Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold564
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: 45506
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.33
Warning! 1139 characters in sequence are not A, C, G, or T
Found at i:2071 original size:6 final size:6
Alignment explanation
Indices: 2056--2091 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
2046 GTAAAGCTAC
*
2056 AAAAAA AAAAAG AAAAAG AAAAAG -AAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A
2092 TCAATTACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:2077 original size:11 final size:11
Alignment explanation
Indices: 2057--2091 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
2047 TAAAGCTACA
*
2057 AAAAAAAAAAG
1 AAAAGAAAAAG
2068 AAAAAGAAAAAG
1 -AAAAGAAAAAG
2080 AAAAGAAAAAG
1 AAAAGAAAAAG
2091 A
1 A
2092 TCAATTACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:2083 original size:17 final size:17
Alignment explanation
Indices: 2057--2091 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2047 TAAAGCTACA
2057 AAAAAAAAAAGAAAAAG
1 AAAAAAAAAAGAAAAAG
*
2074 AAAAAGAAAAGAAAAAG
1 AAAAAAAAAAGAAAAAG
2091 A
1 A
2092 TCAATTACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAGAAAAAG
Found at i:2392 original size:22 final size:22
Alignment explanation
Indices: 2346--2391 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
2336 TGGTTTATCC
*
2346 TTTGTAATAAAAACATATTATT
1 TTTGTAATAAAAACATAGTATT
*
2368 TTTGTAA-AAAAATATAGTATT
1 TTTGTAATAAAAACATAGTATT
2389 TTT
1 TTT
2392 TAAGTAAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (22 bp):
TTTGTAATAAAAACATAGTATT
Found at i:6688 original size:3 final size:3
Alignment explanation
Indices: 6668--6739 Score: 51
Period size: 3 Copynumber: 24.3 Consensus size: 3
6658 TGTTATTAAT
* * * *
6668 TTA TTA TTT TTA TAA TTA TTA TTA TTA TTA -TA GTTT TCTA TT- TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA T-TA TTA TTA
* *
6713 ATA TTA TTA TTA ATA TTA TTA -TA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
6740 GAAATAAAAT
Statistics
Matches: 52, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
2 5 0.10
3 44 0.85
4 3 0.06
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:7277 original size:18 final size:18
Alignment explanation
Indices: 7254--7292 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
7244 TTGTATATTG
7254 ATTGAAT-GTGAAATTGAA
1 ATTGAATAGTGAAATT-AA
*
7272 ATTGAATAGTGATATTAA
1 ATTGAATAGTGAAATTAA
7290 ATT
1 ATT
7293 TAGTATGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.44, C:0.00, G:0.18, T:0.38
Consensus pattern (18 bp):
ATTGAATAGTGAAATTAA
Found at i:7448 original size:22 final size:23
Alignment explanation
Indices: 7412--7454 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
7402 CTTTGCCGAT
7412 CAGGCACTTTATGTGTCGTATTC
1 CAGGCACTTTATGTGTCGTATTC
7435 CAGGCAC-TTATGTGTCGTAT
1 CAGGCACTTTATGTGTCGTAT
7455 ATTGATCAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (23 bp):
CAGGCACTTTATGTGTCGTATTC
Found at i:12328 original size:137 final size:138
Alignment explanation
Indices: 12165--12440 Score: 545
Period size: 137 Copynumber: 2.0 Consensus size: 138
12155 ACTATAATAT
12165 GAATATTAAAATAGTGTTAAGATAACTATATAAAAACTTTCAATAAATAAATTTTTTATTAAATA
1 GAATATTAAAATAGTGTTAAGATAACTATATAAAAACTTTCAATAAATAAATTTTTTATTAAATA
12230 TTAAAATAATATAATCTAAATATTTTTTTAAAAATTTTTAAAAATAATATGGACGAGTCTAAAAT
66 TTAAAATAATATAATCTAAATATTTTTTTAAAAATTTTTAAAAATAATATGGACGAGTCTAAAAT
12295 GGGCTTGA
131 GGGCTTGA
12303 GAATATTAAAA-AGTGTTAAGATAACTATATAAAAACTTTCAATAAATAAATTTTTTATTAAATA
1 GAATATTAAAATAGTGTTAAGATAACTATATAAAAACTTTCAATAAATAAATTTTTTATTAAATA
12367 TTAAAATAATATAATCTAAATATTTTTTTAAAAATTTTTAAAAATAATATGGACGAGTCTAAAAT
66 TTAAAATAATATAATCTAAATATTTTTTTAAAAATTTTTAAAAATAATATGGACGAGTCTAAAAT
12432 GGGCTTGA
131 GGGCTTGA
12440 G
1 G
12441 TTAATGCAAA
Statistics
Matches: 138, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
137 127 0.92
138 11 0.08
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.38
Consensus pattern (138 bp):
GAATATTAAAATAGTGTTAAGATAACTATATAAAAACTTTCAATAAATAAATTTTTTATTAAATA
TTAAAATAATATAATCTAAATATTTTTTTAAAAATTTTTAAAAATAATATGGACGAGTCTAAAAT
GGGCTTGA
Found at i:12794 original size:18 final size:17
Alignment explanation
Indices: 12767--12800 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12757 TATTTAAATG
12767 TTAAAAAGTGAATATTAA
1 TTAAAAAGTGAA-ATTAA
*
12785 TTAAATAGTGAAATTA
1 TTAAAAAGTGAAATTA
12801 TCAAAAATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (17 bp):
TTAAAAAGTGAAATTAA
Found at i:13440 original size:20 final size:20
Alignment explanation
Indices: 13415--13454 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
13405 ATCTAATAAA
13415 ATATAA-TTAATATATTTTAT
1 ATATAATTTAA-ATATTTTAT
13435 ATATAATTTAAATATTTTAT
