Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008620.1 Hibiscus syriacus cultivar Beakdansim tig00111582_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: 13158977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 64
Found at i:1757428 original size:43 final size:43
Alignment explanation
Indices: 1757371--1757470 Score: 139
Period size: 43 Copynumber: 2.3 Consensus size: 43
1757361 TTTGTTAACC
*
1757371 AAAAACGCCACAATAGGTAACGATATATAGAGGCGTTTAT-TT
1 AAAAACGCCGCAATAGGTAACGATATATAGAGGCGTTTATCTT
* * * *
1757413 AACAAACGCCGCAATAGGTATCGATATTTAGCGGCGTTTGTCTT
1 AA-AAACGCCGCAATAGGTAACGATATATAGAGGCGTTTATCTT
1757457 AAAAACGCCGCAAT
1 AAAAACGCCGCAAT
1757471 TAGTGTTAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
42 2 0.04
43 45 0.88
44 4 0.08
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (43 bp):
AAAAACGCCGCAATAGGTAACGATATATAGAGGCGTTTATCTT
Found at i:1757483 original size:43 final size:43
Alignment explanation
Indices: 1757373--1757494 Score: 133
Period size: 43 Copynumber: 2.8 Consensus size: 43
1757363 TGTTAACCAA
* * * * *
1757373 AAACGCCACAATAGGTAACGATATATAGAGGCGTTTATTTAAC
1 AAACGCCGCAATAGGTATCAATATTTAGCGGCGTTTATTTAAC
* *
1757416 AAACGCCGCAATAGGTATCGATATTTAGCGGCGTTTGTCTTAA-
1 AAACGCCGCAATAGGTATCAATATTTAGCGGCGTTTAT-TTAAC
1757459 AAACGCCGCAATTAGTGT-T-AATATTTAGCGGCGTTT
1 AAACGCCGCAA-TAG-GTATCAATATTTAGCGGCGTTT
1757495 TTATCACAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
43 60 0.86
44 8 0.11
45 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (43 bp):
AAACGCCGCAATAGGTATCAATATTTAGCGGCGTTTATTTAAC
Found at i:1757506 original size:43 final size:43
Alignment explanation
Indices: 1757392--1757539 Score: 122
Period size: 43 Copynumber: 3.4 Consensus size: 43
1757382 AATAGGTAAC
* * *
1757392 GATATATAGAGGCGTTTATT-TAACAAACGCCGCAA-TAG-GTAT
1 GATATTTAGCGGCGTTT-TTATCACAAACGCCGCAATTAGTGT-T
* * * *
1757434 CGATATTTAGCGGCGTTTGTCTTAAAAACGCCGCAATTAGTGTT
1 -GATATTTAGCGGCGTTTTTATCACAAACGCCGCAATTAGTGTT
* * * * *
1757478 AATATTTAGCGGCGTTTTTATCACAAACGTCACAATAAATGTT
1 GATATTTAGCGGCGTTTTTATCACAAACGCCGCAATTAGTGTT
* *
1757521 GATATTTCGCGGCATTTTT
1 GATATTTAGCGGCGTTTTT
1757540 TTGTGAAAAC
Statistics
Matches: 85, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
42 1 0.01
43 78 0.92
44 4 0.05
45 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (43 bp):
GATATTTAGCGGCGTTTTTATCACAAACGCCGCAATTAGTGTT
Found at i:1757594 original size:44 final size:44
Alignment explanation
Indices: 1757546--1757686 Score: 140
Period size: 44 Copynumber: 3.2 Consensus size: 44
1757536 TTTTTTGTGA
* * * * *
1757546 AAACGGCGCAATAGGTCTGGTATTTAACGGCGTTTTTAGGGTAC
1 AAACGCCGCGATAGGTCTGGAATATAACGGCGTTTTTAGGATAC
* * *
1757590 AAACGCCGCGATAGGACTGGAATATAGCGTCGTTTTTAGGATAC
1 AAACGCCGCGATAGGTCTGGAATATAACGGCGTTTTTAGGATAC
* * * * **
1757634 AAACACCGCGATAGGTCT-TATATATAGCGGCATTTTTTTGATAC
1 AAACGCCGCGATAGGTCTGGA-ATATAACGGCGTTTTTAGGATAC
1757678 AAACGCCGC
1 AAACGCCGC
1757687 TAAATAACAC
Statistics
Matches: 80, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
43 1 0.01
44 79 0.99
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (44 bp):
AAACGCCGCGATAGGTCTGGAATATAACGGCGTTTTTAGGATAC
Found at i:1761356 original size:13 final size:13
Alignment explanation
Indices: 1761338--1761362 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1761328 TCAAACCAAA
1761338 GGAGAAATAAAGC
1 GGAGAAATAAAGC
1761351 GGAGAAATAAAG
1 GGAGAAATAAAG
1761363 AAATAAGAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.32, T:0.08
Consensus pattern (13 bp):
GGAGAAATAAAGC
Found at i:1761861 original size:39 final size:40
Alignment explanation
Indices: 1761791--1761885 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 40
1761781 TCCAAATATT
*
1761791 TTGCGGCGTTTTTGTTTAAAAACGACACTAAAGTA-ACACTA
1 TTGCGGCG--TTTGTGTAAAAACGACACTAAAGTACACACTA
* * * *
1761832 TTGCGGCGTTTGTGTAAAAACGCCGCTAAATTACTACTCTA
1 TTGCGGCGTTTGTGTAAAAACGACACTAAAGTAC-ACACTA
1761873 TTGCGGCGTTTGT
1 TTGCGGCGTTTGT
1761886 TGAAAAAATG
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
39 21 0.45
41 26 0.55
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (40 bp):
TTGCGGCGTTTGTGTAAAAACGACACTAAAGTACACACTA
Found at i:1761874 original size:41 final size:40
Alignment explanation
Indices: 1761801--1761987 Score: 130
Period size: 41 Copynumber: 4.5 Consensus size: 40
1761791 TTGCGGCGTT
* * * * * *
1761801 TTTGTTTAAAAACGACACTAAAGTA-ACACTATTGCGGCG
1 TTTGTGTAAAAACGCCGCTAAATTACACTCTATTACGGCG
*
1761840 TTTGTGTAAAAACGCCGCTAAATTACTACTCTATTGCGGCG
1 TTTGTGTAAAAACGCCGCTAAATTAC-ACTCTATTACGGCG
* * *
1761881 TTTGTTGAAAAAATGCCACTATAA--ACATCTCTATTACGGCG
1 TTTG-TGTAAAAACGCCGCTA-AATTACA-CTCTATTACGGCG
* * * *
1761922 TTT-TAGCTATAAATGCTGCTAAATTACCACTCTATTACGGCT
1 TTTGT-G-TAAAAACGCCGCTAAATTA-CACTCTATTACGGCG
*
1761964 TTTGTTTAAAAAAACGCCGCTAAA
1 TTTGTGT--AAAAACGCCGCTAAA
1761988 GTATCATTTT
Statistics
Matches: 117, Mismatches: 18, Indels: 22
0.75 0.11 0.14
Matches are distributed among these distances:
39 22 0.19
40 4 0.03
41 45 0.38
42 29 0.25
43 17 0.15
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32
Consensus pattern (40 bp):
TTTGTGTAAAAACGCCGCTAAATTACACTCTATTACGGCG
Found at i:1770080 original size:37 final size:37
Alignment explanation
Indices: 1769926--1770135 Score: 143
Period size: 37 Copynumber: 5.8 Consensus size: 37
1769916 ATTTTTTTAG
* * * *
1769926 TATATATTATATATAGTTTGAAATCA-TTTTAAAAATA
1 TATATATTATATA-ATTTTAAAAACATTTTTGAAAATA
* *
1769963 TTTATATTATATAGTTTATGAAAAACA-TTTTGAAAATA
1 TATATATTATATAATTT-T-AAAAACATTTTTGAAAATA
** * *
1770001 TA-ATA-TATAGT--TTTTAAAATTA-GTTTGAAAGTA
1 TATATATTATA-TAATTTTAAAAACATTTTTGAAAATA
* *
1770034 -A-ATAATATATAATTTTTAAAACATTTTTGAAAATA
1 TATATATTATATAATTTTAAAAACATTTTTGAAAATA
* * * *
1770069 TATATATTATATAGTTTAAAAAACATTTTGGGAAA-A
1 TATATATTATATAATTTTAAAAACATTTTTGAAAATA
* *
1770105 TATATATTATATAATTTGTGAAAATATTTTT
1 TATATATTATATAATTT-TAAAAACATTTTT
1770136 ATATATTATT
Statistics
Matches: 136, Mismatches: 27, Indels: 20
0.74 0.15 0.11
Matches are distributed among these distances:
32 5 0.04
33 18 0.13
34 9 0.07
35 12 0.09
36 24 0.18
37 52 0.38
38 16 0.12
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (37 bp):
TATATATTATATAATTTTAAAAACATTTTTGAAAATA
Found at i:1770127 original size:24 final size:23
Alignment explanation
Indices: 1770095--1770140 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
1770085 TAAAAAACAT
1770095 TTTGGGAAAATATATATTATATAA
1 TTTGGGAAAATAT-TATTATATAA
* *
1770119 TTTGTGAAAATATTTTTATATA
1 TTTGGGAAAATATTATTATATA
1770141 TTATTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (23 bp):
TTTGGGAAAATATTATTATATAA
Found at i:1771471 original size:12 final size:13
Alignment explanation
Indices: 1771454--1771494 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
1771444 TATATACATT
1771454 TTTTATTAT-TTA
1 TTTTATTATCTTA
1771466 TTTTATT-TCTTA
1 TTTTATTATCTTA
1771478 TTATTATTATCTT-
1 TT-TTATTATCTTA
1771491 TTTT
1 TTTT
1771495 CTAATATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 1 0.04
12 14 0.54
13 7 0.27
14 4 0.15
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTATTATCTTA
Found at i:1771545 original size:4 final size:4
Alignment explanation
Indices: 1771538--1771609 Score: 56
Period size: 4 Copynumber: 17.0 Consensus size: 4
1771528 ACCCTTTTTC
* * * *
1771538 ATTT ATTTT ATTT -TTAT TTTT CTTT ATTT ATTT CTTT ATTT ATCTT TTTT
1 ATTT A-TTT ATTT ATT-T ATTT ATTT ATTT ATTT ATTT ATTT AT-TT ATTT
1771588 ATTT ATTGTT ATTT ATTT ATTT
1 ATTT A-T-TT ATTT ATTT ATTT
1771610 TTTTCTTCTT
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
3 2 0.04
4 40 0.71
5 11 0.20
6 3 0.05
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.76
Consensus pattern (4 bp):
ATTT
Found at i:1771549 original size:5 final size:5
Alignment explanation
Indices: 1771539--1771642 Score: 58
Period size: 5 Copynumber: 20.4 Consensus size: 5
1771529 CCCTTTTTCA
* *
1771539 TTTAT TTTATT TTTAT TTT-T CTTTA- TTTAT TTCTTT ATTTAT CTT-T
1 TTTAT TTTA-T TTTAT TTTAT -TTTAT TTTAT TT-TAT -TTTAT TTTAT
* *
1771585 TTTA- TTTAT TGTTA- TTTA- TTTAT TTTTT TCTTCTT CTTTAT TTTAT
1 TTTAT TTTAT T-TTAT TTTAT TTTAT TTTAT T-TT-AT -TTTAT TTTAT
1771631 TTTAT TTTAT TT
1 TTTAT TTTAT TT
1771643 ATGTATATTC
Statistics
Matches: 80, Mismatches: 6, Indels: 26
0.71 0.05 0.23
Matches are distributed among these distances:
4 19 0.24
5 39 0.49
6 15 0.19
7 6 0.08
8 1 0.01
ACGTcount: A:0.15, C:0.06, G:0.01, T:0.78
Consensus pattern (5 bp):
TTTAT
Found at i:1771555 original size:76 final size:81
Alignment explanation
Indices: 1771399--1771555 Score: 200
Period size: 82 Copynumber: 2.0 Consensus size: 81
1771389 TTATTTTCCC
* * ** *
1771399 TTATTATGTTTTTTCCTAATATTTTATTTTATGTATTTATATATATATATACATTTTTTATTATT
1 TTATTATCTTTTTTCCTAATATTTTATTTTATG-ATTGATATATATATATACACCTTTTATCATT
1771464 TATTTTATTTCTTATTA
65 TATTTTATTTCTTATTA
*
1771481 TTATTATCTTTTTT-CTAATATTTTGTTTGTATG-TTGATATATATAT-TAC-CCTTTT-TCATT
1 TTATTATCTTTTTTCCTAATATTTTATTT-TATGATTGATATATATATATACACCTTTTATCATT
1771541 TATTTTATTT-TTATT
65 TATTTTATTTCTTATT
1771556 TTTCTTTATT
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
76 5 0.07
77 14 0.21
78 4 0.06
79 3 0.04
80 12 0.18
81 13 0.19
82 17 0.25
ACGTcount: A:0.24, C:0.06, G:0.04, T:0.66
Consensus pattern (81 bp):
TTATTATCTTTTTTCCTAATATTTTATTTTATGATTGATATATATATATACACCTTTTATCATTT
ATTTTATTTCTTATTA
Found at i:1771557 original size:22 final size:22
Alignment explanation
Indices: 1771546--1771637 Score: 68
Period size: 23 Copynumber: 4.2 Consensus size: 22
1771536 TCATTTATTT
*
1771546 TATTT-TTATTTTTCTTTA-TT
1 TATTTCTTATTTTTATTTATTT
*
1771566 TATTTCTT-TATTTATCTT-TTT
1 TATTTCTTATTTTTAT-TTATTT
* *
1771587 TATTTATTGTTATTTATTTATTT
1 TATTTCTTATT-TTTATTTATTT
*
1771610 T-TTTCTTCTTCTTTATTTTATTT
1 TATTTCTTATT-TTTA-TTTATTT
1771633 TATTT
1 TATTT
1771638 TATTTATGTA
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
20 10 0.18
21 13 0.23
22 14 0.25
23 17 0.30
