Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008212.1 Hibiscus syriacus cultivar Beakdansim tig00110834_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: 343056
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 1 of 2
Found at i:1508 original size:19 final size:19
Alignment explanation
Indices: 1484--1554 Score: 133
Period size: 19 Copynumber: 3.7 Consensus size: 19
1474 GAATGCAATT
1484 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
1503 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
*
1522 AGTGCATCGATGCATGAGG
1 AGTGCATCGATGCATAAGG
1541 AGTGCATCGATGCA
1 AGTGCATCGATGCA
1555 CCTACTTAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 51 1.00
ACGTcount: A:0.30, C:0.17, G:0.32, T:0.21
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGG
Found at i:2297 original size:18 final size:18
Alignment explanation
Indices: 2274--2335 Score: 79
Period size: 18 Copynumber: 3.3 Consensus size: 18
2264 GGATATATAC
2274 AGTGGTTCTTCGGGACAT
1 AGTGGTTCTTCGGGACAT
**
2292 AGTGGTTCTTCGAAACAAT
1 AGTGGTTCTTCGGGAC-AT
*
2311 CAGTGGTCCTTCGGGACAT
1 -AGTGGTTCTTCGGGACAT
2330 AGTGGT
1 AGTGGT
2336 CCTTTGAGAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 20 0.54
19 4 0.11
20 13 0.35
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.31
Consensus pattern (18 bp):
AGTGGTTCTTCGGGACAT
Found at i:2346 original size:18 final size:18
Alignment explanation
Indices: 2274--2346 Score: 74
Period size: 18 Copynumber: 3.9 Consensus size: 18
2264 GGATATATAC
* *
2274 AGTGGTTCTTCGGGACAT
1 AGTGGTCCTTCGAGACAT
* *
2292 AGTGGTTCTTCGAAACAAT
1 AGTGGTCCTTCGAGAC-AT
*
2311 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGAGACAT
*
2330 AGTGGTCCTTTGAGACA
1 AGTGGTCCTTCGAGACA
2347 AATATCCAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
18 29 0.63
19 4 0.09
20 13 0.28
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTCGAGACAT
Found at i:6887 original size:47 final size:45
Alignment explanation
Indices: 6831--6928 Score: 135
Period size: 47 Copynumber: 2.1 Consensus size: 45
6821 ATGACTTAAT
*
6831 TTATTTTGTTTAGTTTGTTTATTACTTAATTCAAGTGAAT-GGTTTTA
1 TTATTTTGTTTAGTTTGTTTATTACTT--TTCAAGAGAATAGG-TTTA
* *
6878 TTATTTTGTTTATTTTGTTTATTACTTTTGAAGAGAATAGGTTTA
1 TTATTTTGTTTAGTTTGTTTATTACTTTTCAAGAGAATAGGTTTA
6923 TTATTT
1 TTATTT
6929 AGTGAAATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
45 19 0.40
46 2 0.04
47 26 0.55
ACGTcount: A:0.23, C:0.03, G:0.14, T:0.59
Consensus pattern (45 bp):
TTATTTTGTTTAGTTTGTTTATTACTTTTCAAGAGAATAGGTTTA
Found at i:10522 original size:40 final size:40
Alignment explanation
Indices: 10464--10541 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
10454 CAGAAAGACA
**
10464 CAGATGATGATCCGCGCCTCTT-TTGTGTGTGTCATAATTG
1 CAGATGATGATCCGCGCCT-TTCTTGTACGTGTCATAATTG
* *
10504 CAGATGGTGATCCTCGCCTTTCTTGTACGTGTCATAAT
1 CAGATGATGATCCGCGCCTTTCTTGTACGTGTCATAAT
10542 ATGCGTGTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 2 0.06
40 31 0.94
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.37
Consensus pattern (40 bp):
CAGATGATGATCCGCGCCTTTCTTGTACGTGTCATAATTG
Found at i:11538 original size:2 final size:2
Alignment explanation
Indices: 11531--11562 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11521 CTAATATTCA
11531 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11563 TTAAAAGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22021 original size:144 final size:144
Alignment explanation
Indices: 21849--22137 Score: 470
Period size: 144 Copynumber: 2.0 Consensus size: 144
21839 TCTTAAAATA
* * * * * *
21849 CATAAGACACCATAATAAAAGATATAATTAAAGTCTAGAAACATAAATGACAAACACATAATGTT
1 CATAAAACACCATAATAAAAAACATAATTAAAGCCAAGAAACATAAATGACAAACACATAATATT
* *
21914 TTTGTTCTTTGACACAACATTCTAAAATTTCAGGCAATACTTGTGACATCTGATACTCCAGTATT
66 TTTGTTATTTGACACAACATTCTAAAATTTCAAGCAATACTTGTGACATCTGATACTCCAGTATT
*
21979 AGAATCATCATTCT
131 ACAATCATCATTCT
*
21993 CATAAAACACCATAATAAAAAACATAATTAAAGCCAATAAACATAAATGACAAACACATAATATT
1 CATAAAACACCATAATAAAAAACATAATTAAAGCCAAGAAACATAAATGACAAACACATAATATT
* *
22058 TTTGTTATTTGGCACAACATTCTCAAATTTCAAGCAATACTTGTGACATCTGATACTCCAGTATT
66 TTTGTTATTTGACACAACATTCTAAAATTTCAAGCAATACTTGTGACATCTGATACTCCAGTATT
22123 ACAATCATCATTCT
131 ACAATCATCATTCT
22137 C
1 C
22138 TATTTCCTCC
Statistics
Matches: 133, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
144 133 1.00
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (144 bp):
CATAAAACACCATAATAAAAAACATAATTAAAGCCAAGAAACATAAATGACAAACACATAATATT
TTTGTTATTTGACACAACATTCTAAAATTTCAAGCAATACTTGTGACATCTGATACTCCAGTATT
ACAATCATCATTCT
Found at i:25668 original size:27 final size:27
Alignment explanation
Indices: 25626--25679 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
25616 TCGATGTCTA
25626 AAGGTCTAAGACAGAGTTGTTCACTTT
1 AAGGTCTAAGACAGAGTTGTTCACTTT
*
25653 AAGGTCTAAGATAGAGTTGTTCACTTT
1 AAGGTCTAAGACAGAGTTGTTCACTTT
25680 CTCCAATGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (27 bp):
AAGGTCTAAGACAGAGTTGTTCACTTT
Found at i:36647 original size:90 final size:90
Alignment explanation
Indices: 36484--36749 Score: 471
Period size: 90 Copynumber: 3.0 Consensus size: 90
36474 TAATCCTGAA
* *
36484 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCTCTAATATGAT
1 TATTAAATTACAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCTCTAATATGAT
36549 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
*
36574 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCTCTAATATGAT
1 TATTAAATTACAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCTCTAATATGAT
36639 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
*
36664 TATTAAATTACAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGAT
1 TATTAAATTACAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCTCTAATATGAT
* *
36728 TAGGGTACCTTGGCTATAAAAG
66 TAGGGTAACTTGGATATAAAAG
36750 TGTGTGTTAG
Statistics
Matches: 170, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
89 31 0.18
90 139 0.82
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (90 bp):
TATTAAATTACAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCTCTAATATGAT
TAGGGTAACTTGGATATAAAAGGAT
Found at i:52567 original size:18 final size:18
Alignment explanation
Indices: 52544--52592 Score: 98
Period size: 18 Copynumber: 2.7 Consensus size: 18
52534 TTCAACGTCA
52544 GTCAACGGTCAATGGTCG
1 GTCAACGGTCAATGGTCG
52562 GTCAACGGTCAATGGTCG
1 GTCAACGGTCAATGGTCG
52580 GTCAACGGTCAAT
1 GTCAACGGTCAAT
52593 AGCTGACTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.22
Consensus pattern (18 bp):
GTCAACGGTCAATGGTCG
Found at i:53227 original size:30 final size:30
Alignment explanation
Indices: 53169--53230 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
53159 TTTGGATCAG
* ***
53169 AATTTAATCAAAATTTCACTTTGGTCCTCA
1 AATTTAATCAAAATTTCAATTCAATCCTCA
*
53199 AATTTAATTAAAATTTCAATTCAATCCTCA
1 AATTTAATCAAAATTTCAATTCAATCCTCA
53229 AA
1 AA
53231 AATAATTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.40, C:0.18, G:0.03, T:0.39
Consensus pattern (30 bp):
AATTTAATCAAAATTTCAATTCAATCCTCA
Found at i:55168 original size:14 final size:14
Alignment explanation
Indices: 55149--55201 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
55139 TTTATATATA
55149 TATATATATGTATG
1 TATATATATGTATG
*
55163 TATATATATATGTGTG
1 --TATATATATGTATG
* *
55179 TGTTTATATGTATG
1 TATATATATGTATG
55193 TATATATAT
1 TATATATAT
55202 ATCGAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
14 18 0.58
16 13 0.42
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (14 bp):
TATATATATGTATG
Found at i:55168 original size:16 final size:16
Alignment explanation
Indices: 55147--55203 Score: 82
Period size: 16 Copynumber: 3.7 Consensus size: 16
55137 GGTTTATATA
55147 TATATATATATGTATG
1 TATATATATATGTATG
*
55163 TATATATATATGTGTG
1 TATATATATATGTATG
*
55179 TGT-T-TATATGTATG
1 TATATATATATGTATG
55193 TATATATATAT
1 TATATATATAT
55204 CGAAAAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
14 11 0.31
15 2 0.06
16 22 0.63
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (16 bp):
TATATATATATGTATG
Found at i:55168 original size:18 final size:18
Alignment explanation
Indices: 55145--55203 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 18
55135 AAGGTTTATA
55145 TATATATATATATGTATG
1 TATATATATATATGTATG
* *
55163 TATATATATATGTGTGTG
1 TATATATATATATGTATG
* *
55181 T-T-TATATGTATGTATA
1 TATATATATATATGTATG
55197 TATATAT
1 TATATAT
55204 CGAAAAAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
16 11 0.33
17 2 0.06
18 20 0.61
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.53
Consensus pattern (18 bp):
TATATATATATATGTATG
Found at i:56479 original size:25 final size:23
Alignment explanation
Indices: 56434--56485 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 23
56424 GTTTTCAAAA
*
56434 AACGTCAACGTCGGTTAACAATC
1 AACGTCAACGTCGGTCAACAATC
*
56457 AACGATCAACAGTTGGTCAACAATC
1 AACG-TCAAC-GTCGGTCAACAATC
56482 AACG
1 AACG
56486 GTCAGTCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 4 0.16
24 5 0.20
25 16 0.64
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (23 bp):
AACGTCAACGTCGGTCAACAATC
Found at i:58439 original size:27 final size:27
Alignment explanation
Indices: 58386--58439 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
58376 ACGAGTGTGC
*
58386 AATATGCAATTTAACTGCAACATAGAT
1 AATATGCAATTTAACTGCAACACAGAT
* * * *
