Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010654.1 Corchorus olitorius cultivar O-4 contig10686, 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: 7221
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Found at i:1969 original size:4 final size:4
Alignment explanation
Indices: 1949--2129 Score: 57
Period size: 4 Copynumber: 46.5 Consensus size: 4
1939 AATAGGTAGC
** *
1949 TAAA -AAA T-AA T-AA TAAA TAAA TAAA TAGG T-AA TAAC TAAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA T-AAA TAAA
* * *
1994 -AAGA TAAA T-AG TAAA TAAA TAGA TGATAA TTAA -AAA TAAA TAAA -AAGA
1 TAA-A TAAA TAAA TAAA TAAA TAAA T-A-AA TAAA TAAA TAAA TAAA TAA-A
* * * *
2042 TAAA T-AG TAAA TAAA TAGA TAATA GTTAA -AAA TAAA TAAA TAGA -AAA
1 TAAA TAAA TAAA TAAA TAAA TAA-A -TAAA TAAA TAAA TAAA TAAA TAAA
* * * *
2089 -AAA T-AG TGAA TAAA TAGA TAATA GTTAA T-AA TAAA TAAA TA
1 TAAA TAAA TAAA TAAA TAAA TAA-A -TAAA TAAA TAAA TAAA TA
2130 GAAAAGAATA
Statistics
Matches: 130, Mismatches: 26, Indels: 42
0.66 0.13 0.21
Matches are distributed among these distances:
3 32 0.25
4 80 0.62
5 12 0.09
6 6 0.05
ACGTcount: A:0.66, C:0.01, G:0.08, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:1983 original size:19 final size:19
Alignment explanation
Indices: 1949--2111 Score: 91
Period size: 19 Copynumber: 8.9 Consensus size: 19
1939 AATAGGTAGC
1949 TAAA-AAATA-ATAATAAA
1 TAAATAAATAGATAATAAA
* *
1966 TAAATAAATAGGTAATAAC
1 TAAATAAATAGATAATAAA
* *
1985 TAAAATAAAAAGATAA-ATAG
1 T-AAATAAATAGATAATA-AA
*
2005 TAAATAAATAGATGAT-AA
1 TAAATAAATAGATAATAAA
*
2023 TTAA-AAAT--A-AATAAA
1 TAAATAAATAGATAATAAA
2038 -AAGATAAATAG-TAAATAAA
1 TAA-ATAAATAGAT-AATAAA
* *
2057 TAGAT-AATAGTTAA-AAA
1 TAAATAAATAGATAATAAA
*
2074 TAAATAAATAGA-AAAAAA
1 TAAATAAATAGATAATAAA
2092 TAGTGAATAAATAGATAATA
1 TA---AATAAATAGATAATA
2112 GTTAATAATA
Statistics
Matches: 111, Mismatches: 15, Indels: 35
0.69 0.09 0.22
Matches are distributed among these distances:
14 3 0.03
15 4 0.04
16 4 0.04
17 17 0.15
18 26 0.23
19 29 0.26
20 15 0.14
21 10 0.09
22 3 0.03
ACGTcount: A:0.66, C:0.01, G:0.09, T:0.25
Consensus pattern (19 bp):
TAAATAAATAGATAATAAA
Found at i:2040 original size:44 final size:44
Alignment explanation
Indices: 1951--2154 Score: 214
Period size: 46 Copynumber: 4.5 Consensus size: 44
1941 TAGGTAGCTA
* * * *
1951 AAAAATAAT-AATAAATAAATAAATAGGTAATAACTAAAATAAAAAG
1 AAAAATAGTAAATAAATAGAT-AATAGTTAA-AAAT-AAATAAAAAG
* * *
