Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010564.1 Corchorus capsularis cultivar CVL-1 contig10585, 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: 32787
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:268 original size:13 final size:13
Alignment explanation
Indices: 250--277 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
240 CTTGACCTCC
250 ATGGCTAGGTAGA
1 ATGGCTAGGTAGA
263 ATGGCTAGGTAGA
1 ATGGCTAGGTAGA
276 AT
1 AT
278 AACAAGTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.07, G:0.36, T:0.25
Consensus pattern (13 bp):
ATGGCTAGGTAGA
Found at i:5460 original size:3 final size:3
Alignment explanation
Indices: 5445--5499 Score: 94
Period size: 3 Copynumber: 18.3 Consensus size: 3
5435 TTTGATCGTC
5445 TCT TCT TAC- TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT T-CT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
5490 TCT TCT TCT T
1 TCT TCT TCT T
5500 TGTTTTCCTT
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 1 0.02
3 48 0.96
4 1 0.02
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:7647 original size:1 final size:1
Alignment explanation
Indices: 7641--7666 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
7631 GAATGAAGGC
7641 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
7667 CCACTTCACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:20217 original size:2 final size:2
Alignment explanation
Indices: 20210--20238 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20200 TAAAAATAAA
20210 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 A
20239 ACCACGTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27925 original size:21 final size:21
Alignment explanation
Indices: 27900--27940 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
27890 CCCACAAAAT
*
27900 TAAATGTCTAACAGAGTTCTA
1 TAAATCTCTAACAGAGTTCTA
27921 TAAATCTCTAACAGAGTTCT
1 TAAATCTCTAACAGAGTTCT
27941 TGATCAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (21 bp):
TAAATCTCTAACAGAGTTCTA
Found at i:31462 original size:333 final size:332
Alignment explanation
Indices: 30155--32787 Score: 3169
Period size: 333 Copynumber: 8.0 Consensus size: 332
30145 AACGGTGTTC
* * *
30155 TTGGTTTAGATGAATTTAGATATTTCAACGAGTCTTGACGCAAAAAATCATACAAAACTGAACCG
1 TTGG-TTAGATGAATATAGATATTTCAACGAGTCTTGGCGCAAAAAATCATGCAAAACTGAACCG
*
30220 GAGCACCCGAACGCATTTTTAGCAAAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAAATTT
65 GAGCACCCGAACGCATTTTT-GC-CAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAAATTT
*
30285 TGCAAAAATTGATCCGAAAAATTTTTCCTCAATTTTTGGCTACAATACTCAT-AAAAATATATAA
128 TGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCTACAATACTCATAAAAAATATATAA
* * * *
30349 TTCAACCCCAAAAAAATTGATGTGCTTTTCACGCTTCTAATATTGATTTTCCTATATTTTTCCGA
193 TTCAACGCCAAAAAGATTGATGGGCTTTTCACGCTTCTAATATCGATTTTCCTATATTTTTCCGA
* * * *
30414 ATTAATTTCTCATTAAAACGACGCATGATTCTGATACTTGT-ACAATCAAATCCTTAAATCCATT
258 ATTAATTTCTCATTAAATCGACACATGATTCTGATGCTCGTCA-AATCAAATCCTTAAATCCATT
*
30478 GTGGCTGGGAT
322 GTGGCTGAGAT
* *
30489 TTGGTTAGATGAATATAGATATTTCAACGAGTCTTGACGCAAAAAATCATGCAAAACTGAACCAG
1 TTGGTTAGATGAATATAGATATTTCAACGAGTCTTGGCGCAAAAAATCATGCAAAACTGAACCGG
