Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008062.1 Hibiscus syriacus cultivar Beakdansim tig00110557_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: 2089609
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1487599 original size:24 final size:24
Alignment explanation
Indices: 1487565--1487616 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
1487555 TTAAACATAA
*
1487565 ATAAACGAACATAACCGAACGAAC
1 ATAAACAAACATAACCGAACGAAC
1487589 ATAAACAAACATAACCGAACGAAC
1 ATAAACAAACATAACCGAACGAAC
1487613 ATAA
1 ATAA
1487617 CCGAACGTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.58, C:0.23, G:0.10, T:0.10
Consensus pattern (24 bp):
ATAAACAAACATAACCGAACGAAC
Found at i:1487615 original size:14 final size:14
Alignment explanation
Indices: 1487568--1487623 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
1487558 AACATAAATA
1487568 AACGAACATAACCG
1 AACGAACATAACCG
1487582 AACGAACAT-A---
1 AACGAACATAACCG
*
1487592 AACAAACATAACCG
1 AACGAACATAACCG
1487606 AACGAACATAACCG
1 AACGAACATAACCG
1487620 AACG
1 AACG
1487624 TTCACGAACG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
10 8 0.22
11 1 0.03
13 1 0.03
14 26 0.72
ACGTcount: A:0.54, C:0.27, G:0.12, T:0.07
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:1493701 original size:29 final size:29
Alignment explanation
Indices: 1493620--1493714 Score: 79
Period size: 29 Copynumber: 3.1 Consensus size: 29
1493610 CATCATAATA
*
1493620 ATTAAATTAAATTTTTTATATTAATTATAATT
1 ATTAAA-TAAA-TTTTT-TATTAATTAGAATT
*
1493652 ATTATATTGAAA-TTTTT-TTAATTAGAATT
1 ATTA-AAT-AAATTTTTTATTAATTAGAATT
*
1493681 ATTAAAT-AATTTATTTATTAATTATGATTT
1 ATTAAATAAATTT-TTTATTAATTA-GAATT
1493711 ATTA
1 ATTA
1493715 GATTAGAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
26 2 0.04
27 2 0.04
28 5 0.09
29 22 0.42
30 9 0.17
31 4 0.08
32 5 0.09
33 4 0.08
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (29 bp):
ATTAAATAAATTTTTTATTAATTAGAATT
Found at i:1496303 original size:18 final size:18
Alignment explanation
Indices: 1496280--1496315 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1496270 AGACGTTTAT
*
1496280 ATTTATCCATAGACGTTG
1 ATTTATACATAGACGTTG
*
1496298 ATTTATACATGGACGTTG
1 ATTTATACATAGACGTTG
1496316 CCCAACCTAT
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:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (18 bp):
ATTTATACATAGACGTTG
Found at i:1506328 original size:53 final size:53
Alignment explanation
Indices: 1506266--1506384 Score: 202
Period size: 53 Copynumber: 2.2 Consensus size: 53
1506256 GTGTGGTAGT
* * *
1506266 ACTTTATTTTGTTTGCTATGTTTTCTTTATTATTGTAGTGTTTGTTTAAAAGG
1 ACTTTATTTTGTTTACTATATTTTCTTTATTATTGTAGTGTTTATTTAAAAGG
*
1506319 ACTTTATTTTGTTTACTATATTTTCTTTGTTATTGTAGTGTTTATTTAAAAGG
1 ACTTTATTTTGTTTACTATATTTTCTTTATTATTGTAGTGTTTATTTAAAAGG
1506372 ACTTTATTTTGTT
1 ACTTTATTTTGTT
1506385 ACTGCTTTGT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 62 1.00
ACGTcount: A:0.20, C:0.06, G:0.14, T:0.60
Consensus pattern (53 bp):
ACTTTATTTTGTTTACTATATTTTCTTTATTATTGTAGTGTTTATTTAAAAGG
Found at i:1515476 original size:67 final size:67
Alignment explanation
Indices: 1515396--1515521 Score: 173
Period size: 67 Copynumber: 1.9 Consensus size: 67
1515386 GAGCTAAAAA
* * * *
1515396 AGCAACGAGTCGAGTAATAAATTTTCTCAACGAGCATC-AGTCGAGTAAAATTTTAACGACCTTA
1 AGCAACGAGTCGAGCAATAAATTTCCTCAACGAGCA-CAAGTCGAATAAAACTTTAACGACCTTA
1515460 ATG
65 ATG
* * *
1515463 AGCAACGATTCGAGCAATAAATTTCCTTATCGAGCACAAGTCGAATAAAACTTTAACGA
1 AGCAACGAGTCGAGCAATAAATTTCCTCAACGAGCACAAGTCGAATAAAACTTTAACGA
1515522 GTAACGAGTC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 1 0.02
67 50 0.98
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (67 bp):
AGCAACGAGTCGAGCAATAAATTTCCTCAACGAGCACAAGTCGAATAAAACTTTAACGACCTTAA
TG
Found at i:1515537 original size:58 final size:58
Alignment explanation
Indices: 1515457--1515576 Score: 150
Period size: 58 Copynumber: 2.1 Consensus size: 58
1515447 TTTAACGACC
* * *
1515457 TTAATGAGCAACGATTCGAGCAATAAATTTCCTTATCGAGCACAAGTCGAATAAAACT
1 TTAACGAGCAACGAGTCGAGCAACAAATTTCCTTATCGAGCACAAGTCGAATAAAACT
* * * ** * *
1515515 TTAACGAGTAACGAGTCGAGCAACAAATTTTCTTATTGAGCATGAGTTGAATAAAATT
1 TTAACGAGCAACGAGTCGAGCAACAAATTTCCTTATCGAGCACAAGTCGAATAAAACT
1515573 TTAA
1 TTAA
1515577 AAAGTTTAAC
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (58 bp):
TTAACGAGCAACGAGTCGAGCAACAAATTTCCTTATCGAGCACAAGTCGAATAAAACT
Found at i:1518336 original size:30 final size:30
Alignment explanation
Indices: 1518300--1518357 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
1518290 GTGGCGTTTA
1518300 GGGGCTGGCTTCTGCTGTTGTGGATTCGAG
1 GGGGCTGGCTTCTGCTGTTGTGGATTCGAG
*
1518330 GGGGCTGGTTTCTGCTGTTGTGGATTCG
1 GGGGCTGGCTTCTGCTGTTGTGGATTCG
1518358 TGACATTCGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.05, C:0.16, G:0.43, T:0.36
Consensus pattern (30 bp):
GGGGCTGGCTTCTGCTGTTGTGGATTCGAG
Found at i:1527937 original size:16 final size:15
Alignment explanation
Indices: 1527918--1527996 Score: 62
Period size: 16 Copynumber: 5.4 Consensus size: 15
1527908 ATAATAAAAT
*
1527918 AAAAATTATTGAATAC
1 AAAAATTATT-AATAA
1527934 AAAAATTAATT-A-AA
1 AAAAATT-ATTAATAA
*
1527948 CAAAA--A-TAAT-A
1 AAAAATTATTAATAA
1527959 AAAAATTATTGAATAA
1 AAAAATTATT-AATAA
1527975 AAAAATTAATTAATAA
1 AAAAATT-ATTAATAA
1527991 AAAAAT
1 AAAAAT
1527997 AAAAAGGGGA
Statistics
Matches: 51, Mismatches: 3, Indels: 18
0.71 0.04 0.25
Matches are distributed among these distances:
10 1 0.02
11 7 0.14
13 1 0.02
14 6 0.12
15 4 0.08
16 26 0.51
17 6 0.12
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (15 bp):
AAAAATTATTAATAA
Found at i:1527969 original size:41 final size:40
Alignment explanation
Indices: 1527901--1528001 Score: 152
Period size: 41 Copynumber: 2.5 Consensus size: 40
1527891 AATAAATTTA
* *
1527901 TAATTAAATAATAAAAT-AAAAATTATTGAATACAAAAAT
1 TAATTAAATAAAAAAATAAAAAATTATTGAATAAAAAAAT
*
1527940 TAATTAAACAAAAATAATAAAAAATTATTGAATAAAAAAAT
1 TAATTAAATAAAAA-AATAAAAAATTATTGAATAAAAAAAT
1527981 TAATT-AATAAAAAAATAAAAA
1 TAATTAAATAAAAAAATAAAAA
1528002 GGGGAAAAGT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
39 20 0.36
40 10 0.18
41 26 0.46
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (40 bp):
TAATTAAATAAAAAAATAAAAAATTATTGAATAAAAAAAT
Found at i:1530937 original size:19 final size:20
Alignment explanation
Indices: 1530894--1530941 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1530884 TCTAAATCCT
*
1530894 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
1530914 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
1530933 TTTTCAAAA
1 TTTTCAAAA
1530942 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:1531855 original size:34 final size:33
Alignment explanation
Indices: 1531801--1531871 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
1531791 CCTTACAAAC
* * *
1531801 TCCCTAGTTTTTTCTGGGCTAAACTAGAACTTT
1 TCCCTAGCTTTTACTGGGCTAAACTAGAACCTT
*
1531834 TCCCTAGCTTTTACATGGGCTAAGCTAGAACCTT
1 TCCCTAGCTTTTAC-TGGGCTAAACTAGAACCTT
1531868 TCCC
1 TCCC
1531872 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 12 0.36
34 21 0.64
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.37
Consensus pattern (33 bp):
TCCCTAGCTTTTACTGGGCTAAACTAGAACCTT
Found at i:1532224 original size:20 final size:20
Alignment explanation
Indices: 1532199--1532239 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1532189 CTGTTAGACA
1532199 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
* *
1532219 GGGGGAATCTGTACCCGCTG
1 GGGGGAATCGGTACCCCCTG
1532239 G
1 G
1532240 ACAATCTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.27, G:0.41, T:0.17
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCCTG
Found at i:1533336 original size:14 final size:14
Alignment explanation
Indices: 1533317--1533358 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1533307 ACAATTTTGG
1533317 TATTTTATTTATTT
1 TATTTTATTTATTT
*
1533331 TATTTTA-TTAATT
1 TATTTTATTTATTT
*
1533344 GATTTTTATTTATTT
1 TA-TTTTATTTATTT
1533359 AGATAAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 6 0.26
14 12 0.52
15 5 0.22
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (14 bp):
TATTTTATTTATTT
Found at i:1533998 original size:30 final size:32
Alignment explanation
Indices: 1533940--1533999 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
1533930 ATTAATAATA
* *
1533940 AAATATATTTTTTAAAATTATTATAATTTATT
1 AAATATATTTTTTAAAATGATCATAATTTATT
1533972 AAAT-TATTTTTTAAAATGATCA-AATTTA
1 AAATATATTTTTTAAAATGATCATAATTTA
1534000 AATATATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 6 0.23
31 16 0.62
32 4 0.15
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (32 bp):
AAATATATTTTTTAAAATGATCATAATTTATT