1 ATATAATTTAAATATTTTAT
13455 TGAAATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATAATTTAAATATTTTAT
Found at i:14438 original size:16 final size:16
Alignment explanation
Indices: 14417--14452 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
14407 TAGATTATGC
14417 ATTTTGAGTTCAAATT
1 ATTTTGAGTTCAAATT
*
14433 ATTTTGAGTTGAAATT
1 ATTTTGAGTTCAAATT
14449 ATTT
1 ATTT
14453 AATGTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.53
Consensus pattern (16 bp):
ATTTTGAGTTCAAATT
Found at i:15172 original size:56 final size:56
Alignment explanation
Indices: 15089--15222 Score: 177
Period size: 56 Copynumber: 2.4 Consensus size: 56
15079 ATATGAAAGT
* * *
15089 TTGAA-TTTTTT-T-CAAATTAGTCCTTGAACTTGGTAATTGTTTC-CACATTAGGG
1 TTGAATTTTTTTGTCCAAGTTAGTCCTTGAAATTGGTAATTG-TTCACAAATTAGGG
*
15142 TTGAATTTTTTTGTCCAAGTTAGTCCTTGAAATTGGTAATTGTTCACAAATTGGGG
1 TTGAATTTTTTTGTCCAAGTTAGTCCTTGAAATTGGTAATTGTTCACAAATTAGGG
15198 TATGAATTTTTTTAGTCCAAGTTAG
1 T-TGAATTTTTTT-GTCCAAGTTAG
15223 CCCCTGATAT
Statistics
Matches: 71, Mismatches: 4, Indels: 7
0.87 0.05 0.09
Matches are distributed among these distances:
53 5 0.07
54 6 0.08
55 4 0.06
56 34 0.48
57 11 0.15
58 11 0.15
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.45
Consensus pattern (56 bp):
TTGAATTTTTTTGTCCAAGTTAGTCCTTGAAATTGGTAATTGTTCACAAATTAGGG
Found at i:23233 original size:29 final size:30
Alignment explanation
Indices: 23184--23261 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 30
23174 TAGTGCACAC
* * *
23184 ACAATCACTCGGCCCATCAACATCGCTCAT
1 ACAATCACTCGGCCCAGCAACAGCACTCAT
* *
23214 ACAATCAC-AGGCCCAGCAACAGCACTGAT
1 ACAATCACTCGGCCCAGCAACAGCACTCAT
*
23243 ACAGTCACTCGGCCCAGCA
1 ACAATCACTCGGCCCAGCA
23262 CTTCAATCGA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 23 0.57
30 17 0.43
ACGTcount: A:0.32, C:0.38, G:0.15, T:0.14
Consensus pattern (30 bp):
ACAATCACTCGGCCCAGCAACAGCACTCAT
Found at i:23957 original size:116 final size:117
Alignment explanation
Indices: 23837--24046 Score: 300
Period size: 116 Copynumber: 1.8 Consensus size: 117
23827 ATAAAATAGA
** * *
23837 AATTTACTTTTCCATTTTTAATATAA-TAGAAATTCTTTTAAGTAAGGCAATATTTTGAATATTT
1 AATTTACTTTAACATTTTTAATA-AAGTAGAAATTCTTTTAAATAAGGCAATATTCTGAATATTT
23901 CTATATTATTTCA-TTTAATAAAATA-AAATGTTGTTTTGAATAAAGTAATTGT
65 CTATATTATTTCATTTTAA-AAAATATAAATGTTGTTTTGAATAAAGTAATTGT
* ** *
23953 AATTTACTTTAATATTTTTAATAAAGTAGATTTTCTTTTAAATAAGTCAATATTCTGAATATTTC
1 AATTTACTTTAACATTTTTAATAAAGTAGAAATTCTTTTAAATAAGGCAATATTCTGAATATTTC
*
24018 TATATTATTTTATTTTAAAAAATATAAAT
66 TATATTATTTCATTTTAAAAAATATAAAT
24047 AATAAAAAGT
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
115 2 0.02
116 71 0.87
117 9 0.11
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.49
Consensus pattern (117 bp):
AATTTACTTTAACATTTTTAATAAAGTAGAAATTCTTTTAAATAAGGCAATATTCTGAATATTTC
TATATTATTTCATTTTAAAAAATATAAATGTTGTTTTGAATAAAGTAATTGT
Found at i:27878 original size:15 final size:15
Alignment explanation
Indices: 27858--27891 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
27848 ACAAAACTGA
27858 TACGCCTAATTCTTT
1 TACGCCTAATTCTTT
27873 TACGCCTAATTCTTT
1 TACGCCTAATTCTTT
27888 TACG
1 TACG
27892 AAATTCTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.09, T:0.44
Consensus pattern (15 bp):
TACGCCTAATTCTTT
Found at i:28367 original size:125 final size:126
Alignment explanation
Indices: 28118--28529 Score: 675
Period size: 125 Copynumber: 3.3 Consensus size: 126
28108 TTAGGCCAAA
*
28118 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGTTTCTTTCAGTACTTTTGCTGACAAAGC
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
* * * *
28183 A-TGTGTTTAAAGCGTTTTTGACACTATTTGCTTAGAAACGTCTACTCAAAATTATTTTTT
66 ATTCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
* *
28243 CAGGAGCTACTGTAGCAAAAACGCATCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
*
28308 ATTCTGCTTAAAGCGTTTTTGACGCTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
66 ATTCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
*
28369 CAGGAG-TACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGTTGACAAAGC
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
* * *
28433 ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTTCTCGAAACTATTTTTT
66 ATTCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
* * *
28494 TAGTAGCTACTGTAGCAAAAGCGCTTCCACGTGGGA
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGA
28530 ATTTTTTTAA
Statistics
Matches: 267, Mismatches: 18, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
125 179 0.67
126 88 0.33
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (126 bp):
CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
ATTCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
Found at i:28690 original size:97 final size:96
Alignment explanation
