Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022777.1 Corchorus olitorius cultivar O-4 contig22810, 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: 26438
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:149 original size:13 final size:13
Alignment explanation
Indices: 131--157 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
121 GTCATCGGAT
131 TCCTTCAATTCAA
1 TCCTTCAATTCAA
144 TCCTTCAATTCAA
1 TCCTTCAATTCAA
157 T
1 T
158 ATGTATGGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.41
Consensus pattern (13 bp):
TCCTTCAATTCAA
Found at i:1089 original size:334 final size:338
Alignment explanation
Indices: 400--1328 Score: 926
Period size: 334 Copynumber: 2.8 Consensus size: 338
390 CGCAAAGGCC
* * *
400 CCTTGAAATATCTATATTCAT-TGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTA
1 CCTTGAAATATCTATATTCATCT-AATCAAATCTCAGCCACATTGGATTCAAGAATTTGTTTTTA
** * * * * * * * * * *
464 CGAGTTTCTGAATTTTGTTTCAATTTAATTAGAAATCAATT-TGGAAAAAAAAATGGAAAACCGA
65 CGAGCATCTAAATCTTGATTCGATTTAATAAGAAATAAATTCAGCAAAAGAAAA-GGAAAAACGA
* * * * *
528 TATTAGAAGC-CCAAAAATCCCGTCAATCT-TTTTGGCGTTCAATTATACATTTTTTATGAGTAT
129 TATTAGAAACGTCAAAAA-CCCTTCAAT-TGTTTTGGCGTTGAATTATATATTTTTTATGAGTAT
* ** * ** * * *
591 TGTGGGAAAAAATTGA-GAAAAAATTTTC--G---A--TTT---AGTTTTTAGCCGAAATCGTGT
192 TCT-GCCAAAAATTGAGGAAAAACTTTTCGAGTCAATTTTTGCAAAATTTTAACCAAAATCATGT
* * **
645 AC-AA--ATTAC-G---GTTTTTTGGCTAAAAACGTGTTTCGGGACCCCGGTTAAGTTTTGCATG
256 ACTAACCATCACAGTTTTTTTTTTGGCTAAAAACCCGTTTCGGGACCCCGGTTAAGTTTTGCATG
* *
703 ATTTTTGGTAAAAAGAAT
321 ATTTTAGGCAAAAAGAAT
* * *
721 CCTTGAAATATCTATATTCATCTAATCAAATCTCAGCTACATTGGATTCACGGATTTGTTTTTAC
1 CCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTCAAGAATTTGTTTTTAC
* * * * *
786 GAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAATTTAG-AAAA-AAATGG-AAAATGATA
66 GAGCATCTAAATCTTGATTCGATTTAATAAGAAATAAATTCAGCAAAAGAAAAGGAAAAACGATA
** * * * *
848 TTAGAAGTGTCAAAAATCCTTCAATTTTTTTGGCGTTGAGTTATATATTTTTTATGAGTATTGTG
131 TTAGAAACGTCAAAAACCCTTCAATTGTTTTGGCGTTGAATTATATATTTTTTATGAGTATTCTG
** * * * *
913 CCAAAAAATTGAGGAAAAGTTTTTTGAGTCAGTTTTT-C-TAATTTTAACCAAAATCGTGTACTA
196 CC-AAAAATTGAGGAAAAACTTTTCGAGTCAATTTTTGCAAAATTTTAACCAAAATCATGTACTA
* * *
976 ACCATCACGGTTTTTTTTTTGGCTAAAAACCCGTTTCGAGG-CCCC-GTCTCAGTTTTTCATGAT
260 ACCATCACAGTTTTTTTTTTGGCTAAAAACCCGTTTCG-GGACCCCGGT-TAAGTTTTGCATGAT
* *
1039 TTTAGGCAGAAAGACT
323 TTTAGGCAAAAAGAAT
* ** *
1055 CTTTGAAATATCTATATTCATCTAATTGAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTAC
1 CCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTCAAGAATTTGTTTTTAC
* * *
1120 GAGCATCTGAATCTTGATTCGATTTAATAAGGAATAAATTCGGCAAAAGAAAAGGAAAAACGATA
66 GAGCATCTAAATCTTGATTCGATTTAATAAGAAATAAATTCAGCAAAAGAAAAGGAAAAACGATA
