Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006938.1 Corchorus capsularis cultivar CVL-1 contig06959, 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: 23661
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:5220 original size:28 final size:28
Alignment explanation
Indices: 5181--5252 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 28
5171 ACACATAGCT
* * *
5181 TTTGAGCCTCACCTAAACTTGGAGTTTC
1 TTTGAGCCTCACCTAAACCTGAAGCTTC
5209 TTTGAGCCTCACCT-AACCTGAAGCTTC
1 TTTGAGCCTCACCTAAACCTGAAGCTTC
* *
5236 TTTTAGACTCACCTAAA
1 TTTGAGCCTCACCTAAA
5253 ACCCTAGACA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
27 22 0.58
28 16 0.42
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.33
Consensus pattern (28 bp):
TTTGAGCCTCACCTAAACCTGAAGCTTC
Found at i:9881 original size:13 final size:13
Alignment explanation
Indices: 9865--9912 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
9855 AGAATAGAGA
9865 AGAGAAAAAGAAC
1 AGAGAAAAAGAAC
*
9878 AGAGAAAGAG-A-
1 AGAGAAAAAGAAC
9889 AGAGAAAAAGAAC
1 AGAGAAAAAGAAC
*
9902 AGAGAAGAAGA
1 AGAGAAAAAGA
9913 GGTGAGAGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 9 0.30
12 2 0.07
13 19 0.63
ACGTcount: A:0.67, C:0.04, G:0.29, T:0.00
Consensus pattern (13 bp):
AGAGAAAAAGAAC
Found at i:9892 original size:24 final size:25
Alignment explanation
Indices: 9854--9907 Score: 101
Period size: 24 Copynumber: 2.2 Consensus size: 25
9844 AAGAGAGGCT
9854 GAGAATAGAGAAGAGAAAAAGAACA
1 GAGAATAGAGAAGAGAAAAAGAACA
9879 GAGAA-AGAGAAGAGAAAAAGAACA
1 GAGAATAGAGAAGAGAAAAAGAACA
9903 GAGAA
1 GAGAA
9908 GAAGAGGTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 24 0.83
25 5 0.17
ACGTcount: A:0.65, C:0.04, G:0.30, T:0.02
Consensus pattern (25 bp):
GAGAATAGAGAAGAGAAAAAGAACA
Found at i:13115 original size:28 final size:28
Alignment explanation
Indices: 13075--13129 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
13065 GTAAAACTTT
13075 TGAGATTGGCCAATCGGCCTATTAATTA
1 TGAGATTGGCCAATCGGCCTATTAATTA
13103 TGAGATTGGCCAATCGGCCTATTAATT
1 TGAGATTGGCCAATCGGCCTATTAATT
13130 TTGGGAACAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (28 bp):
TGAGATTGGCCAATCGGCCTATTAATTA
Found at i:15704 original size:24 final size:23
Alignment explanation
Indices: 15660--15704 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
15650 TCTAAAGAAT
* * *
15660 TTGGGGATGGTGCATAAGATTAA
1 TTGGGGATGATGAAAAAGATTAA
15683 TTGGGGATGATGAAAAATGATT
1 TTGGGGATGATGAAAAA-GATT
15705 TGGGTATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.33, C:0.02, G:0.33, T:0.31
Consensus pattern (23 bp):
TTGGGGATGATGAAAAAGATTAA
Found at i:15716 original size:220 final size:221
Alignment explanation
