Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017801.1 Corchorus olitorius cultivar O-4 contig17834, 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: 33886
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:79 original size:2 final size:2
Alignment explanation
Indices: 72--109 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
62 TTTCTTCTTT
72 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
110 CAAAAGTAAA
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):
TA
Found at i:6520 original size:190 final size:184
Alignment explanation
Indices: 6107--6657 Score: 785
Period size: 190 Copynumber: 3.0 Consensus size: 184
6097 AAGTGGATAT
* * *
6107 TGTTTCATAAATAACAAAACAGAGTTTTAGAATGATCATTGTTTGAGCAAATCATTTTAGGAAAC
1 TGTTTCATAAATAACTAAACAGAG-TTTAGAATGATCATTGTTTGAGCAAAACATTTTAGGAAAA
* *
6172 ACTTTTTCCTTTTCTGGAAAAAGC-TTGTTAGGTGATGATGGGGTTACTTTCTCGAATTCTCGTT
65 ACTTTTTCCTTTTTTGG-AAAAGCATTGTTAGGTGATGGTGGGGTTACTTTCTCGAATTCTCGTT
6236 TAGTG-T---T-TA-AAGGCAAACTGACCTTAAAACCTTGCAAATAGTGATTGAAA
129 TAGTGTTACATATACAAGGCAAACTGACCTTAAAACCTTGCAAATAGTGATTGAAA
*
6286 TGTTTCATAAATAACTAAACAGAGTTTAGAATGATCACTGTTTGAGCAAAACATTTTAGGAAAAA
1 TGTTTCATAAATAACTAAACAGAGTTTAGAATGATCATTGTTTGAGCAAAACATTTTAGGAAAAA
* *
6351 CTTTTTTCTTTTTTGGAAAAGCTTTTATTATTAGGTGATGGTGGGGTTACTTTCTCGAATTCTCG
66 CTTTTTCCTTTTTTGGAAAAGC----ATTGTTAGGTGATGGTGGGGTTACTTTCTCGAATTCTCG
* *
6416 TTTAGTGCTTACATATACAAGGCAAGCTGACCTTAAAACCTTACAAATAGTGATTGAAAA
127 TTTAGTG-TTACATATACAAGGCAAACTGACCTTAAAACCTTGCAAATAGTGATTG-AAA
*
6476 TGTTTCATAAATAACTAATCAGAGTTTAGAATGATCATTGTTTGAGCAAAACATTTTAGGAAAAA
1 TGTTTCATAAATAACTAAACAGAGTTTAGAATGATCATTGTTTGAGCAAAACATTTTAGGAAAAA
* * * *
6541 CTTTTTCCTTTTTTGGAAAA-AACTTGTTAGGTGATGGTAGAGTTACTTTCTCGAATTCTTGTTT
66 CTTTTTCCTTTTTTGGAAAAGCA-TTGTTAGGTGATGGTGGGGTTACTTTCTCGAATTCTCGTTT
* * *
6605 AGTGTTTACAATATACAAGGGAAAATGACCTTAAAACTTTGCAAATAGTGATT
130 AGTG-TTAC-ATATACAAGGCAAACTGACCTTAAAACCTTGCAAATAGTGATT
6658 ACTTTCTCGA
Statistics
Matches: 333, Mismatches: 24, Indels: 22
0.88 0.06 0.06
Matches are distributed among these distances:
177 6 0.02
178 52 0.16
179 23 0.07
182 43 0.13
184 1 0.00
185 1 0.00
186 45 0.14
187 39 0.12
188 2 0.01
189 36 0.11
190 85 0.26
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.37
Consensus pattern (184 bp):
TGTTTCATAAATAACTAAACAGAGTTTAGAATGATCATTGTTTGAGCAAAACATTTTAGGAAAAA
CTTTTTCCTTTTTTGGAAAAGCATTGTTAGGTGATGGTGGGGTTACTTTCTCGAATTCTCGTTTA
GTGTTACATATACAAGGCAAACTGACCTTAAAACCTTGCAAATAGTGATTGAAA
Found at i:6723 original size:72 final size:73
Alignment explanation
Indices: 6583--6729 Score: 242
Period size: 72 Copynumber: 2.0 Consensus size: 73