* * * *
30554 AGCACCTGAACACATTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTGGGTTAAAATTTTG
66 AGCACCCGAACGCATTTTT-GCCAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAAATTTTG
* * *
30619 TAAAAATTGACCCGAAAAA--TTT--T--A-----GGCAAAAATACTCAT-AAAAA-ATATAATT
130 CAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCTACAATACTCATAAAAAATATATAATT
* *
30671 CAACGCCAAAAAGATTGATGGGCTTTTCACGCTTCTTATATC-AGTTTTCCTATA-TTTTCCCAA
195 CAACGCCAAAAAGATTGATGGGCTTTTCACGCTTCTAATATCGA-TTTTCCTATATTTTTCCGAA
* * * *
30734 TTAATTTCTCAATAAATCGACACATGATTATGATGCTTGTCAAATCAAATCCATAAATCCATTGT
259 TTAATTTCTCATTAAATCGACACATGATTCTGATGCTCGTCAAATCAAATCCTTAAATCCATTGT
30799 GGCTGAGAT
324 GGCTGAGAT
* * * ** *
30808 TTAGTTAGATGAATATAAATATTTCAACAAGTCTTGGCGCAAAAAATCATATAAAACTGAACTGG
1 TTGGTTAGATGAATATAGATATTTCAACGAGTCTTGGCGCAAAAAATCATGCAAAACTGAACCGG
* * * ** * * * * *
30873 AGTATCGGAACGCATTTAAAGCCAAAAACAGTGATAGTCAGTAGAAGATTTGGGCTAAAATTTTG
66 AGCACCCGAACGCATTT-TTGCCAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAAATTTTG
** * * *
30938 CAAAAATTGACCCGAAATTTTTTTTTCCTCAATTTTAGGCCT-GAATACCCATAAAAAATATATA
130 CAAAAATTGACCCGAAA--AATTTTTCCTCAATTTTTGG-CTACAATACTCATAAAAAATATATA
*
31002 ATTCAACGCCAAAAAGATTGATGGGCTTTTCACACTTCTAATATCGATTTTCCTATATTTTTCCG
192 ATTCAACGCCAAAAAGATTGATGGGCTTTTCACGCTTCTAATATCGATTTTCCTATATTTTTCCG
* * * *
31067 GATTATTTTCTCATTAAATCCACACATGATTCTGATGCTCGTCAAATCAAATCCTTAAATCCACT
257 AATTAATTTCTCATTAAATCGACACATGATTCTGATGCTCGTCAAATCAAATCCTTAAATCCATT
*
31132 GTGGGTGAGAT
322 GTGGCTGAGAT
* *
31143 TTGGTTAGATGAATATAGATATTTCAACGAGTCTTGGCGCAAAAAATCATGCAAAAATTAACCGG
1 TTGGTTAGATGAATATAGATATTTCAACGAGTCTTGGCGCAAAAAATCATGCAAAACTGAACCGG
* * **
31208 AGCACCCGAACGCATTTATTGGCTAAAACCGTGAAAGTTAGTACACGATTTGGGCTAAAATTTTG
66 AGCACCCGAACGCATTT-TTGCCAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAAATTTTG
* * * **
31273 CAAAAATTGACCCGAAAATTTTTTCCTTAATTTTTGGCTACAATACTTATAAGGAATATATAATT
130 CAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCTACAATACTCATAAAAAATATATAATT
* * * *
31338 CAACGCCAGAAAGATTTATGGGCATTTCACGCTTCTAATATCGAATTTCCTATATTTTTCCGAAT
195 CAACGCCAAAAAGATTGATGGGCTTTTCACGCTTCTAATATCGATTTTCCTATATTTTTCCGAAT
* ** *
31403 TAATTTCTCATTAAATAGACACATGATTCTGATGCTCGTCTTATCAAATCCTGAAATCCATTGTG
260 TAATTTCTCATTAAATCGACACATGATTCTGATGCTCGTCAAATCAAATCCTTAAATCCATTGTG
*
31468 GCTGTGAT
325 GCTGAGAT
** * *
31476 TTGGTTAGATGAATATAGATATTTCAGTGAGTCTTGGCGCAAAAAATCTTGCAAAACTGAACCAG
1 TTGGTTAGATGAATATAGATATTTCAACGAGTCTTGGCGCAAAAAATCATGCAAAACTGAACCGG
* * *
31541 AGCACCCGAATGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTGGCCTAAAATTTTT
66 AGCACCCGAACGCATTTTT-GCCAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAAATTTTG
* *
31606 CAAAAATTGACCGGAAAAATTTTTCCTCGATTTTTGGCTACAATACTCATAAAACAA-ATATAAT
130 CAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCTACAATACTCATAAAA-AATATATAAT
* * * * *
31670 TCAACGCCAAAAAAGATTGATTGGCATGTCACGCTTCTAATATCGATTTTCTTTTA-TTTTCCGA
194 TCAACGCC-AAAAAGATTGATGGGCTTTTCACGCTTCTAATATCGATTTTCCTATATTTTTCCGA
* *
31734 ATTAATTTCTCATTAGATCG--AC---A-T-TGATGCTCGTCAAATCAAATCCTGAAATCCATTG
258 ATTAATTTCTCATTAAATCGACACATGATTCTGATGCTCGTCAAATCAAATCCTTAAATCCATTG
