Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 21 of 170
Found at i:5536910 original size:45 final size:43
Alignment explanation
Indices: 5536817--5536912 Score: 120
Period size: 45 Copynumber: 2.2 Consensus size: 43
5536807 CTTAGGGAGG
* ** *
5536817 CAAGATCTGTTTCTTTGATCTACTTCATGCCAGTACATGAAGA
1 CAAGATCTGTTTCTTGGATCTACTTCACACCAGTACAGGAAGA
**
5536860 CAAGATCTGTTTTCTTGGATCTACTTCACCACCAGTATGGGAAGA
1 CAAGATCTG-TTTCTTGGATCTACTTCA-CACCAGTACAGGAAGA
5536905 CAAGATCT
1 CAAGATCT
5536913 TTTGTAGTCA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 9 0.20
44 17 0.38
45 19 0.42
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (43 bp):
CAAGATCTGTTTCTTGGATCTACTTCACACCAGTACAGGAAGA
Found at i:5538212 original size:14 final size:13
Alignment explanation
Indices: 5538179--5538218 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
5538169 TTAGCCTCTC
5538179 CATTTTT-ACTTTT
1 CATTTTTCA-TTTT
5538192 CATTTTTCATTTT
1 CATTTTTCATTTT
5538205 CATCTTTTCATTTT
1 CAT-TTTTCATTTT
5538219 TTTCACATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (13 bp):
CATTTTTCATTTT
Found at i:5538213 original size:21 final size:20
Alignment explanation
Indices: 5538179--5538219 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
5538169 TTAGCCTCTC
*
5538179 CATTTTTACTTTTCATTTTT
1 CATTTTCACTTTTCATTTTT
5538199 CATTTTCATCTTTTCATTTTT
1 CATTTTCA-CTTTTCATTTTT
5538220 TTCACATCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (20 bp):
CATTTTCACTTTTCATTTTT
Found at i:5538220 original size:8 final size:7
Alignment explanation
Indices: 5538179--5538219 Score: 50
Period size: 6 Copynumber: 6.0 Consensus size: 7
5538169 TTAGCCTCTC
5538179 CATTTTT
1 CATTTTT
*
5538186 -ACTTTT
1 CATTTTT
5538192 CATTTTT
1 CATTTTT
5538199 CA-TTTT
1 CATTTTT
5538205 CATCTTTT
1 CAT-TTTT
5538213 CATTTTT
1 CATTTTT
5538220 TTCACATCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
6 11 0.38
7 11 0.38
8 7 0.24
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (7 bp):
CATTTTT
Found at i:5542405 original size:9 final size:9
Alignment explanation
Indices: 5542391--5542432 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
5542381 TGTGAAGGTT
5542391 AAAAATAAA
1 AAAAATAAA
5542400 AAAAATAAA
1 AAAAATAAA
5542409 AAAAA-ACAA
1 AAAAATA-AA
*
5542418 AACATATAAA
1 AA-AAATAAA
5542428 AAAAA
1 AAAAA
5542433 CGCACGAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
8 1 0.04
9 20 0.71
10 6 0.21
11 1 0.04
ACGTcount: A:0.86, C:0.05, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAATAAA
Found at i:5542419 original size:17 final size:18
Alignment explanation
Indices: 5542390--5542433 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
5542380 ATGTGAAGGT
*
5542390 TAAAAATAA-AAAAAATA
1 TAAAAAAAACAAAAAATA
*
5542407 -AAAAAAAACAAAACATA
1 TAAAAAAAACAAAAAATA
5542424 TAAAAAAAAC
1 TAAAAAAAAC
5542434 GCACGAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 7 0.30
17 7 0.30
18 9 0.39
ACGTcount: A:0.82, C:0.07, G:0.00, T:0.11
Consensus pattern (18 bp):
TAAAAAAAACAAAAAATA
Found at i:5542419 original size:19 final size:19
Alignment explanation
Indices: 5542391--5542432 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5542381 TGTGAAGGTT
*
5542391 AAAAATAAAAAAAATAAAA
1 AAAAACAAAAAAAATAAAA
* *
5542410 AAAAACAAAACATATAAAA
1 AAAAACAAAAAAAATAAAA
5542429 AAAA
1 AAAA
5542433 CGCACGAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.86, C:0.05, G:0.00, T:0.10
Consensus pattern (19 bp):
AAAAACAAAAAAAATAAAA
Found at i:5542433 original size:18 final size:17
Alignment explanation
Indices: 5542390--5542433 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
5542380 ATGTGAAGGT
5542390 TAAAAATAAA-AAAAATA
1 TAAAAA-AAACAAAAATA
5542407 -AAAAAAAACAAAACATA
1 TAAAAAAAACAAAA-ATA
5542424 TAAAAAAAAC
1 TAAAAAAAAC
5542434 GCACGAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 3 0.12
16 9 0.38
17 3 0.12
18 9 0.38
ACGTcount: A:0.82, C:0.07, G:0.00, T:0.11
Consensus pattern (17 bp):
TAAAAAAAACAAAAATA
Found at i:5542521 original size:23 final size:25
Alignment explanation
Indices: 5542477--5542530 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
5542467 CTTATGAACA
** *
5542477 TATATATTTTATATAAAGAAATATG
1 TATATATACTATATAAAGAAATACG
*
5542502 TATATATACTATAT-AA-AAATGCG
1 TATATATACTATATAAAGAAATACG
5542525 TATATA
1 TATATA
5542531 AGTTTAGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 11 0.44
24 2 0.08
25 12 0.48
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (25 bp):
TATATATACTATATAAAGAAATACG
Found at i:5562306 original size:96 final size:96
Alignment explanation
Indices: 5562185--5562365 Score: 258
Period size: 96 Copynumber: 1.9 Consensus size: 96
5562175 ACAAAAGGAA
* * *
5562185 TAAACACGAAGAAGAAGAGCTTGAAAAGGTGA-CAG-AAAGCTATAAGCTTAAACGAAAGCCACC
1 TAAACACGAAAAAGAAGAGCTTGAAAAGGT-ATCAGAAAAG-TATAAACTTAAACGAAAGCAACC
* *
5562248 ATCACCGTCATTGGAACGCGAAAAGCAGATCGC
64 ATCACCGTCATCGGAACCCGAAAAGCAGATCGC
*
5562281 TAAACTCGAAAAAGAAGAGCTTGAAAAGGTATCAGAAAAGTATAAACTTAAACGAAAGCAACCAT
1 TAAACACGAAAAAGAAGAGCTTGAAAAGGTATCAGAAAAGTATAAACTTAAACGAAAGCAACCAT
* *
5562346 CGCCTTCATCGGAACCCGAA
66 CACCGTCATCGGAACCCGAA
5562366 GCAATCACCT
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
95 1 0.01
96 70 0.93
97 4 0.05
ACGTcount: A:0.44, C:0.20, G:0.20, T:0.15
Consensus pattern (96 bp):
TAAACACGAAAAAGAAGAGCTTGAAAAGGTATCAGAAAAGTATAAACTTAAACGAAAGCAACCAT
CACCGTCATCGGAACCCGAAAAGCAGATCGC
Found at i:5585822 original size:50 final size:52
Alignment explanation
Indices: 5585715--5585832 Score: 168
Period size: 50 Copynumber: 2.3 Consensus size: 52
5585705 AAAAATGAGT
* * * * *
5585715 TTACTTAATGCATGACTTAATTTAATGATGCAGACTTAAATTAACATGGGAG
1 TTACATAATGCATGACATAATTTAATGATGCAAACTTAAACTAACATGAGAG
*
5585767 TTACATAATGCATGTCATAATTT-ATGATGCAAACTT-AACTAACATGAGAG
1 TTACATAATGCATGACATAATTTAATGATGCAAACTTAAACTAACATGAGAG
5585817 TTACATAATGCATGAC
1 TTACATAATGCATGAC
5585833 TTTATTAAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 27 0.46
51 12 0.20
52 20 0.34
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (52 bp):
TTACATAATGCATGACATAATTTAATGATGCAAACTTAAACTAACATGAGAG
Found at i:5589734 original size:34 final size:34
Alignment explanation
Indices: 5589663--5589747 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 34
5589653 ATGACTCAAA
* *
5589663 AACAAGCTAATAAATTTAGCTTCTTACTCCCACT
1 AACAAGCTAACAAACTTAGCTTCTTACTCCCACT
** *
5589697 AACAAGCTAACAAACTTAGCTT-TCTACTTTCATT
1 AACAAGCTAACAAACTTAGCTTCT-TACTCCCACT
*
5589731 AACAAGTTAACAAACTT
1 AACAAGCTAACAAACTT
5589748 CCTAGAATCA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
33 1 0.02
34 43 0.98
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.32
Consensus pattern (34 bp):
AACAAGCTAACAAACTTAGCTTCTTACTCCCACT
Found at i:5592054 original size:86 final size:91
Alignment explanation
Indices: 5591901--5592066 Score: 243
Period size: 86 Copynumber: 1.9 Consensus size: 91
5591891 ACTTTTTCAA
* * * *
5591901 AAAAAAAAGAGAAGCAATTAAGCCCCTGCTTTTTTTTTTGCACTCAATTGGGTACTTGAATTTTC
1 AAAAAAAAGAGAAGCAATTAAGCCCCTACTTTTTTTTTTGCACTAAATTGGATACTTGAATTGTC
5591966 AAAATGCATAAAAAATGCCTCAAATT
66 AAAATGCATAAAAAATGCCTCAAATT
*
5591992 AAAAAAAA-A-AA-CAATTAAGTCCCTAC-TTTTTTTTT-CACTAAATTGGATACTTGAATTGTC
1 AAAAAAAAGAGAAGCAATTAAGCCCCTACTTTTTTTTTTGCACTAAATTGGATACTTGAATTGTC
*
5592052 AAAATGCATCAAAAA
66 AAAATGCATAAAAAA
5592067 GACCATTTGA
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
86 36 0.52
87 9 0.13
88 13 0.19
89 2 0.03
90 1 0.01
91 8 0.12
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (91 bp):
AAAAAAAAGAGAAGCAATTAAGCCCCTACTTTTTTTTTTGCACTAAATTGGATACTTGAATTGTC
AAAATGCATAAAAAATGCCTCAAATT
Found at i:5592175 original size:10 final size:10
Alignment explanation
Indices: 5592162--5592217 Score: 53
Period size: 10 Copynumber: 5.8 Consensus size: 10
5592152 AAAATATAAA
5592162 AATAAAAATT
1 AATAAAAATT
5592172 AAT-AAAATT
1 AATAAAAATT
* *
5592181 TATAAGAATT
1 AATAAAAATT
* **
5592191 ATTAAATTTT
1 AATAAAAATT
5592201 AATAAAAATT
1 AATAAAAATT
5592211 -ATAAAAA
1 AATAAAAA
5592218 ATTGTAAAAA
Statistics
Matches: 35, Mismatches: 10, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
9 15 0.43
10 20 0.57
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (10 bp):
AATAAAAATT
Found at i:5592190 original size:19 final size:20
Alignment explanation
Indices: 5592162--5592286 Score: 73
Period size: 19 Copynumber: 6.3 Consensus size: 20
5592152 AAAATATAAA
5592162 AATAAAAATTAATAAAATTT
1 AATAAAAATTAATAAAATTT
* * *
5592182 -ATAAGAATTATTAAATTTT
1 AATAAAAATTAATAAAATTT
*
5592201 AATAAAAATTATAAAAAATTGT
1 AATAAAAATTA-ATAAAATT-T
* * *
5592223 AA-AAAATTATAAAAAAAATGT
1 AATAAAA--ATTAATAAAATTT
*
5592244 AA-AAAAATT-ATAAAA-TA
1 AATAAAAATTAATAAAATTT
*
5592261 AATAGAAA-TATATAAAATTT
1 AATAAAAATTA-ATAAAATTT
*
5592281 TATAAA
1 AATAAA
5592287 GTCGTAAGAA
Statistics
Matches: 79, Mismatches: 17, Indels: 18
0.69 0.15 0.16
Matches are distributed among these distances:
17 3 0.04
18 9 0.11
19 24 0.30
20 14 0.18
21 16 0.20
22 10 0.13
23 3 0.04
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
AATAAAAATTAATAAAATTT
Found at i:5592218 original size:10 final size:10
Alignment explanation
Indices: 5592204--5592258 Score: 67
Period size: 10 Copynumber: 5.3 Consensus size: 10
5592194 AAATTTTAAT
5592204 AAAAATTATA
