Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011977.1 Corchorus olitorius cultivar O-4 contig12010, 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: 19263
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Found at i:6810 original size:15 final size:15
Alignment explanation
Indices: 6790--6826 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
6780 CAAGAGACGT
**
6790 TTTTCAAGAAAATTG
1 TTTTCAAGAAAAAGG
6805 TTTTCAAGAAAAAGG
1 TTTTCAAGAAAAAGG
6820 TTTTCAA
1 TTTTCAA
6827 AAATGAGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.38
Consensus pattern (15 bp):
TTTTCAAGAAAAAGG
Found at i:9270 original size:67 final size:67
Alignment explanation
Indices: 9158--9475 Score: 456
Period size: 67 Copynumber: 4.6 Consensus size: 67
9148 TTTAGAAGTG
9158 CACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAAGAA
1 CACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAAGAA
9223 TA
66 TA
* * *
9225 CACTGGAAGATGGTTTGCTAGAAAAAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAAGAA
1 CACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAAGAA
9290 TA
66 TA
* * *
9292 CACCGGAAGATGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTTATTAAGGAA
1 CACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAAGAA
9357 TA
66 TA
* *
9359 CACCGGAAGACAGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCGTTTAGGAT
1 CACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTC-ATTA--A-
*
9424 TTTTAGAAGAA
62 ----AGAA-TA
* *
9435 CACCAGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGA
1 CACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGA
9476 GACACCAGAA
Statistics
Matches: 226, Mismatches: 16, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
67 180 0.80
68 3 0.01
70 1 0.00
75 3 0.01
76 39 0.17
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (67 bp):
CACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAAGAA
TA
Found at i:9551 original size:39 final size:39
Alignment explanation
Indices: 9491--9569 Score: 124
Period size: 39 Copynumber: 2.0 Consensus size: 39
9481 CAGAAGATGG
9491 TTTCTCAACGATTTTCAGAAGTTGATCGGAAGACGATCT
1 TTTCTCAACGATTTTCAGAAGTTGATCGGAAGACGATCT
* *
9530 TTTCTCAA-GATCTTTCCGAAGTTGATCGGAAGATGATCT
1 TTTCTCAACGAT-TTTCAGAAGTTGATCGGAAGACGATCT
9569 T
1 T
9570 GTCAAAAAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 3 0.08
39 34 0.92
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (39 bp):
TTTCTCAACGATTTTCAGAAGTTGATCGGAAGACGATCT
Found at i:9826 original size:64 final size:65
Alignment explanation
Indices: 9549--10018 Score: 578
Period size: 65 Copynumber: 7.3 Consensus size: 65
9539 ATCTTTCCGA
* * * * * *
9549 AGTTGATCGGAAGATGATCTTGTCAAAAAGTGCACCAGAAGAGGGTTTTCTCAACAATTCTCAGG
1 AGTTGATCGGAAGACGATCTTGTCAAGAAGTACTCCAGAAGATGGTTTTCTCAACAATTTTCAGG
* *
9614 AGATGATCGGAAGACGATCTGGTCAAGAAGTACTCCAGAAGATGGTTTTCTCAACAATTCTT-AG
1 AGTTGATCGGAAGACGATCTTGTCAAGAAGTACTCCAGAAGATGGTTTTCTCAACAATT-TTCAG
9678 G
65 G
* * * * * *
9679 AGATGTTCGGAAGACGATCTTGTCAAGAAGTACTCTAGAAGATGGTTTTCTGAACAATTCTCAAG
1 AGTTGATCGGAAGACGATCTTGTCAAGAAGTACTCCAGAAGATGGTTTTCTCAACAATTTTCAGG
* * * *
9744 AGATGATCGGAAGACGATCTTGTCAAGAAGTAGTCCAGAAGATGG-TTTCTCAAGAGTTTTCAGG
1 AGTTGATCGGAAGACGATCTTGTCAAGAAGTACTCCAGAAGATGGTTTTCTCAACAATTTTCAGG
9808 AGTTGATCGGAAGACGATCTTGTCAAGAAGTACTCCAGAAGATGGTTTTCTCAACAATTTTCA-G
1 AGTTGATCGGAAGACGATCTTGTCAAGAAGTACTCCAGAAGATGGTTTTCTCAACAATTTTCAGG
* * * * *
