Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002637.1 Hibiscus syriacus cultivar Beakdansim tig00005377_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: 3156206
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 14
Found at i:1760978 original size:24 final size:24
Alignment explanation
Indices: 1760946--1760994 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1760936 TGCACTCGCC
1760946 TGATATGTCTCACTAGCTAACCTT
1 TGATATGTCTCACTAGCTAACCTT
1760970 TGATATGTCTCACTAGCTAACCTT
1 TGATATGTCTCACTAGCTAACCTT
1760994 T
1 T
1760995 CTTAACGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.39
Consensus pattern (24 bp):
TGATATGTCTCACTAGCTAACCTT
Found at i:1761598 original size:10 final size:11
Alignment explanation
Indices: 1761573--1761605 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1761563 ACCTTAGCGA
1761573 AATTTTCCCAT
1 AATTTTCCCAT
1761584 AATTTTCCC-T
1 AATTTTCCCAT
*
1761594 AATTTTTCCAT
1 AATTTTCCCAT
1761605 A
1 A
1761606 GTGGTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.27, C:0.24, G:0.00, T:0.48
Consensus pattern (11 bp):
AATTTTCCCAT
Found at i:1764406 original size:16 final size:16
Alignment explanation
Indices: 1764360--1764407 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
1764350 AAAAATGAAT
*
1764360 TTTGAAAGTTAGAGTGA
1 TTTGAAAGTTA-AGTAA
1764377 -TT-AAAGTATAAGTAA
1 TTTGAAAGT-TAAGTAA
1764392 TTTGAAAGTTAAGTAA
1 TTTGAAAGTTAAGTAA
1764408 CTAAATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
15 9 0.33
16 13 0.48
17 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (16 bp):
TTTGAAAGTTAAGTAA
Found at i:1774786 original size:21 final size:21
Alignment explanation
Indices: 1774756--1774796 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1774746 CTGAGACCCT
*
1774756 AGTATTGATAATCCTATAATG
1 AGTATCGATAATCCTATAATG
* *
1774777 AGTATCGATACTCCTGTAAT
1 AGTATCGATAATCCTATAAT
1774797 AAAATTCCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (21 bp):
AGTATCGATAATCCTATAATG
Found at i:1786346 original size:4 final size:4
Alignment explanation
Indices: 1786337--1786365 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1786327 AGAAAGCTCC
1786337 TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT T
1786366 GCATTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:1788830 original size:26 final size:26
Alignment explanation
Indices: 1788800--1788865 Score: 66
Period size: 26 Copynumber: 2.5 Consensus size: 26
1788790 TGGATTCTCT
1788800 AAATAATTTTAATATAATT-TTATTTTTA
1 AAATAATTTTAATAT-ATTATTA--TTTA
*
1788828 ATATAA-TTT-ATATATTATTATTTA
1 AAATAATTTTAATATATTATTATTTA
*
1788852 AAATAATTTAAATA
1 AAATAATTTTAATA
1788866 AAAATATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
24 9 0.28
25 5 0.16
26 10 0.31
27 3 0.09
28 5 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
AAATAATTTTAATATATTATTATTTA
Found at i:1788894 original size:107 final size:103
Alignment explanation
Indices: 1788766--1788993 Score: 327
Period size: 107 Copynumber: 2.2 Consensus size: 103
1788756 TATTTTTAAG
*
1788766 TTAAA-TTATTTTTATTTTGTGATTTGGATTCTCTAAATAATTTTAATATAATTTTATTTTTAAT
1 TTAAACTTATTTTTATTTTGTGATTTGGATTCTCTAAATAATTTT-A-A-AATTTTATTTGTAAT
*
1788830 ATAATTTATATATTATTATTT-AAAATAATT-TAAATAAAAATA
63 ATAATTTAGATA-TATTATTTAAAAATAATTGT-AA-AAAAATA
*
1788872 TTAAACTTATTTTTATTTTGTGATTTGGATTCTCTAAATAATTTTAAAATTTTATTTGTAATCTA
1 TTAAACTTATTTTTATTTTGTGATTTGGATTCTCTAAATAATTTTAAAATTTTATTTGTAATATA
1788937 ATTTAGATATATTATTTAAAAATAATTGTAAAAAAATA
66 ATTTAGATATATTATTTAAAAATAATTGTAAAAAAATA
* **
1788975 TTGAACTCGTTTTTATTTT
1 TTAAACTTATTTTTATTTT
1788994 TAAGTCTTAC
Statistics
Matches: 113, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
103 31 0.27
104 35 0.31
105 2 0.02
106 6 0.05
107 39 0.35
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.53
Consensus pattern (103 bp):
TTAAACTTATTTTTATTTTGTGATTTGGATTCTCTAAATAATTTTAAAATTTTATTTGTAATATA
ATTTAGATATATTATTTAAAAATAATTGTAAAAAAATA
Found at i:1790597 original size:24 final size:24
Alignment explanation
Indices: 1790565--1790626 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
1790555 GAACAAACTC
* *
1790565 GTTTGTAAGCTCGTGTATGATCTT
1 GTTTATAAGCTCGTGTATGAGCTT
*
1790589 GTTTATAAGCTCATGTATGAGCTT
1 GTTTATAAGCTCGTGTATGAGCTT
1790613 GTTTATCAA-CTCGT
1 GTTTAT-AAGCTCGT
1790627 TTGTTCATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 31 0.94
25 2 0.06
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.44
Consensus pattern (24 bp):
GTTTATAAGCTCGTGTATGAGCTT
Found at i:1791655 original size:2 final size:2
Alignment explanation
Indices: 1791648--1791689 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1791638 ACATAACCCA
1791648 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1791690 CAGATTAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1793533 original size:2 final size:2
Alignment explanation
Indices: 1793520--1793555 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1793510 TTTTAAGAAA
1793520 AT AT AT -T A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1793556 TTGTAAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1795285 original size:3 final size:3
Alignment explanation
Indices: 1795279--1795346 Score: 84
Period size: 3 Copynumber: 23.0 Consensus size: 3
1795269 ATTATTTATT
* * *
1795279 TAA TAA TAA TAA TAT TAA TAA TAA TAA T-A TAT TAA TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1795326 TAA TAA TAA AAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
1795347 ATAGATGAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
2 2 0.04
3 52 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1795997 original size:22 final size:22
Alignment explanation
Indices: 1795969--1796023 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1795959 CATTATGAAT
*
1795969 TTCTTCTCCTTCTTCAGATGAG
1 TTCTTCTCATTCTTCAGATGAG
*
1795991 TTCTTCTCATTCTTCAGATTAG
1 TTCTTCTCATTCTTCAGATGAG
1796013 TTCTTCTCATT
1 TTCTTCTCATT
1796024 ATGAACTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.15, C:0.25, G:0.09, T:0.51
Consensus pattern (22 bp):
TTCTTCTCATTCTTCAGATGAG
Found at i:1796396 original size:22 final size:22
Alignment explanation
Indices: 1796341--1796398 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
1796331 AATAAAGCTT
* *
1796341 TCATATTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
1796363 TCATCTTTGAAGAGAGAATCTG
1 TCATCTTTGAAGAGAGAATCTA
1796385 TCATCTTTGAAGAG
1 TCATCTTTGAAGAG
1796399 TGTAGATGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:1804287 original size:14 final size:13
Alignment explanation
Indices: 1804268--1804306 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 13
1804258 CAAACATAAA
1804268 AAATGAAAAGATGC
1 AAATG-AAAGATGC
1804282 AAATGAAA-ATGC
1 AAATGAAAGATGC
1804294 AAATGCAAAGATG
1 AAATG-AAAGATG
1804307 TAAAATGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.39
13 6 0.26
14 8 0.35
ACGTcount: A:0.56, C:0.08, G:0.21, T:0.15
Consensus pattern (13 bp):
AAATGAAAGATGC
Found at i:1804320 original size:27 final size:26
Alignment explanation
Indices: 1804268--1804321 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
1804258 CAAACATAAA
*
1804268 AAATGAAAAGATGCAAATGAAAATGC
1 AAATGAAAAGATGAAAATGAAAATGC
* *
1804294 AAATGCAAAGATGTAAAATGTAAATGC
1 AAATGAAAAGATG-AAAATGAAAATGC
1804321 A
1 A
1804322 TGTATGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.56, C:0.07, G:0.19, T:0.19
Consensus pattern (26 bp):
AAATGAAAAGATGAAAATGAAAATGC
Found at i:1809117 original size:18 final size:19
Alignment explanation
Indices: 1809090--1809134 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1809080 TCGTAATCTT
*
1809090 AAATAGAATATATTTAT-TA
1 AAATA-AATAGATTTATATA
1809109 AAATAAATAGATTTATATA
1 AAATAAATAGATTTATATA
*
1809128 AATTAAA
1 AAATAAA
1809135 GTTTAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (19 bp):
AAATAAATAGATTTATATA
Found at i:1809481 original size:9 final size:9
Alignment explanation
Indices: 1809467--1809496 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
1809457 TAAAAATATC
1809467 ATATATTTT
1 ATATATTTT
1809476 ATATATTTTT
1 ATATA-TTTT
1809486 ATATATTTT
1 ATATATTTT
1809495 AT
1 AT
1809497 TAATTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
ATATATTTT
Found at i:1810761 original size:7 final size:7
Alignment explanation
Indices: 1810743--1810777 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
1810733 ATATAGTGTG
1810743 CTTGCCCA
1 CTTG-CCA
*
1810751 CTTGTCA
1 CTTGCCA
1810758 CTTGCCA
1 CTTGCCA
1810765 CTTGCCA
1 CTTGCCA
1810772 CTTGCC
1 CTTGCC
1810778 CACGGAAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 21 0.84
8 4 0.16
ACGTcount: A:0.11, C:0.43, G:0.14, T:0.31
Consensus pattern (7 bp):
CTTGCCA
Found at i:1810997 original size:5 final size:5
Alignment explanation
Indices: 1810987--1811162 Score: 352
Period size: 5 Copynumber: 35.2 Consensus size: 5
1810977 TGATTTAAGA
1810987 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1811037 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1811087 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1811137 ATTAT ATTAT ATTAT ATTAT ATTAT A
1 ATTAT ATTAT ATTAT ATTAT ATTAT A
1811163 ATCTCTTGTT
Statistics
Matches: 171, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 171 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:1816226 original size:29 final size:29
Alignment explanation
Indices: 1816165--1816226 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
1816155 TTAATAATTT
*
1816165 ATTATATATTATTAAAATAAAAGTATAAT
1 ATTATATATTATTAAAATAAAAGTATAAC
* *
1816194 ATTATATATTA-TAATAATATAATTATAAC
1 ATTATATATTATTAA-AATAAAAGTATAAC
1816223 ATTA
1 ATTA
1816227 GAAAATATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 3 0.10
