Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022252.1 Corchorus olitorius cultivar O-4 contig22285, 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: 4927
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.36
Found at i:1461 original size:22 final size:22
Alignment explanation
Indices: 1434--1973 Score: 187
Period size: 22 Copynumber: 24.8 Consensus size: 22
1424 ATTACACTAT
*
1434 TTTTGATGACC-TCCTTATGAAA
1 TTTTGATAACCTTCC-TATGAAA
1456 TTTTGATAACCTTCCTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* ** *
1478 TTTTAATAACGATACTAT-AGAA
1 TTTTGATAACCTTCCTATGA-AA
* **
1500 TTTTGAGAACCTTTTTAT-AAA
1 TTTTGATAACCTTCCTATGAAA
** * *
1521 TTTTTTTTAACATTCTTATGAAA
1 -TTTTGATAACCTTCCTATGAAA
* *
1544 TTTT-ATTAACC-TCTCTAAGGAA
1 TTTTGA-TAACCTTC-CTATGAAA
*
1566 TTTTGA-AGATC-TCACTATGAAA
1 TTTTGATA-ACCTTC-CTATGAAA
* *
1588 ATTTGATAA-CTTCCCAATGAAA
1 TTTTGATAACCTT-CCTATGAAA
** *
1610 TTTTGATAACCATTTTTATGAGA
1 TTTTGATAACC-TTCCTATGAAA
* *
1633 TGTTGATAACC-TCCATATGATA
1 TTTTGATAACCTTCC-TATGAAA
* * * *
1655 TATTGTTAACC-ACGTTATGAAA
1 TTTTGATAACCTTC-CTATGAAA
* * * *
1677 ATTTAAAAATC-TCCATATG-AA
1 TTTTGATAACCTTCC-TATGAAA
* *
1698 TTGTT-AGTAATC-ACACTATGAAA
1 TT-TTGA-TAACCTTC-CTATGAAA
* *
1721 TTTTGATAATC-ACACTATGAAA
1 TTTTGATAACCTTC-CTATGAAA
*
1743 TTGTGATAACC-TCGCTATGAAA
1 TTTTGATAACCTTC-CTATGAAA
* *
1765 TTTTGATAAACCTCCCTATAAAA
1 TTTTGAT-AACCTTCCTATGAAA
* *
1788 TTTTGACAACCTCCCTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* *
1810 TCTTGATAA-----CTA-CAAA
1 TTTTGATAACCTTCCTATGAAA
* **
1826 TTTTGATAATC-TCCTTATGATT
1 TTTTGATAACCTTCC-TATGAAA
* *
1848 TTTTGATAATCTCCCTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* * *
1870 TTTT-TTAA-CATACTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* *
1890 TTTTGATAACCCTCTTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* ** *
1912 TTTTGA-AAACTAAACTAAGAAA
1 TTTTGATAACCT-TCCTATGAAA
**
1934 TTTTGATAACCTTTATATGAAA
1 TTTTGATAACCTTCCTATGAAA
* *
1956 TTTTGATATCCTCCCTAT
1 TTTTGATAACCTTCCTAT
1974 TACTCCATAA
Statistics
Matches: 390, Mismatches: 94, Indels: 68
0.71 0.17 0.12
Matches are distributed among these distances:
16 11 0.03
17 3 0.01
20 14 0.04
21 23 0.06
22 282 0.72
23 54 0.14
24 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
TTTTGATAACCTTCCTATGAAA
Found at i:1806 original size:45 final size:45
Alignment explanation
Indices: 1713--1818 Score: 133
Period size: 45 Copynumber: 2.4 Consensus size: 45
1703 AGTAATCACA
* * * *
1713 CTATGAAATTTTGAT-AATCACACTATGAAATTGTGATAACCTCG
1 CTATGAAATTTTGATAAACCACACTATAAAATTGTGACAACCTCC
* * *
1757 CTATGAAATTTTGATAAACCTCCCTATAAAATTTTGACAACCTCC
1 CTATGAAATTTTGATAAACCACACTATAAAATTGTGACAACCTCC
*
