Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 37 of 135
Found at i:9459977 original size:149 final size:148
Alignment explanation
Indices: 9459555--9459970 Score: 399
Period size: 149 Copynumber: 2.8 Consensus size: 148
9459545 CGTCGTTGCG
* ** * * *
9459555 GCCTCAACCTTTCCCATCGCATCTTCTAAGGTACTGGGTTCACCGTTGCAGCCTCAACCTTTCCC
1 GCCTCAACCTTTCCCTTCAAATCTTC-ATGGTATTGGGTTCACCGTTGCGGCCTCAACCTTTCCC
* ** * * * *
9459620 TTCAAATCTTC-ATGGTACTGGGTTCACCTTTGCAGACTCAACCTTTCCCATCACGTCTTCTAAG
65 ATCATGTCTTCTAAGGTACTGGGTTC-GCTTTGCAGCCTCAACCTTTCCCTTCACGTCTTCTAAG
** **
9459684 GTACCAAGTTTGTTATTATG
129 GTACCAAGTTTGCCATTACA
* *** * *
9459704 GCCTCAACCTTTCCCTTCAAATCTTCATGGTATCGGGTTCGTTGTTACGACCTCAACCTTTCCCA
1 GCCTCAACCTTTCCCTTCAAATCTTCATGGTATTGGGTTCACCGTTGCGGCCTCAACCTTTCCCA
* * * *
9459769 T--TGCATCTTCTAAGGTACCGGGTTCGCCATTGCAACCTGAACCTTT-CCTATCACGTCTTCTA
66 TCATG--TCTTCTAAGGTACTGGGTTCG-CTTTGCAGCCTCAACCTTTCCCT-TCACGTCTTCTA
* ** *
9459831 AGGTATCGGGTTTGCCATTGCA
127 AGGTACCAAGTTTGCCATTACA
* ** * * *
9459853 GCCTGAACCTTTCTTTTTAAATTTTCATGGTATTGGGTTTACCGTTGCGGCCTCAACCTTTCCCA
1 GCCTCAACCTTTCCCTTCAAATCTTCATGGTATTGGGTTCACCGTTGCGGCCTCAACCTTTCCCA
*
9459918 TCATGTCTTCTAAGGTACTGGGTTCGCTGTTACAGCCTCAACCTTTCCCTTCA
66 TCATGTCTTCTAAGGTACTGGGTTCGCT-TTGCAGCCTCAACCTTTCCCTTCA
9459971 AATCTTCATG
Statistics
Matches: 210, Mismatches: 48, Indels: 18
0.76 0.17 0.07
Matches are distributed among these distances:
148 38 0.18
149 167 0.80
150 3 0.01
151 2 0.01
ACGTcount: A:0.19, C:0.30, G:0.17, T:0.35
Consensus pattern (148 bp):
GCCTCAACCTTTCCCTTCAAATCTTCATGGTATTGGGTTCACCGTTGCGGCCTCAACCTTTCCCA
TCATGTCTTCTAAGGTACTGGGTTCGCTTTGCAGCCTCAACCTTTCCCTTCACGTCTTCTAAGGT
ACCAAGTTTGCCATTACA
Found at i:9459980 original size:99 final size:100
Alignment explanation
Indices: 9459516--9459977 Score: 334
Period size: 99 Copynumber: 4.7 Consensus size: 100
9459506 GCCTTAATTC
* * * **
9459516 TTCCCATCACGTCTTCTAAGG-ATCGGGTTCG-TCGTTGCGGCCTCAACCTTTCCCATCGCATCT
1 TTCCCATCAAGTCTTCTAAGGTATCGGGTTCGCT-GTTGCAGCCTCAACCTTTCCCTTCAAATCT
* *
9459579 TCTAAGGTACTGGGTTCACCGTTGCAGCCTCAACCT
65 TCTAAGGTACCGGGTTCACCATTGCAGCCTCAACCT
* * * * * * **
9459615 TTCCCTTCAAATCTTC-ATGGTA-CTGGGTTCACCT-TTGCAGACTCAACCTTTCCCATCACGTC
1 TTCCCATCAAGTCTTCTAAGGTATC-GGGTTC-GCTGTTGCAGCCTCAACCTTTCCCTTCAAATC
** **** ***
9459677 TTCTAAGGTACCAAGTTTGTTATTATGGCCTCAACCT
64 TTCTAAGGTACCGGGTTCACCATTGCAGCCTCAACCT
* * * * *
9459714 TTCCCTTCAAATCTTC-ATGGTATCGGGTTCGTTGTTAC-GACCTCAACCTTTCCCATTGC--AT
1 TTCCCATCAAGTCTTCTAAGGTATCGGGTTCGCTGTTGCAG-CCTCAACCTTTCCC-TT-CAAAT
* * *
9459775 CTTCTAAGGTACCGGGTTCGCCATTGCAACCTGAACCT
63 CTTCTAAGGTACCGGGTTCACCATTGCAGCCTCAACCT
* * * ** * ** * *
9459813 TTCCTATCACGTCTTCTAAGGTATCGGGTTTGCCATTGCAGCCTGAACCTTTCTTTTTAAATTTT
1 TTCCCATCAAGTCTTCTAAGGTATCGGGTTCGCTGTTGCAGCCTCAACCTTTCCCTTCAAATCTT
* ** * * *
9459878 C-ATGGTATTGGGTTTACCGTTGCGGCCTCAACCT
66 CTAAGGTACCGGGTTCACCATTGCAGCCTCAACCT
* *
9459912 TTCCCATCATGTCTTCTAAGGTA-CTGGGTTCGCTGTTACAGCCTCAACCTTTCCCTTCAAATCT
1 TTCCCATCAAGTCTTCTAAGGTATC-GGGTTCGCTGTTGCAGCCTCAACCTTTCCCTTCAAATCT
9459976 TC
65 TC
9459978 ATGTTTCCTT
Statistics
Matches: 278, Mismatches: 71, Indels: 28
0.74 0.19 0.07
Matches are distributed among these distances:
98 7 0.03
99 234 0.84
100 34 0.12
101 3 0.01
ACGTcount: A:0.18, C:0.30, G:0.17, T:0.35
Consensus pattern (100 bp):
TTCCCATCAAGTCTTCTAAGGTATCGGGTTCGCTGTTGCAGCCTCAACCTTTCCCTTCAAATCTT
CTAAGGTACCGGGTTCACCATTGCAGCCTCAACCT
Found at i:9460219 original size:17 final size:17
Alignment explanation
Indices: 9460197--9460233 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
9460187 GTCTAAGTCC
9460197 TATAACTGATGTGCTAT
1 TATAACTGATGTGCTAT
9460214 TATAACTGATGTGCTAT
1 TATAACTGATGTGCTAT
9460231 TAT
1 TAT
9460234 GTTGTTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (17 bp):
TATAACTGATGTGCTAT
Found at i:9486534 original size:6 final size:6
Alignment explanation
Indices: 9486512--9486572 Score: 65
Period size: 6 Copynumber: 10.5 Consensus size: 6
9486502 GTTTAAATTG
* *
9486512 ATTTAA ATTTAT TTTTAA ATTTAA ATTT-- ATCTTAA ATTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA ATTTAA
*
9486558 ATTAAA ATTTAA ATT
1 ATTTAA ATTTAA ATT
9486573 GATTCAAAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
4 2 0.04
5 6 0.13
6 35 0.78
7 2 0.04
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (6 bp):
ATTTAA
Found at i:9486548 original size:17 final size:16
Alignment explanation
Indices: 9486512--9486572 Score: 77
Period size: 17 Copynumber: 3.6 Consensus size: 16
9486502 GTTTAAATTG
9486512 ATTTAAATTTATTTTTAA
1 ATTTAAATTTA--TTTAA
9486530 ATTTAAATTTATCTTAA
1 ATTTAAATTTAT-TTAA
*
9486547 ATTTAAATTTAATTAAA
1 ATTTAAATTT-ATTTAA
9486564 ATTTAAATT
1 ATTTAAATT
9486573 GATTCAAAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
16 1 0.03
17 26 0.65
18 13 0.32
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTTAAATTTATTTAA
Found at i:9486560 original size:11 final size:11
Alignment explanation
Indices: 9486503--9486569 Score: 55
Period size: 11 Copynumber: 6.0 Consensus size: 11
9486493 TTAAGTTGGG
*
9486503 TTTAAA-TTGA
1 TTTAAATTTAA
*
9486513 TTTAAATTTATT
1 TTTAAATTTA-A
9486525 TTTAAATTTAAA
1 TTTAAATTT-AA
** *
9486537 TTTATCTTAAA
1 TTTAAATTTAA
9486548 TTTAAATTTAA
1 TTTAAATTTAA
*
9486559 TTAAAATTTAA
1 TTTAAATTTAA
9486570 ATTGATTCAA
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
10 6 0.14
11 22 0.50
12 15 0.34
13 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:9487343 original size:19 final size:17
Alignment explanation
Indices: 9487316--9487365 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 17
9487306 CATTAAATTT
*
9487316 ATAATTAATAATAAATAA
1 ATAAATAATAATAAAT-A
*
9487334 CATAAATAATAATTAATA
1 -ATAAATAATAATAAATA
9487352 AT-AATAATAATAAA
1 ATAAATAATAATAAA
9487366 CAAATAACGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 11 0.39
17 2 0.07
18 1 0.04
19 14 0.50
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAATAATAATAAATA
Found at i:9487357 original size:16 final size:16
Alignment explanation
Indices: 9487311--9487362 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
9487301 AAGTACATTA
*
9487311 AATTTATAATTAATAAT
1 AATTAATAA-TAATAAT
* *
9487328 AAATAA-CATAAATAAT
1 AATTAATAAT-AATAAT
9487344 AATTAATAATAATAAT
1 AATTAATAATAATAAT
9487360 AAT
1 AAT
9487363 AAACAAATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
15 1 0.04
16 21 0.75
17 6 0.21
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
AATTAATAATAATAAT
Found at i:9487364 original size:26 final size:26
Alignment explanation
Indices: 9487316--9487365 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
9487306 CATTAAATTT
*
9487316 ATAATTAATAATAAATAACATAAATA
1 ATAATTAATAATAAATAAAATAAATA
9487342 ATAATTAATAAT-AATAATAATAAA
1 ATAATTAATAATAAATAA-AATAAA
9487366 CAAATAACGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (26 bp):
ATAATTAATAATAAATAAAATAAATA
Found at i:9488496 original size:29 final size:28
Alignment explanation
Indices: 9488455--9488705 Score: 134
Period size: 29 Copynumber: 8.6 Consensus size: 28
9488445 ATATAGTCCA
* *
9488455 AAAATTACATTTTTATCCCTGAGCTTTCC
1 AAAATTCCATTTTTA-CCCTGAACTTTCC
* * *
9488484 AAAATTCCATTTTAACCTTG-ATTTGTCC
1 AAAATTCCATTTTTACCCTGAACTT-TCC
* *
9488512 AAAAATTACATTTTTACCCTTAAACTTTCC
1 -AAAATTCCATTTTTACCC-TGAACTTTCC
* * *
9488542 AAAATTCTATTTTGACCCT-AATTTGTCC
1 AAAATTCCATTTTTACCCTGAACTT-TCC
* * ** *
9488570 AAAAAATACATTTTTACCCCCAAACTTTCT
1 -AAAATTCCATTTTTA-CCCTGAACTTTCC
* * *
9488600 AAAATTCCA-TTTTAACCTCG-ATTTGTCTA
1 AAAATTCCATTTTTACCCT-GAACTT-TC-C
* *
9488629 AAAATTACATTTTTATCCCCGAACTTTCC
1 AAAATTCCATTTTTA-CCCTGAACTTTCC
* * *
9488658 ATAATTCCATTTTTAACCCTAAATTTTCC
1 AAAATTCCATTTTT-ACCCTGAACTTTCC
9488687 AAAAATTACCA-TTTTACCC
1 -AAAATT-CCATTTTTACCC
9488706 CCGAATGTCT
Statistics
Matches: 166, Mismatches: 39, Indels: 34
0.69 0.16 0.14
Matches are distributed among these distances:
27 11 0.07
28 18 0.11
29 95 0.57
30 27 0.16
31 15 0.09
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.40
Consensus pattern (28 bp):
AAAATTCCATTTTTACCCTGAACTTTCC
Found at i:9488512 original size:28 final size:28
Alignment explanation
Indices: 9488481--9488573 Score: 89
Period size: 28 Copynumber: 3.2 Consensus size: 28
9488471 CCCTGAGCTT
*
9488481 TCCAAAATTCCATTTTAACCTTGATTTG
1 TCCAAAATTCCATTTTAACCTTAATTTG
* * *
9488509 TCCAAAAATTACATTTTTACCCTTAAACTT-
1 TCC-AAAATTCCA-TTTTAACCTT-AATTTG
* * *
9488539 TCCAAAATTCTATTTTGACCCTAATTTG
1 TCCAAAATTCCATTTTAACCTTAATTTG
9488567 TCCAAAA
1 TCCAAAA
9488574 AATACATTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
27 4 0.08
28 17 0.33
29 15 0.29
30 12 0.24
31 3 0.06
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.40
Consensus pattern (28 bp):
TCCAAAATTCCATTTTAACCTTAATTTG
Found at i:9488540 original size:58 final size:57
Alignment explanation
Indices: 9488450--9488706 Score: 293
Period size: 58 Copynumber: 4.4 Consensus size: 57
9488440 TCCCTATATA
** * *
9488450 GTCCAAAAATTACATTTTTATCCCTGAGCTTTCCAAAATTCCATTTTAACCTTGATTT
1 GTCCAAAAATTACATTTTTA-CCCCAAACTTTCCAAAATTCCATTTTAACCTTAATTT
* * * *
9488508 GTCCAAAAATTACATTTTTACCCTTAAACTTTCCAAAATTCTATTTTGACCCTAATTT
1 GTCCAAAAATTACATTTTTACCC-CAAACTTTCCAAAATTCCATTTTAACCTTAATTT
* * **
9488566 GTCCAAAAAATACATTTTTACCCCCAAACTTTCTAAAATTCCATTTTAACCTCGATTT
1 GTCCAAAAATTACATTTTTA-CCCCAAACTTTCCAAAATTCCATTTTAACCTTAATTT
* * * *
9488624 GTCTAAAAATTACATTTTTATCCCCGAACTTTCCATAATTCCATTTTTAACCCTAAATTT
1 GTCCAAAAATTACATTTTTA-CCCCAAACTTTCCAAAATTCCA-TTTTAA-CCTTAATTT
9488684 -TCCAAAAATTACCA-TTTTACCCC
1 GTCCAAAAATTA-CATTTTTACCCC
9488707 CGAATGTCTA
Statistics
Matches: 171, Mismatches: 23, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
57 3 0.02
58 135 0.79
59 24 0.14
60 9 0.05
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (57 bp):
GTCCAAAAATTACATTTTTACCCCAAACTTTCCAAAATTCCATTTTAACCTTAATTT
Found at i:9488654 original size:116 final size:118
Alignment explanation
Indices: 9488450--9488739 Score: 358
Period size: 116 Copynumber: 2.5 Consensus size: 118
9488440 TCCCTATATA
* * * * *
9488450 GTCCAAAAATTACATTTTTATCCCTGAGCTTTCCAAAATTCCATTTTAACCTTGATTTGTCCAAA
1 GTCCAAAAATTACATTTTTACCCCCGAACTTTCTAAAATTCCATTTTAACCTCGATTTGTCCAAA
* * *
9488515 AATTACATTTTTACCCTTAAACTTTCCAAAATTCTA-TTTTGACCCT-AATTT
66 AATTACATTTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCTAAATTT
* * *
9488566 GTCCAAAAAATACATTTTTACCCCCAAACTTTCTAAAATTCCATTTTAACCTCGATTTGTCTAAA
1 GTCCAAAAATTACATTTTTACCCCCGAACTTTCTAAAATTCCATTTTAACCTCGATTTGTCCAAA
* *
9488631 AATTACATTTTTATCCC-CGAACTTTCCATAATTCCATTTTTAACCCTAAATTT
66 AATTACATTTTTA-CCCTCAAACTTTCCAAAATTCCATTTTTAACCCTAAATTT
* *
9488684 -TCCAAAAATTACCA-TTTTACCCCCGAA-TGTCTAAAATTTTCCATTGTTGACCTCGA
1 GTCCAAAAATTA-CATTTTTACCCCCGAACTTTCTAAAA--TTCCATT-TTAACCTCGA
9488740 ACCTTTTGAA
Statistics
Matches: 150, Mismatches: 17, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
116 93 0.62
117 34 0.23
118 14 0.09
119 9 0.06
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (118 bp):
GTCCAAAAATTACATTTTTACCCCCGAACTTTCTAAAATTCCATTTTAACCTCGATTTGTCCAAA
AATTACATTTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCTAAATTT
Found at i:9488868 original size:59 final size:56
Alignment explanation
Indices: 9488597--9488879 Score: 205
Period size: 59 Copynumber: 4.8 Consensus size: 56
9488587 CCCCAAACTT
* ** *
9488597 TCTAAAATTCCA-TTTTAA-CCTCGATTTGTCTAAAAATTA-CATTTTTATCCCCGAACTT
1 TCTAAAATTTCATTTTTAACCCTAAATTT-TC-AAAAATTACCA-TTTTA-CCCCGAA-TG
* * *
9488655 TCCATAATTCCATTTTTAACCCTAAATTTTCCAAAAATTACCATTTTACCCCCGAATG
1 TCTAAAATTTCATTTTTAACCCTAAATTTT-CAAAAATTACCATTTTA-CCCCGAATG
* * * * * *
