Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003547.1 Hibiscus syriacus cultivar Beakdansim tig00007479_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 114764
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:9099 original size:12 final size:12
Alignment explanation
Indices: 9082--9108 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
9072 CCTGGTGAGA
9082 ATGCAAATAAAT
1 ATGCAAATAAAT
9094 ATGCAAATAAAT
1 ATGCAAATAAAT
9106 ATG
1 ATG
9109 TTGACATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.07, G:0.11, T:0.26
Consensus pattern (12 bp):
ATGCAAATAAAT
Found at i:20421 original size:17 final size:17
Alignment explanation
Indices: 20396--20435 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
20386 GTGTGTTGTT
*
20396 CATTAAAGCATGTATTG
1 CATTTAAGCATGTATTG
*
20413 CATTTAAGCATGTATTT
1 CATTTAAGCATGTATTG
20430 CATTTA
1 CATTTA
20436 GGGAAGTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (17 bp):
CATTTAAGCATGTATTG
Found at i:22012 original size:27 final size:27
Alignment explanation
Indices: 21965--22022 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
21955 CGGGTTAGTA
21965 AAAAAAATAAAAAAATCAGAAAAAATCT
1 AAAAAAATAAAAAAA-CAGAAAAAATCT
* *
21993 AAAAAAATGAAATAAA-AGAAAAAATTT
1 AAAAAAAT-AAAAAAACAGAAAAAATCT
22020 AAA
1 AAA
22023 GAGGGCGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 13 0.48
28 8 0.30
29 6 0.22
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (27 bp):
AAAAAAATAAAAAAACAGAAAAAATCT
Found at i:26628 original size:14 final size:14
Alignment explanation
Indices: 26609--26637 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
26599 TGACTTGTCT
26609 AGAAATTACTTGAC
1 AGAAATTACTTGAC
26623 AGAAATTACTTGAC
1 AGAAATTACTTGAC
26637 A
1 A
26638 TGGGATGGGA
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:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (14 bp):
AGAAATTACTTGAC
Found at i:28358 original size:30 final size:30
Alignment explanation
Indices: 28322--28380 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
28312 ACAGAACAAA
28322 ACGGGGAACGAAATCCCATGCAGAATCAGG
1 ACGGGGAACGAAATCCCATGCAGAATCAGG
* *
28352 ACGGGGAATGAAGTCCCATGCAGAATCAG
1 ACGGGGAACGAAATCCCATGCAGAATCAG
28381 AAATGCATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.36, C:0.22, G:0.31, T:0.12
Consensus pattern (30 bp):
ACGGGGAACGAAATCCCATGCAGAATCAGG
Found at i:35611 original size:17 final size:17
Alignment explanation
Indices: 35580--35612 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
35570 TTATATATTA
35580 TTAAATATAAAAATAAT
1 TTAAATATAAAAATAAT
35597 TTAAA-ATAAATAATAA
1 TTAAATATAAA-AATAA
35613 AAAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAATATAAAAATAAT
Found at i:35647 original size:10 final size:10
Alignment explanation
Indices: 35632--35664 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
35622 TATTATTAAC
35632 AATTTAAAAT
1 AATTTAAAAT
35642 AATTTAAAAT
1 AATTTAAAAT
35652 AATTTAAAAT
1 AATTTAAAAT
35662 AAT
1 AAT
35665 CATTGTCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
AATTTAAAAT
Found at i:46113 original size:2 final size:2
Alignment explanation
Indices: 46106--46175 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
46096 ACATTCTTGC
46106 AT 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 AT
46148 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
46176 GTGTGTGTGT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50750 original size:34 final size:34
Alignment explanation
Indices: 50707--50772 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
50697 GTCATACTAA
50707 GATTCAAACTCCTAAAAATATGATAAAATTTTAG
1 GATTCAAACTCCTAAAAATATGATAAAATTTTAG
* *
50741 GATTCAAACTCCTAAAGATATGATAGAATTTT
1 GATTCAAACTCCTAAAAATATGATAAAATTTT
50773 GCTAGGATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (34 bp):
GATTCAAACTCCTAAAAATATGATAAAATTTTAG
Found at i:50827 original size:34 final size:34
Alignment explanation
Indices: 50707--50828 Score: 92
Period size: 34 Copynumber: 3.7 Consensus size: 34
50697 GTCATACTAA
* *
50707 GATTCAAACTCCTAAAAATATGATAAAATTTTAG
1 GATTCAAACTCCTAAAAATAGGATAAAATTTTAT
* * *
50741 GATTCAAACTCCTAAAGATATGATAGAA-TTT-T
1 GATTCAAACTCCTAAAAATAGGATAAAATTTTAT
* * * * *
50773 G-CT-AGGA-TTCAAAAAATAGGATATAATTTTAT
1 GATTCA-AACTCCTAAAAATAGGATAAAATTTTAT
* *
50805 GATTTAAACTCCTAAAGATAGGAT
1 GATTCAAACTCCTAAAAATAGGAT
50829 CCACAAGCAC
Statistics
Matches: 67, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
30 15 0.22
31 5 0.07
32 3 0.04
33 5 0.07
34 39 0.58
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (34 bp):
GATTCAAACTCCTAAAAATAGGATAAAATTTTAT
Found at i:51129 original size:24 final size:23
Alignment explanation
Indices: 51097--51164 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 23
