Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012913.1 Kokia drynarioides strain JFW-HI SEQ_127929, 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: 213083
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 81 characters in sequence are not A, C, G, or T
Found at i:591 original size:17 final size:16
Alignment explanation
Indices: 563--598 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
553 TTATTATAAA
563 TTATTATTAATATCAT
1 TTATTATTAATATCAT
*
579 TTATTAGTTAATATTAT
1 TTATTA-TTAATATCAT
596 TTA
1 TTA
599 AAATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (16 bp):
TTATTATTAATATCAT
Found at i:1347 original size:17 final size:17
Alignment explanation
Indices: 1320--1373 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
1310 TTTTAATTTT
*
1320 ATTTTAATTTAAAATAA
1 ATTTAAATTTAAAATAA
* *
1337 GTTTGAATTTAAAATAA
1 ATTTAAATTTAAAATAA
*
1354 ATTTAAATTTAAAGTAA
1 ATTTAAATTTAAAATAA
1371 ATT
1 ATT
1374 CAAACTTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:10036 original size:101 final size:101
Alignment explanation
Indices: 9915--10097 Score: 276
Period size: 101 Copynumber: 1.8 Consensus size: 101
9905 ATAAAACGAG
* * * * *
9915 CTGTATTTTTACATATTCATAAATTAATTCGTACTTATTTTATCTTATAATTTTAAGCATTCCGT
1 CTGTACTTTTACATATTCATAAATTAATCCGCACTCATTTGATCTTATAATTTTAAGCATTCCGT
*
9980 TATCCTTTTATTTAAAAGAAAACATCACAAAAGGAA
66 TATCCTTTCATTTAAAAGAAAACATCACAAAAGGAA
* ** *
10016 CTGTACTTTTACATATTCATAAATTAGTCCGCACTCATTTGATCTTATAATTTTAAGTGTTCTGT
1 CTGTACTTTTACATATTCATAAATTAATCCGCACTCATTTGATCTTATAATTTTAAGCATTCCGT
10081 TATCCTTTCATTTAAAA
66 TATCCTTTCATTTAAAA
10098 AGATTTAAGA
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 72 1.00
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (101 bp):
CTGTACTTTTACATATTCATAAATTAATCCGCACTCATTTGATCTTATAATTTTAAGCATTCCGT
TATCCTTTCATTTAAAAGAAAACATCACAAAAGGAA
Found at i:10644 original size:22 final size:22
Alignment explanation
Indices: 10607--10648 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
10597 CAGTTTAATA
10607 AAATTTATAAAAATTTTATTTTT
1 AAATTTATAAAAA-TTTATTTTT
*
10630 AAATTT-TAAATATTTATTT
1 AAATTTATAAAAATTTATTT
10649 AATTATTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 5 0.28
23 6 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
AAATTTATAAAAATTTATTTTT
Found at i:11061 original size:6 final size:6
Alignment explanation
Indices: 11050--11077 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
11040 CAGCTAACTC
11050 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
11078 TCAGCTGATT
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:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTCT
Found at i:17414 original size:29 final size:29
Alignment explanation
Indices: 17340--17420 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 29
17330 TAAATATCAT
*
17340 ATTTATACATAAATTTTAATTTAATGTGTA
1 ATTTATACATAAATTTTAATTTAA-GTATA
*
17370 ATTTAATACATTAATTTTAATTTAA-TATA
1 ATTT-ATACATAAATTTTAATTTAAGTATA
*
17399 ATTATATACATAAATTTGAATT
1 ATT-TATACATAAATTTTAATT
17421 ATAGTTGTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
29 21 0.47
30 5 0.11
31 19 0.42
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (29 bp):
ATTTATACATAAATTTTAATTTAAGTATA
Found at i:20097 original size:34 final size:34
Alignment explanation
Indices: 20054--20125 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 34
20044 CAAAATGATT
20054 TCCTTCTCTCATTTAGATGTATTTTACCATTGTA
1 TCCTTCTCTCATTTAGATGTATTTTACCATTGTA
*
20088 TCCTTCTCTCATTTAGATGTATTTTACCATTGTT
1 TCCTTCTCTCATTTAGATGTATTTTACCATTGTA
20122 TCCT
1 TCCT
20126 CCAGGTCAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.18, C:0.22, G:0.08, T:0.51
Consensus pattern (34 bp):
TCCTTCTCTCATTTAGATGTATTTTACCATTGTA
Found at i:24849 original size:12 final size:12
Alignment explanation
Indices: 24834--24858 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24824 ATAAAATAAA
24834 ATAAATAAATCC
1 ATAAATAAATCC
24846 ATAAATAAATCC
1 ATAAATAAATCC
24858 A
1 A
24859 ATTGTAATTA
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:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAAATAAATCC
Found at i:26167 original size:10 final size:10
Alignment explanation
Indices: 26152--26176 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
26142 TTTAATCAAC
26152 AAAAAAAGAA
1 AAAAAAAGAA
26162 AAAAAAAGAA
1 AAAAAAAGAA
26172 AAAAA
1 AAAAA
26177 CAGTGATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:26291 original size:27 final size:27
Alignment explanation
Indices: 26261--26341 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 27
26251 ACCAAATAAT
*
26261 AAATTTTTCTCTACATTTAATGCCTTA
1 AAATTTTTCTCTACATTTAATACCTTA
*
26288 AAATTTTTC-CATACATTTAATATCTTA
1 AAATTTTTCTC-TACATTTAATACCTTA
** * *
26315 ATGTCTTTTCTCTTCATTTAATCCCTT
1 AAAT-TTTTCTCTACATTTAATACCTT
26342 TTTTTGTATA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
26 1 0.02
27 25 0.57
28 17 0.39
29 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.02, T:0.51
Consensus pattern (27 bp):
AAATTTTTCTCTACATTTAATACCTTA
Found at i:31130 original size:36 final size:36
Alignment explanation
Indices: 31078--31148 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
31068 TGGAACAGCC
* * *
31078 CCTAAATTGCTTCCTTCAATTCCTCCATTGTTCCCT
1 CCTAAATTGCTCCCTTCAATTCCGCCATTCTTCCCT
31114 CCTAAATTGCTCCCTTCAATTCCGCCATTCTTCCC
1 CCTAAATTGCTCCCTTCAATTCCGCCATTCTTCCC
31149 ACCAAAATGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.17, C:0.39, G:0.06, T:0.38
Consensus pattern (36 bp):
CCTAAATTGCTCCCTTCAATTCCGCCATTCTTCCCT
Found at i:32388 original size:15 final size:15
Alignment explanation
Indices: 32368--32419 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
32358 TTTTATCAGA
32368 TTTTTTAATTAATAT
1 TTTTTTAATTAATAT
* *
32383 TTTTTTCATT-TTAT
1 TTTTTTAATTAATAT
* *
32397 TTTTGTGATTAATAT
1 TTTTTTAATTAATAT
32412 TATTTTTA
1 T-TTTTTA
32420 TCTTTTGATT
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
14 11 0.39
15 13 0.46
16 4 0.14
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (15 bp):
TTTTTTAATTAATAT
Found at i:37405 original size:20 final size:18
Alignment explanation
Indices: 37366--37401 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
37356 CCACCAAAAA
37366 TAAAATATATATTTAAAT
1 TAAAATATATATTTAAAT
*
37384 TAAATTATATATTTAAAT
1 TAAAATATATATTTAAAT
37402 ATTATATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAAATATATATTTAAAT
Found at i:42053 original size:2 final size:2
Alignment explanation
Indices: 42046--42075 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
42036 AATTCGATTG
