Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 82 of 318
Found at i:28038311 original size:39 final size:38
Alignment explanation
Indices: 28038194--28038322 Score: 115
Period size: 36 Copynumber: 3.4 Consensus size: 38
28038184 GATCCGATTG
* *
28038194 AAACACGAGAATTTCTTGTTTTGAAAACACGAGAATTTTA
1 AAACACGAG-ATTT-TTTTTTTGAAAACACGAAAATTTTA
* * * *
28038234 AGACA-TA-ATATTTTTTTT-AAAAC-C-AAAATTTATG
1 AAACACGAGATTTTTTTTTTGAAAACACGAAAATTT-TA
28038268 AAACACGAGATTTTTTTTTTGAAAACACGAAAATTTTCA
1 AAACACGAGATTTTTTTTTTGAAAACACGAAAATTTT-A
*
28038307 AAACACCGAAATTTTT
1 AAACA-CGAGATTTTT
28038323 GAAAACAAGA
Statistics
Matches: 70, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
33 6 0.09
34 6 0.09
35 6 0.09
36 16 0.23
37 8 0.11
38 2 0.03
39 13 0.19
40 13 0.19
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (38 bp):
AAACACGAGATTTTTTTTTTGAAAACACGAAAATTTTA
Found at i:28038329 original size:35 final size:35
Alignment explanation
Indices: 28038283--28038445 Score: 170
Period size: 35 Copynumber: 4.7 Consensus size: 35
28038273 CGAGATTTTT
**
28038283 TTTTTGAAAACACGAAAATTTTCAAAACACCGAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
* ** *
28038318 TTTTTGAAAACAAGAGGATTTTTGAAATA-CGAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCG-AAA
* *
28038353 ATTTTGAAAACACGAAAATTTTTGAAACACGGAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
**
28038388 TTTTTG-AAA-ACGAAAATTTTTGAAACACAAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
* * *
28038421 TTTTTAGAAGACACTAAAAATTTTG
1 TTTTT-GAAAACACGAAAATTTTTG
28038446 GAAAATGGAT
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
33 27 0.26
34 6 0.06
35 60 0.57
36 12 0.11
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.30
Consensus pattern (35 bp):
TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
Found at i:28038658 original size:20 final size:19
Alignment explanation
Indices: 28038619--28038666 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
28038609 ACGAATATAT
28038619 ATTTTTGAAACACGAGAAAA
1 ATTTTTGAAACACG-GAAAA
*
28038639 ATTTTTGAAGGCAC-GAAAA
1 ATTTTTGAA-ACACGGAAAA
28038658 A-TTTTGAAA
1 ATTTTTGAAA
28038667 AATAGAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 7 0.28
19 6 0.24
20 9 0.36
21 3 0.12
ACGTcount: A:0.46, C:0.08, G:0.17, T:0.29
Consensus pattern (19 bp):
ATTTTTGAAACACGGAAAA
Found at i:28039040 original size:7 final size:7
Alignment explanation
Indices: 28039024--28039116 Score: 75
Period size: 7 Copynumber: 13.3 Consensus size: 7
28039014 GAATTGAAAC
28039024 TCTTTTT
1 TCTTTTT
*
28039031 T-TTCTT
1 TCTTTTT
*
28039037 T-TTTCT
1 TCTTTTT
28039043 TCTTTTT
1 TCTTTTT
28039050 TCCTTTTT
1 T-CTTTTT
*
28039058 CCTTTTT
1 TCTTTTT
*
28039065 TCTCTTT
1 TCTTTTT
28039072 TC-TTTT
1 TCTTTTT
*
28039078 TCTTCTT
1 TCTTTTT
28039085 TCTTTTTT
1 TC-TTTTT
*
28039093 TCTTTCT
1 TCTTTTT
*
28039100 TCTTTCTC
1 TCTTT-TT
28039108 TCTTTTT
1 TCTTTTT
28039115 TC
1 TC
28039117 CTGGCCTGCT
Statistics
Matches: 67, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
6 14 0.21
7 36 0.54
8 17 0.25
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (7 bp):
TCTTTTT
Found at i:28039078 original size:28 final size:28
Alignment explanation
Indices: 28039038--28039114 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 28
28039028 TTTTTTCTTT
28039038 TTTCTTCTTTTTTCCTTTTTCCTTTTTTC
1 TTTCTTC-TTTTTCCTTTTTCCTTTTTTC
*
28039067 TCTT-TTCTTTTT-CTTCTTTCTTTTTTTC
1 T-TTCTTCTTTTTCCTT-TTTCCTTTTTTC
*
28039095 TTTCTTCTTTCTCTCTTTTT
1 TTTCTTCTTTTTC-CTTTTT
28039115 TCCTGGCCTG
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
27 5 0.12
28 24 0.59
29 7 0.17
30 5 0.12
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (28 bp):
TTTCTTCTTTTTCCTTTTTCCTTTTTTC
Found at i:28039081 original size:35 final size:34
Alignment explanation
Indices: 28039025--28039102 Score: 93
Period size: 35 Copynumber: 2.3 Consensus size: 34
28039015 AATTGAAACT
* *
28039025 CTTTTTTTTCTTTTTTCTTCTTTTTTCCTTTTTC
1 CTTTTTTCTCTTTTTTCTTCTTCTTTCCTTTTTC
* * *
28039059 CTTTTTTCTCTTTTCTTTTTCTTCTTTCTTTTTTT
1 CTTTTTTCTCTTTT-TTCTTCTTCTTTCCTTTTTC
*
28039094 CTTTCTTCT
1 CTTTTTTCT
28039103 TTCTCTCTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
34 13 0.35
35 24 0.65
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (34 bp):
CTTTTTTCTCTTTTTTCTTCTTCTTTCCTTTTTC
Found at i:28039096 original size:15 final size:15
Alignment explanation
Indices: 28039027--28039096 Score: 65
Period size: 15 Copynumber: 4.7 Consensus size: 15
28039017 TTGAAACTCT
*
28039027 TTTTTTTCTTTTTTC
1 TTTTTTTCTTCTTTC
28039042 TTCTTTTTTCCTT-TTTC
1 -T-TTTTTT-CTTCTTTC
*
28039059 CTTTTTTC-TCTTT-
1 TTTTTTTCTTCTTTC
*
28039072 TCTTTTTCTTCTTTC
1 TTTTTTTCTTCTTTC
28039087 TTTTTTTCTT
1 TTTTTTTCTT
28039097 TCTTCTTTCT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
13 7 0.16
14 9 0.20
15 15 0.33
16 1 0.02
17 10 0.22
18 3 0.07
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTTCTTCTTTC
Found at i:28039102 original size:15 final size:15
Alignment explanation
Indices: 28039024--28039104 Score: 64
Period size: 15 Copynumber: 5.5 Consensus size: 15
28039014 GAATTGAAAC
* *
28039024 TCTTTTTTTTCTTTTT
1 TCTTCTTTTT-TTCTT
*
28039040 TCTTCTTTTTTCCTT
1 TCTTCTTTTTTTCTT
*
28039055 T-TTCCTTTTTTC--
1 TCTTCTTTTTTTCTT
28039067 TCTT-TTCTTTTTC-T
1 TCTTCTT-TTTTTCTT
28039081 TCTTTCTTTTTTTCTT
1 TC-TTCTTTTTTTCTT
28039097 TCTTCTTT
1 TCTTCTTT
28039105 CTCTCTTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
12 2 0.04
13 8 0.15
14 11 0.21
15 18 0.34
16 14 0.26
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TCTTCTTTTTTTCTT
Found at i:28039106 original size:39 final size:39
Alignment explanation
Indices: 28039030--28039108 Score: 99
Period size: 39 Copynumber: 2.0 Consensus size: 39
28039020 AAACTCTTTT
*
28039030 TTTTCTTTTTTCTTCTTTTTTCCTTTTTCCTTTTTTCTC
1 TTTTCTTTTTTCTTCTTTTTTCCTTTTTCCTTCTTTCTC
* *
28039069 TTTTC-TTTTTCTTCTTTCTTT-TTTTCTTTCTTCTTTCTC
1 TTTTCTTTTTTCTTCTTT-TTTCCTTT-TTCCTTCTTTCTC
28039108 T
1 T
28039109 CTTTTTTCCT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
38 15 0.43
39 20 0.57
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (39 bp):
TTTTCTTTTTTCTTCTTTTTTCCTTTTTCCTTCTTTCTC
Found at i:28039111 original size:15 final size:13
Alignment explanation
Indices: 28039031--28039112 Score: 66
Period size: 13 Copynumber: 6.2 Consensus size: 13
28039021 AACTCTTTTT
28039031 TTTCTTTTTTCTTC
1 TTTC-TTTTTCTTC
*
28039045 -TT-TTTTCCTT-
1 TTTCTTTTTCTTC
28039055 TTTCCTTTTT-TCTC
1 TTT-CTTTTTCT-TC
28039069 TTTTCTTTTTCTTC
1 -TTTCTTTTTCTTC
28039083 TTTCTTTTT-TTC
1 TTTCTTTTTCTTC
28039095 TTTCTTCTTTCTCTC
1 TTTCTT-TTTCT-TC
28039110 TTT
1 TTT
28039113 TTTCCTGGCC
Statistics
Matches: 56, Mismatches: 2, Indels: 19
0.73 0.03 0.25
Matches are distributed among these distances:
11 9 0.16
12 10 0.18
13 19 0.34
14 9 0.16
15 9 0.16
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTCTTTTTCTTC
Found at i:28039246 original size:14 final size:15
Alignment explanation
Indices: 28039229--28039268 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
28039219 GCTGTTTTTT
28039229 CTTTTTTTTTGGGC-
1 CTTTTTTTTTGGGCG
28039243 CTTTTCTTTTTGGGCTG
1 CTTTT-TTTTTGGGC-G
28039260 CTTTTTTTT
1 CTTTTTTTT
28039269 GCTTTGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 5 0.22
15 9 0.39
16 4 0.17
17 5 0.22
ACGTcount: A:0.00, C:0.15, G:0.17, T:0.68
Consensus pattern (15 bp):
CTTTTTTTTTGGGCG
Found at i:28039269 original size:15 final size:15
Alignment explanation
Indices: 28039231--28039298 Score: 52
Period size: 15 Copynumber: 4.5 Consensus size: 15
28039221 TGTTTTTTCT
28039231 TTTTTTTTGGGC--C
1 TTTTTTTTGGGCTGC
28039244 TTTTCTTTTTGGGCTGC
1 -TTT-TTTTTGGGCTGC
***
28039261 TTTTTTTTGCTTTG-
1 TTTTTTTTGGGCTGC
*
28039275 TTTTTTTTGGGCTGA
1 TTTTTTTTGGGCTGC
28039290 TTTGTTTTT
1 TTT-TTTTT
28039299 TTTTGTGTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
14 14 0.33
15 20 0.47
16 8 0.19
17 1 0.02
ACGTcount: A:0.01, C:0.10, G:0.21, T:0.68
Consensus pattern (15 bp):
TTTTTTTTGGGCTGC
Found at i:28039303 original size:29 final size:31
Alignment explanation
Indices: 28039249--28039313 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 31
28039239 GGGCCTTTTC
*
28039249 TTTTTGGGCTGCTTTTTTTTGCTTTGT-TT-
1 TTTTTGGGCTGATTTTTTTTGCTTTGTGTTG
*
28039278 TTTTTGGGCTGATTTGTTTTT-TTTTGTGTTG
1 TTTTTGGGCTGATTT-TTTTTGCTTTGTGTTG
28039309 TTTTT
1 TTTTT
28039314 TTTAATTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 19 0.61
30 7 0.23
31 5 0.16
ACGTcount: A:0.02, C:0.06, G:0.22, T:0.71
Consensus pattern (31 bp):
TTTTTGGGCTGATTTTTTTTGCTTTGTGTTG
Found at i:28039437 original size:3 final size:3
Alignment explanation
Indices: 28039431--28039462 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
28039421 TTTTTTTTCT
28039431 TTC TTC TTC TTTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC T
28039463 CCTCCTACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:28039442 original size:19 final size:19
Alignment explanation
Indices: 28039418--28039460 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
28039408 TTAAATTTTT
*
28039418 TTCTTT-TTTTTCTTTCTTC
1 TTCTTTCTTCTTC-TTCTTC
28039437 TTCTTTCTTCTTCTTCTTC
1 TTCTTTCTTCTTCTTCTTC
28039456 TTCTT
1 TTCTT
28039461 CTCCTCCTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (19 bp):
TTCTTTCTTCTTCTTCTTC
Found at i:28039563 original size:10 final size:10
Alignment explanation
Indices: 28039528--28039577 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
28039518 ACGCCGGTAC
