Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005177.1 Corchorus capsularis cultivar CVL-1 contig05195, 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: 5425
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Found at i:1630 original size:13 final size:13
Alignment explanation
Indices: 1614--1638 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1604 CTATAATGCA
1614 ATATGCAAATGTG
1 ATATGCAAATGTG
1627 ATATGCAAATGT
1 ATATGCAAATGT
1639 CATAAAGTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (13 bp):
ATATGCAAATGTG
Found at i:2147 original size:33 final size:33
Alignment explanation
Indices: 2105--2197 Score: 132
Period size: 34 Copynumber: 2.8 Consensus size: 33
2095 AGGAGGCTTT
2105 GAAGAATTGAAATTGAAACATTGAATTGAATTC
1 GAAGAATTGAAATTGAAACATTGAATTGAATTC
*
2138 GAAGAATTGAAAATGAAACATTGAAATTGAATTC
1 GAAGAATTGAAATTGAAACATTG-AATTGAATTC
* * * *
2172 GAAGAATTCAAGTTGAAGCATGGAAT
1 GAAGAATTGAAATTGAAACATTGAAT
2198 AATTGAAGCG
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 25 0.47
34 28 0.53
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.27
Consensus pattern (33 bp):
GAAGAATTGAAATTGAAACATTGAATTGAATTC
Found at i:2171 original size:34 final size:33
Alignment explanation
Indices: 2105--2179 Score: 132
Period size: 33 Copynumber: 2.2 Consensus size: 33
2095 AGGAGGCTTT
*
2105 GAAGAATTGAAATTGAAACATTGAATTGAATTC
1 GAAGAATTGAAAATGAAACATTGAATTGAATTC
2138 GAAGAATTGAAAATGAAACATTGAAATTGAATTC
1 GAAGAATTGAAAATGAAACATTG-AATTGAATTC
2172 GAAGAATT
1 GAAGAATT
2180 CAAGTTGAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 22 0.55
34 18 0.45
ACGTcount: A:0.48, C:0.05, G:0.19, T:0.28
Consensus pattern (33 bp):
GAAGAATTGAAAATGAAACATTGAATTGAATTC
Found at i:2372 original size:8 final size:7
Alignment explanation
Indices: 2355--2490 Score: 79
Period size: 8 Copynumber: 18.9 Consensus size: 7
2345 AATTTGAATA
2355 ATTGAA-
1 ATTGAAG
2361 ATTGAAG
1 ATTGAAG
2368 CATTGAAGG
1 -ATTGAA-G
2377 ATTGAA-
1 ATTGAAG
2383 ATTGAAG
1 ATTGAAG
* *
2390 CACTAAAG
1 -ATTGAAG
2398 -TTGAA-
1 ATTGAAG
2403 ATTGAAG
1 ATTGAAG
2410 CATTGAAG
1 -ATTGAAG
2418 AATTGAA-
1 -ATTGAAG
*
2425 ATTGAAAC
1 ATTG-AAG
2433 ATTGAAG
1 ATTGAAG
2440 AATTGAA-
1 -ATTGAAG
*
2447 ATTGAAAC
1 ATTG-AAG
*
2455 ACTGAAGG
1 ATTGAA-G
2463 ATTGAA-
1 ATTGAAG
2469 ATTGAAG
1 ATTGAAG
2476 CATTGAAAG
1 -ATTG-AAG
2485 ATTGAA
1 ATTGAA
2491 TTTGAATTTG
Statistics
Matches: 104, Mismatches: 9, Indels: 33
0.71 0.06 0.23
Matches are distributed among these distances:
6 34 0.33
7 10 0.10
8 56 0.54
9 4 0.04
ACGTcount: A:0.46, C:0.06, G:0.22, T:0.26
Consensus pattern (7 bp):
ATTGAAG
Found at i:2372 original size:14 final size:14
Alignment explanation
Indices: 2369--2483 Score: 78
