Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023910.1 Corchorus olitorius cultivar O-4 contig23943, 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, 684
Length: 1141
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Found at i:541 original size:154 final size:154
Alignment explanation
Indices: 1--981 Score: 1489
Period size: 154 Copynumber: 6.3 Consensus size: 154
* * * * * *
1 TTTGGTCAGATTAGTCCATTGTGAACTTTTTAGTCTTATTTGGTAAAACTTGTTATTTTGGACCT
1 TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG-CTCATTTGG-AACACTTGTTATTTTGGGCCT
* * * *
66 ATCAGGGCCCATTAGTAACGTATTTGAATCTTCTTCGATTTGGCAAACCTCAATGCTTTT-ATTC
64 ATCGGGGCCCATTAGTTACGTA-TTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTC
* * *
130 CTATTGTTTATGGCCTAATTGTAATCAT
128 C-ATTGTTTATGGCATAACTATAATCAT
* *
158 TTTGGTGAGATTAGCCCACTCGTGAAGTTTTTTAGTCTTCATTTAGTAACACTTGTTATTTTGGG
1 TTTGGTGAGATTAGTCCACT-GTGAAG-TTTTTAG-C-TCATTT-GGAACACTTGTTATTTTGGG
* * * * *
223 CCTATCGGGGCTCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGTAAACCTCAAAGCTTTTCTT
61 CCTATCGGGGCCCATTAGTTACGTATTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTT
288 TCCATTGTTTATTGGCATAACTATAATCAT
126 TCCATTGTTTA-TGGCATAACTATAATCAT
318 TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTAT
1 TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTAT
*
383 CGGGGCCCATTAGTTACGTATTGAATCGTCTTCGATTTGGTAAACCTCAATGCTTTTCTTTCCAT
66 CGGGGCCCATTAGTTACGTATTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCAT
448 TGTTTATGGCATAACTATAATCAT
131 TGTTTATGGCATAACTATAATCAT
472 TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTAT
1 TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTAT
* * *
537 CGGGGCTCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCAT
66 CGGGGCCCATTAGTTACGTATTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCAT
602 TGTTTATGGCATAACTATAATCAT
131 TGTTTATGGCATAACTATAATCAT
626 TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA-TTTGGGCCTAT
1 TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTAT
* * * * *
690 CGGGGCTCATTAGTTCCGTTTTTAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCCTTCCAT
66 CGGGGCCCATTAGTTACGTATTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCAT
*
755 TGTTTATGGCCTAACTATAATCAT
131 TGTTTATGGCATAACTATAATCAT
* **
779 TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGCAGTACTTGTTATTTTGGGCCTAT
1 TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTAT
* * * * *
844 TGGGGCCCATTAGTGACGTATTGGATCGTCTTCGATTTAGAAAACCTCAATGCTTTTCTTTCCAT
66 CGGGGCCCATTAGTTACGTATTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCAT
*
909 TGTTTATGGCCTAACTATAATCAT
131 TGTTTATGGCATAACTATAATCAT
* *
933 CTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTT
1 TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTT
982 ATGGCCTAAC
Statistics
Matches: 766, Mismatches: 51, Indels: 17
0.92 0.06 0.02
Matches are distributed among these distances:
153 147 0.19
154 355 0.46
155 91 0.12
156 6 0.01
157 18 0.02
158 12 0.02
159 57 0.07
160 79 0.10
161 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.42
Consensus pattern (154 bp):
TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTAT
CGGGGCCCATTAGTTACGTATTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCAT
TGTTTATGGCATAACTATAATCAT
Found at i:783 original size:307 final size:308
Alignment explanation
Indices: 1--981 Score: 1525
Period size: 307 Copynumber: 3.2 Consensus size: 308
* * * * *
1 TTTGGTCAGATTAGTCCATTGTGAACTTTTTAGTCTTATTTGGTAAAACTTGTTATTTTGGACCT
