Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397262.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_67.0, 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: 8984705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 112788 characters in sequence are not A, C, G, or T
File 10 of 20
Found at i:3425827 original size:22 final size:23
Alignment explanation
Indices: 3425799--3425849 Score: 77
Period size: 25 Copynumber: 2.2 Consensus size: 23
3425789 CCTCAAGTAG
3425799 TCTATAAAT-CAACATATTGCTT
1 TCTATAAATACAACATATTGCTT
3425821 TCTATAAATACACAACATATTGCTT
1 TCTATAAAT--ACAACATATTGCTT
3425846 TCTA
1 TCTA
3425850 CCGGAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 9 0.35
25 17 0.65
ACGTcount: A:0.37, C:0.20, G:0.04, T:0.39
Consensus pattern (23 bp):
TCTATAAATACAACATATTGCTT
Found at i:3426230 original size:2 final size:2
Alignment explanation
Indices: 3426223--3426248 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3426213 ATAGTTTTAG
3426223 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3426249 TGTGCAATCA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3451496 original size:19 final size:19
Alignment explanation
Indices: 3451453--3451542 Score: 55
Period size: 20 Copynumber: 4.7 Consensus size: 19
3451443 AAAGTATAAC
*
3451453 AAAAGAAAAAAGATAGGAAAA
1 AAAAG-AAAAAGA-AGCAAAA
3451474 AAAAGAAAAAGAAGC-AAA
1 AAAAGAAAAAGAAGCAAAA
*
3451492 GAAA-AAAAAG-AG-AAAA
1 AAAAGAAAAAGAAGCAAAA
* *
3451508 ATTAAAAAAAAAGATA-TAAAA
1 A--AAAGAAAAAGA-AGCAAAA
3451529 AGAAAGAAAAAGAA
1 A-AAAGAAAAAGAA
3451543 AGGAGGATAT
Statistics
Matches: 57, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
16 5 0.09
17 6 0.11
18 9 0.16
19 9 0.16
20 17 0.30
21 11 0.19
ACGTcount: A:0.78, C:0.01, G:0.16, T:0.06
Consensus pattern (19 bp):
AAAAGAAAAAGAAGCAAAA
Found at i:3451544 original size:14 final size:13
Alignment explanation
Indices: 3451470--3451544 Score: 55
Period size: 14 Copynumber: 5.5 Consensus size: 13
3451460 AAAAGATAGG
3451470 AAAAA-AAAGAAA
1 AAAAAGAAAGAAA
*
3451482 AAGAAGCAAAGAAA
1 AAAAAG-AAAGAAA
3451496 AAAAAGAGAA-AAA
1 AAAAAGA-AAGAAA
* *
3451509 TTAAAAAAAAAGATAT
1 --AAAAAGAAAGA-AA
3451525 AAAAAGAAAGAAA
1 AAAAAGAAAGAAA
3451538 AAGAAAG
1 AA-AAAG
3451545 GAGGATATCA
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
12 4 0.08
13 7 0.14
14 30 0.61
15 7 0.14
16 1 0.02
ACGTcount: A:0.79, C:0.01, G:0.15, T:0.05
Consensus pattern (13 bp):
AAAAAGAAAGAAA
Found at i:3466626 original size:22 final size:20
Alignment explanation
Indices: 3466601--3466643 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
3466591 TTTAACTATC
*
3466601 AATTATTAATAAATTCATATTA
1 AATTAATAATAAA-T-ATATTA
*
3466623 AATTAATACTAAATATATTA
1 AATTAATAATAAATATATTA
3466643 A
1 A
3466644 TAAGTTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 1 0.05
22 11 0.58
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (20 bp):
AATTAATAATAAATATATTA
Found at i:3466790 original size:21 final size:22
Alignment explanation
Indices: 3466766--3466809 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
3466756 TGAAATCATT
*
3466766 ATTAAAAATTATT-ATTTTTTA
1 ATTAAAAATTATTAATATTTTA
*
3466787 ATTATAAATTATTAATATTTTA
1 ATTAAAAATTATTAATATTTTA
3466809 A
1 A
3466810 ACAAATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTAAAAATTATTAATATTTTA
Found at i:3466816 original size:27 final size:27
Alignment explanation
Indices: 3466786--3466906 Score: 96
Period size: 27 Copynumber: 4.7 Consensus size: 27
3466776 ATTATTTTTT
*
3466786 AATTATAAATTATTAATATTTTAAACA
1 AATTATAAATTATTAATATTTTAAATA
** *
3466813 AATTATAAAAAATTAATATTTCAAATTA
1 AATTATAAATTATTAATATTTTAAA-TA
** *
3466841 AAAAATAAA--ATGAA-ATTTT---T-
1 AATTATAAATTATTAATATTTTAAATA
* *
3466861 AATTATAAATTATAAATACTTTAAATA
1 AATTATAAATTATTAATATTTTAAATA
3466888 AATTATAAATTATT-ATATT
1 AATTATAAATTATTAATATT
3466907 AAAATATTAA
Statistics
Matches: 72, Mismatches: 14, Indels: 17
0.70 0.14 0.17
Matches are distributed among these distances:
20 7 0.10
21 1 0.01
22 4 0.06
23 4 0.06
25 4 0.06
26 9 0.12
27 35 0.49
28 8 0.11
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (27 bp):
AATTATAAATTATTAATATTTTAAATA
Found at i:3468978 original size:2 final size:2
Alignment explanation
Indices: 3468971--3469000 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3468961 TCTTGTAGTG
3468971 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3469001 GTATGTATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3470572 original size:17 final size:17
Alignment explanation
Indices: 3470553--3470585 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
3470543 TTAAAATTAA
3470553 AAAAATAA-TTATTTTT
1 AAAAATAACTTATTTTT
3470569 AAAAATAACTTATTTTT
1 AAAAATAACTTATTTTT
3470586 GAGAGGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
AAAAATAACTTATTTTT
Found at i:3475264 original size:2 final size:2
Alignment explanation
Indices: 3475257--3475285 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3475247 TCTTATCTTG
3475257 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
3475286 CAGTTTACTC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3478794 original size:23 final size:23
Alignment explanation
Indices: 3478766--3478811 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
3478756 TATGTAAAAA
3478766 ATATAGTGATACTATATGTTAAT
1 ATATAGTGATACTATATGTTAAT
*
3478789 ATATAGTGATATTATATGTTAAT
1 ATATAGTGATACTATATGTTAAT
3478812 GTGACGTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.02, G:0.13, T:0.46
Consensus pattern (23 bp):
ATATAGTGATACTATATGTTAAT
Found at i:3478936 original size:22 final size:23
Alignment explanation
Indices: 3478889--3478934 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
3478879 TTATAATTAA
**
3478889 TTAATAATAAAAAATTATTTAAT
1 TTAATAATAAAAAATTATAAAAT
3478912 TTAA-AATAAAAAA-TATAAAAT
1 TTAATAATAAAAAATTATAAAAT
3478933 TT
1 TT
3478935 TATGTAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 9 0.43
23 4 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
TTAATAATAAAAAATTATAAAAT
Found at i:3478970 original size:28 final size:27
Alignment explanation
Indices: 3478898--3478971 Score: 76
Period size: 30 Copynumber: 2.6 Consensus size: 27
3478888 ATTAATAATA
*
3478898 AAAAATTATTTAATTTAAAATAAAAAAT
1 AAAAATTATTTAA-ATAAAATAAAAAAT
* *
3478926 ATAAAATTTTATGTAAATATAATAAAAAAT
1 A-AAAA--TTATTTAAATAAAATAAAAAAT
3478956 AAAAATATATTTAAAT
1 AAAAAT-TATTTAAAT
3478972 TACATGTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
27 1 0.03
28 9 0.24
29 8 0.21
30 13 0.34
31 7 0.18
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (27 bp):
AAAAATTATTTAAATAAAATAAAAAAT
Found at i:3479067 original size:30 final size:28
Alignment explanation
Indices: 3479028--3479105 Score: 93
Period size: 30 Copynumber: 2.7 Consensus size: 28
3479018 AACGGTTAAT
*
3479028 AATAAAAATTTATTTAATTTAAAATAAAA
1 AATAAAAATTTATTTAA-ATAAAATAAAA
* * *
3479057 AATATAAAATTTCATGTAAATATAATAATA
1 AATA-AAAATTT-ATTTAAATAAAATAAAA
3479087 AATAAAAATTTATTTAAAT
1 AATAAAAATTTATTTAAAT
3479106 TGCATATATT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
28 7 0.17
29 11 0.26
30 19 0.45
31 5 0.12
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (28 bp):
AATAAAAATTTATTTAAATAAAATAAAA
Found at i:3479264 original size:15 final size:15
Alignment explanation
Indices: 3479244--3479274 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3479234 TTTGGTCTAC
3479244 CTGTAATATCATTTG
1 CTGTAATATCATTTG
3479259 CTGTAATATCATTTG
1 CTGTAATATCATTTG
3479274 C
1 C
3479275 GTGTTTTGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (15 bp):
CTGTAATATCATTTG
Found at i:3484420 original size:2 final size:2
Alignment explanation
Indices: 3484415--3484448 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3484405 TATATATAGT
*
3484415 GA GA GA GA GA GA GA CA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3484449 ACTAAAACCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3510318 original size:23 final size:23
Alignment explanation
Indices: 3510269--3510369 Score: 121
Period size: 23 Copynumber: 4.3 Consensus size: 23
3510259 TTTTCAAGAG
* * *
3510269 TCACGAACTTGGACTTTGTCTTGA
1 TCACGAACTTCGCCGTTG-CTTGA
***
3510293 TCACGAACTTCGTTTTTGCTTGA
1 TCACGAACTTCGCCGTTGCTTGA
*
3510316 TCACGAACTTCGCTGTTGCTTGA
1 TCACGAACTTCGCCGTTGCTTGA
*
3510339 TCACGAACTTCACCGTTGCTTGA
1 TCACGAACTTCGCCGTTGCTTGA
3510362 TCACGAAC
1 TCACGAAC
3510370 ATTATCTTCA
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
23 55 0.79
24 15 0.21
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.35
Consensus pattern (23 bp):