29 26 0.90
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (29 bp):
ATTATATATTATTAAAATAAAAGTATAAC
Found at i:1816252 original size:21 final size:21
Alignment explanation
Indices: 1816181--1816266 Score: 70
Period size: 22 Copynumber: 4.0 Consensus size: 21
1816171 TATTATTAAA
1816181 ATAAAAGTATAATATTATATATT
1 ATAAAAGTATAATA-TA-ATATT
*
1816204 ATAATAA-TATAATTATAACATT
1 ATAA-AAGTATAA-TATAATATT
*
1816226 AGAAAA-TATAATATAATATT
1 ATAAAAGTATAATATAATATT
*
1816246 ATTAAAATTATCAATA-AATAT
1 A-TAAAAGTAT-AATATAATAT
1816267 ATTTTAATAA
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
20 9 0.17
21 11 0.20
22 15 0.28
23 15 0.28
24 4 0.07
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
ATAAAAGTATAATATAATATT
Found at i:1816321 original size:30 final size:28
Alignment explanation
Indices: 1816272--1816342 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 28
1816262 AATATATTTT
**
1816272 AATAATCAATATTTTTATTAAAATGATACTAA
1 AATAAT-AATATTACTATT-AAAT-ATA-TAA
1816304 AATAAT-ATATTACTATTAAATATATAA
1 AATAATAATATTACTATTAAATATATAA
1816331 AATAATAATATT
1 AATAATAATATT
1816343 TTGAGTGTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
27 9 0.25
28 8 0.22
29 4 0.11
30 9 0.25
32 6 0.17
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (28 bp):
AATAATAATATTACTATTAAATATATAA
Found at i:1817067 original size:23 final size:23
Alignment explanation
Indices: 1817000--1817098 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 23
1816990 AATTTTTTTA
*
1817000 TATTATT-AAAATAT-AT-TATT
1 TATTATTAAAAATATAATAAATT
1817020 TAATTATTAAAAATATAA-AAA--
1 T-ATTATTAAAAATATAATAAATT
1817041 TATTA-TAAAAATATATATAAATT
1 TATTATTAAAAATATA-ATAAATT
*
1817064 TATTATTTAAAATATAATAAATAAT
1 TATTATTAAAAATATAATAAAT--T
1817089 TATT-TTAAAA
1 TATTATTAAAA
1817099 TATTTTAATC
Statistics
Matches: 65, Mismatches: 3, Indels: 18
0.76 0.03 0.21
Matches are distributed among these distances:
19 10 0.15
20 6 0.09
21 10 0.15
22 7 0.11
23 13 0.20
24 14 0.22
25 5 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TATTATTAAAAATATAATAAATT
Found at i:1817076 original size:43 final size:42
Alignment explanation
Indices: 1816999--1817091 Score: 118
Period size: 41 Copynumber: 2.2 Consensus size: 42
1816989 GAATTTTTTT
*
1816999 ATATTATTAAAATATATTATTTAATTATTAAAAATATAA-AA
1 ATATTATAAAAATATATTATTTAATTATTAAAAATATAATAA
*
1817040 ATATTATAAAAATATATATAAATTT-ATTATTTAAAATATAATAA
1 ATATTATAAAAATATAT-T--ATTTAATTATTAAAAATATAATAA
1817084 ATAATTAT
1 AT-ATTAT
1817092 TTTAAAATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
41 16 0.36
42 1 0.02
43 15 0.33
44 8 0.18
45 5 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (42 bp):
ATATTATAAAAATATATTATTTAATTATTAAAAATATAATAA
Found at i:1817099 original size:23 final size:22
Alignment explanation
Indices: 1817001--1817101 Score: 93
Period size: 23 Copynumber: 4.6 Consensus size: 22
1816991 ATTTTTTTAT
* **
1817001 ATTA-TTAAAATATATTATTTA
1 ATTATTTAAAATATAATAAATA
*
1817022 ATTATTAAAAATATAA-AAAT-
1 ATTATTTAAAATATAATAAATA
* *
1817042 ATTA-TAAAAATATATATAAATTT
1 ATTATTTAAAATATA-ATAAA-TA
1817065 ATTATTTAAAATATAATAAATA
1 ATTATTTAAAATATAATAAATA
1817087 ATTATTTTAAAATAT
1 ATTA-TTTAAAATAT
1817102 TTTAATCGAA
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
19 10 0.15
20 5 0.07
21 9 0.13
22 15 0.22
23 19 0.28
24 9 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTATTTAAAATATAATAAATA
Found at i:1824143 original size:20 final size:20
Alignment explanation
Indices: 1824118--1824172 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
1824108 TTTCTAGTTA
* *
1824118 AACAATATCGATAATGTAAG
1 AACAATATCAATAATGCAAG
* *
1824138 AACAATATCAATACTGCATG
1 AACAATATCAATAATGCAAG
1824158 AACAATATCAATAAT
1 AACAATATCAATAAT
1824173 ATTCTTGCAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.51, C:0.15, G:0.09, T:0.25
Consensus pattern (20 bp):
AACAATATCAATAATGCAAG
Found at i:1832332 original size:14 final size:14
Alignment explanation
Indices: 1832300--1832346 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
1832290 AATAAGTATT
1832300 AAAATA-AAA-AAA
1 AAAATAGAAATAAA
1832312 AATAATAGAAATAAA
1 AA-AATAGAAATAAA
1832327 AAAATAGAAATAAA
1 AAAATAGAAATAAA
1832341 AGAAAT
1 A-AAAT
1832347 TATAAAGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.06
13 4 0.13
14 16 0.52
15 9 0.29
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (14 bp):
AAAATAGAAATAAA
Found at i:1833767 original size:106 final size:106
Alignment explanation
Indices: 1833582--1833787 Score: 322
Period size: 106 Copynumber: 1.9 Consensus size: 106
1833572 TGTATTGCTC
*
1833582 CGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGACTCTGGAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
** *
1833647 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTATCT
66 ACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTATCT
* * * *
1833688 CGAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
* *
1833753 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG
66 ACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTG
1833788 TTGTCTTAAG
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
106 90 1.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.33
Consensus pattern (106 bp):
CGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTATCT
Found at i:1835133 original size:16 final size:17
Alignment explanation
Indices: 1835112--1835149 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1835102 ACCCACCTTA
*
1835112 TTTTTTGTTCT-TTCTC
1 TTTTTTCTTCTGTTCTC
*
1835128 TTTTTTCTTTTGTTCTC
1 TTTTTTCTTCTGTTCTC
1835145 TTTTT
1 TTTTT
1835150 CAATTTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (17 bp):
TTTTTTCTTCTGTTCTC
Found at i:1845826 original size:2 final size:2
Alignment explanation
Indices: 1845819--1845851 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1845809 AGTTATATGA
1845819 AT AT AT AT AT AT 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
1845852 ATAACTTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1845922 original size:22 final size:22
Alignment explanation
Indices: 1845885--1845930 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
1845875 AAATAATAGT
*
1845885 AATAATAAGTATTAAAATAAAAA
1 AATAATAAGTAAT-AAATAAAAA
1845908 AATAAT-AGTAATAAATAAAAA
1 AATAATAAGTAATAAATAAAAA
1845929 AA
1 AA
1845931 CAGAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.50
22 5 0.23
23 6 0.27
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (22 bp):
AATAATAAGTAATAAATAAAAA
Found at i:1845929 original size:23 final size:23
Alignment explanation
Indices: 1845885--1845930 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
1845875 AAATAATAGT
* *
1845885 AATAATAAGTATTAAAATAAAAA
1 AATAATAAGTAATAAAAAAAAAA
*
1845908 AATAAT-AGTAATAAATAAAAAA
1 AATAATAAGTAATAAAAAAAAAA
1845930 A
1 A
1845931 CAGAAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (23 bp):
AATAATAAGTAATAAAAAAAAAA
Found at i:1845938 original size:18 final size:17
Alignment explanation
Indices: 1845899--1845941 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
1845889 ATAAGTATTA
* *
1845899 AAATAAAAAAATAATAG
1 AAATAAAAAAAAAACAG
*
1845916 TAATAAATAAAAAAACAG
1 AAATAAA-AAAAAAACAG
1845934 AAATAAAA
1 AAATAAAA
1845942 GAAATTATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (17 bp):
AAATAAAAAAAAAACAG
Found at i:1845979 original size:2 final size:2
Alignment explanation
Indices: 1845972--1846002 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1845962 AATCAAAGTA
1845972 AT AT AT AT AT 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 A
1846003 AAATAAACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1851051 original size:16 final size:18
Alignment explanation
Indices: 1851019--1851053 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1851009 ATATAAAAAC
1851019 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
1851037 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
1851053 A
1 A
1851054 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:1851111 original size:18 final size:18
Alignment explanation
Indices: 1851058--1851111 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
1851048 TAAATAAATG
1851058 AGTAAAATATATAA-AA-A
1 AGTAAAATA-ATAATAATA
**
1851075 AGTAAAAGCAT-ATATATA
1 AGTAAAATAATAATA-ATA
1851093 AGTAAAATAATAATAATA
1 AGTAAAATAATAATAATA
1851111 A
1 A
1851112 AAAAAAAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
15 1 0.03
16 3 0.10
17 8 0.28
18 14 0.48
19 3 0.10
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (18 bp):
AGTAAAATAATAATAATA
Found at i:1851213 original size:31 final size:32
Alignment explanation
Indices: 1851170--1851246 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 32
1851160 GGAAATATAT
* *
1851170 AAATATATATATATAATAACACTAATA-AAAA
1 AAATATACATATATAATAAAACTAATAGAAAA
* *
1851201 AAATATACATATATAATAAAATTAATAGAAAG
1 AAATATACATATATAATAAAACTAATAGAAAA
* *
1851233 TAATATGCATATAT
1 AAATATACATATAT
1851247 GACAAGAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 24 0.62
32 15 0.38
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.31
Consensus pattern (32 bp):
AAATATACATATATAATAAAACTAATAGAAAA
Found at i:1851682 original size:35 final size:35
Alignment explanation
Indices: 1851612--1851711 Score: 128
Period size: 35 Copynumber: 2.7 Consensus size: 35
1851602 GTGCTTGTGG
* *
1851612 ATCCTATCTTTAGGAGTTTAAACCATAGCAAAATTCT
1 ATCCTAT-TTTAGGAGTTGAATCC-TAGCAAAATTCT
*
1851649 ATCCTATTTTAGGAGTTGAATCCTAGCAGAATTCT
1 ATCCTATTTTAGGAGTTGAATCCTAGCAAAATTCT
*
1851684 ATCCTATTTTTGAGAGATTGAATCCTAG
1 ATCCTATTTTAG-GAG-TTGAATCCTAG
1851712 TAGGACGAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
35 22 0.39
36 17 0.30
