Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024098.1 Corchorus olitorius cultivar O-4 contig24131, 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: 4645
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Found at i:364 original size:22 final size:22
Alignment explanation
Indices: 320--416 Score: 87
Period size: 22 Copynumber: 4.5 Consensus size: 22
310 CATTGTTAGG
*
320 TTATC-AAAGTTTATTATGG-AA
1 TTATCAAAATTTTA-TATGGTAA
*
341 TTTATCACAATTTTATA-GGTAA
1 -TTATCAAAATTTTATATGGTAA
* *
363 TTATCAAAATTTCATATGGTAG
1 TTATCAAAATTTTATATGGTAA
* *
385 TTATCAAAA-TTT-TAGGGTAG
1 TTATCAAAATTTTATATGGTAA
405 TTATCAAAATTT
1 TTATCAAAATTT
417 CATAAAAATA
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
20 16 0.25
21 20 0.31
22 22 0.34
23 6 0.09
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.43
Consensus pattern (22 bp):
TTATCAAAATTTTATATGGTAA
Found at i:368 original size:21 final size:21
Alignment explanation
Indices: 342--416 Score: 98
Period size: 20 Copynumber: 3.6 Consensus size: 21
332 ATTATGGAAT
* *
342 TTATCACAATTTTATAGGTAA
1 TTATCAAAATTTTATAGGTAG
*
363 TTATCAAAATTTCATATGGTAG
1 TTATCAAAATTTTATA-GGTAG
*
385 TTATCAAAATTTTA-GGGTAG
1 TTATCAAAATTTTATAGGTAG
405 TTATCAAAATTT
1 TTATCAAAATTT
417 CATAAAAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
20 17 0.35
21 14 0.29
22 17 0.35
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (21 bp):
TTATCAAAATTTTATAGGTAG
Found at i:381 original size:43 final size:42
Alignment explanation
Indices: 320--420 Score: 123
Period size: 43 Copynumber: 2.4 Consensus size: 42
310 CATTGTTAGG
* * *
320 TTATCAAAGTTT-ATTATGGAATTTATCACAATTTTATAGGTAA
1 TTATCAAAATTTCA-TATGGAAGTTATCAAAATTTTA-AGGTAA
* * *
363 TTATCAAAATTTCATATGGTAGTTATCAAAATTTTAGGGTAG
1 TTATCAAAATTTCATATGGAAGTTATCAAAATTTTAAGGTAA
405 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
421 AAAATATTCA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
42 20 0.39
43 30 0.59
44 1 0.02
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.43
Consensus pattern (42 bp):
TTATCAAAATTTCATATGGAAGTTATCAAAATTTTAAGGTAA
Found at i:543 original size:55 final size:55
Alignment explanation
Indices: 484--594 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
474 ACTAATATAT
484 ATATATATATATATAAATTTTTGAACGTTGGCATTTAAAAAAGGCAAATAATACA
1 ATATATATATATATAAATTTTTGAACGTTGGCATTTAAAAAAGGCAAATAATACA
539 ATATATATATATATAAATTTTTGAACGTTGGCATTTAAAAAAGGCAAATAATACA
1 ATATATATATATATAAATTTTTGAACGTTGGCATTTAAAAAAGGCAAATAATACA
594 A
1 A
595 AACACCGGCG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.34
Consensus pattern (55 bp):
ATATATATATATATAAATTTTTGAACGTTGGCATTTAAAAAAGGCAAATAATACA
Found at i:1008 original size:22 final size:22
Alignment explanation
Indices: 967--1009 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
957 GACAAACTTG
**
967 TAACCTAAATGACCTGAGAAGT
1 TAACCTAAATGACCCAAGAAGT
*
989 TAACCTGAATGACCCAAGAAG
1 TAACCTAAATGACCCAAGAAG
