Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 4 of 135
Found at i:1205608 original size:16 final size:16
Alignment explanation
Indices: 1205576--1205608 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1205566 TATCATTATA
1205576 TGTTTAAATTTATAAT
1 TGTTTAAATTTATAAT
1205592 TGTTATAAATTTA-AAT
1 TGTT-TAAATTTATAAT
1205608 T
1 T
1205609 AAATTTTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (16 bp):
TGTTTAAATTTATAAT
Found at i:1207598 original size:72 final size:72
Alignment explanation
Indices: 1207511--1207657 Score: 285
Period size: 72 Copynumber: 2.0 Consensus size: 72
1207501 GATTTTAAAT
1207511 AAAATCCTCTTTTTTTTTTTCACTTTTTAACATACGGATATCCTTCACCGTATCATTAAAAAAAA
1 AAAATCCTCTTTTTTTTTTTCACTTTTTAACATACGGATATCCTTCACCGTATCATTAAAAAAAA
1207576 AATCTGA
66 AATCTGA
*
1207583 AAAATCCTGTTTTTTTTTTTCACTTTTTAACATACGGATATCCTTCACCGTATCATTAAAAAAAA
1 AAAATCCTCTTTTTTTTTTTCACTTTTTAACATACGGATATCCTTCACCGTATCATTAAAAAAAA
1207648 AATCTGA
66 AATCTGA
1207655 AAA
1 AAA
1207658 TATAAAACCT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.39
Consensus pattern (72 bp):
AAAATCCTCTTTTTTTTTTTCACTTTTTAACATACGGATATCCTTCACCGTATCATTAAAAAAAA
AATCTGA
Found at i:1214479 original size:46 final size:46
Alignment explanation
Indices: 1214371--1214526 Score: 255
Period size: 46 Copynumber: 3.5 Consensus size: 46
1214361 TACGTATGAT
* *
1214371 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
1214414 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGTTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1214460 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1214506 CACTTATCACTTTGTCACTTG
1 CACTTATCACTTTGTCACTTG
1214527 TCACTAATCA
Statistics
Matches: 104, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
43 10 0.10
44 5 0.05
45 20 0.19
46 69 0.66
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:1215591 original size:39 final size:42
Alignment explanation
Indices: 1215536--1215630 Score: 133
Period size: 39 Copynumber: 2.3 Consensus size: 42
1215526 NNNTTATTAA
*
1215536 AATTTTAAAATTTTTTTAAAAT-ACTTTTTTAA-TTT-TTTT
1 AATTTTAAAATATTTTTAAAATAACTTTTTTAATTTTATTTT
*
1215575 AATTTTAAAATATTTTTAAAATAATTTTTTTAATTTTTATTTT
1 AATTTTAAAATATTTTTAAAATAACTTTTTTAA-TTTTATTTT
1215618 AATTTTTAAAATA
1 AA-TTTTAAAATA
1215631 AATTTTTGGT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
39 21 0.43
40 9 0.18
42 3 0.06
43 6 0.12
44 10 0.20
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (42 bp):
AATTTTAAAATATTTTTAAAATAACTTTTTTAATTTTATTTT
Found at i:1229168 original size:15 final size:15
Alignment explanation
Indices: 1229148--1229178 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1229138 AATATTTTTT
*
1229148 AAATAAATTATAAAA
1 AAATAAATAATAAAA
1229163 AAATAAATAATAAAA
1 AAATAAATAATAAAA
1229178 A
1 A
1229179 CTCCAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATAAATAATAAAA
Found at i:1231092 original size:16 final size:16
Alignment explanation
Indices: 1231073--1231103 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1231063 TTATAAATGA
1231073 TTAAATATATATATTT
1 TTAAATATATATATTT
1231089 TTAAATATATATATT
1 TTAAATATATATATT
1231104 AATTTTTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAAATATATATATTT
Found at i:1256042 original size:2 final size:2
Alignment explanation
Indices: 1256035--1256063 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1256025 TTTCGCTAAC
1256035 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1256064 GTTCTGCTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1256363 original size:25 final size:23
Alignment explanation
Indices: 1256305--1256365 Score: 61
Period size: 25 Copynumber: 2.6 Consensus size: 23
1256295 AATATTCAAA
* *
1256305 AAATAAAAAAAATTCAAAATTTT
1 AAATAAAAAAAGTTCAAAATTTC
*
1256328 AAA-AATTAAAAGTTCATAAAATTTC
1 AAATAA-AAAAAGTTC--AAAATTTC
1256353 AAATAAAAAAAGT
1 AAATAAAAAAAGT
1256366 ATGAAGTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
22 2 0.07
23 10 0.33
25 16 0.53
26 2 0.07
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (23 bp):
AAATAAAAAAAGTTCAAAATTTC
Found at i:1261387 original size:30 final size:31
Alignment explanation
Indices: 1261330--1261404 Score: 125
Period size: 30 Copynumber: 2.5 Consensus size: 31
1261320 TTACAATTTG
1261330 GTCACTGAACTATTCAAAAATTTTTATTTAA
1 GTCACTGAACTATTCAAAAATTTTTATTTAA
*
1261361 GTCACTAAACTATTCAAAAA-TTTTATTTAA
1 GTCACTGAACTATTCAAAAATTTTTATTTAA
*
1261391 GTCATTGAACTATT
1 GTCACTGAACTATT
1261405 AAGTTTTTCT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 22 0.54
31 19 0.46
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (31 bp):
GTCACTGAACTATTCAAAAATTTTTATTTAA
Found at i:1267841 original size:25 final size:25
Alignment explanation
Indices: 1267812--1267863 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
1267802 AAAATTGGTA
*
1267812 AGACATTTTCCATT-TTTCTCTAAGC
1 AGACATTTTCCATTCTCT-TCTAAGC
1267837 AGACATTTTCCATTCTCTTCTAAGC
1 AGACATTTTCCATTCTCTTCTAAGC
1267862 AG
1 AG
1267864 CAGACATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (25 bp):
AGACATTTTCCATTCTCTTCTAAGC
Found at i:1272760 original size:14 final size:15
Alignment explanation
Indices: 1272738--1272814 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
1272728 TTACCAAACA
1272738 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
1272752 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
1272767 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
1272787 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
1272801 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
1272815 ACTGCCAAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:1272779 original size:20 final size:20
Alignment explanation
Indices: 1272754--1272793 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1272744 AATATTTTCC
*
1272754 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
1272774 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
1272794 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:1272799 original size:34 final size:35
Alignment explanation
Indices: 1272742--1272808 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
1272732 CAAACACCAG
*
1272742 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
1272777 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
1272809 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:1272815 original size:14 final size:14
Alignment explanation
Indices: 1272777--1272816 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1272767 ACAGAAAAGT
*
1272777 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
1272791 AAATCATTTTACGG
1 AAAACATTTTACAG
1272805 AAAACATTTTAC
1 AAAACATTTTAC
1272817 TGCCAAACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:1287960 original size:47 final size:47
Alignment explanation
Indices: 1287907--1288000 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
1287897 AAACTGAGCA
*
1287907 GAAGTATTAATGGATAGATTTGCAAAATAGCTAACAATGAATGCACT
1 GAAGTATTAATGGATAGATCTGCAAAATAGCTAACAATGAATGCACT
1287954 GAAGTATTAATGGATAGATCTGCAAAATAGCTAACAATGAATGCACT
1 GAAGTATTAATGGATAGATCTGCAAAATAGCTAACAATGAATGCACT
1288001 TACTTTCTCA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.27
Consensus pattern (47 bp):
GAAGTATTAATGGATAGATCTGCAAAATAGCTAACAATGAATGCACT
Found at i:1313689 original size:6 final size:6
Alignment explanation
Indices: 1313678--1313715 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
1313668 TTAAAATAGT
*
1313678 TTAGGG TTAGGG TTACGG TTAGGG TTAGGG TTAGGG TT
1 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TT
1313716 TTGTTAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.16, C:0.03, G:0.45, T:0.37
Consensus pattern (6 bp):
TTAGGG
Found at i:1313830 original size:34 final size:35
Alignment explanation
Indices: 1313766--1313882 Score: 134
Period size: 34 Copynumber: 3.4 Consensus size: 35
1313756 TTTTAAAAAA
* * *
1313766 TAAATTAGGGTTT-GGAGTTTTTTTAAAAATTAAT
1 TAAATTAGGGTTTATGAGTGTTTTAAAAAATTAAT
* *
1313800 TAAGTTAGGTTTTATG-G-GTTTTAAATAAATTAAT
1 TAAATTAGGGTTTATGAGTGTTTTAAA-AAATTAAT
* *
1313834 TAAATTAGGGTTTA-GAGTTTTTTTAAAAATTAAT
1 TAAATTAGGGTTTATGAGTGTTTTAAAAAATTAAT
1313868 TAAATTAGGGTTTAT
1 TAAATTAGGGTTTAT
1313883 TTTTAAAAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
33 7 0.10
34 55 0.80
35 7 0.10
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (35 bp):
TAAATTAGGGTTTATGAGTGTTTTAAAAAATTAAT
Found at i:1314274 original size:125 final size:124
Alignment explanation
Indices: 1313974--1314346 Score: 507
Period size: 124 Copynumber: 3.0 Consensus size: 124
1313964 GTAGTTTCAA
* * *
1313974 AAAAATTAATTTTGAGAAGACAGTTCTGAAAAAATGGTGTCAAAAACGCTTTAAGCAAGATGCAC
1 AAAAA-TAATTTTGAGAAGACGGTTCTGAACAAATGGTGTCAAAAACGCTTCAAGCAAGATGCAC
** * *
1314039 TGTCAGCAAAAATATTGAAAAAAGCTCTCATATGGACGCTCTTTTTTTACATTAGTTCTTG
65 TGTCAGCAAAAATA-TGAAAAAAGCTCTCACGTGGACGCTCTTTTTATACAGTAGTTCTTG
* * * *
