Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022396.1 Corchorus olitorius cultivar O-4 contig22429, 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: 9349
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Found at i:2488 original size:331 final size:331
Alignment explanation
Indices: 3--3214 Score: 2980
Period size: 333 Copynumber: 9.8 Consensus size: 331
1 TG
* * * * *
3 TAACTCAACGCCAATGAAATTTAAGGGCTTTTCAGTCTTCTAATATAATTTTTCCTATTTTTTCG
1 TAACTCAACGCCAATAAAATTGAAGGGCTTTTCAGGCTTCTAATATCATTTTTCCTATTTTTCCG
* * * * *
68 AATTAATTTCTAATTAAATTGAAACAAAATTTAGATGCTC-TTAAAACCTTATCCTTAAATCCAT
66 AATTAATTTCTAATTAAATCGAAACATAATTCAGATGCTCGTAAAAAAC-TATCCTTAAATCCAT
** * * **
132 TGTGTTTGAGATTTGGTTAGAAGAAAATTGATATTTTAAGGAGTCTTGCTGCCAAAAATCATGCA
130 TGTGGCTGAGATTTGGTTAGATGAATATAAATATTTTAAGGAGTCTTGCTGCCAAAAATCATGCA
* * * * *
197 AAACTGTGCCGGTG-CCAAGAACGCGTTTTTAACCAAAAAGCTGTGAT-G--AGTACGCGATTTC
195 AAACTATGTCGGGGCCCAAGAACGCGTTTTTAGCCAAAAA-CTGTGATGGTTAGTACACGATTTC
* * *
258 GGCCAAAATTTTGTAAAAACTGTCCCGAAAAATTTTT-CTTAATTTTTGGCCACAACACTCATAA
259 GGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTCCTCAATTTTTGGCCACAATACTCATAA
322 AAAATATA
324 AAAATATA
* * * * ** * * * *
330 TAATTCGAA-TCCAA-AACGACTGAAGGGCTTTAGATGCTTC-AATTTTCGTATTTCCTATTTTT
1 TAACTC-AACGCCAATAA-AATTGAAGGGCTTTTCAGGCTTCTAA-TATCATTTTTCCTA--TTT
* ** * *
392 TTCCTAATTAATTTCTAATTAAATCGAAACACGATTCAGATGCTCGT-AAAAACAAATCCTTCAA
61 TTCCGAATTAATTTCTAATTAAATCGAAACATAATTCAGATGCTCGTAAAAAAC-TATCCTTAAA
* * * * * ** *
456 TCCAATGTGGCTGAGAATTGGTTAGATGAATATAGATATTTCAATGAAACTTGGTGCCAAAAATC
125 TCCATTGTGGCTGAGATTTGGTTAGATGAATATAAATATTTTAAGGAGTCTTGCTGCCAAAAATC
* *
521 ATGCAAAACAATGTCGAGGCCCAAGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGA
190 ATGCAAAACTATGTCGGGGCCCAAGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGA
* * *
586 TTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATGTTTCCTCAATTTTTGACCACAACACTC
255 TTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTCCTCAATTTTTGGCCACAATACTC
651 ATAAAAAATATA
320 ATAAAAAATATA
* ** * ** * * *
663 TAATTCAAATCCAA-AAAGACTGAAGGGCTTTAGATGCTTC-AATTTTCATATTTCCTATTTTTT
1 TAACTCAACGCCAATAAA-ATTGAAGGGCTTTTCAGGCTTCTAA-TATCATTTTTCCTA-TTTTT
* * * * *
726 CCCTAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAAA-AATCCTTCAATA
63 -CCGAATTAATTTCTAATTAAATCGAAACATAATTCAGATGCTCGTAAAAAACTATCCTTAAATC
* * * * * * ** *
790 CAATGTGGCTGAGAATTGGTTAAATGAATATAGATATTTCAATGACACTTGGC-GCCAATAATCA
