Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011058.1 Corchorus olitorius cultivar O-4 contig11091, 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, 743
Length: 1239
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Found at i:288 original size:154 final size:154
Alignment explanation
Indices: 1--526 Score: 738
Period size: 154 Copynumber: 3.4 Consensus size: 154
* * *
1 TTATGGCCTAACTATAATCATTTTGGGGAGATTAGTCCACTGTGAAGTTTTTA-ACTATTTGGAA
1 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCCCATTTGGAA
*
65 CACTTGTTATTTTGGGCCTATAGGGGCCCATTAGTGAT-GTTTTGAATCGTCTTCGATTTGGCAA
66 CACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTG-TCGTTTTGAATCGTCTTCGATTTGGCAA
*
129 CCCTCAATGCTTTTCTTTCCATTGT
130 ACCTCAATGCTTTTCTTTCCATTGT
* * *
154 TTATGGCCTAACTATAATTATTTAGGTGAGATTAGTCCACTGGGAAGTTTTTAGCCCATTTGGAA
1 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCCCATTTGGAA
* * *
219 CACTTGTTATTTTGAGCCTATCGGGGCCCATTAATGTCGTTTTGAATCGTCTTCGATTTAGCAAA
66 CACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGTCGTTTTGAATCGTCTTCGATTTGGCAAA
*
284 CCTCAATGTTTTTCTTTCCATTGT
131 CCTCAATGCTTTTCTTTCCATTGT
* * *
308 TTATGGCCTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTATCTCATTTGGAA
1 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCCCATTTGGAA
* * ** *
373 CACTAT-TTATTTTGGGCCTATCGGGGCCCATTAGT-TCCATTTTAAATTATTTTCGATTTGGC-
66 CACT-TGTTATTTTGGGCCTATCGGGGCCCATTAGTGT-CGTTTTGAATCGTCTTCGATTTGGCA
* *
435 AACAATCAATGCTTTACTTTCCATTGT
129 AAC-CTCAATGCTTTTCTTTCCATTGT
* * ** *
462 TTATGGCCCAACTATAATCATTTTGGTGAGATTAGTCTACTAAGAAGTTTTTAGCTCATTTGGAA
1 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCCCATTTGGAA
527 ATGCTTTTCG
Statistics
Matches: 333, Mismatches: 35, Indels: 9
0.88 0.09 0.02
Matches are distributed among these distances:
153 54 0.16
154 278 0.83
155 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.41
Consensus pattern (154 bp):
TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCCCATTTGGAA
CACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGTCGTTTTGAATCGTCTTCGATTTGGCAAA
CCTCAATGCTTTTCTTTCCATTGT
Found at i:593 original size:84 final size:84
Alignment explanation
Indices: 442--610 Score: 275
Period size: 84 Copynumber: 2.0 Consensus size: 84
432 GGCAACAATC
* * *
442 AATGCTTTACTTTCCATTGTTTATGGCCCAACTATAATCATTTTGGTGAGATTAGTCTACTAAGA
1 AATGCTTTACGTTCCACTGTTTATGGCCCAACTATAATCATTTTGGTGAGATTAGTCCACTAAGA
507 AGTTTTTAGCTCATTTGGA
66 AGTTTTTAGCTCATTTGGA
* * **
526 AATGCTTTTCGTTCCACTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGA
1 AATGCTTTACGTTCCACTGTTTATGGCCCAACTATAATCATTTTGGTGAGATTAGTCCACTAAGA
591 AGTTTTTAGCTCATTTGGA
66 AGTTTTTAGCTCATTTGGA
610 A
1 A
611 CACCTTTTAT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
84 78 1.00
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (84 bp):
AATGCTTTACGTTCCACTGTTTATGGCCCAACTATAATCATTTTGGTGAGATTAGTCCACTAAGA
AGTTTTTAGCTCATTTGGA
Found at i:733 original size:238 final size:238
Alignment explanation
Indices: 288--761 Score: 698
Period size: 238 Copynumber: 2.0 Consensus size: 238
278 AGCAAACCTC
* * * *
288 AATGTTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGA
1 AATGCTTTTCGTTCCACTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGA
* **
353 AGTTTTTATCTCATTTGGAACACTATTTATTTTGGGCCTATCGGGGCCCATTAGTTCCATTTTAA
66 AGTTTTTAGCTCATTTGGAACACTATTTATTTTGGGCCTATCGGGGCCCATTAGTGACATTTTAA
* * *
418 ATTATTTTCGATTTGGCAACAATCAATGCTTTACTTTCCATTGTTTATGGCCCAACTATAATCAT
131 ATCATCTTCGATTTGGCAACAATCAATGCTTTACGTTCCATTGTTTATGGCCCAACTATAATCAT
* * * * *
483 TTTGGTGAGATTAGTCTACTAAGAAGTTTTTAGCTCATTTGGA
196 TATGGGGAGATTAGTCCACTAACAAGTTTTTAACTCATTTGGA
526 AATGCTTTTCGTTCCACTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGA
1 AATGCTTTTCGTTCCACTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGA
* *
591 AGTTTTTAGCTCATTTGGAACACCT-TTTATTTTGGGCCTATCGGGGCCCATTAGTGACTTTTTG
66 AGTTTTTAGCTCATTTGGAACA-CTATTTATTTTGGGCCTATCGGGGCCCATTAGTGACATTTTA
* ** * * * *
655 AATCGTCTTCGATTTGGCAACCCTGAATGCTTTTCGTTCCATTGTTTATGGTCTAACTATAATCA
130 AATCATCTTCGATTTGGCAACAATCAATGCTTTACGTTCCATTGTTTATGGCCCAACTATAATCA
**
720 TTATGGGGAGATTAGTCCACTGTCAAGTTTTTAACTCATTTG
195 TTATGGGGAGATTAGTCCACTAACAAGTTTTTAACTCATTTG
762 AACACTTGTT
Statistics
Matches: 209, Mismatches: 26, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
238 207 0.99
239 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.42
Consensus pattern (238 bp):
AATGCTTTTCGTTCCACTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGA
AGTTTTTAGCTCATTTGGAACACTATTTATTTTGGGCCTATCGGGGCCCATTAGTGACATTTTAA
ATCATCTTCGATTTGGCAACAATCAATGCTTTACGTTCCATTGTTTATGGCCCAACTATAATCAT
TATGGGGAGATTAGTCCACTAACAAGTTTTTAACTCATTTGGA
Found at i:990 original size:154 final size:154
Alignment explanation
Indices: 526--1237 Score: 1076
Period size: 154 Copynumber: 4.6 Consensus size: 154
516 CTCATTTGGA
*
526 AATGCTTTTCGTTCCACTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGA
1 AATGCTTTTCATTCCACTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGA
* * *
591 AGTTTTTAGCTCATTTGGAACACCTT-TTATTTTGGGCCTATCGGGGCCCATTAGTGACTTTTTG
66 AGTTTTTAACTCATTTGGAACA-CTTGTTATTTTGGGCCTATAGGGGCCCATTAGTGACGTTTTG
*
655 AATCGTCTTCGATTTGGCAACCCTG
130 AATCGTCTTCGATTTGGCAACCCTC
* * * * * *
680 AATGCTTTTCGTTCCATTGTTTATGGTCTAACTATAATCATTATGGGGAGATTAGTCCACTGTCA
1 AATGCTTTTCATTCCACTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGA
*
745 AGTTTTTAACTCATTT-GAACACTTGTTATTTTGGGCCTATAGGGGCCCATTAGTGACGTTTCGA
66 AGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATAGGGGCCCATTAGTGACGTTTTGA
* *
809 ATCGTCTTCGATATGGCAAACCTC
131 ATCGTCTTCGATTTGGCAACCCTC
* *
833 AATGTTTTTCATTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGA
1 AATGCTTTTCATTCCACTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGA
* * * *
898 AGGTTTTAACTCATTCGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT-TCTGTTTTG
66 AGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATAGGGGCCCATTAGTGAC-GTTTTG
*
962 AATCGTCTTCGATTTGGCAACCCAC
130 AATCGTCTTCGATTTGGCAACCCTC
*
987 AATGCTTTTCATTCCACTGTTTATGGCCTAACTATAATCATTTTGGAGAGATTAGTCCACTGTGA
1 AATGCTTTTCATTCCACTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGA
*
1052 AGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATAGGGGCCCATTAGTGACGTTCTGA
66 AGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATAGGGGCCCATTAGTGACGTTTTGA
*
1117 ATCGTCTTCGATTTGGCAACCCTG
131 ATCGTCTTCGATTTGGCAACCCTC
** *
1141 AATGCTTTT--TTTTAATGTTTATGGCCTAACTATAATCATTTTGGTGTAGATTAGTCCACTGTG