Indices: 28576--28841 Score: 288
Period size: 87 Copynumber: 2.9 Consensus size: 96
28566 CCTAAATCCA
*
28576 AAACCCTAATGTATTTGATTTTTTCTTTAAAAACCTTAAACACTAAACCCTAATCTAATTTTTTA
1 AAACCCTAATTTATTTGA-TTTTTCTTTAAAAACCTTAAACACTAAACCCTAATCTAATTTTTTA
28641 AAAATTTTATAATTAATTTACTCAAGTA-ACCT
65 AAAA-TTTATAATTAATTTACTCAAGTAGACCT
* * * * *
28673 TAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTT--ACCCT-AA---T-AT-GATTTTTTTA
1 AAACCCTAATTTATTTGATTTTTCTTTAAAAA-CCTTAAACACTAAACCCTAATCTAATTTTTTA
*
28730 AAAA-TT-TAATTAATTTACTCAAGTAGCCCT
65 AAAATTTATAATTAATTTACTCAAGTAGACCT
* * * * * *
28760 AAACCCTAATTTAATTAATTTTTATTTAAATA-CTATAAACACGAAACCCTAATCTAA-TTTTGA
1 AAACCCTAATTTATTTGATTTTTCTTTAAAAACCT-TAAACACTAAACCCTAATCTAATTTTTTA
28823 AAAATTTATAATTAATTTA
65 AAAATTTATAATTAATTTA
28842 ATTAAGAAAC
Statistics
Matches: 138, Mismatches: 18, Indels: 28
0.75 0.10 0.15
Matches are distributed among these distances:
85 2 0.01
86 20 0.14
87 31 0.22
88 3 0.02
89 14 0.10
90 2 0.01
91 1 0.01
92 1 0.01
93 11 0.08
94 5 0.04
95 15 0.11
96 13 0.09
97 20 0.14
ACGTcount: A:0.39, C:0.16, G:0.03, T:0.42
Consensus pattern (96 bp):
AAACCCTAATTTATTTGATTTTTCTTTAAAAACCTTAAACACTAAACCCTAATCTAATTTTTTAA
AAATTTATAATTAATTTACTCAAGTAGACCT
Found at i:28835 original size:95 final size:93
Alignment explanation
Indices: 28576--28864 Score: 238
Period size: 95 Copynumber: 3.1 Consensus size: 93
28566 CCTAAATCCA
* * * *
28576 AAACCCTAATGTATTTGATTTTTTCTTTAAAAACCT-TAAACACTAAACCCTAATCTAATTTTTT
1 AAACCCTAATTTATTT-AATTTTT-TTTAAATA-CTATAAACACCAAACCCTAATCTAA-TTTTT
*
28640 AAAAATTTTATAATTAATTTACTCAAGTAACCT
62 AAAAA-TTTATAATTAATTTACTCAAGTACCCT
* * ** ** * *
28673 TAACCCTAATTTATTTGATTTTTCCT---TA--A-AAAC-CCTTACCCTAATATGATTTTTTTAA
1 AAACCCTAATTTATTTAATTTTTTTTAAATACTATAAACACCAAACCCTAATCT-A-ATTTTTAA
28731 AAA-TT-TAATTAATTTACTCAAGTAGCCCT
64 AAATTTATAATTAATTTACTCAAGTA-CCCT
* * *
28760 AAACCCTAATTTAATTAATTTTTATTTAAATACTATAAACACGAAACCCTAATCTAATTTTGAAA
1 AAACCCTAATTTATTTAATTTTT-TTTAAATACTATAAACACCAAACCCTAATCTAATTTTTAAA
* * *
28825 AATTTATAATTAATTTAATTAAGAAACCCT
65 AATTTATAATTAATTTACTCAAG-TACCCT
*
28855 AAACTCTAAT
1 AAACCCTAAT
28865 CCCTTATTTA
Statistics
Matches: 149, Mismatches: 28, Indels: 32
0.71 0.13 0.15
Matches are distributed among these distances:
86 19 0.13
87 25 0.17
88 11 0.07
89 15 0.10
91 2 0.01
92 1 0.01
93 10 0.07
94 7 0.05
95 39 0.26
96 6 0.04
97 14 0.09
ACGTcount: A:0.40, C:0.16, G:0.03, T:0.40
Consensus pattern (93 bp):
AAACCCTAATTTATTTAATTTTTTTTAAATACTATAAACACCAAACCCTAATCTAATTTTTAAAA
ATTTATAATTAATTTACTCAAGTACCCT
Found at i:31432 original size:18 final size:18
Alignment explanation
Indices: 31409--31466 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
31399 TGGGGAATAA
31409 TTTTATAT-TCTTTTACAT
1 TTTTATATAT-TTTTACAT
31427 TTTTATATATTTTTACA-
1 TTTTATATATTTTTACAT
* *
31444 GTCTATATA-TTTTACACT
1 TTTTATATATTTTTACA-T
31462 TTTTA
1 TTTTA
31467 CGATTTTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 7 0.21
17 7 0.21
18 18 0.55
19 1 0.03
ACGTcount: A:0.26, C:0.10, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTATATATTTTTACAT
Found at i:31530 original size:20 final size:20
Alignment explanation
Indices: 31487--31555 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
31477 AGTTTTATTC
* *
31487 TATTTTTAATAAATTTTTAA-
1 TATTTTTATTAAA-ATTTAAT
31507 TATTTTTATTAAAATTTAAT
1 TATTTTTATTAAAATTTAAT
* *
31527 TATTCTTA-TAAACTTT-AT
1 TATTTTTATTAAAATTTAAT
31545 TGATTTTTATT
1 T-ATTTTTATT
31556 TTTATCATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
18 3 0.07
19 18 0.44
20 20 0.49
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (20 bp):
TATTTTTATTAAAATTTAAT
Found at i:32112 original size:20 final size:21
Alignment explanation
Indices: 32084--32122 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
32074 TATTTGAATT
32084 TTAAATTGACCCA-AGTCAAA
1 TTAAATTGACCCACAGTCAAA
*
32104 TTAACTTGACCCACAGTCA
1 TTAAATTGACCCACAGTCA
32123 TTGTGAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.26, G:0.10, T:0.26
Consensus pattern (21 bp):
TTAAATTGACCCACAGTCAAA
Found at i:33341 original size:33 final size:33
Alignment explanation
Indices: 33299--33364 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
33289 GGCATAAAAG
33299 ATGAGCCCACAAGTAAATGGTACTTGATGAGAT
1 ATGAGCCCACAAGTAAATGGTACTTGATGAGAT
33332 ATGAGCCCACAAGTAAATGGTACTTGATGAGAT
1 ATGAGCCCACAAGTAAATGGTACTTGATGAGAT
33365 TTTTCTTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.24
Consensus pattern (33 bp):
ATGAGCCCACAAGTAAATGGTACTTGATGAGAT
Found at i:36353 original size:21 final size:20
Alignment explanation
Indices: 36323--36395 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 20
36313 TCTTATTAGT
36323 AAAAAATTATAAAAATTGTA
1 AAAAAATTATAAAAATTGTA
*
36343 AAAAAATTTATAAAGATTGT-
