Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008746.1 Hibiscus syriacus cultivar Beakdansim tig00111835_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: 2013901
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 10
Found at i:1409494 original size:22 final size:21
Alignment explanation
Indices: 1409443--1409494 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
1409433 TCAAAATTAT
*
1409443 AAAATATATATATAGTTTTTG
1 AAAATATATATATAGTTTTCG
*
1409464 AAGATATATAGTATAGTTTTCG
1 AAAATATATA-TATAGTTTTCG
*
1409486 AAAACATAT
1 AAAATATAT
1409495 TTTTGAAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.40
Consensus pattern (21 bp):
AAAATATATATATAGTTTTCG
Found at i:1409539 original size:41 final size:39
Alignment explanation
Indices: 1409467--1409627 Score: 158
Period size: 41 Copynumber: 4.2 Consensus size: 39
1409457 GTTTTTGAAG
**
1409467 ATATATAGTATAG-TTTTCGAAAAC-ATATTTTTGAAAAC
1 ATATATA-TATAGTTTTTTTAAAACGATATTTTTGAAAAC
*
1409505 ATATAATATATAGTTTTTTTTAAAACGATTTTTTTGAAAAC
1 ATAT-ATATATAG-TTTTTTTAAAACGATATTTTTGAAAAC
* *
1409546 ATATATAATATA-TAATTTTTGAAAA-TATATTTTTGAAAAC
1 ATATAT-ATATAGT--TTTTTTAAAACGATATTTTTGAAAAC
*
1409586 ATATA-ATATAG-TTTTTTAAAACGGT-TTTTTG-AAAC
1 ATATATATATAGTTTTTTTAAAACGATATTTTTGAAAAC
1409621 ATATATA
1 ATATATA
1409628 GTTTTTTGAA
Statistics
Matches: 104, Mismatches: 9, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
35 9 0.09
36 16 0.15
37 1 0.01
38 14 0.13
39 4 0.04
40 29 0.28
41 31 0.30
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (39 bp):
ATATATATATAGTTTTTTTAAAACGATATTTTTGAAAAC
Found at i:1409565 original size:40 final size:39
Alignment explanation
Indices: 1409467--1409627 Score: 158
Period size: 40 Copynumber: 4.2 Consensus size: 39
1409457 GTTTTTGAAG
* **
1409467 ATATATAGTATAGTTTTCGAAAAC-ATATTTTTGAAAAC
1 ATATATAATATAGTTTTTTAAAACGATATTTTTGAAAAC
*
1409505 ATATA-ATATATAGTTTTTTTTAAAACGATTTTTTTGAAAAC
1 ATATATA-ATATAG--TTTTTTAAAACGATATTTTTGAAAAC
*
1409546 ATATATAATATA-TAATTTTTGAAAA-TATATTTTTGAAAAC
1 ATATATAATATAGT--TTTTT-AAAACGATATTTTTGAAAAC
*
1409586 --ATATAATATAGTTTTTTAAAACGGT-TTTTTG-AAAC
1 ATATATAATATAGTTTTTTAAAACGATATTTTTGAAAAC
1409621 ATATATA
1 ATATATA
1409628 GTTTTTTGAA
Statistics
Matches: 103, Mismatches: 8, Indels: 25
0.76 0.06 0.18
Matches are distributed among these distances:
35 4 0.04
36 10 0.10
37 12 0.12
38 21 0.20
39 1 0.01
40 27 0.26
41 27 0.26
42 1 0.01
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (39 bp):
ATATATAATATAGTTTTTTAAAACGATATTTTTGAAAAC
Found at i:1409576 original size:81 final size:76
Alignment explanation
Indices: 1409467--1409627 Score: 218
Period size: 81 Copynumber: 2.1 Consensus size: 76
1409457 GTTTTTGAAG
*
1409467 ATAT-ATAGTATAGTTTTCGAAAACATATTTTTGAAAACATATAATATATAGTTTTTTTTAAAAC
1 ATATAATAGTATAATTTTCGAAAACATATTTTTGAAAACATAT-A-ATATAG--TTTTTTAAAAC
*
1409531 GATTTTTTTGAAAACAT
62 G-GTTTTTTG-AAACAT
* *
1409548 ATATAATA-TATAATTTTTGAAAATATATTTTTGAAAACATATAATATAGTTTTTTAAAACGGTT
1 ATATAATAGTATAATTTTCGAAAACATATTTTTGAAAACATATAATATAGTTTTTTAAAACGGTT
1409612 TTTTGAAACAT
66 TTTTGAAACAT
1409623 ATATA
1 ATATA
1409628 GTTTTTTGAA
Statistics
Matches: 75, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
75 11 0.15
76 7 0.09
77 12 0.16
79 6 0.08
80 1 0.01
81 35 0.47
82 3 0.04
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (76 bp):
ATATAATAGTATAATTTTCGAAAACATATTTTTGAAAACATATAATATAGTTTTTTAAAACGGTT
TTTTGAAACAT
Found at i:1409579 original size:15 final size:14
Alignment explanation
Indices: 1409555--1409589 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1409545 CATATATAAT
1409555 ATATAATTTTTGAAA
1 ATAT-ATTTTTGAAA
1409570 ATATATTTTTGAAA
1 ATATATTTTTGAAA
*
1409584 ACATAT
1 ATATAT
1409590 AATATAGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (14 bp):
ATATATTTTTGAAA
Found at i:1409633 original size:19 final size:19
Alignment explanation
Indices: 1409609--1409650 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
1409599 TTTTAAAACG
1409609 GTTTTTTG-AAACATATATA
1 GTTTTTTGAAAACATA-ATA
1409628 GTTTTTTGAAAACATAATA
1 GTTTTTTGAAAACATAATA
1409647 GTTT
1 GTTT
1409651 GAATATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.48
Consensus pattern (19 bp):
GTTTTTTGAAAACATAATA
Found at i:1411019 original size:39 final size:39
Alignment explanation
Indices: 1410976--1411052 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
1410966 TAATTTCTCA
1410976 AATTTTATCTTATCTT-AACCCTAATATTAATTCTTTTTT
1 AATTTTATCTTAT-TTCAACCCTAATATTAATTCTTTTTT
* *
1411015 AATTTTATTTTATTTCAACCCTAATTTTAATTCTTTTT
1 AATTTTATCTTATTTCAACCCTAATATTAATTCTTTTT
1411053 CCTTTTTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 2 0.06
39 33 0.94
ACGTcount: A:0.27, C:0.14, G:0.00, T:0.58
Consensus pattern (39 bp):
AATTTTATCTTATTTCAACCCTAATATTAATTCTTTTTT
Found at i:1411060 original size:39 final size:38
Alignment explanation
Indices: 1410976--1411069 Score: 116
Period size: 39 Copynumber: 2.4 Consensus size: 38
1410966 TAATTTCTCA
* *
1410976 AATTTTATCTTATCTTAACCCTAATATTAATTCTTTTTT
1 AATTTTATTTTAT-TTAACCCTAATATTAATTCTTTTTC
*
1411015 AATTTTATTTTATTTCAACCCTAATTTTAATTCTTTTTC
1 AATTTTATTTTATTT-AACCCTAATATTAATTCTTTTTC
**
1411054 CTTTTTATATTTATTT
1 AATTTTAT-TTTATTT
1411070 TAATATTTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
38 2 0.04
39 39 0.81
40 7 0.15
ACGTcount: A:0.26, C:0.14, G:0.00, T:0.61
Consensus pattern (38 bp):
AATTTTATTTTATTTAACCCTAATATTAATTCTTTTTC
Found at i:1411090 original size:13 final size:12
Alignment explanation
Indices: 1411055--1411096 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
1411045 TTCTTTTTCC
1411055 TTTTTATATTTA
1 TTTTTATATTTA
*
1411067 TTTTAATATTTA
1 TTTTTATATTTA
1411079 TTTTTATCATTTTA
1 TTTTTAT-A-TTTA
1411093 TTTT
1 TTTT
1411097 ATCATTTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 17 0.65
13 1 0.04
14 8 0.31
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTATATTTA
Found at i:1411097 original size:13 final size:13
Alignment explanation
Indices: 1411063--1411103 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1411053 CCTTTTTATA
1411063 TTTATTTTA--AT
1 TTTATTTTATCAT
1411074 ATTTATTTTTATCAT
1 -TTTA-TTTTATCAT
1411089 TTTATTTTATCAT
1 TTTATTTTATCAT
1411102 TT
1 TT
1411104 AACATTCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 4 0.15
13 16 0.62
14 4 0.15
15 2 0.08
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTATTTTATCAT
Found at i:1428626 original size:2 final size:2
Alignment explanation
Indices: 1428621--1428661 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1428611 ACATACATAC
1428621 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1428662 ACCTTGTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1431947 original size:144 final size:144
Alignment explanation
Indices: 1431687--1431974 Score: 477
Period size: 144 Copynumber: 2.0 Consensus size: 144
1431677 AAGAAATATA
* * * *
1431687 ATAAAATACCATAATAAAAAACATAATTAAAGTCTAGAAACATAAATGATAAACACATAATGTTT
1 ATAAAACACCATAATAAAAAACATAATTAAAGCCTAGAAACATAAATGACAAACACATAATATTT
1431752 TTGTTCTTTGGCACAACATTATAAAATTTCAGGCAATACTTGTGACATCTGATACTCCAGTATTA
66 TTGTTCTTTGGCACAACATTATAAAATTTCAGGCAATACTTGTGACATCTGATACTCCAGTATTA
1431817 CAATCATCATTCTC
131 CAATCATCATTCTC
* *
1431831 ATAAAACATCATAATAAAAGACATAATTAAAGCCTAGAAACATAAATGACAAACACATAATATTT
1 ATAAAACACCATAATAAAAAACATAATTAAAGCCTAGAAACATAAATGACAAACACATAATATTT
* * * * *
1431896 TTGTTCTTTGGCAGAACATTCTCAAATTTCAGGCAATACTTGTGTCATCTGATACTCTAGTATTA
66 TTGTTCTTTGGCACAACATTATAAAATTTCAGGCAATACTTGTGACATCTGATACTCCAGTATTA
1431961 CAATCATCATTCTC
131 CAATCATCATTCTC
1431975 TATTTCCTCC
Statistics
Matches: 133, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
144 133 1.00
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.32
Consensus pattern (144 bp):
ATAAAACACCATAATAAAAAACATAATTAAAGCCTAGAAACATAAATGACAAACACATAATATTT
TTGTTCTTTGGCACAACATTATAAAATTTCAGGCAATACTTGTGACATCTGATACTCCAGTATTA
CAATCATCATTCTC
Found at i:1439539 original size:30 final size:30
Alignment explanation
Indices: 1439505--1439564 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1439495 GGCTAAGCAC
1439505 CAAATAGCACA-GTGACTTGGCCACCAATGT
1 CAAATAGCACATG-GACTTGGCCACCAATGT
* *
1439535 CAAATAGTACATGGACTTGGCCACCCATGT
1 CAAATAGCACATGGACTTGGCCACCAATGT
1439565 TGAACAATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.22
