Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011518.1 Corchorus olitorius cultivar O-4 contig11551, 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: 2631
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Found at i:331 original size:154 final size:154
Alignment explanation
Indices: 1--1489 Score: 2400
Period size: 154 Copynumber: 9.7 Consensus size: 154
* * * *
1 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCAACTTTGAAGTTTCT
1 TTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
* *
66 AGCACATTTTGGAACACTTGTTATTTTGGGTCCGTATCGGGGTCCGATTAGTTCCGTTTTGAAAT
66 AGCTCA-TTTGGAACACTTGTTATTTTGGG-CC-TATCGGGG-CCCATTAGTTCCGTTTTG-AAT
131 CGTCTTCGATTTGGCAAACCTCAATGCTT
126 CGTCTTCGATTTGGCAAACCTCAATGCTT
*
160 TTCTTTCCTATTG-TTATGGACTAACTATAATCAGTTTGGTGTAGATTAGTCCACTGTGAAGTTT
1 TTCTTTCC-ATTGTTTATGGACTAACTATAATCATTTTGGTG-AGATTAGTCCACTGTGAAGTTT
* * *
224 TTAGCTCTCATTTGGAACACTTG-TA-TTTGGGTCTATC-GGGCCCACTAGTTCCATTTTGAATC
64 TTAG--CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATC
*
286 GTCTTCGATTTGGCAAACCTCAAAGCTT
127 GTCTTCGATTTGGCAAACCTCAATGCTT
* *
314 TTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGATGAGATTAGTCCAATGTGAAGTTTTT
1 TTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
*
379 AGCTCATTTGGAACACATGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCT
66 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCT
*
444 TCGATTTGGCAAACCTCAAAGCTT
131 TCGATTTGGCAAACCTCAATGCTT
*
468 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
1 TTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
533 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCT
66 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCT
598 TCGATTTGGCAAACCTCAATGCTT
131 TCGATTTGGCAAACCTCAATGCTT
*
622 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
1 TTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
* ** *
687 AGCTCATTTGAAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTTT
66 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCT
*
752 TCGATTTAGCAAACCTCAATGCTT
131 TCGATTTGGCAAACCTCAATGCTT
*
776 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG-TTTT
1 TTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
** * *
840 ATTTCATTCGGAACACTTGTTATTTTGGGCCTATCGGGGCTCATTAGTTCCGTTTTGAATCGTCT
66 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCT
905 TCGATTTGGCAAACCTCAATGCTT
131 TCGATTTGGCAAACCTCAATGCTT
**
929 TTCTTTCCATTGTTTAT-GACCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACATTT
1 TTCTTTCCATTGTTTATGGA-CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT
* ** * *
993 TAGCTCATTTGGAATACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAAACGTC
65 TAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTC
*
1058 TTCGATTTGGCAAACCTGAATGCTT
130 TTCGATTTGGCAAACCTCAATGCTT
*
1083 TTCTTTCCATTGTTTATTGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
1 TTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
* *
1148 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTTGAATCATCT
66 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCT
* *
1213 TCGATTGGGC--ACCTCAGTGCTT
131 TCGATTTGGCAAACCTCAATGCTT
* * *
1235 TTCCTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTT
1 TTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
* **
1300 AGCTCATTTGGAACACTTGTTATTTTTGGCCTATCGGGGCCCATTAGTTCTATTTTGAATCGTCT
66 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCT
*
1365 TCGATTTGGCAAACCTTAATGCTT
131 TCGATTTGGCAAACCTCAATGCTT
*
1389 TTCTTTCTATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
1 TTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
1454 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
66 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
1490 TGATACGAAT
Statistics
Matches: 1239, Mismatches: 78, Indels: 31
0.92 0.06 0.02
Matches are distributed among these distances:
151 16 0.01
152 143 0.12
153 180 0.15
154 790 0.64
155 17 0.01
156 3 0.00
157 4 0.00
158 1 0.00
159 40 0.03
160 29 0.02
161 13 0.01
162 3 0.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (154 bp):
TTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCT
TCGATTTGGCAAACCTCAATGCTT
Found at i:977 original size:461 final size:461
Alignment explanation
Indices: 1--1489 Score: 2398
Period size: 461 Copynumber: 3.2 Consensus size: 461
* * * *
1 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCAACTTTGAAGTTTCT
1 TTCTTTCCATTGTTTATGACCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
* *
66 AGCACATTTTGGAACACTTGTTATTTTGGGTCCGTATCGGGGTCCGATTAGTTCCGTTTTGAAAT
66 AGCTCA-TTTGGAACACTTGTTATTTTGGG-CC-TATCGGGG-CCCATTAGTTCCGTTTTG-AAT
*
131 CGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCTATTG-TTATGGACTAACTATAATCAGT
126 CGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC-ATTGTTTATGGACTAACTATAATCATT
*
195 TTGGTGTAGATTAGTCCACTGTGAAGTTTTTAGCTCTCATTTGGAACACTTG-TA-TTTGGGTCT
190 TTGGTG-AGATTAGTCCACTGTGAAGTTTTTAG--CTCATTTGGAACACTTGTTATTTTGGGCCT
* * *
258 ATC-GGGCCCACTAGTTCCATTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCC
252 ATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
* * *
322 ATTGTTTATGGACTAACTATAATCATTTTGATGAGATTAGTCCAATGTGAAGTTTTTAGCTCATT
