Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007823.1 Hibiscus syriacus cultivar Beakdansim tig00110160_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: 6287495
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 33
Found at i:1727490 original size:23 final size:22
Alignment explanation
Indices: 1727448--1727490 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1727438 AAATTTATTA
*
1727448 ATATAATTTAAAGAATATATAT
1 ATATAATTTAAAGAACATATAT
*
1727470 ATATATATTTAAATAACATAT
1 ATATA-ATTTAAAGAACATAT
1727491 TTATTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
ATATAATTTAAAGAACATATAT
Found at i:1727727 original size:115 final size:115
Alignment explanation
Indices: 1727493--1727727 Score: 285
Period size: 115 Copynumber: 2.0 Consensus size: 115
1727483 TAACATATTT
* * * **
1727493 ATTTATTTAGAAATATCAGAAAATGGCTTATAGGTGCTTTAAGACAGCTCTTTCTTTTGATATTA
1 ATTTATTTAAAAATATCAGAAAATGGCTTATAGGTGCTTTAAGACAGCTATTTCCTTCAATATTA
* ** * * **
1727558 AAAAATAAATAAATAATAATAATAAATTATTTTAATATAGTAAGATATTT
66 AAAAATAAATAAATAATAATAACAAATTATTAAAATATAATAAAATATAA
* *
1727608 ATTTATTTAAAAATATTAGAAAATGGCTTATAGTTGCTTTAAGACAGCTATTTCCTTCAATATTA
1 ATTTATTTAAAAATATCAGAAAATGGCTTATAGGTGCTTTAAGACAGCTATTTCCTTCAATATTA
** *
1727673 AAAAATAAATAAATAACTAA-AACATTTTCTTAAAATGATAATAAAATA-AA
66 AAAAATAAATAAATAA-TAATAACAAATTATTAAAAT-ATAATAAAATATAA
1727723 ATTTA
1 ATTTA
1727728 AACATAAATA
Statistics
Matches: 101, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
115 89 0.88
116 12 0.12
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.38
Consensus pattern (115 bp):
ATTTATTTAAAAATATCAGAAAATGGCTTATAGGTGCTTTAAGACAGCTATTTCCTTCAATATTA
AAAAATAAATAAATAATAATAACAAATTATTAAAATATAATAAAATATAA
Found at i:1727912 original size:15 final size:16
Alignment explanation
Indices: 1727894--1727953 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
1727884 AATAATAATC
1727894 AAAATGAAAGAA-ATT
1 AAAATGAAAGAATATT
* *
1727909 AAAA-GCAATAATATT
1 AAAATGAAAGAATATT
1727924 AAAATGAAA-AATATAT
1 AAAATGAAAGAATAT-T
*
1727940 TAAATGAAA-AATAT
1 AAAATGAAAGAATAT
1727954 CCAACTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
14 5 0.13
15 16 0.42
16 17 0.45
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.25
Consensus pattern (16 bp):
AAAATGAAAGAATATT
Found at i:1727946 original size:16 final size:17
Alignment explanation
Indices: 1727919--1727953 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1727909 AAAAGCAATA
1727919 ATATTAAAATGAAAAAT
1 ATATTAAAATGAAAAAT
1727936 ATATT-AAATGAAAAAT
1 ATATTAAAATGAAAAAT
1727952 AT
1 AT
1727954 CCAACTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (17 bp):
ATATTAAAATGAAAAAT
Found at i:1731355 original size:31 final size:31
Alignment explanation
Indices: 1731319--1731415 Score: 124
Period size: 31 Copynumber: 3.1 Consensus size: 31
1731309 ATAATGGTGG
* *
1731319 AGTGACCATTTTATTACAAATTGATAATATT
1 AGTGACCATTTTATTACAAATCGATAACATT
* *
1731350 AGTGACCATTTTATTACCAATCGATAACGTT
1 AGTGACCATTTTATTACAAATCGATAACATT
* *
1731381 AGTGACCATTTTGTTATC-AATCGATAACGTT
1 AGTGACCATTTTATTA-CAAATCGATAACATT
1731412 AGTG
1 AGTG
1731416 GAAAATTTGT
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
31 59 0.98
32 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.38
Consensus pattern (31 bp):
AGTGACCATTTTATTACAAATCGATAACATT
Found at i:1731425 original size:31 final size:31
Alignment explanation
Indices: 1731348--1731427 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
1731338 ATTGATAATA
* * * *
1731348 TTAGTGACCATTTTATTACCAATCGATAACG
1 TTAGTGACAAATTTGTTATCAATCGATAACG
* *
1731379 TTAGTGACCATTTTGTTATCAATCGATAACG
1 TTAGTGACAAATTTGTTATCAATCGATAACG
1731410 TTAGTGGA-AAATTTGTTA
1 TTAGT-GACAAATTTGTTA
1731428 CTTTTGAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 42 0.95
32 2 0.05
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (31 bp):
TTAGTGACAAATTTGTTATCAATCGATAACG
Found at i:1736528 original size:19 final size:20
Alignment explanation
Indices: 1736504--1736542 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1736494 GAAATTTAAA
1736504 ATTTTC-TTATATTTTATAT
1 ATTTTCTTTATATTTTATAT
*
1736523 ATTTTCTTTGTATTTTATAT
1 ATTTTCTTTATATTTTATAT
1736543 GAATGATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (20 bp):
ATTTTCTTTATATTTTATAT
Found at i:1740309 original size:2 final size:2
Alignment explanation
Indices: 1740292--1740325 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1740282 TTAGATGATT
*
1740292 AG AG GG AG AG -G AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1740326 TTTATGTTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1740716 original size:60 final size:58
Alignment explanation
Indices: 1740644--1740782 Score: 161
Period size: 58 Copynumber: 2.4 Consensus size: 58
1740634 GGATGAACTT
* *** * *
1740644 GAATATTCAAAAGTTTGGGGACTAATATAGAAAGATAGTCATAGTCTAGGGATAAAATTA
1 GAATATTTAAAAGTTTAAAGACTAATATAGAAAG--AGTCATAATCTAGAGATAAAATTA
* * * * *
1740704 GAATATTTAAAAGTTTAAAGACTACTTTAGAATGAGTCATAATTTAGATATAAAATTA
1 GAATATTTAAAAGTTTAAAGACTAATATAGAAAGAGTCATAATCTAGAGATAAAATTA
1740762 GAATATTTAAAAGTTTAAAGA
1 GAATATTTAAAAGTTTAAAGA
1740783 TCAATTTAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
58 41 0.60
60 27 0.40
ACGTcount: A:0.46, C:0.05, G:0.17, T:0.32
Consensus pattern (58 bp):
GAATATTTAAAAGTTTAAAGACTAATATAGAAAGAGTCATAATCTAGAGATAAAATTA
Found at i:1740778 original size:29 final size:29
Alignment explanation
Indices: 1740694--1740783 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 29
1740684 ATAGTCTAGG
1740694 GATAAAATTAGAATATTTAAAAGTTTAAA
1 GATAAAATTAGAATATTTAAAAGTTTAAA
** * * * *
1740723 GACT-ACTTTAGAATGAGTCATAA-TTTAGA
1 GA-TAAAATTAGAAT-ATTTAAAAGTTTAAA
*
1740752 TATAAAATTAGAATATTTAAAAGTTTAAA
1 GATAAAATTAGAATATTTAAAAGTTTAAA
1740781 GAT
1 GAT
1740784 CAATTTAAAA
Statistics
Matches: 43, Mismatches: 14, Indels: 8
0.66 0.22 0.12
Matches are distributed among these distances:
28 6 0.14
29 31 0.72
30 6 0.14
ACGTcount: A:0.49, C:0.03, G:0.12, T:0.36
Consensus pattern (29 bp):
GATAAAATTAGAATATTTAAAAGTTTAAA
Found at i:1740910 original size:14 final size:14
Alignment explanation
Indices: 1740891--1740924 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1740881 CTATTGCGAT
*
1740891 AAAAGTCGCATAAA
1 AAAAGTCACATAAA
*
1740905 AAAAGTTACATAAA
1 AAAAGTCACATAAA
1740919 AAAAGT
1 AAAAGT
1740925 TATACTCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.62, C:0.09, G:0.12, T:0.18
Consensus pattern (14 bp):
AAAAGTCACATAAA
Found at i:1740925 original size:14 final size:14
Alignment explanation
Indices: 1740899--1740926 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1740889 ATAAAAGTCG
1740899 CATAAAAAAAGTTA
1 CATAAAAAAAGTTA
1740913 CATAAAAAAAGTTA
1 CATAAAAAAAGTTA
1740927 TACTCTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (14 bp):
CATAAAAAAAGTTA
Found at i:1746016 original size:17 final size:17
Alignment explanation
Indices: 1745994--1746047 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
1745984 ATACATAAAG
1745994 TCCTGCACTCATCTTCT
1 TCCTGCACTCATCTTCT
1746011 TCCTG--CT-AT-TTCTT
1 TCCTGCACTCATCTTC-T
1746025 TCCTGCACTCATCTTCT
1 TCCTGCACTCATCTTCT
1746042 TCCTGC
1 TCCTGC
1746048 TATTTCTTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 3 0.09
14 8 0.25
15 2 0.06
16 2 0.06
17 14 0.44
18 3 0.09
ACGTcount: A:0.09, C:0.39, G:0.07, T:0.44
Consensus pattern (17 bp):
TCCTGCACTCATCTTCT
Found at i:1746032 original size:31 final size:31
Alignment explanation
Indices: 1745994--1746055 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1745984 ATACATAAAG
1745994 TCCTGCACTCATCTTCTTCCTGCTATTTCTT
1 TCCTGCACTCATCTTCTTCCTGCTATTTCTT
1746025 TCCTGCACTCATCTTCTTCCTGCTATTTCTT
1 TCCTGCACTCATCTTCTTCCTGCTATTTCTT
1746056 ACTTTGGCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.10, C:0.35, G:0.06, T:0.48
Consensus pattern (31 bp):
TCCTGCACTCATCTTCTTCCTGCTATTTCTT
Found at i:1746936 original size:114 final size:115
Alignment explanation
Indices: 1746736--1746964 Score: 433
Period size: 114 Copynumber: 2.0 Consensus size: 115
1746726 TAGTAGGCCT
*
1746736 CACTAAAAACCCCCTTCATGATTAACGGAACTTGAAAATAGTTCCTTAATCAGCGGAAGGAGGAA
1 CACTAAAAACCCCCTTCATGATTAACGGAACTTGAAAATAGTTCCTTAATCAACGGAAGGAGGAA
1746801 AAGAGTGCCCTAGGAATTCATTAATCTT-AACATTACAAAGTAATAAAAA
66 AAGAGTGCCCTAGGAATTCATTAATCTTAAACATTACAAAGTAATAAAAA
1746850 CACTAAAAACCCCCTTCATGATTAACGGAACTTGAAAATAGTTCCTTAATCAACGGAAGGAGGAA
1 CACTAAAAACCCCCTTCATGATTAACGGAACTTGAAAATAGTTCCTTAATCAACGGAAGGAGGAA
1746915 AAGAGTGCCCTAGGAATTCATTAATCTTAAAACATTACAAAGTAATAAAA
66 AAGAGTGCCCTAGGAATTCATTAATCTT-AAACATTACAAAGTAATAAAA
1746965 GCTTAATCTC
Statistics
Matches: 112, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
114 92 0.82
116 20 0.18
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.24
Consensus pattern (115 bp):
CACTAAAAACCCCCTTCATGATTAACGGAACTTGAAAATAGTTCCTTAATCAACGGAAGGAGGAA
AAGAGTGCCCTAGGAATTCATTAATCTTAAACATTACAAAGTAATAAAAA
Found at i:1750339 original size:10 final size:10
Alignment explanation
Indices: 1750326--1750350 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1750316 ACAAAACCTT
1750326 ACATTCCAAA
1 ACATTCCAAA
1750336 ACATTCCAAA
1 ACATTCCAAA
1750346 ACATT
1 ACATT
1750351 TAGGGTTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (10 bp):
ACATTCCAAA
Found at i:1757341 original size:24 final size:24
Alignment explanation
Indices: 1757313--1757365 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
1757303 GGATATAATG
1757313 GGACAAAATTGAGAATACCTTCGC
1 GGACAAAATTGAGAATACCTTCGC
1757337 GGACAAAATTGAGAATACCTTCGC
1 GGACAAAATTGAGAATACCTTCGC
*
1757361 TGACA
1 GGACA
1757366 GCACACACGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (24 bp):
GGACAAAATTGAGAATACCTTCGC
Found at i:1758765 original size:239 final size:239
Alignment explanation
Indices: 1758346--1758824 Score: 942
Period size: 239 Copynumber: 2.0 Consensus size: 239
1758336 TGCTTAGCAT
1758346 GTCATCAAATGCACTGACGGTGATGGCTTCACAACTCTCGGAGGCAGAAGAAAGGGAGCGCGGTT
1 GTCATCAAATGCACTGACGGTGATGGCTTCACAACTCTCGGAGGCAGAAGAAAGGGAGCGCGGTT
1758411 TGGTTGGTCGTGGGCGGTGGAATCAAGTACGCTCAATAAATGATGCAAAGAACCTGCTTCATACT
66 TGGTTGGTCGTGGGCGGTGGAATCAAGTACGCTCAATAAATGATGCAAAGAACCTGCTTCATACT
1758476 TGTTTAATGCTACTGCAGAATCAAGGTGGCTTATACAAATAGAATCTGAAAAGTTTCTTTCCAAC
131 TGTTTAATGCTACTGCAGAATCAAGGTGGCTTATACAAATAGAATCTGAAAAGTTTCTTTCCAAC
1758541 TTGCTCTTTCTACTGCTGACTTTAGTTATCTGACACTTGAAGTA
196 TTGCTCTTTCTACTGCTGACTTTAGTTATCTGACACTTGAAGTA