1314100 -GAAATAATTTTGAGAAGACGGTTTTGAACAAATGGTGTCAAAAATGCTTCAAGCAAGATGTACT
1 AAAAATAATTTTGAGAAGACGGTTCTGAACAAATGGTGTCAAAAACGCTTCAAGCAAGATGCACT
*
1314164 GTCAGCAAAAATACTGAAAAAAAGCTCTCACGTGG-CACTCTTTTTATACAGTAGTTCTTG
66 GTCAGCAAAAATA-TG-AAAAAAGCTCTCACGTGGACGCTCTTTTTATACAGTAGTTCTTG
* * * *
1314224 AAAAATAATTTTCAGAAGATGGTTCTGAACAAATGGCGTCAAAAACGCTTCAAGCAGGATGCACT
1 AAAAATAATTTTGAGAAGACGGTTCTGAACAAATGGTGTCAAAAACGCTTCAAGCAAGATGCACT
* * * *
1314289 GTTAGCAAAATTGATGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTTCT
66 GTCAGCAAAAAT-ATGAAAAAAGCTCTCACGTGGACGCTCTTTTTATACAGTAGTTCT
1314347 GGTTTGGCCT
Statistics
Matches: 217, Mismatches: 26, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
124 108 0.50
125 108 0.50
126 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.29
Consensus pattern (124 bp):
AAAAATAATTTTGAGAAGACGGTTCTGAACAAATGGTGTCAAAAACGCTTCAAGCAAGATGCACT
GTCAGCAAAAATATGAAAAAAGCTCTCACGTGGACGCTCTTTTTATACAGTAGTTCTTG
Found at i:1317765 original size:18 final size:18
Alignment explanation
Indices: 1317739--1317781 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1317729 GACTGAGAAA
* *
1317739 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
1317757 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
1317775 AGGATAC
1 AGGATAC
1317782 GCACCTAGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.28, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:1318376 original size:7 final size:7
Alignment explanation
Indices: 1318366--1318397 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
1318356 TTATATACAT
1318366 AATACTA
1 AATACTA
1318373 AATACTA
1 AATACTA
1318380 AATACTA
1 AATACTA
1318387 AATACTA
1 AATACTA
1318394 AATA
1 AATA
1318398 TGAAACGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:1318862 original size:27 final size:27
Alignment explanation
Indices: 1318824--1318875 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1318814 AAATATATAT
*
1318824 TTTTTATTTTTTTAATTTTAAAATACA
1 TTTTAATTTTTTTAATTTTAAAATACA
*
1318851 TTTTAATTTTTTTATTTTTAAAATA
1 TTTTAATTTTTTTAATTTTAAAATA
1318876 AAATTTTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTTAATTTTTTTAATTTTAAAATACA
Found at i:1319633 original size:20 final size:19
Alignment explanation
Indices: 1319583--1319635 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
1319573 AATAAAAATT
1319583 AATTAAAATTACATAATAAA
1 AATTAAAATTA-ATAATAAA
* * *
1319603 AAATATTAATTAATATTCAAA
1 AATTA-AAATTAATAAT-AAA
1319624 AATTAAAATTAA
1 AATTAAAATTAA
1319636 CCCGACCATT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (19 bp):
AATTAAAATTAATAATAAA
Found at i:1322286 original size:14 final size:14
Alignment explanation
Indices: 1322263--1322292 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1322253 TTTGATGTAT
*
1322263 TATATTTATAAAAA
1 TATATATATAAAAA
1322277 TATATATATAAAAA
1 TATATATATAAAAA
1322291 TA
1 TA
1322293 AAAAATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TATATATATAAAAA
Found at i:1322915 original size:24 final size:24
Alignment explanation
Indices: 1322888--1322936 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1322878 ATGGTAAAAC
*
1322888 ATAATGCTAAAATCATAATATATT
1 ATAATACTAAAATCATAATATATT
* *
1322912 ATAATACTAAAATCTTAGTATATT
1 ATAATACTAAAATCATAATATATT
1322936 A
1 A
1322937 CTTTAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (24 bp):
ATAATACTAAAATCATAATATATT
Found at i:1330499 original size:561 final size:562
Alignment explanation
Indices: 1329764--1330886 Score: 2239
Period size: 561 Copynumber: 2.0 Consensus size: 562
1329754 GTTAAAATAA
1329764 CAAACGTCAAGCTAACATGAATAATAAATTTAACCCTCAAATTTTACATATTATATCAATTTAGT
1 CAAACGTCAAGCTAACATGAATAATAAATTTAACCCTCAAATTTTACATATTATATCAATTTAGT
1329829 CATGATTTAAAAATATTAACCCTCAAAATTTATAAATAATCTCAATTTGATCCTAATTCTAAAAA
66 CATGATTTAAAAATATTAACCCTCAAAATTTATAAATAATCTCAATTTGATCCTAATTCTAAAAA
1329894 ATTCAAAGAAATCTATAAAAATACATAAATATTTTAAATATATAATAATAATTTTAAATTTTATA
131 ATTCAAAGAAATCTATAAAAATACATAAATATTTTAAATATATAATAATAATTTTAAATTTTATA
1329959 TCAGTATTTATATTAATATTAAATAAATATAATTATAGTATTATATTTGAAAAGTATGACTAAAT
196 TCAGTATTTATATTAATATTAAATAAATATAATTATAGTATTATATTTGAAAAGTATGACTAAAT
1330024 TCCAAATTCTCAAAAAGTACATGGATTTATCGCATATTTTACCCAAAAAGTTCTAACCACGACCT
261 TCCAAATTCTCAAAAAGTACATGGATTTATCGCATATTTTACCCAAAAAGTTCTAACCACGACCT
1330089 AGTCCGGTTTAAATCATGGCAAATATAAGTTCGGTTCTTTATGTTTTTCATTTACTTAAATGCTG
326 AGTCCGGTTTAAATCATGGCAAATATAAGTTCGGTTCTTTATGTTTTTCATTTACTTAAATGCTG
1330154 AAATTTGTACCGATCAATATGGAACGAGAATGAAAGCTTGGAAATATTCAAAAAAAACCTTTGGA
391 AAATTTGTACCGATCAATATGGAACGAGAATGAAAGCTTGGAAATATTCAAAAAAAACCTTTGGA
1330219 GCTTCAACTTTTTCTGAATTTACTTGCAGACTAACACCAAATTGTATCAAATTTTCAACCTGTTT
456 GCTTCAACTTTTTCTGAATTTACTTGCAGACTAACACCAAATTGTATCAAATTTTCAACCTGTTT
1330284 GAAAATTCTTTCCTTTACAAGAATTACGTTTGGCTTTAATCG
521 GAAAATTCTTTCCTTTACAAGAATTACGTTTGGCTTTAATCG
1330326 CAAACGTCAAG-TAACATGAATAATAAATTTAACCCTCAAATTTTACATATTATATCAATTTAGT
1 CAAACGTCAAGCTAACATGAATAATAAATTTAACCCTCAAATTTTACATATTATATCAATTTAGT
1330390 CATGATTTAAAAATATTAACCCTCAAAATTTATAAATAATCTCAATTTGATCCTAATTCTAAAAA
66 CATGATTTAAAAATATTAACCCTCAAAATTTATAAATAATCTCAATTTGATCCTAATTCTAAAAA
1330455 ATTCAAAGAAATCTATAAAAATACATAAATATTTTAAATATATAATAATAATTTTAAATTTTATA
131 ATTCAAAGAAATCTATAAAAATACATAAATATTTTAAATATATAATAATAATTTTAAATTTTATA
1330520 TCAGTATTTATATTAATATTAAATAAATATAATTATAGTATTATATTTGAAAAGTATGACTAAAT
196 TCAGTATTTATATTAATATTAAATAAATATAATTATAGTATTATATTTGAAAAGTATGACTAAAT
1330585 TCCAAATTCTCAAAAAGTACATGGATTTATCGCATATTTTACCCAAAAAGTTCTAACCACGACCT
261 TCCAAATTCTCAAAAAGTACATGGATTTATCGCATATTTTACCCAAAAAGTTCTAACCACGACCT
1330650 AGTCCGGTTTAAATCATGGCAAATATAAGTTCGGTTCTTTATGTTTTTCATTTACTTAAATGCTG
326 AGTCCGGTTTAAATCATGGCAAATATAAGTTCGGTTCTTTATGTTTTTCATTTACTTAAATGCTG
1330715 AAATTTGTACCGATCAATATGGAACGAGAATGAAAGCTTGGAAATATTCAAAAAAAACCTTTGGA
391 AAATTTGTACCGATCAATATGGAACGAGAATGAAAGCTTGGAAATATTCAAAAAAAACCTTTGGA
1330780 GCTTCAACTTTTTCTGAATTTACTTGCAGACTAACACCAAATTGTATCAAATTTTCAACCTGTTT
456 GCTTCAACTTTTTCTGAATTTACTTGCAGACTAACACCAAATTGTATCAAATTTTCAACCTGTTT
1330845 GAAAATTCTTTCCTTTACAAGAATTACGTTTGGCTTTAATCG
521 GAAAATTCTTTCCTTTACAAGAATTACGTTTGGCTTTAATCG
1330887 TATGCATCAT
Statistics
Matches: 561, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
561 550 0.98
562 11 0.02
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (562 bp):
CAAACGTCAAGCTAACATGAATAATAAATTTAACCCTCAAATTTTACATATTATATCAATTTAGT
CATGATTTAAAAATATTAACCCTCAAAATTTATAAATAATCTCAATTTGATCCTAATTCTAAAAA
ATTCAAAGAAATCTATAAAAATACATAAATATTTTAAATATATAATAATAATTTTAAATTTTATA
TCAGTATTTATATTAATATTAAATAAATATAATTATAGTATTATATTTGAAAAGTATGACTAAAT
TCCAAATTCTCAAAAAGTACATGGATTTATCGCATATTTTACCCAAAAAGTTCTAACCACGACCT
AGTCCGGTTTAAATCATGGCAAATATAAGTTCGGTTCTTTATGTTTTTCATTTACTTAAATGCTG
AAATTTGTACCGATCAATATGGAACGAGAATGAAAGCTTGGAAATATTCAAAAAAAACCTTTGGA
GCTTCAACTTTTTCTGAATTTACTTGCAGACTAACACCAAATTGTATCAAATTTTCAACCTGTTT
GAAAATTCTTTCCTTTACAAGAATTACGTTTGGCTTTAATCG
Found at i:1334602 original size:83 final size:84
Alignment explanation
Indices: 1334489--1334656 Score: 329
Period size: 83 Copynumber: 2.0 Consensus size: 84
1334479 TTATATGATT
1334489 ATTTAATTTATAAAATGTTTATTTTAAGTTGTTTAGTGATGAATTATATTTGTGAAATTAATTGA
1 ATTTAATTTATAAAATGTTTATTTTAAGTTGTTTAGTGATGAATTATATTTGTGAAATTAATTGA
1334554 TTAAATAATATTTTATTTG
66 TTAAATAATATTTTATTTG
1334573 ATTTAATTTAT-AAATGTTTATTTTAAGTTGTTTAGTGATGAATTATATTTGTGAAATTAATTGA
1 ATTTAATTTATAAAATGTTTATTTTAAGTTGTTTAGTGATGAATTATATTTGTGAAATTAATTGA
1334637 TTAAATAATATTTTATTTG
66 TTAAATAATATTTTATTTG
1334656 A
1 A
1334657 GATTTATTTA
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
83 73 0.87
84 11 0.13
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (84 bp):
ATTTAATTTATAAAATGTTTATTTTAAGTTGTTTAGTGATGAATTATATTTGTGAAATTAATTGA
TTAAATAATATTTTATTTG
Found at i:1341835 original size:2 final size:2
Alignment explanation
Indices: 1341828--1341860 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1341818 TTGGTTCCTA
*
1341828 TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1341861 TTCCTTTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:1355082 original size:3 final size:3
Alignment explanation
Indices: 1355074--1355098 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1355064 TTTTCCCTTA
1355074 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
1355099 AGCATCCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:1371726 original size:16 final size:16
Alignment explanation
Indices: 1371696--1371735 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1371686 ATATTTCATG
*
1371696 CATTTCAT-CAATAAT
1 CATTTCATAAAATAAT
1371711 CATTTCATAAAATAAT
1 CATTTCATAAAATAAT
*
1371727 TATTTCATA
1 CATTTCATA
1371736 TATTTCATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (16 bp):
CATTTCATAAAATAAT
Found at i:1372229 original size:6 final size:6
Alignment explanation
Indices: 1372192--1372234 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
1372182 CCAAACACAC
