Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012900.1 Corchorus capsularis cultivar CVL-1 contig12921, 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: 5681
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:221 original size:36 final size:36
Alignment explanation
Indices: 156--272 Score: 128
Period size: 36 Copynumber: 3.2 Consensus size: 36
146 GTCAGTGGCG
* * *
156 TTATAGCCAAATATTGGGCGAC-TATGGCCAGCGGCT
1 TTATAGCCAAAGATTGGGCGACTTA-GGCCATCGGCA
**** *
192 TTATAGCCATTTTTTGGGCGACTTAGGCCATCAGCA
1 TTATAGCCAAAGATTGGGCGACTTAGGCCATCGGCA
* *
228 TTATAGCGAAAGATTAGGCGACTTAGGCCATCGGCA
1 TTATAGCCAAAGATTGGGCGACTTAGGCCATCGGCA
264 TTATAGCCA
1 TTATAGCCA
273 GAAACAGAGC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
36 64 0.97
37 2 0.03
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.27
Consensus pattern (36 bp):
TTATAGCCAAAGATTGGGCGACTTAGGCCATCGGCA
Found at i:573 original size:45 final size:44
Alignment explanation
Indices: 510--596 Score: 111
Period size: 45 Copynumber: 2.0 Consensus size: 44
500 TTGCCAACAC
* **
510 CATGTGGAAGAGAGTATAATTCTTGTCATTGGAAGCACCACCCT
1 CATGTGGAAGAGAGTATAAATAATGTCATTGGAAGCACCACCCT
* * *
554 CATGTTGGAGGAGAGTATAAATAATGTCGTTGGAAGCGCCACC
1 CATG-TGGAAGAGAGTATAAATAATGTCATTGGAAGCACCACC
597 ACCCTGGAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 4 0.11
45 32 0.89
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.25
Consensus pattern (44 bp):
CATGTGGAAGAGAGTATAAATAATGTCATTGGAAGCACCACCCT
Found at i:797 original size:17 final size:17
Alignment explanation
Indices: 770--818 Score: 80
Period size: 17 Copynumber: 2.9 Consensus size: 17
760 GCGTCAATAT
*
770 CATGTTAGAAGCGCAAC
1 CATGTTGGAAGCGCAAC
*
787 CTTGTTGGAAGCGCAAC
1 CATGTTGGAAGCGCAAC
804 CATGTTGGAAGCGCA
1 CATGTTGGAAGCGCA
819 TATAAATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (17 bp):
CATGTTGGAAGCGCAAC
Found at i:856 original size:44 final size:44
Alignment explanation
Indices: 788--1116 Score: 254
Period size: 45 Copynumber: 7.2 Consensus size: 44
778 AAGCGCAACC
* *
788 TTGTTGGAAGCG-CA--ACCATGTTGGAAGCGCATATAAATTTA
1 TTGTTGGAAGCGCCACCATCATGTTGGAAGAGCATATAAATTTA
* * * **
829 TCGCTGGAAGCGCCACCCTCATGTTGGAAGAGTGTATAAATTT-
1 TTGTTGGAAGCGCCACCATCATGTTGGAAGAGCATATAAATTTA
* * *
872 TGTGATTGGAGGCGCCACAATCATGTTGGAAGCGCATATAAATTTA
1 T-TG-TTGGAAGCGCCACCATCATGTTGGAAGAGCATATAAATTTA
* *
918 TTGTTGGAAGCGCCACCATCATGTTGGAAAGAGCGTATAAATTTTTTTT
1 TTGTTGGAAGCGCCACCATCATGTTGG-AAGAGCATATAAA----TTTA
* * * * ** *
967 TGTGATTGGAGGCGTCACCATCATTTTGGAAGTG-AGTATAGGTTTTG
1 T-TG-TTGGAAGCGCCACCATCATGTTGGAAGAGCA-TATA-AATTTA
* * *
1014 TCTGTTGGAAGCGCCATCACACCGTGTTGGAAGTGCATATAAATTTTA
1 T-TGTTGGAAGCGCCA-C-CATCATGTTGGAAGAGCATATAAA-TTTA
*
1062 TTGTTGGAAGCGCCACCATCATGTTGGAAAGAGCGTATAAATTTTCA
1 TTGTTGGAAGCGCCACCATCATGTTGG-AAGAGCATATAAA-TTT-A
1109 TTGTTGGA
1 TTGTTGGA
1117 GGAAGGTGAT
Statistics
Matches: 226, Mismatches: 41, Indels: 36
0.75 0.14 0.12
Matches are distributed among these distances:
41 10 0.04
42 2 0.01
43 1 0.00
44 44 0.19
45 55 0.24
46 27 0.12
47 30 0.13
48 21 0.09
49 5 0.02