42046 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
42076 GTTATTGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47334 original size:28 final size:30
Alignment explanation
Indices: 47293--47373 Score: 107
Period size: 28 Copynumber: 2.8 Consensus size: 30
47283 CATAATAACG
*
47293 TAAAAG-A-AAAAAAAAAGAAAGAAAATGA
1 TAAAAGAATAAAAAAAAAGAAAGAAAATAA
* *
47321 T-AAAGAAT-TAAAAAAGGAAAGAAAATAA
1 TAAAAGAATAAAAAAAAAGAAAGAAAATAA
47349 TAAAAGAATAAAAAAAAAGAAAGAA
1 TAAAAGAATAAAAAAAAAGAAAGAA
47374 CGAAAGACAA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
27 4 0.09
28 20 0.45
29 7 0.16
30 13 0.30
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.10
Consensus pattern (30 bp):
TAAAAGAATAAAAAAAAAGAAAGAAAATAA
Found at i:49071 original size:170 final size:168
Alignment explanation
Indices: 48762--49274 Score: 563
Period size: 170 Copynumber: 3.1 Consensus size: 168
48752 TGCGGATTCT
* *
48762 CCACAGCTCGTGTGAGCATATATGGTTACATGTTACAATTACAGCTCGTATGAGCATTACAGGTT
1 CCACAGCTCGTGTGAGCATATATGGTTACATGTTA-TATTACAGCTCGTGTGAGCATTACAGGTT
* * * ** * *
48827 ATATGAGTGCTAGTCTTGGATGTCTTATTGATGGCTGAGGTTTTGCATTAGTTGCAGATTCTTCA
65 ATATGGGTGCTAGTCTTAGATGTC-TATCGATGGCTGAGGTCCTGCATTAGTTGCGGATTCTCCA
* *
48892 CAGCTCGTGTGAGCAGCATCGTGTAGCCTAACATCTCGAC
129 CAACTCGTGTGAGCAGCATCGTGTAACCTAACATCTCGAC
48932 CCACAGCTCGTGTGAGCATATATGGTTACATGTTATAGTTACAGCTCGTGTGAGCATTACAGGTT
1 CCACAGCTCGTGTGAGCATATATGGTTACATGTTATA-TTACAGCTCGTGTGAGCATTACAGGTT
* *
48997 ATATGGGTGCTAGTCTTAGATGTACTATCGATGGTTGAGGTCCTGCATTGGTTGCGGATTCTCCA
65 ATATGGGTGCTAGTCTTAGATGT-CTATCGATGGCTGAGGTCCTGCATTAGTTGCGGATTCTCCA
* * *
49062 CATCTCGTGTGAGTAGCATCGCGTAACCTAACATCTCGAC
129 CAACTCGTGTGAGCAGCATCGTGTAACCTAACATCTCGAC
** * * *
49102 CCACAGCTCGTGTGAGC----A-GG-CCCA---T-T-TCACAGCTCGTGTGAGCATTACATGTTT
1 CCACAGCTCGTGTGAGCATATATGGTTACATGTTATATTACAGCTCGTGTGAGCATTACAGGTTA
* * *
49156 TAT-GGTGTTGGTCTTAGATGTCCTA-CTGATGGCTGAGGTCC-GACATTTA-TTACGG-TTCCT
66 TATGGGTGCTAGTCTTAGATGT-CTATC-GATGGCTGAGGTCCTG-CA-TTAGTTGCGGATT-CT
* * ** *
49216 CCACAACTCATGTGAGCAGCATCGTGTATCCCCACATCTCAAC
126 CCACAACTCGTGTGAGCAGCATCGTGTAACCTAACATCTCGAC
*
49259 CCACAGCTTGTGTGAG
1 CCACAGCTCGTGTGAG
49275 TAGACCCATT
Statistics
Matches: 302, Mismatches: 35, Indels: 25
0.83 0.10 0.07
Matches are distributed among these distances:
156 4 0.01
157 91 0.30
158 30 0.10
160 1 0.00
161 1 0.00
164 2 0.01
165 2 0.01
166 1 0.00
169 1 0.00
170 168 0.56
171 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31
Consensus pattern (168 bp):
CCACAGCTCGTGTGAGCATATATGGTTACATGTTATATTACAGCTCGTGTGAGCATTACAGGTTA
TATGGGTGCTAGTCTTAGATGTCTATCGATGGCTGAGGTCCTGCATTAGTTGCGGATTCTCCACA
ACTCGTGTGAGCAGCATCGTGTAACCTAACATCTCGAC
Found at i:49261 original size:157 final size:158
Alignment explanation
Indices: 48972--49303 Score: 429
Period size: 157 Copynumber: 2.1 Consensus size: 158
48962 TGTTATAGTT
*
48972 ACAGCTCGTGTGAGCATTACAGGTTATATGGGTGCTAGTCTTAGATGTACTATCGATGGTTGAGG
1 ACAGCTCGTGTGAGCATTACAGGTTATATGGGTGCTAGTCTTAGATGTACTATCGATGGCTGAGG
* * * * * * *
49037 TCCTGCATTGGTTGCGGATTCTCCACATCTCGTGTGAGTAGCATCGCGTAACCTAACATCTCGAC
66 TCCTGCATTGATTACGGATTCTCCACAACTCATGTGAGCAGCATCGCGTAACCCAACATCTCAAC
*
49102 CCACAGCTCGTGTGAGCAGGCCCATTTC
131 CCACAGCTCGTGTGAGCAGACCCATTTC
* * * * *
49130 ACAGCTCGTGTGAGCATTACATGTTTTAT-GGTGTTGGTCTTAGATGTCCTA-CTGATGGCTGAG
1 ACAGCTCGTGTGAGCATTACAGGTTATATGGGTGCTAGTCTTAGATGTACTATC-GATGGCTGAG
* * * *
49193 GTCC-GACATTTATTACGG-TTCCTCCACAACTCATGTGAGCAGCATCGTGTATCCCCACATCTC
65 GTCCTG-CATTGATTACGGATT-CTCCACAACTCATGTGAGCAGCATCGCGTAACCCAACATCTC
* *
49256 AACCCACAGCTTGTGTGAGTAGACCCATTTC
128 AACCCACAGCTCGTGTGAGCAGACCCATTTC
49287 ACAGCTCGTGTGAGCAT
1 ACAGCTCGTGTGAGCAT
49304 ATATGGTTAC
Statistics
Matches: 151, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
156 4 0.03
157 120 0.79
158 27 0.18
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.30
Consensus pattern (158 bp):
ACAGCTCGTGTGAGCATTACAGGTTATATGGGTGCTAGTCTTAGATGTACTATCGATGGCTGAGG
TCCTGCATTGATTACGGATTCTCCACAACTCATGTGAGCAGCATCGCGTAACCCAACATCTCAAC
CCACAGCTCGTGTGAGCAGACCCATTTC
Found at i:51256 original size:45 final size:45
Alignment explanation
Indices: 51203--51324 Score: 133
Period size: 45 Copynumber: 2.7 Consensus size: 45
51193 TCAACATCAC
*
51203 CCTG-ACCCTCAACACC-CTCAACACCTTC-ACTAACAACACCCTTA
1 CCTGAACCCTCACCACCTCTC-ACACCTTCAAC-AACAACACCCTTA
* * **
51247 CCTGAACCCTCACCACCTCTCTCACCTTCAACACCCTCACCCTTA
1 CCTGAACCCTCACCACCTCTCACACCTTCAACAACAACACCCTTA
* * *
51292 CCCGAACCCTCACCACCTCCCTCACCTTCAACA
1 CCTGAACCCTCACCACCTCTCACACCTTCAACA
51325 CCCTTAACAC
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
44 4 0.06
45 59 0.87
46 5 0.07
ACGTcount: A:0.26, C:0.52, G:0.02, T:0.19
Consensus pattern (45 bp):
CCTGAACCCTCACCACCTCTCACACCTTCAACAACAACACCCTTA
Found at i:51282 original size:27 final size:27
Alignment explanation
Indices: 51252--51389 Score: 75
Period size: 27 Copynumber: 5.4 Consensus size: 27
51242 CCTTACCTGA
51252 ACCCTCACCACCTCTCTCACCTTCAAC
1 ACCCTCACCACCTCTCTCACCTTCAAC
*
51279 ACCCT---CACC-CT-T-ACC--CGA-
1 ACCCTCACCACCTCTCTCACCTTCAAC
*
51297 ACCCTCACCACCTCCCTCACCTTCAAC
1 ACCCTCACCACCTCTCTCACCTTCAAC
* * * *
51324 ACCCTTAACACC-CTCATC-CTTACTCGA-
1 ACCCTCACCACCTCTC-TCACCT--TCAAC
* * *
51351 ACCCTTACCACCTCCCTCATCTTCAAC
1 ACCCTCACCACCTCTCTCACCTTCAAC
*
51378 ACCCTCAACACC
1 ACCCTCACCACC
51390 CTTATCCTTA
Statistics
Matches: 81, Mismatches: 15, Indels: 30
0.64 0.12 0.24
Matches are distributed among these distances:
18 5 0.06
19 2 0.02
21 7 0.09
22 2 0.02
23 3 0.04
24 7 0.09
26 9 0.11
27 40 0.49
28 6 0.07
ACGTcount: A:0.24, C:0.54, G:0.01, T:0.21
Consensus pattern (27 bp):
ACCCTCACCACCTCTCTCACCTTCAAC
Found at i:51318 original size:54 final size:54
Alignment explanation
Indices: 51269--51425 Score: 217
Period size: 54 Copynumber: 2.9 Consensus size: 54
51259 CCACCTCTCT
*
51269 CACCTTCAACACCCTCACCCTTACCCGAACCCTCACCACCTCCCTCACCTTCAA
1 CACCTTCAACACCCTCATCCTTACCCGAACCCTCACCACCTCCCTCACCTTCAA
* * *
51323 CACCCTT-AACACCCTCATCCTTACTCGAACCCTTACCACCTCCCTCATCTTCAA
1 CA-CCTTCAACACCCTCATCCTTACCCGAACCCTCACCACCTCCCTCACCTTCAA
* * ** *
51377 CACCCTCAACACCCTTATCCTTACCCTCACCCTCACTACCTCCCTCACC
1 CACCTTCAACACCCTCATCCTTACCCGAACCCTCACCACCTCCCTCACC
51426 CTCATCCTCA
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
53 3 0.03
54 82 0.92
55 4 0.04
ACGTcount: A:0.23, C:0.54, G:0.01, T:0.22
Consensus pattern (54 bp):
CACCTTCAACACCCTCATCCTTACCCGAACCCTCACCACCTCCCTCACCTTCAA
Found at i:51325 original size:45 final size:45
Alignment explanation
Indices: 51239--51384 Score: 166
Period size: 45 Copynumber: 3.0 Consensus size: 45
51229 TCACTAACAA
* *