37 18 0.32
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (35 bp):
ATCCTATTTTAGGAGTTGAATCCTAGCAAAATTCT
Found at i:1852472 original size:106 final size:105
Alignment explanation
Indices: 1852172--1852734 Score: 536
Period size: 109 Copynumber: 5.3 Consensus size: 105
1852162 AATATTGTTC
* * * *
1852172 CGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTCCGCTGCGAAGTTGAAATTGGCTCT-GAAATGGAAAATTGTTTGTTGACA
** * ** * * * *
1852237 GTCAGTCACCCCTTTGCTGTGAAGTTGAGCTTGTGCTGTCT
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * * * *
1852278 CGAGTCTAATATCCTTCGTTGTGAAGATGAAATTGACTCTG-AA-CG-AAA-T-CTTGTTGACAA
1 CGAGTCCAATATCCTCCGCTGCGAAGTTGAAATTGGCTCTGAAATGGAAAATTGTTTGTTGACAA
*
1852338 TCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * *
1852378 CGAGTCCAATATCCTTCGCTACGAAGTTGAAATTGGCTCTGAAATTTGAAAAATGTTTGTTGACA
1 CGAGTCCAATATCCTCCGCTGCGAAGTTGAAATTGGCTCTGAAA-TGGAAAATTGTTTGTTGACA
*
1852443 ACCAGCCGTCCCTTCGTTATGAAGTTGAACTTGTGTTGTCT
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * ** *
1852484 CGAGTGGCACGATATCCTCCGTCGTG-G-AGTTGAAA-TCGCGGATGAAACT-GAAAAGTTGTTC
1 CGAGT--C-CAATATCCTCCG-C-TGCGAAGTTGAAATTGGC-TCTGAAA-TGGAAAA-TTGTTT
*
1852545 ATTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
58 GTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * *
1852593 CGGGTAGCACGATATCCTCCGTCGTG-G-AGTTGAAATCGGCTCTGGAATTGGGAAATTGTTTGT
1 CGAGT--C-CAATATCCTCCG-C-TGCGAAGTTGAAATTGGCTCT-GAAATGGAAAATTGTTTGT
*
1852656 TGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
60 TGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
1852702 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
1 CGAGTCCAATATCCTCCGCTGCGAAGTTGAAAT
1852735 CGCGGATGGC
Statistics
Matches: 387, Mismatches: 52, Indels: 36
0.81 0.11 0.08
Matches are distributed among these distances:
100 77 0.20
101 3 0.01
102 3 0.01
103 2 0.01
104 6 0.02
105 4 0.01
106 106 0.27
107 1 0.00
108 9 0.02
109 164 0.42
110 11 0.03
111 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.33
Consensus pattern (105 bp):
CGAGTCCAATATCCTCCGCTGCGAAGTTGAAATTGGCTCTGAAATGGAAAATTGTTTGTTGACAA
CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:1853333 original size:33 final size:33
Alignment explanation
Indices: 1853296--1853361 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1853286 GTCTTGAAAG
*
1853296 AGATAGAAT-TTGTTTCAAGGGAAACGATCTCAA
1 AGATA-AATGTTGTTTCAAGAGAAACGATCTCAA
* *
1853329 AGATATATGTTGTTTCATGAGAAACGATCTCAA
1 AGATAAATGTTGTTTCAAGAGAAACGATCTCAA
1853362 GGGAAACAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 2 0.07
33 27 0.93
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (33 bp):
AGATAAATGTTGTTTCAAGAGAAACGATCTCAA
Found at i:1853452 original size:36 final size:36
Alignment explanation
Indices: 1853407--1853789 Score: 307
Period size: 36 Copynumber: 10.9 Consensus size: 36
1853397 GAAGATTTTG
* *
1853407 TGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
1853443 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * * *
1853480 AGTTCCAAAAGAAACTGTCTCAAGGGGGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * *
1853516 TGTTTCAA-AGAAAACATAT-T-----TA-A-ATATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
*
1853545 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
1853581 TATTTCAAGGGAAAATGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
1853617 TATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * *
1853654 TGTTTCAAGGGAAATTATCTCAAGAGAGACGAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATT
* * * * *
1853691 TATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATT
* *
1853719 ATGTTTTAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 -TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
1853756 TGTTTCAAGGGAAACTGTCTCAAGAGGGACAAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1853790 CTCTTCTAGT
Statistics
Matches: 279, Mismatches: 43, Indels: 50
0.75 0.12 0.13
Matches are distributed among these distances:
28 4 0.01
29 30 0.11
30 5 0.02
32 1 0.00
34 2 0.01
35 4 0.01
36 148 0.53
37 81 0.29
38 4 0.01
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:1853562 original size:102 final size:101
Alignment explanation
Indices: 1853441--1853624 Score: 269
Period size: 102 Copynumber: 1.8 Consensus size: 101
1853431 GGAGACAAAA
* *
1853441 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA-TTCCAAAAGAAAATGTCTCAAGAG
* * *
1853506 GGACGAAATTTGTTTCAAAGAAAACATATTTAAATAT
65 AGACAAAATTTATTTCAAAGAAAACATATTTAAATAT
* * * **
1853543 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAAATGTCTCAAGAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAAATGTCTCAAGAGA
1853608 GACAAAATTTATTTCAA
66 GACAAAATTTATTTCAA
1853625 GGGAAACTGT
Statistics
Matches: 72, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
101 34 0.47
102 38 0.53
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (101 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAAATGTCTCAAGAGA
GACAAAATTTATTTCAAAGAAAACATATTTAAATAT
Found at i:1853574 original size:138 final size:138
Alignment explanation
Indices: 1853407--1853661 Score: 377
Period size: 138 Copynumber: 1.8 Consensus size: 138
1853397 GAAGATTTTG
* * * *
1853407 TGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAAATGTCTCAAGAGAGA
* * *
1853472 CAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGGGACGAAA-TTTGTTTCAAAGAAAACATATT
66 CAAAACTTA-TTCCAAAAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAAGAAAACATATT
1853536 TAAATATTT
130 TAAATATTT
* *
1853545 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAAATGTCTCAAGAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAAATGTCTCAAGAGAGA
* * **
1853610 CAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAA
66 CAAAACTTATTCCAAAAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAA
1853662 GGGAAATTAT
Statistics
Matches: 103, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
137 26 0.25
138 77 0.75
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.27
Consensus pattern (138 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAAATGTCTCAAGAGAGA
CAAAACTTATTCCAAAAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAAGAAAACATATTT
AAATATTT
Found at i:1853839 original size:35 final size:35
Alignment explanation
Indices: 1853720--1853839 Score: 100
Period size: 35 Copynumber: 3.4 Consensus size: 35
1853710 TCAATGTTTA
*
1853720 TGTTTTAAGAGAAACTGTCTCAAGGGAGACAAAAT-T
1 TGTTTTAAGA-AAACTGTCTCAAGAGAGAC-AAATCT
* * * *
1853756 TGTTTCAAGGGAAACTGTCTCAAGAGGGACAAAAC-
1 TGTTTTAA-GAAAACTGTCTCAAGAGAGACAAATCT
* * * * *
1853791 TCTTCTAGTGAAAACGGTCTCAAGCGAGACAAATCT
1 TGTTTTA-AGAAAACTGTCTCAAGAGAGACAAATCT
1853827 TGTTTTAAGAAAA
1 TGTTTTAAGAAAA
1853840 ACAATCATGA
Statistics
Matches: 63, Mismatches: 17, Indels: 9
0.71 0.19 0.10
Matches are distributed among these distances:
35 33 0.52
36 29 0.46
37 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.26
Consensus pattern (35 bp):
TGTTTTAAGAAAACTGTCTCAAGAGAGACAAATCT
Found at i:1854298 original size:18 final size:18
Alignment explanation
Indices: 1854271--1854306 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1854261 TGTTGAATCC
*
1854271 CCAAAGATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
1854289 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
1854307 TTGATGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.33, G:0.08, T:0.17
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:1855313 original size:14 final size:16
Alignment explanation
Indices: 1855296--1855374 Score: 58
Period size: 17 Copynumber: 4.9 Consensus size: 16
1855286 TTTTTGTCCC
1855296 TTTC-TTTT-TTCTTT
1 TTTCTTTTTATTCTTT
1855310 TTTCTTTTTATTCTTTT
1 TTTCTTTTTATTC-TTT
1855327 TTTGCTTTTGT-TT-TTT
1 TTT-CTTTT-TATTCTTT
* *
1855343 GCTTCTTTTTTTTCTTT
1 -TTTCTTTTTATTCTTT
*
1855360 TTGCCTTTTTATTCT
1 TT-TCTTTTTATTCT
1855375 GATTGAATCT
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
14 4 0.08
15 5 0.10
16 14 0.27
17 21 0.40
18 7 0.13
19 1 0.02
ACGTcount: A:0.03, C:0.14, G:0.05, T:0.78
Consensus pattern (16 bp):
TTTCTTTTTATTCTTT
Found at i:1855323 original size:9 final size:8
Alignment explanation
Indices: 1855296--1855361 Score: 57
Period size: 9 Copynumber: 8.1 Consensus size: 8
1855286 TTTTTGTCCC
1855296 TTTC-TTT
1 TTTCTTTT
1855303 TTTC-TTT
1 TTTCTTTT
1855310 TTTCTTTT
1 TTTCTTTT
1855318 TATTCTTTT
1 T-TTCTTTT
1855327 TTTGCTTTT
1 TTT-CTTTT
*
1855336 GTTT-TTTG
1 -TTTCTTTT
*
1855344 CTTCTTTTT
1 TTTC-TTTT
1855353 TTTCTTTT
1 TTTCTTTT
1855361 T
1 T
1855362 GCCTTTTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
7 13 0.27
8 14 0.29
9 19 0.39
10 3 0.06
ACGTcount: A:0.02, C:0.12, G:0.05, T:0.82
Consensus pattern (8 bp):
TTTCTTTT
Found at i:1855334 original size:25 final size:24
Alignment explanation
Indices: 1855300--1855374 Score: 80
Period size: 25 Copynumber: 3.0 Consensus size: 24
1855290 TGTCCCTTTC
1855300 TTTTTTCTTTTTTCTTTTTATTCT
1 TTTTTTCTTTTTTCTTTTTATTCT
**
1855324 TTTTTTGCTTTTGTT-TTTTGCTTCTT
1 TTTTTT-CTTTT-TTCTTTTTATTC-T
*
1855350 TTTTTTCTTTTTGCCTTTTTATTCT
1 TTTTTTCTTTTT-TCTTTTTATTCT
1855375 GATTGAATCT
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
24 7 0.17
25 18 0.44
26 16 0.39
ACGTcount: A:0.03, C:0.13, G:0.05, T:0.79
Consensus pattern (24 bp):
TTTTTTCTTTTTTCTTTTTATTCT
Found at i:1858593 original size:16 final size:18
Alignment explanation
Indices: 1858561--1858595 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1858551 ATATAAAAAC
1858561 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
1858579 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
1858595 A
1 A
1858596 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:1858631 original size:20 final size:20
