Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold352
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: 630196
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 1 of 4
Found at i:3546 original size:19 final size:17
Alignment explanation
Indices: 3517--3571 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 17
3507 TTAAAATATT
3517 TTTTAATAAATTAAAAAA
1 TTTT-ATAAATTAAAAAA
3535 TCATTTATAAATTAAATAAA
1 T--TTTATAAATTAAA-AAA
*
3555 TTTTATTAA-TAAAAAA
1 TTTTATAAATTAAAAAA
3571 T
1 T
3572 ACGTTACAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
16 4 0.12
17 4 0.12
18 8 0.24
19 10 0.30
20 7 0.21
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTTATAAATTAAAAAA
Found at i:4007 original size:18 final size:19
Alignment explanation
Indices: 3966--4001 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3956 AATTATTTAA
*
3966 ATTAATATTAATTAATAAT
1 ATTAATATTAATTAAAAAT
3985 ATTAAT-TTAATTAAAAA
1 ATTAATATTAATTAAAAA
4002 ATTTAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTAATATTAATTAAAAAT
Found at i:8826 original size:831 final size:832
Alignment explanation
Indices: 7221--8885 Score: 3296
Period size: 831 Copynumber: 2.0 Consensus size: 832
7211 GATATGACTC
7221 CAAGTTGTCTTTTGAATGCATGTGCTTATATGAACAGTATATGCCATTTCTTTGTTAGATGTATC
1 CAAGTTGTCTTTTGAATGCATGTGCTTATATGAACAGTATATGCCATTTCTTTGTTAGATGTATC
7286 ATCTGTAGATATTTAGATTTTATTCCTAGTTGTCTCTCAAATACGTGTTCTTATATGAACAATAT
66 ATCTGTAGATATTTAGATTTTATTCCTAGTTGTCTCTCAAATACGTGTTCTTATATGAACAATAT
7351 ATGTGGCAATAGAGTTTCTTTTGGCAATGGACATGCCTAGGTTAGTATTGTTTTGTCTTCTTTTT
131 ATGTGGCAATAGAGTTTCTTTTGGCAATGGACATGCCTAGGTTAGTATTGTTTTGTCTTCTTTTT
7416 TTTTTTTAAAAAAAAAAGAGAAGAAAAGAGGTGGTTGTGCTATGGTGGTTTGCTTATTATATCGA
196 TTTTTTTAAAAAAAAAAGAGAAGAAAAGAGGTGGTTGTGCTATGGTGGTTTGCTTATTATATCGA
7481 GTGAGGTTAAGCCGTTAAAGCTTTCAGTTCCTGTACAATCAAGTACAGGAGGCTCTGTAATCATG
261 GTGAGGTTAAGCCGTTAAAGCTTTCAGTTCCTGTACAATCAAGTACAGGAGGCTCTGTAATCATG
7546 AGCTAATATACTTTTCTCAGTCTTCCATTCCCTTTCTTGTTTCATGGTCCTTGATATTCAGTCTT
326 AGCTAATATACTTTTCTCAGTCTTCCATTCCCTTTCTTGTTTCATGGTCCTTGATATTCAGTCTT
7611 GGGCATATAGGAATAAAATCATATTAACAGTTCATCCTGACCTTAATCACTAAACCCTACTGCCA
391 GGGCATATAGGAATAAAATCATATTAACAGTTCATCCTGACCTTAATCACTAAACCCTACTGCCA
7676 TGGCATTACTATGAGCTCCTAAACAAAATGACAGAGCTGCGTGGTAGAAAGGTTATGATCTTCTT
456 TGGCATTACTATGAGCTCCTAAACAAAATGACAGAGCTGCGTGGTAGAAAGGTTATGATCTTCTT
7741 ATTACCTTTTTCATAAAAATTTTTGTGGGGTCTGTTGTTCTTTATTTGCTTCTTGGTAATACTTA
521 ATTACCTTTTTCATAAAAATTTTTGTGGGGTCTGTTGTTCTTTATTTGCTTCTTGGTAATACTTA
*
7806 TTTCACTTCCTCGCCTTGCTTTGCATTAGAAATCAAAATACAAGGAGGGAAGTCATGCTGGTGCA
586 TTTCACTTCCTCGCCTTGCTTTGCATTAGAAATCAAAATACAAGGAGGGAAGTCATACTGGTGCA
7871 GTTCTTGGTCTAGCTTGGAACAGGGAATACAGGTTATTTTGATCTATCAGGTTTTGCTTTTCTTG
651 GTTCTTGGTCTAGCTTGGAACAGGGAATACAGGTTATTTTGATCTATCAGGTTTTGCTTTTCTTG
7936 CTTTAATGGAAATTTATGAGGAAATTAGTTCTTCTCATAGATCTTTTCATTTAAAAAAAAAAACA
716 CTTTAATGGAAATTTATGAGGAAATTAGTTCTTCTCATAGATCTTTTCATTTAAAAAAAAAAACA
8001 GGAATATCCTTGCTAGTGCAAGTGCTGACAAACAAGTTAAGATTTGGGACGT
781 GGAATATCCTTGCTAGTGCAAGTGCTGACAAACAAGTTAAGATTTGGGACGT
8053 CAAGTTGTCTTTTGAATGCATGTGCTTATATGAACAGTATATGCCATTTCTTTGTTAGATGTATC
1 CAAGTTGTCTTTTGAATGCATGTGCTTATATGAACAGTATATGCCATTTCTTTGTTAGATGTATC
8118 ATCTGTAGATATTTAGATTTTATTCCTAGTTGTCTCTCAAATACGTGTTCTTATATGAACAATAT
66 ATCTGTAGATATTTAGATTTTATTCCTAGTTGTCTCTCAAATACGTGTTCTTATATGAACAATAT
8183 ATGTGGCAATAGAGTTTCTTTTGGCAATGGACATGCCTAGGTTAGTATTGTTTTGTCTTC-TTTT
131 ATGTGGCAATAGAGTTTCTTTTGGCAATGGACATGCCTAGGTTAGTATTGTTTTGTCTTCTTTTT
8247 TTTTTTTAAAAAAAAAAGAGAAGAAAAGAGGTGGTTGTGCTATGGTGGTTTGCTTATTATATCGA
196 TTTTTTTAAAAAAAAAAGAGAAGAAAAGAGGTGGTTGTGCTATGGTGGTTTGCTTATTATATCGA
8312 GTGAGGTTAAGCCGTTAAAGCTTTCAGTTCCTGTACAATCAAGTACAGGAGGCTCTGTAATCATG
261 GTGAGGTTAAGCCGTTAAAGCTTTCAGTTCCTGTACAATCAAGTACAGGAGGCTCTGTAATCATG
8377 AGCTAATATACTTTTCTCAGTCTTCCATTCCCTTTCTTGTTTCATGGTCCTTGATATTCAGTCTT
326 AGCTAATATACTTTTCTCAGTCTTCCATTCCCTTTCTTGTTTCATGGTCCTTGATATTCAGTCTT
8442 GGGCATATAGGAATAAAATCATATTAACAGTTCATCCTGACCTTAATCACTAAACCCTACTGCCA
391 GGGCATATAGGAATAAAATCATATTAACAGTTCATCCTGACCTTAATCACTAAACCCTACTGCCA
8507 TGGCATTACTATGAGCTCCTAAACAAAATGACAGAGCTGCGTGGTAGAAAGGTTATGATCTTCTT
456 TGGCATTACTATGAGCTCCTAAACAAAATGACAGAGCTGCGTGGTAGAAAGGTTATGATCTTCTT
8572 ATTACCTTTTTCATAAAAATTTTTGTGGGGTCTGTTGTTCTTTATTTGCTTCTTGGTAATACTTA
521 ATTACCTTTTTCATAAAAATTTTTGTGGGGTCTGTTGTTCTTTATTTGCTTCTTGGTAATACTTA
8637 TTTCACTTCCTCGCCTTGCTTTGCATTAGAAATCAAAATACAAGGAGGGAAGTCATACTGGTGCA
586 TTTCACTTCCTCGCCTTGCTTTGCATTAGAAATCAAAATACAAGGAGGGAAGTCATACTGGTGCA
*
8702 GTTCTTGGTCTAGCTTGGAACAGGGAATACAGGTTATTTTGATCTATCTGGTTTTGCTTTTCTTG
651 GTTCTTGGTCTAGCTTGGAACAGGGAATACAGGTTATTTTGATCTATCAGGTTTTGCTTTTCTTG
*
8767 CTTTAATGGAAATTTATGAGGAAATTAGTTCTTCTCATAGATCTTTTCATTTTAAAAAAAAAACA
716 CTTTAATGGAAATTTATGAGGAAATTAGTTCTTCTCATAGATCTTTTCATTTAAAAAAAAAAACA
8832 GGAATATCCTTGCTAGTGCAAGTGCTGACAAACAAGTTAAGATTTGGGACGT
781 GGAATATCCTTGCTAGTGCAAGTGCTGACAAACAAGTTAAGATTTGGGACGT
8884 CA
1 CA
8886 CTGCTGGAAA
Statistics
Matches: 830, Mismatches: 3, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
831 640 0.77
832 190 0.23
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (832 bp):
CAAGTTGTCTTTTGAATGCATGTGCTTATATGAACAGTATATGCCATTTCTTTGTTAGATGTATC
ATCTGTAGATATTTAGATTTTATTCCTAGTTGTCTCTCAAATACGTGTTCTTATATGAACAATAT
ATGTGGCAATAGAGTTTCTTTTGGCAATGGACATGCCTAGGTTAGTATTGTTTTGTCTTCTTTTT
TTTTTTTAAAAAAAAAAGAGAAGAAAAGAGGTGGTTGTGCTATGGTGGTTTGCTTATTATATCGA
GTGAGGTTAAGCCGTTAAAGCTTTCAGTTCCTGTACAATCAAGTACAGGAGGCTCTGTAATCATG
AGCTAATATACTTTTCTCAGTCTTCCATTCCCTTTCTTGTTTCATGGTCCTTGATATTCAGTCTT
GGGCATATAGGAATAAAATCATATTAACAGTTCATCCTGACCTTAATCACTAAACCCTACTGCCA
TGGCATTACTATGAGCTCCTAAACAAAATGACAGAGCTGCGTGGTAGAAAGGTTATGATCTTCTT
ATTACCTTTTTCATAAAAATTTTTGTGGGGTCTGTTGTTCTTTATTTGCTTCTTGGTAATACTTA
TTTCACTTCCTCGCCTTGCTTTGCATTAGAAATCAAAATACAAGGAGGGAAGTCATACTGGTGCA
GTTCTTGGTCTAGCTTGGAACAGGGAATACAGGTTATTTTGATCTATCAGGTTTTGCTTTTCTTG
CTTTAATGGAAATTTATGAGGAAATTAGTTCTTCTCATAGATCTTTTCATTTAAAAAAAAAAACA
GGAATATCCTTGCTAGTGCAAGTGCTGACAAACAAGTTAAGATTTGGGACGT
Found at i:14269 original size:27 final size:27
Alignment explanation
Indices: 14207--14270 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
14197 ATTAAAATTT
* *
14207 AAATAAAT-TAAAAATATTTAATTATA
1 AAATAAATATAAAAATATTCAATCATA
* *
14233 TATTAAATATAAAAATATTCAATCATA
1 AAATAAATATAAAAATATTCAATCATA
*
14260 AAATATATATA
1 AAATAAATATA
14271 TATATATATA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 6 0.20
27 24 0.80
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (27 bp):
AAATAAATATAAAAATATTCAATCATA
Found at i:15539 original size:50 final size:50
Alignment explanation
Indices: 15481--15582 Score: 168
Period size: 50 Copynumber: 2.0 Consensus size: 50
15471 TATAAGTATC
* *
15481 CATTCCTCATTTGTGCAGCGCAAGCTAAAAGTAGCCAGACTTAGAGTCAA
1 CATTCCTCATCTGTGCAGCGCAAGCTAAAAGTAGCCAGACTTACAGTCAA
* *
15531 CATTCCTCATCTGTGCAGTGCAAGCTAAAAGTAGCCAGACTTACAGTGAA
1 CATTCCTCATCTGTGCAGCGCAAGCTAAAAGTAGCCAGACTTACAGTCAA
15581 CA
1 CA
15583 GCCTAAAGTC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.24
Consensus pattern (50 bp):
CATTCCTCATCTGTGCAGCGCAAGCTAAAAGTAGCCAGACTTACAGTCAA
Found at i:17450 original size:2 final size:2
Alignment explanation
Indices: 17443--17472 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17433 TAACTTTACA
17443 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17473 GCACATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19129 original size:7 final size:7
Alignment explanation
Indices: 19111--19161 Score: 50
Period size: 7 Copynumber: 7.1 Consensus size: 7
19101 TAAATTTAGA
19111 TTTAAA-
1 TTTAAAT
19117 TTTAAAT
1 TTTAAAT
19124 TTTAAAAT
1 TTT-AAAT
*
19132 TTTAGAT
1 TTTAAAT
19139 TTTAAAT
1 TTTAAAT
*
19146 TTATGAAT
1 TT-TAAAT
*
19154 TTAAAAT
1 TTTAAAT
19161 T
1 T
19162 CTTTATTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
6 6 0.16
7 18 0.49
8 13 0.35
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (7 bp):
TTTAAAT
Found at i:21742 original size:12 final size:12
Alignment explanation
Indices: 21725--21757 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
21715 CATAAAATAT
21725 AAAAATAATAAA
1 AAAAATAATAAA
21737 AAAAATAAT-AA
1 AAAAATAATAAA
*
21748 TAAAATAATA
1 AAAAATAATA
21758 TAATTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAAATAATAAA
Found at i:21830 original size:14 final size:15
Alignment explanation
Indices: 21799--21833 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
21789 GCACTTGCAT
*
21799 GTGCCACGTGTCCAA
1 GTGCCAAGTGTCCAA
21814 GTGCCAAGTGT-CAA
1 GTGCCAAGTGTCCAA
21828 GTGCCA
1 GTGCCA
21834 TATAATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.23, C:0.29, G:0.29, T:0.20
Consensus pattern (15 bp):
GTGCCAAGTGTCCAA
Found at i:26831 original size:80 final size:80
Alignment explanation
Indices: 26687--26834 Score: 190
Period size: 80 Copynumber: 1.9 Consensus size: 80
26677 AACTGGGTTA
* * * * **
26687 GAGTATCCCTTTAGAGATGATAGGGTTGGAGTACCCCTAGAGATAAAAAATTTGGTATTATGGAA
1 GAGTATCCCTTGAGAGATGATAGGGTTGGAGCACCCCTAGAAATAAAAAATATGACATTATGGAA
26752 GTATAAATGAGATTG
66 GTATAAATGAGATTG
* * * *
26767 GAGTATCCCTTCGA-AGATGGTAGGGTTGGAGCATCCCTAGAAATGAAAAATATGACATTTTGGA
1 GAGTATCCCTT-GAGAGATGATAGGGTTGGAGCACCCCTAGAAATAAAAAATATGACATTATGGA
26831 AGTA
65 AGTA
26835 AAAACGGGGT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
80 56 0.98
81 1 0.02
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.28
