Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167993.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_25, 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: 17943224
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 94000 characters in sequence are not A, C, G, or T
File 33 of 100
Found at i:6129616 original size:14 final size:14
Alignment explanation
Indices: 6129576--6129621 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
6129566 ATAAATTTTA
*
6129576 TATAATTTTA-AAT
1 TATAATTTAATAAT
6129589 TATAA-TTAATTAAT
1 TATAATTTAA-TAAT
6129603 TATAATTTAATAAT
1 TATAATTTAATAAT
*
6129617 CATAA
1 TATAA
6129622 ATGATATACT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
12 3 0.11
13 5 0.18
14 16 0.57
15 4 0.14
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
TATAATTTAATAAT
Found at i:6139656 original size:13 final size:13
Alignment explanation
Indices: 6139638--6139662 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6139628 TTTAAGCAAA
6139638 TAATTATTTCATT
1 TAATTATTTCATT
6139651 TAATTATTTCAT
1 TAATTATTTCAT
6139663 GTGGTTATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (13 bp):
TAATTATTTCATT
Found at i:6142457 original size:14 final size:14
Alignment explanation
Indices: 6142417--6142462 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
6142407 ATAAATTTTA
*
6142417 TATAATTTTA-AAT
1 TATAATTTAATAAT
6142430 TATAA-TTAATTAAT
1 TATAATTTAA-TAAT
6142444 TATAATTTAATAAT
1 TATAATTTAATAAT
*
6142458 CATAA
1 TATAA
6142463 ATGATACACT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
12 3 0.11
13 5 0.18
14 16 0.57
15 4 0.14
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
TATAATTTAATAAT
Found at i:6152798 original size:17 final size:16
Alignment explanation
Indices: 6152763--6152798 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
6152753 TTAATTTTAT
*
6152763 TTAATGATAAATATTC
1 TTAATGATAAAGATTC
6152779 TTAATGATAAAGAGTTC
1 TTAATGATAAAGA-TTC
6152796 TTA
1 TTA
6152799 GTAAATAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.42
Consensus pattern (16 bp):
TTAATGATAAAGATTC
Found at i:6153493 original size:2 final size:2
Alignment explanation
Indices: 6153486--6153510 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6153476 GCCCTCCACA
6153486 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6153511 AAGTGCAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6157376 original size:13 final size:13
Alignment explanation
Indices: 6157348--6157384 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
6157338 TTGAGAAAAA
6157348 AATTATTATA-TC
1 AATTATTATATTC
6157360 AATTATTATATTC
1 AATTATTATATTC
6157373 AATTATTATATT
1 AATTATTATATT
6157385 AATGTTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (13 bp):
AATTATTATATTC
Found at i:6157433 original size:27 final size:21
Alignment explanation
Indices: 6157373--6157418 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
6157363 TATTATATTC
6157373 AATTATTATATTAATGTTAAT
1 AATTATTATATTAATGTTAAT
6157394 AATTATTATATTAATGTTAAT
1 AATTATTATATTAATGTTAAT
6157415 AATT
1 AATT
6157419 TATATTCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (21 bp):
AATTATTATATTAATGTTAAT
Found at i:6162652 original size:73 final size:73
Alignment explanation
Indices: 6162573--6162715 Score: 223
Period size: 73 Copynumber: 2.0 Consensus size: 73
6162563 TGAAATACTC
* * *
6162573 TTATACTTTACTAGAATAACTAAAATAAAATTATTTTAAAAGATTAGAGATTGAAATAAAATAAT
1 TTATACTTTACTAGAATAACCAAAATAAAATGATTTTAAAAGATTAGAGATTCAAATAAAATAAT
6162638 TTATAGGA
66 TTATAGGA
* * * *
6162646 TTATACTTTACTAGAATAACCAAAATAAAATGATTTTAAGAGGTTTGAGATTCAAATAGAATAAT
1 TTATACTTTACTAGAATAACCAAAATAAAATGATTTTAAAAGATTAGAGATTCAAATAAAATAAT
6162711 TTATA
66 TTATA
6162716 AGTTAAGGAT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 63 1.00
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.36
Consensus pattern (73 bp):
TTATACTTTACTAGAATAACCAAAATAAAATGATTTTAAAAGATTAGAGATTCAAATAAAATAAT
TTATAGGA
Found at i:6169349 original size:20 final size:20
Alignment explanation
Indices: 6169324--6169373 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 20
6169314 CTCCACATAG
6169324 GGGATTGATCACC-CAAGCAA
1 GGGATTGATC-CCTCAAGCAA
6169344 GGGATTGATCCCTTCAAGCAA
1 GGGATTGATCCC-TCAAGCAA
6169365 GGGATTGAT
1 GGGATTGAT
6169374 TGGGTAAGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.07
20 10 0.36
21 16 0.57
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (20 bp):
GGGATTGATCCCTCAAGCAA
Found at i:6170195 original size:14 final size:15
Alignment explanation
Indices: 6170158--6170198 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
6170148 GTATCAAATT
6170158 TATTTCTAAGCTGCCC
1 TATTTCTAA-CTGCCC
*
6170174 TATTTCTAACTGTCC
1 TATTTCTAACTGCCC
6170189 T-TTTCTAACT
1 TATTTCTAACT
6170199 TTGTCATGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 9 0.38
15 6 0.25
16 9 0.38
ACGTcount: A:0.20, C:0.27, G:0.07, T:0.46
Consensus pattern (15 bp):
TATTTCTAACTGCCC
Found at i:6176399 original size:73 final size:73
Alignment explanation
Indices: 6176268--6176413 Score: 186
Period size: 73 Copynumber: 2.0 Consensus size: 73
6176258 AAAAATCATT
* * * *
6176268 CTCAAACTCTACTAGAATAATCAAAGTAAAATCATTTTAAAAGGTTAAGGTTTGAAATAAAATAA
1 CTCAAACTCTACTAGAATAACCAAAATAAAATCATTTTAAAAGGTTAAGGATTCAAATAAAATAA
*
6176333 TTTATAAG
66 TCTATAAG
* * * * *
6176341 CTCATACTTTACTAGAATAACCAAAATGAAATCATTTTAAAAGGTT-AGAGATTCAAATACAATG
1 CTCAAACTCTACTAGAATAACCAAAATAAAATCATTTTAAAAGGTTAAG-GATTCAAATAAAATA
6176405 ATCTATAAG
65 ATCTATAAG
6176414 TTAATGATCA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
72 2 0.03
73 60 0.97
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.31
Consensus pattern (73 bp):
CTCAAACTCTACTAGAATAACCAAAATAAAATCATTTTAAAAGGTTAAGGATTCAAATAAAATAA
TCTATAAG
Found at i:6179475 original size:18 final size:18
Alignment explanation
Indices: 6179452--6179487 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
6179442 TTTGGACAAT
6179452 GTTTTAGAACTTCAAAAC
1 GTTTTAGAACTTCAAAAC
6179470 GTTTTAGAACTTCAAAAC
1 GTTTTAGAACTTCAAAAC
6179488 TGTAAGATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (18 bp):
GTTTTAGAACTTCAAAAC
Found at i:6192307 original size:14 final size:16
Alignment explanation
Indices: 6192268--6192322 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
6192258 TTTTTATTTA
*
6192268 TATATATTTATATAAT
1 TATATATTTAAATAAT
*
6192284 TATATTTTTAAAT-AT
1 TATATATTTAAATAAT
*
6192299 T-TATATTTAAAAAAT
1 TATATATTTAAATAAT
*
6192314 AATAT-TTTA
1 TATATATTTA
6192323 TTAATTTCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
14 9 0.28
15 9 0.28
16 14 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATATATTTAAATAAT
Found at i:6198752 original size:13 final size:13
Alignment explanation
Indices: 6198722--6198762 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
6198712 TAATAATTTT
*
6198722 AAATATTATATTA
1 AAATATTATATAA
*
6198735 TAATATTATATAA
1 AAATATTATATAA
6198748 AAATA--ATATAA
1 AAATATTATATAA
6198759 AAAT
1 AAAT
6198763 TTTGAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 10 0.40
13 15 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AAATATTATATAA
Found at i:6199395 original size:16 final size:17
Alignment explanation
Indices: 6199374--6199406 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6199364 TCTAATCAAA
6199374 TTTTTA-TATTTAAATT
1 TTTTTATTATTTAAATT
*
6199390 TTTTTATTATTTTAATT
1 TTTTTATTATTTAAATT
6199407 AATAAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTATTATTTAAATT
Found at i:6199833 original size:2 final size:2
Alignment explanation
Indices: 6199826--6199853 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6199816 ATTTCCCCAG
6199826 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
6199854 CCCCTCCCTC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:6200412 original size:22 final size:22
Alignment explanation
Indices: 6200384--6200425 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
6200374 TAATAATTAT
*
6200384 TATTATAATTATGATTAAAAAA
1 TATTATAATTATAATTAAAAAA
6200406 TATTATAATTATAATTAAAA
1 TATTATAATTATAATTAAAA
6200426 TTTTTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTATAATTATAATTAAAAAA
Found at i:6200545 original size:13 final size:14
Alignment explanation
Indices: 6200517--6200545 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6200507 GATATAATAA
6200517 AATAAATTTATATT
1 AATAAATTTATATT
6200531 AATAAATTT-TATT
1 AATAAATTTATATT
6200544 AA
1 AA
6200546 AATTGATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATAAATTTATATT
Found at i:6201070 original size:2 final size:2
Alignment explanation
Indices: 6201063--6201097 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
6201053 TATGAACATT
* *
6201063 TA TA TA TA TA TA TA TA TA TA TT TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6201098 TTAGAAAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:6201240 original size:3 final size:3
Alignment explanation
Indices: 6201232--6201260 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6201222 AACATCACCA
6201232 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
6201261 CCCATAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:6207935 original size:22 final size:24
Alignment explanation
Indices: 6207902--6207957 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 24
6207892 ATAATTATTT
*
6207902 TATAAAAA-TTTATTTAAAT-ATA
1 TATAAAAATTTTATTAAAATAATA
6207924 T-TAAAAATTTTATTAAAATAATA
1 TATAAAAATTTTATTAAAATAATA
*
6207947 TATACAAATTT
1 TATAAAAATTT
6207958 AAAAATCGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 6 0.21
22 11 0.38
23 4 0.14
24 8 0.28
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
TATAAAAATTTTATTAAAATAATA
Found at i:6208819 original size:14 final size:14
Alignment explanation
Indices: 6208800--6208848 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
6208790 AATTAAAAAT
6208800 AATTATAATAATAA
1 AATTATAATAATAA
6208814 AATTATTAA-AATTAA
1 AATTA-TAATAA-TAA
*
6208829 ATATTATAATGATAA
1 A-ATTATAATAATAA
6208844 AATTA
1 AATTA
6208849 AATTAAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
14 11 0.37
15 14 0.47
16 5 0.17
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (14 bp):
AATTATAATAATAA
Found at i:6209051 original size:21 final size:22
Alignment explanation
Indices: 6209027--6209076 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
6209017 AGTACATACT
6209027 ATTTATTTATT-ATATAATAAA
1 ATTTATTTATTAATATAATAAA
* * *
6209048 ATTTATCTGTTAATTTAATAAA
1 ATTTATTTATTAATATAATAAA
6209070 A-TTATTT
1 ATTTATTT
6209077 TAAAATGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (22 bp):
ATTTATTTATTAATATAATAAA
Found at i:6209570 original size:18 final size:16
Alignment explanation
Indices: 6209533--6209571 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
6209523 TGAATTTTAA
*
6209533 ATAAATTTAAAAGATG
1 ATAAATTTAAAACATG
6209549 ATAAATTTAAAATCATTG
1 ATAAATTTAAAA-CA-TG
6209567 ATAAA
1 ATAAA
6209572 AAATAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 1 0.05
18 7 0.35
ACGTcount: A:0.56, C:0.03, G:0.08, T:0.33
Consensus pattern (16 bp):
ATAAATTTAAAACATG
Found at i:6209621 original size:18 final size:18
Alignment explanation
Indices: 6209594--6209631 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
6209584 TTACAAATAG
6209594 ATGATGATGATCATCATC
1 ATGATGATGATCATCATC
*
6209612 ATGATTATGATCATCATC
1 ATGATGATGATCATCATC
6209630 AT
1 AT
6209632 CATTGTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (18 bp):
ATGATGATGATCATCATC
Found at i:6209771 original size:20 final size:20
Alignment explanation
Indices: 6209748--6209793 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
6209738 GTAAAATTTG
6209748 TAAAATTTTTAA-AAAATAAT
1 TAAAATTTTTAATAAAAT-AT
6209768 TAAAA-TTTTAATAAAATAT
1 TAAAATTTTTAATAAAATAT
6209787 TAAAATT
1 TAAAATT
6209794 GATAGATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAAATTTTTAATAAAATAT
Found at i:6210651 original size:18 final size:19
Alignment explanation
Indices: 6210606--6210651 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
6210596 CTTACTATAT
*
6210606 TTTTAAAAATTTATATCAA
1 TTTTAAAAATTTATATAAA
*
6210625 TAATT-AAAA-TTATATAAA
1 T-TTTAAAAATTTATATAAA
6210643 TTTTAAAAA
1 TTTTAAAAA
6210652 AATAATTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 5
0.73 0.10 0.17
Matches are distributed among these distances:
17 2 0.09
18 13 0.59
19 5 0.23
20 2 0.09
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTTAAAAATTTATATAAA
Found at i:6210755 original size:27 final size:26
Alignment explanation
Indices: 6210717--6210779 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 26
6210707 ATAAAATAAA
*
6210717 ATAATATTATTTGATCTAATCTTATTT
1 ATAATATTATTTGATATAATCTTA-TT
* *
6210744 ATAATATTATTTTATATTATCTTATT
1 ATAATATTATTTGATATAATCTTATT
*
6210770 ATAATTTTAT
1 ATAATATTAT
6210780 GTATTAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 11 0.34
27 21 0.66
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.59
Consensus pattern (26 bp):
ATAATATTATTTGATATAATCTTATT
Found at i:6219707 original size:46 final size:46
Alignment explanation
Indices: 6219655--6219746 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
6219645 AGTATTTTTG
* *
6219655 GAGTCACTTTTGTATAGGGTGGCAGAGGTGTTAAAAGGAAGGTTAA
1 GAGTCACTTTTGCATAGAGTGGCAGAGGTGTTAAAAGGAAGGTTAA
*
6219701 GAGTCACTTTTGCATAGAGTGGCGGAGGTGTTAAAAGGAAGGTTAA
1 GAGTCACTTTTGCATAGAGTGGCAGAGGTGTTAAAAGGAAGGTTAA
6219747 ATCTTATGCG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.30, C:0.08, G:0.35, T:0.27
Consensus pattern (46 bp):
GAGTCACTTTTGCATAGAGTGGCAGAGGTGTTAAAAGGAAGGTTAA
Found at i:6229921 original size:17 final size:18
Alignment explanation
Indices: 6229901--6229944 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
6229891 ACTTTTTCTC
*
6229901 AAAAATTGATTTTTT-TG
1 AAAAATTGATTTTTTAAG
*
6229918 -AAAATTTATTTTTTAAG
1 AAAAATTGATTTTTTAAG
6229935 AAAAATTGAT
1 AAAAATTGAT
6229945 ACTTTCAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 13 0.59
17 1 0.05
18 8 0.36
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (18 bp):
AAAAATTGATTTTTTAAG
Found at i:6229959 original size:60 final size:57
Alignment explanation
Indices: 6229815--6230175 Score: 402
Period size: 60 Copynumber: 6.1 Consensus size: 57
6229805 TCTTGTGCAG
* * * * * * *
6229815 GAAAAATTGAAACTTTTAACTTTTCCCTAAAAATATTCTTTTGAAACTTTAATTTCGA
1 GAAAAATTGATACTTTCAACTTTTCTC-AAAAATATTTTTTTGAAAATTTATTTTCAA
* *
6229873 GGAAAATTGATACTTTCAACTTTTTCTCAAAAATTGATTTTTTTGAAAATTTATTTTTTAA
1 GAAAAATTGATACTTTCAAC-TTTTCTCAAAAA-T-ATTTTTTTGAAAATTTA-TTTTCAA
6229934 GAAAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTTGAAAACTTTGATTTTCAA
1 GAAAAATTGATACTTTCAACTTTTCT-CAAAAATATTTTTTTGAAAA-TTT-ATTTTCAA
* *
6229994 GGAAAATTGATACTTTCAACTTTTCTTCAAAAACCT-TTTTTTTGAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTC-TCAAAAA--TATTTTTTTGAAAATTTATTTTCAA
* * * *
6230053 AAAAAATTGATACTTTCAACTTTCTCCCAAAAAAATTTTTTTGGAAACTTTGATTTTCAA
1 GAAAAATTGATACTTTCAACTTT-TCTCAAAAATATTTTTTT-GAAAATTT-ATTTTCAA
* * *
6230113 GAAAAATTGATACTTTCAACTTTTCCTCAAAAAATCTTTTTTTGAAATTTTA-TTTAAA
1 GAAAAATTGATACTTTCAACTTTT-CTC-AAAAATATTTTTTTGAAAATTTATTTTCAA
6230171 GAAAA
1 GAAAA
6230176 TAAAAATAAA
Statistics
Matches: 262, Mismatches: 25, Indels: 32
0.82 0.08 0.10
Matches are distributed among these distances:
58 39 0.15
59 63 0.24
60 104 0.40
61 55 0.21
62 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (57 bp):
GAAAAATTGATACTTTCAACTTTTCTCAAAAATATTTTTTTGAAAATTTATTTTCAA
Found at i:6229966 original size:119 final size:118
Alignment explanation
Indices: 6229815--6230167 Score: 482
Period size: 119 Copynumber: 3.0 Consensus size: 118
6229805 TCTTGTGCAG
* * * * *
6229815 GAAAAATTGAAACTTTTAACTTTTC-CCTAAAAATATTCTTTTGAAACTTT-AATTTCGAGGAAA
1 GAAAAATTGATACTTTCAACTTTTCTCC-AAAAATATTTTTTTGAAACTTTGATTTTCAAGGAAA
*
6229878 ATTGATACTTTCAACTTTTTCTCAAAAATTGATTTTTTTGAAAATTTATTTTTTAA
65 ATTGATACTTTCAACTTTTTCTCAAAAAAT--TTTTTTTGAAAATTTATTTTTTAA
6229934 GAAAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTTGAAAACTTTGATTTTCAAGGAAA
1 GAAAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTTG-AAACTTTGATTTTCAAGGAAA
*
6229999 ATTGATACTTTCAAC-TTTTCTTCAAAAACCTTTTTTTTGAAAATTTA-TTTTTAA
65 ATTGATACTTTCAACTTTTTC-TCAAAAA-ATTTTTTTTGAAAATTTATTTTTTAA
* * *
6230053 AAAAAATTGATACTTTCAAC-TTTCTCCCAAAAAAATTTTTTTGGAAACTTTGATTTTCAAGAAA
1 GAAAAATTGATACTTTCAACTTTTCT-CCAAAAATATTTTTTT-GAAACTTTGATTTTCAAGGAA
* *
6230117 AATTGATACTTTCAACTTTTCCTCAAAAAATCTTTTTTTGAAATTTTATTT
64 AATTGATACTTTCAACTTTTTCTCAAAAAAT-TTTTTTTGAAAATTTATTT
6230168 AAAGAAAATA
Statistics
Matches: 212, Mismatches: 12, Indels: 19
0.87 0.05 0.08
Matches are distributed among these distances:
118 6 0.03
119 135 0.64
120 37 0.17
121 33 0.16
122 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (118 bp):
GAAAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTTGAAACTTTGATTTTCAAGGAAAA
TTGATACTTTCAACTTTTTCTCAAAAAATTTTTTTTGAAAATTTATTTTTTAA
Found at i:6230193 original size:12 final size:11
Alignment explanation
