Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005204.1 Corchorus capsularis cultivar CVL-1 contig05222, 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, 880
Length: 1467
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Found at i:1186 original size:322 final size:319
Alignment explanation
Indices: 1--1358 Score: 1272
Period size: 332 Copynumber: 4.2 Consensus size: 319
* * * * *
1 TATAGATATTTCAAGTAGTATTTATGCCAAAAACCATGCAAAACTGAGTCGGGGCCCCGAA-ATG
1 TATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGTCGGGGCCCAGAACA--
* * * * * * *
65 CGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCAGCTAAAA-TCTG----ATCCGA--
64 CGTTTTTAGCCAAAAAC--CG-TGGTAAGTAAACGATTTCGGCTAAAATTTTGCAAAAACTGACC
* * * * * * **
123 AAATTTATTTTTC-TCAATTTCTTGCCATAATACTCTGAAAGTTTAAACAATTCAATGCCAAAAA
126 CAATTT-TTTTTCTTC-ATTTCTTGCCACAATA--CT-AAA--ATATATAATTAAACACCAAAAA
* * * * *
187 GATTAAAGCATTTTTCACGCTTCTAATAACGTTTTTCCATTTTTTTCCGAATTAATTTCTAACTA
184 AATTAAAGGATTTTTCACGCTTCTAATATCGTTTTTCCA-TTTTTTCCGATTTAATTTCTAATTA
* * *
252 AATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCGTTAAATCGAATATGGCTGGAAT-TCGG
248 AATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCGAATGTGGCTGGAATAT-GG
316 TTCAATGAA
312 -TCAATGAA
* *
325 TATAGATACTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGTCGGGGCCCAAAAACAC
1 TATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGTCGGGGCCC-AGAACAC
* * * *
390 GTATTTAGCCAAAAACTGTGATAAGTAAACGATTTCGGCTAAACTTTTGCAAAAACTGACCCAAA
65 GTTTTTAGCCAAAAACCGTGGTAAGTAAACGATTTCGGCTAAAATTTTGCAAAAACTGACCC-AA
* * *
455 TTTTTTTTTCCCTTCATTTCTTTGCCACAATACTAAAAAATATAAATATAATTCAACGCCAAAAA
129 -TTTTTTTT--CTTCATTTC-TTGCCACAATACTAAAATATAT-AAT-TAA-AC-AC-CAAAAAA
* *
520 ATTGAAGGATTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGATTTTATTTCTAATTAA
185 ATTAAAGGATTTTTCACGCTTCTAATATCGTTTTTCCA-TTTTTTCCGATTTAATTTCTAATTAA
* ** *
585 ATTGAAACAAGATTCAGATTTTCGTAAAAGCAAATCCTTAAATCGAATGTGGCTGTG-ATATGGT
249 ATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCGAATGTGGCTG-GAATATGGT
*
649 CGATGAA
313 CAATGAA
* * * * * * * *
656 TATAGATATTACAGGGAGTCTTTATGCTAAAAATCTTGCAAAACTGAGTTGAGGCCTC-GTAACG
1 TATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGTCGGGGCC-CAG-AACA
* * * * * * *
720 CGTTTTTAGCCAAAAACCGTGATGGTTAGTATATGATTTTCGGCTAAAA--AT---AGATCCGA-
64 CGTTTTTAGCCAAAAACC--G-TGGTAAGTAAACGA-TTTCGGCTAAAATTTTGCAAAAACTGAC
* * * *
779 --ATATTTTTTTTC-TCAATTTCTTGCCACAATACTCTGAAAATTTAAACAATTCAACGCCAAAA
125 CCA-ATTTTTTTTCTTC-ATTTCTTGCCACAATA--CT-AAAA--TATATAATTAAACACCAAAA
* * * *
841 AGATTAAAGGGTTTTTAACGCTTCTAATATCGTTTTTTCA-TTTTTCCGATTTAATTTCTAATTA
183 AAATTAAAGGATTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCGATTTAATTTCTAATTA
** * * *
905 AATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTGTTAAATCGAATGTGGCTTGAATTTGAT
248 AATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCGAATGTGGCTGGAATATG-G
*
970 TCGATGAA
312 TCAATGAA
**
978 TGCAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGTCGGGGTCCCAGAACAC
1 TATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGTCGGGG-CCCAGAACAC
*