1 AAAAAA-TTATAAAAATTGTA
*** **
36363 AAACTTTTATAAAAATCATA
1 AAAAAATTATAAAAATTGTA
36383 AAAAAA-TATAAAA
1 AAAAAATTATAAAA
36396 TGTACCAAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
19 17 0.41
20 12 0.29
21 12 0.29
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.30
Consensus pattern (20 bp):
AAAAAATTATAAAAATTGTA
Found at i:36580 original size:9 final size:9
Alignment explanation
Indices: 36566--36734 Score: 55
Period size: 9 Copynumber: 17.9 Consensus size: 9
36556 TTTTGGTATG
36566 ATAATTTTT
1 ATAATTTTT
36575 ATAATTTTTTT
1 ATAA--TTTTT
*
36586 ATAA-ATTT
1 ATAATTTTT
*
36594 ATATTTCTTT
1 ATAATT-TTT
*
36604 ATATTTTTT
1 ATAATTTTT
36613 ATAATTTTCT
1 ATAATTTT-T
* *
36623 -TACTGCTTT
1 ATAAT-TTTT
*
36632 ATAAAATTTT
1 AT-AATTTTT
36642 ATAATTTTT
1 ATAATTTTT
36651 GCGGGAATAA-TTTT
1 ------ATAATTTTT
36665 ATAATTTTT
1 ATAATTTTT
36674 -TACATTTTT
1 ATA-ATTTTT
36683 AT-ATATTTT
1 ATAAT-TTTT
* * *
36692 A-CAGTTCT
1 ATAATTTTT
36700 AT-ATATTTT
1 ATAAT-TTTT
36709 ATAATTTTT
1 ATAATTTTT
*
36718 ATTATTTTT
1 ATAATTTTT
*
36727 ATAGTTTT
1 ATAATTTT
36735 ATTCTATTTT
Statistics
Matches: 121, Mismatches: 17, Indels: 44
0.66 0.09 0.24
Matches are distributed among these distances:
8 19 0.16
9 63 0.52
10 21 0.17
11 10 0.08
14 4 0.03
15 4 0.03
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.62
Consensus pattern (9 bp):
ATAATTTTT
Found at i:36690 original size:10 final size:10
Alignment explanation
Indices: 36661--36823 Score: 54
Period size: 9 Copynumber: 17.5 Consensus size: 10
36651 GCGGGAATAA
36661 TTTTATA-AT
1 TTTTATATAT
*
36670 TTTT-TACAT
1 TTTTATATAT
36679 TTTTATATA-
1 TTTTATATAT
* *
36688 -TTT-TACAG
1 TTTTATATAT
*
36696 TTCTATATA-
1 TTTTATATAT
36705 TTTTATA-AT
1 TTTTATATAT
36714 TTTTAT-TA-
1 TTTTATATAT
*
36722 TTTT-TATAG
1 TTTTATATAT
*
36731 TTTTATTCTAT
1 TTTTA-TATAT
*
36742 TTTTA-ATCAA
1 TTTTATAT-AT
*
36752 TTTTAAATAT
1 TTTTATATAT
* *
36762 TTTTATTAAAA
1 TTTTA-TATAT
*
36773 TTTAAT-TAT
1 TTTTATATAT
*
36782 TTTTATA-AA
1 TTTTATATAT
36791 TTTTAT-TGAT
1 TTTTATAT-AT
36801 TTTTAT-T-T
1 TTTTATATAT
36809 TTTTATCAT-T
1 TTTTAT-ATAT
36819 TTTTA
1 TTTTA
36824 CCACATGTCA
Statistics
Matches: 116, Mismatches: 19, Indels: 37
0.67 0.11 0.22
Matches are distributed among these distances:
7 4 0.03
8 19 0.16
9 43 0.37
10 34 0.29
11 16 0.14
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (10 bp):
TTTTATATAT
Found at i:36691 original size:17 final size:17
Alignment explanation
Indices: 36661--36725 Score: 69
Period size: 17 Copynumber: 3.8 Consensus size: 17
36651 GCGGGAATAA
*
36661 TTTTATAATTTTTTACAT
1 TTTTAT-ATATTTTACAT
*
36679 TTTTATATATTTTACAG
1 TTTTATATATTTTACAT
* *
36696 TTCTATATATTTTATAAT
1 TTTTATATATTTTA-CAT
36714 TTTTAT-TATTTT
1 TTTTATATATTTT
36726 TATAGTTTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
17 28 0.70
18 12 0.30
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (17 bp):
TTTTATATATTTTACAT
Found at i:36734 original size:17 final size:18
Alignment explanation
Indices: 36705--36806 Score: 89
Period size: 20 Copynumber: 5.3 Consensus size: 18
36695 GTTCTATATA
*
36705 TTTTATAATTTTTATTAT
1 TTTTATAAATTTTATTAT
*
36723 TTTTAT-AGTTTTATTCTAT
1 TTTTATAAATTTTA-T-TAT
* *
36742 TTTTAATCAATTTTAAATAT
1 TTTT-ATAAATTTT-ATTAT
*
36762 TTTTATTAAAATTTAATTAT
1 TTTTA-T-AAATTTTATTAT
36782 TTTTATAAATTTTATTGAT
1 TTTTATAAATTTTATT-AT
36801 TTTTAT
1 TTTTAT
36807 TTTTTTATCA
Statistics
Matches: 69, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
17 6 0.09
18 16 0.23
19 17 0.25
20 19 0.28
21 10 0.14
22 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTTATAAATTTTATTAT
Found at i:36803 original size:39 final size:38
Alignment explanation
Indices: 36705--36807 Score: 102
Period size: 39 Copynumber: 2.7 Consensus size: 38
36695 GTTCTATATA
* ** *
36705 TTTTATAATTTTTATTATTTTTA-TAGTTTTATTCTAT
1 TTTTATAAATTTTATTATTTTTATTAAATTTAATCTAT
* *
36742 TTTTAATCAATTTTAAATATTTTTATTAAAATTTAAT-TAT
1 TTTT-ATAAATTTT-ATTATTTTTATT-AAATTTAATCTAT
36782 TTTTATAAATTTTATTGATTTTTATT
1 TTTTATAAATTTTATT-ATTTTTATT
36808 TTTTTATCAT
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
37 4 0.08
38 9 0.17
39 26 0.49
40 8 0.15
41 6 0.11
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (38 bp):
TTTTATAAATTTTATTATTTTTATTAAATTTAATCTAT
Found at i:36804 original size:20 final size:19
Alignment explanation
Indices: 36705--36804 Score: 64
Period size: 18 Copynumber: 5.2 Consensus size: 19
36695 GTTCTATATA
*
36705 TTTTATAATTTTTATTA-T
1 TTTTATAAATTTTATTATT
*
36723 TTTTAT-AGTTTTATTCTATT
1 TTTTATAAATTTTA-T-TATT
* * *
36743 TTTAATCAATTTTA-AATAT
1 TTTTATAAATTTTATTAT-T
*
36762 TTTTATTAAAATTTAATTA-T
1 TTTTA-T-AAATTTTATTATT
36782 TTTTATAAATTTTATTGATT
1 TTTTATAAATTTTATT-ATT
36802 TTT
1 TTT
36805 ATTTTTTTAT
Statistics