* * *
1185 TTAGAAACGTGAATAACCCTTCAATTGTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTCTG
131 TTAGAAACGTCAAAAACCCTTCAATTGTTTTGGCGTTGAATTATATATTTTTTATGAGTATTCTG
* * *
1250 GCAAAAATTGAGGAAAAACTTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTAA
196 CCAAAAATTGAGGAAAAACTTTTCGAGTCAATTTTTGCAAAATTTTAACCAAAATCATGTACTAA
1315 CCATCACAGTTTTT
261 CCATCACAGTTTTT
1329 GGCTAAAAAC
Statistics
Matches: 504, Mismatches: 76, Indels: 39
0.81 0.12 0.06
Matches are distributed among these distances:
317 2 0.00
318 64 0.13
319 17 0.03
320 3 0.01
321 98 0.19
322 2 0.00
326 3 0.01
327 18 0.04
328 2 0.00
330 4 0.01
331 1 0.00
333 2 0.00
334 146 0.29
335 6 0.01
336 35 0.07
337 66 0.13
338 35 0.07
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (338 bp):
CCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTCAAGAATTTGTTTTTAC
GAGCATCTAAATCTTGATTCGATTTAATAAGAAATAAATTCAGCAAAAGAAAAGGAAAAACGATA
TTAGAAACGTCAAAAACCCTTCAATTGTTTTGGCGTTGAATTATATATTTTTTATGAGTATTCTG
CCAAAAATTGAGGAAAAACTTTTCGAGTCAATTTTTGCAAAATTTTAACCAAAATCATGTACTAA
CCATCACAGTTTTTTTTTTGGCTAAAAACCCGTTTCGGGACCCCGGTTAAGTTTTGCATGATTTT
AGGCAAAAAGAAT
Found at i:3207 original size:322 final size:326
Alignment explanation
Indices: 2460--3342 Score: 1021
Period size: 322 Copynumber: 2.7 Consensus size: 326
2450 TTTAGTCGAT
* * *
2460 AAAGACTCCTTGAAATATATATATTCATCTAACCGAATCTCAGCCACATTGGATTTAAGGATTTG
1 AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATATAAGGATTTG
2525 ATTTTTACGAGCATCTGAATCTTT-TTTCGATTTAATTAGAAATAAATTCGG---AAAAATGGAA
66 -TTTTTACGAGCATCTGAATCTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAATGGAA
* * * **
2586 AAATGATATTAGAATCGTAAAAAAGCCCTTCAATTTTTTTTGGCTTCAAATTATATATTTTTTCT
130 AAATGATATTAGAAGCGT-GAAAAGACCTTCAA-TTTTTTTGG-TTTGAATTATATATTTTTTCT
2651 GAGTATTGTAGCAAAAAATTGAG-AAAAACTTTTCGGGTCAGTTTTTGTAAAATTTTAACCGAAA
192 GAGTATTGTAGCAAAAAATTGAGAAAAAAC-TTT----TCAG---TTGTAAAATTTTAACCGAAA
* * * * * *
2715 TTGTGTACTCATTCAAAATTGGTTTTTCGCTAAAAATGTGTTCCGAGGATCCACCTCAATTTTGA
249 TCGTGTACTCATT---AACTGGTTTTTCGCTAAAAACGCGTTCCGAGGACCCAACTCAATTTTGA
* * *
2780 ATGATTTTTGACTCCG
311 ATGATTTCTGACGCAG
* * *
2796 --AGACTACTTGAAATATCTATACTCATCAAACCAAATCTCAGCCACATTGGATATAAGGATTTG
1 AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATATAAGGATTTG
* *
2859 TTTTTACGAACATCTGAATC-TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATATTGGA
66 TTTTTACGAGCATCTGAATCTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAA-A-TGGA
* * * * *
2923 ATAACGATATTAGAAGCGTGAAAAGACCGTCAATCTTTTTGGTGTTGAATTATATATTTTTTCTA
129 AAAATGATATTAGAAGCGTGAAAAGACCTTCAATTTTTTTGGT-TTGAATTATATATTTTTTCTG
* * * ** *
2988 AATATTTTTGCAAAAAAATTGAGAAAAAACTTTTC-G-TGTAAGGTTTTAGCCGAAATCGTGTAC
