Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 9 of 173
Found at i:2436661 original size:64 final size:64
Alignment explanation
Indices: 2436524--2436661 Score: 179
Period size: 65 Copynumber: 2.1 Consensus size: 64
2436514 ATAATACTTA
* * *
2436524 AATAACGAAATTAAAATAAAATCATCACATATTTTATATTAGCCAAAGAAAGTAGTTAACAATAC
1 AATAACAAAACTAAAATAAAATCATCACATATTTTATACTAGCC-AAGAAAGTAGTTAACAATAC
* ** *
2436589 AATAACAAAACTAAAATCAAATCATCATGTGTTTTATACTAGTCC-AGAAAGTAGTTAACAATAC
1 AATAACAAAACTAAAATAAAATCATCACATATTTTATACTAG-CCAAGAAAGTAGTTAACAATAC
*
2436653 AATTACAAA
1 AATAACAAA
2436662 TAAAAATAAC
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
64 27 0.42
65 35 0.55
66 2 0.03
ACGTcount: A:0.51, C:0.14, G:0.08, T:0.28
Consensus pattern (64 bp):
AATAACAAAACTAAAATAAAATCATCACATATTTTATACTAGCCAAGAAAGTAGTTAACAATAC
Found at i:2444768 original size:13 final size:14
Alignment explanation
Indices: 2444750--2444778 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2444740 TTATCCTCAT
2444750 AAAATTATTA-AAA
1 AAAATTATTATAAA
2444763 AAAATTATTATAAA
1 AAAATTATTATAAA
2444777 AA
1 AA
2444779 CTGAACGCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAATTATTATAAA
Found at i:2447453 original size:103 final size:104
Alignment explanation
Indices: 2447268--2447474 Score: 380
Period size: 103 Copynumber: 2.0 Consensus size: 104
2447258 TAAAGTACAA
*
2447268 TGACTAAATCACAACTTTCATAAGTAATGGGACTATTGGTAGAATTTAACATTTTCTTTCCACTT
1 TGACTAAATCACAACTTTCATAAGTAATAGGACTATTGGTAGAATTTAACATTTTCTTTCCACTT
2447333 TTCTATTCAACCAAGCACACCCTGAAGACCATGTAGGTG
66 TTCTATTCAACCAAGCACACCCTGAAGACCATGTAGGTG
*
2447372 TGACTAAATCACAACTTTCATAAGTAATAGGACTA-TGGTAGAATTTAACATTTTCTTTCGACTT
1 TGACTAAATCACAACTTTCATAAGTAATAGGACTATTGGTAGAATTTAACATTTTCTTTCCACTT
*
2447436 TTCTATTCAACCGAGCACACCCTGAAGACCATGTAGGTG
66 TTCTATTCAACCAAGCACACCCTGAAGACCATGTAGGTG
2447475 CCACTTTTCA
Statistics
Matches: 100, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
103 66 0.66
104 34 0.34
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (104 bp):
TGACTAAATCACAACTTTCATAAGTAATAGGACTATTGGTAGAATTTAACATTTTCTTTCCACTT
TTCTATTCAACCAAGCACACCCTGAAGACCATGTAGGTG
Found at i:2452339 original size:31 final size:31
Alignment explanation
Indices: 2452301--2452362 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
2452291 GGAATGATGT
2452301 GTAAGACCATAACTCAACTATGACAACATTG
1 GTAAGACCATAACTCAACTATGACAACATTG
2452332 GTAAGACCATAACTCAACTATGACAACATTG
1 GTAAGACCATAACTCAACTATGACAACATTG
2452363 AGAGTTCACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.23, G:0.13, T:0.23
Consensus pattern (31 bp):
GTAAGACCATAACTCAACTATGACAACATTG
Found at i:2452460 original size:67 final size:66
Alignment explanation
Indices: 2452332--2452700 Score: 389
Period size: 67 Copynumber: 5.5 Consensus size: 66
2452322 GACAACATTG
* ** * * * * * * *
2452332 GTAAGACCATAACTCAACTATGACAACATTGAGAGTTCACCATGATATTAAACATCGGGTATAAT
1 GTAAGACCATAGCTCGGCTATGGCAACATAGAGAGTCCGCCA-GACATTAAACATGGGGTATGAT
2452397 GT
65 GT
* * * *
2452399 GTAAGAACC-TAGCTCGGCTATGGCAACGTAGTGAGTCTGCCAGTACATTAAAAATGGGGTATGA
1 GTAAG-ACCATAGCTCGGCTATGGCAACATAGAGAGTCCGCCAG-ACATTAAACATGGGGTATGA
*
2452463 TAT
64 TGT
* * * ** *
2452466 GTAAGACCATAGCTCGACTATGGCAACAAAGAAAGTTTGCTAGATCATTAAACATGGGGTATGAT
1 GTAAGACCATAGCTCGGCTATGGCAACATAGAGAGTCCGCCAGA-CATTAAACATGGGGTATGAT
2452531 GT
65 GT
* * * *
2452533 GTAAGACCTTAGCTCGGCTATGACAACATAGAGAGTCCGCCAGAACATTAAACGTGGGGTTTGAT
1 GTAAGACCATAGCTCGGCTATGGCAACATAGAGAGTCCGCCAG-ACATTAAACATGGGGTATGAT
2452598 GT
65 GT
* * *
2452600 GTAAGACCATAGCTCGGCTATGGCAACATAGAGAGTCCACCAGGACATTAAACATGAGGTATAAT
1 GTAAGACCATAGCTCGGCTATGGCAACATAGAGAGTCCGCCA-GACATTAAACATGGGGTATGAT
2452665 GT
65 GT
* * * *
2452667 GTAAGGCCCTAGCTCGACTATGACAACATAGAGA
1 GTAAGACCATAGCTCGGCTATGGCAACATAGAGA
2452701 TTCTATTGGG
Statistics
Matches: 251, Mismatches: 45, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
66 5 0.02
67 241 0.96
68 5 0.02
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (66 bp):
GTAAGACCATAGCTCGGCTATGGCAACATAGAGAGTCCGCCAGACATTAAACATGGGGTATGATG
T
Found at i:2452726 original size:134 final size:132
Alignment explanation
Indices: 2452332--2452700 Score: 450
Period size: 134 Copynumber: 2.8 Consensus size: 132
2452322 GACAACATTG
* * * * *
2452332 GTAAGACCATAACTCAACTATGACAACATTGAGAGTTCACCATGATATTAAACATCGGGTATAAT
1 GTAAGACCATAGCTCGACTATGGCAACATAGAGAGTTCACCA-GACATTAAACAT-GGGTATAAT
* * * * *
2452397 GTGTAAGAACCTAGCTCGGCTATGGCAACGTAGTGAGTCTGCCAGTACATTAAAAATGGGGTATG
64 GTGTAAGACCCTAGCTCGGCTATGACAACATAGAGAGTCTGCCAGAACATTAAAAATGGGGTATG
2452462 ATAT
129 ATAT
* * ** * *
2452466 GTAAGACCATAGCTCGACTATGGCAACAAAGAAAGTTTGCTAGATCATTAAACATGGGGTATGAT
1 GTAAGACCATAGCTCGACTATGGCAACATAGAGAGTTCACCAGA-CATTAAACAT-GGGTATAAT
* * ** *
2452531 GTGTAAGACCTTAGCTCGGCTATGACAACATAGAGAGTCCGCCAGAACATTAAACGTGGGGTTTG
64 GTGTAAGACCCTAGCTCGGCTATGACAACATAGAGAGTCTGCCAGAACATTAAAAATGGGGTATG
*
2452596 ATGT
129 ATAT
* *
2452600 GTAAGACCATAGCTCGGCTATGGCAACATAGAGAGTCCACCAGGACATTAAACATGAGGTATAAT
1 GTAAGACCATAGCTCGACTATGGCAACATAGAGAGTTCACCA-GACATTAAACATG-GGTATAAT
* *
2452665 GTGTAAGGCCCTAGCTCGACTATGACAACATAGAGA
64 GTGTAAGACCCTAGCTCGGCTATGACAACATAGAGA
2452701 TTCTATTGGG
Statistics
Matches: 198, Mismatches: 34, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
133 3 0.02
134 193 0.97
135 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (132 bp):
GTAAGACCATAGCTCGACTATGGCAACATAGAGAGTTCACCAGACATTAAACATGGGTATAATGT
GTAAGACCCTAGCTCGGCTATGACAACATAGAGAGTCTGCCAGAACATTAAAAATGGGGTATGAT
AT
Found at i:2461402 original size:26 final size:26
Alignment explanation
Indices: 2461367--2461418 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
2461357 AATGTGAAAG
*
2461367 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
2461393 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
2461419 TTTCATTGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:2461474 original size:104 final size:103
Alignment explanation
Indices: 2461289--2461658 Score: 600
Period size: 103 Copynumber: 3.6 Consensus size: 103
2461279 TGTATATAAA
** * * *
2461289 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
*
2461353 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCCG
65 TTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCCG
2461392 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
2461457 TTGAAATGAAAAGGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGAAAA-GGGGGTTGCTATGTGCTGATTCCCCCG
2461497 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
*
2461562 TGAAATAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* **
2461600 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGGGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
2461659 ATAACGGCTA
Statistics
Matches: 253, Mismatches: 10, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
103 111 0.44
104 109 0.43
105 33 0.13
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:2476451 original size:14 final size:14
Alignment explanation
Indices: 2476400--2476444 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
2476390 TTTATTTTTA
2476400 TTATAATATTTTATT
1 TTATAATA-TTTATT
*
2476415 ATATCAAT-TTTATT
1 TTAT-AATATTTATT
2476429 TTATAATATTTATT
1 TTATAATATTTATT
2476443 TT
1 TT
2476445 TAGATATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 3 0.12
14 17 0.65
15 3 0.12
16 3 0.12
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (14 bp):
TTATAATATTTATT
Found at i:2481002 original size:38 final size:39
Alignment explanation
Indices: 2480950--2481023 Score: 123
Period size: 38 Copynumber: 1.9 Consensus size: 39
2480940 AATAAAATTC
2480950 TCTCTTAATTAGTTTGTTGATTAAGTTTAGATGAAGTCA
1 TCTCTTAATTAGTTTGTTGATTAAGTTTAGATGAAGTCA
* *
2480989 TCTC-TAATTAGTTTGTTGTTTATGTTTAGATGAAG
1 TCTCTTAATTAGTTTGTTGATTAAGTTTAGATGAAG