28039528 TCTT-TCTTT
1 TCTTCTCTTT
* *
28039537 TCTTCTCCTC
1 TCTTCTCTTT
28039547 T-TTCTCTTT
1 TCTTCTCTTT
28039556 TCTTCTCTTT
1 TCTTCTCTTT
*
28039566 TCTTCTTTTT
1 TCTTCTCTTT
28039576 TC
1 TC
28039578 CTTCGAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TCTTCTCTTT
Found at i:28039575 original size:19 final size:19
Alignment explanation
Indices: 28039532--28039574 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
28039522 CGGTACTCTT
28039532 TCTTTTCTTCTCCTCTTTC
1 TCTTTTCTTCTCCTCTTTC
28039551 TCTTTTCTTCT-CT-TTTC
1 TCTTTTCTTCTCCTCTTTC
28039568 TTCTTTT
1 -TCTTTT
28039575 TTCCTTCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.17
18 8 0.35
19 11 0.48
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TCTTTTCTTCTCCTCTTTC
Found at i:28039883 original size:30 final size:30
Alignment explanation
Indices: 28039826--28039942 Score: 121
Period size: 30 Copynumber: 3.9 Consensus size: 30
28039816 TGTAATTTTT
* * *
28039826 AGAAAATTTA-GGATTAAAATAAAATTTAA
1 AGAAAGTTTAGGGGTTAAAATGAAATTTAA
* * *
28039855 TGAAAGTTTAGGGGTTTAAGTGAAATTTAA
1 AGAAAGTTTAGGGGTTAAAATGAAATTTAA
* *
28039885 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAGTTTAGGGGTTAAAATGAAATTTAA
* *
28039914 GGAAAAGTTTAGGGGTTAAAATGCAATTT
1 AG-AAAGTTTAGGGGTTAAAATGAAATTT
28039943 TTATTTTTAA
Statistics
Matches: 71, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
29 10 0.14
30 61 0.86
ACGTcount: A:0.45, C:0.02, G:0.21, T:0.32
Consensus pattern (30 bp):
AGAAAGTTTAGGGGTTAAAATGAAATTTAA
Found at i:28039962 original size:13 final size:15
Alignment explanation
Indices: 28039938--28039971 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
28039928 GTTAAAATGC
28039938 AATTTTTATTTTT-A
1 AATTTTTATTTTTGA
28039952 AATTTTT-TTTTTGA
1 AATTTTTATTTTTGA
28039966 AATTTT
1 AATTTT
28039972 GAAAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
AATTTTTATTTTTGA
Found at i:28040393 original size:54 final size:55
Alignment explanation
Indices: 28040208--28040425 Score: 306
Period size: 54 Copynumber: 4.1 Consensus size: 55
28040198 CACGTGAGCC
* *
28040208 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTG-AA
* *
28040263 AAGGATCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAG--A---AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTGAA
* * *
28040314 AAGGCTCAACTCACCTCTCGCAATATGAGATGGTTTTTGAAAAATAGAAATT-AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
28040368 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
28040423 AAG
1 AAG
28040426 TAGAAATTGA
Statistics
Matches: 146, Mismatches: 10, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
50 14 0.10
51 32 0.22
52 1 0.01
54 51 0.35
55 36 0.25
56 6 0.04
57 6 0.04
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (55 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
Found at i:28040404 original size:105 final size:104
Alignment explanation
Indices: 28040208--28040417 Score: 323
Period size: 106 Copynumber: 2.0 Consensus size: 104
28040198 CACGTGAGCC
* * *
28040208 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAACAGAATTTGCAAAAGGATCAAC
1 AAGGCTCAACTCACCTCTCGCAATATGAGATGATTTTTGAAAACAGAAATT-CAAAAGGATCAAC
*
28040273 TCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAGAAA
65 TCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAA
* * *
28040314 AAGGCTCAACTCACCTCTCGCAATATGAGATGGTTTTTGAAAAATAGAAATT-AAAAGGCTCAAC
1 AAGGCTCAACTCACCTCTCGCAATATGAGATGATTTTTG-AAAACAGAAATTCAAAAGGATCAAC
28040378 TCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA
65 TCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA
28040418 TTGAAAAGTA
Statistics
Matches: 96, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
104 16 0.17
105 34 0.35
106 36 0.38
107 10 0.10
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.29
Consensus pattern (104 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGATGATTTTTGAAAACAGAAATTCAAAAGGATCAACT
CACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA
Found at i:28040423 original size:14 final size:14
Alignment explanation
Indices: 28040404--28040438 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
28040394 GAGTTGATTT
28040404 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
**
28040418 TTGAAAAGTAGAAA
1 TTGAAAAACAGAAA
28040432 TTGAAAA
1 TTGAAAA
28040439 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.03, G:0.17, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:28040719 original size:15 final size:16
Alignment explanation
Indices: 28040686--28040719 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28040676 GTTGATTTTG
* *
28040686 AAAAGCATAGATTGAA
1 AAAAACATAAATTGAA
28040702 AAAAACATAAATTGAA
1 AAAAACATAAATTGAA
28040718 AA
1 AA
28040720 TACCTCAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.18
Consensus pattern (16 bp):
AAAAACATAAATTGAA
Found at i:28040761 original size:90 final size:87
Alignment explanation
Indices: 28040538--28040780 Score: 298
Period size: 85 Copynumber: 2.8 Consensus size: 87
28040528 AAAATAAAAT
* *
28040538 TTGAAAAGACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAGTTGA-TTTGAA
1 TTGAAAATACCTCAGC-TGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTGAA
*** *
28040602 AAGTAGAATTAGTGAAGCAGAAA
65 AAGTAGAATTAAAAAAACAGAAA
* *
28040625 TTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTGAA
1 TTGAAAATACCTCAGCTGTGGCC-TGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTGAA
*
28040688 AAGCATAG-ATTGAAAAAAACATAAA
65 AAG--TAGAATT-AAAAAAACAGAAA
28040713 TTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTG
1 TTGAAAATACCTCAGC-TGTG-GCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTGA-TTTTG
28040777 AAAA
63 AAAA
28040781 ACAAAAATTA
Statistics
Matches: 135, Mismatches: 11, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
84 3 0.02
85 33 0.24
86 9 0.07
87 18 0.13
88 27 0.20
90 33 0.24
91 9 0.07
92 3 0.02
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (87 bp):
TTGAAAATACCTCAGCTGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTGAAA
AGTAGAATTAAAAAAACAGAAA
Found at i:28041219 original size:191 final size:192
Alignment explanation
Indices: 28040738--28042116 Score: 2613
Period size: 192 Copynumber: 7.2 Consensus size: 192
28040728 CATGTGAGCC
** *
28040738 GAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGGCTTAACT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTGAAAAACAAAAATTAAAAGGCTTAACT
28040803 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
65 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
* **
28040868 AACTCATTTCTCGCAATATGAGTTGATTTTTTTTTAAAATTTAAAAATACCTCAACGTGTCTT
130 AACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
*
28040931 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGACTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
*
28040996 ACCTCTCGTAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
28041061 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
28041123 GAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
28041187 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
28041252 ACTCACTTCTCGCAATATGAGTTGA-TTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
28041313 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
28041378 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
**
28041443 ACTCACTTCTCGCAATATGAGTTGATTTTTTT-TTAAATTTAAAAATACCTCAACGTGTCTT
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
28041504 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
28041569 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
28041634 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
28041696 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
*
28041761 ATCTCTCGCAATATGAGTC-ATGTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
66 ACCTCTCGCAATATGAGTCAAT-TTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
28041825 AACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
130 AACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
28041888 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
28041953 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
28042018 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
28042080 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
28042117 CCTTGTAAAG
Statistics
Matches: 1165, Mismatches: 16, Indels: 11
0.98 0.01 0.01
Matches are distributed among these distances:
190 69 0.06
191 431 0.37
192 633 0.54
193 32 0.03
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (192 bp):
GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
Found at i:28041390 original size:122 final size:122
Alignment explanation
Indices: 28041245--28041471 Score: 305
Period size: 122 Copynumber: 1.9 Consensus size: 122
28041235 GCGTGCCCCG
* * * * **
28041245 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTAAA-A-AATTTAAAAATACCTCAACGT
1 AGGCTCAACTCACCTCTCGCAATATGAG-TCA-ATTTAAAACATAAACTAAAAATACCTCAACGT
* ** *
28041308 GTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
64 GCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
* **
28041367 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCAACGTGC
28041432 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT
66 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT
28041472 TTTTTAAATT
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
120 6 0.07
121 3 0.03
122 81 0.90
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.30
Consensus pattern (122 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCAACGTGC
CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
Found at i:28053951 original size:51 final size:49
Alignment explanation
Indices: 28053874--28054011 Score: 156
Period size: 51 Copynumber: 2.8 Consensus size: 49
28053864 GAGATTTTTT
* *
28053874 TTTTGAAAAC-ATGAAAATTTTCAAAACACCGAAATTTTTGAAACAA-GAGGA
1 TTTTGAAAACGA--AAAATTTTGAAAACA-CGAAATTTTTGAAACAAGGA-AA
*
28053925 TTTTGAAATACGAAAAATTTTGAAAACACGAAAATTTTTGAAACACGGAAA
1 TTTTGAAA-ACGAAAAATTTTGAAAACACG-AAATTTTTGAAACAAGGAAA
* *
28053976 TTTTGAAAACGAAAATTTTTG-AAACACAAAATTTTT
1 TTTTGAAAACGAAAAATTTTGAAAACACGAAATTTTT
28054012 AGAAGACACT
Statistics
Matches: 78, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
48 8 0.10
49 6 0.08
50 14 0.18
51 45 0.58
52 4 0.05
53 1 0.01
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.30
Consensus pattern (49 bp):
TTTTGAAAACGAAAAATTTTGAAAACACGAAATTTTTGAAACAAGGAAA
Found at i:28053952 original size:34 final size:34
Alignment explanation
Indices: 28053874--28054010 Score: 140
Period size: 34 Copynumber: 4.1 Consensus size: 34
28053864 GAGATTTTTT
* ** *
28053874 TTTTGAAAACATGAAAATTTTCAAAACACCGAAAT
1 TTTTGAAAACAAGAAAATTTTTGAAACA-CGAAAA
** *
28053909 TTTTG-AAACAAGAGGA-TTTTGAAATACGAAAAA
1 TTTTGAAAACAAGAAAATTTTTGAAACACG-AAAA
* *
28053942 TTTTGAAAACACGAAAATTTTTGAAACACGGAAA
1 TTTTGAAAACAAGAAAATTTTTGAAACACGAAAA
28053976 TTTTGAAAAC--GAAAATTTTTGAAACAC-AAAA
1 TTTTGAAAACAAGAAAATTTTTGAAACACGAAAA
28054007 TTTT
1 TTTT
28054011 TAGAAGACAC
Statistics
Matches: 86, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
31 7 0.08
32 19 0.22
33 15 0.17
34 29 0.34
35 16 0.19
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.30
Consensus pattern (34 bp):
TTTTGAAAACAAGAAAATTTTTGAAACACGAAAA
Found at i:28054006 original size:16 final size:17
Alignment explanation
Indices: 28053873--28054031 Score: 139
Period size: 16 Copynumber: 9.4 Consensus size: 17
28053863 CGAGATTTTT
*
28053873 TTTTTGAAAACATGAAAA
1 TTTTTG-AAACACGAAAA
**
28053891 TTTTCAAAACACCG-AAA
1 TTTTTGAAACA-CGAAAA
* **
28053908 TTTTTGAAACAAGAGGA
1 TTTTTGAAACACGAAAA
*
28053925 -TTTTGAAATACGAAAA
1 TTTTTGAAACACGAAAA
*
28053941 ATTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
*
28053959 TTTTTGAAACACGGAAA
1 TTTTTGAAACACGAAAA
28053976 -TTTTGAAA-ACGAAAA
1 TTTTTGAAACACGAAAA
28053991 TTTTTGAAACAC-AAAA
1 TTTTTGAAACACGAAAA
*
28054007 TTTTTAGAAGACACTAAAA
1 TTTTT-GAA-ACACGAAAA
*
28054026 ATTTTG
1 TTTTTG
28054032 GAAAATGGAT
Statistics
Matches: 115, Mismatches: 17, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
15 6 0.05
16 38 0.33
17 38 0.33
18 25 0.22
19 8 0.07
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.30
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:28054612 original size:7 final size:7
Alignment explanation
Indices: 28054600--28054648 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
28054590 TGAAACTCTT
28054600 TTTTTTC
1 TTTTTTC
28054607 TTTTTTC
1 TTTTTTC
*
28054614 -TTCTTC
1 TTTTTTC
28054620 TTTTTTC
1 TTTTTTC
*
28054627 TTTCTTC
1 TTTTTTC
*
28054634 TTTCTCTC
1 TTT-TTTC
28054642 TTTTTTC
1 TTTTTTC
28054649 CTGGCCTGCT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
6 5 0.15
7 24 0.71
8 5 0.15
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTTTC
Found at i:28054622 original size:13 final size:14
Alignment explanation
Indices: 28054604--28054636 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
28054594 ACTCTTTTTT
28054604 TTCTTTTTTC-TTC
1 TTCTTTTTTCTTTC
28054617 TTCTTTTTTCTTTC
1 TTCTTTTTTCTTTC
28054631 TTCTTT
1 TTCTTT
28054637 CTCTCTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TTCTTTTTTCTTTC
Found at i:28054631 original size:11 final size:11
Alignment explanation
Indices: 28054598--28054648 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
28054588 ATTGAAACTC
28054598 TTTTT-TTTCT
1 TTTTTCTTTCT
28054608 TTTTTCTTCTTCT
1 TTTTTC-T-TTCT
28054621 TTTTTCTTTCT
1 TTTTTCTTTCT
* *
28054632 TCTTTCTCTCT
1 TTTTTCTTTCT
28054643 TTTTTC
1 TTTTTC
28054649 CTGGCCTGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
10 5 0.14
11 18 0.51
12 2 0.06
13 10 0.29
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTCTTTCT
Found at i:28054645 original size:20 final size:20
Alignment explanation
Indices: 28054602--28054645 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
28054592 AAACTCTTTT
* *
28054602 TTTTCTTTTTTCTTCTTCTT
1 TTTTCTTTCTTCTTCTTCTC
28054622 TTTTCTTTCTTCTT-TCTCTC
1 TTTTCTTTCTTCTTCT-TCTC
28054642 TTTT
1 TTTT
28054646 TTCCTGGCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTCTTTCTTCTTCTTCTC
Found at i:28054773 original size:14 final size:15
Alignment explanation
Indices: 28054756--28054793 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
28054746 GGCTGTTTTT
28054756 CTTTTTTTTTGGGC-
1 CTTTTTTTTTGGGCG
*
28054770 CTTTTCTTTTGGGCTG
1 CTTTTTTTTTGGGC-G
28054786 CTTTTTTT
1 CTTTTTTT
28054794 GCTTTGGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 13 0.65
16 7 0.35
ACGTcount: A:0.00, C:0.16, G:0.18, T:0.66
Consensus pattern (15 bp):
CTTTTTTTTTGGGCG
Found at i:28054957 original size:3 final size:3
Alignment explanation
Indices: 28054951--28054982 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
28054941 CTTTTTTTCT
28054951 TTC TTC TTC TTTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC T
28054983 CCTCCTACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:28054976 original size:22 final size:22
Alignment explanation
Indices: 28054938--28054982 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
28054928 TGTTAAATTT
*
28054938 TTTCTTTTTTTCTTTCTTCTTC
1 TTTCTTTTCTTCTTTCTTCTTC
28054960 TTTCTTCTTCTTC-TTCTTCTTC
1 TTTCTT-TTCTTCTTTCTTCTTC
28054982 T
1 T
28054983 CCTCCTACAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTCTTTTCTTCTTTCTTCTTC
Found at i:28055386 original size:30 final size:29
Alignment explanation
Indices: 28055346--28055447 Score: 116
Period size: 30 Copynumber: 3.4 Consensus size: 29
28055336 AATTAGGATT
*
28055346 AAAATGAAATTTAATGAAAGTTTAGGAGTC
1 AAAATGAAATTTAAAGAAAGTTTAGG-GTC
* *
28055376 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTT-AGGGTC
*
28055406 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTA-GGGTC
*
28055436 AAAATGCAATTT
1 AAAATGAAATTT
28055448 TTATTTTTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
29 3 0.05
30 56 0.90
31 3 0.05
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (29 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGTC
Found at i:28055468 original size:14 final size:15
Alignment explanation
Indices: 28055443--28055477 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
28055433 GTCAAAATGC
*
28055443 AATTTTTATTTTTTA
1 AATTTTTATTTTTGA
28055458 AATTTTT-TTTTTGA
1 AATTTTTATTTTTGA
28055472 AATTTT
1 AATTTT
28055478 GAAAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
AATTTTTATTTTTGA
Found at i:28055776 original size:21 final size:21
Alignment explanation
Indices: 28055752--28055800 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
28055742 CTGTTGAATT
28055752 GATTCTTTTTTTGTTCAAATC
1 GATTCTTTTTTTGTTCAAATC
* *
28055773 GATTC-ATTTTTGTTTAAATC
1 GATTCTTTTTTTGTTCAAATC
*
28055793 AATTCTTT
1 GATTCTTT
28055801 GTTGTTTAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.22, C:0.12, G:0.08, T:0.57
Consensus pattern (21 bp):
GATTCTTTTTTTGTTCAAATC
Found at i:28055782 original size:20 final size:19
Alignment explanation
Indices: 28055759--28055816 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
28055749 ATTGATTCTT
*
28055759 TTTTTGTTCAAATCGATTC
1 TTTTTGTTCAAATCAATTC
*
28055778 ATTTTTGTTTAAATCAATTC
1 -TTTTTGTTCAAATCAATTC
* *
28055798 TTTGTTGTTTAACTCAATT
1 TTT-TTGTTCAAATCAATT
28055817 TAAACTCCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 3 0.09
20 31 0.91
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTTGTTCAAATCAATTC
Found at i:28056519 original size:18 final size:17
Alignment explanation
Indices: 28056486--28056533 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
28056476 ATATTTAAAA
28056486 AATTTAG-AAAAAATAT
1 AATTTAGAAAAAAATAT
28056502 AATTTAGAAAAAACATAT
1 AATTTAGAAAAAA-ATAT
* *
28056520 AAATTATAAAAAAA
1 AATTTAGAAAAAAA
28056534 ATTATAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 7 0.25
17 6 0.21
18 15 0.54
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (17 bp):
AATTTAGAAAAAAATAT
Found at i:28056539 original size:19 final size:18
Alignment explanation
Indices: 28056493--28056540 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
28056483 AAAAATTTAG
*
28056493 AAAAAATATAATTTAGAA
1 AAAAAATATAAATTAGAA
* *
28056511 AAAACATATAAATTATAA
1 AAAAAATATAAATTAGAA
28056529 AAAAAATTATAA
1 AAAAAA-TATAA
28056541 GAATAAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (18 bp):
AAAAAATATAAATTAGAA
Found at i:28059456 original size:26 final size:26
Alignment explanation
Indices: 28059434--28059488 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
28059424 TTTTTATGTG
28059434 TTAAAATATA-TATATTAAATTATTA
1 TTAAAATATAGTATATTAAATTATTA
* * *
28059459 TTATATTATAGTATATTATATTATATA
1 TTAAAATATAGTATATTAAATTAT-TA
28059486 TTA
1 TTA
28059489 TATTATATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 8 0.32
26 12 0.48
27 5 0.20
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
TTAAAATATAGTATATTAAATTATTA
Found at i:28059465 original size:5 final size:5
Alignment explanation
Indices: 28059439--28059496 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
28059429 ATGTGTTAAA
* *
28059439 ATATAT ATATT AAATT ATTATT ATATT ATAGT ATATT ATATTAT ATATT