Period size: 14 Copynumber: 8.1 Consensus size: 14
2359 AAATTGAAGC
*
2369 ATTGAAGGATTGAA
1 ATTGAAGCATTGAA
*
2383 ATTGAAGCACT-AA
1 ATTGAAGCATTGAA
2396 AGTTGAA--ATTGAA
1 A-TTGAAGCATTGAA
*
2409 GCATTGAAGAATTGAA
1 --ATTGAAGCATTGAA
*
2425 ATTGAAACATTGAAGA
1 ATTGAAGCATTG-A-A
2441 ATTGAA--ATTGAAA
1 ATTGAAGCATTG-AA
* *
2454 CACTGAAGGATTGAA
1 -ATTGAAGCATTGAA
2469 ATTGAAGCATTGAA
1 ATTGAAGCATTGAA
2483 A
1 A
2484 GATTGAATTT
Statistics
Matches: 82, Mismatches: 8, Indels: 22
0.73 0.07 0.20
Matches are distributed among these distances:
12 2 0.02
13 6 0.07
14 53 0.65
15 4 0.05
16 17 0.21
ACGTcount: A:0.46, C:0.06, G:0.22, T:0.26
Consensus pattern (14 bp):
ATTGAAGCATTGAA
Found at i:2373 original size:22 final size:22
Alignment explanation
Indices: 2348--2546 Score: 210
Period size: 22 Copynumber: 9.2 Consensus size: 22
2338 CATTTGGAAT
*
2348 TTGAATAATTGAAATTGAAGCA
1 TTGAAGAATTGAAATTGAAGCA
*
2370 TTGAAGGATTGAAATTGAAGCA
1 TTGAAGAATTGAAATTGAAGCA
* *
2392 CT-AA-AGTTGAAATTGAAGCA
1 TTGAAGAATTGAAATTGAAGCA
*
2412 TTGAAGAATTGAAATTGAAACA
1 TTGAAGAATTGAAATTGAAGCA
*
2434 TTGAAGAATTGAAATTGAAACA
1 TTGAAGAATTGAAATTGAAGCA
* *
2456 CTGAAGGATTGAAATTGAAGCA
1 TTGAAGAATTGAAATTGAAGCA
* *
2478 TTGAA-AGATTGAATTTGAA--T
1 TTGAAGA-ATTGAAATTGAAGCA
* *
2498 TTGAAGAATTGCAATTGAAACA
1 TTGAAGAATTGAAATTGAAGCA
* * * *
2520 TCGAAGGATTGAATTTGAAGAA
1 TTGAAGAATTGAAATTGAAGCA
2542 TTGAA
1 TTGAA
2547 ATATTAAAGC
Statistics
Matches: 146, Mismatches: 25, Indels: 12
0.80 0.14 0.07
Matches are distributed among these distances:
20 30 0.21
21 5 0.03
22 111 0.76
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.29
Consensus pattern (22 bp):
TTGAAGAATTGAAATTGAAGCA
Found at i:2438 original size:86 final size:86
Alignment explanation
Indices: 2348--2546 Score: 267
Period size: 86 Copynumber: 2.3 Consensus size: 86
2338 CATTTGGAAT
*
2348 TTGAATAATTGAAATTGAAGCATTGAAGGATTGAAATTGAAGCACT-AAAG-TTGAAATTGAAGC
1 TTGAAGAATTGAAATTGAAGCATTGAAGGATTGAAATTGAAGCACTGAAAGATTGAAATTGAA--
2411 ATTGAAGAATTGAAATTGAAACA
64 ATTGAAGAATTGAAATTGAAACA
* * * * *
2434 TTGAAGAATTGAAATTGAAACACTGAAGGATTGAAATTGAAGCATTGAAAGATTGAATTTGAATT
1 TTGAAGAATTGAAATTGAAGCATTGAAGGATTGAAATTGAAGCACTGAAAGATTGAAATTGAAAT
*
2499 TGAAGAATTGCAATTGAAACA
66 TGAAGAATTGAAATTGAAACA
* * * *
2520 TCGAAGGATTGAATTTGAAGAATTGAA
1 TTGAAGAATTGAAATTGAAGCATTGAA
2547 ATATTAAAGC
Statistics
Matches: 98, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
86 84 0.86
87 4 0.04
88 10 0.10
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.29
Consensus pattern (86 bp):
TTGAAGAATTGAAATTGAAGCATTGAAGGATTGAAATTGAAGCACTGAAAGATTGAAATTGAAAT
TGAAGAATTGAAATTGAAACA
Found at i:2473 original size:36 final size:35
Alignment explanation
Indices: 2433--2548 Score: 111
