Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013026.1 Corchorus capsularis cultivar CVL-1 contig13047, 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: 9854
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Found at i:949 original size:33 final size:33
Alignment explanation
Indices: 899--1055 Score: 194
Period size: 33 Copynumber: 4.7 Consensus size: 33
889 CCGCGCAACA
899 CCGGCCACAAGACCGGCCACGCGACATGGCCATGT
1 CCGGCCAC-A-ACCGGCCACGCGACATGGCCATGT
934 CCGGCCATC-ACCGGCCACGCGACATGGCCATGT
1 CCGGCCA-CAACCGGCCACGCGACATGGCCATGT
* *
967 CCGGCCATC-ACCGGCCACGCGACATGGACATGG
1 CCGGCCA-CAACCGGCCACGCGACATGGCCATGT
* ** *
1000 CCGGCTACAACCGGCCAAACGAC-TCGGCCATGC
1 CCGGCCACAACCGGCCACGCGACAT-GGCCATGT
1033 CCGGCCACAACCGGCCACGCGAC
1 CCGGCCACAACCGGCCACGCGAC
1056 CCTTTGTCTA
Statistics
Matches: 109, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
32 2 0.02
33 99 0.91
35 7 0.06
36 1 0.01
ACGTcount: A:0.22, C:0.43, G:0.27, T:0.08
Consensus pattern (33 bp):
CCGGCCACAACCGGCCACGCGACATGGCCATGT
Found at i:2874 original size:38 final size:37
Alignment explanation
Indices: 2818--2938 Score: 143
Period size: 38 Copynumber: 3.2 Consensus size: 37
2808 AATCACAGAT
* * *
2818 AGGTCATCTATCAACAGTTTTCAAGTTCGACTAGAAAC
1 AGGTCATCTTTCAGCAGTTATCAAGTT-GACTAGAAAC
*
2856 AGGTCATCTTTCAGCAGTTATCAAGTTGACTGGAAAC
1 AGGTCATCTTTCAGCAGTTATCAAGTTGACTAGAAAC
* * * * *
2893 AGGTCATCTTTTAGCAATTATCAAAATTGACTGGAGAC
1 AGGTCATCTTTCAGCAGTTATC-AAGTTGACTAGAAAC
2931 AGGTCATC
1 AGGTCATC
2939 AAAGGTCATC
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
37 29 0.39
38 45 0.61
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (37 bp):
AGGTCATCTTTCAGCAGTTATCAAGTTGACTAGAAAC
Found at i:2981 original size:36 final size:38
Alignment explanation
Indices: 2941--3024 Score: 111
Period size: 38 Copynumber: 2.3 Consensus size: 38
2931 AGGTCATCAA
2941 AGGTCATCTTCCAA-A-TTATAAAAG-TCGACTGGAAAC
1 AGGTCATCTTCCAACACTTAT-AAAGTTCGACTGGAAAC
* * *
2977 AGGTCGTCTTTCAACACTTATCAAGTTCGACTGGAAAC
1 AGGTCATCTTCCAACACTTATAAAGTTCGACTGGAAAC
3015 AGGTCATCTT
1 AGGTCATCTT
3025 TCGACAATCA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
36 12 0.29
37 4 0.10
38 25 0.61
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (38 bp):
AGGTCATCTTCCAACACTTATAAAGTTCGACTGGAAAC
Found at i:3047 original size:35 final size:36
Alignment explanation
Indices: 2965--3060 Score: 122
Period size: 35 Copynumber: 2.6 Consensus size: 36
2955 ATTATAAAAG
* *
2965 TCGACTGGAAACAGGTCGTCTTTCAACACTTATCAAGT
1 TCGACTGGAAACAGGTCATCTTTCAACA--TATCAAGA
*
3003 TCGACTGGAAACAGGTCATCTTTCGACA-ATCAAGA
1 TCGACTGGAAACAGGTCATCTTTCAACATATCAAGA
* *
3038 TCGATTGGAAACAAGTCATCTTT
