Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 176 of 185
Found at i:53520041 original size:27 final size:28
Alignment explanation
Indices: 53520011--53520068 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
53520001 AAAGTATTCT
53520011 AAAA-ATATTTTAAAAATAAAAAATAAA
1 AAAATATATTTTAAAAATAAAAAATAAA
*
53520038 AAAATGTATTTTAAAAATAAAAAATAAA
1 AAAATATATTTTAAAAATAAAAAATAAA
53520066 AAA
1 AAA
53520069 TAAATATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 4 0.14
28 25 0.86
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (28 bp):
AAAATATATTTTAAAAATAAAAAATAAA
Found at i:53520047 original size:39 final size:35
Alignment explanation
Indices: 53519987--53520072 Score: 109
Period size: 39 Copynumber: 2.3 Consensus size: 35
53519977 AAAAAAATTT
53519987 TAAAAAATAAAAAAAAAGTATTCTAAAAATATTTTAAAAA
1 TAAAAAAT-AAAAAAAAGTATTCTAAAAATA----AAAAA
* *
53520027 TAAAAAATAAAAAAATGTATTTTAAAAATAAAAAA
1 TAAAAAATAAAAAAAAGTATTCTAAAAATAAAAAA
53520062 TAAAAAATAAA
1 TAAAAAATAAA
53520073 TATATTTATT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
35 16 0.36
39 20 0.45
40 8 0.18
ACGTcount: A:0.71, C:0.01, G:0.02, T:0.26
Consensus pattern (35 bp):
TAAAAAATAAAAAAAAGTATTCTAAAAATAAAAAA
Found at i:53524728 original size:17 final size:16
Alignment explanation
Indices: 53524704--53524775 Score: 54
Period size: 17 Copynumber: 4.0 Consensus size: 16
53524694 GAGGATTTTC
53524704 CTCAACAGAAAATATT
1 CTCAACAGAAAATATT
*
53524720 CTGCAACAGTTAGAAAATTTT
1 CT-CAAC----AGAAAATATT
*
53524741 CCTCAACTGAAAAATATT
1 -CTCAACAG-AAAATATT
53524759 CTACAACAGAAAATATT
1 CT-CAACAGAAAATATT
53524776 TTGAAAAAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 15
0.70 0.06 0.24
Matches are distributed among these distances:
16 2 0.05
17 15 0.34
18 12 0.27
21 13 0.30
22 2 0.05
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (16 bp):
CTCAACAGAAAATATT
Found at i:53530590 original size:17 final size:16
Alignment explanation
Indices: 53530566--53530637 Score: 54
Period size: 17 Copynumber: 4.0 Consensus size: 16
53530556 GAGGATTTTC
53530566 CTCAACAGAAAATATT
1 CTCAACAGAAAATATT
*
53530582 CTGCAACAGTCAGAAAATTTT
1 CT-C-A-A--CAGAAAATATT
*
53530603 CCTCAACTGAAAAATATT
1 -CTCAACAG-AAAATATT
53530621 CTACAACAGAAAATATT
1 CT-CAACAGAAAATATT
53530638 TTGAAAAAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 15
0.70 0.06 0.24
Matches are distributed among these distances:
16 2 0.05
17 13 0.30
18 13 0.30
19 2 0.05
20 1 0.02
21 11 0.25
22 2 0.05
ACGTcount: A:0.46, C:0.19, G:0.08, T:0.26
Consensus pattern (16 bp):
CTCAACAGAAAATATT
Found at i:53531346 original size:14 final size:14
Alignment explanation
Indices: 53531327--53531355 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
53531317 AAGTAATTTT
53531327 TAATTTCTTAGTAA
1 TAATTTCTTAGTAA
53531341 TAATTTCTTAGTAA
1 TAATTTCTTAGTAA
53531355 T
1 T
53531356 CAGGACTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (14 bp):
TAATTTCTTAGTAA
Found at i:53545625 original size:166 final size:166
Alignment explanation
Indices: 53545351--53545674 Score: 524
Period size: 166 Copynumber: 2.0 Consensus size: 166
53545341 GATTGTTGTC
53545351 CAAGCGATGTTCTGAAAAATGAATAAATTCTTGTTTTTCCAGATGCACCAAGTGATTATTCCAAA
1 CAAGCGATGTTCTGAAAAATGAATAAATTCTTGTTTTTCCAGATGCACCAAGTGATTATTCCAAA
* * *
53545416 AAAACACGACCAAATCATGTCACATTCCTGCAACCTCATGTGACAACAAAGGTTAAAAGAAAATT
66 AAAACACGACCAAATCATGTCACATCCCTGCAACCTCATGTGACAACAAAAGTTAAAAGAAAATC
53545481 AAAACCGAAAAGATTTAGAGAAAAACCATGTGACAA
131 AAAACCGAAAAGATTTAGAGAAAAACCATGTGACAA
* * * * *
53545517 CAAGCGATGTTTTGGAAAATGAATAAATTCTTGTTTTTCCAGGTGCACCAAGTGGTTATTTCAAA
1 CAAGCGATGTTCTGAAAAATGAATAAATTCTTGTTTTTCCAGATGCACCAAGTGATTATTCCAAA
* * *
53545582 AAGACACGATCAAAT-AGTGTCACGTCCCTGCAACCTCATGTGACAACAAAAGTTAAAAGAAAAT
66 AAAACACGACCAAATCA-TGTCACATCCCTGCAACCTCATGTGACAACAAAAGTTAAAAGAAAAT
*
53545646 CAATACCGAAAAGATTTAGAGAAAAACCA
130 CAAAACCGAAAAGATTTAGAGAAAAACCA
53545675 GTATTATTGA
Statistics
Matches: 145, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
165 1 0.01
166 144 0.99
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (166 bp):
CAAGCGATGTTCTGAAAAATGAATAAATTCTTGTTTTTCCAGATGCACCAAGTGATTATTCCAAA
AAAACACGACCAAATCATGTCACATCCCTGCAACCTCATGTGACAACAAAAGTTAAAAGAAAATC
AAAACCGAAAAGATTTAGAGAAAAACCATGTGACAA
Found at i:53547077 original size:24 final size:25
Alignment explanation
Indices: 53547050--53547119 Score: 79
Period size: 26 Copynumber: 2.8 Consensus size: 25
53547040 TTTTTTTCTT
* *
53547050 TTTTTGGTA-TATTTTTGTAAATAA
1 TTTTTGATATTATTTTGGTAAATAA
* *
53547074 TTTTTTATATTATTTTGGTAAATATT
1 TTTTTGATATTATTTTGGTAAATA-A
*
53547100 TTTTTTATATTATTTTGGTA
1 TTTTTGATATTATTTTGGTA
53547120 TTTTTTTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.17
25 13 0.32
26 20 0.50
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (25 bp):
TTTTTGATATTATTTTGGTAAATAA
Found at i:53547121 original size:22 final size:23
Alignment explanation
Indices: 53547074--53547146 Score: 78
Period size: 26 Copynumber: 3.1 Consensus size: 23
53547064 TTGTAAATAA
53547074 TTTTTTATATTATTTTGGTAAATATT
1 TTTTTTATATTATTTTGG---ATATT
53547100 TTTTTTATATTATTTTGG-TATT
1 TTTTTTATATTATTTTGGATATT
* *
53547122 TTTTTTAT-TTCTTTTGTGTTATT
1 TTTTTTATATTATTTTG-GATATT
53547145 TT
1 TT
53547147 AGTAAAACAC
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
21 7 0.16
22 13 0.30
23 6 0.14
26 18 0.41
ACGTcount: A:0.18, C:0.01, G:0.08, T:0.73
Consensus pattern (23 bp):
TTTTTTATATTATTTTGGATATT
Found at i:53547127 original size:26 final size:26
Alignment explanation
Indices: 53547059--53547119 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
53547049 TTTTTTGGTA
* *
53547059 TATTTTTGTAAATA-ATTTTTTATAT
1 TATTTTGGTAAATATTTTTTTTATAT
53547084 TATTTTGGTAAATATTTTTTTTATAT
1 TATTTTGGTAAATATTTTTTTTATAT
53547110 TATTTTGGTA
1 TATTTTGGTA
53547120 TTTTTTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
25 13 0.39
26 20 0.61
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (26 bp):
TATTTTGGTAAATATTTTTTTTATAT
Found at i:53554472 original size:3 final size:3
Alignment explanation
Indices: 53554464--53554506 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
53554454 ATGTATAAAT
* *
53554464 ATA ATA ATA ATA CTA ATA ATA ATA ATA ATA ATA ATA GTA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
53554507 CGATATAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:53556998 original size:46 final size:46
Alignment explanation
Indices: 53556890--53557143 Score: 406
Period size: 46 Copynumber: 5.6 Consensus size: 46
53556880 TACATATGAT
* *
53556890 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
53556933 CACTTATCACTTTGTTACTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* * *
53556979 CACTTATCACTTTGTTACTTGATCAGATAAGTGTAGTTAAAACTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
53557025 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGTTAAAACTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
53557071 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
53557117 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
53557144 AGTACTCAAA
Statistics
Matches: 198, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
43 10 0.05
44 4 0.02
45 20 0.10
46 164 0.83
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:53563292 original size:166 final size:166
Alignment explanation
Indices: 53563013--53563333 Score: 525
Period size: 166 Copynumber: 1.9 Consensus size: 166
53563003 GATTGTTGTC
* *
53563013 CAAGCGATGTTCTGGAAAATGAATAAATTCTTGTTTTTCCAGATGCACCAAGTGATTATTCTAAA
1 CAAGCGATGTTCTGGAAAATGAATAAATTCTTGTTTTTCCAAATGCACCAAGTGATTATTCCAAA
* * * * *
53563078 AAAACACGACCAAATAGTGTCACGTTCTTGCAACCTCATGTGACAACAAATGTTAAAAGAAAATC
66 AAAACACGACCAAATAGTATCACGTCCCTGCAACCTCACGTGACAACAAAGGTTAAAAGAAAATC
**
53563143 AAGACCGAAAAGATTTAGAGAAAAACCATGTGACAA
131 AAGACAAAAAAGATTTAGAGAAAAACCATGTGACAA
* *
53563179 CAAGGGATGTTCTGGAAAATGAATAAATTCTTGTTTTTCCAAATGCACCAAGTGGTTATTCCAAA
1 CAAGCGATGTTCTGGAAAATGAATAAATTCTTGTTTTTCCAAATGCACCAAGTGATTATTCCAAA
* *
53563244 AAGACACGATCAAATAGTATCACGTCCCTGCAACCTCACGTGACAACAAAGGTTAAAAGAAAATC
66 AAAACACGACCAAATAGTATCACGTCCCTGCAACCTCACGTGACAACAAAGGTTAAAAGAAAATC
53563309 AAGACAAAAAAGATTTAGAGAAAAA
131 AAGACAAAAAAGATTTAGAGAAAAA
53563334 TCAGTATTAC
Statistics
Matches: 142, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
166 142 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24
Consensus pattern (166 bp):
CAAGCGATGTTCTGGAAAATGAATAAATTCTTGTTTTTCCAAATGCACCAAGTGATTATTCCAAA
AAAACACGACCAAATAGTATCACGTCCCTGCAACCTCACGTGACAACAAAGGTTAAAAGAAAATC
AAGACAAAAAAGATTTAGAGAAAAACCATGTGACAA
Found at i:53567452 original size:21 final size:22
Alignment explanation
Indices: 53567394--53567460 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 22
53567384 TTTTTTAAGC
53567394 TTATT-ATTAGTATAATTTAAA
1 TTATTAATTAGTATAATTTAAA
* * *
53567415 ATA-TAA-TATTATCATTTAAA
1 TTATTAATTAGTATAATTTAAA
*