1802 CTATGAAATCTTGATAA
1 CTATGAAATTTTGATAA
1819 CTACAAATTT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 15 0.28
45 38 0.72
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (45 bp):
CTATGAAATTTTGATAAACCACACTATAAAATTGTGACAACCTCC
Found at i:2117 original size:22 final size:22
Alignment explanation
Indices: 2056--2132 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
2046 AAATACCACA
* * *
2056 ATGAAATTTTGGTAATCACATTT
1 ATGAAATTTTGATAACCTC-TTT
*
2079 -TGAAAATTTGATAACCTCTTT
1 ATGAAATTTTGATAACCTCTTT
*
2100 ATGAAATTTTGATAACCTCTCT
1 ATGAAATTTTGATAACCTCTTT
2122 AT-ACAATTTTG
1 ATGA-AATTTTG
2133 TTGACAATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
21 4 0.09
22 42 0.91
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTCTTT
Found at i:2141 original size:12 final size:12
Alignment explanation
Indices: 2124--2149 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2114 ACCTCTCTAT
2124 ACAATTTTGTTG
1 ACAATTTTGTTG
2136 ACAATTTTGTTG
1 ACAATTTTGTTG
2148 AC
1 AC
2150 CCCTCTATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (12 bp):
ACAATTTTGTTG
Found at i:2180 original size:22 final size:21
Alignment explanation
Indices: 2155--2236 Score: 76
Period size: 22 Copynumber: 3.8 Consensus size: 21
2145 TTGACCCCTC
*
2155 TATGAAATTTTGATATTCACAT
1 TATGAAATTTTGATA-ACACAT
* * *
2177 TATGTAATTTTGATAACCTCGT
1 TATGAAATTTTGATAA-CACAT
*
2199 TTTGAAATTTTGATAACA-ACT
1 TATGAAATTTTGATAACACA-T
2220 CTATGAAATTTTGATAA
1 -TATGAAATTTTGATAA
2237 TTTTCCTATA
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
21 2 0.04
22 46 0.96
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.44
Consensus pattern (21 bp):
TATGAAATTTTGATAACACAT
Found at i:2372 original size:22 final size:21
Alignment explanation
Indices: 2355--2504 Score: 104
Period size: 22 Copynumber: 6.9 Consensus size: 21
2345 TTATAACCTT
2355 CATATGAAATTTTGATAACCA
1 CATATGAAATTTTGATAACCA
**
2376 CACTAAAAAATTTTGATAACCA
1 CA-TATGAAATTTTGATAACCA
* *
2398 CACTATGAAATATTGATAACCTC
1 CA-TATGAAATTTTGATAACC-A
** * * *
2421 CCCATGAAATATTAATAACCTC
1 CATATGAAATTTTGATAACC-A
* *
2443 CTTATGAAATTTTGTTAACCA
1 CATATGAAATTTTGATAACCA
*
2464 CACTATGAAATTCTT-ATAACCT
1 CA-TATGAAATT-TTGATAACCA
* *
2486 CGCTATGACATTTTGATAA
1 C-ATATGAAATTTTGATAA
2505 TATCTCTGAT
Statistics
Matches: 103, Mismatches: 20, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
21 5 0.05
22 95 0.92
23 3 0.03
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.33
Consensus pattern (21 bp):
CATATGAAATTTTGATAACCA
Found at i:2405 original size:44 final size:44
Alignment explanation
Indices: 2343--2740 Score: 231
Period size: 44 Copynumber: 9.2 Consensus size: 44
2333 AAATTGTGAC
