Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024478.1 Corchorus olitorius cultivar O-4 contig24511, 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: 13828
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.36
Found at i:2890 original size:21 final size:21
Alignment explanation
Indices: 2862--2901 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2852 AATTTGTCTG
*
2862 TAAATATAT-AGTTTTTTTTA
1 TAAATATATAAGTATTTTTTA
2882 TAAACTATATAAGTATTTTT
1 TAAA-TATATAAGTATTTTT
2902 AGTACAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 5 0.29
22 8 0.47
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (21 bp):
TAAATATATAAGTATTTTTTA
Found at i:9075 original size:14 final size:14
Alignment explanation
Indices: 9056--9084 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
9046 TGGTTCCCTC
9056 TATTATTAAATGAA
1 TATTATTAAATGAA
9070 TATTATTAAATGAA
1 TATTATTAAATGAA
9084 T
1 T
9085 GGGGTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (14 bp):
TATTATTAAATGAA
Found at i:9372 original size:22 final size:22
Alignment explanation
Indices: 9323--9378 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
9313 TTATGACCTC
* *
9323 CTTATGAAATATTGATAACATT
1 CTTATGAAATTTTAATAACATT
*
9345 CCTATGAAATTTTAATAACGATT
1 CTTATGAAATTTTAATAAC-ATT
*
9368 -TTATGGAATTT
1 CTTATGAAATTT
9379 CGAGAACCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 25 0.89
23 3 0.11
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.43
Consensus pattern (22 bp):
CTTATGAAATTTTAATAACATT
Found at i:9466 original size:22 final size:22
Alignment explanation
Indices: 9414--9467 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
9404 TAAACCTTCT
* *
9414 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGTAAACCTCAC
* *
9436 TAAGGAATTTTG-AAGACCTCAC
1 TATGAAATTTTGTAA-ACCTCAC
9458 TATGAAATTT
1 TATGAAATTT
9468 GTTTATTTCC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGTAAACCTCAC
Found at i:9533 original size:22 final size:23
Alignment explanation
Indices: 9480--9540 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
9470 TTATTTCCCA
*
9480 ATGAAATTTTGATAACCAACACT
1 ATGAAATATTGATAACCAACACT
**
9503 ATGAAATATTGATAACCTCCA-T
1 ATGAAATATTGATAACCAACACT
*
9525 ATGATATATTGATAAC
1 ATGAAATATTGATAAC
9541 TACGTTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 16 0.47
23 18 0.53
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.33
Consensus pattern (23 bp):
ATGAAATATTGATAACCAACACT
Found at i:9605 original size:21 final size:22
Alignment explanation
Indices: 9568--9626 Score: 77
Period size: 21 Copynumber: 2.7 Consensus size: 22
9558 AAAACCTCCA
*
9568 TATG-AATTGTTATTAATCACAC
1 TATGAAATTGTGA-TAATCACAC
*
9590 TTTGAAATT-TGATAATCACAC
1 TATGAAATTGTGATAATCACAC
9611 TATGAAATTGTGATAA
1 TATGAAATTGTGATAA
9627 CCTTGCTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 17 0.53
22 11 0.34
23 4 0.12
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (22 bp):
TATGAAATTGTGATAATCACAC
Found at i:9675 original size:15 final size:15
Alignment explanation
Indices: 9655--9684 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9645 ATAAGTTTTC
9655 CTATAAAATTATGAT
1 CTATAAAATTATGAT
*
9670 CTATAAAATTTTGAT
1 CTATAAAATTATGAT
