Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019071.1 Corchorus olitorius cultivar O-4 contig19104, 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: 60886
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1308 original size:16 final size:16
Alignment explanation
Indices: 1287--1326 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
1277 TAAAAGGTAA
1287 TTTCATGATCTACTAC
1 TTTCATGATCTACTAC
1303 TTTCATGATCTACTAC
1 TTTCATGATCTACTAC
1319 TTTCATGA
1 TTTCATGA
1327 AGGACTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.25, C:0.23, G:0.07, T:0.45
Consensus pattern (16 bp):
TTTCATGATCTACTAC
Found at i:2150 original size:21 final size:22
Alignment explanation
Indices: 2115--2158 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
2105 ATATTGTCAT
2115 TCAATTCATTTTTTTAACTAAA
1 TCAATTCATTTTTTTAACTAAA
2137 TCAATTCA-TTTTTTAACTAAA
1 TCAATTCATTTTTTTAACTAAA
2158 T
1 T
2159 TATTGTTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (22 bp):
TCAATTCATTTTTTTAACTAAA
Found at i:3238 original size:44 final size:44
Alignment explanation
Indices: 3188--3276 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
3178 TTTATTAATA
3188 TTTCTTGGAATTGTACTAGTTATTTTGTTCTTATTTGTTAAGAC
1 TTTCTTGGAATTGTACTAGTTATTTTGTTCTTATTTGTTAAGAC
3232 TTTCTTGGAATTGTACTAGTTATTTTGTTCTTATTTGTTAAGAC
1 TTTCTTGGAATTGTACTAGTTATTTTGTTCTTATTTGTTAAGAC
3276 T
1 T
3277 CTCCAAATGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.20, C:0.09, G:0.16, T:0.55
Consensus pattern (44 bp):
TTTCTTGGAATTGTACTAGTTATTTTGTTCTTATTTGTTAAGAC
Found at i:3609 original size:66 final size:67
Alignment explanation
Indices: 3493--3624 Score: 221
Period size: 66 Copynumber: 2.0 Consensus size: 67
3483 CCCAATCCCA
* *
3493 CCACCTTGCTCCTATAATTTTTTTTTTTTTATCAAATTGTATTTAATCAAAGATTAGCAACTTGC
1 CCACCATGCTCCTATAA--TTTTTTTTTTTATCAAATTGTATTTAATCAAAGATTAACAACTTGC
3558 AATC
64 AATC
3562 CCACCATGCTCCTATAA-TTTTTTTTTTATCAAATTGTATTTAATCAAAGATTAACAACTTGCA
1 CCACCATGCTCCTATAATTTTTTTTTTTATCAAATTGTATTTAATCAAAGATTAACAACTTGCA
3625 CCTATAACAT
Statistics
Matches: 61, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
66 45 0.74
69 16 0.26
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.43
Consensus pattern (67 bp):
CCACCATGCTCCTATAATTTTTTTTTTTATCAAATTGTATTTAATCAAAGATTAACAACTTGCAA
TC
Found at i:3799 original size:29 final size:30
Alignment explanation
Indices: 3758--3822 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
3748 ATTTGTACGG
3758 TTTT-GACATTTTAC-CTCATAAAC-TTTAA
1 TTTTGGACATTTTACTCTC-TAAACTTTTAA
*
3786 TTTTGGACATTTTACTCTCTGAACTTTTAA
1 TTTTGGACATTTTACTCTCTAAACTTTTAA
3816 -TTTGGAC
1 TTTTGGAC
3823 CCTTTTTAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
28 4 0.12
29 21 0.64
30 8 0.24
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.48
Consensus pattern (30 bp):
TTTTGGACATTTTACTCTCTAAACTTTTAA
Found at i:12150 original size:20 final size:21
Alignment explanation
Indices: 12125--12164 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
