Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1326
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: 34993
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:418 original size:26 final size:27
Alignment explanation
Indices: 389--454 Score: 86
Period size: 26 Copynumber: 2.5 Consensus size: 27
379 AAGGAATTCG
389 GTCATTTTACCCTTAG-GGTTATTT-TA
1 GTCATTTTACCCTTAGCGG-TATTTCTA
415 GTCATTTTACCCTCTAGCGGTATTTCTA
1 GTCATTTTACCCT-TAGCGGTATTTCTA
443 --CATTTTACCCTT
1 GTCATTTTACCCTT
455 GAAGACGGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
25 1 0.03
26 24 0.65
27 8 0.22
28 4 0.11
ACGTcount: A:0.18, C:0.23, G:0.12, T:0.47
Consensus pattern (27 bp):
GTCATTTTACCCTTAGCGGTATTTCTA
Found at i:3139 original size:45 final size:45
Alignment explanation
Indices: 3070--3757 Score: 888
Period size: 45 Copynumber: 15.3 Consensus size: 45
3060 TTCACTGCAG
* * *
3070 TACAAGAAGACAAGATCTGTTATCTTCAGTCTACTTCGCTGCCAA
1 TACAGGAAGACAAGACCTGCTATCTTCAGTCTACTTCGCTGCCAA
* *
3115 TACAGGAAGACAAGACCTGCTATCTTTAGTCTACTTTGCTGCCAA
1 TACAGGAAGACAAGACCTGCTATCTTCAGTCTACTTCGCTGCCAA
* *
3160 TATAGGAAGACAAAACCTGCTATCTTC-GATCTACTTCGCTGCCAA
1 TACAGGAAGACAAGACCTGCTATCTTCAG-TCTACTTCGCTGCCAA
** *
3205 TACAGGAAGACAAGATTTGCTATCTTCAGTCTAC-TCGCTGCTAA
1 TACAGGAAGACAAGACCTGCTATCTTCAGTCTACTTCGCTGCCAA
*
3249 TACAGGAAGACAAGACCTGCTATCTTC-GATCTACTTCGCTGTCAA
1 TACAGGAAGACAAGACCTGCTATCTTCAG-TCTACTTCGCTGCCAA
* * * * *
3294 TACAGGAAGACAAGATCTGCTATCTTCAATCAACTTCGTTGACAA
1 TACAGGAAGACAAGACCTGCTATCTTCAGTCTACTTCGCTGCCAA
* **
3339 TACAGGAAGACAAGACATGCTATCTTC-GATCTACTTCATTGCCAA
1 TACAGGAAGACAAGACCTGCTATCTTCAG-TCTACTTCGCTGCCAA
* *
3384 TATAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGCTGCCAA
1 TACAGGAAGACAAGACCTGCTATCTTCAGTCTACTTCGCTGCCAA
* * * *
3429 TATAGGAAGACAAGACCTGCTATCTT-TGATCTACTTCACTGTCAA
1 TACAGGAAGACAAGACCTGCTATCTTCAG-TCTACTTCGCTGCCAA
*
3474 TATAGGAAGACAAGACCTGCTATCTTCAGTCTACTTCGCTGCCAA
1 TACAGGAAGACAAGACCTGCTATCTTCAGTCTACTTCGCTGCCAA
*
3519 TACAGGAAGACAAGACCTGCTATCTTCAGTCTTCTTCGCTGCCAA
1 TACAGGAAGACAAGACCTGCTATCTTCAGTCTACTTCGCTGCCAA
* * * * *
3564 TACAGGAAGATAAGACATGTTATCTTTAATCTACTTCGCTGCCAA
1 TACAGGAAGACAAGACCTGCTATCTTCAGTCTACTTCGCTGCCAA
* * *
3609 TACAGGAAGACAATACATGCTATCTTC-GATCTACTTCGTTGCCAA
1 TACAGGAAGACAAGACCTGCTATCTTCAG-TCTACTTCGCTGCCAA
* *
3654 TACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGCTACCAA
1 TACAGGAAGACAAGACCTGCTATCTTCAGTCTACTTCGCTGCCAA
* * ** *
3699 TACAGGAAGATAAGACCT-CTATCTT-TGATCTACTTCATTACCAA
1 TACAGGAAGACAAGACCTGCTATCTTCAG-TCTACTTCGCTGCCAA
3743 TACAGGAAGACAAGA
1 TACAGGAAGACAAGA
3758 TCTGTTATTT
Statistics
Matches: 565, Mismatches: 66, Indels: 25
0.86 0.10 0.04
Matches are distributed among these distances:
43 2 0.00
44 76 0.13
45 483 0.85
46 4 0.01
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.28
Consensus pattern (45 bp):
TACAGGAAGACAAGACCTGCTATCTTCAGTCTACTTCGCTGCCAA
Found at i:5090 original size:6 final size:6
Alignment explanation
Indices: 5079--5129 Score: 54
Period size: 6 Copynumber: 9.0 Consensus size: 6
5069 TTGGCCTTTC
* *
5079 CTTTTT CTTTTT C-TTTT CTTCTT CTTTTT -TTTTT CTTGTT -TTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
5124 ATTTTT
1 CTTTTT
5130 TTGATTGAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
5 14 0.37