1 TTTGGTGAGATTAGTCCACTGTGAACTTTTTAG-CTCATTTGG-AACACTTGTTATTTTGGGCCT
* * *
66 ATCAGGGCCCATTAGTAACGTATTTGAATCTTCTTCGATTTGGCAAACCTCAATGCTTTT-ATTC
64 ATCGGGGCCCATTAGTTACGT-TTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCATTC
* * *
130 CTATTGTTTATGGCCTAATTGTAATCATTTTGGTGAGATTAGCCCACTCGTGAAGTTTTTTAGTC
128 C-ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT-GTGAAG-TTTTTAG-C
*
195 TTCATTTAGTAACACTTGTTATTTTGGGCCTATCGGGGCTCATTAGTTCCGTTTTGAATCGTCTT
189 -TCATTT-GCAACACTTGTTATTTTGGGCCTATCGGGGCTCATTAGTTCCGTTTTGAATCGTCTT
* *
260 CGATTTGGTAAACCTCAAAGCTTTTCTTTCCATTGTTTATTGGCATAACTATAATCAT
252 CGATTTGGAAAACCTCAATGCTTTTCTTTCCATTGTTTA-TGGCATAACTATAATCAT
*
318 TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTAT
1 TTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTAT
* * *
383 CGGGGCCCATTAGTTACGTATTGAATCGTCTTCGATTTGGTAAACCTCAATGCTTTTCTTTCCAT
66 CGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCATTCCAT
*
448 TGTTTATGGCATAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTG
131 TGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTG
* *
513 GAACACTTGTTATTTTGGGCCTATCGGGGCTCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGC
196 CAACACTTGTTATTTTGGGCCTATCGGGGCTCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGA
578 AAACCTCAATGCTTTTCTTTCCATTGTTTATGGCATAACTATAATCAT
261 AAACCTCAATGCTTTTCTTTCCATTGTTTATGGCATAACTATAATCAT
*
626 TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA-TTTGGGCCTAT
1 TTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTAT
* * * *
690 CGGGGCTCATTAGTTCCGTTTTTAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCCTTCCAT
66 CGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCATTCCAT
755 TGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTG
131 TGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTG
** * * ** * * *
820 CAGTACTTGTTATTTTGGGCCTATTGGGGCCCATTAGTGACGTATTGGATCGTCTTCGATTTAGA
196 CAACACTTGTTATTTTGGGCCTATCGGGGCTCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGA
*
885 AAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCAT
261 AAACCTCAATGCTTTTCTTTCCATTGTTTATGGCATAACTATAATCAT
*
933 CTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTT
1 TTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTT
982 ATGGCCTAAC
Statistics
Matches: 623, Mismatches: 40, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
307 282 0.45
308 71 0.11
309 93 0.15
310 6 0.01
311 1 0.00
312 7 0.01
313 6 0.01
314 77 0.12
315 42 0.07
316 8 0.01
317 30 0.05
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.42
Consensus pattern (308 bp):
TTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTAT
CGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCATTCCAT
TGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTG
CAACACTTGTTATTTTGGGCCTATCGGGGCTCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGA
AAACCTCAATGCTTTTCTTTCCATTGTTTATGGCATAACTATAATCAT
Found at i:957 original size:461 final size:469
Alignment explanation
Indices: 2--981 Score: 1582
Period size: 461 Copynumber: 2.1 Consensus size: 469
1 T
* * * *
2 TTGGTCAGATTAGTCCATTGTGAACTTTTTAGTCTTATTTGGTAAAACTTGTTATTTTGGACCTA
1 TTGGTGAGATTAGTCCACTGTGAACTTTTTAG-CTCATTTGG-AACACTTGTTATTTTGGACCTA
*
67 TCAGGGCCCATTAGTAACGTATTTGAATCTTCTTCGATTTGGCAAACCTCAATGCTTTTATTCCT
64 TCAGGGCCCATTAGTAACGTATTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTATTCCT
* * *
132 ATTGTTTATGGCCTAATTGTAATCATTTTGGTGAGATTAGCCCACTCGTGAAGTTTTTTAGTCTT
129 ATTGTTTATGGCATAACTATAATCATTTTGGTGAGATTAGCCCACTCGTGAAGTTTTTTAGTCTT