1 ATAT-T ATATT ATATT A-TATT ATATT ATATT ATATT ATA-T-T ATATT
28059488 ATATT ATAT
1 ATATT ATAT
28059497 AAATAAGTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
5 31 0.69
6 10 0.22
7 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (5 bp):
ATATT
Found at i:28059475 original size:10 final size:9
Alignment explanation
Indices: 28059440--28059497 Score: 61
Period size: 8 Copynumber: 6.7 Consensus size: 9
28059430 TGTGTTAAAA
28059440 TATATATAT
1 TATATATAT
*
28059449 TAAAT-TAT
1 TATATATAT
28059457 TAT-TATAT
1 TATATATAT
28059465 TATAGTATAT
1 TATA-TATAT
28059475 TATAT-TA-
1 TATATATAT
28059482 TATATTATAT
1 TATA-TATAT
28059492 TATATA
1 TATATA
28059498 AATAAGTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
7 5 0.12
8 14 0.34
9 9 0.22
10 13 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (9 bp):
TATATATAT
Found at i:28059487 original size:12 final size:12
Alignment explanation
Indices: 28059442--28059497 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
28059432 TGTTAAAATA
*
28059442 TATATATTAAAT
1 TATATATTATAT
28059454 TAT-TATTATATT
1 TATATATTATA-T
28059466 ATAGTATATTATAT
1 -TA-TATATTATAT
28059480 TATATATTATAT
1 TATATATTATAT
28059492 TATATA
1 TATATA
28059498 AATAAGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.15
12 20 0.51
13 4 0.10
14 2 0.05
15 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:28060833 original size:18 final size:19
Alignment explanation
Indices: 28060810--28060848 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
28060800 ATATATAGAT
28060810 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
28060828 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
28060847 AT
1 AT
28060849 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:28061366 original size:18 final size:19
Alignment explanation
Indices: 28061345--28061385 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
28061335 AATGAAATGA
28061345 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
28061363 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
28061382 GAAA
1 GAAA
28061386 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:28065658 original size:51 final size:50
Alignment explanation
Indices: 28065499--28065655 Score: 251
Period size: 51 Copynumber: 3.1 Consensus size: 50
28065489 ACTTCTGATC
* *
28065499 AGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATA
1 AGTGACAAGTGATAAGTGGTAG-CTTAGCTACACTTATCTGATCAGTGACA
* *
28065550 AGTGACAAATGATAAGTGGTAGCTTAGCTACTCTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
*
28065600 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAGTGACA
28065651 AGTGA
1 AGTGA
28065656 TAAATGTGAT
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
50 46 0.47
51 52 0.53
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (50 bp):
AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
Found at i:28076967 original size:43 final size:41
Alignment explanation
Indices: 28076918--28077002 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 41
28076908 TTATTGTATG
28076918 ATATTATA-TGA-AATAATGAAAATATTATTTATTATTTATTATT
1 ATATTATATTGACAAT--TGAAAA-ATTATTTATT-TTTATTATT
* *
28076961 ATATTATATTGACAATTGAAAAATTTTTTATTTTTGTTATT
1 ATATTATATTGACAATTGAAAAATTATTTATTTTTATTATT
28077002 A
1 A
28077003 AATTTATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
41 9 0.24
42 9 0.24
43 14 0.37
44 3 0.08
45 3 0.08
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.53
Consensus pattern (41 bp):
ATATTATATTGACAATTGAAAAATTATTTATTTTTATTATT
Found at i:28082798 original size:37 final size:39
Alignment explanation
Indices: 28082733--28082917 Score: 98
Period size: 38 Copynumber: 4.7 Consensus size: 39
28082723 TTATAGTATC
* * *
28082733 ATATATTATG-ATTTGAGTAAATTCATATAAGAATAT-TG
1 ATATATTAAGAATTTTATTAAATT-ATATAAGAATATATG
** *
28082771 AT-TATTAAGAATTTTATTAAATTATATATTTTAAT-TATA
1 ATATATTAAGAATTTTATTAAATTATATA--AGAATATATG
* * * *** *
28082810 ATATATTTAATAATAATTATGTTAATT-TATATTTATAGTATC
1 ATATA-TTAAGAAT-TTTAT-TAAATTATATAAGAATA-TATG
* * *
28082852 ATATATTATG-ATTTGAGTAAATTCATATAAGAATAT-TG
1 ATATATTAAGAATTTTATTAAATT-ATATAAGAATATATG
28082890 AT-TATTAAGAATTTTATTAAATTATATA
1 ATATATTAAGAATTTTATTAAATTATATA
28082918 TTTTAATTAT
Statistics
Matches: 110, Mismatches: 24, Indels: 27
0.68 0.15 0.17
Matches are distributed among these distances:
37 22 0.20
38 33 0.30
39 9 0.08
40 15 0.14
41 10 0.09
42 16 0.15
43 5 0.05
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.48
Consensus pattern (39 bp):
ATATATTAAGAATTTTATTAAATTATATAAGAATATATG
Found at i:28082820 original size:15 final size:15
Alignment explanation
Indices: 28082785--28082836 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
28082775 TTAAGAATTT
*
28082785 TATTAAATTAT-ATA
1 TATTTAATTATAATA
28082799 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
28082813 TATTTAATAATAAT-
1 TATTTAATTATAATA
28082827 TATGTTAATT
1 TAT-TTAATT
28082837 TATATTTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:28082934 original size:16 final size:16
Alignment explanation
Indices: 28082913--28082954 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
28082903 TTATTAAATT
*
28082913 ATATATTTTAATTATA
1 ATATATTTTAATAATA
28082929 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
28082944 AT-TATGTTTAA
1 ATATAT-TTTAA
28082955 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:28082934 original size:119 final size:119
Alignment explanation
Indices: 28082723--28082951 Score: 458
Period size: 119 Copynumber: 1.9 Consensus size: 119
28082713 TTTGAGTAAA
28082723 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
1 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
28082788 TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATAT
66 TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATAT
28082842 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
1 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
28082907 TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
66 TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
28082952 TAAATATGAT
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
119 110 1.00
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (119 bp):
TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATAT
Found at i:28082939 original size:15 final size:15
Alignment explanation
Indices: 28082904--28082945 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28082894 TTAAGAATTT
*
28082904 TATTAAATTAT-ATA
1 TATTTAATTATAATA
28082918 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
28082932 TATTTAATAATAAT
1 TATTTAATTATAAT
28082946 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:28083213 original size:16 final size:16
Alignment explanation
Indices: 28083189--28083245 Score: 105
Period size: 16 Copynumber: 3.6 Consensus size: 16
28083179 ATTCCAATAT
28083189 TCCAATACACCTCTAA
1 TCCAATACACCTCTAA
*
28083205 TCCATTACACCTCTAA
1 TCCAATACACCTCTAA
28083221 TCCAATACACCTCTAA
1 TCCAATACACCTCTAA
28083237 TCCAATACA
1 TCCAATACA
28083246 GCGAACCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.26
Consensus pattern (16 bp):
TCCAATACACCTCTAA
Found at i:28096226 original size:27 final size:27
Alignment explanation
Indices: 28096186--28096326 Score: 171
Period size: 27 Copynumber: 5.2 Consensus size: 27
28096176 AGGAAGCGTC
*
28096186 CTGGTGGCTATGCCACAAATATCTGAT
1 CTGGTGGCTCTGCCACAAATATCTGAT
*
28096213 CTGGTGGCTCTGCCACATATATCTG-T
1 CTGGTGGCTCTGCCACAAATATCTGAT
* *
28096239 CCTGGTGGCTATGCCACAATTATCTGAT
1 -CTGGTGGCTCTGCCACAAATATCTGAT
*
28096267 CTGGTGGCTCTGCCACATAA-ATCTGTT
1 CTGGTGGCTCTGCCACA-AATATCTGAT
* *
28096294 TTGGTGGCTCCGCCAC-AATATCTGTAT
1 CTGGTGGCTCTGCCACAAATATCTG-AT
28096321 CTGGTG
1 CTGGTG
28096327 ACTTCGTCAC
Statistics
Matches: 97, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
25 2 0.02
26 6 0.06
27 87 0.90
28 2 0.02
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.33
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAAATATCTGAT
Found at i:28096265 original size:54 final size:53
Alignment explanation
Indices: 28096183--28096326 Score: 216
Period size: 54 Copynumber: 2.7 Consensus size: 53
28096173 TGGAGGAAGC
*
28096183 GTCCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCAC-AATATCTGATCTGGTGGCTCTGCCACATAAATCT
28096237 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATAAATCT
1 GTCCTGGTGGCTATGCCACAA-TATCTGATCTGGTGGCTCTGCCACATAAATCT
** **
28096291 GTTTTGGTGGCTCCGCCACAATATCTGTATCTGGTG
1 GTCCTGGTGGCTATGCCACAATATCTG-ATCTGGTG
28096327 ACTTCGTCAC
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
53 8 0.10
54 75 0.90
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.33
Consensus pattern (53 bp):
GTCCTGGTGGCTATGCCACAATATCTGATCTGGTGGCTCTGCCACATAAATCT
Found at i:28096338 original size:81 final size:80
Alignment explanation
Indices: 28096186--28096344 Score: 198
Period size: 81 Copynumber: 2.0 Consensus size: 80
28096176 AGGAAGCGTC
* *
28096186 CTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCTGTCCTGGTGGCTAT
1 CTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCCGCCACATATATCTGTCCTGGTGACTAT
28096251 GCCACAATTATCTGAT
66 GCCACAA-TATCTGAT
* * * *
28096267 CTGGTGGCTCTGCCACATAA-ATCTGTTTTGGTGGCTCCGCCACA-ATATCTGTATCTGGTGACT
1 CTGGTGGCTATGCCACA-AATATCTGATCTGGTGGCTCCGCCACATATATCTGT-CCTGGTGACT
*
28096330 -TCGTCACAATATCTG
64 AT-GCCACAATATCTG
28096345 GCAGCCTCGC
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
80 15 0.22
81 51 0.75
82 2 0.03
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.33
