Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016364.1 Corchorus olitorius cultivar O-4 contig16397, 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: 1889
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Found at i:765 original size:331 final size:320
Alignment explanation
Indices: 9--1810 Score: 1903
Period size: 331 Copynumber: 5.5 Consensus size: 320
1 TGATGGGT
* *
9 TTTTTCACTCTTCTAATACCGTTTTCCCATTCTTTTCCGAATTTTTTTCTAATTAAATCGAAACA
1 TTTTTCACGCTTCTAATATCGTTTTCCCATTCTTTTCCGAA-TTTTTTCTAATTAAATCGAAACA
74 AAATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATATGTCTGAGATTTTGTTTGATGAATA
65 AAATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATATGTCTGAGATTTTGTTTGATGAATA
* * * ** * *
139 CAGATATTTCAAGGAGTCTTTCTGCCAAAAATCTTGTAAAACAT-AATCGGGGCTCCTGAACGCG
130 TAGATATTTCAAGGAGTCTTTCTGCCAAAACTCATACAAAAC-TGAGTCGGGGCTCCGGAACGCG
* ** *
203 TTATTAGCTAAAAACCATGATGGTTAGTACAC-TATTTCGGCTAAAAACTGACCCGAAATGTTTT
194 TTTTTAGCTAAAAACCATGATGAAT-GTACACGAATTT-GGCTAAAAACTGACCCGAAATGTTTT
* * * * * * *
267 TTCTCAATTTTTTGCCATAATACTCAGAAAAAATATATAATTCAACGCTAAAAATCTTGACCGGA
257 TCCTCAATTTTTTGCCACAATACTCTGAAAAAATATATAATTCAACGCCAAAAATATTGA-AGGG
* * * * *
332 TTTTT-ACGCTTC-AGATATCGTTTTTCCATTTTTTTCTGAATTAATTTCTAATTAAATAGAAAC
1 TTTTTCACGCTTCTA-ATATCGTTTTCCCATTCTTTTCCGAATT-TTTTCTAATTAAATCGAAAC
* * ** * * * **
395 AAAATTCAGATTCTCTTAAAAACAAATCCTTGTATCCAATGTGGCTGAGATTTGGTCCGATGAAT
64 AAAATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATATGTCTGAGATTTTGTTTGATGAAT
* * ** ** *
460 ATAGATATTTCAAAGAGTCTTTGTTTCAAAACTCATACAAAGTTGAGCCGGGGCTCCGGAACGCG
129 ATAGATATTTCAAGGAGTCTTTCTGCCAAAACTCATACAAAACTGAGTCGGGGCTCCGGAACGCG
* *
525 TTTTTAGCCAAAAACCATAATGAATGTACACGAATTTGGCTAAAATTTTGCAAAAACTGACCCGA
194 TTTTTAGCTAAAAACCATGATGAATGTACACGAATTTGGC--------T--AAAAACTGACCCG-
* * *
590 AAAT-TTTTTACCTCAATTTCTTGCCACAATACTCTGAAAAAATATATAATTCAACGCGAAAAAG
248 AAATGTTTTT-CCTCAATTTTTTGCCACAATACTCTGAAAAAATATATAATTCAACGCCAAAAAT
654 ATTGAAGGG
312 ATTGAAGGG
* * *
663 TTTTTCACTCTTCTAATAGCGTTTTCCCATTCTTTTCCGAATTTTTTCTAATTAAATCGAACCAA
1 TTTTTCACGCTTCTAATATCGTTTTCCCATTCTTTTCCGAATTTTTTCTAATTAAATCGAAACAA
* *
728 AATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATATGTCTGAGATTTTGTTTGATAAATAC
