Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 9 of 213
Found at i:2581602 original size:26 final size:29
Alignment explanation
Indices: 2581555--2581609 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
2581545 CGCATAAGTG
2581555 TATATATATTATAAATATTTAAAG-TTAA
1 TATATATATTATAAATATTTAAAGCTTAA
2581583 TATATATATTAT-AATA-TTAAAGCTTAA
1 TATATATATTATAAATATTTAAAGCTTAA
2581610 AAGTTAAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 6 0.23
27 8 0.31
28 12 0.46
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (29 bp):
TATATATATTATAAATATTTAAAGCTTAA
Found at i:2581698 original size:13 final size:13
Alignment explanation
Indices: 2581678--2581723 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
2581668 AATGAAGGAG
*
2581678 AGAAAGAAACGAA
1 AGAAAGAAAAGAA
* *
2581691 ACAAAG-AAGGAA
1 AGAAAGAAAAGAA
2581703 AGAAAGAAAAGAA
1 AGAAAGAAAAGAA
2581716 AGAAAGAA
1 AGAAAGAA
2581724 GGAGAATAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 10 0.36
13 18 0.64
ACGTcount: A:0.72, C:0.04, G:0.24, T:0.00
Consensus pattern (13 bp):
AGAAAGAAAAGAA
Found at i:2581700 original size:25 final size:25
Alignment explanation
Indices: 2581671--2581728 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
2581661 AATGGAAAAT
*
2581671 GAAGGAGAGAAAGAAACGAAACAAA
1 GAAGGAGAGAAAGAAAAGAAACAAA
* *
2581696 GAAGGAAAGAAAGAAAAGAAAGAAA
1 GAAGGAGAGAAAGAAAAGAAACAAA
2581721 GAAGGAGA
1 GAAGGAGA
2581729 ATAGTTAGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.66, C:0.03, G:0.31, T:0.00
Consensus pattern (25 bp):
GAAGGAGAGAAAGAAAAGAAACAAA
Found at i:2581709 original size:4 final size:4
Alignment explanation
Indices: 2581678--2581723 Score: 56
Period size: 4 Copynumber: 11.0 Consensus size: 4
2581668 AATGAAGGAG
* *
2581678 AGAA AGAA ACGAA ACAA AGAA GGAA AGAA AGAAA AGAA AGAA AGAA
1 AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AG-AA AGAA AGAA AGAA
2581724 GGAGAATAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
4 28 0.78
5 8 0.22
ACGTcount: A:0.72, C:0.04, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:2582010 original size:30 final size:28
Alignment explanation
Indices: 2581956--2582011 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
2581946 AATTGTAGAA
*
2581956 TAAATTGTAAATTTTGAGTATTAGGGAC
1 TAAATTGTAAATTTTGAATATTAGGGAC
2581984 TAAATTGTGAAAATTTTGAA-ATTTAGGG
1 TAAATTGT--AAATTTTGAATA-TTAGGG
2582012 GTTTAAGTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 8 0.33
29 1 0.04
30 15 0.62
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.39
Consensus pattern (28 bp):
TAAATTGTAAATTTTGAATATTAGGGAC
Found at i:2582415 original size:24 final size:24
Alignment explanation
Indices: 2582388--2582434 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2582378 ATTGAAATGG
2582388 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
2582412 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
2582435 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:2582643 original size:41 final size:41
Alignment explanation
Indices: 2582599--2582733 Score: 154
Period size: 40 Copynumber: 3.4 Consensus size: 41
2582589 GACTTCGAGT
*
2582599 CGATGAGACACTGGGTGTCAATTTATTACTTCGGATTAATT
1 CGATGAGACACTGGGTGTCAATTTATTACTTCGGATTAATC
* * *
2582640 CGATGAGGCACTGGGTGCCAA--T-TTACTTCGGTTTAA-C
1 CGATGAGACACTGGGTGTCAATTTATTACTTCGGATTAATC
* * **
2582677 CGATAAGACACTGGGTGTTAATTTATTACTTCAAATT-ATC
1 CGATGAGACACTGGGTGTCAATTTATTACTTCGGATTAATC
*
2582717 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
2582734 CCAAACTGGT
Statistics
Matches: 77, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
37 17 0.22
38 13 0.17
39 3 0.04
40 25 0.32
41 19 0.25
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (41 bp):
CGATGAGACACTGGGTGTCAATTTATTACTTCGGATTAATC
Found at i:2582901 original size:20 final size:20
Alignment explanation
Indices: 2582876--2582914 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2582866 TGAATATGGA
2582876 ATGGATAAAGCAATTGCATT
1 ATGGATAAAGCAATTGCATT
2582896 ATGGATAAAGCAATTGCAT
1 ATGGATAAAGCAATTGCAT
2582915 AAATGAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (20 bp):
ATGGATAAAGCAATTGCATT
Found at i:2591391 original size:22 final size:22
Alignment explanation
Indices: 2591366--2591407 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2591356 ATACAAACAT
2591366 TAATAATAAAAT-ATTAGCAATA
1 TAATAATAAAATGA-TAGCAATA
2591388 TAATAATAAAATGATAGCAA
1 TAATAATAAAATGATAGCAA
2591408 CAGTAGCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.29
Consensus pattern (22 bp):
TAATAATAAAATGATAGCAATA
Found at i:2597359 original size:27 final size:23
Alignment explanation
Indices: 2597308--2597355 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
2597298 TTTTTCAAAG
2597308 AATTTTTTAAATAAATAAGAAAT
1 AATTTTTTAAATAAATAAGAAAT
2597331 AATTTTTTAAATAAATAAGAAAT
1 AATTTTTTAAATAAATAAGAAAT
2597354 AA
1 AA
2597356 ATAAACTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (23 bp):
AATTTTTTAAATAAATAAGAAAT
Found at i:2601039 original size:6 final size:6
Alignment explanation
Indices: 2600993--2601038 Score: 56
Period size: 6 Copynumber: 7.3 Consensus size: 6
2600983 AATATGAGTT
* *
2600993 GAAAGA GAATGA GAAAGA GAAAGA TGATAAGA GAAAGA GATAGA GA
1 GAAAGA GAAAGA GAAAGA GAAAGA -GA-AAGA GAAAGA GAAAGA GA
2601039 TCCTTGTGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
6 27 0.77
7 4 0.11
8 4 0.11
ACGTcount: A:0.59, C:0.00, G:0.33, T:0.09
Consensus pattern (6 bp):
GAAAGA
Found at i:2601334 original size:14 final size:14
Alignment explanation
Indices: 2601315--2601345 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2601305 TATTTTCTGA
2601315 TGTTTGATTGAATC
1 TGTTTGATTGAATC
2601329 TGTTTGATTGAATC
1 TGTTTGATTGAATC
2601343 TGT
1 TGT
2601346 GTAAAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.23, T:0.52
Consensus pattern (14 bp):
TGTTTGATTGAATC
Found at i:2605481 original size:24 final size:24
Alignment explanation
Indices: 2605453--2605508 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
2605443 CTCCCTTCAA
*
2605453 TCGTAGACGTAGCCCTTCTCCAAT
1 TCGTAGACGGAGCCCTTCTCCAAT
* *
2605477 TCGTAGGCGGAGCCGTTCTCCAAT
1 TCGTAGACGGAGCCCTTCTCCAAT
*
2605501 TCGCAGAC
1 TCGTAGAC
2605509 CTCTTCGTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.32, G:0.23, T:0.25
Consensus pattern (24 bp):
TCGTAGACGGAGCCCTTCTCCAAT
Found at i:2607815 original size:18 final size:18
Alignment explanation
Indices: 2607792--2607832 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2607782 ATATTACAAA
*
2607792 ATTTTGATGAT-AAACATG
1 ATTTTGATCATGAAA-ATG
2607810 ATTTTGATCATGAAAATG
1 ATTTTGATCATGAAAATG
2607828 ATTTT
1 ATTTT
2607833 CCAATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.44
Consensus pattern (18 bp):
ATTTTGATCATGAAAATG
Found at i:2608286 original size:6 final size:7
Alignment explanation
Indices: 2608267--2608313 Score: 71
Period size: 7 Copynumber: 7.0 Consensus size: 7
2608257 TATTTATTAA
2608267 GGTTTTT
1 GGTTTTT
2608274 GGTTTTT
1 GGTTTTT
2608281 GGTTTTT
1 GGTTTTT
2608288 GGTTTTT
1 GGTTTTT
*
2608295 GGTATTT
1 GGTTTTT
2608302 -GTTTTT
1 GGTTTTT
2608308 -GTTTTT
1 GGTTTTT
2608314 ATTTTATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
6 11 0.29
7 27 0.71
ACGTcount: A:0.02, C:0.00, G:0.26, T:0.72
Consensus pattern (7 bp):
GGTTTTT
Found at i:2624320 original size:16 final size:17
Alignment explanation
Indices: 2624299--2624338 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
2624289 GATTTGAATC
2624299 ATATATAAGTATAT-AT
1 ATATATAAGTATATCAT
*
2624315 ATATATATGTATATGCAT
1 ATATATAAGTATAT-CAT
2624333 ATATAT
1 ATATAT
2624339 TTTTTTATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 13 0.62
18 8 0.38
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (17 bp):
ATATATAAGTATATCAT
Found at i:2631306 original size:3 final size:3
Alignment explanation
Indices: 2631298--2631322 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2631288 TTTCTCTCTC
2631298 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
2631323 ATTTTCTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:2637044 original size:18 final size:19
Alignment explanation
Indices: 2637021--2637056 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2637011 CATAGCTTGG
*
2637021 TATTATATTATA-AATAAT
1 TATTATATAATACAATAAT
2637039 TATTATATAATACAATAA
1 TATTATATAATACAATAA
2637057 AAGAATCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (19 bp):
TATTATATAATACAATAAT
Found at i:2643997 original size:15 final size:15
Alignment explanation
Indices: 2643977--2644008 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2643967 ACATATGTGG
*
2643977 AAAATAAAATAAGAT
1 AAAATAAAATAACAT
2643992 AAAATAAAATAACAT
1 AAAATAAAATAACAT
2644007 AA
1 AA
2644009 TATATAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (15 bp):
AAAATAAAATAACAT
Found at i:2644053 original size:25 final size:25
Alignment explanation
Indices: 2644006--2644053 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
2643996 TAAAATAACA
* *
2644006 TAATATATAAACAATATACATATTT
1 TAATATATAAAAAACATACATATTT
* *
2644031 TAATGTATAAAAAACATAGATAT
1 TAATATATAAAAAACATACATAT
2644054 ACATGTATAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.35
Consensus pattern (25 bp):
TAATATATAAAAAACATACATATTT
Found at i:2644259 original size:3 final size:3
Alignment explanation
Indices: 2644244--2644276 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
2644234 AATAGTAAGG
*
2644244 ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2644277 CTAAACAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2644259 original size:12 final size:12
Alignment explanation
Indices: 2644228--2644273 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
2644218 TGAATATAAA
*
2644228 AATAGTAATAGT
1 AATAATAATAGT
**
2644240 AAGGATAATAGT
1 AATAATAATAGT
*
2644252 AATAATAATAAT
1 AATAATAATAGT
2644264 AATAATAATA
1 AATAATAATA
2644274 ATACTAAACA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (12 bp):
AATAATAATAGT
Found at i:2644265 original size:18 final size:18
Alignment explanation
Indices: 2644210--2644276 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 18