Consensus pattern (80 bp):
CTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCCGCCACATATATCTGTCCTGGTGACTAT
GCCACAATATCTGAT
Found at i:28100293 original size:19 final size:19
Alignment explanation
Indices: 28100257--28100293 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28100247 GTATGCCATT
**
28100257 TTTTAAATACATTTTTTTA
1 TTTTAAATACATAATTTTA
28100276 TTTTAAATACATAATTTT
1 TTTTAAATACATAATTTT
28100294 CTCAAACGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTAAATACATAATTTTA
Found at i:28101627 original size:16 final size:15
Alignment explanation
Indices: 28101601--28101635 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
28101591 TGATGTGAAT
28101601 AATATAAAATATTAA
1 AATATAAAATATTAA
*
28101616 AATATCAAAATATTAG
1 AATAT-AAAATATTAA
28101632 AATA
1 AATA
28101636 ATAATTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATATAAAATATTAA
Found at i:28101819 original size:20 final size:21
Alignment explanation
Indices: 28101777--28101819 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
28101767 CTTTTTTTAG
* *
28101777 AATAATAATTAAATATACGAA
1 AATAATAATTAAATACACAAA
*
28101798 AATAAT-ATTATATACACAAA
1 AATAATAATTAAATACACAAA
28101818 AA
1 AA
28101820 GGTATATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (21 bp):
AATAATAATTAAATACACAAA
Found at i:28102517 original size:12 final size:12
Alignment explanation
Indices: 28102470--28102521 Score: 50
Period size: 12 Copynumber: 4.0 Consensus size: 12
28102460 GGAAAAGGTA
*
28102470 ATTTTTTTTTAT
1 ATTTTTTATTAT
*
28102482 ATTTGTTTTGTATAT
1 A-TT-TTTTAT-TAT
28102497 ATATTTTTATTAT
1 AT-TTTTTATTAT
28102510 ATTTTTTATTAT
1 ATTTTTTATTAT
28102522 GATGTATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
12 11 0.32
13 7 0.21
14 11 0.32
15 5 0.15
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (12 bp):
ATTTTTTATTAT
Found at i:28102872 original size:22 final size:23
Alignment explanation
Indices: 28102844--28102894 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 23
28102834 TAGGTTTTTC
*
28102844 TTTTCTTTTTT-TGGGTTAGGTT
1 TTTTCTTTTTTGGGGGTTAGGTT
28102866 TTTTCTTTTTTGGGGGGGTTAGGTT
1 TTTTCTTTTTT--GGGGGTTAGGTT
28102891 TTTT
1 TTTT
28102895 TTGGGGGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 11 0.44
25 14 0.56
ACGTcount: A:0.04, C:0.04, G:0.27, T:0.65
Consensus pattern (23 bp):
TTTTCTTTTTTGGGGGTTAGGTT
Found at i:28102893 original size:26 final size:26
Alignment explanation
Indices: 28102820--28102895 Score: 88
Period size: 26 Copynumber: 3.0 Consensus size: 26
28102810 GTTTCTTGGT
28102820 TTTTTTGGGGGGGTTAGGTTTTTCTTTTC
1 TTTTTTGGGGGGGTTAGG--TTT-TTTTC
*
28102849 TTTTTT---TGGGTTAGG-TTTTTTC
1 TTTTTTGGGGGGGTTAGGTTTTTTTC
28102871 TTTTTTGGGGGGGTTAGGTTTTTTT
1 TTTTTTGGGGGGGTTAGGTTTTTTT
28102896 TGGGGGAGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
22 11 0.27
23 2 0.05
25 8 0.20
26 14 0.34
29 6 0.15
ACGTcount: A:0.04, C:0.04, G:0.30, T:0.62
Consensus pattern (26 bp):
TTTTTTGGGGGGGTTAGGTTTTTTTC
Found at i:28104009 original size:147 final size:147
Alignment explanation
Indices: 28103749--28104167 Score: 639
Period size: 147 Copynumber: 2.9 Consensus size: 147
28103739 CATGTGTGAT
*
28103749 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTG-AAAACAGAAATTGAAATTACC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAATTACC
* *
28103812 TCAGCGTGTCTCGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGA
66 TCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGA
*
28103877 AATTACCTCAGTGTGTC
131 AATTACCTCAGCGTGTC
* * *
28103894 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAAAAATTTAAAATACC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAATTACC
* ** * *
28103959 TCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATACGAGTTGAATTTTGAAAACAGAAATTGA
66 TCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGA
28104024 AATTACCTCAGCGTGTC
131 AATTACCTCAGCGTGTC
** *
28104041 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTT-AACAACAGAAATTGAAATTACC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAATTACC
* *
28104105 TCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAGTATGAGTTGATTTTTTTG-AAACAGAAAT
66 TCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAACAGAAAT
28104168 AAAAACATCA
Statistics
Matches: 245, Mismatches: 25, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
145 34 0.14
146 64 0.26
147 142 0.58
148 5 0.02
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Consensus pattern (147 bp):
CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAATTACC
TCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGA
AATTACCTCAGCGTGTC
Found at i:28104118 original size:74 final size:73
Alignment explanation
Indices: 28103749--28104167 Score: 621
Period size: 72 Copynumber: 5.7 Consensus size: 73
28103739 CATGTGTGAT
*
28103749 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAATTACCTC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAATTACCTC
28103814 AGCGTGT-
66 AGCGTGTC
*
28103821 CTCGAGGCTTAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAACAGAAATTGAAATTACCT
1 CT-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAATTACCT
*
28103885 CAGTGTGTC
65 CAGCGTGTC
* * *
28103894 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAAAAATTTAAAATACC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTG-AAAACAGAAATTGAAATTACC
*
28103959 TCAGCATGTC
64 TCAGCGTGTC
* ** * *
28103969 TTGAGGCTCAACTCATTTCTCGCAATACGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAATTACCTC
28104033 AGCGTGTC
66 AGCGTGTC
** *
28104041 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTAACAACAGAAATTGAAATTACCT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAA-AACAGAAATTGAAATTACCT
28104106 CAGCGTGTC
65 CAGCGTGTC
*
28104115 CTGAGGCTCAACTCACCTCTCGCAGTATGAGTTGATTTTTTTG-AAACAGAAAT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAACAGAAAT
28104168 AAAAACATCA
Statistics
Matches: 313, Mismatches: 26, Indels: 15
0.88 0.07 0.04
Matches are distributed among these distances:
72 129 0.41
73 53 0.17
74 68 0.22
75 63 0.20
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Consensus pattern (73 bp):
CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAATTACCTC
AGCGTGTC
Found at i:28115018 original size:72 final size:74
Alignment explanation
Indices: 28114744--28115044 Score: 325
Period size: 72 Copynumber: 4.3 Consensus size: 74
28114734 NNNNNNNNNN
*
28114744 TCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAATTACCTCAGTGTGT-CTGAGGCTCA
1 TCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCA
28114808 ACTCA-CTC
66 ACTCATCTC
* * *
28114816 TCGCAATATGAGTTGATTTTTTTTGAAAAACAAAAATTTTAAA--ACCTCAGC-T-TCTTGA-GC
1 TCGCAATATGAGTTGA--TTTTTTGAAAAACAGAAA-TTGAAATTACCTCAGCGTGTCCTGAGGC
*
28114876 -C-ACTCATTTC
63 TCAACTCATCTC
* *
28114886 TCGC-ATACGAGTTGA-ATTTTG-AAAA-AGAAATTGAAATTA-CTCAGCGTGTCCTGAGGCTCA
1 TCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCA
*
28114946 ACTCATTTC
66 ACTCATCTC
* *
28114955 TCGCAATA-GAG-TGATTTTTTTAACAACAGAAATTTGAAATTACCTCAGCGTGTCCTGA-GCTC
1 TCGCAATATGAGTTGATTTTTTGAAAAACAGAAA-TTGAAATTACCTCAGCGTGTCCTGAGGCTC
*
28115017 AA-TCACCTC
65 AACTCATCTC
*
28115026 TCGCAGTATGAG-TGATTTT
1 TCGCAATATGAGTTGATTTT
28115045 GAAACTAGAA
Statistics
Matches: 194, Mismatches: 16, Indels: 38
0.78 0.06 0.15
Matches are distributed among these distances:
63 5 0.03
64 10 0.05
65 6 0.03
66 10 0.05
67 2 0.01
68 4 0.02
69 35 0.18
70 13 0.07
71 20 0.10
72 45 0.23
73 22 0.11
74 17 0.09
75 5 0.03
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (74 bp):
TCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCA
ACTCATCTC
Found at i:28115828 original size:13 final size:13
Alignment explanation
Indices: 28115810--28115834 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28115800 GGGTTTCGCC
28115810 TTGATCCCTTTTT
1 TTGATCCCTTTTT
28115823 TTGATCCCTTTT
1 TTGATCCCTTTT
28115835 GGGTTTTCAT
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:0.08, C:0.24, G:0.08, T:0.60
Consensus pattern (13 bp):
TTGATCCCTTTTT
Found at i:28126880 original size:16 final size:15
Alignment explanation
Indices: 28126854--28126888 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
28126844 TGATGTGAAT
28126854 AATATAAAATATTAA
1 AATATAAAATATTAA
*
28126869 AATATCAAAATATTAG
1 AATAT-AAAATATTAA
28126885 AATA
1 AATA
28126889 ATAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATATAAAATATTAA
Found at i:28127073 original size:20 final size:21
Alignment explanation
Indices: 28127031--28127073 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
28127021 CTTTTTTTAG
* *
28127031 AATAATAATTAAATATACGAA
1 AATAATAATTAAATACACAAA
*
28127052 AATAAT-ATTATATACACAAA
1 AATAATAATTAAATACACAAA
28127072 AA
1 AA
28127074 GGTATATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (21 bp):
AATAATAATTAAATACACAAA
Found at i:28127766 original size:11 final size:12
Alignment explanation
Indices: 28127725--28127775 Score: 50
Period size: 12 Copynumber: 4.0 Consensus size: 12
28127715 GAAAAGGTAA
28127725 ATTTTTT-TTAT
1 ATTTTTTATTAT
*
28127736 ATTTGTTTTGTATAT
1 A-TT-TTTTAT-TAT
28127751 ATATTTTTATTAT
1 AT-TTTTTATTAT
28127764 ATTTTTTATTAT
1 ATTTTTTATTAT
28127776 GATGTATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
11 1 0.03
12 12 0.35
13 9 0.26
14 7 0.21
15 5 0.15
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.73
Consensus pattern (12 bp):
ATTTTTTATTAT
Found at i:28128105 original size:23 final size:21
Alignment explanation
Indices: 28128073--28128142 Score: 94
