Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold351
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: 34202
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:2216 original size:17 final size:17
Alignment explanation
Indices: 2194--2241 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
2184 TATTATAATT
2194 ATTTTATTTTCTTTTA-A
1 ATTTTATTTT-TTTTATA
* *
2211 ATTTTAGTTTTTCTATA
1 ATTTTATTTTTTTTATA
2228 ATTTT-TTTTTTTTA
1 ATTTTATTTTTTTTA
2242 GCAATTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (17 bp):
ATTTTATTTTTTTTATA
Found at i:2514 original size:23 final size:22
Alignment explanation
Indices: 2466--2514 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2456 TAAATTTCCA
***
2466 TTTTTATTTTTAATAATTATTT
1 TTTTTATTTTTAATAATTACAG
2488 TTTTTATTTTTAATAGATTACAG
1 TTTTTATTTTTAATA-ATTACAG
2511 TTTT
1 TTTT
2515 CTTAAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTTTATTTTTAATAATTACAG
Found at i:3407 original size:12 final size:13
Alignment explanation
Indices: 3390--3418 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3380 TAATAATTTT
3390 ATTTTTAAAT-TA
1 ATTTTTAAATATA
3402 ATTTTTAAATATA
1 ATTTTTAAATATA
3415 ATTT
1 ATTT
3419 AATTTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTTTAAATATA
Found at i:4114 original size:23 final size:22
Alignment explanation
Indices: 4088--4190 Score: 72
Period size: 23 Copynumber: 4.7 Consensus size: 22
4078 TATTTAAAAT
4088 TTATTATATAAATTTTTTTTACA
1 TTATTATATAAATTTTTTTTA-A
* *
4111 TTATTATA-CAATTTATTTATAA
1 TTATTATATAAATTT-TTTTTAA
*
4133 TCTATTGTATATAA-TTTTTTT-A
1 T-TATTATATA-AATTTTTTTTAA
* * *
4155 TTA-TATATAAATATTATAT-A
1 TTATTATATAAATTTTTTTTAA
4175 TTATTCATATAAATTT
1 TTATT-ATATAAATTT
4191 AATTAAATTC
Statistics
Matches: 63, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
19 2 0.03
20 13 0.21
21 3 0.05
22 18 0.29
23 23 0.37
24 2 0.03
25 2 0.03
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (22 bp):
TTATTATATAAATTTTTTTTAA
Found at i:4114 original size:46 final size:47
Alignment explanation
Indices: 4064--4153 Score: 119
Period size: 46 Copynumber: 1.9 Consensus size: 47
4054 ATTTGATAAA
** *
4064 ATTATTATATTATATATTTAAAATTTATTATATA-AATTTTTTTTAC
1 ATTATTATACAATATATTTAAAATCTATTATATATAATTTTTTTTAC
* * *
4110 ATTATTATACAATTTATTTATAATCTATTGTATATAATTTTTTT
1 ATTATTATACAATATATTTAAAATCTATTATATATAATTTTTTT
4154 ATTATATATA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
46 28 0.76
47 9 0.24
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (47 bp):
ATTATTATACAATATATTTAAAATCTATTATATATAATTTTTTTTAC
Found at i:4281 original size:16 final size:15
Alignment explanation
Indices: 4230--4317 Score: 53
Period size: 14 Copynumber: 6.1 Consensus size: 15
4220 TATTAATTAA
*
4230 TATTATTATTATA-T
1 TATTTTTATTATATT
* * *
4244 TATTTTAATTCTA-A
1 TATTTTTATTATATT
4258 T-TTTTTATTATATT
1 TATTTTTATTATATT
*
4272 TATATTTTATTA-AAT
1 TAT-TTTTATTATATT
*
4287 TATTTAT-TTATATT
1 TATTTTTATTATATT
4301 T-TGTTTTATTTATATT
1 TAT-TTTTA-TTATATT
4317 T
1 T
4318 TTAATTTTTA
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
13 13 0.23
14 21 0.38
15 6 0.11
16 16 0.29
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.68
Consensus pattern (15 bp):
TATTTTTATTATATT