Matches: 63, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
17 6 0.10
18 18 0.29
19 9 0.14
20 17 0.27
21 12 0.19
22 1 0.02
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTTATAAATTTTATTATT
Found at i:37165 original size:91 final size:91
Alignment explanation
Indices: 36987--37163 Score: 250
Period size: 91 Copynumber: 2.0 Consensus size: 91
36977 ACAAGAACAA
* * * * ** * *
36987 GAGCTTAATTGTTTTTTTTTTTTTTAAGTTTGAGAGGCTTTTTTATGCATTTTGATAGTTCAAGT
1 GAGCGTAATTGGTTTTTTTTTTTTAAAGTTTGAGAGCCTTTTGCATGCATTTTGACAGCTCAAGT
*
37052 ACCCAATTGAGTGGGAATAAAAGCTG
66 ACCCAATTGAGTGGGAAAAAAAGCTG
37078 GAGCGTAATTGGTTTTTTTTTTTTAAAGTTTGACG-GCCTTTTGCATGCATTTTG-CAGCTCAAG
1 GAGCGTAATTGGTTTTTTTTTTTTAAAGTTTGA-GAGCCTTTTGCATGCATTTTGACAGCTCAAG
37141 TACCCAATTGAGTGGGAAAAAAA
65 TACCCAATTGAGTGGGAAAAAAA
37164 AGAGAGTAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
90 29 0.38
91 46 0.61
92 1 0.01
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.41
Consensus pattern (91 bp):
GAGCGTAATTGGTTTTTTTTTTTTAAAGTTTGAGAGCCTTTTGCATGCATTTTGACAGCTCAAGT
ACCCAATTGAGTGGGAAAAAAAGCTG
Found at i:37308 original size:88 final size:92
Alignment explanation
Indices: 37136--37308 Score: 205
Period size: 88 Copynumber: 1.9 Consensus size: 92
37126 ATTTTGCAGC
* * * * *
37136 TCAAGTACCCAATTGAGTGGGAAAAAAAAGAGAGTAAAAGCTTAATTGCTTTTTTTGAAAAATTT
1 TCAAGTACCCAATTAAGT-GGAAAAAAAAAACAGTAAAAGCTTAATTACCTTTTTTGAAAAATTT
* * *
37201 GAAGTCCTTTTTTATGCATTTTGAAAAT
65 AAAGTACTTTTTTAAGCATTTTGAAAAT
37229 TCAAGTACCCAATTAAGT-GAAAAAAAAAACA-T-AAA-CTTAATTACCTTTTTTGAAAAAATTT
1 TCAAGTACCCAATTAAGTGGAAAAAAAAAACAGTAAAAGCTTAATTACCTTTTTTG-AAAAATTT
37290 AAAG-AC-TTTTTACAGCATT
65 AAAGTACTTTTTTA-AGCATT
37309 AAACCTTACA
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
87 6 0.09
88 21 0.30
89 14 0.20
90 1 0.01
91 11 0.16
93 17 0.24
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.34
Consensus pattern (92 bp):
TCAAGTACCCAATTAAGTGGAAAAAAAAAACAGTAAAAGCTTAATTACCTTTTTTGAAAAATTTA
AAGTACTTTTTTAAGCATTTTGAAAAT
Found at i:40241 original size:16 final size:19
Alignment explanation
Indices: 40222--40263 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 19
40212 ATCACAACAA
40222 AACAACTC-TTAT-TTG-G
1 AACAACTCTTTATATTGAG
40238 AACAAC-CTTTATATTGAG
1 AACAACTCTTTATATTGAG
40256 AACAACTC
1 AACAACTC
40264 ACGTTAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.05
16 10 0.45
17 3 0.14
18 7 0.32
19 1 0.05
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (19 bp):
AACAACTCTTTATATTGAG
Found at i:40436 original size:14 final size:14
Alignment explanation
Indices: 40417--40450 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
40407 ATAAGAAATA
40417 AAAAACCCAAACCC
1 AAAAACCCAAACCC
40431 AAAAACCCAAACCC
1 AAAAACCCAAACCC
40445 AAAAAC
1 AAAAAC
40451 AGGCCCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.62, C:0.38, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAACCCAAACCC
Found at i:41542 original size:19 final size:19
Alignment explanation
Indices: 41514--41550 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
41504 CCTTTGCACC
*
41514 TTTTTCTTTTATTTTTTAT
1 TTTTTATTTTATTTTTTAT
41533 TTTTTATTTTATTTTTTA
1 TTTTTATTTTATTTTTTA
41551 CAATCTCAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTATTTTATTTTTTAT
Found at i:42060 original size:30 final size:31
Alignment explanation
Indices: 42012--42112 Score: 97
Period size: 30 Copynumber: 3.4 Consensus size: 31
42002 GCAAAAAATA
* *
42012 AAAATT-ACAGTTTAACCCCAATAC-TTTTTG
1 AAAATTCACATTTTGACCCCAA-ACTTTTTTG
* *
42042 AAATTTC-CATTTTGACCCCAAACTTTTTTT
1 AAAATTCACATTTTGACCCCAAACTTTTTTG
* *
42072 AAAATTCACATTTTGA-CCCAAAATTTTCT-
1 AAAATTCACATTTTGACCCCAAACTTTTTTG
42101 AAAATT-ACATTT
1 AAAATTCACATTT
42113 CGGCCCTTAA
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
28 6 0.10
29 8 0.13
30 39 0.64
31 8 0.13
ACGTcount: A:0.36, C:0.20, G:0.04, T:0.41
Consensus pattern (31 bp):
AAAATTCACATTTTGACCCCAAACTTTTTTG
Found at i:42077 original size:31 final size:30
Alignment explanation
Indices: 42036--42136 Score: 84
Period size: 29 Copynumber: 3.4 Consensus size: 30
42026 ACCCCAATAC
* *
42036 TTTTTGAAATTTC-CATTTTGACCCCAAACTT
1 TTTTTAAAATTTCACATTTTGA-CCCAAA-AT
42067 TTTTTAAAA-TTCACATTTTGACCCAAAAT
1 TTTTTAAAATTTCACATTTTGACCCAAAAT
* * * *
42096 TTTCTAAAA-TT-ACATTTCGGCCCTTAAAT
1 TTTTTAAAATTTCACATTTTGACCC-AAAAT
42125 TTTCTTAAAATT
1 TTT-TTAAAATT
42137 GCCCTTTAAC
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
28 10 0.17
29 18 0.31
30 14 0.24
31 17 0.29
ACGTcount: A:0.32, C:0.19, G:0.05, T:0.45
Consensus pattern (30 bp):
TTTTTAAAATTTCACATTTTGACCCAAAAT
Found at i:42136 original size:30 final size:30
Alignment explanation
Indices: 42049--42136 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 30
42039 TTGAAATTTC
* * *
42049 CATTTTGACCCCAAACTTTTTTTAAAATTCA