Consensus pattern (80 bp):
GAGTATCCCTTGAGAGATGATAGGGTTGGAGCACCCCTAGAAATAAAAAATATGACATTATGGAA
GTATAAATGAGATTG
Found at i:29653 original size:20 final size:20
Alignment explanation
Indices: 29594--29666 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
29584 ACATGGTCTA
***
29594 GTATCGATACATTACAAGCAT
1 GTATCGATACATTA-ACTTAT
* **
29615 GTATTGATACATTTGCTTAT
1 GTATCGATACATTAACTTAT
29635 GTATCGATACATTAACTTATT
1 GTATCGATACATTAACTTA-T
*
29656 ATATCGATACA
1 GTATCGATACA
29667 AATTGTAAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 18 0.44
21 23 0.56
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.38
Consensus pattern (20 bp):
GTATCGATACATTAACTTAT
Found at i:33904 original size:51 final size:50
Alignment explanation
Indices: 33837--33951 Score: 176
Period size: 51 Copynumber: 2.3 Consensus size: 50
33827 AATTAACTAG
* * *
33837 ATGTATCGATATATTGAATAATGTATCGATACATCTAGGTAACAAAACAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGGAA-AAAACAGA
* *
33888 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGGAAAAAACATA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGGAAAAAACAGA
33938 ATGTATCGATACAT
1 ATGTATCGATACAT
33952 GTACTGTTCA
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
50 21 0.36
51 38 0.64
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (50 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGGAAAAAACAGA
Found at i:35566 original size:22 final size:24
Alignment explanation
Indices: 35538--35584 Score: 80
Period size: 22 Copynumber: 2.0 Consensus size: 24
35528 AACATTAACC
35538 CCATAAGCAATTTTA-CAAG-CTA
1 CCATAAGCAATTTTATCAAGTCTA
35560 CCATAAGCAATTTTATCAAGTCTA
1 CCATAAGCAATTTTATCAAGTCTA
35584 C
1 C
35585 TTAGCATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 15 0.65
23 4 0.17
24 4 0.17
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.30
Consensus pattern (24 bp):
CCATAAGCAATTTTATCAAGTCTA
Found at i:36385 original size:27 final size:23
Alignment explanation
Indices: 36355--36409 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
36345 ACGGAGAGAG
36355 AAAAAAATAAAAAGATGAAAAGAAAA
1 AAAAAAATAAAAA-A-G-AAAGAAAA
* *
36381 AAAAAAGTAAAAAAGAAGGAAAA
1 AAAAAAATAAAAAAGAAAGAAAA
36404 AAAAAA
1 AAAAAA
36410 GGGTGGCCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 13 0.48
24 1 0.04
25 1 0.04
26 12 0.44
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (23 bp):
AAAAAAATAAAAAAGAAAGAAAA
Found at i:36392 original size:11 final size:11
Alignment explanation
Indices: 36372--36410 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
36362 TAAAAAGATG
36372 AAAAGAAAAAA
1 AAAAGAAAAAA
36383 AAAAGTAAAAAA
1 AAAAG-AAAAAA
* *
36395 GAAGGAAAAAA
1 AAAAGAAAAAA
36406 AAAAG
1 AAAAG
36411 GGTGGCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:36901 original size:32 final size:32
Alignment explanation
Indices: 36836--36898 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
36826 TGTATTTGTA
*
36836 TTTATATATTTTTATATTTAAAATATTATATT
1 TTTATATATTTTTACATTTAAAATATTATATT
36868 TTTATATATTTTTTACATATTAATAAT-TTAT
1 TTTATATA-TTTTTACAT-TTAA-AATATTAT
36899 TTTATTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 8 0.30
33 8 0.30
34 8 0.30
35 3 0.11
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (32 bp):
TTTATATATTTTTACATTTAAAATATTATATT
Found at i:37261 original size:19 final size:18
Alignment explanation
Indices: 37231--37280 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
37221 GGACATAAGT
*
37231 AAAAAA-AAAAAAGAGAG
1 AAAAAAGAAAAAAAAGAG
37248 AAAGAAAGAAAAAAAAGAG
1 AAA-AAAGAAAAAAAAGAG
37267 AAAAAAGAAAAAAA
1 AAAAAAGAAAAAAA
37281 GGACAAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 3 0.10
18 14 0.47
19 13 0.43
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAAAAAAGAG
Found at i:37261 original size:21 final size:19
Alignment explanation
Indices: 37231--37280 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
37221 GGACATAAGT
*
37231 AAAAA-AAAAAAAGAGAGA
1 AAAAAGAAAAAAAAAGAGA
37249 AAGAAAG-AAAAAAAAGAGA
1 AA-AAAGAAAAAAAAAGAGA
37268 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
37281 GGACAAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAAAAAAAGAGA
Found at i:37270 original size:9 final size:9
Alignment explanation
Indices: 37238--37281 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
37228 AGTAAAAAAA
37238 AAAAAGAGAG
1 AAAAA-AGAG
*
37248 AAAGAAAGAA
1 AAA-AAAGAG
37258 AAAAAAGAG
1 AAAAAAGAG
37267 AAAAAAGA-
1 AAAAAAGAG
37275 AAAAAAG
1 AAAAAAG
37282 GACAAGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 7 0.23
9 13 0.42
10 9 0.29
11 2 0.06
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
AAAAAAGAG
Found at i:37673 original size:23 final size:23
Alignment explanation
Indices: 37645--37690 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
37635 CATGTCATAT
* *
37645 TTATTTTCTATATTATATTTTAA
1 TTATTTTCTATATCATATATTAA
*
37668 TTATTTTTTATATCATATATTAA
1 TTATTTTCTATATCATATATTAA
37691 AAATATGATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (23 bp):
TTATTTTCTATATCATATATTAA
Found at i:38103 original size:23 final size:24
Alignment explanation
Indices: 38077--38127 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
38067 TAAAATGAAT
38077 TTATATAAATT-TCTATATGTTAA
1 TTATATAAATTATCTATATGTTAA
* *
38100 TTAT-TAATTTATCTATATTTTAA
1 TTATATAAATTATCTATATGTTAA
38123 -TATAT
1 TTATAT
38128 TCATATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (24 bp):
TTATATAAATTATCTATATGTTAA
Found at i:38386 original size:15 final size:14
Alignment explanation
Indices: 38367--38422 Score: 67
Period size: 15 Copynumber: 3.8 Consensus size: 14
38357 AATAATATGT
38367 TTAAATTATTTTTAA
1 TTAAATT-TTTTTAA
* *
38382 ATAAATTTTATTAA
1 TTAAATTTTTTTAA
38396 TTATAATTTTATTTAA
1 TTA-AATTTT-TTTAA
38412 TTAAATTTTTT
1 TTAAATTTTTT
38423 AAAAATATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 10 0.29
15 18 0.51
16 7 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTAAATTTTTTTAA
Found at i:39995 original size:13 final size:13
Alignment explanation
Indices: 39977--40001 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39967 ACTGAAGTAA
39977 TGTATCGATACAT
1 TGTATCGATACAT
39990 TGTATCGATACA
1 TGTATCGATACA
40002 ATCTGAAAAA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:40602 original size:23 final size:24
Alignment explanation
Indices: 40557--40603 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
40547 CAAAGAATTG
*
40557 AACACAAATTCAATTAAGCACAAA
1 AACACAAATTCAATTAAGAACAAA
40581 AACACAAA-TCAATTGAA-AACAAA
1 AACACAAATTCAATT-AAGAACAAA
40604 TTTTCAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.62, C:0.19, G:0.04, T:0.15
Consensus pattern (24 bp):
AACACAAATTCAATTAAGAACAAA
Found at i:43644 original size:13 final size:13
Alignment explanation
Indices: 43626--43651 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43616 CTATTTATGA
43626 TGTATCGATACAC
1 TGTATCGATACAC
43639 TGTATCGATACAC
1 TGTATCGATACAC
43652 ACAAATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:43796 original size:22 final size:22
Alignment explanation
Indices: 43741--43796 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
43731 ACAGTGACCT
43741 ATGAACAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
43763 ATGAA-AGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
43784 ATGAACAGTGATG
1 ATGAACAGTGATG
43797 AATAGTGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.27
Consensus pattern (22 bp):
ATGAACAGTGATGTATCGATAC
Found at i:43902 original size:53 final size:53
Alignment explanation
Indices: 43838--43974 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
43828 CTACTTCCAA
43838 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* *
43891 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
43944 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
43975 TATGTAATTT
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 67 0.84
54 13 0.16
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:43969 original size:20 final size:21
Alignment explanation
Indices: 43944--44014 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 21
43934 GCCAATGTCC
**
43944 TGTATCGATACATAT-TTGTG
1 TGTATCGATACATATGTAATG
*
43964 TGTATCGATAC-TATGTAATT
1 TGTATCGATACATATGTAATG
**
43984 TGTATCGATACAT-TCAAATG
1 TGTATCGATACATATGTAATG
44004 TGTATCGATAC
1 TGTATCGATAC
44015 TTTTCAGGGT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
19 3 0.07
20 39 0.91
21 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41
Consensus pattern (21 bp):
TGTATCGATACATATGTAATG
Found at i:44080 original size:21 final size:21
Alignment explanation
Indices: 44054--44094 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
44044 GTCAACCTTG
44054 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
44075 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
44095 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:44824 original size:24 final size:24
Alignment explanation
Indices: 44780--44825 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
44770 GTGATTTGTA
** *
44780 AATTTAAAATATATTTTATTTTTT
1 AATTTAAAATATAGCTAATTTTTT
44804 AATTTAAAATATAGCTAATTTT
1 AATTTAAAATATAGCTAATTTT
44826 GTTTTGCTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
AATTTAAAATATAGCTAATTTTTT
Found at i:44962 original size:16 final size:18
Alignment explanation
Indices: 44913--44963 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
