Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007849.1 Hibiscus syriacus cultivar Beakdansim tig00110206_pilon, whole genome shotgun sequence
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: 3141433
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 12
Found at i:859220 original size:6 final size:6
Alignment explanation
Indices: 859209--859331 Score: 246
Period size: 6 Copynumber: 20.5 Consensus size: 6
859199 TCTCGTCTCG
859209 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
859257 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
859305 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
859332 AATACGTGTC
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 117 1.00
ACGTcount: A:0.00, C:0.16, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:859433 original size:20 final size:20
Alignment explanation
Indices: 859410--859560 Score: 167
Period size: 20 Copynumber: 7.4 Consensus size: 20
859400 CTTTTTAACG
* *
859410 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTCAATCGCA
*
859430 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTCAATCGCA
* *
859450 TTGCGATTTTCTTCTAAATCGCG
1 TTGCGA--TTC-TCTCAATCGCA
* *
859473 TTGCGACTCTCTCAATCGCG
1 TTGCGATTCTCTCAATCGCA
*
859493 TTGCGACTCTCTCAATCGCA
1 TTGCGATTCTCTCAATCGCA
**
859513 TTGCGATTCAATCAATCGCA
1 TTGCGATTCTCTCAATCGCA
**
859533 TTGCGATTCAATCAATCGCA
1 TTGCGATTCTCTCAATCGCA
859553 TTGCGATT
1 TTGCGATT
859561 TTCTTCTAAA
Statistics
Matches: 116, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
20 97 0.84
21 2 0.02
22 3 0.03
23 14 0.12
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.34
Consensus pattern (20 bp):
TTGCGATTCTCTCAATCGCA
Found at i:859573 original size:83 final size:81
Alignment explanation
Indices: 859408--859581 Score: 190
Period size: 83 Copynumber: 2.1 Consensus size: 81
859398 TTCTTTTTAA
* ** * * *
859408 CGTTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCG
1 CGTTGCGACTCTATAAATCGCATTGCGATTCAATCAATCGCATTGCGA-TTTCATC-AAATCGCA
*
859473 TTGCGACTCTCTCAATCG
64 TTGCGACTCTCTAAATCG
* *
859491 CGTTGCGACTCTCTCAATCGCATTGCGATTCAATCAATCGCATTGCGA-TTCAATC-AATCGCAT
1 CGTTGCGACTCTATAAATCGCATTGCGATTCAATCAATCGCATTGCGATTTC-ATCAAATCGCAT
*
859554 TGCGATTTTCTTCTAAATCG
65 TGCGA--CTC-TCTAAATCG
859574 CGTTGCGA
1 CGTTGCGA
859582 ACTTGGAAGC
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
80 12 0.16
81 3 0.04
82 4 0.05
83 58 0.75
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (81 bp):
CGTTGCGACTCTATAAATCGCATTGCGATTCAATCAATCGCATTGCGATTTCATCAAATCGCATT
GCGACTCTCTAAATCG
Found at i:859658 original size:20 final size:20
Alignment explanation
Indices: 859408--859685 Score: 112
Period size: 20 Copynumber: 13.6 Consensus size: 20
859398 TTCTTTTTAA
* *
859408 CGTTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
859428 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
859448 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
859471 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
859491 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* *** *
859511 CATTGCGATTCAATCAATCG
1 CGTTGCGATTTTCTAAATCG
* *** *
859531 CATTGCGATTCAATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
859551 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
859574 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
859595 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
859613 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
859635 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
859655 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
859674 CGTTGCGATTTT
1 CGTTGCGATTTT
859686 ATTGGTCATT
Statistics
Matches: 207, Mismatches: 40, Indels: 23
0.77 0.15 0.09
Matches are distributed among these distances:
18 2 0.01
19 17 0.08
20 141 0.68
21 14 0.07
22 6 0.03
23 27 0.13
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:859675 original size:19 final size:20
Alignment explanation
Indices: 859635--859685 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
859625 TTCTTTTTAA
*
859635 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
859655 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
859674 CGTTGCGATTTT
1 CGTTGCGATTTT
859686 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:867333 original size:11 final size:11
Alignment explanation
Indices: 867319--867356 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
867309 CTCCTAAAAC
867319 TAAATAATATA
1 TAAATAATATA
867330 TAAATAATATA
1 TAAATAATATA
867341 T--ATAATATA
1 TAAATAATATA
867350 TTAAATA
1 -TAAATA
867357 TTTAATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.33
10 1 0.04
11 12 0.50
12 3 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TAAATAATATA
Found at i:877126 original size:18 final size:17
Alignment explanation
Indices: 877105--877138 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
877095 ATTTTCAAAA
*
877105 TAGTATCGATACTCAATT
1 TAGTATCAATAC-CAATT
877123 TAGTATCAATACCAAT
1 TAGTATCAATACCAAT
877139 ATGACATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (17 bp):
TAGTATCAATACCAATT
Found at i:879649 original size:3 final size:3
Alignment explanation
Indices: 879641--879698 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
879631 ATAACAATAC
879641 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
879689 AGA AGA AGA A
1 AGA AGA AGA A
879699 CCCAGAAAAG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:880744 original size:28 final size:27
Alignment explanation
Indices: 880701--880780 Score: 71
Period size: 25 Copynumber: 3.1 Consensus size: 27
880691 ATATATAACC
880701 TAATATT-TTATTTTAATAATAAATTAT
1 TAATATTATT-TTTTAATAATAAATTAT
*
880728 TAATATTATTTTGTTAA-AA-ATATTAT
1 TAATATTATTTT-TTAATAATAAATTAT
* * *
880754 T-TTATTATTATTTAATAGTAAA-TAT
1 TAATATTATTTTTTAATAATAAATTAT
880779 TA
1 TA
880781 TTCTTAATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
24 4 0.09
25 13 0.30
26 9 0.21
27 11 0.26
28 6 0.14
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (27 bp):
TAATATTATTTTTTAATAATAAATTAT
Found at i:882301 original size:5 final size:5
Alignment explanation
Indices: 882291--882322 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
882281 ATGATTTTTT
882291 AATTA AATTA AATTA AATTA AATATA AATTA A
1 AATTA AATTA AATTA AATTA AAT-TA AATTA A
882323 TATTTTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATTA
Found at i:883627 original size:33 final size:33
Alignment explanation
Indices: 883585--883659 Score: 150
Period size: 33 Copynumber: 2.3 Consensus size: 33
883575 GAATATCTAT
883585 CGAGAACCTGTTGCACTAGGCTCTTATGCAGAA
1 CGAGAACCTGTTGCACTAGGCTCTTATGCAGAA
883618 CGAGAACCTGTTGCACTAGGCTCTTATGCAGAA
1 CGAGAACCTGTTGCACTAGGCTCTTATGCAGAA
883651 CGAGAACCT
1 CGAGAACCT
883660 AAGTTATATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.23
Consensus pattern (33 bp):
CGAGAACCTGTTGCACTAGGCTCTTATGCAGAA
Found at i:886347 original size:2 final size:2
Alignment explanation
Indices: 886340--886364 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
886330 AATCATTTAC
886340 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
886365 TTAAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:886377 original size:14 final size:15
Alignment explanation
Indices: 886340--886383 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
886330 AATCATTTAC
* *
886340 TATATATATATATATA
1 TATATATATTTA-AAA
886356 TATATATATTTAAAA
1 TATATATATTTAAAA
886371 TAT-TATATTTAAA
1 TATATATATTTAAA
886384 CACTTAACGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 10 0.38
15 5 0.19
16 11 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATATATATTTAAAA
Found at i:886725 original size:15 final size:15
Alignment explanation
Indices: 886705--886756 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
886695 AAAAGCAAAA
886705 AAGAAATAAATAAAT
1 AAGAAATAAATAAAT
886720 AAGAAAT-AAT-AAT
1 AAGAAATAAATAAAT
*
886733 AATAAATAAA-ATAAT
1 AAGAAATAAATA-AAT
*
886748 AATAAATAA
1 AAGAAATAA
886757 TAATAATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 9 0.27
14 5 0.15
15 19 0.58
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (15 bp):
AAGAAATAAATAAAT
Found at i:886732 original size:3 final size:3
Alignment explanation
Indices: 886724--886768 Score: 65
Period size: 3 Copynumber: 14.7 Consensus size: 3
886714 ATAAATAAGA
886724 AAT AAT AAT AAT AAAT AA- AAT AAT AAT AAAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AA
886769 AAAAAATTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 2 0.05
3 31 0.79
4 6 0.15
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:886748 original size:28 final size:29
Alignment explanation
Indices: 886708--886775 Score: 97
Period size: 28 Copynumber: 2.4 Consensus size: 29
886698 AGCAAAAAAG
886708 AAAT-AAATAAATAAGAAATAATAATAAT
1 AAATAAAATAAATAAGAAATAATAATAAT
*
886736 AAATAAAAT-AATAATAAATAATAATAAT
1 AAATAAAATAAATAAGAAATAATAATAAT
*
886764 -AATAAAAAAAAT
1 AAATAAAATAAAT
886776 TAAAAACCCA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
27 7 0.19
28 25 0.69
29 4 0.11
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.25
Consensus pattern (29 bp):
AAATAAAATAAATAAGAAATAATAATAAT
Found at i:886755 original size:25 final size:24
Alignment explanation
Indices: 886709--886762 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
886699 GCAAAAAAGA
886709 AATAAATAAATAAGAAATAATAAT
1 AATAAATAAATAAGAAATAATAAT
*
886733 AATAAATAAAATAA-TAATAAATAAT
1 AATAAAT-AAATAAGAAAT-AATAAT
886758 AATAA
1 AATAA
886763 TAATAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 10 0.37
25 17 0.63
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (24 bp):
AATAAATAAATAAGAAATAATAAT
Found at i:886837 original size:43 final size:43
Alignment explanation
