Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019810.1 Corchorus olitorius cultivar O-4 contig19843, 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: 7361
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:2559 original size:111 final size:110
Alignment explanation
Indices: 2365--2591 Score: 400
Period size: 111 Copynumber: 2.1 Consensus size: 110
2355 CGTAGCCATA
* * *
2365 AGTGCCTTTCCTTTTTGTTGTTTCTGGCCTATGTAGCCCATTAAAAAAATCTACATTTTGACTTG
1 AGTGCCTTTCCTTGTTGATGATTCTGGCCTATGTAGCCCATTAAAAAAATCTACATTTTGACTTG
2430 GAGTGAGTGCACCCTTAGGAGTGCTGCACTAGTTGCACCTCCAGG
66 GAGTGAGTGCACCCTTAGGAGTGCTGCACTAGTTGCACCTCCAGG
*
2475 AGTGCCTTTCCTTGTTGATGATTCTGGCCTATGTAGCCCATTAAAAAAAATCTATATTTTGACTT
1 AGTGCCTTTCCTTGTTGATGATTCTGGCCTATGTAGCCCATT-AAAAAAATCTACATTTTGACTT
*
2540 GGAGTGAGTGCACCCTTAGGAGTGCTGCACTGGTTGCACCTCCAGG
65 GGAGTGAGTGCACCCTTAGGAGTGCTGCACTAGTTGCACCTCCAGG
2586 AGTGCC
1 AGTGCC
2592 CTTCAGCTTA
Statistics
Matches: 111, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
110 39 0.35
111 72 0.65
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (110 bp):
AGTGCCTTTCCTTGTTGATGATTCTGGCCTATGTAGCCCATTAAAAAAATCTACATTTTGACTTG
GAGTGAGTGCACCCTTAGGAGTGCTGCACTAGTTGCACCTCCAGG
Found at i:2968 original size:14 final size:14
Alignment explanation
Indices: 2949--3097 Score: 76
Period size: 14 Copynumber: 11.1 Consensus size: 14
2939 CGTCAAAGGC
*
2949 ATGTGGCATTCGCG
1 ATGTGGTATTCGCG
* *
2963 ATGTGGTATTTGCA
1 ATGTGGTATTCGCG
2977 ATGTGGTATTCGCG
1 ATGTGGTATTCGCG
* * ***
2991 ACGT--CAAAGGC-
1 ATGTGGTATTCGCG
* *
3002 ATGTGGCATTCCCG
1 ATGTGGTATTCGCG
* *
3016 ATGTGGTATTTGCA
1 ATGTGGTATTCGCG
3030 ATGTGGTATTCGCG
1 ATGTGGTATTCGCG
* * ***
3044 ACGT--CAAAGGC-
1 ATGTGGTATTCGCG
*
3055 ATGTGGCATTCGCG
1 ATGTGGTATTCGCG
* *
3069 ATGTGGTATTTGCA
1 ATGTGGTATTCGCG
3083 ATGTGGTATTCGCG
1 ATGTGGTATTCGCG
3097 A
1 A
3098 CGTCAAAGGC
Statistics
Matches: 94, Mismatches: 35, Indels: 12
0.67 0.25 0.09
Matches are distributed among these distances:
11 6 0.06
12 6 0.06
13 7 0.07
14 75 0.80
ACGTcount: A:0.20, C:0.17, G:0.32, T:0.32
Consensus pattern (14 bp):
ATGTGGTATTCGCG
Found at i:2980 original size:53 final size:53
Alignment explanation
Indices: 2912--3173 Score: 461
Period size: 53 Copynumber: 4.9 Consensus size: 53
2902 AAGGCATGTG
2912 GTGGTATTTGCAATGTGGTATTCGCGACGTCAAAGGCATGTGGCATTCGCGAT
1 GTGGTATTTGCAATGTGGTATTCGCGACGTCAAAGGCATGTGGCATTCGCGAT
*
2965 GTGGTATTTGCAATGTGGTATTCGCGACGTCAAAGGCATGTGGCATTCCCGAT
1 GTGGTATTTGCAATGTGGTATTCGCGACGTCAAAGGCATGTGGCATTCGCGAT
3018 GTGGTATTTGCAATGTGGTATTCGCGACGTCAAAGGCATGTGGCATTCGCGAT
1 GTGGTATTTGCAATGTGGTATTCGCGACGTCAAAGGCATGTGGCATTCGCGAT
3071 GTGGTATTTGCAATGTGGTATTCGCGACGTCAAAGGCATGTGGCATTCGCGAT
1 GTGGTATTTGCAATGTGGTATTCGCGACGTCAAAGGCATGTGGCATTCGCGAT
* * * * * *
3124 ATTGTATTTGCGATGTGGTATTCGTGACGTCAAAAGCATGTGGCGTTCGC
1 GTGGTATTTGCAATGTGGTATTCGCGACGTCAAAGGCATGTGGCATTCGC
3174 TTCAAACATC
Statistics
