Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009555.1 Corchorus olitorius cultivar O-4 contig09587, 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: 1811
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:1089 original size:322 final size:322
Alignment explanation
Indices: 563--1184 Score: 846
Period size: 322 Copynumber: 1.9 Consensus size: 322
553 TGCCACACTA
** *
563 CTCAGAAAAATATATAATTCAACGCCAAAAAGATTAAATGTTTTTTCACGCTTCTAATATCATTT
1 CTCAGAAAAATATATAATTCAACGCCAAAAAGATTAAATGGATTTTCACGCTTCTAATATCAGTT
* * *
628 TTCCAACTTTTTTTTCCGAATTAATTTCTAATTAAATTGAAACAAGATTCAATTCTAATAAAAAC
66 TTCC-ACATTTTTTTCAGAATTAATTTCTAATTAAATTGAAACAAGATTCAATACTAATAAAAAC
* *
693 ATATCCTTAAATCCAATGTGGCTGAGATTTGGTTACGTGAATATAGATATCTCAAGAAGCCTTTG
130 AAATCCTTAAATCCAATGTGGCTGAGATTTGGTTACGTGAATATAGAAATCTCAAGAAGCCTTTG
*
758 CGCCCAAAATCAT-CTAAAATTGAGCCGGGATCCGGAACGCGTTGT-TAGCCAAAAACCATGATG
195 CACCCAAAATCATGC-AAAATTGAGCCGGGATCCGGAACGCGTT-TCTAGCCAAAAACCATGATG
* * *
821 GTTAGTAAACGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTTCTCAATATTTTGCAAAAATT
258 GTTAGTAAACGATTTCGGCTAAAAACCGACCCAAAAAGTTTTTTTCTCAATATTTTGCAAAAATT
* *
886 CTCAGAAAAAATATATAATTCAACGCCAAAAGGATT-GATGGGATTTTCACGCTTCTAAATATC-
1 CTCAG-AAAAATATATAATTCAACGCCAAAAAGATTAAAT-GGATTTTCACGCTTCT-AATATCA
* **
949 GTTTTCC-CATTTTTTT-AGAATTAATTTCTAGCTT-AATTGAAACAAGATTCAGATACTCGTAA
63 GTTTTCCACATTTTTTTCAGAATTAATTTCTA-ATTAAATTGAAACAAGATTCA-ATACTAATAA
* * * * * *
1011 AAACAAATCCTTATATCGAATGTGGCTGAGATTTGGTTA-GATGAATATAGAAATTTTAAGGAGT
126 AAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTACG-TGAATATAGAAATCTCAAGAAGC
* * * *
1075 CTTTGCATCCAAAATCATGCAAAATTGAGGCGGGCTCCGGAACGCGTTTCTAGCCAAAAACCGTG
190 CTTTGCACCCAAAATCATGCAAAATTGAGCCGGGATCCGGAACGCGTTTCTAGCCAAAAACCATG
* *
1140 ATGGTTAGTACACGATTTTGGCTAAAAACCGACCCAAAAAGTTTT
255 ATGGTTAGTAAACGATTTCGGCTAAAAACCGACCCAAAAAGTTTT
1185 CATTCAATTT
Statistics
Matches: 262, Mismatches: 29, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
321 32 0.12
322 167 0.64
323 8 0.03
324 49 0.19
325 6 0.02
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (322 bp):
CTCAGAAAAATATATAATTCAACGCCAAAAAGATTAAATGGATTTTCACGCTTCTAATATCAGTT
TTCCACATTTTTTTCAGAATTAATTTCTAATTAAATTGAAACAAGATTCAATACTAATAAAAACA