2644200 ACAATAACAA
* *
2644210 AATATTAATGAAT-ATAAA
1 AATAGTAAT-AATAATAAT
* **
2644228 AATAGTAATAGTAAGGAT
1 AATAGTAATAATAATAAT
2644246 AATAGTAATAATAATAAT
1 AATAGTAATAATAATAAT
*
2644264 AATAATAATAATA
1 AATAGTAATAATA
2644277 CTAAACAACA
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
17 2 0.05
18 37 0.95
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (18 bp):
AATAGTAATAATAATAAT
Found at i:2645599 original size:15 final size:15
Alignment explanation
Indices: 2645573--2645605 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
2645563 TTTGATGATT
2645573 TTGGGCTATTGGGCTG
1 TTGGGCTATTGGG-TG
2645589 TTGGG-TATTGGGTG
1 TTGGGCTATTGGGTG
2645603 TTG
1 TTG
2645606 TAATTGGGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 7 0.41
16 5 0.29
ACGTcount: A:0.06, C:0.06, G:0.45, T:0.42
Consensus pattern (15 bp):
TTGGGCTATTGGGTG
Found at i:2667449 original size:17 final size:17
Alignment explanation
Indices: 2667427--2667460 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2667417 ATCCACTAAT
*
2667427 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
2667444 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
2667461 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:2672087 original size:17 final size:17
Alignment explanation
Indices: 2672065--2672098 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2672055 ATCCACTAAT
*
2672065 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
2672082 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
2672099 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:2672556 original size:5 final size:5
Alignment explanation
Indices: 2672546--2672597 Score: 104
Period size: 5 Copynumber: 10.4 Consensus size: 5
2672536 CACTTGAGAC
2672546 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
2672596 AT
1 AT
2672598 TAGATATTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 47 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:2672971 original size:11 final size:11
Alignment explanation
Indices: 2672936--2672971 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
2672926 TTTTATTGTC
2672936 ATTTTACTATT
1 ATTTTACTATT
*
2672947 ATATTACTATT
1 ATTTTACTATT
*
2672958 ATTTTATTATT
1 ATTTTACTATT
2672969 ATT
1 ATT
2672972 GTTTAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTTTACTATT
Found at i:2675263 original size:44 final size:44
Alignment explanation
Indices: 2675188--2675271 Score: 136
Period size: 44 Copynumber: 1.9 Consensus size: 44
2675178 ATAATAATTT
2675188 TTTTTGCAATATTTATAATTTTTTAATTTTTAATAATTTTATTC
1 TTTTTGCAATATTTATAATTTTTTAATTTTTAATAATTTTATTC
2675232 TTTTTGCAAT-TTTAT-ATTATTTTAATATTTTAATAATTTT
1 TTTTTGCAATATTTATAATT-TTTTAAT-TTTTAATAATTTT
2675272 TTCCCATTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
42 3 0.08
43 12 0.32
44 23 0.61
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (44 bp):
TTTTTGCAATATTTATAATTTTTTAATTTTTAATAATTTTATTC
Found at i:2676056 original size:15 final size:15
Alignment explanation
Indices: 2676036--2676074 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
2676026 GAAATAAAAT
*
2676036 TTGAGTCTAGTCAAG
1 TTGAGTCGAGTCAAG
*
2676051 TTGAGTCGAGTCGAG
1 TTGAGTCGAGTCAAG
*
2676066 TCGAGTCGA
1 TTGAGTCGA
2676075 ATGAAGTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.23, C:0.15, G:0.33, T:0.28
Consensus pattern (15 bp):
TTGAGTCGAGTCAAG
Found at i:2676273 original size:18 final size:19
Alignment explanation
Indices: 2676251--2676294 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
2676241 TAAATTCTAA
*
2676251 AAATTTTATAAA-TATTTT
1 AAATTTTAAAAATTATTTT
*
2676269 GAATTTTAAAAATTATTTT
1 AAATTTTAAAAATTATTTT
2676288 AAATTTT
1 AAATTTT
2676295 TTTTTGTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
AAATTTTAAAAATTATTTT
Found at i:2676278 original size:27 final size:28
Alignment explanation
Indices: 2676243--2676296 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
2676233 TTATAAAATA
2676243 AATTCTAAAAATT-TTATAAATATTTTG
1 AATTCTAAAAATTATTATAAATATTTTG
* * *
2676270 AATTTTAAAAATTATTTTAAATTTTTT
1 AATTCTAAAAATTATTATAAATATTTT
2676297 TTTGTATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (28 bp):
AATTCTAAAAATTATTATAAATATTTTG
Found at i:2682463 original size:20 final size:22
Alignment explanation
Indices: 2682424--2682463 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2682414 ACACTTCTCG
*
2682424 AGGTATCACGATATCCACCTCT
1 AGGTATCACGACATCCACCTCT
2682446 AGGTATC-CGACA-CCACCT
1 AGGTATCACGACATCCACCT
2682464 TCGTCAATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 4 0.24
22 7 0.41
ACGTcount: A:0.28, C:0.35, G:0.15, T:0.23
Consensus pattern (22 bp):
AGGTATCACGACATCCACCTCT
Found at i:2690627 original size:31 final size:31
Alignment explanation
Indices: 2690583--2690648 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
2690573 TTAATATAAT
* * *
2690583 ATTTGGTAATTGAATTTGACAATTTTTTTTA
1 ATTTGATAATTGAACTTGACAATTTTTCTTA
* *
2690614 ATTTGATATTTGAACTTGACTATTTTTCTTA
1 ATTTGATAATTGAACTTGACAATTTTTCTTA
2690645 ATTT
1 ATTT
2690649 AGTACTTGTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.06, G:0.11, T:0.56
Consensus pattern (31 bp):
ATTTGATAATTGAACTTGACAATTTTTCTTA
Found at i:2691822 original size:18 final size:18
Alignment explanation
Indices: 2691799--2691841 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2691789 GAATAGGTTT
2691799 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
2691817 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
2691835 TTAATTA
1 TTAATTA
2691842 CACTTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:2707275 original size:19 final size:19
Alignment explanation
Indices: 2707251--2707288 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2707241 GCTTCCTTGC
2707251 CATAGAAAATAAGCCTATT
1 CATAGAAAATAAGCCTATT
2707270 CATAGAAAATAAGCCTATT
1 CATAGAAAATAAGCCTATT
2707289 TCAGCTACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (19 bp):
CATAGAAAATAAGCCTATT
Found at i:2708404 original size:14 final size:14
Alignment explanation
Indices: 2708385--2708412 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2708375 ACAACCCCAG
2708385 AACAATAGAAGAGT
1 AACAATAGAAGAGT
2708399 AACAATAGAAGAGT
1 AACAATAGAAGAGT
2708413 TAAGTTAAAG
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:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
AACAATAGAAGAGT
Found at i:2715490 original size:20 final size:21
Alignment explanation
Indices: 2715449--2715495 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
2715439 GGCCCGGTCC
2715449 ATTTTTTAATAAAATACTAAAA
1 ATTTTTTAATAAAATAC-AAAA
2715471 ATTTATTTAA-AAAATA-AAAA
1 ATTT-TTTAATAAAATACAAAA
2715491 ATTTT
1 ATTTT
2715496 AAAAAAAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.04
20 8 0.33
22 10 0.42
23 5 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTTTTTAATAAAATACAAAA
Found at i:2716364 original size:58 final size:57
Alignment explanation
Indices: 2716297--2716412 Score: 171
Period size: 58 Copynumber: 2.0 Consensus size: 57
2716287 TTTACCGTAT
* *
2716297 AAACACTTT-GGTATTGTACTCATAATAATATTTTATAATAATTTCTTTTAAGAATAAA
1 AAACACTTTGGGTATTGTACTCATAAAAATA-TTTATAATAATCT-TTTTAAGAATAAA
* *
2716355 AAACTCTTTGGGTATTTTACTCATAAAAATATTTATAATAATCTTTTTAAGAATAAA
1 AAACACTTTGGGTATTGTACTCATAAAAATATTTATAATAATCTTTTTAAGAATAAA
2716412 A
1 A
2716413 TTAGCATGGA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
57 14 0.26
58 20 0.38
59 19 0.36
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (57 bp):
AAACACTTTGGGTATTGTACTCATAAAAATATTTATAATAATCTTTTTAAGAATAAA
Found at i:2716434 original size:56 final size:59
Alignment explanation
Indices: 2716308--2716436 Score: 149
Period size: 59 Copynumber: 2.2 Consensus size: 59
2716298 AACACTTTGG
* * * * * *
2716308 TATTGTACTCATAATAATATTTTATAATAATTTCTTTTAAGAATAAAAAACTCTTTGGG
1 TATTTTACTCATAAAAATATTTTATAATAATCTCTTTTAAGAATAAAAAACGCTATGGA
*
2716367 TATTTTACTCATAAAAATA-TTTATAATAATCT-TTTTAAGAATAAAATTA-GC-ATGGA
1 TATTTTACTCATAAAAATATTTTATAATAATCTCTTTTAAGAATAAAA-AACGCTATGGA
*
2716423 TGTTTTACTCATAA
1 TATTTTACTCATAA
2716437 GATTTTTACT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
56 16 0.26
57 15 0.25
58 13 0.21
59 17 0.28
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (59 bp):
TATTTTACTCATAAAAATATTTTATAATAATCTCTTTTAAGAATAAAAAACGCTATGGA
Found at i:2719734 original size:6 final size:6
Alignment explanation
Indices: 2719723--2719747 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2719713 ACCATACGCA
2719723 TGCATC TGCATC TGCATC TGCATC T
1 TGCATC TGCATC TGCATC TGCATC T
2719748 TCAACTCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (6 bp):
TGCATC
Found at i:2724422 original size:21 final size:22
Alignment explanation
Indices: 2724393--2724439 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
2724383 CAGAAGGAGT
2724393 GAGTAGTACT-TCGCAGCAGGTG
1 GAGTAGTACTCT-GCAGCAGGTG
2724415 GAGT-GTACTCTGCAGCAGGTG
1 GAGTAGTACTCTGCAGCAGGTG
2724436 GAGT
1 GAGT
2724440 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.21, C:0.17, G:0.38, T:0.23
Consensus pattern (22 bp):
GAGTAGTACTCTGCAGCAGGTG
Found at i:2726232 original size:13 final size:13
Alignment explanation
Indices: 2726216--2726241 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2726206 TTATAACTTG
2726216 AATTTAATATTTA
1 AATTTAATATTTA
2726229 AATTTAATATTTA
1 AATTTAATATTTA
2726242 TTTTTCAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATTTAATATTTA
Found at i:2727997 original size:15 final size:16
Alignment explanation
Indices: 2727977--2728013 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2727967 GATTTTTCCC
*
2727977 TAAAAA-AATCAAATA
1 TAAAAATAATAAAATA
2727992 TAAAAATAATAAAATA
1 TAAAAATAATAAAATA
2728008 TAAAAA
1 TAAAAA
2728014 GCATCAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (16 bp):
TAAAAATAATAAAATA
Found at i:2736387 original size:17 final size:17
Alignment explanation
Indices: 2736362--2736396 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2736352 TCACTGGAAA
2736362 ATTAAATTTTAACAACT
1 ATTAAATTTTAACAACT
* *
2736379 ATTAGATTTTAGCAACT
