Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003047.1 Hibiscus syriacus cultivar Beakdansim tig00006340_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: 59569
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:13772 original size:28 final size:29
Alignment explanation
Indices: 13731--13785 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
13721 TAAAAAAAAA
*
13731 CCCAAAAATTAATT-TATTAGGAAAATAAC
1 CCCAAAAATGAATTAT-TTAGGAAAATAAC
*
13760 CCCAAAAA-GAATTATTTGGGAAAATA
1 CCCAAAAATGAATTATTTAGGAAAATA
13786 CCTCTAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.51, C:0.13, G:0.11, T:0.25
Consensus pattern (29 bp):
CCCAAAAATGAATTATTTAGGAAAATAAC
Found at i:17349 original size:21 final size:21
Alignment explanation
Indices: 17323--17362 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
17313 GATTATATAT
17323 TTTCAAAATATAAAAATGATG
1 TTTCAAAATATAAAAATGATG
17344 TTTCAAAATATAAAAATGA
1 TTTCAAAATATAAAAATGA
17363 AAATAGTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (21 bp):
TTTCAAAATATAAAAATGATG
Found at i:23398 original size:20 final size:20
Alignment explanation
Indices: 23373--23412 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
23363 CAGATTGCCC
23373 AGAGGGTACCGATACCCCCA
1 AGAGGGTACCGATACCCCCA
23393 AGAGGGTACCGATACCCCCA
1 AGAGGGTACCGATACCCCCA
23413 TGTAAGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.35, G:0.25, T:0.10
Consensus pattern (20 bp):
AGAGGGTACCGATACCCCCA
Found at i:25207 original size:2 final size:2
Alignment explanation
Indices: 25200--25240 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
25190 TCTTAGCAGC
25200 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25241 CAATTGGTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25269 original size:19 final size:19
Alignment explanation
Indices: 25245--25283 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
25235 ATATATCAAT
25245 TGGTTATCTTGTTTAAAAA
1 TGGTTATCTTGTTTAAAAA
25264 TGGTTATCTTGTTTAAAAA
1 TGGTTATCTTGTTTAAAAA
25283 T
1 T
25284 TATAGAGTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.05, G:0.15, T:0.49
Consensus pattern (19 bp):
TGGTTATCTTGTTTAAAAA
Found at i:25450 original size:18 final size:18
Alignment explanation
Indices: 25423--25471 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
25413 GAAATTTAAG
25423 ATTTTATATTCGATTGAA
1 ATTTTATATTCGATTGAA
* *
25441 ATTTTGTATTCGATTTAA
1 ATTTTATATTCGATTGAA
*
25459 ATATTATATTCGA
1 ATTTTATATTCGA
25472 ATATCACAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.51
Consensus pattern (18 bp):
ATTTTATATTCGATTGAA
Found at i:25936 original size:22 final size:23
Alignment explanation
Indices: 25902--25945 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
25892 ATTTAAATTT
* *
25902 TATACAAGTAGTATCGATACCCC
1 TATACAAGGAGTACCGATACCCC
25925 TATA-AAGGAGTACCGATACCC
1 TATACAAGGAGTACCGATACCC
25946 ATACGCTCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (23 bp):
TATACAAGGAGTACCGATACCCC
Found at i:28272 original size:199 final size:198
Alignment explanation
Indices: 27863--28315 Score: 487
Period size: 199 Copynumber: 2.3 Consensus size: 198
27853 ATACTACGAT
* ** * * * *
27863 TCTAATCTTATAAATTATGAAAATTTCCAGATTGAATTCCCCAAAATACTCCTCGAAAATGCCTA
1 TCTAATCTTATAAATTACG-AAATTTTTAGATT-AACTACCCAAAATACCCCTCCAAAATGCCTA
*
27928 CCAACCATTTTAGCTTCTTCTTCATGCACAAAAGCAAGCTTTGGAACCATTTTCCACGCGATTTG
64 CCAACCATTTTAGCTTCTTCTTCATGCACAAAAGCAAGCTTTGGAACCATTTTCAACGCGATTTG
* * ** * * *
27993 TAGCCAACTTATAATGTCTCGTATGTATCGATATTACCCTCAGTTGAAAGATAATTTATAATATT
129 TAGCCAACTTACAATATCTCGTATGTATCGATATTACCCTCAACTCAAAGATAAATTACAATATT
*
28058 ATGCC
194 ACGCC
* * * *
28063 TTTGATCTTATAAATTACGAAATTTTTGGATTAACTACCCATAAATACCCCTCCAATATGCCTAT
1 TCTAATCTTATAAATTACGAAATTTTTAGATTAACTACCCA-AAATACCCCTCCAAAATGCCTA-
* * * * * * *
28128 CGAACCATTTTTAGTTTTTTCTTTATGCACAAAA-CAAGTTTTGGAATCATTTTCAATGCGATTT
