Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold198
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: 3915534
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 240068 characters in sequence are not A, C, G, or T
File 2 of 13
Found at i:227941 original size:43 final size:42
Alignment explanation
Indices: 227824--228051 Score: 262
Period size: 43 Copynumber: 5.3 Consensus size: 42
227814 AAGATATATT
* *
227824 TTTAGTGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTAT--TC
1 TTTAGCGGCGTTTTTG-GAAAAGCGCCGCTAAAGGTC-ATGGTC
* * * *
227866 TATAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGTCCTGGTC
1 TTTAGCGGCGTTT-TTGGAAAAGCGCCGCTAAAGGTCATGGTC
* * * *
227909 TTTAGTGGCGCTTTTTGTAAAAGTGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCG-TTTTTGGAAAAGCGCCGCTAAAGGTCATGGTC
* *
227952 TTTAGCGGCGTTTTTTGTAAAAGCGCCGCTAAAAGGTTATGGTC
1 TTTAGCGGCG-TTTTTGGAAAAGCGCCGCT-AAAGGTCATGGTC
227996 TTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTT-TTGGAAAAGCGCCGCTAAAGGTCATGGTC
*
228039 TTTAGTGGCGTTT
1 TTTAGCGGCGTTT
228052 ATTTATAAAA
Statistics
Matches: 159, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
41 1 0.01
42 30 0.19
43 89 0.56
44 39 0.25
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (42 bp):
TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:228024 original size:87 final size:87
Alignment explanation
Indices: 227824--228072 Score: 292
Period size: 87 Copynumber: 2.9 Consensus size: 87
227814 AAGATATATT
* * * *
227824 TTTAGTGGCGTTTG-TGAGAAAAGCGCCGCTAAAGGTCTAT--TCTATAGCGGCGTTTGTGGGAA
1 TTTAGTGGCGTTTGTTG-GAAAAGCGCCGCTAAAGGTCT-TGGTCTTTAGCGGCGTTTTTTGTAA
* *
227886 AAGCGCCACT-AAAGGTCCTGGTC
64 AAGCGCCGCTAAAAGGTCATGGTC
* *
227909 TTTAGTGGCGCTTT-TTGTAAAAGTGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTTTTGTAAA
1 TTTAGTGGCG-TTTGTTGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTTTTGTAAA
*
227973 AGCGCCGCTAAAAGGTTATGGTC
65 AGCGCCGCTAAAAGGTCATGGTC
* * * *
227996 TTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGTGGCGTTTATTTATAAA
1 TTTAGTGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTT-TTTGTAAA
* *
228061 AACTCCGCTAAA
65 AGCGCCGCTAAA
228073 GTTAGCGACG
Statistics
Matches: 140, Mismatches: 17, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
84 1 0.01
85 29 0.21
86 35 0.25
87 58 0.41
88 17 0.12
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (87 bp):
TTTAGTGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTTTTGTAAAA
GCGCCGCTAAAAGGTCATGGTC
Found at i:228171 original size:22 final size:22
Alignment explanation
Indices: 228143--228188 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
228133 TTTAGCGGCG
*
228143 CTAAAAAA-CGCCGCCTAAAGGC
1 CTAAAAAAGCGCCG-CTAAAAGC
228165 CTAAAAAAGCGCCGCTAAAAGC
1 CTAAAAAAGCGCCGCTAAAAGC
228187 CT
1 CT
228189 GTTTTGGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.41, C:0.30, G:0.17, T:0.11
Consensus pattern (22 bp):
CTAAAAAAGCGCCGCTAAAAGC
Found at i:231123 original size:16 final size:16
Alignment explanation
Indices: 231102--231140 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
231092 AAATATTTGA
231102 AGAAGTTCAGAAGAAT
1 AGAAGTTCAGAAGAAT
231118 AGAAGTTCAGAAGAAT
1 AGAAGTTCAGAAGAAT
231134 AGAAGTT
1 AGAAGTT
231141 GGGGTTGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.49, C:0.05, G:0.26, T:0.21
Consensus pattern (16 bp):
AGAAGTTCAGAAGAAT
Found at i:237359 original size:15 final size:14
Alignment explanation
Indices: 237336--237365 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
237326 CTCTCTTCTT
237336 TCTTTTTTTCTTTC
1 TCTTTTTTTCTTTC
237350 TCTTTCTTTTCTTTC
1 TCTTT-TTTTCTTTC
237365 T
1 T
237366 AATTTTGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (14 bp):
TCTTTTTTTCTTTC
Found at i:237371 original size:27 final size:26
Alignment explanation
Indices: 237318--237371 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
237308 AGGTCGTGCG
**
237318 TCTTTCTCCTCTCTTCTTTCTTTTTT
1 TCTTTCTCCTCTCTTCTTTCTAATTT
* *
237344 TCTTTCTCTTTCTTTTCTTTCTAATTT
1 TCTTTCTC-CTCTCTTCTTTCTAATTT
237371 T
1 T
237372 GCATGTTCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.04, C:0.26, G:0.00, T:0.70
Consensus pattern (26 bp):
TCTTTCTCCTCTCTTCTTTCTAATTT
Found at i:238554 original size:30 final size:30
Alignment explanation
Indices: 238494--238554 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
238484 CCCGATTCGT
*
238494 GCTGTACTAAAATTAAGTCGCGTGTGAAAA
1 GCTGTACTAAAATTAAGTCGCGTCTGAAAA
238524 GCTGTACTAAAATTAAGTCGCGTACT-AAAA
1 GCTGTACTAAAATTAAGTCGCGT-CTGAAAA
238554 G
1 G
238555 ATTCGTGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (30 bp):
GCTGTACTAAAATTAAGTCGCGTCTGAAAA
Found at i:245253 original size:55 final size:55
Alignment explanation
Indices: 245189--245305 Score: 191
Period size: 55 Copynumber: 2.1 Consensus size: 55
245179 GATAATTATT
*
245189 ACTTTAGTCCCCTTATTAATTTTTAATCTATAATCCAACTTTCACCCTATATGCG
1 ACTTTAGTCCCCTTATTAATTTTTAATCTATAATCCAACTTTCACCCTATACGCG
* * *
245244 ACTTTAGTCCCCTTATTAATTTTTAATCTATAATTCAACTTTTACCTTATACGCG
1 ACTTTAGTCCCCTTATTAATTTTTAATCTATAATCCAACTTTCACCCTATACGCG
245299 A-TTTAGT
1 ACTTTAGT
245306 TCTTATACTA
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
54 6 0.10
55 52 0.90
ACGTcount: A:0.27, C:0.22, G:0.06, T:0.44
Consensus pattern (55 bp):
ACTTTAGTCCCCTTATTAATTTTTAATCTATAATCCAACTTTCACCCTATACGCG
Found at i:247522 original size:20 final size:20
Alignment explanation
Indices: 247497--247565 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
247487 TCGTCCAGAG
247497 TAATGTCAACATGTACATCA
1 TAATGTCAACATGTACATCA
247517 TAATGTCAACATG-A-ATCA
1 TAATGTCAACATGTACATCA
***
247535 T-A-GTTTGCATGTACATCA
1 TAATGTCAACATGTACATCA
247553 TAATGTCAACATG
1 TAATGTCAACATG
247566 AATCATAGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
16 6 0.15
17 2 0.05
18 10 0.26
19 2 0.05
20 19 0.49
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (20 bp):
TAATGTCAACATGTACATCA
Found at i:247546 original size:36 final size:36
Alignment explanation
Indices: 247506--247581 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
247496 GTAATGTCAA
247506 CATGTACATCATAATGTCAACATGAATCATAGTTTG
1 CATGTACATCATAATGTCAACATGAATCATAGTTTG
247542 CATGTACATCATAATGTCAACATGAATCATAGTTTG
1 CATGTACATCATAATGTCAACATGAATCATAGTTTG
247578 CATG
1 CATG
247582 CATTTTCAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (36 bp):
CATGTACATCATAATGTCAACATGAATCATAGTTTG
Found at i:248156 original size:17 final size:17
Alignment explanation
Indices: 248134--248169 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
248124 TGTAGGTAAT
248134 TTGCAATAAATAGGCCA
1 TTGCAATAAATAGGCCA
248151 TTGCAATAAATAGGCCA
1 TTGCAATAAATAGGCCA
248168 TT
1 TT
248170 AAGCTCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.28
Consensus pattern (17 bp):
TTGCAATAAATAGGCCA
Found at i:250819 original size:12 final size:12
Alignment explanation
Indices: 250801--250894 Score: 68
Period size: 12 Copynumber: 7.7 Consensus size: 12
250791 TTAATAAAAT
250801 AAATAAAATTAA
1 AAATAAAATTAA
*
250813 CAATAAAATTAA
1 AAATAAAATTAA
250825 AAATAAAGATTAA
1 AAATAAA-ATTAA
**
250838 ATTTAAAATT--
1 AAATAAAATTAA
*
250848 AAATCAAAATGAA
1 AAAT-AAAATTAA
*
250861 AGATAAAGA-TAA
1 AAATAAA-ATTAA
*
250873 AAATGAGAAATAAA
1 AAAT-A-AAATTAA
250887 AAATAAAA
1 AAATAAAA
250895 CTATGAAATG
Statistics
Matches: 63, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
10 2 0.03
11 5 0.08
12 31 0.49
13 17 0.27
14 8 0.13
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.22
Consensus pattern (12 bp):
AAATAAAATTAA
Found at i:250825 original size:18 final size:19
Alignment explanation
Indices: 250804--250850 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
250794 ATAAAATAAA
250804 TAAAATTAACA-A-TAAAAT
1 TAAAATTAA-AGATTAAAAT
* *
250822 TAAAAATAAAGATTAAATT
1 TAAAATTAAAGATTAAAAT
250841 TAAAATTAAA
1 TAAAATTAAA
250851 TCAAAATGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 1 0.04
18 9 0.38
19 14 0.58
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
TAAAATTAAAGATTAAAAT
Found at i:250838 original size:7 final size:6
Alignment explanation
Indices: 250804--250850 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
250794 ATAAAATAAA
* *
250804 TAAAAT TAACAA- TAAAAT TAAAAA TAAAGAT TAAATT TAAAAT TAAA
1 TAAAAT TAA-AAT TAAAAT TAAAAT TAAA-AT TAAAAT TAAAAT TAAA
250851 TCAAAATGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
5 2 0.06
6 25 0.74
7 7 0.21
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (6 bp):
TAAAAT
Found at i:250838 original size:19 final size:19
Alignment explanation
Indices: 250816--250886 Score: 56
Period size: 18 Copynumber: 3.8 Consensus size: 19
250806 AAATTAACAA
*
250816 TAAAATTAAAAATAAAGAT
1 TAAAATGAAAAATAAAGAT
** *
250835 T-AAATTTAAAATTAA-AT
1 TAAAATGAAAAATAAAGAT
* *
250852 CAAAATGAAAGATAAAGAT
1 TAAAATGAAAAATAAAGAT
* *
250871 AAAAATGAGAAATAAA
1 TAAAATGAAAAATAAA
250887 AAATAAAACT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
17 2 0.05
18 22 0.55
19 16 0.40
ACGTcount: A:0.66, C:0.01, G:0.08, T:0.24
Consensus pattern (19 bp):
TAAAATGAAAAATAAAGAT
Found at i:264239 original size:32 final size:32
Alignment explanation