24 3 0.05
ACGTcount: A:0.15, C:0.07, G:0.01, T:0.77
Consensus pattern (22 bp):
TATTTCTTATTTTTATTTATTT
Found at i:1771755 original size:25 final size:24
Alignment explanation
Indices: 1771724--1771787 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 24
1771714 TTGCTATATC
1771724 TTTTTATTATTTGTTTTTTGCTTTA
1 TTTTTATTATTTGTTTTTT-CTTTA
*
1771749 TTTTTA-T-TTT-TATTTTCTTTA
1 TTTTTATTATTTGTTTTTTCTTTA
*
1771770 TTTTATTTTATTTGTTTT
1 TTTT-TATTATTTGTTTT
1771788 ATTCATTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
21 9 0.28
22 6 0.19
23 4 0.12
24 4 0.12
25 9 0.28
ACGTcount: A:0.12, C:0.03, G:0.05, T:0.80
Consensus pattern (24 bp):
TTTTTATTATTTGTTTTTTCTTTA
Found at i:1771775 original size:14 final size:14
Alignment explanation
Indices: 1771751--1771790 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1771741 TTGCTTTATT
*
1771751 TTTATTTTTATTTTC
1 TTTA-TTTTATTTTA
1771766 TTTATTTTATTTTA
1 TTTATTTTATTTTA
*
1771780 TTTGTTTTATT
1 TTTATTTTATT
1771791 CATTTTCACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 19 0.83
15 4 0.17
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.80
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:1772848 original size:19 final size:19
Alignment explanation
Indices: 1772824--1772863 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1772814 GATTATAATC
1772824 TTTATCTCATTAACTTTTT
1 TTTATCTCATTAACTTTTT
1772843 TTTATCTCATTAACTTTTT
1 TTTATCTCATTAACTTTTT
1772862 TT
1 TT
1772864 CCATTCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATCTCATTAACTTTTT
Found at i:1774704 original size:98 final size:94
Alignment explanation
Indices: 1774447--1774706 Score: 290
Period size: 95 Copynumber: 2.7 Consensus size: 94
1774437 AGATTATAAT
* * *
1774447 ATTATATATATACAATAAAGCTTGAGCTATCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTA
1 ATTATA-ATATGCAATAAAGATTGAGCTAT-CCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTA
* * *
1774512 TGGATAAGATTAAGCTAAACTGATAAAGGTG
64 TGAATAAAATCAAGCTAAACTGATAAAGGTG
* * * *
1774543 ATTATAATATGCAATAAAGCTCGAGTTATCCATCTAGAGCAATTGGTTAAATGCCCCGGCTTTAT
1 ATTATAATATGCAATAAAGATTGAGCTATCC-TCTAGAGCAATTGGTTAAACGCCCCGGCTTTAT
**
1774608 GAATAATAATCAA-CTAGCCTGATAAAGGTG
65 GAATAA-AATCAAGCTAAACTGATAAAGGTG
* * *
1774638 ATTATAATAT-CTATACAACGATATTGAGCTGTCTCTCTAGAGCAATTGGTTAAACGCCCCGACT
1 ATTATAATATGCAATA-AA-G--ATTGAGCTATC-CTCTAGAGCAATTGGTTAAACGCCCCGGCT
1774702 TTATG
61 TTATG
1774707 GATCAGCTAG
Statistics
Matches: 140, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
94 6 0.04
95 83 0.59
96 11 0.08
98 39 0.28
99 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (94 bp):
ATTATAATATGCAATAAAGATTGAGCTATCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATG
AATAAAATCAAGCTAAACTGATAAAGGTG
Found at i:1775694 original size:83 final size:83
Alignment explanation
Indices: 1775551--1776322 Score: 872
Period size: 83 Copynumber: 9.4 Consensus size: 83
1775541 TGACATGTTG
* * * * *
1775551 AAAGACCTTCGAGTTCGATTACACTCAGCTAAAAGGCACGTCATTTACAGCATAACTCAAGGCTA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
* *
1775616 GAAGGGTTACCTGTCAAC
66 GAAGGGCTATCTGTCAAC
* * * *
1775634 AAAGAGCTTCGAGTTCGATTACACTAACCTCAAAGGCACATCATTTGCAGCATAGTTCAAGGCAA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
1775699 GAAGGGCTA-CATG-C--C
66 GAAGGGCTATC-TGTCAAC
* *
1775714 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAA-GCACATTCATTTGCAGCAAAGCTCAAGTCA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACA-TCATTTGCAGCATAGCTCAAGGCA
*
1775778 AGAAGGGCTATATG-C--C
65 AGAAGGGCTATCTGTCAAC
* * *
1775794 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGACGCATCATTTGTAGCATAGCTCAAGGCAA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
1775859 GAAGGGCTATCT-TCTAAC
66 GAAGGGCTATCTGTC-AAC
* * * * * *
1775877 AAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGACACATCATTTACATCATAACTCAAGGCT
1 -AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCA
* *
1775942 ATAAGGGTTATCTGTCAAC
65 AGAAGGGCTATCTGTCAAC
*
1775961 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCTA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
* *
1776026 GAAGGGCTATTTGCCAAC
66 GAAGGGCTATCTGTCAAC
* * * * * * *
1776044 AAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCACATAATTTGTAACATAACTTAA-GAAG
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCA-
* *
1776108 AGAAGGGTTATC--T-ACC
65 AGAAGGGCTATCTGTCAAC
* * *
1776124 AAAGACCTTTGAGTTCAATTACACTCAGCTCAAAGGCACATCATTTGCAGTATAGCTCAAGGCAA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
* * * *
1776189 AAAAGGATATCTGCCAAC
66 GAAGGGCTATCTGTCAAC
* * * * * *
1776207 AAAAGACCTTCGAGTTCGATTACATTCAACTCAGAGGCAAATCAAATTTACAGCATAACTCAAGG
1 -AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC--ATTTGCAGCATAGCTCAAGG
*
1776272 CAAGAAGGGTTATCTGTCAAC
63 CAAGAAGGGCTATCTGTCAAC
* * *
1776293 AAA-A-TTGTCGAGTTCGATTCCATTCAGCTC
1 AAAGACCT-TCGAGTTCGATTACACTCAGCTC
1776323 GATGACACAT
Statistics
Matches: 586, Mismatches: 84, Indels: 37
0.83 0.12 0.05
Matches are distributed among these distances:
79 5 0.01
80 197 0.34
81 5 0.01
82 3 0.01
83 208 0.35
84 129 0.22
85 5 0.01
86 34 0.06
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (83 bp):
AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
GAAGGGCTATCTGTCAAC
Found at i:1776885 original size:26 final size:27
Alignment explanation
Indices: 1776851--1776904 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
1776841 TTGGAAATTA
* *
1776851 TATAATATATGGTTTTT-AAAAATATT
1 TATAATATATAGTTTTTGAAAAACATT
*
1776877 TATATTATATAGTTTTTGAAAAACATT
1 TATAATATATAGTTTTTGAAAAACATT
1776904 T
1 T
1776905 TAAAAATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (27 bp):
TATAATATATAGTTTTTGAAAAACATT
Found at i:1776886 original size:28 final size:27
Alignment explanation
Indices: 1776848--1776904 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
1776838 ATTTTGGAAA
*
1776848 TTATATAATATATGGTTTTT-AAAAATAT
1 TTATATAATATA--GTTTTTGAAAAACAT
*
1776876 TTATATTATATAGTTTTTGAAAAACAT
1 TTATATAATATAGTTTTTGAAAAACAT
1776903 TT
1 TT
1776905 TAAAAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 6 0.23
27 9 0.35
28 11 0.42
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (27 bp):
TTATATAATATAGTTTTTGAAAAACAT
Found at i:1776919 original size:38 final size:37
Alignment explanation
Indices: 1776864--1777068 Score: 189
Period size: 38 Copynumber: 5.6 Consensus size: 37
1776854 AATATATGGT
* *
1776864 TTTTAAAAATATTTATATTATATAGTTTTTGAAAAACA
1 TTTTGAAAATATATATATTATATAGTTTTT-AAAAACA
*
1776902 TTTTAAAAATATATATATTATA-ATGTTTTTAAAAAACA
1 TTTTGAAAATATATATATTATATA-GTTTTT-AAAAACA
**
1776940 TTTTG---A-ATATA-A-TATATAGTTTTTAAAATTA
1 TTTTGAAAATATATATATTATATAGTTTTTAAAAACA
* *
1776971 TTTTGAAAGTATATA-A-TATATAATTTTT-AAAACA
1 TTTTGAAAATATATATATTATATAGTTTTTAAAAACA
*
1777005 TTTTTTGAAAATATATATATTATATAGTTTTAAAAAAACA
1 --TTTTGAAAATATATATATTATATAGTTTT-TAAAAACA
*
1777045 TTTTGGGAAA-ATATATATTATATA
1 TTTT-GAAAATATATATATTATATA
1777069 ATTTGTGAAA
Statistics
Matches: 141, Mismatches: 13, Indels: 26
0.78 0.07 0.14
Matches are distributed among these distances:
31 10 0.07
32 10 0.07
33 2 0.01
34 9 0.06
35 18 0.13
36 14 0.10
37 2 0.01
38 66 0.47
39 4 0.03
40 6 0.04
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (37 bp):
TTTTGAAAATATATATATTATATAGTTTTTAAAAACA
Found at i:1776935 original size:64 final size:62
Alignment explanation
Indices: 1776815--1776936 Score: 149
Period size: 64 Copynumber: 1.9 Consensus size: 62
1776805 ATTTTTAGTA
* **
1776815 TATATTATATATAGTTTGAAATCATTTTGGAAATTATATAATATATGGTTTTTAAAAATATT
1 TATATTATATATAGTTTGAAAACATTTTAAAAATTATATAATATATGGTTTTTAAAAATATT
* *
1776877 TATATTATATAGT-TTTTGAAAAACATTTTAAAAATATATATATTATAAT-GTTTTTAAAAA
1 TATATTATATA-TAGTTTG-AAAACATTTTAAAAAT-TATATAATAT-ATGGTTTTTAAAAA
1776937 ACATTTTGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
62 15 0.29
63 14 0.27
64 20 0.39
65 2 0.04
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (62 bp):
TATATTATATATAGTTTGAAAACATTTTAAAAATTATATAATATATGGTTTTTAAAAATATT
Found at i:1776990 original size:35 final size:34
Alignment explanation
Indices: 1776946--1777040 Score: 118
Period size: 36 Copynumber: 2.6 Consensus size: 34
1776936 AACATTTTGA
*
1776946 ATATAATATATAGTTTTTAAAATTATTTTGAAAGT
1 ATATAATATATAGTTTTTAAAATT-TTTTGAAAAT
*
1776981 ATATAATATATAATTTTTAAAACATTTTTTGAAAAT
1 ATATAATATATAGTTTTT-AAA-ATTTTTTGAAAAT
*
1777017 ATATATATTATATAGTTTTAAAAA
1 ATATA-A-TATATAGTTTTTAAAA
1777041 AACATTTTGG
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
35 17 0.33
36 18 0.35
37 7 0.13
38 10 0.19
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.47
Consensus pattern (34 bp):
ATATAATATATAGTTTTTAAAATTTTTTGAAAAT
Found at i:1777078 original size:24 final size:23
Alignment explanation
Indices: 1777046--1777091 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
1777036 AAAAAAACAT
1777046 TTTGGGAAAATATATATTATATAA
1 TTTGGGAAAATAT-TATTATATAA
* *
1777070 TTTGTGAAAATATTTTTATATA
1 TTTGGGAAAATATTATTATATA
1777092 TTATTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (23 bp):
TTTGGGAAAATATTATTATATAA
Found at i:1777118 original size:14 final size:15
Alignment explanation
Indices: 1777083--1777155 Score: 60
Period size: 15 Copynumber: 4.8 Consensus size: 15
1777073 GTGAAAATAT
* *
1777083 TTTTATATATTATTA
1 TTTTATTTATTTTTA
1777098 TTTTATTTATTTTTA
1 TTTTATTTATTTTTA
*
1777113 -TTTATTTATTTTCTT
1 TTTTATTTATTTT-TA
*
1777128 TCTTTA-TTATTATTA
1 T-TTTATTTATTTTTA
*
1777143 TTATTATTAATTT
1 TT-TTATTTATTT
1777156 CTTTTTATGT
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
14 13 0.28
15 19 0.41
16 10 0.22
17 4 0.09
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTATTTATTTTTA
Found at i:1777133 original size:13 final size:13
Alignment explanation
Indices: 1777084--1777141 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
1777074 TGAAAATATT
*
1777084 TTTATATATTATTA
1 TTTATTTATT-TTA
1777098 TTTTATTTATTTTTA