Alignment explanation
Indices: 1858606--1858643 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1858596 AATGAGTAAA
1858606 ATATATAAAAAAGTAAAAGC
1 ATATATAAAAAAGTAAAAGC
* *
1858626 ATATATATATAAGTAAAA
1 ATATATAAAAAAGTAAAA
1858644 TAATAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (20 bp):
ATATATAAAAAAGTAAAAGC
Found at i:1858755 original size:31 final size:32
Alignment explanation
Indices: 1858712--1858788 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 32
1858702 GGAAATATAT
* *
1858712 AAATATATATATATAATAACACTAATA-AAAA
1 AAATATACATATATAATAAAACTAATAGAAAA
* *
1858743 AAATATACATATATAATAAAATTAATAGAAAG
1 AAATATACATATATAATAAAACTAATAGAAAA
* *
1858775 TAATATGCATATAT
1 AAATATACATATAT
1858789 GACAAGAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 24 0.62
32 15 0.38
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.31
Consensus pattern (32 bp):
AAATATACATATATAATAAAACTAATAGAAAA
Found at i:1859224 original size:35 final size:37
Alignment explanation
Indices: 1859162--1859253 Score: 109
Period size: 35 Copynumber: 2.6 Consensus size: 37
1859152 GGATCCTATC
* * *
1859162 TTTAG-GAGTTTAAAACATAGCAAAATTCTATCATAT
1 TTTAGAGAGTTTGAATCCTAGCAAAATTCTATCATAT
* *
1859198 TTTAG-GAG-TTGAATCCTAGCAGAATTCTATCCTAT
1 TTTAGAGAGTTTGAATCCTAGCAAAATTCTATCATAT
*
1859233 TTTTGAGAGTTTGAATCCTAG
1 TTTAGAGAGTTTGAATCCTAG
1859254 TAGGACGAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
35 26 0.54
36 11 0.23
37 11 0.23
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (37 bp):
TTTAGAGAGTTTGAATCCTAGCAAAATTCTATCATAT
Found at i:1863017 original size:155 final size:156
Alignment explanation
Indices: 1862696--1863015 Score: 486
Period size: 155 Copynumber: 2.1 Consensus size: 156
1862686 CTCCACCTGC
* *
1862696 GGCAAAAAATAGAATGACCAAAATAACAAAGATTAAAACTAGAATACAGATGAGTTCAGAAGGGT
1 GGCAAAAAATAAAAGGACCAAAATAACAAAGATTAAAACTAGAATACA-ATGAGTTCAGAAGGGT
* * * *
1862761 GACAATGCACCAAAAATATTTTCTAGGAGGCATTGACAAGATCTAGACCTTAAGCTCCAATCTTT
65 GACAACGCACCAAAAATATTTTCTAGGAGGCATCGAAAAGATCTAGACCTCAAGCTCCAATCTTT
1862826 TTCAATAAAATTATTAGTTCCTTGAGA
130 TTCAATAAAATTATTAGTTCCTTGAGA
*
1862853 GGCAAAAAATAAAAGGACCAAAATAGA-AAAGATTAAAACTAGAATGC-ATGAGTTCAGAAGGGT
1 GGCAAAAAATAAAAGGACCAAAATA-ACAAAGATTAAAACTAGAATACAATGAGTTCAGAAGGGT
* * *
1862916 GACTACGCACCAAAAATATTTTCTAGGAGGCATCGAAAAGATCTAGACCTCAAGCTCC-GTTTTT
65 GACAACGCACCAAAAATATTTTCTAGGAGGCATCGAAAAGATCTAGACCTCAAGCTCCAATCTTT
*
1862980 TTTAATAAAATTATTAGTTCCTT-AGGA
130 TTCAATAAAATTATTAGTTCCTTGA-GA
1863007 GGCAAAAAA
1 GGCAAAAAA
1863016 ATTCCAGAAT
Statistics
Matches: 150, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
153 1 0.01
154 37 0.25
155 69 0.46
157 42 0.28
158 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (156 bp):
GGCAAAAAATAAAAGGACCAAAATAACAAAGATTAAAACTAGAATACAATGAGTTCAGAAGGGTG
ACAACGCACCAAAAATATTTTCTAGGAGGCATCGAAAAGATCTAGACCTCAAGCTCCAATCTTTT
TCAATAAAATTATTAGTTCCTTGAGA
Found at i:1870676 original size:18 final size:18
Alignment explanation
Indices: 1870653--1870695 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
1870643 CTTTAGATTA
*
1870653 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
1870671 TTTATTTAATTATTATCT
1 TTTATTTAATTATTATCT
1870689 TTTATTT
1 TTTATTT
1870696 TAAAAACAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:1870793 original size:29 final size:28
Alignment explanation
Indices: 1870756--1870810 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 28
1870746 TTTTATTTAA
1870756 CACTTTTTTTGT-TTTAT-TTTTATTTTCC
1 CACTTTTTTT-TATTT-TGTTTTATTTTCC
1870784 CACTTCTTTTTTATTTTGTTTTATTTT
1 CACTT-TTTTTTATTTTGTTTTATTTT
1870811 TATTTTCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.11, C:0.13, G:0.04, T:0.73
Consensus pattern (28 bp):
CACTTTTTTTTATTTTGTTTTATTTTCC
Found at i:1870822 original size:30 final size:33
Alignment explanation
Indices: 1870762--1870845 Score: 86
Period size: 35 Copynumber: 2.5 Consensus size: 33
1870752 TTAACACTTT
**
1870762 TTTTGTTTTATTTTTATTTTCCCACTTCTTTT-TTA
1 TTTTGTTTTATTTTTATTTT--C-CTTCTTTTAACA
1870797 TTTTGTTTTATTTTTATTTT-C-TCTTTTAACA
1 TTTTGTTTTATTTTTATTTTCCTTCTTTTAACA
1870828 TTTT-TTTTATATTTTATT
1 TTTTGTTTTAT-TTTTATT
1870846 ATTTTTCTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
30 12 0.27
31 13 0.29
35 20 0.44
ACGTcount: A:0.14, C:0.10, G:0.02, T:0.74
Consensus pattern (33 bp):
TTTTGTTTTATTTTTATTTTCCTTCTTTTAACA
Found at i:1877653 original size:35 final size:36
Alignment explanation
Indices: 1877584--1877655 Score: 110
Period size: 35 Copynumber: 2.0 Consensus size: 36
1877574 ATTTTTATTA
* *
1877584 TTTCTTTTGAACTCAATTTTTTTTTCATTTAGTACT
1 TTTCTTTTGAACTCAATTTTTCTTTCATTCAGTACT
*
1877620 TTTCTTTTGAATTCAA-TTTTCTTTCATTCAGTACT
1 TTTCTTTTGAACTCAATTTTTCTTTCATTCAGTACT
1877655 T
1 T
1877656 CGTTTTATCC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 18 0.55
36 15 0.45
ACGTcount: A:0.19, C:0.15, G:0.06, T:0.60
Consensus pattern (36 bp):
TTTCTTTTGAACTCAATTTTTCTTTCATTCAGTACT
Found at i:1881069 original size:2 final size:2
Alignment explanation
Indices: 1881062--1881088 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1881052 CATTTTGAAA
1881062 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1881089 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1881840 original size:18 final size:19
Alignment explanation
Indices: 1881817--1881853 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
1881807 CTACGTTTAT
1881817 TTTTCAAAATCAAA-ATAG
1 TTTTCAAAATCAAAGATAG
1881835 TTTTCAAAATCAAAGATAG
1 TTTTCAAAATCAAAGATAG
1881854 ACTTTGGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (19 bp):
TTTTCAAAATCAAAGATAG
Found at i:1883376 original size:18 final size:18
Alignment explanation
Indices: 1883353--1883393 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1883343 ACACATTTGA
*
1883353 TCCTCTGGTCGTGCTTGT
1 TCCTCTGGTCGAGCTTGT
*
1883371 TCCTCTGGTGGAGCTTGT
1 TCCTCTGGTCGAGCTTGT
1883389 TCCTC
1 TCCTC
1883394 GTGCTGTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.02, C:0.29, G:0.27, T:0.41
Consensus pattern (18 bp):
TCCTCTGGTCGAGCTTGT
Found at i:1902946 original size:32 final size:32
Alignment explanation
Indices: 1902874--1902952 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 32
1902864 TGGGTGACGA
1902874 ATGGTGCTCCATGCGTTTTGCATGGGTAACAC
1 ATGGTGCTCCATGCGTTTTGCATGGGTAACAC
**** **
1902906 GCCATGCTCCATGCGTTTTGCATGGGTGTCAC
1 ATGGTGCTCCATGCGTTTTGCATGGGTAACAC
*
1902938 ATGGTGCTCAATGCG
1 ATGGTGCTCCATGCG
1902953 AGATAAGGGT
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.30
Consensus pattern (32 bp):
ATGGTGCTCCATGCGTTTTGCATGGGTAACAC
Found at i:1904329 original size:20 final size:20
Alignment explanation
Indices: 1904301--1904351 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1904291 TTTTATCACA
*
1904301 TCAAATTCTCTCAATTTCTC
1 TCAAATTCTCTCAACTTCTC
*
1904321 TCAATTTCTCTCAACTTCTC
1 TCAAATTCTCTCAACTTCTC
*
1904341 TCAAATACTCT
1 TCAAATTCTCT
1904352 TATATTCTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.43
Consensus pattern (20 bp):
TCAAATTCTCTCAACTTCTC
Found at i:1904332 original size:12 final size:10
Alignment explanation
Indices: 1904301--1904344 Score: 70
Period size: 10 Copynumber: 4.4 Consensus size: 10
1904291 TTTTATCACA
*
1904301 TCAAATTCTC
1 TCAATTTCTC
1904311 TCAATTTCTC
1 TCAATTTCTC
1904321 TCAATTTCTC
1 TCAATTTCTC
*
1904331 TCAACTTCTC
1 TCAATTTCTC
1904341 TCAA
1 TCAA
1904345 ATACTCTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.25, C:0.32, G:0.00, T:0.43
Consensus pattern (10 bp):
TCAATTTCTC
Found at i:1904351 original size:10 final size:10
Alignment explanation
Indices: 1904301--1904361 Score: 68
Period size: 10 Copynumber: 6.1 Consensus size: 10
1904291 TTTTATCACA
1904301 TCAAATTCTC
1 TCAAATTCTC
*
1904311 TCAATTTCTC
1 TCAAATTCTC
*
1904321 TCAATTTCTC
1 TCAAATTCTC
*
1904331 TCAACTTCTC
1 TCAAATTCTC
*
1904341 TCAAATACTC
1 TCAAATTCTC
* *
1904351 TTATATTCTC
1 TCAAATTCTC
1904361 T
1 T
1904362 GTTTAATATA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 44 1.00
ACGTcount: A:0.25, C:0.30, G:0.00, T:0.46
Consensus pattern (10 bp):
TCAAATTCTC
Found at i:1906496 original size:12 final size:12
Alignment explanation
Indices: 1906479--1906503 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1906469 ACCTACTCAG
1906479 GACGACGACGAT
1 GACGACGACGAT
1906491 GACGACGACGAT
1 GACGACGACGAT
1906503 G
1 G
1906504 GTGATGATGA
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:0.32, C:0.24, G:0.36, T:0.08
Consensus pattern (12 bp):
GACGACGACGAT
Found at i:1906776 original size:35 final size:33
Alignment explanation
Indices: 1906737--1906821 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
1906727 GTATTTCAGT
1906737 TAATTTTGTT-TATTACCATTTAATATCGGTTATTG
1 TAATTTTGTTATATTACCATTTAATA-C--TTATTG
*
1906772 TAATTTGGTTATCATTTACCATTTAATACTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATACTTATTG
* *
1906807 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
1906822 TAAAATTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 2 0.05
38 13 0.30
ACGTcount: A:0.26, C:0.08, G:0.12, T:0.54
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATACTTATTG
Found at i:1910378 original size:49 final size:50
Alignment explanation
Indices: 1910315--1910424 Score: 145
Period size: 51 Copynumber: 2.2 Consensus size: 50
1910305 GATACCTACA
* *
1910315 TCGCGCCT-TATATAATTATATCAG-TTAAAGGTATGGCGCGGCCCCTGCC
1 TCGCG-CTATATATAATTATATCAGATTAAAGGTAAGGCGCAGCCCCTGCC
*
1910364 -CTGCGCTATATATAATTATGTCAGAATTAAAGGTAAGGCGCAGCCCCTGCC
1 TC-GCGCTATATATAATTATATCAG-ATTAAAGGTAAGGCGCAGCCCCTGCC
1910415 TCGCGCTATA
1 TCGCGCTATA
1910425 CCCCTACGTG
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
48 3 0.06
49 18 0.34
