Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014487.1 Corchorus capsularis cultivar CVL-1 contig14508, 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: 49281
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1927 original size:14 final size:14
Alignment explanation
Indices: 1908--1934 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1898 GTCATTTTAA
1908 TAAAAAGGAACAAT
1 TAAAAAGGAACAAT
1922 TAAAAAGGAACAA
1 TAAAAAGGAACAA
1935 GAGGGAGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.07, G:0.15, T:0.11
Consensus pattern (14 bp):
TAAAAAGGAACAAT
Found at i:20490 original size:5 final size:5
Alignment explanation
Indices: 20482--20508 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
20472 TCTATTCTAT
20482 ATTAA ATTAA ATTAA ATTAA ATTAA AT
1 ATTAA ATTAA ATTAA ATTAA ATTAA AT
20509 ATTTATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATTAA
Found at i:21354 original size:114 final size:114
Alignment explanation
Indices: 21141--21364 Score: 285
Period size: 114 Copynumber: 1.9 Consensus size: 114
21131 TCATCTTCGG
*
21141 AAGATGGTAGGAAAAGTGTTCAGAAATTAACAAGGAACAAATGCTTATTTATTTTCCTTAATTAA
1 AAGATGGTAGGAAAAGTGTTAAGAAATT-A-AAGGAACAAATGCTTATTTATTTTCCTTAATTAA
** * * *
21206 TGGAATTCAATAATTCATAGCTTAATTACAATTCCCTCTCTTTTCAATTTA
64 TAAAATTCAATAATTAATAGATTAATAACAATTCCCTCTCTTTTCAATTTA
*
21257 AAGATGGTAGGAGAAGTGTTAAGAACATT-AAGGAACAAATGCTTATTTATTTTCCTTAATTAAT
1 AAGATGGTAGGAAAAGTGTTAAGAA-ATTAAAGGAACAAATGCTTATTTATTTTCCTTAATTAAT
* *
21321 AAAATTC-ATAGCTTAAT-GAATTACA-AACTATTCCCTCTCTTTTC
65 AAAATTCAATA-ATTAATAG-ATTA-ATAACAATTCCCTCTCTTTTC
21365 CCTCCAAAAA
Statistics
Matches: 95, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
113 4 0.04
114 64 0.67
115 1 0.01
116 23 0.24
117 3 0.03
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (114 bp):
AAGATGGTAGGAAAAGTGTTAAGAAATTAAAGGAACAAATGCTTATTTATTTTCCTTAATTAATA
AAATTCAATAATTAATAGATTAATAACAATTCCCTCTCTTTTCAATTTA
Found at i:21666 original size:18 final size:18
Alignment explanation
Indices: 21643--21677 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
21633 TCAATTCCAG
21643 TACTACT-TTTCACTTAAA
1 TACTACTCTTTCA-TTAAA
21661 TACTACTCTTTCATTAA
1 TACTACTCTTTCATTAA
21678 CCTCTTGCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (18 bp):
TACTACTCTTTCATTAAA
Found at i:22949 original size:40 final size:39
Alignment explanation
Indices: 22900--22977 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
22890 TCCCTCCTAA
*
22900 ATAATTAAGGAAACAAATTAAATTCAGGTTTAGCTCCCTG
1 ATAATTAAGGAAACAAATTAAATCCAGGTTTAGC-CCCTG
* *
22940 ATAATTAAGGTAAGAAATTAAATCCAGGTTTAGCCCCT
1 ATAATTAAGGAAACAAATTAAATCCAGGTTTAGCCCCT
22978 AGTTATAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.29
Consensus pattern (39 bp):
ATAATTAAGGAAACAAATTAAATCCAGGTTTAGCCCCTG
Found at i:24902 original size:3 final size:3
Alignment explanation
Indices: 24894--24921 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
24884 TTCCCTCCCA
24894 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
24922 GATAACCCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:32310 original size:1 final size:1
Alignment explanation
Indices: 32270--32299 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
32260 GAAACTTGCC
*
32270 TTTTTTTTTTTTTTTTTTCTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
32300 CATCATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:32415 original size:2 final size:2
Alignment explanation
Indices: 32408--32439 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
32398 TATACATGTG
32408 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32440 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33675 original size:2 final size:2
Alignment explanation
Indices: 33664--33704 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
33654 TTGCTTTTGA
*
