Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015078.1 Corchorus olitorius cultivar O-4 contig15111, 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: 14909
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:520 original size:2 final size:2
Alignment explanation
Indices: 509--550 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
499 AGTTTAGACT
* * *
509 TA TA TA -A TA TA TA TA GA TA TA GA TA TA GA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
550 T
1 T
551 TATTACGGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (2 bp):
TA
Found at i:2196 original size:81 final size:79
Alignment explanation
Indices: 2063--2222 Score: 302
Period size: 81 Copynumber: 2.0 Consensus size: 79
2053 GCAGGGAAAA
2063 ATCCCCAATATTTTTTTTTCCTACGTAAGGAAGATTTTTGAGATCTTATTTTTAATTAAACCTGT
1 ATCCCCAATATTTTTTTTTCCTACGTAAGGAAGATTTTTGAGATCTTATTTTTAATTAAACCTGT
2128 TTAATTTAATTAAT
66 TTAATTTAATTAAT
2142 ATCCCCAATATTTTTTATTTTCCTACGTAAGGAAGATTTTTGAGATCTTATTTTTAATTAAACCT
1 ATCCCCAATA-TTTTT-TTTTCCTACGTAAGGAAGATTTTTGAGATCTTATTTTTAATTAAACCT
2207 GTTTAATTTAATTAAT
64 GTTTAATTTAATTAAT
2223 TTATTATTAT
Statistics
Matches: 79, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
79 10 0.13
80 5 0.06
81 64 0.81
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.48
Consensus pattern (79 bp):
ATCCCCAATATTTTTTTTTCCTACGTAAGGAAGATTTTTGAGATCTTATTTTTAATTAAACCTGT
TTAATTTAATTAAT
Found at i:2370 original size:22 final size:22
Alignment explanation
Indices: 2323--2383 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
2313 TTCAATATTT
*
2323 TTATGAAATTTTGATAACTATC
1 TTATGAAATTTTGATAACCATC
*
2345 TTATTAAATTTTGATAACCA-C
1 TTATGAAATTTTGATAACCATC
*
2366 GTTATGGAATTTTGATAA
1 -TTATGAAATTTTGATAA
2384 TTTACCTATG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 1 0.03
22 33 0.97
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.44
Consensus pattern (22 bp):
TTATGAAATTTTGATAACCATC
Found at i:2444 original size:23 final size:23
Alignment explanation
Indices: 2418--2472 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
2408 GATAACCTAA
*
2418 CTATGAAATTTTAATAAACCTTG
1 CTATGAAATTTTAATAAACCTTC
*
2441 CTATAAAATTTTAATAAACCTTC
1 CTATGAAATTTTAATAAACCTTC
2464 CTATGAAAT
1 CTATGAAAT
2473 GTTGTAACCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.38
Consensus pattern (23 bp):
CTATGAAATTTTAATAAACCTTC
Found at i:4316 original size:23 final size:21
Alignment explanation
Indices: 4201--4336 Score: 75
Period size: 21 Copynumber: 6.3 Consensus size: 21
4191 TGATAGCTAC
* *
4201 CCTATTAAATTTTGATAACC-A
1 CCTATGAAATTTT-ATAACCTT
4222 CC-ATGAAATTTTGATAA--TT
1 CCTATGAAATTTT-ATAACCTT
* * *
4241 ACCTATAAAATTGTGATAAAC-T
1 -CCTATGAAATT-TTATAACCTT
* * *
4263 CCATAAGAAACTTTGATAACCTA
1 CC-TATGAAA-TTTTATAACCTT
* *
4286 ACTATGAAATTTTAATAAACTTT
1 CCTATGAAATTTT-AT-AACCTT
4309 CCTATGAAATTTTATAACCTT
1 CCTATGAAATTTTATAACCTT
4330 CCTATGA
1 CCTATGA
4337 TTTTTGATAA
Statistics
Matches: 89, Mismatches: 15, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
20 16 0.18
21 30 0.34
22 24 0.27
23 19 0.21
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (21 bp):
CCTATGAAATTTTATAACCTT
Found at i:4333 original size:21 final size:22
Alignment explanation
Indices: 4181--4346 Score: 114
Period size: 22 Copynumber: 7.7 Consensus size: 22
4171 TGAATATTTT
* *
4181 TATGAAATTTTGAT-AGCTACCC
1 TATGAAATTTTGATAACCT-TCC
* *
4203 TATTAAATTTTGATAACC-ACC
1 TATGAAATTTTGATAACCTTCC
4224 -ATGAAATTTTGATAA--TTACC
1 TATGAAATTTTGATAACCTT-CC
* * *
4244 TATAAAATTGTGATAAAC-TCC
1 TATGAAATTTTGATAACCTTCC
