Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 5 of 199
Found at i:1487605 original size:31 final size:29
Alignment explanation
Indices: 1487541--1487606 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
1487531 TTAATGGTAT
*
1487541 AGGGACTAAATTGATCCATTTAATAGTAG
1 AGGGACTAAATTGATCCATTTAATAATAG
* * *
1487570 AGGGACTAATTTGATCAGATCTTTATAATAG
1 AGGGACTAAATTGATC-CAT-TTAATAATAG
1487601 AGGGAC
1 AGGGAC
1487607 CTCCCAGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 15 0.48
30 2 0.06
31 14 0.45
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (29 bp):
AGGGACTAAATTGATCCATTTAATAATAG
Found at i:1490581 original size:30 final size:28
Alignment explanation
Indices: 1490531--1490620 Score: 92
Period size: 28 Copynumber: 3.1 Consensus size: 28
1490521 ATTTTTATTA
** *
1490531 TTTATTATTTTTTTAATTTTAAAATACT
1 TTTATTAAATTTTAAATTTTAAAATACT
1490559 TTTATTAAATTTTAAATTTTTTAAAACTACT
1 TTTATTAAATTTTAAA--TTTTAAAA-TACT
* * *
1490590 TTT-TTAATTTTTTAATTTTAAAATATT
1 TTTATTAAATTTTAAATTTTAAAATACT
1490617 TTTA
1 TTTA
1490621 AAATACTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
27 6 0.12
28 21 0.40
30 18 0.35
31 7 0.13
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (28 bp):
TTTATTAAATTTTAAATTTTAAAATACT
Found at i:1490603 original size:31 final size:29
Alignment explanation
Indices: 1490547--1490620 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 29
1490537 ATTTTTTTAA
1490547 TTTTAAAATACTTTTATTAAATTTTAAATT
1 TTTTAAAATACTTTTATTAAATTTT-AATT
*
1490577 TTTTAAAACTACTTTT-TTAATTTTTTAA--
1 TTTTAAAA-TACTTTTATTAA-ATTTTAATT
*
1490605 TTTTAAAATATTTTTA
1 TTTTAAAATACTTTTA
1490621 AAATACTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
27 6 0.15
28 8 0.21
30 14 0.36
31 11 0.28
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.59
Consensus pattern (29 bp):
TTTTAAAATACTTTTATTAAATTTTAATT
Found at i:1490640 original size:38 final size:38
Alignment explanation
Indices: 1490566--1490647 Score: 118
Period size: 39 Copynumber: 2.2 Consensus size: 38
1490556 ACTTTTATTA
1490566 AATTTT-AAATTTTTTAAAACTACTTTTTTAATTTTTT
1 AATTTTAAAATTTTTTAAAACTACTTTTTTAATTTTTT
1490603 AATTTTAAAATATTTTTAAAA-TACTTTTTTTAA-TTTTT
1 AATTTTAAAAT-TTTTTAAAACTAC-TTTTTTAATTTTTT
1490641 -ATTTTAA
1 AATTTTAA
1490648 TTTTTAAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
37 13 0.31
38 12 0.29
39 17 0.40
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (38 bp):
AATTTTAAAATTTTTTAAAACTACTTTTTTAATTTTTT
Found at i:1505172 original size:20 final size:20
Alignment explanation
Indices: 1505147--1505186 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1505137 GTTCTTGTCA
1505147 TAACATGTC-AGATGTGATTC
1 TAACATGTCGA-ATGTGATTC
1505167 TAACATGTCGAATGTGATTC
1 TAACATGTCGAATGTGATTC
1505187 CGACATGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (20 bp):
TAACATGTCGAATGTGATTC
Found at i:1505192 original size:20 final size:20
Alignment explanation
Indices: 1505148--1505193 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1505138 TTCTTGTCAT
*
1505148 AACATGTCAGATGTGATTCT
1 AACATGTCAGATGTGATTCC
1505168 AACATGTC-GAATGTGATTCC
1 AACATGTCAG-ATGTGATTCC
*
1505188 GACATG
1 AACATG
1505194 CTAGACACAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (20 bp):
AACATGTCAGATGTGATTCC
Found at i:1506071 original size:16 final size:17
Alignment explanation
Indices: 1506027--1506071 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
1506017 AACCAAACCC
1506027 AAAATATTTTTTATTTCA
1 AAAATA-TTTTTATTTCA
* *
1506045 AGAATAATTTTATTT-A
1 AAAATATTTTTATTTCA
1506061 AAAATATTTTT
1 AAAATATTTTT
1506072 TCTTCGAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 10 0.43
17 8 0.35
18 5 0.22
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
AAAATATTTTTATTTCA
Found at i:1506072 original size:17 final size:18
Alignment explanation
Indices: 1506027--1506072 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
1506017 AACCAAACCC
1506027 AAAATATTTTTTATTTCA
1 AAAATATTTTTTATTTCA
* *
1506045 AGAATA-ATTTTATTT-A
1 AAAATATTTTTTATTTCA
1506061 AAAATATTTTTT
1 AAAATATTTTTT
1506073 CTTCGAAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 6 0.26
17 12 0.52
18 5 0.22
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (18 bp):
AAAATATTTTTTATTTCA
Found at i:1514318 original size:23 final size:24
Alignment explanation
Indices: 1514263--1514322 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
1514253 TATAGTATTT
*
1514263 TTTAATTGTTTGTGAACATGTTCAA
1 TTTAA-TGTTTATGAACATGTTCAA
1514288 -TTATATGTTTATGAACATGTT-AA
1 TTTA-ATGTTTATGAACATGTTCAA
1514311 TTTAATGTTTAT
1 TTTAATGTTTAT
1514323 AAATAAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
23 10 0.31
24 21 0.66
25 1 0.03
ACGTcount: A:0.30, C:0.05, G:0.13, T:0.52
Consensus pattern (24 bp):
TTTAATGTTTATGAACATGTTCAA
Found at i:1523820 original size:13 final size:13
Alignment explanation
Indices: 1523802--1523826 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1523792 TCAAATTTTA
1523802 AATATTTTATTCT
1 AATATTTTATTCT
1523815 AATATTTTATTC
1 AATATTTTATTC
1523827 GAACATATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (13 bp):
AATATTTTATTCT
Found at i:1524420 original size:36 final size:37
Alignment explanation
Indices: 1524338--1524422 Score: 95
Period size: 36 Copynumber: 2.3 Consensus size: 37
1524328 AAAATTTATA
* * *
1524338 TTTAATACAATAAATATTTATTTATATTTGTTTGTGTT
1 TTTAATATAA-AAACATTTATTTATATTTGTTAGTGTT
1524376 TTTAATATAAAAACATTTA-TTATATTTGTGGTAGTG-T
1 TTTAATATAAAAACATTTATTTATATTTGT--TAGTGTT
1524413 TTT-ATATAAA
1 TTTAATATAAA
1524423 TAATTTTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
36 17 0.40
37 12 0.29
38 13 0.31
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.53
Consensus pattern (37 bp):
TTTAATATAAAAACATTTATTTATATTTGTTAGTGTT
Found at i:1524677 original size:20 final size:22
Alignment explanation
Indices: 1524635--1524680 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
1524625 CTAATCTGAT
*
1524635 GTCACTTTAAAATTTTATTTTG
1 GTCACTTTAAAATGTTATTTTG
1524657 GTCACTTT-AAATGTT-TTTTG
1 GTCACTTTAAAATGTTATTTTG
1524677 GTCA
1 GTCA
1524681 ATTTTGGACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.39
21 6 0.26
22 8 0.35
ACGTcount: A:0.24, C:0.11, G:0.13, T:0.52
Consensus pattern (22 bp):
GTCACTTTAAAATGTTATTTTG
Found at i:1525231 original size:5 final size:5
Alignment explanation
Indices: 1525221--1525301 Score: 82
Period size: 5 Copynumber: 16.6 Consensus size: 5
1525211 TAAAAAATAT
* *
1525221 TATTA TATTA TAGTAA TGATTA TGTT- T-TTA TATTA TATTA TTATTA
1 TATTA TATTA TA-TTA T-ATTA TATTA TATTA TATTA TATTA -TATTA
1525267 -A-TA TATTA TATTA TATTA TATTA TATTA TA-TA TAT
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT
1525302 ACATAAAACA
Statistics
Matches: 65, Mismatches: 3, Indels: 16
0.77 0.04 0.19
Matches are distributed among these distances:
3 4 0.06
4 8 0.12
5 41 0.63
6 11 0.17
7 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (5 bp):
TATTA
Found at i:1525331 original size:15 final size:15
Alignment explanation
Indices: 1525311--1525352 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
1525301 TACATAAAAC
*
1525311 AAAAGAAAGAATAGA
1 AAAAGAAAGAAAAGA
1525326 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAAGA
*
1525341 AACAGAATAGAA
1 AAAAGAA-AGAA
1525353 GAGACGAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (15 bp):
AAAAGAAAGAAAAGA
Found at i:1526476 original size:24 final size:24
Alignment explanation
Indices: 1526444--1526599 Score: 210
Period size: 24 Copynumber: 6.5 Consensus size: 24
1526434 ACTTTAGCGC
1526444 GCTCTCTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
1526468 GCTCTCTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
1526492 GCTCTCTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
* *
1526516 GCTCTCTTATTATTATCACGTTGGT
1 GCTCTCTGA-TATTAGCACGTTGGT
***
1526541 GCTCTCTGATATTTAGCACGGCAGT
1 GCTCTCTGATA-TTAGCACGTTGGT
* *
1526566 GCTCTCTG-T-TTAGCACATTTGT
1 GCTCTCTGATATTAGCACGTTGGT
1526588 GCTCTCTG-TATT
1 GCTCTCTGATATT
1526600 TGTTCCGTAT
Statistics
Matches: 118, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
22 18 0.15
23 2 0.02
24 59 0.50
25 39 0.33
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.40
Consensus pattern (24 bp):
GCTCTCTGATATTAGCACGTTGGT
Found at i:1527432 original size:17 final size:17
Alignment explanation
Indices: 1527410--1527443 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1527400 ATGTGGCATG
*
1527410 TACCTAGGTAATGTATA
1 TACCTAAGTAATGTATA
*
1527427 TACCTAAGTGATGTATA
1 TACCTAAGTAATGTATA
1527444 AGGGTTAGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (17 bp):
TACCTAAGTAATGTATA
Found at i:1528393 original size:11 final size:11
Alignment explanation
Indices: 1528362--1528404 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
1528352 TATTTTTAAA
*
1528362 ATTTAAAAAGT
1 ATTTTAAAAGT
1528373 ATTTTCAAAAGT
1 ATTTT-AAAAGT
*
1528385 ATTTTAAAAAT
1 ATTTTAAAAGT
1528396 ATTTTAAAA
1 ATTTTAAAA
1528405 TTAAAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 18 0.62
12 11 0.38
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (11 bp):
ATTTTAAAAGT
Found at i:1528447 original size:16 final size:16
Alignment explanation
Indices: 1528426--1528471 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
1528416 AAAAGTATTT
1528426 TAAAAATATTTTAAAA
1 TAAAAATATTTTAAAA
*
1528442 TAAAAAAATTTTAAAA
1 TAAAAATATTTTAAAA
1528458 -AATAAATATATTTA
1 TAA-AAATAT-TTTA
1528472 TTATATCGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 2 0.08
16 20 0.77
17 4 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAAAATATTTTAAAA
Found at i:1551733 original size:21 final size:21
Alignment explanation
Indices: 1551707--1551746 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1551697 ACTAAGTGTG
1551707 GGCTTAATTAGTAATTAAAAT
1 GGCTTAATTAGTAATTAAAAT
*
1551728 GGCTTAATTAGTTATTAAA
1 GGCTTAATTAGTAATTAAA
1551747 TTTTAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (21 bp):