Consensus pattern (30 bp):
CAAATAGCACATGGACTTGGCCACCAATGT
Found at i:1440413 original size:27 final size:27
Alignment explanation
Indices: 1440375--1440427 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
1440365 CCCTTGAGAT
1440375 AATTTCTTTCATACCTAATATTGTTTC
1 AATTTCTTTCATACCTAATATTGTTTC
1440402 AATTTCTTTCATACCTAATATTGTTT
1 AATTTCTTTCATACCTAATATTGTTT
1440428 TACTCGAGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.17, G:0.04, T:0.53
Consensus pattern (27 bp):
AATTTCTTTCATACCTAATATTGTTTC
Found at i:1441047 original size:49 final size:49
Alignment explanation
Indices: 1440975--1441074 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
1440965 AAATTATCTT
1440975 CAGGAAATTAAACTTCCTCAGCGTAAAGGAACAATGTTGTCTTCAGATG
1 CAGGAAATTAAACTTCCTCAGCGTAAAGGAACAATGTTGTCTTCAGATG
1441024 CAGGAAATTAAACTTCCTCAGCGTAAAGGAACAATGTTGTCTTCAGATG
1 CAGGAAATTAAACTTCCTCAGCGTAAAGGAACAATGTTGTCTTCAGATG
1441073 CA
1 CA
1441075 CAGTGACCCA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (49 bp):
CAGGAAATTAAACTTCCTCAGCGTAAAGGAACAATGTTGTCTTCAGATG
Found at i:1441723 original size:17 final size:16
Alignment explanation
Indices: 1441697--1441728 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1441687 TAGTCATTTT
1441697 TATTTTTTATTTTATA
1 TATTTTTTATTTTATA
1441713 TATTTTATTATTTTAT
1 TATTTT-TTATTTTAT
1441729 TAAATATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
TATTTTTTATTTTATA
Found at i:1441726 original size:8 final size:8
Alignment explanation
Indices: 1441696--1441730 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
1441686 TTAGTCATTT
1441696 TTATTTT-
1 TTATTTTA
1441703 TTATTTTA
1 TTATTTTA
1441711 TATATTTTA
1 T-TATTTTA
1441720 TTATTTTA
1 TTATTTTA
1441728 TTA
1 TTA
1441731 AATATTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 7 0.27
8 11 0.42
9 8 0.31
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TTATTTTA
Found at i:1441735 original size:22 final size:21
Alignment explanation
Indices: 1441694--1441735 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1441684 TTTTAGTCAT
**
1441694 TTTTATTTTTTATTTTATATA
1 TTTTATTTTTTATTAAATATA
1441715 TTTTATTATTTTATTAAATAT
1 TTTTATT-TTTTATTAAATAT
1441736 TAATATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTATTTTTTATTAAATATA
Found at i:1442172 original size:10 final size:10
Alignment explanation
Indices: 1442156--1442189 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1442146 CATTTAAATG
1442156 ATAAACGAAC
1 ATAAACGAAC
*
1442166 GTAAACGAAC
1 ATAAACGAAC
*
1442176 AAAAACGAAC
1 ATAAACGAAC
1442186 ATAA
1 ATAA
1442190 TAAATGAACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.62, C:0.18, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1443668 original size:35 final size:36
Alignment explanation
Indices: 1443605--1443673 Score: 106
Period size: 35 Copynumber: 1.9 Consensus size: 36
1443595 ATATATAATC
1443605 ATATAATATAGTTTTTGAAAATACTTTTGAAAACAT
1 ATATAATATAGTTTTTGAAAATACTTTTGAAAACAT
*
1443641 ATATAATATAG-TTTTG-AAATCATTTTTGAAAAC
1 ATATAATATAGTTTTTGAAAAT-ACTTTTGAAAAC
1443674 GTATTTTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
34 4 0.13
35 16 0.52
36 11 0.35
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (36 bp):
ATATAATATAGTTTTTGAAAATACTTTTGAAAACAT
Found at i:1443671 original size:47 final size:46
Alignment explanation
Indices: 1443616--1443717 Score: 118
Period size: 47 Copynumber: 2.2 Consensus size: 46
1443606 TATAATATAG
1443616 TTTTTGAAAA-TACTTTTGAAAACATATATAATATA-GTTTTGAAATCA
1 TTTTTGAAAACTACTTTTG-AAA-ATATATAATATAGGTTTTGAAAT-A
* * *
1443663 TTTTTGAAAACGTATTTTTGAAAATGTATAATATATGGTTTTGAAATT
1 TTTTTGAAAAC-TACTTTTGAAAATATATAATATA-GGTTTTGAAATA
1443711 TTTTTGA
1 TTTTTGA
1443718 TAACGTATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
47 21 0.44
48 10 0.21
49 17 0.35
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.47
Consensus pattern (46 bp):
TTTTTGAAAACTACTTTTGAAAATATATAATATAGGTTTTGAAATA
Found at i:1443681 original size:14 final size:14
Alignment explanation
Indices: 1443662--1443691 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1443652 TTTTGAAATC
1443662 ATTTTTGAAAACGT
1 ATTTTTGAAAACGT
*
1443676 ATTTTTGAAAATGT
1 ATTTTTGAAAACGT
1443690 AT
1 AT
1443692 AATATATGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (14 bp):
ATTTTTGAAAACGT
Found at i:1443726 original size:34 final size:34
Alignment explanation
Indices: 1443677--1443775 Score: 117
Period size: 34 Copynumber: 2.8 Consensus size: 34
1443667 TGAAAACGTA
*
1443677 TTTTTGAAAATGTATAATATATGGTTTTGAAATT
1 TTTTTGAAAACGTATAATATATGGTTTTGAAATT
* *
1443711 TTTTTGATAACGTATAATATATGGTTTTGAAAATAGA
1 TTTTTGAAAACGTATAATATATGGTTTTG-AAAT--T
* * *
1443748 TTTTTGAAAATGTATAATAAATAGTTTT
1 TTTTTGAAAACGTATAATATATGGTTTT
1443776 TTAAAAAACA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
34 27 0.49
35 4 0.07
37 24 0.44
ACGTcount: A:0.37, C:0.01, G:0.14, T:0.47
Consensus pattern (34 bp):
TTTTTGAAAACGTATAATATATGGTTTTGAAATT
Found at i:1443738 original size:83 final size:85
Alignment explanation
Indices: 1443606--1443762 Score: 196
Period size: 83 Copynumber: 1.9 Consensus size: 85
1443596 TATATAATCA
*
1443606 TATAATATAGTTTTTGAAAATACTTTTGAAAACATATATAATATAGTTTTG-AAAT-CATTTTTG
1 TATAATATAGGTTTTGAAAATACTTTTGAAAACATATATAATATAGTTTTGAAAATACATTTTTG
1443669 AAAACGTATTTTTGAAAATG
66 AAAACGTATTTTTGAAAATG
** * * * *
1443689 TATAATATATGGTTTTG-AAATTTTTTTGATAACGTATA-ATATATGGTTTTGAAAATAGATTTT
1 TATAATATA-GGTTTTGAAAATACTTTTGAAAACATATATA-ATATAGTTTTGAAAATACATTTT
*
1443752 TGAAAATGTAT
64 TGAAAACGTAT
1443763 AATAAATAGT
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
82 1 0.02
83 36 0.58
84 10 0.16
85 15 0.24
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.45
Consensus pattern (85 bp):
TATAATATAGGTTTTGAAAATACTTTTGAAAACATATATAATATAGTTTTGAAAATACATTTTTG
AAAACGTATTTTTGAAAATG
Found at i:1443827 original size:36 final size:37
Alignment explanation
Indices: 1443712--1443956 Score: 171
Period size: 38 Copynumber: 6.6 Consensus size: 37
1443702 TTTGAAATTT
* * * * *
1443712 TTTTGATAACGTATAATATAT-GGTTTTGAAAATAGAT
1 TTTTGAAAACGTATAATATATAGATTTTTAAAA-ACAG
* * *
1443749 TTTTGAAAATGTATAATAAATAGTTTTTTAAAAAACAG
1 TTTTGAAAACGTATAATATATAGATTTTT-AAAAACAG
* *
1443787 TTTTGAAAACGTATAATATATA-ATTTTTCAAAACGG
1 TTTTGAAAACGTATAATATATAGATTTTTAAAAACAG
* *
1443823 TTTTGAAAACATATAATATATAGATTTTTAAAAACAA
1 TTTTGAAAACGTATAATATATAGATTTTTAAAAACAG
* * * *
1443860 TTTTGGAGA--TAT-ATAATATAG-TTTTTAAAAATATA
1 TTTTGAAAACGTATAAT-ATATAGATTTTTAAAAACA-G
* * * *
1443895 TTTTGAAAAACATATAATATATGGTTTTTTTTAAAAA-TG
1 TTTTG-AAAACGTATAATATATAG--ATTTTTAAAAACAG
* * *
1443934 TTTTTAAAACATAAAATATATAG
1 TTTTGAAAACGTATAATATATAG
1443957 TTACTTTGAA
Statistics
Matches: 169, Mismatches: 27, Indels: 23
0.77 0.12 0.11
Matches are distributed among these distances:
34 13 0.08
35 15 0.09
36 29 0.17
37 41 0.24
38 51 0.30
39 10 0.06
41 10 0.06
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.42
Consensus pattern (37 bp):
TTTTGAAAACGTATAATATATAGATTTTTAAAAACAG
Found at i:1445198 original size:16 final size:17
Alignment explanation
Indices: 1445177--1445209 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1445167 CTTTTATTCC
1445177 TTTTATTTAC-TTATTT
1 TTTTATTTACTTTATTT
1445193 TTTTATTTACTTTATTT
1 TTTTATTTACTTTATTT
1445210 CAATCGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTATTTACTTTATTT
Found at i:1448695 original size:15 final size:15
Alignment explanation
Indices: 1448675--1448727 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
1448665 ATTTTATTAA
1448675 TATGTGAATGTGTTC
1 TATGTGAATGTGTTC
** *
1448690 TATGTGAAAATGTTT
1 TATGTGAATGTGTTC
* *
1448705 TATATAAATGTGTTC
1 TATGTGAATGTGTTC
1448720 TATGTGAA
1 TATGTGAA
1448728 GATGCTTTAT
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.30, C:0.04, G:0.21, T:0.45
Consensus pattern (15 bp):
TATGTGAATGTGTTC
Found at i:1448757 original size:30 final size:30
Alignment explanation
Indices: 1448679--1448746 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
1448669 TATTAATATG
*
1448679 TGAATGTGTTCTATGTGAAAATGTTTTATA
1 TGAATGTGTTCTATGTGAAAATGCTTTATA
* *
1448709 TAAATGTGTTCTATGTGAAGATGCTTTATA
1 TGAATGTGTTCTATGTGAAAATGCTTTATA
1448739 TGAATGTG
1 TGAATGTG