Found at i:1534338 original size:19 final size:19
Alignment explanation
Indices: 1534314--1534351 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1534304 CAAAATAAAA
* *
1534314 AAATATTTTAAATTACAAT
1 AAATATTTAAAATCACAAT
1534333 AAATATTTAAAATCACAAT
1 AAATATTTAAAATCACAAT
1534352 CGTAAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATATTTAAAATCACAAT
Found at i:1535968 original size:42 final size:42
Alignment explanation
Indices: 1535906--1535999 Score: 145
Period size: 42 Copynumber: 2.3 Consensus size: 42
1535896 TTCCCTGAAA
* *
1535906 TCCCGTG-TTGTTTCATGTAATTCGTTTTTCGGAAAATGTTT
1 TCCCGTGTTTGTTTCAAGTAATTCGTTTTCCGGAAAATGTTT
*
1535947 TCCCGTGTTTGTTTCAAGTAATTCGTTTTCCGGAGAATGTTT
1 TCCCGTGTTTGTTTCAAGTAATTCGTTTTCCGGAAAATGTTT
*
1535989 TCCAGTGTTTG
1 TCCCGTGTTTG
1536000 GTTGGAGGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
41 7 0.15
42 41 0.85
ACGTcount: A:0.16, C:0.16, G:0.21, T:0.47
Consensus pattern (42 bp):
TCCCGTGTTTGTTTCAAGTAATTCGTTTTCCGGAAAATGTTT
Found at i:1536410 original size:23 final size:23
Alignment explanation
Indices: 1536390--1536434 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1536380 ATTAATATTT
1536390 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
1536413 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
1536435 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:1536785 original size:14 final size:14
Alignment explanation
Indices: 1536753--1536787 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1536743 CATTTTACGG
*
1536753 AAAACATTTTCTAA
1 AAAATATTTTCTAA
*
1536767 AAAATATTTTTTAA
1 AAAATATTTTCTAA
1536781 AAAATAT
1 AAAATAT
1536788 AATTTATTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (14 bp):
AAAATATTTTCTAA
Found at i:1536819 original size:15 final size:15
Alignment explanation
Indices: 1536801--1536878 Score: 54
Period size: 15 Copynumber: 5.3 Consensus size: 15
1536791 TTATTTCCAG
1536801 AATTCAAATTTCAAT
1 AATTCAAATTTCAAT
** **
1536816 AATTCATTTTTTTA-
1 AATTCAAATTTCAAT
*
1536830 AATTCAAATTTCACT
1 AATTCAAATTTCAAT
* *
1536845 AATT-AATTTTTTAAT
1 AATTCAA-ATTTCAAT
1536860 AATTCAAA-TTCTAAT
1 AATTCAAATTTC-AAT
1536875 AATT
1 AATT
1536879 TATTTTACTC
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
14 13 0.29
15 30 0.67
16 2 0.04
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (15 bp):
AATTCAAATTTCAAT
Found at i:1536839 original size:29 final size:30
Alignment explanation
Indices: 1536801--1536884 Score: 109
Period size: 29 Copynumber: 2.8 Consensus size: 30
1536791 TTATTTCCAG
* *
1536801 AATTCAAATTTCAATAATTCATTTTTTTA-
1 AATTCAAATTTCAATAATTAATTTTTTAAT
*
1536830 AATTCAAATTTCACTAATTAATTTTTTAAT
1 AATTCAAATTTCAATAATTAATTTTTTAAT
*
1536860 AATTCAAA-TTCTAATAATTTATTTT
1 AATTCAAATTTC-AATAATTAATTTT
1536885 ACTCTATTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
29 29 0.60
30 19 0.40
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (30 bp):
AATTCAAATTTCAATAATTAATTTTTTAAT
Found at i:1541805 original size:17 final size:17
Alignment explanation
Indices: 1541780--1541813 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1541770 TTATCTTGAT
1541780 AATAAATTTTAATAAAA
1 AATAAATTTTAATAAAA
* *
1541797 AATATATTTTATTAAAA
1 AATAAATTTTAATAAAA
1541814 CACGTTATCT
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATAAATTTTAATAAAA
Found at i:1560185 original size:3 final size:3
Alignment explanation
Indices: 1560177--1560203 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1560167 TTATAACTCT
1560177 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1560204 AAAAATGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1561053 original size:25 final size:26
Alignment explanation
Indices: 1561000--1561055 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
1560990 TTTAAAATAT
1561000 ATTTTAACACATCTAATTATTACTCA
1 ATTTTAACACATCTAATTATTACTCA
* *
1561026 ATTTTAA-ATATCTAATGTATTA-TTA
1 ATTTTAACACATCTAAT-TATTACTCA
1561051 ATTTT
1 ATTTT
1561056 GGAACAAAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 15 0.56
26 12 0.44
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (26 bp):
ATTTTAACACATCTAATTATTACTCA
Found at i:1561566 original size:179 final size:179
Alignment explanation
Indices: 1561274--1561637 Score: 556
Period size: 179 Copynumber: 2.0 Consensus size: 179
1561264 TTATATAAAA
* *
1561274 ATTA-AATGTTTTTTAATTAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAA
1 ATTATAATATTTTTTAATTAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAA
*
1561338 AAATTTCAGATAATTTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAA
66 AAATTTCAGATAA-TTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTAGATCTTAA
* * * *
1561403 ATTATTAATTGGGTTTTAAATGGTTTGGACTT-AGCCCATATGTTATATAT
130 ATTATTAATTGGATTTCAAATGATTTGG-CTTGAACCCATATGTTATATAT
1561453 ATTATAATATTTTTTAATTAAAAAAACAGTTTACAATTAATTTAAATAATATAT-ATTATAAAAT
1 ATTATAATATTTTTTAATT-AAAAAA-AGTTTACAATTAATTTAAATAATATATAATTATAAAAT
* *
1561517 AAAAATTTTATATAA-TTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTAGATCTTA
64 AAAAATTTCAGATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTAGATCTTA
* *
1561581 AATTATTAATTGGATTTCAAATGATTTGGGTTGAACTCATATGTTATATAT
129 AATTATTAATTGGATTTCAAATGATTTGGCTTGAACCCATATGTTATATAT
*
1561632 AATATA
1 ATTATA
1561638 TTTAAAATTT
Statistics
Matches: 169, Mismatches: 12, Indels: 8
0.89 0.06 0.04
Matches are distributed among these distances:
178 2 0.01
179 99 0.59
180 13 0.08
181 29 0.17
182 26 0.15
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (179 bp):
ATTATAATATTTTTTAATTAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAA
AAATTTCAGATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTAGATCTTAAA
TTATTAATTGGATTTCAAATGATTTGGCTTGAACCCATATGTTATATAT
Found at i:1561852 original size:17 final size:18
Alignment explanation
Indices: 1561830--1561863 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1561820 GTGGAGCTGG
1561830 TGATTT-GTTTATTATAA
1 TGATTTCGTTTATTATAA
*
1561847 TGATTTCTTTTATTATA
1 TGATTTCGTTTATTATA
1561864 GTTTCTTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.03, G:0.09, T:0.62
Consensus pattern (18 bp):
TGATTTCGTTTATTATAA
Found at i:1572568 original size:21 final size:21
Alignment explanation
Indices: 1572542--1572584 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1572532 AGAAATCAGA
1572542 ATGGAGTGTTACCCTCCGAAG
1 ATGGAGTGTTACCCTCCGAAG
1572563 ATGGAGTGTTACCCTCCGAAG
1 ATGGAGTGTTACCCTCCGAAG
1572584 A
1 A
1572585 GGAACCCGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (21 bp):
ATGGAGTGTTACCCTCCGAAG
Found at i:1582712 original size:2 final size:2
Alignment explanation
Indices: 1582707--1582741 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1582697 TTTTATTATT
1582707 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1582742 GTTTGAAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1582768 original size:38 final size:38
Alignment explanation
Indices: 1582725--1582966 Score: 94
Period size: 38 Copynumber: 6.3 Consensus size: 38
1582715 TATATATATA
1582725 TATATATATATATTATAGTTTGAAATCATTTTGAAAAC
1 TATATATATATATTATAGTTTGAAATCATTTTGAAAAC
* * *** *
1582763 TATATAATATATGGGTTTCTAAAAAT-AAAACATTTTGAAAA-
1 TATAT-ATATAT---ATTAT-AGTTTGAAATCATTTTGAAAAC
** * *
1582804 TATATA-ATATATGGT-TTTTGAAAACATTTTTTGAAAAC
1 TATATATATATATTATAGTTTGAAATCA--TTTTGAAAAC
* * **
1582842 -ATATATATTATATAAT-TTTTGAAATTTTTTTTG-AAAC
1 TATATATA-TATATTATAGTTTGAAA-TCATTTTGAAAAC
* * *
1582879 CATATATAT-TA-TATAGTTTTTAAAACCATTTTTGAAAAC
1 TATATATATATATTATAG--TTTGAAATCA-TTTTGAAAAC
* **
1582918 T-TATATA-ATA-TATAGTTTTAAAATCATTTTGAAATT
1 TATATATATATATTATAG-TTTGAAATCATTTTGAAAAC
1582954 TATATAATATATA
1 TATAT-ATATATA
1582967 GTTTAAAAAA
Statistics
Matches: 155, Mismatches: 27, Indels: 43
0.69 0.12 0.19
Matches are distributed among these distances:
34 1 0.01
35 8 0.05
36 13 0.08
37 32 0.21
38 45 0.29
39 31 0.20
40 1 0.01
41 5 0.03
42 17 0.11
43 2 0.01
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (38 bp):
TATATATATATATTATAGTTTGAAATCATTTTGAAAAC
Found at i:1582836 original size:13 final size:13
Alignment explanation
Indices: 1582818--1582843 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1582808 TAATATATGG
1582818 TTTTTGAAAACAT
1 TTTTTGAAAACAT
1582831 TTTTTGAAAACAT
1 TTTTTGAAAACAT
1582844 ATATATTATA
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:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
TTTTTGAAAACAT
Found at i:1582846 original size:37 final size:36
Alignment explanation
Indices: 1582795--1583081 Score: 206
Period size: 38 Copynumber: 8.0 Consensus size: 36
1582785 AAATAAAACA
* *
1582795 TTTTGAAAATATATAATATATGGTTTTTGAAAACATT
1 TTTTGAAAACATATAATATATAG-TTTTGAAAACATT
