Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014347.1 Corchorus capsularis cultivar CVL-1 contig14368, 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: 3400
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Found at i:758 original size:51 final size:51
Alignment explanation
Indices: 690--810 Score: 161
Period size: 51 Copynumber: 2.4 Consensus size: 51
680 TAAGACCTTG
* * *
690 ACAATAAAAATTGAATCTTTGTATAGTAAGGGTTGAGTTCTAGTAATTTTA
1 ACAATAAAAATTGAATCTTTATATAGTAAGAGTTGAGTTCTAGTAATTCTA
* * * * * *
741 GCCATAAAAATTAAATCTTTATGTAGTAAGAGTTGGGTTTTAGTAATTCTA
1 ACAATAAAAATTGAATCTTTATATAGTAAGAGTTGAGTTCTAGTAATTCTA
792 ACAATAAAAATTGAATCTT
1 ACAATAAAAATTGAATCTT
811 GATAGTTTTT
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.38
Consensus pattern (51 bp):
ACAATAAAAATTGAATCTTTATATAGTAAGAGTTGAGTTCTAGTAATTCTA
Found at i:1634 original size:38 final size:38
Alignment explanation
Indices: 1602--1914 Score: 473
Period size: 38 Copynumber: 8.2 Consensus size: 38
1592 AATTAAGGAC
1602 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
*
1640 CAAAGTAATAGTAATCGGTAAAATTGATAATTAAGAGT
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
* *
1678 CAAAGTAATAGTAATCAGTAAAATTGATAATTGAGAGC
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
* *
1716 CAAAAGTAATAGTAATCAATAAAATTGATAATTAAGAGC
1 C-AAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
*
1755 CAAAGTAATAGTAATCAGTAGAATTGATAATTAAGAGT
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
* *
1793 CAAAGTAAGAATAATCAGTAAAATTGATAATTAAGAGT
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
* * *
1831 CAAAGTAAGAATAATCAGTAAAATTGATAATTAACAGT
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
* * * *
1869 CAAAGTAAGAATAATCAGTAAAATTGATAATCAAGGGT
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
*
1907 CAAGGTAA
1 CAAAGTAA
1915 AAATATTAAT
Statistics
Matches: 257, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
38 221 0.86
39 36 0.14
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.27
Consensus pattern (38 bp):
CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
Found at i:1856 original size:153 final size:152
Alignment explanation
Indices: 1592--1904 Score: 484
Period size: 153 Copynumber: 2.1 Consensus size: 152
1582 ACCCCAGTAA
* * *
1592 AATTAAGGACCAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAATAGTAATCG
1 AATTAAGGACCAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATCA
* * * *
1657 GTAAAATTGATAATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAATTGAGAGCCAAAAG
66 GTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAATTAACAGCC-AAAG
* *
1722 TAATAGTAATCAATAAAATTGAT
130 TAAGAATAATCAATAAAATTGAT
*
1745 AATTAA-GAGCCAAAGTAATAGTAATCAGTAGAATTGATAATTAAGAGTCAAAGTAAGAATAATC
1 AATTAAGGA-CCAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATC
*
1809 AGTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAATTAACAGTCAAAG
65 AGTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAATTAACAGCCAAAG
*
1874 TAAGAATAATCAGTAAAATTGAT
130 TAAGAATAATCAATAAAATTGAT
*
1897 AATCAAGG
1 AATTAAGG
1905 GTCAAGGTAA
Statistics
Matches: 145, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
152 31 0.21
153 114 0.79
ACGTcount: A:0.50, C:0.07, G:0.16, T:0.27
Consensus pattern (152 bp):
AATTAAGGACCAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATCA
GTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAATTAACAGCCAAAGT
AAGAATAATCAATAAAATTGAT
Found at i:1887 original size:19 final size:19
Alignment explanation
Indices: 1790--1887 Score: 83
Period size: 19 Copynumber: 5.2 Consensus size: 19
1780 GATAATTAAG
1790 AGTCAAAGTAAGAATAATC
1 AGTCAAAGTAAGAATAATC
* * * * *
1809 AGTAAAATTGATAATTAA-G
1 AGTCAAAGTAAGAA-TAATC
1828 AGTCAAAGTAAGAATAATC
1 AGTCAAAGTAAGAATAATC
* * * *
1847 AGTAAAATTGATAATTAA-C
1 AGTCAAAGTAAGAA-TAATC
1866 AGTCAAAGTAAGAATAATC
1 AGTCAAAGTAAGAATAATC
1885 AGT
1 AGT
1888 AAAATTGATA
Statistics
Matches: 57, Mismatches: 18, Indels: 8
0.69 0.22 0.10
Matches are distributed among these distances:
18 6 0.11
19 45 0.79
20 6 0.11
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.26
Consensus pattern (19 bp):
AGTCAAAGTAAGAATAATC
Found at i:1900 original size:16 final size:16
Alignment explanation
Indices: 1841--1901 Score: 50
Period size: 16 Copynumber: 3.4 Consensus size: 16
1831 CAAAGTAAGA
1841 ATAATCAGTAAAATTG
1 ATAATCAGTAAAATTG
* *
1857 ATAATTAACAGTCAAAGTAAG
1 ATAA-T--CAGT-AAAAT-TG