66 AATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATATGTCTGAGATTTTGTTTGATGAATAT
* * * * *
793 AGATATTTTAAGGAGTCTCTCTGGCAAAAATCATGCAAAACTGAGTCGGGGCTCCGGAACGCGTT
131 AGATATTTCAAGGAGTCTTTCTGCCAAAACTCATACAAAACTGAGTCGGGGCTCCGGAACGCGTT
* * * * *
858 TTTAGCTAAAAACCATGATG-GTGTACACTAATTCGGCTAAAAACTGACCCTAAATGTTTTTTCT
196 TTTAGCTAAAAACCATGATGAATGTACACGAATTTGGCTAAAAACTGACCCGAAATGTTTTTCCT
* * * * *
922 CAATTTTTTGTCATAATACT-TAGAAAAAATATATAATTCAACGCCAAAAATCTTGACATGA
261 CAATTTTTTGCCACAATACTCT-GAAAAAATATATAATTCAACGCCAAAAATATTGA-AGGG
* * * * * *
983 TTTTT-ACGCTTCTGATATCATTTTTCCATTTTTTTCTGAATTAATTTCTAATTAAATCGAAACA
1 TTTTTCACGCTTCTAATATCGTTTTCCCATTCTTTTCCGAATT-TTTTCTAATTAAATCGAAACA
* * * ** * * *
1047 AAATTAAGATGCTCTTAAAAACAAATCCTTATTTCCAATATGGCTGAGATTTGGTTCGATGAATA
65 AAATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATATGTCTGAGATTTTGTTTGATGAATA
* ** * *
1112 TAGATATTTCAAGGAGTCTTTATGCCAAAACTCA-AGCAAAGTTGAGTCTGGGCTCCGGAATGCG
130 TAGATATTTCAAGGAGTCTTTCTGCCAAAACTCATA-CAAAACTGAGTCGGGGCTCCGGAACGCG
* * *
1176 TTTTTAGCCAAAAACC--G-T-AACGTACACGATTTTGGCTAAAATTTTGCAAAAACTGACCCGA
194 TTTTTAGCTAAAAACCATGATGAATGTACACGAATTTGGC--------T--AAAAACTGACCCGA
* * *
1237 AATGTTTTTACCTCAATCTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGA
249 AATGTTTTT-CCTCAATTTTTTGCCACAATACTCTGAAAAAATATATAATTCAACGCCAAAAATA
1302 TTGAAGGG
313 TTGAAGGG
* * * * *
1310 TTTTTTTCACTCTTATAATACCGTTTCCCCATTCTTTTCCGAATTTTTTACTAATTATATCGAAA
1 --TTTTTCACGCTTCTAATATCGTTTTCCCATTCTTTTCCGAATTTTTT-CTAATTAAATCGAAA
* * *
1375 CAAGATTCAGATTCTCGTAAAAACAAATCCTTAAATCCAATATGTCTAAGATTTTGTTTGATGAA
63 CAAAATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATATGTCTGAGATTTTGTTTGATGAA
* * *
1440 TATAGATATTTCAAGGAGTCTTTCTGCAAACAAATCATGCAAAACTGAGTCGGGGCTCCGGAACG
128 TATAGATATTTCAAGGAGTCTTTCTGCCAA-AACTCATACAAAACTGAGTCGGGGCTCCGGAACG
* ** *
1505 CGTTTTTATCTAAAAACCATGATGGTTAGTACACG-ATTTCGGCTAAAAACTGACCCGAAATAAT
192 CGTTTTTAGCTAAAAACCATGATGAAT-GTACACGAATTT-GGCTAAAAACTGACCCGAAAT-GT
** * *
1569 TTTTTTTGAATTTTTTTGCCGA-AATACT-TAGAAAAAAATATATAATTCAACGCCAAGAATATT
254 TTTTCCTCAA-TTTTTTGCC-ACAATACTCT-G-AAAAAATATATAATTCAACGCCAAAAATATT
1632 GAAGGG
315 GAAGGG
* * * * * *
1638 TTTTTTCACGCCTCTAATATCATTTTTCCA-T-TTTCCCGAATTTATTTCAAATTAAATCGGAAC