AATCCTTAAATCCAATGTGGCTGAGATTTGGTTACGTGAATATAGAAATCTCAAGAAGCCTTTGC
ACCCAAAATCATGCAAAATTGAGCCGGGATCCGGAACGCGTTTCTAGCCAAAAACCATGATGGTT
AGTAAACGATTTCGGCTAAAAACCGACCCAAAAAGTTTTTTTCTCAATATTTTGCAAAAATT
Found at i:1562 original size:811 final size:810
Alignment explanation
Indices: 1--1668 Score: 2950
Period size: 811 Copynumber: 2.1 Consensus size: 810
* * *
1 AACCATGGTGGTTAGTAAACGATTTCGGCTAAAAACTGACCCGAAACTTTTTTTTCTCAATTTTT
1 AACCATGATGGTTAGTAAACGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTTCTCAATATTT
*
66 TGCAAAAATTCTCAGAAAAAATATATAATTCAACGCCAAAAGGATTGGCGGGATTGTCACGCTTC
66 TGCAAAAATTCTCAGAAAAAATATATAATTCAACGCCAAAAGGATTGACGGGATTGTCACGCTTC
*
131 TAAATATCGTTTTCCCATTTTTCTGAATTAATTTCTAGTTTAATTGAAACAAGATTCAGATACTC
131 TAAATATCGTTTTCCCATTTTTCTGAATTAATTTCTAGCTTAATTGAAACAAGATTCAGATACTC
196 GTAAAAACAAATCCTTATATCGAATGTGGCTGAGATTTGGTTAGATGAATATAGAAATTTTAAGG
196 GTAAAAACAAATCCTTATATCGAATGTGGCTGAGATTTGGTTAGATGAATATAGAAATTTTAAGG
261 AGTCTTTGCACCCAAAATCATGCAAAATTGAGGCGGGCTCCGGAACGCGTTTCTAGCCAAAAACC
261 AGTCTTTGCACCCAAAATCATGCAAAATTGAGGCGGGCTCCGGAACGCGTTTCTAGCCAAAAACC
*
326 GTGATGGTTAGTGCACGATTTTGGCTAAAAACCGACCCAAAAAGTTTTCATTCAATTTCTACCAT
326 GTGATGGTTAGTACACGATTTTGGCTAAAAACCGACCCAAAAAGTTTTCATTCAATTTCTACCAT
391 AGCGTAGTCGGTTCAATCAGTCTCCGCAAAGGTATTATAATAGTAAAACCGATTTACGGTTTGAA
391 AGCGTAGTCGGTTCAATCAGTCTCCGCAAAGGTATTATAATAGTAAAACCGATTTACGGTTTGAA
*
456 AGCTATGGCATTTTTAGCCAAAAAACGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCTAA
456 AGCTATGGCATTTTTAGCCAAAAAACGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCTAA
521 AATTGACCCGAAAAATTTTCCTCAATTTTTTTTGCCACACTACTCAGAAAAATATATAATTCAAC
521 AATTGACCCGAAAAATTTTCCTCAATTTTTTTTGCCACACTACTCAGAAAAATATATAATTCAAC
* * *
586 GCCAAAAAGATTAAATGTTTTTTCACGCTTCTAATATCATTTTTCCAACTTTTTTTTCCGAATTA
586 GCCAAAAAGATAAAATATTTTTTCACGCTTCTAATATCATTTTTCCAACTTTCTTTTCCGAATTA
* *
651 ATTTCTAATTAAATTGAAACAAGATTCAATTCTAATAAAAACATATCCTTAAATCCAATGTGGCT
651 ATTTCTAATTAAATCGAAACAAGATTCAATTCTAATAAAAACAAATCCTTAAATCCAATGTGGCT
716 GAGATTTGGTTACGTGAATATAGATATCTCAAGAAGCCTTTGCGCCCAAAATCATCTAAAATTGA
716 GAGATTTGGTTACGTGAATATAGATATCTCAAGAAGCCTTTGCGCCCAAAATCATCTAAAATTGA
*
781 GCCGGGATCCGGAACGCGTTGTTAGCCAAA
781 GCCGGGATCCAGAACGCGTTGTTAGCCAAA
811 AACCATGATGGTTAGTAAACGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTTCTCAATATTT
1 AACCATGATGGTTAGTAAACGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTTCTCAATATTT
* *
876 TGCAAAAATTCTCAGAAAAAATATATAATTCAACGCCAAAAGGATTGATGGGATTTTCACGCTTC
66 TGCAAAAATTCTCAGAAAAAATATATAATTCAACGCCAAAAGGATTGACGGGATTGTCACGCTTC
*
941 TAAATATCGTTTTCCCATTTTTTTAGAATTAATTTCTAGCTTAATTGAAACAAGATTCAGATACT
131 TAAATATCGTTTTCCCATTTTTCT-GAATTAATTTCTAGCTTAATTGAAACAAGATTCAGATACT
1006 CGTAAAAACAAATCCTTATATCGAATGTGGCTGAGATTTGGTTAGATGAATATAGAAATTTTAAG
195 CGTAAAAACAAATCCTTATATCGAATGTGGCTGAGATTTGGTTAGATGAATATAGAAATTTTAAG
*
1071 GAGTCTTTGCATCCAAAATCATGCAAAATTGAGGCGGGCTCCGGAACGCGTTTCTAGCCAAAAAC
260 GAGTCTTTGCACCCAAAATCATGCAAAATTGAGGCGGGCTCCGGAACGCGTTTCTAGCCAAAAAC
1136 CGTGATGGTTAGTACACGATTTTGGCTAAAAACCGACCCAAAAAGTTTTCATTCAATTTCTACCA
325 CGTGATGGTTAGTACACGATTTTGGCTAAAAACCGACCCAAAAAGTTTTCATTCAATTTCTACCA
* * *
1201 TAGCGTAGTCGGTTCAATCAGTCTCCGCAAAGGTGTTATAATAGTAAAACTGATTTATGGTTTGA
390 TAGCGTAGTCGGTTCAATCAGTCTCCGCAAAGGTATTATAATAGTAAAACCGATTTACGGTTTGA
*
1266 AAGCTATGGCATTTTTAGCCAAAAAAACGTGATGGTTAATACACGATTTCGGCTAAAATTTTGTT
455 AAGCTATGGCATTTTTAGCC-AAAAAACGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCT
* *
1331 AAATTTGACCCGAAAAATTTTCCTCAA-TTTTTTTGCCACACTACTCAGAAAAAATATATAATTT
519 AAAATTGACCCGAAAAATTTTCCTCAATTTTTTTTGCCACACTACTCAG-AAAAATATATAATTC
*
1395 AATGCCAAAAAGATAAAATATTTTTTCACGCTTCTAATATCATTTTTCCAAC-TTCTTTT-CGAA
583 AACGCCAAAAAGATAAAATATTTTTTCACGCTTCTAATATCATTTTTCCAACTTTCTTTTCCGAA
* *
1458 TTAATTTCTAATTAAATCGAAACAAGATTCAGATTCTAGTAAAAACAAATCCTTAAATTCAATGT
648 TTAATTTCTAATTAAATCGAAACAAGATTCA-ATTCTAATAAAAACAAATCCTTAAATCCAATGT
* *
1523 GGCTGAGATTTGTTTAC-TAGAATATAGATATTTCAAGAAGCCTTTGCGCCCAAAATCATCTAAA
712 GGCTGAGATTTGGTTACGT-GAATATAGATATCTCAAGAAGCCTTTGCGCCCAAAATCATCTAAA
*
1587 ATTGAGCCGGGCTCCAGAACGCGTTGTTAGCCAAA
776 ATTGAGCCGGGATCCAGAACGCGTTGTTAGCCAAA
* * * *
1622 AACCATGATAG-AAGTACACGATTTTGGCTAAAAACTGACCCGTAAAA
1 AACCATGATGGTTAGTAAACGATTTCGGCTAAAAACTGACCCG-AAAA
1669 ACAAATTCTT
Statistics
Matches: 819, Mismatches: 33, Indels: 11
0.95 0.04 0.01
Matches are distributed among these distances:
810 210 0.26
811 478 0.58
812 131 0.16
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (810 bp):
AACCATGATGGTTAGTAAACGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTTCTCAATATTT
TGCAAAAATTCTCAGAAAAAATATATAATTCAACGCCAAAAGGATTGACGGGATTGTCACGCTTC
TAAATATCGTTTTCCCATTTTTCTGAATTAATTTCTAGCTTAATTGAAACAAGATTCAGATACTC
GTAAAAACAAATCCTTATATCGAATGTGGCTGAGATTTGGTTAGATGAATATAGAAATTTTAAGG
AGTCTTTGCACCCAAAATCATGCAAAATTGAGGCGGGCTCCGGAACGCGTTTCTAGCCAAAAACC
GTGATGGTTAGTACACGATTTTGGCTAAAAACCGACCCAAAAAGTTTTCATTCAATTTCTACCAT
AGCGTAGTCGGTTCAATCAGTCTCCGCAAAGGTATTATAATAGTAAAACCGATTTACGGTTTGAA
AGCTATGGCATTTTTAGCCAAAAAACGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCTAA
AATTGACCCGAAAAATTTTCCTCAATTTTTTTTGCCACACTACTCAGAAAAATATATAATTCAAC
GCCAAAAAGATAAAATATTTTTTCACGCTTCTAATATCATTTTTCCAACTTTCTTTTCCGAATTA
ATTTCTAATTAAATCGAAACAAGATTCAATTCTAATAAAAACAAATCCTTAAATCCAATGTGGCT
GAGATTTGGTTACGTGAATATAGATATCTCAAGAAGCCTTTGCGCCCAAAATCATCTAAAATTGA
GCCGGGATCCAGAACGCGTTGTTAGCCAAA
Found at i:1776 original size:167 final size:168
Alignment explanation
Indices: 1496--1811 Score: 440
Period size: 167 Copynumber: 1.9 Consensus size: 168
1486 TCAGATTCTA
* * *
1496 GTAAAAACAAATCCTTAAATTCAATGTGGCTGAGATTTGTTTACTAGAATATAGATATTTCAAGA
1 GTAAAAACAAATCCTTAAATTCAATGTGGCTGAGATTTGGTTAATAGAATATAGAAATTTCAAGA
*
1561 AGCCTTTGCGCCCAAAATCATCTAAAATTGAGCCGGGCTCCAGAACGCGTTGTTAGCCAAAAACC
66 AGCCTTTGAGCCCAAAATCATCTAAAATTGAGCCGGGCTCCAGAACGCGTTGTTAGCCAAAAACC
1626 ATGATAG-AAGTACACGATTTTGGCTAAAAACTGACCC
131 ATGATAGTAAGTACACGATTTTGGCTAAAAACTGACCC
* * * *
1663 GTAAAAACAAATTCTTATA-TCGAATGTGGCTGAGATTTGGTTAGAT-GAATATAGAAATTTTAT
1 GTAAAAACAAATCCTTAAATTC-AATGTGGCTGAGATTTGGTTA-ATAGAATATAGAAATTTCAA
* * * * * * *
1726 GGAGTCTTTGAGCCTAAAATCATGTGAAATTGAGCCGGGCTCCGGAACGCGTTTTTAGCCAAAAA
64 GAAGCCTTTGAGCCCAAAATCATCTAAAATTGAGCCGGGCTCCAGAACGCGTTGTTAGCCAAAAA
* *
1791 CCATGATGGTTAGTACACGAT
129 CCATGATAGTAAGTACACGAT
Statistics
Matches: 129, Mismatches: 17, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
166 2 0.02
167 116 0.90
168 11 0.09
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.28
Consensus pattern (168 bp):
GTAAAAACAAATCCTTAAATTCAATGTGGCTGAGATTTGGTTAATAGAATATAGAAATTTCAAGA
AGCCTTTGAGCCCAAAATCATCTAAAATTGAGCCGGGCTCCAGAACGCGTTGTTAGCCAAAAACC
ATGATAGTAAGTACACGATTTTGGCTAAAAACTGACCC
Done.