58413 AATATGCACTTTTAGTGCAAGACAGAT
1 AATATGCAATTTAACTGCAACACAGAT
58440 GCATAGGTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (27 bp):
AATATGCAATTTAACTGCAACACAGAT
Found at i:67727 original size:2 final size:2
Alignment explanation
Indices: 67720--67750 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
67710 GACCTAATTC
67720 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 A
67751 ACTATTGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:69603 original size:37 final size:38
Alignment explanation
Indices: 69562--69678 Score: 128
Period size: 37 Copynumber: 3.0 Consensus size: 38
69552 CGTTTGTTAA
*
69562 ACAAACGCCGCAATAGGTGTTAATATTTAGCGACGTT-
1 ACAAACGCCGCAATAGGTGTTAATATTTAGCGGCGTTC
* * *
69599 ACAAACGCCGCAATAGGTTTTAGTGTTTAGCGGCGTTTTTCCC
1 ACAAACGCCGCAATAGGTGTTAATATTTAGCGGCG---TT--C
* *
69642 ACAAACGCCGCAATAGGTGTTCAGATTTAGCGGCGTT
1 ACAAACGCCGCAATAGGTGTTAATATTTAGCGGCGTT
69679 TTTCTCACAA
Statistics
Matches: 65, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
37 31 0.48
40 4 0.06
43 30 0.46
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.28
Consensus pattern (38 bp):
ACAAACGCCGCAATAGGTGTTAATATTTAGCGGCGTTC
Found at i:69723 original size:86 final size:80
Alignment explanation
Indices: 69562--69725 Score: 204
Period size: 86 Copynumber: 2.0 Consensus size: 80
69552 CGTTTGTTAA
* * *
69562 ACAAACGCCGCAATAGGTGTTAATATTTAGCGACGTTACAAACGCCGCAATAGGTTTTAGTGTTT
1 ACAAACGCCGCAATAGGTGTTAAGATTTAGCGACGTTACAAACGACGCAATAGGTTTTAGTATTT
69627 AGCGGCGTTTTTCCC
66 AGCGGCGTTTTTCCC
* *
69642 ACAAACGCCGCAATAGGTGTTCAGATTTAGCGGCGTTTTTCTCACAAACGACGCAATAGGTTTTG
1 ACAAACGCCGCAATAGGTGTTAAGATTTAGCGACG----T-T-ACAAACGACGCAATAGGTTTT-
*
69707 AG-ATTTAGCGGTGTTTTTC
59 AGTATTTAGCGGCGTTTTTC
69726 TCATAGGCGC
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
80 32 0.45
84 1 0.01
85 1 0.01
86 35 0.49
87 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (80 bp):
ACAAACGCCGCAATAGGTGTTAAGATTTAGCGACGTTACAAACGACGCAATAGGTTTTAGTATTT
AGCGGCGTTTTTCCC
Found at i:69747 original size:43 final size:43
Alignment explanation
Indices: 69599--69728 Score: 190
Period size: 43 Copynumber: 3.0 Consensus size: 43
69589 TAGCGACGTT
* *
69599 ACAAACGCCGCAATAGGTTTT-AGTGTTTAGCGGCGTTTTTCCC
1 ACAAACGCCGCAATAGGTTTTCAG-ATTTAGCGGCGTTTTTCTC
*
69642 ACAAACGCCGCAATAGGTGTTCAGATTTAGCGGCGTTTTTCTC
1 ACAAACGCCGCAATAGGTTTTCAGATTTAGCGGCGTTTTTCTC
* * *
69685 ACAAACGACGCAATAGGTTTTGAGATTTAGCGGTGTTTTTCTC
1 ACAAACGCCGCAATAGGTTTTCAGATTTAGCGGCGTTTTTCTC
69728 A
1 A
69729 TAGGCGCCGC
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
43 77 0.97
44 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (43 bp):
ACAAACGCCGCAATAGGTTTTCAGATTTAGCGGCGTTTTTCTC
Found at i:70164 original size:15 final size:15
Alignment explanation
Indices: 70144--70176 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
70134 GCTGATATAC
70144 TGCTTCTCTCTGTGT
1 TGCTTCTCTCTGTGT
70159 TGCTTCTCTCTGTGT
1 TGCTTCTCTCTGTGT
70174 TGC
1 TGC
70177 CGTTGCTTCT
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:0.00, C:0.27, G:0.21, T:0.52
Consensus pattern (15 bp):
TGCTTCTCTCTGTGT
Found at i:77770 original size:48 final size:47
Alignment explanation
Indices: 77698--77857 Score: 196
Period size: 48 Copynumber: 3.3 Consensus size: 47
77688 TTAATTTTAG
* *
77698 CACCATCATTTATGGTCGATCCATGCACGTGTTATTCTTCAATTCCAT
1 CACCATCATTTATGGT-GAACCATGCACGTGTTGTTCTTCAATTCCAT
* *
77746 CACCATCATTTATGGCTGAACCATGCACGTGTTGTTCTTCAATTCTAG
1 CACCATCATTTATGG-TGAACCATGCACGTGTTGTTCTTCAATTCCAT
* * * *
77794 CACCATCATTTATGGTTGAACCATGCATGTTTTGTCCTTCAATTTCAGT
1 CACCATCATTTATGG-TGAACCATGCACGTGTTGTTCTTCAATTCCA-T
*
77843 -GCCATCATTTATGGT
1 CACCATCATTTATGGT
77858 CGGGCTATGC
Statistics
Matches: 98, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
47 1 0.01
48 96 0.98
49 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.38
Consensus pattern (47 bp):
CACCATCATTTATGGTGAACCATGCACGTGTTGTTCTTCAATTCCAT
Found at i:81534 original size:2 final size:2
Alignment explanation
Indices: 81529--81577 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
81519 TGGATGCACT
81529 TA TA TA 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
81571 TA TA TA T
1 TA TA TA T
81578 TTAGAAAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:83158 original size:2 final size:2
Alignment explanation
Indices: 83151--83184 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
83141 CATTGTAAAC
*
83151 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
83185 TCATATGCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:88164 original size:201 final size:190
Alignment explanation
Indices: 88030--88393 Score: 561
Period size: 190 Copynumber: 1.9 Consensus size: 190
88020 GAAGTAGTTT
* *
88030 CTCATTGCTAAATCGCAGTCGATCTGGGTCTTTTTCTAGACATGAAGACATTAGTTTGAATTTTG
1 CTCATTGCTAAATCGCAGCCGATCTGGGTCTTCTTCTAGACATGAAGACATTAGTTTGAATTTTG
* *
88095 ACCGGAAGGTAGTTCATCGTTGCTACCATGCAGTCAATGTGCTCTTGAGTTGAGTGAAATCAAAC
66 ACCGGAAGGTAGTTCCTCGTTGCTACCATGCGGTCAATGTGCTCTTGAGTTGAGTGAAATCAAAC
* *
88160 TTGAAAGCTTTGGTCGACAGAGAGCTCTTCTCGACTTAAGCTATGTCGAAATATGGGTTC
131 TTGAAAGCTTTGGTCGACAAATAGCTCTTCTCGACTTAAGCTATGTCGAAATATGGGTTC
* * * *
88220 CTCGTTGCTAAATCGCAGCCGATTTGGGTCTTCTTCTAGACTTGAAGACCTTAGTTTGAATTTTG
1 CTCATTGCTAAATCGCAGCCGATCTGGGTCTTCTTCTAGACATGAAGACATTAGTTTGAATTTTG
** * * *
88285 AATGGAAGGTAGTTCCTCGTTGCTACCATGCGGTCAATGTGCTCTTAAGTTGAGTGGAATTGAAA
66 ACCGGAAGGTAGTTCCTCGTTGCTACCATGCGGTCAATGTGCTCTTGAGTTGAGT-GAAATCAAA
*
88350 -TTGAAAGCTTTGGTAGACAAATAGCTC-TCTCGACTTAAGCTATG
130 CTTGAAAGCTTTGGTCGACAAATAGCTCTTCTCGACTTAAGCTATG
88394 CAATTAAGGA
Statistics
Matches: 157, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
189 17 0.11
190 133 0.85
191 7 0.04
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.33
Consensus pattern (190 bp):
CTCATTGCTAAATCGCAGCCGATCTGGGTCTTCTTCTAGACATGAAGACATTAGTTTGAATTTTG
ACCGGAAGGTAGTTCCTCGTTGCTACCATGCGGTCAATGTGCTCTTGAGTTGAGTGAAATCAAAC
TTGAAAGCTTTGGTCGACAAATAGCTCTTCTCGACTTAAGCTATGTCGAAATATGGGTTC
Found at i:88972 original size:13 final size:13
Alignment explanation
Indices: 88954--88978 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
88944 TTCTCTCATA
88954 AAAAATAAAAAAT
1 AAAAATAAAAAAT
88967 AAAAATAAAAAA
1 AAAAATAAAAAA
88979 AGACTGAAAT
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:89289 original size:21 final size:21
Alignment explanation
Indices: 89265--89315 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
89255 AGTTGGCGAT
*
89265 TTCCTAGGAGAAACTAATTAC
1 TTCCCAGGAGAAACTAATTAC
* *
89286 TTCCCAGAAGAAACTGATTAC
1 TTCCCAGGAGAAACTAATTAC
89307 TTCCCAGGA
1 TTCCCAGGA
89316 AAAATTCCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (21 bp):
TTCCCAGGAGAAACTAATTAC
Found at i:95732 original size:18 final size:18
Alignment explanation
Indices: 95681--95736 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
95671 GAAAGCCACA
*
95681 AAAAAACACCAACCAAGC
1 AAAAAACACGAACCAAGC
* *
95699 --AAAATACG-AGCAAGC
1 AAAAAACACGAACCAAGC
95714 AAAAAACACGAACCAAGC
1 AAAAAACACGAACCAAGC
95732 AAAAA
1 AAAAA
95737 TCAAGCAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 6 0.20
16 6 0.20
17 7 0.23
18 11 0.37
ACGTcount: A:0.62, C:0.25, G:0.11, T:0.02
Consensus pattern (18 bp):
AAAAAACACGAACCAAGC
Found at i:95744 original size:33 final size:33
Alignment explanation
Indices: 95681--95744 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
95671 GAAAGCCACA
*
95681 AAAAAACACCAACCAAGCAAAATACGAGCAAGC
1 AAAAAACACCAACCAAGCAAAATACAAGCAAGC
*
95714 AAAAAACACGAACCAAGCAAAA-ATCAAGCAA
1 AAAAAACACCAACCAAGCAAAATA-CAAGCAA
95745 AAAAATAACC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.61, C:0.25, G:0.11, T:0.03
Consensus pattern (33 bp):
AAAAAACACCAACCAAGCAAAATACAAGCAAGC
Found at i:95754 original size:27 final size:29
Alignment explanation
Indices: 95709--95765 Score: 82
Period size: 27 Copynumber: 2.0 Consensus size: 29
95699 AAAATACGAG
*
95709 CAAGCAAAAAACACGAACCAAGCAAAAAT
1 CAAGCAAAAAACACGAACCAAACAAAAAT
*
95738 CAAGCAAAAAA-A-TAACCAAACAAAAAT
1 CAAGCAAAAAACACGAACCAAACAAAAAT
95765 C
1 C
95766 GTCAAGGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 14 0.54
28 1 0.04
29 11 0.42
ACGTcount: A:0.65, C:0.23, G:0.07, T:0.05
Consensus pattern (29 bp):
CAAGCAAAAAACACGAACCAAACAAAAAT
Found at i:96387 original size:14 final size:15
Alignment explanation
Indices: 96345--96407 Score: 67
Period size: 14 Copynumber: 4.2 Consensus size: 15
96335 ATTTAATCCT
*
96345 TTTAATTTAAATTTTG
1 TTTAATTT-AATTTTA
* *
96361 TTTTATTT-CTTTTA
1 TTTAATTTAATTTTA
96375 TTTAA-TTAATTTTA
1 TTTAATTTAATTTTA
96389 TTTAATTTAATTTTCA
1 TTTAATTTAATTTT-A
96405 TTT
1 TTT
96408 TCATTTTCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
13 2 0.05
14 18 0.46
15 8 0.21
16 11 0.28
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (15 bp):
TTTAATTTAATTTTA
Found at i:97133 original size:21 final size:21
Alignment explanation
Indices: 97109--97149 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
97099 TAAGAACCAT
**
97109 AAATCCCCAATTCTTTCCCCC
1 AAATCCCCAACCCTTTCCCCC
97130 AAATCCCCAACCCTTTCCCC
1 AAATCCCCAACCCTTTCCCC
97150 TCATCGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.51, G:0.00, T:0.24
Consensus pattern (21 bp):
AAATCCCCAACCCTTTCCCCC
Found at i:97720 original size:13 final size:13
Alignment explanation