* *
1372192 CAGTAAA CAGTAA TCAGTAA CGGTAG CAGTAA CAGTAA CAGTA
1 CAGT-AA CAGTAA -CAGTAA CAGTAA CAGTAA CAGTAA CAGTA
1372235 TTCAACACAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
6 21 0.68
7 10 0.32
ACGTcount: A:0.44, C:0.16, G:0.21, T:0.19
Consensus pattern (6 bp):
CAGTAA
Found at i:1382370 original size:2 final size:2
Alignment explanation
Indices: 1382363--1382389 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1382353 CTTCTTTTAC
1382363 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 A
1382390 AAGTTGAGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1407866 original size:25 final size:25
Alignment explanation
Indices: 1407832--1407881 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1407822 TAAATCTTAC
*
1407832 CTTAGTTTTTTATTTTATTGAAAAT
1 CTTACTTTTTTATTTTATTGAAAAT
1407857 CTTACTTTTTTATTTTATTGAAAAT
1 CTTACTTTTTTATTTTATTGAAAAT
1407882 TTTGGAAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.60
Consensus pattern (25 bp):
CTTACTTTTTTATTTTATTGAAAAT
Found at i:1408609 original size:24 final size:24
Alignment explanation
Indices: 1408561--1408610 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1408551 AGATTCCCAT
* *
1408561 TATTAGCTCTCATGAGCATCTCGA
1 TATTAGCTCTCATGAGCAACCCGA
1408585 TATTAGCTCT-ATTGAGCAACCCGA
1 TATTAGCTCTCA-TGAGCAACCCGA
1408609 TA
1 TA
1408611 CATGGCTCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (24 bp):
TATTAGCTCTCATGAGCAACCCGA
Found at i:1408819 original size:11 final size:11
Alignment explanation
Indices: 1408805--1408830 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1408795 AGACCAAATT
1408805 GAATAGGTGAA
1 GAATAGGTGAA
1408816 GAATAGGTGAA
1 GAATAGGTGAA
1408827 GAAT
1 GAAT
1408831 TGACGGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.35, T:0.19
Consensus pattern (11 bp):
GAATAGGTGAA
Found at i:1409399 original size:33 final size:33
Alignment explanation
Indices: 1409357--1409493 Score: 105
Period size: 33 Copynumber: 4.1 Consensus size: 33
1409347 AATTGATGGA
* *
1409357 TAAGACCATAACTGGGTTATGGCACTATGAACG
1 TAAGACCATAACTGGGCTATGGCACTATGAATG
** * * * * *
1409390 TAAGACCATAGTTGGACCATGGCAGTTTTTACATG
1 TAAGACCATAACTGGGCTATGGCA-CTATGA-ATG
* * *
1409425 TAAGACCATAGCTGGGCTATGGCATTCTG-ATG
1 TAAGACCATAACTGGGCTATGGCACTATGAATG
* * *
1409457 ATAAGACCATAACTTGGTTATGGCACTACGAATG
1 -TAAGACCATAACTGGGCTATGGCACTATGAATG
1409491 TAA
1 TAA
1409494 AGGATGAATG
Statistics
Matches: 80, Mismatches: 20, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
32 3 0.04
33 45 0.56
34 9 0.11
35 23 0.29
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (33 bp):
TAAGACCATAACTGGGCTATGGCACTATGAATG
Found at i:1410382 original size:25 final size:25
Alignment explanation
Indices: 1410348--1410397 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1410338 TAAATCTTAC
*
1410348 CTTAGTTTTTTATTTTATTGAAAAT
1 CTTACTTTTTTATTTTATTGAAAAT
1410373 CTTACTTTTTTATTTTATTGAAAAT
1 CTTACTTTTTTATTTTATTGAAAAT
1410398 TTTGGAAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.60
Consensus pattern (25 bp):
CTTACTTTTTTATTTTATTGAAAAT
Found at i:1411125 original size:24 final size:24
Alignment explanation
Indices: 1411077--1411126 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1411067 AGATTCCCAT
* *
1411077 TATTAGCTCTCATGAGCATCTCGA
1 TATTAGCTCTCATGAGCAACCCGA
1411101 TATTAGCTCT-ATTGAGCAACCCGA
1 TATTAGCTCTCA-TGAGCAACCCGA
1411125 TA
1 TA
1411127 CATGGCTCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (24 bp):
TATTAGCTCTCATGAGCAACCCGA
Found at i:1411463 original size:11 final size:11
Alignment explanation
Indices: 1411449--1411474 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1411439 AGACCAAATT
1411449 GAATAGGTGAA
1 GAATAGGTGAA
1411460 GAATAGGTGAA
1 GAATAGGTGAA
1411471 GAAT
1 GAAT
1411475 TGACGGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.35, T:0.19
Consensus pattern (11 bp):
GAATAGGTGAA
Found at i:1412043 original size:33 final size:33
Alignment explanation
Indices: 1412001--1412137 Score: 105
Period size: 33 Copynumber: 4.1 Consensus size: 33
1411991 AATTGATGGA
* *
1412001 TAAGACCATAACTGGGTTATGGCACTATGAACG
1 TAAGACCATAACTGGGCTATGGCACTATGAATG
** * * * * *
1412034 TAAGACCATAGTTGGACCATGGCAGTTTTTACATG
1 TAAGACCATAACTGGGCTATGGCA-CTATGA-ATG
* * *
1412069 TAAGACCATAGCTGGGCTATGGCATTCTG-ATG
1 TAAGACCATAACTGGGCTATGGCACTATGAATG
* * *
1412101 ATAAGACCATAACTTGGTTATGGCACTACGAATG
1 -TAAGACCATAACTGGGCTATGGCACTATGAATG
1412135 TAA
1 TAA
1412138 AGGATGAATG
Statistics
Matches: 80, Mismatches: 20, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
32 3 0.04
33 45 0.56
34 9 0.11
35 23 0.29
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (33 bp):
TAAGACCATAACTGGGCTATGGCACTATGAATG
Found at i:1413418 original size:27 final size:26
Alignment explanation
Indices: 1413388--1413476 Score: 119
Period size: 25 Copynumber: 3.5 Consensus size: 26
1413378 TGGATCTCTA
* *
1413388 GAGCTTCCCGATTAAAGGCTCTTTTAT
1 GAGCTTCCCGATTAATGGCTCTTTT-G
1413415 GAGCTTCCCGATTAATGGCT-TTTTG
1 GAGCTTCCCGATTAATGGCTCTTTTG
*
1413440 GAGCTTCCCGATTAATGGCTC-TCTG
1 GAGCTTCCCGATTAATGGCTCTTTTG
*
1413465 GAGCTTTCCGAT
1 GAGCTTCCCGAT
1413477 ATTTGGCTCG
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
25 34 0.60
26 4 0.07
27 19 0.33
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (26 bp):
GAGCTTCCCGATTAATGGCTCTTTTG
Found at i:1413485 original size:25 final size:25
Alignment explanation
Indices: 1413377--1413476 Score: 110
Period size: 25 Copynumber: 3.9 Consensus size: 25
1413367 GTCTCGATAT
* *
1413377 ATGGATCTCTAGAGCTTCCCGATTA
1 ATGGCTCTCTGGAGCTTCCCGATTA
* * *
1413402 AAGGCTCTTTTATGAGCTTCCCGATTA
1 ATGGCTC-TCT-GGAGCTTCCCGATTA
* *
1413429 ATGGCTTTTTGGAGCTTCCCGATTA
1 ATGGCTCTCTGGAGCTTCCCGATTA
*
1413454 ATGGCTCTCTGGAGCTTTCCGAT
1 ATGGCTCTCTGGAGCTTCCCGAT
1413477 ATTTGGCTCG
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
25 39 0.62
26 5 0.08
27 19 0.30
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (25 bp):
ATGGCTCTCTGGAGCTTCCCGATTA
Found at i:1413494 original size:50 final size:51
Alignment explanation
Indices: 1413440--1413553 Score: 119
Period size: 50 Copynumber: 2.3 Consensus size: 51
1413430 TGGCTTTTTG
* * * *
1413440 GAGCTTCCCGATTA-ATGGCTCTC-TGGAGCTTTCC-GATATTTGGCTCGCAA
1 GAGCTTCCCGATTACATAGCTCACAT-GAGC-TTCCTGATATATGGCTCGAAA
* *
1413490 GAGCTTCTCG-TTACATAGCTCACATGAGCTTCCTGTTATATGGCTCGAAA
1 GAGCTTCCCGATTACATAGCTCACATGAGCTTCCTGATATATGGCTCGAAA
*
1413540 GAGCTTCCTGATTA
1 GAGCTTCCCGATTA
1413554 TATGCTCGAT
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
49 7 0.13
50 41 0.79
51 4 0.08
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (51 bp):
GAGCTTCCCGATTACATAGCTCACATGAGCTTCCTGATATATGGCTCGAAA
Found at i:1413560 original size:25 final size:25
Alignment explanation
Indices: 1413480--1413562 Score: 82
Period size: 25 Copynumber: 3.3 Consensus size: 25
1413470 TTCCGATATT
* *
1413480 TGGCTCGCAAGAGCTT-CTCGTTACA
1 TGGCTCGAAAGAGCTTCCT-GTTATA
* *
1413505 TAGCTC-ACATGAGCTTCCTGTTATA
1 TGGCTCGA-AAGAGCTTCCTGTTATA
1413530 TGGCTCGAAAGAGCTTCCTGATTATA
1 TGGCTCGAAAGAGCTTCCTG-TTATA
1413556 T-GCTCGA
1 TGGCTCGA
1413563 TTTGGCATAC
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
25 39 0.81
26 9 0.19
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (25 bp):
TGGCTCGAAAGAGCTTCCTGTTATA
Found at i:1414035 original size:11 final size:11
Alignment explanation
Indices: 1414019--1414043 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1414009 CGTAAAGGTT
1414019 GGAAGCTGGTC
1 GGAAGCTGGTC
1414030 GGAAGCTGGTC
1 GGAAGCTGGTC
1414041 GGA
1 GGA
1414044 GCTACATCGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.16, G:0.48, T:0.16
Consensus pattern (11 bp):
GGAAGCTGGTC
Found at i:1416347 original size:22 final size:20
Alignment explanation
Indices: 1416301--1416347 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
1416291 TTATTAATTG
* *
1416301 TGAATATTAAAAATATATGT
1 TGAAAATTAAAAATATATAT
1416321 T-AAAATTAAACAATATATAT
1 TGAAAATTAAA-AATATATAT
1416341 ATGAAAA
1 -TGAAAA
1416348 AAGGGGCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 8 0.36
20 9 0.41
21 1 0.05
22 4 0.18
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.34
Consensus pattern (20 bp):
TGAAAATTAAAAATATATAT
Found at i:1418286 original size:13 final size:14
Alignment explanation
Indices: 1418264--1418292 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1418254 TATTTTTGTT
1418264 TTTTACTAATATAA
1 TTTTACTAATATAA
1418278 TTTTA-TAATATAA
1 TTTTACTAATATAA
1418291 TT
1 TT
1418293 GTTCAAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTTACTAATATAA
Found at i:1418812 original size:18 final size:20
Alignment explanation
Indices: 1418777--1418813 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
1418767 ATATAATTTT
*
1418777 AAAATATATATAATACATCA
1 AAAATATATATAAAACATCA
1418797 AAAATAT-TA-AAAACATC
1 AAAATATATATAAAACATC
1418814 GAAATAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 7 0.44