193 AGTATTGTAGC-AAAAAATTGAGAAAAAACTTTTCAGTTGTAAAATTTTAACCGAAATCGTGTAC
* * * * ** *
3051 T-ATT-ACT-GTTTTTGGTTAAAAACGCGTTTCG-GGGCCCAAACTCTGTTTTGCATGATTTCT-
257 TCATTAACTGGTTTTTCGCTAAAAACGCGTTCCGAGGACCC-AACTCAATTTTGAATGATTTCTG
3111 A-GCAG
321 ACGCAG
*
3116 AAAGACTCCTTGAAATATCTACATTCATCTAACCAAATCTCAGCCACATTGG-TATAAGGATTTG
1 AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATATAAGGATTTG
3180 TTTTTACGAGCATCTGAATCTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAA-GGAAA
66 TTTTTACGAGCATCTGAATCTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAATGGAAA
* * *
3244 AATGATCTTAGAAGTGTGAAAA-ACCCTTCAATTTTTTTGGCCTTGAATTATATATTTTTTCTGA
131 AATGATATTAGAAGCGTGAAAAGA-CCTTCAATTTTTTTGG-TTTGAATTATATATTTTTTCTGA
* *
3308 GTATTGTGGCAAAAAATTGAGAAAATACTTTTCAG
194 GTATTGTAGCAAAAAATTGAGAAAAAACTTTTCAG
3343 GTCAATTTTT
Statistics
Matches: 473, Mismatches: 58, Indels: 49
0.82 0.10 0.08
Matches are distributed among these distances:
318 23 0.05
319 66 0.14
320 2 0.00
321 37 0.08
322 118 0.25
323 2 0.00
327 3 0.01
328 24 0.05
332 3 0.01
333 47 0.10
334 57 0.12
335 1 0.00
336 38 0.08
337 26 0.05
338 26 0.05
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (326 bp):
AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATATAAGGATTTG
TTTTTACGAGCATCTGAATCTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAATGGAAA
AATGATATTAGAAGCGTGAAAAGACCTTCAATTTTTTTGGTTTGAATTATATATTTTTTCTGAGT
ATTGTAGCAAAAAATTGAGAAAAAACTTTTCAGTTGTAAAATTTTAACCGAAATCGTGTACTCAT
TAACTGGTTTTTCGCTAAAAACGCGTTCCGAGGACCCAACTCAATTTTGAATGATTTCTGACGCA
G
Found at i:4044 original size:665 final size:670
Alignment explanation
Indices: 2769--4714 Score: 2294
Period size: 665 Copynumber: 2.9 Consensus size: 670
2759 GAGGATCCAC
* * ** * *
2769 CTCAATTTTGAATGATTTTT-GACTCCGAGACTAC-TTGAAATATCTATACTCATCAAACCAAAT
1 CTCAATTTTGCATGATTTTTAG-CGCAAAGACT-CGTTGAAATATCTATATTCATCGAACCAAAT
* ** * ** *
2832 CTCAGCCACA-TTGGATATAAGGATTTGTTTTTACGAACATCTGAATCTTGTTTCGATTTAATTA
64 CTCAGCCACATTTGTATATAAAAATTTGTTTTTACGAGCATCCAAATCTTGTTTCAATTTAATTA
* * * * *
2896 GAAATTAATTCGGAAAAAAATATTGGAATAACGATATTAGAAGCGTGAAAAGACCGTCAATCTTT
129 GAAATTAATTCGG-AAAAAA-A-TGGAAAAACAATATTAGAAGCGTGCAAAGCCCGTCAATATTT
* * * * *
2961 TTGGTGTTGAATTATATATTTTTTCTAAATATTTTTGCAAAAAAATTGAGAAAAAACTTTTCGTG
191 TTGGCGTTGAA-TATATA----TTATGAATA-TTTTG-TAAAAATTTGAG-----ACTTTTCG-G
* * * * * * *
3026 TA--AGGTTTTAGCCGAAATCGTGTACT----ATTACTG-TTTTTGGTTAAAAACGCGTTTCGGG
243 -AGCAGTTTTTAGCCGAAATCATGTACTAACCATCAC-GATTTTTGGCTAAAAACGAGTTT-TGT
* *** ** * * * * *
3084 GCCCAAACTCTGTTTTGCATGATTTCTAGCAGAAAGACTCCTTGAAATATCTACATTCATCTAAC
305 ACCCCGGCTCAATTTTGAATGATTTTTGGCAGAAAGACTCTTTGAAATATCTATATTCATCTAAC
* *
3149 CAAATCTCAGCCACATTGG-TATAAGGATTTGTTTTTACGAGCATCTGAATCTTTGTTTCGATTT
