Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019652.1 Corchorus olitorius cultivar O-4 contig19685, 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: 13739
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Found at i:2404 original size:998 final size:992
Alignment explanation
Indices: 1--3509 Score: 5658
Period size: 998 Copynumber: 3.5 Consensus size: 992
1 AAGCCAAAAAACCGTGAT-ATTAAATACACGATTTCGGCTAAAATTTTACAAAAATTGACCCGAA
1 AAGCC-AAAAACCGTGATGA-TAAATACACGATTTCGGCTAAAATTTTACAAAAATTGACCCGAA
*
65 AGATATTTTCTCAATTTTTAGCCATAATACTTATAAAAATTATATAATTAATCACCAAAAATATT
64 AGATATTTTCTCAATTTTTAGCCATAATACTCATAAAAATTATATAATTAATCACCAAAAATATT
130 GAAAAGCTTTTTGACGCTTTTAATATCGTTTTTTCATATTTTTTTGAATTAATTTCTAATTAAAT
129 GAAAAGCTTTTTGACGCTTTTAATATCGTTTTTTCATATTTTTTTGAATTAATTTCTAATTAAAT
* * *
195 CGAAATAAGATTCAGATACTCGTAAAAACAAATTCTTAAATACAATTTGGCTAAGATTTTATTAG
194 CGAAACAAGATTCAGATACTCGTAAAAACAAATTCTTAAATGCAATGTGGCTAAGATTTTATTAG
* *
260 ATGAATATAGATATTTTAAGGAGTGCCAGTGCCAAAAATCATGCAAAACTGAGCTGGTGCTCCGA
259 ATGAATATAGATATTTTAAGGAGTGTCAGCGCCAAAAATCATGCAAAACTGAGCTGGTGC-CCGA
325 AACGTGTTTTTAGCCAAAAACCGTG-ATGGTACACGATTTTGGTTAGAATTTTACAAAAAATGAC
323 AACGTGTTTTTAGCCAAAAACCGTGTAT-GTACACGATTTTGGTTAGAATTTTACAAAAAATGAC
* * ** *
389 CCGGAATTTTTTTCCTTAATTCATGGATAAAATACTCATAAAATATATATAATTGAACGGCAAAA
387 CCGAAAATTTTTTCCTTAATTTTTGGATAAAATACTCATAAAATATATATAATTTAACGGCAAAA
*
454 AGATTGGAGGACTTTTCACGTTTTTAATATCGTTTTTCATATTTTTCTAAATTAATTTCTAATTA
452 AGATTGGAGGACTTTTCACGTTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTA
*
519 AATTTAAACAAGATTCAGATGCTTGTAAAAACAAATTCTTAAATCCAATGTGGTTGAGATTTGAT
517 AATTTAAACAAGATTCAGATGCTTGTAAAAACAAATTC-TAAATCCAATGTGGCTGAGA-TTGAT
* * * * * *
584 TAGTTG-TATAGAGATATCTCAAGGAGTCTTGGCACCAAAAATTAGGAAAAACTGAGCCGGGGAC
580 TAGATGAT-TATAGATATCTCAAGGAGTCTTGGCGCCAAAAATCATGAAAAACTGAGCCGGGGCC
648 CTAGAACGCTTTTTTATCCAAAAAGTGTGATGGTTATTACACGAGCCGAAAGATGTTTCCTCAAT
644 CTAGAACGCTTTTTTATCCAAAAAGTGTGATGGTTATTACACGAGCCGAAAGATGTTTCCTCAAT
* *
713 TTTTGAATAAAATACGCAAAGAAATGACTCGGAATA-ATTTTCCTCAATTTTTAGCAACAATACT
709 TTTTGGATAAAATACGCAAAAAAATGACTCGGAATATATTTTCCTCAATTTTTAGCAACAATACT
* * *
777 CATAAAAAATATATTATTTAACGCCAAAAAGATTGAATGGCTTTTCACGCTTCTAATACCGTTTT
774 CATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATACCGTTTT
* *
842 TCATATTTTTTCCGAATTAATTTCTAATTAAAACAAAACATGATTTAGATGCTTTTCAAAACAAT
839 TCATATTTTTTCCGAATTAATTTCTAATTAAAACGAAACATGATTTAGATGCTTGT-AAAACAAT
*
907 GGCTGGGATATGGTTAGATGAATATAGATATTTCAAGCAGTCTCGACGCCAAAAATCATTCAAAA
903 GGCTGGGATATGGTTAGATGAATATAGATATTTCAAGCAGTCTCGGCGCCAAAAATCATTCAAAA