* **
1582832 TTTTGAAAACATATATATTATATAATTTTTG-AAATTTT
1 TTTTGAAAACATATA-A-TATAT-AGTTTTGAAAACATT
* *
1582870 TTTTGAAACCATATATATTATATAGTTTTTAAAACCA-T
1 TTTTGAAAACATATA-A-TATATAGTTTTGAAAA-CATT
1582908 TTTTGAAAACTTATATAATATATAGTTTT-AAAATCA--
1 TTTTGAAAAC--ATATAATATATAGTTTTGAAAA-CATT
** **
1582944 TTTTGAAATTTATATAATATATAGTTTAAAAAAACA-T
1 TTTTGAAA-ACATATAATATATAGTTT-TGAAAACATT
*
1582981 TTTTG-AAACATAT-A-ATATAGTTTT-AAAAC-GT
1 TTTTGAAAACATATAATATATAGTTTTGAAAACATT
* *
1583012 TTTTGAAAAC-TATAACATATAG-TTTGAAAACGTT
1 TTTTGAAAACATATAATATATAGTTTTGAAAACATT
* *
1583046 TTTT-AAAATTATATAATATATGGTTTTGAAATACAT
1 TTTTGAAAA-CATATAATATATAGTTTTGAAA-ACAT
1583082 ATTATATAAA
Statistics
Matches: 206, Mismatches: 23, Indels: 42
0.76 0.08 0.15
Matches are distributed among these distances:
31 14 0.07
32 8 0.04
33 24 0.12
34 6 0.03
35 30 0.15
36 19 0.09
37 37 0.18
38 52 0.25
39 11 0.05
40 5 0.02
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (36 bp):
TTTTGAAAACATATAATATATAGTTTTGAAAACATT
Found at i:1583032 original size:68 final size:72
Alignment explanation
Indices: 1582788--1583077 Score: 224
Period size: 68 Copynumber: 4.1 Consensus size: 72
1582778 TTTCTAAAAA
* *** *
1582788 TAAAA-CATTTTGAAAA-TATATAATATATGGTTTTTGAAAACATTTTTTGAAAACATATATATT
1 TAAAATCATTTTGAAAACTATATAATATATAGTTTAAAAAAACA-TTTTTGAAAAC-TATATAAT
*
1582851 ATATAATTTT
64 ATAT-AGTTT
* ** * * ** *
1582861 TGAAATTTTTTTTGAAACCATATATATTATATAGTTTTTAAAACCATTTTTGAAAACTTATATAA
1 T-AAAATCATTTTGAAAAC-TATATAATATATAGTTTAAAAAAACATTTTTGAAAAC-TATATAA
1582926 TATATAGTTT
63 TATATAGTTT
**
1582936 TAAAATCATTTTGAAATTTATATAATATATAGTTTAAAAAAACATTTTTG-AAAC-ATAT-A-AT
1 TAAAATCATTTTGAAAACTATATAATATATAGTTTAAAAAAACATTTTTGAAAACTATATAATAT
1582997 ATAGTTT
66 ATAGTTT
* * * * * *
1583004 TAAAA-CGTTTTTGAAAAC--TATAACATATAGTTT--GAAAACGTTTTTTAAAATTATATAATA
1 TAAAATC-ATTTTGAAAACTATATAATATATAGTTTAAAAAAACATTTTTGAAAACTATATAATA
*
1583064 TATGGTTT
65 TATAGTTT
*
1583072 TGAAAT
1 TAAAAT
1583078 ACATATTATA
Statistics
Matches: 177, Mismatches: 30, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
64 10 0.06
65 3 0.02
66 18 0.10
67 2 0.01
68 34 0.19
69 1 0.01
70 4 0.02
72 4 0.02
73 29 0.16
74 15 0.08
75 13 0.07
76 22 0.12
77 22 0.12
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (72 bp):
TAAAATCATTTTGAAAACTATATAATATATAGTTTAAAAAAACATTTTTGAAAACTATATAATAT
ATAGTTT
Found at i:1583178 original size:23 final size:22
Alignment explanation
Indices: 1583118--1583179 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 22
1583108 TATCATATAG
*
1583118 TATTTTAT-TCTTTTTTATTTTT
1 TATTTTATCT-TTTTTTATTATT
*
1583140 TATTTGT-TTTTGTTTTTATTATT
1 TATTT-TATCTT-TTTTTATTATT
1583163 TATTTTATCCTTTTTTT
1 TATTTTAT-CTTTTTTT
1583180 TGGTGTTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
22 8 0.24
23 23 0.70
24 2 0.06
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (22 bp):
TATTTTATCTTTTTTTATTATT
Found at i:1584832 original size:13 final size:13
Alignment explanation
Indices: 1584816--1584854 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
1584806 TTTGTGTACT
1584816 TTACAATCTGTGA
1 TTACAATCTGTGA
1584829 TTACAATCTGTGA
1 TTACAATCTGTGA
1584842 TTACAATCTGTGA
1 TTACAATCTGTGA
1584855 ATCAATTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTACAATCTGTGA
Found at i:1587448 original size:29 final size:29
Alignment explanation
Indices: 1587414--1587469 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1587404 TCCCAACACA
* *
1587414 TAGGTCGACATGCCCTCCGGGTGACCTTG
1 TAGGTCGACATGCACTCCGGGCGACCTTG
*
1587443 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGACATGCACTCCGGGCGACCT
1587470 ACCCTTGCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.14, C:0.34, G:0.30, T:0.21
Consensus pattern (29 bp):
TAGGTCGACATGCACTCCGGGCGACCTTG
Found at i:1590569 original size:15 final size:15
Alignment explanation
Indices: 1590549--1590579 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1590539 TTATCATCCG
1590549 TCATCAAAATTCAAA
1 TCATCAAAATTCAAA
1590564 TCATCAAAATTCAAA
1 TCATCAAAATTCAAA
1590579 T
1 T
1590580 TGATGATGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (15 bp):
TCATCAAAATTCAAA
Found at i:1596385 original size:26 final size:25
Alignment explanation
Indices: 1596329--1596386 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
1596319 TTTATACACC
* *
1596329 AAAATA-TTATTAGGTTAATAATAA
1 AAAATATTTAATAAGTTAATAATAA
*
1596353 AATATATTTAATAAGTTAATATATAA
1 AAAATATTTAATAAGTTAATA-ATAA
1596379 AAAATATT
1 AAAATATT
1596387 ATGAATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 5 0.18
25 12 0.43
26 11 0.39
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (25 bp):
AAAATATTTAATAAGTTAATAATAA
Found at i:1601209 original size:14 final size:14
Alignment explanation
Indices: 1601190--1601220 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1601180 TACGTGGCAG
1601190 TCTTCTGCTTTTTT
1 TCTTCTGCTTTTTT
*
1601204 TCTTCTTCTTTTTT
1 TCTTCTGCTTTTTT
1601218 TCT
1 TCT
1601221 AAAGCGCGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.74
Consensus pattern (14 bp):
TCTTCTGCTTTTTT
Found at i:1601234 original size:2 final size:2
Alignment explanation
Indices: 1601229--1601256 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1601219 CTAAAGCGCG
1601229 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1601257 AAATGATATC
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):
TA
Found at i:1603913 original size:15 final size:15
Alignment explanation
Indices: 1603893--1603931 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
1603883 TCTACTTTCA
1603893 CATTAAACATATTAG
1 CATTAAACATATTAG
1603908 CATTAAACATATTAG
1 CATTAAACATATTAG
1603923 CATTAAACA
1 CATTAAACA
1603932 ACCACGCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (15 bp):
CATTAAACATATTAG
Found at i:1604872 original size:15 final size:16
Alignment explanation
Indices: 1604854--1604887 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1604844 GTCGGATCAT
1604854 ATTAAGTCAGAT-CGG
1 ATTAAGTCAGATGCGG
*
1604869 ATTAAGTCGGATGCGG
1 ATTAAGTCAGATGCGG
1604885 ATT
1 ATT
1604888 TTAACCTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (16 bp):
ATTAAGTCAGATGCGG
Found at i:1606974 original size:22 final size:22
Alignment explanation
Indices: 1606946--1607410 Score: 488
Period size: 22 Copynumber: 21.5 Consensus size: 22
1606936 ATAATATATT
1606946 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
1606968 TTTTAAAATAAATCAATAT-ATA
1 TTTTAAAATAAATCAAT-TCATA
*
1606990 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
** ***
1607012 TTTT-AAAT-TTTTTTTTCATA
1 TTTTAAAATAAATCAATTCATA
1607032 TTTTAAAATAAATC-A-TCATA
1 TTTTAAAATAAATCAATTCATA
*
1607052 TTTT-AAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
* ***
1607073 -TTTAAAATAATTTTTTTCATA
1 TTTTAAAATAAATCAATTCATA
1607094 TTTT-AAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
*
1607115 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
* ***
1607137 TTTTAAAATAATTTTTTTCCATA
1 TTTTAAAATAAATCAATT-CATA
*
1607160 TTTTAAAATAAATCAATTTATA
1 TTTTAAAATAAATCAATTCATA
*
1607182 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
**
1607204 TTTTAAAATAAAT-TTTTCTATA
1 TTTTAAAATAAATCAATTC-ATA
1607226 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
* ***
1607248 TTTTAAAATAATTTTTTTCATA
1 TTTTAAAATAAATCAATTCATA
1607270 TTTTAAAATAAATCAA-TCAATA
1 TTTTAAAATAAATCAATTC-ATA
*
1607292 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
***
1607314 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATTCATA
** ***
1607336 TTTT-AAAT-TTTTTTTTCATA
1 TTTTAAAATAAATCAATTCATA
*
1607356 TTTCAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
1607378 TTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
1607400 TTTTAAAATAA
1 TTTTAAAATAA
1607411 TTTTTAAAAT
Statistics
Matches: 365, Mismatches: 61, Indels: 34
0.79 0.13 0.07
Matches are distributed among these distances:
19 9 0.02
20 36 0.10
21 55 0.15
22 242 0.66
23 23 0.06
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.46
Consensus pattern (22 bp):
TTTTAAAATAAATCAATTCATA
Found at i:1607016 original size:66 final size:65
Alignment explanation
Indices: 1606962--1607415 Score: 577
Period size: 66 Copynumber: 7.0 Consensus size: 65
1606952 AATAAATCAA
*
1606962 TTCATATTTTAAAATAAATCAATATATATTTTAAAATAAATCAATCCATATTTT-AAAT-TTTTT
1 TTCATATTTTAAAATAAATCAAT-TATATTTTAAAATAAATCAATCCATATTTTAAAATAATTTT
1607025 T
65 T
*
1607026 TTCATATTTTAAAATAAATC-ATCATATTTT-AAATAAATCAATCCATA-TTTAAAATAATTTTT
1 TTCATATTTTAAAATAAATCAATTATATTTTAAAATAAATCAATCCATATTTTAAAATAATTTTT
1607088 TTCATATTTT-AAATAAATCAATTCATATTTTAAAATAAATCAATCCATATTTTAAAATAATTTT
1 TTCATATTTTAAAATAAATCAATT-ATATTTTAAAATAAATCAATCCATATTTTAAAATAATTTT
