Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005879.1 Corchorus capsularis cultivar CVL-1 contig05897, 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: 2566
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.34
Found at i:2193 original size:35 final size:35
Alignment explanation
Indices: 2104--2213 Score: 134
Period size: 35 Copynumber: 3.1 Consensus size: 35
2094 TCATATTTTT
* *
2104 ACTCTTTACCATTTTTTCTTTACTGGATTACTCTTT
1 ACTCTTTACCATTTTTTCTTTACT-GATTACCCTTC
* *
2140 ACTCTTCACCA-TTCTTCTTTACTGACTT-CCCTTC
1 ACTCTTTACCATTTTTTCTTTACTGA-TTACCCTTC
* *
2174 ACTCTTTACCATTTTTTCTTTACTGATTACTCTTT
1 ACTCTTTACCATTTTTTCTTTACTGATTACCCTTC
2209 ACTCT
1 ACTCT
2214 ACTCTTTACC
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
34 18 0.29
35 35 0.56
36 10 0.16
ACGTcount: A:0.16, C:0.28, G:0.04, T:0.52
Consensus pattern (35 bp):
ACTCTTTACCATTTTTTCTTTACTGATTACCCTTC
Found at i:2210 original size:7 final size:7
Alignment explanation
Indices: 2190--2469 Score: 92
Period size: 7 Copynumber: 41.1 Consensus size: 7
2180 TACCATTTTT
2190 TCTTTAC
1 TCTTTAC
**
2197 TGATTAC
1 TCTTTAC
2204 TCTTTAC
1 TCTTTAC
2211 TC--TAC
1 TCTTTAC
2216 TCTTTAC
1 TCTTTAC
*
2223 CCTTTAC
1 TCTTTAC
**
2230 -CATTTTT
1 TC-TTTAC
2237 TCTTTAC
1 TCTTTAC
**
2244 TGATTAC
1 TCTTTAC
2251 TC-TT-C
1 TCTTTAC
2256 TCTTTAC
1 TCTTTAC
2263 TCTTTAC
1 TCTTTAC
2270 TCTTTAC
1 TCTTTAC
* *
2277 CCTTT-T
1 TCTTTAC
2283 TCTTTAC
1 TCTTTAC
**
2290 TGATTAC
1 TCTTTAC
2297 TCTTTTAC
1 TC-TTTAC
*
2305 TTTTTAC
1 TCTTTAC
2312 -CATTTTAC
1 TC--TTTAC
2320 T-TTGT--
1 TCTT-TAC
**
2325 TGATTAC
1 TCTTTAC
2332 TCTTTAC
1 TCTTTAC
*
2339 TCTTCAC
1 TCTTTAC
*
2346 -CATTT-T
1 TC-TTTAC
2352 TCTTTAC
1 TCTTTAC
**
2359 TGATTAC
1 TCTTTAC
2366 TCTTTAC
1 TCTTTAC
2373 TC--TAC
1 TCTTTAC
2378 TCTTTAC
1 TCTTTAC
*
2385 CCTTTAC
1 TCTTTAC
**
2392 -CATTTTTT
1 TC--TTTAC
2400 TCTTTAC
1 TCTTTAC
**
2407 TGATTAC
1 TCTTTAC
2414 TC-TT-C
1 TCTTTAC
2419 TCTTTAC
1 TCTTTAC
2426 TCTTTAC
1 TCTTTAC
**
2433 -CATTTTT
1 TC-TTTAC
2440 TCTTTAC
1 TCTTTAC
**
2447 TGATTAC
1 TCTTTAC
2454 TCATTTAC
1 TC-TTTAC
*
2462 TTTTTAC
1 TCTTTAC
2469 T
1 T
2470 GATTACCATT
Statistics
Matches: 195, Mismatches: 50, Indels: 56
0.65 0.17 0.19
Matches are distributed among these distances:
5 18 0.09
6 22 0.11
7 134 0.69
8 20 0.10
9 1 0.01
ACGTcount: A:0.16, C:0.25, G:0.03, T:0.56
Consensus pattern (7 bp):
TCTTTAC
Found at i:2222 original size:19 final size:19
Alignment explanation
Indices: 2200--2273 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