6573 GATGGTAGAG
* * *
6583 TTACTTTCTCGAATTCTTGTTTAGTGTTTACAATATACAAGGGAAAATGACCTTAAAACTTTGCA
1 TTACTTTCTCGAATTCTTGTTCAGTGTTTACAATATACAAGGCAAAATGACCTTAAAACCTTGCA
6648 AATAGTGA
66 AATAGTGA
**
6656 TTACTTTCTCGAATTCTTGTTCAGTGTTTAC-ATATACAAGGCAAGCTGACCTTAAAACCTTGCA
1 TTACTTTCTCGAATTCTTGTTCAGTGTTTACAATATACAAGGCAAAATGACCTTAAAACCTTGCA
6720 AATAGTGA
66 AATAGTGA
6728 TT
1 TT
6730 GAAATGTTTC
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
72 39 0.57
73 30 0.43
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (73 bp):
TTACTTTCTCGAATTCTTGTTCAGTGTTTACAATATACAAGGCAAAATGACCTTAAAACCTTGCA
AATAGTGA
Found at i:9618 original size:128 final size:128
Alignment explanation
Indices: 9388--9619 Score: 428
Period size: 128 Copynumber: 1.8 Consensus size: 128
9378 TAAGGACACC
*
9388 TGCTCGGAAAAGACCAAATTGGAGTTCAACATGACATCATTTGCATGAAGTCATGTTAGTAATGT
1 TGCTCGGAAAAGACCAAATTGGAGTTCAACATGACATCATTTGCATGAAGTCATGTTACTAATGT
*
9453 CATACTATGGTTAAAGGCTAGTCAATTTCGTGTCTTAGTAATGTCATATTTCGTGCCTTATTA
66 CATACTATGGTTAAAGGCTAGTCAATTTCGTGCCTTAGTAATGTCATATTTCGTGCCTTATTA
*
9516 TGCTCGGAAAAGGCCAAATTGGAGTTCAACATGACATCATTTGCATGAAGTCATGTTACTAATGT
1 TGCTCGGAAAAGACCAAATTGGAGTTCAACATGACATCATTTGCATGAAGTCATGTTACTAATGT
*
9581 CATATTATGGTTAAAGGCTAGTCAATTTCGTGCCTTAGT
66 CATACTATGGTTAAAGGCTAGTCAATTTCGTGCCTTAGT
9620 CTTTTTGACC
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
128 100 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (128 bp):
TGCTCGGAAAAGACCAAATTGGAGTTCAACATGACATCATTTGCATGAAGTCATGTTACTAATGT
CATACTATGGTTAAAGGCTAGTCAATTTCGTGCCTTAGTAATGTCATATTTCGTGCCTTATTA
Found at i:13354 original size:42 final size:42
Alignment explanation
Indices: 13307--13387 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
13297 TAAGGATCAA
*
13307 GATTTGAGTTAAGTATTTCTTTATTTACAAAGAATTTTCTAT
1 GATTTGAGTTAAGTATTTCTTAATTTACAAAGAATTTTCTAT
* *
13349 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAGTTAAGTATTTCTTAATTTACAAAGAATTTTC
13388 AAGACTTAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (42 bp):
GATTTGAGTTAAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:14469 original size:20 final size:20
Alignment explanation
Indices: 14431--14470 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
14421 TTTATCTCAC
14431 TTAGGGTTTGTCATTTCATGG
1 TTAGGGTTTG-CATTTCATGG
14452 TTAGGGTTTG-AGTTTCATG
1 TTAGGGTTTGCA-TTTCATG
14471 TCATGTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.06
20 7 0.39
21 10 0.56
ACGTcount: A:0.15, C:0.07, G:0.30, T:0.47
Consensus pattern (20 bp):
TTAGGGTTTGCATTTCATGG
Found at i:14474 original size:25 final size:24
Alignment explanation
