Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 120 of 145
Found at i:40097706 original size:17 final size:17
Alignment explanation
Indices: 40097642--40097706 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 17
40097632 TAAAAAACAG
40097642 AAAAAGGACAAACAAATA
1 AAAAAGGA-AAACAAATA
**
40097660 AAAAAACAAATA-AAATGA
1 AAAAAGGAAA-ACAAAT-A
*
40097678 AATAAAGAAAAACAAATA
1 AA-AAAGGAAAACAAATA
40097696 AAAAAGGAAAA
1 AAAAAGGAAAA
40097707 GGACAAACAA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
17 14 0.37
18 14 0.37
19 10 0.26
ACGTcount: A:0.77, C:0.06, G:0.09, T:0.08
Consensus pattern (17 bp):
AAAAAGGAAAACAAATA
Found at i:40097733 original size:96 final size:94
Alignment explanation
Indices: 40097557--40097733 Score: 234
Period size: 96 Copynumber: 1.9 Consensus size: 94
40097547 TAAAAATAAT
* * * *
40097557 AAACAAATAAAAAATAGAAAAATGAAATAAAGAAAAACAAATAAAAAAGAGAAAAATGAAATAAA
1 AAACAAATAAAAAACAAAAAAATGAAATAAAGAAAAACAAATAAAAAAGAGAAAAATCAAACAAA
*
40097622 GAAAAACAAATAAAAAACAGAAAAAGGAC
66 GAAAAACAAAAAAAAAACAGAAAAAGGAC
40097651 AAACAAATAAAAAAACAAATAAAATGAAATAAAGAAAAACAAATAAAAAAG-GAAAAGGA-CAAA
1 AAACAAAT-AAAAAACAAA-AAAATGAAATAAAGAAAAACAAATAAAAAAGAGAAAA--ATCAAA
* *
40097714 CAAATAAAAA-ATAAAAAAAA
62 CAAAGAAAAACAAAAAAAAAA
40097734 TGACAATAGG
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
94 8 0.11
95 21 0.29
96 42 0.58
97 1 0.01
ACGTcount: A:0.77, C:0.06, G:0.09, T:0.08
Consensus pattern (94 bp):
AAACAAATAAAAAACAAAAAAATGAAATAAAGAAAAACAAATAAAAAAGAGAAAAATCAAACAAA
GAAAAACAAAAAAAAAACAGAAAAAGGAC
Found at i:40099098 original size:23 final size:22
Alignment explanation
Indices: 40099072--40099125 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
40099062 TAATTAAAAT
* *
40099072 TAAAATTAAAATTATTTTTTTAA
1 TAAAATTAAAATTA-ATTGTTAA
* *
40099095 TAAAATAAAAATTAATTGTTAT
1 TAAAATTAAAATTAATTGTTAA
40099117 TAAAATTAA
1 TAAAATTAA
40099126 TTGTTAGTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 13 0.50
23 13 0.50
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TAAAATTAAAATTAATTGTTAA
Found at i:40099120 original size:22 final size:23
Alignment explanation
Indices: 40099070--40099122 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
40099060 TTTAATTAAA
* * *
40099070 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATAAAAATTATATTGTT
*
40099093 AATAAAATAAAAATTA-ATTGTT
1 ATTAAAATAAAAATTATATTGTT
40099115 ATTAAAAT
1 ATTAAAAT
40099123 TAATTGTTAG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 11 0.44
23 14 0.56
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATAAAAATTATATTGTT
Found at i:40099123 original size:16 final size:16
Alignment explanation
Indices: 40099102--40099140 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
40099092 TAATAAAATA
*
40099102 AAAATTAATTGTTATT
1 AAAATTAATTGTTAGT
40099118 AAAATTAATTGTTAGT
1 AAAATTAATTGTTAGT
40099134 AAAATTA
1 AAAATTA
40099141 TCAAATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.44
Consensus pattern (16 bp):
AAAATTAATTGTTAGT
Found at i:40099202 original size:66 final size:67
Alignment explanation
Indices: 40099129--40099271 Score: 252
Period size: 68 Copynumber: 2.1 Consensus size: 67
40099119 AAATTAATTG
*
40099129 TTAGTAAAATTATCAAATTATTAATTG-TTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
1 TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAACAAAATCTAACATTT
40099193 GA
66 GA
*
40099195 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAAATTATCAAATTATTAATTG-ATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
40099260 TGA
65 TGA
40099263 TTAGTAAAA
1 TTAGTAAAA
40099272 CAAACTTGAT
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
66 26 0.36
68 46 0.64
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (67 bp):
TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAACAAAATCTAACATTT
GA
Found at i:40099225 original size:9 final size:9
Alignment explanation
Indices: 40099213--40099240 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
40099203 TTTATCAAAT
40099213 TATTAATTG
1 TATTAATTG
40099222 TATTAATTG
1 TATTAATTG
40099231 TATTAATTG
1 TATTAATTG
40099240 T
1 T
40099241 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:40099377 original size:22 final size:23
Alignment explanation
Indices: 40099335--40099380 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
40099325 GTAAATAAAC
40099335 TTAAAATAAAAAACTATTATATT
1 TTAAAATAAAAAACTATTATATT
40099358 TTAAAATTAAAAAA-TA-TATATT
1 TTAAAA-TAAAAAACTATTATATT
40099380 T
1 T
40099381 AATATTTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.32
23 8 0.36
24 7 0.32
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
TTAAAATAAAAAACTATTATATT
Found at i:40102216 original size:22 final size:22
Alignment explanation
Indices: 40102191--40102258 Score: 127
Period size: 22 Copynumber: 3.1 Consensus size: 22
40102181 ATCCTATCTA
40102191 AATTTCCTTCCAAAATTCTCTC
1 AATTTCCTTCCAAAATTCTCTC
*
40102213 AATTTCCTTTCAAAATTCTCTC
1 AATTTCCTTCCAAAATTCTCTC
40102235 AATTTCCTTCCAAAATTCTCTC
1 AATTTCCTTCCAAAATTCTCTC
40102257 AA
1 AA
40102259 ACTCTCAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTTCCTTCCAAAATTCTCTC
Found at i:40102264 original size:30 final size:30
Alignment explanation
Indices: 40102230--40102288 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
40102220 TTTCAAAATT
* * *
40102230 CTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCAAAAATCCTCTCAAA
40102260 CTCTCAAATTCCTTCAAAAATCCTCTCAA
1 CTCTCAAATTCCTTCAAAAATCCTCTCAA
40102289 TTTCCTTCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (30 bp):
CTCTCAAATTCCTTCAAAAATCCTCTCAAA
Found at i:40102273 original size:52 final size:52
Alignment explanation
Indices: 40102208--40102307 Score: 157
Period size: 52 Copynumber: 1.9 Consensus size: 52
40102198 TTCCAAAATT
* * *
40102208 CTCTCAATTTCCTTTC-AAAATTCTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATTCC-TTCAAAAATCCTCTCAATTTCCTTCCAAAAATCTCTCAAA
40102260 CTCTCAAATTCCTTCAAAAATCCTCTCAATTTCCTTCCAAAAATCTCT
1 CTCTCAAATTCCTTCAAAAATCCTCTCAATTTCCTTCCAAAAATCTCT
40102308 AAAATCCATA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 3 0.07
52 41 0.93
ACGTcount: A:0.30, C:0.32, G:0.00, T:0.38
Consensus pattern (52 bp):
CTCTCAAATTCCTTCAAAAATCCTCTCAATTTCCTTCCAAAAATCTCTCAAA
Found at i:40102285 original size:22 final size:22
Alignment explanation
Indices: 40102260--40102312 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
40102250 TTCTCTCAAA
40102260 CTCTCAAATTCCTT-CAAAAAT
1 CTCTCAAATTCCTTCCAAAAAT
*
40102281 CCTCTCAATTTCCTTCCAAAAAT
1 -CTCTCAAATTCCTTCCAAAAAT
*
40102304 CTCTAAAAT
1 CTCTCAAAT
40102313 CCATATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 20 0.74
23 7 0.26
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.34
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAAAT
Found at i:40102383 original size:31 final size:31
Alignment explanation
Indices: 40102345--40102409 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
40102335 TTCAATTTCA
*
40102345 TTTTTTAAGATAATTTTAAATATTTTT-ATAT
1 TTTTTTAAAATAATTTTAAAT-TTTTTAATAT
40102376 TTTTTTAAAATAATTTTAAATTTTTTAATAT
1 TTTTTTAAAATAATTTTAAATTTTTTAATAT
40102407 TTT
1 TTT
40102410 CAACAATGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (31 bp):
TTTTTTAAAATAATTTTAAATTTTTTAATAT
Found at i:40102386 original size:21 final size:20
Alignment explanation
Indices: 40102358--40102401 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
40102348 TTTAAGATAA
* *
40102358 TTTTAAATATTTTTATATTT
1 TTTTAAATAATTTTAAATTT
40102378 TTTTAAAATAATTTTAAATTT
1 TTTT-AAATAATTTTAAATTT
40102399 TTT
1 TTT
40102402 AATATTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTAAATAATTTTAAATTT
Found at i:40105211 original size:23 final size:23
Alignment explanation
Indices: 40105164--40105225 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
40105154 NNNNNNNNNN
*
40105164 AACCCTAACCTATTTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
40105187 AACCCTAACCTTAATTT-ATGT-AA
1 AACCCTAACC-TAATTTAAT-TAAA
* *
40105210 AATCCTAACATAATTT
1 AACCCTAACCTAATTT
40105226 TACCTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 6 0.18
23 22 0.65
24 6 0.18
ACGTcount: A:0.42, C:0.21, G:0.02, T:0.35
Consensus pattern (23 bp):
AACCCTAACCTAATTTAATTAAA
Found at i:40105279 original size:56 final size:56
Alignment explanation
Indices: 40105219--40105399 Score: 301
Period size: 56 Copynumber: 3.2 Consensus size: 56
40105209 AAATCCTAAC
* * * * *
40105219 ATAATTTTACCTAATTTGATAATCTTACTAACCATTAAC-ACATTTTTTGGGGCTTA
1 ATAATTTTACATAATTTGATAATTTTACTAATCATTAACAAAAGTTTTT-GGGCTTA
40105275 ATAATTTTACATAATTTGATAATTTTACTAATCATTAACAAAAGTTTTTGGGCTTA
1 ATAATTTTACATAATTTGATAATTTTACTAATCATTAACAAAAGTTTTTGGGCTTA
40105331 ATAATTTTACATAATTTGATAATTTTACTAATCATTAACAAAAGTTTTTGGGCTTA
1 ATAATTTTACATAATTTGATAATTTTACTAATCATTAACAAAAGTTTTTGGGCTTA
40105387 ATAATTTTACATA
1 ATAATTTTACATA
40105400 GTTTTACATA
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
56 112 0.94
57 7 0.06
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.44
Consensus pattern (56 bp):
ATAATTTTACATAATTTGATAATTTTACTAATCATTAACAAAAGTTTTTGGGCTTA
Found at i:40116698 original size:33 final size:33
Alignment explanation
Indices: 40116656--40116722 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
40116646 CGAAGGTTCA
40116656 AACTTATGTTTTCCTTTTGGAAGTGCTATGGGC
1 AACTTATGTTTTCCTTTTGGAAGTGCTATGGGC
*
40116689 AACTTATGTTTTCCTTTTGGGAGTGCTATGGGC
1 AACTTATGTTTTCCTTTTGGAAGTGCTATGGGC
40116722 A
1 A
40116723 TTACCATTGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.18, C:0.15, G:0.25, T:0.42
Consensus pattern (33 bp):
AACTTATGTTTTCCTTTTGGAAGTGCTATGGGC
Found at i:40128091 original size:16 final size:16
Alignment explanation
Indices: 40128070--40128107 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
40128060 TTGATTTGCT
*
40128070 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
40128086 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
40128102 AATACA
1 ATTACA
40128108 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:40132183 original size:188 final size:189
Alignment explanation
Indices: 40131854--40132232 Score: 751
Period size: 188 Copynumber: 2.0 Consensus size: 189
40131844 AATTATTTAA
40131854 ATATATATTATAGTAAAATTTTAAAAAAGTATTTGTGGTTGATTAGACTTGTTAACTTGATTTCA
1 ATATATATTATAGTAAAATTTTAAAAAAGTATTTGTGGTTGATTAGACTTGTTAACTTGATTTCA
40131919 GTTAAATCATAGTTAATTATTCAAGGAAAATAATGTGTATATATATAATTAGACACAAAAAGGAT
66 GTTAAATCATAGTTAATTATTCAAGGAAAATAATGTGTATATATATAATTAGACACAAAAAGGAT
40131984 AAGCAAATTTATCAATAAGATGAGCCATCCGGACAATAATCTAAAATTATAAGTTGTTT
131 AAGCAAATTTATCAATAAGATGAGCCATCCGGACAATAATCTAAAATTATAAGTTGTTT
40132043 ATATATATTAT-GTAAAATTTTAAAAAAGTATTTGTGGTTGATTAGACTTGTTAACTTGATTTCA
1 ATATATATTATAGTAAAATTTTAAAAAAGTATTTGTGGTTGATTAGACTTGTTAACTTGATTTCA
40132107 GTTAAATCATAGTTAATTATTCAAGGAAAATAATGTGTATATATATAATTAGACACAAAAAGGAT
66 GTTAAATCATAGTTAATTATTCAAGGAAAATAATGTGTATATATATAATTAGACACAAAAAGGAT
40132172 AAGCAAATTTATCAATAAGATGAGCCATCCGGACAATAATCTAAAATTATAAGTTGTTT
131 AAGCAAATTTATCAATAAGATGAGCCATCCGGACAATAATCTAAAATTATAAGTTGTTT