1758585 GTCATCAAATGCACTGACGGTGATGGCTTCACAACTCTCGGAGGCAGAAGAAAGGGAGCGCGGTT
1 GTCATCAAATGCACTGACGGTGATGGCTTCACAACTCTCGGAGGCAGAAGAAAGGGAGCGCGGTT
1758650 TGGTTGGTCGTGGGCGGTGGAATCAAGTACGCTCAATAAATGATGCAAAGAACCTGCTTCAATAC
66 TGGTTGGTCGTGGGCGGTGGAATCAAGTACGCTCAATAAATGATGCAAAGAACCTGCTTC-ATAC
1758715 TTGTTTAATGCTACTGCAGAATCAAGGT-GCTTATACAAATAGAATCTGAAAAGTTTCTTTCCAA
130 TTGTTTAATGCTACTGCAGAATCAAGGTGGCTTATACAAATAGAATCTGAAAAGTTTCTTTCCAA
1758779 CTTGCTCTTTCTACTGCTGACTTTAGTTATCTGACACTTGAAGTA
195 CTTGCTCTTTCTACTGCTGACTTTAGTTATCTGACACTTGAAGTA
1758824 G
1 G
1758825 CCTGTTTGTG
Statistics
Matches: 239, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
239 207 0.87
240 32 0.13
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (239 bp):
GTCATCAAATGCACTGACGGTGATGGCTTCACAACTCTCGGAGGCAGAAGAAAGGGAGCGCGGTT
TGGTTGGTCGTGGGCGGTGGAATCAAGTACGCTCAATAAATGATGCAAAGAACCTGCTTCATACT
TGTTTAATGCTACTGCAGAATCAAGGTGGCTTATACAAATAGAATCTGAAAAGTTTCTTTCCAAC
TTGCTCTTTCTACTGCTGACTTTAGTTATCTGACACTTGAAGTA
Found at i:1758845 original size:11 final size:11
Alignment explanation
Indices: 1758829--1758853 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1758819 AAGTAGCCTG
1758829 TTTGTGTTTTA
1 TTTGTGTTTTA
1758840 TTTGTGTTTTA
1 TTTGTGTTTTA
1758851 TTT
1 TTT
1758854 TTTTGGTTGA
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:0.08, C:0.00, G:0.16, T:0.76
Consensus pattern (11 bp):
TTTGTGTTTTA
Found at i:1761903 original size:22 final size:22
Alignment explanation
Indices: 1761878--1761939 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 22
1761868 CATATGAAAT
* *
1761878 TGTCCTGAAAGACCTGTGAGTA
1 TGTCCCGAAAGACCTATGAGTA
*
1761900 TGTCCCGAAGGACCTATGAGT-
1 TGTCCCGAAAGACCTATGAGTA
* *
1761921 TGTACCGAAGGACCTATGA
1 TGTCCCGAAAGACCTATGA
1761940 AACCCTCGAC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 18 0.50
22 18 0.50
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.24
Consensus pattern (22 bp):
TGTCCCGAAAGACCTATGAGTA
Found at i:1761930 original size:21 final size:22
Alignment explanation
Indices: 1761888--1761939 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
1761878 TGTCCTGAAA
* *
1761888 GACCTGTGAGTATGTCCCGAAG
1 GACCTATGAGTATGTACCGAAG
1761910 GACCTATGAGT-TGTACCGAAG
1 GACCTATGAGTATGTACCGAAG
1761931 GACCTATGA
1 GACCTATGA
1761940 AACCCTCGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (22 bp):
GACCTATGAGTATGTACCGAAG
Found at i:1762547 original size:64 final size:65
Alignment explanation
Indices: 1762477--1762597 Score: 149
Period size: 64 Copynumber: 1.9 Consensus size: 65
1762467 TTCCTTTAGA
* * *
1762477 GGGTATCGATACCCTA-CTTAAGGTATCGGTACCCTC-ATGGCATTCTGTGATT-TTTCGTTCAA
1 GGGTATCGATACCC-AGCTGAAGGTATCGATACCCTCAAT-ACATTCTGTGATTCTTTCGTTCAA
1762539 GG
64 GG
* **
1762541 GGGTATCGGTACCCAGCTGGGGGTATCGATACCCTCAATACATTCTGTGATTCTTTC
1 GGGTATCGATACCCAGCTGAAGGTATCGATACCCTCAATACATTCTGTGATTCTTTC
1762598 ATTTGAGAGG
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
63 1 0.02
64 41 0.85
65 6 0.12
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.33
Consensus pattern (65 bp):
GGGTATCGATACCCAGCTGAAGGTATCGATACCCTCAATACATTCTGTGATTCTTTCGTTCAAGG
Found at i:1766421 original size:24 final size:24
Alignment explanation
Indices: 1766385--1766438 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1766375 TAATAGCTTC
* * *
1766385 TTTGCTGATATCACAGAAATAACA
1 TTTGCCGACATCACAAAAATAACA
1766409 TTTGCCGACATCACAAAAATAACA
1 TTTGCCGACATCACAAAAATAACA
1766433 TTTGCC
1 TTTGCC
1766439 AATGGATTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.28
Consensus pattern (24 bp):
TTTGCCGACATCACAAAAATAACA
Found at i:1768826 original size:21 final size:22
Alignment explanation
Indices: 1768780--1768839 Score: 86
Period size: 21 Copynumber: 2.8 Consensus size: 22
1768770 TGTGAAATTA
* *
1768780 TCCCAAAGGACCTGTGAGTATG
1 TCCCGAAGGACCTATGAGTATG
1768802 TCCCGAAGGACCTATGAGT-TG
1 TCCCGAAGGACCTATGAGTATG
*
1768823 TCCCGAATGACCTATGA
1 TCCCGAAGGACCTATGA
1768840 ACCCTCGACT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
21 18 0.51
22 17 0.49
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (22 bp):
TCCCGAAGGACCTATGAGTATG
Found at i:1770359 original size:109 final size:109
Alignment explanation
Indices: 1770197--1770414 Score: 427
Period size: 109 Copynumber: 2.0 Consensus size: 109
1770187 TCACCAAATT
*
1770197 TTGAAACTTTACAATTTAATCATTAACCCGGTATTGGAGATGTTATATTGTGCATGGATTTAATT
1 TTGAAACTTTACAATTTAATCATTAACCCGGTATTGAAGATGTTATATTGTGCATGGATTTAATT
1770262 GCTTAATTATCTGTTTTCAATTTTCTAATTGTAGGAAATTTATA
66 GCTTAATTATCTGTTTTCAATTTTCTAATTGTAGGAAATTTATA
1770306 TTGAAACTTTACAATTTAATCATTAACCCGGTATTGAAGATGTTATATTGTGCATGGATTTAATT
1 TTGAAACTTTACAATTTAATCATTAACCCGGTATTGAAGATGTTATATTGTGCATGGATTTAATT
1770371 GCTTAATTATCTGTTTTCAATTTTCTAATTGTAGGAAATTTATA
66 GCTTAATTATCTGTTTTCAATTTTCTAATTGTAGGAAATTTATA
1770415 AGTGAAGATA
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 108 1.00
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (109 bp):
TTGAAACTTTACAATTTAATCATTAACCCGGTATTGAAGATGTTATATTGTGCATGGATTTAATT
GCTTAATTATCTGTTTTCAATTTTCTAATTGTAGGAAATTTATA
Found at i:1770842 original size:23 final size:23
Alignment explanation
Indices: 1770812--1770855 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1770802 ATTAATCGGG
*
1770812 TTGGATACTGTATAGACAAAGGA
1 TTGGATACTCTATAGACAAAGGA
1770835 TTGGATACTCTATAGACAAAG
1 TTGGATACTCTATAGACAAAG
1770856 ACTATCCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (23 bp):
TTGGATACTCTATAGACAAAGGA
Found at i:1771157 original size:14 final size:14
Alignment explanation
Indices: 1771140--1771182 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
1771130 GGTAAAACAT
1771140 ATTAAATAAATATA
1 ATTAAATAAATATA
* *
1771154 ATTATATAACTATA
1 ATTAAATAAATATA
1771168 ATTAAA-AAATA-A
1 ATTAAATAAATATA
1771180 ATT
1 ATT
1771183 TGGGGCTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 4 0.16
13 4 0.16
14 17 0.68
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (14 bp):
ATTAAATAAATATA
Found at i:1774669 original size:45 final size:45
Alignment explanation
Indices: 1774618--1774703 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
1774608 TCTCTCATAT
* *
1774618 TGTTGGAGCTATTACCAACATTACCCAACTTATTTCCTAAGGCTA
1 TGTTGGAGATATTACCAACATTACACAACTTATTTCCTAAGGCTA
* *
1774663 TGTTGGAGATATTACTAGCATTACACAACTTATTTCCTAAG
1 TGTTGGAGATATTACCAACATTACACAACTTATTTCCTAAG
1774704 ATCTCTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (45 bp):
TGTTGGAGATATTACCAACATTACACAACTTATTTCCTAAGGCTA
Found at i:1783288 original size:54 final size:54
Alignment explanation
Indices: 1783227--1783721 Score: 560
Period size: 54 Copynumber: 9.2 Consensus size: 54
1783217 TTTCATGGTT
* * * * * *
1783227 TTGCACACATATTGTCGATACAGTAATTCACAACCTCATTGTGATTTACGTAGG
1 TTGCACACATAGTGTCAATACGGTAATTCACAAACTCATTATGAATTACGTAGG
* * *
1783281 TTACACACATAGTGCCAATACGGTAATTCACAAACTCATTGTGAATTACGTAGG
1 TTGCACACATAGTGTCAATACGGTAATTCACAAACTCATTATGAATTACGTAGG
* ** * *
1783335 TTGCACATATAGTGTTGATACGGTAATTCACAAACTTATTATGAATTACATAGG
1 TTGCACACATAGTGTCAATACGGTAATTCACAAACTCATTATGAATTACGTAGG
* * * * *
1783389 TTGTACACATGGTGTCAATATGGTAATTCACAAACTCATTATGAATTACTTAGT
1 TTGCACACATAGTGTCAATACGGTAATTCACAAACTCATTATGAATTACGTAGG
* * *
1783443 TTGCACACATAGTGCCAATACGATAATTCACAAACTCATTATGAATTACTTAGG
1 TTGCACACATAGTGTCAATACGGTAATTCACAAACTCATTATGAATTACGTAGG
* ** * * *
1783497 TTGCACACATAGAGAAAATACGGTAATTTATAAACTCATTATGAATTACTTAGG
1 TTGCACACATAGTGTCAATACGGTAATTCACAAACTCATTATGAATTACGTAGG
* * * * * * ** *
1783551 TTGGACGCATAGTGCCAATACGATAATTCACAGACACATTATGAATTATTTAAG
1 TTGCACACATAGTGTCAATACGGTAATTCACAAACTCATTATGAATTACGTAGG
* ** *
1783605 TTGTACACATAGT-TCCAATACAATAATTCACAAACTCATTATGAATTACTTAGG
1 TTGCACACATAGTGT-CAATACGGTAATTCACAAACTCATTATGAATTACGTAGG
** * * *
1783659 TTTAACACATAGTGTCAATACGGTAATTCACAAACTTATTATTAATTACTTAGG
1 TTGCACACATAGTGTCAATACGGTAATTCACAAACTCATTATGAATTACGTAGG
1783713 TTGCACACA
1 TTGCACACA
1783722 CTGTGCTGAT
Statistics
Matches: 375, Mismatches: 64, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
54 374 1.00
55 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (54 bp):
TTGCACACATAGTGTCAATACGGTAATTCACAAACTCATTATGAATTACGTAGG
Found at i:1783520 original size:162 final size:161
Alignment explanation
Indices: 1783227--1783721 Score: 621
Period size: 162 Copynumber: 3.1 Consensus size: 161
1783217 TTTCATGGTT
* * * * * * * * *
1783227 TTGCACACATATTGTCGATACAGTAATTCACAACCTCATTGTGATTTACGTAGGTTACACACATA
1 TTGCACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTA-GTTGCACACATA
* * * * **
1783292 GTGCCAATACGGTAATTCACAAACTCATTGTGAATTACGTAGGTTGCACATATAGTGTTGATACG
65 GTGCCAATACGATAATTCACAAACTCATTATGAATTACTTAGGTTGCACACATAGTGTAAATACG
*
1783357 GTAATTCACAAACTTATTATGAATTACATAGG
130 GTAATTCACAAACTTATTATGAATTACTTAGG
* * * *
1783389 TTGTACACATGGTGTCAATATGGTAATTCACAAACTCATTATGAATTACTTAGTTTGCACACATA
1 TTGCACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAG-TTGCACACATA
* *
1783454 GTGCCAATACGATAATTCACAAACTCATTATGAATTACTTAGGTTGCACACATAGAGAAAATACG
65 GTGCCAATACGATAATTCACAAACTCATTATGAATTACTTAGGTTGCACACATAGTGTAAATACG
* * *
1783519 GTAATTTATAAACTCATTATGAATTACTTAGG
130 GTAATTCACAAACTTATTATGAATTACTTAGG
* * * * * * *
1783551 TTGGACGCATAGTGCCAATACGATAATTCACAGACACATTATGAATTATTTAAGTTGTACACATA
1 TTGCACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTT-AGTTGCACACATA
* * ** *
1783616 GTTCCAATACAATAATTCACAAACTCATTATGAATTACTTAGGTTTAACACATAGTGTCAATACG
65 GTGCCAATACGATAATTCACAAACTCATTATGAATTACTTAGGTTGCACACATAGTGTAAATACG
*
1783681 GTAATTCACAAACTTATTATTAATTACTTAGG
130 GTAATTCACAAACTTATTATGAATTACTTAGG
1783713 TTGCACACA
1 TTGCACACA
1783722 CTGTGCTGAT
Statistics
Matches: 285, Mismatches: 46, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
161 1 0.00
162 282 0.99
163 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (161 bp):
TTGCACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGTTGCACACATAG
TGCCAATACGATAATTCACAAACTCATTATGAATTACTTAGGTTGCACACATAGTGTAAATACGG
TAATTCACAAACTTATTATGAATTACTTAGG
Found at i:1784179 original size:20 final size:20
Alignment explanation
Indices: 1784154--1784206 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
1784144 TTCTGATTAC
1784154 GGTATCGATACCTTCCTCTT
1 GGTATCGATACCTTCCTCTT
*
1784174 GGTATCGATACCTTTCTCTT
1 GGTATCGATACCTTCCTCTT
1784194 GGTATCGATACCT
1 GGTATCGATACCT
1784207 ACACCAGAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (20 bp):
GGTATCGATACCTTCCTCTT