Indices: 6230172--6230232 Score: 52
Period size: 11 Copynumber: 5.4 Consensus size: 11
6230162 TTATTTAAAG
6230172 AAAATAAAAAT
1 AAAATAAAAAT
6230183 AAAAGTAAAAAT
1 AAAA-TAAAAAT
*
6230195 AAATTAAAAA-
1 AAAATAAAAAT
* *
6230205 AATAATGAGAAGT
1 AA-AAT-AAAAAT
*
6230218 AAAACAAAAAT
1 AAAATAAAAAT
6230229 AAAA
1 AAAA
6230233 ATAAGATAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
10 2 0.05
11 20 0.51
12 15 0.38
13 2 0.05
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.16
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:6230204 original size:119 final size:118
Alignment explanation
Indices: 6229959--6230207 Score: 261
Period size: 119 Copynumber: 2.1 Consensus size: 118
6229949 TCAACTTTTC
* * *
6229959 TCCAAAAATATTTTTTTGAAAACTTTGATTTTCAAGGAAAATTGATACTTTCAACTTTTCTTCAA
1 TCCAAAAAAATTTTTTTGAAAACTTTGATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAA
** * * ** ** * ***
6230024 AAACCTTTTTTTTGAAAATTTATTTTTAAAAAAAATTGATACTTTCAACTTTC
66 AAACCTTTTTTTTGAAAATTTATTTAGAAAAAAAAATGAAAAGTAAAAATAAA
*
6230077 TCCCAAAAAAATTTTTTTGGAAACTTTGATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCA
1 T-CCAAAAAAATTTTTTTGAAAACTTTGATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCA
* *
6230142 AAAA-ATCTTTTTTTGAAATTTTATTTAAAGAAAATAAAAAT-AAAAGTAAAAATAAA
65 AAAACCT-TTTTTTTGAAAATTTATTT--AGAAAA-AAAAATGAAAAGTAAAAATAAA
*
6230198 T-TAAAAAAAT
1 TCCAAAAAAAT
6230208 AATGAGAAGT
Statistics
Matches: 107, Mismatches: 19, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
118 2 0.02
119 89 0.83
121 11 0.10
122 5 0.05
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.41
Consensus pattern (118 bp):
TCCAAAAAAATTTTTTTGAAAACTTTGATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAA
AAACCTTTTTTTTGAAAATTTATTTAGAAAAAAAAATGAAAAGTAAAAATAAA
Found at i:6231328 original size:11 final size:11
Alignment explanation
Indices: 6231302--6231372 Score: 65
Period size: 11 Copynumber: 6.3 Consensus size: 11
6231292 TATTTAAAAT
*
6231302 AATAATAATAAA
1 AATAAAAAT-AA
6231314 AATAAAAATAA
1 AATAAAAATAA
* *
6231325 AATAGAGATAA
1 AATAAAAATAA
6231336 AATAAAAATATA
1 AATAAAAATA-A
6231348 AATACAAAA-AA
1 AATA-AAAATAA
6231359 AAGTAAAAA-AA
1 AA-TAAAAATAA
6231370 AAT
1 AAT
6231373 GAAGAGAATA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
10 1 0.02
11 30 0.59
12 16 0.31
13 4 0.08
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.18
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:6231343 original size:6 final size:6
Alignment explanation
Indices: 6231302--6231371 Score: 58
Period size: 6 Copynumber: 12.2 Consensus size: 6
6231292 TATTTAAAAT
* * * *
6231302 AATAAT AATAAA AATAAA AAT-AA AATAGA GAT-AA AATAAA AATATA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
*
6231348 AATACAA AA-AAA AGTAAA AA-AAA A
1 AATA-AA AATAAA AATAAA AATAAA A
6231372 TGAAGAGAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
5 15 0.29
6 33 0.65
7 3 0.06
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:6231359 original size:17 final size:16
Alignment explanation
Indices: 6231308--6231371 Score: 58
Period size: 17 Copynumber: 3.8 Consensus size: 16
6231298 AAATAATAAT
6231308 AATAAAAATAAAAATAA
1 AATAAAAATAAAAA-AA
* *
6231325 AATAGAGATAAAATAAA
1 AATAAAAATAAAA-AAA
*
6231342 AATATAAATACAAAAAA
1 AATAAAAATA-AAAAAA
6231359 AAGTAAAAA-AAAA
1 AA-TAAAAATAAAA
6231372 TGAAGAGAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
16 3 0.08
17 27 0.69
18 9 0.23
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.16
Consensus pattern (16 bp):
AATAAAAATAAAAAAA
Found at i:6231359 original size:22 final size:22
Alignment explanation
Indices: 6231311--6231372 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
6231301 TAATAATAAT
*
6231311 AAAAATAAAAATAAAATAGAGA
1 AAAAATAAAAATAAAATACAGA
* *
6231333 TAAAATAAAAATATAAATACAAA
1 AAAAATAAAAATA-AAATACAGA
6231356 AAAAAGTAAAAA-AAAAT
1 AAAAA-TAAAAATAAAAT
6231373 GAAGAGAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
22 16 0.47
23 12 0.35
24 6 0.18
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (22 bp):
AAAAATAAAAATAAAATACAGA
Found at i:6233720 original size:19 final size:19
Alignment explanation
Indices: 6233684--6233720 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6233674 CCTTATCATT
**
6233684 TTTCAAAATTTATTTTTTA
1 TTTCAAAATTTAAATTTTA
6233703 TTTCAAAATTTAAATTTT
1 TTTCAAAATTTAAATTTT
6233721 CAAAATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTCAAAATTTAAATTTTA
Found at i:6238113 original size:27 final size:27
Alignment explanation
Indices: 6238083--6238135 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
6238073 ATACAAGTAA
*
6238083 ATTTTGATAATTTTTTATATAATTTTG
1 ATTTTGATAATTTTTAATATAATTTTG
6238110 ATTTTGATAATTTTTAATATAATTTT
1 ATTTTGATAATTTTTAATATAATTTT
6238136 AATAACCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (27 bp):
ATTTTGATAATTTTTAATATAATTTTG
Found at i:6238121 original size:15 final size:14
Alignment explanation
Indices: 6238083--6238123 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 14
6238073 ATACAAGTAA
6238083 ATTTTGATAATTTT
1 ATTTTGATAATTTT
*
6238097 -TTAT-ATAATTTT
1 ATTTTGATAATTTT
6238109 GATTTTGATAATTTT
1 -ATTTTGATAATTTT
6238124 TAATATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
12 8 0.36
13 3 0.14
14 3 0.14
15 8 0.36
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.63
Consensus pattern (14 bp):
ATTTTGATAATTTT
Found at i:6238134 original size:21 final size:21
Alignment explanation
Indices: 6238110--6238197 Score: 88
Period size: 21 Copynumber: 4.2 Consensus size: 21
6238100 TATAATTTTG
* *
6238110 ATTTTGATAATTTTTAATATA
1 ATTTTGATAACTTTTGATATA
* * *
6238131 ATTTTAATAACCTTTGATATT
1 ATTTTGATAACTTTTGATATA
* * *
6238152 AGTTTGGTTACTTTTGATATA
1 ATTTTGATAACTTTTGATATA
*
6238173 ATTTTGATAACTGTTGATA-A
1 ATTTTGATAACTTTTGATATA
6238193 ATTTT
1 ATTTT
6238198 TTTATATAAC
Statistics
Matches: 52, Mismatches: 15, Indels: 1
0.76 0.22 0.01
Matches are distributed among these distances:
20 6 0.12
21 46 0.88
ACGTcount: A:0.32, C:0.05, G:0.10, T:0.53
Consensus pattern (21 bp):
ATTTTGATAACTTTTGATATA
Found at i:6238433 original size:22 final size:22
Alignment explanation
Indices: 6238407--6238643 Score: 187
Period size: 22 Copynumber: 10.8 Consensus size: 22
6238397 GACTATTATG
*
6238407 TTATCTATGATTTACTACTAAA
1 TTATCAATGATTTACTACTAAA
* * *
6238429 CTATCAATGATATATTACTAAA
1 TTATCAATGATTTACTACTAAA
*
6238451 TTATCAATGATTTACTATTAAA
1 TTATCAATGATTTACTACTAAA
* * *
6238473 TTAGT-ATTGATTTGCTACTAAT
1 TTA-TCAATGATTTACTACTAAA
* * *
6238495 TTATAAATGATTTACTATTAAG
1 TTATCAATGATTTACTACTAAA
* * *
6238517 CTATAAATGATTTATTACTAAA
1 TTATCAATGATTTACTACTAAA
* *
6238539 TTATTAATGATTTACTACTAAG
1 TTATCAATGATTTACTACTAAA
*
6238561 TTATCGATGCATTGT--TA-TAAA
1 TTATCAATG-ATT-TACTACTAAA
* *
6238582 GTTAT-AACTGATTTACTATTAAT
1 -TTATCAA-TGATTTACTACTAAA
* *
6238605 TTATCAATGAATTACTACAAAA
1 TTATCAATGATTTACTACTAAA
* *
6238627 TTATCAATAATTAACTA
1 TTATCAATGATTTACTA
6238644 ATTTACTACT
Statistics
Matches: 169, Mismatches: 36, Indels: 20
0.75 0.16 0.09
Matches are distributed among these distances:
20 1 0.01
21 8 0.05
22 150 0.89
23 9 0.05
24 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (22 bp):
TTATCAATGATTTACTACTAAA
Found at i:6238461 original size:44 final size:44
Alignment explanation
Indices: 6238407--6238742 Score: 191
Period size: 44 Copynumber: 7.5 Consensus size: 44
6238397 GACTATTATG
* * *
6238407 TTATCTATGATTTACTACTAAACTATCAATGATATATTACTAAA
1 TTATCAATGATTTACTATTAAATTATCAATGATATATTACTAAA
* * ** *
6238451 TTATCAATGATTTACTATTAAATTAGT-ATTGATTTGCTACTAAT
1 TTATCAATGATTTACTATTAAATTA-TCAATGATATATTACTAAA
* ** * *
6238495 TTATAAATGATTTACTATTAAGCTATAAATGATTTATTACTAAA
1 TTATCAATGATTTACTATTAAATTATCAATGATATATTACTAAA
* * * * *
6238539 TTATTAATGATTTACTACTAAGTTATCGATGCAT-TGTTA-TAAA
1 TTATCAATGATTTACTATTAAATTATCAATG-ATATATTACTAAA
* * *
6238582 GTTAT-AACTGATTTACTATTAATTTATCAATGA-ATTACTACAAAA
1 -TTATCAA-TGATTTACTATTAAATTATCAATGATA-TATTACTAAA
* * * * ** *
6238627 TTATCAATAATTAACTAATTTACTACTAAATTATCATTGATTTACAATTAAA
1 TTATC-------AA-TGATTTACTATTAAATTATCAATGATATATTACTAAA
* * * *
6238679 TTATTAATGATTTACTATTAAGTTATCAATAGTTTACATT--TAAA
1 TTATCAATGATTTACTATTAAATTATCAAT-G-ATATATTACTAAA
*
6238723 TTATCAATAATTTACTATTA
1 TTATCAATGATTTACTATTA
6238743 TGTTATTATA
Statistics
Matches: 226, Mismatches: 47, Indels: 38
0.73 0.15 0.12
Matches are distributed among these distances:
43 8 0.04
44 172 0.76
45 9 0.04
46 2 0.01
52 35 0.15
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (44 bp):