40132231 AT
1 AT
40132233 TATTGCATTA
Statistics
Matches: 190, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
188 179 0.94
189 11 0.06
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (189 bp):
ATATATATTATAGTAAAATTTTAAAAAAGTATTTGTGGTTGATTAGACTTGTTAACTTGATTTCA
GTTAAATCATAGTTAATTATTCAAGGAAAATAATGTGTATATATATAATTAGACACAAAAAGGAT
AAGCAAATTTATCAATAAGATGAGCCATCCGGACAATAATCTAAAATTATAAGTTGTTT
Found at i:40132349 original size:7 final size:7
Alignment explanation
Indices: 40132337--40132361 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
40132327 ATTGTTGGTA
40132337 TTATAAT
1 TTATAAT
40132344 TTATAAT
1 TTATAAT
40132351 TTATAAT
1 TTATAAT
40132358 TTAT
1 TTAT
40132362 TATTGACTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTATAAT
Found at i:40132522 original size:55 final size:56
Alignment explanation
Indices: 40132438--40132550 Score: 219
Period size: 55 Copynumber: 2.0 Consensus size: 56
40132428 TTGTTTTTTC
40132438 TTCTTTATATTCTAAACAAAATAAGAAAGAAC-AAAAAAAGAAATATTTTATTGCA
1 TTCTTTATATTCTAAACAAAATAAGAAAGAACAAAAAAAAGAAATATTTTATTGCA
40132493 TTCTTTATATTCTAAACAAAATAAGAAAGAACAAAAAAAAGAAATATTTTATTGCA
1 TTCTTTATATTCTAAACAAAATAAGAAAGAACAAAAAAAAGAAATATTTTATTGCA
40132549 TT
1 TT
40132551 ATTATCTATA
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 32 0.56
56 25 0.44
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.32
Consensus pattern (56 bp):
TTCTTTATATTCTAAACAAAATAAGAAAGAACAAAAAAAAGAAATATTTTATTGCA
Found at i:40132572 original size:55 final size:54
Alignment explanation
Indices: 40132441--40132563 Score: 174
Period size: 55 Copynumber: 2.2 Consensus size: 54
40132431 TTTTTTCTTC
* *
40132441 TTTATATTCTAAACAAAATAAGAAAGAACAAAAAAAGAAATATTTTATTGCATTC
1 TTTATATACT-AACAAAATAAGAAAGAACAAAAAAAGAAATATTTTATTGCATTA
*
40132496 TTTATATTCTAAACAAAATAAGAAAGAACAAAAAAAAGAAATATTTTATTGCATTA
1 TTTATATACT-AACAAAATAAGAAAGAAC-AAAAAAAGAAATATTTTATTGCATTA
*
40132552 TTATCTATACTA
1 TT-TATATACTA
40132564 TTTAATAAGT
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
55 29 0.46
56 28 0.44
57 6 0.10
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.33
Consensus pattern (54 bp):
TTTATATACTAACAAAATAAGAAAGAACAAAAAAAGAAATATTTTATTGCATTA
Found at i:40151884 original size:51 final size:49
Alignment explanation
Indices: 40151751--40151936 Score: 219
Period size: 51 Copynumber: 3.7 Consensus size: 49
40151741 NNNNNNNTGA
* * *
40151751 TGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAAAGAT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAG-T
* ** * *
40151801 AGGTCGTATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAG-T
* * *
40151851 TCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGT
1 T-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGT
*
40151901 GATGGTCACATGTGTAGTACTATGTGCATGCTACTA
1 --TGGTCACATGTGTAGTACTATGTGCAGGCTACTA
40151937 TGTGAATCCG
Statistics
Matches: 113, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
50 42 0.37
51 70 0.62
52 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.31
Consensus pattern (49 bp):
TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGT
Found at i:40151940 original size:26 final size:26
Alignment explanation
Indices: 40151860--40151940 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
40151850 TTCGATCACG
*
40151860 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCATGCTACTA
* * *
40151886 CGTGTA-T-CGGATAGTG-ATGGTCAC-A
1 TGTGTAGTAC-TAT-GTGCATGCT-ACTA
40151911 TGTGTAGTACTATGTGCATGCTACTA
1 TGTGTAGTACTATGTGCATGCTACTA
40151937 TGTG
1 TGTG
40151941 AATCCGCATC
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
24 1 0.02
25 17 0.41
26 22 0.54
27 1 0.02
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.35
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCATGCTACTA
Found at i:40152055 original size:42 final size:43
Alignment explanation
Indices: 40151948--40152159 Score: 256
Period size: 43 Copynumber: 5.0 Consensus size: 43
40151938 GTGAATCCGC
*
40151948 ATCATTGAATATAAATGTGGTTGCTAAGTGCTGATTCCACCGT
1 ATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGT
* * *
40151991 ATCCTTGACAGT-GAAAGG-GGTTGCTATGTGCTGATTCC-CCGT
1 ATCATTGA-A-TATAAAGGTGGTTGCTAAGTGCTGATTCCACCGT
*
40152033 ATCATTGAATATAAAGGTGGTTGCTAAGTGCAGATTCCACCGT
1 ATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGT
* * * * *
40152076 ATCCTTGACTGTGAAAGG-GGTTACTATGTGCTGATTCC-CCGT
1 ATCATTGAATAT-AAAGGTGGTTGCTAAGTGCTGATTCCACCGT
*
40152118 ATCATTGATTAT-AAGGTGGTTGCTAAGTGCTGATTCCACCGT
1 ATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGT
40152160 GTAACGGTTA
Statistics
Matches: 142, Mismatches: 19, Indels: 17
0.80 0.11 0.10
Matches are distributed among these distances:
40 5 0.04
41 24 0.17
42 46 0.32
43 56 0.39
44 10 0.07
45 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (43 bp):
ATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGT
Found at i:40152091 original size:85 final size:85
Alignment explanation
Indices: 40151948--40152159 Score: 372
Period size: 85 Copynumber: 2.5 Consensus size: 85
40151938 GTGAATCCGC
*
40151948 ATCATTGAATATAAATGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGACAGTGAAAGGGGTT
1 ATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGACAGTGAAAGGGGTT
*
40152013 GCTATGTGCTGATTCCCCGT
66 ACTATGTGCTGATTCCCCGT
* *
40152033 ATCATTGAATATAAAGGTGGTTGCTAAGTGCAGATTCCACCGTATCCTTGACTGTGAAAGGGGTT
1 ATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGACAGTGAAAGGGGTT
40152098 ACTATGTGCTGATTCCCCGT
66 ACTATGTGCTGATTCCCCGT
*
40152118 ATCATTGATTAT-AAGGTGGTTGCTAAGTGCTGATTCCACCGT
1 ATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGT
40152160 GTAACGGTTA
Statistics
Matches: 121, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
84 29 0.24
85 92 0.76
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (85 bp):
ATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGACAGTGAAAGGGGTT
ACTATGTGCTGATTCCCCGT
Found at i:40172444 original size:5 final size:5
Alignment explanation
Indices: 40172434--40172463 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
40172424 TTCTTCGTGT
40172434 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
40172464 AAAATTATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:40172690 original size:30 final size:29
Alignment explanation
Indices: 40172653--40172782 Score: 113
Period size: 30 Copynumber: 4.4 Consensus size: 29
40172643 CAAAAAATAT
*
40172653 AAATTACATTTTGGCCCCTAAATTTTTCA
1 AAATTACATTTTGACCCCTAAATTTTTCA
*
40172682 ACAATTACATTTTGACCCCTAACTTTTTCTA
1 A-AATTACATTTTGACCCCTAAATTTTTC-A
* *
40172713 AATTTACATCTTGACCCCTAATATTTTGT--
1 AAATTACATTTTGACCCCTAA-ATTTT-TCA
** * *
40172742 AAATTACATTCGGGCCCCTAAA-CTTTCTA
1 AAATTACATTTTGACCCCTAAATTTTTC-A
40172771 GAAATTACATTT
1 -AAATTACATTT
40172783 CAGCCTCATA
Statistics
Matches: 81, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
26 1 0.01
27 2 0.02
28 1 0.01
29 17 0.21
30 53 0.65
31 6 0.07
32 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (29 bp):
AAATTACATTTTGACCCCTAAATTTTTCA
Found at i:40173523 original size:13 final size:13
Alignment explanation
Indices: 40173505--40173546 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
40173495 CCTGAAGAAG
40173505 AAGAAGAAAAAGA
1 AAGAAGAAAAAGA
40173518 AAGAAGAAAAAGA
1 AAGAAGAAAAAGA
* *
40173531 GAGAAAAAAGAAGA
1 AAGAAGAAA-AAGA
40173545 AA
1 AA
40173547 AATAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 20 0.80
14 5 0.20
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAGAAGAAAAAGA
Found at i:40173540 original size:11 final size:10
Alignment explanation
Indices: 40173499--40173548 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
40173489 GTTCGGCCTG
*
40173499 AAGAAG-AAG
1 AAGAAGAAAA
40173508 AAGAA-AAAGA
1 AAGAAGAAA-A
40173518 AAGAAG-AAA
1 AAGAAGAAAA
40173527 AAGAGAGAAAA
1 AAGA-AGAAAA
40173538 AAGAAGAAAA
1 AAGAAGAAAA
40173548 A
1 A
40173549 TAAAAAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
9 12 0.34
10 16 0.46
11 7 0.20
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (10 bp):
AAGAAGAAAA
Found at i:40173547 original size:9 final size:9
Alignment explanation
Indices: 40173499--40173548 Score: 55
Period size: 9 Copynumber: 5.2 Consensus size: 9
40173489 GTTCGGCCTG
*
40173499 AAGAAGAAG
1 AAGAAGAAA
*
40173508 AAGAAAAAGA
1 AAGAAGAA-A
40173518 AAGAAGAAA
1 AAGAAGAAA
40173527 AAGAGAGAAAA
1 AAGA-AG-AAA
40173538 AAGAAGAAA
1 AAGAAGAAA
40173547 AA
1 AA
40173549 TAAAAAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
9 17 0.49
10 11 0.31
11 7 0.20
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (9 bp):
AAGAAGAAA
Found at i:40173676 original size:14 final size:15
Alignment explanation
Indices: 40173657--40173685 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40173647 CAAGCAGCCC
40173657 ACAGCA-AAAAAAAA
1 ACAGCAGAAAAAAAA
40173671 ACAGCAGAAAAAAAA
1 ACAGCAGAAAAAAAA
40173686 GGGAAAGCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.14, G:0.10, T:0.00
Consensus pattern (15 bp):
ACAGCAGAAAAAAAA
Found at i:40174506 original size:17 final size:17
Alignment explanation
Indices: 40174468--40174648 Score: 148
Period size: 17 Copynumber: 10.3 Consensus size: 17
40174458 GTTTTTTTAA
* *
40174468 AAAAATTTCTCGTATTTC
1 AAAAATTT-TCGTGTTTT
* *
40174486 AAAAATTGTCATGTTTT
1 AAAAATTTTCGTGTTTT
40174503 AAAAATTTTCGTGTTTT
1 AAAAATTTTCGTGTTTT
* * *
40174520 CAATAATTCTCGTGTTTC
1 -AAAAATTTTCGTGTTTT
* *
40174538 ACAAATTTTCGTGTTTC
1 AAAAATTTTCGTGTTTT
40174555 AAAAATTTTCGTGTTTT
1 AAAAATTTTCGTGTTTT
*
40174572 CAAGAATTTTTCGTGTTTT
1 -AA-AAATTTTCGTGTTTT
* *
40174591 CAAAAATTCTCGTGTTTAAA
1 -AAAAATTTTCGTGTTT--T
* *
40174611 AAAAAATTT-GTGTTTA
1 AAAAATTTTCGTGTTTT
**
40174627 AAAAAAATTCGTGTTTT
1 AAAAATTTTCGTGTTTT
40174644 AAAAA
1 AAAAA
40174649 AAAGTTGTGT
Statistics
Matches: 135, Mismatches: 22, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
16 9 0.07
17 61 0.45
18 41 0.30
19 24 0.18
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.45
Consensus pattern (17 bp):
AAAAATTTTCGTGTTTT
Found at i:40174521 original size:35 final size:35
Alignment explanation
Indices: 40174468--40174648 Score: 172
Period size: 35 Copynumber: 5.1 Consensus size: 35
40174458 GTTTTTTTAA
* * *
40174468 AAAAATTTCTCGT-ATTTCAAAAATTGTCATGTTTT
1 AAAAATTT-TCGTGTTTTCAAAAATTCTCGTGTTTT
* *
40174503 AAAAATTTTCGTGTTTTCAATAATTCTCGTGTTTC
1 AAAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTT
* *
40174538 ACAAATTTTCGTG-TTTCAAAAATTTTCGTGTTTT
1 AAAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTT
* *
40174572 CAAGAATTTTTCGTGTTTTCAAAAATTCTCGTGTTTAAA
1 -AA-AAATTTTCGTGTTTTCAAAAATTCTCGTGTTT--T
* ** *
40174611 AAAAAATTT-GTGTTTAAAAAAAAT-TCGTGTTTT
1 AAAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTT
40174644 AAAAA
1 AAAAA
40174649 AAAGTTGTGT
Statistics
Matches: 121, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
33 5 0.04
34 22 0.18
35 46 0.38
36 22 0.18
37 24 0.20
38 2 0.02
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.45
Consensus pattern (35 bp):
AAAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTT
Found at i:40174538 original size:52 final size:53
Alignment explanation
Indices: 40174471--40174613 Score: 189
Period size: 52 Copynumber: 2.7 Consensus size: 53
40174461 TTTTTAAAAA
* * * * *
40174471 AATTTCTCGTATTTCAAAAATTGTCATGTTTTAAAAATTTTCGTGTTTTCAAT
1 AATTTCTCGTGTTTCAAAAATTCTCGTGTTTAAAAAATTTTCGTGTTTTCAAG
* * *
40174524 AA-TTCTCGTGTTTCACAAATTTTCGTGTTTCAAAAATTTTCGTGTTTTCAAG
1 AATTTCTCGTGTTTCAAAAATTCTCGTGTTTAAAAAATTTTCGTGTTTTCAAG
*
40174576 AATTTTTCGTGTTTTCAAAAATTCTCGTGTTTAAAAAA
1 AATTTCTCGTG-TTTCAAAAATTCTCGTGTTTAAAAAA
40174614 AAATTTGTGT
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
52 46 0.59
53 9 0.12
54 23 0.29
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (53 bp):
AATTTCTCGTGTTTCAAAAATTCTCGTGTTTAAAAAATTTTCGTGTTTTCAAG
Found at i:40174650 original size:18 final size:18
Alignment explanation
Indices: 40174581--40174665 Score: 95
Period size: 18 Copynumber: 4.8 Consensus size: 18
40174571 TCAAGAATTT
* *
40174581 TTCGTGTTTT-CAAAAAT
1 TTCGTGTTTTAAAAAAAA
*
40174598 TCTCGTGTTTAAAAAAAAA
1 T-TCGTGTTTTAAAAAAAA
*
40174617 TTTGTG-TTTAAAAAAAA
1 TTCGTGTTTTAAAAAAAA
40174634 TTCGTGTTTTAAAAAAAA
1 TTCGTGTTTTAAAAAAAA
40174652 GTT-GTGTTTTAAAA
1 -TTCGTGTTTTAAAA
40174666 TTCACGTGTT
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
17 16 0.28
18 34 0.59
19 8 0.14
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.41
Consensus pattern (18 bp):
TTCGTGTTTTAAAAAAAA
Found at i:40183233 original size:76 final size:76
Alignment explanation
Indices: 40183026--40183935 Score: 897
Period size: 76 Copynumber: 11.8 Consensus size: 76
40183016 TTTTAAGAAT
* *
40183026 TATTTTTCAATTTTTATTTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
40183091 TCACATGCC-GAGG
66 T--CAT-CCTGAGG
* ** * *
40183104 TATCTTT-AATTTCTATTTTTTTTAAAAAATCAACTTATATTGCGAGAGCTGAGTTGAGCCTCGG
1 TATTTTTCAATTTCTA-TTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
40183168 GTCATCCTGAGG
65 GTCATCCTGAGG
** * *
40183180 TATTTTTCAATTTCTATTTTTCAAAAAAAGAAACTCATAATGCGAGAGGTGAGTTGAGCCTCGAG
1 TATTTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
40183245 TCATCCTGAGG
66 TCATCCTGAGG
* *
40183256 TATTTTTCAATTTCTGTTTTTCAAAAAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
1 TATTTTTCAATTTCTATTTTTC--AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
40183321 GGTCA-CGCTGAGG
64 GGTCATC-CTGAGG
* * ** *
40183334 TA-TTTTCAATTTCTACTTTTC-AAATAATCAACTCATATTGCGAGAACTGAGTTGAGCCTCGAG
1 TATTTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
*
40183397 CCA-CGCTGAGG
66 TCATC-CTGAGG
* *
40183408 TA-TTTTCAATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGG
1 TATTTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
**
40183470 CTGCAAGCTGAGG
66 -T-CATCCTGAGG
* *
40183483 TATTTTTTAATTTCT-TTTTAAAAAAATCAAATCAAGAATCAACTCATAATGCGAGAGGTGAGTT
1 TATTTTTCAATTTCTATTTT-------TCAAA--AA-AATCAACTCATATTGCGAGAGGTGAGTT
* *
40183547 GAGTCTCGGGTCACATGCC-GAAG
56 GAGCCTCGGGT--CAT-CCTGAGG
*
40183570 TATCTTT-AATTTCTATGTTTTCAAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
1 TATTTTTCAATTTCTAT-TTTTC----AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
*
40183634 TTGGGTCACATCCTGAGG
61 TCGGGT--CATCCTGAGG
* * *
40183652 TA-TTTTCAATTTCTGTTTTTC-AAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAGG
1 TATTTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
40183715 TCATCCTGAGG
66 TCATCCTGAGG
* * * *
40183726 TA-TTTTCAATTTCTGTTTTTCAAAAAAATCAACCCATATTGCGAGAAGTGAGTTGAGCCTCAGG
1 TATTTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
* *
40183790 TCACATGCTGACG
66 T--CATCCTGAGG
* * * *
40183803 TATATTTT-AATTTCTA-CTTTCTAAAAAATCAACTCATGTTGTGAGAGGTGAGTTGA-CTCTCG
1 TAT-TTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC-CTCG
* * *
40183865 GGTCACACGCCGAGA
64 GGTCA-TC-CTGAGG
* * * * * *
40183880 TATTTTTTAATTTCT-GTTTTC-CAAAGATCAACTCATAATCCGAGAGGTGAGTTGAG
1 TATTTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
40183936 TTTCGGATAG
Statistics
Matches: 711, Mismatches: 78, Indels: 87
0.81 0.09 0.10
Matches are distributed among these distances:
73 38 0.05
74 97 0.14
75 58 0.08
76 170 0.24
77 100 0.14
78 109 0.15
79 4 0.01
81 12 0.02
82 56 0.08
83 2 0.00
84 1 0.00
85 3 0.00
86 10 0.01
87 47 0.07
88 4 0.01
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (76 bp):
TATTTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
TCATCCTGAGG
Found at i:40183311 original size:154 final size:154
Alignment explanation
Indices: 40183026--40183935 Score: 886
Period size: 154 Copynumber: 5.9 Consensus size: 154
40183016 TTTTAAGAAT
* *
40183026 TATTTTTCAATTTTTATTTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTCAATTTCTATTTTT-CAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAG
* * *** * *
40183091 TCACATGCC-GAGGTATCTTT-AATTTCTATTTTT-TTTAAAAAATCAACTTATATTGCGAGAGC
65 T--CAT-CCTGAGGTATTTTTCAATTTCTGTTTTTCAAAAAAAAATCAACTCATATTGCGAGAGG
40183153 TGAGTTGAGCCTCGGGT-CATCCTGAGG
127 TGAGTTGAGCCTCGGGTACATCCTGAGG
** *
40183180 TATTTTTCAATTTCTATTTTTCAAAAAAAGAAACTCATAATGCGAGAGGTGAGTTGAGCCTCGAG
1 TATTTTTCAATTTCTATTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAG
*
40183245 TCATCCTGAGGTATTTTTCAATTTCTGTTTTTCAAAAAAAAATTAACTCATATTGCGAGAGGTGA
65 TCATCCTGAGGTATTTTTCAATTTCTGTTTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGA
40183310 GTTGAGCCTCGGGT-CA-CGCTGAGG
130 GTTGAGCCTCGGGTACATC-CTGAGG
* * ** *
40183334 TA-TTTTCAATTTCTACTTTTCAAATAATCAACTCATATTGCGAGAACTGAGTTGAGCCTCGAGC
1 TATTTTTCAATTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGT
*
40183398 CA-CGCTGAGGTA-TTTTCAATTTCTGTTTTTC----AAAAATCAACTCATATTGCGAGAAGTGA
66 CATC-CTGAGGTATTTTTCAATTTCTGTTTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGA
* **
40183457 GTTGAGCCTCGGGCTGCAAGCTGAGG
130 GTTGAGCCTCGGG-TACATCCTGAGG
* *
40183483 TATTTTTTAATTTCT-TTTTAAAAAAATCAAATCAAGAATCAACTCATAATGCGAGAGGTGAGTT
1 TATTTTTCAATTTCTATTTT-------TC-AA--AA-AATCAACTCATATTGCGAGAGGTGAGTT
* * * * *
40183547 GAGTCTCGGGTCACATGCC-GAAGTATCTTT-AATTTCTATGTTTTCAAAAAAAAAAATCAACTC
55 GAGCCTCGAGT--CAT-CCTGAGGTATTTTTCAATTTCTGT-TTTTC--AAAAAAAAATCAACTC
*
40183610 ATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACATCCTGAGG
114 ATATTGCGAGAGGTGAGTTGAGCCTCGGGT-ACATCCTGAGG
* *
40183652 TA-TTTTCAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTC-AGG
1 TATTTTTCAATTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGA-G
* *
40183715 TCATCCTGAGGTA-TTTTCAATTTCTGTTTTTC--AAAAAAATCAACCCATATTGCGAGAAGTGA
65 TCATCCTGAGGTATTTTTCAATTTCTGTTTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGA
* * *
40183777 GTTGAGCCTCAGGTCACATGCTGACG
130 GTTGAGCCTCGGGT-ACATCCTGAGG
* * *
40183803 TATATTTT-AATTTCTA-CTTTCTAAAAAATCAACTCATGTTGTGAGAGGTGAGTTGA-CTCTCG
1 TAT-TTTTCAATTTCTATTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC-CTCG
* * * * * * * * *
40183865 GGTCACACGCCGAGATATTTTTTAATTTCTG-TTTTC---CAAAGATCAACTCATAATCCGAGAG
63 AGTCA-TC-CTGAGGTATTTTTCAATTTCTGTTTTTCAAAAAAAAATCAACTCATATTGCGAGAG
40183926 GTGAGTTGAG
126 GTGAGTTGAG
40183936 TTTCGGATAG
Statistics
Matches: 639, Mismatches: 71, Indels: 93
0.80 0.09 0.12
Matches are distributed among these distances:
147 39 0.06
148 1 0.00
149 13 0.02
150 11 0.02
151 79 0.12
152 104 0.16
153 66 0.10
154 120 0.19
155 22 0.03
156 18 0.03
157 2 0.00
158 34 0.05
159 3 0.00
160 33 0.05
161 2 0.00
162 17 0.03
163 9 0.01
164 1 0.00
168 12 0.02
169 53 0.08
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (154 bp):
TATTTTTCAATTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGT
CATCCTGAGGTATTTTTCAATTTCTGTTTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAG
TTGAGCCTCGGGTACATCCTGAGG
Found at i:40183930 original size:228 final size:226
Alignment explanation
Indices: 40183026--40183935 Score: 1009
Period size: 228 Copynumber: 3.9 Consensus size: 226
40183016 TTTTAAGAAT
* * *
40183026 TATTTTTCAATTTTTATTTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
* * *
40183091 TCACATGCCGAGGTATCTTTAATTTCTATTTTTTTTAAAAAATCAACTTATATTGCGAGAGCTGA
66 TCACATGCCGAGGTATCTTTAATTTCTA-TCTTTCTAAAAAATCAACTCATATTGCGAGAGCTGA
* * **
40183156 GTTGAGCCTCGGGTCA-TCCTGAGGTATTTTTCAATTTCTATTTTTCAAAAAAAGAAACTCATAA
130 GTTGAGCCTCGGGTCACACCTGAGGTA-TTTTCAATTTCT-GTTTTC-AAAAAATCAACTCATAA
40183220 TGCGAGAGGTGAGTTGAGCCTCGAGTCATCCTGAGG
192 TGCGAGAGGTGAGTTGAGCCTCG-GTCATCCTGAGG
*
40183256 TATTTTTCAATTTCTGTTTTTCAAAAAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
1 TATTTTTCAATTTCTGTTTTTC--AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
* * *
40183321 GGTCAC--GCTGAGGTAT-TTTCAATTTCTA-CTTT-TCAAATAATCAACTCATATTGCGAGAAC
64 GGTCACATGCCGAGGTATCTTT-AATTTCTATCTTTCT-AAAAAATCAACTCATATTGCGAGAGC
*
40183381 TGAGTTGAGCCTCGAG-C-CACGCTGAGGTATTTTCAATTTCTGTTTTTC-AAAAATCAACTCAT
127 TGAGTTGAGCCTCGGGTCACAC-CTGAGGTATTTTCAATTTCTG-TTTTCAAAAAATCAACTCAT
* * **
40183443 ATTGCGAGAAGTGAGTTGAGCCTCGGGCTGCAAGCTGAGG
190 AATGCGAGAGGTGAGTTGAGCCTC-GG-T-CATCCTGAGG
* *
40183483 TATTTTTTAATTTCT-TTTTAAAAAAATCAAATCAAGAATCAACTCATAATGCGAGAGGTGAGTT
1 TATTTTTCAATTTCTGTTTT-------TCAAA--AA-AATCAACTCATATTGCGAGAGGTGAGTT
* * * *
40183547 GAGTCTCGGGTCACATGCCGAAGTATCTTTAATTTCTATGTTTTCAAAAAAAAAAATCAACTCAT
56 GAGCCTCGGGTCACATGCCGAGGTATCTTTAATTTCTAT-CTTTC----TAAAAAATCAACTCAT
* *
40183612 ATTGCGAGAGGTGAGTTGAGCCTTGGGTCACATCCTGAGGTATTTTCAATTTCTGTTTTTCAAAA
116 ATTGCGAGAGCTGAGTTGAGCCTCGGGTCACA-CCTGAGGTATTTTCAATTTCTG-TTTTCAAAA
* *
40183677 AATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAGGTCATCCTGAGG
179 AATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC-GGTCATCCTGAGG
* * *
40183726 TA-TTTTCAATTTCTGTTTTTCAAAAAAATCAACCCATATTGCGAGAAGTGAGTTGAGCCTCAGG
1 TATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
* * * * * *
40183790 TCACATGCTGACGTATATTTTAATTTCTA-CTTTCTAAAAAATCAACTCATGTTGTGAGAGGTGA
66 TCACATGCCGAGGTAT-CTTTAATTTCTATCTTTCTAAAAAATCAACTCATATTGCGAGAGCTGA
* * * * *
40183854 GTTGA-CTCTCGGGTCACACGCCGAGATATTTTTTAATTTCTGTTTTCCAAAGATCAACTCATAA
130 GTTGAGC-CTCGGGTCACAC-CTGAGGTA-TTTTCAATTTCTGTTTTCAAAAAATCAACTCATAA
*
40183918 TCCGAGAGGTGAGTTGAG
192 TGCGAGAGGTGAGTTGAG
40183936 TTTCGGATAG
Statistics
Matches: 583, Mismatches: 58, Indels: 80
0.81 0.08 0.11
Matches are distributed among these distances:
225 35 0.06
226 6 0.01
227 44 0.08
228 132 0.23
229 15 0.03
230 37 0.06
231 3 0.01
232 49 0.08
233 51 0.09
234 52 0.09
236 21 0.04
237 3 0.01
238 3 0.01
242 48 0.08
243 15 0.03
244 30 0.05
245 39 0.07
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (226 bp):
TATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
TCACATGCCGAGGTATCTTTAATTTCTATCTTTCTAAAAAATCAACTCATATTGCGAGAGCTGAG
TTGAGCCTCGGGTCACACCTGAGGTATTTTCAATTTCTGTTTTCAAAAAATCAACTCATAATGCG
AGAGGTGAGTTGAGCCTCGGTCATCCTGAGG
Found at i:40184113 original size:5 final size:5
Alignment explanation
Indices: 40184103--40184133 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
40184093 TTCTTCGTGT
40184103 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
40184134 ATATATTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:40184142 original size:15 final size:15
Alignment explanation
Indices: 40184106--40184141 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
