Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold143
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1221646
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Warning! 499 characters in sequence are not A, C, G, or T
File 4 of 8
Found at i:423713 original size:30 final size:31
Alignment explanation
Indices: 423641--424071 Score: 478
Period size: 31 Copynumber: 13.8 Consensus size: 31
423631 TTCATCTTTT
*
423641 TTCTTCAAAGTCCACGACTTAGTGGCAATCTC
1 TTCTTCAAAGTCCACGACTCAGTGGC-ATCTC
*
423673 TTC-TCAAAGTCCACGACTCAGTGGCATCCC
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTC
* * *
423703 TTC-CCAAAGTCCATGACTCAGTGGCATCTT
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTC
423733 TTCTTCAAAGTCCACGACTCAGTGGCAATCTC
1 TTCTTCAAAGTCCACGACTCAGTGGC-ATCTC
* * *
423765 TTC-TCAAAGTCCACGACTCAGTGGCTTATT
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTC
* *
423795 TTCTTCAAAGTCCACAACTCAGTGACATCTC
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTC
* * * *
423826 TT-TTCTAAGTCCATGACTTAGTGGCATTCTG
1 TTCTTCAAAGTCCACGACTCAGTGGCA-TCTC
* *
423857 TTCTTCCAAGTCCACAACTCAGTGGCATCTTC
1 TTCTTCAAAGTCCACGACTCAGTGGCATC-TC
*
423889 TTTCTTCAAAGTCCACGACTCAGTGGCATCTTTT
1 -TTCTTCAAAGTCCACGACTCAGTGGCATC--TC
* * *
423923 TTCTTCAAAGTCCACAACTCAATGGTATCTC
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTC
* * * *
423954 TT-TTCTAAGTCCACGACTCAGAGCCATCCTT
1 TTCTTCAAAGTCCACGACTCAGTGGCAT-CTC
* * *
423985 TTCTTCCAAGTCCATGACTCAGTGGCATCTT
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTC
*
424016 TTCTTCAAAGTCCACGACTTAGTGGCATCTC
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTC
* *
424047 TTC-CCAAAGTCCACGACTCTGTGGC
1 TTCTTCAAAGTCCACGACTCAGTGGC
424072 GTCTTTTTCT
Statistics
Matches: 336, Mismatches: 53, Indels: 22
0.82 0.13 0.05
Matches are distributed among these distances:
30 95 0.28
31 134 0.40
32 52 0.15
33 53 0.16
34 2 0.01
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (31 bp):
TTCTTCAAAGTCCACGACTCAGTGGCATCTC
Found at i:424133 original size:33 final size:33
Alignment explanation
Indices: 423864--424823 Score: 825
Period size: 33 Copynumber: 29.8 Consensus size: 33
423854 CTGTTCTTCC
* **
423864 AAGTCCACAACTCAGTGGCATCTTCTTT-CTTCA
1 AAGTCCACAACTCCGTGGCATCTT-TTTCCTTTT
* * * **
423897 AAGTCCACGACTCAGTGGCATCTTTTTTCTTCA
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
** *
423930 AAGTCCACAACTCAATGGTATCTCTTTT-C---T
1 AAGTCCACAACTCCGTGGCATCT-TTTTCCTTTT
* * * * * **
423960 AAGTCCACGACTCAGAGCCATCCTTTT-CTTCC
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
** * **
423992 AAGTCCATGACTCAGTGGCATC-TTTT-CTTCA
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
* ** * **
424023 AAGTCCACGACTTAGTGGCATC-TCTTCC--CA
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
* * * *
424053 AAGTCCACGACTCTGTGGCGTCTTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
* * *
424086 AAAGCCCACAACTCCATGGAATCTTTTTCCTTTT
1 -AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
424120 AAGTCCACAACTCCGTGGCA-C-----CCTTTT
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
* *
424147 AAGTCCATAACTCTGTGGCATCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
* * *
424180 AAGTCCACAACTCCATGGCACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
* * *
424213 AAGTCCACAACTCTGTGGCACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
* *
424246 AAGTCCATAACTCCGTGGCATC-TTTTCTTTTT
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
* * * * *
424278 AAGCCCACGACTCTGCGGCACTCTTTTTCCATTT
1 AAGTCCACAACTCCGTGGCA-TCTTTTTCCTTTT
*
424312 AAGTCCACAACTCCGTGGTA-C-----CCTTTT
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
* *
424339 AAGTCCACAACTTCATGGCATCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
*
424372 AAGTCGACAACTCCGTGGCACTCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCA-TCTTTTTCCTTTT
* *
424406 AAGTCCACAACACCGTGGTACTCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCA-TCTTTTTCCTTTT
* * * *
424440 AAGTCCACAACCCCATGGCACCTTTTTCCCTTT
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
* * *
424473 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTC
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
*
424506 AAGTCCACAACTCCGTGGCATC-TTTTCTTTTT
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
* *
424538 AAGCCCACGACTCCGTGGCACTCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCA-TCTTTTTCCTTTT
*
424572 AAGTCCATAACTCCGTGGCA-C-----CCTTTT
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
424599 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
424632 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCA-TCTTTTTCCTTTT
* *
424666 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
* * *
424699 AAGTCCACAACTCCGTGGTA-CCTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
** * *
424731 AAGTCCATTACTCCGTGGCACCCTTTTCCCTTTT
1 AAGTCCACAACTCCGTGGCA-TCTTTTTCCTTTT
* * * *
424765 AAGCCCACACCTCCATGGCATCCCTTTTTCC-TGT
1 AAGTCCACAACTCCGTGGCAT--CTTTTTCCTTTT
** * *
424799 AAGTCTGCAACTCCATGGCACCTTT
1 AAGTCCACAACTCCGTGGCATCTTT
424824 AAGTCCAATA
Statistics
Matches: 771, Mismatches: 118, Indels: 77
0.80 0.12 0.08
Matches are distributed among these distances:
27 71 0.09
28 3 0.00
29 5 0.01
30 38 0.05
31 35 0.05
32 104 0.13
33 293 0.38
34 215 0.28
35 7 0.01
ACGTcount: A:0.20, C:0.31, G:0.13, T:0.35
Consensus pattern (33 bp):
AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
Found at i:424476 original size:260 final size:260
Alignment explanation
Indices: 424082--424786 Score: 1045
Period size: 260 Copynumber: 2.7 Consensus size: 260
424072 GTCTTTTTCT
* *
424082 TTTTAAAGCCCACAACTCCATGGAATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCA--C----
1 TTTT-AAGTCCACAACTCCATGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACTCTTTT
* *
424141 -CCTTTTAAGTCCATAACTCTGTGGCA-TCTTTTTCCTTTTAAGTCCACAACTCCATGGCACCTT
65 TCCTTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCATGGCACCTT
* * *
424204 GTTCCTTTTAAGTCCACAACTCTGTGGCACCTTGTTCCTTTTAAGTCCATAACTCCGTGGCATCT
130 TTTCCTTTTAAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCATCT
* *
424269 TTTCTTTTTAAGCCCACGACTCTGCGGCACTCTTTTTCCATTTAAGTCCACAACTCCGTGGTACC
195 TTTCTTTTTAAGCCCACGACTCCGCGGCACTCTTTTTCCATTTAAGTCCACAACTCCGTGGCACC
424334 C
260 C
* *
424335 TTTTAAGTCCACAACTTCATGGCATCTTTTTCCTTTTAAGTCGACAACTCCGTGGCACTCTTTTT
1 TTTTAAGTCCACAACTCCATGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACTCTTTTT
* * *
424400 CCTTTTAAGTCCACAACACCGTGGTACTCTTTTTCCTTTTAAGTCCACAACCCCATGGCACCTTT
66 CCTTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCATGGCACCTTT
* *
424465 TTCCCTTTAAGTCCACAACTCCGTGGCACCTTGTTCCTTTCAAGTCCACAACTCCGTGGCATCTT
131 TTCCTTTTAAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCATCTT
* * *
424530 TTCTTTTTAAGCCCACGACTCCGTGGCACTCTTTTTCCTTTTAAGTCCATAACTCCGTGGCACCC
196 TTCTTTTTAAGCCCACGACTCCGCGGCACTCTTTTTCCATTTAAGTCCACAACTCCGTGGCACCC
*
424595 TTTTAAGTCCACAACTCCGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACTCTTTTT
1 TTTTAAGTCCACAACTCCATGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACTCTTTTT
* * *
424660 CCTTTTAAGTCCACAACTCCGTGGCAC-CTTGTTCCTTTTAAGTCCACAACTCCGTGGTACC-TT
66 CCTTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCATGGCACCTTT
* ** * * *
424723 TTCTTTTTAAGTCCATTACTCCGTGGCACCCTT-TTCCCTTTTAAGCCCACACCTCCATGGCATC
131 TTCCTTTTAAGTCCACAACTCCGTGGCA-CCTTGTT-CCTTTTAAGTCCACAACTCCGTGGCATC
424787 CCTTTTTCCT
Statistics
Matches: 406, Mismatches: 36, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
252 49 0.12
253 4 0.01
254 1 0.00
258 28 0.07
259 80 0.20
260 244 0.60
ACGTcount: A:0.19, C:0.32, G:0.13, T:0.36
Consensus pattern (260 bp):
TTTTAAGTCCACAACTCCATGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACTCTTTTT
CCTTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCATGGCACCTTT
TTCCTTTTAAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCATCTT
TTCTTTTTAAGCCCACGACTCCGCGGCACTCTTTTTCCATTTAAGTCCACAACTCCGTGGCACCC
Found at i:424606 original size:193 final size:189
Alignment explanation
Indices: 424053--424792 Score: 799
Period size: 193 Copynumber: 3.8 Consensus size: 189
424043 TCTCTTCCCA
* * ** * * * * * *
424053 AAGTCCACGACTCTGTGGCGTCTTTTTCTTTTTAAAGCCCACAACTCCATGGAATCTTTTTCCTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCCTTTT-AAGTCCACAACTCCGTGGCACCTTGTTCCTT
* *
424118 TTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCATAACTCTGTGGCATCTTTTTCCTTTTAAG
65 TTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCTTTTTCCTTTTAAG
* *
424183 TCCACAACTCCATGGCACCTTGTTCCTTTTAAGTCCACAACTCTGTGGCAC-CTTGTTCCTTTT
130 TCCACAACTCCATGGCACC----TCCTTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * * * * * * * *
424246 AAGTCCATAACTCCGTGGCATC-TTTTCTTTTTAAGCCCACGACTCTGCGGCACTCTTTTTCCAT
1 AAGTCCACAACTCCGTGGCACCTTTTTCCTTTTAAGTCCACAACTCCGTGGCAC-CTTGTTCCTT
* * *
424310 TTAAGTCCACAACTCCGTGGTACCCTTTTAAGTCCACAACTTCATGGCATCTTTTTCCTTTTAAG
65 TTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCTTTTTCCTTTTAAG
* * * *
424375 TCGACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACACCGTGGTACTCTTTTTCCTTTT
130 TCCACAACTCCATGGCAC-C----TCCTTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * *
424440 AAGTCCACAACCCCATGGCACCTTTTTCCCTTTAAGTCCACAACTCCGTGGCACCTTGTTCCTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTGTTCCTTT
* * * *
424505 CAAGTCCACAACTCCGTGGCATCTTTTCTTTTTAAGCCCACGACTCCGTGGCACTCTTTTTCCTT
66 TAAGTCCACAACTCCGTGGCA-C----CCTTTTAAGTCCACAACTCCGTGGCA-TCTTTTTCCTT
* *
424570 TTAAGTCCATAACTCCGTGGCA-C-CCTTTTAAGTCCACAACTCCGTGGCA-TCTTTTTCCTTTT
125 TTAAGTCCACAACTCCATGGCACCTCCTTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
424632 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTGTTCCTT
1 AAGTCCACAACTCCGTGGCAC-CTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTGTTCCTT
* ** * *
424697 TTAAGTCCACAACTCCGTGGTACCTTTTCTTTTTAAGTCCATTACTCCGTGGCACCCTTTTCCCT
65 TTAAGTCCACAACTCCGTGGCACC----C-TTTTAAGTCCACAACTCCGTGGCA-TCTTTTTCCT
* * *
424762 TTTAAGCCCACACCTCCATGGCATC-CCTTTT
124 TTTAAGTCCACAACTCCATGGCACCTCCTTTT
424793 TCCTGTAAGT
Statistics
Matches: 469, Mismatches: 61, Indels: 33
0.83 0.11 0.06
Matches are distributed among these distances:
188 1 0.00
191 15 0.03
192 128 0.27
193 182 0.39
194 64 0.14
195 26 0.06
198 1 0.00
199 21 0.04
200 31 0.07
ACGTcount: A:0.19, C:0.32, G:0.13, T:0.36
Consensus pattern (189 bp):
AAGTCCACAACTCCGTGGCACCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTGTTCCTTT
TAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCTTTTTCCTTTTAAGT
CCACAACTCCATGGCACCTCCTTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
Found at i:424907 original size:51 final size:48
Alignment explanation
Indices: 424818--425286 Score: 338
Period size: 49 Copynumber: 9.9 Consensus size: 48
424808 ACTCCATGGC
* * * * *
424818 ACCTTTAAGTCCAATATTGCT-GCCTTGAATCAGTATATTGGTACCTTT
1 ACCTATAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TT
*
424866 ACCATCATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
1 ACC-T-ATAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
* * * *
424916 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGG------
1 ACCTATAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
* * * *
424958 --C----AGCCCAATATCGCTAGCCTTGAATCAACATATGGGCACCTT
1 ACCTATAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
* * * * ** * * *
425000 CATCT-TAAAACCGATGTCATTGGCCTTGAATTAGCACATTGGCATCTT
1 -ACCTATAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
* * * *
425048 CATCTTTAAGTCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT
1 -ACCTATAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TT
* * * *
425098 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT
1 ACCTATAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
* * * **
425146 CATCTTTAAGTCTGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT
1 -ACCTATAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TT
* * * *
425196 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT
1 ACCTATAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
* * * **
425244 CATCTTTAA-ATCCGATATCATTGGCCTTGAATCAGCATATTGG
1 -ACCTATAAGA-CCAATATCGCTGGCCTTGAATCAGCATATTGG
425287 TATCTTTAAC
Statistics
Matches: 345, Mismatches: 55, Indels: 41
0.78 0.12 0.09
Matches are distributed among these distances:
36 29 0.08
40 1 0.00
45 1 0.00
48 76 0.22
49 194 0.56
50 22 0.06
51 22 0.06
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (48 bp):
ACCTATAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
Found at i:425017 original size:84 final size:84
Alignment explanation
Indices: 424875--425043 Score: 250
Period size: 84 Copynumber: 2.0 Consensus size: 84
424865 TACCATCATA
* * * * *
424875 AGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGCTGGC
1 AGCCCAATATCGCTAGCCTTGAATCAACATATGGGCACCTTATCTTTAAAACCAATGTCACTGGC
424940 CTTGAATCAGCACATTGGC
66 CTTGAATCAGCACATTGGC
* *
424959 AGCCCAATATCGCTAGCCTTGAATCAACATATGGGCACCTTCATC-TTAAAACCGATGTCATTGG
1 AGCCCAATATCGCTAGCCTTGAATCAACATATGGGCACCTT-ATCTTTAAAACCAATGTCACTGG
*
425023 CCTTGAATTAGCACATTGGC
65 CCTTGAATCAGCACATTGGC
425043 A
1 A
425044 TCTTCATCTT
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
84 73 0.96
85 3 0.04
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (84 bp):
AGCCCAATATCGCTAGCCTTGAATCAACATATGGGCACCTTATCTTTAAAACCAATGTCACTGGC
CTTGAATCAGCACATTGGC
Found at i:425078 original size:49 final size:49
Alignment explanation
Indices: 424965--425286 Score: 414
Period size: 49 Copynumber: 6.6 Consensus size: 49
424955 TGGCAGCCCA
* * * *
424965 ATATCGCTAGCCTTGAATCAACATATGGGCACCTTCATC-TTAAAACCG
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCG
* ** * * * *
425013 ATGTCATTGGCCTTGAATTAGCACATTGGCATCTTCATCTTTAAGTCCG
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCG
* *
425062 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCG
* * * *
425111 ATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCTG
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCG
* *
425160 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCG
* *
425209 ATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAA-ATCCG
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGA-CCG
**
425258 ATATCATTGGCCTTGAATCAGCATATTGG
1 ATATCGCTGGCCTTGAATCAGCATATTGG
425287 TATCTTTAAC
Statistics
Matches: 232, Mismatches: 40, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
48 31 0.13
49 201 0.87
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (49 bp):
ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCG
Found at i:425151 original size:98 final size:98
Alignment explanation
Indices: 424965--425379 Score: 530
Period size: 98 Copynumber: 4.2 Consensus size: 98
424955 TGGCAGCCCA
* * * * * * **
424965 ATATCGCTAGCCTTGAATCAACATATGGGCACCTTCATC-TTAAAACCGATGTCATTGGCCTTGA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCTGGCCTTGA
* *
425029 ATTAGCACATTGGCATCTTCATCTTTAAGTCCG
66 ATCAGCACATTGGCACCTTCATCTTTAAGTCCG
425062 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCTGGCCTTGA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCTGGCCTTGA
*
425127 ATCAGCACATTGGCACCTTCATCTTTAAGTCTG
66 ATCAGCACATTGGCACCTTCATCTTTAAGTCCG
