Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000390.1 Hibiscus syriacus cultivar Beakdansim tig00000716_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 60439
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:2264 original size:21 final size:20
Alignment explanation
Indices: 2240--2279 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
2230 CCATGAACAG
2240 TGCTACAGTGTACCGATGCAT
1 TGCTA-AGTGTACCGATGCAT
*
2261 TGCTATGTGTACCGATGCA
1 TGCTAAGTGTACCGATGCA
2280 CAAAAACATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (20 bp):
TGCTAAGTGTACCGATGCAT
Found at i:2331 original size:21 final size:21
Alignment explanation
Indices: 2302--2342 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2292 ATATAAATTC
*
2302 TGTATCGATGCAG-TGCTACAG
1 TGTACCGATGC-GCTGCTACAG
2323 TGTACCGATGCGCTGCTACA
1 TGTACCGATGCGCTGCTACA
2343 ATACTATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (21 bp):
TGTACCGATGCGCTGCTACAG
Found at i:3077 original size:23 final size:22
Alignment explanation
Indices: 3051--3096 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
3041 CACTAGGGCA
*
3051 TATGAAATTTGTCCTGAAGGACC
1 TATG-AATTTGTCCCGAAGGACC
*
3074 TATGTATTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
3096 T
1 T
3097 CTGTATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.33
Consensus pattern (22 bp):
TATGAATTTGTCCCGAAGGACC
Found at i:3085 original size:22 final size:22
Alignment explanation
Indices: 3057--3102 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
3047 GGCATATGAA
*
3057 ATTTGTCCTGAAGGACCTATGT
1 ATTTGTCCCGAAGGACCTATGT
*
3079 ATTTGTCCCGAAGGACCTCTGT
1 ATTTGTCCCGAAGGACCTATGT
3101 AT
1 AT
3103 ATTTTATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (22 bp):
ATTTGTCCCGAAGGACCTATGT
Found at i:9460 original size:21 final size:21
Alignment explanation
Indices: 9436--9484 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
9426 AAAGAAATGG
9436 AAGATAAAGTGAAGCTTATCC
1 AAGATAAAGTGAAGCTTATCC
*
9457 AAGATAAAGTGAAGGTTATCC
1 AAGATAAAGTGAAGCTTATCC
9478 AAGATAA
1 AAGATAA
9485 TCTTAAGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.22
Consensus pattern (21 bp):
AAGATAAAGTGAAGCTTATCC
Found at i:12140 original size:24 final size:26
Alignment explanation
Indices: 12090--12140 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 26
12080 TGAGCAGCTC
* *
12090 AAAAATATAATATATTAAGATTTTTA
1 AAAAATATAATATATTAAGAATATTA
*
12116 AAAAATA-AAT-TATTAATAATATTA
1 AAAAATATAATATATTAAGAATATTA
12140 A
1 A
12141 CATTTATGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 12 0.55
25 3 0.14
26 7 0.32
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (26 bp):
AAAAATATAATATATTAAGAATATTA
Found at i:13072 original size:22 final size:21
Alignment explanation
Indices: 13047--13117 Score: 87
Period size: 22 Copynumber: 3.5 Consensus size: 21
13037 TCCAACCCTC
13047 ATCTCTACTCCACAACATCTCT
1 ATCTCTACT-CACAACATCTCT
13069 A--TCT-CT-ACAACATCTCT
1 ATCTCTACTCACAACATCTCT
*
13086 ATCTCTACTCTATAACATCTCT
1 ATCTCTACTC-ACAACATCTCT
13108 ATCTCTACTC
1 ATCTCTACTC
13118 TAAAGATGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
17 12 0.28
19 5 0.12
20 5 0.12
22 21 0.49
ACGTcount: A:0.27, C:0.37, G:0.00, T:0.37
Consensus pattern (21 bp):
ATCTCTACTCACAACATCTCT
Found at i:13080 original size:17 final size:17
Alignment explanation
Indices: 13046--13093 Score: 80
Period size: 17 Copynumber: 2.9 Consensus size: 17
13036 CTCCAACCCT
*
13046 CATCTCTA-CTCCACAA
1 CATCTCTATCTCTACAA
13062 CATCTCTATCTCTACAA
1 CATCTCTATCTCTACAA
13079 CATCTCTATCTCTAC
1 CATCTCTATCTCTAC
13094 TCTATAACAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 8 0.27
17 22 0.73
ACGTcount: A:0.27, C:0.40, G:0.00, T:0.33
Consensus pattern (17 bp):
CATCTCTATCTCTACAA
Found at i:13118 original size:22 final size:22
Alignment explanation
Indices: 13063--13119 Score: 96
Period size: 22 Copynumber: 2.5 Consensus size: 22
13053 ACTCCACAAC
13063 ATCTCTATCTCTACAACATCTCT
1 ATCTCTA-CTCTACAACATCTCT
*
13086 ATCTCTACTCTATAACATCTCT
1 ATCTCTACTCTACAACATCTCT
13108 ATCTCTACTCTA
1 ATCTCTACTCTA
13120 AAGATGAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 26 0.79
23 7 0.21
ACGTcount: A:0.26, C:0.33, G:0.00, T:0.40
Consensus pattern (22 bp):
ATCTCTACTCTACAACATCTCT
Found at i:14411 original size:23 final size:24
Alignment explanation
Indices: 14360--14419 Score: 72