1 TCGACTGGAAACAGGTCATCTTT
3061 AAGTAGTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
35 27 0.51
38 26 0.49
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (36 bp):
TCGACTGGAAACAGGTCATCTTTCAACATATCAAGA
Found at i:3158 original size:54 final size:51
Alignment explanation
Indices: 3095--3265 Score: 171
Period size: 54 Copynumber: 3.4 Consensus size: 51
3085 AGGAGGGGGG
*
3095 CATTCCAACAACTTTTCAGCATTCCAACAACTTTTTAGTAGCCCCCAAGGAGGA
1 CATTCCAACAACTTTTCAG--TTCCAAC-ACTTTTCAGTAGCCCCCAAGGAGGA
* * * * *
3149 CATTGCAACAACTTTTCAG---------TTTTCGGTCGCTCCCAAGGAGGGG
1 CATTCCAACAACTTTTCAGTTCCAACACTTTTCAGTAGCCCCCAAGGA-GGA
3192 CATTCCAACAACTTTTCAGTTTCCAACAGCTTTTCAGTAGCCCCCAAGGAGGA
1 CATTCCAACAACTTTTCAG-TTCCAACA-CTTTTCAGTAGCCCCCAAGGAGGA
3245 CATTCCAACAACTTTTCAGTT
1 CATTCCAACAACTTTTCAGTT
3266 TTCAGTTGCT
Statistics
Matches: 94, Mismatches: 11, Indels: 26
0.72 0.08 0.20
Matches are distributed among these distances:
42 16 0.17
43 20 0.21
52 2 0.02
53 21 0.22
54 35 0.37
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (51 bp):
CATTCCAACAACTTTTCAGTTCCAACACTTTTCAGTAGCCCCCAAGGAGGA
Found at i:3206 original size:43 final size:42
Alignment explanation
Indices: 3126--3311 Score: 158
Period size: 42 Copynumber: 4.2 Consensus size: 42
3116 TTCCAACAAC
* * *
3126 TTTTTAGTAGCCCCCAAGGAGGACATTGCAACAACTTTTCAG
1 TTTTCAGTAGCTCCCAAGGAGGACATTCCAACAACTTTTCAG
* * *
3168 TTTTCGGTCGCTCCCAAGGAGGGGCATTCCAACAACTTTTCAGTTTCCAACAG
1 TTTTCAGTAGCTCCCAAGGA-GGACATTCCAACAAC---T---TTT----CAG
*
3221 CTTTTCAGTAGCCCCCAAGGAGGACATTCCAACAACTTTTCAG
1 -TTTTCAGTAGCTCCCAAGGAGGACATTCCAACAACTTTTCAG
* * * *
3264 TTTTCAGTTGCTCCCAAGGGGGGCATTCCAACAGC-TTTCAG
1 TTTTCAGTAGCTCCCAAGGAGGACATTCCAACAACTTTTCAG
3305 TTTTCAG
1 TTTTCAG
3312 GGCATTCCAA
Statistics
Matches: 117, Mismatches: 15, Indels: 25
0.75 0.10 0.16
Matches are distributed among these distances:
41 13 0.11
42 46 0.39
43 16 0.14
46 1 0.01
47 3 0.03
49 3 0.03
50 1 0.01
53 17 0.15
54 17 0.15
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (42 bp):
TTTTCAGTAGCTCCCAAGGAGGACATTCCAACAACTTTTCAG
Found at i:3217 original size:18 final size:18
Alignment explanation
Indices: 3194--3229 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3184 AGGAGGGGCA
3194 TTCCAACAACTTTTCAGT
1 TTCCAACAACTTTTCAGT
*
3212 TTCCAACAGCTTTTCAGT
1 TTCCAACAACTTTTCAGT
3230 AGCCCCCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.28, G:0.08, T:0.39
Consensus pattern (18 bp):
TTCCAACAACTTTTCAGT
Found at i:3236 original size:96 final size:95
Alignment explanation
Indices: 3088--3307 Score: 352
Period size: 96 Copynumber: 2.3 Consensus size: 95
3078 CCCCAAGAGG
* *