51 31 0.58
52 1 0.02
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.27
Consensus pattern (50 bp):
TCGCGCTATATATAATTATATCAGATTAAAGGTAAGGCGCAGCCCCTGCC
Found at i:1910824 original size:35 final size:36
Alignment explanation
Indices: 1910757--1910841 Score: 120
Period size: 35 Copynumber: 2.4 Consensus size: 36
1910747 ATGATATTAA
*
1910757 TAATAATAAGTCATATCATCTTATGAATAAATATTT
1 TAATAATAAGTCATATCATCTTATGAATAAATATGT
* *
1910793 TAATAATAATTTATAT-AT-TTGATGAATAAATATGT
1 TAATAATAAGTCATATCATCTT-ATGAATAAATATGT
1910828 TAATAATAAGTCAT
1 TAATAATAAGTCAT
1910842 GTCCCTTAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
34 2 0.05
35 27 0.63
36 14 0.33
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (36 bp):
TAATAATAAGTCATATCATCTTATGAATAAATATGT
Found at i:1927041 original size:111 final size:111
Alignment explanation
Indices: 1926902--1927126 Score: 432
Period size: 111 Copynumber: 2.0 Consensus size: 111
1926892 AAAATAAATA
*
1926902 ACAATATACAAAACAACCATCCATTAAAATAAAACTTAAGTATCCATAAGGAACTCTGACCAAAT
1 ACAACATACAAAACAACCATCCATTAAAATAAAACTTAAGTATCCATAAGGAACTCTGACCAAAT
*
1926967 AAGACTAGTTCATGGTGGGTTCAAATATTCCAAAAAACAAGGCATG
66 AAGACTAGTTCATGGTGGGTTCAAATAGTCCAAAAAACAAGGCATG
1927013 ACAACATACAAAACAACCATCCATTAAAATAAAACTTAAGTATCCATAAGGAACTCTGACCAAAT
1 ACAACATACAAAACAACCATCCATTAAAATAAAACTTAAGTATCCATAAGGAACTCTGACCAAAT
1927078 AAGACTAGTTCATGGTGGGTTCAAATAGTCCAAAAAACAAGGCATG
66 AAGACTAGTTCATGGTGGGTTCAAATAGTCCAAAAAACAAGGCATG
1927124 ACA
1 ACA
1927127 TTAATCTGTT
Statistics
Matches: 112, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 112 1.00
ACGTcount: A:0.46, C:0.20, G:0.13, T:0.21
Consensus pattern (111 bp):
ACAACATACAAAACAACCATCCATTAAAATAAAACTTAAGTATCCATAAGGAACTCTGACCAAAT
AAGACTAGTTCATGGTGGGTTCAAATAGTCCAAAAAACAAGGCATG
Found at i:1928449 original size:19 final size:19
Alignment explanation
Indices: 1928376--1928450 Score: 84
Period size: 18 Copynumber: 4.0 Consensus size: 19
1928366 TGAATTTGAG
1928376 AATGAGTATGAATCT-AAA
1 AATGAGTATGAATCTGAAA
*
1928394 AATGAGTATAAATCT-AAA
1 AATGAGTATGAATCTGAAA
* *
1928412 AATGAGTTATGGATATGAAA
1 AATGAG-TATGAATCTGAAA
1928432 AA-GAGATATGAATCTGAAA
1 AATGAG-TATGAATCTGAAA
1928451 TGTGAAAGTA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
18 23 0.48
19 20 0.42
20 5 0.10
ACGTcount: A:0.51, C:0.04, G:0.19, T:0.27
Consensus pattern (19 bp):
AATGAGTATGAATCTGAAA
Found at i:1936560 original size:23 final size:22
Alignment explanation
Indices: 1936534--1936576 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1936524 ACTATAGGGC
* *
1936534 GATTCTAGCTTGAATTTCAACTT
1 GATTCAAGCATGAA-TTCAACTT
1936557 GATTCAAGCATGAATTCAAC
1 GATTCAAGCATGAATTCAAC
1936577 CTCTATTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (22 bp):
GATTCAAGCATGAATTCAACTT
Found at i:1938766 original size:235 final size:234
Alignment explanation
Indices: 1938356--1938828 Score: 732
Period size: 235 Copynumber: 2.0 Consensus size: 234
1938346 TCTATCCCTC
* *
1938356 CAAACTATCGCTAATGACGAACAACAACATCTCTTCCACTGTCACCAAAAAAGACTATAATCCAA
1 CAAACTATCACTAATGACGAACAACAACATCCCTTCCACTGTCACCAAAAAAGACTATAATCCAA
* ** *
1938421 ACCCTAACATGCGCCCAATGGACTCAATGGCATGCCAATTGTATCCAAAGTAACTTGACTTCGAA
66 ACCCTAACATGAGCCCAATAAACTCAATGGCATGCCAATTGTATCCAAAGTAACTTGACATCGAA
* * *
1938486 GGTTGTATTCATTTTAGCTTGACACATATGAAATTTATCTTAACATAGTTGAGCCTTAGCTCCTT
131 GGGTATATTCATTTTAGCTTGACACATATGAAACTTATCTTAACATAGTTGAGCCTTAGCTCCTT
*
1938551 ATCATGTCATAACTTACATTCATATTGCAACATTTCTTA
196 ATCATGTCATAACTTACATTCATATTGCAACATTGCTTA
* * * *
1938590 CAAACTATCACTAGTGACGAACACCAACATCCCTTCTACTGTCGCCAAAAAAGGA-TCATAATCC
1 CAAACTATCACTAATGACGAACAACAACATCCCTTCCACTGTCACCAAAAAA-GACT-ATAATCC
* * **
1938654 AAACCCTAACATGAGCCTAATAAACTCTATGGCATGCCAATTGTATTTAAAGTAACTTGACATCG
64 AAACCCTAACATGAGCCCAATAAACTCAATGGCATGCCAATTGTATCCAAAGTAACTTGACATCG
* * *
1938719 ATGGGTATATTCATTTTAGCTTGACACATATGAAACTTATCTTAACATAGTTTAGCCTTATCTCC
129 AAGGGTATATTCATTTTAGCTTGACACATATGAAACTTATCTTAACATAGTTGAGCCTTAGCTCC
1938784 TTATCATGTCATAACTTACATTCATATTGCAACATTGCTTA
194 TTATCATGTCATAACTTACATTCATATTGCAACATTGCTTA
1938825 CAAA
1 CAAA
1938829 GATGATTTTG
Statistics
Matches: 216, Mismatches: 21, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
234 47 0.22
235 169 0.78
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.31
Consensus pattern (234 bp):
CAAACTATCACTAATGACGAACAACAACATCCCTTCCACTGTCACCAAAAAAGACTATAATCCAA
ACCCTAACATGAGCCCAATAAACTCAATGGCATGCCAATTGTATCCAAAGTAACTTGACATCGAA
GGGTATATTCATTTTAGCTTGACACATATGAAACTTATCTTAACATAGTTGAGCCTTAGCTCCTT
ATCATGTCATAACTTACATTCATATTGCAACATTGCTTA
Found at i:1946685 original size:13 final size:13
Alignment explanation
Indices: 1946664--1946720 Score: 69
Period size: 13 Copynumber: 4.4 Consensus size: 13
1946654 ACAATAAGCA
1946664 TCATAAATGCGCG
1 TCATAAATGCGCG
* *
1946677 TCGTAAATGCGTG
1 TCATAAATGCGCG
**
1946690 TCATAAATGCATG
1 TCATAAATGCGCG
*
1946703 TCATAAATGCACG
1 TCATAAATGCGCG
1946716 TCATA
1 TCATA
1946721 GATTTATGAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (13 bp):
TCATAAATGCGCG
Found at i:1950905 original size:42 final size:42
Alignment explanation
Indices: 1950846--1950944 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 42
1950836 ATCAATAATT
* * *
1950846 CAATT-AATTTTGGTCATGGAAACATGCATTTATTCACCAA-C
1 CAATTCAATTTAGATCATGGAAACATGCATTAATTCA-CAATC
* *
1950887 CAATTCAATTTAGATCATGGTAACATGTATTAATTCACAATC
1 CAATTCAATTTAGATCATGGAAACATGCATTAATTCACAATC
1950929 CAATTCAATTTA-ATCA
1 CAATTCAATTTAGATCA
1950945 AGGCAACAAG
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
41 12 0.24
42 39 0.76
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.35
Consensus pattern (42 bp):
CAATTCAATTTAGATCATGGAAACATGCATTAATTCACAATC
Found at i:1957853 original size:16 final size:17
Alignment explanation
Indices: 1957825--1957856 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1957815 TGAAGAGAGA
1957825 ATGAAGAAGAAAGAAAG
1 ATGAAGAAGAAAGAAAG
1957842 ATGAAG-AGAAAGAAA
1 ATGAAGAAGAAAGAAA
1957857 ATAAAAAGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.66, C:0.00, G:0.28, T:0.06
Consensus pattern (17 bp):
ATGAAGAAGAAAGAAAG
Found at i:1965370 original size:22 final size:22
Alignment explanation
Indices: 1965345--1965387 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1965335 TAACTCCCGA
* *
1965345 AATTATATCATGTAACCCCTGG
1 AATTAAATCAAGTAACCCCTGG
*
1965367 AATTAAATCAAGTAACTCCTG
1 AATTAAATCAAGTAACCCCTG
1965388 ATATTAACAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (22 bp):
AATTAAATCAAGTAACCCCTGG
Found at i:1965393 original size:22 final size:21
Alignment explanation
Indices: 1965335--1965394 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
1965325 TCAACTGTTA
* * *
1965335 TAACTCCCGAAATTATATCATG
1 TAACTCCTG-AATTAAATCAAG
*
1965357 TAACCCCTGGAATTAAATCAAG
1 TAACTCCT-GAATTAAATCAAG
1965379 TAACTCCTGATATTAA
1 TAACTCCTGA-ATTAA
1965395 CAAATTGTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
21 2 0.06
22 28 0.90
23 1 0.03
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.30
Consensus pattern (21 bp):
TAACTCCTGAATTAAATCAAG
Found at i:1967735 original size:16 final size:16
Alignment explanation
Indices: 1967716--1967750 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1967706 TGATAACACA
1967716 TTCAGTGTCAAACATC
1 TTCAGTGTCAAACATC
1967732 TTCAGTGTCAAACATC
1 TTCAGTGTCAAACATC
1967748 TTC
1 TTC
1967751 GAATACACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (16 bp):
TTCAGTGTCAAACATC
Found at i:1975145 original size:44 final size:45
Alignment explanation
Indices: 1975094--1975198 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 45
1975084 TGTTAGAATT
* * *
1975094 CCAACTTATTTCTCT-CACTATGTTGGAGTTATTACCAGCATTAC
1 CCAACTTATTTCTCTAAACTATGTTGGAGCTATTACCACCATTAC
*
1975138 CCAACTTATTT-TTTAAACTATGTTGGAGCTATTACCACCATTAC
1 CCAACTTATTTCTCTAAACTATGTTGGAGCTATTACCACCATTAC
*
1975182 CCAAATTATTTC-CTAAA
1 CCAACTTATTTCTCTAAA
1975199 TTTTCTCATT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
43 2 0.04
44 51 0.96
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.38
Consensus pattern (45 bp):
CCAACTTATTTCTCTAAACTATGTTGGAGCTATTACCACCATTAC
Found at i:1975580 original size:26 final size:26
Alignment explanation
Indices: 1975544--1975596 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 26
1975534 TGCAACATCG
1975544 AAAACACAAACAATAA-AAACATAAAAC
1 AAAACACAAACAA-AATAAAC-TAAAAC
1975571 AAAA-ACAAACAAAATAAACTAAAAC
1 AAAACACAAACAAAATAAACTAAAAC
1975596 A
1 A
1975597 TGAGAAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 9 0.36
26 12 0.48
27 4 0.16
ACGTcount: A:0.75, C:0.17, G:0.00, T:0.08
Consensus pattern (26 bp):
AAAACACAAACAAAATAAACTAAAAC
Found at i:1984119 original size:46 final size:46
Alignment explanation
Indices: 1984069--1984410 Score: 345
Period size: 46 Copynumber: 7.3 Consensus size: 46
1984059 TTTATTTATG
* *
1984069 GCATCCTTTCATGCATTTTATTTATGACATTCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAAT
* ** **
1984115 GCATCCTTTCATGAATTTTATTCGTGGCATCCTTTTGTGCCTTAAT
1 GCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAAT
** *
1984161 GCATCCTTTCATGCATTTTATTCGTGGCATCCTTTCGTGCCTTAAT
1 GCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAAT
* * *
1984207 GCATCTTTTCATGCATTTTATTTGTGGCATCCTTTCATGCATTTTATTCAT
1 GCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGC--CTTA---AT
* * *
1984258 GGCATTCTTTCATGC--CTTA---AT-GCATCCTTTCATTCCTTAAT
1 -GCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAAT
* * *
1984299 GCACCCTTTCATGCACTTTATTTATGGCATCCTTTCATGCATTTTATTTAT
1 GCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGC--CTTA---AT
* *
1984350 GGCATCCATTCATGCATTTTATTTATGGCATCCTTTTATGCCTTAAT