370 CAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTTGTTTCGATTT
* *
3213 AATTAGAAATAAATTCGGAAAAAAAAGGAAAAATGATCTTAGAAGTGTGAAAAACCCTTCAATTT
435 AATTAGAAATAAATTCGGAAAAAAAAGGAAAAACGATATTAGAAGTGTG-AAAACCCTTCAATTT
*
3278 TTTTGGCCTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGA-GAAAATACTTTTCA
499 TTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAA-ACTTTTC-
* * *
3342 GGTCAATTTTTGCAAAATTTTAGTCAAAATTGTGTAC-TTTTTTTTGCCAACGAAATCATGTACT
562 GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTTTTTTTTTGCCAACGAAATCATGTACT
* ** * * *
3406 AATTATCACGGTTTTTTGCCTAAAAACGCGTTCCGGAGTCTCGG
627 AATTATCACGGTTTTTGGCAAAAAAACGCATTCCGGAGTCCCGA
* * * *
3450 GTCAATTTTGCATGATTTTTGGCGCAAAGACTCTTTGAAATATCTATATTTATCGAACCAAATCT
1 CTCAATTTTGCATGATTTTTAGCGCAAAGACTCGTTGAAATATCTATATTCATCGAACCAAATCT
* *
3515 CAGCCACA-TTGTATATAAAAATTTGTTTTTACGAGTATCTAAATCTTGTTTCAATTTAATTAGA
66 CAGCCACATTTGTATATAAAAATTTGTTTTTACGAGCATCCAAATCTTGTTTCAATTTAATTAGA
* ** *
3579 AATTATTTCGGAAAAAAATAATGGAAAAACAATATTAGAAGCGTG-AGAAGTTCGTCAATCTTTT
131 AATTAATTCGG--AAAAA-AATGGAAAAACAATATTAGAAGCGTGCA-AAGCCCGTCAATATTTT
* * * * *
3643 TGGCGTTGAA-ATATA-TAT-AAT-TTTT-TGAATATTT-TG-C-TTTCGGGGCAGTTTTTAGCT
192 TGGCGTTGAATATATATTATGAATATTTTGTAAAAATTTGAGACTTTTCGGAGCAGTTTTTAGCC
* * *
3700 GAAATCATGTACTAATCATCACGATTTTTGGCTGAAAACGAGTTTCATG-GCCCCGGCTCAATTT
257 GAAATCATGTACTAACCATCACGATTTTTGGCTAAAAACGAGTTT--TGTACCCCGGCTCAATTT
*
3764 TGAATGATTTTTGGCAGAAAGACTCTTTGAAATATCTATATTCATGTAACCAAATCTCAGCCACA
320 TGAATGATTTTTGGCAGAAAGACTCTTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACA
* *
3829 ATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTTGTTTCGATTTAATTAGATATTAATT
385 ATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTTGTTTCGATTTAATTAGAAATAAATT
* *
3894 C-GAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAACCCCTTCAATTTTTTTGGCGTTGAATT
450 CGGAAAAAAAAGGAAAAACGATATTAGAAGTGTGAAAA-CCCTTCAATTTTTTTGGCGTTGAATT
*
3958 ATATATTTTTTCTGAGTATTATGGCAAAAAATTGAGGAAAAACTTTTCGGTTCAATTTTTGCAAA
514 ATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCGG-TCAATTTTTGCAAA
* *
4023 ATTTTAGCCGAAATCGTGTACTTTTTTTTTGCCAACGAGATCGTGTACTAATTATCACGGTTTTT
578 ATTTTAGCCGAAATCGTGTACTTTTTTTTTGCCAACGAAATCATGTACTAATTATCACGGTTTTT
4088 GGCAAAAAAACGCATTCCGGAGTCCCGA
643 GGCAAAAAAACGCATTCCGGAGTCCCGA
*
4116 CTCAATTTTGCATGATTTTTAGCGTAAAGACTCGTTGAAATATCTATATTCATCGAACCAAATCT
1 CTCAATTTTGCATGATTTTTAGCGCAAAGACTCGTTGAAATATCTATATTCATCGAACCAAATCT
* * *
4181 CAGCCACATTTGTATATAAGAATTTGTTTTTACGAGCATCCGAATCTTGTTTCGATTTAATTAGA
66 CAGCCACATTTGTATATAAAAATTTGTTTTTACGAGCATCCAAATCTTGTTTCAATTTAATTAGA
*
4246 AATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGCAAAGCCCGTCAATATTTTTGGC