Indices: 264189--264292 Score: 122
Period size: 32 Copynumber: 3.3 Consensus size: 32
264179 GAATGGCTAC
* *
264189 AAGCCATAAGT-ACAGTAATATGATTGGCACA
1 AAGCCATCAGTAATAGTAATATGATTGGCACA
* *
264220 GAGCCATCAGTAGTAGTAATATGATTGGCACA
1 AAGCCATCAGTAATAGTAATATGATTGGCACA
* *
264252 CAA-CCATCAGTAATGGTAATATGACTGGCACA
1 -AAGCCATCAGTAATAGTAATATGATTGGCACA
*
264284 AAGACATCA
1 AAGCCATCA
264293 ATAGCATCGC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
31 11 0.18
32 49 0.80
33 1 0.02
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.22
Consensus pattern (32 bp):
AAGCCATCAGTAATAGTAATATGATTGGCACA
Found at i:264328 original size:26 final size:26
Alignment explanation
Indices: 264298--264351 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
264288 CATCAATAGC
*
264298 ATCGCAGCAAAGCTACCAGCAACAGT
1 ATCGCAACAAAGCTACCAGCAACAGT
* **
264324 ATCGCAACAAAGCTGCCATTAACAGT
1 ATCGCAACAAAGCTACCAGCAACAGT
264350 AT
1 AT
264352 ATGTGGCCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.39, C:0.28, G:0.17, T:0.17
Consensus pattern (26 bp):
ATCGCAACAAAGCTACCAGCAACAGT
Found at i:264508 original size:24 final size:24
Alignment explanation
Indices: 264481--264527 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
264471 GGTCATACAA
* *
264481 ATCATAGACAAATCAGTCATTTAC
1 ATCACAGACAAATCAATCATTTAC
*
264505 ATCACGGACAAATCAATCATTTA
1 ATCACAGACAAATCAATCATTTA
264528 ACCCTGAGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.28
Consensus pattern (24 bp):
ATCACAGACAAATCAATCATTTAC
Found at i:267578 original size:18 final size:17
Alignment explanation
Indices: 267555--267593 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
267545 CTCTTTTTGC
267555 TCTTTTTCATTCTCTTTT
1 TCTTTTTCATT-TCTTTT
*
267573 TCTTTTTTTATTTCTTTT
1 TC-TTTTTCATTTCTTTT
267591 TCT
1 TCT
267594 GTCTTCCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 1 0.05
18 10 0.53
19 8 0.42
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (17 bp):
TCTTTTTCATTTCTTTT
Found at i:270070 original size:16 final size:16
Alignment explanation
Indices: 270046--270076 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
270036 TGGACCAAGA
270046 TTTCCTGATTCTTGAT
1 TTTCCTGATTCTTGAT
*
270062 TTTCTTGATTCTTGA
1 TTTCCTGATTCTTGA
270077 AATCTTGATT
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:0.13, C:0.16, G:0.13, T:0.58
Consensus pattern (16 bp):
TTTCCTGATTCTTGAT
Found at i:270467 original size:27 final size:27
Alignment explanation
Indices: 270437--270628 Score: 221
Period size: 27 Copynumber: 7.2 Consensus size: 27
270427 ATTACGGTCG
* *
270437 TTTTACCCATCGGGGGTATTTTGATAA
1 TTTTACCCTTCGAGGGTATTTTGATAA
* *
270464 TTTTACCCTTTG-GGGTA-TTTCAGTAA
1 TTTTACCCTTCGAGGGTATTTTGA-TAA
* * *
270490 TTGTACCCTTTGAGGGTATTTTGGTAA
1 TTTTACCCTTCGAGGGTATTTTGATAA
*
270517 TTTTACCCTTCGAGGGTATTTCGATAA
1 TTTTACCCTTCGAGGGTATTTTGATAA
*
270544 TTTTA-CCTTTGAGGGTATTTCT-ATAA
1 TTTTACCCTTCGAGGGTATTT-TGATAA
*
270570 TTTTACCCTTCGAGGGTATTTCGATAA
1 TTTTACCCTTCGAGGGTATTTTGATAA
* * *
270597 TTTTACCCTTCAAGGGTATTTCGGTAA
1 TTTTACCCTTCGAGGGTATTTTGATAA
270624 TTTTA
1 TTTTA
270629 TGGCCCAACC
Statistics
Matches: 143, Mismatches: 16, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
25 4 0.03
26 42 0.29
27 94 0.66
28 3 0.02
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.44
Consensus pattern (27 bp):
TTTTACCCTTCGAGGGTATTTTGATAA
Found at i:270507 original size:53 final size:54
Alignment explanation
Indices: 270450--270628 Score: 249
Period size: 53 Copynumber: 3.4 Consensus size: 54
270440 TACCCATCGG
* *
270450 GGGTATTTTGATAATTTTACCCTTTG-GGGTATTTC-AGTAATTGTACCCTTTGA
1 GGGTATTTTGATAATTTTACCCTTCGAGGGTATTTCGA-TAATTTTACCCTTTGA
*
270503 GGGTATTTTGGTAATTTTACCCTTCGAGGGTATTTCGATAATTTTA-CCTTTGA
1 GGGTATTTTGATAATTTTACCCTTCGAGGGTATTTCGATAATTTTACCCTTTGA
**
270556 GGGTATTTCT-ATAATTTTACCCTTCGAGGGTATTTCGATAATTTTACCCTTCAA
1 GGGTATTT-TGATAATTTTACCCTTCGAGGGTATTTCGATAATTTTACCCTTTGA
* *
270610 GGGTATTTCGGTAATTTTA
1 GGGTATTTTGATAATTTTA
270629 TGGCCCAACC
Statistics
Matches: 113, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
53 74 0.65
54 38 0.34
55 1 0.01
ACGTcount: A:0.22, C:0.14, G:0.20, T:0.45
Consensus pattern (54 bp):
GGGTATTTTGATAATTTTACCCTTCGAGGGTATTTCGATAATTTTACCCTTTGA
Found at i:270546 original size:80 final size:80
Alignment explanation
Indices: 270437--270628 Score: 271
Period size: 80 Copynumber: 2.4 Consensus size: 80
270427 ATTACGGTCG
* * *
270437 TTTTACCCATCGGGGGTATTTTGATAATTTTACCCTTTG-GGGTATTTC-AGTAATTGTACCCTT
1 TTTTACCCTTCGAGGGTATTTCGATAATTTTA-CCTTTGAGGGTATTTCTA-TAATTGTACCCTT
* * *
270500 TGAGGGTATTTTGGTAA
64 CGAGGGTATTTCGATAA
*
270517 TTTTACCCTTCGAGGGTATTTCGATAATTTTACCTTTGAGGGTATTTCTATAATTTTACCCTTCG
1 TTTTACCCTTCGAGGGTATTTCGATAATTTTACCTTTGAGGGTATTTCTATAATTGTACCCTTCG
270582 AGGGTATTTCGATAA
66 AGGGTATTTCGATAA
* *
270597 TTTTACCCTTCAAGGGTATTTCGGTAATTTTA
1 TTTTACCCTTCGAGGGTATTTCGATAATTTTA
270629 TGGCCCAACC
Statistics
Matches: 101, Mismatches: 9, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
79 6 0.06
80 94 0.93
81 1 0.01
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.44
Consensus pattern (80 bp):
TTTTACCCTTCGAGGGTATTTCGATAATTTTACCTTTGAGGGTATTTCTATAATTGTACCCTTCG
AGGGTATTTCGATAA
Found at i:273212 original size:22 final size:22
Alignment explanation
Indices: 273187--273236 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
273177 TATTAAGTTC
** *
273187 AATTATAACTATAAAATTAAAA
1 AATTATAAAAATAAAAATAAAA
*
273209 AATTAAAAAAATAAAAATAAAA
1 AATTATAAAAATAAAAATAAAA
*
273231 ATTTAT
1 AATTAT
273237 TCTTACCATT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTATAAAAATAAAAATAAAA
Found at i:274842 original size:19 final size:19
Alignment explanation
Indices: 274818--274861 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
274808 ATTTTAAAGT
274818 TGAAAATAC-GTGTTTGTTA
1 TGAAAA-ACAGTGTTTGTTA
*
274837 TGAAAAACAGTGTTTGTTG
1 TGAAAAACAGTGTTTGTTA
274856 TGAAAA
1 TGAAAA
274862 CTTATTTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.09
19 21 0.91
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (19 bp):
TGAAAAACAGTGTTTGTTA
Found at i:275427 original size:27 final size:28
Alignment explanation
Indices: 275391--275449 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
275381 AGTAGAGCTG
*
275391 CCAGTACAGTAT-A-TGTGGCAAAGGCA
1 CCAGTACAGTATGAGTGTGGCAAAGCCA
*
275417 CCAGTATCAGTATGAGTGTGGCAGAGCCA
1 CCAGTA-CAGTATGAGTGTGGCAAAGCCA
275446 CCAG
1 CCAG
275450 AAACAGTACT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 6 0.21
27 6 0.21
28 1 0.04
29 15 0.54
ACGTcount: A:0.31, C:0.22, G:0.29, T:0.19
Consensus pattern (28 bp):
CCAGTACAGTATGAGTGTGGCAAAGCCA
Found at i:275456 original size:29 final size:27
Alignment explanation
Indices: 275396--275457 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 27
275386 AGCTGCCAGT
* *
275396 ACAGTATATGTGGCAAAGGCACCAGTA
1 ACAGTATATGTGGCAAAGCCACCAGAA
* *
275423 TCAGTATGAGTGTGGCAGAGCCACCAGAA
1 ACAGTAT-A-TGTGGCAAAGCCACCAGAA
275452 ACAGTA
1 ACAGTA
275458 CTTCCTCCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 6 0.21
28 1 0.04
29 21 0.75
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.18
Consensus pattern (27 bp):
ACAGTATATGTGGCAAAGCCACCAGAA
Found at i:285504 original size:8 final size:8
Alignment explanation
Indices: 285478--285530 Score: 51
Period size: 8 Copynumber: 7.0 Consensus size: 8
285468 ATCTGAGTAA
285478 AAATGAAT
1 AAATGAAT
*
285486 ATAATGGAT
1 A-AATGAAT
285495 AAATGAAT
1 AAATGAAT
285503 -AA-G--T
1 AAATGAAT
*
285507 AAATGAGT
1 AAATGAAT
285515 AAATGAAT
1 AAATGAAT
285523 AAATGAAT
1 AAATGAAT
285531 CAAGCAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
4 1 0.03
5 2 0.05
6 2 0.05
7 2 0.05
8 23 0.62
9 7 0.19
ACGTcount: A:0.57, C:0.00, G:0.17, T:0.26
Consensus pattern (8 bp):
AAATGAAT
Found at i:293140 original size:5 final size:5
Alignment explanation
Indices: 293132--293157 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
293122 GAGATGGAAT
293132 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
293158 TGTTCGAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:293157 original size:26 final size:26
Alignment explanation
Indices: 293106--293158 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
293096 TGAAGTTTTC
* * *
293106 TCGAATCGAGTCGAGTGAGATGGAAT
1 TCGAATCGAATCGAATGAGATCGAAT
293132 TCGAATCGAATCGAATCGA-ATCGAAT
1 TCGAATCGAATCGAAT-GAGATCGAAT
293158 T
1 T
293159 GTTCGAGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 21 0.91
27 2 0.09
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (26 bp):
TCGAATCGAATCGAATGAGATCGAAT
Found at i:293816 original size:9 final size:9
Alignment explanation
Indices: 293802--293838 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
293792 TATAGTTTGA
293802 TATTCGAAT
1 TATTCGAAT
293811 TATTCGAAT
1 TATTCGAAT
*
293820 TATTCGAGT
1 TATTCGAAT
293829 TATTCGAAT
1 TATTCGAAT
293838 T
1 T
293839 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:293909 original size:9 final size:9
Alignment explanation
Indices: 293892--293922 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
293882 TCGAGTTGAT
293892 TCGAATAAC
1 TCGAATAAC
*
293901 TCGATTAAC
