Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021092.1 Corchorus olitorius cultivar O-4 contig21125, 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: 66457
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1289 original size:12 final size:12
Alignment explanation
Indices: 1272--1297 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1262 AATATTTGGA
1272 ATCATTATTATT
1 ATCATTATTATT
1284 ATCATTATTATT
1 ATCATTATTATT
1296 AT
1 AT
1298 TATGTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (12 bp):
ATCATTATTATT
Found at i:3063 original size:42 final size:43
Alignment explanation
Indices: 3008--3102 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 43
2998 AGTGCATTAC
*
3008 CTAA-ATTATA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTATACCTCCATCTCTAGATAATTCATCAAAATAAAG
*
3049 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTATA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
3094 CTAATATTA
1 CTAATATTA
3103 ATTGTTGCTT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
41 4 0.09
42 5 0.11
45 38 0.81
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (43 bp):
CTAATATTATACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:5469 original size:60 final size:60
Alignment explanation
Indices: 5375--5537 Score: 220
Period size: 60 Copynumber: 2.7 Consensus size: 60
5365 GGTAATTGCT
* * * *
5375 CAAATAAGGGTCTAACGTT-TGCCAAAATGTTCAAATAAGGGCCCGATCTTTTAATTAGGA
1 CAAATAAGGGCCTAACGTTAT-CGAAAATGCTCAAATAAGGGCCCAATCTTTTAATTAGGA
* * * * *
5435 CAAATACGGGCCTAACGTTATCGAAAATGCTCAAATAAGTGTCCAATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCAATCTTTTAATTAGGA
*
5495 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAAAAAGGGCC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCC
5538 TGGCGTCGGT
Statistics
Matches: 89, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
60 88 0.99
61 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCAATCTTTTAATTAGGA
Found at i:5470 original size:31 final size:31
Alignment explanation
Indices: 5435--5538 Score: 92
Period size: 31 Copynumber: 3.4 Consensus size: 31
5425 TTAATTAGGA
*
5435 CAAATACGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
* * **
5466 CAAATAAGTGTCC-AATC-TT-T-TAATTTGGC-
1 CAAATAAG-GGCCTAA-CGTTATCGAAAAT-GCT
5495 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
*
5526 CAAAAAAGGGCCT
1 CAAATAAGGGCCT
5539 GGCGTCGGTT
Statistics
Matches: 55, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
28 4 0.07
29 15 0.27
30 6 0.11
31 26 0.47
32 4 0.07
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCT
Found at i:5626 original size:12 final size:12
Alignment explanation
Indices: 5609--5633 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5599 GCAAACCTTA
5609 GGCTCTTATTTG
1 GGCTCTTATTTG
5621 GGCTCTTATTTG
1 GGCTCTTATTTG
5633 G
1 G
5634 CCAAATTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.28, T:0.48
Consensus pattern (12 bp):
GGCTCTTATTTG
Found at i:12618 original size:11 final size:11
Alignment explanation
Indices: 12602--12632 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
12592 TTATAGTTCA
12602 TATAAATAATT
1 TATAAATAATT
12613 TATAAATAATT
1 TATAAATAATT
*
12624 TATGAATAA
1 TATAAATAA
12633 ACGACGAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (11 bp):
TATAAATAATT
Found at i:17866 original size:42 final size:42
Alignment explanation
Indices: 17807--17889 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
17797 GCTAAGGATC
*
17807 ATGATTTGAGTTGAGTATTTCTTAATTTAGAAAGAATTTTCT
1 ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCT
*
17849 ATGATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
17890 AAGACTTAGC
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:0.30, C:0.06, G:0.17, T:0.47
Consensus pattern (42 bp):
ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCT
Found at i:26851 original size:27 final size:31