131 AATTAATTCGGAAAAAAATGGAAAAACAATATTAGAAGCGTGCAAAGCCCGTCAATATTTTTGGC
* **
4311 GTTGAATTATATATTTTTCTGAATATTTTGTAAAAATTTGAGAAAAACTTTTCGGATTAGTTTTT
196 GTTGAA-TATATA---TTATGAATATTTTGTAAAAATTTGAG----ACTTTTCGGAGCAGTTTTT
* * * * *
4376 AGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAATGTGTTTTGTATCCCGGCTCAGT
253 AGCCGAAATCATGTACTAACCATCACGATTTTTGGCTAAAAACGAGTTTTGTACCCCGGCTCAAT
* * * * * *
4441 TTTAAATTATTTTTGGCAGAAAGA-TTTCTTGAAATA--TATATTTATCTAACAAAATCTTAGCC
318 TTTGAATGATTTTTGGCAGAAAGACTCT-TTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* *
4503 ACAATGGATTTAAGAATTTGTTTTTACGAGCATCTTAATCTTTGTTTCGATTTAATTAGAAATAA
382 ACAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTTGTTTCGATTTAATTAGAAATAA
* * * *
4568 ATTCGGGAAAAAAAAAGAAAAACGATATTAGAAATGTGAAATATCCTTCAATTTTTTTGGCGTTA
447 ATTC-GGAAAAAAAAGGAAAAACGATATTAGAAGTGTGAAA-ACCCTTCAATTTTTTTGGCGTTG
* * * *
4633 AATTATATATTTTTTCCGAGTA-TGTGGTAAAAAATTGAGGAAAAACTTTTCGGATCACTTTTTA
510 AATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCGG-TCAATTTTTG
*
4697 CAAAATTTTAACCGAAAT
574 CAAAATTTTAGCCGAAAT
4715 TGTATACCAT
Statistics
Matches: 1100, Mismatches: 124, Indels: 85
0.84 0.09 0.06
Matches are distributed among these distances:
660 1 0.00
661 26 0.02
662 1 0.00
664 56 0.05
665 226 0.21
666 200 0.18
667 61 0.06
668 1 0.00
669 5 0.00
670 2 0.00
671 7 0.01
672 4 0.00
673 10 0.01
674 3 0.00
677 87 0.08
678 58 0.05
679 118 0.11
680 59 0.05
681 166 0.15
682 8 0.01
683 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (670 bp):
CTCAATTTTGCATGATTTTTAGCGCAAAGACTCGTTGAAATATCTATATTCATCGAACCAAATCT
CAGCCACATTTGTATATAAAAATTTGTTTTTACGAGCATCCAAATCTTGTTTCAATTTAATTAGA
AATTAATTCGGAAAAAAATGGAAAAACAATATTAGAAGCGTGCAAAGCCCGTCAATATTTTTGGC
GTTGAATATATATTATGAATATTTTGTAAAAATTTGAGACTTTTCGGAGCAGTTTTTAGCCGAAA
TCATGTACTAACCATCACGATTTTTGGCTAAAAACGAGTTTTGTACCCCGGCTCAATTTTGAATG
ATTTTTGGCAGAAAGACTCTTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGAT
TTAAGGATTTGTTTTTACGAGCATCTGAATCTTTGTTTCGATTTAATTAGAAATAAATTCGGAAA
AAAAAGGAAAAACGATATTAGAAGTGTGAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATT
TTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCGGTCAATTTTTGCAAAATTTTAGC
CGAAATCGTGTACTTTTTTTTTGCCAACGAAATCATGTACTAATTATCACGGTTTTTGGCAAAAA
AACGCATTCCGGAGTCCCGA
Found at i:13337 original size:24 final size:24
Alignment explanation
Indices: 13310--13390 Score: 135
Period size: 24 Copynumber: 3.4 Consensus size: 24
13300 AAGCCCAGCT
*
13310 ATGCATTGGGGTTCTCATCCCATC
1 ATGCATTGGGGTTCTCATGCCATC
*
13334 ATGCATTGGCGTTCTCATGCCATC
1 ATGCATTGGGGTTCTCATGCCATC
13358 ATGCATTGGGGTTCTCATGCCATC
1 ATGCATTGGGGTTCTCATGCCATC
*
13382 ATGGATTGG
1 ATGCATTGG
13391 TGTGGCTGTA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (24 bp):