Period size: 23 Copynumber: 2.5 Consensus size: 24
14350 AATGTAAGTT
14360 TTTATAATATT-TATTTTTCAATAA
1 TTTA-AATATTATATTTTTCAATAA
*
14384 TTTAAATTTTATATTTTATC-ATAA
1 TTTAAATATTATATTTT-TCAATAA
14408 -TTAAATATTATA
1 TTTAAATATTATA
14420 AATTTATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 16 0.50
24 14 0.44
25 2 0.06
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTAAATATTATATTTTTCAATAA
Found at i:14425 original size:24 final size:24
Alignment explanation
Indices: 14380--14426 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
14370 TTATTTTTCA
* *
14380 ATAATTTAAATTTTATATTTTATC
1 ATAATTTAAATATTATAATTTATC
14404 ATAA-TTAAATATTATAAATTTAT
1 ATAATTTAAATATTAT-AATTTAT
14427 TTTTTAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
ATAATTTAAATATTATAATTTATC
Found at i:15045 original size:2 final size:2
Alignment explanation
Indices: 15038--15076 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
15028 AGTTCATAGA
15038 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15077 ATAAAACTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17513 original size:21 final size:20
Alignment explanation
Indices: 17428--17584 Score: 75
Period size: 21 Copynumber: 7.8 Consensus size: 20
17418 AATGACCAAT
** *
17428 AAAATCGCAACGCGA-AATA
1 AAAATCGCAACGCGATTTTC
***
17447 AAAATCGCAACGCGATCCCC
1 AAAATCGCAACGCGATTTTC
* ** *
17467 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGA-TTTTC
*
17487 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTC
* * *
17508 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGAT-TTTC
* ** *
17529 AAATTCGCATTGTGATTTTCC
1 AAAATCGCAACGCGATTTT-C
* * *
17550 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTC
17570 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
17585 ACACATAAAT
Statistics
Matches: 102, Mismatches: 30, Indels: 11
0.71 0.21 0.08
Matches are distributed among these distances:
19 16 0.16
20 41 0.40
21 45 0.44
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTC
Found at i:17594 original size:20 final size:20
Alignment explanation
Indices: 17571--17743 Score: 100
Period size: 20 Copynumber: 8.7 Consensus size: 20
17561 GCGAATATGA
17571 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* * * *
17591 AAATTGTAACGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
17611 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAACCAT
****
17631 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTAACCAT
* * *
17651 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
17671 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
17691 AAATCGTAACG-ATAATCCGT
1 AAATCGCAACGCGTAA-CCAT
* *
17711 AAATCGCAACGAG-AATCCGT
1 AAATCGCAACGCGTAA-CCAT
17731 AAATCGCAACGCG
1 AAATCGCAACGCG
17744 ATATTTAAAG
Statistics
Matches: 128, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
19 2 0.02
20 124 0.97
21 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:17634 original size:40 final size:40
Alignment explanation
Indices: 17598--17741 Score: 191
Period size: 40 Copynumber: 3.6 Consensus size: 40
17588 CATAAATTGT
17598 AACGCGTATCCGTAAATCGCAACGTGTATCCGTAAATCGC
1 AACGCGTATCCGTAAATCGCAACGTGTATCCGTAAATCGC
** * * *
17638 AACGCGTATGGGTAAATCGCAATGCGTATCCGTATATCGC
1 AACGCGTATCCGTAAATCGCAACGTGTATCCGTAAATCGC
* *
17678 AACGCGTATCCGTAAATCGTAACGAT-AATCCGTAAATCGC
1 AACGCGTATCCGTAAATCGCAACG-TGTATCCGTAAATCGC
* *
17718 AACGAGAATCCGTAAATCGCAACG
1 AACGCGTATCCGTAAATCGCAACG
17742 CGATATTTAA
Statistics
Matches: 88, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
40 88 1.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.22
Consensus pattern (40 bp):
AACGCGTATCCGTAAATCGCAACGTGTATCCGTAAATCGC
Found at i:17636 original size:60 final size:59
Alignment explanation
Indices: 17551--17743 Score: 197
Period size: 60 Copynumber: 3.2 Consensus size: 59
17541 TGATTTTCCA
* ** * * * *
17551 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATTGTAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CGTAAATCGCAACGCGTATCCGT
* *** *
17611 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCGTAAATCGCAACGCGTATCCGT
* * ** * *
17671 ATATCGCAACGCGTATCCGTAAATCGTAACGATAATCCGTAAATCGCAACGAGAATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCGTAAATCGCAACGCGTATCCGT
17731 AAATCGCAACGCG
1 AAATCGCAACGCG
17744 ATATTTAAAG
Statistics