51087 TTTCCTTTTT
51097 TTTTCATGTAATATTTTTTTTTAC
1 TTTT-ATGTAATATTTTTTTTTAC
51121 ATTTTATGT-AT-TTTCTTTTTTAC
1 -TTTTATGTAATATTT-TTTTTTAC
51144 -TTTA-GTATATATTTTTATTTT
1 TTTTATGTA-ATATTTTT-TTTT
51165 TTTTAGATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
20 2 0.05
21 4 0.11
22 7 0.18
23 17 0.45
24 4 0.11
25 4 0.11
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.69
Consensus pattern (23 bp):
TTTTATGTAATATTTTTTTTTAC
Found at i:51253 original size:9 final size:9
Alignment explanation
Indices: 51236--51365 Score: 50
Period size: 9 Copynumber: 13.4 Consensus size: 9
51226 TATATATATA
*
51236 TTTACTTTT
1 TTTATTTTT
51245 TTTA-TTTT
1 TTTATTTTT
51253 TTTATTTTAT
1 TTTATTTT-T
*
51263 ATATATATTATT
1 -T-T-TATTTTT
51275 TTTACTTTTTAT
1 TTTA--TTTT-T
*
51287 TATTATTTTA
1 T-TTATTTTT
*
51297 TTTATTTGT
1 TTTATTTTT
*
51306 TTTA-TTTC
1 TTTATTTTT
*
51314 TATATTTTT
1 TTTATTTTT
51323 TTCT-TCTTTT
1 TT-TAT-TTTT
*
51333 TCTTCTTTTT
1 T-TTATTTTT
51343 CTTTATTTTT
1 -TTTATTTTT
* *
51353 TATATTTAT
1 TTTATTTTT
51362 TTTA
1 TTTA
51366 CTTACTATTT
Statistics
Matches: 92, Mismatches: 14, Indels: 30
0.68 0.10 0.22
Matches are distributed among these distances:
8 13 0.14
9 34 0.37
10 21 0.23
11 12 0.13
12 4 0.04
13 8 0.09
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.75
Consensus pattern (9 bp):
TTTATTTTT
Found at i:51290 original size:32 final size:30
Alignment explanation
Indices: 51230--51290 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
51220 TATATATATA
*
51230 TATATATTTACTTTTTTTATTTTTTTATTT
1 TATATATATACTTTTTTTATTTTTTTATTT
51260 TATATATATA-TTATTTTTACTTTTTATTATT
1 TATATATATACTT-TTTTTA-TTTTT-TTATT
51291 ATTTTATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 2 0.07
30 15 0.56
31 5 0.19
32 5 0.19
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (30 bp):
TATATATATACTTTTTTTATTTTTTTATTT
Found at i:51471 original size:15 final size:15
Alignment explanation
Indices: 51453--51482 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
51443 TATTTATTTC
51453 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
51468 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
51483 ACATGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:54487 original size:8 final size:8
Alignment explanation
Indices: 54476--54556 Score: 56
Period size: 8 Copynumber: 9.8 Consensus size: 8
54466 CAAAAAGGGC
54476 AAAAAGAA
1 AAAAAGAA
54484 AAAAGAGAA
1 AAAA-AGAA
* *
54493 AAGAAGCA
1 AAAAAGAA
*
54501 AAAAAGCA
1 AAAAAGAA
*
54509 AAAAAGGA
1 AAAAAGAA
*
54517 AAAAACAA
1 AAAAAGAA
54525 GAACAAA-AA
1 -AA-AAAGAA
*
54534 AGAAAGAA
1 AAAAAGAA
*
54542 CAAAAATAA
1 -AAAAAGAA
54551 AAAAAG
1 AAAAAG
54557 GGAACAAAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
7 3 0.05
8 35 0.60
9 17 0.29
10 3 0.05
ACGTcount: A:0.78, C:0.06, G:0.15, T:0.01
Consensus pattern (8 bp):
AAAAAGAA
Found at i:54534 original size:13 final size:14
Alignment explanation
Indices: 54478--54547 Score: 54
Period size: 14 Copynumber: 4.9 Consensus size: 14
54468 AAAAGGGCAA
*
54478 AAAGAA-AAAAGAG
1 AAAGAACAAAAAAG
54491 AAAAGAAGCAAAAAAG
1 -AAAGAA-CAAAAAAG
* *
54507 CAAAAAAGGAAAAAA-
1 -AAAGAA-CAAAAAAG
*
54522 CAAGAACAAAAAAG
1 AAAGAACAAAAAAG
54536 AAAGAACAAAAA
1 AAAGAACAAAAA
54548 TAAAAAAAGG
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
13 6 0.13
14 21 0.47
16 18 0.40
ACGTcount: A:0.77, C:0.07, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAGAACAAAAAAG
Found at i:54538 original size:20 final size:21
Alignment explanation
Indices: 54475--54554 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 21
54465 ACAAAAAGGG
*
54475 CAAAAAGAAAAAAGAGAAAAGAA
1 CAAAAACAAAAAAG-GAAAA-AA
54498 GCAAAAAAGCAAAAAAGGAAAAAA
1 -C-AAAAA-CAAAAAAGGAAAAAA
* *
54522 CAAGAACAAAAAA-GAAAGAA
1 CAAAAACAAAAAAGGAAAAAA
*
54542 CAAAAATAAAAAA
1 CAAAAACAAAAAA
54555 AGGGAACAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
20 17 0.35
21 7 0.14
22 4 0.08
23 1 0.02
24 3 0.06
25 10 0.20
26 7 0.14
ACGTcount: A:0.78, C:0.07, G:0.14, T:0.01
Consensus pattern (21 bp):
CAAAAACAAAAAAGGAAAAAA
Found at i:55634 original size:18 final size:18
Alignment explanation
Indices: 55611--55646 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
55601 TCAACATCAA
* *
55611 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
55629 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
55647 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:56115 original size:36 final size:35
Alignment explanation
Indices: 56075--56372 Score: 191
Period size: 36 Copynumber: 8.5 Consensus size: 35
56065 ACTCATGATT
* * *
56075 GTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACC
1 GTTTCTCTTAAAACAA-ATTTGTCTCTCTTGAGACA
* * * **
56111 GTTT-TCACTAGAAGAGTTTTGTCTCTCTTGAGACA
1 GTTTCTC-TTAAAACAAATTTGTCTCTCTTGAGACA