425160 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCTGGCCTTGA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCTGGCCTTGA
*
425225 ATCAGCACATTGGCACCTTCATCTTTAAATCCG
66 ATCAGCACATTGGCACCTTCATCTTTAAGTCCG
** * * * * *
425258 ATATCATTGGCCTTGAATCAGCATATTGGTATCTTTAACATTCCTAAGCCCAATGTCGCTGACCT
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC-TT--TAAGACCAATGTCGCTGGCCT
** * * ***
425323 TGTCTCAGCACATTGGCA--TTCTTCTTCAAGTTTA
63 TGAATCAGCACATTGGCACCTTCATCTTTAAGTCCG
* *
425357 ATGTCGCTGGCCATGAATCAGCA
1 ATATCGCTGGCCTTGAATCAGCA
425380 CATTATCATT
Statistics
Matches: 282, Mismatches: 32, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
97 35 0.12
98 181 0.64
99 31 0.11
101 35 0.12
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (98 bp):
ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCTGGCCTTGA
ATCAGCACATTGGCACCTTCATCTTTAAGTCCG
Found at i:426212 original size:13 final size:13
Alignment explanation
Indices: 426194--426221 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
426184 CATTATTCAA
426194 TGTATCGATACAT
1 TGTATCGATACAT
426207 TGTATCGATACAT
1 TGTATCGATACAT
426220 TG
1 TG
426222 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:429333 original size:49 final size:49
Alignment explanation
Indices: 429264--429653 Score: 382
Period size: 49 Copynumber: 7.9 Consensus size: 49
429254 CCATTGGCAC
*
429264 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* *
429313 CTTTAAGTCCAATATAGCTGGCCTTGAATTAGCATATTGGCACCTTTAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * *
429362 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG-----T-AC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * * *
429405 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGACGTCTTTGTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGC-AC-CT-TCAT
* * * * *
429457 CTTTAAGTCCAATGTCGCTGGCATTGAATCAGCACATTGGCACCTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
*
429506 C-TTAAGTCCAATATCA-CTGGCCTTGAATCAGCATATTGGCGCCCTCGTCAT
1 CTTTAAGTCCAATAT-AGCTGGCCTTGAATCAGCATATTGGC-ACCT--TCAT
* * * *
429557 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC----T-TCAT
* * * * *
429612 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA
429654 TCTTTATCAC
Statistics
Matches: 283, Mismatches: 38, Indels: 34
0.80 0.11 0.10
Matches are distributed among these distances:
43 37 0.13
44 1 0.00
48 34 0.12
49 90 0.32
50 1 0.00
51 6 0.02
52 74 0.26
55 39 0.14
56 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32
Consensus pattern (49 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
Found at i:429484 original size:52 final size:52
Alignment explanation
Indices: 429405--429650 Score: 257
Period size: 52 Copynumber: 4.8 Consensus size: 52
429395 ACATTGGTAC
429405 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGACGTCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGACGTCTTTGTCAT
* * * * * * *
429457 CTTTAAGTCCAATGTCGCTGGCATTGAATCAGCACATTGGC-AC-CT-CCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGACGTCTTTGTCAT
* * * * *
429506 C-TTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCGCCCTCGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGACGTCTTTGTCAT
* * * *
429557 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGACGT-C--TTTGTCAT
* * * *
429612 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTG
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
429651 GCATCTTTAT
Statistics
Matches: 157, Mismatches: 30, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
48 35 0.22
49 5 0.03
50 1 0.01
51 5 0.03
52 72 0.46
53 1 0.01
55 38 0.24
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (52 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGACGTCTTTGTCAT
Found at i:429556 original size:100 final size:99
Alignment explanation
Indices: 429264--429595 Score: 437
Period size: 100 Copynumber: 3.4 Consensus size: 99
429254 CCATTGGCAC
* * * *
429264 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTTTAAGTCCAATAT-
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCCATC-TTAAGTCCAATATC
* *
429328 AGCTGGCCTTGAATTAGCATATTGGC-ACCT-TTAT
65 A-CTGGCCTTGAATCAGCATATTGGCGACCTGTCAT
* *
429362 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGTA---CC-T-TTAAGTCCAATATCG
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCCATCTTAAGTCCAATATCA
* * *
429422 CTGGCCTTGAATCAGCATATTGACGTCTTTGTCAT
66 CTGGCCTTGAATCAGCATATTGGCGAC-CTGTCAT
* *
429457 CTTTAAGTCCAATGTCGCTGGCATTGAATCAGCACATTGGCACCTCCATCTTAAGTCCAATATCA
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCCATCTTAAGTCCAATATCA
*
429522 CTGGCCTTGAATCAGCATATTGGCGCCCTCGTCAT
66 CTGGCCTTGAATCAGCATATTGGCGACCT-GTCAT
*
429557 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTG
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
429596 ACATCCTTTT
Statistics
Matches: 205, Mismatches: 19, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
92 35 0.17
93 1 0.00
94 1 0.00
95 43 0.21
98 41 0.20
99 2 0.01
100 82 0.40
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (99 bp):
CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCCATCTTAAGTCCAATATCA
CTGGCCTTGAATCAGCATATTGGCGACCTGTCAT
Found at i:429784 original size:53 final size:53
Alignment explanation
Indices: 429697--429867 Score: 177
Period size: 53 Copynumber: 3.2 Consensus size: 53
429687 CCAATATTGC
* * * * *
429697 TGGCCTTGAATCCGCATATTGG-AGTCTTCGTCATCTTTGAAACCCAATGTCGT
1 TGGCCGTGAATCAGCACATTGGCATTCTTCCTCATCTTT-AAACCCAATGTCGT
* * * *
429750 TGGCCTTGAATCAGCACATTGGCATTC-TCCTCATCTTCAAGA-CTAATGTCGC
1 TGGCCGTGAATCAGCACATTGGCATTCTTCCTCATCTTTAA-ACCCAATGTCGT
** * * *
429802 TGATCGTGAATCAGCACATTGACATTCTTTCTCATCTTTAAACCCAATATCGT
1 TGGCCGTGAATCAGCACATTGGCATTCTTCCTCATCTTTAAACCCAATGTCGT
429855 TGGCCGTGAATCA
1 TGGCCGTGAATCA
429868 ACGTATTGGT
Statistics
Matches: 96, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
52 34 0.35
53 59 0.61
54 3 0.03
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.33
Consensus pattern (53 bp):
TGGCCGTGAATCAGCACATTGGCATTCTTCCTCATCTTTAAACCCAATGTCGT
Found at i:430508 original size:32 final size:32
Alignment explanation
Indices: 430472--430539 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
430462 TTTAACGATT
430472 TGTATCAATACATAAGTGTTGTATCGATACAA
1 TGTATCAATACATAAGTGTTGTATCGATACAA
* *
430504 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCAATACATAAGTGTTGTATCGATACAA
430536 TGTA
1 TGTA
430540 CAGTTACGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCAATACATAAGTGTTGTATCGATACAA
Found at i:430509 original size:13 final size:13
Alignment explanation
Indices: 430491--430515 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
430481 ACATAAGTGT
430491 TGTATCGATACAA
1 TGTATCGATACAA
430504 TGTATCGATACA
1 TGTATCGATACA
430516 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:430528 original size:19 final size:19
Alignment explanation
Indices: 430470--430534 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
430460 ATTTTAACGA
*
430470 TTTGTATCAATACATAAGT
1 TTTGTATCGATACATAAGT
*
430489 GTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
430504 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
430521 TTTGTATCGATACA
1 TTTGTATCGATACA
430535 ATGTACAGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:430605 original size:13 final size:13
Alignment explanation
Indices: 430587--430611 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
430577 ATTACTCAAA
430587 TGTATCGATACAT
1 TGTATCGATACAT
430600 TGTATCGATACA
1 TGTATCGATACA
430612 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:430664 original size:52 final size:52
Alignment explanation
Indices: 430620--430749 Score: 215
Period size: 52 Copynumber: 2.5 Consensus size: 52
430610 CACTGATCTT
*
430620 TGTATCGATACATGCAGGAAAATTTGCCTAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGAAAATTTGCCCAGATGTATCGATACACTATGAAA
* * *
430672 TGTATTGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGAAAATTTGCCCAGATGTATCGATACACTATGAAA
430724 TGTATCGATACATGCAGGCAAAATTT
1 TGTATCGATACATGCAGG-AAAATTT
430750 CATATTTCGG
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
52 65 0.92
53 6 0.08
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGAAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:433997 original size:222 final size:222
Alignment explanation
Indices: 433611--434041 Score: 799
Period size: 222 Copynumber: 1.9 Consensus size: 222
433601 TAGGCATCCG
* *
433611 ATCATGCCTAGCTCGAAATGATCGGTGGCGACTCCAAAATTTCGGTCACTTCGTAGTGACCATTG
1 ATCATGCCTAGCCCGAAATGATCGGTGACGACTCCAAAATTTCGGTCACTTCGTAGTGACCATTG
* *
433676 AAGATCAATTAGATGGGCGATTCATCTACCGATCTTCCCCCTTTAATTAACATACTTCCTATCAT
66 AAGATCAATTAGATGGGCGATTCATCTACCGATCTTCCCCCTTTAATCAACATACTTCCCATCAT
*
433741 GCCATAGAAATCCCCAATCGCGAGGGATATTAAGTCGAGCGCGCCTCATTTGCCCTATCGCCGGG
131 GCCATAGAAATCCCCAATCGCGAGGGATATTAAGTCGAACGCGCCTCATTTGCCCTATCGCCGGG
433806 GTCGAGCGCACGTTACTACAGCATCTA
196 GTCGAGCGCACGTTACTACAGCATCTA
*
433833 ATCATGCCTAGCCCGAAATGATTGGTGACGACTCCAAAATTTCGGTCACTTCGTAGTGACCATTG
1 ATCATGCCTAGCCCGAAATGATCGGTGACGACTCCAAAATTTCGGTCACTTCGTAGTGACCATTG
433898 AAGATCAATTAGATGGGCGATTCATCTACCGATCTTCCCCCTTTAATCAACATACTTCCCATCAT
66 AAGATCAATTAGATGGGCGATTCATCTACCGATCTTCCCCCTTTAATCAACATACTTCCCATCAT
433963 GCCATAGAAATCCCCAATCGCGAGGGATATTAAGTCGAACGCGCCTCATTTGCCCTATCGCCGGG
131 GCCATAGAAATCCCCAATCGCGAGGGATATTAAGTCGAACGCGCCTCATTTGCCCTATCGCCGGG
*
434028 GTCGAGTGCACGTT
196 GTCGAGCGCACGTT
434042 GCGACAGCTT
Statistics
Matches: 202, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
222 202 1.00
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (222 bp):
ATCATGCCTAGCCCGAAATGATCGGTGACGACTCCAAAATTTCGGTCACTTCGTAGTGACCATTG
AAGATCAATTAGATGGGCGATTCATCTACCGATCTTCCCCCTTTAATCAACATACTTCCCATCAT
GCCATAGAAATCCCCAATCGCGAGGGATATTAAGTCGAACGCGCCTCATTTGCCCTATCGCCGGG
GTCGAGCGCACGTTACTACAGCATCTA
Found at i:437948 original size:11 final size:11
Alignment explanation
Indices: 437928--437979 Score: 77
Period size: 11 Copynumber: 4.7 Consensus size: 11
437918 AGTCAAAAGT
*
437928 AAAAACACAAA
1 AAAAAAACAAA
437939 AAAAAAACAAA
1 AAAAAAACAAA
*
437950 ACAAAAACAAA
1 AAAAAAACAAA
*
437961 AAAAACACAAA
1 AAAAAAACAAA
437972 AAAAAAAC
1 AAAAAAAC
437980 GTGCAAAGGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 36 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:439362 original size:30 final size:31
Alignment explanation
Indices: 439261--440086 Score: 557
Period size: 33 Copynumber: 25.9 Consensus size: 31
439251 ATCTCTCTTC
* *
439261 TCAAAGTCCATGACCCAGTGGCATCTTTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATC--TTTTCT
* *
439294 TCAAAGTCCACGACTTAGTGGCAATCTCTTC-
1 TCAAAGTCCACGACTCAGTGGC-ATCTTTTCT
**
439325 TCAAAGTCCACGACTCAGTGGCATCCCTTC-
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCT
* *
439355 CCAAAGTCCACAACTCAGTGGCATCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCT
* *
439386 TCAAAGTCCACAACTCAGTGGCAATCTCTTC-
1 TCAAAGTCCACGACTCAGTGGC-ATCTTTTCT
*
439417 TCAAAGTCCACGACTCAGTGGCTTCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCT
*
439448 TCAAAGTCCACAACTCAGTGGCATCTTTT-T
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCT
* * *
439478 TCTAAGTCCACGACTTAGTAGCATTCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCA-TCTTTTCT
* *
439510 TCCAAGTCCACGACTCAATGGCATCTTCTTTCT
1 TCAAAGTCCACGACTCAGTGGCATC-T-TTTCT
*
439543 TCAAAGTCCACGACTTAGTGGCATCTTTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATC--TTTTCT
* * *
439576 TCAAAGTCCACAACTCAATGGTAT-TTCTT-T
1 TCAAAGTCCACGACTCAGTGGCATCTT-TTCT
*
439606 TCTAAGTCCACGACTCAGTGGCATCCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCAT-CTTTTCT
* *
439638 TCCAAGTCCATGACTCAGTGGCATCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCT
*
439669 TCAAAGTCCACGACTCAGTGGCATCTCTTC-
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCT
* *
439699 -CAAAAGTCCACGACTCTGTGGCACCTTTTTCTTT
1 TC-AAAGTCCACGACTCAGTGGCATC-TTTTC--T
* * *
439733 TTAAAGCCCACAACTTC-GTGGCATCTTTTTCCT
1 TCAAAGTCCACGAC-TCAGTGGCATC-TTTT-CT
** * * *
439766 TTTAAGTCCACAACTCCGTGGCACCTTGTTCCT
1 TCAAAGTCCACGACTCAGTGGCATCTT-TT-CT
** * *
439799 TTTAAGTCCACAACTCCA-TGGCACCTTGTTCCT
1 TCAAAGTCCACGACT-CAGTGGCATCTT-TT-CT
** * **
439832 TTTAAGTCCACAACTTTGTGGCATCTTTTCCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTT-CT
** * *
439864 TTTAAGCCCACGACTCCGTGGCACTCTTTTTCCAT
1 TCAAAGTCCACGACTCAGTGGCA-TC-TTTT-C-T
* * * * *
439899 T-TAAGTCCACAACTCCGTGGCAGC-CTT-T
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCT
* *
439927 T--AAGTCCACAACTCTGTGGCATCTTTTTCCT
1 TCAAAGTCCACGACTCAGTGGCATC-TTTT-CT
** * *
439958 TTTAAGTCCACAACTCCGTGGCACTCTTTTTCCT
1 TCAAAGTCCACGACTCAGTGGCA-TC-TTTT-CT
** ** * *
439992 TTTAAGTCCATAACTCCGTGGCACCTTGTTCCT
1 TCAAAGTCCACGACTCAGTGGCATCTT-TT-CT
** * *
440025 TTTAAGTCCACAACTCCGTGGCATCTTTTCTT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTC-T
** * *
440057 TTTAAGCCCACGACTCCGTGGCACTCTTTT
1 TCAAAGTCCACGACTCAGTGGCA-TCTTTT
440087 TCCTTTTAAG
Statistics
Matches: 682, Mismatches: 73, Indels: 76
0.82 0.09 0.09
Matches are distributed among these distances:
27 20 0.03
28 2 0.00
29 3 0.00
30 103 0.15
31 145 0.21
32 111 0.16
33 208 0.30
34 85 0.12
35 5 0.01
ACGTcount: A:0.21, C:0.30, G:0.14, T:0.34
Consensus pattern (31 bp):
TCAAAGTCCACGACTCAGTGGCATCTTTTCT
Found at i:439444 original size:62 final size:62
Alignment explanation
Indices: 439261--439721 Score: 502
Period size: 62 Copynumber: 7.4 Consensus size: 62
439251 ATCTCTCTTC
* * * * * *
439261 TCAAAGTCCATGACCCAGTGGCATCTTTTTTCTTCAAAGTCCACGACTTAGTGGCAATCTCTTC-
1 TCAAAGTCCACGACTCAGTGGCATC--TCTTC-TCAAAGTCCACGACTCAGTGGCATTCTTTTCT
* * *
439325 TCAAAGTCCACGACTCAGTGGCATCCCTTCCCAAAGTCCACAACTCAGTGGCA-TCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTCTTCTCAAAGTCCACGACTCAGTGGCATTCTTTTCT
*
439386 TCAAAGTCCACAACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGC-TTCTTTTCT
1 TCAAAGTCCACGACTCAGTGGC-ATCTCTTCTCAAAGTCCACGACTCAGTGGCATTCTTTTCT
* * * * * *
439448 TCAAAGTCCACAACTCAGTGGCATCTTTTTTCTAAGTCCACGACTTAGTAGCATTCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTCTTCTCAAAGTCCACGACTCAGTGGCATTCTTTTCT
* * * *
439510 TCCAAGTCCACGACTCAATGGCATCTTCTTTCTTCAAAGTCCACGACTTAGTGGCATCTTTTTTC
1 TCAAAGTCCACGACTCAGTGGCATC-TC-TTC-TCAAAGTCCACGACTCAGTGGCAT-TCTTTTC
439575 T
62 T
* * * * * * *
439576 TCAAAGTCCACAACTCAATGGTATTTCTTTTCTAAGTCCACGACTCAGTGGCATCCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTCTTCTCAAAGTCCACGACTCAGTGGCATTCTTTTCT
* * * *
439638 TCCAAGTCCATGACTCAGTGGCATCTTTTCTTCAAAGTCCACGACTCAGTGGCA-TCTCTTC-
1 TCAAAGTCCACGACTCAGTGGCATCTCTTC-TCAAAGTCCACGACTCAGTGGCATTCTTTTCT
*
439699 -CAAAAGTCCACGACTCTGTGGCA
1 TC-AAAGTCCACGACTCAGTGGCA
439722 CCTTTTTCTT
Statistics
Matches: 339, Mismatches: 48, Indels: 23
0.83 0.12 0.06
Matches are distributed among these distances:
60 7 0.02
61 84 0.25
62 124 0.37
63 45 0.13
64 27 0.08
65 24 0.07
66 28 0.08
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.32
Consensus pattern (62 bp):
TCAAAGTCCACGACTCAGTGGCATCTCTTCTCAAAGTCCACGACTCAGTGGCATTCTTTTCT
Found at i:439519 original size:93 final size:92
Alignment explanation
Indices: 439261--440079 Score: 528
Period size: 93 Copynumber: 8.6 Consensus size: 92
439251 ATCTCTCTTC