6 24 0.63
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.82
Consensus pattern (6 bp):
CTTTTT
Found at i:5129 original size:17 final size:17
Alignment explanation
Indices: 5083--5129 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
5073 CCTTTCCTTT
*
5083 TTCTTTTTCTTTTCTTC
1 TTCTTTTTTTTTTCTTC
*
5100 TTCTTTTTTTTTTCTTG
1 TTCTTTTTTTTTTCTTC
5117 TT-TTTTTATTTTT
1 TTCTTTTT-TTTTT
5130 TTGATTGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 5 0.19
17 22 0.81
ACGTcount: A:0.02, C:0.13, G:0.02, T:0.83
Consensus pattern (17 bp):
TTCTTTTTTTTTTCTTC
Found at i:5131 original size:11 final size:11
Alignment explanation
Indices: 5079--5131 Score: 61
Period size: 11 Copynumber: 4.7 Consensus size: 11
5069 TTGGCCTTTC
5079 CTTTTTCTTTTT
1 CTTTTT-TTTTT
* *
5091 CTTTTCTTCTT
1 CTTTTTTTTTT
5102 CTTTTTTTTTT
1 CTTTTTTTTTT
*
5113 CTTGTTTTTTT
1 CTTTTTTTTTT
*
5124 ATTTTTTT
1 CTTTTTTT
5132 GATTGAATCT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
11 29 0.85
12 5 0.15
ACGTcount: A:0.02, C:0.13, G:0.02, T:0.83
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:17184 original size:18 final size:18
Alignment explanation
Indices: 17136--17442 Score: 240
Period size: 18 Copynumber: 17.3 Consensus size: 18
17126 TTTTAAAAAA
*
17136 AAAACACGAAAGTTTTTG
1 AAAACACGAAAATTTTTG
*
17154 -AATCAC-AAGAATTTTTG
1 AAAACACGAA-AATTTTTG
*
17171 AAAACCCGAAAATTTTTG
1 AAAACACGAAAATTTTTG
* * *
17189 GAAACATGAAGATTTTTG
1 AAAACACGAAAATTTTTG
*
17207 -AAACACGACAATTTTTG
1 AAAACACGAAAATTTTTG
* ** *
17224 AAACACAAGAATTTTTTTT
1 AAA-ACACGAAAATTTTTG
* * * *
17243 AAAGCGC-AAACTTTTTT
1 AAAACACGAAAATTTTTG
*
17260 AAAACACTG-AAATTTGTG
1 AAAACAC-GAAAATTTTTG
* *
17278 -AAACACGAGAATTGTTG
1 AAAACACGAAAATTTTTG
17295 AAAACACGAAAATTTTTG
1 AAAACACGAAAATTTTTG
* *
17313 AAAATATGAAAATTTTTG
1 AAAACACGAAAATTTTTG
*
17331 AAAACACAAAAATTTTTG
1 AAAACACGAAAATTTTTG
*
17349 -AAACACAAAAATTTTTAG
1 AAAACACGAAAATTTTT-G
17367 AAAACACGAAAACTTTTTG
1 AAAACACGAAAA-TTTTTG
* * *
17386 -AATCACTAGAA-TTTTG
1 AAAACACGAAAATTTTTG
*
17402 AAAACACGTAAATTTTTG
1 AAAACACGAAAATTTTTG
*
17420 -AAACATCG-GAATTTTTG
1 AAAACA-CGAAAATTTTTG
17437 AAAACA
1 AAAACA
17443 TGTGGATTTT
Statistics
Matches: 228, Mismatches: 45, Indels: 32
0.75 0.15 0.10
Matches are distributed among these distances:
16 8 0.04
17 87 0.38
18 102 0.45
19 26 0.11
20 5 0.02
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (18 bp):
AAAACACGAAAATTTTTG
Found at i:17241 original size:36 final size:34
Alignment explanation
Indices: 17137--17442 Score: 215
Period size: 35 Copynumber: 8.7 Consensus size: 34
17127 TTTAAAAAAA
* *
17137 AAACACGAAAGTTTTTGAATCACAAG-AATTTTTG
1 AAACACGAAAATTTTTGAA-AACAAGAAATTTTTG
* * *
17171 AAAACCCGAAAATTTTTGGAAACATGAAGATTTTTG
1 -AAACACGAAAATTTTTGAAAACAAGAA-ATTTTTG
* * *
17207 AAACACGACAATTTTTGAAACACAAGAATTTTTTTT
1 AAACACGAAAATTTTTGAAA-ACAAGAA-ATTTTTG
* * * * *
17243 AAA-GCGCAAACTTTTTTAAAACACTGAAATTTGTG
1 AAACACG-AAAATTTTTGAAAACA-AGAAATTTTTG
* * *
17278 AAACACGAGAATTGTTGAAAACACGAAAATTTTTG
1 AAACACGAAAATTTTTGAAAACAAG-AAATTTTTG
* * *
17313 AAAATATGAAAATTTTTGAAAACACAAAAATTTTTG
1 -AAACACGAAAATTTTTGAAAACA-AGAAATTTTTG
* *
17349 AAACACAAAAATTTTTAGAAAACACGAAAACTTTTTG
1 AAACACGAAAATTTTT-GAAAACAAG-AAA-TTTTTG
* * * *
17386 AATCACTAGAA-TTTTGAAAACACGTAAATTTTTG