Found at i:4307 original size:28 final size:28
Alignment explanation
Indices: 4225--4310 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 28
4215 ATATTTATTA
*
4225 ATTAATATTA-TTATTATA-TTAT-TTTA
1 ATTAA-ATTATTTATTATATTTATATTTT
* *
4251 ATTCTAATTTTTTATTATATTTATATTTT
1 ATT-AAATTATTTATTATATTTATATTTT
*
4280 ATTAAATTATTTATTTATATTT-TGTTTT
1 ATTAAATTATTTA-TTATATTTATATTTT
4308 ATT
1 ATT
4311 TATATTTTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
26 6 0.12
27 9 0.18
28 20 0.41
29 14 0.29
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (28 bp):
ATTAAATTATTTATTATATTTATATTTT
Found at i:4398 original size:21 final size:23
Alignment explanation
Indices: 4361--4402 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
4351 TTTATAATCA
4361 TTAATATTTTTTGTTATTTTTTT
1 TTAATATTTTTTGTTATTTTTTT
4384 TTAA-ATTTTTT-TTATTTTT
1 TTAATATTTTTTGTTATTTTT
4403 AATTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.42
22 7 0.37
23 4 0.21
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (23 bp):
TTAATATTTTTTGTTATTTTTTT
Found at i:4403 original size:17 final size:16
Alignment explanation
Indices: 4377--4415 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
4367 TTTTTTGTTA
4377 TTTTTTTTTAAATTTT
1 TTTTTTTTTAAATTTT
4393 TTTTATTTTT-AATTTT
1 TTTT-TTTTTAAATTTT
4409 TTTTTTT
1 TTTTTTT
4416 AAATTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.14
16 14 0.64
17 5 0.23
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTTTTTTAAATTTT
Found at i:4424 original size:17 final size:17
Alignment explanation
Indices: 4377--4426 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
4367 TTTTTTGTTA
4377 TTTTTTTTTAAATT-TT
1 TTTTTTTTTAAATTATT
4393 TTTTATTTTT--A--ATT
1 TTTT-TTTTTAAATTATT
4407 TTTTTTTTTAAATTATT
1 TTTTTTTTTAAATTATT
4424 TTT
1 TTT
4427 ATAATTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 11
0.72 0.00 0.28
Matches are distributed among these distances:
13 5 0.18
14 6 0.21
15 2 0.07
16 4 0.14
17 11 0.39
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTTTTTAAATTATT
Found at i:4518 original size:10 final size:10
Alignment explanation
Indices: 4503--4579 Score: 54
Period size: 10 Copynumber: 7.7 Consensus size: 10
4493 AATTAATAAA
4503 ATTTTTTATT
1 ATTTTTTATT
4513 ATTTTTTATT
1 ATTTTTTATT
*
4523 -TTTTTTTTT
1 ATTTTTTATT
4532 ATTTTATT-TT
1 ATTTT-TTATT
*
4542 ATTACTTT-TT
1 ATT-TTTTATT
* *
4552 ATTTATCTAAT
1 ATTT-TTTATT
4563 -TTTTTTATT
1 ATTTTTTATT
4572 ATTATTTT
1 ATT-TTTT
4580 TCTTAATTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 13
0.73 0.10 0.18
Matches are distributed among these distances:
9 12 0.23
10 33 0.62
11 8 0.15
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (10 bp):
ATTTTTTATT
Found at i:4564 original size:24 final size:23
Alignment explanation
Indices: 4516--4593 Score: 70
Period size: 24 Copynumber: 3.4 Consensus size: 23
4506 TTTTATTATT
* * *
4516 TTTTATT-TTTTTTTTTATTTTA
1 TTTTATTATTTTTATTTATCTAA
4538 TTTTATTACTTTTTATTTATCTAA
1 TTTTATTA-TTTTTATTTATCTAA
* * *
4562 TTTTTTTATTATTATTTTTCTTAA
1 TTTTATTATTTTTATTTATC-TAA
4586 -TTTATTAT
1 TTTTATTAT
4594 ATATAGTTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
22 7 0.15
23 17 0.37
24 22 0.48
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTATTATTTTTATTTATCTAA
Found at i:4569 original size:32 final size:32
Alignment explanation
Indices: 4506--4577 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
4496 TAATAAAATT
* * **
4506 TTTTATTATTTTTTATTTTTTTTTTTATTTTA
1 TTTTATTACTTTTTATTTTCTAATTTATTTTA
4538 TTTTATTACTTTTTATTTATCTAATTT-TTTTA
1 TTTTATTACTTTTTATTT-TCTAATTTATTTTA
4570 TTATTATT
1 TT-TTATT
4578 TTTCTTAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 24 0.71
33 10 0.29
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (32 bp):
TTTTATTACTTTTTATTTTCTAATTTATTTTA
Found at i:4593 original size:23 final size:23
Alignment explanation
Indices: 4537--4593 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
4527 TTTTTATTTT
*
4537 ATTTTATTACTTTTTATTTATCTA
1 ATTTTATTA-TTATTATTTATCTA
* *
4561 ATTTTTTTATTATTATTTTTCTTA
1 ATTTTATTATTATTATTTATC-TA
4585 A-TTTATTAT
1 ATTTTATTAT
4594 ATATAGTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 17 0.61
24 11 0.39
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (23 bp):
ATTTTATTATTATTATTTATCTA
Found at i:4661 original size:30 final size:28
Alignment explanation
Indices: 4621--4696 Score: 86
Period size: 30 Copynumber: 2.8 Consensus size: 28
4611 ATATTTATTA
*
4621 ATATTATTTATTTTAATTTATTCATAGATT
1 ATATAATTTATTTTAATTTATT-AT-GATT
* *
4651 ATATAATTTATTATAATTTATTATTATT
1 ATATAATTTATTTTAATTTATTATGATT
4679 -TA-AATTTA-TTTAATTTAT
1 ATATAATTTATTTTAATTTAT
4697 ATTTTATTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
25 9 0.21
26 6 0.14
27 2 0.05
28 3 0.07
29 2 0.05
30 20 0.48
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (28 bp):
ATATAATTTATTTTAATTTATTATGATT
Found at i:4700 original size:15 final size:14
Alignment explanation
Indices: 4612--4735 Score: 60
Period size: 16 Copynumber: 8.4 Consensus size: 14
4602 TAATAAGAAA
*
4612 TATTTATTAATA-T
1 TATTTATTTATATT
4625 TATTTATTT-TAATT
1 TATTTATTTAT-ATT
*
4639 TATTCATAGATTATA-T
1 TATT--TA-TTTATATT
*
4655 AATTTA-TTATAATT
1 TATTTATTTAT-ATT
*
4669 TATTATTATTTAAATT
1 TA-T-TTATTTATATT
4685 TATTTAATTTATATTT
1 TATTT-ATTTATA-TT
4701 TATTTATTTATTATT
1 TATTTATTTA-TATT
*
4716 TCATTTCA-TTATAAT
1 T-ATTT-ATTTATATT
4731 TATTT
1 TATTT
4736 TATATGTATA
Statistics
Matches: 88, Mismatches: 7, Indels: 31
0.70 0.06 0.25
Matches are distributed among these distances:
12 5 0.06
13 10 0.11
14 15 0.17
15 20 0.23
16 30 0.34
17 7 0.08
18 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (14 bp):
TATTTATTTATATT
Found at i:4702 original size:16 final size:16
Alignment explanation
Indices: 4661--4751 Score: 55
Period size: 16 Copynumber: 5.7 Consensus size: 16
4651 ATATAATTTA
* *
4661 TTATAATTTATTATTAT
1 TTATATTTTATT-TAAT
*
4678 TTA-AATTTATTTAAT
1 TTATATTTTATTTAAT
4693 TTATATTTTATTT-AT
1 TTATATTTTATTTAAT
* *
4708 TTATTATTTCATTTCA-
1 TTA-TATTTTATTTAAT
*
4724 TTATA-ATTATTTTATAT
1 TTATATTTTA-TTTA-AT
*
4741 GTATATTTTAT
1 TTATATTTTAT
4752 AAAATAATAT
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
14 2 0.03
15 16 0.27
16 29 0.49
17 9 0.15
18 3 0.05
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (16 bp):
TTATATTTTATTTAAT
Found at i:4710 original size:40 final size:43
Alignment explanation
Indices: 4612--4715 Score: 115
Period size: 46 Copynumber: 2.3 Consensus size: 43