1 AAAAATTATA
*
5592214 AAAAATTGTA
1 AAAAATTATA
5592224 AAAAATTATAAA
1 AAAAATTAT--A
5592236 AAAAATGTA-A
1 AAAAAT-TATA
5592246 AAAAATTATA
1 AAAAATTATA
5592256 AAA
1 AAA
5592259 TAAATAGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 2 0.05
10 28 0.72
12 7 0.18
13 2 0.05
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (10 bp):
AAAAATTATA
Found at i:5592225 original size:29 final size:29
Alignment explanation
Indices: 5592170--5592225 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
5592160 AAAATAAAAA
* * *
5592170 TTAATAAAATTTATAAGAATTATTAAATT
1 TTAATAAAAATTATAAAAATTAGTAAATT
5592199 TTAATAAAAATTATAAAAAATT-GTAAA
1 TTAATAAAAATTAT-AAAAATTAGTAAA
5592226 AAATTATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 17 0.74
30 6 0.26
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (29 bp):
TTAATAAAAATTATAAAAATTAGTAAATT
Found at i:5592227 original size:20 final size:21
Alignment explanation
Indices: 5592204--5592263 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 21
5592194 AAATTTTAAT
*
5592204 AAAAATTATAAAAAATTGT-A
1 AAAAATTATAAAAAAATGTAA
5592224 AAAAATTATAAAAAAAATGTAA
1 AAAAATTAT-AAAAAAATGTAA
5592246 AAAAATTATAAAATAAAT
1 AAAAATTATAAAA-AAAT
5592264 AGAAATATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 9 0.25
21 13 0.36
22 14 0.39
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (21 bp):
AAAAATTATAAAAAAATGTAA
Found at i:5592238 original size:22 final size:23
Alignment explanation
Indices: 5592194--5592263 Score: 85
Period size: 22 Copynumber: 3.2 Consensus size: 23
5592184 AAGAATTATT
*
5592194 AAATTTTAATAAAAATTAT--AAA
1 AAATTGTAA-AAAAATTATAAAAA
5592216 AAATTGT-AAAAAATTATAAAAA
1 AAATTGTAAAAAAATTATAAAAA
*
5592238 AAA-TGTAAAAAAATTATAAAAT
1 AAATTGTAAAAAAATTATAAAAA
5592260 AAAT
1 AAAT
5592264 AGAAATATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
20 9 0.21
21 4 0.10
22 29 0.69
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (23 bp):
AAATTGTAAAAAAATTATAAAAA
Found at i:5592344 original size:20 final size:20
Alignment explanation
Indices: 5592274--5592347 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 20
5592264 AGAAATATAT
* * *
5592274 AAAATTTTATAAAGTCGTAAG
1 AAAATTATA-AAATTCGTAAA
* *
5592295 AAGATTATAAAAAAT-GTAAA
1 AAAATTAT-AAAATTCGTAAA
*
5592315 GAAA-TATAAAATTCGTAAA
1 AAAATTATAAAATTCGTAAA
5592334 AAAATTATAAAATT
1 AAAATTATAAAATT
5592348 TATCATACCA
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
18 5 0.12
19 11 0.26
20 15 0.36
21 10 0.24
22 1 0.02
ACGTcount: A:0.58, C:0.03, G:0.09, T:0.30
Consensus pattern (20 bp):
AAAATTATAAAATTCGTAAA
Found at i:5592626 original size:10 final size:9
Alignment explanation
Indices: 5592600--5592654 Score: 58
Period size: 9 Copynumber: 6.0 Consensus size: 9
5592590 TTAAAACTTA
5592600 ATAATTTTT
1 ATAATTTTT
5592609 ATAATTTTT
1 ATAATTTTT
*
5592618 ATAACTTTT
1 ATAATTTTT
*
5592627 ATTGATTTTT
1 A-TAATTTTT
*
5592637 ATTGATTTTT
1 A-TAATTTTT
5592647 AT-ATTTTT
1 ATAATTTTT
5592655 TGCCACATGT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
8 6 0.14
9 19 0.45
10 17 0.40
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (9 bp):
ATAATTTTT
Found at i:5592973 original size:89 final size:89
Alignment explanation
Indices: 5592760--5592985 Score: 276
Period size: 89 Copynumber: 2.5 Consensus size: 89
5592750 TCAAATGAGC
* * * * * * *
5592760 TTTTTGATTCATTTTGACAGTTTAAGTACCCAATTAAGCGTAAAATAAAAGCAGGGGCTTAATTG
1 TTTTTGATGCATTTTGAAAGTTTAAGTACCCAATTGAGTGCAAAA-AAAAGCAGGGGCTTAACTA
*
5592825 CTTTTTTGAAAAAGTTTGATGGCAT
65 CTTTTTTGAAAAAGTTTGAGGGCAT
* * * *
5592850 TTTTT-ATGTATTTTAAAAGTTTAAGTACCCAATTGAGTGCAAAAAAAAGTAGGGGCTTAACTAT
1 TTTTTGATGCATTTTGAAAGTTTAAGTACCCAATTGAGTGCAAAAAAAAGCAGGGGCTTAACTAC
5592914 TTTTTTCGAAAAAGTTTGAGGGC-T
66 TTTTTT-GAAAAAGTTTGAGGGCAT
* * * *
5592938 TTTTTGATGCATTTTGAAAGTTCAAATGCCTAATTGAGTGCAAAAAAA
1 TTTTTGATGCATTTTGAAAGTTTAAGTACCCAATTGAGTGCAAAAAAA
5592986 GGACTTAATT
Statistics
Matches: 116, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
88 28 0.24
89 83 0.72
90 5 0.04
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (89 bp):
TTTTTGATGCATTTTGAAAGTTTAAGTACCCAATTGAGTGCAAAAAAAAGCAGGGGCTTAACTAC
TTTTTTGAAAAAGTTTGAGGGCAT
Found at i:5597392 original size:14 final size:14
Alignment explanation
Indices: 5597373--5597399 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5597363 TCTCTATGTA
5597373 AAAAGAAAAAAAAG
1 AAAAGAAAAAAAAG
5597387 AAAAGAAAAAAAA
1 AAAAGAAAAAAAA
5597400 CTCTGATGAT
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:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAAAG
Found at i:5601034 original size:31 final size:31
Alignment explanation
Indices: 5600998--5601058 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
5600988 CAAAAACACA
* *
5600998 AAAACAAAATCTGGGTCTTCGAGTTTAATTC
1 AAAACAAAAACTGGGTCTTCGAGTTAAATTC
* *
5601029 AAAACAAAAACTGGGTGTTTGAGTTAAATT
1 AAAACAAAAACTGGGTCTTCGAGTTAAATT
5601059 TTTTTTTCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.31
Consensus pattern (31 bp):
AAAACAAAAACTGGGTCTTCGAGTTAAATTC
Found at i:5609382 original size:25 final size:24
Alignment explanation
Indices: 5609347--5609440 Score: 84
Period size: 25 Copynumber: 3.8 Consensus size: 24
5609337 CTTCAATGTT
5609347 CAATTTGGTACTTGAGTTTTTTTC
1 CAATTTGGTACTTGAGTTTTTTTC
*
5609371 CTAATTTGGTACTTGA-ATTTTTT-
1 C-AATTTGGTACTTGAGTTTTTTTC
* *
5609394 CAACTTGATACTTGAGGTTTGTTTGGTCC
1 CAATTTGGTACTTGA-GTTT-TTT--T-C
*
5609423 CAATTTGGTACTTAAGTT
1 CAATTTGGTACTTGAGTT
5609441 CGAGTTTAAC
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
22 12 0.22
23 1 0.02
24 9 0.16
25 17 0.31
27 1 0.02
28 3 0.05
29 12 0.22
ACGTcount: A:0.20, C:0.13, G:0.18, T:0.49
Consensus pattern (24 bp):
CAATTTGGTACTTGAGTTTTTTTC
Found at i:5610669 original size:20 final size:21
Alignment explanation
Indices: 5610633--5610671 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
5610623 TTGATATTGT
*
5610633 TTTTAAGAAATGTATCGATTA
1 TTTTAAGAAAAGTATCGATTA
5610654 TTTTAA-AAAAGTATCGAT
1 TTTTAAGAAAAGTATCGAT
5610672 ACCAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (21 bp):
TTTTAAGAAAAGTATCGATTA
Found at i:5610877 original size:20 final size:20
Alignment explanation
Indices: 5610846--5610903 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
5610836 TTTTGATGTG
*
5610846 TTAAAATGATTTTAACTTGA
1 TTAAAATCATTTTAACTTGA
** *
5610866 TTGGAATCATTTTAACTTGG
1 TTAAAATCATTTTAACTTGA
*
5610886 TTAAAATCATTTTCACTT
1 TTAAAATCATTTTAACTT
5610904 AATTTTAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (20 bp):
TTAAAATCATTTTAACTTGA
Found at i:5617266 original size:12 final size:11
Alignment explanation
Indices: 5617248--5617327 Score: 65
Period size: 12 Copynumber: 7.0 Consensus size: 11
5617238 TTGTTGCCGC
5617248 TATTATTATTA
1 TATTATTATTA
5617259 TCATTATTATTTA
1 T-ATTATTA-TTA
5617272 TATTATTATTA
1 TATTATTATTA
*
5617283 TTATCATTATTA
1 -TATTATTATTA
*
5617295 T-TTATCT-TTC
1 TATTAT-TATTA
*
5617305 TTTTATTATTTA
1 TATTATTA-TTA
*
5617317 TATTAGTATTA
1 TATTATTATTA
5617328 GAATAGTAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
10 7 0.12
11 13 0.23
12 32 0.57
13 4 0.07
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64
Consensus pattern (11 bp):
TATTATTATTA
Found at i:5617313 original size:27 final size:27
Alignment explanation
Indices: 5617248--5617299 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
5617238 TTGTTGCCGC
5617248 TATTATTATTATCATTATTATTTATAT
1 TATTATTATTATCATTATTATTTATAT
5617275 TATTATTATTATCATTATTATTTAT
1 TATTATTATTATCATTATTATTTAT
5617300 CTTTCTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (27 bp):
TATTATTATTATCATTATTATTTATAT
Found at i:5617314 original size:3 final size:3
Alignment explanation
Indices: 5617248--5617296 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
5617238 TTGTTGCCGC
* *
5617248 TAT TAT TAT TAT CAT TAT TAT T-T ATAT TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
5617293 TAT T
1 TAT T
5617297 TATCTTTCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
2 1 0.03
3 38 0.95
4 1 0.03
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:5623616 original size:17 final size:17
Alignment explanation
Indices: 5623590--5623623 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5623580 GCCAGGAGTG
5623590 TTAATCGACAATGGATA
1 TTAATCGACAATGGATA
* *
5623607 TTAATTGACAGTGGATA
1 TTAATCGACAATGGATA
5623624 CACGCTGAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (17 bp):
TTAATCGACAATGGATA
Found at i:5627428 original size:37 final size:37
Alignment explanation
Indices: 5627387--5627497 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 37
5627377 AAAGAAAGAG
*
5627387 ATCATATGTCGGTATGGAATGCCATAAAAGA-CTATAT
1 ATCATATGTCGGTATGGAATGCCAGAAAAGATC-ATAT
* *
5627424 ATCATATCTCAGTATGGAATGCCAGAAAAGATCATAT
1 ATCATATGTCGGTATGGAATGCCAGAAAAGATCATAT
*
5627461 ATCATATGTCGGTATGGAATGCCAGAAAGGATCATAT
1 ATCATATGTCGGTATGGAATGCCAGAAAAGATCATAT
5627498 CTAACAATGC
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
37 66 0.99
38 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (37 bp):
ATCATATGTCGGTATGGAATGCCAGAAAAGATCATAT
Found at i:5629085 original size:44 final size:44
Alignment explanation
Indices: 5629019--5629443 Score: 406
Period size: 44 Copynumber: 9.5 Consensus size: 44
5629009 CTACCATAGT
