Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007823.1 Hibiscus syriacus cultivar Beakdansim tig00110160_pilon, whole genome shotgun sequence
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: 6287495
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 33
Found at i:4964679 original size:183 final size:183
Alignment explanation
Indices: 4964293--4964679 Score: 636
Period size: 183 Copynumber: 2.1 Consensus size: 183
4964283 ATTAAAGTTT
* *
4964293 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAATCATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
**
4964358 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAATTTTTT
66 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
* *
4964423 TATTTTATAATTATATATTATTTAAATTATTTGTAAACTGTTTTTTAATTAAA
131 TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTAATTAAA
4964476 AAATATTAAATATATTATATATAACATATGGGCT-AAGCCCAAACCATTTAAAACCCAATTAATA
1 AAATATTAAATATATTATATATAACATATGGGCTCAA-CCCAAACCATTTAAAACCCAATTAATA
* *
4964540 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAATTTTATCTAAAATT
65 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAA-ATTATATAAAATT
4964605 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATTAAA
129 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTT-AATTAAA
* *
4964660 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
4964680 AATTAGAAAA
Statistics
Matches: 191, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
182 2 0.01
183 124 0.65
184 65 0.34
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.43
Consensus pattern (183 bp):
AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTAATTAAA
Found at i:4964825 original size:15 final size:15
Alignment explanation
Indices: 4964805--4964833 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4964795 AAAAAAAGTT
4964805 TGGTTAATTCGGTTA
1 TGGTTAATTCGGTTA
4964820 TGGTTAATTCGGTT
1 TGGTTAATTCGGTT
4964834 CGATCGGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.07, G:0.28, T:0.48
Consensus pattern (15 bp):
TGGTTAATTCGGTTA
Found at i:4970830 original size:18 final size:17
Alignment explanation
Indices: 4970807--4970848 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
4970797 TGCCTTCTCT
4970807 TTCAAAGGCGTTTTCAAC
1 TTCAAAGG-GTTTTCAAC
*
4970825 TTCAAAATGGTTTTCAAC
1 TTC-AAAGGGTTTTCAAC
4970843 TTCAAA
1 TTCAAA
4970849 ATGTAATCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 3 0.14
18 15 0.68
19 4 0.18
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (17 bp):
TTCAAAGGGTTTTCAAC
Found at i:4970849 original size:18 final size:18
Alignment explanation
Indices: 4970816--4970851 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
4970806 TTTCAAAGGC
4970816 GTTTTCAACTTCAAAATG
1 GTTTTCAACTTCAAAATG
4970834 GTTTTCAACTTCAAAATG
1 GTTTTCAACTTCAAAATG
4970852 TAATCTTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (18 bp):
GTTTTCAACTTCAAAATG
Found at i:4976899 original size:19 final size:19
Alignment explanation
Indices: 4976875--4976912 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4976865 AGATTGGGAC
4976875 TGTGTCGAGCTCAGATTTA
1 TGTGTCGAGCTCAGATTTA
*
4976894 TGTGTCGAGGTCAGATTTA
1 TGTGTCGAGCTCAGATTTA
4976913 GGTTGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.13, G:0.29, T:0.37
Consensus pattern (19 bp):
TGTGTCGAGCTCAGATTTA
Found at i:4977873 original size:17 final size:17
Alignment explanation
Indices: 4977847--4977880 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4977837 CATGGTGTTT
4977847 AGAACCGGCCCGATCAA
1 AGAACCGGCCCGATCAA
* *
4977864 AGAACTGGCCCGGTCAA
1 AGAACCGGCCCGATCAA
4977881 TGAATCGGTC
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:0.32, C:0.32, G:0.26, T:0.09
Consensus pattern (17 bp):
AGAACCGGCCCGATCAA
Found at i:4985931 original size:19 final size:19
Alignment explanation
Indices: 4985909--4985947 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
4985899 TTACAACCAG
4985909 CTGACCCAAAGCCCAAGAT
1 CTGACCCAAAGCCCAAGAT
*
4985928 CTGACCCGAAGCCCAAGAT
1 CTGACCCAAAGCCCAAGAT
4985947 C
1 C
4985948 CGACTCGATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.38, G:0.18, T:0.10
Consensus pattern (19 bp):
CTGACCCAAAGCCCAAGAT
Found at i:4994949 original size:23 final size:22
Alignment explanation
Indices: 4994913--4994958 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
4994903 TGATTTTGGG
4994913 TTTCATTTGATTCGATTTCTTGTT
1 TTTCATTTGATTCGA--TCTTGTT
*
4994937 TTTC-TTTGGTTCGATCTTGTT
1 TTTCATTTGATTCGATCTTGTT
4994958 T
1 T
4994959 GTCCGGAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
23 9 0.43
24 4 0.19
ACGTcount: A:0.09, C:0.13, G:0.15, T:0.63
Consensus pattern (22 bp):
TTTCATTTGATTCGATCTTGTT
Found at i:4995477 original size:15 final size:15
Alignment explanation
Indices: 4995459--4995532 Score: 73
Period size: 15 Copynumber: 5.1 Consensus size: 15
4995449 AAATTCTAAA
4995459 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
4995474 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
** *
4995489 TCA-TCGAAT-AATA-
1 T-ATTTAAATAAAAAT
4995502 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
4995517 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
4995532 T
1 T
4995533 CATCGATAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
12 1 0.02
13 5 0.11
14 6 0.13
15 33 0.72
16 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:4995507 original size:43 final size:42
Alignment explanation
Indices: 4995458--4995547 Score: 171
Period size: 43 Copynumber: 2.1 Consensus size: 42
4995448 GAAATTCTAA
4995458 ATATTTAAATAAAAATTATTTATATAAAAATTCATCGAATAAT
1 ATATTTAAATAAAAATTATTTATATAAAAATTCATCG-ATAAT
4995501 ATATTTAAATAAAAATTATTTATATAAAAATTCATCGATAAT
1 ATATTTAAATAAAAATTATTTATATAAAAATTCATCGATAAT
4995543 ATATT
1 ATATT
4995548 ATTTTATTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 10 0.21
43 37 0.79
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.41
Consensus pattern (42 bp):
ATATTTAAATAAAAATTATTTATATAAAAATTCATCGATAAT
Found at i:4998710 original size:200 final size:200
Alignment explanation
Indices: 4998367--4998740 Score: 597
Period size: 200 Copynumber: 1.9 Consensus size: 200
4998357 AATGTAAATG
* * * *
4998367 AATTTAGATAGCCGTTAACTTAAACCCTATTATCAAGATAGCCAAAATCATCCAAGACTGGCATC
1 AATTTAGATAGCCATTAACTGAAACCCTATTATCAAGATAGCCAAAATCATCAAAGACTGACATC
* *
4998432 AACTCTCACAGAAAGAAACAAGAATAAATTAGATCAATGGAACCCTCGCCAGAATAAAACTCTCA
66 AACTCTCACAGAAAGAAACAAGAATAAATTAGATCAATAGAACCCTCGCCAGAATAAAACTCTAA
*
4998497 CAAAATGCAAAAATGAC-CAAAAAAGAACAATTAAAACCCCTAATCCATAATTTAGAATGATTTC
131 CAAAATGCAAAAATG-CTCAAAAAAGAACAATTAAAAACCCTAATCCATAATTTAGAATGATTTC
4998561 CTCCCC
195 CTCCCC
4998567 AATTTAGATAGCCATTAACTGAAACCCTATTATCAAGATAGCCAAAATCATCAAAGACTGACATC
1 AATTTAGATAGCCATTAACTGAAACCCTATTATCAAGATAGCCAAAATCATCAAAGACTGACATC
* * * * **
4998632 AACTCTCACAGAATGCAACAGGATTTCATTAGATCAATAGAACCCTCGCCAGAATAAAACTCTAA
66 AACTCTCACAGAAAGAAACAAGAATAAATTAGATCAATAGAACCCTCGCCAGAATAAAACTCTAA
* *
4998697 TAAAATGCAAAAATGCTCTAAAAAGAACAATTAAAAACCCTAAT
131 CAAAATGCAAAAATGCTCAAAAAAGAACAATTAAAAACCCTAAT
4998741 TTTTAGCTCT
Statistics
Matches: 158, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
199 1 0.01
200 157 0.99
ACGTcount: A:0.45, C:0.22, G:0.10, T:0.22
Consensus pattern (200 bp):
AATTTAGATAGCCATTAACTGAAACCCTATTATCAAGATAGCCAAAATCATCAAAGACTGACATC
AACTCTCACAGAAAGAAACAAGAATAAATTAGATCAATAGAACCCTCGCCAGAATAAAACTCTAA
CAAAATGCAAAAATGCTCAAAAAAGAACAATTAAAAACCCTAATCCATAATTTAGAATGATTTCC
TCCCC
Found at i:4999753 original size:21 final size:23
Alignment explanation
Indices: 4999655--4999758 Score: 71
Period size: 23 Copynumber: 4.8 Consensus size: 23
4999645 TAATAGTAGT
*
4999655 AATA-ATAATATA-ATA-TTCGA
1 AATATATAATATATATATTTCAA
*
4999675 AATATGTAATATATAT-TTTC--
1 AATATATAATATATATATTTCAA
** *
4999695 AATA-A-ACCATATATATTTTAA
1 AATATATAATATATATATTTCAA
* *
4999716 AGTATATAATATGTATATTTCAA
1 AATATATAATATATATATTTCAA
4999739 AATTATATATATATATATAT
1 AA-TATATA-ATATATATAT
4999759 ATATATTAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
18 7 0.11
19 3 0.05
20 8 0.13
21 10 0.16
22 6 0.10
23 13 0.21
24 6 0.10
25 9 0.15
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (23 bp):
AATATATAATATATATATTTCAA
Found at i:5001321 original size:13 final size:14
Alignment explanation
Indices: 5001288--5001326 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
5001278 AACCTGGGCC
5001288 AAATAAAA-AAAAG
1 AAATAAAATAAAAG
*
5001301 AAAGAAAATAAAA-
1 AAATAAAATAAAAG
5001314 AAATAAAATAAAA
1 AAATAAAATAAAA
5001327 TTAATAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (14 bp):
AAATAAAATAAAAG
Found at i:5001326 original size:18 final size:18
Alignment explanation
Indices: 5001288--5001337 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
5001278 AACCTGGGCC
5001288 AAATAAAAAAA-AGAAAGA
1 AAATAAAAAAATA-AAAGA
*
5001306 AAATAAAAAAATAAAATA
1 AAATAAAAAAATAAAAGA
* *
5001324 AAATTAATAAATAA
1 AAATAAAAAAATAA
5001338 TAAATCATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 27 0.96
19 1 0.04
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (18 bp):
AAATAAAAAAATAAAAGA
Found at i:5001341 original size:21 final size:24
Alignment explanation
Indices: 5001308--5001402 Score: 66
Period size: 23 Copynumber: 4.2 Consensus size: 24
5001298 AAGAAAGAAA
5001308 ATAA-AAA-AATAAA-ATAA-AAT
1 ATAATAAATAATAAACATAATAAT
5001328 -TAATAAATAATAAATCATAATAAT
1 ATAATAAATAATAAA-CATAATAAT
* * *
5001352 ATAATAAGTAATATATAT-AT-AT
1 ATAATAAATAATAAACATAATAAT
5001374 ATAATATAAT-ATAATAC-T-ATAAT
1 ATAATA-AATAATAA-ACATAATAAT
5001397 ATAATA
1 ATAATA
5001403 TACTTATAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 15
0.74 0.07 0.19
Matches are distributed among these distances:
19 3 0.05
20 3 0.05
21 6 0.10
22 14 0.23
23 17 0.28
24 5 0.08
25 12 0.20
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (24 bp):
ATAATAAATAATAAACATAATAAT
Found at i:5001342 original size:25 final size:25