1 TCGAATAAC
293910 TCGAATAAC
1 TCGAATAAC
293919 TCGA
1 TCGA
293923 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:299235 original size:23 final size:23
Alignment explanation
Indices: 299194--299255 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
299184 ATGTGACGAG
* *
299194 CCTCCGTGCGCG-CACGCCTTCA
1 CCTCCGTACGCGCCACGCCTGCA
* *
299216 CCTCCGTACGTGCCACGCCTGCG
1 CCTCCGTACGCGCCACGCCTGCA
299239 CCTCCGTACGCGCCACG
1 CCTCCGTACGCGCCACG
299256 TCACACCGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 10 0.29
23 24 0.71
ACGTcount: A:0.10, C:0.50, G:0.24, T:0.16
Consensus pattern (23 bp):
CCTCCGTACGCGCCACGCCTGCA
Found at i:305305 original size:6 final size:6
Alignment explanation
Indices: 305294--305339 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
305284 AAAAAGAAGA
* * * *
305294 AAAATC AAAATC AAAATC AAAATC AAAGTA AAAATG AAAATG AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
305340 AGAGAGAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.70, C:0.09, G:0.07, T:0.15
Consensus pattern (6 bp):
AAAATC
Found at i:306233 original size:7 final size:7
Alignment explanation
Indices: 306216--306258 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
306206 CGAGTCAAAA
306216 AAAAGATG
1 AAAA-ATG
306224 AAAAATG
1 AAAAATG
306231 AAAAAGTG
1 AAAAA-TG
306239 -AAAATG
1 AAAAATG
306245 AAAAAT-
1 AAAAATG
306251 AAAAATG
1 AAAAATG
306258 A
1 A
306259 TGGAGAGGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 8 0.25
7 18 0.56
8 6 0.19
ACGTcount: A:0.70, C:0.00, G:0.16, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:308464 original size:129 final size:129
Alignment explanation
Indices: 307512--308450 Score: 1610
Period size: 129 Copynumber: 7.3 Consensus size: 129
307502 TAATGAATAT
*
307512 TTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGACAAATCTTATCTTCAAGAGTAAGGAAG
1 TTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGACAAATCTTATCTTCAAGAGTAAGGAAG
*
307577 CAGATTTAAGCCACAAGTCCTATATCCCTGGCCAGCAGTGGAATAGGTTGGGAAATTACAGATC
66 CAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATC
* * *
307641 TTGTCCCCCTAAGCAGTAGCGAAGCAGATCGAAGACGACAAATCTTATCTTCAAAAGTAAGGAAG
1 TTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGACAAATCTTATCTTCAAGAGTAAGGAAG
* * * * *
307706 CAAATTTAAGCCAGAAGTCCTATATCCCTGGTTAGTAGTGGAATAGGTTGAGAAATTACAGATC
66 CAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATC
307770 TTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGACAAATCTTATCTTCAAGAGTAAGGAAG
1 TTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGACAAATCTTATCTTCAAGAGTAAGGAAG
*
307835 CAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATG
66 CAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATC
307899 TTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGACAAATCTTATCTTCAAGAGTAAGGAAG
1 TTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGACAAATCTTATCTTCAAGAGTAAGGAAG
*
307964 CAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATG
66 CAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATC
* *
308028 TTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACAAATCTTATCTTCAAGAGTAAGGAAG
1 TTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGACAAATCTTATCTTCAAGAGTAAGGAAG
**
308093 CAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTCAGGAAATTACAGATC
66 CAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATC
*
308157 TTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGACAAATCTTATCATCAAGAGTAAGGAAG
1 TTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGACAAATCTTATCTTCAAGAGTAAGGAAG
* * *
308222 CAGATTTAAGCCAAAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGTAATTATAGATC
66 CAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATC
* *
308286 TTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGACGAATTTTATCTTCAAGAGTAAGGAAG
1 TTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGACAAATCTTATCTTCAAGAGTAAGGAAG
* *
308351 CAGATTTAAGCCACAAGTCCTATATCCCTGGTTAGCAGTGGAATAGGTTGGGAAATTACATATC
66 CAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATC
* * * *
308415 TTATCTCCCTAAG-TGTTAGTGGAGCAGATAGAAGAC
1 TTGTCTCCCTAAGCAG-TAGCGGAGCAGATCGAAGAC
308451 AGCGAATCCT
Statistics
Matches: 765, Mismatches: 44, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
128 1 0.00
129 764 1.00
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (129 bp):
TTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGACAAATCTTATCTTCAAGAGTAAGGAAG
CAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATC
Found at i:313826 original size:12 final size:13
Alignment explanation
Indices: 313799--313832 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
313789 AGGCCATAAA
313799 GTTTCAAAGTTGG
1 GTTTCAAAGTTGG
313812 GTTTCAAAG-TGG
1 GTTTCAAAGTTGG
313824 GTTTCAAAG
1 GTTTCAAAG
313833 GATAAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.26, C:0.09, G:0.29, T:0.35
Consensus pattern (13 bp):
GTTTCAAAGTTGG
Found at i:313869 original size:13 final size:13
Alignment explanation
Indices: 313851--313877 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
313841 TTTCATCATG
313851 GTTGGGTTTCAAA
1 GTTGGGTTTCAAA
313864 GTTGGGTTTCAAA
1 GTTGGGTTTCAAA
313877 G
1 G
313878 GATAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.33, T:0.37
Consensus pattern (13 bp):
GTTGGGTTTCAAA
Found at i:317263 original size:11 final size:11
Alignment explanation
Indices: 317247--317272 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
317237 CTACTGTAAT
317247 TTGATTATACA
1 TTGATTATACA
317258 TTGATTATACA
1 TTGATTATACA
317269 TTGA
1 TTGA
317273 GTATCCATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.46
Consensus pattern (11 bp):
TTGATTATACA
Found at i:327667 original size:41 final size:41
Alignment explanation
Indices: 327622--327726 Score: 120
Period size: 41 Copynumber: 2.6 Consensus size: 41
327612 CAATACATTG
*
327622 GCACGAAGACTGCTAGGCTCAAAGCCTGATATAACACACCA
1 GCACGAAGACTGCTAGGCACAAAGCCTGATATAACACACCA
* * * * **
327663 GCACGAAGCCTGCTAGGCACAAGGCTTGATATAATACACTG
1 GCACGAAGACTGCTAGGCACAAAGCCTGATATAACACACCA
* * *
327704 GCACGAAGCCTACTAAGCACAAA
1 GCACGAAGACTGCTAGGCACAAA
327727 ACTCGAATAT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.36, C:0.28, G:0.21, T:0.15
Consensus pattern (41 bp):
GCACGAAGACTGCTAGGCACAAAGCCTGATATAACACACCA
Found at i:327776 original size:37 final size:38
Alignment explanation
Indices: 327730--327891 Score: 166
Period size: 38 Copynumber: 4.3 Consensus size: 38
327720 GCACAAAACT
*
327730 CGAATATCACCGGCACAAAGCCTATTAGGCATGG-GCT
1 CGAATATCACCGGCACAAAGCCTATTAGGCATGGAGCC
* *
327767 CGAATATCACTGGCACAAAGCCTGA-TAGGCACGGAGCC
1 CGAATATCACCGGCACAAAGCCT-ATTAGGCATGGAGCC
* ** * * * *
327805 CAAATATCACTAGCATAAAGCCTGTTAGGTATGAAGCC
1 CGAATATCACCGGCACAAAGCCTATTAGGCATGGAGCC
* * * * *
327843 CGAATATCATCGACACAAAACCTGTTATGCATGGAGCC
1 CGAATATCACCGGCACAAAGCCTATTAGGCATGGAGCC
327881 CGAATATCACC
1 CGAATATCACC
327892 ACGTTTCTAT
Statistics
Matches: 101, Mismatches: 21, Indels: 5
0.80 0.17 0.04
Matches are distributed among these distances:
37 30 0.30
38 71 0.70
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.19
Consensus pattern (38 bp):
CGAATATCACCGGCACAAAGCCTATTAGGCATGGAGCC
Found at i:332966 original size:18 final size:16
Alignment explanation
Indices: 332945--332979 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
332935 TGGGGTTTTC
332945 TTTCTTTTCTTCTTTTGT
1 TTTCTTTTC--CTTTTGT
332963 TTTCTTTTCCTTTTGT
1 TTTCTTTTCCTTTTGT
332979 T
1 T
332980 CTTTTTGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.77
Consensus pattern (16 bp):
TTTCTTTTCCTTTTGT
Found at i:332977 original size:16 final size:17
Alignment explanation
Indices: 332945--332992 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
332935 TGGGGTTTTC
332945 TTTCTTTTCTTCTTTTGT
1 TTTCTTTTC-TCTTTTGT
332963 TTTCTTTTC-CTTTTGT
1 TTTCTTTTCTCTTTTGT
* *
332979 TCT-TTTTGTCTTTT
1 TTTCTTTTCTCTTTT
332993 TACTTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 4 0.15
16 14 0.52
18 9 0.33
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.77
Consensus pattern (17 bp):
TTTCTTTTCTCTTTTGT
Found at i:332981 original size:24 final size:22
Alignment explanation
Indices: 332939--332984 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 22
332929 CCTTTTTGGG
332939 GTTTTCTTTCTTTTCTTCTTTT
1 GTTTTCTTTCTTTTCTTCTTTT
*
332961 GTTTTCTTTTCCTTTTGTTCTTTT
1 GTTTTC-TTT-CTTTTCTTCTTTT
332985 TGTCTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.29
23 3 0.14
24 12 0.57
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.76
Consensus pattern (22 bp):
GTTTTCTTTCTTTTCTTCTTTT
Found at i:333979 original size:23 final size:26
Alignment explanation
Indices: 333953--334000 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
333943 TCAGCCATGA
333953 GTATA-TGTT-TTTGGCGG-TTAACC
1 GTATACTGTTATTTGGCGGCTTAACC
333976 GTATACTGTTATTTGGCGGCTTAAC
1 GTATACTGTTATTTGGCGGCTTAAC
334001 TGCACTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.23
24 4 0.18
25 8 0.36
26 5 0.23
ACGTcount: A:0.19, C:0.15, G:0.25, T:0.42
Consensus pattern (26 bp):
GTATACTGTTATTTGGCGGCTTAACC
Found at i:337430 original size:48 final size:49
Alignment explanation
