Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007495.1 Corchorus capsularis cultivar CVL-1 contig07516, 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: 18747
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:1767 original size:24 final size:24
Alignment explanation
Indices: 1732--1780 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
1722 GAGGCAAGTA
1732 AGCTAAAAGAATCAACATCACAGC
1 AGCTAAAAGAATCAACATCACAGC
*
1756 AGCTAAAGGAATCAACATCACAGC
1 AGCTAAAAGAATCAACATCACAGC
1780 A
1 A
1781 ACATCATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.49, C:0.24, G:0.14, T:0.12
Consensus pattern (24 bp):
AGCTAAAAGAATCAACATCACAGC
Found at i:3203 original size:41 final size:40
Alignment explanation
Indices: 3145--3356 Score: 280
Period size: 41 Copynumber: 5.2 Consensus size: 40
3135 TCATATGCAT
*
3145 AAAGCAAACACAATCAAAGTCTTAATTCAGGTTAATTAAGA
1 AAAGCAAACACAGTCAAAGTCTTAATTCAGG-TAATTAAGA
3186 AAAGCAAACACAGTCAAAGTCTTAATTCAGGGTAATTAAGA
1 AAAGCAAACACAGTCAAAGTCTTAATTCA-GGTAATTAAGA
* *
3227 AAAGTAAACACAGTTAAAGTCTTAATTCATGGTAATTAAGA
1 AAAGCAAACACAGTCAAAGTCTTAATTCA-GGTAATTAAGA
* * *
3268 AAAACAAACACAATCAAAGTCTCAATTCATGGTAATTAAGA
1 AAAGCAAACACAGTCAAAGTCTTAATTCA-GGTAATTAAGA
* * * *
3309 AAAGTAAATACAGTCAAGGACTTAATTCAGGGTAATTAAGTA
1 AAAGCAAACACAGTCAAAGTCTTAATTCA-GGTAATTAAG-A
3351 AAAGCA
1 AAAGCA
3357 GTTCAAGTAC
Statistics
Matches: 151, Mismatches: 18, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
41 143 0.95
42 8 0.05
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.24
Consensus pattern (40 bp):
AAAGCAAACACAGTCAAAGTCTTAATTCAGGTAATTAAGA
Found at i:3287 original size:82 final size:81
Alignment explanation
Indices: 3145--3393 Score: 292
Period size: 82 Copynumber: 3.1 Consensus size: 81
3135 TCATATGCAT
* * * *
3145 AAAGCAAACACAATCAAAGTCTTAATTCAGGTTAATTAAGAAAAGCAAACACAGTCAAAGTCTTA
1 AAAGTAAACACAGTCAAAGTCTTAATTCAGG-TAATTAAGAAAAACAAACACAATCAAAGTCTTA
3210 ATTCAGGGTAATTAAGA
65 ATTCAGGGTAATTAAGA
* *
3227 AAAGTAAACACAGTTAAAGTCTTAATTCATGGTAATTAAGAAAAACAAACACAATCAAAGTCTCA
1 AAAGTAAACACAGTCAAAGTCTTAATTCA-GGTAATTAAGAAAAACAAACACAATCAAAGTCTTA
*
3292 ATTCATGGTAATTAAGA
65 ATTCAGGGTAATTAAGA
* * * * * **
3309 AAAGTAAATACAGTCAAGGACTTAATTCAGGGTAATTAAG--TAA-AAGCA-GTTC-AAGTACTT
1 AAAGTAAACACAGTCAAAGTCTTAATTCA-GGTAATTAAGAAAAACAAACACAATCAAAGT-CTT
3369 AATTCAGGGTAATTAAGTA
64 AATTCAGGGTAATTAAG-A
3388 AAAGTA
1 AAAGTA
3394 GTTAAAGGAC
Statistics
Matches: 146, Mismatches: 18, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
77 4 0.03
78 20 0.14
79 11 0.08
80 2 0.01
82 107 0.73
83 2 0.01
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.25
Consensus pattern (81 bp):
AAAGTAAACACAGTCAAAGTCTTAATTCAGGTAATTAAGAAAAACAAACACAATCAAAGTCTTAA
TTCAGGGTAATTAAGA
Found at i:3372 original size:37 final size:36
Alignment explanation
Indices: 3310--3463 Score: 188
Period size: 37 Copynumber: 4.2 Consensus size: 36
3300 TAATTAAGAA
3310 AAGTAAATA-CAGTCAAGGACTTAATTCAGGGTAATT
1 AAGTAAA-AGCAGTCAAGGACTTAATTCAGGGTAATT
*
3346 AAGTAAAAGCAGTTCAAGTACTTAATTCAGGGTAATT
1 AAGTAAAAGCAG-TCAAGGACTTAATTCAGGGTAATT
* * * *
3383 AAGTAAAAGTAGTTAAAGGACTTAATTTCAAGGAAATT
1 AAGTAAAAGCAG-TCAAGGACTTAA-TTCAGGGTAATT
*
3421 AAGTAAAAGCAG-CACA-GACTTAATTCAGGATAATT
1 AAGTAAAAGCAGTCA-AGGACTTAATTCAGGGTAATT
3456 AAGTAAAA
1 AAGTAAAA
3464 CAAGCACAGA
Statistics
Matches: 103, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
35 18 0.17
36 18 0.17