Indices: 97702--97726 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
97692 GAGTCAACCT
97702 GTTGACTTTGACC
1 GTTGACTTTGACC
97715 GTTGACTTTGAC
1 GTTGACTTTGAC
97727 TTTGACCAAA
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:0.20, G:0.24, T:0.40
Consensus pattern (13 bp):
GTTGACTTTGACC
Found at i:103016 original size:23 final size:23
Alignment explanation
Indices: 102986--103037 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
102976 CAATCGAGAC
*
102986 GTGACACATGTAACCATACGATA
1 GTGACACATGTAACCATACAATA
103009 GTGACACATGTAACCATACAATA
1 GTGACACATGTAACCATACAATA
103032 GTGACA
1 GTGACA
103038 TGTAAGCACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.21
Consensus pattern (23 bp):
GTGACACATGTAACCATACAATA
Found at i:104006 original size:18 final size:18
Alignment explanation
Indices: 103981--104057 Score: 92
Period size: 18 Copynumber: 4.6 Consensus size: 18
103971 ACCGGTCACA
103981 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
* *
103999 ATCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
*
104017 ACCTGACCC-A----TTG
1 ACCCGACCCGACCCGTTG
104030 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
104048 ACCCGACCCG
1 ACCCGACCCG
104058 TTGACCGTTG
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
13 10 0.21
14 1 0.02
17 1 0.02
18 36 0.75
ACGTcount: A:0.18, C:0.48, G:0.19, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:104024 original size:13 final size:13
Alignment explanation
Indices: 104003--104078 Score: 53
Period size: 13 Copynumber: 5.3 Consensus size: 13
103993 CCGTTGATCC
104003 GACCCGACCCGTT
1 GACCCGACCCGTT
* * *
104016 TACCTGACCCATT
1 GACCCGACCCGTT
104029 GACCCGACCCGACCCGTT
1 GACCCG-----ACCCGTT
104047 GACCCGACCCGTT
1 GACCCGACCCGTT
*
104060 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
104075 GACC
1 GACC
104079 GTTGACCGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
13 25 0.51
15 12 0.24
18 12 0.24
ACGTcount: A:0.17, C:0.43, G:0.21, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:104036 original size:31 final size:31
Alignment explanation
Indices: 103985--104063 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
103975 GTCACAACCC
*
103985 GACCCGACCCGTTGATCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* * *
104016 TACCTGACCCATTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
104047 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
104064 GTTGACCCGT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.18, C:0.46, G:0.20, T:0.16
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:104050 original size:8 final size:8
Alignment explanation
Indices: 104039--104085 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
104029 GACCCGACCC
104039 GACCCGTT
1 GACCCGTT
104047 GACCC---
1 GACCCGTT
104052 GACCCGTT
1 GACCCGTT
104060 GA-CCGTT
1 GACCCGTT
104067 GACCCGTT
1 GACCCGTT
104075 GA-CCGTT
1 GACCCGTT
104082 GACC
1 GACC
104086 GAAGTTGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
5 5 0.15
7 14 0.41
8 15 0.44
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:104067 original size:7 final size:7
Alignment explanation
Indices: 104055--104086 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
104045 TTGACCCGAC
104055 CCGTTGA
1 CCGTTGA
104062 CCGTTGA
1 CCGTTGA
104069 CCCGTTGA
1 -CCGTTGA
104077 CCGTTGA
1 CCGTTGA
104084 CCG
1 CCG
104087 AAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:104072 original size:15 final size:15
Alignment explanation
Indices: 104039--104085 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
104029 GACCCGACCC
*
104039 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
104052 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
104067 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
104082 GACC
1 GACC
104086 GAAGTTGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:105407 original size:18 final size:18
Alignment explanation
Indices: 105381--105416 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
105371 TCGAAAGGAC
*
105381 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
105399 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
105417 CGGGTGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:106537 original size:23 final size:23
Alignment explanation
Indices: 106511--106584 Score: 96
Period size: 23 Copynumber: 3.2 Consensus size: 23
106501 AATTCTATTA
*
106511 TGATCCTGACCTGGATTCTGATC
1 TGATCATGACCTGGATTCTGATC
*
106534 TGAT-ATTGACATGGATTCTGATC
1 TGATCA-TGACCTGGATTCTGATC
*
106557 TGATACATGACCTGGATTCTGATA
1 TGAT-CATGACCTGGATTCTGATC
106581 TGAT
1 TGAT
106585 ACTTGACTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
23 24 0.55
24 19 0.43
25 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (23 bp):
TGATCATGACCTGGATTCTGATC
Found at i:106572 original size:24 final size:24
Alignment explanation
Indices: 106517--106591 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
106507 ATTATGATCC
106517 TGACCTGGATTCTGATCTGATA-T
1 TGACCTGGATTCTGATCTGATACT
* *
106540 TGACATGGATTCTGATCTGATACA
1 TGACCTGGATTCTGATCTGATACT
*
106564 TGACCTGGATTCTGATATGATACT
1 TGACCTGGATTCTGATCTGATACT
106588 TGAC
1 TGAC
106592 TTGAATTATG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.36
Consensus pattern (24 bp):
TGACCTGGATTCTGATCTGATACT
Found at i:106717 original size:35 final size:35
Alignment explanation
Indices: 106670--106744 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
106660 TGGAGGAAGA
* *
106670 TTACTTGGAGGCTCCTTGGCTGTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTGTGTGCTCAGGGCC
*
106705 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTGTGTGCTCAGGGCC
106740 TTACT
1 TTACT
106745 GTTCGTGACG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.09, C:0.28, G:0.29, T:0.33
Consensus pattern (35 bp):
TTACTTGCAGGCTCCTCGGCTGTGTGCTCAGGGCC
Found at i:108786 original size:18 final size:18
Alignment explanation
Indices: 108761--108837 Score: 92
Period size: 18 Copynumber: 4.6 Consensus size: 18
108751 ACCGGTCACA
108761 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
* *
108779 ATCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
*
108797 ACCTGACCC-A----TTG
1 ACCCGACCCGACCCGTTG
108810 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
108828 ACCCGACCCG
1 ACCCGACCCG
108838 TTGACCGTTG
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
13 10 0.21
14 1 0.02
17 1 0.02
18 36 0.75
ACGTcount: A:0.18, C:0.48, G:0.19, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:108804 original size:13 final size:13
Alignment explanation
Indices: 108783--108858 Score: 53
Period size: 13 Copynumber: 5.3 Consensus size: 13
108773 CCGTTGATCC
108783 GACCCGACCCGTT
1 GACCCGACCCGTT
* * *
108796 TACCTGACCCATT
1 GACCCGACCCGTT
108809 GACCCGACCCGACCCGTT
1 GACCCG-----ACCCGTT
108827 GACCCGACCCGTT
1 GACCCGACCCGTT
*
108840 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
108855 GACC
1 GACC
108859 GTTGACCGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
13 25 0.51
15 12 0.24
18 12 0.24
ACGTcount: A:0.17, C:0.43, G:0.21, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:108816 original size:31 final size:31
Alignment explanation
Indices: 108765--108843 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
108755 GTCACAACCC
*
108765 GACCCGACCCGTTGATCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* * *
108796 TACCTGACCCATTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
108827 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
108844 GTTGACCCGT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.18, C:0.46, G:0.20, T:0.16
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:108830 original size:8 final size:8
Alignment explanation
Indices: 108819--108865 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
108809 GACCCGACCC
108819 GACCCGTT
1 GACCCGTT
108827 GACCC---
1 GACCCGTT
108832 GACCCGTT
1 GACCCGTT
108840 GA-CCGTT
1 GACCCGTT
108847 GACCCGTT
1 GACCCGTT
108855 GA-CCGTT
1 GACCCGTT
108862 GACC
1 GACC
108866 GAAGTTGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
5 5 0.15
7 14 0.41
8 15 0.44
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:108847 original size:7 final size:7
Alignment explanation
Indices: 108835--108866 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
108825 TTGACCCGAC
108835 CCGTTGA
1 CCGTTGA
108842 CCGTTGA
1 CCGTTGA
108849 CCCGTTGA
1 -CCGTTGA
108857 CCGTTGA
1 CCGTTGA
108864 CCG
1 CCG
108867 AAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:108852 original size:15 final size:15
Alignment explanation
Indices: 108819--108865 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
108809 GACCCGACCC
*
108819 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
108832 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
108847 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
108862 GACC
1 GACC
108866 GAAGTTGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:110187 original size:18 final size:18
Alignment explanation
Indices: 110161--110196 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
110151 TCGAAAGGAC
*
110161 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
110179 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
110197 CGGGTGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:111317 original size:23 final size:23
Alignment explanation
Indices: 111291--111364 Score: 96