Alignment explanation
Indices: 5001314--5001364 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
5001304 GAAAATAAAA
5001314 AAAT-AAAATAAAATTAATAAATAAT
1 AAATCAAAATAAAA-TAATAAATAAT
* * *
5001339 AAATCATAATAATATAATAAGTAAT
1 AAATCAAAATAAAATAATAAATAAT
5001364 A
1 A
5001365 TATATATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (25 bp):
AAATCAAAATAAAATAATAAATAAT
Found at i:5001355 original size:15 final size:14
Alignment explanation
Indices: 5001316--5001402 Score: 62
Period size: 13 Copynumber: 6.4 Consensus size: 14
5001306 AAATAAAAAA
5001316 ATAA-AATA-AAAT
1 ATAATAATATAAAT
5001328 -TAATAAATAATAAAT
1 ATAAT-AAT-ATAAAT
5001343 CATAATAATAT-AAT
1 -ATAATAATATAAAT
* *
5001357 A-AGTAATATATAT
1 ATAATAATATAAAT
5001370 ATATATAATAT-AAT
1 ATA-ATAATATAAAT
*
5001384 ATAATACTAT-AAT
1 ATAATAATATAAAT
5001397 ATAATA
1 ATAATA
5001403 TACTTATAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 17
0.73 0.06 0.20
Matches are distributed among these distances:
11 3 0.05
12 7 0.11
13 22 0.36
14 10 0.16
15 12 0.20
16 3 0.05
17 4 0.07
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (14 bp):
ATAATAATATAAAT
Found at i:5001355 original size:18 final size:18
Alignment explanation
Indices: 5001315--5001404 Score: 87
Period size: 18 Copynumber: 4.9 Consensus size: 18
5001305 AAAATAAAAA
* *
5001315 AATAAAATAAAAT-TAAT
1 AATATAATATAATATAAT
5001332 AA-ATAATA-AATCATAAT
1 AATATAATATAAT-ATAAT
5001349 AATATAATAAGTAATATATAT
1 AATATAAT-A-TAATATA-AT
5001370 ATATATAATATAATATAAT
1 A-ATATAATATAATATAAT
*
5001389 ACTATAATATAATATA
1 AATATAATATAATATA
5001405 CTTATAAATA
Statistics
Matches: 63, Mismatches: 2, Indels: 15
0.79 0.03 0.19
Matches are distributed among these distances:
15 3 0.05
16 5 0.08
17 8 0.13
18 19 0.30
19 4 0.06
20 10 0.16
21 7 0.11
22 7 0.11
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (18 bp):
AATATAATATAATATAAT
Found at i:5001357 original size:5 final size:5
Alignment explanation
Indices: 5001347--5001404 Score: 59
Period size: 5 Copynumber: 11.6 Consensus size: 5
5001337 ATAAATCATA
*
5001347 ATAAT ATAAT AAGTAAT AT-AT ATATAT ATAAT ATAAT AT-A- ATACT
1 ATAAT ATAAT -A-TAAT ATAAT ATA-AT ATAAT ATAAT ATAAT ATAAT
5001392 ATAAT ATAAT ATA
1 ATAAT ATAAT ATA
5001405 CTTATAAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
3 2 0.04
4 5 0.11
5 27 0.60
6 7 0.16
7 4 0.09
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:5001463 original size:38 final size:39
Alignment explanation
Indices: 5001390--5001481 Score: 111
Period size: 38 Copynumber: 2.4 Consensus size: 39
5001380 TAATATAATA
5001390 CTATAATATA-ATATA-CTTATAAATATTTTCAAAAACT
1 CTATAATATATATATATCTTATAAATATTTTCAAAAACT
* *
5001427 CTATAATATATATATATTTTCA-AAATGTTTTC-AAAACT
1 CTATAATATATATATATCTT-ATAAATATTTTCAAAAACT
* *
5001465 ATATTATATATATATAT
1 CTATAATATATATATAT
5001482 ATATATATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
37 10 0.21
38 26 0.54
39 11 0.23
40 1 0.02
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.45
Consensus pattern (39 bp):
CTATAATATATATATATCTTATAAATATTTTCAAAAACT
Found at i:5001476 original size:2 final size:2
Alignment explanation
Indices: 5001464--5001499 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5001454 TTTTCAAAAC
5001464 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5001500 TCAAAATGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5001490 original size:54 final size:52
Alignment explanation
Indices: 5001428--5001534 Score: 153
Period size: 54 Copynumber: 2.0 Consensus size: 52
5001418 TCAAAAACTC
* **
5001428 TATAATATATATATATTTTCAAAATGT-TTTCAAAACTATATTATATATATATA
1 TATAATATATATATATATTCAAAATGTCTTAAAAAACTATA-TAT-TATATATA
5001481 TATATATATATATATATATTCAAAATGTCTTAAAAAACTATATATTATATATA
1 TATA-ATATATATATATATTCAAAATGTCTTAAAAAACTATATATTATATATA
5001534 T
1 T
5001535 GTTTTCAATT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
53 13 0.27
54 25 0.51
55 11 0.22
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.46
Consensus pattern (52 bp):
TATAATATATATATATATTCAAAATGTCTTAAAAAACTATATATTATATATA
Found at i:5001594 original size:23 final size:23
Alignment explanation
Indices: 5001568--5001617 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
5001558 TATATATTAT
5001568 ATATATATT-TAAAATGTTTCAAA
1 ATATATATTAT-AAATGTTTCAAA
*
5001591 ATATATATTATATATGTTTCAAA
1 ATATATATTATAAATGTTTCAAA
5001614 ATAT
1 ATAT
5001618 TTCAAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (23 bp):
ATATATATTATAAATGTTTCAAA
Found at i:5001676 original size:36 final size:36
Alignment explanation
Indices: 5001481--5001677 Score: 197
Period size: 39 Copynumber: 5.4 Consensus size: 36
5001471 TATATATATA
* * **
5001481 TATATATATATATATATATTCAAAATGTCTTAAAAAAC
1 TATATAT-TATATATTTTTTCAAAATGT-TTTCAAAAC
** *
5001519 TATATATTATATATATGTTTTCAATTTTTTTTCAAAAAC
1 TATATATTATATAT-T-TTTTCAAAATGTTTTC-AAAAC
*
5001558 TATATATTATATATATATTT-AAAATG-TTTCAAAA-
1 TATATATTATATAT-TTTTTCAAAATGTTTTCAAAAC
* * *
5001592 TATATATTATATA-TGTTTCAAAAT-ATTTCAAAAT
1 TATATATTATATATTTTTTCAAAATGTTTTCAAAAC
5001626 TATATATTATATATTTTTTCAAAATGTTTTCAAAAC
1 TATATATTATATATTTTTTCAAAATGTTTTCAAAAC
*
5001662 TACATATTATATATTT
1 TATATATTATATATTT
5001678 GCAAAATCCA
Statistics
Matches: 135, Mismatches: 16, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
32 4 0.03
33 13 0.10
34 26 0.19
35 14 0.10
36 27 0.20
37 10 0.07
38 12 0.09
39 29 0.21
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.48
Consensus pattern (36 bp):
TATATATTATATATTTTTTCAAAATGTTTTCAAAAC
Found at i:5001683 original size:34 final size:35
Alignment explanation
Indices: 5001481--5001684 Score: 191
Period size: 34 Copynumber: 5.7 Consensus size: 35
5001471 TATATATATA
**
5001481 TATATATATATATATATATTCAAAATGTCTTAAAAAAC
1 TATATAT-TATATATAT-TTCAAAATGT-TTTCAAAAC
** *
5001519 TATATATTATATATATGTTTTCAATTTTTTTTCAAAAAC
1 TATATATTATATATA---TTTCAAAATGTTTTC-AAAAC
*
5001558 TATATATTATATATATATTTAAAATG-TTTCAAAA-
1 TATATATTATATATAT-TTCAAAATGTTTTCAAAAC
* * *
5001592 TATATATTATATATGTTTCAAAAT-ATTTCAAAAT
1 TATATATTATATATATTTCAAAATGTTTTCAAAAC
*
5001626 TATATATTATATATTTTTTCAAAATGTTTTCAAAAC
1 TATATATTATATA-TATTTCAAAATGTTTTCAAAAC
* *
5001662 TACATATTATATAT-TTGCAAAAT
1 TATATATTATATATATTTCAAAAT
5001685 CCATTTTAAA
Statistics
Matches: 141, Mismatches: 16, Indels: 22
0.79 0.09 0.12
Matches are distributed among these distances:
33 15 0.11
34 36 0.26
35 15 0.11
36 25 0.18
37 13 0.09
38 9 0.06
39 27 0.19
40 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (35 bp):
TATATATTATATATATTTCAAAATGTTTTCAAAAC
Found at i:5001731 original size:13 final size:14
Alignment explanation
Indices: 5001702--5001729 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5001692 AAAAAACTAT
5001702 ATACGTTTTCAAAA
1 ATACGTTTTCAAAA
5001716 ATACGTTTTCAAAA
1 ATACGTTTTCAAAA
5001730 TATATATACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
ATACGTTTTCAAAA
Found at i:5001762 original size:30 final size:31
Alignment explanation
Indices: 5001709--5001768 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
5001699 TATATACGTT
5001709 TTCAAAAATACGTTTTCAAAATA-TATATAC
1 TTCAAAAATACGTTTTCAAAATATTATATAC
* *
5001739 TTCACAAATTACG-TTTGAAAATATTATATA
1 TTCA-AAAATACGTTTTCAAAATATTATATA
5001769 TATATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (31 bp):
TTCAAAAATACGTTTTCAAAATATTATATAC
Found at i:5001770 original size:2 final size:2
Alignment explanation
Indices: 5001759--5001795 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
5001749 ACGTTTGAAA
5001759 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A
5001796 ATAATGAAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5004223 original size:18 final size:19
Alignment explanation
Indices: 5004199--5004252 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 19
5004189 ATAAACCATA
5004199 ATAATATAATAAGTAATAC-
1 ATAATATAATAA-TAATACT
5004218 AT-ATATAAT-ATAATACT
1 ATAATATAATAATAATACT
5004235 ATAATATAATATATAATA
1 ATAATATAATA-ATAATA
5004253 TACTTATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 6 0.19
17 3 0.10
18 14 0.45
19 2 0.06
20 6 0.19
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (19 bp):
ATAATATAATAATAATACT
Found at i:5004260 original size:13 final size:12
Alignment explanation
Indices: 5004199--5004254 Score: 71
Period size: 12 Copynumber: 4.7 Consensus size: 12
5004189 ATAAACCATA
5004199 ATAATATAATA-
1 ATAATATAATAT
*
5004210 AGTAATA-CATAT
1 A-TAATATAATAT
5004222 ATAATATAATACT
1 ATAATATAATA-T
5004235 ATAATATAATAT
1 ATAATATAATAT
5004247 ATAATATA
1 ATAATATA
5004255 CTTATAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
11 9 0.23
12 18 0.46
13 12 0.31
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (12 bp):
ATAATATAATAT
Found at i:5004285 original size:31 final size:32
Alignment explanation
Indices: 5004244--5004304 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
5004234 TATAATATAA
*
5004244 TATATAATATACT-TATAAATATTTTCAAAAAC
1 TATATAATATA-TATATAAATATATTCAAAAAC
*
5004276 TATAT-ATATATATATATATATATTCAAAA
1 TATATAATATATATATAAATATATTCAAAA
5004305 TGTTTTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 1 0.04
31 20 0.77
32 5 0.19
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.43
Consensus pattern (32 bp):
TATATAATATATATATAAATATATTCAAAAAC
Found at i:5004399 original size:77 final size:75
Alignment explanation
Indices: 5004238--5004522 Score: 331
Period size: 77 Copynumber: 3.7 Consensus size: 75
5004228 TAATACTATA
* * *
5004238 ATATAATATATAATATACTT-ATAAATATTTTCAAAAACTATATATATATATATATATATATTCA
1 ATATATTATAT-ATATA-TTCA-AAATGTTTTCAAAAACTATATAT-TATATATATGT-T-TTCA
* *
5004302 AAATGTTTTCAAAACT
60 AAATATTTTCAAAAAT
* ** *
5004318 ATATATTATATATATATTCAAAATGTTTTAAAAAACTATATATTATATATATGTTTTCAATTTTT
1 ATATATTATATATATATTCAAAATGTTTTCAAAAACTATATATTATATATATGTTTTCAA-AATA
5004383 TTTTCAAAAAAT
65 TTTTC-AAAAAT
* * *
5004395 ATATATTATATGTATATTTAAAATGTTTTCAAAAATTATATATTATATATATGTTTTCAAAATAT