* *
31792 -GGGTGTGAT
323 TGGCTGAGAT
* * *
31801 TTGGTT--ATGAATATAGATATTTCAATGAGTCATGGCGCAAAAAATCATGCAAAACTGTACCGG
1 TTGGTTAGATGAATATAGATATTTCAACGAGTCTTGGCGCAAAAAATCATGCAAAACTGAACCGG
* * *
31864 AGCA-CCGAAACGCATTTTTATCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAACATTTT
66 AGCACCCG-AACGCATTTTT-GCCAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAAATTTT
31928 GCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCTACAATACTCATAAAAAATATATAAT
129 GCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCTACAATACTCATAAAAAATATATAAT
* * * *
31993 TCAACGCCAAAAAGATTGATGGGCATTTCACGTTTCTAATATCGATTTTCCTTTTTTTTTCCTG-
194 TCAACGCCAAAAAGATTGATGGGCTTTTCACGCTTCTAATATCGATTTTCCTATATTTTTCC-GA
* ** *
32057 ATTAATTTCTCATTAAATCGACATATGATTCTGATATTCGTCAAATCAAATCCTTCAATCCATTG
258 ATTAATTTCTCATTAAATCGACACATGATTCTGATGCTCGTCAAATCAAATCCTTAAATCCATTG
*
32122 TGGCTCAGAT
323 TGGCTGAGAT
* * * * *
32132 TTGGTCAGATGAATATAGATATTTCAATGAGTCTTGGCGTAGAAAATCATGCAAAACTGAGCCGG
1 TTGGTTAGATGAATATAGATATTTCAACGAGTCTTGGCGCAAAAAATCATGCAAAACTGAACCGG
* ** * * *
32197 AGTACTGGAACACATTTTTAGCCAAAAACCGCGATGGTTAGTACAAGATTTGGGCTAAAATTTTG
66 AGCACCCGAACGCATTTTT-GCCAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAAATTTTG
* * * * * *
32262 CAAAAATTGATCCGAAAAAATTTTCCTCAATTTTTGGCCAGAATACTTATAAAAAATATATAGTT
130 CAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCTACAATACTCATAAAAAATATATAATT
* * * *
32327 CAAAGCCAAAAAGATTGATGGGCTTTTCACGTTTCTAATATTGATTTTCCTATATTTTTCCGGAT
195 CAACGCCAAAAAGATTGATGGGCTTTTCACGCTTCTAATATCGATTTTCCTATATTTTTCCGAAT
* * * * * * *
32392 TATTTTCTCAGTAAATAGATATACGATTCTGATGCTCGTCAAATCAAATCCTTAAATCCTTTGTG
260 TAATTTCTCATTAAATCGACACATGATTCTGATGCTCGTCAAATCAAATCCTTAAATCCATTGTG
*
32457 GGTGAGAT
325 GCTGAGAT
* * * * **
32465 TTGGTTAGATGAATATAGTTATTTCAAGGAGTCTT-TCTGCCGAAAAATCATGCAAAACTGAGTC
1 TTGGTTAGATGAATATAGATATTTCAACGAGTCTTGGC-G-CAAAAAATCATGCAAAACTGAACC
* * ** * * * * *
32529 GGGGC-CCCGAAATGTGTTTTTGGCTAAAAACCGTGATGGTTAGTACACAATTTCGACTAAAATA
64 GGAGCACCCG-AACGCATTTTT-GCCAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAAATT
* * * * * *
32593 TTGCAAAAACTGACCC-AAAATTTTTTTCCTCCATTTTTTGCCACAATACTCAGAAAAACATATA
127 TTGCAAAAATTGACCCGAAAA-ATTTTTCCTCAATTTTTGGCTACAATACTCATAAAAA-ATATA
* * ** * * * *
32657 TAATTCAACACCAAAAATATTGAAAGGTTTTTCATGCTTCTAATATC-ATTTTTCCATTTTTTGT
190 TAATTCAACGCCAAAAAGATTGATGGGCTTTTCACGCTTCTAATATCGA-TTTTCC-TATATT-T
* * * * * * * * * * *
32721 TTTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAATCCTTAAAT
252 TTCCGAATTAATTTCTCATTAAATCGACACATGATTCTGATGCTCGTCAAATCAAATCCTTAAAT
32786 CC
317 CC
Statistics
Matches: 1989, Mismatches: 261, Indels: 95
0.85 0.11 0.04
Matches are distributed among these distances:
319 198 0.10
320 56 0.03
321 18 0.01
322 47 0.02
323 202 0.10
324 1 0.00
325 16 0.01
326 33 0.02
327 2 0.00
328 3 0.00
329 1 0.00
330 33 0.02
331 13 0.01
332 75 0.04
333 770 0.39
334 215 0.11
335 249 0.13
336 4 0.00
337 53 0.03
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (332 bp):
TTGGTTAGATGAATATAGATATTTCAACGAGTCTTGGCGCAAAAAATCATGCAAAACTGAACCGG
AGCACCCGAACGCATTTTTGCCAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAAATTTTGC
AAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCTACAATACTCATAAAAAATATATAATTC
AACGCCAAAAAGATTGATGGGCTTTTCACGCTTCTAATATCGATTTTCCTATATTTTTCCGAATT
AATTTCTCATTAAATCGACACATGATTCTGATGCTCGTCAAATCAAATCCTTAAATCCATTGTGG
CTGAGAT
Found at i:32009 original size:656 final size:659
Alignment explanation
Indices: 30155--32787 Score: 3136
Period size: 656 Copynumber: 4.0 Consensus size: 659
30145 AACGGTGTTC
* *
30155 TTGGTTTAGATGAATTTAGATATTTCAACGAGTCTTGACGCAAAAAATCATACAAAACTGAACCG
1 TTGG-TTAGATGAATATAGATATTTCAACGAGTCTTGGCGCAAAAAATCATACAAAACTGAACCG
* *
30220 GAGCACCCGAACGCATTTTTAGCAAAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAAATTT
65 GAGCACCCGAACGCATTTTTAGC-CAAAAACCGTGATGGTTAGTACAAGATTTGGGCTAAAATTT
30285 TGCAAAAATTGATCCGAAAAATTTTTCCTCAATTTTTGGCTACAATACTCAT-AAAAATATATAA
129 TGCAAAAATTGATCCGAAAAATTTTTCCTCAATTTTTGGCTACAATACTCATAAAAAATATATAA
* * * *
30349 TTCAACCCCAAAAAAATTGATGTGCTTTTCACGCTTCTAATATTGATTTTCCTATATTTTTCCGA
194 TTCAACGCCAAAAAGATTGATGGGCTTTTCACGCTTCTAATATCGATTTTCCTATATTTTTCCGA
* * *
30414 ATTAATTTCTCATTAAAACGACGCATGATTCTGATACTTGT-ACAATCAAATCCTTAAATCCATT
259 ATTAATTTCTCATTAAATCGA--C--GATTCTGATGCTCGTCA-AATCAAATCCTTAAATCCATT
* * *
30478 GTGGCTGGGATTTGGTTAGATGAATATAGATATTTCAACGAGTCTTGACGCAAAAAATCATGCAA
319 GTGGGTGAGATTTGGTTA-ATGAATATAGATATTTCAACGAGTCTTGGCGCAAAAAATCATGCAA
* * * *
30543 AACTGAACCAGAGCACCTGAACACATTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTGGG
383 AACTGTACCGGAGCACC-GAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTGGG
* * * *
30608 TTAAAATTTTGTAAAAATTGACCCGAAAAA--TTT--T--A-----GGCAAAAATACTCAT-AAA
447 CTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCTACAATACTCATAAAA
* *
30661 AA-ATATAATTCAACGCCAAAAAGATTGATGGGCTTTTCACGCTTCTTATATC-AGTTTTCCTAT
512 AATATATAATTCAACGCCAAAAAGATTGATGGGCATTTCACGCTTCTAATATCGA-TTTTCCTAT
* * * *
30724 A-TTTTCCCAATTAATTTCTCAATAAATCGACACATGATTATGATGCTTGTCAAATCAAATCCAT
576 ATTTTTCCGAATTAATTTCTCATTAAATCGACACATGATTCTGATGCTCGTCAAATCAAATCC-T
30788 AAATCCATTGTGGCTGAGAT
640 AAATCCATTGTGGCTGAGAT
* * * * *
30808 TTAGTTAGATGAATATAAATATTTCAACAAGTCTTGGCGCAAAAAATCATATAAAACTGAACTGG
1 TTGGTTAGATGAATATAGATATTTCAACGAGTCTTGGCGCAAAAAATCATACAAAACTGAACCGG
* * * ** * * * *
30873 AGTATCGGAACGCATTTAAAGCCAAAAACAGTGATAGTCAGTAGAAGATTTGGGCTAAAATTTTG
66 AGCACCCGAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACAAGATTTGGGCTAAAATTTTG
* ** * * *
30938 CAAAAATTGACCCGAAATTTTTTTTTCCTCAATTTTAGGCCT-GAATACCCATAAAAAATATATA
131 CAAAAATTGATCCGAAA--AATTTTTCCTCAATTTTTGG-CTACAATACTCATAAAAAATATATA
*
31002 ATTCAACGCCAAAAAGATTGATGGGCTTTTCACACTTCTAATATCGATTTTCCTATATTTTTCCG
193 ATTCAACGCCAAAAAGATTGATGGGCTTTTCACGCTTCTAATATCGATTTTCCTATATTTTTCCG
* * * *
31067 GATTATTTTCTCATTAAATCCACACATGATTCTGATGCTCGTCAAATCAAATCCTTAAATCCACT
258 AATTAATTTCTCATTAAAT-C-GAC--GATTCTGATGCTCGTCAAATCAAATCCTTAAATCCATT
31132 GTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAACGAGTCTTGGCGCAAAAAATCATGCAA
319 GTGGGTGAGATTTGGTTA-ATGAATATAGATATTTCAACGAGTCTTGGCGCAAAAAATCATGCAA
* * * **
31197 AAAT-TAACCGGAGCACCCGAACGCATTTATT-GGCTAAAACCGTGAAAGTTAGTACACGATTTG
383 AACTGT-ACCGGAGCA-CCGAACGCATTT-TTAGCCAAAAACCGTGATGGTTAGTACACGATTTG
* * *
