Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016390.1 Corchorus capsularis cultivar CVL-1 contig16411, 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: 3937
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Found at i:1213 original size:22 final size:22
Alignment explanation
Indices: 1176--1235 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
1166 AGAAAGATGC
*
1176 AATCAGTAAA-AGGTAAAATGGT
1 AATCAGTAAAGA-GTAAAATGAT
*
1198 AATCAGTAAAGAGTAAAGTGAT
1 AATCAGTAAAGAGTAAAATGAT
* *
1220 GATTAGTAAAGAGTAA
1 AATCAGTAAAGAGTAA
1236 TAGAAGTCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 32 0.97
23 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.23, T:0.23
Consensus pattern (22 bp):
AATCAGTAAAGAGTAAAATGAT
Found at i:1301 original size:55 final size:55
Alignment explanation
Indices: 1232--1541 Score: 433
Period size: 55 Copynumber: 5.6 Consensus size: 55
1222 TTAGTAAAGA
*
1232 GTAATAG-AAGTCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATCAGAGTTAAG
1 GTAATAGTAA-TCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAG
* * * * *
1287 GTAATAGTGATCAGTAAATCAGTAATTAAGTAAAAAGAGGTAAATCAGAGTCAAA
1 GTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAG
** *
1342 GTAGCAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATCAGAGTTAAG
1 GTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAG
* * * * * *
1397 GTAATAGTGATCAGTAAATCAATAATTAAGTAAAAAGAGGTAAATCAGAGTCAAA
1 GTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAG
**
1452 GTAGCAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAG
1 GTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAG
* *
1507 GTAATAGTAATCAGTAAATCAGTAATCAGGTAAAA
1 GTAATAGTAATCAGTAAATCAGTAATTAAGTAAAA
1542 GATAGTAATC
Statistics
Matches: 219, Mismatches: 35, Indels: 2
0.86 0.14 0.01
Matches are distributed among these distances:
55 218 1.00
56 1 0.00
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.25
Consensus pattern (55 bp):
GTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAG
Found at i:1358 original size:110 final size:110
Alignment explanation
Indices: 1242--1541 Score: 555
Period size: 110 Copynumber: 2.7 Consensus size: 110
1232 GTAATAGAAG
1242 TCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATCAGAGTTAAGGTAATAGTGATCAGTAAATC
1 TCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATCAGAGTTAAGGTAATAGTGATCAGTAAATC
1307 AGTAATTAAGTAAAAAGAGGTAAATCAGAGTCAAAGTAGCAGTAA
66 AGTAATTAAGTAAAAAGAGGTAAATCAGAGTCAAAGTAGCAGTAA
1352 TCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATCAGAGTTAAGGTAATAGTGATCAGTAAATC
1 TCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATCAGAGTTAAGGTAATAGTGATCAGTAAATC