1 -GCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAAT
1984397 GCATCCTTTCATGC
1 GCATCCTTTCATGC
1984411 CTTAATGCAT
Statistics
Matches: 248, Mismatches: 30, Indels: 36
0.79 0.10 0.11
Matches are distributed among these distances:
40 12 0.05
41 2 0.01
42 3 0.01
44 3 0.01
45 2 0.01
46 159 0.64
47 3 0.01
48 6 0.02
50 6 0.02
51 4 0.02
52 48 0.19
ACGTcount: A:0.19, C:0.23, G:0.12, T:0.46
Consensus pattern (46 bp):
GCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAAT
Found at i:1984196 original size:92 final size:95
Alignment explanation
Indices: 1984043--1984410 Score: 412
Period size: 92 Copynumber: 3.9 Consensus size: 95
1984033 ATGCCTTAAT
* * *
1984043 GCATACTTTCATGCATTTTATTTATGGCATCCTTTCATGCATTTTATTTATGACATTCTTTCATG
1 GCATCCTTTCATGCA-TTTA--TATGGCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATG
* *
1984108 CCTTAATGCATCCTTTCATGAATTTTATTCGTG
63 CCTTAATGCATCCTTTCATGCATTTTATTTGTG
** * ** *
1984141 GCATCCTTTTGTGC-CTTA-AT-GCATCCTTTCATGCATTTTATTCGTGGCATCCTTTCGTGCCT
1 GCATCCTTTCATGCATTTATATGGCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCT
*
1984203 TAATGCATCTTTTCATGCATTTTATTTGTG
66 TAATGCATCCTTTCATGCATTTTATTTGTG
* * *
1984233 GCATCCTTTCATGCATTTTATTCATGGCATTCTTTCATGC--CTTA---AT-GCATCCTTTCATT
1 GCATCCTTTCATGCA-TTTA-T-ATGGCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATG
* * *
1984292 CCTTAATGCACCCTTTCATGCACTTTATTTATG
63 CCTTAATGCATCCTTTCATGCATTTTATTTGTG
* *
1984325 GCATCCTTTCATGCATTTTATTTATGGCATCCATTCATGCATTTTATTTATGGCATCCTTTTATG
1 GCATCCTTTCATGCA-TTTA--TATGGCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATG
1984390 CCTTAATGCATCCTTTCATGC
63 CCTTAATGCATCCTTTCATGC
1984411 CTTAATGCAT
Statistics
Matches: 227, Mismatches: 30, Indels: 26
0.80 0.11 0.09
Matches are distributed among these distances:
92 151 0.67
93 5 0.02
94 6 0.03
96 6 0.03
97 4 0.02
98 55 0.24
ACGTcount: A:0.19, C:0.23, G:0.12, T:0.46
Consensus pattern (95 bp):
GCATCCTTTCATGCATTTATATGGCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCT
TAATGCATCCTTTCATGCATTTTATTTGTG
Found at i:1984287 original size:20 final size:20
Alignment explanation
Indices: 1984259--1984430 Score: 119
Period size: 20 Copynumber: 7.7 Consensus size: 20
1984249 TTTATTCATG
*
1984259 GCATTCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
1984279 GCATCCTTTCATTCCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
1984299 GCACCCTTTCATGCACTTTATTTAT
1 GCATCCTTTCATGC-C-TTA---AT
*
1984324 GGCATCCTTTCATGCATTTTATTTAT
1 -GCATCCTTTCATGC--CTTA---AT
* *
1984350 GGCATCCATTCATGCATTTTATTTAT
1 -GCATCCTTTCATGC--CTTA---AT
*
1984376 GGCATCCTTTTATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
1984397 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
1984417 GCATCCTTTCATGC
1 GCATCCTTTCATGC
1984431 ATTTTATTTA
Statistics
Matches: 133, Mismatches: 12, Indels: 14
0.84 0.08 0.09
Matches are distributed among these distances:
20 63 0.47
21 3 0.02
22 3 0.02
24 3 0.02
25 2 0.02
26 59 0.44
ACGTcount: A:0.20, C:0.26, G:0.10, T:0.44
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:1984331 original size:164 final size:159
Alignment explanation
Indices: 1984010--1984364 Score: 430
Period size: 164 Copynumber: 2.2 Consensus size: 159
1984000 CATTAAATTT
* *
1984010 CATTTTATTTCTGGCCTCTTTTCATGCCTTAATGCATACTTTCATGCATTTTATTTATGGCATCC
1 CATTTTA-TTCTGGCATCCTTTCATGCCTTAATGCATACTTTCATGCATTTTATTTATGGCATCC
* * *
1984075 TTTCATGCATTTTATTTATGACATTCTTTCATGCCTTAATGCATCCTTTCATGAATTTTATTCGT
65 TTTCATGCATTTTATTCATGACATTCTTTCATGCCTTAATGCATCCTTTCAT--ATCTTA-T-AT
* **
1984140 GGCATCCTTTTGTGCCTTAATGCATCCTTTCATG
126 GGCACCCTTTCATGCCTTAATGCATCCTTTCATG
* *
1984174 CATTTTATTCGTGGCATCCTTTCGTGCCTTAATGCAT-CTTTTCATGCATTTTATTTGTGGCATC
1 CATTTTATTC-TGGCATCCTTTCATGCCTTAATGCATAC-TTTCATGCATTTTATTTATGGCATC
*
1984238 CTTTCATGCATTTTATTCATGGCATTCTTTCATGCCTTAATGCATCCTTTCAT-TCCTTA-AT-G
64 CTTTCATGCATTTTATTCATGACATTCTTTCATGCCTTAATGCATCCTTTCATAT-CTTATATGG
1984300 CACCCTTTCATGCACTTTATTTATGGCATCCTTTCATG
128 CACCCTTTCATGC-C-TTA---AT-GCATCCTTTCATG
* *
1984338 CATTTTATTTATGGCATCCATTCATGC
1 CATTTTA-TTCTGGCATCCTTTCATGC
1984365 ATTTTATTTA
Statistics
Matches: 167, Mismatches: 14, Indels: 20
0.83 0.07 0.10
Matches are distributed among these distances:
158 11 0.07
159 2 0.01
160 3 0.02
161 1 0.01
162 3 0.02
163 6 0.04
164 139 0.83
165 2 0.01
ACGTcount: A:0.19, C:0.23, G:0.12, T:0.46
Consensus pattern (159 bp):
CATTTTATTCTGGCATCCTTTCATGCCTTAATGCATACTTTCATGCATTTTATTTATGGCATCCT
TTCATGCATTTTATTCATGACATTCTTTCATGCCTTAATGCATCCTTTCATATCTTATATGGCAC
CCTTTCATGCCTTAATGCATCCTTTCATG
Found at i:1984375 original size:30 final size:26
Alignment explanation
Indices: 1984306--1984382 Score: 136
Period size: 26 Copynumber: 3.0 Consensus size: 26
1984296 AATGCACCCT
* *
1984306 TTCATGCACTTTATTTATGGCATCCT
1 TTCATGCATTTTATTTATGGCATCCA
1984332 TTCATGCATTTTATTTATGGCATCCA
1 TTCATGCATTTTATTTATGGCATCCA
1984358 TTCATGCATTTTATTTATGGCATCC
1 TTCATGCATTTTATTTATGGCATCC
1984383 TTTTATGCCT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.47
Consensus pattern (26 bp):
TTCATGCATTTTATTTATGGCATCCA
Found at i:1984421 original size:92 final size:94
Alignment explanation
Indices: 1984029--1984442 Score: 410
Period size: 92 Copynumber: 4.4 Consensus size: 94
1984019 TCTGGCCTCT
*
1984029 TTTCATGCCTTA-AT-GCATACTTTCATGCATTTTATTTATGGCATCCTTTCATGCATTTTATTT
1 TTTCATGCCTTATATGGCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCATTTTATTT
* *
1984092 ATGACATTCTTTCATGCCTTAATGCATCC
66 ATGGCATCCTTTCATGCCTTAATGCATCC
** * ** *
1984121 TTTCATGAATTTTATTCGTGGCATCCTTTTGTGC--CTTA---AT-GCATCCTTTCATGCATTTT
1 TTTCATG--CCTTA-T-ATGGCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCATTTT
** * *
1984180 ATTCGTGGCATCCTTTCGTGCCTTAATGCATCT
62 ATTTATGGCATCCTTTCATGCCTTAATGCATCC
* * * * *
1984213 TTTCATGCATTTTATTTGTGGCATCCTTTCATGCATTTTATTCATGGCATTCTTTCATGC--CTT
1 TTTCATGC--CTTA--TATGGCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCATTTT
* *
1984276 A---AT-GCATCCTTTCATTCCTTAATGCACCC
62 ATTTATGGCATCCTTTCATGCCTTAATGCATCC
*
1984305 TTTCATGCACTTTATTTATGGCATCCTTTCATGCATTTTATTTATGGCATCCATTCATGCATTTT
1 TTTCATGC-C-TTA--TATGGCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCATTTT
*
1984370 ATTTATGGCATCCTTTTATGCCTTAATGCATCC
62 ATTTATGGCATCCTTTCATGCCTTAATGCATCC
1984403 TTTCATGCCTTA-AT-GCATCCTTTCATGCATTTTATTTATG
1 TTTCATGCCTTATATGGCATCCTTTCATGCATTTTATTTATG
1984443 TATTCGGTTT
Statistics
Matches: 266, Mismatches: 34, Indels: 44
0.77 0.10 0.13
Matches are distributed among these distances:
92 180 0.68
93 7 0.03
94 9 0.03
96 9 0.03
97 6 0.02
98 55 0.21
ACGTcount: A:0.19, C:0.22, G:0.12, T:0.47
Consensus pattern (94 bp):
TTTCATGCCTTATATGGCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCATTTTATTT
ATGGCATCCTTTCATGCCTTAATGCATCC
Found at i:1984438 original size:118 final size:121
Alignment explanation
Indices: 1984010--1984442 Score: 456
Period size: 118 Copynumber: 3.7 Consensus size: 121
1984000 CATTAAATTT
* * *
1984010 CATTTTATTTC-TGGCCT-CTTTTCATGCCTTAATGCATACTTTCATGCATTTTATTTATGGCAT
1 CATTTTA-TTCATGGCATCCTTTT-ATGCCTTAATGCATCCTTTCATGCA-CTTA--TATGGCAT
* * *
1984073 CCTTTCATGCATTTTATTTATGACATTCTTTCATGC--CTTA---AT-GCATCCTTTCATG
61 CCTTTCATGCATTTTATTTATGGCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATG
* * * * *
1984128 AATTTTATTCGTGGCATCCTTTTGTGCCTTAATGCATCCTTTCATGCATTTTATTCGTGGCATCC
1 CATTTTATTCATGGCATCCTTTTATGCCTTAATGCATCCTTTCATGCA-CTTA-T-ATGGCATCC
* * * *
1984193 TTTCGTGC--CTTA---AT-GCATCTTTTCATGCATTTTATTTGTGGCATCCTTTCATG
63 TTTCATGCATTTTATTTATGGCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATG
* * * *
1984246 CATTTTATTCATGGCATTCTTTCATGCCTTAATGCATCCTTTCATTC-CTTA-AT-GCACCCTTT
1 CATTTTATTCATGGCATCCTTTTATGCCTTAATGCATCCTTTCATGCACTTATATGGCATCCTTT
* *
1984308 CATGCACTTTATTTATGGCATCCTTTCATGCATTTTATTTATGGCATCCATTCATG
66 CATGCATTTTATTTATGGCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATG
*
1984364 CATTTTATTTATGGCATCCTTTTATGCCTTAATGCATCCTTTCATGC-CTTA-AT-GCATCCTTT
1 CATTTTATTCATGGCATCCTTTTATGCCTTAATGCATCCTTTCATGCACTTATATGGCATCCTTT
1984426 CATGCATTTTATTTATG
66 CATGCATTTTATTTATG
1984443 TATTCGGTTT
Statistics
Matches: 268, Mismatches: 32, Indels: 30
0.81 0.10 0.09
Matches are distributed among these distances:
112 23 0.09
113 3 0.01
114 6 0.02
116 6 0.02
117 8 0.03
118 217 0.81
119 5 0.02
ACGTcount: A:0.19, C:0.23, G:0.12, T:0.47
Consensus pattern (121 bp):
CATTTTATTCATGGCATCCTTTTATGCCTTAATGCATCCTTTCATGCACTTATATGGCATCCTTT
CATGCATTTTATTTATGGCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATG
Found at i:1987182 original size:2 final size:2
Alignment explanation
Indices: 1987175--1987217 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1987165 GCCAATTGAT
1987175 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1987217 T
1 T
1987218 CTTAAGCTAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1989429 original size:23 final size:22
Alignment explanation
Indices: 1989373--1989451 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 22
1989363 GAACCCTCAT
*
1989373 GGGGTATCGATTCCCC-T--AG
1 GGGGAATCGATTCCCCTTCAAG
1989392 GGTGGAATCGATTCCCCTTCAAAG
1 GG-GGAATCGATTCCCCTTC-AAG
*
1989416 GGGGAATCGGTTCCCCTTCAAG
1 GGGGAATCGATTCCCCTTCAAG
*
1989438 GGGGTATCGATTCC
1 GGGGAATCGATTCC
1989452 ATCTTCTCTA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
19 2 0.04
20 13 0.25
21 1 0.02
22 15 0.29
23 16 0.31
24 4 0.08
ACGTcount: A:0.19, C:0.25, G:0.30, T:0.25
Consensus pattern (22 bp):
GGGGAATCGATTCCCCTTCAAG
Found at i:1998988 original size:46 final size:46
Alignment explanation
Indices: 1998928--1999020 Score: 132
Period size: 46 Copynumber: 2.0 Consensus size: 46
1998918 CGTTAAATTT
* *
1998928 CATTTTATTTATGACCTCCTTTCATGCCTTAATGCATCATTTCATG
