Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009062.1 Corchorus olitorius cultivar O-4 contig09090, 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, 847
Length: 1413
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.43
Found at i:689 original size:153 final size:153
Alignment explanation
Indices: 4--1413 Score: 2135
Period size: 153 Copynumber: 9.2 Consensus size: 153
1 GCT
*
4 TTTCTTTTCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTT
1 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTT
* * **
69 TATCTCATTTGGAACAATTTTTATTTTGGTATCTATCTACGGCCCATTAGTTCCGTTTTGGAATC
66 TAGCTCATTTGGAACACTTTTTATTTTGG-ATCTATC-GGGGCCCATTAGTTCCGTTTT-GAATC
134 GTCTTCGAATTTGGCAACCCTCAATGC
128 GTCTTCG-ATTTGGCAACCCTCAATGC
* * * * * *
161 TTTTCTTTTCAGTTGTTTATGGCGTAAGTGTAATCATTTTGGTGAGATTAGTCCTCTGTGAAGTT
1 -TTTCTTTCCA-TTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTT
* * * * ** * * ** * *
226 CTTAGTTCATTTGCAACAATTTTTATTTTGGGCCAATCGGGGGCCATTAGTGACGCTTTGAATCA
64 TTTAGCTCATTTGGAACACTTTTTATTTTGGATCTATCGGGGCCCATTAGTTCCGTTTTGAATCG
291 TCTTCGATTTGGCAACCCTCAATGC
129 TCTTCGATTTGGCAACCCTCAATGC
* *
316 TTTTCTTTTCATTGTTTATGTCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTT
1 -TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTT
* *
381 TTATCTCATTTGGAACACTTTTTATTTTGGATCTATCGCGGCCCATTAGTTCCGTTTTGAACTCG
65 TTAGCTCATTTGGAACACTTTTTATTTTGGATCTATCGGGGCCCATTAGTTCCGTTTTGAA-TCG
446 TCTTCGATTTGGCAACCCTCAATGC
129 TCTTCGATTTGGCAACCCTCAATGC
*
471 -TTC-TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT
1 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTT
*
534 TAGCTCATTTGGAACACTTTTTATTTTGGATCTATCGCGGCCCATTAGTTCCGTTTTGAATCGTC
66 TAGCTCATTTGGAACACTTTTTATTTTGGATCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTC
599 TTCGATTTGGCAACCCTCAATGC
131 TTCGATTTGGCAACCCTCAATGC
* *
622 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCTCTGTGAAGTTTT
1 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTT
* * *
687 TAGCTAATTTGGAACAGTTTTTATTTTGTG-CCTATCGGGGCCCATTAGTTCCGTTTTGAATCGT
66 TAGCTCATTTGGAACACTTTTTATTTTG-GATCTATCGGGGCCCATTAGTTCCGTTTTGAATCGT
751 CTTCGATTTGGCAACCCTCAATGC
130 CTTCGATTTGGCAACCCTCAATGC
* * * * * * *
775 TTTTCTTTTCATTGTTTATGGCGTAAGTGTAATCATTTTGGTGAGATTAGTCCTCTGTGAAGTTC
1 -TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTT
* * * ** * * ** * *
840 TTAGTTCATTTGCAACAATTTTTATTTTGGGCCAATCGGGGGCCATTAGTGACGCTTTGAATCAT
65 TTAGCTCATTTGGAACACTTTTTATTTTGGATCTATCGGGGCCCATTAGTTCCGTTTTGAATCGT
*
905 CTTCGATTTGGCAAGCCTCAATGC
130 CTTCGATTTGGCAACCCTCAATGC
*
929 TTTTCTTT-CTTTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTT
1 -TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTT
* *
993 TTAGCTCATTTGTAACACTTTTTATTTTGGATCTTTCGGGGCCCGACTTAGTTCCGTTTTGTAAT
65 TTAGCTCATTTGGAACACTTTTTATTTTGGATCTATCGGGGCCC-A-TTAGTTCCGTTTTG-AAT