Indices: 337335--337443 Score: 159
Period size: 48 Copynumber: 2.2 Consensus size: 49
337325 ACTTAATTAC
*
337335 TTTAATATTAAATTAATATAATATTTATCAAGATAAATATAAGATTAAA
1 TTTAATATTAAATTAATAGAATATTTATCAAGATAAATATAAGATTAAA
* *
337384 TTTAATATTGAATTAATAGAATA-TTATCAAGATAAGTATTAA-ATTAAA
1 TTTAATATTAAATTAATAGAATATTTATCAAGATAAATA-TAAGATTAAA
*
337432 TTAAATATTAAA
1 TTTAATATTAAA
337444 ACTATTAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
48 30 0.56
49 24 0.44
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (49 bp):
TTTAATATTAAATTAATAGAATATTTATCAAGATAAATATAAGATTAAA
Found at i:353141 original size:63 final size:65
Alignment explanation
Indices: 353069--353195 Score: 186
Period size: 63 Copynumber: 2.0 Consensus size: 65
353059 TTCGTTTTCC
* * *
353069 ATTTTCATTTTCAGTTTAGAGAAAACCATAATAATTTCTAGATGA-TT-TCATTTCTCCATTTTG
1 ATTTTCATTTTCAGTTTAGAGAAAACCATAATAATTTCCAAATGATTTCTCAGTTCTCCATTTTG
* * *
353132 ATTTTCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGATTTCTCAGTTCTCCATTTT
1 ATTTTCATTTTCAGTTTAGAGAAAACCATAATAATTTCCAAATGATTTCTCAGTTCTCCATTTT
353196 TTTCATTTAT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
63 40 0.71
64 2 0.04
65 14 0.25
ACGTcount: A:0.29, C:0.17, G:0.09, T:0.46
Consensus pattern (65 bp):
ATTTTCATTTTCAGTTTAGAGAAAACCATAATAATTTCCAAATGATTTCTCAGTTCTCCATTTTG
Found at i:357116 original size:10 final size:10
Alignment explanation
Indices: 357101--357140 Score: 71
Period size: 10 Copynumber: 4.0 Consensus size: 10
357091 ATATTGCAAT
357101 ATTTAAAAAA
1 ATTTAAAAAA
357111 ATTTAAAAAA
1 ATTTAAAAAA
*
357121 ATTTAAAAAT
1 ATTTAAAAAA
357131 ATTTAAAAAA
1 ATTTAAAAAA
357141 TAAATAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
ATTTAAAAAA
Found at i:361244 original size:26 final size:26
Alignment explanation
Indices: 361197--361246 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
361187 AGTTCTATAA
* *
361197 AATTTAAATCATTATGAGAAAAATAT
1 AATTTAAATCACTATCAGAAAAATAT
*
361223 AATTTAAATCACTATCATAAAAAT
1 AATTTAAATCACTATCAGAAAAAT
361247 TTGCAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.34
Consensus pattern (26 bp):
AATTTAAATCACTATCAGAAAAATAT
Found at i:370936 original size:73 final size:73
Alignment explanation
Indices: 370829--371112 Score: 541
Period size: 73 Copynumber: 3.9 Consensus size: 73
370819 AAACAGACCT
*
370829 TTTTTTCCCACCCATTTAGTAGTAATCTTTCTATTTCCCTCCAATTCCCAATATCTCGTTACCCA
1 TTTTTGCCCACCCATTTAGTAGTAATCTTTCTATTTCCCTCCAATTCCCAATATCTCGTTACCCA
370894 AACAAACA
66 AACAAACA
370902 TTTTTGCCCACCCATTTAGTAGTAATCTTTCTATTTCCCTCCAATTCCCAATATCTCGTTACCCA
1 TTTTTGCCCACCCATTTAGTAGTAATCTTTCTATTTCCCTCCAATTCCCAATATCTCGTTACCCA
370967 AACAAACA
66 AACAAACA
370975 TTTTTGCCCACCCATTTAGTAGTAATCTTTCTATTTCCCTCCAATTCCCAATATCTCGTTACCCA
1 TTTTTGCCCACCCATTTAGTAGTAATCTTTCTATTTCCCTCCAATTCCCAATATCTCGTTACCCA
371040 AACAAACA
66 AACAAACA
* *
371048 TTTTTGCCCACCCATTTAGTAGTAATCTTTCTATTTCCCTCCAATTCTCAATATCTCATTACCCA
1 TTTTTGCCCACCCATTTAGTAGTAATCTTTCTATTTCCCTCCAATTCCCAATATCTCGTTACCCA
371113 TGTTAGGCCA
Statistics
Matches: 208, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 208 1.00
ACGTcount: A:0.26, C:0.31, G:0.05, T:0.37
Consensus pattern (73 bp):
TTTTTGCCCACCCATTTAGTAGTAATCTTTCTATTTCCCTCCAATTCCCAATATCTCGTTACCCA
AACAAACA
Found at i:378103 original size:52 final size:52
Alignment explanation
Indices: 378018--378118 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
378008 TAAGGAAAAG
* *
378018 TAATGGACAGCAACTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAACTTAAGACCTCATTTATAGCTCGGTTGAAGCTCAAACAA
*
378070 TAATAGACAGCAGCTTAAGACCTCATTTATAGCTCGGTTGAAGCTCAAA
1 TAATAGACAGCAACTTAAGACCTCATTTATAGCTCGGTTGAAGCTCAAA
378119 TATGTGCATG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.26
Consensus pattern (52 bp):
TAATAGACAGCAACTTAAGACCTCATTTATAGCTCGGTTGAAGCTCAAACAA
Found at i:381475 original size:18 final size:18
Alignment explanation
Indices: 381452--381486 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
381442 CATTGGATAA
381452 TATGAAAGAATGATAAAT
1 TATGAAAGAATGATAAAT
*
381470 TATGAATGAATGATAAA
1 TATGAAAGAATGATAAA
381487 CATTAGATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TATGAAAGAATGATAAAT
Found at i:382914 original size:19 final size:20
Alignment explanation
Indices: 382877--382914 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
382867 GCCCTTACTT
382877 CTTAAATTTTATAGTTTTGC
1 CTTAAATTTTATAGTTTTGC
382897 CTTAAATTTTAT-GTTTTG
1 CTTAAATTTTATAGTTTTG
382915 TACAAAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.24, C:0.08, G:0.11, T:0.58
Consensus pattern (20 bp):
CTTAAATTTTATAGTTTTGC
Found at i:383128 original size:16 final size:16
Alignment explanation
Indices: 383076--383130 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
383066 ATTTGGTTCA
383076 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
* *
383092 CTATAATTGAATAGAG
1 CTGTAATGGAATAGAG
*
383108 CTGTAATGGAATAAAG
1 CTGTAATGGAATAGAG
*
383124 TTGTAAT
1 CTGTAAT
383131 CAGTAGTTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.40, C:0.05, G:0.24, T:0.31
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:383163 original size:46 final size:44
Alignment explanation
Indices: 383112--383205 Score: 111
Period size: 44 Copynumber: 2.1 Consensus size: 44
383102 ATAGAGCTGT
* *
383112 AATGGAATA-AAGTTGTAATCAGTAGTTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGAA-CTGTAAT-AGTA-TTC-ATGTGTTTGGTTGAATAG
*
383158 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATAG
1 AATGGAATAGAACTGTAATAGTATTCATGTGTTTGGTTGAATAG
383202 AATG
1 AATG
383206 ATGTTGTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
43 1 0.02
44 21 0.49
45 4 0.09
46 15 0.35
47 2 0.05
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATTCATGTGTTTGGTTGAATAG
Found at i:383536 original size:41 final size:41
Alignment explanation
Indices: 383488--383640 Score: 173
Period size: 41 Copynumber: 3.7 Consensus size: 41
383478 ACCATGGGTG
* * *
383488 GCGTTTTTGAAGAAGCATCGCTAATGCACTGGGCTTTAGTA
1 GCGTTTTTGAAGAAGCACCGCTAATGCTCTGGGCTTTAGCA
* * * *
383529 GCATTTTTGAAGAAGCGCCGCTAATGCTCTGGGCATTAGCG
1 GCGTTTTTGAAGAAGCACCGCTAATGCTCTGGGCTTTAGCA
* * *
383570 GTGTTTTTGAAGAAAGCACCGCTATTGCTCTGGGATTTAGCA
1 GCGTTTTTGAAG-AAGCACCGCTAATGCTCTGGGCTTTAGCA
* *
383612 GCGTTTTT-TAGAAAGCGCCGCTAATGCTC
1 GCGTTTTTGAAG-AAGCACCGCTAATGCTC
383641 AGGGGATTTT
Statistics
Matches: 93, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
41 62 0.67
42 31 0.33
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.31
Consensus pattern (41 bp):
GCGTTTTTGAAGAAGCACCGCTAATGCTCTGGGCTTTAGCA
Found at i:383921 original size:14 final size:14
Alignment explanation
Indices: 383883--383922 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
383873 TTGTGCTGTA
*
383883 GGTTTAAGGCTTGG
1 GGTTTAAGGTTTGG
**
383897 GGTTTGGGGTTTGG
1 GGTTTAAGGTTTGG
383911 GGTTTAAGGTTT
1 GGTTTAAGGTTT
383923 AGCGTTTACG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.10, C:0.03, G:0.45, T:0.42
Consensus pattern (14 bp):
GGTTTAAGGTTTGG
Found at i:384035 original size:21 final size:21
Alignment explanation
Indices: 384002--384042 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
383992 TCGGGCTTGA
* * *
384002 TGTTTATGGTTTACGGTTTAG
1 TGTTAATGATTTAAGGTTTAG
384023 TGTTAATGATTTAAGGTTTA
1 TGTTAATGATTTAAGGTTTA
384043 CAATGCATGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.02, G:0.24, T:0.51
Consensus pattern (21 bp):
TGTTAATGATTTAAGGTTTAG
Found at i:385580 original size:31 final size:31
Alignment explanation
Indices: 385506--385581 Score: 134
Period size: 31 Copynumber: 2.5 Consensus size: 31
385496 TTTGATTTTA
*
385506 ATTGGTTTTTGCAGCTAAGATGGTACCTTCT
1 ATTGGTTTTTGCTGCTAAGATGGTACCTTCT
385537 ATTGGTTTTTGCTGCTAAGATGGTACCTTCT
1 ATTGGTTTTTGCTGCTAAGATGGTACCTTCT
*
385568 ATTGATTTTTGCTG
1 ATTGGTTTTTGCTG
385582 TTAAATCAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.17, C:0.14, G:0.22, T:0.46
Consensus pattern (31 bp):
ATTGGTTTTTGCTGCTAAGATGGTACCTTCT
Found at i:387800 original size:43 final size:43
Alignment explanation
Indices: 387752--387839 Score: 124
Period size: 43 Copynumber: 2.0 Consensus size: 43
387742 ACCTTCAGCA
* * *
387752 GCGTTTGT-GGTTAAAGCGCCGCTAAAGATCATGTTCTTTAACG
1 GCGTTTGTAGG-TAAAGCGCAGCTAAAGAACATGATCTTTAACG
*
387795 GCGTTTGTAGGTAAAGCGCAGCTAAAGAACATGATCTTTAGCG
1 GCGTTTGTAGGTAAAGCGCAGCTAAAGAACATGATCTTTAACG
387838 GC
1 GC
387840 ATTTTTTCTC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 38 0.95
44 2 0.05
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.28
Consensus pattern (43 bp):
GCGTTTGTAGGTAAAGCGCAGCTAAAGAACATGATCTTTAACG
Found at i:388477 original size:20 final size:21
Alignment explanation
Indices: 388446--388484 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
388436 ATAATGTTTT
*
388446 TTTTTATGAATATGTATATTA
1 TTTTTATGAATATATATATTA
388467 TTTTTAT-AATATATATAT
1 TTTTTATGAATATATATAT
388485 GACCTTTAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (21 bp):
TTTTTATGAATATATATATTA
Found at i:388555 original size:43 final size:43
Alignment explanation
Indices: 388499--388673 Score: 217
Period size: 43 Copynumber: 4.1 Consensus size: 43
388489 TTTAGCGATA