ATGCATTGGGGTTCTCATGCCATC
Found at i:19514 original size:3 final size:3
Alignment explanation
Indices: 19496--19558 Score: 108
Period size: 3 Copynumber: 20.3 Consensus size: 3
19486 TAGTTCCACC
19496 TAA TAAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
19543 TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
19559 GGGATTAAGC
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
3 52 0.90
4 6 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:20085 original size:43 final size:44
Alignment explanation
Indices: 20028--20155 Score: 170
Period size: 43 Copynumber: 2.9 Consensus size: 44
20018 TCTATTTTGA
*
20028 ATTCTGAGATTTAGGGTTTGGTCATTGATTTGGGGTTTTTCTT-
1 ATTCTGAGATTTAGGGTTTTGTCATTGATTTGGGGTTTTTCTTG
* * *
20071 ATTCTGAGAATTAGGGTTTTGTCATTGATGTGGGTGTTCTATTTTTG
1 ATTCTGAGATTTAGGGTTTTGTCATTGATTTGGG-GTT-T-TTCTTG
*
20118 ATTCTCAGATTTAGGGTTTTGTCATTGATTT-GGGTTTT
1 ATTCTGAGATTTAGGGTTTTGTCATTGATTTGGGGTTTT
20156 GTTTTGTTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
43 32 0.43
44 4 0.05
45 4 0.05
46 6 0.08
47 28 0.38
ACGTcount: A:0.16, C:0.07, G:0.27, T:0.51
Consensus pattern (44 bp):
ATTCTGAGATTTAGGGTTTTGTCATTGATTTGGGGTTTTTCTTG
Found at i:20132 original size:47 final size:47
Alignment explanation
Indices: 20005--20152 Score: 191
Period size: 47 Copynumber: 3.2 Consensus size: 47
19995 CTGTTACTCT
*
20005 TTGATTTGGGTCG-TCTA-TTTTGAATTCTGAGATTTAGGGTTTGGTCA
1 TTGATTTGGGT-GTTCTATTTTTG-ATTCTGAGATTTAGGGTTTTGTCA
* *
20052 TTGATTTGGG-GTT-T-TTCTT-ATTCTGAGAATTAGGGTTTTGTCA
1 TTGATTTGGGTGTTCTATTTTTGATTCTGAGATTTAGGGTTTTGTCA
* *
20095 TTGATGTGGGTGTTCTATTTTTGATTCTCAGATTTAGGGTTTTGTCA
1 TTGATTTGGGTGTTCTATTTTTGATTCTGAGATTTAGGGTTTTGTCA
20142 TTGATTTGGGT
1 TTGATTTGGGT
20153 TTTGTTTTGT
Statistics
Matches: 87, Mismatches: 8, Indels: 12
0.81 0.07 0.11
Matches are distributed among these distances:
43 31 0.36
44 3 0.03
45 6 0.07
46 5 0.06
47 42 0.48
ACGTcount: A:0.16, C:0.07, G:0.27, T:0.50
Consensus pattern (47 bp):
TTGATTTGGGTGTTCTATTTTTGATTCTGAGATTTAGGGTTTTGTCA
Found at i:23234 original size:25 final size:26
Alignment explanation
Indices: 23206--23260 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
23196 CGTGTTAATA
* *
23206 AAAATTTTAAATTACTATAAT-TTCT
1 AAAATTATAAATTACAATAATATTCT
* *
23231 AAAATTATATATTTCAATAATATTCT
1 AAAATTATAAATTACAATAATATTCT
23257 AAAA
1 AAAA
23261 ATTAAGGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 17 0.68
26 8 0.32
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (26 bp):
AAAATTATAAATTACAATAATATTCT
Found at i:23456 original size:13 final size:13
Alignment explanation
Indices: 23421--23449 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