1 AATGCTTTTCATTCCACTGTTTATGGCCTAACTATAATCATTTTGGTG-AGATTAGTCCACTGTG
* * * *
1204 AAATTTTTAGCTAATTTTGAACACTTG-TATTTTG
65 AAGTTTTTAACTCATTTGGAACACTTGTTATTTTG
1238 CG
Statistics
Matches: 509, Mismatches: 44, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
152 43 0.08
153 175 0.34
154 290 0.57
155 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.40
Consensus pattern (154 bp):
AATGCTTTTCATTCCACTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGA
AGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATAGGGGCCCATTAGTGACGTTTTGA
ATCGTCTTCGATTTGGCAACCCTC
Found at i:1030 original size:545 final size:545
Alignment explanation
Indices: 1--1071 Score: 1686
Period size: 545 Copynumber: 2.0 Consensus size: 545
1 TTATGGCCTAACTATAATCATTTTGGGGAGATTAGTCCACTGTGAAGTTTTTAACTATTTGGAAC
1 TTATGGCCTAACTATAATCATTTTGGGGAGATTAGTCCACTGTGAAGTTTTTAACTATTTGGAAC
66 ACTTGTTATTTTGGGCCTATAGGGGCCCATTAGTGATGTTTTGAATCGTCTTCGATTTGGCAACC
66 ACTTGTTATTTTGGGCCTATAGGGGCCCATTAGTGATGTTTTGAATCGTCTTCGATTTGGCAACC
* * *
131 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTAGGTGAGATTAGTCCACTG
131 CTCAATGCTTTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTAGGGGAGATTAGTCCACTG
* * * *
196 GGAAGTTTTTAGCCCATTTGGAACACTTGTTATTTTGAGCCTATCGGGGCCCATTAATGTCGTTT
196 GCAAGTTTTTAACCCATTTGGAACACTTGTTATTTTGAGCCTATAGGGGCCCATTAATGACGTTT
* * *
261 TGAATCGTCTTCGATTTAGCAAACCTCAATGTTTTTCTTTCCATTGTTTATGGCCTAACTATAAT
261 CGAATCGTCTTCGATATAGCAAACCTCAATGTTTTTCATTCCATTGTTTATGGCCTAACTATAAT
* * * *
326 CATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTATCTCATTTGGAACACTATTTATTTTGGGCC
326 CATTTTGGTGAGATTAGTCCACTGTGAAGGTTTTAACTCATTCGGAACACTATTTATTTTGGGCC
* * *
391 TATCGGGGCCCATTAGTTCCATTTTAAATTATTTTCGATTTGGCAACAATCAATGCTTTACTTTC
391 TATCGGGGCCCATTAGTTCCATTTTAAATCATCTTCGATTTGGCAACAATCAATGCTTTACATTC
* * * *
456 CATTGTTTATGGCCCAACTATAATCATTTTGGTGAGATTAGTCTACTAAGAAGTTTTTAGCTCAT
456 CACTGTTTATGGCCCAACTATAATCATTTTGGAGAGATTAGTCCACTAAGAAGTTTTTAACTCAT
521 TTGGAAATGCTTTTCGTTCCACTGT
521 TTGGAAATGCTTTTCGTTCCACTGT
* *
546 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
1 TTATGGCCTAACTATAATCATTTTGGGGAGATTAGTCCACTGTGAAGTTTTTAACT-ATTTGGAA
*
611 CACCTT-TTATTTTGGGCCTATCGGGGCCCATTAGTGACT-TTTTGAATCGTCTTCGATTTGGCA
65 CA-CTTGTTATTTTGGGCCTATAGGGGCCCATTAGTGA-TGTTTTGAATCGTCTTCGATTTGGCA
* *
674 ACCCTGAATGCTTTTCGTTCCATTGTTTATGGTCTAACTATAATCA-TTATGGGGAGATTAGTCC
128 ACCCTCAATGCTTTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTA-GGGGAGATTAGTCC
* * * *
738 ACTGTCAAGTTTTTAACTCATTT-GAACACTTGTTATTTTGGGCCTATAGGGGCCCATTAGTGAC
192 ACTGGCAAGTTTTTAACCCATTTGGAACACTTGTTATTTTGAGCCTATAGGGGCCCATTAATGAC
*
802 GTTTCGAATCGTCTTCGATATGGCAAACCTCAATGTTTTTCATTCCATTGTTTATGGCCTAACTA
257 GTTTCGAATCGTCTTCGATATAGCAAACCTCAATGTTTTTCATTCCATTGTTTATGGCCTAACTA
867 TAATCATTTTGGTGAGATTAGTCCACTGTGAAGGTTTTAACTCATTCGGAACACT-TGTTATTTT
322 TAATCATTTTGGTGAGATTAGTCCACTGTGAAGGTTTTAACTCATTCGGAACACTAT-TTATTTT
** * * *
931 GGGCCTATCGGGGCCCATTAGTTCTGTTTTGAATCGTCTTCGATTTGGCAACCCA-CAATGCTTT
386 GGGCCTATCGGGGCCCATTAGTTCCATTTTAAATCATCTTCGATTTGGCAA-CAATCAATGCTTT
* * **
995 TCATTCCACTGTTTATGGCCTAACTATAATCATTTTGGAGAGATTAGTCCACTGTGAAGTTTTTA
450 ACATTCCACTGTTTATGGCCCAACTATAATCATTTTGGAGAGATTAGTCCACTAAGAAGTTTTTA
