Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012300.1 Corchorus capsularis cultivar CVL-1 contig12321, 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: 3912
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.31
Found at i:577 original size:17 final size:17
Alignment explanation
Indices: 555--589 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
545 AGTGAAAGGG
* *
555 TTGTTTTTGGAATAAAA
1 TTGTTTTCGAAATAAAA
572 TTGTTTTCGAAATAAAA
1 TTGTTTTCGAAATAAAA
589 T
1 T
590 GATGTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.14, T:0.46
Consensus pattern (17 bp):
TTGTTTTCGAAATAAAA
Found at i:1865 original size:18 final size:16
Alignment explanation
Indices: 1834--1868 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
1824 ATGCATGTTG
1834 AAAAAAAGAAAAGAGA
1 AAAAAAAGAAAAGAGA
1850 AAAAAGAAGAAAAAGAGA
1 AAAAA-AAG-AAAAGAGA
1868 A
1 A
1869 GGAAATGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 3 0.18
18 9 0.53
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAAAAGAGA
Found at i:2706 original size:35 final size:35
Alignment explanation
Indices: 2659--3027 Score: 469
Period size: 35 Copynumber: 10.6 Consensus size: 35
2649 TGTAGTCATC
* * *
2659 AGGTCAGTGTTGATCTAATTCCAAGAAGTTTCCAG
1 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
*
2694 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTGCAG
1 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
2729 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
1 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
*
2764 AGGTCAGAGTTGATCTCATTCCAAAAAGTTTTCAG
1 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
* *
2799 AGGTCAGAGTTGATCTCATTGCAAGGAGTTTTCAG
1 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
* *
2834 AGGTCAGAGTTGATCTCATTGCAAGCAGTTTTCAG
1 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
2869 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
1 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
* *
2904 AGGTCAGAGTTGATCTCATTTCAAGAAGTTTCCA-
1 AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
* * * * *
2938 ACGATCAGAGTTGATCGCATTTC-AGTAGTTTCCA-
1 A-GGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
* * * *
2972 ACGATCAGAGTTGATCACATTTTC-AGAAGTTTCCA-
1 A-GGTCAGAGTTGATCTCA-TTCCAAGAAGTTTTCAG
* *
3007 ACGATCAGAGTTGATCGCATT
1 A-GGTCAGAGTTGATCTCATT
3028 TTCAGTAGTT
Statistics
Matches: 313, Mismatches: 19, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
34 31 0.10
35 282 0.90
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (35 bp):
AGGTCAGAGTTGATCTCATTCCAAGAAGTTTTCAG
Found at i:3028 original size:35 final size:35
Alignment explanation
Indices: 2907--3158 Score: 312
Period size: 35 Copynumber: 7.5 Consensus size: 35
2897 TTTTCAGAGG
* *
2907 TCAGAGTTGATCTCA-TTTCAAGAAGTTTCCAACGA
1 TCAGAGTTGATCGCATTTTC-AGTAGTTTCCAACGA
2942 TCAGAGTTGATCGCA-TTTCAGTAGTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
* *
2976 TCAGAGTTGATCACATTTTCAGAAGTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
3011 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
* *
3046 TCAGAGTTGATCGCATTTTCAGTATTTTGCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
3081 TC-------A---CATTTTCAGTAGTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
* *
