Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009087.1 Corchorus capsularis cultivar CVL-1 contig09108, 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: 2881
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Found at i:437 original size:154 final size:154
Alignment explanation
Indices: 1--2128 Score: 2993
Period size: 154 Copynumber: 13.9 Consensus size: 154
* * *
1 GTGCTGTTTTAAATCGGCTTCAATTTGGC-AACCAACAAAGCTTTTCTTTTCAATTGTTTACGAC
1 GTGCTGTTTTGAATCGTCTTCGATTTGGCAAACC-ACAAAGCTTTTC-TTTCAATTGTTTACGAC
*
65 CTAACTATAATCATTTTGATGAGATTAGTCCATTG-GTAAGTTTTTAGCTCATTCAGAACACTTT
64 CTAACTATAATCATTTTGATGAGATTAGTCCATTGTG-AAGTTTTTAGCTCATTCAGAACACTTG
129 TTATTTCGGGCCTTT-GGAGGCCCATTA
128 TTATTTCGGGCCTTTCGG-GGCCCATTA
* * * * *
156 GTGCTGTTTTAAATCGGCTTCAATTTTGGC-AACCAACAAAACTTTTCTTTCAAATGTTTACGAC
1 GTGCTGTTTTGAATCGTCTTCGA-TTTGGCAAACC-ACAAAGCTTTTCTTTCAATTGTTTACGAC
220 CTAACTATAATCATTTTGATGAGATTAGTCCATTG-GTAAGTTTTTAGCTCATTCAGAACACTTG
64 CTAACTATAATCATTTTGATGAGATTAGTCCATTGTG-AAGTTTTTAGCTCATTCAGAACACTTG
*
284 TTATTTCGGGCCATTCGGGGCCCATTA
128 TTATTTCGGGCCTTTCGGGGCCCATTA
* * * * * * * * *
311 GTGCTATTTTGAATCGTATTCGATATGACAAACCGCAAAGCTTTTCTTTCCATTGTTTATGGCAT
1 GTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGACCT
* * * *
376 AACTATAATCATTTTGGTGATATTAGTCCACTGTGTAGTTTTTAGCTCATTCAGAACACTTGTTA
66 AACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTA
441 TTTCGGGCCTTTCGGGGCCCATTA
131 TTTCGGGCCTTTCGGGGCCCATTA
* * * *
465 GTGCTATTTTGAATCGTATTCGATTTGGCAAACCACAATA-CTTTTCTTTCAATTGTTTATGGCC
1 GTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAA-AGCTTTTCTTTCAATTGTTTACGACC
* *
529 TAACTATAATCATTTTGTTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTTTT
65 TAACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTT
594 ATTTCGGGCCTTT-GGAGGCCCATTA
130 ATTTCGGGCCTTTCGG-GGCCCATTA
* * * * *
619 GTGCTGTTTTAAATCGGCTTCAATTTGGC-AACCAACAAAACTTTTCTTTCAAATGTTTACGACC
1 GTGCTGTTTTGAATCGTCTTCGATTTGGCAAACC-ACAAAGCTTTTCTTTCAATTGTTTACGACC
* *
683 TAACTATAATCATTTTGATGAGATTAGTCCATTGCGAAGTTTTTAGCTCATTCAGAACACTTTTT
65 TAACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTT
748 ATTTCGGGCCTTTCGGGGCCCATTA
130 ATTTCGGGCCTTTCGGGGCCCATTA
* * * * * * * *
773 GTGTTGTTTTAAATCGGCTTCAATTTCGC-AACCAACAAAGCTTTTCTTTAAAATGCTTACGACC
1 GTGCTGTTTTGAATCGTCTTCGATTTGGCAAACC-ACAAAGCTTTTCTTTCAATTGTTTACGACC
837 TAACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTT
65 TAACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTT
*
902 ATTTCGGGTCTTTCGGGGCCCATTA
130 ATTTCGGGCCTTTCGGGGCCCATTA
* * *
927 TTGCTATTTTGAATTGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGACCT
1 GTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGACCT
*
992 AACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTTTTA
66 AACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTA
1057 TTTCGGGCCTTT-GGAGGCCCATTA
131 TTTCGGGCCTTTCGG-GGCCCATTA