*
1417 AATAATTAAGTAAAAAGAGGTAAATCAGAGTCAAAGTAGCAGTAA
66 AGTAATTAAGTAAAAAGAGGTAAATCAGAGTCAAAGTAGCAGTAA
* *
1462 TCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAATAGTAATCAGTAAATC
1 TCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATCAGAGTTAAGGTAATAGTGATCAGTAAATC
* *
1527 AGTAATCAGGTAAAA
66 AGTAATTAAGTAAAA
1542 GATAGTAATC
Statistics
Matches: 184, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
110 184 1.00
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.25
Consensus pattern (110 bp):
TCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATCAGAGTTAAGGTAATAGTGATCAGTAAATC
AGTAATTAAGTAAAAAGAGGTAAATCAGAGTCAAAGTAGCAGTAA
Found at i:1563 original size:18 final size:17
Alignment explanation
Indices: 1510--1564 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
1500 AGTTAAGGTA
1510 ATAGTAATCAGTAAAT-
1 ATAGTAATCAGTAAATG
* *
1526 -CAGTAATCAGGTAAAAG
1 ATAGTAATCA-GTAAATG
1543 ATAGTAATCAGTAAATTG
1 ATAGTAATCAGTAAA-TG
1561 ATAG
1 ATAG
1565 GCAAGGTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
15 8 0.26
16 5 0.16
17 5 0.16
18 13 0.42
ACGTcount: A:0.47, C:0.07, G:0.18, T:0.27
Consensus pattern (17 bp):
ATAGTAATCAGTAAATG
Found at i:1998 original size:86 final size:84
Alignment explanation
Indices: 1849--2215 Score: 252
Period size: 86 Copynumber: 4.2 Consensus size: 84
1839 ATCTGAAAGG
* * * * * * **
1849 GTAAAATGGTAGTTAGTAAGAGTAAAAGGTAATCATTAAAAAGTAAGAAGGTAATCAACAAGAGT
1 GTAAAATAGTAATCAGTAAGAGTAAAAAGTAATCAGTAAAAAGTAA-AAGGAAATCAGTAAGAGT
1914 GAAATA-AT-AGTCAGTAAAAAA
65 GAAA-AGATGA-TCAGT-AAAAA
*
1935 GTAAAATAGTAATCAGTAAGAGTGAAAAAGTAA-CAAGTAAGAAGTAAAAGGAAATCAGTAAGAG
1 GTAAAATAGTAATCAGTAAGAGT-AAAAAGTAATC-AGTAAAAAGTAAAAGGAAATCAGTAAGAG
* *
1999 TGAAAAGGTGATCAGTAAAGA
64 TGAAAAGATGATCAGTAAAAA
* * * *
2020 GTAAAA-AGCTAATCAGTAAGAAATAAAAAGGTAATCAGTAAAAAGCAAAAGGCAATCAGTAAAA
1 GTAAAATAG-TAATCAGTAAG-AGTAAAAA-GTAATCAGTAAAAAGTAAAAGGAAATCAGT-AAG
*
2084 AGT-AAAAGAGTAATCAGTAAAAAAAGGA
62 AGTGAAAAGA-TGATCAGT---AAAA--A
* * * *
2112 GCAGAAAATGGTAATCAGTAAAAGAGTAAAATGGTAATCAGTAAAAAGTAAGAAGGTAATCAGTA
1 G--TAAAATAGTAATCAGT--AAGAGTAAAA-AGTAATCAGTAAAAAGTAA-AAGGAAATCAGT-
* *
2177 AAGAGT---AA-A--ATCCGTAAAGA
59 AAGAGTGAAAAGATGATCAGTAAAAA
2197 GTAAAATAGTAATCAGTAA
1 GTAAAATAGTAATCAGTAA
2216 AAGATAACCA
Statistics
Matches: 229, Mismatches: 30, Indels: 49
0.74 0.10 0.16
Matches are distributed among these distances:
81 2 0.01
83 14 0.06
84 2 0.01
85 29 0.13
86 78 0.34
87 35 0.15
90 8 0.03
92 2 0.01
93 1 0.00
94 14 0.06
95 24 0.10
96 20 0.09
ACGTcount: A:0.54, C:0.06, G:0.21, T:0.19
Consensus pattern (84 bp):