9685 AACCTCCTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (15 bp):
CTATAAAATTATGAT
Found at i:9763 original size:22 final size:23
Alignment explanation
Indices: 9738--9882 Score: 112
Period size: 22 Copynumber: 6.6 Consensus size: 23
9728 CCCTATGATT
9738 TTTTGATAACCTCATC-ATGAAA
1 TTTTGATAACCTCATCTATGAAA
* * * *
9760 TTTTGTTAATCTC-CCAATGAAA
1 TTTTGATAACCTCATCTATGAAA
9782 TTTTGAT---CTACATACTATGAAA
1 TTTTGATAACCT-CAT-CTATGAAA
9804 TTTTGATAACC-C-TCTTATGAAA
1 TTTTGATAACCTCATC-TATGAAA
* * *
9826 TTTTGA-AAACTAAACTATGAAA
1 TTTTGATAACCTCATCTATGAAA
9848 TTTTGATAACCT--TCATATGAAA
1 TTTTGATAACCTCATC-TATGAAA
*
9870 TTTTGATATCCTC
1 TTTTGATAACCTC
9883 CCCGAAATGT
Statistics
Matches: 98, Mismatches: 12, Indels: 25
0.73 0.09 0.19
Matches are distributed among these distances:
19 2 0.02
20 1 0.01
21 6 0.06
22 82 0.84
23 6 0.06
25 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (23 bp):
TTTTGATAACCTCATCTATGAAA
Found at i:10026 original size:22 final size:22
Alignment explanation
Indices: 10001--10364 Score: 122
Period size: 22 Copynumber: 16.6 Consensus size: 22
9991 TATCACATTT
*
10001 TGAAAATTTGATAACCTCCTTA
1 TGAAATTTTGATAACCTCCTTA
* *
10023 TGAAATTTTGATAA-TTTCTCTA
1 TGAAATTTTGATAACCTCCT-TA
* * *
10045 TAAAATTTTGTTGA-CTCCTTTA
1 TGAAATTTTGATAACCTCC-TTA
* * *
10067 TGAAATTTTGATAATCACATTA
1 TGAAATTTTGATAACCTCCTTA
* * *
10089 TGTAATTTTGATAACCTCGTTT
1 TGAAATTTTGATAACCTCCTTA
**
10111 TGAAATTTTGATAACAACAC-TA
1 TGAAATTTTGATAACCTC-CTTA
* *
10133 TAAAATTTTGATAATCTTCC-TA
1 TGAAATTTTGATAA-CCTCCTTA
* * *
10155 T-AAATTTTTATAATCTGATCTCTA
1 TGAAATTTTGATAACCT--CCT-TA
* *
10179 CGAAATTTCGATAA--TCACTCTA
1 TGAAATTTTGATAACCTC-CT-TA
*
10201 TGAAA-TTTGATAACCTTC-TA
1 TGAAATTTTGATAACCTCCTTA
*
10221 TCAAATTTT-AGT-A-CTCCTTA
1 TGAAATTTTGA-TAACCTCCTTA
* * *
10241 TGAAATTGAGACTTTTATAACCTTCATA
1 TGAAA-T-----TTTGATAACCTCCTTA
**
10269 TGAAATTTTGATAACCTCCCCA
1 TGAAATTTTGATAACCTCCTTA
*
10291 TG-----TAG-TAACCTCCTTA
1 TGAAATTTTGATAACCTCCTTA
* *
10307 TGAAATTTTGTTAACCACAC-TA
1 TGAAATTTTGATAACCTC-CTTA
10329 TGAAATTCTT-ATAACCT-CTCTA
1 TGAAATT-TTGATAACCTCCT-TA
*
10351 TGACATTTTGATAA
1 TGAAATTTTGATAA
10365 TCTCTTTGAT
Statistics
Matches: 252, Mismatches: 54, Indels: 72
0.67 0.14 0.19
Matches are distributed among these distances:
16 11 0.04
17 2 0.01
19 3 0.01
20 16 0.06
21 30 0.12
22 151 0.60
23 10 0.04
24 2 0.01
25 10 0.04
26 4 0.02
27 3 0.01
28 10 0.04
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCCTTA
Found at i:10096 original size:44 final size:45
Alignment explanation
Indices: 9978--10146 Score: 170
Period size: 44 Copynumber: 3.8 Consensus size: 45
9968 GAAATACCAC
* * *
9978 TATGAAATTTTGGT-ATCACATTTTGAAAATTTGATAACCTCC-T
1 TATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCCTT
** * * *
10021 TATGAAATTTTGATAATTTC-TCTATAAAATTTTGTTGA-CTCCTT
1 TATGAAATTTTGATAATCACAT-TATGAAATTTTGATAACCTCCTT
* *
10065 TATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGTT
1 TATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCCTT
* *
10110 T-TGAAATTTTGATAA-CAACACTATAAAATTTTGATAA
1 TATGAAATTTTGATAATC-ACATTATGAAATTTTGATAA
10147 TCTTCCTATA
Statistics
Matches: 102, Mismatches: 18, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
43 19 0.19