19 2 0.12
20 7 0.44
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.27
Consensus pattern (20 bp):
AAAATATATATAAAACATCA
Found at i:1419054 original size:61 final size:61
Alignment explanation
Indices: 1418988--1419111 Score: 239
Period size: 61 Copynumber: 2.0 Consensus size: 61
1418978 AACAACAAAA
1418988 TAGTAGCAACATAATAGTAAAATGGTAGCAAAATAGGGAGAAAACAATAAGAAAATAATAT
1 TAGTAGCAACATAATAGTAAAATGGTAGCAAAATAGGGAGAAAACAATAAGAAAATAATAT
*
1419049 TAGTAGCAACATAATAGTAAAATGGTAGCAAAATAGTGAGAAAACAATAAGAAAATAATAT
1 TAGTAGCAACATAATAGTAAAATGGTAGCAAAATAGGGAGAAAACAATAAGAAAATAATAT
1419110 TA
1 TA
1419112 AAAACAAAAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.56, C:0.06, G:0.17, T:0.21
Consensus pattern (61 bp):
TAGTAGCAACATAATAGTAAAATGGTAGCAAAATAGGGAGAAAACAATAAGAAAATAATAT
Found at i:1427923 original size:37 final size:37
Alignment explanation
Indices: 1427881--1427955 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
1427871 AGCAAAAAAA
1427881 ACTTGGTTTAAGGTTGTCTTTAACTGAGACTTGGTTT
1 ACTTGGTTTAAGGTTGTCTTTAACTGAGACTTGGTTT
1427918 ACTTGGTTTAAGGTTGTCTTTAACTGAGACTTGGTTT
1 ACTTGGTTTAAGGTTGTCTTTAACTGAGACTTGGTTT
1427955 A
1 A
1427956 GTTAGAATTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.20, C:0.11, G:0.24, T:0.45
Consensus pattern (37 bp):
ACTTGGTTTAAGGTTGTCTTTAACTGAGACTTGGTTT
Found at i:1429488 original size:29 final size:29
Alignment explanation
Indices: 1429433--1429488 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
1429423 GTTTAATGGG
* *
1429433 CAATTGTATACATGAACTTTGGTTTTGTA
1 CAATTGTATACATGAAATTTGGATTTGTA
* * *
1429462 CAATTTTATACATTAAATTTTGATTTG
1 CAATTGTATACATGAAATTTGGATTTG
1429489 ATCCAATTCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.48
Consensus pattern (29 bp):
CAATTGTATACATGAAATTTGGATTTGTA
Found at i:1432531 original size:30 final size:30
Alignment explanation
Indices: 1432497--1432559 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
1432487 ACTTATTTTA
1432497 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* *
1432527 TTGTTAATTTTGTTATTATTTTAGAGCCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
1432557 TTG
1 TTG
1432560 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.05, G:0.13, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:1436000 original size:11 final size:12
Alignment explanation
Indices: 1435983--1436014 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1435973 GTCCATTATA
1435983 CTTTCTTTTTCT
1 CTTTCTTTTTCT
1435995 -TTTC-TTTTCT
1 CTTTCTTTTTCT
1436005 CTTTCTTTTT
1 CTTTCTTTTT
1436015 TTTGCTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 6 0.33
11 8 0.44
12 4 0.22
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (12 bp):
CTTTCTTTTTCT
Found at i:1436009 original size:16 final size:15
Alignment explanation
Indices: 1435984--1436017 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1435974 TCCATTATAC
*
1435984 TTTCTTTTTCTTTTCT
1 TTTCTCTTTCTTTT-T
1436000 TTTCTCTTTCTTTTT
1 TTTCTCTTTCTTTTT
1436015 TTT
1 TTT
1436018 GCTTATTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTCTCTTTCTTTTT
Found at i:1438643 original size:6 final size:6
Alignment explanation
Indices: 1438589--1438624 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
1438579 TTAATAAATT
*
1438589 TATTTA TATTTA TATTTA TATTTA TATTTA TTTTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
1438625 ATTCCTGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TATTTA
Found at i:1440930 original size:14 final size:15
Alignment explanation
Indices: 1440911--1440943 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
1440901 AGAATAGATT
1440911 TTTAATTAA-ATAAA
1 TTTAATTAATATAAA
1440925 TTTAATTAATTATAAA
1 TTTAATTAA-TATAAA
1440941 TTT
1 TTT
1440944 TAAACCCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
16 8 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTAATTAATATAAA
Found at i:1447077 original size:20 final size:20
Alignment explanation
Indices: 1447037--1447097 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 20
1447027 TACTCCAATC
* *
1447037 TATTTTT-TAAATTTTGAAT
1 TATTTTTATAATTTTTAAAT
1447056 T-TCTTTTAT--TTTTTAAA-
1 TAT-TTTTATAATTTTTAAAT
1447073 TATTTTTATAATTTTTAAAT
1 TATTTTTATAATTTTTAAAT
1447093 TATTT
1 TATTT
1447098 ATTAATATAG
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
17 7 0.21
18 8 0.24
19 13 0.38
20 6 0.18
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
TATTTTTATAATTTTTAAAT
Found at i:1447103 original size:19 final size:19
Alignment explanation
Indices: 1447065--1447103 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1447055 TTTCTTTTAT
*
1447065 TTTTTAAATATTTTTATAA
1 TTTTTAAATATTTATATAA
1447084 TTTTTAAATTATTTAT-TAA
1 TTTTTAAA-TATTTATATAA
1447103 T
1 T
1447104 ATAGCATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTTAAATATTTATATAA
Found at i:1448457 original size:99 final size:99
Alignment explanation
Indices: 1448286--1448503 Score: 436
Period size: 99 Copynumber: 2.2 Consensus size: 99
1448276 TAATAATATT
1448286 AAAAGAAATTCACACATTAATTAAGGCGGATTATGTTCTTGCTTTGAATCATTAGTGTAATTTTT
1 AAAAGAAATTCACACATTAATTAAGGCGGATTATGTTCTTGCTTTGAATCATTAGTGTAATTTTT
1448351 TGAATTTTTGTTTTAAGCTGTATTTTTTCTACCA
66 TGAATTTTTGTTTTAAGCTGTATTTTTTCTACCA
1448385 AAAAGAAATTCACACATTAATTAAGGCGGATTATGTTCTTGCTTTGAATCATTAGTGTAATTTTT
1 AAAAGAAATTCACACATTAATTAAGGCGGATTATGTTCTTGCTTTGAATCATTAGTGTAATTTTT
1448450 TGAATTTTTGTTTTAAGCTGTATTTTTTCTACCA
66 TGAATTTTTGTTTTAAGCTGTATTTTTTCTACCA
1448484 AAAAGAAATTCACACATTAA
1 AAAAGAAATTCACACATTAA
1448504 ATGTTGATGT
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 119 1.00
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.43
Consensus pattern (99 bp):
AAAAGAAATTCACACATTAATTAAGGCGGATTATGTTCTTGCTTTGAATCATTAGTGTAATTTTT
TGAATTTTTGTTTTAAGCTGTATTTTTTCTACCA
Found at i:1458936 original size:15 final size:16
Alignment explanation
Indices: 1458911--1458944 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1458901 AAATTGTAAT
1458911 TTTATTATTTTAATAA
1 TTTATTATTTTAATAA
*
1458927 TTTA-TATTTTTATAA
1 TTTATTATTTTAATAA
1458942 TTT
1 TTT
1458945 TTTCTTCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTATTTTAATAA
Found at i:1459428 original size:249 final size:250
Alignment explanation
Indices: 1458978--1459477 Score: 993
Period size: 249 Copynumber: 2.0 Consensus size: 250
1458968 ATAAATTATA
1458978 AAAGATTTAAATAAAAAAAAAGGAAATTTTAAGTAAATAACATGTTGGATTTTAATGAAATTGTA
1 AAAGATTTAAATAAAAAAAAAGGAAATTTTAAGTAAATAACATGTTGGATTTTAATGAAATTGTA
1459043 TTTAAGGATAAGTTTTTGTTAGATTCAAATGACTGTCACGTCTTCATCTTGAGGAATACTTTAAT
66 TTTAAGGATAAGTTTTTGTTAGATTCAAATGACTGTCACGTCTTCATCTTGAGGAATACTTTAAT
1459108 TCTTAACTATGTTCAAAACAAAATATTCTGTAAAAGAAAAAGTATACTAAATCAATACACATATC
131 TCTTAACTATGTTCAAAACAAAATATTCTGTAAAAGAAAAAGTATACTAAATCAATACACATATC
1459173 ACAATGTATTGTGAACATATATATTTCTTGCCATCGGAAAAATTAATATTTATTT
196 ACAATGTATTGTGAACATATATATTTCTTGCCATCGGAAAAATTAATATTTATTT
1459228 AAAGATTTAAA-AAAAAAAAAGGAAATTTTAAGTAAATAACATGTTGGATTTTAATGAAATTGTA
1 AAAGATTTAAATAAAAAAAAAGGAAATTTTAAGTAAATAACATGTTGGATTTTAATGAAATTGTA
1459292 TTTAAGGATAAGTTTTTGTTAGATTCAAATGACTGTCACGTCTTCATCTTGAGGAATACTTTAAT
66 TTTAAGGATAAGTTTTTGTTAGATTCAAATGACTGTCACGTCTTCATCTTGAGGAATACTTTAAT
1459357 TCTTAACTATGTTCAAAACAAAATATTCTGTAAAAGAAAAAGTATACTAAATCAATACACATATC
131 TCTTAACTATGTTCAAAACAAAATATTCTGTAAAAGAAAAAGTATACTAAATCAATACACATATC
1459422 ACAATGTATTGTGAACATATATATTTCTTGCCATCGGAAAAATTAATATTTATTT
196 ACAATGTATTGTGAACATATATATTTCTTGCCATCGGAAAAATTAATATTTATTT
1459477 A
1 A
1459478 CATGCCAATT
Statistics
Matches: 250, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
249 239 0.96
250 11 0.04
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (250 bp):
AAAGATTTAAATAAAAAAAAAGGAAATTTTAAGTAAATAACATGTTGGATTTTAATGAAATTGTA
TTTAAGGATAAGTTTTTGTTAGATTCAAATGACTGTCACGTCTTCATCTTGAGGAATACTTTAAT
TCTTAACTATGTTCAAAACAAAATATTCTGTAAAAGAAAAAGTATACTAAATCAATACACATATC
ACAATGTATTGTGAACATATATATTTCTTGCCATCGGAAAAATTAATATTTATTT
Found at i:1462245 original size:22 final size:22
Alignment explanation
Indices: 1462220--1462263 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1462210 ACCAGCGAGG
1462220 ATTTGATAGTACTAGAATACGT
1 ATTTGATAGTACTAGAATACGT
1462242 ATTTGATAGTACTAGAATACGT
1 ATTTGATAGTACTAGAATACGT
1462264 TGTTTGGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (22 bp):
ATTTGATAGTACTAGAATACGT
Found at i:1462323 original size:21 final size:22
Alignment explanation
Indices: 1462313--1462355 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 22
1462303 TCTTTAATTA
1462313 TAAAAT-ATTATTTTATACATT
1 TAAAATAATTATTTTATACATT
1462334 TAAAATAATTATATTTAATACA
1 TAAAATAATTAT-TTT-ATACA
1462356 AATATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 5 0.26
23 3 0.16
24 5 0.26
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (22 bp):
TAAAATAATTATTTTATACATT
Found at i:1463034 original size:24 final size:24