44903 TTATGCTACA
44913 TATATATATATATTAATTTG
1 TATATATATAT-TTAA-TTG
44933 TATATATCATATTTAA-TG
1 TATATAT-ATATTTAATTG
44951 TAT-TATATATTTA
1 TATATATATATTTA
44964 TATAAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 7 0.23
17 3 0.10
18 5 0.17
20 11 0.37
21 4 0.13
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (18 bp):
TATATATATATTTAATTG
Found at i:45009 original size:20 final size:21
Alignment explanation
Indices: 44957--45011 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 21
44947 AATGTATTAT
*
44957 ATATTTATATAAATTTTAATTT
1 ATATTTATATAAATTTTAA-TA
44979 ATCATTTTATATAAATTTTAA-A
1 AT-A-TTTATATAAATTTTAATA
45001 ATATTTATATA
1 ATATTTATATA
45012 TTTTTATCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 8 0.27
21 1 0.03
22 4 0.13
23 1 0.03
24 16 0.53
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
ATATTTATATAAATTTTAATA
Found at i:45460 original size:32 final size:33
Alignment explanation
Indices: 45398--45462 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
45388 GTATCTCTTA
*
45398 AGAGACGACATTCATTCTTAAGACTATTAAATT
1 AGAGACGACATTCATTCTCAAGACTATTAAATT
* * *
45431 AGAGACGATATTTATT-TCAAGGCTATTAAATT
1 AGAGACGACATTCATTCTCAAGACTATTAAATT
45463 TAATATAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (33 bp):
AGAGACGACATTCATTCTCAAGACTATTAAATT
Found at i:46273 original size:150 final size:150
Alignment explanation
Indices: 46107--46414 Score: 582
Period size: 150 Copynumber: 2.1 Consensus size: 150
46097 CATAATTTTT
*
46107 ATATTATTAAATCTTTAAGTAGCTTTTAGTATTATTTTAATATCATCATAGTAATCTATTCATTA
1 ATATTATTAAATCTTTAAGTAGCTTTTAGTATTATTTTAATATCATCATAGTAATCTAATCATTA
46172 AGGTAATTTTATCATTAGAATTTGATTTA-TAATTATTAATTTTTAAAAATTTAATATCATTTTG
66 AGGTAATTTTATCATTAGAATTTGA-TTAGTAATTATTAATTTTTAAAAATTTAATATCATTTTG
46236 TTTGATATTATCAAAAATTAA
130 TTTGATATTATCAAAAATTAA
46257 ATATTATTAAATCTTTAAGTAGCTTTTAGTATTATTTTAATATCATCATAGTAATCTAATCATTA
1 ATATTATTAAATCTTTAAGTAGCTTTTAGTATTATTTTAATATCATCATAGTAATCTAATCATTA
46322 AGGTAATTTTATCATTAGAATTTGATTAGTAATTATTAATTTTTAAAAATTTAATATCATTTTGT
66 AGGTAATTTTATCATTAGAATTTGATTAGTAATTATTAATTTTTAAAAATTTAATATCATTTTGT
*
46387 TTGATATTATTAAAAATTAA
131 TTGATATTATCAAAAATTAA
46407 ATATTATT
1 ATATTATT
46415 TTATTTAAAA
Statistics
Matches: 155, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
149 3 0.02
150 152 0.98
ACGTcount: A:0.38, C:0.06, G:0.07, T:0.49
Consensus pattern (150 bp):
ATATTATTAAATCTTTAAGTAGCTTTTAGTATTATTTTAATATCATCATAGTAATCTAATCATTA
AGGTAATTTTATCATTAGAATTTGATTAGTAATTATTAATTTTTAAAAATTTAATATCATTTTGT
TTGATATTATCAAAAATTAA
Found at i:47525 original size:15 final size:16
Alignment explanation
Indices: 47505--47536 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
47495 TAATTAATTT
47505 TTAAATTAT-TTTTAA
1 TTAAATTATATTTTAA
47520 TTAAATTATATTTTAA
1 TTAAATTATATTTTAA
47536 T
1 T
47537 ACATGCATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTAAATTATATTTTAA
Found at i:48964 original size:13 final size:14
Alignment explanation
Indices: 48917--48964 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
48907 AGGGAGACTG
48917 AGAAAAGAAAG-AAA
1 AGAAAA-AAAGAAAA
*
48931 AGAAAAAAAGAGAA
1 AGAAAAAAAGAAAA
*
48945 GGAAAAAAAGAAAA
1 AGAAAAAAAGAAAA
48959 AGAAAA
1 AGAAAA
48965 GGTATAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 4 0.14
14 25 0.86
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AGAAAAAAAGAAAA
Found at i:48973 original size:20 final size:20
Alignment explanation
Indices: 48917--48966 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 20
48907 AGGGAGACTG
48917 AGAAAA-GAAAGAAAAGAAAAAA
1 AGAAAAGGAAA-AAAAG--AAAA
*
48939 AGAGAAGGAAAAAAAGAAAA
1 AGAAAAGGAAAAAAAGAAAA
48959 AGAAAAGG
1 AGAAAAGG
48967 TATAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 11 0.44
22 10 0.40
23 4 0.16
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (20 bp):
AGAAAAGGAAAAAAAGAAAA
Found at i:49043 original size:28 final size:26
Alignment explanation
Indices: 49012--49079 Score: 77
Period size: 25 Copynumber: 2.6 Consensus size: 26
49002 TTGTTATTTT
*
49012 ATATGTTTTATGTATATTTTATAAGTAA
1 ATAT-TTTTATATATATTTT-TAAGTAA
* *
49040 ATATATTTATAT-TATTTTTAATTAA
1 ATATTTTTATATATATTTTTAAGTAA
49065 AT-TTTTTATATATAT
1 ATATTTTTATATATAT
49080 CTATATCATA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 8 0.23
25 11 0.31
26 6 0.17
27 6 0.17
28 4 0.11
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (26 bp):
ATATTTTTATATATATTTTTAAGTAA
Found at i:49354 original size:14 final size:12
Alignment explanation
Indices: 49323--49369 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
49313 TTCATATATT
49323 TATATTTTTTAA
1 TATATTTTTTAA
*
49335 TTTATTTTTTACA
1 TATATTTTTTA-A
49348 TCATATTATTTTAA
1 T-ATATT-TTTTAA
49362 T-TATTTTT
1 TATATTTTT
49370 ATATTATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
11 3 0.10
12 14 0.47
13 2 0.07
14 6 0.20
15 5 0.17
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (12 bp):
TATATTTTTTAA
Found at i:49377 original size:11 final size:11
Alignment explanation
Indices: 49350--49384 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
49340 TTTTTACATC
49350 ATATTA-TTTT
1 ATATTATTTTT
49360 A-ATTATTTTT
1 ATATTATTTTT
49370 ATATTATTTTT
1 ATATTATTTTT
49381 ATAT
1 ATAT
49385 CGTTTCTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 4 0.17
10 6 0.26
11 13 0.57
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
ATATTATTTTT
Found at i:51550 original size:2 final size:2
Alignment explanation
Indices: 51539--51567 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
51529 TATTATCCGA
51539 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51568 GTAAATTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:51929 original size:18 final size:19
Alignment explanation
Indices: 51906--51947 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
51896 ATATAATTTT
51906 TTAATTT-TGTAAAAATAA
1 TTAATTTATGTAAAAATAA
*
51924 TTAATTTAATGTAAAAATTA
1 TTAATTT-ATGTAAAAATAA
51944 TTAA
1 TTAA
51948 AAAAAAGATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
20 14 0.67
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
TTAATTTATGTAAAAATAA
Found at i:52097 original size:22 final size:22
Alignment explanation
Indices: 52060--52109 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 22
52050 AATTTTAAAA
52060 ATTTTATTATTATATTATATTTTAT
1 ATTTTATTA-TAT-TTAT-TTTTAT
*
52085 ATTTTATTTTATTTATTTTTAT
1 ATTTTATTATATTTATTTTTAT
52107 ATT
1 ATT
52110 ACATTTACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 9 0.38
23 4 0.17
24 3 0.12
25 8 0.33
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (22 bp):
ATTTTATTATATTTATTTTTAT
Found at i:52115 original size:17 final size:17
Alignment explanation
Indices: 52062--52116 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 17
52052 TTTTAAAAAT
*
52062 TTTATTATTATATTATA
1 TTTATTTTTATATTATA
52079 TTTTATATTTTAT-TT-TA
1 -TTTAT-TTTTATATTATA
*
52096 TTTATTTTTATATTACA
1 TTTATTTTTATATTATA
52113 TTTA
1 TTTA
52117 CATAATATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
15 6 0.19
16 7 0.22
17 7 0.22
18 7 0.22
19 5 0.16
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTATTTTTATATTATA
Found at i:52115 original size:22 final size:24
Alignment explanation
Indices: 52069--52115 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
52059 AATTTTATTA
**
52069 TTATATTATATTTTATATTTTATT
1 TTATATTATATTTTATATTACATT
52093 TTAT-TTAT-TTTTATATTACATT
1 TTATATTATATTTTATATTACATT
52115 T
1 T
52116 ACATAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 13 0.62
23 4 0.19
24 4 0.19
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (24 bp):
TTATATTATATTTTATATTACATT
Found at i:52739 original size:19 final size:19
Alignment explanation
Indices: 52704--52756 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
52694 ACTAGGCACA
*
52704 TGAT-TTTTTAAGTTATT-
1 TGATATTTTTAATTTATTG
52721 TGATATTTTTAATTATATTG
1 TGATATTTTTAATT-TATTG
*
52741 TAATATTTTTAATTTA
1 TGATATTTTTAATTTA
52757 AAATATATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 4 0.13
18 8 0.26
19 6 0.19
20 13 0.42
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (19 bp):
TGATATTTTTAATTTATTG
Found at i:53407 original size:3 final size:3
Alignment explanation
Indices: 53393--53438 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
53383 TCAAATCTCC
* *
53393 TCT TCC TCT TCT TCT TCT TCT TCT TCT TCT TCG TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
53439 AATCTTAAGC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.35, G:0.02, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:57217 original size:16 final size:17
Alignment explanation
Indices: 57184--57217 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
57174 CCCTTTCTTC
57184 TTTCTCTGATGATTTTTA
1 TTTCTCTGAT-ATTTTTA
57202 TTTCTCTGAT-TTTTTA
1 TTTCTCTGATATTTTTA
57218 GCTTTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.15, C:0.12, G:0.09, T:0.65
Consensus pattern (17 bp):
TTTCTCTGATATTTTTA
Found at i:59757 original size:36 final size:36
Alignment explanation
Indices: 59685--59757 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 36
59675 TCTGTCACTG
* **
59685 CCACATTCCGAGTCTCAAAACCAAGCTAAGTTATTA
1 CCACAATCCGAGTCTCAAAACCAAGCTAAGCGATTA
* * * *
59721 CCACAATCTGAGTCTCAAAACCAGGTTGAGCGATTA
1 CCACAATCCGAGTCTCAAAACCAAGCTAAGCGATTA
59757 C
1 C
59758 TTTTGTCCCC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.23