31260 GGCTAAAATTTTGCAAAAATTGACCCGAAAATTTTTTCCTTAATTTTTGGCTACAATACTTATAA
445 GGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCTACAATACTCATAA
** * * *
31325 GGAATATATAATTCAACGCCAGAAAGATTTATGGGCATTTCACGCTTCTAATATCGAATTTCCTA
510 AAAATATATAATTCAACGCCAAAAAGATTGATGGGCATTTCACGCTTCTAATATCGATTTTCCTA
* **
31390 TATTTTTCCGAATTAATTTCTCATTAAATAGACACATGATTCTGATGCTCGTCTTATCAAATCCT
575 TATTTTTCCGAATTAATTTCTCATTAAATCGACACATGATTCTGATGCTCGTCAAATCAAATCCT
*
31455 GAAATCCATTGTGGCTGTGAT
640 -AAATCCATTGTGGCTGAGAT
** * * *
31476 TTGGTTAGATGAATATAGATATTTCAGTGAGTCTTGGCGCAAAAAATCTTGCAAAACTGAACCAG
1 TTGGTTAGATGAATATAGATATTTCAACGAGTCTTGGCGCAAAAAATCATACAAAACTGAACCGG
* * * *
31541 AGCACCCGAATGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTGGCCTAAAATTTTT
66 AGCACCCGAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACAAGATTTGGGCTAAAATTTTG
*
31606 CAAAAATTGA-CCGGAAAAATTTTTCCTCGATTTTTGGCTACAATACTCATAAAACAA-ATATAA
131 CAAAAATTGATCC-GAAAAATTTTTCCTCAATTTTTGGCTACAATACTCATAAAA-AATATATAA
* * * * *
31669 TTCAACGCCAAAAAAGATTGATTGGCATGTCACGCTTCTAATATCGATTTTCTTTTA-TTTTCCG
194 TTCAACGCC-AAAAAGATTGATGGGCTTTTCACGCTTCTAATATCGATTTTCCTATATTTTTCCG
* *
31733 AATTAATTTCTCATTAGATCGAC-A-T-TGATGCTCGTCAAATCAAATCCTGAAATCCATTG-GG
258 AATTAATTTCTCATTAAATCGACGATTCTGATGCTCGTCAAATCAAATCCTTAAATCCATTGTGG
* * *
31794 GTGTGATTTGGTT-ATGAATATAGATATTTCAATGAGTCATGGCGCAAAAAATCATGCAAAACTG
323 GTGAGATTTGGTTAATGAATATAGATATTTCAACGAGTCTTGGCGCAAAAAATCATGCAAAACTG
* * *
31858 TACCGGAGCACCGAAACGCATTTTTATCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAC
388 TACCGGAGCACCG-AACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAA
31923 ATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCTACAATACTCATAAAAAATAT
452 ATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCTACAATACTCATAAAAAATAT
* * *
31988 ATAATTCAACGCCAAAAAGATTGATGGGCATTTCACGTTTCTAATATCGATTTTCCTTTTTTTTT
517 ATAATTCAACGCCAAAAAGATTGATGGGCATTTCACGCTTCTAATATCGATTTTCCTATATTTTT
* ** *
32053 CCTG-ATTAATTTCTCATTAAATCGACATATGATTCTGATATTCGTCAAATCAAATCCTTCAATC
582 CC-GAATTAATTTCTCATTAAATCGACACATGATTCTGATGCTCGTCAAATCAAATCC-TAAATC
*
32117 CATTGTGGCTCAGAT
645 CATTGTGGCTGAGAT
* * * * * *
32132 TTGGTCAGATGAATATAGATATTTCAATGAGTCTTGGCGTAGAAAATCATGCAAAACTGAGCCGG
1 TTGGTTAGATGAATATAGATATTTCAACGAGTCTTGGCGCAAAAAATCATACAAAACTGAACCGG
* ** * *
32197 AGTACTGGAACACATTTTTAGCCAAAAACCGCGATGGTTAGTACAAGATTTGGGCTAAAATTTTG
66 AGCACCCGAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACAAGATTTGGGCTAAAATTTTG
* * * * *
32262 CAAAAATTGATCCGAAAAAATTTTCCTCAATTTTTGGCCAGAATACTTATAAAAAATATATAGTT
131 CAAAAATTGATCCGAAAAATTTTTCCTCAATTTTTGGCTACAATACTCATAAAAAATATATAATT
* * * *
32327 CAAAGCCAAAAAGATTGATGGGCTTTTCACGTTTCTAATATTGATTTTCCTATATTTTTCCGGAT
196 CAACGCCAAAAAGATTGATGGGCTTTTCACGCTTCTAATATCGATTTTCCTATATTTTTCCGAAT
* * * *
32392 TATTTTCTCAGTAAATAGATATACGATTCTGATGCTCGTCAAATCAAATCCTTAAATCCTTTGTG
261 TAATTTCTCATTAAATCG----ACGATTCTGATGCTCGTCAAATCAAATCCTTAAATCCATTGTG
* * * *
32457 GGTGAGATTTGGTTAGATGAATATAGTTATTTCAAGGAGTCTT-TCTGCCGAAAAATCATGCAAA
322 GGTGAGATTTGGTTA-ATGAATATAGATATTTCAACGAGTCTTGGC-G-CAAAAAATCATGCAAA
* * * * ** * * * * *
32521 ACTG-AGTCGGGGCCCCGAAATGTGTTTTTGGCTAAAAACCGTGATGGTTAGTACACAATTTCGA