51239 CACCCTTACCTGAACCCTCACCACCTCTCTCACCTTCAACACCCT
1 CACCCTTACCCGAACCCTCACCACCTCCCTCACCTTCAACACCCT
51284 CACCCTTACCCGAACCCTCACCACCTCCCTCACCTTCAACACCCTT
1 CACCCTTACCCGAACCCTCACCACCTCCCTCACCTTCAACACCC-T
* * *
51330 AACACCCTCATCCTTACTCGAACCCTTACCACCTCCCTCATCTTCAACACCCT
1 --CA----C--CCTTACCCGAACCCTCACCACCTCCCTCACCTTCAACACCCT
51383 CA
1 CA
51385 ACACCCTTAT
Statistics
Matches: 87, Mismatches: 5, Indels: 12
0.84 0.05 0.12
Matches are distributed among these distances:
45 42 0.48
46 1 0.01
48 2 0.02
51 2 0.02
52 1 0.01
53 1 0.01
54 38 0.44
ACGTcount: A:0.23, C:0.53, G:0.02, T:0.22
Consensus pattern (45 bp):
CACCCTTACCCGAACCCTCACCACCTCCCTCACCTTCAACACCCT
Found at i:52566 original size:21 final size:20
Alignment explanation
Indices: 52520--52591 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 20
52510 AATAAATTCA
52520 TTAATAATAATAATAATAATA-
1 TTAATAATAA-AAT-ATAATAT
*
52541 ATAATAATAAAATA-AATGAGT
1 TTAATAATAAAATATAAT-A-T
52562 TTAATAAT-AAATATAATAT
1 TTAATAATAAAATATAATAT
52581 TTAA-AATAAAA
1 TTAATAATAAAA
52592 AAAAAGTTGA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
18 6 0.14
19 10 0.23
20 9 0.20
21 19 0.43
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (20 bp):
TTAATAATAAAATATAATAT
Found at i:52571 original size:3 final size:3
Alignment explanation
Indices: 52521--52555 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
52511 ATAAATTCAT
52521 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
52556 ATGAGTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:53023 original size:58 final size:58
Alignment explanation
Indices: 52951--53183 Score: 218
Period size: 58 Copynumber: 4.1 Consensus size: 58
52941 TTTCGACGGT
52951 AAAATCCCATTTTTAACCCAAAAACTTCCAAAAATTCTGTTTTTACCCTCGAACTTCCA
1 AAAATCCCATTTTTAACCC-AAAACTTCCAAAAATTCTGTTTTTACCCTCGAACTTCCA
* * * *
53010 AACATTCCA-TTTTAACCCCGAAACTTCCAAAAATTTTGTTTTTACCCTCGAACTTCCA
1 AAAATCCCATTTTTAA-CCCAAAACTTCCAAAAATTCTGTTTTTACCCTCGAACTTCCA
* * *
53068 AAAATCCCATTTTTGACCTCAAAACTTCC----A-T-T-TTTAT-CCC-CAAACTTCCA
1 AAAATCCCATTTTTAACC-CAAAACTTCCAAAAATTCTGTTTTTACCCTCGAACTTCCA
* ** * * *
53118 AAAATGCCATTTTTGCCCCGAAACTTTCAAAAATTCCAT-TTTTTGCCCTCGAACTTCCA
1 AAAATCCCATTTTTAACCCAAAACTTCCAAAAATT-C-TGTTTTTACCCTCGAACTTCCA
*
53177 AATATCC
1 AAAATCC
53184 ATTATCGACC
Statistics
Matches: 143, Mismatches: 18, Indels: 26
0.76 0.10 0.14
Matches are distributed among these distances:
49 8 0.06
50 25 0.17
51 3 0.02
52 4 0.03
53 2 0.01
54 2 0.01
55 1 0.01
57 5 0.03
58 55 0.38
59 38 0.27
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.33
Consensus pattern (58 bp):
AAAATCCCATTTTTAACCCAAAACTTCCAAAAATTCTGTTTTTACCCTCGAACTTCCA
Found at i:53080 original size:29 final size:29
Alignment explanation
Indices: 52973--53186 Score: 164
Period size: 29 Copynumber: 7.7 Consensus size: 29
52963 TTAACCCAAA
**
52973 AACTTCCAAAAATTCTGTTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* *
53002 AACTTCCAAACATTCCATTTTAACCC-CG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
***
53030 AAACTTCCAAAAATTTTGTTTTTACCCTCG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
*
53060 AACTTCCAAAAATCCCA-TTTT----T-G
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* * *
53083 -ACCT-CAAAACTTCCATTTTTATCCC-CA
1 AACTTCCAAAAATTCCATTTTTA-CCCTCG
* *
53110 AACTTCCAAAAATGCCATTTTTGCCC-CG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* *
53138 AAACTTTCAAAAATTCCATTTTTTGCCCTCG
1 -AACTTCCAAAAATTCCA-TTTTTACCCTCG
*
53169 AACTTCCAAATA-TCCATT
1 AACTTCCAAAAATTCCATT
53187 ATCGACCTCG
Statistics
Matches: 145, Mismatches: 26, Indels: 29
0.73 0.13 0.14
Matches are distributed among these distances:
21 9 0.06
22 7 0.05
23 1 0.01
24 1 0.01
28 15 0.10
29 89 0.61
30 21 0.14
31 2 0.01
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:53111 original size:21 final size:21
Alignment explanation
Indices: 53065--53117 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
53055 CCTCGAACTT
* *
53065 CCAAAAATCCCATTTTTGACC
1 CCAAAACTTCCATTTTTGACC
*
53086 TCAAAACTTCCATTTTT-ATCC
1 CCAAAACTTCCATTTTTGA-CC
53107 CC-AAACTTCCA
1 CCAAAACTTCCA
53118 AAAATGCCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.32, C:0.34, G:0.02, T:0.32
Consensus pattern (21 bp):
CCAAAACTTCCATTTTTGACC
Found at i:53149 original size:79 final size:80
Alignment explanation
Indices: 53009--53160 Score: 193
Period size: 79 Copynumber: 1.9 Consensus size: 80
52999 TCGAACTTCC
****
53009 AAACATTCCATTTTAACCCCGAAACTTCCAAAAATTTTGTTTTTACCCTCGAACTTCCAAAAATC
1 AAACATTCCATTTTAACCCCGAAACTTCCAAAAATGCCATTTTTACCCTCGAACTTCCAAAAATC
53074 CCATTTTTGACCTCA
66 CCATTTTTGACCTCA
* * *
53089 AAAC-TTCCATTTTTATCCCC-AAACTTCCAAAAATGCCATTTTTGCCC-CGAAACTTTCAAAAA
1 AAACATTCCA-TTTTAACCCCGAAACTTCCAAAAATGCCATTTTTACCCTCG-AACTTCCAAAAA
*
53151 TTCCATTTTT
64 TCCCATTTTT
53161 TGCCCTCGAA
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.76
80 13 0.21
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (80 bp):
AAACATTCCATTTTAACCCCGAAACTTCCAAAAATGCCATTTTTACCCTCGAACTTCCAAAAATC
CCATTTTTGACCTCA
Found at i:53186 original size:108 final size:108
Alignment explanation
Indices: 53002--53201 Score: 269
Period size: 108 Copynumber: 1.9 Consensus size: 108
52992 TTTACCCTCG
* * *
53002 AACTTCCAAACATTCCATTTTAACCCCGAAACTTCCAAAAATTTTGTTTTTACCCTCGAACTTCC
1 AACTTCCAAAAATGCCATTTTAACCCCGAAACTTCCAAAAATTATGTTTTTACCCTCGAACTTCC
* *
53067 AAAAATCCCATTTTTGACCTCAAAACTTCCATTTTTATCCCCA
66 AAAAATCCCATTATCGACCTCAAAACTTCCATTTTTATCCCCA
** * *
53110 AACTTCCAAAAATGCCATTTTTGCCCCGAAACTTTCAAAAATTCCAT-TTTTTGCCCTCGAACTT
1 AACTTCCAAAAATGCCATTTTAACCCCGAAACTTCCAAAAATT--ATGTTTTTACCCTCGAACTT
* *
53174 CCAAATAT-CCATTATCGACCTCGAAACT
64 CCAAAAATCCCATTATCGACCTCAAAACT
53202 CTCAAAATTA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
108 55 0.70
109 23 0.29
110 1 0.01
ACGTcount: A:0.32, C:0.30, G:0.06, T:0.33
Consensus pattern (108 bp):
AACTTCCAAAAATGCCATTTTAACCCCGAAACTTCCAAAAATTATGTTTTTACCCTCGAACTTCC
AAAAATCCCATTATCGACCTCAAAACTTCCATTTTTATCCCCA
Found at i:53199 original size:59 final size:58
Alignment explanation
Indices: 53085--53208 Score: 144
Period size: 59 Copynumber: 2.1 Consensus size: 58
53075 CATTTTTGAC
* * *
53085 CTCAAAACTTCCATTTTTATCCCCAAACTTCCAAAAATGCCATTTTTGCCCCGAAACT
1 CTCAAAAATTCCATTTTTATCCCCAAACTTCCAAAAATGCCATTATCGCCCCGAAACT
* * * *
53143 TTCAAAAATTCCATTTTT-TGCCCTCGAACTTCCAAATAT-CCATTATCGACCTCGAAACT
1 CTCAAAAATTCCATTTTTAT-CCC-CAAACTTCCAAAAATGCCATTATCG-CCCCGAAACT
53202 CTCAAAA
1 CTCAAAA
53209 TTACCCTTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
57 1 0.02
58 26 0.47
59 28 0.51
ACGTcount: A:0.32, C:0.31, G:0.06, T:0.31