Consensus pattern (36 bp):
CCACAATCCGAGTCTCAAAACCAAGCTAAGCGATTA
Found at i:63913 original size:41 final size:41
Alignment explanation
Indices: 63862--63948 Score: 165
Period size: 41 Copynumber: 2.1 Consensus size: 41
63852 AAAAGGATAA
*
63862 TTTTTTTCCTTTTAAAATTTTGGAGATAACTGACGAATTTT
1 TTTTTTTCCTTCTAAAATTTTGGAGATAACTGACGAATTTT
63903 TTTTTTTCCTTCTAAAATTTTGGAGATAACTGACGAATTTT
1 TTTTTTTCCTTCTAAAATTTTGGAGATAACTGACGAATTTT
63944 TTTTT
1 TTTTT
63949 ACTAATCCCT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.25, C:0.10, G:0.11, T:0.53
Consensus pattern (41 bp):
TTTTTTTCCTTCTAAAATTTTGGAGATAACTGACGAATTTT
Found at i:63970 original size:22 final size:22
Alignment explanation
Indices: 63945--63989 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
63935 ACGAATTTTT
63945 TTTTACTAATCCCTAACTTCTC
1 TTTTACTAATCCCTAACTTCTC
*
63967 TTTTACTAATCCCTAATTTCTC
1 TTTTACTAATCCCTAACTTCTC
63989 T
1 T
63990 GCTGTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTTACTAATCCCTAACTTCTC
Found at i:74005 original size:21 final size:21
Alignment explanation
Indices: 73981--74057 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
73971 AATTTATCCA
73981 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
74002 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* *
74023 AATGTATCGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
74044 AATGTATCGATACA
1 AATGTATCGATACA
74058 GGGTCCCAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 3 0.06
21 48 0.94
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:74117 original size:19 final size:19
Alignment explanation
Indices: 74093--74162 Score: 71
Period size: 19 Copynumber: 4.0 Consensus size: 19
74083 AATTCAACAA
74093 TTTGTATCGATACATAATT
1 TTTGTATCGATACATAATT
74112 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAATT
* *
74127 --TGTATTGATACATAAGT
1 TTTGTATCGATACATAATT
*
74144 ATTGTATCGATACATAATT
1 TTTGTATCGATACATAATT
74163 AGCTACTGCC
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
13 10 0.24
15 2 0.05
17 2 0.05
19 28 0.67
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (19 bp):
TTTGTATCGATACATAATT
Found at i:74137 original size:32 final size:32
Alignment explanation
Indices: 74095--74157 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
74085 TTCAACAATT
* *
74095 TGTATCGATACATAATTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
*
74127 TGTATTGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
74158 TAATTAGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:74218 original size:13 final size:13
Alignment explanation
Indices: 74200--74225 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
74190 CATTTTTCTG
74200 TGTATCGATACAT
1 TGTATCGATACAT
74213 TGTATCGATACAT
1 TGTATCGATACAT
74226 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:74222 original size:33 final size:33
Alignment explanation
Indices: 74180--74246 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
74170 GCCAAGGAAA
***
74180 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
74213 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
74246 T
1 T
74247 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:76701 original size:54 final size:51
Alignment explanation
Indices: 76569--76963 Score: 178
Period size: 52 Copynumber: 7.5 Consensus size: 51
76559 TTGAGTTTCT
* * * * *
76569 CAATTCTCCACAATCGGGGATATTCCAACTCTGATTTTATTTTCAAACCAC
1 CAATTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC
* *
76620 TAATT-TTCTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACAC
1 CAATTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC--AAAACAC
* * * ** * *
76673 CAATTTCTTCACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTC
1 CAA-TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC--CAAAACAC
* * ** * ***
76726 CAACCCCGTTATTTC-CGA--GGGGATACTTTAACTCCGACTTTATTTCCAAAATGT
1 CAA-----TT-CTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC
** * * * * * *
76780 TGATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACAC
1 CAATTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC
* * * * * * *
76831 TAATTTTTCCACAATCGGGAACACTTCAA-TCCCGGTTTTATTTTCAAAACAC
1 CAATTCTT-CACAATCGGGGATACTCCAACT-CCGATTTTATTTCCAAAACAC
* * *
76883 CAATT-TTC-CTTTAATCGAGGATACTCCAACTCTGATTTTATTTCCAAAAATAC
1 CAATTCTTCAC---AATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAACAC
* *
76936 CAATTTTTCACAATCGAGGATACTCCAA
1 CAATTCTTCACAATCGGGGATACTCCAA
76964 TCTCGTTATT
Statistics
Matches: 255, Mismatches: 62, Indels: 53
0.69 0.17 0.14
Matches are distributed among these distances:
48 4 0.02
49 4 0.02
50 3 0.01
51 70 0.27
52 83 0.33
53 29 0.11
54 30 0.12
55 19 0.07
56 2 0.01
57 8 0.03
58 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (51 bp):
CAATTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC
Found at i:76984 original size:28 final size:28
Alignment explanation
Indices: 76948--77024 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
76938 ATTTTTCACA
* * * *
76948 ATCGAGGATACTCCAATCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
76976 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
77004 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
77025 GCTTTATTCC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.25
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:90798 original size:55 final size:54
Alignment explanation
Indices: 90497--91523 Score: 997
Period size: 55 Copynumber: 18.3 Consensus size: 54
90487 GCTTTTTAGC
**
90497 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGT
1 CCTCAAAGAGCAGGAC-CC----CTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGT
90557 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
1 CCTCAAAGAGCAGGAC-CC----CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
* * *
90616 CCTCAAAGAGCGGGACACATTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTCAGT
1 CCTCAAAGAGCAGGAC-C----CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
**
90675 CCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTC-GT
1 CCTCAAAGAGCAGGA--C---CCCTTTT-AAAGCCCACACAAGTTGGTGGCACC--TTCAGT
*
90736 CCCCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGT
1 CCTCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT--CAGT
*
90791 CCTCAAAGAGTAGGACACCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
1 CCTCAAAGAGCAGG--A-C--C-CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
* *
90851 CCTCAAAGAGCGGGACGCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
1 CCTCAAAGAGCAGGAC-C----CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
* * *
90910 CCTCAAAGAGCGGGATGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTCAGT
1 CCTCAAAGAGCAGGA--CC---CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
**
90969 CCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGT
1 CCTCAAAGAGCAGGA--C---CCCTTTT-AAAGCCCACACAAGTTGGTGGCACC-TTCAGT
* ** **
91030 CCCCAAAGAGCAGGACCCCTTTCGAAGCCCACACAAGTTGGTGGCATTTTTCAGT
1 CCTCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTCAGT
* * *
91085 CCTCAAAGAGCAAGACACCTTTCAAAGCCCACACAAGTTGGTGG------CA-T
1 CCTCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
* * *
91132 CCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGT
1 CCTCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTCAGT
* ** **
91187 CCCCAAAGAGCAGGACCCCTTTCGAAGCCCACACAAGTTGGTGGCATTTTCCAGT
1 CCTCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGT
* *
91242 CCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGG------CA-T
1 CCTCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
* *
91289 CCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGT
1 CCTCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTCAGT
* * * * **
91344 CCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTAGTGGCATTTTCCAGT
1 CCTCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGT
* *
91399 CCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGT
1 CCTCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTCAGT
* * * * *
91454 CCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGT
1 CCTCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTCAGT
91509 CCTCAAAGAGCAGGA
1 CCTCAAAGAGCAGGA
91524 TACACTTTAT
Statistics
Matches: 846, Mismatches: 69, Indels: 109
0.83 0.07 0.11
Matches are distributed among these distances:
47 85 0.10
48 4 0.00
52 2 0.00
54 9 0.01
55 347 0.41
56 12 0.01
57 2 0.00
58 2 0.00
59 191 0.23
60 119 0.14
61 67 0.08
62 6 0.01
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (54 bp):
CCTCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
Found at i:91034 original size:294 final size:283
Alignment explanation
Indices: 90497--91524 Score: 1233
Period size: 294 Copynumber: 3.7 Consensus size: 283
90487 GCTTTTTAGC
*
90497 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCA
1 CCTCAAAGAGCAGGACACC-TTTC----AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCA
*
90562 AAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAG
61 AAGAGCAGGACACC---TC--TTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAG
* * * *
90626 CGGGACACATTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGAT
121 CAGGACGC-CTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGAT
90691 GCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTC-GTCCCCAAAGAGCAGGACCCC
185 GCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC-TTTCAGTCCCCAAAGAGCAGGACCCC
*