GTAAAATAGTAATCAGTAAGAGTAAAAAGTAATCAGTAAAAAGTAAAAGGAAATCAGTAAGAGTG
AAAAGATGATCAGTAAAAA
Found at i:2026 original size:22 final size:22
Alignment explanation
Indices: 1818--2186 Score: 227
Period size: 22 Copynumber: 16.8 Consensus size: 22
1808 AATAGCATGC
*
1818 AATCAGTAAAAAGTAAAAA-GT
1 AATCAGTAAAGAGTAAAAAGGT
* * *
1839 -ATCTG-AAAGGGTAAAATGGT
1 AATCAGTAAAGAGTAAAAAGGT
* *
1859 AGTTAGT-AAGAGT-AAAAGGT
1 AATCAGTAAAGAGTAAAAAGGT
* * *
1879 AATCATTAAAAAGTAAGAAGGT
1 AATCAGTAAAGAGTAAAAAGGT
1901 AATCA--ACAAGAGTGAAATAA--T
1 AATCAGTA-AAGAGT-AAA-AAGGT
* *
1922 AGTCAGTAAAAAAGTAAAATA-GT
1 AATCAGT-AAAGAGTAAAA-AGGT
1945 AATCAGT-AAGAGTGAAAAA-GT
1 AATCAGTAAAGAGT-AAAAAGGT
*
1966 AA-CAAGT-AAGAAGT-AAAAGGA
1 AATC-AGTAAAG-AGTAAAAAGGT
*
1987 AATCAGT-AAGAGTGAAAAGGT
1 AATCAGTAAAGAGTAAAAAGGT
* *
2008 GATCAGTAAAGAGTAAAAAGCT
1 AATCAGTAAAGAGTAAAAAGGT
*
2030 AATCAGT-AAGAAATAAAAAGGT
1 AATCAGTAAAG-AGTAAAAAGGT
* * *
2052 AATCAGTAAAAAG-CAAAAGGC
1 AATCAGTAAAGAGTAAAAAGGT
*
2073 AATCAGTAAAAAGT-AAAAGAGT
1 AATCAGTAAAGAGTAAAAAG-GT
*
2095 AATCAGTAAAAAAAGGAGCAGAAAATGGT
1 AATCAGT----AAA-GAGTA-AAAA-GGT
*
2124 AATCAGTAAAAGAGTAAAATGGT
1 AATCAGT-AAAGAGTAAAAAGGT
* *
2147 AATCAGTAAAAAGTAAGAAGGT
1 AATCAGTAAAGAGTAAAAAGGT
2169 AATCAGTAAAGAGTAAAA
1 AATCAGTAAAGAGTAAAA
2187 TCCGTAAAGA
Statistics
Matches: 274, Mismatches: 42, Indels: 63
0.72 0.11 0.17
Matches are distributed among these distances:
19 9 0.03
20 25 0.09
21 87 0.32
22 96 0.35
23 26 0.09
24 4 0.01
25 4 0.01
26 7 0.03
27 2 0.01
29 13 0.05
30 1 0.00
ACGTcount: A:0.54, C:0.06, G:0.21, T:0.18
Consensus pattern (22 bp):
AATCAGTAAAGAGTAAAAAGGT
Found at i:2188 original size:16 final size:16
Alignment explanation
Indices: 2169--2208 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
2159 GTAAGAAGGT
2169 AATCAGTAAAGAGTAA
1 AATCAGTAAAGAGTAA
*
2185 AATCCGTAAAGAGTAA
1 AATCAGTAAAGAGTAA
2201 AAT-AGTAA
1 AATCAGTAA
2209 TCAGTAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.55, C:0.07, G:0.17, T:0.20
Consensus pattern (16 bp):
AATCAGTAAAGAGTAA
Found at i:2200 original size:45 final size:46
Alignment explanation
Indices: 1866--2208 Score: 127
Period size: 43 Copynumber: 7.7 Consensus size: 46
1856 GGTAGTTAGT
* * * *
1866 AAGAGTAAAA-GGTAATCATTAAAA-AGTAAGAAGGTAATCA--AC
1 AAGAGTAAAATCGTAAACAGTAAAATAGTAAGAAGGTAATCAGTAA
* ** ** * *
1908 AAGAGTGAAATAATAGTCAGTAAAAAAGTAA-AATAGTAATCAGT--
1 AAGAGTAAAATCGTAAACAGTAAAATAGTAAGAA-GGTAATCAGTAA
* * *
1952 AAGAGTGAAAA-AGT-AACAAGTAAGA-AGTAA-AAGGAAATCAGT--
1 AAGAGT-AAAATCGTAAAC-AGTAAAATAGTAAGAAGGTAATCAGTAA
* * * * * *
1994 AAGAGTGAAAA-GGTGATCAGT-AAAGAGTAAAAAGCTAATCAGTAA
1 AAGAGT-AAAATCGTAAACAGTAAAATAGTAAGAAGGTAATCAGTAA
