Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019625.1 Corchorus olitorius cultivar O-4 contig19658, 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: 37335
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:48 original size:30 final size:30
Alignment explanation
Indices: 11--224 Score: 338
Period size: 30 Copynumber: 7.1 Consensus size: 30
1 GTTACAGATA
*
11 ATTGCTTTACTTTAATCCTGGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
* *
41 GTTGCTTTATTTTAATCCTGTTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
* *
71 GTTGCTTTATTTTAATCCTGGTTGAGGATA
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
101 ATTGCTTTATTTTAATCCTGGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
*
131 GTTGCTTTATTTTAATCCTGGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
* *
161 ATTACTTCATTTTAATCCTGGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
* *
191 ATTGCTTTATTTTAACCCTGGTTTAGGATC
1 ATTGCTTTATTTTAATCCTGGTTGAGGATC
221 ATTG
1 ATTG
225 TTTCATCAGT
Statistics
Matches: 169, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 169 1.00
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.46
Consensus pattern (30 bp):
ATTGCTTTATTTTAATCCTGGTTGAGGATC
Found at i:363 original size:39 final size:39
Alignment explanation
Indices: 315--401 Score: 122
Period size: 39 Copynumber: 2.2 Consensus size: 39
305 TTTGAATTTT
*
315 GATCATTGCTTTATCAGTCGTGTTTC-AGTCATGATTTAG
1 GATCATTGCTTTATCAGTCGTATTTCGA-TCATGATTTAG
* **
354 GATTATTGCTTTATCAGTTTTATTTCGATCATGATTTAG
1 GATCATTGCTTTATCAGTCGTATTTCGATCATGATTTAG
393 GATCATTGC
1 GATCATTGC
402 CTATTAGTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
39 41 0.98
40 1 0.02
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.46
Consensus pattern (39 bp):
GATCATTGCTTTATCAGTCGTATTTCGATCATGATTTAG
Found at i:424 original size:39 final size:39
Alignment explanation
Indices: 343--416 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
333 CGTGTTTCAG
* * *
343 TCATGATTTAGGATTATTGCTTTATCAGTTTTATTTCGA
1 TCATGATTTAGGATCATTGCTCTATCAGTTTAATTTCGA
*
382 TCATGATTTAGGATCATTGC-CTATTAG-TTAATTTC
1 TCATGATTTAGGATCATTGCTCTATCAGTTTAATTTC
417 AGAATCATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 7 0.23
38 5 0.16
39 19 0.61
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.49
Consensus pattern (39 bp):
TCATGATTTAGGATCATTGCTCTATCAGTTTAATTTCGA
Found at i:810 original size:27 final size:27
Alignment explanation
Indices: 746--845 Score: 103
Period size: 27 Copynumber: 3.7 Consensus size: 27
736 AGGTCATTCG
* * *
746 GGGGCATTTTGGTCATTTTTCA-ATTACA
1 GGGGCATTTTAGTCA-TTTGCACA-TCCA
*
774 GGGGCATTTTGGTCATTTGCACATCCA
1 GGGGCATTTTAGTCATTTGCACATCCA
* *
801 GGGGCATTTTAATCATTTGCACGTCCA
1 GGGGCATTTTAGTCATTTGCACATCCA
* *
828 TGGGCATTCTAGTCATTT
1 GGGGCATTTTAGTCATTT
846 TAAGTTCACA
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
27 47 0.75
28 16 0.25
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (27 bp):
GGGGCATTTTAGTCATTTGCACATCCA
Found at i:13458 original size:25 final size:25
Alignment explanation
Indices: 13428--13482 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
13418 CAGAAATACC
* *
13428 GAAAAAGAAAAGAAAAATGGAAAAAG
1 GAAAAAG-AAAGAAAAACGCAAAAAG
13454 GAAAAAGAAAGAAAAACGCAAAAAG
1 GAAAAAGAAAGAAAAACGCAAAAAG
13479 GAAA
1 GAAA
13483 CCATGTTAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 20 0.74
26 7 0.26
ACGTcount: A:0.73, C:0.04, G:0.22, T:0.02
Consensus pattern (25 bp):
GAAAAAGAAAGAAAAACGCAAAAAG
Found at i:14718 original size:27 final size:25
Alignment explanation
Indices: 14688--14755 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 25
14678 TACTTCTTGA
* *
14688 TTACTGATTACCAATTTTTTTCTCTTT
1 TTACTGATTACC--GTTTTTACTCTTT
*
14715 TTACTGACTACCGTTTTTACTCTTT
1 TTACTGATTACCGTTTTTACTCTTT