Matches: 107, Mismatches: 24, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
59 1 0.01
60 105 0.98
61 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (59 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACCGTAAATCGCAACGCGTATCCGT
Found at i:18260 original size:20 final size:20
Alignment explanation
Indices: 18236--18310 Score: 98
Period size: 19 Copynumber: 3.8 Consensus size: 20
18226 TGCAGAAGAG
***
18236 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
18256 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
*
18277 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
18296 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
18311 CGCAACGTGA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 18 0.38
20 15 0.31
21 15 0.31
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:18351 original size:19 final size:19
Alignment explanation
Indices: 18329--18459 Score: 103
Period size: 19 Copynumber: 7.7 Consensus size: 19
18319 GAAACCAAAA
*
18329 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
18348 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
18362 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
18381 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
18395 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
18414 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
18428 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
18447 TCGCGTTGCGATT
1 TCGCGTTGCGATT
18460 CTCTCGTTGC
Statistics
Matches: 87, Mismatches: 10, Indels: 30
0.69 0.08 0.24
Matches are distributed among these distances:
14 30 0.34
16 7 0.08
17 8 0.09
19 42 0.48
ACGTcount: A:0.10, C:0.24, G:0.23, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:18370 original size:14 final size:14
Alignment explanation
Indices: 18351--18473 Score: 84
Period size: 14 Copynumber: 7.7 Consensus size: 14
18341 TTTCATTTCG
18351 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
18365 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
18384 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
18398 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
18417 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
18431 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
18450 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
18464 CGTTGCGATT
1 CGTTGCGATT
18474 TTCATTTCAA
Statistics
Matches: 88, Mismatches: 6, Indels: 30
0.71 0.05 0.24
Matches are distributed among these distances:
14 40 0.45
15 2 0.02
16 7 0.08
17 7 0.08
18 2 0.02
19 30 0.34
ACGTcount: A:0.09, C:0.24, G:0.24, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:18376 original size:33 final size:33
Alignment explanation
Indices: 18334--18481 Score: 278
Period size: 33 Copynumber: 4.5 Consensus size: 33
18324 CAAAATCGCA
18334 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
18367 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
18400 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
18433 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
18466 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
18482 AACCCAAAGA
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 113 1.00
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:20449 original size:93 final size:93
Alignment explanation
Indices: 20161--20473 Score: 578
Period size: 93 Copynumber: 3.4 Consensus size: 93
20151 TAGATTGCTT
* *
20161 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTC
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
20226 TTTGTCTTTGTTTTGTC-TTTGG-TGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
20252 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT-ACAATGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
20316 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
20344 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
20409 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
20437 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
20474 AATACCCTGA
Statistics
Matches: 215, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
90 31 0.14
91 52 0.24
92 52 0.24
93 80 0.37
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:20651 original size:52 final size:53
Alignment explanation
Indices: 20571--20680 Score: 159
Period size: 52 Copynumber: 2.1 Consensus size: 53
20561 TAGTTTACTT
* * * **
20571 TCGCAACACGAAACTTAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACACGAAACTCAAAATCGCAACGACAAAATCGCAACGCGAAACCAAAA
*
20624 TCGCAACGCGAAAC-CAAAATCGCAACGACAAAATCGCAACGCGAAACCAAAA
1 TCGCAACACGAAACTCAAAATCGCAACGACAAAATCGCAACGCGAAACCAAAA
20676 TCGCA
1 TCGCA
20681 TTGCGATTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
52 38 0.75
53 13 0.25
ACGTcount: A:0.46, C:0.27, G:0.17, T:0.09
Consensus pattern (53 bp):
TCGCAACACGAAACTCAAAATCGCAACGACAAAATCGCAACGCGAAACCAAAA
Found at i:20655 original size:14 final size:14
Alignment explanation
Indices: 20638--20664 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20628 AACGCGAAAC
20638 CAAAATCGCAACGA
1 CAAAATCGCAACGA
20652 CAAAATCGCAACG
1 CAAAATCGCAACG
20665 CGAAACCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.30, G:0.15, T:0.07
Consensus pattern (14 bp):
CAAAATCGCAACGA
Found at i:20686 original size:19 final size:19
Alignment explanation
Indices: 20603--20680 Score: 103
Period size: 19 Copynumber: 4.4 Consensus size: 19
20593 GCAACGAGAG
**
20603 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
20622 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
20641 AATCGCAA--CG--A-CAA
1 AATCGCAACGCGAAACCAA
20655 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
20674 AATCGCA
1 AATCGCA
20681 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
14 11 0.21
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 35 0.67
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:20698 original size:19 final size:19
Alignment explanation
Indices: 20676--20813 Score: 134
Period size: 19 Copynumber: 7.8 Consensus size: 19
20666 GAAACCAAAA
*
20676 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
20695 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
20709 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
20728 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
20744 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
20761 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
20780 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
20799 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
20814 AAGTTTAATG
Statistics
Matches: 94, Mismatches: 15, Indels: 20
0.73 0.12 0.16
Matches are distributed among these distances:
14 17 0.18
16 8 0.09
17 8 0.09
19 61 0.65
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:20717 original size:14 final size:14
Alignment explanation
Indices: 20698--20754 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
20688 TTTCATTTCG
20698 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
20712 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
20729 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
20745 CGTTGCGATT
1 CGTTGCGATT
20755 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:20723 original size:33 final size:33
Alignment explanation
Indices: 20681--20811 Score: 181
Period size: 33 Copynumber: 3.8 Consensus size: 33
20671 CAAAATCGCA
20681 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
20714 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
20747 TTGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGA---T--TCTCTCG
*
20785 TTGCGATTCTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
20812 TTAAGTTTAA
Statistics
Matches: 87, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
33 56 0.64
35 1 0.01
36 1 0.01
38 29 0.33
ACGTcount: A:0.10, C:0.21, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:22769 original size:14 final size:14
Alignment explanation
Indices: 22750--22785 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
22740 ATTGTTTAAT
22750 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
22764 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
22778 TGATTTGT
1 TGATTTGT
22786 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:22904 original size:19 final size:19
Alignment explanation
Indices: 22888--22985 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
22878 AAAAATGACT
22888 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
22907 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
22926 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
22940 ATCGCAATGCGAAATTAAA
1 ATCGCAATGCGAAATGAAA
22959 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
22979 ATCGCAA
1 ATCGCAA
22986 CGAGAGAATC