Found at i:1790352 original size:54 final size:54
Alignment explanation
Indices: 1790293--1790749 Score: 627
Period size: 54 Copynumber: 8.4 Consensus size: 54
1790283 TTTTGTACAT
* *
1790293 ATAGTGCTGATACGGTAATTCACAACCTCATTGA-GAATTA-TGTAGGTTGCATAC
1 ATAGTGCTGATACGGTAATTCACAAACTCATT-ATGAATTACT-TAGGTTGCACAC
* * *
1790347 ATAGTGCAGATAATGGTAATTCACAAACTCATTATGAATTACTTAGATTGCACAC
1 ATAGTGCTGAT-ACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGCACAC
* *
1790402 GTAGTGCTGATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTACACAC
1 ATAGTGCTGATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGCACAC
* * *
1790456 ATAGTACCGATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGCACAT
1 ATAGTGCTGATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGCACAC
*
1790510 ATAGTGCT-AGTACGGTAATTCACAAACTCATTATAAATTACTTAGGTTGCACAC
1 ATAGTGCTGA-TACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGCACAC
* * * * *
1790564 ATAGTGGC-AATACGATAATTCACAAACTCGTTATGAATTACTTAAGTTGTACAC
1 ATAGT-GCTGATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGCACAC
** *
1790618 ATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTACACAC
1 ATAGTGCTGATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGCACAC
**
1790672 ATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGCACAC
1 ATAGTGCTGATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGCACAC
*
1790726 ATAGTG-TCGATGCGGTAATTCACA
1 ATAGTGCT-GATACGGTAATTCACA
1790750 GCATATACAT
Statistics
Matches: 362, Mismatches: 33, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
53 3 0.01
54 311 0.86
55 47 0.13
56 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (54 bp):
ATAGTGCTGATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGCACAC
Found at i:1791070 original size:20 final size:20
Alignment explanation
Indices: 1791045--1791094 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
1791035 AGACTGAATA
1791045 GTATCGATACCTCTCCTATG
1 GTATCGATACCTCTCCTATG
1791065 GTATCGATACCTCTCCTATG
1 GTATCGATACCTCTCCTATG
1791085 GTATCGATAC
1 GTATCGATAC
1791095 TTCTATTCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.34
Consensus pattern (20 bp):
GTATCGATACCTCTCCTATG
Found at i:1794138 original size:31 final size:31
Alignment explanation
Indices: 1794050--1794127 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
1794040 GTGTCGAGGG
*
1794050 TTACCTATGTTCTTCGGGACATATGGGTTGT
1 TTACCTATGTTCTTCGGGACATATGGATTGT
1794081 TTACCTATGTTCTTCGGGACATATGGATTGT
1 TTACCTATGTTCTTCGGGACATATGGATTGT
*
1794112 TTACCTAGGTTCTTCG
1 TTACCTATGTTCTTCG
1794128 AAATCAATGG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.17, C:0.18, G:0.23, T:0.42
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGATTGT
Found at i:1794880 original size:21 final size:21
Alignment explanation
Indices: 1794856--1794929 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
1794846 AGTAGCAATA
1794856 CATCGGTACACTGTAACAGTG
1 CATCGGTACACTGTAACAGTG
1794877 CATCGGTACACTGTAACAGTG
1 CATCGGTACACTGTAACAGTG
* **
1794898 CATCGGTACACTATAGTAGTG
1 CATCGGTACACTGTAACAGTG
*
1794919 CATCGATACAC
1 CATCGGTACAC
1794930 AATTTATATT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (21 bp):
CATCGGTACACTGTAACAGTG
Found at i:1796149 original size:22 final size:21
Alignment explanation
Indices: 1796112--1796158 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
1796102 CGTAATCACA
* *
1796112 AAAGTGCCTTAGCACTAATAC
1 AAAGTGCCTCAACACTAATAC
*
1796133 TAAAGTGCCTCAACACTGATAC
1 -AAAGTGCCTCAACACTAATAC
1796155 AAAG
1 AAAG
1796159 GTGTATTCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.21
Consensus pattern (21 bp):
AAAGTGCCTCAACACTAATAC
Found at i:1798771 original size:6 final size:6
Alignment explanation
Indices: 1798760--1798790 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1798750 AAATGACTCC
1798760 TTATAA TTATAA TTATAA TTATAA TTATAA T
1 TTATAA TTATAA TTATAA TTATAA TTATAA T
1798791 GTTATATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTATAA
Found at i:1799395 original size:3 final size:3
Alignment explanation
Indices: 1799380--1799479 Score: 103
Period size: 3 Copynumber: 32.7 Consensus size: 3
1799370 TTCATTTAAA
* *
1799380 TAT TAT T-T ATAT TAT TAT TAT TAT TAT AAT TAT TAT TAT TAT AAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
1799425 TAT AAT TAC TAA TAT TAT TAT TATT TAT TAT TAA TAT TAT TAT TAAA
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T-AT
1799472 TAT TAT TA
1 TAT TAT TA
1799480 CAAGCCCAAA
Statistics
Matches: 80, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
2 1 0.01
3 73 0.91
4 6 0.08
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:1801600 original size:16 final size:16
Alignment explanation
Indices: 1801579--1801636 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 16
1801569 TCTTTCAAAT
1801579 TTTTTAT-TACTTATTA
1 TTTTTATATA-TTATTA
1801595 TTTTTATATATTATTA
1 TTTTTATATATTATTA
*
1801611 TTTTT-TATTTTATTTA
1 TTTTTATATATTA-TTA
1801627 TTTATTATAT
1 TTT-TTATAT
1801637 TCAAGAATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
15 6 0.16
16 24 0.65
17 4 0.11
18 3 0.08
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTATATATTATTA
Found at i:1801631 original size:23 final size:24
Alignment explanation
Indices: 1801577--1801634 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
1801567 TTTCTTTCAA
*
1801577 ATTT-TTTATTACTTATTATTTTT
1 ATTTATTTATTATTTATTATTTTT
* *
1801600 ATATA-TTATTATTTTTTA-TTTT
1 ATTTATTTATTATTTATTATTTTT
1801622 ATTTATTTATTAT
1 ATTTATTTATTAT
1801635 ATTCAAGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 8 0.28
23 21 0.72
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (24 bp):
ATTTATTTATTATTTATTATTTTT
Found at i:1801637 original size:13 final size:13
Alignment explanation
Indices: 1801589--1801637 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
1801579 TTTTTATTAC
*
1801589 TTATTATTTTTAT
1 TTATTATATTTAT
*
1801602 ATATTATTATTT-T
1 TTATTA-TATTTAT
*
1801615 TTATTTTATTTAT
1 TTATTATATTTAT
1801628 TTATTATATT
1 TTATTATATT
1801638 CAAGAATTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 5 0.17
13 20 0.69
14 4 0.14
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTATTATATTTAT
Found at i:1803067 original size:43 final size:43
Alignment explanation
Indices: 1803000--1803085 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
1802990 TGGCTTTAGA
* *
1803000 GAAGTTAGGAGGGAAAGTTATCCCCTATATGTAAAGTTTTGTT
1 GAAGTTAGGACGGAAAGATATCCCCTATATGTAAAGTTTTGTT
* *
1803043 GAAGTTAGGACTGAAAGATGTCCCCTATATGTAAAGTTTTGTT
1 GAAGTTAGGACGGAAAGATATCCCCTATATGTAAAGTTTTGTT
1803086 TGATGCACGG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.35
Consensus pattern (43 bp):
GAAGTTAGGACGGAAAGATATCCCCTATATGTAAAGTTTTGTT
Found at i:1803378 original size:15 final size:15
Alignment explanation
Indices: 1803342--1803380 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1803332 AATTTACATG
1803342 TTTACATTT-GCATA
1 TTTACATTTGGCATA
*
1803356 TTTACATTTGGCATC
1 TTTACATTTGGCATA
*
1803371 TTTGCATTTG
1 TTTACATTTG
1803381 TATTTTTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.21, C:0.15, G:0.13, T:0.51
Consensus pattern (15 bp):
TTTACATTTGGCATA
Found at i:1806614 original size:17 final size:17
Alignment explanation
Indices: 1806592--1806624 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1806582 CAGCAAAGAA
1806592 AGGAAAAAAGAAAAAAG
1 AGGAAAAAAGAAAAAAG
1806609 AGGAAAAAAGAAAAAA
1 AGGAAAAAAGAAAAAA
1806625 AAAGAGGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
AGGAAAAAAGAAAAAAG
Found at i:1806616 original size:10 final size:10
Alignment explanation
Indices: 1806601--1806647 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
1806591 AAGGAAAAAA
1806601 GAAAAAAGAG
1 GAAAAAAGAG
*
1806611 GAAAAAAGAA
1 GAAAAAAGAG
*
1806621 AAAAAAAGAG
1 GAAAAAAGAG
*
1806631 GAAAGAAATA-
1 GAAA-AAAGAG
1806641 GAAAAAA
1 GAAAAAA
1806648 AACAAAAGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
9 3 0.10
10 24 0.77
11 4 0.13
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (10 bp):
GAAAAAAGAG
Found at i:1806627 original size:20 final size:20
Alignment explanation
Indices: 1806602--1806667 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
1806592 AGGAAAAAAG
1806602 AAAAAAGAGGAAAAAAGAAA
1 AAAAAAGAGGAAAAAAGAAA
*
1806622 AAAAAAGAGGAAAGAAATAGAA
1 AAAAAAGAGGAAA-AAAGA-AA
* *
1806644 AAAAAACA-AAAGAAAAGAAA
1 AAAAAAGAGGAA-AAAAGAAA
1806664 AAAA
1 AAAA
1806668 TTAAATCAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 19 0.49
21 10 0.26
22 10 0.26
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (20 bp):
AAAAAAGAGGAAAAAAGAAA
Found at i:1806635 original size:17 final size:18
Alignment explanation
Indices: 1806592--1806666 Score: 55
Period size: 20 Copynumber: 3.9 Consensus size: 18
1806582 CAGCAAAGAA
1806592 AGGAAA-AAAGAAAAAAG
1 AGGAAAGAAAGAAAAAAG
1806609 AGGAAA-AAAGAAAAAAAAAG
1 AGGAAAGAAAG---AAAAAAG
*
1806629 AGGAAAGAAATAGAAAAAAA
1 AGGAAAG-AA-AGAAAAAAG
**
1806649 ACAAAAGAAAAGAAAAAA
1 AGGAAAG-AAAGAAAAAA
1806667 ATTAAATCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
17 10 0.20
19 8 0.16
20 27 0.55
22 2 0.04
23 2 0.04
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.01
Consensus pattern (18 bp):
AGGAAAGAAAGAAAAAAG
Found at i:1806659 original size:10 final size:10
Alignment explanation
Indices: 1806614--1806664 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
1806604 AAAAGAGGAA
*
1806614 AAAAGAAAAA
1 AAAAGAAAAG
1806624 AAAAGAGGAAAG
1 AAAAGA--AAAG
1806636 AAATAGAAAA-
1 AAA-AGAAAAG
*
1806646 AAAACAAAAG
1 AAAAGAAAAG
1806656 AAAAGAAAA
1 AAAAGAAAA
1806665 AAATTAAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
9 5 0.15
10 17 0.50
11 3 0.09
12 6 0.18
13 3 0.09
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (10 bp):
AAAAGAAAAG
Found at i:1811212 original size:50 final size:53
Alignment explanation
Indices: 1811070--1811214 Score: 140
Period size: 50 Copynumber: 2.8 Consensus size: 53
1811060 AGAAATCTTG
* * * *
1811070 GCAGAAGCCACAAGAAATGAAGAATGTTTGTCAAATGTTTTACAAACATCTGA
1 GCAGAAACCACAGGAAAAGATGAATGTTTGTCAAATGTTTTACAAACATCTGA
* * * * *
1811123 GCAG-AAGCA-AGAAAAATGATGAATATGTTGTCAACTGTTTTAC-ATC-TC-GA
1 GCAGAAACCACAGGAAAA-GATGAATGT-TTGTCAAATGTTTTACAAACATCTGA
1811173 -CAGAAACCACAGGAAAAGATGAATGTATTGTCAAATGTTTTA
1 GCAGAAACCACAGGAAAAGATGAATGT-TTGTCAAATGTTTTA
1811215 TGAACCAGTG
Statistics
Matches: 74, Mismatches: 14, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
49 3 0.04