* * *
56146 GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACA
1 GTTTCTCTTAAAACAAA-TTTGTCTCTCTTGAGACA
*
56182 GTTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACA
1 GTTTCTCTTAAAACAAATTT-GTCTCTCTTGAGACA
* * * * *
56218 GTTTCCCTTGAAACAAA-----ATAT-TTGA-ATA
1 GTTTCTCTTAAAACAAATTTGTCTCTCTTGAGACA
* *
56246 TGTTT-TCTTTGAAACAAATTTCGTCTCCCTTGAGACA
1 -GTTTCTC-TTAAAACAAATTT-GTCTCTCTTGAGACA
* ** *
56283 GTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAAC-AA-ATTTGTCTCTCTTGAGACA
* * *
56320 GTTTCTCTTGAAACAATTTTCGTCTATCTTGAGACA
1 GTTTCTCTTAAAACAAATTT-GTCTCTCTTGAGACA
* *
56356 GTTTCCCTTGAAACAAA
1 GTTTCTCTTAAAACAAA
56373 ATCTTTGAAT
Statistics
Matches: 209, Mismatches: 35, Indels: 36
0.75 0.12 0.13
Matches are distributed among these distances:
28 3 0.01
29 18 0.09
30 2 0.01
35 34 0.16
36 118 0.56
37 31 0.15
38 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (35 bp):
GTTTCTCTTAAAACAAATTTGTCTCTCTTGAGACA
Found at i:56319 original size:138 final size:137
Alignment explanation
Indices: 56131--56435 Score: 430
Period size: 138 Copynumber: 2.2 Consensus size: 137
56121 GAAGAGTTTT
*
56131 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCTCTTGAAAC
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCTCTTGAAAC
* * * ** *
56196 AAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCTTTGAAAC
66 AAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATATTTCCCCTAAAAC
56261 AAATTTC
131 AAATTTC
** * * *
56268 GTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
1 GTCTCCCTTGAGACAGTTTCCCTTGAAAC-AAATTTTATCTCTCTTGAGACAGTTTCTCTTGAAA
* * *
56333 CAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCTAAAA
65 CAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATATTTCCCCTAAAA
*
56398 CAAATTTT
130 CAAATTTC
* * *
56406 GTCTCCCTTGAGACAATTACTCTTGAAACA
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACA
56436 CAAAATCTTC
Statistics
Matches: 147, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
137 26 0.18
138 121 0.82
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.39
Consensus pattern (137 bp):
GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCTCTTGAAAC
AAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATATTTCCCCTAAAAC
AAATTTC
Found at i:56434 original size:65 final size:67
Alignment explanation
Indices: 56330--56487 Score: 196
Period size: 67 Copynumber: 2.4 Consensus size: 67
56320 GTTTCTCTTG
** * * **
56330 AAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATTTATTTCCC
1 AAACAAATTTT-GTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCCC
56392 CTA
65 CTA
* *
56395 AAACAAATTTTGTCTCCCTTGAGACAATTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCCCC
56460 TA
66 TA
*
56462 AAACATAATTTTGTTTCCCTTGAGAC
1 AAACA-AATTTTGTCTCCCTTGAGAC
56488 CGTTTCTCAT
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 24 0.30
66 8 0.10
67 29 0.36
68 19 0.24
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (67 bp):
AAACAAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCCCC
TA
Found at i:56464 original size:67 final size:65
Alignment explanation
Indices: 56321--56487 Score: 192
Period size: 65 Copynumber: 2.5 Consensus size: 65
56311 CTTGAGACAG
* * ** * * **
56321 TTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTT
1 TTTCCCTTAAAACAAATTTT-GTCTCCCTTGAGACAATTACCCTTGAAACAAAATCTTCAAATTT
56385 A
65 A
* *
56386 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAATTACTCTTGAAACACAAAATCTTCAAATT
1 TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAATTACCCTTG-AA-ACAAAATCTTCAAATT
56451 TA
64 TA
*
56453 TTTCCCTTAAAACATAATTTTGTTTCCCTTGAGAC
1 TTTCCCTTAAAACA-AATTTTGTCTCCCTTGAGAC
56488 CGTTTCTCAT
Statistics
Matches: 86, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
65 30 0.35
66 8 0.09
67 29 0.34
68 19 0.22
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (65 bp):
TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACAAAATCTTCAAATTTA
Found at i:57183 original size:109 final size:109
Alignment explanation
Indices: 56974--57272 Score: 378
Period size: 109 Copynumber: 2.8 Consensus size: 109
56964 TATCCACGAC
* * * *
56974 TTCAACTCCACGACAGAGGATATCGTGCTACCCGAGATAACACAAGTTCAACTTCACAACGAAGG
1 TTCAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCACAACGAAGG
* * * *
57039 GACGGCTGGTTGTCAACGAACAACTTTTCAGTTTCATCTGC-GAT
66 GACGGCTGGTTGTCAACAAACAACTTTTCAATTTCA-CAGCTAAT
* *
57083 TTTAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACACAAGATCAACTTCACAACGAAGG
1 TTCAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCACAACGAAGG
* *
57148 GACGGCTGGTTGTCAACAAAC-ATTTTTCAAATTTCAGAGCTAAT
66 GACGGCTGGTTGTCAACAAACAACTTTTC-AATTTCACAGCTAAT
* *
57192 TTCAACTTCGCA-G-CGAAGGATAT--TG-GACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 TTCAAC-TC-CACGACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCACAACGAA
*
57252 GGGACGGCTGATTGTCAACAA
64 GGGACGGCTGGTTGTCAACAA
57273 GATTTCGTTC
Statistics
Matches: 169, Mismatches: 17, Indels: 11
0.86 0.09 0.06
Matches are distributed among these distances:
106 53 0.31
107 2 0.01
108 8 0.05
109 101 0.60
110 3 0.02
111 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.22
Consensus pattern (109 bp):
TTCAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCACAACGAAGG
GACGGCTGGTTGTCAACAAACAACTTTTCAATTTCACAGCTAAT
Found at i:57267 original size:106 final size:104
Alignment explanation
Indices: 57006--57428 Score: 437
Period size: 106 Copynumber: 4.0 Consensus size: 104
56996 TCGTGCTACC
* * *
57006 CGAGATAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTTTCAGT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAAC-A-TTTTCAGT
** * * * * *
57071 TTCATCTGC-GATTTTAACTCCAC-GACGGAGGATATCGTGCCACT
64 TTCA-GAGCTAATTTCAACTTCACAG-CGAAGGATAT--TG-GACT
* * *
57115 CGAGACAACACAAGATCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACATTTTTCAAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACA-TTTTC-AGT
*
57180 TTCAGAGCTAATTTCAACTTCGCAGCGAAGGATATTGGACT
64 TTCAGAGCTAATTTCAACTTCACAGCGAAGGATATTGGACT
*
57221 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAAC-AAGA-TTTC-G-TT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACATTTTCAGTTT
* * *
57282 CAGAG-TCAATTTCATCTTCACAACGAAGGATATTAGACT
66 CAGAGCT-AATTTCAACTTCACAGCGAAGGATATTGGACT
* * * * * *
57321 CGAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCAGT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAAC-ATTT-TCAGT
* * * *
57386 TCCAGAACCAATTTCAACTTCACAGCGGAGGATATTGGACT
64 TTCAGAGCTAATTTCAACTTCACAGCGAAGGATATTGGACT
57427 CG
1 CG
57429 GAACAATATT
Statistics
Matches: 268, Mismatches: 35, Indels: 25
0.82 0.11 0.08
Matches are distributed among these distances:
99 1 0.00
100 80 0.30
101 2 0.01
102 1 0.00
103 6 0.02
104 1 0.00
105 4 0.01
106 86 0.32
107 2 0.01
108 8 0.03
109 76 0.28
110 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.23
Consensus pattern (104 bp):
CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACATTTTCAGTTT
CAGAGCTAATTTCAACTTCACAGCGAAGGATATTGGACT
Found at i:57401 original size:206 final size:212
Alignment explanation
Indices: 57006--57428 Score: 511
Period size: 206 Copynumber: 2.0 Consensus size: 212
56996 TCGTGCTACC
* *
57006 CGAGATAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTTTCAGT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACGAACAAC-TTTCAGT
* * * * *
57071 TTCATCTGCGATTTTAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACACAAGATCAACT
65 TTCAACTGCAATTTCAACTCCACAACGAAGGATATC-TG-CACTCGAGACAACACAAGATCAACT
** * * * * *
57136 TCACAACGAAGGGACGGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCTAATTTCAACTTC
128 TCACAACGAAGGGACGGCTGACTGTCAACAAACAATTTCCAAATTCCAGAACCAATTTCAACTTC
*
57201 GCAGCGAAGGATATTGGACT
193 ACAGCGAAGGATATTGGACT
*
57221 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAAC-AA-GA-TTTC-G-T
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACGAACAACTTTCAGTT
* * * * *
57281 TCAGAGT-CAATTTCATCTTCACAACGAAGGATAT-TAG-ACTCGAGACAGCACAAGCTCAACTT
66 TCA-ACTGCAATTTCAACTCCACAACGAAGGATATCT-GCACTCGAGACAACACAAGATCAACTT
* * * *
57343 CACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCAGTTCCAGAACCAATTTCAACTTCA
129 CACAACGAAGGGACGGCTGACTGTCAACAAACAATTTCCAAATTCCAGAACCAATTTCAACTTCA
*
57408 CAGCGGAGGATATTGGACT
194 CAGCGAAGGATATTGGACT
57427 CG
1 CG
57429 GAACAATATT
Statistics
Matches: 180, Mismatches: 26, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
206 96 0.53
207 1 0.01
208 1 0.01
209 25 0.14
210 2 0.01
211 4 0.02
213 1 0.01
214 2 0.01
215 48 0.27
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.23
Consensus pattern (212 bp):
CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACGAACAACTTTCAGTT
TCAACTGCAATTTCAACTCCACAACGAAGGATATCTGCACTCGAGACAACACAAGATCAACTTCA
CAACGAAGGGACGGCTGACTGTCAACAAACAATTTCCAAATTCCAGAACCAATTTCAACTTCACA
GCGAAGGATATTGGACT
Found at i:58286 original size:34 final size:34
Alignment explanation
Indices: 58243--58367 Score: 120
Period size: 34 Copynumber: 3.8 Consensus size: 34
58233 TTCGTCCTAC
58243 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
58277 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
*
58312 GCTAGGATTC--A-----AAAAATATGATAGAATTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
58341 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
58368 CCACAAGCAC
Statistics
Matches: 74, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
27 6 0.08
29 4 0.05
30 14 0.19
34 38 0.51
35 4 0.05
37 8 0.11
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.32
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:58665 original size:23 final size:22