1 -TTTTTCACGCTTCTAATATCGTTTTCCCATTCTTTTCCGAATTT-TTTCTAATTAAATCGAAAC
* * * * * * * *
1701 AAGATTCAGATGCTCGTAAAAATAAATCCATATATCCAATATGCCTGAGATTTAGTTAGATGAAT
64 AAAATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATATGTCTGAGATTTTGTTTGATGAAT
* * *
1766 ATTAGATATTTCAAGGAGTCTTTCTACCAAAAATCATGCAAAACT
129 A-TAGATATTTCAAGGAGTCTTTCTGCCAAAACTCATACAAAACT
1811 AAGCCAGAAT
Statistics
Matches: 1225, Mismatches: 199, Indels: 108
0.80 0.13 0.07
Matches are distributed among these distances:
317 13 0.01
318 2 0.00
319 84 0.07
320 166 0.14
321 13 0.01
322 176 0.14
323 5 0.00
325 98 0.08
326 50 0.04
327 67 0.05
328 88 0.07
329 9 0.01
330 139 0.11
331 213 0.17
332 86 0.07
333 2 0.00
334 1 0.00
335 3 0.00
336 10 0.01
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (320 bp):
TTTTTCACGCTTCTAATATCGTTTTCCCATTCTTTTCCGAATTTTTTCTAATTAAATCGAAACAA
AATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATATGTCTGAGATTTTGTTTGATGAATAT
AGATATTTCAAGGAGTCTTTCTGCCAAAACTCATACAAAACTGAGTCGGGGCTCCGGAACGCGTT
TTTAGCTAAAAACCATGATGAATGTACACGAATTTGGCTAAAAACTGACCCGAAATGTTTTTCCT
CAATTTTTTGCCACAATACTCTGAAAAAATATATAATTCAACGCCAAAAATATTGAAGGG
Found at i:1477 original size:651 final size:651
Alignment explanation
Indices: 5--1807 Score: 2696
Period size: 651 Copynumber: 2.8 Consensus size: 651
1 TGAT
5 GGGTTTTTTCACTCTTCTAATACCGTTTTCCCATTCTTTTCCGAATTTTTTTCTAATTAAATCGA
1 GGGTTTTTTCACTCTTCTAATACCGTTTTCCCATTCTTTTCCGAA-TTTTTTCTAATTAAATCGA
70 AACAAAATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATATGTCTGAGATTTTGTTTGATG
65 AACAAAATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATATGTCTGAGATTTTGTTTGATG
* * * *
135 AATACAGATATTTCAAGGAGTCTTTCTGCCAAAAATCTTGTAAAACAT-AATCGGGGCTCCTGAA
130 AATACAGATATTTCAAGGAGTCTTTCTG-CAAAAATCATGCAAAAC-TGAGTCGGGGCTCCGGAA
*
199 CGCGTTATTAGCTAAAAACCATGATGGTTAGTACACTATTTCGGCTAAAAACTGACCCGAAATGT
193 CGCGTTTTTAGCTAAAAACCATGATGGTTAGTACACTATTTCGGCTAAAAACTGACCCGAAATGT
* * *
264 TTTTTCTCAATTTTTTGCCATAATACTCAGAAAAAATATATAATTCAACGCTAAAAATCTTGACC
258 TTTTTCTCAATTTTTTGCCATAATACTTAGAAAAAATATATAATTCAACGCCAAAAATCTTGACA
* * *
329 GGATTTTTACGCTTCAGATATCGTTTTTCCATTTTTTTCTGAATTAATTTCTAATTAAATAGAAA
323 GGATTTTTACGCTTCTGATATCATTTTTCCATTTTTTTCTGAATTAATTTCTAATTAAATCGAAA