Alignment explanation
Indices: 1463007--1463052 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1462997 ATTAGTAAGT
1463007 CAAATAAACTATACTAATAAATGC
1 CAAATAAACTATACTAATAAATGC
* *
1463031 CAAATATATTATACTAATAAAT
1 CAAATAAACTATACTAATAAAT
1463053 ACTAAATCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.30
Consensus pattern (24 bp):
CAAATAAACTATACTAATAAATGC
Found at i:1464994 original size:24 final size:24
Alignment explanation
Indices: 1464967--1465018 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1464957 TTAGTAAGTC
*
1464967 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
1464991 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
1465015 AAAT
1 AAAT
1465019 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:1472696 original size:13 final size:12
Alignment explanation
Indices: 1472674--1472704 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
1472664 TGCAATTCTC
1472674 AAAAAAAAAAGA
1 AAAAAAAAAAGA
1472686 AAAAGAAAAAAGA
1 AAAA-AAAAAAGA
1472699 AAAAAA
1 AAAAAA
1472705 CAGTAGCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:1478807 original size:6 final size:6
Alignment explanation
Indices: 1478793--1478832 Score: 62
Period size: 6 Copynumber: 6.5 Consensus size: 6
1478783 TTCCAGAACA
*
1478793 AGAAGGG AGAAGG AGAAGG AGAAGG AGAAGA AGAAGG AGA
1 AGAA-GG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGA
1478833 TGGATGGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 27 0.87
7 4 0.13
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (6 bp):
AGAAGG
Found at i:1499910 original size:50 final size:51
Alignment explanation
Indices: 1499846--1499980 Score: 166
Period size: 51 Copynumber: 2.7 Consensus size: 51
1499836 CCGACACATT
* * ** * *
1499846 TAGTAGCCTACACATAGTACTACACACGTGATCAA-GCTTTCCT-GTTCACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAAGGCCAT-CTGGTACACA
*
1499896 TAGTAACCTGCACATAGTACTACACACGTGACCAAGGCCATCTGGTACACA
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAAGGCCATCTGGTACACA
* *
1499947 TAGTAGCCTGCATATAGTACTACACATGTGACCA
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA
1499981 TTATCTATCG
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
50 34 0.47
51 39 0.53
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.24
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCAAGGCCATCTGGTACACA
Found at i:1499969 original size:51 final size:50
Alignment explanation
Indices: 1499803--1499980 Score: 164
Period size: 51 Copynumber: 3.5 Consensus size: 50
1499793 TTCAGTGGTT
* * * * *
1499803 TGCACATAGTACCACCCATGTGACCATTGTCATCC-G-ACACATTTAGTAGCC
1 TGCACATAGTACTACACACGTGACCA-AGCCATCCTGTACACA--TAGTAGCC
* * ** * * *
1499854 TACACATAGTACTACACACGTGATCAAGCTTTCCTGTTCACGTAGTAACC
1 TGCACATAGTACTACACACGTGACCAAGCCATCCTGTACACATAGTAGCC
1499904 TGCACATAGTACTACACACGTGACCAAGGCCAT-CTGGTACACATAGTAGCC
1 TGCACATAGTACTACACACGTGACCAA-GCCATCCT-GTACACATAGTAGCC
* *
1499955 TGCATATAGTACTACACATGTGACCA
1 TGCACATAGTACTACACACGTGACCA
1499981 TTATCTATCG
Statistics
Matches: 102, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
50 38 0.37
51 61 0.60
52 3 0.03
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (50 bp):
TGCACATAGTACTACACACGTGACCAAGCCATCCTGTACACATAGTAGCC
Found at i:1499996 original size:51 final size:51
Alignment explanation
Indices: 1499846--1500027 Score: 165
Period size: 51 Copynumber: 3.6 Consensus size: 51
1499836 CCGACACATT
* * ** * *
1499846 TAGTAGCCTACACATAGTACTACACACGTGATCAA-GCTTTCCTG-TTCACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAAGGCCAT-CTGATACACA
* *
1499896 TAGTAACCTGCACATAGTACTACACACGTGACCAAGGCCATCTGGTACACA
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAAGGCCATCTGATACACA
* * * * *
1499947 TAGTAGCCTGCATATAGTACTACACATGTGACCATTA-TCTATC-GATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA--AGGCCATCTGATACACA
* * *
1499998 TAGTAGCCTGCACTTTGTACTACATACGTG
1 TAGTAGCCTGCACATAGTACTACACACGTG
1500028 CTCATAGGTA
Statistics
Matches: 109, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
50 35 0.32
51 69 0.63
52 4 0.04
53 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCAAGGCCATCTGATACACA
Found at i:1500847 original size:43 final size:43
Alignment explanation
Indices: 1500758--1500847 Score: 155
Period size: 43 Copynumber: 2.1 Consensus size: 43
1500748 TTCATAAATA
*
1500758 TTTATCACTCTGGCAAGTTTTACACCTTTTCAATTTAGGCTAT
1 TTTATCACTCTGGCAAGTTTTACACCTTTTCAATTTAGCCTAT
1500801 TTTATCACTCTGGCAAGTTTTACACCTTTTCAATTTAGTCCT-T
1 TTTATCACTCTGGCAAGTTTTACACCTTTTCAATTTAG-CCTAT
1500844 TTTA
1 TTTA
1500848 ACTAATTAAC
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
43 43 0.96
44 2 0.04
ACGTcount: A:0.22, C:0.21, G:0.10, T:0.47
Consensus pattern (43 bp):
TTTATCACTCTGGCAAGTTTTACACCTTTTCAATTTAGCCTAT
Found at i:1501187 original size:54 final size:54
Alignment explanation
Indices: 1501085--1501188 Score: 145
Period size: 54 Copynumber: 1.9 Consensus size: 54
1501075 TCATCGAATT
* * **
1501085 TAGTGGTCTTGAACCACTATTTCTGACACTACTAAAAATTGGGTTGTTACTTAC
1 TAGTGGTCTTGAACCACTATTTCTGACACCACTAAAAATTAGACTGTTACTTAC
* * *
1501139 TAGTGGTCTTGAACCACTGTTTTTGACACCACTGAAAATTAGACTGTTAC
1 TAGTGGTCTTGAACCACTATTTCTGACACCACTAAAAATTAGACTGTTAC
1501189 AGTAAGTGTT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (54 bp):
TAGTGGTCTTGAACCACTATTTCTGACACCACTAAAAATTAGACTGTTACTTAC
Found at i:1505225 original size:22 final size:24
Alignment explanation
Indices: 1505179--1505225 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
1505169 AAGATTATAG
* *
1505179 ATAAGTTATCAAACTTTTAAATAA
1 ATAAGTTAACAAACTTTCAAATAA
1505203 ATAAGTTAAC-AA-TTTCAAATAA
1 ATAAGTTAACAAACTTTCAAATAA
1505225 A
1 A
1505226 CAAATTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.48
23 2 0.10
24 9 0.43
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (24 bp):
ATAAGTTAACAAACTTTCAAATAA
Found at i:1505835 original size:133 final size:134
Alignment explanation
Indices: 1505667--1505952 Score: 531
Period size: 133 Copynumber: 2.1 Consensus size: 134
1505657 TTTAATTATT
*
1505667 TTAATAATTATTATTTTTGGTTGCCTTATTAATTTTTTTTATAGTTTTGCATTAATCCGAAATGG
1 TTAATAATTTTTATTTTTGG-TGCCTTATTAATTTTTTTTATAGTTTTGCATTAATCCGAAATGG
1505732 ATTTGAATAACCCTTTATCCAGAATAATTTTAGATGT-TCATGTTATTAATTTTTACATTTTTAT
65 ATTTGAATAACCCTTTATCCAGAATAATTTTAGATGTGT-ATGTTATTAATTTTTACATTTTTAT
1505796 AAATTA
129 AAATTA
1505802 TTAATAATTTTTATTTTTGG-GCCTTATTAATTTTTTTTATAGTTTTGCATTAATCCGAAATGGA
1 TTAATAATTTTTATTTTTGGTGCCTTATTAATTTTTTTTATAGTTTTGCATTAATCCGAAATGGA
1505866 TTTGAATAACCCTTTATCCAGAATAATTTTAGATGTGTATGTTATTAATTTTTACATTTTTATAA
66 TTTGAATAACCCTTTATCCAGAATAATTTTAGATGTGTATGTTATTAATTTTTACATTTTTATAA
1505931 ATTA
131 ATTA
1505935 TTAATAATTTTTATTTTT
1 TTAATAATTTTTATTTTT
1505953 TAAATTTTTA
Statistics
Matches: 149, Mismatches: 1, Indels: 4
0.97 0.01 0.03
Matches are distributed among these distances:
133 129 0.87
134 1 0.01
135 19 0.13
ACGTcount: A:0.30, C:0.08, G:0.09, T:0.52
Consensus pattern (134 bp):
TTAATAATTTTTATTTTTGGTGCCTTATTAATTTTTTTTATAGTTTTGCATTAATCCGAAATGGA
TTTGAATAACCCTTTATCCAGAATAATTTTAGATGTGTATGTTATTAATTTTTACATTTTTATAA
ATTA
Found at i:1505975 original size:25 final size:26
Alignment explanation
Indices: 1505907--1505978 Score: 69
Period size: 25 Copynumber: 2.8 Consensus size: 26
1505897 GATGTGTATG
* *
1505907 TTATTAAT-TTTTACATTTTTATAAA
1 TTATTAATAATTTAAATTTTTATAAA
**
1505932 TTATTAATAATTTTTATTTTT-TAAA
1 TTATTAATAATTTAAATTTTTATAAA
*
1505957 TTTTTAA-AATTATAAATTTTTA
1 TTATTAATAATT-TAAATTTTTA
1505979 GTATTTTTTC
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
24 4 0.11
25 25 0.66
26 9 0.24
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (26 bp):
TTATTAATAATTTAAATTTTTATAAA
Found at i:1512613 original size:24 final size:23
Alignment explanation
Indices: 1512575--1512621 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
1512565 ATTCACTAAA
*
1512575 AAAATTTAAACCCTAAATCACTT
1 AAAATTTAAACCCTAAACCACTT
*
1512598 AAAATTTCAAATCCTAAACCACTT
1 AAAATTT-AAACCCTAAACCACTT
1512622 TTTTTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (23 bp):
AAAATTTAAACCCTAAACCACTT
Found at i:1516837 original size:29 final size:29
Alignment explanation
Indices: 1516795--1516852 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1516785 TTCCTCATTA
1516795 ACCATTTGACTAGCATTACTACAAGTTTT
1 ACCATTTGACTAGCATTACTACAAGTTTT
1516824 ACCATTTGACTAGCATTACTACAAGTTTT
1 ACCATTTGACTAGCATTACTACAAGTTTT
1516853 CTTTGGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (29 bp):
ACCATTTGACTAGCATTACTACAAGTTTT
Found at i:1518326 original size:283 final size:283
Alignment explanation
Indices: 1517819--1518387 Score: 1129
Period size: 283 Copynumber: 2.0 Consensus size: 283
1517809 CATGTGATTA
1517819 GTGATTACCCTGTGAGTGTTAACATAGATGAGGTGATTAGACAATAATGTGGAGGAGGAGGTTCC
1 GTGATTACCCTGTGAGTGTTAACATAGATGAGGTGATTAGACAATAATGTGGAGGAGGAGGTTCC
1517884 TTTGGTTAAAGGGGAAGAGTGGGCTGATATAGAAGCATGAGGAGAAAGTGATGTGTTAAAGTAAA