*
197 CATTTAGTAACACTTGTTATTTTGGGCCTATCGGGGCTCATTAGTTCCGTTTTGAATCGTCTTCG
194 CATTTAGGAACACTTGTTATTTTGGGCCTATCGGGGCTCATTAGTTCCGTTTTGAATCGTCTTCG
* *
262 ATTTGGTAAACCTCAAAGCTTTTCTTTCCATTGTTTATTGGCATAACTATAATCATTTTGGTGAG
259 ATTTGGCAAACCTCAAAGCTTTTCCTTCCATTGTTTATTGGCATAACTATAATCATTTTGGTGAG
*
327 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCA
324 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGCAACACTTGTTATTTTGGGCCTATCGGGGCCCA
* * *
392 TTAGTTACGTATTGAATCGTCTTCGATTTGGTAAACCTCAATGCTTTTCTTTCCATTGTTTATGG
389 TTAGTGACGTATTGAATCGTCTTCGATTTAGAAAACCTCAATGCTTTTCTTTCCATTGTTTATGG
*
457 CATAACTATAATCATT
454 CATAACTATAATCATC
* *
473 TTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC
1 TTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGACCTATC
* * ** *
538 GGGGCTCATTAGTTCCGT-TTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC-A
66 AGGGCCCATTAGTAACGTATTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTT-ATTCCTA
*
601 TTGTTTATGGCATAACTATAATCATTTTGGTGAGATTAGTCCACT-GTGAAG-TTTTTAG-C-TC
130 TTGTTTATGGCATAACTATAATCATTTTGGTGAGATTAGCCCACTCGTGAAGTTTTTTAGTCTTC
*
662 ATTT-GGAACACTTGTTA-TTTGGGCCTATCGGGGCTCATTAGTTCCGTTTTTAATCGTCTTCGA
195 ATTTAGGAACACTTGTTATTTTGGGCCTATCGGGGCTCATTAGTTCCGTTTTGAATCGTCTTCGA
* *
725 TTTGGCAAACCTCAATGCTTTTCCTTCCATTGTTTA-TGGCCTAACTATAATCATTTTGGTGAGA
260 TTTGGCAAACCTCAAAGCTTTTCCTTCCATTGTTTATTGGCATAACTATAATCATTTTGGTGAGA
** *
789 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGCAGTACTTGTTATTTTGGGCCTATTGGGGCCCAT
325 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGCAACACTTGTTATTTTGGGCCTATCGGGGCCCAT
*
854 TAGTGACGTATTGGATCGTCTTCGATTTAGAAAACCTCAATGCTTTTCTTTCCATTGTTTATGGC
390 TAGTGACGTATTGAATCGTCTTCGATTTAGAAAACCTCAATGCTTTTCTTTCCATTGTTTATGGC
*
919 CTAACTATAATCATC
455 ATAACTATAATCATC
934 TTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTT
1 TTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTT
982 ATGGCCTAAC
Statistics
Matches: 475, Mismatches: 33, Indels: 12
0.91 0.06 0.02
Matches are distributed among these distances:
461 209 0.44
462 78 0.16
463 12 0.03
464 6 0.01
465 1 0.00
466 7 0.01
467 6 0.01
468 79 0.17
469 40 0.08
470 8 0.02
471 29 0.06
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.42
Consensus pattern (469 bp):
TTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGACCTATC
AGGGCCCATTAGTAACGTATTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTATTCCTAT
TGTTTATGGCATAACTATAATCATTTTGGTGAGATTAGCCCACTCGTGAAGTTTTTTAGTCTTCA
TTTAGGAACACTTGTTATTTTGGGCCTATCGGGGCTCATTAGTTCCGTTTTGAATCGTCTTCGAT
TTGGCAAACCTCAAAGCTTTTCCTTCCATTGTTTATTGGCATAACTATAATCATTTTGGTGAGAT
TAGTCCACTGTGAAGTTTTTAGCTCATTTGCAACACTTGTTATTTTGGGCCTATCGGGGCCCATT
AGTGACGTATTGAATCGTCTTCGATTTAGAAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCA
TAACTATAATCATC
Found at i:1021 original size:68 final size:68
Alignment explanation
Indices: 912--1049 Score: 267
Period size: 68 Copynumber: 2.0 Consensus size: 68
902 TTTCCATTGT
912 TTATGGCCTAACTATAATCATCTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAA
1 TTATGGCCTAACTATAATCATCTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAA
977 CAC
66 CAC
*
980 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAA
1 TTATGGCCTAACTATAATCATCTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAA
1045 CAC
66 CAC
1048 TT
1 TT
1050 GTTAATTTGG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.38
Consensus pattern (68 bp):
TTATGGCCTAACTATAATCATCTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAA
CAC
Done.