Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008942.1 Hibiscus syriacus cultivar Beakdansim tig00112261_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2383254
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 11
Found at i:399299 original size:38 final size:37
Alignment explanation
Indices: 399185--399302 Score: 137
Period size: 38 Copynumber: 3.1 Consensus size: 37
399175 TAAAATGTTT
* * * *
399185 ACTTCTCTTTACGAGTAATTCAAGAATAACAAAGATTT
1 ACTTCTCTTTACGAGAAAGTCAAG-ATAACAAAGGTTG
* * * *
399223 ATTTCTCTTCACGAGGAAGTCAAGGATAACAAATGTTG
1 ACTTCTCTTTACGAGAAAGTCAA-GATAACAAAGGTTG
399261 ACTTCTCTTTACGAGAAAGTCAATGATAACAAAGGTTG
1 ACTTCTCTTTACGAGAAAGTCAA-GATAACAAAGGTTG
399299 ACTT
1 ACTT
399303 ATCGTCAAGA
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
38 66 0.99
39 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (37 bp):
ACTTCTCTTTACGAGAAAGTCAAGATAACAAAGGTTG
Found at i:399315 original size:76 final size:76
Alignment explanation
Indices: 399177--399325 Score: 192
Period size: 76 Copynumber: 2.0 Consensus size: 76
399167 CAAGGAATTA
* * * * * * * *
399177 AAATGTTTACTTCTCTTTACGAGTAATTCAAGAATAACAAAGATTTATTTCTCTTCACGAGGAAG
1 AAATGTTGACTTCTCTTTACGAGAAAGTCAAGAATAACAAAGATTGACTTATCGTCAAGAGGAAG
399242 TCAAGGATAAC
66 TCAAGGATAAC
*
399253 AAATGTTGACTTCTCTTTACGAGAAAGTCAATG-ATAACAAAGGTTGACTTATCGTCAAGAGGAA
1 AAATGTTGACTTCTCTTTACGAGAAAGTCAA-GAATAACAAAGATTGACTTATCGTCAAGAGGAA
*
399317 GTCATGGAT
65 GTCAAGGAT
399326 TGACTCTGCT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
76 61 0.98
77 1 0.02
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (76 bp):
AAATGTTGACTTCTCTTTACGAGAAAGTCAAGAATAACAAAGATTGACTTATCGTCAAGAGGAAG
TCAAGGATAAC
Found at i:399319 original size:38 final size:38
Alignment explanation
Indices: 399235--399325 Score: 110
Period size: 38 Copynumber: 2.4 Consensus size: 38
399225 TTCTCTTCAC
* * * * *
399235 GAGGAAGTCAAGGATAACAAATGTTGACTTCTCTTTAC
1 GAGGAAGTCAAGGATAACAAAGGTTGACTTATCGTCAA
* *
399273 GAGAAAGTCAATGATAACAAAGGTTGACTTATCGTCAA
1 GAGGAAGTCAAGGATAACAAAGGTTGACTTATCGTCAA
*
399311 GAGGAAGTCATGGAT
1 GAGGAAGTCAAGGAT
399326 TGACTCTGCT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.25
Consensus pattern (38 bp):
GAGGAAGTCAAGGATAACAAAGGTTGACTTATCGTCAA
Found at i:399421 original size:167 final size:167
Alignment explanation
Indices: 399235--399550 Score: 472
Period size: 167 Copynumber: 1.9 Consensus size: 167
399225 TTCTCTTCAC
* * * *
399235 GAGGAAGTCAAGGATAACAAATGTTGACTTCTCTTTACGAGAAAGTCAATGATAACAAAGGTTGA
1 GAGGAAGTCAAGAATAACAAAGGTTGACTTCTCTTTACAAGAAAGTCAAGGATAACAAAGGTTGA
* *
399300 CTTATCGTCAAGAGGAAGTCATGGATTGACTCTGCTGGGGAGTCAGA-AATAACAAAGATTGACT
66 CTTATCGTCAAGAGGAAGTCAAGGATTGACTCTGCTAGGGAGTCA-ACAATAACAAAGATTGACT
399364 TCTCTTAACGAGAAAGTCAAAGGCTGAATTTTCTTTAT
130 TCTCTTAACGAGAAAGTCAAAGGCTGAATTTTCTTTAT
*
399402 GAGGAAGTCAAGAATAACAAAGGTTGACTTCTCTTTACAAGGAAGTCAAGGATAACAAAGGTTGA
1 GAGGAAGTCAAGAATAACAAAGGTTGACTTCTCTTTACAAGAAAGTCAAGGATAACAAAGGTTGA
* * * * * *
399467 CTTGTCTTCACGAGGAAGTCAAGGATTGACTCTGGTAGGGAGTCAACGATAACAAAGGTTGACTT
66 CTTATCGTCAAGAGGAAGTCAAGGATTGACTCTGCTAGGGAGTCAACAATAACAAAGATTGACTT
* * *
399532 CTCTTTATGAGGAAGTCAA
131 CTCTTAACGAGAAAGTCAA
399551 GGATAACAAA
Statistics
Matches: 132, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
166 1 0.01
167 131 0.99
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (167 bp):
GAGGAAGTCAAGAATAACAAAGGTTGACTTCTCTTTACAAGAAAGTCAAGGATAACAAAGGTTGA
CTTATCGTCAAGAGGAAGTCAAGGATTGACTCTGCTAGGGAGTCAACAATAACAAAGATTGACTT
CTCTTAACGAGAAAGTCAAAGGCTGAATTTTCTTTAT
Found at i:399436 original size:205 final size:205
Alignment explanation
Indices: 399107--399488 Score: 494
Period size: 205 Copynumber: 1.9 Consensus size: 205
399097 TCTCATGAGA
* *
399107 AGGAAGTCAAAGATTGACTCTACTGGGAAGACAAAAATAACAAAGATTCAATTCTCTTCACAAGG
1 AGGAAGTCAAAGATTGACTCTACTGGGAAGACAAAAATAACAAAGATTCAATTCTCTTAACAAGA
* * * * * * * * * *
399172 AATTAAAATGTTTACTTCTCTTTACGAGTAATTCAAGAATAACAAAGATTTATTTCTCTTCACGA
66 AAGTAAAAGGCTGAATTCTCTTTACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCACAA
* *
399237 GGAAGTCAAGGATAACAAATGTTGACTTCTCTTTACGAGAAAGTCAATGATAACAAAGGTTGACT
131 GGAAGTCAAGGATAACAAAGGTTGACTTCTCTTCACGAGAAAGTCAATGATAACAAAGGTTGACT
399302 TATCGTCAAG
196 TATCGTCAAG
** * * * * * * *
399312 AGGAAGTCATGGATTGACTCTGCTGGGGAGTCAGAAATAACAAAGATTGACTTCTCTTAACGAGA
1 AGGAAGTCAAAGATTGACTCTACTGGGAAGACAAAAATAACAAAGATTCAATTCTCTTAACAAGA
* * * * *
399377 AAGTCAAAGGCTGAATTTTCTTTATGAGGAAGTCAAGAATAACAAAGGTTGACTTCTCTTTACAA
66 AAGTAAAAGGCTGAATTCTCTTTACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCACAA
* *
399442 GGAAGTCAAGGATAACAAAGGTTGACTTGTCTTCACGAGGAAGTCAA
131 GGAAGTCAAGGATAACAAAGGTTGACTTCTCTTCACGAGAAAGTCAA
399489 GGATTGACTC
Statistics
Matches: 147, Mismatches: 30, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
205 147 1.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.27
Consensus pattern (205 bp):
AGGAAGTCAAAGATTGACTCTACTGGGAAGACAAAAATAACAAAGATTCAATTCTCTTAACAAGA
AAGTAAAAGGCTGAATTCTCTTTACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCACAA
GGAAGTCAAGGATAACAAAGGTTGACTTCTCTTCACGAGAAAGTCAATGATAACAAAGGTTGACT
TATCGTCAAG
Found at i:399437 original size:38 final size:38
Alignment explanation
Indices: 399381--399489 Score: 146
Period size: 38 Copynumber: 2.9 Consensus size: 38
399371 ACGAGAAAGT
* * * *
399381 CAAAGGCTGAATTTTCTTTATGAGGAAGTCAAGAATAA
1 CAAAGGTTGACTTCTCTTTACGAGGAAGTCAAGAATAA
* *
399419 CAAAGGTTGACTTCTCTTTACAAGGAAGTCAAGGATAA
1 CAAAGGTTGACTTCTCTTTACGAGGAAGTCAAGAATAA
* *
399457 CAAAGGTTGACTTGTCTTCACGAGGAAGTCAAG
1 CAAAGGTTGACTTCTCTTTACGAGGAAGTCAAG
399490 GATTGACTCT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 62 1.00
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.27
Consensus pattern (38 bp):
CAAAGGTTGACTTCTCTTTACGAGGAAGTCAAGAATAA
Found at i:399545 original size:100 final size:100
Alignment explanation
Indices: 399407--399621 Score: 288
Period size: 100 Copynumber: 2.1 Consensus size: 100
399397 TTTATGAGGA
* * *
399407 AGTCAAGAATAACAAAGGTTGACTTCTCTTTACAAGGAAGTCAAGGATAACAAAGGTTGACTTGT
1 AGTCAAGAATAACAAAGGTTGACTTCTCTTTACAAGGAAGTCAAGGATAACAAAGATAGACTTCT
* *
399472 CTTCACGAGGAAGTCAAGGATTGACTCTGGTAGGG
66 CTTAACGAGGAAGTCAAGAATTGACTCTGGTAGGG
** *
399507 AGTCAACG-ATAACAAAGGTTGACTTCTCTTTATGAGGAAGTCAAGGATAACAAATATAGACTTC
1 AGTCAA-GAATAACAAAGGTTGACTTCTCTTTACAAGGAAGTCAAGGATAACAAAGATAGACTTC
* * *
399571 TCTTAATGAGGAAGTCAATAATTGACTCCTCTGGGAGGG
65 TCTTAACGAGGAAGTCAAGAATTGA---CTCTGGTAGGG
399610 AGTCAAGAATAA
1 AGTCAAGAATAA
399622 AAAATATTAA
Statistics
Matches: 99, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
100 77 0.78
101 1 0.01
102 1 0.01
103 20 0.20
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.26
Consensus pattern (100 bp):
AGTCAAGAATAACAAAGGTTGACTTCTCTTTACAAGGAAGTCAAGGATAACAAAGATAGACTTCT
CTTAACGAGGAAGTCAAGAATTGACTCTGGTAGGG
Found at i:399558 original size:38 final size:38
Alignment explanation
Indices: 399507--399588 Score: 119
Period size: 38 Copynumber: 2.2 Consensus size: 38
399497 TCTGGTAGGG
* * *
399507 AGTCAACGATAACAAAGGTTGACTTCTCTTTATGAGGA
1 AGTCAACGATAACAAAGATAGACTTCTCTTAATGAGGA
* *
399545 AGTCAAGGATAACAAATATAGACTTCTCTTAATGAGGA
1 AGTCAACGATAACAAAGATAGACTTCTCTTAATGAGGA
399583 AGTCAA
1 AGTCAA
399589 TAATTGACTC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (38 bp):
AGTCAACGATAACAAAGATAGACTTCTCTTAATGAGGA
Found at i:418557 original size:32 final size:30
Alignment explanation
Indices: 418485--418608 Score: 126
Period size: 32 Copynumber: 4.0 Consensus size: 30
418475 CTGAAGGACA
* *
418485 TGTCCATATGTTCCGAAGAACATAGGTAA-C
1 TGTCCATATGTCCCAAAG-ACATAGGTAACC
*
418515 AGTCCATATGTCCCAAATGACATAGGTAATCC
1 TGTCCATATGTCCCAAA-GACATAGGTAA-CC
*
418547 TGTCCATATGTCCCAAAGGACATAGGAAAACC
1 TGTCCATATGTCCCAAA-GACATAGG-TAACC
* *
418579 -ATCCATATGTCTCGAAAGACATAGGTAACC
1 TGTCCATATGTC-CCAAAGACATAGGTAACC
418609 CTCGACTCTT
Statistics
Matches: 80, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
30 28 0.35
31 19 0.24
32 31 0.39
33 2 0.03
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.23
Consensus pattern (30 bp):
TGTCCATATGTCCCAAAGACATAGGTAACC
Found at i:418603 original size:63 final size:62
Alignment explanation
Indices: 418485--418606 Score: 158
Period size: 62 Copynumber: 2.0 Consensus size: 62
418475 CTGAAGGACA
* * *
418485 TGTCCATATGTTCCGAAGAACATAGGTAACAGTCCATATGTCCCAAATGACATAGGTAATCC
1 TGTCCATATGTCCCAAAGAACATAGGAAACAGTCCATATGTCCCAAATGACATAGGTAATCC
* *
418547 TGTCCATATGTCCCAAAGGACATAGGAAAACCA-TCCATATGTCTCGAAA-GACATAGGTAA
1 TGTCCATATGTCCCAAAGAACATAGG-AAA-CAGTCCATATGTC-CCAAATGACATAGGTAA
418607 CCCTCGACTC
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
62 23 0.44
63 23 0.44
64 6 0.12
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (62 bp):
TGTCCATATGTCCCAAAGAACATAGGAAACAGTCCATATGTCCCAAATGACATAGGTAATCC
Found at i:424619 original size:134 final size:134
Alignment explanation
Indices: 424447--424942 Score: 518
Period size: 134 Copynumber: 3.7 Consensus size: 134
424437 ATTTTTAATT
* * ** * * *
424447 CACTTCACTGCTATTCAGGGAAGATTGAATCAAATTTGATTTTCTTTAATGCTCTTCAGGAACAC
1 CACTTCACTGATCTTCAGGGAAGATTGAATTGAATTTGATTTTCTTCACTGCTCTTCAGGAAGAC
* *
424512 CAAATATGAAAGGAGAAGAATTTGTTCCACTACTCTTTAGGAGAGATTAGAATCAAGGAAATTTT
66 CAAATATGAAAGGAGAAGAATCTGTTCCACTACTCTTTAGGAGAGATTAGACTCAAGGAAATTTT
424577 GATC
131 GATC
* * * *
424581 CACTTCACTGATCTTCATGGAAGATTGAATTGAATTTGATTTGCTTCGCTGCTCTTCAGGAAGTC
1 CACTTCACTGATCTTCAGGGAAGATTGAATTGAATTTGATTTTCTTCACTGCTCTTCAGGAAGAC
* * ** * *
424646 CAAATCTGAAAGGAGAAGAATCTGGTCCGTTACTCTTTA-GAGGAGATCAGACTCGAGGAAATTT
66 CAAATATGAAAGGAGAAGAATCTGTTCCACTACTCTTTAGGA-GAGATTAGACTCAAGGAAATTT
*
424710 TGTTC
130 TGATC
* * ** * *
424715 CACTTCACT-ACTCTTCATGGAAGATTGAATTTAATTTGATTTGGTT-AGTTGCTCTTTAGGAAG
1 CACTTCACTGA-TCTTCAGGGAAGATTGAATTGAATTTGATTTTCTTCA-CTGCTCTTCAGGAAG
* * * * * * *
424778 ACCAATTCTGAAA-GATAAAGAATCTGCTCCACTATTCTTTAGGGGAGATTAGACTCAAGAAAAT
64 ACCAAATATGAAAGGA-GAAGAATCTGTTCCACTACTCTTTAGGAGAGATTAGACTCAAGGAAAT
*
424842 TTTGAAC
128 TTTGATC
* * * * *
424849 CACTTCACTGCTCTTCAGGGAAGATTCAATAGAATTTGATTTGT-TTCGCTGCTATTCAGGAAGA
1 CACTTCACTGATCTTCAGGGAAGATTGAATTGAATTTGATTT-TCTTCACTGCTCTTCAGGAAGA
* * *
424913 CAAAATATGAAAGAAG-AGAAATATGTTCCA
65 CCAAATATGAAAGGAGAAG-AATCTGTTCCA
424943 TTTTTTTGGG
Statistics
Matches: 297, Mismatches: 55, Indels: 20
0.80 0.15 0.05
Matches are distributed among these distances:
133 7 0.02
134 288 0.97
135 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (134 bp):
CACTTCACTGATCTTCAGGGAAGATTGAATTGAATTTGATTTTCTTCACTGCTCTTCAGGAAGAC
CAAATATGAAAGGAGAAGAATCTGTTCCACTACTCTTTAGGAGAGATTAGACTCAAGGAAATTTT
GATC
Found at i:426445 original size:22 final size:22
Alignment explanation
Indices: 426420--426464 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
426410 TTCCATTAAA
*
426420 TTCTTTTCCTTTT-TTCTTATTT
1 TTCTTTT-ATTTTCTTCTTATTT
426442 TTCTTTTATTTTCTTCTTATTT
1 TTCTTTTATTTTCTTCTTATTT
426464 T
1 T
426465 CTTCTTCTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.78