TCACGAACTTCGCCGTTGCTTGA
Found at i:3510338 original size:46 final size:47
Alignment explanation
Indices: 3510269--3510369 Score: 134
Period size: 46 Copynumber: 2.2 Consensus size: 47
3510259 TTTTCAAGAG
* ****
3510269 TCACGAACTTGGACTTTGTCTTGATCACGAACTTCGTTTTTGCTTGA
1 TCACGAACTTCGACTTTGTCTTGATCACGAACTTCACCGTTGCTTGA
3510316 TCACGAACTTCG-CTGTTG-CTTGATCACGAACTTCACCGTTGCTTGA
1 TCACGAACTTCGACT-TTGTCTTGATCACGAACTTCACCGTTGCTTGA
3510362 TCACGAAC
1 TCACGAAC
3510370 ATTATCTTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
46 34 0.71
47 14 0.29
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.35
Consensus pattern (47 bp):
TCACGAACTTCGACTTTGTCTTGATCACGAACTTCACCGTTGCTTGA
Found at i:3511839 original size:9 final size:9
Alignment explanation
Indices: 3511825--3511858 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
3511815 ATGAAAAAAA
3511825 ATTTTGAGC
1 ATTTTGAGC
3511834 ATTTTGAGC
1 ATTTTGAGC
*
3511843 ATTTTTAAGC
1 A-TTTTGAGC
3511853 ATTTTG
1 ATTTTG
3511859 GAATGATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.50
Consensus pattern (9 bp):
ATTTTGAGC
Found at i:3512046 original size:22 final size:22
Alignment explanation
Indices: 3512021--3512157 Score: 82
Period size: 22 Copynumber: 6.3 Consensus size: 22
3512011 TTTGGGTATC
3512021 GCGTGACTAATTTTTAGGCATT
1 GCGTGACTAATTTTTAGGCATT
* * **
3512043 GCGTGACTTA-CTTTAGAAATT
1 GCGTGACTAATTTTTAGGCATT
* * * *
3512064 GCGTAACTGA--CTTAGGGTATT
1 GCGTGACTAATTTTTA-GGCATT
* *
3512085 GCGTGACTAATTTTTAAGTATT
1 GCGTGACTAATTTTTAGGCATT
* * * *
3512107 GCGTGATTAGTTTGTAAGCATT
1 GCGTGACTAATTTTTAGGCATT
* * *
3512129 GCGTGACTTATTAGTAAGGCATT
1 GCGTGACTAATT-TTTAGGCATT
3512152 GCGTGA
1 GCGTGA
3512158 TTAGTTAGTA
Statistics
Matches: 87, Mismatches: 24, Indels: 7
0.74 0.20 0.06
Matches are distributed among these distances:
20 3 0.03
21 28 0.32
22 41 0.47
23 15 0.17
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (22 bp):
GCGTGACTAATTTTTAGGCATT
Found at i:3512152 original size:23 final size:24
Alignment explanation
Indices: 3512104--3512231 Score: 151
Period size: 23 Copynumber: 5.6 Consensus size: 24
3512094 ATTTTTAAGT
*
3512104 ATTGCGTGA-TTAGTTTGTAA-GC
1 ATTGCGTGACTTAGTTAGTAAGGC
3512126 ATTGCGTGACTTA-TTAGTAAGGC
1 ATTGCGTGACTTAGTTAGTAAGGC
3512149 ATTGCGTGA-TTAGTTAGTAAGGC
1 ATTGCGTGACTTAGTTAGTAAGGC
** *
3512172 ATTGTATGAC-TAGTTAGTAAGGT
1 ATTGCGTGACTTAGTTAGTAAGGC
*
3512195 ATTGCATGAC-TAGTTAGTAAGGC
1 ATTGCGTGACTTAGTTAGTAAGGC
* *
3512218 ATTGTGTAACTTAG
1 ATTGCGTGACTTAG
3512232 GTATTGCTTA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
22 18 0.20
23 71 0.77
24 3 0.03
ACGTcount: A:0.27, C:0.09, G:0.27, T:0.37
Consensus pattern (24 bp):
ATTGCGTGACTTAGTTAGTAAGGC
Found at i:3520934 original size:35 final size:35
Alignment explanation
Indices: 3520869--3520936 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
3520859 GTTGTTTTGC
**
3520869 GTGAAGTAATACTTCACTTGTTTTAATTATTCTGT
1 GTGAAGTAATACTTCACTTGTAATAATTATTCTGT
* **
3520904 GTGAAGTAATGCTTCACTTGTAATGGTTATTCT
1 GTGAAGTAATACTTCACTTGTAATAATTATTCT
3520937 CATTATTCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.46
Consensus pattern (35 bp):
GTGAAGTAATACTTCACTTGTAATAATTATTCTGT
Found at i:3527484 original size:23 final size:23
Alignment explanation
Indices: 3527454--3527542 Score: 133
Period size: 23 Copynumber: 3.9 Consensus size: 23
3527444 NNNNNNNNNN
3527454 AACTTCGCCGTTGCTTGATCACG
1 AACTTCGCCGTTGCTTGATCACG
*
3527477 AACTTCGCTGTTGCTTGATCACG
1 AACTTCGCCGTTGCTTGATCACG
* *
3527500 AACTTCGCTGCTGCTTGATCACG
1 AACTTCGCCGTTGCTTGATCACG
* *
3527523 AACTTCGTCGTTACTTGATC
1 AACTTCGCCGTTGCTTGATC
3527543 TTCACCTCAG
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.18, C:0.28, G:0.20, T:0.34
Consensus pattern (23 bp):
AACTTCGCCGTTGCTTGATCACG
Found at i:3527621 original size:18 final size:18
Alignment explanation
Indices: 3527585--3527622 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3527575 NNNNNNNNNC
* *
3527585 TCTCAATCTTCGAATGCT
1 TCTCAATCTTCAAAAGCT
3527603 TCTCAATCTTCAAAAGCT
1 TCTCAATCTTCAAAAGCT
3527621 TC
1 TC
3527623 CGAATGAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.29, G:0.08, T:0.37
Consensus pattern (18 bp):
TCTCAATCTTCAAAAGCT
Found at i:3554111 original size:12 final size:13
Alignment explanation
Indices: 3554087--3554115 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3554077 TTTTCTCTAC
3554087 CTTTTCTTTTTTT
1 CTTTTCTTTTTTT
3554100 CTTTTC-TTTTTT
1 CTTTTCTTTTTTT
3554112 CTTT
1 CTTT
3554116 CTTCTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
CTTTTCTTTTTTT
Found at i:3555185 original size:61 final size:60
Alignment explanation
Indices: 3554955--3555443 Score: 550
Period size: 61 Copynumber: 8.2 Consensus size: 60
3554945 GTCTTAAAAA
* * *
3554955 TTAAAAATTAAAAATTCTTAAACTTGATTCAGGCTTGATCTATCTCAAATA-A-GTTCGAC
1 TTAAAAATTAAAAATTCTTAGACTTGATTCAGGCTCGACCTATCTCAAA-ACAGGTTCGAC
* * * * * *
3555014 TTAAAAGTCAAAAATTCTTAGACTTGATCCAGGTTCAACCTATCTCAAAACAAGTTCGAC
1 TTAAAAATTAAAAATTCTTAGACTTGATTCAGGCTCGACCTATCTCAAAACAGGTTCGAC
* * *
3555074 TTTAAAAATTAAAAATTCCTA-ACTTGATTCAGGCTCGACTTATCTCAAAACAGGTTTGAC
1 -TTAAAAATTAAAAATTCTTAGACTTGATTCAGGCTCGACCTATCTCAAAACAGGTTCGAC
* * * *
3555134 TTAAAAATTAAAAATTCCTAGACTTAGATTTAGGCTCGACTTATCTTAAAACAGGTTCGAC
1 TTAAAAATTAAAAATTCTTAGACTT-GATTCAGGCTCGACCTATCTCAAAACAGGTTCGAC
* * * * * *
3555195 TTAAAAGTTAAAAATTCCTAAACTCGA-TCTAGGCTCGACTTATCTCACAACAGGTTCGAC
1 TTAAAAATTAAAAATTCTTAGACTTGATTC-AGGCTCGACCTATCTCAAAACAGGTTCGAC
*
3555255 TTTAAAAATTAAAAATTCTTAGAC-TGAAATCAGGCTCGACCTATCTCAAAACAGGTTCGA-
1 -TTAAAAATTAAAAATTCTTAGACTTG-ATTCAGGCTCGACCTATCTCAAAACAGGTTCGAC
* * * * * *
3555315 TT-----TTAAAAATTCTTAGATTTGATCCAGTCTCGACCTATCTCACAATAGATTCGAC
1 TTAAAAATTAAAAATTCTTAGACTTGATTCAGGCTCGACCTATCTCAAAACAGGTTCGAC
* * *
3555370 TTTAAAAATTAAAAATTTTTAAACTTGATTCAAGCTCGACCTATCTCAAAACAGGTTCGAC
1 -TTAAAAATTAAAAATTCTTAGACTTGATTCAGGCTCGACCTATCTCAAAACAGGTTCGAC
3555431 TTAAAAATTAAAA
1 TTAAAAATTAAAA
3555444 TGTGAACTTA
Statistics
Matches: 365, Mismatches: 48, Indels: 33
0.82 0.11 0.07
Matches are distributed among these distances:
54 42 0.12
55 2 0.01
56 2 0.01
58 1 0.00
59 65 0.18
60 88 0.24
61 163 0.45
62 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (60 bp):
TTAAAAATTAAAAATTCTTAGACTTGATTCAGGCTCGACCTATCTCAAAACAGGTTCGAC
Found at i:3555249 original size:121 final size:121
Alignment explanation
Indices: 3554955--3555443 Score: 572
Period size: 121 Copynumber: 4.1 Consensus size: 121
3554945 GTCTTAAAAA
* * * *
3554955 TTAAAAATTAAAAATTCTTAAACTTGATTCAGGCTTGA-TCTATCTCA-AATAAGTTCGAC-TTA
1 TTAAAAATTAAAAATTCCTAAACTTGATTCAGGCTCGACT-TATCTCACAACAGGTTCGACTTTA
* * * * * *
3555017 AAAGTCAAAAATTCTTAGACTTGATCCAGGTTCAACCTATCTCAAAACAAGTTCGAC
65 AAAATTAAAAATTCTTAGACTTGATTCAGGCTCGACCTATCTCAAAACAGGTTCGAC
* *
3555074 TTTAAAAATTAAAAATTCCT-AACTTGATTCAGGCTCGACTTATCTCAAAACAGGTTTGAC-TTA
1 -TTAAAAATTAAAAATTCCTAAACTTGATTCAGGCTCGACTTATCTCACAACAGGTTCGACTTTA
* * * *
3555137 AAAATTAAAAATTCCTAGACTTAGATTTAGGCTCGACTTATCTTAAAACAGGTTCGAC
65 AAAATTAAAAATTCTTAGACTT-GATTCAGGCTCGACCTATCTCAAAACAGGTTCGAC
* *
3555195 TTAAAAGTTAAAAATTCCTAAACTCGA-TCTAGGCTCGACTTATCTCACAACAGGTTCGACTTTA
1 TTAAAAATTAAAAATTCCTAAACTTGATTC-AGGCTCGACTTATCTCACAACAGGTTCGACTTTA
*
3555259 AAAATTAAAAATTCTTAGAC-TGAAATCAGGCTCGACCTATCTCAAAACAGGTTCGA-
65 AAAATTAAAAATTCTTAGACTTG-ATTCAGGCTCGACCTATCTCAAAACAGGTTCGAC
* * * * * * * *
3555315 TT-----TTAAAAATTCTTAGATTTGATCCAGTCTCGACCTATCTCACAATAGATTCGACTTTAA
1 TTAAAAATTAAAAATTCCTAAACTTGATTCAGGCTCGACTTATCTCACAACAGGTTCGACTTTAA
* * *
3555375 AAATTAAAAATTTTTAAACTTGATTCAAGCTCGACCTATCTCAAAACAGGTTCGAC
66 AAATTAAAAATTCTTAGACTTGATTCAGGCTCGACCTATCTCAAAACAGGTTCGAC
3555431 TTAAAAATTAAAA
1 TTAAAAATTAAAA
3555444 TGTGAACTTA
Statistics
Matches: 317, Mismatches: 37, Indels: 29
0.83 0.10 0.08
Matches are distributed among these distances:
115 95 0.30
116 5 0.02
119 24 0.08
120 73 0.23
121 98 0.31
122 22 0.07
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (121 bp):
TTAAAAATTAAAAATTCCTAAACTTGATTCAGGCTCGACTTATCTCACAACAGGTTCGACTTTAA
AAATTAAAAATTCTTAGACTTGATTCAGGCTCGACCTATCTCAAAACAGGTTCGAC
Found at i:3555347 original size:54 final size:53
Alignment explanation
Indices: 3555263--3555379 Score: 146
Period size: 54 Copynumber: 2.2 Consensus size: 53
3555253 ACTTTAAAAA
* *
3555263 TTAAAAATTCTTAGACTGAAATCAGGCTCGACCTATCTCAAAACAGGTTCGATT
1 TTAAAAATTCTTAGACTG-AATCAGGCTCGACCTATCTCAAAACAGATTCGACT
* * * *
3555317 TTAAAAATTCTTAGATTTG-ATCCAGTCTCGACCTATCTCACAATAGATTCGACT
1 TTAAAAATTCTTAGA-CTGAAT-CAGGCTCGACCTATCTCAAAACAGATTCGACT
3555371 TTAAAAATT