53567435 TTATTAATTA-TATTATTTAAA
1 TTATTAATTAGTATAATTTAAA
53567456 GTTAT
1 -TTAT
53567461 CATACATTAG
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
20 15 0.41
21 16 0.43
22 6 0.16
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (22 bp):
TTATTAATTAGTATAATTTAAA
Found at i:53573248 original size:16 final size:16
Alignment explanation
Indices: 53573227--53573258 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
53573217 CTATTTTTTA
53573227 ATTTAATGTATTATTT
1 ATTTAATGTATTATTT
*
53573243 ATTTAATTTATTATTT
1 ATTTAATGTATTATTT
53573259 TTCACATGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (16 bp):
ATTTAATGTATTATTT
Found at i:53581275 original size:5 final size:5
Alignment explanation
Indices: 53581265--53581297 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
53581255 TTCTCTCAGG
53581265 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT
53581298 GAATCAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:53587702 original size:101 final size:102
Alignment explanation
Indices: 53587583--53587767 Score: 259
Period size: 101 Copynumber: 1.8 Consensus size: 102
53587573 AAAGTCATGG
* * * *
53587583 TCACGTGTGTAGTACTATGTACAGGCTACTACGTGTACCGGAAT-G--ATAGGTCGCATGTATAG
1 TCACGTGTGTAGTACTATGTACAGGCTACTACATGTACC-AAATAGTAAT-GGTCACATATATAG
53587645 TACTATGTGCAGGCTACTATGCGTACCACATAGTTTCGA
64 TACTATGTGCAGGCTACTATGCGTACCACATAGTTTCGA
** * *
53587684 TCACGTGTGTAGTACTATGTGTAGGCTACTACATGTATCAAATAGTAATGGTCACATATGTAGTA
1 TCACGTGTGTAGTACTATGTACAGGCTACTACATGTACCAAATAGTAATGGTCACATATATAGTA
53587749 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
53587768 TGAACCGAAC
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
100 3 0.04
101 36 0.49
102 32 0.44
103 2 0.03
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTACAGGCTACTACATGTACCAAATAGTAATGGTCACATATATAGTA
CTATGTGCAGGCTACTATGCGTACCACATAGTTTCGA
Found at i:53587710 original size:51 final size:51
Alignment explanation
Indices: 53587642--53587767 Score: 146
Period size: 51 Copynumber: 2.5 Consensus size: 51
53587632 GTCGCATGTA
* * * *
53587642 TAGTACTATGTGCAGGCTACTATGCGTACCACATAGT-TTCGATCACGTGTG
1 TAGTACTATGTGCAGGCTACTATGCGTACCAAATAGTAAT-GATCACATATG
* *** * *
53587693 TAGTACTATGTGTAGGCTACTACATGTATCAAATAGTAATGGTCACATATG
1 TAGTACTATGTGCAGGCTACTATGCGTACCAAATAGTAATGATCACATATG
53587744 TAGTACTATGTGCAGGCTACTATG
1 TAGTACTATGTGCAGGCTACTATG
53587768 TGAACCGAAC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
51 60 0.98
52 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (51 bp):
TAGTACTATGTGCAGGCTACTATGCGTACCAAATAGTAATGATCACATATG
Found at i:53587827 original size:45 final size:45
Alignment explanation
Indices: 53587771--53587865 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 45
53587761 TACTATGTGA
* *
53587771 ACCGAACATCATTGATTAGTAAAGTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTGATTAATAAAGTGGTTGCTATGTGCTGAATCC
* *
53587816 ACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAAGTGGTTGCTATGTGCTGAATCC
53587861 ACCGA
1 ACCGA
53587866 GTATCTGTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAAGTGGTTGCTATGTGCTGAATCC
Found at i:53588011 original size:37 final size:38
Alignment explanation
Indices: 53587940--53588012 Score: 105
Period size: 37 Copynumber: 1.9 Consensus size: 38
53587930 AGGTGTGGAA
53587940 TTGAATTGAATATCGACTTAGAAATGAAAAAGTGAATT
1 TTGAATTGAATATCGACTTAGAAATGAAAAAGTGAATT
* *
53587978 TTGAATTGAATTTTGA-TT-GAAAGTGAAAAAGTGAA
1 TTGAATTGAATATCGACTTAGAAA-TGAAAAAGTGAA
53588013 ATTATGAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 4 0.12
37 14 0.44
38 14 0.44
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.33
Consensus pattern (38 bp):
TTGAATTGAATATCGACTTAGAAATGAAAAAGTGAATT
Found at i:53593586 original size:34 final size:35
Alignment explanation
Indices: 53593531--53593597 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
53593521 CAAACACCAG
*
53593531 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
53593566 AAAACATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
53593598 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:53595492 original size:31 final size:32
Alignment explanation
Indices: 53595447--53595506 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
53595437 TCATTTCGAC
53595447 TCTTTTTCAAAAGGTTGATGGTC-AAATTTGAT
1 TCTTTTTCAAAAGGTTG-TGGTCTAAATTTGAT
53595479 TCTTTTT-AAAAGGTTGTGGTCTAAATTT
1 TCTTTTTCAAAAGGTTGTGGTCTAAATTT
53595507 AGCTTAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 5 0.19
31 15 0.56
32 7 0.26
ACGTcount: A:0.27, C:0.08, G:0.18, T:0.47
Consensus pattern (32 bp):
TCTTTTTCAAAAGGTTGTGGTCTAAATTTGAT
Found at i:53597437 original size:11 final size:10
Alignment explanation
Indices: 53597418--53597457 Score: 64
Period size: 11 Copynumber: 4.0 Consensus size: 10
53597408 ATGTAACGAC
53597418 AAATAATAAA
1 AAATAATAAA
53597428 AAATTAATAAA
1 AAA-TAATAAA
53597439 AAATAA-AAA
1 AAATAATAAA
53597448 AAATAATAAA
1 AAATAATAAA
53597458 TGTTATAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.32
10 9 0.32
11 10 0.36
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (10 bp):
AAATAATAAA
Found at i:53597650 original size:30 final size:30
Alignment explanation
Indices: 53597614--53597682 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
53597604 TTTTTTTTTC
53597614 TAATTTTTAATAAAAATTAAATATTTCTTA
1 TAATTTTTAATAAAAATTAAATATTTCTTA
* * * *
53597644 TAATTTTTTATTAAAATTTAATATTTTTTA
1 TAATTTTTAATAAAAATTAAATATTTCTTA
*
53597674 TAAATTTTA
1 TAATTTTTA
53597683 TTGATTTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (30 bp):
TAATTTTTAATAAAAATTAAATATTTCTTA
Found at i:53599104 original size:12 final size:12
Alignment explanation
Indices: 53599087--53599112 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53599077 GTTTGCTTGT
53599087 ACTTCATTACTG
1 ACTTCATTACTG
53599099 ACTTCATTACTG
1 ACTTCATTACTG
53599111 AC
1 AC
53599113 ATGAATAATT
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:0.27, C:0.27, G:0.08, T:0.38
Consensus pattern (12 bp):
ACTTCATTACTG
Found at i:53599873 original size:22 final size:22
Alignment explanation
Indices: 53599847--53599891 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
53599837 AAAATTATAA
* *
53599847 AAATAGAAAAATATATAAGCAT
1 AAATACAAAAATATAAAAGCAT
*
53599869 AAATACAAAAATCTAAAAGCAT
1 AAATACAAAAATATAAAAGCAT
53599891 A
1 A
53599892 TATGACTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.64, C:0.09, G:0.07, T:0.20
Consensus pattern (22 bp):
AAATACAAAAATATAAAAGCAT
Found at i:53612650 original size:20 final size:21
Alignment explanation
Indices: 53612609--53612668 Score: 52
Period size: 20 Copynumber: 2.8 Consensus size: 21
53612599 TATGATGGTT
* *
53612609 TTCAGTTATTGAATGAATTTTTA
1 TTCAATTATTTAATG-A-TTTTA
*
53612632 TT-ATATTATTT-ATGATTTTT
1 TTCA-ATTATTTAATGATTTTA
53612652 TTCAATTATTTAATGAT
1 TTCAATTATTTAATGAT
53612669 ATTTCAATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
20 13 0.42
21 7 0.23
22 4 0.13
23 7 0.23
ACGTcount: A:0.30, C:0.03, G:0.08, T:0.58
Consensus pattern (21 bp):
TTCAATTATTTAATGATTTTA
Found at i:53612651 original size:21 final size:21
Alignment explanation
Indices: 53612607--53612668 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
53612597 TTTATGATGG
* *
53612607 TTTTCAGTTATTGAATGAATTT
1 TTTTCAATTATTTAATG-ATTT
53612629 TTATT-ATATTATTT-ATGATTT
1 TT-TTCA-ATTATTTAATGATTT
53612650 TTTTCAATTATTTAATGAT
1 TTTTCAATTATTTAATGAT
53612669 ATTTCAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
20 9 0.26
21 12 0.35
22 6 0.18
23 7 0.21
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.60
Consensus pattern (21 bp):
TTTTCAATTATTTAATGATTT
Found at i:53612672 original size:23 final size:22
Alignment explanation
Indices: 53612607--53612672 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
53612597 TTTATGATGG
* *
53612607 TTTTCAGTTATTGAATGAATTT
1 TTTTCAATTATTTAATGAATTT
53612629 TTATT-ATATTATTT-ATG-ATTT
1 TT-TTCA-ATTATTTAATGAATTT
53612650 TTTTCAATTATTTAATGATATTT
1 TTTTCAATTATTTAATGA-ATTT
53612673 CAATCATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
20 9 0.25
21 10 0.28
22 6 0.17
23 11 0.31
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.61
Consensus pattern (22 bp):
TTTTCAATTATTTAATGAATTT
Found at i:53612749 original size:14 final size:14
Alignment explanation
Indices: 53612720--53612761 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
53612710 TTGAACTCGA
53612720 ATTTAGAGAATTCAAG
1 ATTTAGAG--TTCAAG
*
53612736 ATTTAGGGTTCAAG
1 ATTTAGAGTTCAAG
53612750 ATTTAGAGTTCA
1 ATTTAGAGTTCA
53612762 TGTTTAAGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 17 0.71
16 7 0.29
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (14 bp):
ATTTAGAGTTCAAG
Found at i:53619277 original size:3 final size:3
Alignment explanation
Indices: 53619269--53619301 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
53619259 GCATTTTTGA
53619269 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