* *
972 TGAACCGGGGCCAGAAACGTGTTTT
968 TGAACCGGGGCCAGGAACGCGTTTT
* * * * * *
997 TAGCCAAAAACCTTGATGATAATTACATGATTTTGGCTAAAATTTTGCAAAAATTGACCCGAAAG
1 AAGCCAAAAACCGTGATGATAAATACACGATTTCGGCTAAAATTTTACAAAAATTGACCCGAAAG
* *
1062 ATATTTTCTCATTTTTTAGCCATAATACTCATAAAAATTATATAAATAATCACCAAAAATATTGA
66 ATATTTTCTCAATTTTTAGCCATAATACTCATAAAAATTATATAATTAATCACCAAAAATATTGA
* * *
1127 AAAGCTTTTTGGCGCTATTAATATCGTTTTTTCATATTTTTTTTGAATTAATTTCTGATTAAATC
131 AAAGCTTTTTGACGCTTTTAATATCGTTTTTTCATA-TTTTTTTGAATTAATTTCTAATTAAATC
*
1192 AAAACAAGATTCAGATACTCGTAAAAACAAATTCTTAAATGCAATGTGGCTAAGATTTTATTAGA
195 GAAACAAGATTCAGATACTCGTAAAAACAAATTCTTAAATGCAATGTGGCTAAGATTTTATTAGA
* *
1257 TGAATATAGATATTTGAAGGAGTGTCAGCGCCAAAAATCATGCAATACTGAGCTGGTGTCCCGAA
260 TGAATATAGATATTTTAAGGAGTGTCAGCGCCAAAAATCATGCAAAACTGAGCTGGTG-CCCGAA
*
1322 ACGTGTTTTTAGCTAAAAACCGTGATACTTAGTACACGATTTTGGTTAGAATTTTACAAAAAATG
324 ACGTGTTTTTAGCCAAAAACCGTG-TA--T-GTACACGATTTTGGTTAGAATTTTACAAAAAATG
* * * *
1387 ACCTG-AAA---TTTCTTTAATTTTTGGATAAAATACTCGTAAAATATATATATAATTTAACGGA
385 ACCCGAAAATTTTTTCCTTAATTTTTGGATAAAATACTCAT-AAA-ATATATATAATTTAACGGC
*
1448 AAAAAGATTGGAGGACTTTTCACATTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTA
448 AAAAAGATTGGAGGACTTTTCACGTTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTA
*
1513 ATTAAATTTAAACAAGATTCAGATGCTTGTAAAAACAAATTCTAAAATCCAATGTGGCTAAGATT
513 ATTAAATTTAAACAAGATTCAGATGCTTGTAAAAACAAATTCT-AAATCCAATGTGGCTGAGATT
* * *
1578 CGGTTAGATGATTATAGATATCTTAAGGAGTCTTGGCGCCAAAAATCATTAAAAACTGAGCCGGG
577 -GATTAGATGATTATAGATATCTCAAGGAGTCTTGGCGCCAAAAATCATGAAAAACTGAGCCGGG
* * * *
1643 GCCCTAAAACGTTTTTTTATCCAAAAAGTGTGATGGTTATTACACGAACCGAAAGATGTTTCCTT
641 GCCCTAGAACGCTTTTTTATCCAAAAAGTGTGATGGTTATTACACGAGCCGAAAGATGTTTCCTC
* * *
1708 AATTTTTGGATAAAATACGCAAAAAAATGACCCGGAATATTTTTTCC-CAATTTTTAGCAACAAC
706 AATTTTTGGATAAAATACGCAAAAAAATGACTCGGAATATATTTTCCTCAATTTTTAGCAACAAT
*
1772 ACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGTTTCTAATACCGT
771 ACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATACCGT
* *
1837 TTTTCCATATTTTTTCTGAATTAATTTCTAATTAAAACGAAACATGATTCAGATGCTTGTAAAAC
836 TTTT-CATATTTTTTCCGAATTAATTTCTAATTAAAACGAAACATGATTTAGATGCTTGTAAAA-
* *
1902 CAATGGCTAGGATATGGTTAGATGAATATAGATATTTCAAGCAGTCTCGGCGCCAAAATTCATTC
899 CAATGGCTGGGATATGGTTAGATGAATATAGATATTTCAAGCAGTCTCGGCGCCAAAAATCATTC
* *
1967 AAAATGAACCAGGCCCAGGAACGCGTTTT
964 AAAATGAACCGGGGCCAGGAACGCGTTTT
*
1996 AAGCCAAAAACCGTGAT-ATTAAATACACGATTTCAGCTAAAATTTTACAAAAATTGACCCGAAA
1 AAGCCAAAAACCGTGATGA-TAAATACACGATTTCGGCTAAAATTTTACAAAAATTGACCCGAAA