Consensus pattern (22 bp):
TTCTTTTATTTTCTTCTTATTT
Found at i:426450 original size:11 final size:12
Alignment explanation
Indices: 426429--426470 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 12
426419 ATTCTTTTCC
426429 TTTT-TTCTTAT
1 TTTTCTTCTTAT
426440 TTTTCTT-TTA-
1 TTTTCTTCTTAT
426450 TTTTCTTCTTA-
1 TTTTCTTCTTAT
426461 TTTTCTTCTT
1 TTTTCTTCTT
426471 CTTCAAGCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 7 0.24
11 20 0.69
12 2 0.07
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTCTTCTTAT
Found at i:463251 original size:47 final size:44
Alignment explanation
Indices: 463157--463274 Score: 146
Period size: 47 Copynumber: 2.6 Consensus size: 44
463147 GTAACTATGC
* * *
463157 AAATAAGTTTATGAGCTTACGGAATAATGGCAAGTATATTGGAA
1 AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGGAA
* * *
463201 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--T-AATGGCAAGTATATTGGAA
*
463248 AAATAAGCTTACGAGCTTATGGGATAA
1 AAATAAGCTTACGAGCTTATGGAATAA
463275 ATTGTAAGAG
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
44 23 0.36
45 1 0.02
46 1 0.02
47 39 0.61
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGGAA
Found at i:481557 original size:18 final size:18
Alignment explanation
Indices: 481531--481569 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
481521 TCATCTTCTA
* *
481531 ATTTTTTTAATTACTTTT
1 ATTTATTTAATCACTTTT
*
481549 ATTTATTTAATCGCTTTT
1 ATTTATTTAATCACTTTT
481567 ATT
1 ATT
481570 ATCTTTTACT
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:0.23, C:0.08, G:0.03, T:0.67
Consensus pattern (18 bp):
ATTTATTTAATCACTTTT
Found at i:486170 original size:21 final size:22
Alignment explanation
Indices: 486141--486181 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
486131 CATATCCTTA
*
486141 ATTTCTTCTTCCAGTTGTTTGC
1 ATTTCTTCTTCCAATTGTTTGC
*
486163 ATTT-TTCTTCTAATTGTTT
1 ATTTCTTCTTCCAATTGTTT
486182 ATTCGGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.12, C:0.17, G:0.10, T:0.61
Consensus pattern (22 bp):
ATTTCTTCTTCCAATTGTTTGC
Found at i:491952 original size:17 final size:16
Alignment explanation
Indices: 491921--491958 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
491911 CTTGTTGATT
491921 TTATTAATATTAATTA
1 TTATTAATATTAATTA
*
491937 TTATTATTATTTAATTA
1 TTATTAATA-TTAATTA
491954 TTATT
1 TTATT
491959 GTTTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATTAATATTAATTA
Found at i:496016 original size:131 final size:131
Alignment explanation
Indices: 495782--496029 Score: 392
Period size: 131 Copynumber: 1.9 Consensus size: 131
495772 ATAACTTTCA
* *
495782 AATTAATATTGAATTTTAGGATGAAATAGTAGTATATCTTCATTTCAATTGGAGTAATGAACGAC
1 AATTAATATTGAATTTTAGGATGAAATAGTAATATATCTTCATTTCAATTGGAGTAATAAACGAC
*
495847 TGCTTTAATGCATGAGAGGTCATTTATTCTTGATTGGAAATAATTAGATATTATCGTTTTCTCTC
66 TGCTTTAAGGCATGAGAGGTCATTTATTCTTGATTGGAAATAATTAGATATTATCGTTTTCTCTC
495912 G
131 G
* * **
495913 AATTAATATTGAATTTTATGATGAAATAGTAATATCA-CTTCATTTCGATTGGAGTAATAAATTA
1 AATTAATATTGAATTTTAGGATGAAATAGTAATAT-ATCTTCATTTCAATTGGAGTAATAAACGA
*
495977 TTGCTTTAAGGCATGAGAGGTCATTTATTCTAT-ATTGGAAATAATTAGATATT
65 CTGCTTTAAGGCATGAGAGGTCATTTATTCT-TGATTGGAAATAATTAGATATT
496030 GTTGTTCTCT
Statistics
Matches: 107, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
131 105 0.98
132 2 0.02
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (131 bp):
AATTAATATTGAATTTTAGGATGAAATAGTAATATATCTTCATTTCAATTGGAGTAATAAACGAC
TGCTTTAAGGCATGAGAGGTCATTTATTCTTGATTGGAAATAATTAGATATTATCGTTTTCTCTC
G
Found at i:510708 original size:24 final size:24
Alignment explanation
Indices: 510614--510717 Score: 127
Period size: 24 Copynumber: 4.3 Consensus size: 24
510604 TTCGATATCA
* *
510614 TAGATCTCCATCACCTACGCGTCG
1 TAGATCTCCATCACCTATGCATCG
* * *
510638 TTGATCTCCTTCACCTATGCGTCG
1 TAGATCTCCATCACCTATGCATCG
* *
510662 TAGATCTCCATCACCTATACATTG
1 TAGATCTCCATCACCTATGCATCG
* *
510686 TAGATCTCCATCACCTTTGCATTG
1 TAGATCTCCATCACCTATGCATCG
510710 TAGATCTC
1 TAGATCTC
510718 GTTCGATAGT
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 70 1.00
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.34
Consensus pattern (24 bp):
TAGATCTCCATCACCTATGCATCG
Found at i:518015 original size:3 final size:3
Alignment explanation
Indices: 518007--518102 Score: 156
Period size: 3 Copynumber: 32.0 Consensus size: 3
517997 TTAATATATT
* *
518007 TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
518055 TTA TAA TAA TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
518103 ATTCATATGG
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 87 1.00
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:518422 original size:36 final size:38
Alignment explanation
Indices: 518381--518484 Score: 140
Period size: 41 Copynumber: 2.7 Consensus size: 38
518371 AAGGTTAAAC
518381 AAGTTCTTCTCATTATGAACTTC-CTT-TTCTTCAGAT
1 AAGTTCTTCTCATTATGAACTTCTCTTCTTCTTCAGAT
*
518417 GAGTTCTTCTCATTATGAACTCTCTTCTTCCTTCTTCAGAT
1 AAGTTCTTCTCATTATGAACT-TC-TCTT-CTTCTTCAGAT
*
518458 AAATTCTTCTCATTATGAACTTTCTCT
1 AAGTTCTTCTCATTATGAAC-TTCTCT
518485 GGAAAAGTTG
Statistics
Matches: 59, Mismatches: 3, Indels: 8
0.84 0.04 0.11
Matches are distributed among these distances:
36 20 0.34
37 2 0.03
39 3 0.05
40 3 0.05
41 30 0.51
42 1 0.02
ACGTcount: A:0.21, C:0.24, G:0.08, T:0.47
Consensus pattern (38 bp):
AAGTTCTTCTCATTATGAACTTCTCTTCTTCTTCAGAT
Found at i:518607 original size:41 final size:40
Alignment explanation
Indices: 518519--518621 Score: 143
Period size: 41 Copynumber: 2.5 Consensus size: 40
518509 AAAGTCGAAC
* * *
518519 AAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTTAGAT
1 AAATTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGAT
* * *
518559 GAGTTCTTCTCATTATGAACTCTTTTATTCCTTCTTCAGAT
1 AAATTCTTCTCATTATGAACT-TCTTATTCCTTCTTCAGAT
518600 AAATTCTTCTCATTATGAACTT
1 AAATTCTTCTCATTATGAACTT
518622 TCTCTGGAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
40 20 0.37
41 34 0.63
ACGTcount: A:0.23, C:0.20, G:0.07, T:0.50
Consensus pattern (40 bp):
AAATTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGAT
Found at i:518630 original size:142 final size:149
Alignment explanation
Indices: 518360--518735 Score: 504
Period size: 142 Copynumber: 2.6 Consensus size: 149
518350 TAAGTGATGA
* ** *
518360 ATTTGAACAAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTC--CT-TTTCTTCAGATGAGTT
1 ATTTAAAC-AAAAGGTCGAACAAATTCTTCTCATTATGAACTTCTTCTCTTTCTTCAGATGAGTT
*
518422 CTTCTCATTATGAACTCTCTTCTTCCTTCTTCAGATAAATTCTTCTCATTATGAACTTTCTCTGG
65 CTTCTCATTATGAACTCTCTTATTCCTTCTTCAGATAAATTCTTCTCATTATGAACTTTCTCTGG
*
518487 AAAAG-T-T-GAT-GT-T-G
130 AAAAGTTATCCATAGTATGG
* *
518501 A-TTAAACTAAA-GTCGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTTAGATGAGTT
1 ATTTAAACAAAAGGTCGAACAAATTCTTCTCATTATGAACTTCTTC-TCTTTCTTCAGATGAGTT
*
518564 CTTCTCATTATGAACTCTTTTATTCCTTCTTCAGATAAATTCTTCTCATTATGAACTTTCTCTGG
65 CTTCTCATTATGAACTCTCTTATTCCTTCTTCAGATAAATTCTTCTCATTATGAACTTTCTCTGG
518629 AAAAGTTAATCCATCAAGTGATGG
130 AAAAGTT-ATCCAT--AGT-ATGG
* * *
518653 ATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTT
1 ATTTAAACAAAAGGTCGAACAAATTCTTCTCATTATGAACTTCTTC-TCTTTCTTCAGATGAGTT
518718 CTTCTCATTATGAACTCT
65 CTTCTCATTATGAACTCT
518736 ACCTGGAAAA
Statistics
Matches: 204, Mismatches: 15, Indels: 19
0.86 0.06 0.08
Matches are distributed among these distances:
138 27 0.13
139 3 0.01
140 6 0.03
141 2 0.01
142 83 0.41
143 1 0.00
145 1 0.00
146 2 0.01
149 2 0.01
151 1 0.00
152 2 0.01
153 8 0.04
154 66 0.32
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.41
Consensus pattern (149 bp):
ATTTAAACAAAAGGTCGAACAAATTCTTCTCATTATGAACTTCTTCTCTTTCTTCAGATGAGTTC
TTCTCATTATGAACTCTCTTATTCCTTCTTCAGATAAATTCTTCTCATTATGAACTTTCTCTGGA
AAAGTTATCCATAGTATGG
Found at i:518761 original size:113 final size:113
Alignment explanation
Indices: 518562--518998 Score: 734
Period size: 113 Copynumber: 3.9 Consensus size: 113
518552 TTTAGATGAG
* *
518562 TTCTTCTCATTATGAAC-TCTTTTATTCCTTCTTCAGATAAATTCTTCTCATTATGAACT-TTCT
1 TTCTTCTCATTATGAACTTC-TTCA-TCCTTCTTCAGATGAATTCTTCTCATTATGAACTCTTC-
* * *
518625 CTGGAAAAGTTAATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAAA
63 CTGGAAAAGATAATCCATCAAGTGATAGATTTAAACAAAAGGTTGAACAAA
* *
518676 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
1 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAATTCTTCTCATTATGAACTCTTCCTG
518741 GAAAAGATAATCCATCAAGTGATAGATTTAAACAAAAGGTTGAACAAA
66 GAAAAGATAATCCATCAAGTGATAGATTTAAACAAAAGGTTGAACAAA
* * *
518789 TTCTTCTCATTATGAACTTCTTCATCCTTCTTTAGATGAGTTCTTCTCATTATGAACTCTTTCTG
1 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAATTCTTCTCATTATGAACTCTTCCTG
518854 GAAAAGATAATCCATCAAGTGATAGATTTAAACAAAAGGTTGAACAAA
66 GAAAAGATAATCCATCAAGTGATAGATTTAAACAAAAGGTTGAACAAA
*
518902 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAATTCTTCTCATTATGAACTCTTTCTG
1 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAATTCTTCTCATTATGAACTCTTCCTG
518967 GAAAAGATAATCCATCAAGTGATAGATTTAAA
66 GAAAAGATAATCCATCAAGTGATAGATTTAAA
518999 TCTTTGCTAA
Statistics
Matches: 309, Mismatches: 12, Indels: 5
0.95 0.04 0.02
Matches are distributed among these distances:
113 285 0.92
114 22 0.07
115 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.38
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAATTCTTCTCATTATGAACTCTTCCTG
GAAAAGATAATCCATCAAGTGATAGATTTAAACAAAAGGTTGAACAAA
Found at i:519876 original size:114 final size:114
Alignment explanation
Indices: 519676--519889 Score: 401
Period size: 114 Copynumber: 1.9 Consensus size: 114
519666 CATGCAGTTC
* *
519676 ATCTTTTAATTCTAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGAACA
1 ATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGAACA
519741 CTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAATTT
66 CTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAATTT
519790 ATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGAACA
1 ATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGAACA
*
519855 CTTCCAGAAGATGTTATTGGGTCTTCTTATTTCTA
66 CTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTA
519890 AATTCAATAA
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 97 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (114 bp):
ATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGAACA
CTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAATTT
Found at i:519976 original size:83 final size:84
Alignment explanation
Indices: 519824--520046 Score: 308
Period size: 83 Copynumber: 2.7 Consensus size: 84
519814 TTGGGGTTCA
* * ** *
519824 TACCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATTG-GGTC-TTCTTATTT
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATATTT
*
519887 CTAAATTCAATAACTAATTT
65 CTAAATTCAATAACTAATTC
*
519907 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATATTTC
* **
519972 -AAATTCAATAATTGGTTC
66 TAAATTCAATAACTAATTC
* *
519990 TGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGTACATT
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
520047 GCATTTGTTC
Statistics