127 CATTGTGGCTGAGATTTGGTTAGATGAATATAAATATTTTAAGGAGTCTT-GCTGCCAAAAATCA
* * * *
854 TGCAAAACTGTGCCGGGGCCCAAGAACGCGTTTTTAACCAAAAACTGTGATGGTTAGCACACGAT
191 TGCAAAACTATGTCGGGGCCCAAGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGAT
* *
919 TTCGGCCAAAATTTTGCAAAAACAGTCCCAAAAAATTTTTCCTCAATTTTTGGCCACAATACTCA
256 TTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTCCTCAATTTTTGGCCACAATACTCA
984 TAAAAAATATA
321 TAAAAAATATA
* *
995 TAAATCAACGCCAATAAAATTGAAGGGCTTTTCTAGGCTTCT-A-AT-A----T-C-ATTTTTCG
1 TAACTCAACGCCAATAAAATTGAAGGGCTTTTC-AGGCTTCTAATATCATTTTTCCTATTTTTCC
* * *
1051 GAATAAATTTCTAATTAAATCGAAACATAATTCAGATGCTCGTAAAAAATTATTCTTAAATCCAT
65 GAATTAATTTCTAATTAAATCGAAACATAATTCAGATGCTCGTAAAAAACTATCCTTAAATCCAT
*
1116 TGTGGCTGAGATTTGGATAGATGAATATAAATATTTTAAGGAGTCTTGCTGCCAAAAATCATGCA
130 TGTGGCTGAGATTTGGTTAGATGAATATAAATATTTTAAGGAGTCTTGCTGCCAAAAATCATGCA
* * *
1181 AAACTAAGTCGGGGACCC-AGAACGCGCGTTTTTAGCCAAAAACAGTGATGATTAGTACACGATT
195 AAACTATGTCGGGG-CCCAAGAA--CGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATT
* * *
1245 TTGACCAAAATTTTGCAAAAACTATCCCGAAAAATTTTTCCTCAATTTTTGGCCACAATACTCAT
257 TCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTCCTCAATTTTTGGCCACAATACTCAT
*
1310 AAAAAATATG
322 AAAAAATATA
* * * * *
1320 TAACTCAACGCCAATAAATTTTAAGGGCTATTCAGGCTTCTAATATAATTTTTCCTATTTTTTTC
1 TAACTCAACGCCAATAAAATTGAAGGGCTTTTCAGGCTTCTAATATCATTTTTCCTA-TTTTTCC
* * *
1385 GAATTAATTTCTAATTAAATCGAAACATAATTCTGATGCTCGTAAAAAATTATTCTTAAATCCAT
65 GAATTAATTTCTAATTAAATCGAAACATAATTCAGATGCTCGTAAAAAACTATCCTTAAATCCAT
*
1450 TGTGACTGAGATTTGGTTAGATGAATATAAATATTTTAAGGAGTCTTGCTGCCAAAAATCATGCA
130 TGTGGCTGAGATTTGGTTAGATGAATATAAATATTTTAAGGAGTCTTGCTGCCAAAAATCATGCA
* * * * *
1515 AAACTAAGTCGGGGCCCCAGAACGCGCGTTTTT--CAAAAAAATAGTGATGTTTAGTACACGATT
195 AAACTATGTCGGGGCCCAAGAA--CGCGTTTTTAGCCAAAAACT-GTGATGGTTAGTACACGATT
* * *
1578 TCGGCCAAAATTTTGCAAAAACTGTCTCG-AAAATATTTCCTCAATTTTTTGCCACAATACTCAT
257 TCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTCCTCAATTTTTGGCCACAATACTCAT
1642 AACAAAA-ATTA
322 AA-AAAATA-TA
* * * * *
1653 TAATTCAACGCCGATAATATTAAAGGGCTTTTTCAGGCTTCTAATATAATTTTTCCTATTTTTCC
1 TAACTCAACGCCAATAAAATTGAAGGGC-TTTTCAGGCTTCTAATATCATTTTTCCTATTTTTCC
* * * * *
1718 G-----------AATT---T-GAAACATAATTCAGATGCTCATAAAAAATTATTCATAAATCTAT
65 GAATTAATTTCTAATTAAATCGAAACATAATTCAGATGCTCGTAAAAAACTATCCTTAAATCCAT
* * * * *
1768 TGTGCCTGAGATTTGGTTAGATGACTATAAATGTTTTAAGGAGTTTTGCCGCCAAAAATCATGCA
130 TGTGGCTGAGATTTGGTTAGATGAATATAAATATTTTAAGGAGTCTTGCTGCCAAAAATCATGCA