50 28 0.38
51 12 0.16
52 12 0.16
53 19 0.26
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (53 bp):
GCAGAAACCACAGGAAAAGATGAATGTTTGTCAAATGTTTTACAAACATCTGA
Found at i:1811615 original size:22 final size:22
Alignment explanation
Indices: 1811586--1811640 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
1811576 ATCTACACTC
* *
1811586 TTCAAAGATGATATATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
1811608 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
1811630 TTCAAAGATGA
1 TTCAAAGATGA
1811641 AAACTTTATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:1812238 original size:113 final size:113
Alignment explanation
Indices: 1812040--1813599 Score: 2426
Period size: 113 Copynumber: 13.8 Consensus size: 113
1812030 TAGCAAAGAT
*
1812040 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATTAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1812105 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
1812153 TCAAATCCACCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1812218 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
1812266 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1812331 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
1812379 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1812444 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
1812492 TCAAATCCATCATCTGATGGATCAGCTTTTCCAAAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1812557 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
1812605 TCAAATCCATCATCTGATGGATCAGCTTTTCCA-AAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1812669 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
1812717 TCAAATCCATCATCTGATGGATCAGCTTTTCCAAAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1812782 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
****
1812830 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* *
1812895 AGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * ****
1812943 TCAAATCTATCA-CTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATC-TGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
* *
1813007 AAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * ****
1813056 TCAAATCTATCA-CTTGATAGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATC-TGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
* *
1813120 AAGAAGGATGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * ****
1813169 TCAAATCTATCA-CTTGATAGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATC-TGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
* *
1813233 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTTGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
1813282 CCAAATCCATCA-CTTGATGGATCAGCTTTTCTAGAGAAAGTTCATAATAAGAAGAACTCATCTG
1 TCAAATCCATCATC-TGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
* * * *
1813346 AAGAAGGAAGAAGAAGTTCATAATGAGAATAATTTATTCAATCTTTTGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * * ** * *
1813395 TCAAATACATCATTTGATGGATCAACATTGCCAGGTAGAGTTCACAATGAGAAGAACTCGTCATC
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAA--C-TCATC
* *
1813460 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
63 TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
1813511 TCAAATCCATCA-CTTGATAGATCAGC--TT-GAGAGAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATC-TGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
1813572 AAGAA-GAAGAAG---TTCATAATGAGAAGAA
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAA
1813600 CTAATCTGAA
Statistics
Matches: 1380, Mismatches: 60, Indels: 21
0.94 0.04 0.01
Matches are distributed among these distances:
106 16 0.01
109 7 0.01
110 12 0.01
111 1 0.00
112 113 0.08
113 1156 0.84
114 1 0.00
115 1 0.00
116 73 0.05
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (113 bp):
TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:1813585 original size:36 final size:36
Alignment explanation
Indices: 1813545--1813623 Score: 140
Period size: 36 Copynumber: 2.2 Consensus size: 36
1813535 GCTTGAGAGA
* *
1813545 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG
1 AAGTTCATAATGAGAAGAACTAATCTGAAAAAGAAG
1813581 AAGTTCATAATGAGAAGAACTAATCTGAAAAAGAAG
1 AAGTTCATAATGAGAAGAACTAATCTGAAAAAGAAG
1813617 AAGTTCA
1 AAGTTCA
1813624 AGAATGTTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.49, C:0.10, G:0.20, T:0.20
Consensus pattern (36 bp):
AAGTTCATAATGAGAAGAACTAATCTGAAAAAGAAG
Found at i:1813705 original size:30 final size:30
Alignment explanation
Indices: 1813669--1813729 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
1813659 TTTTGAATGA
1813669 CTCTATCACAGAAAGGAAATAGGTCAACAT
1 CTCTATCACAGAAAGGAAATAGGTCAACAT
1813699 CTCTATCACAGAAAGGAAATAGGTCAACAT
1 CTCTATCACAGAAAGGAAATAGGTCAACAT
1813729 C
1 C
1813730 ATCCCCAGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.20
Consensus pattern (30 bp):
CTCTATCACAGAAAGGAAATAGGTCAACAT
Found at i:1813932 original size:3 final size:3
Alignment explanation
Indices: 1813917--1814016 Score: 112
Period size: 3 Copynumber: 32.7 Consensus size: 3
1813907 TTCATTTAAA
*
1813917 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT AAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
1813962 TAT AAT TAC TAA TAT TAT TAT TATT TAT TAT TAA TAT TAT TAT TAAA
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T-AT
1814009 TAT TAT TA
1 TAT TAT TA
1814017 CAAGCCCAAA
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
2 1 0.01
3 75 0.91
4 6 0.07
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:1815587 original size:100 final size:99
Alignment explanation
Indices: 1815421--1815607 Score: 216
Period size: 100 Copynumber: 1.9 Consensus size: 99
1815411 TTTTTAAAAT
* * * * *
1815421 AAATTATTTTTAATATTTATTTTTCAATATCGAAGAAAAGGGCAGTCTTAATACAACTGGATGTC
1 AAATTATTTTTAATATTTATTTTTCAATATCAAAGAAAAGAGCAGTCTTAAGACAACTAGAAGTC
*
1815486 CTACTCTGGTA-TTTTAAAATTAAATATTATAAA
66 CTACTCTGATATTTTTAAAATTAAATATTATAAA
* ** * *
1815519 AAATTATTATTTAAT-TTTATATTTATTAATATCAAAGAAAAGAGCTTTCTTAAGGCACCTAGAA
1 AAATTATT-TTTAATATTTAT-TTT-TCAATATCAAAGAAAAGAGCAGTCTTAAGACAACTAGAA
**
1815583 GTCCTTTTCTGATATTTTTAAAATT
63 GTCCTACTCTGATATTTTTAAAATT
1815608 TTTTTATAAT
Statistics
Matches: 72, Mismatches: 13, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
98 13 0.18
99 9 0.12
100 40 0.56
101 10 0.14
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (99 bp):
AAATTATTTTTAATATTTATTTTTCAATATCAAAGAAAAGAGCAGTCTTAAGACAACTAGAAGTC
CTACTCTGATATTTTTAAAATTAAATATTATAAA
Found at i:1820688 original size:2 final size:2
Alignment explanation
Indices: 1820683--1820730 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1820673 AGGGTTTTTT
1820683 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1820725 TA TA TA
1 TA TA TA
1820731 AGTGTTTGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1821000 original size:43 final size:43
Alignment explanation
Indices: 1820950--1821215 Score: 236
Period size: 43 Copynumber: 6.2 Consensus size: 43
1820940 TGAGAACAAA
*
1820950 AAACGCCGCAATAGGTCA-ATATATATTACGGCGTTTTTGGA-AC
1 AAACGCCGCAAAAGGTCAGATATATA--ACGGCGTTTTTGGACAC
* * *
1820993 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATATATAACGGCGTTTTTGGACAC
* * ** * *
1821036 AAATGCCGCAAAAGAG-CATACCTAT-ACTGGCGCTTTTAGA-AC
1 AAACGCCGCAAAAG-GTCAGATATATAAC-GGCGTTTTTGGACAC
** *
1821078 AAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGACAC
1 AAACGCCGCAAAAGGTCAGATATATAACGGCGTTTTTGGACAC
* ** * **
1821121 AAACGCTGCAAAAGGTCAGACCTATAACGGCATTTTTAAACAC
1 AAACGCCGCAAAAGGTCAGATATATAACGGCGTTTTTGGACAC
* * ** * *
1821164 AAACGTCGCAAAAAGTCAGACCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATATATAACGGCGTTTTTGGACAC
1821207 AAACGCCGC
1 AAACGCCGC
1821216 TAATTACCTT
Statistics
Matches: 188, Mismatches: 28, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
41 1 0.01
42 47 0.25
43 133 0.71
44 7 0.04
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCAGATATATAACGGCGTTTTTGGACAC
Found at i:1821084 original size:85 final size:85
Alignment explanation
Indices: 1820950--1821215 Score: 340
Period size: 85 Copynumber: 3.1 Consensus size: 85
1820940 TGAGAACAAA
* ** * *
1820950 AAACGCCGCAATAGGTCA-ATATATATTACGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAGAT
1 AAACGCCGCAAAAGGTCAGACCTATA--ACGGCGTTTTTAGAACAAACGCCGCAAAAGGTCAGAC
1821014 CTATAGCGGCGTTTTTGGATAC
64 CTATAGCGGCGTTTTTGGATAC
* * *
1821036 AAATGCCGCAAAAGAG-CATACCTAT-ACTGGCGCTTTTAGAACAAACGCCGCAAAAGGTCAGAC
1 AAACGCCGCAAAAG-GTCAGACCTATAAC-GGCGTTTTTAGAACAAACGCCGCAAAAGGTCAGAC
*
1821099 CTATAGCGGCGTTTTTGGACAC
64 CTATAGCGGCGTTTTTGGATAC
* * * * *
1821121 AAACGCTGCAAAAGGTCAGACCTATAACGGCATTTTTAAACACAAACGTCGCAAAAAGTCAGACC
1 AAACGCCGCAAAAGGTCAGACCTATAACGGCGTTTTTAGA-ACAAACGCCGCAAAAGGTCAGACC
1821186 TATAGCGGCGTTTTTGGATAC
65 TATAGCGGCGTTTTTGGATAC
1821207 AAACGCCGC
1 AAACGCCGC
1821216 TAATTACCTT
Statistics
Matches: 156, Mismatches: 18, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
84 3 0.02
85 82 0.53
86 66 0.42
87 5 0.03
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22
Consensus pattern (85 bp):
AAACGCCGCAAAAGGTCAGACCTATAACGGCGTTTTTAGAACAAACGCCGCAAAAGGTCAGACCT
ATAGCGGCGTTTTTGGATAC
Found at i:1821187 original size:128 final size:128
Alignment explanation
Indices: 1820978--1821215 Score: 320
Period size: 128 Copynumber: 1.9 Consensus size: 128
1820968 ATATATATTA
* * * ** * *
1820978 CGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATACAAATGCC
1 CGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAGACCTATAACGGCATTTTTAAACACAAACGCC
*
1821043 GCAAAAGAGCATACCTATA-CTGGCGCTTTTAGA-ACAAACGCCGCAAAAGGTCAGACCTATAG
66 GCAAAAGAGCAGACCTATAGC-GGCGCTTTTAGATACAAACGCCGCAAAAGGTCAGACCTATAG
* *
1821105 CGGCGTTTTTGGACACAAACGCTGCAAAAGGTCAGACCTATAACGGCATTTTTAAACACAAACGT
1 CGGCGTTTTTGGA-ACAAACGCCGCAAAAGGTCAGACCTATAACGGCATTTTTAAACACAAACGC
* *
1821170 CGCAAAA-AGTCAGACCTATAGCGGCGTTTTTGGATACAAACGCCGC
65 CGCAAAAGAG-CAGACCTATAGCGGCGCTTTTAGATACAAACGCCGC
1821216 TAATTACCTT
Statistics
Matches: 95, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
127 15 0.16
128 68 0.72
129 12 0.13
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.21
Consensus pattern (128 bp):
CGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAGACCTATAACGGCATTTTTAAACACAAACGCC
GCAAAAGAGCAGACCTATAGCGGCGCTTTTAGATACAAACGCCGCAAAAGGTCAGACCTATAG
Found at i:1822454 original size:20 final size:20
Alignment explanation