1607152 T
65 T
*
1607153 TTCCATATTTTAAAATAAATCAATTTATATTTTAAAATAAATCAATCCATATTTTAAAATAA-AT
1 TT-CATATTTTAAAATAAATCAA-TTATATTTTAAAATAAATCAATCCATATTTTAAAATAATTT
1607217 TT
64 TT
* *** * *
1607219 TTCTATATTTTAAAATAAATCAATTCATATTTTAAAATAATTTTTTTCATATTTTAAAATAA-AT
1 TTC-ATATTTTAAAATAAATCAATT-ATATTTTAAAATAAATCAATCCATATTTTAAAATAATTT
**
1607283 CA
64 TT
* * *** * *
1607285 ATCAATATTTTAAAATAAATCAATCCATATTTTAAAATAAATTTTTTCATATTTT-AAAT-TTTT
1 TTC-ATATTTTAAAATAAATCAAT-TATATTTTAAAATAAATCAATCCATATTTTAAAATAATTT
1607348 TT
64 TT
* *
1607350 TTCATATTTCAAAATAAATCAATTCATATTTTAAAATAAATCAATCTATATTTTAAAATAATTTT
1 TTCATATTTTAAAATAAATCAATT-ATATTTTAAAATAAATCAATCCATATTTTAAAATAATTTT
1607415 T
65 T
1607416 AAAATATATT
Statistics
Matches: 346, Mismatches: 28, Indels: 30
0.86 0.07 0.07
Matches are distributed among these distances:
60 3 0.01
61 30 0.09
62 24 0.07
63 9 0.03
64 80 0.23
65 31 0.09
66 120 0.35
67 47 0.14
68 2 0.01
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (65 bp):
TTCATATTTTAAAATAAATCAATTATATTTTAAAATAAATCAATCCATATTTTAAAATAATTTTT
Found at i:1612183 original size:2 final size:2
Alignment explanation
Indices: 1612176--1612207 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1612166 CTTCCTAGTC
1612176 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1612208 GGGCTTTAAA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1620188 original size:31 final size:31
Alignment explanation
Indices: 1620153--1620221 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
1620143 CTAATCTTGC
* *
1620153 TTAAATAGATTATTTTAAATATTTAAGTACT
1 TTAAATAGATTATTTTAAATACTTAAATACT
*
1620184 TTAAATTGATTATTTTAAATACTTAAATACT
1 TTAAATAGATTATTTTAAATACTTAAATACT
1620215 TTAAATA
1 TTAAATA
1620222 AATAATAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (31 bp):
TTAAATAGATTATTTTAAATACTTAAATACT
Found at i:1630730 original size:2 final size:2
Alignment explanation
Indices: 1630725--1630756 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1630715 TTTTGTCCTA
1630725 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
1630757 TATTATTCAT
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:1631066 original size:17 final size:17
Alignment explanation
Indices: 1631044--1631079 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1631034 TTATTGGTGG
1631044 TTTATCTTGTTTATGAC
1 TTTATCTTGTTTATGAC
1631061 TTTATCTTGTTTATGAC
1 TTTATCTTGTTTATGAC
1631078 TT
1 TT
1631080 CAGTAATTAT
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:0.17, C:0.11, G:0.11, T:0.61
Consensus pattern (17 bp):
TTTATCTTGTTTATGAC
Found at i:1634164 original size:16 final size:16
Alignment explanation
Indices: 1634143--1634173 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1634133 TAATAAATAA
1634143 ACGAACATAAACGAAT
1 ACGAACATAAACGAAT
1634159 ACGAACATAAACGAA
1 ACGAACATAAACGAA
1634174 CAATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.19, G:0.13, T:0.10
Consensus pattern (16 bp):
ACGAACATAAACGAAT
Found at i:1634261 original size:10 final size:10
Alignment explanation
Indices: 1634244--1634274 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1634234 ATAAACGAAC
1634244 ACGAACATAA
1 ACGAACATAA
*
1634254 ATGAACATAA
1 ACGAACATAA
1634264 ACGAACATAA
1 ACGAACATAA
1634274 A
1 A
1634275 ACGTTGGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.61, C:0.16, G:0.10, T:0.13
Consensus pattern (10 bp):
ACGAACATAA
Found at i:1635387 original size:14 final size:14
Alignment explanation
Indices: 1635370--1635424 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 14
1635360 AATGAACATA
1635370 AACGAACATAACCG
1 AACGAACATAACCG
1635384 AACGAACAT-A---
1 AACGAACATAACCG
*
1635394 AACAAACATAACCG
1 AACGAACATAACCG
* *
1635408 AACGAATATAAACG
1 AACGAACATAACCG
1635422 AAC
1 AAC
1635425 ATAATTGAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
10 8 0.24
11 1 0.03
13 1 0.03
14 23 0.70
ACGTcount: A:0.56, C:0.24, G:0.11, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:1635435 original size:24 final size:24
Alignment explanation
Indices: 1635363--1635428 Score: 114
Period size: 24 Copynumber: 2.8 Consensus size: 24
1635353 ATAAATGAAT
1635363 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
*
1635387 GAACATAAACAAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
*
1635411 GAATATAAACGAACATAA
1 GAACATAAACGAACATAA
1635429 TTGAACGTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.58, C:0.21, G:0.11, T:0.11
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:1639171 original size:9 final size:9
Alignment explanation
Indices: 1639157--1639194 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
1639147 ATTAACTAAA
1639157 ATTATTTAT
1 ATTATTTAT
1639166 ATTATTTAT
1 ATTATTTAT
*
1639175 A-TATTACAT
1 ATTATT-TAT
1639184 ATTATTTAT
1 ATTATTTAT
1639193 AT
1 AT
1639195 ATTACAGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 4 0.16
9 17 0.68
10 4 0.16
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (9 bp):
ATTATTTAT
Found at i:1639187 original size:18 final size:18
Alignment explanation
Indices: 1639164--1639200 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1639154 AAAATTATTT
1639164 ATATTATTTATATATTAC
1 ATATTATTTATATATTAC
1639182 ATATTATTTATATATTAC
1 ATATTATTTATATATTAC
1639200 A
1 A
1639201 GTGTTTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATTATTTATATATTAC
Found at i:1640689 original size:20 final size:20
Alignment explanation
Indices: 1640666--1640711 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
1640656 AAGCGCAGCT
1640666 TGAATAGTTA-AATCGCAACG
1 TGAATAG-TACAATCGCAACG
*
1640686 TGAATAGTACAATTGCAACG
1 TGAATAGTACAATCGCAACG
1640706 TGAATA
1 TGAATA
1640712 ATAAAATCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (20 bp):
TGAATAGTACAATCGCAACG
Found at i:1641135 original size:21 final size:20
Alignment explanation
Indices: 1641081--1641207 Score: 200
Period size: 20 Copynumber: 6.2 Consensus size: 20
1641071 CATATAGATT
* * *
1641081 CGTTGTGATTTTATTATTTA
1 CGTTGCGATTTTACTATTCA
1641101 CGTTGCGATTTTACTATTCA
1 CGTTGCGATTTTACTATTCA
*
1641121 AGTTGCGATTTTTACTATTCA
1 CGTTGCGA-TTTTACTATTCA
1641142 CGTTGCGATTTTTACTATTCA
1 CGTTGCGA-TTTTACTATTCA
1641163 CGTTGCGATTTTACTATTCA
1 CGTTGCGATTTTACTATTCA
1641183 CGTTGCGATTTTACTATTCA
1 CGTTGCGATTTTACTATTCA
1641203 CGTTG
1 CGTTG
1641208 TGAATTTGAC
Statistics
Matches: 101, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
20 61 0.60
21 40 0.40
ACGTcount: A:0.20, C:0.17, G:0.16, T:0.48
Consensus pattern (20 bp):
CGTTGCGATTTTACTATTCA
Found at i:1641220 original size:41 final size:40
Alignment explanation
Indices: 1641081--1641207 Score: 200
Period size: 41 Copynumber: 3.1 Consensus size: 40
1641071 CATATAGATT
* * *
1641081 CGTTGTGATTTTATTATTTACGTTGCGATTTTACTATTCA
1 CGTTGCGATTTTACTATTCACGTTGCGATTTTACTATTCA
*
1641121 AGTTGCGATTTTTACTATTCACGTTGCGATTTTTACTATTCA
1 CGTTGCGA-TTTTACTATTCACGTTGCGA-TTTTACTATTCA
1641163 CGTTGCGATTTTACTATTCACGTTGCGATTTTACTATTCA
1 CGTTGCGATTTTACTATTCACGTTGCGATTTTACTATTCA
1641203 CGTTG
1 CGTTG
1641208 TGAATTTGAC
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
40 23 0.29
41 38 0.47
42 19 0.24
ACGTcount: A:0.20, C:0.17, G:0.16, T:0.48
Consensus pattern (40 bp):
CGTTGCGATTTTACTATTCACGTTGCGATTTTACTATTCA
Found at i:1641226 original size:20 final size:20
Alignment explanation
Indices: 1641101--1641278 Score: 121
Period size: 20 Copynumber: 8.8 Consensus size: 20
1641091 TTATTATTTA
*
1641101 CGTTGCG-ATTTTACTATT-
1 CGTTGCGAATTTGACTATTG
* * *
1641119 CAAGTTGCGATTTTTACTATTCA
1 C--GTTGCGAATTTGACTATT-G
* * *
1641142 CGTTGCGATTTTTACTATTCA
1 CGTTGCGAATTTGACTATT-G
* *
1641163 CGTTGCG-ATTTTACTATTCA
1 CGTTGCGAATTTGACTATT-G
* *
1641183 CGTTGCG-ATTTTACTATTCA
1 CGTTGCGAATTTGACTATT-G
* *
1641203 CGTTGTGAATTTGACTATCG
1 CGTTGCGAATTTGACTATTG
* *
1641223 CGTTACGAATTTGACTTTTG
1 CGTTGCGAATTTGACTATTG
* *
1641243 TGTTGCAAATTTGACTATTG
1 CGTTGCGAATTTGACTATTG
1641263 CGTTGCGAATTTGACT
1 CGTTGCGAATTTGACT
1641279 TCTGTGTTGC
Statistics
Matches: 138, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
18 1 0.01
20 90 0.65
21 46 0.33
23 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.18, T:0.44
Consensus pattern (20 bp):
CGTTGCGAATTTGACTATTG
Found at i:1641254 original size:40 final size:40
Alignment explanation
Indices: 1641210--1641288 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
1641200 TCACGTTGTG
*
1641210 AATTTGACTATCGCGTTACGAATTTGACTTTTGTGTTGCA
1 AATTTGACTATCGCGTTACGAATTTGACTTCTGTGTTGCA
* *
1641250 AATTTGACTATTGCGTTGCGAATTTGACTTCTGTGTTGC
1 AATTTGACTATCGCGTTACGAATTTGACTTCTGTGTTGC
1641289 GATTTACAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (40 bp):
AATTTGACTATCGCGTTACGAATTTGACTTCTGTGTTGCA