1 ATTAAATTTTAACAACT
2736396 A
1 A
2736397 AGAGTACGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (17 bp):
ATTAAATTTTAACAACT
Found at i:2737358 original size:51 final size:51
Alignment explanation
Indices: 2737302--2737398 Score: 149
Period size: 51 Copynumber: 1.9 Consensus size: 51
2737292 GTTGTTGCTT
* *
2737302 TGGTTAAGATACTTAGTAGTTTGTTTTAATTTTTGAAGATTTTATGGCTAG
1 TGGTTAAGATACTTAGTAATTTGTTTTAATTATTGAAGATTTTATGGCTAG
* * *
2737353 TGGTTAAGTTACTTATTAATTTGTTTTAGTTATTGAAGATTTTATG
1 TGGTTAAGATACTTAGTAATTTGTTTTAATTATTGAAGATTTTATG
2737399 TCTCAATACT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.26, C:0.03, G:0.20, T:0.52
Consensus pattern (51 bp):
TGGTTAAGATACTTAGTAATTTGTTTTAATTATTGAAGATTTTATGGCTAG
Found at i:2738029 original size:13 final size:13
Alignment explanation
Indices: 2738011--2738035 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2738001 AATATTGCCT
2738011 TTATTATTATTTG
1 TTATTATTATTTG
2738024 TTATTATTATTT
1 TTATTATTATTT
2738036 TTTAGAAAAA
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:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
TTATTATTATTTG
Found at i:2738863 original size:18 final size:16
Alignment explanation
Indices: 2738840--2738875 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
2738830 ATAGGGTTTT
2738840 TAAAAGTATATTATAAAA
1 TAAAAGT-TATTA-AAAA
2738858 TAAAAGTTATTAAAAA
1 TAAAAGTTATTAAAAA
2738874 TA
1 TA
2738876 TATTATATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (16 bp):
TAAAAGTTATTAAAAA
Found at i:2738960 original size:39 final size:38
Alignment explanation
Indices: 2738916--2738991 Score: 98
Period size: 39 Copynumber: 2.0 Consensus size: 38
2738906 CATCACAAAG
* * *
2738916 TTAAAATAATAATGTATGATAATAATAAAATAAAATAAT
1 TTAAAATAATAATGCATAATAA-AATAAAAAAAAATAAT
* *
2738955 TTAAAATAATAGTGCATAATAAAGTAAAAAAAAATAA
1 TTAAAATAATAATGCATAATAAAATAAAAAAAAATAA
2738992 GTAACTGAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
38 13 0.41
39 19 0.59
ACGTcount: A:0.63, C:0.01, G:0.07, T:0.29
Consensus pattern (38 bp):
TTAAAATAATAATGCATAATAAAATAAAAAAAAATAAT
Found at i:2739056 original size:23 final size:23
Alignment explanation
Indices: 2739030--2739074 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2739020 ATAATGTCAA
2739030 TAATAATAATAATAA-TAATAAAT
1 TAATAATAA-AATAATTAATAAAT
* *
2739053 TAATATTAAACTAATTAATAAA
1 TAATAATAAAATAATTAATAAA
2739075 ACAATGGGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
TAATAATAAAATAATTAATAAAT
Found at i:2739999 original size:11 final size:11
Alignment explanation
Indices: 2739979--2740045 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
2739969 CAAAAATTAA
2739979 AAAAAGTATTTT
1 AAAAA-TATTTT
2739991 AAAAATATTTT
1 AAAAATATTTT
2740002 --AAA-A-TTT
1 AAAAATATTTT
* *
2740009 AAAAA-AATTA
1 AAAAATATTTT
2740019 AAAAAGTATTTT
1 AAAAA-TATTTT
*
2740031 AAAAAAATTTT
1 AAAAATATTTT
2740042 AAAA
1 AAAA
2740046 TTAAAAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
7 3 0.07
8 1 0.02
9 7 0.15
10 7 0.15
11 15 0.33
12 13 0.28
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:2740006 original size:43 final size:42
Alignment explanation
Indices: 2739952--2740097 Score: 199
Period size: 43 Copynumber: 3.5 Consensus size: 42
2739942 ACCAAAAATT
2739952 TATTTTAAAAATTAAAACAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATTAAAA-AAAAATTAAAAAAAGTATTTTAAAAA
*
2739996 TATTTTAAAATT-TAAAAAAATT-AAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAAAATTAAAAAAAGTATTTTAAAAA
* * *
2740036 AATTTTAAAATTAAAAAAATTAA-AAAAAAAAGTATTTTAAAAG
1 TATTTTAAAATTAAAAAAA--AATTAAAAAAAGTATTTTAAAAA
2740079 TATTTTAAAATTAAAAAAA
1 TATTTTAAAATTAAAAAAA
2740098 TAAAAATATT
Statistics
Matches: 92, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
40 29 0.32
41 12 0.13
42 2 0.02
43 43 0.47
44 6 0.07
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.34
Consensus pattern (42 bp):
TATTTTAAAATTAAAAAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:2740019 original size:9 final size:9
Alignment explanation
Indices: 2740002--2740063 Score: 54
Period size: 9 Copynumber: 6.6 Consensus size: 9
2739992 AAAATATTTT
*
2740002 AAAATTTAA
1 AAAAATTAA
2740011 AAAAATTAA
1 AAAAATTAA
2740020 AAAAGTATTTTAA
1 AAAA--A--TTAA
*
2740033 AAAAATT-T
1 AAAAATTAA
*
2740041 TAAAATTAA
1 AAAAATTAA
2740050 AAAAATTAA
1 AAAAATTAA
2740059 AAAAA
1 AAAAA
2740064 AAAGTATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
8 6 0.14
9 27 0.63
11 2 0.05
13 8 0.19
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (9 bp):
AAAAATTAA
Found at i:2740062 original size:17 final size:17
Alignment explanation
Indices: 2740029--2740062 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2740019 AAAAAGTATT
**
2740029 TTAAAAAAATTTTAAAA
1 TTAAAAAAATTAAAAAA
2740046 TTAAAAAAATTAAAAAA
1 TTAAAAAAATTAAAAAA
2740063 AAAAGTATTT
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TTAAAAAAATTAAAAAA
Found at i:2740077 original size:11 final size:11
Alignment explanation
Indices: 2740063--2740088 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2740053 AATTAAAAAA
2740063 AAAAGTATTTT
1 AAAAGTATTTT
2740074 AAAAGTATTTT
1 AAAAGTATTTT
2740085 AAAA
1 AAAA
2740089 TTAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:2752931 original size:19 final size:19
Alignment explanation
Indices: 2752907--2753057 Score: 212
Period size: 19 Copynumber: 7.8 Consensus size: 19
2752897 AATTTTTGAG
2752907 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
2752926 GATATGCAATCCAAGATAT
1 GATATGCAATCTTAGATAT
2752945 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
2752966 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
** *
2752985 GATATATAATTTTAGATAT
1 GATATGCAATCTTAGATAT
*
2753004 GATATGCAATCTTAGAGAT
1 GATATGCAATCTTAGATAT
**
2753023 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
2753042 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
2753058 ATATATGATT
Statistics
Matches: 114, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
19 97 0.85
21 17 0.15
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:2752952 original size:40 final size:38
Alignment explanation
Indices: 2752914--2753057 Score: 234
Period size: 38 Copynumber: 3.7 Consensus size: 38
2752904 GAGGATATGC
**
2752914 AATCTTAGATATGATATGCAATCCAAGATATGATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATGATATAT
2752952 GCAATCTTAGATATGATATGCAATCTTAGATATGATATAT
1 --AATCTTAGATATGATATGCAATCTTAGATATGATATAT
* *
2752992 AATTTTAGATATGATATGCAATCTTAGAGATGATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATGATATAT
2753030 AATCTTAGATATGATATGCAATCTTAGA
1 AATCTTAGATATGATATGCAATCTTAGA
2753058 ATATATGATT
Statistics
Matches: 99, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
38 63 0.64
40 36 0.36
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.37
Consensus pattern (38 bp):
AATCTTAGATATGATATGCAATCTTAGATATGATATAT
Found at i:2754491 original size:98 final size:98
Alignment explanation
Indices: 2754371--2754567 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
2754361 TTAAAAATAA
* * *
2754371 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTAATTTC
2754436 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
2754469 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTAATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTAATTTC
*
2754534 TTAAATCTTGGATGAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
2754567 T
1 T
2754568 TTTATTGTAC
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTAATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:2754731 original size:94 final size:94
Alignment explanation
Indices: 2754570--2754759 Score: 380
Period size: 94 Copynumber: 2.0 Consensus size: 94
2754560 TTTAAAGTTT
2754570 TATTGTACAAGTATTTTGGCCCAATTCATTTTGGGGAAAATTAGAATGCTGTGCCCTAACGCATT
1 TATTGTACAAGTATTTTGGCCCAATTCATTTTGGGGAAAATTAGAATGCTGTGCCCTAACGCATT
2754635 GGGTGTGGTATCTTCTTTCTCTGAAATAA
66 GGGTGTGGTATCTTCTTTCTCTGAAATAA
2754664 TATTGTACAAGTATTTTGGCCCAATTCATTTTGGGGAAAATTAGAATGCTGTGCCCTAACGCATT
1 TATTGTACAAGTATTTTGGCCCAATTCATTTTGGGGAAAATTAGAATGCTGTGCCCTAACGCATT
2754729 GGGTGTGGTATCTTCTTTCTCTGAAATAA
66 GGGTGTGGTATCTTCTTTCTCTGAAATAA
2754758 TA
1 TA
2754760 AGGGTCTTAA
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 96 1.00
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (94 bp):
TATTGTACAAGTATTTTGGCCCAATTCATTTTGGGGAAAATTAGAATGCTGTGCCCTAACGCATT
GGGTGTGGTATCTTCTTTCTCTGAAATAA
Found at i:2758775 original size:20 final size:20
Alignment explanation
Indices: 2758739--2758794 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
2758729 AAAATATTTC
*
2758739 AAAA-AAAAAGAGGAAAAAG-
1 AAAAGAAAAAG-GAAAAAAGT
2758758 AAAAGGAAAAAGGAAAAAAGT
1 AAAA-GAAAAAGGAAAAAAGT
*
2758779 AAAAGAAAAAGTAAAA
1 AAAAGAAAAAGGAAAA
2758795 GGAGAGGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 4 0.12
20 18 0.56
21 10 0.31
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.04
Consensus pattern (20 bp):
AAAAGAAAAAGGAAAAAAGT
Found at i:2758787 original size:12 final size:12
Alignment explanation
Indices: 2758753--2758795 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
2758743 AAAAAGAGGA
* *
2758753 AAAAGAAAAGGA
1 AAAAGAAAAAGT
2758765 AAAAGGAAAAAAGT
1 AAAA-G-AAAAAGT
2758779 AAAAGAAAAAGT
1 AAAAGAAAAAGT
2758791 AAAAG
1 AAAAG
2758796 GAGAGGCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 16 0.59
13 2 0.07
14 9 0.33
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (12 bp):
AAAAGAAAAAGT
Found at i:2760244 original size:132 final size:132
Alignment explanation
Indices: 2760002--2760618 Score: 1022
Period size: 132 Copynumber: 4.7 Consensus size: 132
2759992 AACAGATCAG
* *
2760002 TGAAAATTGTAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATC-AACGACGGCGAATCTTATC
1 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAA-GACAGCGAATCTTATC
*
2760066 TTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAA
65 TTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAA
2760131 GGT
130 GGT
* *
2760134 TGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCGAAGACAGCGAATCTTATCT
1 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACAGCGAATCTTATCT
*
2760199 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAAAAG
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAG
2760264 GT
131 GT
** *
2760266 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATAT
1 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACAGCGAATCTTATCT
* *
2760331 TTCCAAGATAGTGGGAAGCAGATTTAAGCCATCAAGCCTTGTCTCCCTGAGCAGCCGCGGAGAAG
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAG
2760396 GT
131 GT
* * *
2760398 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGAAGCAGATCGAAGACAACAAATCTTATCT
1 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACAGCGAATCTTATCT
* *
2760463 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTTTCCCTGAGCAGCAGCGGAGTAG
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAG
2760528 GT
131 GT
* * * *
2760530 TGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAAAC-GACAAATCATATC
1 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACAG-CGAATCTTATC
2760594 TTTCCAAGATAGTGGGAAGCAGATT
65 TTTCCAAGATAGTGGGAAGCAGATT
2760619 AAAGTCGACA
Statistics
Matches: 454, Mismatches: 29, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
132 452 1.00
133 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (132 bp):
TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACAGCGAATCTTATCT
TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAG
GT
Found at i:2760729 original size:84 final size:83
Alignment explanation
Indices: 2760633--2761011 Score: 309
Period size: 84 Copynumber: 4.4 Consensus size: 83
2760623 TCGACAATCC
* *
2760633 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCATAGATCTTATCCCTCTGAAGTTGCAGAG
1 TATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAATCA-AGATCTTATCCCTCTGAAGTTACAGAG
*
2760698 AGCAAATCGCATCTAGTCT
65 AGCAGATCGCATCTAGTCT
* * * * *
2760717 TATCTCCCTAAAGTTGCAGTGGAGCAGACTAAGTAAACAAG-TCTTATCCTTCTAAAGTTACAGT
1 TATCTCCCTAAAGTTGCAGTGGAGCAGATTAA--AATCAAGATCTTATCCCTCTGAAGTTACAGA
* * *
2760781 GAGGCAGA-CTGAAGATGGCAAATCT
64 GA-GCAGATC-G--CAT--CTAGTCT
* * * *
2760806 TATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAATTACAGATCTTATCTCTCTGAAGTTACAGAG
1 TATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAATCA-AGATCTTATCCCTCTGAAGTTACAGAG
2760871 AGCAGATCGCATCTAGTCT
65 AGCAGATCGCATCTAGTCT
* * * * *
2760890 TATCTCCCTGAAGTTACGGTGGA-CAAGACTAAGTAAGCAAG-TCTTAT-CCTCCTGAAGTTACA
1 TATCTCCCTAAAGTTGCAGTGGAGC-AGATTAA--AATCAAGATCTTATCCCT-CTGAAGTTACA
* * * * *
2760952 GTGAGGCAGATTGAAGATGGCAAATCT
62 GAGA-GCAGATCG--CAT--CTAGTCT
* *
2760979 TATCTTCCTGAAGTTGCAGTGGAGCAGATTAAA
1 TATCTCCCTAAAGTTGCAGTGGAGCAGATTAAA
2761012 GCCGACAATC
Statistics
Matches: 235, Mismatches: 39, Indels: 39
0.75 0.12 0.12
Matches are distributed among these distances:
83 3 0.01
84 103 0.44
85 16 0.07
86 9 0.04
87 8 0.03
88 8 0.03
89 87 0.37
90 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (83 bp):
TATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAATCAAGATCTTATCCCTCTGAAGTTACAGAGA
GCAGATCGCATCTAGTCT
Found at i:2760827 original size:89 final size:88
Alignment explanation
Indices: 2760714--2761436 Score: 361
Period size: 89 Copynumber: 8.3 Consensus size: 88
2760704 TCGCATCTAG
* *
2760714 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAGTAAACAAGTCTTATCCTTCTAAAGTTACA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACAAGTCTTATCCTTCTGAAGTTACA
2760779 GTGAGGCAGACTGAAGATGGCAAA
66 GTGAGGCAGA-TGAAGATGGCAAA
* *
2760803 TCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAA--AATTAC-AGATCTTAT-CTCTCTGAAGT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAA--ACAAG-TCTTATCCT-TCTGAAGT
* * * *
2760864 TACAGAGA-GCAGATCG--CAT--CTAG
62 TACAGTGAGGCAGAT-GAAGATGGCAAA
* * * *
2760887 TCTTATCTCCCTGAAGTTACGGTGGA-CAAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTAC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGC-AGACTAAGTAAACAAGTCTTATCCTTCTGAAGTTAC
2760951 AGTGAGGCAGATTGAAGATGGCAAA
65 AGTGAGGCAGA-TGAAGATGGCAAA
* * *** * * * *
2760976 TCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAA-TCCTAT-CTCCCTAAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAACAAGTCTTATCCT-TCTGAAGTTA
* * * * *
2761039 CAGTG-GAGCGGATTAAAATTAG-AGA
64 CAGTGAG-GCAGATGAAGA-TGGCAAA
* * * * * * * *
2761064 TCTTATCTCTCTGAAGTTACAG-AGAGCAGA-T-CG-CATCTAA-TCTTAT-CTCCCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAAC-AAGTCTTATCCT-TCTGAAGTTA
* * * * *
2761123 CGGTG-GACA-AGGCTAAG-TAAGCAAG
64 CAGTGAGGCAGATG--AAGAT-GGCAAA
* ** *
2761148 TCTTATC-CTCCTGAAGTTACAGT-GAGGCAGACTGAAG-ATGGCAAATCTTAT-CTTCCTGAAG
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGTA-AACAAGTCTTATCCTT-CTGAAG
* * *
2761209 TTGCAGTG-GAGCAGATTAA-A-GCCGATAA
61 TTACAGTGAG-GCAGATGAAGATGGC-A-AA
* * * * * *
2761237 TCCTATCTTCCTGAAGTTGCAGTAGAGCGGATTAA--AATCACAGATCTTAT-CTCTCTGAAGTT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACA-AG-TCTTATCCT-TCTGAAGTT
* * * * *
2761299 GCAGAGA-GCAGATCG--CAT--CTAG
63 ACAGTGAGGCAGAT-GAAGATGGCAAA
* * * *
2761321 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGGAAGCAAGTCTTATCCTCCTGAAGTTACA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACAAGTCTTATCCTTCTGAAGTTACA
2761386 GTGAGGCAGACTGAAGATGGCAAA
66 GTGAGGCAGA-TGAAGATGGCAAA
2761410 TCTTATCTCCCTGAAGTTGCAGTGGAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAG
2761437 TATATTGAAG
Statistics
Matches: 487, Mismatches: 89, Indels: 116
0.70 0.13 0.17
Matches are distributed among these distances:
82 2 0.00
83 7 0.01
84 150 0.31
85 25 0.05
86 15 0.03
87 24 0.05
88 65 0.13
89 187 0.38
90 11 0.02
91 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (88 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACAAGTCTTATCCTTCTGAAGTTACA
GTGAGGCAGATGAAGATGGCAAA
Found at i:2760838 original size:173 final size:173
Alignment explanation
Indices: 2760628--2761011 Score: 608
Period size: 173 Copynumber: 2.2 Consensus size: 173
2760618 TAAAGTCGAC
* * * * * *
2760628 AATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCATAGATCTTATCCCTCTGAAGTTG
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCCCTCTGAAGTTA
*
2760693 CAGAGAGCAAATCGCATCTAGTCTTATCTCCCTAAAGTTGCAGTGGAGC-AGACTAAGTAAACAA
66 CAGAGAGCAAATCGCATCTAGTCTTATCTCCCTAAAGTTACAGTGGA-CAAGACTAAGTAAACAA
*
2760757 GTCTTATCCTTCTAAAGTTACAGTGAGGCAGACTGAAGATGGCA
130 GTCTTATCCTCCTAAAGTTACAGTGAGGCAGACTGAAGATGGCA
* *
2760801 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAATTACAGATCTTATCTCTCTGAAGTTA
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCCCTCTGAAGTTA
* * * *
2760866 CAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTACGGTGGACAAGACTAAGTAAGCAAG
66 CAGAGAGCAAATCGCATCTAGTCTTATCTCCCTAAAGTTACAGTGGACAAGACTAAGTAAACAAG
* *
2760931 TCTTATCCTCCTGAAGTTACAGTGAGGCAGATTGAAGATGGCA
131 TCTTATCCTCCTAAAGTTACAGTGAGGCAGACTGAAGATGGCA
2760974 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAA
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAA
2761012 GCCGACAATC
Statistics
Matches: 194, Mismatches: 16, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
172 1 0.01
173 193 0.99
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (173 bp):
AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCCCTCTGAAGTTA
CAGAGAGCAAATCGCATCTAGTCTTATCTCCCTAAAGTTACAGTGGACAAGACTAAGTAAACAAG
TCTTATCCTCCTAAAGTTACAGTGAGGCAGACTGAAGATGGCA
Found at i:2761067 original size:217 final size:217
Alignment explanation
Indices: 2760801--2761436 Score: 1110
Period size: 217 Copynumber: 2.9 Consensus size: 217
2760791 GAAGATGGCA
* *
2760801 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAATTACAGATCTTATCTCTCTGAAGTTA
1 AATCCTATCTTCCTGAAGTTGCAGTGGAGCGGATTAAAATTACAGATCTTATCTCTCTGAAGTTA
*
2760866 CAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTACGGTGGACAAGACTAAGTAAGCAAG
66 CAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCGGTGGACAAGACTAAGTAAGCAAG
*
2760931 TCTTATCCTCCTGAAGTTACAGTGAGGCAGATTGAAGATGGCAAATCTTATCTTCCTGAAGTTGC
131 TCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCTTATCTTCCTGAAGTTGC
2760996 AGTGGAGCAGATTAAAGCCGAC
196 AGTGGAGCAGATTAAAGCCGAC
* * *
2761018 AATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATTAGAGATCTTATCTCTCTGAAGTTA
1 AATCCTATCTTCCTGAAGTTGCAGTGGAGCGGATTAAAATTACAGATCTTATCTCTCTGAAGTTA
* *
2761083 CAGAGAGCAGATCGCATCTAATCTTATCTCCCTGAAGTTGCGGTGGACAAGGCTAAGTAAGCAAG
66 CAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCGGTGGACAAGACTAAGTAAGCAAG
2761148 TCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCTTATCTTCCTGAAGTTGC
131 TCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCTTATCTTCCTGAAGTTGC
*
2761213 AGTGGAGCAGATTAAAGCCGAT
196 AGTGGAGCAGATTAAAGCCGAC
* * *
2761235 AATCCTATCTTCCTGAAGTTGCAGTAGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTG
1 AATCCTATCTTCCTGAAGTTGCAGTGGAGCGGATTAAAATTACAGATCTTATCTCTCTGAAGTTA
* ** *
2761300 CAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGGAAGCAAG
66 CAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCGGTGGACAAGACTAAGTAAGCAAG
*
2761365 TCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGC
131 TCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCTTATCTTCCTGAAGTTGC
2761430 AGTGGAG
196 AGTGGAG
2761437 TATATTGAAG
Statistics
Matches: 396, Mismatches: 23, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
217 396 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (217 bp):
AATCCTATCTTCCTGAAGTTGCAGTGGAGCGGATTAAAATTACAGATCTTATCTCTCTGAAGTTA
CAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCGGTGGACAAGACTAAGTAAGCAAG
TCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCTTATCTTCCTGAAGTTGC
AGTGGAGCAGATTAAAGCCGAC
Found at i:2761121 original size:173 final size:173
Alignment explanation
Indices: 2760628--2761087 Score: 498
Period size: 173 Copynumber: 2.6 Consensus size: 173
2760618 TAAAGTCGAC
* * * * * * *
2760628 AATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATC-ATAGATCTTATC-CCTCTGAAGT
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAA-CGACAGATCCTATCTCC-CTAAAGT
* * *** * * * *
2760691 TGCAGAGAGCAAATCGCATCTAGTCTTATCTCCCTAAAGTTGCAGTGGAGC-AGACTAAGTAAAC