9488713 TCTAAAATTTTCCATTGTTGACCTCGAACCTTTT-GAAAATTTCCATTTTACCCCTGAATG
1 TCTAAAA-TTT-CATTTTTAACC-CTAA-ATTTTCAAAAATTACCATTTTACCCC-GAATG
** * * ** *
9488773 TCTAAAAAATCTATTTTTGATCCTGAACCTTTCAAAAATTACCATTTTACCCTCGAGTG
1 TCTAAAATTTC-ATTTTTAACCCT-AAATTTTCAAAAATTACCATTTTACCC-CGAATG
9488832 TCTAAAATTTCATTTTTAACCCTAAATTTTCCCAAAAATTACCATTTT
1 TCTAAAATTTCATTTTTAACCCTAAATTTT--CAAAAATTACCATTTT
9488880 GCACTCGGGT
Statistics
Matches: 180, Mismatches: 30, Indels: 29
0.75 0.13 0.12
Matches are distributed among these distances:
57 5 0.03
58 32 0.18
59 90 0.50
60 46 0.26
61 3 0.02
62 4 0.02
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40
Consensus pattern (56 bp):
TCTAAAATTTCATTTTTAACCCTAAATTTTCAAAAATTACCATTTTACCCCGAATG
Found at i:9491538 original size:21 final size:22
Alignment explanation
Indices: 9491514--9491561 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
9491504 TTACGTCCCA
*
9491514 CTCCATCTCTCC-TCCTTATTT
1 CTCCATCTCGCCTTCCTTATTT
*
9491535 CTCC-TCTCGCCTTCGTTATTT
1 CTCCATCTCGCCTTCCTTATTT
9491556 CTCCAT
1 CTCCAT
9491562 TTAGGAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 6 0.26
21 16 0.70
22 1 0.04
ACGTcount: A:0.08, C:0.42, G:0.04, T:0.46
Consensus pattern (22 bp):
CTCCATCTCGCCTTCCTTATTT
Found at i:9521586 original size:15 final size:16
Alignment explanation
Indices: 9521561--9521603 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
9521551 TCCCGAATCT
9521561 CTCAGTCTTCATAG-TA
1 CTCA-TCTTCATAGATA
9521577 CTCATCTTCATAGATA
1 CTCATCTTCATAGATA
*
9521593 -TCATCATCATA
1 CTCATCTTCATA
9521604 ATCATCATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 19 0.76
16 6 0.24
ACGTcount: A:0.30, C:0.26, G:0.07, T:0.37
Consensus pattern (16 bp):
CTCATCTTCATAGATA
Found at i:9528250 original size:5 final size:5
Alignment explanation
Indices: 9528235--9528271 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
9528225 ATTTTGTTAT
*
9528235 TTTTA TATTA TTTTA TTTTA -TTTA -TTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
9528272 TATTAATCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 8 0.28
5 21 0.72
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:9528262 original size:13 final size:14
Alignment explanation
Indices: 9528235--9528270 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
9528225 ATTTTGTTAT
9528235 TTTTATATTATTTTA
1 TTTTAT-TTATTTTA
9528250 TTTTATTTA-TTTA
1 TTTTATTTATTTTA
9528263 TTTTATTT
1 TTTTATTT
9528271 TTATTAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 12 0.57
14 3 0.14
15 6 0.29
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTATTTATTTTA
Found at i:9528265 original size:18 final size:19
Alignment explanation
Indices: 9528236--9528271 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
9528226 TTTTGTTATT
9528236 TTTATATTATTTTATTTTA
1 TTTATATTATTTTATTTTA
9528255 TTTAT-TTATTTTATTTT
1 TTTATATTATTTTATTTT
9528272 TATTAATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTATATTATTTTATTTTA
Found at i:9548851 original size:16 final size:16
Alignment explanation
Indices: 9548804--9548858 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
9548794 AACCCGATCC
9548804 ATAAATATCTCTA-GTA
1 ATAAATATCTCTACG-A
*
9548820 ATAACATAAACTCTACGA
1 ATAA-AT-ATCTCTACGA
*
9548838 ATAAATATCTCTACAA
1 ATAAATATCTCTACGA
9548854 ATAAA
1 ATAAA
9548859 ACAACTAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 17 0.52
17 4 0.12
18 11 0.33
19 1 0.03
ACGTcount: A:0.51, C:0.16, G:0.04, T:0.29
Consensus pattern (16 bp):
ATAAATATCTCTACGA
Found at i:9552943 original size:7 final size:7
Alignment explanation
Indices: 9552931--9552957 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
9552921 TGTTGTTTAG
9552931 ATCTTGC
1 ATCTTGC
9552938 ATCTTGC
1 ATCTTGC
9552945 ATCTTGC
1 ATCTTGC
9552952 ATCTTG
1 ATCTTG
9552958 AGTGTCCCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.26, G:0.15, T:0.44
Consensus pattern (7 bp):
ATCTTGC
Found at i:9553922 original size:58 final size:58
Alignment explanation
Indices: 9553847--9553971 Score: 173
Period size: 58 Copynumber: 2.2 Consensus size: 58
9553837 TTCATATTTT
* * *
9553847 AATAATAATTATATTAAAAATATTATTAAATTACA-TATTA-TTTTATTAAATTGTATTC
1 AATAATAATTATATT-AAAATATAATTAAATTA-ATTAATATTTTTATTAAATTATATTC
* *
9553905 AATAATAATTATGTTAAAATATAATTAAATTAATTAATATTTTTATTAAATTATATTT
1 AATAATAATTATATTAAAATATAATTAAATTAATTAATATTTTTATTAAATTATATTC
9553963 AATAATAAT
1 AATAATAAT
9553972 CATTAAAATT
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
56 1 0.02
57 20 0.33
58 39 0.65
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (58 bp):
AATAATAATTATATTAAAATATAATTAAATTAATTAATATTTTTATTAAATTATATTC
Found at i:9554162 original size:16 final size:16
Alignment explanation
Indices: 9554141--9554178 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
9554131 TGAATTACTG
9554141 ATTACAACTCTATTCC
1 ATTACAACTCTATTCC
* *
9554157 ATTACACCTCTATTTC
1 ATTACAACTCTATTCC
9554173 ATTACA
1 ATTACA
9554179 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:9554690 original size:73 final size:74
Alignment explanation
Indices: 9554550--9554692 Score: 175
Period size: 73 Copynumber: 1.9 Consensus size: 74
9554540 CGGTTCATGA
* * *
9554550 CCTCTCAAAGTTTAAATTTTTTCAATTTAATCTTTTGTAAATTTATATTATAATTCTCCTAAAAA
1 CCTCTCAAAGTTTAAATTTTTACAATTTAATCTTTTGT-AATATATATTATAATCCTCCTAAAAA
9554615 TATAAATAAG
65 TATAAATAAG
* * * *
9554625 CCTC-CAAGGTTTAAGATTTTTACAATTT-TTCTTTTTGT-ATATATATTATAGTCCTTCTAAAA
1 CCTCTCAAAGTTTAA-ATTTTTACAATTTAATC-TTTTGTAATATATATTATAATCCTCCTAAAA
9554687 ATATAA
64 ATATAA
9554693 TTAGACCCCT
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
73 26 0.44
74 11 0.19
75 22 0.37
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.46
Consensus pattern (74 bp):
CCTCTCAAAGTTTAAATTTTTACAATTTAATCTTTTGTAATATATATTATAATCCTCCTAAAAAT
ATAAATAAG
Found at i:9566059 original size:332 final size:332
Alignment explanation
Indices: 9565510--9566171 Score: 1180
Period size: 332 Copynumber: 2.0 Consensus size: 332
9565500 TTCGAAAGCT
* *
9565510 TCAATCCCCATCTCTAGACATCTCAGCCATTGGACTTTACATACGGGATATAAGAGATCTGGCCA
1 TCAATCCCCATCTCTAGACATCTCAGCCATTGGACCTTACATACGGGATATAAAAGATCTGGCCA
9565575 GGCATTTCTGGTGTTGTTGTTTTCAACATGTCTCCCGTGAAGGAAATTTTATGGCTCATCTCCTA
66 GGCATTTCTGGTGTTGTTGTTTTCAACATGTCTCCCGTGAAGGAAATTTTATGGCTCATCTCCTA
* ** *
9565640 ACTATGGAGGGACTTTAGGGAGGTGATCGGAGTTTTTTGTAAGAAGAGCCACCTGATTTTGTGCA
131 ACTATAGAGGGACTTTAGGGAGGCAATCGGAGTTTTATGTAAGAAGAGCCACCTGATTTTGTGCA
9565705 ATTAGTTGTTCATAGAGACTAATGCCGGGCGTGGTGGAGGGAGAGAATCGTCCACTTCCATCGGT
196 ATTAGTTGTTCATAGAGACTAATGCCGGGCGTGGTGGAGGGAGAGAATCGTCCACTTCCATCGGT
*
9565770 CAGTCTACTCTTTGATTTAGATCGAGGGGATTCAGTCGGTTGCTCTCAGTTTCCTCTGCTAGTTG
261 CAGTCTACTCTTTGATTTAGATCGAGGGGATTCAGACGGTTGCTCTCAGTTTCCTCTGCTAGTTG
9565835 GTGGTTC
326 GTGGTTC
*
9565842 TCAATCCCCATCTCTGGACATCTCAGCCATTGGACCTTACATACGGGATATAAAAGATCTGGCCA
1 TCAATCCCCATCTCTAGACATCTCAGCCATTGGACCTTACATACGGGATATAAAAGATCTGGCCA
*
9565907 GGCATTTCTGGTGTTGTTGTTTTCAACATGTCTCCCGTGAAGGAAATTTTGTGGCTCATCTCCTA
66 GGCATTTCTGGTGTTGTTGTTTTCAACATGTCTCCCGTGAAGGAAATTTTATGGCTCATCTCCTA
* * * *
9565972 GCTATAGAGGGACTTTAGGGAGGCAATCGTAGTTTTATGTAAGGAGAGCTACCTGATTTTGTGCA
131 ACTATAGAGGGACTTTAGGGAGGCAATCGGAGTTTTATGTAAGAAGAGCCACCTGATTTTGTGCA
* *
9566037 ATTAGTTGTTGATAGGGACTAATGCCGGGCGTGGTGGAGGGAGAGAATCGTCCACTTCCATCGGT
196 ATTAGTTGTTCATAGAGACTAATGCCGGGCGTGGTGGAGGGAGAGAATCGTCCACTTCCATCGGT
*
9566102 CAGTCTACTCTTTGATTTGGATCGAGGGGATTCAGACGGTTGCTCTCAGTTTCCTCTGCTAGTTG
261 CAGTCTACTCTTTGATTTAGATCGAGGGGATTCAGACGGTTGCTCTCAGTTTCCTCTGCTAGTTG
9566167 GTGGT
326 GTGGT
9566172 GCTCTGGGCT
Statistics
Matches: 314, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
332 314 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (332 bp):
TCAATCCCCATCTCTAGACATCTCAGCCATTGGACCTTACATACGGGATATAAAAGATCTGGCCA
GGCATTTCTGGTGTTGTTGTTTTCAACATGTCTCCCGTGAAGGAAATTTTATGGCTCATCTCCTA
ACTATAGAGGGACTTTAGGGAGGCAATCGGAGTTTTATGTAAGAAGAGCCACCTGATTTTGTGCA
ATTAGTTGTTCATAGAGACTAATGCCGGGCGTGGTGGAGGGAGAGAATCGTCCACTTCCATCGGT
CAGTCTACTCTTTGATTTAGATCGAGGGGATTCAGACGGTTGCTCTCAGTTTCCTCTGCTAGTTG
GTGGTTC
Found at i:9568299 original size:70 final size:70
Alignment explanation
Indices: 9568220--9568356 Score: 211
Period size: 70 Copynumber: 2.0 Consensus size: 70
9568210 ATTCTCCACA
* * *
9568220 ACCCTCCAAGAATTTATAACAAATTAATAAACCCTATATGCATTAAGATATTTCAATGTGTTATT
1 ACCCTCCAAGAATTTATAACAAATTAATAAACCCTATAAGCATTAAGATATTTAAATGTATTATT
9568285 AATTC
66 AATTC
* ** *
9568290 ACCCTCCAAGAATTTATGACAAATTGGTAAACCCTATAAGCTTTAAGATATTTAAATGTATTATT
1 ACCCTCCAAGAATTTATAACAAATTAATAAACCCTATAAGCATTAAGATATTTAAATGTATTATT
9568355 AA
66 AA
9568357 GACTTTGTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
70 60 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (70 bp):
ACCCTCCAAGAATTTATAACAAATTAATAAACCCTATAAGCATTAAGATATTTAAATGTATTATT
AATTC
Found at i:9569736 original size:28 final size:28
Alignment explanation
Indices: 9569705--9569766 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
9569695 AAAATGAGAC
* *
9569705 TTTGGA-TGCCCGGGGGTAAAATGGTAAT
1 TTTGGACT-CCCGAGGGCAAAATGGTAAT
**
9569733 TTTGGACTTTCGAGGGCAAAATGGTAAT
1 TTTGGACTCCCGAGGGCAAAATGGTAAT
9569761 TTTGGA
1 TTTGGA
9569767 AAAAATTTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.26, C:0.10, G:0.32, T:0.32
Consensus pattern (28 bp):
TTTGGACTCCCGAGGGCAAAATGGTAAT
Found at i:9569795 original size:59 final size:59
Alignment explanation
Indices: 9569732--9569945 Score: 203
Period size: 59 Copynumber: 3.7 Consensus size: 59
9569722 AAAATGGTAA
* * *
9569732 TTTTGGAC-T-TTCGAGGGCAAAATGGTAATTTTG-GAAAAAATTTAGGGTTAAAAATGAAG
1 TTTTGGACATATT-GAGGGTAAAATGGTAATTTTGAG-AAAAA-TTAGGGTCAAAAATGAAT
* * * *
9569791 TTTTGG--ATGTTCGGGGGTAAAATGATAATTTTTAGAAAAATT-GGGATCAAAAATAGAAT
1 TTTTGGACATATT-GAGGGTAAAATGGTAATTTTGAGAAAAATTAGGG-TCAAAAAT-GAAT
* * * *
9569850 TTTTGGACAT-TTGAGGGTAAAATGGTAATTTTTAGAAGAATTAGGATCAAAAACGGAAT
1 TTTTGGACATATTGAGGGTAAAATGGTAATTTTGAGAAAAATTAGGGTCAAAAA-TGAAT
9569909 TTTTGGACATATTG-GGGTAAAATGGTAATTTTG-GAAA
1 TTTTGGACATATTGAGGGTAAAATGGTAATTTTGAGAAA
9569946 TGTCGGGGTT
Statistics
Matches: 132, Mismatches: 13, Indels: 21
0.80 0.08 0.13
Matches are distributed among these distances:
57 3 0.02
58 13 0.10
59 106 0.80
60 8 0.06
61 2 0.02
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (59 bp):
TTTTGGACATATTGAGGGTAAAATGGTAATTTTGAGAAAAATTAGGGTCAAAAATGAAT
Found at i:9569822 original size:28 final size:28
Alignment explanation
Indices: 9569705--9569822 Score: 69
Period size: 28 Copynumber: 4.1 Consensus size: 28
9569695 AAAATGAGAC
** *
9569705 TTTGGATGCCCGGGGGTAAAATGGTAAT
1 TTTGGATGTTCGGGGGTAAAATGATAAT
* * *
9569733 TTTGGACT-TTCGAGGGCAAAATGGTAAT
1 TTTGGA-TGTTCGGGGGTAAAATGATAAT
** ** * *
9569761 TTTGGAAAAAATTTAGGGTTAAAAATGA-AGT
1 TTTGG---ATGTTCGGGGGT-AAAATGATAAT
9569792 TTTGGATGTTCGGGGGTAAAATGATAAT
1 TTTGGATGTTCGGGGGTAAAATGATAAT
9569820 TTT
1 TTT
9569823 TAGAAAAATT
Statistics
Matches: 65, Mismatches: 18, Indels: 14
0.67 0.19 0.14
Matches are distributed among these distances:
27 7 0.11
28 39 0.60
29 1 0.02
31 12 0.18
32 6 0.09
ACGTcount: A:0.31, C:0.06, G:0.29, T:0.34
Consensus pattern (28 bp):
TTTGGATGTTCGGGGGTAAAATGATAAT
Found at i:9569871 original size:29 final size:28
Alignment explanation
Indices: 9569839--9570259 Score: 203
Period size: 29 Copynumber: 14.6 Consensus size: 28
9569829 AATTGGGATC
*
9569839 AAAAATAGAATTTTTGGACATTTGAGGGT
1 AAAAATGGAATTTTTGGA-ATTTGAGGGT
*
9569868 -AAAATGGTAATTTTTAGAAGAA-TT-AGGAT
1 AAAAATGG-AATTTTT-G--GAATTTGAGGGT
*
9569897 CAAAAACGGAATTTTTGGACATATTG-GGGT
1 -AAAAATGGAATTTTTGGA-AT-TTGAGGGT
*
9569927 -AAAATGGTAA-TTTTGGAAATGTCG-GGGTT