50 10 0.04
51 21 0.09
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.32
Consensus pattern (44 bp):
TTGTTGGAAGCGCCACCATCATGTTGGAAGAGCATATAAATTTA
Found at i:906 original size:20 final size:20
Alignment explanation
Indices: 877--946 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 20
867 AATTTTGTGA
*
877 TTGGAGGCGCCACAATCATG
1 TTGGAAGCGCCACAATCATG
* * *
897 TTGGAAGCGCATATAAATTTATTG
1 TTGGAAGCGC-CA-CAA-TCA-TG
*
921 TTGGAAGCGCCACCATCATG
1 TTGGAAGCGCCACAATCATG
941 TTGGAA
1 TTGGAA
947 AGAGCGTATA
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
20 17 0.45
21 3 0.08
22 3 0.08
23 3 0.08
24 12 0.32
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.27
Consensus pattern (20 bp):
TTGGAAGCGCCACAATCATG
Found at i:1274 original size:26 final size:26
Alignment explanation
Indices: 1238--1291 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
1228 TTCTTTCCAA
*
1238 CACCATATGCTTCTGACTATATGAAG
1 CACCATATGCTTCCGACTATATGAAG
1264 CACCATATGCTTCCGACTATATGAAG
1 CACCATATGCTTCCGACTATATGAAG
1290 CA
1 CA
1292 GCGATGACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (26 bp):
CACCATATGCTTCCGACTATATGAAG
Found at i:1829 original size:76 final size:77
Alignment explanation
Indices: 1739--1880 Score: 241
Period size: 76 Copynumber: 1.9 Consensus size: 77
1729 TTGTTTTTTT
* *
1739 AAGCTACATAGGCTATAGGCATTGTAAGCCATTT-TTTTTAAGCTGCATAGGCTATAGGCGTTGT
1 AAGCTACATAGGCTATAGGCATTGTAAGCCATTTCTTTTTAAGCTACATAGGCTATAGGCATTGT
1803 ACGCTCTCTTTC
66 ACGCTCTCTTTC
* *
1815 AAGCTACATTGGCTATAGGCATTGTAAGCCTTTTCTTTTTAAGCTACATAGGCTATAGGCATTGT
1 AAGCTACATAGGCTATAGGCATTGTAAGCCATTTCTTTTTAAGCTACATAGGCTATAGGCATTGT
1880 A
66 A
1881 AGCCTTTTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
76 32 0.52
77 29 0.48
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.36
Consensus pattern (77 bp):
AAGCTACATAGGCTATAGGCATTGTAAGCCATTTCTTTTTAAGCTACATAGGCTATAGGCATTGT
ACGCTCTCTTTC
Found at i:1870 original size:40 final size:40
Alignment explanation
Indices: 1720--1910 Score: 237
Period size: 40 Copynumber: 4.8 Consensus size: 40
1710 TGTAGGCGTA
*
1720 GTAAGCCTTTTGTTTTTTTAAGCTACATAGGCTATAGGCATT
1 GTAAGCC-TTT-TCTTTTTAAGCTACATAGGCTATAGGCATT
* * *
1762 GTAAGCCATTT-TTTTTAAGCTGCATAGGCTATAGGCGTT
1 GTAAGCCTTTTCTTTTTAAGCTACATAGGCTATAGGCATT
* * * *
1801 GTACG-C-TCTC-TTTCAAGCTACATTGGCTATAGGCATT
1 GTAAGCCTTTTCTTTTTAAGCTACATAGGCTATAGGCATT
1838 GTAAGCCTTTTCTTTTTAAGCTACATAGGCTATAGGCATT
1 GTAAGCCTTTTCTTTTTAAGCTACATAGGCTATAGGCATT
* *
1878 GTAAGCCTTTTTTTTTTAAAGCTGCATAGGCTA
1 GTAAGCCTTTTCTTTTT-AAGCTACATAGGCTA
1911 GAAGTGTCAA
Statistics
Matches: 129, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
37 29 0.22
38 2 0.02
39 33 0.26
40 42 0.33
41 16 0.12
42 7 0.05
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (40 bp):
GTAAGCCTTTTCTTTTTAAGCTACATAGGCTATAGGCATT
Found at i:2000 original size:106 final size:109
Alignment explanation
Indices: 1888--2152 Score: 333
Period size: 109 Copynumber: 2.4 Consensus size: 109
1878 GTAAGCCTTT
* * * * *
1888 TTTTTTTAA-AGCTGCATAGGCTAGAAGT-GTCAACAAGGAGGGGCACTCCTGGAGGTGCAATCA
