Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011601.1 Corchorus olitorius cultivar O-4 contig11634, 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: 3831
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Found at i:183 original size:30 final size:30
Alignment explanation
Indices: 149--212 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
139 ATAGTTGTTA
*
149 TTTTGGGCCTATAGGGGCCCATTAGTGACG
1 TTTTGGGCCTATAGGGGCCCATTAGTGAAG
179 TTTTGGGCCTATAGGGGCCCATTAGTGAAG
1 TTTTGGGCCTATAGGGGCCCATTAGTGAAG
209 TTTT
1 TTTT
213 TAACTCATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.17, C:0.17, G:0.31, T:0.34
Consensus pattern (30 bp):
TTTTGGGCCTATAGGGGCCCATTAGTGAAG
Found at i:483 original size:154 final size:154
Alignment explanation
Indices: 203--534 Score: 520
Period size: 154 Copynumber: 2.2 Consensus size: 154
193 GGGCCCATTA
* *
203 GTGAAGTTTTTAACTCATTTGGAACACTTGTGATTTTGGGCCTATAGGGGCCCATTAGTGATGTT
1 GTGAAGTTTTTAACTCATTTGGAACACTTGTGATTTTGGGCCTATAGGGGCCCATTAATGACGTT
* * ** *
268 TTGAATCGTTTTCGATTTGGCAACCCTCAATTCTTTTCTTTCCATTGTTTATGGCCTAACTATAA
66 TTGAATCATCTTCGATTTGGCAACAATCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAA
333 TCATTTTGGTGAGATTAGTCCACT
131 TCATTTTGGTGAGATTAGTCCACT
* * * **
357 GTGAAGTTTTTATCTCATTTGGAACACTTGTTATTTTGGGCCTATAGGGGCCTATTAATTCCGTT
1 GTGAAGTTTTTAACTCATTTGGAACACTTGTGATTTTGGGCCTATAGGGGCCCATTAATGACGTT
422 TTGAATCATCTTCGATTTGGCAACAATCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAA
66 TTGAATCATCTTCGATTTGGCAACAATCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAA
*
487 TCATTTTGGTGAGATTATTCCACT
131 TCATTTTGGTGAGATTAGTCCACT
** *
511 AAGAAGTTTTTAGCTCATTTGGAA
1 GTGAAGTTTTTAACTCATTTGGAA
535 ATGCTTTTCG
Statistics
Matches: 162, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
154 162 1.00
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (154 bp):
GTGAAGTTTTTAACTCATTTGGAACACTTGTGATTTTGGGCCTATAGGGGCCCATTAATGACGTT
TTGAATCATCTTCGATTTGGCAACAATCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAA
TCATTTTGGTGAGATTAGTCCACT
Found at i:711 original size:216 final size:217
Alignment explanation
Indices: 336--750 Score: 665
Period size: 216 Copynumber: 1.9 Consensus size: 217
326 ACTATAATCA
*
336 TTTTGGTGAGATTAGTCCACTGTGAAGTTTTTATCTCATTTGGAACACTTGTTATTTTGGGCCTA
1 TTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTA
* * *
401 TAGGGGCCTATTAATTCCGTTTTGAATCATCTTCGATTTGGCAACAATCAATGCTTTTCTTTCCA
66 TAGGGGCCTATTAATTCCGTTTGGAATCATCTTCGATTTGACAACAATAAATGCTTTTCTTTCCA
* * *
466 TTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTATTCCACTAAGAAGTTTTTAGCTCATTT
131 TTGTTTATGGCCTAACTATAAGCATTTTGGTGAGATTAGTCCACTAAGAAGTTTTTAGCTAATTT
531 GGAAATGCTTTTCGTTCCATTG
196 GGAAATGCTTTTCGTTCCATTG
*
553 TTTTGGTGACGATTAGTCCACTGTGAAG-TTTTAGCTCATTTGGAACACTT-TTATTTTGGGCGT
1 TTTTGGTGA-GATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
* * **
616 ATCGGGG-CTCATTAGTTCCGTTTGGAATCATCTTCGATTTGACAACCCTAAATGCTTTTCTTTC
65 ATAGGGGCCT-ATTAATTCCGTTTGGAATCATCTTCGATTTGACAACAATAAATGCTTTTCTTTC
**
680 CATTGTTTATGGCCTAACTATAAGCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTAAT
129 CATTGTTTATGGCCTAACTATAAGCATTTTGGTGAGATTAGTCCACTAAGAAGTTTTTAGCTAAT
