Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010571.1 Corchorus capsularis cultivar CVL-1 contig10592, 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: 25353
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:11116 original size:2 final size:2
Alignment explanation
Indices: 11109--11134 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11099 TACTTTTATC
11109 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
11135 GAAACCATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23597 original size:334 final size:317
Alignment explanation
Indices: 22763--23921 Score: 1035
Period size: 322 Copynumber: 3.6 Consensus size: 317
22753 CCATGATGGT
* * * *
22763 AAAAATGACCCGAAAGATTTTT-CCTCGA-TTTTTGACAAAAATACTCATAAAATATATATAATT
1 AAAAATGACCC-AAA-ATTTTTATCTCAATTTTTTG-CCACAATACTCA-AAAA-ATATATAATT
* * * * **
22826 CAATGCCAAAAAAATTGGAGGATTTTTCACGCTTTTAATGCCGTTTTT-CATATTTTTTCTGAAT
61 CAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCAT-TTTTTTC-GAAT
*
22890 TAATTT-TGAATTAAATCGAAACAAGATTCGGATGTAC-GTAAAAACAAATCCTTAAATCCAATG
124 TAATTTCT-AATTAAATCGAAACAAGATTCAGAT-T-CTGTAAAAACAAATCCTTAAATCCAATG
* * *
22953 TAGTTAAGATTTGATTAGATAAATAAAGATATTTCAAGGAGT-TTTGGCGCAAAAAGTCATGCAA
186 TAGCTGAGATTTGATTAGATAAATAAAGATATTTCAAGGAGTCTTT-GC-CCAAAA-TCATGC-A
* * * * *
23017 AACAAAGCCGTA-GCCCCGGAACGC-GTTTTAG-TAAAAACCCGTGATGCTTAGTACACGATTTC
247 AATATAGTCG-AGGCCCCGGAACGCTTTTTTAGCCAAAAA-CCGTGATG-TTAGTACACGATTTC
23079 GGCTAAAAAC
309 GGCT-AAAAC
* * * ** *
23089 TAACACGA---AACGTTTTTATCTCAATTTTTTGCCACAATACTCATAAAAAACATTATAATTCA
1 AAAAATGACCCAAAATTTTTATCTCAATTTTTTGCCACAATACTC--AAAAAATA-TATAATTCA
* * * * * * *
23151 ACGCCAAAAAGATTGACGAGCTTTTTCATGCTTCTAATATCATTTTTCCATTTTTCT-AAATTAA
63 ACGCCAAAAAAATTGAAG-GGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCGAATTAA
* * * * *
23215 TTTCTAATTACAGCGAAACAAGATTCATATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT
127 TTTCTAATTAAATCGAAACAAGATTCAGATTCT-GTAAAAACAAATCCTTAAATCCAATGTAGCT
* * * * * * * *
23280 TACATTTGGTTCGATCAATATAGATATTTCAAGGACTCTTTGCACCACAAATCATGCAAATTTGA
191 GAGATTTGATTAGATAAATAAAGATATTTCAAGGAGTCTTTGC-CCA-AAATCATGCAAATAT-A
* *
23345 GTCGGGGCTCCGGAACGCTTTTTTAGCCAAAAACCGTGATGGTGTTAGTACACGATTTCGGCTAA
253 GTCGAGGCCCCGGAACGCTTTTTTAGCCAAAAACCGTGA---TGTTAGTACACGATTTCGGCTAA
23410 AATTTTGC
315 AA-----C