Indices: 886790--886871 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
886780 AACCCATATA
* * *
886790 ATATAAATTTTTAAAATTGTTTCTT-TTAAAAACTATATATTAT
1 ATATAAATTTTTAAAAATATTT-TTATAAAAAACTATATATTAT
886833 ATATAAATTTTTAAAAATATTTTTATAAAAAACTATATA
1 ATATAAATTTTTAAAAATATTTTTATAAAAAACTATATA
886872 ATTTTCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
42 2 0.06
43 33 0.94
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.48
Consensus pattern (43 bp):
ATATAAATTTTTAAAAATATTTTTATAAAAAACTATATATTAT
Found at i:886901 original size:32 final size:33
Alignment explanation
Indices: 886832--886920 Score: 117
Period size: 32 Copynumber: 2.7 Consensus size: 33
886822 CTATATATTA
* *
886832 TATATAAATTTTTAAAAATATTTTTATAAAAAAC
1 TATAT-AATTTTCAAAAATGTTTTTATAAAAAAC
*
886866 TATATAATTTTCAAAAATGTTTTT-TTAAAAAC
1 TATATAATTTTCAAAAATGTTTTTATAAAAAAC
* *
886898 TATATAATTTCCAAAACTGTTTT
1 TATATAATTTTCAAAAATGTTTT
886921 AAAAATTATA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
32 28 0.56
33 17 0.34
34 5 0.10
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (33 bp):
TATATAATTTTCAAAAATGTTTTTATAAAAAAC
Found at i:886907 original size:108 final size:107
Alignment explanation
Indices: 886813--887122 Score: 277
Period size: 104 Copynumber: 2.9 Consensus size: 107
886803 AAATTGTTTC
* * *
886813 TTTTAAAAACTATATATTATATATAAATTTTTAAAAATATTTTTATAAA-A-A-ACTATATAA-T
1 TTTTAAAAACTATATATTATATATAAATTTTCAAAAATATTTTCAAAAACATATACTATATAAGT
*
886874 TTTC-AAAAATGTTTTTTTAAAAACTATATAATTTCCAAAACTG
66 TTTCAAAAAATG--TTTTCAAAAACTATATAATTTCCAAAACTG
* * * *
886917 TTTTAAAAATTATATATTATATATAAGTTTTCAAAAATGTTTTCAAAAACTATATATTATATAAG
1 TTTTAAAAACTATATATTATATATAAATTTTCAAAAATATTTTCAAAAAC-ATATACTATATAAG
*
886982 TTTTCAAAAAATGTTTTCAAAAACTATATATTATATAAGTTTTCAAAA-TG
65 TTTTCAAAAAATGTTTTCAAAAAC-------TATATAA-TTTCCAAAACTG
* *
887032 ATTTTAAAAA-TCATATATTATATAT--ATTTTCTAAAAATGTTTT-AAAAACTATATATTATAT
1 -TTTTAAAAACT-ATATATTATATATAAATTTTC-AAAAATATTTTCAAAAAC-ATATACTATAT
* *
887093 -AGTTTTC-ATAAGTGTTTT-AAAAACTATATA
62 AAGTTTTCAAAAAATGTTTTCAAAAACTATATA
887123 TTATATATAT
Statistics
Matches: 177, Mismatches: 12, Indels: 34
0.79 0.05 0.15
Matches are distributed among these distances:
104 49 0.28
106 1 0.01
107 1 0.01
108 18 0.10
109 5 0.03
110 7 0.04
111 6 0.03
112 9 0.05
113 7 0.04
114 23 0.13
115 21 0.12
116 30 0.17
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (107 bp):
TTTTAAAAACTATATATTATATATAAATTTTCAAAAATATTTTCAAAAACATATACTATATAAGT
TTTCAAAAAATGTTTTCAAAAACTATATAATTTCCAAAACTG
Found at i:886958 original size:39 final size:39
Alignment explanation
Indices: 886898--887166 Score: 316
Period size: 39 Copynumber: 7.1 Consensus size: 39
886888 TTTTAAAAAC
* * *
886898 TATATAA-TTTCCAAAACTGTTTTAAAAATTATATATTA
1 TATATAAGTTTTCAAAAATGTTTTAAAAACTATATATTA
886936 TATATAAGTTTTCAAAAATGTTTTCAAAAACTATATA-T-
1 TATATAAGTTTTCAAAAATGTTTT-AAAAACTATATATTA
886974 TATATAAGTTTTCAAAAAATGTTTTCAAAAACTATATA-T-
1 TATATAAGTTTTC-AAAAATGTTTT-AAAAACTATATATTA
887013 TATATAAGTTTTC-AAAATGATTTTAAAAA-TCATATATTA
1 TATATAAGTTTTCAAAAATG-TTTTAAAAACT-ATATATTA
887052 TATAT-A-TTTTCTAAAAATGTTTTAAAAACTATATA-T-
1 TATATAAGTTTTC-AAAAATGTTTTAAAAACTATATATTA
* *
887088 TATAT-AGTTTTCATAAGTGTTTTAAAAACTATATATTA
1 TATATAAGTTTTCAAAAATGTTTTAAAAACTATATATTA
*
887126 TATAT-A-TTTTC-AAAATGTTTTTAGAAACTATATATTA
1 TATATAAGTTTTCAAAAATG-TTTTAAAAACTATATATTA
887163 TATA
1 TATA
887167 CACATTTTTA
Statistics
Matches: 209, Mismatches: 8, Indels: 29
0.85 0.03 0.12
Matches are distributed among these distances:
36 32 0.15
37 55 0.26
38 46 0.22
39 65 0.31
40 11 0.05
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (39 bp):
TATATAAGTTTTCAAAAATGTTTTAAAAACTATATATTA
Found at i:886971 original size:38 final size:37
Alignment explanation
Indices: 886898--887166 Score: 336
Period size: 37 Copynumber: 7.2 Consensus size: 37
886888 TTTTAAAAAC
* * *
886898 TATATAA-TTTCCAAAACTGTTTTAAAAATTATATATT
1 TATATAAGTTTTCAAAAATGTTTTAAAAACTATATA-T
886935 ATATATAAGTTTTCAAAAATGTTTTCAAAAACTATATAT
1 -TATATAAGTTTTCAAAAATGTTTT-AAAAACTATATAT
886974 TATATAAGTTTTCAAAAAATGTTTTCAAAAACTATATAT
1 TATATAAGTTTTC-AAAAATGTTTT-AAAAACTATATAT
887013 TATATAAGTTTTC-AAAATGATTTTAAAAA-TCATATAT
1 TATATAAGTTTTCAAAAATG-TTTTAAAAACT-ATATAT
887050 TATATATA-TTTTCTAAAAATGTTTTAAAAACTATATAT
1 TATATA-AGTTTTC-AAAAATGTTTTAAAAACTATATAT
* *
887088 TATAT-AGTTTTCATAAGTGTTTTAAAAACTATATAT
1 TATATAAGTTTTCAAAAATGTTTTAAAAACTATATAT
*
887124 TATATATA-TTTTC-AAAATGTTTTTAGAAACTATATAT
1 TATATA-AGTTTTCAAAAATG-TTTTAAAAACTATATAT
887161 TATATA
1 TATATA
887167 CACATTTTTA
Statistics
Matches: 210, Mismatches: 8, Indels: 27
0.86 0.03 0.11
Matches are distributed among these distances:
36 33 0.16
37 60 0.29
38 46 0.22
39 60 0.29
40 11 0.05
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (37 bp):
TATATAAGTTTTCAAAAATGTTTTAAAAACTATATAT
Found at i:887174 original size:39 final size:37
Alignment explanation
Indices: 886785--887166 Score: 301
Period size: 37 Copynumber: 10.3 Consensus size: 37
886775 TTAAAAACCC
* *
886785 ATATAATATAAATTTTTAAAATTGTTTCTTTTAAAAACTAT
1 ATATTATATAAATTTTCAAAA-TG--T-TTTTAAAAACTAT
* * *
886826 ATATTATATATAAATTTTTAAAAATATTTTTATAAA--A-
1 ATA-T-TATATAAA-TTTTCAAAATGTTTTTAAAAACTAT
* **
886863 A-ACTATAT-AATTTTCAAAAATGTTTTT-TTAA--A-
1 ATATTATATAAATTTTC-AAAATGTTTTTAAAAACTAT
* * *
886895 A-ACTATAT-AATTTCCAAAACTG-TTTTAAAAATTAT
1 ATATTATATAAATTTTCAAAA-TGTTTTTAAAAACTAT
*
886930 ATATTATATATAAGTTTTCAAAAATGTTTTCAAAAACTAT
1 ATATTATATA-AA-TTTTC-AAAATGTTTTTAAAAACTAT
* *
886970 ATATTATATAAGTTTTCAAAAAATGTTTTCAAAAACTAT
1 ATATTATATAAATTTTC--AAAATGTTTTTAAAAACTAT
* *
887009 ATATTATATAAGTTTTCAAAATGATTTTAAAAA-TCAT
1 ATATTATATAAATTTTCAAAATGTTTTTAAAAACT-AT
*
887046 ATATTATATATATTTTCTAAAAATG-TTTTAAAAACTAT
1 ATATTATATAAATTTTC--AAAATGTTTTTAAAAACTAT
* *
887084 ATATTATAT-AGTTTTCATAA-GTGTTTTAAAAACTAT
1 ATATTATATAAATTTTCAAAATGT-TTTTAAAAACTAT
* *
887120 ATATTATATATATTTTCAAAATGTTTTTAGAAACTAT
1 ATATTATATAAATTTTCAAAATGTTTTTAAAAACTAT
887157 ATATTATATA
1 ATATTATATA
887167 CACATTTTTA
Statistics
Matches: 290, Mismatches: 27, Indels: 52
0.79 0.07 0.14
Matches are distributed among these distances:
31 8 0.03
32 26 0.09
33 12 0.04
34 7 0.02
35 4 0.01
36 30 0.10
37 67 0.23
38 30 0.10
39 52 0.18
40 33 0.11
41 4 0.01
42 1 0.00
43 8 0.03
44 8 0.03
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.46
Consensus pattern (37 bp):
ATATTATATAAATTTTCAAAATGTTTTTAAAAACTAT
Found at i:893253 original size:33 final size:34
Alignment explanation
Indices: 893216--893284 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
893206 ATTTGGCAAG
* *
893216 TTGGAAATTTCATC-TTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTTGGTAGGTGGCCAACTTA
893249 TTGGAAAATTCATCTTTGGTAGGTGGCCAACTTA
1 TTGGAAAATTCATCTTTGGTAGGTGGCCAACTTA
893283 TT
1 TT
893285 TTTCATCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
33 13 0.39
34 20 0.61
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.39
Consensus pattern (34 bp):
TTGGAAAATTCATCTTTGGTAGGTGGCCAACTTA
Found at i:897019 original size:114 final size:114
Alignment explanation
Indices: 896819--897030 Score: 381
Period size: 114 Copynumber: 1.9 Consensus size: 114
896809 TTTTAAACCA
*
896819 GGTAGACTTATAAAGATGTAGAATAATATATCATACCTTGTCAACAGCTTCAGAGTAAGATCCAT
1 GGTAGACTTATAAAGATGTAGAATAATATACCATACCTTGTCAACAGCTTCAGAGTAAGATCCAT
896884 GATGATCCTGCAAATTGCGGAAAACAGATATGTTCAGAATGGTTTTAAC
66 GATGATCCTGCAAATTGCGGAAAACAGATATGTTCAGAATGGTTTTAAC
* *
896933 GGTAGACTTGTAAAGATGTAGAATAATATACCATACCTTGTCAGA-AGCTTCAGAGTTAGATCCA
1 GGTAGACTTATAAAGATGTAGAATAATATACCATACCTTGTCA-ACAGCTTCAGAGTAAGATCCA
896997 TGATGATCCTGCAAATTGCGGAAAACAGATATGT
65 TGATGATCCTGCAAATTGCGGAAAACAGATATGT
897031 GATATAAATA
Statistics
Matches: 94, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
114 93 0.99
115 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.28
Consensus pattern (114 bp):
GGTAGACTTATAAAGATGTAGAATAATATACCATACCTTGTCAACAGCTTCAGAGTAAGATCCAT
GATGATCCTGCAAATTGCGGAAAACAGATATGTTCAGAATGGTTTTAAC
Found at i:897062 original size:32 final size:32
Alignment explanation
Indices: 897025--897089 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
897015 CGGAAAACAG
897025 ATATGTGATATAAATAAATTGAACTAACAAAA
1 ATATGTGATATAAATAAATTGAACTAACAAAA
* * *
897057 ATATGTGATATACATGAATTGGACTAACAAAA
1 ATATGTGATATAAATAAATTGAACTAACAAAA
897089 A
1 A
897090 GGAATAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.28
Consensus pattern (32 bp):
ATATGTGATATAAATAAATTGAACTAACAAAA
Found at i:897918 original size:27 final size:27
Alignment explanation
Indices: 897863--897920 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
897853 TTGCACCATT
* *
897863 TCAATGGCTGAATTAAGCTTGAATACC
1 TCAATGGCTGAATTAAGCCTCAATACC
*
897890 TCAATGGCTGAATTAAGCCTCAATCCC
1 TCAATGGCTGAATTAAGCCTCAATACC
897917 TCAA
1 TCAA
897921 CTTGTCGCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.28
Consensus pattern (27 bp):
TCAATGGCTGAATTAAGCCTCAATACC
Found at i:903638 original size:29 final size:29
Alignment explanation
Indices: 903574--903639 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
903564 CAAAGTCCAT
* *
903574 TGCTATAACTAGAGCAATTGAAAGGTCAC
1 TGCTATAACTAGAGCAATTAAAAGGTCAA
*
903603 TGCTATAACT-GAAGCAATTAAAAGTTCAA
1 TGCTATAACTAG-AGCAATTAAAAGGTCAA
*
903632 TGGTATAA
1 TGCTATAA
903640 ACGATACATC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 1 0.03
29 31 0.97
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (29 bp):
TGCTATAACTAGAGCAATTAAAAGGTCAA
Found at i:903658 original size:31 final size:31
Alignment explanation
Indices: 903623--903685 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
903613 GAAGCAATTA
* * *
903623 AAAGTTCAATGGTATAAACGATACATCACCT
1 AAAGTTCAATAGTATAAAAGATACACCACCT
* *
903654 AAAGTTTAGTAGTATAAAAGATACACCACCT