53619302 TCAATGCTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:53619942 original size:17 final size:19
Alignment explanation
Indices: 53619917--53619952 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
53619907 TATAATTTTT
53619917 AAATATAT-AATACATCAA
1 AAATATATAAATACATCAA
53619935 AAAT-TATAAATACATCAA
1 AAATATATAAATACATCAA
53619953 GATAAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (19 bp):
AAATATATAAATACATCAA
Found at i:53620071 original size:30 final size:30
Alignment explanation
Indices: 53620037--53620095 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
53620027 ACTTAACAAG
*
53620037 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCATCTAAAATAATAACAAAATTAA
* *
53620067 CAAATGCATTTAAAATAATAACAAGATTA
1 CAAATGCATCTAAAATAATAACAAAATTA
53620096 TCAATAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.56, C:0.14, G:0.05, T:0.25
Consensus pattern (30 bp):
CAAATGCATCTAAAATAATAACAAAATTAA
Found at i:53620156 original size:14 final size:14
Alignment explanation
Indices: 53620122--53620160 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
53620112 TATACAATAT
*
53620122 CAAAATAATAACAA
1 CAAAATAGTAACAA
*
53620136 TAAAATAGTAACAA
1 CAAAATAGTAACAA
*
53620150 CATAATAGTAA
1 CAAAATAGTAA
53620161 AATGGTAGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.64, C:0.10, G:0.05, T:0.21
Consensus pattern (14 bp):
CAAAATAGTAACAA
Found at i:53620873 original size:9 final size:9
Alignment explanation
Indices: 53620856--53620884 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
53620846 TGAAAAAAAA
53620856 AATAA-AAC
1 AATAATAAC
53620864 AATAATAAC
1 AATAATAAC
53620873 AATAATAAC
1 AATAATAAC
53620882 AAT
1 AAT
53620885 CACATAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.25
9 15 0.75
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (9 bp):
AATAATAAC
Found at i:53623975 original size:16 final size:17
Alignment explanation
Indices: 53623943--53623977 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
53623933 CAATTCATAA
53623943 TATAACTAAAATATTTT
1 TATAACTAAAATATTTT
*
53623960 TATAACT-AATTATTTT
1 TATAACTAAAATATTTT
53623976 TA
1 TA
53623978 AAATTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (17 bp):
TATAACTAAAATATTTT
Found at i:53633668 original size:10 final size:10
Alignment explanation
Indices: 53633653--53633683 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
53633643 TCTAATTTGG
53633653 TTTTTGTTTT
1 TTTTTGTTTT
53633663 TTTTTGTTTT
1 TTTTTGTTTT
53633673 TTTTTGTTTT
1 TTTTTGTTTT
53633683 T
1 T
53633684 CATAATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:53636510 original size:29 final size:31
Alignment explanation
Indices: 53636448--53636521 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 31
53636438 ACTACTAAAA
**
53636448 TAGTCACTTTTGTTTGGTTCATGTTACATTT
1 TAGTCACTTTTGTTTGGTAAATGTTACATTT
*
53636479 TAGTCACTTTTGTTT-G-AAATGTTACGTTT
1 TAGTCACTTTTGTTTGGTAAATGTTACATTT
*
53636508 TAGTCACTTATGTT
1 TAGTCACTTTTGTT
53636522 ATCATGTTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 23 0.59
30 1 0.03
31 15 0.38
ACGTcount: A:0.19, C:0.12, G:0.16, T:0.53
Consensus pattern (31 bp):
TAGTCACTTTTGTTTGGTAAATGTTACATTT
Found at i:53638010 original size:13 final size:13
Alignment explanation
Indices: 53637992--53638021 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
53637982 TTGAAACCAA
53637992 AATAAACAATAAT
1 AATAAACAATAAT
*
53638005 AATAAATAATAAT
1 AATAAACAATAAT
53638018 AATA
1 AATA
53638022 TTATTATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (13 bp):
AATAAACAATAAT
Found at i:53639822 original size:44 final size:44
Alignment explanation
Indices: 53639774--53639978 Score: 127
Period size: 44 Copynumber: 4.6 Consensus size: 44
53639764 GCCATATTCG
*
53639774 ATCTACTCCACTACTGCTTAGGGAGATAAGATCT-ATAATCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAAATCTCATAA-CTTCA
* * * * *
53639818 ATCTATTCCACTGCCTAC-TAGGGAGATAAAATCAC-TGGA-TTCA
1 ATCTACTCCACT-ACTGCTTAGGGAGATAAAATCTCAT-AACTTCA
* * ** * * *
53639861 ATGTACTCCACTGTAAT-CACAGGGAGGTAAAATCTGCCATTACTT-G
1 ATCTACTCCAC--TACTGCTTAGGGAGATAAAATCT--CATAACTTCA
* ** *
53639907 ATCTACTCCACTACTGCTTAGGGAGACATGATCTGA-AATCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAAATCTCATAA-CTTCA
*
53639951 ACCTACTCCACTACTGCTTAGGGAGATA
1 ATCTACTCCACTACTGCTTAGGGAGATA
53639979 GGATTTGCAA
Statistics
Matches: 120, Mismatches: 28, Indels: 26
0.69 0.16 0.15
Matches are distributed among these distances:
42 1 0.01
43 18 0.15
44 69 0.57
45 17 0.14
46 12 0.10
47 3 0.03
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (44 bp):
ATCTACTCCACTACTGCTTAGGGAGATAAAATCTCATAACTTCA
Found at i:53639973 original size:133 final size:132
Alignment explanation
Indices: 53639706--53639978 Score: 347
Period size: 133 Copynumber: 2.1 Consensus size: 132
53639696 CGCAACGTCG
* * * * **
53639706 GGGAGATAGAATTACTGGCTTCAAAGTACTCCATTGTAACCTTAGGGAGGTAAAATTCGCCATAT
1 GGGAGATAAAATCACTGGATTCAAAGTACTCCACTGTAACCACAGGGAGGTAAAATTCGCCATAT
* * * *
53639771 TCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGCCTAC
66 TCGATCTACTCCACTACTGCTTAGGGAGACAAGATCTATAATCTTCAACCTACTCCACTGACTAC
53639836 TA
131 TA
* *
53639838 GGGAGATAAAATCACTGGATTCAATGTACTCCACTGTAATCACAGGGAGGTAAAA-TCTGCCATT
1 GGGAGATAAAATCACTGGATTCAAAGTACTCCACTGTAACCACAGGGAGGTAAAATTC-GCCA-T
*
53639902 ACTT-GATCTACTCCACTACTGCTTAGGGAGACATGATCTGA-AATCTTCAACCTACTCCACT-A
64 A-TTCGATCTACTCCACTACTGCTTAGGGAGACAAGATCT-ATAATCTTCAACCTACTCCACTGA
*
53639964 CTGCTTA
127 CTAC-TA
53639971 GGGAGATA
1 GGGAGATA
53639979 GGATTTGCAA
Statistics
Matches: 122, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
131 2 0.02
132 54 0.44
133 63 0.52
134 3 0.02
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (132 bp):
GGGAGATAAAATCACTGGATTCAAAGTACTCCACTGTAACCACAGGGAGGTAAAATTCGCCATAT
TCGATCTACTCCACTACTGCTTAGGGAGACAAGATCTATAATCTTCAACCTACTCCACTGACTAC
TA
Found at i:53639991 original size:44 final size:44
Alignment explanation
Indices: 53639909--53639994 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
53639899 ATTACTTGAT
*
53639909 CTACTCCACTACTGCTTAGGGAGACATGATCTGAAATCTTCAAC
1 CTACTCCACTACTGCTTAGGGAGACAGGATCTGAAATCTTCAAC
* * *
53639953 CTACTCCACTACTGCTTAGGGAGATAGGATTTGCAATCTTCA
1 CTACTCCACTACTGCTTAGGGAGACAGGATCTGAAATCTTCA
53639995 GTCTGCTCCG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (44 bp):
CTACTCCACTACTGCTTAGGGAGACAGGATCTGAAATCTTCAAC
Found at i:53640096 original size:88 final size:88
Alignment explanation
Indices: 53639997--53640907 Score: 1297
Period size: 88 Copynumber: 10.4 Consensus size: 88
53639987 AATCTTCAGT
* * * ** * *
53639997 CTGCTCCGCTGTCAATGCAGGAAGGCAAGATCTGTTATCTTTGACCTGCTCGA-CTACAACCGAT
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATC-ACAACCGA-
*
53640061 G-GAGGCAAGGTTTGTGTCTTCGAT
64 GAGAGGCAAGGTTTGTGTCTTCGAC
* * ** * * ** * *
53640085 CTGCTTCGCTGTCAATGTAGGAATGCAAGATCTGCTATTTTTTACCTGCTTCCCT-ACAACCGAG
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGC-TCCATCACAACCGAG
* * * * *
53640149 GGAGGTAAAGTTTGTATTTTCGAC
65 AGAGGCAAGGTTTGTGTCTTCGAC
*
53640173 CTGCTTCGCTTTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
53640238 GAGGCAAGGTTTGTGTCTTCGAC
66 GAGGCAAGGTTTGTGTCTTCGAC
53640261 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
*
53640326 GAGGCAAGGTTTGAGTCTTCGAC
66 GAGGCAAGGTTTGTGTCTTCGAC
* * * *
53640349 CTGCTTCACTTTCAATGCATGAAGGCAAGATCTTTTGTCTTCAACTAGCTCCATCACAACCGAGA
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
53640414 GAGGCAAGGTTTGTGTCTTCGAC
66 GAGGCAAGGTTTGTGTCTTCGAC
* *
53640437 CTGCTTCGCTGTCAATGCAGGAATGCAAGATCTTTTGTCTTTAACCAGCTCCATCACAACCGAGA
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
* *
53640502 GAGGCAAGGTTTGAGACTTCGAC
66 GAGGCAAGGTTTGTGTCTTCGAC
* *
53640525 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACAAGCTCTATCACAACCGAGA
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
* *
53640590 GAGGCAAGGTTTGAGTCTTCGAT
66 GAGGCAAGGTTTGTGTCTTCGAC
* *
53640613 CTGCTTCGCTGTTAATGAAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
*
53640678 GAGGCAAGGTTTGAGTCTTCGAC
66 GAGGCAAGGTTTGTGTCTTCGAC
* *
53640701 CTGCTTCGCTGTCAATGCATGAAGGCAAGATCTTTTGTCTTCAACTAGCTCCATCACAACCGAGA
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
* *
53640766 GAGGCAAGGTTTATGTCTTCGAT
66 GAGGCAAGGTTTGTGTCTTCGAC
* * * *
53640789 CTGCTTCACCGCCAATGAAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
* * *
53640854 GAGGCAATGTTTATGTTTTCGAC
66 GAGGCAAGGTTTGTGTCTTCGAC
* *
53640877 CTGCTTCACTGTCAATGCAGGAAGGAAAGAT
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGAT
53640908 TTGTAACTTC
Statistics
Matches: 744, Mismatches: 75, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
87 5 0.01
88 737 0.99
89 2 0.00
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (88 bp):
CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
GAGGCAAGGTTTGTGTCTTCGAC
Found at i:53641777 original size:13 final size:13