TTATCAATGATTTACTATTAAATTATCAATGATATATTACTAAA
Found at i:6238468 original size:66 final size:64
Alignment explanation
Indices: 6238392--6238761 Score: 224
Period size: 66 Copynumber: 5.5 Consensus size: 64
6238382 AAGTTATTTT
* ** *
6238392 TGATTGACTATTATGTTATCTATGATTTACTACTAAACTATCAATGATATATTACTAAATTATCA
1 TGATTTACTATTAAATTAT-TATGATTTACTACTAAATTATCAATGATATATTA-TAAATTATCA
6238457 A
64 A
* * * * * * ** *
6238458 TGATTTACTATTAAATTAGTATTGATTTGCTACTAATTTATAAATGATTTACTATTAAGCTATAA
1 TGATTTACTATTAAATTATTA-TGATTTACTACTAAATTATCAATGATATATTA-TAAATTATCA
6238523 A
64 A
* * * * *
6238524 TGATTTATTACTAAATTATTAATGATTTACTACTAAGTTATCGATGCAT-TGTTATAAAGTTAT-
1 TGATTTACTATTAAATTATT-ATGATTTACTACTAAATTATCAATG-ATATATTATAAA-TTATC
6238587 AA
63 AA
* * * * *
6238589 CTGATTTACTATTAATTTATCAATGAATTACTACAAAATTATCAATAATTAACTAATTTACTACT
1 -TGATTTACTATTAAATTAT-TATGATTTACTACTAAATTATCAATGA-T-A-T-A--T--TA-T
*
6238654 AAATTATCAT
55 AAATTATCAA
* * * * *
6238664 TGATTTACAATTAAATTATTAATGATTTACTATTAAGTTATCAATAGTTTACATT-TAAATTATC
1 TGATTTACTATTAAATTATT-ATGATTTACTACTAAATTATCAAT-G-ATATATTATAAATTATC
6238728 AA
63 AA
* ** *
6238730 TAATTTACTATTATGTTATTATACATTTACTA
1 TGATTTACTATTAAATTATTAT-GATTTACTA
6238762 TTATGTTATC
Statistics
Matches: 231, Mismatches: 52, Indels: 42
0.71 0.16 0.13
Matches are distributed among these distances:
65 10 0.04
66 163 0.71
67 3 0.01
68 1 0.00
69 1 0.00
70 1 0.00
72 2 0.01
74 44 0.19
75 6 0.03
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.45
Consensus pattern (64 bp):
TGATTTACTATTAAATTATTATGATTTACTACTAAATTATCAATGATATATTATAAATTATCAA
Found at i:6238748 original size:22 final size:22
Alignment explanation
Indices: 6238642--6238901 Score: 116
Period size: 22 Copynumber: 11.9 Consensus size: 22
6238632 AATAATTAAC
* *
6238642 TAATTTACTACTAAATTATCAT
1 TAATTTACTATTAAATTATCAA
* * *
6238664 TGATTTACAATTAAATTATTAA
1 TAATTTACTATTAAATTATCAA
* *
6238686 TGATTTACTATTAAGTTATCAA
1 TAATTTACTATTAAATTATCAA
*
6238708 TAGTTTAC-ATTTAAATTATCAA
1 TAATTTACTA-TTAAATTATCAA
** *
6238730 TAATTTACTATTATGTTAT-TA
1 TAATTTACTATTAAATTATCAA
** *
6238751 TACATTTACTATTATGTTATCAT
1 TA-ATTTACTATTAAATTATCAA
* * * * * *
6238774 TGATTTATTGCTT-AGTTTTTAA
1 TAATTTACT-ATTAAATTATCAA
* **
6238796 TTATTTACTACAAAATTAT-AA
1 TAATTTACTATTAAATTATCAA
* * * * **
6238817 CAATTTTATTACTAAATTAACCG
1 TAA-TTTACTATTAAATTATCAA
* * * * * *
6238840 TGATTCATTATCAAGTTATCAG
1 TAATTTACTATTAAATTATCAA
* *
6238862 TAATTTA-AATTAAATTATCCA
1 TAATTTACTATTAAATTATCAA
6238883 TAATTTACTATTAAATTAT
1 TAATTTACTATTAAATTAT
6238902 TTAACTATTA
Statistics
Matches: 175, Mismatches: 54, Indels: 18
0.71 0.22 0.07
Matches are distributed among these distances:
21 23 0.13
22 147 0.84
23 5 0.03
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.47
Consensus pattern (22 bp):
TAATTTACTATTAAATTATCAA
Found at i:6238903 original size:15 final size:16
Alignment explanation
Indices: 6238885--6238918 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
6238875 ATTATCCATA
6238885 ATTT-ACTATTAAATT
1 ATTTAACTATTAAATT
*
6238900 ATTTAACTATTAAGTT
1 ATTTAACTATTAAATT
6238916 ATT
1 ATT
6238919 AATAATTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (16 bp):
ATTTAACTATTAAATT
Found at i:6239084 original size:22 final size:22
Alignment explanation
Indices: 6239059--6239105 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
6239049 ACTAAAACTG
*
6239059 ATTTACCATTAAGTTATCATTA
1 ATTTACCATTAAGTTATCAATA
* *
6239081 ATTTACTATTTAGTTATCAATA
1 ATTTACCATTAAGTTATCAATA
6239103 ATT
1 ATT
6239106 GACTACAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.49
Consensus pattern (22 bp):
ATTTACCATTAAGTTATCAATA
Found at i:6239117 original size:22 final size:22
Alignment explanation
Indices: 6239069--6239117 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
6239059 ATTTACCATT
* * **
6239069 AAGTTATCATTAATTTACTATT
1 AAGTTATCAATAATTGACTACA
*
6239091 TAGTTATCAATAATTGACTACA
1 AAGTTATCAATAATTGACTACA
6239113 AAGTT
1 AAGTT
6239118 GTTACTTGTT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (22 bp):
AAGTTATCAATAATTGACTACA
Found at i:6239451 original size:22 final size:22
Alignment explanation
Indices: 6239439--6239539 Score: 103
Period size: 22 Copynumber: 4.6 Consensus size: 22
6239429 TACTTTTAAG
6239439 TTATCAATAATTTATTACTAAA
1 TTATCAATAATTTATTACTAAA
* *
6239461 TTATCAATAATTTATTTCTAAT
1 TTATCAATAATTTATTACTAAA
* * * *
6239483 TTATGAACAATTTGTTATTAAA
1 TTATCAATAATTTATTACTAAA
* * * *
6239505 TTATGAATGATTTATCATTAAA
1 TTATCAATAATTTATTACTAAA
*
6239527 TTATTAATAATTT
1 TTATCAATAATTT
6239540 CTATTAAATT
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 65 1.00
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.50
Consensus pattern (22 bp):
TTATCAATAATTTATTACTAAA
Found at i:6239474 original size:44 final size:44
Alignment explanation
Indices: 6239426--6239519 Score: 109
Period size: 44 Copynumber: 2.1 Consensus size: 44
6239416 GTTATTAGTT
*
6239426 ATTTACTTT-TAAGTTATCAATAATTTATTACTAAATTATCAATA
1 ATTTA-TTTCTAAGTTATCAACAATTTATTACTAAATTATCAATA
* * * * * *
6239470 ATTTATTTCTAATTTATGAACAATTTGTTATTAAATTATGAATG
1 ATTTATTTCTAAGTTATCAACAATTTATTACTAAATTATCAATA
6239514 ATTTAT
1 ATTTAT
6239520 CATTAAATTA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 3 0.07
44 39 0.93
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.50
Consensus pattern (44 bp):
ATTTATTTCTAAGTTATCAACAATTTATTACTAAATTATCAATA
Found at i:6239475 original size:11 final size:11
Alignment explanation
Indices: 6239439--6239539 Score: 58
Period size: 11 Copynumber: 9.2 Consensus size: 11
6239429 TACTTTTAAG
*
6239439 TTATCAATAAT
1 TTATTAATAAT
* *
6239450 TTATTACTAAA
1 TTATTAATAAT
*
6239461 TTATCAATAAT
1 TTATTAATAAT
**
6239472 TTATTTCTAAT
1 TTATTAATAAT
* *
6239483 TTATGAACAAT
1 TTATTAATAAT
* * *
6239494 TTGTTATTAAA
1 TTATTAATAAT
* *
6239505 TTATGAATGAT
1 TTATTAATAAT
* * *
6239516 TTATCATTAAA
1 TTATTAATAAT
6239527 TTATTAATAAT
1 TTATTAATAAT
6239538 TT
1 TT
6239540 CTATTAAATT
Statistics
Matches: 60, Mismatches: 30, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
11 60 1.00
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.50
Consensus pattern (11 bp):
TTATTAATAAT
Found at i:6239539 original size:44 final size:42
Alignment explanation
Indices: 6239434--6239549 Score: 106
Period size: 44 Copynumber: 2.7 Consensus size: 42
6239424 TTATTTACTT
* * *
6239434 TTAAGTTATCAATAATTTATTACTAAATTATCAATAATTTATT
1 TTAAATTATCAATAATTT-TTATTAAATTATCAATAATTTATA
* * * * *
6239477 TCTAATTTATGAACAATTTGTTATTAAATTATGAATGATTTATCA
1 T-TAAATTATCAATAATTT-TTATTAAATTATCAATAATTTAT-A
* *
6239522 TTAAATTATTAATAATTTCTATTAAATT
1 TTAAATTATCAATAATTTTTATTAAATT
6239550 GTTGGCAATT
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
43 10 0.17
44 48 0.81
45 1 0.02
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (42 bp):
TTAAATTATCAATAATTTTTATTAAATTATCAATAATTTATA
Found at i:6239859 original size:22 final size:20
Alignment explanation
Indices: 6239792--6239860 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 20
6239782 TTTTCAATTG
*
6239792 TTTACTACAAATTATTATCGA
1 TTTACAACAAATTATTAT-GA
* *
6239813 TTTACCACTAAATTATTTATAA
1 TTTACAAC-AAATTA-TTATGA
6239835 TTTACAACAAAGTTATTACTGA
1 TTTACAACAAA-TTATTA-TGA
6239857 TTTA
1 TTTA
6239861 TATTAAATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 13 0.32
22 23 0.57
23 4 0.10
ACGTcount: A:0.39, C:0.13, G:0.04, T:0.43
Consensus pattern (20 bp):
TTTACAACAAATTATTATGA
Found at i:6239893 original size:22 final size:21
Alignment explanation
Indices: 6239844--6240022 Score: 112
Period size: 22 Copynumber: 8.2 Consensus size: 21
6239834 ATTTACAACA
*
6239844 AAGTTATTACTGATTTA-TATT
1 AAGTTATCA-TGATTTATTATT
*
6239865 AAATTATGCATGATTTATTATT
1 AAGTTAT-CATGATTTATTATT
* *
6239887 AAGTTATCACTAATTAATTATT
1 AAGTTATCA-TGATTTATTATT
* *
6239909 ATGTTATCGATGATTTACTATT
1 AAGTTATC-ATGATTTATTATT
*
6239931 AAGTTA-AATTGATTTACTT-TT
1 AAGTTATCA-TGATTTA-TTATT
* * * *
6239952 AAGTTTTCAATAATTAACTATT
1 AAGTTATC-ATGATTTATTATT
* *
6239974 AAATTATCAATTATTTATTATT
1 AAGTTATC-ATGATTTATTATT
* * *
6239996 AATTTATCATTGACTTACTATT
1 AAGTTATCA-TGATTTATTATT
6240018 AAGTT
1 AAGTT
6240023 TTTATAATTT
Statistics
Matches: 121, Mismatches: 27, Indels: 19
0.72 0.16 0.11
Matches are distributed among these distances:
20 1 0.01
21 31 0.26
22 87 0.72
23 2 0.02
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (21 bp):
AAGTTATCATGATTTATTATT
Found at i:6240030 original size:65 final size:64
Alignment explanation