* * * * * ** * *
1833 AAACTAAGTTGGGGCCCCAGAAAGTGCTTTTTTAGCCAAAAACAATGATGATT-GTACATGATTT
195 AAACTATGTCGGGGCCCAAG-AA-CGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGA-TT
*
1897 TCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTCCTCAATTTTTGGCCACAACACTCAT
257 TCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTCCTCAATTTTTGGCCACAATACTCAT
*
1962 AAAAAATATT
322 AAAAAATATA
* ** * ** * * *
1972 TAAATCAAATCCAA-AAAGACTGAAGGGCTTTAGACGCTTC-AATTTTCATTTTT-TTAATTTTT
1 TAACTCAACGCCAATAAA-ATTGAAGGGCTTTTCAGGCTTCTAA-TATCATTTTTCCT-ATTTTT
* *
2034 CCGAATTAAATTCTAATTAAATCGAAACATAATTCAGATGCTCGTAAAAAGA-AATCCTTAAATC
63 CCGAATTAATTTCTAATTAAATCGAAACATAATTCAGATGCTCGTAAAAA-ACTATCCTTAAATC
* * * * * ** *
2098 CATTGTGGCTGAGAATTGGTTAGATAAATATAGATATTTCAATGACACTTGGTGCCAAAAATCAT
127 CATTGTGGCTGAGATTTGGTTAGATGAATATAAATATTTTAAGGAGTCTTGCTGCCAAAAATCAT
* * * *
2163 GCAAAACTGTGTCGCGGCCCAAGAACGCATTTTTAGCCAAAAACTGTGAAGGTTAGTACACGATT
192 GCAAAACTATGTCGGGGCCCAAGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATT
* * ** *
2228 TCAGCCAAAATTTTGCAACAACTGTCCCGAAAAACATTTCCTCAATTTTTGGGCACAATACTCAT
257 TCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTCCTCAATTTTTGGCCACAATACTCAT
2293 AAAAAATATA
322 AAAAAATATA
* * * * *
2303 TAACTCAATGCCAATAAAATTTAATGGCTTTTCAGGTTTCTACTATCATTTTTCCTATTTTTCCG
1 TAACTCAACGCCAATAAAATTGAAGGGCTTTTCAGGCTTCTAATATCATTTTTCCTATTTTTCCG
* * *
2368 AATTAATTTCTAATTAAATCGAAACATAATTCAGATGGTCATAAAAAACTATCCATAAATCCATT
66 AATTAATTTCTAATTAAATCGAAACATAATTCAGATGCTCGTAAAAAACTATCCTTAAATCCATT
* * * * *
2433 GTGCCTGAGATTTAGTTAGATGACTATAAATGTTTTAAGGAGTCTTGCCGCCAAAAATCATGCAA
131 GTGGCTGAGATTTGGTTAGATGAATATAAATATTTTAAGGAGTCTTGCTGCCAAAAATCATGCAA
* * *
2498 AACTAAGTCGGGGCCC-CGTAACGCGTGTTTTTAGCCAAAAAC----A--G-T-G---ACTATTT
196 AACTATGTCGGGGCCCAAG-AACGC--GTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTT
* ** * ** *
2551 CGGCTAAAATTTTGCAAAAAACTGAT-CCGAAAGTTTTTTCCTCAAATTACGACCA-AATTACTC
258 CGGCCAAAATTTTGC-AAAAACTG-TCCCGAAAAATTTTTCCTCAATTTTTGGCCACAA-TACTC
*
2614 AT-AAAAATGTA
320 ATAAAAAATATA
* * * * * ** * * *
2625 TAACTCAATG-TAAAAAAGATTAAAGGGCTTTTCACGCTTCGGATATCGTTTTTCTTATTTATCC
1 TAACTCAACGCCAATAAA-ATTGAAGGGCTTTTCAGGCTTCTAATATCATTTTTCCTATTTTTCC
* ** * * * *
2689 GAATTAATTTCTAATTAAATCGAAA-TTGGTTTCTA-CTACTCGTAAAAATA-AATCATTAAATC
65 GAATTAATTTCTAATTAAATCGAAACAT-AATTC-AGATGCTCGTAAAAA-ACTATCCTTAAATC
* * * * * * *
2751 CAATGAT-GTTGAGAATTGGTAAGATGAATATAGATATTTCAATGAGTCTTGGC-GCCAAAAATC
127 CATTG-TGGCTGAGATTTGGTTAGATGAATATAAATATTTTAAGGAGTCTT-GCTGCCAAAAATC