4602 TAATAAGAAA
*
4612 TATTTATTAATATTATTTATTTTAATTTATTCATAGATTATATAATT
1 TATTTATT--TATTA-TTATTTAAATTTATT-ATAGATTATATAATT
*
4659 TATTATAATTTATTATTATTTAAATTTATT-TA-ATT-TATATTT
1 TATT-T-ATTTATTATTATTTAAATTTATTATAGATTATATAATT
4701 TATTTATTTATTATT
1 TATTTATTTATTATT
4716 TCATTTCATT
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
40 10 0.19
41 1 0.02
42 10 0.19
43 3 0.06
44 2 0.04
46 14 0.26
47 9 0.17
48 1 0.02
49 3 0.06
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (43 bp):
TATTTATTTATTATTATTTAAATTTATTATAGATTATATAATT
Found at i:4777 original size:14 final size:15
Alignment explanation
Indices: 4758--4791 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
4748 TTATAAAATA
4758 ATATT-TTTTTTATT
1 ATATTATTTTTTATT
4772 ATATTTATTTTTTATT
1 ATA-TTATTTTTTATT
4788 ATAT
1 ATAT
4792 CTTCAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 3 0.17
15 3 0.17
16 12 0.67
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
ATATTATTTTTTATT
Found at i:4856 original size:3 final size:3
Alignment explanation
Indices: 4848--4939 Score: 54
Period size: 3 Copynumber: 31.7 Consensus size: 3
4838 ATACTAATTA
* * *
4848 ATT ATT ATT ATAA ATT -TT TTT TTT ATT -TT A-T ATT -TT ATT ATT
1 ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
4890 -TT -TT ATTT ATT ATT ATT ATT ATT ATA ATTT ATCT ATA ATT ATT -TT
1 ATT ATT A-TT ATT ATT ATT ATT ATT ATT A-TT AT-T ATT ATT ATT ATT
4935 ATT AT
1 ATT AT
4940 ATGCTTTTTT
Statistics
Matches: 72, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
2 14 0.19
3 48 0.67
4 10 0.14
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:4891 original size:23 final size:24
Alignment explanation
Indices: 4849--4912 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 24
4839 TACTAATTAA
* *
4849 TTATTATTATAAATTTTTTTTTTAT
1 TTATTATTAT-TATTATTTTTTTAT
4874 TT-TATATT-TTATTA-TTTTTTAT
1 TTAT-TATTATTATTATTTTTTTAT
4896 TTATTATTATTATTATT
1 TTATTATTATTATTATT
4913 ATAATTTATC
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
22 14 0.42
23 10 0.30
24 3 0.09
25 6 0.18
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (24 bp):
TTATTATTATTATTATTTTTTTAT
Found at i:4912 original size:26 final size:26
Alignment explanation
Indices: 4848--4939 Score: 89
Period size: 26 Copynumber: 3.5 Consensus size: 26
4838 ATACTAATTA
* *
4848 ATTATTATTATAAATTTTTTTTTTATT
1 ATTATTATTAT-TATTTTTTATTTATT
*
4875 -TTATATTTTATTATTTTTTATTTATT
1 ATTAT-TATTATTATTTTTTATTTATT
** * *
4901 ATTATTATTATTATAATTTATCTATA
1 ATTATTATTATTATTTTTTATTTATT
4927 ATTATT-TTATTAT
1 ATTATTATTATTAT
4940 ATGCTTTTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
25 7 0.13
26 39 0.71
27 9 0.16
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.68
Consensus pattern (26 bp):
ATTATTATTATTATTTTTTATTTATT
Found at i:4981 original size:29 final size:28
Alignment explanation
Indices: 4842--4990 Score: 94
Period size: 29 Copynumber: 5.3 Consensus size: 28
4832 TATTTTATAC
*
4842 TAATTAA-TTATTATTATAAATTTTTTT-
1 TAATTAATTTATTATTAT-TATTTTTTTA
* *
4869 T--TTATTTTATATTTTATTA-TTTTTTA
1 TAATTAATTTAT-TATTATTATTTTTTTA
* * * * *
4895 TTTATTATTATTATTATTATAATTTATCTA
1 -TAATTAAT-TTATTATTATTATTTTTTTA
* *
4925 TAATTATTTTATTA-TATGCTTTTTTTTTA
1 TAATTAATTTATTATTAT--TATTTTTTTA