GGCTTAATTAGTAATTAAAAT
Found at i:1551852 original size:81 final size:82
Alignment explanation
Indices: 1551763--1551928 Score: 298
Period size: 81 Copynumber: 2.0 Consensus size: 82
1551753 TTTTGTTAAC
1551763 ATATTTTTATTTTAATAATTAAATTTAAATAAAAATGTTAAC-TAATAAATAGTAATTAAGCCGG
1 ATATTTTTATTTTAATAATTAAATTTAAATAAAAATGTTAACTTAATAAATAGTAATTAAGCCGG
1551827 ATACGAATTGGATGGAA
66 ATACGAATTGGATGGAA
* *
1551844 ATATTTTTATTTTAATAATTAAATTTAAATAAAAGTGTTAACTTAATAAATAGTAATTAAGTCGG
1 ATATTTTTATTTTAATAATTAAATTTAAATAAAAATGTTAACTTAATAAATAGTAATTAAGCCGG
*
1551909 ATATGAATTGGATGGAA
66 ATACGAATTGGATGGAA
1551926 ATA
1 ATA
1551929 GAAGATTGAG
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
81 41 0.51
82 40 0.49
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.39
Consensus pattern (82 bp):
ATATTTTTATTTTAATAATTAAATTTAAATAAAAATGTTAACTTAATAAATAGTAATTAAGCCGG
ATACGAATTGGATGGAA
Found at i:1555224 original size:5 final size:6
Alignment explanation
Indices: 1555206--1555231 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1555196 CATAGGATCT
1555206 AATAAA AATAAA AATAAA AATAAA AA
1 AATAAA AATAAA AATAAA AATAAA AA
1555232 GTCGAGTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AATAAA
Found at i:1559135 original size:60 final size:60
Alignment explanation
Indices: 1559041--1559158 Score: 227
Period size: 60 Copynumber: 2.0 Consensus size: 60
1559031 TTGTTTGATA
1559041 GATGTACTTGGACTACCGGAGTTTGAAAAACATTGATGACATGTCCAAGTTGAAAAAATT
1 GATGTACTTGGACTACCGGAGTTTGAAAAACATTGATGACATGTCCAAGTTGAAAAAATT
*
1559101 GATGTACTTGGACTACCGGAGTTTGAAAAGCATTGATGACATGTCCAAGTTGAAAAAA
1 GATGTACTTGGACTACCGGAGTTTGAAAAACATTGATGACATGTCCAAGTTGAAAAAA
1559159 AAATTAATTG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (60 bp):
GATGTACTTGGACTACCGGAGTTTGAAAAACATTGATGACATGTCCAAGTTGAAAAAATT
Found at i:1559821 original size:61 final size:61
Alignment explanation
Indices: 1559756--1559876 Score: 154
Period size: 61 Copynumber: 2.0 Consensus size: 61
1559746 TTTAATTTTT
* * *
1559756 TTGAAAAG-TTTAGAAGTAGAAATAAATTGACAATTTTTGTAAACGTTGAGGACTAAATTTA
1 TTGAAAAGTTTTAGAA-TAGAAATAAAATGACAAATTTTATAAACGTTGAGGACTAAATTTA
** * * *
1559817 TTGAATTGTTTTAGAATTGAATTAAAATGACAAATTTTATAAACGTTGAGGGCTAAATTT
1 TTGAAAAGTTTTAGAATAGAAATAAAATGACAAATTTTATAAACGTTGAGGACTAAATTT
1559877 GTTATTAGGC
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
61 44 0.86
62 7 0.14
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.37
Consensus pattern (61 bp):
TTGAAAAGTTTTAGAATAGAAATAAAATGACAAATTTTATAAACGTTGAGGACTAAATTTA
Found at i:1579474 original size:3 final size:3
Alignment explanation
Indices: 1579468--1579520 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
1579458 TATGTGGTGC
1579468 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1579516 CAT CA
1 CAT CA
1579521 AATCTTTGAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:1583039 original size:16 final size:16
Alignment explanation
Indices: 1583018--1583053 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1583008 TGGAGTATTA
*
1583018 TTATATTATATTAAAT
1 TTATATTACATTAAAT
*
1583034 TTATATTACATTATAT
1 TTATATTACATTAAAT
1583050 TTAT
1 TTAT
1583054 CTGTTAGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATATTACATTAAAT
Found at i:1586573 original size:5 final size:5
Alignment explanation
Indices: 1586565--1586590 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1586555 AAGTTGTAAG
1586565 ATTTT ATTTT ATTTT ATTTT ATTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT A
1586591 AACACTTGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:1589913 original size:52 final size:52
Alignment explanation
Indices: 1589842--1590091 Score: 386
Period size: 52 Copynumber: 4.9 Consensus size: 52
1589832 ATCAAGTGAC
* **
1589842 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
* *
1589894 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC------
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
*
1589940 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
1589992 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
* *
1590044 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGACAA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
1590092 AGTGATAAGT
Statistics
Matches: 182, Mismatches: 10, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
46 44 0.24
52 138 0.76
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.28
Consensus pattern (52 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
Found at i:1589948 original size:98 final size:98
Alignment explanation
Indices: 1589828--1590102 Score: 406
Period size: 98 Copynumber: 2.7 Consensus size: 98
1589818 TTTGAGTACT
* **
1589828 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
* *
1589893 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTACACTTA
1589926 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
*
1589991 AAAAGTGATAAGTGATAGCTTCGGCTACACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTACACTTA
* *
1590024 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
*
1590089 CAAAGTGATAAGTG
60 C-AAGTGAAAAGTG
1590103 GCTACACTTA
Statistics
Matches: 161, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
98 106 0.66
104 44 0.27
105 11 0.07
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTACACTTA
Found at i:1590112 original size:37 final size:37
Alignment explanation
Indices: 1590065--1590174 Score: 161
Period size: 37 Copynumber: 3.0 Consensus size: 37
1590055 TAATAGCTTC
* *
1590065 GGCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
* *
1590102 GGCTACACTTATCTGATCAAGAAACAAAGTGATAGGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
*
1590139 GGCTACACTTATCTGATC-AGGGAC-AAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
1590174 G
1 G
1590175 ATCATACGTA
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
35 11 0.17
36 4 0.06
37 51 0.77
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (37 bp):
GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
Found at i:1591503 original size:58 final size:59
Alignment explanation
Indices: 1591427--1591598 Score: 226
Period size: 58 Copynumber: 3.1 Consensus size: 59
1591417 CATGTGAACA
*
1591427 TGTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCGTCGGTAAGTGATATG
1 TGTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
1591486 TGTGA-TATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATA--
1 TGTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
* *
1591542 TGTG---A--T--TT-CGTGTAAGACCATAGTTGGGCTATGGCATCGGTATGTGAT-T-
1 TGTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
1591591 TGTGATTA
1 TGTGATTA
1591599 CGTGTAAGAC
Statistics
Matches: 106, Mismatches: 3, Indels: 15
0.85 0.02 0.12
Matches are distributed among these distances:
49 42 0.40
50 2 0.02
52 2 0.02
54 1 0.01
56 4 0.04
58 50 0.47
59 5 0.05
ACGTcount: A:0.23, C:0.13, G:0.31, T:0.34
Consensus pattern (59 bp):
TGTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
Found at i:1591536 original size:28 final size:28
Alignment explanation
Indices: 1591446--1591536 Score: 71
Period size: 28 Copynumber: 3.2 Consensus size: 28
1591436 GTGATTCCGT
*
1591446 GTAAGACCATAGCTGGGCTATGGCGTCG
1 GTAAGACCATAGCTGGGCTATGGCATCG
** * *
1591474 GTAAG-TGATATG-TGTGATATGTG-ATTCCG
1 GTAAGACCATA-GCTGGGCTATG-GCA-T-CG
1591503 TGTAAGACCATAGCTGGGCTATGGCATCG
1 -GTAAGACCATAGCTGGGCTATGGCATCG
1591532 GTAAG
1 GTAAG
1591537 TGATATGTGA
Statistics
Matches: 46, Mismatches: 9, Indels: 16
0.65 0.13 0.23
Matches are distributed among these distances:
27 10 0.22
28 13 0.28
29 4 0.09
30 8 0.17
31 11 0.24
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.27
Consensus pattern (28 bp):
GTAAGACCATAGCTGGGCTATGGCATCG
Found at i:1591559 original size:49 final size:49
Alignment explanation
Indices: 1591487--1591629 Score: 232
Period size: 49 Copynumber: 2.9 Consensus size: 49
1591477 AGTGATATGT
* *
1591487 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
* *
1591536 GTGATATGTGATTTCGTGTAAGACCATAGTTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
* *
1591585 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCG
1591630 AGAAAACGAA
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 88 1.00
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.32
Consensus pattern (49 bp):
GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
Found at i:1594836 original size:52 final size:52
Alignment explanation
Indices: 1594765--1595014 Score: 386
Period size: 52 Copynumber: 4.9 Consensus size: 52
1594755 ATCAAGTGAC
* **
1594765 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
* *
1594817 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC------
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
*
1594863 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
1594915 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
* *
1594967 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGACAA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
1595015 AGTGATAAGT
Statistics
Matches: 182, Mismatches: 10, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
46 44 0.24
52 138 0.76
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.28
Consensus pattern (52 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
Found at i:1594871 original size:98 final size:98
Alignment explanation
Indices: 1594751--1595025 Score: 406
Period size: 98 Copynumber: 2.7 Consensus size: 98
1594741 TTTGAGTACT
* **
1594751 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
* *
1594816 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTACACTTA
1594849 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
*
1594914 AAAAGTGATAAGTGATAGCTTCGGCTACACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTACACTTA
* *
1594947 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
*
1595012 CAAAGTGATAAGTG
60 C-AAGTGAAAAGTG
1595026 GCTACACTTA
Statistics
Matches: 161, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
98 106 0.66