64 CCAACCA-TTTTAGCTTCTTCTTCATGCACAAAAGCAAGCTTTGGAACCATTTTCAACGCGATTT
* * * *** *
28192 TTAGCC-GCTTACAATATCTCGTATGTGTCGATATTGGTCTCAACTCAAAGATAAATTCCAATAT
128 GTAGCCAACTTACAATATCTCGTATGTATCGATATTACCCTCAACTCAAAGATAAATTACAATAT
*
28256 TACGTC
193 TACGCC
* * *
28262 TCTAATCTTATAAATTACAAAATTTTTTAGATTAACTACCTGAAAATGCCCCTC
1 TCTAATCTTATAAATTACGAAA-TTTTTAGATTAACTACC-CAAAATACCCCTC
28316 AAACGTACCT
Statistics
Matches: 207, Mismatches: 41, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
198 7 0.03
199 97 0.47
200 79 0.38
201 24 0.12
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (198 bp):
TCTAATCTTATAAATTACGAAATTTTTAGATTAACTACCCAAAATACCCCTCCAAAATGCCTACC
AACCATTTTAGCTTCTTCTTCATGCACAAAAGCAAGCTTTGGAACCATTTTCAACGCGATTTGTA
GCCAACTTACAATATCTCGTATGTATCGATATTACCCTCAACTCAAAGATAAATTACAATATTAC
GCC
Found at i:29037 original size:2 final size:2
Alignment explanation
Indices: 29030--29083 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
29020 TGGACTAAAC
29030 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29072 TA TA TA TA TA TA
1 TA TA TA TA TA TA
29084 GCCACCCAAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32106 original size:96 final size:96
Alignment explanation
Indices: 31971--32146 Score: 291
Period size: 96 Copynumber: 1.8 Consensus size: 96
31961 TTACATTTTT
* *
31971 CAGTGAAAGTTCCAATCTATCCATGGCACCCCAACCCCCGTCTCAGCCCAAGCGACCTCGAAGGT
1 CAGTGAAAGTTCCAATCTATCCATGGCACCCCAAACCCCGTCTCAGCCCAAGCGACCTCGAAGAT
32036 CTGCTGCAACAGACGCGGTCGTTGCACTTTG
66 CTGCTGCAACAGACGCGGTCGTTGCACTTTG
* * *
32067 CAGTGAAAGTTTCGATCTAAT-CATGGCACCCCAAACCCCGTCTCAGCCCAGGCGACCTCGAAGA
1 CAGTGAAAGTTCCAATCT-ATCCATGGCACCCCAAACCCCGTCTCAGCCCAAGCGACCTCGAAGA
32131 TCTGCTGCAACAGACG
65 TCTGCTGCAACAGACG
32147 TGGTGGATAG
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
96 72 0.97
97 2 0.03
ACGTcount: A:0.25, C:0.35, G:0.22, T:0.19
Consensus pattern (96 bp):
CAGTGAAAGTTCCAATCTATCCATGGCACCCCAAACCCCGTCTCAGCCCAAGCGACCTCGAAGAT
CTGCTGCAACAGACGCGGTCGTTGCACTTTG
Found at i:32340 original size:16 final size:16
Alignment explanation
Indices: 32316--32388 Score: 110
Period size: 16 Copynumber: 4.6 Consensus size: 16
32306 TAAATAAACG
32316 AACATAAACGAACACA
1 AACATAAACGAACACA
*
32332 AATATAAACGAACACA
1 AACATAAACGAACACA
*
32348 AACATAAACGAACACG
1 AACATAAACGAACACA
* *
32364 AACATAAATGAACACG
1 AACATAAACGAACACA
32380 AACATAAAC
1 AACATAAAC
32389 ATTGGACCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.60, C:0.22, G:0.08, T:0.10
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:33083 original size:24 final size:24
Alignment explanation
Indices: 33056--33102 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
33046 TAAATGAATG
33056 AACATAAACGAACATAACCGAACA
1 AACATAAACGAACATAACCGAACA
*
33080 AACATAAACGAACATAACTGAAC
1 AACATAAACGAACATAACCGAAC
33103 GTTCACGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.57, C:0.23, G:0.09, T:0.11
Consensus pattern (24 bp):
AACATAAACGAACATAACCGAACA
Found at i:33436 original size:33 final size:33
Alignment explanation
Indices: 33385--33447 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
33375 GGCGACCTCG
* *
33385 AAGGTCTGCTGAAACAGACGCAGTGGATGCTCA
1 AAGGTCTGATGAAACAGACACAGTGGATGCTCA
* * *
33418 AAGGTCTGATGCATCAGACACGGTGGATGC
1 AAGGTCTGATGAAACAGACACAGTGGATGC
33448 ATCCTTTGCG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.29, C:0.21, G:0.32, T:0.19
Consensus pattern (33 bp):
AAGGTCTGATGAAACAGACACAGTGGATGCTCA
Found at i:35021 original size:68 final size:68
Alignment explanation
Indices: 34912--35045 Score: 232
Period size: 68 Copynumber: 2.0 Consensus size: 68
34902 TTGCGAAGGT
* *
34912 ATTCCTTTCACGCTTGGAATTGTGATACTTTCAAAAACATTGCCACAAAGTGGGGCAAATTATTA
1 ATTCCTTTCACGCTTAGAATTGGGATACTTTCAAAAACATTGCCACAAAGTGGGGCAAATTATTA
34977 GCA
66 GCA
* *
