Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006792.1 Corchorus capsularis cultivar CVL-1 contig06813, 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: 41756
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:15 original size:2 final size:2
Alignment explanation
Indices: 10--34 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1 GTGTGTGTC
10 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
35 CCATATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:458 original size:29 final size:28
Alignment explanation
Indices: 378--460 Score: 91
Period size: 27 Copynumber: 3.0 Consensus size: 28
368 TACATAAAAT
* * *
378 TATATTTCAATAATAGTATAATTA-AAA
1 TATATTTTAAAAATAGTACAATTAGAAA
*
405 TATATTTTAATAAT-GT-CAATTTAGAAA
1 TATATTTTAAAAATAGTACAA-TTAGAAA
432 TATATTTTAAAAAATAGTACAATTAGAAA
1 TATATTTT-AAAAATAGTACAATTAGAAA
461 AATAAAGTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
25 2 0.04
26 5 0.10
27 24 0.50
28 5 0.10
29 9 0.19
30 3 0.06
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.40
Consensus pattern (28 bp):
TATATTTTAAAAATAGTACAATTAGAAA
Found at i:568 original size:4 final size:4
Alignment explanation
Indices: 559--598 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
549 ATTAAAGTTT
559 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
599 GAAATAATTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:3118 original size:29 final size:31
Alignment explanation
Indices: 3086--3152 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
3076 ATGCAATTTG
3086 GGATATAACGTTAC-AAAA-CAAGCAATTAA
1 GGATATAACGTTACGAAAATCAAGCAATTAA
*
3115 GGATATAATGTTACGAAAATCAAGCAATTAA
1 GGATATAACGTTACGAAAATCAAGCAATTAA
3146 GGATATA
1 GGATATA
3153 GTCCGTTAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 13 0.37
30 4 0.11
31 18 0.51
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.24
Consensus pattern (31 bp):
GGATATAACGTTACGAAAATCAAGCAATTAA
Found at i:3306 original size:31 final size:31
Alignment explanation
Indices: 3271--3411 Score: 160
Period size: 31 Copynumber: 4.6 Consensus size: 31
3261 CCCTAACTGA
3271 TTATATCCTTAATTGCTTGAAATCGAAAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACG
* *
3302 TTATATCCTTAATTGCTCGAAATCAAAAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACG
* ** * *
3333 TTATATCCTTAGTTGCTTG-TTTTG-TAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACG
*** *
3362 TTATATCCTTAATTGCTTGTGGTAGAAAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACG
*
3393 TTATATCCTAAATTGCTTG
1 TTATATCCTTAATTGCTTG
3412 CTTATCATCT
Statistics
Matches: 93, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
29 22 0.24
30 3 0.03
31 68 0.73
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (31 bp):
TTATATCCTTAATTGCTTGAAATCGAAAACG
Found at i:3391 original size:60 final size:60
Alignment explanation
Indices: 3298--3411 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
3288 TGAAATCGAA
* *
3298 AACGTTATATCCTTAATTGCTCGAAATCAAAAACGTTATATCCTTAGTTGCTTGTTTTGT
1 AACGTTATATCCTTAATTGCTCGAAATCAAAAACGTTATATCCTAAATTGCTTGTTTTGT
* ***
3358 AACGTTATATCCTTAATTGCTTGTGGT-AGAAAACGTTATATCCTAAATTGCTTG
1 AACGTTATATCCTTAATTGCTCGAAATCA-AAAACGTTATATCCTAAATTGCTTG
3412 CTTATCATCT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 1 0.02