1 AAACACGAAAATTTTTGAAAACAAG-AAATTTTTG
*
17420 AAACATCG-GAATTTTTGAAAACA
1 AAACA-CGAAAATTTTTGAAAACA
17443 TGTGGATTTT
Statistics
Matches: 213, Mismatches: 44, Indels: 28
0.75 0.15 0.10
Matches are distributed among these distances:
34 18 0.08
35 103 0.48
36 78 0.37
37 14 0.07
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (34 bp):
AAACACGAAAATTTTTGAAAACAAGAAATTTTTG
Found at i:17433 original size:71 final size:68
Alignment explanation
Indices: 17178--17442 Score: 207
Period size: 71 Copynumber: 3.7 Consensus size: 68
17168 TTGAAAACCC
* * * **
17178 GAAAATTTTTGGAAACA-TGAAGATTTTTGAAACACGACAATTTTTGAAACACAAGAATTTTTTT
1 GAAAATTTTTGAAAACACT-AA-ATTTTTGAAACACG-GAATTTTTGAAA-ACACGAAAATTTTT
* **
17242 TAAA-GC
62 GAAATAT
* * * *
17248 GCAAACTTTTTTAAAACACTGAAATTTGTGAAACACGAGAATTGTTGAAAACACGAAAATTTTTG
1 G-AAAATTTTTGAAAACACT-AAATTTTTGAAACACG-GAATTTTTGAAAACACGAAAATTTTTG
17313 AAAATAT
63 -AAATAT
* **
17320 GAAAATTTTTGAAAACACAAAAATTTTTGAAACACAAAAATTTTTAGAAAACACGAAAACTTTTT
1 GAAAATTTTTGAAAACAC-TAAATTTTTGAAACAC-GGAATTTTT-GAAAACACGAAAA-TTTTT
17385 G-AATCACT
62 GAAAT-A-T
*
17393 -AGAA-TTTTGAAAACACGTAAATTTTTGAAACATCGGAATTTTTGAAAACA
1 GAAAATTTTTGAAAACAC-TAAATTTTTGAAACA-CGGAATTTTTGAAAACA
17443 TGTGGATTTT
Statistics
Matches: 160, Mismatches: 24, Indels: 22
0.78 0.12 0.11
Matches are distributed among these distances:
70 19 0.12
71 111 0.69
72 23 0.14
73 7 0.04
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (68 bp):
GAAAATTTTTGAAAACACTAAATTTTTGAAACACGGAATTTTTGAAAACACGAAAATTTTTGAAA
TAT
Found at i:17451 original size:18 final size:18
Alignment explanation
Indices: 17397--17453 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
17387 ATCACTAGAA
* *
17397 TTTTGAAAACACGTAAAT
1 TTTTGAAAACATGTGAAT
17415 TTTTG-AAACATCG-GAAT
1 TTTTGAAAACAT-GTGAAT
*
17432 TTTTGAAAACATGTGGAT
1 TTTTGAAAACATGTGAAT
17450 TTTT
1 TTTT
17454 TTTTACACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 14 0.42
18 19 0.58
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (18 bp):
TTTTGAAAACATGTGAAT
Found at i:17662 original size:20 final size:19
Alignment explanation
Indices: 17637--17682 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
17627 GACACAAAAA
*
17637 TTTTGAAACACAGGAATTTT
1 TTTTGAAA-ACACGAATTTT
17657 TTTTGAAAACACGAATTTT
1 TTTTGAAAACACGAATTTT
17676 TTTTGAA
1 TTTTGAA
17683 TTTTTTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (19 bp):
TTTTGAAAACACGAATTTT
Found at i:18011 original size:9 final size:9
Alignment explanation
Indices: 17997--18074 Score: 70
Period size: 10 Copynumber: 8.4 Consensus size: 9
17987 AATTGAACCC
17997 TTTTCTCTT
1 TTTTCTCTT
18006 TTTTCTTCTT
1 TTTTC-TCTT
18016 TTTT-TCTT
1 TTTTCTCTT
*
18024 TTTTCTTTT
1 TTTTCTCTT
18033 TTTTCTCTGT
1 TTTTCTCT-T
* *
18043 TTTTTTCCGT
1 TTTTCT-CTT
*
18053 CTTTCTCTT
1 TTTTCTCTT
18062 CTTTT-TCTT
1 -TTTTCTCTT
18071 TTTT
1 TTTT
18075 GGCCTGTTGG
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
8 12 0.21
9 21 0.38
10 22 0.39
11 1 0.02
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (9 bp):
TTTTCTCTT
Found at i:18023 original size:18 final size:17
Alignment explanation
Indices: 17997--18046 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
17987 AATTGAACCC
*
17997 TTTTCTCTTTTTTCTTCT
1 TTTTTTCTTTTTTCTT-T