Indices: 6239854--6240036 Score: 172
Period size: 65 Copynumber: 2.8 Consensus size: 64
6239844 AAGTTATTAC
* * * * ** *
6239854 TGATTTATATTAAATTATGCA-TGATTTATTATTAAGTTATCACTAATTAATTATTATGTTATCG
1 TGATTTATATTAAATTAT-CATTGATTTACTATTAAGTT-TTAATAATTAACTATTAAATTATCA
6239918 A
64 A
* * *
6239919 TGATTTACTATTAAGTTA-AATTGATTTACTTTTAAGTTTTCAATAATTAACTATTAAATTATCA
1 TGATTTA-TATTAAATTATCATTGATTTACTATTAAGTTTT-AATAATTAACTATTAAATTATCA
6239983 A
64 A
* * * * *
6239984 TTATTTATTATTAATTTATCATTGACTTACTATTAAGTTTTTATAATTTACTA
1 TGATTTA-TATTAAATTATCATTGATTTACTATTAAGTTTTAATAATTAACTA
6240037 CTGTCAATTA
Statistics
Matches: 96, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
64 2 0.02
65 66 0.69
66 28 0.29
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.51
Consensus pattern (64 bp):
TGATTTATATTAAATTATCATTGATTTACTATTAAGTTTTAATAATTAACTATTAAATTATCAA
Found at i:6240080 original size:22 final size:22
Alignment explanation
Indices: 6240052--6240101 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
6240042 AATTAATTAT
6240052 TATTAAACTAAAACTAATTTAC
1 TATTAAACTAAAACTAATTTAC
* ** *
6240074 TATTAAATTATTACTAATTTAG
1 TATTAAACTAAAACTAATTTAC
6240096 TATTAA
1 TATTAA
6240102 GTTATTATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (22 bp):
TATTAAACTAAAACTAATTTAC
Found at i:6240106 original size:22 final size:22
Alignment explanation
Indices: 6240064--6240374 Score: 102
Period size: 22 Copynumber: 14.3 Consensus size: 22
6240054 TTAAACTAAA
6240064 ACTAATTTACTATTAAATTATT
1 ACTAATTTACTATTAAATTATT
* *
6240086 ACTAATTTAGTATTAAGTTATT
1 ACTAATTTACTATTAAATTATT
* * * *
6240108 ATTAATTTA-TTTCTAAGTTATC
1 ACTAATTTACTAT-TAAATTATT
* * * *
6240130 A-AAATTAACTACTAAATTATC
1 ACTAATTTACTATTAAATTATT
* *
6240151 ACTTATTT-TTATTAAATTA-T
1 ACTAATTTACTATTAAATTATT
* * * * ***
6240171 CCTTGATTTAGTACTGTGTTATT
1 AC-TAATTTACTATTAAATTATT
* * *
6240194 A-TACATTTACAACTAAATTATA
1 ACTA-ATTTACTATTAAATTATT
* *
6240216 ATTGATTTA-TCATT-AATGTATT
1 ACTAATTTACT-ATTAAAT-TATT
* * * *
6240238 A-TGTATATATTATTATATTATT
1 ACT-AATTTACTATTAAATTATT
* ** *
6240260 ACTGATTTACTAAAAAATTATC
1 ACTAATTTACTATTAAATTATT
* * *
6240282 AATTATTTACTAGTAAATTATT
1 ACTAATTTACTATTAAATTATT
* * *
6240304 ATTTATTTACTATTAAATTATC
1 ACTAATTTACTATTAAATTATT
* * * *
6240326 ACTAATTTAATACTAAGTTACT
1 ACTAATTTACTATTAAATTATT
* *
6240348 AATAA-TTACTATTAAGTTA-T
1 ACTAATTTACTATTAAATTATT
6240368 ACTAATT
1 ACTAATT
6240375 ACATTTAAGT
Statistics
Matches: 210, Mismatches: 64, Indels: 31
0.69 0.21 0.10
Matches are distributed among these distances:
20 6 0.03
21 48 0.23
22 150 0.71
23 6 0.03
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.48
Consensus pattern (22 bp):
ACTAATTTACTATTAAATTATT
Found at i:6240375 original size:20 final size:20
Alignment explanation
Indices: 6240310--6240385 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 20
6240300 TATTATTTAT
*
6240310 TTACTATTAAATTATCACTAA
1 TTACTATTAAGTTAT-ACTAA
* * *
6240331 TTTAATACTAAGTTACTAATAA
1 -TTACTATTAAGTTA-TACTAA
6240353 TTACTATTAAGTTATACTAA
1 TTACTATTAAGTTATACTAA
6240373 TTAC-ATTTAAGTT
1 TTACTA-TTAAGTT
6240386 TTTAATGATT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 1 0.02
20 16 0.36
21 12 0.27
22 15 0.33
23 1 0.02
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.45
Consensus pattern (20 bp):
TTACTATTAAGTTATACTAA
Found at i:6244184 original size:8 final size:8
Alignment explanation
Indices: 6244171--6244201 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
6244161 ATTAAACTTA
6244171 AATAAATT
1 AATAAATT
6244179 AATAAATT
1 AATAAATT
6244187 AATAAATT
1 AATAAATT
6244195 ATATAAA
1 A-ATAAA
6244202 CTCTATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.77
9 5 0.23
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AATAAATT
Found at i:6244185 original size:68 final size:68
Alignment explanation
Indices: 6244113--6244256 Score: 188
Period size: 68 Copynumber: 2.1 Consensus size: 68
6244103 ATTAAAATTT
*
6244113 TAAATAGTTTAATTTTATATAAACTC-TTTTCAATATTAATTGATTTAAATTAAACTTAAATAAA
1 TAAATAGTTTAA-ATTATATAAACTCATTTTCAATATTAATTGATTTAAATTAAACTTAAATAAA
6244177 TTAA
65 TTAA
* * * *
6244181 TAAAT--TAATAAATTATATAAACTCTATTTTTAATTTTAATTGATTTAAATTAAACTTATATAA
1 TAAATAGT-TTAAATTATATAAACTC-ATTTTCAATATTAATTGATTTAAATTAAACTTAAATAA
6244244 ATTAA
64 ATTAA
6244249 TAAA-AGTT
1 TAAATAGTT
6244257 ATATATTTAA
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
66 13 0.20
67 3 0.05
68 48 0.74
69 1 0.02
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.46
Consensus pattern (68 bp):
TAAATAGTTTAAATTATATAAACTCATTTTCAATATTAATTGATTTAAATTAAACTTAAATAAAT
TAA
Found at i:6252232 original size:22 final size:21
Alignment explanation
Indices: 6252180--6252240 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 21
6252170 AATCAACAAC
*
6252180 AAAAATTAACTTAAATTCAAA
1 AAAAATTAACTTAAAATCAAA
*
6252201 ATAAACTTAACTTGAATAAT-AAA
1 A-AAAATTAACTT-AA-AATCAAA
6252224 AAAAATTAA-TTCAAAAT
1 AAAAATTAACTT-AAAAT
6252241 TAAATTGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
20 3 0.09
21 5 0.15
22 17 0.52
23 6 0.18
24 2 0.06
ACGTcount: A:0.61, C:0.08, G:0.02, T:0.30
Consensus pattern (21 bp):
AAAAATTAACTTAAAATCAAA
Found at i:6253132 original size:2 final size:2
Alignment explanation
Indices: 6253125--6253172 Score: 80
Period size: 2 Copynumber: 24.0 Consensus size: 2
6253115 GAGCTTCTTT
6253125 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
6253167 TA TA TA
1 TA TA TA
6253173 GGCTCCTAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 42 0.95
3 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:6255084 original size:14 final size:13
Alignment explanation
Indices: 6255051--6255105 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 13
6255041 GAAGTTCTCT
6255051 ACTAAAAATTATTAA
1 ACTAAAAATTA--AA
6255066 A-TAAAAATTAAA
1 ACTAAAAATTAAA
6255078 ATCT-AAAATTAAA
1 A-CTAAAAATTAAA
*
6255091 ACAAATAAATTAAA
1 ACTAA-AAATTAAA
6255105 A
1 A
6255106 GGTCTTGCTA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
12 4 0.11
13 11 0.31
14 19 0.54
15 1 0.03
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.27
Consensus pattern (13 bp):
ACTAAAAATTAAA
Found at i:6255326 original size:10 final size:10
Alignment explanation
Indices: 6255311--6255344 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
6255301 TATAAATTTG
6255311 AATTTTATTA
1 AATTTTATTA
6255321 AATTTTATTAA
1 AATTTTATT-A
6255332 AATTTTTATTA
1 AA-TTTTATTA
6255343 AA
1 AA
6255345 CCAATTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.41
11 6 0.27
12 7 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
AATTTTATTA
Found at i:6255340 original size:12 final size:11
Alignment explanation
Indices: 6255311--6255344 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
6255301 TATAAATTTG
6255311 AATTTTATT-A
1 AATTTTATTAA
6255321 AATTTTATTAA
1 AATTTTATTAA
6255332 AATTTTTATTAA
1 AA-TTTTATTAA
6255344 A
1 A
6255345 CCAATTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 9 0.41
11 3 0.14
12 10 0.45
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
AATTTTATTAA
Found at i:6260707 original size:2 final size:2
Alignment explanation
Indices: 6260700--6260726 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6260690 TCAAGAGATT
6260700 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
6260727 TAGGCACCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6265663 original size:31 final size:30
Alignment explanation
Indices: 6265619--6265762 Score: 123
Period size: 30 Copynumber: 4.8 Consensus size: 30
6265609 AATGATTTAT
*
6265619 ATTAAGAATTTATTTAAATATAAATTAAAAG
1 ATTAAAAATTTATTTAAATATAAATT-AAAG
* * *
6265650 TTTAAAGATTTATTTGAATATAAATTAAAG
1 ATTAAAAATTTATTTAAATATAAATTAAAG
* * * * *
6265680 ACTAAAAACTTATTTGAGTGTAAATTAAAG
1 ATTAAAAATTTATTTAAATATAAATTAAAG
* * * *
6265710 ATTAAGAGTTTATTTAAATGT-AA-TAAAA
1 ATTAAAAATTTATTTAAATATAAATTAAAG
*
6265738 ATATAAAAATTTATCTAAATA-AAAT
1 AT-TAAAAATTTATTTAAATATAAAT
6265763 AATAAAATAT
Statistics
Matches: 89, Mismatches: 21, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
28 6 0.07
29 18 0.20
30 43 0.48
31 22 0.25
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.38
Consensus pattern (30 bp):
ATTAAAAATTTATTTAAATATAAATTAAAG
Found at i:6271719 original size:31 final size:30
Alignment explanation
Indices: 6271684--6271749 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 30
6271674 ATGTTATCAG
6271684 TAAATCAAATGATAATAATTTATTAATAAAA
1 TAAATCAAATGATAATAATTTATTAAT-AAA
* * * *
6271715 TAAATTATATGATAATATTTTATTAATGAA