90755 TTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGT
249 TTTTAAAGCCCACACAAGTTGGTGGCACTT-TCAGT
* **
90791 CCTCAAAGAGTAGGACACCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTC
1 CCTCAAAGAGCAGGACACCTT-T-C----AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC
* * *
90855 AAAGAGCGGGACGCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGA
60 AAAGAGCAGGACAC-----CTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGA
* * *
90919 GCGGGATGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGA
120 GCAGGACGCC-TTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGA
90984 TGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACCCC
184 TGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACCCC
** *
91049 TTTCGAAGCCCACACAAGTTGGTGGCATTTTTCAGT
249 TTTTAAAGCCCACACAAGTTGGTGGCA-CTTTCAGT
*
91085 CCTCAAAGAGCAAGACACCTTTCAAAGCCCACACAAGTTGGTGG-------CA-TCCTCAAAGAG
1 CCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAG
* *
91142 CAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCCCAAAGAGCAGGAC-CC-
66 CAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCT
** ** * *
91205 --CTTTCGAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA--C----ACCT
131 TTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGATGCTTTTTCTT
* * *
91262 TTCAAAGCCCACACAAGTTGGTGG-------CA-TCCTCAAAGAGCAGGACACCTCTTAAAGCCC
195 TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACCCCTTTTAAAGCCC
91319 ACACAAGTTGGTGGCACCTTTCAGT
260 ACACAAGTTGGTGGCA-CTTTCAGT
* *
91344 CCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTAGTGGCATTTTCCAGTCCTCAAAGAG
1 CCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAG
91409 CAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCT
66 CAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCT
* * *
91474 TTC----AAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGAT
131 TTCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTCAGTCCTCAAAGAGCAGGAT
91525 ACACTTTATT
Statistics
Matches: 663, Mismatches: 45, Indels: 78
0.84 0.06 0.10
Matches are distributed among these distances:
259 90 0.14
260 2 0.00
266 2 0.00
267 135 0.20
268 5 0.01
271 2 0.00
272 27 0.04
273 19 0.03
276 31 0.05
277 18 0.03
281 17 0.03
282 2 0.00
288 21 0.03
292 1 0.00
293 7 0.01
294 250 0.38
295 32 0.05
296 1 0.00
299 1 0.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (283 bp):
CCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAG
CAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCT
TTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTT
TCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACCCCTTTTAAAGCCCA
CACAAGTTGGTGGCACTTTCAGT
Found at i:91284 original size:157 final size:159
Alignment explanation
Indices: 90520--91523 Score: 1022
Period size: 157 Copynumber: 6.0 Consensus size: 159
90510 GACGCCTTTT
* *
90520 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTT
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACC-TTTC----
* *
90585 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACACATTTTCTTTTAAAGCC
61 AAAGCCCACACAAGTTGGTGG---C--CAGTCCTCAAAGAGCAGGACAC-----CTCTTAAAGCC
* * *
90650 CACCCAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGATGCTTTTTC
116 CACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGA--C----CC
* * * *
90699 TTTTCAAAGCCCACACAAGTTGGTGGCACCTTTT-C-GTCCCCAAAGAGCAGGACCCCTTTTAAA
1 CTTTCAAAGCCCACACAAGTTGGTGGCA--TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAA
*
90762 GCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGTAGGACACCTTCTCCTTTTAAAGCCC
64 GCCCACACAAGTTGGTGG------CCAGTCCTCAAAGAGCAGGACA-C--CT-C--TTAAAGCCC
* * *
90827 ACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCGGGACGCTTTTT
117 ACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGAC-C----C
* ** * **
90874 CTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCGGGATGCCTTTTCTTTT
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACC-TTTC----
* ** *
90938 AAAGCCCACCCAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGC
61 AAAGCCCACACAAGTTGGTGG---C--CAGTCCTCAAAGAGCAGGA--C---ACCTCTT-AAAGC
91003 CCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACCC
115 CCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACCC
* * *
91048 CTTTCGAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAAGACACCTTTCAAAGC
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGC
91113 CCACACAAGTTGGTGG-CA-TCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGG
66 CCACACAAGTTGGTGGCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGG
*
91176 CACCTTTTAGTCCCCAAAGAGCAGGACCC
131 CACCTTTCAGTCCCCAAAGAGCAGGACCC
*
91205 CTTTCGAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGC
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGC
91270 CCACACAAGTTGGTGG-CA-TCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGG
66 CCACACAAGTTGGTGGCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGG
*
91333 CACCTTTCAGTCCCCAAAGAGCAGGACAC
131 CACCTTTCAGTCCCCAAAGAGCAGGACCC
*
91362 CTTTCAAAGCCCACACAAGTTAGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAG
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCT-TTCAAAG
* *
91426 CCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCT-TTCAAAGCCCACACGA
65 CCCACACAAGTTGGTGG---C---CAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAA
* * *
91490 GTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGA
123 GTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGA
91524 TACACTTTAT
Statistics
Matches: 728, Mismatches: 58, Indels: 92
0.83 0.07 0.10
Matches are distributed among these distances:
157 278 0.38
158 6 0.01
161 1 0.00
163 16 0.02
164 6 0.01
165 63 0.09
170 20 0.03
173 7 0.01
174 71 0.10
175 67 0.09
176 49 0.07
177 4 0.01
178 47 0.06
179 85 0.12
180 4 0.01
181 4 0.01
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (159 bp):
CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGC
CCACACAAGTTGGTGGCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGG
CACCTTTCAGTCCCCAAAGAGCAGGACCC
Found at i:94237 original size:51 final size:51
Alignment explanation
Indices: 94180--94565 Score: 271
Period size: 52 Copynumber: 7.4 Consensus size: 51
94170 AATTCTCCAC
* * * *
94180 AATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTAT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCTAT
* *
94231 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAA-TTTCTTCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCC--AAAACACCAATTTTC-T-AT
* * ** * * **
94285 AATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAA-CCTCGTTAT
1 AATCGGGGATACTCCAACCCCGATTTTAT-TTC--CAAAACACCAATTTTC--TAT
** * *****
94338 TTTCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAATGTTGATTTT-TCAT
1 AATC--GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCT-AT
* * * * *
94391 AATCGGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAATTTTTCCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAA-TTTTCTAT
* * *
94443 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTTCTTT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAA-TTTTCTAT
* * * *
94495 AATCGGGGATACTCCAACTCTGATTTTATTTCCAAAAATACCAATTTT-TCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCC-AAAACACCAATTTTCT-AT
*
94547 AATCGAGGATACTCCAACC
1 AATCGGGGATACTCCAACC
94566 TCGTTATTTC
Statistics
Matches: 261, Mismatches: 56, Indels: 35
0.74 0.16 0.10
Matches are distributed among these distances:
51 64 0.25
52 108 0.41
53 37 0.14
54 27 0.10
55 19 0.07
56 2 0.01
57 4 0.02
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.32
Consensus pattern (51 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCTAT
Found at i:94356 original size:28 final size:27
Alignment explanation
Indices: 94286--94361 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
94276 TTTCTTCACA
94286 ATCGGGGATACTCCAACCCCGTTAATC
1 ATCGGGGATACTCCAACCCCGTTAATC
* *
94313 ATCGGGGATACTCCAACCTCGTT-ATT
1 ATCGGGGATACTCCAACCCCGTTAATC
*
94339 TTCGAGGGGATACTCCAACCCCG
1 ATC--GGGGATACTCCAACCCCG
94362 ACTTTATTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 4 0.09
27 22 0.51
28 17 0.40
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.24
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTAATC
Found at i:94584 original size:28 final size:28
Alignment explanation
Indices: 94548--94624 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
94538 ATTTTTCACA
* * *
94548 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
94576 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
94604 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
94625 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:94648 original size:263 final size:263
Alignment explanation
Indices: 94175--94675 Score: 817
Period size: 263 Copynumber: 1.9 Consensus size: 263
94165 TTCTCAATTC
* * *
94175 TCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
*
94240 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
* * *
94305 CGTTAATCATCGGGGATACTCCAACCTCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATT
131 CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATT
* *
94370 TCCAAAATGTTGATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAAT
196 CCCAAAATATTGATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAAT
94435 TTT
261 TTT
* *
94438 TCCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTTCTTTAATCGGGG
1 TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAA-TTTTCTATAATCGGGG
* *
94503 ATACTCCAACTCTGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAACC
65 ATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACC
* * *
94566 TCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTA
130 CCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTA
*
94631 TTCCCAAAATATTGATTTTTCATAATTGGGGATACTCCAACCCCG
194 TTCCCAAAATATTGATTTTTCATAATCGGGGATACTCCAACCCCG
94676 TTATTTTTTA
Statistics
Matches: 219, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
262 28 0.13
263 152 0.69
264 39 0.18
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (263 bp):
TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATT
CCCAAAATATTGATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAAT
TTT
Found at i:94698 original size:28 final size:28
Alignment explanation
Indices: 94658--94712 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
94648 TTTCATAATT
94658 GGGGATACTCCAACCCCG-TTATTTTTTA
1 GGGGATACTCCAACCCCGATT-TTTTTTA
*
94686 GGGGATACTCCAATCCCGATTTTTTTT
1 GGGGATACTCCAACCCCGATTTTTTTT
94713 CTAATCATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 23 0.92
29 2 0.08
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGATTTTTTTTA
Found at i:97145 original size:13 final size:13
Alignment explanation
Indices: 97127--97152 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
97117 TACACAAAGT
97127 ATGTATCGATACA
1 ATGTATCGATACA
97140 ATGTATCGATACA
1 ATGTATCGATACA
97153 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:97171 original size:34 final size:32
Alignment explanation
Indices: 97109--97173 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
97099 TAGCCAAACT
**
97109 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAATGTATCGATACAA
97141 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACAC-AAAAAA-TGTATCGATACA
97174 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 13 0.45
33 4 0.14
34 12 0.41
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATGTATCGATACAA
Found at i:100832 original size:17 final size:17
Alignment explanation
Indices: 100810--100844 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
100800 TCCTGTATAA
100810 TTCAAAAA-AATAATTTT
1 TTCAAAAATAA-AATTTT
100827 TTCAAAAATAAAATTTT
1 TTCAAAAATAAAATTTT
100844 T
1 T
100845 GAAAGATTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (17 bp):
TTCAAAAATAAAATTTT
Found at i:104014 original size:15 final size:16
Alignment explanation
Indices: 103984--104017 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
103974 GTAATTAATT
103984 TATTAAAATATTTTTA
1 TATTAAAATATTTTTA
*
104000 TATTAAAA-GTTTTTA
1 TATTAAAATATTTTTA
104015 TAT
1 TAT
104018 ATTTTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
TATTAAAATATTTTTA
Found at i:104897 original size:27 final size:27
Alignment explanation
Indices: 104867--104925 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
104857 GTATTAAAAT
* *
104867 TTATATAAATAAAAA-ATTTAAATATAA
1 TTATA-AAATAAAAATATATAAAAATAA
*
104894 TTATAATATAAAAATATATAAAAATAA
1 TTATAAAATAAAAATATATAAAAATAA
104921 -TATAA
1 TTATAA
104926 TACATAAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 13 0.46
27 15 0.54
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (27 bp):
TTATAAAATAAAAATATATAAAAATAA
Found at i:104914 original size:10 final size:11
Alignment explanation
Indices: 104896--104925 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
104886 AAATATAATT
104896 ATAATATAAAA
1 ATAATATAAAA
104907 AT-ATATAAAA
1 ATAATATAAAA
104917 ATAATATAA
1 ATAATATAA
104926 TACATAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:105242 original size:27 final size:27
Alignment explanation
Indices: 105195--105267 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
105185 TAATAAATAA
*
105195 AATTTTATATTATA-TAAAATTTA-AT
1 AATTTTATATTATATTTAAATTTATAT
* * *
105220 ATATTTTATATTATATTTTAATTTTTTT
1 A-ATTTTATATTATATTTAAATTTATAT
105248 AATTTTATATTATATTTAAA
1 AATTTTATATTATATTTAAA
105268 ATAATTATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
25 1 0.03
26 13 0.32
27 24 0.60
28 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
AATTTTATATTATATTTAAATTTATAT
Found at i:120533 original size:2 final size:2
Alignment explanation
Indices: 120528--120558 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
120518 TACATATATA
120528 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
120559 ATAACATAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:122627 original size:180 final size:180
Alignment explanation
Indices: 122354--122991 Score: 799
Period size: 196 Copynumber: 3.5 Consensus size: 180
122344 AGATGAAGAT
*
122354 GGCAAAGGAAACTGAAACT-GATGTTGGAGTTGATGACATAAGTGGACAGCTCCAAAGAGTGTTG
1 GGCAAAGGAAACTGAAACTAGA-GTTGGAGTTGATGACATAAGTGGACAACTCCAAAGAGTGTTG
*
122418 AACGTATAGATTAGGGAAATGTGGGCATGCACGCAGGCACTGGCGCTGGCACGGACCGTGACATT
65 AATGTATAGATTAGGGAAATGTGGGCATGCACGCAGGCACTGGCGCTGGCACGGACCGTGACATT
*
122483 TGGTTACCTGTCTTTTGTGCGTCTGAATCTTACTGTCTTGAATTCAGATGG
130 TGGTTACCTGTCTTTTGTGCGTCTGAATCTTACTGTCTTGAATTCAGATAG
* *
122534 GGCAAAGGAAACTGAAACTAGAGTTGGAGTTGATGACATAAGTGGACGACTCCAAAGAGTGTTGC
1 GGCAAAGGAAACTGAAACTAGAGTTGGAGTTGATGACATAAGTGGACAACTCCAAAGAGTGTTGA
*
122599 ATGTACAGATTAGGGAAATGTGGGCATGCGCAGGCACTGGCACTGGCACTGGCACTGGCACTGGC
66 ATGTATAGATTAGGGAAATGTGGGCAT------GCAC--GCA--GGCACTGG--C--G--CTGGC
* * *
122664 ATGGACCGTGACGTTTGGTTACCTGTCTTTTGTGCGTCTGAATCTTACTGTCTTGATTTCAGATA
115 ACGGACCGTGACATTTGGTTACCTGTCTTTTGTGCGTCTGAATCTTACTGTCTTGAATTCAGATA
122729 G
180 G
*
122730 GGCAAAGGAAACTGAAACTAGCGTTGGAGTTGATGACATAAGTGGACAACTCCAAAGAGTGTTGA
1 GGCAAAGGAAACTGAAACTAGAGTTGGAGTTGATGACATAAGTGGACAACTCCAAAGAGTGTTGA
* ** * * * * * *
122795 ATGTATAGATTA-GGAAATGTAGGTGTGCAAG--GGCGCTGGTGCAGGCACAGA-C-TAACATTT
66 ATGTATAGATTAGGGAAATGTGGGCATGCACGCAGGCACTGGCGCTGGCACGGACCGTGACATTT
* * *
122855 GGTTATCTGTCTTTTGTGAGT-TCGAATCTTACAGTCTTGAATTCAGATAG
131 GGTTACCTGTCTTTTGTGCGTCT-GAATCTTACTGTCTTGAATTCAGATAG
* * * *
122905 GGCAAAGGAAACTGAATCTGGAGTCGGAGTTGATGACATAAGTGGACAACT--ACAGAGTGTTGA
1 GGCAAAGGAAACTGAAACTAGAGTTGGAGTTGATGACATAAGTGGACAACTCCAAAGAGTGTTGA
* *
122968 ATGTATAGATTATGAAAATGTGGG
66 ATGTATAGATTAGGGAAATGTGGG
122992 TGCGTGGGAC
Statistics
Matches: 404, Mismatches: 35, Indels: 44
0.84 0.07 0.09
Matches are distributed among these distances:
173 23 0.06
174 10 0.02
175 97 0.24
176 1 0.00
177 7 0.02
179 1 0.00
180 84 0.21
181 2 0.00
183 7 0.02
186 4 0.01
187 1 0.00
188 3 0.01
189 3 0.01
190 8 0.02
192 1 0.00
194 1 0.00
195 11 0.03
196 140 0.35
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.27
Consensus pattern (180 bp):
GGCAAAGGAAACTGAAACTAGAGTTGGAGTTGATGACATAAGTGGACAACTCCAAAGAGTGTTGA
ATGTATAGATTAGGGAAATGTGGGCATGCACGCAGGCACTGGCGCTGGCACGGACCGTGACATTT
GGTTACCTGTCTTTTGTGCGTCTGAATCTTACTGTCTTGAATTCAGATAG
Found at i:122642 original size:6 final size:6
Alignment explanation
Indices: 122631--122664 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
122621 GGCATGCGCA
122631 GGCACT GGCACT GGCACT GGCACT GGCACT GGCA
1 GGCACT GGCACT GGCACT GGCACT GGCACT GGCA
122665 TGGACCGTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.32, G:0.35, T:0.15
Consensus pattern (6 bp):
GGCACT
Found at i:125741 original size:33 final size:33
Alignment explanation
Indices: 125701--125769 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
125691 CTATACTTCA
125701 TTCTTAAGCTATATAAATAAAAGATTCCAACAC
1 TTCTTAAGCTATATAAATAAAAGATTCCAACAC
* *
125734 TTCTTAAGCTATATAAATAAAGGATTTCAACAC
1 TTCTTAAGCTATATAAATAAAAGATTCCAACAC
125767 TTC
1 TTC
125770 AACTTCCAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (33 bp):
TTCTTAAGCTATATAAATAAAAGATTCCAACAC
Found at i:128958 original size:29 final size:30
Alignment explanation
Indices: 128915--128973 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
128905 TTTTTTATTT
128915 TTTTATCTAATAATTAACTATATAAAATAA
1 TTTTATCTAATAATTAACTATATAAAATAA
* *
128945 TTTTATGT-ATAATTAATTATATAAAATAA
1 TTTTATCTAATAATTAACTATATAAAATAA
128974 ATAAATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (30 bp):
TTTTATCTAATAATTAACTATATAAAATAA
Found at i:128985 original size:29 final size:29
Alignment explanation
Indices: 128923--128985 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
128913 TTTTTTATCT
* ** *
128923 AATAATTAACTATATAAAATAATTTTATG
1 AATAATTAACTATATAAAATAAATAAATA
* *
128952 TATAATTAATTATATAAAATAAATAAATA
1 AATAATTAACTATATAAAATAAATAAATA
128981 AATAA
1 AATAA
128986 ACATGGATAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (29 bp):
AATAATTAACTATATAAAATAAATAAATA
Found at i:129404 original size:16 final size:16
Alignment explanation
Indices: 129383--129413 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
129373 AAGACTTAGT
*
129383 TTCATCACTCAATTGC
1 TTCATCACTAAATTGC
129399 TTCATCACTAAATTG
1 TTCATCACTAAATTG
129414 TGCGCGAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.39
Consensus pattern (16 bp):
TTCATCACTAAATTGC
Found at i:130416 original size:22 final size:21
Alignment explanation
Indices: 130390--130430 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
130380 CAACTCAAAA
* *
130390 TAAAAATAAACAAAATAAAATT
1 TAAAAA-AAAAAAAAAAAAATT
130412 TAAAAAAAAAAAAAAAAAA
1 TAAAAAAAAAAAAAAAAAA
130431 CCAAAAACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.83, C:0.02, G:0.00, T:0.15
Consensus pattern (21 bp):
TAAAAAAAAAAAAAAAAAATT
Found at i:138820 original size:14 final size:14