18015 TTTTTTCTTTTTTCTTT
1 TTTTTTCTTTTTTCTTT
18032 TTTTTCTCTGTTTTT
1 TTTTT-TCT-TTTTT
18047 TTCCGTCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 6 0.21
18 18 0.62
19 5 0.17
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (17 bp):
TTTTTTCTTTTTTCTTT
Found at i:18031 original size:15 final size:16
Alignment explanation
Indices: 18006--18035 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17996 CTTTTCTCTT
18006 TTTTCTTCTTTTTTTC
1 TTTTCTTCTTTTTTTC
18022 TTTT-TTCTTTTTTT
1 TTTTCTTCTTTTTTT
18036 TCTCTGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTCTTCTTTTTTTC
Found at i:18035 original size:27 final size:28
Alignment explanation
Indices: 17997--18074 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 28
17987 AATTGAACCC
17997 TTTTCTCTTTTTTCT-TCTTTTTTTCTT
1 TTTTCTCTTTTTTCTCTCTTTTTTTCTT
* * *
18024 TTTTCTTTTTTTTCTCTGTTTTTTTCCGT
1 TTTTCTCTTTTTTCTCTCTTTTTTT-CTT
* *
18053 CTTTCTCTTCTTT-T-TCTTTTTT
1 TTTTCTCTTTTTTCTCTCTTTTTT
18075 GGCCTGTTGG
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
27 21 0.50
28 9 0.21
29 12 0.29
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (28 bp):
TTTTCTCTTTTTTCTCTCTTTTTTTCTT
Found at i:18336 original size:4 final size:4
Alignment explanation
Indices: 18327--18418 Score: 69
Period size: 4 Copynumber: 24.8 Consensus size: 4
18317 TAATTTTCTT
*
18327 TTTC TTTC -TTC -TTC -TTC TTTC -TTC TTCCCC TTTTC T-TC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT--TC TT-TC TTTC TTTC TTTC
*
18373 -TTC TTTA TTT- TTTC TTTC TTTC TTTC -TTC TTT- TTT- TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
18416 TTT
1 TTT
18419 TTCTCTTCTC
Statistics
Matches: 75, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
3 30 0.40
4 40 0.53
5 2 0.03
6 3 0.04
ACGTcount: A:0.01, C:0.25, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:18425 original size:25 final size:26
Alignment explanation
Indices: 18357--18427 Score: 112
Period size: 25 Copynumber: 2.8 Consensus size: 26
18347 CTTCTTCCCC
18357 TTTTC-TTCTTTCTTTCTTCTTTATT
1 TTTTCTTTCTTTCTTTCTTCTTTATT
18382 TTTTCTTTCTTTCTTTCTTCTTT-TT
1 TTTTCTTTCTTTCTTTCTTCTTTATT
18407 TTTTCTTTCTTT-TTCTCTTCT
1 TTTTCTTTCTTTCTT-TCTTCT
18428 CCTTCATTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
24 2 0.05
25 25 0.57
26 17 0.39
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.77
Consensus pattern (26 bp):
TTTTCTTTCTTTCTTTCTTCTTTATT
Found at i:18888 original size:29 final size:30
Alignment explanation
Indices: 18764--18889 Score: 123
Period size: 29 Copynumber: 4.3 Consensus size: 30
18754 GGGGCCAATG
*
18764 TGTAATTTTAAGAAAATTTAGGGGTCAAAA
1 TGTAATTTCAAGAAAATTTAGGGGTCAAAA
* * ** * *
18794 TATAATTT-AAAAAAACCTAGTGGTTAAAA
1 TGTAATTTCAAGAAAATTTAGGGGTCAAAA
**
18823 CATAATTTCAAGAAAATTTAGGGGTCAAAA
1 TGTAATTTCAAGAAAATTTAGGGGTCAAAA
* *
18853 TGCAATTTCAA-AAAATTTA-GGGTACGAAA
1 TGTAATTTCAAGAAAATTTAGGGGT-CAAAA
18882 TGTAATTT
1 TGTAATTT
18890 TTTTTAAAAC
Statistics
Matches: 77, Mismatches: 17, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
28 4 0.05
29 42 0.55
30 31 0.40
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.32
Consensus pattern (30 bp):
TGTAATTTCAAGAAAATTTAGGGGTCAAAA
Found at i:19207 original size:82 final size:80
Alignment explanation
Indices: 19114--19865 Score: 842