1 TTAAAAATT
3555380 AAAAATTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
53 2 0.04
54 51 0.93
55 2 0.04
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (53 bp):
TTAAAAATTCTTAGACTGAATCAGGCTCGACCTATCTCAAAACAGATTCGACT
Found at i:3556761 original size:21 final size:21
Alignment explanation
Indices: 3556714--3556809 Score: 86
Period size: 22 Copynumber: 4.4 Consensus size: 21
3556704 TGGAATTCAG
3556714 TAAAAAATCTAATGAAAA-TTTA
1 TAAAAAATC-AAT-AAAATTTTA
* * *
3556736 CAAAAAATCAATACAACTTTA
1 TAAAAAATCAATAAAATTTTA
**
3556757 TAAAAAATTCTTTAAAATTTTA
1 TAAAAAA-TCAATAAAATTTTA
**
3556779 TAAAAAATTCTTTAAAATTTTA
1 TAAAAAA-TCAATAAAATTTTA
3556801 TAAAAAATC
1 TAAAAAATC
3556810 CGTTGAATTT
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
20 3 0.05
21 15 0.23
22 47 0.72
ACGTcount: A:0.55, C:0.08, G:0.01, T:0.35
Consensus pattern (21 bp):
TAAAAAATCAATAAAATTTTA
Found at i:3556820 original size:21 final size:22
Alignment explanation
Indices: 3556753--3556808 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
3556743 TCAATACAAC
3556753 TTTATAAAAAATTCTTTAAAAT
1 TTTATAAAAAATTCTTTAAAAT
3556775 TTTATAAAAAATTCTTTAAAAT
1 TTTATAAAAAATTCTTTAAAAT
3556797 TTTATAAAAAAT
1 TTTATAAAAAAT
3556809 CCGTTGAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTATAAAAAATTCTTTAAAAT
Found at i:3561371 original size:23 final size:22
Alignment explanation
Indices: 3561337--3561396 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
3561327 ACTCCATGAA
*
3561337 GGGAATAAGTGAGACG-GCAGG
1 GGGAATATGTGAGACGAGCAGG
* *
3561358 GTGAGAATATGTGACACGACTCAGG
1 G-G-GAATATGTGAGACGA-GCAGG
3561383 GGGAATATGTGAGA
1 GGGAATATGTGAGA
3561397 ATATGTGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
21 1 0.03
22 1 0.03
23 23 0.74
24 1 0.03
25 5 0.16
ACGTcount: A:0.33, C:0.10, G:0.40, T:0.17
Consensus pattern (22 bp):
GGGAATATGTGAGACGAGCAGG
Found at i:3561692 original size:47 final size:46
Alignment explanation
Indices: 3561480--3561692 Score: 178
Period size: 47 Copynumber: 4.6 Consensus size: 46
3561470 TGTGTGACAC
** * * *
3561480 AATTGTGACACGATAGGGTTTAGAGTTTGTGACATGCCATGGAGGG
1 AATTGTGACACGCCAAGGTTTAGAGTTTGTGACACGCCATGGAGAG
** * * * *
3561526 AATTCGTGACACG-GGAGGATTCAGAGTTTGTAATACGCCATGGAGGG
1 AATT-GTGACACGCCAAGG-TTTAGAGTTTGTGACACGCCATGGAGAG
* ** * * * *
3561573 AATCCGTGACACGTTAGGGTTCATAGTTTGTGACACACCATGGAGAG
1 AAT-TGTGACACGCCAAGGTTTAGAGTTTGTGACACGCCATGGAGAG
* *
3561620 AATTGTGACACGCC-AGAGTTTAGAGTTTATGACATGCCATGGAGAG
1 AATTGTGACACGCCAAG-GTTTAGAGTTTGTGACACGCCATGGAGAG
*
3561666 AATCTGTGATACGCCAAGGTTTAGAGT
1 AAT-TGTGACACGCCAAGGTTTAGAGT
3561693 GTGTCAGATA
Statistics
Matches: 134, Mismatches: 26, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
45 1 0.01
46 41 0.31
47 88 0.66
48 4 0.03
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (46 bp):
AATTGTGACACGCCAAGGTTTAGAGTTTGTGACACGCCATGGAGAG
Found at i:3562367 original size:31 final size:31
Alignment explanation
Indices: 3562326--3562528 Score: 282
Period size: 31 Copynumber: 6.6 Consensus size: 31
3562316 GTGTCAGCGT
3562326 TGGCGTGTAACAACATTTGACTTGATATGCA
1 TGGCGTGTAACAACATTTGACTTGATATGCA
* * * **
3562357 TGACGTGTAACAATATTT-ACTTGGTATATA
1 TGGCGTGTAACAACATTTGACTTGATATGCA
*
3562387 TGGAGTGTAACAACATTTGACTTGATATGCA
1 TGGCGTGTAACAACATTTGACTTGATATGCA
*
3562418 TGGCGTGTAACAATATTTGACTTGATATGCA
1 TGGCGTGTAACAACATTTGACTTGATATGCA
* * *
3562449 TGGCATGTAACAACATTTTATTTGATATGCA
1 TGGCGTGTAACAACATTTGACTTGATATGCA
* *
3562480 TGGCCTGTAACAACATTTGACTTGACATGCA
1 TGGCGTGTAACAACATTTGACTTGATATGCA
*
3562511 TGGTGTGTAACAACATTT
1 TGGCGTGTAACAACATTT
3562529 ATTTCTTTCT
Statistics
Matches: 148, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
30 24 0.16
31 124 0.84
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (31 bp):
TGGCGTGTAACAACATTTGACTTGATATGCA
Found at i:3566600 original size:23 final size:23
Alignment explanation
Indices: 3566574--3566645 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 23
3566564 TGTTGCACAT
* *
3566574 CATTTTTTAAATATGTTACATGC
1 CATTTTTTAAAAATGTTACACGC
3566597 CATTTTTTAAAAATGTTACACGC
1 CATTTTTTAAAAATGTTACACGC
* * * *
3566620 CATGTTTAAAAAATGATGCACGC
1 CATTTTTTAAAAATGTTACACGC
3566643 CAT
1 CAT
3566646 GTTAAAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.38
Consensus pattern (23 bp):
CATTTTTTAAAAATGTTACACGC
Found at i:3566646 original size:23 final size:23
Alignment explanation
Indices: 3566590--3566691 Score: 84
Period size: 23 Copynumber: 4.5 Consensus size: 23
3566580 TTAAATATGT
* * * *
3566590 TACATGCCATTTTTTAAAAATGT
1 TACACGCCATGTTTAAAAAATGA
3566613 TACACGCCATGTTTAAAAAATGA
1 TACACGCCATGTTTAAAAAATGA
*
3566636 TGCACGCCATG-TTAAAAAAT-A
1 TACACGCCATGTTTAAAAAATGA
* * * * *
3566657 T-TACGCACAAGTTCAAAAATTGT
1 TACACGC-CATGTTTAAAAAATGA
3566680 TACACGCCATGT
1 TACACGCCATGT
3566692 GACATGCCCT
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
20 4 0.06
21 5 0.08
22 16 0.25
23 34 0.54
24 4 0.06
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (23 bp):
TACACGCCATGTTTAAAAAATGA
Found at i:3568967 original size:27 final size:27
Alignment explanation
Indices: 3568929--3569034 Score: 110
Period size: 27 Copynumber: 4.0 Consensus size: 27
3568919 ATAGCATGTA
3568929 TAACATGATGTGTAATAATTAAATTTT
1 TAACATGATGTGTAATAATTAAATTTT
* * *
3568956 TAACATGGTGTGTAAAAATTATATTTTT
1 TAACATGATGTGTAATAATTA-AATTTT
* * * * *
3568984 TAATATAACGTGCAACAATTAAATTTT
1 TAACATGATGTGTAATAATTAAATTTT
3569011 TAACATGA---GTAATAATTAAATTTT
1 TAACATGATGTGTAATAATTAAATTTT
3569035 CAAAATGACG
Statistics
Matches: 64, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
24 14 0.22
27 30 0.47
28 20 0.31
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (27 bp):
TAACATGATGTGTAATAATTAAATTTT
Found at i:3570754 original size:2 final size:2
Alignment explanation
Indices: 3570747--3570780 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3570737 TTGTTGAATA
3570747 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3570781 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3584665 original size:86 final size:85
Alignment explanation
Indices: 3584567--3584732 Score: 228
Period size: 86 Copynumber: 1.9 Consensus size: 85
3584557 TTCTGTAATG
* * * * *
3584567 AATTTGAGAAGAAAAAGCAAAGTTGAAATTGCAG-TTTCTACTAATGAATGAGTTC-TCGGTGCA
1 AATTTGAAAAGAAAAAGAAAAGTTGAAATTGCAGATTT-AACTAATGAATCAGTTCTTCGAT-CA
*
3584630 TAAATTTCTTTGTTCAATAACAT
64 T-AATTACTTTGTTCAATAACAT
*
3584653 AATTTGAAAAGAAAAGGAAAAGTTGAAATTGCAGATTTAACTAATGAATCAGTTCTTCGATCATA
1 AATTTGAAAAGAAAAAGAAAAGTTGAAATTGCAGATTTAACTAATGAATCAGTTCTTCGATCATA
3584718 ATTACTTTGTTCAAT
66 ATTACTTTGTTCAAT
3584733 GATTTCTTTT
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
85 15 0.21
86 49 0.69
87 7 0.10
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (85 bp):
AATTTGAAAAGAAAAAGAAAAGTTGAAATTGCAGATTTAACTAATGAATCAGTTCTTCGATCATA
ATTACTTTGTTCAATAACAT
Found at i:3585288 original size:2 final size:2
Alignment explanation
Indices: 3585281--3585305 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3585271 TTCTTCAAGG
3585281 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3585306 AGTAATTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3607830 original size:28 final size:30
Alignment explanation
Indices: 3607799--3607867 Score: 88
Period size: 32 Copynumber: 2.3 Consensus size: 30
3607789 GAATATGATA
*
3607799 TGTAATAACA-A-TATTTTTCAACATGGTG
1 TGTAATAACAGATTATTTTTCAACATGGCG
*
3607827 TGTAATAACAGTATTTTTTTTTCAACATGGCG
1 TGTAATAACAG-A-TTATTTTTCAACATGGCG
3607859 TGTAATAAC
1 TGTAATAAC
3607868 TTTTTTTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 10 0.29
30 1 0.03
32 24 0.69
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (30 bp):
TGTAATAACAGATTATTTTTCAACATGGCG
Found at i:3607954 original size:21 final size:20
Alignment explanation
Indices: 3607926--3607984 Score: 91
Period size: 21 Copynumber: 2.9 Consensus size: 20
3607916 GTATTTTTTT
3607926 TAACATGGCGTGTAACAACC
1 TAACATGGCGTGTAACAACC
*
3607946 TAACTATGGCGTGTAACAACT
1 TAAC-ATGGCGTGTAACAACC
3607967 TAACCATGGCGTGTAACA
1 TAA-CATGGCGTGTAACA
3607985 TGTTTGTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 4 0.11
21 31 0.86
22 1 0.03
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (20 bp):
TAACATGGCGTGTAACAACC
Found at i:3608085 original size:45 final size:45
Alignment explanation
Indices: 3608014--3608163 Score: 151
Period size: 45 Copynumber: 3.3 Consensus size: 45
3608004 ACAATTTAAC
* * * *
3608014 CATGGCGTGTCACACATTTTTATACATGGCATGTAATAACCTAAT
1 CATGACGTGTAACACGTTTTTGTACATGGCATGTAATAACCTAAT
* * * *