384 ACTGTA-CCGGAGCACCG-AACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTGGG
* * * * * * *
32585 CTAAAATATTGCAAAAACTGACCC-AAAATTTTTTTCCTCCATTTTTTGCCACAATACTCAGAAA
447 CTAAAATTTTGCAAAAATTGACCCGAAAA-ATTTTTCCTCAATTTTTGGCTACAATACTCATAAA
* * ** ** *
32649 AACATATATAATTCAACACCAAAAATATTGAAAGGTTTTTCATGCTTCTAATATC-ATTTTTCCA
511 AA-ATATATAATTCAACGCCAAAAAGATTGATGGGCATTTCACGCTTCTAATATCGA-TTTTCC-
* * * * * * * * * * * * *
32713 TTTTTTGTTTTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAAT
573 TATATT-TTTCCGAATTAATTTCTCATTAAATCGACACATGATTCTGATGCTCGTCAAATCAAAT
32778 CCTTAAATCC
637 CC-TAAATCC
Statistics
Matches: 1696, Mismatches: 227, Indels: 97
0.84 0.11 0.05
Matches are distributed among these distances:
651 53 0.03
652 72 0.04
653 28 0.02
654 263 0.16
655 53 0.03
656 482 0.28
657 5 0.00
658 15 0.01
659 32 0.02
660 4 0.00
661 2 0.00
662 1 0.00
663 32 0.02
664 16 0.01
665 16 0.01
666 99 0.06
667 220 0.13
668 245 0.14
669 7 0.00
670 51 0.03
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (659 bp):
TTGGTTAGATGAATATAGATATTTCAACGAGTCTTGGCGCAAAAAATCATACAAAACTGAACCGG
AGCACCCGAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACAAGATTTGGGCTAAAATTTTG
CAAAAATTGATCCGAAAAATTTTTCCTCAATTTTTGGCTACAATACTCATAAAAAATATATAATT
CAACGCCAAAAAGATTGATGGGCTTTTCACGCTTCTAATATCGATTTTCCTATATTTTTCCGAAT
TAATTTCTCATTAAATCGACGATTCTGATGCTCGTCAAATCAAATCCTTAAATCCATTGTGGGTG
AGATTTGGTTAATGAATATAGATATTTCAACGAGTCTTGGCGCAAAAAATCATGCAAAACTGTAC
CGGAGCACCGAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAAATTT
TGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCTACAATACTCATAAAAAATATATAA
TTCAACGCCAAAAAGATTGATGGGCATTTCACGCTTCTAATATCGATTTTCCTATATTTTTCCGA
ATTAATTTCTCATTAAATCGACACATGATTCTGATGCTCGTCAAATCAAATCCTAAATCCATTGT
GGCTGAGAT
Found at i:32288 original size:989 final size:991
Alignment explanation
Indices: 30162--32673 Score: 3271
Period size: 989 Copynumber: 2.5 Consensus size: 991
30152 TTCTTGGTTT
* * *
30162 AGATGAATTTAGATATTTCAACGAGTCTTGACGCAAAAAATCATACAAAACTGAACCGGAGCACC
1 AGATGAATATAGATATTTCAACGAGTCTTGGCGCAAAAAATCATGCAAAACTGAACCGGAGCACC
*
30227 CGAACGCATTTTTAGCAAAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAAATTTTGCAAAA
66 CGAACGCATTTTTAGC-CAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAAATTTTGCAAAA
* *
30292 ATTGATCCGAAAAATTTTTCCTCAATTTTTGGCTACAATACTCATAAAAATATATAATTCAACCC
130 ATTGATCCGAAAAATTTTTCCTCAATTTTTGGCTACAATACTTATAAAAATATATAATTCAACGC
* *
30357 CAAAAAAATTGATGTGCTTTTCACGCTTCTAATATTGATTTTCCTATATTTTTCCGAATTAATTT
195 CAAAAAGATTGATGGGCTTTTCACGCTTCTAATATTGATTTTCCTATATTTTTCCGAATTAATTT
* * * *
30422 CTCATTAAA-ACGACGCATGATTCTGATACTTGTACAATCAAATCCTTAAATCCATTGTGGCTGG
260 CTCATTAAATA-GACACATGATTCTGATGCTCGT-CAATCAAATCCTTAAATCCATTGTGGCTGA
*
30486 GATTTGGTTAGATGAATATAGATATTTCAACGAGTCTTGACGCAAAAAATCATGCAAAACTGAAC
323 GATTTGGTTAGATGAATATAGATATTTC-AGGAGTCTTGACGCAAAAAATCATGCAAAACTGAAC
* ** **
30551 CAGAGCACCTGAACACATTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTGGGTTAAAATT
387 CAGAGCACCCGAATGCATTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTGGACTAAAATT
*
30616 TTGT-AAAAATTGACCCGAAAAA--TTT--T-A-----GGCAAAAATACTCAT-AAA-AAATATA