Period size: 23 Copynumber: 3.2 Consensus size: 23
111281 AATTCTATTA
*
111291 TGATCCTGACCTGGATTCTGATC
1 TGATCATGACCTGGATTCTGATC
*
111314 TGAT-ATTGACATGGATTCTGATC
1 TGATCA-TGACCTGGATTCTGATC
*
111337 TGATACATGACCTGGATTCTGATA
1 TGAT-CATGACCTGGATTCTGATC
111361 TGAT
1 TGAT
111365 ACTTGACTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
23 24 0.55
24 19 0.43
25 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (23 bp):
TGATCATGACCTGGATTCTGATC
Found at i:111352 original size:24 final size:24
Alignment explanation
Indices: 111297--111371 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
111287 ATTATGATCC
111297 TGACCTGGATTCTGATCTGATA-T
1 TGACCTGGATTCTGATCTGATACT
* *
111320 TGACATGGATTCTGATCTGATACA
1 TGACCTGGATTCTGATCTGATACT
*
111344 TGACCTGGATTCTGATATGATACT
1 TGACCTGGATTCTGATCTGATACT
111368 TGAC
1 TGAC
111372 TTGAATTATG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.36
Consensus pattern (24 bp):
TGACCTGGATTCTGATCTGATACT
Found at i:111496 original size:35 final size:35
Alignment explanation
Indices: 111449--111523 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
111439 TGGAGGAAGA
* *
111449 TTACTTGGAGGCTCCTTGGCTGTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTGTGTGCTCAGGGCC
*
111484 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTGTGTGCTCAGGGCC
111519 TTACT
1 TTACT
111524 GTTCGTGACG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.09, C:0.28, G:0.29, T:0.33
Consensus pattern (35 bp):
TTACTTGCAGGCTCCTCGGCTGTGTGCTCAGGGCC
Found at i:113207 original size:451 final size:454
Alignment explanation
Indices: 112167--113287 Score: 1488
Period size: 455 Copynumber: 2.5 Consensus size: 454
112157 CAATAAAATA
* * * *
112167 TTGGTGTCAAAATAACCACCATTTTTAAAATTGTGTCAATATGATCACTTAACTATTTAATTAGT
1 TTGGTGTCAAAATAACCACCATTTTTAAAATTGAGTTAATATGACCACTTAACTATTTAATTGGT
* * * * *
112232 ATCATTCAAGCCACATGTCATTAATACTTAACGAGATGATGATGTGTCAATTAACATAATTACTA
66 ATCATTCAAGCCACATGCCATTAATATTTAACGAGATGCTGACGTGTCAGTTAACATAATTACTA
* * *
112297 TAATTACATATTTGATCCTCAATATTTTTACATTTAACCAATTTGATCCTAATTTTGATTTAATT
131 TAATTACATATTTGATCATCAATATTTTTACATTTAATCAATTTGGTCCTAATTTTGATTTAATT
* *
112362 TAATAAATTAACCACTT-AATCAAGAGGTAATAAATGTCACCATACGATCGTGACACATGTAAGC
196 TAATAAATTAACCA-TTCAATCAAGAGGTAATAAATGCCACCATACGATCATGACACATGTAAGC
* *
112426 ATCTGAATGGATTTTTTTTAATTAATTTATTTAAATTTATGTTCAATTCAATCGCGACACATGTT
260 ATCTGAATGGA-TGTTTTTAATTAATTTATTTAAATTTATGTTCAATTCAATCGCGACACATGTC
* * *
112491 ATCATTGATTGGGTTGAAAATAAATGGAGACTGTAATTTCTTGTACGTCACTGCATCATTTGAAT
324 ATCATTGATTGGATTGAAAATAAATGGAGAATGTAATCTCTTGTACGTCACTGCATCATTTGAAT
* ** *
112556 TTTATTAATTACACTGTAATTTTATTTATTAGAGTAAACTACTTGAATGACCACTTAACTATATG
389 TTTATTAATTACACTGTAATTTTACTTATTAGAGTAAACTACTTGAATGAAAACTTAACAATATG
112621 G
454 G
*
112622 TTGGTGTCAAAATAACCACCATTTTCAAAATT-A-TATCAATATGACCACTTAACTATTTAATTG
1 TTGGTGTCAAAATAACCACCATTTTTAAAATTGAGT-T-AATATGACCACTTAACTATTTAATTG
* * * * * *
112685 GCATCATTAAAGCTACATGCCATTAATATTTAACGAGATGCCGACATGTTAGTTAACATAATTAC
64 GTATCATTCAAGCCACATGCCATTAATATTTAACGAGATGCTGACGTGTCAGTTAACATAATTAC
* * * * *
112750 TATAATTGCATATTTAATCTTTAATATTTTTACATTTAATTAATTTGGTCCTAATTTTGATTTAA
129 TATAATTACATATTTGATCATCAATATTTTTACATTTAATCAATTTGGTCCTAATTTTGATTTAA
* * * * *
112815 TCTATTAAATTAACCATTCAATCAATAGGTGATACATGCCACCATACGATCATGACACATGTAAG
194 TTTAATAAATTAACCATTCAATCAAGAGGTAATAAATGCCACCATACGATCATGACACATGTAAG
* * * * * * *
112880 CA-CTTGAATGGA-GTTTTTATTTATTTTA-TTATATTTATTTTCAA-TCTAATCGTGATACGTG
259 CATC-TGAATGGATGTTTTTAATTAATTTATTTAAATTTATGTTCAATTC-AATCGCGACACATG
* **
112941 TCATCATTGATTGGATT-AAAATAAATGGGAGAATGTAATCTCTTGTAGGTTGCTGCATCATTTG
322 TCATCATTGATTGGATTGAAAATAAAT-GGAGAATGTAATCTCTTGTACGTCACTGCATCATTTG
* * * *
113005 AATTTTATTAATTGCACTTTAATTTTACTT-TTAGGGTAAAATTA-TTGAATGAAAACTTAACAA
386 AATTTTATTAATTACACTGTAATTTTACTTATTAGAGT-AAACTACTTGAATGAAAACTTAACAA
*
113068 TTTGG
450 TATGG
* * *
113073 TTGGTGTCAAAATAACCACTATTTTTAAAATTGAGTTAATATAACCACTTAGCTATTTAATTGGT
1 TTGGTGTCAAAATAACCACCATTTTTAAAATTGAGTTAATATGACCACTTAACTATTTAATTGGT
* * * * *
113138 ATAATTCAAGCCATATGCCATTAATATTTAACGGGATGCTAACGTGTCAGTTAACATAATTGCTA
66 ATCATTCAAGCCACATGCCATTAATATTTAACGAGATGCTGACGTGTCAGTTAACATAATTACTA
* * * *
113203 TAATTACACATTTGATCATCAATATTTTTACATTGAATCATTTTGGTCTTAATTTTGATTTAATT
131 TAATTACATATTTGATCATCAATATTTTTACATTTAATCAATTTGGTCCTAATTTTGATTTAATT
*
113268 TAATAAATTAATCATTCAAT
196 TAATAAATTAACCATTCAAT
113288 AACGGGATGC
Statistics
Matches: 576, Mismatches: 81, Indels: 22
0.85 0.12 0.03
Matches are distributed among these distances:
451 220 0.38
452 106 0.18
453 15 0.03
454 3 0.01
455 232 0.40
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (454 bp):
TTGGTGTCAAAATAACCACCATTTTTAAAATTGAGTTAATATGACCACTTAACTATTTAATTGGT
ATCATTCAAGCCACATGCCATTAATATTTAACGAGATGCTGACGTGTCAGTTAACATAATTACTA
TAATTACATATTTGATCATCAATATTTTTACATTTAATCAATTTGGTCCTAATTTTGATTTAATT
TAATAAATTAACCATTCAATCAAGAGGTAATAAATGCCACCATACGATCATGACACATGTAAGCA
TCTGAATGGATGTTTTTAATTAATTTATTTAAATTTATGTTCAATTCAATCGCGACACATGTCAT
CATTGATTGGATTGAAAATAAATGGAGAATGTAATCTCTTGTACGTCACTGCATCATTTGAATTT
TATTAATTACACTGTAATTTTACTTATTAGAGTAAACTACTTGAATGAAAACTTAACAATATGG
Found at i:113329 original size:97 final size:97
Alignment explanation
Indices: 113198--113384 Score: 257
Period size: 97 Copynumber: 1.9 Consensus size: 97
113188 TTAACATAAT
** * * *
113198 TGCTATAATTACACATTTGATCATCAATATTTTTACATTGAATCATTTTGGTCTTAATTTTGATT
1 TGCTATAATTACACATTTGATCATCAATATTTTTACATTGAATCAAGTTGATCCTAATCTTGATT
*
113263 TAATTTAATAAATTAATCATTCAATAACGGGA
66 TAATTTAATAAATTAACCATTCAATAACGGGA
* * * * *
113295 TGCTATAATTATATATTTGATCCTCGATATTTTTACATTTAATCAAGTTGATCCTAATCTTGATT
1 TGCTATAATTACACATTTGATCATCAATATTTTTACATTGAATCAAGTTGATCCTAATCTTGATT
* *
113360 TAGTTTATTAAATTAACCATTCAAT
66 TAATTTAATAAATTAACCATTCAAT
113385 CAGTTGGTGA
Statistics
Matches: 77, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
97 77 1.00
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45
Consensus pattern (97 bp):
TGCTATAATTACACATTTGATCATCAATATTTTTACATTGAATCAAGTTGATCCTAATCTTGATT
TAATTTAATAAATTAACCATTCAATAACGGGA
Found at i:114272 original size:14 final size:14
Alignment explanation
Indices: 114250--114280 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
114240 GAATAGAGTT
*
114250 TTTACTTAAATTTA
1 TTTAATTAAATTTA
114264 TTTAATTAAATTTA
1 TTTAATTAAATTTA
114278 TTT
1 TTT
114281 TCAATCTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTAATTAAATTTA
Found at i:114700 original size:14 final size:14
Alignment explanation
Indices: 114681--114715 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
114671 GAATAGAGTT
* *
114681 TTTATTTATTTTAA
1 TTTATTTAATTAAA
114695 TTTATTTAATTAAA
1 TTTATTTAATTAAA
114709 TTTATTT
1 TTTATTT
114716 TTAATCCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTATTTAATTAAA
Found at i:115000 original size:438 final size:430
Alignment explanation
Indices: 114001--115245 Score: 1321
Period size: 438 Copynumber: 2.9 Consensus size: 430
113991 AATTACTATG
* * *
114001 TTTAAAATTGTGTCAATATGACAATTTAACTATTTAGTTGGTATCATTCAAGTCACATGTCATTT
1 TTTAAAATTGTGTCAATATGAC-ATTTAACTATTTAATTGGTATCATTCAAGCCACATGTCATTA
* * * *
114066 ATATTTAATGAGATCCTGACGTGTCAGTTAACATAATTGTTATAATTATATATTTGATCCTCAAT
65 ATATTTAACGAGATCATGACGTGTCAGTTAACATAATTGCTATAATTAAATATTTGATCCTCAAT
* * * *
114131 ATTTTTACATTTAATCAAATTGATCCTAATTTTAATTTAATTTAATAAAGTAATAATTTAATCAG
130 ATTTTTACATTTAATCAATTTGGTCCTAATTTTAATTTAATTTAATAAATTAATCA-TTAAT-AG
* * *
114196 AAAGTGACACATATCA-CATACGATCGTGACACATGTAAGCA-TCTGAATAGAGTTTTTACTTA-
193 AGAGTGACACATGTCACCATACGATCGTGACACATGTAAGCACT-TGAATAGAGTTTTTATTTAT
* * * * * * * *
114258 -AATTTATTTAATTAAATTTATTTTCAATCTAATCACGACACGTGTCATCGTCGATTAGGTTGAA
257 TAATTTATTTAATTAAATTTATTTTCAATCCAATCGCAAAAAGTGTCATCATTGATTGGGTTGAA
* * * * * * * *
114322 AATAAACCT--ACATCTTTTGAATTTTATTATTCGT-ACTT--TAATTAT-ATTTTTAGGGTAA-
322 AATAAA-TTGGAGA-C--CTGAA-TTTCTTGTACGTCACTTCATAATT-TGAATTTTA--TTAAT
* * *
114380 ACTACTTTAATGACCACTTAATTATAGGATTCATGACAAAATAACCACCATT
379 TCTACTTTAATGACCACTTAATTAAAAGATTCATGACAAAATAACCACCATT
* * *
114432 TTTAAAATTGTGTCAATATGACCATTTAAC-ATTTAATTGGTATTATTCAAGGCACATGCCATTA
1 TTTAAAATTGTGTCAATATGA-CATTTAACTATTTAATTGGTATCATTCAAGCCACATGTCATTA
* * * *
114496 ATATTTAACGGGA-CATTGATGTGTCAGTTAACATAATTGCTATAATTAAACATTTGATCTTCAA
65 ATATTTAACGAGATCA-TGACGTGTCAGTTAACATAATTGCTATAATTAAATATTTGATCCTCAA
* * *
114560 TATTTTTACATTTAATCAATTTGGTCATAATTTTTATTTAATTTAATAAATTAATCATTCAATTG
129 TATTTTTACATTTAATCAATTTGGTCCTAATTTTAATTTAATTTAATAAATTAATCATT-AATAG
* *
114625 AGAGTTGACACATGTAACCATACAATCGTGACACATGTAAGCACTTGAATAGAGTTTTTATTTAT
193 AGAG-TGACACATGTCACCATACGATCGTGACACATGTAAGCACTTGAATAGAGTTTTTATTTA-
* * *
114690 TTTAATTTATTTAATTAAATTTATTTTTAATCCAATCGCAAAAAGTGTCAACATTTATTGGGTTG
256 -TTAATTTATTTAATTAAATTTATTTTCAATCCAATCGCAAAAAGTGTCATCATTGATTGGGTTG
* * * * *
114755 AAAATAAATTGGAGACCAGAATTTCTTGTAGGTCACTTCATTATTTGAATTTTATTAATTGTAGT
320 AAAATAAATTGGAGACCTGAATTTCTTGTACGTCACTTCATAATTTGAATTTTATTAATTCTACT
* **** * ** *
114820 TTAATTTTATTTTTTAGGA-TAAAATATTGGTGTCAAAATAACCACCATT
385 TTAA--TGACCACTTA--ATTAAAAGATTCATGACAAAATAACCACCATT
* *
114869 TTTAAAATTGTGTCAATATGATCACTTAACTATTTAATTAGTATCATTCAAGCCACATGTCATTA
1 TTTAAAATTGTGTCAATATGA-CATTTAACTATTTAATTGGTATCATTCAAGCCACATGTCATTA
* * * * *
114934 ATACTTAACGAGATGATGACGTGTCAATTAACATAATTACTATAATTACATATTTGATCCTCAAT