1 CATTTTATTCATGACATCCTTTCATGCCTTAATGCATCATTTCATG
* * * *
1998974 CATTTTATTCATGACATCCTTTTATGCGTTAATGCATCCTTTTATG
1 CATTTTATTCATGACATCCTTTCATGCCTTAATGCATCATTTCATG
1999020 C
1 C
1999021 CTTAATGCAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.22, C:0.23, G:0.10, T:0.46
Consensus pattern (46 bp):
CATTTTATTCATGACATCCTTTCATGCCTTAATGCATCATTTCATG
Found at i:1999015 original size:66 final size:66
Alignment explanation
Indices: 1998944--1999089 Score: 220
Period size: 66 Copynumber: 2.2 Consensus size: 66
1998934 ATTTATGACC
* * * *
1998944 TCCTTTCATGCCTTAATGCATCATTTCATGCATTTTATTCATGACATCCTTTTATGCGTTAATGC
1 TCCTTTCATGCCTTAATGCATCATTTCATGCATTTTATTAATGACATCATTTCATGCCTTAATGC
1999009 A
66 A
* * *
1999010 TCCTTTTATGCCTTAATGCATCATTTTATGCATTTTATTAATGGCATCATTTCATGCCTTAATGC
1 TCCTTTCATGCCTTAATGCATCATTTCATGCATTTTATTAATGACATCATTTCATGCCTTAATGC
1999075 A
66 A
*
1999076 TCTTTTCATGCCTT
1 TCCTTTCATGCCTT
1999090 TTATTTATGG
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 71 1.00
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (66 bp):
TCCTTTCATGCCTTAATGCATCATTTCATGCATTTTATTAATGACATCATTTCATGCCTTAATGC
A
Found at i:1999067 original size:46 final size:45
Alignment explanation
Indices: 1999002--1999138 Score: 195
Period size: 46 Copynumber: 3.0 Consensus size: 45
1998992 CTTTTATGCG
* *
1999002 TTAAT-GCATCCTTTTATGCCTTAATGCATCATTTTATGCATTTTA
1 TTAATGGCATCATTTCATGCCTTAATGCATC-TTTTATGCATTTTA
*
1999047 TTAATGGCATCATTTCATGCCTTAATGCATCTTTTCATGCCTTTTA
1 TTAATGGCATCATTTCATGCCTTAATGCATCTTTT-ATGCATTTTA
* * *
1999093 TTTATGGCATCTTTTCATGCCTTAATGCATCTTTCATGCATTTTA
1 TTAATGGCATCATTTCATGCCTTAATGCATCTTTTATGCATTTTA
1999138 T
1 T
1999139 ATATGTATTT
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
45 19 0.23
46 64 0.77
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.48
Consensus pattern (45 bp):
TTAATGGCATCATTTCATGCCTTAATGCATCTTTTATGCATTTTA
Found at i:1999102 original size:26 final size:25
Alignment explanation
Indices: 1999027--1999115 Score: 91
Period size: 26 Copynumber: 3.7 Consensus size: 25
1999017 ATGCCTTAAT
*
1999027 GCATCATTTT-ATGCATTTTATTAATG
1 GCATC-TTTTCATGCCTTTTATT-ATG
*
1999053 GCATCATTTCATGCC--TTA--AT-
1 GCATCTTTTCATGCCTTTTATTATG
1999073 GCATCTTTTCATGCCTTTTATTTATG
1 GCATCTTTTCATGCCTTTTA-TTATG
1999099 GCATCTTTTCATGCCTT
1 GCATCTTTTCATGCCTT
1999116 AATGCATCTT
Statistics
Matches: 53, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
20 14 0.26
21 2 0.04
22 3 0.06
24 3 0.06
25 5 0.09
26 26 0.49
ACGTcount: A:0.20, C:0.20, G:0.11, T:0.48
Consensus pattern (25 bp):
GCATCTTTTCATGCCTTTTATTATG
Found at i:2000942 original size:18 final size:18
Alignment explanation
Indices: 2000907--2000945 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2000897 TATGACTAGT
*
2000907 AGGACTGACATTACTTAA
1 AGGACTGACATAACTTAA
* *
2000925 AGGACTGATATAATTTAA
1 AGGACTGACATAACTTAA
2000943 AGG
1 AGG
2000946 GCTGGCATGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (18 bp):
AGGACTGACATAACTTAA
Found at i:2002981 original size:2 final size:2
Alignment explanation
Indices: 2002976--2003002 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2002966 TTTTCTTAAT
2002976 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 T
2003003 GTGCATAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2004279 original size:3 final size:3
Alignment explanation
Indices: 2004271--2004338 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
2004261 CCCTGCCACG
2004271 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2004319 ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT AT
2004339 CTCTCTGATA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2007000 original size:24 final size:24
Alignment explanation
Indices: 2006966--2007021 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
2006956 CTATTCTTTC
2006966 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
*
2006990 GCTTCAGTTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
2007014 GCTTCAAT
1 GCTTCAAT
2007022 CGAACTTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:2007284 original size:30 final size:30
Alignment explanation
Indices: 2007248--2007313 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
2007238 AGTGAACTGG
*
2007248 CGGTTCAAACCGGTTTTGTCGGTTTCCAGT
1 CGGTTCAAACCGGTTTTGTCGGTTTCCAGC
** * * *
2007278 CGGTTCACTCCGGTTTTTTGGGTTTTCAGC
1 CGGTTCAAACCGGTTTTGTCGGTTTCCAGC
2007308 CGGTTC
1 CGGTTC
2007314 TTCCGATTCT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.09, C:0.24, G:0.27, T:0.39
Consensus pattern (30 bp):
CGGTTCAAACCGGTTTTGTCGGTTTCCAGC
Found at i:2011745 original size:3 final size:3
Alignment explanation
Indices: 2011737--2011868 Score: 108
Period size: 3 Copynumber: 43.0 Consensus size: 3
2011727 TCGTCCGATT
**
2011737 TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA CAA TTA TATA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA T-TA TTA TTA
* * * *
2011783 CTA CTA TTA TATA TGA -TA TTA TTA TCA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
2011827 TTA TTAA TTA CATG TTG TTA TTA TTA TTA TATA TTA TTA TTA
1 TTA TT-A TTA -TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
2011869 AATAATATTA
Statistics
Matches: 107, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
2 4 0.04
3 88 0.82
4 15 0.14
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:2011813 original size:23 final size:23
Alignment explanation
Indices: 2011738--2011868 Score: 75
Period size: 23 Copynumber: 5.9 Consensus size: 23
2011728 CGTCCGATTT
*
2011738 TATTATTATTATTATTATTAT--
1 TATTATTATGATTATTATTATCA
**
2011759 TATTATATACAATTATATATTATACTA
1 TATTAT-TATGATTAT-TATTAT-C-A
2011786 CTATTATATATGA-TATTATTATCA
1 -TATTAT-TATGATTATTATTATCA
* *
2011810 TATTATTATTATTATTATTATTA
1 TATTATTATGATTATTATTATCA
* *
2011833 -ATTA-CATG-TTGTTATTAT--
1 TATTATTATGATTATTATTATCA
2011851 TATTA-TAT-ATTATTATTA
1 TATTATTATGATTATTATTA
2011869 AATAATATTA
Statistics
Matches: 89, Mismatches: 11, Indels: 22
0.73 0.09 0.18
Matches are distributed among these distances:
19 14 0.16
20 9 0.10
21 8 0.09
22 15 0.17
23 22 0.25
24 1 0.01
25 1 0.01
26 6 0.07
27 3 0.03
28 10 0.11
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (23 bp):
TATTATTATGATTATTATTATCA
Found at i:2011876 original size:16 final size:13
Alignment explanation
Indices: 2011737--2011878 Score: 100
Period size: 13 Copynumber: 11.0 Consensus size: 13
2011727 TCGTCCGATT
2011737 TTAT-TATTATTA
1 TTATATATTATTA
2011749 TTAT-TATTATTA
1 TTATATATTATTA
**
2011761 TTATATACAATTA
1 TTATATATTATTA
* *
2011774 TATATTATACTACTA
1 T-TA-TATATTATTA
2011789 TTATATATGATATTA
1 TTATATAT--TATTA
2011804 TTATCATATTATTA
1 TTAT-ATATTATTA
2011818 TTAT-TATTATTA
1 TTATATATTATTA
* *
2011830 -T-TA-ATTACATG
1 TTATATATTA-TTA
*
2011841 TTGT-TATTATTA
1 TTATATATTATTA
2011853 TTATATATTATTA
1 TTATATATTATTA
* *
2011866 TTAAATAATATTA
1 TTATATATTATTA
2011879 CAAGCCCAAA
Statistics
Matches: 105, Mismatches: 13, Indels: 23
0.74 0.09 0.16
Matches are distributed among these distances:
10 5 0.05
11 2 0.02
12 29 0.28
13 35 0.33
14 13 0.12
15 17 0.16
16 4 0.04
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (13 bp):
TTATATATTATTA
Found at i:2011924 original size:20 final size:20
Alignment explanation
Indices: 2011901--2011955 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
2011891 AATAAATCGG
2011901 GGCCCAATTACAAGTTTGGA
1 GGCCCAATTACAAGTTTGGA
2011921 GGCCCAATTACAAGTTTGGA
1 GGCCCAATTACAAGTTTGGA
* *
2011941 GGTCCATTTACAAGT
1 GGCCCAATTACAAGT
2011956 AAAGGCTCGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (20 bp):
GGCCCAATTACAAGTTTGGA
Found at i:2013189 original size:18 final size:17
Alignment explanation
Indices: 2013159--2013203 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
2013149 TTTAAGACTA
*
2013159 AATTATAATATTATTAT
1 AATTATAATATTATGAT
2013176 AATTATATATATTATGAT
1 AATTATA-ATATTATGAT
2013194 AATTCATAAT
1 AATT-ATAAT
2013204 TTAATCTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 7 0.28
18 15 0.60
19 3 0.12
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (17 bp):
AATTATAATATTATGAT
Found at i:2013746 original size:11 final size:11
Alignment explanation
Indices: 2013730--2013759 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
2013720 AATAAATTTA
2013730 TTTTAATTTTG
1 TTTTAATTTTG
2013741 TTTTAATTTTG
1 TTTTAATTTTG
2013752 TTTTAATT
1 TTTTAATT
2013760 ATTTTACTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (11 bp):
TTTTAATTTTG
Found at i:2019780 original size:22 final size:22
Alignment explanation
Indices: 2019755--2019829 Score: 141
Period size: 22 Copynumber: 3.4 Consensus size: 22
2019745 CTACATTCTG
*
2019755 CAAAGATGATAGATTCTATTTT
1 CAAAGATGATAGATTCTCTTTT
2019777 CAAAGATGATAGATTCTCTTTT
1 CAAAGATGATAGATTCTCTTTT
2019799 CAAAGATGATAGATTCTCTTTT
1 CAAAGATGATAGATTCTCTTTT
2019821 CAAAGATGA
1 CAAAGATGA
2019830 AAGCATTATC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (22 bp):
CAAAGATGATAGATTCTCTTTT
Found at i:2020549 original size:20 final size:20
Alignment explanation
Indices: 2020521--2020569 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
2020511 TCTAGAAAAT
* * *
2020521 TAAATCCTCCGGGTGATTTG
1 TAAAACCTCCGGGTAATCTG
2020541 TAAAACCTCCGGGTAATCTG
1 TAAAACCTCCGGGTAATCTG
*
2020561 TGAAACCTC
1 TAAAACCTC
2020570 AAGGTAGGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (20 bp):
TAAAACCTCCGGGTAATCTG
Found at i:2020591 original size:119 final size:119
Alignment explanation
Indices: 2020440--2020703 Score: 447
Period size: 119 Copynumber: 2.2 Consensus size: 119
2020430 CCCACAAAAT
*
2020440 TATAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAAAACGATTTTCAAAGTTTCTCATT
1 TATAAAACCTCAAGGTAGGATGTTTTCGCATGAAAATGAGAAAACGATTTTCAAAGTTTCTCATT