1 TAAATCAAATGATAATAATTTATTAATAAA
6271745 TAAAT
1 TAAAT
6271750 TTTATAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 7 0.23
31 24 0.77
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.41
Consensus pattern (30 bp):
TAAATCAAATGATAATAATTTATTAATAAA
Found at i:6271743 original size:17 final size:17
Alignment explanation
Indices: 6271691--6271743 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 17
6271681 CAGTAAATCA
6271691 AATGATAATAATTTATT
1 AATGATAATAATTTATT
* *
6271708 AAT-AAAATAAATTA-T
1 AATGATAATAATTTATT
*
6271723 -ATGATAATATTTTATT
1 AATGATAATAATTTATT
6271739 AATGA
1 AATGA
6271744 ATAAATTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
14 2 0.07
15 9 0.32
16 10 0.36
17 7 0.25
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (17 bp):
AATGATAATAATTTATT
Found at i:6271764 original size:31 final size:31
Alignment explanation
Indices: 6271697--6271764 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
6271687 ATCAAATGAT
* * *
6271697 AATAATTTATTAATAAAATAAATTATATGAT
1 AATATTTTATTAATAAAATAAATTATATAAA
* *
6271728 AATATTTTATTAAT-GAATAAATTTTATAAA
1 AATATTTTATTAATAAAATAAATTATATAAA
6271758 ATATATT
1 A-ATATT
6271765 AATTTATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 13 0.42
31 18 0.58
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (31 bp):
AATATTTTATTAATAAAATAAATTATATAAA
Found at i:6271775 original size:14 final size:13
Alignment explanation
Indices: 6271758--6271800 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
6271748 ATTTTATAAA
6271758 ATATATTAATTTAT
1 ATATATTAATTT-T
*
6271772 ATATATTTATTTT
1 ATATATTAATTTT
*
6271785 AAATATTAATATTT
1 ATATATTAAT-TTT
6271799 AT
1 AT
6271801 TCATTAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATATATTAATTTT
Found at i:6278112 original size:2 final size:2
Alignment explanation
Indices: 6278107--6278136 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
6278097 CTCTCATCTA
*
6278107 AT AT AT AA 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
6278137 TATTTCTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6280671 original size:23 final size:22
Alignment explanation
Indices: 6280643--6280686 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
6280633 ATATTAGTTC
6280643 TTTATT-TATTCTCTTTTTAACTA
1 TTTATTAT-TTCTC-TTTTAACTA
6280666 TTTATTATTTCTCTTTTAACT
1 TTTATTATTTCTCTTTTAACT
6280687 TTATAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 8 0.40
23 11 0.55
24 1 0.05
ACGTcount: A:0.20, C:0.14, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTATTATTTCTCTTTTAACTA
Found at i:6280682 original size:22 final size:23
Alignment explanation
Indices: 6280643--6280686 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
6280633 ATATTAGTTC
6280643 TTTATTTATTCTCTTTTTAACTA
1 TTTATTTATTCTCTTTTTAACTA
6280666 TTTA-TTATT-TCTCTTTTAACT
1 TTTATTTATTCTCT-TTTTAACT
6280687 TTATAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 3 0.15
22 13 0.65
23 4 0.20
ACGTcount: A:0.20, C:0.14, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTATTTATTCTCTTTTTAACTA
Found at i:6282674 original size:18 final size:18
Alignment explanation
Indices: 6282651--6282689 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
6282641 TAGAAGGATG
*
6282651 AAAACACAAAGATGATTA
1 AAAACACAAAAATGATTA
6282669 AAAACACAAAAATGATTA
1 AAAACACAAAAATGATTA
6282687 AAA
1 AAA
6282690 TATGTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.67, C:0.10, G:0.08, T:0.15
Consensus pattern (18 bp):
AAAACACAAAAATGATTA
Found at i:6290312 original size:2 final size:2
Alignment explanation
Indices: 6290301--6290345 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
6290291 GAGCATTCGT
* * *
6290301 TA TA -A TA TA TA TA TA TA TA TA TA TT TA TT TA TA TT 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
6290342 TA TA
1 TA TA
6290346 ATTTGTTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:6291709 original size:2 final size:2
Alignment explanation
Indices: 6291702--6291731 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6291692 TCTCAATAAA
6291702 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
6291732 CTAAATCGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6304251 original size:15 final size:17
Alignment explanation
Indices: 6304220--6304257 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
6304210 ACTACAAATC
6304220 TTAATTACCTCATGATA
1 TTAATTACCTCATGATA
6304237 TTAATTA-CT-ATGATA
1 TTAATTACCTCATGATA
*
6304252 ATAATT
1 TTAATT
6304258 TTAACTGTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 11 0.55
16 2 0.10
17 7 0.35
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (17 bp):
TTAATTACCTCATGATA
Found at i:6307375 original size:2 final size:2
Alignment explanation
Indices: 6307370--6307398 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6307360 TATGAGTTAG
6307370 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 A
6307399 CATACAATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6317564 original size:18 final size:18
Alignment explanation
Indices: 6317519--6317566 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
6317509 GCCACTTGAA
* *
6317519 ATATCCTGTAAACTTATG
1 ATATCCTATTAACTTATG
6317537 ATATCCTATTAACTTATG
1 ATATCCTATTAACTTATG
6317555 ATATCCTATTAA
1 ATATCCTATTAA
6317567 TACCAGATGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (18 bp):
ATATCCTATTAACTTATG
Found at i:6321400 original size:55 final size:55
Alignment explanation
Indices: 6321333--6321443 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
6321323 TGTGGTTATA
*
6321333 ATAAATTCAAGTGTATGATCATTATCGATTTTTTGAACAGTTCTAGAATGTCTAG
1 ATAAATCCAAGTGTATGATCATTATCGATTTTTTGAACAGTTCTAGAATGTCTAG
6321388 ATAAATCCAAGTGTATGATCATTATCGATTTTTTGAACAGTTCTAGAATGTCTAG
1 ATAAATCCAAGTGTATGATCATTATCGATTTTTTGAACAGTTCTAGAATGTCTAG
6321443 A
1 A
6321444 CTCCGACAGG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (55 bp):
ATAAATCCAAGTGTATGATCATTATCGATTTTTTGAACAGTTCTAGAATGTCTAG
Found at i:6321846 original size:15 final size:15
Alignment explanation
Indices: 6321826--6321858 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
6321816 CATCGTGCAG
6321826 CTCACCTCGAATATA
1 CTCACCTCGAATATA
6321841 CTCACCTCGAATATA
1 CTCACCTCGAATATA
6321856 CTC
1 CTC
6321859 TTACATTTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.30, C:0.36, G:0.06, T:0.27
Consensus pattern (15 bp):
CTCACCTCGAATATA
Found at i:6322215 original size:21 final size:21
Alignment explanation
Indices: 6322190--6322254 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
6322180 AAATTTAATA
6322190 TAATATATATAATATTATTTT
1 TAATATATATAATATTATTTT
*
6322211 TAATATA-A-ATTA-TA-TTT
1 TAATATATATAATATTATTTT
6322228 TAATTATATATAAATATAATATTTT
1 TAA-TATATAT-AATAT--TATTTT
6322253 TA
1 TA
6322255 TTAAATTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
17 6 0.18
18 6 0.18
19 4 0.12
20 1 0.03
21 10 0.29
24 2 0.06
25 5 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TAATATATATAATATTATTTT
Found at i:6322218 original size:17 final size:17
Alignment explanation
Indices: 6322196--6322231 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
6322186 AATATAATAT
6322196 ATATAATATTAT-TTTTA
1 ATATAA-ATTATATTTTA
6322213 ATATAAATTATATTTTA
1 ATATAAATTATATTTTA
6322230 AT
1 AT
6322232 TATATATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATATAAATTATATTTTA
Found at i:6322224 original size:24 final size:24
Alignment explanation
Indices: 6322183--6322258 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 24
6322173 ATTTAATAAA
6322183 TTTAATATAATATATATAATATTATT
1 TTTAATATAA-AT-TATAATATTATT
* *
6322209 TTTAATATAAATTAT-ATTTTAAT
1 TTTAATATAAATTATAATATTATT
*
6322232 TAT-ATATAAA-TATAATATT-TT
1 TTTAATATAAATTATAATATTATT
6322253 TATTAA
1 T-TTAA
6322259 ATTATTATCT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
21 5 0.12
22 12 0.29
23 9 0.22
24 3 0.07
25 2 0.05
26 10 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTAATATAAATTATAATATTATT
Found at i:6322255 original size:21 final size:20
Alignment explanation
Indices: 6322192--6322255 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 20
6322182 ATTTAATATA
6322192 ATATATATAATAT-TATTTTT
1 ATATATA-AATATATATTTTT
6322212 A-ATATAAAT-TATATTTTAATT
1 ATATATAAATATATA-TTT--TT
6322233 ATATATAAATATAATATTTTT
1 ATATATAAATAT-ATATTTTT
6322254 AT
1 AT
6322256 TAAATTATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 13
0.74 0.00 0.26
Matches are distributed among these distances:
17 1 0.03
18 5 0.14
19 8 0.22
20 1 0.03