1 -TTTATTTA-TTTTA
*
1777113 TTTATTTATTTTC
1 TTTATTTATTTTA
*
1777126 TTTCTTTATTATTA
1 TTTATTTATT-TTA
1777140 TT
1 TT
1777142 ATTATTATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
13 13 0.35
14 12 0.32
15 10 0.27
16 2 0.05
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:1777140 original size:23 final size:23
Alignment explanation
Indices: 1777084--1777155 Score: 69
Period size: 23 Copynumber: 3.1 Consensus size: 23
1777074 TGAAAATATT
1777084 TTTATATATTA-TTATTTTATTTA
1 TTTAT-TATTATTTATTTTATTTA
* *
1777107 TTT-TTATTTATTTATTTTCTTTC
1 TTTATTA-TTATTTATTTTATTTA
*
1777130 TTTATTATTA-TTATTATTATTAA
1 TTTATTATTATTTATT-TTATTTA
1777153 TTT
1 TTT
1777156 CTTTTTATGT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
21 2 0.05
22 9 0.22
23 26 0.65
24 3 0.08
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (23 bp):
TTTATTATTATTTATTTTATTTA
Found at i:1778464 original size:75 final size:80
Alignment explanation
Indices: 1778380--1778565 Score: 208
Period size: 75 Copynumber: 2.4 Consensus size: 80
1778370 TTATTCCTAG
* *
1778380 TTATTTTATTTTATTTTCTCTT-ATTATGTTTTTTCTTAATATTTTATTT-TATG-T-ATTTATA
1 TTATTTTATTTTATTTT-TCTTAATTAT-TTTATTC-TAATATTTTATTTGTATGTTGATATATA
*
1778441 TATA-TA-CATTTTTTA-
63 TATATTACCATTTTTCAT
* *
1778456 TTA-TTTATTTTATTATTTATTAATTATTTTATTCTAATATTTTGTTTGTATGTTGATATATATA
1 TTATTTTATTTTATT-TTTCTTAATTATTTTATTCTAATATTTTATTTGTATGTTGATATATATA
*
1778520 TATTACCCTTTTTCAT
65 TATTACCATTTTTCAT
*
1778536 TTATTTTATTTTATTTTTCTTTATTTATTT
1 TTATTTTATTTTATTTTTC-TTAATTATTT
1778566 ATCTCTTTTA
Statistics
Matches: 92, Mismatches: 8, Indels: 15
0.80 0.07 0.13
Matches are distributed among these distances:
74 12 0.13
75 24 0.26
76 11 0.12
77 10 0.11
78 2 0.02
79 7 0.08
80 6 0.07
81 20 0.22
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (80 bp):
TTATTTTATTTTATTTTTCTTAATTATTTTATTCTAATATTTTATTTGTATGTTGATATATATAT
ATTACCATTTTTCAT
Found at i:1778468 original size:12 final size:12
Alignment explanation
Indices: 1778451--1778476 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1778441 TATATACATT
1778451 TTTTATTATTTA
1 TTTTATTATTTA
1778463 TTTTATTATTTA
1 TTTTATTATTTA
1778475 TT
1 TT
1778477 AATTATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTATTATTTA
Found at i:1778541 original size:4 final size:4
Alignment explanation
Indices: 1778534--1778640 Score: 51
Period size: 4 Copynumber: 24.5 Consensus size: 4
1778524 ACCCTTTTTC
*
1778534 ATTT ATTTT ATTT -TATT -TTT CTTT ATTT ATTT ATCTCT -TTT ATTT
1 ATTT A-TTT ATTT AT-TT ATTT ATTT ATTT ATTT AT-T-T ATTT ATTT
*
1778579 ATTGTT ATTT ATTT ATTT ATTCTT ATTT ATTCT -TCTT TTTT ATTTT ATTTT
1 A-T-TT ATTT ATTT ATTT A-T-TT ATTT ATT-T AT-TT ATTT A-TTT A-TTT
1778630 ATTTT ATTT AT
1 A-TTT ATTT AT
1778641 GTATATTTTG
Statistics
Matches: 87, Mismatches: 2, Indels: 28
0.74 0.02 0.24
Matches are distributed among these distances:
3 4 0.05
4 49 0.56
5 27 0.31
6 7 0.08
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:1778548 original size:10 final size:9
Alignment explanation
Indices: 1778535--1778638 Score: 81
Period size: 10 Copynumber: 11.2 Consensus size: 9
1778525 CCCTTTTTCA
1778535 TTTATTTTAT
1 TTTA-TTTAT
*
1778545 TTTATTTTT
1 TTTATTTAT
1778554 CTTTATTTA-
1 -TTTATTTAT
* *
1778563 TTTATCTCT
1 TTTATTTAT
1778572 TTTATTTAT
1 TTTATTTAT
1778581 TGTTATTTA-
1 T-TTATTTAT
1778590 TTTATTTAT
1 TTTATTTAT
1778599 TCTTATTTAT
1 T-TTATTTAT
*
1778609 TCTT-CTT-T
1 T-TTATTTAT
1778617 TTTATTTTAT
1 TTTA-TTTAT
1778627 TTTATTTTAT
1 TTTA-TTTAT
1778637 TT
1 TT
1778639 ATGTATATTT
Statistics
Matches: 78, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
7 2 0.03
8 15 0.19
9 18 0.23
10 43 0.55
ACGTcount: A:0.17, C:0.06, G:0.01, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:1778577 original size:17 final size:15
Alignment explanation
Indices: 1778539--1778638 Score: 70
Period size: 14 Copynumber: 6.8 Consensus size: 15
1778529 TTTTCATTTA
1778539 TTTTATTTTATTTTTC
1 TTTTA-TTTATTTTTC
1778555 -TTTATTTATTTATCTC
1 TTTTATTTATTT-T-TC
*
1778571 TTTTATTTATTGTT-
1 TTTTATTTATTTTTC
*
1778585 ATTTATTTATTTATTC
1 TTTTATTTATTT-TTC
*
1778601 --TTATTTATTCTTC
1 TTTTATTTATTTTTC
*
1778614 -TTT-TTTA-TTTTA
1 TTTTATTTATTTTTC
1778626 TTTTATTTTATTT
1 TTTTA-TTTATTT
1778639 ATGTATATTT
Statistics
Matches: 68, Mismatches: 6, Indels: 20
0.72 0.06 0.21
Matches are distributed among these distances:
12 3 0.04
13 10 0.15
14 28 0.41
15 12 0.18
16 5 0.07
17 10 0.15
ACGTcount: A:0.17, C:0.06, G:0.01, T:0.76
Consensus pattern (15 bp):
TTTTATTTATTTTTC
Found at i:1778590 original size:31 final size:30
Alignment explanation
Indices: 1778539--1778623 Score: 104
Period size: 31 Copynumber: 2.9 Consensus size: 30
1778529 TTTTCATTTA
*
1778539 TTTTATTTTATTTTTCTTTATTTATTTATCTC
1 TTTTA-TTTATTCTTCTTTATTTATTTAT-TC
* *
1778571 TTTTATTTATTGTTATTTATTTATTTATTC
1 TTTTATTTATTCTTCTTTATTTATTTATTC
1778601 --TTATTTATTCTTCTTT-TTTATTT
1 TTTTATTTATTCTTCTTTATTTATTT
1778624 TATTTTATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
27 7 0.14
28 14 0.29
30 2 0.04
31 21 0.43
32 5 0.10
ACGTcount: A:0.16, C:0.07, G:0.01, T:0.75
Consensus pattern (30 bp):
TTTTATTTATTCTTCTTTATTTATTTATTC
Found at i:1778595 original size:18 final size:18
Alignment explanation
Indices: 1778572--1778609 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1778562 ATTTATCTCT
*
1778572 TTTATTTATTGTTATTTA
1 TTTATTTATTCTTATTTA
1778590 TTTATTTATTCTTATTTA
1 TTTATTTATTCTTATTTA
1778608 TT
1 TT
1778610 CTTCTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTATTTATTCTTATTTA
Found at i:1778609 original size:45 final size:46
Alignment explanation
Indices: 1778535--1778640 Score: 139
Period size: 45 Copynumber: 2.3 Consensus size: 46
1778525 CCCTTTTTCA
1778535 TTTATTTTATTTTATTTTTCTTTATTTATT-TATCTCTTTTA-TTTAT
1 TTTATTTTA-TTTATTTTTCTTTATTTATTCT-TCTCTTTTATTTTAT
*
1778581 TGTTA-TTTATTTATTTATTC-TTATTTATTCTTCTTTTTTATTTTAT
1 T-TTATTTTATTTATTT-TTCTTTATTTATTCTTCTCTTTTATTTTAT
1778627 TTTATTTTATTTAT
1 TTTATTTTATTTAT
1778641 GTATATTTTG
Statistics
Matches: 54, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
45 27 0.50
46 24 0.44
47 3 0.06
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.75
Consensus pattern (46 bp):
TTTATTTTATTTATTTTTCTTTATTTATTCTTCTCTTTTATTTTAT
Found at i:1778620 original size:13 final size:13
Alignment explanation
Indices: 1778560--1778622 Score: 56
Period size: 13 Copynumber: 4.7 Consensus size: 13
1778550 TTTTCTTTAT
1778560 TTATTTATCTCTT-
1 TTATTTAT-TCTTC
* *
1778573 TTATTTATTGTTAT
1 TTATTTATTCTT-C
*
1778587 TTATTTATTTATTC
1 TTATTTA-TTCTTC
1778601 TTATTTATTCTTC
1 TTATTTATTCTTC
*
1778614 TTTTTTATT
1 TTATTTATT
1778623 TTATTTTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
12 3 0.07
13 21 0.50
14 14 0.33
15 4 0.10
ACGTcount: A:0.17, C:0.08, G:0.02, T:0.73
Consensus pattern (13 bp):
TTATTTATTCTTC
Found at i:1778647 original size:15 final size:14
Alignment explanation
Indices: 1778529--1778655 Score: 55
Period size: 14 Copynumber: 8.7 Consensus size: 14
1778519 ATATTACCCT
*
1778529 TTTTCATTTATTTTA
1 TTTT-ATTTATTATA
* *
1778544 TTTTATTT-TTCTT
1 TTTTATTTATTATA
* *
1778557 TATTTATTTA-TCTC
1 T-TTTATTTATTATA
*
1778571 TTTTATTTATTGT-
1 TTTTATTTATTATA
1778584 TATTTATTTATT-TA
1 T-TTTATTTATTATA
* *
1778598 TTCTTATTTATTCTTCTT
1 TT-TTATTTA---TTATA
*
1778616 TTTTATTTTATTTTA
1 TTTTA-TTTATTATA
1778631 TTTTATTTATGTATA
1 TTTTATTTAT-TATA
*
1778646 TTTTGTTTAT
1 TTTTATTTAT
1778656 ATGTTTTTAT
Statistics
Matches: 91, Mismatches: 9, Indels: 24
0.73 0.07 0.19
Matches are distributed among these distances:
13 15 0.16
14 40 0.44
15 24 0.26
17 5 0.05
18 7 0.08
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.74
Consensus pattern (14 bp):
TTTTATTTATTATA
Found at i:1778741 original size:28 final size:28
Alignment explanation
Indices: 1778709--1778764 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
1778699 ACTTTTCATC
*
1778709 TTTGCTATATCTTTT-TATTATTTGTTTT
1 TTTGCTATAT-TTTTATATTATTTATTTT
* *
1778737 TTTGCTTTATTTTTATTTTATTTATTTT
1 TTTGCTATATTTTTATATTATTTATTTT
1778765 CTTTTCTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.75
Consensus pattern (28 bp):
TTTGCTATATTTTTATATTATTTATTTT
Found at i:1787893 original size:15 final size:15
Alignment explanation
Indices: 1787873--1787903 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1787863 CAACAGATAA
1787873 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
1787888 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
1787903 A
1 A
1787904 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:1788525 original size:45 final size:45
Alignment explanation
Indices: 1788451--1788568 Score: 146
Period size: 45 Copynumber: 2.6 Consensus size: 45
1788441 TGAGGAACGT
* * * *
1788451 TCTTGCTCTTTTCTGTGAAAGACGCCAAGTCGTAAACAATGGTTGA
1 TCTT-CTCATTTCTCTGAAAGATGCCAAGTCATAAACAATGGTTGA
* * *
1788497 TCTTCTCCTTTCTCTGAAGGATGCCAAGTCATAATCAATGGTTGA
1 TCTTCTCATTTCTCTGAAAGATGCCAAGTCATAAACAATGGTTGA
* *
1788542 TCTGCTCATTTCTTTGAAAGATGCCAA
1 TCTTCTCATTTCTCTGAAAGATGCCAA
1788569 ATTGGGGAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
45 58 0.94
46 4 0.06
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (45 bp):
TCTTCTCATTTCTCTGAAAGATGCCAAGTCATAAACAATGGTTGA
Found at i:1788601 original size:85 final size:85
Alignment explanation
Indices: 1788495--1788706 Score: 250
Period size: 85 Copynumber: 2.5 Consensus size: 85
1788485 AACAATGGTT
*
1788495 GATCTT-CTCCTTTCTCTGAAGGATGCCAAGTCATAATCAATGGTTGATCTGCTCATTTCTTTGA
1 GATCTTGCTCCTTTCTCTGAAGGATGCCAAGTCATAATCAATGGTTGATCTGCTCATTTCTCTGA
** ** *
1788559 A-AGATGCCAAATTGGGGAAT
66 AGA-ACACCAAATCAGGGAAC
* * * * *
1788579 TATCTTGCTCCTTTCTTTGAAGGA-GATCAAGTCATAATCAGTGGTTGGTCTGCTCATTTCTCTG
1 GATCTTGCTCCTTTCTCTGAAGGATG-CCAAGTCATAATCAATGGTTGATCTGCTCATTTCTCTG
1788643 AAGAACACCAAATCAGGGAAC
65 AAGAACACCAAATCAGGGAAC
* * * *
1788664 GATCTTGCTCCTTCCTCTAAAGGATGCCAAGTCGTGATCAATG
1 GATCTTGCTCCTTTCTCTGAAGGATGCCAAGTCATAATCAATG