* * * *
394 CAAAATTCAGATTCTCTTAAAAACAAATCCTTGTATCCAATGTGGCTGAGATTTGGTCCGATGAA
388 CAAAATTCAGATGCTCTTAAAAACAAATCCTTATATCCAATATGGCTGAGATTTGGTTCGATGAA
* * **
459 TATAGATATTTCAAAGAGTCTTTGTTTCAAAACTCATA-CAAAGTTGAGCCGGGGCTCCGGAACG
453 TATAGATATTTCAAGGAGTCTTTATACCAAAACTCA-AGCAAAGTTGAGCCGGGGCTCCGGAACG
*
523 CGTTTTTAGCCAAAAACCATAATGAATGTACACGAATTTGGCTAAAATTTTGCAAAAACTGACCC
517 CGTTTTTAGCCAAAAACC--AATGAACGTACACGAATTTGGCTAAAATTTTGCAAAAACTGACCC
* *
588 GAAAATTTTTTACCTCAATTTCTTGCCACAATACTCTGAAAAAATATATAATTCAACGCGAAAAA
580 GAAAATTTTTTACCTCAATTTCTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAA
653 GATTGAA
645 GATTGAA
*
660 GGG-TTTTTCACTCTTCTAATAGCGTTTTCCCATTCTTTTCCGAATTTTTTCTAATTAAATCGAA
1 GGGTTTTTTCACTCTTCTAATACCGTTTTCCCATTCTTTTCCGAATTTTTTCTAATTAAATCGAA
* *
724 CCAAAATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATATGTCTGAGATTTTGTTTGATAA
66 ACAAAATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATATGTCTGAGATTTTGTTTGATGA
* *
789 ATACAGATATTTTAAGGAGTCTCTCTGGCAAAAATCATGCAAAACTGAGTCGGGGCTCCGGAACG
131 ATACAGATATTTCAAGGAGTCTTTCT-GCAAAAATCATGCAAAACTGAGTCGGGGCTCCGGAACG
* *
854 CGTTTTTAGCTAAAAACCATGATGG-T-GTACACTAATTCGGCTAAAAACTGACCCTAAATGTTT
195 CGTTTTTAGCTAAAAACCATGATGGTTAGTACACTATTTCGGCTAAAAACTGACCCGAAATGTTT
* *
917 TTTCTCAATTTTTTGTCATAATACTTAGAAAAAATATATAATTCAACGCCAAAAATCTTGACATG
260 TTTCTCAATTTTTTGCCATAATACTTAGAAAAAATATATAATTCAACGCCAAAAATCTTGACAGG
982 ATTTTTACGCTTCTGATATCATTTTTCCATTTTTTTCTGAATTAATTTCTAATTAAATCGAAACA
325 ATTTTTACGCTTCTGATATCATTTTTCCATTTTTTTCTGAATTAATTTCTAATTAAATCGAAACA
* *
1047 AAATTAAGATGCTCTTAAAAACAAATCCTTATTTCCAATATGGCTGAGATTTGGTTCGATGAATA
390 AAATTCAGATGCTCTTAAAAACAAATCCTTATATCCAATATGGCTGAGATTTGGTTCGATGAATA
* * * *
1112 TAGATATTTCAAGGAGTCTTTATGCCAAAACTCAAGCAAAGTTGAGTCTGGGCTCCGGAATGCGT
455 TAGATATTTCAAGGAGTCTTTATACCAAAACTCAAGCAAAGTTGAGCCGGGGCTCCGGAACGCGT
* *
1177 TTTTAGCCAAAAACC-GT-AACGTACACGATTTTGGCTAAAATTTTGCAAAAACTGACCCG-AAA
520 TTTTAGCCAAAAACCAATGAACGTACACGAATTTGGCTAAAATTTTGCAAAAACTGACCCGAAAA
1239 TGTTTTTACCTCAATCTT-TTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGAT
585 T-TTTTTACCTCAAT-TTCTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGAT
1303 TGAA
648 TGAA
* * *
1307 GGGTTTTTTTCACTCTTATAATACCGTTTCCCCATTCTTTTCCGAATTTTTTACTAATTATATCG