Alignment explanation
Indices: 58634--58695 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
58624 CTTTTCTTTT
58634 TTTTCATGTAATATTTTTTTTAC
1 TTTT-ATGTAATATTTTTTTTAC
*
58657 ATTTTATGT-ATTTTCTTTTTTAC
1 -TTTTATGTAATATT-TTTTTTAC
58680 -TTTA-GTATATATTTTT
1 TTTTATGTA-ATATTTTT
58696 ATTTTTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
20 2 0.06
21 7 0.21
22 8 0.24
23 12 0.36
24 4 0.12
ACGTcount: A:0.21, C:0.06, G:0.05, T:0.68
Consensus pattern (22 bp):
TTTTATGTAATATTTTTTTTAC
Found at i:58692 original size:24 final size:23
Alignment explanation
Indices: 58649--58694 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
58639 ATGTAATATT
*
58649 TTTTTTACATTTTATGTATTTTC
1 TTTTTTACATTTTATATATTTTC
58672 TTTTTTAC-TTTAGTATATATTTT
1 TTTTTTACATTT--TATATATTTT
58695 TATTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 8 0.40
24 9 0.45
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTTTTACATTTTATATATTTTC
Found at i:58787 original size:9 final size:9
Alignment explanation
Indices: 58770--58891 Score: 50
Period size: 10 Copynumber: 12.4 Consensus size: 9
58760 TATATATATA
*
58770 TTTACTTTT
1 TTTATTTTT
58779 TTTA-TTTT
1 TTTATTTTT
58787 TTTATTATATAT
1 TTTATT-T-T-T
* *
58799 ATATATTATT
1 -TTTATTTTT
58809 TTTACTTTTT
1 TTTA-TTTTT
*
58819 TATTA-TTAT
1 T-TTATTTTT
58828 TTTATTTATT
1 TTTATTT-TT
*
58838 TCTTCTTTTT
1 T-TTATTTTT
58848 CTTTATTTTTT
1 -TTTA-TTTTT
*
58859 TCTTCTTTTT
1 T-TTATTTTT
58869 CTTTATTTTT
1 -TTTATTTTT
* *
58879 TATATTTAT
1 TTTATTTTT
58888 TTTA
1 TTTA
58892 CTTACTATTT
Statistics
Matches: 86, Mismatches: 13, Indels: 28
0.68 0.10 0.22
Matches are distributed among these distances:
8 11 0.13
9 24 0.28
10 26 0.30
11 19 0.22
12 1 0.01
13 5 0.06
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTATTTTT
Found at i:58796 original size:30 final size:30
Alignment explanation
Indices: 58762--58847 Score: 99
Period size: 30 Copynumber: 2.9 Consensus size: 30
58752 TTTATATATA
*
58762 TATATATATTTACTT-TTTTTATTTTTTTAT
1 TATATATATTTA-TTATTTTTACTTTTTTAT
*
58792 TATATATATATATTATTTTTACTTTTTTAT
1 TATATATATTTATTATTTTTACTTTTTTAT
58822 TAT-TAT-TTTATTTATTTCTT-CTTTTT
1 TATATATATTTA-TTATTT-TTACTTTTT
58848 CTTTATTTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
28 3 0.06
29 17 0.34
30 30 0.60
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (30 bp):
TATATATATTTATTATTTTTACTTTTTTAT
Found at i:58877 original size:21 final size:21
Alignment explanation
Indices: 58828--58879 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
58818 TTATTATTAT
*
58828 TTTATTTATTTCTTCTTTTTC
1 TTTATTTTTTTCTTCTTTTTC
58849 TTTATTTTTTTCTTCTTTTTC
1 TTTATTTTTTTCTTCTTTTTC
58870 TTTATTTTTT
1 TTTATTTTTT
58880 ATATTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTATTTTTTTCTTCTTTTTC
Found at i:58994 original size:15 final size:15
Alignment explanation
Indices: 58970--59007 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
58960 AATTTATTTA
*
58970 TTTATTTATTACCTT
1 TTTATCTATTACCTT
58985 TTTATCTATTACCTT
1 TTTATCTATTACCTT
59000 TTTATCTA
1 TTTATCTA
59008 ACATGGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.21, C:0.16, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTATCTATTACCTT
Found at i:64491 original size:29 final size:27
Alignment explanation
Indices: 64429--64502 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 27
64419 TATTTATTCC
64429 ATTTTTATTTTATTTATTTCCCCCTTTT
1 ATTTTTATTTT-TTTATTTCCCCCTTTT
*
64457 ACTTTTTATTTTTTTTTCTTCTTCCCC-TTT
1 A-TTTTTATTTTTTTAT-TTC--CCCCTTTT
*
64487 ATTTTATATTATTTTA
1 ATTTT-TATTTTTTTA
64503 CTTTTTATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
28 5 0.13
29 17 0.45
30 12 0.32
31 4 0.11
ACGTcount: A:0.15, C:0.16, G:0.00, T:0.69
Consensus pattern (27 bp):
ATTTTTATTTTTTTATTTCCCCCTTTT
Found at i:66465 original size:2 final size:2
Alignment explanation
Indices: 66458--66488 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
66448 TTCAACAATC
66458 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
66489 CACACGAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:66826 original size:15 final size:15
Alignment explanation
Indices: 66806--66836 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
66796 AATAAACCAT
66806 TATAAAGGGTATAGG
1 TATAAAGGGTATAGG
66821 TATAAAGGGTATAGG
1 TATAAAGGGTATAGG
66836 T
1 T
66837 TTGAGTCTCT
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:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (15 bp):
TATAAAGGGTATAGG
Found at i:71931 original size:12 final size:12
Alignment explanation
Indices: 71914--71938 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
71904 CTCAAACAGA
71914 GAGAATGAACGT
1 GAGAATGAACGT
71926 GAGAATGAACGT
1 GAGAATGAACGT
71938 G
1 G