1 CATTTCGA-CCCAAAATTTTCTTAAAATTCA
*
42080 CATTTTGACCCAAAATTTTC-TAAAATT-A
1 CATTTCGACCCAAAATTTTCTTAAAATTCA
* *
42108 CATTTCGGCCCTTAAATTTTCTTAAAATT
1 CATTTCGACCC-AAAATTTTCTTAAAATT
42137 GCCCTTTAAC
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
28 10 0.20
29 15 0.30
30 17 0.34
31 8 0.16
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.42
Consensus pattern (30 bp):
CATTTCGACCCAAAATTTTCTTAAAATTCA
Found at i:42630 original size:12 final size:12
Alignment explanation
Indices: 42615--42679 Score: 53
Period size: 12 Copynumber: 5.2 Consensus size: 12
42605 AGCGGCCAAA
42615 AAGAAGGAAGAG
1 AAGAAGGAAGAG
* *
42627 AAGAAAGAAAAG
1 AAGAAGGAAGAG
42639 AAAGAAGAGAAGA-
1 -AAGAAG-GAAGAG
*
42652 AAGAA-AAAGAG
1 AAGAAGGAAGAG
42663 AGAGAGAGGAAGAG
1 A-AGA-AGGAAGAG
42677 AAG
1 AAG
42680 GGAGGCGCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
10 4 0.10
11 1 0.02
12 18 0.44
13 8 0.20
14 10 0.24
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (12 bp):
AAGAAGGAAGAG
Found at i:42668 original size:21 final size:22
Alignment explanation
Indices: 42612--42675 Score: 85
Period size: 21 Copynumber: 2.9 Consensus size: 22
42602 AACAGCGGCC
*
42612 AAAAAGAAGGAAGAGAAGAAAG
1 AAAAAGAAAGAAGAGAAGAAAG
42634 -AAAAGAAAGAAGAGAAGAAAG
1 AAAAAGAAAGAAGAGAAGAAAG
*
42655 AAAAAGAGAGAGAGAGGAAGA
1 AAAAAGAAAGA-AGA-GAAGA
42676 GAAGGGAGGC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
21 20 0.54
22 9 0.24
23 3 0.08
24 5 0.14
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAGAAGAGAAGAAAG
Found at i:42779 original size:19 final size:20
Alignment explanation
Indices: 42755--42804 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
42745 GGGGTGACCC
* *
42755 GAAGAAGAAAGAAA-AAAAG
1 GAAGAAAAAAGAAAGAAAAA
42774 GAAGAAAAAAGAAAGAAAAA
1 GAAGAAAAAAGAAAGAAAAA
*
42794 GAAGGAAAAAG
1 GAAGAAAAAAG
42805 GGAAATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (20 bp):
GAAGAAAAAAGAAAGAAAAA
Found at i:42941 original size:24 final size:26
Alignment explanation
Indices: 42889--42945 Score: 82
Period size: 24 Copynumber: 2.2 Consensus size: 26
42879 CGACCCGCAT
42889 CAGCCCAGCAGCCCAAATAAAAAACAG
1 CAGCCCAGCAGCCC-AATAAAAAACAG
*
42916 CAGCCCAGCAGCCC-A-AAAAAATAG
1 CAGCCCAGCAGCCCAATAAAAAACAG
42940 CAGCCC
1 CAGCCC
42946 CTAAAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 14 0.48
25 1 0.03
27 14 0.48
ACGTcount: A:0.44, C:0.37, G:0.16, T:0.04
Consensus pattern (26 bp):
CAGCCCAGCAGCCCAATAAAAAACAG
Found at i:42943 original size:16 final size:18
Alignment explanation
Indices: 42922--42959 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
42912 ACAGCAGCCC
42922 AGCAG-CCC-AAAAAAAT
1 AGCAGCCCCTAAAAAAAT
42938 AGCAGCCCCTAAAAAAAT
1 AGCAGCCCCTAAAAAAAT
42956 AGCA
1 AGCA
42960 AACAGCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 5 0.25
17 3 0.15
18 12 0.60
ACGTcount: A:0.53, C:0.26, G:0.13, T:0.08
Consensus pattern (18 bp):
AGCAGCCCCTAAAAAAAT
Found at i:43094 original size:32 final size:30
Alignment explanation
Indices: 43058--43116 Score: 73
Period size: 32 Copynumber: 1.9 Consensus size: 30
43048 CAGCAGACCA
*
43058 GCCCAGAAGGCCCACAGCGCCAGGCCCAGTTT
1 GCCCAGAAGGCCAACAG-GCC-GGCCCAGTTT
* *
43090 GCCCAGCAGTCCAACAGGCCGGCCCAG
1 GCCCAGAAGGCCAACAGGCCGGCCCAG
43117 CAGCAGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 7 0.29
31 3 0.12
32 14 0.58
ACGTcount: A:0.22, C:0.42, G:0.29, T:0.07
Consensus pattern (30 bp):
GCCCAGAAGGCCAACAGGCCGGCCCAGTTT
Found at i:43672 original size:36 final size:37
Alignment explanation
Indices: 43618--43708 Score: 123
Period size: 37 Copynumber: 2.5 Consensus size: 37
43608 GGTACTTCTT
* *
43618 AAAAAAATTCCGTG-TTTCAACAATTCTCGTG-AATA
1 AAAAAAATTTCGTGTTTTCAAAAATTCTCGTGTAATA
**
43653 AAAAAAATTTCGTGTTTTCAAAAATTCTCGTGTTTTA
1 AAAAAAATTTCGTGTTTTCAAAAATTCTCGTGTAATA
*
43690 AAAAAATTTTCGTGTTTTC
1 AAAAAAATTTCGTGTTTTC
43709 GTGTTTTCAA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
35 13 0.27
36 16 0.33
37 20 0.41
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (37 bp):
AAAAAAATTTCGTGTTTTCAAAAATTCTCGTGTAATA
Found at i:43675 original size:18 final size:18
Alignment explanation
Indices: 43654--44250 Score: 165
Period size: 18 Copynumber: 32.3 Consensus size: 18
43644 TCGTGAATAA
43654 AAAAAATTTCGTGTTTTC
1 AAAAAATTTCGTGTTTTC
*
43672 -AAAAATTCTCGTGTTTTA
1 AAAAAATT-TCGTGTTTTC
43690 AAAAAATTTTCGTG--TT-
1 AAAAAA-TTTCGTGTTTTC
43706 ------T-TCGTGTTTTC
1 AAAAAATTTCGTGTTTTC
43717 AAAAAAAATTCTCGTG-TTTC
1 --AAAAAATT-TCGTGTTTTC
* *
43737 AAAAATTTTCATGTTTTC
1 AAAAAATTTCGTGTTTTC
* *
43755 AAAATTTTCATGTTTTCATGTTTTC
1 AAAA-----A-AT-TTCGTGTTTTC
*
43780 AAAAAATTTCTCGTGTTTTT
1 AAAAAA-TT-TCGTGTTTTC
* * *
43800 AAAAAAATTCGTATTTTT
1 AAAAAATTTCGTGTTTTC
*
43818 AAAAAA-TTCATGTTTTC
1 AAAAAATTTCGTGTTTTC
* *
43835 -GAAATTTTCGTGTTTTC