104 44 0.27
105 11 0.07
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTACACTTA
Found at i:1595035 original size:37 final size:37
Alignment explanation
Indices: 1594988--1595097 Score: 161
Period size: 37 Copynumber: 3.0 Consensus size: 37
1594978 TAATAGCTTC
* *
1594988 GGCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
* *
1595025 GGCTACACTTATCTGATCAAGAAACAAAGTGATAGGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
*
1595062 GGCTACACTTATCTGATC-AGGGAC-AAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
1595097 G
1 G
1595098 ATCATACGTA
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
35 11 0.17
36 4 0.06
37 51 0.77
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (37 bp):
GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
Found at i:1602148 original size:24 final size:24
Alignment explanation
Indices: 1602107--1602167 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
1602097 TTTACGTGCT
*
1602107 TATTTTTA-AATTTATTAAGTAATA
1 TATTTTTATAATTTATTAA-AAATA
*
1602131 TATTTTTATCATTT-TTAAAAATA
1 TATTTTTATAATTTATTAAAAATA
*
1602154 TATATTTATTAATT
1 TATTTTTA-TAATT
1602168 AAATGAGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
23 11 0.35
24 16 0.52
25 4 0.13
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
TATTTTTATAATTTATTAAAAATA
Found at i:1607192 original size:39 final size:39
Alignment explanation
Indices: 1607134--1607214 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 39
1607124 ATTTTGAGAG
*
1607134 TTAAAATATAATTTTACTATATATATACATGCATATTTA
1 TTAAAATATAATTTGACTATATATATACATGCATATTTA
* *
1607173 TTAAAGTATAATTTGACTATATATATACATTCATATTTA
1 TTAAAATATAATTTGACTATATATATACATGCATATTTA
1607212 TTA
1 TTA
1607215 TTTATGAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (39 bp):
TTAAAATATAATTTGACTATATATATACATGCATATTTA
Found at i:1608349 original size:29 final size:29
Alignment explanation
Indices: 1608299--1608370 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
1608289 AGTTCATACC
*
1608299 TTTATAAATTTTAAAGGATTAAATTA-AATT
1 TTTAT-AATTTTAAAGGATTAAAATATAA-T
** *
1608329 TTTATAATTTTAGGGGGTTAAAATATAAT
1 TTTATAATTTTAAAGGATTAAAATATAAT
1608358 TTTA-AATTTTAAA
1 TTTATAATTTTAAA
1608371 TTTTTTATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
28 7 0.20
29 21 0.60
30 7 0.20
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (29 bp):
TTTATAATTTTAAAGGATTAAAATATAAT
Found at i:1608559 original size:101 final size:101
Alignment explanation
Indices: 1608398--1608595 Score: 308
Period size: 101 Copynumber: 2.0 Consensus size: 101
1608388 AAGGATCAAA
* * *
1608398 ATCTACTCTCGTGAAAAAAAAATAAAAAAGATATATGATCGTAACTTTTCACCCAATTAAGCCAT
1 ATCTACTCTCGTGAAAAAAAAATAAAAAAGATATATCATCGTAACTTCTCACCCAATTAAGACAT
1608463 TATCGA-AAAAAAGAAATAATTGTTTAAACCTTGAC
66 TATCGACAAAAAAGAAATAATTGTTTAAACCTTGAC
* * * *
1608498 ATCTGCTCTCGTTAAAAAAAATTAAAAAAAGATATATCATCGTAACTTCTCACCCAATTAAGATA
1 ATCTACTCTCGTGAAAAAAAAAT-AAAAAAGATATATCATCGTAACTTCTCACCCAATTAAGACA
*
1608563 TTATTGACAAAAAAGAAATAATTGTTTAAACCT
65 TTATCGACAAAAAAGAAATAATTGTTTAAACCT
1608596 GTACGTGAGT
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
100 20 0.23
101 43 0.49
102 25 0.28
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.29
Consensus pattern (101 bp):
ATCTACTCTCGTGAAAAAAAAATAAAAAAGATATATCATCGTAACTTCTCACCCAATTAAGACAT
TATCGACAAAAAAGAAATAATTGTTTAAACCTTGAC
Found at i:1610872 original size:5 final size:6
Alignment explanation
Indices: 1610855--1610880 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1610845 ATATATTAAA
1610855 TATTTT TATTTT TATTTT TATTTT TA
1 TATTTT TATTTT TATTTT TATTTT TA
1610881 ATCAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TATTTT
Found at i:1610912 original size:16 final size:16
Alignment explanation
Indices: 1610873--1610912 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1610863 TTTTTATTTT
*
1610873 TATTTTTAATCAAATA
1 TATTTTTTATCAAATA
* *
1610889 TACTTTTTATTAAATA
1 TATTTTTTATCAAATA
1610905 TATTTTTT
1 TATTTTTT
1610913 GGACTTTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTTTTTATCAAATA
Found at i:1616444 original size:27 final size:27
Alignment explanation
Indices: 1616414--1616483 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
1616404 AATAATCAAT
*
1616414 TCAATATCCAACAATGTTAAAACATA-A
1 TCAATATCCAACAAT-TCAAAACATATA
* *
1616441 TCAATATCTAACCAATTCAAGACATATA
1 TCAATATCCAA-CAATTCAAAACATATA
*
1616469 TCAAAATCCAACAAT
1 TCAATATCCAACAAT
1616484 CTAAAATCTG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.50, C:0.21, G:0.03, T:0.26
Consensus pattern (27 bp):
TCAATATCCAACAATTCAAAACATATA
Found at i:1622276 original size:21 final size:22
Alignment explanation
Indices: 1622250--1622296 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
1622240 CTCTGCTCAA
*
1622250 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
1622271 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
1622293 ACTC
1 ACTC
1622297 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:1629243 original size:16 final size:16
Alignment explanation
Indices: 1629212--1629263 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
1629202 GATGTTAACA
*
1629212 TTATTTTGAGTTTCATT
1 TTATTTCGA-TTTCATT
*
1629229 TTATATT-TATTTCATT
1 TTAT-TTCGATTTCATT
*
1629245 TCATTTCGATTTCATT
1 TTATTTCGATTTCATT
1629261 TTA
1 TTA
1629264 CTTTGGGTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
15 2 0.07
16 20 0.69
17 5 0.17
18 2 0.07
ACGTcount: A:0.21, C:0.10, G:0.06, T:0.63
Consensus pattern (16 bp):
TTATTTCGATTTCATT
Found at i:1637148 original size:113 final size:113
Alignment explanation
Indices: 1636950--1637176 Score: 436
Period size: 113 Copynumber: 2.0 Consensus size: 113
1636940 AATGGATAAG
*
1636950 GTAGTAACAATTGTGCACTATTAAACTATCTCATGTAAGAGAAATTTGTGACCTTTCTGACTACA
1 GTAGTAACAATTGTGCACTATTAAACTATCTCATGTAAGAGAAATTTGTGACCTTTCTGACCACA
1637015 GGTTAACCCTAAGTTGAAAGCTCAAACATTCAATTACCATATTGGAGA
66 GGTTAACCCTAAGTTGAAAGCTCAAACATTCAATTACCATATTGGAGA
*
1637063 GTAGTAACAATTGTGCACTATTAAACTATCTCATGTAAGAGAAGTTTGTGACCTTTCTGACCACA
1 GTAGTAACAATTGTGCACTATTAAACTATCTCATGTAAGAGAAATTTGTGACCTTTCTGACCACA
1637128 GGTTAACCCTAAGTTGAAAGCTCAAACATTCAATTACCATATTGGAGA
66 GGTTAACCCTAAGTTGAAAGCTCAAACATTCAATTACCATATTGGAGA
1637176 G
1 G
1637177 ACCTCTCCAT
Statistics
Matches: 112, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 112 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (113 bp):
GTAGTAACAATTGTGCACTATTAAACTATCTCATGTAAGAGAAATTTGTGACCTTTCTGACCACA
GGTTAACCCTAAGTTGAAAGCTCAAACATTCAATTACCATATTGGAGA
Found at i:1651440 original size:16 final size:16
Alignment explanation
Indices: 1651419--1651486 Score: 102
Period size: 16 Copynumber: 4.2 Consensus size: 16
1651409 TTTGGTTCGC
1651419 TGTATTGGATTAGAGA
1 TGTATTGGATTAGAGA
1651435 TGTATTGGATTAGA-A
1 TGTATTGGATTAGAGA
*
1651450 GTGTATTGGATTAGAGG
1 -TGTATTGGATTAGAGA
*
1651467 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGA
1651483 TGTA
1 TGTA
1651487 ATAGCAAATC
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
15 1 0.02
16 48 0.98
ACGTcount: A:0.28, C:0.00, G:0.34, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGA
Found at i:1651455 original size:32 final size:32
Alignment explanation
Indices: 1651419--1651486 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
1651409 TTTGGTTCGC
1651419 TGTATTGGATTAGAGATGTATTGGATTAGAAG
1 TGTATTGGATTAGAGATGTATTGGATTAGAAG
* *
1651451 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGATGTATTGGATTAGAAG
1651483 TGTA
1 TGTA
1651487 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.28, C:0.00, G:0.34, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGATGTATTGGATTAGAAG
Found at i:1651823 original size:157 final size:157
Alignment explanation
Indices: 1651616--1651925 Score: 530
Period size: 157 Copynumber: 2.0 Consensus size: 157
1651606 CCCTTAGCAT
*
1651616 AAATTTATTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTATCAA
1 AAATTTATTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
* * *
1651681 TAATGAATATTTTAATCATATTTAAACATAATTATTATTAAACATATTTTAATTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTATAATTAAAATATATAA
1651746 TTTAATAAAATTCTTAATAATTACCAA
131 TTTAATAAAATTCTTAATAATTACCAA
* * * *
1651773 AAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTGATAAGATTATTAATATGAA
1 AAATTTATTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
* *
1651838 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATACTTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTATAATTAAAATATATAA
1651903 TTTAATAAAATTCTTAATAATTA
131 TTTAATAAAATTCTTAATAATTA
1651926 ATATTCTTAT
Statistics
Matches: 143, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
157 143 1.00
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (157 bp):
AAATTTATTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTATAATTAAAATATATAA
TTTAATAAAATTCTTAATAATTACCAA
Found at i:1665396 original size:28 final size:30
Alignment explanation
Indices: 1665327--1665381 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
1665317 TTCGTATTTA
*
1665327 AAAATATTAAATATTATTATAAAAATATTG
1 AAAATATAAAATATTATTATAAAAATATTG
1665357 AAAATATAAAAT-TTATTA-AAAAATA
1 AAAATATAAAATATTATTATAAAAATA
1665382 ATTTAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 7 0.29
29 6 0.25
30 11 0.46
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (30 bp):
AAAATATAAAATATTATTATAAAAATATTG
Found at i:1673230 original size:11 final size:10
Alignment explanation
Indices: 1673216--1673280 Score: 55
Period size: 11 Copynumber: 6.4 Consensus size: 10
1673206 AAAATTTAAA
1673216 AAAAGTATTTT
1 AAAA-TATTTT
1673227 AAAATATTTT
1 AAAATATTTT
*
1673237 AAAA-A--TA
1 AAAATATTTT
*
1673244 AAAATATTTAA
1 AAAATATTT-T
1673255 AAAAGTATTTT
1 AAAA-TATTTT
1673266 AAAATATTTTT
1 AAAATA-TTTT
1673277 AAAA
1 AAAA
1673281 ATAAAAAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
7 5 0.11
8 1 0.02
9 1 0.02
10 13 0.28
11 21 0.46
12 5 0.11
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (10 bp):