Found at i:1641287 original size:20 final size:21
Alignment explanation
Indices: 1641203--1641290 Score: 94
Period size: 20 Copynumber: 4.4 Consensus size: 21
1641193 TTACTATTCA
*
1641203 CGTTGTGAATTTGACTATC-G
1 CGTTGCGAATTTGACTATCTG
* *
1641223 CGTTACGAATTTGACT-TTTG
1 CGTTGCGAATTTGACTATCTG
* *
1641243 TGTTGCAAATTTGACTAT-TG
1 CGTTGCGAATTTGACTATCTG
1641263 CGTTGCGAATTTGACT-TCTG
1 CGTTGCGAATTTGACTATCTG
*
1641283 TGTTGCGA
1 CGTTGCGA
1641291 TTTACAAATT
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 2 0.04
20 53 0.95
21 1 0.02
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.42
Consensus pattern (21 bp):
CGTTGCGAATTTGACTATCTG
Found at i:1641576 original size:13 final size:13
Alignment explanation
Indices: 1641558--1641583 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1641548 ATCGGTGGCT
1641558 TGAGTCTTGAGTC
1 TGAGTCTTGAGTC
1641571 TGAGTCTTGAGTC
1 TGAGTCTTGAGTC
1641584 ATGGCGTCGG
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:0.15, C:0.15, G:0.31, T:0.38
Consensus pattern (13 bp):
TGAGTCTTGAGTC
Found at i:1647579 original size:2 final size:2
Alignment explanation
Indices: 1647572--1647596 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1647562 ATTGAAGAAC
1647572 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1647597 AGTGGATGAC
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1651973 original size:43 final size:43
Alignment explanation
Indices: 1651912--1651997 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
1651902 AACCAACCTG
1651912 GACTATATCTTGTTCATGCATTCAGAAACTTCGATAAAAGCAA
1 GACTATATCTTGTTCATGCATTCAGAAACTTCGATAAAAGCAA
1651955 GACTATATCTTGTTCATGCATTCAGAAACTTCGATAAAAGCAA
1 GACTATATCTTGTTCATGCATTCAGAAACTTCGATAAAAGCAA
1651998 AAGTCGATGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (43 bp):
GACTATATCTTGTTCATGCATTCAGAAACTTCGATAAAAGCAA
Found at i:1656181 original size:159 final size:159
Alignment explanation
Indices: 1655892--1656210 Score: 620
Period size: 159 Copynumber: 2.0 Consensus size: 159
1655882 AACAGTTCTT
1655892 ACTTCTCCAACTGTTTCTCCTGATATCTGTCAAACACCATCCACAATTACGCACTAATGATCATC
1 ACTTCTCCAACTGTTTCTCCTGATATCTGTCAAACACCATCCACAATTACGCACTAATGATCATC
*
1655957 AGGCCTAATACTATCAAGGATTATGCACTGATGACCGATTTTGTCCAGGATTTTCCAGCAAATTC
66 AGGCCTAATACTATCAAGGATTATGCACTGATGACCGATGTTGTCCAGGATTTTCCAGCAAATTC
1656022 TTTTACCAAATACAGTAACTTGAATAATA
131 TTTTACCAAATACAGTAACTTGAATAATA
1656051 ACTTCTCCAACTGTTTCTCCTGATATCTGTCAAACACCATCCACAATTACGCACTAATGATCATC
1 ACTTCTCCAACTGTTTCTCCTGATATCTGTCAAACACCATCCACAATTACGCACTAATGATCATC
1656116 AGGCCTAATACTATCAAGGATTATGCACTGATGACCGATGTTGTCCAGGATTTTCCAGCAAATTC
66 AGGCCTAATACTATCAAGGATTATGCACTGATGACCGATGTTGTCCAGGATTTTCCAGCAAATTC
*
1656181 TTTTACCAAATACAGTAAGTTGAATAATA
131 TTTTACCAAATACAGTAACTTGAATAATA
1656210 A
1 A
1656211 ACCTAGATGA
Statistics
Matches: 158, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
159 158 1.00
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.31
Consensus pattern (159 bp):
ACTTCTCCAACTGTTTCTCCTGATATCTGTCAAACACCATCCACAATTACGCACTAATGATCATC
AGGCCTAATACTATCAAGGATTATGCACTGATGACCGATGTTGTCCAGGATTTTCCAGCAAATTC
TTTTACCAAATACAGTAACTTGAATAATA
Found at i:1656568 original size:23 final size:23
Alignment explanation
Indices: 1656519--1656569 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1656509 GTGTTATATT
**
1656519 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
1656542 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
1656565 ATATT
1 ATATT
1656570 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:1656621 original size:19 final size:19
Alignment explanation
Indices: 1656557--1656635 Score: 67
Period size: 19 Copynumber: 4.3 Consensus size: 19
1656547 TTAAATATCT
1656557 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
* *
1656576 TTATT-ATATTAATATTAA
1 TTATTAATAATATTATTAA
* * *
1656594 ATATAAATAATATTATTCA
1 TTATTAATAATATTATTAA
*
1656613 TTATTAATAAT-TTAATAA
1 TTATTAATAATATTATTAA
1656631 -TATTA
1 TTATTA
1656636 TTTCTATGAA
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
17 5 0.11
18 10 0.21
19 32 0.68
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:1656650 original size:27 final size:26
Alignment explanation
Indices: 1656599--1656688 Score: 80
Period size: 25 Copynumber: 3.5 Consensus size: 26
1656589 ATTAAATATA
1656599 AATAATATTA-TTCATTATTAATAATTT
1 AATAATATTATTTC--TATTAATAATTT
*
1656626 AATAATATTATTTCTATGAATTAA--T
1 AATAATATTATTTCTATTAA-TAATTT
* *
1656651 AATAATATAAATT-TATTAATAATTT
1 AATAATATTATTTCTATTAATAATTT
*
1656676 ATTATATATTATT
1 AATA-ATATTATT
1656689 AAAATAAAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
23 3 0.06
24 5 0.10
25 16 0.31
26 11 0.22
27 13 0.25
28 3 0.06
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (26 bp):
AATAATATTATTTCTATTAATAATTT
Found at i:1656651 original size:30 final size:27
Alignment explanation
Indices: 1656599--1656653 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 27
1656589 ATTAAATATA
*
1656599 AATAATATTATTCATTATTAATAATTT
1 AATAATATTATTCATAATTAATAATTT
1656626 AATAATATTATTTCTATGAATTAATAAT
1 AATAATATTA-TTC-AT-AATTAATAAT
1656654 AATATAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 10 0.42
28 3 0.12
29 2 0.08
30 9 0.38
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (27 bp):
AATAATATTATTCATAATTAATAATTT
Found at i:1656758 original size:21 final size:23
Alignment explanation
Indices: 1656734--1656779 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
1656724 TTGATTATTT
1656734 TATTATAGTATTA-AAATA-TAA
1 TATTATAGTATTAGAAATATTAA
*
1656755 TATTATATTATTAGAAATATTAA
1 TATTATAGTATTAGAAATATTAA
1656778 TA
1 TA
1656780 AATATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.55
22 5 0.23
23 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (23 bp):
TATTATAGTATTAGAAATATTAA
Found at i:1656758 original size:26 final size:25
Alignment explanation
Indices: 1656679--1656765 Score: 72
Period size: 26 Copynumber: 3.5 Consensus size: 25
1656669 ATAATTTATT
*
1656679 ATATATTATTA-A-AATAAAATATA
1 ATATTTTATTATATAATAAAATATA
* *
1656702 ATATTTATATTAGATAATATAAT-TGA
1 ATATTT-TATTATATAATAAAATAT-A
* *
1656728 TTATTTTATTATAGTATTAAAATATA
1 ATATTTTATTATA-TAATAAAATATA
*
1656754 ATATTATATTAT
1 ATATTTTATTAT
1656766 TAGAAATATT
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
23 5 0.10
24 5 0.10
25 8 0.16
26 31 0.62
27 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (25 bp):
ATATTTTATTATATAATAAAATATA
Found at i:1656780 original size:26 final size:24
Alignment explanation
Indices: 1656751--1656813 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
1656741 GTATTAAAAT
1656751 ATAATATTATATTATTAGAA-ATATTA
1 ATAATA-TATATT-TTA-AATATATTA
*
1656777 ATAA-ATATATTTTAAATATTTTA
1 ATAATATATATTTTAAATATATTA
1656800 ATAAT-TAATATTTT
1 ATAATAT-ATATTTT
1656814 GATTAAAAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 13 0.39
24 13 0.39
25 1 0.03
26 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
ATAATATATATTTTAAATATATTA
Found at i:1656787 original size:21 final size:22
Alignment explanation
Indices: 1656742--1656811 Score: 54
Period size: 23 Copynumber: 3.0 Consensus size: 22
1656732 TTTATTATAG
*
1656742 TATTAAAATA-TAATATTATAT
1 TATTAAAATATTAATATAATAT
1656763 TATTAGAAATATTAATA-AATAT
1 TATTA-AAATATTAATATAATAT
* *
1656785 ATTTTAAATATTTTAATAATTAATAT
1 -TATTAAA-ATATTAAT-A-TAATAT
1656811 T
1 T
1656812 TTGATTAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
21 5 0.13
22 11 0.28
23 16 0.41
24 1 0.03
25 1 0.03
26 5 0.13
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (22 bp):
TATTAAAATATTAATATAATAT
Found at i:1657088 original size:40 final size:41
Alignment explanation
Indices: 1657010--1657101 Score: 125
Period size: 40 Copynumber: 2.3 Consensus size: 41
1657000 TTCTTCTAAC
* *
1657010 CAAACACTGGAAAATATTTTCCGAAAAACGAATTCGTGAAA
1 CAAACACGGGAAAACATTTTCCGAAAAACGAATTCGTGAAA
* *
1657051 CAAATACGGGAAAACATTTTTC-AAAAACG-ATTACGTGAAA
1 CAAACACGGGAAAACATTTTCCGAAAAACGAATT-CGTGAAA
1657091 CAAACACGGGA
1 CAAACACGGGA
1657102 TTTCAGAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
39 3 0.07
40 24 0.53
41 18 0.40
ACGTcount: A:0.47, C:0.17, G:0.16, T:0.20
Consensus pattern (41 bp):
CAAACACGGGAAAACATTTTCCGAAAAACGAATTCGTGAAA
Found at i:1657141 original size:29 final size:29
Alignment explanation
Indices: 1657099--1657163 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
1657089 AACAAACACG
*
1657099 GGATTTCAGAGAAAACTAATTCCATAATT
1 GGATTTCAGAGAAAACCAATTCCATAATT
* **
1657128 GGATTTCGGAGAAAACCAATTCTGTAATT
1 GGATTTCAGAGAAAACCAATTCCATAATT
*
1657157 GGTTTTC
1 GGATTTC
1657164 CCCAAACAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (29 bp):
GGATTTCAGAGAAAACCAATTCCATAATT