Period size: 82 Copynumber: 9.5 Consensus size: 80
19104 CGTGTGACTT
* *
19114 GAGGCTGAACTCACCTCTAGCAATATGAGTTGATTTTTTTTGAAAGAACAGAAATTTTAAAAAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAA-AACAGAAA-TTTAAAAAAA
* * *
19179 TACCTCGGTATGAGCCT
64 TACCTCGGCATGTGCCC
* * * * * * *
19196 GATGCTCAACTCACCTTTCACAATATGAGTTGA--TTGTTTGAAAAGCATAAA-TT-GAAAAATA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTTAAAAAAATA
*
19257 CCTCAGC--GTGACCC
66 CCTCGGCATGTG-CCC
* * *
19271 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGGAAAAAACA-AAAATT-GAAAAAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTG-AAAAACAGAAATTTAAAAAAAT
*
19334 ACCTCAGCATGTGCCC
65 ACCTCGGCATGTGCCC
** *
19350 GAGGCTCAACTCACCTCTCTTAATATGAGTTGATTTTTTTTGAAAAGCAGAAA-TT-AAAAAATA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTTAAAAAAATA
*
19413 CCTCAGCATGTGACCC
66 CCTCGGCATGTG-CCC
* * *
19429 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTT-AAAAATAGAAATTTAAATGAAAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTTAAA-AAAAT
*
19492 ACTTCGGCATGTGACCC
65 ACCTCGGCATGTG-CCC
*
19509 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAAACAGAAA-TT-GAAAAAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTTGAAAAACAGAAATTTAAAAAAAT
*
19572 ACCTCAGC--GTGACCC
65 ACCTCGGCATGTG-CCC
* * *
19587 GAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTTTGGAAAAAATAGAAATTTAAAAGAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTG-AAAAACAGAAATTTAAAA-AAA
* *
19652 TACCTCGACATGTGTCC
64 TACCTCGGCATGTGCCC
* * * * *
19669 GAGGCTTAACTCACCTCTCGTAATATGAGTTAATTTTTTTGGAAAAAATAGAAATTTAAAAGAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTG-AAAAACAGAAATTTAAAA-AAA
* *
19734 TACCTCGACATGTGTCC
64 TACCTCGGCATGTGCCC
* *
19751 GAGGCTCAACTCACCTCTCGTAATATGAGTTGA---CTTTTGAAAAAACAGAAATTTAAAAGAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTG-AAAAACAGAAATTTAAAA-AAA
*
19813 TACCTCGGCATG-ACCC
64 TACCTCGGCATGTGCCC
*
19829 GAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
19866 AAAAAAAAAC
Statistics
Matches: 588, Mismatches: 58, Indels: 49
0.85 0.08 0.07
Matches are distributed among these distances:
74 2 0.00
75 32 0.05
76 12 0.02
77 27 0.05
78 141 0.24
79 125 0.21
80 75 0.13
81 11 0.02
82 150 0.26
83 13 0.02
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (80 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTTAAAAAAATA
CCTCGGCATGTGCCC
Found at i:28349 original size:17 final size:17
Alignment explanation
Indices: 28299--28602 Score: 152
Period size: 18 Copynumber: 17.4 Consensus size: 17
28289 TTTTTTTAAA
28299 AAAACACGAAAATTTTTG
1 AAAACACGAAAA-TTTTG
* * *
28317 -AATCAAGAGAATTTTTG
1 AAAACACGA-AAATTTTG
*
28334 AAAACCCGAAAATTTTTG
1 AAAACACGAAAA-TTTTG
* * *
28352 GAAACACGAAGATTTTT
1 AAAACACGAAAATTTTG
*
28369 AAAACACGACAATTTTTG
1 AAAACACGA-AAATTTTG
* * * *
28387 AACACAAGAAATTTTTTT
1 AAAACACGAAA-ATTTTG
* ** *
28405 TAAA-GTGCAAAATTTTTT
1 AAAACACG-AAAA-TTTTG
*
28423 AAAACACTG-AAATTGTG
1 AAAACAC-GAAAATTTTG
*
28440 -AAACACGAGAATTGTTG
1 AAAACACGAAAATT-TTG
28457 AAAACACGAAAATTTTTG
1 AAAACACGAAAA-TTTTG
* * *
28475 AAAATATGAAAAATTTG
1 AAAACACGAAAATTTTG
* *
28492 AAAACGCGAAAATTTTT
1 AAAACACGAAAATTTTG
* *
28509 TAAACACAAAAATTTTAG
1 AAAACACGAAAATTTT-G
28527 AAAACACGAAAACTTTTTG
1 AAAACACGAAAA--TTTTG