* *
388499 TTTGTGGGTAAAGCGCCACTAAAGATCATGTTCTTTAGCTGCG
1 TTTGTGGGTAAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCG
* * * *
388542 TTTGT-GATAAAAGCGTCGCTAAAGATCATGTTCCTTAGCGGCT
1 TTTGTGGGT-AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCG
* *
388585 TTTGTGGGTAAAGCGCCGCTAAAGGTCATGTTCTTTAACGGCG
1 TTTGTGGGTAAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCG
* * * * *
388628 TTTGTGGGTAAAGCACCGCTAAAAAACATGATCTTTAGCAGCG
1 TTTGTGGGTAAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCG
388671 TTT
1 TTT
388674 TTTCTCATAA
Statistics
Matches: 111, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
42 2 0.02
43 107 0.96
44 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (43 bp):
TTTGTGGGTAAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCG
Found at i:389828 original size:14 final size:15
Alignment explanation
Indices: 389798--389829 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
389788 ACCAAAACCG
389798 CTATTGCTTTTTCCA
1 CTATTGCTTTTTCCA
389813 CTATTGCTTTTT-CA
1 CTATTGCTTTTTCCA
389827 CTA
1 CTA
389830 AGCATGTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.16, C:0.25, G:0.06, T:0.53
Consensus pattern (15 bp):
CTATTGCTTTTTCCA
Found at i:389940 original size:27 final size:27
Alignment explanation
Indices: 389902--389960 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
389892 TTTAGCCTTC
*
389902 AACAAGGCATTGGGTAAAAATTTTTCT
1 AACATGGCATTGGGTAAAAATTTTTCT
389929 AACATGGCATTGGGTAAAAATTTTTCT
1 AACATGGCATTGGGTAAAAATTTTTCT
389956 AACAT
1 AACAT
389961 TTTTTCCAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (27 bp):
AACATGGCATTGGGTAAAAATTTTTCT
Found at i:390876 original size:16 final size:16
Alignment explanation
Indices: 390855--390886 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
390845 GTATGATCTT
390855 AAAGATTAATTCAAAG
1 AAAGATTAATTCAAAG
390871 AAAGATTAATTCAAAG
1 AAAGATTAATTCAAAG
390887 TCCTCTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.25
Consensus pattern (16 bp):
AAAGATTAATTCAAAG
Found at i:393129 original size:27 final size:27
Alignment explanation
Indices: 393091--393282 Score: 244
Period size: 27 Copynumber: 7.1 Consensus size: 27
393081 TTACACTATT
**
393091 ATGACCGAAATACCCTTATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
*
393118 ATGACCAAAATACCCCCATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * * *
393145 ATGATCGAAATACCCTCATAAGCTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* *
393172 ATGACCAAAATA-CCCCATATGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * *
393198 ATGATCAAAATTCCCCCATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
393225 ATGACCGAAATACCCCCGA-AGGGTAAA
1 ATGACCGAAATACCCCC-ATAGGGTAAA
*
393252 ATGACTGAAATACCCCCATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
393279 ATGA
1 ATGA
393283 TTTTTATACC
Statistics
Matches: 142, Mismatches: 20, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
26 22 0.15
27 119 0.84
28 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.19
Consensus pattern (27 bp):
ATGACCGAAATACCCCCATAGGGTAAA
Found at i:393225 original size:80 final size:80
Alignment explanation
Indices: 393091--393283 Score: 262
Period size: 80 Copynumber: 2.4 Consensus size: 80
393081 TTACACTATT
* * *
393091 ATGACCGAAATACCCTTATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAAATGATCGAAAT
1 ATGACCGAAATACCC-CATAGGGTAAAATGATCAAAATACCCCCATAGGGTAAAATGACCGAAAT
*
393156 ACCCTC-ATAAGCTAAA
65 ACCCCCGA-AAGCTAAA
* * *
393172 ATGACCAAAATACCCCATATGGTAAAATGATCAAAATTCCCCCATAGGGTAAAATGACCGAAATA
1 ATGACCGAAATACCCCATAGGGTAAAATGATCAAAATACCCCCATAGGGTAAAATGACCGAAATA
* *
393237 CCCCCGAAGGGTAAA
66 CCCCCGAAAGCTAAA
*
393252 ATGACTGAAATACCCCCATAGGGTAAAATGAT
1 ATGACCGAAATA-CCCCATAGGGTAAAATGAT
393284 TTTTATACCC
Statistics
Matches: 98, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
80 65 0.66
81 33 0.34
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.19
Consensus pattern (80 bp):
ATGACCGAAATACCCCATAGGGTAAAATGATCAAAATACCCCCATAGGGTAAAATGACCGAAATA
CCCCCGAAAGCTAAA
Found at i:393698 original size:28 final size:28
Alignment explanation
Indices: 393658--393759 Score: 150
Period size: 28 Copynumber: 3.6 Consensus size: 28
393648 GTAATGTCAT
*
393658 TGTATTGAGCTAAGGCCCACACTGATAC
1 TGTATTGGGCTAAGGCCCACACTGATAC
**
393686 TGTATTGGGCTAAGGCCCACGTTGATAC
1 TGTATTGGGCTAAGGCCCACACTGATAC
*
393714 TGTATTGGGCTAAGGCCCACACTGCTAC
1 TGTATTGGGCTAAGGCCCACACTGATAC
**
393742 TAAATTGGGCTAAGGCCC
1 TGTATTGGGCTAAGGCCC
393760 TTGTTGTACT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 66 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (28 bp):
TGTATTGGGCTAAGGCCCACACTGATAC
Found at i:395700 original size:13 final size:13
Alignment explanation
Indices: 395682--395714 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
395672 TTCTTTATTA
395682 CTTTTGAGAAGTG
1 CTTTTGAGAAGTG
395695 CTTTTGAGAAGTG
1 CTTTTGAGAAGTG
395708 CTTTTGA
1 CTTTTGA
395715 CAAATTTGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.21, C:0.09, G:0.27, T:0.42
Consensus pattern (13 bp):
CTTTTGAGAAGTG
Found at i:400882 original size:19 final size:19
Alignment explanation
Indices: 400836--400884 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
400826 AACAGCTTCA
* *
400836 AAATATTAAACAGAAGAGG
1 AAATATAAAACAGAAGAAG
*
400855 AACTAATAAAACAGAAGAAG
1 AAAT-ATAAAACAGAAGAAG
400875 AAATATAAAA
1 AAATATAAAA
400885 GAAACTCTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.65, C:0.06, G:0.14, T:0.14
Consensus pattern (19 bp):
AAATATAAAACAGAAGAAG
Found at i:401659 original size:27 final size:27
Alignment explanation
Indices: 401452--401648 Score: 276
Period size: 27 Copynumber: 7.3 Consensus size: 27
401442 ATAATGGGCC
*
401452 TAAAATGACCGAAATACCC-CTGAAGGG
1 TAAAATGATCGAAATACCCTC-GAAGGG
*
401479 TAAAATGAACGAAATACCCTCGAAGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
*
401506 TAAAATGATTGAAATACCCTCGAAGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
401533 TAAAATGA-CTGAAATACCC-CTGAAGGG
1 TAAAATGATC-GAAATACCCTC-GAAGGG
* *
401560 TAAAATGATCGAAATACCC-CCAATGCG
1 TAAAATGATCGAAATACCCTCGAA-GGG
401587 TAAAATGATCGAAATACCCTCGAAGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
*
401614 TAAAATGATCGAAATACCCTCGAATGG
1 TAAAATGATCGAAATACCCTCGAAGGG
401641 TAAAATGA
1 TAAAATGA
401649 CTATTATACC
Statistics
Matches: 155, Mismatches: 9, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
26 3 0.02
27 147 0.95
28 5 0.03
ACGTcount: A:0.42, C:0.19, G:0.20, T:0.19
Consensus pattern (27 bp):
TAAAATGATCGAAATACCCTCGAAGGG
Found at i:402020 original size:28 final size:28
Alignment explanation
Indices: 401982--402097 Score: 178
Period size: 28 Copynumber: 4.1 Consensus size: 28
401972 TACTGCACTG
* * *
401982 CACTGGTTACTGTATTCGGTTAAGGCCCA
1 CACT-GTTACTGTAATGGGCTAAGGCCCA
*
402011 CACTGTTACTGTATTGGGCTAAGGCCCA
1 CACTGTTACTGTAATGGGCTAAGGCCCA
402039 CACTGTTACTGTAATGGGCTAAGGCCCA
1 CACTGTTACTGTAATGGGCTAAGGCCCA
*
402067 CACTATTACTGTAATGGGCTAAGGCCCA
1 CACTGTTACTGTAATGGGCTAAGGCCCA
402095 CAC
1 CAC
402098 CATACTGTTA
Statistics
Matches: 83, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
28 79 0.95
29 4 0.05
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (28 bp):
CACTGTTACTGTAATGGGCTAAGGCCCA
Found at i:408005 original size:40 final size:40
Alignment explanation
Indices: 407940--408027 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 40
407930 GTGACAGTTT
* *
407940 GGGCCTTAGCCCATCTCAGTACAGTGTTAAAAATGCAATA
1 GGGCCTTAACCCATCTCAGTACAGTGTCAAAAATGCAATA
* * * *
407980 GGGCTTTAACCCATCTTAGTGCAGTGTCAAAAATGCAGTA
1 GGGCCTTAACCCATCTCAGTACAGTGTCAAAAATGCAATA
408020 GGGCCTTA
1 GGGCCTTA
408028 GCCTGTCACA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.26
Consensus pattern (40 bp):
GGGCCTTAACCCATCTCAGTACAGTGTCAAAAATGCAATA
Found at i:410302 original size:17 final size:17
Alignment explanation
Indices: 410280--410316 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
410270 GCTTCGCATC
410280 CTTAGGCTCCCACATGG
1 CTTAGGCTCCCACATGG
410297 CTTAGGCTCCCACATGG
1 CTTAGGCTCCCACATGG
410314 CTT
1 CTT
410317 CCTCAATGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.16, C:0.35, G:0.22, T:0.27
Consensus pattern (17 bp):
CTTAGGCTCCCACATGG
Found at i:414395 original size:26 final size:26
Alignment explanation
Indices: 414366--414427 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
414356 TACCCACAGT
414366 AGTTTCAGAATATCATAACATATATC
1 AGTTTCAGAATATCATAACATATATC
* *
414392 AGTTTCAGAATATCATAGCATGTATC
1 AGTTTCAGAATATCATAACATATATC
*
414418 AATTTCAGAA
1 AGTTTCAGAA
414428 CACTTACGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (26 bp):
AGTTTCAGAATATCATAACATATATC
Found at i:417812 original size:21 final size:22
Alignment explanation
Indices: 417788--417832 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
417778 TAATGTCTAA
417788 AAGCTTAGC-AAAACTCTAGAG
1 AAGCTTAGCAAAAACTCTAGAG
417809 AAGCTTAGCAAAAACTCTAGAG
1 AAGCTTAGCAAAAACTCTAGAG
417831 AA
1 AA
417833 CCAATGTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.18
Consensus pattern (22 bp):
AAGCTTAGCAAAAACTCTAGAG
Found at i:425156 original size:18 final size:18
Alignment explanation