1010 GCTAAGAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.19
Consensus pattern (22 bp):
TAACCTAAATGACCCAAGAAGT
Found at i:1877 original size:31 final size:31
Alignment explanation
Indices: 1839--1897 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1829 TATGCTAGAC
*
1839 AAATAAGGATATAATATACGTTTCAAAAATT
1 AAATAAGGATATAATAGACGTTTCAAAAATT
*
1870 AAATAAGGGTATAATAGACGTTTCAAAA
1 AAATAAGGATATAATAGACGTTTCAAAA
1898 CTTTTACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.51, C:0.07, G:0.14, T:0.29
Consensus pattern (31 bp):
AAATAAGGATATAATAGACGTTTCAAAAATT
Found at i:2736 original size:21 final size:21
Alignment explanation
Indices: 2711--2780 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
2701 TTAATTACTC
2711 AAAAAGTTATAACGGTTATGAA
1 AAAAAGTTATAACGGTTATG-A
*
2733 AAAAAG-T-TAA---TTACT-C
1 AAAAAGTTATAACGGTTA-TGA
*
2749 AAAAAGCTATAACGGTTATGA
1 AAAAAGTTATAACGGTTATGA
2770 AAAAAGTTATA
1 AAAAAGTTATA
2781 TATGTATCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 15
0.68 0.05 0.27
Matches are distributed among these distances:
16 6 0.16
17 4 0.11
18 4 0.11
20 4 0.11
21 14 0.37
22 6 0.16
ACGTcount: A:0.51, C:0.07, G:0.14, T:0.27
Consensus pattern (21 bp):
AAAAAGTTATAACGGTTATGA
Found at i:2744 original size:38 final size:37
Alignment explanation
Indices: 2701--2778 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 37
2691 TTTACAATAC
*
2701 TTAATTACTCAAAAAGTTATAACGGTTATGAAAAAAAG
1 TTAATTACTCAAAAAGCTATAACGGTTATG-AAAAAAG
2739 TTAATTACTCAAAAAGCTATAACGGTTATGAAAAAAG
1 TTAATTACTCAAAAAGCTATAACGGTTATGAAAAAAG
2776 TTA
1 TTA
2779 TATATGTATC
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 10 0.26
38 29 0.74
ACGTcount: A:0.49, C:0.09, G:0.13, T:0.29
Consensus pattern (37 bp):
TTAATTACTCAAAAAGCTATAACGGTTATGAAAAAAG
Found at i:3381 original size:70 final size:70
Alignment explanation
Indices: 3268--3412 Score: 272
Period size: 70 Copynumber: 2.1 Consensus size: 70
3258 TAACTCCGAA
3268 ACACAACATATGAGCATTGATTACACAAATAACACATTCGAAATAAACATTTTCTCCAAAACAAC
1 ACACAACATATGAGCATTGATTACACAAATAACACATTCGAAATAAACATTTTCTCCAAAACAAC
*
3333 GTTCT
66 GTTCG
*
3338 ACACAACATATGAGCATTGATTACACAAATAACACATTTGAAATAAACATTTTCTCCAAAACAAC
1 ACACAACATATGAGCATTGATTACACAAATAACACATTCGAAATAAACATTTTCTCCAAAACAAC
3403 GTTCG
66 GTTCG
3408 ACACA
1 ACACA
3413 CAAAAATGCA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 73 1.00
ACGTcount: A:0.45, C:0.23, G:0.08, T:0.25
Consensus pattern (70 bp):
ACACAACATATGAGCATTGATTACACAAATAACACATTCGAAATAAACATTTTCTCCAAAACAAC
GTTCG
Found at i:3872 original size:22 final size:22
Alignment explanation
Indices: 3798--3931 Score: 111
Period size: 22 Copynumber: 6.3 Consensus size: 22
3788 ATAATGATGC
* *
3798 GAAAATTTGATAA-CATCATTAT
1 GAAATTTTGATAATCA-CACTAT
*
3820 GAAATTTCGAT-A--AC-CTAT
1 GAAATTTTGATAATCACACTAT
* *
3838 GAAAATTTT-ATAAACACACTGT
1 G-AAATTTTGATAATCACACTAT
* *
3860 GAAATTTTGATAACCAAACTAT
1 GAAATTTTGATAATCACACTAT
*
3882 GAAATTTTGATAATCTC-CATAT
1 GAAATTTTGATAATCACAC-TAT