Indices: 1822429--1822467 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1822419 GAGATCCCCA
1822429 AGTGCGAGGCCAGCCTGAAG
1 AGTGCGAGGCCAGCCTGAAG
1822449 AGTGCGAGGCCAGCCTGAA
1 AGTGCGAGGCCAGCCTGAA
1822468 AGAAGATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.38, T:0.10
Consensus pattern (20 bp):
AGTGCGAGGCCAGCCTGAAG
Found at i:1824737 original size:83 final size:82
Alignment explanation
Indices: 1824646--1825000 Score: 443
Period size: 83 Copynumber: 4.3 Consensus size: 82
1824636 TATGACAATT
*
1824646 GCGGCGTTTG-GTATTAAAACACCACTAAAGTACGAGTCTATAGCGGCGTTTGTGTA-AAAACGC
1 GCGGCGTTTGTGTA--AAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTG-GTATAAAACGC
1824709 CACAAAAGTACGTGTCTATA
63 CACAAAAGTACGTGTCTATA
* *
1824729 GCGACGTTTGTGTAAAAATGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTATTAAAACGCCA
1 GCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTA-TAAAACGCCA
1824794 CAAAAGTACGTGTCTATA
65 CAAAAGTACGTGTCTATA
*
1824812 GCGGCGTTTGTGTAAAAATGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTATTAAAACGCCA
1 GCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTA-TAAAACGCCA
*
1824877 CAAAAGTATGTGTCTATA
65 CAAAAGTACGTGTCTATA
* * * * * * * *
1824895 GCGGCGTTTGTATAAAAACGCCACTACATTACGATTATTTAGCGGCGTTT-TTATACAAACGTCA
1 GCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTATA-AAACGCCA
* * * *
1824959 CTAAAGTATAGTAT-TTTA
65 CAAAAGTA-CGTGTCTATA
*
1824977 -CGGCGTTTGT-TCAAAACGCCACTA
1 GCGGCGTTTGTGTAAAAACGCCACTA
1825001 TATGTAAACA
Statistics
Matches: 248, Mismatches: 19, Indels: 13
0.89 0.07 0.05
Matches are distributed among these distances:
80 13 0.05
81 15 0.06
82 54 0.22
83 163 0.66
84 3 0.01
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.28
Consensus pattern (82 bp):
GCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTATAAAACGCCAC
AAAAGTACGTGTCTATA
Found at i:1824938 original size:41 final size:41
Alignment explanation
Indices: 1824646--1825000 Score: 392
Period size: 41 Copynumber: 8.6 Consensus size: 41
1824636 TATGACAATT
* *
1824646 GCGGCGTTTGGTATTAAAACACCACTAAAGTACGAGTCTATA
1 GCGGCGTTT-GTATAAAAACGCCACTAAAGTACGAGTCTATA
* * *
1824688 GCGGCGTTTGTGTAAAAACGCCACAAAAGTACGTGTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATA
* * *
1824729 GCGACGTTTGTGTAAAAATGCCACTAAAGTACGAGTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATA
* * *
1824770 GCGGCGTTTGGTATTAAAACGCCACAAAAGTACGTGTCTATA
1 GCGGCGTTT-GTATAAAAACGCCACTAAAGTACGAGTCTATA
* *
1824812 GCGGCGTTTGTGTAAAAATGCCACTAAAGTACGAGTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATA
* * * *
1824853 GCGGCGTTTGGTATTAAAACGCCACAAAAGTATGTGTCTATA
1 GCGGCGTTT-GTATAAAAACGCCACTAAAGTACGAGTCTATA
* * * * *
1824895 GCGGCGTTTGTATAAAAACGCCACTACATTACGATTATTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATA
* * * * * *
1824936 GCGGCGTTTTTATACAAACGTCACTAAAGTA-TAGTATTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGT-CTATA
*
1824977 -CGGCGTTTGT-TCAAAACGCCACTA
1 GCGGCGTTTGTATAAAAACGCCACTA
1825001 TATGTAAACA
Statistics
Matches: 263, Mismatches: 47, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
39 11 0.04
40 11 0.04
41 161 0.61
42 80 0.30
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.28
Consensus pattern (41 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATA
Found at i:1824961 original size:124 final size:124
Alignment explanation
Indices: 1824646--1824966 Score: 414
Period size: 124 Copynumber: 2.6 Consensus size: 124
1824636 TATGACAATT
* *
1824646 GCGGCGTTTGGTATTAAAACACCACTAAAGTACGAGTCTATAGCGGCGTTTGTGTAAAAACGCCA
1 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGATTCTATAGCGGCGTTTGTGTAAAAACGCCA
* * * *
1824711 CAAAAGTACGTGTCTATAGCGACGTTTGTGTAAAAATGCCACTAAAGTACGAGTCTATA
66 CTAAAGTACGAGTCTATAGCGACGTTTGTGTAAAAACGCCACAAAAGTACGAGTCTATA
* *
1824770 GCGGCGTTTGGTATTAAAACGCCACAAAAGTACG-TGTCTATAGCGGCGTTTGTGTAAAAATGCC
1 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAT-TCTATAGCGGCGTTTGTGTAAAAACGCC
* * *
1824834 ACTAAAGTACGAGTCTATAGCGGCGTTTG-GTATTAAAACGCCACAAAAGTATGTGTCTATA
65 ACTAAAGTACGAGTCTATAGCGACGTTTGTGTA--AAAACGCCACAAAAGTACGAGTCTATA
* * * * * * * * *
1824895 GCGGCGTTT-GTATAAAAACGCCACTACATTACGATTATTTAGCGGCGTTTTTATACAAACGTCA
1 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGATTCTATAGCGGCGTTTGTGTAAAAACGCCA
1824959 CTAAAGTA
66 CTAAAGTA
1824967 TAGTATTTTA
Statistics
Matches: 171, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
123 3 0.02
124 135 0.79
125 33 0.19
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.27
Consensus pattern (124 bp):
GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGATTCTATAGCGGCGTTTGTGTAAAAACGCCA
CTAAAGTACGAGTCTATAGCGACGTTTGTGTAAAAACGCCACAAAAGTACGAGTCTATA
Found at i:1831793 original size:3 final size:3
Alignment explanation
Indices: 1831785--1831823 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
1831775 TATTTACTTC
*
1831785 TGA TGA TGA TTA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1831824 GAGTGAGGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:1832046 original size:17 final size:18
Alignment explanation
Indices: 1832024--1832057 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1832014 GTTAGAATTG
1832024 TTTTTAT-TTTTTAGTTC
1 TTTTTATCTTTTTAGTTC
1832041 TTTTTATCTTTTTAGTT
1 TTTTTATCTTTTTAGTT
1832058 GTATCGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.76
Consensus pattern (18 bp):
TTTTTATCTTTTTAGTTC
Found at i:1850262 original size:60 final size:61
Alignment explanation
Indices: 1850172--1850298 Score: 179
Period size: 60 Copynumber: 2.1 Consensus size: 61
1850162 TTTATATTTT
*
1850172 AAAG-TACACAAATAGTACTCCAACTATAAGGTATTGTTTTGTTGAGTCTCCCAACCATTA
1 AAAGTTACACAAATAGTACTCCAACTATAAGGTATTGCTTTGTTGAGTCTCCCAACCATTA
* * * *
1850232 AAAGTTACA-AAATGGT-CTCCTAACTATAAGGTATTGCTTTGTTGAGTCTCTCGACTATTA
1 AAAGTTACACAAATAGTACTCC-AACTATAAGGTATTGCTTTGTTGAGTCTCCCAACCATTA
1850292 AAAGTTA
1 AAAGTTA
1850299 TAAATTGATC
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
59 4 0.07
60 52 0.87
61 4 0.07
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (61 bp):
AAAGTTACACAAATAGTACTCCAACTATAAGGTATTGCTTTGTTGAGTCTCCCAACCATTA
Found at i:1850316 original size:60 final size:60
Alignment explanation
Indices: 1850193--1850318 Score: 171
Period size: 60 Copynumber: 2.1 Consensus size: 60
1850183 ATAGTACTCC
* * * *
1850193 AACTATAAGGTATTGTTTTGTTGAGTCTCCCAACCATTAAAAGTTACAAAATGGTCTCCT
1 AACTATAAGGTATTGCTTTGTTGAGTCTCCCAACCATTAAAAGTTACAAAATGATCACAT
* * * * *
1850253 AACTATAAGGTATTGCTTTGTTGAGTCTCTCGACTATTAAAAGTTATAAATTGATCACAT
1 AACTATAAGGTATTGCTTTGTTGAGTCTCCCAACCATTAAAAGTTACAAAATGATCACAT
1850313 AACTAT
1 AACTAT
1850319 TCATATGTTC
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (60 bp):
AACTATAAGGTATTGCTTTGTTGAGTCTCCCAACCATTAAAAGTTACAAAATGATCACAT
Found at i:1851207 original size:21 final size:22
Alignment explanation
Indices: 1851177--1851222 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1851167 TGAAATTTCC
* *
1851177 TAAAATTCGAA-TTTTCTTCTT
1 TAAAACTCGAAGTTTTCTTCAT
1851198 TAAAACTCGAAGTTTTCTTCAT
1 TAAAACTCGAAGTTTTCTTCAT
1851220 TAA
1 TAA
1851223 TATACACATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.46
Consensus pattern (22 bp):
TAAAACTCGAAGTTTTCTTCAT
Found at i:1853661 original size:18 final size:18
Alignment explanation
Indices: 1853638--1853686 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
1853628 AGAAAGACAC
1853638 GAAAAGGAGAAGGAACGT
1 GAAAAGGAGAAGGAACGT
1853656 GAAAAGGAGAAGGAACGT
1 GAAAAGGAGAAGGAACGT
*
1853674 GAAATGGA-AAGGA
1 GAAAAGGAGAAGGA
1853687 GGGCTGAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 5 0.17
18 25 0.83
ACGTcount: A:0.51, C:0.04, G:0.39, T:0.06
Consensus pattern (18 bp):
GAAAAGGAGAAGGAACGT
Found at i:1860469 original size:20 final size:20
Alignment explanation
Indices: 1860446--1860493 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1860436 CCAGGAAGAA
1860446 TCGAACCGAGTTGACCCAAC
1 TCGAACCGAGTTGACCCAAC
** **
1860466 TCGAACTAAGTTGACCTGAC
1 TCGAACCGAGTTGACCCAAC
1860486 TCGAACCG
1 TCGAACCG
1860494 TTGACCGGCC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.31, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGAACCGAGTTGACCCAAC
Found at i:1864254 original size:36 final size:37
Alignment explanation
Indices: 1864207--1864287 Score: 121
Period size: 37 Copynumber: 2.2 Consensus size: 37
1864197 TTTAAAAAAT
*
1864207 ATATATGAA-TTTATCTAAAAAGAATAAACTATGTG-A
1 ATATATAAATTTTATCTAAAAAGAAT-AACTATGTGCA
*
1864243 ATATATAAATTTTATCTAAAAAGAATAATTATGTGCA
1 ATATATAAATTTTATCTAAAAAGAATAACTATGTGCA
1864280 ATATATAA
1 ATATATAA
1864288 CAAAGACAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
36 16 0.39
37 25 0.61
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.36
Consensus pattern (37 bp):
ATATATAAATTTTATCTAAAAAGAATAACTATGTGCA
Found at i:1865827 original size:36 final size:37
Alignment explanation
Indices: 1865758--1865838 Score: 128
Period size: 36 Copynumber: 2.2 Consensus size: 37
1865748 TTTAAAAATT
* *
1865758 ATATATGAATTTTATCTAAAAAGAATAACTATGTGTA
1 ATATATAAATTTTATCTAAAAAGAATAACTATGTGCA
*
1865795 ATATATAAATTTTATCT-AAAAGAATAATTATGTGCA
1 ATATATAAATTTTATCTAAAAAGAATAACTATGTGCA
1865831 ATATATAA
1 ATATATAA
1865839 CAAAGACAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
36 25 0.61
37 16 0.39
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.38
Consensus pattern (37 bp):
ATATATAAATTTTATCTAAAAAGAATAACTATGTGCA
Found at i:1871324 original size:33 final size:36
Alignment explanation
Indices: 1871229--1871332 Score: 117
Period size: 33 Copynumber: 3.0 Consensus size: 36
1871219 ATCCCATTAT
* * **
1871229 CATTTTTC-AACAAACATCTATTAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
* *
1871265 TATTTTTCAAAGAAGCATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1871301 CA-TTTTCAAA-AAAC-TTTACCAAACTTTGAAAA
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAA
1871333 TACGAAATTT
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
33 18 0.31
34 3 0.05
35 8 0.14
36 13 0.22
37 17 0.29
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:1883316 original size:21 final size:21
Alignment explanation
Indices: 1883287--1883352 Score: 56
Period size: 21 Copynumber: 3.5 Consensus size: 21
1883277 ATTTTTCAAA
*
1883287 AAAAACATTTACCAAACTTTG
1 AAAATCATTTACCAAACTTTG
*
1883308 AAAATCATTT-TCAAA-----
1 AAAATCATTTACCAAACTTTG
1883323 AAAA-CATTTACCAAACTTTG
1 AAAATCATTTACCAAACTTTG
*
1883343 AAAATTATTT
1 AAAATCATTT