40184096 TTCGTGTTTT
*
40184106 TATTTTATTTTATTT
1 TATTTTATTTTATTA
40184121 TATTTTATTTTATATA
1 TATTTTATTTTAT-TA
40184137 TATTT
1 TATTT
40184142 AAAAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
TATTTTATTTTATTA
Found at i:40184394 original size:29 final size:29
Alignment explanation
Indices: 40184329--40184462 Score: 108
Period size: 30 Copynumber: 4.5 Consensus size: 29
40184319 ATACAAAAAA
* *
40184329 TATAAATTACATTTTGGCCACTGAACTTTT
1 TATAAATTACATTTTGACC-CTTAACTTTT
*
40184359 TAAAAATTACATTTTGACCCTTAACTTTT
1 TATAAATTACATTTTGACCCTTAACTTTT
* * *
40184388 TCTAAATTTACATCTTGACCCCTAA-TATTT
1 TATAAA-TTACATTTTGACCCTTAACT-TTT
* ** * * *
40184418 TGTAAATTACATTCGGGCCTCTAAACTTTC
1 TATAAATTACATTTTGACC-CTTAACTTTT
*
40184448 TAGAAATTACATTTT
1 TATAAATTACATTTT
40184463 AGCCTCATAT
Statistics
Matches: 81, Mismatches: 19, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
29 23 0.28
30 57 0.70
31 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.43
Consensus pattern (29 bp):
TATAAATTACATTTTGACCCTTAACTTTT
Found at i:40184468 original size:30 final size:30
Alignment explanation
Indices: 40184434--40184500 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
40184424 TTACATTCGG
40184434 GCCTCTAAACTTT-CTAGAAATTACATTTTA
1 GCCTCTAAACTTTCCTA-AAATTACATTTTA
* * *
40184464 GCCTC-ATATTTTCCTAAAATTACATTTTT
1 GCCTCTAAACTTTCCTAAAATTACATTTTA
40184493 GCCT-TAAA
1 GCCTCTAAA
40184501 AACTTTACAC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
29 23 0.74
30 8 0.26
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.42
Consensus pattern (30 bp):
GCCTCTAAACTTTCCTAAAATTACATTTTA
Found at i:40185027 original size:23 final size:24
Alignment explanation
Indices: 40184991--40185058 Score: 61
Period size: 23 Copynumber: 2.9 Consensus size: 24
40184981 AGGTTTCGAA
*
40184991 GGAGAAAGAAAAGAAAAGGAAAGG
1 GGAGAAAGAAAAGAAAAGAAAAGG
* *
40185015 GGAG-AAGAGAAGAGAAGAAAA-G
1 GGAGAAAGAAAAGAAAAGAAAAGG
*
40185037 AGAGAAA-ACGAAAGAAAAGAAA
1 GGAGAAAGA--AAAGAAAAGAAA
40185059 GAAAAAAAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
22 5 0.14
23 16 0.46
24 14 0.40
ACGTcount: A:0.65, C:0.01, G:0.34, T:0.00
Consensus pattern (24 bp):
GGAGAAAGAAAAGAAAAGAAAAGG
Found at i:40185029 original size:10 final size:10
Alignment explanation
Indices: 40185016--40185072 Score: 59
Period size: 9 Copynumber: 6.0 Consensus size: 10
40185006 AAGGAAAGGG
*
40185016 GAGAAGAGAA
1 GAGAAGAAAA
40185026 GAGAAGAAAA
1 GAGAAGAAAA
40185036 GAG-AGAAAA
1 GAGAAGAAAA
40185045 CGA-AAGAAAA
1 -GAGAAGAAAA
40185055 GA-AAGAAAA
1 GAGAAGAAAA
*
40185064 -AAAAGAAAA
1 GAGAAGAAAA
40185073 AGTAGAGAGA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
8 1 0.02
9 22 0.51
10 20 0.47
ACGTcount: A:0.72, C:0.02, G:0.26, T:0.00
Consensus pattern (10 bp):
GAGAAGAAAA
Found at i:40185074 original size:19 final size:19
Alignment explanation
Indices: 40185029--40185072 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
40185019 AAGAGAAGAG
* *
40185029 AAGAAAAGAGAGAAAACGA
1 AAGAAAAGAAAGAAAACAA
40185048 AAGAAAAGAAAGAAAA-AA
1 AAGAAAAGAAAGAAAACAA
40185066 AAGAAAA
1 AAGAAAA
40185073 AGTAGAGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.77, C:0.02, G:0.20, T:0.00
Consensus pattern (19 bp):
AAGAAAAGAAAGAAAACAA
Found at i:40185475 original size:15 final size:15
Alignment explanation
Indices: 40185457--40185488 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
40185447 CCCAATCTGC
*
40185457 AGAAAAAAAGAAAAA
1 AGAAAAAAACAAAAA
40185472 AGAAAAAAACAAAAA
1 AGAAAAAAACAAAAA
40185487 AG
1 AG
40185489 GCCCGAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.84, C:0.03, G:0.12, T:0.00
Consensus pattern (15 bp):
AGAAAAAAACAAAAA
Found at i:40186127 original size:18 final size:18
Alignment explanation
Indices: 40186062--40186200 Score: 144
Period size: 17 Copynumber: 7.9 Consensus size: 18
40186052 TTTTTTTAAA
*
40186062 AAAAATTCTCGT-ATTTC
1 AAAAATTCTCGTGTTTTC
*
40186079 AAAAATTGTCGTGTTTT-
1 AAAAATTCTCGTGTTTTC
* *
40186096 AAAATTTTTCGTGTTTTC
1 AAAAATTCTCGTGTTTTC
*
40186114 AATAATTCTCGTG-TTTC
1 AAAAATTCTCGTGTTTTC
* *
40186131 ACAAATT-TC-TGTGATTC
1 AAAAATTCTCGTGT-TTTC
*
40186148 AAAAATTTTCGTGTTTTC
1 AAAAATTCTCGTGTTTTC
*
40186166 AAGAAATTGTCGTGTTTTC
1 AA-AAATTCTCGTGTTTTC
40186185 AAAAATTCTCGTGTTT
1 AAAAATTCTCGTGTTT
40186201 AAAAAAAATT
Statistics
Matches: 101, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
15 2 0.02
16 2 0.02
17 44 0.44
18 33 0.33
19 20 0.20
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (18 bp):
AAAAATTCTCGTGTTTTC
Found at i:40186131 original size:52 final size:52
Alignment explanation
Indices: 40186064--40186206 Score: 171
Period size: 52 Copynumber: 2.7 Consensus size: 52
40186054 TTTTTAAAAA
* * *
40186064 AAATTCTCGTATTTCAAAAATTGTCGTGTTTTAAAATTTTTCGTGTTTTCAA-
1 AAATTCTCGTGTTTCAAAAATT-TCGTGTTTAAAAAATTTTCGTGTTTTCAAG
* * * *
40186116 TAATTCTCGTGTTTCACAAATTTCTGTGATTCAAAAATTTTCGTGTTTTCAAG
1 AAATTCTCGTGTTTCAAAAATTTC-GTGTTTAAAAAATTTTCGTGTTTTCAAG
*
40186169 AAATTGTCGTGTTTTCAAAAATTCTCGTGTTTAAAAAA
1 AAATTCTCGTG-TTTCAAAAATT-TCGTGTTTAAAAAA
40186207 AATTTTGTGT
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
51 2 0.03
52 43 0.57
53 9 0.12
54 20 0.26
55 2 0.03
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.45
Consensus pattern (52 bp):
AAATTCTCGTGTTTCAAAAATTTCGTGTTTAAAAAATTTTCGTGTTTTCAAG
Found at i:40186206 original size:18 final size:18
Alignment explanation
Indices: 40186060--40186243 Score: 101
Period size: 18 Copynumber: 10.4 Consensus size: 18
40186050 TGTTTTTTTA
*
40186060 AAAAAAATTCTCGTATTT
1 AAAAAAATTCTCGTGTTT
* *
40186078 -CAAAAATTGTCGTGTTT
1 AAAAAAATTCTCGTGTTT
* * *
40186095 -TAAAATTTTTCGTGTTT
1 AAAAAAATTCTCGTGTTT
** *
40186112 TCAATAATTCTCGTGTTT
1 AAAAAAATTCTCGTGTTT
* * * *
40186130 CACAAATTTCT-GTGATT
1 AAAAAAATTCTCGTGTTT
* *
40186147 -CAAAAATTTTCGTGTTTT
1 AAAAAAATTCTCGTG-TTT
* * *
40186165 CAAGAAATTGTCGTGTTT
1 AAAAAAATTCTCGTGTTT
**
40186183 TCAAAAATTCTCGTGTTT
1 AAAAAAATTCTCGTGTTT
*
40186201 AAAAAAAATT-TTGTGTTT
1 -AAAAAAATTCTCGTGTTT
*
40186219 AAAAAAAAT-TCGTGTTTT
1 AAAAAAATTCTCGTG-TTT
40186237 AAAAAAA
1 AAAAAAA
40186244 AGTTGTGTTT
Statistics
Matches: 127, Mismatches: 33, Indels: 12
0.74 0.19 0.07
Matches are distributed among these distances:
16 6 0.05
17 48 0.38
18 55 0.43
19 18 0.14
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (18 bp):
AAAAAAATTCTCGTGTTT
Found at i:40186209 original size:19 final size:18
Alignment explanation
Indices: 40186148--40186258 Score: 93
Period size: 18 Copynumber: 6.1 Consensus size: 18
40186138 TCTGTGATTC
* **
40186148 AAAAATTTTCGTGTTTTC
1 AAAAAATTTCGTGTTTAA
* *
40186166 AAGAAATTGTCGTGTTT-T
1 AAAAAATT-TCGTGTTTAA
*
40186184 CAAAAATTCTCGTGTTTAA
1 AAAAAATT-TCGTGTTTAA
*
40186203 AAAAAATTTTGTGTTTAA
1 AAAAAATTTCGTGTTTAA
40186221 AAAAAA-TTCGTGTTTTAA
1 AAAAAATTTCGTG-TTTAA
*
40186239 AAAAAAGTT-GTGTTTCAA
1 AAAAAATTTCGTGTTT-AA
40186257 AA
1 AA
40186259 CTCACGTGTT
Statistics
Matches: 78, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
17 8 0.10
18 53 0.68
19 17 0.22
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.41
Consensus pattern (18 bp):
AAAAAATTTCGTGTTTAA
Found at i:40197774 original size:6 final size:6
Alignment explanation
Indices: 40197759--40197799 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
40197749 TGGGGCATAC
* * *
40197759 GAGCCA GAGCCT GAGCTA GAGCCA AAGCCA GAGCCA GAGCC
1 GAGCCA GAGCCA GAGCCA GAGCCA GAGCCA GAGCCA GAGCC
40197800 TAAGCGGTTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.32, C:0.32, G:0.32, T:0.05
Consensus pattern (6 bp):
GAGCCA
Found at i:40197782 original size:18 final size:18
Alignment explanation
Indices: 40197759--40197804 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
40197749 TGGGGCATAC
* * *
40197759 GAGCCAGAGCCTGAGCTA
1 GAGCCAAAGCCAGAGCCA
40197777 GAGCCAAAGCCAGAGCCA
1 GAGCCAAAGCCAGAGCCA
*
40197795 GAGCCTAAGC
1 GAGCCAAAGC
40197805 GGTTGCATAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.30, G:0.30, T:0.07
Consensus pattern (18 bp):
GAGCCAAAGCCAGAGCCA
Found at i:40198262 original size:48 final size:48
Alignment explanation
Indices: 40198196--40198304 Score: 141
Period size: 48 Copynumber: 2.3 Consensus size: 48
40198186 GTATTTATTT
* *
40198196 AATTAGAT-CAATTCCAACATTAAAAC-TTGGAACAAACTTTGTAATATA
1 AATTAGATAC-ATTACAACATTAAAACGAT-GAACAAACTTTGTAATATA
**
40198244 AATTAGATACATTACAACATTAAAACGATGATTAAACTTTGTAATATA
1 AATTAGATACATTACAACATTAAAACGATGAACAAACTTTGTAATATA
*
40198292 AATTAGGTACATT
1 AATTAGATACATT
40198305 GGGTTACATA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
48 52 0.96
49 2 0.04
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (48 bp):
AATTAGATACATTACAACATTAAAACGATGAACAAACTTTGTAATATA
Found at i:40206786 original size:18 final size:18
Alignment explanation
Indices: 40206763--40206801 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
40206753 TGCACTTGCA
*
40206763 AGCTCACCTAAAGATGCG
1 AGCTCAACTAAAGATGCG
* *
40206781 AGCTCAACTCAAGTTGCG
1 AGCTCAACTAAAGATGCG
40206799 AGC
1 AGC
40206802 ATATTAAAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.31, C:0.28, G:0.23, T:0.18
Consensus pattern (18 bp):
AGCTCAACTAAAGATGCG
Found at i:40209686 original size:29 final size:29
Alignment explanation
Indices: 40209653--40209714 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
40209643 AAAGTTGCCA
*
40209653 AGCACCTAGCGAGCTTGGGATTTAAAAAG
1 AGCACCTAGCAAGCTTGGGATTTAAAAAG
* *
40209682 AGCACCTAGCAAGCTTGGGATTTGAAAGG
1 AGCACCTAGCAAGCTTGGGATTTAAAAAG
40209711 AGCA
1 AGCA
40209715 TCGTTAATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.18, G:0.29, T:0.19
Consensus pattern (29 bp):
AGCACCTAGCAAGCTTGGGATTTAAAAAG
Found at i:40215140 original size:126 final size:127
Alignment explanation
Indices: 40214914--40215166 Score: 472
Period size: 126 Copynumber: 2.0 Consensus size: 127
40214904 TTCCTTATGA
*
40214914 GCAAAAATAATTCCTTCTTTTAATCCACTCATTGACGACTGCTTTAGACTTGTTTGGTAAGAAAG
1 GCAAAAATAATTCCTTCTTTCAATCCACTCATTGACGACTGCTTTAGACTTGTTTGGTAAGAAAG
**
40214979 ATGATTTTTAAAAAAAATCTAAAATAGTTAAAGCTTTTATATAAGAACATGAACTGAAAGTT
66 ATGATTTAAAAAAAAAATCTAAAATAGTTAAAGCTTTTATATAAGAACATGAACTGAAAGTT
40215041 GCAAAAATAATTCCTTCTTTCAATCCACTCATTGACGACTGC-TTAGACTTGTTTGGTAAGAAAG
1 GCAAAAATAATTCCTTCTTTCAATCCACTCATTGACGACTGCTTTAGACTTGTTTGGTAAGAAAG
40215105 ATGATTTAAAAAAAAAATCTAAAATAGTTAAAGCTTTTATATAAGAACATGAACTGAAAGTT
66 ATGATTTAAAAAAAAAATCTAAAATAGTTAAAGCTTTTATATAAGAACATGAACTGAAAGTT
40215167 TTTATCTTTA
Statistics
Matches: 123, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
126 82 0.67
127 41 0.33
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (127 bp):
GCAAAAATAATTCCTTCTTTCAATCCACTCATTGACGACTGCTTTAGACTTGTTTGGTAAGAAAG
ATGATTTAAAAAAAAAATCTAAAATAGTTAAAGCTTTTATATAAGAACATGAACTGAAAGTT
Found at i:40215415 original size:34 final size:34
Alignment explanation
Indices: 40215372--40215439 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
40215362 TTGCCTATGT
40215372 GTTCTTAACAACCAAGTAAATTAATCTCGAATAA
1 GTTCTTAACAACCAAGTAAATTAATCTCGAATAA
* *
40215406 GTTCTTAACAACTAAGTAAATTCATCTCGAATAA