AAAATATTTT
Found at i:1673247 original size:39 final size:39
Alignment explanation
Indices: 1673204--1673289 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
1673194 AATAAACACA
1673204 AAAAAATTTAAAAAAAGTATTTTAAAATA-TTTTAAAAAT
1 AAAAAATTT-AAAAAAGTATTTTAAAATATTTTTAAAAAT
1673243 AAAAATATTTAAAAAAGTATTTTAAAATATTTTTAAAAAT
1 AAAAA-ATTTAAAAAAGTATTTTAAAATATTTTTAAAAAT
1673283 AAAAAAT
1 AAAAAAT
1673290 ATATATTTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
39 26 0.58
40 19 0.42
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (39 bp):
AAAAAATTTAAAAAAGTATTTTAAAATATTTTTAAAAAT
Found at i:1673253 original size:40 final size:40
Alignment explanation
Indices: 1673203--1673288 Score: 147
Period size: 40 Copynumber: 2.1 Consensus size: 40
1673193 AAATAAACAC
1673203 AAAAAAATTTAAAAAAAGTATTTTAAAATA-TTTTAAAAAT
1 AAAAAAATTT-AAAAAAGTATTTTAAAATATTTTTAAAAAT
*
1673243 AAAAATATTTAAAAAAGTATTTTAAAATATTTTTAAAAAT
1 AAAAAAATTTAAAAAAGTATTTTAAAATATTTTTAAAAAT
1673283 AAAAAA
1 AAAAAA
1673289 TATATATTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
39 19 0.44
40 24 0.56
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (40 bp):
AAAAAAATTTAAAAAAGTATTTTAAAATATTTTTAAAAAT
Found at i:1683748 original size:17 final size:17
Alignment explanation
Indices: 1683706--1683748 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1683696 ATTATTGAAC
1683706 TAATTTTTTCTATTTTA
1 TAATTTTTTCTATTTTA
*
1683723 AAATATTTTT-TATTTATA
1 TAAT-TTTTTCTATTT-TA
1683741 TAATTTTT
1 TAATTTTT
1683749 AATTAAACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TAATTTTTTCTATTTTA
Found at i:1687886 original size:236 final size:231
Alignment explanation
Indices: 1687477--1687947 Score: 879
Period size: 236 Copynumber: 2.0 Consensus size: 231
1687467 TTGTAACCGG
1687477 ATTTTGCTTAAAGTATCGAGCTCATTGCGGTCCAACATGTCTGAACTATAGGATTCACTATCACC
1 ATTTTGCTTAAAGTATCGAGCTCATTGCGGTCCAACATGTCTGAACTATAGGATTCACTATCACC
1687542 AATCTACATCATCGAGAAACCTGGAGGGGTAGCTACAAATCCTGAAAGGATTAGATCTTATAGAG
66 AATCTACATCATCGAGAAACCTGGAGGGGTAGCTACAAATCCTGAAAGGATTAGATCTTATAGAG
1687607 AGATACCTCCATTTTTAATAGGGGTAACCACGATCCCGGAAATGTTTAGTATTTAATAGAGATTG
131 AGATACCTCCATTTTTAATAGGGGTAACCACGATCCCGGAAATGTTTAGTATTTAATAGAGATTG
*
1687672 TCACGAACCCGTAAAGAATCAGTTTCTGTGAATTCC
196 TCACGAACCCATAAAGAATCAGTTTCTGTGAATTCC
1687708 ATTTTGCTTAAAGTATCGAGCTCATTGCGGTCCAACATGTCTGAACTATAGGATTCACTATCACC
1 ATTTTGCTTAAAGTATCGAGCTCATTGCGGTCCAACATGTCTGAACTATAGGATTCACTATCACC
1687773 AATCTACATCATCGAGAAACCTAGAGGGGAGGGGTAGCTACAAATCCTGAAAGGATTAGATCTTA
66 AATCTACATCATCGAGAAACCT-----GGAGGGGTAGCTACAAATCCTGAAAGGATTAGATCTTA
1687838 TAGAGAGATACCTCCATTTTTAATAGGGGTAACCACGATCCCGGAAATGTTTAGTATTTAATAGA
126 TAGAGAGATACCTCCATTTTTAATAGGGGTAACCACGATCCCGGAAATGTTTAGTATTTAATAGA
*
1687903 GATTGTCACGAACCCATAAAGAATTAGTTTCTGTGAATTCC
191 GATTGTCACGAACCCATAAAGAATCAGTTTCTGTGAATTCC
1687944 ATTT
1 ATTT
1687948 AGGAGGGGTA
Statistics
Matches: 233, Mismatches: 2, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
231 87 0.37
236 146 0.63
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (231 bp):
ATTTTGCTTAAAGTATCGAGCTCATTGCGGTCCAACATGTCTGAACTATAGGATTCACTATCACC
AATCTACATCATCGAGAAACCTGGAGGGGTAGCTACAAATCCTGAAAGGATTAGATCTTATAGAG
AGATACCTCCATTTTTAATAGGGGTAACCACGATCCCGGAAATGTTTAGTATTTAATAGAGATTG
TCACGAACCCATAAAGAATCAGTTTCTGTGAATTCC
Found at i:1700958 original size:113 final size:114
Alignment explanation
Indices: 1700748--1700958 Score: 275
Period size: 113 Copynumber: 1.9 Consensus size: 114
1700738 AAGTAGGGAC
* *** *
1700748 GGATCTAGGGGTGAAGTTAGAAAATTATTTTAGGTGGTTAGAAATAAATAATAAATTTTAGGAGG
1 GGATCTAGGGGTGAAGCTAGAAAATTATTTTAGGTCACTAGAAATAAATAATAAATTTAAGGAGG
** *
1700813 CCAAAGTGTAATTTTACTATTATATTAACTTATGCATTAAAGCAAGGGT
66 CCAAAGTACAATTTTACCATTATATTAACTTATGCATTAAAGCAAGGGT
* *
1700862 GGATCTAGGGGTGAAGCTAGAAAATT-TATTTAGG-CACTAGAAATGAATAATGAATTTAAGG-G
1 GGATCTAGGGGTGAAGCTAGAAAATTAT-TTTAGGTCACTAGAAATAAATAATAAATTTAAGGAG
* *
1700924 AGCTAAATTACAATTTTACCATTATATTAACTTAT
65 -GCCAAAGTACAATTTTACCATTATATTAACTTAT
1700959 AAATTTATAA
Statistics
Matches: 83, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
112 1 0.01
113 51 0.61
114 31 0.37
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.34
Consensus pattern (114 bp):
GGATCTAGGGGTGAAGCTAGAAAATTATTTTAGGTCACTAGAAATAAATAATAAATTTAAGGAGG
CCAAAGTACAATTTTACCATTATATTAACTTATGCATTAAAGCAAGGGT
Found at i:1704149 original size:23 final size:23
Alignment explanation
Indices: 1704123--1704176 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
1704113 TGATTTTAAA
* *
1704123 ATTTTGAATTATTTAGTAATAAT
1 ATTTAGAATTATTTAATAATAAT
*
1704146 ATTTAGAATTATTTAATGATAAT
1 ATTTAGAATTATTTAATAATAAT
1704169 ATTTAGAA
1 ATTTAGAA
1704177 AAAATCTAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (23 bp):
ATTTAGAATTATTTAATAATAAT
Found at i:1704342 original size:14 final size:15
Alignment explanation
Indices: 1704313--1704346 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1704303 GTCACACATA
*
1704313 TTTTGTTCTTTCAAT
1 TTTTTTTCTTTCAAT
1704328 TTTTTTTCTTT-AAT
1 TTTTTTTCTTTCAAT
1704342 TTTTT
1 TTTTT
1704347 GGTTTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.12, C:0.09, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTTTTCTTTCAAT
Found at i:1710273 original size:5 final size:6
Alignment explanation
Indices: 1710258--1710283 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1710248 TAACTTTGAC
1710258 AAAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AA
1710284 TTATTAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:1712035 original size:89 final size:88
Alignment explanation
Indices: 1711921--1712755 Score: 573
Period size: 89 Copynumber: 9.5 Consensus size: 88
1711911 TCCGATAGGG
* ** * *
1711921 TGACACAGTTGAGCATCTTGTAGTAACAGGTGAATCTATGTCTTCGGTCGAGGTTTTGTCTCCCG
1 TGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACTATGTC-CCGGTCGAGGTTTTGTCTCCCG
* * *
1711986 CCTCTGTCGAGAATCCTGTCAGGA
65 ACTCTATCGAGACTCCTGTCAGGA
* * * * *
1712010 TG-CTAGAGTTGAGTGTCTTGTAGTAACAGTTGAATCTATATCCTTGGTGGAGGTTTTGTCTCCC
1 TGAC-AGAGTTGAGTGTCTTGTAGTAACAGGTGAAACTATGTCC-CGGTCGAGGTTTTGTCTCCC
* * * * *
1712074 GATTCT-GCTGAGAATACTGTCAGGT
64 GACTCTATC-GAGACTCCTGTCAGGA
* * * * * *
1712099 TGATAGAGTCGAGTGTCTTGTAGTAACAGGTGAAACCATGTCGCTGTCTAGGTTTTGTCTCCCGA
1 TGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACTATGTCCCGGTCGAGGTTTTGTCTCCCGA
*
1712164 CTCTACCGAGACTCCTGAT-AGGA
66 CTCTATCGAGACTCCTG-TCAGGA
* * * * * *
1712187 TGACAGAGTTGTGTTTCATGTAGTAACAGGTGAAACTATATCCCCGGTTGAGGTTTTGTCCCCCG
1 TGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACTATGT-CCCGGTCGAGGTTTTGTCTCCCG
* *
1712252 GCTCTA-CAGAGACTCCTGTTAGG-
65 ACTCTATC-GAGACTCCTGTCAGGA
* * * * * ** * *
1712275 TGGACAAAGTTGAGTGTTTTGCAGTAACAAGTGAAACTGTGTCCCTTTTGAGCTTTTGTCTCCCG
1 T-GACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACTATGTCCCGGTCGAGGTTTTGTCTCCCG
* * *
1712340 ACTCTATCGAGACTCCTATTAGGTT
65 ACTCTATCGAGACTCCTGTCAGG-A
* ** * * * *
1712365 TGACAGAGTTGAGTGTCCTGTAGTAACAGGTGAAACCGTGTCCTAGGTTGAGGTTTGGTCTCCTG
1 TGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACTATGTCC-CGGTCGAGGTTTTGTCTCCCG
** *
1712430 ACTCTA-CTGAGACTATTGT-AGGT
65 ACTCTATC-GAGACTCCTGTCAGGA
* * * * *
1712453 TGACAGCA-TT--GTG--ATGTAGTAACAGGTGAAACCATGTTCCCGGTCGAAGTTTTATCTCCT
1 TGACAG-AGTTGAGTGTCTTGTAGTAACAGGTGAAACTATG-TCCCGGTCGAGGTTTTGTCTCCC
* * * * ** *
1712513 AACTCTACCGAGACTCTTATTGGGT
64 GACTCTATCGAGACTCCTGTCAGGA
** * * * * *
1712538 TGTTAGAGTTGAGTTTCTTGTAGTAACAAGTGAAACCATGTCTCCTGTC-AGGGTTTTGTTTCCC
1 TGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACTATGTC-CCGGTCGA-GGTTTTGTCTCCC
* * * * * * *
1712602 TACTTTACCGAGACTCATATTAGGT
64 GACTCTATCGAGACTCCTGTCAGGA
* * * ** * * **
1712627 TGACAGAGTTGAGTGTTTTATACTAACAGGTG-AACCGTGTCCCCGGTCAAGGTTCTGTCTCCTA
1 TGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACTATGT-CCCGGTCGAGGTTTTGTCTCCCG
* * * *
1712691 ACTCTACCGAGAATCCTATCAGGT
65 ACTCTATCGAGACTCCTGTCAGGA
*
1712715 TGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCATGT
1 TGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACTATGT
1712756 GAAACTAAAG
Statistics
Matches: 599, Mismatches: 118, Indels: 58
0.77 0.15 0.07
Matches are distributed among these distances:
84 52 0.09
85 13 0.02
86 3 0.01
87 2 0.00
88 192 0.32
89 307 0.51
90 30 0.05
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.33
Consensus pattern (88 bp):
TGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACTATGTCCCGGTCGAGGTTTTGTCTCCCGA
CTCTATCGAGACTCCTGTCAGGA
Found at i:1712197 original size:177 final size:176
Alignment explanation
Indices: 1711936--1712753 Score: 704
Period size: 177 Copynumber: 4.6 Consensus size: 176
1711926 CAGTTGAGCA
* * * * ** *
1711936 TCTTGTAGTAACAGGTGAATCTATGTCTTCGGTCGAGGTTTTGTCTCCCGCCTCTGTCGAGAATC
1 TCTTGTAGTAACAGGTGAAACCATGTC-CCGGTCGAGGTTTTGTCTCCCGACTCTACCGAGACTC
* * * * * * *
1712001 CTGTCAGGATG-CTAGAGTTGAGTGTCTTGTAGTAACAGTTGAATCTATATCCTTGGTGGAGGTT
65 CTAT-AGGTTGAC-AGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCATATCCCTGGTTGAGGTT
* * * * *
1712065 TTGTCTCCCGATTCTGCTGAGAATACTGTCAGGTTGATAGAGTCGAGTG
128 TTGTCTCCCGACTCTACTGAGACTACTGTTAGGTTGACAGAGTCGAGTG
* * *
1712114 TCTTGTAGTAACAGGTGAAACCATGTCGCTGTCTAGGTTTTGTCTCCCGACTCTACCGAGACTCC
1 TCTTGTAGTAACAGGTGAAACCATGTCCCGGTCGAGGTTTTGTCTCCCGACTCTACCGAGACTCC
* * * * * *
1712179 TGATAGGATGACAGAGTTGTGTTTCATGTAGTAACAGGTGAAACTATATCCCCGGTTGAGGTTTT
66 T-ATAGGTTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCATATCCCTGGTTGAGGTTTT
* * * * * * *
1712244 GTCCCCCGGCTCTACAGAGACTCCTGTTAGGTGGACAAAGTTGAGTG
130 GTCTCCCGACTCTACTGAGACTACTGTTAGGTTGACAGAGTCGAGTG
* * * ** ** * * *
1712291 TTTTGCAGTAACAAGTGAAACTGTGTCCCTTTTGAGCTTTTGTCTCCCGACTCTATCGAGACTCC
1 TCTTGTAGTAACAGGTGAAACCATGTCCCGGTCGAGGTTTTGTCTCCCGACTCTACCGAGACTCC
* * *
1712356 TATTAGGTTTGACAGAGTTGAGTGTCCTGTAGTAACAGGTGAAACCGTGT-CCTAGGTTGAGGTT
66 TA-TAGG-TTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCATATCCCT-GGTTGAGGTT