1 AAAAATGG-AATTTTTGG-AAT-TTGAGGG-T
* *
9569956 AAAAATGGAATTTTTTAGAATTTTAGGGGT
1 AAAAATGGAA-TTTTTGGAATTTGA-GGGT
*
9569986 AAAAATGGAATTTTTTAGAATTTTTG-GGGTT
1 AAAAATGGAA-TTTTTGGAA--TTTGAGGG-T
* *
9570017 AAAAATGGAATTTTTGGGAGTTCGAGGGT
1 AAAAATGGAATTTTT-GGAATTTGAGGGT
* *
9570046 AAAAATGGAATTTTTTGAAGTTTCG-GGATT
1 AAAAATGGAATTTTTGGAA-TTT-GAGG-GT
9570076 AAAAATGGAATTTTT---A---G-GGGT
1 AAAAATGGAATTTTTGGAATTTGAGGGT
*
9570097 AAAAATGTAATTTTTGGAATTTTG-GGGT
1 AAAAATGGAATTTTTGGAA-TTTGAGGGT
* *
9570125 CAAAAATGGGATTTTTAGAAGTTTGAGGGT
1 -AAAAATGGAATTTTTGGAA-TTTGAGGGT
* *
9570155 AAAAATGTAATTTTTAGAAGTTTCGA-GGT
1 AAAAATGGAATTTTTGGAA-TTT-GAGGGT
* * *** *
9570184 CAAAATGCAATTTTCCAAAAGTTTTAGGGTT
1 AAAAATGGAATTTT-TGGAA-TTTGAGGG-T
** *
9570215 AAAAATATAATTTTTGGAAGTTTTAGGGT
1 AAAAATGGAATTTTTGGAA-TTTGAGGGT
*
9570244 AAAAATGTAATTTTTG
1 AAAAATGGAATTTTTG
9570260 TAAGTTTTGG
Statistics
Matches: 315, Mismatches: 38, Indels: 78
0.73 0.09 0.18
Matches are distributed among these distances:
21 15 0.05
22 3 0.01
24 1 0.00
27 3 0.01
28 33 0.10
29 115 0.37
30 100 0.32
31 40 0.13
32 5 0.02
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (28 bp):
AAAAATGGAATTTTTGGAATTTGAGGGT
Found at i:9569963 original size:30 final size:30
Alignment explanation
Indices: 9569948--9570279 Score: 223
Period size: 29 Copynumber: 11.5 Consensus size: 30
9569938 TTTGGAAATG
*
9569948 TCGGGGTTAAAAATGGAATTTTTTAGAATTT
1 TCGGGGTTAAAAATGGAA-TTTTTAGAAGTT
* *
9569979 TAGGGG-TAAAAATGGAATTTTTTAGAATTT
1 TCGGGGTTAAAAATGGAA-TTTTTAGAAGTT
* * *
9570009 TTGGGGTTAAAAATGGAATTTTTGGGAG-T
1 TCGGGGTTAAAAATGGAATTTTTAGAAGTT
*
9570038 TCGAGGG-TAAAAATGGAATTTTTTGAAGTT
1 TCG-GGGTTAAAAATGGAATTTTTAGAAGTT
*
9570068 TCGGGATTAAAAATGGAATTTTT---A---
1 TCGGGGTTAAAAATGGAATTTTTAGAAGTT
* *
9570092 --GGGG-TAAAAATGTAATTTTTGGAA-TT
1 TCGGGGTTAAAAATGGAATTTTTAGAAGTT
* * *
9570118 TTGGGGTCAAAAATGGGATTTTTAGAAGTT
1 TCGGGGTTAAAAATGGAATTTTTAGAAGTT
*
9570148 T-GAGGG-TAAAAATGTAATTTTTAGAAGTT
1 TCG-GGGTTAAAAATGGAATTTTTAGAAGTT
* * * * *
9570177 TCGAGG-TCAAAATGCAATTTTCCAAAAGTT
1 TCGGGGTTAAAAATGGAATTTT-TAGAAGTT
** ** *
9570207 TTAGGGTTAAAAATATAATTTTTGGAAGTT
1 TCGGGGTTAAAAATGGAATTTTTAGAAGTT
** *
9570237 TTAGGG-TAAAAATGTAATTTTT-GTAAGTT
1 TCGGGGTTAAAAATGGAATTTTTAG-AAGTT
* *
9570266 TTGGGGTCAAAAAT
1 TCGGGGTTAAAAAT
9570280 ATAATTTTAA
Statistics
Matches: 247, Mismatches: 35, Indels: 39
0.77 0.11 0.12
Matches are distributed among these distances:
21 15 0.06
22 3 0.01
24 1 0.00
27 1 0.00
28 5 0.02
29 102 0.41
30 92 0.37
31 28 0.11
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.38
Consensus pattern (30 bp):
TCGGGGTTAAAAATGGAATTTTTAGAAGTT
Found at i:9569971 original size:59 final size:59
Alignment explanation
Indices: 9569833--9570179 Score: 233
Period size: 59 Copynumber: 6.0 Consensus size: 59
9569823 TAGAAAAATT
* * * *
9569833 GGGATCAAAAATAGAA-TTTTTGGACATTTGAGGGT-AAAATGGTAATTTTTAGAAGAATT-
1 GGGATTAAAAATGGAATTTTTTGGA-ATTTGAGGGTAAAAATGG-AATTTTTGGAA-ATTTC
* * * *
9569892 AGGATCAAAAACGGAA-TTTTTGGACATATTG-GGGT-AAAATGGTAA-TTTTGGAAATGTC
1 GGGATTAAAAATGGAATTTTTTGGA-AT-TTGAGGGTAAAAATGG-AATTTTTGGAAATTTC
* * * * * *
9569950 GGGGTTAAAAATGGAATTTTTTAGAATTTTAGGGGTAAAAATGGAATTTTTTAGAATTTTT
1 GGGATTAAAAATGGAATTTTTTGGAATTTGA-GGGTAAAAATGGAA-TTTTTGGAAATTTC
* * * * * *
9570011 GGGGTTAAAAATGGAATTTTTGGGAGTTCGAGGGTAAAAATGGAATTTTTTGAAGTTTC
1 GGGATTAAAAATGGAATTTTTTGGAATTTGAGGGTAAAAATGGAATTTTTGGAAATTTC
* *
9570070 GGGATTAAAAATGGAA-TTTTT---A---G-GGGTAAAAATGTAATTTTTGG-AATTTT
1 GGGATTAAAAATGGAATTTTTTGGAATTTGAGGGTAAAAATGGAATTTTTGGAAATTTC
* * * * * * *
9570120 GGGGTCAAAAATGGGA-TTTTTAGAAGTTTGAGGGTAAAAATGTAATTTTTAGAAGTTTC
1 GGGATTAAAAATGGAATTTTTTGGAA-TTTGAGGGTAAAAATGGAATTTTTGGAAATTTC
9570179 G
1 G
9570180 AGGTCAAAAT
Statistics
Matches: 234, Mismatches: 37, Indels: 34
0.77 0.12 0.11
Matches are distributed among these distances:
50 22 0.09
51 19 0.08
52 1 0.00
53 1 0.00
57 5 0.02
58 45 0.19
59 82 0.35
60 24 0.10
61 35 0.15
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (59 bp):
GGGATTAAAAATGGAATTTTTTGGAATTTGAGGGTAAAAATGGAATTTTTGGAAATTTC
Found at i:9570109 original size:80 final size:80
Alignment explanation
Indices: 9570003--9570171 Score: 211
Period size: 80 Copynumber: 2.1 Consensus size: 80
9569993 GAATTTTTTA
* *
9570003 GAATTTTT-GGGGTTAAAAATGGAATTTTTGGGAGTTCGAGGGT-AAAAATGGAATTTTTTGAAG
1 GAATTTTTAGGGGTTAAAAATGGAATTTTTGGAAGTTCG-GGGTCAAAAATGGAATTTTTAGAAG
*
9570066 TTTCG-GGATTAAAAATG
65 TTT-GAGG-GTAAAAATG
* * * *
9570083 GAATTTTTAGGGG-TAAAAATGTAATTTTTGGAATTTTGGGGTCAAAAATGGGATTTTTAGAAGT
1 GAATTTTTAGGGGTTAAAAATGGAATTTTTGGAAGTTCGGGGTCAAAAATGGAATTTTTAGAAGT
9570147 TTGAGGGTAAAAATG
66 TTGAGGGTAAAAATG
*
9570162 TAATTTTTAG
1 GAATTTTTAG
9570172 AAGTTTCGAG
Statistics
Matches: 78, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 22 0.28
80 52 0.67
81 4 0.05
ACGTcount: A:0.33, C:0.02, G:0.27, T:0.38
Consensus pattern (80 bp):
GAATTTTTAGGGGTTAAAAATGGAATTTTTGGAAGTTCGGGGTCAAAAATGGAATTTTTAGAAGT
TTGAGGGTAAAAATG
Found at i:9570158 original size:109 final size:111
Alignment explanation
Indices: 9569976--9570179 Score: 313
Period size: 109 Copynumber: 1.9 Consensus size: 111
9569966 TTTTTTAGAA
* * *
9569976 TTTTAGGGGTAAAAATGGAATTTTTTAGAATTTTTGGGGTTAAAAATGGAATTTTTGGGAGTTCG
1 TTTTAGGGGTAAAAATGGAATTTTTTAGAATTTTTGGGGTCAAAAATGGAATTTTTAGAAGTTCG
*
9570041 AGGGTAAAAATGGAATTTTTTGAAGTTTCGGGATTAAAAATGGAAT
66 AGGGTAAAAATGGAATTTTTAGAAGTTTCGGGATTAAAAATGGAAT
* * * *
9570087 TTTTAGGGGTAAAAATGTAA-TTTTTGGAA-TTTTGGGGTCAAAAATGGGATTTTTAGAAGTTTG
1 TTTTAGGGGTAAAAATGGAATTTTTTAGAATTTTTGGGGTCAAAAATGGAATTTTTAGAAGTTCG
*
9570150 AGGGTAAAAATGTAATTTTTAGAAGTTTCG
66 AGGGTAAAAATGGAATTTTTAGAAGTTTCG
9570180 AGGTCAAAAT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
109 57 0.68
110 8 0.10
111 19 0.23
ACGTcount: A:0.33, C:0.02, G:0.26, T:0.39
Consensus pattern (111 bp):
TTTTAGGGGTAAAAATGGAATTTTTTAGAATTTTTGGGGTCAAAAATGGAATTTTTAGAAGTTCG
AGGGTAAAAATGGAATTTTTAGAAGTTTCGGGATTAAAAATGGAAT
Found at i:9570309 original size:89 final size:89
Alignment explanation
Indices: 9570135--9570331 Score: 222
Period size: 89 Copynumber: 2.2 Consensus size: 89
9570125 CAAAAATGGG
* * * *
9570135 ATTTTTAGAAGTTTGAGGGTAAAAATGTAATTTTTAGAAGTTTCGAGGTCAAAATGCAATTTTCC
1 ATTTTTGGAAGTTTTAGGGTAAAAATGTAATTTTTAGAAGTTTCGAGGTCAAAATACAATTTTCA
** *
9570200 AAAAGTTTTAGGGTTAAAAATATA
66 AAAAGTTCAAGGGTTAAAAATACA
* * *
9570224 ATTTTTGGAAGTTTTAGGGTAAAAATGTAATTTTT-GTAAGTTTTGGGGTCAAAAATATAATTTT
1 ATTTTTGGAAGTTTTAGGGTAAAAATGTAATTTTTAG-AAGTTTCGAGGTC-AAAATACAATTTT
*
9570288 -AAAGAAGTTCAAGGG-TCAAAATACA
64 CAAA-AAGTTCAAGGGTTAAAAATACA
*
9570313 ATTTCTGGACAG-TTTAGGG
1 ATTTTTGGA-AGTTTTAGGG
9570332 ACCTTCAGAA
Statistics
Matches: 92, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
88 1 0.01
89 69 0.75
90 22 0.24
ACGTcount: A:0.37, C:0.06, G:0.21, T:0.37
Consensus pattern (89 bp):
ATTTTTGGAAGTTTTAGGGTAAAAATGTAATTTTTAGAAGTTTCGAGGTCAAAATACAATTTTCA
AAAAGTTCAAGGGTTAAAAATACA
Found at i:9570316 original size:60 final size:59
Alignment explanation
Indices: 9570146--9570316 Score: 166
Period size: 60 Copynumber: 2.8 Consensus size: 59
9570136 TTTTTAGAAG
* *
9570146 TTTGAGGGTAAAAATGTAATTTTTAGAAGTTTCGA-GGTCAAAATGCAATTTTCCAAAAGT
1 TTTG-GGGTAAAAATATAATTTTTAGAAG-TTCAAGGGTCAAAATGCAATTTTCCAAAAGT
* * ** * * ***
9570206 TTTAGGGTTAAAAATATAATTTTTGGAAGTTTTAGGGTAAAAATGTAATTTT-TGTAAGT
1 TTT-GGGGTAAAAATATAATTTTTAGAAGTTCAAGGGTCAAAATGCAATTTTCCAAAAGT
* *
9570265 TTTGGGGTCAAAAATATAATTTTAAAGAAGTTCAAGGGTCAAAATACAATTT
1 TTTGGGGT-AAAAATATAATTTT-TAGAAGTTCAAGGGTCAAAATGCAATTT
9570317 CTGGACAGTT
Statistics
Matches: 89, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
58 4 0.04
59 24 0.27
60 60 0.67
61 1 0.01
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.37
Consensus pattern (59 bp):
TTTGGGGTAAAAATATAATTTTTAGAAGTTCAAGGGTCAAAATGCAATTTTCCAAAAGT
Found at i:9572220 original size:6 final size:6
Alignment explanation
Indices: 9572211--9572314 Score: 87
Period size: 6 Copynumber: 17.8 Consensus size: 6
9572201 TTAATATTAT
* *
9572211 TTTAAA TTT-AA -TTAAA TTTAAA TTTAAA -GTAAA TTTAAA TAAGTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
* *
9572258 TTTAAA TTTAAGA --TAAA TTTAAA TTTAAA ATT-AA TTTAAA ATT-AA
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
9572303 TTTAAA CTTTAA
1 TTTAAA -TTTAA
9572315 TTAAAAATCA
Statistics
Matches: 79, Mismatches: 8, Indels: 21
0.73 0.07 0.19
Matches are distributed among these distances:
4 3 0.04
5 19 0.24
6 46 0.58
7 6 0.08
8 5 0.06
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:9572229 original size:17 final size:16
Alignment explanation
Indices: 9572211--9572285 Score: 109
Period size: 17 Copynumber: 4.7 Consensus size: 16
9572201 TTAATATTAT
*
9572211 TTTAAATTTAATTAAA
1 TTTAAATTTAAGTAAA
9572227 TTTAAATTTAAAGTAAA
1 TTTAAATTT-AAGTAAA
9572244 TTTAAA--TAAGTAAA
1 TTTAAATTTAAGTAAA
9572258 TTTAAATTTAAGATAAA
1 TTTAAATTTAAG-TAAA
9572275 TTTAAATTTAA
1 TTTAAATTTAA
9572286 AATTAATTTA
Statistics
Matches: 54, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
14 13 0.24
15 1 0.02
16 13 0.24
17 27 0.50
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (16 bp):
TTTAAATTTAAGTAAA
Found at i:9572234 original size:11 final size:11
Alignment explanation
Indices: 9572211--9572319 Score: 68
Period size: 11 Copynumber: 10.0 Consensus size: 11
9572201 TTAATATTAT
*
9572211 TTTAAATTTAA
1 TTTAAATTAAA
9572222 -TTAAATTTAAA
1 TTTAAA-TTAAA
*
9572233 TTTAAAGTAAA
1 TTTAAATTAAA
9572244 TTTAAA-T-AA
1 TTTAAATTAAA
*
9572253 -GTAAATTTAAA
1 TTTAAA-TTAAA
9572264 TTTAAGA-TAAA
1 TTTAA-ATTAAA
9572275 TTTAAATTTAAA
1 TTTAAA-TTAAA
* *
9572287 ATTAATTTAAA
1 TTTAAATTAAA
* *
9572298 ATTAATTTAAA
1 TTTAAATTAAA
9572309 CTTT-AATTAAA
1 -TTTAAATTAAA
9572320 AATCAAAAGC
Statistics
Matches: 80, Mismatches: 8, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
8 4 0.05
9 2 0.03
10 8 0.10
11 47 0.59
12 18 0.22
13 1 0.01
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:9572261 original size:31 final size:31
Alignment explanation
Indices: 9572223--9572281 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
9572213 TAAATTTAAT
9572223 TAAATTTAAATTTAA-AGTAAATTTAAATAAG
1 TAAATTTAAATTTAAGA-TAAATTTAAATAAG
9572254 TAAATTTAAATTTAAGATAAATTTAAAT
1 TAAATTTAAATTTAAGATAAATTTAAAT
9572282 TTAAAATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (31 bp):
TAAATTTAAATTTAAGATAAATTTAAATAAG
Found at i:9572293 original size:17 final size:17
Alignment explanation
Indices: 9572211--9572302 Score: 102
Period size: 17 Copynumber: 5.6 Consensus size: 17
9572201 TTAATATTAT
*
9572211 TTTAAATTT-AATTAAA
1 TTTAAATTTAAAATAAA
*
9572227 TTTAAATTTAAAGTAAA
1 TTTAAATTTAAAATAAA
*
9572244 TTTAAA--T-AAGTAAA
1 TTTAAATTTAAAATAAA
*
9572258 TTTAAATTTAAGATAAA
1 TTTAAATTTAAAATAAA
*
9572275 TTTAAATTTAAAATTAA
1 TTTAAATTTAAAATAAA
*
9572292 TTTAAAATTAA
1 TTTAAATTTAA
9572303 TTTAAACTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
14 13 0.20
15 1 0.02
16 10 0.15
17 42 0.64
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:9572321 original size:23 final size:22
Alignment explanation
Indices: 9572279--9572322 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
9572269 GATAAATTTA
*
9572279 AATTTAAAATTAATTTAAAATT
1 AATTTAAAATTAATTAAAAATT
*
9572301 AATTTAAACTTTAATTAAAAAT
1 AATTTAAA-ATTAATTAAAAAT
9572323 CAAAAGCCCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTTAAAATTAATTAAAAATT
Found at i:9573759 original size:54 final size:54
Alignment explanation
Indices: 9573690--9573817 Score: 188
Period size: 54 Copynumber: 2.4 Consensus size: 54
9573680 TGCGATTTAT
*
9573690 GATTTTTTATATGTTTAAAACGATTGTCATGTTGGAAT-ATCATTTCTTTTGAAT-