1 AAAGTTCAATAGTATAAAAGATACACCACCT
903685 A
1 A
903686 CGATTCAGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.25
Consensus pattern (31 bp):
AAAGTTCAATAGTATAAAAGATACACCACCT
Found at i:905583 original size:17 final size:18
Alignment explanation
Indices: 905552--905586 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
905542 TATCATTATG
*
905552 TATTTTTTATTAAAAAAT
1 TATTTTTTATGAAAAAAT
905570 TATTTTTT-TGAAAAAAT
1 TATTTTTTATGAAAAAAT
905587 ATTAAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TATTTTTTATGAAAAAAT
Found at i:906379 original size:9 final size:10
Alignment explanation
Indices: 906363--906388 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
906353 GTCATATATG
906363 TAAAAAAAAT
1 TAAAAAAAAT
906373 TAAAAAAAAT
1 TAAAAAAAAT
906383 TAAAAA
1 TAAAAA
906389 TTTTTAATAG
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:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (10 bp):
TAAAAAAAAT
Found at i:923661 original size:12 final size:12
Alignment explanation
Indices: 923632--923667 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
923622 GTATATTTAT
923632 TATTTTATAAAA
1 TATTTTATAAAA
923644 TA-TTTATAAAA
1 TATTTTATAAAA
923655 TATTTTATAAAA
1 TATTTTATAAAA
923667 T
1 T
923668 TAAAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.48
12 12 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TATTTTATAAAA
Found at i:923831 original size:64 final size:61
Alignment explanation
Indices: 923706--923831 Score: 155
Period size: 61 Copynumber: 2.0 Consensus size: 61
923696 GACAAACTCT
* *
923706 CAAGCATAAACAATTTCAACTTATTGACTTCGAAGCAGTAGGCTTTACATTCAATAATTTG
1 CAAGCATAAACAATTTCAAATCATTGACTTCGAAGCAGTAGGCTTTACATTCAATAATTTG
* * * *
923767 CAAGCTTAGACAATTTCAAATCATTCGACTTTGAAGCAGT-GGCCTTTTTACATTCAATACTTTG
1 CAAGCATAAACAATTTCAAATCATT-GACTTCGAAGCAGTAGG-C--TTTACATTCAATAATTTG
923831 C
1 C
923832 TAAGAATCTT
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
61 23 0.42
62 14 0.25
64 18 0.33
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (61 bp):
CAAGCATAAACAATTTCAAATCATTGACTTCGAAGCAGTAGGCTTTACATTCAATAATTTG
Found at i:928920 original size:30 final size:28
Alignment explanation
Indices: 928884--928947 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
928874 AGTTGATACA
*
928884 ATATTTTAAAAGAATAAATTTAAGATTTAT
1 ATATTTT-AAA-AATAAATTTAAGAATTAT
* * *
928914 ATATTTTTAAACTAAATTTAATAATTAT
1 ATATTTTAAAAATAAATTTAAGAATTAT
928942 ATATTT
1 ATATTT
928948 CATATTTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 21 0.70
29 2 0.07
30 7 0.23
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (28 bp):
ATATTTTAAAAATAAATTTAAGAATTAT
Found at i:929202 original size:21 final size:21
Alignment explanation
Indices: 929178--929220 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
929168 TATTACCTTA
929178 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
929199 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
929220 A
1 A
929221 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:929238 original size:35 final size:35
Alignment explanation
Indices: 929189--929274 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
929179 ATTGAAGTAT
** * *
929189 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* * *
929224 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
*
929259 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
929275 TTACTGTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:929457 original size:29 final size:29
Alignment explanation
Indices: 929405--929462 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
929395 GCAAACGAAA
* *
929405 TAAATGTTGGGGGACTGTATTGCAAGTTT
1 TAAATGTTGGGGGACTGAAATGCAAGTTT
929434 TAAATGTTGGGGGACCT-AAATGCAAGTTT
1 TAAATGTTGGGGGA-CTGAAATGCAAGTTT
929463 CAAAAATGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.28, C:0.09, G:0.29, T:0.34
Consensus pattern (29 bp):
TAAATGTTGGGGGACTGAAATGCAAGTTT
Found at i:930944 original size:35 final size:36
Alignment explanation
Indices: 930893--930973 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 36
930883 AACACAATCA
* *
930893 TCAATTATATTATAAACCCCAAA-ATCC-AGAATACT
1 TCAATTACATTATAAACCCCAAATA-CCAAAAATACT
* *
930928 TCAATTACATTTTAAACCTCAAATACCAAAAATACT
1 TCAATTACATTATAAACCCCAAATACCAAAAATACT
930964 TCAATTACAT
1 TCAATTACAT
930974 GCCCAACCTC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
35 22 0.55
36 18 0.45
ACGTcount: A:0.46, C:0.22, G:0.01, T:0.31
Consensus pattern (36 bp):
TCAATTACATTATAAACCCCAAATACCAAAAATACT
Found at i:931810 original size:35 final size:34
Alignment explanation
Indices: 931764--931864 Score: 112
Period size: 35 Copynumber: 2.9 Consensus size: 34
931754 TTTTGAGAAT
* * * *
931764 GTATTATGAATTTGGGGTTGGGCATGTAATTGAA
1 GTATTTTGAATTTGGGGTTGAGAATGTAATTAAA
* *
931798 GTATTTTAGAATTTGAGGTTTAGAATGTAATTAAA
1 GTATTTT-GAATTTGGGGTTGAGAATGTAATTAAA
* *
931833 GTATTTTGAAATTTGGGGTTTATAATGTAATT
1 GTATTTTG-AATTTGGGGTTGAGAATGTAATT
931865 GATGATTGTA
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
34 7 0.12
35 50 0.88
ACGTcount: A:0.31, C:0.01, G:0.25, T:0.44
Consensus pattern (34 bp):
GTATTTTGAATTTGGGGTTGAGAATGTAATTAAA
Found at i:932473 original size:20 final size:20
Alignment explanation
Indices: 932437--932474 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
932427 AACATTAATT
*
932437 AAAATATATTAATTTTATGG
1 AAAATATATTAAATTTATGG
932457 AAAATA-ATTATAATTTAT
1 AAAATATATTA-AATTTAT
932475 TTTATAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
AAAATATATTAAATTTATGG
Found at i:937803 original size:30 final size:30
Alignment explanation
Indices: 937769--937850 Score: 101
Period size: 35 Copynumber: 2.6 Consensus size: 30
937759 ACCAAACCCG
*
937769 TCCCCGTCCCCGTTTAACATAAACGGTTTT
1 TCCCCGTCCCCGTTTAACATAAACGATTTT
*
937799 TCCCCATCCCGTCCCCGTTTAGCATAAACGATTTT
1 T---C--CCCGTCCCCGTTTAACATAAACGATTTT
937834 TCCCCGTCCCCGTTTAA
1 TCCCCGTCCCCGTTTAA
937851 TTTGTTTTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
30 15 0.34
32 1 0.02
33 1 0.02
35 27 0.61
ACGTcount: A:0.18, C:0.38, G:0.12, T:0.32
Consensus pattern (30 bp):
TCCCCGTCCCCGTTTAACATAAACGATTTT
Found at i:937817 original size:35 final size:35
Alignment explanation
Indices: 937771--937843 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
937761 CAAACCCGTC
*
937771 CCCGTCCCCGTTTAACATAAACGGTTTTTCCCCAT
1 CCCGTCCCCGTTTAACATAAACGATTTTTCCCCAT
* *
937806 CCCGTCCCCGTTTAGCATAAACGATTTTTCCCCGT
1 CCCGTCCCCGTTTAACATAAACGATTTTTCCCCAT
937841 CCC
1 CCC
937844 CGTTTAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.18, C:0.40, G:0.12, T:0.30
Consensus pattern (35 bp):
CCCGTCCCCGTTTAACATAAACGATTTTTCCCCAT
Found at i:938455 original size:22 final size:25
Alignment explanation
Indices: 938400--938456 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
938390 GCCCCGATAA
938400 TATATATATATATATTTTATATTAAT
1 TATATATATATATATTTTATATT-AT
*
938426 TATATATATA-ATATTTTATATTTT
1 TATATATATATATATTTTATATTAT
*
938450 TTTATAT
1 TATATAT
938457 TAATTATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 7 0.24
25 12 0.41
26 10 0.34
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
TATATATATATATATTTTATATTAT
Found at i:938460 original size:35 final size:36
Alignment explanation
Indices: 938396--938477 Score: 130
Period size: 35 Copynumber: 2.3 Consensus size: 36
938386 CCCTGCCCCG
*
938396 ATAATATATATATATATATTTTATATTAATTATATAT
1 ATAATAT-TTTATATATATTTTATATTAATTATATAT
*
938433 ATAATATTTTATAT-TTTTTTATATTAATTATATAT
1 ATAATATTTTATATATATTTTATATTAATTATATAT
938468 ATAATATTTT
1 ATAATATTTT
938478 TGGGTTCGGG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 30 0.70
36 6 0.14
37 7 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (36 bp):
ATAATATTTTATATATATTTTATATTAATTATATAT
Found at i:941462 original size:25 final size:25
Alignment explanation
Indices: 941428--941482 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
941418 AATTACATAT
941428 ACTTATTATAAGGATAATATTCTCA
1 ACTTATTATAAGGATAATATTCTCA
*
941453 ACTTATTATAAGGATATTATTCTCA
1 ACTTATTATAAGGATAATATTCTCA
941478 ACTTA
1 ACTTA
941483 ATTTACTCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (25 bp):
ACTTATTATAAGGATAATATTCTCA
Found at i:946343 original size:2 final size:2
Alignment explanation
Indices: 946336--946361 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
946326 GTGACATGTA
946336 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
946362 TTTCAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:952479 original size:11 final size:11
Alignment explanation
Indices: 952459--952540 Score: 53
Period size: 11 Copynumber: 7.3 Consensus size: 11
952449 TTAATTATTT
*
952459 TTATTCTAATA
1 TTATTTTAATA
*
952470 TTATTTTAATG
1 TTATTTTAATA
952481 TT-TTTTAA-A
1 TTATTTTAATA
*
952490 GTTATTAT-ATA
1 -TTATTTTAATA
952501 TATATTTATAACTA
1 T-TATTT-TAA-TA
*
952515 TTATATTTATTA
1 TTAT-TTTAATA
*
952527 TTATTTTACTA
1 TTATTTTAATA
952538 TTA
1 TTA
952541 ACGTATATAA
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
10 10 0.18
11 28 0.50
12 7 0.12
13 6 0.11
14 5 0.09
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:952611 original size:17 final size:18
Alignment explanation
Indices: 952583--952620 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
952573 TATTATTATC
*
952583 ATTATATGTATATTTTTT
1 ATTATATGTATACTTTTT
952601 ATTATAT-TATACTTTTT
1 ATTATATGTATACTTTTT
952618 ATT
1 ATT
952621 TTTACTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (18 bp):
ATTATATGTATACTTTTT
Found at i:952731 original size:16 final size:16
Alignment explanation
Indices: 952710--952743 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
952700 CATGTATTTA
952710 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
952726 TATTATTTTACTTTAT