1883353 TTTCAAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
14 5 0.15
15 8 0.24
20 8 0.24
21 13 0.38
ACGTcount: A:0.48, C:0.15, G:0.03, T:0.33
Consensus pattern (21 bp):
AAAATCATTTACCAAACTTTG
Found at i:1883331 original size:35 final size:35
Alignment explanation
Indices: 1883243--1883353 Score: 143
Period size: 35 Copynumber: 3.1 Consensus size: 35
1883233 CCATTATTAT
* * * *
1883243 TTTTC-AATAAACATCTATCAAACTTTGAAAAACTA
1 TTTTCAAAAAAACATTTACCAAACTTTGAAAATC-A
1883278 TTTTTCAAAAAAAACATTTACCAAACTTTGAAAATCA
1 -TTTTC-AAAAAAACATTTACCAAACTTTGAAAATCA
*
1883315 TTTTCAAAAAAACATTTACCAAACTTTGAAAATTA
1 TTTTCAAAAAAACATTTACCAAACTTTGAAAATCA
1883350 TTTT
1 TTTT
1883354 TTCAAAATTA
Statistics
Matches: 68, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
35 33 0.49
36 10 0.15
37 1 0.01
38 24 0.35
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.36
Consensus pattern (35 bp):
TTTTCAAAAAAACATTTACCAAACTTTGAAAATCA
Found at i:1887738 original size:49 final size:49
Alignment explanation
Indices: 1887685--1887890 Score: 322
Period size: 49 Copynumber: 4.2 Consensus size: 49
1887675 TTTATGTTGA
*
1887685 AAATGTACCGTTATGCATTTAACTTTCATTAGTGACACCTTTTATGCCG
1 AAATGCACCGTTATGCATTTAACTTTCATTAGTGACACCTTTTATGCCG
* *
1887734 AAATGCACCGTTATGCATTTAACTTTTATTAGTGACACTTTTTATGCCG
1 AAATGCACCGTTATGCATTTAACTTTCATTAGTGACACCTTTTATGCCG
* * *
1887783 AAATGCACCGTTATGCATTTAATTTTCATTAGTGGCACATTTTATGCCG
1 AAATGCACCGTTATGCATTTAACTTTCATTAGTGACACCTTTTATGCCG
* * * *
1887832 AAATGCACCGTTATACATTTAACTTTCATTAGCGGCACCTTTCATGCCG
1 AAATGCACCGTTATGCATTTAACTTTCATTAGTGACACCTTTTATGCCG
1887881 AAATGCACCG
1 AAATGCACCG
1887891 ATTTAAACAT
Statistics
Matches: 145, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 145 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.36
Consensus pattern (49 bp):
AAATGCACCGTTATGCATTTAACTTTCATTAGTGACACCTTTTATGCCG
Found at i:1891225 original size:13 final size:14
Alignment explanation
Indices: 1891207--1891235 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1891197 CTTTCCTTAA
1891207 TTTTTC-TTTATTT
1 TTTTTCATTTATTT
1891220 TTTTTCATTTATTT
1 TTTTTCATTTATTT
1891234 TT
1 TT
1891236 CTAGGTACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTCATTTATTT
Found at i:1905746 original size:90 final size:90
Alignment explanation
Indices: 1905630--1905807 Score: 293
Period size: 90 Copynumber: 2.0 Consensus size: 90
1905620 TAATCCCGAA
* * * *
1905630 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTGATATGAT
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
*
1905695 TAGGGTAACTTGGATATAAAAGGAT
66 TAGAGTAACTTGGATATAAAAGGAT
*
1905720 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACTCTAATATGAC
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
*
1905785 TAGAGTAACTTGGCTATAAAAGG
66 TAGAGTAACTTGGATATAAAAGG
1905808 GTGTGTTAGG
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 81 1.00
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (90 bp):
TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
TAGAGTAACTTGGATATAAAAGGAT
Found at i:1918477 original size:36 final size:36
Alignment explanation
Indices: 1918432--1918525 Score: 179
Period size: 36 Copynumber: 2.6 Consensus size: 36
1918422 AATATATGAA
*
1918432 TTTTAATGTCGATAGCGTTTTTCATCGGACCCGGAT
1 TTTTAATGTCGATAGCGTTTTTCACCGGACCCGGAT
1918468 TTTTAATGTCGATAGCGTTTTTCACCGGACCCGGAT
1 TTTTAATGTCGATAGCGTTTTTCACCGGACCCGGAT
1918504 TTTTAATGTCGATAGCGTTTTT
1 TTTTAATGTCGATAGCGTTTTT
1918526 GGATCCTGGT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.41
Consensus pattern (36 bp):
TTTTAATGTCGATAGCGTTTTTCACCGGACCCGGAT
Found at i:1923133 original size:17 final size:17
Alignment explanation
Indices: 1923089--1923126 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1923079 TGGAGAATTG
*
1923089 TTATGATAAATTATAAA
1 TTATTATAAATTATAAA
*
1923106 TTATTAAAAATTA-AAA
1 TTATTATAAATTATAAA
1923122 TTATT
1 TTATT
1923127 TTTAAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
TTATTATAAATTATAAA
Found at i:1926252 original size:24 final size:25
Alignment explanation
Indices: 1926225--1926281 Score: 91
Period size: 24 Copynumber: 2.4 Consensus size: 25
1926215 TATGCGAGAT
1926225 CATCCGAGGC-CATCCGACCGAGGG
1 CATCCGAGGCGCATCCGACCGAGGG
*
1926249 CATCCGA-GCGCATCCGACCGAGGT
1 CATCCGAGGCGCATCCGACCGAGGG
1926273 CATCCGAGG
1 CATCCGAGG
1926282 GGTAGGTCAC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 2 0.07
24 27 0.90
25 1 0.03
ACGTcount: A:0.21, C:0.37, G:0.32, T:0.11
Consensus pattern (25 bp):
CATCCGAGGCGCATCCGACCGAGGG
Found at i:1926324 original size:29 final size:29
Alignment explanation
Indices: 1926282--1926337 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
1926272 TCATCCGAGG
1926282 GGTAGGTCACCATGCACGCTAGGCGACAT
1 GGTAGGTCACCATGCACGCTAGGCGACAT
*
1926311 GGTAGGTCTCCATGCACGCTAGGCGAC
1 GGTAGGTCACCATGCACGCTAGGCGAC
1926338 CTTGTCCTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.29, G:0.32, T:0.18
Consensus pattern (29 bp):
GGTAGGTCACCATGCACGCTAGGCGACAT
Found at i:1926735 original size:13 final size:14
Alignment explanation
Indices: 1926717--1926749 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1926707 GGTTAGGGTT
1926717 AGTTTA-GGTTTAG
1 AGTTTAGGGTTTAG
1926730 AGTTTAGGGTTTAG
1 AGTTTAGGGTTTAG
*
1926744 GGTTTA
1 AGTTTA
1926750 ATTAGTTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.45
Consensus pattern (14 bp):
AGTTTAGGGTTTAG
Found at i:1926940 original size:30 final size:30
Alignment explanation
Indices: 1926871--1926976 Score: 115
Period size: 30 Copynumber: 3.5 Consensus size: 30
1926861 TTTAGTTAAT
* * * *
1926871 TAGTTTTTTAGTAGTAAATTATAATTAAAAAA
1 TAGTTTATTAGTTG-AAGTTAT-ATTAAAGAA
**
1926903 TCA-TTTATTAGTTTTAGTTATATTAAAGAA
1 T-AGTTTATTAGTTGAAGTTATATTAAAGAA
1926933 TAGTTTATTAGTTGAAGTTATATTAAAGAA
1 TAGTTTATTAGTTGAAGTTATATTAAAGAA
*
1926963 TTGTTTATTAGTTG
1 TAGTTTATTAGTTG
1926977 TTTAAGGGAA
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
29 1 0.02
30 47 0.75
31 5 0.08
32 9 0.14
33 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.48
Consensus pattern (30 bp):
TAGTTTATTAGTTGAAGTTATATTAAAGAA
Found at i:1927058 original size:15 final size:16
Alignment explanation
Indices: 1927030--1927063 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
1927020 GTTTGTTACT
1927030 TTATAAGTTTATTATA
1 TTATAAGTTTATTATA
1927046 TTATAAG-TTATTATA
1 TTATAAGTTTATTATA
1927061 TTA
1 TTA
1927064 AATTTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TTATAAGTTTATTATA
Found at i:1928483 original size:21 final size:21
Alignment explanation
Indices: 1928457--1928499 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1928447 TCATGACTTC
1928457 CTCCAAAACTTAGATGGTCGT
1 CTCCAAAACTTAGATGGTCGT
1928478 CTCCAAAACTTAGATGGTCGT
1 CTCCAAAACTTAGATGGTCGT
1928499 C
1 C
1928500 GTCAGGTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (21 bp):
CTCCAAAACTTAGATGGTCGT
Found at i:1929454 original size:14 final size:14
Alignment explanation
Indices: 1929433--1929741 Score: 155
Period size: 14 Copynumber: 23.3 Consensus size: 14
1929423 ATTAGTAATA
1929433 ATTATTAAATCATT
1 ATTATTAAATCATT
*
1929447 AGTATTAAATCATT
1 ATTATTAAATCATT
*
1929461 ATTA-TAAA--ATC
1 ATTATTAAATCATT
* *
1929472 ATGACTAAATC---
1 ATTATTAAATCATT
1929483 ATTATTAAATCATT
1 ATTATTAAATCATT
*
1929497 ACTATTAAATCATT
1 ATTATTAAATCATT
*
1929511 ATTA-T-AATGATT
1 ATTATTAAATCATT
1929523 ATTATTAAATCA--
1 ATTATTAAATCATT
*
1929535 A-TATT--ATAATT
1 ATTATTAAATCATT
*
1929546 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
1929558 ATTACTAAATCATT
1 ATTATTAAATCATT
*
1929572 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
1929584 ATTACTAAATCATT
1 ATTATTAAATCATT
*
1929598 ATTA-T-AATGATT
1 ATTATTAAATCATT
* *
1929610 ATCACTAAATCATT
1 ATTATTAAATCATT
*
1929624 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
1929636 ATTATCAAATCATT
1 ATTATTAAATCATT
*
1929650 ACTAAATCATCAAATCATT
1 A-T---T-ATTAAATCATT
* *
1929669 AAATATTAAA--ATA
1 -ATTATTAAATCATT
* *
1929682 AATACTAAATCATT
1 ATTATTAAATCATT
*
1929696 AAATATTAAAATCATT
1 -ATTATT-AAATCATT
*
1929712 ATTA-T-AATTATT
1 ATTATTAAATCATT
*
1929724 ATTACTAAATCATT
1 ATTATTAAATCATT
1929738 ATTA
1 ATTA
1929742 AATCATAATA
Statistics
Matches: 232, Mismatches: 31, Indels: 64
0.71 0.09 0.20
Matches are distributed among these distances:
9 3 0.01
11 20 0.09
12 73 0.31
13 15 0.06
14 85 0.37
15 14 0.06
16 9 0.04
18 1 0.00
19 11 0.05
20 1 0.00
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (14 bp):
ATTATTAAATCATT
Found at i:1929572 original size:26 final size:26
Alignment explanation
Indices: 1929543--1929650 Score: 191
Period size: 26 Copynumber: 4.2 Consensus size: 26
1929533 CAATATTATA
1929543 ATTATTATAATGATTATTACTAAATC
1 ATTATTATAATGATTATTACTAAATC
1929569 ATTATTATAATGATTATTACTAAATC
1 ATTATTATAATGATTATTACTAAATC
*
1929595 ATTATTATAATGATTATCACTAAATC
1 ATTATTATAATGATTATTACTAAATC
1929621 ATTATTATAATGATTATTA-TCAAATC
1 ATTATTATAATGATTATTACT-AAATC
1929647 ATTA
1 ATTA
1929651 CTAAATCATC
Statistics
Matches: 79, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
25 1 0.01
26 78 0.99
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (26 bp):
ATTATTATAATGATTATTACTAAATC
Found at i:1929680 original size:8 final size:9
Alignment explanation
Indices: 1929642--1929808 Score: 54
Period size: 8 Copynumber: 18.9 Consensus size: 9
1929632 GATTATTATC
1929642 AAATCATTA
1 AAATCATTA
*
1929651 CTAAATCA-TC
1 --AAATCATTA
1929661 AAATCATT-
1 AAATCATTA
1929669 AAAT-ATTA
1 AAATCATTA
* *
1929677 AAATAAATA
1 AAATCATTA
1929686 CTAAATCATT-
1 --AAATCATTA
1929696 AAAT-ATTA
1 AAATCATTA
1929704 AAATCATTA
1 AAATCATTA
** *
1929713 TTATAATTA
1 AAATCATTA
** * *
1929722 TTATTACT-
1 AAATCATTA
1929730 AAATCATTA
1 AAATCATTA
1929739 TTAAATCA-T-
1 --AAATCATTA
1929748 -AAT-ATTA
1 AAATCATTA
1929755 AAATCATTACA
1 AAATCATT--A
*
1929766 AAATCA-TC
1 AAATCATTA
1929774 AAATCATT-
1 AAATCATTA
1929782 AAAT-ATTA
1 AAATCATTA
1929790 AAATCATTA
1 AAATCATTA
1929799 TTAAATCATT
1 --AAATCATT
1929809 TTTATGGTTA
Statistics
Matches: 121, Mismatches: 14, Indels: 42
0.68 0.08 0.24
Matches are distributed among these distances:
5 1 0.01
6 4 0.03
7 9 0.07
8 43 0.36
9 28 0.23
10 3 0.02
11 33 0.27
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (9 bp):
AAATCATTA
Found at i:1929724 original size:12 final size:12
Alignment explanation
Indices: 1929699--1929763 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
1929689 AATCATTAAA
*
1929699 TATTAAAATCAT
1 TATTATAATCAT
*