9872 A--TGATCGGAAGACGATCTTATTAAGAAGTA-TATCGGAAGA-GGGTTTCTCAACAATTTTCAG
1 AGTTGATCGGAAGACGATCTTGTCAAGAAGTACT-CCAGAAGATGGTTTTCTCAACAATTTTCAG
*
9933 A
65 G
* * * * * * **
9934 AGTTGGTCGGAAGATGATCTTTTCAAGAAGTACACTAGAAGATGGTTTT-TCAAAAATTTTCAAA
1 AGTTGATCGGAAGACGATCTTGTCAAGAAGTACTCCAGAAGATGGTTTTCTCAACAATTTTCAGG
9998 AGTTGATCGGAAGACGATCTT
1 AGTTGATCGGAAGACGATCTT
10019 CTTAAAAAGT
Statistics
Matches: 351, Mismatches: 45, Indels: 19
0.85 0.11 0.05
Matches are distributed among these distances:
61 20 0.06
62 34 0.10
64 122 0.35
65 174 0.50
66 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.29
Consensus pattern (65 bp):
AGTTGATCGGAAGACGATCTTGTCAAGAAGTACTCCAGAAGATGGTTTTCTCAACAATTTTCAGG
Found at i:9938 original size:126 final size:127
Alignment explanation
Indices: 9542--10081 Score: 570
Period size: 126 Copynumber: 4.2 Consensus size: 127
9532 TCTCAAGATC
* * * * *
9542 TTTCCGAAGTTGATCGGAAGATGATCTTGTCAAAAAGTGCACCAGAAGAGGGTTTTCTCAACAAT
1 TTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTTCTCAACAAT
* *
9607 TCTCAGGAGATGATCGGAAGACGATCTGGTCAAGAAGTACTCCAGAAGATGGTTTTCTCAACAAT
66 TCTCA--AGATGATCGGAAGACGATCTTGTCAAGAAGTACTCCAGAAGA-GGGTTTCTCAACAAT
* * * * * *
9672 TCTT-AGGAGATGTTCGGAAGACGATCTTGTCAAGAAGTACTCTAGAAGATGGTTTTCTGAACAA
1 T-TTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTTCTCAACAA
* * * *
9736 TTCTCAAGAGATGATCGGAAGACGATCTTGTCAAGAAGTAGTCCAGAAGATGGTTTCTCAAGAGT
65 TTCTC-A-AGATGATCGGAAGACGATCTTGTCAAGAAGTACTCCAGAAGAGGGTTTCTCAACAAT
* *
9801 TTTCAGGAGTTGATCGGAAGACGATCTTGTCAAGAAGTACTCCAGAAGATGGTTTTCTCAACAAT
1 TTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTTCTCAACAAT
* * * * *
9866 TTTC-AGATGATCGGAAGACGATCTTATTAAGAAGTA-TATCGGAAGAGGGTTTCTCAACAAT
66 TCTCAAGATGATCGGAAGACGATCTTGTCAAGAAGTACT-CCAGAAGAGGGTTTCTCAACAAT
* * * * *
9927 TTTCAGAAGTTGGTCGGAAGATGATCTTTTCAAGAAGTACACTAGAAGATGGTTTT-TCAAAAAT
1 TTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTTCTCAACAAT
* * * * * * **
9991 TTTCAAAAGTTGATCGGAAGACGATCTTCTTAAAAAGTAC-ACAGGAAGATAGTTTCTCGGAA-A
66 TCTC--AAGATGATCGGAAGACGATCTTGTCAAGAAGTACTCCA-GAAGAGGGTTTCTC--AACA
**
10054 GG
126 AT
*
10056 TTTCAGAAGCTGATCGGAAGACGATC
1 TTTCAGAAGTTGATCGGAAGACGATC
10082 ACCGAAAGAC
Statistics
Matches: 351, Mismatches: 48, Indels: 23
0.83 0.11 0.05
Matches are distributed among these distances:
125 12 0.03
126 98 0.28
127 1 0.00
128 43 0.12
129 96 0.27
130 98 0.28
131 3 0.01
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (127 bp):
TTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTTCTCAACAAT
TCTCAAGATGATCGGAAGACGATCTTGTCAAGAAGTACTCCAGAAGAGGGTTTCTCAACAAT
Found at i:10029 original size:64 final size:65
Alignment explanation
Indices: 9529--10081 Score: 563
Period size: 65 Copynumber: 8.6 Consensus size: 65
9519 GAAGACGATC
* * * * * * *
9529 TTTTCTCAA-GATCTTTCCGAAGTTGATCGGAAGATGATCTTGTCAAAAAGTGCACCAGAAGAGG
1 TTTTCTCAACAAT-TTTCAGAAGATGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATG
9593 G
65 G
* * * *
9594 TTTTCTCAACAATTCTCAGGAGATGATCGGAAGACGATCTGGTCAAGAAGTACTCCAGAAGATGG
1 TTTTCTCAACAATTTTCAGAAGATGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGG
* * * *
9659 TTTTCTCAACAATTCTT-AGGAGATGTTCGGAAGACGATCTTGTCAAGAAGTACTCTAGAAGATG
1 TTTTCTCAACAATT-TTCAGAAGATGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATG
9723 G
65 G
* * **
9724 TTTTCTGAACAATTCTCA-AGAGATGATCGGAAGACGATCTTGTCAAGAAGTAGTCCAGAAGATG