1448747 CTTTACGTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.29, C:0.04, G:0.22, T:0.44
Consensus pattern (30 bp):
TGAATGTGTTCTATGTGAAAATGCTTTATA
Found at i:1448896 original size:23 final size:24
Alignment explanation
Indices: 1448870--1448921 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
1448860 GTTCTAGCCA
*
1448870 GTCCTTCGGGA-CAATTCTACGTG
1 GTCCTTCGGGATAAATTCTACGTG
*
1448893 GTCCTTCGGGATAAATTCTAGGTG
1 GTCCTTCGGGATAAATTCTACGTG
1448917 GTCCT
1 GTCCT
1448922 CTGAGACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.17, C:0.23, G:0.27, T:0.33
Consensus pattern (24 bp):
GTCCTTCGGGATAAATTCTACGTG
Found at i:1448932 original size:24 final size:24
Alignment explanation
Indices: 1448870--1448940 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 24
1448860 GTTCTAGCCA
*
1448870 GTCCTTCGGGAC-AATTCTACGTG
1 GTCCTTCGAGACAAATTCTACGTG
* * *
1448893 GTCCTTCGGGATAAATTCTAGGTG
1 GTCCTTCGAGACAAATTCTACGTG
*
1448917 GTCC-TCTGAGACAAA-TCTATGTG
1 GTCCTTC-GAGACAAATTCTACGTG
1448940 G
1 G
1448941 CACTTCAGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
23 21 0.51
24 20 0.49
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (24 bp):
GTCCTTCGAGACAAATTCTACGTG
Found at i:1448959 original size:24 final size:24
Alignment explanation
Indices: 1448932--1448978 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1448922 CTGAGACAAA
*
1448932 TCTATGTGGCACTTCAGTGCATAT
1 TCTACGTGGCACTTCAGTGCATAT
*
1448956 TCTACGTGGCACTTCGGTGCATA
1 TCTACGTGGCACTTCAGTGCATA
1448979 AAACAAAGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.34
Consensus pattern (24 bp):
TCTACGTGGCACTTCAGTGCATAT
Found at i:1454224 original size:68 final size:68
Alignment explanation
Indices: 1454144--1454280 Score: 256
Period size: 68 Copynumber: 2.0 Consensus size: 68
1454134 GTGACTAAAG
1454144 TGTAAGAATTTAAAATTTGATGGTTTAATTTGAGTAAATTAAAAAGTTCAATAATTGATTTTGGG
1 TGTAAGAATTTAAAATTTGATGGTTTAATTTGAGTAAATTAAAAAGTTCAATAATTGATTTTGGG
1454209 AAT
66 AAT
* *
1454212 TGTAAGAATTTAAAATTTGATGGTTTAATTTGAGTAAATTGAAAAGTTCAATGATTGATTTTGGG
1 TGTAAGAATTTAAAATTTGATGGTTTAATTTGAGTAAATTAAAAAGTTCAATAATTGATTTTGGG
1454277 AAT
66 AAT
1454280 T
1 T
1454281 TTTGTCTAGG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.38, C:0.01, G:0.19, T:0.42
Consensus pattern (68 bp):
TGTAAGAATTTAAAATTTGATGGTTTAATTTGAGTAAATTAAAAAGTTCAATAATTGATTTTGGG
AAT
Found at i:1455532 original size:15 final size:15
Alignment explanation
Indices: 1455512--1455596 Score: 57
Period size: 15 Copynumber: 5.7 Consensus size: 15
1455502 ATTTTATTAA
1455512 TATGTGAATATGTTC
1 TATGTGAATATGTTC
*
1455527 TATGTGAAAATGCTT-
1 TATGTGAATATG-TTC
* * *
1455542 TATATAAATGTGTTC
1 TATGTGAATATGTTC
*
1455557 TATGTGAAGATGCTT-
1 TATGTGAATATG-TTC
* * *
1455572 TATATGAATGTGCTC
1 TATGTGAATATGTTC
*
1455587 TACGTGAATA
1 TATGTGAATA
1455597 AAGGATACCT
Statistics
Matches: 50, Mismatches: 16, Indels: 8
0.68 0.22 0.11
Matches are distributed among these distances:
14 3 0.06
15 43 0.86
16 4 0.08
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (15 bp):
TATGTGAATATGTTC
Found at i:1455556 original size:30 final size:30
Alignment explanation
Indices: 1455522--1455594 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
1455512 TATGTGAATA
1455522 TGTTCTATGTGAAAATGCTTTATATAAATG
1 TGTTCTATGTGAAAATGCTTTATATAAATG
* *
1455552 TGTTCTATGTGAAGATGCTTTATATGAATG
1 TGTTCTATGTGAAAATGCTTTATATAAATG
* *
1455582 TGCTCTACGTGAA
1 TGTTCTATGTGAA
1455595 TAAAGGATAC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.41
Consensus pattern (30 bp):
TGTTCTATGTGAAAATGCTTTATATAAATG
Found at i:1455775 original size:24 final size:24
Alignment explanation
Indices: 1455728--1455775 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1455718 TAAATCTATA
*
1455728 TGGCACTTCAGTGCATATTCTACG
1 TGGCACTTCAGTGCAAATTCTACG
* * *
1455752 TGGCACTTCGGTGGAAATTTTACG
1 TGGCACTTCAGTGCAAATTCTACG
1455776 AGCAGTGGTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (24 bp):
TGGCACTTCAGTGCAAATTCTACG
Found at i:1460431 original size:55 final size:55
Alignment explanation
Indices: 1460367--1460664 Score: 499
Period size: 55 Copynumber: 5.4 Consensus size: 55
1460357 CCACTGTCAC
* * *
1460367 TACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACATAAAGTGCCCA
1 TACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCA
* *
1460422 TACGGAAATTCATAAACTCATTATGAATTTCTTAATTTTTCACACAAAGTGCCCA
1 TACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCA
* *
1460477 TACAGAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGACCA
1 TACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCA
*
1460532 TACGGAAATTCATAAACTCATTATGAATTTTTTAGTTTTGCACACAAAGTGCCCA
1 TACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCA
*
1460587 TACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGTCCA
1 TACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCA
*
1460642 TACAGAAATTCATAAA-TCATTAT
1 TACGGAAATTCATAAACTCATTAT
1460665 ATGATCTATT
Statistics
Matches: 228, Mismatches: 15, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
54 7 0.03
55 221 0.97
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.35
Consensus pattern (55 bp):
TACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCA
Found at i:1464312 original size:16 final size:16
Alignment explanation
Indices: 1464291--1464325 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1464281 GGTATTACCC
1464291 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
1464307 GACCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
1464323 GAC
1 GAC
1464326 ATGTAAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.14, T:0.37
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:1464617 original size:14 final size:14
Alignment explanation
Indices: 1464595--1464641 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
1464585 TGAAAAGGAA
*
1464595 AATTAATATAGTTT
1 AATTTATATAGTTT
1464609 AATTTATATA----
1 AATTTATATAGTTT
1464619 AA-TTATATAGTTT
1 AATTTATATAGTTT
1464632 AATTTATATA
1 AATTTATATA
1464642 AATAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:1464628 original size:23 final size:24
Alignment explanation
Indices: 1464594--1464644 Score: 95
Period size: 23 Copynumber: 2.2 Consensus size: 24
1464584 ATGAAAAGGA
1464594 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
1464618 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
1464641 AAAT
1 AAAT
1464645 AAAAAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 22 0.81
24 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:1464911 original size:13 final size:14
Alignment explanation
Indices: 1464895--1464952 Score: 52
Period size: 13 Copynumber: 4.4 Consensus size: 14
1464885 TATACATACA
1464895 TATTAT-ATAAAAT
1 TATTATAATAAAAT
1464908 TATT-TAATAAAAT
1 TATTATAATAAAAT
* *
1464921 TATTAAAATGTAAAT
1 TATTATAAT-AAAAT
1464936 TA-TATAA-AAAAT
1 TATTATAATAAAAT
*
1464948 GATTA
1 TATTA
1464953 ATTAGGTGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
12 6 0.17
13 17 0.47
14 7 0.19
15 6 0.17
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (14 bp):
TATTATAATAAAAT
Found at i:1465256 original size:14 final size:14
Alignment explanation
Indices: 1465237--1465316 Score: 85
Period size: 14 Copynumber: 5.7 Consensus size: 14
1465227 TCTATTTACA
1465237 TTAGGGTTTAAGGT
1 TTAGGGTTTAAGGT
1465251 TTAGGGTTT-AGTGT
1 TTAGGGTTTAAG-GT
*
1465265 TTATGGG-TTAAAGT
1 TTA-GGGTTTAAGGT
1465279 TTAGGG-TTAAGGGT
1 TTAGGGTTTAA-GGT
* *
1465293 TTATGATTTAAGGT
1 TTAGGGTTTAAGGT
1465307 TTAGGGTTTA
1 TTAGGGTTTA
1465317 TATAAAATTA
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
13 9 0.16
14 38 0.69
15 8 0.15
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.45
Consensus pattern (14 bp):
TTAGGGTTTAAGGT
Found at i:1465280 original size:28 final size:28
Alignment explanation
Indices: 1465244--1465316 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
1465234 ACATTAGGGT
* *
1465244 TTAAGGTTTAGGGTTTAGTGTTTATGGG
1 TTAAGGTTTAGGGTTTAGGGTTTATGAG
* * *
1465272 TTAAAGTTTAGGGTTAAGGGTTTATGAT
1 TTAAGGTTTAGGGTTTAGGGTTTATGAG
1465300 TTAAGGTTTAGGGTTTA
1 TTAAGGTTTAGGGTTTA
1465317 TATAAAATTA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.45
Consensus pattern (28 bp):
TTAAGGTTTAGGGTTTAGGGTTTATGAG
Found at i:1465317 original size:21 final size:21
Alignment explanation