66 TTTGGTTAAAGGGGAAGAGTGGGCTGATATAGAAGCATGAGGAGAAAGTGATGTGTTAAAGTAAA
1517949 AGAATGGTTAATTTTTTTCTTAGTGTGAGAAAGACAGCCCTATTTTTCATTTTTGCTATTTTCTG
131 AGAATGGTTAATTTTTTTCTTAGTGTGAGAAAGACAGCCCTATTTTTCATTTTTGCTATTTTCTG
1518014 GCGTGATCTATTTGTTGTAATGAAATAGGTTTTTCTTGCATAATCACGAATCAACTGTGAATTTG
196 GCGTGATCTATTTGTTGTAATGAAATAGGTTTTTCTTGCATAATCACGAATCAACTGTGAATTTG
1518079 ATTATTTTAACTTTTGTTATTTG
261 ATTATTTTAACTTTTGTTATTTG
1518102 GTGATTACCCTGTGAGTGTTAACATAGATGAGGTGATTAGACAATAATGTGGAGGAGGAGGTTCC
1 GTGATTACCCTGTGAGTGTTAACATAGATGAGGTGATTAGACAATAATGTGGAGGAGGAGGTTCC
*
1518167 TTTGGTTAAAGGGGAAGAGTGGGTTGATATAGAAGCATGAGGAGAAAGTGATGTGTTAAAGTAAA
66 TTTGGTTAAAGGGGAAGAGTGGGCTGATATAGAAGCATGAGGAGAAAGTGATGTGTTAAAGTAAA
1518232 AGAATGGTTAATTTTTTTCTTAGTGTGAGAAAGACAGCCCTATTTTTCATTTTTGCTATTTTCTG
131 AGAATGGTTAATTTTTTTCTTAGTGTGAGAAAGACAGCCCTATTTTTCATTTTTGCTATTTTCTG
1518297 GCGTGATCTATTTGTTGTAATGAAATAGGTTTTTCTTGCATAATCACGAATCAACTGTGAATTTG
196 GCGTGATCTATTTGTTGTAATGAAATAGGTTTTTCTTGCATAATCACGAATCAACTGTGAATTTG
1518362 ATTATTTTAACTTTTGTTATTTG
261 ATTATTTTAACTTTTGTTATTTG
1518385 GTG
1 GTG
1518388 GGTTTAATGT
Statistics
Matches: 285, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
283 285 1.00
ACGTcount: A:0.28, C:0.09, G:0.25, T:0.38
Consensus pattern (283 bp):
GTGATTACCCTGTGAGTGTTAACATAGATGAGGTGATTAGACAATAATGTGGAGGAGGAGGTTCC
TTTGGTTAAAGGGGAAGAGTGGGCTGATATAGAAGCATGAGGAGAAAGTGATGTGTTAAAGTAAA
AGAATGGTTAATTTTTTTCTTAGTGTGAGAAAGACAGCCCTATTTTTCATTTTTGCTATTTTCTG
GCGTGATCTATTTGTTGTAATGAAATAGGTTTTTCTTGCATAATCACGAATCAACTGTGAATTTG
ATTATTTTAACTTTTGTTATTTG
Found at i:1532151 original size:75 final size:75
Alignment explanation
Indices: 1532026--1532176 Score: 268
Period size: 75 Copynumber: 2.0 Consensus size: 75
1532016 GCAAAGGGTA
* *
1532026 TAAAACTTCTTGTAATAAAAAACCATCTTTATTTATATATACAAATACAAGTCTCCCCGCCCAAC
1 TAAAACTTCTTGTAATAAAAAACCATCTTTATTTATATATACAAATACAAGGCCCCCCGCCCAAC
1532091 CCCCCCCCCC
66 CCCCCCCCCC
1532101 TAAAACTTCTTGTAATAAAAAACCATCTTTATTTATATTATACAAA-ACAAGGCCCCCCGCCCAA
1 TAAAACTTCTTGTAATAAAAAACCATCTTTATTTATA-TATACAAATACAAGGCCCCCCGCCCAA
1532165 CCCCCCCCCCC
65 CCCCCCCCCCC
1532176 T
1 T
1532177 TTTCTTTAGC
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
75 65 0.89
76 8 0.11
ACGTcount: A:0.34, C:0.35, G:0.05, T:0.26
Consensus pattern (75 bp):
TAAAACTTCTTGTAATAAAAAACCATCTTTATTTATATATACAAATACAAGGCCCCCCGCCCAAC
CCCCCCCCCC
Found at i:1535384 original size:41 final size:41
Alignment explanation
Indices: 1535327--1535417 Score: 164
Period size: 41 Copynumber: 2.2 Consensus size: 41
1535317 AAATGGGGTA
1535327 TGGGAGTGGCTTAGATACAAAAGGGACTGTGCCTCAGGTGT
1 TGGGAGTGGCTTAGATACAAAAGGGACTGTGCCTCAGGTGT
*
1535368 TGGGAGTGGCTTAGATACAAAAGGGTCTGTGCCTCAGGTGT
1 TGGGAGTGGCTTAGATACAAAAGGGACTGTGCCTCAGGTGT
*
1535409 TGGGGGTGG
1 TGGGAGTGG
1535418 AGAGTTTGAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.21, C:0.13, G:0.41, T:0.25
Consensus pattern (41 bp):
TGGGAGTGGCTTAGATACAAAAGGGACTGTGCCTCAGGTGT
Found at i:1544242 original size:29 final size:31
Alignment explanation
Indices: 1544168--1544251 Score: 91
Period size: 31 Copynumber: 2.8 Consensus size: 31
1544158 ATTAAATCAA
* * * **
1544168 AATTAAAGTTTCAAGTATACATTTAAACCAC
1 AATTAAAGTTTCATGTATATAATTGCACCAC
* *
1544199 AATTAGAGTTTCATGTGTATAATTGCACCA-
1 AATTAAAGTTTCATGTATATAATTGCACCAC
1544229 AATTAAAG-TTCATGTATATAATT
1 AATTAAAGTTTCATGTATATAATT
1544252 TTACATTATA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 14 0.32
30 7 0.16
31 23 0.52
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (31 bp):
AATTAAAGTTTCATGTATATAATTGCACCAC
Found at i:1560715 original size:21 final size:21
Alignment explanation
Indices: 1560655--1560781 Score: 141
Period size: 21 Copynumber: 6.0 Consensus size: 21
1560645 TTTGGGTGGA
* *
1560655 TCAGCTCTCACAAGCTTC-GAT
1 TCAGCTCTTACGAGCTTCTG-T
* * **
1560676 TTAGCTCTCACGATATTCTGT
1 TCAGCTCTTACGAGCTTCTGT
* *
1560697 TTAGCTCGTT-TGAGCTTCTGT
1 TCAGCTC-TTACGAGCTTCTGT
1560718 TCAGCTCTTACGAGCTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
1560739 TCAGCTCTTACGAGCTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
*
1560760 TCAGCTCTTATGAGCTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
1560781 T
1 T
1560782 AACGATGTAC
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
20 2 0.02
21 88 0.96
22 2 0.02
ACGTcount: A:0.16, C:0.26, G:0.18, T:0.40
Consensus pattern (21 bp):
TCAGCTCTTACGAGCTTCTGT
Found at i:1560734 original size:63 final size:63
Alignment explanation
Indices: 1560655--1560781 Score: 159
Period size: 63 Copynumber: 2.0 Consensus size: 63
1560645 TTTGGGTGGA
* * *
1560655 TCAGCTCTCACAAGCTTC-GATTTAGCTCTCACGATATTCTGTTTAGCTCGTT-TGAGCTTCTGT
1 TCAGCTCTCACAAGCTTCTG-TTCAGCTCTCACGAGATTCTGTTCAGCTC-TTATGAGCTTCTGT
* * * *
1560718 TCAGCTCTTACGAGCTTCTGTTCAGCTCTTACGAGCTTCTGTTCAGCTCTTATGAGCTTCTGT
1 TCAGCTCTCACAAGCTTCTGTTCAGCTCTCACGAGATTCTGTTCAGCTCTTATGAGCTTCTGT
1560781 T
1 T
1560782 AACGATGTAC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 52 0.95
64 1 0.02
ACGTcount: A:0.16, C:0.26, G:0.18, T:0.40
Consensus pattern (63 bp):
TCAGCTCTCACAAGCTTCTGTTCAGCTCTCACGAGATTCTGTTCAGCTCTTATGAGCTTCTGT
Found at i:1562467 original size:31 final size:31
Alignment explanation
Indices: 1562426--1562491 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
1562416 ACAGGCTGAG
* *
1562426 ACACGACCGTGTGTTCTTATTTCGAATGTCC
1 ACACGACCGTGTGTTCCTATTTCAAATGTCC
*
1562457 ACACGGCCGTGTGTTCCTATTTCAAATGTCC
1 ACACGACCGTGTGTTCCTATTTCAAATGTCC
1562488 ACAC
1 ACAC
1562492 CGCCTAAGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.32
Consensus pattern (31 bp):
ACACGACCGTGTGTTCCTATTTCAAATGTCC
Found at i:1563852 original size:2 final size:2
Alignment explanation
Indices: 1563841--1563881 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1563831 TTTTTTTTCT
*
1563841 TG TG TA TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1563882 ATTAATAAGA
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:0.02, C:0.00, G:0.46, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1565020 original size:2 final size:2
Alignment explanation
Indices: 1565013--1565038 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1565003 TATGTTCATA
1565013 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
1565039 CGCGCTCGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1570538 original size:18 final size:18
Alignment explanation
Indices: 1570499--1570539 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1570489 TTAGCAGTCT
*
1570499 AATTATAATTTTTTATTT
1 AATTATAATTTTTTATTA
1570517 AATTATTAATTTTTT-TTA
1 AATTA-TAATTTTTTATTA
1570535 AATTA
1 AATTA
1570540 GGTTTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
AATTATAATTTTTTATTA
Found at i:1579025 original size:32 final size:32
Alignment explanation
Indices: 1578967--1579031 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
1578957 CACTTTTCAT
** *
1578967 GCTTCTGGTTTAGACCTGGACTATCTTTTTAG
1 GCTTCTGGTTTAGACCTAAACCATCTTTTTAG
1578999 GCTTCTGGTTTAGACCTAAACCATCTTTTTAG
1 GCTTCTGGTTTAGACCTAAACCATCTTTTTAG
1579031 G
1 G
1579032 TTTGAAGGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (32 bp):
GCTTCTGGTTTAGACCTAAACCATCTTTTTAG
Found at i:1584455 original size:63 final size:63
Alignment explanation
Indices: 1584377--1584503 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
1584367 TATCTGCAAG
1584377 TGAGTTCTAAAATTCTCTGATGCCTTGGTGCCATTTATAATTGTTGTTTTCAGTTTATTGCCT
1 TGAGTTCTAAAATTCTCTGATGCCTTGGTGCCATTTATAATTGTTGTTTTCAGTTTATTGCCT
1584440 TGAGTTCTAAAATTCTCTGATGCCTTGGTGCCATTTATAATTGTTGTTTTCAGTTTATTGCCT
1 TGAGTTCTAAAATTCTCTGATGCCTTGGTGCCATTTATAATTGTTGTTTTCAGTTTATTGCCT
1584503 T
1 T
1584504 TCATTCTGCT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.19, C:0.16, G:0.17, T:0.48
Consensus pattern (63 bp):
TGAGTTCTAAAATTCTCTGATGCCTTGGTGCCATTTATAATTGTTGTTTTCAGTTTATTGCCT
Found at i:1599043 original size:98 final size:99
Alignment explanation
Indices: 1598873--1599071 Score: 391
Period size: 98 Copynumber: 2.0 Consensus size: 99
1598863 TTTTTTTTTT
1598873 TTAATTTTCATTTTTATTATTAGATTAGACACAAACTAACCTCTCAAACCTTTTTAAAAACTTTC
1 TTAATTTTCATTTTTATTATTAGATTAGACACAAACTAACCTCTCAAACCTTTTTAAAAACTTTC
1598938 TTTTTCCTTTTATTGATCCAATGAGTTTACAAGA
66 TTTTTCCTTTTATTGATCCAATGAGTTTACAAGA
1598972 TTAATTTTCA-TTTTATTATTAGATTAGACACAAACTAACCTCTCAAACCTTTTTAAAAACTTTC
1 TTAATTTTCATTTTTATTATTAGATTAGACACAAACTAACCTCTCAAACCTTTTTAAAAACTTTC
1599036 TTTTTCCTTTTATTGATCCAATGAGTTTACAAGA
66 TTTTTCCTTTTATTGATCCAATGAGTTTACAAGA
1599070 TT
1 TT
1599072 TGGGGTGATC
Statistics
Matches: 100, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
98 90 0.90
99 10 0.10
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.45
Consensus pattern (99 bp):
TTAATTTTCATTTTTATTATTAGATTAGACACAAACTAACCTCTCAAACCTTTTTAAAAACTTTC
TTTTTCCTTTTATTGATCCAATGAGTTTACAAGA
Found at i:1612107 original size:18 final size:18
Alignment explanation