Period size: 17 Copynumber: 3.5 Consensus size: 21
28128063 GGTTTCTTGG
*
28128073 TTTTTTTTTTTGGGTTAGGTT
1 TTTTTTTTTTTTGGTTAGGTT
28128094 TTTCTTTTTTTTTGGTTAGG--
1 TTT-TTTTTTTTTGGTTAGGTT
28128114 --TTTTTTTTTTGGTTAGGTT
1 TTTTTTTTTTTTGGTTAGGTT
28128133 TTTTTTTTTT
1 TTTTTTTTTT
28128143 GGGAGGGCTT
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
17 16 0.37
18 1 0.02
21 11 0.26
22 15 0.35
ACGTcount: A:0.04, C:0.01, G:0.19, T:0.76
Consensus pattern (21 bp):
TTTTTTTTTTTTGGTTAGGTT
Found at i:28130159 original size:20 final size:20
Alignment explanation
Indices: 28130120--28130159 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
28130110 CACGTGACAA
*
28130120 AAAAATAAAAATTATATTTT
1 AAAAATAAAAATTAAATTTT
28130140 AAAAA-AAAAATTAAACTTTT
1 AAAAATAAAAATTAAA-TTTT
28130160 TCTACCACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAATAAAAATTAAATTTT
Found at i:28134508 original size:140 final size:140
Alignment explanation
Indices: 28134256--28134536 Score: 562
Period size: 140 Copynumber: 2.0 Consensus size: 140
28134246 TGTCAAATGG
28134256 AACTCAAACTTCATGTACAACCACATAAACTGTTTAAGGCACGAATATAAATTGAAAACAAATTT
1 AACTCAAACTTCATGTACAACCACATAAACTGTTTAAGGCACGAATATAAATTGAAAACAAATTT
28134321 GGAAAATTTCGTTACCTTATTCTCCAAAACAGATTTGGACAAATTCGAGGATTTTACACAAGGTA
66 GGAAAATTTCGTTACCTTATTCTCCAAAACAGATTTGGACAAATTCGAGGATTTTACACAAGGTA
28134386 AATCAAGAGA
131 AATCAAGAGA
28134396 AACTCAAACTTCATGTACAACCACATAAACTGTTTAAGGCACGAATATAAATTGAAAACAAATTT
1 AACTCAAACTTCATGTACAACCACATAAACTGTTTAAGGCACGAATATAAATTGAAAACAAATTT
28134461 GGAAAATTTCGTTACCTTATTCTCCAAAACAGATTTGGACAAATTCGAGGATTTTACACAAGGTA
66 GGAAAATTTCGTTACCTTATTCTCCAAAACAGATTTGGACAAATTCGAGGATTTTACACAAGGTA
28134526 AATCAAGAGA
131 AATCAAGAGA
28134536 A
1 A
28134537 TAACAAATCA
Statistics
Matches: 141, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
140 141 1.00
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (140 bp):
AACTCAAACTTCATGTACAACCACATAAACTGTTTAAGGCACGAATATAAATTGAAAACAAATTT
GGAAAATTTCGTTACCTTATTCTCCAAAACAGATTTGGACAAATTCGAGGATTTTACACAAGGTA
AATCAAGAGA
Found at i:28134941 original size:23 final size:22
Alignment explanation
Indices: 28134889--28134941 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
28134879 TCCACATCTT
*
28134889 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
28134911 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
28134934 TTTCTTTT
1 TTTCTTTT
28134942 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:28143900 original size:12 final size:12
Alignment explanation
Indices: 28143883--28143907 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28143873 AGTTCGATTA
28143883 AAAAAATATTTT
1 AAAAAATATTTT
28143895 AAAAAATATTTT
1 AAAAAATATTTT
28143907 A
1 A
28143908 TTTTACTGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAAAATATTTT
Found at i:28144250 original size:19 final size:18
Alignment explanation
Indices: 28144206--28144256 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 18
28144196 AAAATTTAAA
28144206 ATATA-TTTTATTTTTTT
1 ATATATTTTTATTTTTTT
28144223 ATATATTTTTATTTTTTT
1 ATATATTTTTATTTTTTT
28144241 A-ATGATTTTTAATTTT
1 ATAT-ATTTTT-ATTTT
28144257 AAATTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.23
18 19 0.61
19 5 0.16
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (18 bp):
ATATATTTTTATTTTTTT
Found at i:28144665 original size:26 final size:28
Alignment explanation
Indices: 28144626--28144683 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
28144616 TTGGATAAAC
**
28144626 AATTGAAAAGGTAAAATTAAAGA-TGGA
1 AATTGAAAAGGTAAAAACAAAGATTGGA
*
28144653 AATTGAAGA-GTAAAAACAAAGATTGGA
1 AATTGAAAAGGTAAAAACAAAGATTGGA
28144680 AATT
1 AATT
28144684 AGAATTAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.55, C:0.02, G:0.21, T:0.22
Consensus pattern (28 bp):
AATTGAAAAGGTAAAAACAAAGATTGGA
Found at i:28148231 original size:42 final size:45
Alignment explanation
Indices: 28148168--28148332 Score: 135
Period size: 49 Copynumber: 3.6 Consensus size: 45
28148158 CTTCGTTTTC
** *
28148168 TCGATGCCATAGTTCAACTATGGTCTTACACAT-C-T-TCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATACATATCACAT-A
*
28148211 T-GATGCCATAGCCCAGCTATGGTCTTACATGTAATCACATATCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACA---CAT-ACATATCACATA
* *
28148259 TCGATGCCATAGCCCAGCTATGGTCTTACACGGATCACATATCTCA-C
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC--AT-ACATATCACATA
* * *
28148306 T-GATGCCATATCACAGATATGGTCTTA
1 TCGATGCCATAGCCCAGCTATGGTCTTA
28148333 TATATATCAC
Statistics
Matches: 102, Mismatches: 10, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
42 25 0.25
43 1 0.01
45 2 0.02
46 23 0.23
47 2 0.02
48 15 0.15
49 34 0.33
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (45 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATACATATCACATA
Found at i:28148269 original size:49 final size:47
Alignment explanation
Indices: 28148203--28148332 Score: 163
Period size: 49 Copynumber: 2.7 Consensus size: 47
28148193 TTACACATCT
*
28148203 TCACATAATGATGCCATAGCCCAGCTATGGTCTTACATGTAATCACATA
1 TCACAT-ATGATGCCATAGCCCAGCTATGGTCTTACACG-AATCACATA
*
28148252 TCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGGATCACATA
1 TCACATAT-GATGCCATAGCCCAGCTATGGTCTTACACGAATCACATA
* * * * *
28148300 TCTCA-CTGATGCCATATCACAGATATGGTCTTA
1 TCACATATGATGCCATAGCCCAGCTATGGTCTTA
28148333 TATATATCAC
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
46 23 0.32
47 1 0.01
48 14 0.19
49 35 0.48
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (47 bp):
TCACATATGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATA
Found at i:28148428 original size:31 final size:31
Alignment explanation
Indices: 28148393--28148510 Score: 184
Period size: 31 Copynumber: 3.8 Consensus size: 31
28148383 CTTGTCACTT
*
28148393 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
28148424 GTAGCCGGTA-CTACCACTTTTCACTGATCAG
1 GTAGCC-GAAGCTACCACTTTTCACTGATCAG
*
28148455 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
28148486 GTAGCTGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
28148511 TGTCATTTGT
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
30 2 0.03
31 76 0.95
32 2 0.03
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:28148596 original size:50 final size:51
Alignment explanation
Indices: 28148486--28148614 Score: 190
Period size: 50 Copynumber: 2.5 Consensus size: 51
28148476 CACTGATCAG
* * *
28148486 GTAGCTGAAGCTACCACTTTTCACTTGTCATTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
*
28148537 GTAGCCGAAGCTATCACTTATCACTT-TCACTTTTTC-TTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCA-TTTGTCATTGATCAGATAAGT
*
28148587 GTAGTCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
28148615 TGCCATGGTC
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
50 42 0.59
51 29 0.41
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
Found at i:28152322 original size:19 final size:19
Alignment explanation
Indices: 28152284--28152343 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
28152274 ATCAAATTTG
*
28152284 TTAATTATGATTAAAATTAAT
1 TTAATTAAGATT--AATTAAT
* *
28152305 TTAATTAAGTTTAATTAAG
1 TTAATTAAGATTAATTAAT
* *
28152324 CTAATTAGGATTAATTAAT
1 TTAATTAAGATTAATTAAT
28152343 T
1 T
28152344 ACTAAACTTA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
19 21 0.68
21 10 0.32
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (19 bp):
TTAATTAAGATTAATTAAT
Found at i:28153112 original size:23 final size:22
Alignment explanation
Indices: 28153059--28153113 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 22
28153049 AGTTCATATG
* * *
28153059 GTATGATTGTATTTGAATTTTT
1 GTATGTTTGAATTTGAATTTGT
* *
28153081 ATATATTTGAATTATGAATTTGT
1 GTATGTTTGAATT-TGAATTTGT
28153104 GTATGTTTGA
1 GTATGTTTGA
28153114 CAGTAATTTG
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.55
Consensus pattern (22 bp):
GTATGTTTGAATTTGAATTTGT
Found at i:28153190 original size:12 final size:12
Alignment explanation
Indices: 28153168--28153197 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
28153158 GAATTAAATC
28153168 ATAAA-TAATTG
1 ATAAATTAATTG
28153179 ATAAATTAATTG
1 ATAAATTAATTG
28153191 ATAAATT
1 ATAAATT
28153198 GAATATCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (12 bp):
ATAAATTAATTG
Found at i:28158469 original size:20 final size:20
Alignment explanation
Indices: 28158440--28158484 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
28158430 AGCACATATA
* *
28158440 TTCATAAAATTTTAGAATTT
1 TTCATAAAATTTTACAACTT
*
28158460 TTCATCAAATTTTACAACTT
1 TTCATAAAATTTTACAACTT
28158480 TTCAT
1 TTCAT
28158485 TTTAGTCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (20 bp):
TTCATAAAATTTTACAACTT
Found at i:28161416 original size:43 final size:43
Alignment explanation
Indices: 28161296--28161453 Score: 155
Period size: 43 Copynumber: 3.7 Consensus size: 43
28161286 AGCTTGTACA
* * * *
28161296 ATGCCAATGTCCCAGATGTGGGCTTACATGT-AATCAAATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAATCAAATA-CG
* *
28161339 ATGCC-ACTATCCCAGACAG-GGTCTTACATG-AAATCAAATACG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAAATCAAATACG
*
28161381 ATGCCAACGTCCCAGACGTGGTATTACACGTAAATCATAAGT-CG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAATCA-AA-TACG
* *
28161425 ATGCCAACGCCCCAGACATGGTCTTACAC
1 ATGCCAACGTCCCAGACGTGGTCTTACAC
28161454 AAAAACACAT
Statistics
Matches: 97, Mismatches: 10, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
41 1 0.01
42 25 0.26
43 39 0.40
44 31 0.32