* * * *
1712420 TGGTCTCCTGACTCTACTGAGACTATTG-TAGGTTGAC--AG-C-ATTG
128 TTGTCTCCCGACTCTACTGAGACTACTGTTAGGTTGACAGAGTCGAGTG
** * * **
1712464 TGATGTAGTAACAGGTGAAACCATGTTCCCGGTCGAAGTTTTATCTCCTAACTCTACCGAGACTC
1 TCTTGTAGTAACAGGTGAAACCATG-TCCCGGTCGAGGTTTTGTCTCCCGACTCTACCGAGACTC
* * ** * * * *
1712529 TTATTGGGTTGTTAGAGTTGAGTTTCTTGTAGTAACAAGTGAAACCATGTCTCCT-G-TCAGGGT
65 CTA-TAGGTTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCATATC-CCTGGTTGA-GGT
* * * * * *
1712592 TTTGTTTCCCTACTTTACCGAGACT-CATATTAGGTTGACAGAGTTGAGTG
127 TTTGTCTCCCGACTCTACTGAGACTAC-TGTTAGGTTGACAGAGTCGAGTG
* * * * * * ** *
1712642 TTTTATACTAACAGGTG-AACCGTGTCCCCGGTCAAGGTTCTGTCTCCTAACTCTACCGAGAATC
1 TCTTGTAGTAACAGGTGAAACCATGT-CCCGGTCGAGGTTTTGTCTCCCGACTCTACCGAGACTC
1712706 CTATCAGGTTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCAT
65 CTAT-AGGTTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCAT
1712754 GTGAAACTAA
Statistics
Matches: 514, Mismatches: 109, Indels: 35
0.78 0.17 0.05
Matches are distributed among these distances:
172 2 0.00
173 82 0.16
174 45 0.09
175 5 0.01
176 5 0.01
177 266 0.52
178 109 0.21
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (176 bp):
TCTTGTAGTAACAGGTGAAACCATGTCCCGGTCGAGGTTTTGTCTCCCGACTCTACCGAGACTCC
TATAGGTTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCATATCCCTGGTTGAGGTTTTG
TCTCCCGACTCTACTGAGACTACTGTTAGGTTGACAGAGTCGAGTG
Found at i:1712565 original size:262 final size:262
Alignment explanation
Indices: 1712095--1712753 Score: 636
Period size: 262 Copynumber: 2.5 Consensus size: 262
1712085 GAATACTGTC
* * * *
1712095 AGGTTGATAGAGTCGAGTGTCTTGTAGTAACAGGTGAAACCATGTCGCTGTCTAGGTTTTGTCTC
1 AGGTTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCGTGTC-CTGTCTAGGTTTGGTCTC
* *
1712160 CCGACTCTACCGAGACTCCTGATAGGATGACAGAGTTGTGTTTCATGTAGTAACAGGTGAAACTA
65 CCGACTCTACCGAGACTACTGATAGGATGACAGAGTTGTG--T-ATGTAGTAACAGGTGAAACCA
* * * ** *
1712225 TATCCCCGGTTGAGGTTTTGTCCCCCGGCTCTACAGAGACTCCTGTTAGGTGGACAAAGTTGAGT
127 TATCCCCGGTCGAAGTTTTATCCCCCAACTCTACAGAGACTCCTATTAGGTGGACAAAGTTGAGT
** ** *
1712290 GTTTTGCAGTAACAAGTGAAACTGTGTC-CCT-TTTGAGCTTTTGTCTCCCGACTCTATCGAGAC
192 GTTTTGCAGTAACAAGTGAAACCATGTCTCCTGTCAG-GCTTTTGTCTCCCGACTCTACCGAGAC
*
1712353 TCCTATT
256 TCATATT
*
1712360 AGGTTTGACAGAGTTGAGTGTCCTGTAGTAACAGGTGAAACCGTGTCCTAGGT-TGAGGTTTGGT
1 AGG-TTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCGTGTCCT--GTCT-AGGTTTGGT
* * * *
1712424 CTCCTGACTCTACTGAGACTATTG-TAGGTTGACAGCA-TTGTG-ATGTAGTAACAGGTGAAACC
62 CTCCCGACTCTACCGAGACTACTGATAGGATGACAG-AGTTGTGTATGTAGTAACAGGTGAAACC
* * * * * * * * ** *
1712486 ATGTTCCCGGTCGAAGTTTTATCTCCTAACTCTACCGAGACTCTTATTGGGTTGTTAGAGTTGAG
126 ATATCCCCGGTCGAAGTTTTATCCCCCAACTCTACAGAGACTCCTATTAGGTGGACAAAGTTGAG
* * * * *
1712551 T-TTCTTGTAGTAACAAGTGAAACCATGTCTCCTGTCAGGGTTTTGTTTCCCTACTTTACCGAGA
191 TGTT-TTGCAGTAACAAGTGAAACCATGTCTCCTGTCAGGCTTTTGTCTCCCGACTCTACCGAGA
1712615 CTCATATT
255 CTCATATT
* * * * *
1712623 AGGTTGACAGAGTTGAGTGTTTTATACTAACAGGTG-AACCGTGTCCCCGGTCAAGGTTCT-GTC
1 AGGTTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCGTGT--CCTGTCTAGGTT-TGGTC
** * * * *
1712686 TCCTAACTCTACCGAGAATCCT-ATCAGGTTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAA
63 TCCCGACTCTACCGAGACTACTGAT-AGGATGACAGAGTT--GTGT-ATGTAGTAACAGGTGAAA
1712750 CCAT
124 CCAT
1712754 GTGAAACTAA
Statistics
Matches: 324, Mismatches: 51, Indels: 37
0.79 0.12 0.09
Matches are distributed among these distances:
261 39 0.12
262 132 0.41
263 36 0.11
264 5 0.02
265 5 0.02
266 76 0.23
267 31 0.10
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (262 bp):
AGGTTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCGTGTCCTGTCTAGGTTTGGTCTCC
CGACTCTACCGAGACTACTGATAGGATGACAGAGTTGTGTATGTAGTAACAGGTGAAACCATATC
CCCGGTCGAAGTTTTATCCCCCAACTCTACAGAGACTCCTATTAGGTGGACAAAGTTGAGTGTTT
TGCAGTAACAAGTGAAACCATGTCTCCTGTCAGGCTTTTGTCTCCCGACTCTACCGAGACTCATA
TT
Found at i:1713045 original size:20 final size:20
Alignment explanation
Indices: 1713022--1713061 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1713012 TAGTATGATG
1713022 ATTATGATGTTAGTTTATGT
1 ATTATGATGTTAGTTTATGT
1713042 ATTATGATGTTAGTTTATGT
1 ATTATGATGTTAGTTTATGT
1713062 TTTAGTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.20, T:0.55
Consensus pattern (20 bp):
ATTATGATGTTAGTTTATGT
Found at i:1721543 original size:69 final size:69
Alignment explanation
Indices: 1721432--1721572 Score: 264
Period size: 69 Copynumber: 2.0 Consensus size: 69
1721422 ATGAAATTGG
*
1721432 GTTTTGATTAAATTTGTAATCGAGTCGAATTAAACCTCTGAACCGGAGTAATGCTCTTTCAATAT
1 GTTTTGATTAAATTTATAATCGAGTCGAATTAAACCTCTGAACCGGAGTAATGCTCTTTCAATAT
1721497 TGTT
66 TGTT
*
1721501 GTTTTGATTAAATTTATAATCGAGTCGAATTAAACCTCTGAACCGGAGTAATGCTCTTTGAATAT
1 GTTTTGATTAAATTTATAATCGAGTCGAATTAAACCTCTGAACCGGAGTAATGCTCTTTCAATAT
1721566 TGTT
66 TGTT
1721570 GTT
1 GTT
1721573 GTTTTACTCC
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (69 bp):
GTTTTGATTAAATTTATAATCGAGTCGAATTAAACCTCTGAACCGGAGTAATGCTCTTTCAATAT
TGTT
Found at i:1723366 original size:7 final size:7
Alignment explanation
Indices: 1723349--1723378 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
1723339 TATATATATA
1723349 TATTCAAT
1 TATT-AAT
1723357 TATTAAT
1 TATTAAT
1723364 TATTAAT
1 TATTAAT
1723371 TATTAAT
1 TATTAAT
1723378 T
1 T
1723379 TTTTTATAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.82
8 4 0.18
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (7 bp):
TATTAAT
Found at i:1725817 original size:30 final size:29
Alignment explanation
Indices: 1725742--1725836 Score: 91
Period size: 31 Copynumber: 3.1 Consensus size: 29
1725732 TTTTATTATA
* * *
1725742 CCTTTAAAATTTTAAAAAATTTCAATTAGCT
1 CCTTTGAAATTTTTAAAAATTTC-ATTA-AT
*
1725773 CCCTTGAAATTTTTAAAAATTTCATTAAT
1 CCTTTGAAATTTTTAAAAATTTCATTAAT
* *
1725802 CCTTTCGATATTTTTAAAAATGTTAATTAAAT
1 CCTTT-GAAATTTTTAAAAAT-TTCATT-AAT
1725834 CCT
1 CCT
1725837 AAAATTTTTG
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
29 5 0.09
30 18 0.33
31 25 0.46
32 6 0.11
ACGTcount: A:0.38, C:0.14, G:0.04, T:0.44
Consensus pattern (29 bp):
CCTTTGAAATTTTTAAAAATTTCATTAAT
Found at i:1725924 original size:30 final size:30
Alignment explanation
Indices: 1725890--1725946 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1725880 TTTTTATTAT
* *
1725890 GCCTTTGAAATTTTTAAAAATTCTAATTGA
1 GCCTTTCAAAATTTTAAAAATTCTAATTGA
* *
1725920 GCCTTTCAAAATTTTATAAATTTTAAT
1 GCCTTTCAAAATTTTAAAAATTCTAAT
1725947 AAGACCCTCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.46
Consensus pattern (30 bp):
GCCTTTCAAAATTTTAAAAATTCTAATTGA
Found at i:1730695 original size:18 final size:17
Alignment explanation
Indices: 1730669--1730703 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1730659 AATATTAAGA
*
1730669 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
1730686 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
1730704 TTAATAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:1730715 original size:120 final size:120
Alignment explanation
Indices: 1730562--1730845 Score: 446
Period size: 120 Copynumber: 2.4 Consensus size: 120
1730552 TAATTGAAAA
* * *
1730562 TATATATTTT-ATTAAATTATATTTAATAATAATTATGTTAAATTATATTTCATAGTATTATATA
1 TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTCACAGTATCATATA
* *
1730626 TTATGATTTTAGAAAATTCATATAAGAATATTTAA-TATTAAGAATTTTATTAAAT
66 TTATGATTTCAGAAAATTAATATAAGAATA-TTAATTATTAAGAATTTTATTAAAT
* * *
1730681 TATATATTTTAATTAAAATATATTTAATAGTAATTATGTTAATTTATATTTTACAGTATCATATA
1 TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTCACAGTATCATATA
*
1730746 TTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
66 TTATGATTTCAGAAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
*
1730801 TATATATTTTAATTAAAATATATTTAATAAAAATTATGTTTAAAT
1 TATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
1730846 ATGATTAAAT
Statistics
Matches: 150, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
119 14 0.09
120 131 0.87
121 5 0.03
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTCACAGTATCATATA
TTATGATTTCAGAAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
Found at i:1730817 original size:18 final size:17
Alignment explanation
Indices: 1730789--1730823 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1730779 ATTATTAAGA
*
1730789 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
1730806 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
1730824 TTAATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:1730823 original size:16 final size:16
Alignment explanation
Indices: 1730789--1730843 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
1730779 ATTATTAAGA
1730789 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
1730806 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
*
1730822 A-TTTAATAAAAAT-T
1 ATTTTAATTAAAATAT
1730836 ATGTTTAA
1 AT-TTTAA
1730844 ATATGATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 2 0.06
15 11 0.32
16 10 0.29
17 5 0.15
18 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:1731080 original size:16 final size:16
Alignment explanation
Indices: 1731059--1731110 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
1731049 GATTTGCTAT
1731059 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
1731075 TACACCTTTAATCCAA
1 TACACCTCTAATCCAA
1731091 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1731107 TACA
1 TACA
1731111 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.27
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:1736999 original size:22 final size:20
Alignment explanation
Indices: 1736973--1737013 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
1736963 TGCAATCGTA
1736973 TATTAGACATATTGTATTTTTC
1 TATTA-ACATA-TGTATTTTTC
*
1736995 TATTAATATATGTATTTTT
1 TATTAACATATGTATTTTT
1737014 AAAAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 4 0.22
22 5 0.28
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.59
Consensus pattern (20 bp):
TATTAACATATGTATTTTTC
