Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010863.1 Corchorus capsularis cultivar CVL-1 contig10884, 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: 2736
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Found at i:672 original size:321 final size:321
Alignment explanation
Indices: 11--794 Score: 1107
Period size: 321 Copynumber: 2.4 Consensus size: 321
1 TTTTTACTAG
* * * * *
11 AATAATCAGAAAAAAAATATAACTCAACGCCAAAAAGATTGACAGACTTTTCACGCTTCTGATAT
1 AATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGACTTTTCACGCTTCTAATAT
* * * *
76 TATTTTTTC-ATTTTTTCCGAATTAATTTCTAATCAAATTGAATTATGATTTAGATGCTCGTAAA
66 CA-TTTTTCAATTTTTTCCGAATTAATTTCTAATTAAATCGAAATATGATTTAGATGCTCGTAAA
* *
140 AACAAATCCTTATATCCAATGTGGCTGACATTTGGTTTCAATGTATATAGACATTTCGAGGAGTC
130 AACAAATACTTATATCCAATGTGGCTGACATTTGGTTTCAATGTATATAGACATTTCAAGGAGTC
*
205 TTTGTCCCAAAAATCATGCGAAATTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTG
195 TTTGT-CCAAAAATCATGCGAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTG
*
270 ATGATTAGTACACAATTTCGGCTAAAAACTTACCCGAAAATTTTTTTCCCAATTTTTTGCCAC
259 ATGAGTAGTACACAATTTCGGCTAAAAACTTACCCGAAAATTTTTTTCCCAATTTTTTGCCAC
* * * *
333 AATACTCAG-AAAAATATATAATTCAACGCCAAAAATATTGTCGGCCTTTTCACGCTTCCAATAT
1 AATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGACTTTTCACGCTTCTAATAT
*
397 CATTTTTCAATTTTTTCCGAATTAATTTCTAATTAAATCGAAATATAATTTAGATGCTCGTACAA
66 CATTTTTCAATTTTTTCCGAATTAATTTCTAATTAAATCGAAATATGATTTAGATGCTCGTA-AA
* * * *
462 AA-AAATACTTATATCGAATGTGGCTGACATTTGG-TTCAATGTATATAGATATTTCAAGTATTC
130 AACAAATACTTATATCCAATGTGGCTGACATTTGGTTTCAATGTATATAGACATTTCAAGGAGTC
* * **
525 TTTCCGT-CAAAAATCATGCGAAATTGAGCCGGGGCTTCGGAACGCGTTTTTCGCCAAAATTCGT
195 TTT--GTCCAAAAATCATGCGAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGT
* ** *
589 GATG-GTAGTAGATGATTTCGGCTAAAAA-TTGACCCGAAAATTTTTTTCTCAATTTTTTGCCAC
258 GATGAGTAGTACACAATTTCGGCTAAAAACTT-ACCCGAAAATTTTTTTCCCAATTTTTTGCCAC
* *
652 AATACTCAGAAAAGAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATA
1 AATACTCAGAAAA-AATATATAATTCAACGCCAAAAAGATTGACGGACTTTTCACGCTTCTAATA
* ** *
717 TCATTTTTCCATTTTTTTCCGAATTAATTTCTTGTTAAATCGAAATATGATTTAGATG-TTGTAA
65 TCATTTTT-CAATTTTTTCCGAATTAATTTCTAATTAAATCGAAATATGATTTAGATGCTCGTAA
*
781 AAACAAATTCTTAT
129 AAACAAATACTTAT
795 TGTGGCTGAC
Statistics
Matches: 412, Mismatches: 41, Indels: 19
0.87 0.09 0.04
Matches are distributed among these distances:
318 2 0.00
319 60 0.15
320 97 0.24
321 194 0.47
322 59 0.14
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (321 bp):
AATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGACTTTTCACGCTTCTAATAT
CATTTTTCAATTTTTTCCGAATTAATTTCTAATTAAATCGAAATATGATTTAGATGCTCGTAAAA
ACAAATACTTATATCCAATGTGGCTGACATTTGGTTTCAATGTATATAGACATTTCAAGGAGTCT
TTGTCCAAAAATCATGCGAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGAT
GAGTAGTACACAATTTCGGCTAAAAACTTACCCGAAAATTTTTTTCCCAATTTTTTGCCAC
Found at i:1468 original size:321 final size:319
Alignment explanation
Indices: 813--2736 Score: 2615
Period size: 321 Copynumber: 6.0 Consensus size: 319
803 ACATTTGGCG
* * ** *
813 GGGCTTCGGAACGCGTTTGTAGTAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAAACT
1 GGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGGCT-AAAAACT
* * * *
878 TACCCGAAAATTTTTTTCCCAATTTTTTGTCACAATACTTAGAAAAA-ATATATAATTCAAATCC
65 TACCCGAAAA-TTTTTTCCCAATTTTTTGCCACAATACTCAAAAAAATATATATAATTCAACTCC
*
942 AAAAATATTGACGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTCCGAATTAATTTCTAA
129 AAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTCCGAATTAATTTCTAA
* *
1007 TTAAATCGAAATAAGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGTTGGCATTT
194 TTAAATCGAAATAAGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTT
*
1072 GGTTCAATGTATATAGATATTTCAAGGAGTTTTTGCGCCAAAAATCATGCAAAATTGAGCA
259 GGTTCAATGTATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGCA
* * *
1133 GGGCTTCTGGAACGCGTTTTTAGCCAAAAACCGTAATGGTTAGTACACGATTTCGGCTAAAAACT
1 GGGC-TCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGGCTAAAAACT
* *
1198 TACCCGAAAAATTTTTCCCACTTTTTTTTGCCACAATACTCAAAAAAATATATATAATTCAACTC
65 TACCCGAAAATTTTTTCCCA--ATTTTTTGCCACAATACTCAAAAAAATATATATAATTCAACTC
* *
1263 CAAAAAGATTGACGGG-TTTTCACCCTTCTAATATCATTTTTCCATTTTTTTCCGAATTAATTTA