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 38 0.55
20 15 0.22
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:22966 original size:52 final size:53
Alignment explanation
Indices: 22888--23003 Score: 209
Period size: 52 Copynumber: 2.2 Consensus size: 53
22878 AAAAATGACT
22888 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
22940 ATCGCAATGCGAAATTAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
22993 ATCGC-ATGCGA
1 ATCGCAATGCGA
23004 TTTCATTTCG
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
52 34 0.55
53 28 0.45
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:23028 original size:19 final size:19
Alignment explanation
Indices: 22994--23232 Score: 279
Period size: 19 Copynumber: 13.7 Consensus size: 19
22984 AACGAGAGAA
22994 TCGCA-TGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
23011 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
23030 TCGCATTGCGA--TT-ATC
1 TCGCATTGCGATTTTCATT
23046 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
23063 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
23082 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
23098 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
23115 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
23134 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
23153 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
*
23169 TCG--TTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
23186 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
23204 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
23220 TCGCATTGCGATT
1 TCGCATTGCGATT
23233 CTCTCGTTGC
Statistics
Matches: 191, Mismatches: 8, Indels: 44
0.79 0.03 0.18
Matches are distributed among these distances:
14 33 0.17
16 19 0.10
17 21 0.11
18 8 0.04
19 99 0.52
20 11 0.06
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:23066 original size:52 final size:52
Alignment explanation
Indices: 22999--23232 Score: 311
Period size: 52 Copynumber: 4.5 Consensus size: 52
22989 GAGAATCGCA
22999 TGCGA-TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGT
*
23050 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGT
*
23102 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-ATCTCG--T
* *
23159 TGCGATTTTC---TCG--TTGCGATTTTTATTTCCGCATTGCGATTTTCAT-GT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTATC-TCGT
*
23207 TGGGATTTTCATTTCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
23233 CTCTCGTTGC
Statistics
Matches: 163, Mismatches: 7, Indels: 24
0.84 0.04 0.12
Matches are distributed among these distances:
48 10 0.06
50 2 0.01
51 11 0.07
52 102 0.63
53 18 0.11
54 5 0.03
55 4 0.02
57 11 0.07
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGT
Found at i:23091 original size:71 final size:69
Alignment explanation
Indices: 22994--23246 Score: 270
Period size: 71 Copynumber: 3.6 Consensus size: 69
22984 AACGAGAGAA
* * *
22994 TCGCA-TGCGA-TTTCATTTCGCATTGCGATTTTCATTTCGCA-TTGCGATTATCTCGTTGCGAT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTGCG-ATTTGC-ATT-TCGCATTGCGAT
23056 TTTCATT
63 TTTCATT
* *
23063 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATT-T-TCATTGCGATTTGCATTTCGCATTGCGATT
23128 TTCATT
64 TTCATT
* **
23134 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATTTTTATTTCCGCATTGCGAT
1 TCGCATTGCGATTTTCATTTCGCATTGCGA-TTT-TCATTGCGATTTGCATTT-CGCATTGCGAT
23199 TTTCA--
63 TTTCATT
* *
23204 T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATT-T-TCATTGCGATT
23247 GTAATTTCCG
Statistics
Matches: 169, Mismatches: 7, Indels: 18
0.87 0.04 0.09
Matches are distributed among these distances:
66 2 0.01
67 37 0.22
69 6 0.04
70 6 0.04
71 86 0.51
72 23 0.14
73 9 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (69 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTGCGATTTGCATTTCGCATTGCGATTTT
CATT
Found at i:23238 original size:67 final size:70
Alignment explanation
Indices: 23049--23265 Score: 307
Period size: 71 Copynumber: 3.1 Consensus size: 70
23039 GATTATCTCG
*
23049 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCA-TTCG-ATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTAAT
23114 TT-CGCA
64 TTCCGCA
* *
23120 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATTTTTAT
1 TTGCGATTTTCA-TTCG-ATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTAAT
23185 TTCCGCA
64 TTCCGCA