60 46 0.98
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (60 bp):
AACGTTATATCCTTAATTGCTCGAAATCAAAAACGTTATATCCTAAATTGCTTGTTTTGT
Found at i:4325 original size:3 final size:3
Alignment explanation
Indices: 4317--4372 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
4307 TGAAATTAGG
4317 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4365 ATT ATT AT
1 ATT ATT AT
4373 GAAAATACGG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:4508 original size:30 final size:31
Alignment explanation
Indices: 4470--4550 Score: 130
Period size: 31 Copynumber: 2.6 Consensus size: 31
4460 CGTTACAAAA
4470 CAAGCAATTAAGGATATAACT-TTTT-GATTT
1 CAAGCAATTAAGGATATAA-TGTTTTCGATTT
*
4500 CGAGCAATTAAGGATATAATGTTTTCGATTT
1 CAAGCAATTAAGGATATAATGTTTTCGATTT
4531 CAAGCAATTAAGGATATAAT
1 CAAGCAATTAAGGATATAAT
4551 CAGTTAGGGC
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
29 1 0.02
30 22 0.47
31 24 0.51
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (31 bp):
CAAGCAATTAAGGATATAATGTTTTCGATTT
Found at i:4742 original size:29 final size:31
Alignment explanation
Indices: 4668--4734 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
4658 TCTAACGGAC
4668 TATATCCTTAATTGCTCGCTTTTCGTAACGT
1 TATATCCTTAATTGCTCGCTTTTCGTAACGT
*
4699 TATATCCTTAATTGCTTG-TTTT-GTAACGT
1 TATATCCTTAATTGCTCGCTTTTCGTAACGT
4728 TATATCC
1 TATATCC
4735 CAAATTGCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
30 4 0.11
31 17 0.49
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (31 bp):
TATATCCTTAATTGCTCGCTTTTCGTAACGT
Found at i:8784 original size:120 final size:120
Alignment explanation
Indices: 8571--8791 Score: 442
Period size: 120 Copynumber: 1.8 Consensus size: 120
8561 TCCACATAAC
8571 AATTACTATGGAAACCAAGAGTTTGCCCATAATCGATACTATGATTCATATCCAAATTACCAACA
1 AATTACTATGGAAACCAAGAGTTTGCCCATAATCGATACTATGATTCATATCCAAATTACCAACA
8636 ATGGAGTGATCCACCATATGAACTTGCCCCTCCAAGTCTTCTTGAGGAGACTTTT
66 ATGGAGTGATCCACCATATGAACTTGCCCCTCCAAGTCTTCTTGAGGAGACTTTT
8691 AATTACTATGGAAACCAAGAGTTTGCCCATAATCGATACTATGATTCATATCCAAATTACCAACA
1 AATTACTATGGAAACCAAGAGTTTGCCCATAATCGATACTATGATTCATATCCAAATTACCAACA
8756 ATGGAGTGATCCACCATATGAACTTGCCCCTCCAAG
66 ATGGAGTGATCCACCATATGAACTTGCCCCTCCAAG
8792 GCCTACATGG
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 101 1.00
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (120 bp):
AATTACTATGGAAACCAAGAGTTTGCCCATAATCGATACTATGATTCATATCCAAATTACCAACA
ATGGAGTGATCCACCATATGAACTTGCCCCTCCAAGTCTTCTTGAGGAGACTTTT
Found at i:10620 original size:12 final size:13
Alignment explanation
Indices: 10603--10632 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
10593 TAAGAAAATG
10603 AAAAAAAAG-GAA
1 AAAAAAAAGAGAA
10615 AAAAAAAAGAGAA
1 AAAAAAAAGAGAA
10628 AAAAA
1 AAAAA
10633 GTGAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAGAA
Found at i:10639 original size:20 final size:20
Alignment explanation
Indices: 10615--10660 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
10605 AAAAAAGGAA
*
10615 AAAAAAAAGAGAAAAAAAGTG
1 AAAAAAAAGA-AAAGAAAGTG
10636 AAAAAAAAGAAAAGAAAGTG
1 AAAAAAAAGAAAAGAAAGTG
10656 AAAAA
1 AAAAA
10661 TGGAACACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.04
Consensus pattern (20 bp):