128 CAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTCCA--TTTTTCCGAATTAATTTC
*
1327 TAATTAAATCGAAATATGATTTAGATGCT-GTAAAAACAAATCCTTATATCCAATGTGGCTGACA
191 TAATTAAATCGAAATAAGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACA
** * *
1391 TTTGGTTCAATGTATATAGATATTTTGAGGAGTCTTTGTC-CCAAAAATCATGCGAAATTGAGCC
256 TTTGGTTCAATGTATATAGATATTTCAAGGAGTCTTTG-CGCCAAAAATCATGCAAAATTGAGCA
* * * * * *
1455 GGGGTGCGGAACGCGTTTTTAGCAAAAAACAGTGATGGTTATTACACAATTTCGACTAAAAACTT
1 GGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGGCTAAAAACTT
* * ** **
1520 ACCCGAAATTTTTTTTTCACAATTTTTTGCCACAATACTTTGAAAAAATAT-T-TAATTCGGCTC
66 ACCCGAAA--ATTTTTTCCCAATTTTTTGCCACAATAC-TCAAAAAAATATATATAATTCAACTC
* * * *
1583 CAAAAAGATTGACGGGCTTTTCACGCTTCTGACATCATTTTTCAATTTTTTTTCGAATTAATTTC
128 CAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTCCA--TTTTTCCGAATTAATTTC
* * * *
1648 TAATTAAATCGAAATATGATTTAGATGCTCGTAAAAACAAATACTTATATCGAATGTGGTTGACA
191 TAATTAAATCGAAATAAGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACA
* * * * *
1713 TTTGTTTCAATGTCTATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATCCGAAATTGAGTA
256 TTTGGTTCAATGTATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGCA
*
1777 GGGGCTCCGGAATGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGGCTAAAAAAC
1 -GGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGGCT-AAAAAC
* * * * * *
1842 TTACCCGAAAATTTTTTTCCCAATTTTTTGCAACACTAGTC--AGAAAGATATATAATTCAACGC
64 TTACCCGAAAA-TTTTTTCCCAATTTTTTGCCACAATACTCAAAAAAATATATATAATTCAACTC
* * *
1905 CAAAAAGATTGACGGGCTTTTCACGGTGCTAATATAATTTTTCCA-TTTTCCGAATTAATTTCTA
128 CAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTCCGAATTAATTTCTA
* *
1969 ATTAAATCCAAATAAGATTTAGATGCTCGTAAAAACAAATCCTTATATTCAATGTGGCT-AGCAT
193 ATTAAATCGAAATAAGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGA-CAT
* * *
2033 TTTGTTCAATGTATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGTAAAATTGAGCA
257 TTGGTTCAATGTATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGCA
* * * *
2096 GTGCTTCCGGAACGCGTTTTTAGCCAAAAACCGTAATGGTTAGTACACGATTTCGGCTAAAATCT
1 GGGC-TCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGGCTAAAAACT
*
2161 TACCCGAAAATTTTTTCCCAATTTTTTGCCACAATACT-AAAAAATATATATATAATTCAATTCC
65 TACCCGAAAATTTTTTCCCAATTTTTTGCCACAATACTCAAAAAA-ATATATATAATTCAACTCC
* * * *
2225 AAAAAGATTGACGAG-TTTTCACCCTTCTAATGTCATTTTTCCATTTTTTTCCGAATTAATTTAT
129 AAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTCCA--TTTTTCCGAATTAATTTCT
* * * * *
2289 AATTAAACCGAAATATGATTTAGATGCT-GTAAAAACAAATCTTTATATCCAATGTGACTAACAT
192 AATTAAATCGAAATAAGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACAT
* * *
2353 TTGGTTCAATGTCTATAGATATTTCAAGGTGTCTTTGCGCCAAAAATCATGCGAAATTGAGTC-
257 TTGGTTCAATGTATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAG-CA
* *
2416 GAGGCTCCAGAATGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGGCTAAAAACT
1 G-GGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGGCTAAAAACT
* * * * * *
2481 TACCCGAAATTTTTTTTCCCAATTTTTTGCAACAATAGTC--AGAAAGATATATAATTCAACGCC
65 TACCCGAAA-ATTTTTTCCCAATTTTTTGCCACAATACTCAAAAAAATATATATAATTCAACTCC
* * *
2544 AAAAAGATTGACGGGCTTTTCACGGTGCTAATATAATTTTTCCA-TTTTCCGAATTAATTTCTAA
129 AAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTCCGAATTAATTTCTAA
* *
2608 TTAAATCCAAATAAGATTTAGATGCTCGTAAAAACAAATCCTTATATTCAATGTGGCT-AGCATT
194 TTAAATCGAAATAAGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGA-CATT
* * *
2672 TTGTTCAATGTATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGTAAAATTGAGCA
258 TGGTTCAATGTATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGCA
2734 GGG
1 GGG
Statistics
Matches: 1411, Mismatches: 158, Indels: 73
0.86 0.10 0.04
Matches are distributed among these distances:
317 71 0.05
318 133 0.09
319 248 0.18
320 229 0.16
321 319 0.23
322 268 0.19
323 127 0.09
324 16 0.01
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (319 bp):
GGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGGCTAAAAACTT
ACCCGAAAATTTTTTCCCAATTTTTTGCCACAATACTCAAAAAAATATATATAATTCAACTCCAA
AAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTCCGAATTAATTTCTAATT
AAATCGAAATAAGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGG
TTCAATGTATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGCA
Done.