4954 TAATTAATTTACTTATTATTATTTTTTTA
1 TAATTAATTTA-TTATTATTATTTTTTTA
*
4983 TAAATAAT
1 TAATTAAT
4991 GATTTATTTT
Statistics
Matches: 95, Mismatches: 15, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
25 9 0.09
26 5 0.05
27 10 0.11
28 6 0.06
29 50 0.53
30 12 0.13
31 3 0.03
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.66
Consensus pattern (28 bp):
TAATTAATTTATTATTATTATTTTTTTA
Found at i:5029 original size:22 final size:21
Alignment explanation
Indices: 4968--5030 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
4958 TAATTTACTT
* *
4968 ATTATTATTTTTTTATAAATA
1 ATTATTTTTTTTTTATAATTA
* * *
4989 ATGATTTATTTTAT-TAATTA
1 ATTATTTTTTTTTTATAATTA
5009 ATTATTTTTTTTTTATGAATTA
1 ATTATTTTTTTTTTAT-AATTA
5031 TTAAATTATA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 16 0.50
21 11 0.34
22 5 0.16
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (21 bp):
ATTATTTTTTTTTTATAATTA
Found at i:5815 original size:23 final size:23
Alignment explanation
Indices: 5789--5855 Score: 56
Period size: 23 Copynumber: 3.2 Consensus size: 23
5779 GATGATCCGC
5789 GCTAAGTCCCGAAGAGCATTCGT
1 GCTAAGTCCCGAAGAGCATTCGT
* * * *
5812 GCT-AGT---G-A-TGTATCCGG
1 GCTAAGTCCCGAAGAGCATTCGT
5829 GCTAAGTCCCGAAGAGCATTCGT
1 GCTAAGTCCCGAAGAGCATTCGT
5852 GCTA
1 GCTA
5856 GTATGTATCC
Statistics
Matches: 30, Mismatches: 8, Indels: 12
0.60 0.16 0.24
Matches are distributed among these distances:
17 8 0.27
18 4 0.13
19 1 0.03
21 1 0.03
22 4 0.13
23 12 0.40
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (23 bp):
GCTAAGTCCCGAAGAGCATTCGT
Found at i:5901 original size:39 final size:40
Alignment explanation
Indices: 5779--6113 Score: 382
Period size: 39 Copynumber: 8.7 Consensus size: 40
5769 AAGTCTCGAC
*
5779 GATG-ATCCGCGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
5818 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
*
5858 -ATGTATCCGGG-TAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
5896 GATGTATCCGGGCTAAGTCCCG-AGAGGCATTC-TGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGA-GCATTCGTGCTAGT
5935 GATGTATCC-GGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
*
5974 AGATG-ATCCGGGCT-AGTCTCG-AGAAGCATT-GTGCTAGT
1 -GATGTATCCGGGCTAAGTCCCGAAG-AGCATTCGTGCTAGT
* * *
6012 GATGTATCCGGACTAAGTTCCG-A-AGCATT-TTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
** * * * *
6049 GAT-TATCCATG-TAA-ACCCCAAAATGCATTCGTGCTGGT
1 GATGTATCCGGGCTAAGTCCCGAAGA-GCATTCGTGCTAGT
* *
6087 G-TATATCCGGGCTAGGT-CCGAAGAGCA
1 GATGTATCCGGGCTAAGTCCCGAAGAGCA
6114 ATCACATGCT
Statistics
Matches: 257, Mismatches: 21, Indels: 37
0.82 0.07 0.12
Matches are distributed among these distances:
34 2 0.01
35 4 0.02
36 6 0.02
37 26 0.10
38 78 0.30
39 84 0.33
40 57 0.22
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
Found at i:6009 original size:116 final size:116
Alignment explanation
Indices: 5779--6056 Score: 383
Period size: 116 Copynumber: 2.4 Consensus size: 116
5769 AAGTCTCGAC
*
5779 GATG-ATCCGCGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
1 GATGTATCCGGGCTAAGTCCCGAAG-GCATTC-TGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
5843 AGCATTCGTGCTAGTATGTATCCGGGTAAGTCCCGAAGAGCATTCATGCTAGT
64 AGCATTCGTGCTAGTATGTATCCGGGTAAGTCCCGAAGAGCATTCATGCTAGT