71939 TTGCATGGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (12 bp):
GAGAATGAACGT
Found at i:72037 original size:33 final size:33
Alignment explanation
Indices: 71996--72079 Score: 134
Period size: 33 Copynumber: 2.5 Consensus size: 33
71986 GCGACCTACC
*
71996 CTCGCTCGGCTT-CCCTCGGATTCCCTCGCATAG
1 CTCGCTCGG-TTGCCCTCGGATGCCCTCGCATAG
72029 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
*
72062 CTCGCTCAGTTGCCCTCG
1 CTCGCTCGGTTGCCCTCG
72080 CATAGCTCGT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
32 2 0.04
33 46 0.96
ACGTcount: A:0.08, C:0.42, G:0.24, T:0.26
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
Found at i:72101 original size:23 final size:23
Alignment explanation
Indices: 72043--72102 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
72033 CTCGGTTGCC
72043 CTCGGATGCCCTCGCATAGCTCG
1 CTCGGATGCCCTCGCATAGCTCG
* *
72066 CTCAGTTGCCCTCGCATAGCTCG
1 CTCGGATGCCCTCGCATAGCTCG
* *
72089 TTCGGATGGCCTCG
1 CTCGGATGCCCTCG
72103 GTCGGATGGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.12, C:0.37, G:0.27, T:0.25
Consensus pattern (23 bp):
CTCGGATGCCCTCGCATAGCTCG
Found at i:72107 original size:14 final size:14
Alignment explanation
Indices: 72085--72199 Score: 70
Period size: 14 Copynumber: 7.4 Consensus size: 14
72075 CCTCGCATAG
*
72085 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
72099 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
*
72113 CTCGGATGCTCTCAGATGGC
1 CTC-G--G---TCGGATGGC
72133 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
*
72147 CTCGGATGCTCTCAGATGGC
1 CTC-G--G---TCGGATGGC
72167 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
*
72181 CTCAGTC-GATTGGC
1 CTCGGTCGGA-TGGC
72195 CTCGG
1 CTCGG
72200 ATGCCCAGCG
Statistics
Matches: 81, Mismatches: 7, Indels: 26
0.71 0.06 0.23
Matches are distributed among these distances:
13 2 0.02
14 49 0.60
15 2 0.02
17 4 0.05
19 2 0.02
20 22 0.27
ACGTcount: A:0.10, C:0.30, G:0.36, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:72117 original size:10 final size:11
Alignment explanation
Indices: 72090--72171 Score: 57
Period size: 10 Copynumber: 7.4 Consensus size: 11
72080 CATAGCTCGT
72090 TCGGATGGCCTC
1 TCGGATGG-CTC
72102 GGTCGGATGGC-C
1 --TCGGATGGCTC
72114 TCGGAT-GCTC
1 TCGGATGGCTC
*
72124 TCAGATGGCCTC
1 TCGGATGG-CTC
72136 GGTCGGATGGC-C
1 --TCGGATGGCTC
72148 TCGGAT-GCTC
1 TCGGATGGCTC
*
72158 TCAGATGGC-C
1 TCGGATGGCTC
72168 TCGG
1 TCGG
72172 TCGGATGGCC
Statistics
Matches: 57, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
9 4 0.07
10 28 0.49
11 3 0.05
12 5 0.09
13 2 0.04
14 15 0.26
ACGTcount: A:0.11, C:0.29, G:0.37, T:0.23
Consensus pattern (11 bp):
TCGGATGGCTC
Found at i:72131 original size:34 final size:34
Alignment explanation
Indices: 72093--72183 Score: 182
Period size: 34 Copynumber: 2.7 Consensus size: 34
72083 AGCTCGTTCG
72093 GATGGCCTCGGTCGGATGGCCTCGGATGCTCTCA
1 GATGGCCTCGGTCGGATGGCCTCGGATGCTCTCA
72127 GATGGCCTCGGTCGGATGGCCTCGGATGCTCTCA
1 GATGGCCTCGGTCGGATGGCCTCGGATGCTCTCA
72161 GATGGCCTCGGTCGGATGGCCTC
1 GATGGCCTCGGTCGGATGGCCTC
72184 AGTCGATTGG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 57 1.00
ACGTcount: A:0.11, C:0.30, G:0.36, T:0.23
Consensus pattern (34 bp):
GATGGCCTCGGTCGGATGGCCTCGGATGCTCTCA
Found at i:72132 original size:20 final size:20
Alignment explanation
Indices: 72107--72171 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
72097 GCCTCGGTCG
72107 GATGGCCTCGGATGCTCTCA
1 GATGGCCTCGGATGCTCTCA
*
72127 GATGGCCTC-G--G---TCG
1 GATGGCCTCGGATGCTCTCA
72141 GATGGCCTCGGATGCTCTCA
1 GATGGCCTCGGATGCTCTCA
72161 GATGGCCTCGG
1 GATGGCCTCGG
72172 TCGGATGGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
14 11 0.30
15 1 0.03
17 2 0.05
19 1 0.03
20 22 0.59
ACGTcount: A:0.12, C:0.29, G:0.35, T:0.23
Consensus pattern (20 bp):
GATGGCCTCGGATGCTCTCA
Found at i:76849 original size:2 final size:2
Alignment explanation
Indices: 76842--76873 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
76832 ACAAAAAGTA
76842 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
76874 TTACTCTCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:78240 original size:23 final size:21
Alignment explanation
Indices: 78203--78256 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
78193 TGGTTCAACC
*
78203 TAAATTTTTT-TTATTTTTTAT
1 TAAATTTTTTAGTA-TTTTTAT
78224 TAAATATTTTTAGTATTTTTAT
1 TAAAT-TTTTTAGTATTTTTAT
*
78246 TTAATTTTTTA
1 TAAATTTTTTA
78257 AATAATTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 11 0.38
22 16 0.55
23 2 0.07
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (21 bp):
TAAATTTTTTAGTATTTTTAT
Found at i:80424 original size:60 final size:60
Alignment explanation
Indices: 80352--80489 Score: 154
Period size: 61 Copynumber: 2.3 Consensus size: 60