Period size: 36 Copynumber: 3.5 Consensus size: 35
2423 AAATTGAAAC
2433 ATTGAAGAATTGAAATTGAAACACTGAAGGATTGAA
1 ATTGAAGAATTGAAATTGAAACA-TGAAGGATTGAA
* * *
2469 ATTGAAGCATTGAAA--G--A-TTGAA--TTTGAA
1 ATTGAAGAATTGAAATTGAAACATGAAGGATTGAA
* *
2497 TTTGAAGAATTGCAATTGAAACATCGAAGGATTGAA
1 ATTGAAGAATTGAAATTGAAACAT-GAAGGATTGAA
*
2533 TTTGAAGAATTGAAAT
1 ATTGAAGAATTGAAAT
2549 ATTAAAGCAT
Statistics
Matches: 63, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
28 17 0.27
30 5 0.08
32 2 0.03
33 1 0.02
34 4 0.06
36 34 0.54
ACGTcount: A:0.44, C:0.05, G:0.22, T:0.29
Consensus pattern (35 bp):
ATTGAAGAATTGAAATTGAAACATGAAGGATTGAA
Found at i:2506 original size:64 final size:67
Alignment explanation
Indices: 2354--2547 Score: 249
Period size: 64 Copynumber: 3.0 Consensus size: 67
2344 GAATTTGAAT
* * * *
2354 AATTGAAATTGAAGCATTGAAGGATTGAAATTGAAGCACT-AAAG-TTGAAATTGAAGCATTG-A
1 AATTGAAATTGAAACATTGAAGAATTGAAATTGAAACACTGAAGGATTGAAATTGAAGCATTGAA
2416 AG
66 AG
2418 AATTGAAATTGAAACATTGAAGAATTGAAATTGAAACACTGAAGGATTGAAATTGAAGCATTGAA
1 AATTGAAATTGAAACATTGAAGAATTGAAATTGAAACACTGAAGGATTGAAATTGAAGCATTGAA
2483 AG
66 AG
* * * * *
2485 -ATTGAATTTG-AA-TTTGAAGAATTGCAATTGAAACA-TCGAAGGATTGAATTTGAAGAATTGA
1 AATTGAAATTGAAACATTGAAGAATTGAAATTGAAACACT-GAAGGATTGAAATTGAAGCATTGA
2546 AA
65 AA
2548 TATTAAAGCA
Statistics
Matches: 117, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
63 1 0.01
64 82 0.70
65 5 0.04
66 26 0.22
67 3 0.03
ACGTcount: A:0.45, C:0.06, G:0.22, T:0.28
Consensus pattern (67 bp):
AATTGAAATTGAAACATTGAAGAATTGAAATTGAAACACTGAAGGATTGAAATTGAAGCATTGAA
AG
Found at i:2604 original size:22 final size:22
Alignment explanation
Indices: 2576--2625 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
2566 CCTTTGAAGA
2576 ATTGAAGCATGGAAATTAAAGT
1 ATTGAAGCATGGAAATTAAAGT
* * * *
2598 ATTGAAGCCTTGACATTGAAGT
1 ATTGAAGCATGGAAATTAAAGT
2620 ATTGAA
1 ATTGAA
2626 AAATTGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (22 bp):
ATTGAAGCATGGAAATTAAAGT
Found at i:2638 original size:36 final size:36
Alignment explanation
Indices: 2613--2684 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
2603 AGCCTTGACA
*
2613 TTGAAGTATTGAAAAATTGAAATTGAAACATTGAAT
1 TTGAAGCATTGAAAAATTGAAATTGAAACATTGAAT
**
2649 TTGAAGCATTGAAAAATTGAAATTGAGGCATTGAAT
1 TTGAAGCATTGAAAAATTGAAATTGAAACATTGAAT
2685 AATGGAGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.44, C:0.04, G:0.19, T:0.32
Consensus pattern (36 bp):
TTGAAGCATTGAAAAATTGAAATTGAAACATTGAAT
Found at i:2658 original size:14 final size:14
Alignment explanation
Indices: 2610--2662 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
2600 TGAAGCCTTG
2610 ACATTGAAGTATTGAA
1 ACATTGAA--ATTGAA
*
2626 AAATTGAAATTGAA