1 GTTCTTAACAACCAAGTAAATTAATCTCGAATAA
40215440 CAGAGAGTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.31
Consensus pattern (34 bp):
GTTCTTAACAACCAAGTAAATTAATCTCGAATAA
Found at i:40216296 original size:10 final size:9
Alignment explanation
Indices: 40216248--40216306 Score: 50
Period size: 10 Copynumber: 6.2 Consensus size: 9
40216238 TAAATTTTAA
40216248 AATATTTTT
1 AATATTTTT
40216257 ATATAATTTTT
1 A-AT-ATTTTT
40216268 -ATACTTTTTT
1 AATA--TTTTT
*
40216278 AATAATTTT
1 AATATTTTT
40216287 AATGATTTTT
1 AAT-ATTTTT
40216297 AAT-TTTTT
1 AATATTTTT
40216305 AA
1 AA
40216307 ATTAAAATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
8 8 0.19
9 10 0.24
10 15 0.36
11 9 0.21
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
AATATTTTT
Found at i:40216403 original size:5 final size:5
Alignment explanation
Indices: 40216393--40216421 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
40216383 AAAATGTTAA
40216393 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
40216422 GACCGATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:40231521 original size:50 final size:50
Alignment explanation
Indices: 40231454--40232029 Score: 295
Period size: 50 Copynumber: 11.5 Consensus size: 50
40231444 TTTGGAAAGT
* * *
40231454 AAGATTCGCCATCGTGGCTTTAATCTTTTTAACTGTAATGTCGGGGAAGC
1 AAGATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
* * * * * * * * *
40231504 AAGATTCACCGTTGTGGCTTTAAT-TTGCTTCACTGTATTGCCTGGAAATGT
1 AAGATTCGCCGTTGTGGCTTTAATCTT-TTTAACTGCAATGTCGGGGAA-GC
* * * *
40231555 AAGATTCGCTGCTGTAGCTTTAATCTTTTTAA-TCGCAATGTCAGGG-AGAC
1 AAGATTCGCCGTTGTGGCTTTAATCTTTTTAACT-GCAATGTCGGGGAAG-C
*** * * ** ** * * * *
40231605 CTTATTCACCGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGGAGGT
1 AAGATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
* * * * ***
40231655 AAGATTCGTCGTTGTGACTTTAATCCTTTTAGCTGC-ATGTCGAAAAAGC
1 AAGATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
* ** * * * * * * *
40231704 AAGATTCACCGTTGTGGCTTTAATCTGCTTCACTACATTGCCAGAGAATGT
1 AAGATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAA-GC
* * * **
40231755 AAGATTCGCTGTTGTAGCTTTAATCTTTTTAACCGCAATGTCAAGGAAGC
1 AAGATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
** * * * ** ** * * * *
40231805 TGGATACGCCATTGTGGTTTTAATCTGCTCCACTGC-ATCGCCAGGAAAGT
1 AAGATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAAT-GTCGGGGAAGC
* * * * *
40231855 AACACTCGCCGCTGTGGCTTTACTCTTTTTAACTGCAATGTCGGGGAAGA
1 AAGATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
* * *** * *
40231905 AAGATTCACCG-TGTGGCTTTAATCTATTCCGCTGC-ATCGCCTGGGG-AGT
1 AAGATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAAT-GTC-GGGGAAGC
* *
40231954 AAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
1 AAGATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
* * *
40232004 ATGATTCGCTGTTGTAGCTTTAATCT
1 AAGATTCGCCGTTGTGGCTTTAATCT
40232030 GTTCCACTGC
Statistics
Matches: 371, Mismatches: 139, Indels: 32
0.68 0.26 0.06
Matches are distributed among these distances:
48 2 0.01
49 72 0.19
50 221 0.60
51 74 0.20
52 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (50 bp):
AAGATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
Found at i:40231729 original size:99 final size:100
Alignment explanation
Indices: 40231447--40232040 Score: 524
Period size: 100 Copynumber: 5.9 Consensus size: 100
40231437 CGTAACTTTT
* ** * * * **
40231447 GGAAAGTAAGATTCGCCATCGTGGCTTTAATCTTTTTAACTGTAATGTCGGGGAAGCAAGATTCA
1 GGAAGGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGAAGAAGCAAGATTCA
* * * *
40231512 CCGTTGTGGCTTTAATTTGCTT-CACTGTATTGCCT
66 CCGTTGTGGCTTTAATCTG-TTCCACTGCATCGCCA
* * * * ***
40231547 GGAAATGTAAGATTCGCTGCTGTAGCTTTAATCTTTTTAA-TCGCAATGTC-AGGGAGACCTTAT
1 GG-AAGGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACT-GCAATGTCGAAGAAG-CAAGAT
* *
40231610 TCACCGTTGTGGCTTTAATCTGTTCCACTGCACCGCCT
63 TCACCGTTGTGGCTTTAATCTGTTCCACTGCATCGCCA
* * * *
40231648 GGGAGGTAAGATTCG-TCGTTGT-GACTTTAATCCTTTTAGCTGC-ATGTCGAAAAAGCAAGATT
1 GGAAGGTAAGATTCGCT-GTTGTAG-CTTTAATCTTTTTAACTGCAATGTCGAAGAAGCAAGATT
* *
40231710 CACCGTTGTGGCTTTAATCTGCTT-CACTACATTGCCA
64 CACCGTTGTGGCTTTAATCTG-TTCCACTGCATCGCCA
* * ** *
40231747 GAGAATGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACCGCAATGTC-AAGGAAGCTGGATA
1 G-GAAGGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGAA-GAAGCAAGATT
* * * *
40231811 CGCCATTGTGGTTTTAATCTGCTCCACTGCATCGCCA
64 CACCGTTGTGGCTTTAATCTGTTCCACTGCATCGCCA
* * * * * * * ** *
40231848 GGAAAGTAACACTCGCCGCTGTGGCTTTACTCTTTTTAACTGCAATGTCGGGGAAGAAAGATTCA
1 GGAAGGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGAAGAAGCAAGATTCA
* * *
40231913 CCG-TGTGGCTTTAATCTATTCCGCTGCATCGCCT
66 CCGTTGTGGCTTTAATCTGTTCCACTGCATCGCCA
* ** *
40231947 GG-GGAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCATGATTC
1 GGAAG-GTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGAAGAAGCAAGATTC
* * *
40232011 GCTGTTGTAGCTTTAATCTGTTCCACTGCA
65 ACCGTTGTGGCTTTAATCTGTTCCACTGCA
40232041 CCGTTTGGGA
Statistics
Matches: 394, Mismatches: 82, Indels: 36
0.77 0.16 0.07
Matches are distributed among these distances:
99 123 0.31
100 152 0.39
101 119 0.30
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.34
Consensus pattern (100 bp):
GGAAGGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGAAGAAGCAAGATTCA
CCGTTGTGGCTTTAATCTGTTCCACTGCATCGCCA
Found at i:40231922 original size:200 final size:199
Alignment explanation
Indices: 40231467--40232043 Score: 712
Period size: 200 Copynumber: 2.9 Consensus size: 199
40231457 ATTCGCCATC
* *
40231467 GTGGCTTTAATCTTTTTAACTGTAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATTTGC
1 GTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGC
* * *
40231532 TTCACTGTATTGCCTGGAAATGTAAGATTCGCTGCTGTAGCTTTAATCTTTTTAATCGCAATGTC
66 TTCACTGCATTGCCTGG-AATGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACCGCAATGTC
* * * * * * * *
40231597 AGGGAGACCTTATTCACCGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGGAGGTAAGATTC
130 AGGGA-AGCTGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCACCGCCAGGAAAGTAACACTC
* *
40231662 GTCGTT
194 GCCGCT
* * * ***
40231668 GTGACTTTAATCCTTTTAGCTGC-ATGTCGAAAAAGCAAGATTCACCGTTGTGGCTTTAATCTGC
1 GTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGC
* *
40231732 TTCACTACATTGCCAGAGAATGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACCGCAATGTC
66 TTCACTGCATTGCCTG-GAATGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACCGCAATGTC
* * * * * *
40231797 AAGGAAGCTGGATACGCCATTGTGGTTTTAATCTGCTCCACTGCATCGCCAGGAAAGTAACACTC
130 AGGGAAGCT-GATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCACCGCCAGGAAAGTAACACTC
40231862 GCCGCT
194 GCCGCT
* * *
40231868 GTGGCTTTACTCTTTTTAACTGCAATGTCGGGGAAGAAAGATTCACCG-TGTGGCTTTAATCT-A
1 GTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGC
* * * *
40231931 TTCCGCTGCATCGCCTGGGGA-GTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGT
66 TT-CACTGCATTGCCT-GGAATGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACCGCAATGT
* * *
40231995 CGGGGAAGCATGATTCGCTGTTGTAGCTTTAATCTGTTCCACTGCACCG
129 CAGGGAAGC-TGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCACCG
40232044 TTTGGGAAGA
Statistics
Matches: 317, Mismatches: 53, Indels: 14
0.83 0.14 0.04
Matches are distributed among these distances:
199 85 0.27
200 191 0.60
201 41 0.13
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (199 bp):
GTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGC
TTCACTGCATTGCCTGGAATGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACCGCAATGTCA
GGGAAGCTGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCACCGCCAGGAAAGTAACACTCGC
CGCT
Found at i:40232051 original size:50 final size:50
Alignment explanation
Indices: 40231886--40232052 Score: 147
Period size: 50 Copynumber: 3.4 Consensus size: 50
40231876 ACTCTTTTTA
* * * * * *
40231886 ACTGCAATGTCGGGGAAGAAAGATTCACCG-TGTGGCTTTAATCTATTCC
1 ACTGCAACGTCTGGGAAGCAAGATTCGCTGTTGTAGCTTTAATCTATTCC
* * * * * * **
40231935 GCTGCATCGCCTGGGGAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTA
1 ACTGCAACGTCTGGGAAGCAAGATTCGCTGTTGTAGCTTTAATCTATTCC
* * * *
40231985 ACTGCAATGTCGGGGAAGCATGATTCGCTGTTGTAGCTTTAATCTGTTCC
1 ACTGCAACGTCTGGGAAGCAAGATTCGCTGTTGTAGCTTTAATCTATTCC
* *
40232035 ACTGCACCGTTTGGGAAG
1 ACTGCAACGTCTGGGAAG
40232053 ATAAGATCTG
Statistics
Matches: 89, Mismatches: 28, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
49 21 0.24
50 68 0.76
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (50 bp):
ACTGCAACGTCTGGGAAGCAAGATTCGCTGTTGTAGCTTTAATCTATTCC
Found at i:40232186 original size:44 final size:44
Alignment explanation
Indices: 40232163--40232401 Score: 131
Period size: 44 Copynumber: 5.2 Consensus size: 44
40232153 TTTTAATCAG
* *
40232163 CTCCACTGTAATCTCAGAGAGATAGGATTACTAGCTTCAATCTA
1 CTCCACTGTAATCTCAGAGAGATAAGATCACTAGCTTCAATCTA
* * * * *
40232207 CTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTTAATCTGATGCGATCTA
1 CTCCACTGTAATCTCAGAGAGATAAGA--TC--AC--T-AGCT--T-CAATCTA
* *** **
40232261 CTCTACTGTAA-CTTCAGAGAGATAAGATC-CTTTATTCTAATCCG
1 CTCCACTGTAATC-TCAGAGAGATAAGATCACTAGCTTC-AATCTA
* * * * *
40232305 CTCCACTGTAATCTCAGGGAGGTAGGATTACTAGCTTCAATCTG
1 CTCCACTGTAATCTCAGAGAGATAAGATCACTAGCTTCAATCTA
* * * ** * *
40232349 CTCCGCTGTAATCTTAGGGAGATAAGATTTCTGGCTTCAATCTC
1 CTCCACTGTAATCTCAGAGAGATAAGATCACTAGCTTCAATCTA
40232393 CTCCACTGT
1 CTCCACTGT
40232402 TGCTTAGGGA
Statistics
Matches: 149, Mismatches: 32, Indels: 28
0.71 0.15 0.13
Matches are distributed among these distances:
43 1 0.01
44 100 0.67
45 6 0.04
46 3 0.02
47 1 0.01
48 1 0.01
49 1 0.01
50 1 0.01
51 3 0.02
52 2 0.01
53 2 0.01
54 28 0.19
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (44 bp):
CTCCACTGTAATCTCAGAGAGATAAGATCACTAGCTTCAATCTA
Found at i:40232289 original size:142 final size:142
Alignment explanation
Indices: 40232106--40232391 Score: 473
Period size: 142 Copynumber: 2.0 Consensus size: 142
40232096 GAGATAAGAC
* *
40232106 CTGATGTGATCTACTCTACTGTAACTTCAAAAAGATAAGATCATTTATTTTAATCAGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAAAAAGATAAGATCATTTATTCTAATCAGCTCCACTG
40232171 TAATCTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATT
66 TAATCTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATT
*
40232236 TCTGGCTTTAAT
131 TCTGGCTTCAAT
* * * *
40232248 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTCTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAAAAAGATAAGATCATTTATTCTAATCAGCTCCACTG
* * * *
40232313 TAATCTCAGGGAGGTAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTTAGGGAGATAAGATT
66 TAATCTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATT
40232378 TCTGGCTTCAAT
131 TCTGGCTTCAAT
40232390 CT
1 CT
40232392 CCTCCACTGT
Statistics
Matches: 133, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
142 133 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (142 bp):
CTGATGCGATCTACTCTACTGTAACTTCAAAAAGATAAGATCATTTATTCTAATCAGCTCCACTG
TAATCTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATT
TCTGGCTTCAAT
Found at i:40233669 original size:13 final size:13