2020505 TAATGTTCTAGAAAATTAAATCCTCCGGGTGATTTGTAAAACCTCCGGGTAATC
66 TAATGTTCTAGAAAATTAAATCCTCCGGGTGATTTGTAAAACCTCCGGGTAATC
* * ***
2020559 TGTGAAACCTCAAGGTAGGATGTTTTCGCATGAAAATGAGAAAGTTATTTTCAAAGTTTCTCATT
1 TATAAAACCTCAAGGTAGGATGTTTTCGCATGAAAATGAGAAAACGATTTTCAAAGTTTCTCATT
* * *
2020624 TAATGTTCTAGAAAATTAAATCCTTCGGGTGATTTGTAAAACCTCCGGGTCATT
66 TAATGTTCTAGAAAATTAAATCCTCCGGGTGATTTGTAAAACCTCCGGGTAATC
2020678 TATAAAACCTCAAGGTAGGATGTTTT
1 TATAAAACCTCAAGGTAGGATGTTTT
2020704 TTATTTTTGA
Statistics
Matches: 134, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
119 134 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.34
Consensus pattern (119 bp):
TATAAAACCTCAAGGTAGGATGTTTTCGCATGAAAATGAGAAAACGATTTTCAAAGTTTCTCATT
TAATGTTCTAGAAAATTAAATCCTCCGGGTGATTTGTAAAACCTCCGGGTAATC
Found at i:2020672 original size:20 final size:20
Alignment explanation
Indices: 2020649--2020688 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2020639 TTAAATCCTT
* *
2020649 CGGGTGATTTGTAAAACCTC
1 CGGGTCATTTATAAAACCTC
2020669 CGGGTCATTTATAAAACCTC
1 CGGGTCATTTATAAAACCTC
2020689 AAGGTAGGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (20 bp):
CGGGTCATTTATAAAACCTC
Found at i:2020845 original size:3 final size:3
Alignment explanation
Indices: 2020837--2020970 Score: 105
Period size: 3 Copynumber: 44.0 Consensus size: 3
2020827 TCGTCCGGTT
*
2020837 TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TATA TAA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA T-TA TTA
* * * *
2020883 -TA CTA CTA TTA TATA TGA -TA TTA TTA TCA -TA TTA TTA TTA TTAA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
* * * *
2020927 TTA CATG TTA TTA TTA TTA TATA TTA TTA ATA TTT TTA TTA TTA
1 TTA -TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
2020971 AATAATATTA
Statistics
Matches: 106, Mismatches: 15, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
2 6 0.06
3 84 0.79
4 16 0.15
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:2020862 original size:20 final size:20
Alignment explanation
Indices: 2020837--2020968 Score: 118
Period size: 18 Copynumber: 7.0 Consensus size: 20
2020827 TCGTCCGGTT
2020837 TTATTATTATTATTATTATA
1 TTATTATTATTATTATTATA
*
2020857 TTATTATTATATATAATTATA
1 TTATTATTAT-TATTATTATA
* *
2020878 -TATTA-TACTACTATTATA
1 TTATTATTATTATTATTATA
* *
2020896 -TATGA-TATTATTATCATA
1 TTATTATTATTATTATTATA
*
2020914 TTATTATTATTA--ATTACA
1 TTATTATTATTATTATTATA
*
2020932 -TGTTATTATTATTA-TATA
1 TTATTATTATTATTATTATA
* *
2020950 TTATTAATATTTTTATTAT
1 TTATTATTATTATTATTAT
2020969 TAAATAATAT
Statistics
Matches: 89, Mismatches: 16, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
17 10 0.11
18 29 0.33
19 18 0.20
20 23 0.26
21 9 0.10
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (20 bp):
TTATTATTATTATTATTATA
Found at i:2020879 original size:23 final size:23
Alignment explanation
Indices: 2020837--2020968 Score: 96
Period size: 23 Copynumber: 5.7 Consensus size: 23
2020827 TCGTCCGGTT
2020837 TTATTAT-TATTATTATTATATTA
1 TTATTATATATTATTA-TATATTA
*
2020860 TTATTATATATAATTATATATTA
1 TTATTATATATTATTATATATTA
* *
2020883 -TACTA-CTATTATATATGATATTA
1 TTATTATATATTAT-TAT-ATATTA
*
2020906 TTATCATATTATTATTAT-TAATTA
1 TTATTATA-TATTATTATAT-ATTA
* *
2020930 CATGTTAT-TATTATTATATATTA
1 -TTATTATATATTATTATATATTA
* *
2020953 TTAATAT-TTTTATTAT
1 TTATTATATATTATTAT
2020969 TAAATAATAT
Statistics
Matches: 86, Mismatches: 14, Indels: 19
0.72 0.12 0.16
Matches are distributed among these distances:
21 5 0.06
22 19 0.22
23 34 0.40
24 15 0.17
25 7 0.08
26 6 0.07
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (23 bp):
TTATTATATATTATTATATATTA
Found at i:2020920 original size:54 final size:52
Alignment explanation
Indices: 2020847--2020970 Score: 134
Period size: 54 Copynumber: 2.4 Consensus size: 52
2020837 TTATTATTAT
*
2020847 TATTATTATATTATTATTA-TATATAATTATATATTATACTACTATTATATATGA
1 TATTATTATATTATTATTATTAT-TAATTACATATTAT--TACTATTATATATGA
* *
2020901 TATTATTATCA-TATTATTATTATTAATTACATGTTATTATTATTATATAT--
1 TATTATTAT-ATTATTATTATTATTAATTACATATTATTACTATTATATATGA
*
2020951 TATTA--ATATTTTTATTATTA
1 TATTATTATATTATTATTATTA
2020971 AATAATATTA
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
47 1 0.02
48 12 0.19
50 5 0.08
52 12 0.19
54 29 0.46
55 4 0.06
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (52 bp):
TATTATTATATTATTATTATTATTAATTACATATTATTACTATTATATATGA
Found at i:2022242 original size:18 final size:17
Alignment explanation
Indices: 2022205--2022285 Score: 62
Period size: 18 Copynumber: 4.6 Consensus size: 17
2022195 TTTAAGACTA
2022205 AATTATAATATTATTAT
1 AATTATAATATTATTAT
2022222 AATTATATATATTATGT-T
1 AATTATA-ATATTAT-TAT
2022240 AATTCATAAT-TTAATCTAT
1 AATT-ATAATATT-AT-TAT
*
2022259 ATAGTTATAATATTA-AAT
1 A-A-TTATAATATTATTAT
2022277 -ATTATAATA
1 AATTATAATA
2022286 GGACTAGTGA
Statistics
Matches: 54, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
15 8 0.15
16 1 0.02
17 9 0.17
18 19 0.35
19 6 0.11
20 7 0.13
21 4 0.07
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (17 bp):
AATTATAATATTATTAT
Found at i:2022783 original size:187 final size:188
Alignment explanation
Indices: 2022417--2022788 Score: 683
Period size: 187 Copynumber: 2.0 Consensus size: 188
2022407 GTGGGAATTT
* * *
2022417 TAATCCTTCTCCATACGTAACCGACTCTCGAACTCATTTTTCTGGTAAGCAGACTCGATTTGTAT
1 TAATCCTTCTCCACACGTAACCGACTCCCGAACTCATTTTTCTGGTAAGCAGACTCGAGTTGTAT
* *
2022482 TATTTTAATATTATTTTTAGGAATTTTTTATTAAAATAATATGATATTTTGGTGACCAATCTCAC
66 TATTTTAATATTATTCTTAGGAATTTTTTATTAAAATAATATGACATTTTGGTGACCAATCTCAC
2022547 CAAATTAAAAGATTGGTGGCGACTCTACAATTTGGTGTTTTATCTGATTCATGGATTC
131 CAAATTAAAAGATTGGTGGCGACTCTACAATTTGGTGTTTTATCTGATTCATGGATTC
2022605 TAATCCTTCTCCACACGTAACCGACTCCCGAACTCATTTTTCTGGTAAGCAGACTCGAGTTGTAT
1 TAATCCTTCTCCACACGTAACCGACTCCCGAACTCATTTTTCTGGTAAGCAGACTCGAGTTGTAT
2022670 TATTTTAATATTATTCTTAGGAA-TTTTTATTAAAATAATATGACATTTTGGTGACCAATCTCAC
66 TATTTTAATATTATTCTTAGGAATTTTTTATTAAAATAATATGACATTTTGGTGACCAATCTCAC
*
2022734 CAAATTAAAAGATTGGTGGTGACTCTACAATTTGGTGTTTTATCTGATTCATGGA
131 CAAATTAAAAGATTGGTGGCGACTCTACAATTTGGTGTTTTATCTGATTCATGGA
2022789 AGATAAACAC
Statistics
Matches: 178, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
187 94 0.53
188 84 0.47
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.40
Consensus pattern (188 bp):
TAATCCTTCTCCACACGTAACCGACTCCCGAACTCATTTTTCTGGTAAGCAGACTCGAGTTGTAT
TATTTTAATATTATTCTTAGGAATTTTTTATTAAAATAATATGACATTTTGGTGACCAATCTCAC
CAAATTAAAAGATTGGTGGCGACTCTACAATTTGGTGTTTTATCTGATTCATGGATTC
Found at i:2023402 original size:12 final size:12
Alignment explanation
Indices: 2023385--2023427 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
2023375 TCCATTTGTA
2023385 ATAATAATATAT
1 ATAATAATATAT
*
2023397 ATAATAATTTAT
1 ATAATAATATAT
* *
2023409 ATATTAAAATAT
1 ATAATAATATAT
2023421 ATAATAA
1 ATAATAA
2023428 CATAACACTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATAATAATATAT
Found at i:2024093 original size:20 final size:20
Alignment explanation
Indices: 2024066--2024151 Score: 136
Period size: 20 Copynumber: 4.3 Consensus size: 20
2024056 TGAGAGACTG
*
2024066 ACAAATGACCCAAAGGCTTT
1 ACAAATGACCCGAAGGCTTT
*
2024086 ATAAATGACCCGAAGGCTTT
1 ACAAATGACCCGAAGGCTTT
*
2024106 ACAAATGACCTGAAGGCTTT
1 ACAAATGACCCGAAGGCTTT
*
2024126 ACAAATGACTCGAAGGCTTT
1 ACAAATGACCCGAAGGCTTT
2024146 ACAAAT
1 ACAAAT
2024152 TCGTGAGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (20 bp):
ACAAATGACCCGAAGGCTTT
Found at i:2025577 original size:42 final size:42
Alignment explanation
Indices: 2025531--2025636 Score: 112
Period size: 42 Copynumber: 2.6 Consensus size: 42
2025521 AGGTCTTTAG
** *
2025531 CATGCCCCGCATAGATTATTTTTGA-TGAAAATGGGCCTTCAA
1 CATGCCCCAAATAGATTATTTCTGACTG-AAATGGGCCTTCAA
* * * *
2025573 CATGCCCTAAATATATTATTTCTGACTGAAATGGGCCTTTAG
1 CATGCCCCAAATAGATTATTTCTGACTGAAATGGGCCTTCAA
2025615 CATGCCCC--AT-GATTATTTCTGA
1 CATGCCCCAAATAGATTATTTCTGA
2025637 ATAGGTTTTC
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
39 11 0.20
40 2 0.04
42 39 0.72
43 2 0.04
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (42 bp):
CATGCCCCAAATAGATTATTTCTGACTGAAATGGGCCTTCAA
Found at i:2031742 original size:20 final size:20
Alignment explanation
Indices: 2031717--2031757 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2031707 AGCCTTCTGT
2031717 TTGCTCTCTGT-GTTATTTCC
1 TTGCTCT-TGTGGTTATTTCC
*
2031737 TTGCTCTTGTGGTTGTTTCC
1 TTGCTCTTGTGGTTATTTCC
2031757 T
1 T
2031758 CTCTTGCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.02, C:0.22, G:0.20, T:0.56
Consensus pattern (20 bp):
TTGCTCTTGTGGTTATTTCC
Found at i:2032300 original size:10 final size:10
Alignment explanation
Indices: 2032285--2032335 Score: 60
Period size: 10 Copynumber: 5.7 Consensus size: 10
2032275 ACCATTTGTA
2032285 ATAATAATAT
1 ATAATAATAT
2032295 ATAATAAT-T
1 ATAATAATAT
2032304 -T-AT-ATAT
1 ATAATAATAT
2032311 -TAAT-ATAT
1 ATAATAATAT
2032319 ATAATAATAT
1 ATAATAATAT
2032329 ATAATAA
1 ATAATAA
2032336 CATAACACTC
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
6 2 0.05
7 4 0.11
8 7 0.19
9 5 0.14
10 19 0.51
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
ATAATAATAT
Found at i:2032309 original size:12 final size:11
Alignment explanation
Indices: 2032285--2032335 Score: 61
Period size: 12 Copynumber: 4.6 Consensus size: 11
2032275 ACCATTTGTA
2032285 ATAATAA-TAT
1 ATAATAATTAT
2032295 ATAATAATTTAT
1 ATAATAA-TTAT
*
2032307 ATATTAATATAT
1 ATAATAAT-TAT
2032319 ATAATAA-TAT
1 ATAATAATTAT
2032329 ATAATAA
1 ATAATAA
2032336 CATAACACTC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
10 17 0.47
11 1 0.03
12 18 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
ATAATAATTAT
Done.