Alignment explanation
Indices: 53641759--53641783 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53641749 ATTATCCAAA
53641759 AATAATAAAGAAG
1 AATAATAAAGAAG
53641772 AATAATAAAGAA
1 AATAATAAAGAA
53641784 ATTGATTGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (13 bp):
AATAATAAAGAAG
Found at i:53643371 original size:13 final size:13
Alignment explanation
Indices: 53643352--53643387 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
53643342 ATTGACCTCT
*
53643352 CCTTTTTTTTTTC
1 CCTTTTTTTTCTC
*
53643365 TCTTTTTTTTCTC
1 CCTTTTTTTTCTC
53643378 CCTTTTTTTT
1 CCTTTTTTTT
53643388 ACTTCGATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (13 bp):
CCTTTTTTTTCTC
Found at i:53643418 original size:12 final size:12
Alignment explanation
Indices: 53643397--53643444 Score: 69
Period size: 12 Copynumber: 3.8 Consensus size: 12
53643387 TACTTCGATT
*
53643397 TTTTGATTTTTG
1 TTTTGTTTTTTG
53643409 ATTTTGTTTTTTTG
1 -TTTTG-TTTTTTG
53643423 TTTTGTTTTTTG
1 TTTTGTTTTTTG
53643435 TTTTGTTTTT
1 TTTTGTTTTT
53643445 CCTTCTTCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
12 17 0.52
13 10 0.30
14 6 0.18
ACGTcount: A:0.04, C:0.00, G:0.15, T:0.81
Consensus pattern (12 bp):
TTTTGTTTTTTG
Found at i:53652779 original size:18 final size:17
Alignment explanation
Indices: 53652751--53652794 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 17
53652741 GAACAAGTAA
53652751 AAAATTAAAAATTAAAAAT
1 AAAA-TAAAAA-TAAAAAT
53652770 AAAATAAAAATAAAAAT
1 AAAATAAAAATAAAAAT
53652787 AAAGATAA
1 AAA-ATAA
53652795 TTCTTTGCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.42
18 10 0.42
19 4 0.17
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20
Consensus pattern (17 bp):
AAAATAAAAATAAAAAT
Found at i:53652787 original size:6 final size:6
Alignment explanation
Indices: 53652750--53652794 Score: 56
Period size: 6 Copynumber: 7.3 Consensus size: 6
53652740 CGAACAAGTA
*
53652750 AAAAATT AAAAATT AAAAAT -AAAAT AAAAAT AAAAAT AAAGAT AA
1 AAAAA-T AAAAA-T AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AA
53652795 TTCTTTGCTC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
5 5 0.14
6 19 0.53
7 12 0.33
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (6 bp):
AAAAAT
Found at i:53659113 original size:30 final size:30
Alignment explanation
Indices: 53659073--53659149 Score: 118
Period size: 30 Copynumber: 2.6 Consensus size: 30
53659063 GACATAAATG
* *
53659073 GGGTTACCGTGTTCGTCAGTGAGTTGAACC
1 GGGTTGCCGTGTTCGTCAGTGAGTTGAACA
* *
53659103 GGGTTGCCGTGTTCGTCGGTGAGTTGAATA
1 GGGTTGCCGTGTTCGTCAGTGAGTTGAACA
53659133 GGGTTGCCGTGTTCGTC
1 GGGTTGCCGTGTTCGTC
53659150 TCTCAAATCA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.12, C:0.18, G:0.38, T:0.32
Consensus pattern (30 bp):
GGGTTGCCGTGTTCGTCAGTGAGTTGAACA
Found at i:53659585 original size:22 final size:22
Alignment explanation
Indices: 53659524--53659589 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 22
53659514 AGCGTAGGAG
* *
53659524 GTCGTAGATTCGAATGTACATA
1 GTCGTATATTCGAATGTGCATA
*
53659546 GTCGGTTGTGAATTCGAATGTGCATA
1 GTC-G-TAT--ATTCGAATGTGCATA
53659572 GTCGTATATTCGAATGTG
1 GTCGTATATTCGAATGTG
53659590 TTAAAATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
22 14 0.39
23 1 0.03
24 3 0.08
25 1 0.03
26 17 0.47
ACGTcount: A:0.26, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
GTCGTATATTCGAATGTGCATA
Found at i:53660243 original size:31 final size:31
Alignment explanation
Indices: 53660208--53660268 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
53660198 ATAACACATG
53660208 AGTGACTTAAATA-AGAACTTTCAAATAATTC
1 AGTGACTTAAATAGA-AACTTTCAAATAATTC
*
53660239 AGTGACTTAAATAGAAACTTTCTAATAATT
1 AGTGACTTAAATAGAAACTTTCAAATAATT
53660269 TAGTAATCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.34
Consensus pattern (31 bp):
AGTGACTTAAATAGAAACTTTCAAATAATTC
Found at i:53662885 original size:98 final size:98
Alignment explanation
Indices: 53662716--53662913 Score: 396
Period size: 98 Copynumber: 2.0 Consensus size: 98
53662706 TGACATGTCA
53662716 TTTTATGCATTTCAAAACAGTATGCGAGATAATGAACATTACACTTATAGCATATAAACTTACGG
1 TTTTATGCATTTCAAAACAGTATGCGAGATAATGAACATTACACTTATAGCATATAAACTTACGG
53662781 TATCACTCTGGTCTTCCCTCTCTTGTCATATGC
66 TATCACTCTGGTCTTCCCTCTCTTGTCATATGC
53662814 TTTTATGCATTTCAAAACAGTATGCGAGATAATGAACATTACACTTATAGCATATAAACTTACGG
1 TTTTATGCATTTCAAAACAGTATGCGAGATAATGAACATTACACTTATAGCATATAAACTTACGG
53662879 TATCACTCTGGTCTTCCCTCTCTTGTCATATGC
66 TATCACTCTGGTCTTCCCTCTCTTGTCATATGC
53662912 TT
1 TT
53662914 CACGCTTTTC
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 100 1.00
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.36
Consensus pattern (98 bp):
TTTTATGCATTTCAAAACAGTATGCGAGATAATGAACATTACACTTATAGCATATAAACTTACGG
TATCACTCTGGTCTTCCCTCTCTTGTCATATGC
Found at i:53669859 original size:14 final size:14
Alignment explanation
Indices: 53669840--53669881 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
53669830 AAAGTATTTT
*
53669840 AAAATTAAAAATTA
1 AAAATTAAAAAATA
53669854 AAAATTAAAAAATA
1 AAAATTAAAAAATA
53669868 AAAA-TAGAAAAATA
1 AAAATTA-AAAAATA
53669882 TATATTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 2 0.08
14 24 0.92
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (14 bp):
AAAATTAAAAAATA
Found at i:53669864 original size:8 final size:7
Alignment explanation
Indices: 53669840--53669872 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
53669830 AAAGTATTTT
53669840 AAAATTA
1 AAAATTA
53669847 AAAATTA
1 AAAATTA
53669854 AAAATTA
1 AAAATTA
*
53669861 AAAAATA
1 AAAATTA
53669868 AAAAT
1 AAAAT
53669873 AGAAAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATTA
Found at i:53670177 original size:27 final size:27
Alignment explanation
Indices: 53670143--53670197 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
53670133 ATTCAACCTA
53670143 TTATTTATTATGATAAGTA-ATTTTTAT
1 TTATTTATTATGATAA-TATATTTTTAT
**
53670170 TTATTTATTATTTTAATATATTTTTAT
1 TTATTTATTATGATAATATATTTTTAT
53670197 T
1 T
53670198 GAAATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (27 bp):
TTATTTATTATGATAATATATTTTTAT
Found at i:53670227 original size:12 final size:13
Alignment explanation
Indices: 53670160--53670224 Score: 53
Period size: 14 Copynumber: 4.9 Consensus size: 13
53670150 TTATGATAAG
*
53670160 TAATTTTTATTTAT
1 TAATTTTTA-TTAA
* *
53670174 TTATTATT-TTAA
1 TAATTTTTATTAA
*
53670186 TATATTTTTATTGA
1 TA-ATTTTTATTAA
53670200 -AATTTTTATTAAA
1 TAATTTTTATT-AA
53670213 TAATTTTTATTA
1 TAATTTTTATTA
53670225 TAAAATATCA
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
12 13 0.32
13 8 0.20
14 19 0.47
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (13 bp):
TAATTTTTATTAA
Found at i:53672018 original size:30 final size:31
Alignment explanation
Indices: 53671970--53672034 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
53671960 TTAATAGTTA
53671970 TAAA-AAATTTTATCATTATATTAAATTATT-
1 TAAATAAATTTTATCATTATATTAAATT-TTG
*
53672000 TAAATAAA-TTTATTATTATATTAAATTTTG
1 TAAATAAATTTTATCATTATATTAAATTTTG
53672030 TAAAT
1 TAAAT
53672035 CTTATTTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 2 0.06
30 27 0.84
31 3 0.09
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (31 bp):
TAAATAAATTTTATCATTATATTAAATTTTG
Found at i:53672024 original size:17 final size:17
Alignment explanation
Indices: 53671978--53672027 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
53671968 TATAAAAAAT
*
53671978 TTTATCATTATATTAAA
1 TTTATTATTATATTAAA
*
53671995 -TTA-T-TTA-AATAAA
1 TTTATTATTATATTAAA
53672008 TTTATTATTATATTAAA
1 TTTATTATTATATTAAA
53672025 TTT
1 TTT
53672028 TGTAAATCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 8
0.70 0.08 0.22
Matches are distributed among these distances:
13 5 0.19
14 6 0.23
15 1 0.04
16 6 0.23
17 8 0.31
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTATTATTATATTAAA
Found at i:53672051 original size:26 final size:25
Alignment explanation
Indices: 53672004--53672053 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 25
53671994 ATTATTTAAA
53672004 TAAATTTATTATTATATTAAATTTTG
1 TAAATTTATTATTATA-TAAATTTTG
53672030 TAAATCTTATTTATTATA-AAATTT
1 TAAAT-TTA-TTATTATATAAATTT
53672054 ATTTTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 11 0.50
27 3 0.14
28 8 0.36
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (25 bp):
TAAATTTATTATTATATAAATTTTG
Found at i:53675123 original size:17 final size:17
Alignment explanation
Indices: 53675103--53675135 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53675093 TACTTAAATA
53675103 TGTATTTGTAATTATAT
1 TGTATTTGTAATTATAT
*
53675120 TGTATTTGTATTTATA
1 TGTATTTGTAATTATA
53675136 AACTCGGAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (17 bp):
TGTATTTGTAATTATAT
Found at i:53676403 original size:23 final size:22
Alignment explanation
Indices: 53676346--53676404 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
53676336 AAAAGCTATC
*