Alignment explanation
Indices: 40233653--40233678 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40233643 TTAGCCTTTC
40233653 CATTTTTCATTTT
1 CATTTTTCATTTT
40233666 CATTTTTCATTTT
1 CATTTTTCATTTT
40233679 TTTACTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (13 bp):
CATTTTTCATTTT
Found at i:40234592 original size:13 final size:12
Alignment explanation
Indices: 40234574--40234607 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
40234564 TTTTCTCTCA
40234574 TTTTATTTTGAT
1 TTTTATTTTGAT
40234586 CTTTTATTTTGAT
1 -TTTTATTTTGAT
*
40234599 TTTGATTTT
1 TTTTATTTT
40234608 TCTTCTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.15, C:0.03, G:0.09, T:0.74
Consensus pattern (12 bp):
TTTTATTTTGAT
Found at i:40234602 original size:6 final size:6
Alignment explanation
Indices: 40234573--40234647 Score: 50
Period size: 6 Copynumber: 12.8 Consensus size: 6
40234563 TTTTTCTCTC
* * *
40234573 ATTTT- ATTTTG ATCTTTT ATTTTG ATTTTG ATTTTT CTTCTT- -TTTT-
1 ATTTTG ATTTTG AT-TTTG ATTTTG ATTTTG ATTTTG ATT-TTG ATTTTG
* * *
40234619 ATTTTG ATCTTG ATTTTG CTTTTG CTTTT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTT
40234648 TTTTTTTTTG
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
4 2 0.03
5 11 0.19
6 38 0.66
7 7 0.12
ACGTcount: A:0.12, C:0.08, G:0.09, T:0.71
Consensus pattern (6 bp):
ATTTTG
Found at i:40234608 original size:41 final size:40
Alignment explanation
Indices: 40234563--40234648 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 40
40234553 TTATTCTTTC
*
40234563 TTTTTC-TCTCATTTTATTTTGATCTTTTATTTTGATTTTGA
1 TTTTTCTTCT-ATTTTATTTTGATC-TTGATTTTGATTTTGA
* * *
40234604 TTTTTCTTCTTTTTTATTTTGATCTTGATTTTGCTTTTGC
1 TTTTTCTTCTATTTTATTTTGATCTTGATTTTGATTTTGA
40234644 TTTTT
1 TTTTT
40234649 TTTTTTTTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
40 18 0.45
41 19 0.47
42 3 0.08
ACGTcount: A:0.10, C:0.10, G:0.08, T:0.71
Consensus pattern (40 bp):
TTTTTCTTCTATTTTATTTTGATCTTGATTTTGATTTTGA
Found at i:40234632 original size:34 final size:33
Alignment explanation
Indices: 40234594--40234658 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 33
40234584 ATCTTTTATT
*
40234594 TTGATTTTGATTTTTCTTCTTTTTTATTTTGATC
1 TTGATTTTGATTTTGCTT-TTTTTTATTTTGATC
* *
40234628 TTGATTTTGCTTTTGCTTTTTTTTTTTTTGA
1 TTGATTTTGATTTTGCTTTTTTTTATTTTGA
40234659 GATCGGATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 12 0.43
34 16 0.57
ACGTcount: A:0.09, C:0.08, G:0.11, T:0.72
Consensus pattern (33 bp):
TTGATTTTGATTTTGCTTTTTTTTATTTTGATC
Found at i:40234649 original size:41 final size:39
Alignment explanation
Indices: 40234574--40234656 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 39
40234564 TTTTCTCTCA
*
40234574 TTTTATTTTGATCTTTTATTTTGATTTTGATTTTTCTTCTT
1 TTTTATTTTGATCTTTGATTTTGATTTTGATTTTT-TT-TT
* *
40234615 TTTTATTTTGATC-TTGATTTTGCTTTTGCTTTTTTTTT
1 TTTTATTTTGATCTTTGATTTTGATTTTGATTTTTTTTT
40234653 TTTT
1 TTTT
40234657 GAGATCGGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
38 6 0.15
39 2 0.05
40 18 0.46
41 13 0.33
ACGTcount: A:0.10, C:0.07, G:0.08, T:0.75
Consensus pattern (39 bp):
TTTTATTTTGATCTTTGATTTTGATTTTGATTTTTTTTT
Found at i:40234651 original size:28 final size:29
Alignment explanation
Indices: 40234585--40234652 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 29
40234575 TTTATTTTGA
* *
40234585 TCTTTTATTTTGATTTTGATTTTTCTTCT
1 TCTTTTATTTTGATCTTGATTTTGCTTCT
40234614 T-TTTTATTTTGATCTTGATTTTGCTT-T
1 TCTTTTATTTTGATCTTGATTTTGCTTCT
*
40234641 TGCTTTTTTTTT
1 T-CTTTTATTTT
40234653 TTTTGAGATC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 2 0.06
28 23 0.68
29 9 0.26
ACGTcount: A:0.09, C:0.09, G:0.09, T:0.74
Consensus pattern (29 bp):
TCTTTTATTTTGATCTTGATTTTGCTTCT
Found at i:40236147 original size:36 final size:36
Alignment explanation
Indices: 40236105--40236176 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
40236095 TATATTATTC
40236105 ATCTCATCTTCTTTTCTCCTTGAGACTGATTTTTTT
1 ATCTCATCTTCTTTTCTCCTTGAGACTGATTTTTTT
40236141 ATCTCATCTTCTTTTCTCCTTGAGACTGATTTTTTT
1 ATCTCATCTTCTTTTCTCCTTGAGACTGATTTTTTT
40236177 TACTCTCTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.14, C:0.22, G:0.08, T:0.56
Consensus pattern (36 bp):
ATCTCATCTTCTTTTCTCCTTGAGACTGATTTTTTT
Found at i:40239079 original size:44 final size:44
Alignment explanation
Indices: 40239016--40239103 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
40239006 TGAAATAGAA
40239016 TGATAAAAGTAAGAATTTTAAAAGAAACATGTAATGTAAAAGAT
1 TGATAAAAGTAAGAATTTTAAAAGAAACATGTAATGTAAAAGAT
40239060 TGATAAAAGTAAGAATTTTAAAAGAAACATGTAATGTAAAAGAT
1 TGATAAAAGTAAGAATTTTAAAAGAAACATGTAATGTAAAAGAT
40239104 CAATGATGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.55, C:0.02, G:0.16, T:0.27
Consensus pattern (44 bp):
TGATAAAAGTAAGAATTTTAAAAGAAACATGTAATGTAAAAGAT
Found at i:40243382 original size:158 final size:156
Alignment explanation
Indices: 40243138--40243595 Score: 535
Period size: 158 Copynumber: 2.9 Consensus size: 156
40243128 AACAAAAGAT
* * * * * * *
40243138 CATGCATTCAACCTAACATAACGGGAACACATGTATATCATAAACACTTTTTCATTGTCAATTCT
1 CATGCATTCAGCCTAACACAACTGGATCACAGGTATATCAT-AACACTTTTTAATT-TCAATTCA
* * * * **
40243203 AGAATATTAAAATCTAATTT-GGGTTCTGATTTTTTTGGTCTTTGTCTGGTATGAGTACAAGAAC
64 AAAATATTTAAATCTAATTTGGGGTTCTGATTTTTTTGGTCTTAGTCCGGTACAAGTACAAGAAC
* * *
40243267 TAGAAGCCTAAAAAATAACAACATAACAC
129 TAGAAG-CAAAAAAAGAACAACAGAACAC
* * *
40243296 CATGCATTCAGCCTAATACAACTGGATCATAGGTATATCCTATACACTATTTTAATTTCAATTCA
1 CATGCATTCAGCCTAACACAACTGGATCACAGGTATATCATA-ACACT-TTTTAATTTCAATTCA
* * *
40243361 AAAATATTTTAATCTAATTTGGGGTTCTAATTTTTTTTGTCTTAGTCCGGTACAAGTACAAGAAC
64 AAAATATTTAAATCTAATTTGGGGTTCTGATTTTTTTGGTCTTAGTCCGGTACAAGTACAAGAAC
40243426 TAGAAGCAAAAAAAGAACAACAGAACAC
129 TAGAAGCAAAAAAAGAACAACAGAACAC
* * *
40243454 CATCCATTCAGCCTAACACAACTGGATCACAGGTATATCGTAACACTTTTTTAATTTCAATTCCA
1 CATGCATTCAGCCTAACACAACTGGATCACAGGTATATCATAACAC-TTTTTAATTTCAATTCAA
* * * * * ***
40243519 AATTATTTAAATCTAATTTGGGGATCTGA--TTTTTGTTCTCAGTCTGGTACAAGTATGGGAACT
65 AAATATTTAAATCTAATTTGGGGTTCTGATTTTTTTGGTCTTAGTCCGGTACAAGTACAAGAACT
*
40243582 AGAAGCCAAAAAAG
130 AGAAGCAAAAAAAG
40243596 GACAGCATAT
Statistics
Matches: 257, Mismatches: 39, Indels: 11
0.84 0.13 0.04
Matches are distributed among these distances:
155 40 0.16
157 46 0.18
158 120 0.47
159 51 0.20
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (156 bp):
CATGCATTCAGCCTAACACAACTGGATCACAGGTATATCATAACACTTTTTAATTTCAATTCAAA
AATATTTAAATCTAATTTGGGGTTCTGATTTTTTTGGTCTTAGTCCGGTACAAGTACAAGAACTA
GAAGCAAAAAAAGAACAACAGAACAC
Found at i:40243809 original size:83 final size:82
Alignment explanation
Indices: 40243671--40243874 Score: 329
Period size: 83 Copynumber: 2.5 Consensus size: 82
40243661 TTGAGATGGT
* * *
40243671 TAACATATTTTGTTTGTTTTTTTAAATGATTTGTTGAAATGGTTGGTTAACATCTTACTTCTATA
1 TAACATATTTTTTTTGTTTTTTGAAATGATTTGTTGAAATGGTTGGTTAACATCTTACTGCTATA
40243736 GGATCATTTTGTTAGCA
66 GGATCATTTTGTTAGCA
40243753 TAACATATTTCTTTTTGTTTTTTGAAATGATTTGTTGAAATGGTTGGTTAACATCTTACTGCTAT
1 TAACATATTT-TTTTTGTTTTTTGAAATGATTTGTTGAAATGGTTGGTTAACATCTTACTGCTAT
* *
40243818 AGGATTATTTTGTTAGTA
65 AGGATCATTTTGTTAGCA
*
40243836 TAACAT-TTTTTGTTTGTTTTTTGAAATGTTTTGTTGAAA
1 TAACATATTTTT-TTTGTTTTTTGAAATGATTTGTTGAAA
40243875 GATGTATACA
Statistics
Matches: 114, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
81 2 0.02
82 39 0.34
83 73 0.64
ACGTcount: A:0.25, C:0.07, G:0.16, T:0.52
Consensus pattern (82 bp):
TAACATATTTTTTTTGTTTTTTGAAATGATTTGTTGAAATGGTTGGTTAACATCTTACTGCTATA
GGATCATTTTGTTAGCA
Found at i:40246229 original size:6 final size:6
Alignment explanation
Indices: 40246218--40246246 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
40246208 CATTATGCCC
40246218 ATACAT ATACAT ATACAT ATACAT ATACA
1 ATACAT ATACAT ATACAT ATACAT ATACA
40246247 CTTATAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (6 bp):
ATACAT
Found at i:40250536 original size:30 final size:30
Alignment explanation
Indices: 40250502--40250558 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
40250492 TCAATGCAAC
* *
40250502 TATAT-AAAAATAATATTATTAATATTTTGA
1 TATATGAAAAATAAAATT-TAAATATTTTGA
*
40250532 TATATGAAATATAAAATTTAAATATTT
1 TATATGAAAAATAAAATTTAAATATTT
40250559 CTCATGCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 13 0.57
31 10 0.43
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (30 bp):
TATATGAAAAATAAAATTTAAATATTTTGA
Found at i:40253882 original size:18 final size:17
Alignment explanation
Indices: 40253835--40253887 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
40253825 ATTTAATTTT
*
40253835 TTTTGTTTATTTTTATTG
1 TTTT-TTTATTTTAATTG
*
40253853 TTATTTTGATTTTAATTG
1 TT-TTTTTATTTTAATTG
40253871 TTTTTATTATTTTAATT
1 TTTTT-TTATTTTAATT
40253888 TTTATCATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 3 0.10
18 25 0.83
19 2 0.07
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.74
Consensus pattern (17 bp):
TTTTTTTATTTTAATTG
Found at i:40270805 original size:28 final size:28
Alignment explanation
Indices: 40270767--40270831 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
40270757 AAATTGGGTA
*
40270767 TTACAAATATGGTTGTTAGAATCTAACCG
1 TTAC-AATATGATTGTTAGAATCTAACCG
* *
40270796 TTACAATATGATTGTTGGAATCTGACCG
1 TTACAATATGATTGTTAGAATCTAACCG
*
40270824 TTGCAATA
1 TTACAATA
40270832 GGGCCATTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 28 0.88
29 4 0.12
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.35
Consensus pattern (28 bp):
TTACAATATGATTGTTAGAATCTAACCG
Found at i:40272230 original size:27 final size:27
Alignment explanation
Indices: 40272198--40272262 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
40272188 TAAGCTTTCA
*
40272198 TAATCAAAATGTCAAATGGCATTCAAT
1 TAATCAAAATCTCAAATGGCATTCAAT
* *
40272225 TAATCAAAGTCTCAAATGGCATTCGAT
1 TAATCAAAATCTCAAATGGCATTCAAT
40272252 TAATCAAAATC
1 TAATCAAAATC
40272263 AAAGTGAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (27 bp):
TAATCAAAATCTCAAATGGCATTCAAT
Found at i:40272298 original size:24 final size:24
Alignment explanation
Indices: 40272258--40272313 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
40272248 CGATTAATCA
*
40272258 AAATCAAAGTGAAATTTC-ATTATC
1 AAATCAAACTGAAATTTCAATT-TC
40272282 AAATCAAACT-AACATTTCAATTTC
1 AAATCAAACTGAA-ATTTCAATTTC
40272306 AGAATCAA
1 A-AATCAA
40272314 GATGGCATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 2 0.07
24 17 0.61
25 9 0.32
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.30
Consensus pattern (24 bp):
AAATCAAACTGAAATTTCAATTTC
Found at i:40275217 original size:29 final size:29
Alignment explanation
Indices: 40275175--40275233 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
40275165 GAAATTGATC
40275175 TTTATTCACATCTAATGATCGTACAATCA
1 TTTATTCACATCTAATGATCGTACAATCA
40275204 TTTATTCACATCTAATGATCGTACAATCA
1 TTTATTCACATCTAATGATCGTACAATCA
40275233 T
1 T
40275234 CGGAGTACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (29 bp):
TTTATTCACATCTAATGATCGTACAATCA
Found at i:40284205 original size:25 final size:24
Alignment explanation