1 ATATATTATATATATATTCAAAATGTTTTCAAAAACTATATATTATATATATGTTTTCAAAATAT
*
5004460 TTTCAAAATT
66 TTTCAAAAAT
* *
5004470 ATATATTATATATATTTTTTCAAAATGTTTTC-AAAACTACATATTATATATAT
1 ATATATTATATATA--TATTCAAAATGTTTTCAAAAACTATATATTATATATAT
5004523 TTGCAAAATC
Statistics
Matches: 179, Mismatches: 21, Indels: 14
0.84 0.10 0.07
Matches are distributed among these distances:
75 23 0.13
76 32 0.18
77 85 0.47
78 23 0.13
79 6 0.03
80 10 0.06
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.47
Consensus pattern (75 bp):
ATATATTATATATATATTCAAAATGTTTTCAAAAACTATATATTATATATATGTTTTCAAAATAT
TTTCAAAAAT
Found at i:5004477 original size:38 final size:37
Alignment explanation
Indices: 5004260--5004524 Score: 291
Period size: 38 Copynumber: 6.9 Consensus size: 37
5004250 ATATACTTAT
*
5004260 AAATATTTTCAAAAACTATATATATATATATATATATATTCA
1 AAATGTTTTC-AAAACTATATAT-TATATATAT-T-T-TTCA
*
5004302 AAATGTTTTCAAAACTATATATTATATATA-TATTCA
1 AAATGTTTTCAAAACTATATATTATATATATTTTTCA
*
5004338 AAATGTTTTAAAAAACTATATATTATATATATGTTTTCA
1 AAATGTTTT-CAAAACTATATATTATATATAT-TTTTCA
** * * * *
5004377 ATTTTTTTTTCAAAAAATATATATTATATGTATATTT-A
1 A-AATGTTTTC-AAAACTATATATTATATATATTTTTCA
*
5004415 AAATGTTTTCAAAAATTATATATTATATATATGTTTTCA
1 AAATGTTTTC-AAAACTATATATTATATATAT-TTTTCA
* *
5004454 AAATATTTTCAAAATTATATATTATATATATTTTTTCA
1 AAATGTTTTCAAAACTATATATTATATATA-TTTTTCA
*
5004492 AAATGTTTTCAAAACTACATATTATATATATTT
1 AAATGTTTTCAAAACTATATATTATATATATTT
5004525 GCAAAATCCA
Statistics
Matches: 194, Mismatches: 21, Indels: 21
0.82 0.09 0.09
Matches are distributed among these distances:
36 13 0.07
37 49 0.25
38 59 0.30
39 20 0.10
40 32 0.16
41 12 0.06
42 9 0.05
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (37 bp):
AAATGTTTTCAAAACTATATATTATATATATTTTTCA
Found at i:5004569 original size:14 final size:14
Alignment explanation
Indices: 5004550--5004577 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5004540 AAAAAACTAT
5004550 ATACGTTTTCAAAA
1 ATACGTTTTCAAAA
5004564 ATACGTTTTCAAAA
1 ATACGTTTTCAAAA
5004578 CATATAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
ATACGTTTTCAAAA
Found at i:5004624 original size:2 final size:2
Alignment explanation
Indices: 5004617--5004658 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
5004607 TTGAAATTAT
5004617 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
5004659 ATAATATGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5004665 original size:8 final size:9
Alignment explanation
Indices: 5004617--5004665 Score: 52
Period size: 8 Copynumber: 5.8 Consensus size: 9
5004607 TTGAAATTAT
5004617 TATATAT-A
1 TATATATAA
5004625 TATATAT-A
1 TATATATAA
5004633 TATATAT-A
1 TATATATAA
*
5004641 TATATATTA
1 TATATATAA
5004650 TACTATATAA
1 TA-TATATAA
5004660 TA-ATAT
1 TATATAT
5004666 GAAGCCCTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
8 27 0.71
9 3 0.08
10 8 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (9 bp):
TATATATAA
Found at i:5007151 original size:5 final size:5
Alignment explanation
Indices: 5007119--5007170 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
5007109 AACCTGGACC
* *
5007119 AAATA AAA-A AAAGA AAGAAA ATAATA AAATA AAATA AAATA AAAT- AAATA
1 AAATA AAATA AAATA AA-ATA A-AATA AAATA AAATA AAATA AAATA AAATA
5007169 AA
1 AA
5007171 TAATAAACCA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 8 0.20
5 26 0.63
6 6 0.15
7 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (5 bp):
AAATA
Found at i:5007157 original size:31 final size:31
Alignment explanation
Indices: 5007119--5007177 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
5007109 AACCTGGACC
5007119 AAATAAAA-AAAAGAAAGAAAATAATAAAATA
1 AAATAAAATAAAAGAAA-AAAATAATAAAATA
* *
5007150 AAATAAAATAAAATAAATAAATAATAAA
1 AAATAAAATAAAAGAAAAAAATAATAAA
5007178 CCATAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (31 bp):
AAATAAAATAAAAGAAAAAAATAATAAAATA
Found at i:5007171 original size:18 final size:17
Alignment explanation
Indices: 5007119--5007173 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
5007109 AACCTGGACC
* *
5007119 AAATAAAAAAAAGAAAGA
1 AAAT-AAAAAAATAAATA
*
5007137 AAATAATAAAATAAAATA
1 AAATAAAAAAAT-AAATA
5007155 AAATAAAATAAATAAATA
1 AAATAAAA-AAATAAATA
5007173 A
1 A
5007174 TAAACCATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 6 0.19
18 21 0.68
19 4 0.13
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (17 bp):
AAATAAAAAAATAAATA
Found at i:5007186 original size:31 final size:31
Alignment explanation
Indices: 5007116--5007191 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 31
5007106 CCGAACCTGG
5007116 ACCAAATAAAA-AAAAGAAAGAAAATAATAAA
1 ACCAAATAAAATAAAAGAAAGAAAATAAT-AA
** * *
5007147 ATAAAATAAAATAAAATAAA-TAAATAATAA
1 ACCAAATAAAATAAAAGAAAGAAAATAATAA
*
5007177 ACCATAATAATATAA
1 ACCA-AATAAAATAA
5007192 TAAGTAATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
30 4 0.11
31 25 0.69
32 7 0.19
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (31 bp):
ACCAAATAAAATAAAAGAAAGAAAATAATAA
Found at i:5007207 original size:18 final size:17
Alignment explanation
Indices: 5007186--5007238 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 17
5007176 AACCATAATA
5007186 ATATAATAAGTAATATAT
1 ATATAATAA-TAATATAT
5007204 ATATAAT-ATAATATTAT
1 ATATAATAATAATA-TAT
5007221 ACTATAATATATAATATA
1 A-TATAATA-ATAATATA
5007239 CCTATAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 5 0.16
17 5 0.16
18 13 0.42
19 2 0.06
20 6 0.19
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
ATATAATAATAATATAT
Found at i:5007213 original size:23 final size:24
Alignment explanation
Indices: 5007183--5007238 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
5007173 ATAAACCATA
5007183 ATAATATAATA-AGTAATAT-ATAT
1 ATAATATAATATA-TAATATAATAT
*
5007206 ATAATATAATATTATACTATAATAT
1 ATAATATAATA-TATAATATAATAT
5007231 ATAATATA
1 ATAATATA
5007239 CCTATAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 11 0.38
24 5 0.17
25 13 0.45
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (24 bp):
ATAATATAATATATAATATAATAT
Found at i:5007226 original size:13 final size:14
Alignment explanation
Indices: 5007183--5007233 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
5007173 ATAAACCATA
5007183 ATAATATA-ATAAGT
1 ATAATATATATAA-T
5007197 A-ATATATATATAAT
1 ATA-ATATATATAAT
*
5007211 ATAATAT-TATACT
1 ATAATATATATAAT
5007224 ATAATATATA
1 ATAATATATA
5007234 ATATACCTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
13 13 0.41
14 14 0.44
15 5 0.16
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (14 bp):
ATAATATATATAAT
Found at i:5007226 original size:20 final size:19
Alignment explanation
Indices: 5007186--5007237 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
5007176 AACCATAATA
* *
5007186 ATATAATA-AGTAATATAT
1 ATATAATATAATATTATAT
5007204 ATATAATATAATATTATACT
1 ATATAATATAATATTATA-T
5007224 ATA-ATATATAATAT
1 ATATA-ATATAATAT
5007238 ACCTATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 8 0.28
19 8 0.28
20 13 0.45
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (19 bp):
ATATAATATAATATTATAT
Found at i:5007243 original size:18 final size:17
Alignment explanation
Indices: 5007200--5007249 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
5007190 AATAAGTAAT
5007200 ATATA-TATAATATAATA
1 ATATACTATAATAT-ATA
*
5007217 TTATACTATAATATATA
1 ATATACTATAATATATA
5007234 ATATACCTATAA-ATAT
1 ATATA-CTATAATATAT
5007250 TTTCAAAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATACTATAATATATA
Found at i:5007265 original size:34 final size:32
Alignment explanation
Indices: 5007228--5007289 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
5007218 TATACTATAA
** *
5007228 TATATAATATACCTATAAATATTTTCAAAAAC
1 TATATAATATATATATAAATATATTCAAAAAC
*
5007260 TATATAATATATATATATATATATTCAAAA
1 TATATAATATATATATAAATATATTCAAAA
5007290 TGTTTTCAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (32 bp):
TATATAATATATATATAAATATATTCAAAAAC
Found at i:5007313 original size:40 final size:38
Alignment explanation
Indices: 5007244--5007510 Score: 281
Period size: 37 Copynumber: 6.8 Consensus size: 38
5007234 ATATACCTAT
*
5007244 AAATATTTTCAAAAACTATATAATATATATATATATATATTCA
1 AAATGTTTTC-AAAACTATAT-AT-TATATATATAT-T-TTCA
5007287 AAATGTTTTCAAAACTATATATTATATATATA--TTCA
1 AAATGTTTTCAAAACTATATATTATATATATATTTTCA
* *
5007323 AAATGTTTTAAAAAACTATATATTATATATATGTTTTCA
1 AAATGTTTT-CAAAACTATATATTATATATATATTTTCA
** *
5007362 ATTTTTTTTTTCAAAAACTATATATTATATATATA-TTT-A
1 A--AATGTTTTC-AAAACTATATATTATATATATATTTTCA
* * *
5007401 AAATGTTTTCAAAAATTATATATTATATGTATGTTTTCAA
1 AAATGTTTTC-AAAACTATATATTATATATATATTTTC-A
* * *
5007441 AAATATTTTCAAAATTTATATATTATATATATTTTTTCA
1 AAATGTTTTCAAAA-CTATATATTATATATATATTTTCA
*
5007480 AAATGTTTTCAAAACTAAATATTATATATAT
1 AAATGTTTTCAAAACTATATATTATATATAT
5007511 TTGCAAAATC
Statistics
Matches: 194, Mismatches: 20, Indels: 25
0.81 0.08 0.10
Matches are distributed among these distances:
36 13 0.07
37 47 0.24
38 18 0.09
39 25 0.13
40 44 0.23
41 28 0.14
42 10 0.05
43 9 0.05
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.48
Consensus pattern (38 bp):
AAATGTTTTCAAAACTATATATTATATATATATTTTCA
Found at i:5007385 original size:78 final size:76
Alignment explanation
Indices: 5007244--5007510 Score: 295
Period size: 78 Copynumber: 3.4 Consensus size: 76
5007234 ATATACCTAT
* * *
5007244 AAATATTTTCAAAAACTATATAATATATATATATATATATTC-AAAATGTTTTC-AAAACTATAT
1 AAATGTTTT-AAAAACTATAT-AT-TATATATATGT-T-TTCAAAAATATTTTCAAAAACTATAT
5007307 ATTATATATATATTCA
61 ATTATATATATATTCA
*** *
5007323 AAATGTTTTAAAAAACTATATATTATATATATGTTTTCAATTTTTTTTTTCAAAAACTATATATT
1 AAATGTTTT-AAAAACTATATATTATATATATGTTTTCAA-AAATATTTTCAAAAACTATATATT
*
5007388 ATATATATATTTA
64 ATATATATATTCA
* * **
5007401 AAATGTTTTCAAAAATTATATATTATATGTATGTTTTCAAAAATATTTTCAAAATTTATATATTA
1 AAATGTTTT-AAAAACTATATATTATATATATGTTTTCAAAAATATTTTCAAAAACTATATATTA
*
5007466 TATATATTTTTTCA