Indices: 1465278--1465317 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1465268 TGGGTTAAAG
*
1465278 TTTAGGGTTAAGGGTTTATGA
1 TTTAAGGTTAAGGGTTTATGA
*
1465299 TTTAAGGTTTAGGGTTTAT
1 TTTAAGGTTAAGGGTTTAT
1465318 ATAAAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (21 bp):
TTTAAGGTTAAGGGTTTATGA
Found at i:1465599 original size:2 final size:2
Alignment explanation
Indices: 1465588--1465787 Score: 98
Period size: 2 Copynumber: 102.0 Consensus size: 2
1465578 ATAGTGTTTC
1465588 TA TA -A TA TA TA TA 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 TA TA TA TA TA TA TA
* * * *
1465629 TA TA -A TT TA TA GA T- TA CT- TA TA T- TA GT- TA TA CA TA CA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA
* * * *
1465668 TA TA TA CTA TA T- TA -A TA TA AA T- TA TA -A TT TG TA AA CTA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * * *
1465708 TA T- TT TA TA TA GTT TA TA CA TA TA TA GTT TA TA TA CA TA CA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * * *
1465751 TA TA GTT TA TA TA CA TA CA TA CA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1465788 GAAAATTAAA
Statistics
Matches: 146, Mismatches: 34, Indels: 36
0.68 0.16 0.17
Matches are distributed among these distances:
1 11 0.08
2 127 0.87
3 8 0.05
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1465742 original size:17 final size:17
Alignment explanation
Indices: 1465713--1465767 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 17
1465703 CTATATATTT
1465713 TATATAG-TT-TATACA
1 TATATAGTTTATATACA
1465728 TATATAGTTTATATACATACA
1 TATATAG-TT-TAT--ATACA
1465749 TATATAGTTTATATACA
1 TATATAGTTTATATACA
1465766 TA
1 TA
1465768 CATACATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
15 7 0.21
17 8 0.24
18 1 0.03
19 4 0.12
20 2 0.06
21 12 0.35
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.45
Consensus pattern (17 bp):
TATATAGTTTATATACA
Found at i:1466055 original size:19 final size:19
Alignment explanation
Indices: 1465974--1466055 Score: 76
Period size: 19 Copynumber: 4.3 Consensus size: 19
1465964 ATAAAATCTC
*
1465974 AATTCTCAATTTCCCTCCA
1 AATTCTCAATTTCCCTCTA
* * *
1465993 AATTTTTCTA-TTCCCTTTA
1 AA-TTCTCAATTTCCCTCTA
* *
1466012 AATTTTTCAATTGCCCTCTA
1 AA-TTCTCAATTTCCCTCTA
*
1466032 AATTCTCAATTTCCCTATA
1 AATTCTCAATTTCCCTCTA
1466051 AATTC
1 AATTC
1466056 CCAAATAAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
19 37 0.73
20 14 0.27
ACGTcount: A:0.27, C:0.27, G:0.01, T:0.45
Consensus pattern (19 bp):
AATTCTCAATTTCCCTCTA
Found at i:1466201 original size:15 final size:15
Alignment explanation
Indices: 1466181--1466219 Score: 64
Period size: 13 Copynumber: 2.7 Consensus size: 15
1466171 ATATACTTTT
1466181 TATAGTTTATACATA
1 TATAGTTTATACATA
1466196 TATAG-TT-TACATA
1 TATAGTTTATACATA
1466209 TATAGTTTATA
1 TATAGTTTATA
1466220 TATAGTTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 11 0.50
14 4 0.18
15 7 0.32
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (15 bp):
TATAGTTTATACATA
Found at i:1466220 original size:11 final size:11
Alignment explanation
Indices: 1466193--1466232 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1466183 TAGTTTATAC
1466193 ATATATAGTTT
1 ATATATAGTTT
1466204 ACATATATAGTTT
1 --ATATATAGTTT
*
1466217 ATATATAGTTC
1 ATATATAGTTT
1466228 ATATA
1 ATATA
1466233 AACATAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 15 0.58
13 11 0.42
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (11 bp):
ATATATAGTTT
Found at i:1466232 original size:13 final size:12
Alignment explanation
Indices: 1466193--1466362 Score: 69
Period size: 13 Copynumber: 14.2 Consensus size: 12
1466183 TAGTTTATAC
*
1466193 ATATATAGTTTAC
1 ATATATAG-TTAT
1466206 ATATATAGTT-T
1 ATATATAGTTAT
1466217 ATATATAGTTCAT
1 ATATATAGTT-AT
* *
1466230 ATAAACATAATT-T
1 AT--ATATAGTTAT
1466243 ATATATA-TATAT
1 ATATATAGT-TAT
*
1466255 ATATATAACTTAT
1 ATATAT-AGTTAT
1466268 A-ATA-A-TTAT
1 ATATATAGTTAT
*
1466277 ATAGTTTATA-ATAT
1 ATA---TATAGTTAT
*
1466291 AAATATAGTTTAT
1 ATATATAG-TTAT
1466304 ATATATAGTT-T
1 ATATATAGTTAT
*
1466315 ATATATAAGCTTTT
1 ATATAT-AG-TTAT
1466329 AT-TATA--TAT
1 ATATATAGTTAT
1466338 ATATATA-TATAT
1 ATATATAGT-TAT
1466350 ATATATA-TTAT
1 ATATATAGTTAT
1466361 AT
1 AT
1466363 TTTTTTCAAT
Statistics
Matches: 127, Mismatches: 9, Indels: 44
0.71 0.05 0.24
Matches are distributed among these distances:
9 9 0.07
10 7 0.06
11 31 0.24
12 28 0.22
13 36 0.28
14 10 0.08
15 6 0.05
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (12 bp):
ATATATAGTTAT
Found at i:1466249 original size:2 final size:2
Alignment explanation
Indices: 1466242--1466362 Score: 73
Period size: 2 Copynumber: 63.5 Consensus size: 2
1466232 AAACATAATT
1466242 TA TA TA TA TA TA TA TA TA TA -A CT- TA TA -A TA -A T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * * *
1466280 GTT TA TA -A TA TA AA TA TA GTT TA TA TA TA TA GTT TA TA TA TA
1 -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA
** *
1466322 -A GC T- TT TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1466360 TA T
1 TA T
1466363 TTTTTTCAAT
Statistics
Matches: 94, Mismatches: 11, Indels: 28
0.71 0.08 0.21
Matches are distributed among these distances:
1 10 0.11
2 81 0.86
3 3 0.03
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1468087 original size:68 final size:68
Alignment explanation
Indices: 1467993--1468121 Score: 158
Period size: 68 Copynumber: 1.9 Consensus size: 68
1467983 TAATATAATA
*
1467993 TTTTCAAAACTATTATATAGACTATTTTTCTAAATGT-TTTCCAAA-CTATATATTATTTTCAAA
1 TTTTCAAAACTATTATATAGACTATTTTT-TAAAT-TATTT-CAAATATATATATTATTTTCAAA
1468056 ATATTT
63 ATATTT
* *
1468062 TTTTC-AAACTA-TATAATATATTATTTTTTAAATTAATTTCAAATATATATATTATTTTCA
1 TTTTCAAAACTATTAT-ATAGACTATTTTTTAAATT-ATTTCAAATATATATATTATTTTCA
1468122 TATGGGTGGG
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
66 1 0.02
67 12 0.23
68 35 0.66
69 5 0.09
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (68 bp):
TTTTCAAAACTATTATATAGACTATTTTTTAAATTATTTCAAATATATATATTATTTTCAAAATA
TTT
Found at i:1470617 original size:18 final size:18
Alignment explanation
Indices: 1470588--1470713 Score: 189
Period size: 18 Copynumber: 7.0 Consensus size: 18
1470578 GCGTAGAATT
* *
1470588 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTG
*
1470606 TGTCCTGAAGGACCACTG
1 TGTCCCGAAGGACCACTG
1470624 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTG
*
1470642 TGTCCCGAAAGACCACTG
1 TGTCCCGAAGGACCACTG
*
1470660 TGTCCCGAATGACCACTG
1 TGTCCCGAAGGACCACTG
* *
1470678 TATCTCGAAGGACCACTG
1 TGTCCCGAAGGACCACTG
1470696 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTG
1470714 ATAATCCCTC
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 97 1.00
ACGTcount: A:0.24, C:0.32, G:0.25, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTG
Found at i:1475256 original size:21 final size:21
Alignment explanation
Indices: 1475231--1475281 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
1475221 TCTAGAAAAG
1475231 GGATCGATCCATTACGGGAAA
1 GGATCGATCCATTACGGGAAA
*
1475252 GGATCGATCCATTAGGGGAAA
1 GGATCGATCCATTACGGGAAA
1475273 GGATCGATC
1 GGATCGATC
1475282 TGTTTACAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.18, G:0.31, T:0.20
Consensus pattern (21 bp):
GGATCGATCCATTACGGGAAA
Found at i:1477199 original size:17 final size:17
Alignment explanation
Indices: 1477177--1477210 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1477167 TTTTACTTAG
1477177 GTTATTGTTCATTTTCA
1 GTTATTGTTCATTTTCA
1477194 GTTATTGTTCATTTTCA
1 GTTATTGTTCATTTTCA
1477211 AGGCTCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.12, T:0.59
Consensus pattern (17 bp):
GTTATTGTTCATTTTCA
Found at i:1484106 original size:25 final size:25
Alignment explanation
Indices: 1484074--1484154 Score: 92
Period size: 28 Copynumber: 3.1 Consensus size: 25
1484064 TTCCAAGATT
1484074 TTATAATTTTGAAATTTTAATTTAA
1 TTATAATTTTGAAATTTTAATTTAA
*
1484099 TTATAATTTTGAGAATATTTTTATTTAA
1 TTATAATTTT--GAA-ATTTTAATTTAA
* *
1484127 ATATAATTTT-AAATTTTAAATTTTA
1 TTATAATTTTGAAATTTT-AATTTAA
1484152 TTA
1 TTA
1484155 ATTTTATTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
24 5 0.11
25 19 0.40
27 3 0.06
28 20 0.43
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (25 bp):
TTATAATTTTGAAATTTTAATTTAA
Found at i:1485242 original size:29 final size:29
Alignment explanation