452 TT-TCAAAAATTGA-CCGAAAAATTTTTCCTCATTTTTGGCAACAATACTCATAAAACAAATATA
* * *
30668 ATTCAACGCC-AAAAAGATTGATGGGCTTTTCACGCTTCTTATATCAGTTTTCCTATATTTTCCC
515 ATTCAACGCCAAAAAAGATTGATGGGCATGTCACGCTTCTAATATCAGTTTTCCTATATTTTCCC
*
30732 AATTAATTTCTCAATAAATCGACACATGATTATGATGCTTGTCAAATCAAATCCATAAATCCATT
580 AATTAATTTCTCAATAAATCGA-ACA--ATTATGATGCTCGTCAAATCAAATCCATAAATCCATT
* *
30797 GTGGCTGAGATTTAGTTAGATGAATATAAATATTTCAACAAGTCTTGGCGCAAAAAATCATATAA
642 GTGGCTGAGATTTAGTTA-ATGAATATAAATATTTCAACAAGTCATGGCGCAAAAAATCATACAA
* * * * *
30862 AACTGAACTGGAGTATCGGAACGCATTTAAAGCCAAAAACAGTGATAGTCAGTAGAAGATTTGGG
706 AACTGAACCGGAGCACCGAAACGCATTTAAAGCCAAAAACAGTGATAGTCAGTACAAGATTTGGG
** *
30927 CTAAAATTTTGCAAAAATTGACCCGAAATTTTTTTTTCCTCAATTTTAGGCCTGAATACCCATAA
771 CTAAAATTTTGCAAAAATTGACCCGAAA-TAATTTTTCCTCAATTTTAGGCCTCAATACCCATAA
*
30992 AAAATATATAATTCAACGCCAAAAAGATTGATGGGCTTTTCACACTTCTAATATCGATTTTCCTA
835 AAAATATATAATTCAACGCCAAAAAGATTGATGGGCATTTCACACTTCTAATATCGATTTTCCTA
* *
31057 TATTTTTCCGGATTATTTTCTCATTAAATCCACACATGATTCTGATGCTCGTCAAATCAAATCCT
900 TATTTTTCCGGATTAATTTCTCATTAAATCCACACATGATTCTGATACTCGTCAAATCAAATCCT
* * *
31122 TAAATCCACTGTGGGTGAGATTTGGTT
965 TAAATCCACTGTGGCTCAGATTTGGTC
* *
31149 AGATGAATATAGATATTTCAACGAGTCTTGGCGCAAAAAATCATGCAAAAATTAACCGGAGCACC
1 AGATGAATATAGATATTTCAACGAGTCTTGGCGCAAAAAATCATGCAAAACTGAACCGGAGCACC
* * **
31214 CGAACGCATTTATT-GGCTAAAACCGTGAAAGTTAGTACACGATTTGGGCTAAAATTTTGCAAAA
66 CGAACGCATTT-TTAGCCAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAAATTTTGCAAAA
* * * *
31278 ATTGACCCGAAAATTTTTTCCTTAATTTTTGGCTACAATACTTATAAGGAATATATAATTCAACG
130 ATTGATCCGAAAAATTTTTCCTCAATTTTTGGCTACAATACTTATAA-AAATATATAATTCAACG
* * * * *
31343 CCAGAAAGATTTATGGGCATTTCACGCTTCTAATATCGAATTTCCTATATTTTTCCGAATTAATT
194 CCAAAAAGATTGATGGGCTTTTCACGCTTCTAATATTGATTTTCCTATATTTTTCCGAATTAATT
* * *
31408 TCTCATTAAATAGACACATGATTCTGATGCTCGTCTTATCAAATCCTGAAATCCATTGTGGCTGT
259 TCTCATTAAATAGACACATGATTCTGATGCTCGTC-AATCAAATCCTTAAATCCATTGTGGCTGA
* *
31473 GATTTGGTTAGATGAATATAGATATTTCAGTGAGTCTTGGCGCAAAAAATCTTGCAAAACTGAAC
323 GATTTGGTTAGATGAATATAGATATTTCAG-GAGTCTTGACGCAAAAAATCATGCAAAACTGAAC
* *
31538 CAGAGCACCCGAATGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTGGCCTAAAATT
387 CAGAGCACCCGAATGCATTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTGGACTAAAATT
*
31603 TTTCAAAAATTGACCGGAAAAATTTTTCCTCGATTTTTGGCTACAATACTCATAAAACAAATATA
452 TTTCAAAAATTGACC-GAAAAATTTTTCCTC-ATTTTTGGCAACAATACTCATAAAACAAATATA
* * *
31668 ATTCAACGCCAAAAAAGATTGATTGGCATGTCACGCTTCTAATATC-GATTTTCTTTTATTTTCC
515 ATTCAACGCCAAAAAAGATTGATGGGCATGTCACGCTTCTAATATCAG-TTTTCCTATATTTTCC
* * *
31732 GAATTAATTTCTCATTAGATCG-AC-A-T-TGATGCTCGTCAAATCAAATCC-TGAAATCCATTG
579 CAATTAATTTCTCAATAAATCGAACAATTATGATGCTCGTCAAATCAAATCCAT-AAATCCATTG
* * * * ** *
31792 -GGGTGTGATTTGGTT-ATGAATATAGATATTTCAATGAGTCATGGCGCAAAAAATCATGCAAAA
643 TGGCTGAGATTTAGTTAATGAATATAAATATTTCAACAAGTCATGGCGCAAAAAATCATACAAAA
* ** * * * * * *
31855 CTGTACCGGAGCACCGAAACGCATTTTTATCCAAAAACCGTGATGGTTAGTACACGATTTTGGCT
708 CTGAACCGGAGCACCGAAACGCATTTAAAGCCAAAAACAGTGATAGTCAGTACAAGATTTGGGCT
* * *
31920 AACATTTTGCAAAAATTGACCCGAAA-AATTTTTCCTCAATTTTTGG-CTACAATACTCATAAAA
773 AAAATTTTGCAAAAATTGACCCGAAATAATTTTTCCTCAATTTTAGGCCT-CAATACCCATAAAA