Indices: 1612084--1612118 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1612074 ATACATTTGT
* *
1612084 AGTGAAGAATATGAGAAG
1 AGTGAAAAATAAGAGAAG
1612102 AGTGAAAAATAAGAGAA
1 AGTGAAAAATAAGAGAA
1612119 TGAAAAAACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.29, T:0.14
Consensus pattern (18 bp):
AGTGAAAAATAAGAGAAG
Found at i:1614551 original size:16 final size:16
Alignment explanation
Indices: 1614517--1614550 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1614507 AATATTTTAT
1614517 AAAGAATTTTATATTA
1 AAAGAATTTTATATTA
1614533 AAAGAATTTT-TATTA
1 AAAGAATTTTATATTA
1614548 AAA
1 AAA
1614551 ATAAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (16 bp):
AAAGAATTTTATATTA
Found at i:1626720 original size:72 final size:72
Alignment explanation
Indices: 1626592--1626735 Score: 263
Period size: 71 Copynumber: 2.0 Consensus size: 72
1626582 AATGCTATCT
* *
1626592 TTTTTTTTATTTACCAAAATATTATAAATTTTTTTATTTACCAAAATATATCAAAAAATAAAAAT
1 TTTTTTTTATTTAACAAAAAATTATAAATTTTTTTATTTACCAAAATATATCAAAAAATAAAAAT
1626657 AAAAACC
66 AAAAACC
1626664 TTTTTTTTA-TTAACAAAAAATTATAAATTTTTTTATTTACCAAAATATATCAAAAAATAAAAAT
1 TTTTTTTTATTTAACAAAAAATTATAAATTTTTTTATTTACCAAAATATATCAAAAAATAAAAAT
1626728 AAAAACC
66 AAAAACC
1626735 T
1 T
1626736 GCAAAAAAAA
Statistics
Matches: 70, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
71 61 0.87
72 9 0.13
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (72 bp):
TTTTTTTTATTTAACAAAAAATTATAAATTTTTTTATTTACCAAAATATATCAAAAAATAAAAAT
AAAAACC
Found at i:1626790 original size:27 final size:27
Alignment explanation
Indices: 1626756--1626814 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
1626746 AACTTGAGGT
* *
1626756 GGCACCAAAGGTGCTAAAGTGATTGGC
1 GGCACCAAAGGTGCCAAAGAGATTGGC
*
1626783 GGCACCAAATGTGCCAAAGAGATTGGC
1 GGCACCAAAGGTGCCAAAGAGATTGGC
1626810 GGCAC
1 GGCAC
1626815 TGGATTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.31, C:0.22, G:0.32, T:0.15
Consensus pattern (27 bp):
GGCACCAAAGGTGCCAAAGAGATTGGC
Found at i:1627306 original size:19 final size:19
Alignment explanation
Indices: 1627282--1627344 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
1627272 TCTAATTAAG
1627282 TAATAATTCTATTTTACTT
1 TAATAATTCTATTTTACTT
** ***
1627301 TAATAAGTT-TATTAAAAAG
1 TAATAA-TTCTATTTTACTT
*
1627320 TAATAACTCTATTTTACTT
1 TAATAATTCTATTTTACTT
1627339 TAATAA
1 TAATAA
1627345 ACTATTGCTT
Statistics
Matches: 31, Mismatches: 11, Indels: 4
0.67 0.24 0.09
Matches are distributed among these distances:
18 1 0.03
19 28 0.90
20 2 0.06
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.48
Consensus pattern (19 bp):
TAATAATTCTATTTTACTT
Found at i:1627408 original size:18 final size:17
Alignment explanation
Indices: 1627379--1627413 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1627369 GTAATGTTTC
*
1627379 AAAAAATGTTTTTAGGA
1 AAAAAATGTTTTAAGGA
1627396 AAAAAATGTTTTTAAGGA
1 AAAAAATG-TTTTAAGGA
1627414 GAAGTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (17 bp):
AAAAAATGTTTTAAGGA
Found at i:1628510 original size:27 final size:27
Alignment explanation
Indices: 1628468--1628556 Score: 144
Period size: 27 Copynumber: 3.3 Consensus size: 27
1628458 TTTAGTCCTA
1628468 TGCCGCCAATCTCTTTGGCACCTTTGG
1 TGCCGCCAATCTCTTTGGCACCTTTGG
*
1628495 T-CGGGCCAATCTCTTTGGCACCTTTGG
1 TGC-CGCCAATCTCTTTGGCACCTTTGG
*
1628522 TGCCGCCAATCACTTTGGCACCTTTGG
1 TGCCGCCAATCTCTTTGGCACCTTTGG
1628549 TGCCGCCA
1 TGCCGCCA
1628557 CAGGTTTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
26 1 0.02
27 55 0.96
28 1 0.02
ACGTcount: A:0.12, C:0.34, G:0.24, T:0.30
Consensus pattern (27 bp):
TGCCGCCAATCTCTTTGGCACCTTTGG
Found at i:1629474 original size:26 final size:26
Alignment explanation
Indices: 1629444--1629495 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1629434 AGTAAAAAAG
1629444 AATGTTCTAATGTTTTCTCATAACAC
1 AATGTTCTAATGTTTTCTCATAACAC
1629470 AATGTTCTAATGTTTTCTCATAACAC
1 AATGTTCTAATGTTTTCTCATAACAC
1629496 CCTCGAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (26 bp):
AATGTTCTAATGTTTTCTCATAACAC
Found at i:1631329 original size:22 final size:23
Alignment explanation
Indices: 1631304--1631346 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1631294 AATAAGTAGG
* *
1631304 CTTTCAA-AGGTGAAGTTTATCC
1 CTTTCAAGAGATGAACTTTATCC
1631326 CTTTCAAGAGATGAACTTTAT
1 CTTTCAAGAGATGAACTTTAT
1631347 GGCTAGTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.37
Consensus pattern (23 bp):
CTTTCAAGAGATGAACTTTATCC
Found at i:1637749 original size:21 final size:22
Alignment explanation
Indices: 1637725--1637769 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
1637715 AAATTTAGTG
1637725 TTAAGATAAAATAT-TGTTTAA
1 TTAAGATAAAATATGTGTTTAA
* * *
1637746 TTAATATAAATTTTGTGTTTAA
1 TTAAGATAAAATATGTGTTTAA
1637768 TT
1 TT
1637770 TTAAATTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
TTAAGATAAAATATGTGTTTAA
Found at i:1640146 original size:67 final size:67
Alignment explanation
Indices: 1640038--1640463 Score: 843
Period size: 67 Copynumber: 6.4 Consensus size: 67
1640028 GCTGCATGAT
*
1640038 TGGAGTGAGGTTTATGAGTGCCCCTTACCGTGGGGTTTCTAACCCAAAACTTTTTGCAATTCTAT
1 TGGAGTCAGGTTTATGAGTGCCCCTTACCGTGGGGTTTCTAACCCAAAACTTTTTGCAATTCTAT
1640103 TA
66 TA
1640105 TGGAGTCAGGTTTATGAGTGCCCCTTACCGTGGGGTTTCTAACCCAAAACTTTTTGCAATTCTAT
1 TGGAGTCAGGTTTATGAGTGCCCCTTACCGTGGGGTTTCTAACCCAAAACTTTTTGCAATTCTAT
1640170 TA
66 TA
1640172 TGGAGTCAGGTTTATGAGTGCCCCTTACCGTGGGGTTTCTAACCCAAAACTTTTTGCAATTCTAT
1 TGGAGTCAGGTTTATGAGTGCCCCTTACCGTGGGGTTTCTAACCCAAAACTTTTTGCAATTCTAT
1640237 TA
66 TA
1640239 TGGAGTCAGGTTTATGAGTGCCCCTTACCGTGGGGTTTCTAACCCAAAACTTTTTGCAATTCTAT
1 TGGAGTCAGGTTTATGAGTGCCCCTTACCGTGGGGTTTCTAACCCAAAACTTTTTGCAATTCTAT
1640304 TA
66 TA
1640306 TGGAGTCAGGTTTATGAGTGCCCCTTACCGTGGGGTTTCTAACCCAAAACTTTTTGCAATTCTAT
1 TGGAGTCAGGTTTATGAGTGCCCCTTACCGTGGGGTTTCTAACCCAAAACTTTTTGCAATTCTAT
1640371 TA
66 TA
1640373 TGGAGTCAGGTTTATGAGTGCCCCTTACCGTGGGGTTTCTAACCCAAAACTTTTTGCAATTCTAT
1 TGGAGTCAGGTTTATGAGTGCCCCTTACCGTGGGGTTTCTAACCCAAAACTTTTTGCAATTCTAT
1640438 TA
66 TA
1640440 TGGAGTCAGGTTTATGAGTGCCCC
1 TGGAGTCAGGTTTATGAGTGCCCC
1640464 CCCCCCCCCC
Statistics
Matches: 358, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 358 1.00
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (67 bp):
TGGAGTCAGGTTTATGAGTGCCCCTTACCGTGGGGTTTCTAACCCAAAACTTTTTGCAATTCTAT
TA
Found at i:1650885 original size:33 final size:33
Alignment explanation
Indices: 1650845--1651030 Score: 110
Period size: 33 Copynumber: 5.5 Consensus size: 33
1650835 GTTTAATGAA
* *
1650845 AAGACCATAACTGGGTTATGACACTTTGAATGT
1 AAGACCATAACTGGGCTATGGCACTTTGAATGT
*** * * * *
1650878 AAGACCATGGTTGGACCATGGCAGTATAGATACATGTGT
1 AAGACCATAACTGGGCTATGGCACT-TTG--A-A--TGT
*
1650917 AAGACCATAACTGGGCTATGGCA-TTCTG-ATAAT
1 AAGACCATAACTGGGCTATGGCACTT-TGAAT-GT
* * ***
1650950 AAGACCATAATTGGGTTATGGCACTACAAATGT
1 AAGACCATAACTGGGCTATGGCACTTTGAATGT
*
1650983 AAGAACATAACTGGGCTATGGCA-TTCTG-ATGAT
1 AAGACCATAACTGGGCTATGGCACTT-TGAATG-T
1651016 AAGACCATAACTGGG
1 AAGACCATAACTGGG
1651031 TTGTGACACT
Statistics
Matches: 112, Mismatches: 29, Indels: 24
0.68 0.18 0.15
Matches are distributed among these distances:
32 5 0.04
33 75 0.67
34 6 0.05
36 1 0.01
37 2 0.02
38 2 0.02
39 21 0.19
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (33 bp):
AAGACCATAACTGGGCTATGGCACTTTGAATGT
Found at i:1650996 original size:66 final size:66
Alignment explanation
Indices: 1650914--1651052 Score: 233
Period size: 66 Copynumber: 2.1 Consensus size: 66
1650904 TAGATACATG
* * *
1650914 TGTAAGACCATAACTGGGCTATGGCATTCTGATAATAAGACCATAATTGGGTTATGGCACTACAA
1 TGTAAGAACATAACTGGGCTATGGCATTCTGATAATAAGACCATAACTGGGTTATGACACTACAA
1650979 A
66 A
* *
1650980 TGTAAGAACATAACTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTGTGACACTACAA
1 TGTAAGAACATAACTGGGCTATGGCATTCTGATAATAAGACCATAACTGGGTTATGACACTACAA
1651045 A
66 A
1651046 TGTAAGA
1 TGTAAGA
1651053 TCATGGCAGG
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (66 bp):
TGTAAGAACATAACTGGGCTATGGCATTCTGATAATAAGACCATAACTGGGTTATGACACTACAA
A
Found at i:1651052 original size:33 final size:33
Alignment explanation
Indices: 1650914--1651052 Score: 129
Period size: 33 Copynumber: 4.2 Consensus size: 33
1650904 TAGATACATG
* * **
1650914 TGTAAGACCATAACTGGGCTATGGCA-TTCTGA
1 TGTAAGACCATAACTGGGTTATGGCACTACAAA
* *
1650946 TAATAAGACCATAATTGGGTTATGGCACTACAAA
1 T-GTAAGACCATAACTGGGTTATGGCACTACAAA
* * * **
1650980 TGTAAGAACATAACTGGGCTATGGCA-TTCTGA
1 TGTAAGACCATAACTGGGTTATGGCACTACAAA
* *
1651012 TGATAAGACCATAACTGGGTTGTGACACTACAAA
1 TG-TAAGACCATAACTGGGTTATGGCACTACAAA
1651046 TGTAAGA
1 TGTAAGA
1651053 TCATGGCAGG
Statistics
Matches: 83, Mismatches: 20, Indels: 7
0.75 0.18 0.06
Matches are distributed among these distances:
32 6 0.07
33 68 0.82
34 9 0.11
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (33 bp):
TGTAAGACCATAACTGGGTTATGGCACTACAAA
Found at i:1651085 original size:66 final size:66