1929711 TATTATAATTAT
1 TATTATAATCAT
1929723 TATTACTAAATCAT
1 TATTA-T-AATCAT
1929737 TATTA-AATCAT
1 TATTATAATCAT
*
1929748 AATATTAAAATCAT
1 --TATTATAATCAT
1929762 TA
1 TA
1929764 CAAAATCATC
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
11 6 0.13
12 17 0.38
13 6 0.13
14 16 0.36
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.45
Consensus pattern (12 bp):
TATTATAATCAT
Found at i:1929725 original size:88 final size:86
Alignment explanation
Indices: 1929616--1929801 Score: 247
Period size: 88 Copynumber: 2.1 Consensus size: 86
1929606 GATTATCACT
1929616 AAATCATTATTATAATGATTATTA-TCAAATCATTACTAAATCATCAAATCATT-AAAT-ATTAA
1 AAATCATTATTATAATGATTATTACT-AAATCATTACTAAATCAT--AAT-ATTAAAATCATTAA
1929678 AATAA--ATACTAAATCATTAAATATTA
62 AA-AATCAT-C-AAATCATTAAATATTA
* * *
1929704 AAATCATTATTATAATTATTATTACTAAATCATTATTAAATCATAATATTAAAATCATTACAAAA
1 AAATCATTATTATAATGATTATTACTAAATCATTACTAAATCATAATATTAAAATCATTAAAAAA
1929769 TCATCAAATCATTAAATATTA
66 TCATCAAATCATTAAATATTA
1929790 AAATCATTATTA
1 AAATCATTATTA
1929802 AATCATTTTT
Statistics
Matches: 90, Mismatches: 3, Indels: 12
0.86 0.03 0.11
Matches are distributed among these distances:
85 3 0.03
86 37 0.41
87 7 0.08
88 42 0.47
89 1 0.01
ACGTcount: A:0.51, C:0.10, G:0.01, T:0.39
Consensus pattern (86 bp):
AAATCATTATTATAATGATTATTACTAAATCATTACTAAATCATAATATTAAAATCATTAAAAAA
TCATCAAATCATTAAATATTA
Found at i:1929737 original size:26 final size:25
Alignment explanation
Indices: 1929699--1929763 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 25
1929689 AATCATTAAA
*
1929699 TATTA-AAATCATTATTATAATTAT
1 TATTATAAATCATTATTATAATCAT
1929723 TATTACTAAATCATTATTA-AATCAT
1 TATTA-TAAATCATTATTATAATCAT
1929748 AATATTA-AAATCATTA
1 --TATTATAAATCATTA
1929764 CAAAATCATC
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
24 5 0.14
25 14 0.39
26 12 0.33
27 5 0.14
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.45
Consensus pattern (25 bp):
TATTATAAATCATTATTATAATCAT
Found at i:1929791 original size:113 final size:113
Alignment explanation
Indices: 1929590--1929808 Score: 334
Period size: 113 Copynumber: 1.9 Consensus size: 113
1929580 GATTATTACT
* *
1929590 AAATCATTATTATAATGATTATCACTAAATCATTATTATAATGATTATTATCAAATCATTACTAA
1 AAATCATTATTATAATGATTATCACTAAATCATTATTATAATCATTATTA-CAAATCATTACAAA
1929655 ATCATCAAATCATTAAATATTAAAATAAATACTAAATCATTAAATATTA
65 ATCATCAAATCATTAAATATTAAAATAAATACTAAATCATTAAATATTA
* *
1929704 AAATCATTATTATAATTATTATTACTAAATCATTATTA-AATCATAATATTA-AAATCATTACAA
1 AAATCATTATTATAATGATTATCACTAAATCATTATTATAATCAT--TATTACAAATCATTACAA
* * *
1929767 AATCATCAAATCATTAAATATTAAAATCATTATTAAATCATT
64 AATCATCAAATCATTAAATATTAAAATAAATACTAAATCATT
1929809 TTTATGGTTA
Statistics
Matches: 96, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
113 55 0.57
114 36 0.38
115 5 0.05
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.39
Consensus pattern (113 bp):
AAATCATTATTATAATGATTATCACTAAATCATTATTATAATCATTATTACAAATCATTACAAAA
TCATCAAATCATTAAATATTAAAATAAATACTAAATCATTAAATATTA
Found at i:1929794 original size:35 final size:33
Alignment explanation
Indices: 1929741--1929807 Score: 98
Period size: 35 Copynumber: 2.0 Consensus size: 33
1929731 AATCATTATT
1929741 AAATCATAATATTAAAATCATTACAAAATCATC
1 AAATCATAATATTAAAATCATTACAAAATCATC
**
1929774 AAATCATTAAATATTAAAATCATTATTAAATCAT
1 AAATCA-T-AATATTAAAATCATTACAAAATCAT
1929808 TTTTATGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 6 0.20
34 1 0.03
35 23 0.77
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (33 bp):
AAATCATAATATTAAAATCATTACAAAATCATC
Found at i:1929808 original size:27 final size:27
Alignment explanation
Indices: 1929661--1929798 Score: 121
Period size: 27 Copynumber: 5.3 Consensus size: 27
1929651 CTAAATCATC
* *
1929661 AAATCATTAAATATTAAAATAAATACT
1 AAATCATTAAATATTAAAATCATTACT
*
1929688 AAATCATTAAATATTAAAATCATTATT
1 AAATCATTAAATATTAAAATCATTACT
* * * *
1929715 ATAATTATT-ATTACT-AAATCATTATT
1 A-AATCATTAAATATTAAAATCATTACT
*
1929741 AAATCA-T-AATATTAAAATCATTACA
1 AAATCATTAAATATTAAAATCATTACT
*
1929766 AAATCATCAAATCATT-AAAT-ATTA--
1 AAATCATTAAAT-ATTAAAATCATTACT
1929790 AAATCATTA
1 AAATCATTA
1929799 TTAAATCATT
Statistics
Matches: 93, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
24 13 0.14
25 19 0.20
26 16 0.17
27 36 0.39
28 9 0.10
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (27 bp):
AAATCATTAAATATTAAAATCATTACT
Found at i:1929945 original size:21 final size:21
Alignment explanation
Indices: 1929919--1929998 Score: 62
Period size: 21 Copynumber: 4.0 Consensus size: 21
1929909 TTATAATTTC
1929919 ATTATTACTAATAATTACTAA
1 ATTATTACTAATAATTACTAA
* *
1929940 ATTATTACT-ATCAAATCATTAA
1 ATTATTACTAAT--AATTACTAA
* *
1929962 A-TATTAATAATAATT--T-C
1 ATTATTACTAATAATTACTAA
*
1929979 ATTATTACTAATCATTACTA
1 ATTATTACTAATAATTACTA
1929999 TCAAATCATT
Statistics
Matches: 45, Mismatches: 7, Indels: 14
0.68 0.11 0.21
Matches are distributed among these distances:
17 1 0.02
18 13 0.29
20 6 0.13
21 15 0.33
22 10 0.22
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTATTACTAATAATTACTAA
Found at i:1929999 original size:49 final size:49
Alignment explanation
Indices: 1929932--1930155 Score: 294
Period size: 49 Copynumber: 4.6 Consensus size: 49
1929922 ATTACTAATA
*
1929932 ATTACTAAATTATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1929982 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
* *
1930031 ATTACTAATCATTATTACCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
* * * * *
1930080 ATTACTAATTATTACTA-AATAATTATTATAATTTTAA-ATATAAATTCATT
1 ATTACTAATCATTACTATCA-AATCATTA-AATATTAATA-ATAATTTCATT
* *
1930130 ATTA--AATCATGATTATCAAATCATTA
1 ATTACTAATCATTACTATCAAATCATTA
1930156 CTAAAGAAAA
Statistics
Matches: 156, Mismatches: 14, Indels: 10
0.87 0.08 0.06
Matches are distributed among these distances:
48 16 0.10
49 113 0.72
50 27 0.17
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
Found at i:1930044 original size:13 final size:14
Alignment explanation
Indices: 1930026--1930058 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1930016 AATAATAATT
*
1930026 TCATTATTA-CTAA
1 TCATTATTACCAAA
1930039 TCATTATTACCAAA
1 TCATTATTACCAAA
1930053 TCATTA
1 TCATTA
1930059 AATATTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.42
Consensus pattern (14 bp):
TCATTATTACCAAA
Found at i:1930948 original size:26 final size:26
Alignment explanation
Indices: 1930919--1931012 Score: 77
Period size: 27 Copynumber: 3.5 Consensus size: 26
1930909 TTAACTTGAT
1930919 TGATTGATTACTAAT-ATTACTAATAA
1 TGATTGATTA-TAATGATTACTAATAA
*
1930945 TGATTTGATATTTAATGATT--TAATAA
1 TGA-TTGAT-TATAATGATTACTAATAA
*
1930971 TAATATGATTTAGTAATGATTACTAATAA
1 TGAT-TGA-TTA-TAATGATTACTAATAA
* *
1931000 TTATTTATTATAA
1 TGATTGATTATAA
1931013 ATATTTAATG
Statistics
Matches: 55, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
25 1 0.02
26 18 0.33
27 21 0.38
28 6 0.11
29 9 0.16
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (26 bp):
TGATTGATTATAATGATTACTAATAA
Found at i:1931390 original size:14 final size:14
Alignment explanation
Indices: 1931371--1931397 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1931361 CACATACACA
1931371 ACAACAAAAAATAG
1 ACAACAAAAAATAG
1931385 ACAACAAAAAATA
1 ACAACAAAAAATA
1931398 ATAAATTACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.15, G:0.04, T:0.07
Consensus pattern (14 bp):
ACAACAAAAAATAG
Found at i:1931390 original size:17 final size:17
Alignment explanation
Indices: 1931368--1931400 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1931358 TTACACATAC
1931368 ACAACAACAAAA-AATAG
1 ACAACAA-AAAATAATAG
1931385 ACAACAAAAAATAATA
1 ACAACAAAAAATAATA
1931401 AATTACCCGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.73, C:0.15, G:0.03, T:0.09
Consensus pattern (17 bp):
ACAACAAAAAATAATAG
Found at i:1931831 original size:21 final size:21
Alignment explanation
Indices: 1931798--1931846 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1931788 AATATAATAT
1931798 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
1931819 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
1931840 ATTAACT
1 A-TAACT
1931847 AAATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:1932473 original size:29 final size:29
Alignment explanation
Indices: 1932408--1932548 Score: 201
Period size: 29 Copynumber: 4.8 Consensus size: 29
1932398 CATGCATATC
* * *
1932408 TCGCCCTGAGTTCATGGTGACCTCTCCTTGG
1 TCGCCCGGAGTGCATGGCGA-C-CTCCTTGG
*
1932439 TCGCCCGGAGTGCATGGAGACCTCCTTGG
1 TCGCCCGGAGTGCATGGCGACCTCCTTGG
1932468 TCGCCCGGAGTGCATGGCGACCTCCTTGG
1 TCGCCCGGAGTGCATGGCGACCTCCTTGG
*
1932497 TCACCCGGAGTGCATGGCGACCTCCTTGG
1 TCGCCCGGAGTGCATGGCGACCTCCTTGG
* *
1932526 TCGCCCAGAGTGCATGACGACCT
1 TCGCCCGGAGTGCATGGCGACCT
1932549 ACGGCTTCAC
Statistics
Matches: 102, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
29 84 0.82
30 1 0.01
31 17 0.17
ACGTcount: A:0.13, C:0.33, G:0.30, T:0.23
Consensus pattern (29 bp):
TCGCCCGGAGTGCATGGCGACCTCCTTGG
Found at i:1939240 original size:12 final size:12
Alignment explanation
Indices: 1939210--1939252 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
1939200 CTTGTTTGTT
1939210 ATTAGTTAGTTC
1 ATTAGTTAGTTC
1939222 A--AGTTAGTTC
1 ATTAGTTAGTTC
* *
1939232 ATTAGTTAGCTG
1 ATTAGTTAGTTC
1939244 ATTAGTTAG
1 ATTAGTTAG
1939253 CAGTTGTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 10 0.37
12 17 0.63
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.44
Consensus pattern (12 bp):
ATTAGTTAGTTC
Found at i:1941393 original size:18 final size:18
Alignment explanation
Indices: 1941364--1941417 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
1941354 ATAATATAAG
1941364 TTTATA-TATAAACTATA
1 TTTATATTATAAACTATA
1941381 TTTATATTATAAACTATA
1 TTTATATTATAAACTATA
* *
1941399 -TAATTATTATAAGCTATA
1 TTTA-TATTATAAACTATA
1941417 T
1 T
1941418 ATAAAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 8 0.25
18 24 0.75
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (18 bp):
TTTATATTATAAACTATA
Found at i:1941456 original size:13 final size:13
Alignment explanation
Indices: 1941438--1941485 Score: 69
Period size: 13 Copynumber: 3.5 Consensus size: 13
1941428 TGTTTATGTG
1941438 AACTATATATATA
1 AACTATATATATA
*
1941451 AACTATGTATATA
1 AACTATATATATA
1941464 AACTATATATGTATA
1 AACTATATA--TATA
1941479 AACTATA
1 AACTATA
1941486 AAAAGTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
13 20 0.65
15 11 0.35