Indices: 425129--425167 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
425119 TGGGCTTTTC
425129 ATTTCTTGG-TCAGTTCA
1 ATTTCTTGGTTCAGTTCA
425146 ATTTACTTGGTTCAGTTCA
1 ATTT-CTTGGTTCAGTTCA
425165 ATT
1 ATT
425168 GGACCACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.20
18 5 0.25
19 11 0.55
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.49
Consensus pattern (18 bp):
ATTTCTTGGTTCAGTTCA
Found at i:426393 original size:22 final size:24
Alignment explanation
Indices: 426350--426393 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
426340 CTGTAAATTT
426350 ATGGGGAAAATGGTAGCAAGATGG
1 ATGGGGAAAATGGTAGCAAGATGG
*
426374 ATGGGG-ATATGGT-GCAAGAT
1 ATGGGGAAAATGGTAGCAAGAT
426394 CTTGTGGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 6 0.32
24 6 0.32
ACGTcount: A:0.34, C:0.05, G:0.41, T:0.20
Consensus pattern (24 bp):
ATGGGGAAAATGGTAGCAAGATGG
Found at i:431735 original size:18 final size:18
Alignment explanation
Indices: 431712--431747 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
431702 TCATTTTTTC
*
431712 ATTTCTCATTTCTTATTT
1 ATTTCTCATTTCTCATTT
431730 ATTTCTCATTTCTCATTT
1 ATTTCTCATTTCTCATTT
431748 CATTATGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTCTCATTTCTCATTT
Found at i:444358 original size:39 final size:39
Alignment explanation
Indices: 444315--444662 Score: 363
Period size: 39 Copynumber: 8.9 Consensus size: 39
444305 ATTAAAACTG
* *
444315 AATGCACATACTTTCCCCTATTGTACTTCGGTACCCCTA
1 AATGCACATACGTGCCCCTATTGTACTTCGGTACCCCTA
* * * * *
444354 AATGCATATACGTGCCCCTGTTGTACTTTGGTACCCTTG
1 AATGCACATACGTGCCCCTATTGTACTTCGGTACCCCTA
* * * *
444393 AATGCACATATGTGCCCCTGTTGTACTTCGATACCTCTA
1 AATGCACATACGTGCCCCTATTGTACTTCGGTACCCCTA
* * * * * **
444432 GATGTAGATACGTGCCCCTGTTGTACTTTGGTACCCCGG
1 AATGCACATACGTGCCCCTATTGTACTTCGGTACCCCTA
** * * *
444471 AATGCACCCACATGCCCCTGTTATACTTCGGTACCCCTA
1 AATGCACATACGTGCCCCTATTGTACTTCGGTACCCCTA
* *
444510 AATGCACATATGTGCCCCTATTGTACTTCGATACCCCTA
1 AATGCACATACGTGCCCCTATTGTACTTCGGTACCCCTA
* * * * * *
444549 AATACACATACGTTCCCATTTTGTACTTTGGTACCCCTG
1 AATGCACATACGTGCCCCTATTGTACTTCGGTACCCCTA
* *
444588 AATGCACCTACGTGCCCCTATTGTACTTCGATACCCCTA
1 AATGCACATACGTGCCCCTATTGTACTTCGGTACCCCTA
* * * *
444627 ACTGCACAGACATGCCCCTATTGTACTTTGGTACCC
1 AATGCACATACGTGCCCCTATTGTACTTCGGTACCC
444663 GTGATTTGCA
Statistics
Matches: 247, Mismatches: 62, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
39 247 1.00
ACGTcount: A:0.22, C:0.31, G:0.16, T:0.31
Consensus pattern (39 bp):
AATGCACATACGTGCCCCTATTGTACTTCGGTACCCCTA
Found at i:444662 original size:117 final size:116
Alignment explanation
Indices: 444319--444654 Score: 411
Period size: 117 Copynumber: 2.9 Consensus size: 116
444309 AAACTGAATG
* * * ** *
444319 CACATACTTTCCCCTATTGTACTTCGGTACCCCTAAATGCATATACGTGCCCCTGTTGTACTTTG
1 CACATACGTTCCCCTATTGTACTTTGGTACCCCTGAATGCACCTACGTGCCCCTGTTGTACTTCG
* * * * *
444384 GTACCCTTGAATGCACATATGTGCCCCTGTTGTACTTCGATACCTCTAGATG
66 GTACCCCT-AATGCACATATGTGCCCCTATTGTACTTCGATACCCCTAAATA
* * * * * * * *
444436 TAGATACGTGCCCCTGTTGTACTTTGGTACCCCGGAATGCACCCACATGCCCCTGTTATACTTCG
1 CACATACGTTCCCCTATTGTACTTTGGTACCCCTGAATGCACCTACGTGCCCCTGTTGTACTTCG
444501 GTACCCCTAAATGCACATATGTGCCCCTATTGTACTTCGATACCCCTAAATA
66 GTACCCCT-AATGCACATATGTGCCCCTATTGTACTTCGATACCCCTAAATA
* * *
444553 CACATACGTTCCCATTTTGTACTTTGGTACCCCTGAATGCACCTACGTGCCCCTATTGTACTTCG
1 CACATACGTTCCCCTATTGTACTTTGGTACCCCTGAATGCACCTACGTGCCCCTGTTGTACTTCG
* * **
444618 ATACCCCTAACTGCACAGACATGCCCCTATTGTACTT
66 GTACCCCTAA-TGCACATATGTGCCCCTATTGTACTT
444655 TGGTACCCGT
Statistics
Matches: 184, Mismatches: 34, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
116 2 0.01
117 182 0.99
ACGTcount: A:0.22, C:0.31, G:0.15, T:0.32
Consensus pattern (116 bp):
CACATACGTTCCCCTATTGTACTTTGGTACCCCTGAATGCACCTACGTGCCCCTGTTGTACTTCG
GTACCCCTAATGCACATATGTGCCCCTATTGTACTTCGATACCCCTAAATA
Found at i:445825 original size:21 final size:20
Alignment explanation
Indices: 445786--445826 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
445776 CCCCTGCAGT
* *
445786 TGAAAATTTCTATCTTTTTC
1 TGAAAAATTCTATATTTTTC
445806 TGAAAAATTCTATATGTTTTC
1 TGAAAAATTCTATAT-TTTTC
445827 GATTTAGTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.29, C:0.12, G:0.07, T:0.51
Consensus pattern (20 bp):
TGAAAAATTCTATATTTTTC
Found at i:457570 original size:23 final size:22
Alignment explanation
Indices: 457540--457612 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 22
457530 AATGACCATT
457540 AATTAGGGGGTTAGAATTTATAA
1 AATTAGGGGG-TAGAATTTATAA
* **
457563 AATTAGGGGAG-AAAACTCCA-AA
1 AATTAGGGG-GTAGAA-TTTATAA
457585 AATTAGGGGGTAAGAATTTATAA
1 AATTAGGGGGT-AGAATTTATAA
457608 AATTA
1 AATTA
457613 CCATGAATTG
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
21 1 0.03
22 16 0.41
23 21 0.54
24 1 0.03
ACGTcount: A:0.45, C:0.04, G:0.23, T:0.27
Consensus pattern (22 bp):
AATTAGGGGGTAGAATTTATAA
Found at i:468210 original size:7 final size:8
Alignment explanation
Indices: 468188--468212 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
468178 TTAAATAATT
468188 TTTAAAAA
1 TTTAAAAA
468196 TTTAAAAA
1 TTTAAAAA
468204 TTTAAAAA
1 TTTAAAAA
468212 T
1 T
468213 ATTTAATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TTTAAAAA
Found at i:468216 original size:18 final size:19
Alignment explanation
Indices: 468177--468218 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
468167 TTATTATATT
*
468177 TTTAAATAATTTTTAAAAA
1 TTTAAATAATTTTAAAAAA
468196 TTTAAA-AA-TTTAAAAATA
1 TTTAAATAATTTTAAAAA-A
468214 TTTAA
1 TTTAA
468219 TGATGCGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 7 0.33
18 8 0.38
19 6 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTAAATAATTTTAAAAAA
Found at i:470296 original size:26 final size:26
Alignment explanation
Indices: 470266--470317 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
470256 AGTGGTATAA
* *
470266 AATTTAAATCATTATGATAAAAATAT
1 AATTTAAATCACTATCATAAAAATAT
* *
470292 AATTTAGATCACTATCCTAAAAATAT
1 AATTTAAATCACTATCATAAAAATAT
470318 GCAAAATATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (26 bp):
AATTTAAATCACTATCATAAAAATAT
Found at i:476156 original size:20 final size:20
Alignment explanation
Indices: 476128--476170 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
476118 CTCTATTTTC
476128 TTTTGAATTAGAAATACCAA
1 TTTTGAATTAGAAATACCAA
* *
476148 TTTTTAATTAGAAATAGCAA
1 TTTTGAATTAGAAATACCAA
476168 TTT
1 TTT
476171 CCTCGTGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (20 bp):
TTTTGAATTAGAAATACCAA
Found at i:476503 original size:16 final size:15
Alignment explanation
Indices: 476482--476516 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
476472 TAAGATCTTG
476482 TATATCTAGATAAAAA
1 TATATCTAGA-AAAAA
*
476498 TATATCTATAAAAAA
1 TATATCTAGAAAAAA
476513 TATA
1 TATA
476517 GATAATAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (15 bp):
TATATCTAGAAAAAA
Found at i:478403 original size:35 final size:34
Alignment explanation
Indices: 478357--478429 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 34
478347 AGGTAAATAA
*
478357 TATAAAAAAATATTA-ATATAATATTCTAATA-TAT
1 TATAAAAAAATA-TAGAAATAA-ATTCTAATACTAT
*
478391 TATAAATAAAATATAGAAATAAGTTCTAATACTAT
1 TATAAA-AAAATATAGAAATAAATTCTAATACTAT
478426 TATA
1 TATA
478430 TATTAGAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
34 16 0.47
35 18 0.53
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (34 bp):
TATAAAAAAATATAGAAATAAATTCTAATACTAT
Found at i:490053 original size:30 final size:29
Alignment explanation
Indices: 490019--490104 Score: 77
Period size: 29 Copynumber: 3.0 Consensus size: 29
490009 TTTCAAATAA
490019 TTATTACAAA-TATAAAAAAATATTTAAAAT
1 TTATTA-AAATTATAAAAAAATA-TTAAAAT
* *
490049 TTATTAAAATTATAATAAATTATTAAAAT
1 TTATTAAAATTATAAAAAAATATTAAAAT
** * * *
490078 CAATTAAACTGAT-AAAAATTATTAAAA
1 TTATTAAAATTATAAAAAAATATTAAAA
490105 ATACTTTCCG
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
28 13 0.27
29 19 0.40
30 16 0.33
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.37
Consensus pattern (29 bp):
TTATTAAAATTATAAAAAAATATTAAAAT
Found at i:490083 original size:29 final size:28
Alignment explanation
Indices: 490033--490104 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
490023 TACAAATATA
* ** *
490033 AAAAAATATTTAAAATTTATTAAAATTAT
1 AAAAATTA-TTAAAATCAATTAAAATGAT
*
490062 AATAAATTATTAAAATCAATTAAACTGAT
1 AA-AAATTATTAAAATCAATTAAAATGAT
490091 AAAAATTATTAAAA
1 AAAAATTATTAAAA
490105 ATACTTTCCG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 12 0.32
29 20 0.54
30 5 0.14
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (28 bp):
AAAAATTATTAAAATCAATTAAAATGAT
Found at i:496037 original size:28 final size:27
Alignment explanation
Indices: 495979--496076 Score: 117
Period size: 28 Copynumber: 3.6 Consensus size: 27
495969 TTAGATGGTA
*
495979 GCCACAAGGGCTTTCC-TTCAAGATTT
1 GCCACAAAGGCTTTCCTTTCAAGATTT
*
496005 GCCACAAAGGCTATTCCTTTTAAGATTT
1 GCCACAAAGGCT-TTCCTTTCAAGATTT
* * *
496033 TCCACAAAGGCTTTTCCATTCGAGATTT
1 GCCACAAAGGC-TTTCCTTTCAAGATTT
*
496061 GACACAAAGGCTTTCC
1 GCCACAAAGGCTTTCC
496077 CTTTTCTGAC
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