1 GGG-TTTTTTCACTCTTCTAATACCGTTTTCCCATTCTTTTCCGAATTTTTT-CTAATTAAATCG
* * *
1372 AAACAAGATTCAGATTCTCGTAAAAACAAATCCTTAAATCCAATATGTCTAAGATTTTGTTTGAT
64 AAACAAAATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATATGTCTGAGATTTTGTTTGAT
*
1437 GAATATAGATATTTCAAGGAGTCTTTCTGCAAACAAATCATGCAAAACTGAGTCGGGGCTCCGGA
129 GAATACAGATATTTCAAGGAGTCTTTCTGC-AA-AAATCATGCAAAACTGAGTCGGGGCTCCGGA
* *
1502 ACGCGTTTTTATCTAAAAACCATGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAATA
192 ACGCGTTTTTAGCTAAAAACCATGATGGTTAGTACACTATTTCGGCTAAAAACTGACCCGAAAT-
* * * * *
1567 ATTTTTTTTGAATTTTTTTGCCGA-AATACTTAGAAAAAAATATATAATTCAACGCCAAGAATAT
256 GTTTTTTCTCAA-TTTTTTGCC-ATAATACTTAG-AAAAAATATATAATTCAACGCCAAAAATCT
* * * * * * *
1631 TGA-AGGGTTTTTTCACGCCTCTAATATCATTTTTCCA--TTTTCCCGAATTTATTTCAAATTAA
318 TGACA-GGATTTTT-ACGCTTCTGATATCATTTTTCCATTTTTTTCTGAATTAATTTCTAATTAA
* * * * * * *
1693 ATCGGAACAAGATTCAGATGCTCGTAAAAATAAATCCATATATCCAATATGCCTGAGATTTAGTT
381 ATCGAAACAAAATTCAGATGCTCTTAAAAACAAATCCTTATATCCAATATGGCTGAGATTTGGTT
* * * *
1758 AGATGAATATTAGATATTTCAAGGAGTCTTTCTACCAAAAATCATGCAAA
446 CGATGAATA-TAGATATTTCAAGGAGTCTTTATACCAAAACTCAAGCAAA
1808 ACTAAGCCAG
Statistics
Matches: 1047, Mismatches: 82, Indels: 37
0.90 0.07 0.03
Matches are distributed among these distances:
646 4 0.00
647 104 0.10
648 3 0.00
649 46 0.04
650 99 0.09
651 345 0.33
652 3 0.00
653 192 0.18
654 50 0.05
655 106 0.10
656 74 0.07
657 21 0.02
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (651 bp):
GGGTTTTTTCACTCTTCTAATACCGTTTTCCCATTCTTTTCCGAATTTTTTCTAATTAAATCGAA
ACAAAATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATATGTCTGAGATTTTGTTTGATGA
ATACAGATATTTCAAGGAGTCTTTCTGCAAAAATCATGCAAAACTGAGTCGGGGCTCCGGAACGC
GTTTTTAGCTAAAAACCATGATGGTTAGTACACTATTTCGGCTAAAAACTGACCCGAAATGTTTT
TTCTCAATTTTTTGCCATAATACTTAGAAAAAATATATAATTCAACGCCAAAAATCTTGACAGGA
TTTTTACGCTTCTGATATCATTTTTCCATTTTTTTCTGAATTAATTTCTAATTAAATCGAAACAA
AATTCAGATGCTCTTAAAAACAAATCCTTATATCCAATATGGCTGAGATTTGGTTCGATGAATAT
AGATATTTCAAGGAGTCTTTATACCAAAACTCAAGCAAAGTTGAGCCGGGGCTCCGGAACGCGTT
TTTAGCCAAAAACCAATGAACGTACACGAATTTGGCTAAAATTTTGCAAAAACTGACCCGAAAAT
TTTTTACCTCAATTTCTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGA
A
Done.