2190 TCTTTACTGA
*
2200 TTACTCTTTACTCTACTCT
1 TTACTCTTTACTCTTCTCT
* * *
2219 TTACCCTTTACCATTTTTTCT
1 TTACTCTTTA-C-TCTTCTCT
**
2240 TTACTGATTACTCTTCTCT
1 TTACTCTTTACTCTTCTCT
2259 TTACTCTTTACTCTT
1 TTACTCTTTACTCTT
2274 TACCCTTTTT
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
19 28 0.67
20 2 0.05
21 12 0.29
ACGTcount: A:0.15, C:0.28, G:0.01, T:0.55
Consensus pattern (19 bp):
TTACTCTTTACTCTTCTCT
Found at i:2231 original size:47 final size:46
Alignment explanation
Indices: 2177--2301 Score: 198
Period size: 47 Copynumber: 2.7 Consensus size: 46
2167 TCCCTTCACT
2177 CTTTACCATTTTTTCTTTACTGATTACTCTTTACTCTACTCTTTACC
1 CTTTACCATTTTTTCTTTACTGATTACTCTTT-CTCTACTCTTTACC
* *
2224 CTTTACCATTTTTTCTTTACTGATTACTCTTCTCTTTACTCTTTACT
1 CTTTACCATTTTTTCTTTACTGATTACTCTT-TCTCTACTCTTTACC
*
2271 CTTTACC-CTTTTTCTTTACTGATTACTCTTT
1 CTTTACCATTTTTTCTTTACTGATTACTCTTT
2302 TACTTTTTAC
Statistics
Matches: 74, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
45 1 0.01
46 22 0.30
47 50 0.68
48 1 0.01
ACGTcount: A:0.15, C:0.26, G:0.02, T:0.56
Consensus pattern (46 bp):
CTTTACCATTTTTTCTTTACTGATTACTCTTTCTCTACTCTTTACC
Found at i:2285 original size:163 final size:164
Alignment explanation
Indices: 2101--2432 Score: 521
Period size: 163 Copynumber: 2.0 Consensus size: 164
2091 GATTCATATT
*
2101 TTTACTCTTTACCATTTTTTCTTTACTGGATTACTC-TTTACTCTTCACCATTCTT-CTTTACTG
1 TTTACTCTTTACCACTTTTTCTTTACT-GATTACTCTTTTACTCTTCACCATT-TTACTTTACTG
*
2164 ACTT-CCCTTCACTCTTTACCATTTTTTCTTTACTGATTACTCTTTACTCTACTCTTTACCCTTT
64 A-TTACCCTTCACTCTTCACCA-TTTTTCTTTACTGATTACTCTTTACTCTACTCTTTACCCTTT
2228 ACCA-TTTTTTCTTTACTGATTACTCTTCTCTTTACTC
127 ACCATTTTTTTCTTTACTGATTACTCTTCTCTTTACTC
* * **
2265 TTTACTCTTTACC-CTTTTTCTTTACTGATTACTCTTTTACTTTTTACCATTTTACTTTGTTGAT
1 TTTACTCTTTACCACTTTTTCTTTACTGATTACTCTTTTACTCTTCACCATTTTACTTTACTGAT
* *
2329 TACTCTTTACTCTTCACCATTTTTCTTTACTGATTACTCTTTACTCTACTCTTTACCCTTTACCA
66 TACCCTTCACTCTTCACCATTTTTCTTTACTGATTACTCTTTACTCTACTCTTTACCCTTTACCA
2394 TTTTTTTCTTTACTGATTACTCTTCTCTTTACTC
131 TTTTTTTCTTTACTGATTACTCTTCTCTTTACTC
2428 TTTAC
1 TTTAC
2433 CATTTTTTCT
Statistics
Matches: 156, Mismatches: 8, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
162 58 0.37
163 85 0.54
164 13 0.08
ACGTcount: A:0.16, C:0.27, G:0.03, T:0.55
Consensus pattern (164 bp):
TTTACTCTTTACCACTTTTTCTTTACTGATTACTCTTTTACTCTTCACCATTTTACTTTACTGAT
TACCCTTCACTCTTCACCATTTTTCTTTACTGATTACTCTTTACTCTACTCTTTACCCTTTACCA