1788707 AAAATTCAAT
Statistics
Matches: 105, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
84 6 0.06
85 97 0.92
86 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (85 bp):
GATCTTGCTCCTTTCTCTGAAGGATGCCAAGTCATAATCAATGGTTGATCTGCTCATTTCTCTGA
AGAACACCAAATCAGGGAAC
Found at i:1793038 original size:40 final size:40
Alignment explanation
Indices: 1792983--1793089 Score: 160
Period size: 40 Copynumber: 2.7 Consensus size: 40
1792973 TTTCTGATAG
* *
1792983 TGTGGAGCGAAGGCGCATTTCAGGGGGTGCACTTTGTTGA
1 TGTGGAGCGAAGGCGCGTTTCAGGGGGTGCACATTGTTGA
* * *
1793023 TGTGGAGCGAAGGCGCGTTTTAGGAGCTGCACATTGTTGA
1 TGTGGAGCGAAGGCGCGTTTCAGGGGGTGCACATTGTTGA
*
1793063 TGTAGAGCGAAGGCGCGTTTCAGGGGG
1 TGTGGAGCGAAGGCGCGTTTCAGGGGG
1793090 CACCTTCCAG
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.19, C:0.15, G:0.41, T:0.25
Consensus pattern (40 bp):
TGTGGAGCGAAGGCGCGTTTCAGGGGGTGCACATTGTTGA
Found at i:1797047 original size:17 final size:16
Alignment explanation
Indices: 1797016--1797049 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1797006 TACGTGAGGA
1797016 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
1797032 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
1797049 T
1 T
1797050 ACTATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:1807188 original size:16 final size:16
Alignment explanation
Indices: 1807154--1807187 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
1807144 CACGTGAGGA
1807154 TTATTTTCTTTTTATT
1 TTATTTTCTTTTTATT
1807170 TTATTTATCTTTTTATT
1 TTATTT-TCTTTTTATT
1807187 T
1 T
1807188 ACTGTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (16 bp):
TTATTTTCTTTTTATT
Found at i:1808167 original size:135 final size:132
Alignment explanation
Indices: 1807951--1808394 Score: 538
Period size: 133 Copynumber: 3.3 Consensus size: 132
1807941 AGATCGAGAA
* *
1807951 ACGTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGTAGACTT-TCTCCACTATTAC
1 ACGTTGATTCATTCCACTATTCTTTAGGGAAGATTGAATCGAGGCAGACTTGT-TCCACTATTAC
* * * * * * *
1808015 TCAGGGAAGATCAAATCTTGAAGGATAGGGATTTTGTTTCGCTTCTTCTTGATGGAAAATTAGAT
65 TC-GGGAATATCAAATCTTGAAAGAGAGGGA-TTTGTTTCGCTTTTTC-TGAAGGAAAATCATAT
*
1808080 CTGGGG
127 ATGGGG
* *
1808086 ACGTTGATTCATTCCACTATTCTTTAGGGAAGATTGAATCGAGGCAAACTTGTTCCACTGTTACT
1 ACGTTGATTCATTCCACTATTCTTTAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTATTACT
* * *
1808151 CGGTGAATATCAAATCTTGAATGAGAGGGATCTG-TTCAGCTTTTTACTGAGGGAAAATCATATA
66 CGG-GAATATCAAATCTTGAAAGAGAGGGATTTGTTTC-GCTTTTT-CTGAAGGAAAATCATATA
1808215 TGCGGG
128 TG-GGG
* * * * * *
1808221 -CGTTGATTCATTCCACTGTTAC-TTATGAAAAATTGAATCGAGGCCGATTTGTTCCACTATTAC
1 ACGTTGATTCATTCCACTATT-CTTTAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTATTAC
**
1808284 TATGGAATATCAAATCTTGAAAGAGAGGGATTTGTTTCGCTTTTTCCTGAAGGAAAATCATATAT
65 TCGGGAATATCAAATCTTGAAAGAGAGGGATTTGTTTCGCTTTTT-CTGAAGGAAAATCATATAT
1808349 GGGG
129 GGGG
*
1808353 ATGTTGATTCATTCCACTATT-TTTCAGGGAAGATTGAATCGA
1 ACGTTGATTCATTCCACTATTCTTT-AGGGAAGATTGAATCGA
1808395 ATTCGATTTG
Statistics
Matches: 267, Mismatches: 32, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
132 5 0.02
133 89 0.33
134 84 0.31
135 88 0.33
136 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (132 bp):
ACGTTGATTCATTCCACTATTCTTTAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTATTACT
CGGGAATATCAAATCTTGAAAGAGAGGGATTTGTTTCGCTTTTTCTGAAGGAAAATCATATATGG
GG
Found at i:1808833 original size:167 final size:169
Alignment explanation
Indices: 1808554--1808892 Score: 655
Period size: 167 Copynumber: 2.0 Consensus size: 169
1808544 CTCGCAACCA
1808554 CCAAATAATGGAGTTTGTCTCGACATGAGTGTTAGTTCAATCTCTCACTTTTTGGGACTTTGAAT
1 CCAAATAATGGAGTTTGTCTCGACATGAGTGTTAGTTCAA-CTCTCACTTTTTGGGACTTTGAAT
1808619 TGGTTATTTTGTTTTTCAAAAATTTCATTTTTCAGAAGAGATTTAAATGAGAAACTTAGGAAATT
65 TGGTTATTTTGTTTTTCAAAAATTTCATTTTTCAGAAGAGATTTAAATGAGAAACTTAGGAAATT
1808684 GTTTTCTTATTTTTTTTACCGAAAACATGAAAACATCTTG
130 GTTTTCTTATTTTTTTTACCGAAAACATGAAAACATCTTG
1808724 CCAAATAATGGAGTTTGTCTCGACATGAGTGTTAGTTCAA-TCTCAC-TTTTGGGACTTTGAATT
1 CCAAATAATGGAGTTTGTCTCGACATGAGTGTTAGTTCAACTCTCACTTTTTGGGACTTTGAATT
1808787 GGTTATTTTGTTTTTCAAAAATTTCATTTTTCAGAAGAGATTTAAATGAGAAACTTAGGAAATTG
66 GGTTATTTTGTTTTTCAAAAATTTCATTTTTCAGAAGAGATTTAAATGAGAAACTTAGGAAATTG
1808852 TTTTCTTATTTTTTTTACCGAAAACATGAAAACATCTTG
131 TTTTCTTATTTTTTTTACCGAAAACATGAAAACATCTTG
1808891 CC
1 CC
1808893 CGAAGGACTT
Statistics
Matches: 169, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
167 123 0.73
168 6 0.04
170 40 0.24
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (169 bp):
CCAAATAATGGAGTTTGTCTCGACATGAGTGTTAGTTCAACTCTCACTTTTTGGGACTTTGAATT
GGTTATTTTGTTTTTCAAAAATTTCATTTTTCAGAAGAGATTTAAATGAGAAACTTAGGAAATTG
TTTTCTTATTTTTTTTACCGAAAACATGAAAACATCTTG
Found at i:1811770 original size:6 final size:6
Alignment explanation
Indices: 1811759--1811855 Score: 63
Period size: 6 Copynumber: 14.8 Consensus size: 6
1811749 GAATTCATCT
1811759 TTTTTC TTTTTCC TCTTTTC TTTTTC TTTTTC -TTTTC TTTTCGTC TTTTTC
1 TTTTTC TTTTT-C T-TTTTC TTTTTC TTTTTC TTTTTC TTTT--TC TTTTTC
* * *
1811810 TATATTTTC TCTTTTA TGTTTTC -TCTTC TTTTTTC TTCTTC TTTTT
1 --T-TTTTC T-TTTTC T-TTTTC TTTTTC -TTTTTC TTTTTC TTTTT
1811856 TATATTTTCT
Statistics
Matches: 73, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
5 9 0.12
6 30 0.41
7 18 0.25
8 11 0.15
9 5 0.07
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (6 bp):
TTTTTC
Found at i:1811822 original size:25 final size:24
Alignment explanation
Indices: 1811777--1811870 Score: 61
Period size: 25 Copynumber: 3.9 Consensus size: 24
1811767 TTTCCTCTTT
* *
1811777 TCTTTTTCTTTTTCTTTTCTTTTCG
1 TCTTTTTCTTATT-TTCTCTTTTCG
*
1811802 TCTTTTTCTATATTTTCTCTTTTATG
1 TCTTTTTCT-TATTTTCTCTTTT-CG
* * *
1811828 T-TTTCTCTTCTTTTTTCTTCTTC-
1 TCTTTTTCTTATTTTCTCTT-TTCG
*
1811851 T-TTTTT-ATATTTTCTCTTTT
1 TCTTTTTCTTATTTTCTCTTTT
1811871 TTTAATATAT
Statistics
Matches: 55, Mismatches: 11, Indels: 10
0.72 0.14 0.13
Matches are distributed among these distances:
21 2 0.04
22 9 0.16
23 5 0.09
24 9 0.16
25 25 0.45
26 5 0.09
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.74
Consensus pattern (24 bp):
TCTTTTTCTTATTTTCTCTTTTCG
Found at i:1811839 original size:47 final size:47
Alignment explanation
Indices: 1811759--1811870 Score: 135
Period size: 47 Copynumber: 2.4 Consensus size: 47
1811749 GAATTCATCT
* * *
1811759 TTTTTCT-T-TTTCCTCTTTTCTTTTTCTTTTTCTTTTCTT-TTCGTC
1 TTTTTCTATATTTTCTCTTTTATTTTTCTTCTTCTTTT-TTCTTCGTC
*
1811804 TTTTTCTATATTTTCTCTTTTATGTTTTC-TCTTCTTTTTTCTTCTTC
1 TTTTTCTATATTTTCTCTTTTAT-TTTTCTTCTTCTTTTTTCTTCGTC
1811851 TTTTT-TATATTTTCTCTTTT
1 TTTTTCTATATTTTCTCTTTT
1811871 TTTAATATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
45 7 0.12
46 18 0.31
47 29 0.49
48 5 0.08
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.75
Consensus pattern (47 bp):
TTTTTCTATATTTTCTCTTTTATTTTTCTTCTTCTTTTTTCTTCGTC
Found at i:1811865 original size:14 final size:14
Alignment explanation
Indices: 1811802--1811871 Score: 50
Period size: 15 Copynumber: 4.6 Consensus size: 14
1811792 TTTCTTTTCG
1811802 TCTTTTTCTATATTT
1 TCTTTTT-TATATTT
* *
1811817 TCTCTTTTATGTTTT
1 TCTTTTTTAT-ATTT
* *
1811832 CTCTTCTTTTTTCTTCT
1 -TCTT-TTTTATATT-T
1811849 TCTTTTTTATATTT
1 TCTTTTTTATATTT
1811863 TCTCTTTTT
1 TCT-TTTTT
1811872 TTAATATATA
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
14 7 0.16
15 21 0.49
16 9 0.21
17 6 0.14
ACGTcount: A:0.07, C:0.17, G:0.01, T:0.74
Consensus pattern (14 bp):
TCTTTTTTATATTT
Found at i:1811865 original size:20 final size:18
Alignment explanation
Indices: 1811840--1811878 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1811830 TTCTCTTCTT
*
1811840 TTTTCTTCTTCTTTTTTATA
1 TTTTC-TCTT-TTTTTAATA
1811860 TTTTCTCTTTTTTTAATA
1 TTTTCTCTTTTTTTAATA
1811878 T
1 T
1811879 ATATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 4 0.22
20 5 0.28
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTCTCTTTTTTTAATA
Found at i:1811868 original size:16 final size:16
Alignment explanation
Indices: 1811796--1811872 Score: 72
Period size: 16 Copynumber: 4.8 Consensus size: 16
1811786 TTTTCTTTTC
1811796 TTTTCGTCTTTTTCTATA
1 TTTTC-TCTTTTT-TATA
*
1811814 TTTTCTC--TTTTATG
1 TTTTCTCTTTTTTATA
1811828 TTTTCTCTTCTTTT-T-
1 TTTTCTCTT-TTTTATA
*
1811843 TCTTCTTCTTTTTTATA
1 TTTTC-TCTTTTTTATA
1811860 TTTTCTCTTTTTT
1 TTTTCTCTTTTTT
1811873 TAATATATAT
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
14 10 0.20
15 11 0.22
16 14 0.28
17 10 0.20
18 5 0.10
ACGTcount: A:0.06, C:0.17, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTTCTCTTTTTTATA
Found at i:1811871 original size:17 final size:17
Alignment explanation
Indices: 1811796--1811874 Score: 62
Period size: 17 Copynumber: 4.9 Consensus size: 17
1811786 TTTTCTTTTC
*
1811796 TTTTCGTCTTTTTCTATA
1 TTTTC-TCTTTTTTTATA
*
1811814 TTTTCTC---TTTTATG
1 TTTTCTCTTTTTTTATA
*
1811828 TTTTCTCTTCTTTT-T-
1 TTTTCTCTTTTTTTATA
*
1811843 TCTTCT-TCTTTTTTATA
1 TTTTCTCT-TTTTTTATA
1811860 TTTTCTCTTTTTTTA
1 TTTTCTCTTTTTTTA
1811875 ATATATATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
14 13 0.27
15 10 0.20
16 2 0.04
17 18 0.37
18 6 0.12
ACGTcount: A:0.08, C:0.16, G:0.03, T:0.73
Consensus pattern (17 bp):
TTTTCTCTTTTTTTATA
Found at i:1811880 original size:2 final size:2
Alignment explanation
Indices: 1811875--1811902 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1811865 TCTTTTTTTA
1811875 AT 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 AT
1811903 TATTATGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1814718 original size:18 final size:18
Alignment explanation
Indices: 1814695--1814730 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1814685 TATTGTATAA
1814695 AAATAACAATAATAATAG
1 AAATAACAATAATAATAG
* *
1814713 AAATAATAATATTAATAG
1 AAATAACAATAATAATAG
1814731 CATCGGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.28
Consensus pattern (18 bp):
AAATAACAATAATAATAG