Matches: 201, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 201 1.00
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (53 bp):
GTGGTATTTGCAATGTGGTATTCGCGACGTCAAAGGCATGTGGCATTCGCGAT
Found at i:3209 original size:14 final size:14
Alignment explanation
Indices: 3190--3258 Score: 102
Period size: 14 Copynumber: 4.9 Consensus size: 14
3180 CATCAAAGGC
*
3190 ATGTGGTATTTGCA
1 ATGTGGTATTCGCA
3204 ATGTGGTATTCGCA
1 ATGTGGTATTCGCA
* *
3218 ATGTGGCATTCGCG
1 ATGTGGTATTCGCA
3232 ATGTGGTATTCGCA
1 ATGTGGTATTCGCA
*
3246 ATGTGGCATTCGC
1 ATGTGGTATTCGC
3259 GATATAGTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 49 1.00
ACGTcount: A:0.19, C:0.16, G:0.30, T:0.35
Consensus pattern (14 bp):
ATGTGGTATTCGCA
Found at i:3235 original size:28 final size:28
Alignment explanation
Indices: 3190--3270 Score: 117
Period size: 28 Copynumber: 2.9 Consensus size: 28
3180 CATCAAAGGC
* * *
3190 ATGTGGTATTTGCAATGTGGTATTCGCA
1 ATGTGGCATTCGCGATGTGGTATTCGCA
3218 ATGTGGCATTCGCGATGTGGTATTCGCA
1 ATGTGGCATTCGCGATGTGGTATTCGCA
* *
3246 ATGTGGCATTCGCGATATAGTATTC
1 ATGTGGCATTCGCGATGTGGTATTC
3271 CTTCTTCCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.36
Consensus pattern (28 bp):
ATGTGGCATTCGCGATGTGGTATTCGCA
Found at i:3334 original size:19 final size:19
Alignment explanation
Indices: 3310--3383 Score: 67
Period size: 19 Copynumber: 3.7 Consensus size: 19
3300 GGCATGTGGC
3310 ATGGTACTCGCGATATGGT
1 ATGGTACTCGCGATATGGT
* * *
3329 ATGGTATTCGCGACGCTAAAGGC
1 ATGGTACTCGCGA---T-ATGGT
*
3352 ATGGTACTCGCGATGTGGT
1 ATGGTACTCGCGATATGGT
*
3371 ATGGTATTCGCGA
1 ATGGTACTCGCGA
3384 CGCTAAAGGC
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
19 26 0.60
20 1 0.02
22 1 0.02
23 15 0.35
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (19 bp):
ATGGTACTCGCGATATGGT
Found at i:3362 original size:23 final size:23
Alignment explanation
Indices: 3329--3406 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 23
3319 GCGATATGGT
*
3329 ATGGTATTCGCGACGCTAAAGGC
1 ATGGTACTCGCGACGCTAAAGGC
* *
3352 ATGGTACTCGCGATG-T---GGT
1 ATGGTACTCGCGACGCTAAAGGC
*
3371 ATGGTATTCGCGACGCTAAAGGC
1 ATGGTACTCGCGACGCTAAAGGC
3394 ATGGTACTCGCGA
1 ATGGTACTCGCGA
3407 TGTGGTATTC
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
19 15 0.34
20 1 0.02
22 1 0.02
23 27 0.61
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (23 bp):
ATGGTACTCGCGACGCTAAAGGC
Found at i:3371 original size:42 final size:42
Alignment explanation
Indices: 3307--3414 Score: 207
Period size: 42 Copynumber: 2.6 Consensus size: 42
3297 AGTGGCATGT
*
3307 GGCATGGTACTCGCGATATGGTATGGTATTCGCGACGCTAAA
1 GGCATGGTACTCGCGATGTGGTATGGTATTCGCGACGCTAAA
3349 GGCATGGTACTCGCGATGTGGTATGGTATTCGCGACGCTAAA
1 GGCATGGTACTCGCGATGTGGTATGGTATTCGCGACGCTAAA
3391 GGCATGGTACTCGCGATGTGGTAT
1 GGCATGGTACTCGCGATGTGGTAT
3415 TCGCAATTGC
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.27
Consensus pattern (42 bp):
GGCATGGTACTCGCGATGTGGTATGGTATTCGCGACGCTAAA