Consensus pattern (58 bp):
CTCAAAAATTCCATTTTTATCCCCAAACTTCCAAAAATGCCATTATCGCCCCGAAACT
Found at i:64645 original size:196 final size:195
Alignment explanation
Indices: 64371--64725 Score: 595
Period size: 196 Copynumber: 1.8 Consensus size: 195
64361 ATGAGATACG
* * *
64371 GAGAAGCAGGCCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGATCAAATTC
1 GAGAAGCAGGCCGAAGCAATAAAAGGTTAGCTTCCTAATGAGATACTGAGAAGTGAACCAAATTC
* *
64436 ATCTTCCTGATGAGATACAAAGAAGC-GAATTGAAACAAGCGATGTGGTCATCTTCCTGATGAGA
66 ATCTTCCTGATGAGATACAAAGAAGCAG-ATTGAAACAAGCGATGCGGTCATCTTCCTAATGAGA
64500 TACTGAGAAGAAGACCAAATCAAACCCACGTTCGATCTTTGAACTCCAGCTTCTTGATGCGACAC
130 TACTGAGAAGAAGACCAAATCAAACCCACGTTCGATCTTTGAACTCCAGCTTCTTGATGCGACAC
64565 T
195 T
* *
64566 GAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCCTAATGAGATACTGAGAAGTGAACCAAATT
1 GAGAAGCAGGCCGAAGCAATAAAA-GGTTAGCTTCCTAATGAGATACTGAGAAGTGAACCAAATT
* * *
64631 CGTCTTCTTGATGAGATACAGAGAAGCAGATTGAAACAAGCGATGCGGTCATCTTCCTAATGAGA
65 CATCTTCCTGATGAGATACAAAGAAGCAGATTGAAACAAGCGATGCGGTCATCTTCCTAATGAGA
64696 TACTGAGAAGAAGACCAAATCAAACCCACG
130 TACTGAGAAGAAGACCAAATCAAACCCACG
64726 CTCAAAGCGA
Statistics
Matches: 148, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
195 22 0.15
196 125 0.84
197 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (195 bp):
GAGAAGCAGGCCGAAGCAATAAAAGGTTAGCTTCCTAATGAGATACTGAGAAGTGAACCAAATTC
ATCTTCCTGATGAGATACAAAGAAGCAGATTGAAACAAGCGATGCGGTCATCTTCCTAATGAGAT
ACTGAGAAGAAGACCAAATCAAACCCACGTTCGATCTTTGAACTCCAGCTTCTTGATGCGACACT
Found at i:64939 original size:207 final size:206
Alignment explanation
Indices: 64268--64912 Score: 508
Period size: 196 Copynumber: 3.2 Consensus size: 206
64258 GACCATCCAC
* * * * *
64268 AAAC-AGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACC----CAAAC-GAGGCTC
1 AAACAAGCGAT-CGGTCATCTTCCTAATAAGATACTAAGAAGAAGACCAAATCAAACAAACGCTC
* * * * * * * *
64327 AAAGCGAGCAAAATCTTCGAACCTCAACTTC-CTGATGAGATACGGAGAAGCAGGCCGAAGCAAT
65 AAAGCGAACAAAATCTTTGAACCCCAGCTTCTC-GATGAGACACTGAGAAGCAGGTCGAAGTAAT
* ** * * * ** * *
64391 AAAA-GGTTAGCTTCCTGATGAGATACTGAGAAGTGGATCAAATTCATCTTCCTGATGAGATACA
129 AAAACGATTAGCTTCCCAATGAAATACTGAGAAGTGAACCAAAACCATCTTCCTGATGAAACACA
* **
64455 AAGAAGC-GAATTG
194 GAGAAGCAG-ATCA
* * * *
64468 AAACAAGCGATGTGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAAT----CAAAC-C-C
1 AAACAAGCGAT-CGGTCATCTTCCTAATAAGATACTAAGAAGAAGACCAAATCAAACAAACGCTC
** * * * *
64527 --A-CGTTC--GATCTTTGAACTCCAGCTTCTTGATGCGACACTGAGAAGCAGGTCGAAGTAATA
65 AAAGCGAACAAAATCTTTGAACCCCAGCTTCTCGATGAGACACTGAGAAGCAGGTCGAAGTAATA
* * * * ** * * * *
64587 AAATGGTTAGCTTCCTAATGAGATACTGAGAAGTGAACCAAATTCGTCTTCTTGATGAGATACAG
130 AAACGATTAGCTTCCCAATGAAATACTGAGAAGTGAACCAAAACCATCTTCCTGATGAAACACAG
**
64652 AGAAGCAGATTG
195 AGAAGCAGATCA
* * **
64664 AAACAAGCGATGCGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
1 AAACAAGCGAT-CGGTCATCTTCCTAATAAGATACTAAGAAGAAGACCAAATCAAACAAACGCTC
** *
64729 AAAGCGAACAAAATCTTTGAACCCCAGCTTCTCGATGAGATTCTGAGAAGTAGGTCGAAGTAATA
65 AAAGCGAACAAAATCTTTGAACCCCAGCTTCTCGATGAGACACTGAGAAGCAGGTCGAAGTAATA
* * *
64794 AAACGATTAGCTTCCCGATGAAATA-TGGGGAAGTGAACCAAAACCATCTTCCTGATGAAACATA
130 AAACGATTAGCTTCCCAATGAAATACT-GAGAAGTGAACCAAAACCATCTTCCTGATGAAACACA
*
64858 GAGAAGTAGATCA
194 GAGAAGCAGATCA
* * * *
64871 AAACAAG-TAT-GGTCGTCTTCTTGATAAGATACTAAGAAGAAG
1 AAACAAGCGATCGGTCATCTTCCTAATAAGATACTAAGAAGAAG
64913 GCTAAGTCAA
Statistics
Matches: 367, Mismatches: 57, Indels: 38
0.79 0.12 0.08
Matches are distributed among these distances:
195 45 0.12
196 115 0.31
197 4 0.01
198 1 0.00
200 8 0.02
201 45 0.12
202 2 0.01
204 28 0.08
205 3 0.01
206 3 0.01
207 113 0.31
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (206 bp):
AAACAAGCGATCGGTCATCTTCCTAATAAGATACTAAGAAGAAGACCAAATCAAACAAACGCTCA
AAGCGAACAAAATCTTTGAACCCCAGCTTCTCGATGAGACACTGAGAAGCAGGTCGAAGTAATAA
AACGATTAGCTTCCCAATGAAATACTGAGAAGTGAACCAAAACCATCTTCCTGATGAAACACAGA
GAAGCAGATCA
Found at i:67189 original size:30 final size:29
Alignment explanation
Indices: 67121--67513 Score: 296
Period size: 29 Copynumber: 13.7 Consensus size: 29
67111 GGTCCCTAAC
* *
67121 CTTCCAAAAATTCCGTTTTTACCCCCGAA
1 CTTCCAAAAATTCCATTTTTACCCTCGAA
* * *
67150 CTTTCAAAAATCCCATTTTTAACCTCGAAA
1 CTTCCAAAAATTCCATTTTTACCCTCG-AA
* *
67180 CTTCTAAAAATTCTATTTTTACCCTCGAA
1 CTTCCAAAAATTCCATTTTTACCCTCGAA
*
67209 CTTCCAAAAATTCCATTTTTAACCTCGAAA
1 CTTCCAAAAATTCCATTTTTACCCTCG-AA
* *
67239 CTTTCAAAAATTCTATTTTTACCCTCGAA
1 CTTCCAAAAATTCCATTTTTACCCTCGAA
*
67268 CTTCCAAAAATTCCATTTTCAACCC-CGAAA
1 CTTCCAAAAATTCCATTTT-TACCCTCG-AA
* *
67298 CTTCCAAAAATTCAAATTTTACCCTCGAA
1 CTTCCAAAAATTCCATTTTTACCCTCGAA
** *
67327 CTTTAAAAAATCCCA--TTT----T-G-A
1 CTTCCAAAAATTCCATTTTTACCCTCGAA
* * * *
67348 C-CCCAAAACTTCCATTTTTACCCCCAAA
1 CTTCCAAAAATTCCATTTTTACCCTCGAA
* * *
67376 CTTCCAACAATGCCATTTTTAACCC-CAAAA
1 CTTCCAAAAATTCCATTTTT-ACCCTC-GAA
* *
67406 CTTCCAAAAATTTCATTTTTGCCCTCGAA
1 CTTCCAAAAATTCCATTTTTACCCTCGAA
*
67435 CTTCC-AAAATCTCCATTTTCGA-CCTCGAAA
1 CTTCCAAAAAT-TCCATTTT-TACCCTCG-AA
* * * *
67465 C-TCCCAAAATTACC-CTTTTGCCCCCGAA
1 CTTCCAAAAATT-CCATTTTTACCCTCGAA
*
67493 -TATCTAAAAATTCCATTTTTA
1 CT-TCCAAAAATTCCATTTTTA
67514 AACCCCAAAT
Statistics
Matches: 285, Mismatches: 53, Indels: 52
0.73 0.14 0.13
Matches are distributed among these distances:
20 8 0.03
21 2 0.01
22 4 0.01
23 1 0.00
27 3 0.01
28 11 0.04
29 146 0.51
30 110 0.39
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (29 bp):
CTTCCAAAAATTCCATTTTTACCCTCGAA
Found at i:67218 original size:59 final size:59
Alignment explanation
Indices: 67121--67473 Score: 361
Period size: 59 Copynumber: 6.2 Consensus size: 59
67111 GGTCCCTAAC
** * *
67121 CTTCCAAAAATTCCGTTTTTACCCCCGAACTTTCAAAAATCCCATTTTTAACCTCGAAA
1 CTTCCAAAAATTCTATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCTCGAAA
* *
67180 CTTCTAAAAATTCTATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCTCGAAA
1 CTTCCAAAAATTCTATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCTCGAAA
* * * *
67239 CTTTCAAAAATTCTATTTTTACCCTCGAACTTCCAAAAATTCCATTTTCAACCCCGAAA
1 CTTCCAAAAATTCTATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCTCGAAA
* * **
67298 CTTCCAAAAATTCAAATTTTACCCTCGAACTTTAAAAAATCCCA--TTT----T-G--A
1 CTTCCAAAAATTCTATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCTCGAAA
* * * * * * * * *
67348 C-CCCAAAACTTCCATTTTTACCCCCAAACTTCCAACAATGCCATTTTTAACCCCAAAA
1 CTTCCAAAAATTCTATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCTCGAAA
* **
67406 CTTCCAAAAATT-TCATTTTTGCCCTCGAACTTCC-AAAATCTCCATTTTCGACCTCGAAA
1 CTTCCAAAAATTCT-ATTTTTACCCTCGAACTTCCAAAAATC-CCATTTTTAACCTCGAAA
*
67465 CTCCCAAAA