* * *
28546 -AATCACTAGAATTTTG
1 AAAACACGAAAATTTTG
*
28562 AAAACACGTAAATTTTTG
1 AAAACACG-AAAATTTTG
* *
28580 -AAACACCGGAATTTTTG
1 AAAACA-CGAAAATTTTG
28597 AAAACA
1 AAAACA
28603 TGTTGAGTTT
Statistics
Matches: 213, Mismatches: 53, Indels: 40
0.70 0.17 0.13
Matches are distributed among these distances:
15 1 0.00
16 15 0.07
17 80 0.38
18 109 0.51
19 3 0.01
20 5 0.02
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (17 bp):
AAAACACGAAAATTTTG
Found at i:28403 original size:53 final size:53
Alignment explanation
Indices: 28300--28602 Score: 131
Period size: 53 Copynumber: 5.8 Consensus size: 53
28290 TTTTTTAAAA
* * * **
28300 AAACACGAAAATTTTTGAATCAAGAGAATTTTTGAAAACCCGAAAATTTTTGG
1 AAACACGAAAATTTTTAAAACAAGACAATTTTTGAAAACAAGAAAATTTTTGG
* * * * **
28353 AAACACGAAGATTTTTAAAACACGACAATTTTTGAACACAAGAAATTTTTTTT
1 AAACACGAAAATTTTTAAAACAAGACAATTTTTGAAAACAAGAAAATTTTTGG
** * * * * * *
28406 AAA-GTGCAAAATTTTTTAAAACACTGA-AA-TTGTG-AAACACGAGAATTGTTGA
1 AAACACG-AAAA-TTTTTAAAACA-AGACAATTTTTGAAAACAAGAAAATTTTTGG
* * ** ** *
28458 AAACACGAAAATTTTTGAAAATATGA-AAAATTTGAAAACGCGAAAATTTTT-T
1 AAACACGAAAATTTTT-AAAACAAGACAATTTTTGAAAACAAGAAAATTTTTGG
* * * * * * *
28510 AAACACAAAAATTTTAGAAAACACGAAAACTTTTTGAATCACTAG--AA-TTTTGA
1 AAACACGAAAATTTT-TAAAACAAGACAA-TTTTTGAA-AACAAGAAAATTTTTGG
* * * *
28563 AAACACGTAAATTTTTGAAACACCG-GAATTTTTGAAAACA
1 AAACACGAAAATTTTTAAAACA-AGACAATTTTTGAAAACA
28603 TGTTGAGTTT
Statistics
Matches: 188, Mismatches: 49, Indels: 29
0.71 0.18 0.11
Matches are distributed among these distances:
50 2 0.01
51 18 0.10
52 59 0.31
53 85 0.45
54 19 0.10
55 5 0.03
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.30
Consensus pattern (53 bp):
AAACACGAAAATTTTTAAAACAAGACAATTTTTGAAAACAAGAAAATTTTTGG
Found at i:28514 original size:70 final size:69
Alignment explanation
Indices: 28438--28602 Score: 176
Period size: 70 Copynumber: 2.3 Consensus size: 69
28428 ACTGAAATTG
*
28438 TGAAACACGAGAATTGTTGAAAACACGAAAA-TTTTTGAAAAT-A-TGAAAAATTTGAAAACGCG
1 TGAAACACGAGAATT-TTGAAAACACGAAAACTTTTTG--AATCACT-AAAAATTTGAAAACACG
28500 AAAATTTT
62 AAAATTTT
* * * * * *
28508 TTAAACACAAAAATTTTAGAAAACACGAAAACTTTTTGAATCACTAGAATTTTGAAAACACGTAA
1 TGAAACACGAGAATTTT-GAAAACACGAAAACTTTTTGAATCACTAAAAATTTGAAAACACGAAA
28573 ATTTT
65 ATTTT
28578 TGAAACACCG-GAATTTTTGAAAACA
1 TGAAACA-CGAGAA-TTTTGAAAACA
28603 TGTTGAGTTT
Statistics
Matches: 79, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
69 5 0.06
70 62 0.78
71 12 0.15
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.28
Consensus pattern (69 bp):
TGAAACACGAGAATTTTGAAAACACGAAAACTTTTTGAATCACTAAAAATTTGAAAACACGAAAA
TTTT
Found at i:28596 original size:35 final size:35
Alignment explanation
Indices: 28309--28602 Score: 145
Period size: 35 Copynumber: 8.4 Consensus size: 35
28299 AAAACACGAA
* * * *
28309 AATTTTTG-AATCAAGAGAATTTTTGAAA-ACCCGAA
1 AATTTTTGAAAACACGAAAATTTTTGAAACA-CCG-G
* * * *
28344 AATTTTTGGAAACACGAAGATTTTTAAAACA-CGAC
1 AATTTTTGAAAACACGAAAATTTTTGAAACACCG-G
* * * * *** **
28379 AATTTTTGAACACAAGAAATTTTTTTTAAAGTGCAA
1 AATTTTTGAAAACACGAAA-ATTTTTGAAACACCGG
* *
28415 AATTTTTTAAAACACTG-AAA-TTGTGAAACA-CGAG
1 AATTTTTGAAAACAC-GAAAATTTTTGAAACACCG-G
* ** *
28449 AATTGTTGAAAACACGAAAATTTTTGAAA-ATATGA
1 AATTTTTGAAAACACGAAAATTTTTGAAACA-CCGG