** * *
439261 TCAAAGTCCATGACCCAGTGGCATCTTTTTTCTTCAAAGTCCACGACTTAGTGGCAATCTCTTCT
1 TCAAAGTCCACAACTCAGTGGCATCTTTTTTC-T--AAGTCCACGACTCAGTGGCAATCTCTTCT
**
439326 CAAAGTCCACGACTCAGTGGCATCCCTTC-
63 CAAAGTCCACGACTCAGTGGCATCTTTTCT
* * *
439355 CCAAAGTCCACAACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCAATCTCTTCTCA
1 TCAAAGTCCACAACTCAGTGGCATCTTTT-TTCTAAGTCCACGACTCAGTGGCAATCTCTTCTCA
*
439420 AAGTCCACGACTCAGTGGCTTCTTTTCT
65 AAGTCCACGACTCAGTGGCATCTTTTCT
* * * * *
439448 TCAAAGTCCACAACTCAGTGGCATCTTTTTTCTAAGTCCACGACTTAGTAGCATTCTTTTCTTCC
1 TCAAAGTCCACAACTCAGTGGCATCTTTTTTCTAAGTCCACGACTCAGTGGCAATCTCTTC-TCA
*
439513 AAGTCCACGACTCAATGGCATCTTCTTTCT
65 AAGTCCACGACTCAGTGGCATC-T-TTTCT
* * * * * * *
439543 TCAAAGTCCACGACTTAGTGGCATCTTTTTTCTTCAAAGTCCACAACTCAATGG-TATTTCTTTT
1 TCAAAGTCCACAACTCAGTGGCATCTTTTTTC-T--AAGTCCACGACTCAGTGGCAATCTCTTCT
*
439607 CTAAGTCCACGACTCAGTGGCATCCTTTTCT
63 CAAAGTCCACGACTCAGTGGCAT-CTTTTCT
* ** *
439638 TCCAAGTCCATGACTCAGTGGCATCTTTTCTTCAAAGTCCACGACTCAGTGGC-ATCTCTTC-CA
1 TCAAAGTCCACAACTCAGTGGCATCTTTT-TTCTAAGTCCACGACTCAGTGGCAATCTCTTCTC-
* *
439701 AAAGTCCACGACTCTGTGGCACCTTTTTCTTT
64 AAAGTCCACGACTCAGTGGCATC-TTTTC--T
* * * * * * *
439733 TTAAAGCCCACAACTTC-GTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGC-ACCTTGTT
1 TCAAAGTCCACAAC-TCAGTGGCATC-TTTT--TTCTAAGTCCACGACTCAGTGGCAATC-TCTT
** * *
439796 CCTTTTAAGTCCACAACTCCA-TGGCACCTTGTTCCT
61 -C-TCAAAGTCCACGACT-CAGTGGCATCTT-TT-CT
** ** * * * * *
439832 TTTAAGTCCACAACTTTGTGGCATCTTTTCCTTTTAAGCCCACGACTCCGTGGCACTCT-TTTTC
1 TCAAAGTCCACAACTCAGTGGCATCTTTT--TTCTAAGTCCACGACTCAGTGGCAATCTCTTCT-
* * * *
439896 CATTTAAGTCCACAACTCCGTGGCAGC-CTT-T
63 CA---AAGTCCACGACTCAGTGGCATCTTTTCT
* * * * * *
439927 T--AAGTCCACAACTCTGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACTCTTTTTC
1 TCAAAGTCCACAACTCAGTGGCATC-TTTT--TTCTAAGTCCACGACTCAGTGGCAATC-TCTT-
** ** * *
439990 CTTTTAAGTCCATAACTCCGTGGCACCTTGTTCCT
61 C-TCAAAGTCCACGACTCAGTGGCATCTT-TT-CT
** * * * *
440025 TTTAAGTCCACAACTCCGTGGCATCTTTTCTTTTTAAGCCCACGACTCCGTGGCA
1 TCAAAGTCCACAACTCAGTGGCATC-TTT-TTTCTAAGTCCACGACTCAGTGGCA
440080 CTCTTTTTCC
Statistics
Matches: 597, Mismatches: 84, Indels: 83
0.78 0.11 0.11
Matches are distributed among these distances:
92 81 0.14
93 117 0.20
94 77 0.13
95 91 0.15
96 37 0.06
97 31 0.05
98 50 0.08
99 65 0.11
100 45 0.08
101 3 0.01
ACGTcount: A:0.21, C:0.30, G:0.14, T:0.34
Consensus pattern (92 bp):
TCAAAGTCCACAACTCAGTGGCATCTTTTTTCTAAGTCCACGACTCAGTGGCAATCTCTTCTCAA
AGTCCACGACTCAGTGGCATCTTTTCT
Found at i:439786 original size:33 final size:33
Alignment explanation
Indices: 439358--440311 Score: 661
Period size: 33 Copynumber: 29.8 Consensus size: 33
439348 TCCCTTCCCA
* **
439358 AAGTCCACAACTCAGTGGCATC-TTTT-CTTCA
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
* * **
439389 AAGTCCACAACTCAGTGGCAATC-TCTT-C-TCA
1 AAGTCCACAACTCCGTGGC-ATCTTTTTCCTTTT
* * * **
439420 AAGTCCACGACTCAGTGGCTTC-TTTT-CTTCA
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
* *
439451 AAGTCCACAACTCAGTGGCATC-TTTT--TTCT
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
* ** * **
439481 AAGTCCACGACTTAGTAGCAT-TCTTTT-CTTCC
1 AAGTCCACAACTCCGTGGCATCT-TTTTCCTTTT
* ** **
439513 AAGTCCACGACTCAATGGCATCTTCTTT-CTTCA
1 AAGTCCACAACTCCGTGGCATCTT-TTTCCTTTT
* ** * **
439546 AAGTCCACGACTTAGTGGCATCTTTTTTCTTCA
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
** * * *
439579 AAGTCCACAACTCAATGGTAT-TTCTT--TTCT
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
* * * **
439609 AAGTCCACGACTCAGTGGCATCCTTTT-CTTCC
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
** * **
439641 AAGTCCATGACTCAGTGGCATC-TTTT-CTTCA
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
* * * **
439672 AAGTCCACGACTCAGTGGCATC-TCTTCC--AA
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
* * * *
439702 AAGTCCACGACTCTGTGGCACCTTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
* *
439735 AAAGCCCACAACTTCGTGGCATCTTTTTCCTTTT
1 -AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
* *
439769 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
* * *
439802 AAGTCCACAACTCCATGGCACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
**
439835 AAGTCCACAACTTTGTGGCATC-TTTTCCTTTT
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
* * *
439867 AAGCCCACGACTCCGTGGCACTCTTTTTCCATTT
1 AAGTCCACAACTCCGTGGCA-TCTTTTTCCTTTT
*
439901 AAGTCCACAACTCCGTGGCA------GCCTTTT
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
*
439928 AAGTCCACAACTCTGTGGCATCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
439961 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCA-TCTTTTTCCTTTT
* * *
439995 AAGTCCATAACTCCGTGGCACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
*
440028 AAGTCCACAACTCCGTGGCATC-TTTTCTTTTT
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
* *
440060 AAGCCCACGACTCCGTGGCACTCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCA-TCTTTTTCCTTTT
** *
440094 AAGTCCACAACTTTGTGGCA-C-----CTTTTT
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
* *
440121 AAGTCCACAACTCCGTGACATCTTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
* * *
440154 AAGTCCATAACTCCGTGGCACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
* * * *
440187 AAATCCACAACTCCGTGGTA-CCTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
* * * *
440219 AAGTCCACGACTCTGTGGCACCCTTTTCCCTTTT
1 AAGTCCACAACTCCGTGGCA-TCTTTTTCCTTTT
* * * *
440253 AAGCCCACACCTCCATGGCATCCCTTTTTCC-TGT
1 AAGTCCACAACTCCGTGGCAT--CTTTTTCCTTTT
** * *
440287 AAGTCTGCAACTCCATGGCACCTTT
1 AAGTCCACAACTCCGTGGCATCTTT
440312 AAGTCTAATA
Statistics
Matches: 770, Mismatches: 117, Indels: 71
0.80 0.12 0.07
Matches are distributed among these distances:
27 46 0.06
28 1 0.00
30 69 0.09
31 110 0.14
32 142 0.18
33 242 0.31
34 153 0.20
35 7 0.01
ACGTcount: A:0.21, C:0.30, G:0.14, T:0.36
Consensus pattern (33 bp):
AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
Found at i:440068 original size:193 final size:190
Alignment explanation
Indices: 439731--440316 Score: 829
Period size: 193 Copynumber: 3.0 Consensus size: 190
439721 ACCTTTTTCT
*
439731 TTTTAAAGCCCACAACT-TCGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTGT
1 TTTT-AAGTCCACAACTCT-GTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTGT
* *
439795 TCCTTTTAAGTCCACAACTCCATGGCACCTTGTTCCTTTTAAGTCCACAACTTTGTGGCATCTTT
64 TCCTTTTAAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCTGTGGCATCTTT
439860 TCCTTTTAAGCCCACGACTCCGTGGCACTCTTTTTCCATTTAAGTCCACAACTCCGTGGCAGCC
129 TCCTTTTAAGCCCACGACTCCGTGGCACTCTTTTTCC-TTTAAGTCCACAACTCCGTGGCA-CC
*
439924 TTTTAAGTCCACAACTCTGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACTCTTTTT
1 TTTTAAGTCCACAACTCTGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCAC-CTTGTT
* *
439989 CCTTTTAAGTCCATAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCATCTTTT
65 CCTTTTAAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCTGTGGCATCTTTT
* **
440054 CTTTTTAAGCCCACGACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTTTGTGGCACC
130 CCTTTTAAGCCCACGACTCCGTGGCACTCTTTTTCC-TTTAAGTCCACAACTCCGTGGCACC
* * * *
440116 TTTTTAAGTCCACAACTCCGTGACATCTTTTTCTTTTTAAGTCCATAACTCCGTGGCACCTTGTT
1 -TTTTAAGTCCACAACTCTGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTGTT
* * * * *
440181 CCTTTTAAATCCACAACTCCGTGGTACCTT-TTCTTTTTAAGTCCACGACTCTGTGGCACCCTTT
65 CCTTTTAAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCTGTGGCA-TCTTT
* * * ** *
440245 TCCCTTTTAAGCCCAC-ACCTCCATGGCATCCCTTTTTCCTGTAAGTCTGCAACTCCATGGCACC
129 T-CCTTTTAAGCCCACGA-CTCCGTGGCA-CTCTTTTTCCTTTAAGTCCACAACTCCGTGGCACC
440309 -TTTAAGTC
1 TTTTAAGTC
440317 TAATATTGTT
Statistics
Matches: 355, Mismatches: 31, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
191 33 0.09
192 91 0.26
193 222 0.63
194 9 0.03
ACGTcount: A:0.19, C:0.31, G:0.13, T:0.37
Consensus pattern (190 bp):
TTTTAAGTCCACAACTCTGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTGTTC
CTTTTAAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCTGTGGCATCTTTTC
CTTTTAAGCCCACGACTCCGTGGCACTCTTTTTCCTTTAAGTCCACAACTCCGTGGCACC
Found at i:440145 original size:27 final size:27
Alignment explanation
Indices: 440090--440147 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
440080 CTCTTTTTCC
** *
440090 TTTTAAGTCCACAACTTTGTGGCACCT
1 TTTTAAGTCCACAACTCCGTGACACCT
*
440117 TTTTAAGTCCACAACTCCGTGACATCT
1 TTTTAAGTCCACAACTCCGTGACACCT
440144 TTTT
1 TTTT
440148 CTTTTTAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.26, G:0.12, T:0.40
Consensus pattern (27 bp):
TTTTAAGTCCACAACTCCGTGACACCT
Found at i:440251 original size:159 final size:159
Alignment explanation
Indices: 439702--440261 Score: 625
Period size: 159 Copynumber: 3.5 Consensus size: 159
439692 TCTCTTCCAA
* * *
439702 AAGTCCACGACTCTGTGGCACCTTTTTCTTTTTAAAGCCCACAACTTCGTGGCATCTTTTTCCTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTTT-AAGCCCACAACTCCGTGGCATCTTTTTCCTT
* * * *
439767 TTAAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCATGGCACCTTGTTCCT
65 TTAAGTCCACAACTCTGTGGCACC----T--TTTTAAGTCCACAACTCCGTGGCATCTTTTTCCT
* ** *
439832 TTTAAGTCCACAACTTTGTGGCATCTT-TTCCTTTT
124 TTTAAGTCCATAACTCCGTGGCACCTTGTTCCTTTT
* * ** * *
439867 AAGCCCACGACTCCGTGGCACTCTTTTTCCATTTAAGTCCACAACTCCGTGGCA------GCCTT
1 AAGTCCACAACTCCGTGGCAC-CTTTTTCTTTTTAAGCCCACAACTCCGTGGCATCTTTTTCCTT
*
439926 TTAAGTCCACAACTCTGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACTCTTTTTCC
65 TTAAGTCCACAACTCTGTGGCA-C-----CTTTTTAAGTCCACAACTCCGTGGCA-TCTTTTTCC
439991 TTTTAAGTCCATAACTCCGTGGCACCTTGTTCCTTTT
123 TTTTAAGTCCATAACTCCGTGGCACCTTGTTCCTTTT
* *
440028 AAGTCCACAACTCCGTGGCATC-TTTTCTTTTTAAGCCCACGACTCCGTGGCACTCTTTTTCCTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAGCCCACAACTCCGTGGCA-TCTTTTTCCTT
* * *
440092 TTAAGTCCACAACTTTGTGGCACCTTTTTAAGTCCACAACTCCGTGACATCTTTTTCTTTTTAAG
65 TTAAGTCCACAACTCTGTGGCACCTTTTTAAGTCCACAACTCCGTGGCATCTTTTTCCTTTTAAG
440157 TCCATAACTCCGTGGCACCTTGTTCCTTTT
130 TCCATAACTCCGTGGCACCTTGTTCCTTTT
* * * * * * *
440187 AAATCCACAACTCCGTGGTACC-TTTTCTTTTTAAGTCCACGACTCTGTGGCACCCTTTTCCCTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAGCCCACAACTCCGTGGCA-TCTTTTTCCTT
*
440251 TTAAGCCCACA
65 TTAAGTCCACA
440262 CCTCCATGGC
Statistics
Matches: 343, Mismatches: 36, Indels: 38
0.82 0.09 0.09
Matches are distributed among these distances:
159 186 0.54
160 57 0.17
161 26 0.08
165 39 0.11
166 35 0.10
ACGTcount: A:0.19, C:0.31, G:0.13, T:0.37
Consensus pattern (159 bp):
AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAGCCCACAACTCCGTGGCATCTTTTTCCTTT
TAAGTCCACAACTCTGTGGCACCTTTTTAAGTCCACAACTCCGTGGCATCTTTTTCCTTTTAAGT
CCATAACTCCGTGGCACCTTGTTCCTTTT
Found at i:440395 original size:51 final size:48
Alignment explanation
Indices: 440327--440447 Score: 143
Period size: 48 Copynumber: 2.5 Consensus size: 48
440317 TAATATTGTT
* * * *
440327 GCCTTGAATCAGTATATTGGTACCTTTACCATCATAAGCCCAATATCGCTG
1 GCCTTGAATCAGCATATTGGCACC-TTACC-T-ATAAGACAAATATCGCTG
* * *
440378 GCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACAAATGTCGCTG
1 GCCTTGAATCAGCATATTGGCACCTTACCTATAAGACAAATATCGCTG
*
440426 GCCTTGAATCAGCACATTGGCA
1 GCCTTGAATCAGCATATTGGCA
440448 GCCCAATATC
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
48 35 0.56
49 1 0.02
50 4 0.06
51 22 0.35
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (48 bp):
GCCTTGAATCAGCATATTGGCACCTTACCTATAAGACAAATATCGCTG
Found at i:440530 original size:49 final size:50
Alignment explanation
Indices: 440465--440581 Score: 137
Period size: 52 Copynumber: 2.3 Consensus size: 50
440455 ATCGCTAGCT
* * * ** *
440465 TTGAATCAACATATTGGCACCTT-CATCTTTAAGACCGATATCGTTGGCC
1 TTGAATCAGCACATTGGCACCTTACATCTTTAAGACCAATATCGCCGACC
* *
440514 TTGAATCAGCACATTGGCACCTTAACCATCTTTAAGTCCAATGTCGCCGACC
1 TTGAATCAGCACATTGGCACCTT-A-CATCTTTAAGACCAATATCGCCGACC
440566 TTGAATCAGCACATTG
1 TTGAATCAGCACATTG
440582 CCTTGAATCA
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
49 21 0.37
52 36 0.63
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.30
Consensus pattern (50 bp):
TTGAATCAGCACATTGGCACCTTACATCTTTAAGACCAATATCGCCGACC
Found at i:440587 original size:18 final size:18
Alignment explanation
Indices: 440564--440599 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
440554 ATGTCGCCGA
440564 CCTTGAATCAGCACATTG
1 CCTTGAATCAGCACATTG
440582 CCTTGAATCAGCACATTG
1 CCTTGAATCAGCACATTG
440600 GCACCTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (18 bp):
CCTTGAATCAGCACATTG
Found at i:440624 original size:70 final size:70
Alignment explanation
Indices: 440511--440651 Score: 282
Period size: 70 Copynumber: 2.0 Consensus size: 70
440501 GATATCGTTG
440511 GCCTTGAATCAGCACATTGGCACCTTAACCATCTTTAAGTCCAATGTCGCCGACCTTGAATCAGC
1 GCCTTGAATCAGCACATTGGCACCTTAACCATCTTTAAGTCCAATGTCGCCGACCTTGAATCAGC
440576 ACATT
66 ACATT
440581 GCCTTGAATCAGCACATTGGCACCTTAACCATCTTTAAGTCCAATGTCGCCGACCTTGAATCAGC
1 GCCTTGAATCAGCACATTGGCACCTTAACCATCTTTAAGTCCAATGTCGCCGACCTTGAATCAGC
440646 ACATT
66 ACATT
440651 G
1 G
440652 GCATCTTCAT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (70 bp):
GCCTTGAATCAGCACATTGGCACCTTAACCATCTTTAAGTCCAATGTCGCCGACCTTGAATCAGC
ACATT
Found at i:440687 original size:49 final size:49
Alignment explanation
Indices: 440581--440995 Score: 447
Period size: 49 Copynumber: 8.4 Consensus size: 49
440571 TCAGCACATT
*
440581 GCCTTGAATCAGCACATTGGCACCTTAACCATCTTTAAGTCCAATGTCGCCG
1 GCCTTGAATCAGCACATTGGCACCTT---CATCTTTAAGTCCAATGTCGCTG
* * * * *
440633 ACCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCTAATATCGTTG
1 GCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGCTG
* * * *
440682 GCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTTGCTG
1 GCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGCTG
* * *
440731 GCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGCCCGATATCGCTG
1 GCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGCTG
* * * *
440780 GCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCTA
1 GCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGCTG
* * * *
440829 GCCTTGAATCAGCACATTGGCACCTTCATCTTTAAATCCGATATCGTTG
1 GCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGCTG
* * * * * *
440878 GCCTTGAATAAGCATATTGGCATCTTTAACATTCCTAAGACCAATGTCGCTG
1 GCCTTGAATCAGCACATTGGCACCTTCATC-TT--TAAGTCCAATGTCGCTG
* ** * * *
440930 ACCTTGTCTCAGCACATTGGCA--TTCTTCTTCAAGTCTAATGTCGCTG
1 GCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGCTG
* *
440977 GCCATCAATCAGCACATTG
1 GCCTTGAATCAGCACATTG
440996 TCAATCTTCG
Statistics
Matches: 299, Mismatches: 61, Indels: 11
0.81 0.16 0.03
Matches are distributed among these distances:
47 28 0.09
49 213 0.71
50 5 0.02
52 53 0.18
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (49 bp):
GCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGCTG
Found at i:440758 original size:98 final size:98
Alignment explanation
Indices: 440581--440995 Score: 512
Period size: 98 Copynumber: 4.2 Consensus size: 98
440571 TCAGCACATT
* * * *
440581 GCCTTGAATCAGCACATTGGCACCTTAACCATCTTTAAGTCCAATGTCGCCGACCTTGAATCAGC
1 GCCTTGAATCAGCATATTGGCACCTT---TATCTTTAAGACCAATGTCGCTGACCTTGAATCAGC
* * *
440646 ACATTGGCATCTTCATCTTTAAGTCTAATATCGTTG
63 ACATTGGCACCTTCATCTTTAAGTCCAATATCGCTG
* *