Matches: 126, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
82 2 0.02
83 116 0.92
84 8 0.06
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.28
Consensus pattern (84 bp):
TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATATTTC
TAAATTCAATAACTAATTC
Found at i:521206 original size:9 final size:9
Alignment explanation
Indices: 521192--521274 Score: 84
Period size: 9 Copynumber: 9.3 Consensus size: 9
521182 TGACCCCTCA
521192 TTTTTTCTT
1 TTTTTTCTT
521201 TTTTTTC--
1 TTTTTTCTT
*
521208 TTTTTTCTC
1 TTTTTTCTT
521217 TTTTTTCTT
1 TTTTTTCTT
521226 TTTCTTT-TT
1 TTT-TTTCTT
521235 TTCTTTTCTT
1 TT-TTTTCTT
521245 TCTTTTTCTT
1 T-TTTTTCTT
* *
521255 TTCTCTC-T
1 TTTTTTCTT
521263 TTTTTTCTT
1 TTTTTTCTT
521272 TTT
1 TTT
521275 CTTCAAGCAT
Statistics
Matches: 62, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
7 7 0.11
8 6 0.10
9 33 0.53
10 15 0.24
11 1 0.02
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:521220 original size:23 final size:23
Alignment explanation
Indices: 521193--521277 Score: 120
Period size: 23 Copynumber: 3.7 Consensus size: 23
521183 GACCCCTCAT
*
521193 TTTTTCTTTTTTTTCTTTTTTCTC
1 TTTTT-TTCTTTTTCTTTTTTCTC
521217 -TTTTTTCTTTTTCTTTTTT-TC
1 TTTTTTTCTTTTTCTTTTTTCTC
*
521238 TTTTCTTTCTTTTTCTTTTCTCTC
1 TTTT-TTTCTTTTTCTTTTTTCTC
521262 TTTTTTTCTTTTTCTT
1 TTTTTTTCTTTTTCTT
521278 CAAGCATAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
21 2 0.04
22 17 0.30
23 31 0.55
24 6 0.11
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (23 bp):
TTTTTTTCTTTTTCTTTTTTCTC
Found at i:534089 original size:3 final size:3
Alignment explanation
Indices: 534081--534194 Score: 192
Period size: 3 Copynumber: 38.0 Consensus size: 3
534071 ATTTATATAT
* *
534081 TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
534129 TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
534177 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
534195 ATCCATATGG
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 103 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:536583 original size:40 final size:42
Alignment explanation
Indices: 536512--536643 Score: 139
Period size: 40 Copynumber: 3.1 Consensus size: 42
536502 CTTAACATTA
536512 AAAATATATT-TTTTTATCTTAATTTTAAAATATTATAAGAAT
1 AAAAT-TATTATTTTTATCTTAATTTTAAAATATTATAAGAAT
* *
536554 AAAA-TA-TA-TTTTATCTTAAATTTTAAAATATTTTAA-TAT
1 AAAATTATTATTTTTATCTT-AATTTTAAAATATTATAAGAAT
*
536593 AGAAATTTATTTTTATTTTTATCTTAATTTTAAAATATTATAAGATT
1 A-AAA-TTA---TTATTTTTATCTTAATTTTAAAATATTATAAGAAT
536640 AAAA
1 AAAA
536644 AATAAATATT
Statistics
Matches: 74, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
39 13 0.18
40 22 0.30
42 6 0.08
46 22 0.30
47 11 0.15
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (42 bp):
AAAATTATTATTTTTATCTTAATTTTAAAATATTATAAGAAT
Found at i:536713 original size:40 final size:40
Alignment explanation
Indices: 536668--536810 Score: 128
Period size: 40 Copynumber: 3.5 Consensus size: 40
536658 TTAAAGTAAG
536668 AATAAATTATATTTTTAACTTAAATTAAAATTAAGATAAA
1 AATAAATTATATTTTTAACTTAAATTAAAATTAAGATAAA
* *
536708 AATAAA-TATATTTTAAAATTAAAATATTTTAAAATTTAAGATAAA
1 AATAAATTATATTTTTAACTT--AA-A--TTAAAA-TTAAGATAAA
* * * * **
536753 AATATACTT-TATTCTTATCATATTTTAAAATTAAGATAAA
1 AATA-AATTATATTTTTAACTTAAATTAAAATTAAGATAAA
*
536793 AATAAAATATATTTTTAA
1 AATAAATTATATTTTTAA
536811 TGTTAAGATG
Statistics
Matches: 80, Mismatches: 14, Indels: 18
0.71 0.12 0.16
Matches are distributed among these distances:
39 14 0.17
40 27 0.34
41 8 0.10
42 1 0.01
44 7 0.09
45 14 0.17
46 8 0.10
47 1 0.01
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (40 bp):
AATAAATTATATTTTTAACTTAAATTAAAATTAAGATAAA
Found at i:536746 original size:17 final size:17
Alignment explanation
Indices: 536704--536743 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
536694 AAAATTAAGA
*
536704 TAAAAATAAATATATTT
1 TAAAATTAAATATATTT
536721 TAAAATTAAA-ATATTT
1 TAAAATTAAATATATTT
536737 TAAAATT
1 TAAAATT
536744 TAAGATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAAATTAAATATATTT
Found at i:536755 original size:45 final size:44
Alignment explanation
Indices: 536692--536807 Score: 132
Period size: 41 Copynumber: 2.7 Consensus size: 44
536682 TTAACTTAAA
536692 TTAAAATTAAGATAAAAATAAATATATTTTAAAATTAAAATATT
1 TTAAAATTAAGATAAAAATAAATATATTTTAAAATTAAAATATT
* *** **
536736 TTAAAATTTAAGAT---AA-AAATATACTTTATTCTTATCATATT
1 TTAAAA-TTAAGATAAAAATAAATATATTTTAAAATTAAAATATT
536777 TTAAAATTAAGATAAAAATAAAATATATTTT
1 TTAAAATTAAGATAAAAAT-AAATATATTTT
536808 TAATGTTAAG
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
40 7 0.12
41 25 0.42
42 2 0.03
43 2 0.03
44 6 0.10
45 17 0.29
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (44 bp):
TTAAAATTAAGATAAAAATAAATATATTTTAAAATTAAAATATT
Found at i:537215 original size:61 final size:61
Alignment explanation
Indices: 537116--537240 Score: 205
Period size: 61 Copynumber: 2.0 Consensus size: 61
537106 CAGGTGACGA
* **
537116 TATGTGTCATGATGTTTGGTAATTAGTGCCATGTGGCATGATCTGATTTGAAGATTAAGTT
1 TATGTGTCATGATATTTGGTAATTAGTGCCATAAGGCATGATCTGATTTGAAGATTAAGTT
* *
537177 TATGTGTCATGATATTTGGTAATTAGTGCCATAAGGCATGATCTGATTTGATGATTGAGTT
1 TATGTGTCATGATATTTGGTAATTAGTGCCATAAGGCATGATCTGATTTGAAGATTAAGTT
537238 TAT
1 TAT
537241 TTGGATTTAT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.42
Consensus pattern (61 bp):
TATGTGTCATGATATTTGGTAATTAGTGCCATAAGGCATGATCTGATTTGAAGATTAAGTT
Found at i:538607 original size:14 final size:14
Alignment explanation
Indices: 538588--538627 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
538578 AATGGGAAGT
538588 AATCCCTGCA-AATA
1 AATCCCTGCATAA-A
538602 AATCCCTGCATAAA
1 AATCCCTGCATAAA
*
538616 AATCTCTGCATA
1 AATCCCTGCATA
538628 TAGATTTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 22 0.92
15 2 0.08
ACGTcount: A:0.40, C:0.28, G:0.07, T:0.25
Consensus pattern (14 bp):
AATCCCTGCATAAA
Found at i:540517 original size:40 final size:42
Alignment explanation
Indices: 540446--540577 Score: 139
Period size: 40 Copynumber: 3.1 Consensus size: 42
540436 CTTAACATTA
540446 AAAATATATT-TTTTTATCTTAATTTTAAAATATTATAAGAAT
1 AAAAT-TATTATTTTTATCTTAATTTTAAAATATTATAAGAAT
* *
540488 AAAA-TA-TA-TTTTATCTTAAATTTTAAAATATTTTAA-TAT
1 AAAATTATTATTTTTATCTT-AATTTTAAAATATTATAAGAAT
*
540527 AGAAATTTATTTTTATTTTTATCTTAATTTTAAAATATTATAAGATT
1 A-AAA-TTA---TTATTTTTATCTTAATTTTAAAATATTATAAGAAT
540574 AAAA
1 AAAA
540578 AATAAATATT
Statistics
Matches: 74, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
39 13 0.18
40 22 0.30
42 6 0.08
46 22 0.30
47 11 0.15
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (42 bp):
AAAATTATTATTTTTATCTTAATTTTAAAATATTATAAGAAT
Found at i:540665 original size:16 final size:16
Alignment explanation
Indices: 540644--540675 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
540634 AGATAAAAAT
540644 AATATTTTAAAATTAA
1 AATATTTTAAAATTAA
540660 AATATTTTAAAATTAA
1 AATATTTTAAAATTAA
540676 GATAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATATTTTAAAATTAA
Found at i:541141 original size:61 final size:61
Alignment explanation
Indices: 541042--541166 Score: 205
Period size: 61 Copynumber: 2.0 Consensus size: 61
541032 CAGGTGACGA
* **
541042 TATGTGTCATGATGTTTGGTAATTAGTGCCATGTGGCATGATCTGATTTGAAGATTAAGTT
1 TATGTGTCATGATATTTGGTAATTAGTGCCATAAGGCATGATCTGATTTGAAGATTAAGTT
* *
541103 TATGTGTCATGATATTTGGTAATTAGTGCCATAAGGCATGATCTGATTTGATGATTGAGTT
1 TATGTGTCATGATATTTGGTAATTAGTGCCATAAGGCATGATCTGATTTGAAGATTAAGTT
541164 TAT
1 TAT
541167 TTGGATTTAT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.42
Consensus pattern (61 bp):
TATGTGTCATGATATTTGGTAATTAGTGCCATAAGGCATGATCTGATTTGAAGATTAAGTT
Found at i:542438 original size:4 final size:4
Alignment explanation
Indices: 542429--542460 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
542419 CAATGCATAT
*
542429 ATAA ATAA ATAA ATAA ATAA ATAA ATAC ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
542461 TTGAACAGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:542530 original size:14 final size:14
Alignment explanation
Indices: 542511--542550 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
542501 AATGGGAAGT
542511 AATCCCTGCA-AATA
1 AATCCCTGCATAA-A
542525 AATCCCTGCATAAA
1 AATCCCTGCATAAA
*
542539 AATCTCTGCATA
1 AATCCCTGCATA
542551 TAGATAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 22 0.92
15 2 0.08
ACGTcount: A:0.40, C:0.28, G:0.07, T:0.25
Consensus pattern (14 bp):
AATCCCTGCATAAA
Found at i:553036 original size:34 final size:36
Alignment explanation
Indices: 552992--553093 Score: 154
Period size: 34 Copynumber: 2.9 Consensus size: 36
552982 ATTCGTCCTA
552992 CTAGGATTCAAACTCCTAAAAATATGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATATGATAGAATTTT
* *
553027 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATATGATAGAATTTT
*
553062 GCTAGGATTCAAATTCCTAAAAATATGATAGA
1 -CTAGGATTCAAACTCCTAAAAATATGATAGA
553094 GTTCTACTAT
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
34 29 0.49
35 3 0.05
37 27 0.46
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATATGATAGAATTTT
Found at i:553450 original size:24 final size:23
Alignment explanation
Indices: 553405--553457 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
553395 TTTCATGTAA
*
553405 TATTTTTTACATTTTATGTATTT
1 TATTTTTTACATTTTATATATTT
*
553428 TCTTTTTTAC-TTTAGTATATATTT
1 TATTTTTTACATTT--TATATATTT
553452 TATTTT
1 TATTTT
553458 ATTTTTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 3 0.12
23 9 0.36
24 13 0.52
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.70
Consensus pattern (23 bp):
TATTTTTTACATTTTATATATTT
Found at i:553555 original size:29 final size:29
Alignment explanation
Indices: 553522--553579 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
553512 TATATATATA
* *
553522 TATATATATTTTACTTTTT-TTTTTTTATT
1 TATATATATATTA-TTTTTACTTTTTTATT
553551 TATATATATATTATTTTTACTTTTTTATT
1 TATATATATATTATTTTTACTTTTTTATT
553580 ATTATTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.72
Consensus pattern (29 bp):
TATATATATATTATTTTTACTTTTTTATT
Found at i:553569 original size:35 final size:37
Alignment explanation
Indices: 553499--553588 Score: 121
Period size: 35 Copynumber: 2.4 Consensus size: 37
553489 TTATTATCAG
*
553499 TTTTATTAATTTATATATATATATATATATATTTTACTT
1 TTTTATT--TTTATTTATATATATATATATATTTTACTT
*
553538 TTTTTTTTTTATTTATATATATAT-TAT-TTTTACTT
1 TTTTATTTTTATTTATATATATATATATATTTTACTT
*
553573 TTTTATTATTATTTAT
1 TTTTATTTTTATTTAT
553589 TTATTTGTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
35 22 0.47
36 3 0.06
37 16 0.34
39 6 0.13
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (37 bp):
TTTTATTTTTATTTATATATATATATATATTTTACTT
Found at i:553626 original size:9 final size:9
Alignment explanation
Indices: 553612--553643 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
553602 TTCTATATTT
553612 TTTTTCTTC
1 TTTTTCTTC
553621 TTTTTCTTC
1 TTTTTCTTC
*
553630 TTTTTCTTA
1 TTTTTCTTC
553639 TTTTT
1 TTTTT
553644 ATATTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:553654 original size:21 final size:20