1 CTTCCAAAA
67474 TTACCCTTTT
Statistics
Matches: 239, Mismatches: 43, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
49 32 0.13
50 2 0.01
51 3 0.01
52 1 0.00
57 2 0.01
58 6 0.03
59 193 0.81
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (59 bp):
CTTCCAAAAATTCTATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCTCGAAA
Found at i:67366 original size:21 final size:20
Alignment explanation
Indices: 67339--67381 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
67329 TTAAAAAATC
*
67339 CCATTTTGACCCCAAAACTT
1 CCATTTTTACCCCAAAACTT
*
67359 CCATTTTTACCCCCAAACTT
1 CCATTTTTACCCCAAAACTT
67379 CCA
1 CCA
67382 ACAATGCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.28, C:0.40, G:0.02, T:0.30
Consensus pattern (20 bp):
CCATTTTTACCCCAAAACTT
Found at i:67378 original size:49 final size:50
Alignment explanation
Indices: 67314--67411 Score: 126
Period size: 49 Copynumber: 2.0 Consensus size: 50
67304 AAAATTCAAA
* * * *
67314 TTTTACCCTCGAACTTTAAAAAATCCCA-TTTTGACCCCAAAACTTCCAT
1 TTTTACCCCCAAACTTCAAAAAATCCCATTTTTAACCCCAAAACTTCCAT
* * *
67363 TTTTACCCCCAAACTTCCAACAATGCCATTTTTAACCCCAAAACTTCCA
1 TTTTACCCCCAAACTTCAAAAAATCCCATTTTTAACCCCAAAACTTCCA
67412 AAAATTTCAT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
49 22 0.54
50 19 0.46
ACGTcount: A:0.33, C:0.34, G:0.03, T:0.31
Consensus pattern (50 bp):
TTTTACCCCCAAACTTCAAAAAATCCCATTTTTAACCCCAAAACTTCCAT
Found at i:67432 original size:108 final size:108
Alignment explanation
Indices: 67243--67437 Score: 284
Period size: 108 Copynumber: 1.8 Consensus size: 108
67233 TCGAAACTTT
* * * * *
67243 CAAAAATTCTATTTTTACCCTCGAACTTCCAAAAATTCCATTTTCAACCCCGAAACTTCCAAAAA
1 CAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATGCCATTTTCAACCCCAAAACTTCCAAAAA
67308 TTCAAATTTTACCCTCGAACTTTAAAAAATCCCATTTTGACCC
66 TTCAAATTTTACCCTCGAACTTTAAAAAATCCCATTTTGACCC
* * *
67351 CAAAACTTCCATTTTTACCCCCAAACTTCCAACAATGCCATTTTTAACCCCAAAACTTCCAAAAA
1 CAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATGCCATTTTCAACCCCAAAACTTCCAAAAA
* *
67416 TTTC-ATTTTTGCCCTCGAACTT
66 -TTCAAATTTTACCCTCGAACTT
67438 CCAAAATCTC
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
108 73 0.96
109 3 0.04
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (108 bp):
CAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATGCCATTTTCAACCCCAAAACTTCCAAAAA
TTCAAATTTTACCCTCGAACTTTAAAAAATCCCATTTTGACCC
Found at i:67460 original size:29 final size:29
Alignment explanation
Indices: 67350--67475 Score: 94
Period size: 30 Copynumber: 4.3 Consensus size: 29
67340 CATTTTGACC
* * *
67350 CCAAAACTTCCATTTT-TACCCCCAAACTT
1 CCAAAA-TTCCATTTTCGACCTCGAAACTT
* ** * *
67379 CCAACAATGCCATTTTTAACCCCAAAACTT
1 CCAA-AATTCCATTTTCGACCTCGAAACTT
* * *
67409 CCAAAAATTTCATTTTTGCCCTCG-AACTT
1 CC-AAAATTCCATTTTCGACCTCGAAACTT
*
67438 CCAAAATCTCCATTTTCGACCTCGAAACTC
1 CCAAAAT-TCCATTTTCGACCTCGAAACTT
67468 CCAAAATT
1 CCAAAATT
67476 ACCCTTTTGC
Statistics
Matches: 79, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
28 5 0.06
29 33 0.42
30 39 0.49
31 2 0.03
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.30
Consensus pattern (29 bp):
CCAAAATTCCATTTTCGACCTCGAAACTT
Found at i:68666 original size:21 final size:21
Alignment explanation
Indices: 68640--68680 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
68630 CAGTTTAAAA
68640 AATATAAAGACAAAAAACATC
1 AATATAAAGACAAAAAACATC
** *
68661 AATATACTGACAAACAACAT
1 AATATAAAGACAAAAAACAT
68681 GCAGCCAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.61, C:0.17, G:0.05, T:0.17
Consensus pattern (21 bp):
AATATAAAGACAAAAAACATC
Found at i:69427 original size:12 final size:12
Alignment explanation
Indices: 69363--69428 Score: 50
Period size: 12 Copynumber: 5.6 Consensus size: 12
69353 AAATTATGAA
*
69363 ACATACACTTAC
1 ACATACATTTAC
69375 ACATACATTT--
1 ACATACATTTAC
*
69385 TC-TACATTTAC
1 ACATACATTTAC
*
69396 ACATTA-ATTATGAA
1 ACA-TACATT-T-AC
69410 ACATACATTTAC
1 ACATACATTTAC
69422 ACATACA
1 ACATACA
69429 AACTAAGTCT
Statistics
Matches: 42, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
9 7 0.17
10 1 0.02
11 1 0.02
12 20 0.48
13 6 0.14
14 7 0.17
ACGTcount: A:0.42, C:0.23, G:0.02, T:0.33
Consensus pattern (12 bp):
ACATACATTTAC
Found at i:74938 original size:20 final size:19
Alignment explanation
Indices: 74910--74980 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
74900 ACAAAAATTA
*
74910 AAAAATTCAAAATAATTTT
1 AAAATTTCAAAATAATTTT
74929 CAAAATTTCAAAAT-ATTTT
1 -AAAATTTCAAAATAATTTT
*
74948 TAAATTTCAAAAT-ATTTAT
1 AAAATTTCAAAATAATTT-T
*
74967 AAGAAATTCAAAAT
1 AA-AATTTCAAAAT
74981 TTATATTTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
18 16 0.36
19 7 0.16
20 22 0.49
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.38
Consensus pattern (19 bp):
AAAATTTCAAAATAATTTT
Found at i:74954 original size:18 final size:19
Alignment explanation
Indices: 74910--74964 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 19
74900 ACAAAAATTA
*
74910 AAAAATTCAAAATAATTTTC
1 AAAATTTCAAAAT-ATTTTC
74930 AAAATTTCAAAATATTTT-
1 AAAATTTCAAAATATTTTC
*
74948 TAAATTTCAAAATATTT
1 AAAATTTCAAAATATTT
74965 ATAAGAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
18 16 0.48
19 5 0.15
20 12 0.36
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATTTCAAAATATTTTC
Found at i:78454 original size:22 final size:21
Alignment explanation
Indices: 78429--78471 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
78419 TGTTGACCTC
78429 TTTTTCTT-TTCAATTTGTTAGA
1 TTTTT-TTATTCAA-TTGTTAGA
78451 TTTTTTTAATTCAATTGTTAG
1 TTTTTTT-ATTCAATTGTTAG
78472 TTTAAAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 2 0.11
22 12 0.63
23 5 0.26
ACGTcount: A:0.21, C:0.07, G:0.09, T:0.63
Consensus pattern (21 bp):
TTTTTTTATTCAATTGTTAGA
Found at i:78830 original size:18 final size:17
Alignment explanation
Indices: 78793--78826 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
78783 AATTACTAAA
78793 AATCATTAAAAAGAAAT
1 AATCATTAAAAAGAAAT
*
78810 AATCATTTAAAA-AAAT
1 AATCATTAAAAAGAAAT
78826 A
1 A
78827 TAATTCCGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (17 bp):
AATCATTAAAAAGAAAT
Found at i:101432 original size:16 final size:17
Alignment explanation
Indices: 101411--101444 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
101401 TTTAGTTGAG
101411 AAAATT-ATTTAATTAA
1 AAAATTAATTTAATTAA
*
101427 AAAATTAATTTATTTAA
1 AAAATTAATTTAATTAA
101444 A
1 A
101445 TTAATTGAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAATTAATTTAATTAA
Found at i:108155 original size:15 final size:16
Alignment explanation