1 ACATTGAAATTGAA
*
2640 ACATTGAATTTGAA
1 ACATTGAAATTGAA
*
2654 GCATTGAAA
1 ACATTGAAA
2663 AATTGAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 25 0.78
16 7 0.22
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.30
Consensus pattern (14 bp):
ACATTGAAATTGAA
Found at i:2740 original size:18 final size:16
Alignment explanation
Indices: 2717--2750 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
2707 CACCATGGAT
2717 CATTGAAGTAAATTGAAG
1 CATTGAAG-AAA-TGAAG
2735 CATTGAAGAAATGAAG
1 CATTGAAGAAATGAAG
2751 AAAGAGATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 3 0.19
18 8 0.50
ACGTcount: A:0.47, C:0.06, G:0.24, T:0.24
Consensus pattern (16 bp):
CATTGAAGAAATGAAG
Found at i:3813 original size:26 final size:24
Alignment explanation
Indices: 3766--3813 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
3756 TACTGATTAC
*
3766 CATTTTTACTTTTGCTATTTTTAT
1 CATTTTTACTTTTGCTACTTTTAT
*
3790 CATTTTTACTCTTTTCTTACTTTT
1 CATTTTTACT-TTTGC-TACTTTT
3814 TTTACTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 10 0.50
25 4 0.20
26 6 0.30
ACGTcount: A:0.15, C:0.17, G:0.02, T:0.67
Consensus pattern (24 bp):
CATTTTTACTTTTGCTACTTTTAT
Found at i:3851 original size:27 final size:27
Alignment explanation
Indices: 3802--3871 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
3792 TTTTTACTCT
*
3802 TTTCTTACT-TTTTTTACTAATTACCC
1 TTTCTTACTCTCTTTTACTAATTACCC
*
3828 TTTCCTTACTCTCTTTTA-TTATTACCAC
1 TTT-CTTACTCTCTTTTACTAATTACC-C
3856 TTT-TTACTCTTCTTTT
1 TTTCTTACTC-TCTTTT
3872 TCTCTTATAC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
26 9 0.24
27 19 0.50
28 10 0.26
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (27 bp):
TTTCTTACTCTCTTTTACTAATTACCC
Found at i:3935 original size:14 final size:14
Alignment explanation
Indices: 3918--4087 Score: 65
Period size: 14 Copynumber: 12.4 Consensus size: 14
3908 TGATCACCTT
3918 TTACTCTTTACTGA
1 TTACTCTTTACTGA
* *
3932 TTACTCCTTACTAA
1 TTACTCTTTACTGA
*
3946 TTAC-CATTTAGCT-C
1 TTACTC-TTTA-CTGA
**
3960 TTACTGATTACT-A
1 TTACTCTTTACTGA
*
3973 TTTTACTC-TGACTGA
1 --TTACTCTTTACTGA
3988 TTAC-CTTTTACTGA
1 TTACTC-TTTACTGA
*
4002 TTACT-ATTACCTGA
1 TTACTCTTTA-CTGA
4016 TTACT-TTT--T-A
1 TTACTCTTTACTGA
* * **
4026 CTACTCTTTGCCATTT
1 TTACTCTTT-AC-TGA
4042 TTACT-TTTACTGA
1 TTACTCTTTACTGA
**
4055 TTACTCTTTACTTT
1 TTACTCTTTACTGA
*
4069 TTCCTCTTTACTGA
1 TTACTCTTTACTGA
4083 TTACT
1 TTACT
4088 ATTTTACCCT
Statistics
Matches: 115, Mismatches: 24, Indels: 34
0.66 0.14 0.20
Matches are distributed among these distances:
10 5 0.04
11 4 0.03
12 1 0.01
13 16 0.14
14 73 0.63
15 12 0.10
16 4 0.03
ACGTcount: A:0.21, C:0.22, G:0.06, T:0.51
Consensus pattern (14 bp):
TTACTCTTTACTGA
Found at i:3962 original size:21 final size:20