* * * * *
5629019 AAATATTATATCCCTAAAGTTGCAATGGAGCAGATTAAAGCTAA
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC
* * * * *
5629063 AAATCCTATAC-CTCTGAAGTTGCAGTGG-GTCTGATTGAATATACCATAG
1 AAATCTTAT-CTCCCTGAAGTTGCAGTGGAG-CAGATT--A-A-AGC-TAC
* * * * * * *
5629112 GAATCTTATCTTCATAAATTTGCAATGGAGCAGATGAAAGCTAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC
* * * *
5629156 CAATCTTATCCCCCTGAAGTTGTATTGGAGCAGATTAAAGCTAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC
* * * *
5629200 AAGTCTTATCTCCCTGAAGTTTCAATGGAGCAAATTAAAGCTAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC
* *
5629244 CAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCTAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC
* *
5629288 AAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCTAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC
* * * *
5629332 CAATCTTATCTCTCTAAAGTTGTAGTGGAGCAGATTAAAGCTAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC
* * *
5629376 AAATCTTATCTCCCTGAAGTTGTAGTGGAGTAGATTGAAG-TAAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCT-AC
* * *
5629420 AAATCTTATTTCTCTAAAGTTGCA
1 AAATCTTATCTCCCTGAAGTTGCA
5629444 ATGGGGCAAG
Statistics
Matches: 309, Mismatches: 62, Indels: 20
0.79 0.16 0.05
Matches are distributed among these distances:
43 2 0.01
44 273 0.88
45 2 0.01
46 2 0.01
47 2 0.01
48 3 0.01
49 24 0.08
50 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (44 bp):
AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC
Found at i:5631305 original size:3 final size:3
Alignment explanation
Indices: 5631231--5631287 Score: 69
Period size: 3 Copynumber: 19.0 Consensus size: 3
5631221 TGCCTCTATG
* * * * *
5631231 ATT ATT ATT GTT ACT GTT ATT AAT ATT ATT ATT ATT ATT ATT ATT ATC
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5631279 ATT ATT ATT
1 ATT ATT ATT
5631288 TATCTTTCTT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:5635500 original size:20 final size:20
Alignment explanation
Indices: 5635448--5635500 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
5635438 ATTTTGATGT
*
5635448 GTTAAAATGATTTAAACTTG
1 GTTAAAATCATTTAAACTTG
** * **
5635468 GTTGGAATTATTTGGACTTG
1 GTTAAAATCATTTAAACTTG
5635488 GTTAAAATCATTT
1 GTTAAAATCATTT
5635501 TCACTTTATT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (20 bp):
GTTAAAATCATTTAAACTTG
Found at i:5647826 original size:21 final size:22
Alignment explanation
Indices: 5647784--5647827 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
5647774 GTTATGAGAA
*
5647784 TTTAAGAATTTGGTTGAAAATC
1 TTTAAGAATTTGATTGAAAATC
*
5647806 TTTAAGAA-TTGATTGAGAATC
1 TTTAAGAATTTGATTGAAAATC
5647827 T
1 T
5647828 CAATCAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (22 bp):
TTTAAGAATTTGATTGAAAATC
Found at i:5647891 original size:73 final size:73
Alignment explanation
Indices: 5647784--5648082 Score: 296
Period size: 73 Copynumber: 4.2 Consensus size: 73
5647774 GTTATGAGAA
* * *
5647784 TTTAAGAATTT---GGTTGAAAATCTTTAAGAATTGATTGAGAATCTCAATCAATAATGTTAAAT
1 TTTAAGAATTTAGGGGTTGAAAATCTTTAAGATTTGATTGAGAATCTTAATCAACAATGTTAAAT
* *
5647846 GGATCATT
66 GGAGCACT
* *
5647854 TTTAAGAATTTAGGGGTTGAAAATCTGTAAGATTTGATTGCA-AATTTTAATCAACAATGTTAAA
1 TTTAAGAATTTAGGGGTTGAAAATCTTTAAGATTTGATTG-AGAATCTTAATCAACAATGTTAAA
5647918 TGGAGCACT
65 TGGAGCACT
* * *
5647927 TTTGAGGATTTAGGGATTTGGTTGAAAATCTTTAAAATTTGATTGAGAATCTTAATCAACAATGT
1 TTTAAGAATTTA-GG----GGTTGAAAATCTTTAAGATTTGATTGAGAATCTTAATCAACAATGT
5647992 TAAATGGAGCACT
61 TAAATGGAGCACT
* * * * * * * *
5648005 TTT--GAGTTT---GG-TCAAAATCTTTCAGATTTAATTGAAAATTTTTATGAACAATGTT-AAT
1 TTTAAGAATTTAGGGGTTGAAAATCTTTAAGATTTGATTGAGAATCTTAATCAACAATGTTAAAT
5648063 GGAGCACT
66 GGAGCACT
*
5648071 TTTTAGAATTTA
1 TTTAAGAATTTA
5648083 AAATCTTTAA
Statistics
Matches: 193, Mismatches: 23, Indels: 27
0.79 0.09 0.11
Matches are distributed among these distances:
66 14 0.07
67 36 0.19
68 7 0.04
70 11 0.06
73 60 0.31
74 3 0.02
76 4 0.02
77 1 0.01
78 57 0.30
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.39
Consensus pattern (73 bp):
TTTAAGAATTTAGGGGTTGAAAATCTTTAAGATTTGATTGAGAATCTTAATCAACAATGTTAAAT
GGAGCACT
Found at i:5648884 original size:422 final size:410
Alignment explanation
Indices: 5648034--5648782 Score: 1099
Period size: 422 Copynumber: 1.8 Consensus size: 410
5648024 TTTCAGATTT
* **
5648034 AATTGAAAATTTTTATGAACAATGTTAATGGAGCACTTTTTAGAATTTAAAATCTTTAAAATGAT
1 AATTGAAAATTTTAACCAACAATGTTAATGGAGCACTTTTTAGAATTTAAAATCTTTAAAATGAT
5648099 TGAGAATCTTAAGTAGATAACTTTTAGTTTGTATCTTTATATATAGTGGAGCAATATCAGCTTAA
66 TGAGAATCTTAAGTAGATAACTTTTAGTTTGTATCTTTATATATAGTGGAGCAATATCAGCTTAA
*
5648164 TTCTTTTATATGATATAATTTAAAAATTAATATTTTTCATGATAATAATTTGTCATGTGTAATTC
131 TTCTTTTATATGATATAATTTAAAAATTAATATTTTTCATGATAATAAATTGTCATGTGTAATTC
*
5648229 TTGATTATATTGAAAAAAAATTATTCAATGCAAATTTCTTCTAAAAATATAGTGACAAATTTGGA
196 TTGATTATATTGAAAAAAAATTATTCAATGCAAATTTCTTATAAAAATATAGTGACAAATTTGGA
*
5648294 ATTAAAAAAAAATCATATATTTTATTAATATCTCCAATATTCCTATTGTATAATAAAAAGTATTA
261 ATT-AAAAAAAATCATATATTTGATTAATATCTCCAATATTCCTATTGTATAATAAAAAGTATTA
*** *** ** *
5648359 GACTAATAAAAAATTTTTGGTTGAAAATCAATAATGTTAAATGGAGCACTTTTGAGAATTTAGGG
325 GACTAATAAAAAATAAAT-GTTGAAAATCAATAATAAAAAATGGAGCAAATTTCAGAATTTA--G
* * * * **
5648424 ATTTGGTTGAAATCTTTCAGATTT
387 ATTTGGTTAAAATATTTAAAATGA
5648448 AATTGAAAATTTTAACCAACAATGTTAATGGAGCACTTTTTAGAATTTATTGAAAATCTTTAAGA
1 AATTGAAAATTTTAACCAACAATGTTAATGGAGCACTTTTTAGAA--T-TT-AAAATCTTTAA-A
* *
5648513 TTTGATTGAGAATCTTAAGTAGATAA-TTTTAGTTTGTATCTTTATATATATAGTGTAGCAATAT
61 -ATGATTGAGAATCTTAAGTAGATAACTTTTAGTTTGTATC-TT-TATATATAGTGGAGCAATAT
* * *
5648577 CAGCTTAAATTTTTTTATATGATATAATTTAAAAATTGATATTTTTCATGATAATAAATTGTGAT
123 CAGCTT-AATTCTTTTATATGATATAATTTAAAAATTAATATTTTTCATGATAATAAATTGTCAT
5648642 GTGTAATTCTTGATTATATTGAAAAAAAATTATTCAATGCAAATTTCTTATAAAAATATAGTGAC
187 GTGTAATTCTTGATTATATTGAAAAAAAATTATTCAATGCAAATTTCTTATAAAAATATAGTGAC
* *
5648707 AAATTTGGAA-T-AAAAAATTCTATATATTTGATTAATATCTCCAATATTCCTATTGTATAATCA
252 AAATTTGGAATTAAAAAAAATC-ATATATTTGATTAATATCTCCAATATTCCTATTGTATAATAA
5648770 AAAGTATTAGACT
316 AAAGTATTAGACT
5648783 GTATTTAGTA
Statistics
Matches: 312, Mismatches: 13, Indels: 14
0.92 0.04 0.04
Matches are distributed among these distances:
414 42 0.13
416 1 0.00
417 2 0.01
418 11 0.04
419 23 0.07
420 79 0.25
421 26 0.08
422 128 0.41
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.41
Consensus pattern (410 bp):
AATTGAAAATTTTAACCAACAATGTTAATGGAGCACTTTTTAGAATTTAAAATCTTTAAAATGAT
TGAGAATCTTAAGTAGATAACTTTTAGTTTGTATCTTTATATATAGTGGAGCAATATCAGCTTAA
TTCTTTTATATGATATAATTTAAAAATTAATATTTTTCATGATAATAAATTGTCATGTGTAATTC
TTGATTATATTGAAAAAAAATTATTCAATGCAAATTTCTTATAAAAATATAGTGACAAATTTGGA
ATTAAAAAAAATCATATATTTGATTAATATCTCCAATATTCCTATTGTATAATAAAAAGTATTAG
ACTAATAAAAAATAAATGTTGAAAATCAATAATAAAAAATGGAGCAAATTTCAGAATTTAGATTT
GGTTAAAATATTTAAAATGA
Found at i:5653520 original size:43 final size:43
Alignment explanation
Indices: 5653457--5653620 Score: 156
Period size: 43 Copynumber: 3.9 Consensus size: 43
5653447 TACCGTAACA
* * ** *
5653457 ATGCC-ATATCCCAGATATGGTCTTACATGTAATCTCGTATCG
1 ATGCCAATAGCCCAGACATGGTCTTACACATAATCTCATATCG
* * *
5653499 ATGCCAATAGCCCAGCCATGGTCTTACACAAAATCACATATCG
1 ATGCCAATAGCCCAGACATGGTCTTACACATAATCTCATATCG
* * *
5653542 ATGCCAAT-GTCCTAGACATGGTCTTACACGA-AGTCTCATATCA
1 ATGCCAATAG-CCCAGACATGGTCTTACAC-ATAATCTCATATCG
* * *
5653585 ATGGC-ATATCCCAGATATGGTCTTACACATAATCTC
1 ATGCCAATAGCCCAGACATGGTCTTACACATAATCTC
5653621 GGTAACCCTA
Statistics
Matches: 99, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
41 1 0.01
42 30 0.30
43 67 0.68
44 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (43 bp):
ATGCCAATAGCCCAGACATGGTCTTACACATAATCTCATATCG
Found at i:5654905 original size:15 final size:15
Alignment explanation
Indices: 5654880--5654919 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
5654870 CCCATTCGTA
5654880 TGAACCCCTAGGTGTG
1 TGAA-CCCTAGGTGTG
5654896 TGAACCCTAGGTGTG
1 TGAACCCTAGGTGTG
*
5654911 TAAACCCTA
1 TGAACCCTA
5654920 ATGTGCAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (15 bp):
TGAACCCTAGGTGTG
Found at i:5654986 original size:28 final size:28
Alignment explanation
Indices: 5654915--5654986 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 28
5654905 GGTGTGTAAA
*
5654915 CCCTAATGTGCAAACCCCTAGGTGCGAT
1 CCCTAAAGTGCAAACCCCTAGGTGCGAT
* * * *
5654943 CCCTAATGAGCGAACCCCTAGGTGTGA-
1 CCCTAAAGTGCAAACCCCTAGGTGCGAT
*
5654970 CCTTTAAAGTGCAAACC
1 CC-CTAAAGTGCAAACC
5654987 TACATGTGCA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 2 0.06
28 34 0.94
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.21
Consensus pattern (28 bp):
CCCTAAAGTGCAAACCCCTAGGTGCGAT
Found at i:5657698 original size:23 final size:23
Alignment explanation
Indices: 5657629--5657698 Score: 61
Period size: 25 Copynumber: 2.9 Consensus size: 23
5657619 TAGCTCGAAA
*
5657629 GAGCGTTC-CGTTATTAGCTCTCAT
1 GAGC-TTCTCGTTA-TAGCTCTTAT
* * *
5657653 GAGCTTCTCATTATATAGTTCTTGT
1 GAGCTTCTC-GT-TATAGCTCTTAT
5657678 GAGCTTCTCGTTATAGCTCTT
1 GAGCTTCTCGTTATAGCTCTT
5657699 CGGAGTATCC
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
23 12 0.32
24 6 0.16
25 17 0.46
26 2 0.05
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (23 bp):
GAGCTTCTCGTTATAGCTCTTAT