** * * *
23418 AAAAATTGACCCAAAAAATTTGTCATCAATTTTTTTCCAGAATACTCAGGAAAAATATATAATTC
1 AAAAA-TGACCCAAAATTTTTATC-TCAATTTTTTGCCACAATACTCA--AAAAATATATAATTC
* *
23483 AATGCCAAAGAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCGAATTT
62 AACGCCAAA-AAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCGAATTA
** *
23548 ATTTCTAATTAAATCGAAACAAGATTCAGATTCTTGTAAAGCCAAATCCTTAAATCCAATGTAAC
126 ATTTCTAATTAAATCGAAACAAGATTCAGATTC-TGTAAAAACAAATCCTTAAATCCAATGTAGC
* * * *
23613 TGAGATTTGATTAGATAAATAAAGATATTTGAAGGAGTCTTTATGCCGAAAACCTTGCAAAATAT
190 TGAGATTTGATTAGATAAATAAAGATATTTCAAGGAGTC-TT-TGCCCAAAATCATGC-AAATAT
* * *
23678 AGTCGAGGCCCCGAAACGCGTTTTTTAGCCAAAAAACCGTGA---TCGTACATGATTTTCGGC--
252 AGTCGAGGCCCCGGAACGC-TTTTTTAGCC-AAAAACCGTGATGTTAGTACACGA-TTTCGGCTA
23738 -AA-
314 AAAC
* * * *
23740 AAAACTGACCCAAATTTTCTTTTCTCAATTTTTTGCCACAATACTCATAAAATATAATAATTCAA
1 AAAAATGACCCAAAATTT-TTATCTCAATTTTTTGCCACAATACTCAAAAAATAT-ATAATTCAA
* * * * * *
23805 CGCCAAAAAGATTGATGGGATTTTCAAGCTTGTAATATCGTTTTTCCGTTTTTTTTTCCGAATTA
64 CGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCC--ATTTTTTT-CGAATTA
*
23870 ATTTCTAATTAAATCGAAACAAGATTCAGATACTGGTAAAAACAAATCCTTA
126 ATTTCTAATTAAATCGAAACAAGATTCAGATTCT-GTAAAAACAAATCCTTA
23922 TATCAGCTGC
Statistics
Matches: 677, Mismatches: 110, Indels: 96
0.77 0.12 0.11
Matches are distributed among these distances:
319 42 0.06
320 16 0.02
321 47 0.07
322 192 0.28
323 52 0.08
324 37 0.05
325 22 0.03
326 7 0.01
328 2 0.00
329 4 0.01
330 10 0.01
331 7 0.01
332 1 0.00
333 57 0.08
334 147 0.22
335 20 0.03
336 14 0.02
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (317 bp):
AAAAATGACCCAAAATTTTTATCTCAATTTTTTGCCACAATACTCAAAAAATATATAATTCAACG
CCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCGAATTAATTTC
TAATTAAATCGAAACAAGATTCAGATTCTGTAAAAACAAATCCTTAAATCCAATGTAGCTGAGAT
TTGATTAGATAAATAAAGATATTTCAAGGAGTCTTTGCCCAAAATCATGCAAATATAGTCGAGGC
CCCGGAACGCTTTTTTAGCCAAAAACCGTGATGTTAGTACACGATTTCGGCTAAAAC
Found at i:24171 original size:204 final size:203
Alignment explanation
Indices: 23837--24205 Score: 535
Period size: 204 Copynumber: 1.8 Consensus size: 203
23827 TTCAAGCTTG
* *
23837 TAATATCGTTTTTCCGTTTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATA
1 TAATATCGTTTTTCCATTTTTTTTTCCGAATTAATTTATAATTAAATCGAAACAAGATTCAGATA
* * * * *
23902 CTGGTAAAAACAAATCCTTATATCAGCTGCGGATGAGATTTGTTTCGATGAATATAGATATTTCA