440682 GCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTTGCTGGCCTTGAATCAGCACA
1 GCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCTGACCTTGAATCAGCACA
* *
440747 TTGGCACCTTCATCTTTAAGCCCGATATCGCTG
66 TTGGCACCTTCATCTTTAAGTCCAATATCGCTG
440780 GCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCT-AGCCTTGAATCAGCAC
1 GCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCTGA-CCTTGAATCAGCAC
* * *
440844 ATTGGCACCTTCATCTTTAAATCCGATATCGTTG
65 ATTGGCACCTTCATCTTTAAGTCCAATATCGCTG
* * * **
440878 GCCTTGAATAAGCATATTGGCATCTTTAACATTCCTAAGACCAATGTCGCTGACCTTGTCTCAGC
1 GCCTTGAATCAGCATATTGGCACCTTTATC-TT--TAAGACCAATGTCGCTGACCTTGAATCAGC
* * * *
440943 ACATTGGCA--TTCTTCTTCAAGTCTAATGTCGCTG
63 ACATTGGCACCTTCATCTTTAAGTCCAATATCGCTG
* * *
440977 GCCATCAATCAGCACATTG
1 GCCTTGAATCAGCATATTG
440996 TCAATCTTCG
Statistics
Matches: 277, Mismatches: 32, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
98 181 0.65
99 35 0.13
101 60 0.22
102 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (98 bp):
GCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCTGACCTTGAATCAGCACA
TTGGCACCTTCATCTTTAAGTCCAATATCGCTG
Found at i:441805 original size:19 final size:19
Alignment explanation
Indices: 441781--441827 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
441771 AAACAGTAAA
441781 TGTATCGATGCATAAATGT
1 TGTATCGATGCATAAATGT
441800 TGTATCGATGCATAAATGT
1 TGTATCGATGCATAAATGT
441819 TGTATCGAT
1 TGTATCGAT
441828 ACAATGTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (19 bp):
TGTATCGATGCATAAATGT
Found at i:445061 original size:19 final size:20
Alignment explanation
Indices: 445037--445091 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
445027 GTATCGATAT
* *
445037 ATTGTATCGATACATGTTC-
1 ATTGTATCAATACATGCTCA
*
445056 ATTGTATCAATACATACTCA
1 ATTGTATCAATACATGCTCA
445076 ATTGTATCAATACATG
1 ATTGTATCAATACATG
445092 AAAGTGGCAG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (20 bp):
ATTGTATCAATACATGCTCA
Found at i:445177 original size:33 final size:33
Alignment explanation
Indices: 445122--445188 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
445112 AAGTGAAATG
*
445122 TATCGATACATGAGATAATGTATCGATACATTA
1 TATCAATACATGAGATAATGTATCGATACATTA
*
445155 TATCAATACATGAAGA-ATTGTATCGATACATTA
1 TATCAATACATG-AGATAATGTATCGATACATTA
445188 T
1 T
445189 GCCCAATGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 28 0.90
34 3 0.10
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.34
Consensus pattern (33 bp):
TATCAATACATGAGATAATGTATCGATACATTA
Found at i:446758 original size:20 final size:19
Alignment explanation
Indices: 446729--446766 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
446719 AATGTCACGA
446729 AATGTGTATCGATACAATG
1 AATGTGTATCGATACAATG
446748 AATGATGTATCGATACAAT
1 AATG-TGTATCGATACAAT
446767 TTTTTTCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (19 bp):
AATGTGTATCGATACAATG
Found at i:446875 original size:21 final size:20
Alignment explanation
Indices: 446827--446876 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
446817 TATAGGCATA
*
446827 TATCGATACATTCACTTATG
1 TATCGATACATTAACTTATG
* *
446847 TATTGATACATTAACTTGTTG
1 TATCGATACATTAACTT-ATG
446868 TATCGATAC
1 TATCGATAC
446877 CAATTGTAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (20 bp):
TATCGATACATTAACTTATG
Found at i:447888 original size:78 final size:77
Alignment explanation
Indices: 447757--447917 Score: 180
Period size: 78 Copynumber: 2.1 Consensus size: 77
447747 AAGAGAAAAC
* * * * * * * *
447757 CTAATTTAGTTTATTAGGTAGAAACTAGCGAGGTTGGCATCTTTTAGGGAGGTTAAACCCTATT-
1 CTAATTTAGTTAATTAGGTAAAAACTAACAAGGTTAGCATATGTTAGGAAGGTTAAACCCTATTG
447821 AAAAAAGAAAAGT
66 AAAAAA-AAAAGT
* * *
447834 CTAATTTAGTTAATTAGGTAAAAAACTAATAAGGTTAGCATATGTTAGGAAGGTTAAGCTCTATT
1 CTAATTTAGTTAATTAGGT-AAAAACTAACAAGGTTAGCATATGTTAGGAAGGTTAAACCCTATT
*
447899 GAAAGAAAAAAGT
65 GAAAAAAAAAAGT
*
447912 CCAATT
1 CTAATT
447918 AGGTTGCTTA
Statistics
Matches: 69, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
77 18 0.26
78 46 0.67
79 5 0.07
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (77 bp):
CTAATTTAGTTAATTAGGTAAAAACTAACAAGGTTAGCATATGTTAGGAAGGTTAAACCCTATTG
AAAAAAAAAAGT
Found at i:448147 original size:60 final size:59
Alignment explanation
Indices: 448073--448222 Score: 169
Period size: 60 Copynumber: 2.5 Consensus size: 59
448063 AAAAGGTTAA
* * *
448073 CTTTATCTACTTAAGTGGAAGACCAATAAAGTTA-ACATTTTTAGTTTTTTGTTAAGATC-G
1 CTTTATC-AATTAAGTGGAAGACCAATAAAGTCAGA-ATTTTTAGTTTTATGTTAAG-TCTG
* *
448133 TTTTATCAAGTTAAGTGGAAGACCAATAGAGTCAGAATTTTTAGTTTTATGTTAAGTCTG
1 CTTTATCAA-TTAAGTGGAAGACCAATAAAGTCAGAATTTTTAGTTTTATGTTAAGTCTG
* * *
448193 CTTTAGTGAATTAAGTAGAAGACTAATAAA
1 CTTTA-TCAATTAAGTGGAAGACCAATAAA
448223 AATGACACTT
Statistics
Matches: 76, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
59 3 0.04
60 69 0.91
61 4 0.05
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (59 bp):
CTTTATCAATTAAGTGGAAGACCAATAAAGTCAGAATTTTTAGTTTTATGTTAAGTCTG
Found at i:451696 original size:17 final size:17
Alignment explanation
Indices: 451674--451707 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
451664 TGAGATACAT
451674 TTTTTTCTTTTTCATTG
1 TTTTTTCTTTTTCATTG
451691 TTTTTTCTTTTTCATTG
1 TTTTTTCTTTTTCATTG
451708 ATATTTCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTTTTCTTTTTCATTG
Found at i:451714 original size:17 final size:17
Alignment explanation
Indices: 451677--451714 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
451667 GATACATTTT
* *
451677 TTTCTTTTTCATTGTTT
1 TTTCTTTTTCATTGATA
451694 TTTCTTTTTCATTGATA
1 TTTCTTTTTCATTGATA
451711 TTTC
1 TTTC
451715 ATGTTTTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.13, G:0.05, T:0.71
Consensus pattern (17 bp):
TTTCTTTTTCATTGATA
Found at i:452122 original size:21 final size:21
Alignment explanation
Indices: 452096--452135 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
452086 ACAACAAAGA
452096 GGTTAGCTTC-CTTAGTGAAGG
1 GGTTAG-TTCTCTTAGTGAAGG
*
452117 GGTTAGTTCTTTTAGTGAA
1 GGTTAGTTCTCTTAGTGAA
452136 TAGGTCAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.20, C:0.10, G:0.30, T:0.40
Consensus pattern (21 bp):
GGTTAGTTCTCTTAGTGAAGG
Found at i:452191 original size:22 final size:22
Alignment explanation
Indices: 452163--452240 Score: 102
Period size: 22 Copynumber: 3.5 Consensus size: 22
452153 TGTTATAGTC
* *
452163 ATGTACATACTGTTATAATGAT
1 ATGTACATATTATTATAATGAT
* *
452185 ATGTACATGTTATTATATTGAT
1 ATGTACATATTATTATAATGAT
* *
452207 ATGTACATATTATTACAGTGAT
1 ATGTACATATTATTATAATGAT
452229 ATGTACATATTA
1 ATGTACATATTA
452241 ATTGTAAGTG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.44
Consensus pattern (22 bp):
ATGTACATATTATTATAATGAT
Found at i:453285 original size:22 final size:22
Alignment explanation
Indices: 453257--453312 Score: 80
Period size: 20 Copynumber: 2.6 Consensus size: 22
453247 TGAATAAGAT
453257 AATATGTATATATAGTAAAAAC
1 AATATGTATATATAGTAAAAAC
*
453279 AATATG--TATATAGTAAAAAT
1 AATATGTATATATAGTAAAAAC
*
453299 AATATATATATATA
1 AATATGTATATATA
453313 TATTGCATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 18 0.60
22 12 0.40
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (22 bp):
AATATGTATATATAGTAAAAAC
Found at i:453778 original size:16 final size:16
Alignment explanation
Indices: 453744--453791 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
453734 GTTTCCTTTC
*
453744 TAACAATTTTTATCT-T
1 TAAC-ATTTTTATTTAT
453760 TAACATTTTTATTTAT
1 TAACATTTTTATTTAT
* *
453776 TAATATTATTATTTAT
1 TAACATTTTTATTTAT
453792 CATTAGACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 9 0.32
16 19 0.68
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.60
Consensus pattern (16 bp):
TAACATTTTTATTTAT
Found at i:455374 original size:28 final size:30
Alignment explanation
Indices: 455316--455374 Score: 68
Period size: 31 Copynumber: 2.0 Consensus size: 30
455306 GGAAGACGAA
* *
455316 AAAAAAAGAACATGATACTTTGAGTATATAT
1 AAAAAAAGAACATGATAATTTGAG-ACATAT
*
455347 AAAAGAAGAACATGATAATTT-A-ACATAT
1 AAAAAAAGAACATGATAATTTGAGACATAT
455375 TTATTTTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
28 5 0.20
30 1 0.04
31 19 0.76
ACGTcount: A:0.54, C:0.07, G:0.12, T:0.27
Consensus pattern (30 bp):
AAAAAAAGAACATGATAATTTGAGACATAT
Found at i:460117 original size:20 final size:20
Alignment explanation
Indices: 460092--460192 Score: 103
Period size: 20 Copynumber: 4.8 Consensus size: 20
460082 GTAAATCCAG
*
460092 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGAAC
460112 AATGTATCGATACAATGAAC
1 AATGTATCGATACAATGAAC
* *
460132 AATGTATCGATACATCTAGGACCCAG
1 AATGTATCGATACA---ATGA---AC
460158 AATGTATCGATACAATGAAC
1 AATGTATCGATACAATGAAC
* *
460178 AATATATCAATACAA
1 AATGTATCGATACAA
460193 ATTATGAAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
20 47 0.69
23 6 0.09
26 15 0.22
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAATGAAC
Found at i:460172 original size:66 final size:67
Alignment explanation
Indices: 460063--460192 Score: 190
Period size: 66 Copynumber: 1.9 Consensus size: 67
460053 GCCTGAATAA
* * * * *
460063 AATGTATCGATACATCTGGGTAAATCCAGAATGTATCGATACAATGAGCAATGTATCGATACAAT
1 AATGTATCGATACATCTAGG--AACCCAGAATGTATCGATACAATGAACAATATATCAATACAAT
460128 GAAC
64 GAAC
460132 AATGTATCGATACATCTAGG-ACCCAGAATGTATCGATACAATGAACAATATATCAATACAA
1 AATGTATCGATACATCTAGGAACCCAGAATGTATCGATACAATGAACAATATATCAATACAA
460193 ATTATGAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
66 37 0.66
69 19 0.34
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.25
Consensus pattern (67 bp):
AATGTATCGATACATCTAGGAACCCAGAATGTATCGATACAATGAACAATATATCAATACAATGA
AC
Found at i:463930 original size:20 final size:20
Alignment explanation
Indices: 463905--463942 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
463895 GTATCGATAC
*
463905 AATGTATTGATACATTTCGT
1 AATGTATCGATACATTTCGT
463925 AATGTATCGATACATTTC
1 AATGTATCGATACATTTC
463943 CTTGGCAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (20 bp):
AATGTATCGATACATTTCGT
Found at i:463980 original size:13 final size:13
Alignment explanation
Indices: 463962--464013 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
463952 AGCTTCGTAG
463962 CGATACATTGTAT
1 CGATACATTGTAT
463975 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
463994 CGATACATTGTAT
1 CGATACATTGTAT
464007 CGATACA
1 CGATACA
464014 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:463994 original size:19 final size:19
Alignment explanation
Indices: 463970--464034 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
463960 AGCGATACAT
463970 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
463989 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
464002 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
464021 TGTATCGATACAAA
1 TGTATCGATACAAA
464035 TTGTTGAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 2 0.05
18 1 0.03
19 24 0.62
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:464003 original size:32 final size:32
Alignment explanation
Indices: 463962--464032 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
463952 AGCTTCGTAG
463962 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
463994 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
464026 CGATACA
1 CGATACA
464033 AATTGTTGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:468946 original size:78 final size:78
Alignment explanation
Indices: 468846--469047 Score: 223
Period size: 79 Copynumber: 2.6 Consensus size: 78
468836 ATAAAATCGA
* * * * *
468846 GGTTAGAGTATCCCCTCGAAATAACAGGGTTGGAGTATCACT-GATTAT-AAAAATTGGT-ATTT
1 GGTTGGAGTATCCCCTTGAAATAACGGGGTTGGAGTATC-CTCGATTATGAAAAATCGATGA-TT
* **
468908 TGAAAATGAA-ATTGG
64 TAAAAAT-AAGACCGG
* *
468923 GGTTGGAGTATCCGCTTGAAAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAATCGATGATTT
1 GGTTGGAGTATCCCCTTG-AAATAACGGGGTTGGAGTATCCTCGATTATGAAAAATCGATGATTT
*
468988 AAAAATAAGGCCGG
65 AAAAATAAGACCGG
*
469002 GGTTGAAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCTCGAT
1 GGTTGGAGTATCCCCTT-GAAATAACGGGGTTGGAGTATCCTCGAT
469048 AAAATAACGG
Statistics
Matches: 106, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
77 17 0.16
78 27 0.25
79 60 0.57
80 2 0.02
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (78 bp):
GGTTGGAGTATCCCCTTGAAATAACGGGGTTGGAGTATCCTCGATTATGAAAAATCGATGATTTA
AAAATAAGACCGG
Found at i:469033 original size:28 final size:27
Alignment explanation
Indices: 468999--469073 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 27
468989 AAAATAAGGC
* * *
468999 CGGGGTTGAAGTATCCCCTTGGAAATAA
1 CGGGGTTGGAGTATCCCCAT-AAAATAA
*
469027 CGGGGTTGGAGTATCCTCGATAAAATAA
1 CGGGGTTGGAGTATCC-CCATAAAATAA
469055 CGGGGTTGGAGTATCCCCA
1 CGGGGTTGGAGTATCCCCA
469074 ATTGTGAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 2 0.05
28 37 0.90
29 2 0.05
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.24
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCATAAAATAA
Found at i:469118 original size:51 final size:51
Alignment explanation
Indices: 469059--469174 Score: 178
Period size: 51 Copynumber: 2.3 Consensus size: 51
469049 AAATAACGGG
* *
469059 GTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCAATTGTGAAAAATTGGTATTTTAGAAATAAAATCGGA
* * * *
469110 GTTGGAGTATCCCCGATTGTGGAAATTTGGTATTTTAGAAATAAAATCGGG
1 GTTGGAGTATCCCCAATTGTGAAAAATTGGTATTTTAGAAATAAAATCGGA
469161 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
469175 TCGAAAATAA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCCAATTGTGAAAAATTGGTATTTTAGAAATAAAATCGGA
Found at i:469119 original size:107 final size:107
Alignment explanation
Indices: 468921--469123 Score: 264
Period size: 107 Copynumber: 1.9 Consensus size: 107
468911 AAATGAAATT
* * *
468921 GGGGTTGGAGTATCCGCTTGAAAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAATCGATGAT
1 GGGGTTGGAGTATCCGCATGAAAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATCGATGAT
** *
468986 TTAAAAATAAGGCCGGGGTTGAAGTATCCCCTTGGAAATAAC
66 TTAAAAATAAAACCGGAGTTGAAGTATCCCCTTGGAAATAAC
* * * *
469028 GGGGTTGGAGTATCCTCGAT-AAAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATTGGTGT
1 GGGGTTGGAGTATCCGC-ATGAAAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATCGATGA
** * *
469092 TTTGGAAATAAAATCGGAGTTGGAGTATCCCC
65 TTTAAAAATAAAACCGGAGTTGAAGTATCCCC
469124 GATTGTGGAA
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
107 80 0.99
108 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.27
Consensus pattern (107 bp):
GGGGTTGGAGTATCCGCATGAAAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATCGATGAT
TTAAAAATAAAACCGGAGTTGAAGTATCCCCTTGGAAATAAC
Found at i:469152 original size:158 final size:157
Alignment explanation
Indices: 468952--469241 Score: 366
Period size: 158 Copynumber: 1.8 Consensus size: 157
468942 AAATAACGGG
* **
468952 GTTGGAGTATCCTCGATTGTGAAAAATCGATGATTTAAAAATAAGGCCGGGGTTGAAGTATCCCC
1 GTTGGAGTATCCCCGATTGTGAAAAATCGATGATTTAAAAATAAAACCGGGGTTGAAGTATCCCC
* * *** * * * *
469017 TTGGAAATAACGGGGTTGGAGTATCCTCGATAAAATAACGGGGTTGGAGTATCCCCAATTGTGAA
66 TCGAAAATAACGAAATTGGAGTA-CCCCGATAAAATAACGGGGTTAGAGTACCCCCAATTATGAA
469082 AAATTGGTGTTTTGGAAATAAAATCGGA
130 AAATTGGTGTTTTGGAAATAAAATCGGA
* * * * * * *
