Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019077.1 Corchorus olitorius cultivar O-4 contig19110, 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: 11142
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:689 original size:25 final size:24
Alignment explanation
Indices: 655--701 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
645 ACGTTTGCAC
655 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
*
680 AAATATCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
702 TGTAAGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:756 original size:45 final size:42
Alignment explanation
Indices: 692--780 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 42
682 ATATCTAAGA
692 ATTTAATTAATGTAAGTATTTCAGTTATTATAGTATTATTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATA-TA-TA-TATTAC
* *
737 ATTTAATTAATGTACGTATTTTAGTTATTATATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATATTAC
779 AT
1 AT
781 AGGAATTAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
42 8 0.19
43 2 0.05
44 2 0.05
45 30 0.71
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.52
Consensus pattern (42 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATATTAC
Found at i:1537 original size:11 final size:11
Alignment explanation
Indices: 1521--1550 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1511 TAACCATAAA
1521 AGCCCGGCCCG
1 AGCCCGGCCCG
1532 AGCCCGGCCCG
1 AGCCCGGCCCG
1543 -GCCCGGCC
1 AGCCCGGCC
1551 TGTATACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.42
11 11 0.58
ACGTcount: A:0.07, C:0.57, G:0.37, T:0.00
Consensus pattern (11 bp):
AGCCCGGCCCG
Found at i:1705 original size:21 final size:21
Alignment explanation
Indices: 1680--1762 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 21
1670 TATCTTAGAT
1680 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
1701 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
* **
1722 ATAAATAATGA-GTTCAAAATAA
1 AT-AATAAT-ATATTTTAAATAA
1744 ATAAATAATATATATTTAA
1 AT-AATAATATAT-TTTAA
1763 TTACTAAATG
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
21 18 0.37
22 21 0.43
23 10 0.20
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:1713 original size:25 final size:25
Alignment explanation
Indices: 1682--1730 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1672 TCTTAGATAT
*
1682 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
1707 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
1731 GAGTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Found at i:8934 original size:335 final size:328
Alignment explanation
Indices: 8319--11125 Score: 2384
Period size: 335 Copynumber: 8.5 Consensus size: 328
8309 AAATGACCCA
* * ** *
8319 AAAGATTTTTCCTCAATTTTTGTCAAAAATACTCATAAATTATATATATTTCAACGCCAAAAAGA
1 AAAGATTTTTCCTCAATTTTAG-CCAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGA
* * * *
8384 TTGTAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTTGAATTAATTTCTAATTAAA
65 TTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAA
* * * * *
8449 TCGAAATAAAATTAATTCAGATGCACGTTAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTA
130 TCG-AA-ACAA--GATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTG
* * * * *
8514 ATTAGATGAAT-T-GAGATATTTCAAGGAGTCTCGGCGCCAAAAATAATGCAAAACAGAGCCGTA
191 ATTAGATGAATATAGA-ATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGACCCG-G
** * *
8577 G-CCATAGAATGCATTTTTAGCC-AAAACCGTGATGTTAGTACACGATTTCGGCTAAAATTTTGC
254 GCCCCGA-AACGCGTTTTTAGCCAAAAACCGTGATG-TAGTACACGATTTCGGCTAAAATTTTGC
8640 AAAAATTGAGCCG
317 AAAAATTGA-CCG
* ** * *