64 TACAGAGAGCAGATAAAATCTAGTCTTATCTCCCTGAAGTTACAGAGGA-CAAGACTAAGTAAGC
* *
2760755 AAGTCTTATCCTTCTAAAGTTACAGTGAGGCAGACTGAAGATGGCA
128 AAGTCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCA
** * * *
2760801 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAATTACAGATCTTATCTCTCTGAAGTTA
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAACGACAGATCCTATCTCCCTAAAGTTA
*** * *
2760866 CAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTACGGTGGACAAGACTAAGTAAGCAAG
66 CAGAGAGCAGATAAAATCTAGTCTTATCTCCCTGAAGTTACAGAGGACAAGACTAAGTAAGCAAG
*
2760931 TCTTATCCTCCTGAAGTTACAGTGAGGCAGATTGAAGATGGCA
131 TCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCA
*
2760974 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACA-ATCCTATCTCCCTAAAGTT
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAA-ACGACAGATCCTATCTCCCTAAAGTT
* * * *
2761038 GCAGTGGAGCGGATTAAAAT-TAGAGATCTTATCTCTCTGAAGTTACAGAG
65 ACAG-AGAGCAGA-TAAAATCT--AG-TCTTATCTCCCTGAAGTTACAGAG
2761088 AGCAGATCGC
Statistics
Matches: 247, Mismatches: 31, Indels: 14
0.85 0.11 0.05
Matches are distributed among these distances:
172 1 0.00
173 209 0.85
174 11 0.04
175 3 0.01
176 2 0.01
177 21 0.09
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (173 bp):
AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAACGACAGATCCTATCTCCCTAAAGTTA
CAGAGAGCAGATAAAATCTAGTCTTATCTCCCTGAAGTTACAGAGGACAAGACTAAGTAAGCAAG
TCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCA
Found at i:2761336 original size:390 final size:388
Alignment explanation
Indices: 2760611--2761436 Score: 1026
Period size: 390 Copynumber: 2.1 Consensus size: 388
2760601 GATAGTGGGA
* *
2760611 AGCAGATTAAAGTCGACAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCATAGATC
1 AGCAGATTAAAGACGACAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCAGAGATC
* *
2760676 TTATCCCTCTGAAGTTGCAGAGAGCAAATCGCATCTAGTCTTATCTCCCTAAAGTTGCAGTGGAG
66 TTATCCCTCTGAAGTTACAGAGAGCAAATCGCATCTAATCTTATCTCCCTAAAGTTGCAGTGGAG
*
2760741 CAGACTAAGTAAACAAGTCTTATCCTTCTAAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCT
131 CAGACTAAGTAAACAAGTCTTATCCTCCTAAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCT
** *
2760806 TATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAATTACAGATCTTATCTCTCTGAAGTTACAGAG
196 TATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAACGACAGATCCTATCTCTCTGAAGTTACAGAG
*** * * *
2760871 AGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTACGGTGGACAAGACTAAGTAAGCAAGTCTTA
261 AGCAGATAAAATCCAGTCTTATCTCCCTGAAGTTACAGAGGACAAGACTAAGTAAGCAAGTCTTA
* * * *
2760936 TCCTCCTGAAGTTACAGT-GAGGCAGATTGAA-GATGGCAAATCTTATCTTCCTGAAGTTGCAGT
326 TCCTCCTGAAGTTACAGTGGA-GCAGACT-AAGGA-AGCAAATCTTATCCTCCTGAAGTTACAGT
2760999 GG
388 -G
* *
2761001 AGCAGATTAAAGCCGACAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATTAGAGATC
1 AGCAGATTAAAGACGACAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCAGAGATC
* * * *
2761066 TTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCTAATCTTATCTCCCTGAAGTTGCGGTGGA-
66 TTATCCCTCTGAAGTTACAGAGAGCAAATCGCATCTAATCTTATCTCCCTAAAGTTGCAGTGGAG
* * *
2761130 CAAGGCTAAGTAAGCAAGTCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCAAATC
131 C-AGACTAAGTAAACAAGTCTTATCCTCCTAAAGTTACAGTGAGGCAGACTGAAGATGGCAAATC
* * *
2761195 TTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATA-ATCCTATCT-TCCTGAAGTTGCA
195 TTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAA-ACGACAGATCCTATCTCT-CTGAAGTTACA
* * * * * *
2761258 GTAGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGA-GAGC-AGA-T-CG-CATC
258 G-AGAGCAGA-TAAAATC-CAG-TCTTATCTCCCTGAAGTTACAGAGGA-CAAGACTAAGTAAGC
* * * *
2761318 TAGTCTTAT-CTCCCTGAAGTTGCAGTGGAGTAGACTAAGGAAGCAAGTCTTATCCTCCTGAAGT
318 AAGTCTTATCCT-CCTGAAGTTACAGTGGAGCAGACTAAGGAAGCAAATCTTATCCTCCTGAAGT
2761382 TACAGTG
382 TACAGTG
* * * * * *
2761389 AGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAG
1 A-GCAGATTAAAGACGAC-AATCCTATCTCCCTAAAGTTGCAGTGGAG
2761437 TATATTGAAG
Statistics
Matches: 377, Mismatches: 46, Indels: 26
0.84 0.10 0.06
Matches are distributed among these distances:
388 2 0.01
389 42 0.11
390 289 0.77
391 12 0.03
392 5 0.01
393 7 0.02
394 20 0.05
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (388 bp):
AGCAGATTAAAGACGACAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCAGAGATC
TTATCCCTCTGAAGTTACAGAGAGCAAATCGCATCTAATCTTATCTCCCTAAAGTTGCAGTGGAG
CAGACTAAGTAAACAAGTCTTATCCTCCTAAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCT
TATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAACGACAGATCCTATCTCTCTGAAGTTACAGAG
AGCAGATAAAATCCAGTCTTATCTCCCTGAAGTTACAGAGGACAAGACTAAGTAAGCAAGTCTTA
TCCTCCTGAAGTTACAGTGGAGCAGACTAAGGAAGCAAATCTTATCCTCCTGAAGTTACAGTG
Found at i:2761377 original size:128 final size:129
Alignment explanation
Indices: 2761193--2761431 Score: 286
Period size: 128 Copynumber: 1.9 Consensus size: 129
2761183 AGATGGCAAA
* * ** * *
2761193 TCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTTCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAGATAATCCTATCCTCCTGAAGTTACA
* * * *
2761258 GT-AGAGCGGA-TTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAG
66 GTGAG-GCAGACTGAAAATCACAAATCTTATCTCCCTGAAGTTGCAGAGAGCAGATCGCATCTAG
* * * *
2761321 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGGAAGCA-AGTCTTATCCTCCTGAAGTTAC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAG-ATAATCCTATCCTCCTGAAGTTAC
* **
2761385 AGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAG
65 AGTGAGGCAGACTGAAAATCACAAATCTTATCTCCCTGAAGTTGCAG
2761432 TGGAGTATAT
Statistics
Matches: 91, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
128 59 0.65
129 32 0.35
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (129 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAGATAATCCTATCCTCCTGAAGTTACA
GTGAGGCAGACTGAAAATCACAAATCTTATCTCCCTGAAGTTGCAGAGAGCAGATCGCATCTAG
Found at i:2761446 original size:45 final size:44
Alignment explanation
Indices: 2760714--2761438 Score: 236
Period size: 44 Copynumber: 16.7 Consensus size: 44
2760704 TCGCATCTAG
* * * *
2760714 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGACT-AAGTAAACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAG-AAGCAAA
* * * * *
2760758 TCTTATC-CTTCTAAAGTTACAGT-GAGGCAGACTGAAGATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GTAGACTGAAGA-AGCAAA
* * * * *
2760803 TCTTATCTTCCTGAAGTTGCAGTGGAGCAGA-TTAA-AATTACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGAA--GCAAA
* * * * * * * * *
2760847 TCTTATCTCTCTGAAGTTACAG-AGAGCAGA-T--CGCATCTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGAAGCAAA
* * ** *
2760887 TCTTATCTCCCTGAAGTTACGGTGGACAAGACT-AAGTAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAG-AAGCAAA
* * * *
2760931 TCTTATC-CTCCTGAAGTTACAGT-GAGGCAGATTGAAGATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GTAGACTGAAGA-AGCAAA
* * * * **
2760976 TCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCCG-ACAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGAAGCA-AA
* * ** * * *
2761020 TCCTATCTCCCTAAAGTTGCAGTGGAGCGGA-TTAAAATTAG-AGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGA--AGCAAA
* * * * * * * *
2761064 TCTTATCTCTCTGAAGTTACAG-AGAGCAGA-T--CGCATCTAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGAAGCAAA
* ** * *
2761104 TCTTATCTCCCTGAAGTTGCGGTGGACAAGGCT-AAGTAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAG-AAGCAAA
* * *
2761148 TCTTATC-CTCCTGAAGTTACAGT-GAGGCAGACTGAAGATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GTAGACTGAAGA-AGCAAA
* * * * **
2761193 TCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCCG-ATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGAAGCA-AA
* * * ** * *
2761237 TCCTATCTTCCTGAAGTTGCAGTAGAGCGGA-TTAA-AATCACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGAAGCA-A-A
* * * * * * * *
2761281 TCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T--CGCATCTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGAAGCAAA
*
2761321 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACT-AAGGAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAA-GAAGCAAA
* * *
2761365 TCTTATC-CTCCTGAAGTTACAGT-GAGGCAGACTGAAGATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GTAGACTGAAGA-AGCAAA
2761410 TCTTATCTCCCTGAAGTTGCAGTGGAGTA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTA
2761439 TATTGAAGCA
Statistics
Matches: 516, Mismatches: 118, Indels: 93
0.71 0.16 0.13
Matches are distributed among these distances:
39 1 0.00
40 62 0.12
41 16 0.03
42 7 0.01
43 48 0.09
44 241 0.47
45 132 0.26
46 9 0.02
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGAAGCAAA
Found at i:2761674 original size:19 final size:19
Alignment explanation
Indices: 2761650--2761762 Score: 154
Period size: 19 Copynumber: 5.8 Consensus size: 19
2761640 AATTTTTGAG
*
2761650 GATATGCAATTTTAGATAT
1 GATATGCAATCTTAGATAT
**
2761669 GATATGCAATCCAAGATAT
1 GATATGCAATCTTAGATAT
2761688 GATAGATGCAATCTTAGATAT
1 GAT--ATGCAATCTTAGATAT
*
2761709 GATATGCAATCTTAGAGAT
1 GATATGCAATCTTAGATAT
**
2761728 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
2761747 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
2761763 ATATATGATT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
19 64 0.79
21 17 0.21
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:2761748 original size:38 final size:39
Alignment explanation
Indices: 2761656--2761762 Score: 153
Period size: 40 Copynumber: 2.7 Consensus size: 39
2761646 TGAGGATATG
* ** *
2761656 CAATTTTAGATATGATATGCAATCCAAGATATGATAGAT
1 CAATCTTAGATATGATATGCAATCTTAGAGATGATAGAT
*
2761695 GCAATCTTAGATATGATATGCAATCTTAGAGATGATATAT
1 -CAATCTTAGATATGATATGCAATCTTAGAGATGATAGAT
2761735 -AATCTTAGATATGATATGCAATCTTAGA
1 CAATCTTAGATATGATATGCAATCTTAGA
2761763 ATATATGATT
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
38 28 0.45
40 34 0.55
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (39 bp):
CAATCTTAGATATGATATGCAATCTTAGAGATGATAGAT
Found at i:2763199 original size:98 final size:98
Alignment explanation
Indices: 2763079--2763275 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
2763069 TTAAAAATAA
* *