**
2343 TTTT-ATAACCTTCA-TATGAAATTTTGATAACCACACTAAAAAA
1 TTTTGATAACC-TCACTATGAAATTTTGATAACCACACTATGAAA
* * * * *
2386 TTTTGATAACCACACTATGAAATATTGATAACCTCCCCATGAAA
1 TTTTGATAACCTCACTATGAAATTTTGATAACCACACTATGAAA
* * *
2430 TATTAATAACCTC-CTTATGAAATTTTGTTAACCACACTATGAAA
1 TTTTGATAACCTCAC-TATGAAATTTTGATAACCACACTATGAAA
* *
2474 TTCTT-ATAACCTCGCTATGACATTTTGAT----A-A-TAT----
1 TT-TTGATAACCTCACTATGAAATTTTGATAACCACACTATGAAA
* * *** * *
2508 CTCTGATAACCTTTTTATAAAATTGTGATAACCACACTATGAAA
1 TTTTGATAACCTCACTATGAAATTTTGATAACCACACTATGAAA
** * * ***
2552 TTTCAATAACCTTCA-TAAGAAATTTTAATAACTTGATCTTATGAAA
1 TTTTGATAACC-TCACTATGAAATTTTGATAACCACA-C-TATGAAA
* * * *
2598 TTTTGGTAACCACACTATGAAATTTTGATAACCTTC-CCATGAAA
1 TTTTGATAACCTCACTATGAAATTTTGATAACC-ACACTATGAAA
* * *
2642 TTTTGATAACTTC-CATATGAAATTTTGGTAACCACACTATGGAA
1 TTTTGATAACCTCAC-TATGAAATTTTGATAACCACACTATGAAA
* * * * *
2686 TTTCGATAACCT-TCTCATGAAATTATAATAACCATC-TTATGAAA
1 TTTTGATAACCTCACT-ATGAAATTTTGATAACCA-CACTATGAAA
2730 TTTTGATAACC
1 TTTTGATAACC
2741 ACATAGAGAC
Statistics
Matches: 266, Mismatches: 63, Indels: 51
0.70 0.17 0.13
Matches are distributed among these distances:
33 1 0.00
34 19 0.07
38 4 0.02
39 2 0.01
40 4 0.02
43 10 0.04
44 186 0.70
45 9 0.03
46 30 0.11
47 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (44 bp):
TTTTGATAACCTCACTATGAAATTTTGATAACCACACTATGAAA
Found at i:2428 original size:66 final size:66
Alignment explanation
Indices: 2347--2743 Score: 300
Period size: 66 Copynumber: 5.8 Consensus size: 66
2337 TGTGACTTTT
** * **
2347 ATAACCTTCATATGAAATTTTGATAACCACAC-TAAAAAATTTTGATAACCACACTATGAAATAT
1 ATAACCTTCCCATGAAATTTTAATAACCACACTTATGAAATTTTGATAACCACACTATGAAAT-T
2411 TG
65 TG
* * * *
2413 ATAACCTCCCCATGAAATATTAATAACCTC-CTTATGAAATTTTGTTAACCACACTATGAAATTC
1 ATAACCTTCCCATGAAATTTTAATAACCACACTTATGAAATTTTGATAACCACACTATGAAATT-
*
2477 TT
65 TG
* * * * * *
2479 ATAACC-TCGCTATGACATTTTGATAATATCTCTGATAACCTTTTTATAAAATTGTGATAACCAC
1 ATAACCTTC-CCATGA-AATTT--TAATAAC-C--A-CA-C---TTATGAAATTTTGATAACCAC
*
2543 ACTATGAAATTTCA
54 ACTATGAAATTT-G
** * *** *
2557 ATAACCTTCATAAGAAATTTTAATAACTTGATCTTATGAAATTTTGGTAACCACACTATGAAATT
1 ATAACCTTCCCATGAAATTTTAATAACCACA-CTTATGAAATTTTGATAACCACACTATGAAA-T
2622 TTG
64 TTG
* ** * * *
2625 ATAACCTTCCCATGAAATTTTGATAACTTC-CATATGAAATTTTGGTAACCACACTATGGAATTT
1 ATAACCTTCCCATGAAATTTTAATAACCACACTTATGAAATTTTGATAACCACACTATGAAATTT
2689 CG
66 -G
* * *
2691 ATAACCTTCTCATGAAATTATAATAACCA-TCTTATGAAATTTTGATAACCACA
1 ATAACCTTCCCATGAAATTTTAATAACCACACTTATGAAATTTTGATAACCACA
2744 TAGAGACAAG
Statistics
Matches: 264, Mismatches: 47, Indels: 40
0.75 0.13 0.11
Matches are distributed among these distances:
65 6 0.02
66 138 0.52
67 3 0.01
68 52 0.20