1 TATTATATTACATTAT
952742 TA
1 TA
952744 AATTATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:952748 original size:21 final size:22
Alignment explanation
Indices: 952724--952774 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
952714 ATATTACATT
*
952724 ATTATTATTTTACTTTATTA-A
1 ATTATTATTTTACGTTATTATA
* *
952745 ATTATTTTTTTTCGTTATTATA
1 ATTATTATTTTACGTTATTATA
*
952767 TTTATTAT
1 ATTATTAT
952775 ATATATATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTATTATTTTACGTTATTATA
Found at i:956146 original size:20 final size:21
Alignment explanation
Indices: 956109--956162 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
956099 AAAAAAAGAA
956109 AAGAAGCAAAAAAGGAAAAAAC
1 AAGAA-CAAAAAAGGAAAAAAC
*
956131 AAGAACAAAAAA-GAAAGAAC
1 AAGAACAAAAAAGGAAAAAAC
* *
956151 AAAAATAAAAAA
1 AAGAACAAAAAA
956163 AGGGAACAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 17 0.59
21 7 0.24
22 5 0.17
ACGTcount: A:0.78, C:0.07, G:0.13, T:0.02
Consensus pattern (21 bp):
AAGAACAAAAAAGGAAAAAAC
Found at i:957748 original size:36 final size:36
Alignment explanation
Indices: 957651--957909 Score: 248
Period size: 36 Copynumber: 7.3 Consensus size: 36
957641 ATTGAAAACA
* *
957651 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
* *
957687 TTTCTCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAA-TAAATTTTGTCTCTCTTGAGACAG
957724 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
* * * *
957760 TTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACA-G
* * * *
957789 TTTTCTTTGAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
** * *
957825 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTT-GAAATAAATTTTGTCTCTCTTGAGACAG
* * *
957862 TTTCTCTTGAAA-CAATTTTCGTCTATCTTGAGACAG
1 TTTCCCTTGAAATAAATTTT-GTCTCTCTTGAGACAG
957898 TTTCCCTTGAAA
1 TTTCCCTTGAAA
957910 CAAAATCTTT
Statistics
Matches: 183, Mismatches: 28, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
28 2 0.01
29 19 0.10
30 2 0.01
35 6 0.03
36 89 0.49
37 65 0.36
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
Found at i:957770 original size:73 final size:73
Alignment explanation
Indices: 957651--957920 Score: 290
Period size: 73 Copynumber: 3.8 Consensus size: 73
957641 ATTGAAAACA
* * *
957651 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATTTTGTCTCTCT
1 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCT
957716 TGAGACAG
66 TGAGACAG
*
957724 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAA-------TAT-T
1 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCT
*
957781 TGA-ATATG
66 TGAGACA-G
* * * * ** * * *
957789 TTTTCTTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCT
957854 TGAGACAG
66 TGAGACAG
* * *
957862 TTTCTCTTGAAA-CAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTG
1 TTTCCCTTGAAATAAATTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT-TTTG
957921 AATTTATTTC
Statistics
Matches: 158, Mismatches: 27, Indels: 23
0.76 0.13 0.11
Matches are distributed among these distances:
64 2 0.01
65 49 0.31
66 2 0.01
72 8 0.05
73 91 0.58
74 6 0.04
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (73 bp):
TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCT
TGAGACAG
Found at i:957772 original size:138 final size:136
Alignment explanation
Indices: 957599--957976 Score: 495
Period size: 138 Copynumber: 2.7 Consensus size: 136
957589 TTTTTAAAAC
* * * * *
957599 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
1 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAACATTGAATATATTTCCCTTGAAAC
* * *
957664 AAATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCC
65 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCC
957729 CTTGAAA
130 CTTGAAA
* * * *
957736 TAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCTTTGAAA
1 -AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACA-TTGAATATATTTCCCTTGAAA
* * * *
957801 CAAATTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTC
64 CAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTC
*
957866 TCTTGAAA
129 CCTTGAAA
* * * * * *
957874 CAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCTAAAA
1 AAATTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAAA-CATTGAATATATTTCCCTTGAAA
*
957939 CAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACA
64 CAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
957977 CAAAATCTTC
Statistics
Matches: 206, Mismatches: 31, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
137 10 0.05
138 196 0.95
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (136 bp):
AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACATTGAATATATTTCCCTTGAAACA
AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCC
TTGAAA
Found at i:957799 original size:102 final size:103
Alignment explanation
Indices: 957687--957876 Score: 303
Period size: 102 Copynumber: 1.9 Consensus size: 103
957677 CTTGAGATAG
*
957687 TTTCTCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTT-GAAATAAATTTTGTCTCTC
1 TTTCTCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGGAAATAAATTTTGTCTCTC
957751 TTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
65 TTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
** * *
957790 TTTCT-TTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGGAAATAAATTTTGTCTCTCT
*
957854 TGAGACAGTTTCTCTTGAAACAA
66 TGAGACAGTTTCCCTTGAAACAA
957877 TTTTCGTCTA
Statistics
Matches: 80, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
101 28 0.35
102 47 0.59
103 5 0.06
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.42
Consensus pattern (103 bp):
TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGGAAATAAATTTTGTCTCTCT
TGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
Found at i:957910 original size:36 final size:36
Alignment explanation
Indices: 957790--957913 Score: 162
Period size: 37 Copynumber: 3.4 Consensus size: 36
957780 TTGAATATGT
*
957790 TTTCT-TTGAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * *
957825 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
*
957862 TTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAG
1 TTTCTCTTGAAACAAATTTT-GTCTCTCTTGAGACAG
*
957898 TTTCCCTTGAAACAAA
1 TTTCTCTTGAAACAAA
957914 ATCTTTGAAT
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
35 10 0.13
36 33 0.43
37 34 0.44
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:957975 original size:65 final size:65
Alignment explanation
Indices: 957871--958045 Score: 217
Period size: 67 Copynumber: 2.6 Consensus size: 65
957861 GTTTCTCTTG
** * **
957871 AAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCT
1 AAACAAATTTT-GTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCT
957935 A
65 A
* *
957936 AAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG-AA-ACAAAATCTTCAAATTTATTTCCCC
958001 TA
64 TA
* * *
958003 AAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACAA
1 AAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
958046 CAGATATCTT
Statistics
Matches: 95, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
65 25 0.26
66 12 0.13
67 31 0.33
68 27 0.28
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.37
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
Found at i:958005 original size:67 final size:67
Alignment explanation
Indices: 957862--958044 Score: 219
Period size: 68 Copynumber: 2.7 Consensus size: 67
957852 CTTGAGACAG
* * ** * **
957862 TTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAAT
1 TTTCCCTTAAAACAAATTTT-GTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAAT
957924 TTA
65 TTA
* *
957927 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATT
1 TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
957992 TA
66 TA
* * *
957994 TTTCCCTTAAAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACA
1 TTTCCCTTAAAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
958045 ACAGATATCT
Statistics
Matches: 100, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
65 31 0.31
66 8 0.08
67 29 0.29
68 32 0.32
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (67 bp):
TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
TA
Found at i:958809 original size:106 final size:105
Alignment explanation
Indices: 958649--959102 Score: 535
Period size: 106 Copynumber: 4.3 Consensus size: 105
958639 GCCATCCGCG
* *
958649 ATTTCAACTCCAC-GACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGA
1 ATTTCAACTTCACAG-CGAAGGATAT--TGG-ACTCGAGACAACACAAGTTCAACTTCACAACGA
* *
958713 AGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
62 AGGGACGGCTGATTGTCAAC-AACAATTTCTCAATTTCAGAGCCA
* * * *
958758 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * *
958823 ACTGCTGCTTGTTAACAACAATTTTTCAAATTTCAGAGCCA
66 ACGGCTGATTGTCAACAACAATTTCTC-AATTTCAGAGCCA
* *
958864 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGAAAACACAAGTTCAACTTCACAATGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * *
958929 ACGGCTGATTGTCAACAA-GATTT-T---GTTCAGAGTCA
66 ACGGCTGATTGTCAACAACAATTTCTCAATTTCAGAGCCA
* * * *
958964 ATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGCTCAACTTCACAGCGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * ** * *
959029 GCGGCTGACTGTCAACAAACAATTTCCCGGTTCCAGAACCA
66 ACGGCTGATTGTCAAC-AACAATTTCTCAATTTCAGAGCCA
959070 ATTTCAACTTCACAGC-AGAGGATATTGGACTCG
1 ATTTCAACTTCACAGCGA-AGGATATTGGACTCG
959103 GAACAATATT
Statistics
Matches: 298, Mismatches: 38, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
100 82 0.28
101 2 0.01
102 4 0.01
104 1 0.00
105 14 0.05
106 171 0.57
107 3 0.01
109 21 0.07
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (105 bp):
ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
ACGGCTGATTGTCAACAACAATTTCTCAATTTCAGAGCCA
Found at i:959073 original size:206 final size:210