21 7 0.19
22 8 0.22
23 4 0.11
24 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATATAAATATATATTTTT
Found at i:6322275 original size:42 final size:41
Alignment explanation
Indices: 6322182--6322301 Score: 108
Period size: 42 Copynumber: 2.9 Consensus size: 41
6322172 AATTTAATAA
6322182 ATTT-AATATAATATATATAATAT--TATTTTTAATATAAATTAT
1 ATTTAAAT-TAATATATA-AATATAATATTTTT-AT-TAAATTAT
*
6322224 ATTTTAATT-ATATATAAATATAATATTTTTATTAAATTATT
1 ATTTAAATTAATATATAAATATAATATTTTTATTAAATTA-T
* * *
6322265 ATCTTAAATTAAAATATTAA-ATAATAGTTTTA-TAAAT
1 AT-TTAAATTAATATATAAATATAATATTTTTATTAAAT
6322302 AGAAAATATA
Statistics
Matches: 68, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
40 12 0.18
41 17 0.25
42 29 0.43
43 10 0.15
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (41 bp):
ATTTAAATTAATATATAAATATAATATTTTTATTAAATTAT
Found at i:6336801 original size:24 final size:24
Alignment explanation
Indices: 6336766--6336822 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
6336756 CGAGACAATG
6336766 TTATT-AATTAAAAATAATTATTT
1 TTATTAAATTAAAAATAATTATTT
* *
6336789 TTATTAAATTAAATATATTTATTT
1 TTATTAAATTAAAAATAATTATTT
*
6336813 TCTTTTAAAT
1 T-TATTAAAT
6336823 ATCTAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 5 0.17
24 17 0.59
25 7 0.24
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
TTATTAAATTAAAAATAATTATTT
Found at i:6338238 original size:2 final size:2
Alignment explanation
Indices: 6338233--6338258 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6338223 AAAAAAAAAA
6338233 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
6338259 TCTTGAAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6355919 original size:18 final size:17
Alignment explanation
Indices: 6355881--6355932 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
6355871 TCAGCCCCCC
6355881 TTTTTTGT-TTTTT-TT
1 TTTTTTGTATTTTTGTT
6355896 TGTTTTTGTATTTTTGTAT
1 T-TTTTTGTATTTTTGT-T
**
6355915 TTTTTAATATTTTTGTT
1 TTTTTTGTATTTTTGTT
6355932 T
1 T
6355933 AATTTAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 1 0.03
16 7 0.23
17 7 0.23
18 14 0.45
19 2 0.06
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.81
Consensus pattern (17 bp):
TTTTTTGTATTTTTGTT
Found at i:6355938 original size:18 final size:18
Alignment explanation
Indices: 6355904--6355941 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
6355894 TTTGTTTTTG
*
6355904 TATTTTTGTATTTTTTAA
1 TATTTTTGTATTATTTAA
6355922 TATTTTTGT-TTAATTTAA
1 TATTTTTGTATT-ATTTAA
6355940 TA
1 TA
6355942 AAATAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (18 bp):
TATTTTTGTATTATTTAA
Found at i:6361352 original size:19 final size:20
Alignment explanation
Indices: 6361320--6361357 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
6361310 GCTATTAAAT
6361320 ATAAAAAAAATACA-ATCAC
1 ATAAAAAAAATACATATCAC
* *
6361339 ATAAAAATATTACATATCA
1 ATAAAAAAAATACATATCA
6361358 TAAACTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.63, C:0.13, G:0.00, T:0.24
Consensus pattern (20 bp):
ATAAAAAAAATACATATCAC
Found at i:6371944 original size:29 final size:29
Alignment explanation
Indices: 6371912--6371978 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
6371902 CTAATCATGC
* * *
6371912 AAATCATGCTAAATATCATGCTAATATA-T
1 AAATCATACCAAAAATCATGC-AATATATT
*
6371941 AAATTATACCAAAAATCATGCAATATATT
1 AAATCATACCAAAAATCATGCAATATATT
6371970 AAATTCATA
1 AAA-TCATA
6371979 AAAGATATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 6 0.19
29 21 0.68
30 4 0.13
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.33
Consensus pattern (29 bp):
AAATCATACCAAAAATCATGCAATATATT
Found at i:6372005 original size:14 final size:14
Alignment explanation
Indices: 6371988--6372093 Score: 50
Period size: 14 Copynumber: 6.6 Consensus size: 14
6371978 AAAAGATATT
6371988 ATGCAAAAATTATC
1 ATGCAAAAATTATC
6372002 ATGCAATAATATAAAATATC
1 ATGCAA-AA-AT----TATC
*
6372022 ATACAAAAATTATC
1 ATGCAAAAATTATC
**
6372036 ATGCAATAAAAACATC
1 ATGC-A-AAAATTATC
6372052 ATGCAATAATATAAAATATC
1 ATGCAA-AA-AT----TATC
*
6372072 ATACAAAAATTATC
1 ATGCAAAAATTATC
6372086 ATGCAAAA
1 ATGCAAAA
6372094 TATAAAATAA
Statistics
Matches: 70, Mismatches: 8, Indels: 28
0.66 0.08 0.26
Matches are distributed among these distances:
14 25 0.36
15 6 0.09
16 14 0.20
18 4 0.06
19 4 0.06
20 17 0.24
ACGTcount: A:0.56, C:0.13, G:0.05, T:0.26
Consensus pattern (14 bp):
ATGCAAAAATTATC
Found at i:6372023 original size:20 final size:19
Alignment explanation
Indices: 6371993--6372102 Score: 75
Period size: 20 Copynumber: 6.3 Consensus size: 19
6371983 ATATTATGCA
6371993 AAAATTATCATGCAATAATAT
1 AAAA-TATCATGCAA-AATAT
*
6372014 AAAATATCATACAAAA-AT
1 AAAATATCATGCAAAATAT
6372032 ----TATCATGC--AATA-
1 AAAATATCATGCAAAATAT
*
6372044 AAAACATCATGCAATAATAT
1 AAAATATCATGCAA-AATAT
*
6372064 AAAATATCATACAAAA-AT
1 AAAATATCATGCAAAATAT
6372082 ----TATCATGCAAAATAT
1 AAAATATCATGCAAAATAT
6372097 AAAATA
1 AAAATA
6372103 AATCACACAA
Statistics
Matches: 69, Mismatches: 6, Indels: 30
0.66 0.06 0.29
Matches are distributed among these distances:
12 2 0.03
13 1 0.01
14 18 0.26
15 2 0.03
16 7 0.10
18 4 0.06
19 10 0.14
20 21 0.30
21 4 0.06
ACGTcount: A:0.57, C:0.12, G:0.04, T:0.27
Consensus pattern (19 bp):
AAAATATCATGCAAAATAT
Found at i:6372054 original size:50 final size:48
Alignment explanation
Indices: 6371951--6372093 Score: 195
Period size: 50 Copynumber: 3.0 Consensus size: 48
6371941 AAATTATACC
* * *
6371951 AAAAATCATGCAAT-ATATTAAAT-TCATA-AAAGA-TATTATGCAAA
1 AAAAATCATGCAATAATATAAAATATCATACAAAAATTATCATGCAAA
**
6371995 AATTATCATGCAATAATATAAAATATCATACAAAAATTATCATGCAATA
1 AAAAATCATGCAATAATATAAAATATCATACAAAAATTATCATGCAA-A
6372044 AAAACATCATGCAATAATATAAAATATCATACAAAAATTATCATGCAAA
1 AAAA-ATCATGCAATAATATAAAATATCATACAAAAATTATCATGCAAA
6372093 A
1 A
6372094 TATAAAATAA
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
44 12 0.14
45 8 0.09
46 5 0.06
47 4 0.05
48 9 0.10
49 5 0.06
50 43 0.50
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.28
Consensus pattern (48 bp):
AAAAATCATGCAATAATATAAAATATCATACAAAAATTATCATGCAAA
Found at i:6372115 original size:33 final size:34
Alignment explanation
Indices: 6372049--6372116 Score: 95
Period size: 33 Copynumber: 2.0 Consensus size: 34
6372039 CAATAAAAAC
*
6372049 ATCATGCAATAATATAAAATATCATACAAAAATT
1 ATCATGCAATAATATAAAATATAATACAAAAATT
*
6372083 ATCATGCAA-AATATAAAATA-AATCACACAAATT
1 ATCATGCAATAATATAAAATATAAT-ACAAAAATT
6372116 A
1 A
6372117 ATATATTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
32 2 0.06
33 20 0.65
34 9 0.29
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.26
Consensus pattern (34 bp):
ATCATGCAATAATATAAAATATAATACAAAAATT
Found at i:6373236 original size:22 final size:22
Alignment explanation
Indices: 6373210--6373258 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
6373200 TGTTTTTATT
**
6373210 TTTTATTTTTTGGTTTTCTAAC
1 TTTTATTTTTTACTTTTCTAAC
6373232 TTTTATTTTTTACTTTTCTAAC
1 TTTTATTTTTTACTTTTCTAAC
6373254 TTTTA
1 TTTTA
6373259 ACAAATTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.16, C:0.10, G:0.04, T:0.69
Consensus pattern (22 bp):
TTTTATTTTTTACTTTTCTAAC
Found at i:6373328 original size:6 final size:6
Alignment explanation
Indices: 6373319--6373388 Score: 77
Period size: 6 Copynumber: 11.7 Consensus size: 6
6373309 TAAAAATCCC
** * * * *
6373319 AATTAA AATTAA AACCAA CATTAA AATGAA AATTAA AATGAA AATGAA
1 AATTAA AATTAA AATTAA AATTAA AATTAA AATTAA AATTAA AATTAA
*
6373367 AATTGA AATTAA AATTAA AATT
1 AATTAA AATTAA AATTAA AATT
6373389 TTGGGGCTTT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.27
Consensus pattern (6 bp):
AATTAA
Found at i:6373332 original size:18 final size:19
Alignment explanation
Indices: 6373305--6373351 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
6373295 TTAAAATTGA
*
6373305 AAAATAAAAATCCCA-ATT
1 AAAATAAAAATCCAACATT
*
6373323 AAAATTAAAA-CCAACATT
1 AAAATAAAAATCCAACATT
*
6373341 AAAATGAAAAT
1 AAAATAAAAAT
6373352 TAAAATGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.64, C:0.13, G:0.02, T:0.21
Consensus pattern (19 bp):
AAAATAAAAATCCAACATT
Found at i:6374187 original size:9 final size:9
Alignment explanation
Indices: 6374170--6374200 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
6374160 TGCAACATGT
*
6374170 AATGGATGC
1 AATGAATGC
6374179 AATGAATGC
1 AATGAATGC
6374188 AATGAATGC
1 AATGAATGC
6374197 AATG
1 AATG
6374201 CATGACATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.42, C:0.10, G:0.26, T:0.23