44 76 0.75
45 7 0.07
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (45 bp):
TATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCCTT
Found at i:10103 original size:88 final size:87
Alignment explanation
Indices: 9978--10142 Score: 231
Period size: 88 Copynumber: 1.9 Consensus size: 87
9968 GAAATACCAC
* * *** *
9978 TATGAAATTTTGGTATCACATTTTGAAAATTTGATAACCTCCTTATGAAATTTTGATAATTTCTC
1 TATGAAATTTTGATATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAACAC
10043 TATAAAATTTTGTTGACTCCTT
66 TATAAAATTTTGTTGACTCCTT
* * * *
10065 TATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGTTTTGAAATTTTGATAACAACA
1 TATGAAATTTTGAT-ATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAACA
10130 CTATAAAATTTTG
65 CTATAAAATTTTG
10143 ATAATCTTCC
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
87 13 0.19
88 54 0.81
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (87 bp):
TATGAAATTTTGATATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAACAC
TATAAAATTTTGTTGACTCCTT
Found at i:10412 original size:22 final size:21
Alignment explanation
Indices: 10387--10624 Score: 197
Period size: 22 Copynumber: 10.8 Consensus size: 21
10377 CCTTTTTATA
*
10387 AAATTGTGATAACCACACTATG
1 AAATTTTGATAACCAC-CTATG
** * *
10409 AAATTTCAATAACCTTCCTAAG
1 AAATTTTGATAACC-ACCTATG
*
10431 AAATTTTAATAACCTGATCCTATG
1 AAATTTTGATAACC--A-CCTATG
*
10455 AAATTTTGGTAACCACGCTATG
1 AAATTTTGATAACCAC-CTATG
*
10477 AAATTTTGGTAACCACGCTATG
1 AAATTTTGATAACCAC-CTATG
* *
10499 AAATTTTGATAACCTTCCCATG
1 AAATTTTGATAACC-ACCTATG
**
10521 AAATTTTGATAACTTCCATATG
1 AAATTTTGATAACCACC-TATG
*
10543 AAATTTTGGTAACCACACTATG
1 AAATTTTGATAACCAC-CTATG
* * *
10565 GAGTTTTGATAACCTCCTTATG
1 AAATTTTGATAACCACC-TATG
* * *
10587 AAATTATAATAACCATCTTATG
1 AAATTTTGATAACCA-CCTATG
10609 AAATTTTGATAACCAC
1 AAATTTTGATAACCAC
10625 ATAGAGACAA
Statistics
Matches: 176, Mismatches: 31, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
21 6 0.03
22 149 0.85
23 4 0.02
24 17 0.10
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.34
Consensus pattern (21 bp):
AAATTTTGATAACCACCTATG
Found at i:10480 original size:68 final size:66
Alignment explanation
Indices: 10387--10533 Score: 170
Period size: 68 Copynumber: 2.2 Consensus size: 66
10377 CCTTTTTATA
* *
10387 AAATTGTGATAACCACACTATGAAATTTCAATAACCTTC-CTAAGAAATTTTAATAACCTGATCC
1 AAATTTTGATAACCACACTATGAAATTTCAATAACC-ACGCTAAGAAATTTTAATAACCT--TCC
*
10451 TATG
63 CATG
* * *** * *
10455 AAATTTTGGTAACCACGCTATGAAATTTTGGTAACCACGCTATGAAATTTTGATAACCTTCCCAT
1 AAATTTTGATAACCACACTATGAAATTTCAATAACCACGCTAAGAAATTTTAATAACCTTCCCAT
10520 G
66 G
10521 AAATTTTGATAAC
1 AAATTTTGATAAC
10534 TTCCATATGA
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
66 18 0.27
67 1 0.01
68 48 0.72
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (66 bp):
AAATTTTGATAACCACACTATGAAATTTCAATAACCACGCTAAGAAATTTTAATAACCTTCCCAT
G
Found at i:10827 original size:20 final size:20
Alignment explanation
Indices: 10789--10827 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
10779 TATTGACATT
10789 TAAAAAATTGAAATTAAAAG
1 TAAAAAATTGAAATTAAAAG
*
10809 TAAAATATT-AAATTCAAAA
1 TAAAAAATTGAAATT-AAAA
10828 AATAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAG
Done.