2481024 CTAAAACCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
38 29 0.88
39 4 0.12
ACGTcount: A:0.26, C:0.07, G:0.19, T:0.49
Consensus pattern (39 bp):
TCTCTTAATTAGTTTGTTGATTAAGTTTAGATGAAGTCA
Found at i:2490979 original size:43 final size:43
Alignment explanation
Indices: 2490898--2491053 Score: 149
Period size: 43 Copynumber: 3.7 Consensus size: 43
2490888 CAATGTCATA
* * * *
2490898 TCCCAGATATGGTCTTAAATGAAATCTCGTATCGATGCCAATAG
1 TCCCAGACATGGTCTTACACGAAATCTCATATCGATGCCAAT-G
* *
2490942 -CCCA-ACCAAT-GTTTTACACGAAATCACATATCGATGCCAATG
1 TCCCAGA-C-ATGGTCTTACACGAAATCTCATATCGATGCCAATG
* * *
2490984 TCCCAGACATGGTCTTACACGAATTCTCATATCGATGTC-ATA
1 TCCCAGACATGGTCTTACACGAAATCTCATATCGATGCCAATG
* * *
2491026 TCTCAGATATGGTCTTACACGTAATCTC
1 TCCCAGACATGGTCTTACACGAAATCTC
2491054 GGTAACCCTA
Statistics
Matches: 92, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
42 30 0.33
43 59 0.64
44 3 0.03
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACACGAAATCTCATATCGATGCCAATG
Found at i:2500061 original size:14 final size:14
Alignment explanation
Indices: 2500042--2500073 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
2500032 AGGTCATTTA
2500042 GCCCAACCAAACTG
1 GCCCAACCAAACTG
2500056 GCCCAACCAAACTG
1 GCCCAACCAAACTG
2500070 GCCC
1 GCCC
2500074 GGTGGTTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.47, G:0.16, T:0.06
Consensus pattern (14 bp):
GCCCAACCAAACTG
Found at i:2505148 original size:14 final size:14
Alignment explanation
Indices: 2505129--2505160 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
2505119 AGGTCATTTA
2505129 GCCCAACCAAACTG
1 GCCCAACCAAACTG
2505143 GCCCAACCAAACTG
1 GCCCAACCAAACTG
2505157 GCCC
1 GCCC
2505161 GGTGGTTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.47, G:0.16, T:0.06
Consensus pattern (14 bp):
GCCCAACCAAACTG
Found at i:2507359 original size:5 final size:5
Alignment explanation
Indices: 2507349--2507378 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
2507339 TGCCAAAGAT
2507349 TTGAA TTGAA TTGAA TTGAA TATGAA TTGA
1 TTGAA TTGAA TTGAA TTGAA T-TGAA TTGA
2507379 TGTTAAACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
TTGAA
Found at i:2511054 original size:110 final size:109
Alignment explanation
Indices: 2510820--2511204 Score: 592
Period size: 109 Copynumber: 3.5 Consensus size: 109
2510810 TCGATTAAAT
* *
2510820 GAGAAAAATTGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCCAAATGCAAAACATTGC
1 GAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTT-CCAAACGCAAAACATTGC
*
2510885 ATTATTTCG-AAAGTTTTTTAAAAGGATATTTAGCCATTTGGTTGAAC
65 CTTATTT-GAAAAG--TTTTAAAAGGATATTTAGCCATTTGGTTGAAC
*
2510932 GAGAAAAATCGACACCCAGCACCTTAGGGCACGTTCTCTCGAATTTCCCAAACGCAAAACATTGC
1 GAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTT-CCAAACGCAAAACATTGC
* *
2510997 CTTATTTGAAAAGTTTTAAAAGGATATTAAGCCATTTGGTTGAAT
65 CTTATTTGAAAAGTTTTAAAAGGATATTTAGCCATTTGGTTGAAC
* * *
2511042 GAGAAAATTCGACACCCAGCACCTTAGGGCATGTTTCCTCGAATTTCCAAACGCAAAACATTGCC
1 GAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTGCC
* * * *
2511107 TTATTTTAAAATTTTTAAAAAGATATTTAGCTATTTGGTTGAAC
66 TTATTTGAAAAGTTTTAAAAGGATATTTAGCCATTTGGTTGAAC
*
2511151 GAGAAAAATCGACACCCAGCACCTTATGGCACGTTTTCTCGAATTTCCAAACGC
1 GAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAACGC
2511205 TAAATATTAC
Statistics
Matches: 252, Mismatches: 20, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
109 107 0.42
110 72 0.29
111 1 0.00
112 72 0.29
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (109 bp):
GAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTGCC
TTATTTGAAAAGTTTTAAAAGGATATTTAGCCATTTGGTTGAAC
Found at i:2511464 original size:32 final size:34
Alignment explanation
Indices: 2511428--2511492 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
2511418 AAATATATAA
*
2511428 ATATTATAAAA-TATGAAAA-AATATGTATATGT
1 ATATTATAAAATTATGAAAATAATATATATATGT
* *
2511460 ATATTTTAAAATTATTAAAATAATATATATATG
1 ATATTATAAAATTATGAAAATAATATATATATG
2511493 AGTATGTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 10 0.36
33 7 0.25
34 11 0.39
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (34 bp):
ATATTATAAAATTATGAAAATAATATATATATGT
Found at i:2519872 original size:16 final size:17
Alignment explanation
Indices: 2519851--2519886 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2519841 ACTTTTAATT
*
2519851 TTTAAC-TAAATCAATA
1 TTTAACATAAATCAACA
2519867 TTTAACATAAATCAACA
1 TTTAACATAAATCAACA
2519884 TTT
1 TTT
2519887 TTATTTAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (17 bp):
TTTAACATAAATCAACA
Found at i:2524007 original size:4 final size:4
Alignment explanation
Indices: 2523988--2524028 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
2523978 GTAATACATA
*
2523988 TAAT TAA- TAAG T-AT TAAT TAAT TAAT TAAT TAAT TAAT TAA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAA
2524029 AAAGACAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
3 5 0.15
4 29 0.85
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (4 bp):
TAAT
Found at i:2527477 original size:46 final size:46
Alignment explanation
Indices: 2527410--2527502 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
2527400 TACTACACAA
2527410 AGGACACTAGATCCCAATAGACATTCTAAGATTGTGTCGCGTCATC
1 AGGACACTAGATCCCAATAGACATTCTAAGATTGTGTCGCGTCATC
2527456 AGGACACTAGATCCCAATAGACATTCTAAGATTGTGTCGCGTCATC
1 AGGACACTAGATCCCAATAGACATTCTAAGATTGTGTCGCGTCATC
2527502 A
1 A
2527503 CCTTAAATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (46 bp):
AGGACACTAGATCCCAATAGACATTCTAAGATTGTGTCGCGTCATC
Found at i:2535405 original size:31 final size:30
Alignment explanation
Indices: 2535361--2535418 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
2535351 TTTTTAATTT
2535361 TTTAAAATATTTATATTATTTTAATTTAATA
1 TTTAAAATATTTATA-TATTTTAATTTAATA
*
2535392 TTTAATAAT-TTTATATATTTTTATTTA
1 TTTAA-AATATTTATATATTTTAATTTA
2535419 TTGAACTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 11 0.44
31 11 0.44
32 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
TTTAAAATATTTATATATTTTAATTTAATA
Found at i:2535418 original size:30 final size:31
Alignment explanation
Indices: 2535340--2535418 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 31
2535330 TAGGCTCACC
* *
2535340 TATATACTTTTTTTTTAATTTTTTAAAATATT
1 TATATA-TTTTTATTTAATTATTTAAAATATT
*
2535372 TATATTATTTTAATTTAA-TATTTAATAAT-TT
1 TATA-TATTTTTATTTAATTATTTAA-AATATT
2535403 TATATATTTTTATTTA
1 TATATATTTTTATTTA
2535419 TTGAACTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 11 0.27
31 12 0.29
32 16 0.39
33 2 0.05
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (31 bp):
TATATATTTTTATTTAATTATTTAAAATATT
Found at i:2543876 original size:131 final size:131
Alignment explanation
Indices: 2543643--2543933 Score: 459
Period size: 131 Copynumber: 2.3 Consensus size: 131
2543633 TAGTGTACCG
2543643 ACTTAAACTCTTTCTAAGAACATGAT----G-ACAACTGTTCTGATTGTGACTCGTGAAGAAGAA
1 ACTTAAACTCTTTCTAAGAACATGATGGCAGTACAACTGTTCTGATTGTGACTCGTGAAGAAGAA
* * * *
2543703 GAGTAAGGCTAAACGCTATATCTATATATAGTGTCCCCACTGGTGACTGAGTATATGTCCTAAGC
66 GAGGAAGGCTAAACGCTAAATCTATAAATAGTGTCCCCACTGGTGACTGAGTATATGTCCTAAAC
2543768 A
131 A
* *
2543769 ACTTAAACTCTTTCTAAGAACATGATGGCAGTATAACTGTTCTGATTGTGACTCGTGGAGAAGAA
1 ACTTAAACTCTTTCTAAGAACATGATGGCAGTACAACTGTTCTGATTGTGACTCGTGAAGAAGAA
*
2543834 GAGGAAGGCTAAACGCTAAATCTATAAATAGTG-CCCAGACTGGTGACTGAGTATATGTCCTAAA
66 GAGGAAGGCTAAACGCTAAATCTATAAATAGTGTCCC-CACTGGTGACTGAGTATATGTCCTAAA
2543898 CA
130 CA
*
2543900 ACTCAAACTCTTTCTAAGAACATGATGGCAGTAC
1 ACTTAAACTCTTTCTAAGAACATGATGGCAGTAC
2543934 TGTTTGTATA
Statistics
Matches: 150, Mismatches: 9, Indels: 7
0.90 0.05 0.04
Matches are distributed among these distances:
126 26 0.17
130 4 0.03
131 120 0.80
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (131 bp):