12115 TAAAAACTAC
12125 AAGAACTCCG-AATGGAGTAT
1 AAGAACTCCGCAATGGAGTAT
*
12145 AAGAACTCCGCGATGGAGTA
1 AAGAACTCCGCAATGGAGTA
12165 AAAACCATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.38, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
AAGAACTCCGCAATGGAGTAT
Found at i:22780 original size:29 final size:28
Alignment explanation
Indices: 22733--22793 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 28
22723 AAGCTAACAT
*
22733 AAATAAACCACATCTACCTACCAAATACAC
1 AAATAAACCAAATCTACCTACC--ATACAC
22763 AAATAAA-CAAATCTACCTACCATACAC
1 AAATAAACCAAATCTACCTACCATACAC
22790 AAAT
1 AAAT
22794 TACAAACTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 10 0.33
29 13 0.43
30 7 0.23
ACGTcount: A:0.52, C:0.30, G:0.00, T:0.18
Consensus pattern (28 bp):
AAATAAACCAAATCTACCTACCATACAC
Found at i:23077 original size:17 final size:17
Alignment explanation
Indices: 23052--23094 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
23042 AATCATATAT
*
23052 CTCTCTATACGTTCAAA
1 CTCTCTATACGCTCAAA
*
23069 CTCTTTATACGCTCAAA
1 CTCTCTATACGCTCAAA
*
23086 TTCTCTATA
1 CTCTCTATA
23095 TGCTGACATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.28, G:0.05, T:0.40
Consensus pattern (17 bp):
CTCTCTATACGCTCAAA
Found at i:32836 original size:42 final size:43
Alignment explanation
Indices: 32789--32872 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 43
32779 GTGTTTTGGC
32789 TTATCGTGTCTCGTGTCGA-AATCGTGTCG-GACACGATTAAAA
1 TTATCGTGTCTCGTGTC-ATAATCGTGTCGTGACACGATTAAAA
*
32831 TTATCGTGTTTCGTGTCATAATCGTGTCGTTGACACGATTAA
1 TTATCGTGTCTCGTGTCATAATCGTGTCG-TGACACGATTAA
32873 CACGGTTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
41 1 0.03
42 26 0.68
44 11 0.29
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.36
Consensus pattern (43 bp):
TTATCGTGTCTCGTGTCATAATCGTGTCGTGACACGATTAAAA
Found at i:34521 original size:12 final size:12
Alignment explanation
Indices: 34502--34532 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
34492 TACCCTATGT
34502 AAACACGACACG
1 AAACACGACACG
*
34514 AGACACGACACG
1 AAACACGACACG
34526 AAACACG
1 AAACACG
34533 GATTGCCAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.48, C:0.32, G:0.19, T:0.00
Consensus pattern (12 bp):
AAACACGACACG
Found at i:35840 original size:19 final size:20
Alignment explanation
Indices: 35790--35847 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
35780 GCTGCTCTAA
35790 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGTA-C
* * *
35811 TAATATAATCTGTACAGT-G
1 TAATCTCATCTGTACAGTAC
35830 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
35848 TGCTAAACAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (20 bp):
TAATCTCATCTGTACAGTAC
Found at i:36476 original size:16 final size:16
Alignment explanation
Indices: 36455--36485 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
36445 TTCGTTTCTC
36455 AACTGCCTCAAATTTT
1 AACTGCCTCAAATTTT
36471 AACTGCCTCAAATTT
1 AACTGCCTCAAATTT