65 TATATA--TATTCA
* *
5007480 AAATGTTTTCAAAACTAAATATTATATATAT
1 AAATGTTTTAAAAACTATATATTATATATAT
5007511 TTGCAAAATC
Statistics
Matches: 160, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
75 3 0.02
76 2 0.01
77 41 0.26
78 82 0.51
79 32 0.20
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.48
Consensus pattern (76 bp):
AAATGTTTTAAAAACTATATATTATATATATGTTTTCAAAAATATTTTCAAAAACTATATATTAT
ATATATATTCA
Found at i:5007420 original size:26 final size:28
Alignment explanation
Indices: 5007391--5007444 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
5007381 ATATATTATA
5007391 TATATATT-TA-AAATGTTTTCAAAAAT
1 TATATATTATATAAATGTTTTCAAAAAT
**
5007417 TATATATTATATGTATGTTTTCAAAAAT
1 TATATATTATATAAATGTTTTCAAAAAT
5007445 ATTTTCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 8 0.33
27 2 0.08
28 14 0.58
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.48
Consensus pattern (28 bp):
TATATATTATATAAATGTTTTCAAAAAT
Found at i:5008628 original size:125 final size:125
Alignment explanation
Indices: 5008406--5008655 Score: 500
Period size: 125 Copynumber: 2.0 Consensus size: 125
5008396 GCCAACCTAG
5008406 GTCTTCTTATTGACTTAAAGACCTCAGTTTAAACTTCATCCGGAAAGTAGTTCCTCGCTTCTACC
1 GTCTTCTTATTGACTTAAAGACCTCAGTTTAAACTTCATCCGGAAAGTAGTTCCTCGCTTCTACC
5008471 ATATAGCTGATACGTCATCGAGCAGAATGGAATCGAACTTGAAAGTTTTCGTTGACAGAT
66 ATATAGCTGATACGTCATCGAGCAGAATGGAATCGAACTTGAAAGTTTTCGTTGACAGAT
5008531 GTCTTCTTATTGACTTAAAGACCTCAGTTTAAACTTCATCCGGAAAGTAGTTCCTCGCTTCTACC
1 GTCTTCTTATTGACTTAAAGACCTCAGTTTAAACTTCATCCGGAAAGTAGTTCCTCGCTTCTACC
5008596 ATATAGCTGATACGTCATCGAGCAGAATGGAATCGAACTTGAAAGTTTTCGTTGACAGAT
66 ATATAGCTGATACGTCATCGAGCAGAATGGAATCGAACTTGAAAGTTTTCGTTGACAGAT
5008656 AGCCCTTCTC
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
125 125 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (125 bp):
GTCTTCTTATTGACTTAAAGACCTCAGTTTAAACTTCATCCGGAAAGTAGTTCCTCGCTTCTACC
ATATAGCTGATACGTCATCGAGCAGAATGGAATCGAACTTGAAAGTTTTCGTTGACAGAT
Found at i:5010438 original size:175 final size:175
Alignment explanation
Indices: 5010091--5010445 Score: 667
Period size: 175 Copynumber: 2.0 Consensus size: 175
5010081 CCTTCCCCTA
5010091 ATGTTGAAACCCTAATTCAATTTGGACTTAGGCTGGGTCAGGCCCCCTAACCAGGTTTACTGGGT
1 ATGTTGAAACCCTAATTCAATTTGGACTTAGGCTGGGTCAGGCCCCCTAACCAGGTTTACTGGGT
5010156 CATGCTACCCAGTTGGGCTCCTTACTGGACCATGCTGGACTCCCCGAACCTAGACCAATAAAAAA
66 CATGCTACCCAGTTGGGCTCCTTACTGGACCATGCTGGACTCCCCGAACCTAGACCAATAAAAAA
5010221 AAGAAAGAAAATAATATAATAAGTAATATAATACTAAAAATATAT
131 AAGAAAGAAAATAATATAATAAGTAATATAATACTAAAAATATAT
5010266 ATGTTGAAACCCTAATTCAATTTGGACTTAGGCTGGGTCAGGCCCCCTAACCAGGTTTACTGGGT
1 ATGTTGAAACCCTAATTCAATTTGGACTTAGGCTGGGTCAGGCCCCCTAACCAGGTTTACTGGGT
5010331 CATGCTACCCAGTTGGGCTCCTTACTGGACCAATGCTGGACTCCCCGAACCTAGACCAA-ATAAA
66 CATGCTACCCAGTTGGGCTCCTTACTGGACC-ATGCTGGACTCCCCGAACCTAGACCAATA-AAA
5010395 AAAAGAAAGAAAATAATATAATAAGTAATATAATACTAAAATATAATAT
129 AAAAGAAAGAAAATAATATAATAAGTAATATAATACTAAAA-AT-ATAT
5010444 AT
1 AT
5010446 AATATACTTA
Statistics
Matches: 176, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
175 97 0.55
176 71 0.40
177 2 0.01
178 6 0.03
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (175 bp):
ATGTTGAAACCCTAATTCAATTTGGACTTAGGCTGGGTCAGGCCCCCTAACCAGGTTTACTGGGT
CATGCTACCCAGTTGGGCTCCTTACTGGACCATGCTGGACTCCCCGAACCTAGACCAATAAAAAA
AAGAAAGAAAATAATATAATAAGTAATATAATACTAAAAATATAT
Found at i:5010451 original size:12 final size:12
Alignment explanation
Indices: 5010407--5010451 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
5010397 AAGAAAGAAA
5010407 ATAATATAATA-
1 ATAATATAATAT
5010418 AGTAATATAATACT
1 A-TAATATAATA-T
*
5010432 AAAATATAATAT
1 ATAATATAATAT
5010444 ATAATATA
1 ATAATATA
5010452 CTTATAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 1 0.03
12 18 0.62
13 9 0.31
14 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (12 bp):
ATAATATAATAT
Found at i:5010510 original size:38 final size:39
Alignment explanation
Indices: 5010457--5010717 Score: 336
Period size: 38 Copynumber: 6.8 Consensus size: 39
5010447 ATATACTTAT
* *
5010457 AAATATTTTCAAAAACTATATAATATATATATATTTTCA
1 AAATGTTTTCAAAAACTATATATTATATATATATTTTCA
* *
5010496 AAATGTTTTC-AAAACTATATATTATATATTTATATTCA
1 AAATGTTTTCAAAAACTATATATTATATATATATTTTCA
* * *
5010534 AAAAGTTTTAAAAAACTATATATTATATATATGTTTTC-
1 AAATGTTTTCAAAAACTATATATTATATATATATTTTCA
* * *
5010572 AATTTTTTTCAAAAACTATGTATTATATATATA-TTT-A
1 AAATGTTTTCAAAAACTATATATTATATATATATTTTCA
* *
5010609 AAATGTTTTCAAAAATTATATATTATATATATGTTTTCA
1 AAATGTTTTCAAAAACTATATATTATATATATATTTTCA
* *
5010648 AAATATTTTCAAAAATTATATATTATATATAT-TTTTGCA
1 AAATGTTTTCAAAAACTATATATTATATATATATTTT-CA
*
5010687 AAATGTTTTC-AAAACTACATATTATATATAT
1 AAATGTTTTCAAAAACTATATATTATATATAT
5010718 TTGCAAAATC
Statistics
Matches: 193, Mismatches: 24, Indels: 11
0.85 0.11 0.05
Matches are distributed among these distances:
37 31 0.16
38 86 0.45
39 76 0.39
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.47
Consensus pattern (39 bp):
AAATGTTTTCAAAAACTATATATTATATATATATTTTCA
Found at i:5010522 original size:77 final size:77
Alignment explanation
Indices: 5010435--5010747 Score: 318
Period size: 77 Copynumber: 4.1 Consensus size: 77
5010425 TAATACTAAA
* *
5010435 ATATAATATATAATATACTT-ATAAATATTTTCAAAAACTATATAATATATATATATTTTCAAAA
1 ATATATTATAT-ATATATTTCA-AAATATTTTCAAAAACTATATAATATATATATATTTTCAAAA
*
5010499 TGTTTTC-AAAACT
64 TATTTTCAAAAACT
* * * * *
5010512 ATATATTATATATTTATATTCAAAA-AGTTTTAAAAAACTATATATTATATATATGTTTTC-AAT
1 ATATATTATATATATAT-TTCAAAATA-TTTTCAAAAACTATATAATATATATATATTTTCAAAA
*
5010575 TTTTTTCAAAAACT
64 TATTTTCAAAAACT
* * * * *
5010589 ATGTATTATATATATATTT-AAAATGTTTTCAAAAATTATATATTATATATATGTTTTCAAAATA
1 ATATATTATATATATATTTCAAAATATTTTCAAAAACTATATAATATATATATATTTTCAAAATA
*
5010653 TTTTCAAAAATT
66 TTTTCAAAAACT
* * * *
5010665 ATATATTATATATATTTTTGCAAAATGTTTTC-AAAACTACAT-AT-TATATATATTTGCAAAAT
1 ATATATTATATATATATTT-CAAAATATTTTCAAAAACTATATAATATATATATATTTTCAAAAT
*
5010727 CCATTTTTAAAAAACT
65 --A-TTTTCAAAAACT
5010743 ATATA
1 ATATA
5010748 CGTTTTCAAA
Statistics
Matches: 200, Mismatches: 25, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
75 51 0.25
76 47 0.23
77 75 0.38
78 27 0.14
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (77 bp):
ATATATTATATATATATTTCAAAATATTTTCAAAAACTATATAATATATATATATTTTCAAAATA
TTTTCAAAAACT
Found at i:5010628 original size:26 final size:28
Alignment explanation
Indices: 5010599--5010650 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
5010589 ATGTATTATA
5010599 TATATATT-TA-AAATGTTTTCAAAAAT
1 TATATATTATATAAATGTTTTCAAAAAT
*
5010625 TATATATTATATATATGTTTTCAAAA
1 TATATATTATATAAATGTTTTCAAAA
5010651 TATTTTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 8 0.35
27 2 0.09
28 13 0.57
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (28 bp):
TATATATTATATAAATGTTTTCAAAAAT
Found at i:5010764 original size:14 final size:14
Alignment explanation
Indices: 5010745--5010772 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5010735 AAAAAACTAT
5010745 ATACGTTTTCAAAA
1 ATACGTTTTCAAAA
5010759 ATACGTTTTCAAAA
1 ATACGTTTTCAAAA
5010773 CATATAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
ATACGTTTTCAAAA
Found at i:5015539 original size:11 final size:11
Alignment explanation
Indices: 5015525--5015588 Score: 51
Period size: 11 Copynumber: 5.8 Consensus size: 11
5015515 GACTAATATG
5015525 AAAATAATAAT
1 AAAATAATAAT
*
5015536 AAAACAATAATT
1 AAAATAATAA-T
* *
5015548 AAAGTAATATT
1 AAAATAATAAT
*
5015559 AAACAT-ATCA-
1 AAA-ATAATAAT
*
5015569 AAAGTAATAAT
1 AAAATAATAAT
5015580 AAAATAATA
1 AAAATAATA
5015589 TTGCAAATAA
Statistics
Matches: 39, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
9 1 0.03
10 6 0.15
11 23 0.59
12 9 0.23
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.27
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:5015941 original size:63 final size:64
Alignment explanation
Indices: 5015805--5015941 Score: 165
Period size: 63 Copynumber: 2.2 Consensus size: 64
5015795 AGATATACGG
* * *
5015805 TGACTAAATTATAAATAAAATTAAATTAAAATACTGAATTAAAATATATGAAAACTTATTATAG
1 TGACTAAATTATAAATAAAATAAAATTAAAATACTGAATTAAAACATATGAAAACTTATTATAA
* *
5015869 TGACTAAATTAT-AATAAAGA-AAAATTAAAATA-TATAATTAAAACATATGAAAA-TTAATTTT
1 TGACTAAATTATAAATAAA-ATAAAATTAAAATACT-GAATTAAAACATATGAAAACTT-ATTAT
5015930 AA
63 AA
*
5015932 TGACCAAATT
1 TGACTAAATT
5015942 GCATAGATAC
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
62 3 0.05
63 48 0.75
64 13 0.20
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (64 bp):
TGACTAAATTATAAATAAAATAAAATTAAAATACTGAATTAAAACATATGAAAACTTATTATAA
Found at i:5016954 original size:3 final size:3
Alignment explanation
Indices: 5016946--5017008 Score: 53
Period size: 3 Copynumber: 22.0 Consensus size: 3
5016936 TTGTAATATG
* *
5016946 TAA TAA TAA TATT TAT TAA TAA TAA TAA -AA -AA T-A TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
5016989 TTA TAA TAA T-A TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
5017009 AAATGAAACG
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
2 8 0.16
3 41 0.80
4 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:5017558 original size:139 final size:139
Alignment explanation
Indices: 5017233--5017574 Score: 435
Period size: 138 Copynumber: 2.5 Consensus size: 139
5017223 CAAAAAATTT
**
5017233 GAACAAGTTCTTCTTATTATGAACTTCTTCTTTATCTTCAGATGAG-TCATTCTCATTATGAAC-
1 GAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATGAGTTC-TTCTCATTATGAACT
* * * * * * *
5017296 TCCTTCTGGAAATGTTGATCCTCAAAAGAAGGGTTGTTGATTCAGCTTCATATGTGATGAATTTA
65 TCCTTCTGAAAATGTTGATCCTCAAAAGAAGGCTTGTTCATTCAACTCCATAGGTGATGAATTCA
*
5017361 AGACAAGGTT
130 AGACAAGGTC
* * * *
5017371 GAACAATTTCTTCTTATAATAAACTTCTTCTTCCTATTCAGATGAGTTCTTCTCATTATGAACTT
1 GAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTT
* *
5017436 CC-TCTGAAAATGTTGATCCTCAAGAG-AGGTTCTTCTTTCATTCAACTCCATAGGTGATGAA-T