Found at i:1814853 original size:24 final size:24
Alignment explanation
Indices: 1814826--1814880 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
1814816 ATTGTTTAGA
*
1814826 TTAATGTGGTTTAGAGATTT-TAAG
1 TTAAAGTGGTTTAG-GATTTCTAAG
*
1814850 TTAAAGTGGTTTAGGGTTTCTAAG
1 TTAAAGTGGTTTAGGATTTCTAAG
1814874 TTAAAGT
1 TTAAAGT
1814881 TATTTAGGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.29, C:0.02, G:0.25, T:0.44
Consensus pattern (24 bp):
TTAAAGTGGTTTAGGATTTCTAAG
Found at i:1814886 original size:24 final size:24
Alignment explanation
Indices: 1814846--1814891 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1814836 TTAGAGATTT
*
1814846 TAAGTTAAAGTGGTTTAGGGTTTC
1 TAAGTTAAAGTGATTTAGGGTTTC
*
1814870 TAAGTTAAAGTTATTTAGGGTT
1 TAAGTTAAAGTGATTTAGGGTT
1814892 GATTTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.02, G:0.26, T:0.43
Consensus pattern (24 bp):
TAAGTTAAAGTGATTTAGGGTTTC
Found at i:1817475 original size:102 final size:101
Alignment explanation
Indices: 1817294--1817526 Score: 277
Period size: 102 Copynumber: 2.3 Consensus size: 101
1817284 AATGCATCCT
* ** * * * *
1817294 CTTGAACTTAAAGTCATTGTGCCATATGGGTTTTGAACATACTGTTGTGTTGATGGCATTTTCAT
1 CTTGAACTTAAAGGCA-TGTTTCATATGGGTATTGAACAGACTATTGTGTTGATGGCATTTCCAT
* * **
1817359 TTTGACGTTTAAGAAATTGACAGAGGAATGCCTTTCC
65 GTTAACGTGGAAGAAATTGACAGAGGAATGCCTTTCC
*
1817396 CTTGAACTTAAAGGCATAGTTTCATATGGGTATTGAACAGACTATTGTGTTGATGGTATTTCCAT
1 CTTGAACTTAAAGGCAT-GTTTCATATGGGTATTGAACAGACTATTGTGTTGATGGCATTTCCAT
* * * *
1817461 GTTAAGGTGGAAGAAGTTGGCAGATGAATGCCTTTCC
65 GTTAACGTGGAAGAAATTGACAGAGGAATGCCTTTCC
* *
1817498 CTTGAACTTGAAGGGATGTTTCCATATGG
1 CTTGAACTTAAAGGCATGTTT-CATATGG
1817527 ATTATTCATG
Statistics
Matches: 111, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
101 5 0.05
102 106 0.95
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (101 bp):
CTTGAACTTAAAGGCATGTTTCATATGGGTATTGAACAGACTATTGTGTTGATGGCATTTCCATG
TTAACGTGGAAGAAATTGACAGAGGAATGCCTTTCC
Found at i:1819067 original size:23 final size:24
Alignment explanation
Indices: 1819023--1819087 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 24
1819013 CACATAATTT
*
1819023 TCCCAAAGGACCACAAAGG-TTTG
1 TCCCAAAGGACCACATAGGTTTTG
* *
1819046 TCTCAAAGGACCACATATGTTTTG
1 TCCCAAAGGACCACATAGGTTTTG
* *
1819070 TCCCGAATGACCACATAG
1 TCCCAAAGGACCACATAG
1819088 AACCCTCGAC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 16 0.47
24 18 0.53
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.23
Consensus pattern (24 bp):
TCCCAAAGGACCACATAGGTTTTG
Found at i:1825746 original size:24 final size:24
Alignment explanation
Indices: 1825692--1825772 Score: 75
Period size: 23 Copynumber: 3.6 Consensus size: 24
1825682 ATTTACACCG
1825692 AAAGG-CCACATAA-TTT-TCCC-
1 AAAGGACCACATAATTTTGTCCCT
* * * *
1825712 GAAGGATCACATAGGTTTTGTCTC-
1 AAAGGACCACATA-ATTTTGTCCCT
1825736 AAAGGACCACATAATTTTGTCCCT
1 AAAGGACCACATAATTTTGTCCCT
1825760 AAA-GACCACATAA
1 AAAGGACCACATAA
1825773 AAGCCTTGAC
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
20 4 0.08
21 6 0.12
23 21 0.44
24 17 0.35
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (24 bp):
AAAGGACCACATAATTTTGTCCCT
Found at i:1827891 original size:153 final size:152
Alignment explanation
Indices: 1827613--1827911 Score: 404
Period size: 153 Copynumber: 2.0 Consensus size: 152
1827603 TTCACGTGAA
* *
1827613 CCCCTAAGATATTTGATGGGATGAGACAATATGACATGACAGAGTTTCTCTTAAAAAGTTGAAAG
1 CCCCTAAGATATTTGATGGGATAAGACAATATGACATGACAGAGTTTCTCTGAAAAAGTTGAAAG
* * * *
1827678 CACTTTTTATGGGATGTGCATTCCCTTTCCGTCAGAGTTCCTCTGCGTGTTTCAGTTAATAATAA
66 CACTTCTTATGGGATGTGCATTCCCTTTCCGTCAGAGTTCCTCTGCATGCTTCAATTAATAATAA
*
1827743 GCAGAAAATGATGTTCCTAGTTT
131 GCAG-AAATGATATTCCTAGTTT
* * * * *
1827766 CCCCTAATATGTTTGATGGGATAAGATAGTATGACATGATAG-GTATTCTCTGAAAAAGTTGAAA
1 CCCCTAAGATATTTGATGGGATAAGACAATATGACATGACAGAGT-TTCTCTGAAAAAGTTGAAA
* * *
1827830 GCGCTTCTTGTGGGATGCT-CATTCCCTTTTCGTCAGAGTTCCTCTGCATGCTTCAATTAATAAT
65 GCACTTCTTATGGGATG-TGCATTCCCTTTCCGTCAGAGTTCCTCTGCATGCTTCAATTAATAAT
**
1827894 TGGCAGAAATGATATTCC
129 AAGCAGAAATGATATTCC
1827912 CAGTCGAGGA
Statistics
Matches: 127, Mismatches: 17, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
152 13 0.10
153 113 0.89
154 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (152 bp):
CCCCTAAGATATTTGATGGGATAAGACAATATGACATGACAGAGTTTCTCTGAAAAAGTTGAAAG
CACTTCTTATGGGATGTGCATTCCCTTTCCGTCAGAGTTCCTCTGCATGCTTCAATTAATAATAA
GCAGAAATGATATTCCTAGTTT
Found at i:1828075 original size:169 final size:170
Alignment explanation
Indices: 1827766--1828143 Score: 453
Period size: 169 Copynumber: 2.2 Consensus size: 170
1827756 TTCCTAGTTT
* * ** * * *
1827766 CCCCTAATATGTTTGATGGGATAAGATAGTATGACAT-G-ATAGGTATTCTCTGAAAAAGTTGAA
1 CCCCTAATATGTTTGATGGGATAAAACAAAATGACATGGCA-AAG-ATTCTCAGAAAAAGTTAAA
* *
1827829 AGCGCTTCTTGTGGGATGCTCATTCCCTTTTCGTCAGAGTTCCTCTGCATGCTTCAATTAATAAT
64 AGCGCTTCTTGTGGGATGCGCATTCCCTTTTCGTCAGAGTTCCTCTGCATACTTCAATTAATAAT
* * *
1827894 TGGCAGAAATGATATTCCCAGTCGAGGAACTATTCAA-ATCAA
129 AGGAAGAAATGATATTCCCAGTCGAGGAACTACT-AACATCAA
* * * *
1827936 -CCTTAAATATGTTTGAT-GGATGAGACAAAATGACATGGCAAAGATTCTCAGAAAAATTTAAAA
1 CCCCT-AATATGTTTGATGGGATAAAACAAAATGACATGGCAAAGATTCTCAGAAAAAGTTAAAA
* * * * *
1827999 GCGCTTCTTGTGGGATGCGCTTTCCCTTTTTGTTAGAGTTCCTCTTCATACTTCAGTTGAA-AAT
65 GCGCTTCTTGTGGGATGCGCATTCCCTTTTCGTCAGAGTTCCTCTGCATACTTCAATT-AATAAT
* *
1828063 AGGAAGAAATGATGTTCCCAGTCGGGGAACTACTAACATCAA
129 AGGAAGAAATGATATTCCCAGTCGAGGAACTACTAACATCAA
*
1828105 CCCCTAATATGTTTGATGGGATAAAACAATATGACATGG
1 CCCCTAATATGTTTGATGGGATAAAACAAAATGACATGG
1828144 TGTGCAAATG
Statistics
Matches: 176, Mismatches: 25, Indels: 14
0.82 0.12 0.07
Matches are distributed among these distances:
168 2 0.01
169 135 0.77
170 38 0.22
171 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (170 bp):
CCCCTAATATGTTTGATGGGATAAAACAAAATGACATGGCAAAGATTCTCAGAAAAAGTTAAAAG
CGCTTCTTGTGGGATGCGCATTCCCTTTTCGTCAGAGTTCCTCTGCATACTTCAATTAATAATAG
GAAGAAATGATATTCCCAGTCGAGGAACTACTAACATCAA
Found at i:1829114 original size:12 final size:13
Alignment explanation
Indices: 1829092--1829129 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
1829082 TTTTGAATAT
1829092 TAAAAACATTACA
1 TAAAAACATTACA
*
1829105 TAAAAA-ATTAAA
1 TAAAAACATTACA
*
1829117 TAAAAATATTACA
1 TAAAAACATTACA
1829130 ATTATTATGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (13 bp):
TAAAAACATTACA
Found at i:1829547 original size:21 final size:21
Alignment explanation
Indices: 1829523--1829568 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1829513 AAACCATGCA
*
1829523 GGCTCAGAATGTAACCCAGTG
1 GGCTCAGAATATAACCCAGTG
*
1829544 GGCTCAGAATATAACCCTGTG
1 GGCTCAGAATATAACCCAGTG
1829565 GGCT
1 GGCT
1829569 TGGTATGTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (21 bp):
GGCTCAGAATATAACCCAGTG
Found at i:1830412 original size:24 final size:24
Alignment explanation
Indices: 1830375--1830423 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1830365 ACAAACCACC
*
1830375 TATTTAATATAAAAAATATTTAAA
1 TATTTAATAAAAAAAATATTTAAA
* **
1830399 TATTTACTAAAAAATTTATTTAAA
1 TATTTAATAAAAAAAATATTTAAA
1830423 T
1 T
1830424 GAAAAATTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
TATTTAATAAAAAAAATATTTAAA
Found at i:1831600 original size:26 final size:27
Alignment explanation
Indices: 1831571--1831629 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 27
1831561 AGGTTTAGGC
1831571 AGGAGTTCCGGGCAAGAGTTCGTGG-T
1 AGGAGTTCCGGGCAAGAGTTCGTGGCT
* * *
1831597 AGGAGTTCCTGGCACGATTTCGTGGCT
1 AGGAGTTCCGGGCAAGAGTTCGTGGCT
1831624 -GGAGTT
1 AGGAGTT
1831630 TTGGGCGGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 28 0.97
27 1 0.03
ACGTcount: A:0.17, C:0.17, G:0.39, T:0.27
Consensus pattern (27 bp):
AGGAGTTCCGGGCAAGAGTTCGTGGCT
Found at i:1835617 original size:21 final size:21
Alignment explanation
Indices: 1835592--1835636 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1835582 ATTATAGAAC
1835592 AAACTTGAAATACATAACAAT
1 AAACTTGAAATACATAACAAT
* *
1835613 AAACTTGAAATCCATAATAAT
1 AAACTTGAAATACATAACAAT
1835634 AAA
1 AAA
1835637 TCAAAGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.58, C:0.13, G:0.04, T:0.24
Consensus pattern (21 bp):
AAACTTGAAATACATAACAAT
Found at i:1839601 original size:14 final size:14
Alignment explanation
Indices: 1839584--1839634 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
1839574 AATTTAAAGC
* *
1839584 TTAGGGTTTAGGGT
1 TTAGGATTTAGAGT
1839598 TTAGGATTTAGAGT
1 TTAGGATTTAGAGT
*
1839612 TTAAGATTTATGA-T
1 TTAGGATTTA-GAGT
*
1839626 TTATGATTT
1 TTAGGATTT
1839635 TTTAAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 30 0.94
15 2 0.06
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.49
Consensus pattern (14 bp):
TTAGGATTTAGAGT
Found at i:1840872 original size:51 final size:50
Alignment explanation
Indices: 1840752--1840873 Score: 194
Period size: 51 Copynumber: 2.4 Consensus size: 50
1840742 ATTTAATAAA
*
1840752 ATAAGTTCTTTTAG-T-ATAAGGAAGAGAATTGAAATTAGGGCTAGGATT
1 ATAAGTTCTTTTAGTTAATAAGGAAGAGAATTGAAATTAGGGCAAGGATT
*
1840800 ATAAGTTCTTTTAGTAAAATAAGGAAGAGAATTGAAATTAGGGCAAGGATT
1 ATAAGTTCTTTTAGT-TAATAAGGAAGAGAATTGAAATTAGGGCAAGGATT
1840851 ATAAGTTCTTTTAGTTTAATAAG
1 ATAAGTTCTTTTAG-TTAATAAG
1840874 ATGTAAAAAT
Statistics
Matches: 67, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
48 14 0.21
51 52 0.78
52 1 0.01
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.34
Consensus pattern (50 bp):
ATAAGTTCTTTTAGTTAATAAGGAAGAGAATTGAAATTAGGGCAAGGATT
Found at i:1841955 original size:21 final size:21
Alignment explanation
Indices: 1841931--1841982 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
1841921 CGCCACTAAA
*
1841931 GTATGCACAATAGCGGCGTTT
1 GTATACACAATAGCGGCGTTT
1841952 GTATACACAATAGCGGCGTTT
1 GTATACACAATAGCGGCGTTT
1841973 GTATACACAA
1 GTATACACAA
1841983 ATGCCACTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (21 bp):
GTATACACAATAGCGGCGTTT