Found at i:3565 original size:77 final size:78
Alignment explanation
Indices: 3473--3617 Score: 247
Period size: 77 Copynumber: 1.9 Consensus size: 78
3463 TCTTTCAATG
* *
3473 TCAATGTCAAAGGCATATGGTGTTCGCGAGACTATCACCTTCTTTCAACGTCAAAA-CATATGGT
1 TCAATGTCAAAGGCATATGGTGTTCGCGAAACTATCACCCTCTTTCAACGTCAAAAGCATATGGT
3537 GTTTGTGCCTCTT
66 GTTTGTGCCTCTT
* *
3550 TCAATGTCAAAGGCATATGGTGTTTGCGAAACTATCACCCTCTTTCAATGTCAAAAGCATATGGT
1 TCAATGTCAAAGGCATATGGTGTTCGCGAAACTATCACCCTCTTTCAACGTCAAAAGCATATGGT
3615 GTT
66 GTT
3618 CGCGAAGTCT
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
77 52 0.83
78 11 0.17
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (78 bp):
TCAATGTCAAAGGCATATGGTGTTCGCGAAACTATCACCCTCTTTCAACGTCAAAAGCATATGGT
GTTTGTGCCTCTT
Found at i:3646 original size:30 final size:30
Alignment explanation
Indices: 3610--3670 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
3600 TCAAAAGCAT
*
3610 ATGGTGTTCGCGAAGTCTCACCTCCTTCCA
1 ATGGTGTTAGCGAAGTCTCACCTCCTTCCA
3640 ATGGTGTTAGCGAAGTCTCACCTCCTTCCA
1 ATGGTGTTAGCGAAGTCTCACCTCCTTCCA
3670 A
1 A
3671 CGTCCTGAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.31, G:0.20, T:0.30
Consensus pattern (30 bp):
ATGGTGTTAGCGAAGTCTCACCTCCTTCCA
Found at i:3826 original size:55 final size:55
Alignment explanation
Indices: 3760--3870 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
3750 TTAAGTCGCC
3760 CAATACATACTAGCTATGCCACTGGCTCTTGCGCCTCTTACTTGCTGTGATGCAA
1 CAATACATACTAGCTATGCCACTGGCTCTTGCGCCTCTTACTTGCTGTGATGCAA
*
3815 CAATACATACTAGCTATGCCACTGGCTCTTGCGCCTCTTACTTGTTGTGATGCAA
1 CAATACATACTAGCTATGCCACTGGCTCTTGCGCCTCTTACTTGCTGTGATGCAA
3870 C
1 C
3871 TGGCTTCTAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.32
Consensus pattern (55 bp):
CAATACATACTAGCTATGCCACTGGCTCTTGCGCCTCTTACTTGCTGTGATGCAA
Found at i:4156 original size:46 final size:46
Alignment explanation
Indices: 4089--4373 Score: 359
Period size: 46 Copynumber: 6.3 Consensus size: 46
4079 ATTTTTGAAA
* *
4089 TCTATATGGTAGCTCTTATGTGAGCACCCTTTTTCAGAAAGAATAC
1 TCTATACGGTAGCTCTTATGTGAGCACCCTTCTTCAGAAAGAATAC
*
4135 TCTATACGGTAGCTCTTATGTGAGCGCCCTTCTTCAGAAAGAATAC
1 TCTATACGGTAGCTCTTATGTGAGCACCCTTCTTCAGAAAGAATAC
* * * *
4181 TCTATATGGTAGCTCTTATGTGAGCACCTTTCTTCGGAAAAAAATAC
1 TCTATACGGTAGCTCTTATGTGAGCACCCTTCTTCAG-AAAGAATAC
*
4228 TCTATACGGTAGCTCCTATGTGAGCACCCTTCTTCAGAAAGAATAC
1 TCTATACGGTAGCTCTTATGTGAGCACCCTTCTTCAGAAAGAATAC
* * * *
4274 TCTATGCAGTAACTCTTATGTGAGCACCCATCTTCAGAAAGAATA-
1 TCTATACGGTAGCTCTTATGTGAGCACCCTTCTTCAGAAAGAATAC
* * *
4319 -C--T-C--TAGCTCTTATATGAGCACCCATCTTCAGAAAAGAATTC
1 TCTATACGGTAGCTCTTATGTGAGCACCCTTCTTCAG-AAAGAATAC
*
4360 TCTATATGGTAGCT
1 TCTATACGGTAGCT
4374 TCTTGCAAAG
Statistics
Matches: 208, Mismatches: 22, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
39 26 0.12
40 7 0.03
41 1 0.00
42 2 0.01
44 2 0.01
46 124 0.60
47 46 0.22
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (46 bp):