1 TTTTCTCAACAATTTTCAGA-AGATGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATG
9788 G
65 G
* * * * *
9789 -TTTCTCAAGAGTTTTCAGGAGTTGATCGGAAGACGATCTTGTCAAGAAGTACTCCAGAAGATGG
1 TTTTCTCAACAATTTTCAGAAGATGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGG
* * * * *
9853 TTTTCTCAACAATTTTC---AGATGATCGGAAGACGATCTTATTAAGAAGTATATCGGAAGA-GG
1 TTTTCTCAACAATTTTCAGAAGATGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGG
* * * * * *
9914 GTTTCTCAACAATTTTCAGAAGTTGGTCGGAAGATGATCTTTTCAAGAAGTACACTAGAAGATGG
1 TTTTCTCAACAATTTTCAGAAGATGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGG
* * * * * * *
9979 TTTT-TCAAAAATTTTCAAAAGTTGATCGGAAGACGATCTTCTTAAAAAGTACA-CAGGAAGATA
1 TTTTCTCAACAATTTTCAGAAGATGATCGGAAGACGATCTTGTCAAGAAGTACACCA-GAAGATG
10042 G
65 G
** *
10043 -TTTCTCGGAA-AGGTTTCAGAAGCTGATCGGAAGACGATC
1 TTTTCTC--AACAATTTTCAGAAGATGATCGGAAGACGATC
10082 ACCGAAAGAC
Statistics
Matches: 413, Mismatches: 61, Indels: 28
0.82 0.12 0.06
Matches are distributed among these distances:
61 18 0.04
62 35 0.08
63 4 0.01
64 141 0.34
65 210 0.51
66 5 0.01
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (65 bp):
TTTTCTCAACAATTTTCAGAAGATGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGG
Found at i:10300 original size:25 final size:26
Alignment explanation
Indices: 10259--10307 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
10249 CAATCCTTTT
* *
10259 AAGATTGAATTGTAAGATAGTTCACG
1 AAGATTGAATTGGAAGACAGTTCACG
10285 AAGA-TGAATTGGAAGACAGTTCA
1 AAGATTGAATTGGAAGACAGTTCA
10308 AAGGATAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.27
Consensus pattern (26 bp):
AAGATTGAATTGGAAGACAGTTCACG
Found at i:10350 original size:50 final size:50
Alignment explanation
Indices: 10285--10433 Score: 237
Period size: 50 Copynumber: 3.0 Consensus size: 50
10275 ATAGTTCACG
*
10285 AAGA-TGAATTGGAAGACAGTTCAAAGGATAAGCGGAAAACGGTCCTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
* *
10334 AAGATTGAATTTGAAGACAGTTCAAAGGATAAGCGGATGACGGTCCTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
* * *
10384 AAGATTGAATTGGGAGACAGTTTAAAGGATAAGCGGAAGACGATCCTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
10434 TATATTGGAC
Statistics
Matches: 91, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
49 4 0.04
50 87 0.96
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.26
Consensus pattern (50 bp):
AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
Found at i:17794 original size:27 final size:27
Alignment explanation
Indices: 17737--17798 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
17727 GGAATTTTGG
* * * * *
17737 GGTCATTTGCATGTCCAGGGGCGTTTT
1 GGTCATTTGCACGTCCAAGGGCATCTC
*
17764 GGTCATTTGCACGTTCAAGGGCATCTC
1 GGTCATTTGCACGTCCAAGGGCATCTC
17791 GGTCATTT
1 GGTCATTT
17799 TAAGCACTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.15, C:0.21, G:0.29, T:0.35
Consensus pattern (27 bp):
GGTCATTTGCACGTCCAAGGGCATCTC
Found at i:19156 original size:22 final size:22
Alignment explanation
Indices: 19111--19172 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 22
19101 CGGCTGAGAA
* *
19111 AAGAAGAAGAAGCAAACGAGGG
1 AAGAAGAAGAAGCAAAAGAAGG
* *
19133 AAGAAGAAGAAGGAAAATAAGG
1 AAGAAGAAGAAGCAAAAGAAGG
*
19155 AA-AA-AAAAAG-AAAAGAAG
1 AAGAAGAAGAAGCAAAAGAAG
19173 CTCGACTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 7 0.21
20 5 0.15
21 2 0.06
22 20 0.59
ACGTcount: A:0.66, C:0.03, G:0.29, T:0.02
Consensus pattern (22 bp):
AAGAAGAAGAAGCAAAAGAAGG
Done.