Found at i:1842154 original size:82 final size:82
Alignment explanation
Indices: 1842054--1842373 Score: 333
Period size: 82 Copynumber: 3.9 Consensus size: 82
1842044 ATTGCGATGT
* * * * * *
1842054 TTTTTACACAAACGCCACTATATATCAAGCTATTGCAGCGTTTTTTACATAAACGCTACTAAAGA
1 TTTTCACAAAAACACCACTATATATCAAGCTATAGCAGCGTTTTTTACATAAACGCCACTAAAGT
* * * **
1842119 ACACGTTTGTCGTGGTG
66 ACACATTTGTAGCGGCA
* * * *
1842136 TTTACTCAAAAACACCACTATATAT-ATGATATAGCAGC-TTTTTTACATAAACGCCACTAAAGT
1 TTTTCACAAAAACACCACTATATATCAAGCTATAGCAGCGTTTTTTACATAAACGCCACTAAAGT
** *
1842199 ACATGTTT-TAGCAGCA
66 ACACATTTGTAGCGGCA
** * * * *
1842215 TTTTCACAAAAACACCACTATATATCTGGCTATAGCGGTGTTTTTTATACAAACGCCACTAAAGT
1 TTTTCACAAAAACACCACTATATATCAAGCTATAGCAGCGTTTTTTACATAAACGCCACTAAAGT
** *
1842280 ATGCATTTTTAGCGGCA
66 ACACATTTGTAGCGGCA
* *
1842297 TTTTCACAAAAATACCACTATATATCTAA-CTATAGCGGCGTTTTTTACATAAACGCCACTAAAG
1 TTTTCACAAAAACACCACTATATATC-AAGCTATAGCAGCGTTTTTTACATAAACGCCACTAAAG
*
1842361 TACGCATTTGTAG
65 TACACATTTGTAG
1842374 TGGTGTTTCC
Statistics
Matches: 196, Mismatches: 38, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
79 26 0.13
80 38 0.19
81 37 0.19
82 95 0.48
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.33
Consensus pattern (82 bp):
TTTTCACAAAAACACCACTATATATCAAGCTATAGCAGCGTTTTTTACATAAACGCCACTAAAGT
ACACATTTGTAGCGGCA
Found at i:1842356 original size:41 final size:41
Alignment explanation
Indices: 1842215--1842357 Score: 110
Period size: 41 Copynumber: 3.5 Consensus size: 41
1842205 TTTAGCAGCA
** *
1842215 TTTTCACAAAAACACCACTATATATCTGGCTATAGCGGTGT
1 TTTTCACAAAAACACCACTATATATCTAACTATAGCGGCGT
* * * * * ** * *
1842256 TTTTTATACAAACGCCACTAAAGTATGC-ATTTTTAGCGGC-A
1 TTTTCACAAAAACACCACTATA-TAT-CTAACTATAGCGGCGT
*
1842297 TTTTCACAAAAATACCACTATATATCTAACTATAGCGGCGT
1 TTTTCACAAAAACACCACTATATATCTAACTATAGCGGCGT
* * *
1842338 TTTTTACATAAACGCCACTA
1 TTTTCACAAAAACACCACTA
1842358 AAGTACGCAT
Statistics
Matches: 73, Mismatches: 25, Indels: 8
0.69 0.24 0.08
Matches are distributed among these distances:
39 1 0.01
40 12 0.16
41 49 0.67
42 10 0.14
43 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.33
Consensus pattern (41 bp):
TTTTCACAAAAACACCACTATATATCTAACTATAGCGGCGT
Found at i:1846074 original size:18 final size:18
Alignment explanation
Indices: 1846031--1846074 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1846021 AAACGTATAG
1846031 TTTATATTATTAAATATTA
1 TTTA-ATTATTAAATATTA
* * *
1846050 ATAAATTATTAATTATTA
1 TTTAATTATTAAATATTA
1846068 TTTAATT
1 TTTAATT
1846075 TTTTAATGAA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTAATTATTAAATATTA
Found at i:1848822 original size:21 final size:21
Alignment explanation
Indices: 1848796--1848839 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1848786 GGAAGCCATT
1848796 GATGAAAGATT-GAAACTTTGG
1 GATGAAAGATTCG-AACTTTGG
1848817 GATGAAAGATTCGAACTTTGG
1 GATGAAAGATTCGAACTTTGG
1848838 GA
1 GA
1848840 AGATGAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.36, C:0.07, G:0.30, T:0.27
Consensus pattern (21 bp):
GATGAAAGATTCGAACTTTGG
Found at i:1851552 original size:16 final size:15
Alignment explanation
Indices: 1851526--1851555 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
1851516 ATCACCTACG
1851526 AAAAAGAAAGAAAGA
1 AAAAAGAAAGAAAGA
1851541 AAAAAGAGAAGAAAG
1 AAAAAGA-AAGAAAG
1851556 GATATATATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAGAAAGA
Found at i:1851679 original size:28 final size:28
Alignment explanation
Indices: 1851630--1851687 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
1851620 GGGATAAGGT
*
1851630 TTTTCACACGTAGGACAGCGAACCAACC
1 TTTTCACACGTAGGACAACGAACCAACC
* * *
1851658 TTTTCACACGTTGTATAACGAACCAACC
1 TTTTCACACGTAGGACAACGAACCAACC
1851686 TT
1 TT
1851688 ACTTTTGTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (28 bp):
TTTTCACACGTAGGACAACGAACCAACC
Found at i:1852369 original size:38 final size:37
Alignment explanation
Indices: 1852313--1852384 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 37
1852303 TACTAATAGA
* *
1852313 TAATAAAAAATGATAAATTAAT-AATCTATTAATTTTT
1 TAATAAAAAATAAAAAATTAATAAAT-TATTAATTTTT
*
1852350 TAATAAAAAATAAAAAAATTATTAAATTATTAATT
1 TAATAAAAAAT-AAAAAATTAATAAATTATTAATT
1852385 AATATTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
37 11 0.37
38 16 0.53
39 3 0.10
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (37 bp):
TAATAAAAAATAAAAAATTAATAAATTATTAATTTTT
Found at i:1854232 original size:24 final size:24
Alignment explanation
Indices: 1854202--1854272 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
1854192 ATACATGACA
*
1854202 TGAATTCTGTTCTGATTTCTTATC
1 TGAATTCTGTTCTGATTTCTGATC
*
1854226 T-AGATTCTGTTCTGATATCTGATC
1 TGA-ATTCTGTTCTGATTTCTGATC
*
1854250 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTCTGTTCTGATTTCTGAT
1854273 ATCTCCGTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
23 1 0.02
24 39 0.95
25 1 0.02
ACGTcount: A:0.18, C:0.14, G:0.15, T:0.52
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATC
Found at i:1854459 original size:16 final size:16
Alignment explanation
Indices: 1854438--1854469 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1854428 GGTAGTGTTC
*
1854438 ATGTTTTAAAATATAT
1 ATGTTTTAAAAGATAT
1854454 ATGTTTTAAAAGATAT
1 ATGTTTTAAAAGATAT
1854470 GTATCTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (16 bp):
ATGTTTTAAAAGATAT
Found at i:1864576 original size:15 final size:16
Alignment explanation
Indices: 1864556--1864595 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
1864546 CGGATATTGC
*
1864556 GGGTACCCGATAAT-T
1 GGGTACCCGAAAATAT
*
1864571 GGGTACCCAAAAATAT
1 GGGTACCCGAAAATAT
1864587 GGGTACCCG
1 GGGTACCCG
1864596 GATTTACACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.30, C:0.23, G:0.28, T:0.20
Consensus pattern (16 bp):
GGGTACCCGAAAATAT
Found at i:1869904 original size:36 final size:36
Alignment explanation
Indices: 1869857--1869929 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
1869847 CCTTAGGTCC
*
1869857 ATAAGGAATTACCAGCTTGATCGATGTTAAACCTAT
1 ATAAGGAATTACCAGCTTGATCGAAGTTAAACCTAT
*
1869893 ATAAGGAATTACCAGTTTGATCGAAGTTAAACCTAT
1 ATAAGGAATTACCAGCTTGATCGAAGTTAAACCTAT
1869929 A
1 A
1869930 GAGACTTCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.30
Consensus pattern (36 bp):
ATAAGGAATTACCAGCTTGATCGAAGTTAAACCTAT
Found at i:1872287 original size:29 final size:29
Alignment explanation
Indices: 1872255--1872336 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 29
1872245 ATTTTTTAGC
* ***
1872255 ATTTAAATTTCAGTACCTTTATTTATTTT
1 ATTTAAATTTCAATACCTTTATTTACAAT
* *
1872284 ATTTACATTTCAATATCTTTATTTACAAT
1 ATTTAAATTTCAATACCTTTATTTACAAT
* *
1872313 ATTTATATTTCAATACTTTTATTT
1 ATTTAAATTTCAATACCTTTATTT
1872337 TTTGGTATTT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.30, C:0.11, G:0.01, T:0.57
Consensus pattern (29 bp):
ATTTAAATTTCAATACCTTTATTTACAAT
Found at i:1872326 original size:14 final size:13
Alignment explanation
Indices: 1872290--1872336 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 13
1872280 TTTTATTTAC
1872290 ATTTCAATATCTTT
1 ATTTCAATAT-TTT
1872304 ATTTACAATATTTAT
1 ATTT-CAATATTT-T
1872319 ATTTCAATACTTTT
1 ATTTCAATA-TTTT
1872333 ATTT
1 ATTT
1872337 TTTGGTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 16 0.53
15 14 0.47
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (13 bp):
ATTTCAATATTTT
Found at i:1875303 original size:19 final size:20
Alignment explanation
Indices: 1875269--1875310 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1875259 ATAACTACCT
1875269 TTTTATCATTTGCATTTGCA
1 TTTTATCATTTGCATTTGCA
* *
1875289 TTTTA-CATTTTCATTTTCA
1 TTTTATCATTTGCATTTGCA
1875308 TTT
1 TTT
1875311 GTATTCACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.19, C:0.14, G:0.05, T:0.62
Consensus pattern (20 bp):
TTTTATCATTTGCATTTGCA
Found at i:1875340 original size:28 final size:26
Alignment explanation
Indices: 1875277--1875352 Score: 75
Period size: 28 Copynumber: 2.9 Consensus size: 26
1875267 CTTTTTATCA
* *
1875277 TTTGCATTTGCATTTTACAT-TTTCAT
1 TTTGCATTTGTA-TTCACATATTTCAT
1875303 TTT-CATTTGTATTCACATATTTGCAT
1 TTTGCATTTGTATTCACATATTT-CAT
* *
1875329 CTTTGCATTTGTGTTCGCATATTT
1 -TTTGCATTTGTATTCACATATTT
1875353 ACATATGTAC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
24 6 0.14
25 10 0.24
26 6 0.14
27 3 0.07
28 17 0.40
ACGTcount: A:0.18, C:0.16, G:0.11, T:0.55
Consensus pattern (26 bp):
TTTGCATTTGTATTCACATATTTCAT
Found at i:1875365 original size:28 final size:28
Alignment explanation
Indices: 1875306--1875395 Score: 99
Period size: 28 Copynumber: 3.2 Consensus size: 28
1875296 TTTTCATTTT
* * *
1875306 CATTTGTATTCACATATTTGCATCTTTG
1 CATTTGTATTCGCATATTTGCATATGTG
* * *
1875334 CATTTGTGTTCGCATATTTACATATGTA
1 CATTTGTATTCGCATATTTGCATATGTG
* * *
1875362 CATTTGCATTCGCGTCTTTGCATATGTG
1 CATTTGTATTCGCATATTTGCATATGTG
1875390 CATTTG
1 CATTTG
1875396 CATCTATACA
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.47
Consensus pattern (28 bp):
CATTTGTATTCGCATATTTGCATATGTG
Found at i:1878504 original size:42 final size:42
Alignment explanation
Indices: 1878449--1878539 Score: 137
Period size: 42 Copynumber: 2.2 Consensus size: 42
1878439 CTTGTTAGTG
* * *
1878449 AGTCTTTCGAGCATACTGATTAAATCCATCGGGTCTTCTGTT
1 AGTCTTTCGAGCATACTGATTAAATCCATCAGGTCATATGTT
**
1878491 AGTCTTTCGAGCATGTTGATTAAATCCATCAGGTCATATGTT
1 AGTCTTTCGAGCATACTGATTAAATCCATCAGGTCATATGTT
1878533 AGTCTTT
1 AGTCTTT
1878540 AGAGAAAGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.40
Consensus pattern (42 bp):
AGTCTTTCGAGCATACTGATTAAATCCATCAGGTCATATGTT
Found at i:1878551 original size:42 final size:42
Alignment explanation
Indices: 1878465--1878552 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 42
1878455 TCGAGCATAC
* * * * * *
1878465 TGATTAAATCCATCGGGTCTTCTGTTAGTCTTTCGAGCATGT
1 TGATTAAATCCATCAGGTCATATGTTAGTCTTTAGAGAAAGT
1878507 TGATTAAATCCATCAGGTCATATGTTAGTCTTTAGAGAAAGT
1 TGATTAAATCCATCAGGTCATATGTTAGTCTTTAGAGAAAGT