1997 ATAAATAGTAAATAAATAGATGATAATTAAAAATAAATAAAAAG
1 AAAAATAGTAAATAAATAGATAATAGTTAAAAATAAATAAAAAG
* *
2041 ATAAATAGTAAATAAATAGATAATAGTTAAAAATAAATAAATAGAA
1 AAAAATAGTAAATAAATAGATAATAGTTAAAAATAAATAAA-A-AG
* * *
2087 AAAAATAGTGAATAAATAGATAATAGTTAATAATAAATAAATAG
1 AAAAATAGTAAATAAATAGATAATAGTTAAAAATAAATAAAAAG
*
2131 AAAAGAATAGTGAATAAATA-ATAA
1 -AAA-AATAGTAAATAAATAGATAA
2155 AAAATCTTTT
Statistics
Matches: 138, Mismatches: 15, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
44 50 0.36
45 11 0.08
46 67 0.49
47 10 0.07
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (44 bp):
AAAAATAGTAAATAAATAGATAATAGTTAAAAATAAATAAAAAG
Found at i:2042 original size:25 final size:24
Alignment explanation
Indices: 2005--2131 Score: 92
Period size: 25 Copynumber: 5.5 Consensus size: 24
1995 AGATAAATAG
2005 TAAATAAATAGATGATAATTAAAAA
1 TAAATAAATAGAT-ATAATTAAAAA
* *
2030 TAAATAAAAAGATA-AA-T---AG
1 TAAATAAATAGATATAATTAAAAA
*
2049 TAAATAAATAGATAATAGTTAAAAA
1 TAAATAAATAGAT-ATAATTAAAAA
*
2074 TAAATAAATAGA-A-AA--AAATAG
1 TAAATAAATAGATATAATTAAA-AA
* * *
2095 TGAATAAATAGATAATAGTTAATAA
1 TAAATAAATAGAT-ATAATTAAAAA
2120 TAAATAAATAGA
1 TAAATAAATAGA
2132 AAAGAATAGT
Statistics
Matches: 78, Mismatches: 12, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
19 13 0.17
20 4 0.05
21 13 0.17
22 3 0.04
23 4 0.05
24 2 0.03
25 37 0.47
26 2 0.03
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (24 bp):
TAAATAAATAGATATAATTAAAAA
Found at i:2105 original size:46 final size:46
Alignment explanation
Indices: 1999--2154 Score: 219
Period size: 46 Copynumber: 3.5 Consensus size: 46
1989 ATAAAAAGAT
* * * *
1999 AAATAGTAAATAAATAGATGATAATTAAAAATAAATAAA-A-AGAT
1 AAATAGTAAATAAATAGATAATAGTTAAAAATAAATAAATAGAAAA
2043 AAATAGTAAATAAATAGATAATAGTTAAAAATAAATAAATAGAAAA
1 AAATAGTAAATAAATAGATAATAGTTAAAAATAAATAAATAGAAAA
* *
2089 AAATAGTGAATAAATAGATAATAGTTAATAATAAATAAATAGAAAA
1 AAATAGTAAATAAATAGATAATAGTTAAAAATAAATAAATAGAAAA
* *
2135 GAATAGTGAATAAATA-ATAA
1 AAATAGTAAATAAATAGATAA
2155 AAAATCTTTT
Statistics
Matches: 103, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
44 37 0.36
45 5 0.05
46 61 0.59
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (46 bp):
AAATAGTAAATAAATAGATAATAGTTAAAAATAAATAAATAGAAAA
Found at i:2146 original size:25 final size:25
Alignment explanation
Indices: 2072--2151 Score: 87
Period size: 25 Copynumber: 3.4 Consensus size: 25
2062 AATAGTTAAA
*
2072 AATAAATAAATAGAAAAAAATAGTG