3608059 CATGACGTGTAACATGTTTTTGTACATGGCGTGTAACACCCTAA-
1 CATGACGTGTAACACGTTTTTGTACATGGCATGTAATAACCTAAT
* ** *
3608103 CTAT-AGCGTGTCACACGTTTTTGTACATAACATGTAATAATCTAAT
1 C-ATGA-CGTGTAACACGTTTTTGTACATGGCATGTAATAACCTAAT
*
3608149 CATGGCGTGTAACAC
1 CATGACGTGTAACAC
3608164 CCTAATCATG
Statistics
Matches: 83, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
44 2 0.02
45 80 0.96
46 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (45 bp):
CATGACGTGTAACACGTTTTTGTACATGGCATGTAATAACCTAAT
Found at i:3608130 original size:90 final size:88
Alignment explanation
Indices: 3607951--3608162 Score: 244
Period size: 90 Copynumber: 2.4 Consensus size: 88
3607941 CAACCTAACT
* * * * * **
3607951 ATGGCGTGTAACAACTTAACCATGGCGTGTAACATGTTTGTATATGACGTGCAACAATTTAACCA
1 ATGGCATGTAATAACCTAATCATGGCGTGTAACATGTTTGTACATGACGTGCAACAACCTAACCA
*
3608016 TGGCGTGTCACACATTTTTATAC
66 TAGCGTGTCACACATTTTTATAC
* * * *
3608039 ATGGCATGTAATAACCTAATCATGACGTGTAACATGTTTTTGTACATGGCGTGTAACACCCTAAC
1 ATGGCATGTAATAACCTAATCATGGCGTGTAACATG--TTTGTACATGACGTGCAACAACCTAAC
* * *
3608104 TATAGCGTGTCACACGTTTTTGTAC
64 CATAGCGTGTCACACATTTTTATAC
** *
3608129 ATAACATGTAATAATCTAATCATGGCGTGTAACA
1 ATGGCATGTAATAACCTAATCATGGCGTGTAACA
3608163 CCCTAATCAT
Statistics
Matches: 103, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
88 31 0.30
90 72 0.70
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (88 bp):
ATGGCATGTAATAACCTAATCATGGCGTGTAACATGTTTGTACATGACGTGCAACAACCTAACCA
TAGCGTGTCACACATTTTTATAC
Found at i:3608168 original size:21 final size:21
Alignment explanation
Indices: 3608135--3608249 Score: 70
Period size: 21 Copynumber: 5.3 Consensus size: 21
3608125 GTACATAACA
* *
3608135 TGTAATAATCTAATCATGGCG
1 TGTAACAACCTAATCATGGCG
* *
3608156 TGTAACACCCTAATCATGGTG
1 TGTAACAACCTAATCATGGCG
* * **
3608177 TGTCAC-ACGTTTTTGTACATGGCG
1 TGTAACAAC---CTAAT-CATGGCG
* *
3608201 TGTAACAACCTAACCATGGCA
1 TGTAACAACCTAATCATGGCG
* * *
3608222 TGTAACAACCTAACCATGACA
1 TGTAACAACCTAATCATGGCG
3608243 TGTAACA
1 TGTAACA
3608250 TGTTTTTATA
Statistics
Matches: 72, Mismatches: 17, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
20 1 0.01
21 55 0.76
22 1 0.01
23 2 0.03
24 11 0.15
25 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTAACAACCTAATCATGGCG
Found at i:3608244 original size:26 final size:22
Alignment explanation
Indices: 3608193--3608249 Score: 82
Period size: 21 Copynumber: 2.7 Consensus size: 22
3608183 ACGTTTTTGT
*
3608193 ACATGGCGTGTAACAACCTAAC
1 ACATGGCATGTAACAACCTAAC
3608215 -CATGGCATGTAACAACCTAAC
1 ACATGGCATGTAACAACCTAAC
*
3608236 -CATGACATGTAACA
1 ACATGGCATGTAACA
3608250 TGTTTTTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.39, C:0.26, G:0.16, T:0.19
Consensus pattern (22 bp):
ACATGGCATGTAACAACCTAAC
Found at i:3608255 original size:66 final size:66
Alignment explanation
Indices: 3608083--3608273 Score: 204
Period size: 66 Copynumber: 2.9 Consensus size: 66
3608073 TGTTTTTGTA
* ** * * *
3608083 CATGGCGTGTAACACCCTAACTAT-AGCGTGTCACACGTTTTTGTACATAACATGTAATAATCTA
1 CATGGCGTGTAACACCCTAACCATGA-CGTGTCACACGTTTTTGTACATGGCGTGTAACAACCTA
*
3608147 AT
65 AC
* **
3608149 CATGGCGTGTAACACCCTAATCATGGTGTGTCACACGTTTTTGTACATGGCGTGTAACAACCTAA
1 CATGGCGTGTAACACCCTAACCATGACGTGTCACACGTTTTTGTACATGGCGTGTAACAACCTAA
3608214 C
66 C
* * * * * * * *
3608215 CATGGCATGTAACAACCTAACCATGACATGTAACATGTTTTTATACACGGTGTGTAACA
1 CATGGCGTGTAACACCCTAACCATGACGTGTCACACGTTTTTGTACATGGCGTGTAACA
3608274 TTCTGGCATG
Statistics
Matches: 103, Mismatches: 21, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
66 103 1.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (66 bp):
CATGGCGTGTAACACCCTAACCATGACGTGTCACACGTTTTTGTACATGGCGTGTAACAACCTAA
C
Found at i:3612027 original size:38 final size:38
Alignment explanation
Indices: 3611963--3612045 Score: 121
Period size: 38 Copynumber: 2.2 Consensus size: 38
3611953 ATATAACAAG
* * *
3611963 GTTTCATATTACAAGCAAGAATTGCATTCAACTAAAAT
1 GTTTCATATTACAAACAAAAACTGCATTCAACTAAAAT
* *
3612001 GTTTCATATTATAAACAAAAACTGCATTCAACTATAAT
1 GTTTCATATTACAAACAAAAACTGCATTCAACTAAAAT
3612039 GTTTCAT
1 GTTTCAT
3612046 GATATTCATA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.35
Consensus pattern (38 bp):
GTTTCATATTACAAACAAAAACTGCATTCAACTAAAAT
Found at i:3612193 original size:31 final size:31
Alignment explanation
Indices: 3612146--3612217 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
3612136 AAAGAATTAG
* * ** *
3612146 TCCTTATATTATAAAGTTATGTTCAATTTAT
1 TCCTTATACTACAAAGTTATGAACAATTTAA
* *
3612177 TCCTTGTACTACAAAGTTTTGAACAATTTAA
1 TCCTTATACTACAAAGTTATGAACAATTTAA
3612208 TCCTTATACT
1 TCCTTATACT
3612218 TTACTATTTT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.32, C:0.15, G:0.07, T:0.46
Consensus pattern (31 bp):
TCCTTATACTACAAAGTTATGAACAATTTAA
Found at i:3613298 original size:22 final size:21
Alignment explanation
Indices: 3613273--3613313 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3613263 ATTTTAACAA
3613273 ATTTAAAATAATTTTTTATTAT
1 ATTT-AAATAATTTTTTATTAT
*
3613295 ATTTAATTAATTTTTTATT
1 ATTTAAATAATTTTTTATT
3613314 TTTTATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTTAAATAATTTTTTATTAT
Found at i:3614241 original size:41 final size:41
Alignment explanation
Indices: 3614195--3614274 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
3614185 AAATCTATAC
* *
3614195 TTATCATAACATATTATATCTTAATAATTCAACTTAATAAT
1 TTATCATAACATATTATATCTCAATAATTCAACCTAATAAT
* *
3614236 TTATCATAATATATTATATCTCAATAATTTAACCTAATA
1 TTATCATAACATATTATATCTCAATAATTCAACCTAATA
3614275 TCTCAATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (41 bp):
TTATCATAACATATTATATCTCAATAATTCAACCTAATAAT
Found at i:3614751 original size:21 final size:22
Alignment explanation
Indices: 3614727--3614774 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
3614717 TGTATTTAAT
3614727 TTAAAATAAAAAT-ATAAAAAA
1 TTAAAATAAAAATAATAAAAAA
*
3614748 TT-AATTAAAAATAATAAAAAA
1 TTAAAATAAAAATAATAAAAAA
*
3614769 ATAAAA
1 TTAAAA
3614775 ATTTGTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 9 0.41
21 11 0.50
22 2 0.09
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (22 bp):
TTAAAATAAAAATAATAAAAAA
Found at i:3614759 original size:11 final size:9
Alignment explanation
Indices: 3614731--3614776 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
3614721 TTTAATTTAA
3614731 AATAAAAAT
1 AATAAAAAT
3614740 -ATAAAAAATT
1 AAT-AAAAA-T
3614750 AATTAAAAAT
1 AA-TAAAAAT
3614760 AATAAAAA-
1 AATAAAAAT
3614768 AATAAAAAT
1 AATAAAAAT
3614777 TTGTTTAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
8 10 0.31
9 11 0.34
10 4 0.12
11 6 0.19
12 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AATAAAAAT
Found at i:3615770 original size:16 final size:16
Alignment explanation
Indices: 3615749--3615782 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3615739 ATTATTTAAA
* *
3615749 ATATTTTTATTATTTT
1 ATATTTATATAATTTT
3615765 ATATTTATATAATTTT
1 ATATTTATATAATTTT
3615781 AT
1 AT
3615783 TTAAAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATATTTATATAATTTT
Found at i:3617332 original size:15 final size:16
Alignment explanation
Indices: 3617293--3617334 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
3617283 CTGTATGAAT
*
3617293 TTTTCTTTCTTAGTAC
1 TTTTCTTTCATAGTAC
* *
3617309 TTTTGTTTCAT-GTTC
1 TTTTCTTTCATAGTAC
3617324 TTTTCTTTCAT
1 TTTTCTTTCAT
3617335 TCTCTTTATC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.10, C:0.17, G:0.07, T:0.67
Consensus pattern (16 bp):
TTTTCTTTCATAGTAC
Found at i:3623214 original size:19 final size:20
Alignment explanation
Indices: 3623175--3623212 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3623165 TTTCGATCTC
3623175 ATACTTTTAATATAAAAAAT
1 ATACTTTTAATATAAAAAAT
3623195 ATACTTATTAAT-TAAAAA
1 ATACTT-TTAATATAAAAA
3623213 TAAATTCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (20 bp):
ATACTTTTAATATAAAAAAT
Found at i:3623222 original size:21 final size:21
Alignment explanation
Indices: 3623175--3623233 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
3623165 TTTCGATCTC
*
3623175 ATACTT-TTAATATAAAAAAT
1 ATACTTATTAATATAAAAAAA
3623195 ATACTTATTAAT-TAAAAATAA
1 ATACTTATTAATATAAAAA-AA
* * *
3623216 ATTCTTATAAATCTAAAA
1 ATACTTATTAATATAAAA
3623234 TTTTACTGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 12 0.36
21 16 0.48
22 5 0.15
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (21 bp):
ATACTTATTAATATAAAAAAA
Found at i:3627969 original size:15 final size:16
Alignment explanation
Indices: 3627946--3627979 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3627936 TACTTGATTG