1878549 TGAT
1 TGAT
1878553 AGGTTATTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (42 bp):
TGATTAAATCCATCAGGTCATATGTTAGTCTTTAGAGAAAGT
Found at i:1878859 original size:102 final size:102
Alignment explanation
Indices: 1878663--1879385 Score: 659
Period size: 102 Copynumber: 7.1 Consensus size: 102
1878653 TTTTCAAAAA
* * * * *
1878663 AAAAGGAAAATCTTATCTCACTTGATATTGTTTTTCTTAAAACAAATTTTATCTCACTTGAGACA
1 AAAAGAAAAATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-TTTGTCTCGCTTGAGACA
* ** *
1878728 GTGTCATTTGAAACTCAAATTTTAAGATCATTTCAATC
65 GTTTCCCTTGAAACACAAATTTTAAGATCATTTCAATC
* * *
1878766 AAAAGAACAAATTTTATCTCAGTTGAGATTGTTTTTCTTAAAACAAA-TTGTCTCACTTAAGACA
1 AAAAGAA-AAATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCTTGAGACA
*
1878830 GTTTCCCTTGAAACAAAAATTTTAAGATCATTTCAATC
65 GTTTCCCTTGAAACACAAATTTTAAGATCATTTCAATC
* **
1878868 AAAATAACAAATTTTATCTCACTTGAGATTACTTTTCTTAAAACAAAATTTGTCTCGCTTGAGAC
1 AAAAGAA-AAATTTTATCTCACTTGAGATTGTTTTTCTTAAAAC-AAATTTGTCTCGCTTGAGAC
** * * *
1878933 AGTTTAACTTGAAACACAATATTTTAAAAT--TTTCACTT
64 AGTTTCCCTTGAAACACAA-ATTTTAAGATCATTTCAATC
* * * * * * *
1878971 GAAA-TAAATTTTTTTCTCACTTGAGATTGCTTTTCTTAAAA-AAA-TTATCTCGCTTGAGACAA
1 AAAAGAAAAATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCTTGAGACAG
** * *
1879033 TTTCCCTTGAAACACAAATTTTGAA-ATTGTTTCAGTT
66 TTTCCCTTGAAACACAAATTTT-AAGATCATTTCAATC
* * * * **
1879070 GAAA-CAAAATTTTAGCTCACTTGAAATCCTTTTTCTTAAAACAAATTTTGTCTCGCTTGAGACA
1 AAAAGAAAAATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-TTTGTCTCGCTTGAGACA
* * ** **
1879134 ATTTCCCTTGAAACATAAATTTTGAA-ATTGTTTCGCTC
65 GTTTCCCTTGAAACACAAATTTT-AAGATCATTTCAATC
* * * *
1879172 GAAAG--AGATTTT-TATCACTTGAGATTG-TTTTCTTAAAACAAATTTTGTCTCTCTTGAGACA
1 AAAAGAAAAATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-TTTGTCTCGCTTGAGACA
* ** *
1879233 GTTTCACTTGAAACACAAGCTTTAAGATCATTTCACTC
65 GTTTCCCTTGAAACACAAATTTTAAGATCATTTCAATC
* * * * *
1879271 AAAAAGGAAATTTTTATCTCACTTGAGATTGTTTCTCTTGAAACAAATTTCATCTTC-CTTGAGA
1 -AAAAGAAAAATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTT-GTC-TCGCTTGAGA
* * *
1879335 GAAATTT-CCTTGAAACACAAAGTTTAAGATCATTT-AACTC
63 -CAGTTTCCCTTGAAACACAAATTTTAAGATCATTTCAA-TC
1879375 AAAAAGAAAAA
1 -AAAAGAAAAA
1879386 AAAACCCACT
Statistics
Matches: 523, Mismatches: 76, Indels: 41
0.82 0.12 0.06
Matches are distributed among these distances:
97 7 0.01
98 35 0.07
99 103 0.20
100 17 0.03
101 38 0.07
102 148 0.28
103 36 0.07
104 124 0.24
105 15 0.03
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (102 bp):
AAAAGAAAAATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCTTGAGACAG
TTTCCCTTGAAACACAAATTTTAAGATCATTTCAATC
Found at i:1879817 original size:44 final size:44
Alignment explanation
Indices: 1879753--1879982 Score: 187
Period size: 44 Copynumber: 5.2 Consensus size: 44
1879743 TTAGAGGAGT
* * *
1879753 TGGATCAACATTACCC-TTTTGCTTGATTCCATCACAGAATGAGG
1 TGGATCAACATT-CCCTTTTTGCTCGATTTCATCACAGAAAGAGG
* * ** * *
1879797 GGGATCAACATTCCCTTTTTGCTCAATTTTGTCATAGAAAGAGT
1 TGGATCAACATTCCCTTTTTGCTCGATTTCATCACAGAAAGAGG
* * * *
1879841 TGGATCAACA-TCACCTTTTTGCTCAATTTCATCATATAAAGAGT
1 TGGATCAACATTC-CCTTTTTGCTCGATTTCATCACAGAAAGAGG
* * * * * * *
1879885 TGGATTAGCGTCACCCTTTTT-TTCGATTCCATCACAGAATGAGG
1 TGGATCAACAT-TCCCTTTTTGCTCGATTTCATCACAGAAAGAGG
* * * * *
1879929 TGGATCAATATTCCCTTTTTGCTAGGTTTCATCACTGAAGGAGG
1 TGGATCAACATTCCCTTTTTGCTCGATTTCATCACAGAAAGAGG
1879973 TGGATCAACA
1 TGGATCAACA
1879983 CGATTGAAGG
Statistics
Matches: 145, Mismatches: 36, Indels: 10
0.76 0.19 0.05
Matches are distributed among these distances:
43 13 0.09
44 124 0.86
45 7 0.05
46 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Consensus pattern (44 bp):
TGGATCAACATTCCCTTTTTGCTCGATTTCATCACAGAAAGAGG
Found at i:1880195 original size:22 final size:21
Alignment explanation
Indices: 1880156--1880210 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
1880146 TTTAATTGAT
*
1880156 AAAAATA-AAAATATAAATATAA
1 AAAAATAGAAAA-A-AAATAGAA
1880178 AAAAATATGAAAAAAAATAGAA
1 AAAAATA-GAAAAAAAATAGAA
*
1880200 ATAAATAGAAA
1 AAAAATAGAAA
1880211 TAAATCCTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 4 0.14
22 20 0.69
23 1 0.03
24 4 0.14
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (21 bp):
AAAAATAGAAAAAAAATAGAA
Found at i:1880207 original size:10 final size:10
Alignment explanation
Indices: 1880168--1880215 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
1880158 AAATAAAAAT
*
1880168 ATAAATATAA
1 ATAAATAGAA
*
1880178 AAAAATATGAAA
1 ATAAATA-G-AA
*
1880190 AAAAATAGAA
1 ATAAATAGAA
1880200 ATAAATAGAA
1 ATAAATAGAA
1880210 ATAAAT
1 ATAAAT
1880216 CCTCACATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 23 0.70
11 1 0.03
12 9 0.27
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (10 bp):
ATAAATAGAA
Found at i:1892324 original size:3 final size:3
Alignment explanation
Indices: 1892316--1892354 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1892306 TTTGTGACTT
1892316 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1892355 GAATTTAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1894031 original size:22 final size:23
Alignment explanation
Indices: 1894000--1894042 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1893990 TTTTTATATC
*
1894000 TTTTATTTTCGGTTCTGACTTTT
1 TTTTATTTTCGGTTCTAACTTTT
*
1894023 TTTTA-TTTCGTTTCTAACTT
1 TTTTATTTTCGGTTCTAACTT
1894043 ATTAACTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.12, C:0.14, G:0.09, T:0.65
Consensus pattern (23 bp):
TTTTATTTTCGGTTCTAACTTTT
Found at i:1894241 original size:29 final size:29
Alignment explanation
Indices: 1894209--1894305 Score: 101
Period size: 29 Copynumber: 3.3 Consensus size: 29
1894199 ATTTTTCAGC
*
1894209 ATTTAAATTTC-ATAACCTTTATTTCTTTT
1 ATTTACATTTCAAT-ACCTTTATTTCTTTT
* * *
1894238 ATTTACATTTAAATATCTTTATTTAC-ATT
1 ATTTACATTTCAATACCTTTATTT-CTTTT
*
1894267 ATTTATATTTCAATACCTTTATTT-TTGTT
1 ATTTACATTTCAATACCTTTATTTCTT-TT
1894296 ATTTACATTT
1 ATTTACATTT
1894306 TGCCGCATAA
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
29 52 0.95
30 3 0.05
ACGTcount: A:0.29, C:0.11, G:0.01, T:0.59
Consensus pattern (29 bp):
ATTTACATTTCAATACCTTTATTTCTTTT
Found at i:1897323 original size:27 final size:29
Alignment explanation
Indices: 1897267--1897328 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 29
1897257 CCTAAAAACT
*
1897267 ACCCTAAAATGAAACTCACTACACCCTAA
1 ACCCAAAAATGAAACTCACTACACCCTAA
* *
1897296 ACCCAAAAAT-AATCTCAC-ACACCGTAA
1 ACCCAAAAATGAAACTCACTACACCCTAA
*
1897323 AACCAA
1 ACCCAA
1897329 CCCTATGGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 13 0.45
28 7 0.24
29 9 0.31
ACGTcount: A:0.48, C:0.34, G:0.03, T:0.15
Consensus pattern (29 bp):
ACCCAAAAATGAAACTCACTACACCCTAA
Found at i:1897963 original size:6 final size:6
Alignment explanation
Indices: 1897943--1897997 Score: 58
Period size: 6 Copynumber: 8.5 Consensus size: 6
1897933 TTGGACCTGT
1897943 AAATAA AATATATA AATATAA AAATAA AAATAA AAATAA AAA-ACA ATAATAA
1 AAATAA AA-ATA-A AA-ATAA AAATAA AAATAA AAATAA AAATA-A A-AATAA
1897995 AAA
1 AAA
1897998 CAATAATATC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
5 1 0.02
6 25 0.57
7 10 0.23
8 8 0.18
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (6 bp):
AAATAA
Found at i:1897978 original size:13 final size:13
Alignment explanation
Indices: 1897943--1897997 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
1897933 TTGGACCTGT
1897943 AAATAAAATATATAA
1 AAATAAAA-ATA-AA
*
1897958 ATATAAAAAT-AA
1 AAATAAAAATAAA
1897970 AAATAAAAATAAA
1 AAATAAAAATAAA
* *
1897983 AAACAATAATAAA
1 AAATAAAAATAAA
1897996 AA
1 AA
1897998 CAATAATATC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
12 11 0.31
13 15 0.43
14 2 0.06
15 7 0.20
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATAAAAATAAA
Found at i:1897985 original size:20 final size:21
Alignment explanation
Indices: 1897943--1897985 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
1897933 TTGGACCTGT
* *
1897943 AAATAAAATATATAAATATAA
1 AAATAAAATATAAAAATAAAA
1897964 AAATAAAA-ATAAAAATAAAA
1 AAATAAAATATAAAAATAAAA
1897984 AA
1 AA
1897986 CAATAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (21 bp):
AAATAAAATATAAAAATAAAA
Found at i:1897998 original size:12 final size:12
Alignment explanation
Indices: 1897965--1898005 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
1897955 TAAATATAAA
* *
1897965 AATAAAAATAAA
1 AATAAAAACAAT
1897977 AATAAAAAACAAT
1 AAT-AAAAACAAT
1897990 AATAAAAACAAT
1 AATAAAAACAAT
1898002 AATA
1 AATA
1898006 TCGATATCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (12 bp):
AATAAAAACAAT
Found at i:1898418 original size:135 final size:135
Alignment explanation
Indices: 1898197--1898621 Score: 516
Period size: 135 Copynumber: 3.2 Consensus size: 135
1898187 CATTCCACTA
** * *
1898197 CTCTTCAGGGAA-AATTGAATCGAGGTTGATTTATTTCACTGCTCTTCAAGAAGACCAAATCTGA
1 CTCTTCAGGGAAGAA-TGAATCGAACTTGATTTGTTTCACTGCTCTTCAGGAAGACCAAATCTGA
* * *
1898261 AAGAAGAAGAATTTGTTACGCTACTCTTTAGGGGATATTAGACTCGAGAAAAATTTTGATCCATT
65 AAGAAGAAGAATATGCTCCGCTACTCTTTAGGGGATATTAGACTCGAGAAAAATTTTGATCCATT
1898326 TCGATG
130 TCGATG
* * * * **
1898332 TTCTTTAGGGAAGAATGAATCGAACTTGACTTGTTTCATTGCTCTTCAGGAATTCCAAATCTGAA
1 CTCTTCAGGGAAGAATGAATCGAACTTGATTTGTTTCACTGCTCTTCAGGAAGACCAAATCTGAA
* * *
1898397 AGAATAAGAGTATGCTCCGCTACTCTTTAGGGGATATTAGACTCGCGAAAAATTTTGATCCAGTT
66 AGAAGAAGAATATGCTCCGCTACTCTTTAGGGGATATTAGACTCGAGAAAAATTTTGATCCA-TT
*
1898462 T-GCTG
130 TCGATG
* ** * * *
1898467 CTCTTCAAGGAAGTTTGAATCGAACTTGATTTGCTTCGCTACTCTTCAGGAAGACCAAATCTGAA
1 CTCTTCAGGGAAGAATGAATCGAACTTGATTTGTTTCACTGCTCTTCAGGAAGACCAAATCTGAA
** * * * * *
1898532 AGAAGAAGAATATGCTCTACTACTCTTTATGGGAGATCAGACTCGAG-AAAACTTTGATCCACTT
66 AGAAGAAGAATATGCTCCGCTACTCTTTAGGGGATATTAGACTCGAGAAAAATTTTGATCCATTT
1898596 C-ACTG
131 CGA-TG
*
1898601 CTCTTCAGGGAAGATTGAATC
1 CTCTTCAGGGAAGAATGAATC
1898622 AGAATAGTCA
Statistics