37 46 0.45
38 21 0.20
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.27
Consensus pattern (36 bp):
AAGTAAAAGCAGTCAAGGACTTAATTCAGGGTAATT
Found at i:3515 original size:41 final size:41
Alignment explanation
Indices: 3412--3930 Score: 770
Period size: 41 Copynumber: 12.9 Consensus size: 41
3402 ACTTAATTTC
*
3412 AAGGAAATTAAGTAAA-AGC-AGCACAGACTTAA-TTC-AGG
1 AAGGAAATTAGGTAAAGA-CAAGCACAGACTTAATTTCAAGG
* *
3450 -A--TAATTAAGTAAA-ACAAGCACAGACTTAATTTCAAGG
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
*
3487 AAGGAAATTAGGTAAAGATAAGCACAGACTTAATTTCAAGG
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
* * *
3528 AAGAAAATTTGGTAAAGACGAGCACAGACTTAATTTCAAGG
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
* * * *
3569 AAGGAAATTAGGTAGAGATAAGCACATACTTTATTTCAAGG
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
*
3610 AAGGAAATTAGGTAAAGACAAGCACAGACTTTATTTCAAGG
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
*
3651 AAGGAAATTAGGTAAAGACAAGCACAGACTT-TTTTCAAGG
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
3691 AAGGAAATTAGGTAAA-ACAAGCACAGACTTAATTTCAAGG
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
3731 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
* *
3772 AAGGACATTAGGTAAGGACAAGCACAGACTTAATTTCAAGG
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
* * * *
3813 AAGGAAATTAGGTAAGGATAAGCACATACTTAATTTCAGGG
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
3854 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
* *
3895 AAGGAAATTAGGTAAAGACAAGCATAGAATTAATTT
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTT
3931 AGGATAATTA
Statistics
Matches: 440, Mismatches: 32, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
34 1 0.00
35 25 0.06
36 3 0.01
37 4 0.01
38 1 0.00
39 14 0.03
40 58 0.13
41 334 0.76
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22
Consensus pattern (41 bp):
AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
Found at i:3892 original size:244 final size:245
Alignment explanation
Indices: 3447--3918 Score: 831
Period size: 244 Copynumber: 1.9 Consensus size: 245
3437 GACTTAATTC
*
3447 AGGATAATTAAGTAAAACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGATAAGCAC
1 AGGATAATTAAGTAAAACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCAC
* *
3512 AGACTTAATTTCAAGGAAGAAAATTTGGTAAAGACGAGCACAGACTTAATTTCAAGGAAGGAAAT
66 AGACTTAATTTCAAGGAAGAAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAAT
* *
3577 TAGGTAGAGATAAGCACATACTTTATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTT
131 TAGGTAGAGATAAGCACATACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTA
3642 ATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTTTTTCAAGGA
196 ATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTTTTTCAAGGA
*
3692 AGGA-AATTAGGTAAAACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCAC
1 AGGATAATTAAGTAAAACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCAC
* * *
3756 AGACTTAATTTCAAGGAAGGACATTAGGTAAGGACAAGCACAGACTTAATTTCAAGGAAGGAAAT
66 AGACTTAATTTCAAGGAAGAAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAAT
*
3821 TAGGTA-AGGATAAGCACATACTTAATTTCAGGGAAGGAAATTAGGTAAAGACAAGCACAGACTT
131 TAGGTAGA-GATAAGCACATACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTT
3885 AATTTCAAGGAAGGAAATTAGGTAAAGACAAGCA
195 AATTTCAAGGAAGGAAATTAGGTAAAGACAAGCA
3919 TAGAATTAAT
Statistics
Matches: 216, Mismatches: 10, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