8653 AAAGACTTTTCCTCAATTTCTAGAGAAAATACTCATAAAAAATATATAGTTCAACGCCAAAAAAA
1 AAAGATTTTTCCTCAATTT-TAGCCAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGA
* * * ** * *
8718 TTGAAAGTCTTTTTCACGCTTCTAATATCGTTTTTCCTACTTTACTTCCAAATTAATTTTTGATT
65 TTGAAGGAC-TTTTCACGCTTCTAATATCGTTTTTCCTA-TTT-TTTCTGAATTAATTTCTAATT
* * * * * * *
8783 AAATCGAAACAAGATTTAGATACTCGTGAAAACAAATCCTTAAGTACAATGTGCCTGAGATTTGG
127 AAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGA
* *
8848 TTAGATGAATATAGATATATTTTAAGGAGTCTTGGCGCAAAAAATCATGCAAAACTGACCCGAGG
192 TTAGATGAATATAGA-ATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGACCCG-GG
* * *
8913 CCCCGAAACACATTTTTAGCCAAAAATCCGTGATG--GTATACGATTTCGGCT-AAATTTTGCAA
255 CCCCGAAACGCGTTTTTAGCCAAAAA-CCGTGATGTAGTACACGATTTCGGCTAAAATTTTGC-A
*
8975 AAAATTGGCCCG
318 AAAATT-GACCG
* * * * * * *
8987 AAATATTTTTTC-CATTTTTTGGCCACAATACTCATAAAAAATATAAAATTCAACACCAAAAAGA
1 AAAGATTTTTCCTCA-ATTTTAGCCAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGA
* * * *
9051 TTGAAAGG-CTTCTCATGCTTCAAATATCGTTTTTCCTATTTCTTT-TCAAATTAATTTCTAATT
65 TTG-AAGGACTTTTCACGCTTCTAATATCGTTTTTCCTATTT-TTTCT-GAATTAATTTCTAATT
* * * * * *
9114 AAATCGAAACATGATTCAAATGCTCGTAAAAACAAATCCATAAATCCAATGTGGTTAAGATTTGG
127 AAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGA
* * * * ** *
9179 TTAGATGAATATA-AATATTACAAGGAGTTTTGCCACTGAAAATCATGCAAAACTTACCCGGGGC
192 TTAGATGAATATAGAATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGACCC-GGGC
* *
9243 CCCGGAACGCGTTTTT--CCAAAAAACCGTGATG--GTACACGATTTCGGCTAAAATTTTGTAAA
256 CCCGAAACGCGTTTTTAGCC-AAAAACCGTGATGTAGTACACGATTTCGGCTAAAATTTTGCAAA
* *
9304 AGTTGACATG
320 AATTGAC-CG
* * *
9314 AAATATTTTTCCTCAATTTTTAGCCACAATACTCATAATATATATATATATATATATATAATTGA
1 AAAGATTTTTCCTCAA-TTTTAGCCAAAATACTC-------ATA-A-A-A-A-ATATATAATTCA
* * * * * * *
9379 ACACCAAAAAAATTGGAGGACTTGTCACGTTTTTAATATCGTTCTTT-C-ATATTTTCTGAATTA
53 ACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTT-TTTCCTATTTTTTCTGAATTA
* * * **
9442 ATTTCTAATTAAATTGAAACAAGATTCAGATACTCGTAAAAACAAATGCTTAAATCCAATGAAGC
117 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
* * *
9507 TGAGATTTGATTAGATGAATATAGAA-ATCTCAAAGAGTCTTGGCGCCAAAAATCATGGAAAACT
182 TGAGATTTGATTAGATGAATATAGAATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACT
* * * * * ** * *
9571 TAGCAGGAGCCACAAAACGCGTTTTTAGCCAAAAATTGTGATGACTATTTCACGATTTCGGCTAA
247 GACCCGG-GCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATG--TAGTACACGATTTCGGCTAA
* **
9636 TATTTTGC-AAAATTTTCTCG
309 AATTTTGCAAAAATTGAC-CG
* * * * *
9656 AAAG-TTATTTGCTCAACTTATAGCCACAATAATCATAAAAATTATATAATTCAACGCCAAAAAG
1 AAAGATT-TTTCCTCAA-TTTTAGCCAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAG
** * *
9720 ATTGAAGGGTTTTTCATGCTTCTAATATCGTTTTTCCTATTATTTTCTGAATTAATTTTTAATTA
64 ATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCCTATT-TTTTCTGAATTAATTTCTAATTA
*** * * *** *
9785 AATCGAAATGTGATTCAGATGATTGT-TTCACAAATCCTTAAATCCAATGTAGCTGA-ATTT--T
128 AATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGAT
* * * * * * ** ** * * *
9846 TAATATAAATGTAG-ATAGTTCAAAGAGTCTCGGAACCAAAAATCATATAACACTGAACCGGG-T
193 T-AGATGAATATAGAATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGACCCGGGCC
* *
9909 CC----CGCTTTTTTAGCCAAAAACC--------GT----GATTTCGGCTAATATTTTGCAAAAA
257 CCGAAACGCGTTTTTAGCCAAAAACCGTGATGTAGTACACGATTTCGGCTAAAATTTTGCAAAAA
9958 TTGACCAG
322 TTGACC-G
* * * * * * * *
9966 AAATATTTTTTCTCAATTTTGGTCTAAAATACTCATAAAATATACATAATTCAACTCCAAAAATA
1 AAAGATTTTTCCTCAATTTTAG-CCAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGA
* * *
10031 TTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTCTGAATTAATTTCTAATTAAA
65 TTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAA
*
10095 TCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTGAGATTTGATTA
130 TCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTA
* * * * *
10160 GATGAATATAG-ATATTTCAAGAAGTCTCGACGCCAAAAATCATGCAAAACTGAGCCGTGGCCTC
195 GATGAATATAGAATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGACCCG-GGCCCC
* ***
10224 GAAACGCGTTTTTAGCAAAATAACCGTGATGCTTAGTACACGATTTCTATTAAAATTTTGCAAAA
259 GAAACGCGTTTTTAGCCAAA-AACCGTGATG--TAGTACACGATTTCGGCTAAAATTTTGCAAAA
10289 ATTGACCCG
321 ATTGA-CCG
* * * * * * * *
10298 AAA-ATTTCT-CTCAATTTTTGGCTAAAATAATCATGAAATATATATAATTGTTTTAGCGCCAAA
1 AAAGATTTTTCCTCAA-TTTTAGCCAAAATACTCATAAAAAATATATAA----TTCAACGCCAAA
* * * * * *
10361 AAGATTGGAGGACTTTTCACACATT-TCATATCGTTTTTCATATTTTTTCTAAATTAATTTCCAA
61 AAGATTGAAGGACTTTTCACGC-TTCTAATATCGTTTTTCCTATTTTTTCTGAATTAATTTCTAA
* *
10425 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATACAATGTGGATGAGATTT
125 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
* * * * * ** *
10490 AATTAGATAAATAT-GGATATCTCAAGGA-TCTTGGTGTTAAAAAGCATGCAAAACTGACCCGGG
190 GATTAGATGAATATAGAATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGACCC-GG
* * * * * * *
10553 GTCCTGGAACACG-TTTTAGCCTAAAACCGTGATGATTATTACATGATTTCGGCTAAAATTTTGC
254 GCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATG--TAGTACACGATTTCGGCTAAAATTTTGC
10617 AAAAATTGACCCG
317 AAAAATTGA-CCG
* * * * *
10630 AAAGATATTTCCTCAAGTCTTGGCTAAAATAATCAATAAAAAATTATATATAATTCAACGCCAAA
1 AAAGATTTTTCCTCAA-TTTTAGCCAAAATACTC-AT-AAAAA--ATATATAATTCAACGCCAAA
* ** * * *
10695 AATATTGAAGGGTTTTTTTACGCTTCTAGTATCGTTTTTCCTATTTTTTCCGAATTAATTTCTAA
61 AAGATTGAA-GGACTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCTGAATTAATTTCTAA
* * * * *
10760 TTAAATCGAAACAAGATTTAGATGTTCATAAAAAGAAATCCTTAAATCCAATGTGACTGAGATTT
125 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
* * * * *
10825 GATTAGATGAATGTAG-ATTTTTCAAGGAGTCTTGGCACCAAAAATTATGCAAAACTGACTCGGT
190 GATTAGATGAATATAGAATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGACCCGG-
* ** * ** *
10889 G-CGC-ATAACGCGTTTTTAGTAAAAAAAAAAACCGTGA--TAGTACACGCTTTCATCTAATATT
254 GCCCCGA-AACGCGTTTTTAG-----CCAAAAACCGTGATGTAGTACACGATTTCGGCTAAAATT
**
10950 TTGCAAATGTTGACCTG
313 TTGCAAAAATTGACC-G
* * * *
10967 AAACATTTTTCCTCAATTTTAGCCACAATACTCATAAAATATATATAATTCAATGCC-AAAAGAA
1 AAAGATTTTTCCTCAATTTTAGCCAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAG-A
* * *
11031 TTGAAGGGCTTTTCACGCTTCTAATATTG-TTTTCTCTATTTTTTC-GAATTAATTTTTAATTAA
65 TTGAAGGACTTTTCACGCTTCTAATATCGTTTTTC-CTATTTTTTCTGAATTAATTTCTAATTAA
* * * *
11094 ATCGAAACATGA-TCAGATACTTGTAAGAACAA
129 ATCGAAACAAGATTCAGATGCTCGTAAAAACAA
11126 TGGTTGGGAA
Statistics
Matches: 2003, Mismatches: 361, Indels: 223
0.77 0.14 0.09
Matches are distributed among these distances:
308 43 0.02
309 51 0.03
310 89 0.04
311 47 0.02
312 4 0.00
313 2 0.00
317 14 0.01
318 4 0.00
323 17 0.01
326 2 0.00
327 44 0.02
328 37 0.02
329 112 0.06
330 112 0.06
331 158 0.08
332 169 0.08
333 121 0.06
334 226 0.11
335 335 0.17
336 63 0.03
337 76 0.04
338 141 0.07
339 21 0.01
340 45 0.02
341 15 0.01
342 33 0.02
343 22 0.01
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (328 bp):
AAAGATTTTTCCTCAATTTTAGCCAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGAT
TGAAGGACTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAAT
CGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAG
ATGAATATAGAATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGACCCGGGCCCCGA
AACGCGTTTTTAGCCAAAAACCGTGATGTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGA
CCG
Done.