Indices: 15333--15751 Score: 666
Period size: 220 Copynumber: 1.9 Consensus size: 221
15323 ATTTTCCACC
* *
15333 ATCATATAGATGTGGTTTATTCAATTAATTAGATCCCTAAAATATGGATTAAAGCACTGTTTAAA
1 ATCATATAGACGTGGTTTATTCAATTAATTAGAT-CCAAAAATATGGATTAAAGCACTGTTTAAA
* * * *
15398 GTCAAATTTGTGTATATGAGAAAATAGCAATTTCTAAAGAATTTGGGAATTGTGCATATGATTAT
65 GTCAAATTTGTGTATATGAGAAAATAGCAATCTCTAAAGAATTTGGGAATGGTGCATAAGATTAA
* *
15463 TTGGGGATGGTGAGAAATGATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTCAC-AT
130 TTGGGGATGATGAAAAATGATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTCACAAT
15527 TTTGTTTAATTATGAGATGGCGCTAAA
195 TTTGTTTAATTATGAGATGGCGCTAAA
* *
15554 ATCATATAGACGTGGTTTATTCAATTAATTAGAAT-GAAAAATATGGTTTAAAGCACCT-TTTAA
1 ATCATATAGACGTGGTTTATTCAATTAATTAG-ATCCAAAAATATGGATTAAAGCA-CTGTTTAA
* *
15617 AGTCCAATTTGTGTATATGAGAAAAT-GTCAATCTCTAAAGAATTTGGGGATGGTGCATAAGATT
64 AGTCAAATTTGTGTATATGAGAAAATAG-CAATCTCTAAAGAATTTGGGAATGGTGCATAAGATT
15681 AATTGGGGATGATGAAAAATGATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTCACA
128 AATTGGGGATGATGAAAAATGATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTCACA
15746 ATTTTG
193 ATTTTG
15752 ACTTTAAAAA
Statistics
Matches: 182, Mismatches: 12, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
219 1 0.01
220 140 0.77
221 39 0.21
222 2 0.01
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.36
Consensus pattern (221 bp):
ATCATATAGACGTGGTTTATTCAATTAATTAGATCCAAAAATATGGATTAAAGCACTGTTTAAAG
TCAAATTTGTGTATATGAGAAAATAGCAATCTCTAAAGAATTTGGGAATGGTGCATAAGATTAAT
TGGGGATGATGAAAAATGATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTCACAATT
TTGTTTAATTATGAGATGGCGCTAAA
Found at i:16130 original size:221 final size:220
Alignment explanation
Indices: 15742--16349 Score: 968
Period size: 221 Copynumber: 2.8 Consensus size: 220
15732 TACTGAATTT
* *
15742 CACAATTTTGACTTTAAAAAGT-TCTTTAAACCATATTTTTCATTCTAATTAATTGAATAAACCA
1 CACAAATTTGACTTTAAAAAGTGT-TTTAATCCATATTTTTCATTCTAATTAATTGAATAAACCA
* *
15806 CGTCTATACGATTTTAGCGCCCTCTCATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAATG
65 CGTCTATATGATTTTAGCGCCATCTCATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAATG
15871 ATATACTTTATACCCAAATCATTTCTCATCATCCCCAATTAATCTTATGCACCATCCCCAAATTC
130 ATATACTTTATACCCAAATCATTTCTCATCATCCCCAATTAATCTTATGCACCATCCCCAAATTC
* *
15936 TTTAGAGATTGACATTTTTTCGTATA
195 TTTAGAGATTGACATTTTCTCATATA
** *
15962 CACAAATTTGACTTTAAAAAGTGTTTTAATCCATATTTTAGGGA-TCTAATTAATTGAATAAACG
1 CACAAATTTGACTTTAAAAAGTGTTTTAATCCATATTTT--TCATTCTAATTAATTGAATAAACC
* * *
16026 ACATATATATGATTCTAGCGCCATCTCATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAAT
64 ACGTCTATATGATTTTAGCGCCATCTCATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAAT
* *
16091 GATATACTTTATACCCAAATCATTTTTCATTATCCCCAATTAATCTTATGCACCATCCCCAAATT
129 GATATACTTTATACCCAAATCATTTCTCATCATCCCCAATTAATCTTATGCACCATCCCCAAATT
16156 CTTTAGAGATTGACATTTTCTCATATA
194 CTTTAGAGATTGACATTTTCTCATATA
* *
16183 CACAAATTGGACTTTAAAAAGTGCTTTAATCCATATTTTTCATTCTAATTAATTGAATAAACCAC
1 CACAAATTTGACTTTAAAAAGTGTTTTAATCCATATTTTTCATTCTAATTAATTGAATAAACCAC
* ** *
16248 GTCTATATGATTTTAGCGACATCTCATAATTAAACAAAATGTGAAATTCAGTATCCCCAAACTGA
66 GTCTATATGATTTTAGCGCCATCTCATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAATGA
* * *
16313 TATACTATATACCCAAATCATTTCTCACCATTCCCAA
131 TATACTTTATACCCAAATCATTTCTCATCATCCCCAA
16350 ATTCTTTAGA
Statistics
Matches: 353, Mismatches: 31, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
219 1 0.00
220 146 0.41
221 205 0.58
222 1 0.00
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.35
Consensus pattern (220 bp):
CACAAATTTGACTTTAAAAAGTGTTTTAATCCATATTTTTCATTCTAATTAATTGAATAAACCAC
GTCTATATGATTTTAGCGCCATCTCATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAATGA
TATACTTTATACCCAAATCATTTCTCATCATCCCCAATTAATCTTATGCACCATCCCCAAATTCT
TTAGAGATTGACATTTTCTCATATA
Found at i:16496 original size:31 final size:30
Alignment explanation
Indices: 16460--16550 Score: 84
Period size: 28 Copynumber: 3.0 Consensus size: 30
16450 ATATGATGGT
16460 GGAAAATAAATTTAAGAAAAAATTAAGAAAA
1 GGAAAATAAA-TTAAGAAAAAATTAAGAAAA
*
16491 GGAAAA-AGAA--AAGAAAAAATTTAGAAAA
1 GGAAAATA-AATTAAGAAAAAATTAAGAAAA
16519 --AAAAGGTGAAATTAAGAAAAAATTTAAGAAAA
1 GGAAAA--T-AAATTAAGAAAAAA-TTAAGAAAA
16551 AATATACAAC
Statistics
Matches: 50, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
26 4 0.08
28 17 0.34
29 2 0.04
30 2 0.04
31 17 0.34
32 8 0.16
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.16
Consensus pattern (30 bp):
GGAAAATAAATTAAGAAAAAATTAAGAAAA
Found at i:16644 original size:21 final size:21
Alignment explanation
Indices: 16618--16689 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 21
16608 AAAAAATTTA
16618 AGAAAAGAAATTGATAAAAGC
1 AGAAAAGAAATTGATAAAAGC
* *
16639 AGAAAACGGAGAA--GAAAAGGAAGA
1 AGAAAA--GA-AATTGATAA--AAGC
16663 AGAAAAGAAATTGATAAAAGC
1 AGAAAAGAAATTGATAAAAGC
16684 AGAAAA
1 AGAAAA
16690 CGGAGAAGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
21 17 0.43
22 6 0.15
23 6 0.15
24 11 0.28
ACGTcount: A:0.64, C:0.04, G:0.24, T:0.08
Consensus pattern (21 bp):
AGAAAAGAAATTGATAAAAGC
Found at i:16656 original size:12 final size:12
Alignment explanation
Indices: 16639--16713 Score: 54
Period size: 12 Copynumber: 6.5 Consensus size: 12
16629 TGATAAAAGC
16639 AGAAAACGG-AGA
1 AGAAAA-GGAAGA
16651 AGAAAAGGAAGA
1 AGAAAAGGAAGA
16663 AGAAAA-GAA-A
1 AGAAAAGGAAGA
* * *