*
2060 GATATTTTCTCAATTTTTAGCCATAATACTTATAAAAGATTATATAATTAATCACCAAAAATATT
65 GATATTTTCTCAATTTTTAGCCATAATACTCATAAAA-ATTATATAATTAATCACCAAAAATATT
*
2125 GAAAAGCTTTTTGACGCTTTTAATATCGTTCTTTCATATTTTTTTTGAATTAATTTCTAATTAAA
129 GAAAAGCTTTTTGACGCTTTTAATATCGTTTTTTCATA-TTTTTTTGAATTAATTTCTAATTAAA
*
2190 TCGAAACAAGATTCAGATACTCGTAAAAACAAATTCTTAAATGCAATGTGGCTAAGATTTTAGTA
193 TCGAAACAAGATTCAGATACTCGTAAAAACAAATTCTTAAATGCAATGTGGCTAAGATTTTATTA
2255 GATGAATATAGATATTTTAAGGAGTGTCAGCGCCAAAAATCATGCAAAACTGAGCTGGTGCCCGG
258 GATGAATATAGATATTTTAAGGAGTGTCAGCGCCAAAAATCATGCAAAACTGAGCTGGTGCCC-G
* * *
2320 AAACATGTTTTTAGCCAAAAACTGTG-AT-TACACGATTTTGATTAGAATTTTACAAAAAATGAC
322 AAACGTGTTTTTAGCCAAAAACCGTGTATGTACACGATTTTGGTTAGAATTTTACAAAAAATGAC
*
2383 CCGAAAATTTTTTCCTTAATTTTTGGATAAAATACTCATAAAATATATATAGTTTAACGGCAAAA
387 CCGAAAATTTTTTCCTTAATTTTTGGATAAAATACTCATAAAATATATATAATTTAACGGCAAAA
* * *
2448 AGATTGGAGGACTTTTCACGGTTTTAGTATCGTTTTTTATATTTTTCTGAATTAATTTCTAATTA
452 AGATTGGAGGACTTTTCACGTTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTA
2513 AATTTAAACAAGATTCAGATGCTTGTAAAAACAAA---T---T-CAATGTGGCTGAGATATGATT
517 AATTTAAACAAGATTCAGATGCTTGTAAAAACAAATTCTAAATCCAATGTGGCTGAGAT-TGATT
* *
2571 AGATGAATATAGATATCTCAAGGAGTCTTGGCGCAAAAAATCATGAAAAACTGAGCCGGGGCCCT
581 AGATGATTATAGATATCTCAAGGAGTCTTGGCGCCAAAAATCATGAAAAACTGAGCCGGGGCCCT
*
2636 AGAACGCTTTTTTATCCAAAAAGTGCGATGGTTATTACACGAGCCGAAAGATGTTTCCTCAATTT
646 AGAACGCTTTTTTATCCAAAAAGTGTGATGGTTATTACACGAGCCGAAAGATGTTTCCTCAATTT
*
2701 TTGGAGAAAATACGCAAAAAAAATGACTCGG-AT-TATTTTCCTCAATTTTTAGCAACAATACTC
711 TTGGATAAAATACGC-AAAAAAATGACTCGGAATATATTTTCCTCAATTTTTAGCAACAATACTC
*
2764 ATAAAAAATATATAATTCAACGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATACCGTTTTT
775 ATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATACCGTTTTT
2829 CATATTTTTTCCGAATTAATTTCTAATTAAAACGAAACATGATTTAGATGCTTGTTAAAACAATG
840 CATATTTTTTCCGAATTAATTTCTAATTAAAACGAAACATGATTTAGATGCTTG-TAAAACAATG
*
2894 GCTGGGATATGGTTAGATGAATATAGATATTTCAAGCAGTCTCGGCGCAGAAAAATCATTCAAAA
904 GCTGGGATATGGTTAGATGAATATAGATATTTCAAGCAGTCTCGGCGC-CAAAAATCATTCAAAA
2959 TGAACCGGGGCCAGGAACGCGTTTT
968 TGAACCGGGGCCAGGAACGCGTTTT
* * * * *
2984 TAGCCAAAAATCGTTATGATAATTACACGATTTCGGCTAAAATTTTACAAAAATTGACCCAAAAG
1 AAGCCAAAAACCGTGATGATAAATACACGATTTCGGCTAAAATTTTACAAAAATTGACCCGAAAG
*
3049 ATATTTTCTCAA-TTTTAGCCATAATAATCATAAAAATTATATAATTAATCACCAAAAATATTGA
66 ATATTTTCTCAATTTTTAGCCATAATACTCATAAAAATTATATAATTAATCACCAAAAATATTGA
* * *
3113 AAAGCTTTTTGACGCTGTTAATATTGTTTTTTCATATTTTTTTGAATTAATATCTAATTAAATCG