AAAAAAAAGAAAAGAAAGTG
Found at i:10644 original size:11 final size:11
Alignment explanation
Indices: 10597--10660 Score: 64
Period size: 11 Copynumber: 6.1 Consensus size: 11
10587 TCCAAATAAG
10597 AAAA-TGAAAA
1 AAAAGTGAAAA
10607 AAAAG-GAAAA
1 AAAAGTGAAAA
**
10617 AAAAAAGAGAAA
1 AAAAGTGA-AAA
10629 AAAAGTGAAAA
1 AAAAGTGAAAA
10640 AAAA--GAAAA
1 AAAAGTGAAAA
*
10649 GAAAGTGAAAA
1 AAAAGTGAAAA
10660 A
1 A
10661 TGGAACACTC
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
9 8 0.18
10 13 0.30
11 14 0.32
12 9 0.20
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (11 bp):
AAAAGTGAAAA
Found at i:17212 original size:28 final size:28
Alignment explanation
Indices: 17181--17241 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
17171 TAAAATTTCC
*
17181 TAAATCAATTTAATATAAACAAATCAAT
1 TAAACCAATTTAATATAAACAAATCAAT
** * *
17209 TAAACCTTTTTCATTTAAACAAATCAAT
1 TAAACCAATTTAATATAAACAAATCAAT
17237 TAAAC
1 TAAAC
17242 ATTTCCTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (28 bp):
TAAACCAATTTAATATAAACAAATCAAT
Found at i:17257 original size:30 final size:28
Alignment explanation
Indices: 17196--17263 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
17186 CAATTTAATA
* **
17196 TAAACAAATCAATTAAACCTTTTTCATT
1 TAAACAAATCAATTAAACATTTTAAATT
17224 TAAACAAATCAATTAAACATTTCCTAAATT
1 TAAACAAATCAATTAAACATTT--TAAATT
17254 TAAACAAATC
1 TAAACAAATC
17264 TAATATAACC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
28 21 0.60
30 14 0.40
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.34
Consensus pattern (28 bp):
TAAACAAATCAATTAAACATTTTAAATT
Found at i:25745 original size:42 final size:41
Alignment explanation
Indices: 25652--25770 Score: 170
Period size: 42 Copynumber: 2.9 Consensus size: 41
25642 GACCCTTCTA
* * *
25652 AATAATTAAGGAAATAAATTAAATCTAGGTTTA--CCCCGT
1 AATAATTAAGGTAAGAAATTAAATCCAGGTTTAGCCCCCGT
*
25691 ACTAATTAAGGTAAGAAATTAAATCCAGGTTTAGCCTCCCGT
1 AATAATTAAGGTAAGAAATTAAATCCAGGTTTAGCC-CCCGT
*
25733 AATAATTAAGGTAAGAAATTAAATCCAGATTTAGCCCC
1 AATAATTAAGGTAAGAAATTAAATCCAGGTTTAGCCCC
25771 TAGTTATAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
39 29 0.41
41 3 0.04
42 39 0.55
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (41 bp):
AATAATTAAGGTAAGAAATTAAATCCAGGTTTAGCCCCCGT
Found at i:28996 original size:2 final size:2
Alignment explanation
Indices: 28989--29021 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
28979 ACATTTGTAC
28989 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29022 CTTTAATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29181 original size:16 final size:16
Alignment explanation
Indices: 29160--29192 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
29150 TTGAAGAAAT
29160 CCAGATACATCTAAAA
1 CCAGATACATCTAAAA
29176 CCAGATACATCTAAAA
1 CCAGATACATCTAAAA
29192 C
1 C
29193 TCAATCCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.27, G:0.06, T:0.18
Consensus pattern (16 bp):
CCAGATACATCTAAAA
Found at i:41064 original size:3 final size:3
Alignment explanation
Indices: 41056--41082 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
41046 TTCAAGCTTT
41056 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
41083 GTTATCAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Done.