Consensus pattern (9 bp):
AATGAATGC
Found at i:6376219 original size:14 final size:14
Alignment explanation
Indices: 6376200--6376231 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
6376190 GTCTTCATTT
6376200 TTTTCTCATTTTCA
1 TTTTCTCATTTTCA
6376214 TTTTCTCATTTTCA
1 TTTTCTCATTTTCA
6376228 TTTT
1 TTTT
6376232 TTCAATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTCTCATTTTCA
Found at i:6379541 original size:35 final size:35
Alignment explanation
Indices: 6379475--6379575 Score: 139
Period size: 35 Copynumber: 2.9 Consensus size: 35
6379465 GTAATAAAAC
* *
6379475 ATCATGCAATAATATAAAATTATCATGCAAACATTT
1 ATCATGCAATAATATAAAA-TATCATACAAACAGTT
* * *
6379511 ATCATACAATACTATAAAATATCATCCAAACAGTT
1 ATCATGCAATAATATAAAATATCATACAAACAGTT
*
6379546 ATCATGCAATAATATTAAATATCATACAAA
1 ATCATGCAATAATATAAAATATCATACAAA
6379576 AAATACAATA
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 40 0.70
36 17 0.30
ACGTcount: A:0.50, C:0.16, G:0.04, T:0.31
Consensus pattern (35 bp):
ATCATGCAATAATATAAAATATCATACAAACAGTT
Found at i:6379585 original size:29 final size:31
Alignment explanation
Indices: 6379552--6379612 Score: 90
Period size: 29 Copynumber: 2.0 Consensus size: 31
6379542 AGTTATCATG
*
6379552 CAATAATATTAAAT-ATCATACAAA-AAATA
1 CAATAATATAAAATAATCATACAAATAAATA
6379581 CAATAATATAAAATAAATCATACAAATAAATA
1 CAATAATATAAAAT-AATCATACAAATAAATA
6379613 TATTAATGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 13 0.46
31 10 0.36
32 5 0.18
ACGTcount: A:0.64, C:0.10, G:0.00, T:0.26
Consensus pattern (31 bp):
CAATAATATAAAATAATCATACAAATAAATA
Found at i:6379646 original size:20 final size:20
Alignment explanation
Indices: 6379623--6379660 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6379613 TATTAATGAT
*
6379623 CATGCAACTAAATTATTATC
1 CATGCAAATAAATTATTATC
6379643 CATGCAAATAAATTATTA
1 CATGCAAATAAATTATTA
6379661 GTAATGCAAA
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:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (20 bp):
CATGCAAATAAATTATTATC
Found at i:6379667 original size:20 final size:20
Alignment explanation
Indices: 6379624--6379671 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
6379614 ATTAATGATC
* *
6379624 ATGCAACTAAATTATTATCC
1 ATGCAAATAAATTATTATCA
6379644 ATGCAAATAAATTATTAGT-A
1 ATGCAAATAAATTATTA-TCA
6379664 ATGCAAAT
1 ATGCAAAT
6379672 TCATTCAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.33
Consensus pattern (20 bp):
ATGCAAATAAATTATTATCA
Found at i:6379869 original size:17 final size:18
Alignment explanation
Indices: 6379849--6379886 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
6379839 AATAATTAAT
*
6379849 AAAAATAAATAAAAAC-A
1 AAAAATAAAAAAAAACTA
6379866 AAAAATAAAAAAAAACTA
1 AAAAATAAAAAAAAACTA
6379884 AAA
1 AAA
6379887 TCAAAATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.84, C:0.05, G:0.00, T:0.11
Consensus pattern (18 bp):
AAAAATAAAAAAAAACTA
Found at i:6379872 original size:23 final size:24
Alignment explanation
Indices: 6379846--6379892 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
6379836 CATAATAATT
*
6379846 AATAAAAATAAA-TAAAAACAAAA
1 AATAAAAAAAAACTAAAAACAAAA
*
6379869 AATAAAAAAAAACTAAAATCAAAA
1 AATAAAAAAAAACTAAAAACAAAA
6379893 TCAAATTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.13
Consensus pattern (24 bp):
AATAAAAAAAAACTAAAAACAAAA
Found at i:6380816 original size:18 final size:17
Alignment explanation
Indices: 6380802--6380860 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 17
6380792 TAAAAAATCC
6380802 AAATCCAAATTAAAAATTA
1 AAATCCAAATT-AAAA-TA
*
6380821 AAATCAAAATTAAAATTA
1 AAATCCAAATTAAAA-TA
6380839 AAA-CCAAAATTAAAATTA
1 AAATCC-AAATTAAAA-TA
6380857 AAAT
1 AAAT
6380861 TTTTGAGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.03
18 25 0.69
19 10 0.28
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATCCAAATTAAAATA
Found at i:6380818 original size:19 final size:19
Alignment explanation
Indices: 6380787--6380853 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
6380777 TTAAATCAAA
*
6380787 AAAATTAAAAAATCCAAATC
1 AAAATT-AAAAATCAAAATC
* *
6380807 CAAATTAAAAATTAAAATC
1 AAAATTAAAAATCAAAATC
* *
6380826 AAAATT-AAAATTAAAACC
1 AAAATTAAAAATCAAAATC
6380844 AAAATTAAAA
1 AAAATTAAAA
6380854 TTAAAATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
18 17 0.41
19 19 0.46
20 5 0.12
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAATTAAAAATCAAAATC
Found at i:6380823 original size:6 final size:6
Alignment explanation
Indices: 6380808--6380861 Score: 72
Period size: 6 Copynumber: 8.8 Consensus size: 6
6380798 ATCCAAATCC
* **
6380808 AAATTAA AAATTA AAATCA AAATTA AAATTA AAACCA AAATTA AAATTA
1 AAATT-A AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
6380857 AAATT
1 AAATT
6380862 TTTGAGTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
6 36 0.88
7 5 0.12
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (6 bp):
AAATTA
Found at i:6380830 original size:25 final size:26
Alignment explanation
Indices: 6380786--6380841 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
6380776 ATTAAATCAA
* *
6380786 AAAAATTAAAAAATCCAAATCCAAATT
1 AAAAATT-AAAAATCAAAATCAAAATT
*
6380813 AAAAATT-AAAATCAAAATTAAAATT
1 AAAAATTAAAAATCAAAATCAAAATT
6380838 AAAA
1 AAAA
6380842 CCAAAATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 19 0.73
27 7 0.27
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.23
Consensus pattern (26 bp):
AAAAATTAAAAATCAAAATCAAAATT
Found at i:6382142 original size:2 final size:2
Alignment explanation
Indices: 6382135--6382164 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6382125 TTATACATAC
6382135 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
6382165 GACAAACTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6382370 original size:6 final size:6
Alignment explanation
Indices: 6382359--6382391 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
6382349 TCTTGGGTTG
6382359 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT
6382392 TCAAGTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:6391884 original size:14 final size:15
Alignment explanation
Indices: 6391855--6391888 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
6391845 TTTAAATTTG
*
6391855 AATTTTATTATCAAT
1 AATTTTATTATAAAT
6391870 AATTTT-TTATAAAT
1 AATTTTATTATAAAT
6391884 AATTT
1 AATTT
6391889 ATAAATTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (15 bp):
AATTTTATTATAAAT
Found at i:6395557 original size:42 final size:42
Alignment explanation
Indices: 6395444--6395558 Score: 167
Period size: 42 Copynumber: 2.7 Consensus size: 42
6395434 GAACTGACCG
* * ** *
6395444 CTGAGAACAAACGCTTGCAAGAGGAAAATAGGCAGTTGAGTA
1 CTGAGAATAAACACTTAAAAGAGGAAAATGGGCAGTTGAGTA
*
6395486 CTGAGAATAGACACTTAAAAGAGGAAAATGGGCAGTTGAGTA
1 CTGAGAATAAACACTTAAAAGAGGAAAATGGGCAGTTGAGTA
*
6395528 CTGAGAATAAACACTTAAAAGACGAAAATGG
1 CTGAGAATAAACACTTAAAAGAGGAAAATGG
6395559 AAGCTTGAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.44, C:0.12, G:0.26, T:0.17
Consensus pattern (42 bp):
CTGAGAATAAACACTTAAAAGAGGAAAATGGGCAGTTGAGTA
Found at i:6396013 original size:33 final size:33
Alignment explanation
Indices: 6395969--6396031 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
6395959 TATCATGAAT
*
6395969 ATGTTTTCTTTTTCCTTCTCTGATGCACTTTTC
1 ATGTTTCCTTTTTCCTTCTCTGATGCACTTTTC
*
6396002 ATGTTTCCTTTTTCCTTCTCTGATTCACTT
1 ATGTTTCCTTTTTCCTTCTCTGATGCACTT
6396032 ATTCTGATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.10, C:0.25, G:0.08, T:0.57
Consensus pattern (33 bp):
ATGTTTCCTTTTTCCTTCTCTGATGCACTTTTC
Found at i:6396043 original size:33 final size:33
Alignment explanation
Indices: 6395976--6396043 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
6395966 AATATGTTTT
*
6395976 CTTTTTCCTTCTCTGATGCACTTTTCATGTTTC
1 CTTTTTCCTTCTCTGATGCACTTTTCATGATTC
*
6396009 CTTTTTCCTTCTCTGATTCACTTATTC-TGATTC
1 CTTTTTCCTTCTCTGATGCACTT-TTCATGATTC
6396042 CT
1 CT
6396044 ATCTGTTGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 29 0.91
34 3 0.09
ACGTcount: A:0.10, C:0.28, G:0.07, T:0.54
Consensus pattern (33 bp):
CTTTTTCCTTCTCTGATGCACTTTTCATGATTC
Found at i:6399381 original size:13 final size:13
Alignment explanation
Indices: 6399363--6399387 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6399353 TATAGTATAA
6399363 TTTTACTTTTTAC
1 TTTTACTTTTTAC
6399376 TTTTACTTTTTA
1 TTTTACTTTTTA
6399388 GTTGGTTAAT
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:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTACTTTTTAC
Done.