Alignment explanation
Indices: 138801--138827 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
138791 TTATTAATAA
138801 TAAATAAATAAATT
1 TAAATAAATAAATT
138815 TAAATAAATAAAT
1 TAAATAAATAAAT
138828 ATATTAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAATAAATAAATT
Found at i:138885 original size:21 final size:21
Alignment explanation
Indices: 138822--138889 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
138812 ATTTAAATAA
138822 ATAAATA-TATTAATTAT-TT
1 ATAAATATTATTAATTATATT
* * * * *
138841 TTAAATATAAAATAA-TAAAAT
1 ATAAATAT-TATTAATTATATT
138862 ATAAATATTATTAATTATATT
1 ATAAATATTATTAATTATATT
138883 ATAAATA
1 ATAAATA
138890 AATAAAAATA
Statistics
Matches: 35, Mismatches: 10, Indels: 6
0.69 0.20 0.12
Matches are distributed among these distances:
19 6 0.17
20 6 0.17
21 23 0.66
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAAATATTATTAATTATATT
Found at i:138915 original size:37 final size:36
Alignment explanation
Indices: 138850--138931 Score: 89
Period size: 37 Copynumber: 2.3 Consensus size: 36
138840 TTTAAATATA
* *
138850 AAAT-AATAAAATATAAATATTATTAATTATATTAT
1 AAATAAATAAAATATAAATATCATGAATTATATTAT
*
138885 AAATAAATAAAA-ATAATTATATCATGAATTATTTTAT
1 AAATAAATAAAATATAA--ATATCATGAATTATATTAT
138922 -AATCAAATAA
1 AAAT-AAATAA
138932 TAAACAAGCT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
35 8 0.20
36 10 0.25
37 22 0.55
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.39
Consensus pattern (36 bp):
AAATAAATAAAATATAAATATCATGAATTATATTAT
Found at i:139712 original size:2 final size:2
Alignment explanation
Indices: 139705--139730 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
139695 GCATAGGCAC
139705 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
139731 ATAGAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:140454 original size:24 final size:26
Alignment explanation
Indices: 140403--140460 Score: 93
Period size: 24 Copynumber: 2.3 Consensus size: 26
140393 TGGATGGCTA
*
140403 GTCAACAAAAGCCACCCTTTGTGTTT
1 GTCAACAAAAGCCACCCTATGTGTTT
140429 GTCAACAAAAGCCA-CC-ATGTGTTT
1 GTCAACAAAAGCCACCCTATGTGTTT
140453 GTCAACAA
1 GTCAACAA
140461 TGGTGGTTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 15 0.48
25 2 0.06
26 14 0.45
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (26 bp):
GTCAACAAAAGCCACCCTATGTGTTT
Found at i:140532 original size:28 final size:27
Alignment explanation
Indices: 140448--140546 Score: 98
Period size: 27 Copynumber: 3.8 Consensus size: 27
140438 AGCCACCATG
* *
140448 TGTTTGTCAACAATGGTGG-TTACTTTG
1 TGTTTGTCAAAAATGGTGGCTT-CTTTT
* *
140475 TATTTGTCAAAAATGGTGGTTTCTTTT
1 TGTTTGTCAAAAATGGTGGCTTCTTTT
* *
140502 TGTTTGTCAAAAATTGTGG---CTTGT
1 TGTTTGTCAAAAATGGTGGCTTCTTTT
*
140526 TGTTTGTCAAAATTGGTGGCT
1 TGTTTGTCAAAAATGGTGGCT
140547 AATTTTTATT
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
24 21 0.34
27 38 0.62
28 2 0.03
ACGTcount: A:0.20, C:0.09, G:0.24, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGCTTCTTTT
Found at i:140533 original size:24 final size:24
Alignment explanation
Indices: 140477--140546 Score: 79
Period size: 24 Copynumber: 2.8 Consensus size: 24
140467 TTACTTTGTA
* *
140477 TTTGTCAAAAATGGTGGTTTCTTTTTG
1 TTTGTCAAAAATTGTGG---CTTGTTG
140504 TTTGTCAAAAATTGTGGCTTGTTG
1 TTTGTCAAAAATTGTGGCTTGTTG
140528 TTTGTC-AAAATTGGTGGCT
1 TTTGTCAAAAATT-GTGGCT
140547 AATTTTTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
23 6 0.15
24 18 0.45
27 16 0.40
ACGTcount: A:0.20, C:0.09, G:0.24, T:0.47
Consensus pattern (24 bp):
TTTGTCAAAAATTGTGGCTTGTTG
Found at i:145051 original size:24 final size:26
Alignment explanation
Indices: 145000--145057 Score: 93
Period size: 24 Copynumber: 2.3 Consensus size: 26
144990 TGGGTGGCTA
*
145000 GTCAACAAAAGCCACCCTTTGTGTTT
1 GTCAACAAAAGCCACCCTATGTGTTT
145026 GTCAACAAAAGCCA-CC-ATGTGTTT
1 GTCAACAAAAGCCACCCTATGTGTTT
145050 GTCAACAA
1 GTCAACAA
145058 TGGTGGTTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 15 0.48
25 2 0.06
26 14 0.45
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (26 bp):
GTCAACAAAAGCCACCCTATGTGTTT
Found at i:145129 original size:28 final size:27
Alignment explanation
Indices: 145045--145143 Score: 98
Period size: 27 Copynumber: 3.8 Consensus size: 27
145035 AGCCACCATG
* *
145045 TGTTTGTCAACAATGGTGG-TTACTTTG
1 TGTTTGTCAAAAATGGTGGCTT-CTTTT
* *
145072 TATTTGTCAAAAATGGTGGTTTCTTTT
1 TGTTTGTCAAAAATGGTGGCTTCTTTT
* *
145099 TGTTTGTCAAAAATTGTGG---CTTGT
1 TGTTTGTCAAAAATGGTGGCTTCTTTT
*
145123 TGTTTGTCAAAATTGGTGGCT
1 TGTTTGTCAAAAATGGTGGCT
145144 AATTTTTATT
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
24 21 0.34
27 38 0.62
28 2 0.03
ACGTcount: A:0.20, C:0.09, G:0.24, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGCTTCTTTT
Found at i:145130 original size:24 final size:24
Alignment explanation
Indices: 145074--145143 Score: 79
Period size: 24 Copynumber: 2.8 Consensus size: 24
145064 TTACTTTGTA
* *
145074 TTTGTCAAAAATGGTGGTTTCTTTTTG
1 TTTGTCAAAAATTGTGG---CTTGTTG
145101 TTTGTCAAAAATTGTGGCTTGTTG
1 TTTGTCAAAAATTGTGGCTTGTTG
145125 TTTGTC-AAAATTGGTGGCT
1 TTTGTCAAAAATT-GTGGCT
145144 AATTTTTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
23 6 0.15
24 18 0.45
27 16 0.40
ACGTcount: A:0.20, C:0.09, G:0.24, T:0.47
Consensus pattern (24 bp):
TTTGTCAAAAATTGTGGCTTGTTG
Found at i:147023 original size:14 final size:15
Alignment explanation
Indices: 146996--147028 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
146986 ATAAATAGAC
*
146996 AATCTATAATAAAAT
1 AATCTATAACAAAAT
147011 AATCTAT-ACAAAAT
1 AATCTATAACAAAAT
147025 AATC
1 AATC
147029 GAAAAAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCTATAACAAAAT
Found at i:147550 original size:16 final size:16
Alignment explanation
Indices: 147501--147554 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
147491 AGTATAAGAT
147501 TTTAATTTTTTAT-T-
1 TTTAATTTTTTATCTA
*
147515 TTAAATCTTTTTCA-CTTA
1 TTTAAT-TTTTT-ATC-TA
147533 TTTAATTTTTTATCTA
1 TTTAATTTTTTATCTA
147549 TTTAAT
1 TTTAAT
147555 AACAATTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 5 0.16
15 5 0.16
16 10 0.31
17 7 0.22
18 5 0.16
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTAATTTTTTATCTA
Found at i:147964 original size:18 final size:17
Alignment explanation
Indices: 147934--147967 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
147924 AGAGAATCAT
*
147934 ATTTTTTTGACGAAAAG
1 ATTTTTTTAACGAAAAG
147951 ATTTTTTATAACGAAAA
1 ATTTTTT-TAACGAAAA
147968 TTTTTTGACG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (17 bp):
ATTTTTTTAACGAAAAG
Found at i:148393 original size:30 final size:31
Alignment explanation
Indices: 148341--148398 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
148331 AAAAATGAAA
* *
148341 TAAAGAATAATTTTTGACAAAAT-TTTTCCT
1 TAAAGAATAATTTTTAAAAAAATATTTTCCT
148371 TAAA-AATATATTTTTAAAAAAATATTTT
1 TAAAGAATA-ATTTTTAAAAAAATATTTT
148399 AGAGAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 4 0.17
30 16 0.67
31 4 0.17
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (31 bp):
TAAAGAATAATTTTTAAAAAAATATTTTCCT
Found at i:148904 original size:15 final size:15
Alignment explanation
Indices: 148886--148920 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
148876 TTATTTAGAT
148886 TTAATTGATTTTTAG
1 TTAATTGATTTTTAG
148901 TTAATTGATTTTTAG
1 TTAATTGATTTTTAG
*
148916 CTAAT
1 TTAAT
148921 AGTCCTAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (15 bp):
TTAATTGATTTTTAG
Found at i:151333 original size:42 final size:41
Alignment explanation
Indices: 151287--151384 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 41
151277 TTTCATTCAA
*
151287 GATCAAGCAAAATCCTTAATGAAAACTAAAGCTATTGTTAAG
1 GATCAAGCAAAATCCTT-AGGAAAACTAAAGCTATTGTTAAG
* *
151329 GATCAAGCAAAATGCCTTAGGAAAACTTAAGCTATTGTTTAG
1 GATCAAGCAAAAT-CCTTAGGAAAACTAAAGCTATTGTTAAG
* *
151371 AACCAAGCAAAATC
1 GATCAAGCAAAATC
151385 TACAAGGAAC
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
41 1 0.02
42 45 0.90
43 4 0.08
ACGTcount: A:0.44, C:0.16, G:0.15, T:0.24
Consensus pattern (41 bp):
GATCAAGCAAAATCCTTAGGAAAACTAAAGCTATTGTTAAG
Found at i:154464 original size:20 final size:21
Alignment explanation
Indices: 154441--154490 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
154431 TCTTAAAAGT
*
154441 TTTTATTTAAATTT-AATTAA
1 TTTTATTTAAATTTAAATCAA
* **
154461 TTTTAGTTATCTTTAAATCAA
1 TTTTATTTAAATTTAAATCAA
154482 TTTTATTTA
1 TTTTATTTA
154491 TTTTTTATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTTATTTAAATTTAAATCAA
Found at i:154484 original size:30 final size:28
Alignment explanation
Indices: 154450--154506 Score: 69
Period size: 30 Copynumber: 2.0 Consensus size: 28
154440 TTTTTATTTA
*
154450 AATTTAATTAATTTTAGTTATCTTTAAATC
1 AATTTAATTAATTTT--TTATATTTAAATC
* *
154480 AATTTTATTTATTTTTTATATTTAAAT
1 AATTTAATTAATTTTTTATATTTAAAT
154507 TATATATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 11 0.46
30 13 0.54
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (28 bp):
AATTTAATTAATTTTTTATATTTAAATC
Found at i:157464 original size:22 final size:21
Alignment explanation
Indices: 157405--157464 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 21
157395 AAATATTAAT
157405 TATTTAA-TATTATAATGTAA
1 TATTTAATTATTATAATGTAA
*
157425 TATTTACATTTTTATAATGTAA
1 TATTTA-ATTATTATAATGTAA
157447 TAGTTTTAATTATT-TAAT
1 TA--TTTAATTATTATAAT
157465 AATATATAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 6 0.18