Alignment explanation
Indices: 958649--959102 Score: 541
Period size: 206 Copynumber: 2.2 Consensus size: 210
958639 GCCATCCGCG
* * *
958649 ATTTCAACTCCAC-GACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGA
1 ATTTCAACTTCACAG-CGAAGGATAT--TGG-ACTCGAGAAAACACAAGTTCAACTTCACAACGA
*
958713 AGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAG
62 AGGGACGGCTGATTGTCAACAAACAACTTCT--ATTTCAGAGCCAATTTCAACTTCACAACGAAG
* * * * *
958778 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGCTTGTTAACAACA
125 GATATTAGACTCCAGACAACACAAGCTCAACTTCACGACGAAGGGACGGCTGCTTGTCAACAACA
* * *
958843 ATTTTTCAAATTTCAGAGCCA
190 ATTTTCCAAATTCCAGAACCA
*
958864 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGAAAACACAAGTTCAACTTCACAATGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGAAAACACAAGTTCAACTTCACAACGAAGGG
* * *
958929 ACGGCTGATTGTCAAC-AA-GA-TT-T-TGTTCAGAGTCAATTTCAACTTCACAGCGAAGGATAT
66 ACGGCTGATTGTCAACAAACAACTTCTAT-TTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
* * *
958989 TAGACTCGAGACAGCACAAGCTCAACTTCAC-AGCGAAGGGGCGGCTGAC-TGTCAACAAACAA-
130 TAGACTCCAGACAACACAAGCTCAACTTCACGA-CGAAGGGACGGCTG-CTTGTCAAC-AACAAT
***
959051 TTTCCCGGTTCCAGAACCA
192 TTTCCAAATTCCAGAACCA
959070 ATTTCAACTTCACAGC-AGAGGATATTGGACTCG
1 ATTTCAACTTCACAGCGA-AGGATATTGGACTCG
959103 GAACAATATT
Statistics
Matches: 211, Mismatches: 22, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
205 3 0.01
206 121 0.57
207 6 0.03
208 1 0.00
209 2 0.01
210 1 0.00
211 2 0.01
212 50 0.24
213 3 0.01
215 21 0.10
216 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (210 bp):
ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGAAAACACAAGTTCAACTTCACAACGAAGGG
ACGGCTGATTGTCAACAAACAACTTCTATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
AGACTCCAGACAACACAAGCTCAACTTCACGACGAAGGGACGGCTGCTTGTCAACAACAATTTTC
CAAATTCCAGAACCA
Found at i:960343 original size:16 final size:16
Alignment explanation
Indices: 960322--960355 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
960312 CATGTATTTA
960322 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
960338 TATTATTTTACTTTAT
1 TATTATATTACATTAT
960354 TA
1 TA
960356 AATTATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:960360 original size:21 final size:22
Alignment explanation
Indices: 960336--960386 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
960326 ATATTACATT
*
960336 ATTATTATTTTACTTTATTA-A
1 ATTATTATTTTACGTTATTATA
* *
960357 ATTATTTTTTTTCGTTATTATA
1 ATTATTATTTTACGTTATTATA
*
960379 TTTATTAT
1 ATTATTAT
960387 ATATATATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTATTATTTTACGTTATTATA
Found at i:960391 original size:2 final size:2
Alignment explanation
Indices: 960375--960412 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
960365 TTTTCGTTAT
*
960375 TA TA TT TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
960413 CATAATGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:964007 original size:6 final size:6
Alignment explanation
Indices: 963996--964041 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
963986 TATTAAAAAT
* *
963996 ATTAAA ATTAAA ATTAAA ATTAAA A--AGAT ATTAAA TTTAAA ATTAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTA-AA ATTAAA ATTAAA ATTAA
964042 CTTTTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
4 1 0.03
5 2 0.06
6 29 0.88
7 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (6 bp):
ATTAAA
Found at i:966074 original size:4 final size:4
Alignment explanation
Indices: 966065--966089 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
966055 CTCTATAGTC
966065 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
966090 CTTTTATTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:968148 original size:2 final size:2
Alignment explanation
Indices: 968141--968181 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
968131 TTAAACAATT
**
968141 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA GC TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
968182 AAAGTTTTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:973821 original size:88 final size:88
Alignment explanation
Indices: 973721--973901 Score: 326
Period size: 88 Copynumber: 2.1 Consensus size: 88
973711 ATGATTATAT
*
973721 ATAAATATTATTCATATATATTATTATAAAATTTAAATATATTTTAATTATCAATTGGATTACAT
1 ATAAATATTATTCATATATATTATTATAAAATTTAAATATATTTTAATTATCAATTGAATTACAT
973786 TTTATAATAATTGATACTAATGA
66 TTTATAATAATTGATACTAATGA
*
973809 ATAAATATTATTCATATATATTATTATAAAATTTAAATATATTTTAATTATCAATTGAATTATAT
1 ATAAATATTATTCATATATATTATTATAAAATTTAAATATATTTTAATTATCAATTGAATTACAT
* *
973874 TTTCTAATAATTGATATTAATGA
66 TTTATAATAATTGATACTAATGA
973897 ATAAA
1 ATAAA
973902 ACCTTAAAAA
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (88 bp):
ATAAATATTATTCATATATATTATTATAAAATTTAAATATATTTTAATTATCAATTGAATTACAT
TTTATAATAATTGATACTAATGA
Found at i:974160 original size:17 final size:15
Alignment explanation
Indices: 974117--974160 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
974107 TCTAATTTAA
974117 AATTAATTTAAAATT
1 AATTAATTTAAAATT
*
974132 ATTTCAATTTAAAATAT
1 AATT-AATTTAAAAT-T
974149 AATTATATTTAA
1 AATTA-ATTTAA
974161 TTTAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 3 0.12
16 11 0.46
17 10 0.42
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTAATTTAAAATT
Found at i:976608 original size:20 final size:20
Alignment explanation
Indices: 976583--976629 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
976573 CGTGTCTTAG
976583 AAGATTGCTCCCTAACATAA
1 AAGATTGCTCCCTAACATAA
* *
976603 AAGATTGCTCTCTAATATAA
1 AAGATTGCTCCCTAACATAA
*
976623 AATATTG
1 AAGATTG
976630 TCCTCGGTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (20 bp):
AAGATTGCTCCCTAACATAA
Found at i:995390 original size:23 final size:23
Alignment explanation
Indices: 995359--995431 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
995349 ATAGGTAAAA
* *
995359 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGTGCTT
*
995382 ATATAATGTAATAGGTAGTGTTT
1 ATATAATGTAATAGGTAGTGCTT
995405 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGTGCTT
995428 ATAT
1 ATAT
995432 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:995821 original size:22 final size:22
Alignment explanation
Indices: 995777--995821 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
995767 ATTACATAAC
* *
995777 TTTAAAAAAATTATCGATCCTT
1 TTTAAAAAAAGTATCGATACTT
* *
995799 TTTATAAAAAGTATGGATACTT
1 TTTAAAAAAAGTATCGATACTT
995821 T
1 T
995822 CAATATAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (22 bp):
TTTAAAAAAAGTATCGATACTT
Found at i:995870 original size:23 final size:23
Alignment explanation
Indices: 995839--995911 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
995829 ATAAGTAAAA
*
995839 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
995862 ATATAATGTAATATGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
995885 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
995908 ATAT
1 ATAT
995912 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:995982 original size:480 final size:478
Alignment explanation
Indices: 994938--996784 Score: 3150
Period size: 484 Copynumber: 3.8 Consensus size: 478
994928 TTTTTACATG
* *
994938 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTG-TCTATATTTTTTTCACTGTGGAAAATAT
1 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTTC-ATACTTTTTTCACTGTGGAAAACAT
*
995002 TAATTTAAGGTTATCTTTTAAGTGAGTTTTAAGATATTAACTTAGTAATTATAGGCGTCTAATGA
65 TAATTTAAGG--------T---T-AGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGA
995067 TTTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATA
118 TTTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATA
995132 TTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAA
183 TTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAA
* * * *
995197 AACAATAAAATATTTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAAGTGAAAAACATGAA
248 AACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAA
995262 ACACTATT-AAAAAAATTGAAACATAAATTACATAACTTT-AAAAAAATATCGATCCTTTTTATA
313 ACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAATATCGATCCTTTTTATA
995325 AAAAGTATTA-ACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAAT
378 AAAAGTA-TAGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAAT
*
995389 GTAATAGGTAGTGTTTATATAATGTAATAGGTAGTGC
442 GTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGC
* *
995426 TTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTACATACTTTTTTCACTGTGGAAAACATT
1 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTTCATACTTTTTTCACTGTGGAAAACATT
* *
995491 AACTTAAGGTTAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTATG
66 AATTTAAGGTTAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACG
995556 TTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCT
131 TTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCT
995621 TTGGTTAATATTCG-TAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATA
196 TTGGTTAATATT-GTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATA
995685 ATTTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAA
260 A-TTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAA
* * * *
995750 AAATAAATGAAATATAAATTACATAACTTTAAAAAAATTATCGATCCTTTTTATAAAAAGTATGG
324 AAA-AATTGAAACATAAATTACATAACTTTAAAAAAAATATCGATCCTTTTTATAAAAAGTATAG
* * *
995815 ATACTTTCAATATAATAAGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTAG
388 ACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAG
*
995880 CGTTTATATAATGTAATAGGTAGTGG
453 CGTTTATATAATGTAATAGGTAGTGC
995906 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTTCATACTTTTTTCACTGTGGAAAACATT
1 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTTCATACTTTTTTCACTGTGGAAAACATT