26 11 0.18
27 9 0.15
28 40 0.66
29 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.32
Consensus pattern (27 bp):
GCCACAAAGGCTTTCCTTTCAAGATTT
Found at i:500702 original size:3 final size:3
Alignment explanation
Indices: 500696--500760 Score: 94
Period size: 3 Copynumber: 21.7 Consensus size: 3
500686 AAAATTTAAG
* * * *
500696 AAT AAT ATT AAT AAT AAT AAT GAT GAT GAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
500744 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
500761 ATAAATATAT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:500892 original size:15 final size:15
Alignment explanation
Indices: 500866--500898 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
500856 AAATAAAAGG
*
500866 AAAAATAATAATACT
1 AAAAATAATAATAAT
500881 AAAAATAATAATAAT
1 AAAAATAATAATAAT
500896 AAA
1 AAA
500899 TTAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAATAATAATAAT
Found at i:505298 original size:25 final size:25
Alignment explanation
Indices: 505270--505323 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
505260 TGTAGTGGCA
*
505270 AGGTGGCGACACAGGTGTGCCAAGG
1 AGGTGGCGACACAGGTGTGACAAGG
* *
505295 AGGTGGCGTCACAGGTGTGATAAGG
1 AGGTGGCGACACAGGTGTGACAAGG
505320 AGGT
1 AGGT
505324 CAGAGGTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.15, G:0.44, T:0.17
Consensus pattern (25 bp):
AGGTGGCGACACAGGTGTGACAAGG
Found at i:505789 original size:35 final size:35
Alignment explanation
Indices: 505744--505816 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
505734 ATTCTTCCCT
505744 TTTTCCTCTCTGAATAGCCGAATTTTCCCTTTTTC
1 TTTTCCTCTCTGAATAGCCGAATTTTCCCTTTTTC
505779 TTTTCCTCTCTGAATAGCCGAATTTTCCCTTTTTC
1 TTTTCCTCTCTGAATAGCCGAATTTTCCCTTTTTC
505814 TTT
1 TTT
505817 CTTTTTCTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.14, C:0.27, G:0.08, T:0.51
Consensus pattern (35 bp):
TTTTCCTCTCTGAATAGCCGAATTTTCCCTTTTTC
Found at i:506602 original size:27 final size:27
Alignment explanation
Indices: 506566--506719 Score: 173
Period size: 27 Copynumber: 5.7 Consensus size: 27
506556 GTAATGGGCC
* * *
506566 TAAAAATACCGAAACACCCTCGATGGG
1 TAAAATTACCAAAATACCCTCGATGGG
* * *
506593 TAAAATTACCAAAATACTCTTGAAGGG
1 TAAAATTACCAAAATACCCTCGATGGG
* * * *
506620 TAAAATTATCGAAGTACCCCCGATGGG
1 TAAAATTACCAAAATACCCTCGATGGG
** *
506647 TAAAATTAATAAAATACCTTCGATGGG
1 TAAAATTACCAAAATACCCTCGATGGG
* *
506674 TAAAATTATCTAAATACCCTCGATGGG
1 TAAAATTACCAAAATACCCTCGATGGG
506701 TAAAATTACCAAAATACCC
1 TAAAATTACCAAAATACCC
506720 CTTGAAGGGA
Statistics
Matches: 102, Mismatches: 25, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 102 1.00
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (27 bp):
TAAAATTACCAAAATACCCTCGATGGG
Found at i:506648 original size:54 final size:52
Alignment explanation
Indices: 506581--506761 Score: 211
Period size: 54 Copynumber: 3.3 Consensus size: 52
506571 ATACCGAAAC
*
506581 ACCCTCGATGGGTAAAATTACCAAAATACTCTTGAAGGGTAAAATTATCGAAGT
1 ACCCCCGATGGGTAAAATTACCAAAATAC-CTTGAAGGGTAAAATTATCGAA-T
** * *
506635 ACCCCCGATGGGTAAAATTAATAAAATACCTTCGATGGGTAAAATTATCTAAAT
1 ACCCCCGATGGGTAAAATTACCAAAATACCTT-GAAGGGTAAAATTATC-GAAT
* *
506689 ACCCTCGATGGGTAAAATTACCAAAATACCCCTTGAAGGGAAAAATTATCGTAAT
1 ACCCCCGATGGGTAAAATTACCAAAATA--CCTTGAAGGGTAAAATTATCG-AAT
*
506744 A-CCCCGTTAGGGTAAAAT
1 ACCCCCGAT-GGGTAAAAT
506762 GAATGCTAGG
Statistics
Matches: 108, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
53 3 0.03
54 72 0.67
55 29 0.27
56 4 0.04
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.25
Consensus pattern (52 bp):
ACCCCCGATGGGTAAAATTACCAAAATACCTTGAAGGGTAAAATTATCGAAT
Found at i:506760 original size:28 final size:26
Alignment explanation
Indices: 506616--506761 Score: 84
Period size: 27 Copynumber: 5.4 Consensus size: 26
506606 ATACTCTTGA
* *
506616 AGGGTAAAATTATCGAAGTACCCCCGAT
1 AGGGTAAAATTATCTAA-TA-CCCCGTT
** * *
506644 -GGGTAAAATTAATAAAATACCTTCGAT
1 AGGGTAAAATT-ATCTAATACC-CCGTT
*
506671 -GGGTAAAATTATCTAAATACCCTCGAT
1 AGGGTAAAATTATCT-AATACCC-CGTT
* *
506698 -GGGTAAAATTACCAAAATACCCC-TT
1 AGGGTAAAATTATC-TAATACCCCGTT
*
506723 GAAGGGAAAAATTATCGTAATACCCCGTT
1 --AGGGTAAAATTATC-TAATACCCCGTT
506752 AGGGTAAAAT
1 AGGGTAAAAT
506762 GAATGCTAGG
Statistics
Matches: 95, Mismatches: 14, Indels: 19
0.74 0.11 0.15
Matches are distributed among these distances:
25 1 0.01
26 5 0.05
27 64 0.67
28 23 0.24
29 2 0.02
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (26 bp):
AGGGTAAAATTATCTAATACCCCGTT
Found at i:506922 original size:27 final size:27
Alignment explanation
Indices: 506884--506953 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
506874 GAGGAAGTAT
*
506884 TGTTTCTGGTGGCTCTACCACA-ATCAC
1 TGTTACTGGTGGCTCTACCACATAT-AC
* *
506911 TGTTACTGGTGGCTTTGCCACATATAC
1 TGTTACTGGTGGCTCTACCACATATAC
*
506938 TG-TACTGGTAGCTCTA
1 TGTTACTGGTGGCTCTA
506954 TTGCGTTATT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
26 11 0.31
27 23 0.64
28 2 0.06
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (27 bp):
TGTTACTGGTGGCTCTACCACATATAC
Found at i:508956 original size:23 final size:23
Alignment explanation
Indices: 508926--508973 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
508916 TGAGAGGCGT
508926 GTTAAGAAGGCCAGGTTTGATGG
1 GTTAAGAAGGCCAGGTTTGATGG
508949 GTTAAGAAGGCCAGGTTTGATGG
1 GTTAAGAAGGCCAGGTTTGATGG
508972 GT
1 GT
508974 CGATTCAGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.08, G:0.40, T:0.27
Consensus pattern (23 bp):
GTTAAGAAGGCCAGGTTTGATGG
Found at i:512962 original size:25 final size:25
Alignment explanation
Indices: 512934--512987 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
512924 TGTAGTGGCA
*
512934 AGGTGGGGACACAGGTGTGGCAAGG
1 AGGTGGCGACACAGGTGTGGCAAGG
* *
512959 AGGTGGCGTCACAGGTGTGGTAAGG
1 AGGTGGCGACACAGGTGTGGCAAGG
512984 AGGT
1 AGGT
512988 TAGAGGTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.22, C:0.11, G:0.50, T:0.17
Consensus pattern (25 bp):
AGGTGGCGACACAGGTGTGGCAAGG
Found at i:513136 original size:24 final size:21
Alignment explanation
Indices: 513103--513149 Score: 58
Period size: 24 Copynumber: 2.1 Consensus size: 21
513093 TCAAATGAGT
*
513103 GATTTAAGGAGTGGATCATGGAG
1 GATTTAAGGAGAGGAT--TGGAG
513126 GATTTCAAGGAGAGGATTGGAG
1 GATTT-AAGGAGAGGATTGGAG
513148 GA
1 GA
513150 GTGATTTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 5 0.23
24 10 0.45
ACGTcount: A:0.32, C:0.04, G:0.40, T:0.23
Consensus pattern (21 bp):
GATTTAAGGAGAGGATTGGAG
Found at i:514211 original size:27 final size:27
Alignment explanation
Indices: 514170--514365 Score: 184
Period size: 27 Copynumber: 7.2 Consensus size: 27
514160 GTAATAAGCC
* *
514170 TAAAA-TACCGAAATACCCTCGATA-GG
1 TAAAATTATCGAAATACCCCCGA-AGGG
*
514196 TAAAATTATAGAAATACCCCCGAAGGG
1 TAAAATTATCGAAATACCCCCGAAGGG
* * * * *
514223 TAAAGTCATTGAAATACCCTC-AATAGG
1 TAAAATTATCGAAATACCCCCGAA-GGG
* * *
514250 TAAATTTA-CTGAAATACCCTCGATGGG
1 TAAAATTATC-GAAATACCCCCGAAGGG
514277 TAAAATTATCGAAATACCCCCGAAGGG
1 TAAAATTATCGAAATACCCCCGAAGGG
*
514304 TAAAATTACCGAAATACCCCCCGAAGGG
1 TAAAATTATCGAAATA-CCCCCGAAGGG
* * *
514332 TAAAATTACCGTAATACCCCCGTTAGGG
1 TAAAATTATCGAAATACCCCCG-AAGGG
514360 TAAAAT
1 TAAAAT
514366 GACAGCTAGG
Statistics
Matches: 143, Mismatches: 19, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
26 8 0.06
27 97 0.68
28 38 0.27
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (27 bp):
TAAAATTATCGAAATACCCCCGAAGGG
Found at i:515590 original size:75 final size:75
Alignment explanation
Indices: 515467--515618 Score: 304
Period size: 75 Copynumber: 2.0 Consensus size: 75
515457 GGCCTAATGA
515467 GCTTTATTTTCCAATTCAAGTGGCAAATGACATACCTTTCCAAAAACTAACCGATAAGGAGTCAT
1 GCTTTATTTTCCAATTCAAGTGGCAAATGACATACCTTTCCAAAAACTAACCGATAAGGAGTCAT
515532 TCCTAACGGT
66 TCCTAACGGT
515542 GCTTTATTTTCCAATTCAAGTGGCAAATGACATACCTTTCCAAAAACTAACCGATAAGGAGTCAT
1 GCTTTATTTTCCAATTCAAGTGGCAAATGACATACCTTTCCAAAAACTAACCGATAAGGAGTCAT
515607 TCCTAACGGT
66 TCCTAACGGT
515617 GC
1 GC
515619 CTTAAAAGTA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (75 bp):
GCTTTATTTTCCAATTCAAGTGGCAAATGACATACCTTTCCAAAAACTAACCGATAAGGAGTCAT
TCCTAACGGT
Found at i:524840 original size:68 final size:68
Alignment explanation
Indices: 524731--524865 Score: 209
Period size: 68 Copynumber: 2.0 Consensus size: 68
524721 AAAATTAAGC
* * *
524731 TGTTCGAATGTGTTAGATTCACTGATCAAAGCACCATCATTTATGTTGTTTTATTTAGTAAATGT
1 TGTTCGAATGTGTTAAATTCACTGATCAAAGCACCAGCATTTATGTTGTTTTATTTAATAAATGT
524796 AGT
66 AGT
* *
524799 TGTTCGAATGTGTTAAATTCACT-ATTCAATGCACTAGCATTTATGTTGTTTTATTTAATAAATG
1 TGTTCGAATGTGTTAAATTCACTGA-TCAAAGCACCAGCATTTATGTTGTTTTATTTAATAAATG
524863 TAG
65 TAG
524866 CTATCCGAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
67 1 0.02
68 60 0.98
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (68 bp):
TGTTCGAATGTGTTAAATTCACTGATCAAAGCACCAGCATTTATGTTGTTTTATTTAATAAATGT
AGT
Found at i:524875 original size:68 final size:68
Alignment explanation
Indices: 524735--524880 Score: 195
Period size: 68 Copynumber: 2.1 Consensus size: 68
524725 TTAAGCTGTT
* * * *
524735 CGAATGTGTTAGATTCACTGATCAAAGCACCATCATTTATGTTGTTTTATTTAGTAAATGTAGTT