Indices: 1485209--1485305 Score: 76
Period size: 29 Copynumber: 3.2 Consensus size: 29
1485199 CAATGTAATT
1485209 CATTTTACTTGTCAATTGAATTTTCTTTG
1 CATTTTACTTGTCAATTGAATTTTCTTTG
* *
1485238 CATTTT-C-TG-AAATTGACTTACAATATTAT-TTTT
1 CATTTTACTTGTCAATTG------AAT-TT-TCTTTG
1485271 CATTTTACTTGTCAATTGAATTTTCTTTG
1 CATTTTACTTGTCAATTGAATTTTCTTTG
1485300 CATTTT
1 CATTTT
1485306 CTGAAAATGA
Statistics
Matches: 52, Mismatches: 4, Indels: 24
0.65 0.05 0.30
Matches are distributed among these distances:
26 5 0.10
27 2 0.04
28 2 0.04
29 17 0.33
30 3 0.06
32 3 0.06
33 11 0.21
34 2 0.04
35 2 0.04
36 5 0.10
ACGTcount: A:0.24, C:0.13, G:0.08, T:0.55
Consensus pattern (29 bp):
CATTTTACTTGTCAATTGAATTTTCTTTG
Found at i:1485278 original size:62 final size:62
Alignment explanation
Indices: 1485207--1485333 Score: 245
Period size: 62 Copynumber: 2.0 Consensus size: 62
1485197 ATCAATGTAA
*
1485207 TTCATTTTACTTGTCAATTGAATTTTCTTTGCATTTTCTGAAATTGACTTACAATATTATTT
1 TTCATTTTACTTGTCAATTGAATTTTCTTTGCATTTTCTGAAAATGACTTACAATATTATTT
1485269 TTCATTTTACTTGTCAATTGAATTTTCTTTGCATTTTCTGAAAATGACTTACAATATTATTT
1 TTCATTTTACTTGTCAATTGAATTTTCTTTGCATTTTCTGAAAATGACTTACAATATTATTT
1485331 TTC
1 TTC
1485334 GTAAGTCATT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.26, C:0.13, G:0.08, T:0.53
Consensus pattern (62 bp):
TTCATTTTACTTGTCAATTGAATTTTCTTTGCATTTTCTGAAAATGACTTACAATATTATTT
Found at i:1485441 original size:30 final size:27
Alignment explanation
Indices: 1485377--1485441 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
1485367 ACAAACACTT
1485377 AAAATATTATTATTTTATATATTTAATA
1 AAAATA-TATTATTTTATATATTTAATA
**
1485405 TTAATATATTATTTTAATATCATTTGAATA
1 AAAATATATTATTTT-ATAT-ATTT-AATA
1485435 AAAATAT
1 AAAATAT
1485442 TAATTATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 9 0.30
28 8 0.27
29 4 0.13
30 9 0.30
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (27 bp):
AAAATATATTATTTTATATATTTAATA
Found at i:1485442 original size:28 final size:26
Alignment explanation
Indices: 1485384--1485443 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 26
1485374 CTTAAAATAT
*
1485384 TATTATTTTATATATTTAATATTAATA
1 TATTATTTTATATATTTAATA-TAAAA
1485411 TATTATTTTAATATCATTTGAATA-AAAA
1 TATTATTTT-ATAT-ATTT-AATATAAAA
1485439 TATTA
1 TATTA
1485444 ATTATTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 9 0.31
28 12 0.41
29 4 0.14
30 4 0.14
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (26 bp):
TATTATTTTATATATTTAATATAAAA
Found at i:1485663 original size:25 final size:24
Alignment explanation
Indices: 1485634--1485695 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
1485624 CCCGTAAAAT
**
1485634 ATAATATAATTATTTTAATATTTTA
1 ATAATATAATTATTTTAATA-AGTA
1485659 ATAATA-ATATTATTTTAATAAGTA
1 ATAATATA-ATTATTTTAATAAGTA
1485683 ATTAATATAATTA
1 A-TAATATAATTA
1485696 GTAATATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 4 0.12
25 27 0.84
26 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
ATAATATAATTATTTTAATAAGTA
Found at i:1486891 original size:17 final size:17
Alignment explanation
Indices: 1486865--1486898 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1486855 TATCATTTAA
*
1486865 ATAAATAAATAAATTAT
1 ATAAAAAAATAAATTAT
1486882 ATAAAAAAATAAATTAT
1 ATAAAAAAATAAATTAT
1486899 TGATAGAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAAAAAATAAATTAT
Found at i:1491914 original size:43 final size:43
Alignment explanation
Indices: 1491817--1491976 Score: 169
Period size: 43 Copynumber: 3.7 Consensus size: 43
1491807 GGGTGACCCC
* * * * *
1491817 TTCTTCAGATAACTCACTTTCGCTA-GTTTATGCCAAGGGAAGTA
1 TTCTTCAGATGACTCCCTTTCGC-AGGTTTA-GTCAAGTGAAATA
*
1491861 TTCTTCAGATGACTCCCTTTCGCAGGTTTAGTCATGTGAAATA
1 TTCTTCAGATGACTCCCTTTCGCAGGTTTAGTCAAGTGAAATA
* * * * *
1491904 TTCTTCAGATGACTTCCTTTCGCGGGTTAAGTCAGGTGAAATG
1 TTCTTCAGATGACTCCCTTTCGCAGGTTTAGTCAAGTGAAATA
* * *
1491947 TTCTTCAGATGAGTCCCCTTCGCGGGTTTA
1 TTCTTCAGATGACTCCCTTTCGCAGGTTTA
1491977 AGCCACGTGA
Statistics
Matches: 100, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
43 74 0.74
44 26 0.26
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (43 bp):
TTCTTCAGATGACTCCCTTTCGCAGGTTTAGTCAAGTGAAATA
Found at i:1499783 original size:11 final size:10
Alignment explanation
Indices: 1499761--1499795 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
1499751 AGCTACTCTC
1499761 TAGCTCCCTT
1 TAGCTCCCTT
1499771 TAGCTCCCATT
1 TAGCTCCC-TT
1499782 TAGCT-CCTT
1 TAGCTCCCTT
1499791 TAGCT
1 TAGCT
1499796 AGCCTTGAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 7 0.29
10 10 0.42
11 7 0.29
ACGTcount: A:0.14, C:0.34, G:0.11, T:0.40
Consensus pattern (10 bp):
TAGCTCCCTT
Found at i:1504760 original size:65 final size:64
Alignment explanation
Indices: 1504647--1504802 Score: 188
Period size: 65 Copynumber: 2.4 Consensus size: 64
1504637 ATAAGACTTA
* * * * *
1504647 GTGCATCGGTACACTAATTACATTCGATGTTTCAAAAGAGCCAGGAGTGCATCGATGCATGGTAT
1 GTGCATCGGTACACAAAATGCATTCGATATTTCAAAAGAGCCAAGAGTGCATCGATGCATGG-AT
* ** * *
1504712 GTGCATCGGTACACAAAATGCATTCGGTATTTCAATAA-ATTCAAGAGTGCATTGATGCATGGCT
1 GTGCATCGGTACACAAAATGCATTCGATATTTCAA-AAGAGCCAAGAGTGCATCGATGCATGGAT
*
1504776 GTGCATCGGTACACAAAATGTATTCGA
1 GTGCATCGGTACACAAAATGCATTCGA
1504803 AATAGGGTGT
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
64 26 0.33
65 50 0.64
66 2 0.03
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (64 bp):
GTGCATCGGTACACAAAATGCATTCGATATTTCAAAAGAGCCAAGAGTGCATCGATGCATGGAT
Found at i:1506638 original size:23 final size:22
Alignment explanation
Indices: 1506604--1506703 Score: 73
Period size: 23 Copynumber: 4.6 Consensus size: 22
1506594 CACTGTATAG
1506604 TGTATCGATGCACATTCAAGGAA
1 TGTATCGATGCACATTCAAGG-A
* *
1506627 TGTATCGGTGCACCTTCATA-G-
1 TGTATCGATGCACATTCA-AGGA
*
1506648 TGTATCGATGCATATTCAAGGGA
1 TGTATCGATGCACATTCAA-GGA
* * * * *
1506671 TGCATCGGTACACTTTCTA-G-
1 TGTATCGATGCACATTCAAGGA
1506691 TGTATCGATGCAC
1 TGTATCGATGCAC
1506704 TTTGCAAAAA
Statistics
Matches: 59, Mismatches: 14, Indels: 11
0.70 0.17 0.13
Matches are distributed among these distances:
20 11 0.19
21 16 0.27
22 1 0.02
23 30 0.51
24 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (22 bp):
TGTATCGATGCACATTCAAGGA
Found at i:1506655 original size:44 final size:44
Alignment explanation
Indices: 1506584--1506703 Score: 156
Period size: 44 Copynumber: 2.8 Consensus size: 44
1506574 ACCCGACAAG
*
1506584 TGTATCGATGCA-CTGT-ATAGTGTATCGATGCACATTCAAGGAA
1 TGTATCGGTGCACCT-TCATAGTGTATCGATGCACATTCAAGGAA
* *
1506627 TGTATCGGTGCACCTTCATAGTGTATCGATGCATATTCAAGGGA
1 TGTATCGGTGCACCTTCATAGTGTATCGATGCACATTCAAGGAA
* * *
1506671 TGCATCGGTACACTTTC-TAGTGTATCGATGCAC
1 TGTATCGGTGCACCTTCATAGTGTATCGATGCAC
1506704 TTTGCAAAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
43 27 0.40
44 41 0.60
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (44 bp):
TGTATCGGTGCACCTTCATAGTGTATCGATGCACATTCAAGGAA
Found at i:1510551 original size:22 final size:21
Alignment explanation
Indices: 1510509--1510548 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1510499 GAGATTATTT
*
1510509 TCATTTTTTAGTTTTGAAATA
1 TCATTTTTTAGTTTTAAAATA
1510530 TCATTTTTGTA-TTTTAAAA
1 TCATTTTT-TAGTTTTAAAA
1510549 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.57
Consensus pattern (21 bp):
TCATTTTTTAGTTTTAAAATA
Found at i:1514412 original size:27 final size:27
Alignment explanation
Indices: 1514368--1514420 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1514358 ATGTTACTAG
* *
1514368 TATAACAATAAAAGAAAAAATATAAAA
1 TATAACAATAAAACAAAAAAGATAAAA
1514395 TATAA-AATATAAACAAAAAAGATAAA
1 TATAACAATA-AAACAAAAAAGATAAA
1514421 GTAAGTGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.19
Consensus pattern (27 bp):
TATAACAATAAAACAAAAAAGATAAAA
Found at i:1514747 original size:28 final size:27
Alignment explanation
Indices: 1514684--1514747 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
1514674 TCAAATGAGG
1514684 AAATTAAAGAAAAAAAGACAATATAAAA
1 AAATT-AAGAAAAAAAGACAATATAAAA
* *
1514712 AAGGTTAAGAAAAAAATCGA-AATCTAAAA
1 AA-ATTAAGAAAAAAA--GACAATATAAAA
1514741 AAATTAA
1 AAATTAA
1514748 ATTTAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
28 16 0.53
29 12 0.40
30 2 0.07
ACGTcount: A:0.69, C:0.05, G:0.09, T:0.17
Consensus pattern (27 bp):
AAATTAAGAAAAAAAGACAATATAAAA