1043 GTTTTTAGCCAAAAACCGTGGTGAGTAAACGATTTCGGCTAAAATTTTGCAAAAACTGACCCAAT
65 GTTTTTAGCCAAAAACCGTGGTAAGTAAACGATTTCGGCTAAAATTTTGCAAAAACTGACCCAAT
* *
1108 TTTTTTTCTTCATTTCTTGGCCACAATGCT-AAATATATAATTAAACACCAAAAAAAAATTGAAG
130 TTTTTTTCTTCATTTCTT-GCCACAATACTAAAATATATAATTAAACACC--AAAAAAATTAAAG
* *
1172 GATTTATCACGCTTCTAATATCATTTTTCCATTTTTTTCCCCGAATTT-ATTTCTAATTAAATCG
192 GATTTTTCACGCTTCTAATATCGTTTTTCCA-TTTTTT--CCG-ATTTAATTTCTAATTAAATCG
* ** * * *
1236 AAACAAGATTTAGATTTTCTTAAAAATAAATCCTTAAATCGAATGTGGCTGGGATATGGTCAATG
253 AAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCGAATGTGGCTGGAATATGGTCAATG
1301 AA
318 AA
* * *
1303 TATAGATATTTTAGGGAGT-TTATACGCCAAAAATCTTGCAAAACTGAGTCGAGGGC
1 TATAGATATTTCAAGGAGTCTT-TACGCCAAAAATCATGCAAAACTGAGTCG-GGGC
1359 TCGAGGTCCC
Statistics
Matches: 845, Mismatches: 131, Indels: 115
0.77 0.12 0.11
Matches are distributed among these distances:
318 12 0.01
319 11 0.01
320 15 0.02
321 97 0.11
322 120 0.14
323 60 0.07
324 84 0.10
325 73 0.09
326 101 0.12
327 10 0.01
328 5 0.01
329 12 0.01
330 10 0.01
331 81 0.10
332 129 0.15
333 4 0.00
334 10 0.01
335 11 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (319 bp):
TATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGTCGGGGCCCAGAACACG
TTTTTAGCCAAAAACCGTGGTAAGTAAACGATTTCGGCTAAAATTTTGCAAAAACTGACCCAATT
TTTTTTCTTCATTTCTTGCCACAATACTAAAATATATAATTAAACACCAAAAAAATTAAAGGATT
TTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCGATTTAATTTCTAATTAAATCGAAACAAGA
TTCAGATGCTCGTAAAAACAAATCCTTAAATCGAATGTGGCTGGAATATGGTCAATGAA
Found at i:1440 original size:653 final size:654
Alignment explanation
Indices: 1--1464 Score: 2001
Period size: 653 Copynumber: 2.2 Consensus size: 654
* * * * * * * * *
1 TATAGATATTTCAAGTAGTATTTATGCCAAAAACCATGCAAAACTGAGTCG-GGGC-CCCGAAAT
1 TATAGATATTACAGGGAGTCTTTACGCCAAAAATCTTGCAAAACTGAGTCGAGGCCTCCCGAAAC
* *
64 GCGTTTTTAGCCAAAAACTGTGATGGTTAGTAC-ACGATTTCAGCTAAAATCTGATCCGAAAATT
66 GCGTTTTTAGCCAAAAACCGTGATGGTTAGT-CTACGATTTCAGCTAAAAACTGATCCGAAAATT
* * *
128 TATTTTTCTCAATTTCTTGCCATAATACTCTGAAAGTTTAAACAATTCAATGCCAAAAAGATTAA
130 T-TTTTTCTCAATTTCTTGCCACAATACTCTGAAAATTTAAACAATTCAACGCCAAAAAGATTAA
*
193 AGCATTTTTCACGCTTCTAATAACGTTTTTCCATTTTTTTCCGAATTAATTTCTAACTAAATCGA
194 AGCATTTTTAACGCTTCTAATAACGTTTTTCCA-TTTTTTCCGAATTAATTTCTAACTAAATCGA
* *
258 AACAAGATTTAGATGCTCGTAAAAACAAATCGTTAAATCGAATATGGCTGGAATTCGGTTCAATG
258 AACAAGATTCAGATGCTCGTAAAAACAAATCGTTAAATCGAATATGGCTGGAATTCGATTCAATG
*
323 AATATAGATACTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGTCGGGGCCCAAAAAC
323 AATACAGATACTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGTCGGGGCCCAAAAAC
* *
388 ACGTATTTAGCCAAAAACTGTGATAAGTAAACGATTTCGGCTAAACTTTTGCAAAAACTGACCCA
388 ACGTATTTAGCCAAAAACCGTGATAAGTAAACGATTTCGGCTAAAATTTTGCAAAAACTGACCCA
* * ***
453 AATTTTTTTTTCCCTTCATTTCTTTGCCACAATACTAAAAAATATAAATATAATTCAACGCCAAA
453 AATTTTTTTTT-CCTTCATTTCTTGGCCACAATACTAAAAAATATAAATATAATACAACAAAAAA
* * *
518 AAATTGAAGGATTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGATTTTATTTCTAATT
517 AAATTGAAGGATTTATCACGCTTCTAATATCATTTTTCCATTTTTTTCCGAATTTATTTCTAATT
* * *
583 AAATTGAAACAAGATTCAGATTTTCGTAAAAGCAAATCCTTAAATCGAATGTGGCTGTGATATGG