53676346 TACAAATCAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
*
53676367 TACAGAATCGTATCTTCTAAAGAT
1 TACA-AATCATATCTTCT-AAGAT
*
53676391 TACATATCATATCT
1 TACAAATCATATCT
53676405 AAGATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 4 0.13
22 7 0.23
23 11 0.35
24 9 0.29
ACGTcount: A:0.41, C:0.19, G:0.07, T:0.34
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:53679823 original size:2 final size:2
Alignment explanation
Indices: 53679816--53679856 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
53679806 GTCAATACAT
* *
53679816 AC AC AC AC AC GC AC AC AC AC AC AC AC AC AC AT AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
53679857 TATATATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.46, G:0.02, T:0.02
Consensus pattern (2 bp):
AC
Found at i:53679857 original size:10 final size:10
Alignment explanation
Indices: 53679812--53679858 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
53679802 CATAGTCAAT
53679812 ACATACACAC
1 ACATACACAC
*
53679822 ACACGCACACAC
1 ACA--TACACAC
*
53679834 ACACACACAC
1 ACATACACAC
53679844 ACATACACAC
1 ACATACACAC
53679854 ACATA
1 ACATA
53679859 TATATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 24 0.73
12 9 0.27
ACGTcount: A:0.49, C:0.43, G:0.02, T:0.06
Consensus pattern (10 bp):
ACATACACAC
Found at i:53682745 original size:15 final size:15
Alignment explanation
Indices: 53682707--53682760 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
53682697 TTTTACAAAT
*
53682707 TAAAATATAATTATA
1 TAAAAAATAATTATA
53682722 -AAAAGAATAATTATA
1 TAAAA-AATAATTATA
* *
53682737 TTAAAAATAAATAATA
1 TAAAAAAT-AATTATA
53682753 TAAAAAAT
1 TAAAAAAT
53682761 TTCAATATGG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
14 4 0.12
15 12 0.38
16 16 0.50
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (15 bp):
TAAAAAATAATTATA
Found at i:53686604 original size:20 final size:19
Alignment explanation
Indices: 53686579--53686642 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 19
53686569 TTAAAATTTT
*
53686579 AAAAATATTAAAAAATTATA
1 AAAAATATTTAAAAA-TATA
53686599 AAAAATATTTTTAAAAAT-TA
1 AAAAATA--TTTAAAAATATA
*
53686619 AAAATTATTTAAAAAGTATA
1 AAAAATATTTAAAAA-TATA
53686639 AAAA
1 AAAA
53686643 GAATATAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 8 0.21
19 1 0.03
20 21 0.55
21 1 0.03
22 7 0.18
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAAATATTTAAAAATATA
Found at i:53686633 original size:40 final size:40
Alignment explanation
Indices: 53686566--53686642 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
53686556 CTTAACTAAT
* *
53686566 TTTTTAAAATTTTAAAAATATTAAAAAATTATAAAAAATA
1 TTTTTAAAATATTAAAAATATTAAAAAAGTATAAAAAATA
*
53686606 TTTTTAAAA-ATTAAAAATTATTTAAAAAGTATAAAAA
1 TTTTTAAAATATTAAAAA-TATTAAAAAAGTATAAAAA
53686643 GAATATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 7 0.21
40 26 0.79
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (40 bp):
TTTTTAAAATATTAAAAATATTAAAAAAGTATAAAAAATA
Found at i:53686681 original size:51 final size:49
Alignment explanation
Indices: 53686562--53686689 Score: 138
Period size: 51 Copynumber: 2.6 Consensus size: 49
53686552 AACACTTAAC
*
53686562 TAAT-TTTTTAAAATTTTAAAAATATTAAAAAATTATAAAAAATATTTT
1 TAATATTTTTAAAATTTTAAAAATATTAAAAAAATATAAAAAATATTTT
** * *
53686610 TAA-AAATTAAAAATTATTTAAAAAGTA-TAAAAAGAATATAAAATATATTTTT
1 TAATATTTTTAAAA-T-TTTAAAAA-TATTAAAAA-AATATAAAAAATA-TTTT
53686662 TAATATTTTTAAAATTTTAAAAA-ATTAA
1 TAATATTTTTAAAATTTTAAAAATATTAA
53686690 TTAAACGTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
48 9 0.14
49 2 0.03
50 17 0.27
51 21 0.33
52 8 0.12
53 7 0.11
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (49 bp):
TAATATTTTTAAAATTTTAAAAATATTAAAAAAATATAAAAAATATTTT
Found at i:53703668 original size:22 final size:21
Alignment explanation
Indices: 53703622--53703670 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
53703612 GAATTAATGC
* *
53703622 TTTTTATATTTTTAAAATCTT
1 TTTTTATAGTTTTAAAATCTA
53703643 TTTTTATAAGTTTTAAGAAT-TA
1 TTTTTAT-AGTTTTAA-AATCTA
53703665 TTTTTA
1 TTTTTA
53703671 ATCATTTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 7 0.29
22 14 0.58
23 3 0.12
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (21 bp):
TTTTTATAGTTTTAAAATCTA
Found at i:53710256 original size:35 final size:35
Alignment explanation
Indices: 53710208--53710275 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 35
53710198 ATACACTATC
53710208 TTAGAACTTAATTAGGATTACGAAAATTATATTAG
1 TTAGAACTTAATTAGGATTACGAAAATTATATTAG
*
53710243 TTAGAA-TTGAATTAGGATTATGAAAATTATATT
1 TTAGAACTT-AATTAGGATTACGAAAATTATATT
53710276 TATATATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 2 0.06
35 29 0.94
ACGTcount: A:0.43, C:0.03, G:0.15, T:0.40
Consensus pattern (35 bp):
TTAGAACTTAATTAGGATTACGAAAATTATATTAG
Found at i:53715044 original size:5 final size:5
Alignment explanation
Indices: 53715031--53715070 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
53715021 TATATATATT
* *
53715031 TTTTA TTTTC TTTTA TTTTC TTTTA TTTTCA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A TTTTA TTTT
53715071 TCCTAAAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:53715044 original size:10 final size:10
Alignment explanation
Indices: 53715031--53715070 Score: 71
Period size: 10 Copynumber: 3.9 Consensus size: 10
53715021 TATATATATT
53715031 TTTTATTTTC
1 TTTTATTTTC
53715041 TTTTATTTTC
1 TTTTATTTTC
53715051 TTTTATTTTC
1 TTTTATTTTC
53715061 ATTTTATTTT
1 -TTTTATTTT
53715071 TCCTAAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 20 0.69
11 9 0.31
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTATTTTC
Found at i:53715680 original size:3 final size:3
Alignment explanation
Indices: 53715672--53715727 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
53715662 TGTTTTTTAA
* *
53715672 ATT ATT ATTT ATT ATT ATC ATT ATT ATT A-T ATT ATAT ATT ATC ATT
1 ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT
*
53715718 ATT ACT ATT A
1 ATT ATT ATT A
53715728 CTATCTCTAC
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
2 2 0.05
3 36 0.82
4 6 0.14
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:53715711 original size:24 final size:22
Alignment explanation
Indices: 53715672--53715726 Score: 83
Period size: 24 Copynumber: 2.4 Consensus size: 22
53715662 TGTTTTTTAA
53715672 ATTATTATTTATTATTATCATT
1 ATTATTATTTATTATTATCATT
53715694 ATTATTATATTATATATTATCATT
1 ATTATTAT-TTAT-TATTATCATT
*
53715718 ATTACTATT
1 ATTATTATT
53715727 ACTATCTCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 8 0.27
23 5 0.17
24 17 0.57
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTATTATTTATTATTATCATT
Found at i:53715711 original size:27 final size:27
Alignment explanation
Indices: 53715674--53715727 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
53715664 TTTTTTAAAT
* * *
53715674 TATTATTTATTATTATCATTATTATTA
1 TATTATATATTATCATCATTACTATTA
*
53715701 TATTATATATTATCATTATTACTATTA
1 TATTATATATTATCATCATTACTATTA
53715728 CTATCTCTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (27 bp):
TATTATATATTATCATCATTACTATTA
Found at i:53715827 original size:26 final size:24
Alignment explanation
Indices: 53715766--53715827 Score: 70
Period size: 26 Copynumber: 2.5 Consensus size: 24
53715756 ACTTTATATA
* *
53715766 ATATATATATATATGCATTTTTTT
1 ATATATATATACACGCATTTTTTT
53715790 ATATATAGTATACACGCATTGTTTTT
1 ATATATA-TATACACGCATT-TTTTT
*
53715816 TTATATGATATA
1 ATATAT-ATATA
53715828 TATATATGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 7 0.22
25 10 0.31
26 14 0.44
27 1 0.03
ACGTcount: A:0.34, C:0.06, G:0.08, T:0.52
Consensus pattern (24 bp):
ATATATATATACACGCATTTTTTT
Found at i:53716076 original size:22 final size:21
Alignment explanation
Indices: 53716029--53716071 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
53716019 CAAACATATA
*
53716029 TATATACATTTTTTTGAATTAT
1 TATAAACATTTTTTT-AATTAT
53716051 TATAAACATTTTTTT-ATTAT
1 TATAAACATTTTTTTAATTAT
53716071 T
1 T
53716072 CTATATATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
22 14 0.70
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (21 bp):
TATAAACATTTTTTTAATTAT
Found at i:53719887 original size:35 final size:35
Alignment explanation
Indices: 53719839--53719906 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 35
53719829 ATACACTATC
53719839 TTAGAACTTAATTAGGATTACGAAAATTATATTAG
1 TTAGAACTTAATTAGGATTACGAAAATTATATTAG
*
53719874 TTAGAA-TTGAATTAGGATTATGAAAATTATATT
1 TTAGAACTT-AATTAGGATTACGAAAATTATATT
53719907 TATATATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 2 0.06
35 29 0.94
ACGTcount: A:0.43, C:0.03, G:0.15, T:0.40
Consensus pattern (35 bp):
TTAGAACTTAATTAGGATTACGAAAATTATATTAG
Found at i:53721230 original size:15 final size:15
Alignment explanation
Indices: 53721185--53721231 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
53721175 TTGCATAATC
*
53721185 ATTAATTTATTCTTT
1 ATTAATTTATTTTTT
*