Found at i:1659432 original size:18 final size:18
Alignment explanation
Indices: 1659411--1659451 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1659401 ATCATATTAA
1659411 TTTTTGTAA-TTTTCGGAT
1 TTTTTG-AATTTTTCGGAT
*
1659429 TTTTTGAATTTTTCTGAT
1 TTTTTGAATTTTTCGGAT
1659447 TTTTT
1 TTTTT
1659452 TATATTTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.15, C:0.05, G:0.12, T:0.68
Consensus pattern (18 bp):
TTTTTGAATTTTTCGGAT
Found at i:1659849 original size:17 final size:17
Alignment explanation
Indices: 1659829--1659863 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1659819 AAAAGTAAAA
*
1659829 TTTAGCGGATATATTTT
1 TTTAGCAGATATATTTT
*
1659846 TTTATCAGATATATTTT
1 TTTAGCAGATATATTTT
1659863 T
1 T
1659864 GTTTATATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.11, T:0.57
Consensus pattern (17 bp):
TTTAGCAGATATATTTT
Found at i:1659959 original size:84 final size:84
Alignment explanation
Indices: 1659861--1660029 Score: 248
Period size: 84 Copynumber: 2.0 Consensus size: 84
1659851 CAGATATATT
* *
1659861 TTTGTTTATATCACATGTTTCATTTATCGGACAAAAATTATTTGTCTTTTTCGTCTTTTTCATAT
1 TTTGTTTATATCACATGTTTCATTTATCGGACAAAAATTAGTTGTCTTTTTCGTCTTTGTCATAT
* *
1659926 CTTTATTAACACAAGAATG
66 CCTTACTAACACAAGAATG
* * * *
1659945 TTTGTTTATGTCACATGTTTCATTTATCGGACAAAAATTGGTTGTCTTTTTCTTCTTTGTCTTAT
1 TTTGTTTATATCACATGTTTCATTTATCGGACAAAAATTAGTTGTCTTTTTCGTCTTTGTCATAT
* *
1660010 CCTTGCTAACATAAGAATG
66 CCTTACTAACACAAGAATG
1660029 T
1 T
1660030 GTAAAGAGGG
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
84 75 1.00
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.49
Consensus pattern (84 bp):
TTTGTTTATATCACATGTTTCATTTATCGGACAAAAATTAGTTGTCTTTTTCGTCTTTGTCATAT
CCTTACTAACACAAGAATG
Found at i:1660579 original size:42 final size:42
Alignment explanation
Indices: 1660528--1660619 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
1660518 GTTTCCAGAT
** *
1660528 TCGCAACGCGAACTTGGACTGTCGCAACGAATTTGGAATAAA
1 TCGCAACGCGAACTTCAACTATCGCAACGAATTTGGAATAAA
* *
1660570 TCGTAACGCGAACTTCAACTATCGCAACGAATTTGGAATCAA
1 TCGCAACGCGAACTTCAACTATCGCAACGAATTTGGAATAAA
1660612 TCGCAACG
1 TCGCAACG
1660620 AATTTGGAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.22
Consensus pattern (42 bp):
TCGCAACGCGAACTTCAACTATCGCAACGAATTTGGAATAAA
Found at i:1660667 original size:103 final size:101
Alignment explanation
Indices: 1660528--1660718 Score: 310
Period size: 103 Copynumber: 1.9 Consensus size: 101
1660518 GTTTCCAGAT
* * **
1660528 TCGCAACGCGAACTTGGACTGTCGCAACGAATTTGGAATAAATCGTAACGCGAACTTCAACTATC
1 TCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTCAACTATC
1660593 GCAACGAATTTGGAATCAATCGCAACGAATTTGGAAAA
66 GCAACGAATTTGGAA--AATCGCAACGAATTTGGAAAA
* *
1660631 TCGCAACGTGAACTTCGACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTCGACTATC
1 TCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTCAACTATC
1660696 GCAACGAATTTGGAAAATCGCAA
66 GCAACGAATTTGGAAAATCGCAA
1660719 TGCAAACTTC
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
101 8 0.10
103 74 0.90
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (101 bp):
TCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTCAACTATC
GCAACGAATTTGGAAAATCGCAACGAATTTGGAAAA
Found at i:1660668 original size:61 final size:63
Alignment explanation
Indices: 1660549--1660680 Score: 205
Period size: 61 Copynumber: 2.1 Consensus size: 63
1660539 ACTTGGACTG
* *
1660549 TCGCAACGAATTTGGAATAAATCGTAACGCGAACTTCAACTATCGCAACGAATTTGGAATCAA
1 TCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCAACTATCGCAACGAATTTGGAATAAA
* *
1660612 TCGCAACGAATTTGG-A-AAATCGCAACGTGAACTTCGACTATCGCAACGAATTTGGAATAAA
1 TCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCAACTATCGCAACGAATTTGGAATAAA
*
1660673 TCACAACG
1 TCGCAACG
1660681 CGAACTTCGA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
61 48 0.75
62 1 0.02
63 15 0.23
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (63 bp):
TCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCAACTATCGCAACGAATTTGGAATAAA
Found at i:1660687 original size:42 final size:40
Alignment explanation
Indices: 1660611--1660775 Score: 225
Period size: 40 Copynumber: 4.2 Consensus size: 40
1660601 TTTGGAATCA
*
1660611 ATCGCAACGAATTTGGAAAATCGCAACGTGAACTTCGACT
1 ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
*
1660651 ATCGCAACGAATTTGGAATAAATCACAACGCGAACTTCGACT
1 ATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTCGACT
* *
1660693 ATCGCAACGAATTTGGAAAATCGCAATGCAAACTTCGACT
1 ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
*
1660733 ATCG---C-AA--TGCAAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
1660767 ATCGCAACG
1 ATCGCAACG
1660776 CGAACTTGAA
Statistics
Matches: 111, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
34 28 0.25
36 2 0.02
37 2 0.02
40 40 0.36
41 2 0.02
42 37 0.33
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (40 bp):
ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
Found at i:1660716 original size:61 final size:60
Alignment explanation
Indices: 1660567--1660718 Score: 137
Period size: 61 Copynumber: 2.5 Consensus size: 60
1660557 AATTTGGAAT
* * * * * *
1660567 AAATCGTAACGCGAACTTC-AACTATCGCAACGAATTTGGAATCAATCGCAACGAATTTGGA
1 AAATCGCAACG-GAACTTCGAA-AATCGCAACGAATTTGGAATAAATCACAACGAACTTCGA
**
1660628 AAATCGCAACGTGAACTTCGACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTCGA
1 AAATCGCAACG-GAACTTCGAAAATCGCAACGAATTTGGAATAAATCACAA--CGAACTTCGA
** * *
1660691 CTATCGCAAC-GAATTTGGAAAATCGCAA
1 AAATCGCAACGGAACTTCGAAAATCGCAA
1660719 TGCAAACTTC
Statistics
Matches: 75, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
61 58 0.77
62 1 0.01
63 16 0.21
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (60 bp):
AAATCGCAACGGAACTTCGAAAATCGCAACGAATTTGGAATAAATCACAACGAACTTCGA
Found at i:1660752 original size:34 final size:34
Alignment explanation
Indices: 1660709--1660773 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
1660699 ACGAATTTGG
*
1660709 AAAATCGCAATGCAAACTTCGACTATCGCAATGC
1 AAAATCGCAACGCAAACTTCGACTATCGCAATGC
*
1660743 AAAATCGCAACGCGAACTTCGACTATCGCAA
1 AAAATCGCAACGCAAACTTCGACTATCGCAA
1660774 CGCGAACTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.38, C:0.28, G:0.15, T:0.18
Consensus pattern (34 bp):
AAAATCGCAACGCAAACTTCGACTATCGCAATGC
Found at i:1660772 original size:21 final size:21
Alignment explanation
Indices: 1660746--1660800 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
1660736 GCAATGCAAA
1660746 ATCGCAACGCGAACTTCG-ACT
1 ATCGCAACGCGAACTT-GAACT
1660767 ATCGCAACGCGAACTTGAACT
1 ATCGCAACGCGAACTTGAACT
*
1660788 ATCGCAATGCGAA
1 ATCGCAACGCGAA
1660801 TATGTAAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGAACT
Found at i:1660838 original size:21 final size:21
Alignment explanation
Indices: 1660812--1660860 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
1660802 ATGTAAATCA
1660812 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
*
1660833 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
1660854 TTGCGAT
1 TTGCGAT
1660861 TTTCCAAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.18, C:0.20, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGCGATAGTCCAAGTTCGCG
Found at i:1665536 original size:13 final size:14
Alignment explanation
Indices: 1665518--1665554 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
1665508 GATATGATTT
1665518 TATTTAATTATTA-
1 TATTTAATTATTAC
1665531 TATTTAA-TATTAC
1 TATTTAATTATTAC
*
1665544 TTTTTAATTAT
1 TATTTAATTAT
1665555 ATAATAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 5 0.24
13 13 0.62
14 3 0.14
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTTAATTATTAC
Found at i:1669125 original size:2 final size:2
Alignment explanation
Indices: 1669118--1669169 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1669108 GGTAATTTTA
1669118 AT AT AT AT AT 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 AT AT AT AT AT
1669160 AT AT AT AT AT
1 AT AT AT AT AT
1669170 GTTTAGTTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1672649 original size:22 final size:22
Alignment explanation
Indices: 1672621--1672703 Score: 148
Period size: 22 Copynumber: 3.8 Consensus size: 22
1672611 TTCTAGAACC
*
1672621 AAAGGCAATGTGCTTCAGGCTA
1 AAAGGCAATCTGCTTCAGGCTA
*
1672643 AAAGGCAATGTGCTTCAGGCTA
1 AAAGGCAATCTGCTTCAGGCTA
1672665 AAAGGCAATCTGCTTCAGGCTA
1 AAAGGCAATCTGCTTCAGGCTA
1672687 AAAGGCAATCTGCTTCA
1 AAAGGCAATCTGCTTCA
1672704 ATCCTGTGTT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 60 1.00
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (22 bp):
AAAGGCAATCTGCTTCAGGCTA
Found at i:1673498 original size:21 final size:21
Alignment explanation
Indices: 1673472--1673550 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 21