1 AAAAAATTTCGTGTTTTC
** *
43852 AAAATTTTTAGTG---TC
1 AAAAAATTTCGTGTTTTC
*
43867 AAAAAATTCTCATG-TTTC
1 AAAAAATT-TCGTGTTTTC
*
43885 AAAAATTTTCGTGTTTTC
1 AAAAAATTTCGTGTTTTC
*
43903 AAAAAAGTTCCCGTGTTTTC
1 AAAAAA-TT-TCGTGTTTTC
*
43923 AAAAATTTCATGTTTTGGTGTTTTC
1 AAAAA----A---TTTCGTGTTTTC
*
43948 AAAAAATTCTCGTGTTTTTTTA
1 AAAAAATT-TCGTG---TTTTC
* * *
43970 AAAAAAATTCATGTTTTTA
1 AAAAAATTTCGTG-TTTTC
* *
43989 AAAAAAATT-ATGTTTTC
1 AAAAAATTTCGTGTTTTC
* *
44006 -GAAATTTTCGTGTTTTC
1 AAAAAATTTCGTGTTTTC
**
44023 AAAATTTTTCGTG---TC
1 AAAAAATTTCGTGTTTTC
*
44038 AAAAAATTCTCATG-TTTC
1 AAAAAATT-TCGTGTTTTC
*
44056 AAAAATTTTCGTGTTTTC
1 AAAAAATTTCGTGTTTTC
*
44074 AAAAAAGTTCCCGTGTTTTC
1 AAAAAA-TT-TCGTGTTTTC
*
44094 AAAAATTTCATGTTTTGGTGTTTTC
1 AAAAA----A---TTTCGTGTTTTC
*
44119 AAAAAATTCTCGTGTTTTTTTA
1 AAAAAATT-TCGTG---TTTTC
* * *
44141 AAAAAAATTCATGTTTTTA
1 AAAAAATTTCGTG-TTTTC
* *
44160 AAAAAAATT-ATGTTTTC
1 AAAAAATTTCGTGTTTTC
* *
44177 -GAAATTTTCGTGTTTTC
1 AAAAAATTTCGTGTTTTC
** *
44194 AAAATTTTTAGTG---TC
1 AAAAAATTTCGTGTTTTC
*
44209 AAAAAATTCTCATG-TTTC
1 AAAAAATT-TCGTGTTTTC
*
44227 AAAAATTTTCGTGTTTTC
1 AAAAAATTTCGTGTTTTC
44245 AAAAAA
1 AAAAAA
44251 GTATACCAAT
Statistics
Matches: 442, Mismatches: 69, Indels: 136
0.68 0.11 0.21
Matches are distributed among these distances:
8 5 0.01
9 1 0.00
10 2 0.00
15 24 0.05
16 23 0.05
17 65 0.15
18 131 0.30
19 55 0.12
20 50 0.11
21 15 0.03
22 22 0.05
23 1 0.00
24 3 0.01
25 41 0.09
26 4 0.01
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.46
Consensus pattern (18 bp):
AAAAAATTTCGTGTTTTC
Found at i:43675 original size:19 final size:19
Alignment explanation
Indices: 43653--43708 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
43643 CTCGTGAATA
43653 AAAAAAATTTCGTGTTTTC
1 AAAAAAATTTCGTGTTTTC
43672 --AAAAATTCTCGTGTTTT-
1 AAAAAAATT-TCGTGTTTTC
43689 AAAAAAATTTTCGTGTTTTC
1 AAAAAAA-TTTCGTGTTTTC
43709 GTGTTTTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
17 7 0.22
18 9 0.28
19 14 0.44
20 2 0.06
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (19 bp):
AAAAAAATTTCGTGTTTTC
Found at i:43677 original size:17 final size:17
Alignment explanation
Indices: 43655--44109 Score: 84
Period size: 17 Copynumber: 25.9 Consensus size: 17
43645 CGTGAATAAA
43655 AAAAATTTCGTGTTTTC
1 AAAAATTTCGTGTTTTC
*
43672 AAAAATTCTCGTGTTTTAA
1 AAAAATT-TCGTGTTTT-C
43691 AAAAATTTTCGTG---T-
1 AAAAA-TTTCGTGTTTTC
43705 -----TTTCGTGTTTTC
1 AAAAATTTCGTGTTTTC
43717 AAAAAAAATTCTCGTG-TTTC
1 ---AAAAATT-TCGTGTTTTC
*
43737 AAAAATTTTCATGTTTTC
1 AAAAA-TTTCGTGTTTTC
* *
43755 AAAATTTTCATGTTTTC
1 AAAAATTTCGTGTTTTC
43772 ----A--T-GT--TTTC
1 AAAAATTTCGTGTTTTC
*
43780 AAAAAATTTCTCGTGTTTTTA
1 -AAAAA-TT-TCGTG-TTTTC
* * *
43801 AAAAAATTCGTATTTTT
1 AAAAATTTCGTGTTTTC
* *
43818 AAAAAATTCATGTTTTC
1 AAAAATTTCGTGTTTTC
* *
43835 GAAATTTTCGTGTTTTC
1 AAAAATTTCGTGTTTTC
* *
43852 -AAAATTT-TTAG-TGTC
1 AAAAATTTCGT-GTTTTC
*
43867 AAAAAATTCTCATG-TTTC
1 -AAAAATT-TCGTGTTTTC
43885 AAAAATTTTCGTGTTTTC
1 AAAAA-TTTCGTGTTTTC
*
43903 AAAAAAGTTCCCGTGTTTTC
1 -AAAAA-TT-TCGTGTTTTC
43923 AAAAATTTCATGTTTTGGTGTTTTC
1 AAAAATTTC--------GTGTTTTC
*
43948 AAAAAATTCTCGTGTTTTTTTAA
1 -AAAAATT-TCGTG---TTTT-C
* * *
43971 AAAAAATTCATGTTTTTAA
1 AAAAATTTCGTG-TTTT-C
* *
43990 AAAAAATT-ATGTTTTC
1 AAAAATTTCGTGTTTTC
* *
44006 GAAATTTTCGTGTTTTC
1 AAAAATTTCGTGTTTTC
*
44023 AAAATTTTTCGTG---TC
1 AAAA-ATTTCGTGTTTTC
*
44038 AAAAAATTCTCATG-TTTC
1 -AAAAATT-TCGTGTTTTC
44056 AAAAATTTTCGTGTTTTC
1 AAAAA-TTTCGTGTTTTC
*
44074 AAAAAAGTTCCCGTGTTTTC
1 -AAAAA-TT-TCGTGTTTTC
*
44094 AAAAATTTCATGTTTT
1 AAAAATTTCGTGTTTT
44110 GGTGTTTTCA
Statistics
Matches: 333, Mismatches: 41, Indels: 128
0.66 0.08 0.25
Matches are distributed among these distances:
8 11 0.03
10 1 0.00
11 2 0.01
13 1 0.00
15 8 0.02
16 21 0.06
17 106 0.32
18 59 0.18
19 54 0.16
20 31 0.09
21 12 0.04
22 10 0.03
25 8 0.02
26 7 0.02
27 2 0.01
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (17 bp):
AAAAATTTCGTGTTTTC
Found at i:43711 original size:27 final size:28
Alignment explanation
Indices: 43680--43735 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
43670 TCAAAAATTC
*
43680 TCGTGTTTT-AAAAAAATTTTCGTGTTT
1 TCGTGTTTTAAAAAAAATTCTCGTGTTT
43707 TCGTGTTTTCAAAAAAAATTCTCGTGTTT
1 TCGTGTTTT-AAAAAAAATTCTCGTGTTT
43736 CAAAAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 9 0.35
29 17 0.65
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (28 bp):
TCGTGTTTTAAAAAAAATTCTCGTGTTT
Found at i:43721 original size:63 final size:63
Alignment explanation
Indices: 43653--43834 Score: 203
Period size: 65 Copynumber: 2.9 Consensus size: 63
43643 CTCGTGAATA
* * *
43653 AAAAAAATT-TCGTGTTTTCAAAAATTCTCGTGTTTTAAAAAAATTTTCGTGTTTTCGTGTTTTC
1 AAAAAAATTCTCGTGTTTTCAAAAATTCTCATGTTTT--AAAAATTTTCATGTTTTCATGTTTTC
* *