Indices: 40284158--40284227 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 24
40284148 GAATGTAAAT
* *
40284158 AAGTGTACATTTGGGATATAAAACA
1 AAGTATACATTTGGGA-AAAAAACA
*
40284183 AAGTATACATTTGGGAAGAAAAATA
1 AAGTATACATTTGGGAA-AAAAACA
*
40284208 AAGTATACAATTTAGGAAAA
1 AAGTATAC-ATTTGGGAAAA
40284228 TTACAAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
24 1 0.03
25 30 0.77
26 8 0.21
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.26
Consensus pattern (24 bp):
AAGTATACATTTGGGAAAAAAACA
Found at i:40286579 original size:7 final size:7
Alignment explanation
Indices: 40286532--40286642 Score: 80
Period size: 7 Copynumber: 15.9 Consensus size: 7
40286522 GACGATCGAG
40286532 AATTGAA
1 AATTGAA
* *
40286539 AACTGGA
1 AATTGAA
*
40286546 AATTGGA
1 AATTGAA
*
40286553 AATTGGA
1 AATTGAA
*
40286560 AATTGAG
1 AATTGAA
40286567 AATTGAA
1 AATTGAA
*
40286574 AATTGAG
1 AATTGAA
* *
40286581 GATTGAG
1 AATTGAA
40286588 AATTGAA
1 AATTGAA
*
40286595 AATTGAG
1 AATTGAA
* *
40286602 GATTAAA
1 AATTGAA
40286609 AATT-AA
1 AATTGAA
* *
40286615 GGATTGAG
1 -AATTGAA
40286623 AATTGAA
1 AATTGAA
*
40286630 AATTTAA
1 AATTGAA
40286637 AATTGA
1 AATTGA
40286643 GTATTGAGTT
Statistics
Matches: 81, Mismatches: 21, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
6 2 0.02
7 78 0.96
8 1 0.01
ACGTcount: A:0.48, C:0.01, G:0.23, T:0.29
Consensus pattern (7 bp):
AATTGAA
Found at i:40286601 original size:21 final size:21
Alignment explanation
Indices: 40286561--40286650 Score: 101
Period size: 21 Copynumber: 4.3 Consensus size: 21
40286551 GAAATTGGAA
40286561 ATTGAGAATTGAAAATTGAGG
1 ATTGAGAATTGAAAATTGAGG
40286582 ATTGAGAATTGAAAATTGAGG
1 ATTGAGAATTGAAAATTGAGG
* * * *
40286603 ATTAAAAATT-AAGGATTGAGA
1 ATTGAGAATTGAA-AATTGAGG
* * *
40286624 ATTGAAAATTTAAAATTGAGT
1 ATTGAGAATTGAAAATTGAGG
40286645 ATTGAG
1 ATTGAG
40286651 TTAAAAAGAA
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
20 2 0.03
21 55 0.93
22 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (21 bp):
ATTGAGAATTGAAAATTGAGG
Found at i:40287097 original size:17 final size:17
Alignment explanation
Indices: 40287077--40287109 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40287067 AGCAAATGCC
40287077 TTTAA-AATAATAACAAA
1 TTTAACAATAA-AACAAA
40287094 TTTAACAATAAAACAA
1 TTTAACAATAAAACAA
40287110 GTGTTATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (17 bp):
TTTAACAATAAAACAAA
Found at i:40287430 original size:22 final size:22
Alignment explanation
Indices: 40287391--40287432 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
40287381 CAATAAAGTT
**
40287391 TTACCATTATTATTTTTTAATA
1 TTACCATTATTAAATTTTAATA
*
40287413 TTACTATTATTAAATTTTAA
1 TTACCATTATTAAATTTTAA
40287433 AAATATAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (22 bp):
TTACCATTATTAAATTTTAATA
Found at i:40287682 original size:3 final size:3
Alignment explanation
Indices: 40287674--40287729 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
40287664 TAGCAACTTG
40287674 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
40287722 AAT AAT AA
1 AAT AAT AA
40287730 ATCTTTCTTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:40288272 original size:6 final size:6
Alignment explanation
Indices: 40288257--40288285 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
40288247 GGAAGCAAAG
40288257 AGTG-T AGTGTT AGTGTT AGTGTT AGTGTT
1 AGTGTT AGTGTT AGTGTT AGTGTT AGTGTT
40288286 GACGAAGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.17, C:0.00, G:0.34, T:0.48
Consensus pattern (6 bp):
AGTGTT
Found at i:40293190 original size:16 final size:16
Alignment explanation
Indices: 40293169--40293210 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
40293159 TTATTAAATT
*
40293169 ATATATTTTAATTATA
1 ATATATTTTAATAATA
40293185 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
40293200 AT-TATGTTTAA
1 ATATAT-TTTAA
40293211 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:40293195 original size:15 final size:15
Alignment explanation
Indices: 40293160--40293201 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
40293150 TTAAGAATTT
*
40293160 TATTAAATTAT-ATA
1 TATTTAATTATAATA
40293174 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
40293188 TATTTAATAATAAT
1 TATTTAATTATAAT
40293202 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:40293445 original size:16 final size:16
Alignment explanation
Indices: 40293424--40293476 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
40293414 TTGATTTGCT
* *
40293424 ATTACAATTCTATTCC
1 ATTACACTTCTAATCC
*
40293440 ATTACACTTCTAATCT
1 ATTACACTTCTAATCC
*
40293456 ATTACACCTCTAATCC
1 ATTACACTTCTAATCC
40293472 ATTAC
1 ATTAC
40293477 GCCTCTATTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTACACTTCTAATCC
Found at i:40293481 original size:16 final size:16
Alignment explanation
Indices: 40293432--40293493 Score: 70
Period size: 16 Copynumber: 3.9 Consensus size: 16
40293422 CTATTACAAT
* *
40293432 TCTATTCCATTACACT
1 TCTAATCCATTACACC
*
40293448 TCTAATCTATTACACC
1 TCTAATCCATTACACC
*
40293464 TCTAATCCATTACGCC
1 TCTAATCCATTACACC
* *
40293480 TCTATTCCAATACA
1 TCTAATCCATTACA
40293494 GCGAACCGAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.29, C:0.32, G:0.02, T:0.37
Consensus pattern (16 bp):
TCTAATCCATTACACC
Found at i:40307559 original size:53 final size:53
Alignment explanation
Indices: 40307476--40307583 Score: 189
Period size: 53 Copynumber: 2.0 Consensus size: 53
40307466 ATACTGGTAG
*
40307476 TATTAAATATAAACCTATCTTAATATATTTGCATCTTCAAAATTGAGGAAGCT
1 TATTAAATATAAACCTATCTTAATACATTTGCATCTTCAAAATTGAGGAAGCT
* *
40307529 TATTAAATATAAACCTATGTTACTACATTTGCATCTTCAAAATTGAGGAAGCT
1 TATTAAATATAAACCTATCTTAATACATTTGCATCTTCAAAATTGAGGAAGCT
40307582 TA
1 TA
40307584 ACATGTTAAC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (53 bp):
TATTAAATATAAACCTATCTTAATACATTTGCATCTTCAAAATTGAGGAAGCT
Found at i:40313706 original size:27 final size:27
Alignment explanation
Indices: 40313668--40313721 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
40313658 AACAGAACAG
*
40313668 AACTCAATTCATGTTAAAAATAAATTT
1 AACTCAATTCATGTCAAAAATAAATTT
*
40313695 AACTCATTTCATGTCAAAAATAAATTT
1 AACTCAATTCATGTCAAAAATAAATTT
40313722 TCTTTAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (27 bp):
AACTCAATTCATGTCAAAAATAAATTT
Found at i:40313982 original size:117 final size:118
Alignment explanation
Indices: 40313775--40314009 Score: 348
Period size: 117 Copynumber: 2.0 Consensus size: 118
40313765 TCACTGTGCA
* * * * * *
40313775 CTGCTAGTTATTCTTGGACTACATGGGCTGTAAACAGAAATTTCTAGGTTCAAATCTAGTCATGT
1 CTGCTAATTATTCTTGGACTACATAGGCTGTAAAAAGAAATTTCAAGATTCAAATCTAGCCATGT
40313840 CTTGTGTATGGTATTGAATTTTTATATGCATCATTATTATCTCTGTATTCTTT
66 CTTGTGTATGGTATTGAATTTTTATATGCATCATTATTATCTCTGTATTCTTT
* * *
40313893 CTGCTAATTATTCTTGG-CTAGATAGGTTGTAAAAAGAAATTTCAAGATTCAAATCTGGCCATGA
1 CTGCTAATTATTCTTGGACTACATAGGCTGTAAAAAGAAATTTCAAGATTCAAATCTAGCCATG-
* *
40313957 T-TTGTGTATGGTATTGAATTTTTATATGCCTCTTTATTATCTCTGTATTCTTT
65 TCTTGTGTATGGTATTGAATTTTTATATGCATCATTATTATCTCTGTATTCTTT
40314010 TTAGTGGTTG
Statistics
Matches: 105, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
117 88 0.84
118 17 0.16
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.44
Consensus pattern (118 bp):
CTGCTAATTATTCTTGGACTACATAGGCTGTAAAAAGAAATTTCAAGATTCAAATCTAGCCATGT
CTTGTGTATGGTATTGAATTTTTATATGCATCATTATTATCTCTGTATTCTTT
Found at i:40331153 original size:42 final size:42
Alignment explanation
Indices: 40331086--40331194 Score: 182
Period size: 42 Copynumber: 2.6 Consensus size: 42
40331076 ACAGCCTAGC
*
40331086 ACACGGCTTGGCACACAGGCATGTGAGGCCATTTCGAAAGTT
1 ACACGGCTTGGCACACAGGCGTGTGAGGCCATTTCGAAAGTT
*
40331128 ACACGGCTTGGCACATAGGCGTGTGAGGCCATTTCGAAAGTT
1 ACACGGCTTGGCACACAGGCGTGTGAGGCCATTTCGAAAGTT
* *
40331170 ACACGGCCTAGCACACAGGCGTGTG
1 ACACGGCTTGGCACACAGGCGTGTG
40331195 GCTTGGCCGT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.25, C:0.25, G:0.30, T:0.20
Consensus pattern (42 bp):
ACACGGCTTGGCACACAGGCGTGTGAGGCCATTTCGAAAGTT
Found at i:40333998 original size:14 final size:14
Alignment explanation
Indices: 40333979--40334005 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40333969 CCATTGAAAA
40333979 ATGGGTTGTTACAT
1 ATGGGTTGTTACAT
40333993 ATGGGTTGTTACA
1 ATGGGTTGTTACA
40334006 AAGGAAGCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.07, G:0.30, T:0.41
Consensus pattern (14 bp):
ATGGGTTGTTACAT
Found at i:40336331 original size:24 final size:23
Alignment explanation
Indices: 40336297--40336343 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
40336287 AGTTGTACAG
40336297 AGAAAATTTTCTAAAGCATTATTTT
1 AGAAAATTTTCTAAAG-A-TATTTT
40336322 AGAAAA-TTTCTAAAGATATTTT
1 AGAAAATTTTCTAAAGATATTTT
40336344 TCTTATTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.27
23 1 0.05
24 9 0.41
25 6 0.27
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (23 bp):
AGAAAATTTTCTAAAGATATTTT
Found at i:40339264 original size:24 final size:23
Alignment explanation
Indices: 40339230--40339276 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
40339220 AGTTGTACAG
40339230 AGAAAATTTTCTAAAGCATTATTTT
1 AGAAAATTTTCTAAAG-A-TATTTT
40339255 AGAAAA-TTTCTAAAGATATTTT
1 AGAAAATTTTCTAAAGATATTTT
40339277 TCTTATTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.27
23 1 0.05
24 9 0.41
25 6 0.27
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (23 bp):
AGAAAATTTTCTAAAGATATTTT
Found at i:40348459 original size:62 final size:59
Alignment explanation
Indices: 40348392--40348505 Score: 165
Period size: 62 Copynumber: 1.9 Consensus size: 59
40348382 AGTGATTATC
* * * *
40348392 TTAATATTAAATTTAATTTAATGTTTATCTTGTAGATAAATATTTTATTAATTTAATAAAAT
1 TTAATATTAAATCTAATCTAATATTTATC-T-T-GATAAATATTATATTAATTTAATAAAAT
40348454 TTAATATTAAATCTAATCTAATATTTATCTTGATAAATATTATATTAATTTA
1 TTAATATTAAATCTAATCTAATATTTATCTTGATAAATATTATATTAATTTA
40348506 TTTTAAAGTG
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
59 20 0.42
60 1 0.02
61 1 0.02
62 26 0.54
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (59 bp):
TTAATATTAAATCTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATAAAAT
Found at i:40349311 original size:22 final size:22
Alignment explanation
Indices: 40349286--40349341 Score: 80
Period size: 20 Copynumber: 2.6 Consensus size: 22
40349276 ATCTGCAAAC
40349286 TTTCAATTTACTACAACATGTG
1 TTTCAATTTACTACAACATGTG
*
40349308 TTTCAA--TACTATAACATGTG
1 TTTCAATTTACTACAACATGTG
40349328 TTTCAATTGTACTA
1 TTTCAATT-TACTA
40349342 ATAGTTGTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 19 0.63
22 6 0.20
23 5 0.17
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (22 bp):
TTTCAATTTACTACAACATGTG
Found at i:40359545 original size:17 final size:16
Alignment explanation
Indices: 40359518--40359564 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
40359508 AAATTTGAGA
40359518 ATAAA-AAATAAAAAT
1 ATAAATAAATAAAAAT
40359533 CATAAATAAATAAGAAAT
1 -ATAAATAAATAA-AAAT
*
40359551 AGAAATAAA-AAAAA
1 ATAAATAAATAAAAA
40359565 AGAACAAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 3 0.11
16 7 0.25