Found at i:5663893 original size:12 final size:12
Alignment explanation
Indices: 5663876--5663900 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5663866 GCCAGGCAGT
5663876 AGAAGAAGAAAA
1 AGAAGAAGAAAA
5663888 AGAAGAAGAAAA
1 AGAAGAAGAAAA
5663900 A
1 A
5663901 ATAGAGATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AGAAGAAGAAAA
Found at i:5664857 original size:30 final size:30
Alignment explanation
Indices: 5664821--5664889 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
5664811 ATGTTAGCGG
* *
5664821 GTGACTGTTTTGTTATTTTCTTAAAGTTTA
1 GTGACTGTTTTGTTATTTTCTCAAAGTTGA
5664851 GTGACTGTTTTGTTATTTTCTCAAAGTTGA
1 GTGACTGTTTTGTTATTTTCTCAAAGTTGA
5664881 GTGACTGTT
1 GTGACTGTT
5664890 GGTGTAGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.19, C:0.09, G:0.20, T:0.52
Consensus pattern (30 bp):
GTGACTGTTTTGTTATTTTCTCAAAGTTGA
Found at i:5668931 original size:29 final size:29
Alignment explanation
Indices: 5668889--5668975 Score: 147
Period size: 29 Copynumber: 3.0 Consensus size: 29
5668879 CTCAGAGCCC
5668889 CCCATGTGCAATGCTATAAGTTATTTAGA
1 CCCATGTGCAATGCTATAAGTTATTTAGA
**
5668918 CCCATGTGTGATGCTATAAGTTATTTAGA
1 CCCATGTGCAATGCTATAAGTTATTTAGA
*
5668947 CTCATGTGCAATGCTATAAGTTATTTAGA
1 CCCATGTGCAATGCTATAAGTTATTTAGA
5668976 AAGTGCTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (29 bp):
CCCATGTGCAATGCTATAAGTTATTTAGA
Found at i:5674932 original size:17 final size:18
Alignment explanation
Indices: 5674888--5674945 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 18
5674878 ATAATTAATT
*
5674888 AATT-TTAAAAATTAAAA
1 AATTATTAAAAATTATAA
* *
5674905 AACTATAAAAAATT-TAA
1 AATTATTAAAAATTATAA
5674922 AATTATT-AAAATTATAA
1 AATTATTAAAAATTATAA
*
5674939 AAATATT
1 AATTATT
5674946 TTCTAATATT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
16 6 0.18
17 19 0.58
18 8 0.24
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
AATTATTAAAAATTATAA
Found at i:5674941 original size:18 final size:19
Alignment explanation
Indices: 5674894--5674942 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 19
5674884 AATTAATTTT
*
5674894 AAAAATTA-AAAAACTATA
1 AAAAATTATAAAAATTATA
5674912 AAAAATT-T-AAAATTAT-
1 AAAAATTATAAAAATTATA
*
5674928 TAAAATTATAAAAAT
1 AAAAATTATAAAAAT
5674943 ATTTTCTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 6 0.23
17 8 0.31
18 12 0.46
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATTATAAAAATTATA
Found at i:5681435 original size:15 final size:16
Alignment explanation
Indices: 5681417--5681446 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5681407 CATTAATAAA
5681417 ATCAT-TATTTTTTTT
1 ATCATATATTTTTTTT
5681432 ATCATATATTTTTTT
1 ATCATATATTTTTTT
5681447 AACACAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (16 bp):
ATCATATATTTTTTTT
Found at i:5684273 original size:27 final size:28
Alignment explanation
Indices: 5684241--5684313 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 28
5684231 TGTGTGTCGC
*
5684241 CACACAGTCGTGTGGTAGGCCGTGTATGG
1 CACAC-GTCGTGTGGTAGGCCGTGTAAGG
*
5684270 CACACGGTCGTGTGGTAGGTCGTGTAAGG
1 CACAC-GTCGTGTGGTAGGCCGTGTAAGG
*
5684299 CACACGACAGTGTGG
1 CACACGTC-GTGTGG
5684314 ACCTTTTTGG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 2 0.05
29 37 0.95
ACGTcount: A:0.19, C:0.21, G:0.38, T:0.22
Consensus pattern (28 bp):
CACACGTCGTGTGGTAGGCCGTGTAAGG
Found at i:5684279 original size:29 final size:29
Alignment explanation
Indices: 5684241--5684304 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
5684231 TGTGTGTCGC
* *
5684241 CACACAGTCGTGTGGTAGGCCGTGTATGG
1 CACACGGTCGTGTGGTAGGCCGTGTAAGG
*
5684270 CACACGGTCGTGTGGTAGGTCGTGTAAGG
1 CACACGGTCGTGTGGTAGGCCGTGTAAGG
5684299 CACACG
1 CACACG
5684305 ACAGTGTGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.19, C:0.22, G:0.38, T:0.22
Consensus pattern (29 bp):
CACACGGTCGTGTGGTAGGCCGTGTAAGG
Found at i:5684802 original size:5 final size:5
Alignment explanation
Indices: 5684788--5684900 Score: 93
Period size: 5 Copynumber: 22.4 Consensus size: 5
5684778 ATGGGGGTAG
* * * * * *
5684788 GATAT GATTT GATTT GATTT GATAT GATAT GATAT GATAA GCTAT GATTT
1 GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT
* * * * * *
5684838 GATTT GATTT GATTT GATAT GATAT GATAG GATAT CATCT G-TAT GAAATAT
1 GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT G--ATAT
5684889 GATAT GATAT GA
1 GATAT GATAT GA
5684901 AATATTAAGA
Statistics
Matches: 91, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
4 3 0.03
5 84 0.92
7 4 0.04
ACGTcount: A:0.34, C:0.03, G:0.20, T:0.43
Consensus pattern (5 bp):
GATAT
Found at i:5684845 original size:40 final size:40
Alignment explanation
Indices: 5684790--5684866 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
5684780 GGGGGTAGGA
5684790 TATGATTTGATTTGATTTGATATGATATGATATGATAAGC
1 TATGATTTGATTTGATTTGATATGATATGATATGATAAGC
*
5684830 TATGATTTGATTTGATTTGATTTGATATGATATGATA
1 TATGATTTGATTTGATTTGATATGATATGATATGATA
5684867 GGATATCATC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.31, C:0.01, G:0.19, T:0.48
Consensus pattern (40 bp):
TATGATTTGATTTGATTTGATATGATATGATATGATAAGC
Found at i:5687153 original size:25 final size:25
Alignment explanation
Indices: 5687125--5687175 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
5687115 AAGTGTCAAG
*
5687125 TTTAG-TACCAAATTAAACCAAAAAA
1 TTTAGATACCAAATTAAA-AAAAAAA
5687150 TTTAGATACCAAATTAAAAAAAAAA
1 TTTAGATACCAAATTAAAAAAAAAA
5687175 T
1 T
5687176 CAAATTTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.59, C:0.12, G:0.04, T:0.25
Consensus pattern (25 bp):
TTTAGATACCAAATTAAAAAAAAAA
Found at i:5690799 original size:21 final size:22
Alignment explanation
Indices: 5690757--5690806 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
5690747 GAATTTTAAA
* *
5690757 TTATTTTTATATATATATATTT
1 TTATTTTTATATAAATAAATTT
*
5690779 TTATTTTTTTA-AAATAAATTT
1 TTATTTTTATATAAATAAATTT
5690800 TTATTTT
1 TTATTTT
5690807 ATTTTCATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTATTTTTATATAAATAAATTT
Found at i:5691169 original size:20 final size:21
Alignment explanation
Indices: 5691130--5691177 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
5691120 TTTGATTGAC
*
5691130 AAAATATAATATTACTTTAAA
1 AAAATATAATATCACTTTAAA
*
5691151 AAAATATCATATCAC-TTAAA
1 AAAATATAATATCACTTTAAA
*
5691171 AACATAT
1 AAAATAT
5691178 TTTTACTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAATATAATATCACTTTAAA
Found at i:5701788 original size:94 final size:94
Alignment explanation
Indices: 5701627--5701813 Score: 356
Period size: 94 Copynumber: 2.0 Consensus size: 94
5701617 CAGCTAAATT
5701627 TGGTTTGGTACTGGGAGGACAGAGGAGAAATCTTAGTAAGCCAAGTTCTGGAGTATTAGCAAGAG
1 TGGTTTGGTACTGGGAGGACAGAGGAGAAATCTTAGTAAGCCAAGTTCTGGAGTATTAGCAAGAG
5701692 CTTATGTGATGAAAGCTAAGAGGGATGTC
66 CTTATGTGATGAAAGCTAAGAGGGATGTC
*
5701721 TGGTTTGGTACTGGGAGGACAGATGAGAAATCTTAGTAAGCCAAGTTCTGGAGTATTAGCAAGAG
1 TGGTTTGGTACTGGGAGGACAGAGGAGAAATCTTAGTAAGCCAAGTTCTGGAGTATTAGCAAGAG
*
5701786 CTTATGTGGTGAAAGCTAAGAGGGATGT
66 CTTATGTGATGAAAGCTAAGAGGGATGT
5701814 TGATCTACCT
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 91 1.00
ACGTcount: A:0.30, C:0.10, G:0.33, T:0.26
Consensus pattern (94 bp):
TGGTTTGGTACTGGGAGGACAGAGGAGAAATCTTAGTAAGCCAAGTTCTGGAGTATTAGCAAGAG
CTTATGTGATGAAAGCTAAGAGGGATGTC
Found at i:5717073 original size:43 final size:43
Alignment explanation
Indices: 5717026--5717107 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
5717016 TCTTACATGT
*
5717026 AATCACGTAACGGTGCCGCTGTCCCACACAGGGTCTTACTCGA
1 AATCACATAACGGTGCCGCTGTCCCACACAGGGTCTTACTCGA
** * *
5717069 AATCACATCTCGTTGCCTCTGTCCCACACAGGGTCTTAC
1 AATCACATAACGGTGCCGCTGTCCCACACAGGGTCTTAC
5717108 ACAAGAACAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.22, C:0.34, G:0.20, T:0.24
Consensus pattern (43 bp):
AATCACATAACGGTGCCGCTGTCCCACACAGGGTCTTACTCGA
Found at i:5723299 original size:17 final size:17
Alignment explanation
Indices: 5723279--5723320 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
5723269 TGGACTGTTA
* *
5723279 TTTTATTTGGTTTTTAT
1 TTTTATTTGGATTTGAT
*
5723296 TTTTATTTTGATTTGAT
1 TTTTATTTGGATTTGAT
5723313 TTTTATTT
1 TTTTATTT
5723321 ATTATTGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.10, T:0.76
Consensus pattern (17 bp):
TTTTATTTGGATTTGAT
Found at i:5724829 original size:13 final size:13
Alignment explanation
Indices: 5724811--5724835 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5724801 TCTTATTTTC
5724811 TTTCTCATCACTA
1 TTTCTCATCACTA
5724824 TTTCTCATCACT
1 TTTCTCATCACT
5724836 TTCTCTTATT
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:0.20, C:0.32, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTCTCATCACTA
Found at i:5725289 original size:11 final size:13
Alignment explanation
Indices: 5725269--5725300 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
5725259 AATAAATTAA
5725269 TAAAATATCAT-T
1 TAAAATATCATAT
5725281 TAAAA-ATCATAT
1 TAAAATATCATAT
5725293 TAAAATAT
1 TAAAATAT
5725301 TAATAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATCATAT
Found at i:5732164 original size:14 final size:16
Alignment explanation
Indices: 5732130--5732166 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
5732120 TTTATAATAT
*
5732130 AAATTCAATGATTATA
1 AAATTTAATGATTATA
5732146 AAATTTAAT-ATTA-A