43717 AAAAAAAATTCTCGTG-TTTCAAAAATTTTCATGTTTTCAAAATTTTCATGTTTTCATGTTTTC
1 -AAAAAAATTCTCGTGTTTTCAAAAATTCTCATGTTTTAAAAATTTTCATGTTTTCATGTTTTC
* * *
43780 AAAAAATTTCTCGTGTTTTTAAAAAAATTCGT-AT-TTTTAAAAA-ATTCATGTTTTC
1 AAAAAAATTCTCGTG-TTTT-CAAAAATTC-TCATGTTTTAAAAATTTTCATGTTTTC
43835 GAAATTTTCG
Statistics
Matches: 102, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
62 14 0.14
63 34 0.33
64 11 0.11
65 37 0.36
66 6 0.06
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (63 bp):
AAAAAAATTCTCGTGTTTTCAAAAATTCTCATGTTTTAAAAATTTTCATGTTTTCATGTTTTC
Found at i:43744 original size:46 final size:45
Alignment explanation
Indices: 43660--43754 Score: 131
Period size: 46 Copynumber: 2.1 Consensus size: 45
43650 ATAAAAAAAA
*
43660 TTTCGTGTTTTCAAAAATTCTCGTGTTTTAAAAAAATTTTCGTGT
1 TTTCGTGTTTTCAAAAATTCTCGTGTTTTAAAAAAATTTTCATGT
*
43705 TTTCGTGTTTTCAAAAAAAATTCTCGTG-TTT-CAAAAATTTTCATGT
1 TTTCGTGTTTTC---AAAAATTCTCGTGTTTTAAAAAAATTTTCATGT
43751 TTTC
1 TTTC
43755 AAAATTTTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
45 12 0.27
46 17 0.38
47 3 0.07
48 13 0.29
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.48
Consensus pattern (45 bp):
TTTCGTGTTTTCAAAAATTCTCGTGTTTTAAAAAAATTTTCATGT
Found at i:43755 original size:8 final size:8
Alignment explanation
Indices: 43742--43780 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
43732 GTTTCAAAAA
43742 TTTTCATG
1 TTTTCATG
**
43750 TTTTCAAAA
1 TTTTC-ATG
43759 TTTTCATG
1 TTTTCATG
43767 TTTTCATG
1 TTTTCATG
43775 TTTTCA
1 TTTTCA
43781 AAAAATTTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
8 20 0.77
9 6 0.23
ACGTcount: A:0.21, C:0.13, G:0.08, T:0.59
Consensus pattern (8 bp):
TTTTCATG
Found at i:43920 original size:37 final size:36
Alignment explanation
Indices: 43771--43938 Score: 98
Period size: 34 Copynumber: 4.7 Consensus size: 36
43761 TTCATGTTTT
* * *
43771 CATGTTTTCAAAAAATTTCTCGTGTTTTTAAAAAAATTCG
1 CATGTTTTC-AAAAA-TT-TCATG-TTTTCAAAAAATTCC
* * * **
43811 TAT-TTTT-AAAAAATTCATGTTTTC--GAAATTTT
1 CATGTTTTCAAAAATTTCATGTTTTCAAAAAATTCC
* * * * *
43843 CGTGTTTTCAAAATTTTTA-G-TGTCAAAAAATTCT
1 CATGTTTTCAAAAATTTCATGTTTTCAAAAAATTCC
*
43877 CATG-TTTCAAAAATTTTCGTGTTTTCAAAAAAGTTCC
1 CATGTTTTCAAAAA-TTTCATGTTTTCAAAAAA-TTCC
*
43914 CGTGTTTTCAAAAATTTCATGTTTT
1 CATGTTTTCAAAAATTTCATGTTTT
43939 GGTGTTTTCA
Statistics
Matches: 96, Mismatches: 23, Indels: 21
0.69 0.16 0.15
Matches are distributed among these distances:
32 9 0.09
33 13 0.14
34 23 0.24
35 5 0.05
36 10 0.10
37 21 0.22
38 9 0.09
39 4 0.04
40 2 0.02
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (36 bp):
CATGTTTTCAAAAATTTCATGTTTTCAAAAAATTCC
Found at i:44044 original size:171 final size:171
Alignment explanation
Indices: 43748--44252 Score: 903
Period size: 171 Copynumber: 3.0 Consensus size: 171
43738 AAAATTTTCA
* **
43748 TGTTTTCAAAATTTTCATGTTTTCATGTTTTCAAAAAATTTCTCGTG--TTTTT-AAAAAAATTC
1 TGTTTTCAAAAATTTCATGTTTTGGTGTTTTCAAAAAA-TTCTCGTGTTTTTTTAAAAAAAATTC
* *
43810 GTATTTTT--AAAAAATTCATGTTTTCGAAATTTTCGTGTTTTCAAAATTTTTAGTGTCAAAAAA
65 ATGTTTTTAAAAAAAATT-ATGTTTTCGAAATTTTCGTGTTTTCAAAATTTTTAGTGTCAAAAAA
43873 TTCTCATGTTTCAAAAATTTTCGTGTTTTCAAAAAAGTTCCCG
129 TTCTCATGTTTCAAAAATTTTCGTGTTTTCAAAAAAGTTCCCG
43916 TGTTTTCAAAAATTTCATGTTTTGGTGTTTTCAAAAAATTCTCGTGTTTTTTTAAAAAAAATTCA
1 TGTTTTCAAAAATTTCATGTTTTGGTGTTTTCAAAAAATTCTCGTGTTTTTTTAAAAAAAATTCA
*
43981 TGTTTTTAAAAAAAATTATGTTTTCGAAATTTTCGTGTTTTCAAAATTTTTCGTGTCAAAAAATT
66 TGTTTTTAAAAAAAATTATGTTTTCGAAATTTTCGTGTTTTCAAAATTTTTAGTGTCAAAAAATT
44046 CTCATGTTTCAAAAATTTTCGTGTTTTCAAAAAAGTTCCCG
131 CTCATGTTTCAAAAATTTTCGTGTTTTCAAAAAAGTTCCCG
44087 TGTTTTCAAAAATTTCATGTTTTGGTGTTTTCAAAAAATTCTCGTGTTTTTTTAAAAAAAATTCA
1 TGTTTTCAAAAATTTCATGTTTTGGTGTTTTCAAAAAATTCTCGTGTTTTTTTAAAAAAAATTCA
44152 TGTTTTTAAAAAAAATTATGTTTTCGAAATTTTCGTGTTTTCAAAATTTTTAGTGTCAAAAAATT
66 TGTTTTTAAAAAAAATTATGTTTTCGAAATTTTCGTGTTTTCAAAATTTTTAGTGTCAAAAAATT
44217 CTCATGTTTCAAAAATTTTCGTGTTTTCAAAAAAGT
131 CTCATGTTTCAAAAATTTTCGTGTTTTCAAAAAAGT
44253 ATACCAATTT
Statistics
Matches: 325, Mismatches: 7, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
167 8 0.02
168 35 0.11
169 5 0.02
170 16 0.05
171 253 0.78
172 8 0.02
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (171 bp):
TGTTTTCAAAAATTTCATGTTTTGGTGTTTTCAAAAAATTCTCGTGTTTTTTTAAAAAAAATTCA
TGTTTTTAAAAAAAATTATGTTTTCGAAATTTTCGTGTTTTCAAAATTTTTAGTGTCAAAAAATT
CTCATGTTTCAAAAATTTTCGTGTTTTCAAAAAAGTTCCCG
Found at i:44230 original size:17 final size:18
Alignment explanation
Indices: 44210--44249 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
44200 TTTAGTGTCA
44210 AAAAATTCTCATG-TTTC
1 AAAAATTCTCATGTTTTC
* *
44227 AAAAATTTTCGTGTTTTC
1 AAAAATTCTCATGTTTTC
44245 AAAAA
1 AAAAA
44250 AGTATACCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (18 bp):
AAAAATTCTCATGTTTTC
Done.