Found at i:1514749 original size:15 final size:15
Alignment explanation
Indices: 1514721--1514763 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1514711 AAAGGTTAAG
*
1514721 AAAAAAATCGAAATCT
1 AAAAAAAT-TAAATCT
*
1514737 AAAAAAATTAAATTT
1 AAAAAAATTAAATCT
*
1514752 AAAAAATTTAAA
1 AAAAAAATTAAA
1514764 AAAACAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (15 bp):
AAAAAAATTAAATCT
Found at i:1530385 original size:15 final size:16
Alignment explanation
Indices: 1530349--1530388 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1530339 TAAGACAATG
*
1530349 AAAAATATAGATAATA
1 AAAAAGATAGATAATA
1530365 AAAAAGATAGATAA-A
1 AAAAAGATAGATAATA
*
1530380 ATAAAGATA
1 AAAAAGATA
1530389 AGGATAGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (16 bp):
AAAAAGATAGATAATA
Found at i:1538145 original size:29 final size:29
Alignment explanation
Indices: 1538110--1538191 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1538100 AAACTAAATT
*
1538110 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1538139 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
1538168 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1538192 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:1542912 original size:29 final size:29
Alignment explanation
Indices: 1542877--1542958 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1542867 AAACTAAATT
*
1542877 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1542906 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
1542935 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1542959 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:1546520 original size:20 final size:21
Alignment explanation
Indices: 1546495--1546546 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1546485 TTTCCCCAAT
*
1546495 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
1546515 TCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1546536 TCGCAATGCGA
1 TCGCAATGCGA
1546547 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1546560 original size:20 final size:20
Alignment explanation
Indices: 1546535--1546648 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
1546525 AATTGGGAAA
*
1546535 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1546555 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
1546575 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
1546596 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1546616 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
1546636 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1546649 TTACATAGCG
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1546580 original size:61 final size:61
Alignment explanation
Indices: 1546532--1546648 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
1546522 GCGAATTGGG
* * * *
1546532 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAATGCGATAATAC
* * * *
1546593 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAATGCGAT
1546649 TTACATAGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAATGCGATAATAC
Found at i:1547205 original size:19 final size:19
Alignment explanation
Indices: 1547167--1547233 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1547157 TTCGAGAATG
1547167 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
1547187 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
1547206 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
1547225 AAAATCGCA
1 AAAATCGCA
1547234 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:1547251 original size:19 final size:19
Alignment explanation
Indices: 1547229--1547413 Score: 174
Period size: 19 Copynumber: 10.1 Consensus size: 19
1547219 GAAACCAAAA
*
1547229 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1547248 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1547267 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
1547286 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
1547306 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
1547322 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1547339 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1547353 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1547372 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1547392 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1547412 TC
1 TC
1547414 AACCAAAAGA
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 20 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 60 0.43
20 49 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1547306 original size:39 final size:38
Alignment explanation
Indices: 1547229--1547413 Score: 174
Period size: 33 Copynumber: 5.1 Consensus size: 38
1547219 GAAACCAAAA
*
1547229 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
1547267 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * **
1547306 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* **
1547339 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
1547372 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
1547412 TC
1 TC
1547414 AACCAAAAGA
Statistics
Matches: 124, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
31 3 0.02
33 38 0.31
34 10 0.08
35 1 0.01
36 3 0.02
38 21 0.17
39 30 0.24
40 18 0.15
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:1547390 original size:20 final size:20
Alignment explanation
Indices: 1547356--1547413 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1547346 GCGATTCTCT
**
1547356 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
1547376 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
1547396 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
1547414 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:1549498 original size:42 final size:42
Alignment explanation
Indices: 1549415--1549537 Score: 106
Period size: 42 Copynumber: 2.9 Consensus size: 42
1549405 GCCCGACTCG
* * * * * * *
1549415 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAAAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1549457 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
* * * * *
1549499 ACTGTCATT-GTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
1549538 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 2 0.03
42 63 0.94
43 2 0.03
ACGTcount: A:0.24, C:0.36, G:0.17, T:0.24
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
Found at i:1550915 original size:14 final size:14
Alignment explanation
Indices: 1550896--1550931 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1550886 ATTGTTTAAT
1550896 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1550910 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1550924 TGATTTGT
1 TGATTTGT
1550932 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1551082 original size:19 final size:19
Alignment explanation
Indices: 1551058--1551116 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
1551048 GAAATTAGCG
1551058 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1551077 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1551091 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1551110 TTGCGAT
1 TTGCGAT
1551117 AGTAATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 7 0.21
19 13 0.39
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1551082 original size:33 final size:34
Alignment explanation
Indices: 1551039--1551115 Score: 104
Period size: 33 Copynumber: 2.3 Consensus size: 34
1551029 AAAAGTACTA
*
1551039 TCGCAATGCGAAAT-TAGCGTTGCGATTTTCATT
1 TCGCATTGCGAAATCTAGCGTTGCGATTTTCATT
* **
1551072 TCGCATTGCG-ATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATCTAGCGTTGCGATTTTCATT
1551105 TCGCATTGCGA
1 TCGCATTGCGA
1551116 TAGTAATTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 2 0.05
33 36 0.95
ACGTcount: A:0.18, C:0.22, G:0.21, T:0.39
Consensus pattern (34 bp):
TCGCATTGCGAAATCTAGCGTTGCGATTTTCATT
Found at i:1553426 original size:12 final size:12
Alignment explanation
Indices: 1553409--1553433 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1553399 TCTTCGGGGA
1553409 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1553421 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1553433 C
1 C
1553434 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1553642 original size:24 final size:24