Alignment explanation
Indices: 26793--26864 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 31
26783 GCTTAAATAC
* *
26793 CAAAAAAATCCCTTAACTTTTTCATTTGGGA
1 CAAATAAATCCCTTAACTTTTTCATTTAGGA
26824 CAAATAAATCCCTT-A-TTTTT-A-TTAGGA
1 CAAATAAATCCCTTAACTTTTTCATTTAGGA
26851 CAAATAAATCCCTT
1 CAAATAAATCCCTT
26865 TGCTTTCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 19 0.49
28 1 0.03
29 5 0.13
30 1 0.03
31 13 0.33
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.36
Consensus pattern (31 bp):
CAAATAAATCCCTTAACTTTTTCATTTAGGA
Found at i:27898 original size:31 final size:28
Alignment explanation
Indices: 27836--27907 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
27826 TTTGAAAGCA
*
27836 AAGGGATTTATTTGTCCCAAAAAAAGAT
1 AAGGGATTTATTTGTCCAAAAAAAAGAT
*
27864 AAGGGATTTATTTGTTCCAAATGAAAAAGTT
1 AAGGGATTTATTTG-TCCAAA--AAAAAGAT
*
27895 AAGGG-TTTTTTTG
1 AAGGGATTTATTTG
27908 GTATTTAATC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 14 0.37
29 5 0.13
30 7 0.18
31 12 0.32
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (28 bp):
AAGGGATTTATTTGTCCAAAAAAAAGAT
Found at i:28821 original size:20 final size:20
Alignment explanation
Indices: 28796--28843 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
28786 GCCATTTCCT
28796 TCCTTTCCTTTAAAAAACCC
1 TCCTTTCCTTTAAAAAACCC
28816 TCCTTTCCTTTAAAAAACCC
1 TCCTTTCCTTTAAAAAACCC
28836 TCCTTTCC
1 TCCTTTCC
28844 CATCCTATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.25, C:0.38, G:0.00, T:0.38
Consensus pattern (20 bp):
TCCTTTCCTTTAAAAAACCC
Found at i:29193 original size:31 final size:31
Alignment explanation
Indices: 29147--29210 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
29137 AGTACGAGTT
* *
29147 TTGTAAAACTTTTGAATCGTCTATTATACCC
1 TTGTAAAACTATTGAATCGCCTATTATACCC
* *
29178 TTGTTAAACTATTGAATCGCCTATTATGCCC
1 TTGTAAAACTATTGAATCGCCTATTATACCC
29209 TT
1 TT
29211 ATTTTTCGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.42
Consensus pattern (31 bp):
TTGTAAAACTATTGAATCGCCTATTATACCC
Found at i:31186 original size:12 final size:12
Alignment explanation
Indices: 31169--31194 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31159 TGAAACACCA
31169 AATAAAATTACT
1 AATAAAATTACT
31181 AATAAAATTACT
1 AATAAAATTACT
31193 AA
1 AA
31195 ACGCCCCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (12 bp):
AATAAAATTACT
Found at i:31415 original size:56 final size:56
Alignment explanation
Indices: 31346--31514 Score: 275
Period size: 56 Copynumber: 3.0 Consensus size: 56
31336 TCCGTTTCCT
* *
31346 TTTCACACAATAAATATTATAATAAATCATATCCCCCTATTTTTACTTAATTATTC
1 TTTCACACAATAAATGTTATAATAAATCATATCCCCCTATTTCTACTTAATTATTC
* * * *
31402 TTTCACACAATAAATGTTATGATAAATCCTATCTCCCTATTTCTACTTAATTATTA
1 TTTCACACAATAAATGTTATAATAAATCATATCCCCCTATTTCTACTTAATTATTC
*
31458 TTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATTC
1 TTTCACACAATAAATGTTATAATAAATCATATCCCCCTATTTCTACTTAATTATTC
31514 T
1 T
31515 ACAAAATAAA
Statistics
Matches: 102, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 102 1.00
ACGTcount: A:0.36, C:0.21, G:0.02, T:0.42
Consensus pattern (56 bp):
TTTCACACAATAAATGTTATAATAAATCATATCCCCCTATTTCTACTTAATTATTC
Found at i:31639 original size:42 final size:42
Alignment explanation
Indices: 31580--31660 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
31570 TAAGGATCAG
31580 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
*
31622 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
31661 AAGACTTAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:34469 original size:29 final size:28
Alignment explanation
Indices: 34407--34469 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
34397 AACTTGTAGC
** *
34407 ATTTGGATGTTTTGCTTCATGAATTTTA
1 ATTTGGACATTTTGCTTCATGAATTTCA
*
34435 ATTTTGGACATTTTGCTTCCTGAACTTTCA
1 A-TTTGGACATTTTGCTTCATGAA-TTTCA
34465 ATTTG
1 ATTTG