Indices: 14382--14475 Score: 65
Period size: 25 Copynumber: 4.0 Consensus size: 24
14372 TGGATGACAT
14382 GTTAGGGTTTGGTTTTCATGTCATG
1 GTTAGGGTTTGG-TTTCATGTCATG
** *
14407 GTTAGGGTTTAACCTTT-ATCTCA--
1 GTTAGGGTTT--GGTTTCATGTCATG
* *
14430 CTTAGGGTTT-G--TCATTTCATG
1 GTTAGGGTTTGGTTTCATGTCATG
14451 GTTAGGGTTTGAGTTTCATGTCATG
1 GTTAGGGTTTG-GTTTCATGTCATG
14476 TCTTTTTTTG
Statistics
Matches: 52, Mismatches: 8, Indels: 18
0.67 0.10 0.23
Matches are distributed among these distances:
18 1 0.02
19 5 0.10
21 9 0.17
23 10 0.19
25 24 0.46
26 3 0.06
ACGTcount: A:0.16, C:0.12, G:0.27, T:0.46
Consensus pattern (24 bp):
GTTAGGGTTTGGTTTCATGTCATG
Found at i:14652 original size:42 final size:42
Alignment explanation
Indices: 14606--14688 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
14596 TGATTTGGTT
*
14606 ATTAATATTTAATTTTAGTTTGATTTAAATCATATTTAGATA
1 ATTAATATTTAATTTTAGTTTGATTTAAATAATATTTAGATA
*
14648 ATTAATGTTTAATTTTAGTTTGATTTAAATAATATTTAGAT
1 ATTAATATTTAATTTTAGTTTGATTTAAATAATATTTAGAT
14689 TTAGTTAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.37, C:0.01, G:0.08, T:0.53
Consensus pattern (42 bp):
ATTAATATTTAATTTTAGTTTGATTTAAATAATATTTAGATA
Found at i:14906 original size:62 final size:62
Alignment explanation
Indices: 14826--15034 Score: 265
Period size: 62 Copynumber: 3.4 Consensus size: 62
14816 TTGATATGGG
* * * *
14826 TTTAATTTTTCTTACAAATTATATTTATAATTTCCCTTACTAATCATGTTTATTTATGTCGA
1 TTTAATTTTCCTTACAAATCATGTTTATAATTTCCCTTACTAATCATGTTTATTTATGTGGA
* * * *
14888 TTTAATTTTCCTCACAAATCATGTTTATGATTTTCCTAACTAATCATGTTTATTTATGTGGA
1 TTTAATTTTCCTTACAAATCATGTTTATAATTTCCCTTACTAATCATGTTTATTTATGTGGA
* * * * * * * *
14950 TTTAATTTTTCTTAGAAACCATGTTTATAATGTCCCTTACAAATCATGTTTGTTTATTTGGG
1 TTTAATTTTCCTTACAAATCATGTTTATAATTTCCCTTACTAATCATGTTTATTTATGTGGA
*
15012 TTTAATTTTCCTTGCAAATCATG
1 TTTAATTTTCCTTACAAATCATG
15035 GTTAATACAT
Statistics
Matches: 123, Mismatches: 24, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
62 123 1.00
ACGTcount: A:0.27, C:0.14, G:0.09, T:0.50
Consensus pattern (62 bp):
TTTAATTTTCCTTACAAATCATGTTTATAATTTCCCTTACTAATCATGTTTATTTATGTGGA
Found at i:14920 original size:25 final size:25
Alignment explanation
Indices: 14892--14940 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
14882 TGTCGATTTA
*
14892 ATTTTCCTCACAAATCATGTTTATG
1 ATTTTCCTAACAAATCATGTTTATG
*
14917 ATTTTCCTAACTAATCATGTTTAT
1 ATTTTCCTAACAAATCATGTTTAT
14941 TTATGTGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (25 bp):
ATTTTCCTAACAAATCATGTTTATG
Found at i:17946 original size:105 final size:103
Alignment explanation
Indices: 17790--17988 Score: 299
Period size: 105 Copynumber: 1.9 Consensus size: 103