1058 CGTCTTCGATTTGGCAACCCTCAATGC
127 CGTCTTCGATTTGGCAACCCTCAATGC
1085 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTT
1 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTT
*
1150 TAGCTCATTTGTAACACTTTTTATTTTGGATCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTC
66 TAGCTCATTTGGAACACTTTTTATTTTGGATCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTC
1215 TTCGATTTGGCAACCCTCAATGC
131 TTCGATTTGGCAACCCTCAATGC
*
1238 TTTCTTTCCATTGTTTATGGCCTAACTATAATGATTTTGGTGAGATTAGTCCACTTTGAAGTTTT
1 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTT
*
1303 TAGCTCATTTGGAACACTTTTTATTTTGGATCTAACGGGGCCCATTAGTTCCGTTTTGAATCGTC
66 TAGCTCATTTGGAACACTTTTTATTTTGGATCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTC
1368 TTCGATTTGGCAACCCTCAATGC
131 TTCGATTTGGCAACCCTCAATGC
1391 TTTCTTTCCATTGTTTATGGCCT
1 TTTCTTTCCATTGTTTATGGCCT
Statistics
Matches: 1152, Mismatches: 89, Indels: 27
0.91 0.07 0.02
Matches are distributed among these distances:
151 28 0.02
152 119 0.10
153 433 0.38
154 255 0.22
155 76 0.07
156 137 0.12
157 15 0.01
158 14 0.01
159 75 0.07
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.43
Consensus pattern (153 bp):
TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTT
TAGCTCATTTGGAACACTTTTTATTTTGGATCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTC
TTCGATTTGGCAACCCTCAATGC
Found at i:1222 original size:616 final size:613
Alignment explanation
Indices: 4--1411 Score: 2473
Period size: 616 Copynumber: 2.3 Consensus size: 613
1 GCT
*
4 TTTCTTTTCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTT
1 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTT
* * **
69 TATCTCATTTGGAACAATTTTTATTTTGGTATCTATCTACGGCCCATTAGTTCCGTTTTGGAATC
66 TAGCTCATTTGGAACAATTTTTATTTT-GTGTCTATC-GGGGCCCATTAGTTCCGTTTT-GAATC
134 GTCTTCGAATTTGGCAACCCTCAATGCTTTTCTTTTCAGTTGTTTATGGCGTAAGTGTAATCATT
128 GTCTTCG-ATTTGGCAACCCTCAATGCTTTTCTTTTCA-TTGTTTATGGCGTAAGTGTAATCATT
199 TTGGTGAGATTAGTCCTCTGTGAAGTTCTTAGTTCATTTGCAACAATTTTTATTTTGGGCCAATC
191 TTGGTGAGATTAGTCCTCTGTGAAGTTCTTAGTTCATTTGCAACAATTTTTATTTTGGGCCAATC
264 GGGGGCCATTAGTGACGCTTTGAATCATCTTCGATTTGGCAACCCTCAATGCTTTTCTTTTCATT
256 GGGGGCCATTAGTGACGCTTTGAATCATCTTCGATTTGGCAACCCTCAATGCTTTTCTTTTCATT
* *
329 GTTTATGTCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTATCTCATTTGG
321 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGG
394 AACACTTTTTATTTTGGATCTATCGCGGCCCATTAGTTCCGTTTTGAACTCGTCTTCGATTTGGC
386 AACACTTTTTATTTTGGATCTATCGCGGCCCATTAGTTCCGTTTTGAACTCGTCTTCGATTTGGC
459 AACCCTCAATGCTTCTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
451 AACCCTCAATGCTTCTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
524 GTGAAGTTTTTAGCTCATTTGGAACACTTTTTATTTTGGATCTATCGCGGCCCATTAGTTCCGTT
516 GTGAAGTTTTTAGCTCATTTGGAACACTTTTTATTTTGGATCTATCGCGGCCCATTAGTTCCGTT