14740 TTACTGATTACC-TTTT
1 TTACTGATTACCGTTTT
14756 CCTCTCTTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 4 0.11
25 22 0.59
27 11 0.30
ACGTcount: A:0.18, C:0.21, G:0.06, T:0.56
Consensus pattern (25 bp):
TTACTGATTACCGTTTTTACTCTTT
Found at i:14762 original size:25 final size:25
Alignment explanation
Indices: 14688--14763 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 25
14678 TACTTCTTGA
*
14688 TTACTGATTACCAATTTTTTTCTCTTT
1 TTACTGATTACC-A-TTTTCTCTCTTT
* *
14715 TTACTGACTACCGTTTT-TACTCTTT
1 TTACTGATTACCATTTTCT-CTCTTT
14740 TTACTGATTACC-TTTTCCTCTCTT
1 TTACTGATTACCATTTT-CTCTCTT
14764 GCTAACTACT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
24 5 0.12
25 26 0.60
26 1 0.02
27 11 0.26
ACGTcount: A:0.16, C:0.24, G:0.05, T:0.55
Consensus pattern (25 bp):
TTACTGATTACCATTTTCTCTCTTT
Found at i:14816 original size:7 final size:7
Alignment explanation
Indices: 14804--14873 Score: 52
Period size: 7 Copynumber: 9.4 Consensus size: 7
14794 TATTACCATG
14804 TTTACTC
1 TTTACTC
*
14811 TTTACTT
1 TTTACTC
14818 TTTACTC
1 TTTACTC
14825 ATTGCTA-TCC
1 -TT--TACT-C
*
14835 TTTACTG
1 TTTACTC
14842 TTTACTC
1 TTTACTC
*
14849 TTTTACTG
1 -TTTACTC
*
14857 ATTACTC
1 TTTACTC
14864 TTTACTC
1 TTTACTC
14871 TTT
1 TTT
14874 GCCATTATCA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
7 34 0.69
8 9 0.18
9 3 0.06
10 3 0.06
ACGTcount: A:0.16, C:0.23, G:0.04, T:0.57
Consensus pattern (7 bp):
TTTACTC
Found at i:14855 original size:15 final size:15
Alignment explanation
Indices: 14835--14866 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
14825 ATTGCTATCC
*
14835 TTTACTGTTTACTCT
1 TTTACTGATTACTCT
14850 TTTACTGATTACTCT
1 TTTACTGATTACTCT
14865 TT
1 TT
14867 ACTCTTTGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.19, G:0.06, T:0.59
Consensus pattern (15 bp):
TTTACTGATTACTCT
Found at i:15160 original size:32 final size:32
Alignment explanation
Indices: 15124--15184 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
15114 CTTTAATTCT
**
15124 AATTACTATTTTAAGTTTTGAATTTGATTGCC
1 AATTACTATTTTAACCTTTGAATTTGATTGCC
*
15156 AATTACTATTTTACCCTTTGAATTTGATT
1 AATTACTATTTTAACCTTTGAATTTGATT
15185 TCTAGTTACC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.28, C:0.11, G:0.10, T:0.51
Consensus pattern (32 bp):
AATTACTATTTTAACCTTTGAATTTGATTGCC
Found at i:15199 original size:32 final size:32
Alignment explanation
Indices: 15140--15206 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
15130 TATTTTAAGT
*
15140 TTTGAATTTGATTGCCAATTACTATTTTACCC
1 TTTGAATTTGATTGCCAATTACCATTTTACCC
* * *
15172 TTTGAATTTGATTTCTAGTTACCATTTTACCC
1 TTTGAATTTGATTGCCAATTACCATTTTACCC
15204 TTT
1 TTT
15207 ACTGACTGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.22, C:0.18, G:0.09, T:0.51
Consensus pattern (32 bp):
TTTGAATTTGATTGCCAATTACCATTTTACCC
Found at i:15741 original size:44 final size:44
Alignment explanation
Indices: 15673--15857 Score: 289
Period size: 44 Copynumber: 4.2 Consensus size: 44
15663 ATTTTAAGAG
* * * *
15673 GCCCAACAGAAAGTAAAAACAAGACCCAAGCCTATGTAATGTGGAA
1 GCCCAACAG-AA-TAAAAACAAGACCCAAACCCATTTAATATGGAA
*
15719 GCCCAACAGAATAAAAGCAAGACCCAAACCCATTTAATATGGAA
1 GCCCAACAGAATAAAAACAAGACCCAAACCCATTTAATATGGAA
15763 GCCCAACAGAATAAAAACAAGACCCAAACCCATTTAATATGGAA
1 GCCCAACAGAATAAAAACAAGACCCAAACCCATTTAATATGGAA
* *
15807 GCCCAACAGAATAAAAACAAGACCCAAACCCATTTGACATGGAA
1 GCCCAACAGAATAAAAACAAGACCCAAACCCATTTAATATGGAA
15851 GCCCAAC
1 GCCCAAC
15858 CAAAAAAATT
Statistics
Matches: 131, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
44 120 0.92
45 2 0.02
46 9 0.07
ACGTcount: A:0.47, C:0.26, G:0.15, T:0.12
Consensus pattern (44 bp):
GCCCAACAGAATAAAAACAAGACCCAAACCCATTTAATATGGAA
Found at i:15745 original size:21 final size:21
Alignment explanation
Indices: 15720--15833 Score: 52