80342 AACGTAATGA
* * *
80352 ATAGTCGGATGACCATTTCGTAACTTTTGATAGTCGA-AGGACTCAACAAAGCAACACTCT
1 ATAGTCGGATGACCATTTCGTAACTTTTAATAGTCGAGA-GACTCAACAAAACAACACCCT
* * * * * *
80412 ATAGTCGAATGACTATTTTTGTAATTTTTAATAGTCGAGAGACTTAACAAAATAACACCCT
1 ATAGTCGGATGACCA-TTTCGTAACTTTTAATAGTCGAGAGACTCAACAAAACAACACCCT
*
80473 ATAATCGGA-GACCATTT
1 ATAGTCGGATGACCATTT
80490 GTTTACTTTA
Statistics
Matches: 64, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
59 3 0.05
60 17 0.27
61 43 0.67
62 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (60 bp):
ATAGTCGGATGACCATTTCGTAACTTTTAATAGTCGAGAGACTCAACAAAACAACACCCT
Found at i:80777 original size:21 final size:21
Alignment explanation
Indices: 80753--80813 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
80743 ACTGTTATAG
**
80753 TACTAACGTGACAATTTACTC
1 TACTAACACGACAATTTACTC
*
80774 TACTAACACGACAATCTACTC
1 TACTAACACGACAATTTACTC
80795 TACTAACACGACAATTTAC
1 TACTAACACGACAATTTAC
80814 GATGTTGACG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.38, C:0.28, G:0.07, T:0.28
Consensus pattern (21 bp):
TACTAACACGACAATTTACTC
Found at i:80916 original size:21 final size:21
Alignment explanation
Indices: 80886--80944 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
80876 AATATAACAG
80886 ATGGAATGTCATGTCAATAAC
1 ATGGAATGTCATGTCAATAAC
* * * *
80907 ATGGATTGTCACGTAAATACC
1 ATGGAATGTCATGTCAATAAC
* * *
80928 GTGGACTGTCATATCAA
1 ATGGAATGTCATGTCAA
80945 CACCGTAACG
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (21 bp):
ATGGAATGTCATGTCAATAAC
Found at i:82124 original size:5 final size:5
Alignment explanation
Indices: 82104--82241 Score: 91
Period size: 5 Copynumber: 28.8 Consensus size: 5
82094 TCCGGGACTT
* * * **
82104 TTAT- TTATA TTTATA TTATA -TATA GTATA TTTTA -TATA GTATA TGGTA
1 TTATA TTATA -TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
82152 TTATA -TAGTA TT-TA -TATA TTATA TTATA TTATA TTATA TTATATA
1 TTATA TTA-TA TTATA TTATA TTATA TTATA TTATA TTATA -T-TATA
* *
82197 TTAGTA TTAT- TT-TA TTAT- TTAT- TTATA TTACA TTAT- TAATA TTAT
1 TTA-TA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTAT
82242 TTTTGGTTTT
Statistics
Matches: 107, Mismatches: 12, Indels: 29
0.72 0.08 0.20
Matches are distributed among these distances:
3 2 0.02
4 32 0.30
5 56 0.52
6 13 0.12
7 4 0.04
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.59
Consensus pattern (5 bp):
TTATA
Found at i:82127 original size:2 final size:2
Alignment explanation
Indices: 82109--82197 Score: 50
Period size: 2 Copynumber: 46.5 Consensus size: 2
82099 GACTTTTATT
* * *
82109 TA TA TT TA TA T- TA TA TA TA GTA TA T- TT TA TA TA GTA TA TGG
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA T-A
*
82150 TA T- TA TA TA GTA TT TA TA TA T- TA TA T- TA TA T- TA TA T- TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
82188 TA T- TA TA TA T
1 TA TA TA TA TA T
82198 TAGTATTATT
Statistics
Matches: 68, Mismatches: 7, Indels: 24
0.69 0.07 0.24
Matches are distributed among these distances:
1 8 0.12
2 53 0.78
3 7 0.10
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (2 bp):
TA
Found at i:82155 original size:33 final size:34
Alignment explanation
Indices: 82116--82211 Score: 95
Period size: 38 Copynumber: 2.7 Consensus size: 34
82106 ATTTATATTT
82116 ATATTATATA-TAGTATATTTTATATAGTATATG
1 ATATTATATAGTAGTATATTTTATATAGTATATG
* * * *
82149 GTATTATATAGTATTTATATATTATATTATATTATATT
1 ATATTATATAGTA-GTATAT-TT-TA-TATAGTATATG
*
82187 ATATTATATATTAGTATTATTTTAT
1 ATATTATATAGTAGTA-TATTTTAT
82212 TATTTATTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
33 9 0.18
34 2 0.04
35 6 0.12
36 4 0.08
37 6 0.12
38 23 0.46
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (34 bp):
ATATTATATAGTAGTATATTTTATATAGTATATG
Found at i:82175 original size:7 final size:7
Alignment explanation
Indices: 82105--82241 Score: 63
Period size: 7 Copynumber: 18.9 Consensus size: 7
82095 CCGGGACTTT
82105 TATT-TA
1 TATTATA
82111 TATT-TA
1 TATTATA
82117 TATTATA
1 TATTATA
82124 TATAGTATA
1 TAT--TATA
*
82133 TTTTATA
1 TATTATA
*
82140 TAGTATATGG
1 TA-T-TAT-A
82150 TATTATA
1 TATTATA
* *
82157 TAGTATT
1 TATTATA
82164 TATATATTA
1 TAT-TA-TA
82173 TATTATA
1 TATTATA
82180 T-TATATTA
1 TAT-TA-TA
82188 TATTATA
1 TATTATA
82195 TATTAGTA
1 TATTA-TA
82203 TTATT-T-
1 -TATTATA
*
82209 TATTATT
1 TATTATA
82216 TATT-TA
1 TATTATA
*
82222 TATTACA
1 TATTATA
82229 TTATTA-A
1 -TATTATA
82236 TATTAT
1 TATTAT
82242 TTTTGGTTTT
Statistics
Matches: 103, Mismatches: 10, Indels: 35
0.70 0.07 0.24
Matches are distributed among these distances:
5 4 0.04
6 22 0.21
7 36 0.35
8 20 0.19
9 19 0.18
10 2 0.02
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.58
Consensus pattern (7 bp):
TATTATA
Found at i:83313 original size:23 final size:21
Alignment explanation