1 AAATTTAATGATTATA
5732160 AAATTTA
1 AAATTTA
5732167 GTACCTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 8 0.40
15 4 0.20
16 8 0.40
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (16 bp):
AAATTTAATGATTATA
Found at i:5749191 original size:4 final size:4
Alignment explanation
Indices: 5749182--5749227 Score: 92
Period size: 4 Copynumber: 11.5 Consensus size: 4
5749172 TATCTAAACA
5749182 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
5749228 TTGTTTGTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:5749351 original size:4 final size:4
Alignment explanation
Indices: 5749342--5749411 Score: 140
Period size: 4 Copynumber: 17.5 Consensus size: 4
5749332 TATCTAAACA
5749342 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5749390 ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT AT
5749412 TTATTGTTTG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 66 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:5749493 original size:23 final size:23
Alignment explanation
Indices: 5749448--5749493 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
5749438 TTATTAACAT
* *
5749448 TGTTCGTGAACATGTTTGTTTAA
1 TGTTCGTGAACATGTTCGATTAA
5749471 TGTTCGTGAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
5749494 GTTAAATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.11, G:0.22, T:0.43
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:5751379 original size:125 final size:124
Alignment explanation
Indices: 5751157--5751408 Score: 450
Period size: 125 Copynumber: 2.0 Consensus size: 124
5751147 CATAAAGTGA
* *
5751157 ATTTGCGATTCCTTGTTTCCCACTTAAACTATAAACAGTTGAGTTACCATTTAATTCAAGACAAT
1 ATTTGCGATTCCTGGTTTCCCACTTAAACTATAAACAGTTGAGTTACCAGTTAATTCAAGACAAT
5751222 AATATCAATGTTTTATTGGTGAAGGTGTCACCCCTCTCCACCCCCATTTTATTATTAATT
66 AATATCAATGTTTTATTGGTGAAGGTGTCACCCCTC-CCACCCCCATTTTATTATTAATT
5751282 ATTTGCGATTCCTGGTTTCCCACTTAAACTATAAACAGTTGAGTTACCAGTTAATTCAAGACAAT
1 ATTTGCGATTCCTGGTTTCCCACTTAAACTATAAACAGTTGAGTTACCAGTTAATTCAAGACAAT
* **
5751347 AATATCAATGTTTTATTGGTGAAGGTGTCACCCTTCCCACCCCTGTTTTATTATTAATT
66 AATATCAATGTTTTATTGGTGAAGGTGTCACCCCTCCCACCCCCATTTTATTATTAATT
5751406 ATT
1 ATT
5751409 ATTATATTTT
Statistics
Matches: 122, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
124 24 0.20
125 98 0.80
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (124 bp):
ATTTGCGATTCCTGGTTTCCCACTTAAACTATAAACAGTTGAGTTACCAGTTAATTCAAGACAAT
AATATCAATGTTTTATTGGTGAAGGTGTCACCCCTCCCACCCCCATTTTATTATTAATT
Found at i:5756199 original size:14 final size:14
Alignment explanation
Indices: 5756175--5756208 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5756165 TTAAAAAATG
*
5756175 TATTATTTATAAAA
1 TATTATATATAAAA
*
5756189 TTTTATATATAAAA
1 TATTATATATAAAA
5756203 TATTAT
1 TATTAT
5756209 TGTATAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTATATATAAAA
Found at i:5762040 original size:35 final size:35
Alignment explanation
Indices: 5762001--5762071 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
5761991 GTACCACCAT
5762001 CGAGCCCTTTACTGATAACTGAACTAGTTCTTTGG
1 CGAGCCCTTTACTGATAACTGAACTAGTTCTTTGG
5762036 CGAGCCCTTTACTGATAACTGAACTAGTTCTTTGG
1 CGAGCCCTTTACTGATAACTGAACTAGTTCTTTGG
5762071 C
1 C
5762072 AAGAAGAGAG
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:0.23, C:0.24, G:0.20, T:0.34
Consensus pattern (35 bp):
CGAGCCCTTTACTGATAACTGAACTAGTTCTTTGG
Found at i:5767798 original size:49 final size:49
Alignment explanation
Indices: 5767707--5767803 Score: 124
Period size: 49 Copynumber: 2.0 Consensus size: 49
5767697 ATCTATTTAT
* * * * *
5767707 AGGTTGAAAAACCTTATTCTAGTCAATATCAAATAGATGAAGTGTAGTA
1 AGGTTGAAAAACCTTATTCTAATCAATAGCAAATAAAAGAAGTATAGTA
*
5767756 AGGTTGAAAAACCTTATTCTAATTAAT-GCAAAATAAAAGAAGTATAGT
1 AGGTTGAAAAACCTTATTCTAATCAATAGC-AAATAAAAGAAGTATAGT
5767804 TCTATATGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
48 1 0.02
49 40 0.98
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.30
Consensus pattern (49 bp):
AGGTTGAAAAACCTTATTCTAATCAATAGCAAATAAAAGAAGTATAGTA
Found at i:5769796 original size:6 final size:6
Alignment explanation
Indices: 5769785--5769809 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5769775 TGGTAATGTG
5769785 AACACC AACACC AACACC AACACC A
1 AACACC AACACC AACACC AACACC A
5769810 TGCACATGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (6 bp):
AACACC
Found at i:5770105 original size:29 final size:28
Alignment explanation
Indices: 5770002--5770100 Score: 155
Period size: 28 Copynumber: 3.5 Consensus size: 28
5769992 AAAAATAAAA
* *
5770002 ATTTACTAAAATATTACAATTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
5770030 ATTTACCAAAATATTACAACTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
5770058 ATTTACCAAAATATTTA-AACTTTTTTATT
1 ATTTACCAAAATA-TTACAACTTTTTT-TT
5770087 ATTTACCAAAATAT
1 ATTTACCAAAATAT
5770101 ATAAAAAAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
28 49 0.73
29 18 0.27
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (28 bp):
ATTTACCAAAATATTACAACTTTTTTTT
Found at i:5770202 original size:27 final size:27
Alignment explanation
Indices: 5770172--5770243 Score: 126
Period size: 27 Copynumber: 2.7 Consensus size: 27
5770162 CCCCAATGGT
5770172 ATTGGCGGCACCAATGGTGCCAATACC
1 ATTGGCGGCACCAATGGTGCCAATACC
*
5770199 ATTGGCGGCACCAATTGTGCCAATACC
1 ATTGGCGGCACCAATGGTGCCAATACC
*
5770226 ATTGGCGGCACCACTGGT
1 ATTGGCGGCACCAATGGT
5770244 ATTATTTATA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.24, C:0.29, G:0.26, T:0.21
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAATACC
Found at i:5770317 original size:29 final size:29
Alignment explanation
Indices: 5770270--5770325 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
5770260 CTACCCAGCT
* *
5770270 GAAGAGAGAAAAATAAAAAAAAGAAAGCA
1 GAAGACAGAAAAATAAAAAAAAAAAAGCA
* *
5770299 GAAGACAGAAAATTCAAAAAAAAAAAG
1 GAAGACAGAAAAATAAAAAAAAAAAAG
5770326 AAGAGTTGGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.71, C:0.05, G:0.18, T:0.05
Consensus pattern (29 bp):
GAAGACAGAAAAATAAAAAAAAAAAAGCA
Found at i:5770406 original size:21 final size:20
Alignment explanation
Indices: 5770382--5770432 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 20
5770372 AATCATTGAT
5770382 TATATTATTGT-TATTATTTTG
1 TATATT-TTGTATATT-TTTTG
5770403 TATATTTTGTAATATTTTTTG
1 TATATTTTGT-ATATTTTTTG
5770424 TAATATTTT
1 T-ATATTTT
5770433 TTGTTGTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 4 0.15
21 12 0.44
22 11 0.41
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (20 bp):
TATATTTTGTATATTTTTTG
Found at i:5770420 original size:19 final size:21
Alignment explanation
Indices: 5770382--5770420 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
5770372 AATCATTGAT
*
5770382 TATATTATTGTTATTATTTTG
1 TATATTATTGTTAATATTTTG
5770403 TATATT-TTG-TAATATTTT
1 TATATTATTGTTAATATTTT
5770421 TTGTAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.67
Consensus pattern (21 bp):
TATATTATTGTTAATATTTTG
Found at i:5770504 original size:3 final size:3
Alignment explanation
Indices: 5770498--5770526 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5770488 ATTATTATTA
5770498 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
5770527 AGTATGAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:5770742 original size:14 final size:13
Alignment explanation
Indices: 5770705--5770768 Score: 53
Period size: 12 Copynumber: 5.1 Consensus size: 13
5770695 ATAATTTTAG
5770705 TGTGTATTA-TTT
1 TGTGTATTATTTT
* *
5770717 TGAGTATAATTTAT
1 TGTGTATTATTT-T
5770731 TGTGTATTA-TTT
1 TGTGTATTATTTT
*
5770743 TGTGTAATA-TTT
1 TGTGTATTATTTT
* *
5770755 TGAGTATAATTTT
1 TGTGTATTATTTT
5770768 T
1 T
5770769 TTTTAAGTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
12 25 0.61
13 8 0.20
14 8 0.20
ACGTcount: A:0.25, C:0.00, G:0.16, T:0.59
Consensus pattern (13 bp):
TGTGTATTATTTT
Found at i:5770754 original size:26 final size:26
Alignment explanation
Indices: 5770696--5770754 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
5770686 GTAAAATTAA
5770696 TAAT-TTTAGTGTGTATTATTTTGAG
1 TAATATTTAGTGTGTATTATTTTGAG
* *
5770721 T-ATAATTTATTGTGTATTATTTTGTG
1 TAAT-ATTTAGTGTGTATTATTTTGAG
5770747 TAATATTT
1 TAATATTT
5770755 TGAGTATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
24 2 0.07
25 1 0.03
26 24 0.83
27 2 0.07
ACGTcount: A:0.25, C:0.00, G:0.15, T:0.59
Consensus pattern (26 bp):
TAATATTTAGTGTGTATTATTTTGAG
Found at i:5771357 original size:18 final size:18
Alignment explanation
Indices: 5771314--5771358 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
5771304 TTGACATGGT
* *
5771314 TGGTGGTGAAGAAGAATG
1 TGGTGGCGAAGAAGAAGG
**
5771332 TGCCGGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
5771350 TGGTGGCGA
1 TGGTGGCGA
5771359 TCATTGGGAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.29, C:0.09, G:0.47, T:0.16
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:5775828 original size:18 final size:18
Alignment explanation
Indices: 5775807--5775869 Score: 74
Period size: 18 Copynumber: 3.4 Consensus size: 18
5775797 AATATATTTC
5775807 ATAAAATATATATGCTAA
1 ATAAAATATATATGCTAA
***
5775825 ATAAAATA-ATAAAATAA
1 ATAAAATATATATGCTAA
5775842 CTATAAAATATATATGCTAA
1 --ATAAAATATATATGCTAA
5775862 ATAAAATA
1 ATAAAATA