65 ATATTTAACGAGATCATGACGTGTCAGTTAACATAATTGCTATAATTAAATATTTGATCCTCAAT
* *
114999 ATTTTTACATTTAACCAATTTGGTCCTAATTTTGATTTAATTTAATAAATTAA-CTACTTAATCA
130 ATTTTTACATTTAATCAATTTGGTCCTAATTTTAATTTAATTTAATAAATTAATC-A-TTAAT-A
* * * * *
115063 -AGAGGTAACAAATGTCACCATACGATCGTGACACATGTAAGCACCTGAATGGAGTTTTT-TTAA
192 GAGA-GTGACACATGTCACCATACGATCGTGACACATGTAAGCACTTGAATAGAGTTTTTATTTA
* * * * *
115126 TTAATTTA--T--TTAAATTTATGTTCAATTCAATCGCGACACA-TGTTATCATTGATTGGGTTG
256 TTAATTTATTTAATTAAATTTATTTTCAATCCAATCGC-AAAAAGTGTCATCATTGATTGGGTTG
* *
115186 AAAATAAATTGGAGA-CTGTAATTTCTTGTACGTCACTGCATCATTTGAATTTTATTAATT
320 AAAATAAATTGGAGACCTG-AATTTCTTGTACGTCACTTCATAATTTGAATTTTATTAATT
115246 ACACTGTAAT
Statistics
Matches: 686, Mismatches: 99, Indels: 58
0.81 0.12 0.07
Matches are distributed among these distances:
429 7 0.01
430 149 0.22
431 162 0.24
432 13 0.02
433 11 0.02
434 9 0.01
435 78 0.11
436 7 0.01
437 56 0.08
438 190 0.28
439 4 0.01
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (430 bp):
TTTAAAATTGTGTCAATATGACATTTAACTATTTAATTGGTATCATTCAAGCCACATGTCATTAA
TATTTAACGAGATCATGACGTGTCAGTTAACATAATTGCTATAATTAAATATTTGATCCTCAATA
TTTTTACATTTAATCAATTTGGTCCTAATTTTAATTTAATTTAATAAATTAATCATTAATAGAGA
GTGACACATGTCACCATACGATCGTGACACATGTAAGCACTTGAATAGAGTTTTTATTTATTAAT
TTATTTAATTAAATTTATTTTCAATCCAATCGCAAAAAGTGTCATCATTGATTGGGTTGAAAATA
AATTGGAGACCTGAATTTCTTGTACGTCACTTCATAATTTGAATTTTATTAATTCTACTTTAATG
ACCACTTAATTAAAAGATTCATGACAAAATAACCACCATT
Found at i:126253 original size:19 final size:19
Alignment explanation
Indices: 126229--126272 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
126219 GAACTTGAAT
126229 GGTCAATTAGAAATATTAA
1 GGTCAATTAGAAATATTAA
126248 GGTCAATTAGAAATATTAA
1 GGTCAATTAGAAATATTAA
126267 GGTCAA
1 GGTCAA
126273 CATTTATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.30
Consensus pattern (19 bp):
GGTCAATTAGAAATATTAA
Found at i:130541 original size:22 final size:22
Alignment explanation
Indices: 130516--130565 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
130506 TTTGTTTTTT
* *
130516 TATATGATACATTTTATTATTA
1 TATATAATACATATTATTATTA
*
130538 TATATAATATATATTATTATTA
1 TATATAATACATATTATTATTA
130560 TATATA
1 TATATA
130566 TTTAGCGTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (22 bp):
TATATAATACATATTATTATTA
Found at i:130554 original size:19 final size:17
Alignment explanation
Indices: 130530--130566 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
130520 TGATACATTT
130530 TATTATTATATATAATATA
1 TATTATTAT-TAT-ATATA
130549 TATTATTATTATATATA
1 TATTATTATTATATATA
130566 T
1 T
130567 TTAGCGTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATTATTATTATATATA
Found at i:130606 original size:2 final size:2
Alignment explanation
Indices: 130601--130627 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
130591 TCTTGTTAAT
130601 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
130628 TATTTAATTA
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:133428 original size:5 final size:5
Alignment explanation
Indices: 133399--133537 Score: 75
Period size: 5 Copynumber: 28.2 Consensus size: 5
133389 ACACTTAGTA
* *
133399 TATAT TA-AT ATATAT TA-AG TATAT TATAT T-TA- TATAT TATAT GGTACA-
1 TATAT TATAT -TATAT TATAT TATAT TATAT TATAT TATAT TATAT --TATAT
*
133447 TATAAT TGATA- TATAT TATTAT TATAT TATAT TTTA- TATAT TATAT
1 TAT-AT T-ATAT TATAT TA-TAT TATAT TATAT TATAT TATAT TATAT
* *
133493 ATATTAT TATAT T-TAT AATA- TAAACT T-TA- TATAT TATAT TATAT
1 -TA-TAT TATAT TATAT TATAT TATA-T TATAT TATAT TATAT TATAT
133537 T
1 T
133538 GTAATATACC
Statistics
Matches: 104, Mismatches: 10, Indels: 40
0.68 0.06 0.26
Matches are distributed among these distances:
3 2 0.02
4 24 0.23
5 56 0.54
6 14 0.13
7 8 0.08
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (5 bp):
TATAT
Found at i:133460 original size:38 final size:38
Alignment explanation
Indices: 133418--133509 Score: 98
Period size: 38 Copynumber: 2.4 Consensus size: 38
133408 ATATATTAAG
133418 TATATTATATTTATATATTATATGGTACATATAATTGATA
1 TATATTATATTTATATATTATATGGTACATATAA-T-ATA
* ** * *
133458 TATATTAT-TAT-TATATTATATTTTATATATTATATA
1 TATATTATATTTATATATTATATGGTACATATAATATA
133494 TATTATTATATTTATA
1 TA-TATTATATTTATA
133510 ATATAAACTT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
36 5 0.12
37 7 0.16
38 19 0.44
39 4 0.09
40 8 0.19
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (38 bp):
TATATTATATTTATATATTATATGGTACATATAATATA
Found at i:133508 original size:9 final size:10
Alignment explanation
Indices: 133397--133514 Score: 62
Period size: 9 Copynumber: 12.6 Consensus size: 10
133387 ATACACTTAG
*
133397 TATATATTAA
1 TATATATTAT
133407 TATATATTA-
1 TATATATTAT
133416 -AGTATATTA-
1 TA-TATATTAT
*
133425 TATTTATATAT
1 TATATAT-TAT
**
133436 TATATGGTA-
1 TATATATTAT
*
133445 CATATA--AT
1 TATATATTAT
133453 TGATATA-TAT
1 T-ATATATTAT
133463 TAT-TATTA-
1 TATATATTAT
133471 TATTATATT-T
1 TA-TATATTAT
133481 TATATATTA-
1 TATATATTAT
133490 TATATATTAT
1 TATATATTAT
133500 TATAT-TTAT
1 TATATATTAT
*
133509 AATATA
1 TATATA
133515 AACTTTATAT
Statistics
Matches: 86, Mismatches: 8, Indels: 28
0.70 0.07 0.23
Matches are distributed among these distances:
7 1 0.01
8 5 0.06
9 48 0.56
10 28 0.33
11 4 0.05
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (10 bp):
TATATATTAT
Found at i:133523 original size:32 final size:31
Alignment explanation
Indices: 133419--133545 Score: 98
Period size: 32 Copynumber: 4.0 Consensus size: 31
133409 TATATTAAGT
* **
133419 ATATTATATTTATATATTATATGGTACATATAA
1 ATATTATATATAT-TATTATATTATA-ATATAA
* * * *
133452 TTGA-TATATATTATTATTATATTATATTTTAT
1 AT-ATTATATA-TATTATTATATTATAATATAA
133484 ATATTATATATATTATTATATTTATAATATAA
1 ATATTATATATATTATTATA-TTATAATATAA
*
133516 ACT-TTATATAT-TATATTATATTGTAATATA
1 A-TATTATATATAT-TATTATATTATAATATA
133546 CCTATTTATT
Statistics
Matches: 76, Mismatches: 12, Indels: 14
0.75 0.12 0.14
Matches are distributed among these distances:
31 21 0.28
32 34 0.45
33 17 0.22
34 4 0.05
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (31 bp):
ATATTATATATATTATTATATTATAATATAA
Found at i:133545 original size:10 final size:10
Alignment explanation
Indices: 133466--133545 Score: 53
Period size: 9 Copynumber: 8.2 Consensus size: 10
133456 TATATATTAT
*
133466 TATTATATTA
1 TATTATAATA
*
133476 TATT-TTATA
1 TATTATAATA
133485 TATTAT-ATA
1 TATTATAATA
*
133494 TATTATTATA
1 TATTATAATA
133504 T-TTATAATA
1 TATTATAATA
133513 TAAACTT-T-ATA
1 T--A-TTATAATA
*
133524 TATTATATTA
1 TATTATAATA
*
133534 TATTGTAATA
1 TATTATAATA
133544 TA
1 TA
133546 CCTATTTATT
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
8 2 0.04
9 26 0.46
10 21 0.38
11 4 0.07
12 1 0.02
13 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (10 bp):
TATTATAATA
Found at i:134708 original size:5 final size:5
Alignment explanation
Indices: 134688--134729 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
134678 AATCCTTTTC
134688 ATTTA ATTT- -TTT- ATTTA ATTTA ATTTA ATTTAA ATTTA ATTT
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTT-A ATTTA ATTT
134730 TTTATCTACT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 3 0.09
4 3 0.09
5 23 0.68
6 5 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
ATTTA
Found at i:134725 original size:16 final size:15
Alignment explanation
Indices: 134688--134729 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
134678 AATCCTTTTC
134688 ATTTAATTT--TTT-
1 ATTTAATTTAATTTA
134700 ATTTAATTTAATTTA
1 ATTTAATTTAATTTA
134715 ATTTAAATTTAATTT
1 ATTT-AATTTAATTT
134730 TTTATCTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 9 0.35
14 3 0.12
15 4 0.15
16 10 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTTAATTTAATTTA
Found at i:140637 original size:22 final size:21
Alignment explanation
Indices: 140604--140645 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
140594 AGGATAAATT
140604 ATGAGACTATATGTGAAATGAA
1 ATGAGACTATAT-TGAAATGAA
*
140626 ATGAGTAC-ATATTTAAATGA
1 ATGAG-ACTATATTGAAATGA
140646 TGAGATTGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 7 0.39
22 9 0.50
23 2 0.11
ACGTcount: A:0.45, C:0.05, G:0.19, T:0.31
Consensus pattern (21 bp):
ATGAGACTATATTGAAATGAA
Found at i:141054 original size:22 final size:21
Alignment explanation
Indices: 141004--141054 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 21
140994 GACACATACT
*
141004 TGGTCCTT-AGAATATGTATA
1 TGGTCCTTAAGAATATCTATA
* * *
141024 TGATTCTTAAGGAATATCTATG
1 TGGTCCTTAA-GAATATCTATA
141046 TGGTCCTTA
1 TGGTCCTTA
141055 TGGACATTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 6 0.26
21 1 0.04
22 16 0.70
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (21 bp):
TGGTCCTTAAGAATATCTATA
Found at i:141096 original size:23 final size:23
Alignment explanation
Indices: 141059--141131 Score: 96
Period size: 23 Copynumber: 3.2 Consensus size: 23
141049 TCCTTATGGA
*
141059 CATTT-TATATGGCACTTCGGTG
1 CATTTCTACATGGCACTTCGGTG
141081 CATTTCTA-ATCGGCACTTCGGTG
1 CATTTCTACAT-GGCACTTCGGTG
* *
141104 CAATTCTACGTGGCACTTCGGTG
1 CATTTCTACATGGCACTTCGGTG
141127 CATTT
1 CATTT
141132 ATACGAGATG
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
22 7 0.16
23 37 0.82
24 1 0.02
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.37
Consensus pattern (23 bp):
CATTTCTACATGGCACTTCGGTG
Found at i:145904 original size:2 final size:2
Alignment explanation