1 GATTGTTTATATGTTTAAAACGATTGTCATGTTGGAATAATC--TTCTTTTGAATC
* *
9573744 TATTGTTTATATGTTTAAATCGATTGTCATGTTGGAATAATGCTTCTTTTGAATC
1 GATTGTTTATATGTTTAAAACGATTGTCATGTTGGAATAAT-CTTCTTTTGAATC
9573799 GATTGTTTATATGTTTAAA
1 GATTGTTTATATGTTTAAA
9573818 TCGACTGTTA
Statistics
Matches: 67, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
54 46 0.69
55 20 0.30
56 1 0.01
ACGTcount: A:0.27, C:0.07, G:0.16, T:0.50
Consensus pattern (54 bp):
GATTGTTTATATGTTTAAAACGATTGTCATGTTGGAATAATCTTCTTTTGAATC
Found at i:9576447 original size:39 final size:39
Alignment explanation
Indices: 9576404--9576535 Score: 119
Period size: 39 Copynumber: 3.4 Consensus size: 39
9576394 AGCCGTGCTA
* *
9576404 TGTTTACAGTGTCACAGTCAGATCGAA-ATAGC-ATCGCAG
1 TGTTTACAGTGTCACAGCCAGATC-AATATAGCTA-CACAG
* * *
9576443 TGTTTACAATGTCACTGCCAGTTCAATATAGCTACACAG
1 TGTTTACAGTGTCACAGCCAGATCAATATAGCTACACAG
* * * *
9576482 TGTTTACGGTGTCACTGCCA-ACTCAATATAG-TATTACGG
1 TGTTTACAGTGTCACAGCCAGA-TCAATATAGCTA-CACAG
9576521 TGTTTACAGTGTCAC
1 TGTTTACAGTGTCAC
9576536 CGTCAGTTCA
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
38 4 0.05
39 73 0.94
40 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (39 bp):
TGTTTACAGTGTCACAGCCAGATCAATATAGCTACACAG
Found at i:9576624 original size:39 final size:39
Alignment explanation
Indices: 9576520--9576625 Score: 158
Period size: 39 Copynumber: 2.7 Consensus size: 39
9576510 TAGTATTACG
* *
9576520 GTGTTTACAGTGTCACCGTCAGTTCAGTGTTGTATTGTA
1 GTGTTTACAGTGTCACTGCCAGTTCAGTGTTGTATTGTA
* *
9576559 GTGTTTACAGTGTCACTGCTAATTCAGTGTTGTATTGTA
1 GTGTTTACAGTGTCACTGCCAGTTCAGTGTTGTATTGTA
* *
9576598 GTGTTTATAGTGTCACTACCAGTTCAGT
1 GTGTTTACAGTGTCACTGCCAGTTCAGT
9576626 AATTTGATAA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 59 1.00
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.42
Consensus pattern (39 bp):
GTGTTTACAGTGTCACTGCCAGTTCAGTGTTGTATTGTA
Found at i:9582602 original size:24 final size:24
Alignment explanation
Indices: 9582575--9582825 Score: 187
Period size: 24 Copynumber: 10.5 Consensus size: 24
9582565 ACATAGGCTT
* *
9582575 ACGAGTGTAAACATGTGCAAGTTG
1 ACGAGCGTAAACGTGTGCAAGTTG
* **
9582599 ACGAGCGTAAACGTATATAAGTTG
1 ACGAGCGTAAACGTGTGCAAGTTG
* * * *
9582623 ACAAGCGTAAGCGTGTGTAAGCTG
1 ACGAGCGTAAACGTGTGCAAGTTG
9582647 ACGAGCGTAAACGTGTGCAAGTTG
1 ACGAGCGTAAACGTGTGCAAGTTG
* * ** *
9582671 ACGAGCGTAAACATATATAAGCTG
1 ACGAGCGTAAACGTGTGCAAGTTG
* * *
9582695 ACGAGCATAAATGTGTGCAAGCTG
1 ACGAGCGTAAACGTGTGCAAGTTG
* * * * * *
9582719 ATGAGCGTAAACATATGTAAGCTA
1 ACGAGCGTAAACGTGTGCAAGTTG
* * ** *
9582743 ACGAGCATAAACGTATATAAGCTG
1 ACGAGCGTAAACGTGTGCAAGTTG
* ** **
9582767 ACGAGCGTAAACGTATATAAACTG
1 ACGAGCGTAAACGTGTGCAAGTTG
* *
9582791 ATGAGCATAAACGTGTGCAAGTTG
1 ACGAGCGTAAACGTGTGCAAGTTG
9582815 ACGAGCGTAAA
1 ACGAGCGTAAA
9582826 TGTATATGAG
Statistics
Matches: 179, Mismatches: 48, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 179 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (24 bp):
ACGAGCGTAAACGTGTGCAAGTTG
Found at i:9582610 original size:72 final size:72
Alignment explanation
Indices: 9582532--9582832 Score: 323
Period size: 72 Copynumber: 4.2 Consensus size: 72
9582522 CATTGAATTA
* * * *
9582532 CGTAAACGTATATAAGCTGACGAGCATAAATGTACATAGGCTTACGAGTGTAAACATGTGCAAGT
1 CGTAAACGTATATAAGCTGACGAGCATAAACGTACATAAGCTGACGAGCGTAAACATGTGCAAGT
9582597 TGACGAG
66 TGACGAG
* * * * *** *
9582604 CGTAAACGTATATAAGTTGACAAGCGTAAGCGTGTGTAAGCTGACGAGCGTAAACGTGTGCAAGT
1 CGTAAACGTATATAAGCTGACGAGCATAAACGTACATAAGCTGACGAGCGTAAACATGTGCAAGT
9582669 TGACGAG
66 TGACGAG
* * **** * * * *
9582676 CGTAAACATATATAAGCTGACGAGCATAAATGTGTGCAAGCTGATGAGCGTAAACATATGTAAGC
1 CGTAAACGTATATAAGCTGACGAGCATAAACGTACATAAGCTGACGAGCGTAAACATGTGCAAGT
*
9582741 TAACGAG
66 TGACGAG
* * * * * * *
9582748 CATAAACGTATATAAGCTGACGAGCGTAAACGTATATAAACTGATGAGCATAAACGTGTGCAAGT
1 CGTAAACGTATATAAGCTGACGAGCATAAACGTACATAAGCTGACGAGCGTAAACATGTGCAAGT
9582813 TGACGAG
66 TGACGAG
*
9582820 CGTAAATGTATAT
1 CGTAAACGTATAT
9582833 GAGTCGACAT
Statistics
Matches: 188, Mismatches: 41, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
72 188 1.00
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (72 bp):
CGTAAACGTATATAAGCTGACGAGCATAAACGTACATAAGCTGACGAGCGTAAACATGTGCAAGT
TGACGAG
Found at i:9582831 original size:48 final size:48
Alignment explanation
Indices: 9582532--9582832 Score: 284
Period size: 48 Copynumber: 6.3 Consensus size: 48
9582522 CATTGAATTA
*
9582532 CGTAAACGTATATAAGCTGACGAGCATAAA--TGTACATAGGCTT-ACGAG
1 CGTAAACGTATATAAGCTGACGAGCATAAACGTGTGCA-A-G-TTGACGAG
* * * ** * * * ** *
9582580 TGTAAACATGTGCAAGTTGACGAGCGTAAACGTATATAAGTTGACAAG
1 CGTAAACGTATATAAGCTGACGAGCATAAACGTGTGCAAGTTGACGAG
* * * *
9582628 CGTAAGCGTGTGTAAGCTGACGAGCGTAAACGTGTGCAAGTTGACGAG
1 CGTAAACGTATATAAGCTGACGAGCATAAACGTGTGCAAGTTGACGAG
* * * *
9582676 CGTAAACATATATAAGCTGACGAGCATAAATGTGTGCAAGCTGATGAG
1 CGTAAACGTATATAAGCTGACGAGCATAAACGTGTGCAAGTTGACGAG
* * * * ** *
9582724 CGTAAACATATGTAAGCTAACGAGCATAAACGTATATAAGCTGACGAG
1 CGTAAACGTATATAAGCTGACGAGCATAAACGTGTGCAAGTTGACGAG
* *
9582772 CGTAAACGTATATAAACTGATGAGCATAAACGTGTGCAAGTTGACGAG
1 CGTAAACGTATATAAGCTGACGAGCATAAACGTGTGCAAGTTGACGAG
*
9582820 CGTAAATGTATAT
1 CGTAAACGTATAT
9582833 GAGTCGACAT
Statistics
Matches: 206, Mismatches: 44, Indels: 6
0.80 0.17 0.02
Matches are distributed among these distances:
47 2 0.01
48 199 0.97
49 1 0.00
50 4 0.02
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (48 bp):
CGTAAACGTATATAAGCTGACGAGCATAAACGTGTGCAAGTTGACGAG
Found at i:9588976 original size:3 final size:3
Alignment explanation
Indices: 9588970--9589010 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
9588960 TAATAATAAT
9588970 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
9589011 TAATAATAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:9589015 original size:3 final size:3
Alignment explanation
Indices: 9589009--9589053 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
9588999 CAACAACAAC
9589009 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
9589054 GAAATTAAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:9589448 original size:24 final size:24
Alignment explanation
Indices: 9589410--9589608 Score: 170
Period size: 24 Copynumber: 8.3 Consensus size: 24
9589400 TAAACGTTAT
*
9589410 AAGCTAACGAGCGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
* *
9589434 AAGTTGACGAGCGTAAA--TGTAC
1 AAGCTGACGAGCGTAAACGTGTGC
*
9589456 ATAAGCTGATGAGCGTAATA-GTGTGC
1 --AAGCTGACGAGCGTAA-ACGTGTGC
* * **
9589482 AAGCTGACGAGTGTAAACGTATAT
1 AAGCTGACGAGCGTAAACGTGTGC
* * *
9589506 AAGCTGATGAGTGTAAATGTGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
* * * **
9589530 AAGCTGAGGAGCGTAAACATATAT
1 AAGCTGACGAGCGTAAACGTGTGC
* *
9589554 AAGCTGACAAGCATAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
* *
9589578 AAGCTGACGAGTGTAAACGTATGC
1 AAGCTGACGAGCGTAAACGTGTGC
9589602 AAGCTGA
1 AAGCTGA
9589609 TGATGTAACA
Statistics
Matches: 136, Mismatches: 34, Indels: 10
0.76 0.19 0.06
Matches are distributed among these distances:
22 4 0.03
23 1 0.01
24 126 0.93
25 1 0.01
26 4 0.03
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.22
Consensus pattern (24 bp):
AAGCTGACGAGCGTAAACGTGTGC
Found at i:9589470 original size:48 final size:48
Alignment explanation
Indices: 9589398--9589608 Score: 255
Period size: 48 Copynumber: 4.4 Consensus size: 48
9589388 CATTGAATTA
* *
9589398 CGTAAACGT-TATAAGCTAACGAGCGTAAACGTGTGCAAGTTGACGAG
1 CGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGACGAG
* * *
9589445 CGTAAATGTACATAAGCTGATGAGCGTAATA-GTGTGCAAGCTGACGAG
1 CGTAAACGTATATAAGCTGACGAGCGTAA-ACGTGTGCAAGCTGACGAG
* * * * *
9589493 TGTAAACGTATATAAGCTGATGAGTGTAAATGTGTGCAAGCTGAGGAG
1 CGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGACGAG
* * *
9589541 CGTAAACATATATAAGCTGACAAGCATAAACGTGTGCAAGCTGACGAG
1 CGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGACGAG
* **
9589589 TGTAAACGTATGCAAGCTGA
1 CGTAAACGTATATAAGCTGA
9589609 TGATGTAACA
Statistics
Matches: 139, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
47 9 0.06
48 129 0.93
49 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (48 bp):
CGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGACGAG
Found at i:9592018 original size:52 final size:52
Alignment explanation
Indices: 9591940--9592175 Score: 427
Period size: 52 Copynumber: 4.5 Consensus size: 52
9591930 ATGCAAAAGA
*
9591940 TCCGATTACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGG
1 TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGG
*
9591992 TCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTATAAGG
1 TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGG
9592044 TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGG
1 TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGG
* *
9592096 TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTTCGGATTATGAGG
1 TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGG
*
9592148 TCCGATGACAATGTGTCATCGTGAGTAT
1 TCCGATGACTATGTGTCATCGTGAGTAT
9592176 TAAATGACAA
Statistics
Matches: 178, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 178 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (52 bp):
TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGG
Found at i:9592249 original size:62 final size:62
Alignment explanation
Indices: 9592124--9592249 Score: 148
Period size: 62 Copynumber: 2.0 Consensus size: 62
9592114 TCGTGAGTAT
* * * **
9592124 ATGAATCCTTTTCGGATTATGAGGTCCGATGACAATGTGTCATCGTGAGTATTAAATGACAA
1 ATGAATCCTTTACGGATTATAAGATCCGATGACAATGTGTCATCGTGAGTACCAAATGACAA
** *
9592186 ATGAATCCTATTACGGATTA-AAGATCCGATGACTCTGTGTTATCGTGAGTTACCAAATG-CAA
1 ATGAATCCT-TTACGGATTATAAGATCCGATGACAATGTGTCATCGTGAG-TACCAAATGACAA
9592248 AT
1 AT
9592250 TGAAACCAAC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
62 38 0.70
63 16 0.30
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (62 bp):
ATGAATCCTTTACGGATTATAAGATCCGATGACAATGTGTCATCGTGAGTACCAAATGACAA
Found at i:9615752 original size:19 final size:20
Alignment explanation
Indices: 9615723--9615760 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
9615713 TAATTGTTGG
9615723 TTTCAAATTTTTTTCTTTTT
1 TTTCAAATTTTTTTCTTTTT
9615743 TTTC-AATTTTTTTCTTTT
1 TTTCAAATTTTTTTCTTTT
9615761 ATATTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTCAAATTTTTTTCTTTTT
Found at i:9616233 original size:15 final size:15
Alignment explanation
Indices: 9616213--9616245 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
9616203 AATATTTTAA
9616213 AAATTA-TAAAAATAT
1 AAATTATTAAAAAT-T
9616228 AAATTATTAAAAATT
1 AAATTATTAAAAATT
9616243 AAA
1 AAA
9616246 ATTTAATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATTATTAAAAATT
Found at i:9616842 original size:20 final size:20
Alignment explanation
Indices: 9616819--9616907 Score: 74
Period size: 20 Copynumber: 4.2 Consensus size: 20
9616809 ACAAAAACTA
9616819 AAAAAATTCAAAATAATTTT
1 AAAAAATTCAAAATAATTTT
* *
9616839 AAAATATTTAAAAT-ATTTAT
1 AAAAAATTCAAAATAATTT-T
*
9616859 AAAAATTTCAAAATTTATATTTTT
1 AAAAAATTCAAAA--TA-A-TTTT
*
9616883 AAAAAATTTATAAA-AATTTT
1 AAAAAATTCA-AAATAATTTT
9616903 AAAAA
1 AAAAA
9616908 TTTTGAAGAA
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
19 4 0.07
20 32 0.58
21 1 0.02
22 2 0.04
24 10 0.18
25 6 0.11
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAAAATTCAAAATAATTTT
Found at i:9616848 original size:9 final size:9
Alignment explanation
Indices: 9616819--9616955 Score: 73
Period size: 9 Copynumber: 14.8 Consensus size: 9
9616809 ACAAAAACTA
*
9616819 AAAAAATTC
1 AAAAAATTT
9616828 AAAATAATTTT