469110 GTTGGAGTATCCCCGATTGTGGAAATTTGGT-ATTTTAGAAATAAAATCGGGGTTGGAGTATCCC
1 GTTGGAGTATCCCCGATTGTGAAAAATCGATGA-TTTAAAAATAAAACCGGGGTTGAAGTATCCC
* *
469174 CTCGAAAATAACGAAATTGGAGTACCCCGATGAAATAACGGGGTTAGAGTACCCCCGATTATGAA
65 CTCGAAAATAACGAAATTGGAGTACCCCGATAAAATAACGGGGTTAGAGTACCCCCAATTATGAA
469239 AAA
130 AAA
469242 ATAATATTTT
Statistics
Matches: 110, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
157 39 0.35
158 71 0.65
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (157 bp):
GTTGGAGTATCCCCGATTGTGAAAAATCGATGATTTAAAAATAAAACCGGGGTTGAAGTATCCCC
TCGAAAATAACGAAATTGGAGTACCCCGATAAAATAACGGGGTTAGAGTACCCCCAATTATGAAA
AATTGGTGTTTTGGAAATAAAATCGGA
Found at i:471676 original size:20 final size:20
Alignment explanation
Indices: 471651--471757 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
471641 AAAATGCCTG
*
471651 AATGTATCGATACATTGTA-A
1 AATGTATCGATACAATG-AGA
* *
471671 AATGTATCAATACAATGAGC
1 AATGTATCGATACAATGAGA
471691 AATGTATCGATACAAT----
1 AATGTATCGATACAATGAGA
* *
471707 -A--TAGCGATACAATGAGC
1 AATGTATCGATACAATGAGA
471724 AATGTATCGATACAATGCA-A
1 AATGTATCGATACAATG-AGA
471744 AATGTATCGATACA
1 AATGTATCGATACA
471758 TCTAGGTAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
13 11 0.15
15 1 0.01
18 1 0.01
19 1 0.01
20 56 0.79
21 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACAATGAGA
Found at i:471820 original size:13 final size:13
Alignment explanation
Indices: 471773--471802 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
471763 GTAAACCCAG
471773 AATGTATCGATAC
1 AATGTATCGATAC
471786 AATGTATCGATAC
1 AATGTATCGATAC
471799 AATG
1 AATG
471803 AACAATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:472668 original size:45 final size:43
Alignment explanation
Indices: 472529--472723 Score: 177
Period size: 42 Copynumber: 4.5 Consensus size: 43
472519 AAAAGAGCAC
* * *
472529 GTCCTGCT-TTTCGAGGA-TAAAGGAAAAAAGGAAAACGAAA-TG-
1 GTCCTGCTCTTT-GAGGACAAAAGGAAAGAA-GAAAA-TAAAGTGT
* * *
472571 GTCCTACTCTTTGAGGAC-AAACGAAAGAGGAAAAATAAAGTGT
1 GTCCTGCTCTTTGAGGACAAAAGGAAAGAAG-AAAATAAAGTGT
* ** *
472614 GTCATGCTCTTTGAGGACAAAAGAGAAAAGAAGGGAATGAAGTGT
1 GTCCTGCTCTTTGAGGACAAAAG-G-AAAGAAGAAAATAAAGTGT
*
472659 GTCCTGCTCTTTGAGGA-TAAAGGAAAGAAGAAAATAAAGTGT
1 GTCCTGCTCTTTGAGGACAAAAGGAAAGAAGAAAATAAAGTGT
*
472701 GTCCTACTCTTTGAGGACTAAAA
1 GTCCTGCTCTTTGAGGAC-AAAA
472724 AGTGTCACCA
Statistics
Matches: 124, Mismatches: 19, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
41 4 0.03
42 58 0.47
43 20 0.16
44 10 0.08
45 26 0.21
46 6 0.05
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.22
Consensus pattern (43 bp):
GTCCTGCTCTTTGAGGACAAAAGGAAAGAAGAAAATAAAGTGT
Found at i:472794 original size:61 final size:61
Alignment explanation
Indices: 472702--473725 Score: 694
Period size: 61 Copynumber: 16.9 Consensus size: 61
472692 ATAAAGTGTG
* * *
472702 TCCTACTCTTTGAGGACTA-AAAAGTGTCACCAAATCGTGTGGGCTTTGAAAAGGAAAGGCA
1 TCCTACTCTTTGAGGACTAGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCA
** * *
472763 TCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTATGGGCTTTGCAAAGAGAAA-GCA
1 TCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAG-GAAAGGCA
* * * * *
472824 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTAGGCTTTGAAAAGAAAAGGCG
1 TCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCA
* *
472885 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTG-AAAGGAAAAGGGA
1 TCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGG-AAAGGCA
*
472946 TCCTACTCTTTGAGGACTAGAAAAATGCCACCAACTTGTGTGGGCTTT-AAAAGGGAAAAG-A
1 TCCTACTCTTTGAGGACTAG-AAAATGCCACCAACTTGTGTGGGCTTTGAAAA-GGAAAGGCA
***** *** *** * ** * * **
473007 ----AGGAAATGAAGTG-C--G-TCCTGCTCTTTAA--GGATAAGGG---GGAATAAAGTGA-G-
1 TCCTACTCTTTG-AG-GACTAGAAAATGC-CACCAACTTG-TGTGGGCTTTGAA-AAGGAAAGGC
473057 -
61 A
* * * ** * **
473057 TCTTGCTCTTTGAGGACTAGGAGGTGCCACCAACTTGTGTGGGCTTTG-AAAGGAAAATGTG
1 TCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGG-AAAGGCA
* * ** * * *
473118 TCCTGCTCTTTGAGAACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGCG
1 TCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAG--GAAAGGCA
* * *** * *
473180 TCCTGCTCTTTGAGGACTGGAGGGTGCCACCAACTCGTGTGGGCTTTG-AAAGGAAAAGGGCG
1 TCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGG-AAA-GGCA
* ** * *
473242 TCCTGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAAGGCA
1 TCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAG---GAAAGGCA
** * ** * *
473305 TCCTGGTCTTTAAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGCA
1 TCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAG--GAAAGGCA
* *** * *
473367 TCCTGCTCTTTGAGGACTAGAGGGTGCCACCAACTCGTGTGGGCTTTG-AAAGGAAAAGGCG
1 TCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGG-AAAGGCA
* ** * *
473428 TCCTGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAAGGCA
1 TCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAG---GAAAGGCA
* * *** * * **
473491 TCCTGCTCTTTGAGGACTGGAGGGTGCCACCAACTCGTGTGGGC-TTG-CAAGGAGAAGGTG
1 TCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGA-AAGGCA
* * *
473551 TCCTGCTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGCG
1 TCCTACTCTTTGAGGACTAGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAAGG-AAAGGCA
** * *
473612 TCCTACTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCA
1 TCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCA
* *
473672 TCTTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGG
1 TCCTACTCTTTGAGGACTAGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAAGG
473726 GAAAAGAAGG
Statistics
Matches: 792, Mismatches: 116, Indels: 110
0.78 0.11 0.11
Matches are distributed among these distances:
51 1 0.00
52 5 0.01
53 6 0.01
54 9 0.01
55 7 0.01
56 8 0.01
57 7 0.01
58 5 0.01
59 5 0.01
60 147 0.19
61 286 0.36
62 150 0.19
63 131 0.17
64 25 0.03
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.25
Consensus pattern (61 bp):
TCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCA
Found at i:473154 original size:60 final size:60
Alignment explanation
Indices: 473060--473731 Score: 869
Period size: 60 Copynumber: 10.9 Consensus size: 60
473050 AAGTGAGTCT
* * * *
473060 TGCTCTTTGAGGACTAGGAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAATGTGTCC
1 TGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCC
* *
473121 TGCTCTTTGAGAACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGCGTCC
1 TGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG-GAAAAGGCGTCC
* * * *
473183 TGCTCTTTGAGGACTGGAGGGTGCCACCAACTCGTGTGGGCTTTGAAAGGAAAAGGGCGTCC
1 TGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-GGCGTCC
* *
473245 TGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAAGGCATCC
1 TGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG--GAAAAGGCGTCC
* * * *
473308 TGGTCTTTAAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGCATCC
1 TGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG-GAAAAGGCGTCC
* * *
473370 TGCTCTTTGAGGACTAGAGGGTGCCACCAACTCGTGTGGGCTTTGAAAGGAAAAGGCGTCC
1 TGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCC
* *
473431 TGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAAGGCATCC
1 TGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG--GAAAAGGCGTCC
* * * ** * *
473494 TGCTCTTTGAGGACTGGAGGGTGCCACCAACTCGTGTGGGC-TTGCAAGGAGAAGGTGTCC
1 TGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCC
473554 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCC
1 TGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCC
* * * *
473615 TACTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCATCT
1 TGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCC
*
473675 TGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGGAAAAG
1 TGCTCTTTGAGGACT--AAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GGAAAAG
473732 AAGGAAATGA
Statistics
Matches: 539, Mismatches: 56, Indels: 30
0.86 0.09 0.05
Matches are distributed among these distances:
60 152 0.28
61 107 0.20
62 118 0.22
63 136 0.25
64 26 0.05
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (60 bp):
TGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCC
Found at i:473298 original size:123 final size:122
Alignment explanation
Indices: 473060--473731 Score: 872
Period size: 124 Copynumber: 5.5 Consensus size: 122
473050 AAGTGAGTCT
* * * *
473060 TGCTCTTTGAGGACT-AGGAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAATGTGTCCTGC
1 TGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGC
*
473124 TCTTTGAGAACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGCGTCC
65 TCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAG-AAAAAGGCGTCC
* * * *
473183 TGCTCTTTGAGGACTGGAGGGTGCCACCAACTCGTGTGGGCTTTGAAAGGAAAAGGGCGTCCTGC
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-GGCGTCCTGC
*
473248 TCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAAGGCATCC
65 TCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAG--AAAAAGGCGTCC
* * * *
473308 TGGTCTTTAAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGCATCCTG
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG-GAAAAGGCGTCCTG
* * * *
473372 CTCTTTGAGGACTAGAGGGTGCCACCAACTCGTGTGGGCTTT-GAAAGGAAAAGGCGTCC
64 CTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGCGTCC
* *
473431 TGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAAGGCATCCT
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG--GAAAAGGCGTCCT
* * * ** * * *
473495 GCTCTTTGAGGACTGGAGGGTGCCACCAACTCGTGTGGGC-TT-GCAAGGAGAAGGTGTCC
63 GCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGCGTCC
* *
473554 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTACT
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCT
* *
473619 CTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAG-AAAAGGCATCT
66 CTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGCGTCC
*
473675 TGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGGAAAAG
1 TGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GGAAAAG
473732 AAGGAAATGA
Statistics
Matches: 495, Mismatches: 41, Indels: 26
0.88 0.07 0.05
Matches are distributed among these distances:
120 22 0.04
121 48 0.10
122 34 0.07
123 149 0.30
124 158 0.32
125 55 0.11
126 29 0.06
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (122 bp):
TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCT
CTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGCGTCC
Found at i:473628 original size:184 final size:185
Alignment explanation
Indices: 473060--473723 Score: 984
Period size: 184 Copynumber: 3.6 Consensus size: 185
473050 AAGTGAGTCT
* * * *
473060 TGCTCTTTGAGGACTAGGAGGTGCCACCAACTTGTGTGGGCTTT-GAAAGGAAAATGTG--TCCT
1 TGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAG-GCATCCT
*
473122 GCTCTTTGAGAACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGCGTCCTGCT
64 GCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGCGTCCTGCT
*
473187 CTTTGAGGACTGGAGGGTGCCACCAACTCGTGTGGGCTTTGAAAGGAAAAGGGCGTCC
129 CTTTGAGGACTAGAGGGTGCCACCAACTCGTGTGGGCTTTGAAAGGAAAA-GGCGTCC
473245 TGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAAGGCATCCTG
1 TGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAG-AAAAAAGGCATCCTG
* * *
473310 GTCTTTAAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGCATCCTGCTC
65 CTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGCGTCCTGCTC
473375 TTTGAGGACTAGAGGGTGCCACCAACTCGTGTGGGCTTTGAAAGGAAAAGGCGTCC
130 TTTGAGGACTAGAGGGTGCCACCAACTCGTGTGGGCTTTGAAAGGAAAAGGCGTCC
473431 TGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAAGGCATCCTG
1 TGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAG-AAAAAAGGCATCCTG
* * * ** * * *
473496 CTCTTTGAGGACTGGAGGGTGCCACCAACTCGTGTGGGC-TT-GCAAG-GAGAAGGTGTCCTGCT
65 CTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGCGTCCTGCT
* * * *
473558 CTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCC
129 CTTTGAGGACTAGAGGGTGCCACCAACTCGTGTGGGCTTTGAAAGGAAAAGGCGTCC
* *
473615 TACTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAG--AAAAGGCATCTTGC
1 TGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGCATCCTGC
*
473678 TCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
66 TCTTTGAGGACT--AAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
473724 GGGAAAAGAA
Statistics
Matches: 439, Mismatches: 32, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
181 25 0.06
182 22 0.05
183 2 0.00
184 140 0.32
185 24 0.05
186 90 0.21
187 136 0.31
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (185 bp):
TGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGCATCCTGC
TCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGCGTCCTGCTCT
TTGAGGACTAGAGGGTGCCACCAACTCGTGTGGGCTTTGAAAGGAAAAGGCGTCC
Found at i:473928 original size:61 final size:62
Alignment explanation
Indices: 473782--474058 Score: 375
Period size: 61 Copynumber: 4.5 Consensus size: 62
473772 GAAGGAAAAT
* * * *
473782 AAAGTGCGTCTTGCTCTTTGAGGACT-AGGAGGTGCCACCAACTTGTGTGGGCTTT--GAAGGA
1 AAAG-GCGTCCTGCTCTTTGAGGACTAAAGA-GTGCCACCAACTTGTGTGGGCTTTAAAAAGAA
* * * *
473843 GAAGACGTCCTGCTCTTTGAGGACTAAAGAGTGCCACCAATTTGTGTGGGCTTT-AAAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAGAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAA
*
473904 AAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAGAGTGCCACCAACTTGTGTGGGCTTTAAAAAG-AA
*
473967 AAAGGCGTCCTGCTCTTTAAGGACTAAAG-GTGCCACCAACTTGTGTGGGCTTTAAAAAGAA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAGAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAA
*
474028 AAAGGGCGTCTTGCTCTTTGAGGACTGAAAG
1 AAA-GGCGTCCTGCTCTTTGAGGACT-AAAG
474059 GGCTAAAAGA
Statistics
Matches: 196, Mismatches: 14, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
60 42 0.21
61 66 0.34
62 55 0.28
63 33 0.17
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (62 bp):
AAAGGCGTCCTGCTCTTTGAGGACTAAAGAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAA
Found at i:480379 original size:78 final size:78
Alignment explanation
Indices: 480227--480411 Score: 214
Period size: 78 Copynumber: 2.4 Consensus size: 78
480217 AGATAAAACG
* *
480227 GGGTTGGAGTATCCCCGATTATGGAAAATTGGTGTTCCAGAAATAAAATCGAGGTTGGAGTATCC
1 GGGTTGGAGTATCACCGATTATGAAAAATTGGTGTTCCAGAAATAAAATCGAGGTTGGAGTATCC
**
480292 CTCGGAAATAACA
66 CTCAAAAATAACA
* * ** * *
480305 GGGTTGGAGTATCACTGATTAT-AAAAATTGGTATT-TTGAAAATGAAATCGGGGTTGGAGTATC
1 GGGTTGGAGTATCACCGATTATGAAAAATTGGTGTTCCAG-AAATAAAATCGAGGTTGGAGTAT-
*
480368 CCCTCAAAAATAACG
64 CCCTCAAAAATAACA
*
480383 GGGTTGGAGTATC-CTCGATTGTGAAAAAT
1 GGGTTGGAGTATCAC-CGATTATGAAAAAT
480412 CGATGATTTA
Statistics
Matches: 90, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
76 1 0.01
77 33 0.37
78 50 0.56
79 6 0.07
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.28
Consensus pattern (78 bp):
GGGTTGGAGTATCACCGATTATGAAAAATTGGTGTTCCAGAAATAAAATCGAGGTTGGAGTATCC
CTCAAAAATAACA
Found at i:480472 original size:28 final size:28
Alignment explanation
Indices: 480434--480505 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
480424 AATAAGGCCA
* *
480434 GGGTTGAAGTATCCCC-TTGGAAATAACG
1 GGGTTGGAGTATCCCCGAT-GAAATAACG
480462 GGGTTGGAGTATCCCCGATGAAATAACG
1 GGGTTGGAGTATCCCCGATGAAATAACG
*
480490 GGATTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