** * * *
2039 GAA-A-TAAAAAGGTAATCAGTAAAA-AGCAA-AAGGCAATCAGTAA
1 -AAGAGTAAAATCGTAAACAGTAAAATAGTAAGAAGGTAATCAGTAA
** * * *
2082 AA-AGTAAAAGAGTAATCAGTAAAAAAAGGAGCAGAAAATGGTAATCAGTAA
1 AAGAGTAAAATCGTAAACAGT-AAAATAGTA--AG--AA-GGTAATCAGTAA
* *
2133 AAGAGTAAAATGGTAATCAGTAAAA-AGTAAGAAGGTAATCAGT-A
1 AAGAGTAAAATCGTAAACAGTAAAATAGTAAGAAGGTAATCAGTAA
*
2177 AAGAGTAAAATCCGTAAAGAGTAAAATAGTAA
1 AAGAGTAAAAT-CGTAAACAGTAAAATAGTAA
2209 TCAGTAAAAG
Statistics
Matches: 242, Mismatches: 32, Indels: 50
0.75 0.10 0.15
Matches are distributed among these distances:
41 2 0.01
42 41 0.17
43 62 0.26
44 56 0.23
45 31 0.13
46 9 0.04
47 1 0.00
48 2 0.01
50 5 0.02
51 17 0.07
52 16 0.07
ACGTcount: A:0.55, C:0.06, G:0.21, T:0.18
Consensus pattern (46 bp):
AAGAGTAAAATCGTAAACAGTAAAATAGTAAGAAGGTAATCAGTAA
Found at i:2216 original size:22 final size:22
Alignment explanation
Indices: 1818--2187 Score: 202
Period size: 21 Copynumber: 16.9 Consensus size: 22
1808 AATAGCATGC
* *
1818 AATCAGTAAAAAGTAAAA-AGT
1 AATCAGTAAAGAGTAAAATGGT
* *
1839 -ATCTG-AAAGGGTAAAATGGT
1 AATCAGTAAAGAGTAAAATGGT
* *
1859 AGTTAGT-AAGAGTAAAA-GGT
1 AATCAGTAAAGAGTAAAATGGT
* *
1879 AATCATTAAAAAGTAAGAA-GGT
1 AATCAGTAAAGAGTAA-AATGGT
* **
1901 AATCA--ACAAGAGTGAAATAAT
1 AATCAGTA-AAGAGTAAAATGGT
* * *
1922 AGTCAGTAAAAAAGTAAAATAGT
1 AATCAGT-AAAGAGTAAAATGGT
*
1945 AATCAGT-AAGAGTGAAAA-AGT
1 AATCAGTAAAGAGT-AAAATGGT
*
1966 AA-CAAGT-AAGAAGTAAAA-GGA
1 AATC-AGTAAAG-AGTAAAATGGT
1987 AATCAGT-AAGAGTGAAAA-GGT
1 AATCAGTAAAGAGT-AAAATGGT
* * *
2008 GATCAGTAAAGAGTAAAAAGCT
1 AATCAGTAAAGAGTAAAATGGT
* *
2030 AATCAGT-AAGAAATAAAAAGGT
1 AATCAGTAAAG-AGTAAAATGGT
* * *
2052 AATCAGTAAAAAGCAAAA-GGC
1 AATCAGTAAAGAGTAAAATGGT
*
2073 AATCAGTAAAAAGTAAAA-GAGT
1 AATCAGTAAAGAGTAAAATG-GT
*
2095 AATCAGTAAAAAAAGGAGCAGAAAATGGT
1 AATCAGT----AAA-GAG--TAAAATGGT
2124 AATCAGTAAAAGAGTAAAATGGT
1 AATCAGT-AAAGAGTAAAATGGT
*
2147 AATCAGTAAAAAGTAAGAA-GGT
1 AATCAGTAAAGAGTAA-AATGGT
2169 AATCAGTAAAGAGTAAAAT
1 AATCAGTAAAGAGTAAAAT
2188 CCGTAAAGAG
Statistics
Matches: 278, Mismatches: 41, Indels: 59
0.74 0.11 0.16
Matches are distributed among these distances:
19 9 0.03
20 20 0.07
21 99 0.36
22 87 0.31
23 36 0.13
24 1 0.00
25 3 0.01
26 7 0.03
27 2 0.01
29 13 0.05
30 1 0.00
ACGTcount: A:0.54, C:0.06, G:0.21, T:0.19
Consensus pattern (22 bp):
AATCAGTAAAGAGTAAAATGGT
Found at i:2244 original size:21 final size:21
Alignment explanation
Indices: 2211--2300 Score: 67
Period size: 21 Copynumber: 4.3 Consensus size: 21
2201 AATAGTAATC
*
2211 AGTAAAAGA-TAACCAGTAAG
1 AGTAAAATAGTAACCAGTAAG
*
2231 AGTAAAATAGTAACTAGTAAG
1 AGTAAAATAGTAACCAGTAAG
* * **
2252 AGCAAAGT-GATAATTAGTAAG
1 AGTAAAATAG-TAACCAGTAAG