Alignment explanation
Indices: 3932--4012 Score: 74
Period size: 21 Copynumber: 3.9 Consensus size: 20
3922 TCTTTACTGA
*
3932 TTACTCCTTACTAATTACCAT
1 TTACT-CTTACTGATTACCAT
*
3953 TTAGCTCTTACTGATTACTATT
1 TTA-CTCTTACTGATTACCA-T
* *
3975 TTACTCTGACTGATTACCTT
1 TTACTCTTACTGATTACCAT
*
3995 TTACTGATTACT-ATTACC
1 TTACT-CTTACTGATTACC
4013 TGATTACTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
20 12 0.24
21 32 0.64
22 6 0.12
ACGTcount: A:0.25, C:0.23, G:0.06, T:0.46
Consensus pattern (20 bp):
TTACTCTTACTGATTACCAT
Found at i:4128 original size:26 final size:27
Alignment explanation
Indices: 4082--4149 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 27
4072 CTCTTTACTG
**
4082 ATTACTATTTT-ACCCTCTTGAACTTA
1 ATTACTATTTTCATTCTCTTGAACTTA
*
4108 ATTACTATTTTCATTCT-TTGAATTTA
1 ATTACTATTTTCATTCTCTTGAACTTA
* *
4134 ATCACCATTTGTCATT
1 ATTACTATTT-TCATT
4150 TTACTCTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 27 0.77
27 8 0.23
ACGTcount: A:0.26, C:0.19, G:0.04, T:0.50
Consensus pattern (27 bp):
ATTACTATTTTCATTCTCTTGAACTTA
Found at i:4183 original size:33 final size:32
Alignment explanation
Indices: 4122--4191 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
4112 CTATTTTCAT
4122 TCTTTGAATTTAATCACCATTTGTCATTTTAC
1 TCTTTGAATTTAATCACCATTTGTCATTTTAC
* *
4154 TCTTTGGATTTAATTACCATTT-TACCATTTTAC
1 TCTTTGAATTTAATCACCATTTGT--CATTTTAC
4187 TCTTT
1 TCTTT
4192 ACCGATTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 1 0.03
32 20 0.59
33 13 0.38
ACGTcount: A:0.23, C:0.19, G:0.06, T:0.53
Consensus pattern (32 bp):
TCTTTGAATTTAATCACCATTTGTCATTTTAC
Found at i:4229 original size:16 final size:17
Alignment explanation
Indices: 4181--4236 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 17
4171 CATTTTACCA
4181 TTTTACTCTTTACCGAT
1 TTTTACTCTTTACCGAT
*
4198 TATTCCCTACTTTTTACC-AT
1 T-TT---TACTCTTTACCGAT
4218 TTTTACTCTTTACCGAT
1 TTTTACTCTTTACCGAT
4235 TT
1 TT
4237 ACTGATTACT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
16 10 0.31
17 5 0.16
18 2 0.06
19 2 0.06
20 3 0.09
21 10 0.31
ACGTcount: A:0.18, C:0.25, G:0.04, T:0.54
Consensus pattern (17 bp):
TTTTACTCTTTACCGAT
Found at i:4271 original size:40 final size:40
Alignment explanation
Indices: 4227--4302 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
4217 TTTTTACTCT
* *
4227 TTACCGATTTACTGATTACTTCTTTTACTTTTACTCTTAA
1 TTACCGACTTACTGATTACTTCTTTTACTTTCACTCTTAA
4267 TTACCGACTTACTGATTACTTCTTTTACTTTCACTC
1 TTACCGACTTACTGATTACTTCTTTTACTTTCACTC
4303 CATTTTACTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.21, C:0.24, G:0.05, T:0.50
Consensus pattern (40 bp):
TTACCGACTTACTGATTACTTCTTTTACTTTCACTCTTAA
Found at i:4381 original size:14 final size:14