5896 GATGTATCCGGGCTAAGTCCCGAGAGGCATTCTGCTAGTGATGTATCC-GGCTAAGTCCCGAAGA
1 GATGTATCCGGGCTAAGTCCCGA-AGGCATTCTGCTAGTGATGTATCCGGGCTAAGTCCCGAAGA
* *
5960 GCATTCGTGCTAGTA-GATGATCCGGGCT-AGTCTCG-AGAAGCATT-GTGCTAGT
65 GCATTCGTGCTAGTATG-T-ATCCGGG-TAAGTCCCGAAG-AGCATTCATGCTAGT
* * *
6012 GATGTATCCGGACTAAGTTCCGAA-GCATTTTGCTAGTGAT-TATCC
1 GATGTATCCGGGCTAAGTCCCGAAGGCATTCTGCTAGTGATGTATCC
6057 ATGTAAACCC
Statistics
Matches: 149, Mismatches: 6, Indels: 16
0.87 0.04 0.09
Matches are distributed among these distances:
113 5 0.03
114 15 0.10
115 2 0.01
116 62 0.42
117 39 0.26
118 24 0.16
119 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (116 bp):
GATGTATCCGGGCTAAGTCCCGAAGGCATTCTGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAG
CATTCGTGCTAGTATGTATCCGGGTAAGTCCCGAAGAGCATTCATGCTAGT
Found at i:9840 original size:42 final size:42
Alignment explanation
Indices: 9783--9943 Score: 187
Period size: 42 Copynumber: 3.8 Consensus size: 42
9773 TAGGGTTATG
9783 TGTGATTTCGTGTAAGACCATATCTGGGATATGGCATCGATA
1 TGTGATTTCGTGTAAGACCATATCTGGGATATGGCATCGATA
* * * *
9825 TGTGATTTTGTGTAAGACCATGTTTGGGACATGGCATCGATA
1 TGTGATTTCGTGTAAGACCATATCTGGGATATGGCATCGATA
* ** * * *
9867 TGAGACATCGTGTAATACCATAGCTGGGCTATCGGCATCGATA
1 TGTGATTTCGTGTAAGACCATATCTGGGATAT-GGCATCGATA
** * *
9910 TGTGATCCCATATAAGACCATATCTGGGATATGG
1 TGTGATTTCGTGTAAGACCATATCTGGGATATGG
9944 AATTGGCATC
Statistics
Matches: 95, Mismatches: 23, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
42 62 0.65
43 33 0.35
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (42 bp):
TGTGATTTCGTGTAAGACCATATCTGGGATATGGCATCGATA
Found at i:12439 original size:51 final size:51
Alignment explanation
Indices: 12344--12458 Score: 131
Period size: 51 Copynumber: 2.3 Consensus size: 51
12334 GATGGTTAGG
* * ***
12344 TCACATGTGTAGTACTAAGTCCAGGCTACTATGCGTACCCGATAGCTTCGA
1 TCACATGTGTGGTACTAAGTCCAGGCCACTATGCGTAAAAGATAGCTTCGA
* * * * *
12395 TCACATGTGTGGTACTAAGTGCATGCCACTATGTGTAAAAGATAGCTTTGG
1 TCACATGTGTGGTACTAAGTCCAGGCCACTATGCGTAAAAGATAGCTTCGA
*
12446 TCACAAGTGTGGT
1 TCACATGTGTGGT
12459 CCTATGTGAA
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (51 bp):
TCACATGTGTGGTACTAAGTCCAGGCCACTATGCGTAAAAGATAGCTTCGA
Found at i:22936 original size:47 final size:47
Alignment explanation
Indices: 22817--23261 Score: 804
Period size: 47 Copynumber: 9.5 Consensus size: 47
22807 TTCGGGACTC
* * * * * * *
22817 ATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
*
22864 GTCACATATAT--ACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
22909 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
22956 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
23003 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
23050 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
23097 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
23144 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
23191 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
23238 ATCACATATATACACTTTCACATT
1 ATCACATATATACACTTTCACATT
23262 TATTCAAATA
Statistics
Matches: 387, Mismatches: 9, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
45 38 0.10
47 349 0.90
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
Done.