1 AAAA-AA-TTT
*
9616839 AAAATATTT
1 AAAAAATTT
*
9616848 AAAATATTT
1 AAAAAATTT
9616857 ATAAAAATTT
1 A-AAAAATTT
*
9616867 -CAAAATTT
1 AAAAAATTT
* **
9616875 -ATATTTTT
1 AAAAAATTT
9616883 AAAAAATTT
1 AAAAAATTT
9616892 ATAAAAATTTT
1 A-AAAAA-TTT
*
9616903 AAAAATTTT
1 AAAAAATTT
* *
9616912 GAAGAATATAT
1 -AA-AAAATTT
*
9616923 AAAAAAGTT
1 AAAAAATTT
*
9616932 -AAAATTTT
1 AAAAAATTT
9616940 AAAAAATTT
1 AAAAAATTT
*
9616949 CAAAAAT
1 AAAAAAT
9616956 ATAATTTTTG
Statistics
Matches: 97, Mismatches: 22, Indels: 18
0.71 0.16 0.13
Matches are distributed among these distances:
8 17 0.18
9 43 0.44
10 23 0.24
11 14 0.14
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (9 bp):
AAAAAATTT
Found at i:9616922 original size:44 final size:43
Alignment explanation
Indices: 9616819--9616910 Score: 111
Period size: 44 Copynumber: 2.2 Consensus size: 43
9616809 ACAAAAACTA
* * *
9616819 AAAAAATTCAAAA-TA-A-TTTTAAAATATTTAAAATATTTAT
1 AAAAATTTCAAAATTATATTTTTAAAAAATTTAAAAAATTTAT
9616859 AAAAATTTCAAAATTTATATTTTTAAAAAATTTATAAAAATTT-T
1 AAAAATTTCAAAA-TTATATTTTTAAAAAATTTA-AAAAATTTAT
9616903 AAAAATTT
1 AAAAATTT
9616911 TGAAGAATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
40 12 0.27
42 2 0.05
43 1 0.02
44 22 0.50
45 7 0.16
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.42
Consensus pattern (43 bp):
AAAAATTTCAAAATTATATTTTTAAAAAATTTAAAAAATTTAT
Found at i:9616936 original size:64 final size:64
Alignment explanation
Indices: 9616819--9616938 Score: 149
Period size: 64 Copynumber: 1.9 Consensus size: 64
9616809 ACAAAAACTA
* *
9616819 AAAAAATTCAAAATAATTTTAAAATATTTAAAATATTTATAAAAATTTCAAAATTTATATTTTT
1 AAAAAATTCAAAATAATTTTAAAATATTTAAAATATATATAAAAAGTTCAAAATTTATATTTTT
*
9616883 AAAAAATTTATAAA-AATTTTAAAA-ATTTTGAAGAATATATA-AAAAAGTT-AAAATTT
1 AAAAAATTCA-AAATAATTTTAAAATA-TTT-AA-AATATATATAAAAAGTTCAAAATTT
9616939 TAAAAAATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
63 1 0.02
64 29 0.59
65 12 0.24
66 7 0.14
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.40
Consensus pattern (64 bp):
AAAAAATTCAAAATAATTTTAAAATATTTAAAATATATATAAAAAGTTCAAAATTTATATTTTT
Found at i:9616947 original size:10 final size:10
Alignment explanation
Indices: 9616817--9616954 Score: 56
Period size: 10 Copynumber: 13.6 Consensus size: 10
9616807 CAACAAAAAC
*
9616817 TAAAAAAATT
1 TAAAAAATTT
*
9616827 CAAAATAATTT
1 TAAAA-AATTT
*
9616838 TAAAATA-TT
1 TAAAAAATTT
*
9616847 TAAAATA-TT
1 TAAAAAATTT
9616856 TATAAAAATTT
1 TA-AAAAATTT
*
9616867 CAAAATTTATATTTT
1 TAAAA---A-A-TTT
9616882 TAAAAAA-TT
1 TAAAAAATTT
9616891 TATAAAAATTT
1 TA-AAAAATTT
9616902 T-AAAAATTT
1 TAAAAAATTT
* * *
9616911 TGAAGAATATA
1 TAAAAAAT-TT
*
9616922 TAAAAAA-GT
1 TAAAAAATTT
9616931 T--AAAATTT
1 TAAAAAATTT
9616939 TAAAAAATTT
1 TAAAAAATTT
*
9616949 CAAAAA
1 TAAAAA
9616955 TATAATTTTT
Statistics
Matches: 98, Mismatches: 15, Indels: 30
0.69 0.10 0.21
Matches are distributed among these distances:
7 4 0.04
8 2 0.02
9 27 0.28
10 34 0.35
11 21 0.21
12 1 0.01
13 1 0.01
14 1 0.01
15 7 0.07
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (10 bp):
TAAAAAATTT
Found at i:9618349 original size:24 final size:24
Alignment explanation
Indices: 9618316--9618374 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
9618306 AAAAATAATA
* * *
9618316 TTTCAGTTAAATTTTGTTTAATTG
1 TTTCAATTAAATTCTATTTAATTG
*
9618340 TTTCAATTAAATTCTATTTATTTG
1 TTTCAATTAAATTCTATTTAATTG
9618364 TTT-AAGTTAAA
1 TTTCAA-TTAAA
9618375 CTCTTATTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 2 0.07
24 28 0.93
ACGTcount: A:0.31, C:0.05, G:0.08, T:0.56
Consensus pattern (24 bp):
TTTCAATTAAATTCTATTTAATTG
Found at i:9620334 original size:24 final size:24
Alignment explanation
Indices: 9620306--9620368 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
9620296 AGAAATAATC
*
9620306 TTTCAGTTAAACTCTGTTTAGTTG
1 TTTCAGTTAAACTCTATTTAGTTG
* * *
9620330 TTTCAATTAGACTCTATTTATTTG
1 TTTCAGTTAAACTCTATTTAGTTG
* *
9620354 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
9620369 TATTAGTCTA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.24, C:0.14, G:0.13, T:0.49
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTAGTTG
Found at i:9629089 original size:49 final size:48
Alignment explanation
Indices: 9628931--9629304 Score: 231
Period size: 49 Copynumber: 7.7 Consensus size: 48
9628921 TACCATGAAG
* * * *
9628931 CATGAAGGGAAAGGATTAAGCCGCGATGGTGAACCTTATATCTCAAAA
1 CATGAAGGGAAAGGTTTAAGCCGCAATGGCGAACCTTATACCTCAAAA
* * * * * * * * *
9628979 AATGAAGGGAAAGATTTAAGTCGCAACGACAAATC-TAGTACCACGAAGA
1 CATGAAGGGAAAGGTTTAAGCCGCAATGGCGAACCTTA-TACCTC-AAAA
** * * *
9629028 CACAAAGCGAAAGGTTTAAGTCGCAATGGGGAACCTTATACCTCAAAA
1 CATGAAGGGAAAGGTTTAAGCCGCAATGGCGAACCTTATACCTCAAAA
* * * * *
9629076 GCATGAAGGGAAAGATTTAAGCCACAACGGCGAATC-TAGTACCACGAAGATA
1 -CATGAAGGGAAAGGTTTAAGCCGCAATGGCGAACCTTA-TACCTC-AA-A-A
* * *
9629128 CA--AAGGGAAAGGCTTAAGCCGCAATGGTGAACCTTATACCTCAGAAG
1 CATGAAGGGAAAGGTTTAAGCCGCAATGGCGAACCTTATACCTCA-AAA
* ** * * * * *
9629175 CATTAAGAAAAAGATTTAAGCCGCAACGACGAATC-TAGTACCATGAAAA
1 CATGAAGGGAAAGGTTTAAGCCGCAATGGCGAACCTTA-TACC-TCAAAA
* * * *
9629224 CATAAAGGGAAAGGTTTAAGTCGCAATGACGAACCTTGTACCTCAGAAA
1 CATGAAGGGAAAGGTTTAAGCCGCAATGGCGAACCTTATACCTCA-AAA
* *
9629273 -ATGAAGGG-AAGGATTTAAACCGCAATAGCGAA
1 CATGAAGGGAAAGG-TTTAAGCCGCAATGGCGAA
9629305 TCCAGTACCA
Statistics
Matches: 242, Mismatches: 67, Indels: 34
0.71 0.20 0.10
Matches are distributed among these distances:
47 8 0.03
48 62 0.26
49 159 0.66
50 9 0.04
51 3 0.01
52 1 0.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (48 bp):
CATGAAGGGAAAGGTTTAAGCCGCAATGGCGAACCTTATACCTCAAAA
Found at i:9629112 original size:98 final size:97
Alignment explanation
Indices: 9628935--9629368 Score: 478
Period size: 98 Copynumber: 4.4 Consensus size: 97
9628925 ATGAAGCATG
* * * * *
9628935 AAGGGAAAGGATTAAGCCGCGATGGTGAACCTTATATCTCAAAAAATGAAGGGAAAGATTTAAGT
1 AAGGGAAAGGTTTAAGCCGCAATGGTGAACCTTATACCTCAAAACATGAAGGGAAAGATTTAAGC
*
9629000 CGCAACGACAAATCTAGTACCACGAAGACACA
66 CGCAACGACGAATCTAGTACCACGAAGACACA
* * *
9629032 AAGCGAAAGGTTTAAGTCGCAATGGGGAACCTTATACCTCAAAAGCATGAAGGGAAAGATTTAAG
1 AAGGGAAAGGTTTAAGCCGCAATGGTGAACCTTATACCTCAAAA-CATGAAGGGAAAGATTTAAG
* * *
9629097 CCACAACGGCGAATCTAGTACCACGAAGATACA
65 CCGCAACGACGAATCTAGTACCACGAAGACACA
* * * **
9629130 AAGGGAAAGGCTTAAGCCGCAATGGTGAACCTTATACCTCAGAAGCATTAAGAAAAAGATTTAAG
1 AAGGGAAAGGTTTAAGCCGCAATGGTGAACCTTATACCTCA-AAACATGAAGGGAAAGATTTAAG
* * *
9629195 CCGCAACGACGAATCTAGTACCATGAAAACATA
65 CCGCAACGACGAATCTAGTACCACGAAGACACA
* ** * * *
9629228 AAGGGAAAGGTTTAAGTCGCAATGACGAACCTTGTACCTCAGAAA-ATGAAGGGAAGGATTTAAA
1 AAGGGAAAGGTTTAAGCCGCAATGGTGAACCTTATACCTCA-AAACATGAAGGGAAAGATTTAAG
* * * **
9629292 CCGCAA-TAGCGAATCCAGTACCACGAAAATGTCA
65 CCGCAACGA-CGAATCTAGTACCACGAAGA-CACA
* * * *
9629326 AA-AGAAAGGTTTTAAACCGTAACGGTGAACCTTATACCTCAAA
1 AAGGGAAAGG-TTTAAGCCGCAATGGTGAACCTTATACCTCAAA
9629369 CGTGAAAAGG
Statistics
Matches: 281, Mismatches: 51, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
96 1 0.00
97 84 0.30
98 194 0.69
99 2 0.01
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.18
Consensus pattern (97 bp):
AAGGGAAAGGTTTAAGCCGCAATGGTGAACCTTATACCTCAAAACATGAAGGGAAAGATTTAAGC
CGCAACGACGAATCTAGTACCACGAAGACACA
Found at i:9629268 original size:196 final size:195
Alignment explanation
Indices: 9628935--9629368 Score: 541
Period size: 196 Copynumber: 2.2 Consensus size: 195
9628925 ATGAAGCATG
* * ** *
9628935 AAGGGAAAGGATTAAGCCGCGATGGTGAACCTTATATCTCAAAAAATGAAGGGAAAGATTTAAGT
1 AAGGGAAAGGATTAAGCCGCAATGGTGAACCTTATACCTCAAAAAATGAAGAAAAAGATTTAAGC
* **
9629000 CGCAACGACAAATCTAGTACCACGAAGACACAAAGCGAAAGGTTTAAGTCGCAATGGGGAACCTT
66 CGCAACGACAAATCTAGTACCACGAAAACACAAAGCGAAAGGTTTAAGTCGCAATGACGAACCTT
* * * *
9629065 ATACCTCA-AAAGCATGAAGGGAAAGATTTAAGCCACAACGGCGAATCTAGTACCACGAAGAT-A
131 ATACCTCAGAAA--ATGAAGGGAAAGATTTAAACCACAACAGCGAATCCAGTACCACGAAAATGA
9629128 CA
194 CA
* ** *
9629130 AAGGGAAAGGCTTAAGCCGCAATGGTGAACCTTATACCTCAGAAGCATTAAGAAAAAGATTTAAG
1 AAGGGAAAGGATTAAGCCGCAATGGTGAACCTTATACCTCA-AAAAATGAAGAAAAAGATTTAAG
* * * *
9629195 CCGCAACGACGAATCTAGTACCATGAAAACATAAAGGGAAAGGTTTAAGTCGCAATGACGAACCT
65 CCGCAACGACAAATCTAGTACCACGAAAACACAAAGCGAAAGGTTTAAGTCGCAATGACGAACCT
* * * * *
9629260 TGTACCTCAGAAAATGAAGGGAAGGATTTAAACCGCAATAGCGAATCCAGTACCACGAAAATGTC
130 TATACCTCAGAAAATGAAGGGAAAGATTTAAACCACAACAGCGAATCCAGTACCACGAAAATGAC
9629325 A
195 A
* * * * *
9629326 AA-AGAAAGGTTTTAAACCGTAACGGTGAACCTTATACCTCAAA
1 AAGGGAAAGG-ATTAAGCCGCAATGGTGAACCTTATACCTCAAA
9629369 CGTGAAAAGG
Statistics
Matches: 205, Mismatches: 30, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
195 88 0.43
196 114 0.56
197 3 0.01
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.18
Consensus pattern (195 bp):
AAGGGAAAGGATTAAGCCGCAATGGTGAACCTTATACCTCAAAAAATGAAGAAAAAGATTTAAGC
CGCAACGACAAATCTAGTACCACGAAAACACAAAGCGAAAGGTTTAAGTCGCAATGACGAACCTT
ATACCTCAGAAAATGAAGGGAAAGATTTAAACCACAACAGCGAATCCAGTACCACGAAAATGACA
Found at i:9643387 original size:49 final size:49
Alignment explanation
Indices: 9643330--9643667 Score: 285
Period size: 49 Copynumber: 6.9 Consensus size: 49
9643320 TCAAAAAATG
* * * * *
9643330 AAGGGAAAGATTTAAGCCGCAACGACAAATCTAGTACCACGAGGACACA
1 AAGGGAAAGATTTAAGTCGCAATGGCGAATCTAGTACCACGAAGACACA
* * * * **
9643379 AAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTA-TACCTC-AAAAGCATG
1 AAGGGAAAGATTTAAGTCGCAATGGCGAATC-TAGTACCACGAAGA-CACA
* * * *
9643428 AAGGGAAAGATTTAAGCCACAACGGCGAATCTAGTACCACGAAGATACA
1 AAGGGAAAGATTTAAGTCGCAATGGCGAATCTAGTACCACGAAGACACA
* * * * **
9643477 AAGGGAAAGAGTTAAGTCGTAATGGCGAACCTTA-TACCTCAGAAG-CATT
1 AAGGGAAAGATTTAAGTCGCAATGGCGAATC-TAGTACCAC-GAAGACACA
9643526 AAGGGAAAGATTTAAGTCGCAATGGCGAATCTAGTACCACGAAGACACA
1 AAGGGAAAGATTTAAGTCGCAATGGCGAATCTAGTACCACGAAGACACA
* * * * * * * *
9643575 AAGGAAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTC-AAAAAATGA
1 AAGGGAAAGATTTAAGTCGCAATGGCGAATCTAGTACCACGAAGACA-CA
* * *
9643624 AA-GG-AAGAATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGA
1 AAGGGAAAG-ATTTAAGTCGCAATGGCGAATCTAGTACCACGAAGA
9643668 TGTCAAAGGA
Statistics
Matches: 224, Mismatches: 54, Indels: 22
0.75 0.18 0.07
Matches are distributed among these distances:
47 3 0.01
48 39 0.17
49 171 0.76
50 11 0.05
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.17
Consensus pattern (49 bp):
AAGGGAAAGATTTAAGTCGCAATGGCGAATCTAGTACCACGAAGACACA
Found at i:9643462 original size:98 final size:97
Alignment explanation
Indices: 9643285--9643711 Score: 554
Period size: 98 Copynumber: 4.4 Consensus size: 97
9643275 AAGCATGAAA
* * * *
9643285 GGAAAGGATTAAGCCGCGATGGCGAACCTTATATCTCAAAAAATGAAGGGAAAGATTTAAGCCGC
1 GGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTCAAAAAATGAAGGGAAAGATTTAAGCCGC
* * *
9643350 AACGACAAATCTAGTACCACGAGGACACAAAG
66 AACGGCGAATCTAGTACCACGAAGACACAAAG
* *
9643382 GGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTCAAAAGCATGAAGGGAAAGATTTAAGCCA
1 GGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTCAAAA-AATGAAGGGAAAGATTTAAGCCG
*
9643447 CAACGGCGAATCTAGTACCACGAAGATACAAAG
65 CAACGGCGAATCTAGTACCACGAAGACACAAAG
* ** * *
9643480 GGAAAGAG-TTAAGTCGTAATGGCGAACCTTATACCTCAGAAGCATTAAGGGAAAGATTTAAGTC
1 GGAAAG-GTTTAAGTCGCAATGGCGAACCTTATACCTCA-AAAAATGAAGGGAAAGATTTAAGCC
*
9643544 GCAATGGCGAATCTAGTACCACGAAGACACAAAG
64 GCAACGGCGAATCTAGTACCACGAAGACACAAAG
* * *
9643578 GAAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAAAAAATGAAAGG-AAGAATTTAAGCCG
1 GGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTCAAAAAATGAAGGGAAAG-ATTTAAGCCG
* **
9643642 CAACGGCGAATCCAGTACCACGAAGATGTCAAA-
65 CAACGGCGAATCTAGTACCACGAAGA-CACAAAG