1 TTTTTTTAAGAGCTACATAGGCCAGAA-TCATCAACAAGGAAGGGCACTCCTGGAGGTGCAACCA
*
1951 GTGCAACACTCCTAAGGGTGCAC-CTGCTCCAAGTCAAAATA-AAA
65 GTGCAACACTCCTAAGGGTGCACTC-ACTCCAAGTCAAAATATAAA
*
1995 TTTTTTTAATGGGCTACATAGGCCAGAATCATCAACAAGGAAGGGCACTCCTGGAGGTGCAACCA
1 TTTTTTTAA-GAGCTACATAGGCCAGAATCATCAACAAGGAAGGGCACTCCTGGAGGTGCAACCA
* * *
2060 GTGCAGCACTCCTATGGGTGCACTCACTCCAAGTCAAAATATAGA
65 GTGCAACACTCCTAAGGGTGCACTCACTCCAAGTCAAAATATAAA
* * * *
2105 TTTTTTTAATGGGCTACATAAGCCAGAATCAACAA-AAGGAAAGGCACT
1 TTTTTTTAA-GAGCTACATAGGCCAGAATCATCAACAAGGAAGGGCACT
2153 TTTGGTTACG
Statistics
Matches: 140, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
107 9 0.06
108 1 0.01
109 94 0.67
110 36 0.26
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.23
Consensus pattern (109 bp):
TTTTTTTAAGAGCTACATAGGCCAGAATCATCAACAAGGAAGGGCACTCCTGGAGGTGCAACCAG
TGCAACACTCCTAAGGGTGCACTCACTCCAAGTCAAAATATAAA
Found at i:2015 original size:109 final size:110
Alignment explanation
Indices: 1917--2152 Score: 361
Period size: 109 Copynumber: 2.2 Consensus size: 110
1907 GCTAGAAGTG
* * *
1917 TCAACAAGGAGGGGCACTCCTGGAGGTGCAATCAGTGCAACACTCCTAAGGGTGCAC-CTGCTCC
1 TCAACAAGGAAGGGCACTCCTGGAGGTGCAACCAGTGCAACACTCCTAAGGGTGCACTC-ACTCC
1981 AAGTCAAAATA-AAATTTTTTTAATGGGCTACATAGGCCAGAATCA
65 AAGTCAAAATATAAATTTTTTTAATGGGCTACATAGGCCAGAATCA
* *
2026 TCAACAAGGAAGGGCACTCCTGGAGGTGCAACCAGTGCAGCACTCCTATGGGTGCACTCACTCCA
1 TCAACAAGGAAGGGCACTCCTGGAGGTGCAACCAGTGCAACACTCCTAAGGGTGCACTCACTCCA
* *
2091 AGTCAAAATATAGATTTTTTTAATGGGCTACATAAGCCAGAATCA
66 AGTCAAAATATAAATTTTTTTAATGGGCTACATAGGCCAGAATCA
* *
2136 ACAA-AAGGAAAGGCACT
1 TCAACAAGGAAGGGCACT
2153 TTTGGTTACG
Statistics
Matches: 116, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
109 80 0.69
110 36 0.31
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.21
Consensus pattern (110 bp):
TCAACAAGGAAGGGCACTCCTGGAGGTGCAACCAGTGCAACACTCCTAAGGGTGCACTCACTCCA
AGTCAAAATATAAATTTTTTTAATGGGCTACATAGGCCAGAATCA
Found at i:2220 original size:68 final size:68
Alignment explanation
Indices: 2110--2240 Score: 174
Period size: 68 Copynumber: 1.9 Consensus size: 68
2100 ATAGATTTTT
* * *
2110 TTAATGGGCTACATAAGCCAGAATCAACAAAAGGAAAGGCACTTTTGGTTACGATCCTTGCTGGA
1 TTAATGGGCTACATAAGCCAGAAGCAACAAAAGGAAAGGCACTTATGGCTACGATCCTTGCTGGA
2175 ATC
66 ATC
* * * **
2178 TTAATTGGCTACATAAGCCAGAAGCATCACAGAGGAAA-GCACTTATGGCTGTGATCCTTGCTG
1 TTAATGGGCTACATAAGCCAGAAGCAACA-AAAGGAAAGGCACTTATGGCTACGATCCTTGCTG
2241 AATATGGAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
68 47 0.87
69 7 0.13
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (68 bp):
TTAATGGGCTACATAAGCCAGAAGCAACAAAAGGAAAGGCACTTATGGCTACGATCCTTGCTGGA
ATC
Found at i:2585 original size:18 final size:18
Alignment explanation
Indices: 2558--2593 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2548 CCATTATTTT
2558 TGTCAACAGCTCCAGATC
1 TGTCAACAGCTCCAGATC
* *
2576 TGTCAGCAGCTCCTGATC
1 TGTCAACAGCTCCAGATC
2594 ATGTGCAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.33, G:0.19, T:0.25
Consensus pattern (18 bp):
TGTCAACAGCTCCAGATC
Done.