Indices: 108124--108156 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
108114 CCAAAATCGT
*
108124 TTAATTTTTTTTATAA
1 TTAATTTTTTATATAA
108140 TTAATTTTTTAT-TAA
1 TTAATTTTTTATATAA
108155 TT
1 TT
108157 TATTATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTAATTTTTTATATAA
Found at i:111589 original size:15 final size:15
Alignment explanation
Indices: 111569--111599 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
111559 TACATAAGTA
111569 TTATTATATATTATT
1 TTATTATATATTATT
111584 TTATTATATATTATT
1 TTATTATATATTATT
111599 T
1 T
111600 ATATCAAAAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTATTATATATTATT
Found at i:114545 original size:6 final size:6
Alignment explanation
Indices: 114534--114574 Score: 64
Period size: 6 Copynumber: 6.5 Consensus size: 6
114524 AAGGAGATCA
114534 GTTAGG GTTAGG GTTAGG GTTAGG GTTAGG GCATTAGG GTT
1 GTTAGG GTTAGG GTTAGG GTTAGG GTTAGG G--TTAGG GTT
114575 TTTATATATG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 27 0.82
8 6 0.18
ACGTcount: A:0.17, C:0.02, G:0.46, T:0.34
Consensus pattern (6 bp):
GTTAGG
Found at i:117414 original size:28 final size:28
Alignment explanation
Indices: 117383--117451 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
117373 TCCCGATGTG
* * *
117383 ACACACATTAAGCGTTGAATCAAATCTA
1 ACACGCATTAAGCGCTGAATCAAATATA
**
117411 ACACGCATTAAATGCTGAATCAAATATA
1 ACACGCATTAAGCGCTGAATCAAATATA
*
117439 ACATGCATTAAGC
1 ACACGCATTAAGC
117452 ATTGGATCTC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (28 bp):
ACACGCATTAAGCGCTGAATCAAATATA
Found at i:118653 original size:19 final size:18
Alignment explanation
Indices: 118613--118664 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
118603 AGATTGAGAT
* * *
118613 AAAACAAAAATATGATAA
1 AAAAAAAAAACATGAAAA
118631 AAAAAAAAAACATGAAAA
1 AAAAAAAAAACATGAAAA
* *
118649 CAAAATAAATACATGA
1 -AAAAAAAAAACATGA
118665 TTAGCATAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 15 0.54
19 13 0.46
ACGTcount: A:0.73, C:0.08, G:0.06, T:0.13
Consensus pattern (18 bp):
AAAAAAAAAACATGAAAA
Found at i:127070 original size:44 final size:44
Alignment explanation
Indices: 126981--127068 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 44
126971 TAGTGTCAAG
* * *
126981 TTAAGAGTTAGAATATGTGGTTAAAATAAGAAGATTAGGAAAAA
1 TTAAGAATTAGAATATGTAGTTAAAATAAGAAGATTAAGAAAAA
* *
127025 TTAAGAATTAGAATGTGTAGTCT-AAATAAGAAAGGTTAAGAAAA
1 TTAAGAATTAGAATATGTAGT-TAAAATAAG-AAGATTAAGAAAA
127069 TTCAAGGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
44 25 0.68
45 12 0.32
ACGTcount: A:0.50, C:0.01, G:0.22, T:0.27
Consensus pattern (44 bp):
TTAAGAATTAGAATATGTAGTTAAAATAAGAAGATTAAGAAAAA
Found at i:128694 original size:6 final size:6
Alignment explanation
Indices: 128683--128721 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
128673 TGATCAAAAT
* * *
128683 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
128722 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:130197 original size:18 final size:20
Alignment explanation
Indices: 130165--130214 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 20
130155 CTTTGAGTGA
130165 ATAAAAGCA-ATGTGAG-GGT
1 ATAAAAGCATA-GTGAGTGGT
*
130184 -TAAGAGCATAGTGAGTGGT
1 ATAAAAGCATAGTGAGTGGT
130203 ATAAAAGCATAG
1 ATAAAAGCATAG
130215 AACATGTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 12 0.46
19 4 0.15
20 10 0.38
ACGTcount: A:0.42, C:0.06, G:0.30, T:0.22
Consensus pattern (20 bp):
ATAAAAGCATAGTGAGTGGT
Found at i:133227 original size:16 final size:16
Alignment explanation
Indices: 133206--133241 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
133196 ACAATAGCGG
133206 ATTATAAATAGTGGTA
1 ATTATAAATAGTGGTA
133222 ATTATAAATAGTGGTA
1 ATTATAAATAGTGGTA
133238 ATTA
1 ATTA
133242 AGTACATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.17, T:0.39
Consensus pattern (16 bp):
ATTATAAATAGTGGTA
Found at i:137612 original size:13 final size:13
Alignment explanation
Indices: 137594--137619 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
137584 ACTTTTGTAT
137594 GCCTTGCATTTGA
1 GCCTTGCATTTGA
137607 GCCTTGCATTTGA
1 GCCTTGCATTTGA
137620 CTATTTGTGA
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:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (13 bp):
GCCTTGCATTTGA
Found at i:144479 original size:29 final size:28
Alignment explanation
Indices: 144437--144493 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
144427 AGAACACGTC
* *
144437 ATTTTTTATAATTAAGTTATTATTTTAT
1 ATTTTTTATAATTAAGTAATTAATTTAT
144465 ATTTTTTAATAATTAAGTAATTAATTTAT
1 ATTTTTT-ATAATTAAGTAATTAATTTAT
144494 CGCATATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (28 bp):
ATTTTTTATAATTAAGTAATTAATTTAT
Found at i:146992 original size:14 final size:16
Alignment explanation
Indices: 146975--147007 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
146965 AAATAAAATT
146975 ATTAAAAAT-AT-TAA
1 ATTAAAAATCATATAA
146989 ATTAAAAATCATATAA
1 ATTAAAAATCATATAA
147005 ATT
1 ATT
147008 TTTTCAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 2 0.12
16 6 0.35
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTAAAAATCATATAA
Found at i:148872 original size:51 final size:52
Alignment explanation
Indices: 148809--148923 Score: 162
Period size: 51 Copynumber: 2.2 Consensus size: 52
148799 GAATCCATAA
148809 ACTCACGATGACAAAGT-GTCATCAAACCTTTAATCCATAAAGGATTCATTT
1 ACTCACGATGACAAAGTAGTCATCAAACCTTTAATCCATAAAGGATTCATTT
** * *
148860 ACTCACGATGAC-ACTTAGTCATTAGACCTTTAATCCATAAAGGATTCATTT
1 ACTCACGATGACAAAGTAGTCATCAAACCTTTAATCCATAAAGGATTCATTT
* *
148911 GCTCATGATGACA
1 ACTCACGATGACA
148924 CTTAGTCATC
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
50 2 0.04
51 54 0.96
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (52 bp):
ACTCACGATGACAAAGTAGTCATCAAACCTTTAATCCATAAAGGATTCATTT
Found at i:148924 original size:51 final size:51
Alignment explanation
Indices: 148834--148932 Score: 180
Period size: 51 Copynumber: 1.9 Consensus size: 51
148824 GTGTCATCAA
148834 ACCTTTAATCCATAAAGGATTCATTTACTCACGATGACACTTAGTCATTAG
1 ACCTTTAATCCATAAAGGATTCATTTACTCACGATGACACTTAGTCATTAG
* *
148885 ACCTTTAATCCATAAAGGATTCATTTGCTCATGATGACACTTAGTCAT
1 ACCTTTAATCCATAAAGGATTCATTTACTCACGATGACACTTAGTCAT
148933 CGGACCCTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.34
Consensus pattern (51 bp):
ACCTTTAATCCATAAAGGATTCATTTACTCACGATGACACTTAGTCATTAG
Found at i:151967 original size:2 final size:2
Alignment explanation
Indices: 151960--151985 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
151950 AGAGAAGATC
151960 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