589 TTGAATCGTCTTCGATTTGGCAACCCTCAATGC
581 TTGAATCGTCTTCGATTTGGCAACCCTCAATGC
* *
622 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCTCTGTGAAGTTTT
1 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTT
* * *
687 TAGCTAATTTGGAACAGTTTTTATTTTGTGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTC
66 TAGCTCATTTGGAACAATTTTTATTTTGTGTCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTC
752 TTCGATTTGGCAACCCTCAATGCTTTTCTTTTCATTGTTTATGGCGTAAGTGTAATCATTTTGGT
131 TTCGATTTGGCAACCCTCAATGCTTTTCTTTTCATTGTTTATGGCGTAAGTGTAATCATTTTGGT
817 GAGATTAGTCCTCTGTGAAGTTCTTAGTTCATTTGCAACAATTTTTATTTTGGGCCAATCGGGGG
196 GAGATTAGTCCTCTGTGAAGTTCTTAGTTCATTTGCAACAATTTTTATTTTGGGCCAATCGGGGG
* *
882 CCATTAGTGACGCTTTGAATCATCTTCGATTTGGCAAGCCTCAATGCTTTTC-TTTCTTTGTTTA
261 CCATTAGTGACGCTTTGAATCATCTTCGATTTGGCAACCCTCAATGCTTTTCTTTTCATTGTTTA
*
946 TGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGTAACAC
326 TGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACAC
* *
1011 TTTTTATTTTGGATCTTTCGGGGCCCGACTTAGTTCCGTTTTGTAA-TCGTCTTCGATTTGGCAA
391 TTTTTATTTTGGATCTATCGCGGCCC-A-TTAGTTCCGTTTTG-AACTCGTCTTCGATTTGGCAA
1075 CCCTCAATGCTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
453 CCCTCAATGC-TTC-TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
* * *
1140 TTGAAGTTTTTAGCTCATTTGTAACACTTTTTATTTTGGATCTATCGGGGCCCATTAGTTCCGTT
516 GTGAAGTTTTTAGCTCATTTGGAACACTTTTTATTTTGGATCTATCGCGGCCCATTAGTTCCGTT
1205 TTGAATCGTCTTCGATTTGGCAACCCTCAATGC
581 TTGAATCGTCTTCGATTTGGCAACCCTCAATGC
*
1238 TTTCTTTCCATTGTTTATGGCCTAACTATAATGATTTTGGTGAGATTAGTCCACTTTGAAGTTTT
1 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTT
* *
1303 TAGCTCATTTGGAACACTTTTTATTTTG-GATCTAACGGGGCCCATTAGTTCCGTTTTGAATCGT
66 TAGCTCATTTGGAACAATTTTTATTTTGTG-TCTATCGGGGCCCATTAGTTCCGTTTTGAATCGT
*
1367 CTTCGATTTGGCAACCCTCAATGC-TTTCTTTCCATTGTTTATGGC
130 CTTCGATTTGGCAACCCTCAATGCTTTTCTTTTCATTGTTTATGGC
1412 CT
Statistics
Matches: 756, Mismatches: 28, Indels: 15
0.95 0.04 0.02
Matches are distributed among these distances:
612 97 0.13
613 148 0.20
614 72 0.10
615 38 0.05
616 308 0.41
617 7 0.01
618 86 0.11
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.43
Consensus pattern (613 bp):
TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTT
TAGCTCATTTGGAACAATTTTTATTTTGTGTCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTC
TTCGATTTGGCAACCCTCAATGCTTTTCTTTTCATTGTTTATGGCGTAAGTGTAATCATTTTGGT
GAGATTAGTCCTCTGTGAAGTTCTTAGTTCATTTGCAACAATTTTTATTTTGGGCCAATCGGGGG
CCATTAGTGACGCTTTGAATCATCTTCGATTTGGCAACCCTCAATGCTTTTCTTTTCATTGTTTA
TGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACAC
TTTTTATTTTGGATCTATCGCGGCCCATTAGTTCCGTTTTGAACTCGTCTTCGATTTGGCAACCC
TCAATGCTTCTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA
GTTTTTAGCTCATTTGGAACACTTTTTATTTTGGATCTATCGCGGCCCATTAGTTCCGTTTTGAA
TCGTCTTCGATTTGGCAACCCTCAATGC
Done.