1878 AATAATCAGTAAAATTG
1 -ATAATCAGTAAAATTG
1895 ATAATCA
1 ATAATCA
1902 AGGGTCAAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
16 11 0.31
17 2 0.06
18 4 0.11
19 8 0.23
20 4 0.11
21 2 0.06
22 4 0.11
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.28
Consensus pattern (16 bp):
ATAATCAGTAAAATTG
Found at i:2068 original size:33 final size:32
Alignment explanation
Indices: 1987--2073 Score: 138
Period size: 32 Copynumber: 2.7 Consensus size: 32
1977 GGGAGAGAGT
*
1987 AAAAGAGTAATCAGTAATTAAGAAAGGAAGTA
1 AAAAGACTAATCAGTAATTAAGAAAGGAAGTA
*
2019 AAAAGATTAATCAGTAATTAAGAAAGGAAGTA
1 AAAAGACTAATCAGTAATTAAGAAAGGAAGTA
2051 AAAAGGACTAATCAGTAAATTAA
1 AAAA-GACTAATCAGT-AATTAA
2074 TAATTAAGAA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
32 35 0.69
33 10 0.20
34 6 0.12
ACGTcount: A:0.56, C:0.05, G:0.18, T:0.21
Consensus pattern (32 bp):
AAAAGACTAATCAGTAATTAAGAAAGGAAGTA
Found at i:2308 original size:14 final size:14
Alignment explanation
Indices: 2285--2323 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
2275 GAGTTGTATG
2285 GTAAAAAGTAATCA
1 GTAAAAAGTAATCA
*
2299 GTAAAGAGTAATCA
1 GTAAAAAGTAATCA
*
2313 TTAAAAAGTAA
1 GTAAAAAGTAA
2324 AAATGGCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.56, C:0.05, G:0.15, T:0.23
Consensus pattern (14 bp):
GTAAAAAGTAATCA
Found at i:2905 original size:38 final size:38
Alignment explanation
Indices: 2873--3184 Score: 480
Period size: 38 Copynumber: 8.2 Consensus size: 38
2863 AATTAAGGAC
2873 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
* *
2911 CAAAGTAATAGTAATCGGTAAAATTGATAATTAAGAGC
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
2949 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
*
2987 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGC
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
*
3025 CAAAGTAATAGTAATCAGTAGAATTGATAATTAAGAGT
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
* * *
3063 CAAAGTAAGAATAATCAGTAGAATTGATAATTAAGAGT
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
* * * *
3101 AAAAGTAAGAATAATCAGTAAAATTGATAATTAACAGT
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
* * * *
3139 CAAAGTAAGAATAATCAGTAAAATTGATAATCAAGGGT
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
*
3177 CAAGGTAA
1 CAAAGTAA
3185 AAATATTAAT
Statistics
Matches: 257, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 257 1.00
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.27
Consensus pattern (38 bp):
CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
Found at i:3120 original size:19 final size:19
Alignment explanation
Indices: 3064--3161 Score: 83
Period size: 19 Copynumber: 5.2 Consensus size: 19
3054 ATTAAGAGTC
3064 AAAGTAAGAATAATCAGTA
1 AAAGTAAGAATAATCAGTA
* * * * *
3083 GAATTGATAATTAA-GAGTA
1 AAAGTAAGAA-TAATCAGTA
3102 AAAGTAAGAATAATCAGTA
1 AAAGTAAGAATAATCAGTA
* * * *
3121 AAATTGATAATTAA-CAGTC
1 AAAGTAAGAA-TAATCAGTA
3140 AAAGTAAGAATAATCAGTA
1 AAAGTAAGAATAATCAGTA
3159 AAA
1 AAA
3162 TTGATAATCA
Statistics
Matches: 57, Mismatches: 18, Indels: 8
0.69 0.22 0.10
Matches are distributed among these distances:
18 6 0.11
19 45 0.79
20 6 0.11
ACGTcount: A:0.55, C:0.05, G:0.15, T:0.24
Consensus pattern (19 bp):
AAAGTAAGAATAATCAGTA
Found at i:3170 original size:16 final size:16
Alignment explanation
Indices: 3111--3171 Score: 50
Period size: 16 Copynumber: 3.4 Consensus size: 16
3101 AAAAGTAAGA
3111 ATAATCAGTAAAATTG
1 ATAATCAGTAAAATTG
* *
3127 ATAATTAACAGTCAAAGTAAG
1 ATAA-T--CAGT-AAAAT-TG
3148 AATAATCAGTAAAATTG
1 -ATAATCAGTAAAATTG
3165 ATAATCA
1 ATAATCA
3172 AGGGTCAAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
16 11 0.31
17 2 0.06
18 4 0.11
19 8 0.23
20 4 0.11
21 2 0.06
22 4 0.11
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.28
Consensus pattern (16 bp):
ATAATCAGTAAAATTG
Found at i:3338 original size:33 final size:32
Alignment explanation
Indices: 3257--3343 Score: 138
Period size: 32 Copynumber: 2.7 Consensus size: 32
3247 GGGAGAGAGT
*
3257 AAAAGAGTAATCAGTAATTAAGAAAGGAAGTA
1 AAAAGACTAATCAGTAATTAAGAAAGGAAGTA
*
3289 AAAAGATTAATCAGTAATTAAGAAAGGAAGTA
1 AAAAGACTAATCAGTAATTAAGAAAGGAAGTA
3321 AAAAGGACTAATCAGTAAATTAA
1 AAAA-GACTAATCAGT-AATTAA
3344 TAATTAAGAA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
32 35 0.69
33 10 0.20
34 6 0.12
ACGTcount: A:0.56, C:0.05, G:0.18, T:0.21
Consensus pattern (32 bp):
AAAAGACTAATCAGTAATTAAGAAAGGAAGTA
Done.