5775870 ATAAAATAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
17 6 0.17
18 16 0.44
19 8 0.22
20 6 0.17
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (18 bp):
ATAAAATATATATGCTAA
Found at i:5775849 original size:37 final size:37
Alignment explanation
Indices: 5775807--5775884 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
5775797 AATATATTTC
5775807 ATAAAATATATATGCTAAATAAAATAATAAAATAACT
1 ATAAAATATATATGCTAAATAAAATAATAAAATAACT
5775844 ATAAAATATATATGCTAAATAAAATAATAAAATAACT
1 ATAAAATATATATGCTAAATAAAATAATAAAATAACT
5775881 ATAA
1 ATAA
5775885 TATACATTAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (37 bp):
ATAAAATATATATGCTAAATAAAATAATAAAATAACT
Found at i:5775900 original size:37 final size:37
Alignment explanation
Indices: 5775807--5775900 Score: 127
Period size: 37 Copynumber: 2.5 Consensus size: 37
5775797 AATATATTTC
* *
5775807 ATAAAATATATATGCTAAATAAAATAATAAAATAACT
1 ATAAAATACATATACTAAATAAAATAATAAAATAACT
* *
5775844 ATAAAATATATATGCTAAATAAAATAATAAAATAACT
1 ATAAAATACATATACTAAATAAAATAATAAAATAACT
*
5775881 ATAATATACAT-TACATAAAT
1 ATAAAATACATATAC-TAAAT
5775901 TTTAAACACA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
36 2 0.04
37 51 0.96
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (37 bp):
ATAAAATACATATACTAAATAAAATAATAAAATAACT
Found at i:5776027 original size:37 final size:38
Alignment explanation
Indices: 5775986--5776159 Score: 151
Period size: 39 Copynumber: 4.6 Consensus size: 38
5775976 CTTCCCTCTT
*
5775986 CTTCTTT-TTTTTTTCTCTTCTCCTTTCCCTTTCTTTC
1 CTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
*
5776023 CTTCTTTCTTTCTTTTTTCTTCT-CTTCTCCTTTTCTTCTTC
1 CTTCTTTCTTT-TTTTCTCTTCTCCTT-TCCTTTTC-T-TTC
* *
5776064 TTTCTTTCCTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
* * * * * * *
5776102 TTTCCTCTCCTTTCTT-TCTT-T-CTTCCCTCTCCTTTC
1 CTT-CTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
* *
5776138 TTTCTTTCCTTTTTTCTCTTCT
1 CTTCTTTCTTTTTTTCTCTTCT
5776160 GCCCCACCAC
Statistics
Matches: 116, Mismatches: 12, Indels: 18
0.79 0.08 0.12
Matches are distributed among these distances:
35 10 0.09
36 19 0.16
37 9 0.08
38 16 0.14
39 28 0.24
40 19 0.16
41 15 0.13
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (38 bp):
CTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
Found at i:5776029 original size:18 final size:17
Alignment explanation
Indices: 5776008--5776159 Score: 76
Period size: 18 Copynumber: 9.1 Consensus size: 17
5775998 TTCTCTTCTC
5776008 CTTTCCCTTTCTTTCCTT
1 CTTT-CCTTTCTTTCCTT
*
5776026 CTTT-CTTTCTTT-TTT
1 CTTTCCTTTCTTTCCTT
*
5776041 C-TTCTCTTCTCCTTTTCTT
1 CTTTC-CTT-T-CTTTCCTT
5776060 C-TT-CTTTCTTTCCTT
1 CTTTCCTTTCTTTCCTT
*
5776075 TTTTCTCTTCTCCTTTCC-T
1 CTTTC-CTT-T-CTTTCCTT
5776094 -TTT-CTTTCTTTCC-T
1 CTTTCCTTTCTTTCCTT
*
5776108 C--TCCTTTCTTTCTTT
1 CTTTCCTTTCTTTCCTT
* * *
5776123 CTTCCCTCTCCTTTCTTT
1 CTTTCCT-TTCTTTCCTT
5776141 CTTTCCTTT-TTTCTCTT
1 CTTTCCTTTCTTTC-CTT
5776158 CT
1 CT
5776160 GCCCCACCAC
Statistics
Matches: 107, Mismatches: 10, Indels: 35
0.70 0.07 0.23
Matches are distributed among these distances:
13 1 0.01
14 18 0.17
15 13 0.12
16 21 0.20
17 12 0.11
18 29 0.27
19 7 0.07
20 6 0.06
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (17 bp):
CTTTCCTTTCTTTCCTT
Found at i:5776061 original size:34 final size:35
Alignment explanation
Indices: 5776018--5776159 Score: 114
Period size: 35 Copynumber: 4.0 Consensus size: 35
5776008 CTTTCCCTTT
*
5776018 CTTTCCTTCTTTCTTTCTTT-TTTCTTCTCTTCTC
1 CTTTTCTTCTTTCTTTCTTTCTTTCTTCTCTTCTC
*
5776052 CTTTTCTTC-TTCTTTCTTTCCTTTTTTCTCTTCTC
1 CTTTTCTTCTTTCTTTCTTT-CTTTCTTCTCTTCTC
* *
5776087 CTTTCCTTTTCTTTCTTTCCTCTCCTTTCTT-TCTT-T-
1 CTTT--TCTTCTTTCTTT-CT-TTCTTTCTTCTCTTCTC
* * *
5776123 CTTCCCTCTCCTTTCTTTCTTTCCTTTTTTCTCTTCT
1 CTT--TTCTTCTTTCTTTCTTT-CTTTCTTCTCTTCT
5776160 GCCCCACCAC
Statistics
Matches: 86, Mismatches: 10, Indels: 21
0.74 0.09 0.18
Matches are distributed among these distances:
33 10 0.12
34 9 0.10
35 25 0.29
36 17 0.20
37 6 0.07
38 10 0.12
39 8 0.09
40 1 0.01
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (35 bp):
CTTTTCTTCTTTCTTTCTTTCTTTCTTCTCTTCTC
Found at i:5776081 original size:74 final size:76
Alignment explanation
Indices: 5775972--5776159 Score: 186
Period size: 74 Copynumber: 2.6 Consensus size: 76
5775962 TTTTTTTTTC
*
5775972 CTTTCTTCCCTCTTCTTCTT-TTT-TTT--TTCTCTTCTCCTT-TCCCTTT-C-TTTCCTTCTTT
1 CTTTCTTCCCTC-TCTTCTTCTTTCTTTCCTT-TTTTCTCCTTCT-CCTTTCCTTTTCCTTCTTT
*
5776030 -CT-TTCTTT-TTT
63 CCTCTCCTTTCTTT
* *
5776041 CTTCTCTTCTCCTTTTCTTCTTCTTTCTTTCCTTTTTTCT-CTTCTCCTTTCCTTTTCTTTCTTT
1 CTT-TCTTC-CC-TCTCTTCTTCTTTCTTTCCTTTTTTCTCCTTCTCCTTTCCTTTTCCTTCTTT
5776105 CCTCTCCTTTCTTT
63 CCTCTCCTTTCTTT
*
5776119 CTTTCTTCCCTCTCCT-TTCTTTCTTTCCTTTTTTCT-CTTCT
1 CTTTCTTCCCTCTCTTCTTCTTTCTTTCCTTTTTTCTCCTTCT
5776160 GCCCCACCAC
Statistics
Matches: 100, Mismatches: 6, Indels: 21
0.79 0.05 0.17
Matches are distributed among these distances:
69 3 0.03
70 5 0.05
71 9 0.09
72 4 0.04
73 11 0.11
74 32 0.32
75 16 0.16
76 4 0.04
77 10 0.10
78 6 0.06
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (76 bp):
CTTTCTTCCCTCTCTTCTTCTTTCTTTCCTTTTTTCTCCTTCTCCTTTCCTTTTCCTTCTTTCCT
CTCCTTTCTTT
Found at i:5776096 original size:19 final size:19
Alignment explanation
Indices: 5775981--5776114 Score: 82
Period size: 19 Copynumber: 6.9 Consensus size: 19
5775971 CCTTTCTTCC
* **
5775981 CTCTTCTTCTTTTTTTTTT
1 CTCTTCTCCTTTCCTTTTT
5776000 CTCTTCTCCTTTCCCTTTCTT
1 CTCTTCTCCTTT-CCTTT-TT
*
5776021 -TCCTTCTTTCTTT-CTTTTT
1 CT-CTTC-TCCTTTCCTTTTT
5776040 -TCTTCT-CTTCTCC-TTTT
1 CTCTTCTCCTT-TCCTTTTT
*
5776057 CTTCTTCTTTCTTTCCTTTTTT
1 C-TCTTC-TCCTTTCC-TTTTT
5776079 CTCTTCTCCTTTCCTTTTCT
1 CTCTTCTCCTTTCCTTTT-T
* *
5776099 TTCTT-TCCTCTCCTTT
1 CTCTTCTCCTTTCCTTT
5776115 CTTTCTTTCT
Statistics
Matches: 95, Mismatches: 7, Indels: 26
0.74 0.05 0.20
Matches are distributed among these distances:
16 3 0.03
17 6 0.06
18 5 0.05
19 33 0.35
20 24 0.25
21 14 0.15
22 10 0.11
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (19 bp):
CTCTTCTCCTTTCCTTTTT
Found at i:5776119 original size:22 final size:22
Alignment explanation
Indices: 5776014--5776145 Score: 83
Period size: 22 Copynumber: 6.4 Consensus size: 22
5776004 TCTCCTTTCC
* *
5776014 CTTTCTTTCCTT-CT-TTCTTT
1 CTTTCTTTCTTTCCTCTCCTTT
*
5776034 CTTT-TTTCTTCTCTTCTCCTTT
1 CTTTCTTTCTT-TCCTCTCCTTT
*
5776056 -TCTTC-TTCTTT-CTTTCCTTT
1 CT-TTCTTTCTTTCCTCTCCTTT
*
5776076 -TTTCTCTTC--TCCTTTCCTTTT
1 CTTTCT-TTCTTTCCTCTCC-TTT
5776097 CTTTC----TTTCCTCTCCTTT
1 CTTTCTTTCTTTCCTCTCCTTT
*
5776115 CTTTCTTTCTTCCCTCTCCTTT
1 CTTTCTTTCTTTCCTCTCCTTT
5776137 CTTTCTTTC
1 CTTTCTTTC
5776146 CTTTTTTCTC
Statistics
Matches: 89, Mismatches: 7, Indels: 30
0.71 0.06 0.24
Matches are distributed among these distances:
18 8 0.09
19 16 0.18
20 19 0.21
21 9 0.10
22 37 0.42
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (22 bp):
CTTTCTTTCTTTCCTCTCCTTT
Found at i:5776333 original size:28 final size:28
Alignment explanation
Indices: 5776274--5776372 Score: 155
Period size: 28 Copynumber: 3.5 Consensus size: 28
5776264 TTTTTTTGAT
*
5776274 ATATTTTGGTAAATAATAAAAAA-TTTTAA
1 ATATTTTGGTAAATAA-AAAAAAGTTGT-A
5776303 ATATTTTGGTAAATAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
5776331 ATATTTTGGTAAATAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
*
5776359 ATATTTTGATAAAT
1 ATATTTTGGTAAAT
5776373 TTTTATTTTT
Statistics
Matches: 67, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
28 48 0.72
29 19 0.28
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.39
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTGTA
Found at i:5780370 original size:25 final size:25
Alignment explanation
Indices: 5780324--5780372 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
5780314 CTGTCTTTGA
** *
5780324 TAGTATATCCTGAAACTGCTATAGG
1 TAGTATATAATGAAACTACTATAGG
*
5780349 TAGTATATAATGAGACTACTATAG
1 TAGTATATAATGAAACTACTATAG
5780373 ATAGACTATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (25 bp):
TAGTATATAATGAAACTACTATAGG
Found at i:5792061 original size:21 final size:21
Alignment explanation
Indices: 5792022--5792061 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5792012 GGCCATGTAG
*
5792022 AAAACATAAATTTAAAAATGA
1 AAAACATAAATATAAAAATGA
* *
5792043 AAAATATAAATATATAAAT
1 AAAACATAAATATAAAAAT
5792062 TGTTTGTCAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (21 bp):
AAAACATAAATATAAAAATGA
Found at i:5796756 original size:40 final size:40
Alignment explanation
Indices: 5796701--5796780 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
5796691 GGGATCTAAA
5796701 TAGATGTAAAGAATCATAATTAGTACCAAGTTTTCTAGAC
1 TAGATGTAAAGAATCATAATTAGTACCAAGTTTTCTAGAC
5796741 TAGATGTAAAGAATCATAATTAGTACCAAGTTTTCTAGAC
1 TAGATGTAAAGAATCATAATTAGTACCAAGTTTTCTAGAC
5796781 CATACCTCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (40 bp):
TAGATGTAAAGAATCATAATTAGTACCAAGTTTTCTAGAC
Found at i:5799050 original size:13 final size:13
Alignment explanation
Indices: 5799032--5799057 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5799022 TTGAATTATC
5799032 ATCATAATACATA
1 ATCATAATACATA
5799045 ATCATAATACATA
1 ATCATAATACATA
5799058 TGAGAGGAAG
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:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