Alignment explanation
Indices: 553572--553668 Score: 67
Period size: 21 Copynumber: 4.8 Consensus size: 20
553562 TATTTTTACT
* *
553572 TTTTTATTATTATTTATTTA
1 TTTTTCTTATTTTTTATTTA
*
553592 TTTGTT-TTATTTCTATATTT-
1 TTT-TTCTTATTT-TTTATTTA
* * *
553612 TTTTTCTT-CTTTTT-CTTC
1 TTTTTCTTATTTTTTATTTA
553630 TTTTTCTTATTTTTATATTTA
1 TTTTTCTTATTTTT-TATTTA
*
553651 TTTTACTTATTATTTTAT
1 TTTTTCTTATT-TTTTAT
553669 CTTTGTTTTC
Statistics
Matches: 60, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
17 2 0.03
18 10 0.17
19 8 0.13
20 14 0.23
21 23 0.38
22 3 0.05
ACGTcount: A:0.16, C:0.07, G:0.01, T:0.75
Consensus pattern (20 bp):
TTTTTCTTATTTTTTATTTA
Found at i:553683 original size:23 final size:23
Alignment explanation
Indices: 553640--553716 Score: 65
Period size: 23 Copynumber: 3.4 Consensus size: 23
553630 TTTTTCTTAT
*
553640 TTTTATATTTATTTTAC-TTATTA
1 TTTTATATTTGTTTT-CTTTATTA
*
553663 TTTTATCTTTGTTTTCTTTATCT-
1 TTTTATATTTGTTTTCTTTAT-TA
*
553686 TCTTT-TATTTGTTTTCTCT-TTA
1 T-TTTATATTTGTTTTCTTTATTA
553708 TTTTA-ATTT
1 TTTTATATTT
553717 AATTAATTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
21 8 0.18
22 3 0.07
23 30 0.67
24 4 0.09
ACGTcount: A:0.16, C:0.09, G:0.03, T:0.73
Consensus pattern (23 bp):
TTTTATATTTGTTTTCTTTATTA
Found at i:553753 original size:15 final size:15
Alignment explanation
Indices: 553735--553764 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
553725 TATTTATTTC
553735 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
553750 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
553765 ACATGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:556733 original size:15 final size:15
Alignment explanation
Indices: 556708--556798 Score: 57
Period size: 15 Copynumber: 6.1 Consensus size: 15
556698 AGATCTAATC
556708 AAGAACAAAAAG-AA
1 AAGAACAAAAAGCAA
556722 AAGAAGCAAAAAGCAA
1 AAGAA-CAAAAAGCAA
556738 AA-AA-AAAAA-CACA
1 AAGAACAAAAAGCA-A
* *
556751 AAGAA-AAAGAGAAA
1 AAGAACAAAAAGCAA
* *
556765 CAAGAACAAAAGGAAAA
1 -AAGAACAAAAAG-CAA
* *
556782 AAGAGCAAAAATCAA
1 AAGAACAAAAAGCAA
556797 AA
1 AA
556799 AGAAAAAGGG
Statistics
Matches: 61, Mismatches: 8, Indels: 15
0.73 0.10 0.18
Matches are distributed among these distances:
12 2 0.03
13 8 0.13
14 12 0.20
15 19 0.31
16 17 0.28
17 3 0.05
ACGTcount: A:0.75, C:0.10, G:0.14, T:0.01
Consensus pattern (15 bp):
AAGAACAAAAAGCAA
Found at i:557467 original size:21 final size:22
Alignment explanation
Indices: 557421--557470 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
557411 CCCCATCAAT
557421 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
557443 CCTTTGAGCATCAAATGCC-AA
1 CCTTTGAGCATCAAATACCAAA
557464 CCTTTGA
1 CCTTTGA
557471 CCAACACAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:557481 original size:22 final size:21
Alignment explanation
Indices: 557421--557481 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
557411 CCCCATCAAT
* * *
557421 CCTTTGAGCATCAAATACCAAA
1 CCTTTGACCAACAAATGCC-AA
* *
557443 CCTTTGAGCATCAAATGCCAA
1 CCTTTGACCAACAAATGCCAA
557464 CCTTTGACCAACACAATG
1 CCTTTGACCAACA-AATG
557482 ACCTGAGACT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 13 0.37
22 22 0.63
ACGTcount: A:0.36, C:0.30, G:0.11, T:0.23
Consensus pattern (21 bp):
CCTTTGACCAACAAATGCCAA
Found at i:558378 original size:36 final size:36
Alignment explanation
Indices: 558331--558434 Score: 156
Period size: 36 Copynumber: 2.9 Consensus size: 36
558321 GTGCTCACAA
558331 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
*
558367 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
* * *
558404 TTTTCTCCCTTGAGACAG-TTCTCTTGAAACA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
558435 TAAACATTGA
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 1 0.02
36 42 0.67
37 20 0.32
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
Found at i:558516 original size:37 final size:35
Alignment explanation
Indices: 558329--558632 Score: 146
Period size: 36 Copynumber: 9.0 Consensus size: 35
558319 TCGTGCTCAC
*
558329 AATTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
1 AATTGTCTCTCTTGAGACAATTTCCCTTGAAACAA
* *
558364 ACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
1 A-ATTGTCTCTCTTGAGACAATTTCCCTTGAAACAA
* * * *
558400 AATTTTTTCTCCCTTGAGAC-AGTTCTCTTGAAACATA
1 AA--TTGTCTCTCTTGAGACAATTTCCCTTGAAACA-A
* * *
558437 AA------C-ATTGA-AAACATTTCCCTTGAAA-TA
1 AATTGTCTCTCTTGAGACA-ATTTCCCTTGAAACAA
* *
558464 AATTGTCTCTCTTGAGATAGTTTCCCTTGAAACAA
1 AATTGTCTCTCTTGAGACAATTTCCCTTGAAACAA
*
558499 AATTTTGTCTC-CATTGAGACAATTTCTC-TGAAACAA
1 AA--TTGTCTCTC-TTGAGACAATTTCCCTTGAAACAA
* * **
558535 AA------C-ATTGA-AAACATTTCCCTTGAAATGA
1 AATTGTCTCTCTTGAGACA-ATTTCCCTTGAAACAA
* * *
558563 ATTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAA
1 AATTGTCTCTCTTGAGACAATTTCCCTTGAAACAA
* * **
558598 ATTTTGTCTC-CTTTGAGACAGTTTCTATTGAAACA
1 A-ATTGTCTCTC-TTGAGACAATTTCCCTTGAAACA
558633 TAAACTTTGA
Statistics
Matches: 206, Mismatches: 33, Indels: 59
0.69 0.11 0.20
Matches are distributed among these distances:
26 2 0.01
27 14 0.07
28 12 0.06
29 12 0.06
33 1 0.00
34 17 0.08
35 25 0.12
36 87 0.42
37 36 0.17
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (35 bp):
AATTGTCTCTCTTGAGACAATTTCCCTTGAAACAA
Found at i:558606 original size:98 final size:99
Alignment explanation
Indices: 558349--558660 Score: 459
Period size: 99 Copynumber: 3.1 Consensus size: 99
558339 CTTGAGACAG
* * * *
558349 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAA-TAA-TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCAT
*
558414 TGAGAC-AGTTCTCTTGAAACATAAACATTGAAAACA
64 TGAGACAATTTCTC-TGAAACATAAACATTGAAAACA
*
558450 TTTCCCTTGAAATAAATTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCATTG
1 TTTCCCTTGAAATAATTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCATTG
558515 AGACAATTTCTCTGAAACA-AAACATTGAAAACA
66 AGACAATTTCTCTGAAACATAAACATTGAAAACA
*
558548 TTTCCCTTGAAATGAATTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC-AAATTTTGTCTCCTTT
1 TTTCCCTTGAAAT-AATTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCATT
* * *
558612 GAGACAGTTTCTATTGAAACATAAACTTTGAAAACA
65 GAGACAATTTCT-CTGAAACATAAACATTGAAAACA
558648 GTTTCCCTTGAAA
1 -TTTCCCTTGAAA
558661 CAAAATCTTT
Statistics
Matches: 195, Mismatches: 11, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
98 53 0.27
99 97 0.50
100 21 0.11
101 24 0.12
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (99 bp):
TTTCCCTTGAAATAATTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCATTG
AGACAATTTCTCTGAAACATAAACATTGAAAACA
Found at i:558614 original size:36 final size:35
Alignment explanation
Indices: 558548--558801 Score: 126
Period size: 36 Copynumber: 7.4 Consensus size: 35
558538 ATTGAAAACA
** *
558548 TTTCCCTTGAAATGAATTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTGTCTCTCTTGAGACAG
558583 TTTCCCTTGAAACAAATTTTGTCTC-CTTTGAGACAG
1 TTTCCCTTGAAACAAA-TTTGTCTCTC-TTGAGACAG
** * *
558619 TTTCTATTGAAACATAA------ACT-TTGAAAACAG
1 TTTCCCTTGAAACA-AATTTGTCTCTCTTG-AGACAG
* *
558649 TTTCCCTTGAAACAAA-----ATCT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTGTCTCTCTTGAGACA-G
* *
558678 TTTTACATT-AAACAAATTTCGTCTCTCTTGAGACAG
1 -TTTCCCTTGAAACAAATTT-GTCTCTCTTGAGACAG
* * *
558714 TTTCTCTTGAAACAAATTTTGTCTATCTTAAGACATG
1 TTTCCCTTGAAACAAA-TTTGTCTCTCTTGAGACA-G
** * *
558751 TTTTTCTTAAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAAC-AAA-TTTGTCTCTCTTGAGACAG
*
558788 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
558802 TCAATCCTTG
Statistics
Matches: 172, Mismatches: 27, Indels: 39
0.72 0.11 0.16
Matches are distributed among these distances:
28 2 0.01
29 14 0.08
30 29 0.17
35 23 0.13
36 54 0.31
37 31 0.18
38 19 0.11
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (35 bp):
TTTCCCTTGAAACAAATTTGTCTCTCTTGAGACAG
Found at i:558650 original size:30 final size:30
Alignment explanation
Indices: 558615--558673 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
558605 CTCCTTTGAG
*
558615 ACAGTTTCTATTGAAACATAAA-CTTTGAAA
1 ACAGTTTCCATTGAAACA-AAATCTTTGAAA
*
558645 ACAGTTTCCCTTGAAACAAAATCTTTGAA
1 ACAGTTTCCATTGAAACAAAATCTTTGAA
558674 TATGTTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (30 bp):
ACAGTTTCCATTGAAACAAAATCTTTGAAA
Found at i:558801 original size:37 final size:36
Alignment explanation
Indices: 558687--558801 Score: 158
Period size: 36 Copynumber: 3.1 Consensus size: 36
558677 GTTTTACATT
*
558687 AAACAAATTTCGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * * *
558723 AAACAAATTTTGTCTATCTTAAGACATGTTTTTCTTA
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTCTCTTG
*
558760 AAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
558797 AAACA
1 AAACA
558802 TCAATCCTTG
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
36 24 0.36
37 24 0.36
38 19 0.28
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.39
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:558918 original size:32 final size:32
Alignment explanation
Indices: 558843--558954 Score: 149
Period size: 32 Copynumber: 3.5 Consensus size: 32
558833 CCTTGATACA
558843 GTTTCTCTTGAAACACAAAAGAAACCTTTGAAATT
1 GTTTCTCTTGAAACAC-AAA-AAACCTTTGAAA-T
558878 GTTTCTCTTGAAACACAAAAAACCTTTGAAAT
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAAT
*
558910 GTTTCTCTTGAAACAC---AAACCTTTGAGATT
1 GTTTCTCTTGAAACACAAAAAACCTTTGA-AAT
*
558940 GTTTCCCTTGAAACA
1 GTTTCTCTTGAAACA
558955 ATTTTGTCTC
Statistics
Matches: 74, Mismatches: 2, Indels: 7
0.89 0.02 0.08
Matches are distributed among these distances:
29 10 0.14
30 16 0.22
32 17 0.23
33 12 0.16
34 3 0.04
35 16 0.22
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.33
Consensus pattern (32 bp):
GTTTCTCTTGAAACACAAAAAACCTTTGAAAT
Found at i:559018 original size:64 final size:65
Alignment explanation
Indices: 558910--559056 Score: 197
Period size: 66 Copynumber: 2.2 Consensus size: 65
558900 CCTTTGAAAT
* *
558910 GTTTCTCTTGAAACACAAACCTTTGAGATTGTTTCCCTTGAAAC-AATTTTGTCTCCCTTGAGAC
1 GTTTCTCTTGAAACA-AAACCTTTGAGATTATTTCCCTTAAAACAAATTTTGTCTCCCTTGAGAC
558974 A
65 A
* * * *
558975 GTTTCTCTTGAAACAAAATCTTTGAGTTTATTTCCTTTAAAACAAAATTTTGTCTCCCTTGAGGC
1 GTTTCTCTTGAAACAAAACCTTTGAGATTATTTCCCTTAAAAC-AAATTTTGTCTCCCTTGAGAC
*
559040 C
65 A
*
559041 GTTTCTCATGAAACAA
1 GTTTCTCTTGAAACAA
559057 CATATATCTT
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
64 23 0.32
65 15 0.21
66 34 0.47
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (65 bp):
GTTTCTCTTGAAACAAAACCTTTGAGATTATTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACA
Found at i:559765 original size:105 final size:105
Alignment explanation
Indices: 559580--560409 Score: 1291
Period size: 105 Copynumber: 8.0 Consensus size: 105
559570 GCACTCGAGG
* * *
559580 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTAG-TTGTCAACAAACAACTTCTCAATTTCA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCT-GCTTGTCAAC-AACAACTTCTCAATTTCA
*
559644 GAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
64 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