1 AATAAATAAATAGAAAAGAATAGTG
* * * *
2097 AATAAATAGAT--AATAG-TTAAT-
1 AATAAATAAATAGAAAAGAATAGTG
2118 AATAAATAAATAGAAAAGAATAGTG
1 AATAAATAAATAGAAAAGAATAGTG
2143 AATAAATAA
1 AATAAATAA
2152 TAAAAAATCT
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
21 10 0.24
22 3 0.07
23 7 0.17
24 3 0.07
25 19 0.45
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.24
Consensus pattern (25 bp):
AATAAATAAATAGAAAAGAATAGTG
Found at i:4407 original size:74 final size:75
Alignment explanation
Indices: 4290--4495 Score: 200
Period size: 75 Copynumber: 2.8 Consensus size: 75
4280 ACTAATAAAT
* * **** * * *
4290 TGAAAAAAGACAAAAACGGGCCAAAAAAAAACTCCAACATTAAAAGTTGATGGGAGCTATCAGTA
1 TGAAAAAAGACCAAAACGGGGCAAAAAGGCTCTCCCACGTTAAAAGTTGATGGGAGCGATCAGTA
4355 AA-TGCAGAG
66 AATTGCAGAG
* * * * * **
4364 TGCGAAAAA-ACCAACACGGGGCAAAAAGGCTCTTCCACGTTAAAAGTTGAAGGGAGCGCTTGGT
1 TG-AAAAAAGACCAAAACGGGGCAAAAAGGCTCTCCCACGTTAAAAGTTGATGGGAGCGATCAGT
*
4428 AAATTTCAGAG
65 AAATTGCAGAG
* * * *
4439 TGAAAAAAGACCAAAATGGGGCGAAAATGTTCTCCCACGTTAAAAGTTGATGGGAGC
1 TGAAAAAAGACCAAAACGGGGCAAAAAGGCTCTCCCACGTTAAAAGTTGATGGGAGC
4496 CTTTAGTAAT
Statistics
Matches: 104, Mismatches: 25, Indels: 5
0.78 0.19 0.04
Matches are distributed among these distances:
74 50 0.48
75 54 0.52
ACGTcount: A:0.42, C:0.17, G:0.24, T:0.17
Consensus pattern (75 bp):
TGAAAAAAGACCAAAACGGGGCAAAAAGGCTCTCCCACGTTAAAAGTTGATGGGAGCGATCAGTA
AATTGCAGAG
Found at i:4539 original size:2 final size:2
Alignment explanation
Indices: 4527--4558 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
4517 ATTCAAATAC
4527 TA TA TA GTA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA T
4559 TTATTTCACA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6037 original size:435 final size:438
Alignment explanation
Indices: 5203--6160 Score: 1417
Period size: 435 Copynumber: 2.2 Consensus size: 438
5193 GCATTAAATG
* * *
5203 GTCCAACCCATAATTATGAGGGATTAAATAGCATAAAGCGTAAAAATCTAAGGATCATTTGATAA
1 GTCCAACCCATAA--ATGAGGGACTAAATAGCATAAAGCATAAAAGTCT-AGGATCATTTGATAA
*
5268 ATTATCCAGCAAAAAAAATATTGGTTTATGGAGACCAAACATAAAAATTCCCTCTTGAACCCTCC
63 ATAATCCAGCAAAAAAAATATTGGTTTATGGAGACCAAACATAAAAATTCCCTCTTGAACCCTCC
* *
5333 ACGAAACTCATTAATCAAATTCAGCTTTGAGGCCCTTAACGAAAGCCGTAGATCACACAATAACC
128 ACGAAACTCATTAATCAAATTCAGCTTTGAAGCCCTTAACGAAAGCCATAGATCACACAATAACC
*
5398 TTTTAACCGACACTTGAATAACCTCAATCGGACAAGTGGGCAAAAAATTATACGATATCAAATAG
193 TTTTAACCGACACTTGAATAACCTCAATCGGACAAGTGGACAAAAAATTATACGATATCAAATAG