ACTTAAACTCTTTCTAAGAACATGATGGCAGTACAACTGTTCTGATTGTGACTCGTGAAGAAGAA
GAGGAAGGCTAAACGCTAAATCTATAAATAGTGTCCCCACTGGTGACTGAGTATATGTCCTAAAC
A
Found at i:2553725 original size:23 final size:23
Alignment explanation
Indices: 2553655--2553763 Score: 122
Period size: 23 Copynumber: 5.0 Consensus size: 23
2553645 CTTGATCAGT
*
2553655 ATACGACACAT-AATTGCCTGA-
1 ATACGACACATAAAGTGCCTGAG
** *
2553676 A-ACGACACACGAGGTGCCT--G
1 ATACGACACATAAAGTGCCTGAG
2553696 ATACGACACATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCTGAG
*
2553719 ATACGACACATAAAGTGCCTAATG
1 ATACGACACATAAAGTGCCTGA-G
2553743 -TACGACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
2553764 TCGGCAAGGC
Statistics
Matches: 74, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
20 9 0.12
21 22 0.30
23 42 0.57
24 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAG
Found at i:2553960 original size:36 final size:36
Alignment explanation
Indices: 2553920--2554010 Score: 105
Period size: 36 Copynumber: 2.5 Consensus size: 36
2553910 CTTTTCAAAT
*
2553920 TCACATTTCAATTCAATTTCACTTTTTCACTTTCAA-
1 TCACATTTCAATTCAATTT-ACTTTTCCACTTTCAAG
* *
2553956 TCACAATTCAATTCAAATTTACTTTTCCATTTTCAAG
1 TCACATTTCAATTC-AATTTACTTTTCCACTTTCAAG
*
2553993 TCA-ATATTCATTTCAATT
1 TCACAT-TTCAATTCAATT
2554011 CCACACATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
36 32 0.68
37 15 0.32
ACGTcount: A:0.31, C:0.22, G:0.01, T:0.46
Consensus pattern (36 bp):
TCACATTTCAATTCAATTTACTTTTCCACTTTCAAG
Found at i:2554082 original size:16 final size:17
Alignment explanation
Indices: 2554061--2554092 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2554051 TAATAATAAT
2554061 ACTTACCTTA-TATTTC
1 ACTTACCTTATTATTTC
2554077 ACTTACCTTATTATTT
1 ACTTACCTTATTATTT
2554093 GCTTACCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (17 bp):
ACTTACCTTATTATTTC
Found at i:2561649 original size:66 final size:66
Alignment explanation
Indices: 2561543--2561675 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
2561533 GGATCGAGTA
2561543 GAGGGACCAAGCCAGACATTGCCAATTCCATGCAAATGGTGGTAGTTGTATCATGTATATAGAAA
1 GAGGGACCAAGCCAGACATTGCCAATTCCATGCAAATGGTGGTAGTTGTATCATGTATATAGAAA
2561608 G
66 G
2561609 GAGGGACCAAGCCAGACATTGCCAATTCCATGCAAATGGTGGTAGTTGTATCATGTATATAGAAA
1 GAGGGACCAAGCCAGACATTGCCAATTCCATGCAAATGGTGGTAGTTGTATCATGTATATAGAAA
2561674 G
66 G
2561675 G
1 G
2561676 CATCCTTAAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (66 bp):
GAGGGACCAAGCCAGACATTGCCAATTCCATGCAAATGGTGGTAGTTGTATCATGTATATAGAAA
G
Found at i:2563340 original size:17 final size:17
Alignment explanation
Indices: 2563315--2563359 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
2563305 AAATAATATA
2563315 AAATAAAAAATTAATTAT
1 AAAT-AAAAATTAATTAT
* *
2563333 AAATAAAATTTATTTAT
1 AAATAAAAATTAATTAT
*
2563350 AATTAAAAAT
1 AAATAAAAAT
2563360 AAATAAAAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATAAAAATTAATTAT
Found at i:2564088 original size:147 final size:146
Alignment explanation
Indices: 2563796--2564191 Score: 444
Period size: 147 Copynumber: 2.7 Consensus size: 146
2563786 TCACTTAACC
* * *
2563796 CATGTTAATTGTATATATTATAATCTACCATAAAGTTAATTACACATTTAAGGTTTAAGGTTACA
1 CATGTTAATTGTATATATTATAATTTACCATAAAGTTAGTTACACGTTTAAGGTTTAA-GTTACA
* * * * *
2563861 TATCATTAATAAAAAAATGTACATTATAATATCATAATTGTATATAAGCTTACATATCACTATAA
65 TATCATTAATACAAAAGTGTACATTATAATAACATAATTATATATAAGCATACATATCACTATAA
* *
2563926 AGCTACTTTATTTATAT
130 AGCTACCTTAATTATAT
* * *
2563943 CATGGTAATTGTATATATTATAATTTACTATAAAGTTAGTTACATGTTTAAGGTTTAAGCTTACA
1 CATGTTAATTGTATATATTATAATTTACCATAAAGTTAGTTACACGTTTAAGGTTTAAG-TTACA
* ** *
2564008 TATCATTAATACAAAAGTGTACATTATAATAACGTAATTATATATGGGGATACATATCA-T-TAA
65 TATCATTAATACAAAAGTGTACATTATAATAACATAATTATATATAAGCATACATATCACTATAA
* *
2564071 TGATCTTCCTTAATTATAT
130 --AGCTACCTTAATTATAT
* * * * * *
2564090 AATTTTAATTGTATATATTA-AAATTACCATAAAATTAGTTACGCGTTTAAGGTTTATGTTGA-A
1 CATGTTAATTGTATATATTATAATTTACCATAAAGTTAGTTACACGTTTAAGGTTTAAGTT-ACA
* *
2564153 TATCATT-A-ACAAAAGAAAGTACATTATAATATCATAATT
65 TATCATTAATACAAAAG--TGTACATTATAATAACATAATT
2564192 GTACAATTGA
Statistics
Matches: 212, Mismatches: 31, Indels: 14
0.82 0.12 0.05
Matches are distributed among these distances:
143 7 0.03
144 1 0.00
145 32 0.15
146 35 0.17
147 137 0.65
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.40
Consensus pattern (146 bp):
CATGTTAATTGTATATATTATAATTTACCATAAAGTTAGTTACACGTTTAAGGTTTAAGTTACAT
ATCATTAATACAAAAGTGTACATTATAATAACATAATTATATATAAGCATACATATCACTATAAA
GCTACCTTAATTATAT
Found at i:2565550 original size:3 final size:3
Alignment explanation
Indices: 2565542--2565574 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2565532 TTATAAGTGT
2565542 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2565575 ATGAAATCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2567104 original size:22 final size:21
Alignment explanation
Indices: 2567079--2567125 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
2567069 AGTTTTCACC
2567079 ATTTCTAAA-CTTAAGTATCGAT
1 ATTTCTAAATC-T-AGTATCGAT
* *
2567101 ATTTTTACATCTAGTATCGAT
1 ATTTCTAAATCTAGTATCGAT
2567122 ATTT
1 ATTT
2567126 AACCAAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 13 0.59
22 8 0.36
23 1 0.05
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.47
Consensus pattern (21 bp):
ATTTCTAAATCTAGTATCGAT
Found at i:2567551 original size:19 final size:19
Alignment explanation
Indices: 2567527--2567566 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
2567517 ACTCAGGTCC
2567527 GGTGACTGGGCCGAGTAAG
1 GGTGACTGGGCCGAGTAAG
2567546 GGTGACTGGGCCGAGTAAG
1 GGTGACTGGGCCGAGTAAG
2567565 GG
1 GG
2567567 ATGTTACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.15, G:0.50, T:0.15
Consensus pattern (19 bp):
GGTGACTGGGCCGAGTAAG
Found at i:2567670 original size:21 final size:21
Alignment explanation
Indices: 2567644--2567695 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
2567634 CGATGTGTGG
* *
2567644 TGAGATTAGTTACTATAGCGA
1 TGAGATTAGATACTATAGCAA
*
2567665 TGAGATTGGATACTATAGCAA
1 TGAGATTAGATACTATAGCAA
*
2567686 TGAGTTTAGA
1 TGAGATTAGA
2567696 AACAATGATG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.08, G:0.25, T:0.33
Consensus pattern (21 bp):
TGAGATTAGATACTATAGCAA
Found at i:2568002 original size:21 final size:20
Alignment explanation
Indices: 2567960--2567998 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
2567950 TTTGAATAAT
2567960 TAAAAATGTATTTATCATTA
1 TAAAAATGTATTTATCATTA
2567980 TAAAAA-GTATTTAT-ATTA
1 TAAAAATGTATTTATCATTA
2567998 T
1 T
2567999 TATATAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.26
19 8 0.42
20 6 0.32
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (20 bp):
TAAAAATGTATTTATCATTA
Found at i:2580243 original size:16 final size:16
Alignment explanation
Indices: 2580222--2580265 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
2580212 TTGATTTGCT
2580222 ATTACACTTCTATTCC
1 ATTACACTTCTATTCC
2580238 ATTACA-TATCTATTCC
1 ATTACACT-TCTATTCC
*
2580254 ATTACACCTCTA
1 ATTACACTTCTA
2580266 ATGCAATACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 1 0.04
16 24 0.96
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTACACTTCTATTCC
Found at i:2580275 original size:16 final size:16
Alignment explanation
Indices: 2580246--2580291 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
2580236 CCATTACATA
* *
2580246 TCTATTCCATTACACC
1 TCTAATCCAATACACC
*
2580262 TCTAATGCAATACACC
1 TCTAATCCAATACACC
2580278 TCTAATCCAATACA
1 TCTAATCCAATACA
2580292 GCGAACCAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.35, C:0.33, G:0.02, T:0.30
Consensus pattern (16 bp):
TCTAATCCAATACACC
Found at i:2591007 original size:17 final size:17
Alignment explanation
Indices: 2590971--2591018 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
2590961 GTACTTATGA