3106 TCAGAGTTGATCACATTTTCAGTAGTTTCCAACAA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
* * *
3141 TCAAAGGTGATCTCATTT
1 TCAGAGTTGATCGCATTT
3159 CAAGAAATTC
Statistics
Matches: 192, Mismatches: 14, Indels: 22
0.84 0.06 0.10
Matches are distributed among these distances:
25 22 0.11
28 1 0.01
32 1 0.01
34 28 0.15
35 140 0.73
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (35 bp):
TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
Found at i:3082 original size:25 final size:25
Alignment explanation
Indices: 3054--3108 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
3044 GATCAGAGTT
* * *
3054 GATCGCATTTTCAGTATTTTGCAAC
1 GATCACATTTTCAGTAGTTTCCAAC
3079 GATCACATTTTCAGTAGTTTCCAAC
1 GATCACATTTTCAGTAGTTTCCAAC
3104 GATCA
1 GATCA
3109 GAGTTGATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (25 bp):
GATCACATTTTCAGTAGTTTCCAAC
Found at i:3097 original size:60 final size:60
Alignment explanation
Indices: 3019--3143 Score: 205
Period size: 60 Copynumber: 2.1 Consensus size: 60
3009 GATCAGAGTT
* * * *
3019 GATCGCATTTTCAGTAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTGCAAC
1 GATCACATTTTCAGTAGTTTCCAACGATCAGAGTTGATCACATTTTCAGTAGTTTCCAAC
3079 GATCACATTTTCAGTAGTTTCCAACGATCAGAGTTGATCACATTTTCAGTAGTTTCCAAC
1 GATCACATTTTCAGTAGTTTCCAACGATCAGAGTTGATCACATTTTCAGTAGTTTCCAAC
*
3139 AATCA
1 GATCA
3144 AAGGTGATCT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (60 bp):
GATCACATTTTCAGTAGTTTCCAACGATCAGAGTTGATCACATTTTCAGTAGTTTCCAAC
Found at i:3152 original size:95 final size:95
Alignment explanation
Indices: 2984--3158 Score: 296
Period size: 95 Copynumber: 1.8 Consensus size: 95
2974 GATCAGAGTT
* *
2984 GATCACATTTTCAGAAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGATCA
1 GATCACATTTTCAGAAGTTTCCAACGATCAGAGTTGATCACATTTTCAGTAGTTTCCAACAATCA
* *
3049 GAGTTGATCGCATTTTCAGTATTTTGCAAC
66 AAGGTGATCGCATTTTCAGTATTTTGCAAC
*
3079 GATCACATTTTCAGTAGTTTCCAACGATCAGAGTTGATCACATTTTCAGTAGTTTCCAACAATCA
1 GATCACATTTTCAGAAGTTTCCAACGATCAGAGTTGATCACATTTTCAGTAGTTTCCAACAATCA
*
3144 AAGGTGATCTCATTT
66 AAGGTGATCGCATTT
3159 CAAGAAATTC
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
95 74 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.35
Consensus pattern (95 bp):
GATCACATTTTCAGAAGTTTCCAACGATCAGAGTTGATCACATTTTCAGTAGTTTCCAACAATCA
AAGGTGATCGCATTTTCAGTATTTTGCAAC
Found at i:3178 original size:95 final size:95
Alignment explanation
Indices: 2983--3178 Score: 268
Period size: 95 Copynumber: 2.1 Consensus size: 95
2973 CGATCAGAGT
* *
2983 TGATCACATTTTCAGAAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGATC
1 TGATCACATTTTCAGAAGTTTCCAACGATCAGAGTTGATCACATTTTCAGTAGTTTCCAACAATC
* * * * **
3048 AGAGTTGATCGCATTTTCAGTATTTTGCAA
66 AAAGGTGATCGCATTTTCAGAAATTCCCAA
* *
3078 CGATCACATTTTCAGTAGTTTCCAACGATCAGAGTTGATCACATTTTCAGTAGTTTCCAACAATC
1 TGATCACATTTTCAGAAGTTTCCAACGATCAGAGTTGATCACATTTTCAGTAGTTTCCAACAATC
* *
3143 AAAGGTGATCTCA-TTTCAAGAAATTCCCGA
66 AAAGGTGATCGCATTTTC-AGAAATTCCCAA
3173 TGATCA
1 TGATCA
3179 GAGTTGATCC
Statistics
Matches: 87, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
94 4 0.05
95 83 0.95
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (95 bp):
TGATCACATTTTCAGAAGTTTCCAACGATCAGAGTTGATCACATTTTCAGTAGTTTCCAACAATC
AAAGGTGATCGCATTTTCAGAAATTCCCAA
Done.