Indices: 145897--145944 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
145887 AGGTAAAATG
145897 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
145939 AT AT AT
1 AT AT AT
145945 GACTATGAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:146482 original size:23 final size:23
Alignment explanation
Indices: 146455--146500 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
146445 ACATTTTATA
*
146455 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTATACG
146478 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTATACG
146501 AGCTGTGGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.15, C:0.24, G:0.26, T:0.35
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTATACG
Found at i:147627 original size:73 final size:72
Alignment explanation
Indices: 147505--147743 Score: 295
Period size: 73 Copynumber: 3.3 Consensus size: 72
147495 CAATTTGGAT
* * * *
147505 TCAACTTCACGACGAAAGAGTCACCTACT-ATTTCAACTTCACAACGAAGGATATTGTGCCCAAA
1 TCAACTTTACGACGAAAGAGTCACCCA-TGATTTCAACTTCACAAAGAAGGATATCGTGCCC-AA
147569 TAGATCGAC
64 TAGATCGAC
* *
147578 TCAACTTTGCGACGAAAGAGTCTCCCATGATTTCAACTTCACAAAGAAGGATATCGTGCCCAATA
1 TCAACTTTACGACGAAAGAGTCACCCATGATTTCAACTTCACAAAGAAGGATATCGTGCCCAATA
147643 GATCGAC
66 GATCGAC
* * * * * *
147650 ACAACTTTATGACGAAAGAGTCACACACGATTT-AACTTCACAACA-AAAGATATCGTTCCCAAT
1 TCAACTTTACGACGAAAGAGTCACCCATGATTTCAACTTCACAA-AGAAGGATATCGTGCCCAAT
147713 AGATCGAC
65 AGATCGAC
* * *
147721 TCAACTTCACGGCGAATGAGTCA
1 TCAACTTTACGACGAAAGAGTCA
147744 TCTACGACAT
Statistics
Matches: 145, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
71 52 0.36
72 40 0.28
73 53 0.37
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (72 bp):
TCAACTTTACGACGAAAGAGTCACCCATGATTTCAACTTCACAAAGAAGGATATCGTGCCCAATA
GATCGAC
Found at i:147726 original size:71 final size:71
Alignment explanation
Indices: 147505--147743 Score: 293
Period size: 71 Copynumber: 3.3 Consensus size: 71
147495 CAATTTGGAT
* * * *
147505 TCAACTTCACGACGAAAGAGTCACCTACTATTTCAACTTCACAACGAAGGATATTGTGCCCAAAT
1 TCAACTTTACGACGAAAGAGTCACC-ACGATTTCAACTTCACAACAAAGGATATCGTGCCC-AAT
147570 AGATCGAC
64 AGATCGAC
* * *
147578 TCAACTTTGCGACGAAAGAGTCTCCCATGATTTCAACTTCACAA-AGAAGGATATCGTGCCCAAT
1 TCAACTTTACGACGAAAGAGTC-ACCACGATTTCAACTTCACAACA-AAGGATATCGTGCCCAAT
147642 AGATCGAC
64 AGATCGAC
* * * *
147650 ACAACTTTATGACGAAAGAGTCACACACGATTT-AACTTCACAACAAAAGATATCGTTCCCAATA
1 TCAACTTTACGACGAAAGAGTCAC-CACGATTTCAACTTCACAACAAAGGATATCGTGCCCAATA
147714 GATCGAC
65 GATCGAC
* * *
147721 TCAACTTCACGGCGAATGAGTCA
1 TCAACTTTACGACGAAAGAGTCA
147744 TCTACGACAT
Statistics
Matches: 143, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
71 53 0.37
72 38 0.27
73 50 0.35
74 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (71 bp):
TCAACTTTACGACGAAAGAGTCACCACGATTTCAACTTCACAACAAAGGATATCGTGCCCAATAG
ATCGAC
Found at i:147942 original size:2 final size:2
Alignment explanation
Indices: 147911--148039 Score: 69
Period size: 2 Copynumber: 65.0 Consensus size: 2
147901 ATTCAACTTA
*
147911 AT AT AGT AT GT AT -T AT AT AT -T AT ACT -T AT AT AT CAT AT AGT
1 AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT -AT AT A-T
* * *
147952 AT AT AT CAGT AT AT AT -T AA AT AT -T TT AT AT TT AT AT AT -T AT
1 AT AT AT -A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
147993 AT GGT AT AT AT AT TT GAT AT AT AT -T AT -T AT -T AT AT AT AT AT
1 AT -AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
148034 AT AT AT
1 AT AT AT
148040 TATTATTATA
Statistics
Matches: 99, Mismatches: 11, Indels: 34
0.69 0.08 0.24
Matches are distributed among these distances:
1 9 0.09
2 78 0.79
3 11 0.11
4 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (2 bp):
AT
Found at i:148137 original size:40 final size:40
Alignment explanation
Indices: 148033--148137 Score: 94
Period size: 40 Copynumber: 2.6 Consensus size: 40
148023 TATATATATA
* *
148033 TATATATTATTAT-TATAATTATATTATAAACTTCATATAT
1 TATAT-TTATTATATATTATTATATTATAAACTTCATAGAT
* *
148073 TATATTT-TTCATAT-TATATCATATTATAGATA-TT-TTAGAT
1 TATATTTATT-ATATAT-TATTATATTATA-A-ACTTCATAGAT
148113 TATATTTATTATATATTATTATATT
1 TATATTTATTATATATTATTATATT
148138 TTATTATATA
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
38 2 0.04
39 5 0.09
40 39 0.74
41 6 0.11
42 1 0.02
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (40 bp):
TATATTTATTATATATTATTATATTATAAACTTCATAGAT
Found at i:148157 original size:20 final size:19
Alignment explanation
Indices: 148112--148158 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
148102 ATATTTTAGA
*
148112 TTATATTTATTATATATTAT
1 TTAT-TTTATTATATACTAT
148132 TATATTTTATTATATACCTAT
1 T-TATTTTATTATATA-CTAT
148153 TTATTT
1 TTATTT
148159 AATTTAATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATTTTATTATATACTAT
Found at i:148778 original size:15 final size:16
Alignment explanation
Indices: 148748--148783 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
148738 TCGAAAACCA
148748 CAAAATACCAAGCAAG
1 CAAAATACCAAGCAAG
*
148764 CAAAATA-CGAGCAAG
1 CAAAATACCAAGCAAG
148779 CAAAA
1 CAAAA
148784 AACACCAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.58, C:0.22, G:0.14, T:0.06
Consensus pattern (16 bp):
CAAAATACCAAGCAAG
Found at i:149426 original size:6 final size:6
Alignment explanation
Indices: 149417--149467 Score: 56
Period size: 6 Copynumber: 9.0 Consensus size: 6
149407 TTGAATTTTG
*
149417 TTTTAT TTTT-T TTATT-T ATTTAT TTTTAT TTTTAT TTTTA- -TTTAT
1 TTTTAT TTTTAT TT-TTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
149462 TTTTAT
1 TTTTAT
149468 CTACTTTACA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 4 0.10
5 5 0.13
6 30 0.77
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTAT
Found at i:149442 original size:22 final size:22
Alignment explanation
Indices: 149418--149467 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 22
149408 TGAATTTTGT
149418 TTTATTTTT-TTTATTTATTTATT
1 TTTATTTTTATTTA-TT-TTTATT
149441 TTTATTTTTATTT-TTATTTATT
1 TTTATTTTTATTTATT-TTTATT
149463 TTTAT
1 TTTAT
149468 CTACTTTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.54
23 9 0.35
24 3 0.12
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (22 bp):
TTTATTTTTATTTATTTTTATT
Found at i:149460 original size:16 final size:16
Alignment explanation
Indices: 149418--149467 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
149408 TGAATTTTGT
*
149418 TTTATTTTTTTTATTTA
1 TTTATTTTTATT-TTTA
149435 TTTATTTTTATTTTTA
1 TTTATTTTTATTTTTA
149451 TTT-TTATTTATTTTTA
1 TTTATT-TTTATTTTTA
149467 T
1 T
149468 CTACTTTACA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
15 2 0.06
16 18 0.58
17 11 0.35
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTATTTTTATTTTTA
Found at i:153612 original size:76 final size:70
Alignment explanation
Indices: 153485--153673 Score: 195
Period size: 70 Copynumber: 2.6 Consensus size: 70
153475 TCTTATCTTT
* * * * * *
153485 GTATTTTAGTTTAAATAGGTTTTAGAATTTTAAATAAG-TTCTAGGAAATTATTTTTATATTTTA
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATT-TAGGAAATTA-TTTAAAATATT-
153549 ACTTTGTTTTAG
63 A---T-TTTTAG
*
153561 GTATTCTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTA-GAATATTATTTAAAATATTAT
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGGAA-ATTATTTAAAATATTAT
153625 TTTTAG
65 TTTTAG
* *
153631 GTATTTTATTTTAAATA-GTTTTAAGTGTTTTAATTAGGATTTA
1 GTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAGGATTTA
153674 AGATCTTTTT
Statistics
Matches: 100, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
69 5 0.05
70 40 0.40
71 1 0.01
74 1 0.01
75 11 0.11
76 40 0.40
77 2 0.02
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (70 bp):
GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGGAAATTATTTAAAATATTATT
TTTAG
Found at i:154329 original size:18 final size:18
Alignment explanation
Indices: 154285--154326 Score: 77
Period size: 17 Copynumber: 2.4 Consensus size: 18
154275 TCTTAGATTA
154285 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTTTCT
154303 TTTATTTAATT-TTTTCT
1 TTTATTTAATTATTTTCT
154320 TTTATTT
1 TTTATTT
154327 TAAAAACAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTATTTAATTATTTTCT
Found at i:159640 original size:18 final size:18
Alignment explanation
Indices: 159613--159655 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
159603 TCTTAGATTA
159613 TTTT-TTTAATTATTT-TC
1 TTTTATTTAATT-TTTATC
159630 TTTTATTTAATTTTTATC
1 TTTTATTTAATTTTTATC
*
159648 TTTCATTT
1 TTTTATTT
159656 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTATTTAATTTTTATC
Found at i:159777 original size:18 final size:16
Alignment explanation
Indices: 159727--159774 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 16
159717 TTCCCTTTTA
*
159727 TTTATTATTATTTCTT
1 TTTATTATTATTTCAT
159743 TTTAATTATTCATTTCAT
1 TTT-ATTATT-ATTTCAT
159761 TTTATTATATATTT
1 TTTATTAT-TATTT
159775 TCAACTTCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 3 0.11
17 15 0.54
18 10 0.36
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTATTATTATTTCAT
Found at i:163514 original size:64 final size:63
Alignment explanation
Indices: 163444--163590 Score: 179
Period size: 64 Copynumber: 2.3 Consensus size: 63
163434 TGCACTAGGG
** * * *
163444 TGTGCATCACTGCATAAATCAGCTTCGATGTTTCAAAATAATCAGGGTGCATCGATGCAT-GTCT
1 TGTGCATCGGTGCATAAATCA-ATTCGATGTTTCAAAATAACCAGAGTGCATCGATGCATGGT-T
* * * *