Found at i:1739904 original size:27 final size:27
Alignment explanation
Indices: 1739809--1739889 Score: 162
Period size: 27 Copynumber: 3.0 Consensus size: 27
1739799 GATGACGCAC
1739809 AATCTTATCATGGCTATGCTAGGAGAA
1 AATCTTATCATGGCTATGCTAGGAGAA
1739836 AATCTTATCATGGCTATGCTAGGAGAA
1 AATCTTATCATGGCTATGCTAGGAGAA
1739863 AATCTTATCATGGCTATGCTAGGAGAA
1 AATCTTATCATGGCTATGCTAGGAGAA
1739890 CTTGCCTCCA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (27 bp):
AATCTTATCATGGCTATGCTAGGAGAA
Found at i:1744928 original size:31 final size:31
Alignment explanation
Indices: 1744880--1744960 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 31
1744870 AAATGATCAC
* *
1744880 TGAATTATTCGAAAGTTTTCACTTAAGTCAT
1 TGAACTATTTGAAAGTTTTCACTTAAGTCAT
* * *
1744911 TGAACTATTTGAAAGTTTTTATTTAAGTTAT
1 TGAACTATTTGAAAGTTTTCACTTAAGTCAT
*
1744942 TGAACTATTTGAAAATTTT
1 TGAACTATTTGAAAGTTTT
1744961 TATTTAAGGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.47
Consensus pattern (31 bp):
TGAACTATTTGAAAGTTTTCACTTAAGTCAT
Found at i:1744961 original size:31 final size:31
Alignment explanation
Indices: 1744902--1744974 Score: 119
Period size: 31 Copynumber: 2.4 Consensus size: 31
1744892 AAGTTTTCAC
* *
1744902 TTAAGTCATTGAACTATTTGAAAGTTTTTAT
1 TTAAGTTATTGAACTATTTGAAAATTTTTAT
1744933 TTAAGTTATTGAACTATTTGAAAATTTTTAT
1 TTAAGTTATTGAACTATTTGAAAATTTTTAT
*
1744964 TTAAGGTATTG
1 TTAAGTTATTG
1744975 GATTGTTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.33, C:0.04, G:0.14, T:0.49
Consensus pattern (31 bp):
TTAAGTTATTGAACTATTTGAAAATTTTTAT
Found at i:1750243 original size:3 final size:3
Alignment explanation
Indices: 1750237--1750265 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1750227 TCTTTGTTGT
1750237 TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
1750266 TAGAGGTGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.34, T:0.34
Consensus pattern (3 bp):
TGC
Found at i:1750306 original size:24 final size:24
Alignment explanation
Indices: 1750256--1750313 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
1750246 TGCTGCTGCT
* *
1750256 GCTGCTGCTGTAGAGGTGGCTGAG
1 GCTGCTGCTGAAGAGGTGACTGAG
* * *
1750280 GCTGCTGTTGAAGATGTGACTGTG
1 GCTGCTGCTGAAGAGGTGACTGAG
*
1750304 GCTGCAGCTG
1 GCTGCTGCTG
1750314 TGACTGTCTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.14, C:0.17, G:0.41, T:0.28
Consensus pattern (24 bp):
GCTGCTGCTGAAGAGGTGACTGAG
Found at i:1778725 original size:20 final size:19
Alignment explanation
Indices: 1778700--1778738 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1778690 ATGTGTTAAT
1778700 TATAATAAAATATATTAAAA
1 TATAATAAAATA-ATTAAAA
* *
1778720 TATAATTAAGTAATTAAAA
1 TATAATAAAATAATTAAAA
1778739 ATAGATCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (19 bp):
TATAATAAAATAATTAAAA
Found at i:1785539 original size:6 final size:6
Alignment explanation
Indices: 1785528--1785552 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1785518 ATGAGTACGA
1785528 TAAAAT TAAAAT TAAAAT TAAAAT T
1 TAAAAT TAAAAT TAAAAT TAAAAT T
1785553 TTATGTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TAAAAT
Found at i:1787911 original size:16 final size:16
Alignment explanation
Indices: 1787890--1787921 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1787880 GTTTTATGAA
*
1787890 AATTATATAATCAATT
1 AATTATATAAACAATT
1787906 AATTATATAAACAATT
1 AATTATATAAACAATT
1787922 CTAATCAGAA
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:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTATATAAACAATT
Found at i:1789774 original size:14 final size:15
Alignment explanation
Indices: 1789749--1789779 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1789739 CCCTAACTCG
1789749 AAAGGACTACAAGTA
1 AAAGGACTACAAGTA
1789764 AAAGG-CTACAAGTA
1 AAAGGACTACAAGTA
1789778 AA
1 AA
1789780 TTGAAATTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.55, C:0.13, G:0.19, T:0.13
Consensus pattern (15 bp):
AAAGGACTACAAGTA
Found at i:1793930 original size:2 final size:2
Alignment explanation
Indices: 1793923--1793947 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1793913 TGCATTTTAA
1793923 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 A
1793948 ATTTAAAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1796935 original size:3 final size:3
Alignment explanation
Indices: 1796927--1796958 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1796917 TGCAAACTGG
1796927 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1796959 ATGCATAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1798737 original size:12 final size:13
Alignment explanation
Indices: 1798720--1798757 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
1798710 TTGGTGTAAC
1798720 AAATAAAAATA-A
1 AAATAAAAATATA
1798732 AAATAAAAATATA
1 AAATAAAAATATA
*
1798745 TAATAAATAATAT
1 AAATAAA-AATAT
1798758 GCATTTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.48
13 7 0.30
14 5 0.22
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AAATAAAAATATA
Found at i:1801842 original size:31 final size:31
Alignment explanation
Indices: 1801807--1801870 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
1801797 CAATCCAATA
* *
1801807 ACTTAAATAAAAACTTTCGAATAATTTAGTG
1 ACTTAAATAAAAACTTTAGAATAACTTAGTG
* * *
1801838 ACTTAAATGAGAATTTTAGAATAACTTAGTG
1 ACTTAAATAAAAACTTTAGAATAACTTAGTG
1801869 AC
1 AC
1801871 CATTTTGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.34
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTAGAATAACTTAGTG
Found at i:1804391 original size:15 final size:16
Alignment explanation
Indices: 1804366--1804395 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1804356 AACATAAAAG
1804366 AAAATACAAAAAATAA
1 AAAATACAAAAAATAA
1804382 AAAATA-AAAAAATA
1 AAAATACAAAAAATA
1804396 TAAATTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAATACAAAAAATAA
Found at i:1804512 original size:11 final size:11
Alignment explanation
Indices: 1804496--1804528 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1804486 CCCTTCCCCC
1804496 CTCCCTTCTCT
1 CTCCCTTCTCT
1804507 CTCCCTTCTCT
1 CTCCCTTCTCT
1804518 CTTCCC-TCTCT
1 C-TCCCTTCTCT
1804529 TTTTTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (11 bp):
CTCCCTTCTCT
Found at i:1805012 original size:3 final size:3
Alignment explanation
Indices: 1805004--1805031 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1804994 TGTATTTCAA
1805004 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1805032 GTACATTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1805206 original size:125 final size:129
Alignment explanation
Indices: 1804991--1805239 Score: 332
Period size: 125 Copynumber: 2.0 Consensus size: 129
1804981 ATATTACATT
* * * *
1804991 TTTTGTATTTCAATATTATTATTATTATTATTATTATTATTGTACATTAGTGTATATCTTCATGT
1 TTTTGTATTTCAATATTATTATTATTATTATTATTATCATTGAACATTACTATATATCTTCATGT
* * * *
1805056 ATGTATATATATATGTAGTAATG-TTTT-ATTACTTTATTTTAATAT-TTTTTATTATAATAGC
66 ATGTATATATACATATAGTAATGTTTTTAATGACTTTATTTTAATATCATTTTATTATAATAGC
1805117 TTTTGTATTTCAATATTATTATTATT-TTATTATTATCATT-AACATTACTATATATTCTT-AT-
1 TTTTGTATTTCAATATTATTATTATTATTATTATTATCATTGAACATTACTATATA-TCTTCATG
* *
1805178 TAGATGTATATATACATATATTACTGTTTTTAATGACTTTATTTTAATATCATTTTATTATA
65 T--ATGTATATATACATATAGTAATGTTTTTAATGACTTTATTTTAATATCATTTTATTATA
1805240 TTTACTTTTT
Statistics
Matches: 107, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
123 1 0.01
124 13 0.12
125 36 0.34
126 30 0.28
127 17 0.16
128 10 0.09
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (129 bp):
TTTTGTATTTCAATATTATTATTATTATTATTATTATCATTGAACATTACTATATATCTTCATGT
ATGTATATATACATATAGTAATGTTTTTAATGACTTTATTTTAATATCATTTTATTATAATAGC
Found at i:1805536 original size:11 final size:11
Alignment explanation
Indices: 1805520--1805546 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1805510 GTACGTATTG
1805520 TATATGTTCTA
1 TATATGTTCTA
1805531 TATATGTTCTA
1 TATATGTTCTA
1805542 TATAT
1 TATAT
1805547 TTTAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (11 bp):
TATATGTTCTA
Found at i:1809589 original size:16 final size:17
Alignment explanation
Indices: 1809568--1809605 Score: 69
Period size: 16 Copynumber: 2.3 Consensus size: 17
1809558 TCATGAAAAG
1809568 AAAAAAAACAAAAC-AA
1 AAAAAAAACAAAACGAA
1809584 AAAAAAAACAAAACGAA
1 AAAAAAAACAAAACGAA
1809601 AAAAA
1 AAAAA
1809606 GGACAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.87, C:0.11, G:0.03, T:0.00
Consensus pattern (17 bp):
AAAAAAAACAAAACGAA
Found at i:1809591 original size:11 final size:11
Alignment explanation
Indices: 1809568--1809634 Score: 64
Period size: 11 Copynumber: 6.1 Consensus size: 11
1809558 TCATGAAAAG
1809568 AAAAAAAACAA
1 AAAAAAAACAA
*
1809579 AACAAAAA-AA
1 AAAAAAAACAA
*
1809589 AAACAAAACGAA
1 AAAAAAAAC-AA
**
1809601 AAAAAGGACAA
1 AAAAAAAACAA
*
1809612 GAAAAAAACAA
1 AAAAAAAACAA
*
1809623 AAAAAAATCAA
1 AAAAAAAACAA
1809634 A
1 A
1809635 TGCCAGAAAG
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
10 8 0.19
11 27 0.63
12 8 0.19
ACGTcount: A:0.82, C:0.10, G:0.06, T:0.01
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:1809611 original size:17 final size:15
Alignment explanation
Indices: 1809563--1809605 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 15
1809553 AACAGTCATG
1809563 AAAA-GAAAAAAAAC
1 AAAACGAAAAAAAAC
*
1809577 AAAACAAAAAAAAAAC
1 AAAAC-GAAAAAAAAC
1809593 AAAACGAAAAAAA
1 AAAACGAAAAAAA
1809606 GGACAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 4 0.16
15 7 0.28
16 14 0.56
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (15 bp):
AAAACGAAAAAAAAC
Found at i:1812105 original size:145 final size:146
Alignment explanation
Indices: 1811813--1812111 Score: 546
Period size: 145 Copynumber: 2.0 Consensus size: 146
1811803 TTTATTTCTG
1811813 TTTCAAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
1 TTTC-AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
1811878 ATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGG
65 ATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGG
** *
1811943 TATTTTCAATTTTTGCT
130 TATTTTCAAAATCTGCT
1811960 TTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAA
1 TTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAA
*
1812025 TTTCTG-TTTTCAAAATTCAACTCATTTTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGT
66 TTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGT
1812089 ATTTTCAAAATCTGCT
131 ATTTTCAAAATCTGCT
1812105 TTTCAAA
1 TTTCAAA
1812112 TTAAGTTTCA
Statistics
Matches: 148, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
145 77 0.52
146 67 0.45
147 4 0.03
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (146 bp):
TTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAA
TTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGT
ATTTTCAAAATCTGCT
Found at i:1812113 original size:72 final size:73
Alignment explanation
Indices: 1811806--1812111 Score: 510
Period size: 73 Copynumber: 4.2 Consensus size: 73
1811796 TGATGCTTTT
*
1811806 ATTTCTG--TTTCAAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
1 ATTTCTGCTTTTC-AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAG
1811869 GTAATTTCA
65 GTAATTTCA
1811878 ATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGG
1 ATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGG
*
1811943 TATTTTCA
66 TAATTTCA
* *
1811951 ATTTTTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 ATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGG
1812016 TAATTTCA
66 TAATTTCA
*
1812024 ATTTCTG-TTTTCAAAATTCAACTCATTTTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGG
1 ATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGG
*
1812088 TATTTTCA
66 TAATTTCA
**
1812096 AAATCTGCTTTTCAAA
1 ATTTCTGCTTTTCAAA
1812112 TTAAGTTTCA
Statistics
Matches: 220, Mismatches: 11, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
72 74 0.34
73 142 0.65
74 4 0.02
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (73 bp):
ATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGG
TAATTTCA
Found at i:1812183 original size:53 final size:53
Alignment explanation
Indices: 1812117--1812611 Score: 405
Period size: 53 Copynumber: 8.7 Consensus size: 53
1812107 TCAAATTAAG
* *
1812117 TTTCAAAAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTGTT
1 TTTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTCTGTT
* **** *
1812171 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCCGAGGTATTTTTAGT
1 TTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGA-----A---C-CTTTTA---ATTTCT-G-
1812236 TT
52 TT
** ** *
1812238 ATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTCTGGT
1 -T-TTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTCTGTT
*
1812293 TTTCAAAAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTGTT
1 TTTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTCTGTT
* * *** *
1812347 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGT
1 TTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCT---------TTTA---ATTTCT-G-
1812412 TT
52 TT
** ** * * *
1812414 ATGTTTTAAATTGACTCATATTACGAGAGGCGAGTTGAACCTTTTAATTTCTGGT
1 -T-TTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTCTGTT
*
1812469 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTCTGGT
1 TTTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTCTGTT
*
1812523 TTTCAAAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTGTT
1 TTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTCTGTT
*
1812576 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGA
1 TTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGA
1812612 GCCTCGGGGC
Statistics
Matches: 354, Mismatches: 53, Indels: 69
0.74 0.11 0.14
Matches are distributed among these distances:
53 149 0.42
54 102 0.29
55 2 0.01
56 2 0.01
57 10 0.03
58 1 0.00
60 3 0.01
61 2 0.01
62 3 0.01
64 1 0.00
65 10 0.03
66 2 0.01
67 4 0.01
68 2 0.01
69 61 0.17
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.37
Consensus pattern (53 bp):
TTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTCTGTT
Found at i:1812411 original size:176 final size:176
Alignment explanation
Indices: 1812117--1812558 Score: 812
Period size: 176 Copynumber: 2.5 Consensus size: 176
1812107 TCAAATTAAG
*
1812117 TTTCAAAAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTGTTTTTCAAAATCA
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTGTTTTTCAAAATCA
1812182 ACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCCGAGGTATTTTTAGTTTATGTTTTAA
66 ACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCCGAGGTATTTTTAGTTTATGTTTTAA
* *
1812247 ATTGACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTCTGGT
131 ATTGACTCATATTACGAGAGGCGAGTTGAACCTTTTAATTTCTGGT
1812293 TTTCAAAAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTGTTTTTCAAAATCA
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTGTTTTTCAAAATCA
*
1812358 ACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTATGTTTTAA
66 ACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCCGAGGTATTTTTAGTTTATGTTTTAA
1812423 ATTGACTCATATTACGAGAGGCGAGTTGAACCTTTTAATTTCTGGT
131 ATTGACTCATATTACGAGAGGCGAGTTGAACCTTTTAATTTCTGGT
* *
1812469 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTCTGGTTTTCAAAATCA
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTGTTTTTCAAAATCA
* *
1812534 ACTCATATTGCGAGAGGTGGGTTGA
66 ACTCATATTGCGAGAAGTGAGTTGA
1812559 ACCTTTTAAT
Statistics
Matches: 258, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
176 258 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (176 bp):
TTTCAAAAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTGTTTTTCAAAATCA
ACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCCGAGGTATTTTTAGTTTATGTTTTAA
ATTGACTCATATTACGAGAGGCGAGTTGAACCTTTTAATTTCTGGT
Found at i:1812558 original size:229 final size:230
Alignment explanation
Indices: 1812251--1812680 Score: 826
Period size: 229 Copynumber: 1.9 Consensus size: 230
1812241 TTTTAAATTG
1812251 ACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTCTGGTTTTCAAAAATCAACTCATATTGC
1 ACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTCTGGTTTTCAAAAATCAACTCATATTGC
1812316 GAGAGGTGGGTTGAACCTTTTAATTTCTGTTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTT
66 GAGAGGTGGGTTGAACCTTTTAATTTCTGTTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTT
1812381 GAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTATGTTTTAAATTGACTCATATTACGAGAGGCG
131 GAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTATGTTTTAAATTGACTCATATTACGAGAGGCG
1812446 AGTTGAACCTTTTAATTTCTGGTTTTCAAAAATCA
196 AGTTGAACCTTTTAATTTCTGGTTTTCAAAAATCA
1812481 ACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTCTGGTTTTC-AAAATCAACTCATATTGC
1 ACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTCTGGTTTTCAAAAATCAACTCATATTGC
1812545 GAGAGGTGGGTTGAACCTTTTAATTTCTGTTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTT
66 GAGAGGTGGGTTGAACCTTTTAATTTCTGTTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTT
* * *
1812610 GAGCCTCGGGGCGCGCCGAGGTATTTTTAGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTG
131 GAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTATGTTTTAAATTGACTCATATTACGAGAGGCG
1812675 AGTTGA
196 AGTTGA
1812681 GCCTAGCCTC
Statistics
Matches: 197, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
229 151 0.77
230 46 0.23
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (230 bp):
ACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTCTGGTTTTCAAAAATCAACTCATATTGC
GAGAGGTGGGTTGAACCTTTTAATTTCTGTTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTT
GAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTATGTTTTAAATTGACTCATATTACGAGAGGCG
AGTTGAACCTTTTAATTTCTGGTTTTCAAAAATCA
Found at i:1812923 original size:84 final size:83
Alignment explanation
Indices: 1812781--1813013 Score: 279
Period size: 84 Copynumber: 2.8 Consensus size: 83
1812771 CTACTTTTTC
* *
1812781 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
*
1812846 GTTGTTAA-AAAAAATAAAA
66 G-T-TCAATAAAAAATAAAA
** *
1812865 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTCCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
* * ** ***
1812930 GTTCAATTTATATTTTTCA
66 GTTCAA-TAAAAAATAAAA
* * * *
1812949 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTCAAATTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
1813014 ACTTCCAAAA
Statistics
Matches: 127, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
82 3 0.02
83 1 0.01
84 123 0.97
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (83 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
GTTCAATAAAAAATAAAA
Found at i:1813124 original size:212 final size:209
Alignment explanation
Indices: 1812865--1813404 Score: 607
Period size: 217 Copynumber: 2.6 Consensus size: 209
1812855 AAAAATAAAA
**
1812865 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTCCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT-CT
* *
1812930 GTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCAC-G
65 GTTC--TGTAT-GTTTT--AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACAG
* * *
1812994 CCGAGGTATTTTCAAATTCTACTT-CCAA-AAAAATCAACTCATATTGCGAGAGGTAGGTTGAAC
125 CCGAGGAATTTTCAAAATCTACTTGCAAATAAAAATCAACTCATATTGCGAGAGGTAGGTTGAAC
1813057 CTTTTAATTTCTACTTTTTC
190 CTTTTAATTTCTACTTTTTC
* * * *
1813077 AAAATCAGCTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATT-T-
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTCTG
* ** *
1813140 TT-TGTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAG
66 TTCTGTATGTTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACA-GCCGAG
** *
1813204 GAATTTTCAAAATCTGTTTGGCAAATTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGGGT
130 GAATTTTCAAAATCTACTT-GCAAA--------T-AAAAATCAACTCATATTGCGAGAGGTAGGT
1813269 TGAACCTTTTAATTTCTACTTTTTC
185 TGAACCTTTTAATTTCTACTTTTTC
* * *
1813294 AAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGAACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA-TTCT