* *
23192 TTGCGATTTTCA-T-G-TTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATTT
1 TTGCGATTTTCATTCGATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTAATTT
**
23254 CCGTG
66 CCGCA
23259 TTGCGAT
1 TTGCGAT
23266 AGTCAAATGC
Statistics
Matches: 137, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
67 54 0.39
69 1 0.01
70 1 0.01
71 65 0.47
72 16 0.12
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (70 bp):
TTGCGATTTTCATTCGATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTAATTT
CCGCA
Found at i:23254 original size:33 final size:33
Alignment explanation
Indices: 23068--23246 Score: 243
Period size: 33 Copynumber: 5.2 Consensus size: 33
23058 TCATTTCGCA
23068 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
23101 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
*
23137 CATTGCGATTTTCATTTCGCATTGCGATTTTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* *
23172 TTGCGATTTTTATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
23206 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
23239 TTGCGATT
1 TTGCGATT
23247 GTAATTTCCG
Statistics
Matches: 130, Mismatches: 8, Indels: 16
0.84 0.05 0.10
Matches are distributed among these distances:
32 1 0.01
33 61 0.47
34 29 0.22
35 8 0.06
36 6 0.05
38 25 0.19
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:25562 original size:12 final size:12
Alignment explanation
Indices: 25545--25569 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25535 TCTTCGGGGA
25545 CTTTTTCTTCTT
1 CTTTTTCTTCTT
25557 CTTTTTCTTCTT
1 CTTTTTCTTCTT
25569 C
1 C
25570 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:25777 original size:24 final size:24
Alignment explanation
Indices: 25743--25789 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
25733 CTGAAACATC
25743 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
25767 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
25790 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:26526 original size:20 final size:20
Alignment explanation
Indices: 26501--26745 Score: 267
Period size: 20 Copynumber: 12.2 Consensus size: 20
26491 TGCCCTACCG
* *
26501 GATTTACAGATTCTCGTTGC
1 GATTTACGGATTCGCGTTGC
**
26521 GATTTACGGATTATCGTTGC
1 GATTTACGGATTCGCGTTGC
**
26541 GATTTACGGATTATCGTTGC
1 GATTTACGGATTCGCGTTGC
*
26561 GATTTACGGATTCTCGTTGC
1 GATTTACGGATTCGCGTTGC
**
26581 GATTTACGGATTATCGTTGC
1 GATTTACGGATTCGCGTTGC
*
26601 GATTTACGGATACGCGTTGC
1 GATTTACGGATTCGCGTTGC
* * *
26621 GATATACGGATACGCATTGC
1 GATTTACGGATTCGCGTTGC
** *
26641 GATTTACCCATACGCGTTGC
1 GATTTACGGATTCGCGTTGC
* *
26661 GATTTACGGATACACGTTGC
1 GATTTACGGATTCGCGTTGC
*
26681 GATTTACGGATACGCGTTGC
1 GATTTACGGATTCGCGTTGC
*
26701 GATTTATGTG-TTCGCGTTGC
1 GATTTACG-GATTCGCGTTGC
* **
26721 GATTTTCATATTCGCGTTGC
1 GATTTACGGATTCGCGTTGC
26741 GATTT
1 GATTT
26746 TGGAAAAATC
Statistics
Matches: 200, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
20 199 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GATTTACGGATTCGCGTTGC
Found at i:26798 original size:21 final size:21
Alignment explanation
Indices: 26712--26810 Score: 74
Period size: 21 Copynumber: 4.7 Consensus size: 21
26702 ATTTATGTGT
* *
26712 TCGCGTTGCGATTTTC-ATAT
1 TCGCGTTGCGATTTTCAAAAA
*
26732 TCGCGTTGCGATTTTGGAAAAA
1 TCGCGTTGCGATTTT-CAAAAA
** * ** **
26754 TCGCAATGCGAATTTGTACTA
1 TCGCGTTGCGATTTTCAAAAA
* *
26775 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAAAAA
26796 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
26811 GGAAACTGAT
Statistics
Matches: 61, Mismatches: 16, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 15 0.25
21 32 0.52
22 14 0.23
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCAAAAA
Found at i:26806 original size:42 final size:44
Alignment explanation
Indices: 26712--26811 Score: 102
Period size: 42 Copynumber: 2.4 Consensus size: 44
26702 ATTTATGTGT
* *
26712 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAAA
** *
26754 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAAAAA
*
26796 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
26812 GAAACTGATT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
42 25 0.53
43 19 0.40
44 3 0.06
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (44 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAAA
Found at i:31688 original size:23 final size:23