34470 AACCTCTGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 1 0.03
29 23 0.79
30 5 0.17
ACGTcount: A:0.21, C:0.13, G:0.16, T:0.51
Consensus pattern (28 bp):
ATTTGGACATTTTGCTTCATGAATTTCA
Found at i:36416 original size:17 final size:17
Alignment explanation
Indices: 36394--36427 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
36384 TTGGTGCTAG
36394 GGAAAATACTAGGGAAA
1 GGAAAATACTAGGGAAA
**
36411 GGAAAATTTTAGGGAAA
1 GGAAAATACTAGGGAAA
36428 ATTGAAATCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.29, T:0.18
Consensus pattern (17 bp):
GGAAAATACTAGGGAAA
Found at i:38181 original size:23 final size:27
Alignment explanation
Indices: 38129--38178 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
38119 TTATGTTCGT
38129 TTATATTATATATTATATATATAATAA
1 TTATATTATATATTATATATATAATAA
*
38156 TTATATT-TTTATT-TATATA-AATA
1 TTATATTATATATTATATATATAATA
38179 TTAAAATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 6 0.27
26 5 0.23
27 7 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TTATATTATATATTATATATATAATAA
Found at i:38227 original size:40 final size:41
Alignment explanation
Indices: 38143--38229 Score: 108
Period size: 40 Copynumber: 2.1 Consensus size: 41
38133 ATTATATATT
* *
38143 ATATATATAATAATTATATTTTTATTTATATAAATATTAAA
1 ATATATATAATAATTATATTTTTATTCATATAAATATAAAA
*
38184 ATATGTAT-ATAATTATA-TTTTATTCCATAT-AATATAAATA
1 ATATATATAATAATTATATTTTTATT-CATATAAATATAAA-A
38224 ATATAT
1 ATATAT
38230 TTATTCCAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
39 14 0.35
40 19 0.47
41 7 0.17
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.49
Consensus pattern (41 bp):
ATATATATAATAATTATATTTTTATTCATATAAATATAAAA
Found at i:49366 original size:3 final size:3
Alignment explanation
Indices: 49358--49383 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
49348 TAAAATAAAA
49358 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
49384 ATTGTTCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:51908 original size:39 final size:39
Alignment explanation
Indices: 51863--51946 Score: 168
Period size: 39 Copynumber: 2.2 Consensus size: 39
51853 TTGGTTATAC
51863 TTCATAGGGGTGAATATCAAACTTTTCTACTCTCTTCGT
1 TTCATAGGGGTGAATATCAAACTTTTCTACTCTCTTCGT
51902 TTCATAGGGGTGAATATCAAACTTTTCTACTCTCTTCGT
1 TTCATAGGGGTGAATATCAAACTTTTCTACTCTCTTCGT
51941 TTCATA
1 TTCATA
51947 TTGAATATTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (39 bp):
TTCATAGGGGTGAATATCAAACTTTTCTACTCTCTTCGT
Found at i:52197 original size:22 final size:23
Alignment explanation
Indices: 52161--52211 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
52151 TTTGCCCTTC
52161 TTCTCTCTCCCCCCACTAACTAT
1 TTCTCTCTCCCCCCACTAACTAT
* *
52184 TTCTC-CTCCTCCCACTCACTAT
1 TTCTCTCTCCCCCCACTAACTAT
*
52206 CTCTCT
1 TTCTCT
52212 TCATAAGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.14, C:0.49, G:0.00, T:0.37
Consensus pattern (23 bp):
TTCTCTCTCCCCCCACTAACTAT
Found at i:58970 original size:29 final size:30
Alignment explanation
Indices: 58928--59002 Score: 134
Period size: 29 Copynumber: 2.5 Consensus size: 30
58918 GTTTGTATTC
58928 AAAGTGAGCTCGTTGCTTGGCC-AAAAAAA
1 AAAGTGAGCTCGTTGCTTGGCCAAAAAAAA
58957 AAAGTGAGCTCGTTGCTTGGCCAAAAAAAAA
1 AAAGTGAGCTCGTTGCTTGGCC-AAAAAAAA
58988 AAAGTGAGCTCGTTG
1 AAAGTGAGCTCGTTG
59003 TTGCCCCTAC
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
29 22 0.50
31 22 0.50
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.21
Consensus pattern (30 bp):
AAAGTGAGCTCGTTGCTTGGCCAAAAAAAA
Found at i:59629 original size:16 final size:15
Alignment explanation
Indices: 59608--59637 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
59598 GATTTATTCA
59608 ACAAAACATCCAGGTT
1 ACAAAACAT-CAGGTT
59624 ACAAAACATCAGGT
1 ACAAAACATCAGGT
59638 GGTAAAGACC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.23, G:0.13, T:0.17
Consensus pattern (15 bp):
ACAAAACATCAGGTT
Done.