66 CTCGTAAAAACAAATCCTTAAATCAACTGCGGATGAGATTTGGTTCGATGAATACAGATATTTCA
*
23967 AGAAGTATTTTCTGCAGAA-AATCATGCAAAATTGAGCATTTCTAAAAATCATGCAAACGGGATT
131 AGAAGTA-TTTCTGCA-AACAATCATGCAAAACTGAGCATTTCTAAAAATCATGCAAACGGGATT
24031 TTCCCGTTTC
194 TTCCCGTTTC
* * * *
24041 TAATTTCGTTTTTCCATTTTTTTTTTCGAATTTATTTATAATTAAATCGAAACAAGATTCAGATG
1 TAATATCGTTTTTCCATTTTTTTTTCCGAATTAATTTATAATTAAATCGAAACAAGATTCAGATA
* * * *
24106 CTCGTAAAAATAAATCCTTAAATCCAAC-GTGGTTGAGATTTGGTTCGCTGAATACAGATATTTC
66 CTCGTAAAAACAAATCCTTAAAT-CAACTGCGGATGAGATTTGGTTCGATGAATACAGATATTTC
* *
24170 AAGGAGTATTTCTGCAAACAATCATGCTAAACTGAG
130 AAGAAGTATTTCTGCAAACAATCATGCAAAACTGAG
24206 TCGGGTCCCC
Statistics
Matches: 145, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
202 2 0.01
203 23 0.16
204 117 0.81
205 3 0.02
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (203 bp):
TAATATCGTTTTTCCATTTTTTTTTCCGAATTAATTTATAATTAAATCGAAACAAGATTCAGATA
CTCGTAAAAACAAATCCTTAAATCAACTGCGGATGAGATTTGGTTCGATGAATACAGATATTTCA
AGAAGTATTTCTGCAAACAATCATGCAAAACTGAGCATTTCTAAAAATCATGCAAACGGGATTTT
CCCGTTTC
Found at i:24658 original size:319 final size:322
Alignment explanation
Indices: 24023--25253 Score: 2003
Period size: 319 Copynumber: 3.8 Consensus size: 322
24013 AATCATGCAA
* * *
24023 ACGGGATTTTCCCGTTTCTAATTTCGTTTTTCCATTTTTTTTTTCGAATTTATTTATAATTAAAT
1 ACGGGATTTTCCCGCTTCTAATTTCGTTTTTCCA-ATTTTTTTTCGAATTTATTTCTAATTAAAT
*
24088 CGAAACAAGATTCAGATGCTCGTAAAAATAAATCCTTAAATCCAACGTGGTTGAGATTTGGTTCG
65 CGAAACAAGATTCAGAGGCTCGTAAAAATAAATCCTTAAATCCAACGTGGTTGAGA-TTGGTTCG
* *
24153 CTGAATACAGATATTTCAAGGAGTATTTCTGCAAACAATCATGCTAAACTGAGTCGGGTCCCCGA
129 CTGAATACAGATATTTCAAGGAGTATTTCTGCAAAAAATCATGCTAAACTGAGACGGGTCCCCGA
* *
24218 AACGCATTTTTAGCC-AGTAACCGTGATGG--AATACACGATTTCGACTAAAAACTGACCCGAAA
194 AACGCGTTTTTAGCCAAG-AACCGTGATGGATAATACACGATTTCGGCTAAAAACTGACCCGAAA
24280 AATTATTTCTCAATTTTTCACAAAATATATTCAGAAAAATATTTAATTCAACGCCAAAAAAATTC
258 AATTATTTCTCAATTTTTCACAAAATATATTCAGAAAAATATTTAATTCAACGCCAAAAAAATTC
24345 ACGGGATTTTCCCGCTTCTAATTTCGTTTTT-CAATTTTTTTTCGAATTTATTTCTAATTAAATC
1 ACGGGATTTTCCCGCTTCTAATTTCGTTTTTCCAATTTTTTTTCGAATTTATTTCTAATTAAATC
* *
24409 GAAACAAGATTCAGATGCTCGTAAAAATAAATCTTTAAATCCAACGTGGTTGAGATTGGTTCGCT
66 GAAACAAGATTCAGAGGCTCGTAAAAATAAATCCTTAAATCCAACGTGGTTGAGATTGGTTCGCT
* * *
24474 GAATACATATATTTCAAGGACTA-TTCTGCAAAAAATCATGCTAAACTGAGTCGGGTCCCCGAAA