Indices: 83287--83339 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 21
83277 CATTTTATCC
83287 TATTTTCCCTTGAATACTTATTT
1 TATTTTCCC-T-AATACTTATTT
*
83310 TATTTTTTCCCTAATATTTATTT
1 TA--TTTTCCCTAATACTTATTT
83333 TATTTTC
1 TATTTTC
83340 TATAGAATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 5 0.19
23 14 0.52
24 1 0.04
25 7 0.26
ACGTcount: A:0.21, C:0.15, G:0.02, T:0.62
Consensus pattern (21 bp):
TATTTTCCCTAATACTTATTT
Found at i:91226 original size:10 final size:11
Alignment explanation
Indices: 91203--91264 Score: 74
Period size: 11 Copynumber: 5.7 Consensus size: 11
91193 TCTGTTAGAG
91203 TGTTATTAGTT
1 TGTTATTAGTT
*
91214 TGTTA-TGGTT
1 TGTTATTAGTT
*
91224 TGTTATTAGCT
1 TGTTATTAGTT
91235 TGTTATTAGTT
1 TGTTATTAGTT
*
91246 TGTTA-TGGTT
1 TGTTATTAGTT
91256 TGTTGATTA
1 TGTT-ATTA
91265 CTTGGGCTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
10 17 0.40
11 24 0.57
12 1 0.02
ACGTcount: A:0.16, C:0.02, G:0.23, T:0.60
Consensus pattern (11 bp):
TGTTATTAGTT
Found at i:91228 original size:21 final size:22
Alignment explanation
Indices: 91203--91264 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
91193 TCTGTTAGAG
*
91203 TGTTATTAGTTTGTTA-TGGTT
1 TGTTATTAGTTTGTTATTAGTT
*
91224 TGTTATTAGCTTGTTATTAGTT
1 TGTTATTAGTTTGTTATTAGTT
*
91246 TGTTA-TGGTTTGTTGATTA
1 TGTTATTAGTTTGTT-ATTA
91265 CTTGGGCTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 22 0.63
22 13 0.37
ACGTcount: A:0.16, C:0.02, G:0.23, T:0.60
Consensus pattern (22 bp):
TGTTATTAGTTTGTTATTAGTT
Found at i:91239 original size:32 final size:32
Alignment explanation
Indices: 91203--91268 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
91193 TCTGTTAGAG
91203 TGTTATTAGTTTGTTATGGTTTGTT-ATTAGCT
1 TGTTATTAGTTTGTTATGGTTTGTTGATTA-CT
91235 TGTTATTAGTTTGTTATGGTTTGTTGATTACT
1 TGTTATTAGTTTGTTATGGTTTGTTGATTACT
91267 TG
1 TG
91269 GGCTATATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 29 0.88
33 4 0.12
ACGTcount: A:0.15, C:0.03, G:0.23, T:0.59
Consensus pattern (32 bp):
TGTTATTAGTTTGTTATGGTTTGTTGATTACT
Found at i:93043 original size:14 final size:14
Alignment explanation
Indices: 93024--93052 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
93014 TGTTAGAGTG
93024 TTATTAGTTTGTTA
1 TTATTAGTTTGTTA
93038 TTATTAGTTTGTTA
1 TTATTAGTTTGTTA
93052 T
1 T
93053 GATTTGTTGG
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:0.21, C:0.00, G:0.14, T:0.66
Consensus pattern (14 bp):
TTATTAGTTTGTTA
Found at i:95418 original size:13 final size:13
Alignment explanation
Indices: 95400--95425 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
95390 CACAGTTGAT
95400 GTCCAGATTGAAA
1 GTCCAGATTGAAA
95413 GTCCAGATTGAAA
1 GTCCAGATTGAAA
95426 TCACAAGTAT
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:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
GTCCAGATTGAAA
Found at i:96663 original size:23 final size:25
Alignment explanation
Indices: 96610--96668 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
96600 AGCTCGAATC
96610 GAACTCGAAATCAAAAATTGAAGTTT
1 GAACTCGAAATCAAAAA-TGAAGTTT
*
96636 G-ACTCGATATCAAAAA-GAAG-TT
1 GAACTCGAAATCAAAAATGAAGTTT
*
96658 GAACTCAAAAT
1 GAACTCGAAAT
96669 ATTCTCAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 3 0.10
23 11 0.38
25 14 0.48
26 1 0.03
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.24
Consensus pattern (25 bp):
GAACTCGAAATCAAAAATGAAGTTT
Found at i:99750 original size:22 final size:24
Alignment explanation
Indices: 99721--99767 Score: 73
Period size: 21 Copynumber: 2.1 Consensus size: 24
99711 TGATCAAATT
99721 TTTTAAAAAAT-T-AATAT-TTAA
1 TTTTAAAAAATATAAATATATTAA
99742 TTTTAAAAAATATAAATATATTAA
1 TTTTAAAAAATATAAATATATTAA
99766 TT
1 TT
99768 CGAATCGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 11 0.48
22 1 0.04
23 5 0.22
24 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TTTTAAAAAATATAAATATATTAA
Found at i:101581 original size:24 final size:24
Alignment explanation
Indices: 101554--101606 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
101544 TAATTTAAAA
101554 TCTTATATCATTATATCTTCAAAT
1 TCTTATATCATTATATCTTCAAAT
101578 TCTTATATCATTATATCTTCAAAT
1 TCTTATATCATTATATCTTCAAAT
101602 TCTTA
1 TCTTA
101607 AATTTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.32, C:0.17, G:0.00, T:0.51
Consensus pattern (24 bp):
TCTTATATCATTATATCTTCAAAT
Found at i:109043 original size:23 final size:23
Alignment explanation
Indices: 109017--109060 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
109007 AAACAAATAT
109017 GTTCATAAACATTAAATAAACAC
1 GTTCATAAACATTAAATAAACAC
* *
109040 GTTCGTAAATATTAAATAAAC
1 GTTCATAAACATTAAATAAAC
109061 GAATAAGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.30
Consensus pattern (23 bp):
GTTCATAAACATTAAATAAACAC
Done.