2763079 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
2763144 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
2763177 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
* *
2763242 TTAAATCTTGGATGAGTGGATGTTCTTTTTAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
2763275 T
1 T
2763276 TTTATTGTAC
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:2773378 original size:5 final size:5
Alignment explanation
Indices: 2773364--2773419 Score: 105
Period size: 5 Copynumber: 11.4 Consensus size: 5
2773354 AATTATTAAG
2773364 TATA- TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
2773413 TATAT TA
1 TATAT TA
2773420 CAATAAAACA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 4 0.08
5 47 0.92
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:2773453 original size:21 final size:21
Alignment explanation
Indices: 2773421--2773462 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2773411 ATTATATTAC
* *
2773421 AATAAAACAAAATAAATAAAG
1 AATAAAACAAAAGAAAGAAAG
2773442 AATAAATA-AAAAGAAAGAAAG
1 AATAAA-ACAAAAGAAAGAAAG
2773463 GTACTTAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.76, C:0.02, G:0.10, T:0.12
Consensus pattern (21 bp):
AATAAAACAAAAGAAAGAAAG
Found at i:2774784 original size:45 final size:45
Alignment explanation
Indices: 2774725--2774834 Score: 115
Period size: 45 Copynumber: 2.6 Consensus size: 45
2774715 TTTGGTTCGC
* *
2774725 TGTATTGGATTAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
* * ***
2774770 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
2774814 TG--A---AATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
2774835 TAATGGAAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
39 15 0.27
42 1 0.02
44 18 0.33
45 21 0.38
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.34
Consensus pattern (45 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
Found at i:2775001 original size:18 final size:17
Alignment explanation
Indices: 2774980--2775014 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2774970 TTATTATTAA
*
2774980 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
2774998 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
2775015 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:2775147 original size:16 final size:16
Alignment explanation
Indices: 2775128--2775158 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2775118 TTTAAACATA
*
2775128 ATAATTATAATATATT
1 ATAATTAAAATATATT
2775144 ATAATTAAAATATAT
1 ATAATTAAAATATAT
2775159 AATTTAATAA
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAATTAAAATATATT
Found at i:2775181 original size:157 final size:157
Alignment explanation
Indices: 2774868--2775183 Score: 537
Period size: 159 Copynumber: 2.0 Consensus size: 157
2774858 AGAATACCCG
* *
2774868 TAGCATAAATTTGTTTTGGTAAATGGTTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAT
1 TAGCAGAAATTTGTTTTGGTAAATGGTTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAA
* * *
2774933 TATCAATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAAT
66 TATCAATAATAAATAATTTAATCATATTTAAACATAATAATTATTAAATATATTATAATTAAAAT
2774998 ATATAATTTAATAAAATTCTTAATAAT
131 ATATAATTTAATAAAATTCTTAATAAT
**
2775025 TAGCAGAAATTTGTTTTGGTAAATTATTTTATTGTTATTGTTATTTAAATTTTAATAAGATTATT
1 TAGCAGAAATTTGTTTTGGTAAA-T-GGTTATTGTTATTGTTATTTAAATTTTAATAAGATTATT
2775090 AATATCAATAATAAATAATTTAATCATATTTAAACATAATAATTA-T-AATATATTATAATTAAA
64 AATATCAATAATAAATAATTTAATCATATTTAAACATAATAATTATTAAATATATTATAATTAAA
2775153 ATATATAATTTAATAAAATTCTTAATAAT
129 ATATATAATTTAATAAAATTCTTAATAAT
2775182 TA
1 TA
2775184 ATATTCTTAT
Statistics
Matches: 150, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
157 69 0.46
158 2 0.01
159 79 0.53
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (157 bp):
TAGCAGAAATTTGTTTTGGTAAATGGTTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAA
TATCAATAATAAATAATTTAATCATATTTAAACATAATAATTATTAAATATATTATAATTAAAAT
ATATAATTTAATAAAATTCTTAATAAT
Found at i:2775219 original size:61 final size:61
Alignment explanation
Indices: 2775152--2775459 Score: 230
Period size: 61 Copynumber: 5.1 Consensus size: 61
2775142 TTATAATTAA
2775152 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * *
2775213 AATATATGATACT-GTAAAA-T-AT-A-AATTAACATAATTATTAT-TAAATATA-TTATAATTA
1 AATATATAAT-TTAATAAAATTCTTAATAATT-A-AT-ATTCTTATATGAATTTACTCA-AATCA
*
2775271 A
61 T
* *
2775272 AATATATAATTTAATAAAATTCTTAATAATTCATATTCTTATATGAATTTACCCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * *
2775333 AATATATGATACT-GTAAAA-T-AT-A-AATTAACATAATTATTAT-TAAATATA-TTATAATTA
1 AATATATAAT-TTAATAAAATTCTTAATAATT-A-AT-ATTCTTATATGAATTTACTCA-AATCA
*
2775391 A
61 T
2775392 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
2775453 AATATAT
1 AATATAT
2775460 GATACTATAA
Statistics
Matches: 179, Mismatches: 44, Indels: 48
0.66 0.16 0.18
Matches are distributed among these distances:
57 8 0.04
58 8 0.04
59 54 0.30
60 32 0.18
61 61 0.34
62 8 0.04
63 8 0.04
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
Found at i:2775285 original size:14 final size:15
Alignment explanation
Indices: 2775236--2775287 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
2775226 GTAAAATATA
2775236 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
2775251 TATTAAATATATTAT
1 AATTAAATATATTAT
2775266 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
2775279 AATTTAATA
1 AATTAAATA
2775288 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:2775405 original size:14 final size:15
Alignment explanation
Indices: 2775356--2775407 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
2775346 GTAAAATATA
2775356 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
2775371 TATTAAATATATTAT
1 AATTAAATATATTAT
2775386 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
2775399 AATTTAATA
1 AATTAAATA
2775408 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:2775489 original size:120 final size:120
Alignment explanation
Indices: 2775122--2775470 Score: 648
Period size: 120 Copynumber: 2.9 Consensus size: 120
2775112 ATCATATTTA
*
2775122 AACATAATAATTA-T-AATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
2775185 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
2775240 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTCA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
2775305 TATTCTTATATGAATTTACCCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
2775360 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
2775425 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAA
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAA
2775471 TGAAAATTTG
Statistics
Matches: 223, Mismatches: 6, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
118 12 0.05
119 1 0.00
120 210 0.94
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:2775610 original size:24 final size:25
Alignment explanation
Indices: 2775564--2775611 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
2775554 TATGAATTTG
2775564 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
2775590 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
2775612 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:2775688 original size:91 final size:91
Alignment explanation
Indices: 2775539--2775746 Score: 260
Period size: 91 Copynumber: 2.3 Consensus size: 91
2775529 GAATTATAAC
* * * * * * *
2775539 TAATAAATTATATTTTATGAATTTGTATAATTTAAAATAATAATTATTACATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATAATTATTAAATATAATTTAAT-AG
* *
2775604 TAATAT-TAAATTTCATAAACTTCTTGA
65 TAATATAT-AATTTCATAAAATTCTTAA
2775631 TAATAAATTTTCTTATATGAATTTATACAA-TTAAAATAATTAA-TATTAAATATAATTTAATAG
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAA-TAATTATTAAATATAATTTAATAG
*
2775694 TGATATATAATTTCATAAAATTCTTAA
65 TAATATATAATTTCATAAAATTCTTAA
*
2775721 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAATTTTCTTATATGAATTTA
2775747 CTAAAATCAA
Statistics
Matches: 102, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
90 27 0.26
91 47 0.46
92 28 0.27
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATAATTATTAAATATAATTTAATAGT
AATATATAATTTCATAAAATTCTTAA
Found at i:2782165 original size:24 final size:24
Alignment explanation
Indices: 2782138--2782184 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2782128 ATTGAAATGG
2782138 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
2782162 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
2782185 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:2782182 original size:15 final size:15
Alignment explanation
Indices: 2782162--2782211 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
2782152 TGATGAATTT
2782162 ATTGAATTTATATTG
1 ATTGAATTTATATTG
2782177 ATTGAATTGGTATATATAG
1 ATTGAATT--TATAT-T-G
2782196 ATTGAA--TATATTG
1 ATTGAATTTATATTG
2782209 ATT
1 ATT
2782212 ATTTGAATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 4 0.13
14 1 0.03
15 13 0.42
17 5 0.16
18 1 0.03
19 7 0.23
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:2782442 original size:40 final size:41
Alignment explanation
Indices: 2782347--2782448 Score: 134
Period size: 41 Copynumber: 2.5 Consensus size: 41
2782337 ACTTCGAGTC
* * * * *
2782347 GATGAGACACTGGGTGTCAATTTACTACTTTGGATTAATTT
1 GATGAGGCACTGGGTGTCAAATTACTACTTCGAATTAATCT
*
2782388 GATGAGGCACTGGGTGTCAAATTATTACTTCGAATT-ATCT
1 GATGAGGCACTGGGTGTCAAATTACTACTTCGAATTAATCT
*
2782428 GATGAGGCACTGGGTGCCAAA
1 GATGAGGCACTGGGTGTCAAA
2782449 CTGGTGTGTT
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 23 0.43
41 31 0.57
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.32
Consensus pattern (41 bp):
GATGAGGCACTGGGTGTCAAATTACTACTTCGAATTAATCT
Found at i:2801237 original size:5 final size:5
Alignment explanation
Indices: 2801223--2801276 Score: 87
Period size: 5 Copynumber: 11.4 Consensus size: 5
2801213 AATTATTAAG
2801223 TATA- TATAT TATA- T-TAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
2801270 TATAT TA
1 TATAT TA
2801277 CAATAAACAA
Statistics
Matches: 47, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
3 2 0.04
4 6 0.13
5 39 0.83