480506 AATTGTGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 39 0.98
29 1 0.03
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCGATGAAATAACG
Found at i:480552 original size:51 final size:51
Alignment explanation
Indices: 480493--480607 Score: 167
Period size: 51 Copynumber: 2.3 Consensus size: 51
480483 AATAACGGGA
* *
480493 TTGGAGTATCCCCAATTGTGAAAAATTGATGTTTTTGAAATAAAATCAGAG
1 TTGGAGTATCCCCAATTGTGAAAAATTGATATTTTAGAAATAAAATCAGAG
* * * * *
480544 TTGGAGTATCCCCGATTGTGGAAAATTGGTATTTTAGAAATAAAATCGGGG
1 TTGGAGTATCCCCAATTGTGAAAAATTGATATTTTAGAAATAAAATCAGAG
480595 TTGGAGTATCCCC
1 TTGGAGTATCCCC
480608 TTGGAAATAA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.32
Consensus pattern (51 bp):
TTGGAGTATCCCCAATTGTGAAAAATTGATATTTTAGAAATAAAATCAGAG
Found at i:480552 original size:107 final size:107
Alignment explanation
Indices: 480353--480556 Score: 275
Period size: 107 Copynumber: 1.9 Consensus size: 107
480343 AAAATGAAAT
* * *
480353 CGGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCAAAAATAACGGGATTGGAGTATCCCCAATTGTGAAAAATCGATGA
** *
480418 TTTAGAAATAAGGCCAGGGTTGAAGTATCCCCTTGGAAATAA
66 TTTAGAAATAAAACCAGAGTTGAAGTATCCCCTTGGAAATAA
* * *
480460 CGGGGTTGGAGTATCCCC-GATGAAATAACGGGATTGGAGTATCCCCAATTGTGAAAAATTGATG
1 CGGGGTTGGAGTATCCCCTCA-AAAATAACGGGATTGGAGTATCCCCAATTGTGAAAAATCGATG
* * * *
480524 TTTTTGAAATAAAATCAGAGTTGGAGTATCCCC
65 ATTTAGAAATAAAACCAGAGTTGAAGTATCCCC
480557 GATTGTGGAA
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
106 1 0.01
107 82 0.99
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.26
Consensus pattern (107 bp):
CGGGGTTGGAGTATCCCCTCAAAAATAACGGGATTGGAGTATCCCCAATTGTGAAAAATCGATGA
TTTAGAAATAAAACCAGAGTTGAAGTATCCCCTTGGAAATAA
Found at i:480621 original size:28 final size:28
Alignment explanation
Indices: 480590--480663 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
480580 GAAATAAAAT
*
480590 CGGGGTTGGAGTATCCCC-TTGGAAATAA
1 CGGGGTTGGAGTATCCCCGAT-GAAATAA
*
480618 CGGGATTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
480646 CGGGGTTAGAGTACCCCC
1 CGGGGTTGGAGTATCCCC
480664 CGATTATGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 39 0.98
29 1 0.03
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:480692 original size:158 final size:160
Alignment explanation
Indices: 480385--480716 Score: 420
Period size: 158 Copynumber: 2.1 Consensus size: 160
480375 AAATAACGGG
* **
480385 GTTGGAGTATCCTCGATTGTGAAAAATCGATGATTTAGAAATAAGGCCAGGGTTGAAGTATCCCC
1 GTTGGAGTATCCCCGATTGTGAAAAATCGATGATTTAGAAATAAAACCAGGGTTGAAGTATCCCC
* * * *
480450 TTGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGGGATTGGAGTATCCCCAATTGTGAA
66 TTGGAAATAACGGGATTGGAGTATCCCCGATGAAATAACGGGATTAGAGTACCCCCAATTATGAA
*** * *
480515 AAATTGATGTTTTTGAAATA-AAA-TCAGA
131 AAAACAATATTTTTGAAATATAAAGCCAGA
* * * * * *
480543 GTTGGAGTATCCCCGATTGTGGAAAATTGGT-ATTTTAGAAATAAAATCGGGGTTGGAGTATCCC
1 GTTGGAGTATCCCCGATTGTGAAAAATCGATGA-TTTAGAAATAAAACCAGGGTTGAAGTATCCC
* *
480607 CTTGGAAATAACGGGATTGGAGTATCCCCGATGAAATAACGGGGTTAGAGTACCCCCCGATTATG
65 CTTGGAAATAACGGGATTGGAGTATCCCCGATGAAATAACGGGATTAGAGTA-CCCCCAATTATG
* *
480672 AAAAAACAATATTTTT-AAATATAAAGCCGGG
129 AAAAAACAATATTTTTGAAATATAAAGCCAGA
480703 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
480717 TCGAAAATAA
Statistics
Matches: 148, Mismatches: 22, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
157 1 0.01
158 107 0.72
159 24 0.16
160 16 0.11
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (160 bp):
GTTGGAGTATCCCCGATTGTGAAAAATCGATGATTTAGAAATAAAACCAGGGTTGAAGTATCCCC
TTGGAAATAACGGGATTGGAGTATCCCCGATGAAATAACGGGATTAGAGTACCCCCAATTATGAA
AAAACAATATTTTTGAAATATAAAGCCAGA
Found at i:483146 original size:13 final size:13
Alignment explanation
Indices: 483116--483146 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
483106 ATACAATGAG
*
483116 CAATATATCGATA
1 CAATGTATCGATA
483129 CAATGTATCGATA
1 CAATGTATCGATA
483142 CAATG
1 CAATG
483147 AGCAATATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:483166 original size:33 final size:33
Alignment explanation
Indices: 483097--483168 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
483087 AAAATGCCTG
*
483097 AATGTATCGATACAATGAGCAATATATCGATAC
1 AATGTATCGATACAATGAGCAATATATCAATAC
*
483130 AATGTATCGATACAATGAGCAATATGAT-AATGC
1 AATGTATCGATACAATGAGCAATAT-ATCAATAC
483163 AATGTA
1 AATGTA
483169 ATGATAGATC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 34 0.94
34 2 0.06
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (33 bp):
AATGTATCGATACAATGAGCAATATATCAATAC
Found at i:483212 original size:13 final size:13
Alignment explanation
Indices: 483194--483218 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
483184 AAACCCAGAA
483194 TGTATCGATACAT
1 TGTATCGATACAT
483207 TGTATCGATACA
1 TGTATCGATACA
483219 ATGAACAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:486145 original size:20 final size:20
Alignment explanation
Indices: 486120--486194 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
486110 AAAAAGATAG
486120 AATGTATCGATACATTAAAA
1 AATGTATCGATACATTAAAA
* *
486140 AATGTATCGATACATTCATA
1 AATGTATCGATACATTAAAA
* * *
486160 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTAAAA
486180 AATGTATCGATACAT
1 AATGTATCGATACAT
486195 CTCGGTAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTAAAA
Found at i:487864 original size:21 final size:20
Alignment explanation
Indices: 487818--487870 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
487808 GTAGCCAAAC
**
487818 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACCAAAAA
487838 -TGTATCGATACACCAAAAAA
1 TTGTATCGATACACC-AAAAA
487858 TTGTATCGATACA
1 TTGTATCGATACA
487871 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 14 0.48
20 3 0.10
21 12 0.41
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (20 bp):
TTGTATCGATACACCAAAAA
Found at i:494051 original size:13 final size:13
Alignment explanation
Indices: 494033--494071 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
494023 ACATTTTTCT
494033 TTGTATCGATACA
1 TTGTATCGATACA
*
494046 TTGTATTGATACA
1 TTGTATCGATACA
* *
494059 CTGTATCAATACA
1 TTGTATCGATACA
494072 GGGGGATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:494235 original size:20 final size:20
Alignment explanation
Indices: 494192--494237 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
494182 AAATCTTTTG
494192 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
494213 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
494233 CAAAA
1 CAAAA
494238 CCAGCATCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:496659 original size:12 final size:12
Alignment explanation
Indices: 496642--496666 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
496632 TACACCAAGT
496642 ATGTATCGATAC
1 ATGTATCGATAC
496654 ATGTATCGATAC
1 ATGTATCGATAC
496666 A
1 A
496667 CCAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:496686 original size:33 final size:31
Alignment explanation
Indices: 496624--496688 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 31
496614 TAGCCAAACT
**
496624 TGTATCGATACACCAAGTATGTATCGATACA
1 TGTATCGATACACCAAAAATGTATCGATACA
*
496655 TGTATCGATACACCAAAAAATTGTATTGATACA
1 TGTATCGATACACC-AAAAA-TGTATCGATACA
496688 T
1 T
496689 TGGCTTGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 14 0.48
32 3 0.10
33 12 0.41
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (31 bp):
TGTATCGATACACCAAAAATGTATCGATACA
Found at i:499075 original size:20 final size:21
Alignment explanation
Indices: 499052--499097 Score: 85
Period size: 20 Copynumber: 2.2 Consensus size: 21
499042 GAGAAAAAGA
499052 AAAAAAATTAATTTTTGGTT-
1 AAAAAAATTAATTTTTGGTTG
499072 AAAAAAATTAATTTTTGGTTG
1 AAAAAAATTAATTTTTGGTTG
499093 AAAAA
1 AAAAA
499098 TCGGGTTGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (21 bp):
AAAAAAATTAATTTTTGGTTG
Found at i:501592 original size:20 final size:22
Alignment explanation
Indices: 501557--501614 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
501547 TCAAAAGCCC
**
501557 AGAATGTATCTTTACAAT-A-G
1 AGAATGTATCGATACAATCATG
*
501577 ATAATGTATCGATACAATCATG
1 AGAATGTATCGATACAATCATG
*
501599 AGCATGTATCGATACA
1 AGAATGTATCGATACA
501615 TTTACTTATG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 15 0.48
21 1 0.03
22 15 0.48
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.31
Consensus pattern (22 bp):
AGAATGTATCGATACAATCATG
Found at i:507264 original size:67 final size:67
Alignment explanation
Indices: 507100--507342 Score: 267
Period size: 67 Copynumber: 3.6 Consensus size: 67
507090 ACCCAAGCCC
* * * *
507100 AAAAGGG-GTTGACTAAGGCGAAACTGATAAAATCAACTAAAAGAGATCTAG-GCGGAACCTAAG
1 AAAAGGGTGTTGACCAAGGCGAAACCGATAAAATCAACTAAAAGATA-CTAGAGTGGAACCTAAG
507163 TCA
65 TCA
* * * * * *
507166 AAAAGGGTGTTGACTAATGCAAAATCAATAAAGTCAACTAAAAGATACTAGAGTGGAACCTAAGT
1 AAAAGGGTGTTGACCAAGGCGAAACCGATAAAATCAACTAAAAGATACTAGAGTGGAACCTAAGT
507231 CA
66 CA
* * * *
507233 AAAAGGGTGTTGACCAAGGTGAAACCGATAAAGTCAATTAAAAGATACTA-AGGTAGAACCTAAG
1 AAAAGGGTGTTGACCAAGGCGAAACCGATAAAATCAACTAAAAGATACTAGA-GTGGAACCTAAG
**
507297 TTG
65 TCA
* ** *
507300 GAAAGGGAATTGACCAAGGCGAAACCGATAAAACCAACTAAAA
1 AAAAGGGTGTTGACCAAGGCGAAACCGATAAAATCAACTAAAA
507343 TAGACCAAGC
Statistics
Matches: 149, Mismatches: 25, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
66 12 0.08
67 137 0.92
ACGTcount: A:0.46, C:0.14, G:0.22, T:0.18
Consensus pattern (67 bp):
AAAAGGGTGTTGACCAAGGCGAAACCGATAAAATCAACTAAAAGATACTAGAGTGGAACCTAAGT
CA
Found at i:507674 original size:161 final size:163
Alignment explanation
Indices: 507353--507832 Score: 496
Period size: 161 Copynumber: 3.0 Consensus size: 163
507343 TAGACCAAGC
* *
507353 CAAAACCT-ATAAAGCCAA-CAAGTTAGAGGGGTTTGGCTAGGGCAAAACTGATAAAGCCAAC-A
1 CAAAA-CTGATAAAGTCAACCAA-TTAGAAGGG-TTGGCTAGGGCAAAACTGATAAAGCCAACAA
* * * * *
507415 AGTTAAGGGGTTGACCAAGGCGAAACCGATAAAGTCAACCAATTAAAGGGGTTAGTCATAGTGAA
63 AGTTAAGGAGTTGACCAAGGCAAAACCGATAAAGTCAACCAATT-AAGGGGTTAGCCAGAGTAAA
* *
507480 ATCGATAAAGCCAATAGGTTAGAGGGGTTGACTAGGG
127 ACCAATAAAGCCAATAGGTTAGAGGGGTTGACTAGGG
* *
507517 CAAAACTGATAAAGTCAACCAATTAGAAGGGTTGGCTAGGGCAAAA-TCGATAAAACCAACAAAT
1 CAAAACTGATAAAGTCAACCAATTAGAAGGGTTGGCTAGGGCAAAACT-GATAAAGCCAACAAAG
* * * * *
507581 TTGAA-GAGTTGACCAAGGCAAAACTGATAAAGTTAATCAATT-AGGGG-TCGCCAGGGTAAAAC
65 TT-AAGGAGTTGACCAAGGCAAAACCGATAAAGTCAACCAATTAAGGGGTTAGCCAGAGTAAAAC
507643 CAATAAA-CCTAATAGGTTAGAGGGGTTGACTAGGG
129 CAATAAAGCC-AATAGGTTAGAGGGGTTGACTAGGG
** * * *
507678 TGAAACCGATAAAGTCAACCAATTA-AAGGGTTGGCCAAGGCAAAACTGATAAAGCCAAC-AAGT
1 CAAAACTGATAAAGTCAACCAATTAGAAGGGTTGGCTAGGGCAAAACTGATAAAGCCAACAAAGT
* * ** * * * * * *
507741 TAAGGTGGTTGACCAGGGTGAAACCAATAAAGTTAA-TAAGTTAGAGGGGTTAGCTAGGGCAAAA
66 TAAGG-AGTTGACCAAGGCAAAACCGATAAAGTCAACCAA-TTA-AGGGGTTAGCCAGAGTAAAA
* *
507805 CCAATAAAGCCAACAAGTTAGAGGGGTT
128 CCAATAAAGCCAATAGGTTAGAGGGGTT
507833 AGCCGAGGTA
Statistics
Matches: 267, Mismatches: 35, Indels: 29
0.81 0.11 0.09
Matches are distributed among these distances:
158 2 0.01
159 7 0.03
160 57 0.21
161 63 0.24
162 11 0.04
163 62 0.23
164 60 0.22
165 5 0.02
ACGTcount: A:0.40, C:0.15, G:0.26, T:0.19
Consensus pattern (163 bp):
CAAAACTGATAAAGTCAACCAATTAGAAGGGTTGGCTAGGGCAAAACTGATAAAGCCAACAAAGT
TAAGGAGTTGACCAAGGCAAAACCGATAAAGTCAACCAATTAAGGGGTTAGCCAGAGTAAAACCA
ATAAAGCCAATAGGTTAGAGGGGTTGACTAGGG
Found at i:507992 original size:162 final size:161
Alignment explanation
Indices: 507659--508323 Score: 571
Period size: 162 Copynumber: 4.1 Consensus size: 161
507649 ACCTAATAGG
* * * * * *
507659 TTAGAGGGGTT-GACTAGGGTGAAACCGATAAAGTCAACCA-ATTAAAG-GGTTGGCCAAGGCAA
1 TTAGAGGGGTTAG-CCAGGGTGAAACCAATAAAGCCAA-CAGGTTAGAGAGGTTGACCAA-GCAA
* * * ** * ** *
507721 AACTGATAAAGCCAA-CAAGTTA-AGGTGGTTGACCAGGGTGAAACCAATAAAGTTAATAAGTTA
63 AA-TGATAAAGTCAACCAA-TTAGAGG-GGTTGGCCAAGGCAAAACCGATAAAGCCAACAAGTTA
* * * * *
507784 GAGGGGTT-AGCTAGGGCAAAACCAATAAAGCCAA-CAA
125 -AAGGGTTGA-CCAAGGCAAAACCGATAAAGTCAACCAA
* * *
507821 GTTAGAGGGGTTAGCC-GAGGTAAAACCAATAAAGCTAACAGGTTAGAG-GG-TAACCACAGCAA
1 -TTAGAGGGGTTAGCCAG-GGTGAAACCAATAAAGCCAACAGGTTAGAGAGGTTGACCA-AGCAA
* * *
507883 AACTGATAAAGTCAACCAATTAGAGGGGTTGGCCAAGGCGAAATCGATAAAGCCAACAGGTTAAA
63 AA-TGATAAAGTCAACCAATTAGAGGGGTTGGCCAAGGCAAAACCGATAAAGCCAACAAGTTAAA
***
507948 GGGGTTGACCAAGTTGAAACCGATAAAGTCAACCAA
127 -GGGTTGACCAAGGCAAAACCGATAAAGTCAACCAA
* * * * *
507984 TTAGAGGGGTTAGCCAGGGTGAAACTAATAAGGCCAACAGGTTAGAGAGGTTGACTAGGGAAAAA
1 TTAGAGGGGTTAGCCAGGGTGAAACCAATAAAGCCAACAGGTTAGAGAGGTTGACCA-AGCAAAA
* * *
508049 TTGATAAAGCCAACCAATTAGAGGGTTTGGCCAGGGCAAAACCGATAAAGCCAACAAGTTAAAGG
65 -TGATAAAGTCAACCAATTAGAGGGGTTGGCCAAGGCAAAACCGATAAAGCCAACAAGTTAAAGG
* * *
508114 GTTGACCAAGGCAAAACTGAT-GAGTCAACTAA
129 GTTGACCAAGGCAAAACCGATAAAGTCAACCAA
* * * *
508146 TTAGAAGGGTTAGCCAGGGTGAAACCGATAAATCCAATAGGTTAGAGAGGTTGACCAAGTCAAAA
1 TTAGAGGGGTTAGCCAGGGTGAAACCAATAAAGCCAACAGGTTAGAGAGGTTGACCAAG-CAAAA
* * * *
508211 TAGATAAAGTCAACCAATTAGAGGGGGTTGGCCAGGGCAAAACC-ACCAAAGCCAATAGATTTAA
65 T-GATAAAGTCAACCAATTAGA-GGGGTTGGCCAAGGCAAAACCGA-TAAAGCCAACA-AGTTAA
* * * * *
508275 GAGGGTTGACTAAGACAAAATCGATAAAGTTAATCAA
126 -AGGGTTGACCAAGGCAAAACCGATAAAGTCAACCAA
*
508312 TTAGAGAGGTTA
1 TTAGAGGGGTTA
508324 CTCAAGGCAA
Statistics
Matches: 410, Mismatches: 73, Indels: 35
0.79 0.14 0.07
Matches are distributed among these distances:
161 3 0.01
162 202 0.49
163 97 0.24
164 71 0.17
165 20 0.05
166 17 0.04
ACGTcount: A:0.40, C:0.15, G:0.26, T:0.18
Consensus pattern (161 bp):
TTAGAGGGGTTAGCCAGGGTGAAACCAATAAAGCCAACAGGTTAGAGAGGTTGACCAAGCAAAAT
GATAAAGTCAACCAATTAGAGGGGTTGGCCAAGGCAAAACCGATAAAGCCAACAAGTTAAAGGGT
TGACCAAGGCAAAACCGATAAAGTCAACCAA
Found at i:508058 original size:203 final size:202
Alignment explanation
Indices: 507680--508134 Score: 517
Period size: 203 Copynumber: 2.2 Consensus size: 202
507670 GACTAGGGTG
507680 AAACCGATAAAGTCAACCAATTAAAGGGTTGGCCAAGGCAAAACTGATAAAGCCAACAAGTTAAG
1 AAACCGATAAAGTCAACCAATTAAAGGGTTGGCCAAGGCAAAACTGATAAAGCCAACAAGTTAAG
* * * *
507745 GTGGTTGACCAGGGTGAAACCAATAAAGTTAATAAGTTAGAGGGGTTAGCTAGGGCAAAACCAAT
66 GTGGTTGACCAAGGTGAAACCAATAAAGTCAACAAGTTAGAGGGGTTAGCCAGGGCAAAACCAAT
* * *
507810 AAAGCCAACAAGTTAGAGGGGTTAGCCGAGGTAAAACCAATAAAGCTAACAGGTTAGAGGGTAAC
131 AAAGCCAACAAGTTAGAGAGGTTAGACGAGGAAAAACCAATAAAGCTAACAGGTTAGAGGGTAAC
507875 CACAGCA
196 CACAGCA
* * * *
507882 AAACTGATAAAGTCAACCAATTAGAGGGGTTGGCCAAGGCGAAA-TCGATAAAGCCAACAGGTTA
1 AAACCGATAAAGTCAACCAATTA-AAGGGTTGGCCAAGGCAAAACT-GATAAAGCCAACAAGTT-
* * **
507946 AAGG-GGTTGACCAAGTTGAAACCGATAAAGTCAACCAA-TTAGAGGGGTTAGCCAGGGTGAAAC
63 AAGGTGGTTGACCAAGGTGAAACCAATAAAGTCAA-CAAGTTAGAGGGGTTAGCCAGGGCAAAAC
* * * * *** * *
508009 TAATAAGGCCAACAGGTTAGAGAGGTT-GACTAGGGAAAAATTGATAAAGCCAACCA-ATTAGAG
127 CAATAAAGCCAACAAGTTAGAGAGGTTAGACGA-GGAAAAACCAATAAAGCTAA-CAGGTTAGAG
** **
508072 GGTTTGGCCAGGGCA
190 GG--TAACCACAGCA
* *
508087 AAACCGATAAAGCCAA-CAAGTTAAAGGGTTGACCAAGGCAAAACTGAT
1 AAACCGATAAAGTCAACCAA-TTAAAGGGTTGGCCAAGGCAAAACTGAT
508135 GAGTCAACTA
Statistics
Matches: 210, Mismatches: 33, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
202 26 0.12
203 128 0.61
204 31 0.15
205 25 0.12
ACGTcount: A:0.40, C:0.16, G:0.26, T:0.17
Consensus pattern (202 bp):