995971 AATTTAAGGTTAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACG
66 AATTTAAGGTTAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACG
996036 TTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCT
131 TTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCT
*
996101 TTGGTTAATATTGTTAAATTTAAATTTAAATTTTAAATAATATTTTATAAAATATCAAAACAATC
196 TTGGTTAATATTG------TTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATC
*
996166 AAATAATTTTTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTAT
255 AAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTAT
*
996231 TAAAAAAAATTGAAACATAAATTATATAACTTTAAAAAAAATATCGATCCTTTTTATAAAAAGTA
320 TAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAATATCGATCCTTTTTATAAAAAGTA
* * *
996296 TAGATACTTTCAATATAATAGGTAAAAATATGATGTAATAAGTAGCGCTTATATAATATAATAGG
385 TAGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGG
996361 TAGCGTTTATATAATGTAATAGGTAGTGC
450 TAGCGTTTATATAATGTAATAGGTAGTGC
996390 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTTCATACTTTTTTCACTGTGGAAAACATT
1 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTTCATACTTTTTTCACTGTGGAAAACATT
*
996455 AATTTAAGGTTAGTTTTAATATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACG
66 AATTTAAGGTTAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACG
*
996520 TTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTTTTATCT
131 TTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCT
*
996585 TTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAA
196 TTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAA
*
996650 TTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT--AAA
261 TTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAA
* *
996713 AAATTGAAACGTAAATTACATAACTTTAAAAAAAATATCGATCTTTTTTATAAAAAGTATAGACA
326 AAATTGAAACATAAATTACATAACTTTAAAAAAAATATCGATCCTTTTTATAAAAAGTATAGACA
996778 CTTTCAA
391 CTTTCAA
996785 CATATTAAAT
Statistics
Matches: 1299, Mismatches: 46, Indels: 40
0.94 0.03 0.03
Matches are distributed among these distances:
476 249 0.19
477 60 0.05
478 113 0.09
479 26 0.02
480 320 0.25
484 348 0.27
485 65 0.05
486 50 0.04
488 67 0.05
489 1 0.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (478 bp):
TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTTCATACTTTTTTCACTGTGGAAAACATT
AATTTAAGGTTAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACG
TTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCT
TTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAA
TTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAA
AAATTGAAACATAAATTACATAACTTTAAAAAAAATATCGATCCTTTTTATAAAAAGTATAGACA
CTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGT
TTATATAATGTAATAGGTAGTGC
Found at i:996305 original size:22 final size:22
Alignment explanation
Indices: 996261--996305 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
996251 ATTATATAAC
* *
996261 TTTAAAAAAAATATCGATCCTT
1 TTTAAAAAAAATATAGATACTT
* *
996283 TTTATAAAAAGTATAGATACTT
1 TTTAAAAAAAATATAGATACTT
996305 T
1 T
996306 CAATATAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (22 bp):
TTTAAAAAAAATATAGATACTT
Found at i:996349 original size:23 final size:23
Alignment explanation
Indices: 996323--996395 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
996313 ATAGGTAAAA
* *
996323 ATATGATGTAATAAGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
996346 ATATAATATAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
996369 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
996392 ATAT
1 ATAT
996396 TGTAAAGTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:999043 original size:13 final size:13
Alignment explanation
Indices: 999010--999051 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
999000 ATCACAACTG
*
999010 AAATTATAATAAAA
1 AAATTA-AATCAAA
999024 AAATTAAATCAAA
1 AAATTAAATCAAA
*
999037 TAATTAAATCAAA
1 AAATTAAATCAAA
999050 AA
1 AA
999052 CTATTTTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 19 0.76
14 6 0.24
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (13 bp):
AAATTAAATCAAA
Found at i:1005753 original size:32 final size:32
Alignment explanation
Indices: 1005711--1005778 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 32
1005701 ATAGTATTTT
*
1005711 ACATGTTATATTATCACTTTG-GATGATGTAAC
1 ACATGATATATTATCACTTTGAG-TGATGTAAC
*
1005743 ACATGATATATTATCACTTTGAGTGATGTGAC
1 ACATGATATATTATCACTTTGAGTGATGTAAC
1005775 ACAT
1 ACAT
1005779 TACACATCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 32 0.97
33 1 0.03
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.38
Consensus pattern (32 bp):
ACATGATATATTATCACTTTGAGTGATGTAAC
Found at i:1006280 original size:13 final size:13
Alignment explanation
Indices: 1006262--1006292 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1006252 TCGATCATCA
1006262 TTATTTATATATT
1 TTATTTATATATT
1006275 TTATTTATATATT
1 TTATTTATATATT
1006288 TTATT
1 TTATT
1006293 AATTTAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTATTTATATATT
Found at i:1009737 original size:20 final size:19
Alignment explanation
Indices: 1009699--1009738 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1009689 TATATAATTA
*
1009699 ATATTAATATCATTTAAAT
1 ATATTAATATCATTGAAAT
*
1009718 ATATTAAATATTATTGAAAT
1 ATATT-AATATCATTGAAAT
1009738 A
1 A
1009739 AATACATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (19 bp):
ATATTAATATCATTGAAAT
Found at i:1009824 original size:15 final size:16
Alignment explanation
Indices: 1009792--1009825 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1009782 AATTTTGCTA
*
1009792 AAATTTTATATCAAAT
1 AAATATTATATCAAAT
1009808 AAATATTATAT-AAAT
1 AAATATTATATCAAAT
1009823 AAA
1 AAA
1009826 ACAAAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATATTATATCAAAT
Found at i:1013440 original size:17 final size:18
Alignment explanation
Indices: 1013420--1013463 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
1013410 GGTTAATTTT
*
1013420 TTTTATATATAAT-TATA
1 TTTTATATAAAATATATA
*
1013437 TTTTATA-AAAATATGTA
1 TTTTATATAAAATATATA
1013454 TTTTATATAA
1 TTTTATATAA
1013464 CATTAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 4 0.17
17 17 0.74
18 2 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
TTTTATATAAAATATATA
Found at i:1015141 original size:2 final size:2
Alignment explanation
Indices: 1015136--1015168 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1015126 CGTGCGTGTG
1015136 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1015169 GTAACGTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1017186 original size:14 final size:14
Alignment explanation
Indices: 1017167--1017195 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1017157 CAATTCAGTA
1017167 AAAACATGAACCAG
1 AAAACATGAACCAG
1017181 AAAACATGAACCAG
1 AAAACATGAACCAG
1017195 A
1 A
1017196 CAAGTAACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.21, G:0.14, T:0.07
Consensus pattern (14 bp):
AAAACATGAACCAG
Found at i:1017344 original size:2 final size:2
Alignment explanation
Indices: 1017323--1017361 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
1017313 GATATTTCAA
* * *
1017323 AT AT AC AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1017362 CGCACAAGGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:1024521 original size:12 final size:12
Alignment explanation
Indices: 1024504--1024528 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1024494 TTTTGAATAT
1024504 TCCAATTTCATC
1 TCCAATTTCATC
1024516 TCCAATTTCATC
1 TCCAATTTCATC
1024528 T
1 T
1024529 AAATGTGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (12 bp):
TCCAATTTCATC
Found at i:1029076 original size:28 final size:28
Alignment explanation
Indices: 1029042--1029097 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1029032 GCAGTGGGCG
1029042 CGTCTCCATGCATAAGATTCACGGGCCA
1 CGTCTCCATGCATAAGATTCACGGGCCA
1029070 CGTCTCCATGCATAAGATTCACGGGCCA
1 CGTCTCCATGCATAAGATTCACGGGCCA
1029098 TGCATCAGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.32, G:0.21, T:0.21
Consensus pattern (28 bp):
CGTCTCCATGCATAAGATTCACGGGCCA
Found at i:1030727 original size:54 final size:54
Alignment explanation
Indices: 1030616--1030731 Score: 126
Period size: 54 Copynumber: 2.1 Consensus size: 54
1030606 CTTCGTTGTT
* * * * *
1030616 ATCATCATCTTTGTCAAATCTTCCAGACGGAGGACGATTAATATCAACCCCGAC
1 ATCATCATCATTGTCAAATCTTCCAGACGAAGAACGATGAATATCAACCCAGAC
* * * * *
1030670 ATCATCGTCATTGTCGAATCTTTCGGACGAAGAACGATGAATGTCAACACCAG-C
1 ATCATCATCATTGTCAAATCTTCCAGACGAAGAACGATGAATATCAAC-CCAGAC
1030724 ATCATCAT
1 ATCATCAT
1030732 TGATTGAACC
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
54 47 0.94
55 3 0.06
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (54 bp):
ATCATCATCATTGTCAAATCTTCCAGACGAAGAACGATGAATATCAACCCAGAC
Found at i:1038387 original size:16 final size:16
Alignment explanation
Indices: 1038366--1038396 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1038356 AAAACATGGC
1038366 ATTTTTTTATAAAATA
1 ATTTTTTTATAAAATA
*
1038382 ATTTTTTTATTAAAT
1 ATTTTTTTATAAAAT
1038397 GTACTTGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTTTTTATAAAATA
Found at i:1039785 original size:20 final size:19
Alignment explanation
Indices: 1039748--1039786 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1039738 TCTAAACGTG
**
1039748 GATTATAATATTTGATTTT
1 GATTATAATATTAAATTTT
1039767 GATTATAACTATTAAATTTT
1 GATTATAA-TATTAAATTTT
1039787 AGTAATTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.54
Consensus pattern (19 bp):
GATTATAATATTAAATTTT
Found at i:1040760 original size:41 final size:41
Alignment explanation
Indices: 1040723--1040845 Score: 106
Period size: 41 Copynumber: 3.0 Consensus size: 41
1040713 CTATCGCATT
* * * *
1040723 GCGATTTTCCTAATTCGTAATGCGAATACGTAAATCGCAAC