17780 TGATGAAAAA
* * * * *
17790 GGTTTATTTGGAGCCTGCAAAACAGACTGTTAAGGAAGGTTAAGCTTTCCCTATCTCATTTACTT
1 GGTTTATTTGGAGCCTGCAAAACAAACTGTTAAGGAAGGTAAAACTTTCCCTATCCCATATACTT
*
17855 TTACTTATTTTTTAAACCTTTACAAGCAGGACTGCATG
66 TTACTCATTTTTTAAACCTTTACAAGCAGGACTGCATG
* *
17893 GGTTTCATTTGGAGCCTGCAAAAGCAAATTGTTAAGGATGGTAAAACTTTCCCTATCCCATATAC
1 GGTTT-ATTTGGAGCCTGCAAAA-CAAACTGTTAAGGAAGGTAAAACTTTCCCTATCCCATATAC
*
17958 TTTTACTCATTTTTTAAAGCTTTACAAGCAG
64 TTTTACTCATTTTTTAAACCTTTACAAGCAG
17989 AACTCTCTGT
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
103 5 0.06
104 17 0.20
105 63 0.74
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (103 bp):
GGTTTATTTGGAGCCTGCAAAACAAACTGTTAAGGAAGGTAAAACTTTCCCTATCCCATATACTT
TTACTCATTTTTTAAACCTTTACAAGCAGGACTGCATG
Found at i:24163 original size:21 final size:21
Alignment explanation
Indices: 24124--24163 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
24114 CTCGATTAAG
**
24124 TAGGGTTAGGGTATTGTATAA
1 TAGGGTTAGGGTAGGGTATAA
24145 TAGGGTTAGGGTAGGGTAT
1 TAGGGTTAGGGTAGGGTAT
24164 GGGTAGTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.40, T:0.35
Consensus pattern (21 bp):
TAGGGTTAGGGTAGGGTATAA
Found at i:24278 original size:19 final size:19
Alignment explanation
Indices: 24258--24294 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
24248 AATTAATTAT
24258 TTTA-ATATTATATTTTTA
1 TTTATATATTATATTTTTA
24276 TTTATATATTATATTTTTA
1 TTTATATATTATATTTTTA
24295 CTTAAAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATATATTATATTTTTA
Found at i:25615 original size:27 final size:27
Alignment explanation
Indices: 25577--25630 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
25567 TTTAGTAATT
25577 AACACTTCTATTATGAATGTTTGTATA
1 AACACTTCTATTATGAATGTTTGTATA
25604 AACACTTCTATTATGAATGTTTGTATA
1 AACACTTCTATTATGAATGTTTGTATA
25631 GATGTATAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (27 bp):
AACACTTCTATTATGAATGTTTGTATA
Found at i:27043 original size:18 final size:18
Alignment explanation
Indices: 27020--27054 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
27010 AGTTTCCAGT
*
27020 TTCTTTATCGTGGATATA
1 TTCTTTATCATGGATATA
27038 TTCTTTATCATGGATAT
1 TTCTTTATCATGGATAT
27055 GTTCATCTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.11, G:0.14, T:0.51
Consensus pattern (18 bp):
TTCTTTATCATGGATATA
Found at i:31543 original size:3 final size:3
Alignment explanation
Indices: 31535--31565 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
31525 CATTTCTACA
31535 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
31566 TGCTAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Done.