745 TTGGAA
194 TTGGAA
751 CACTTGCTCT
Statistics
Matches: 182, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
215 2 0.01
216 132 0.73
217 30 0.16
218 18 0.10
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (217 bp):
TTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTA
TAGGGGCCTATTAATTCCGTTTGGAATCATCTTCGATTTGACAACAATAAATGCTTTTCTTTCCA
TTGTTTATGGCCTAACTATAAGCATTTTGGTGAGATTAGTCCACTAAGAAGTTTTTAGCTAATTT
GGAAATGCTTTTCGTTCCATTG
Found at i:839 original size:154 final size:154
Alignment explanation
Indices: 553--1424 Score: 1273
Period size: 154 Copynumber: 5.7 Consensus size: 154
543 CGTTCCATTG
* *
553 TTTTGGTGACGATTAGTCCACTGTGAAG-TTTTAGCTCATTTGGAACACTT-TTATTTTGGGCGT
1 TTTTGGTGA-GATTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTTTGGGCCT
* * * * *
616 ATCGGGGCTCATTAGTTCCGTTTGGAATCATCTTCGATTTGACAACCCTAAATGCTTTTCTTTCC
65 ATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCC
*
681 ATTGTTTATGGCCTAACTATAAGCA
130 ATTGTTTATGGCCTAACTATAATCA
* *
706 TTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGCTCTTTTGGGCCTA
1 TTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTTTGGGCCTA
* * *
771 TCGGGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGGTTTTCATTT-A
66 TCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTC-TTTCC
*
835 ATTGTTTATGGTCTAACTATAAGTCGA
130 ATTGTTTATGGCCTAACTATAA-TC-A
* ** **
862 TTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTAATTCGGAATGCTTGTTATTTTGCTCCTA
1 TTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTTTGGGCCTA
* ** * *
927 TTGGGGCCCATTAGTGACGTTTTGAATCATCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCA
66 TCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCA
* *
992 CTGTTTATGCCCTAACTATAATCA
131 TTGTTTATGGCCTAACTATAATCA
* * * * * *
1016 TTTTGGTGAGATTATTCCACTATGAAGTTTTTAGCTCATTTGAAACACTTTTTATTTTGGGCGTA
1 TTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTTTGGGCCTA
* * **
1081 TCGGGGCCCATTAGTTCCGTTTTAAATTGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTTAA
66 TCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCA
1146 TTGTTTATGGCCTAACTATAATCA
131 TTGTTTATGGCCTAACTATAATCA
* *
1170 TTTTGGTGAGATTAGTCCACTGTGAAGTTTTCAGCTAATTTGGAACACTTGTTATTTTGCGCCTA
1 TTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTTTGGGCCTA
** * *
1235 TCGGGGCCCATTAGTGACGTTTTGAATCGTCTTTGATTTGGCAAACCTCAATGCTTTTCTTTCCA
66 TCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCA
*
1300 TAGTTTATGGCCTAACTATAATCA
131 TTGTTTATGGCCTAACTATAATCA
* *
1324 TTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTTTTATTTTGGGCCTA
1 TTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTTTGGGCCTA
*
1389 TCGGGGCCCATTAGTTCCGTTTTGCATCGTCTTCGA
66 TCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGA
1425 ACCCTCAATG
Statistics
Matches: 634, Mismatches: 79, Indels: 11
0.88 0.11 0.02
Matches are distributed among these distances:
152 18 0.03
153 30 0.05
154 447 0.71
155 9 0.01
156 130 0.21
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.41
Consensus pattern (154 bp):
TTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTTTGGGCCTA
TCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCA
TTGTTTATGGCCTAACTATAATCA
Done.