Matches: 244, Mismatches: 42, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
133 2 0.01
134 34 0.14
135 203 0.83
136 5 0.02
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (135 bp):
CTCTTCAGGGAAGAATGAATCGAACTTGATTTGTTTCACTGCTCTTCAGGAAGACCAAATCTGAA
AGAAGAAGAATATGCTCCGCTACTCTTTAGGGGATATTAGACTCGAGAAAAATTTTGATCCATTT
CGATG
Found at i:1903173 original size:19 final size:17
Alignment explanation
Indices: 1903146--1903188 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
1903136 AAAAAAAAAC
*
1903146 AAAACAATTTGAAAGAATA
1 AAAAAAATTTG-AA-AATA
1903165 AAAAAAA-TTGAAAATA
1 AAAAAAATTTGAAAATA
1903181 AAAAAAAT
1 AAAAAAAT
1903189 AAATGAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 11 0.50
17 2 0.09
18 3 0.14
19 6 0.27
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.19
Consensus pattern (17 bp):
AAAAAAATTTGAAAATA
Found at i:1903662 original size:22 final size:23
Alignment explanation
Indices: 1903577--1903651 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
1903567 CGATTCCCCT
1903577 AAGGGGGAATCGGTTCCCCTTCA
1 AAGGGGGAATCGGTTCCCCTTCA
1903600 AAGGGGGAATCGGTTCCCCTTCA
1 AAGGGGGAATCGGTTCCCCTTCA
*
1903623 AAGGGGGAATAGGTTCCCCTTC-
1 AAGGGGGAATCGGTTCCCCTTCA
1903645 AAGGGGG
1 AAGGGGG
1903652 TATTGATTCC
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 7 0.14
23 44 0.86
ACGTcount: A:0.23, C:0.23, G:0.35, T:0.20
Consensus pattern (23 bp):
AAGGGGGAATCGGTTCCCCTTCA
Found at i:1904269 original size:19 final size:19
Alignment explanation
Indices: 1904245--1904283 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1904235 TAACTGAAAT
*
1904245 GTATTCGGCTTCAGTGGTA
1 GTATTCGGCTTCAATGGTA
1904264 GTATTCGGCTTCAATGGTA
1 GTATTCGGCTTCAATGGTA
1904283 G
1 G
1904284 ATAATGTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.18, C:0.15, G:0.31, T:0.36
Consensus pattern (19 bp):
GTATTCGGCTTCAATGGTA
Found at i:1907517 original size:20 final size:20
Alignment explanation
Indices: 1907484--1907523 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1907474 GAGTTTATTT
*
1907484 TCATTTTTCAATTTTGAACA
1 TCATTTTTCAATTTTAAACA
1907504 TCATTTTT-ATATTTTAAACA
1 TCATTTTTCA-ATTTTAAACA
1907524 ATTTCTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.33, C:0.12, G:0.03, T:0.53
Consensus pattern (20 bp):
TCATTTTTCAATTTTAAACA
Found at i:1909713 original size:10 final size:10
Alignment explanation
Indices: 1909700--1909797 Score: 64
Period size: 10 Copynumber: 9.6 Consensus size: 10
1909690 TTTTATTTAA
1909700 TTTTTCTTCT
1 TTTTTCTTCT
1909710 TTTTTCTT-T
1 TTTTTCTTCT
1909719 TCTTTTCTT-T
1 T-TTTTCTTCT
*
1909729 TCTTTTTTTCT
1 T-TTTTCTTCT
1909740 CTTTTTCTT-T
1 -TTTTTCTTCT
1909750 TTCTTT-TTCT
1 TT-TTTCTTCT
1909760 TTCTTT-TTCT
1 TT-TTTCTTCT
*
1909770 TTTTCCTGT-T
1 TTTTTCT-TCT
1909780 TCTTCTTCTTCT
1 T-TT-TTCTTCT
1909792 TTTTTC
1 TTTTTC
1909798 AGGCAAAATA
Statistics
Matches: 74, Mismatches: 4, Indels: 20
0.76 0.04 0.20
Matches are distributed among these distances:
9 8 0.11
10 47 0.64
11 13 0.18
12 6 0.08
ACGTcount: A:0.00, C:0.20, G:0.01, T:0.79
Consensus pattern (10 bp):
TTTTTCTTCT
Found at i:1909734 original size:22 final size:23
Alignment explanation
Indices: 1909706--1909795 Score: 82
Period size: 22 Copynumber: 3.9 Consensus size: 23
1909696 TTAATTTTTC
1909706 TTCTTTTTTCTTTTC-TTTTCTT
1 TTCTTTTTTCTTTTCTTTTTCTT
*
1909728 TTC-TTTTT-TTCTCTTTTTCTT
1 TTCTTTTTTCTTTTCTTTTTCTT
1909749 TT-TCTTTTTC-TTTCTTTTTCTTT
1 TTCT-TTTTTCTTTTCTTTTTC-TT
1909772 TTCCTGTTTCTTCTTCTTCTTTTT
1 TT-CT-TTT-TTCTT-TTCTTTTT
1909796 TCAGGCAAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 14
0.76 0.04 0.19
Matches are distributed among these distances:
20 4 0.07
21 14 0.25
22 17 0.31
23 4 0.07
25 4 0.07
26 3 0.05
27 1 0.02
28 8 0.15
ACGTcount: A:0.00, C:0.20, G:0.01, T:0.79
Consensus pattern (23 bp):
TTCTTTTTTCTTTTCTTTTTCTT
Found at i:1909735 original size:6 final size:6
Alignment explanation
Indices: 1909710--1909789 Score: 75
Period size: 6 Copynumber: 14.3 Consensus size: 6
1909700 TTTTTCTTCT
*
1909710 TTTTTC -TTTTC -TTTTC -TTTTC -TTTT- TTTCTC TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
* *
1909753 TTTTTC --TTTC TTTTTC TTTTTCC TGTTTC TTCTTC TT
1 TTTTTC TTTTTC TTTTTC TTTTT-C TTTTTC TTTTTC TT
1909790 CTTTTTTCAG
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
4 4 0.06
5 22 0.34
6 33 0.52
7 5 0.08
ACGTcount: A:0.00, C:0.20, G:0.01, T:0.79
Consensus pattern (6 bp):
TTTTTC
Found at i:1909743 original size:32 final size:33
Alignment explanation
Indices: 1909700--1909767 Score: 97
Period size: 32 Copynumber: 2.1 Consensus size: 33
1909690 TTTTATTTAA
1909700 TTTTTCTTCTTTTT-TCTTTTC-TTTTCTTTTCTT
1 TTTTTCTTCTTTTTCT-TTTTCTTTTTC-TTTCTT
1909733 TTTTTC-TCTTTTTCTTTTTCTTTTTCTTTCTT
1 TTTTTCTTCTTTTTCTTTTTCTTTTTCTTTCTT
1909765 TTT
1 TTT
1909768 CTTTTTCCTG
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
32 21 0.64
33 12 0.36
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (33 bp):
TTTTTCTTCTTTTTCTTTTTCTTTTTCTTTCTT
Found at i:1909758 original size:38 final size:38
Alignment explanation
Indices: 1909702--1909795 Score: 113
Period size: 38 Copynumber: 2.5 Consensus size: 38
1909692 TTATTTAATT
*
1909702 TTTCTTCTTTTT-TCTTTTCTTT-TCTTTTCTTTTTTTCTC
1 TTTCTTCTTTTTCT-TTTTCTTTCT-TTTTC-TTTTTCCTC
*
1909741 TTT-TTCTTTTTCTTTTTCTTTCTTTTTCTTTTTCCTG
1 TTTCTTCTTTTTCTTTTTCTTTCTTTTTCTTTTTCCTC
*
1909778 TTTCTTCTTCTTCTTTTT
1 TTTCTTCTTTTTCTTTTT
1909796 TCAGGCAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
37 10 0.20
38 34 0.69
39 5 0.10
ACGTcount: A:0.00, C:0.20, G:0.01, T:0.79
Consensus pattern (38 bp):
TTTCTTCTTTTTCTTTTTCTTTCTTTTTCTTTTTCCTC
Found at i:1925939 original size:13 final size:12
Alignment explanation
Indices: 1925921--1925971 Score: 57
Period size: 13 Copynumber: 4.1 Consensus size: 12
1925911 ATTGGACCTG
1925921 TAAATAAAACATA
1 TAAATAAAA-ATA
*
1925934 TAAATATAAATA
1 TAAATAAAAATA
*
1925946 TAAAAAAATAATA
1 TAAATAAA-AATA
*
1925959 TAAATAATAATA
1 TAAATAAAAATA
1925971 T
1 T
1925972 CGATATCGGA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
12 14 0.44
13 18 0.56
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (12 bp):
TAAATAAAAATA
Found at i:1925945 original size:19 final size:18
Alignment explanation
Indices: 1925921--1925965 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
1925911 ATTGGACCTG
* *
1925921 TAAATAAAACATATAAATA
1 TAAATAAAAAAAAT-AATA
1925940 TAAATATAAAAAAATAATA
1 TAAATA-AAAAAAATAATA
1925959 TAAATAA
1 TAAATAA
1925966 TAATATCGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 1 0.04
19 16 0.70
20 6 0.26
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (18 bp):
TAAATAAAAAAAATAATA
Found at i:1926463 original size:21 final size:19
Alignment explanation
Indices: 1926412--1926504 Score: 87
Period size: 20 Copynumber: 4.6 Consensus size: 19
1926402 TAAGATTTAA
1926412 AAAAAGTAAATTTAATATTT
1 AAAAA-TAAATTTAATATTT
*
1926432 AAAAATAAAATTCAATATGTAT
1 AAAAAT-AAATTTAATAT-T-T
1926454 AAAAATAAATTTAATATTTT
1 AAAAATAAATTTAATA-TTT
* * * *
1926474 TAAAATGAATTGAAAATTT
1 AAAAATAAATTTAATATTT
*
1926493 AAAAATCAATTT
1 AAAAATAAATTT
1926505 CACCAAAATT
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
19 13 0.22
20 28 0.47
21 11 0.18
22 8 0.13
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (19 bp):
AAAAATAAATTTAATATTT
Found at i:1928369 original size:2 final size:2
Alignment explanation
Indices: 1928362--1928388 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1928352 CTTTTAAAAC
1928362 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
1928389 CCCCCATCCT
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:1932951 original size:2 final size:2
Alignment explanation
Indices: 1932944--1932975 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1932934 CTTTTAAAAC
1932944 AT AT AT 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 AT AT AT
1932976 GCCCCCATCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1933154 original size:12 final size:12
Alignment explanation
Indices: 1933129--1933209 Score: 58
Period size: 12 Copynumber: 6.8 Consensus size: 12
1933119 ACGGAGATAT
* *
1933129 CAGAAATCAAAA
1 CAGAATTCAGAA
1933141 CAGAATTCAGAA
1 CAGAATTCAGAA
1933153 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* * *
1933165 CATAATCCAGAT
1 CAGAATTCAGAA
**
1933177 CAGAATTCAGGT
1 CAGAATTCAGAA
*
1933189 CATGTA-TCAGAA
1 CA-GAATTCAGAA
1933201 CAGAATTCA
1 CAGAATTCA
1933210 AGTCAGAAAT
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
11 4 0.08
12 45 0.85
13 4 0.08
ACGTcount: A:0.47, C:0.19, G:0.15, T:0.20
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1933221 original size:24 final size:24
Alignment explanation
Indices: 1933172--1933224 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1933162 GAACATAATC
* * *
1933172 CAGATCAGAATTCAGGTCATGTAT
1 CAGAACAGAATTCAAGTCATGAAT
1933196 CAGAACAGAATTCAAGTCA-GAAAT
1 CAGAACAGAATTCAAGTCATG-AAT
1933220 CAGAA
1 CAGAA
1933225 AAAATATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.21
Consensus pattern (24 bp):
CAGAACAGAATTCAAGTCATGAAT
Found at i:1938772 original size:27 final size:27
Alignment explanation
Indices: 1938734--1938797 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
1938724 AAGACAAACA
*
1938734 TAAAATTTTATATTAGAAGTGAACTTT
1 TAAAATTTTATATTAGAAATGAACTTT
1938761 TAAAATTTTATATTAGAAATGAACTTT
1 TAAAATTTTATATTAGAAATGAACTTT
1938788 TAAAATTTTA
1 TAAAATTTTA
1938798 GGAGATAACA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (27 bp):
TAAAATTTTATATTAGAAATGAACTTT
Found at i:1940581 original size:21 final size:21
Alignment explanation
Indices: 1940553--1940604 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
1940543 AAGATAACGG
1940553 TAAAATTAATTATTGTAACAA
1 TAAAATTAATTATTGTAACAA
* * * *
1940574 TGAGATTAAATATTTTAACAA
1 TAAAATTAATTATTGTAACAA
1940595 TAAAATTAAT
1 TAAAATTAAT
1940605 CATAACACTA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (21 bp):
TAAAATTAATTATTGTAACAA
Done.