16673 TTGATAA--AAGC
1 -AGAAAAGGAAGA
16684 AGAAAACGG-AGA
1 AGAAAA-GGAAGA
16696 AGAAAAGGAAGA
1 AGAAAAGGAAGA
16708 AGAAAA
1 AGAAAA
16714 TAAATTGGGG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
10 7 0.14
11 11 0.22
12 32 0.64
ACGTcount: A:0.64, C:0.04, G:0.28, T:0.04
Consensus pattern (12 bp):
AGAAAAGGAAGA
Found at i:16666 original size:45 final size:45
Alignment explanation
Indices: 16617--16720 Score: 199
Period size: 45 Copynumber: 2.3 Consensus size: 45
16607 GAAAAAATTT
16617 AAGAAAAGAAATTGATAAAAGCAGAAAACGGAGAAGAAAAGGAAG
1 AAGAAAAGAAATTGATAAAAGCAGAAAACGGAGAAGAAAAGGAAG
16662 AAGAAAAGAAATTGATAAAAGCAGAAAACGGAGAAGAAAAGGAAG
1 AAGAAAAGAAATTGATAAAAGCAGAAAACGGAGAAGAAAAGGAAG
*
16707 AAGAAAATAAATTG
1 AAGAAAAGAAATTG
16721 GGGAAAATAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.62, C:0.04, G:0.25, T:0.09
Consensus pattern (45 bp):
AAGAAAAGAAATTGATAAAAGCAGAAAACGGAGAAGAAAAGGAAG
Found at i:21945 original size:72 final size:72
Alignment explanation
Indices: 21851--22074 Score: 331
Period size: 72 Copynumber: 3.1 Consensus size: 72
21841 CTAGTCGTTG
* ** * * * *
21851 CCGTGCTTGGTCGAGGTTGGCTCTCCACCGCCTGCCAGTTGGTCTCACTGGACCCTTAAAAGGGT
1 CCGTGCTTGGTCAAGGTTGGCTCTCCACCGCCTGCCAGCAGGTATCTCTGGACCCTTAAGAGGGC
21916 TCTTCAT
66 TCTTCAT
*
21923 CCGTGCTTGGTCAAGGTCGGCTCTCCACCGCCTGCCAGCAGGTATCTCTGGACCCTTAAGAGGGC
1 CCGTGCTTGGTCAAGGTTGGCTCTCCACCGCCTGCCAGCAGGTATCTCTGGACCCTTAAGAGGGC
21988 TCTTCAT
66 TCTTCAT
* * * *
21995 CCGTGCTTGGTCAAGGTTAGCTCTCCACCGCCTACCAGCCGGTATCTCTGGACTCTTAAGAGGGC
1 CCGTGCTTGGTCAAGGTTGGCTCTCCACCGCCTGCCAGCAGGTATCTCTGGACCCTTAAGAGGGC
22060 TCTTCAT
66 TCTTCAT
*
22067 TCGTGCTT
1 CCGTGCTT
22075 ACTACCCGTC
Statistics
Matches: 138, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 138 1.00
ACGTcount: A:0.15, C:0.32, G:0.25, T:0.28
Consensus pattern (72 bp):
CCGTGCTTGGTCAAGGTTGGCTCTCCACCGCCTGCCAGCAGGTATCTCTGGACCCTTAAGAGGGC
TCTTCAT
Found at i:22186 original size:50 final size:50
Alignment explanation
Indices: 22072--22252 Score: 283
Period size: 50 Copynumber: 3.6 Consensus size: 50
22062 TTCATTCGTG
*
22072 CTTACTACCCGTCAATGGGGTGTTACTGCCGATAA-TGTCTCGATCCGGT
1 CTTACTACCCGTCAAGGGGGTGTTACTGCCGATAATTGTCTCGATCCGGT
22121 CTTACTACCCGTCAAGGGGGTGTTACTGCCGATAATTGTCTCGATCCGGT
1 CTTACTACCCGTCAAGGGGGTGTTACTGCCGATAATTGTCTCGATCCGGT
* * * * **
22171 CTTACTACCCATCAAGGGGGTATTACTGCCGATAATGGTCTTGATCCAAT
1 CTTACTACCCGTCAAGGGGGTGTTACTGCCGATAATTGTCTCGATCCGGT
*
22221 CTTACTACCCGTCAAGAGGGTGTTACTGCCGA
1 CTTACTACCCGTCAAGGGGGTGTTACTGCCGA
22253 GAATGATCAA
Statistics
Matches: 121, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
49 34 0.28
50 87 0.72
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (50 bp):