131 GAATACAGATATTTCAAGGAGTATTTCTGCAAAAAATCATGCTAAACTGAGACGGGTCCCCGAAA
* * *
24538 CGCGTTTTTAGCAAAGAACCGTGATGGATAATACACGATTTCGGCT-AAAACTGACCAGAGAAAT
196 CGCGTTTTTAGCCAAGAACCGTGATGGATAATACACGATTTCGGCTAAAAACTGACCCGAAAAAT
* *
24602 TATTTCTCATTTTTTCGCAAAATATATTCAGAAAAATATTTAATTCAACGCCAAAAAAATTC
261 TATTTCTCAATTTTTCACAAAATATATTCAGAAAAATATTTAATTCAACGCCAAAAAAATTC
*
24664 ACGGGATTTTCCCGCTTCTAATTTCGTTTTTCCATTTTTTTTCTCGAATTTATTTCTAATTAAAT
1 ACGGGATTTTCCCGCTTCTAATTTCGTTTTTCCAATTTTTTT-TCGAATTTATTTCTAATTAAAT
*
24729 CGAAACAAGATTCAGAGGCTCGTAAAAATAAATCCTTAAATCCAACGCGGTTGAGATTGGTTCGC
65 CGAAACAAGATTCAGAGGCTCGTAAAAATAAATCCTTAAATCCAACGTGGTTGAGATTGGTTCGC
* ** *
24794 TAAATACAGATATTTCAAGGAGTATTTCTGCAAAAAATCATAATAAACTAAGACGGGTCCCCGAA
130 TGAATACAGATATTTCAAGGAGTATTTCTGCAAAAAATCATGCTAAACTGAGACGGGTCCCCGAA
* * *
24859 ATGCGTTTTTAGCCAAGAACCGTGATGGATAATACACGATTTAGGCTAAAAACTGATCCGAAAAA
195 ACGCGTTTTTAGCCAAGAACCGTGATGGATAATACACGATTTCGGCTAAAAACTGACCCGAAAAA
* * *
24924 TTATTTCTCAGTTTTTCACAAAATATATTCAGAAAAATATTTAATTCAACG-CAAAAAAACTG
260 TTATTTCTCAATTTTTCACAAAATATATTCAGAAAAATATTTAATTCAACGCCAAAAAAATTC
*
24986 ACGGGATTGTCCCGCTTCTAATTTCGTTTTTCC-A-TTTTTTTCGAATTTATTTCTAATTAAATC
1 ACGGGATTTTCCCGCTTCTAATTTCGTTTTTCCAATTTTTTTTCGAATTTATTTCTAATTAAATC
* * * * * *
25049 GAAATAAGTTTCAGAGGCTCGTAAAAATCAAGCTTTAAATCCAACGTGGTTGCGATTGGTTCGCT
66 GAAACAAGATTCAGAGGCTCGTAAAAATAAATCCTTAAATCCAACGTGGTTGAGATTGGTTCGCT
* *
25114 GAATACAGATACTTCAAGGAGTATTTCTGCAAAAAATCATGCTAAACTGAGACGGGTCCCCCAAA
131 GAATACAGATATTTCAAGGAGTATTTCTGCAAAAAATCATGCTAAACTGAGACGGGTCCCCGAAA
*
25179 CGCGTTTTTAGCCAAGAACCGTGATGGATAACACACGATTTCGGCTAAAAACTGACCCGAAAAAT
196 CGCGTTTTTAGCCAAGAACCGTGATGGATAATACACGATTTCGGCTAAAAACTGACCCGAAAAAT
25244 TATTTCTCAA
261 TATTTCTCAA
25254 GCTTCTAGCC
Statistics
Matches: 847, Mismatches: 55, Indels: 17
0.92 0.06 0.02
Matches are distributed among these distances:
318 62 0.07
319 350 0.41
320 114 0.13
321 107 0.13
322 151 0.18
323 63 0.07
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32
Consensus pattern (322 bp):
ACGGGATTTTCCCGCTTCTAATTTCGTTTTTCCAATTTTTTTTCGAATTTATTTCTAATTAAATC
GAAACAAGATTCAGAGGCTCGTAAAAATAAATCCTTAAATCCAACGTGGTTGAGATTGGTTCGCT
GAATACAGATATTTCAAGGAGTATTTCTGCAAAAAATCATGCTAAACTGAGACGGGTCCCCGAAA
CGCGTTTTTAGCCAAGAACCGTGATGGATAATACACGATTTCGGCTAAAAACTGACCCGAAAAAT
TATTTCTCAATTTTTCACAAAATATATTCAGAAAAATATTTAATTCAACGCCAAAAAAATTC
Done.