TTTTTTTCTTTACTGATTACTCTTCTCTTTACTC
Found at i:2299 original size:34 final size:34
Alignment explanation
Indices: 2259--2375 Score: 171
Period size: 34 Copynumber: 3.4 Consensus size: 34
2249 ACTCTTCTCT
*
2259 TTACTCTTTACTCTTTACCCTTTTTCTTTACTGA
1 TTACTCTTTACTCTTTACCATTTTTCTTTACTGA
* * **
2293 TTACTCTTTTACTTTTTACCATTTTACTTTGTTGA
1 TTACTC-TTTACTCTTTACCATTTTTCTTTACTGA
*
2328 TTACTCTTTACTCTTCACCATTTTTCTTTACTGA
1 TTACTCTTTACTCTTTACCATTTTTCTTTACTGA
2362 TTACTCTTTACTCT
1 TTACTCTTTACTCT
2376 ACTCTTTACC
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
34 43 0.60
35 29 0.40
ACGTcount: A:0.16, C:0.24, G:0.03, T:0.56
Consensus pattern (34 bp):
TTACTCTTTACTCTTTACCATTTTTCTTTACTGA
Found at i:2309 original size:27 final size:26
Alignment explanation
Indices: 2247--2309 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
2237 TCTTTACTGA
* * *
2247 TTACTCTTCTCTTTACTCTTTACTCT
1 TTACTTTTTTCTTTACTCATTACTCT
* *
2273 TTACCCTTTTTCTTTACTGATTACTCTT
1 TTA-CTTTTTTCTTTACTCATTACTC-T
2301 TTACTTTTT
1 TTACTTTTT
2310 ACCATTTTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
26 3 0.10
27 22 0.76
28 4 0.14
ACGTcount: A:0.13, C:0.25, G:0.02, T:0.60
Consensus pattern (26 bp):
TTACTTTTTTCTTTACTCATTACTCT
Found at i:2407 original size:41 final size:41
Alignment explanation
Indices: 2329--2455 Score: 148
Period size: 41 Copynumber: 3.0 Consensus size: 41
2319 CTTTGTTGAT
* *
2329 TACTCTTTACTCTTCACCATTTTTCTTTACTGATTACTCTTTACTC
1 TACTCTTTACTCTTTACCA-TTTT-TTT-CT--TTACTCATTACTC
* *
2375 TACTCTTTACCCTTTACCATTTTTTTCTTTACTGATTACTC
1 TACTCTTTACTCTTTACCATTTTTTTCTTTACTCATTACTC
* *
2416 TTCTCTTTACTCTTTACCA-TTTTTTCTTTACTGATTACTC
1 TACTCTTTACTCTTTACCATTTTTTTCTTTACTCATTACTC
2456 ATTTACTTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
40 21 0.28
41 28 0.37
43 2 0.03
44 3 0.04
45 4 0.05
46 17 0.23
ACGTcount: A:0.17, C:0.27, G:0.02, T:0.54
Consensus pattern (41 bp):
TACTCTTTACTCTTTACCATTTTTTTCTTTACTCATTACTC
Found at i:2413 original size:22 final size:22
Alignment explanation
Indices: 2388--2481 Score: 90
Period size: 22 Copynumber: 4.5 Consensus size: 22
2378 TCTTTACCCT
2388 TTACCATTTTTTTCTTTACTGA
1 TTACCATTTTTTTCTTTACTGA
* * **
2410 TTA-C--TCTTCTCTTTACTCT
1 TTACCATTTTTTTCTTTACTGA
2429 TTACCATTT-TTTCTTTACTGA
1 TTACCATTTTTTTCTTTACTGA
**
2450 TTACTCATTTACTT-TTTACTGA
1 TTAC-CATTTTTTTCTTTACTGA
2472 TTACCATTTT
1 TTACCATTTT
2482 ACTCTTTTTC
Statistics
Matches: 57, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
19 14 0.25
20 1 0.02
21 19 0.33
