Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022248.1 Corchorus olitorius cultivar O-4 contig22281, 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: 43842
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:6953 original size:23 final size:23
Alignment explanation
Indices: 6882--6953 Score: 55
Period size: 23 Copynumber: 3.2 Consensus size: 23
6872 TTCTTGTATA
6882 TATTATGTTTA-TTACTAATG-TG
1 TATTATGTTTATTTA-TAATGTTG
* *
6904 ATATTTAT-ATTATTAAT-ATGTAT-
1 -TA-TTATGTTTATTTATAATGT-TG
6927 TATTATGTTTATTTATAATGTTG
1 TATTATGTTTATTTATAATGTTG
6950 TATT
1 TATT
6954 TACTATATAC
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
21 4 0.11
22 13 0.34
23 14 0.37
24 7 0.18
ACGTcount: A:0.31, C:0.01, G:0.10, T:0.58
Consensus pattern (23 bp):
TATTATGTTTATTTATAATGTTG
Found at i:7119 original size:20 final size:21
Alignment explanation
Indices: 7080--7120 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
7070 AAATTTTTCA
7080 TTTAATAAGATAAAAAAATAT
1 TTTAATAAGATAAAAAAATAT
* *
7101 TTTAA-AAGATATAATAATAT
1 TTTAATAAGATAAAAAAATAT
7121 AGTTTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (21 bp):
TTTAATAAGATAAAAAAATAT
Found at i:9866 original size:31 final size:31
Alignment explanation
Indices: 9822--9904 Score: 78
Period size: 31 Copynumber: 2.6 Consensus size: 31
9812 TAATTAATAC
* *
9822 TAAATTATTACAAATTAAAACAAAT-TAAGCAT
1 TAAATTA-AACAAATTAAAA-AAATGAAAGCAT
* ** *
9854 TAAATTAAACAAATCATTAAAATGAAAGCCT
1 TAAATTAAACAAATTAAAAAAATGAAAGCAT
*
9885 TAAATTAAACAAAATAAAAA
1 TAAATTAAACAAATTAAAAA
9905 CTGATAGACC
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
30 4 0.10
31 29 0.73
32 7 0.17
ACGTcount: A:0.60, C:0.10, G:0.04, T:0.27
Consensus pattern (31 bp):
TAAATTAAACAAATTAAAAAAATGAAAGCAT
Found at i:13306 original size:2 final size:2
Alignment explanation
Indices: 13299--13336 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
13289 GTCAAATACA
13299 AT AT AT 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 AT AT AT
13337 GCAGATGGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15331 original size:25 final size:25
Alignment explanation
Indices: 15247--15331 Score: 78
Period size: 22 Copynumber: 3.7 Consensus size: 25
15237 TTAGTAATTA
15247 AATATATATTATTTATTTATTT--T
1 AATATATATTATTTATTTATTTAAT
*
15270 AA-ACT-CATTATTTA-TTATTTAA-
1 AATA-TATATTATTTATTTATTTAAT
*
15292 AATATAT-TT-GTTATTTATTTAAT
1 AATATATATTATTTATTTATTTAAT
*
15315 AATATATATTATATATT
1 AATATATATTATTTATT
15332 ATAAGATAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
21 9 0.19
22 22 0.46
23 11 0.23
24 2 0.04
25 4 0.08
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (25 bp):
AATATATATTATTTATTTATTTAAT
Found at i:22658 original size:2 final size:2
Alignment explanation
Indices: 22651--22683 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
22641 TATAAGATAA
22651 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22684 ATGTCCTTTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23564 original size:22 final size:19
Alignment explanation
Indices: 23523--23561 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