317 ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG-TTTTAGCTCATT
*
387 TGGAACACATGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
381 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
*
452 GCAAACCTCAAAGCTT
446 GCAAACCTCAATGCTT
*
468 TTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
1 TTCTTTCCATTGTTTATGACCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
533 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCT
66 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCT
*
598 TCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTG
131 TCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTG
*
663 AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGAAACACTTGTTATTTTGGGCCTATCGGGGCC
196 AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCC
** * *
728 CATTAGTGACGTTTTGAATCGTTTTCGATTTAGCAAACCTCAATGCTTTTCTTTCCATTGTTTAT
261 CATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTAT
** *
793 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTATTTCATTCGGAACACTT
326 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTAGCTCATTTGGAACACTT
*
858 GTTATTTTGGGCCTATCGGGGCTCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCA
391 GTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCA
923 ATGCTT
456 ATGCTT
**
929 TTCTTTCCATTGTTTATGACCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACATTTT
1 TTCTTTCCATTGTTTATGACCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
* ** * *
994 AGCTCATTTGGAATACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAAACGTCT
66 AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCT
* *
1059 TCGATTTGGCAAACCTGAATGCTTTTCTTTCCATTGTTTATTGACTAACTATAATCATTTTGGTG
131 TCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTG
*
1124 AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCC
196 AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCC
* * * *
1189 CATTAGTTCCGTTTTGAATCATCTTCGATTGGGC--ACCTCAGTGCTTTTCCTTCCATTGTTTAT
261 CATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTAT
*
1252 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAACACT
326 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA-GTTTTAGCTCATTTGGAACACT
* ** *
1317 TGTTATTTTTGGCCTATCGGGGCCCATTAGTTCTATTTTGAATCGTCTTCGATTTGGCAAACCTT
390 TGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTC
1382 AATGCTT
455 AATGCTT
*
1389 TTCTTTCTATTGTTTATGGA-CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT
1 TTCTTTCCATTGTTTAT-GACCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT
1453 TAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
65 TAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG
1490 TGATACGAAT
Statistics
Matches: 957, Mismatches: 59, Indels: 19
0.92 0.06 0.02
Matches are distributed among these distances:
459 85 0.09
460 181 0.19
461 405 0.42
462 169 0.18
463 17 0.02
464 8 0.01
465 2 0.00
466 23 0.02
467 67 0.07
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (461 bp):
TTCTTTCCATTGTTTATGACCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCT
TCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTG
AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCC
CATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTAT
GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTAGCTCATTTGGAACACTT
GTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCA
ATGCTT
Found at i:2432 original size:154 final size:154
Alignment explanation
Indices: 2151--2631 Score: 809
Period size: 154 Copynumber: 3.1 Consensus size: 154
2141 CAATGGGCTT
2151 CATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGTTTCAATACGTCACTAAT
1 CATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGTTTCAATACGTCACTAAT
*
2216 GGGACCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAGTTCACAGTGGACTAATC
66 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAGTTCACAGTGGACTAATC
*
2281 TCACCAAAATGATTATAGTTAGTC
131 TCACCAAAATGATTATAGTTAGGC
2305 CATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGTTTCAATACGTCACTAAT
1 CATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGTTTCAATACGTCACTAAT
* * * * *
2370 GGGCCCCGATAAGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTCCATAGTGAACTAATC
66 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAGTTCACAGTGGACTAATC
*
2435 TCAACAAAATGATTATAGTTAGGC
131 TCACCAAAATGATTATAGTTAGGC
* * * *
2459 CATAAACAATGGAAAGAAAAGTATTGTGGTTTGCCAAATCGTAGACGATTCAATACGTCACTAAT
1 CATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGTTTCAATACGTCACTAAT
* *
2524 GGGCCCCAATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAGTTTACAGTGGACTAATC
66 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAGTTCACAGTGGACTAATC
*
2589 TCACCAAAATGATTATAGTTTGGC
131 TCACCAAAATGATTATAGTTAGGC
**
2613 CATAAACGTTGGAAAGAAA
1 CATAAACAATGGAAAGAAA
Statistics
Matches: 304, Mismatches: 23, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
154 304 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23
Consensus pattern (154 bp):
CATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGTTTCAATACGTCACTAAT
GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAGTTCACAGTGGACTAATC
TCACCAAAATGATTATAGTTAGGC
Done.