*
2590971 TTTTTTTTGTTTTCGAT
1 TTTTTTTTGTTTTCAAT
2590988 TTTTTTTTGTTTT-AACT
1 TTTTTTTTGTTTTCAA-T
*
2591005 TTTATTTTTATTTT
1 TTT-TTTTTGTTTT
2591019 TGTTCTCGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 1 0.04
17 17 0.63
18 9 0.33
ACGTcount: A:0.10, C:0.04, G:0.06, T:0.79
Consensus pattern (17 bp):
TTTTTTTTGTTTTCAAT
Found at i:2591711 original size:6 final size:6
Alignment explanation
Indices: 2591702--2591729 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2591692 AATTATTAGT
2591702 ATTTTA ATTTTA ATTTTA ATTTTA ATTT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTT
2591730 ATCAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
ATTTTA
Found at i:2596403 original size:47 final size:48
Alignment explanation
Indices: 2596333--2596424 Score: 159
Period size: 47 Copynumber: 1.9 Consensus size: 48
2596323 AGTCGAGGCA
*
2596333 ATATATTTTGTTTTATATATTTATTTTGATTTAATAAGATGTCTTACG
1 ATATATTTTGTTTTATATATTTATTATGATTTAATAAGATGTCTTACG
*
2596381 ATATA-TTTGTTTTATATGTTTATTATGATTTAATAAGATGTCTT
1 ATATATTTTGTTTTATATATTTATTATGATTTAATAAGATGTCTT
2596425 CGTAATTCTC
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
47 37 0.88
48 5 0.12
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (48 bp):
ATATATTTTGTTTTATATATTTATTATGATTTAATAAGATGTCTTACG
Found at i:2599750 original size:6 final size:6
Alignment explanation
Indices: 2599739--2599770 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
2599729 GCTTGAGGTG
*
2599739 GGCATA GGCATA GGCATA GGCATA GGTATA GG
1 GGCATA GGCATA GGCATA GGCATA GGCATA GG
2599771 GTGAAGCAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.31, C:0.12, G:0.38, T:0.19
Consensus pattern (6 bp):
GGCATA
Found at i:2600033 original size:22 final size:24
Alignment explanation
Indices: 2599992--2600113 Score: 89
Period size: 23 Copynumber: 5.2 Consensus size: 24
2599982 GTTAAATTAT
2599992 ATTATATTTAAATAATTTAATAT-A
1 ATTAT-TTTAAATAATTTAATATAA
*
2600016 ATTATTTTAAGTAA-TTAATATAA
1 ATTATTTTAAATAATTTAATATAA
*
2600039 ATTATTTTTAAA-ATTTATAATATATA
1 ATTA-TTTTAAATAATT-TAATATA-A
* *
2600065 AATATTTTTAA-AATTTAA-ATATA
1 ATTATTTTAAATAATTTAATATA-A
*
2600088 ATAATATTT-AAT-ATTTAA-ATAA
1 ATTAT-TTTAAATAATTTAATATAA
2600110 ATTA
1 ATTA
2600114 ATATAATAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
22 11 0.13
23 33 0.40
24 18 0.22
25 16 0.20
26 4 0.05
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (24 bp):
ATTATTTTAAATAATTTAATATAA
Found at i:2600077 original size:26 final size:25
Alignment explanation
Indices: 2600033--2600117 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 25
2600023 TAAGTAATTA
2600033 ATATAAATTATTTTTAAAATTTATAAT
1 ATATAAA-TATTTTTAAAATTTA-AAT
2600060 ATATAAATATTTTTAAAATTTAAAT
1 ATATAAATATTTTTAAAATTTAAAT
*
2600085 ATA-ATAATA--TTTAATATTTAAAT
1 ATATA-AATATTTTTAAAATTTAAAT
* *
2600108 AAATTAATAT
1 ATATAAATAT
2600118 AATAATATGT
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
23 19 0.37
24 1 0.02
25 10 0.19
26 15 0.29
27 7 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
ATATAAATATTTTTAAAATTTAAAT
Found at i:2600083 original size:17 final size:17
Alignment explanation
Indices: 2600045--2600104 Score: 54
Period size: 16 Copynumber: 3.7 Consensus size: 17
2600035 ATAAATTATT
*
2600045 TTTAAA-ATTTATAATA
1 TTTAAATATTTATAAAA
* *
2600061 TATAAATATTTTTAAAA
1 TTTAAATATTTATAAAA
* *
2600078 TTTAAATA-TAATAATA
1 TTTAAATATTTATAAAA
2600094 TTT-AATATTTA
1 TTTAAATATTTA
2600105 AATAAATTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
15 4 0.12
16 15 0.44
17 15 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTAAATATTTATAAAA
Found at i:2600092 original size:33 final size:32
Alignment explanation
Indices: 2600055--2600135 Score: 85
Period size: 31 Copynumber: 2.5 Consensus size: 32
2600045 TTTAAAATTT
* *
2600055 ATAATATATAAATATTTTTAA-AATTTAAATATA
1 ATAATAT-TAAATATTTTAAATAAATT-AATATA
*
2600088 ATAATATTTAATA-TTTAAATAAATTAATATA
1 ATAATATTAAATATTTTAAATAAATTAATATA
2600119 ATAATATGTACAATATT
1 ATAATAT-TA-AATATT
2600136 AGTTAATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
31 18 0.45
32 10 0.25
33 11 0.28
34 1 0.03
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (32 bp):
ATAATATTAAATATTTTAAATAAATTAATATA
Found at i:2600787 original size:22 final size:22
Alignment explanation
Indices: 2600744--2600791 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2600734 CGTTGTTCAA
*
2600744 GGTTAGGGTTTTCTATAATTAG
1 GGTTAGGGTTTTCTAGAATTAG
*
2600766 GGTTAGGGTTTT-TAGATTTTAG
1 GGTTAGGGTTTTCTAGA-ATTAG
2600788 GGTT
1 GGTT
2600792 TTAAGAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.19, C:0.02, G:0.31, T:0.48
Consensus pattern (22 bp):
GGTTAGGGTTTTCTAGAATTAG
Found at i:2601209 original size:95 final size:94
Alignment explanation
Indices: 2600790--2601297 Score: 472
Period size: 95 Copynumber: 5.4 Consensus size: 94
2600780 GATTTTAGGG
* * * * * *
2600790 TTTTAAG-AAAAAATAAATAAATAATGGTTTAGGATTTCTTAATTAAATTAATTATAAATTTAAA
1 TTTTAAGAAAAAAATAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTT-AA
* * * **
2600854 AAAATATATATTAGGATTTAGTGTTTATGGT
65 AAAA-ATAGATTAGGGTTTAGGGTTTATAAT
* * *
2600885 TTTT---AAATAAATAAATAAATTAGGGTTTAGGGTTATTTGAGTAAATTAATTATAAAATT-AA
1 TTTTAAGAAAAAAATAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTAAA
2600946 AAAATAGATTAGGGTTTAGGGTTTAGAGTTTAGAGT
66 AAAATAGATTAGGGTTTAGGGTTT--A---TA-A-T
* *
2600982 TTTTAAGAAAAAAATTAACTAGAA-TAGGGTTTAAGGTTA-TTGAGTAAATTAATTATAAATTTA
1 TTTTAAGAAAAAAA-TAAATA-AATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTA
*
2601045 AAAAAATAGATTAAGGTTTAGGG-------T
64 AAAAAATAGATTAGGGTTTAGGGTTTATAAT
* * * * *
2601069 TTTTAAGGAATAAAATCAAATAAATTAGGATTTGGGGTTACTTGAGTAAAATAATTATAAATTTT
1 TTTTAA-GAAAAAAAT-AAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTA
* *
2601134 AAAAAATAGATTAGGGTTTAGTGTTTATAAA
64 AAAAAATAGATTAGGGTTTAGGGTTTATAAT
* * *
2601165 TTTTAAGAAAAAAATCAAATAAATTAGAGTTTGGGGTTACTTGAGTAAATTAATTATAAATTAAA
1 TTTTAAGAAAAAAAT-AAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATT-TA
*
2601230 AAAAAATAGATTAGGGTTTAGGGTTTA-AGGT
64 AAAAAATAGATTAGGGTTTAGGGTTTATA-AT
* * *
2601261 TTTTAA-ATAAAAATTAAATAAGTTAGGGTTTGGGGTT
1 TTTTAAGA-AAAAAATAAATAAATTAGGGTTTAGGGTT
2601298 TAGGGTTAAT
Statistics
Matches: 344, Mismatches: 41, Indels: 56
0.78 0.09 0.13
Matches are distributed among these distances:
87 10 0.03
88 23 0.07
89 43 0.12
90 18 0.05
91 5 0.01
92 1 0.00
93 45 0.13
95 79 0.23
96 44 0.13
97 5 0.01
100 28 0.08
101 41 0.12
102 2 0.01
ACGTcount: A:0.44, C:0.01, G:0.17, T:0.38
Consensus pattern (94 bp):
TTTTAAGAAAAAAATAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTAAA
AAAATAGATTAGGGTTTAGGGTTTATAAT
Found at i:2606480 original size:16 final size:16
Alignment explanation
Indices: 2606447--2606480 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2606437 TAACACTGTT
* *
2606447 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
2606463 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
2606479 AA
1 AA
2606481 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:2609303 original size:21 final size:21
Alignment explanation
Indices: 2609277--2609317 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2609267 AGACGAGCAA
* *
2609277 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
2609298 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
2609318 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:2611254 original size:16 final size:16
Alignment explanation
Indices: 2611221--2611254 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2611211 GGAGATTGTT
* *
2611221 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
2611237 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
2611253 AA
1 AA
2611255 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:2613645 original size:105 final size:104