* * *
2273 AGTCAAATAGTAATCAATAAAG
1 AGTAAAATAGTAACCAGT-AAG
2295 AGTAAA
1 AGTAAA
2301 GGGTGATCAG
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
20 9 0.16
21 37 0.67
22 9 0.16
ACGTcount: A:0.53, C:0.07, G:0.19, T:0.21
Consensus pattern (21 bp):
AGTAAAATAGTAACCAGTAAG
Found at i:2250 original size:42 final size:42
Alignment explanation
Indices: 2203--2285 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 42
2193 AAGAGTAAAA
*
2203 TAGTAATCAGTAAA-AGATAACCAGTAAGAGTAAAATAGTAAC
1 TAGTAA-CAGCAAAGAGATAACCAGTAAGAGTAAAATAGTAAC
* * ** *
2245 TAGTAAGAGCAAAGTGATAATTAGTAAGAGTCAAATAGTAA
1 TAGTAACAGCAAAGAGATAACCAGTAAGAGTAAAATAGTAA
2286 TCAATAAAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
41 5 0.15
42 29 0.85
ACGTcount: A:0.51, C:0.07, G:0.19, T:0.23
Consensus pattern (42 bp):
TAGTAACAGCAAAGAGATAACCAGTAAGAGTAAAATAGTAAC
Found at i:2390 original size:29 final size:28
Alignment explanation
Indices: 2365--2427 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
2355 GTAAAAAGTG
2365 GTAATAAATAAAAGAGAGTAAGAAAAGA
1 GTAATAAATAAAAGAGAGTAAGAAAAGA
***
2393 GTAATTGGTAAAA-AGAGTAAGAAAAGA
1 GTAATAAATAAAAGAGAGTAAGAAAAGA
2420 GTAA-AAAT
1 GTAATAAAT
2428 GATAAAAGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
26 1 0.03
27 18 0.62
28 10 0.34
ACGTcount: A:0.60, C:0.00, G:0.22, T:0.17
Consensus pattern (28 bp):
GTAATAAATAAAAGAGAGTAAGAAAAGA
Found at i:2433 original size:29 final size:28
Alignment explanation
Indices: 2372--2435 Score: 85
Period size: 27 Copynumber: 2.2 Consensus size: 28
2362 GTGGTAATAA
*
2372 ATAAAAGAGAGTAAGAAAAGAGTAATTG
1 ATAAAAGAGAGTAAGAAAAGAGTAAATG
*
2400 GTAAAA-AGAGTAAGAAAAGAGTAAAAATG
1 ATAAAAGAGAGTAAGAAAAGAGT--AAATG
2429 ATAAAAG
1 ATAAAAG
2436 TAGCAAAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 16 0.53
28 5 0.17
29 9 0.30
ACGTcount: A:0.61, C:0.00, G:0.23, T:0.16
Consensus pattern (28 bp):
ATAAAAGAGAGTAAGAAAAGAGTAAATG
Found at i:3343 original size:50 final size:50
Alignment explanation
Indices: 3283--3402 Score: 129
Period size: 48 Copynumber: 2.4 Consensus size: 50
3273 GAAGTCCAGA
* * *
3283 CTTTAATTCAAAGGTGACATTTATTTCACAAATTACTT-TAAAAATTCAAT
1 CTTTTATTCAAAGGTGACATTT-CTTCACAAATTACTTGTAAAAATCCAAT
* * *
3333 CTTTTATTCAAAGGTGTCA--TCTTCACTAATTATTTGTAAAAATCCAAT
1 CTTTTATTCAAAGGTGACATTTCTTCACAAATTACTTGTAAAAATCCAAT
* * *
3381 CTTTTATTTAAAGATGGCATTT
1 CTTTTATTCAAAGGTGACATTT
3403 TGATAATCCC
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
47 12 0.21
48 28 0.48
50 18 0.31
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.42
Consensus pattern (50 bp):
CTTTTATTCAAAGGTGACATTTCTTCACAAATTACTTGTAAAAATCCAAT
Done.