163508 TGTGCATCGGTGCATAAAATCAATTCGATGTTTTAAAATAGCCAGAGTTCATCTATGCATGGTT
1 TGTGCATCGGTGCAT-AAATCAATTCGATGTTTCAAAATAACCAGAGTGCATCGATGCATGGTT
163572 TGTGCATCGGTGCATAAAT
1 TGTGCATCGGTGCATAAAT
163591 TGCATTAAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
63 4 0.06
64 60 0.83
65 8 0.11
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.33
Consensus pattern (63 bp):
TGTGCATCGGTGCATAAATCAATTCGATGTTTCAAAATAACCAGAGTGCATCGATGCATGGTT
Found at i:164848 original size:21 final size:20
Alignment explanation
Indices: 164790--164911 Score: 68
Period size: 24 Copynumber: 5.6 Consensus size: 20
164780 ACCCAACTTA
*
164790 TGTATCGATGCACTGC-TGAG
1 TGTATCGATGCACTTCATG-G
* *
164810 TGCATCGGTGCATCTTCATGG
1 TGTATCGATGCA-CTTCATGG
164831 TGTATCGATGCACATTCATAGGG
1 TGTATCGATGCAC-TTCAT--GG
**
164854 ATGCGTCGATGCACATTCATAGG
1 -TGTATCGATGCAC-TTCAT-GG
*
164877 -GATACATCGATGCACCTTCATAG
1 TG-T--ATCGATGCA-CTTCATGG
164900 TGTATCGATGCA
1 TGTATCGATGCA
164912 TTATGCACAA
Statistics
Matches: 80, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
20 11 0.14
21 29 0.36
22 2 0.03
23 6 0.08
24 31 0.39
25 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (20 bp):
TGTATCGATGCACTTCATGG
Found at i:164863 original size:24 final size:24
Alignment explanation
Indices: 164834--164899 Score: 105
Period size: 24 Copynumber: 2.8 Consensus size: 24
164824 TTCATGGTGT
*
164834 ATCGATGCACATTCATAGGGATGC
1 ATCGATGCACATTCATAGGGATAC
*
164858 GTCGATGCACATTCATAGGGATAC
1 ATCGATGCACATTCATAGGGATAC
*
164882 ATCGATGCACCTTCATAG
1 ATCGATGCACATTCATAG
164900 TGTATCGATG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (24 bp):
ATCGATGCACATTCATAGGGATAC
Found at i:170557 original size:21 final size:21
Alignment explanation
Indices: 170531--170586 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
170521 GGAGCGTGTT
170531 TGCATCGATGCATAGTCAAGG
1 TGCATCGATGCATAGTCAAGG
170552 TGCATCGATGCATAGTCAAGG
1 TGCATCGATGCATAGTCAAGG
*
170573 TGCATCGATACATA
1 TGCATCGATGCATA
170587 AAGTGTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (21 bp):
TGCATCGATGCATAGTCAAGG
Found at i:170740 original size:64 final size:65
Alignment explanation
Indices: 170645--170790 Score: 183
Period size: 64 Copynumber: 2.3 Consensus size: 65
170635 TGCACTAGGG
*
170645 TGTGCATCGGTGCAT-AAATCAACTTCAATGTTTCAAAATAACCATG-GTGCATCGATGCAT-GT
1 TGTGCATCGGTGCATAAAATCAACTTCAATGTTTCAAAATAACCA-GAGTACATCGATGCATGGT
170707 CT
65 -T
* * * * * *
170709 TGTGCATAGGTGTATAAAATCAA-TTCGATGTTTTAAAATAGCCAGAGTACATCGATGTATGGTT
1 TGTGCATCGGTGCATAAAATCAACTTCAATGTTTCAAAATAACCAGAGTACATCGATGCATGGTT
170773 TGTGCATCGGTGCATAAA
1 TGTGCATCGGTGCATAAA
170791 TTGCATTCAA
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
63 1 0.01
64 60 0.86
65 9 0.13
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (65 bp):
TGTGCATCGGTGCATAAAATCAACTTCAATGTTTCAAAATAACCAGAGTACATCGATGCATGGTT
Found at i:172478 original size:22 final size:23
Alignment explanation
Indices: 172448--172497 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 23
172438 TAAAAATACA
172448 TAAATATATTTATCT-A-AATTATT
1 TAAATATATTT-T-TAATAATTATT
172471 TAAA-ATATTTTTAATAATTATT
1 TAAATATATTTTTAATAATTATT
172493 TAAAT
1 TAAAT
172498 TGAATATTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
20 1 0.04
21 2 0.08
22 17 0.71
23 4 0.17
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TAAATATATTTTTAATAATTATT
Found at i:175812 original size:194 final size:193
Alignment explanation
Indices: 175455--175854 Score: 473
Period size: 194 Copynumber: 2.1 Consensus size: 193
175445 GTGTTTTGCT
* * ** *
175455 ACAATATCTCTTTCGTCACATATAAGTTTATTTTAATGCATTATTTGTGATAATATAAATTATCA
1 ACAATATCTCTTTTGTCACATATAAGTTGATTTTAATGCATTATCCGTGATAATATAAATCATCA
** * *
175520 ATAACGAAATCTTATTTAATTTAGTGACGTAACCAACTGTCATATAATATAAATTATAAAGTGAT
66 ATAACGAAATCTTACATAATTTAGTGACATAACCAACTGTCATATAATATAAATTATAAAGTGAC
* * * * *
175585 GTTATGCATAAACGTCATTCATAATATTATTAGGCAACATTTATATTATGTCACTAA-ATATGTG
131 GTTATACATAAACGTCATCCATAATACTATTAGGCAACA-ATATATTACGTCACTAACA-ATGTG
* * *
175649 ACAATATCTCTTTTGTCACATATAGGTTGATTTTAATGTATTATCCGTGATGATATAAATCATCA
1 ACAATATCTCTTTTGTCACATATAAGTTGATTTTAATGCATTATCCGTGATAATATAAATCATCA
* * ** * *
175714 ATAACGAAATTTTACATAATTTAGTGACATAATCAGTTGTCAT-TGAATATTAATTATATAGTGA
66 ATAACGAAATCTTACATAATTTAGTGACATAACCAACTGTCATAT-AATATAAATTATAAAGTGA
* * ** ** *
175778 CGTTATATATAAATGTCATCCATGTTACTATTAGGTGACAATATATTACGTTACTAACAATGTG
130 CGTTATACATAAACGTCATCCATAATACTATTAGGCAACAATATATTACGTCACTAACAATGTG
*
175842 ACAAT-TTTCTTTT
1 ACAATATCTCTTTT
175855 CTTCATGTAT
Statistics
Matches: 173, Mismatches: 31, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
192 7 0.04
193 25 0.14
194 141 0.82
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.40
Consensus pattern (193 bp):
ACAATATCTCTTTTGTCACATATAAGTTGATTTTAATGCATTATCCGTGATAATATAAATCATCA
ATAACGAAATCTTACATAATTTAGTGACATAACCAACTGTCATATAATATAAATTATAAAGTGAC
GTTATACATAAACGTCATCCATAATACTATTAGGCAACAATATATTACGTCACTAACAATGTG
Found at i:182012 original size:22 final size:21
Alignment explanation
Indices: 181975--182016 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
181965 CCATCTCCAT
*
181975 TTCATCATCAACACCATCAAC
1 TTCATCATCAAAACCATCAAC
181996 TTCATCCATCAAAACCATCAA
1 TTCAT-CATCAAAACCATCAA
182017 TTCCGCAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.40, C:0.36, G:0.00, T:0.24
Consensus pattern (21 bp):
TTCATCATCAAAACCATCAAC
Found at i:182356 original size:17 final size:19
Alignment explanation
Indices: 182311--182361 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
182301 AAATTGGAGT
182311 AGAAAAAGAAAGAAAATAC
1 AGAAAAAGAAAGAAAATAC
*
182330 AAAAAGAAGAAA-AAAATA-
1 AGAAA-AAGAAAGAAAATAC
182348 AGAAAAAG-AAGAAA
1 AGAAAAAGAAAGAAA
182362 GAAAAAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 2 0.07
17 6 0.21
18 4 0.14
19 10 0.36
20 6 0.21
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (19 bp):
AGAAAAAGAAAGAAAATAC
Found at i:182370 original size:20 final size:20
Alignment explanation
Indices: 182316--182372 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
182306 GGAGTAGAAA
* *
182316 AAGAAAGAAAATACAAAAAG
1 AAGAAAGAAAAAAGAAAAAG
182336 AAGAAA-AAAATAAGAAAAAG
1 AAGAAAGAAAA-AAGAAAAAG
182356 AAGAAAGAAAAAAGAAA
1 AAGAAAGAAAAAAGAAA
182373 GCAAAGCCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.12
20 25 0.76
21 4 0.12
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.04
Consensus pattern (20 bp):
AAGAAAGAAAAAAGAAAAAG
Found at i:185230 original size:2 final size:2
Alignment explanation
Indices: 185223--185259 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
185213 AGTTATTTTC
185223 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 A
185260 GTTATTATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:186724 original size:22 final size:22
Alignment explanation
Indices: 186693--186772 Score: 97
Period size: 22 Copynumber: 3.6 Consensus size: 22
186683 ATGTGAAATT
* * *
186693 TGTCCAGAAGGACCTATGTATT
1 TGTCCCGAAGGACCTCTGTATA
*
186715 TTTCCCGAAGGACCTCTGTATA
1 TGTCCCGAAGGACCTCTGTATA
*
186737 TGTCCTGAAGGACCTCTGTATA
1 TGTCCCGAAGGACCTCTGTATA
* *
186759 TATCCCAAAGGACC
1 TGTCCCGAAGGACC
186773 ACGTAGACCC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (22 bp):
TGTCCCGAAGGACCTCTGTATA
Found at i:189259 original size:22 final size:21
Alignment explanation
Indices: 189222--189262 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
189212 TCATCTCCAT
189222 TTCATCATCAACACCATCATC
1 TTCATCATCAACACCATCATC
*
189243 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
189263 ATTCTGAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.34, C:0.37, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAACACCATCATC
Found at i:194822 original size:20 final size:20
Alignment explanation
Indices: 194737--194914 Score: 125
Period size: 20 Copynumber: 8.9 Consensus size: 20
194727 CAACTCAAAC
* * *
194737 TCCAATTTCGCAACCCGGTT
1 TCCAAATTCGCAACACGATT
* *
194757 TCCAAATTCGCAACGCGAATA
1 TCCAAATTCGCAACACG-ATT
** *
194778 TGTAAA-TCGCAACAC-ATAAG
1 TCCAAATTCGCAACACGAT--T
194798 T-CAAATTCGCAACACGATT
1 TCCAAATTCGCAACACGATT
* **
194817 TCCAAATTTGCAATGCGATT
1 TCCAAATTCGCAACACGATT
194837 TCCAAATTCGCAACACTGAATT
1 TCCAAATTCGCAACAC-G-ATT
*
194859 T-CAAATTCGCAAC-TGAATT
1 TCCAAATTCGCAACACG-ATT
*
194878 T-CAAATTCGCAACTCGATT
1 TCCAAATTCGCAACACGATT
* *
194897 TTCGAATTCGCAACACGA
1 TCCAAATTCGCAACACGA
194915 ATTTAATTTC
Statistics
Matches: 128, Mismatches: 20, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
18 2 0.02
19 26 0.20
20 76 0.59
21 20 0.16
22 4 0.03
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.27
Consensus pattern (20 bp):
TCCAAATTCGCAACACGATT
Found at i:194848 original size:60 final size:60
Alignment explanation
Indices: 194743--194929 Score: 163
Period size: 60 Copynumber: 3.1 Consensus size: 60
194733 AAACTCCAAT
* * * **
194743 TTCGCAACCCGGTTTCCAAATTCGCAACGCGAATATGTAAA-TCGCAACACAT-AA-GTCAAA
1 TTCGCAA-CCGATTTCCAAATTCGCAATGCG-ATTTCCAAATTCGCAACAC-TGAATGTCAAA
* *
194803 TTCGCAACACGATTTCCAAATTTGCAATGCGATTTCCAAATTCGCAACACTGAATTTCAAA
1 TTCGCAAC-CGATTTCCAAATTCGCAATGCGATTTCCAAATTCGCAACACTGAATGTCAAA
* * * * *
194864 TTCGCAACTGAATTT-CAAATTCGCAACT-CGATTTTCGAATTCGCAACAC-GAAT-TTAAT
1 TTCGCAACCG-ATTTCCAAATTCGCAA-TGCGATTTCCAAATTCGCAACACTGAATGTCAAA
194922 TTCGCAAC
1 TTCGCAAC
194930 AGGTTTTAGT
Statistics