66 CCTTCTGAAAATGTTGATCCTCAAAAGAAGG--CTT-GTTCATTCAACTCCATAGGTGATGAATT
5017498 CAAG-CTAAGGTC
128 CAAGAC-AAGGTC
* *
5017510 GAACAAGTTCTTATTATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTT
1 GAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTT
5017575 TATATAGAAA
Statistics
Matches: 176, Mismatches: 22, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
137 3 0.02
138 77 0.44
139 75 0.43
140 21 0.12
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (139 bp):
GAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTT
CCTTCTGAAAATGTTGATCCTCAAAAGAAGGCTTGTTCATTCAACTCCATAGGTGATGAATTCAA
GACAAGGTC
Found at i:5017840 original size:113 final size:113
Alignment explanation
Indices: 5017619--5017957 Score: 506
Period size: 113 Copynumber: 3.0 Consensus size: 113
5017609 TGTGATAGAG
* *
5017619 TCAAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTTC-TCTTCAGATGAGTTCT
1 TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * * *
5017683 TCTCATTATGAACT-T-CCTATGGAAAAGTTGATCCATCGACTGATGAAT
66 TCTCATTATGAACTCTACC--TGGCAATGTTGATCCATAGAGTGATGAAT
* *
5017731 TCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* *
5017796 TCTCATTATGAACTCTACCTGGCAATGCTGATCCATAAAGTGATGAAT
66 TCTCATTATGAACTCTACCTGGCAATGTTGATCCATAGAGTGATGAAT
5017844 TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * * *
5017909 TATTATTATGAACTCTACCTGGC-ATGTTGATCCATTGAGTGATGGAT
66 TCTCATTATGAACTCTACCTGGCAATGTTGATCCATAGAGTGATGAAT
5017956 TC
1 TC
5017958 GAATCTTTGC
Statistics
Matches: 206, Mismatches: 18, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
112 66 0.32
113 137 0.67
114 1 0.00
115 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (113 bp):
TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
TCTCATTATGAACTCTACCTGGCAATGTTGATCCATAGAGTGATGAAT
Found at i:5018373 original size:22 final size:22
Alignment explanation
Indices: 5018323--5018375 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
5018313 ATCTTTCTTT
*
5018323 TTTGAAAAGAGAATCTATCATC
1 TTTGAAGAGAGAATCTATCATC
*
5018345 TTTGAAGAGAGAATTTATCATC
1 TTTGAAGAGAGAATCTATCATC
5018367 TTTGAAGAG
1 TTTGAAGAG
5018376 TGTAGATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (22 bp):
TTTGAAGAGAGAATCTATCATC
Found at i:5019591 original size:28 final size:28
Alignment explanation
Indices: 5019559--5019613 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
5019549 ACACCAGGAC
5019559 CCTGATATAACTGTTTGATGAACGAAGA
1 CCTGATATAACTGTTTGATGAACGAAGA
*
5019587 CCTGATGTAACTGTTTGATGAACGAAG
1 CCTGATATAACTGTTTGATGAACGAAG
5019614 CAATTTTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.29
Consensus pattern (28 bp):
CCTGATATAACTGTTTGATGAACGAAGA
Found at i:5019865 original size:74 final size:73
Alignment explanation
Indices: 5019753--5019977 Score: 247
Period size: 75 Copynumber: 3.0 Consensus size: 73
5019743 TAACATTTAT
* * *
5019753 TGATACAAACGTTCAAAATGCA-CTAACATTCCTGATTCTGATTAAAAGGGCTTTCAGCATGCCC
1 TGATACAAACATTCAAAATGCATC-AATATTCC-AATTCTGATTAAAAGGGCTTTCAGCATGCCC
5019817 CAATATTTGC
64 CAATATTTGC
* * * * *
5019827 TGATACAAATATTCAAAATG-AGTCAATATTCTTAATTCTGATTGAAATGGGCTTTCAGCCTACC
1 TGATACAAACATTCAAAATGCA-TCAATATTC-CAATTCTGATT-AAAAGGGCTTTCAGCATGCC
*
5019891 CCAGTATTTGC
63 CCAATATTTGC
* * * *
5019902 CGATACAAACGTTCAAAATGCATTAATATTCCAACTTTTGATTAAAATGGGCTTTCAGCATGCCC
1 TGATACAAACATTCAAAATGCATCAATATTCCAA-TTCTGATTAAAA-GGGCTTTCAGCATGCCC
*
5019967 CAACATTTGC
64 CAATATTTGC
5019977 T
1 T
5019978 TCTTGTTGAT
Statistics
Matches: 123, Mismatches: 21, Indels: 13
0.78 0.13 0.08
Matches are distributed among these distances:
73 1 0.01
74 38 0.31
75 83 0.67
76 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.32
Consensus pattern (73 bp):
TGATACAAACATTCAAAATGCATCAATATTCCAATTCTGATTAAAAGGGCTTTCAGCATGCCCCA
ATATTTGC
Found at i:5026121 original size:13 final size:13
Alignment explanation
Indices: 5026103--5026127 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5026093 GATGATCTAA
5026103 TTTTTAAACAGTG
1 TTTTTAAACAGTG
5026116 TTTTTAAACAGT
1 TTTTTAAACAGT
5026128 TTCGTCAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.48
Consensus pattern (13 bp):
TTTTTAAACAGTG
Found at i:5030239 original size:34 final size:35
Alignment explanation
Indices: 5030196--5030264 Score: 131
Period size: 34 Copynumber: 2.0 Consensus size: 35
5030186 GGATCATATG
5030196 CACAACACAACATGTGCATAGC-TTTATATTTTGT
1 CACAACACAACATGTGCATAGCTTTTATATTTTGT
5030230 CACAACACAACATGTGCATAGCTTTTATATTTTGT
1 CACAACACAACATGTGCATAGCTTTTATATTTTGT
5030265 TGAGCTTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 22 0.65
35 12 0.35
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (35 bp):
CACAACACAACATGTGCATAGCTTTTATATTTTGT
Found at i:5032390 original size:37 final size:37
Alignment explanation
Indices: 5032340--5032413 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
5032330 CTGGTGAACA
5032340 AAGTAGTGAACTTCATTTCAGTCAATGATGGATGCAC
1 AAGTAGTGAACTTCATTTCAGTCAATGATGGATGCAC
5032377 AAGTAGTGAACTTCATTTCAGTCAATGATGGATGCAC
1 AAGTAGTGAACTTCATTTCAGTCAATGATGGATGCAC
5032414 TTGAGAAGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (37 bp):
AAGTAGTGAACTTCATTTCAGTCAATGATGGATGCAC
Found at i:5033474 original size:43 final size:44
Alignment explanation
Indices: 5033391--5033477 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 44
5033381 TTGTGCATCA
*
5033391 AACAAAACTTTTACATATAAGAGACAACTTTCAGTCCTAACTTC
1 AACAAAACTTTTACATATAAGAGACAACTTTCACTCCTAACTTC
* * * * *
5033435 AACAAAAC-TTTACATATAGGGGATAACTTTCCCTTCTAACTTC
1 AACAAAACTTTTACATATAAGAGACAACTTTCACTCCTAACTTC
5033478 TCTAAAGCCA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 29 0.78
44 8 0.22
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (44 bp):
AACAAAACTTTTACATATAAGAGACAACTTTCACTCCTAACTTC
Found at i:5034790 original size:2 final size:2
Alignment explanation
Indices: 5034736--5034771 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5034726 TTAATAAAAA
5034736 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5034772 AAAATAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5035297 original size:2 final size:2
Alignment explanation
Indices: 5035290--5035321 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5035280 AATTTTAAGA
5035290 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5035322 AATAAGATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5035331 original size:24 final size:23
Alignment explanation
Indices: 5035304--5035348 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
5035294 ATATATATAT
*
5035304 ATATATATATATATTATAAATAAG
1 ATATATATATAT-TTAGAAATAAG
* *
5035328 ATATTTATTTATTTAGAAATA
1 ATATATATATATTTAGAAATA
5035349 TCAGAAAAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 8 0.44
24 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (23 bp):
ATATATATATATTTAGAAATAAG
Found at i:5035424 original size:18 final size:18
Alignment explanation
Indices: 5035391--5035431 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
5035381 CTCATTTCTT
*
5035391 AATATTAAAAAATAAATA
1 AATATTAAAAAATAAACA
**
5035409 AATATTAAAATTTAAACA
1 AATATTAAAAAATAAACA
5035427 AATAT
1 AATAT
5035432 ATATATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
AATATTAAAAAATAAACA
Found at i:5036116 original size:13 final size:13
Alignment explanation
Indices: 5036100--5036124 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5036090 TTTCCGACGT
5036100 CGGCCACCATCGC
1 CGGCCACCATCGC
5036113 CGGCCACCATCG
1 CGGCCACCATCG
5036125 ACGGTGGCAA
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:0.16, C:0.52, G:0.24, T:0.08
Consensus pattern (13 bp):
CGGCCACCATCGC
Found at i:5036879 original size:3 final size:3
Alignment explanation
Indices: 5036871--5036957 Score: 65
Period size: 3 Copynumber: 30.0 Consensus size: 3
5036861 TTGTAATATG
* *
5036871 TAA TAA TAA TATT TAT TAA TAA TAA TAA -AA -AA T-A TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
5036914 TTA TAA TAA T-A TTA TAA CAA TTA TAA TAA TTA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5036958 AATGGGCCAA
Statistics
Matches: 67, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
2 8 0.12
3 57 0.85
4 2 0.03
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:5040408 original size:49 final size:47
Alignment explanation
Indices: 5040324--5040496 Score: 154
Period size: 49 Copynumber: 3.5 Consensus size: 47
5040314 AATAGAATAA
* *
5040324 AAATAAATAAATAAAAAATGAAGAAAATTTAAATTTT-AAAGGAAAT
1 AAATAAATAAATAAAAAAAGAAAAAAATTTAAATTTTAAAAGGAAAT
*
5040370 AAATAAATAAATAATAAAAAGAGCAAAAAATATTAATTTTTAAAAAGGAAA-
1 AAATAAATAAATAA-AAAAAGA--AAAAAAT-TTAAATTTT-AAAAGGAAAT
* * * *
5040421 AAATGAAA-AAATAAATAAAAGAAAGAAATGTTAAATTTTGAAAGTAAGT
1 AAAT-AAATAAATAAA-AAAAGAAAAAAAT-TTAAATTTTAAAAGGAAAT
* *
5040470 AAAAAAATAACAGAATAAAAAGAAAAA
1 AAATAAATAA-ATAA-AAAAAGAAAAA
5040497 GTAGAAAAGA
Statistics
Matches: 103, Mismatches: 12, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
46 14 0.14
47 6 0.06
48 9 0.09
49 25 0.24
50 21 0.20
51 17 0.17
52 11 0.11
ACGTcount: A:0.67, C:0.01, G:0.10, T:0.22
Consensus pattern (47 bp):
AAATAAATAAATAAAAAAAGAAAAAAATTTAAATTTTAAAAGGAAAT
Found at i:5040411 original size:50 final size:46
Alignment explanation
Indices: 5040324--5040496 Score: 143
Period size: 50 Copynumber: 3.5 Consensus size: 46
5040314 AATAGAATAA
* * *
5040324 AAATAAATAAATAAAAAATGAAGAAAATTTAAATTTTAAAGGAAAT
1 AAATAAATAAATAAAAAAAGAAAAAAATTTAATTTTTAAAGGAAAT
5040370 AAATAAATAAATAATAAAAAGAGCAAAAAATATTAATTTTTAAAAAGGAAA-
1 AAATAAATAAATAA-AAAAAGA--AAAAAAT-TTAATTTTT--AAAGGAAAT
* * * *
5040421 AAATGAAA-AAATAAATAAAAGAAAGAAATGTTAAATTTTGAAAGTAAGT
1 AAAT-AAATAAATAAA-AAAAGAAAAAAAT-TT-AATTTTTAAAGGAAAT
* *
5040470 AAAAAAATAACAGAATAAAAAGAAAAA
1 AAATAAATAA-ATAA-AAAAAGAAAAA
5040497 GTAGAAAAGA
Statistics
Matches: 103, Mismatches: 11, Indels: 22
0.76 0.08 0.16
Matches are distributed among these distances:
46 14 0.14
47 6 0.06