131 AAAGCTTTTTGACGCTTTTAATATCGTTTTTTCATATTTTTTTGAATTAATTTCTAATTAAATCG
*
3178 AAACAAGATTCAGATACTCGTAAAAACAAATTGTTAAATGCAATGTGGCTAAGATTTTATTAGAT
196 AAACAAGATTCAGATACTCGTAAAAACAAATTCTTAAATGCAATGTGGCTAAGATTTTATTAGAT
3243 GAATATAGATATTTTAAGGAGTGTCAGCGCCAAAAATCATGCAAAACTGAGCTGGTGCCCCGAAA
261 GAATATAGATATTTTAAGGAGTGTCAGCGCCAAAAATCATGCAAAACTGAGCTGGTG-CCCGAAA
* *
3308 CGTGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTTGGTTAGAATTTTGCAAAAAATGA
325 CGTGTTTTTAGCCAAAAACCGTG-T--AT-GTACACGATTTTGGTTAGAATTTTACAAAAAATGA
* * * *
3373 CCCAAAAATTTTTTCTTTAATTTTTGGATAAAATACTCATAAAATTTATATAATTTAACGTCAAA
386 CCCGAAAATTTTTTCCTTAATTTTTGGATAAAATACTCATAAAATATATATAATTTAACGGCAAA
*
3438 AAGATTGGAGGACTTTTCATGTTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATT
451 AAGATTGGAGGACTTTTCACGTTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATT
3503 AAATTTA
516 AAATTTA
3510 TATTATCTAA
Statistics
Matches: 2328, Mismatches: 150, Indels: 75
0.91 0.06 0.03
Matches are distributed among these distances:
985 173 0.07
986 65 0.03
987 132 0.06
988 348 0.15
989 18 0.01
991 160 0.07
993 1 0.00
994 36 0.02
995 152 0.07
996 318 0.14
997 10 0.00
998 404 0.17
999 240 0.10
1000 271 0.12
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (992 bp):
AAGCCAAAAACCGTGATGATAAATACACGATTTCGGCTAAAATTTTACAAAAATTGACCCGAAAG
ATATTTTCTCAATTTTTAGCCATAATACTCATAAAAATTATATAATTAATCACCAAAAATATTGA
AAAGCTTTTTGACGCTTTTAATATCGTTTTTTCATATTTTTTTGAATTAATTTCTAATTAAATCG
AAACAAGATTCAGATACTCGTAAAAACAAATTCTTAAATGCAATGTGGCTAAGATTTTATTAGAT
GAATATAGATATTTTAAGGAGTGTCAGCGCCAAAAATCATGCAAAACTGAGCTGGTGCCCGAAAC
GTGTTTTTAGCCAAAAACCGTGTATGTACACGATTTTGGTTAGAATTTTACAAAAAATGACCCGA
AAATTTTTTCCTTAATTTTTGGATAAAATACTCATAAAATATATATAATTTAACGGCAAAAAGAT
TGGAGGACTTTTCACGTTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATT
TAAACAAGATTCAGATGCTTGTAAAAACAAATTCTAAATCCAATGTGGCTGAGATTGATTAGATG
ATTATAGATATCTCAAGGAGTCTTGGCGCCAAAAATCATGAAAAACTGAGCCGGGGCCCTAGAAC
GCTTTTTTATCCAAAAAGTGTGATGGTTATTACACGAGCCGAAAGATGTTTCCTCAATTTTTGGA
TAAAATACGCAAAAAAATGACTCGGAATATATTTTCCTCAATTTTTAGCAACAATACTCATAAAA
AATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATACCGTTTTTCATATT
TTTTCCGAATTAATTTCTAATTAAAACGAAACATGATTTAGATGCTTGTAAAACAATGGCTGGGA
TATGGTTAGATGAATATAGATATTTCAAGCAGTCTCGGCGCCAAAAATCATTCAAAATGAACCGG
GGCCAGGAACGCGTTTT
Found at i:6909 original size:7 final size:7
Alignment explanation
Indices: 6897--6944 Score: 69
Period size: 7 Copynumber: 6.9 Consensus size: 7
6887 GAAACTAGTG
*
6897 TTTTTTT
1 TTTTTTC
6904 TTTTTTC
1 TTTTTTC
6911 TTTTTTC
1 TTTTTTC
6918 TTTTTTC
1 TTTTTTC
*
6925 TTTATTC