TCTATACGGTAGCTCTTATGTGAGCACCCTTCTTCAGAAAGAATAC
Found at i:4251 original size:93 final size:92
Alignment explanation
Indices: 4089--4373 Score: 361
Period size: 93 Copynumber: 3.2 Consensus size: 92
4079 ATTTTTGAAA
*
4089 TCTATATGGTAGCTCTTATGTGAGCACCCTTT-TTCAGAAAGAATACTCTATACGGTAGCTCTTA
1 TCTATATGGTAGCTCTTATGTGAGCA-CCTTTCTTCAGAAAGAATACTCTATACGGTAGCTCCTA
*
4153 TGTGAGCGCCCTTCTTCAGAAAGAATAC
65 TGTGAGCACCCTTCTTCAGAAAGAATAC
* *
4181 TCTATATGGTAGCTCTTATGTGAGCACCTTTCTTCGGAAAAAAATACTCTATACGGTAGCTCCTA
1 TCTATATGGTAGCTCTTATGTGAGCACCTTTCTTCAG-AAAGAATACTCTATACGGTAGCTCCTA
4246 TGTGAGCACCCTTCTTCAGAAAGAATAC
65 TGTGAGCACCCTTCTTCAGAAAGAATAC
*** * ** *
4274 TCTATGCAGTAACTCTTATGTGAGCACCCATCTTCAGAAAGAATA--C--T-C--TAGCTCTTAT
1 TCTATATGGTAGCTCTTATGTGAGCACCTTTCTTCAGAAAGAATACTCTATACGGTAGCTCCTAT
* * *
4332 ATGAGCACCCATCTTCAGAAAAGAATTC
66 GTGAGCACCCTTCTTCAG-AAAGAATAC
4360 TCTATATGGTAGCT
1 TCTATATGGTAGCT
4374 TCTTGCAAAG
Statistics
Matches: 170, Mismatches: 20, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
85 25 0.15
86 18 0.11
87 1 0.01
88 1 0.01
90 1 0.01
91 5 0.03
92 37 0.22
93 82 0.48
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (92 bp):
TCTATATGGTAGCTCTTATGTGAGCACCTTTCTTCAGAAAGAATACTCTATACGGTAGCTCCTAT
GTGAGCACCCTTCTTCAGAAAGAATAC
Found at i:4340 original size:39 final size:40
Alignment explanation
Indices: 4286--4363 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 40
4276 TATGCAGTAA
*
4286 CTCTTATGTGAGCACCCATCTTCAG-AAAGAATACTCTAG
1 CTCTTATATGAGCACCCATCTTCAGAAAAGAATACTCTAG
*
4325 CTCTTATATGAGCACCCATCTTCAGAAAAGAATTCTCTA
1 CTCTTATATGAGCACCCATCTTCAGAAAAGAATACTCTA
4364 TATGGTAGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 24 0.67
40 12 0.33
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (40 bp):
CTCTTATATGAGCACCCATCTTCAGAAAAGAATACTCTAG
Found at i:6142 original size:26 final size:26
Alignment explanation
Indices: 6106--6158 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
6096 ATTAGCATAA
*
6106 GGTATTTCCATAGGATGTTGCCACAG
1 GGTATTTCCATAGGATCTTGCCACAG
*
6132 GGTATTTCCATAGGGTCTTGCCACAG
1 GGTATTTCCATAGGATCTTGCCACAG
6158 G
1 G
6159 AACTGTGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (26 bp):
GGTATTTCCATAGGATCTTGCCACAG
Found at i:6234 original size:3 final size:3
Alignment explanation
Indices: 6226--6254 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6216 CCCATGTCGA
6226 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6255 ATAAATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6370 original size:13 final size:13
Alignment explanation
Indices: 6354--6384 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
6344 TTGCAAGAAC
*
6354 GTATTGCCATAGG
1 GTATTGACATAGG
6367 GTATTGACATAGG
1 GTATTGACATAGG
6380 GTATT
1 GTATT
6385 ACCACATGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.26, C:0.10, G:0.29, T:0.35
Consensus pattern (13 bp):
GTATTGACATAGG
Done.