1673462 ATTAAAATAA
1673472 TATTATTAATTAATAATATTT
1 TATTATTAATTAATAATATTT
* * * *
1673493 TATTATTTATTAAAAATAATA
1 TATTATTAATTAATAATATTT
* *
1673514 TATTAGTTAATTTATTAT-TTT
1 TATTA-TTAATTAATAATATTT
*
1673535 TATTATTTATTAATAA
1 TATTATTAATTAATAA
1673551 ATTAATAATT
Statistics
Matches: 44, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
20 8 0.18
21 28 0.64
22 8 0.18
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (21 bp):
TATTATTAATTAATAATATTT
Found at i:1673505 original size:39 final size:40
Alignment explanation
Indices: 1673461--1673547 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 40
1673451 TTGTTTTTTA
1673461 TATTAAAATAATATTATTAATTAA-TAATA-TTTTATTATT
1 TATTAAAATAATA-TATTAATTAATTAATATTTTTATTATT
* *
1673500 TATTAAAAATAATATATTAGTTAATTTATTATTTTTATTATT
1 TATT-AAAATAATATATTAATTAA-TTAATATTTTTATTATT
1673542 TATTAA
1 TATTAA
1673548 TAAATTAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
39 13 0.31
40 9 0.21
41 6 0.14
42 14 0.33
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (40 bp):
TATTAAAATAATATATTAATTAATTAATATTTTTATTATT
Found at i:1673517 original size:42 final size:43
Alignment explanation
Indices: 1673471--1673564 Score: 131
Period size: 42 Copynumber: 2.2 Consensus size: 43
1673461 TATTAAAATA
1673471 ATATTATTAATTAATAATATTTTATTATTTATTAA-AAA-TAAT
1 ATATTATTAATTAATAAT-TTTTATTATTTATTAATAAATTAAT
* *
1673513 ATATTAGTTAATTTATTATTTTTATTATTTATTAATAAATTAAT
1 ATATTA-TTAATTAATAATTTTTATTATTTATTAATAAATTAAT
1673557 A-ATTATTA
1 ATATTATTA
1673565 TTTGGATTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
42 25 0.53
43 17 0.36
44 5 0.11
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (43 bp):
ATATTATTAATTAATAATTTTTATTATTTATTAATAAATTAAT
Found at i:1678660 original size:21 final size:21
Alignment explanation
Indices: 1678630--1678669 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1678620 AGTCATATCT
*
1678630 AGCCGTTGGGGATG-TTTTGG
1 AGCCGTTGGGAATGATTTTGG
1678650 AGCCGCTTGGGAATGATTTT
1 AGCCG-TTGGGAATGATTTT
1678670 TCTACAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.15, C:0.12, G:0.38, T:0.35
Consensus pattern (21 bp):
AGCCGTTGGGAATGATTTTGG
Found at i:1678724 original size:21 final size:21
Alignment explanation
Indices: 1678698--1678739 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1678688 CCATAATGGG
* *
1678698 GGGAATCGGTACTCCTTCATA
1 GGGAATCGATACCCCTTCATA
1678719 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1678740 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:1678995 original size:29 final size:31
Alignment explanation
Indices: 1678963--1679022 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1678953 AAATTTTGAA
*
1678963 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1678992 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1679023 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1683714 original size:39 final size:39
Alignment explanation
Indices: 1683660--1683752 Score: 141
Period size: 39 Copynumber: 2.4 Consensus size: 39
1683650 CAAGTTTAGG
* *
1683660 TTTTGTTTTATTTTAGTATACGCCATTAAAAATTTTATT
1 TTTTGTTTCATTTTAGTATACGCCATTAAAAACTTTATT
* * *
1683699 TTTTGTTTCATTTTAGTATCCGCCATTGAAAGCTTTATT
1 TTTTGTTTCATTTTAGTATACGCCATTAAAAACTTTATT
1683738 TTTTGTTTCATTTTA
1 TTTTGTTTCATTTTA
1683753 ACAACCAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.23, C:0.11, G:0.10, T:0.57
Consensus pattern (39 bp):
TTTTGTTTCATTTTAGTATACGCCATTAAAAACTTTATT
Found at i:1691743 original size:50 final size:50
Alignment explanation
Indices: 1691668--1691769 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
1691658 TTATCACTAT
1691668 ACAATTTCATCAATAATTGATTTGTCATGTGGGCGAGTAAACAAGAACAG
1 ACAATTTCATCAATAATTGATTTGTCATGTGGGCGAGTAAACAAGAACAG
1691718 ACAATTTCATCAATAATTGATTTGTCATGTGGGCGAGTAAACAAGAACAG
1 ACAATTTCATCAATAATTGATTTGTCATGTGGGCGAGTAAACAAGAACAG
1691768 AC
1 AC
1691770 GCATATTTTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (50 bp):
ACAATTTCATCAATAATTGATTTGTCATGTGGGCGAGTAAACAAGAACAG
Found at i:1695960 original size:19 final size:20
Alignment explanation
Indices: 1695925--1695969 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
1695915 AAATCTCAAT
1695925 ATAAATATCAATAAATTAAA
1 ATAAATATCAATAAATTAAA
*
1695945 ATAAATA-CATTAAATTAAA
1 ATAAATATCAATAAATTAAA
1695964 A-AAATA
1 ATAAATA
1695970 AACCTAAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 5 0.21
19 12 0.50
20 7 0.29
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (20 bp):
ATAAATATCAATAAATTAAA
Found at i:1695977 original size:19 final size:19
Alignment explanation
Indices: 1695936--1695977 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1695926 TAAATATCAA
* *
1695936 TAAATTAAAATAAATACAT
1 TAAATTAAAATAAATAAAC
1695955 TAAATTAAAA-AAATAAACC
1 TAAATTAAAATAAATAAA-C
1695974 TAAA
1 TAAA
1695978 CCCACCATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (19 bp):
TAAATTAAAATAAATAAAC
Found at i:1697368 original size:21 final size:21
Alignment explanation
Indices: 1697342--1697382 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1697332 CGAGTTTTCT
1697342 AATATAA-TATAAATAATCATA
1 AATATAATTAT-AATAATCATA
1697363 AATATAATTATAATAATCAT
1 AATATAATTATAATAATCAT
1697383 GATTTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (21 bp):
AATATAATTATAATAATCATA
Found at i:1697428 original size:17 final size:18
Alignment explanation
Indices: 1697406--1697445 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1697396 ATAATTCATT
* *
1697406 TAAAAAGAT-ACATAATA
1 TAAAAAGATCAAATAAAA
1697423 TAAAAAGATCAAATAAAA
1 TAAAAAGATCAAATAAAA
1697441 TAAAA
1 TAAAA
1697446 TTCAATCAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (18 bp):
TAAAAAGATCAAATAAAA
Found at i:1702896 original size:19 final size:19
Alignment explanation
Indices: 1702874--1702911 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1702864 ATAAATTTTC
1702874 AATAAAAATATATA-GATAA
1 AATAAAAAT-TATACGATAA
*
1702893 AATATAAATTATACGATAA
1 AATAAAAATTATACGATAA
1702912 TTTTAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (19 bp):
AATAAAAATTATACGATAA
Found at i:1703224 original size:28 final size:28
Alignment explanation
Indices: 1703184--1703244 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
1703174 TATACTTCAC
*
1703184 CCATCGTAAAGAGTCCTATTTACGTCAT
1 CCATCGTAAAGAGTCCTATTTACATCAT
*
1703212 CCATCGTAAAGAGTCTTATTTACATCAT
1 CCATCGTAAAGAGTCCTATTTACATCAT
1703240 CCATC
1 CCATC
1703245 TCCTCTACAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (28 bp):
CCATCGTAAAGAGTCCTATTTACATCAT
Found at i:1707948 original size:49 final size:49
Alignment explanation
Indices: 1707888--1707985 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
1707878 GTTATTGGTT
*
1707888 AATCATCCTGCCTATGGATAGGCACAGCAGTTGCCTCCCACCCAGGAAG
1 AATCATCCTGCCTATGGACAGGCACAGCAGTTGCCTCCCACCCAGGAAG
1707937 AATCATCCTGCCTATGGACAGGCACAGCAGTTGCCTCCCACCCAGGAAG
1 AATCATCCTGCCTATGGACAGGCACAGCAGTTGCCTCCCACCCAGGAAG
1707986 CTATGGCCAG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.27, C:0.34, G:0.22, T:0.17
Consensus pattern (49 bp):
AATCATCCTGCCTATGGACAGGCACAGCAGTTGCCTCCCACCCAGGAAG
Found at i:1715972 original size:6 final size:6
Alignment explanation
Indices: 1715954--1715988 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
1715944 TATTATTTAT
*
1715954 TATTAG TAGTAG TATTAG TATTAG TATTAG TATTA
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTA
1715989 CATCCGAGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (6 bp):
TATTAG
Found at i:1717547 original size:16 final size:16
Alignment explanation
Indices: 1717526--1717558 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1717516 AACGGGATAC
1717526 TAAACATTAGGTATGG
1 TAAACATTAGGTATGG
1717542 TAAACATTAGGTATGG
1 TAAACATTAGGTATGG
1717558 T
1 T
1717559 TTTGAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.33
Consensus pattern (16 bp):
TAAACATTAGGTATGG
Found at i:1721887 original size:183 final size:184
Alignment explanation
Indices: 1721675--1722061 Score: 620
Period size: 183 Copynumber: 2.1 Consensus size: 184
1721665 ATTAAATTTT
* *
1721675 AAATTTTAAATATATTATATATAACATATGAGCTCAA-CCCAAATCATTTAAAACCCAATTAATA
1 AAATATTAAATATATTATATATAACATATGAGCT-AAGCCCAAACCATTTAAAACCCAATTAATA
*
1721739 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAAT-TATATAAATTT
65 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATGTATATAAAATT
* * *
1721803 TTTATTTTATAATTATATATTATTTAAATTATTTGTAAACTATTTTTT-AATTAAA
130 TTTATTATATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATTAAA
* *
1721858 AAATATTATATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGAGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
* *