** * * ***
28484 AAAATTTGAAAACGCGAAAATTTTTTAAACACAAA
1 AATTTTTGAAAACACGAAAATTTTTGAAACACCGG
* * **
28519 AATTTTAGAAAACACGAAAACTTTTTGAATCACTAG
1 AATTTTTGAAAACACGAAAA-TTTTTGAAACACCGG
*
28555 AA-TTTTGAAAACACGTAAATTTTTGAAACACCGG
1 AATTTTTGAAAACACGAAAATTTTTGAAACACCGG
28589 AATTTTTGAAAACA
1 AATTTTTGAAAACA
28603 TGTTGAGTTT
Statistics
Matches: 194, Mismatches: 52, Indels: 26
0.71 0.19 0.10
Matches are distributed among these distances:
33 2 0.01
34 37 0.19
35 100 0.52
36 52 0.27
37 3 0.02
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (35 bp):
AATTTTTGAAAACACGAAAATTTTTGAAACACCGG
Found at i:28813 original size:16 final size:17
Alignment explanation
Indices: 28774--28815 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
28764 ACACGAGAAA
*
28774 AAAAATTTTGAAGACAT
1 AAAAATTTTGAAGACAC
28791 AAAAATTTTGAA-ACAC
1 AAAAATTTTGAAGACAC
*
28807 AAGAATTTT
1 AAAAATTTT
28816 TTTGAAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (17 bp):
AAAAATTTTGAAGACAC
Found at i:28834 original size:18 final size:19
Alignment explanation
Indices: 28796--28839 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
28786 GACATAAAAA
*
28796 TTTTGAAACACAAGAATTT
1 TTTTGAAACACAAGAAATT
*
28815 TTTTGAAA-ACACGAAATT
1 TTTTGAAACACAAGAAATT
28833 TTTTGAA
1 TTTTGAA
28840 TATTTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (19 bp):
TTTTGAAACACAAGAAATT
Found at i:29019 original size:15 final size:15
Alignment explanation
Indices: 28993--29046 Score: 56
Period size: 14 Copynumber: 3.5 Consensus size: 15
28983 AAATTAAATT
28993 AAAAATAT-AAATAC
1 AAAAATATAAAATAC
29007 AAAAATATAAAATAC
1 AAAAATATAAAATAC
* *
29022 ATAAAGTACTAATAATAT
1 A-AAAATA-TAA-AATAC
29040 AAAAATA
1 AAAAATA
29047 CGAGTATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
14 8 0.24
15 7 0.21
16 5 0.15
17 8 0.24
18 5 0.15
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.24
Consensus pattern (15 bp):
AAAAATATAAAATAC
Found at i:29154 original size:12 final size:12
Alignment explanation
Indices: 29137--29179 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
29127 GAAACCTTTC
29137 TCTTTTTTCTCT
1 TCTTTTTTCTCT
* *
29149 TCTTTTTTTTTT
1 TCTTTTTTCTCT
*
29161 TCTTTCTTCTCT
1 TCTTTTTTCTCT
29173 TCTTTTT
1 TCTTTTT
29180 CTTTTTGGCC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TCTTTTTTCTCT
Found at i:29168 original size:19 final size:18
Alignment explanation
Indices: 29140--29183 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
29130 ACCTTTCTCT
*
29140 TTTTTCTCTTCTT-T-TTT
1 TTTTTCT-TTCTTCTCTTC
29157 TTTTTCTTTCTTCTCTTC
1 TTTTTCTTTCTTCTCTTC
29175 TTTTTCTTT
1 TTTTTCTTT
29184 TTGGCCTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 5 0.21
17 8 0.33
18 11 0.46
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTCTTTCTTCTCTTC
Found at i:29170 original size:24 final size:24
Alignment explanation
Indices: 29132--29185 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
29122 AAATTGAAAC
* *
29132 CTTTCTCTTTTTTCTCTTCTTTTT
1 CTTTTTCTTTCTTCTCTTCTTTTT
*
29156 TTTTTTCTTTCTTCTCTTCTTTTT
1 CTTTTTCTTTCTTCTCTTCTTTTT
29180 CTTTTT
1 CTTTTT
29186 GGCCTGTTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (24 bp):
CTTTTTCTTTCTTCTCTTCTTTTT
Found at i:29457 original size:3 final size:3
Alignment explanation