559686 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* *
559751 GCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
559791 CAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
559856 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
559896 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCATA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
559961 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
560001 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTT-TCCAATCTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCT-CAATTTCAG
*
560065 AGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * *
560106 CAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTAAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
560171 GCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
560211 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** *
560271 TTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * * ** *
560311 CAACACAAGTTCAACTTCAC-ACGAAGGGACGGCTGGTTGTCAACAACAATTTC-CTGGTTCCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTC-AATTTCAG
* * *
560374 AACCAATTTCAACTTCACGACGGAGGATATTGGACT
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACT
560410 TGGAACAATG
Statistics
Matches: 675, Mismatches: 40, Indels: 20
0.92 0.05 0.03
Matches are distributed among these distances:
99 24 0.04
100 61 0.09
101 4 0.01
102 1 0.00
103 2 0.00
104 39 0.06
105 505 0.75
106 39 0.06
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:560999 original size:34 final size:36
Alignment explanation
Indices: 560955--561054 Score: 168
Period size: 34 Copynumber: 2.8 Consensus size: 36
560945 TTTCGTCCTA
*
560955 CTAGGATTCAAACTCCTAAAAATAGGATATAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
560990 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
561025 GCTAGGATTCAAACTCCTAAAAATAGGATA
1 -CTAGGATTCAAACTCCTAAAAATAGGATA
561055 GAGTTCTACT
Statistics
Matches: 61, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
34 30 0.49
35 3 0.05
37 28 0.46
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
Found at i:561082 original size:37 final size:37
Alignment explanation
Indices: 560952--561065 Score: 162
Period size: 37 Copynumber: 3.2 Consensus size: 37
560942 CATTTTCGTC
*
560952 CTACTAGGATTCAAACTCCTAAAAATAGGATATAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
560989 -T--TAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
561023 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
561060 CTACTA
1 CTACTA
561066 TTATTTAAAT
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
34 32 0.46
35 1 0.01
36 1 0.01
37 35 0.51
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:561388 original size:22 final size:21
Alignment explanation
Indices: 561358--561425 Score: 54
Period size: 23 Copynumber: 3.3 Consensus size: 21
561348 CTTTTCTTTT
561358 TTTTCATGTAATATTTTTTTAC
1 TTTT-ATGTAATATTTTTTTAC
* *
561380 ATTTTATGTATTTTCTTTTTTAC
1 -TTTTATGTAATAT-TTTTTTAC
*
561403 -TTTA-GT-ATATATTTTTA-
1 TTTTATGTAATATTTTTTTAC
561420 TTTTAT
1 TTTTAT
561426 TTTTTTAGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
18 10 0.27
19 2 0.05
20 2 0.05
21 4 0.11
22 7 0.19
23 12 0.32
ACGTcount: A:0.22, C:0.06, G:0.04, T:0.68
Consensus pattern (21 bp):
TTTTATGTAATATTTTTTTAC
Found at i:561415 original size:24 final size:23
Alignment explanation
Indices: 561372--561417 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
561362 CATGTAATAT
*
561372 TTTTTTACATTTTATGTATTTTC
1 TTTTTTACATTTTATATATTTTC
561395 TTTTTTAC-TTTAGTATATATTTT
1 TTTTTTACATTT--TATATATTTT
561418 TATTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 8 0.40
24 9 0.45
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTTTTACATTTTATATATTTTC
Found at i:561462 original size:42 final size:42
Alignment explanation
Indices: 561414--561561 Score: 135
Period size: 42 Copynumber: 3.5 Consensus size: 42
561404 TTAGTATATA
561414 TTTTTATT-TTATTTTTTTAGAATATATATATAAATATATTA-T
1 TTTTTATTATTATTTTTTT--AATATATATATAAATATATTACT
* * * *
561456 TTTTTATTATCAGTTTTATTAATTTATATATATATATATATACTT
1 TTTTTATTATTA-TTTTTTTAATATATATATAAATATAT-TAC-T
* * *
561501 TTTTTATT-TTTTTTTATTTTATATATATATTAAT-T-TTACT
1 TTTTTATTATTATTTT-TTTAATATATATATAAATATATTACT
561541 TTTTTATTATTATTTTATTTA
1 TTTTTATTATTATTTT-TTTA
561562 TTTGTTTTAT
Statistics
Matches: 86, Mismatches: 13, Indels: 15
0.75 0.11 0.13
Matches are distributed among these distances:
40 9 0.10
41 13 0.15
42 26 0.30
43 9 0.10
44 20 0.23
45 9 0.10
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.66
Consensus pattern (42 bp):
TTTTTATTATTATTTTTTTAATATATATATAAATATATTACT
Found at i:561522 original size:40 final size:41
Alignment explanation
Indices: 561408--561560 Score: 127
Period size: 40 Copynumber: 3.7 Consensus size: 41
561398 TTTACTTTAG
*** *
561408 TATATA-TTTTTATT-TTATTTTTTTAGAATATATATATAAA
1 TATATACTTTTT-TTATTATTTTTTTATTTTATATATATATA
* * * *
561448 TATATTATTTTTTATTATCAGTTTTATTAATTTATATATATATA
1 TATA-TACTTTTT-TTATTA-TTTTTTTATTTTATATATATATA
561492 TATATACTTTTTTTATT-TTTTTTTATTTTATATATATAT-
1 TATATACTTTTTTTATTATTTTTTTATTTTATATATATATA
* *
561531 TAATTTTAC-TTTTTTATTATTATTTTATTT
1 T-A-TATACTTTTTTTATTATTTTTTTATTT
561561 ATTTGTTTTA
Statistics
Matches: 94, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
39 1 0.01
40 34 0.36
41 16 0.17
42 12 0.13
43 9 0.10
44 22 0.23
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (41 bp):
TATATACTTTTTTTATTATTTTTTTATTTTATATATATATA
Found at i:561526 original size:32 final size:33
Alignment explanation
Indices: 561488--561551 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
561478 TTTATATATA
* *
561488 TATATATATACTT-TTTTTA-TTTTTTTTTATTT
1 TATATATATA-TTAATTTTACTTTTTTATTATTT
561520 TATATATATATTAATTTTACTTTTTTATTATT
1 TATATATATATTAATTTTACTTTTTTATTATT
561552 ATTTTATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 2 0.07
32 15 0.54
33 11 0.39
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (33 bp):
TATATATATATTAATTTTACTTTTTTATTATTT
Found at i:561543 original size:23 final size:18
Alignment explanation
Indices: 561500--561583 Score: 64
Period size: 19 Copynumber: 4.3 Consensus size: 18
561490 TATATATACT
*
561500 TTTTTTATT-TTTTTTTA
1 TTTTTTATTATTATTTTA
561517 TTTTATATATATATTAATTTTA
1 TTTT-T-TAT-TATT-ATTTTA
561539 CTTTTTTATTATTATTTTA
1 -TTTTTTATTATTATTTTA
*
561558 TTTATTTGTT-TTATTTCTA
1 TTT-TTTATTATTATTT-TA
561577 TATTTTT
1 T-TTTTT
561584 TTTCTTCTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 16
0.76 0.03 0.22
Matches are distributed among these distances:
17 4 0.07
18 10 0.18
19 20 0.36
20 7 0.12
21 5 0.09
22 6 0.11
23 4 0.07
ACGTcount: A:0.21, C:0.02, G:0.01, T:0.75
Consensus pattern (18 bp):
TTTTTTATTATTATTTTA
Found at i:561554 original size:36 final size:36
Alignment explanation
Indices: 561484--561558 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
561474 TTAATTTATA
* * *
561484 TATATATATATATACTTTTTTTATTTTTTTTTATTT
1 TATATATATATATAATTTTTTTATTTATTATTATTT
561520 TATATATATAT-TAATTTTACTTT-TTTATTATTATTT
1 TATATATATATATAATTTT--TTTATTTATTATTATTT
561556 TAT
1 TAT
561559 TTATTTGTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 6 0.18
36 25 0.74
37 3 0.09
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (36 bp):
TATATATATATATAATTTTTTTATTTATTATTATTT
Found at i:561594 original size:8 final size:9
Alignment explanation
Indices: 561582--561607 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
561572 TTCTATATTT
561582 TTTTTCTTC
1 TTTTTCTTC
561591 TTTTTCTTC
1 TTTTTCTTC
561600 TTTTTCTT
1 TTTTTCTT
561608 TATTTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:563879 original size:14 final size:14
Alignment explanation
Indices: 563860--563910 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 14
563850 AAAACCAAAA
563860 TCGGTTTTTTCGGT
1 TCGGTTTTTTCGGT
563874 TCGGTTTTTTTAACGGT
1 TCGG-TTTTTT--CGGT
563891 TCAGG-TTTTTCGGT
1 TC-GGTTTTTTCGGT
563905 TCGGTT
1 TCGGTT
563911 CAGTTTATCG
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 2 0.06
14 11 0.34
15 6 0.19
16 5 0.16
17 6 0.19
18 2 0.06
ACGTcount: A:0.06, C:0.14, G:0.27, T:0.53
Consensus pattern (14 bp):
TCGGTTTTTTCGGT
Found at i:564255 original size:24 final size:24
Alignment explanation
Indices: 564231--564276 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
564221 TAATTTTATA
564231 AAAAC-TTTAAGT-TTTCTTTAAAT
1 AAAACTTTTAAGTATTT-TTTAAAT
*
564254 AATACTTTTAAGTATTTTTTAAA
1 AAAACTTTTAAGTATTTTTTAAA
564277 CAATAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 13 0.65
25 3 0.15
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.50
Consensus pattern (24 bp):
AAAACTTTTAAGTATTTTTTAAAT
Found at i:564281 original size:24 final size:24
Alignment explanation
Indices: 564236--564281 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
564226 TTATAAAAAC
*
564236 TTTAAGTTTTCTTTAAATAATACT
1 TTTAAGTTTTCTTTAAACAATACT
564260 TTTAAGTATTT-TTTAAACAATA
1 TTTAAGT-TTTCTTTAAACAATA
564282 AAAAATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (24 bp):
TTTAAGTTTTCTTTAAACAATACT
Found at i:565905 original size:3 final size:3
Alignment explanation
Indices: 565897--565957 Score: 104
Period size: 3 Copynumber: 20.3 Consensus size: 3
565887 TTTGACGGAC
*
565897 TTA TTA TTA TTA TTA TTA TTA TTA TGA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
565945 TGA TTA TTA TTA T
1 TTA TTA TTA TTA T
565958 ATCAAGTATC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:566023 original size:21 final size:19
Alignment explanation
Indices: 565999--566068 Score: 63
Period size: 18 Copynumber: 3.7 Consensus size: 19
565989 TTAAGGTTTC
565999 TTAAAAATTTTAAAAATTAA
1 TTAAAAATTTTAAAAATT-A
* *
566019 TTTAAAAATATTAAATATTA
1 -TTAAAAATTTTAAAAATTA
*
566039 TT-AAAATTATAAAAA-TA
1 TTAAAAATTTTAAAAATTA
* *
566056 TGAAAATTTTTAA
1 TTAAAAATTTTAA
566069 TTTTAAAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
17 3 0.08
18 18 0.45
19 2 0.05
20 1 0.03
21 16 0.40
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (19 bp):
TTAAAAATTTTAAAAATTA
Found at i:567735 original size:2 final size:2
Alignment explanation
Indices: 567722--567762 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
567712 AACAGTGGTA
*
567722 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
567763 GAGAGAGAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:568026 original size:2 final size:2
Alignment explanation
Indices: 568019--568073 Score: 60
Period size: 2 Copynumber: 28.5 Consensus size: 2
568009 TCGAGTATGG
* * * *
568019 TA TA TA TA TT TA AA T- TA AA TA TA TA TA AA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
568059 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
568074 TAATTTAATT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:568049 original size:10 final size:10
Alignment explanation
Indices: 568034--568127 Score: 59
Period size: 10 Copynumber: 9.3 Consensus size: 10
568024 ATATTTAAAT
568034 TAAATATATA
1 TAAATATATA
568044 TAAATAT-TA
1 TAAATATATA
*
568053 TATATATATA
1 TAAATATATA
*
568063 TATATATATA
1 TAAATATATA
* * *
568073 TTAATTTAATT