* * ** * * * *
2814 TTGCAAAACTGA-GCCGGGGCCCCGGAATGCGTTTTTAGCCATAAACTGTGATGATTAGTACGCG
190 ATGCAAAACT-ATGTCGGGGCCCAAGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACG
* * ** * *
2878 ATTTTGGCTC--AATTTTGCGAAAAACTGACCCGAAATTTTCTTTACTCAATCTTTT-TCCACAA
254 ATTTCGGC-CAAAATTTTGC-AAAAACTGTCCCGAAAAATT-TTTCCTCAAT-TTTTGGCCACAA
* *
2940 TACTCGTAAAAATTATA
315 TACTCATAAAAAATATA
* * * * * * * * *
2957 AAATATCAACTCCAA-AAAGATTGAAAGTCTTTTCATGCTTCTAATATCGTTTTTCTTAATTTTC
1 TAA-CTCAACGCCAATAAA-ATTGAAGGGCTTTTCAGGCTTCTAATATCATTTTTCCTATTTTTC
* * * ** * * *
3021 CAAAATAATTTCTAATTAAATCGAAA-TTGGTTTCCGATGCTCGT-AAAAACAAATTCTTAAATC
64 CGAATTAATTTCTAATTAAATCGAAACAT-AATTCAGATGCTCGTAAAAAAC-TATCCTTAAATC
* * * * * * * * ** *
3084 CAATGTTGTTGAGATTTGATCAGATAAATATAGATATTTCAATTAGTCTTG-TCGCCAAAAAACA
127 CATTGTGGCTGAGATTTGGTTAGATGAATATAAATATTTTAAGGAGTCTTGCT-GCCAAAAATCA
* * * * * ** * ** *
3148 TG-AGAAATTAAGCCGAGACCCCGGAACGCGTTTTTAGCAAAAAACCATGATGGTTAGTACAAGA
191 TGCA-AAACTATGTCGGGGCCCAAGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGA
3212 TTT
255 TTT
3215 GAGCAAACAT
Statistics
Matches: 2427, Mismatches: 348, Indels: 214
0.81 0.12 0.07
Matches are distributed among these distances:
317 3 0.00
318 162 0.07
319 63 0.03
320 56 0.02
321 6 0.00
322 243 0.10
323 124 0.05
324 14 0.01
325 137 0.06
326 7 0.00
327 38 0.02
328 3 0.00
329 134 0.06
330 54 0.02
331 293 0.12
332 356 0.15
333 538 0.22
334 196 0.08
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (331 bp):
TAACTCAACGCCAATAAAATTGAAGGGCTTTTCAGGCTTCTAATATCATTTTTCCTATTTTTCCG
AATTAATTTCTAATTAAATCGAAACATAATTCAGATGCTCGTAAAAAACTATCCTTAAATCCATT
GTGGCTGAGATTTGGTTAGATGAATATAAATATTTTAAGGAGTCTTGCTGCCAAAAATCATGCAA
AACTATGTCGGGGCCCAAGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGG
CCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTCCTCAATTTTTGGCCACAATACTCATAAAA
AATATA
Found at i:4039 original size:320 final size:318
Alignment explanation
Indices: 3667--4285 Score: 784
Period size: 320 Copynumber: 1.9 Consensus size: 318
3657 TCGTAAAAAC
* *
3667 AAATCCTTAAATCCAATGTTGCTGAGATTTGGTCATATAAATATAGATATTTCAACGAGTCTTGA
1 AAATCCTTAAATCCAATGTTGCTGAGATTTGGTCAGATAAATATAAATATTTCAACGAGTCTTGA
* * * * *
3732 CGCCAAAAATCATGCAAAACTGAGTCGGGACTCCGGAACGCGTTATTAGCCAAAAATTGTGATGA
66 CGCCAAAAATCATGCAAAACTGAGACGGGACCCCGGAACCCGTTATTAGCCAAAAATCGTAATGA
** * * * * *
3797 CGTA-TTTA-ATTTTGGTTAAAATTTTGT-AAAAA-TGACCCGAAAAATTTTTCTTTTTCCACAA