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:2801317 original size:20 final size:20
Alignment explanation
Indices: 2801278--2801317 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2801268 ATTATATTAC
* *
2801278 AATAAACAAAATAAATAAAG
1 AATAAACAAAAGAAAGAAAG
*
2801298 AATAAATAAAAGAAAGAAAG
1 AATAAACAAAAGAAAGAAAG
2801318 GTACTTAACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.75, C:0.03, G:0.10, T:0.12
Consensus pattern (20 bp):
AATAAACAAAAGAAAGAAAG
Found at i:2802624 original size:45 final size:45
Alignment explanation
Indices: 2802565--2802674 Score: 115
Period size: 45 Copynumber: 2.6 Consensus size: 45
2802555 TTTGGTTCGC
* *
2802565 TGTATTGGATTAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
* * ***
2802610 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
2802654 TG--A---AATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
2802675 TAATGGAAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
39 15 0.27
42 1 0.02
44 18 0.33
45 21 0.38
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.34
Consensus pattern (45 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
Found at i:2802909 original size:157 final size:153
Alignment explanation
Indices: 2802708--2803019 Score: 518
Period size: 157 Copynumber: 2.0 Consensus size: 153
2802698 AGAATACCCG
* * *
2802708 TAGCATAAATTTGTTTTGGTAAATGGTTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAT
1 TAGCAGAAATTTGTTTTGGTAAATAGTTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAA
* *
2802773 TATCAATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAAT
66 TATCAATAATAAATAATTTAATCATATTTAAACATAA-TA--ATT-AATATATTATAATTAAAAT
2802838 ATATAA-TTAATAAAATTCTTAATAAT
127 ATATAATTTAATAAAATTCTTAATAAT
*
2802864 TAGCAGAAATTTGTTTTGGTAAATTATTTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TAGCAGAAATTTGTTTTGGTAAA-TAGTTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
2802929 ATATCAATAATAAATAATTTAATCATATTTAAACATAATAATTAATATATTATAATTAAAATATA
65 ATATCAATAATAAATAATTTAATCATATTTAAACATAATAATTAATATATTATAATTAAAATATA
2802994 TAATTTAATAAAATTCTTAATAAT
130 TAATTTAATAAAATTCTTAATAAT
2803018 TA
1 TA
2803020 ATATTCTTAT
Statistics
Matches: 148, Mismatches: 6, Indels: 6
0.93 0.04 0.04
Matches are distributed among these distances:
153 24 0.16
154 25 0.17
156 24 0.16
157 75 0.51
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (153 bp):
TAGCAGAAATTTGTTTTGGTAAATAGTTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAA
TATCAATAATAAATAATTTAATCATATTTAAACATAATAATTAATATATTATAATTAAAATATAT
AATTTAATAAAATTCTTAATAAT
Found at i:2803121 original size:14 final size:15
Alignment explanation
Indices: 2803072--2803123 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
2803062 GTAAAATATA
2803072 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
2803087 TATTAAATATATTAT
1 AATTAAATATATTAT
2803102 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
2803115 AATTTAATA
1 AATTAAATA
2803124 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:2803241 original size:14 final size:15
Alignment explanation
Indices: 2803192--2803243 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
2803182 GTAAAATATA
2803192 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
2803207 TATTAAATATATTAT
1 AATTAAATATATTAT
2803222 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
2803235 AATTTAATA
1 AATTAAATA
2803244 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:2803325 original size:120 final size:120
Alignment explanation
Indices: 2802972--2803306 Score: 643
Period size: 120 Copynumber: 2.8 Consensus size: 120
2802962 CATAATAATT
2802972 AATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATT
1 AATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATT
2803037 TACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTATTATTA
66 TACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTATTATTA
*
2803092 AATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTCATATTCTTATATGAATT
1 AATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATT
*
2803157 TACCCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTATTATTA
66 TACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTATTATTA
2803212 AATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATT
1 AATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATT
*
2803277 TACTCAAATCATAATATATGATACTATAAA
66 TACTCAAATCATAATATATGATACTGTAAA
2803307 TGAAAATTTG
Statistics
Matches: 210, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 210 1.00
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (120 bp):
AATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATT
TACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTATTATTA
Found at i:2803445 original size:24 final size:25
Alignment explanation
Indices: 2803399--2803446 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
2803389 TATGAATTTG
2803399 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
2803425 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
2803447 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:2803450 original size:91 final size:91
Alignment explanation
Indices: 2803355--2803581 Score: 216
Period size: 91 Copynumber: 2.5 Consensus size: 91
2803345 TGATTTAATA
* *
2803355 AAATTT-AAAAGAATT-ATAACTAATAAATTATATT-TATGAATTTGTATAATTTAAAATAA-TA
1 AAATTTCAAAA-AATTCATAA-TAATAAATTATATTATATGAATTTATACAA-TTAAAATAATTA
*
2803416 ATTATTACATATAATTTAATAATTAATATT
63 A-TATTAAATATAATTTAATAATTAATATT
* * * * * *
2803446 AAATTTCATAAACTTCTTGATAATAAATTTTCTTATATGAATTTATACAATTAAAATAATTAATA
1 AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTAAAATAATTAATA
* *
2803511 TTAAATATAATTTAAT-AGTGATA-T
66 TTAAATATAATTTAATAATTAATATT
* * *
2803535 ATAATTTCATAAAATTCTTAATAATAAAATGT-TCTTATATGAATTTA
1 A-AATTTCAAAAAATTCATAATAAT-AAAT-TATATTATATGAATTTA
2803582 CTAAAATCAA
Statistics
Matches: 116, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
89 2 0.02
90 26 0.22
91 66 0.57
92 22 0.19
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (91 bp):
AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTAAAATAATTAATA
TTAAATATAATTTAATAATTAATATT
Found at i:2809999 original size:24 final size:24
Alignment explanation
Indices: 2809972--2810018 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2809962 ATTGAAATGG
2809972 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
2809996 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
2810019 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:2810016 original size:15 final size:15
Alignment explanation
Indices: 2809996--2810045 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
2809986 TGATGAATTT
2809996 ATTGAATTTATATTG
1 ATTGAATTTATATTG
2810011 ATTGAATTGGTATATATAG
1 ATTGAATT--TATAT-T-G
2810030 ATTGAA--TATATTG
1 ATTGAATTTATATTG
2810043 ATT
1 ATT
2810046 ATTTGAATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 4 0.13
14 1 0.03
15 13 0.42
17 5 0.16
18 1 0.03
19 7 0.23
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:2810276 original size:40 final size:41
Alignment explanation
Indices: 2810181--2810282 Score: 134
Period size: 41 Copynumber: 2.5 Consensus size: 41
2810171 ACTTCGAGTC
* * * * *
2810181 GATGAGACACTGGGTGTCAATTTACTACTTTGGATTAATTT
1 GATGAGGCACTGGGTGTCAAATTACTACTTCGAATTAATCT
*
2810222 GATGAGGCACTGGGTGTCAAATTATTACTTCGAATT-ATCT
1 GATGAGGCACTGGGTGTCAAATTACTACTTCGAATTAATCT
*
2810262 GATGAGGCACTGGGTGCCAAA
1 GATGAGGCACTGGGTGTCAAA
2810283 CTGGTGTGTT
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 23 0.43
41 31 0.57
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.32
Consensus pattern (41 bp):
GATGAGGCACTGGGTGTCAAATTACTACTTCGAATTAATCT
Found at i:2810767 original size:28 final size:27
Alignment explanation
Indices: 2810717--2810771 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
2810707 TACTTAACTT
* *
2810717 TTAAGTTTTAATATTATAATATATATA
1 TTAACTTTAAATATTATAATATATATA
2810744 TTAACTTTAAATATTTATAATATATATA
1 TTAACTTTAAATA-TTATAATATATATA
2810772 CTCTTATGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (27 bp):
TTAACTTTAAATATTATAATATATATA
Found at i:2813626 original size:60 final size:60
Alignment explanation
Indices: 2813491--2813626 Score: 148
Period size: 60 Copynumber: 2.3 Consensus size: 60
2813481 CTAAATATAA
* * * * ** **
2813491 AAAAAATCAACAAATTTAGCACTCAATATTTACAAAATTTTTCATTTTAGTTTTAATTCT
1 AAAAAATCAAAAAATTTACCACTCAATATTTACAAAATCTATCATTTTAGTCCTAACACT
** *
2813551 AAAAGTTCAATAAATTTGACCA-TCAATATTTACAAAATCTATCATTTTAGTCCTAACACT
1 AAAAAATCAAAAAATTT-ACCACTCAATATTTACAAAATCTATCATTTTAGTCCTAACACT
*
2813611 AAAAAATAAAAAAATT
1 AAAAAATCAAAAAATT
2813627 ATAAAAAAAT
Statistics
Matches: 61, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
60 58 0.95
61 3 0.05
ACGTcount: A:0.46, C:0.14, G:0.04, T:0.36
Consensus pattern (60 bp):
AAAAAATCAAAAAATTTACCACTCAATATTTACAAAATCTATCATTTTAGTCCTAACACT
Found at i:2816542 original size:10 final size:10
Alignment explanation
Indices: 2816510--2816553 Score: 52
Period size: 10 Copynumber: 4.1 Consensus size: 10
2816500 AAAATTTTAA
2816510 TAAATTATAAT
1 TAAATTAT-AT
2816521 TATAATTAATAT
1 TA-AATT-ATAT
2816533 TAAATTATAT
1 TAAATTATAT
*
2816543 TATATTATAT
1 TAAATTATAT
2816553 T
1 T
2816554 TTAATATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 14 0.47
11 6 0.20
12 8 0.27
13 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TAAATTATAT
Found at i:2822212 original size:19 final size:20
Alignment explanation
Indices: 2822188--2822226 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2822178 ATATTTTATA
2822188 TTAAAA-TTTAATAATTTTT
1 TTAAAATTTTAATAATTTTT
*
2822207 TTAAAATTTTATTAATTTTT
1 TTAAAATTTTAATAATTTTT
2822227 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTAAAATTTTAATAATTTTT
Found at i:2822216 original size:11 final size:12
Alignment explanation
Indices: 2822194--2822244 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
2822184 TATATTAAAA
2822194 TTTAATAATTTT
1 TTTAATAATTTT
2822206 TTTAA-AATTTT
1 TTTAATAATTTT
* **
2822217 ATTAATTTTTATT
1 TTTAATAATT-TT
*
2822230 TTTTATAATTTT
1 TTTAATAATTTT
2822242 TTT
1 TTT