3904 GAAATTTTGATAATCACACTAT
1 GAAATTTTGATAATCACACTAT
*
3926 AAAATT
1 GAAATT
3932 GGTAACCGCA
Statistics
Matches: 91, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
18 6 0.07
19 8 0.09
20 1 0.01
21 11 0.12
22 64 0.70
23 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (22 bp):
GAAATTTTGATAATCACACTAT
Found at i:4178 original size:22 final size:21
Alignment explanation
Indices: 4124--4225 Score: 75
Period size: 22 Copynumber: 4.6 Consensus size: 21
4114 ACCCTCCTCC
*
4124 CTATAAAATTTTGATAA-CTA
1 CTATAAAATTTTGATAACCTT
4144 C-ACTACAAATTTTGATAACCTT
1 CTA-TA-AAATTTTGATAACCTT
* *
4166 CGTATAAAATTTTGTTAACGACACT
1 C-TATAAAATTTTGATAAC--C-TT
4191 CTA-AGAAATTTTGATAACCTTT
1 CTATA-AAATTTTGATAACC-TT
*
4213 TTATAAAATTTTG
1 CTATAAAATTTTG
4226 GCAACGTCTG
Statistics
Matches: 65, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
19 1 0.02
20 3 0.05
21 12 0.18
22 27 0.42
23 4 0.06
24 16 0.25
25 2 0.03
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (21 bp):
CTATAAAATTTTGATAACCTT
Found at i:4218 original size:46 final size:43
Alignment explanation
Indices: 4125--4225 Score: 130
Period size: 46 Copynumber: 2.3 Consensus size: 43
4115 CCCTCCTCCC
*
4125 TATAAAATTTTGATAACTACACTACAAATTTTGATAACCTTCG
1 TATAAAATTTTGATAACGACACTACAAATTTTGATAACCTTCG
* * **
4168 TATAAAATTTTGTTAACGACACTCTAAGAAATTTTGATAACCTTTT
1 TATAAAATTTTGATAACGACA--CT-ACAAATTTTGATAACCTTCG
4214 TATAAAATTTTG
1 TATAAAATTTTG
4226 GCAACGTCTG
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
43 19 0.38
45 2 0.04
46 29 0.58
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.41
Consensus pattern (43 bp):
TATAAAATTTTGATAACGACACTACAAATTTTGATAACCTTCG
Found at i:4261 original size:22 final size:23
Alignment explanation
Indices: 4236--4335 Score: 84
Period size: 22 Copynumber: 4.5 Consensus size: 23
4226 GCAACGTCTG
*
4236 TATGGAATTTTGATAA-CTACAC
1 TATGAAATTTTGATAACCTACAC
** *
4258 TATGACGTTTTGATAACCTCCA-
1 TATGAAATTTTGATAACCTACAC
*
4280 TATGAAATTTT-AGTAAAC-ACAC
1 TATGAAATTTTGA-TAACCTACAC
* *
4302 TATGAAAATTTGATAACCTTC-C
1 TATGAAATTTTGATAACCTACAC
*
4324 TATGTAATTTTG
1 TATGAAATTTTG
4336 GTTTGATTGA
Statistics
Matches: 60, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
21 3 0.05
22 51 0.85
23 6 0.10
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (23 bp):
TATGAAATTTTGATAACCTACAC
Found at i:4289 original size:44 final size:45
Alignment explanation
Indices: 4236--4335 Score: 109
Period size: 44 Copynumber: 2.3 Consensus size: 45
4226 GCAACGTCTG
* ***
4236 TATGGAATTTTGA-T-AACTACACTATGACGTTTTGATAACC-TCC
1 TATGAAATTTTGAGTAAAC-ACACTATGAAAATTTGATAACCTTCC
4279 ATATGAAATTTT-AGTAAACACACTATGAAAATTTGATAACCTTCC
1 -TATGAAATTTTGAGTAAACACACTATGAAAATTTGATAACCTTCC
*
4324 TATGTAATTTTG
1 TATGAAATTTTG
4336 GTTTGATTGA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
43 1 0.02
44 40 0.85
45 6 0.13
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (45 bp):
TATGAAATTTTGAGTAAACACACTATGAAAATTTGATAACCTTCC
Done.