17 14 0.50
18 4 0.14
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.17
Consensus pattern (16 bp):
ATAAATAAATAAAAAT
Found at i:40361251 original size:15 final size:18
Alignment explanation
Indices: 40361231--40361267 Score: 53
Period size: 15 Copynumber: 2.2 Consensus size: 18
40361221 AACATCGAGT
40361231 TCATTTC-ATTT-T-ATC
1 TCATTTCAATTTCTCATC
40361246 TCATTTCAATTTCTCATC
1 TCATTTCAATTTCTCATC
40361264 TCAT
1 TCAT
40361268 ATAAACCGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 4 0.21
17 1 0.05
18 7 0.37
ACGTcount: A:0.22, C:0.24, G:0.00, T:0.54
Consensus pattern (18 bp):
TCATTTCAATTTCTCATC
Found at i:40361729 original size:2 final size:2
Alignment explanation
Indices: 40361722--40361746 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40361712 AATCAAAGAC
40361722 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
40361747 ATTCAAATAC
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:40362748 original size:43 final size:43
Alignment explanation
Indices: 40362687--40362927 Score: 333
Period size: 43 Copynumber: 5.6 Consensus size: 43
40362677 TTCTGTGAAA
* *
40362687 AAACGCCGCTAAAGAACATGAGCTTTAGCGGCACTTTACCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
** * *
40362730 AAACGCCGCTAAAGAACATGGCCTTTAGCGACGCTTTACCAAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
* *
40362773 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGC-TTACCAAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
*
40362815 AAACGCCGCTAAAGAACATGATCTTTAACGGCGCTTTACCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
* * * *
40362858 GAACACCGCAAAAGAACATGATCTTTAGCGGCGGTTCT-CCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTT-TACCCAC
*
40362901 AAACGCCACTAAAGAACATGATCTTTA
1 AAACGCCGCTAAAGAACATGATCTTTA
40362928 TCGACACTTT
Statistics
Matches: 177, Mismatches: 19, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
42 40 0.23
43 136 0.77
44 1 0.01
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.19
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
Found at i:40362915 original size:128 final size:128
Alignment explanation
Indices: 40362687--40362927 Score: 349
Period size: 128 Copynumber: 1.9 Consensus size: 128
40362677 TTCTGTGAAA
* * * *
40362687 AAACGCCGCTAAAGAACATGAGCTTTAGCGGCACTTTACCCACAAACGCCGCTAAAGAACATGGC
1 AAACGCCGCTAAAGAACATGAGCTTTAACGGCACTTTACCCACAAACACCGCAAAAGAACATGAC
*
40362752 CTTTAGCGACGCTTTACCAACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTACCAAC
66 CTTTAGCGACGCTTTACCAACAAACGCCACTAAAGAACATGACCTTTAGCGGCGCTTACCAAC
* * * *
40362815 AAACGCCGCTAAAGAACATGATCTTTAACGGCGCTTTACCCACGAACACCGCAAAAGAACATGAT
1 AAACGCCGCTAAAGAACATGAGCTTTAACGGCACTTTACCCACAAACACCGCAAAAGAACATGAC
* * * *
40362880 CTTTAGCGGCGGTTCT-CCCACAAACGCCACTAAAGAACATGATCTTTA
66 CTTTAGCGACGCTT-TACCAACAAACGCCACTAAAGAACATGACCTTTA
40362928 TCGACACTTT
Statistics
Matches: 99, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
128 98 0.99
129 1 0.01
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.19
Consensus pattern (128 bp):
AAACGCCGCTAAAGAACATGAGCTTTAACGGCACTTTACCCACAAACACCGCAAAAGAACATGAC
CTTTAGCGACGCTTTACCAACAAACGCCACTAAAGAACATGACCTTTAGCGGCGCTTACCAAC
Found at i:40362945 original size:43 final size:42
Alignment explanation
Indices: 40362687--40362956 Score: 317
Period size: 43 Copynumber: 6.3 Consensus size: 42
40362677 TTCTGTGAAA
* *
40362687 AAACGCCGCTAAAGAACATGAGCTTTAGCGGCACTTTACCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTA-CCAC
** *
40362730 AAACGCCGCTAAAGAACATGGCCTTTAGCGACGCTTTACCAAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACC-AC
*
40362773 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGC-TTACCAAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACC-AC
*
40362815 AAACGCCGCTAAAGAACATGATCTTTAACGGCGCTTTACCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTA-CCAC
* * * * *
40362858 GAACACCGCAAAAGAACATGATCTTTAGCGGCGGTTCTCCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTT-TACCAC
* * * * *
40362901 AAACGCCACTAAAGAACATGATCTTTATCGACACTTTTATCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGC-TTTACCAC
*
40362944 AAACGCCACTAAA
1 AAACGCCGCTAAA
40362957 AGTACGATTC
Statistics
Matches: 198, Mismatches: 24, Indels: 10
0.85 0.10 0.04
Matches are distributed among these distances:
42 42 0.21
43 151 0.76
44 5 0.03
ACGTcount: A:0.34, C:0.30, G:0.17, T:0.20
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCAC
Found at i:40364646 original size:15 final size:14
Alignment explanation
Indices: 40364610--40364638 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
40364600 AGAAACTAAA
40364610 ATAAAACTAAAAAT
1 ATAAAACTAAAAAT
40364624 ATAAAACTAAAAAT
1 ATAAAACTAAAAAT
40364638 A
1 A
40364639 ATCAAACTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (14 bp):
ATAAAACTAAAAAT
Found at i:40365010 original size:40 final size:40
Alignment explanation
Indices: 40364947--40365031 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
40364937 TAGCTTGAAT
* * *
40364947 ATCAACACTTCAATATTTAATATGTAAGGAATTATCAAAA
1 ATCAACACTTCAATATTTAATATGCAAGAAATTAACAAAA
*
40364987 ATCAACATTTCAATAATTT-ATATGCAAGAAATTAACAAAA
1 ATCAACACTTCAAT-ATTTAATATGCAAGAAATTAACAAAA
40365027 ATCAA
1 ATCAA
40365032 TCTTACAACA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 36 0.90
41 4 0.10
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.31
Consensus pattern (40 bp):
ATCAACACTTCAATATTTAATATGCAAGAAATTAACAAAA
Found at i:40365047 original size:40 final size:40
Alignment explanation
Indices: 40364961--40365068 Score: 101
Period size: 40 Copynumber: 2.7 Consensus size: 40
40364951 ACACTTCAAT
* * * * *
40364961 ATTTAATATGTAAGGAATTATCAAAAATCAACATTTCAATA
1 ATTT-ATATGAAAGAAATTAACAAAAATCAACATTACAACA
*
40365002 ATTTATATGCAAGAAATTAACAAAAATCAATC-TTACAACA
1 ATTTATATGAAAGAAATTAACAAAAATCAA-CATTACAACA
* * * *
40365042 GTTTATGTGAAACAAATTAGCAAAAAT
1 ATTTATATGAAAGAAATTAACAAAAAT
40365069 AAACTATTCA
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
40 51 0.91
41 5 0.09
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.31
Consensus pattern (40 bp):
ATTTATATGAAAGAAATTAACAAAAATCAACATTACAACA
Found at i:40365180 original size:86 final size:85
Alignment explanation
Indices: 40365052--40365380 Score: 365
Period size: 86 Copynumber: 3.8 Consensus size: 85
40365042 GTTTATGTGA
* * * ** * *
40365052 AACAAATTAGCAAAAATAAACT-ATTCATAGTTCATATATTTACCGGCAA-CAGGGCTAAATCTT
1 AACAAATTAGCAAAAATCAA-TGGTTCA-AGTTCATGTATTTACCAACAACCA-GACTAAATTTT
* *
40365115 CAATTTCTATAACGATTTATATGC
63 CAATTT-TATAACAACTTATATGC
* * * * *
40365139 AAAAAATTAGCAAAAATCAGTGGTTCAAGTTCATGTATTTACCAAAAATCAGACTAATTTTTCAA
1 AACAAATTAGCAAAAATCAATGGTTCAAGTTCATGTATTTACCAACAACCAGACTAAATTTTCAA
40365204 TATTTATAACAACTTATATGC
66 T-TTTATAACAACTTATATGC
* *
40365225 AACAAATTAGCAAAAATAAATGGTTCAAGTTCATGCATTTACCAACAACCAGACTAAATTTTCAA
1 AACAAATTAGCAAAAATCAATGGTTCAAGTTCATGTATTTACCAACAACCAGACTAAATTTTCAA
*
40365290 CTTTTATAACAACTTATGTGC
66 -TTTTATAACAACTTATATGC
* ** * * * *
40365311 AACAAATTAGAAAAAATCAACAGTTCAAGTTCATGCATTCATCAACAACCAGACCAAATTTTCAA
1 AACAAATTAGCAAAAATCAATGGTTCAAGTTCATGTATTTACCAACAACCAGACTAAATTTTCAA
*
40365376 CTTTA
66 TTTTA
40365381 ATAAAGTAGA
Statistics
Matches: 209, Mismatches: 29, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
85 4 0.02
86 179 0.86
87 26 0.12
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.31
Consensus pattern (85 bp):
AACAAATTAGCAAAAATCAATGGTTCAAGTTCATGTATTTACCAACAACCAGACTAAATTTTCAA
TTTTATAACAACTTATATGC
Found at i:40365735 original size:85 final size:86
Alignment explanation
Indices: 40365583--40365749 Score: 201
Period size: 85 Copynumber: 2.0 Consensus size: 86
40365573 ATTTACCGAT
* * * * * *
40365583 TTATATACAACAAATTAACACAAATCAACGGTTCAAGTTCATGTATTTACCAAAATCCGAATAAA
1 TTATATACAACAAATTAACAAAAATCAACGGTTCAAGTGCAAGTATTCACCAAAAACCGAACAAA
*
40365648 -TTTACAATTTTTGTAATAAA
66 TTTTACAACTTTTGTAATAAA
* * * * * *
40365668 TTATATGCAACAAATTAGCAAAAATCAACTGTTCAGGTGCAAGTATTCACCAAAAACCGGACCAA
1 TTATATACAACAAATTAACAAAAATCAACGGTTCAAGTGCAAGTATTCACCAAAAACCGAACAAA
*
40365733 TTTTTCAACTTTTGTAA
66 TTTTACAACTTTTGTAA
40365750 AGTAAGAGTT
Statistics
Matches: 67, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
85 53 0.79
86 14 0.21
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (86 bp):
TTATATACAACAAATTAACAAAAATCAACGGTTCAAGTGCAAGTATTCACCAAAAACCGAACAAA
TTTTACAACTTTTGTAATAAA
Found at i:40366886 original size:5 final size:6
Alignment explanation
Indices: 40366856--40366883 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
40366846 AAAGATAATC
40366856 GAAAAT GAAAAT GAAAAT GAAAAT GAAA
1 GAAAAT GAAAAT GAAAAT GAAAAT GAAA
40366884 TGATATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.14
Consensus pattern (6 bp):
GAAAAT
Found at i:40368646 original size:72 final size:71
Alignment explanation
Indices: 40368528--40368673 Score: 265
Period size: 72 Copynumber: 2.0 Consensus size: 71
40368518 TTATTAAAAA
*
40368528 ATTATTTCATTTTGAACAAATGACACTGTTTTACTATGCTAAAAATTTTTTATTTTGTTTTTTAT
1 ATTATTTCATTTTGAACAAATGACACCGTTTTACTATGCTAAAAATTTTTTATTTTGTTTTTTAT
40368593 AAATTG
66 AAATTG
*
40368599 ATTATTTCATTTTGAACAAAATGACGCCGTTTTACTATGCTAAAAATTTTTTATTTTGTTTTTTA
1 ATTATTTCATTTTGAAC-AAATGACACCGTTTTACTATGCTAAAAATTTTTTATTTTGTTTTTTA
40368664 TAAATTG
65 TAAATTG
40368671 ATT
1 ATT
40368674 TATATTTGCG
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
71 17 0.24
72 55 0.76
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.51
Consensus pattern (71 bp):
ATTATTTCATTTTGAACAAATGACACCGTTTTACTATGCTAAAAATTTTTTATTTTGTTTTTTAT
AAATTG
Found at i:40369072 original size:15 final size:16
Alignment explanation
Indices: 40369036--40369073 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
40369026 TCTTAACCCG
*
40369036 ACTCCTAAATCCCTAA
1 ACTCTTAAATCCCTAA
40369052 AC-CTTAAATCCCT-A
1 ACTCTTAAATCCCTAA
40369066 ACTCTTAA
1 ACTCTTAA
40369074 CCCCTCACGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 3 0.15
15 15 0.75
16 2 0.10
ACGTcount: A:0.37, C:0.34, G:0.00, T:0.29
Consensus pattern (16 bp):
ACTCTTAAATCCCTAA
Found at i:40369391 original size:15 final size:16
Alignment explanation
Indices: 40369357--40369399 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
40369347 CCCTAACTTT
*
40369357 TAACCCCTAACACGTC
1 TAACCCCTAACACCTC
40369373 TAACCCCTAA-ACCTC
1 TAACCCCTAACACCTC
40369388 TAACCCTCTAAC
1 TAACCC-CTAAC
40369400 CCCTAAACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.33, C:0.44, G:0.02, T:0.21
Consensus pattern (16 bp):
TAACCCCTAACACCTC
Found at i:40369400 original size:15 final size:14
Alignment explanation
Indices: 40369347--40369405 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 14
40369337 ACCCCTGAAT
* *
40369347 CCCTAACTTTTAAC
1 CCCTAACCTCTAAC
40369361 CCCTAACACGTCTAAC
1 CCCTAAC-C-TCTAAC
40369377 CCCTAAACCTCTAAC
1 CCCT-AACCTCTAAC
*
40369392 CCTCTAACCCCTAA
1 CC-CTAACCTCTAA
40369406 ACCTTAAATC
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
14 7 0.18
15 16 0.42
16 12 0.32
17 3 0.08
ACGTcount: A:0.31, C:0.44, G:0.02, T:0.24
Consensus pattern (14 bp):
CCCTAACCTCTAAC
Done.