36486 CAGAAAAGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.35
Consensus pattern (16 bp):
AACTGCCTCAAATTTT
Found at i:38300 original size:14 final size:13
Alignment explanation
Indices: 38264--38302 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
38254 ATTTTATATT
*
38264 TATAATTATATTTA
1 TATAATTA-ATTAA
38278 TATAATTAATTAA
1 TATAATTAATTAA
38291 TATAATTTAATT
1 TATAA-TTAATT
38303 CTTAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATAATTAATTAA
Found at i:40867 original size:20 final size:20
Alignment explanation
Indices: 40842--40881 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
40832 ATCTTGGTGT
40842 AATTGAAAGAGTATTTTGTC
1 AATTGAAAGAGTATTTTGTC
40862 AATTGAAAGAGTATTTTGTC
1 AATTGAAAGAGTATTTTGTC
40882 TCACCTATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.40
Consensus pattern (20 bp):
AATTGAAAGAGTATTTTGTC
Found at i:40989 original size:29 final size:29
Alignment explanation
Indices: 40904--40990 Score: 71
Period size: 29 Copynumber: 3.2 Consensus size: 29
40894 ATTAACTCAC
*
40904 TCTTGCAGGAGAATGGTATTTATAGATCT
1 TCTTGCAGGAGAATGGTATTTATTGATCT
** *
40933 TCTTG-A-TTG-AT--TATTCTAATT-AAC-
1 TCTTGCAGGAGAATGGTATT-T-ATTGATCT
40957 TCTTGCAGGAGAATGGTATTTATTGATCT
1 TCTTGCAGGAGAATGGTATTTATTGATCT
40986 TCTTG
1 TCTTG
40991 ATTGATTAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 18
0.63 0.10 0.27
Matches are distributed among these distances:
24 9 0.21
25 4 0.10
26 5 0.12
27 6 0.14
28 4 0.10
29 14 0.33
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.44
Consensus pattern (29 bp):
TCTTGCAGGAGAATGGTATTTATTGATCT
Found at i:41097 original size:54 final size:54
Alignment explanation
Indices: 41024--41186 Score: 299
Period size: 54 Copynumber: 3.0 Consensus size: 54
41014 AATAAAATGA
* * *
41024 AACTAATGCTAGTGCTTGTGCTCTTTAGATGAATATGGCTACTATTTGAATGGC
1 AACTAATGCCAGTGGTTGTGCCCTTTAGATGAATATGGCTACTATTTGAATGGC
41078 AACTAATGCCAGTGGTTGTGCCCTTTAGATGAATATGGCTACTATTTGAATGGC
1 AACTAATGCCAGTGGTTGTGCCCTTTAGATGAATATGGCTACTATTTGAATGGC
41132 AACTAATGCCAGTGGTTGTGCCCTTTAGATGAATATGGCTACTATTTGAATGGC
1 AACTAATGCCAGTGGTTGTGCCCTTTAGATGAATATGGCTACTATTTGAATGGC
41186 A
1 A
41187 GCATGTGATA
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 106 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.34
Consensus pattern (54 bp):
AACTAATGCCAGTGGTTGTGCCCTTTAGATGAATATGGCTACTATTTGAATGGC
Found at i:49836 original size:18 final size:19
Alignment explanation
Indices: 49815--49851 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
49805 GATATTGAGC
*
49815 TCAAGCTCGAGC-CGAGTA
1 TCAAGCTCAAGCTCGAGTA
49833 TCAAGCTCAAGCTCGAGTA
1 TCAAGCTCAAGCTCGAGTA
49852 GCTGACTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.30, C:0.27, G:0.24, T:0.19
Consensus pattern (19 bp):
TCAAGCTCAAGCTCGAGTA
Found at i:55493 original size:31 final size:31
Alignment explanation
Indices: 55455--55519 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
55445 ATATCATGTG
55455 GATACTATCACCAAAAAACAAATGATATGCA
1 GATACTATCACCAAAAAACAAATGATATGCA