*
3627946 TAAAGAATCAAA-AAA
1 TAAACAATCAAATAAA
3627961 TAAACAATCAAATAAA
1 TAAACAATCAAATAAA
3627977 TAA
1 TAA
3627980 GCAAGGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.71, C:0.09, G:0.03, T:0.18
Consensus pattern (16 bp):
TAAACAATCAAATAAA
Found at i:3632070 original size:31 final size:31
Alignment explanation
Indices: 3632032--3632090 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
3632022 GGCATTAATG
*
3632032 TCTCTGTCTACAGATTGCGTTGGCTTCTACA
1 TCTCTGTCTACAGATTGCATTGGCTTCTACA
*
3632063 TCTCTGTCTACAGATTGCATTGGGTTCT
1 TCTCTGTCTACAGATTGCATTGGCTTCT
3632091 GCATATGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.15, C:0.24, G:0.20, T:0.41
Consensus pattern (31 bp):
TCTCTGTCTACAGATTGCATTGGCTTCTACA
Found at i:3641692 original size:25 final size:26
Alignment explanation
Indices: 3641664--3641721 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
3641654 TTGCTATTAT
3641664 TAATTTATAAT-TGTTATTGAAAAT-A
1 TAATTTATAATAT-TTATTGAAAATAA
* *
3641689 TAATTAATAATATTTATTTAAAATAA
1 TAATTTATAATATTTATTGAAAATAA
3641715 TAATTTA
1 TAATTTA
3641722 AAAATAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 20 0.71
26 8 0.29
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (26 bp):
TAATTTATAATATTTATTGAAAATAA
Found at i:3654091 original size:55 final size:54
Alignment explanation
Indices: 3654004--3654145 Score: 133
Period size: 55 Copynumber: 2.6 Consensus size: 54
3653994 ACTAAAAGAA
** **
3654004 TTTCTGTTGGAAATGCATCACTAATGGAAAATTTTTTCAGAAATTTTCAAGCAAAAT
1 TTTC-GTTGGAAATGCAT-TTTAATGGAAAATTTCGTCAGAAATTTTCAA-CAAAAT
* * ** *
3654061 TTTCGTTGGAAATGCATTTTAGTGGGAAATTTCGTGGGAAATTTTCAACGAAAT
1 TTTCGTTGGAAATGCATTTTAATGGAAAATTTCGTCAGAAATTTTCAACAAAAT
* * *
3654115 TTT-GTGGGAAATGCTTTTTGAATGAAAAATT
1 TTTCGTTGGAAATGCATTTT-AATGGAAAATT
3654146 CTATTGAAAT
Statistics
Matches: 70, Mismatches: 14, Indels: 5
0.79 0.16 0.06
Matches are distributed among these distances:
53 14 0.20
54 16 0.23
55 23 0.33
56 13 0.19
57 4 0.06
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (54 bp):
TTTCGTTGGAAATGCATTTTAATGGAAAATTTCGTCAGAAATTTTCAACAAAAT
Found at i:3659991 original size:43 final size:43
Alignment explanation
Indices: 3659913--3659994 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
3659903 ATTATCTTTT
*
3659913 CATCTCGAAACTTGAGAAAGACCATCGGAATAACTAGTCATGA
1 CATCTCGAAACTTGAGAAAGACCACCGGAATAACTAGTCATGA
*
3659956 CATCTCTG-AACTTGAGAAAGACCGCCGGAGA-AACTAGTC
1 CATCTC-GAAACTTGAGAAAGACCACCGGA-ATAACTAGTC
3659995 CTAATACGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
43 33 0.94
44 2 0.06
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.20
Consensus pattern (43 bp):
CATCTCGAAACTTGAGAAAGACCACCGGAATAACTAGTCATGA
Found at i:3660438 original size:199 final size:195
Alignment explanation
Indices: 3660099--3660485 Score: 505
Period size: 199 Copynumber: 2.0 Consensus size: 195
3660089 TATCTTCTTT
* * *
3660099 CTTGATCGCTTTGATGTTGAAGACGACGTAATAGTCTCTCTCTTTGCCTTCTCTATTTTCTCCGT
1 CTTGATCGCTTTGATGTTGAAGACGACGTAATAATATCTCTCTTTCCCTTCTCTATTTTCTCCGT
* * *
3660164 TTTTCCAGTTTTCTTGTTGTTACTAGTAGGGTTTAAGCCTCTGTTAAATTTGGTTTCTTGAGCTA
66 TATTCCAGTTTTCTTGTTGTTAC-ACTAGGGTTTAAGCCTCTGTTAAATTTGGTTTCTTGAACTA
* *
3660229 TTCAAAAACTTAAAGCTGCAAAGAAA-AATGAGAAATGTATAGGCTTTGTATATTGTTTTCCTTC
130 TTCAAAAACTTAAAGCAGCAAAGAAAGAA-GAGAAATG-ATAGGCCTTGTATATTGTTTTCCTTC
3660293 GTG
193 GTG
*
3660296 CTTGATCGCTTTGTTGTTGAAGACGACGTAATTTTACAATATCTCTCTTTCCCTTCTCTATTTTC
1 CTTGATCGCTTTGATGTTGAAGACGACGTAA---T--AATATCTCTCTTTCCCTTCTCTATTTTC
* * * *
3660361 TCTGTTATTCCGGTTTTCTTGTTGTT-C-CTAGGGTTT-AGTTCTCTGTTATATTTGGTTTCTTG
61 TCCGTTATTCCAGTTTTCTTGTTGTTACACTAGGGTTTAAG-CCTCTGTTAAATTTGGTTTCTTG
* * *
3660423 AACTGTAT-AAAAACTTAAAGCAGCAAAGAAAGAAGAGAAATGATATGCCTTGTTTATTGTTTT
125 AACTAT-TCAAAAACTTAAAGCAGCAAAGAAAGAAGAGAAATGATAGGCCTTGTATATTGTTTT
3660486 GCTTATTGAA
Statistics
Matches: 166, Mismatches: 16, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
197 30 0.18
198 20 0.12
199 63 0.38
200 4 0.02
201 1 0.01
202 48 0.29
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (195 bp):
CTTGATCGCTTTGATGTTGAAGACGACGTAATAATATCTCTCTTTCCCTTCTCTATTTTCTCCGT
TATTCCAGTTTTCTTGTTGTTACACTAGGGTTTAAGCCTCTGTTAAATTTGGTTTCTTGAACTAT
TCAAAAACTTAAAGCAGCAAAGAAAGAAGAGAAATGATAGGCCTTGTATATTGTTTTCCTTCGTG
Found at i:3663957 original size:12 final size:12
Alignment explanation
Indices: 3663940--3663965 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3663930 AATGAAAGTG
3663940 AAGGGCAAGTCA
1 AAGGGCAAGTCA
3663952 AAGGGCAAGTCA
1 AAGGGCAAGTCA
3663964 AA
1 AA
3663966 AGTCCATTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.15, G:0.31, T:0.08
Consensus pattern (12 bp):
AAGGGCAAGTCA
Found at i:3664218 original size:31 final size:28
Alignment explanation
Indices: 3664180--3664266 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 28
3664170 TATGTCATAA
*
3664180 AGATTAAATTGAATAAAAATATATAATATAT
1 AGATTAAATT-AA-AAAAAT-TAAAATATAT
3664211 AGATTAAATTAAAAAAATTAAAATAT-T
1 AGATTAAATTAAAAAAATTAAAATATAT
* *
3664238 GAGAAATTAAATTAAAAATATTTAAATAT
1 -AG--ATTAAATTAAAAAAATTAAAATAT
3664267 TTTAAATATT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
27 1 0.02
28 9 0.18
29 6 0.12
30 24 0.48
31 10 0.20
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (28 bp):
AGATTAAATTAAAAAAATTAAAATATAT
Found at i:3664786 original size:19 final size:18
Alignment explanation
Indices: 3664756--3664791 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
3664746 TGAATTTCAC
3664756 TTTTTTATTTTTTATTTA
1 TTTTTTATTTTTTATTTA
3664774 TTTTTTATATTTTTATTT
1 TTTTTTAT-TTTTTATTT
3664792 TGTTTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTTATTTTTTATTTA
Found at i:3664801 original size:18 final size:19
Alignment explanation
Indices: 3664764--3664803 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
3664754 ACTTTTTTAT
* *
3664764 TTTTTATTTATTTTTTATA
1 TTTTTATTTATGTTTAATA
3664783 TTTTTATTT-TGTTTAATA
1 TTTTTATTTATGTTTAATA
3664801 TTT
1 TTT
3664804 CAAGTTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.78
Consensus pattern (19 bp):
TTTTTATTTATGTTTAATA
Found at i:3665124 original size:107 final size:108
Alignment explanation
Indices: 3665003--3665211 Score: 316
Period size: 107 Copynumber: 1.9 Consensus size: 108
3664993 TATAAGAAAT
*
3665003 TTTGAGTAAATTTAAATAAAATGTAAA-TTGAATAAGAGTTGAATAA-TTTCAAAAGAATGTGTA
1 TTTGAGTAAATTTAAATAAAAGGTAAATTTG-ATAAGAGTTGAATAAGTTT-AAAAGAATGTGTA
* * *
3665066 TTTATAAATTGTGAAA-TTGTAGCTAAATCAACATATTTTGCTAA
64 TTTATAAATCGTGAAAGTTGCAACTAAATCAACATATTTTGCTAA
*
3665110 TTTGAGTAAATTTAAATAAAAGGTAAATTTGGTAAGAGTTGAATAAGTTTAAAAGAATGTGTATT
1 TTTGAGTAAATTTAAATAAAAGGTAAATTTGATAAGAGTTGAATAAGTTTAAAAGAATGTGTATT
* *
3665175 TGTAAATCGTGAAAGTTGCAACTCAATCAACATATTT
66 TATAAATCGTGAAAGTTGCAACTAAATCAACATATTT
3665212 AGTCATTTTA
Statistics
Matches: 92, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
107 67 0.73
108 25 0.27
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.36
Consensus pattern (108 bp):
TTTGAGTAAATTTAAATAAAAGGTAAATTTGATAAGAGTTGAATAAGTTTAAAAGAATGTGTATT
TATAAATCGTGAAAGTTGCAACTAAATCAACATATTTTGCTAA
Found at i:3668473 original size:11 final size:11
Alignment explanation
Indices: 3668457--3668486 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
3668447 ATTTCAACCA
3668457 AAAAAAAAAAG
1 AAAAAAAAAAG
3668468 AAAAAAAAAAG
1 AAAAAAAAAAG
3668479 AAAGAAAA
1 AAA-AAAA
3668487 GACTCCTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:3668476 original size:15 final size:15
Alignment explanation
Indices: 3668456--3668486 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3668446 CATTTCAACC
3668456 AAAAAAAAAAAGAAA
1 AAAAAAAAAAAGAAA
*
3668471 AAAAAAAGAAAGAAA
1 AAAAAAAAAAAGAAA
3668486 A
1 A
3668487 GACTCCTTAA
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:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAGAAA
Found at i:3669156 original size:13 final size:13
Alignment explanation
Indices: 3669138--3669163 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3669128 GTAGAATGTA
3669138 TAATACCTTTCTG
1 TAATACCTTTCTG
3669151 TAATACCTTTCTG
1 TAATACCTTTCTG
3669164 CCAGAAGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (13 bp):
TAATACCTTTCTG
Found at i:3669668 original size:33 final size:34
Alignment explanation
Indices: 3669612--3669704 Score: 92
Period size: 33 Copynumber: 2.9 Consensus size: 34
3669602 ATTAATTTAT
* *
3669612 TAAAAATATTT-TATAATAT-TATAAT-TAA-AA
1 TAAAAATATTTAAATAAAATATATAATATAAGAA
3669642 TAAAAAATATTTAAATAAAATATATAATATAAGAA
1 T-AAAAATATTTAAATAAAATATATAATATAAGAA
* *