CTTACTACCCGTCAAGGGGGTGTTACTGCCGATAATTGTCTCGATCCGGT
Found at i:22590 original size:91 final size:90
Alignment explanation
Indices: 22430--22599 Score: 234
Period size: 91 Copynumber: 1.9 Consensus size: 90
22420 ACATATACCA
* * * *
22430 CCATCAAAATATGATAAAACATGTAAGTATGATTAAACGATGCTCTTGCATGTTCATATTAGCTT
1 CCATCAAAAAATGATAAAACATGTAAGTATGATTAAACGATGCTCTTGCATGATCATAATAGCTC
22495 AATTTATGCATATAAGCATGTACTT
66 AATTTATGCATATAAGCATGTACTT
* * * * *
22520 CCATCAAAAAATGATAAAAACATGTTA-TCATGCTTAAAGGATGCTTTTGCATGATCATAATATC
1 CCATCAAAAAATGAT-AAAACATGTAAGT-ATGATTAAACGATGCTCTTGCATGATCATAATAGC
22584 TCAATTTATGCATATA
64 TCAATTTATGCATATA
22600 CGAGCAAGTA
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
90 15 0.22
91 54 0.78
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (90 bp):
CCATCAAAAAATGATAAAACATGTAAGTATGATTAAACGATGCTCTTGCATGATCATAATAGCTC
AATTTATGCATATAAGCATGTACTT
Found at i:23207 original size:25 final size:25
Alignment explanation
Indices: 23158--23661 Score: 426
Period size: 25 Copynumber: 20.1 Consensus size: 25
23148 TGGGGATCTA
**
23158 CGCTTGGCGCTCTTC-GGCGTTCTC
1 CGCTTGGCGCTCGACGGGCGTTCTC
23182 CGCTTGGCGCTCGACGGGCGTTCTC
1 CGCTTGGCGCTCGACGGGCGTTCTC
* *
23207 CGCTTGACGCTCGACAGGCGTTCTC
1 CGCTTGGCGCTCGACGGGCGTTCTC
* * *
23232 CACTTGGCGC-CTGGCAGGCGTTCTC
1 CGCTTGGCGCTC-GACGGGCGTTCTC
*
23257 CGCTTGGCGCTCGAGGGACGGGCATTCTC
1 CGCTTGGCGCTC----GACGGGCGTTCTC
* * *
23286 CGCTTGGCCCTCGACTGTCGTTCTC
1 CGCTTGGCGCTCGACGGGCGTTCTC
*
23311 CGCTTGGCGCCTGGA-GGGCGTTCTC
1 CGCTTGGCG-CTCGACGGGCGTTCTC
* * * *
23336 CGATTGGCCCTCGTCTGGCGTTCTC
1 CGCTTGGCGCTCGACGGGCGTTCTC
* *
23361 CACTTGGCGCTGGACGGGCGTTCTC
1 CGCTTGGCGCTCGACGGGCGTTCTC
* * *
23386 CGCCTGGTGCTCGCCGGGCGTTCTC
1 CGCTTGGCGCTCGACGGGCGTTCTC
* * * *
23411 CCCTTGGCGC-CTGGCAGGCATTCTC
1 CGCTTGGCGCTC-GACGGGCGTTCTC
*
23436 CGCTTGGC-CTCGACGGACGTTCTC
1 CGCTTGGCGCTCGACGGGCGTTCTC
* * * * *
23460 CACGTGGCGCCCGTCAGGCGTTCTC
1 CGCTTGGCGCTCGACGGGCGTTCTC
* * * *
23485 CGCTTAGCGTTCGACAGGCGCTCTC
1 CGCTTGGCGCTCGACGGGCGTTCTC
** * * * *
23510 TACTCGGCGCTCGTCAGGCATTCTC
1 CGCTTGGCGCTCGACGGGCGTTCTC
*
23535 CGCTTGGCGCTCGACAGGCGTTCTC
1 CGCTTGGCGCTCGACGGGCGTTCTC
* * * **
23560 CCCTTGGCACTTGGTGGGCGTTCTC
1 CGCTTGGCGCTCGACGGGCGTTCTC
**
23585 CGCTTAACGCTCGACGGGCGTTCTC
1 CGCTTGGCGCTCGACGGGCGTTCTC
* *
23610 CGCTTGGCG-TCCGCCGGGCATTCTC
1 CGCTTGGCGCT-CGACGGGCGTTCTC
*
23635 CGCTTGGCGCTCGACAGGCGTTCTC
1 CGCTTGGCGCTCGACGGGCGTTCTC
23660 CG
1 CG
Statistics
Matches: 374, Mismatches: 93, Indels: 25
0.76 0.19 0.05
Matches are distributed among these distances:
24 35 0.09
25 312 0.83
26 6 0.02
29 21 0.06
ACGTcount: A:0.07, C:0.36, G:0.31, T:0.25
Consensus pattern (25 bp):
CGCTTGGCGCTCGACGGGCGTTCTC
Done.