48 9 0.09
49 19 0.18
50 27 0.26
51 17 0.17
52 11 0.11
ACGTcount: A:0.67, C:0.01, G:0.10, T:0.22
Consensus pattern (46 bp):
AAATAAATAAATAAAAAAAGAAAAAAATTTAATTTTTAAAGGAAAT
Found at i:5041671 original size:6 final size:6
Alignment explanation
Indices: 5041662--5041713 Score: 65
Period size: 6 Copynumber: 9.0 Consensus size: 6
5041652 AACCAGGACC
*
5041662 AAATAA AAATAG AAATAA AAA-ATA AAATAA AAAT-A AAAT-A AAATAA
1 AAATAA AAATAA AAATAA AAATA-A AAATAA AAATAA AAATAA AAATAA
5041708 AAATAA
1 AAATAA
5041714 TTAATAATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
5 11 0.27
6 29 0.71
7 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:5041690 original size:5 final size:5
Alignment explanation
Indices: 5041680--5041709 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
5041670 ATAGAAATAA
5041680 AAAAT AAAAT AAAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT -AAAAT AAAAT AAAAT AAAA
5041710 ATAATTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:5041701 original size:16 final size:16
Alignment explanation
Indices: 5041680--5041713 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
5041670 ATAGAAATAA
5041680 AAAATAAAATAAAAAT
1 AAAATAAAATAAAAAT
5041696 AAAATAAAATAAAAAT
1 AAAATAAAATAAAAAT
5041712 AA
1 AA
5041714 TTAATAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAATAAAATAAAAAT
Found at i:5041713 original size:11 final size:11
Alignment explanation
Indices: 5041662--5041709 Score: 71
Period size: 11 Copynumber: 4.3 Consensus size: 11
5041652 AACCAGGACC
5041662 AAATAAAAATA
1 AAATAAAAATA
5041673 GAAATAAAAAATA
1 -AAAT-AAAAATA
5041686 AAATAAAAATA
1 AAATAAAAATA
5041697 AAAT-AAAATA
1 AAATAAAAATA
5041707 AAA
1 AAA
5041710 ATAATTAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.26
11 11 0.31
12 8 0.23
13 7 0.20
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:5041722 original size:16 final size:16
Alignment explanation
Indices: 5041687--5041746 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
5041677 TAAAAAATAA
*
5041687 AATAAAAATAAAATAA-
1 AATAAAAAT-AATTAAT
5041703 AATAAAAATAATTAAT
1 AATAAAAATAATTAAT
*
5041719 AATAAACCATAA-TAAT
1 AATAAA-AATAATTAAT
5041735 -ATAATAAATAAT
1 AATAA-AAATAAT
5041747 ATATATATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
15 13 0.35
16 20 0.54
17 4 0.11
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (16 bp):
AATAAAAATAATTAAT
Found at i:5041723 original size:3 final size:3
Alignment explanation
Indices: 5041682--5041803 Score: 62
Period size: 3 Copynumber: 40.3 Consensus size: 3
5041672 AGAAATAAAA
* *
5041682 AAT AA- AAT AAA AAT AA- AAT AA- AAT AAA AAT AATT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
*
5041724 ACCAT AAT AAT -AT AAT AAAT AAT ATAT ATAT TAT AAT AAT -AT AAT
1 A--AT AAT AAT AAT AAT -AAT AAT A-AT A-AT AAT AAT AAT AAT AAT
* *
5041769 AAAT AAT ATAT ATAT TAT AAT ACT -AT AAT -AT AAT A
1 -AAT AAT A-AT A-AT AAT AAT AAT AAT AAT AAT AAT A
5041804 TATGTACAAT
Statistics
Matches: 94, Mismatches: 10, Indels: 30
0.70 0.07 0.22
Matches are distributed among these distances:
2 14 0.15
3 57 0.61
4 22 0.23
5 1 0.01
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:5041754 original size:18 final size:16
Alignment explanation
Indices: 5041727--5041803 Score: 85
Period size: 14 Copynumber: 5.2 Consensus size: 16
5041717 ATAATAAACC
5041727 ATAATAATATAATA-A
1 ATAATAATATAATATA
*
5041742 ATAAT-ATAT-ATATT
1 ATAATAATATAATATA
5041756 ATAATAATATAATA-A
1 ATAATAATATAATATA
*
5041771 ATAAT-ATAT-ATATT
1 ATAATAATATAATATA
*
5041785 ATAATACTATAATATA
1 ATAATAATATAATATA
5041801 ATA
1 ATA
5041804 TATGTACAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
13 6 0.12
14 18 0.35
15 17 0.33
16 10 0.20
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (16 bp):
ATAATAATATAATATA
Found at i:5041768 original size:34 final size:34
Alignment explanation
Indices: 5041730--5041837 Score: 129
Period size: 34 Copynumber: 3.3 Consensus size: 34
5041720 ATAAACCATA
5041730 ATAATATAATAAATAATATATATA-T-T-ATA--
1 ATAATATAATAAATAATATATATATTATAATACT
5041759 ATAATATAATAAATAATATATATATTATAATACT
1 ATAATATAATAAATAATATATATATTATAATACT
* * * *
5041793 ATAATATAATATAT-GTACAATATATTATAGTACT
1 ATAATATAATAAATAATA-TATATATTATAATACT
5041827 ATAATATAATA
1 ATAATATAATA
5041838 TACATATAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
29 24 0.35
30 1 0.01
31 1 0.01
32 3 0.04
33 2 0.03
34 38 0.55
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.41
Consensus pattern (34 bp):
ATAATATAATAAATAATATATATATTATAATACT
Found at i:5041816 original size:29 final size:29
Alignment explanation
Indices: 5041727--5041806 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
5041717 ATAATAAACC
5041727 ATAATAATATAATAAATAATATATATATT
1 ATAATAATATAATAAATAATATATATATT
5041756 ATAATAATATAATAAATAATATATATATT
1 ATAATAATATAATAAATAATATATATATT
*
5041785 ATAATACTATAAT--ATAATATAT
1 ATAATAATATAATAAATAATATAT
5041807 GTACAATATA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
27 9 0.18
29 41 0.82
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (29 bp):
ATAATAATATAATAAATAATATATATATT
Found at i:5041844 original size:29 final size:29
Alignment explanation
Indices: 5041727--5041845 Score: 132
Period size: 29 Copynumber: 3.9 Consensus size: 29
5041717 ATAATAAACC
* *
5041727 ATAATAATATAATAAATAATATATATATT
1 ATAATACTATAATAAATAATACATATATT
* *
5041756 ATAATAATATAATAAATAATATATATATT
1 ATAATACTATAATAAATAATACATATATT
5041785 ATAATACTATAATATAATATATGTACAATATATT
1 ATAATACTATAATA-AATA-A--TAC-ATATATT
*
5041819 ATAGTACTATAATATAAT-ATACATATA
1 ATAATACTATAATA-AATAATACATATA
5041846 AATATTTTCA
Statistics
Matches: 82, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
29 47 0.57
30 7 0.09
31 1 0.01
32 1 0.01
33 2 0.02
34 24 0.29
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (29 bp):
ATAATACTATAATAAATAATACATATATT
Found at i:5041913 original size:2 final size:2
Alignment explanation
Indices: 5041906--5041937 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5041896 AACTATATTT
5041906 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5041938 TCAAAATGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5041923 original size:57 final size:58
Alignment explanation
Indices: 5041861--5041972 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 58
5041851 TTTCAAAAAC
* * *
5041861 TATATA-AAATA-TATATGTTTTCAAAATGTTTTC-AAAACTATATTTTATATATATA
1 TATATATAAATATTATATATATTCAAAATGTTTTCAAAAACTATATATTATATATATA
*
5041916 TATATATATATATTATATATATTCAAAATGTTTTCAAAAACTATATATTATATATAT
1 TATATATAAATATTATATATATTCAAAATGTTTTCAAAAACTATATATTATATATAT
5041973 GTTTTCAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
55 6 0.12
56 4 0.08
57 20 0.40
58 20 0.40
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (58 bp):
TATATATAAATATTATATATATTCAAAATGTTTTCAAAAACTATATATTATATATATA
Found at i:5041972 original size:39 final size:38
Alignment explanation
Indices: 5041922--5042133 Score: 271
Period size: 39 Copynumber: 5.7 Consensus size: 38
5041912 TATATATATA
5041922 TATATATTATATATA---TTCAAAATGTTTTCAAAAAC
1 TATATATTATATATATTTTTCAAAATGTTTTCAAAAAC
5041957 TATATATTATATATATGTTTTCAAAATGTTTTCAAAAAC
1 TATATATTATATATAT-TTTTCAAAATGTTTTCAAAAAC
5041996 TATATATTATGTATATATTTTT-AAAATGTTTTCAAAAAC
1 TATATATTA--TATATATTTTTCAAAATGTTTTCAAAAAC
* * *
5042035 TATATATTAAATATGTGTTTTCAAAATGTTTTTAAAAAC
1 TATATATTATATATAT-TTTTCAAAATGTTTTCAAAAAC
* *
5042074 TATATATTGTATATAGTTTTTCAAAATATTTTC----AC
1 TATATATTATATATA-TTTTTCAAAATGTTTTCAAAAAC
5042109 TATATATTATATATA-TTTTCAAAAT
1 TATATATTATATATATTTTTCAAAAT
5042134 CCGTTTTTAG
Statistics
Matches: 159, Mismatches: 9, Indels: 20
0.85 0.05 0.11
Matches are distributed among these distances:
33 10 0.06
35 31 0.19
37 5 0.03
38 4 0.03
39 97 0.61
40 5 0.03
41 7 0.04
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.48
Consensus pattern (38 bp):
TATATATTATATATATTTTTCAAAATGTTTTCAAAAAC
Found at i:5042502 original size:18 final size:18
Alignment explanation
Indices: 5042481--5042532 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 18
5042471 TATTAAATCA
5042481 AAATTAAATATTTTTTTT
1 AAATTAAATATTTTTTTT
* *
5042499 AAA-TAATTATATTTTTT
1 AAATTAAATATTTTTTTT
*
5042516 ACAATAATAATATTTTT
1 A-AATTA-AATATTTTT
5042533 ACCTCAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 13 0.50
18 5 0.19
19 1 0.04
20 7 0.27
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATTAAATATTTTTTTT
Found at i:5042534 original size:17 final size:18
Alignment explanation
Indices: 5042493--5042532 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
5042483 ATTAAATATT
*
5042493 TTTTTTA-AATAATTATA
1 TTTTTTACAATAATAATA
5042510 TTTTTTACAATAATAATA
1 TTTTTTACAATAATAATA
5042528 TTTTT
1 TTTTT
5042533 ACCTCAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTTTACAATAATAATA
Found at i:5042644 original size:3 final size:3
Alignment explanation
Indices: 5042636--5042671 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
5042626 CTCTTTGTAC
* *
5042636 ATT ATT ATT ATT ATT ACT ATT ACT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5042672 CTGAATAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:5043967 original size:18 final size:18
Alignment explanation
Indices: 5043940--5043978 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
5043930 TTGATACTTC
5043940 AATCACTTTAAAGTATAA
1 AATCACTTTAAAGTATAA
*
5043958 AATCATTTTAAAGTATAA
1 AATCACTTTAAAGTATAA
5043976 AAT
1 AAT
5043979 ATTATAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (18 bp):
AATCACTTTAAAGTATAA
Found at i:5051814 original size:54 final size:54
Alignment explanation
Indices: 5051731--5052075 Score: 528
Period size: 54 Copynumber: 6.4 Consensus size: 54
5051721 TTCTTTGAGA
* *
5051731 TGCACACGTAGTGCCTGTACGGTCATTCATCAACATATGATGAATTCCATGGGT
1 TGCACACTTAGTGCCTGTACGGTCATTCATCAACATATGATGAATTCCGTGGGT
* * *
5051785 TGCACACTTAGTGCCTGTACGGACGTTCATCAACATATGATGAATTTCGTGGGT