3669677 TCAAAA-ATTAAAATAAAATA-A-AATATAA
1 TAAAAATATTTAAATAAAATATATAATATAA
3669705 AAAATTAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
30 1 0.02
31 17 0.31
32 7 0.13
33 19 0.35
34 7 0.13
35 3 0.06
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (34 bp):
TAAAAATATTTAAATAAAATATATAATATAAGAA
Found at i:3669670 original size:20 final size:21
Alignment explanation
Indices: 3669623--3669671 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
3669613 AAAAATATTT
*
3669623 TATAATATTATAATTAAAATA
1 TATAATATTATAAATAAAATA
* *
3669644 AAAAATATT-TAAATAAAATA
1 TATAATATTATAAATAAAATA
3669664 TATAATAT
1 TATAATAT
3669672 AAGAATCAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TATAATATTATAAATAAAATA
Found at i:3669725 original size:24 final size:25
Alignment explanation
Indices: 3669697--3669790 Score: 55
Period size: 30 Copynumber: 3.4 Consensus size: 25
3669687 AAATAAAATA
* *
3669697 AAATATAAAAAATTAAAATTTATATA
1 AAATATAAAAAATTAAAA-TAAAATA
*
3669723 ATATAGGTAAAAGAAATTAAAATAAAATA
1 AAATA--T-AAA-AAATTAAAATAAAATA
*
3669752 TATAATATAAAAAATTATATTAAAAAAATA
1 -A-AATATAAAAAATTA-A--AATAAAATA
3669782 AAA-ATAAAA
1 AAATATAAAA
3669791 TGTATAAAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 17
0.71 0.07 0.22
Matches are distributed among these distances:
26 4 0.07
27 12 0.22
28 7 0.13
29 10 0.19
30 18 0.33
31 3 0.06
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (25 bp):
AAATATAAAAAATTAAAATAAAATA
Found at i:3669784 original size:50 final size:50
Alignment explanation
Indices: 3669690--3669784 Score: 111
Period size: 50 Copynumber: 1.9 Consensus size: 50
3669680 AAAATTAAAA
* * * **
3669690 TAAAATAAAATATAAAAAATTAAAATTTATATAATATAGGTAAAAGAAAT
1 TAAAATAAAATATAAAAAATAAAAAATTATATAATAAAAATAAAAGAAAT
* *
3669740 TAAAATAAAATATATAATATAAAAAATTATATTAA-AAAAATAAAA
1 TAAAATAAAATATAAAAAATAAAAAATTATA-TAATAAAAATAAAA
3669785 ATAAAATGTA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
50 34 0.92
51 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.29
Consensus pattern (50 bp):
TAAAATAAAATATAAAAAATAAAAAATTATATAATAAAAATAAAAGAAAT
Found at i:3685598 original size:69 final size:69
Alignment explanation
Indices: 3685487--3685624 Score: 177
Period size: 69 Copynumber: 2.0 Consensus size: 69
3685477 CTACAGTAAC
* **
3685487 AAACTACCATAAACCAGACTTCAAAGTTAATCCTACAATGATATATATGCGGTGATCAATAATTA
1 AAACTACCATAAACCAGACTTCAAAATTAATCCTACAATGATATATATGCGACGATCAATAATTA
3685552 ATTT
66 ATTT
* * * * ** * *
3685556 AAACTACCATGAACTAGATTTCAAAATTAATTCTACGGTGATATATATGTGACGCTCAATAATTA
1 AAACTACCATAAACCAGACTTCAAAATTAATCCTACAATGATATATATGCGACGATCAATAATTA
3685621 ATTT
66 ATTT
3685625 TATGTATTTT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
69 58 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.33
Consensus pattern (69 bp):
AAACTACCATAAACCAGACTTCAAAATTAATCCTACAATGATATATATGCGACGATCAATAATTA
ATTT
Found at i:3686084 original size:2 final size:2
Alignment explanation
Indices: 3686077--3686104 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3686067 AATAATCATC
3686077 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3686105 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3696692 original size:11 final size:11
Alignment explanation
Indices: 3696678--3696711 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
3696668 TACATAAAAC
3696678 TTTATTTTAAA
1 TTTATTTTAAA
3696689 TTTATTTT-AA
1 TTTATTTTAAA
*
3696699 TTGATTTTAAA
1 TTTATTTTAAA
3696710 TT
1 TT
3696712 AAGTGTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (11 bp):
TTTATTTTAAA
Found at i:3697917 original size:2 final size:2
Alignment explanation
Indices: 3697910--3697949 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3697900 ATTGATTCTC
3697910 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3697950 TCAGTGAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3706483 original size:14 final size:15
Alignment explanation
Indices: 3706458--3706487 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3706448 AGTAAATATC
3706458 TTATATATTATTATG
1 TTATATATTATTATG
3706473 TTATA-ATTATTATG
1 TTATATATTATTATG
3706487 T
1 T
3706488 CTTAGTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (15 bp):
TTATATATTATTATG
Found at i:3707045 original size:221 final size:212
Alignment explanation
Indices: 3706547--3707079 Score: 769
Period size: 212 Copynumber: 2.5 Consensus size: 212
3706537 AATATGTTAT
*
3706547 ATATATTTAATTTATACATAAATATTACTATAACTTATAATAAATTTTATTTATATGATTACACT
1 ATATATTTAATTTATACATAAGTATTACTATAACTTATAATAAATTTTATTTATATGATTACACT
* *
3706612 TAATAACTTTATTAATTATCACTTTAGTTTTTATAACATATTGTTTATAATTAGTTATTATTTAT
66 TAATAACTTTATTAGTTATCACTTTAGTTTTTATAACATATTATTTATAATTAGTTATTATTTAT
* * *
3706677 ACAAATTTTAATATAAAACATTATAACATATAAATTGTGTCATTAATGTTATATATATAATAAAG
131 ACAAATTTTAAAATAAAACATTATAACATATAAATTGTATCATTAATGTTATATATATAATAAAA
* *
3706742 TAATATATTATATATAC
196 TAATATATTATATACAA
* * * *
3706759 ATATATTTAATTTGTACATAAGCATTACTACAACTTATAATAGATTTTATTTATATGATTACACT
1 ATATATTTAATTTATACATAAGTATTACTATAACTTATAATAAATTTTATTTATATGATTACACT
*
3706824 TAATAATTTTATTAGTTATCACTTTAGTTTTTATAACATATTATTTATAATTAGTTATTATTTAT
66 TAATAACTTTATTAGTTATCACTTTAGTTTTTATAACATATTATTTATAATTAGTTATTATTTAT
* * * * *
3706889 ACAAATTTGGATGTGAAAATTAAAATATTATAATATATAAGTTGTATTATTAATTTTATATATAT
131 ACAAA-TT---T-T-AAAA-TAAAACATTATAACATATAAATTGTATCATTAATGTTATATATAT
3706954 AAAATAAAATAATATATTATATACAA
189 --AATAAAATAATATATTATATACAA
* * * * * *
3706980 ATATATTTAATTTACACATAAGTATTATTATAATTTATAATATACTTTATTTATATGAGTACACT
1 ATATATTTAATTTATACATAAGTATTACTATAACTTATAATAAATTTTATTTATATGATTACACT
3707045 TAATAACTTTATTAGTTATCACTTTAGTTTTTATA
66 TAATAACTTTATTAGTTATCACTTTAGTTTTTATA
3707080 TTTAATTTAT
Statistics
Matches: 284, Mismatches: 28, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
212 127 0.45
213 2 0.01
216 1 0.00
217 1 0.00
218 3 0.01
219 39 0.14
221 111 0.39
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.47
Consensus pattern (212 bp):
ATATATTTAATTTATACATAAGTATTACTATAACTTATAATAAATTTTATTTATATGATTACACT
TAATAACTTTATTAGTTATCACTTTAGTTTTTATAACATATTATTTATAATTAGTTATTATTTAT
ACAAATTTTAAAATAAAACATTATAACATATAAATTGTATCATTAATGTTATATATATAATAAAA
TAATATATTATATACAA
Found at i:3724088 original size:17 final size:17
Alignment explanation
Indices: 3724066--3724100 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3724056 TTTCAGATGG
3724066 ATTGCAGAATTAAGGCA
1 ATTGCAGAATTAAGGCA
3724083 ATTGCAGAATTAAGGCA
1 ATTGCAGAATTAAGGCA
3724100 A
1 A
3724101 ATACCTGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (17 bp):
ATTGCAGAATTAAGGCA
Found at i:3724324 original size:5 final size:5
Alignment explanation
Indices: 3724314--3724338 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3724304 TGCTTTCCTC
3724314 TCTTT TCTTT TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCTTT TCTTT TCTTT
3724339 ATAAAGCAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TCTTT
Found at i:3744845 original size:22 final size:22
Alignment explanation
Indices: 3744803--3744845 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3744793 GTTTTGTATG
* *
3744803 TTATAGAATAAAGTTTAAAATA
1 TTATAAAATAAAGTTGAAAATA
*
3744825 TTATAAAATAAAGTTGGAAAT
1 TTATAAAATAAAGTTGAAAAT
3744846 CGAATGGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (22 bp):
TTATAAAATAAAGTTGAAAATA
Found at i:3753373 original size:8 final size:8
Alignment explanation
Indices: 3753324--3753387 Score: 51
Period size: 8 Copynumber: 8.1 Consensus size: 8
3753314 CAGTATAACT
3753324 TATATTAA
1 TATATTAA
3753332 TA-ATTTAA
1 TATA-TTAA
* *
3753340 CATAGTAA
1 TATATTAA
* *
3753348 TTTGTTAA
1 TATATTAA
*
3753356 TATACT-A
1 TATATTAA
3753363 TATATTAA
1 TATATTAA
3753371 TATATTAA
1 TATATTAA
*
3753379 TACATTAA
1 TATATTAA
3753387 T
1 T
3753388 GACTTAATGA
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
7 7 0.17
8 34 0.81
9 1 0.02
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (8 bp):
TATATTAA
Found at i:3753671 original size:19 final size:20
Alignment explanation
Indices: 3753647--3753689 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
3753637 AAAATAATAG
3753647 AAGAGATTTTC-TTTTATAA
1 AAGAGATTTTCATTTTATAA
3753666 AAGAGATTTTCATTTTATAA
1 AAGAGATTTTCATTTTATAA
3753686 AAGA
1 AAGA
3753690 AAATATTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.42
Consensus pattern (20 bp):
AAGAGATTTTCATTTTATAA
Found at i:3756221 original size:2 final size:2
Alignment explanation
Indices: 3756214--3756240 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3756204 AATTATTTTG