Alignment explanation
Indices: 1553608--1553661 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1553598 CTGAAACATC
* *
1553608 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
1553632 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
1553656 ATCAAA
1 ATCAAA
1553662 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:1554741 original size:20 final size:20
Alignment explanation
Indices: 1554716--1554786 Score: 133
Period size: 20 Copynumber: 3.5 Consensus size: 20
1554706 ATTCATTTGA
1554716 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
1554736 CTATCGCAACGCAAAAATGG
1 CTATCGCAACGCGAAAATGG
1554756 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1554776 CTATCGCAACG
1 CTATCGCAACG
1554787 AGGAAATCGC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.35, C:0.27, G:0.23, T:0.15
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1554796 original size:34 final size:36
Alignment explanation
Indices: 1554718--1554805 Score: 99
Period size: 40 Copynumber: 2.4 Consensus size: 36
1554708 TCATTTGACT
**
1554718 ATCGCAACGCGAAAATGGCTATCGCAACGCAAAAATGGCT
1 ATCGCAACGCGAAAATGGCTATCGCAACG----AATGGAA
1554758 ATCGCAACGCGAAAATGGCTATCGCAACG-A-GGAA
1 ATCGCAACGCGAAAATGGCTATCGCAACGAATGGAA
*
1554792 ATCGCAATGCGAAA
1 ATCGCAACGCGAAA
1554806 TGAAAATCGC
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
34 15 0.33
35 1 0.02
40 29 0.64
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.14
Consensus pattern (36 bp):
ATCGCAACGCGAAAATGGCTATCGCAACGAATGGAA
Found at i:1554836 original size:14 final size:16
Alignment explanation
Indices: 1554816--1554889 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
1554806 TGAAAATCGC
1554816 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
1554831 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
1554848 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
1554867 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
1554883 -TTGCGAT
1 ATTGCGAT
1554890 AGCCATTTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:1554853 original size:19 final size:19
Alignment explanation
Indices: 1554812--1554879 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
1554802 GAAATGAAAA
1554812 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
1554828 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1554845 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1554864 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
1554880 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1554899 original size:20 final size:20
Alignment explanation
Indices: 1554874--1554911 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1554864 TCGCATTGCG
*
1554874 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
1554894 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
1554912 TCTGTTTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:1555016 original size:14 final size:14
Alignment explanation
Indices: 1554997--1555033 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1554987 CATCAATTAA
1554997 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1555011 ACAAATCATCTTTT
1 ACAAATCAACATTT
1555025 ACAAATCAA
1 ACAAATCAA
1555034 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1556941 original size:20 final size:19
Alignment explanation
Indices: 1556906--1556972 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1556896 GAAACTTAAA
1556906 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
1556925 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
1556945 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
1556964 ATCGCAACG
1 ATCGCAACG
1556973 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1556980 original size:14 final size:14
Alignment explanation
Indices: 1556961--1557018 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1556951 ATGCGAAATG
1556961 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1556975 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
*
1556991 ATGAAATCGCAATGAC
1 A--AAATCGCAACGAC
1557007 AAAATCGCAACG
1 AAAATCGCAACG
1557019 CGAAACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 7 0.19
18 9 0.25
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1557008 original size:32 final size:33
Alignment explanation
Indices: 1556945--1557023 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
1556935 GGAAATGGCT
*
1556945 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
1556978 ATCGCAACGCGAAATG-AAATCGCAATGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1557010 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1557024 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:1557071 original size:14 final size:14
Alignment explanation
Indices: 1557052--1557109 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1557042 TTTCATTTCG
1557052 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1557066 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1557082 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1557098 CGTTGCGATTTT
1 CGTTGCGATTTT
1557110 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1557082 original size:32 final size:33
Alignment explanation
Indices: 1557035--1557117 Score: 159
Period size: 32 Copynumber: 2.5 Consensus size: 33
1557025 ACAAATCGCA
1557035 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1557068 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1557100 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
1557118 ATTACGATAG
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
32 32 0.65
33 17 0.35
ACGTcount: A:0.10, C:0.19, G:0.23, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:1557672 original size:18 final size:18
Alignment explanation
Indices: 1557646--1557690 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1557636 GTCGATCAGA
*
1557646 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1557664 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1557682 TGATGGCTC
1 TGATGGCTC
1557691 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1559035 original size:20 final size:20
Alignment explanation
Indices: 1559010--1559047 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1559000 AATAGTTTCT
1559010 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
1559030 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
1559048 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:1559567 original size:20 final size:20
Alignment explanation
Indices: 1559542--1559635 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1559532 GATTATGTAT
1559542 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1559562 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
1559582 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
1559603 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1559623 TATCGCATTGCGA
1 TATCGCGTTGCGA
1559636 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1559636 original size:20 final size:20
Alignment explanation
Indices: 1559522--1559636 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
1559512 CGCTTTGAAA
*
1559522 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
1559543 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
1559563 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
1559583 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
1559604 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1559624 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1559637 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1559654 original size:21 final size:21
Alignment explanation
Indices: 1559625--1559700 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1559615 ATAGTCAGTA
1559625 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1559646 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1559666 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
*
1559687 TCGCGTTGCGATTT
1 TCGCATTGCGATTT
1559701 ACTTATTCGC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.16, C:0.25, G:0.18, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:1559655 original size:41 final size:41
Alignment explanation
Indices: 1559564--1559698 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
1559554 AAAGTCAGTA
* * * ** *