1 TAAATAT-ATA
*
568084 TAAAT-TAAA
1 TAAATATATA
*
568093 TTAAATTTAT-
1 -TAAATATATA
568103 TAATATTATATA
1 TAA-A-TATATA
*
568115 TATATATATA
1 TAAATATATA
568125 TAA
1 TAA
568128 TTATTTTTAA
Statistics
Matches: 65, Mismatches: 12, Indels: 14
0.71 0.13 0.15
Matches are distributed among these distances:
9 12 0.18
10 38 0.58
11 13 0.20
12 2 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
TAAATATATA
Found at i:568052 original size:17 final size:17
Alignment explanation
Indices: 568032--568067 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
568022 ATATATTTAA
568032 ATTAAATATATATAAAT
1 ATTAAATATATATAAAT
* *
568049 ATTATATATATATATAT
1 ATTAAATATATATAAAT
568066 AT
1 AT
568068 ATATATTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTAAATATATATAAAT
Found at i:570080 original size:14 final size:14
Alignment explanation
Indices: 570061--570098 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
570051 CGTTCGATTA
570061 TATGTTCATTCATT
1 TATGTTCATTCATT
*
570075 TATGTTCGTTCATT
1 TATGTTCATTCATT
570089 TATGTTCATT
1 TATGTTCATT
570099 TATGTTCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (14 bp):
TATGTTCATTCATT
Found at i:570097 original size:24 final size:23
Alignment explanation
Indices: 570069--570118 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 23
570059 TATATGTTCA
570069 TTCATTTATGTTCGTTCATTTATG
1 TTCATTTATGTTCGTT-ATTTATG
*
570093 TTCATTTATGTTCGTTATTTCTG
1 TTCATTTATGTTCGTTATTTATG
570116 TTC
1 TTC
570119 GAACAGATGG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.14, C:0.14, G:0.12, T:0.60
Consensus pattern (23 bp):
TTCATTTATGTTCGTTATTTATG
Found at i:570289 original size:27 final size:26
Alignment explanation
Indices: 570247--570300 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
570237 TTTTTTGTGT
* **
570247 TTGTGTTGTTCTTTTATGTTCGTTTA
1 TTGTGTTGTTCGTTTACATTCGTTTA
570273 TTGTGTTCGTTCGTTTACATTCGTTTA
1 TTGTGTT-GTTCGTTTACATTCGTTTA
570300 T
1 T
570301 GTTCGCTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.09, C:0.11, G:0.19, T:0.61
Consensus pattern (26 bp):
TTGTGTTGTTCGTTTACATTCGTTTA
Found at i:571997 original size:134 final size:134
Alignment explanation
Indices: 571597--572341 Score: 866
Period size: 134 Copynumber: 5.5 Consensus size: 134
571587 ACGAATCAAA
* *
571597 CTCGATTCAATCTTCCCTGAAGTGACAGTGGAATAAATCAACG-CCTCCATATCTGATTTTCCCT
1 CTCGATTCAATCTTCCCT-AAGTGACAGTGGAATGAATCAACGTCC-CCAGATCTGATTTTCCCT
* * * * * *
571661 CAAGAAGAAGCGAAACAGATCCCTTTCTTCCAAGATTTGATATTCCCTGGGTAATAGTGGAACAA
64 CAAGAAGAAGTGGAACAGATCCATTTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAA
*
571726 GTCTAC
129 GTCTGC
* * * *
571732 CTCAATTCAATCTTCCCTAAGTGACTA-TAGAATGAATCAACGTCCCCATATCTGGTATTTCCCT
1 CTCGATTCAATCTTCCCTAAGTGAC-AGTGGAATGAATCAACGTCCCCAGATCTGAT-TTTCCCT
* * ** * * *
571796 CAAGAAAAAGTGGAACATATTTATTTCTTCCAGGATTTGATATTCCATGAGTAACAGTGGAACAA
64 CAAGAAGAAGTGGAACAGATCCATTTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAA
* *
571861 GTTTGT
129 GTCTGC
* * * * * *
571867 CTCGATTCAATCCTCCCTTAGTGATAGTAGAATGAATCAACGTCCCCATATATGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTAAGTGACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCA
* * * * *
571932 AGAAGAAGTAGAATAGATCCATCTCTTTCAAGATTTGATATTCCCTTAGTAACAGTAGAACAAGT
66 AGAAGAAGTGGAACAGATCCATTTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
*
571997 TTGC
131 CTGC
* * ** * *
572001 CTCGATTCAATCTTCCTTAAGTGACAGTGGAATGAATCAACATCCGGAGACCCGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTAAGTGACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCA
* * *
572066 ACAAGAAGTGAAACATAT-CATTTTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
66 AGAAGAAGTGGAACAGATCCA-TTTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
572130 TCTGC
130 TCTGC
* *
572135 CTCGATTCAATCTTCCCTAAGTGACAGTGGAATGAATCAATGTCTCCAGATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTAAGTGACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCA
** * * ** * *
572200 AGAAGAAACGGAACATATCCCTCCCTTTCAAGATTTGTTATTCCTTGAGTAACAGTGGAACAAGT
66 AGAAGAAGTGGAACAGATCCATTTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
572265 CTGC
131 CTGC
* ** * * * * *
572269 CTCGATTCAATCTTCCCTGAGCAAAAATGGAATGAATCGACGTTCCCAGATCTGATTTTCCCCCA
1 CTCGATTCAATCTTCCCTAAGTGACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCA
*
572334 ACAAGAAG
66 AGAAGAAG
572342 CAAAACAAAT
Statistics
Matches: 517, Mismatches: 87, Indels: 13
0.84 0.14 0.02
Matches are distributed among these distances:
133 2 0.00
134 382 0.74
135 133 0.26
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (134 bp):
CTCGATTCAATCTTCCCTAAGTGACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCA
AGAAGAAGTGGAACAGATCCATTTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
CTGC
Found at i:577263 original size:26 final size:25
Alignment explanation
Indices: 577216--577317 Score: 73
Period size: 26 Copynumber: 4.0 Consensus size: 25
577206 GACGAAATTG
* *
577216 TTAGATAGAAAAATAATAAATAAATA
1 TTAGATA-AATAATAAAAAATAAATA
577242 TTAGATAAATAATAAAATAATAAATCA
1 TTAGATAAATAATAAAA-AATAAAT-A
* * *
577269 --AAACAAATAATAAAATAATAAAAA
1 TTAGATAAATAATAAAA-AATAAATA
* * *
577293 TAATAAAAATAATAAAAAATTAAAT
1 TTAGATAAATAATAAAAAA-TAAAT
577318 CAGAGAAAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
24 1 0.02
25 30 0.48
26 31 0.49
27 1 0.02
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.25
Consensus pattern (25 bp):
TTAGATAAATAATAAAAAATAAATA
Found at i:577294 original size:9 final size:9
Alignment explanation
Indices: 577224--577412 Score: 82
Period size: 9 Copynumber: 20.6 Consensus size: 9
577214 TGTTAGATAG
577224 AAAAATAAT
1 AAAAATAAT
*
577233 AAATAAATATT
1 -AA-AAATAAT
577244 AGATAAATAAT
1 A-A-AAATAAT
577255 -AAAATAAT
1 AAAAATAAT
577263 --AAATCAA-
1 AAAAAT-AAT
577270 AACAAATAAT
1 AA-AAATAAT
577280 -AAAATAAT
1 AAAAATAAT
577288 AAAAATAAT
1 AAAAATAAT
577297 AAAAATAAT
1 AAAAATAAT
577306 AAAAAATTAAAT
1 -AAAAA-T-AAT
577318 CAGAGAAA-AAT
1 -A-A-AAATAAT
*
577329 -TAAATAA-
1 AAAAATAAT
*
577336 ATAAATTGAA-
1 A-AAAAT-AAT
577346 AAAAAT-AT
1 AAAAATAAT
577354 AAAAAATAAGT
1 -AAAAATAA-T
577365 CAAAAA-AAT
1 -AAAAATAAT
577374 AAAAA-AAT
1 AAAAATAAT
577382 -AAAATAAAT
1 AAAAAT-AAT
577391 AAAAA-AAT
1 AAAAATAAT
*
577399 AAAAAAAAT
1 AAAAATAAT
577408 AAAAA
1 AAAAA
577413 AGTGAAATGG
Statistics
Matches: 146, Mismatches: 8, Indels: 51
0.71 0.04 0.25
Matches are distributed among these distances:
7 12 0.08
8 34 0.23
9 46 0.32
10 22 0.15
11 24 0.16
12 4 0.03
13 1 0.01
14 3 0.02
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.21
Consensus pattern (9 bp):
AAAAATAAT
Found at i:577380 original size:21 final size:20
Alignment explanation
Indices: 577280--577413 Score: 93
Period size: 17 Copynumber: 6.5 Consensus size: 20
577270 AACAAATAAT
577280 AAAATAATAAAAATAAT-AAA
1 AAAATAA-AAAAATAATCAAA
*
577300 AATAATAAAAAATTAAATCAGAGA
1 AA-AATAAAAAAAT-AATCA-A-A
* *
577324 AAAATTAAATAAATAAATTGAAA
1 AAAA-TAAAAAAAT-AA-TCAAA
577347 AAAATATAAAAAATAAGTCAAA
1 AAAATA-AAAAAATAA-TCAAA
577369 AAAATAAAAAAAT-A--AAA
1 AAAATAAAAAAATAATCAAA
*
577386 TAAATAAAAAAAT-A--AAA
1 AAAATAAAAAAATAATCAAA
577403 AAAATAAAAAA
1 AAAATAAAAAA
577414 GTGAAATGGA
Statistics
Matches: 97, Mismatches: 9, Indels: 19
0.78 0.07 0.15
Matches are distributed among these distances:
17 29 0.30
20 8 0.08
21 15 0.15
22 15 0.15
23 14 0.14
24 14 0.14
25 2 0.02
ACGTcount: A:0.77, C:0.01, G:0.03, T:0.19
Consensus pattern (20 bp):
AAAATAAAAAAATAATCAAA
Found at i:577381 original size:97 final size:97
Alignment explanation
Indices: 577222--577407 Score: 247
Period size: 97 Copynumber: 1.9 Consensus size: 97
577212 ATTGTTAGAT
* * * *
577222 AGAAAAATAATAAATAAATATTAGATAAATAATAAAATAATAAATCAAAACAAATAATAAAATAA
1 AGAAAAATAATAAATAAATATGAAAAAAATAATAAAATAATAAATCAAAACAAATAAAAAAATAA
577287 TAA-AAATAATAAAAATAATAAAAAATTAAATCAG
66 -AATAAATAA-AAAAATAA-AAAAAATTAAATCAG
*
577321 AGAAAAATTAAATAAATAAAT-TGAAAAAAAT-ATAAAA-AATAAGTCAAAA-AAATAAAAAAAT
1 AGAAAAA-T-AATAAATAAATATGAAAAAAATAATAAAATAATAAATCAAAACAAATAAAAAAAT
577382 AAAATAAATAAAAAAATAAAAAAAAT
64 AAAATAAATAAAAAAATAAAAAAAAT
577408 AAAAAAGTGA
Statistics
Matches: 79, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
95 7 0.09
96 10 0.13
97 19 0.24
98 11 0.14
99 13 0.16
100 8 0.10
101 11 0.14
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.21
Consensus pattern (97 bp):
AGAAAAATAATAAATAAATATGAAAAAAATAATAAAATAATAAATCAAAACAAATAAAAAAATAA
AATAAATAAAAAAATAAAAAAAATTAAATCAG
Found at i:577413 original size:9 final size:9
Alignment explanation
Indices: 577263--577413 Score: 92
Period size: 9 Copynumber: 16.1 Consensus size: 9
577253 ATAAAATAAT
*
577263 AAATCAAAAC
1 AAAT-AAAAA
577273 AAATAATAAA
1 AAATAA-AAA
577283 ATAATAAAAA
1 A-AATAAAAA
*
577293 TAATAAAAA
1 AAATAAAAA
*
577302 TAAT-AAAA
1 AAATAAAAA
* **
577310 AATTAAATC
1 AAATAAAAA
* *
577319 AGAGAAAAA
1 AAATAAAAA
*
577328 TTAAATAAATA
1 --AAATAAAAA
*
577339 AATTGAAAAA
1 AAAT-AAAAA
577349 AATATAAAAA
1 AA-ATAAAAA
*
577359 ATAAGTCAAAA
1 A-AA-TAAAAA
577370 AAAT-AAAA
1 AAATAAAAA
*
577378 AAATAAAAT
1 AAATAAAAA
577387 AAAT-AAAA
1 AAATAAAAA
577395 AAATAAAAA
1 AAATAAAAA
577404 AAATAAAAA
1 AAATAAAAA
577413 A
1 A
577414 GTGAAATGGA
Statistics
Matches: 110, Mismatches: 20, Indels: 23
0.72 0.13 0.15
Matches are distributed among these distances:
8 21 0.19
9 45 0.41
10 25 0.23
11 19 0.17
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.19
Consensus pattern (9 bp):
AAATAAAAA
Found at i:577480 original size:13 final size:13
Alignment explanation
Indices: 577462--577490 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
577452 TTACATTTTG
577462 AAATAAAAAAATA
1 AAATAAAAAAATA
577475 AAATAAAAAAATA
1 AAATAAAAAAATA
577488 AAA
1 AAA
577491 ATTGAGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (13 bp):
AAATAAAAAAATA
Found at i:578868 original size:81 final size:78
Alignment explanation
Indices: 578744--579042 Score: 278
Period size: 81 Copynumber: 3.7 Consensus size: 78
578734 TCTTTTCTTG
* * * *
578744 AGCTATGATGTAAATGATGTGCCTTGGAGCTGA--GCATAGTCGAACTCGAAGGTCTTTAGCATA
1 AGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGCA-A-TCGAACTC-AAGGTCTTTGGCAGA
* *
578807 TAACTCTTCTCGACTTA
63 TAAC-CTTCTAGCCTTA
* *
578824 AGCTATGCTGCAAATGATAGTGCCTTTGAGCTGATTGCAATCGAACTCTAAGGTCTTTGGCAGAT
1 AGCTATGCTGCAAATGAT-GTGCCTTGGAGCTGAGTGCAATCGAACTC-AAGGTCTTTGGCAGAT
*
578889 AAACCTTCTAGCCTTG
64 -AACCTTCTAGCCTTA
* * * * * *
578905 AGTTATGTTGCAAATGATATGCCCTTGAAGCTGAGTGTAATCGACCTCAAGGGTCTTTGGCAGAT
1 AGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGTGCAATCGAACTCAA-GGTCTTTGGCAGAT
* *
578970 AGCCATTCTTGCCTTA
64 AACC-TTCTAGCCTTA
* * * * * *
578986 AGCTATACTGCAAATGCTGAGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTT
1 AGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGCAATCGAACTC-AAGGTCTTT
579043 TGTTTCAAGA
Statistics
Matches: 181, Mismatches: 30, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
80 52 0.29
81 122 0.67
82 4 0.02
83 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.30
Consensus pattern (78 bp):
AGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGCAATCGAACTCAAGGTCTTTGGCAGATAA
CCTTCTAGCCTTA
Found at i:579252 original size:37 final size:36
Alignment explanation
Indices: 579165--579257 Score: 107
Period size: 37 Copynumber: 2.5 Consensus size: 36
579155 AACTGTCTCG
* *
579165 GACAAAACTTTGTTTTAAGGGAAATTGTCTCAAAAGA
1 GACAAAACTTTGTTTTGA-GTAAATTGTCTCAAAAGA
**
579202 GACAAAACTTTGTTTTGAGTAAATTAGTCTCAAGCGA
1 GACAAAACTTTGTTTTGAGTAAATT-GTCTCAAAAGA
*
579239 GAC-AACCTCTTGTTTTGAG
1 GACAAAACT-TTGTTTTGAG
579258 AGAAACAATC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
36 10 0.20
37 39 0.80
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.32
Consensus pattern (36 bp):
GACAAAACTTTGTTTTGAGTAAATTGTCTCAAAAGA
Found at i:580885 original size:36 final size:37
Alignment explanation
Indices: 580845--580929 Score: 102
Period size: 38 Copynumber: 2.3 Consensus size: 37
580835 ATGTGTATTG
*
580845 TTTTCTTTTTTA-TTCATTTTTCCTTTGTT-TTCGTTT
1 TTTTCTTTTTTATTTC-TTTTTACTTTGTTATTCGTTT
* *
580881 TTTTCTTTTTTATTTTCTTTTTACTTTTTTATTTGTTT
1 TTTTCTTTTTTA-TTTCTTTTTACTTTGTTATTCGTTT
*
580919 TTCTCTTTTTT
1 TTTTCTTTTTT
580930 CTTCTTCTCT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
36 12 0.29
37 11 0.26
38 19 0.45
ACGTcount: A:0.06, C:0.12, G:0.04, T:0.79
Consensus pattern (37 bp):
TTTTCTTTTTTATTTCTTTTTACTTTGTTATTCGTTT
Found at i:580901 original size:18 final size:18
Alignment explanation
Indices: 580845--580929 Score: 75
Period size: 18 Copynumber: 4.6 Consensus size: 18
580835 ATGTGTATTG
**
580845 TTTTCTTTTTTATTCATT
1 TTTTCTTTTTTATTTGTT
* * *
580863 TTTCCTTTGTT-TTCGTTT
1 TTTTCTTTTTTATTTG-TT
580881 TTTTCTTTTTTATTT-TCT
1 TTTTCTTTTTTATTTGT-T
580899 TTTTACTTTTTTATTTGTT
1 TTTT-CTTTTTTATTTGTT
580918 TTTCTCTTTTTT
1 TTT-TCTTTTTT
580930 CTTCTTCTCT
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
17 4 0.07
18 25 0.45
19 24 0.44
20 2 0.04
ACGTcount: A:0.06, C:0.12, G:0.04, T:0.79
Consensus pattern (18 bp):
TTTTCTTTTTTATTTGTT
Found at i:580901 original size:19 final size:19
Alignment explanation
Indices: 580879--580943 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
580869 TTGTTTTCGT
580879 TTTTTTCTTTTTTATTTTC
1 TTTTTTCTTTTTTATTTTC
*
580898 TTTTTACTTTTTTATTTGT-
1 TTTTTTCTTTTTTATTT-TC
* *
580917 TTTTCTCTTTTTTCTTCTTC
1 TTTTTTCTTTTTTATT-TTC
580937 TCTTTTT
1 T-TTTTT
580944 GTTCTTGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
19 30 0.81
20 3 0.08
21 4 0.11
ACGTcount: A:0.05, C:0.14, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTTTCTTTTTTATTTTC
Found at i:580901 original size:26 final size:27
Alignment explanation
Indices: 580845--580901 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 27
580835 ATGTGTATTG
* * *
580845 TTTTCTTTTTTATTCATTTTTCCTTTG
1 TTTTCGTTTTTATTCATTTTTACTTTC
* *
580872 TTTTCGTTTTT-TTCTTTTTTATTTTC
1 TTTTCGTTTTTATTCATTTTTACTTTC
580898 TTTT
1 TTTT
580902 TACTTTTTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.05, C:0.12, G:0.04, T:0.79
Consensus pattern (27 bp):
TTTTCGTTTTTATTCATTTTTACTTTC
Found at i:580908 original size:26 final size:25
Alignment explanation
Indices: 580879--580948 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 25
580869 TTGTTTTCGT
*
580879 TTTTTTCTTTTTTATTTTCTTTTTAC
1 TTTTTTCTTTTTT-TTCTCTTTTTAC
* *
580905 TTTTTTATTTGTTTTTCTCTTTTTTC
1 TTTTTTCTTT-TTTTTCTCTTTTTAC
* *
580931 TTCTTCTCTTTTTGTTCT
1 TT-TTTTCTTTTTTTTCT
580949 TGATTGGATC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
26 27 0.75
27 9 0.25
ACGTcount: A:0.04, C:0.14, G:0.03, T:0.79
Consensus pattern (25 bp):
TTTTTTCTTTTTTTTCTCTTTTTAC
Found at i:580948 original size:14 final size:15
Alignment explanation
Indices: 580912--580949 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
580902 TACTTTTTTA
*
580912 TTTGTTTTTCTCTTT
1 TTTGTTCTTCTCTTT
*
580927 TTTCTTCTTCTC-TT
1 TTTGTTCTTCTCTTT
580941 TTTGTTCTT
1 TTTGTTCTT
580950 GATTGGATCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.00, C:0.18, G:0.05, T:0.76
Consensus pattern (15 bp):
TTTGTTCTTCTCTTT
Found at i:582369 original size:10 final size:10
Alignment explanation
Indices: 582351--582386 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
582341 AGTTAGCTAG
*
582351 TCTTATATCT
1 TCTTCTATCT
582361 TCTTCTATCT
1 TCTTCTATCT
582371 TCTTCTATCT
1 TCTTCTATCT
582381 TCTTCT
1 TCTTCT
582387 GTCATCGGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.11, C:0.28, G:0.00, T:0.61
Consensus pattern (10 bp):
TCTTCTATCT
Found at i:584030 original size:8 final size:8
Alignment explanation
Indices: 584017--584204 Score: 60
Period size: 8 Copynumber: 22.0 Consensus size: 8
584007 TAAATATTAG
584017 ATAAAAAA
1 ATAAAAAA
* *
584025 ACAAAATA
1 ATAAAAAA
*
584033 ATAAAATA
1 ATAAAAAA
584041 ATAAATCAAA
1 ATAAA--AAA
* *
584051 A-CAAATA
1 ATAAAAAA
584058 ATAAAAAA
1 ATAAAAAA
*
584066 GTAAAAAA
1 ATAAAAAA
584074 ACT-AAAAA
1 A-TAAAAAA
584082 ATAAAAAA
1 ATAAAAAA
*
584090 TTAAATTAGAGA
1 ATAAA--A-A-A
*
584102 A-AAATTAA
1 ATAAA-AAA
584110 ATAAATAAA
1 ATAAA-AAA
*
584119 TTGAAAAAA
1 AT-AAAAAA
584128 ATAAATATAA
1 ATAAA-A-AA
*
584138 A-AGAATAA
1 ATA-AAAAA
584146 ATAAAAATA
1 ATAAAAA-A
584155 ATAATAAAA
1 ATAA-AAAA
* *
584164 ATAAGAGA
1 ATAAAAAA
584172 ATAAAAAA
1 ATAAAAAA
* * *
584180 TATATATAT
1 -ATAAAAAA
584189 ATAAAAAA
1 ATAAAAAA
*
584197 TTAAAAAA
1 ATAAAAAA
584205 GGAAATGGAA
Statistics
Matches: 133, Mismatches: 29, Indels: 36
0.67 0.15 0.18
Matches are distributed among these distances:
7 4 0.03
8 75 0.56
9 33 0.25
10 16 0.12
11 4 0.03
12 1 0.01
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (8 bp):
ATAAAAAA
Found at i:584062 original size:25 final size:25
Alignment explanation
Indices: 584018--584164 Score: 87
Period size: 24 Copynumber: 5.9 Consensus size: 25
584008 AAATATTAGA
584018 TAAA-AAAACAAAATAATAAAATAA-
1 TAAATAAAACAAAATAATAAAA-AAG
584042 TAAATCAAAAC-AAATAATAAAAAAG
1 TAAAT-AAAACAAAATAATAAAAAAG
*
584067 TAAA-AAAACTAAAA-AATAAAAAAT
1 TAAATAAAAC-AAAATAATAAAAAAG
* * * *
584091 TAAATTAGAGAAAA-ATTAAATAAA-
1 TAAATAAAACAAAATAATAAA-AAAG
* *
584115 TAAATTGAAA-AAAATAAATATAAAAGAA
1 TAAA-TAAAACAAAAT-AATA-AAAA-AG
*
584143 TAAATAAAA-ATAATAATAAAAA
1 TAAATAAAACAAAATAATAAAAA
584165 TAAGAGAATA
Statistics
Matches: 100, Mismatches: 10, Indels: 25
0.74 0.07 0.19
Matches are distributed among these distances:
23 5 0.05
24 36 0.36
25 30 0.30
26 14 0.14
27 11 0.11
28 4 0.04
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (25 bp):
TAAATAAAACAAAATAATAAAAAAG
Found at i:584131 original size:14 final size:13
Alignment explanation
Indices: 584034--584158 Score: 61
Period size: 14 Copynumber: 9.8 Consensus size: 13
584024 AACAAAATAA
*
584034 TAAAATAATAAAT
1 TAAAAAAATAAAT
*
584047 CAAAACAAAT-AA-
1 TAAAA-AAATAAAT
*
584059 TAAAAAAGTAAA-
1 TAAAAAAATAAAT
584071 -AAAACTAAA-AAA-
1 TAAAA--AAATAAAT
*
584083 TAAAAAATTAAAT
1 TAAAAAAATAAAT
* *
584096 T-AGAGAA-AAAT
1 TAAAAAAATAAAT
*
584107 TAAATAAATAAAT
1 TAAAAAAATAAAT
584120 TGAAAAAAATAAAT
1 T-AAAAAAATAAAT
*
584134 ATAAAAGAATAAA-
1 -TAAAAAAATAAAT
584147 TAAAAATAATAA
1 TAAAAA-AATAA
584159 TAAAAATAAG
Statistics
Matches: 85, Mismatches: 15, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
11 14 0.16
12 23 0.27
13 23 0.27
14 24 0.28
15 1 0.01
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (13 bp):
TAAAAAAATAAAT
Found at i:584160 original size:12 final size:13
Alignment explanation
Indices: 583995--584178 Score: 79
Period size: 12 Copynumber: 14.4 Consensus size: 13
583985 TGTTAGATAG
583995 AAAAATAATAAAT
1 AAAAATAATAAAT
*
584008 AAATATTAGATAAA-
1 AAA-AATA-ATAAAT
*
584022 AAAACAAAAT-AAT
1 AAAA-ATAATAAAT
584035 -AAAATAATAAAT
1 AAAAATAATAAAT
584047 CAAAACA-AAT-AAT
1 -AAAA-ATAATAAAT
*
584060 AAAAA-AGTAAA-
1 AAAAATAATAAAT
* *
584071 AAAACTAAAAAAT
1 AAAAATAATAAAT
*
584084 AAAAA-ATTAAAT
1 AAAAATAATAAAT
* * *
584096 -TAGAGAA-AAAT
1 AAAAATAATAAAT
*
584107 -TAAATAAATAAATT
1 AAAAAT-AATAAA-T
584121 GAAAAA-AATAAAT
1 -AAAAATAATAAAT
*
584134 ATAAAAGAATAAAT
1 A-AAAATAATAAAT
584148 AAAAATAAT-AAT
1 AAAAATAATAAAT
*
584160 AAAAATAAGAGAAT
1 AAAAATAATA-AAT
584174 AAAAA
1 AAAAA
584179 ATATATATAT
Statistics
Matches: 131, Mismatches: 19, Indels: 41
0.69 0.10 0.21
Matches are distributed among these distances:
11 20 0.15
12 38 0.29
13 28 0.21
14 36 0.27
15 6 0.05
16 3 0.02
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.20
Consensus pattern (13 bp):
AAAAATAATAAAT
Found at i:584173 original size:30 final size:30
Alignment explanation
Indices: 584127--584195 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
584117 AATTGAAAAA
*
584127 AATAAATATAAAAGAATAAATAAAAATA-AT
1 AATAAAAATAAAAGAATAAA-AAAAATATAT
* *
584157 AATAAAAATAAGAGAATAAAAAATATATAT
1 AATAAAAATAAAAGAATAAAAAAAATATAT
584187 ATATAAAAA
1 A-ATAAAAA
584196 ATTAAAAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 6 0.18
30 21 0.62
31 7 0.21
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.23
Consensus pattern (30 bp):
AATAAAAATAAAAGAATAAAAAAAATATAT
Found at i:584271 original size:14 final size:14
Alignment explanation
Indices: 584252--584291 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
584242 TTACATTTTG
584252 AAATAAAAAAAATA
1 AAATAAAAAAAATA
*
584266 AAATAAAAAAATTA
1 AAATAAAAAAAATA
584280 AAA-AATAAAAAA
1 AAATAA-AAAAAA
584292 GGAGTTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 2 0.09
14 21 0.91
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (14 bp):
AAATAAAAAAAATA
Found at i:590257 original size:21 final size:21
Alignment explanation
Indices: 590233--590273 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
590223 ATTTTAAAAA
590233 TAAGATATTTTTAAAATTGTG
1 TAAGATATTTTTAAAATTGTG
*
590254 TAAGATATTTTTAAATTTGT
1 TAAGATATTTTTAAAATTGT
590274 TTTACTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (21 bp):
TAAGATATTTTTAAAATTGTG
Found at i:591762 original size:4 final size:4
Alignment explanation
Indices: 591755--591796 Score: 63
Period size: 4 Copynumber: 11.2 Consensus size: 4
591745 TCATCTAATA
591755 TATT TATT TATT TATT TA-T T-TT TATT TATT TATT TA-T TATT T
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT T
591797 CCATTTATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 7 0.20
4 28 0.80
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:591780 original size:18 final size:18
Alignment explanation
Indices: 591757--591792 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
591747 ATCTAATATA
591757 TTTATTTATTTATTTATT
1 TTTATTTATTTATTTATT
591775 TTTATTTATTTATTTATT
1 TTTATTTATTTATTTATT
591793 ATTTCCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTATTTATTTATTTATT
Found at i:591781 original size:22 final size:21
Alignment explanation
Indices: 591755--591822 Score: 86
Period size: 22 Copynumber: 3.3 Consensus size: 21
591745 TCATCTAATA
591755 TATTTATTTATTTATTTATTTT
1 TATTTATTTATTTA-TTATTTT
*
591777 TATTTATTTATTTATTATTTC
1 TATTTATTTATTTATTATTTT
*
591798 CATTTA-TTA-TTATTATTTT
1 TATTTATTTATTTATTATTTT
*
591817 TCTTTA
1 TATTTA
591823 AATAACATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
19 13 0.32
20 3 0.07