Matches: 108, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
58 11 0.10
59 12 0.11
60 67 0.62
61 18 0.17
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (60 bp):
TTCGCAACCGATTTCCAAATTCGCAATGCGATTTCCAAATTCGCAACACTGAATGTCAAA
Found at i:194930 original size:19 final size:20
Alignment explanation
Indices: 194759--194930 Score: 142
Period size: 20 Copynumber: 8.7 Consensus size: 20
194749 ACCCGGTTTC
*
194759 CAAATTCGCAACGCGAATATGT
1 CAAATTCGCAACACGAAT-T-T
**
194781 -AAA-TCGCAACAC-ATAAGT
1 CAAATTCGCAACACGA-ATTT
194799 CAAATTCGCAACACG-ATTT
1 CAAATTCGCAACACGAATTT
* **
194818 CCAAATTTGCAATGCG-ATTT
1 -CAAATTCGCAACACGAATTT
194838 CCAAATTCGCAACACTGAATTT
1 -CAAATTCGCAACAC-GAATTT
*
194860 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACACGAATTT
* *
194879 CAAATTCGCAACTCGATTTT
1 CAAATTCGCAACACGAATTT
*
194899 CGAATTCGCAACACGAATTT
1 CAAATTCGCAACACGAATTT
*
194919 -AATTTCGCAACA
1 CAAATTCGCAACA
194931 GGTTTTAGTT
Statistics
Matches: 123, Mismatches: 19, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
18 1 0.01
19 34 0.28
20 68 0.55
21 16 0.13
22 4 0.03
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (20 bp):
CAAATTCGCAACACGAATTT
Found at i:195738 original size:12 final size:12
Alignment explanation
Indices: 195717--195750 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
195707 ATCACATTTC
*
195717 CAATACCAAACA
1 CAATATCAAACA
195729 CAATATCAAACA
1 CAATATCAAACA
*
195741 CAATCTCAAA
1 CAATATCAAA
195751 ACCCACAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:198223 original size:18 final size:18
Alignment explanation
Indices: 198200--198235 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
198190 AAGCAAAAGG
198200 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
198218 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
198236 CAACCTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:198412 original size:17 final size:17
Alignment explanation
Indices: 198378--198412 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
198368 CTATGATCTG
198378 TTCAGTTGTTATCTTTT
1 TTCAGTTGTTATCTTTT
*
198395 TTCAGATTGTTGTCTTTT
1 TTCAG-TTGTTATCTTTT
198413 ATCTTTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.11, C:0.11, G:0.14, T:0.63
Consensus pattern (17 bp):
TTCAGTTGTTATCTTTT
Found at i:198648 original size:25 final size:25
Alignment explanation
Indices: 198610--198659 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
198600 AAATCGATTA
*
198610 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
*
198635 AACATTGTTATGGGTATATTATTTG
1 AACATTGTTATGGGTACATTATTTG
198660 GAAAATAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.26, C:0.06, G:0.22, T:0.46
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:199066 original size:18 final size:18
Alignment explanation
Indices: 199045--199081 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
199035 GTAATTGGAG
199045 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
199063 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
199081 T
1 T
199082 ATATATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:200292 original size:20 final size:20
Alignment explanation
Indices: 200269--200342 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 20
200259 TCGCAACGCC
*
200269 AATTTAACTTTCGCGTTGCG
1 AATTTGACTTTCGCGTTGCG
*
200289 AATTTGACTTTCACGTTGCG
1 AATTTGACTTTCGCGTTGCG
*
200309 AATTTGACTATCGCGTTGCG
1 AATTTGACTTTCGCGTTGCG
*
200329 AATTTGACTATCGC
1 AATTTGACTTTCGC
200343 AACGCGAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
AATTTGACTTTCGCGTTGCG
Found at i:200349 original size:20 final size:20
Alignment explanation
Indices: 200306--200350 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
200296 CTTTCACGTT
***
200306 GCGAATTTGACTATCGCGTT
1 GCGAATTTGACTATCGCAAC
200326 GCGAATTTGACTATCGCAAC
1 GCGAATTTGACTATCGCAAC
200346 GCGAA
1 GCGAA
200351 AATCGTAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (20 bp):
GCGAATTTGACTATCGCAAC
Found at i:200350 original size:40 final size:40
Alignment explanation
Indices: 200258--200350 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 40
200248 GAAACGCGAA
* *
200258 ATCGCAACGCCAATTTAACTTTCGCGTTGCGAATTTGACT
1 ATCGCAACGCGAATTTAACTATCGCGTTGCGAATTTGACT
* * *** *
200298 TTCACGTTGCGAATTTGACTATCGCGTTGCGAATTTGACT
1 ATCGCAACGCGAATTTAACTATCGCGTTGCGAATTTGACT
200338 ATCGCAACGCGAA
1 ATCGCAACGCGAA
200351 AATCGTAATG
Statistics
Matches: 40, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (40 bp):
ATCGCAACGCGAATTTAACTATCGCGTTGCGAATTTGACT
Found at i:200368 original size:34 final size:34
Alignment explanation
Indices: 200325--200410 Score: 136
Period size: 34 Copynumber: 2.5 Consensus size: 34
200315 ACTATCGCGT
* *
200325 TGCGAATTTGACTATCGCAACGCGAAAATCGTAA
1 TGCGAATTTGACTATCGCAACGAGAAAATCGAAA
200359 TGCGAATTTGACTATCGCAACGAGAAAATCGAAA
1 TGCGAATTTGACTATCGCAACGAGAAAATCGAAA
* *
200393 CGCGAATTTGACTTTCGC
1 TGCGAATTTGACTATCGC
200411 GTTGCAAAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (34 bp):
TGCGAATTTGACTATCGCAACGAGAAAATCGAAA
Found at i:200627 original size:64 final size:64
Alignment explanation
Indices: 200475--200620 Score: 274
Period size: 64 Copynumber: 2.3 Consensus size: 64
200465 GAAATTTAAC
200475 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
* *
200539 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
200603 AACAAATCAACTTTTACA
1 AACAAATCAACTTTTACA
200621 GGTCAATGTA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 80 1.00
ACGTcount: A:0.50, C:0.18, G:0.01, T:0.30
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
Found at i:212899 original size:2 final size:2
Alignment explanation
Indices: 212892--212962 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
212882 ATGCATAATT
212892 TA TA TA 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
212934 TA 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 TA T
212963 GTTTTTAAAT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:215567 original size:55 final size:55
Alignment explanation
Indices: 215503--215636 Score: 189
Period size: 55 Copynumber: 2.4 Consensus size: 55
215493 GTATAGTCTC
* *
215503 GGTTAGAGAAGATGAACAGAGACCCAAATAGATAAAGAGT-TTCAGTTATATATAG
1 GGTTAGAGAAGATGAACAGAGACACAAATAGATAAAGAGTCTT-AGTTAGATATAG
* * * *
215558 GGTTAGAGAAGATGAACAGAGATAGAAGTAGATGAAGAGTCTTAGTTAGATATAG
1 GGTTAGAGAAGATGAACAGAGACACAAATAGATAAAGAGTCTTAGTTAGATATAG
*
215613 GGTTAGAGAAGATAAACAGAGACA
1 GGTTAGAGAAGATGAACAGAGACA
215637 AAAGAAGAAG
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
55 68 0.97
56 2 0.03
ACGTcount: A:0.44, C:0.07, G:0.28, T:0.22
Consensus pattern (55 bp):
GGTTAGAGAAGATGAACAGAGACACAAATAGATAAAGAGTCTTAGTTAGATATAG
Found at i:216199 original size:114 final size:112
Alignment explanation
Indices: 216023--216236 Score: 279
Period size: 115 Copynumber: 1.9 Consensus size: 112
216013 ATGAATACAA
* * * * * *
216023 ATGAATAAGGGTTGAATTTGGGGTGTTTGATCGAAGAACAAGATATGTTTTGGGTTTTGGTG-TT
1 ATGAACAAGGGTTGAATTTAGAGTGTTTGATCGAAGAAAAAGATAGGGTTTGGGTTTTGGTGTTT
* *
216087 TGTAAAGATTAAAGGAGGGGTTTGGGGATGAACACAAACGAACACAG
66 TGTAAAGATCAAAGGAGGGGTTTCGGGATGAACACAAACGAACACAG
*
216134 ATGAACAAGGGTTGAATTTTTAGAGTGTTTGATCGAA-AAAATAGGATAGGGTTTGGTTTTTGGT
1 ATGAACAAGGGTTGAA--TTTAGAGTGTTTGATCGAAGAAAA-A-GATAGGGTTTGGGTTTTGGT
* *
216198 GTTTTGTAAAGATCAAATGAGGGTTTTCGGGATGAACAC
62 GTTTTGTAAAGATCAAAGGAGGGGTTTCGGGATGAACAC
216237 GGATGAACAA
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
111 15 0.17
112 3 0.03
113 18 0.21
114 18 0.21
115 33 0.38
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.32
Consensus pattern (112 bp):
ATGAACAAGGGTTGAATTTAGAGTGTTTGATCGAAGAAAAAGATAGGGTTTGGGTTTTGGTGTTT
TGTAAAGATCAAAGGAGGGGTTTCGGGATGAACACAAACGAACACAG
Found at i:216654 original size:2 final size:2
Alignment explanation
Indices: 216634--216759 Score: 133
Period size: 2 Copynumber: 65.5 Consensus size: 2
216624 AACTATAGTT
*
216634 TA TA TA T- TA TA T- TA GTA TA TA GTT TA TA TA T- 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
* * *
216674 -A TA -A AA TA TA GTA -A T- TA TA TA TT TA TA TA AA 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
216713 TA TA TA 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
216755 TA TA T
1 TA TA T
216760 TGTAACCCCC
Statistics
Matches: 106, Mismatches: 7, Indels: 22
0.79 0.05 0.16
Matches are distributed among these distances:
1 8 0.08
2 93 0.88
3 5 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:217571 original size:24 final size:24
Alignment explanation
Indices: 217554--217633 Score: 108
Period size: 24 Copynumber: 3.3 Consensus size: 24
217544 ATCAAAACAT
217554 AATCCAGGTCAAGTATCAGATCAA
1 AATCCAGGTCAAGTATCAGATCAA
**
217578 AATCCATATCAAGTATTC-GATCAA
1 AATCCAGGTCAAGTA-TCAGATCAA
* *
217602 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCAGATCAA
217626 AATCCAGG
1 AATCCAGG
217634 GTACAGGTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
23 2 0.04
24 45 0.92
25 2 0.04
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.23
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCAGATCAA
Found at i:222116 original size:2 final size:2
Alignment explanation
Indices: 222109--222137 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
222099 TCTTTTTAAA
222109 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
222138 CCCCCATCCG
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
Done.