23513 TCACTGTACT
23523 TCTGTTGTTCCTTATATTA
1 TCTGTTGTTCCTTATATTA
23542 TCTGTTGTTCCTTATATTA
1 TCTGTTGTTCCTTATATTA
23561 T
1 T
23562 TATTAATTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.59
Consensus pattern (19 bp):
TCTGTTGTTCCTTATATTA
Found at i:23611 original size:17 final size:17
Alignment explanation
Indices: 23589--23642 Score: 99
Period size: 17 Copynumber: 3.2 Consensus size: 17
23579 CTATTTTAAT
23589 TTCTTTTAATTTCATTG
1 TTCTTTTAATTTCATTG
23606 TTCTTTTAATTTCATTG
1 TTCTTTTAATTTCATTG
*
23623 TTCTTGTAATTTCATTG
1 TTCTTTTAATTTCATTG
23640 TTC
1 TTC
23643 GCTGTCTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.17, C:0.13, G:0.07, T:0.63
Consensus pattern (17 bp):
TTCTTTTAATTTCATTG
Found at i:23667 original size:20 final size:20
Alignment explanation
Indices: 23595--23669 Score: 65
Period size: 17 Copynumber: 4.0 Consensus size: 20
23585 TAATTTCTTT
*
23595 TAATTTCATTGTT--CT-TT
1 TAATTTCATTGTTCACTGTC
*
23612 TAATTTCATTGTT--CT-TG
1 TAATTTCATTGTTCACTGTC
*
23629 TAATTTCATTGTTCGCTGTC
1 TAATTTCATTGTTCACTGTC
23649 TAATTTCA-TGATTCACTGTC
1 TAATTTCATTG-TTCACTGTC
23669 T
1 T
23670 TAAGCTTTCT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
17 29 0.57
19 4 0.08
20 18 0.35
ACGTcount: A:0.19, C:0.16, G:0.11, T:0.55
Consensus pattern (20 bp):
TAATTTCATTGTTCACTGTC
Found at i:24073 original size:29 final size:29
Alignment explanation
Indices: 24031--24088 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
24021 TCAATTTTCA
* *
24031 CAATTTTAGCATTTTTTATAACCAAACAG
1 CAATTTTAACATTTTTTAAAACCAAACAG
24060 CAATTTTAACATTTTTTAAAACCAAACAG
1 CAATTTTAACATTTTTTAAAACCAAACAG
24089 GAGGCACAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (29 bp):
CAATTTTAACATTTTTTAAAACCAAACAG
Found at i:24601 original size:187 final size:175
Alignment explanation
Indices: 24298--24660 Score: 566
Period size: 187 Copynumber: 2.0 Consensus size: 175
24288 AAAAAGGAAC
* *
24298 AGGGAAGAAAAAAGGGTCGAAGATCACCTACTGAATTAGGATAATAGATTGATAGAGGGAAAAAA
1 AGGGAAGAAAAAAGGATCGAAGATCACCTACTAAATTAGGATAATAGATTGATAGAGGGAAAAAA
24363 AAGGAACAGATTTTGGGGCTTGGTGCAACTGATGGAAGCCAAAATTTAGATTTAGATATTTAGGG
66 AAGGAACAGATTTTGGGGCTTGGTGCAACTGATGGAAGCCAAAATTTAGATTTAGATATTTAGGG
24428 GTCGAAGATCACCGCTGAATTGAGAGCAACAGATTGATAGAGAGAGAGAA
131 GTCGAAGATCACCGCT--A---AGAGCAACAGATTGATAGAGAGAGAGAA
*
24478 AGGGAAGAAAAAAGGATCGAAGATCGCCTACTAAATTAGGATAATAGATTGATAGAGGAAAAAGG
1 AGGGAAGAAAAAAGGATCGAAGATCACCTACTAAATTAGGATAATAGATTGAT--A-G----AGG
24543 GAAGAAAAAAGGAACAGATTTT-GGGCTTGGTGCAACTGATGGAAGCCAAAATTTAGATTTAGAT
59 GAA-AAAAAAGGAACAGATTTTGGGGCTTGGTGCAACTGATGGAAGCCAAAATTTAGATTTAGAT
*
24607 ATTTAGGGGTCTAAGATCACCGCTAAGAGCAACAGATTGATAGAGAGAGAGAA
123 ATTTAGGGGTCGAAGATCACCGCTAAGAGCAACAGATTGATAGAGAGAGAGAA
24660 A
1 A
24661 AAAAAACAAC
Statistics
Matches: 171, Mismatches: 4, Indels: 14
0.90 0.02 0.07
Matches are distributed among these distances:
180 50 0.29
182 30 0.18
183 1 0.01
185 1 0.01
187 71 0.42
188 18 0.11
ACGTcount: A:0.41, C:0.10, G:0.28, T:0.21
Consensus pattern (175 bp):
AGGGAAGAAAAAAGGATCGAAGATCACCTACTAAATTAGGATAATAGATTGATAGAGGGAAAAAA