582 AAATCGAAACAAGATTCAGATTTTCGTAAAAACAAATCCTTAAATCGAATGTGGCTGGGATATGG
*
648 TCGATGAA
647 TCAATGAA
* * * *
656 TATAGATATTACAGGGAGTCTTTATGCTAAAAATCTTGCAAAACTGAGTTGAGGCCT--CGTAAC
1 TATAGATATTACAGGGAGTCTTTACGCCAAAAATCTTGCAAAACTGAGTCGAGGCCTCCCGAAAC
* * * *
719 GCGTTTTTAGCCAAAAACCGTGATGGTTAGTATATGATTTTCGGCTAAAAA-TAGATCCGAATAT
66 GCGTTTTTAGCCAAAAACCGTGATGGTTAGTCTACGA-TTTCAGCTAAAAACT-GATCCGAAAAT
783 TTTTTTTCTCAATTTCTTGCCACAATACTCTGAAAATTTAAACAATTCAACGCCAAAAAGATTAA
129 TTTTTTTCTCAATTTCTTGCCACAATACTCTGAAAATTTAAACAATTCAACGCCAAAAAGATTAA
** * * * *
848 AGGGTTTTTAACGCTTCTAATATCGTTTTTTCA-TTTTTCCGATTTAATTTCTAATTAAATCGAA
194 AGCATTTTTAACGCTTCTAATAACGTTTTTCCATTTTTTCCGAATTAATTTCTAACTAAATCGAA
* * * * *
912 ACAAGATTCAGATGCTCGTAAAAACAAATTGTTAAATCGAATGTGGCTTGAATTTGATTCGATGA
259 ACAAGATTCAGATGCTCGTAAAAACAAATCGTTAAATCGAATATGGCTGGAATTCGATTCAATGA
* * *
977 ATGCAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGTCGGGGTCCC-AGAAC
324 ATACAGATACTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGTCGGGG-CCCAAAAAC
* * *
1041 ACGTTTTTAGCCAAAAACCGTGGTGAGTAAACGATTTCGGCTAAAATTTTGCAAAAACTGACCC-
388 ACGTATTTAGCCAAAAACCGTGATAAGTAAACGATTTCGGCTAAAATTTTGCAAAAACTGACCCA
* * *
1105 AA-TTTTTTTT-CTTCATTTCTTGGCCACAATGCT-AAATATAT-AAT-TAA-ACACCAAAAAAA
453 AATTTTTTTTTCCTTCATTTCTTGGCCACAATACTAAAAAATATAAATATAATACAACAAAAAAA
1164 AATTGAAGGATTTATCACGCTTCTAATATCATTTTTCCATTTTTTTCCCCGAATTTATTTCTAAT
518 AATTGAAGGATTTATCACGCTTCTAATATCATTTTTCCATTTTTTT--CCGAATTTATTTCTAAT
* * *
1229 TAAATCGAAACAAGATTTAGATTTTCTTAAAAATAAATCCTTAAATCGAATGTGGCTGGGATATG
581 TAAATCGAAACAAGATTCAGATTTTCGTAAAAACAAATCCTTAAATCGAATGTGGCTGGGATATG
1294 GTCAATGAA
646 GTCAATGAA
**
1303 TATAGATATTTTAGGGAGT-TTATACGCCAAAAATCTTGCAAAACTGAGTCGAGGGCTCGAGGTC
1 TATAGATATTACAGGGAGTCTT-TACGCCAAAAATCTTGCAAAACTGAGTCGA-GGC-C----TC
* * ** * *
1367 CCGAAACGCGTTTTTAGCTAGAAACCGTGATTATTAGTCTACGATTTCAACTAAAAACTTATCC-
59 CCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTCTACGATTTCAGCTAAAAACTGATCCG
1431 AAAATTTTTTTTCCTCAATGTT-TTGCCACAATAC
124 AAAATTTTTTTT-CTCAAT-TTCTTGCCACAATAC
1465 GCA
Statistics
Matches: 712, Mismatches: 77, Indels: 41
0.86 0.09 0.05
Matches are distributed among these distances:
645 51 0.07
646 5 0.01
647 130 0.18
648 10 0.01
649 22 0.03
651 8 0.01
652 2 0.00
653 214 0.30
654 36 0.05
655 208 0.29
656 26 0.04
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (654 bp):
TATAGATATTACAGGGAGTCTTTACGCCAAAAATCTTGCAAAACTGAGTCGAGGCCTCCCGAAAC
GCGTTTTTAGCCAAAAACCGTGATGGTTAGTCTACGATTTCAGCTAAAAACTGATCCGAAAATTT
TTTTTCTCAATTTCTTGCCACAATACTCTGAAAATTTAAACAATTCAACGCCAAAAAGATTAAAG
CATTTTTAACGCTTCTAATAACGTTTTTCCATTTTTTCCGAATTAATTTCTAACTAAATCGAAAC
AAGATTCAGATGCTCGTAAAAACAAATCGTTAAATCGAATATGGCTGGAATTCGATTCAATGAAT
ACAGATACTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGTCGGGGCCCAAAAACACG
TATTTAGCCAAAAACCGTGATAAGTAAACGATTTCGGCTAAAATTTTGCAAAAACTGACCCAAAT
TTTTTTTTCCTTCATTTCTTGGCCACAATACTAAAAAATATAAATATAATACAACAAAAAAAAAT
TGAAGGATTTATCACGCTTCTAATATCATTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAAT
CGAAACAAGATTCAGATTTTCGTAAAAACAAATCCTTAAATCGAATGTGGCTGGGATATGGTCAA
TGAA
Done.