151986 GTAAAGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:154239 original size:23 final size:23
Alignment explanation
Indices: 154213--154258 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
154203 TAGTAATTTA
*
154213 TTTTTATTTTTAAAATTTTAATT
1 TTTTTATTTTTAAAATTTAAATT
*
154236 TTTTTATTTTTAGAATTTAAATT
1 TTTTTATTTTTAAAATTTAAATT
154259 CAATGGTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTTATTTTTAAAATTTAAATT
Found at i:155479 original size:18 final size:18
Alignment explanation
Indices: 155444--155484 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
155434 TTGAAGTTTG
*
155444 GTAAATTTATTTAACTTT
1 GTAAATTTATCTAACTTT
155462 GTAAATTTA-CTAAGCTTT
1 GTAAATTTATCTAA-CTTT
155480 G-AAAT
1 GTAAAT
155485 GCTTACCTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (18 bp):
GTAAATTTATCTAACTTT
Found at i:156059 original size:21 final size:21
Alignment explanation
Indices: 156035--156086 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
156025 GGAGTTTTTA
156035 GTATCGATAGTAGTAT-GACTT
1 GTATCGATAGTAGTATCG-CTT
* * *
156056 GTATCGGTAGTTGTCTCGCTT
1 GTATCGATAGTAGTATCGCTT
156077 GTATCGATAG
1 GTATCGATAG
156087 AACTGTCAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (21 bp):
GTATCGATAGTAGTATCGCTT
Found at i:161948 original size:52 final size:52
Alignment explanation
Indices: 161870--162049 Score: 288
Period size: 52 Copynumber: 3.5 Consensus size: 52
161860 CAAAGGTTTA
161870 ATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATCATGAGGTCCG
1 ATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATCATGAGGTCCG
*
161922 ATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCG
1 ATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATCATGAGGTCCG
* * * * * *
161974 ATGACTATGTGTCATCGTGAGTGTATGATTTCTTTACAGAACAAGAGGTCCG
1 ATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATCATGAGGTCCG
*
162026 ATGACTATGTGTCATCATGAGTAT
1 ATGACTATGTGTCATCGTGAGTAT
162050 TAAATGAAAT
Statistics
Matches: 118, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 118 1.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (52 bp):
ATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATCATGAGGTCCG
Found at i:166705 original size:59 final size:61
Alignment explanation
Indices: 166635--166752 Score: 177
Period size: 62 Copynumber: 2.0 Consensus size: 61
166625 ATAATTTTAA
* *
166635 TATTAAATTAATATAATATTTA-T-CAAGATAAATATTAAATTAAATTTAATATTAAATCT
1 TATTAAATTAATAAAATATTTACTACAAGATAAACATTAAATTAAATTTAATATTAAATCT
* *
166694 TATTAAATTAATAAAATATTTATCTACAAGATGAACATTAAATTAAATTTAGTATTAAA
1 TATTAAATTAATAAAATATTTA-CTACAAGATAAACATTAAATTAAATTTAATATTAAA
166753 ACAATCACTT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 21 0.40
61 1 0.02
62 30 0.58
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (61 bp):
TATTAAATTAATAAAATATTTACTACAAGATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:167789 original size:13 final size:13
Alignment explanation
Indices: 167771--167795 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
167761 CTCCCTAATA
167771 GCAATCCTACGTT
1 GCAATCCTACGTT
167784 GCAATCCTACGT
1 GCAATCCTACGT
167796 GGTTTTAAAT
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:0.24, C:0.32, G:0.16, T:0.28
Consensus pattern (13 bp):
GCAATCCTACGTT
Found at i:167867 original size:18 final size:18
Alignment explanation
Indices: 167843--167885 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
167833 GAATAGATTT
167843 TTAATTAAATAAATTTAAA
1 TTAATTAAA-AAATTTAAA
*
167862 -TAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
167879 TTAATTA
1 TTAATTA
167886 TACCTTGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:176721 original size:21 final size:21
Alignment explanation
Indices: 176695--176736 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
176685 ACTATCAGTG
176695 CAAAAGCAACCAA-AACACCAA
1 CAAAAGCAACCAAGAA-ACCAA
*
176716 CAAAAGCACCCAAGAAACCAA
1 CAAAAGCAACCAAGAAACCAA
176737 TTACCAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.60, C:0.33, G:0.07, T:0.00
Consensus pattern (21 bp):
CAAAAGCAACCAAGAAACCAA
Found at i:178494 original size:29 final size:30
Alignment explanation
Indices: 178454--178527 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 30
178444 ACAAAATACT
178454 AACATAAGTGACTAAAACGTAACATT-A-CA
1 AACATAAGTGACTAAAACGTAAC-TTGAGCA
*
178483 AACATAAGTGACTAAAATGTAACTTGAGGCA
1 AACATAAGTGACTAAAACGTAACTTGA-GCA
*
178514 AACAAAAGTGACTA
1 AACATAAGTGACTA
178528 TTTTTATAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 2 0.05
29 23 0.57
31 15 0.38
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.20
Consensus pattern (30 bp):
AACATAAGTGACTAAAACGTAACTTGAGCA
Found at i:182282 original size:22 final size:21
Alignment explanation
Indices: 182258--182386 Score: 116
Period size: 22 Copynumber: 5.9 Consensus size: 21
182248 CATTAAGGAA
*
182258 CACTAGTGTGCTTACTGTTCAA
1 CACTAGTGTGCTT-CTGTTCAG
*
182280 CACTGCGTGTGCTTCTGTTCAG
1 CACT-AGTGTGCTTCTGTTCAG
* *
182302 CACTGCGTGTGCTTCTATTCAG
1 CACT-AGTGTGCTTCTGTTCAG
182324 CACT-GTGTGTACTTCTGTTCAG
1 CACTAGTGTG--CTTCTGTTCAG
*
182346 CACTACATGTGCTTCTGTTCAG
1 CACTA-GTGTGCTTCTGTTCAG
** *
182368 CGTTGTGTGTGCTTCTGTT
1 CACT-AGTGTGCTTCTGTT
182387 TTCCCAGCAG
Statistics
Matches: 92, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
20 5 0.05
22 75 0.82
23 8 0.09
24 4 0.04
ACGTcount: A:0.13, C:0.24, G:0.23, T:0.40
Consensus pattern (21 bp):
CACTAGTGTGCTTCTGTTCAG
Found at i:182339 original size:44 final size:44
Alignment explanation
Indices: 182258--182386 Score: 170
Period size: 44 Copynumber: 2.9 Consensus size: 44
182248 CATTAAGGAA
* *
182258 CACTA-GTGTGCTTACTGTTCAACACTGCGTGTGCTTCTGTTCAG
1 CACTACGTGTGCTT-CTGTTCAGCACTGTGTGTGCTTCTGTTCAG
* * *
182302 CACTGCGTGTGCTTCTATTCAGCACTGTGTGTACTTCTGTTCAG
1 CACTACGTGTGCTTCTGTTCAGCACTGTGTGTGCTTCTGTTCAG
* **
182346 CACTACATGTGCTTCTGTTCAGCGTTGTGTGTGCTTCTGTT
1 CACTACGTGTGCTTCTGTTCAGCACTGTGTGTGCTTCTGTT
182387 TTCCCAGCAG
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
44 65 0.89
45 8 0.11
ACGTcount: A:0.13, C:0.24, G:0.23, T:0.40
Consensus pattern (44 bp):
CACTACGTGTGCTTCTGTTCAGCACTGTGTGTGCTTCTGTTCAG
Found at i:185450 original size:24 final size:24
Alignment explanation
Indices: 185412--185457 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
185402 TAACTGATTA
*
185412 ATTATAATAATATAAAAAATAAGT
1 ATTATAATAAAATAAAAAATAAGT
*
185436 ATTATATTAAAATAAAAAATAA
1 ATTATAATAAAATAAAAAATAA
185458 ATTAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (24 bp):
ATTATAATAAAATAAAAAATAAGT
Found at i:188483 original size:17 final size:17
Alignment explanation
Indices: 188452--188486 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