Alignment explanation
Indices: 2613524--2613961 Score: 489
Period size: 105 Copynumber: 4.1 Consensus size: 104
2613514 AAAAAACAAA
*
2613524 AAAAAAAATTTTTTGGGTGCTGGCCTGTCAATGGTCGGCACCCAGTACACAGTACAAAGAAAAAA
1 AAAAAAAATTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAAGAAAAAA
*
2613589 AATAAATTTTTTTCGTGTCAAAATCAGATAAAAAAATACG
66 AATAAATTTTTTTCGTGTCAGAATCAGAT-AAAAAATACG
2613629 AAAAAAAATTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAAGAAAAAA
1 AAAAAAAATTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAAGAAAAAA
** * *
2613694 AAT-TTTTTTTTTCGTGTCAGAATCAAATAAAAAATACAAAAAAAAATT
66 AATAAATTTTTTTCGTGTCAGAATCAGATAAAAAATAC----------G
* *
2613742 AAAAAAAATTTTTTTAGGTGCTGGCGTGTCAATGGCCGGCACCCAGTACACAGTACAAAG---AA
1 AAAAAAAA-TTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAAGAAAAA
2613804 AAA-AAA----TTTCGTGTCAGAATCAGATAAAAAATACG
65 AAATAAATTTTTTTCGTGTCAGAATCAGATAAAAAATACG
***
2613839 AAAAAAATAAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAA
1 ------A-AAAAAAATTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAA
*
2613904 GAAAAAAAATTTAAAATTTTTTTTCGTGTCAGAATCAGATAAAAAAATAAG
59 GAAAAAAAA--T-AAA-TTTTTTTCGTGTCAGAATCAGAT-AAAAAATACG
2613955 AAAAAAA
1 AAAAAAA
2613962 GTAGAAAAAA
Statistics
Matches: 283, Mismatches: 18, Indels: 60
0.78 0.05 0.17
Matches are distributed among these distances:
103 56 0.20
104 28 0.10
105 67 0.24
106 5 0.02
107 27 0.10
109 6 0.02
110 4 0.01
111 5 0.02
113 8 0.03
114 49 0.17
115 19 0.07
116 9 0.03
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.24
Consensus pattern (104 bp):
AAAAAAAATTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAAGAAAAAA
AATAAATTTTTTTCGTGTCAGAATCAGATAAAAAATACG
Found at i:2613762 original size:114 final size:112
Alignment explanation
Indices: 2613629--2613992 Score: 505
Period size: 114 Copynumber: 3.2 Consensus size: 112
2613619 AAAAAATACG
2613629 AAAAAAAATTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAAGAAAAAA
1 AAAAAAAATTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAAGAAAAAA
* *
2613694 AATTTTTTTTTTCGTGTCAGAATCAAATAAAAAATACAAAAAAAAATT
66 AATTTTTTTTTTCGTGTCAGAATCAGATAAAAAATACAGAAAAAAA-T
* *
2613742 AAAAAAAATTTTTTTAGGTGCTGGCGTGTCAATGGCCGGCACCCAGTACACAGTACAAAGAAAAA
1 AAAAAAAA-TTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAAGAAAAA
2613807 AAA-------TTTCGTGTCAGAATCAGATAAAAAATAC-GAAAAAAAT
65 AAATTTTTTTTTTCGTGTCAGAATCAGATAAAAAATACAGAAAAAAAT
**
2613847 AAAAAAAA-AATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAAGAAAAAA
1 AAAAAAAATTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAAGAAAAAA
2613911 AATTTAAAATTTTTTTTCGTGTCAGAATCAGATAAAAAAATA-AGAAAAAAAGT
66 AA-TT----TTTTTTTTCGTGTCAGAATCAGAT-AAAAAATACAGAAAAAAA-T
*
2613964 AGAAAAAAATTTTTTGGGTGCTGACCTGT
1 A-AAAAAAATTTTTTGGGTGCTGGCCTGT
2613993 AAATATTATA
Statistics
Matches: 222, Mismatches: 11, Indels: 30
0.84 0.04 0.11
Matches are distributed among these distances:
103 54 0.24
105 9 0.04
106 7 0.03
107 27 0.12
113 8 0.04
114 57 0.26
115 19 0.09
116 16 0.07
117 2 0.01
118 7 0.03
119 16 0.07
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.25
Consensus pattern (112 bp):
AAAAAAAATTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAAGAAAAAA
AATTTTTTTTTTCGTGTCAGAATCAGATAAAAAATACAGAAAAAAAT
Found at i:2614049 original size:16 final size:14
Alignment explanation
Indices: 2614023--2614070 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
2614013 TAAATATTCC
*
2614023 TTTTATTTTTACATT
1 TTTTTTTTTTA-ATT
2614038 TTTCTTTTTTTAA-T
1 TTT-TTTTTTTAATT
*
2614052 TTTTTTTTCTAATT
1 TTTTTTTTTTAATT
2614066 TTTTT
1 TTTTT
2614071 CGTATTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 8 0.28
14 10 0.34
15 4 0.14
16 7 0.24
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTTTTTTAATT
Found at i:2614058 original size:13 final size:13
Alignment explanation
Indices: 2614023--2614070 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
2614013 TAAATATTCC
*
2614023 TTTTATTTTTACATT
1 TTTTTTTTTTA-A-T
2614038 TTTCTTTTTTTAAT
1 TTT-TTTTTTTAAT
*
2614052 TTTTTTTTCTAAT
1 TTTTTTTTTTAAT
2614065 TTTTTT
1 TTTTTT
2614071 CGTATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 15 0.50
14 4 0.13
15 4 0.13
16 7 0.23
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTTAAT
Found at i:2614258 original size:118 final size:114
Alignment explanation
Indices: 2614049--2614756 Score: 970
Period size: 118 Copynumber: 6.2 Consensus size: 114
2614039 TTCTTTTTTT
2614049 AATTTTTTTTTCTAATTTTTTTCGTATTTTTTATCTGATTCTGACACGAAAAAAAATTAAAAGTT
1 AATTTTTTTTT-T-ATTTTTTTCGTATTTTTTATCTGATTCTGACACGAAAAAAAA-TAAAA--T
2614114 TTTTTTTCTTTGTACTGTATACTGGGTGCCGGCCATTGACAGGCCAGCACCCAA
61 TTTTTTTCTTTGTACTGTATACTGGGTGCCGGCCATTGACAGGCCAGCACCCAA
2614168 AATTTTTTTTTTATTTTTTTCGTAATTTTTTATCTGATTCTGACACGAAAAAAATAAATAAAATT
1 AATTTTTTTTTTATTTTTTTCGT-ATTTTTTATCTGATTCTGACACG--AAAAA-AAATAAAATT
*
2614233 TTTTTTCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCC-A
62 TTTTTTCTTTGTACTGTATACTGGGTGCCGGCCATTGACAGGCCAGCACCCAA
2614285 AA-TTTTTTTTTATTTTTTTCGTATTTTTTATCTGATTCTGACACGAAAAAAAAATTAAAA--TT
1 AATTTTTTTTTTATTTTTTTCGTATTTTTTATCTGATTCTGACACG-AAAAAAAA-TAAAATTTT
*
2614347 TTTTCTTTGTACTGTATACTGGGT----G-C-TTGACAGGCTAGCACCC-A
64 TTTTCTTTGTACTGTATACTGGGTGCCGGCCATTGACAGGCCAGCACCCAA
*
2614391 AA-TTTTTTTTTATTTTTTTCGTATTTTTTATCTGATTCTGACACGAAAAAAAAT-TAA---TTT
1 AATTTTTTTTTTATTTTTTTCGTATTTTTTATCTGATTCTGACACGAAAAAAAATAAAATTTTTT
* *
2614451 TT-TTTGTACTGTATATTGGGTGCCGGCCATTAACAGGCCAGCACCCAAA
66 TTCTTTGTACTGTATACTGGGTGCCGGCCATTGACAGGCCAGCACCC-AA
*
2614500 AATATTTTTTTTATATTTTTTTCGTA-TTTTTATCTGATTCTGACACGAAAAAAAAT-AATTTTT
1 AAT-TTTTTTTT-TATTTTTTTCGTATTTTTTATCTGATTCTGACACGAAAAAAAATAAAATTTT
* * *
2614563 TTTTCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGTCCAACACCCAAAA
64 TTTTCTTTGTACTGTATACTGGGTGCCGGCCATTGACAGGCCAGCACCC--AA
* *
2614616 AATTTTTTTTTCTAATTTTTTTCGTATTTTTTATCTGATTCTGACACGAAAAAAAATTAATTTTT
1 AATTTTTTTTT-T-ATTTTTTTCGTATTTTTTATCTGATTCTGACACGAAAAAAAATAAAATTTT
* * *
2614681 TTTTCTTTGTACTTTGTACTGGGTGCCGGCCATTGACAGGCCAACA-CCAA
64 TTTTCTTTGTACTGTATACTGGGTGCCGGCCATTGACAGGCCAGCACCCAA
*
2614731 AAATTTTTTTTTATTTTTTTTCGTAT
1 AATTTTTTTTTTA-TTTTTTTCGTAT
2614757 ATCCGTATTT
Statistics
Matches: 546, Mismatches: 18, Indels: 55
0.88 0.03 0.09
Matches are distributed among these distances:
101 18 0.03
102 5 0.01
103 2 0.00
104 1 0.00
105 9 0.02
106 63 0.12
107 16 0.03
108 1 0.00
109 3 0.01
111 39 0.07
112 38 0.07
113 4 0.01
114 29 0.05
115 83 0.15
116 38 0.07
117 46 0.08
118 127 0.23
119 11 0.02
120 10 0.02
121 3 0.01
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (114 bp):
AATTTTTTTTTTATTTTTTTCGTATTTTTTATCTGATTCTGACACGAAAAAAAATAAAATTTTTT
TTCTTTGTACTGTATACTGGGTGCCGGCCATTGACAGGCCAGCACCCAA
Found at i:2615223 original size:22 final size:21
Alignment explanation
Indices: 2615198--2615267 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 21
2615188 ATAAATATAT
2615198 AAAAATACATAAATATTTTCAA
1 AAAAATA-ATAAATATTTTCAA
*
2615220 AAAATATAAT-AATAATTT-AA
1 AAAA-ATAATAAATATTTTCAA
*
2615240 AATATATAAAATAAATATTTTCAA
1 AA-A-A-ATAATAAATATTTTCAA
2615264 AAAA
1 AAAA
2615268 GTAAACTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
20 4 0.10
21 8 0.20
22 13 0.32
23 11 0.28
24 4 0.10
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAAATAATAAATATTTTCAA
Found at i:2615610 original size:31 final size:31
Alignment explanation
Indices: 2615575--2615641 Score: 84
Period size: 29 Copynumber: 2.2 Consensus size: 31
2615565 ATATTAAAAC
*
2615575 TTATTAACATATATATTTTGAAATTATTTAT-
1 TTATTAACAT-TATATTTTGAAATTATATATG
* *
2615606 TTATT-TCATTATATTTTTAAATTATATATG
1 TTATTAACATTATATTTTGAAATTATATATG
2615636 TTATTA
1 TTATTA
2615642 TTTTTTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 18 0.58