1559564 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
1559604 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
1559646 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
1559687 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1559699 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:1559669 original size:20 final size:20
Alignment explanation
Indices: 1559644--1559710 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
1559634 GATTTTCCCA
1559644 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
* * **
1559664 ATTCGCATTGCGATTTTCCCA
1 ATTCGCGTTGCGA-TTTACTT
1559685 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
1559705 ATTCGC
1 ATTCGC
1559711 ATTGTGAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.42
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACTT
Found at i:1559699 original size:41 final size:41
Alignment explanation
Indices: 1559625--1559714 Score: 180
Period size: 41 Copynumber: 2.2 Consensus size: 41
1559615 ATAGTCAGTA
1559625 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1559666 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1559707 TCGCATTG
1 TCGCATTG
1559715 TGAATTGGGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:1561181 original size:13 final size:13
Alignment explanation
Indices: 1561163--1561189 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1561153 CACACACACG
1561163 TTCCAAATTTTAC
1 TTCCAAATTTTAC
1561176 TTCCAAATTTTAC
1 TTCCAAATTTTAC
1561189 T
1 T
1561190 GCAAAATGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.22, G:0.00, T:0.48
Consensus pattern (13 bp):
TTCCAAATTTTAC
Found at i:1567103 original size:24 final size:24
Alignment explanation
Indices: 1567071--1567117 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1567061 TGTTCCTCAC
1567071 TGCTTCCTCGT-CTCTCTTCTTCTA
1 TGCTTCCTCGTCCT-TCTTCTTCTA
1567095 TGCTTCCTCGTCCTTCTTCTTCT
1 TGCTTCCTCGTCCTTCTTCTTCT
1567118 CCAACCATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.02, C:0.38, G:0.09, T:0.51
Consensus pattern (24 bp):
TGCTTCCTCGTCCTTCTTCTTCTA
Found at i:1568546 original size:14 final size:14
Alignment explanation
Indices: 1568524--1568564 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
1568514 TCGATTATAT
*
1568524 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
1568538 GTTCATTTATGTTC
1 GTTCATTTATGTTC
*
1568552 ATTCATTTATGTT
1 GTTCATTTATGTT
1568565 TGAACAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.59
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:1568854 original size:21 final size:20
Alignment explanation
Indices: 1568829--1568880 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
1568819 GTGTTTGTGT
*
1568829 TGTTCGTTTATGTTCATTTT
1 TGTTCGTTTATGTTCATTTA
* *
1568849 TCGTTCGTTTTTGTTCGTTTA
1 T-GTTCGTTTATGTTCATTTA
1568870 TGTTCGTTTAT
1 TGTTCGTTTAT
1568881 CATTTACATG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.08, C:0.12, G:0.17, T:0.63
Consensus pattern (20 bp):
TGTTCGTTTATGTTCATTTA
Found at i:1568879 original size:10 final size:10
Alignment explanation
Indices: 1568829--1568880 Score: 68
Period size: 10 Copynumber: 5.1 Consensus size: 10
1568819 GTGTTTGTGT
1568829 TGTTCGTTTA
1 TGTTCGTTTA
* *
1568839 TGTTCATTTT
1 TGTTCGTTTA
*
1568849 TCGTTCGTTTT
1 T-GTTCGTTTA
1568860 TGTTCGTTTA
1 TGTTCGTTTA
1568870 TGTTCGTTTA
1 TGTTCGTTTA
1568880 T
1 T
1568881 CATTTACATG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
10 28 0.76
11 9 0.24
ACGTcount: A:0.08, C:0.12, G:0.17, T:0.63
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:1570170 original size:3 final size:3
Alignment explanation
Indices: 1570162--1570210 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
1570152 AACAACTGAG
1570162 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1570210 G
1 G
1570211 GGGTTGACGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1570392 original size:19 final size:19
Alignment explanation
Indices: 1570341--1570392 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
1570331 AAATATTCAT
* *
1570341 AGTATTAAAAAATCAATAG
1 AGTAATAAAAAATCAATAA
*
1570360 AGTTAATAACAAATCAATAAA
1 AG-TAATAAAAAATCAAT-AA
1570381 AG-AATAAAAAAT
1 AGTAATAAAAAAT
1570393 GAAATGATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 11 0.41
20 13 0.48
21 3 0.11
ACGTcount: A:0.63, C:0.06, G:0.08, T:0.23
Consensus pattern (19 bp):
AGTAATAAAAAATCAATAA
Found at i:1572001 original size:12 final size:12
Alignment explanation
Indices: 1571984--1572008 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1571974 GGAATTTGGG
1571984 TGTTTTGGTGGA
1 TGTTTTGGTGGA
1571996 TGTTTTGGTGGA
1 TGTTTTGGTGGA
1572008 T
1 T
1572009 CGGTAAGGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.40, T:0.52
Consensus pattern (12 bp):
TGTTTTGGTGGA
Found at i:1581086 original size:24 final size:24
Alignment explanation
Indices: 1581054--1581102 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
1581044 AGTCTTTCTG
1581054 ATGATGTATAAAACATCTACGTAC
1 ATGATGTATAAAACATCTACGTAC
*
1581078 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTACGTAC
1581102 A
1 A
1581103 ATATCATGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (24 bp):
ATGATGTATAAAACATCTACGTAC
Found at i:1589846 original size:80 final size:80
Alignment explanation
Indices: 1589713--1589874 Score: 290
Period size: 80 Copynumber: 2.0 Consensus size: 80
1589703 AAGTCCTTTA
1589713 AACATTCGAGATTCAACTTCTTTGGAATTAATGTTATAAATGAGTAATTGATTTCATTCTCCCAT
1 AACATTCGAGATTCAACTTCTTTGGAATTAATGTTATAAATGAGTAATTGATTTCATTCTCCCAT
1589778 CTTCTCCCATGGTAG
66 CTTCTCCCATGGTAG
* *
1589793 AACATTCGAGATTCAGA-TTCTTTGGAATTAATGTTATAAATGAGTGATTGATTTCATTCTCTCA
1 AACATTCGAGATTCA-ACTTCTTTGGAATTAATGTTATAAATGAGTAATTGATTTCATTCTCCCA
1589857 TCTTCTCCCATGGTAG
65 TCTTCTCCCATGGTAG
1589873 AA
1 AA
1589875 GTCAGTAAAG
Statistics
Matches: 79, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
80 78 0.99
81 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (80 bp):
AACATTCGAGATTCAACTTCTTTGGAATTAATGTTATAAATGAGTAATTGATTTCATTCTCCCAT
CTTCTCCCATGGTAG
Found at i:1594249 original size:19 final size:20
Alignment explanation
Indices: 1594209--1594246 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1594199 TATATGGATA
1594209 GGGGTATCGGTACCCATAAG
1 GGGGTATCGGTACCCATAAG
1594229 GGGGTATCGGTACCCATA
1 GGGGTATCGGTACCCATA
1594247 GGGCACTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.21, G:0.34, T:0.21
Consensus pattern (20 bp):
GGGGTATCGGTACCCATAAG
Found at i:1595044 original size:16 final size:16
Alignment explanation
Indices: 1595007--1595037 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1594997 CATCAAATTC
1595007 AAACATAACAATCCAT
1 AAACATAACAATCCAT
*
1595023 AAACATATCAATCCA
1 AAACATAACAATCCA
1595038 ACAACATCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (16 bp):
AAACATAACAATCCAT
Found at i:1596923 original size:22 final size:21
Alignment explanation
Indices: 1596869--1596945 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 21
1596859 CCAAAACTCG
*
1596869 AAAGGGGCATCGATACCC-TC
1 AAAGGGGTATCGATACCCATC
*
1596889 ATAGGAGGTATCGATACCCATTC
1 AAAGG-GGTATCGATACCCA-TC
* *
1596912 AAAGGGGTATCGATACCTAGC
1 AAAGGGGTATCGATACCCATC
*
1596933 AAGGGGGTATCGA
1 AAAGGGGTATCGA
1596946 AACCTGGTGC
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
20 4 0.08
21 25 0.52
22 13 0.27
23 6 0.12
ACGTcount: A:0.31, C:0.21, G:0.29, T:0.19
Consensus pattern (21 bp):
AAAGGGGTATCGATACCCATC
Found at i:1602685 original size:19 final size:20
Alignment explanation
Indices: 1602645--1602682 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1602635 TATATGGATA
*
1602645 GGGGTATCGGTACCCATAAG
1 GGGGTATCAGTACCCATAAG
1602665 GGGGTATCAGTACCCATA
1 GGGGTATCAGTACCCATA
1602683 GGGCATTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.32, T:0.21
Consensus pattern (20 bp):
GGGGTATCAGTACCCATAAG
Found at i:1608373 original size:2 final size:2
Alignment explanation
Indices: 1608362--1608426 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
1608352 TAAAAGCAAT
1608362 TA TA -A TA TA TA TA 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 TA TA TA TA TA TA TA
1608403 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
1608427 CAATAAAGCT
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 61 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.