22 21 0.37
23 2 0.04
ACGTcount: A:0.18, C:0.21, G:0.03, T:0.57
Consensus pattern (22 bp):
TTACCATTTTTTTCTTTACTGA
Found at i:2414 original size:48 final size:46
Alignment explanation
Indices: 2328--2463 Score: 178
Period size: 46 Copynumber: 3.0 Consensus size: 46
2318 ACTTTGTTGA
*
2328 TTACTCTTTACTCTTCACCA-TTTTTCTTTACTGATTACTCTTTAC
1 TTACTCTTTACTCTTTACCATTTTTTCTTTACTGATTACTCTTTAC
*
2373 TCTACTCTTTACCCTTTACCATTTTTTTCTTTACTGATTA--C--T-C
1 T-TACTCTTTACTCTTTACCA-TTTTTTCTTTACTGATTACTCTTTAC
2416 TT-CTCTTTACTCTTTACCATTTTTTCTTTACTGATTACTCATTTAC
1 TTACTCTTTACTCTTTACCATTTTTTCTTTACTGATTACTC-TTTAC
2462 TT
1 TT
2464 TTTACTGATT
Statistics
Matches: 79, Mismatches: 3, Indels: 17
0.80 0.03 0.17
Matches are distributed among these distances:
40 18 0.23
41 16 0.20
42 2 0.03
43 2 0.03
44 1 0.01
45 2 0.03
46 21 0.27
48 17 0.22
ACGTcount: A:0.17, C:0.26, G:0.02, T:0.55
Consensus pattern (46 bp):
TTACTCTTTACTCTTTACCATTTTTTCTTTACTGATTACTCTTTAC
Found at i:2482 original size:22 final size:22
Alignment explanation
Indices: 2388--2564 Score: 104
Period size: 21 Copynumber: 8.0 Consensus size: 22
2378 TCTTTACCCT
*
2388 TTACCATTTT-TTTCTTTACTGA
1 TTACCATTTTACTT-TTTACTGA
* * **
2410 TTA-C-TCTT-CTCTTTACTCT
1 TTACCATTTTACTTTTTACTGA
2429 TTACCATTTT--TTCTTTACTGA
1 TTACCATTTTACTT-TTTACTGA
2450 TTACTCA-TTTACTTTTTACTGA
1 TTAC-CATTTTACTTTTTACTGA
* *
2472 TTACCATTTTACTCTTTTTCTAA
1 TTACCATTTTACT-TTTTACTGA
*
2495 TTACTATTTTACCTTTTTACTGA
1 TTACCATTTTA-CTTTTTACTGA
*
2518 TTCTATTCC-TTGTACTTTTTACTTGA
1 -T-TA--CCATTTTACTTTTTAC-TGA
*
2544 TTACCA--TTACTTCTTACTGA
1 TTACCATTTTACTTTTTACTGA
2564 T
1 T
2565 CA
Statistics
Matches: 122, Mismatches: 18, Indels: 32
0.71 0.10 0.19
Matches are distributed among these distances:
19 9 0.07
20 10 0.08
21 28 0.23
22 25 0.20
23 26 0.21
24 5 0.04
25 11 0.09
26 7 0.06
27 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.04, T:0.56
Consensus pattern (22 bp):
TTACCATTTTACTTTTTACTGA
Found at i:2497 original size:23 final size:23
Alignment explanation
Indices: 2449--2512 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
2439 TTCTTTACTG
* *
2449 ATTACTCA-TTTACT-TTTTACTG
1 ATTAC-CATTTTACTCTTTTTCTA
2471 ATTACCATTTTACTCTTTTTCTA
1 ATTACCATTTTACTCTTTTTCTA
*
2494 ATTACTATTTTAC-CTTTTT
1 ATTACCATTTTACTCTTTTT
2513 ACTGATTCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 2 0.05
22 17 0.46
23 18 0.49
ACGTcount: A:0.22, C:0.19, G:0.02, T:0.58
Consensus pattern (23 bp):
ATTACCATTTTACTCTTTTTCTA
Done.