30 8 0.26
31 5 0.16
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (31 bp):
TTATTAACATTATATTTTGAAATTATATATG
Found at i:2615644 original size:41 final size:41
Alignment explanation
Indices: 2615597--2615691 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 41
2615587 ATATTTTGAA
*
2615597 ATTATTTATTTATTTCAT-TATAT-TTTTAAATTATATATGTT
1 ATTATTTATTTATTT-ATATATATATTTTAAAATATATATG-T
* *
2615638 ATTATTT-TTTATTTTTATATATATTTTAAAATATTTATGT
1 ATTATTTATTTATTTATATATATATTTTAAAATATATATGT
*
2615678 ATT-TTTATATATTT
1 ATTATTTATTTATTT
2615692 TTTTGAAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
39 4 0.09
40 22 0.47
41 21 0.45
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65
Consensus pattern (41 bp):
ATTATTTATTTATTTATATATATATTTTAAAATATATATGT
Found at i:2615684 original size:10 final size:10
Alignment explanation
Indices: 2615647--2615693 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
2615637 TATTATTTTT
2615647 TATTTTTATA
1 TATTTTTATA
2615657 TATATTTTA-A
1 TAT-TTTTATA
* * *
2615667 AATATTTATG
1 TATTTTTATA
2615677 TATTTTTATA
1 TATTTTTATA
2615687 TATTTTT
1 TATTTTT
2615694 TTGAAATTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
9 4 0.14
10 20 0.69
11 5 0.17
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (10 bp):
TATTTTTATA
Found at i:2615689 original size:18 final size:17
Alignment explanation
Indices: 2615627--2615691 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 17
2615617 TATTTTTAAA
2615627 TTATATATGTTATTATTT
1 TTATATAT-TTATTATTT
*
2615645 TT-TATTTTTATATATATT
1 TTATATATTTAT-TAT-TT
*
2615663 TTAAAATATTTATGTATTT
1 TT-ATATATTTAT-TATTT
2615682 TTATATATTT
1 TTATATATTT
2615692 TTTTGAAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 4 0.11
17 7 0.18
18 13 0.34
19 4 0.11
20 10 0.26
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (17 bp):
TTATATATTTATTATTT
Found at i:2616612 original size:22 final size:22
Alignment explanation
Indices: 2616564--2616612 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
2616554 GCTTTTGTAC
*
2616564 TTTTTAAAATAATTAAATTATAT
1 TTTTTAAAAT-ATTAAATTATAA
*
2616587 TTTTTAAAAT-TTAAAATTTTAA
1 TTTTTAAAATATT-AAATTATAA
2616609 TTTT
1 TTTT
2616613 CACTCAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 2 0.09
22 11 0.48
23 10 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTTAAAATATTAAATTATAA
Found at i:2627609 original size:20 final size:20
Alignment explanation
Indices: 2627553--2627609 Score: 51
Period size: 20 Copynumber: 2.9 Consensus size: 20
2627543 CTATATTTCT
* **
2627553 AAATATCTAAAGATTTTTCA
1 AAATTTCTAAAGATTTACCA
* * * *
2627573 GAATTTATAAGGCTTTACCA
1 AAATTTCTAAAGATTTACCA
2627593 AAATTTCTAAAGATTTA
1 AAATTTCTAAAGATTTA
2627610 TCAATGCTTT
Statistics
Matches: 26, Mismatches: 11, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.39
Consensus pattern (20 bp):
AAATTTCTAAAGATTTACCA
Found at i:2627727 original size:19 final size:20
Alignment explanation
Indices: 2627689--2627733 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
2627679 TTTGATATAA
2627689 CAAAATTTGAAAGGACTCAC
1 CAAAATTTGAAAGGACTCAC
* *
2627709 CAAAATTT-CAAGGATTCAC
1 CAAAATTTGAAAGGACTCAC
2627728 CAAAAT
1 CAAAAT
2627734 ATTTATAGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.47, C:0.20, G:0.11, T:0.22
Consensus pattern (20 bp):
CAAAATTTGAAAGGACTCAC
Found at i:2628291 original size:14 final size:13
Alignment explanation
Indices: 2628272--2628302 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
2628262 ATAATATTAA
2628272 AAAAATTAAAATAT
1 AAAAATTAAAAT-T
2628286 AAAAATTAAAATT
1 AAAAATTAAAATT
2628299 AAAA
1 AAAA
2628303 TTTGAGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AAAAATTAAAATT
Found at i:2634567 original size:4 final size:4
Alignment explanation
Indices: 2634558--2634583 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2634548 TTCTCTTCCC
2634558 CTTT CTTT CTTT CTTT CTTT CTTT CT
1 CTTT CTTT CTTT CTTT CTTT CTTT CT
2634584 ATACCTCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
CTTT
Found at i:2652936 original size:42 final size:41
Alignment explanation
Indices: 2652872--2653073 Score: 237
Period size: 42 Copynumber: 4.9 Consensus size: 41
2652862 ACATTTTCCC
* *
2652872 CAGTGACAAGCACAAGCAATGGTATCTTTGGTGGTTCATCTG
1 CAGT-ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTG
2652914 CAAGTACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTG
1 C-AGTACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTG
* * * * * *
2652956 CAACTACAAGCACGGGCACTGGTTTATTTGGTGGTACATCAG
1 C-AGTACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTG
*
2652998 CAGCTACAAGCACAGGCAATGGCATCTTTGGTGGTACATCTG
1 CAG-TACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTG
* * * *
2653040 CA--ACAAGCACAGGTAGTAGTATTTTTGGTGGTAC
1 CAGTACAAGCACAGGCAATGGTATCTTTGGTGGTAC
2653074 GTTTTTGCCA
Statistics
Matches: 138, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 27 0.20
41 1 0.01
42 107 0.78
43 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (41 bp):
CAGTACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTG
Found at i:2655311 original size:11 final size:11
Alignment explanation
Indices: 2655295--2655321 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2655285 GAGCACTTCA
2655295 TAATCTTATAT
1 TAATCTTATAT
2655306 TAATCTTATAT
1 TAATCTTATAT
2655317 TAATC
1 TAATC
2655322 CTACGTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (11 bp):
TAATCTTATAT
Found at i:2655775 original size:27 final size:28
Alignment explanation
Indices: 2655709--2655789 Score: 146
Period size: 27 Copynumber: 2.9 Consensus size: 28
2655699 CTTGCTTTCA
2655709 AACCCAAATCAGAATGGGTTCATCTTTG
1 AACCCAAATCAGAATGGGTTCATCTTTG
*
2655737 AACCCAAATCAGAATGGGTTCAT-TTTT
1 AACCCAAATCAGAATGGGTTCATCTTTG
2655764 AACCCAAATCAGAATGGGTTCATCTT
1 AACCCAAATCAGAATGGGTTCATCTT
2655790 CGGTGAAAGC
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
27 26 0.51
28 25 0.49
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (28 bp):
AACCCAAATCAGAATGGGTTCATCTTTG
Found at i:2661468 original size:40 final size:40
Alignment explanation
Indices: 2661410--2661548 Score: 151
Period size: 40 Copynumber: 3.5 Consensus size: 40
2661400 ACACACCAGT
2661410 TTGACACCCAGTGCCTCATCGGATAATTCGAAGTGATAAA
1 TTGACACCCAGTGCCTCATCGGATAATTCGAAGTGATAAA
* * * *
2661450 TTGACACCCAGCGTCTCATCGGTTAAATCGAA--G-TAAA
1 TTGACACCCAGTGCCTCATCGGATAATTCGAAGTGATAAA
* * * *
2661487 TTGGCACCCAGTGCCTTATCGAATTAATCCGAAGT-AGTAAA
1 TTGACACCCAGTGCCTCATCGGA-TAATTCGAAGTGA-TAAA
*
2661528 TTGACACCCAGTGTCTCATCG
1 TTGACACCCAGTGCCTCATCG
2661549 ACTCGAAGTC
Statistics
Matches: 79, Mismatches: 15, Indels: 9
0.77 0.15 0.09
Matches are distributed among these distances:
37 21 0.27
38 8 0.10
40 28 0.35
41 22 0.28
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.26
Consensus pattern (40 bp):
TTGACACCCAGTGCCTCATCGGATAATTCGAAGTGATAAA
Found at i:2661744 original size:24 final size:24
Alignment explanation
Indices: 2661707--2661753 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2661697 TATATATACC
2661707 AATTCAATCAATA-TAAATTCAATA
1 AATTCAATCAATATTAAA-TCAATA
2661731 AATTC-ATCACATATTAAATCAAT
1 AATTCAATCA-ATATTAAATCAAT
2661754 CCATTCAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (24 bp):
AATTCAATCAATATTAAATCAATA
Found at i:2663840 original size:30 final size:30
Alignment explanation
Indices: 2663771--2663840 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 30
2663761 GGAGAAGAAG
**
2663771 AACCATAAACATATTGGGTCATTTATGCAAAA
1 AACCA-AAA-ATATTGGACCATTTATGCAAAA
* **
2663803 AA-TAAAAATATTGGACCATTTATTTAAAA
1 AACCAAAAATATTGGACCATTTATGCAAAA
2663832 AACCAAAAA
1 AACCAAAAA
2663841 GGAAGGACAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
29 20 0.65
30 8 0.26
31 1 0.03
32 2 0.06
ACGTcount: A:0.51, C:0.13, G:0.09, T:0.27
