Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010340.1 Corchorus olitorius cultivar O-4 contig10372, 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: 2266
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Found at i:715 original size:162 final size:162
Alignment explanation
Indices: 534--866 Score: 657
Period size: 162 Copynumber: 2.1 Consensus size: 162
524 TCCTCCAATT
534 TTTTTGGCGTTCAGTTATATATATTTTATGAGTATTGTACCCAAAAATTGACGGAATAATTTTTC
1 TTTTTGGCGTTCAGTTATATATATTTTATGAGTATTGTACCCAAAAATTGACGGAATAATTTTTC
599 GGGTCATTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAAA
66 GGGTCATTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAAA
664 GTGTTTCGGGGCCCCGGCTTAGTTTTGCATGA
131 GTGTTTCGGGGCCCCGGCTTAGTTTTGCATGA
*
696 TTTTTGGCGTTCAGTTATATATATTTTATGAGTATTGTAGCCAAAAATTGACGGAATAATTTTTC
1 TTTTTGGCGTTCAGTTATATATATTTTATGAGTATTGTACCCAAAAATTGACGGAATAATTTTTC
761 GGGTCATTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAAA
66 GGGTCATTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAAA
826 GTGTTTCGGGGCCCCGGCTTAGTTTTGCATGA
131 GTGTTTCGGGGCCCCGGCTTAGTTTTGCATGA
858 TTTTTGGCG
1 TTTTTGGCG
867 CCGAGACTCC
Statistics
Matches: 170, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
162 170 1.00
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.39
Consensus pattern (162 bp):
TTTTTGGCGTTCAGTTATATATATTTTATGAGTATTGTACCCAAAAATTGACGGAATAATTTTTC
GGGTCATTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAAA
GTGTTTCGGGGCCCCGGCTTAGTTTTGCATGA
Found at i:1184 original size:494 final size:495
Alignment explanation
Indices: 199--1196 Score: 1170
Period size: 494 Copynumber: 2.0 Consensus size: 495
189 CCCTTCAATT
* * *
199 TTTTTGGCGTTGAATTATATAATTTTTATGAGTATTGTGGCTAAAAATTGAGGAAATAACTTTCG
1 TTTTTGGCGTTCAATTATATAATTTTTATGAGTATTGTAGCCAAAAATTGAGGAAATAACTTTCG
*
264 AGTCAATTATTGCAAAATTCTAGCCGATCGAAACCGTGTAATAATCATCACGGTTTTTGGCTAAA
66 AGTCAATTATTGCAAAATTCTA--CGATCGAAACCGTGTAATAACCATCACGGTTTTTGGCTAAA
* * ** * * *
329 AACGCATTTTGGGTTCCCGACTAAGTTTTGCATGATTTTTTGCGCCAAAACTCTTTGAGATGTCC
129 AAAGCATTTCGGGGCCCCGACTAAGTTTTGCATGATTTTTGGCGCCAAAACTCCTTGAGATATCC
* * *** * * * *
394 ATATTCATTTAATCAAATTTTAGCTAAATTGGATTTAAGAATTTGTTTTTACGAGCATTTGAATC
194 ATACTCATCTAATCAAATCCCAGCCAAATTGAATTTAAGAATTTGTTTTTACAAGCATCTGAATC
* * *
459 TTGCTTCGATTTAATTAGAAATCAATTCAGAAAAATATTGAATACGATACTAAAAGCGTGAAAAT
259 TTGCTTCGATTTAATTAGAAATCAAGTCAGAAAAATATTGAAAACGATACTAAAAGCGTGAAAAG
* * * * * *
524 TCCTCCAATTTTTTTGGCGTTCAGTTATATATATTTTATGAGTATTGTACCCAAAAATTGACGGA
324 GCCTCCAATTTTTTTGGCATTCAATTATATATATTTTATCAGTATTGTACCCAAAAATCGACGAA
* * * * * *
589 ATAATTTTTCGGGTCATTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTT
389 AAAATCTTTCGGATCAATTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTCTC
* * * *