53721200 AAT-ATTTATATCTTTT
1 ATTAATTTAT-T-TTTT
53721216 ATTAATTTATTTTTT
1 ATTAATTTATTTTTT
53721231 A
1 A
53721232 GAGTTAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
14 6 0.23
15 8 0.31
16 6 0.23
17 6 0.23
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (15 bp):
ATTAATTTATTTTTT
Found at i:53730019 original size:13 final size:14
Alignment explanation
Indices: 53730003--53730038 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
53729993 AATTACAAAA
53730003 TTTTATTATTTA-T
1 TTTTATTATTTATT
53730016 TTTTA-TATTTATT
1 TTTTATTATTTATT
53730029 TTTTATTATT
1 TTTTATTATT
53730039 CACACTCGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.29
13 11 0.52
14 4 0.19
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTATTATTTATT
Found at i:53730024 original size:12 final size:12
Alignment explanation
Indices: 53730003--53730035 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
53729993 AATTACAAAA
53730003 TTTTATTATTTAT
1 TTTTA-TATTTAT
53730016 TTTTATATTTAT
1 TTTTATATTTAT
53730028 TTTT-TATT
1 TTTTATATT
53730036 ATTCACACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.20
12 11 0.55
13 5 0.25
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTATATTTAT
Found at i:53737366 original size:11 final size:11
Alignment explanation
Indices: 53737350--53737379 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
53737340 ACAATCACAT
53737350 TGGTGAGATAA
1 TGGTGAGATAA
53737361 TGGTGAGATAA
1 TGGTGAGATAA
53737372 TGGTGAGA
1 TGGTGAGA
53737380 AAGAAATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.40, T:0.27
Consensus pattern (11 bp):
TGGTGAGATAA
Found at i:53740252 original size:15 final size:16
Alignment explanation
Indices: 53740232--53740264 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
53740222 TCTAAAGATT
53740232 TTAATTACTTT-TATA
1 TTAATTACTTTATATA
53740247 TTAATTACTTTATATA
1 TTAATTACTTTATATA
53740263 TT
1 TT
53740265 TAGTTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (16 bp):
TTAATTACTTTATATA
Found at i:53741400 original size:26 final size:25
Alignment explanation
Indices: 53741362--53741412 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
53741352 AAGTTTAAGG
*
53741362 CCCAATATGGAAACACTTGTTCAAGT
1 CCCAATATAGAAACACTTG-TCAAGT
* *
53741388 CCCAATGTAGAAACATTTGTCAAGT
1 CCCAATATAGAAACACTTGTCAAGT
53741413 TTAAAGCCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (25 bp):
CCCAATATAGAAACACTTGTCAAGT
Found at i:53746881 original size:24 final size:24
Alignment explanation
Indices: 53746848--53746895 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
53746838 TCAAGTGAGA
* *
53746848 CTTTATTTTCAACATTTCCATTGT
1 CTTTAGTTTCAACAATTCCATTGT
*
53746872 CTTTAGTTTCAACAATTGCATTGT
1 CTTTAGTTTCAACAATTCCATTGT
53746896 TTTCATCAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.08, T:0.50
Consensus pattern (24 bp):
CTTTAGTTTCAACAATTCCATTGT
Found at i:53749050 original size:14 final size:14
Alignment explanation
Indices: 53749027--53749058 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
53749017 TTTTGTATTG
*
53749027 AAAAGGAAAAAAGA
1 AAAAGAAAAAAAGA
53749041 AAAAGAAAAAAAGA
1 AAAAGAAAAAAAGA
53749055 AAAA
1 AAAA
53749059 TTGGAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAAGA
Found at i:53749382 original size:30 final size:30
Alignment explanation
Indices: 53749337--53749396 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
53749327 ACAAAATGGT
* *
53749337 CACTAAACTATTCAAAATTTTTTATTTAAG
1 CACTAAACTAGTCAAAAGTTTTTATTTAAG
*
53749367 CACTGAACTAGTCAAAAGTTTTTATTTAAG
1 CACTAAACTAGTCAAAAGTTTTTATTTAAG
53749397 TCGCTGAGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (30 bp):
CACTAAACTAGTCAAAAGTTTTTATTTAAG
Found at i:53763918 original size:3 final size:3
Alignment explanation
Indices: 53763910--53763955 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
53763900 CAATCACTTC
53763910 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
53763956 ATTCATTACC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:53766161 original size:50 final size:48
Alignment explanation
Indices: 53766107--53766385 Score: 277
Period size: 50 Copynumber: 5.8 Consensus size: 48
53766097 GGCAGTGAGT
* *
53766107 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACACAGTCCGACGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACAC-GACAGA-GA
*
53766157 GTGCTAGTGTAAGATCATGTCTGGGACATGGCATCGACACGGACAGAGAA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACAC-GACAGAG-A
* *
53766207 GAG-TCAGTGT-AGACCATGTCTGGGACATGGCATC-AGCTCG--AGATGA
1 GTGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGA-CACGACAGA-GA
* *
53766253 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATGGACAGAGAA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACA-CGACAGAG-A
* * * * *
53766303 GAG-TCAGTGTAAGACCTTGTCTGGGACATGACATCGGCTCG--AGATGA
1 GTGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGACACGACAGA-GA
**
53766350 GTGCTAGTGTAAGACCATGTCTAAGACATGGCATCG
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCG
53766386 GCACCGATAT
Statistics
Matches: 194, Mismatches: 21, Indels: 31
0.79 0.09 0.13
Matches are distributed among these distances:
46 11 0.06
47 60 0.31
48 5 0.03
49 30 0.15
50 88 0.45
ACGTcount: A:0.27, C:0.20, G:0.32, T:0.22
Consensus pattern (48 bp):
GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACACGACAGAGA
Found at i:53766362 original size:97 final size:97
Alignment explanation
Indices: 53766112--53766389 Score: 414
Period size: 97 Copynumber: 2.8 Consensus size: 97
53766102 TGAGTGTGCT
* * * * *
53766112 AGTGTAAGACCATGTCTGGGACATGGCATCGACACAGTCCGACGAGTGCTAGTGTAAGATCATGT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTC-G--AGATGAGTGCTAGTGTAAGACCATGT
*
53766177 CTGGGACATGGCATCGACACGGACAGAGAAGAGTC
63 CTGGGACATGGCATCGGCACGGACAGAGAAGAGTC
*
53766212 AGTGT-AGACCATGTCTGGGACATGGCATCAGCTCGAGATGAGTGCTAGTGTAAGACCATGTCTG
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGAGTGCTAGTGTAAGACCATGTCTG
*
53766276 GGACATGGCATCGGCATGGACAGAGAAGAGTC
66 GGACATGGCATCGGCACGGACAGAGAAGAGTC
* * *
53766308 AGTGTAAGACCTTGTCTGGGACATGACATCGGCTCGAGATGAGTGCTAGTGTAAGACCATGTCTA
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGAGTGCTAGTGTAAGACCATGTCTG
*
53766373 AGACATGGCATCGGCAC
66 GGACATGGCATCGGCAC
53766390 CGATATGTGA
Statistics
Matches: 163, Mismatches: 14, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
96 61 0.37
97 70 0.43
98 1 0.01
99 26 0.16
100 5 0.03
ACGTcount: A:0.28, C:0.20, G:0.31, T:0.21
Consensus pattern (97 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGAGTGCTAGTGTAAGACCATGTCTG
GGACATGGCATCGGCACGGACAGAGAAGAGTC
Found at i:53767631 original size:17 final size:16
Alignment explanation
Indices: 53767611--53767657 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
53767601 CGAACGGAGA
53767611 AGAAGAGAAAAAAAAAG
1 AGAA-AGAAAAAAAAAG
*
53767628 AGAAAGAAAGAAGAAAG
1 AGAAAGAAA-AAAAAAG
*
53767645 AAAAAGAAAAAAA
1 AGAAAGAAAAAAA
53767658 GAGAAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 8 0.31
17 18 0.69
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AGAAAGAAAAAAAAAG
Found at i:53767635 original size:21 final size:20
Alignment explanation
Indices: 53767610--53767667 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 20
53767600 CCGAACGGAG
53767610 AAGAAGAGAAAAAAAAAGAGA
1 AAGAAGAGAAAAAAAAAGA-A
*
53767631 AAGAAAGAAGAAAGAAAAAGAA
1 AAG-AAG-AGAAAAAAAAAGAA
*
53767653 AAAAAGAGAAAAAAA
1 AAGAAGAGAAAAAAA
53767668 TTAAAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.25
21 6 0.19
22 6 0.19
23 12 0.38
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
AAGAAGAGAAAAAAAAAGAA
Found at i:53767648 original size:23 final size:19
Alignment explanation
Indices: 53767613--53767667 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 19
53767603 AACGGAGAAG
53767613 AAGAGAAAAAAAAAGAGAAAGA
1 AAGAG-AAAAAAAAGA-AAA-A
53767635 AAGAAGAAAGAAAAAGAAAAA
1 AAG-AGAAA-AAAAAGAAAAA
53767656 AAGAGAAAAAAA
1 AAGAGAAAAAAA
53767668 TTAAAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
19 4 0.13
20 5 0.16
21 4 0.13
22 9 0.29
23 9 0.29
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (19 bp):
AAGAGAAAAAAAAGAAAAA
Found at i:53767651 original size:10 final size:10
Alignment explanation
Indices: 53767620--53767667 Score: 62
Period size: 10 Copynumber: 4.7 Consensus size: 10
53767610 AAGAAGAGAA
53767620 AAAAAAAGAG
1 AAAAAAAGAG
*
53767630 AAAGAAAGAAG
1 AAAAAAAG-AG
53767641 AAAGAAAA-AG
1 AAA-AAAAGAG
53767651 AAAAAAAGAG
1 AAAAAAAGAG
53767661 AAAAAAA
1 AAAAAAA
53767668 TTAAAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 4 0.12
10 21 0.64
11 5 0.15
12 3 0.09
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAG
Found at i:53767941 original size:14 final size:13
Alignment explanation
Indices: 53767924--53767967 Score: 63
Period size: 12 Copynumber: 3.4 Consensus size: 13
53767914 GCAGCAGGCC
53767924 AAAAAAAGAGGAGA
1 AAAAAAAGA-GAGA
53767938 AAAAAAAGAGA-A
