Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009381.1 Corchorus capsularis cultivar CVL-1 contig09402, 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: 57931
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1902 original size:3 final size:3
Alignment explanation
Indices: 1896--1924 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1886 CAGCAGCAGC
1896 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1925 ATGTTGCTAG
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:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2651 original size:39 final size:35
Alignment explanation
Indices: 2608--2700 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 35
2598 TTGGTGGAGG
*
2608 TGGTGAAGGTGATGGTGGTGGCGGTGAGTACTCTACACA
1 TGGTGGAGGTGATGGTGGTGG-GGTG-GT--TCTACACA
*
2647 TGGTGGAGGTGGA-GGT-G-GGGGTGGTTCTATACA
1 TGGTGGAGGT-GATGGTGGTGGGGTGGTTCTACACA
2680 TGGTGGAGGTGATGGTGGTGG
1 TGGTGGAGGTGATGGTGGTGG
2701 TGGAGAGTGG
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
32 2 0.04
33 20 0.42
34 1 0.02
35 4 0.08
36 4 0.08
37 2 0.04
38 1 0.02
39 12 0.25
40 2 0.04
ACGTcount: A:0.16, C:0.08, G:0.49, T:0.27
Consensus pattern (35 bp):
TGGTGGAGGTGATGGTGGTGGGGTGGTTCTACACA
Found at i:2796 original size:21 final size:21
Alignment explanation
Indices: 2770--2844 Score: 78
Period size: 21 Copynumber: 3.4 Consensus size: 21
2760 AAGGATAAAT
*
2770 TGGTGGAGGAGGTGAATGTGG
1 TGGTGGTGGAGGTGAATGTGG
* * *
2791 TGGTGGTGGTGGAGAGTGTGG
1 TGGTGGTGGAGGTGAATGTGG
*
2812 TGGCGGTGGAGGTGAGTATTGTGG
1 TGGTGGTGGAGGTGA--A-TGTGG
2836 TGGTGGTGG
1 TGGTGGTGG
2845 GGAGTTATAG
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
21 29 0.69
24 13 0.31
ACGTcount: A:0.12, C:0.01, G:0.59, T:0.28
Consensus pattern (21 bp):
TGGTGGTGGAGGTGAATGTGG
Found at i:2804 original size:24 final size:24
Alignment explanation
Indices: 2770--2848 Score: 64
Period size: 18 Copynumber: 3.5 Consensus size: 24
2760 AAGGATAAAT
*
2770 TGGTGGAGGAGGTGAATGTGGTGG
1 TGGTGGTGGAGGTGAATGTGGTGG
2794 TGGTGGTGGA---G-A-GT-GTGG
1 TGGTGGTGGAGGTGAATGTGGTGG
*
2812 TGGCGGTGGAGGTGAGTATTGTGGTGG
1 TGGTGGTGGAGGTGA--A-TGTGGTGG
2839 TGGTGG-GGAG
1 TGGTGGTGGAG
2849 TTATAGTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 16
0.69 0.05 0.26
Matches are distributed among these distances:
18 13 0.30
19 2 0.05
20 1 0.02
21 2 0.05
24 10 0.23
26 6 0.14
27 9 0.21
ACGTcount: A:0.13, C:0.01, G:0.59, T:0.27
Consensus pattern (24 bp):
TGGTGGTGGAGGTGAATGTGGTGG
Found at i:3137 original size:24 final size:24
Alignment explanation
Indices: 3101--3170 Score: 59
Period size: 24 Copynumber: 2.9 Consensus size: 24
3091 TGATGGTGGT
**
3101 GGTGGTGAAGGAGGTGGGGGAGAG
1 GGTGGTGGTGGAGGTGGGGGAGAG
* * *
3125 GGTGGTGGTGGAGGAGGGGAATAG
1 GGTGGTGGTGGAGGTGGGGGAGAG
*** *
3149 ACAGGTGGTGGCGGTGGGGGAG
1 GGTGGTGGTGGAGGTGGGGGAG
3171 GTGAAGGAGG
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.19, C:0.03, G:0.64, T:0.14
Consensus pattern (24 bp):
GGTGGTGGTGGAGGTGGGGGAGAG
Found at i:3221 original size:27 final size:27
Alignment explanation
Indices: 3191--3246 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
3181 TGGCGGTGAG
*
3191 GGTGGAGGGGGAGGTGGAGAGTAAACA
1 GGTGGAGGGGGAGGAGGAGAGTAAACA
* * * *
3218 GGTGGTGGGGGCGGAGGTGAGTAGACA
1 GGTGGAGGGGGAGGAGGAGAGTAAACA
3245 GG
1 GG
3247 CGGTGGAGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.23, C:0.05, G:0.59, T:0.12
Consensus pattern (27 bp):
GGTGGAGGGGGAGGAGGAGAGTAAACA