69 9 0.03
70 1 0.00
71 2 0.01
75 7 0.03
77 5 0.02
78 39 0.15
79 2 0.01
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (66 bp):
ATAACCTTCCCATGAAATTTTAATAACCACACTTATGAAATTTTGATAACCACACTATGAAATTT
G
Found at i:2522 original size:23 final size:22
Alignment explanation
Indices: 2496--2540 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
2486 CGCTATGACA
*
2496 TTTTGATAATATCTCTGATAACC
1 TTTTGATAAAAT-TCTGATAACC
* *
2519 TTTTTATAAAATTGTGATAACC
1 TTTTGATAAAATTCTGATAACC
2541 ACACTATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.44
Consensus pattern (22 bp):
TTTTGATAAAATTCTGATAACC
Found at i:2552 original size:22 final size:22
Alignment explanation
Indices: 2527--2743 Score: 140
Period size: 22 Copynumber: 9.8 Consensus size: 22
2517 CCTTTTTATA
*
2527 AAATTGTGATAACCACACTATG
1 AAATTTTGATAACCACACTATG
** * *
2549 AAATTTCAATAACCTTCA-TAAG
1 AAATTTTGATAACC-ACACTATG
* ***
2571 AAATTTTAATAACTTGATCTTATG
1 AAATTTTGATAACCACA-C-TATG
*
2595 AAATTTTGGTAACCACACTATG
1 AAATTTTGATAACCACACTATG
* *
2617 AAATTTTGATAACCTTC-CCATG
1 AAATTTTGATAACC-ACACTATG
2639 AAATTTTGATAACTTC-CA-TATG
1 AAATTTTGATAAC--CACACTATG
*
2661 AAATTTTGGTAACCACACTATG
1 AAATTTTGATAACCACACTATG
* * **
2683 GAATTTCGATAACC-TTCTCATG
1 AAATTTTGATAACCACACT-ATG
* * *
2705 AAATTATAATAACCATC-TTATG
1 AAATTTTGATAACCA-CACTATG
2727 AAATTTTGATAACCACA
1 AAATTTTGATAACCACA
2744 TAGAGACAAG
Statistics
Matches: 149, Mismatches: 32, Indels: 28
0.71 0.15 0.13
Matches are distributed among these distances:
20 1 0.01
21 7 0.05
22 120 0.81
23 5 0.03
24 16 0.11
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATG
Found at i:2577 original size:78 final size:78
Alignment explanation
Indices: 2435--2582 Score: 174
Period size: 78 Copynumber: 1.9 Consensus size: 78
2425 TGAAATATTA
* * * * * * *
2435 ATAACCTCCTTATGAAATTTTGTTAACCACACTATGAAATTCTTATAACCTCGCTATGACATTTT
1 ATAACCTCCTTATAAAATTGTGATAACCACACTATGAAATTCTAATAACCTCGATAAGAAATTTT
*
2500 GATAATATCTCTG
66 AATAATATCTCTG
**
2513 ATAACCTTTTTATAAAATTGTGATAACCACACTATGAAATT-TCAATAACCTTC-ATAAGAAATT
1 ATAACCTCCTTATAAAATTGTGATAACCACACTATGAAATTCT-AATAACC-TCGATAAGAAATT
2576 TTAATAA
64 TTAATAA
2583 CTTGATCTTA
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
77 1 0.02
78 55 0.95
79 2 0.03
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (78 bp):
ATAACCTCCTTATAAAATTGTGATAACCACACTATGAAATTCTAATAACCTCGATAAGAAATTTT
AATAATATCTCTG
Found at i:4753 original size:3 final size:3
Alignment explanation
Indices: 4745--4779 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
4735 AGACAAAGAA
4745 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
4780 AATCTATACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Done.