2822245 GCCACATGCC
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
11 10 0.33
12 12 0.40
13 8 0.27
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTAATAATTTT
Found at i:2824683 original size:56 final size:56
Alignment explanation
Indices: 2824616--2824727 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
2824606 TATAAATTTC
* *
2824616 ATTTTACCCATTCTCCACTCCACTCTCCCCATTCCATTATCGTGTGTCAATTCAAA
1 ATTTTACCCATTCTCCACTCCACTCTCCCCATTCCATTATCATATGTCAATTCAAA
2824672 ATTTTACCCATTCTCCACTCCACTCTCCCCATTCCATTATCATATGTCAATTCAAA
1 ATTTTACCCATTCTCCACTCCACTCTCCCCATTCCATTATCATATGTCAATTCAAA
2824728 CATTACATCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.25, C:0.36, G:0.04, T:0.36
Consensus pattern (56 bp):
ATTTTACCCATTCTCCACTCCACTCTCCCCATTCCATTATCATATGTCAATTCAAA
Found at i:2835411 original size:22 final size:22
Alignment explanation
Indices: 2835384--2835438 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
2835374 ATAATAACAA
*
2835384 CAAAATAGTAACAATACAATAG
1 CAAAATAGTAACAAAACAATAG
*
2835406 CGAAAT-GATAACAAAACAATAG
1 CAAAATAG-TAACAAAACAATAG
*
2835428 CAAAAAAGTAA
1 CAAAATAGTAA
2835439 AACAACAGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 1 0.04
22 25 0.93
23 1 0.04
ACGTcount: A:0.62, C:0.13, G:0.11, T:0.15
Consensus pattern (22 bp):
CAAAATAGTAACAAAACAATAG
Found at i:2838625 original size:27 final size:27
Alignment explanation
Indices: 2838575--2838653 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
2838565 TTGGGGTCTT
* **
2838575 CCTCATCTTCTTCCTCAGTTGAAGAC-
1 CCTCTTCTTCTTCCTCAGAAGAAGACA
*
2838601 CCTTCTTCTTCTTCCTCAGAAGAAGTCA
1 CC-TCTTCTTCTTCCTCAGAAGAAGACA
* * *
2838629 CCTCTTCATCTTCTTCAGAGGAAGA
1 CCTCTTCTTCTTCCTCAGAAGAAGA
2838654 AGCGGCTGGT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
26 2 0.05
27 39 0.91
28 2 0.05
ACGTcount: A:0.22, C:0.32, G:0.13, T:0.34
Consensus pattern (27 bp):
CCTCTTCTTCTTCCTCAGAAGAAGACA
Found at i:2839100 original size:9 final size:9
Alignment explanation
Indices: 2839086--2839150 Score: 94
Period size: 9 Copynumber: 7.2 Consensus size: 9
2839076 ATTCGGCCGG
2839086 TTAACCGAA
1 TTAACCGAA
*
2839095 TTAACCTAA
1 TTAACCGAA
*
2839104 TTACCCGAA
1 TTAACCGAA
2839113 TTAACCGAA
1 TTAACCGAA
2839122 TTAACCGAA
1 TTAACCGAA
*
2839131 TTACCCGAA
1 TTAACCGAA
*
2839140 TTAACCAAA
1 TTAACCGAA
2839149 TT
1 TT
2839151 GAATTACTAC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 49 1.00
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.26
Consensus pattern (9 bp):
TTAACCGAA
Found at i:2839116 original size:27 final size:27
Alignment explanation
Indices: 2839086--2839150 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
2839076 ATTCGGCCGG
*
2839086 TTAACCGAATTAACCTAATTACCCGAA
1 TTAACCGAATTAACCGAATTACCCGAA
2839113 TTAACCGAATTAACCGAATTACCCGAA
1 TTAACCGAATTAACCGAATTACCCGAA
*
2839140 TTAACCAAATT
1 TTAACCGAATT
2839151 GAATTACTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.26
Consensus pattern (27 bp):
TTAACCGAATTAACCGAATTACCCGAA
Found at i:2839285 original size:18 final size:18
Alignment explanation
Indices: 2839245--2839288 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2839235 AATTTTTATG
**
2839245 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
2839263 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
2839281 CTTGGGTT
1 ATTGGGTT
2839289 TGGATTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:2839818 original size:9 final size:9
Alignment explanation
Indices: 2839796--2840008 Score: 92
Period size: 9 Copynumber: 22.2 Consensus size: 9
2839786 ATGATTAAAA
*
2839796 ATAAAAATCA
1 ATAAAAAT-T
*
2839806 ATAAAAGTT
1 ATAAAAATT
2839815 ATAAAAATT
1 ATAAAAATT
2839824 ATAAAAATTT
1 ATAAAAA-TT
2839834 AATAAAAATT
1 -ATAAAAATT
2839844 ATAAAAA-T
1 ATAAAAATT
2839852 ATTAAAAATT
1 A-TAAAAATT
* *
2839862 AGAAAAGTT
1 ATAAAAATT
* *
2839871 TTAAAATTAT
1 ATAAAAAT-T
2839881 ATAAAAATT
1 ATAAAAATT
* *
2839890 GTAAAAA-A
1 ATAAAAATT
2839898 ATGATAAAATAT
1 AT-A-AAAAT-T
2839910 ATAAAAATAT
1 ATAAAAAT-T
*
2839920 AGGAAAAAATT
1 A--TAAAAATT
*
2839931 TTAAAATATT
1 ATAAAA-ATT
* *
2839941 AT-AAAGTC
1 ATAAAAATT
2839949 ATAAGAAAATT
1 AT-A-AAAATT
*
2839960 ATAAAAAAT
1 ATAAAAATT
* *
2839969 GTAAAGAAAT
1 ATAAA-AATT
2839979 AT-AAAATT
1 ATAAAAATT
*
2839987 CGTAAAAAATT
1 -AT-AAAAATT
*
2839998 ATAAACATT
1 ATAAAAATT
2840007 AT
1 AT
2840009 CGTACTAAAA
Statistics
Matches: 155, Mismatches: 29, Indels: 39
0.70 0.13 0.17
Matches are distributed among these distances:
8 9 0.06
9 74 0.48
10 43 0.28
11 21 0.14
12 8 0.05
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.31
Consensus pattern (9 bp):
ATAAAAATT
Found at i:2839837 original size:29 final size:30
Alignment explanation
Indices: 2839796--2839917 Score: 123
Period size: 29 Copynumber: 4.3 Consensus size: 30
2839786 ATGATTAAAA
* *
2839796 ATAAAAA-TCAATAAAAGTTATAAAAAT-T
1 ATAAAAATTTAATAAAAATTATAAAAATAT
2839824 ATAAAAATTTAATAAAAATTATAAAAATAT
1 ATAAAAATTTAATAAAAATTATAAAAATAT
* * * *
2839854 -TAAAAA-TT-AGAAAAGTTTTAAAATTAT
1 ATAAAAATTTAATAAAAATTATAAAAATAT
*
2839881 ATAAAAATTGTAA-AAAAATGAT-AAAATAT
1 ATAAAAATT-TAATAAAAATTATAAAAATAT
2839910 ATAAAAAT
1 ATAAAAAT
2839918 ATAGGAAAAA
Statistics
Matches: 78, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
27 15 0.19
28 15 0.19
29 39 0.50
30 8 0.10
31 1 0.01
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (30 bp):
ATAAAAATTTAATAAAAATTATAAAAATAT
Found at i:2839838 original size:20 final size:20
Alignment explanation
Indices: 2839815--2839906 Score: 86
Period size: 20 Copynumber: 4.8 Consensus size: 20
2839805 AATAAAAGTT
2839815 ATAAAAATTATAAAAATTTA
1 ATAAAAATTATAAAAATTTA
2839835 ATAAAAATTATAAAAA--TA
1 ATAAAAATTATAAAAATTTA
* * *
2839853 TTAAAAATTAGAAAAGTTT-
1 ATAAAAATTATAAAAATTTA
*
2839872 -TAAAATTATATAAAAATTGTA
1 ATAAAAAT-TATAAAAATT-TA
*
2839893 A-AAAAATGATAAAA
1 ATAAAAATTATAAAA
2839907 TATATAAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
18 21 0.36
19 8 0.14
20 24 0.41
21 5 0.09
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (20 bp):
ATAAAAATTATAAAAATTTA
Found at i:2839926 original size:29 final size:27
Alignment explanation
Indices: 2839854--2839945 Score: 76
Period size: 30 Copynumber: 3.1 Consensus size: 27
2839844 ATAAAAATAT
* *
2839854 TAAAAATTAGAAAAGTTTTAAAATTATA
1 TAAAAATTAGAAAAATTATAAAA-TATA
* *
2839882 TAAAAATTGTAAAAAAATGATAAAATATA
1 TAAAAA-T-TAGAAAAATTATAAAATATA
*
2839911 TAAAAATATAGGAAAAAATTTTAAAATATTA
1 TAAAAAT-TA-G-AAAAATTATAAAATA-TA
2839942 TAAA
1 TAAA
2839946 GTCATAAGAA
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
28 9 0.18
29 11 0.22
30 25 0.49
31 6 0.12
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.32
Consensus pattern (27 bp):
TAAAAATTAGAAAAATTATAAAATATA
Found at i:2840002 original size:10 final size:10
Alignment explanation
Indices: 2839808--2840002 Score: 69
Period size: 10 Copynumber: 20.2 Consensus size: 10
2839798 AAAAATCAAT
*
2839808 AAAAGTTAT-
1 AAAAATTATA
2839817 AAAAATTATA
1 AAAAATTATA
*
2839827 AAAATTTA-A
1 AAAAATTATA
2839836 TAAAAATTAT-
1 -AAAAATTATA
*
2839846 AAAAA-TATT
1 AAAAATTATA
*
2839855 AAAAATTA-G
1 AAAAATTATA
*
2839864 AAAAGTT-T-
1 AAAAATTATA
*
2839872 TAAAATTATA
1 AAAAATTATA
*
2839882 TAAAAATTGTAA
1 -AAAAATTAT-A
*
2839894 AAAAATGATA
1 AAAAATTATA
*
2839904 AAATA-TAT-
1 AAAAATTATA
*
2839912 AAAAATATAGGA
1 AAAAAT-TA-TA
*
2839924 AAAAATTTTA
1 AAAAATTATA
*
2839934 AAATATTAT-
1 AAAAATTATA
* *
2839943 -AAAGTCATA
1 AAAAATTATA
2839952 AGAAAATTATA
1 A-AAAATTATA
2839963 AAAAATGTA-A
1 AAAAAT-TATA
*
2839973 AGAAA-TAT-
1 AAAAATTATA
*
2839981 -AAAATTCGTA
1 AAAAATT-ATA
2839991 AAAAATTATA
1 AAAAATTATA
2840001 AA
1 AA
2840003 CATTATCGTA
Statistics
Matches: 135, Mismatches: 28, Indels: 45
0.65 0.13 0.22
Matches are distributed among these distances:
7 3 0.02
8 20 0.15
9 29 0.21
10 45 0.33
11 31 0.23
12 7 0.05
ACGTcount: A:0.63, C:0.01, G:0.06, T:0.30
Consensus pattern (10 bp):
AAAAATTATA
Found at i:2840050 original size:20 final size:17
Alignment explanation
Indices: 2840025--2840074 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 17
2840015 AAAAGAAGCA
2840025 TTTTATAATTTTTCTATAAT
1 TTTTATAATTTTT-TAT--T
2840045 TTTTATAATTTTTTATT
1 TTTTATAATTTTTTATT
2840062 TTTTATCAATTTT
1 TTTTAT-AATTTT
2840075 CGACACATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.24
18 6 0.21
19 3 0.10
20 13 0.45
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTATAATTTTTTATT
Found at i:2840051 original size:9 final size:9
Alignment explanation
Indices: 2840025--2840074 Score: 57
Period size: 10 Copynumber: 5.3 Consensus size: 9
2840015 AAAAGAAGCA
2840025 TTTTATAATT
1 TTTTATAA-T
2840035 TTTCTATAAT
1 TTT-TATAAT
2840045 TTTTATAAT
1 TTTTATAAT
*
2840054 TTTT-TATT
1 TTTTATAAT
2840062 TTTTATCAAT
1 TTTTAT-AAT
2840072 TTT
1 TTT
2840075 CGACACATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 7 0.20
9 11 0.31
10 12 0.34
11 5 0.14
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTTATAAT
Found at i:2840230 original size:8 final size:8
Alignment explanation
Indices: 2840219--2840266 Score: 69
Period size: 8 Copynumber: 5.8 Consensus size: 8
2840209 TTTTAAAAAA
2840219 TTTTATAT
1 TTTTATAT
2840227 TTTTATATT
1 TTTTATA-T
*
2840236 TTTTCTAAT
1 TTTTAT-AT
2840245 TTTTATAT
1 TTTTATAT
2840253 TTTTATAT
1 TTTTATAT
2840261 TTTTAT
1 TTTTAT
2840267 TAAAATTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
8 23 0.64
9 12 0.33
10 1 0.03
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTATAT
Found at i:2840236 original size:26 final size:26
Alignment explanation
Indices: 2840189--2840283 Score: 100
Period size: 26 Copynumber: 3.5 Consensus size: 26
2840179 TTTTTTATGC
2840189 ATTTTATAATTTTTTATCATTTTTAAAAA
1 ATTTTAT-A-TTTTTAT-ATTTTTAAAAA
***
2840218 ATTTTATATTTTTATATTTTTTCTAA
1 ATTTTATATTTTTATATTTTTAAAAA
* *
2840244 TTTTTATATTTTTATATTTTTATTAAA
1 ATTTTATATTTTTATATTTTTA-AAAA
*
2840271 ATTTAATATTTTT
1 ATTTTATATTTTT
2840284 TATAACTTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
26 28 0.50
27 20 0.36
28 1 0.02
29 7 0.12
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (26 bp):
ATTTTATATTTTTATATTTTTAAAAA
Done.