* * *
9643675 GGAAAGGTTTTAAGCCGCAACGGTGAACCTTATACCT
1 GGAAAGG-TTTAAGTCGCAATGGCGAACCTTATACCT
9643712 TAGACGTGAA
Statistics
Matches: 289, Mismatches: 34, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
96 3 0.01
97 85 0.29
98 198 0.69
99 3 0.01
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.18
Consensus pattern (97 bp):
GGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTCAAAAAATGAAGGGAAAGATTTAAGCCGC
AACGGCGAATCTAGTACCACGAAGACACAAAG
Found at i:9659098 original size:23 final size:23
Alignment explanation
Indices: 9659068--9659145 Score: 111
Period size: 23 Copynumber: 3.4 Consensus size: 23
9659058 TGACGTGGCG
*
9659068 TCCAGTCAACAGCTTCTAGAAGA
1 TCCAGTCAGCAGCTTCTAGAAGA
*
9659091 TCCAGTCAGCAACTTCTAGAAGA
1 TCCAGTCAGCAGCTTCTAGAAGA
* *
9659114 TCCAGTCAGCAGCTTCCAGAAGG
1 TCCAGTCAGCAGCTTCTAGAAGA
*
9659137 TCTAGTCAG
1 TCCAGTCAG
9659146 TAAGCATGGA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.22
Consensus pattern (23 bp):
TCCAGTCAGCAGCTTCTAGAAGA
Found at i:9662427 original size:10 final size:10
Alignment explanation
Indices: 9662412--9662437 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
9662402 TAAATAAAGA
9662412 AGAGAATGAG
1 AGAGAATGAG
9662422 AGAGAATGAG
1 AGAGAATGAG
9662432 AGAGAA
1 AGAGAA
9662438 CGTATTTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.38, T:0.08
Consensus pattern (10 bp):
AGAGAATGAG
Found at i:9671615 original size:26 final size:26
Alignment explanation
Indices: 9671586--9671652 Score: 98
Period size: 26 Copynumber: 2.6 Consensus size: 26
9671576 CATGATGCTG
*
9671586 CTCACATGAGCTGTGAAGTGGGCCTA
1 CTCACATGAGCTATGAAGTGGGCCTA
*
9671612 CTCACATGAGCTATGAAGTGGGCCTG
1 CTCACATGAGCTATGAAGTGGGCCTA
* *
9671638 CTCACACGAGTTATG
1 CTCACATGAGCTATG
9671653 GGTCGGGATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (26 bp):
CTCACATGAGCTATGAAGTGGGCCTA
Found at i:9671693 original size:95 final size:95
Alignment explanation
Indices: 9671517--9671695 Score: 259
Period size: 95 Copynumber: 1.9 Consensus size: 95
9671507 TCATGTATTG
* * * *
9671517 CTCACACGAGCTGTGAAATGGGCCTGTTCACACGAGCTGTGGGTCGAGATGTTAAGCTACATGAT
1 CTCACACGAGCTATGAAATGGGCCTGCTCACACGAGCTATGGGTCGAGATGTTAAGCTACACGAT
**
9671582 GCTGCTCACATGAGCTGTGAAGTGGGCCTA
66 GCTGCTCACACAAGCTGTGAAGTGGGCCTA
* * * *
9671612 CTCACATGAGCTATGAAGTGGGCCTGCTCACACGAGTTATGGGTCGGGATGTTAAGCTACACGAT
1 CTCACACGAGCTATGAAATGGGCCTGCTCACACGAGCTATGGGTCGAGATGTTAAGCTACACGAT
*
9671677 GCTGCTCATACAAGCTGTG
66 GCTGCTCACACAAGCTGTG
9671696 GAGAATCCGC
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
95 73 1.00
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.25
Consensus pattern (95 bp):
CTCACACGAGCTATGAAATGGGCCTGCTCACACGAGCTATGGGTCGAGATGTTAAGCTACACGAT
GCTGCTCACACAAGCTGTGAAGTGGGCCTA
Found at i:9671900 original size:158 final size:158
Alignment explanation
Indices: 9671612--9671925 Score: 466
Period size: 158 Copynumber: 2.0 Consensus size: 158
9671602 AGTGGGCCTA
* * *
9671612 CTCACATGAGCTATGAAGTGGGCCTGCTCACACGAGTTATGGGTCGGGATGTTAAGCTACACGAT
1 CTCACACGAGCTATGAAGTGGGCCTGCTCACACAAGTTATGGGTCGAGATGTTAAGCTACACGAT
* * * * *
9671677 GCTGCTCATACAAGCTGTGGAGAATCCGCAACAAATGTCGGATCTCAACCATCGGTAGGACATCT
66 GCTACTCACACAAGCTGTGGAGAATCCACAACAAATGTCGGATCTCAACCATCAGTAAGACATCT
*
9671742 AAGACCAGCACCTATATAACATGTAATG
131 AAGACCAGCACCCATATAACATGTAATG
* * *
9671770 CTCACACGAGCTGTGAAGTGGGCCTGCTCACACAAGTTGTGGGTCGAGATGTTAAGCTACATGAT
1 CTCACACGAGCTATGAAGTGGGCCTGCTCACACAAGTTATGGGTCGAGATGTTAAGCTACACGAT
** * * *
9671835 GCTACTCACACGTGTTGTGGAGAATCTACAACAAATGTTGGATCTCAACCATCAGTAAGACATCT
66 GCTACTCACACAAGCTGTGGAGAATCCACAACAAATGTCGGATCTCAACCATCAGTAAGACATCT
*
9671900 AAGACTAGCACCCATATAACATGTAA
131 AAGACCAGCACCCATATAACATGTAA
9671926 ATCTCGAAAT
Statistics
Matches: 138, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
158 138 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.24
Consensus pattern (158 bp):
CTCACACGAGCTATGAAGTGGGCCTGCTCACACAAGTTATGGGTCGAGATGTTAAGCTACACGAT
GCTACTCACACAAGCTGTGGAGAATCCACAACAAATGTCGGATCTCAACCATCAGTAAGACATCT
AAGACCAGCACCCATATAACATGTAATG
Found at i:9675037 original size:18 final size:18
Alignment explanation
Indices: 9674976--9675037 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
9674966 TAAAAAAAAT
*
9674976 GTGAGGGTTAAAAGCATA
1 GTGAGTGTTAAAAGCATA
* * *
9674994 ATGAGTGAATAAAAGCATT
1 GTGAGTG-TTAAAAGCATA
** *
9675013 GAAAGTGTTAAAAGCATG
1 GTGAGTGTTAAAAGCATA
9675031 GTGAGTG
1 GTGAGTG
9675038 AAAGAGTGAT
Statistics
Matches: 32, Mismatches: 11, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
18 19 0.59
19 13 0.41
ACGTcount: A:0.40, C:0.05, G:0.31, T:0.24
Consensus pattern (18 bp):
GTGAGTGTTAAAAGCATA
Found at i:9676286 original size:22 final size:22
Alignment explanation
Indices: 9676255--9676302 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
9676245 GGATGCCGTG
* * *
9676255 ACATTGGCCTGAAAATGTCACA
1 ACATTAGCCTAAAAATATCACA
*
9676277 ACATTAGCCTAAAAATATCGCA
1 ACATTAGCCTAAAAATATCACA
9676299 ACAT
1 ACAT
9676303 CAAGCCTGGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (22 bp):
ACATTAGCCTAAAAATATCACA
Found at i:9687953 original size:39 final size:40
Alignment explanation
Indices: 9687899--9687978 Score: 126
Period size: 39 Copynumber: 2.0 Consensus size: 40
9687889 TATGCACTCA
9687899 ATGGACACCTTTTGAAGAGTCACAA-TCCTTTCAAATTGG
1 ATGGACACCTTTTGAAGAGTCACAACTCCTTTCAAATTGG
* * *
9687938 ATGGACACCTTTTGAAGGGTCACAACTCTTTTCATATTGG
1 ATGGACACCTTTTGAAGAGTCACAACTCCTTTCAAATTGG
9687978 A
1 A
9687979 CATACCTCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 24 0.65
40 13 0.35
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (40 bp):
ATGGACACCTTTTGAAGAGTCACAACTCCTTTCAAATTGG
Found at i:9692906 original size:39 final size:40
Alignment explanation
Indices: 9692852--9692931 Score: 126
Period size: 39 Copynumber: 2.0 Consensus size: 40
9692842 TATGCACTCA
*
9692852 ATGGACACCTTTTGAAGAGTCACAATCC-TTTCAAATTGG
1 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
* *
9692891 ATGGACACCTTTTGAAGGGTCACAACCCTTTTCATATTGG
1 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
9692931 A
1 A
9692932 CATACCTCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 26 0.70
40 11 0.30
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (40 bp):
ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
Found at i:9701551 original size:50 final size:51
Alignment explanation
Indices: 9701466--9701576 Score: 125
Period size: 50 Copynumber: 2.2 Consensus size: 51
9701456 TGCCTTGTTA
* * * * * * *
9701466 ATATGCGAATATGCTATATTAAGTGATACATGAACATGCTA-GGTTGAATG
1 ATATGCGAACATGCTATATTAAATGACACACGAACATACTATGATTAAATG
* *
9701516 ATATGCGAACATGCTATGTTAAATGACATACGAACATACTATGATTAAATG
1 ATATGCGAACATGCTATATTAAATGACACACGAACATACTATGATTAAATG
*
9701567 ATATACGAAC
1 ATATGCGAAC
9701577 CCTAAAATAT
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
50 34 0.68
51 16 0.32
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.30
Consensus pattern (51 bp):
ATATGCGAACATGCTATATTAAATGACACACGAACATACTATGATTAAATG
Found at i:9701572 original size:26 final size:25
Alignment explanation
Indices: 9701479--9701576 Score: 97
Period size: 25 Copynumber: 3.9 Consensus size: 25
9701469 TGCGAATATG
* * * * *
9701479 CTATATTAAGTGATACATGAACATG
1 CTATGTTAAATGATATACGAACATA
* * * *
9701504 CTAGGTTGAATGATATGCGAACATG
1 CTATGTTAAATGATATACGAACATA
*
9701529 CTATGTTAAATGACATACGAACATA
1 CTATGTTAAATGATATACGAACATA
9701554 CTATGATTAAATGATATACGAAC
1 CTATG-TTAAATGATATACGAAC
9701577 CCTAAAATAT
Statistics
Matches: 59, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
25 43 0.73
26 16 0.27
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (25 bp):
CTATGTTAAATGATATACGAACATA
Found at i:9701597 original size:21 final size:21
Alignment explanation
Indices: 9701573--9701612 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
9701563 AATGATATAC
9701573 GAACCCTAAAATATTGCATGT
1 GAACCCTAAAATATTGCATGT
* *
9701594 GAACCCTCACATATTGCAT
1 GAACCCTAAAATATTGCAT
9701613 ACAAGCCTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.28
Consensus pattern (21 bp):
GAACCCTAAAATATTGCATGT
Found at i:9701778 original size:16 final size:16
Alignment explanation
Indices: 9701759--9701940 Score: 211
Period size: 16 Copynumber: 11.4 Consensus size: 16
9701749 AATGTGCAAA
9701759 CCTACCCATGTGTGAG
1 CCTACCCATGTGTGAG
*
9701775 CCTACCCATGTGTGAA
1 CCTACCCATGTGTGAG
** *
9701791 CCTACTTATGTGCGAG
1 CCTACCCATGTGTGAG
9701807 CCTACCCATGTGTGAG
1 CCTACCCATGTGTGAG
** *
9701823 CCTACCCATGTACGAA
1 CCTACCCATGTGTGAG
* *
9701839 CCTACCTATGTGTGAA
1 CCTACCCATGTGTGAG
**
9701855 CCTACCCATGTACGAG
1 CCTACCCATGTGTGAG
** *
9701871 CCTACCCATGTGCAAA
1 CCTACCCATGTGTGAG
* *
9701887 CCTACTCATGTGTGTG
1 CCTACCCATGTGTGAG
*
9701903 CCTACCCATGTGTGAA
1 CCTACCCATGTGTGAG
9701919 CCTACCCATGTGTGAG
1 CCTACCCATGTGTGAG
9701935 CCTACC
1 CCTACC
9701941 TGAAGTGTGA
Statistics
Matches: 136, Mismatches: 30, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 136 1.00
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (16 bp):
CCTACCCATGTGTGAG
Found at i:9701786 original size:32 final size:32
Alignment explanation
Indices: 9701757--9701940 Score: 242
Period size: 32 Copynumber: 5.8 Consensus size: 32
9701747 CTAATGTGCA
*
9701757 AACCTACCCATGTGTGAGCCTACCCATGTGTG
1 AACCTACCCATGTGCGAGCCTACCCATGTGTG
**
9701789 AACCTACTTATGTGCGAGCCTACCCATGTGTG
1 AACCTACCCATGTGCGAGCCTACCCATGTGTG
* * * *
9701821 AGCCTACCCATGTACGAACCTACCTATGTGTG
1 AACCTACCCATGTGCGAGCCTACCCATGTGTG
* **
9701853 AACCTACCCATGTACGAGCCTACCCATGTGCA
1 AACCTACCCATGTGCGAGCCTACCCATGTGTG
* * *
9701885 AACCTACTCATGTGTGTGCCTACCCATGTGTG
1 AACCTACCCATGTGCGAGCCTACCCATGTGTG
*
9701917 AACCTACCCATGTGTGAGCCTACC
1 AACCTACCCATGTGCGAGCCTACC
9701941 TGAAGTGTGA
Statistics
Matches: 130, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 130 1.00
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (32 bp):
AACCTACCCATGTGCGAGCCTACCCATGTGTG
Found at i:9701811 original size:48 final size:48
Alignment explanation
Indices: 9701750--9701939 Score: 236
Period size: 48 Copynumber: 4.0 Consensus size: 48
9701740 CCTAAACCTA
* *
9701750 ATGTGCAAACCTACCCATGTGTGAGCCTACCCATGTGTGAACCTACTT
1 ATGTGCGAACCTACCCATGTGTGAGCCTACCCATGTGCGAACCTACTT
* * *
9701798 ATGTGCGAGCCTACCCATGTGTGAGCCTACCCATGTACGAACCTACCT
1 ATGTGCGAACCTACCCATGTGTGAGCCTACCCATGTGCGAACCTACTT
* ** * *
9701846 ATGTGTGAACCTACCCATGTACGAGCCTACCCATGTGCAAACCTACTC
1 ATGTGCGAACCTACCCATGTGTGAGCCTACCCATGTGCGAACCTACTT
* ** * * *
9701894 ATGTGTGTGCCTACCCATGTGTGAACCTACCCATGTGTGAGCCTAC
1 ATGTGCGAACCTACCCATGTGTGAGCCTACCCATGTGCGAACCTAC
9701940 CTGAAGTGTG
Statistics
Matches: 121, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 121 1.00
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (48 bp):
ATGTGCGAACCTACCCATGTGTGAGCCTACCCATGTGCGAACCTACTT
Found at i:9701950 original size:17 final size:16
Alignment explanation
Indices: 9701734--9701963 Score: 77
Period size: 16 Copynumber: 14.1 Consensus size: 16
9701724 CATTCTATTA
9701734 TGTGAACCTAAACCTAA-
1 TGTGAACCT--ACCTAAG
* *
9701751 TGTGCAAACCTACCCATG
1 TGTG--AACCTACCTAAG
* * *
9701769 TGTGAGCCTACCCATG
1 TGTGAACCTACCTAAG
* *
9701785 TGTGAACCTACTTATG
1 TGTGAACCTACCTAAG
* * * *
9701801 TGCGAGCCTACCCATG
1 TGTGAACCTACCTAAG
* * *
9701817 TGTGAGCCTACCCATG
1 TGTGAACCTACCTAAG
** *
9701833 TACGAACCTACCTATG
1 TGTGAACCTACCTAAG
* *
9701849 TGTGAACCTACCCATG
1 TGTGAACCTACCTAAG
** * * *
9701865 TACGAGCCTACCCATG
1 TGTGAACCTACCTAAG
** *
9701881 TGCAAACCTA-CTCATG
1 TGTGAACCTACCT-AAG
** * *
9701897 TGTGTGCCTACCCATG
1 TGTGAACCTACCTAAG
* *
9701913 TGTGAACCTACCCATG
1 TGTGAACCTACCTAAG
*
9701929 TGTGAGCCTACCTGAAG