ATCATAATACATA
Found at i:5800303 original size:17 final size:17
Alignment explanation
Indices: 5800281--5800319 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
5800271 ATCATTTGGA
5800281 CCACACAGGCATGTGGG
1 CCACACAGGCATGTGGG
* *
5800298 CCACACGGGCGTGTGGG
1 CCACACAGGCATGTGGG
*
5800315 TCACA
1 CCACA
5800320 TTGGCTGGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.21, C:0.31, G:0.36, T:0.13
Consensus pattern (17 bp):
CCACACAGGCATGTGGG
Found at i:5806683 original size:31 final size:31
Alignment explanation
Indices: 5806608--5806675 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
5806598 TTACAAAATG
* **
5806608 GTCATTGAACTATTTGAAAGTTTTCATTGAA
1 GTCACTGAACTATTCAAAAGTTTTCATTGAA
* *
5806639 GTCACTGAACTATTCAAAAGTTTTTATTTAA
1 GTCACTGAACTATTCAAAAGTTTTCATTGAA
5806670 GTCACT
1 GTCACT
5806676 AGGCTATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.41
Consensus pattern (31 bp):
GTCACTGAACTATTCAAAAGTTTTCATTGAA
Found at i:5819527 original size:9 final size:9
Alignment explanation
Indices: 5819509--5819543 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
5819499 TCTACTCTTC
5819509 TAAA-TTTT
1 TAAATTTTT
5819517 TAAATTTTT
1 TAAATTTTT
5819526 TAAATTTTT
1 TAAATTTTT
5819535 TAAATTTTT
1 TAAATTTTT
5819544 GCTGTAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.15
9 22 0.85
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TAAATTTTT
Found at i:5822894 original size:29 final size:28
Alignment explanation
Indices: 5822862--5822948 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
5822852 TCATAAGAAC
5822862 ATTTTATGAAATTATATTTAATAATAATT
1 ATTTTAT-AAATTATATTTAATAATAATT
* * *
5822891 A-TTT-TAAATTGTATTAAATCAT-A-T
1 ATTTTATAAATTATATTTAATAATAATT
* *
5822915 ATTTTAATTAAAATATATTTAATATTAATT
1 ATTTT-A-TAAATTATATTTAATAATAATT
5822945 ATTT
1 ATTT
5822949 CAAATTTTCA
Statistics
Matches: 44, Mismatches: 8, Indels: 11
0.70 0.13 0.17
Matches are distributed among these distances:
24 2 0.05
25 4 0.09
26 14 0.32
27 1 0.02
28 16 0.36
29 2 0.05
30 5 0.11
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (28 bp):
ATTTTATAAATTATATTTAATAATAATT
Found at i:5823159 original size:137 final size:137
Alignment explanation
Indices: 5823005--5823269 Score: 433
Period size: 137 Copynumber: 1.9 Consensus size: 137
5822995 TAAGAATATG
* *
5823005 AATTATTAAGAATTTTATTAAATTATATACCAAAATTATAATGTATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATACCAAAATTAAAATATATTTAATAATAATTATGTTTA
* *
5823070 AATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAAA
66 AATATGATTAAA-TATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAAA
5823135 TTTCTGCT
130 TTTCTGCT
****
5823143 AATTA-TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATACCAAAATTAAAATATATTTAATAATAATTATGTTTA
*
5823207 AATATGATTAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACATTAACAA
66 AATATGATTAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
5823270 TAATCATTTA
Statistics
Matches: 118, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
136 48 0.41
137 65 0.55
138 5 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (137 bp):
AATTATTAAGAATTTTATTAAATTATATACCAAAATTAAAATATATTTAATAATAATTATGTTTA
AATATGATTAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAAAT
TTCTGCT
Found at i:5823181 original size:18 final size:17
Alignment explanation
Indices: 5823153--5823187 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5823143 AATTATAAGA
*
5823153 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
5823170 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
5823188 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:5823297 original size:155 final size:156
Alignment explanation
Indices: 5823129--5823455 Score: 611
Period size: 155 Copynumber: 2.1 Consensus size: 156
5823119 AAATAACAAT
*
5823129 AACAAATTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATA
1 AACAATTTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATA
5823194 ATAATTATGTTTAAATATGATT-AAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAA
66 ATAATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAA
*
5823258 TAACATTAACAATAATCATTTACCAA
131 TAACAATAACAATAATCATTTACCAA
*
5823284 AACAATTTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATT
1 AACAATTTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATA
5823349 ATAATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAA
66 ATAATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAA
5823414 TAACAATAACAATAATCATTTACCAA
131 TAACAATAACAATAATCATTTACCAA
*
5823440 AACAATTTTATGCTAA
1 AACAATTTTCTGCTAA
5823456 GGGTATTCTA
Statistics
Matches: 167, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
155 85 0.51
156 82 0.49
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (156 bp):
AACAATTTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATA
ATAATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAA
TAACAATAACAATAATCATTTACCAA
Found at i:5823336 original size:18 final size:18
Alignment explanation
Indices: 5823308--5823356 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 18
5823298 AATTATAAGA
5823308 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAATTATAT
5823325 ATTTTAATTAAA--ATAT
1 ATTTTAATTAAATTATAT
5823341 A-TTTAATTATAATTAT
1 ATTTTAATTA-AATTAT
5823357 GTTTAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 8 0.29
16 7 0.25
17 5 0.18
18 8 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTTAATTAAATTATAT
Found at i:5823342 original size:16 final size:16
Alignment explanation
Indices: 5823308--5823362 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
5823298 AATTATAAGA
5823308 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
5823325 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
*
5823341 A-TTTAATTATAAT-T
1 ATTTTAATTAAAATAT
5823355 ATGTTTAA
1 AT-TTTAA
5823363 ATATGATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 2 0.06
15 11 0.32
16 10 0.29
17 5 0.15
18 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:5823572 original size:44 final size:45
Alignment explanation
Indices: 5823507--5823597 Score: 123
Period size: 45 Copynumber: 2.0 Consensus size: 45
5823497 ACCTCTATTC
* * *
5823507 CATTCAACCAAACATAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACATAAGATTAGCTATTACACCTCTAATCCAATA
*
5823551 CATTCAACCAAACAGT-GGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACA-TAAGATTAGCTATTACACCTCTAATCCAATA
5823596 CA
1 CA
5823598 CCTCTAATCC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
44 19 0.46
45 22 0.54
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.29
Consensus pattern (45 bp):
CATTCAACCAAACATAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:5823599 original size:16 final size:16
Alignment explanation
Indices: 5823578--5823646 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
5823568 GATTAGCTAT
5823578 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
5823594 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
5823611 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
5823627 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
5823643 TACA
1 TACA
5823647 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:5823620 original size:33 final size:32
Alignment explanation
Indices: 5823578--5823646 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
5823568 GATTAGCTAT
5823578 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
5823611 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
5823643 TACA
1 TACA
5823647 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.22
33 28 0.78
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:5827743 original size:21 final size:21
Alignment explanation
Indices: 5827717--5827757 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5827707 AGACGAGCAA
* *
5827717 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
5827738 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
5827758 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:5835722 original size:30 final size:30
Alignment explanation
Indices: 5835626--5835708 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
5835616 GACGGTCATC
* *
5835626 ACCATCCCTTTTCATAATTTGATAGCCAAA
1 ACCATCCCTTTTCATAGTTCGATAGCCAAA
* *
5835656 GCTATCCCTTTTCATAGTTCGATAGCCAAA
1 ACCATCCCTTTTCATAGTTCGATAGCCAAA
5835686 ACCATCCCTTTTCATAGTTCGAT
1 ACCATCCCTTTTCATAGTTCGAT
5835709 GATCGTCACC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.35
Consensus pattern (30 bp):
ACCATCCCTTTTCATAGTTCGATAGCCAAA
Found at i:5835725 original size:89 final size:89
Alignment explanation
Indices: 5835538--5835757 Score: 271
Period size: 89 Copynumber: 2.5 Consensus size: 89
5835528 GATGATTGAC
* * * ** *
5835538 CCATCCCTTTTCGTAATTCGATAACCGAAGTTATCCCTTTTTGTAGTTCGACAGCCAAACTATCC
1 CCATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAGTTCGACAGCCAAACCATCC
* * * *
5835603 GTTTTCATTGTTTGACGGTCATCA
66 CTTTTCATAGTTCGACGATCATCA
* * *
5835627 CCATCCCTTTTCATAATTTGATAGCCAAAGCTATCCCTTTTCATAGTTCGATAGCCAAAACCATC
1 CCATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAGTTCGACAGCC-AAACCATC
* *
5835692 CCTTTTCATAGTTCGATGATCGTCA
65 CCTTTTCATAGTTCGACGATCATCA
* *
5835717 CCATCCTTTTTCATAA-TCGATAGTCGAAGCTATCCCTTTTC
