Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009504.1 Corchorus olitorius cultivar O-4 contig09536, 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: 9106
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.28
Found at i:1161 original size:68 final size:67
Alignment explanation
Indices: 1050--1558 Score: 460
Period size: 68 Copynumber: 7.7 Consensus size: 67
1040 AGTAAAGCTC
1050 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGTATTTAAGTT
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTC-TTTTGTATTTAAGTT
1115 TAG
65 TAG
* * * **
1118 TGTTTTCCATTTCCAAAGATACCCTTTCGGTCGAAGGGTCATTTTCG-CCCTT-T-TTT-A----
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGTATTTAAGTTT
1175 AG
66 AG
* * * *
1177 TATTTTATATTTCCAAAAAATACTCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTTAGT
1 TATTTTCTATTTCC-AAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTC-TTTTGTATTTAAGT
1242 TTAG
64 TTAG
* *
1246 TATTTTCTTTTTTCCAAAAATACCCTTTCGGTTGAAGGGTCATTTTCGTCGTTTTGTATTTAAGT
1 TATTTTC-TATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTC-TTTTGTATTTAAGT
1311 TTAG
64 TTAG
* * * * * **
1315 TGTTTTCCATTTCTATAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCACCTAAGTTT
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGTATTTAAGTTT
1380 AG
66 AG
* * * * * ** * * *
1382 TACTTTCTTTTTCCAAAAATGCCCTCTCGGTCGAAGGGTCAATTTCAACTTTTCCATATCT-AGG
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTT--GTATTTAAGT
1446 TTAG
64 TTAG
* * * *
1450 --TTTACT-TTTCCCAAAATACCCTTTCGGTCAAAGGGTCAATTTT-GTCATTCTTCTATTTGAA
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTC-ATTTTCGTC-TT-TTGTATTT-AA
1511 -TTTA-
62 GTTTAG
* * * *
1515 -CTTTT-GATTTCCAAAAATACCCTTTTGGT-GAAAGGGTCAGTTTC
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCG-AAGGGTCATTTTC
1559 ATTATTTTCG
Statistics
Matches: 357, Mismatches: 62, Indels: 46
0.77 0.13 0.10
Matches are distributed among these distances:
59 13 0.04
60 31 0.09
61 1 0.00
62 2 0.01
63 1 0.00
64 6 0.02
65 38 0.11
66 45 0.13
67 61 0.17
68 87 0.24
69 66 0.18
70 6 0.02
ACGTcount: A:0.22, C:0.19, G:0.15, T:0.44
Consensus pattern (67 bp):
TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGTATTTAAGTTT
AG
Found at i:1286 original size:69 final size:67
Alignment explanation
Indices: 1175--1492 Score: 329
Period size: 69 Copynumber: 4.7 Consensus size: 67
1165 CCCTTTTTTA
* * * *
1175 AGTATTTTATATTTCCAAAAAATACTCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTTA
1 AGTATTTTCTTTTTCC-AAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTC-TTTTGCATTTAA
1240 GTTT
64 GTTT
* *
1244 AGTATTTTCTTTTTTCCAAAAATACCCTTTCGGTTGAAGGGTCATTTTCGTCGTTTTGTATTTAA
1 AGTATTTTC-TTTTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTC-TTTTGCATTTAA
1309 GTTT
64 GTTT
* ** * * **
1313 AGTGTTTTCCATTTCTATAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCACCTAAGT
1 AGTATTTTCTTTTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCATTTAAGT
1378 TT
66 TT
* * * * ** *
1380 AGTACTTTCTTTTTCCAAAAATGCCCTCTCGGTCGAAGGGTCAATTTCAACTTTTCCATATCT-A
1 AGTATTTTCTTTTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCAT-T-TAA
*
1444 GGTT
64 GTTT
* * *
1448 AG--TTTAC-TTTTCCCAAAATACCCTTTCGGTCAAAGGGTCAATTTT
1 AGTATTTTCTTTTTCCAAAAATACCCTTTCGGTCGAAGGGTC-ATTTT
1493 GTCATTCTTC
Statistics
Matches: 207, Mismatches: 38, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
65 28 0.14
66 7 0.03
67 59 0.29
68 43 0.21
69 64 0.31
70 6 0.03
ACGTcount: A:0.22, C:0.19, G:0.15, T:0.44
Consensus pattern (67 bp):
AGTATTTTCTTTTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCATTTAAGT
TT
Found at i:1552 original size:131 final size:130
Alignment explanation
Indices: 1391--1628 Score: 295
Period size: 131 Copynumber: 1.8 Consensus size: 130
1381 GTACTTTCTT
* *
1391 TTTCCAAAAATGCCCTCTCGGTCGAAGGGTCAATTTCA-ACTTTTC-CATATCTAGGTTAGTTTA
1 TTTCCAAAAATACCCTCTCGGTCGAAGGGTCAATTTCATA-TTTTCGCATATC-AGGTTAGTCTA
* * *
1454 CTTTTCCCAAAATACCCTTTCGGTCAAAGGGTC-AATTTTGTCATTCTTCTATTTGAATTTACTT
64 C-TTTCCAAAAATACCCTTCCGGTCAAAGGG-CGAACTTTGTCATTCTTCTATTTGAATTTACTT
1518 TTGA
127 TTGA
* * * * *
1522 TTTCCAAAAATACCCTTTTGGT-GAAAGGGTCAGTTTCATTATTTTCGCATTTCAGTTTAGTCTA
1 TTTCCAAAAATACCCTCTCGGTCG-AAGGGTCAATTTCA-TATTTTCGCATATCAGGTTAGTCTA
*
1586 CTTTCCAAAAATGCCCTTCCGGTCAAAGGGCGAACTTTGTCAT
64 CTTTCCAAAAATACCCTTCCGGTCAAAGGGCGAACTTTGTCAT
1629 GTTTTCACGT
Statistics
Matches: 91, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
130 2 0.02
131 68 0.75
132 15 0.16
133 6 0.07
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (130 bp):
TTTCCAAAAATACCCTCTCGGTCGAAGGGTCAATTTCATATTTTCGCATATCAGGTTAGTCTACT
TTCCAAAAATACCCTTCCGGTCAAAGGGCGAACTTTGTCATTCTTCTATTTGAATTTACTTTTGA
Found at i:1614 original size:65 final size:63
Alignment explanation
Indices: 1391--1615 Score: 177
Period size: 65 Copynumber: 3.5 Consensus size: 63
1381 GTACTTTCTT
* * * *
1391 TTTCCAAAAATGCCC-TCTCGGTCGAAGGGTCAATTTCA-ACTTTTCCATATCTAGGTTAGTTTA
1 TTTCCAAAAATACCCTTC-CGGTCAAAGGGTCAATTTCATA-TTTTCCATTTC-AGTTTAGTTTA
1454 C
63 C
* * ** * * * *
1455 TTTTCCCAAAATACCCTTTCGGTCAAAGGGTCAATTTTGTCATTCTTCTATTTGAATTTACTTTT
1 -TTTCCAAAAATACCCTTCCGGTCAAAGGGTCAATTTCAT-ATT-TTCCATTTCAGTTTA-GTTT
1520 GA-
62 -AC
** * * *
1522 TTTCCAAAAATACCCTTTTGGTGAAAGGGTCAGTTTCATTATTTTCGCATTTCAGTTTAGTCTAC
1 TTTCCAAAAATACCCTTCCGGTCAAAGGGTCAATTTCA-TATTTTC-CATTTCAGTTTAGTTTAC
*
1587 TTTCCAAAAATGCCCTTCCGGTCAAAGGG
1 TTTCCAAAAATACCCTTCCGGTCAAAGGG
1616 CGAACTTTGT
Statistics
Matches: 124, Mismatches: 27, Indels: 18
0.73 0.16 0.11
Matches are distributed among these distances:
64 1 0.01
65 60 0.48
66 51 0.41
67 11 0.09
68 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (63 bp):
TTTCCAAAAATACCCTTCCGGTCAAAGGGTCAATTTCATATTTTCCATTTCAGTTTAGTTTAC
Done.