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (13 bp):
AACTATATATATA
Found at i:1941457 original size:28 final size:26
Alignment explanation
Indices: 1941406--1941484 Score: 77
Period size: 28 Copynumber: 2.9 Consensus size: 26
1941396 ATATAATTAT
* * *
1941406 TATAAGCTATATATAAAAATTATGTTTA
1 TATAAACTATATATATAAACTATG--TA
* *
1941434 TGTGAACTATATATATAAACTATGTA
1 TATAAACTATATATATAAACTATGTA
1941460 TATAAACTATATATGTATAAACTAT
1 TATAAACTATATA--TATAAACTAT
1941485 AAAAAGTATA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
26 13 0.31
28 29 0.69
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.41
Consensus pattern (26 bp):
TATAAACTATATATATAAACTATGTA
Found at i:1941699 original size:17 final size:18
Alignment explanation
Indices: 1941672--1941710 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
1941662 ATAAATTATG
*
1941672 TATAGTATATATAAACTA
1 TATAGTATATATAAACCA
1941690 TATA-TATATATAAACCA
1 TATAGTATATATAAACCA
1941707 TATA
1 TATA
1941711 AAGTAAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (18 bp):
TATAGTATATATAAACCA
Found at i:1941795 original size:7 final size:7
Alignment explanation
Indices: 1941785--1941850 Score: 60
Period size: 7 Copynumber: 9.4 Consensus size: 7
1941775 TAGGTTATAA
1941785 AAACCCT
1 AAACCCT
1941792 AAACCCT
1 AAACCCT
**
1941799 AAACATT
1 AAACCCT
* *
1941806 AAATCAT
1 AAACCCT
*
1941813 AAACCAT
1 AAACCCT
** *
1941820 AATTCAT
1 AAACCCT
1941827 AAACCCT
1 AAACCCT
1941834 AAACCCT
1 AAACCCT
1941841 AAACCCT
1 AAACCCT
1941848 AAA
1 AAA
1941851 TACTATACAT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 48 1.00
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (7 bp):
AAACCCT
Found at i:1941959 original size:2 final size:2
Alignment explanation
Indices: 1941952--1942025 Score: 51
Period size: 2 Copynumber: 35.5 Consensus size: 2
1941942 ACTATGTACA
* * *
1941952 AT AT AT AT AA ACT AT AT AT AT AT AT AT AA ACT AT AGT AT AT GT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT A-T AT AT AT
* * *
1941995 AT AT AT AT A- AC CT AT AGT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A
1942026 CAATCTATTT
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
1 1 0.02
2 49 0.88
3 6 0.11
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (2 bp):
AT
Found at i:1941988 original size:61 final size:67
Alignment explanation
Indices: 1941909--1942054 Score: 162
Period size: 61 Copynumber: 2.3 Consensus size: 67
1941899 ACATGTAAAT
* *
1941909 TATATATGT-AACATATAGTACATGTATGTATA-AA-CTAT-GTACA-ATATATATA-AA-CTAT
1 TATATATATAAAC-TATAGTACATGTATATATATAACCTATAGTACATATATATATACAATCTAT
1941967 ATA
65 ATA
* * * *
1941970 TATATATATAAACTATAGTATATGTATATATATAACCTATAGTATATGTATATATACAATCTATT
1 TATATATATAAACTATAGTACATGTATATATATAACCTATAGTACATATATATATACAATCTATA
1942035 TA
66 TA
*
1942037 TATGTTATATAAACTATA
1 TAT-ATATATAAACTATA
1942055 TATGTAACCT
Statistics
Matches: 70, Mismatches: 7, Indels: 9
0.81 0.08 0.10
Matches are distributed among these distances:
61 25 0.36
62 5 0.07
63 4 0.06
64 4 0.06
65 8 0.11
66 2 0.03
67 9 0.13
68 13 0.19
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.41
Consensus pattern (67 bp):
TATATATATAAACTATAGTACATGTATATATATAACCTATAGTACATATATATATACAATCTATA
TA
Found at i:1941997 original size:24 final size:24
Alignment explanation
Indices: 1941964--1942054 Score: 109
Period size: 24 Copynumber: 4.0 Consensus size: 24
1941954 ATATATAAAC
*
1941964 TATATATATATATATAAACTATAG
1 TATATGTATATATATAAACTATAG
*
1941988 TATATGTATATATATAACCTATAG
1 TATATGTATATATATAAACTATAG
* * *
1942012 TATATGTATATATACAATCTAT-T
1 TATATGTATATATATAAACTATAG
1942035 TATATG--T-TATATAAACTATA
1 TATATGTATATATATAAACTATA
1942055 TATGTAACCT
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
20 10 0.17
21 1 0.02
23 6 0.10
24 42 0.71
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (24 bp):
TATATGTATATATATAAACTATAG
Found at i:1942143 original size:64 final size:64
Alignment explanation
Indices: 1942064--1942238 Score: 305
Period size: 64 Copynumber: 2.7 Consensus size: 64
1942054 ATATGTAACC
*
1942064 TATAGTTTATAATCAATAGTTTATAATAATGTACTATATAGTTTATACTTTATAACCTATAGTA
1 TATAATTTATAATCAATAGTTTATAATAATGTACTATATAGTTTATACTTTATAACCTATAGTA
1942128 TATAATTTATAATCAATAGTTTATAATAATGTACTATATAGTTTATACTTTATAACCTATAGTA
1 TATAATTTATAATCAATAGTTTATAATAATGTACTATATAGTTTATACTTTATAACCTATAGTA
* * * *
1942192 TATAATTTATAAACTATAGTTTATATTAATGTACTACATAGTTTATA
1 TATAATTTATAATCAATAGTTTATAATAATGTACTATATAGTTTATA
1942239 TTAATGTTAA
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 106 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (64 bp):
TATAATTTATAATCAATAGTTTATAATAATGTACTATATAGTTTATACTTTATAACCTATAGTA
Found at i:1942298 original size:14 final size:14
Alignment explanation
Indices: 1942281--1942341 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
1942271 TAATATAGTA
1942281 TATAGTTTATAAAC
1 TATAGTTTATAAAC
* * *
1942295 TATACTATATTAA-
1 TATAGTTTATAAAC
*
1942308 TATTAGTTATATTAAC
1 TA-TAGTT-TATAAAC
1942324 TATAGTTTATAAAC
1 TATAGTTTATAAAC
1942338 TATA
1 TATA
1942342 CTATATAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 2 0.05
14 23 0.61
15 11 0.29
16 2 0.05
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.46
Consensus pattern (14 bp):
TATAGTTTATAAAC
Found at i:1942323 original size:65 final size:64
Alignment explanation
Indices: 1942235--1942479 Score: 185
Period size: 65 Copynumber: 3.9 Consensus size: 64
1942225 CTACATAGTT
* * * *
1942235 TATATTAATGTTAATTATCTTAACTATAATTTATATTAATATAGTATATAGTTTATAAACTATAC
1 TATATTAATATTAATTATATTAACTATAATTTATATTAATATAATATATAATTTATAAAC-ATAC
* * * *
1942300 TATATTAATATTAGTTATATTAACTATAGTTTATA--AACTATACTATATAATTTAT-AACATAG
1 TATATTAATATTAATTATATTAACTATAATTTATATTAA-TATAATATATAATTTATAAACATAC
* * * *
1942362 TTTA-T-ATATTAATGTATA--GACTAT--TTTATATTAATATTAAT-TACAAATTATAAACCAT
1 TATATTAATATTAAT-TATATTAACTATAATTTATATTAATA-TAATATATAATTTATAAA-CAT
*
1942420 AT
63 AC
*
1942422 TATATTAATA-TAAGTTAATATTAA-TATTAA-TTATATTAATATTAAT-TATAATATATAA
1 TATATTAATATTAA-TT-ATATTAACTA-TAATTTATATTAATA-TAATATATAATTTATAA
1942480 TTATTTTAAT
Statistics
Matches: 145, Mismatches: 19, Indels: 32
0.74 0.10 0.16
Matches are distributed among these distances:
57 6 0.04
58 10 0.07
59 12 0.08
60 14 0.10
61 10 0.07
62 13 0.09
63 7 0.05
64 17 0.12
65 56 0.39
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (64 bp):
TATATTAATATTAATTATATTAACTATAATTTATATTAATATAATATATAATTTATAAACATAC
Found at i:1942348 original size:14 final size:14
Alignment explanation
Indices: 1942288--1942349 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
1942278 GTATATAGTT
1942288 TATAAACTATACTA
1 TATAAACTATACTA
* *
1942302 TATTAA-TATTAGTTA
1 TATAAACTA-TA-CTA
* * *
1942317 TATTAACTATAGTT
1 TATAAACTATACTA
1942331 TATAAACTATACTA
1 TATAAACTATACTA
1942345 TATAA
1 TATAA
1942350 TTTATAACAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
13 2 0.05
14 24 0.63
15 10 0.26
16 2 0.05
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (14 bp):
TATAAACTATACTA
Found at i:1942445 original size:6 final size:6
Alignment explanation
Indices: 1942418--1942509 Score: 54
Period size: 6 Copynumber: 15.3 Consensus size: 6
1942408 ATTATAAACC
*
1942418 ATATT- ATATTA ATA-TA A-GTTA ATATTA ATATT- A-ATT- ATATTA
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA
*
1942460 ATATTA AT-TATA ATATATA ATTATTTTA ATATTA ATTATAA ATAGTTA
1 ATATTA ATAT-TA ATAT-TA A-TA--TTA ATATTA A-TATTA ATA-TTA
1942508 AT
1 AT
1942510 TAATAAAAAT
Statistics
Matches: 71, Mismatches: 4, Indels: 22
0.73 0.04 0.23
Matches are distributed among these distances:
4 4 0.06
5 16 0.23
6 29 0.41
7 14 0.20
8 4 0.06
9 3 0.04
10 1 0.01
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (6 bp):
ATATTA
Found at i:1942457 original size:153 final size:153
Alignment explanation
Indices: 1942171--1942471 Score: 339
Period size: 153 Copynumber: 2.0 Consensus size: 153
1942161 CTATATAGTT
* *
1942171 TATACTTTATAACCTATAGTATATAATTTATAAACTATAGTTTATATTAATGTACTACATAGTTT
1 TATACTTTATAAACTATACTATATAATTTATAAACTATAGTTTATATTAATGTACTACATAGTTT
* * *** *
1942236 ATATTAATGTTAATTATCTTAACTATAATTTATATTAATATAGTATATAGTTTATAAACTATACT
66 ATATTAATATTAATTATCTAAACTATAAACCATATTAATATAATATATAGTTTATAAACTATACT
*
1942301 ATATTAATATTAGTTATATTAAC
131 ATATTAATATTAATTATATTAAC
* * *
1942324 TATAGTTTATAAACTATACTATATAATTTAT-AAC-ATAGTTTATATATTAATGTA-TAGACTAT
1 TATACTTTATAAACTATACTATATAATTTATAAACTATAG-TT-TATATTAATGTACTACA-TAG
* *
1942386 TTTATATTAATATTAATTA-C-AAATTATAAACCATATT-ATATTAATATA-AGTTAATATTAA-
63 TTTATATTAATATTAATTATCTAAACTATAAACCATATTAATA-TAATATATAGTT--TATAAAC
*
1942446 TATTAATTATATTAATATTAATTATA
125 TA-T-ACTATATTAATATTAATTATA
1942472 ATATATAATT
Statistics
Matches: 125, Mismatches: 15, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
150 7 0.06
151 24 0.19
152 15 0.12
153 79 0.63
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (153 bp):
TATACTTTATAAACTATACTATATAATTTATAAACTATAGTTTATATTAATGTACTACATAGTTT
ATATTAATATTAATTATCTAAACTATAAACCATATTAATATAATATATAGTTTATAAACTATACT
ATATTAATATTAATTATATTAAC
Found at i:1942458 original size:31 final size:27
Alignment explanation
Indices: 1942420--1942500 Score: 90
Period size: 28 Copynumber: 2.8 Consensus size: 27
1942410 TATAAACCAT
*
1942420 ATTATATTAATATAAGTTAATATTAATATTA
1 ATTATATTAATATAA-TT-ATAAT-ATA-TA
1942451 ATTATATTAATATTAATTATAATATATA
1 ATTATATTAATA-TAATTATAATATATA
*
1942479 ATTATTTTAATATTAATTATAA
1 ATTATATTAATA-TAATTATAA
1942501 ATAGTTAATT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
28 23 0.49
29 3 0.06
30 4 0.09
31 14 0.30
32 3 0.06
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (27 bp):
ATTATATTAATATAATTATAATATATA
Found at i:1942473 original size:21 final size:21
Alignment explanation
Indices: 1942387--1942499 Score: 83
Period size: 21 Copynumber: 5.2 Consensus size: 21
1942377 ATAGACTATT
**
1942387 TTATATTAATATTAATTACAAA
1 TTATATTAATATTAA-TATTAA
*
1942409 TTATA-AACCATATT-ATATTAA
1 TTATATTA--ATATTAATATTAA
1942430 -TATAAGTTAATATTAATATTAA
1 TTAT-A-TTAATATTAATATTAA
1942452 TTATATTAATATTAAT-TATAA
1 TTATATTAATATTAATAT-TAA
*
1942473 TATATAATT-ATTTTAATATTAA
1 T-TAT-ATTAATATTAATATTAA
1942495 TTATA
1 TTATA
1942500 AATAGTTAAT
Statistics
Matches: 75, Mismatches: 5, Indels: 24
0.72 0.05 0.23
Matches are distributed among these distances:
20 5 0.07
21 29 0.39
22 28 0.37
23 13 0.17
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.49
Consensus pattern (21 bp):
TTATATTAATATTAATATTAA
Done.