131 C-TACTACACATTTCGGCTAAAATTTT-TCAAAAACTAACAC-AAAAA-TTTT-TTTTGCCACAA
* * * *
3858 TACT-GGTAAAAATATATATAATAAAACG-TAAAAAAGATTGCAGGGCTTTTCGCACTTCTAAAA
191 TACTAGGTAAAAAAATATATAATAAAACGCT-AAAAA-ATTGAAGGGCTTTGCACACTTCTAAAA
* *
3921 TTA-TTTTCCTCTTTTTTCCGAATTAATTTGTAATTAAATCGAAACCTGTTTTCGGTGCTCGTTT
254 -TAGTTTGCCT-TTTTTTCCGAATTAATTTGTAAATAAATCGAAACCTGTTTTCGGTGCTCGTTT
3985 CA
317 CA
* * ** *
3987 AAATCCTTAAATCCAATGTTGCTGAGATTTTGTCAGATGAATATAAATATTTCAGTGAGTCTTGG
1 AAATCCTTAAATCCAATGTTGCTGAGATTTGGTCAGATAAATATAAATATTTCAACGAGTCTTGA
* * *
4052 CGCCAAAAATCATGCAAAACTGAGACGGGGCCCCGGAACCCGTTATTAGTCAAAAATCGTAATGG
66 CGCCAAAAATCATGCAAAACTGAGACGGGACCCCGGAACCCGTTATTAGCCAAAAATCGTAATGA
* *
4117 CTACTACACGATTTCGGCTAATATTTTTCAAAAACTAACACAAAAATTTTTTTTGCTACAATACT
131 CTACTACAC-ATTTCGGCTAAAATTTTTCAAAAACTAACACAAAAATTTTTTTTGCCACAATACT
* ** * *
4182 AGTTAAAAAAATATATAATTCAACGCTAAAAAATTGAAGGGCTTTGCACGCTTCTAATATAGTTT
195 AGGTAAAAAAATATATAATAAAACGCTAAAAAATTGAAGGGCTTTGCACACTTCTAAAATAGTTT
4247 GCCTTTTTTTCCGAATTAATTTGTAAATAAATCGAAACC
260 GCCTTTTTTTCCGAATTAATTTGTAAATAAATCGAAACC
4286 GGTTATGAAA
Statistics
Matches: 256, Mismatches: 35, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
319 38 0.15
320 159 0.62
321 30 0.12
322 25 0.10
323 4 0.02
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (318 bp):
AAATCCTTAAATCCAATGTTGCTGAGATTTGGTCAGATAAATATAAATATTTCAACGAGTCTTGA
CGCCAAAAATCATGCAAAACTGAGACGGGACCCCGGAACCCGTTATTAGCCAAAAATCGTAATGA
CTACTACACATTTCGGCTAAAATTTTTCAAAAACTAACACAAAAATTTTTTTTGCCACAATACTA
GGTAAAAAAATATATAATAAAACGCTAAAAAATTGAAGGGCTTTGCACACTTCTAAAATAGTTTG
CCTTTTTTTCCGAATTAATTTGTAAATAAATCGAAACCTGTTTTCGGTGCTCGTTTCA
Found at i:5649 original size:23 final size:23
Alignment explanation
Indices: 5619--5667 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
5609 GACCTGAATG
5619 AATTTTCCTTAATTTTTGGCCAA
1 AATTTTCCTTAATTTTTGGCCAA
5642 AATTTTCCTTAATTTTTGGCCAA
1 AATTTTCCTTAATTTTTGGCCAA
5665 AAT
1 AAT
5668 ATATAATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.29, C:0.16, G:0.08, T:0.47
Consensus pattern (23 bp):
AATTTTCCTTAATTTTTGGCCAA
Found at i:7631 original size:20 final size:19
Alignment explanation
Indices: 7604--7962 Score: 137
Period size: 20 Copynumber: 17.7 Consensus size: 19
7594 CGCGGCATAT
7604 TCACATTGAACTTTCCCAA
1 TCACATTGAACTTTCCCAA
* *
7623 TCAACATTGAACTTGCCTTAA
1 TC-ACATTGAACTTTCC-CAA
*
7644 TTCACATTCAACTTTCCCAA
1 -TCACATTGAACTTTCCCAA
* * *
7664 TCGACATTGAACTTGCCTTGAT
1 TC-ACATTGAACTTTCC--CAA
**
7686 TCACATCCAACTTTCCCAA
1 TCACATTGAACTTTCCCAA