55486 GATACTATCACCAAAAAACAAATGATATGCA
1 GATACTATCACCAAAAAACAAATGATATGCA
55517 GAT
1 GAT
55520 GGACTAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.51, C:0.18, G:0.11, T:0.20
Consensus pattern (31 bp):
GATACTATCACCAAAAAACAAATGATATGCA
Found at i:57600 original size:427 final size:420
Alignment explanation
Indices: 56922--57698 Score: 1112
Period size: 427 Copynumber: 1.8 Consensus size: 420
56912 AGGACTCAAA
* * *
56922 ACTCAAAAGCCAATGTTTATGTTTCAATTCAAAAAAATGCTTCCGAAATTTGGTGATTTTGATTG
1 ACTCAAAAGCCAATGTTTATGTTTCAATTCAAAAAAATACTTCCCAAATTTGGTGATTTCGATTG
* * * * * **
56987 CCGGTCTATTTAATATCATCTAATTTTCGATCCACATGTCCGATTAATGTTATTTAAGTGTTAGT
66 CAGGTCTATTTAATACCATATAATTTTCGATCCACAGGTCCGATTAAAGTTATTTAAGTGCCAGT
* * * *
57052 TAAAAGGTTATTGCATGATGTACGATTTTCATGAAGGACCCGAAAGCTAAATTTGATCTACGAGT
131 TAAAAGGTTATTGCATGATCTACGACTTTCATGAAGGACCCGAAAGCCAAATTTGATCTACAAGT
* * * * * *
57117 TTCATTAAGGGTTCAAAAGGGAATTTTTATGTTTCAAGATCTCCTTCGATAAACATTTTCTTATT
196 TTCATGAAGGATTCAAAAGAGAATTTTTATGTTTCAAGATCTCCTTCAACAAACATTTTCATATT
* *
57182 TGGATTATTTATCAAATAACCCTCATATTTTTCTACTTTATACTAC-T-TAGTCATTTACTAATT
261 TGGATTATTTATCAAATAACCCTCATATTTTTCTACTTTATACTACTTATAGACATTTACAAATT
57245 CTATCTTAATCGATTTAACGCTTCATCTTTTTTTTTTTCTGTTTGTCCGGTTAAGGTGATTCAGG
326 CTATCTTAATCGATTTAACGCTTCATCTTTTTTTTTTTCTGTTTGTCCGGTTAAGGTGATTCAGG
57310 TAATTTCATGATCTCCAACTTTCATGAAGG
391 TAATTTCATGATCTCCAACTTTCATGAAGG
* * * *
57340 ACTCAAAAGTCAATTTTTATGTTTCAATTCAAAAAAAAAAAAATACTTCCCAAATTTGTTGGTTT
1 ACTCAAAAGCCAATGTTTATGTTTCAATTC------AAAAAAATACTTCCCAAATTTGGTGATTT
* *
57405 CGATTGCAGGTCTCTATTTAATACCATATAATTTTGGATTCACAGGTCCGATTAAAGTTATTTAA
60 CGATTGCAGG--TCTATTTAATACCATATAATTTTCGATCCACAGGTCCGATTAAAGTTATTTAA
* * *
57470 GTGCCGGTTAAAAAGGTTATTGCGTGATCTACGACTTTCATGAAGGATCCGAAAAGCCAAATTTG
123 GTGCCAGTT-AAAAGGTTATTGCATGATCTACGACTTTCATGAAGGACCCG-AAAGCCAAATTTG
57535 ATCTACAAGTTTCATGAAGGATTCAAAAGAGAA-TTTTATGTTTCAAGATCT-CTATCAACAAAC
186 ATCTACAAGTTTCATGAAGGATTCAAAAGAGAATTTTTATGTTTCAAGATCTCCT-TCAACAAAC
*
57598 ATTTTCATATTTGGATTATTTATCAAATGACCCTCATATTTTTCTACTTTATACTACTTATAGAC
250 ATTTTCATATTTGGATTATTTATCAAATAACCCTCATATTTTTCTACTTTATACTACTTATAGAC
* * *
57663 CTTTACAAATTTTATCTTACTCGATTTAACGCTTCA
315 ATTTACAAATTCTATCTTAATCGATTTAACGCTTCA
57699 GTTTTTTCTT
Statistics
Matches: 311, Mismatches: 35, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
418 28 0.09
424 33 0.11
426 55 0.18
427 117 0.38
428 42 0.14
429 36 0.12
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.40
Consensus pattern (420 bp):
ACTCAAAAGCCAATGTTTATGTTTCAATTCAAAAAAATACTTCCCAAATTTGGTGATTTCGATTG
CAGGTCTATTTAATACCATATAATTTTCGATCCACAGGTCCGATTAAAGTTATTTAAGTGCCAGT
TAAAAGGTTATTGCATGATCTACGACTTTCATGAAGGACCCGAAAGCCAAATTTGATCTACAAGT
TTCATGAAGGATTCAAAAGAGAATTTTTATGTTTCAAGATCTCCTTCAACAAACATTTTCATATT
TGGATTATTTATCAAATAACCCTCATATTTTTCTACTTTATACTACTTATAGACATTTACAAATT
CTATCTTAATCGATTTAACGCTTCATCTTTTTTTTTTTCTGTTTGTCCGGTTAAGGTGATTCAGG
TAATTTCATGATCTCCAACTTTCATGAAGG
Done.