1 TTTTTTC
*
6932 TTTATTC
1 TTTTTTC
6939 TTTTTT
1 TTTTTT
6945 TGTTATGAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.04, C:0.10, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTTC
Found at i:6923 original size:21 final size:21
Alignment explanation
Indices: 6897--6950 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
6887 GAAACTAGTG
* *
6897 TTTTTTTTTTTTTCTTTTTTC
1 TTTTTTTTTTATTCTTTATTC
*
6918 TTTTTTCTTTATTCTTTATTC
1 TTTTTTTTTTATTCTTTATTC
*
6939 TTTTTTTGTTAT
1 TTTTTTTTTTAT
6951 GAGACTGAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.06, C:0.09, G:0.02, T:0.83
Consensus pattern (21 bp):
TTTTTTTTTTATTCTTTATTC
Found at i:6950 original size:14 final size:13
Alignment explanation
Indices: 6898--6950 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
6888 AAACTAGTGT
*
6898 TTTTTTTTTTTTC
1 TTTTTTTTTATTC
*
6911 TTTTTTCTTTTTTC
1 TTTTTT-TTTATTC
*
6925 TTTATTCTTTATTC
1 TTT-TTTTTTATTC
6939 TTTTTTTGTTAT
1 TTTTTTT-TTAT
6951 GAGACTGAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
13 9 0.26
14 23 0.68
15 2 0.06
ACGTcount: A:0.06, C:0.09, G:0.02, T:0.83
Consensus pattern (13 bp):
TTTTTTTTTATTC
Found at i:7088 original size:28 final size:28
Alignment explanation
Indices: 7055--7118 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 28
7045 AACTTGTATG
*
7055 ATTTTGACGGTTTGCCCCCTAAACTTTA
1 ATTTTGACAGTTTGCCCCCTAAACTTTA
* * *
7083 ATTTTGGACATTTTGCCCCTTGAACTTTA
1 ATTTT-GACAGTTTGCCCCCTAAACTTTA
7112 ATTTTGA
1 ATTTTGA
7119 AGCCATTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 7 0.23
29 24 0.77
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.44
Consensus pattern (28 bp):
ATTTTGACAGTTTGCCCCCTAAACTTTA
Found at i:8827 original size:31 final size:31
Alignment explanation
Indices: 8747--8830 Score: 89
Period size: 31 Copynumber: 2.6 Consensus size: 31
8737 CGTCATGCCG
8747 TTGATGTGGCAATGCCACGTGGATTGGGTTGGT
1 TTGATGTGGCAATGCCACGTGGATT--GTTGGT
** * * *
8780 TTGGCGGGGCATTGCCACTTGGCATT-TTGGT
1 TTGATGTGGCAATGCCACGTGG-ATTGTTGGT
8811 TTGATGTGGCAATGCCACGT
1 TTGATGTGGCAATGCCACGT
8831 CAGCGGCGTG
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
31 20 0.50
33 17 0.43
34 3 0.08
ACGTcount: A:0.14, C:0.17, G:0.36, T:0.33
Consensus pattern (31 bp):
TTGATGTGGCAATGCCACGTGGATTGTTGGT
Found at i:9449 original size:2 final size:2
Alignment explanation
Indices: 9442--9473 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
9432 TAACCTTCAC
9442 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9474 AAAGAAGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.