23411 AGTCTCATAA
23421 TATGAGTTTAGTT
1 TATGAGTTTAGTT
23434 TATGAGTTTAGTT
1 TATGAGTTTAGTT
23447 TAT
1 TAT
23450 TTGTTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (13 bp):
TATGAGTTTAGTT
Found at i:23778 original size:33 final size:33
Alignment explanation
Indices: 23741--23849 Score: 200
Period size: 33 Copynumber: 3.3 Consensus size: 33
23731 CAATATATAG
*
23741 AAAAAAGATTTTGAGGTGTATAAAAAGCAATTG
1 AAAAAAGATTTTGAGGTGTATAAAAAGCAATTC
23774 AAAAAAGATTTTGAGGTGTATAAAAAGCAATTC
1 AAAAAAGATTTTGAGGTGTATAAAAAGCAATTC
*
23807 AAAAAAGATTTTGAGGTGTATAAAAAGCAACTC
1 AAAAAAGATTTTGAGGTGTATAAAAAGCAATTC
23840 AAAAAAGATT
1 AAAAAAGATT
23850 CTAATTATTT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 74 1.00
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.26
Consensus pattern (33 bp):
AAAAAAGATTTTGAGGTGTATAAAAAGCAATTC
Found at i:24714 original size:26 final size:28
Alignment explanation
Indices: 24670--24721 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
24660 TTAATTGAGT
24670 TTTTTTGGACATTATTAAACTTTTTTCC
1 TTTTTTGGACATTATTAAACTTTTTTCC
* *
24698 TTTTTTGG-CCTTA-TAAAGTTTTTT
1 TTTTTTGGACATTATTAAACTTTTTT
24722 AGTCATCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 10 0.45
27 4 0.18
28 8 0.36
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.60
Consensus pattern (28 bp):
TTTTTTGGACATTATTAAACTTTTTTCC
Found at i:24737 original size:21 final size:21
Alignment explanation
Indices: 24707--24777 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
24697 CTTTTTTGGC
*
24707 CTTATAAAGTTTTTTAGTCAT
1 CTTATTAAGTTTTTTAGTCAT
* *
24728 CTTATTAAGTGTTTTTA-CCTAA
1 CTTATTAAGT-TTTTTAGTC-AT
* *
24750 CTTTATTAAGATTTTTAGTAAT
1 C-TTATTAAGTTTTTTAGTCAT
24772 CTTATT
1 CTTATT
24778 GTGGATTTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
21 15 0.38
22 16 0.41
23 8 0.21
ACGTcount: A:0.28, C:0.10, G:0.08, T:0.54
Consensus pattern (21 bp):
CTTATTAAGTTTTTTAGTCAT
Found at i:25285 original size:87 final size:87
Alignment explanation
Indices: 25184--25349 Score: 296
Period size: 87 Copynumber: 1.9 Consensus size: 87
25174 AAAAAAAAGT
*
25184 TTATAAATTTTTCATTAAACTTAAAAGCTTTTTAAATAGTTTTCTTAAATTTATTCAATCACCTC
1 TTATAAATTTTTCATTAAACTTAAAAGCCTTTTAAATAGTTTTCTTAAATTTATTCAATCACCTC
25249 GTTTAAAATTTTTTTTGTAAGC
66 GTTTAAAATTTTTTTTGTAAGC
* *
25271 TTATAAATTTTTCATTAAACTTAACAGCCTTTTAAATAGTTTTCTTAAATTTATTTAATCACCTC
1 TTATAAATTTTTCATTAAACTTAAAAGCCTTTTAAATAGTTTTCTTAAATTTATTCAATCACCTC
*
25336 GTTTAAGATTTTTT
66 GTTTAAAATTTTTT
25350 GTGATCTTAT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 75 1.00
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (87 bp):
TTATAAATTTTTCATTAAACTTAAAAGCCTTTTAAATAGTTTTCTTAAATTTATTCAATCACCTC
GTTTAAAATTTTTTTTGTAAGC
Done.