45 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAATCAAATACG
Found at i:28164424 original size:43 final size:43
Alignment explanation
Indices: 28164310--28164430 Score: 154
Period size: 43 Copynumber: 2.8 Consensus size: 43
28164300 TATCATATTG
*** * *
28164310 ATGCCAATGTCCCAGACATGGTCTTACACAAAATCATATAACG
1 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCAAATAACA
* *
28164353 ATGCCAATGTCCTAGACATGATCTTACATGTAATCACAATAA-A
1 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCA-AATAACA
*
28164396 ATGCCAATGTCCCAAACATGGTCTTACATGTAATC
1 ATGCCAATGTCCCAGACATGGTCTTACATGTAATC
28164431 TCATCTCGGC
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
43 63 0.94
44 4 0.06
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACATGTAATCAAATAACA
Found at i:28164558 original size:5 final size:5
Alignment explanation
Indices: 28164548--28164574 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
28164538 ACCATTCAGC
28164548 ATTCA ATTCA ATTCA ATTCA ATTCA AT
1 ATTCA ATTCA ATTCA ATTCA ATTCA AT
28164575 AATAAATATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (5 bp):
ATTCA
Found at i:28167834 original size:43 final size:43
Alignment explanation
Indices: 28167786--28167874 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
28167776 TTTATGTCAA
*
28167786 TTGTTAGAGTATATTATACTTATATC-TCAAAGGTATTATTTTC
1 TTGTTAGAGTATATTATACTTATATCAT-AAAGGTATTATTCTC
*
28167829 TTGTTAGAGTATATTGTACTTATATCATAAAGGTATTATTCTC
1 TTGTTAGAGTATATTATACTTATATCATAAAGGTATTATTCTC
28167872 TTG
1 TTG
28167875 GTATCATCTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
43 42 0.98
44 1 0.02
ACGTcount: A:0.29, C:0.09, G:0.13, T:0.48
Consensus pattern (43 bp):
TTGTTAGAGTATATTATACTTATATCATAAAGGTATTATTCTC
Found at i:28171463 original size:28 final size:28
Alignment explanation
Indices: 28171427--28171483 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
28171417 TTTAACAATA
28171427 TAAAAAAATAAATTAATTTATTATTATT
1 TAAAAAAATAAATTAATTTATTATTATT
28171455 TAAAAAAATAAATTAATTTATTATTATT
1 TAAAAAAATAAATTAATTTATTATTATT
28171483 T
1 T
28171484 TCTATCTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TAAAAAAATAAATTAATTTATTATTATT
Found at i:28171547 original size:21 final size:21
Alignment explanation
Indices: 28171508--28171547 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
28171498 ATTAATATAA
* **
28171508 TTTAAAACTAAAATTTTAAAT
1 TTTAAAAATAAAAAATTAAAT
28171529 TTTAAAAATAAAAAATTAA
1 TTTAAAAATAAAAAATTAA
28171548 GATTACAAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
TTTAAAAATAAAAAATTAAAT
Found at i:28175184 original size:26 final size:26
Alignment explanation
Indices: 28175148--28175257 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
28175138 CATGAAATTC
28175148 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28175174 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
28175200 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
28175226 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
28175252 TTATCA
1 TTATCA
28175258 ATTTGTATCA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:28181104 original size:183 final size:183
Alignment explanation
Indices: 28180796--28181162 Score: 734
Period size: 183 Copynumber: 2.0 Consensus size: 183
28180786 TCCTCCTCCT
28180796 AATGACCGAATACTCAAGAGCTTTCTCCTCTCCTTTCTCTTCTCTAACTTTCAGCTATGATGAAC
1 AATGACCGAATACTCAAGAGCTTTCTCCTCTCCTTTCTCTTCTCTAACTTTCAGCTATGATGAAC
28180861 AAAGATGGACAAAACTTTGTTCTTTTCACCCCTTTTTCTTTTAATAAAACTTCATATTTCATCCA
66 AAAGATGGACAAAACTTTGTTCTTTTCACCCCTTTTTCTTTTAATAAAACTTCATATTTCATCCA
28180926 TTTAATTCTTTAATACAAAAGACATGAAATTCTTATCATGAAACATTTACTTA
131 TTTAATTCTTTAATACAAAAGACATGAAATTCTTATCATGAAACATTTACTTA
28180979 AATGACCGAATACTCAAGAGCTTTCTCCTCTCCTTTCTCTTCTCTAACTTTCAGCTATGATGAAC
1 AATGACCGAATACTCAAGAGCTTTCTCCTCTCCTTTCTCTTCTCTAACTTTCAGCTATGATGAAC
28181044 AAAGATGGACAAAACTTTGTTCTTTTCACCCCTTTTTCTTTTAATAAAACTTCATATTTCATCCA
66 AAAGATGGACAAAACTTTGTTCTTTTCACCCCTTTTTCTTTTAATAAAACTTCATATTTCATCCA
28181109 TTTAATTCTTTAATACAAAAGACATGAAATTCTTATCATGAAACATTTACTTA
131 TTTAATTCTTTAATACAAAAGACATGAAATTCTTATCATGAAACATTTACTTA
28181162 A
1 A
28181163 CCCATTATCA
Statistics
Matches: 184, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
183 184 1.00
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.39
Consensus pattern (183 bp):
AATGACCGAATACTCAAGAGCTTTCTCCTCTCCTTTCTCTTCTCTAACTTTCAGCTATGATGAAC
AAAGATGGACAAAACTTTGTTCTTTTCACCCCTTTTTCTTTTAATAAAACTTCATATTTCATCCA
TTTAATTCTTTAATACAAAAGACATGAAATTCTTATCATGAAACATTTACTTA
Found at i:28181177 original size:26 final size:26
Alignment explanation
Indices: 28181141--28181250 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
28181131 CATGAAATTC
*
28181141 TTATCATGAAACATTTACTTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28181167 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
28181193 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
28181219 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
28181245 TTATCA
1 TTATCA
28181251 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:28181748 original size:27 final size:27
Alignment explanation
Indices: 28181710--28181764 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
28181700 TTCATTTTTG
28181710 TTGTTACTCATACTAATGTGTCAATTA
1 TTGTTACTCATACTAATGTGTCAATTA
28181737 TTGTTACTCATACTAATGTGTCAATTA
1 TTGTTACTCATACTAATGTGTCAATTA
28181764 T
1 T
28181765 GAAAATGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.45
Consensus pattern (27 bp):
TTGTTACTCATACTAATGTGTCAATTA
Found at i:28183296 original size:13 final size:13
Alignment explanation
Indices: 28183278--28183305 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
28183268 TGTTTTCATC
28183278 TGCATAATTATTT
1 TGCATAATTATTT
28183291 TGCATAATTATTT
1 TGCATAATTATTT
28183304 TG
1 TG
28183306 AAGTTCGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.11, T:0.54
Consensus pattern (13 bp):
TGCATAATTATTT
Found at i:28187882 original size:46 final size:46
Alignment explanation
Indices: 28187815--28187989 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
28187805 TGTAACCCGC
28187815 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
28187861 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * * ** *
28187911 -C-TCA-CGAACTCGGAATCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
28187954 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
28187990 ATGCTCAACC
Statistics
Matches: 107, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 62 0.58
47 25 0.23
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:28187938 original size:93 final size:93
Alignment explanation
Indices: 28187823--28187993 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
28187813 GCCCATAAGT
* ** *
28187823 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGAATCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
28187888 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
*
28187916 GAACTCGGAATCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGAATCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
28187981 CGAGTTCGGATGC
66 CGAGCTCGGATGC
28187994 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.20
Consensus pattern (93 bp):
GAACTCGGAATCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:28195701 original size:41 final size:42
Alignment explanation
Indices: 28195641--28195719 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 42
28195631 AAACCTATTA
* *
28195641 GGTTTTCATTCAGCTCTTATGAGCTTCTGTTCAACCCTTATG
1 GGTTTCCATTCAGCACTTATGAGCTTCTGTTCAACCCTTATG
* *
28195683 GGTTTCCATT-AGCACTTATGTGCTTCTGTTCAGCCCT
1 GGTTTCCATTCAGCACTTATGAGCTTCTGTTCAACCCT
28195720 CAAGTTTCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
41 24 0.73
42 9 0.27
ACGTcount: A:0.15, C:0.25, G:0.18, T:0.42
Consensus pattern (42 bp):
GGTTTCCATTCAGCACTTATGAGCTTCTGTTCAACCCTTATG
Found at i:28200462 original size:15 final size:15
Alignment explanation
Indices: 28200432--28200462 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28200422 AGTGCTGCTG
*
28200432 ATAAAGGAATAAAAA
1 ATAAAGGAAAAAAAA
28200447 ATAAAGGAAAAAAAA
1 ATAAAGGAAAAAAAA
28200462 A
1 A
28200463 CAGAAAATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (15 bp):
ATAAAGGAAAAAAAA
Found at i:28200707 original size:16 final size:16
Alignment explanation
Indices: 28200666--28200716 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
28200656 TTAAAATAAC
28200666 ATAAAAATATTAA-TTAA
1 ATAAAAA-A-TAATTTAA
*
28200683 TTAACAAAATAATTTAA
1 ATAA-AAAATAATTTAA
*
28200700 ATAAAAAATTATTTAA
1 ATAAAAAATAATTTAA
28200716 A
1 A
28200717 AAATGACCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 15 0.52
17 11 0.38
18 3 0.10
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAAAAAATAATTTAA
Found at i:28200878 original size:41 final size:42
Alignment explanation
Indices: 28200840--28200919 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
28200830 AATTAAATTT
28200840 AAATAACTTTTAAAATA-TATAAAAATAATAAAAATAAATCC
1 AAATAACTTTTAAAATATTATAAAAATAATAAAAATAAATCC
* * * * * *
28200881 AAATTATTTTTTAATTATTTTAAAAATAATAAAATTAAA
1 AAATAACTTTTAAAATATTATAAAAATAATAAAAATAAA
28200920 GAATTATATA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
41 13 0.41
42 19 0.59
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (42 bp):
AAATAACTTTTAAAATATTATAAAAATAATAAAAATAAATCC
Found at i:28203411 original size:14 final size:14
Alignment explanation
Indices: 28203392--28203429 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