AAACCGATAAAGTCAACCAATTAAAGGGTTGGCCAAGGCAAAACTGATAAAGCCAACAAGTTAAG
GTGGTTGACCAAGGTGAAACCAATAAAGTCAACAAGTTAGAGGGGTTAGCCAGGGCAAAACCAAT
AAAGCCAACAAGTTAGAGAGGTTAGACGAGGAAAAACCAATAAAGCTAACAGGTTAGAGGGTAAC
CACAGCA
Found at i:508527 original size:123 final size:122
Alignment explanation
Indices: 508353--508634 Score: 264
Period size: 123 Copynumber: 2.3 Consensus size: 122
508343 AGCCAATAAG
* * * * * * *
508353 TTAGAGGGGTTGACTAGGGCAGAACCAATAAAGTCAACTAATCAAAAGGGTTAGCTAGGGCGAAA
1 TTAGAGGGGTTGGCTAAGGCAAAATC-ATAAAGCCAACCAATCAAAAGGGTTAGCTAGAG-GAAA
* * * * * ** * * *
508418 CT-GATAAAACTAATAAGTTAGAGGGGGTGAA-TAGGGTGAAATCGATAAAGTTAATCAA
64 ATCAATAAAACAAATAAGTTAGAGGGGAT-AACCAAAGCGAAATCAATAAAGTTAAGCAA
** * * *
508476 TTAGAGGGGTTGGCTAAGGCAAAATCGATAAAGCCAACCAATTTAAGGGGTTGGCTAGAGTAAAA
1 TTAGAGGGGTTGGCTAAGGCAAAATC-ATAAAGCCAACCAATCAAAAGGGTTAGCTAGAGGAAAA
*
508541 TCAATAAAGCAAATAAGTTAGAGGGGATAACCAAAGCGAAATCAATAAAGTTAAGCAA
65 TCAATAAAACAAATAAGTTAGAGGGGATAACCAAAGCGAAATCAATAAAGTTAAGCAA
* * *
508599 TTAGA-AGGTTGGCCAAGGCAAAACTCATAAAACCAA
1 TTAGAGGGGTTGGCTAAGGCAAAA-TCATAAAGCCAA
508635 TAGGCTAGAG
Statistics
Matches: 129, Mismatches: 27, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
122 31 0.24
123 98 0.76
ACGTcount: A:0.43, C:0.12, G:0.25, T:0.20
Consensus pattern (122 bp):
TTAGAGGGGTTGGCTAAGGCAAAATCATAAAGCCAACCAATCAAAAGGGTTAGCTAGAGGAAAAT
CAATAAAACAAATAAGTTAGAGGGGATAACCAAAGCGAAATCAATAAAGTTAAGCAA
Found at i:508529 original size:41 final size:41
Alignment explanation
Indices: 507353--508566 Score: 558
Period size: 41 Copynumber: 29.8 Consensus size: 41
507343 TAGACCAAGC
* *
507353 CAAAACCTATAAAGCCAACAAGTTAGAGGGGTTTGGCTAGGG
1 CAAAACCGATAAAGCCAACAAGTTAGAGGGG-TTGGCCAGGG
* * *
507395 CAAAACTGATAAAGCCAACAAGTTA-AGGGGTTGACCAAGG
1 CAAAACCGATAAAGCCAACAAGTTAGAGGGGTTGGCCAGGG
* * * * * **
507435 CGAAACCGATAAAGTCAACCAA-TTAAAGGGGTTAGTCATAG
1 CAAAACCGATAAAGCCAA-CAAGTTAGAGGGGTTGGCCAGGG
** * * * * *
507476 TGAAATCGATAAAGCCAATAGGTTAGAGGGGTTGACTAGGG
1 CAAAACCGATAAAGCCAACAAGTTAGAGGGGTTGGCCAGGG
* * * *
507517 CAAAACTGATAAAGTCAACCAA-TTAGAAGGGTTGGCTAGGG
1 CAAAACCGATAAAGCCAA-CAAGTTAGAGGGGTTGGCCAGGG
* * * * * * * *
507558 CAAAATCGATAAAACCAACAAATTTGAAGAGTTGACCAAGG
1 CAAAACCGATAAAGCCAACAAGTTAGAGGGGTTGGCCAGGG
* ** *
507599 CAAAACTGATAAAGTTAATCAA-TT--AGGGG-TCGCCAGGG
1 CAAAACCGATAAAGCCAA-CAAGTTAGAGGGGTTGGCCAGGG
* * * * * *
507637 TAAAACCAATAAA-CCTAATAGGTTAGAGGGGTTGACTAGGG
1 CAAAACCGATAAAGCC-AACAAGTTAGAGGGGTTGGCCAGGG
** * * *
507678 TGAAACCGATAAAGTCAACCAA-TTA-AAGGGTTGGCCAAGG
1 CAAAACCGATAAAGCCAA-CAAGTTAGAGGGGTTGGCCAGGG
* *
507718 CAAAACTGATAAAGCCAACAAGTTA-AGGTGGTTGACCAGGG
1 CAAAACCGATAAAGCCAACAAGTTAGAGG-GGTTGGCCAGGG
** * ** * * *
507759 TGAAACCAATAAAGTTAATAAGTTAGAGGGGTTAGCTAGGG
1 CAAAACCGATAAAGCCAACAAGTTAGAGGGGTTGGCCAGGG
* *
507800 CAAAACCAATAAAGCCAACAAGTTAGAGGGGTTAGCC-GAGG
1 CAAAACCGATAAAGCCAACAAGTTAGAGGGGTTGGCCAG-GG
* * * * ** **
507841 TAAAACCAATAAAGCTAACAGGTTAGA-GGG-TAACCACAG
1 CAAAACCGATAAAGCCAACAAGTTAGAGGGGTTGGCCAGGG
* * *
507880 CAAAACTGATAAAGTCAACCAA-TTAGAGGGGTTGGCCAAGG
1 CAAAACCGATAAAGCCAA-CAAGTTAGAGGGGTTGGCCAGGG
* * * * * * *
507921 CGAAATCGATAAAGCCAACAGGTTAAAGGGGTTGACCAAGT
1 CAAAACCGATAAAGCCAACAAGTTAGAGGGGTTGGCCAGGG
** * *
507962 TGAAACCGATAAAGTCAACCAA-TTAGAGGGGTTAGCCAGGG
1 CAAAACCGATAAAGCCAA-CAAGTTAGAGGGGTTGGCCAGGG
** ** * * * * *
508003 TGAAACTAATAAGGCCAACAGGTTAGAGAGGTTGACTAGGG
1 CAAAACCGATAAAGCCAACAAGTTAGAGGGGTTGGCCAGGG
* ** *
508044 AAAAATTGATAAAGCCAACCAA-TTAGAGGGTTTGGCCAGGG
1 CAAAACCGATAAAGCCAA-CAAGTTAGAGGGGTTGGCCAGGG
* * *
508085 CAAAACCGATAAAGCCAACAAGTTA-AAGGGTTGACCAAGG
1 CAAAACCGATAAAGCCAACAAGTTAGAGGGGTTGGCCAGGG
* * * * *
508125 CAAAACTGAT-GAGTCAACTAA-TTAGAAGGGTTAGCCAGGG
1 CAAAACCGATAAAGCCAAC-AAGTTAGAGGGGTTGGCCAGGG
** * * * * * * *
508165 TGAAACCGATAAATCCAATAGGTTAGAGAGGTTGACCAAGT
1 CAAAACCGATAAAGCCAACAAGTTAGAGGGGTTGGCCAGGG
** *
508206 CAAAATAGATAAAGTCAACCAA-TTAGAGGGGGTTGGCCAGGG
1 CAAAACCGATAAAGCCAA-CAAGTTAGA-GGGGTTGGCCAGGG
* * * * * * *
508248 CAAAACC-ACCAAAGCCAATAGATTTA-AGAGGGTTGACTAAGA
1 CAAAACCGA-TAAAGCCAACA-AGTTAGAG-GGGTTGGCCAGGG
* ** * * *
508290 CAAAATCGATAAAGTTAATCAA-TTAGAGAGGTT-ACTCAAGG
1 CAAAACCGATAAAGCCAA-CAAGTTAGAGGGGTTGGC-CAGGG
** * * *
508331 CAAAATTGATAAAGCCAATAAGTTAGAGGGGTTGACTAGGG
1 CAAAACCGATAAAGCCAACAAGTTAGAGGGGTTGGCCAGGG
* * * * * * * *
508372 CAGAACCAATAAAGTCAACTAA-TCAAAAGGGTTAGCTAGGG
1 CAAAACCGATAAAGCCAAC-AAGTTAGAGGGGTTGGCCAGGG
* * * * * * ***
508413 CGAAACTGATAAAACTAATAAGTTAGAGGGGGTGAATAGGG
1 CAAAACCGATAAAGCCAACAAGTTAGAGGGGTTGGCCAGGG
** * ** * *
508454 TGAAATCGATAAAGTTAATCAA-TTAGAGGGGTTGGCTAAGG
1 CAAAACCGATAAAGCCAA-CAAGTTAGAGGGGTTGGCCAGGG
* * * *
508495 CAAAATCGATAAAGCCAACCAATTTA-AGGGGTTGGCTAGAG
1 CAAAACCGATAAAGCCAA-CAAGTTAGAGGGGTTGGCCAGGG
* * * * *
508536 TAAAATCAATAAAGCAAATAAGTTAGAGGGG
1 CAAAACCGATAAAGCCAACAAGTTAGAGGGG
508567 ATAACCAAAG
Statistics
Matches: 867, Mismatches: 258, Indels: 95
0.71 0.21 0.08
Matches are distributed among these distances:
37 1 0.00
38 20 0.02
39 38 0.04
40 133 0.15
41 576 0.66
42 94 0.11
43 5 0.01
ACGTcount: A:0.40, C:0.15, G:0.26, T:0.19
Consensus pattern (41 bp):
CAAAACCGATAAAGCCAACAAGTTAGAGGGGTTGGCCAGGG
Found at i:509800 original size:17 final size:15
Alignment explanation
Indices: 509755--509811 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 15
509745 TTTTGTCTAA
* *
509755 TTTTTCTCTTTTCTC
1 TTTTTTTCTTTTTTC
509770 TTTTTTT-TTATTTTC
1 TTTTTTTCTT-TTTTC
509785 ATTTTTTGTCTTTTTTC
1 -TTTTTT-TCTTTTTTC
509802 TTGTTTTTCT
1 TT-TTTTTCT
509812 AGGCATAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
14 2 0.06
15 10 0.29
16 11 0.31
17 10 0.29
18 2 0.06
ACGTcount: A:0.04, C:0.14, G:0.04, T:0.79
Consensus pattern (15 bp):
TTTTTTTCTTTTTTC
Found at i:514841 original size:20 final size:20
Alignment explanation
Indices: 514816--514865 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
514806 CAGTTTCATA
**
514816 TATCGATACAATTGTGCATG
1 TATCGATACAATTGAACATG
514836 TATCGATACAA-TGAACATG
1 TATCGATACAATTGAACATG
514855 TAT-GATACAAT
1 TATCGATACAAT
514866 GTATCAATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 7 0.26
19 9 0.33
20 11 0.41
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (20 bp):
TATCGATACAATTGAACATG
Found at i:515851 original size:33 final size:33
Alignment explanation
Indices: 515809--515875 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
515799 CCGTGTACTA
*
515809 AAGTGCTCATCCATGCACTGCGAGAGTGAAGTG
1 AAGTGCTCATCCATGCACTGCGAAAGTGAAGTG
* **
515842 AAGTGCTCATTCATGTGCTGCGAAAGTGAAGTG
1 AAGTGCTCATCCATGCACTGCGAAAGTGAAGTG
515875 A
1 A
515876 TCAACTCTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (33 bp):
AAGTGCTCATCCATGCACTGCGAAAGTGAAGTG
Found at i:516804 original size:21 final size:21
Alignment explanation
Indices: 516778--516820 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
516768 AGAGCTATTA
**
516778 GAATGAATAAAAATTGTTTTG
1 GAATGAATAAAAAGCGTTTTG
516799 GAATGAATAAAAAGCGTTTTG
1 GAATGAATAAAAAGCGTTTTG
516820 G
1 G
516821 TATAAAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.02, G:0.23, T:0.33
Consensus pattern (21 bp):
GAATGAATAAAAAGCGTTTTG
Found at i:523472 original size:20 final size:20
Alignment explanation
Indices: 523447--523499 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
523437 TCCCGTTGCT
**
523447 ATGTATCGATACAATTCATA
1 ATGTATCGATACAAAGCATA
523467 ATGTATCGATACAAAGCATA
1 ATGTATCGATACAAAGCATA
523487 ATGTATCGATACA
1 ATGTATCGATACA
523500 TACAAGGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACAAAGCATA
Found at i:523800 original size:13 final size:14
Alignment explanation
Indices: 523777--523920 Score: 68
Period size: 14 Copynumber: 9.9 Consensus size: 14
523767 AAATTTAATC
523777 TTTTTTA-TA-TTA
1 TTTTTTATTATTTA
523789 TTTTTTATTATTTA
1 TTTTTTATTATTTA
*
523803 TTATTT-TTATTTA
1 TTTTTTATTATTTA
523816 TTTATTTATT-TTT-
1 TTT-TTTATTATTTA
* *
523829 GTGTTTATTAATTT-
1 TTTTTTATT-ATTTA
*
523843 TTTAATTAATTAATTTA
1 TTT--TTTATT-ATTTA
*
523860 TTTTTTTAATTAATTAA
1 -TTTTTT-ATT-ATTTA
*
523877 TTATTGTTGTTATTATA
1 TT-TT-TTATTATT-TA
523894 TTTTTT-TATATTTA
1 TTTTTTAT-TATTTA
523908 TTTTTTTATTATT
1 -TTTTTTATTATT
523921 ATTCATGTTA
Statistics
Matches: 104, Mismatches: 11, Indels: 31
0.71 0.08 0.21
Matches are distributed among these distances:
12 13 0.12
13 12 0.12
14 21 0.20
15 18 0.17
16 20 0.19
17 15 0.14
18 5 0.05
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (14 bp):
TTTTTTATTATTTA
Found at i:523806 original size:17 final size:17
Alignment explanation
Indices: 523784--523923 Score: 71
Period size: 17 Copynumber: 8.0 Consensus size: 17
523774 ATCTTTTTTA
523784 TATTATTTTTTATTATT
1 TATTATTTTTTATTATT
523801 TATTA-TTTTTATTTATT
1 TATTATTTTTTA-TTATT
*
523818 TATTTATTTTTGTGTTTATT
1 TA-TTATTTTT-T-ATTATT
*
523838 AATT-TTTTAATTAATTAATT
1 TATTATTTT--TT-ATT-ATT
*
523858 TATT-TTTTTAATTAATT
1 TATTATTTTTTATT-ATT
*
523875 AATTATTGTTGTTATTA--
1 TATTATT-TT-TTATTATT
523892 TA-T-TTTTTTA-TATT
1 TATTATTTTTTATTATT
*
523906 TATTTTTTTATTATTATT
1 TATTATTTT-TTATTATT
523924 CATGTTAAAT
Statistics
Matches: 97, Mismatches: 9, Indels: 33
0.70 0.06 0.24
Matches are distributed among these distances:
12 2 0.02
13 3 0.03
14 4 0.04
15 3 0.03
16 11 0.11
17 26 0.27
18 14 0.14
19 12 0.12
20 22 0.23
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
TATTATTTTTTATTATT
Found at i:523815 original size:4 final size:4
Alignment explanation
Indices: 523780--523917 Score: 65
Period size: 4 Copynumber: 34.5 Consensus size: 4
523770 TTTAATCTTT
*
523780 TTTA TATTA TTT- TTTA -TTA TTTA TTATT TTTA TTTA TTTA TTTA TTT-
1 TTTA T-TTA TTTA TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TTTA
* * * * * * *
523827 TTGTG TTTA TTAA TTT- TTTAA TTAA TTAA TTTA TTTT TTTA ATTA ATTA
1 TT-TA TTTA TTTA TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * *
523876 ATTA TTGT- TGTTA TTATA TTT- TTT- TATA TTTA TTTT TTTA TT
1 TTTA TT-TA T-TTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA TT
523918 ATTATTCATG
Statistics
Matches: 106, Mismatches: 15, Indels: 26
0.72 0.10 0.18
Matches are distributed among these distances:
3 16 0.15
4 72 0.68
5 18 0.17
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:523916 original size:56 final size:57
Alignment explanation
Indices: 523781--523923 Score: 131
Period size: 53 Copynumber: 2.6 Consensus size: 57
523771 TTAATCTTTT
* * * * *
523781 TTATATTATTTTT-TA-TTA-TTTATTATTTTTATTTATTTATTTATTTTTGTGTTTA
1 TTATATT-TTTTTATATTTATTTTTTTATTTTTATTAATTAATTAATTATTGTGTTTA
* **
523836 TTA-A-TTTTTTA-ATTAATTAATTTATTTTT-TTAATTAATTAATTATTGT-TGTTA
1 TTATATTTTTTTATATTTATTTTTTTATTTTTATTAATTAATTAATTATTGTGT-TTA
*
523889 TTATATTTTTTTATATTTATTTTTTTATTATTATT
1 TTATATTTTTTTATATTTATTTTTTTATTTTTATT
523924 CATGTTAAAT
Statistics
Matches: 68, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
52 7 0.10
53 24 0.35
54 11 0.16
55 10 0.15
56 14 0.21
57 2 0.03
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (57 bp):
TTATATTTTTTTATATTTATTTTTTTATTTTTATTAATTAATTAATTATTGTGTTTA
Found at i:524492 original size:42 final size:42
Alignment explanation
Indices: 524446--524908 Score: 327
Period size: 42 Copynumber: 10.9 Consensus size: 42
524436 AAAAGGTGAA
* *
524446 AAAGTCTCTAAGGTCAAAGTCGACAGGCAGACTGAGGGTAGG
1 AAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTGAGGGTAGG
* * **
524488 AAAGTCT-TCAGGGTCAAAGCCGACCGGTAGACTGAGGGTAAA
1 AAAGTCTCT-AGGGTCAAAGCCGACAGGCAGACTGAGGGTAGG
* *
524530 AAAGTCTCTAGGGTCAAAGCCGACAGACAGACTTTA-GGTGAGG
1 AAAGTCTCTAGGGTCAAAGCCGACAGGCAGAC-TGAGGGT-AGG
* * * *
524573 -TAGTCT-TCAGGGTCAAAGCCAACAGGCAGACTTAAGGTAAGG
1 AAAGTCTCT-AGGGTCAAAGCCGACAGGCAGACTGAGGGT-AGG
* * * * * *
524615 -CAGTCTCCAGGGTCAAAGCCAATAGGCAGATTGAGGGGTAAG
1 AAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTGA-GGGTAGG
* * * *
524657 AAAGTCTCCAGGGTCAAAGCCGACAAGCAGACTTTA--G-ATG
1 AAAGTCTCTAGGGTCAAAGCCGACAGGCAGAC-TGAGGGTAGG
* * * *
524697 AAGTAGTCTCCAGGGTCAAAGTCGACACGCAGACTGAAGGGTAAG
1 AA--AGTCTCTAGGGTCAAAGCCGACAGGCAGACTG-AGGGTAGG
* ***
524742 AAAATCTCTAGGGTCAAAGCCGACAGGCAGACTTTTGGTAAGG
1 AAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTGAGGGT-AGG
* * * *
524785 -CAGTCTCCAAGGTCAAA-CCTGACAAGCAGACTGAAGGGTAGG
1 AAAGTCTCTAGGGTCAAAGCC-GACAGGCAGACTG-AGGGTAGG
* * * *** *
524827 AAAGTCTCTAAGGTCAAAGTCGACAGGCAAACTTTTGATAAGG
1 AAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTGAGGGT-AGG
* *
524870 -CAGTCTCTAGGGTCAAAGCTGACAGGCAGACTGAAGGGT
1 AAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTG-AGGGT
524909 TGGTCAAAGC
Statistics
Matches: 330, Mismatches: 68, Indels: 45
0.74 0.15 0.10
Matches are distributed among these distances:
40 4 0.01
41 9 0.03
42 214 0.65
43 95 0.29
44 4 0.01
45 4 0.01
ACGTcount: A:0.33, C:0.19, G:0.30, T:0.18
Consensus pattern (42 bp):
AAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTGAGGGTAGG
Found at i:524688 original size:85 final size:84
Alignment explanation
Indices: 524448--524908 Score: 444
Period size: 85 Copynumber: 5.4 Consensus size: 84
524438 AAGGTGAAAA
* * * * * *
524448 AGTCTCTAAGGTCAAAGTCGACAGGCAGACTGAGGGTAGGAAAGTCTTCAGGGTCAAAGCCGACC
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGTAAGAAAGTCTCCAGGGTCAAAGCCGACA
* * ***
524513 GGTAGAC-TGAGGGTAAAAA
66 GGCAGACTTTA-GGTAAGGC
* * * * ** * *
524532 AGTCTCTAGGGTCAAAGCCGACAGACAGACTTTA-GGTGAGGTAGTCTTCAGGGTCAAAGCCAAC
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGAC-TGAGGGTAAGAAAGTCTCCAGGGTCAAAGCCGAC
*
524596 AGGCAGACTTAAGGTAAGGC
65 AGGCAGACTTTAGGTAAGGC
* * *
524616 AGTCTCCAGGGTCAAAGCCAATAGGCAGATTGAGGGGTAAGAAAGTCTCCAGGGTCAAAGCCGAC
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTGA-GGGTAAGAAAGTCTCCAGGGTCAAAGCCGAC
* * *
524681 AAGCAGACTTTAGATGAA-GT
65 AGGCAGACTTTAGGT-AAGGC
* * * *
524701 AGTCTCCAGGGTCAAAGTCGACACGCAGACTGAAGGGTAAGAAAATCTCTAGGGTCAAAGCCGAC
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTG-AGGGTAAGAAAGTCTCCAGGGTCAAAGCCGAC
*
524766 AGGCAGACTTTTGGTAAGGC
65 AGGCAGACTTTAGGTAAGGC
* * * * * *
524786 AGTCTCCAAGGTCAAA-CCTGACAAGCAGACTGAAGGGTAGGAAAGTCTCTAAGGTCAAAGTCGA
1 AGTCTCCAGGGTCAAAGCC-GACAGGCAGACTG-AGGGTAAGAAAGTCTCCAGGGTCAAAGCCGA
* * *
524850 CAGGCAAACTTTTGATAAGGC
64 CAGGCAGACTTTAGGTAAGGC
* *
524871 AGTCTCTAGGGTCAAAGCTGACAGGCAGACTGAAGGGT
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTG-AGGGT
524909 TGGTCAAAGC
Statistics
Matches: 314, Mismatches: 54, Indels: 17
0.82 0.14 0.04
Matches are distributed among these distances:
83 2 0.01
84 91 0.29
85 217 0.69
86 4 0.01
ACGTcount: A:0.33, C:0.20, G:0.30, T:0.18
Consensus pattern (84 bp):
AGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGTAAGAAAGTCTCCAGGGTCAAAGCCGACA
GGCAGACTTTAGGTAAGGC
Found at i:524704 original size:127 final size:126
Alignment explanation
Indices: 524448--525103 Score: 477
Period size: 127 Copynumber: 5.3 Consensus size: 126
524438 AAGGTGAAAA
* * * *
524448 AGTCTCTAAGGTCAAAGTCGACAGGCAGACTGAGGGT-AGGAAAGTCTTCAGGGTCAAAGCCGAC
1 AGTCTCCAGGGTCAAAGTCGACAGGCAGACTGAAGGTAAGG-AAGTCTCCAGGGTCAAAGCCGAC
* * * * * * *
524512 CGGTAGACTGAGGGTAAAAAAGTCTCTAGGGTCAAAGCCGAC-AGACAGACTTTAGGTGAGGT
65 AGGCAGATTGAGGGTAAGAAAGTCTCCAGGGTCAAAGCCGACAAG-CAGACTTTAGATGAAGT
* * * * * * *
524574 AGTCTTCAGGGTCAAAGCCAACAGGCAGACTTAAGGTAAGGCAGTCTCCAGGGTCAAAGCCAATA