3088 AGGGGGGCATTCCAACAACTTTTCAGCATTCCAACAACTTTTTAGTAGCCCCCAAGGAGGACATT
1 AGGGGGGCATTCCAACAACTTTTCAG-TTTCCAACAACTTTTCAGTAGCCCCCAAGGAGGACATT
* *
3153 GCAACAACTTTTCAGTTTTCGGTCGCTCCCA
65 CCAACAACTTTTCAGTTTTCAGTCGCTCCCA
*
3184 AGGAGGGGCATTCCAACAACTTTTCAGTTTCCAACAGCTTTTCAGTAGCCCCCAAGGAGGACATT
1 AGG-GGGGCATTCCAACAACTTTTCAGTTTCCAACAACTTTTCAGTAGCCCCCAAGGAGGACATT
*
3249 CCAACAACTTTTCAGTTTTCAGTTGCTCCCA
65 CCAACAACTTTTCAGTTTTCAGTCGCTCCCA
*
3280 AGGGGGGCATTCCAACAGC-TTTCAGTTT
1 AGGGGGGCATTCCAACAACTTTTCAGTTT
3308 TCAGGGCATT
Statistics
Matches: 116, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
94 9 0.08
95 15 0.13
96 69 0.59
97 23 0.20
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (95 bp):
AGGGGGGCATTCCAACAACTTTTCAGTTTCCAACAACTTTTCAGTAGCCCCCAAGGAGGACATTC
CAACAACTTTTCAGTTTTCAGTCGCTCCCA
Found at i:3322 original size:27 final size:27
Alignment explanation
Indices: 3284--3338 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
3274 CTCCCAAGGG
3284 GGGCATTCCAACAGCTTTCAGTTTTCA
1 GGGCATTCCAACAGCTTTCAGTTTTCA
3311 GGGCATTCCAACAGCTTTCAGTTTTCA
1 GGGCATTCCAACAGCTTTCAGTTTTCA
3338 G
1 G
3339 TTGCTCACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (27 bp):
GGGCATTCCAACAGCTTTCAGTTTTCA
Found at i:3371 original size:68 final size:69
Alignment explanation
Indices: 3245--3374 Score: 199
Period size: 68 Copynumber: 1.9 Consensus size: 69
3235 CCAAGGAGGA
* *
3245 CATTCCAACAACTTTTCAGTTTTCAGTTGCTCCCAAGGGGGGCATTCCAACAGCTTTCAGTTTTC
1 CATTCCAACAACTTTTCAGTTTTCAGTTGCTCACAAGGGGGGCATTACAACAGCTTTCAGTTTTC
3310 AGGG
66 AGGG
* * * *
3314 CATTCCAACAGC-TTTCAGTTTTCAGTTGCTCACAAGGGGGGCATTATAGCAGTTTTCAGTT
1 CATTCCAACAACTTTTCAGTTTTCAGTTGCTCACAAGGGGGGCATTACAACAGCTTTCAGTT
3375 CATCAGTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
68 44 0.80
69 11 0.20
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (69 bp):
CATTCCAACAACTTTTCAGTTTTCAGTTGCTCACAAGGGGGGCATTACAACAGCTTTCAGTTTTC
AGGG
Found at i:3962 original size:27 final size:27
Alignment explanation
Indices: 3924--3981 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
3914 ATATGCGTTG
*
3924 CTTTCTGGGGATCATTTTAATCATACC
1 CTTTCTAGGGATCATTTTAATCATACC
3951 CTTTCTAGGGATCATTTTAATCATACC
1 CTTTCTAGGGATCATTTTAATCATACC
3978 CTTT
1 CTTT
3982 GGGCTTTCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.43
Consensus pattern (27 bp):
CTTTCTAGGGATCATTTTAATCATACC
Found at i:6314 original size:2 final size:2
Alignment explanation
Indices: 6309--6337 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6299 TATATATATA
6309 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
6338 ATTCTTGGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Done.