Alignment explanation
Indices: 4362--4388 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4352 TTCTGATTAC
4362 TTCTTTTACTTTTG
1 TTCTTTTACTTTTG
4376 TTCTTTTACTTTT
1 TTCTTTTACTTTT
4389 ACTGATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.04, T:0.74
Consensus pattern (14 bp):
TTCTTTTACTTTTG
Found at i:4395 original size:36 final size:36
Alignment explanation
Indices: 4349--4421 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
4339 TTGATTATCA
*
4349 TTTTTCTGATTACTTCTTTTACTTTTGTTCTTTTAC
1 TTTTACTGATTACTTCTTTTACTTTTGTTCTTTTAC
4385 TTTTACTGATTACTTCTTTTACTTTTGTTCTTTTAC
1 TTTTACTGATTACTTCTTTTACTTTTGTTCTTTTAC
4421 T
1 T
4422 GATTACTTCC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.12, C:0.16, G:0.05, T:0.66
Consensus pattern (36 bp):
TTTTACTGATTACTTCTTTTACTTTTGTTCTTTTAC
Found at i:4405 original size:16 final size:16
Alignment explanation
Indices: 4275--4447 Score: 103
Period size: 16 Copynumber: 10.9 Consensus size: 16
4265 AATTACCGAC
4275 TTACTGATTACTTCTT
1 TTACTGATTACTTCTT
*
4291 TTACT--TTCACTCCATT
1 TTACTGATT-ACTTC-TT
4307 TTACTGATTACTTCTT
1 TTACTGATTACTTCTT
* * *
4323 CTACGGGTTACTTC-T
1 TTACTGATTACTTCTT
*
4338 CT--TGATTA--TCATT
1 TTACTGATTACTTC-TT
*
4351 TTTCTGATTACTTCTT
1 TTACTGATTACTTCTT
** *
4367 TTACTTTTGTTCTTTTACTT
1 TTACTGAT-TAC--TT-CTT
4387 TTACTGATTACTTCTT
1 TTACTGATTACTTCTT
**
4403 TTACT--TTTGTTCTT
1 TTACTGATTACTTCTT
*
4417 TTACTGATTACTTCCT
1 TTACTGATTACTTCTT
*
4433 CTACTGATTACTTCT
1 TTACTGATTACTTCT
4448 CTTGATTACC
Statistics
Matches: 119, Mismatches: 22, Indels: 32
0.69 0.13 0.18
Matches are distributed among these distances:
11 2 0.02
13 6 0.05
14 14 0.12
15 13 0.11
16 59 0.50
17 10 0.08
18 2 0.02
19 4 0.03
20 9 0.08
ACGTcount: A:0.16, C:0.21, G:0.07, T:0.56
Consensus pattern (16 bp):
TTACTGATTACTTCTT
Found at i:4418 original size:30 final size:32
Alignment explanation
Indices: 4349--4430 Score: 105
Period size: 36 Copynumber: 2.5 Consensus size: 32
4339 TTGATTATCA
*
4349 TTTTTCTGATTACTTCTTTTACTTTTGTTCTTTTAC
1 TTTTACTGATTACTTCTTTTACTTTTG----TTTAC
4385 TTTTACTGATTACTTCTTTTACTTTTG-TT-C
1 TTTTACTGATTACTTCTTTTACTTTTGTTTAC
4415 TTTTACTGATTACTTC
1 TTTTACTGATTACTTC
4431 CTCTACTGAT
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
30 17 0.38
31 2 0.04
36 26 0.58
ACGTcount: A:0.13, C:0.17, G:0.06, T:0.63
Consensus pattern (32 bp):
TTTTACTGATTACTTCTTTTACTTTTGTTTAC
Found at i:4420 original size:110 final size:115
Alignment explanation
Indices: 4238--4513 Score: 337
Period size: 110 Copynumber: 2.4 Consensus size: 115
4228 TACCGATTTA
4238 CTGATTACTTCTTTTACTTTTACTCTTAATTACCGACTTACTGATTACTTCTTTTACTTTCACTC
1 CTGATTACTTCTTTTACTTTTACTCTT-ATTACCGACTTACTGATTACTTCTTTTACTTTCACTC
* * *