1 TGCACACTTAGTGCCTGTACGGTCATTCATCAACATATGATGAATTCCGTGGGT
* * *
5051839 TACACACTTAGTGCCTGTACGGCCATTCATCAACATATGATGAATTCCATGGGT
1 TGCACACTTAGTGCCTGTACGGTCATTCATCAACATATGATGAATTCCGTGGGT
* *
5051893 TGCACACTTAGTCCCTGTACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
1 TGCACACTTAGTGCCTGTACGGTCATTCATCAACATATGATGAATTCCGTGGGT
* *
5051947 TGCACACTTAGTGCATGTACGGTCATTCATCAACATATGATGAATTTCGTGGGT
1 TGCACACTTAGTGCCTGTACGGTCATTCATCAACATATGATGAATTCCGTGGGT
** * * *
5052001 TGCACACTTAGTGCCCATACGATCGTTCATCAACATATGATGAATTCTGTGGGT
1 TGCACACTTAGTGCCTGTACGGTCATTCATCAACATATGATGAATTCCGTGGGT
5052055 TGCACACTTAGTGCCTAGTAC
1 TGCACACTTAGTGCCT-GTAC
5052076 ACATAATACT
Statistics
Matches: 262, Mismatches: 28, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
54 259 0.99
55 3 0.01
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.31
Consensus pattern (54 bp):
TGCACACTTAGTGCCTGTACGGTCATTCATCAACATATGATGAATTCCGTGGGT
Found at i:5056190 original size:73 final size:73
Alignment explanation
Indices: 5056088--5056389 Score: 446
Period size: 72 Copynumber: 4.1 Consensus size: 73
5056078 TCCAAAAGCA
* * * * * * **
5056088 TAAATAAATAAAACGAATTTATATTCTAAACCACGAAAACAAACAATACAAAAATCACCATTTGG
1 TAAA-AAATAATACAAATTTACATACTAAACTATGAAAACAAACAATACCCAAATCACCATTTGG
*
5056153 GGTAAAAAC
65 AGTAAAAAC
5056162 TAAAAAATAATACAAATTTACATACTAAACTATGAAAACAAACAATACCCAAATCACCATTTGGA
1 TAAAAAATAATACAAATTTACATACTAAACTATGAAAACAAACAATACCCAAATCACCATTTGGA
*
5056227 GTAAAAGC
66 GTAAAAAC
* *
5056235 T-AAAAAGAATACAAATTTACATACTAAACTATGAAAACAAACAATACCCAAATCACCATTTGAA
1 TAAAAAATAATACAAATTTACATACTAAACTATGAAAACAAACAATACCCAAATCACCATTTGGA
5056299 GTAAAAAC
66 GTAAAAAC
* *
5056307 TAAAAAA-AATACAAATTTACATATTAAACTATGAAAACAAACAATACCCAAATCACGATTTGGA
1 TAAAAAATAATACAAATTTACATACTAAACTATGAAAACAAACAATACCCAAATCACCATTTGGA
5056371 GTAAAAAC
66 GTAAAAAC
5056379 TAAGAAAATAA
1 TAA-AAAATAA
5056390 GGGAAATTTG
Statistics
Matches: 209, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
72 134 0.64
73 69 0.33
74 6 0.03
ACGTcount: A:0.55, C:0.16, G:0.07, T:0.22
Consensus pattern (73 bp):
TAAAAAATAATACAAATTTACATACTAAACTATGAAAACAAACAATACCCAAATCACCATTTGGA
GTAAAAAC
Found at i:5060212 original size:15 final size:15
Alignment explanation
Indices: 5060186--5060235 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
5060176 GATATTTAGT
*
5060186 GGGCGGGCGGATGTG
1 GGGCGAGCGGATGTG
* *
5060201 GGGCGAGTGGATGCG
1 GGGCGAGCGGATGTG
* *
5060216 GGGTGGGCGGATGTG
1 GGGCGAGCGGATGTG
5060231 GGGCG
1 GGGCG
5060236 GGTAAGGTCT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.08, C:0.12, G:0.66, T:0.14
Consensus pattern (15 bp):
GGGCGAGCGGATGTG
Found at i:5067435 original size:16 final size:16
Alignment explanation
Indices: 5067410--5067440 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5067400 GCTTCTAAAT
*
5067410 TTTTTTGAGTTCAAGC
1 TTTTTCGAGTTCAAGC
5067426 TTTTTCGAGTTCAAG
1 TTTTTCGAGTTCAAG
5067441 TTTCAATATT
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:0.19, C:0.13, G:0.19, T:0.48
Consensus pattern (16 bp):
TTTTTCGAGTTCAAGC
Found at i:5068330 original size:30 final size:29
Alignment explanation
Indices: 5068271--5068331 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
5068261 TTTTTTAATT
* *
5068271 TTTCTAAAAAATTAATTAAGTCCTTAAAC
1 TTTCTAAAAAATCAATTAAGTCCTCAAAC
*
5068300 TTTCTAAAAGAATCAATTAGGTCAC-CAAAC
1 TTTCTAAAA-AATCAATTAAGTC-CTCAAAC
5068330 TT
1 TT
5068332 AGCCAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 9 0.33
30 17 0.63
31 1 0.04
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (29 bp):
TTTCTAAAAAATCAATTAAGTCCTCAAAC
Found at i:5069163 original size:11 final size:11
Alignment explanation
Indices: 5069136--5069172 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
5069126 TTTATCATTG
5069136 TCCCTCCT-TT
1 TCCCTCCTCTT
5069146 TCCCTCCTCTT
1 TCCCTCCTCTT
*
5069157 TCTCTCC-CTT
1 TCCCTCCTCTT
5069167 TCCCTC
1 TCCCTC
5069173 AAACCAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (11 bp):
TCCCTCCTCTT
Found at i:5072765 original size:80 final size:80
Alignment explanation
Indices: 5072662--5072917 Score: 395
Period size: 80 Copynumber: 3.2 Consensus size: 80
5072652 AGGATATATA
**
5072662 TTGGGTAGGGCCCAAGACATATCCTTAGGTTGGTTTCCTTTGCTGTGTGCATAAGGTAACCCTAC
1 TTGGGTA-GGCCCAAGGTATATCCTTAGGTTGGTTTCCTTTGCTGTGTGCATAAGGTAACCCTAC
5072727 GGATCTAAGGATACCC
65 GGATCTAAGGATACCC
*
5072743 TTGGGTAGGCCCAAGGTATATCCTTAGGTTGGTTTCCTTTGATGTGTGCATAAGGTAACCCTACG
1 TTGGGTAGGCCCAAGGTATATCCTTAGGTTGGTTTCCTTTGCTGTGTGCATAAGGTAACCCTACG
*
5072808 AATCTAAGGATACCC
66 GATCTAAGGATACCC
* * * *
5072823 TTGGGTAGACCAAAGGTATATCCTTAGGTTGGTTTCCTTTTTGCTGTGTTCTTAAGGTAACCCTA
1 TTGGGTAGGCCCAAGGTATATCCTTAGGTTGGTTTCC--TTTGCTGTGTGCATAAGGTAACCCTA
**
5072888 CGGATCTAAGGATATTC
64 CGGATCTAAGGATACCC
5072905 TTGGGTAGGCCCA
1 TTGGGTAGGCCCA
5072918 TAGGCCGCAA
Statistics
Matches: 159, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
80 104 0.65
81 7 0.04
82 48 0.30
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.32
Consensus pattern (80 bp):
TTGGGTAGGCCCAAGGTATATCCTTAGGTTGGTTTCCTTTGCTGTGTGCATAAGGTAACCCTACG
GATCTAAGGATACCC
Found at i:5075178 original size:31 final size:31
Alignment explanation
Indices: 5075143--5075208 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
5075133 GTTATAACCC
* *
5075143 GACCCGACCCGA-CCAATTTACCCGACCCGTT
1 GACCCGACCCAATCC-ATTGACCCGACCCGTT
*
5075174 GACCCGACCCAATCCATTGACCTGACCCGTT
1 GACCCGACCCAATCCATTGACCCGACCCGTT
5075205 GACC
1 GACC
5075209 GTTGACCGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.23, C:0.44, G:0.17, T:0.17
Consensus pattern (31 bp):
GACCCGACCCAATCCATTGACCCGACCCGTT
Found at i:5076984 original size:12 final size:12
Alignment explanation
Indices: 5076969--5077032 Score: 53
Period size: 12 Copynumber: 5.4 Consensus size: 12
5076959 TGTTATGATA
5076969 TCTGACCTGGAT
1 TCTGACCTGGAT
*
5076981 TCTGATCT-GAT
1 TCTGACCTGGAT
*
5076992 AT-TGACATGGAT
1 -TCTGACCTGGAT
*
5077004 TCTGATCT-GAT
1 TCTGACCTGGAT
*
5077015 ACATGACCTGGAT
1 TC-TGACCTGGAT
5077028 TCTGA
1 TCTGA
5077033 TATGATACTT
Statistics
Matches: 39, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
11 12 0.31
12 23 0.59
13 4 0.10
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (12 bp):
TCTGACCTGGAT
Found at i:5077040 original size:24 final size:24
Alignment explanation
Indices: 5076955--5077045 Score: 114
Period size: 24 Copynumber: 3.8 Consensus size: 24
5076945 TCTGATTTGA
*
5076955 ATTCTGTTATGATA-TCTGACCTGG
1 ATTCTGATATGATACT-TGACCTGG
* *
5076979 ATTCTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACTTGACCTGG
* *
5077002 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACTTGACCTGG
5077026 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
5077046 TTGAATTATG
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
23 21 0.36
24 38 0.64
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.38
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:5077170 original size:35 final size:35
Alignment explanation
Indices: 5077123--5077197 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
5077113 TGGAGGAAGA
* *
5077123 TTACTTGGAGGCTCCTCGGCTTTGTGCTCAAGGCC
1 TTACTTGCAGGCTCCTCGACTTTGTGCTCAAGGCC
*
5077158 TTACTTGCAGGCTCCTCGACTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGACTTTGTGCTCAAGGCC
5077193 TTACT
1 TTACT
5077198 GTACGTGACG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.12, C:0.29, G:0.25, T:0.33
Consensus pattern (35 bp):
TTACTTGCAGGCTCCTCGACTTTGTGCTCAAGGCC
Found at i:5078916 original size:18 final size:18
Alignment explanation
Indices: 5078893--5078931 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
5078883 ACCGGTCATA
5078893 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
5078911 ACCCGACCTGACCCGTTG
1 ACCCGACCCGACCCGTTG
5078929 ACC
1 ACC
5078932 ATTAACTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.18, C:0.49, G:0.21, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:5078944 original size:14 final size:14
Alignment explanation
Indices: 5078925--5078972 Score: 87
Period size: 14 Copynumber: 3.4 Consensus size: 14
5078915 GACCTGACCC
5078925 GTTGACCATTAACT
1 GTTGACCATTAACT
5078939 GTTGACCATTAACT
1 GTTGACCATTAACT
*
5078953 GTTGACCGTTAACT
1 GTTGACCATTAACT
5078967 GTTGAC
1 GTTGAC
5078973 AGTTGACCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (14 bp):
GTTGACCATTAACT
Found at i:5081384 original size:23 final size:24
Alignment explanation
Indices: 5081344--5081412 Score: 95
Period size: 23 Copynumber: 2.9 Consensus size: 24
5081334 TGAATTATGT
*
5081344 TATGATACCTGACCTGGATTCTGA
1 TATGATACATGACCTGGATTCTGA
* *
5081368 TATGATA-TTGACATGGATTCTGA
1 TATGATACATGACCTGGATTCTGA
*
5081391 TCTGATACATGACCTGGATTCT
1 TATGATACATGACCTGGATTCT
5081413 AATACTTGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 20 0.51
24 19 0.49
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.36
Consensus pattern (24 bp):
TATGATACATGACCTGGATTCTGA
Found at i:5081553 original size:35 final size:35
Alignment explanation
Indices: 5081495--5081569 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
5081485 TGGAGGAAGA
* *
5081495 TTACTTGGAGGCACATCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCACATCGACTTTGTGCTCAGGGCC
* *
5081530 TTACTTGCAGGCTCCTCGACTTTGTGCTCAGGGCC
1 TTACTTGCAGGCACATCGACTTTGTGCTCAGGGCC
5081565 TTACT
1 TTACT
5081570 GTACGTGACG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.13, C:0.28, G:0.27, T:0.32
Consensus pattern (35 bp):
TTACTTGCAGGCACATCGACTTTGTGCTCAGGGCC
Found at i:5091320 original size:86 final size:86
Alignment explanation
Indices: 5091213--5091508 Score: 310
Period size: 86 Copynumber: 3.4 Consensus size: 86
5091203 GAAATATTTG
*
5091213 TTGACCCAACTCCTT-TGTGATGGAATCGAGCGAAATATTTGTAGACCCAACTCATTCTGTGATG
1 TTGA-CCAACTCCTTCTGTGATGGAATCGAGCGAAATATTTGTAGACCCAACTCATTTTGTGATG
** *
5091277 GAATCGAGTTAAATATTGATGT
65 GAATCGAGCGAAATGTTGATGT
* * * * * **