** * *
31983 AATATATAATTCAACGCCAAAAAGATTGATGGGCATTTCACGTTTCTAATATCGATTTTCCTTTT
837 AATATATAATTCAACGCCAAAAAGATTGATGGGCATTTCACACTTCTAATATCGATTTTCCTATA
* * * * *
32048 TTTTTCCTGATTAATTTCTCATTAAATCGACATATGATTCTGATATTCGTCAAATCAAATCCTTC
902 TTTTTCCGGATTAATTTCTCATTAAATCCACACATGATTCTGATACTCGTCAAATCAAATCCTTA
*
32113 AATCCATTGTGGCTCAGATTTGGTC
967 AATCCACTGTGGCTCAGATTTGGTC
* * * * * *
32138 AGATGAATATAGATATTTCAATGAGTCTTGGCGTAGAAAATCATGCAAAACTGAGCCGGAGTACT
1 AGATGAATATAGATATTTCAACGAGTCTTGGCGCAAAAAATCATGCAAAACTGAACCGGAGCACC
* * * *
32203 GGAACACATTTTTAGCCAAAAACCGCGATGGTTAGTACAAGATTTGGGCTAAAATTTTGCAAAAA
66 CGAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAAATTTTGCAAAAA
* * * * *
32268 TTGATCCGAAAAAATTTTCCTCAATTTTTGGCCAGAATACTTATAAAAAATATATAGTTCAAAGC
131 TTGATCCGAAAAATTTTTCCTCAATTTTTGGCTACAATACTTAT-AAAAATATATAATTCAACGC
* * *
32333 CAAAAAGATTGATGGGCTTTTCACGTTTCTAATATTGATTTTCCTATATTTTTCCGGATTATTTT
195 CAAAAAGATTGATGGGCTTTTCACGCTTCTAATATTGATTTTCCTATATTTTTCCGAATTAATTT
* * * * * *
32398 CTCAGTAAATAGATATACGATTCTGATGCTCGTCAAATCAAATCCTTAAATCCTTTGTGGGTGAG
260 CTCATTAAATAGACACATGATTCTGATGCTCGTC-AATCAAATCCTTAAATCCATTGTGGCTGAG
* * * *
32463 ATTTGGTTAGATGAATATAGTTATTTCAAGGAGTCTT-TCTGCCGAAAAATCATGCAAAACTGAG
324 ATTTGGTTAGATGAATATAGATATTTC-AGGAGTCTTGAC-G-CAAAAAATCATGCAAAACTGAA
* * * ** * * * *
32527 TCGGGGC-CCCGAAATGTGTTTTTGGCTAAAAACCGTGATGGTTAGTACACAATTTCGACTAAAA
386 CCAGAGCACCCG-AATGCATTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTGGACTAAAA
* * * * * * * * *
32591 TATTGCAAAAACTGACCCAAAATTTTTTTCCTCCATTTTTTGCCACAATACTCAGAAAAACATAT
450 TTTTTCAAAAATTGACCGAAAA-ATTTTTCCT-CATTTTTGGCAACAATACTCA-TAAAACAAAT
*
32656 ATAATTCAACACCAAAAA
512 ATAATTCAACGCCAAAAA
32674 TATTGAAAGG
Statistics
Matches: 1329, Mismatches: 163, Indels: 62
0.86 0.10 0.04
Matches are distributed among these distances:
986 92 0.07
987 336 0.25
988 8 0.01
989 489 0.37
990 112 0.08
991 145 0.11
993 14 0.01
994 31 0.02
995 1 0.00
996 1 0.00
998 13 0.01
999 5 0.00
1000 18 0.01
1001 64 0.05
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (991 bp):
AGATGAATATAGATATTTCAACGAGTCTTGGCGCAAAAAATCATGCAAAACTGAACCGGAGCACC
CGAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAAATTTTGCAAAAA
TTGATCCGAAAAATTTTTCCTCAATTTTTGGCTACAATACTTATAAAAATATATAATTCAACGCC
AAAAAGATTGATGGGCTTTTCACGCTTCTAATATTGATTTTCCTATATTTTTCCGAATTAATTTC
TCATTAAATAGACACATGATTCTGATGCTCGTCAATCAAATCCTTAAATCCATTGTGGCTGAGAT
TTGGTTAGATGAATATAGATATTTCAGGAGTCTTGACGCAAAAAATCATGCAAAACTGAACCAGA
GCACCCGAATGCATTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTGGACTAAAATTTTTC
AAAAATTGACCGAAAAATTTTTCCTCATTTTTGGCAACAATACTCATAAAACAAATATAATTCAA
CGCCAAAAAAGATTGATGGGCATGTCACGCTTCTAATATCAGTTTTCCTATATTTTCCCAATTAA
TTTCTCAATAAATCGAACAATTATGATGCTCGTCAAATCAAATCCATAAATCCATTGTGGCTGAG
ATTTAGTTAATGAATATAAATATTTCAACAAGTCATGGCGCAAAAAATCATACAAAACTGAACCG
GAGCACCGAAACGCATTTAAAGCCAAAAACAGTGATAGTCAGTACAAGATTTGGGCTAAAATTTT
GCAAAAATTGACCCGAAATAATTTTTCCTCAATTTTAGGCCTCAATACCCATAAAAAATATATAA
TTCAACGCCAAAAAGATTGATGGGCATTTCACACTTCTAATATCGATTTTCCTATATTTTTCCGG
ATTAATTTCTCATTAAATCCACACATGATTCTGATACTCGTCAAATCAAATCCTTAAATCCACTG
TGGCTCAGATTTGGTC
Done.