1060 ACTCATTTGGAA
515 ACTCATTTGGAA
1072 CACTTGTTAT
Statistics
Matches: 480, Mismatches: 40, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
544 1 0.00
545 335 0.70
546 140 0.29
547 4 0.01
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (545 bp):
TTATGGCCTAACTATAATCATTTTGGGGAGATTAGTCCACTGTGAAGTTTTTAACTATTTGGAAC
ACTTGTTATTTTGGGCCTATAGGGGCCCATTAGTGATGTTTTGAATCGTCTTCGATTTGGCAACC
CTCAATGCTTTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTAGGGGAGATTAGTCCACTG
GCAAGTTTTTAACCCATTTGGAACACTTGTTATTTTGAGCCTATAGGGGCCCATTAATGACGTTT
CGAATCGTCTTCGATATAGCAAACCTCAATGTTTTTCATTCCATTGTTTATGGCCTAACTATAAT
CATTTTGGTGAGATTAGTCCACTGTGAAGGTTTTAACTCATTCGGAACACTATTTATTTTGGGCC
TATCGGGGCCCATTAGTTCCATTTTAAATCATCTTCGATTTGGCAACAATCAATGCTTTACATTC
CACTGTTTATGGCCCAACTATAATCATTTTGGAGAGATTAGTCCACTAAGAAGTTTTTAACTCAT
TTGGAAATGCTTTTCGTTCCACTGT
Found at i:1194 original size:307 final size:306
Alignment explanation
Indices: 537--1237 Score: 1108
Period size: 307 Copynumber: 2.3 Consensus size: 306
527 ATGCTTTTCG
*
537 TTCCACTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCT
1 TTCCAATGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCT
602 CATTTGGAACACCTT-TTATTTTGGGCCTATCGGGGCCCATTAGTGACTTTTTGAATCGTCTTCG
66 CATTTGGAACA-CTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACTTTTTGAATCGTCTTCG
** * * * *
666 ATTTGGCAACCCTGAATGCTTTTCGTTCCATTGTTTATGGTCTAACTATAATCATTATGGGGAGA
130 ATTTGGCAACCCACAATGCTTTTCATTCCACTGTTTATGGCCTAACTATAATCATTATGGAGAGA
731 TTAGTCCACTGTCAAGTTTTTAACTCATTTGAACACTTGTTATTTTGGGCCTATAGGGGCCCATT
195 TTAGTCCACTGTCAAGTTTTTAACTCATTTGAACACTTGTTATTTTGGGCCTATAGGGGCCCATT
796 AGTGACGTTTCGAATCGTCTTCGATATGGCAAACCTCAATGTTTTTCA
260 AGTGACGTTTCGAATCGTCTTCGATATGGCAAACCTCAATGTTTTT-A
* * *
844 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGGTTTTAACT
1 TTCCAATGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCT
* *
909 CATTCGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT-TCTGTTTTGAATCGTCTTCG
66 CATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACT-TTTTGAATCGTCTTCG
*
973 ATTTGGCAACCCACAATGCTTTTCATTCCACTGTTTATGGCCTAACTATAATCATTTTGGAGAGA
130 ATTTGGCAACCCACAATGCTTTTCATTCCACTGTTTATGGCCTAACTATAATCATTATGGAGAGA
*
1038 TTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATAGGGGCCCAT
195 TTAGTCCACTGTCAAGTTTTTAACTCATTT-GAACACTTGTTATTTTGGGCCTATAGGGGCCCAT
* * *
1103 TAGTGACG-TTCTGAATCGTCTTCGATTTGGCAACCCTGAATGCTTTTT-
259 TAGTGACGTTTC-GAATCGTCTTCGATATGGCAAACCTCAATG-TTTTTA
* *
1151 TT-TAATGTTTATGGCCTAACTATAATCATTTTGGTGTAGATTAGTCCACTGTGAAATTTTTAGC
1 TTCCAATGTTTATGGCCTAACTATAATCATTTTGGTG-AGATTAGTCCACTGTGAAGTTTTTAGC
* *
1215 TAATTTTGAACACTTG-TATTTTG
65 TCATTTGGAACACTTGTTATTTTG
1238 CG
Statistics
Matches: 364, Mismatches: 24, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
306 44 0.12
307 246 0.68
308 69 0.19
309 5 0.01
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (306 bp):
TTCCAATGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCT
CATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACTTTTTGAATCGTCTTCGA
TTTGGCAACCCACAATGCTTTTCATTCCACTGTTTATGGCCTAACTATAATCATTATGGAGAGAT
TAGTCCACTGTCAAGTTTTTAACTCATTTGAACACTTGTTATTTTGGGCCTATAGGGGCCCATTA
GTGACGTTTCGAATCGTCTTCGATATGGCAAACCTCAATGTTTTTA
Done.