Consensus pattern (30 bp):
AACCAAAAATATTGGACCATTTATGCAAAA
Found at i:2664014 original size:38 final size:38
Alignment explanation
Indices: 2663954--2664029 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
2663944 GTAATAAAAA
* *
2663954 ATGTTAATGAGTTACTGATTTGTAACTTTTCGATAACG
1 ATGTTAATGAGTGACTGATTTGTAACTTTTCGAAAACG
* * *
2663992 ATGTTAATGAGTGATTGGTTTGTCACTTTTCGAAAACG
1 ATGTTAATGAGTGACTGATTTGTAACTTTTCGAAAACG
2664030 TTAGTGATTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.41
Consensus pattern (38 bp):
ATGTTAATGAGTGACTGATTTGTAACTTTTCGAAAACG
Found at i:2665618 original size:20 final size:20
Alignment explanation
Indices: 2665581--2665619 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2665571 TTAATAGTCA
2665581 TTTAACTATTAATATATATT
1 TTTAACTATTAATATATATT
*
2665601 TTTAATTATCTAAT-TATAT
1 TTTAACTAT-TAATATATAT
2665620 AAAAATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTAACTATTAATATATATT
Found at i:2666477 original size:42 final size:42
Alignment explanation
Indices: 2666418--2666583 Score: 217
Period size: 42 Copynumber: 4.0 Consensus size: 42
2666408 TTCCCCAGTG
* *
2666418 ACAAGCACAAGCAATGGTATCTTCGGTGGTACATCTGCAAGT
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAAGT
* *
2666460 ACAAGCGCAGGCAATGGTATCTTTGGTGGTACATCTGCAACT
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAAGT
* ** * * *
2666502 ACAAGCACGGGCAGGGGTTTATTTGGTGGTACATCAGC-AGCT
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAAG-T
*
2666544 ACAAGCACAGGCAATGGCATCTTTGGTGGTACATCTGCAA
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAA
2666584 CAAGCACAGG
Statistics
Matches: 103, Mismatches: 19, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
41 1 0.01
42 101 0.98
43 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (42 bp):
ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAAGT
Found at i:2670549 original size:42 final size:42
Alignment explanation
Indices: 2670493--2670659 Score: 217
Period size: 42 Copynumber: 4.0 Consensus size: 42
2670483 AACTGTGCTT
* * * *
2670493 GTTGCTGATGTACCACCAGAGATGCCATTGCCAGTGCTTGTA
1 GTTGCAGATGTACCACCAAAGATACCATTGCCTGTGCTTGTA
* * * *
2670535 GTTGCAGATGTACCACCAAATAAACCAGTGCCCGTGCTTGTA
1 GTTGCAGATGTACCACCAAAGATACCATTGCCTGTGCTTGTA
*
2670577 GTTGCAGATGTACAACCAAAGATACCATTGCCTGTGCTTGTA
1 GTTGCAGATGTACCACCAAAGATACCATTGCCTGTGCTTGTA
* * * *
2670619 CTTGCAGATTTACCACCGAAGATACCATTGCTTGTGCTTGT
1 GTTGCAGATGTACCACCAAAGATACCATTGCCTGTGCTTGT
2670660 CACTGGGGAA
Statistics
Matches: 108, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 108 1.00
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (42 bp):
GTTGCAGATGTACCACCAAAGATACCATTGCCTGTGCTTGTA
Found at i:2671371 original size:4 final size:4
Alignment explanation
Indices: 2671362--2671390 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
2671352 TAGCACAGCT
2671362 GAAA GAAA GAAA GAAA GAAA GAAA GAAA G
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA G
2671391 GGGGAATGTT
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:2675396 original size:103 final size:105
Alignment explanation
Indices: 2675214--2675420 Score: 364
Period size: 103 Copynumber: 2.0 Consensus size: 105
2675204 AAATAAAAAT
**
2675214 CATATAAAATAGGTAATTGATCCCTTCTTCATGTTTAAAAGCCAAAAAGAGGGTGTTTCCTCTTT
1 CATATAAAATAGGTAATTGATCCC-TCTTCATGCATAAAAGCCAAAAAGAGGGTGTTTCCTCTTT
2675279 AACAAGTTATACCTCCTCCATGACTAACCTATATATATATA
65 AACAAGTTATACCTCCTCCATGACTAACCTATATATATATA
*
2675320 CATATAAAATAGGTAATTGAT-CC-CTTCATGCATAAAAGCCAAAGAGAGGGTGTTTCCTCTTTA
1 CATATAAAATAGGTAATTGATCCCTCTTCATGCATAAAAGCCAAAAAGAGGGTGTTTCCTCTTTA
2675383 ACAAGTTATACCTCCTCCATGACTAACCTATATATATA
66 ACAAGTTATACCTCCTCCATGACTAACCTATATATATA
2675421 AACGTTGGAA
Statistics
Matches: 98, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
103 75 0.77
105 2 0.02
106 21 0.21
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.32
Consensus pattern (105 bp):
CATATAAAATAGGTAATTGATCCCTCTTCATGCATAAAAGCCAAAAAGAGGGTGTTTCCTCTTTA
ACAAGTTATACCTCCTCCATGACTAACCTATATATATATA
Found at i:2676948 original size:16 final size:16
Alignment explanation
Indices: 2676922--2676958 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
2676912 CAAATAAAAT
2676922 AAAATTACATT-ATAA
1 AAAATTACATTAATAA
2676937 AAAATGTACATTAATAA
1 AAAAT-TACATTAATAA
2676954 AAAAT
1 AAAAT
2676959 CATAAAACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.25
16 6 0.30
17 9 0.45
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (16 bp):
AAAATTACATTAATAA
Found at i:2677220 original size:100 final size:99
Alignment explanation
Indices: 2676935--2677275 Score: 325
Period size: 106 Copynumber: 3.3 Consensus size: 99
2676925 ATTACATTAT
* * * *
2676935 AAAAAATGTACATTAATAAAAAATCATAAAACACTAAACTAAACACTAACAATTTATACAACCTA
1 AAAAAAT-TACATTACTAAAAAATCA-CAAA-AC-AAACAAAACACTAACAATTTATA-AATCTA
* ****
2677000 ATCATCAATTACTAACAAAATAACTATAAAATTATTTTTTTA
61 ATCAT-AATTACTAACAAAATAACTAT--AATCATTTAAAAA
* *
2677042 ACAAAATTACATTACTAAAAAATCACAAAACTCTAAACTAAACACTAACAATTTATAAAT-TAAT
1 AAAAAATTACATTACTAAAAAATCACAAAA--C-AAACAAAACACTAACAATTTATAAATCTAAT
2677106 CATAAATTACTAACAAAATAACTATAA-CATTTAAAAA
63 CAT-AATTACTAACAAAATAACTATAATCATTTAAAAA
* *
2677143 AAAAGAATTTACATTACTAATAAATCA-AAAA-ACACAAAACACTAACAATTTATATAATCTAAT
1 AAAA-AA-TTACATTACTAAAAAATCACAAAACAAACAAAACACTAACAATTTATA-AATCTAAT
* **
2677206 CATAAGTTACTAACAAAATAACTATAAAATTATTT--TTA
63 CATAA-TTACTAACAAAATAACTAT--AATCATTTAAAAA
2677244 AAAAAATTACATTACTAAAAAAATCACAAAAC
1 AAAAAATTACATTACT-AAAAAATCACAAAAC
2677276 TCTAAAAAAA
Statistics
Matches: 203, Mismatches: 18, Indels: 31
0.81 0.07 0.12
Matches are distributed among these distances:
98 21 0.10
99 15 0.07
100 36 0.18
101 17 0.08
102 10 0.05
103 22 0.11
104 29 0.14
105 5 0.02
106 42 0.21
107 6 0.03
ACGTcount: A:0.56, C:0.15, G:0.01, T:0.28
Consensus pattern (99 bp):
AAAAAATTACATTACTAAAAAATCACAAAACAAACAAAACACTAACAATTTATAAATCTAATCAT
AATTACTAACAAAATAACTATAATCATTTAAAAA
Found at i:2677540 original size:18 final size:18
Alignment explanation
Indices: 2677499--2677535 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2677489 CGTTTATTGA
2677499 TTTTTTATTAATGTAAAT
1 TTTTTTATTAATGTAAAT
2677517 TTTTTTA-TAATGT-AAT
1 TTTTTTATTAATGTAAAT
2677533 TTT
1 TTT
2677536 ATTTTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.32
17 6 0.32
18 7 0.37
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (18 bp):
TTTTTTATTAATGTAAAT
Found at i:2677545 original size:109 final size:104
Alignment explanation
Indices: 2677290--2677537 Score: 322
Period size: 104 Copynumber: 2.3 Consensus size: 104
2677280 AAAAAAAATA
* * *
2677290 TTTAGTAATGTAAATTCTTTTTTAAAA-AATGTTATAGTTATTTTGTTAGTAATTTATGATTAGT
1 TTTAGTAATGTAAATT-TTTTTAAAAATAATTTTATAGTTATTTTATTAGTAATTTATGATTAGT
*
2677354 TTATAAATTGTTAGTGTTTAGTTTAAGGTTTTGTGATTTT
65 TTATAAATTGTTAGTGTTAAGTTTAAGGTTTTGTGATTTT
* *
2677394 TTTAGTAATGTAATTTTTTTTAAAAATATTTTTATAGTTATTTTATTAGTAATTTATGATTAGGT
1 TTTAGTAATGTAAATTTTTTTAAAAATAATTTTATAGTTATTTTATTAGTAATTTATGATTA-GT
2677459 TATATAAATTGTTAGTGTTAAGTTTAGAGTCGTTTAT-TGA-TTT
65 T-TATAAATTGTTAGTGTTAAGTTTA-AG--GTTT-TGTGATTTT
* **
2677502 TTTATTAATGTAAATTTTTTTATAATGTAATTTTAT
1 TTTAGTAATGTAAATTTTTTTA-AAAATAATTTTAT
2677538 TTTTATTTGA
Statistics
Matches: 125, Mismatches: 11, Indels: 11
0.85 0.07 0.07
Matches are distributed among these distances:
103 9 0.07
104 47 0.38
105 3 0.02
106 23 0.18
107 2 0.02
108 23 0.18
109 17 0.14
110 1 0.01
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.56
Consensus pattern (104 bp):
TTTAGTAATGTAAATTTTTTTAAAAATAATTTTATAGTTATTTTATTAGTAATTTATGATTAGTT
TATAAATTGTTAGTGTTAAGTTTAAGGTTTTGTGATTTT
Found at i:2678849 original size:105 final size:105
Alignment explanation
Indices: 2678724--2678934 Score: 395
Period size: 105 Copynumber: 2.0 Consensus size: 105
2678714 GTGATGAAGG