28203382 GTTTGCCAGT
*
28203392 AAAATGTTTTCCGG
1 AAAATGATTTCCGG
*
28203406 AAAATGATTTCTGG
1 AAAATGATTTCCGG
28203420 AAAATGATTT
1 AAAATGATTT
28203430 ACTTTTCTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (14 bp):
AAAATGATTTCCGG
Found at i:28203443 original size:19 final size:20
Alignment explanation
Indices: 28203413--28203456 Score: 81
Period size: 19 Copynumber: 2.2 Consensus size: 20
28203403 CGGAAAATGA
28203413 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
28203433 TTTCT-GAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
28203452 TTTCT
1 TTTCT
28203457 AGTGTTTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:28203559 original size:14 final size:14
Alignment explanation
Indices: 28203540--28203616 Score: 56
Period size: 14 Copynumber: 5.6 Consensus size: 14
28203530 TGTTTTTACA
28203540 TATATTAATAAATT
1 TATATTAATAAATT
*
28203554 TATATT-TTAAATT
1 TATATTAATAAATT
*
28203567 GT-TTTTAATAAATT
1 -TATATTAATAAATT
28203581 TATACTT--TAAATT
1 TATA-TTAATAAATT
*
28203594 GT-TTTTAATAAATT
1 -TATATTAATAAATT
28203608 TATACTTAA
1 TATA-TTAA
28203617 ATTATTTTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 17
0.68 0.08 0.24
Matches are distributed among these distances:
12 2 0.04
13 18 0.38
14 22 0.46
15 6 0.12
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (14 bp):
TATATTAATAAATT
Found at i:28203616 original size:26 final size:26
Alignment explanation
Indices: 28203544--28203626 Score: 130
Period size: 27 Copynumber: 3.1 Consensus size: 26
28203534 TTTACATATA
*
28203544 TTAATAAATTTATATTTTAAATTGTTT
1 TTAATAAATTTATA-CTTAAATTGTTT
28203571 TTAATAAATTTATACTTTAAATTGTTT
1 TTAATAAATTTATAC-TTAAATTGTTT
*
28203598 TTAATAAATTTATACTTAAATTATTT
1 TTAATAAATTTATACTTAAATTGTTT
28203624 TTA
1 TTA
28203627 CATATATTGC
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
26 13 0.25
27 40 0.75
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (26 bp):
TTAATAAATTTATACTTAAATTGTTT
Found at i:28203903 original size:24 final size:24
Alignment explanation
Indices: 28203876--28203923 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
28203866 TAATAACAAC
28203876 AATATTGTTCAAGTGTATAATTAA
1 AATATTGTTCAAGTGTATAATTAA
28203900 AATATTGTTCAAGTGTATAATTAA
1 AATATTGTTCAAGTGTATAATTAA
28203924 GAGGAAAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.04, G:0.12, T:0.42
Consensus pattern (24 bp):
AATATTGTTCAAGTGTATAATTAA
Found at i:28214067 original size:24 final size:25
Alignment explanation
Indices: 28214039--28214086 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
28214029 ATCATAATAT
28214039 TTTTATAAATATTTT-AATTATTTG
1 TTTTATAAATATTTTAAATTATTTG
**
28214063 TTTTATATTTATTTTAAATTATTT
1 TTTTATAAATATTTTAAATTATTT
28214087 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (25 bp):
TTTTATAAATATTTTAAATTATTTG
Found at i:28214087 original size:14 final size:13
Alignment explanation
Indices: 28214048--28214089 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 13
28214038 TTTTTATAAA
28214048 TATTTTAATTATT
1 TATTTTAATTATT
*
28214061 TGTTTT-A-TATT
1 TATTTTAATTATT
28214072 TATTTTAAATTATT
1 TATTTT-AATTATT
28214086 TATT
1 TATT
28214090 ATATTAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
11 9 0.38
12 1 0.04
13 6 0.25
14 8 0.33
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (13 bp):
TATTTTAATTATT
Found at i:28219058 original size:20 final size:21
Alignment explanation
Indices: 28219035--28219094 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
28219025 CAAGTTTAAT
* *
28219035 AATTATTA-AAATATTATAAA
1 AATTATTAGAAAAACTATAAA
28219055 AATTA-TAGAAAAACTATAAA
1 AATTATTAGAAAAACTATAAA
*
28219075 AATTATAATAAAAAAACTAT
1 AATTAT--TAGAAAAACTAT
28219095 TAGAGATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
19 2 0.06
20 20 0.61
23 11 0.33
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (21 bp):
AATTATTAGAAAAACTATAAA
Found at i:28219061 original size:9 final size:9
Alignment explanation
Indices: 28219035--28219082 Score: 51
Period size: 9 Copynumber: 4.9 Consensus size: 9
28219025 CAAGTTTAAT
28219035 AATTATTAAA
1 AATTA-TAAA
28219045 ATATTATAAA
1 A-ATTATAAA
28219055 AATTATAGAAA
1 AATTAT--AAA
*
28219066 AACTATAAA
1 AATTATAAA
28219075 AATTATAA
1 AATTATAA
28219083 TAAAAAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
9 15 0.45
10 6 0.18
11 12 0.36
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (9 bp):
AATTATAAA
Found at i:28219769 original size:34 final size:33
Alignment explanation
Indices: 28219678--28219795 Score: 109
Period size: 34 Copynumber: 3.5 Consensus size: 33
28219668 TAAAAATTAC
*
28219678 TACTTTTATAAATTTTCATGATAAAA-AATCAAA
1 TACTTTTATAAATTTTCATGA-AAAACAATTAAA
* * *
28219711 GTAC-ATT-T-AATATTCATGATAAACAATTATAA
1 -TACTTTTATAAATTTTCATGAAAAACAATTA-AA
*
28219743 TACTTTTATAAATTTTCATGAAAAACAATTAGAG
1 TACTTTTATAAATTTTCATGAAAAACAATTA-AA
*
28219777 TACATTTAATAAATTTTCA
1 TAC-TTTTATAAATTTTCA
28219796 ACTGAACGAC
Statistics
Matches: 68, Mismatches: 10, Indels: 11
0.76 0.11 0.12
Matches are distributed among these distances:
30 3 0.04
31 17 0.25
32 5 0.07
33 3 0.04
34 26 0.38
35 14 0.21
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (33 bp):
TACTTTTATAAATTTTCATGAAAAACAATTAAA
Found at i:28226128 original size:40 final size:39
Alignment explanation
Indices: 28226073--28226208 Score: 118
Period size: 41 Copynumber: 3.5 Consensus size: 39
28226063 ACCGGAATGG
28226073 CACCCAGTGCCTCATCGAATAGTTCGAAGCAATATAGTGA
1 CACCCAGTGCCTCATCGAATAGTTCGAAG-AATATAGTGA
* ** * *
28226113 CACCCAGTGTCTCATCGGCCTAG-TCGAAG--TAAAGTGG
1 CACCCAGTGCCTCATC-GAATAGTTCGAAGAATATAGTGA
* * *
28226150 TACCCAGTACCTCATCGAATCTA-TCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCGAA--TAGTTCGAAG-AATATAGTGA
*
28226191 CACCCAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
28226209 CTCAAGGTCG
Statistics
Matches: 73, Mismatches: 16, Indels: 13
0.72 0.16 0.13
Matches are distributed among these distances:
36 1 0.01
37 19 0.26
38 7 0.10
40 21 0.29
41 25 0.34
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGAATAGTTCGAAGAATATAGTGA
Found at i:28231474 original size:24 final size:24
Alignment explanation
Indices: 28231444--28231489 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
28231434 CCGTGCAAAC
*
28231444 ACAAAACACCAAAA-ACAAAAAAAA
1 ACAAAACA-AAAAATACAAAAAAAA
28231468 ACAAAACAAAAAATACAAAAAA
1 ACAAAACAAAAAATACAAAAAA
28231490 TATATAAAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.80, C:0.17, G:0.00, T:0.02
Consensus pattern (24 bp):
ACAAAACAAAAAATACAAAAAAAA
Found at i:28231682 original size:22 final size:21
Alignment explanation
Indices: 28231657--28231717 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
28231647 AACAGACAAG
28231657 AAAACAACAGCAAATAGAAAC
1 AAAACAACAGCAAATAGAAAC
* * *
28231678 AAAAAAAACAAGCAAATGGCAAC
1 -AAAACAAC-AGCAAATAGAAAC
**
28231701 AGGACAACAGCAAATAG
1 AAAACAACAGCAAATAG
28231718 GAAAAATGAA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 8 0.26
22 12 0.39
23 11 0.35
ACGTcount: A:0.62, C:0.18, G:0.15, T:0.05
Consensus pattern (21 bp):
AAAACAACAGCAAATAGAAAC
Found at i:28233241 original size:19 final size:19
Alignment explanation
Indices: 28233217--28233256 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
28233207 GTATGCTTTT
28233217 AAGTCCATCATTTGTAATA
1 AAGTCCATCATTTGTAATA
28233236 AAGTCCATCATTTGTAATA
1 AAGTCCATCATTTGTAATA
28233255 AA
1 AA
28233257 AATAATTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (19 bp):
AAGTCCATCATTTGTAATA
Found at i:28233686 original size:14 final size:14
Alignment explanation
Indices: 28233667--28233697 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28233657 TATTTGATTG
28233667 TTAGTCCATCATTT
1 TTAGTCCATCATTT
*
28233681 TTAGTCCATTATTT
1 TTAGTCCATCATTT
28233695 TTA
1 TTA
28233698 TGTCGTGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.16, G:0.06, T:0.55
Consensus pattern (14 bp):
TTAGTCCATCATTT
Found at i:28234401 original size:130 final size:130
Alignment explanation
Indices: 28234025--28234426 Score: 416
Period size: 132 Copynumber: 3.1 Consensus size: 130
28234015 TAATTATTCA
* * *
28234025 TTTAAAAATTCTTTAAAACGAAGACGA-GATTTGATATTTGGCAATTCGTAGAATCGTGCCCTAA
1 TTTAAAAATTCTTTAAAA-TAAG-CGATG-TTCGATATTTGGCAATTCGCAGAATCGTGCCCTAA
* * * * * *
28234089 CGTGTTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCACTTATG
63 CGTGTTGGGTTGCAATTTCTCGTTTGCTCAAAGTAATCGAATATCCCTTTAGAGTTTCACTCATG
28234154 TCT
128 TCT
** * * * * *
28234157 TCCAAAAATCCTTTAAAATAAGGGTGATGTTCGACATTTGACAATTCGCAGAATCGTGCTCTAAC
1 TTTAAAAATTCTTTAAAATAA--GCGATGTTCGATATTTGGCAATTCGCAGAATCGTGCCCTAAC
* * *
28234222 GTGTTGGGTTGCAATTTCTTGTTTGCTCAAAGTAATCGAAGATCCCTTTAGAGTTTCACCCATGT
64 GTGTTGGGTTGCAATTTCTCGTTTGCTCAAAGTAATCGAATATCCCTTTAGAGTTTCACTCATGT
28234287 CT
129 CT
* * *
28234289 TTTAAAAATTCTTTAAACATAAGCGATGTTCGATATTTGGCAATTCG-AGAATCGTACGCTATCG
1 TTTAAAAATTCTTTAAA-ATAAGCGATGTTCGATATTTGGCAATTCGCAGAATCGTGCCCTAACG
* * * * * * * * * *
28234353 TGCTAGGTTACGATTTCTCGTTGGTTCAAAGCAGTTGAATATTCCTTTAG-GTTTTCACTCATGT
65 TGTTGGGTTGCAATTTCTCGTTTGCTCAAAGTAATCGAATATCCCTTTAGAG-TTTCACTCATGT
28234417 -T
129 CT
28234418 TTTACAAAA
1 TTTA-AAAA
28234427 AAAAAATTCT
Statistics
Matches: 223, Mismatches: 41, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
129 6 0.03
130 67 0.30
131 24 0.11
132 120 0.54
133 6 0.03
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (130 bp):
TTTAAAAATTCTTTAAAATAAGCGATGTTCGATATTTGGCAATTCGCAGAATCGTGCCCTAACGT
GTTGGGTTGCAATTTCTCGTTTGCTCAAAGTAATCGAATATCCCTTTAGAGTTTCACTCATGTCT
Done.