21 11 0.27
22 14 0.34
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (21 bp):
TATTTATTTATTTATTATTTT
Found at i:591976 original size:5 final size:5
Alignment explanation
Indices: 591938--592000 Score: 51
Period size: 5 Copynumber: 12.8 Consensus size: 5
591928 TATTATTTGC
* *
591938 ATTTT ATTCT -TTTT GTTTCT ATTTT A-TTT A-TTT ATTTT ATTTT ATTTTT
1 ATTTT ATTTT ATTTT ATTT-T ATTTT ATTTT ATTTT ATTTT ATTTT A-TTTT
* *
591987 ATTTC ATTTG ATTT
1 ATTTT ATTTT ATTT
592001 GTTTATTTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
4 11 0.22
5 29 0.59
6 9 0.18
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.75
Consensus pattern (5 bp):
ATTTT
Found at i:591980 original size:29 final size:30
Alignment explanation
Indices: 591940--592013 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 30
591930 TTATTTGCAT
* * *
591940 TTTATTCT-TTTTGTTTCTATTTTATTT-A
1 TTTATTTTATTTTATTTCTATTTCATTTGA
*
591968 TTTATTTTATTTTATTTTTATTTCATTTGA
1 TTTATTTTATTTTATTTCTATTTCATTTGA
* *
591998 TTT-GTTTATTTAATTT
1 TTTATTTTATTTTATTT
592014 AGTTAACTTC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
28 7 0.18
29 27 0.71
30 4 0.11
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.74
Consensus pattern (30 bp):
TTTATTTTATTTTATTTCTATTTCATTTGA
Found at i:591989 original size:20 final size:20
Alignment explanation
Indices: 591938--592000 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
591928 TATTATTTGC
* *
591938 ATTTTATTCTT-TTTGTTTCT
1 ATTTTATTTTTATTTATTT-T
591958 ATTTTA--TTTATTTATTTT
1 ATTTTATTTTTATTTATTTT
*
591976 ATTTTATTTTTATTTCATTTG
1 ATTTTATTTTTATTT-ATTTT
591997 ATTT
1 ATTT
592001 GTTTATTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
18 9 0.25
19 6 0.17
20 13 0.36
21 8 0.22
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.75
Consensus pattern (20 bp):
ATTTTATTTTTATTTATTTT
Found at i:602845 original size:63 final size:63
Alignment explanation
Indices: 602714--603003 Score: 325
Period size: 63 Copynumber: 4.6 Consensus size: 63
602704 TGTTTACTAT
* * * * * * ** *
602714 AGTCAATCATTAACTTTCTCATTAAGAGAAGTC-AACTTTTGTTATCCCTGACTTATCAGTAG
1 AGTCAATCCTTGACTTCCTCATGAAAAGAAGTCAAACATTTGTTATTTCTGACTCATCAGTAG
* *
602776 AGTCAATCCTTGACTTCCTCATGAAAAGAAGTCAAACATTTGTTATTTTTGACTCATTAGTAG
1 AGTCAATCCTTGACTTCCTCATGAAAAGAAGTCAAACATTTGTTATTTCTGACTCATCAGTAG
* ** ** *
602839 AATCAATTTTTGACTTCCTTGTGAAAATAAGTCAAACATTTGTTATTTCTGACTCATCAGTAG
1 AGTCAATCCTTGACTTCCTCATGAAAAGAAGTCAAACATTTGTTATTTCTGACTCATCAGTAG
* * *
602902 AGTCAATCCTTGACTTTCTCGTGAAAAGAAGTCAAACATTTGTTATTTCTGACTC-CCTAGTAG
1 AGTCAATCCTTGACTTCCTCATGAAAAGAAGTCAAACATTTGTTATTTCTGACTCATC-AGTAG
** * * *
602965 AGTCAATATTTGACTTCCACTTGAAAATAAGTC-AACATT
1 AGTCAATCCTTGACTTCCTCATGAAAAGAAGTCAAACATT
603004 GCAGATTTGG
Statistics
Matches: 194, Mismatches: 32, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
62 35 0.18
63 159 0.82
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (63 bp):
AGTCAATCCTTGACTTCCTCATGAAAAGAAGTCAAACATTTGTTATTTCTGACTCATCAGTAG
Found at i:602977 original size:126 final size:125
Alignment explanation
Indices: 602742--603003 Score: 391
Period size: 126 Copynumber: 2.1 Consensus size: 125
602732 TCATTAAGAG
* *
602742 AAGTCAACTTTTGTTATCCCTGACTTATCAGTAGAGTCAATCCTTGACTTCCTCATGAAAAGAAG
1 AAGTCAACATTTGTTATCCCTGACTCATCAGTAGAGTCAATCCTTGACTTCCTCATGAAAAGAAG
* * * *
602807 TCAAACATTTGTTATTTTTGACTCATTAGTAGAATCAATTTTTGACTTCC-TTGTGAAAAT
66 TCAAACATTTGTTATTTCTGACTCACTAGTAGAATCAATATTTGACTTCCACT-TGAAAAT
** * *
602867 AAGTCAAACATTTGTTATTTCTGACTCATCAGTAGAGTCAATCCTTGACTTTCTCGTGAAAAGAA
1 AAGTC-AACATTTGTTATCCCTGACTCATCAGTAGAGTCAATCCTTGACTTCCTCATGAAAAGAA
* *
602932 GTCAAACATTTGTTATTTCTGACTCCCTAGTAGAGTCAATATTTGACTTCCACTTGAAAAT
65 GTCAAACATTTGTTATTTCTGACTCACTAGTAGAATCAATATTTGACTTCCACTTGAAAAT
602993 AAGTCAACATT
1 AAGTCAACATT
603004 GCAGATTTGG
Statistics
Matches: 123, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
125 11 0.09
126 111 0.90
127 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (125 bp):
AAGTCAACATTTGTTATCCCTGACTCATCAGTAGAGTCAATCCTTGACTTCCTCATGAAAAGAAG
TCAAACATTTGTTATTTCTGACTCACTAGTAGAATCAATATTTGACTTCCACTTGAAAAT
Found at i:603393 original size:35 final size:35
Alignment explanation
Indices: 603370--603638 Score: 378
Period size: 35 Copynumber: 7.7 Consensus size: 35
603360 ACAATTCAGG
* ** *
603370 CTTCATGGAAGAGTAGTGAAGTAAATCAATTCAGC
1 CTTCACGGAAGAGTAGTGAAGTAAAGAAATTCAAC
* *
603405 CTTCACGAAAGAGTAGTGAAGTAAAGAAATCCAAC
1 CTTCACGGAAGAGTAGTGAAGTAAAGAAATTCAAC
* ** *
603440 CTTCACGGAAGAGTAGTGAAGCAAATCAATTCAGC
1 CTTCACGGAAGAGTAGTGAAGTAAAGAAATTCAAC
* * *
603475 CTTCATGAAAGAGTAGCGAAGTAAA-AAATTCAAC
1 CTTCACGGAAGAGTAGTGAAGTAAAGAAATTCAAC
* *
603509 CTTCATGGAAGAGTAGTGAAGTAACGAAATTCAAC
1 CTTCACGGAAGAGTAGTGAAGTAAAGAAATTCAAC
603544 CTTCACGGAAGAGTAGTGAAGTAAAGAAATTCAAC
1 CTTCACGGAAGAGTAGTGAAGTAAAGAAATTCAAC
**
603579 CTTCACGGAAGAGTAGTGAAGTAAAGAAACCCAAC
1 CTTCACGGAAGAGTAGTGAAGTAAAGAAATTCAAC
603614 CTTCACGGAAGAGTAGTGAAGTAAA
1 CTTCACGGAAGAGTAGTGAAGTAAA
603639 TCATTCTTAG
Statistics
Matches: 208, Mismatches: 25, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
34 29 0.14
35 179 0.86
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (35 bp):
CTTCACGGAAGAGTAGTGAAGTAAAGAAATTCAAC
Found at i:603617 original size:139 final size:139
Alignment explanation
Indices: 603370--603638 Score: 403
Period size: 139 Copynumber: 1.9 Consensus size: 139
603360 ACAATTCAGG
** *
603370 CTTCATGGAAGAGTAGTGAAGTAAATCAATTCAGCCTTCACGAAAGAGTAGTGAAGTAAAGAAAT
1 CTTCATGGAAGAGTAGTGAAGTAAAGAAATTCAACCTTCACGAAAGAGTAGTGAAGTAAAGAAAT
** ** * *
603435 CCAACCTTCACGGAAGAGTAGTGAAGCAAATCAATTCAGCCTTCATGAAAGAGTAGCGAAGTAAA
66 CCAACCTTCACGGAAGAGTAGTGAAGCAAAGAAACCCAACCTTCACGAAAGAGTAGCGAAGTAAA
603500 AAATTCAAC
131 AAATTCAAC
* *
603509 CTTCATGGAAGAGTAGTGAAGTAACGAAATTCAACCTTCACGGAAGAGTAGTGAAGTAAAGAAAT
1 CTTCATGGAAGAGTAGTGAAGTAAAGAAATTCAACCTTCACGAAAGAGTAGTGAAGTAAAGAAAT
* * * *
603574 TCAACCTTCACGGAAGAGTAGTGAAGTAAAGAAACCCAACCTTCACGGAAGAGTAGTGAAGTAAA
66 CCAACCTTCACGGAAGAGTAGTGAAGCAAAGAAACCCAACCTTCACGAAAGAGTAGCGAAGTAAA
603639 TCATTCTTAG
Statistics
Matches: 115, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
139 115 1.00
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (139 bp):
CTTCATGGAAGAGTAGTGAAGTAAAGAAATTCAACCTTCACGAAAGAGTAGTGAAGTAAAGAAAT
CCAACCTTCACGGAAGAGTAGTGAAGCAAAGAAACCCAACCTTCACGAAAGAGTAGCGAAGTAAA
AAATTCAAC
Found at i:603847 original size:3 final size:3
Alignment explanation
Indices: 603839--603885 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
603829 CGTCAGAGAA
*
603839 TAT TAT TAT TAT TA- TAT TAT TGT TAT TAT ATAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT
603884 TA
1 TA
603886 CAAGACCCGA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:605022 original size:14 final size:15
Alignment explanation
Indices: 605005--605033 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
604995 ATATAATCGC
605005 TTAATTTT-AATATT
1 TTAATTTTAAATATT
605019 TTAATTTTAAATATT
1 TTAATTTTAAATATT
605034 ACTTTTGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTAATTTTAAATATT
Found at i:609069 original size:23 final size:23
Alignment explanation
Indices: 609039--609082 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
609029 TATGGGACCA
609039 TCTAAATACTTCCTTGATAGCCG
1 TCTAAATACTTCCTTGATAGCCG
* *
609062 TCTAAATACTTGCTTTATAGC
1 TCTAAATACTTCCTTGATAGC
609083 TATTGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (23 bp):
TCTAAATACTTCCTTGATAGCCG
Found at i:610915 original size:3 final size:3
Alignment explanation
Indices: 610909--610995 Score: 151
Period size: 3 Copynumber: 29.7 Consensus size: 3
610899 TTTATTATTT
610909 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
610957 AT- ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATT ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
610996 TTAAAATGTA
Statistics
Matches: 80, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
2 4 0.05
3 76 0.95
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:611505 original size:53 final size:53
Alignment explanation
Indices: 611352--612228 Score: 776
Period size: 53 Copynumber: 17.0 Consensus size: 53
611342 GTTTAAAGAT
* * * *
611352 ATTTGAGATAATACGGTTCCTTCGTGATGAGGACATCTGGCTACCAAAAGATG
1 ATTTGAGATAACACGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATG
* ** * **
611405 A-TTGAGATAACACGGTTCCTTCGTGATGATGATGTTTACCTATCTAAGGATG
1 ATTTGAGATAACACGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATG
* * *
611457 ATTGGAGATAACACGGTTCCTTCGTGATAAGGACATCTGGCTACCTAAGGATG
1 ATTTGAGATAACACGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATG
* * * * *
611510 ATTTTAGATAACTCGGTTCCTTCATGATGAGGACATCTGG---TCAAAAGAT-
1 ATTTGAGATAACACGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATG
* ** *** * * *
611559 AATTGAGATAACACAATTCCTTTACGATGAGGACTTCTGGCTATCAAAAGATG
1 ATTTGAGATAACACGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATG
* * * * * * *
611612 A-TTGAGATAAAATGGTTCCTTCGTGATAAAGATATTTGGCTATCTAATGATG
1 ATTTGAGATAACACGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATG
* * * *
611664 ATTTGAGATAACACAGTTCCTTCGTGATGAGGATATCTAGTTATCTAAGGATG
1 ATTTGAGATAACACGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATG
* ** ** * *
611717 ATTTGAGATAACTCAATTCCTTAATGATGAGGACATCTGG---TCAAAAGAT-
1 ATTTGAGATAACACGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATG
* * ** * * * *
611766 AATTGAGATAACACGATTCCTTCACGATGAGGACTTCTGGGTATCAAAAGATG
1 ATTTGAGATAACACGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATG
*
611819 A-TTGAGATAACACGGTTCCTTCGTGATGAGGACATTTGGCTATCTAAGGATG
1 ATTTGAGATAACACGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATG
* * * *
611871 ATTTAAGATTACACGATTCCATT-GTTATGAGGACATCTGGCTATCTAAGGATG
1 ATTTGAGATAACACGGTTCC-TTCGTGATGAGGACATCTGGCTATCTAAGGATG
* ** * * *
611924 ATTTGAGATAACTCGGTTCCTTTATGATGAGGAC-TTTGG-T-T-AAAAGAT-
1 ATTTGAGATAACACGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATG
* * * * * *
611972 AATTGAGATAACATGGTTCCTTCGCGATGA-GACTTATTGCTATCTAAGGATG
1 ATTTGAGATAACACGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATG
* * *
612024 ATTTGAGATAACACGGTTCCTTCATGATGGGGAAATCTGGCTATCTAAGGATG
1 ATTTGAGATAACACGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATG
* * * **
612077 ATTTGAGATAACTCGGTTCCTTCATGATGAGG-CATCTGG---TCAAAATAT-
1 ATTTGAGATAACACGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATG
* * * ** *
612125 AATTGAGATAACACGATTCCTTTGCAATGAGGACTTCT-GCTATCTAAGGATG
1 ATTTGAGATAACACGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATG
** * * *
612177 ATTTGAGATAACTTGGTTACTTCATGATGAGGACGTCTGGCTATCTAAGGAT
1 ATTTGAGATAACACGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGAT
612229 TTTTGTTTCT
Statistics
Matches: 659, Mismatches: 140, Indels: 50
0.78 0.16 0.06
Matches are distributed among these distances:
47 3 0.00
48 53 0.08
49 82 0.12
50 15 0.02
51 12 0.02
52 207 0.31
53 285 0.43
54 2 0.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (53 bp):
ATTTGAGATAACACGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATG
Done.