243 1 0.00
244 211 0.98
245 4 0.02
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.21
Consensus pattern (245 bp):
AGGATAATTAAGTAAAACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCAC
AGACTTAATTTCAAGGAAGAAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAAT
TAGGTAGAGATAAGCACATACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTA
ATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTTTTTCAAGGA
Found at i:4011 original size:36 final size:35
Alignment explanation
Indices: 3937--4052 Score: 119
Period size: 36 Copynumber: 3.3 Consensus size: 35
3927 ATTTAGGATA
* * *
3937 ATTAAGTAAAA-TCG-AAAGACTTAATTTCAAAGAA
1 ATTAAGTAAAATTAGCAAAGACTTAA-TCCAAAGAG
3971 ATTAAGTAAAATTAGCAAAGACTTAATCCAAAGATG
1 ATTAAGTAAAATTAGCAAAGACTTAATCCAAAGA-G
* * * * *
4007 ATTAAGCAAGATTAGACAAAGACTTAACCCAAGGGG
1 ATTAAGTAAAATTAG-CAAAGACTTAATCCAAAGAG
4043 ATTAAGTAAA
1 ATTAAGTAAA
4053 GAAAAAGACT
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
34 11 0.16
35 9 0.13
36 32 0.47
37 16 0.24
ACGTcount: A:0.50, C:0.11, G:0.16, T:0.23
Consensus pattern (35 bp):
ATTAAGTAAAATTAGCAAAGACTTAATCCAAAGAG
Found at i:4079 original size:32 final size:33
Alignment explanation
Indices: 4043--4251 Score: 158
Period size: 32 Copynumber: 6.2 Consensus size: 33
4033 ACCCAAGGGG
4043 ATTAAGTAAAGAA-AAAGACTTAATTCAGGGTA
1 ATTAAGTAAAGAATAAAGACTTAATTCAGGGTA
* *
4075 ATTAAGT--AGAGTCAAAGACTTAATTCATGGTA
1 ATTAAGTAAAGAAT-AAAGACTTAATTCAGGGTA
* * *
4107 ATTAAGTAGAATCAATAAATGGCTTAATTCAAGGTA
1 ATTAAGTA-AA-GAATAAA-GACTTAATTCAGGGTA
* *
4143 ATTAAGT--AGAGTCAATGACTTAATTCAGGGTA
1 ATTAAGTAAAGAAT-AAAGACTTAATTCAGGGTA
*** * *
4175 ATTAAGTAGTCAATAAAGTGCTTAATTCAGGATA
1 ATTAAGTAAAGAATAAAG-ACTTAATTCAGGGTA
* * **
4209 ATTAAGCAGAGATAATAAAGAACTTAATTCAGGGCG
1 ATTAAGTA-A-AGAATAAAG-ACTTAATTCAGGGTA
4245 ATTAAGT
1 ATTAAGT
4252 GGAGTTAATA
Statistics
Matches: 137, Mismatches: 27, Indels: 22
0.74 0.15 0.12
Matches are distributed among these distances:
30 3 0.02
32 55 0.40
33 6 0.04
34 22 0.16
35 4 0.03
36 47 0.34
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.29
Consensus pattern (33 bp):
ATTAAGTAAAGAATAAAGACTTAATTCAGGGTA
Found at i:4143 original size:36 final size:35
Alignment explanation
Indices: 4056--4272 Score: 184
Period size: 36 Copynumber: 6.3 Consensus size: 35
4046 AAGTAAAGAA
* *
4056 AAAGACTTAATTCAGGGTAATTAAGTAGAGTC---
1 AAAGACTTAATTCAAGGTAATTAAGTAGAATCAAT
*
4088 AAAGACTTAATTCATGGTAATTAAGTAGAATCAAT
1 AAAGACTTAATTCAAGGTAATTAAGTAGAATCAAT
* *
4123 AAATGGCTTAATTCAAGGTAATTAAGTAGAGTCAAT
1 AAA-GACTTAATTCAAGGTAATTAAGTAGAATCAAT
*
4159 ---GACTTAATTCAGGGTAATTAAGTAG--TCAAT
1 AAAGACTTAATTCAAGGTAATTAAGTAGAATCAAT
* *
4189 AAAGTGCTTAATTC-AGGATAATTAAGCAGAGAT-AAT
1 AAAG-ACTTAATTCAAGG-TAATTAAGTAGA-ATCAAT
* ** * * *
4225 AAAGAACTTAATTCAGGGCGATTAAGTGGAGTTAAT
1 AAAG-ACTTAATTCAAGGTAATTAAGTAGAATCAAT
4261 AAAGAACTTAAT
1 AAAG-ACTTAAT
4273 CTAAATAGAG
Statistics
Matches: 153, Mismatches: 18, Indels: 24
0.78 0.09 0.12
Matches are distributed among these distances:
30 5 0.03
32 53 0.35
33 3 0.02
34 18 0.12
35 4 0.03
36 67 0.44
37 3 0.02
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.29
Consensus pattern (35 bp):
AAAGACTTAATTCAAGGTAATTAAGTAGAATCAAT
Found at i:4143 original size:68 final size:66
Alignment explanation
Indices: 4061--4251 Score: 233
Period size: 68 Copynumber: 2.8 Consensus size: 66
4051 AAGAAAAAGA
* *