1 TGTGAACCTACCT-AAG
*
9701946 TGTGAACTTACCTAAG
1 TGTGAACCTACCTAAG
9701962 TG
1 TG
9701964 CAAACTCAAC
Statistics
Matches: 170, Mismatches: 37, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
15 1 0.01
16 138 0.81
17 22 0.13
18 4 0.02
19 5 0.03
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (16 bp):
TGTGAACCTACCTAAG
Found at i:9703344 original size:21 final size:22
Alignment explanation
Indices: 9703320--9703366 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
9703310 CGATCTAAGG
9703320 AAAAATAAAAG-AAACAAAATT
1 AAAAATAAAAGTAAACAAAATT
* *
9703341 AAAAATAAAAGTAAATAGAATT
1 AAAAATAAAAGTAAACAAAATT
9703363 AAAA
1 AAAA
9703367 GAAATAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.17
Consensus pattern (22 bp):
AAAAATAAAAGTAAACAAAATT
Found at i:9703373 original size:15 final size:16
Alignment explanation
Indices: 9703346--9703375 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
9703336 AAATTAAAAA
9703346 TAAAAGTAAATAGAAT
1 TAAAAGTAAATAGAAT
9703362 TAAAAG-AAATAGAA
1 TAAAAGTAAATAGAA
9703376 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (16 bp):
TAAAAGTAAATAGAAT
Found at i:9705173 original size:30 final size:30
Alignment explanation
Indices: 9705139--9705505 Score: 107
Period size: 30 Copynumber: 12.5 Consensus size: 30
9705129 TATGGTGAAG
*
9705139 TCGGGGTTAAAA-GATAGAATTTTT-GAGAAT
1 TCGGGGTTAAAATGAT--AATTTTTGGAGAAA
* *
9705169 TCGGGGGTAAAATGATAATTTTTGGTGAAA
1 TCGGGGTTAAAATGATAATTTTTGGAGAAA
* * *
9705199 CCGGGGTTAAAAATGGT-A-TTTT--AAAAA
1 TCGGGGTT-AAAATGATAATTTTTGGAGAAA
* * *
9705226 GTTTAGGGG-TAAAATGGTAATTTTT-AATGAAA
1 ---TCGGGGTTAAAATGATAATTTTTGGA-GAAA
* ** **
9705258 TCGAGGTTAAAAATG-GGA-TTTTGGA-AGT
1 TCGGGGTT-AAAATGATAATTTTTGGAGAAA
* *
9705286 TCAGGGG-TAAAATGGTAATTTTTGGTGAAA
1 TC-GGGGTTAAAATGATAATTTTTGGAGAAA
* *
9705316 -CTGGGGTTAAAAATG-GAA-TTTTGGA-AAGT
1 TC-GGGGTT-AAAATGATAATTTTTGGAGAA-A
* * *
9705345 TCGGGGGTAAAATGGTAATTTTTGGTGAAA
1 TCGGGGTTAAAATGATAATTTTTGGAGAAA
* *
9705375 -CTGGGGTTAAAATG-GAA-TTTTGGA-AAGT
1 TC-GGGGTTAAAATGATAATTTTTGGAGAA-A
* * * * *
9705403 TTGGGGGTAAAATGGTAATTTTAGGTGAAA
1 TCGGGGTTAAAATGATAATTTTTGGAGAAA
* * *
9705433 TTGGGGTTAAAAATG-GAA-TTTTGGA-AAGT
1 TCGGGGTT-AAAATGATAATTTTTGGAGAA-A
* *
9705462 TCGAGGG-TAAAATGGTAATTTTTGGTGAAA
1 TCG-GGGTTAAAATGATAATTTTTGGAGAAA
*
9705492 TCGAGGTTAAAATG
1 TCGGGGTTAAAATG
9705506 GAATTTTAGA
Statistics
Matches: 248, Mismatches: 52, Indels: 74
0.66 0.14 0.20
Matches are distributed among these distances:
27 11 0.04
28 46 0.19
29 65 0.26
30 88 0.35
31 35 0.14
32 3 0.01
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (30 bp):
TCGGGGTTAAAATGATAATTTTTGGAGAAA
Found at i:9705235 original size:59 final size:59
Alignment explanation
Indices: 9705118--9705542 Score: 511
Period size: 59 Copynumber: 7.3 Consensus size: 59
9705108 ACCTGAGGGC
* ** * * **
9705118 AAAATGGTAA-TTATGGTGAAGTCGGGGTTAAAAGATAGAATTTTTGAGAA-TTCGGGGGT
1 AAAATGGTAATTTTTGGTGAAACCGGGGTTAAAA-ATGGAATTTTGGA-AAGTTTAGGGGT
* * **
9705177 AAAATGATAATTTTTGGTGAAACCGGGGTTAAAAATGGTATTTTAAAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
** * * * *
9705236 AAAATGGTAATTTTTAATGAAATCGAGGTTAAAAATGGGATTTTGG-AAGTTCAGGGGT
1 AAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* **
9705294 AAAATGGTAATTTTTGGTGAAACTGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* *
9705353 AAAATGGTAATTTTTGGTGAAACTGGGGTT-AAAATGGAATTTTGGAAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* ** *
9705411 AAAATGGTAATTTTAGGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAG-TTCGAGGGT
1 AAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTAG-GGGT
* * * *
9705470 AAAATGGTAATTTTTGGTGAAATCGAGGTT-AAAATGGAATTTTAGAAGGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
9705528 AAAATGGTAATTTTT
1 AAAATGGTAATTTTT
9705543 AGAAGTTTCA
Statistics
Matches: 324, Mismatches: 36, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
58 147 0.45
59 157 0.48
60 20 0.06
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
Found at i:9705305 original size:117 final size:116
Alignment explanation
Indices: 9705118--9705542 Score: 534
Period size: 117 Copynumber: 3.6 Consensus size: 116
9705108 ACCTGAGGGC
* * * * *
9705118 AAAATGGTAA-TTATGGTGAAGTCGGGGTTAAAAGATAGAATTTTTGAGAA-TTCGGGGGTAAAA
1 AAAATGGTAATTTTTGGTGAAATCGAGGTT-AAA-ATGGAA-TTTTG-GAAGTTCAGGGGTAAAA
* * * **
9705181 TGATAATTTTTGGTGAAACCGGGGTTAAAAATGGTATTTTAAAAAGTTTAGGGGT
62 TGGTAATTTTTGGTGAAACTGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
** *
9705236 AAAATGGTAATTTTTAATGAAATCGAGGTTAAAAATGGGATTTTGGAAGTTCAGGGGTAAAATGG
1 AAAATGGTAATTTTTGGTGAAATCGAGGTT-AAAATGGAATTTTGGAAGTTCAGGGGTAAAATGG
**
9705301 TAATTTTTGGTGAAACTGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
65 TAATTTTTGGTGAAACTGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* **
9705353 AAAATGGTAATTTTTGGTGAAA-CTGGGGTTAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATG
1 AAAATGGTAATTTTTGGTGAAATC-GAGGTTAAAATGGAATTTTGG-AAGTTCAGGGGTAAAATG
* * *
9705417 GTAATTTTAGGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAG-TTCGAGGGT
64 GTAATTTTTGGTGAAACTGGGGTTAAAAATGGAATTTTGGAAAGTTTAG-GGGT
* *
9705470 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAATGGAATTTTAGAAGGTTTAGGGGTAAAATGG
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAATGGAATTTTGGAA-GTTCAGGGGTAAAATGG
9705535 TAATTTTT
65 TAATTTTT
9705543 AGAAGTTTCA
Statistics
Matches: 271, Mismatches: 29, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
116 22 0.08
117 216 0.80
118 15 0.06
119 18 0.07
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (116 bp):
AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAATGGAATTTTGGAAGTTCAGGGGTAAAATGGT
AATTTTTGGTGAAACTGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
Found at i:9705544 original size:30 final size:28
Alignment explanation
Indices: 9705499--9705555 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 28
9705489 AAATCGAGGT
9705499 TAAAATGGAATTTTAGAAGGTTT-AGGGG
1 TAAAATGGAATTTTAGAA-GTTTCAGGGG
9705527 TAAAATGGTAATTTTTAGAAGTTTCAGGG
1 TAAAATGG-AA-TTTTAGAAGTTTCAGGG
9705556 TCAGAATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 8 0.31
29 6 0.23
30 12 0.46
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.35
Consensus pattern (28 bp):
TAAAATGGAATTTTAGAAGTTTCAGGGG
Found at i:9705556 original size:29 final size:29
Alignment explanation
Indices: 9705465--9705569 Score: 78
Period size: 30 Copynumber: 3.6 Consensus size: 29
9705455 GGAAAGTTCG
* *
9705465 AGGGTAAAATGGTAATTTTTGGTGAA--ATC
1 AGGGTAAAATGGTAATTTTT--AGAAGTTTC
*
9705494 GAGGTTAAAATGG-AA-TTTTAGAAGGTTT-
1 -AGGGTAAAATGGTAATTTTTAGAA-GTTTC
9705522 AGGGGTAAAATGGTAATTTTTAGAAGTTTC
1 A-GGGTAAAATGGTAATTTTTAGAAGTTTC
*
9705552 AGGGTCAGAAT-GTAATTT
1 AGGGT-AAAATGGTAATTT
9705570 CTTGAAATTT
Statistics
Matches: 62, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
26 3 0.05
27 1 0.02
28 14 0.23
29 20 0.32
30 24 0.39
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (29 bp):
AGGGTAAAATGGTAATTTTTAGAAGTTTC
Found at i:9707335 original size:6 final size:6
Alignment explanation
Indices: 9707326--9707398 Score: 50
Period size: 6 Copynumber: 12.8 Consensus size: 6
9707316 GACTTTTCTT
*
9707326 TTTAAA TTTATAA --TAATA TT-AAA TTTAAA -TTAAA TTCAAA TTTAAA
1 TTTAAA TTTA-AA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
9707372 -TTAAA ATTGAA TTTAAA -ATAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
9707399 GATAAAATAA
Statistics
Matches: 52, Mismatches: 7, Indels: 16
0.69 0.09 0.21
Matches are distributed among these distances:
4 1 0.02
5 20 0.38
6 29 0.56
7 2 0.04
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:9707349 original size:17 final size:16
Alignment explanation
Indices: 9707327--9707395 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 16
9707317 ACTTTTCTTT
9707327 TTAAATTTATAA-TAATA
1 TTAAATTTA-AATTAA-A
9707344 TTAAATTTAAATTAAA
1 TTAAATTTAAATTAAA
9707360 TTCAAATTTAAATTAAAA
1 TT-AAATTTAAATT-AAA
* *
9707378 TTGAATTTAAAATAAA
1 TTAAATTTAAATTAAA
9707394 TT
1 TT
9707396 TAAGATAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
16 10 0.21
17 32 0.68
18 5 0.11
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (16 bp):
TTAAATTTAAATTAAA
Found at i:9707359 original size:11 final size:11
Alignment explanation
Indices: 9707343--9707398 Score: 67
Period size: 11 Copynumber: 5.0 Consensus size: 11
9707333 TTATAATAAT
9707343 ATTAAATTTAA
1 ATTAAATTTAA
*
9707354 ATTAAATTCAA
1 ATTAAATTTAA
*
9707365 ATTTAAATTAAA
1 A-TTAAATTTAA
*
9707377 ATTGAATTTAA
1 ATTAAATTTAA
*
9707388 AATAAATTTAA
1 ATTAAATTTAA
9707399 GATAAAATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
11 28 0.74
12 10 0.26
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:9707385 original size:34 final size:34
Alignment explanation
Indices: 9707329--9707395 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
9707319 TTTTCTTTTT
* *
9707329 AAATTTATAATAATATTAAATTTAAATTAAATTC
1 AAATTTATAATAAAATTAAATTTAAAATAAATTC
*
9707363 AAATTTA-AATTAAAATTGAATTTAAAATAAATT
1 AAATTTATAA-TAAAATTAAATTTAAAATAAATT
9707396 TAAGATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 2 0.07
34 27 0.93
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (34 bp):
AAATTTATAATAAAATTAAATTTAAAATAAATTC
Found at i:9707749 original size:19 final size:19
Alignment explanation
Indices: 9707725--9707767 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
9707715 AAACATAAAT
9707725 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
9707744 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
9707763 TAAAT
1 TAAAT
9707768 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:9708444 original size:20 final size:20
Alignment explanation
Indices: 9708419--9708458 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
9708409 AGTCTTCAAG
*
9708419 GTATCGATAGAACTGTAGTT
1 GTATCGATAGAACTGAAGTT
*
9708439 GTATCGGTAGAACTGAAGTT
1 GTATCGATAGAACTGAAGTT
9708459 CTACCGGTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.28, T:0.33
Consensus pattern (20 bp):
GTATCGATAGAACTGAAGTT
Found at i:9708466 original size:20 final size:20
Alignment explanation
Indices: 9708426--9708470 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
9708416 AAGGTATCGA
* * *
9708426 TAGAACTGTAGTTGTATCGG
1 TAGAACTGAAGTTCTACCGG
9708446 TAGAACTGAAGTTCTACCGG
1 TAGAACTGAAGTTCTACCGG
9708466 TAGAA
1 TAGAA
9708471 GTCTCACTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (20 bp):
TAGAACTGAAGTTCTACCGG
Found at i:9708691 original size:17 final size:17
Alignment explanation
Indices: 9708671--9708731 Score: 77
Period size: 17 Copynumber: 3.6 Consensus size: 17
9708661 ATGATGTGAT
*
9708671 ATGAACTGTTATTTTGC
1 ATGAACTGTTATTTCGC
* *
9708688 ATGAACTGTTATTTGGA
1 ATGAACTGTTATTTCGC
* *
9708705 ATGAACTATTATTTCAC
1 ATGAACTGTTATTTCGC
9708722 ATGAACTGTT
1 ATGAACTGTT
9708732 GTTTATTGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (17 bp):
ATGAACTGTTATTTCGC
Found at i:9708743 original size:17 final size:17
Alignment explanation
Indices: 9708733--9708774 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
9708723 TGAACTGTTG
9708733 TTTATTGTGAACTGATAT
1 TTTA-TGTGAACTGATAT
*
9708751 TTTATGTGAACTGCCTAT
1 TTTATGTGAACTG-ATAT
9708769 TTTATG
1 TTTATG
9708775 CGAATTACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.24, C:0.10, G:0.17, T:0.50
Consensus pattern (17 bp):
TTTATGTGAACTGATAT
Found at i:9708769 original size:18 final size:18
Alignment explanation
Indices: 9708748--9708817 Score: 86
Period size: 18 Copynumber: 3.9 Consensus size: 18
9708738 TGTGAACTGA
* *
9708748 TATTTTATGTGAACTGCC
1 TATTTTATGTGAACTACT
* *