1 AAAAAAAGAGAGA
*
53767950 AAAAAAAGAAAGA
1 AAAAAAAGAGAGA
53767963 AAAAA
1 AAAAA
53767968 GGAAAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 11 0.39
13 8 0.29
14 9 0.32
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAGAGA
Found at i:53767954 original size:12 final size:12
Alignment explanation
Indices: 53767924--53767976 Score: 65
Period size: 11 Copynumber: 4.4 Consensus size: 12
53767914 GCAGCAGGCC
53767924 AAAAAAAGAGGAGA
1 AAAAAAAGA-GA-A
53767938 AAAAAAAGAGAA
1 AAAAAAAGAGAA
53767950 AAAAAAAGA-AA
1 AAAAAAAGAGAA
*
53767961 GAAAAAAG-GAA
1 AAAAAAAGAGAA
53767972 AAAAA
1 AAAAA
53767977 TAAAAGTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
11 15 0.42
12 10 0.28
13 2 0.06
14 9 0.25
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAGAA
Found at i:53767959 original size:21 final size:21
Alignment explanation
Indices: 53767935--53767976 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
53767925 AAAAAAGAGG
53767935 AGAAA-AAAAAGAGAAAAAAAA
1 AGAAAGAAAAA-AGAAAAAAAA
*
53767956 AGAAAGAAAAAAGGAAAAAAA
1 AGAAAGAAAAAAGAAAAAAAA
53767977 TAAAAGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (21 bp):
AGAAAGAAAAAAGAAAAAAAA
Found at i:53768488 original size:20 final size:20
Alignment explanation
Indices: 53768465--53768506 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
53768455 TTGTGTTTTC
53768465 AAAAATTT-CAGTATTTCAA
1 AAAAATTTCCAGTATTTCAA
* *
53768484 AAAAATTTCCGGTGTTTCAA
1 AAAAATTTCCAGTATTTCAA
53768504 AAA
1 AAA
53768507 TTTTCATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (20 bp):
AAAAATTTCCAGTATTTCAA
Found at i:53768489 original size:19 final size:19
Alignment explanation
Indices: 53768465--53768524 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
53768455 TTGTGTTTTC
53768465 AAAAATTTCAGTATTTCAA
1 AAAAATTTCAGTATTTCAA
* *
53768484 AAAAATTTCCGGTGTTTC-A
1 AAAAATTT-CAGTATTTCAA
*
53768503 AAAATTTTCA-TATTTTCAA
1 AAAAATTTCAGTA-TTTCAA
53768522 AAA
1 AAA
53768525 TTCTCGTGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
17 1 0.03
18 5 0.15
19 20 0.61
20 7 0.21
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (19 bp):
AAAAATTTCAGTATTTCAA
Found at i:53768502 original size:55 final size:53
Alignment explanation
Indices: 53768442--53768947 Score: 192
Period size: 53 Copynumber: 9.5 Consensus size: 53
53768432 AAAAATTCTA
53768442 GTTTCAAATATCTTT-GTGTTTTCAAAAATTTCAGTATTTCAAAAAAATTTCCGGT
1 GTTTCAAATAT-TTTCGTGTTTTCAAAAATTTCAGTATTTC-AAAAAATTTCC-GT
* * * * *
53768497 GTTTCAAAAATTTTCATATTTTCAAAAATTCTC-GTGTTTTCAAAAAA-TTCCAT
1 GTTTCAAATATTTTCGTGTTTTCAAAAATT-TCAGT-ATTTCAAAAAATTTCCGT
* * * *
53768550 TTTTCAAATTTTTTTCGTGTTTTCTAAAAATTTTCA-TGTTTC-AAAAATTTTCGT
1 GTTTCAAA-TATTTTCGTGTTTTC-AAAAA-TTTCAGTATTTCAAAAAATTTCCGT
* * * *** * *
53768604 GTTTCAAAAATTTTCATATTTTCAAAAA-AAAATTATTTTC-AACAA-TTCTCGT
1 GTTTCAAATATTTTCGTGTTTTCAAAAATTTCAGTA-TTTCAAAAAATTTC-CGT
* * ** * *
53768656 GTTTCACAA-ATTTTCGTGTTTT-AAAATTTTTTATGT-TTAAAAAAAAATTCTTGT
1 GTTTCA-AATATTTTCGTGTTTTCAAAA-ATTTCA-GTATTTCAAAAAATTTC-CGT
* * * * * *
53768710 GTTTCAAAAATTGTCGTGTTTT-AAAAATTTTCA-TGTTTC-TAAAATTTTCTT
1 GTTTCAAATATTTTCGTGTTTTCAAAAA-TTTCAGTATTTCAAAAAATTTCCGT
* * * ** *
53768761 ATTTCAAAAATTTTCGTGTTTTCAAAATTTTGTGTGTTTC-AAAAATCTT-CGT
1 GTTTCAAATATTTTCGTGTTTTCAAAAATTTCAGTATTTCAAAAAAT-TTCCGT
* * * * * * * *
53768813 GTTTTCAAA-AATTCCAATG-TTTCAAAAAATTCCCGTGTTTTAAAAAATGT-CGT
1 G-TTTCAAATATTTTC-GTGTTTTC-AAAAATTTCAGTATTTCAAAAAATTTCCGT
* * * * * *
53768866 GTTTTCAAAAATTTTCGTATTTTTAAGAATTTTC-GTGTTTC-TAAAA-TTCTCGT
1 G-TTTCAAATATTTTCGTGTTTTCAA-AAATTTCAGTATTTCAAAAAATTTC-CGT
* *
53768919 GTTTTAAAAATTTTTCGTGTTTTCAAAAA
1 GTTTCAAATA-TTTTCGTGTTTTCAAAAA
53768948 AATAATTGTT
Statistics
Matches: 342, Mismatches: 76, Indels: 69
0.70 0.16 0.14
Matches are distributed among these distances:
50 1 0.00
51 32 0.09
52 81 0.24
53 97 0.28
54 84 0.25
55 39 0.11
56 8 0.02
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.47
Consensus pattern (53 bp):
GTTTCAAATATTTTCGTGTTTTCAAAAATTTCAGTATTTCAAAAAATTTCCGT
Found at i:53768597 original size:17 final size:17
Alignment explanation
Indices: 53768442--53768947 Score: 297
Period size: 17 Copynumber: 28.6 Consensus size: 17
53768432 AAAAATTCTA
*
53768442 GTTTCAAATATCTTT-GT
1 GTTTCAAAAAT-TTTCGT
53768459 GTTTTCAAAAA-TTTCAGT
1 G-TTTCAAAAATTTTC-GT
* *
53768477 ATTTCAAAAAAATTTCCGGT
1 GTTTC--AAAAATTTTC-GT
*
53768497 GTTTCAAAAATTTTCAT
1 GTTTCAAAAATTTTCGT
* *
53768514 ATTTTCAAAAATTCTCGT
1 -GTTTCAAAAATTTTCGT
* * *
53768532 GTTTTCAAAAAATTCCAT
1 G-TTTCAAAAATTTTCGT
* **
53768550 TTTTCAAATTTTTTTCGT
1 GTTTCAAA-AATTTTCGT
*
53768568 GTTTTCTAAAAATTTTCAT
1 G-TTTC-AAAAATTTTCGT
53768587 GTTTCAAAAATTTTCGT
1 GTTTCAAAAATTTTCGT
*
53768604 GTTTCAAAAATTTTCAT
1 GTTTCAAAAATTTTCGT
* ** *
53768621 ATTTTCAAAAAAAAATT-AT
1 -GTTTC--AAAAATTTTCGT
* *
53768640 -TTTCAACAATTCTCGT
1 GTTTCAAAAATTTTCGT
*
53768656 GTTTCACAAATTTTCGT
1 GTTTCAAAAATTTTCGT
* * **
53768673 GTTTTAAAATTTTTTAT
1 GTTTCAAAAATTTTCGT
*
53768690 GTTTAAAAAAAAATTCTT-GT
1 GTTT---CAAAAATT-TTCGT
*
53768710 GTTTCAAAAATTGTCGT
1 GTTTCAAAAATTTTCGT
* *
53768727 GTTTTAAAAATTTTCAT
1 GTTTCAAAAATTTTCGT
* *
53768744 GTTTCTAAAATTTTCTT
1 GTTTCAAAAATTTTCGT
*
53768761 ATTTCAAAAATTTTCGT
1 GTTTCAAAAATTTTCGT
*
53768778 GTTTTC-AAAATTTTGTGT
1 G-TTTCAAAAATTTT-CGT
*
53768796 GTTTCAAAAATCTTCGT
1 GTTTCAAAAATTTTCGT
* *
53768813 GTTTTCAAAAA-TTCCAAT
1 G-TTTCAAAAATTTTC-GT
**
53768831 GTTTCAAAAAATTCCCGT
1 GTTTC-AAAAATTTTCGT
* * *
53768849 GTTTTAAAAAATGTCGT
1 GTTTCAAAAATTTTCGT
53768866 GTTTTCAAAAATTTTCGT
1 G-TTTCAAAAATTTTCGT
* * *
53768884 ATTTTTAAGAATTTTCGT
1 -GTTTCAAAAATTTTCGT
* *
53768902 GTTTCTAAAATTCTCGT
1 GTTTCAAAAATTTTCGT
*
53768919 GTTTTAAAAATTTTTCGT
1 GTTTCAAAAA-TTTTCGT
53768937 GTTTTCAAAAA
1 G-TTTCAAAAA
53768948 AATAATTGTT
Statistics
Matches: 372, Mismatches: 85, Indels: 62
0.72 0.16 0.12
Matches are distributed among these distances:
15 5 0.01
16 5 0.01
17 175 0.47
18 126 0.34
19 29 0.08
20 30 0.08
21 2 0.01
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.47
Consensus pattern (17 bp):
GTTTCAAAAATTTTCGT
Found at i:53768812 original size:35 final size:35
Alignment explanation
Indices: 53768442--53768947 Score: 198
Period size: 35 Copynumber: 14.3 Consensus size: 35
53768432 AAAAATTCTA
* * **
53768442 GTTTCAAATATCTTT-GTGTTTTCAAAAATTTCAGT
1 GTTTCAAAAAT-TTTCGTGTTTTCAAAATTTTGTGT
* * * *
53768477 ATTTCAAAAAAATTTCCG-GTGTTTCAAAAATTTTCATAT
1 GTTTC--AAAAATTTTCGTGT-TTTC-AAAATTTT-GTGT
* ** ***
53768516 -TTTCAAAAATTCTCGTGTTTTCAAAAAATTCCAT
1 GTTTCAAAAATTTTCGTGTTTTCAAAATTTTGTGT
* ** **
53768550 TTTTCAAATTTTTTTCGTGTTTTCTAAAAATTTT-CAT
1 GTTTCAAA-AATTTTCGTGTTTTC--AAAATTTTGTGT
* *
53768587 GTTTCAAAAATTTTCGTG-TTTCAAAAATTTTCATAT
1 GTTTCAAAAATTTTCGTGTTTTC-AAAATTTT-GTGT
*** * * *
53768623 -TTTCAAAAAAAAAT--TATTTTCAACAATTCT-CGT
1 GTTTC-AAAAATTTTCGTGTTTTCAA-AATTTTGTGT
* * *
53768656 GTTTCACAAATTTTCGTGTTTT-AAAATTTTTTAT
1 GTTTCAAAAATTTTCGTGTTTTCAAAATTTTGTGT
* ** * *
53768690 GTTTAAAAAAAAATTCTTGTGTTTCAAAA-ATTGTCGT
1 GTTT-CAAAAATTTTCGTGT-TTTCAAAATTTTGT-GT
* * *
53768727 GTTTTAAAAATTTTCATG-TTTCTAAAATTTTCT-T
1 GTTTCAAAAATTTTCGTGTTTTC-AAAATTTTGTGT
*
53768761 ATTTCAAAAATTTTCGTGTTTTCAAAATTTTGTGT
1 GTTTCAAAAATTTTCGTGTTTTCAAAATTTTGTGT
* * ****
53768796 GTTTCAAAAATCTTCGTGTTTTCAAAAATTCCAAT
1 GTTTCAAAAATTTTCGTGTTTTCAAAATTTTGTGT
** * * *
53768831 GTTTCAAAAAATTCCCGTGTTTTAAAAAATGTCGTGT
1 GTTTC-AAAAATTTTCGTGTTTT-CAAAATTTTGTGT
* * *
53768868 -TTTCAAAAATTTTCGTATTTTTAAGAATTTT-CGT
1 GTTTCAAAAATTTTCGTGTTTTCAA-AATTTTGTGT
* * *
53768902 GTTTCTAAAATTCTCGTGTTTTAAAAATTTT-TCGT
1 GTTTCAAAAATTTTCGTGTTTTCAAAATTTTGT-GT
53768937 GTTTTCAAAAA
1 G-TTTCAAAAA
53768948 AATAATTGTT
Statistics
Matches: 353, Mismatches: 84, Indels: 67
0.70 0.17 0.13
Matches are distributed among these distances:
33 11 0.03
34 64 0.18
35 132 0.37
36 90 0.25
37 38 0.11
38 17 0.05
39 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.47
Consensus pattern (35 bp):
GTTTCAAAAATTTTCGTGTTTTCAAAATTTTGTGT
Found at i:53768965 original size:36 final size:34
Alignment explanation
Indices: 53768918--53768984 Score: 89
Period size: 36 Copynumber: 1.9 Consensus size: 34
53768908 AAAATTCTCG
* * *
53768918 TGTTTTAAAAATTTTTCGTGTTTTCAAAAAAATAAT
1 TGTTTCAAAAATCTTT-GTATTTT-AAAAAAATAAT
53768954 TGTTTCAAAAATCTTTGTATTTTAAAAAAAT
1 TGTTTCAAAAATCTTTGTATTTTAAAAAAAT
53768985 TTGTATTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 8 0.29
35 6 0.21
36 14 0.50
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.46
Consensus pattern (34 bp):
TGTTTCAAAAATCTTTGTATTTTAAAAAAATAAT
Found at i:53771739 original size:69 final size:70
Alignment explanation
Indices: 53771635--53771778 Score: 168
Period size: 69 Copynumber: 2.1 Consensus size: 70
53771625 AGATTCAATC
* * * * *
53771635 AAATATATTTATAAAACCCTATAAAATTAAGAAATTTTAA-TAAAAAATAT-ATAATATTTTTAA
1 AAATATATTTATAAAACACTATAAAATTAAGAAATTATAATTAAAAAATATAAAAATAGTTATAA
*
53771698 TATTA
66 AATTA
* * *