5091299 TTGACCAACTCATTATGTGATGGAATCGAGCAAAATGTTTGTTGACCCAACTTTTTTTGTGATGG
1 TTGACCAACTCCTTCTGTGATGGAATCGAGCGAAATATTTGTAGACCCAACTCATTTTGTGATGG
*
5091364 AATCAAGCGAAATGTTGATG-
66 AATCGAGCGAAATGTTGATGT
** * * * * * * *
5091384 TTGTTCAACTCCTTCTATGATGGAATCGAACGAAATGTTGATGAAAACTCAAATCATTTTGTGAT
1 TTGACCAACTCCTTCTGTGATGGAATCGAGCGAAATATT--TGTAGACCCAACTCATTTTGTGAT
* *
5091449 GTAATCGAGCGAAATGTTGATAT
64 GGAATCGAGCGAAATGTTGATGT
* *
5091472 TT-AACATACTCCTTCTGTGATGGAATCGATCGAAATA
1 TTGACCA-ACTCCTTCTGTGATGGAATCGAGCGAAATA
5091509 CTGATATTTG
Statistics
Matches: 172, Mismatches: 33, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
85 41 0.24
86 64 0.37
87 38 0.22
88 29 0.17
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (86 bp):
TTGACCAACTCCTTCTGTGATGGAATCGAGCGAAATATTTGTAGACCCAACTCATTTTGTGATGG
AATCGAGCGAAATGTTGATGT
Found at i:5091322 original size:44 final size:41
Alignment explanation
Indices: 5091203--5091376 Score: 206
Period size: 42 Copynumber: 4.1 Consensus size: 41
5091193 GAAATCAAGT
*
5091203 GAAATATTTGTTGACCCAACTCCTTTGTGATGGAATCGAGC
1 GAAATATTTGTTGACCCAACTCATTTGTGATGGAATCGAGC
* *
5091244 GAAATATTTGTAGACCCAACTCATTCTGTGATGGAATCGAGT
1 GAAATATTTGTTGACCCAACTCATT-TGTGATGGAATCGAGC
*
5091286 TAAATATTGATGTTTGA-CCAACTCATTATGTGATGGAATCGAGC
1 GAAATATT--TG-TTGACCCAACTCATT-TGTGATGGAATCGAGC
* * ** *
5091330 AAAATGTTTGTTGACCCAACTTTTTTTGTGATGGAATCAAGC
1 GAAATATTTGTTGACCCAAC-TCATTTGTGATGGAATCGAGC
5091372 GAAAT
1 GAAAT
5091377 GTTGATGTTG
Statistics
Matches: 114, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
41 27 0.24
42 48 0.42
43 3 0.03
44 33 0.29
45 3 0.03
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (41 bp):
GAAATATTTGTTGACCCAACTCATTTGTGATGGAATCGAGC
Found at i:5091377 original size:42 final size:42
Alignment explanation
Indices: 5091203--5091463 Score: 215
Period size: 44 Copynumber: 6.1 Consensus size: 42
5091193 GAAATCAAGT
*
5091203 GAAATATTTGTTGACCCAACTC-CTTTGTGATGGAATCGAGC
1 GAAATATTTGTTGACCCAACTCATTTTGTGATGGAATCGAGC
* * *
5091244 GAAATATTTGTAGACCCAACTCATTCTGTGATGGAATCGAGT
1 GAAATATTTGTTGACCCAACTCATTTTGTGATGGAATCGAGC
* *
5091286 TAAATATTGATGTTTGA-CCAACTCATTATGTGATGGAATCGAGC
1 GAAATATT--TG-TTGACCCAACTCATTTTGTGATGGAATCGAGC
* * ** *
5091330 AAAATGTTTGTTGACCCAACTTTTTTTGTGATGGAATCAAGC
1 GAAATATTTGTTGACCCAACTCATTTTGTGATGGAATCGAGC
* ** * * * *
5091372 GAAATGTTGATGTTG-TTCAACTCCTTCTATGATGGAATCGAAC
1 GAAATATT--TGTTGACCCAACTCATTTTGTGATGGAATCGAGC
* * * * *
5091415 GAAAT-GTTGATGAAAACTCAAATCATTTTGTGATGTAATCGAGC
1 GAAATATTTGTTG---ACCCAACTCATTTTGTGATGGAATCGAGC
5091459 GAAAT
1 GAAAT
5091464 GTTGATATTT
Statistics
Matches: 177, Mismatches: 32, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
40 4 0.02
41 25 0.14
42 56 0.32
43 25 0.14
44 64 0.36
45 3 0.02
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (42 bp):
GAAATATTTGTTGACCCAACTCATTTTGTGATGGAATCGAGC
Found at i:5091441 original size:129 final size:127
Alignment explanation
Indices: 5091204--5091466 Score: 287
Period size: 129 Copynumber: 2.1 Consensus size: 127
5091194 AAATCAAGTG
* *
5091204 AAATATTTGTTGACCCAACTCCTTTGTGATGGAATCGAGCGAAATATTTGTAGACCCAACTCATT
1 AAATGTTTGTTGACCCAACTCCTTTGTGATGGAATCAAGCGAAATATTTGTAGACCCAACTCATT
* *** *** *
5091269 CTGTGATGGAATCGAGTTAAATATTGATGTTTGACCAACTCATTATGTGATGGAATCGAGCA
66 CTATGATGGAATCGAACGAAATATTGATGTAAAACCAAATCATTATGTGATGGAATCGAGCA
** * * **
5091331 AAATGTTTGTTGACCCAACTTTTTTTGTGATGGAATCAAGCGAAATGTTGATGTTG-TTCAACTC
1 AAATGTTTGTTGACCCAAC-TCCTTTGTGATGGAATCAAGCGAAATATT--TGTAGACCCAACTC
* * * *
5091395 CTTCTATGATGGAATCGAACGAAATGTTGATG-AAAACTCAAATCATTTTGTGATGTAATCGAGC
63 ATTCTATGATGGAATCGAACGAAATATTGATGTAAAAC-CAAATCATTATGTGATGGAATCGAGC
*
5091459 G
127 A
5091460 AAATGTT
1 AAATGTT
5091467 GATATTTAAC
Statistics
Matches: 111, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
127 18 0.16
128 27 0.24
129 62 0.56
130 4 0.04
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.34
Consensus pattern (127 bp):
AAATGTTTGTTGACCCAACTCCTTTGTGATGGAATCAAGCGAAATATTTGTAGACCCAACTCATT
CTATGATGGAATCGAACGAAATATTGATGTAAAACCAAATCATTATGTGATGGAATCGAGCA
Found at i:5091457 original size:173 final size:173
Alignment explanation
Indices: 5091219--5091545 Score: 385
Period size: 173 Copynumber: 1.9 Consensus size: 173
5091209 TTTGTTGACC
* * * * *
5091219 CAACTCCTTTGTGATGGAATCGAGCGAAATATTTGTAGACCCAACTCATTCTGTGATGGAATCGA
1 CAACTCCTTTATGATGGAATCGAACGAAATATTTGAAAACCCAAATCATTCTGTGATGGAATCGA
** * * *
5091284 GTTAAATATTGATGTTTGACCA-ACTCATTATGTGATGGAATCGAGC-AAA-A-TG-TTTGTTGA
66 GCGAAATATTGATATTT-AACATACTCATTATGTGATGGAATCGAGCGAAATACTGATAT-TTGA
* *
5091344 CCCAACTTTTTTTGTGATGGAATCAAGCGAAATGTTGATGTTGTT
129 CCCAACTATTTCTGTGATGGAATCAAGCGAAATGTTGATGTTGTT
* * * *
5091389 CAACTCCTTCTATGATGGAATCGAACGAAATGTTGATGAAAACTCAAATCATTTTGTGATGTAAT
1 CAACTCCTT-TATGATGGAATCGAACGAAATATT--TGAAAACCCAAATCATTCTGTGATGGAAT
* * * *
5091454 CGAGCGAAATGTTGATATTTAACATACTCCTTCTGTGATGGAATCGATCGAAATACTGATATTTG
63 CGAGCGAAATATTGATATTTAACATACTCATTATGTGATGGAATCGAGCGAAATACTGATATTTG
*
5091519 ACTCAACTATTTCTGTGATGGAATCAA
128 ACCCAACTATTTCTGTGATGGAATCAA
5091546 ATCTACAAAA
Statistics
Matches: 128, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
170 9 0.07
171 21 0.16
172 3 0.02
173 60 0.47
174 3 0.02
175 1 0.01
176 29 0.23
177 2 0.02
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (173 bp):
CAACTCCTTTATGATGGAATCGAACGAAATATTTGAAAACCCAAATCATTCTGTGATGGAATCGA
GCGAAATATTGATATTTAACATACTCATTATGTGATGGAATCGAGCGAAATACTGATATTTGACC
CAACTATTTCTGTGATGGAATCAAGCGAAATGTTGATGTTGTT
Found at i:5091491 original size:44 final size:44
Alignment explanation
Indices: 5091221--5091543 Score: 145
Period size: 44 Copynumber: 7.5 Consensus size: 44
5091211 TGTTGACCCA
* * *
5091221 ACTCCTT-TGTGATGGAATCGAGCGAAATATTTG-TA--GACCCA-
1 ACTCCTTCTGTGATGGAATCGAGCGAAAT-GTTGATATTTA-ACAT
* ** * * *
5091262 ACTCATTCTGTGATGGAATCGAGTTAAATATTGATGTTTGACCA-
1 ACTCCTTCTGTGATGGAATCGAGCGAAATGTTGATATTT-AACAT
* * * * * *
5091306 ACTCATTATGTGATGGAATCGAGCAAAATGTT--TGTTGACCCA-
1 ACTCCTTCTGTGATGGAATCGAGCGAAATGTTGATATTTA-ACAT
** * * * *
5091348 ACTTTTTTTGTGATGGAATCAAGCGAAATGTTGATGTTGT-TCA-
1 ACTCCTTCTGTGATGGAATCGAGCGAAATGTTGATATT-TAACAT
* * *
5091391 ACTCCTTCTATGATGGAATCGAACGAAATGTTGATGA--AAAC-T
1 ACTCCTTCTGTGATGGAATCGAGCGAAATGTTGAT-ATTTAACAT
* * * *
5091433 CAAATCATTTTGTGATGTAATCGAGCGAAATGTTGATATTTAACAT
1 --ACTCCTTCTGTGATGGAATCGAGCGAAATGTTGATATTTAACAT
* ** *
5091479 ACTCCTTCTGTGATGGAATCGATCGAAATACTGATATTTGAC-T
1 ACTCCTTCTGTGATGGAATCGAGCGAAATGTTGATATTTAACAT
**
5091522 CAACTATTTCTGTGATGGAATC
1 --ACTCCTTCTGTGATGGAATC
5091544 AAATCTACAA
Statistics
Matches: 219, Mismatches: 44, Indels: 34
0.74 0.15 0.11
Matches are distributed among these distances:
41 10 0.05
42 55 0.25
43 33 0.15
44 98 0.45
45 22 0.10
46 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.34
Consensus pattern (44 bp):
ACTCCTTCTGTGATGGAATCGAGCGAAATGTTGATATTTAACAT
Found at i:5091725 original size:20 final size:20
Alignment explanation
Indices: 5091696--5091762 Score: 125
Period size: 20 Copynumber: 3.4 Consensus size: 20
5091686 TGAACTTAGA
*
5091696 TCTTTGCCCACTTTTTGAAT
1 TCTTTTCCCACTTTTTGAAT
5091716 TCTTTTCCCACTTTTTGAAT
1 TCTTTTCCCACTTTTTGAAT
5091736 TCTTTTCCCACTTTTTGAAT
1 TCTTTTCCCACTTTTTGAAT
5091756 TCTTTTC
1 TCTTTTC
5091763 ACACAATATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.55
Consensus pattern (20 bp):
TCTTTTCCCACTTTTTGAAT
Found at i:5103592 original size:17 final size:17
Alignment explanation
Indices: 5103549--5103594 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
5103539 CAGATATTCG
5103549 ATCCGAAAA-TTCGGAT
1 ATCCGAAAATTTCGGAT
* *
5103565 ATCTG-AAATTTTGGAT
1 ATCCGAAAATTTCGGAT
5103581 ATCCGAAAATTTCG
1 ATCCGAAAATTTCG
5103595 AATCGGATTC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 3 0.12
16 14 0.58
17 7 0.29
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (17 bp):
ATCCGAAAATTTCGGAT
Found at i:5103879 original size:12 final size:12
Alignment explanation
Indices: 5103862--5103906 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
5103852 CGTATTTTAG
5103862 TATTTTATATAA
1 TATTTTATATAA
*
5103874 TATTTT-TATTAG
1 TATTTTATA-TAA
5103886 TATTTTATATAA
1 TATTTTATATAA
5103898 TATTATTAT
1 TATT-TTAT
5103907 TGTTATTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 2 0.07
12 20 0.71
13 6 0.21
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (12 bp):
TATTTTATATAA
Found at i:5103882 original size:13 final size:13
Alignment explanation
Indices: 5103864--5103906 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
5103854 TATTTTAGTA
5103864 TTTTATATAATAT
1 TTTTATATAATAT
*
5103877 TTTTAT-TAGTA-
1 TTTTATATAATAT
5103888 TTTTATATAATAT
1 TTTTATATAATAT
*
5103901 TATTAT
1 TTTTAT
5103907 TGTTATTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 6 0.24
12 8 0.32
13 11 0.44
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (13 bp):
TTTTATATAATAT
Found at i:5103890 original size:24 final size:24
Alignment explanation
Indices: 5103854--5103915 Score: 92
Period size: 24 Copynumber: 2.6 Consensus size: 24
5103844 ATTTCAATCG
5103854 TATT-TTAGTATTTTATATAATAT
1 TATTATTAGTATTTTATATAATAT
*
5103877 TTTTATTAGTATTTTATATAATAT
1 TATTATTAGTATTTTATATAATAT
5103901 TATTATT-GTTATTTT
1 TATTATTAG-TATTTT
5103916 CATTTTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
23 4 0.11
24 31 0.89
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.65
Consensus pattern (24 bp):
TATTATTAGTATTTTATATAATAT
Found at i:5107496 original size:17 final size:16
Alignment explanation
Indices: 5107462--5107503 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
5107452 TACATATATT
5107462 AAATATATTAAAACAA
1 AAATATATTAAAACAA
*
5107478 AAATTTATTAAAA-ATA
1 AAATATATTAAAACA-A
5107494 AAATATATTA
1 AAATATATTA
5107504 TTTTGTTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 1 0.04
16 22 0.96
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATATATTAAAACAA
Done.