21 1 0.03
22 18 0.53
23 5 0.15
24 4 0.12
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (21 bp):
TATTTAATTATTATAATGTAA
Found at i:158263 original size:3 final size:3
Alignment explanation
Indices: 158255--158285 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
158245 ATATGTATTT
158255 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
158286 AAGCATGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:160699 original size:17 final size:18
Alignment explanation
Indices: 160679--160723 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
160669 CATACTTATT
160679 TATT-TGTTTT-ATATTTA
1 TATTATGTTTTCAT-TTTA
160696 TATTAT-TTTTCATTTTA
1 TATTATGTTTTCATTTTA
160713 TATTATGTTTT
1 TATTATGTTTT
160724 GCTTCTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 18 0.72
18 7 0.28
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.71
Consensus pattern (18 bp):
TATTATGTTTTCATTTTA
Found at i:161778 original size:14 final size:13
Alignment explanation
Indices: 161740--161792 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
161730 CACATCATTT
*
161740 AAAAATAAAAATA
1 AAAAATAAAATTA
*
161753 AAAACTAAAAAATTA
1 AAAA--ATAAAATTA
161768 AAAAATTAAAATTA
1 AAAAA-TAAAATTA
*
161782 AATAATAAAAT
1 AAAAATAAAAT
161793 AAATTTCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
13 11 0.33
14 11 0.33
15 11 0.33
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAAATAAAATTA
Found at i:161778 original size:22 final size:22
Alignment explanation
Indices: 161746--161797 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
161736 ATTTAAAAAT
* *
161746 AAAAATAAAAACTAAAAAATTA
1 AAAAATTAAAACTAAAAAATAA
* *
161768 AAAAATTAAAATTAAATAATAA
1 AAAAATTAAAACTAAAAAATAA
161790 AATAAATT
1 AA-AAATT
161798 TCTTTGTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (22 bp):
AAAAATTAAAACTAAAAAATAA
Found at i:162282 original size:17 final size:18
Alignment explanation
Indices: 162260--162293 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
162250 AGTTTTTTTT
162260 TCTTTCTCC-CTTTATTC
1 TCTTTCTCCTCTTTATTC
162277 TCTTTCTCCTCTTTATT
1 TCTTTCTCCTCTTTATT
162294 TTTTTTCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.06, C:0.32, G:0.00, T:0.62
Consensus pattern (18 bp):
TCTTTCTCCTCTTTATTC
Found at i:162300 original size:18 final size:17
Alignment explanation
Indices: 162256--162302 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
162246 TACTAGTTTT
162256 TTTTTCTTTCTCCCTTTA
1 TTTTT-TTTCTCCCTTTA
* *
162274 TTCTCTTTCTCCTCTTTA
1 TTTTTTTTCTCC-CTTTA
162292 TTTTTTTTCTC
1 TTTTTTTTCTC
162303 TTTCTTTTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.04, C:0.28, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTTTTTCTCCCTTTA
Found at i:162321 original size:11 final size:11
Alignment explanation
Indices: 162292--162328 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
162282 CTCCTCTTTA
162292 TTTTTTTTCTC
1 TTTTTTTTCTC
*
162303 TTTCTTTTTCCC
1 TTT-TTTTTCTC
162315 TTTTTTTTCTC
1 TTTTTTTTCTC
162326 TTT
1 TTT
162329 CCCCTCTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTTTCTC
Found at i:164794 original size:6 final size:6
Alignment explanation
Indices: 164773--164807 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
164763 TTTCCCATCC
*
164773 AAAATA AAAGTAA AAAATA AAAATA AAAATA AAAA
1 AAAATA AAAAT-A AAAATA AAAATA AAAATA AAAA
164808 AATCAAAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:165503 original size:36 final size:37
Alignment explanation
Indices: 165458--165542 Score: 102
Period size: 36 Copynumber: 2.3 Consensus size: 37
165448 AATTTTTTAT
165458 TTATATTAAATAATAAATATAAAA-TA-AAAATCATAC
1 TTATATTAAATAATAAATA-AAAATTATAAAATCATAC
* * * *
165494 TTATGTTAAATAATAATTAAAAATTATAAAATTATAT
1 TTATATTAAATAATAAATAAAAATTATAAAATCATAC
*
165531 TTATTTTAAATA
1 TTATATTAAATA
165543 GTTAAAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
35 4 0.10
36 19 0.45
37 19 0.45
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (37 bp):
TTATATTAAATAATAAATAAAAATTATAAAATCATAC
Found at i:165585 original size:15 final size:14
Alignment explanation
Indices: 165565--165606 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
165555 ATTTATATTA
165565 AAAATAAGTTAATAT
1 AAAATAA-TTAATAT
*
165580 AAAATAATTTAAAAT
1 AAAATAA-TTAATAT
165595 -AAATAATTAATA
1 AAAATAATTAATA
165607 ATTAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 5 0.21
14 6 0.25
15 13 0.54
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (14 bp):
AAAATAATTAATAT
Found at i:166772 original size:20 final size:20
Alignment explanation
Indices: 166748--166792 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
166738 TTTAATACTT
*
166748 TTTTATT-GTTAGAATTATA
1 TTTTATTAGTTAAAATTATA
*
166767 TCTTTATTATTTAAAATTATA
1 T-TTTATTAGTTAAAATTATA
166788 TTTTA
1 TTTTA
166793 ACATTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 10 0.45
21 11 0.50
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTTATTAGTTAAAATTATA
Found at i:168511 original size:27 final size:26
Alignment explanation
Indices: 168381--168513 Score: 83
Period size: 27 Copynumber: 4.9 Consensus size: 26
168371 GAGAATTCAG
*
168381 ATGACAAAAAGTCTGATCCTGAAGAGA
1 ATGACAAAAA-TCTGATCCTGATGAGA
*** * *
168408 GCAACGAGAAACCTGACTCC-GATGAGA
1 ATGAC-AAAAATCTGA-TCCTGATGAGA
* *
168435 ATGACAAGAAATCTGATTCTGAGGAGA
1 ATGACAA-AAATCTGATCCTGATGAGA
* *
168462 GTGATGC-AAAATCT-AACTCTGATGAGA
1 ATGA--CAAAAATCTGATC-CTGATGAGA
168489 ATGACAACAAATCTGATCCTGATGA
1 ATGACAA-AAATCTGATCCTGATGA
168514 TGGTGAAAAG
Statistics
Matches: 77, Mismatches: 19, Indels: 20
0.66 0.16 0.17
Matches are distributed among these distances:
25 1 0.01
26 5 0.06
27 60 0.78
28 10 0.13
29 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (26 bp):
ATGACAAAAATCTGATCCTGATGAGA
Found at i:185499 original size:20 final size:20
Alignment explanation
Indices: 185452--185526 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
185442 AAAAAGACAT
*
185452 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
185471 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
185492 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
185512 AATGTATCGATACAT
1 AATGTATCGATACAT
185527 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:185520 original size:40 final size:39
Alignment explanation
Indices: 185449--185526 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
185439 GGTAAAAAGA
* *
185449 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
185488 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
185527 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:187245 original size:16 final size:16
Alignment explanation
Indices: 187220--187253 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
187210 ATTCTTTTTT
*
187220 ATTATAGAATTTAGTA
1 ATTATAGAATTCAGTA
*
187236 ATTATTGAATTCAGTA
1 ATTATAGAATTCAGTA
187252 AT
1 AT
187254 ATTTTGGTTC
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:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (16 bp):
ATTATAGAATTCAGTA
Found at i:201691 original size:23 final size:23
Alignment explanation
Indices: 201647--201691 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
201637 ATATAATTAC
* * *
201647 ATTTAAAAATTAATTTTTAATAA
1 ATTTAAAAATTAAATCTCAATAA
*
201670 ATTTAAAATTTAAATCTCAATA
1 ATTTAAAAATTAAATCTCAATA
201692 TTTATGATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (23 bp):
ATTTAAAAATTAAATCTCAATAA
Found at i:202898 original size:19 final size:19
Alignment explanation
Indices: 202874--202913 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
202864 CTTAACCATA
202874 ATTAAGATTTTTTATATTT
1 ATTAAGATTTTTTATATTT
202893 ATTAAGATTTTTTATATTT
1 ATTAAGATTTTTTATATTT
202912 AT
1 AT
202914 AAAGGAAAAT
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:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (19 bp):
ATTAAGATTTTTTATATTT
Found at i:204464 original size:16 final size:16
Alignment explanation
Indices: 204431--204492 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 16
204421 TACCACAAAA
204431 ATAAT-TAAAATATTAT
1 ATAATATAAAA-ATTAT
*
204447 ATAATATAAAAATAAT
1 ATAATATAAAAATTAT
204463 ATAAATATATTAAAATTTAT
1 AT-AATATA--AAAA-TTAT
204483 ATAATATAAA
1 ATAATATAAA
204493 TAATCAACAT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 11 0.28
17 13 0.33
19 10 0.26
20 5 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATAATATAAAAATTAT
Found at i:204488 original size:19 final size:19
Alignment explanation
Indices: 204430--204490 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
204420 ATACCACAAA
204430 AATA-ATTAAAATATTATAT
1 AATATATTAAAAT-TTATAT
*
204449 AATATA--AAAA-TAATAT
1 AATATATTAAAATTTATAT
204465 AAATATATTAAAATTTATAT
1 -AATATATTAAAATTTATAT
204485 AATATA
1 AATATA
204491 AATAATCAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
16 5 0.14
17 6 0.17
18 4 0.11
19 14 0.40
20 6 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATATATTAAAATTTATAT
Found at i:208277 original size:13 final size:15
Alignment explanation
Indices: 208247--208285 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
208237 CTTATTCTTA
208247 TTATTATTTTTAATT
1 TTATTATTTTTAATT
*
208262 TTATT-TTTTTCA-T
1 TTATTATTTTTAATT
208275 TTATTATTTTT
1 TTATTATTTTT
208286 TAATATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 6 0.27
14 11 0.50
15 5 0.23
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (15 bp):
TTATTATTTTTAATT
Done.