*** * *
1813359 GTTC--TA---AAAAAAATCAACTCATATTGCGAAAAGTGAGTTGAGCCTC
65 GTTCTGTATGTTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1813405 AGTTCACATG
Statistics
Matches: 277, Mismatches: 33, Indels: 32
0.81 0.10 0.09
Matches are distributed among these distances:
203 41 0.15
205 25 0.09
206 3 0.01
207 3 0.01
209 2 0.01
210 1 0.00
212 56 0.20
216 33 0.12
217 107 0.39
218 2 0.01
219 2 0.01
220 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (209 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTCTG
TTCTGTATGTTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACAGCCGAGG
AATTTTCAAAATCTACTTGCAAATAAAAATCAACTCATATTGCGAGAGGTAGGTTGAACCTTTTA
ATTTCTACTTTTTC
Found at i:1814028 original size:13 final size:13
Alignment explanation
Indices: 1814010--1814035 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1814000 GGGCCACCCC
1814010 CAAAACCCAATAA
1 CAAAACCCAATAA
1814023 CAAAACCCAATAA
1 CAAAACCCAATAA
1814036 ACCAAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.31, G:0.00, T:0.08
Consensus pattern (13 bp):
CAAAACCCAATAA
Found at i:1814736 original size:17 final size:17
Alignment explanation
Indices: 1814714--1814748 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1814704 AACATAAAAG
1814714 AAAATACAAAAAA-ATAA
1 AAAATA-AAAAAATATAA
1814731 AAAATAAAAAAATATAA
1 AAAATAAAAAAATATAA
1814748 A
1 A
1814749 TTTTTACCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (17 bp):
AAAATAAAAAAATATAA
Found at i:1815366 original size:3 final size:3
Alignment explanation
Indices: 1815358--1815394 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1815348 TGTATTTCAA
1815358 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1815395 GTACATTAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1815550 original size:127 final size:129
Alignment explanation
Indices: 1815367--1815604 Score: 315
Period size: 127 Copynumber: 1.9 Consensus size: 129
1815357 ATATTATTAT
* * * * *
1815367 TATTATTATTATTATTATTATTATTATTGTACATTAGTGTATATCTTCATGTATGTATATATATA
1 TATTATTATTATTATTATTATTATCATTGAACATTACTATATATCTTCATGTATGTATATATACA
* * *
1815432 TGTAGTAATGTTTTT-ATTACTTTATTTTAATAT-TTTTTATTATAATAGCTTTTGTATTTCAA
66 TATAGTAATGTTTTTAATGACTTTATTTTAATATCATTTTATTATAATAGCTTTTGTATTTCAA
*
1815494 TATTATTATTATTTTTATTATTATCATT-AACATTACTATATATTCTT-AT-TAGATGTATATAT
1 TATTATTATTATTATTATTATTATCATTGAACATTACTATATA-TCTTCATGT--ATGTATATAT
* *
1815556 ACATATATTACTGTTTTTAATGACTTTATTTTAATATCATTTTATTATA
63 ACATATAGTAATGTTTTTAATGACTTTATTTTAATATCATTTTATTATA
1815605 TTTACTTTTT
Statistics
Matches: 95, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
125 1 0.01
126 13 0.14
127 54 0.57
128 17 0.18
129 10 0.11
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.57
Consensus pattern (129 bp):
TATTATTATTATTATTATTATTATCATTGAACATTACTATATATCTTCATGTATGTATATATACA
TATAGTAATGTTTTTAATGACTTTATTTTAATATCATTTTATTATAATAGCTTTTGTATTTCAA
Found at i:1815905 original size:11 final size:11
Alignment explanation
Indices: 1815889--1815915 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1815879 GTACGTATTG
1815889 TATATGTTCTA
1 TATATGTTCTA
1815900 TATATGTTCTA
1 TATATGTTCTA
1815911 TATAT
1 TATAT
1815916 TTTTAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (11 bp):
TATATGTTCTA
Found at i:1820260 original size:23 final size:23
Alignment explanation
Indices: 1820230--1820273 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1820220 CAAGATCAAT
* *
1820230 TTGATTGACAGAATGTGTAAATG
1 TTGATTGACAAAATATGTAAATG
1820253 TTGATTGACAAAATATGTAAA
1 TTGATTGACAAAATATGTAAA
1820274 CTTTAAGGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (23 bp):
TTGATTGACAAAATATGTAAATG
Found at i:1820645 original size:17 final size:16
Alignment explanation
Indices: 1820619--1820650 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1820609 AATTGTATAT
1820619 ATTAATTGAAAATTAC
1 ATTAATTGAAAATTAC
1820635 ATTATATTGAAAATTA
1 ATTA-ATTGAAAATTA
1820651 TAATTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (16 bp):
ATTAATTGAAAATTAC
Found at i:1829691 original size:16 final size:16
Alignment explanation
Indices: 1829667--1829698 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1829657 TGTACTTCAC
*
1829667 TATACTTGATTTTGAT
1 TATAATTGATTTTGAT
1829683 TATAATTGATTTTGAT
1 TATAATTGATTTTGAT
1829699 ATTATTTATT
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:0.28, C:0.03, G:0.12, T:0.56
Consensus pattern (16 bp):
TATAATTGATTTTGAT
Found at i:1837440 original size:14 final size:14
Alignment explanation
Indices: 1837421--1837450 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1837411 AGCTTTTGAT
1837421 TATATATATACATA
1 TATATATATACATA
1837435 TATATATATACATA
1 TATATATATACATA
1837449 TA
1 TA
1837451 CTTCAATCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TATATATATACATA
Found at i:1838042 original size:22 final size:22
Alignment explanation
Indices: 1838009--1838051 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1837999 ATTTAAGTGG
**
1838009 TTTTAATATAAATTTTTTTAAC
1 TTTTAATATAAAAATTTTTAAC
1838031 TTTTAA-ACTAAAAATTTTTAA
1 TTTTAATA-TAAAAATTTTTAA
1838052 TCTTCAGACC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTAATATAAAAATTTTTAAC
Found at i:1839682 original size:37 final size:38
Alignment explanation
Indices: 1839632--1839717 Score: 122
Period size: 37 Copynumber: 2.3 Consensus size: 38
1839622 AAAAATTATA
*
1839632 TTTAATACAATAAAACATTTATTATATTTAT-T-TGTTT
1 TTTAATATAATAAAACATTTATTATATTTATGTAT-TTT
*
1839669 TTTAATATAATAAAACATTTATTTTATTTATGGTATTTT
1 TTTAATATAATAAAACATTTATTATATTTAT-GTATTTT
1839708 TTTAATATAA
1 TTTAATATAA
1839718 ATATTTTTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
37 29 0.66
39 14 0.32
40 1 0.02
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.55
Consensus pattern (38 bp):
TTTAATATAATAAAACATTTATTATATTTATGTATTTT
Found at i:1842920 original size:4 final size:4
Alignment explanation
Indices: 1842913--1842954 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
1842903 ATATATATAC
1842913 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1842955 ACCTTCCTGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:1847202 original size:17 final size:17
Alignment explanation
Indices: 1847180--1847215 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1847170 TGGACAAAAT
1847180 AAAAAAGTAGTCATAAA
1 AAAAAAGTAGTCATAAA
1847197 AAAAAAGTAGTCATAAA
1 AAAAAAGTAGTCATAAA
1847214 AA
1 AA
1847216 TTGAATCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.67, C:0.06, G:0.11, T:0.17
Consensus pattern (17 bp):
AAAAAAGTAGTCATAAA
Found at i:1856837 original size:26 final size:26
Alignment explanation
Indices: 1856782--1856840 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
1856772 GTAAAATTTT
* *
1856782 TTTATATTTTTTAAATAATTATTAGT
1 TTTAAATTTTTTAAATAATTATTAGC
1856808 TTTAAATTTTTT-AATAATTTATTTA-C
1 TTTAAATTTTTTAAATAA-TTA-TTAGC
1856834 TTTAAAT
1 TTTAAAT
1856841 CGATCGAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 5 0.17
26 21 0.72
27 3 0.10
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (26 bp):
TTTAAATTTTTTAAATAATTATTAGC
Found at i:1858059 original size:21 final size:21
Alignment explanation
Indices: 1858018--1858059 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1858008 AAATTCATCC
*
1858018 TTAAATTTTAAAACAGTTTAA
1 TTAAATTTTAAAACAGATTAA
*
1858039 TTAAATTCTT-AAACTGATTAA
1 TTAAATT-TTAAAACAGATTAA
1858060 AATATTGTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (21 bp):
TTAAATTTTAAAACAGATTAA
Found at i:1882975 original size:23 final size:26
Alignment explanation
Indices: 1882945--1882999 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
1882935 CATGTGGCAA
1882945 AAAAAATAAAAA-A-T-AAATTTATT
1 AAAAAATAAAAATACTAAAATTTATT
1882968 AAAAAATAAAAATACTTAAAATTTATT
1 AAAAAATAAAAATAC-TAAAATTTATT
1882995 AAAAA
1 AAAAA
1883000 CTATTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 12 0.43
24 1 0.04
26 1 0.04
27 14 0.50
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (26 bp):
AAAAAATAAAAATACTAAAATTTATT
Found at i:1883051 original size:20 final size:20
Alignment explanation
Indices: 1883006--1883055 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1882996 AAAACTATTT
1883006 TTTTAT-AAAAATCGTAAAA
1 TTTTATAAAAAATCGTAAAA
*** *
1883025 AAATATAAAAAATGGTAAAA
1 TTTTATAAAAAATCGTAAAA
1883045 TTTTATAAAAA
1 TTTTATAAAAA
1883056 TCAAACAAAA
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (20 bp):
TTTTATAAAAAATCGTAAAA
Found at i:1883387 original size:19 final size:19
Alignment explanation
Indices: 1883365--1883405 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1883355 TTATAAAAAA
1883365 TTACCATTTTTCTAT-ATTT
1 TTACCATTTTT-TATAATTT
*
1883384 TTACGATTTTTTATAATTT
1 TTACCATTTTTTATAATTT
1883403 TTA
1 TTA
1883406 AATATTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.24, C:0.10, G:0.02, T:0.63
Consensus pattern (19 bp):
TTACCATTTTTTATAATTT
Found at i:1883403 original size:9 final size:9
Alignment explanation
Indices: 1883391--1883458 Score: 52
Period size: 9 Copynumber: 7.6 Consensus size: 9
1883381 TTTTTACGAT
1883391 TTTTTATAA
1 TTTTTATAA
1883400 TTTTTA-AA
1 TTTTTATAA
1883408 TATTTTATTAAA
1 T-TTTTA-T-AA
* * *
1883420 ATATAATAA
1 TTTTTATAA
1883429 TTTTTATAA
1 TTTTTATAA
*
1883438 TTTCTAT--
1 TTTTTATAA
1883445 TTTTTATAA
1 TTTTTATAA
1883454 TTTTT
1 TTTTT
1883459 GTCACATGTC
Statistics
Matches: 45, Mismatches: 8, Indels: 12
0.69 0.12 0.18
Matches are distributed among these distances:
7 6 0.13
8 3 0.07
9 30 0.67
10 1 0.02
11 3 0.07
12 2 0.04
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:1896498 original size:7 final size:7
Alignment explanation
Indices: 1896486--1896518 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
1896476 CATGGTGGAC
1896486 CAAAAAG
1 CAAAAAG
1896493 CAAAAAG
1 CAAAAAG
1896500 CAAAAAG
1 CAAAAAG
1896507 CAAAAAG
1 CAAAAAG
1896514 CAAAA
1 CAAAA
1896519 TTGAAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.73, C:0.15, G:0.12, T:0.00
Consensus pattern (7 bp):
CAAAAAG
Done.