* * *
7705 TTCACATTGAACTTGCCTTGAT
1 -TCACATTGAACTTTCC--CAA
* * *
7727 TCACATTCAAATTTCCTAA
1 TCACATTGAACTTTCCCAA
* *
7746 TTCACATTGAACTTGCCTTAA
1 -TCACATTGAACTTTCC-CAA
* * *
7767 TTCACATTCAAATTTCCTAA
1 -TCACATTGAACTTTCCCAA
* *
7787 TTCACATTGAACTTGCCTTAA
1 -TCACATTGAACTTTCC-CAA
*
7808 TTCACATTCAACTTTCCCAA
1 -TCACATTGAACTTTCCCAA
* * *
7828 TTCACATTGAACTTGCCTTGAT
1 -TCACATTGAACTTTCC--CAA
*
7850 TCACA--CAACTTTCCCAA
1 TCACATTGAACTTTCCCAA
* *
7867 TTCACATTGAACTTGCCTTCAT
1 -TCACATTGAACTTTCC--CAA
* * *
7889 TCATATTCAACTTTTCCAA
1 TCACATTGAACTTTCCCAA
* * *
7908 TTGACATTGAACTTGCCTTCAT
1 -TCACATTGAACTTTCC--CAA
* * *
7930 TCATATTCAACTTTCCAAA
1 TCACATTGAACTTTCCCAA
*
7949 TTGACATTGAACTT
1 -TCACATTGAACTT
7963 GCCTTCATTC
Statistics
Matches: 250, Mismatches: 67, Indels: 45
0.69 0.19 0.12
Matches are distributed among these distances:
17 1 0.00
18 5 0.02
19 16 0.06
20 115 0.46
21 102 0.41
22 11 0.04
ACGTcount: A:0.29, C:0.27, G:0.07, T:0.37
Consensus pattern (19 bp):
TCACATTGAACTTTCCCAA
Found at i:7659 original size:41 final size:41
Alignment explanation
Indices: 7602--7977 Score: 544
Period size: 41 Copynumber: 9.2 Consensus size: 41
7592 TACGCGGCAT
*
7602 ATTCACATTGAACTTTCCCAA-TCAACATTGAACTTGCCTTA
1 ATTCACATTCAACTTTCCCAATTC-ACATTGAACTTGCCTTA
*
7643 ATTCACATTCAACTTTCCCAA-TCGACATTGAACTTGCCTTG
1 ATTCACATTCAACTTTCCCAATTC-ACATTGAACTTGCCTTA
* *
7684 ATTCACATCCAACTTTCCCAATTCACATTGAACTTGCCTTG
1 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTA
* *
7725 ATTCACATTCAAATTTCCTAATTCACATTGAACTTGCCTTA
1 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTA
* *
7766 ATTCACATTCAAATTTCCTAATTCACATTGAACTTGCCTTA
1 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTA
*
7807 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTG
1 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTA
*
7848 ATTCACA--CAACTTTCCCAATTCACATTGAACTTGCCTTC
1 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTA
* * * *
7887 ATTCATATTCAACTTTTCCAATTGACATTGAACTTGCCTTC
1 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTA
* * * *
7928 ATTCATATTCAACTTTCCAAATTGACATTGAACTTGCCTTC
1 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTA
7969 ATTCACATT
1 ATTCACATT
7978 AGCCCTTAAT
Statistics
Matches: 314, Mismatches: 18, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
39 37 0.12
41 275 0.88
42 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.07, T:0.37
Consensus pattern (41 bp):
ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTA
Done.