34980 ATTCCTTTCACGCTTAGAATTGGGATACTTTTAAAAACATTGCCGCAAAGTGGGGCAAATTATTA
1 ATTCCTTTCACGCTTAGAATTGGGATACTTTCAAAAACATTGCCACAAAGTGGGGCAAATTATTA
35045 G
66 G
35046 TAATCAACAA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 62 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (68 bp):
ATTCCTTTCACGCTTAGAATTGGGATACTTTCAAAAACATTGCCACAAAGTGGGGCAAATTATTA
GCA
Found at i:37580 original size:48 final size:48
Alignment explanation
Indices: 37528--37625 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
37518 AACTTTTACA
* *
37528 AATAATTGTTTGTACAGATATTAGATATCATTGCCGATTCCATGCCCT
1 AATAATTGTTTGTACAAATATTAGATATCAGTGCCGATTCCATGCCCT
*
37576 AATAATTGTTTGTACAAATGTTAGATATCAGTGCCGATTCCATGCCCT
1 AATAATTGTTTGTACAAATATTAGATATCAGTGCCGATTCCATGCCCT
37624 AA
1 AA
37626 AGTTTGATTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (48 bp):
AATAATTGTTTGTACAAATATTAGATATCAGTGCCGATTCCATGCCCT
Found at i:39744 original size:34 final size:34
Alignment explanation
Indices: 39701--39772 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
39691 GTTTTGCTCT
39701 GTGGAAGATGATTGGTGGGGCAAGGAATAGAAGG
1 GTGGAAGATGATTGGTGGGGCAAGGAATAGAAGG
39735 GTGGAAGATGATTGGTGGGGCAAGGAATAGAAGG
1 GTGGAAGATGATTGGTGGGGCAAGGAATAGAAGG
39769 GTGG
1 GTGG
39773 CGCTTGTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.31, C:0.03, G:0.49, T:0.18
Consensus pattern (34 bp):
GTGGAAGATGATTGGTGGGGCAAGGAATAGAAGG
Found at i:58302 original size:20 final size:20
Alignment explanation
Indices: 58277--58328 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
58267 CAACGCGATC
58277 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
58297 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
58317 CCAAAATCGCAA
1 CCAGAATCGCAA
58329 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:58345 original size:21 final size:20
Alignment explanation
Indices: 58318--58415 Score: 70
Period size: 20 Copynumber: 4.8 Consensus size: 20
58308 AATCAGTTTC
58318 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
58339 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
58360 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
58380 CCAAATCGCAACGCGAATAT
1 CAAAATCGCAACGCGATTTT
*
58400 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
58416 ACACATAAAT
Statistics
Matches: 57, Mismatches: 19, Indels: 3
0.72 0.24 0.04
Matches are distributed among these distances:
20 29 0.51
21 28 0.49
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:58416 original size:20 final size:20
Alignment explanation
Indices: 58382--58576 Score: 78
Period size: 20 Copynumber: 9.7 Consensus size: 20
58372 GCGATTTTCC
* *
58382 AAATCGCAACGCGAATATGA-
1 AAATCGCAACGCGAACA-CAT
58402 AAATCGCAACGCGAACACAT
1 AAATCGCAACGCGAACACAT
* *
58422 AAATCGCAACGCGTATC-CGT
1 AAATCGCAACGCG-AACACAT
* * *
58442 AAATCGCAACGTGTATC-CGT
1 AAATCGCAACGCG-AACACAT
* ****
58462 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGAACACAT
* * *
58482 AAATCGCAATGCGTATC-CGT
1 AAATCGCAACGCG-AACACAT
* * *
58502 ATATCGCAACGCGTATC-CGT
1 AAATCGCAACGCG-AACACAT
** *
58522 AAATCGCAACGATAATACAT
1 AAATCGCAACGCGAACACAT
* *
58542 AAAATCGCAACGCGTATC-CGT
1 -AAATCGCAACGCG-AACACAT
58563 AAATCGCAACGCGA
1 AAATCGCAACGCGA
58577 TATTTAAAGC
Statistics
Matches: 140, Mismatches: 28, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 121 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGAACACAT
Found at i:58426 original size:40 final size:39
Alignment explanation
Indices: 58382--58576 Score: 201
Period size: 40 Copynumber: 4.9 Consensus size: 39
58372 GCGATTTTCC
* ** *
58382 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CAT
* * *
58422 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCAT
** * * *
58462 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCAT
* ** *
58502 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT
58542 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
58577 TATTTAAAGC
Statistics
Matches: 129, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.01
40 95 0.74
41 33 0.26
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACCAT
Found at i:58450 original size:60 final size:60
Alignment explanation
Indices: 58382--58576 Score: 246
Period size: 60 Copynumber: 3.2 Consensus size: 60
58372 GCGATTTTCC
** * *
58382 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * * *** *
58442 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * **
58502 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
58563 AAATCGCAACGCGA
1 AAATCGCAACGCGA
58577 TATTTAAAGC
Statistics
Matches: 112, Mismatches: 22, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGAATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:59012 original size:32 final size:32
Alignment explanation
Indices: 58942--59009 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 32
58932 ATTTCACTTA
*
58942 GATTTCATTTCGCGTTACGATTCTGTCGTTGC
1 GATTTCATTTCGCGTTACGATTCTCTCGTTGC
* *
58974 GATTTCATTTCGCG-TGCTATTCTCTCGTTGC
1 GATTTCATTTCGCGTTACGATTCTCTCGTTGC
59005 GATTT
1 GATTT
59010 TCAAGTTAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 19 0.58
32 14 0.42
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.46
Consensus pattern (32 bp):
GATTTCATTTCGCGTTACGATTCTCTCGTTGC
Found at i:59151 original size:14 final size:14
Alignment explanation
Indices: 59132--59186 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
59122 GGAATGACTG
59132 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
59146 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
59165 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
59179 TCGCAACG
1 TCGCAACG
59187 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:59199 original size:33 final size:33
Alignment explanation
Indices: 59132--59202 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
59122 GGAATGACTG
***
59132 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
59165 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
59198 TCGCA
1 TCGCA
59203 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:59220 original size:19 final size:19
Alignment explanation
Indices: 59198--59295 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
59188 GAAACCAAAA
*
59198 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
59217 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
59231 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
59250 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
59264 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
59283 TCGCGTTGCGATT
1 TCGCGTTGCGATT
59296 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:59239 original size:14 final size:14
Alignment explanation
Indices: 59220--59309 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
59210 TTTCATTTCG
59220 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
59234 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
59253 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
59267 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
59284 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
59300 CGTTGCGATT
1 CGTTGCGATT
59310 TCATTTCAAC
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:59245 original size:33 final size:33
Alignment explanation
Indices: 59203--59316 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
59193 CAAAATCGCA
59203 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
59236 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
59269 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
59302 TTGCGA-TTTCATTTC
1 TTGCGATTTTCATTTC
59317 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 7 0.09
33 70 0.91
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Done.