33664 AT AT -T AT AT AT AT AT -T AT AT AT A- AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33703 AT
1 AT
33705 GGGAAATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 3 0.09
2 31 0.91
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:33680 original size:11 final size:10
Alignment explanation
Indices: 33664--33704 Score: 52
Period size: 9 Copynumber: 4.4 Consensus size: 10
33654 TTGCTTTTGA
33664 ATAT-TATAT
1 ATATATATAT
33673 ATATAT-TAT
1 ATATATATAT
33682 ATATA-ATAT
1 ATATATATAT
*
33691 ATATGTATAT
1 ATATATATAT
33701 ATAT
1 ATAT
33705 GGGAAATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
9 19 0.68
10 9 0.32
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (10 bp):
ATATATATAT
Found at i:34071 original size:2 final size:2
Alignment explanation
Indices: 34064--34096 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
34054 ATTATGTTAT
34064 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34097 CGTTGTAGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35160 original size:21 final size:20
Alignment explanation
Indices: 35136--35188 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
35126 TGAGTCCTCC
35136 CCTGGTTACAGCCCATCATCG
1 CCTGGTTACAGCCCA-CATCG
* * * *
35157 CCTGGCTATGATCCCACATCT
1 CCTGGTTA-CAGCCCACATCG
35178 CCTGGTTACAG
1 CCTGGTTACAG
35189 TCCAACAAGT
Statistics
Matches: 24, Mismatches: 7, Indels: 3
0.71 0.21 0.09
Matches are distributed among these distances:
20 1 0.04
21 18 0.75
22 5 0.21
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.26
Consensus pattern (20 bp):
CCTGGTTACAGCCCACATCG
Found at i:41188 original size:180 final size:177
Alignment explanation
Indices: 40839--41197 Score: 594
Period size: 180 Copynumber: 2.0 Consensus size: 177
40829 TCCATAAACA
* *
40839 AATCATTTTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATGCTATTTAA
1 AATCATTTTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTCATACTATTTAA
* * *
40904 TCCTTACAATTATATGTTGGATGATTGAATGTTTCGGCTTTAATTGTTTTTTTTTCTATTTGACC
66 TCCTTACAATTATAGGTTGGACGATTGAATGTTTCAGCTTTAATTGTTTTTTTTTCTATTTGACC
*
40969 GATCAAGGTGATTCAGGTGTCTATTTAAAGGTAATTCCATGGTCTAC
131 GATCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTAC
*
41016 AATCA-TTTTTTTGTTGGATTATTTATTAAATGATCCTCGTACTTTTATAATTCATACTATTTAA
1 AATCATTTTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTCATACTATTTAA
* *
41080 TCACTTACAATTATGGGTTGGACGATTGAATGTTTCAGCTTTAATTCTTTTATTTTTTTCTATTT
66 TC-CTTACAATTATAGGTTGGACGATTGAATGTTTCAGCTTTAA-T-TGTT-TTTTTTTCTATTT
41145 GACCGATCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTAC
127 GACCGATCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTAC
41196 AA
1 AA
41198 CTTTCATGAA
Statistics
Matches: 169, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
176 58 0.34
177 42 0.25
178 1 0.01
179 3 0.02
180 65 0.38
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.47
Consensus pattern (177 bp):
AATCATTTTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTCATACTATTTAA
TCCTTACAATTATAGGTTGGACGATTGAATGTTTCAGCTTTAATTGTTTTTTTTTCTATTTGACC
GATCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTAC
Found at i:41833 original size:15 final size:15
Alignment explanation
Indices: 41815--41846 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
41805 GTACTATAGT
41815 TAACAAAAGTAAGAC
1 TAACAAAAGTAAGAC
41830 TAACAAAAGTAAGAC
1 TAACAAAAGTAAGAC
41845 TA
1 TA
41847 TTAATGTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.12, G:0.12, T:0.16
Consensus pattern (15 bp):
TAACAAAAGTAAGAC
Found at i:42292 original size:2 final size:2
Alignment explanation
Indices: 42285--42316 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
42275 AGTAATATTA
42285 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42317 AAGAATGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42298 original size:16 final size:16