1 GCGAATTTCCAAAATCGCAATGCGAATACGTAAATCGCAAC
** * *
1040764 GCGAATTTGGAAAATCGCAATGCGATTACGTAAATCGCAAT
1 GCGAATTTCCAAAATCGCAATGCGAATACGTAAATCGCAAC
* * ** *
1040805 GC-AAATACGTAAATCGCAATGCGAAT-CTGTAAATCACAAC
1 GCGAATTTCCAAAATCGCAATGCGAATAC-GTAAATCGCAAC
1040845 G
1 G
1040846 AGATTCTGAC
Statistics
Matches: 66, Mismatches: 15, Indels: 3
0.79 0.18 0.04
Matches are distributed among these distances:
39 1 0.02
40 30 0.45
41 35 0.53
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (41 bp):
GCGAATTTCCAAAATCGCAATGCGAATACGTAAATCGCAAC
Found at i:1040769 original size:20 final size:20
Alignment explanation
Indices: 1040741--1040839 Score: 119
Period size: 20 Copynumber: 4.9 Consensus size: 20
1040731 CCTAATTCGT
1040741 AATGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
* ** *
1040761 AACGCGAATTTGGAAAATCGC
1 AATGCGAA-TACGTAAATCGC
*
1040782 AATGCGATTACGTAAATCGC
1 AATGCGAATACGTAAATCGC
*
1040802 AATGCAAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
1040822 AATGCGAAT-CTGTAAATC
1 AATGCGAATAC-GTAAATC
1040840 ACAACGAGAT
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
19 1 0.02
20 49 0.75
21 15 0.23
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.22
Consensus pattern (20 bp):
AATGCGAATACGTAAATCGC
Found at i:1041433 original size:24 final size:24
Alignment explanation
Indices: 1041406--1041459 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1041396 GTATTCGAAA
1041406 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1041430 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1041454 TTTGAT
1 TTTGAT
1041460 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1043900 original size:20 final size:21
Alignment explanation
Indices: 1043875--1043984 Score: 167
Period size: 20 Copynumber: 5.5 Consensus size: 21
1043865 TTTATTTGAA
1043875 TATCGCAACGC-GAATATGAC
1 TATCGCAACGCGGAATATGAC
*
1043895 TATCGCAACACGGAA-ATGAC
1 TATCGCAACGCGGAATATGAC
*
1043915 TATCGCAACGCGGAAT-TAAC
1 TATCGCAACGCGGAATATGAC
1043935 TATCGCAACGCGGAAT-TGAC
1 TATCGCAACGCGGAATATGAC
1043955 TATCGCAACGCGGAA-ATGAC
1 TATCGCAACGCGGAATATGAC
1043975 TATCGCAACG
1 TATCGCAACG
1043985 AGTGAATCGC
Statistics
Matches: 83, Mismatches: 4, Indels: 6
0.89 0.04 0.06
Matches are distributed among these distances:
20 80 0.96
21 3 0.04
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (21 bp):
TATCGCAACGCGGAATATGAC
Found at i:1044215 original size:14 final size:14
Alignment explanation
Indices: 1044196--1044232 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1044186 CATCAATTAA
1044196 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1044210 ACAAATCATCTTTT
1 ACAAATCAACATTT
1044224 ACAAATCAA
1 ACAAATCAA
1044233 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1045685 original size:42 final size:42
Alignment explanation
Indices: 1045606--1045698 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
1045596 CCTCTTCAAC
* * *
1045606 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
1045648 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
1045690 GATGACAGG
1 GATGACAGG
1045699 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:1046235 original size:33 final size:33
Alignment explanation
Indices: 1046175--1046258 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 33
1046165 TCTGAAACTT
** * *
1046175 AAAATCGCAACGCGAAAATGACTATCGCAACGAG
1 AAAATCGCAACGCG-AAATGAAAATCGCAACAAC
* *
1046209 AGAATCGCAATGCGAAATGAAAATCGCAACAAC
1 AAAATCGCAACGCGAAATGAAAATCGCAACAAC
1046242 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
1046259 ATGACTATCG
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
33 30 0.71
34 12 0.29
ACGTcount: A:0.48, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACAAC
Found at i:1046270 original size:20 final size:20
Alignment explanation
Indices: 1046245--1046351 Score: 151
Period size: 20 Copynumber: 5.3 Consensus size: 20
1046235 CAACAACAAA
* **
1046245 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAATTTGACT
**
1046265 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAATTTGACT
*
1046285 ATCGCAATGCGAGTTTGACT
1 ATCGCAATGCGAATTTGACT
1046305 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAATTTGACT
*
1046325 ATCGCAATACGAATTTGACT
1 ATCGCAATGCGAATTTGACT
1046345 ATCGCAA
1 ATCGCAA
1046352 CGAGAGAATC
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 81 1.00
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGAATTTGACT
Found at i:1046423 original size:20 final size:20
Alignment explanation
Indices: 1046398--1046501 Score: 121
Period size: 20 Copynumber: 5.5 Consensus size: 20
1046388 GATTCTTTCG
**
1046398 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1046418 TTGCGATAGTCATTTTCGGA
1 TTGCGATAGTCATTTTCGCA
*
1046438 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
1046452 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
1046472 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1046492 TTGCGATAGT
1 TTGCGATAGT
1046502 AAACTATTTT
Statistics
Matches: 71, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
14 7 0.10
16 6 0.08
18 5 0.07
20 53 0.75
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1046453 original size:54 final size:54
Alignment explanation
Indices: 1046360--1046498 Score: 199
Period size: 54 Copynumber: 2.6 Consensus size: 54
1046350 AACGAGAGAA
* ** *
1046360 TCGCAATGCGATTTTCA-TTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAAT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAAT
* **
1046413 TCGCATTGCGATAGTCATTTTCGGATTGCGATTCTCTCGTTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAAT
*
1046467 TTGCATTGCGATAGTCATTTTCGCATTGCGAT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGAT
1046499 AGTAAACTAT
Statistics
Matches: 76, Mismatches: 9, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
53 14 0.18
54 62 0.82
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (54 bp):
TCGCATTGCGATAGTCATTTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAAT
Found at i:1048440 original size:20 final size:20
Alignment explanation
Indices: 1048382--1048451 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
1048372 GAAACTTTAA
* **
1048382 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
1048402 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
1048422 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1048442 ATCGCAACGC
1 ATCGCAACGC
1048452 AAGAATCGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1048490 original size:33 final size:33
Alignment explanation
Indices: 1048381--1048494 Score: 95
Period size: 33 Copynumber: 3.2 Consensus size: 33
1048371 TGAAACTTTA
* *
1048381 AATCGCAACACGAAAATGAAAATCGCAACACGAAAATG
1 AATCGCAACGCG-AAATGAAAATCGC-A-ACG-ACA-G
* **
1048419 ACTATCGCAACGCGAATTTGACTATCGCAACG-CAAG
1 A--ATCGCAACGCGAA-ATGAAAATCGCAACGAC-AG
1048455 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1048488 AATCGCA
1 AATCGCA
1048495 TTGCGATAGT
Statistics
Matches: 63, Mismatches: 8, Indels: 15
0.73 0.09 0.17
Matches are distributed among these distances:
33 21 0.33
34 14 0.22
36 2 0.03
37 1 0.02
38 4 0.06
39 3 0.05
40 18 0.29
ACGTcount: A:0.44, C:0.25, G:0.18, T:0.13
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:1049065 original size:20 final size:19
Alignment explanation
Indices: 1049037--1049110 Score: 80
Period size: 20 Copynumber: 3.7 Consensus size: 19
1049027 GACGCTATGT
1049037 AAATCGCATTGCGATAGTC
1 AAATCGCATTGCGATAGTC
1049056 AAATTCGCATTGCGATTTACGT-
1 AAA-TCGCATTGCGA--TA-GTC
1049078 -AATCGCATTGCGATAGTC
1 AAATCGCATTGCGATAGTC
*
1049096 AGAATCGCGTTGCGA
1 A-AATCGCATTGCGA
1049111 ATCTGGAAAC
Statistics
Matches: 47, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
17 2 0.04
18 2 0.04
19 3 0.06
20 34 0.72
21 2 0.04
22 2 0.04
23 2 0.04
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (19 bp):
AAATCGCATTGCGATAGTC
Found at i:1054696 original size:2 final size:2
Alignment explanation
Indices: 1054691--1054717 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1054681 GGATATATGC
1054691 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1054718 ATTTTATTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1057346 original size:22 final size:21
Alignment explanation
Indices: 1057321--1057369 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
1057311 TACTAAACAT
1057321 ATAATTGTAAATTAATTAAAAA
1 ATAATTGTAAATTAATT-AAAA
* *
1057343 ATAAAATGTAATTTAATTAAAA
1 AT-AATTGTAAATTAATTAAAA
1057365 ATAAT
1 ATAAT
1057370 ATTTATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.09
22 8 0.35
23 13 0.57
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (21 bp):
ATAATTGTAAATTAATTAAAA
Found at i:1064043 original size:15 final size:15
Alignment explanation
Indices: 1064023--1064074 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
1064013 ATATTTAGCT
* *
1064023 GGGCGGACGGATGTG
1 GGGCGGGCGGATGCG
*
1064038 GGGCGGGCGGATGCA
1 GGGCGGGCGGATGCG
*
1064053 GGGCGGGCAGATGCG
1 GGGCGGGCGGATGCG
1064068 GGGCGGG
1 GGGCGGG
1064075 TAATGTCTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.12, C:0.17, G:0.63, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:1067031 original size:2 final size:2
Alignment explanation
Indices: 1067024--1067076 Score: 56
Period size: 2 Copynumber: 27.5 Consensus size: 2
1067014 TCGGGCCGGG
* * * *
1067024 TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1067064 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1067077 TAAATTAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1069814 original size:428 final size:428
Alignment explanation
Indices: 1069017--1069872 Score: 1658
Period size: 428 Copynumber: 2.0 Consensus size: 428
1069007 ATGAATATGA
1069017 AAATATGAGACTTGGACAGTGCATCTAGCAAAGGAAAGAAAATGAAAGCCATTTTTAATGTTTTA