AAGGAACAGATTTTGGGGCTTGGTGCAACTGATGGAAGCCAAAATTTAGATTTAGATATTTAGGG
GTCGAAGATCACCGCTAAGAGCAACAGATTGATAGAGAGAGAGAA
Found at i:30275 original size:14 final size:14
Alignment explanation
Indices: 30256--30284 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
30246 ATTGTCGAAA
30256 CACTAAGCTAGCAT
1 CACTAAGCTAGCAT
30270 CACTAAGCTAGCAT
1 CACTAAGCTAGCAT
30284 C
1 C
30285 CAATAAGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.31, G:0.14, T:0.21
Consensus pattern (14 bp):
CACTAAGCTAGCAT
Found at i:30828 original size:65 final size:65
Alignment explanation
Indices: 30738--30860 Score: 174
Period size: 65 Copynumber: 1.9 Consensus size: 65
30728 GCAAAGCTCT
* * * *
30738 ATAACGGTTGGGAACAAAAAAGAAAAAGGAGAATTGACGGATTAGTAAGAGCAAAGCTGATCTAG
1 ATAACAGTTAGGAACAAAAAAGAAAAAGGAGAATTAACGCATTAGTAAGAGCAAAGCTGATCTAG
* * * *
30803 ATAACAGTTAGGAACAAAAATGAAAAATGAGAATTAACGCTTTAGTCAGAGCAAAGCT
1 ATAACAGTTAGGAACAAAAAAGAAAAAGGAGAATTAACGCATTAGTAAGAGCAAAGCT
30861 CTAAATAACG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
65 50 1.00
ACGTcount: A:0.47, C:0.11, G:0.24, T:0.19
Consensus pattern (65 bp):
ATAACAGTTAGGAACAAAAAAGAAAAAGGAGAATTAACGCATTAGTAAGAGCAAAGCTGATCTAG
Found at i:31027 original size:25 final size:25
Alignment explanation
Indices: 30998--31048 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
30988 AATAAAAAGG
30998 AGAATTAACAAGGATTAGTCTAGGA
1 AGAATTAACAAGGATTAGTCTAGGA
*
31023 AGAATTAACAAGGATTAGTCTGGGA
1 AGAATTAACAAGGATTAGTCTAGGA
31048 A
1 A
31049 CAAAAAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.43, C:0.08, G:0.25, T:0.24
Consensus pattern (25 bp):
AGAATTAACAAGGATTAGTCTAGGA
Found at i:31141 original size:64 final size:64
Alignment explanation
Indices: 30891--31201 Score: 327
Period size: 64 Copynumber: 4.9 Consensus size: 64
30881 ATTGAATCCG
* * *
30891 GTCAGAGCAAAACTCT--ATAACGGTTGGGAACAAAAAAGAAAAAGAAGAACTAAC-A-GATTA
1 GTCAGAGCAAAACTCTAGATAACAGTTGGGAACAAAAAAGAAAAAGGAGAATTAACAAGGATTA
* * *
30951 GTCAGACCAAAACTCTAGATAACAATTGGGAACAAAAAATAAAAAGGAGAATTAACAAGGATTA
1 GTCAGAGCAAAACTCTAGATAACAGTTGGGAACAAAAAAGAAAAAGGAGAATTAACAAGGATTA
* * * *
31015 GTCTAG-G-AAGAATTAACAAGGAT--TAGTCTGGGAACAAAAAAGAAAAAGGAGAACTAAC--G
1 GTC-AGAGCAA-AACT--CTA-GATAACAGT-TGGGAACAAAAAAGAAAAAGGAGAATTAACAAG
31074 GATTA
60 GATTA
* *
31079 GTCAGAGCAAAGCTCTAGATAACAGTTGGGAACAAAAAAGAAAAAGGAAAATTAACAAGGATTA
1 GTCAGAGCAAAACTCTAGATAACAGTTGGGAACAAAAAAGAAAAAGGAGAATTAACAAGGATTA
* * ** * * *
31143 GTCCGAGTAAAGTTCTAGACAACGGTTGGGAACAAAAAAGAAAAAGGAGATTTAACAAG
1 GTCAGAGCAAAACTCTAGATAACAGTTGGGAACAAAAAAGAAAAAGGAGAATTAACAAG
31202 AAGGTGCAAC
Statistics
Matches: 209, Mismatches: 26, Indels: 28
0.79 0.10 0.11
Matches are distributed among these distances:
60 15 0.07
61 3 0.01
62 63 0.30
63 8 0.04
64 81 0.39
65 6 0.03
66 30 0.14
67 3 0.01
ACGTcount: A:0.50, C:0.12, G:0.22, T:0.16
Consensus pattern (64 bp):
GTCAGAGCAAAACTCTAGATAACAGTTGGGAACAAAAAAGAAAAAGGAGAATTAACAAGGATTA
Found at i:31143 original size:128 final size:128
Alignment explanation
Indices: 30915--31145 Score: 399
Period size: 128 Copynumber: 1.8 Consensus size: 128
30905 CTATAACGGT