1721923 TTTAAGATCTAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATGTATCTAAAATTT
66 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATGTATATAAAATTT
1721988 TTATTATATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
131 TTATTATATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
* *
1722042 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
1722062 AATTAGAAAT
Statistics
Matches: 188, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
182 2 0.01
183 123 0.65
184 63 0.34
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (184 bp):
AAATATTAAATATATTATATATAACATATGAGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATGTATATAAAATTT
TTATTATATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
Found at i:1737135 original size:19 final size:18
Alignment explanation
Indices: 1737108--1737166 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 18
1737098 TTTGTTGATT
1737108 TTAAGAAATATATATAATA
1 TTAA-AAATATATATAATA
* *
1737127 TTAATAAATTTAATTTAA-A
1 TTAA-AAATAT-ATATAATA
1737146 TTAAAATATATATATAATA
1 TTAAAA-ATATATATAATA
1737165 TT
1 TT
1737167 TATATATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
18 7 0.22
19 20 0.62
20 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
TTAAAAATATATATAATA
Found at i:1737164 original size:32 final size:32
Alignment explanation
Indices: 1737123--1737192 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
1737113 AAATATATAT
1737123 AATAT-TA-ATAA-ATTTA-AT-TTAAATTAA
1 AATATATATATAATATTTATATATTAAATTAA
* *
1737150 AATATATATATAATATTTATATATTTAATTTA
1 AATATATATATAATATTTATATATTAAATTAA
1737182 AATATATATAT
1 AATATATATAT
1737193 CCGGTCTGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
27 5 0.14
28 2 0.06
29 4 0.11
30 5 0.14
31 2 0.06
32 18 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
AATATATATATAATATTTATATATTAAATTAA
Found at i:1738640 original size:22 final size:23
Alignment explanation
Indices: 1738609--1738651 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1738599 TCTAACCGTC
1738609 CTCCTCATCTCACTCACGTTCCT
1 CTCCTCATCTCACTCACGTTCCT
* *
1738632 CTCC-CATCTGACTCAGGTTC
1 CTCCTCATCTCACTCACGTTC
1738652 TTGCTTTCGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.14, C:0.44, G:0.09, T:0.33
Consensus pattern (23 bp):
CTCCTCATCTCACTCACGTTCCT
Found at i:1750888 original size:16 final size:16
Alignment explanation
Indices: 1750867--1750908 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
1750857 TTATAATTTG
1750867 TAATAATCAATAA-ATT
1 TAATAAT-AATAATATT
1750883 TAATAA-AATAATATT
1 TAATAATAATAATATT
*
1750898 TTATAATAATA
1 TAATAATAATA
1750909 GAATATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 5 0.22
15 8 0.35
16 10 0.43
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
TAATAATAATAATATT
Found at i:1751275 original size:37 final size:37
Alignment explanation
Indices: 1751202--1751276 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
1751192 ATTTGAAAAT
* *
1751202 ATTTATATATTTTCTTTAAAAATTTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAATTTAAAAATCATAAA
*
1751239 ATTTATATAATTTTTTTTACAAAA-TTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTA-AAAATTTAAAAATCATAAA
1751276 A
1 A
1751277 AAGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 14 0.42
38 15 0.45
39 4 0.12
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAATTTAAAAATCATAAA
Found at i:1752692 original size:24 final size:25
Alignment explanation
Indices: 1752645--1752692 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
1752635 ATTATGACAC
* * *
1752645 GTTTTCTTCTACTTTTGTGGCACGT
1 GTTTTCTTCTACTATTCTGACACGT
1752670 GTTTTC-TCTACTATTCTGACACG
1 GTTTTCTTCTACTATTCTGACACG
1752693 ATCTTATGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.12, C:0.23, G:0.17, T:0.48
Consensus pattern (25 bp):
GTTTTCTTCTACTATTCTGACACGT
Found at i:1760699 original size:13 final size:13
Alignment explanation
Indices: 1760681--1760705 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1760671 CTACTTTAAT
1760681 TTAGTATTTTTAG
1 TTAGTATTTTTAG
1760694 TTAGTATTTTTA
1 TTAGTATTTTTA
1760706 AATTTTTAAA
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:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (13 bp):
TTAGTATTTTTAG
Found at i:1769987 original size:12 final size:12
Alignment explanation
Indices: 1769970--1769996 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1769960 AGAAGCTGGT
1769970 TTGGACAAGCTG
1 TTGGACAAGCTG
1769982 TTGGACAAGCTG
1 TTGGACAAGCTG
1769994 TTG
1 TTG
1769997 CTAGCAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.15, G:0.33, T:0.30
Consensus pattern (12 bp):
TTGGACAAGCTG
Found at i:1770988 original size:36 final size:36
Alignment explanation
Indices: 1770948--1771050 Score: 197
Period size: 36 Copynumber: 2.9 Consensus size: 36
1770938 ACGGTGCTGG
1770948 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
1 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
*
1770984 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
1771020 ACATTGATACACGAATGTACCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
1771051 ATACTCAACT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.23
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATAGGATA
Found at i:1777137 original size:15 final size:15
Alignment explanation
Indices: 1777114--1777176 Score: 108
Period size: 15 Copynumber: 4.2 Consensus size: 15
1777104 CGTAGGACTC
1777114 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
1777129 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
1777144 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
1777159 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
1777174 CTA
1 CTA
1777177 TTATACCCTC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.30, C:0.33, G:0.22, T:0.14
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:1777150 original size:30 final size:30
Alignment explanation
Indices: 1777114--1777176 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
1777104 CGTAGGACTC
1777114 CTACATCCCGAAGGACTACGTCCCGAAGGA
1 CTACATCCCGAAGGACTACGTCCCGAAGGA
1777144 CTACATCCCGAAGGACTACGTCCCGAAGGA
1 CTACATCCCGAAGGACTACGTCCCGAAGGA
1777174 CTA
1 CTA
1777177 TTATACCCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.30, C:0.33, G:0.22, T:0.14
Consensus pattern (30 bp):
CTACATCCCGAAGGACTACGTCCCGAAGGA
Found at i:1777303 original size:29 final size:29
Alignment explanation
Indices: 1777261--1777334 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
1777251 TTTCATATGT
1777261 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1777289 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1777318 TCATGTAGCTCATGTCA
1 TCATGTAGCTCATGTCA
1777335 CTTCATATCA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.16
29 38 0.84
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:1777367 original size:12 final size:12
Alignment explanation
Indices: 1777350--1777395 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
1777340 TATCATGTTC
*
1777350 TCATATCACAGG
1 TCATATCACAGA
*
1777362 TCATATCACATA
1 TCATATCACAGA
*
1777374 TCATATCACATA
1 TCATATCACAGA
*
1777386 ACATATCACA
1 TCATATCACA
1777396 TGAACATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.41, C:0.26, G:0.04, T:0.28
Consensus pattern (12 bp):
TCATATCACAGA
Found at i:1777396 original size:12 final size:12
Alignment explanation
Indices: 1777363--1777404 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
1777353 TATCACAGGT
*
1777363 CATATCACATAT
1 CATATCACATAA
1777375 CATATCACATAA
1 CATATCACATAA
1777387 CATATCACATGAA
1 CATATCACAT-AA
1777400 CATAT
1 CATAT
1777405 ATATATCTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 21 0.75
13 7 0.25
ACGTcount: A:0.45, C:0.24, G:0.02, T:0.29
Consensus pattern (12 bp):
CATATCACATAA
Found at i:1777813 original size:64 final size:63
Alignment explanation
Indices: 1777709--1777881 Score: 204
Period size: 64 Copynumber: 2.7 Consensus size: 63
1777699 GAAAGTATGT
* * * ** * * **
1777709 ATCGATGCACTACTGATGCATCAATGCATCAAAGGTATTCGATGTAGT-ATTATTGTTGGGATGC
1 ATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCGATGT-GTCACTATTAATGGGATGC
* *
1777773 ATCGATGCACTCCTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAATGGGATGC
1 ATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCGATGTGTCACTATTAATGGGATGC
1777837 ATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT
1 ATCGATGCACTACTTATGCATCGATGCACG-ATTGCATTCGATGT
1777882 CTTTATTTTA
Statistics
Matches: 94, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
63 3 0.03
64 91 0.97
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.32
Consensus pattern (63 bp):
ATCGATGCACTACTTATGCATCGATGCACGATTGCATTCGATGTGTCACTATTAATGGGATGC
Done.