Alignment explanation
Indices: 42263--42314 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
42253 GAGGTACATA
*
42263 ATATTAATATTTAGTA-
1 ATATTAATATATA-TAT
42279 ATATTAATATATATAT
1 ATATTAATATATATAT
42295 ATA-T-ATATATATAT
1 ATATTAATATATATAT
42309 ATATTA
1 ATATTA
42315 TAAAGAATGG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 13 0.41
15 4 0.12
16 15 0.47
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
ATATTAATATATATAT
Found at i:42673 original size:2 final size:2
Alignment explanation
Indices: 42666--42694 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
42656 TTGTTTTCAT
42666 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 T
42695 GATGGGAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43074 original size:24 final size:25
Alignment explanation
Indices: 43047--43100 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
43037 AAGTGCACGG
*
43047 AGAAAGGA-GATGAAGAGATTCAGA
1 AGAAAGGATGATGAACAGATTCAGA
* *
43071 AGAAA-GATGGTGATCAGATTCAGA
1 AGAAAGGATGATGAACAGATTCAGA
43095 AGAAAG
1 AGAAAG
43101 AGAAATAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.48, C:0.06, G:0.31, T:0.15
Consensus pattern (25 bp):
AGAAAGGATGATGAACAGATTCAGA
Found at i:43847 original size:27 final size:27
Alignment explanation
Indices: 43815--43915 Score: 125
Period size: 27 Copynumber: 3.7 Consensus size: 27
43805 CCTCTGAAGG
43815 GGATGCTGAGAAGGGAAACACTAAAGA
1 GGATGCTGAGAAGGGAAACACTAAAGA
** * *
43842 GGATGCTGAGAACAGAAACAGTAGAGA
1 GGATGCTGAGAAGGGAAACACTAAAGA
*
43869 GGATGCTGAGAAGGGAAAGAC-AATAGA
1 GGATGCTGAGAAGGGAAACACTAA-AGA
43896 GGATGCTGATG-AGGGAAACA
1 GGATGCTGA-GAAGGGAAACA
43916 TCTTCAAGAG
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
26 1 0.02
27 60 0.97
28 1 0.02
ACGTcount: A:0.43, C:0.10, G:0.36, T:0.12
Consensus pattern (27 bp):
GGATGCTGAGAAGGGAAACACTAAAGA
Found at i:48155 original size:24 final size:26
Alignment explanation
Indices: 48095--48155 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 26
48085 TTCAAACCCT
*
48095 AAACTTC-TTTTCTAACAACTTCTTC
1 AAACTTCATTTTCTAACAACATCTTC
48120 AAACTTCA-TTTCTAACAA-ATCTTC
1 AAACTTCATTTTCTAACAACATCTTC
48144 AAA-TTCATTTTC
1 AAACTTCATTTTC
48156 CTTCATTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
23 4 0.12
24 12 0.36
25 17 0.52
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.43
Consensus pattern (26 bp):
AAACTTCATTTTCTAACAACATCTTC
Found at i:48192 original size:26 final size:26
Alignment explanation
Indices: 48163--48230 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
48153 TTCCTTCATT
48163 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
48189 TTAATCATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
48215 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
48231 ATACTAAGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:48193 original size:15 final size:15
Alignment explanation
Indices: 48163--48230 Score: 62
Period size: 15 Copynumber: 5.1 Consensus size: 15
48153 TTCCTTCATT
48163 TTAATCATAAACTAA
1 TTAATCATAAACTAA
48178 TTAA--AT--ACTAA
1 TTAATCATAAACTAA
48189 TTAATCATAAACTAA
1 TTAATCATAAACTAA
*
48204 TT-A-GAT--ACTAA
1 TTAATCATAAACTAA
*
48215 TTAAACATAAACTAA
1 TTAATCATAAACTAA
48230 T
1 T
48231 ATACTAAGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
11 16 0.37
12 1 0.02
13 8 0.19
14 1 0.02
15 17 0.40
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (15 bp):
TTAATCATAAACTAA
Found at i:48517 original size:20 final size:21
Alignment explanation
Indices: 48491--48531 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
48481 ATAAAAATGG
*
48491 GGGGGGGGGTGTTTAGCAAAA
1 GGGGGGTGGTGTTTAGCAAAA
48512 GGGGGGTGGTGTTTAGCAAA
1 GGGGGGTGGTGTTTAGCAAA
48532 CCCCTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.05, G:0.51, T:0.22
Consensus pattern (21 bp):
GGGGGGTGGTGTTTAGCAAAA
Done.