* * * *
5463 ACCGGCAATCAAGACCATAAAATTTCAAAATCATTTTTTAAAATCAAAACATTAAATTTGTCTTT
258 ACCGACAATCAAGACCACAAAATTTCAAAAGCATTTTTTAAAATCAAAACATTAAAATTGTCTTT
* ** **
5528 TGAATCCTTCATGGAAGTTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCATTTTGAT
323 TGAATCCTTCATGGAAGTCGTAGATCACAAAATTACCTTTTAATAGACACTTGAATCACCTTGAT
* * *
5593 CGGACAAGC-AAA-AGAAAAAGTAAAAGAGTTAAAGCCGAAACGTTCAGTC
388 CGGACAAGCAAAACAAAAAAAATAAAAGAATTAAAGCCGAAACGTTCAGTC
* * *
5642 GTCCAACTCA-GAA-GAGGGACTAAATAGCATTAAGCATAAAAGTCTGAGGATCATTTGATAAAT
1 GTCCAACCCATAAATGAGGGACTAAATAGCATAAAGCATAAAAGTCT-AGGATCATTTGATAAAT
* *
5705 AATCCAGCAAACAAAATATTTGTTTATGGAGACCAAACATAAAAATTCCCTCTTGAACCCTCCAC
65 AATCCAGCAAAAAAAATATTGGTTTATGGAGACCAAACATAAAAATTCCCTCTTGAACCCTCCAC
* *
5770 GAAACTCATTAATCAAATTTAGCTTTGAAGCCCTTAACGAAAGCCATAGATCACACAATATCCTT
130 GAAACTCATTAATCAAATTCAGCTTTGAAGCCCTTAACGAAAGCCATAGATCACACAATAACCTT
5835 TTAACCGACACTTGAATAACCTCAATCGGACAAGTGGA-ACAAAAATTATACGATATCAAATAGA
195 TTAACCGACACTTGAATAACCTCAATCGGACAAGTGGACA-AAAAATTATACGATATCAAATAGA
* * *
5899 CCGATAATCAAGACCACAAAATTTCAAAAGCATTTTTTTAAAATGAAAACATTAAAATTG-GTTT
259 CCGACAATCAAGACCACAAAATTTCAAAAGCA-TTTTTTAAAATCAAAACATTAAAATTGTCTTT
* * *
5963 T-AAGTTCTTCATGGAAGTCGTAGATCACAAAATTACGTTTTAATAGACATTTGAATCACCTTGA
323 TGAA-TCCTTCATGGAAGTCGTAGATCACAAAATTACCTTTTAATAGACACTTGAATCACCTTGA
*
6027 TCGGACAAGCAAAACAAAAAAAATAAAAGAATTAAAGCCGAAACGTTTAGTC
387 TCGGACAAGCAAAACAAAAAAAATAAAAGAATTAAAGCCGAAACGTTCAGTC
* * * *
6079 GTCCAACCCATAAATTGTGAGGGACTAAGTAGCATAAAGTATAAAAGTATATGAATCATTTGATA
1 GTCCAACCCATAAA---TGAGGGACTAAATAGCATAAAGCATAAAAGTCTA-GGATCATTTGATA
* *
6144 AATAAACCAACAAAAAA
62 AATAATCCAGCAAAAAA
6161 TGATTTATTT
Statistics
Matches: 464, Mismatches: 44, Indels: 19
0.88 0.08 0.04
Matches are distributed among these distances:
434 3 0.01
435 323 0.70
436 29 0.06
437 42 0.09
438 3 0.01
439 9 0.02
441 1 0.00
442 54 0.12
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (438 bp):
GTCCAACCCATAAATGAGGGACTAAATAGCATAAAGCATAAAAGTCTAGGATCATTTGATAAATA
ATCCAGCAAAAAAAATATTGGTTTATGGAGACCAAACATAAAAATTCCCTCTTGAACCCTCCACG
AAACTCATTAATCAAATTCAGCTTTGAAGCCCTTAACGAAAGCCATAGATCACACAATAACCTTT
TAACCGACACTTGAATAACCTCAATCGGACAAGTGGACAAAAAATTATACGATATCAAATAGACC
GACAATCAAGACCACAAAATTTCAAAAGCATTTTTTAAAATCAAAACATTAAAATTGTCTTTTGA
ATCCTTCATGGAAGTCGTAGATCACAAAATTACCTTTTAATAGACACTTGAATCACCTTGATCGG
ACAAGCAAAACAAAAAAAATAAAAGAATTAAAGCCGAAACGTTCAGTC
Done.