* * **
4265 ATAAGAAACTTTGATAACCTAAC
1 -TATGAAATTTTGATAACCTTCC
* *
4288 TATGAAATTTTAATAAACTTTCC
1 TATGAAATTTTGAT-AACCTTCC
4311 TATGAAATTTT-ATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
*
4332 TATG-ATTTTTGATAA
1 TATGAAATTTTGATAA
4347 TCTCTCTGTG
Statistics
Matches: 112, Mismatches: 22, Indels: 21
0.72 0.14 0.14
Matches are distributed among these distances:
20 21 0.19
21 32 0.29
22 40 0.36
23 19 0.17
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:7291 original size:26 final size:27
Alignment explanation
Indices: 7232--7292 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 27
7222 CTAAATTTCC
*
7232 ATTATTTTAATAATGGATTAATTAAAAT
1 ATTA-TTTAATAATGGATCAATTAAAAT
*
7260 ATTATTTAATAAT-GA-CAATTTAAAT
1 ATTATTTAATAATGGATCAATTAAAAT
7285 ATATATTT
1 AT-TATTT
7293 GAAAAAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 10 0.33
26 7 0.23
27 9 0.30
28 4 0.13
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (27 bp):
ATTATTTAATAATGGATCAATTAAAAT
Found at i:9587 original size:20 final size:20
Alignment explanation
Indices: 9536--9590 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
9526 ATAAGTGGTC
*
9536 AAAATTTGAAGGTCATAACA
1 AAAATTTGAAGTTCATAACA
*
9556 AAAATTTAAAGTTCATAACA
1 AAAATTTGAAGTTCATAACA
9576 AAAATTTGAAGTTCA
1 AAAATTTGAAGTTCA
9591 GGAGATAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.29
Consensus pattern (20 bp):
AAAATTTGAAGTTCATAACA
Found at i:9903 original size:7 final size:7
Alignment explanation
Indices: 9891--9936 Score: 62
Period size: 7 Copynumber: 7.0 Consensus size: 7
9881 TCATATCTAG
9891 TCTTTTT
1 TCTTTTT
9898 TCTTTTT
1 TCTTTTT
9905 TCTTTTT
1 TCTTTTT
*
9912 T-TTTTC
1 TCTTTTT
9918 T-TTTTT
1 TCTTTTT
9924 TCTTTTT
1 TCTTTTT
9931 T-TTTTT
1 TCTTTTT
9937 GCACAAAGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
6 15 0.42
7 21 0.58
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TCTTTTT
Found at i:9904 original size:1 final size:1
Alignment explanation
Indices: 9893--9936 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
9883 ATATCTAGTC
* * * *
9893 TTTTTTCTTTTTTCTTTTTTTTTTCTTTTTTTCTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
9937 GCACAAAGTA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:9916 original size:18 final size:19
Alignment explanation
Indices: 9893--9935 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
9883 ATATCTAGTC
9893 TTTTTTC-TTTTTTCTTTT
1 TTTTTTCTTTTTTTCTTTT
9911 TTTTTTCTTTTTTTCTTTT
1 TTTTTTCTTTTTTTCTTTT
9930 TTTTTT
1 TTTTTT
9936 TGCACAAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (19 bp):
TTTTTTCTTTTTTTCTTTT
Found at i:11232 original size:2 final size:2
Alignment explanation
Indices: 11225--11279 Score: 87
Period size: 2 Copynumber: 28.5 Consensus size: 2
11215 ACAGAACATC
*
11225 AT AT AT AT AT AT GT AT AT AT AT -T AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11265 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
11280 ATTATGCTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 2 0.04
2 47 0.96
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11825 original size:28 final size:28
Alignment explanation
Indices: 11785--11844 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
11775 AAGTACAAGC
11785 CGCCTCCTGTAGCCCAGGAGCCAGGATG
1 CGCCTCCTGTAGCCCAGGAGCCAGGATG
*
11813 CGCCTCCTGTAGCCTAGGAGCCAGGATG
1 CGCCTCCTGTAGCCCAGGAGCCAGGATG
11841 CGCC
1 CGCC
11845 ACCATGTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.17, C:0.37, G:0.32, T:0.15
Consensus pattern (28 bp):
CGCCTCCTGTAGCCCAGGAGCCAGGATG
Done.