1 AGTCTCCAGGGTCAAAGTCGACAGGCAGACTGAAGGTAAGGAAGTCTCCAGGGTCAAAGCCGACA
524639 GGCAGATTGAGGGGTAAGAAAGTCTCCAGGGTCAAAGCCGACAAGCAGACTTTAGATGAAGT
66 GGCAGATTGA-GGGTAAGAAAGTCTCCAGGGTCAAAGCCGACAAGCAGACTTTAGATGAAGT
* * * *
524701 AGTCTCCAGGGTCAAAGTCGACACGCAGACTGAAGGGTAAGAAAATCTCTAGGGTCAAAGCCGAC
1 AGTCTCCAGGGTCAAAGTCGACAGGCAGACTGAA-GGTAAGGAAGTCTCCAGGGTCAAAGCCGAC
** ** * ** *
524766 AGGCAGACTT-TTGGTAAGGCAGTCTCCAAGGTCAAA-CCTGACAAGCAGACTGAAGGGTAGGAA
65 AGGCAGA-TTGAGGGTAAGAAAGTCTCCAGGGTCAAAGCC-GACAAGCAGACTTTA--G-ATGAA
524829 --
125 GT
* * * *** * * * *
524829 AGTCTCTAAGGTCAAAGTCGACAGGCAAACTTTTGATAAGGCAGTCTCTAGGGTCAAAGCTGACA
1 AGTCTCCAGGGTCAAAGTCGACAGGCAGACTGAAGGTAAGGAAGTCTCCAGGGTCAAAGCCGACA
* * * * * * * * *
524894 GGCAGACT----G-AAG--GGT-T----GGTCAAAGCCGATAGGTAGACTTGAGGTGAGGC
66 GGCAGATTGAGGGTAAGAAAGTCTCCAGGGTCAAAGCCGACAAGCAGACTTTAGATGAAGT
* * * * * *
524943 AGTCTCCAAGGTCATAGCCGACAGGCAGATTGAGGGT-AGGAAAGTCTCCAGGGTCAAAACCGAC
1 AGTCTCCAGGGTCAAAGTCGACAGGCAGACTGAAGGTAAGG-AAGTCTCCAGGGTCAAAGCCGAC
* * * * * * * * *
525007 AAGCAGACTGAAGGGTAAGAAAGTCTTCAAGGTTAAAGTCGATATGCAGACTTTAGATGAGGT
65 AGGCAGATTG-AGGGTAAGAAAGTCTCCAGGGTCAAAGCCGACAAGCAGACTTTAGATGAAGT
* * *
525070 AGTCTCCAAGGTCAAAGCCGACAGGCAAACTGAA
1 AGTCTCCAGGGTCAAAGTCGACAGGCAGACTGAA
525104 AGTGGGAAAG
Statistics
Matches: 419, Mismatches: 85, Indels: 51
0.75 0.15 0.09
Matches are distributed among these distances:
112 2 0.00
113 4 0.01
114 55 0.13
115 17 0.04
116 2 0.00
119 2 0.00
120 5 0.01
122 5 0.01
123 2 0.00
126 60 0.14
127 198 0.47
128 60 0.14
129 3 0.01
130 4 0.01
ACGTcount: A:0.33, C:0.19, G:0.30, T:0.18
Consensus pattern (126 bp):
AGTCTCCAGGGTCAAAGTCGACAGGCAGACTGAAGGTAAGGAAGTCTCCAGGGTCAAAGCCGACA
GGCAGATTGAGGGTAAGAAAGTCTCCAGGGTCAAAGCCGACAAGCAGACTTTAGATGAAGT
Found at i:524989 original size:42 final size:42
Alignment explanation
Indices: 524910--525096 Score: 148
Period size: 42 Copynumber: 4.4 Consensus size: 42
524900 CTGAAGGGTT
* * *
524910 GGTCAAAGCCGATAGGTAGACTTGA-GGTGAGG-CAGTCTCCAA
1 GGTCAAAGCCGACAGGCAGA-TTGAGGGT-AGGAAAGTCTCCAA
* *
524952 GGTCATAGCCGACAGGCAGATTGAGGGTAGGAAAGTCTCCAG
1 GGTCAAAGCCGACAGGCAGATTGAGGGTAGGAAAGTCTCCAA
* * * * *
524994 GGTCAAAACCGACAAGCAGACTGAAGGGTAAGAAAGTCTTCAA
1 GGTCAAAGCCGACAGGCAGATTG-AGGGTAGGAAAGTCTCCAA
* * * * * * *
525037 GGTTAAAGTCGATATGCAGACTTTA-GATGAGG-TAGTCTCCAA
1 GGTCAAAGCCGACAGGCAGA-TTGAGGGT-AGGAAAGTCTCCAA
525079 GGTCAAAGCCGACAGGCA
1 GGTCAAAGCCGACAGGCA
525097 AACTGAAAGT
Statistics
Matches: 113, Mismatches: 27, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
41 7 0.06
42 71 0.63
43 34 0.30
44 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.30, T:0.18
Consensus pattern (42 bp):
GGTCAAAGCCGACAGGCAGATTGAGGGTAGGAAAGTCTCCAA
Found at i:533233 original size:17 final size:17
Alignment explanation
Indices: 533213--533268 Score: 77
Period size: 17 Copynumber: 3.6 Consensus size: 17
533203 AAGTAAAAGC
533213 ATGCATGAAATGAAGGT
1 ATGCATGAAATGAAGGT
533230 ATGCATG--A--AA-GT
1 ATGCATGAAATGAAGGT
533242 ATGCATGAAATGAAGGT
1 ATGCATGAAATGAAGGT
533259 ATGCATGAAA
1 ATGCATGAAA
533269 GTAAAAGCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
12 9 0.26
13 2 0.06
14 1 0.03
15 1 0.03
16 2 0.06
17 19 0.56
ACGTcount: A:0.43, C:0.07, G:0.27, T:0.23
Consensus pattern (17 bp):
ATGCATGAAATGAAGGT
Found at i:533267 original size:12 final size:12
Alignment explanation
Indices: 533222--533251 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
533212 CATGCATGAA
*
533222 ATGAAGGTATGC
1 ATGAAAGTATGC
533234 ATGAAAGTATGC
1 ATGAAAGTATGC
533246 ATGAAA
1 ATGAAA
533252 TGAAGGTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.07, G:0.27, T:0.23
Consensus pattern (12 bp):
ATGAAAGTATGC
Found at i:533270 original size:29 final size:29
Alignment explanation
Indices: 533208--533271 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
533198 GCATGAAGTA
*
533208 AAAGCATGCATGAAATGAAGGTATGCATG
1 AAAGTATGCATGAAATGAAGGTATGCATG
533237 AAAGTATGCATGAAATGAAGGTATGCATG
1 AAAGTATGCATGAAATGAAGGTATGCATG
533266 AAAGTA
1 AAAGTA
533272 AAAGCATGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.44, C:0.08, G:0.27, T:0.22
Consensus pattern (29 bp):
AAAGTATGCATGAAATGAAGGTATGCATG
Found at i:533496 original size:4 final size:4
Alignment explanation
Indices: 533459--533586 Score: 67
Period size: 4 Copynumber: 32.8 Consensus size: 4
533449 TTGATCTTAT
533459 TTTA TTTTA TTT- TTTA -TTA TTT- TTTA -TT- TTTA TTTA TTTA TTTA
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * *
533503 TTTA TTGTT TTTA TTAA TTT- TTTAA TTAA TTTA TTT- TTTA ATTA ATTA
1 TTTA TT-TA TTTA TTTA TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTTA
* * *
533551 ATTA TTGT- TGTTA -TTA TATA TTTT TTATA TTTA TTT
1 TTTA TT-TA T-TTA TTTA TTTA TTTA TT-TA TTTA TTT
533587 TTTTTATTAT
Statistics
Matches: 97, Mismatches: 12, Indels: 29
0.70 0.09 0.21
Matches are distributed among these distances:
3 22 0.23
4 61 0.63
5 14 0.14
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:533597 original size:16 final size:16
Alignment explanation
Indices: 533464--533597 Score: 89
Period size: 17 Copynumber: 8.1 Consensus size: 16
533454 CTTATTTTAT
*
533464 TTTATTTTTTATTATTT
1 TTTATTTTTT-TTATTA
533481 TTTATTTTTATTTATTTA
1 TTTATTTTT-TTTA-TTA
533499 TTTATTTATTGTTT-TTA
1 TTTATTT-TT-TTTATTA
* *
533516 -TTAATTTTTTAATTAA
1 TTTATTTTTTTTATT-A
533532 TTTATTTTTTAATTAATTA
1 TTTATTTTTT--TT-ATTA
* * *
533551 ATTATTGTTGTTATTA
1 TTTATTTTTTTTATTA
*
533567 --TATATTTTTTA-TA
1 TTTATTTTTTTTATTA
533580 TTTATTTTTTTTATTA
1 TTTATTTTTTTTATTA
533596 TT
1 TT
533598 CATGTTAAAT
Statistics
Matches: 92, Mismatches: 13, Indels: 25
0.71 0.10 0.19
Matches are distributed among these distances:
13 2 0.02
14 10 0.11
15 14 0.15
16 14 0.15
17 25 0.27
18 10 0.11
19 14 0.15
20 3 0.03
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (16 bp):
TTTATTTTTTTTATTA
Found at i:540446 original size:154 final size:155
Alignment explanation
Indices: 540125--540495 Score: 378
Period size: 154 Copynumber: 2.4 Consensus size: 155
540115 AGTGATTACT
* * *
540125 TAGGACTCGGTTCTAAG-AAAATTAGCAAAATGCCTCTAGGGTATACCTTCAACGTGAAAGTATC
1 TAGGACTCGGTTCTAAGAAAAATTAACAAAATGCCCCTAGGGTATACCTTCAACGTGAAAGTAGC
** *
540189 TTAATAACCTTAAAGGACATAAAAATAATAAGTAAAAGGACGAACCTATCCTAAATGACAACTTT
66 CCAATAACCTTAAAGGACATAAAAATAATAAGTAAAAGGACGAACCTATCATAAATGACAACTTT
** *
540254 GGCATAAAAGTGACCTGGTGACTAC
131 GGCATAAAAGTGACCCAGCGACTAC
* * **
540279 TAGGGCTCGGTTCTAAGAAAAATTAACAAAATGCCCCTAGGGTGTACCTTTGACGTGAAAGT-GC
1 TAGGACTCGGTTCTAAGAAAAATTAACAAAATGCCCCTAGGGTATACCTTCAACGTGAAAGTAGC
* * * * * * * *
540343 CCGATAATCCTT-TAGGACATGAAAAT-ATTA-TAAAAGGATGAACTTATCATAAACAT-ATACC
66 CCAATAA-CCTTAAAGGACATAAAAATAATAAGTAAAAGGACGAACCTATCAT-AA-ATGACAAC
540404 TTTGGCATAAAAGTGACCCAGCGA-TCACC
128 TTTGGCATAAAAGTGACCCAGCGACT-A-C
* * * ** * * * *
540433 TAGGATTCAGTTCTAAGAAAAATTACCAAAAAACCTCTAAGGTATACCTTTAATGTGAAAGTA
1 TAGGACTCGGTTCTAAGAAAAATTAACAAAATGCCCCTAGGGTATACCTTCAACGTGAAAGTA
540496 CCTGGTAACC
Statistics
Matches: 178, Mismatches: 32, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
152 18 0.10
153 30 0.17
154 87 0.49
155 43 0.24
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.26
Consensus pattern (155 bp):
TAGGACTCGGTTCTAAGAAAAATTAACAAAATGCCCCTAGGGTATACCTTCAACGTGAAAGTAGC
CCAATAACCTTAAAGGACATAAAAATAATAAGTAAAAGGACGAACCTATCATAAATGACAACTTT
GGCATAAAAGTGACCCAGCGACTAC
Found at i:541426 original size:31 final size:30
Alignment explanation
Indices: 541377--541435 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
541367 CTCAAGACTT
*
541377 TTTTTCAAAATTTGCAAATTAGTCTCTAATC
1 TTTTTCAAAATTTACAAA-TAGTCTCTAATC
*
541408 TTTTT-AAAATTTAACAAATGGTCTCTAA
1 TTTTTCAAAATTT-ACAAATAGTCTCTAA
541436 CATGTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.44
Consensus pattern (30 bp):
TTTTTCAAAATTTACAAATAGTCTCTAATC
Found at i:542257 original size:5 final size:5
Alignment explanation
Indices: 542247--542301 Score: 67
Period size: 5 Copynumber: 10.8 Consensus size: 5
542237 CCTAGTTTAG
**
542247 AAATA AAATA AAATA AAATA AAATA AAATA ATCTA AAATTA AAA-A AAATTA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAA-TA AAATA AAA-TA
542298 AAAT
1 AAAT
542302 TAACTATTAC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
4 4 0.09
5 30 0.70
6 9 0.21
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (5 bp):
AAATA
Found at i:542411 original size:16 final size:15
Alignment explanation
Indices: 542370--542411 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
542360 CAAAACTTGT
542370 AAAATTGTA-TAAGA
1 AAAATTGTATTAAGA
*
542384 AAAATCTTTATTAAGA
1 AAAAT-TGTATTAAGA
542400 AAAATTGGTATT
1 AAAATT-GTATT
542412 TTAAAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 5 0.22
15 4 0.17
16 14 0.61
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (15 bp):
AAAATTGTATTAAGA
Found at i:547435 original size:15 final size:15
Alignment explanation
Indices: 547415--547448 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
547405 TTTCAGATGT
547415 GTTATGTTAATTATA
1 GTTATGTTAATTATA
547430 GTTATGTTAATTATA
1 GTTATGTTAATTATA
547445 GTTA
1 GTTA
547449 CAAACATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (15 bp):
GTTATGTTAATTATA
Found at i:552514 original size:12 final size:12
Alignment explanation
Indices: 552497--552522 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
552487 TGCCCCCACT
552497 GGGACATGGGTG
1 GGGACATGGGTG
552509 GGGACATGGGTG
1 GGGACATGGGTG
552521 GG
1 GG
552523 TTCCCTAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.62, T:0.15
Consensus pattern (12 bp):
GGGACATGGGTG
Found at i:552993 original size:12 final size:12
Alignment explanation
Indices: 552976--553001 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
552966 AAATTTAAAA
552976 TAAATAAAATAT
1 TAAATAAAATAT
552988 TAAATAAAATAT
1 TAAATAAAATAT
553000 TA
1 TA
553002 TTTCCCATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
TAAATAAAATAT
Found at i:556310 original size:127 final size:126
Alignment explanation
Indices: 555957--556310 Score: 418
Period size: 127 Copynumber: 2.8 Consensus size: 126
555947 TATTATTTTT
*
555957 AATAAAAATAATATTTAATTAAATTTAAAAAAATTTACATTAACAAATTAAAATATT-A--A-T-
1 AATAAAAATAATATTTAATTAAGTTT--AAAAATTTACATTAACAAATTAAAATATTAATTATTA
* **** *
556017 TATTTTTTAAAAATAACAAAA-ATTAAATAAAAATAAAAAGGGTTTTTATTATTATTTTTTAATA
64 TATTTTTTAAAAATAA-AAAATTTTAAATAAAAA-AAAAA-GAAAATTATTATTAATTTTTAATA
556081 A
126 A
* * * *
556082 AATAAAAAATAATATTTAATTAAGTTTAATAAAATTACGTTAAAAAATTAAAATATTAATTGTTA
1 AAT-AAAAATAATATTTAATTAAGTTTAA-AAATTTACATTAACAAATTAAAATATTAATTATTA
* * * *
556147 TGCTTTTATAAAAATAAAAAATTTTAGAATACAAAAATAA-AAAATTATTA-TAATTTTTAATAA
64 T-ATTTTTTAAAAATAAAAAATTTTA-AATAAAAAAAAAAGAAAATTATTATTAATTTTTAATAA
556210 AATAAAAATAATATTTAATTAAGTTTAAAAATTTTACATTAACAAATTAAAATATTAATTATTAT
1 AATAAAAATAATATTTAATTAAGTTTAAAAA-TTTACATTAACAAATTAAAATATTAATTATTAT
*
556275 ATTTTTTAAAAATAAAAAATTTTAAATTAAAAAAAA
65 ATTTTTTAAAAATAAAAAATTTTAAATAAAAAAAAA
556311 GTTTTTTATT
Statistics
Matches: 194, Mismatches: 24, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
124 2 0.01
125 36 0.19
126 48 0.25
127 54 0.28
128 15 0.08
129 7 0.04
130 5 0.03
131 20 0.10
132 7 0.04
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (126 bp):
AATAAAAATAATATTTAATTAAGTTTAAAAATTTACATTAACAAATTAAAATATTAATTATTATA
TTTTTTAAAAATAAAAAATTTTAAATAAAAAAAAAAGAAAATTATTATTAATTTTTAATAA
Found at i:557195 original size:89 final size:87
Alignment explanation
Indices: 557042--557330 Score: 310
Period size: 89 Copynumber: 3.2 Consensus size: 87
557032 ATGCATGGAT
* * * *
557042 TATAAATGTCAAATTACAAGGATTAGACTAATGCATGAATTATATCTGAAAATCAGATTCTTTTT
1 TATAAATATCAGACTACAA-GATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTT
*
557107 TATAGAAAAAAAAGGTTGATTAAT
65 TATAGAAAAAAAA-GTTGATTAAG
* * * *
557131 TGTAAATATCAGACTGCAATGATTAAACTAATGCATGAATTATATCTGAGAATCGGATTCTTTTT
1 TATAAATATCAGACTACAA-GATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTT
* *
557196 CTAT-TAAAAAAAAGTTGATTGAG
65 -TATAGAAAAAAAAGTTGATTAAG
* * * * * *
557219 TATAAATGTTAGACTACAAGAATTAGACTAATGAATAAATTATATCAGAGAATCAGATTTTTTTT
1 TATAAATATCAGACTACAAG-ATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTT
*
557284 TATAGAAAAAAGGAAAAGTTGATTGAG
65 TATAG--AAAA--AAAAGTTGATTAAG
* *
557311 TATAAATGTCAGACTGCAAG
1 TATAAATATCAGACTACAAG
557331 TAACCAATGA
Statistics
Matches: 168, Mismatches: 25, Indels: 11
0.82 0.12 0.05
Matches are distributed among these distances:
87 4 0.02
88 61 0.36
89 64 0.38
90 7 0.04
92 32 0.19
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.34
Consensus pattern (87 bp):
TATAAATATCAGACTACAAGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTT
ATAGAAAAAAAAGTTGATTAAG
Found at i:557260 original size:88 final size:87
Alignment explanation
Indices: 557042--557330 Score: 328
Period size: 88 Copynumber: 3.2 Consensus size: 87
557032 ATGCATGGAT
* * *
557042 TATAAATGTCAAATTACAAGGATTAGACTAATGCATGAATTATATCTGAAAATCAGATTCTTTTT
1 TATAAATGTCAGACTACAA-GATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTT
* * *
557107 TATAGAAAAAAAAGGTTGATTAAT
65 TATA-AAAAAAAAAGTTGATTGAG
* * * * *
557131 TGTAAATATCAGACTGCAATGATTAAACTAATGCATGAATTATATCTGAGAATCGGATTCTTTTT
1 TATAAATGTCAGACTACAA-GATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTT
*
557196 CTAT-TAAAAAAAAGTTGATTGAG
65 -TATAAAAAAAAAAGTTGATTGAG
* * * * *
557219 TATAAATGTTAGACTACAAGAATTAGACTAATGAATAAATTATATCAGAGAATCAGATTTTTTTT
1 TATAAATGTCAGACTACAAG-ATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTT
557284 TATAGAAAAAAGGAAAAGTTGATTGAG
65 TAT--AAAAAA--AAAAGTTGATTGAG
*
557311 TATAAATGTCAGACTGCAAG
1 TATAAATGTCAGACTACAAG
557331 TAACCAATGA
Statistics
Matches: 167, Mismatches: 26, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
87 4 0.02
88 68 0.41
89 56 0.34
90 7 0.04
92 32 0.19
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.34
Consensus pattern (87 bp):
TATAAATGTCAGACTACAAGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTT
ATAAAAAAAAAAGTTGATTGAG
Found at i:559396 original size:19 final size:19
Alignment explanation
Indices: 559372--559435 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
559362 TTTTAGCGAT
559372 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
559391 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
559405 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
559423 TTGTATCGATACA
1 TTGTATCGATACA
559436 ATGTATCGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
19 24 0.62
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:559409 original size:32 final size:32
Alignment explanation
Indices: 559373--559443 Score: 142
Period size: 32 Copynumber: 2.2 Consensus size: 32
559363 TTTAGCGATT
559373 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
559405 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
559437 TGTATCG
1 TGTATCG
559444 CTAAAGCTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:559410 original size:13 final size:13
Alignment explanation
Indices: 559392--559416 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
559382 ACATAAGTGT
559392 TGTATCGATACAA
1 TGTATCGATACAA
559405 TGTATCGATACA
1 TGTATCGATACA
559417 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Done.