9708766 TATTTTATGCGAATTACT
1 TATTTTATGTGAACTACT
*
9708784 TATTCTATGTGAACTACT
1 TATTTTATGTGAACTACT
*
9708802 TATTTTATGAGAACTA
1 TATTTTATGTGAACTA
9708818 TAAGTTGTGT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.46
Consensus pattern (18 bp):
TATTTTATGTGAACTACT
Found at i:9709507 original size:59 final size:61
Alignment explanation
Indices: 9709436--9709552 Score: 166
Period size: 62 Copynumber: 1.9 Consensus size: 61
9709426 ATCATTTTAA
* * * * *
9709436 TATTAAATTAATATAATATTTA-T-CAGGATAAATATTATATTAAATTTAATATTAAATCT
1 TATTAAAATAATAAAATATTTACTACAAGATAAACATTAAATTAAATTTAATATTAAATCT
9709495 TATTAAAATAATAAAATATTTATCTACAAGATAAACATTAAATTAAATTTAATATTAA
1 TATTAAAATAATAAAATATTTA-CTACAAGATAAACATTAAATTAAATTTAATATTAA
9709553 GATAATCACT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 20 0.40
61 1 0.02
62 29 0.58
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (61 bp):
TATTAAAATAATAAAATATTTACTACAAGATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:9709578 original size:20 final size:18
Alignment explanation
Indices: 9709531--9709579 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
9709521 CAAGATAAAC
9709531 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
9709548 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
9709568 ATTAAATTAATA
1 ATTAAATTAATA
9709580 AAATACGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:9714213 original size:20 final size:18
Alignment explanation
Indices: 9714183--9714246 Score: 74
Period size: 20 Copynumber: 3.4 Consensus size: 18
9714173 AGGATGTGAC
9714183 ATAAAAATTATTAAGAATT
1 ATAAAAATTATTAA-AATT
*
9714202 ATAAATAATTATAAATAATT
1 ATAAA-AATTATTAA-AATT
* *
9714222 ATTAAAATTATTGAAATT
1 ATAAAAATTATTAAAATT
9714240 ATAAAAA
1 ATAAAAA
9714247 CTATATACAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
18 10 0.26
19 12 0.32
20 16 0.42
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
ATAAAAATTATTAAAATT
Found at i:9714232 original size:9 final size:9
Alignment explanation
Indices: 9714186--9714245 Score: 59
Period size: 10 Copynumber: 6.4 Consensus size: 9
9714176 ATGTGACATA
9714186 AAAATTATT
1 AAAATTATT
*
9714195 AAGAATTATA
1 AA-AATTATT
*
9714205 AATAATTATA
1 AA-AATTATT
9714215 AATAATTATT
1 AA-AATTATT
9714225 AAAATTATT
1 AAAATTATT
*
9714234 GAAATTA-T
1 AAAATTATT
9714242 AAAA
1 AAAA
9714246 ACTATATACA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
8 4 0.09
9 15 0.33
10 26 0.58
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (9 bp):
AAAATTATT
Found at i:9714455 original size:10 final size:9
Alignment explanation
Indices: 9714427--9714512 Score: 57
Period size: 10 Copynumber: 8.6 Consensus size: 9
9714417 TACTATTAAA
9714427 TTTTA-AAT
1 TTTTATAAT
*
9714435 TTTTAAAAAT
1 TTTT-ATAAT
9714445 TATTTATAAT
1 T-TTTATAAT
9714455 TTATTATAAT
1 TT-TTATAAT
*
9714465 TGTTAAATAAT
1 T-TT-TATAAT
9714476 TTTCTATAAT
1 TTT-TATAAT
9714486 TTTATATAAT
1 TTT-TATAAT
9714496 TATTTAATAAT
1 T-TTT-ATAAT
9714507 TATTTA
1 T-TTTA
9714513 AGAAACTACT
Statistics
Matches: 65, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
8 4 0.06
9 2 0.03
10 37 0.57
11 22 0.34
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (9 bp):
TTTTATAAT
Found at i:9714487 original size:31 final size:31
Alignment explanation
Indices: 9714432--9714512 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 31
9714422 TTAAATTTTA
*
9714432 AATTTTTAAA-AATTATTTATAA-TTTATTAT
1 AATTATTAAATAATTATTTATAATTTTA-TAT
*
9714462 AATTGTTAAATAATT-TTCTATAATTTTATAT
1 AATTATTAAATAATTATT-TATAATTTTATAT
*
9714493 AATTATTTAATAATTATTTA
1 AATTATTAAATAATTATTTA
9714513 AGAAACTACT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
30 11 0.25
31 27 0.61
32 6 0.14
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (31 bp):
AATTATTAAATAATTATTTATAATTTTATAT
Found at i:9714505 original size:21 final size:20
Alignment explanation
Indices: 9714432--9714510 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 20
9714422 TTAAATTTTA
*
9714432 AATTTTTAAAAATTATT-TAT
1 AATTTTT-ATAATTATTATAT
* *
9714452 AATTTATTATAATTGTTAAAT
1 AATTT-TTATAATTATTATAT
9714473 AATTTTCTATAATT-TTATAT
1 AATTTT-TATAATTATTATAT
9714493 AATTATTTAATAATTATT
1 AATT-TTT-ATAATTATT
9714511 TAAGAAACTA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 23 0.47
21 24 0.49
22 2 0.04
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (20 bp):
AATTTTTATAATTATTATAT
Found at i:9714568 original size:31 final size:32
Alignment explanation
Indices: 9714530--9714595 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
9714520 ACTCCAAAAC
9714530 GAATTTGGCA-AA-TGGTTATCCAAGCTCATTT
1 GAATTTGG-ATAATTGGTTATCCAAGCTCATTT
* * *
9714561 GAATTTGGATAATTGGTTGTCCAATCTCTTTT
1 GAATTTGGATAATTGGTTATCCAAGCTCATTT
9714593 GAA
1 GAA
9714596 CGTAAACAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 1 0.03
31 10 0.33
32 19 0.63
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (32 bp):
GAATTTGGATAATTGGTTATCCAAGCTCATTT
Found at i:9717004 original size:20 final size:20
Alignment explanation
Indices: 9716963--9717006 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
9716953 ATTTTTATGA
9716963 TTAACTTAATTAATCACCTAT
1 TTAACTTAATTAAT-ACCTAT
9716984 TTAACCTTAATTAAT-CCTAT
1 TTAA-CTTAATTAATACCTAT
9717004 TTA
1 TTA
9717007 TTATCAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 4 0.18
22 10 0.45
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAACTTAATTAATACCTAT
Found at i:9718384 original size:29 final size:29
Alignment explanation
Indices: 9718347--9718405 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
9718337 TGTTGGCTCC
9718347 AACCTACCTAGTAGCCCATCATGATCCAT
1 AACCTACCTAGTAGCCCATCATGATCCAT
9718376 AACCTACCTAGTAGCCCATCATGATCCAT
1 AACCTACCTAGTAGCCCATCATGATCCAT
9718405 A
1 A
9718406 CACACCCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.34, G:0.10, T:0.24
Consensus pattern (29 bp):
AACCTACCTAGTAGCCCATCATGATCCAT
Found at i:9730085 original size:6 final size:6
Alignment explanation
Indices: 9730074--9730102 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
9730064 AGATGATCAG
9730074 ATACAA ATACAA ATACAA ATACAA ATACA
1 ATACAA ATACAA ATACAA ATACAA ATACA
9730103 GATGCAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
ATACAA
Found at i:9730757 original size:29 final size:28
Alignment explanation
Indices: 9730700--9730771 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
9730690 TATATAAATA
* *
9730700 ATACAGATACAGATATAGTCATGTTAGAG
1 ATACAGTTACAGATATAGT-ATGTCAGAG
9730729 ATACAGTTACAGATATAGT-TGAATCAGAG
1 ATACAGTTACAGATATAGTATG--TCAGAG
*
9730758 ATATAGTTACAGAT
1 ATACAGTTACAGAT
9730772 GCAGTGCAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 2 0.05
29 36 0.95
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (28 bp):
ATACAGTTACAGATATAGTATGTCAGAG
Found at i:9731468 original size:53 final size:53
Alignment explanation
Indices: 9731387--9731501 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 53
9731377 TGTACCCACA
* * * * *
9731387 CCCATGTGTCAGCCCATGTTCCCTAAAATGGTATACACACACCTTGACACACG
1 CCCATGTGTCAACCCATATGCCCTAAAATAGTATACACACACCCTGACACACG
9731440 CCCATGTGTCAACCCATATG-CCTCAAAATAGTATACACACACCCTGACACACG
1 CCCATGTGTCAACCCATATGCCCT-AAAATAGTATACACACACCCTGACACACG
*
9731493 CCTATGTGT
1 CCCATGTGT
9731502 TAGCCCGTGT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
52 3 0.05
53 52 0.95
ACGTcount: A:0.30, C:0.34, G:0.14, T:0.23
Consensus pattern (53 bp):
CCCATGTGTCAACCCATATGCCCTAAAATAGTATACACACACCCTGACACACG
Found at i:9734089 original size:19 final size:19
Alignment explanation
Indices: 9734014--9734092 Score: 68
Period size: 19 Copynumber: 4.2 Consensus size: 19
9734004 AAGGAATAGC
* **
9734014 ATACTGGCTCGTTTGAGCA
1 ATACTGGCTCATAAGAGCA
* **
9734033 ATACTGGTTCATGTGAGCA
1 ATACTGGCTCATAAGAGCA
* * *
9734052 ATACTAGCTTATAAAAGCA
1 ATACTGGCTCATAAGAGCA
*
9734071 ATACTGGCTCGTAAGAGCA
1 ATACTGGCTCATAAGAGCA
9734090 ATA
1 ATA
9734093 TACAGTACTG
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.28
Consensus pattern (19 bp):
ATACTGGCTCATAAGAGCA
Found at i:9740950 original size:18 final size:18
Alignment explanation
Indices: 9740927--9740985 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
9740917 CAGAAGGAAT
* *
9740927 AGCATACTAGCGCGTTTG
1 AGCATACTGGCTCGTTTG
*
9740945 AGCATACTGGCTCATTTG
1 AGCATACTGGCTCGTTTG
*
9740963 AGCAATACTGGCTCGTGTG
1 AGC-ATACTGGCTCGTTTG
9740982 AGCA
1 AGCA
9740986 ATATTGACTC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 19 0.54
19 16 0.46
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (18 bp):
AGCATACTGGCTCGTTTG
Found at i:9740972 original size:19 final size:19
Alignment explanation
Indices: 9740941--9740988 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
9740931 TACTAGCGCG
9740941 TTTGAGC-ATACTGGCTCA
1 TTTGAGCAATACTGGCTCA
*
9740959 TTTGAGCAATACTGGCTCG
1 TTTGAGCAATACTGGCTCA
*
9740978 TGTGAGCAATA
1 TTTGAGCAATA
9740989 TTGACTCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 7 0.26
19 20 0.74
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (19 bp):
TTTGAGCAATACTGGCTCA
Found at i:9745719 original size:3 final size:3
Alignment explanation
Indices: 9745711--9745751 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
9745701 AGCTTTACCT
9745711 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
9745752 TACTTCAGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:9746489 original size:155 final size:155
Alignment explanation
Indices: 9746198--9746653 Score: 716
Period size: 155 Copynumber: 2.9 Consensus size: 155
9746188 GCGGATTCTC
9746198 CACAGCTCGTGTGAG-ATTTACATGATACGGGTGCTGGTCTTGGATGTCCTACCAATGGCTGAGG
1 CACAGCTCGTGTGAGCA-TTACATGATACGGGTGCTGGTCTTGGATGTCCTACCAATGGCTGAGG
* * * * *
9746262 CCCTGCATTTGTTGCGGATTTTCCACAGCTCATGTGAGCAGCATCGTGTAGCTAACATCTCGACT
65 TCCTGCATTTGTTGCGGATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCTAACATCCCGACC
* * ** *
9746327 CATAGCTCATGTGAGGTAGCTCATTT
130 CACAGCTCGTGTGAGCAAGCCCATTT
*
9746353 CACAGCTCGTGTGAGCATTACATGATACGGGTGCTGGTCTTGGATGTCCTATCAATGGCTGAGGT
1 CACAGCTCGTGTGAGCATTACATGATACGGGTGCTGGTCTTGGATGTCCTACCAATGGCTGAGGT
* *
9746418 CCTGCATTTGTTGCGGATTCTCCACAGCTCGTGTGATCTGCATCGTGTAGCTAACATCCCGACCC
66 CCTGCATTTGTTGCGGATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCTAACATCCCGACCC
9746483 ACAGCTCGTGTGAGCAAGCCCATTT
131 ACAGCTCGTGTGAGCAAGCCCATTT
* * *
9746508 CACAGCTCGTGTGAGCATTACATGATACGGGTACTGGTCTTGGATGTCCTACCGATAGCTGAGGT
1 CACAGCTCGTGTGAGCATTACATGATACGGGTGCTGGTCTTGGATGTCCTACCAATGGCTGAGGT
* * * *
9746573 CTTGCATTCGTTGTGGATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAACTAACATCCCGACCC
66 CCTGCATTTGTTGCGGATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCTAACATCCCGACCC
9746638 ACAGCTCGTGTGAGCA
131 ACAGCTCGTGTGAGCA
9746654 TACATGATTA
Statistics
Matches: 277, Mismatches: 23, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
155 276 1.00
156 1 0.00
ACGTcount: A:0.20, C:0.25, G:0.26, T:0.29
Consensus pattern (155 bp):
CACAGCTCGTGTGAGCATTACATGATACGGGTGCTGGTCTTGGATGTCCTACCAATGGCTGAGGT
CCTGCATTTGTTGCGGATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCTAACATCCCGACCC
ACAGCTCGTGTGAGCAAGCCCATTT
Found at i:9748505 original size:22 final size:22
Alignment explanation
Indices: 9748480--9748535 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
9748470 AAAATATAAA
*
9748480 AATAAAATATTTAAAATATTTT
1 AATAAAATATATAAAATATTTT
*
9748502 AATATAAA-ATATACAATATTTT
1 AATA-AAATATATAAAATATTTT
*
9748524 ATTCAAAATATA
1 AAT-AAAATATA
9748536 ATTTAATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 21 0.75
23 7 0.25
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (22 bp):
AATAAAATATATAAAATATTTT
Done.