Alignment explanation
Indices: 1650914--1651090 Score: 198
Period size: 66 Copynumber: 2.7 Consensus size: 66
1650904 TAGATACATG
* * * * * *
1650914 TGTAAGACCATAACTGGGCTATGGCATTCTGATAATAAGACCATAATTGGGTTATGGCACTACAA
1 TGTAAGAACATAACAGGGCTATGGCATGCTGATGATAAGACCATAACTGGGTTATGACACTACAA
1650979 A
66 A
* * *
1650980 TGTAAGAACATAACTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTGTGACACTACAA
1 TGTAAGAACATAACAGGGCTATGGCATGCTGATGATAAGACCATAACTGGGTTATGACACTACAA
1651045 A
66 A
* **
1651046 TGTAAGATCATGGCAGGGAC-ATGGCAATGCATG-TG-TAAGACCATA
1 TGTAAGAACATAACAGGG-CTATGGC-ATGC-TGATGATAAGACCATA
1651091 GTTGGACTAT
Statistics
Matches: 98, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
66 90 0.92
67 6 0.06
68 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.25
Consensus pattern (66 bp):
TGTAAGAACATAACAGGGCTATGGCATGCTGATGATAAGACCATAACTGGGTTATGACACTACAA
A
Found at i:1664647 original size:51 final size:51
Alignment explanation
Indices: 1664586--1664685 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
1664576 CTCAATTTCC
*
1664586 TCTCATTTTGCTCTCAATTTCCT-TCCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAATTTGCTCTCAATTTCCTCT-CAAATTTCTCTCAAATCCATATTTAA
* *
1664637 TCTCAATTTGCTCTCAATTTCCTCTCAAATTTCTCTTAAATCCCTATTT
1 TCTCAATTTGCTCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTT
1664686 TTAATTTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 44 0.98
52 1 0.02
ACGTcount: A:0.24, C:0.28, G:0.02, T:0.46
Consensus pattern (51 bp):
TCTCAATTTGCTCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTTAA
Found at i:1664672 original size:11 final size:11
Alignment explanation
Indices: 1664574--1664669 Score: 60
Period size: 11 Copynumber: 9.0 Consensus size: 11
1664564 CTAAATTATT
1664574 CTCTCAATTTC
1 CTCTCAATTTC
* *
1664585 CTCTCATTTTG
1 CTCTCAATTTC
1664596 CTCTCAATTTC
1 CTCTCAATTTC
1664607 CT-TCCAAATTT-
1 CTCT-C-AATTTC
*
1664618 CTCTCAA-ATC
1 CTCTCAATTTC
* *
1664628 C-AT--ATTTA
1 CTCTCAATTTC
* *
1664636 ATCTCAATTTG
1 CTCTCAATTTC
1664647 CTCTCAATTTC
1 CTCTCAATTTC
1664658 CTCTCAAATTTC
1 CTCTC-AATTTC
1664670 TCTTAAATCC
Statistics
Matches: 63, Mismatches: 13, Indels: 17
0.68 0.14 0.18
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 3 0.05
10 4 0.06
11 42 0.67
12 12 0.19
ACGTcount: A:0.23, C:0.30, G:0.02, T:0.45
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:1664704 original size:15 final size:15
Alignment explanation
Indices: 1664684--1664717 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1664674 AAATCCCTAT
1664684 TTTTAATTTTTTTAA
1 TTTTAATTTTTTTAA
1664699 TTTTAATTTTTTTAA
1 TTTTAATTTTTTTAA
1664714 TTTT
1 TTTT
1664718 TTTTAAATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTAATTTTTTTAA
Found at i:1664723 original size:10 final size:9
Alignment explanation
Indices: 1664683--1664720 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
1664673 TAAATCCCTA
1664683 TTTTTAATT
1 TTTTTAATT
1664692 TTTTTAA--
1 TTTTTAATT
1664699 -TTTTAATT
1 TTTTTAATT
1664707 TTTTTAATT
1 TTTTTAATT
1664716 TTTTT
1 TTTTT
1664721 TAAATCGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
6 6 0.23
9 20 0.77
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTAATT
Found at i:1664832 original size:11 final size:11
Alignment explanation
Indices: 1664816--1664845 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
1664806 CCAGAGAATT
1664816 TATTTTTTAAA
1 TATTTTTTAAA
1664827 TATTTTTT-AA
1 TATTTTTTAAA
1664837 TATTTTTTA
1 TATTTTTTA
1664846 TTTATGCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TATTTTTTAAA
Found at i:1665792 original size:7 final size:7
Alignment explanation
Indices: 1665780--1665805 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1665770 TAGTCGATTG
1665780 GTATTTA
1 GTATTTA
1665787 GTATTTA
1 GTATTTA
1665794 GTATTTA
1 GTATTTA
1665801 GTATT
1 GTATT
1665806 ATATATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:1666475 original size:18 final size:18
Alignment explanation
Indices: 1666452--1666494 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1666442 TGCCAAGTGC
* *
1666452 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
1666470 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
1666488 GTTTCCT
1 GTATCCT
1666495 TTTCCGAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:1668235 original size:14 final size:14
Alignment explanation
Indices: 1668216--1668260 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
1668206 TTTAATTTTT
*
1668216 AACCTTAAATCCTA
1 AACCTTAAACCCTA
1668230 AACCTTAAAACCCTA
1 AACCTT-AAACCCTA
*
1668245 AACCTTAAACCTTA
1 AACCTTAAACCCTA
1668259 AA
1 AA
1668261 AGTAGTGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 15 0.54
15 13 0.46
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (14 bp):
AACCTTAAACCCTA
Found at i:1668238 original size:7 final size:7
Alignment explanation
Indices: 1668216--1668260 Score: 56
Period size: 7 Copynumber: 6.3 Consensus size: 7
1668206 TTTAATTTTT
1668216 AACCTTA
1 AACCTTA
1668223 AATCC-TA
1 AA-CCTTA
1668230 AACCTTAA
1 AACCTT-A
*
1668238 AACCCTA
1 AACCTTA
1668245 AACCTTA
1 AACCTTA
1668252 AACCTTA
1 AACCTTA
1668259 AA
1 AA
1668261 AGTAGTGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 2 0.06
7 23 0.70
8 8 0.24
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (7 bp):
AACCTTA
Found at i:1668246 original size:15 final size:15
Alignment explanation
Indices: 1668216--1668253 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
1668206 TTTAATTTTT
*
1668216 AACCTT-AAATCCTA
1 AACCTTAAAACCCTA
1668230 AACCTTAAAACCCTA
1 AACCTTAAAACCCTA
1668245 AACCTTAAA
1 AACCTTAAA
1668254 CCTTAAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (15 bp):
AACCTTAAAACCCTA
Found at i:1672631 original size:12 final size:12
Alignment explanation
Indices: 1672614--1672638 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1672604 TCTCTGCCTA
1672614 CACTCGCTCGCT
1 CACTCGCTCGCT
1672626 CACTCGCTCGCT
1 CACTCGCTCGCT
1672638 C
1 C
1672639 TCTTTCTCGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.52, G:0.16, T:0.24
Consensus pattern (12 bp):
CACTCGCTCGCT
Found at i:1694338 original size:19 final size:20
Alignment explanation
Indices: 1694295--1694338 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
1694285 TTAAAATACT
* *
1694295 TTTAAAATAAATTTTTTTATT
1 TTTAAAAT-AATTTTTTAATG
1694316 TTTAAAAT-ATTTTTTAATG
1 TTTAAAATAATTTTTTAATG
1694335 TTTA
1 TTTA
1694339 TTTTAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 13 0.62
21 8 0.38
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTAAAATAATTTTTTAATG
Found at i:1702379 original size:32 final size:30
Alignment explanation
Indices: 1702315--1702379 Score: 76
Period size: 32 Copynumber: 2.1 Consensus size: 30
1702305 AAGTTCTGAA
* * *
1702315 TTTTTATTAAATTTTGCAATCAATTTTTAT
1 TTTTTATTAAATTTTCCAATCAATATTAAT
*
1702345 TTTTTAATTAAATTTTACCACTCAATATTAAT
1 TTTTT-ATTAAATTTT-CCAATCAATATTAAT
1702377 TTT
1 TTT
1702380 GATGATTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 5 0.17
31 10 0.34
32 14 0.48
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.57
Consensus pattern (30 bp):
TTTTTATTAAATTTTCCAATCAATATTAAT
Found at i:1708460 original size:22 final size:24
Alignment explanation
Indices: 1708412--1708460 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
1708402 GAGCTTCTTA
* *
1708412 TATATTTTTCTTGAATTTTTCATT
1 TATATTTTTCTTGAATTTTTAAAT
1708436 TATATTTTT-TTGAA-TTTTAAAT
1 TATATTTTTCTTGAATTTTTAAAT
1708458 TAT
1 TAT
1708461 TTGTTAACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 9 0.39
23 5 0.22
24 9 0.39
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (24 bp):
TATATTTTTCTTGAATTTTTAAAT
Found at i:1727413 original size:18 final size:18
Alignment explanation
Indices: 1727390--1727428 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1727380 CCTAGAAATA
*
1727390 GGACGACATAAATCTATT
1 GGACGACATAAATCTACT
*
1727408 GGACGATATAAATCTACT
1 GGACGACATAAATCTACT
1727426 GGA
1 GGA
1727429 TTAGAGTCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (18 bp):
GGACGACATAAATCTACT
Found at i:1739065 original size:45 final size:44
Alignment explanation
Indices: 1738933--1739076 Score: 152
Period size: 45 Copynumber: 3.2 Consensus size: 44
1738923 ATTAATGAAA
*
1738933 ATAAAGGTGATTGCTATGTGCTGATTTCACTGGATACCAATG-GTT
1 ATAAAGGTGATTGCTATGTGCTGATTTCACTGG-TACCATTGAG-T
*
1738978 ATATAA-GTGATTGCTATGTGCTGAATTCACCCT-GTACCATTGAGT
1 ATA-AAGGTGATTGCTATGTGCTGATTTCA--CTGGTACCATTGAGT
* *
1739023 ATAAAGGT-AGTTGCTATGTGCTGATTTCACTGAGTACTATTGATT
1 ATAAAGGTGA-TTGCTATGTGCTGATTTCACTG-GTACCATTGAGT
*
1739068 ATAAGGGTG
1 ATAAAGGTG
1739077 GTGTTGTGTG
Statistics
Matches: 84, Mismatches: 6, Indels: 17
0.79 0.06 0.16
Matches are distributed among these distances:
43 2 0.02
44 3 0.04
45 73 0.87
46 4 0.05
47 2 0.02
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (44 bp):
ATAAAGGTGATTGCTATGTGCTGATTTCACTGGTACCATTGAGT
Done.