1 AAATATGAGACTTGGACAGTGCATCTAGCAAAGGAAAGAAAATGAAAGCCATTTTTAATGTTTTA
1069082 ATGAAATAAATGAAATGCACTAAGAAGCTATGTTAACTCAAAATAGGGTTTTGAGTGAGTGTCTA
66 ATGAAATAAATGAAATGCACTAAGAAGCTATGTTAACTCAAAATAGGGTTTTGAGTGAGTGTCTA
1069147 TTTCCTTGGAAAATAGGATATGAGTATCAGACAGGGATAAGGAAAAAGAAAAGGTCGAAGCAACT
131 TTTCCTTGGAAAATAGGATATGAGTATCAGACAGGGATAAGGAAAAAGAAAAGGTCGAAGCAACT
*
1069212 TAACTTGGGGAAGAGTGCCTAAAATTGGTTCATAACATATTTTGACTTCTCTACCTTGACTACCA
196 TAACTTGGGGAAGAGTACCTAAAATTGGTTCATAACATATTTTGACTTCTCTACCTTGACTACCA
1069277 ATTTCACAAAACTGGGTAGCACACCTACATATAATCAATGAGTAATTGTTTCTAAAAAAGATTCA
261 ATTTCACAAAACTGGGTAGCACACCTACATATAATCAATGAGTAATTGTTTCTAAAAAAGATTCA
*
1069342 GATAGGTGTTGTGATGAAAACAGAAATATTGTGATTTGTTAAAAAGTGTTAGAAATCAATTTCTT
326 GAAAGGTGTTGTGATGAAAACAGAAATATTGTGATTTGTTAAAAAGTGTTAGAAATCAATTTCTT
1069407 TACTAAAAAGCTATTTGCGCCAAATCCAATCAGCATGG
391 TACTAAAAAGCTATTTGCGCCAAATCCAATCAGCATGG
1069445 AAATATGAGACTTGGACAGTGCATCTAGCAAAGGAAAGAAAATGAAAGCCATTTTTAATGTTTTA
1 AAATATGAGACTTGGACAGTGCATCTAGCAAAGGAAAGAAAATGAAAGCCATTTTTAATGTTTTA
*
1069510 ATGAAATAAATGAAATGCACTAGGAAGCTATGTTAACTCAAAATAGGGTTTTGAGTGAGTGTCTA
66 ATGAAATAAATGAAATGCACTAAGAAGCTATGTTAACTCAAAATAGGGTTTTGAGTGAGTGTCTA
1069575 TTTCCTTGGAAAATAGGATATGAGTATCAGACAGGGATAAGGAAAAAGAAAAGGTCGAAGCAACT
131 TTTCCTTGGAAAATAGGATATGAGTATCAGACAGGGATAAGGAAAAAGAAAAGGTCGAAGCAACT
*
1069640 TAACTTGGGGAAGAGTACCTAAAATTGGTTCATGACATATTTTGACTTCTCTACCTTGACTACCA
196 TAACTTGGGGAAGAGTACCTAAAATTGGTTCATAACATATTTTGACTTCTCTACCTTGACTACCA
*
1069705 ATTTCACAAAACTGGGTAGCACACCTACATATATTCAATGAGTAATTGTTTCTAAAAAAGATTCA
261 ATTTCACAAAACTGGGTAGCACACCTACATATAATCAATGAGTAATTGTTTCTAAAAAAGATTCA
1069770 GAAAGGTGTTGTGATGAAAACAGAAATATTGTGATTTGTTAAAAAGTGTTAGAAATCAATTTCTT
326 GAAAGGTGTTGTGATGAAAACAGAAATATTGTGATTTGTTAAAAAGTGTTAGAAATCAATTTCTT
*
1069835 TACTCAAAAGCTATTTGCGCCAAATCCAATCAGCATGG
391 TACTAAAAAGCTATTTGCGCCAAATCCAATCAGCATGG
1069873 GTTATTCAAA
Statistics
Matches: 422, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
428 422 1.00
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (428 bp):
AAATATGAGACTTGGACAGTGCATCTAGCAAAGGAAAGAAAATGAAAGCCATTTTTAATGTTTTA
ATGAAATAAATGAAATGCACTAAGAAGCTATGTTAACTCAAAATAGGGTTTTGAGTGAGTGTCTA
TTTCCTTGGAAAATAGGATATGAGTATCAGACAGGGATAAGGAAAAAGAAAAGGTCGAAGCAACT
TAACTTGGGGAAGAGTACCTAAAATTGGTTCATAACATATTTTGACTTCTCTACCTTGACTACCA
ATTTCACAAAACTGGGTAGCACACCTACATATAATCAATGAGTAATTGTTTCTAAAAAAGATTCA
GAAAGGTGTTGTGATGAAAACAGAAATATTGTGATTTGTTAAAAAGTGTTAGAAATCAATTTCTT
TACTAAAAAGCTATTTGCGCCAAATCCAATCAGCATGG
Found at i:1070815 original size:39 final size:39
Alignment explanation
Indices: 1070755--1070850 Score: 113
Period size: 39 Copynumber: 2.5 Consensus size: 39
1070745 TCATCTGATT
* * *
1070755 TTCTTTTTGGCCCTGATAAATTACAGGAACCTTCAGATA
1 TTCTCTTTGCCCCTGAGAAATTACAGGAACCTTCAGATA
** * *
1070794 TTCTCTTTGTCCCC-GAGAAATTACAGGAATTTTCATATT
1 TTCTCTTTG-CCCCTGAGAAATTACAGGAACCTTCAGATA
1070833 TTCTCTTTGCCCCTGAGA
1 TTCTCTTTGCCCCTGAGA
1070851 CATCAGAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
38 4 0.08
39 41 0.85
40 3 0.06
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.39
Consensus pattern (39 bp):
TTCTCTTTGCCCCTGAGAAATTACAGGAACCTTCAGATA
Found at i:1070873 original size:39 final size:39
Alignment explanation
Indices: 1070830--1070919 Score: 108
Period size: 39 Copynumber: 2.3 Consensus size: 39
1070820 GAATTTTCAT
* * *
1070830 ATTTTCTCTTTGCCCCTGAGACATCAGAATAATCTTCGG
1 ATTTTCTCTTTGCCCCTAAAACATCAGAAGAATCTTCGG
* * * * *
1070869 ATTTTCGCTTTGTCCCTAAAATATCATAAGAATCTTCTG
1 ATTTTCTCTTTGCCCCTAAAACATCAGAAGAATCTTCGG
1070908 ATTTTCTCTTTG
1 ATTTTCTCTTTG
1070920 GTACTGAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.42
Consensus pattern (39 bp):
ATTTTCTCTTTGCCCCTAAAACATCAGAAGAATCTTCGG
Found at i:1070930 original size:39 final size:39
Alignment explanation
Indices: 1070860--1070947 Score: 97
Period size: 39 Copynumber: 2.3 Consensus size: 39
1070850 ACATCAGAAT
* * * *
1070860 AATCTTCGGATTTTCGCTTTGTCCCTAAAATATCATAAG
1 AATCTTCTGATTTTCGCTTTGTCACTAAAATAGCACAAG
* *
1070899 AATCTTCTGATTTTCTCTTTGGT-ACTGAAATAGCACAAG
1 AATCTTCTGATTTTCGCTTT-GTCACTAAAATAGCACAAG
*
1070938 AATTTTCTGA
1 AATCTTCTGA
1070948 ACTTTTCTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 39 0.95
40 2 0.05
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (39 bp):
AATCTTCTGATTTTCGCTTTGTCACTAAAATAGCACAAG
Found at i:1078864 original size:20 final size:20
Alignment explanation
Indices: 1078839--1078881 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1078829 TCTAAAAGCC
*
1078839 CATTTAGGATCATATAGATG
1 CATTTAGGAGCATATAGATG
*
1078859 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
1078879 CAT
1 CAT
1078882 GTGGTGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:1087629 original size:19 final size:19
Alignment explanation
Indices: 1087605--1087642 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1087595 TTGCAAAGAT
1087605 GGTGTATGATTAATACACA
1 GGTGTATGATTAATACACA
*
1087624 GGTGTATGATTACTACACA
1 GGTGTATGATTAATACACA
1087643 TCCGATAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (19 bp):
GGTGTATGATTAATACACA
Found at i:1095880 original size:29 final size:29
Alignment explanation
Indices: 1095833--1095897 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
1095823 ATTGATTATT
*
1095833 TTTAATTTTATATAATTAT-ATATTTAATC
1 TTTAATTTTAAATAATTATCA-ATTTAATC
* *
1095862 TTTACTTTTAAATATTTATCAATTTAAT-
1 TTTAATTTTAAATAATTATCAATTTAATC
*
1095890 TCTAATTT
1 TTTAATTT
1095898 ATTATAATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 6 0.20
29 23 0.77
30 1 0.03
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (29 bp):
TTTAATTTTAAATAATTATCAATTTAATC
Found at i:1101898 original size:42 final size:42
Alignment explanation
Indices: 1101839--1101950 Score: 224
Period size: 42 Copynumber: 2.7 Consensus size: 42
1101829 CCCGAATTCT
1101839 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCC
1101881 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCC
1101923 CGTGTTTGTTTCACGTAATTCGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCC
1101951 AGAATGTAAT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.45
Consensus pattern (42 bp):
CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCC
Found at i:1102187 original size:20 final size:20
Alignment explanation
Indices: 1102142--1102201 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
1102132 TAATTATTAA
* *
1102142 AATATTTAAAATATATTTATT
1 AATATTTATAATA-ATATATT
1102163 AATATTTATAATAATATATT
1 AATATTTATAATAATATATT
* * *
1102183 TATATTTTTAATATTATAT
1 AATATTTATAATAATATAT
1102202 AAAATAATCA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 22 0.65
21 12 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AATATTTATAATAATATATT
Found at i:1102310 original size:29 final size:29
Alignment explanation
Indices: 1102152--1102313 Score: 122
Period size: 29 Copynumber: 5.6 Consensus size: 29
1102142 AATATTTAAA
*
1102152 ATATATTTATTAATATTTATAATAATATATTT
1 ATATATTTAATAATA--TATAATAAT-TATTT
* * * **
1102184 ATATTTTTAATATTATATAA-AATAATCA
1 ATATATTTAATAATATATAATAATTATTT
*
1102212 AT-TATATT-ATAA-ATATAAGATATTATATT
1 ATATAT-TTAATAATATATAATA-ATTAT-TT
* *
1102241 TTAT-TTTAATAATATATAATAATTTTTT
1 ATATATTTAATAATATATAATAATTATTT
1102269 ATATATTTAATAATGA-ATAAT-ATTATTT
1 ATATATTTAATAAT-ATATAATAATTATTT
1102297 ATATATTTCAATAATAT
1 ATATATTT-AATAATAT
1102314 TTTAGTAAAG
Statistics
Matches: 103, Mismatches: 16, Indels: 25
0.72 0.11 0.17
Matches are distributed among these distances:
26 6 0.06
27 6 0.06
28 32 0.31
29 33 0.32
30 14 0.14
32 12 0.12
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (29 bp):
ATATATTTAATAATATATAATAATTATTT
Found at i:1102535 original size:20 final size:20
Alignment explanation
Indices: 1102477--1102526 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
1102467 TTTCCAGATG
1102477 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
1102497 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
1102517 TTTTCCAGAA
1 TTTTCCAGAA
1102527 TTCAAATTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:1102545 original size:15 final size:15
Alignment explanation
Indices: 1102509--1102590 Score: 121
Period size: 15 Copynumber: 5.5 Consensus size: 15
1102499 TTCCAGAAAT
**
1102509 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
1102524 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
1102538 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
1102553 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
1102568 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
1102583 GTAATTCA
1 GTAATTCA
1102591 TTTTCTGTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
14 12 0.20
15 48 0.80
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:1102561 original size:30 final size:30
Alignment explanation
Indices: 1102509--1102590 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
1102499 TTCCAGAAAT
1102509 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
1102538 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
1102568 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
1102591 TTTTCTGTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:1102585 original size:45 final size:44
Alignment explanation
Indices: 1102509--1102595 Score: 147
Period size: 45 Copynumber: 2.0 Consensus size: 44
1102499 TTCCAGAAAT
**
1102509 GTAATTCATTTTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
1 GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
1102553 GTAATTCAAATTCCAGTAATTCAAATTCCAGTAATTCATTTTC
1 GTAATTCAAATTCCAG-AATTCAAATTCCAGTAATTCATTTTC
1102596 TGTAAAACCA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (44 bp):
GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
Done.