Found at i:3225 original size:66 final size:66
Alignment explanation
Indices: 3085--3288 Score: 203
Period size: 66 Copynumber: 3.0 Consensus size: 66
3075 AAACTGGTGG
** * * * * * * * * * *
3085 AGGTGGTGATGGTGGTGGTGGTGAAGGAGGTGGGGGAGAGGGTGGTGGTGGAGGAGGGGAATAGA
1 AGGTGGTGGCGGTGGGGGAGGTGAAGGAGGTGGAGGTGAGGGTGGAGGAGGAGGTGGAGAGTAAA
3150 C
66 C
* *
3151 AGGTGGTGGCGGTGGGGGAGGTGAAGGAGGTGGCGGTGAGGGTGGAGGGGGAGGTGGAGAGTAAA
1 AGGTGGTGGCGGTGGGGGAGGTGAAGGAGGTGGAGGTGAGGGTGGAGGAGGAGGTGGAGAGTAAA
3216 C
66 C
* * * *
3217 AGGTGGTGGGGGCGGAGGTGA-GTAGACAGGCGGTGGAGGTGATGGTGGAGGAGGAGGTGGAGAG
1 AGGTGGTGGCGGTGG-GG-GAGGT-GA-AGGAGGTGGAGGTGAGGGTGGAGGAGGAGGTGGAGAG
3281 TAAAC
62 TAAAC
3286 AGG
1 AGG
3289 CGGAGGAGGT
Statistics
Matches: 116, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
66 67 0.58
67 4 0.03
68 4 0.03
69 41 0.35
ACGTcount: A:0.21, C:0.04, G:0.60, T:0.15
Consensus pattern (66 bp):
AGGTGGTGGCGGTGGGGGAGGTGAAGGAGGTGGAGGTGAGGGTGGAGGAGGAGGTGGAGAGTAAA
C
Found at i:3302 original size:27 final size:27
Alignment explanation
Indices: 3263--3357 Score: 136
Period size: 27 Copynumber: 3.5 Consensus size: 27
3253 AGGTGATGGT
* *
3263 GGAGGAGGAGGTGGAGAGTAAACAGGC
1 GGAGGAGGTGGTGGAGAGTAAACTGGC
3290 GGAGGAGGTGGTGGAGAGTAAACTGGC
1 GGAGGAGGTGGTGGAGAGTAAACTGGC
* *
3317 GGCGGTGGTGGTGGAGAGTAAACTGGC
1 GGAGGAGGTGGTGGAGAGTAAACTGGC
* *
3344 GGCGGCGGTGGTGG
1 GGAGGAGGTGGTGG
3358 CGGTGATTGT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 63 1.00
ACGTcount: A:0.22, C:0.09, G:0.55, T:0.14
Consensus pattern (27 bp):
GGAGGAGGTGGTGGAGAGTAAACTGGC
Found at i:3309 original size:69 final size:69
Alignment explanation
Indices: 3179--3318 Score: 181
Period size: 69 Copynumber: 2.0 Consensus size: 69
3169 AGGTGAAGGA
* * * * * * *
3179 GGTGGCGGTGAGGGTGGAGGGGGAGGTGGAGAGTAAACAGGTGGTGGGGGCGGAGGTGAGTAGAC
1 GGTGGAGGTGAGGGTGGAGGAGGAGGTGGAGAGTAAACAGGCGGAGGAGGCGGAGGAGAGTAAAC
3244 AGGC
66 AGGC
* * *
3248 GGTGGAGGTGATGGTGGAGGAGGAGGTGGAGAGTAAACAGGCGGAGGAGGTGGTGGAGAGTAAAC
1 GGTGGAGGTGAGGGTGGAGGAGGAGGTGGAGAGTAAACAGGCGGAGGAGGCGGAGGAGAGTAAAC
*
3313 TGGC
66 AGGC
3317 GG
1 GG
3319 CGGTGGTGGT
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.23, C:0.06, G:0.57, T:0.14
Consensus pattern (69 bp):
GGTGGAGGTGAGGGTGGAGGAGGAGGTGGAGAGTAAACAGGCGGAGGAGGCGGAGGAGAGTAAAC
AGGC
Found at i:3400 original size:21 final size:21
Alignment explanation
Indices: 3376--3435 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
3366 GTGGAGTATA
*
3376 AACAGGTGGCGAAGGCACAAC
1 AACAGGTGGAGAAGGCACAAC
* * *
3397 AACAGGTGGTGACGGCACTAC
1 AACAGGTGGAGAAGGCACAAC
3418 AACAGGTGGAGAAGGCAC
1 AACAGGTGGAGAAGGCAC
3436 CGGGATTGGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.35, C:0.22, G:0.35, T:0.08
Consensus pattern (21 bp):
AACAGGTGGAGAAGGCACAAC
Found at i:5489 original size:3 final size:3
Alignment explanation
Indices: 5481--5510 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5471 ACATAAATTT
5481 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
5511 AAGATTATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (3 bp):
TGG
Found at i:6928 original size:17 final size:17
Alignment explanation
Indices: 6906--6945 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
6896 TGAATGTGAA
6906 TTAATTCTTTTTGAATG
1 TTAATTCTTTTTGAATG
* *
6923 TTAATTTTTTTTTTAATG
1 TTAA-TTCTTTTTGAATG
6941 TTAAT
1 TTAAT
6946 ATACTATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.25, C:0.03, G:0.07, T:0.65