* * * *
1081 GTGCTGTTTTAAATCGGCTTCAATTTGGC-AACCAACAAAGCTTTTCTTTCAAATGTTTACGACC
1 GTGCTGTTTTGAATCGTCTTCGATTTGGCAAACC-ACAAAGCTTTTCTTTCAATTGTTTACGACC
*
1145 TAACTATAATCATTTTGATGTGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTT
65 TAACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTT
1210 ATTTCGGGCCTTTCGGGGCCCATTA
130 ATTTCGGGCCTTTCGGGGCCCATTA
* * * *
1235 GTGCTGTTTTGAATTGTCTTCGATTTGGCAAGCAACAAAGCTTTTCTTTCAAATGTTTACGACCT
1 GTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGACCT
* *
1300 AACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTCTTA
66 AACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTA
1365 TTTCGGGCCTTTC-GGGCCCATTA
131 TTTCGGGCCTTTCGGGGCCCATTA
* * * * *
1388 GTGCTGTTTTGAATCTTCTTCGATTTGGCAAACCACAAAACTTTTCTTTCCATTGTTTATGGCCT
1 GTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGACCT
* *
1453 AACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTCTTA
66 AACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTA
1518 TTTCGGGCCTTTCGGGGCCCATTA
131 TTTCGGGCCTTTCGGGGCCCATTA
* * * * *
1542 GTGCTGTTTTGAATCGTCTTCAATTTGG---ACCACAAAGATTTTCTTTCCATTGTTTATGGCCT
1 GTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGACCT
*
1604 AACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTA
66 AACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTA
1669 TTTCGGGCCTTTCGGGGCCCATTA
131 TTTCGGGCCTTTCGGGGCCCATTA
* * * * * *
1693 GTGCTATTTTGAATCGTATTCGATTTGGCAAACCACAATGCTTTTCTTTCCAA-TATTTATGGCC
1 GTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTT-CAATTGTTTACGACC
* * * *
1757 TAACAATAAT-ATTTTGATAAGATTAGTCCATTGTGAAGTCTTTA-CTCATTTAGAACACTTGTT
65 TAACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTT
*
1820 ATTTCGGGCCATTCGGGGCCCATTA
130 ATTTCGGGCCTTTCGGGGCCCATTA
* * * * * * * * * * * *
1845 GTGCTATTTTAAATTGTATTCGATATGACAAACCGCAAAGCCTTTCTTTCCATTGTTTATGGCAT
1 GTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGACCT
* * * * *
1910 AACTATAATCATTTTGGTGATATTAGTCCACTGTGTAGTTTTTAGCTTATTCAGAACACTTGTTA
66 AACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTA
1975 TTTCGGGCCTTTCGGGGCCCATTA
131 TTTCGGGCCTTTCGGGGCCCATTA
* * * *
1999 GTGTTGTTTTGAATCGTCTTCGATTTGG---ACCACAAAGCTTTTCTTTCCATTGTTTATGGCCT
1 GTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGACCT
* * * * *
2061 AACTGTAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTCGCTCATTCAGAAGACTTTTTA
66 AACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTA
2126 TTT
131 TTT
2129 AGGTTCGGAT
Statistics
Matches: 1803, Mismatches: 148, Indels: 48
0.90 0.07 0.02
Matches are distributed among these distances:
151 236 0.13
152 102 0.06
153 217 0.12
154 1063 0.59
155 161 0.09
156 24 0.01
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (154 bp):
GTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGACCT
AACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTA
TTTCGGGCCTTTCGGGGCCCATTA
Done.