188442 CATTTTAATT
**
188452 TTTTAAATTTTTAAAAA
1 TTTTAAATTAATAAAAA
188469 TTTTAAATTAATAAAAA
1 TTTTAAATTAATAAAAA
188486 T
1 T
188487 AAAATTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTTAAATTAATAAAAA
Found at i:189276 original size:52 final size:51
Alignment explanation
Indices: 189214--189317 Score: 138
Period size: 52 Copynumber: 2.0 Consensus size: 51
189204 TTATGAATAG
* * *
189214 TTTGAAGTAGGTG-CTTGTCGATGAAGCATTCATAAATTATATATATTTGTTA
1 TTTGAAGTAGGTGTC-TGTCGACGAAGCATTAAGAAATTATATATATTT-TTA
* *
189266 TTTGGAGTAGGTGTCTGTGGACGAAGCATTAAGAAATTATATATATTTTTA
1 TTTGAAGTAGGTGTCTGTCGACGAAGCATTAAGAAATTATATATATTTTTA
189317 T
1 T
189318 ATTATTATGA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
51 4 0.09
52 41 0.89
53 1 0.02
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (51 bp):
TTTGAAGTAGGTGTCTGTCGACGAAGCATTAAGAAATTATATATATTTTTA
Found at i:193148 original size:73 final size:74
Alignment explanation
Indices: 192986--193185 Score: 314
Period size: 74 Copynumber: 2.7 Consensus size: 74
192976 AGAAAAAAAA
* *
192986 TTTGAAGAAGAAAAATGATGTTTGGCAAGAGAGAAAATGAGAGAAAAAAATGGCACCCGACAGTG
1 TTTGAAGAAGAAAAATGATGTTTGACAAGAGAGAAAATGAGAGAAAAAAATGGCAACCGACAGTG
*
193051 GAGGGAAGT
66 GAGAGAAGT
* *
193060 TTTGAAGAATAAAAATGATGTTTGACAAGAGAGAAAATGAGA-AAAAAATATGGCAACTGACAGT
1 TTTGAAGAAGAAAAATGATGTTTGACAAGAGAGAAAATGAGAGAAAAAA-ATGGCAACCGACAGT
193124 GGA-AGAAGT
65 GGAGAGAAGT
* *
193133 TTTGAAGAAGAAAAATGGTGTTTGACAAGAGAAAAAATGAGAGAAAAAAATGG
1 TTTGAAGAAGAAAAATGATGTTTGACAAGAGAGAAAATGAGAGAAAAAAATGG
193186 GGGAAATGGA
Statistics
Matches: 116, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
73 54 0.47
74 62 0.53
ACGTcount: A:0.48, C:0.06, G:0.28, T:0.18
Consensus pattern (74 bp):
TTTGAAGAAGAAAAATGATGTTTGACAAGAGAGAAAATGAGAGAAAAAAATGGCAACCGACAGTG
GAGAGAAGT
Found at i:193636 original size:16 final size:15
Alignment explanation
Indices: 193609--193658 Score: 66
Period size: 16 Copynumber: 3.3 Consensus size: 15
193599 TTTCTCTTAA
*
193609 AAAAATAATTTGTTT
1 AAAAATATTTTGTTT
193624 AAAAATACTTTTGTTT
1 AAAAATA-TTTTGTTT
193640 AAAAAATATTTT-TTT
1 -AAAAATATTTTGTTT
193655 AAAA
1 AAAA
193659 TAATATTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
14 4 0.12
15 10 0.31
16 11 0.34
17 7 0.22
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (15 bp):
AAAAATATTTTGTTT
Found at i:193663 original size:16 final size:15
Alignment explanation
Indices: 193608--193665 Score: 64
Period size: 15 Copynumber: 3.7 Consensus size: 15
193598 TTTTCTCTTA
*
193608 AAAAAATAATTTGTTT
1 AAAAAAT-ATTTTTTT
193624 -AAAAATACTTTTGTTT
1 AAAAAATA-TTTT-TTT
193640 AAAAAATATTTTTTT
1 AAAAAATATTTTTTT
193655 AAAATAATATT
1 AAAA-AATATT
193666 AAACATATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 1 0.03
15 16 0.43
16 13 0.35
17 7 0.19
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (15 bp):
AAAAAATATTTTTTT
Found at i:202966 original size:20 final size:20
Alignment explanation
Indices: 202930--202968 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
202920 GAATAGGGAA
**
202930 TTTTCTCTTCTTTTCTTTCC
1 TTTTCTCTTCTCCTCTTTCC
202950 TTTTCTCTTCTCCTCTTTC
1 TTTTCTCTTCTCCTCTTTC
202969 TCTTCTCTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTCTCTTCTCCTCTTTCC
Found at i:210444 original size:87 final size:85
Alignment explanation
Indices: 210353--210594 Score: 240
Period size: 87 Copynumber: 2.8 Consensus size: 85
210343 TTTTGAAGAA
* * * **
210353 AAACGCCGCTATAAAACATGGTCTTTAGC-AGCGCTTTTTCAACAAACACCGCTAAAGCCCATGG
1 AAACGCCGCTA-AAAACATGGTCTTTAGCGA-CGCTTCTCCAACAAACACCACTAAAGAACATGG
** *
210417 TCTTTAGAGCGGCGCTTCTC-CAC
64 TCTTT--AGCAACACTTCTCTCAC
* **
210440 AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTCTCCCACAAATGCCACTAAAGAACATGGT
1 AAACGCCGCTAAA-AACATGGTCTTTAGCGACGCTTCTCCAACAAACACCACTAAAGAACATGGT
*
210505 CTTTAGCAACACTTTTCTCAC
65 CTTTAGCAACACTTCTCTCAC
* * * * *
210526 AAACGCCGCTAAAAGACATGGTCTTTAACGACACTT-TCTC-ACAAACGCCACTAAAAAACATGA
1 AAACGCCGCTAAAA-ACATGGTCTTTAGCGACGCTTCTC-CAACAAACACCACTAAAGAACATGG
210589 TCTTTA
64 TCTTTA
210595 ACGAAATTTT
Statistics
Matches: 133, Mismatches: 17, Indels: 12
0.82 0.10 0.07
Matches are distributed among these distances:
85 38 0.29
86 38 0.29
87 56 0.42
88 1 0.01
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (85 bp):
AAACGCCGCTAAAAACATGGTCTTTAGCGACGCTTCTCCAACAAACACCACTAAAGAACATGGTC
TTTAGCAACACTTCTCTCAC
Found at i:210565 original size:42 final size:42
Alignment explanation
Indices: 210353--210598 Score: 230
Period size: 43 Copynumber: 5.7 Consensus size: 42
210343 TTTTGAAGAA
* *
210353 AAACGCCGCTATAA-AACATGGTCTTTAGC-AGCGCTTTTTCAAC
1 AAACGCCGCTA-AAGAACATGGTCTTTAACGA-CGCTTTCTC-AC
* ** *
210396 AAACACCGCTAAAGCCCATGGTCTTTAGAGCGGCGC-TTCTCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTA-A-CGACGCTTTCT-CAC
* *
210440 AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTCTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAACGACGCTT-TCTCAC
* * * * *
210483 AAATGCCACTAAAGAACATGGTCTTTAGCAACACTTTTCTCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAACGACGC-TTTCTCAC
*
210526 AAACGCCGCTAAA-AGACATGGTCTTTAACGACACTTTCTCAC
1 AAACGCCGCTAAAGA-ACATGGTCTTTAACGACGCTTTCTCAC
* * *
210568 AAACGCCACTAAAAAACATGATCTTTAACGA
1 AAACGCCGCTAAAGAACATGGTCTTTAACGA
210599 AATTTTTTCC
Statistics
Matches: 170, Mismatches: 23, Indels: 21
0.79 0.11 0.10
Matches are distributed among these distances:
42 43 0.25
43 89 0.52
44 33 0.19
45 5 0.03
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACATGGTCTTTAACGACGCTTTCTCAC
Found at i:211021 original size:115 final size:116
Alignment explanation
Indices: 210896--211128 Score: 432
Period size: 117 Copynumber: 2.0 Consensus size: 116
210886 ACTCAAATTA
* *
210896 CCAAAAAAGAATAAAAATTCTTAACAAAATTGAAAGAAAAAGTGTAAAATTTAG-ACAAAATTTC
1 CCAAAAAAGAACAAAAATTCTTAACAAAATTGAAAGAAAAAGTGTAAAATTTAGAAAAAAATTTC
210960 TAAATTATTCATAATGCTAAATTGCAAAAGACATTACTAGTCAAGGTCCCT
66 TAAATTATTCATAATGCTAAATTGCAAAAGACATTACTAGTCAAGGTCCCT
211011 CCAAAAAAGAACAAAAATTCTTAACAAAATTGAAAGAAAAAGTGTAAAATTTAGATAAAAAATTT
1 CCAAAAAAGAACAAAAATTCTTAACAAAATTGAAAGAAAAAGTGTAAAATTTAGA-AAAAAATTT
211076 CTAAATTATTCATAATGCTAAATTGCAAAAGACATTACTAGTCAAGGTCCCT
65 CTAAATTATTCATAATGCTAAATTGCAAAAGACATTACTAGTCAAGGTCCCT
211128 C
1 C
211129 TTATAGCACA
Statistics
Matches: 114, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
115 53 0.46
117 61 0.54
ACGTcount: A:0.50, C:0.13, G:0.10, T:0.27
Consensus pattern (116 bp):
CCAAAAAAGAACAAAAATTCTTAACAAAATTGAAAGAAAAAGTGTAAAATTTAGAAAAAAATTTC
TAAATTATTCATAATGCTAAATTGCAAAAGACATTACTAGTCAAGGTCCCT
Done.