Indices: 29449--29536 Score: 69
Period size: 3 Copynumber: 29.0 Consensus size: 3
29439 CTTTTCATTT
29449 TTC TTC TTC TTC TTC TTC -TC TT- TTC TTC TTC TTC TTTC TTC TTTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC -TTC
* *
29494 TTTC TTTC TTC TT- TT- TTC TTTC TTTC TTT TTC -TC TTC TCC TTC
1 -TTC -TTC TTC TTC TTC TTC -TTC -TTC TTC TTC TTC TTC TTC TTC
29537 GTTCAACCCC
Statistics
Matches: 74, Mismatches: 4, Indels: 14
0.80 0.04 0.15
Matches are distributed among these distances:
2 10 0.14
3 43 0.58
4 21 0.28
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:29483 original size:25 final size:23
Alignment explanation
Indices: 29448--29531 Score: 104
Period size: 22 Copynumber: 3.7 Consensus size: 23
29438 TCTTTTCATT
*
29448 TTTCTTCTTCTTCTTCTTCTCT-
1 TTTCTTCTTCTTCTTCTTCTTTC
29470 TTTCTTCTTCTTCTTTCTTCTTTC
1 TTTCTTCTTCTTC-TTCTTCTTTC
29494 TTTCTTTCTTCTT-TT-TTCTTTC
1 TTTC-TTCTTCTTCTTCTTCTTTC
*
29516 TTTCTTTTTC-TCTTCT
1 TTTCTTCTTCTTCTTCT
29532 CCTTCGTTCA
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
20 1 0.02
21 7 0.13
22 25 0.45
23 10 0.18
24 4 0.07
25 8 0.15
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTCTTCTTCTTCTTCTTCTTTC
Found at i:29487 original size:29 final size:29
Alignment explanation
Indices: 29438--29529 Score: 100
Period size: 29 Copynumber: 3.1 Consensus size: 29
29428 AAATAATTTT
*
29438 TCTTTTCATTTTTCTTC-TTCTTCTTCTTC
1 TCTTTTC-TTCTTCTTCTTTCTTCTTCTTC
29467 TCTTTTCTTCTTCTTCTTTCTTCTTTCTT-
1 TCTTTTCTTCTTCTTCTTTCTTC-TTCTTC
* *
29496 TC-TTTCTTCTTTTTTCTTTCTTTCTTTTTC
1 TCTTTTCTTC-TTCTTCTTTC-TTCTTCTTC
29526 TCTT
1 TCTT
29530 CTCCTTCGTT
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
28 15 0.28
29 28 0.52
30 10 0.19
31 1 0.02
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.73
Consensus pattern (29 bp):
TCTTTTCTTCTTCTTCTTTCTTCTTCTTC
Found at i:29494 original size:4 final size:4
Alignment explanation
Indices: 29480--29522 Score: 65
Period size: 4 Copynumber: 11.5 Consensus size: 4
29470 TTTCTTCTTC
29480 TTCT TTC- TTCT TTCT TTCT TTC- TTCT TT-T TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT
29523 TTCTCTTCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 9 0.25
4 27 0.75
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:30925 original size:21 final size:20
Alignment explanation
Indices: 30891--30938 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
30881 AAGGAATTAT
30891 AATT-AAAATCATTAACTAAAA
1 AATTAAAAATCATTAA--AAAA
30912 AATTAAAAAT-ATTAAAAAA
1 AATTAAAAATCATTAAAAAA
30931 AATCTAAA
1 AAT-TAAA
30939 TTCAAAGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 7 0.28
20 4 0.16
21 9 0.36
22 5 0.20
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (20 bp):
AATTAAAAATCATTAAAAAA
Found at i:31530 original size:28 final size:28
Alignment explanation
Indices: 31464--31530 Score: 64
Period size: 28 Copynumber: 2.4 Consensus size: 28
31454 ATTTAAGGAG
* * * *
31464 AGTGATTAAATAGAAATATCTAAGTGTG
1 AGTGAATAAATAGAAATATATAAATGTA
**
31492 AGTGACCAAATAG-AATAATATAAATGTA
1 AGTGAATAAATAGAAAT-ATATAAATGTA
31520 AGTGAATAAAT
1 AGTGAATAAAT
31531 TAAAAAATTA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
27 3 0.10
28 28 0.90
ACGTcount: A:0.49, C:0.04, G:0.18, T:0.28
Consensus pattern (28 bp):
AGTGAATAAATAGAAATATATAAATGTA
Done.