53771703 AAATATATGTTATAAAATATTATAAAATTTAA-AAATTATAATTTAAAAATATAAAAATAGTTAT
1 AAATATAT-TTATAAAACACTATAAAA-TTAAGAAATTATAATTAAAAAATATAAAAATAGTTAT
53771767 AAAATTA
64 AAAATTA
53771774 AAATA
1 AAATA
53771779 GTTGCATTTT
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
68 8 0.13
69 23 0.37
70 13 0.21
71 19 0.30
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (70 bp):
AAATATATTTATAAAACACTATAAAATTAAGAAATTATAATTAAAAAATATAAAAATAGTTATAA
AATTA
Found at i:53771755 original size:13 final size:14
Alignment explanation
Indices: 53771728--53771756 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
53771718 AATATTATAA
53771728 AATTTAAAAATTAT
1 AATTTAAAAATTAT
53771742 AATTTAAAAA-TAT
1 AATTTAAAAATTAT
53771755 AA
1 AA
53771757 AAATAGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATTTAAAAATTAT
Found at i:53773266 original size:17 final size:16
Alignment explanation
Indices: 53773219--53773271 Score: 58
Period size: 17 Copynumber: 3.4 Consensus size: 16
53773209 TCGAAAAGTG
*
53773219 AATAAGATTAGAAAAA
1 AATAAGTTTAGAAAAA
53773235 ATATAAGTTT-G--AAA
1 A-ATAAGTTTAGAAAAA
53773249 AATAAGTTTAGACAAAA
1 AATAAGTTTAGA-AAAA
53773266 AATAAG
1 AATAAG
53773272 GTCTTTTAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
13 8 0.26
14 5 0.16
16 2 0.06
17 16 0.52
ACGTcount: A:0.60, C:0.02, G:0.13, T:0.25
Consensus pattern (16 bp):
AATAAGTTTAGAAAAA
Found at i:53776368 original size:3 final size:3
Alignment explanation
Indices: 53776360--53776387 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
53776350 CAATCACTTC
53776360 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
53776388 ATTCATTACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:53777803 original size:3 final size:3
Alignment explanation
Indices: 53777795--53777819 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
53777785 TTGACCCTAA
53777795 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
53777820 AGTCAAATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:53777954 original size:19 final size:18
Alignment explanation
Indices: 53777920--53777955 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
53777910 TGTACTTCAT
53777920 AAAATTTTTAAAAAAATG
1 AAAATTTTTAAAAAAATG
*
53777938 AAAATTATTTTAAAAAAT
1 AAAATT-TTTAAAAAAAT
53777956 CATAAAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
AAAATTTTTAAAAAAATG
Found at i:53778527 original size:13 final size:14
Alignment explanation
Indices: 53778500--53778528 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
53778490 AATATTATAA
53778500 AATTTAAAAATTAT
1 AATTTAAAAATTAT
53778514 AATTTAAAAA-TAT
1 AATTTAAAAATTAT
53778527 AA
1 AA
53778529 AAATAGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATTTAAAAATTAT
Found at i:53778993 original size:5 final size:6
Alignment explanation
Indices: 53778964--53778991 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
53778954 AAACTCAATC
53778964 TTTTTA TTTTTA TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTT
53778992 ATATCATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:53779140 original size:3 final size:3
Alignment explanation
Indices: 53779132--53779169 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
53779122 TTGACAAATG
53779132 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
53779170 TGAACTGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:53781070 original size:5 final size:5
Alignment explanation
Indices: 53781055--53781209 Score: 235
Period size: 5 Copynumber: 30.8 Consensus size: 5
53781045 TTAATTAAAA
* *
53781055 ATATAT ATATT ATATT ATATT A-ACTT A-A-T AAATA AGTTATT ATATT
1 ATAT-T ATATT ATATT ATATT ATA-TT ATATT ATATT A-T-ATT ATATT
53781101 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
53781151 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
53781201 ATATT ATAT
1 ATATT ATAT
53781210 CCTAGAACAA
Statistics
Matches: 141, Mismatches: 3, Indels: 11
0.91 0.02 0.07
Matches are distributed among these distances:
3 2 0.01
4 2 0.01
5 129 0.91
6 5 0.04
7 3 0.02
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:53782908 original size:31 final size:32
Alignment explanation
Indices: 53782872--53782950 Score: 108
Period size: 31 Copynumber: 2.5 Consensus size: 32
53782862 TAAATATGTA
53782872 TTTTTTATTTTTAAAAATA-TTTTAAAATACT
1 TTTTTTATTTTTAAAAATATTTTTAAAATACT
* *
53782903 TTTTTTATTTTT-AAAATATTTTTAACATGCT
1 TTTTTTATTTTTAAAAATATTTTTAAAATACT
53782934 TTTTTTAATTTTCTAAA
1 TTTTTT-ATTTT-TAAA
53782951 TTTTTTTTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
30 6 0.14
31 28 0.67
32 5 0.12
33 1 0.02
34 2 0.05
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (32 bp):
TTTTTTATTTTTAAAAATATTTTTAAAATACT
Found at i:53785896 original size:17 final size:17
Alignment explanation
Indices: 53785871--53785917 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
53785861 GCTTTATTTT
* *
53785871 TATTATATATATACGTA
1 TATTTTATATATACATA
*
53785888 TATTTTATAAATACATA
1 TATTTTATATATACATA
53785905 TATTTTA-ATATAC
1 TATTTTATATATAC
53785918 TTACATACCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 5 0.19
17 21 0.81
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (17 bp):
TATTTTATATATACATA
Found at i:53792791 original size:23 final size:23
Alignment explanation
Indices: 53792765--53792821 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
53792755 ATAAGTGCAA
53792765 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
53792788 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
53792811 CACTGTTATGT
1 CACTGATATGT
53792822 TACCACTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:53792835 original size:37 final size:37
Alignment explanation
Indices: 53792785--53792889 Score: 201
Period size: 37 Copynumber: 2.8 Consensus size: 37
53792775 TAGCCGAAGC
53792785 TACCACTGAAATGTAGCCGAAGCTACCACTGTTATGT
1 TACCACTGAAATGTAGCCGAAGCTACCACTGTTATGT
53792822 TACCACTGAAATGTAGCCGAAGCTACCACTGTTATGT
1 TACCACTGAAATGTAGCCGAAGCTACCACTGTTATGT
*
53792859 TACCACTGAAACGTAGCCGAAGCTACCACTG
1 TACCACTGAAATGTAGCCGAAGCTACCACTG
53792890 ATCAATAACA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (37 bp):
TACCACTGAAATGTAGCCGAAGCTACCACTGTTATGT
Found at i:53794406 original size:26 final size:25
Alignment explanation
Indices: 53794353--53794425 Score: 76
Period size: 26 Copynumber: 2.9 Consensus size: 25
53794343 GCACACCGCA
* * *
53794353 GCTCTT-ATGAGCGTCCAATTATATG
1 GCTCTTCATGAGCTTCCCATTA-AAG
53794378 GCTCTTCATGAGCTTCCCGATTAAAG
1 GCTCTTCATGAGCTTCCC-ATTAAAG
**
53794404 GCTCTTTGTGAGCTTCCCATTA
1 GCTCTTCATGAGCTTCCCATTA
53794426 GTGCTCGCTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
25 10 0.24
26 27 0.66
27 4 0.10
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (25 bp):
GCTCTTCATGAGCTTCCCATTAAAG
Found at i:53794513 original size:24 final size:24
Alignment explanation
Indices: 53794387--53794552 Score: 86
Period size: 24 Copynumber: 6.8 Consensus size: 24
53794377 GGCTCTTCAT
**
53794387 GAGCTTCCCGATTAAAGGCTCTTTG
1 GAGCTTCCC-ATTAATTGCTCTTTG
* *
53794412 TGAGCTTCCCATT-AGTGCTCGCTT-
1 -GAGCTTCCCATTAATTGCTC-TTTG
* * * * **
53794436 GAACTTCCCGTTATATGGCTATCCG
1 GAGCTTCCCATTA-ATTGCTCTTTG
* ** *
53794461 GTGCTTCCTGTTAATTGCTCTTCG
1 GAGCTTCCCATTAATTGCTCTTTG
* *
53794485 AAGCTACCCATTAATTGCTCTTTG
1 GAGCTTCCCATTAATTGCTCTTTG
* *
53794509 GAGCTTCCC-TTTATAGGCTCTTTG
1 GAGCTTCCCATTAAT-TGCTCTTTG
53794533 TGAGCTTCCCATTATATTGC
1 -GAGCTTCCCATTA-ATTGC
53794553 CTAGATAAGT
Statistics
Matches: 103, Mismatches: 29, Indels: 16
0.70 0.20 0.11
Matches are distributed among these distances:
23 14 0.14
24 46 0.45
25 28 0.27
26 13 0.13
27 2 0.02
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.38
Consensus pattern (24 bp):
GAGCTTCCCATTAATTGCTCTTTG
Found at i:53794541 original size:25 final size:24
Alignment explanation
Indices: 53794501--53794548 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
53794491 CCCATTAATT
*
53794501 GCTCTTTGGAGCTTCCCTTTATAG
1 GCTCTTTGGAGCTTCCCATTATAG
53794525 GCTCTTTGTGAGCTTCCCATTATA
1 GCTCTTTG-GAGCTTCCCATTATA
53794549 TTGCCTAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.42
Consensus pattern (24 bp):
GCTCTTTGGAGCTTCCCATTATAG
Found at i:53796022 original size:9 final size:9
Alignment explanation
Indices: 53796008--53796047 Score: 71
Period size: 9 Copynumber: 4.4 Consensus size: 9
53795998 GTTAAACGAA
53796008 TCGAGTTAT
1 TCGAGTTAT
53796017 TCGAGTTAT
1 TCGAGTTAT
*
53796026 TCGAGTTAA
1 TCGAGTTAT
53796035 TCGAGTTAT
1 TCGAGTTAT
53796044 TCGA
1 TCGA
53796048 ATCAACTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:53796118 original size:9 final size:9
Alignment explanation
Indices: 53796100--53796136 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
53796090 TGAGTTTTCG
53796100 AATTCGAAT
1 AATTCGAAT
*
53796109 AATTCAAAT
1 AATTCGAAT
53796118 AATTCGAAT
1 AATTCGAAT
53796127 AATTCGAAT
1 AATTCGAAT
53796136 A
1 A
53796137 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Done.