3756214 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3756241 CTCCCAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3760873 original size:31 final size:30
Alignment explanation
Indices: 3760833--3760905 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
3760823 TTTTTAAAAT
* * *
3760833 TTTTTTTCAATTTAGTCCTT-CAGTATCTTCA
1 TTTTGTTCAATTTAGTCCTTGCACTA-CAT-A
*
3760864 TTTTGTTCAATTTAGTTCTTGCACTACATA
1 TTTTGTTCAATTTAGTCCTTGCACTACATA
3760894 TTTTGTTCAATT
1 TTTTGTTCAATT
3760906 AACCCCTATG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 13 0.35
31 20 0.54
32 4 0.11
ACGTcount: A:0.21, C:0.16, G:0.08, T:0.55
Consensus pattern (30 bp):
TTTTGTTCAATTTAGTCCTTGCACTACATA
Found at i:3761567 original size:143 final size:144
Alignment explanation
Indices: 3761401--3761693 Score: 390
Period size: 146 Copynumber: 2.0 Consensus size: 144
3761391 CTAAAAAAAT
* * *
3761401 TTTCTATAAACAAATTATTTTTCAGTTACGAACCGAACTACAATAAAAAATAAAT-AAAAAATAA
1 TTTCTATAAACAAATTATTTTTCAATTACGAAACGAAATACAATAAAAAATAAATAAAAAAATAA
* ** *
3761465 AAATAATTAGAGCATTAAGATTTGATGTAGGTTTCATTTGGTAAAAATAAAAACTTTTTTTGAAA
66 AAATAATTACAGCATTAAGATTTGACATAGGTTTCATTTGGTAAAAATAAAAACATTTTTTGAAA
3761530 AATTTTTTAATCAC
131 AATTTTTTAATCAC
* * * *
3761544 TTTCTATAGACAAATTATTTTTCAATTATGAAATGAAATATAATAAAAAATAAATACGAAAAAAT
1 TTTCTATAAACAAATTATTTTTCAATTACGAAACGAAATACAATAAAAAATAAATA--AAAAAAT
* * * * *
3761609 AAAAATAATTACCGCATTGAGATTTTACATAGGTTTCATTTTGTAAAACTAAAAACATTTTTTGA
64 AAAAATAATTACAGCATTAAGATTTGACATAGGTTTCATTTGGTAAAAATAAAAACATTTTTTGA
** *
3761674 AATTTTTTTTAATCAT
129 AAAATTTTTTAATCAC
3761690 TTTC
1 TTTC
3761694 CCTTGTTTGC
Statistics
Matches: 128, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
143 48 0.38
146 80 0.62
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.38
Consensus pattern (144 bp):
TTTCTATAAACAAATTATTTTTCAATTACGAAACGAAATACAATAAAAAATAAATAAAAAAATAA
AAATAATTACAGCATTAAGATTTGACATAGGTTTCATTTGGTAAAAATAAAAACATTTTTTGAAA
AATTTTTTAATCAC
Found at i:3764484 original size:2 final size:2
Alignment explanation
Indices: 3764477--3764509 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3764467 CTTGATGGTA
3764477 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
3764510 AATATTGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3772155 original size:26 final size:27
Alignment explanation
Indices: 3772098--3772155 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
3772088 ATTTAAAAAA
* *
3772098 ATTTAAATAAAATTTTATTTTTATTAT
1 ATTTAAATAAAATTTTATATTTATGAT
* *
3772125 ATTTAATTAAATTTTTATATTTA-GAT
1 ATTTAAATAAAATTTTATATTTATGAT
*
3772151 CTTTA
1 ATTTA
3772156 TAATCAATAG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 6 0.23
27 20 0.77
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (27 bp):
ATTTAAATAAAATTTTATATTTATGAT
Found at i:3791784 original size:2 final size:2
Alignment explanation
Indices: 3791777--3791817 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3791767 TCATCTAGTT
3791777 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
3791818 GAAAGAATAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3792427 original size:19 final size:21
Alignment explanation
Indices: 3792403--3792443 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3792393 ATACTTATAT
3792403 ACTATATA-AGT-ATATATTA
1 ACTATATATAGTAATATATTA
3792422 ACTATATATAGTAATATATTA
1 ACTATATATAGTAATATATTA
3792443 A
1 A
3792444 TACACTATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.40
20 3 0.15
21 9 0.45
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (21 bp):
ACTATATATAGTAATATATTA
Found at i:3797158 original size:32 final size:32
Alignment explanation
Indices: 3797118--3797182 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
3797108 GAAAAAAGCC
3797118 CAACAAATCAAACAACATCATGCATGGACTTA
1 CAACAAATCAAACAACATCATGCATGGACTTA
3797150 CAACAAATCAAACAACATCATGCATGGACTTA
1 CAACAAATCAAACAACATCATGCATGGACTTA
3797182 C
1 C
3797183 GTATGCAGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.46, C:0.26, G:0.09, T:0.18
Consensus pattern (32 bp):
CAACAAATCAAACAACATCATGCATGGACTTA
Found at i:3811178 original size:3 final size:3
Alignment explanation
Indices: 3811170--3811198 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3811160 TGAAGTGTAC
3811170 TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
3811199 CAGTACCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:3812567 original size:29 final size:30
Alignment explanation
Indices: 3812523--3812587 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
3812513 CTTTTACAAG
3812523 AATTTTAAATTATTTAAAAAAATTTAAATA
1 AATTTTAAATTATTTAAAAAAATTTAAATA
* ** * *
3812553 AATTTT-AATTCTTTAATTATATTTAATTA
1 AATTTTAAATTATTTAAAAAAATTTAAATA
3812582 AATTTT
1 AATTTT
3812588 TATATTTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 24 0.80
30 6 0.20
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (30 bp):
AATTTTAAATTATTTAAAAAAATTTAAATA
Found at i:3812598 original size:23 final size:22
Alignment explanation
Indices: 3812559--3812616 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
3812549 AATAAATTTT
*
3812559 AATTCTTTA-ATTATATTTAATTA
1 AATT-TTTATATTATA-TTAAATA
*
3812582 AATTTTTATATTTTATTAAATA
1 AATTTTTATATTATATTAAATA
3812604 AATTTTTATATTA
1 AATTTTTATATTA
3812617 CTTGATGATC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 22 0.71
23 9 0.29
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
AATTTTTATATTATATTAAATA
Found at i:3816305 original size:168 final size:168
Alignment explanation
Indices: 3816020--3816323 Score: 423
Period size: 168 Copynumber: 1.8 Consensus size: 168
3816010 CTCCAAAACT
3816020 GGGATTTCATTTTCGTCATATTCTCCTTCTTGCCTAGCTTTCAAGCATTTTAGGGAACCTTGTTC
1 GGGATTTCATTTTCGTCATATTCTCCTTCTTGCCTAGCTTTCAAGCATTTTAGGGAACCTTGTTC
* * * * *
3816085 AAGTGAGATTTTCTTGTTTTCCTCCAAATTCTCTTTTTTACTATCTAAAATGCATTTTGTGGGAC
66 AAGTAAGATTTTCTTGCTTTCCTCCAAAATCTCTTTTTGACTATCAAAAATGCATTTTGTGGGAC
3816150 TTTTAGCAAGTGGGTTTTTCCTGCTGTCCCTTACAAGA
131 TTTTAGCAAGTGGGTTTTTCCTGCTGTCCCTTACAAGA
* * * * * * * * *
3816188 GGGATTTCATTTTCTTTATTTTCTTCTTCTTGCCTAGTTTTGATGCATTTTTTGGG-ACCTTTTT
1 GGGATTTCATTTTCGTCATATTCTCCTTCTTGCCTAGCTTTCAAGCA-TTTTAGGGAACCTTGTT
* * *
3816252 CAAGTAAGTTTTTCTTGCTTTCCTTCAAAATCTCTTTTTGAGC-ATCAAAAATGCATTTTTTGGG
65 CAAGTAAGATTTTCTTGCTTTCCTCCAAAATCTCTTTTTGA-CTATCAAAAATGCATTTTGTGGG
3816316 ACTTTTAG
129 ACTTTTAG
3816324 AAATAGGGTT
Statistics
Matches: 117, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
168 109 0.93
169 8 0.07
ACGTcount: A:0.19, C:0.18, G:0.16, T:0.47
Consensus pattern (168 bp):
GGGATTTCATTTTCGTCATATTCTCCTTCTTGCCTAGCTTTCAAGCATTTTAGGGAACCTTGTTC
AAGTAAGATTTTCTTGCTTTCCTCCAAAATCTCTTTTTGACTATCAAAAATGCATTTTGTGGGAC
TTTTAGCAAGTGGGTTTTTCCTGCTGTCCCTTACAAGA
Found at i:3822024 original size:27 final size:27
Alignment explanation
Indices: 3821869--3822026 Score: 140
Period size: 28 Copynumber: 5.8 Consensus size: 27
3821859 CAGATTGAAG
*
3821869 ATTTAATTATTACACACCATATTAAAAA
1 ATTTAATTATTACACATCATATT-AAAA
*
3821897 ATTTAATTATTACACGTCATATTAAAAA
1 ATTTAATTATTACACATCATATT-AAAA
* ** * *
3821925 ATATAATTATTACATGTTATATTAAAG
1 ATTTAATTATTACACATCATATTAAAA
* * * * *
3821952 ATTTAGTTACTATACTTCACATTAAAA
1 ATTTAATTATTACACATCATATTAAAA
* *
3821979 ATTATAA-TAGTTATA-ATCATGTTAAAA
1 ATT-TAATTA-TTACACATCATATTAAAA
3822006 ATTTAATTATTACACATCATA
1 ATTTAATTATTACACATCATA
3822027 ATGAAAAAAT
Statistics
Matches: 104, Mismatches: 22, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
26 7 0.07
27 45 0.43
28 52 0.50
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.41
Consensus pattern (27 bp):
ATTTAATTATTACACATCATATTAAAA
Found at i:3824358 original size:17 final size:16
Alignment explanation
Indices: 3824335--3824382 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 16
3824325 ATGATAAGTA
3824335 AAAAAAAAATATTTTT
1 AAAAAAAAATATTTTT
3824351 AAATAAAATAATATTTTT
1 AAA-AAAA-AATATTTTT
*
3824369 ATAAATAAAATATT
1 A-AAAAAAAATATT
3824383 AATATTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 3 0.11
17 10 0.36
18 13 0.46
19 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAAAAAAAATATTTTT
Found at i:3824363 original size:18 final size:20
Alignment explanation
Indices: 3824333--3824380 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
3824323 CGATGATAAG
*
3824333 TAAA-AAAAAAATA-TTTT-
1 TAAATAAAATAATATTTTTA
3824350 TAAATAAAATAATATTTTTA
1 TAAATAAAATAATATTTTTA
3824370 TAAATAAAATA
1 TAAATAAAATA
3824381 TTAATATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 4 0.15
18 8 0.30
19 4 0.15
20 11 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAATAAAATAATATTTTTA
Found at i:3824835 original size:17 final size:18
Alignment explanation
Indices: 3824800--3824841 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
3824790 GCACAAAGAA
*
3824800 AGAAAG-AAAAAGATGAG
1 AGAAAGAAAAAAGATAAG
3824817 AGAAAGAAAAAAGA-AAG
1 AGAAAGAAAAAAGATAAG
3824834 AGACAAGA
1 AGA-AAGA
3824842 GATTTTACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.69, C:0.02, G:0.26, T:0.02
Consensus pattern (18 bp):
AGAAAGAAAAAAGATAAG
Found at i:3824842 original size:24 final size:25
Alignment explanation
Indices: 3824794--3824843 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
3824784 AATTGTGCAC
**
3824794 AAAGAAAGAAAGAAAAAGATGAGAG
1 AAAGAAAGAAAGAAAAAGACAAGAG
*
3824819 AAAGAAA-AAAGAAAGAGACAAGAG
1 AAAGAAAGAAAGAAAAAGACAAGAG
3824843 A
1 A
3824844 TTTTACTACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.70, C:0.02, G:0.26, T:0.02
Consensus pattern (25 bp):
AAAGAAAGAAAGAAAAAGACAAGAG
Found at i:3825338 original size:13 final size:12
Alignment explanation
Indices: 3825307--3825340 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3825297 TGATGGTATA
*
3825307 AGTATGAAATTT
1 AGTAAGAAATTT
3825319 AGTAAGAAATTT
1 AGTAAGAAATTT
3825331 AGGTAAGAAA
1 A-GTAAGAAA
3825341 GTTATTGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (12 bp):
AGTAAGAAATTT
Found at i:3835436 original size:15 final size:16
Alignment explanation
Indices: 3835393--3835451 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
3835383 ATAAAAAATT
3835393 AATATTTAAT-TTTAA
1 AATATTTAATATTTAA
* *
3835408 AAAAGTTTTA-ATTTAA
1 AATA-TTTAATATTTAA
3835424 AATA-TTAATATTTAA
1 AATATTTAATATTTAA
*
3835439 ATTATTTAATATT
1 AATATTTAATATT
3835452 ATTACAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
14 3 0.09
15 12 0.34
16 20 0.57
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
AATATTTAATATTTAA
Found at i:3835449 original size:16 final size:15
Alignment explanation
Indices: 3835418--3835451 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
3835408 AAAAGTTTTA
3835418 ATTTAAAATATTAAT
1 ATTTAAAATATTAAT
*
3835433 ATTTAAATTATTTAAT
1 ATTTAAAATA-TTAAT
3835449 ATT
1 ATT
3835452 ATTACAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTAAAATATTAAT
Found at i:3835529 original size:22 final size:22
Alignment explanation
Indices: 3835502--3835545 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3835492 TAATTAATAT
*
3835502 TTTTATTTATAAATTA-AATAAA
1 TTTTATTAAT-AATTATAATAAA
3835524 TTTTATTAATAATTATAATAAA
1 TTTTATTAATAATTATAATAAA
3835546 AATATTTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTTATTAATAATTATAATAAA
Found at i:3835867 original size:19 final size:19
Alignment explanation
Indices: 3835843--3835881 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
3835833 TTAGTGATTG
*
3835843 TAAAAAATATTTTTTATAA
1 TAAAAAATATTTTTGATAA
*
3835862 TAAAAAATGTTTTTGATAA
1 TAAAAAATATTTTTGATAA
3835881 T
1 T
3835882 TTATTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (19 bp):
TAAAAAATATTTTTGATAA
Found at i:3836177 original size:30 final size:30
Alignment explanation
Indices: 3836143--3836208 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
3836133 CAATTAAGTT
*
3836143 TTTATATTTTTATTTTGA-ATCAAATAAATC
1 TTTATATTTTTATTATGAGAT-AAATAAATC
* *
3836173 TTTATATTTTTATTATGAGATAAATTAATT
1 TTTATATTTTTATTATGAGATAAATAAATC
3836203 TTTATA
1 TTTATA
3836209 ACTAATAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 30 0.94
31 2 0.06
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (30 bp):
TTTATATTTTTATTATGAGATAAATAAATC
Found at i:3837361 original size:26 final size:29
Alignment explanation
Indices: 3837331--3837397 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
3837321 AAAATGACTT
3837331 ATTTAATATAAA-AT-A-AAAAT-ATAAAA
1 ATTTAAT-TAAATATAATAAAATAATAAAA
*
3837357 ATTTAATTAAATATAATAAAATAATAATA
1 ATTTAATTAAATATAATAAAATAATAAAA
*
3837386 ATTTATTTAAAT
1 ATTTAATTAAAT
3837398 TAAAGTTCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 4 0.11
26 9 0.26
27 1 0.03
28 5 0.14
29 16 0.46
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (29 bp):
ATTTAATTAAATATAATAAAATAATAAAA
Found at i:3842849 original size:2 final size:2
Alignment explanation
Indices: 3842844--3842873 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3842834 TCCAATCAAA
3842844 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3842874 AAATTCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3844088 original size:19 final size:19
Alignment explanation
Indices: 3844064--3844101 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3844054 GCGTAAGGCT
3844064 CTCTTACATATGTGTCCCA
1 CTCTTACATATGTGTCCCA
3844083 CTCTTACATATGTGTCCCA
1 CTCTTACATATGTGTCCCA
3844102 TATTCTAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.32, G:0.11, T:0.37
Consensus pattern (19 bp):
CTCTTACATATGTGTCCCA
Found at i:3847166 original size:22 final size:23
Alignment explanation
Indices: 3847141--3847185 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3847131 TCATCTTGGT
**
3847141 TAATTAA-TTATTTAAAGAATAA
1 TAATTAACTTATAAAAAGAATAA
3847163 TAATTAACTTATAAAAAGAATAA
1 TAATTAACTTATAAAAAGAATAA
3847186 CCCCTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (23 bp):
TAATTAACTTATAAAAAGAATAA
Found at i:3847971 original size:14 final size:14
Alignment explanation
Indices: 3847949--3847993 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
3847939 ATTTATATTT
* *
3847949 AAACTTAAAAAATA
1 AAACATAAAATATA
3847963 AAACATAAAACTATA
1 AAACATAAAA-TATA
*
3847978 AAAAATAAAATATA
1 AAACATAAAATATA
3847992 AA
1 AA
3847994 TAATTACATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (14 bp):
AAACATAAAATATA
Found at i:3847980 original size:15 final size:14
Alignment explanation
Indices: 3847954--3847993 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
3847944 TATTTAAACT
* *
3847954 TAAAAAATAAAACA
1 TAAAATATAAAAAA
3847968 TAAAACTATAAAAAA
1 TAAAA-TATAAAAAA
3847983 TAAAATATAAA
1 TAAAATATAAA
3847994 TAATTACATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (14 bp):
TAAAATATAAAAAA
Found at i:3847982 original size:22 final size:21
Alignment explanation
Indices: 3847949--3847993 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
3847939 ATTTATATTT
3847949 AAACTTAAAAAATAAAACATA
1 AAACTTAAAAAATAAAACATA
*
3847970 AAACTATAAAAAATAAAATATA
1 AAACT-TAAAAAATAAAACATA
3847992 AA
1 AA
3847994 TAATTACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (21 bp):
AAACTTAAAAAATAAAACATA
Found at i:3850640 original size:26 final size:26
Alignment explanation
Indices: 3850604--3850657 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
3850594 TCCCAACAAT
3850604 GAATATTGGGATCGCCAGATATGTCA
1 GAATATTGGGATCGCCAGATATGTCA
3850630 GAATATTGGGATCGCCAGATATGTCA
1 GAATATTGGGATCGCCAGATATGTCA
3850656 GA
1 GA
3850658 GTTGTTAGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (26 bp):
GAATATTGGGATCGCCAGATATGTCA
Found at i:3854413 original size:6 final size:6
Alignment explanation
Indices: 3854402--3854426 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3854392 ACCTACACAC
3854402 CCTCTT CCTCTT CCTCTT CCTCTT C
1 CCTCTT CCTCTT CCTCTT CCTCTT C
3854427 TTCTAGCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
CCTCTT
Found at i:3860810 original size:13 final size:13
Alignment explanation
Indices: 3860792--3860819 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3860782 TTGTCAATTG
3860792 TTCAATGTAAAGC
1 TTCAATGTAAAGC
3860805 TTCAATGTAAAGC
1 TTCAATGTAAAGC
3860818 TT
1 TT
3860820 TACACACCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (13 bp):
TTCAATGTAAAGC
Found at i:3863236 original size:21 final size:19
Alignment explanation
Indices: 3863201--3863250 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
3863191 CTTGTTTGAA
*
3863201 AATAAAAAATTTATTTCTT
1 AATAAAAAATTTATTACTT
*
3863220 ATATAAAATATTTTATTACTT
1 A-ATAAAA-AATTTATTACTT
3863241 AATAAGAAAA
1 AATAA-AAAA
3863251 CACTTGTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 1 0.04
20 11 0.44
21 13 0.52
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (19 bp):
AATAAAAAATTTATTACTT
Found at i:3863637 original size:27 final size:27
Alignment explanation
Indices: 3863588--3863640 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
3863578 TCAGTTTTTG
**
3863588 AATTTTTTAAATTTAAAATTAAAAAGA
1 AATTTTTTAAAAATAAAATTAAAAAGA
*
3863615 AATTTTTTAAAAAATAAAATAAAAAA
1 AATTTTTT-AAAAATAAAATTAAAAA
3863641 TGATGTGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 8 0.36
28 14 0.64
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (27 bp):
AATTTTTTAAAAATAAAATTAAAAAGA
Done.