1 CCATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTC
5835758 GATTTGTCAA
Statistics
Matches: 111, Mismatches: 19, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
89 70 0.63
90 41 0.37
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.36
Consensus pattern (89 bp):
CCATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAGTTCGACAGCCAAACCATCC
CTTTTCATAGTTCGACGATCATCA
Found at i:5836577 original size:16 final size:15
Alignment explanation
Indices: 5836551--5836580 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5836541 TATCTTATTT
5836551 TAATTACTTAATTAC
1 TAATTACTTAATTAC
5836566 TAATTCACTTAATTA
1 TAATT-ACTTAATTA
5836581 ACCTTGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATTACTTAATTAC
Found at i:5844160 original size:17 final size:18
Alignment explanation
Indices: 5844138--5844177 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
5844128 TTTATCTAAG
* *
5844138 TTTTATAA-TATTAATTT
1 TTTTATAATTATAAATGT
5844155 TTTTATAATTATAAATGT
1 TTTTATAATTATAAATGT
5844173 TTTTA
1 TTTTA
5844178 GAGTTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTTATAATTATAAATGT
Found at i:5850673 original size:2 final size:2
Alignment explanation
Indices: 5850666--5850698 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5850656 TCTGAAGGAA
*
5850666 AT AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5850699 AAGAGCGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5853023 original size:21 final size:20
Alignment explanation
Indices: 5852986--5853024 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
5852976 TTTTAAAATT
* *
5852986 TAAAAATTAATAGAAAATCA
1 TAAAAATTAAAAAAAAATCA
5853006 TAAAAATTTAAAAAAAAAT
1 TAAAAA-TTAAAAAAAAAT
5853025 TATATTTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (20 bp):
TAAAAATTAAAAAAAAATCA
Found at i:5853180 original size:14 final size:14
Alignment explanation
Indices: 5853161--5853189 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5853151 TAATTTTAGA
5853161 TTTTTTATAAATTT
1 TTTTTTATAAATTT
5853175 TTTTTTATAAATTT
1 TTTTTTATAAATTT
5853189 T
1 T
5853190 ATGGTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTTATAAATTT
Found at i:5853198 original size:32 final size:32
Alignment explanation
Indices: 5853146--5853209 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
5853136 TTAACAAAAA
* *
5853146 TTTTATAATTTTAGATTTTTTATA-AATTTTT
1 TTTTATAATTTTAGAGTTTTTAAATAATTTTT
5853177 TTTTATAAATTTTATG-GTTTTTAAATAATTTTT
1 TTTTAT-AATTTTA-GAGTTTTTAAATAATTTTT
5853210 AAATTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 6 0.21
32 14 0.50
33 8 0.29
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (32 bp):
TTTTATAATTTTAGAGTTTTTAAATAATTTTT
Found at i:5854683 original size:21 final size:23
Alignment explanation
Indices: 5854659--5854700 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
5854649 ATATACATGA
5854659 TTATAT-TATCTATTT-TATAAT
1 TTATATGTATCTATTTATATAAT
*
5854680 TTATATGTATGTATTTATATA
1 TTATATGTATCTATTTATATA
5854701 CACATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 8 0.44
23 4 0.22
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (23 bp):
TTATATGTATCTATTTATATAAT
Found at i:5857828 original size:30 final size:30
Alignment explanation
Indices: 5857792--5857851 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
5857782 TATAATTTTC
5857792 ATATGTA-A-TTATTATTTTTAATCTATATAT
1 ATATGTATATTTATT-TTTTT-ATCTATATAT
*
5857822 ATATGTATATTTATTTTTTTATGTATATAT
1 ATATGTATATTTATTTTTTTATCTATATAT
5857852 TTATATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 16 0.59
31 6 0.22
32 5 0.19
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (30 bp):
ATATGTATATTTATTTTTTTATCTATATAT
Found at i:5864354 original size:44 final size:44
Alignment explanation
Indices: 5864304--5864475 Score: 229
Period size: 44 Copynumber: 3.9 Consensus size: 44
5864294 AAGCCAGTAA
* * *
5864304 TCCTATCTCCCTAGTCAGCAGTGAAATGGGTTGAAGATTTTGAG
1 TCCTATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTTTAAG
* * *
5864348 TCCTATCTCGACTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAG
1 TCCTATCTC-CCTAGTCAGCAGTGGAATAGGTTGAAGATTTTAAG
* *
5864393 TCCTATCTCCTTGGTCAGCAGTGGAATAGGTTGAA-ATTTGTAAG
1 TCCTATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTT-TAAG
* *
5864437 TCCTATCTCCCTAATTAGCAGTGGAATAGGTTGAAGATT
1 TCCTATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATT
5864476 GTGAACCTTA
Statistics
Matches: 112, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
43 3 0.03
44 68 0.61
45 41 0.37
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (44 bp):
TCCTATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTTTAAG
Found at i:5864766 original size:51 final size:51
Alignment explanation
Indices: 5864618--5864769 Score: 142
Period size: 51 Copynumber: 3.0 Consensus size: 51
5864608 AAATAGCTGA
* ** * * * * *
5864618 AGTGGAGCGGATTAAAATTGTGGGCAGCGAATCTTATCTCTTTGGCATTAT
1 AGTGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCATTAGCGTTAC
* * * * * * ** *
5864669 AGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCGTTGC
1 AGTGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCATTAGCGTTAC
*
5864720 AGTGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTAACTCATTAGCGTTA
1 AGTGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCATTAGCGTTA
5864770 AGATTGAAAA
Statistics
Matches: 75, Mismatches: 26, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
51 75 1.00
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (51 bp):
AGTGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCATTAGCGTTAC
Found at i:5865089 original size:51 final size:51
Alignment explanation
Indices: 5865009--5865105 Score: 131
Period size: 51 Copynumber: 1.9 Consensus size: 51
5864999 GCATTATAGT
* * * *
5865009 GGAACAGATTAAAGCTAAAGGTAGTGAATCTTGTTTCCCTAGTGTTGTAGC
1 GGAACAGATTAAAGCTAAAGGCAGCGAATCTTATCTCCCTAGTGTTGTAGC
* * *
5865060 GGAACAGATTAAAGCTGAGGGCAGCGAATCTTATCTCTCTAGTGTT
1 GGAACAGATTAAAGCTAAAGGCAGCGAATCTTATCTCCCTAGTGTT
5865106 AAGACTTGAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 39 1.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (51 bp):
GGAACAGATTAAAGCTAAAGGCAGCGAATCTTATCTCCCTAGTGTTGTAGC
Found at i:5865199 original size:169 final size:169
Alignment explanation
Indices: 5864540--5865268 Score: 1016
Period size: 169 Copynumber: 4.3 Consensus size: 169
5864530 ATCTTACTTT
* * * * ** *
5864540 CCTAACGTTACAGCGGAGCAGATTAAAGCTGAAGGTAGCGAATCTTATCTCCCGGGCGTTAAGTC
1 CCTAGCGTTGCAGCGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTAGCGTTAAGAC
* * * *
5864605 TTGAAATAGCTGAAGTGGAGCGGATTAAAATTGTGGGCAGCGAATCTTATCTCTTTGGCATTATA
66 TTGAAAAAGCTGAAGTGGAGCGGATTAAAACTGTGGGCAGCAAATCCTATCTCTTTGGCATTATA
5864670 GTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTC
131 GTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTC
* * **
5864709 CCTAGCGTTGCAGTGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTAACTCATTAGCGTTAAGA-
1 CCTAGCGTTGCAGCGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTAGCGTTAAGAC
* * * ** *
5864773 TTGAAAAAAAGTTGAAGTTGAGCGGATTAAAGCTGTGGGCAGTGAATCCTATCTCTTTGGTATTA
66 TTG--AAAAAGCTGAAGTGGAGCGGATTAAAACTGTGGGCAGCAAATCCTATCTCTTTGGCATTA
5864838 TAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTC
129 TAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTC
* * *
5864879 CCTAGCATTGCAGCAGAGCAGATTAAAGCTGAGGGCAGCG-ATCTTATCTCCCTGGCGTTAAGAC
1 CCTAGCGTTGCAGCGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTAGCGTTAAGAC
*
5864943 TTGAAAAAGCTG-AGTGGAGCGGATTAAAGCTGTGGGCAGCAAATCCTATCTCTTTGGCATTATA
66 TTGAAAAAGCTGAAGTGGAGCGGATTAAAACTGTGGGCAGCAAATCCTATCTCTTTGGCATTATA
*
5865007 GTGGAACAGATTAAAGCTAAAGGTAGTGAATCTTGTTTC
131 GTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTC
* * * * *
5865046 CCTAGTGTTGTAGCGGAACAGATTAAAGCTGAGGGCAGCGAATCTTATCTCTCTAGTGTTAAGAC
1 CCTAGCGTTGCAGCGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTAGCGTTAAGAC
* * *
5865111 TTGAAATAGCTGAAGTGGAGTGGATTAAAACTGTGGGCAGCAAATCCTATTTCTTTGGCATTATA
66 TTGAAAAAGCTGAAGTGGAGCGGATTAAAACTGTGGGCAGCAAATCCTATCTCTTTGGCATTATA
* **
5865176 GTGGAACAGATTAAGGCTAAAGGTAGAAAAT-TTGGTTTC
131 GTGGAACAGATTAAAGCTAAAGGTAGCGAATCTT-GTTTC
* * * * * *
5865215 CCTGGTGTTGTAGTGGAGCAGATTAAAGCTGAAGGCAGCGAATCTCATCTCCCT
1 CCTAGCGTTGCAGCGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCCCT
5865269 GACGATAAAA
Statistics
Matches: 501, Mismatches: 53, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
167 121 0.24
168 45 0.09
169 202 0.40
170 133 0.27
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (169 bp):
CCTAGCGTTGCAGCGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTAGCGTTAAGAC
TTGAAAAAGCTGAAGTGGAGCGGATTAAAACTGTGGGCAGCAAATCCTATCTCTTTGGCATTATA
GTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTC
Found at i:5867042 original size:30 final size:30
Alignment explanation
Indices: 5867006--5867065 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
5866996 TATAATTCTC
5867006 ATATGTA-A-TTATTATTTTTAATCTATATAT
1 ATATGTATATTTATT-TTTTT-ATCTATATAT
*
5867036 ATATGTATATTTATTTTTTTATGTATATAT
1 ATATGTATATTTATTTTTTTATCTATATAT
5867066 TTATATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 16 0.59
31 6 0.22
32 5 0.19
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (30 bp):
ATATGTATATTTATTTTTTTATCTATATAT
Done.