Consensus pattern (17 bp):
TTAATTCTTTTTGAATG
Found at i:6997 original size:25 final size:25
Alignment explanation
Indices: 6945--6997 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
6935 TTAATGTTAA
*
6945 TATACTATATACTATAGTATATTAG
1 TATACTATATACTATACTATATTAG
6970 TATACTATATACTATACTAGTATT-G
1 TATACTATATACTATACTA-TATTAG
6995 TAT
1 TAT
6998 TGTAAATTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 22 0.85
26 4 0.15
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (25 bp):
TATACTATATACTATACTATATTAG
Found at i:17366 original size:1 final size:1
Alignment explanation
Indices: 17360--17393 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
17350 CAAAACAAGC
17360 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
17394 CTAACCATCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:29769 original size:31 final size:31
Alignment explanation
Indices: 29726--29802 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
29716 TCGAAACTAT
* *
29726 AATTTAAGACAATTAA-TTCCATGAACTTCCA
1 AATTTAAAACAATTAACCT-CATGAACTTCCA
*
29757 AATTTAAAACAATTAACCTCATGAACTTTCA
1 AATTTAAAACAATTAACCTCATGAACTTCCA
*
29788 AATTCAAAGACAATT
1 AATTTAAA-ACAATT
29803 TTTTCCTTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
31 33 0.82
32 7 0.17
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.31
Consensus pattern (31 bp):
AATTTAAAACAATTAACCTCATGAACTTCCA
Found at i:38610 original size:29 final size:31
Alignment explanation
Indices: 38545--38629 Score: 97
Period size: 31 Copynumber: 2.8 Consensus size: 31
38535 CTTGAATTTC
**
38545 GGAAGTTCAGAGGGCAAAATGTCCTAGATTT
1 GGAAGTTCAGAGGGCAAAATGTCCTAGAACT
38576 GGAAGTTCAG-GGGACAAAATGTCCT-GAACT
1 GGAAGTTCAGAGGG-CAAAATGTCCTAGAACT
*
38606 -GAAGTTCA-ACGGGCAAAACGTCCT
1 GGAAGTTCAGA-GGGCAAAATGTCCT
38630 TGACGCAATA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
29 18 0.38
30 9 0.19
31 21 0.44
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (31 bp):
GGAAGTTCAGAGGGCAAAATGTCCTAGAACT
Found at i:51725 original size:33 final size:34
Alignment explanation
Indices: 51682--51749 Score: 93
Period size: 36 Copynumber: 2.0 Consensus size: 34
51672 TTTAAAAATT
51682 AAAAGGGT-AGAATATATACATGTCAAAGTTTTA
1 AAAAGGGTAAGAATATATACATGTCAAAGTTTTA
* *
51715 AAAAGTGTAGAAGAATATATGCATGTCAAAGTTTT
1 AAAAGGGT--AAGAATATATACATGTCAAAGTTTT
51750 TTTTTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 7 0.23
36 23 0.77
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (34 bp):
AAAAGGGTAAGAATATATACATGTCAAAGTTTTA
Found at i:57152 original size:24 final size:25
Alignment explanation
Indices: 57118--57164 Score: 87
Period size: 24 Copynumber: 1.9 Consensus size: 25
57108 AGCCATTGCT
57118 TCTTTCTAATTAAATGCATGTTTGA
1 TCTTTCTAATTAAATGCATGTTTGA
57143 TCTTT-TAATTAAATGCATGTTT
1 TCTTTCTAATTAAATGCATGTTT
57165 CAATAAGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.51
Consensus pattern (25 bp):
TCTTTCTAATTAAATGCATGTTTGA
Found at i:57215 original size:27 final size:27
Alignment explanation
Indices: 57184--57248 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
57174 TATTTCTAGA
*
57184 AAACAAGGGAAAGGGACAGTTAAAAAG
1 AAACAAGGGAAAGGGACAATTAAAAAG
*
57211 AAACAAGGGGAAGGGACAATTAAAAAG
1 AAACAAGGGAAAGGGACAATTAAAAAG
*
57238 GAACAGAGGGA
1 AAACA-AGGGA
57249 GGAGTATATG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
27 29 0.88
28 4 0.12
ACGTcount: A:0.54, C:0.08, G:0.32, T:0.06
Consensus pattern (27 bp):
AAACAAGGGAAAGGGACAATTAAAAAG
Done.