654 GGCTAAAAAAGTGTTTCGGGGCCCCGGCTTAGTTTTGCATGA
454 GGCTAAAAAACTGTTCCGGGGCCCCGACTCAGTTTTGCATGA
* *
696 TTTTTGGCGTTCAGTTATAT-ATATTTTATGAGTATTGTAGCCAAAAATTGACGG-AATAATTTT
1 TTTTTGGCGTTCAATTATATAAT-TTTTATGAGTATTGTAGCCAAAAATTGA-GGAAATAA-CTT
* * * * * *
759 TCGGGTCATTTTTTGCAAAATTTTA-G-TCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAA
63 TCGAGTCAATTATTGCAAAATTCTACGATCGAAACCGTGTAATAACCATCACGGTTTTTGGCTAA
** * * * * *
822 AAAAGTGTTTCGGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGATATATC
128 AAAAGCATTTCGGGGCCCCGACTAAGTTTTGCATGATTTTTGGCGCCAAAACTCCTTGAGATATC
* * * *
887 TATACTCATCTAATCAAATCCCAGCCACATTGAATTTAAGGA-TTGTTTTTTCAAGCATCTGAAT
193 CATACTCATCTAATCAAATCCCAGCCAAATTGAATTTAAGAATTTGTTTTTACAAGCATCTGAAT
* * *
951 CTTGTTTCGATTTAATTAGAAATTAAGTCAGAAAAATA-TGAAAAACGATATTAAAAGCGTGAAA
258 CTTGCTTCGATTTAATTAGAAATCAAGTCAGAAAAATATTG-AAAACGATACTAAAAGCGTG-AA
* * * * * * * **** *
1015 AAGGCTTTCAATTTTTTTGGCATTGAATTTTATGTTTTTTATCAGTATTTTTGTTAGAAATCGA-
321 AAGGCCTCCAATTTTTTTGGCATTCAATTATATATATTTTATCAGTATTGTACCCAAAAATCGAC
1079 GAAAAAAATCTTTCGGATCAATTTTTGCAAAAATTTTAG-CAGAAATCGTGTACTAACCATCACG
386 G-AAAAAATCTTTCGGATCAATTTTTGC-AAAATTTTAGTC-GAAATCGTGTACTAACCATCACG
1143 GTTCTCGGCT-AAAAACTCGTTCCGGGG-CCCGACTCAGTTTTGCATGA
448 GTTCTCGGCTAAAAAACT-GTTCCGGGGCCCCGACTCAGTTTTGCATGA
1190 TTTTTGG
1 TTTTTGG
1197 TGCAATCCTT
Statistics
Matches: 419, Mismatches: 73, Indels: 21
0.82 0.14 0.04
Matches are distributed among these distances:
492 2 0.00
493 73 0.17
494 218 0.52
495 50 0.12
496 2 0.00
497 49 0.12
498 25 0.06
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (495 bp):
TTTTTGGCGTTCAATTATATAATTTTTATGAGTATTGTAGCCAAAAATTGAGGAAATAACTTTCG
AGTCAATTATTGCAAAATTCTACGATCGAAACCGTGTAATAACCATCACGGTTTTTGGCTAAAAA
AGCATTTCGGGGCCCCGACTAAGTTTTGCATGATTTTTGGCGCCAAAACTCCTTGAGATATCCAT
ACTCATCTAATCAAATCCCAGCCAAATTGAATTTAAGAATTTGTTTTTACAAGCATCTGAATCTT
GCTTCGATTTAATTAGAAATCAAGTCAGAAAAATATTGAAAACGATACTAAAAGCGTGAAAAGGC
CTCCAATTTTTTTGGCATTCAATTATATATATTTTATCAGTATTGTACCCAAAAATCGACGAAAA
AATCTTTCGGATCAATTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTCTCGG
CTAAAAAACTGTTCCGGGGCCCCGACTCAGTTTTGCATGA
Found at i:1325 original size:329 final size:328
Alignment explanation
Indices: 726--1537 Score: 903
Period size: 328 Copynumber: 2.5 Consensus size: 328
716 ATATTTTATG
* * * * * *
726 AGTATTGTAGCCAAAAATTGACGGAATAATTTTTCGGGTCATTTTTTGCAAAATTTTAGTCGAAA
1 AGTATTTTAGCCAAAAATCGA-GAAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAG-CGAAA
* * * *
791 TCGTGTACTAACCATCACGGTTTTTGGCTAAAAAAGTGTTTCGGGGCCCCGGCTTAGTTTTGCAT
64 TCGTGTACTAACCATCACGGTTTTTGGCT-AAAAACTGTTCCGGGGCCCCGACTCAGTTTTGCAT
* * *
856 GATTTTTGGCGCCGAGACTCCTTGATATATCTATACTCATCTAATCAAATCCCAGCCACATTGAA
128 GATTTTTGGCGCCGAGACTCCTTGAAATATCTATACTCATCTAACCAAATCCCAGACACATTGAA
*
921 TTTAAGGATTGTTTTTTCAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAAGTCAGAAAA
193 TTTAAGGATTGTTTTTTCAAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAAGTCAGAAAA
* * * * * *
986 ATATGAAAAACGATATTAAAAGCGTGAAAAAGGCTTTCAAT-TTTTTTGGCATTGAATTTTATGT
258 ATATGAAAAACAATATTAAAAGCGT-AAAAAGCCCTTAAATCTTTTTTAGC-TCGAA--TTATGT
1050 -TTTTT-ATC
319 ATTTTTCATC
* ** * *
1058 AGTATTTTTGTTAGAAATCGAGAAAAAAATCTTTCGGATCAATTTTTGCAAAAATTTTAGCAGAA
1 AGTATTTTAGCCAAAAATCGAG-AAAAAATCTTTCGGGTCAATTTTTGC-AAAATTTTAGC-GAA
* *
1123 ATCGTGTACTAACCATCACGGTTCTCGGCTAAAAACTCGTTCCGGGG-CCCGACTCAGTTTTGCA
63 ATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACT-GTTCCGGGGCCCCGACTCAGTTTTGCA
* * *
1187 TGATTTTTGGTG-C-A-A-TCCTTGAAATATCTATATTCATCTAACCAAATCTCAGACACATT-A
127 TGATTTTTGGCGCCGAGACTCCTTGAAATATCTATACTCATCTAACCAAATCCCAGACACATTGA
* *
1247 GATTTAAGGATTTGTTTTTTCGAA-CATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCGG
192 -ATTTAAGGA-TTGTTTTTTC-AAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAAGTCAG
* * * * *
1311 AAAAAT-TGGAAAAACAATATTAGAAGTGTTAAAATCCCTTAAATCTTTTTTATCTCGAATTATG
254 AAAAATAT-GAAAAACAATATTAAAAGCGTAAAAAGCCCTTAAATCTTTTTTAGCTCGAATTATG
*
1375 TATTTTTCATT
318 TATTTTTCATC
* * * *
1386 AGTATTTTAGCCAAAAATTGAGAAAATATCTTTCGGGCCAATTTTTGCAAAGTTTTAGCCGAAAT
1 AGTATTTTAGCCAAAAATCGAGAAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAG-CGAAAT
* * * * * * **
1451 CGTGTACTAACTATCATGGTTTTTGGCTAAAAA-TGCGTTTCAGGACCAC-AGCTGTGTTTTGCA
65 CGTGTACTAACCATCACGGTTTTTGGCTAAAAACT--GTTCCGGGGCCCCGA-CTCAGTTTTGCA
*
1514 TGATTTTTGGCACCGAGACTCCTT
127 TGATTTTTGGCGCCGAGACTCCTT
1538 CAATCGTGTA
Statistics
Matches: 402, Mismatches: 59, Indels: 39
0.80 0.12 0.08
Matches are distributed among these distances:
325 1 0.00
326 57 0.14
327 52 0.13
328 83 0.21
329 80 0.20
330 4 0.01
331 7 0.02
332 69 0.17
333 49 0.12
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.37
Consensus pattern (328 bp):
AGTATTTTAGCCAAAAATCGAGAAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCGAAATC
GTGTACTAACCATCACGGTTTTTGGCTAAAAACTGTTCCGGGGCCCCGACTCAGTTTTGCATGAT
TTTTGGCGCCGAGACTCCTTGAAATATCTATACTCATCTAACCAAATCCCAGACACATTGAATTT
AAGGATTGTTTTTTCAAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAAGTCAGAAAAATA
TGAAAAACAATATTAAAAGCGTAAAAAGCCCTTAAATCTTTTTTAGCTCGAATTATGTATTTTTC
ATC
Found at i:1608 original size:39 final size:39
Alignment explanation
Indices: 1554--1631 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
1544 TGTACGTTAA
1554 TCAAAATATTAGCCGAAATCTTGTACGTTAATCAAAATC
1 TCAAAATATTAGCCGAAATCTTGTACGTTAATCAAAATC
*
1593 TCAAAATATTAGCCGAAATCTTGTACTTTAATCAAAATC
1 TCAAAATATTAGCCGAAATCTTGTACGTTAATCAAAATC
1632 ACGGTTTTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (39 bp):
TCAAAATATTAGCCGAAATCTTGTACGTTAATCAAAATC
Done.