30915 TGGGAACAAAAAAGAAAAAGAAGAACTAACAGATTAGTCAGACCAAAACTCTAGATAACAATTGG
1 TGGGAACAAAAAAGAAAAAGAAGAACTAACAGATTAGTCAGACCAAAACTCTAGATAACAATTGG
* *
30980 GAACAAAAAATAAAAAGGAGAATTAACAAGGATTAGTCTAGGAAGAATTAACAAGGATTAGTC
66 GAACAAAAAAGAAAAAGGAAAATTAACAAGGATTAGTCTAGGAAGAATTAACAAGGATTAGTC
* * * * *
31043 TGGGAACAAAAAAGAAAAAGGAGAACTAACGGATTAGTCAGAGCAAAGCTCTAGATAACAGTTGG
1 TGGGAACAAAAAAGAAAAAGAAGAACTAACAGATTAGTCAGACCAAAACTCTAGATAACAATTGG
31108 GAACAAAAAAGAAAAAGGAAAATTAACAAGGATTAGTC
66 GAACAAAAAAGAAAAAGGAAAATTAACAAGGATTAGTC
31146 CGAGTAAAGT
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
128 96 1.00
ACGTcount: A:0.52, C:0.11, G:0.21, T:0.16
Consensus pattern (128 bp):
TGGGAACAAAAAAGAAAAAGAAGAACTAACAGATTAGTCAGACCAAAACTCTAGATAACAATTGG
GAACAAAAAAGAAAAAGGAAAATTAACAAGGATTAGTCTAGGAAGAATTAACAAGGATTAGTC
Found at i:31997 original size:56 final size:56
Alignment explanation
Indices: 31911--32025 Score: 230
Period size: 56 Copynumber: 2.1 Consensus size: 56
31901 TTACGTGATA
31911 TTTTTATATAATTACTTGGCTTATAAGTTAGGTGGTTTAACATTAATTGTAAGAGG
1 TTTTTATATAATTACTTGGCTTATAAGTTAGGTGGTTTAACATTAATTGTAAGAGG
31967 TTTTTATATAATTACTTGGCTTATAAGTTAGGTGGTTTAACATTAATTGTAAGAGG
1 TTTTTATATAATTACTTGGCTTATAAGTTAGGTGGTTTAACATTAATTGTAAGAGG
32023 TTT
1 TTT
32026 CCTCTACTGC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.30, C:0.05, G:0.19, T:0.46
Consensus pattern (56 bp):
TTTTTATATAATTACTTGGCTTATAAGTTAGGTGGTTTAACATTAATTGTAAGAGG
Found at i:36401 original size:1 final size:1
Alignment explanation
Indices: 36395--36430 Score: 63
Period size: 1 Copynumber: 36.0 Consensus size: 1
36385 ACCTCAGAAG
*
36395 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
36431 CAAACAAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:36435 original size:4 final size:4
Alignment explanation
Indices: 36423--36458 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
36413 AAAAAAAAAA
*
36423 AAAC AAAAC AAAC AAAC AAAC AAAC AAAC AAGC AAA
1 AAAC -AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
36459 TTAGATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.75, C:0.22, G:0.03, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:37859 original size:13 final size:15
Alignment explanation
Indices: 37824--37861 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
37814 CATGGCAACC
37824 AGCAGAAGCTCACAA
1 AGCAGAAGCTCACAA
*
37839 AGCCGAAGCTCA-AA
1 AGCAGAAGCTCACAA
37853 AG-AGAAGCT
1 AGCAGAAGCT
37862 AAGGGAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 6 0.29
14 4 0.19
15 11 0.52
ACGTcount: A:0.45, C:0.24, G:0.24, T:0.08
Consensus pattern (15 bp):
AGCAGAAGCTCACAA
Found at i:40410 original size:12 final size:12
Alignment explanation
Indices: 40404--40451 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
40394 ATTTATATTT
40404 CGTTTTAAATTC
1 CGTTTTAAATTC
40416 CGTTTTTAAACTTTC
1 CG-TTTTAAA--TTC
*
40431 CGTTTGAAATTC
1 CGTTTTAAATTC
*
40443 TGTTTTAAA
1 CGTTTTAAA
40452 CTCAGATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 12 0.40
13 7 0.23
14 6 0.20
15 5 0.17
ACGTcount: A:0.25, C:0.15, G:0.10, T:0.50
Consensus pattern (12 bp):
CGTTTTAAATTC
Done.