Alignment explanation
Indices: 31631--31689 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 23
31621 GTACCCCTCT
*
31631 ATATATTATTTTTTTTTCAATTAA
1 ATATA-TATTTTTTATTCAATTAA
31655 ATCAT-TA-TTTTTATTCAA-TAA
1 AT-ATATATTTTTTATTCAATTAA
31676 ATATAATATTTTTT
1 ATAT-ATATTTTTT
31690 GTTATTTCGG
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
20 2 0.07
21 5 0.17
22 12 0.40
23 7 0.23
24 2 0.07
25 2 0.07
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (23 bp):
ATATATATTTTTTATTCAATTAA
Found at i:33963 original size:20 final size:20
Alignment explanation
Indices: 33926--33963 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
33916 TACATTGATA
*
33926 TGAAATTGATTAAGAATGGT
1 TGAAATTGATGAAGAATGGT
33946 TGAAATTGAATGAA-AATG
1 TGAAATTG-ATGAAGAATG
33964 AATTTTGGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.32
Consensus pattern (20 bp):
TGAAATTGATGAAGAATGGT
Found at i:37382 original size:20 final size:20
Alignment explanation
Indices: 37345--37383 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
37335 AGATTGAGTG
* * *
37345 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
37365 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
37384 AGTTTAGAAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:37606 original size:20 final size:21
Alignment explanation
Indices: 37561--37621 Score: 88
Period size: 20 Copynumber: 2.9 Consensus size: 21
37551 TTCCCCTGTG
37561 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
37584 GGGGGAATCGGTTCCCT-AAA
1 GGGGGAATCGGTTCCCTCAAA
*
37604 GGGGGAATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
37622 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 19 0.53
21 1 0.03
22 3 0.08
23 13 0.36
ACGTcount: A:0.21, C:0.25, G:0.33, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:41482 original size:20 final size:20
Alignment explanation
Indices: 41440--41482 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
41430 TTGTTTTCAT
* *
41440 TTTTTAATTTTGAAACATCA
1 TTTTTAATTTTGAAAAATAA
41460 TTTTTATATTTT-AAAAATAA
1 TTTTTA-ATTTTGAAAAATAA
41480 TTT
1 TTT
41483 CTCATAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTTAATTTTGAAAAATAA
Found at i:46961 original size:19 final size:20
Alignment explanation
Indices: 46937--46977 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
46927 GATCGAAATG
46937 AAAAAT-AAAACAAAAAAGT
1 AAAAATAAAAACAAAAAAGT
*
46956 AAAAATAAAAATAAAAAAGT
1 AAAAATAAAAACAAAAAAGT
46976 AA
1 AA
46978 TGGAATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.80, C:0.02, G:0.05, T:0.12
Consensus pattern (20 bp):
AAAAATAAAAACAAAAAAGT
Found at i:49846 original size:18 final size:19
Alignment explanation
Indices: 49823--49864 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
49813 GTAAGAAAAT
*
49823 ATTAAAATAA-TAAAAGCG
1 ATTAAAATAAGTAAAAGCA
49841 ATT-AAATAAGTAAAAGCA
1 ATTAAAATAAGTAAAAGCA
49859 ATTAAA
1 ATTAAA
49865 GTAAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
18 13 0.62
19 2 0.10
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.24
Consensus pattern (19 bp):
ATTAAAATAAGTAAAAGCA
Found at i:55651 original size:18 final size:19
Alignment explanation
Indices: 55624--55660 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
55614 TTCTACGAAT
*
55624 TAAAATTTTAAA-TAATAA
1 TAAAAATTTAAATTAATAA
55642 TAAAAATTTAAATTAATAA
1 TAAAAATTTAAATTAATAA
55661 AATATTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAAATTTAAATTAATAA
Found at i:55832 original size:17 final size:17
Alignment explanation
Indices: 55800--55834 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
55790 AGTAATTACA
55800 AATAATAATAATAATTT
1 AATAATAATAATAATTT
55817 AATATATAATAA-AATTT
1 AATA-ATAATAATAATTT
55834 A
1 A
55835 TACATTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATAATAATAATAATTT
Found at i:58393 original size:21 final size:21
Alignment explanation
Indices: 58369--58446 Score: 122
Period size: 21 Copynumber: 3.7 Consensus size: 21
58359 AAATTACACA
58369 TTTAGTATCTAAACTATCAGT
1 TTTAGTATCTAAACTATCAGT
*
58390 TTTAGTATTTAAACTATCAGT
1 TTTAGTATCTAAACTATCAGT
58411 TTTAGTA-CTTAAACTATCAGT
1 TTTAGTATC-TAAACTATCAGT
*
58432 TTTAGTACCTAAACT
1 TTTAGTATCTAAACT
58447 TTTAATTTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
21 52 0.98
22 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (21 bp):
TTTAGTATCTAAACTATCAGT
Done.