Period size: 21 Copynumber: 5.2 Consensus size: 21
15710 AATGTGGAAG
15720 CCCAACAGAATAAAAGCAAGA
1 CCCAACAGAATAAAAGCAAGA
** * * *
15741 CCCAAACCCATTTAATATGGAAG-
1 CCC-AACAGA-ATAA-AAGCAAGA
*
15764 CCCAACAGAATAAAAACAAGA
1 CCCAACAGAATAAAAGCAAGA
** * * *
15785 CCCAAACCCATTTAATATGGAAG-
1 CCC-AACAGA-ATAA-AAGCAAGA
*
15808 CCCAACAGAATAAAAACAAGA
1 CCCAACAGAATAAAAGCAAGA
15829 CCCAA
1 CCCAA
15834 ACCCATTTGA
Statistics
Matches: 62, Mismatches: 23, Indels: 16
0.61 0.23 0.16
Matches are distributed among these distances:
20 8 0.13
21 17 0.27
22 16 0.26
23 12 0.19
24 9 0.15
ACGTcount: A:0.51, C:0.26, G:0.11, T:0.11
Consensus pattern (21 bp):
CCCAACAGAATAAAAGCAAGA
Found at i:15767 original size:23 final size:23
Alignment explanation
Indices: 15741--15812 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
15731 AAAAGCAAGA
15741 CCCAAACCCATTTAATATGGAAG
1 CCCAAACCCATTTAATATGGAAG
** * ***
15764 CCC-AACAGA-ATAA-AAACAAG
1 CCCAAACCCATTTAATATGGAAG
15784 ACCCAAACCCATTTAATATGGAAG
1 -CCCAAACCCATTTAATATGGAAG
15808 CCCAA
1 CCCAA
15813 CAGAATAAAA
Statistics
Matches: 33, Mismatches: 12, Indels: 8
0.62 0.23 0.15
Matches are distributed among these distances:
20 4 0.12
21 6 0.18
22 8 0.24
23 11 0.33
24 4 0.12
ACGTcount: A:0.46, C:0.28, G:0.11, T:0.15
Consensus pattern (23 bp):
CCCAAACCCATTTAATATGGAAG
Found at i:17626 original size:2 final size:2
Alignment explanation
Indices: 17619--17645 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17609 TCGCTTTTAT
17619 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 T
17646 TGAAGTGCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20317 original size:26 final size:27
Alignment explanation
Indices: 20253--20323 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 27
20243 GAGTGGACTT
**
20253 AAAATGACCAATGTGCCCTTGAATATA
1 AAAATGACCAAAATGCCCTTGAATATA
* * *
20280 CAAATGACCAAAATGCCCTT-AGTGTA
1 AAAATGACCAAAATGCCCTTGAATATA
20306 AAAATGACCAAAATGCCC
1 AAAATGACCAAAATGCCC
20324 CTGGGTGACC
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
26 21 0.55
27 17 0.45
ACGTcount: A:0.42, C:0.23, G:0.14, T:0.21
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCTTGAATATA
Found at i:24194 original size:11 final size:11
Alignment explanation
Indices: 24178--24202 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
24168 ACCCATACCT
24178 AAACTAGAAGA
1 AAACTAGAAGA
24189 AAACTAGAAGA
1 AAACTAGAAGA
24200 AAA
1 AAA
24203 TAAATTATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.08, G:0.16, T:0.08
Consensus pattern (11 bp):
AAACTAGAAGA
Found at i:26119 original size:11 final size:11
Alignment explanation
Indices: 26103--26132 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
26093 GTGTGGTTTC
26103 AAGCTTGGGGA
1 AAGCTTGGGGA
*
26114 AAGCTTAGGGA
1 AAGCTTGGGGA
26125 AAGCTTGG
1 AAGCTTGG
26133 TTTGTGTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.40, T:0.20
Consensus pattern (11 bp):
AAGCTTGGGGA
Found at i:33385 original size:16 final size:15
Alignment explanation
Indices: 33347--33388 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
33337 ATAGAGGTTG
*
33347 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
33362 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
33377 ACTAGAAAACAA
1 AC-AGAAAACAA
33389 AACAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:36652 original size:21 final size:21
Alignment explanation
Indices: 36628--36682 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
36618 GGCTTGGAAT
* **
36628 GGTGATGGCACGGGCATGGCC
1 GGTGGTGGCACGGGCATAACC
*
36649 GGTGGTGGCACGGGCTTAACC
1 GGTGGTGGCACGGGCATAACC
36670 GGTGGTGGCACGG
1 GGTGGTGGCACGG
36683 TGAATGGGCG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.13, C:0.22, G:0.49, T:0.16
Consensus pattern (21 bp):
GGTGGTGGCACGGGCATAACC
Done.