4061 CTTAATTCAGGGTAATTAAGTAGAGTCAAAGACTTAATTCATGGTAATTAAGTAGAATCAATAAA
1 CTTAATTCAAGGTAATTAAGTAGAGTCAAAGACTTAATTCAGGGTAATTAAGTAG--TCAATAAA
4126 -TGG
64 GT-G
*
4129 CTTAATTCAAGGTAATTAAGTAGAGTCAATGACTTAATTCAGGGTAATTAAGTAGTCAATAAAGT
1 CTTAATTCAAGGTAATTAAGTAGAGTCAAAGACTTAATTCAGGGTAATTAAGTAGTCAATAAAGT
4194 G
66 G
* * **
4195 CTTAATTC-AGGATAATTAAGCAGAGATAATAAAGAACTTAATTCAGGGCGATTAAGT
1 CTTAATTCAAGG-TAATTAAGTAGAG-T--CAAAG-ACTTAATTCAGGGTAATTAAGT
4252 GGAGTTAATA
Statistics
Matches: 109, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
65 3 0.03
66 29 0.27
67 2 0.02
68 52 0.48
69 3 0.03
70 20 0.18
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.30
Consensus pattern (66 bp):
CTTAATTCAAGGTAATTAAGTAGAGTCAAAGACTTAATTCAGGGTAATTAAGTAGTCAATAAAGT
G
Found at i:6530 original size:18 final size:18
Alignment explanation
Indices: 6507--6541 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6497 GGTCATTTGG
*
6507 GTTGGGTCAGTCGGTGAT
1 GTTGGGTCAATCGGTGAT
*
6525 GTTGGGTTAATCGGTGA
1 GTTGGGTCAATCGGTGA
6542 AACCCGAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.09, G:0.43, T:0.34
Consensus pattern (18 bp):
GTTGGGTCAATCGGTGAT
Found at i:6639 original size:15 final size:17
Alignment explanation
Indices: 6617--6656 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
6607 CGAGAACCCG
*
6617 ATTATATAATTATAT-T
1 ATTATATAAATATATAT
6633 A-TATATAAATATATAT
1 ATTATATAAATATATAT
6649 ATTATATA
1 ATTATATA
6657 TGTTTTTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 12 0.57
16 3 0.14
17 6 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTATATAAATATATAT
Found at i:6866 original size:29 final size:30
Alignment explanation
Indices: 6824--6886 Score: 103
Period size: 29 Copynumber: 2.1 Consensus size: 30
6814 AACCTTTTAA
6824 AAAAACTGGATGGGATCTTTCCCTAAAT-T
1 AAAAACTGGATGGGATCTTTCCCTAAATCT
6853 AAAAACATGG-TGGGATCTTTCCCTAAATCT
1 AAAAAC-TGGATGGGATCTTTCCCTAAATCT
6883 AAAA
1 AAAA
6887 CTTTGAAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 24 0.75
30 8 0.25
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (30 bp):
AAAAACTGGATGGGATCTTTCCCTAAATCT
Found at i:6896 original size:38 final size:38
Alignment explanation
Indices: 6854--7014 Score: 216
Period size: 39 Copynumber: 4.2 Consensus size: 38
6844 CCCTAAATTA
* *
6854 AAAACATGGTGGGATCTTTCCCTAAATCT-AAAACTTTG
1 AAAACTTGATGGGATCTTTCCCTAAAT-TGAAAACTTTG
* *
6892 AAAACTTGGTGGGATCTTTCCCTAAATTGAAAACATTGG
1 AAAACTTGATGGGATCTTTCCCTAAATTGAAAAC-TTTG
* *
6931 AAAACTTAATGGGATCGTTCCCTAAATTGAAAACTTTGG
1 AAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTT-G
* *
6970 AAAACTTGATGGGATCTTTCCCTAAAGTGAAAACTTTA
1 AAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTTG
7008 AAAACTT
1 AAAACTT
7015 CCTTTTGATT
Statistics
Matches: 110, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.01
38 40 0.36
39 69 0.63
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (38 bp):
AAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTTG
Found at i:7687 original size:21 final size:22
Alignment explanation
Indices: 7652--7703 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
7642 TGCATCGAAG
* *
7652 AAAGCTAAAAGCCCATATGC-AT
1 AAAG-TAACAGCCCAAATGCAAT
*
7674 AAATTAACAGCCCAAATGCAAT
1 AAAGTAACAGCCCAAATGCAAT
7696 AAAGTAAC
1 AAAGTAAC
7704 CAATATAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.50, C:0.21, G:0.12, T:0.17
Consensus pattern (22 bp):
AAAGTAACAGCCCAAATGCAAT
Done.