4303 CATTTTACTGATTACTTCTTCTACGGGTTACTTCTCTTGATTATCATTTTT
65 CATTTTACTGATTACTTCCTCTACGGATTACTTCTCTTGATTACCATTTTT
** ** ** *
4354 CTGATTACTTCTTTTACTTTTGTTCTT-TTA-C-TTTTACTGATTACTTCTTTTACTTT-TGTTC
1 CTGATTACTTCTTTTACTTTTACTCTTATTACCGACTTACTGATTACTTCTTTTACTTTCACTCC
*
4415 -TTTTACTGATTACTTCCTCTACTGATTACTTCTCTTGATTACCATTTTT
66 ATTTTACTGATTACTTCCTCTACGGATTACTTCTCTTGATTACCATTTTT
* * * *
4464 CTAATTACTTTTTTTTACTTTGACTCTTTGATTACTGACTTTACTGATTA
1 CTGATTAC-TTCTTTTACTTTTACTC-TT-ATTACCGAC-TTACTGATTA
4514 ATCTCTTACC
Statistics
Matches: 134, Mismatches: 19, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
110 52 0.39
111 15 0.11
112 25 0.19
113 1 0.01
114 6 0.04
116 25 0.19
117 10 0.07
ACGTcount: A:0.18, C:0.20, G:0.07, T:0.55
Consensus pattern (115 bp):
CTGATTACTTCTTTTACTTTTACTCTTATTACCGACTTACTGATTACTTCTTTTACTTTCACTCC
ATTTTACTGATTACTTCCTCTACGGATTACTTCTCTTGATTACCATTTTT
Found at i:4571 original size:45 final size:47
Alignment explanation
Indices: 4494--4598 Score: 133
Period size: 45 Copynumber: 2.3 Consensus size: 47
4484 TGACTCTTTG
* * * *
4494 ATTACTGACTTTACTGATTAATCTCTTACCTTGATTCTTAATTTTCAA
1 ATTACTGA-TTAACTGATTAATCTATTACCTTGACTCTTAATTATCAA
*
4542 ATTACTGATTAACTGATT-A-CTATTACCTTGACTCTTGATTATCAA
1 ATTACTGATTAACTGATTAATCTATTACCTTGACTCTTAATTATCAA
*
4587 TTTACTGATTAA
1 ATTACTGATTAA
4599 TCTCCTTTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
45 33 0.65
46 1 0.02
47 9 0.18
48 8 0.16
ACGTcount: A:0.30, C:0.17, G:0.08, T:0.46
Consensus pattern (47 bp):
ATTACTGATTAACTGATTAATCTATTACCTTGACTCTTAATTATCAA
Found at i:4658 original size:32 final size:31
Alignment explanation
Indices: 4622--4694 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 31
4612 AATTATCAAT
* *
4622 TTACTGATTAATCCTTCTACCTTGACTCTTAA
1 TTACTGATT-ACCCTTCTACCTTGACCCTTAA
* * *
4654 TTACTGACTTACCCTTTTACTTTGACCCTTAC
1 TTACTGA-TTACCCTTCTACCTTGACCCTTAA
4686 TTACTGATT
1 TTACTGATT
4695 GCTACTTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 2 0.06
32 31 0.89
33 2 0.06
ACGTcount: A:0.22, C:0.26, G:0.07, T:0.45
Consensus pattern (31 bp):
TTACTGATTACCCTTCTACCTTGACCCTTAA
Found at i:4781 original size:38 final size:39
Alignment explanation
Indices: 4688--4781 Score: 109
Period size: 38 Copynumber: 2.4 Consensus size: 39
4678 ACCCTTACTT
* * * *
4688 ACTGATTGCTACTTTTACTTCTTCTCTTAGTTATCAATTT
1 ACTGATTACTACTTTTACTTC-TCTCTTAATTACCAATTG
* *
4728 ACTGATTAATCCTTTTACTTC-CTCTTAATTACCAATTG
1 ACTGATTACTACTTTTACTTCTCTCTTAATTACCAATTG
*
4766 ACTGATTACTTCTTTT
1 ACTGATTACTACTTTT
4782 TCTTTTCACT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
38 28 0.61
40 18 0.39
ACGTcount: A:0.22, C:0.21, G:0.06, T:0.50
Consensus pattern (39 bp):
ACTGATTACTACTTTTACTTCTCTCTTAATTACCAATTG
Done.