1 CGAATGTGTTAAATTCACTGATCAAAGCACCAGCATTTATGTTGTTTTATTTAATAAATGTAGCT
* *
524800 GTT
66 ATC
* *
524803 CGAATGTGTTAAATTCACT-ATTCAATGCACTAGCATTTATGTTGTTTTATTTAATAAATGTAGC
1 CGAATGTGTTAAATTCACTGA-TCAAAGCACCAGCATTTATGTTGTTTTATTTAATAAATGTAGC
524867 TATC
65 TATC
*
524871 CGAATCTGTT
1 CGAATGTGTT
524881 GATTTCACAA
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
67 1 0.01
68 67 0.99
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (68 bp):
CGAATGTGTTAAATTCACTGATCAAAGCACCAGCATTTATGTTGTTTTATTTAATAAATGTAGCT
ATC
Found at i:525275 original size:43 final size:43
Alignment explanation
Indices: 525227--525365 Score: 149
Period size: 43 Copynumber: 3.3 Consensus size: 43
525217 TTGTGATTTT
**
525227 GTGTAAGACCATGTCTAAGACATTGGCATCAATATGAGATTAC
1 GTGTAAGACCATGTCTGGGACATTGGCATCAATATGAGATTAC
* *
525270 GTGTAAGACCATGTCTGGGACATTGGCA-CCATAT-ATGATT-T
1 GTGTAAGACCATGTCTGGGACATTGGCATCAATATGA-GATTAC
* ** * * *
525311 GTGTAAGACCCTGTCTGGGACAGAGGCATCGATATGTGATAAC
1 GTGTAAGACCATGTCTGGGACATTGGCATCAATATGAGATTAC
*
525354 ATGTAAGACCAT
1 GTGTAAGACCAT
525366 ACCGGGATAT
Statistics
Matches: 79, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
41 26 0.33
42 17 0.22
43 36 0.46
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.27
Consensus pattern (43 bp):
GTGTAAGACCATGTCTGGGACATTGGCATCAATATGAGATTAC
Found at i:526975 original size:7 final size:7
Alignment explanation
Indices: 526963--526987 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
526953 AAATCACACG
526963 TAAAGAA
1 TAAAGAA
526970 TAAAGAA
1 TAAAGAA
526977 TAAAGAA
1 TAAAGAA
526984 TAAA
1 TAAA
526988 TTACTAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (7 bp):
TAAAGAA
Found at i:532145 original size:22 final size:22
Alignment explanation
Indices: 532117--532182 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
532107 CTCTCTGATT
* *
532117 ATTAGCACGTTGGTGCTCTCTG
1 ATTAGCACATTAGTGCTCTCTG
* * *
532139 ATTAGCATATTTGTGCTCTATG
1 ATTAGCACATTAGTGCTCTCTG
*
532161 -TATAGCACTTTAGTGCTCTCTG
1 AT-TAGCACATTAGTGCTCTCTG
532183 TTCATTAGTG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 1 0.03
22 34 0.97
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (22 bp):
ATTAGCACATTAGTGCTCTCTG
Found at i:534142 original size:32 final size:32
Alignment explanation
Indices: 534083--534143 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
534073 TTTTCTTATT
* * *
534083 TAGGTACTGAAAGTTTTTTTTTTTTATCAAAG
1 TAGGTACTGAAAGTTTTATTCTATTATCAAAG
534115 TAGGTATCT-AAAGTTTTATTCTATTATCA
1 TAGGTA-CTGAAAGTTTTATTCTATTATCA
534144 CTTTAGGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 23 0.92
33 2 0.08
ACGTcount: A:0.30, C:0.08, G:0.13, T:0.49
Consensus pattern (32 bp):
TAGGTACTGAAAGTTTTATTCTATTATCAAAG
Found at i:534367 original size:176 final size:177
Alignment explanation
Indices: 534099--534570 Score: 451
Period size: 176 Copynumber: 2.7 Consensus size: 177
534089 CTGAAAGTTT
*
534099 TTTTTTTTTATCAAAGTAGGTATCTAAAGTTTTATTCTATTATCACTTTAGGTATAAACTATTAA
1 TTTTTTTTTATCAAAGTAGGTATCTAAAGTTTTATTCTATTATCACTTTAGGTACAAACTATTAA
*** * * ** * *
534164 CTCTTGTTAAAAAAATTTTTCAAACCAATCAAATTATGATACATGACGGTTTTAATTTGTTACCA
66 CTCTTGTTAAAAAAAGAATTAAAACCAATCAAATTATGACACATGAAAGTTTTAATCTATTACCA
*
534229 CTTTAGGTACTTAAACTATGTAAC-TTTTCCTATTTA-AGTACCT-AAC
131 CTTTAGGTACTTAAACTATGCAACTTTTTCC-ATTTAGA-TACCTAAAC
* * * * * *
534275 TTTTTTTTTATTAAAGTAGGTA-CTTGAAA-TTTTATTCTGTTATTACTTTAGGTACCAATTGTT
1 TTTTTTTTTATCAAAGTAGGTATC-T-AAAGTTTTATTCTATTATCACTTTAGGTACAAACTATT
* * * * *
534338 AACT-TTCTTTAAAAACAGAATTAAAACCAATCAAATTCTGACACGTGAAATTTTTAATCTATTA
64 AACTCTT-GTTAAAAAAAGAATTAAAACCAATCAAATTATGACACATGAAAGTTTTAATCTATTA
* *
534402 CCATTTTAGGTACTTAAATTATGCAACTTTTTCCATTTAGATACCTAAA-
128 CCACTTTAGGTACTTAAACTATGCAACTTTTTCCATTTAGATACCTAAAC
* * * ** * * ** *
534451 GTTTTTTTT-TCAGAGCAGGTGCCTAAAGTTTTATT-TAGTTACCATTTTAGGTATC-AACCGTC
1 TTTTTTTTTATCAAAGTAGGTATCTAAAGTTTTATTCTA-TTATCACTTTAGGTA-CAAACTATT
* * * * * *
534513 AACTCTTGGTAAACAAAGAATTCAAACCAAACAAATTATGACACATGACATTTTTAAT
64 AACTCTTGTTAAAAAAAGAATTAAAACCAATCAAATTATGACACATGAAAGTTTTAAT
534571 TAAAAATTGT
Statistics
Matches: 240, Mismatches: 45, Indels: 23
0.78 0.15 0.07
Matches are distributed among these distances:
174 4 0.02
175 81 0.34
176 143 0.60
177 12 0.05
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (177 bp):
TTTTTTTTTATCAAAGTAGGTATCTAAAGTTTTATTCTATTATCACTTTAGGTACAAACTATTAA
CTCTTGTTAAAAAAAGAATTAAAACCAATCAAATTATGACACATGAAAGTTTTAATCTATTACCA
CTTTAGGTACTTAAACTATGCAACTTTTTCCATTTAGATACCTAAAC
Found at i:541604 original size:11 final size:11
Alignment explanation
Indices: 541588--541612 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
541578 CGAATTAACC
541588 AAATTACCCAA
1 AAATTACCCAA
541599 AAATTACCCAA
1 AAATTACCCAA
541610 AAA
1 AAA
541613 GTTCAGTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.24, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATTACCCAA
Found at i:542896 original size:35 final size:35
Alignment explanation
Indices: 542856--542926 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
542846 AAAAGCCAGT
542856 CCAGATAACAGTTATTGATGACAATGAAAGGTATA
1 CCAGATAACAGTTATTGATGACAATGAAAGGTATA
542891 CCAGATAACAGTTATTGATGACAATGAAAGGTATA
1 CCAGATAACAGTTATTGATGACAATGAAAGGTATA
542926 C
1 C
542927 TTATCAACCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (35 bp):
CCAGATAACAGTTATTGATGACAATGAAAGGTATA
Found at i:545518 original size:24 final size:24
Alignment explanation
Indices: 545486--545533 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
545476 ATGGTTAAGT
545486 GGCCTTTACCAAGTTCATTGAAGC
1 GGCCTTTACCAAGTTCATTGAAGC
545510 GGCCTTTACCAAGTTCATTGAAGC
1 GGCCTTTACCAAGTTCATTGAAGC
545534 CATTGAGGGG
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:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (24 bp):
GGCCTTTACCAAGTTCATTGAAGC
Found at i:557539 original size:27 final size:27
Alignment explanation
Indices: 557516--557878 Score: 430
Period size: 27 Copynumber: 13.4 Consensus size: 27
557506 AGAGGTATAA
* * *
557516 CAGTTATTTTAACCTTCGGGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
*
557543 C-GATAATTTTACCCTTCGAGGGTATTT
1 CAG-TCATTTTACCCTTCGAGGGTATTT
557570 -AGGTCATTTTACCCTTCGAGGGTATTT
1 CA-GTCATTTTACCCTTCGAGGGTATTT
*
557597 CAGTCATTTTACCTTTCGAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
557624 -AGGTCATTTTACCCTTCGAGGGTATTT
1 CA-GTCATTTTACCCTTCGAGGGTATTT
557651 CAGTCATTTTACCCTTCGAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
* *
557678 CAGTTATTTTACCCTTCAAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
* * * *
557705 CAATAATTTTACCCTTTGAGGATATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
* *
557732 CGGTAATTTTACCCTTCGAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
* *
557759 C-GATAATTTTACCCTTCGAAGGTATTT
1 CAG-TCATTTTACCCTTCGAGGGTATTT
* *
557786 CAGTAATTTTACCCTTCGATGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
* * *
557813 -TGATCATTTTATCCTTCGAAGGTATTT
1 CAG-TCATTTTACCCTTCGAGGGTATTT
* * *
557840 CGGTAATTTTACCCTTCAAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
*
557867 CGGTCATTTTAC
1 CAGTCATTTTAC
557879 AACCTTTCTG
Statistics
Matches: 297, Mismatches: 29, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
26 4 0.01
27 288 0.97
28 5 0.02
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (27 bp):
CAGTCATTTTACCCTTCGAGGGTATTT
Found at i:559419 original size:29 final size:29
Alignment explanation
Indices: 559377--559434 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
559367 AGGCGACTGT
* *
559377 TGAGCATGTAGGTATGTTGTTCATTTTTA
1 TGAGCACGCAGGTATGTTGTTCATTTTTA
559406 TGAGCACGCAGGTATGTTGTTCATTTTTA
1 TGAGCACGCAGGTATGTTGTTCATTTTTA
559435 GGTCATGGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.21, C:0.10, G:0.24, T:0.45
Consensus pattern (29 bp):
TGAGCACGCAGGTATGTTGTTCATTTTTA
Found at i:559457 original size:20 final size:20
Alignment explanation
Indices: 559432--559473 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
559422 TTGTTCATTT
*
559432 TTAGGTCATGGACTCAATTG
1 TTAGGTCATGGACCCAATTG
559452 TTAGGTCATGGACCCAATTG
1 TTAGGTCATGGACCCAATTG
559472 TT
1 TT
559474 TATGAGCACG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36
Consensus pattern (20 bp):
TTAGGTCATGGACCCAATTG
Found at i:562850 original size:24 final size:24
Alignment explanation
Indices: 562805--562850 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
562795 TGCATAATTA
*
562805 AAAAACAAAAAAAAAACCAAAACC
1 AAAAACAAAAAAAAAACAAAAACC
* *
562829 AAAAACAAAATAAAAATAAAAA
1 AAAAACAAAAAAAAAACAAAAA
562851 TAAAAATTAT
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:0.83, C:0.13, G:0.00, T:0.04
Consensus pattern (24 bp):
AAAAACAAAAAAAAAACAAAAACC
Found at i:562856 original size:24 final size:24
Alignment explanation
Indices: 562803--562856 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
562793 AGTGCATAAT
*
562803 TAAAAAACAAAAAAAAAACCAAAA
1 TAAAAAACAAAAAAAAAACAAAAA
** * *
562827 CCAAAAACAAAATAAAAATAAAAA
1 TAAAAAACAAAAAAAAAACAAAAA
562851 TAAAAA
1 TAAAAA
562857 TTATAAAACT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.81, C:0.11, G:0.00, T:0.07
Consensus pattern (24 bp):
TAAAAAACAAAAAAAAAACAAAAA
Done.