2678724 GGAAAAGAAAGATCAAACTGATGATGCCAACAAGAAAGCAGCAGATGAAAGCAATGAGAATGGAA
1 GGAAAAGAAAGATCAAACTGATGATGCCAACAAGAAAGCAGCAGATGAAAGCAATGAGAATGGAA
2678789 AGGAATATTCGTCCACGCCATCCATGCCCCAAAACAATCT
66 AGGAATATTCGTCCACGCCATCCATGCCCCAAAACAATCT
* * *
2678829 GGAAAAGAAAGATCAGACTGATGATGCCAACAAGAGAGCAGCAGATGAAAGCAATGAGAATGGCA
1 GGAAAAGAAAGATCAAACTGATGATGCCAACAAGAAAGCAGCAGATGAAAGCAATGAGAATGGAA
2678894 AGGAATATTCGTCCACGCCATCCATGCCCCAAAACAATCT
66 AGGAATATTCGTCCACGCCATCCATGCCCCAAAACAATCT
2678934 G
1 G
2678935 CAACCTTCCT
Statistics
Matches: 103, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 103 1.00
ACGTcount: A:0.42, C:0.21, G:0.22, T:0.14
Consensus pattern (105 bp):
GGAAAAGAAAGATCAAACTGATGATGCCAACAAGAAAGCAGCAGATGAAAGCAATGAGAATGGAA
AGGAATATTCGTCCACGCCATCCATGCCCCAAAACAATCT
Found at i:2686556 original size:13 final size:13
Alignment explanation
Indices: 2686538--2686562 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2686528 TTAACTAAAA
2686538 AATATCCATTAGT
1 AATATCCATTAGT
2686551 AATATCCATTAG
1 AATATCCATTAG
2686563 ATGAAAAGAT
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:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (13 bp):
AATATCCATTAGT
Found at i:2688970 original size:123 final size:123
Alignment explanation
Indices: 2688746--2688992 Score: 359
Period size: 123 Copynumber: 2.0 Consensus size: 123
2688736 AAAAGCTGTA
* * *
2688746 GATATTGATGAAAGTGATGAAGATGATGTTAAAGATTTGAAGTCTCCTGTAAAGCCAGGTGGAAA
1 GATATTGACGAAAGTGATGAAGAGGATATTAAAGATTTGAAGTCTCCTGTAAAGCCAGGTGGAAA
* * *
2688811 GGTTCGTGGTGGCAGGGGTGCATCAAAAGGCCCAGCTGGCGGAAGAGGCAGAGGTGGT
66 GGCTCGTGGTGGCAGGGGTGCATCAAAAGGACCAGCTAGCGGAAGAGGCAGAGGTGGT
* * * * *
2688869 GATATTGACGAAAGTGATGAAGAGGATATTAAAGATTTGGAGTCTCCTGTGAAGTCTGGTGGAAG
1 GATATTGACGAAAGTGATGAAGAGGATATTAAAGATTTGAAGTCTCCTGTAAAGCCAGGTGGAAA
* * * *
2688934 GGCTCGTGGTGGTAGGGGTGCATCAACAGGATCAGCTAGTGGAAGAGGCAGAGGTGGT
66 GGCTCGTGGTGGCAGGGGTGCATCAAAAGGACCAGCTAGCGGAAGAGGCAGAGGTGGT
2688992 G
1 G
2688993 GACGGGGTGG
Statistics
Matches: 109, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
123 109 1.00
ACGTcount: A:0.28, C:0.11, G:0.38, T:0.23
Consensus pattern (123 bp):
GATATTGACGAAAGTGATGAAGAGGATATTAAAGATTTGAAGTCTCCTGTAAAGCCAGGTGGAAA
GGCTCGTGGTGGCAGGGGTGCATCAAAAGGACCAGCTAGCGGAAGAGGCAGAGGTGGT
Found at i:2692516 original size:10 final size:10
Alignment explanation
Indices: 2692501--2692525 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2692491 CACCTAAGAA
2692501 AAAAAAAAAG
1 AAAAAAAAAG
2692511 AAAAAAAAAG
1 AAAAAAAAAG
2692521 AAAAA
1 AAAAA
2692526 TAATCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:2706630 original size:15 final size:16
Alignment explanation
Indices: 2706606--2706639 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2706596 ACTAAAGTTC
2706606 AACTTCAAATTTAT-A
1 AACTTCAAATTTATCA
*
2706621 AACTTTAAATTTATCA
1 AACTTCAAATTTATCA
2706637 AAC
1 AAC
2706640 GCTTCATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (16 bp):
AACTTCAAATTTATCA
Found at i:2707668 original size:9 final size:9
Alignment explanation
Indices: 2707654--2707721 Score: 84
Period size: 9 Copynumber: 7.4 Consensus size: 9
2707644 TTTGGTTAAA
2707654 AATTACCCG
1 AATTACCCG
2707663 AATTACCCG
1 AATTACCCG
2707672 AATTACCCG
1 AATTACCCG
*
2707681 AATTAACCG
1 AATTACCCG
2707690 AATTA-CCG
1 AATTACCCG
*
2707698 AAAAATACCCG
1 --AATTACCCG
*
2707709 AATTACCTG
1 AATTACCCG
2707718 AATT
1 AATT
2707722 TTTTTTATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
8 3 0.06
9 42 0.81
10 4 0.08
11 3 0.06
ACGTcount: A:0.40, C:0.26, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:2707880 original size:13 final size:13
Alignment explanation
Indices: 2707862--2707891 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2707852 TTTTAGTTTT
2707862 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
2707875 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
2707888 ATTG
1 ATTG
2707892 AGTTTGGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:2709492 original size:12 final size:12
Alignment explanation
Indices: 2709475--2709501 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2709465 CGATTCATTT
2709475 ATAGTTATTGGG
1 ATAGTTATTGGG
2709487 ATAGTTATTGGG
1 ATAGTTATTGGG
2709499 ATA
1 ATA
2709502 CTATAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.41
Consensus pattern (12 bp):
ATAGTTATTGGG
Found at i:2711158 original size:110 final size:110
Alignment explanation
Indices: 2710950--2711170 Score: 289
Period size: 110 Copynumber: 2.0 Consensus size: 110
2710940 GCCTTTTGAA
* * * * *
2710950 CCACTTTACATACTAGAACAGGGGAAACTCCCTTTAATCTAATGTTTGAAAGAGAGGTCGTGGTC
1 CCACTTCACATACTAGAACAAGGGAAACTCCCTTTAATCTAATATTTGAAACAGAGATCGTGGTC
* * * *
2711015 TCCACTGAAATCATAATCATCTCTTTTAAAACTGCATACTATGAG
66 CCCACTGAAATCATAATCAGCTCCTTTAAAACTGCACACTATGAG
* * * * *
2711060 CCACTTCACATACTGGAACAATGGAAACTCCTTTTGATCTAATATTTGGAACAGAGATCGTGGTC
1 CCACTTCACATACTAGAACAAGGGAAACTCCCTTTAATCTAATATTTGAAACAGAGATCGTGGTC
* * *
2711125 CCCACTGAAATCATAATTAGCTCCTTTAGAACTGCGCACTATGAG
66 CCCACTGAAATCATAATCAGCTCCTTTAAAACTGCACACTATGAG
2711170 C
1 C
2711171 GTGGTCTCAA
Statistics
Matches: 94, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
110 94 1.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.29
Consensus pattern (110 bp):
CCACTTCACATACTAGAACAAGGGAAACTCCCTTTAATCTAATATTTGAAACAGAGATCGTGGTC
CCCACTGAAATCATAATCAGCTCCTTTAAAACTGCACACTATGAG
Found at i:2714655 original size:41 final size:41
Alignment explanation
Indices: 2714604--2714687 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
2714594 CGAACTTGAA
2714604 TAGACAATGTTTTTAGAAGTGTTAAAACTCATTTTAACTTG
1 TAGACAATGTTTTTAGAAGTGTTAAAACTCATTTTAACTTG
2714645 TAGACAATGTTTTTAGAAGTGTTAAAACTCATTTTAACTTG
1 TAGACAATGTTTTTAGAAGTGTTAAAACTCATTTTAACTTG
2714686 TA
1 TA
2714688 TGAATTGTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.42
Consensus pattern (41 bp):
TAGACAATGTTTTTAGAAGTGTTAAAACTCATTTTAACTTG
Found at i:2716869 original size:4 final size:4
Alignment explanation
Indices: 2716860--2716887 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
2716850 ATGGTTCTCC
2716860 GTCT GTCT GTCT GTCT GTCT GTCT GTCT
1 GTCT GTCT GTCT GTCT GTCT GTCT GTCT
2716888 CCTTTCATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.25, T:0.50
Consensus pattern (4 bp):
GTCT
Found at i:2721697 original size:28 final size:28
Alignment explanation
Indices: 2721665--2721721 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
2721655 GTTTTTATTT
*
2721665 TGACAGTTGTACCTGTTTCTGAATAGTG
1 TGACAGTTATACCTGTTTCTGAATAGTG
2721693 TGACAGTTATACCTGTTTCTGAATAGTG
1 TGACAGTTATACCTGTTTCTGAATAGTG
2721721 T
1 T
2721722 TTGATTGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.40
Consensus pattern (28 bp):
TGACAGTTATACCTGTTTCTGAATAGTG
Found at i:2723124 original size:56 final size:55
Alignment explanation
Indices: 2723026--2723166 Score: 203
Period size: 56 Copynumber: 2.5 Consensus size: 55
2723016 CCTTTTATGT
* * * *
2723026 GTATACTCTGTACATGTGTA-TCTATCATAAACTTTTGTCTATGTCAATTGTTGG
1 GTATACTCTGTACATGTGTACTCTATTATAAAATTTTGGCTATGTCAATTGTTGC
*
2723080 GTATACTCTGTATATGTGTACCTCTATTATAAAATTTTGGCTATGTCAATTGTTGC
1 GTATACTCTGTACATGTGTA-CTCTATTATAAAATTTTGGCTATGTCAATTGTTGC
*
2723136 ATATACTCTGTACATGTGTAGCTCTATTATA
1 GTATACTCTGTACATGTGTA-CTCTATTATA
2723167 CTCTGTAGAG
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
54 19 0.25
56 58 0.75
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.44
Consensus pattern (55 bp):
GTATACTCTGTACATGTGTACTCTATTATAAAATTTTGGCTATGTCAATTGTTGC
Found at i:2748369 original size:28 final size:28
Alignment explanation
Indices: 2748332--2748388 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
2748322 TACTAGGTAT
2748332 CCACAAAGTTAAACTAAATGGAAAACCA
1 CCACAAAGTTAAACTAAATGGAAAACCA
2748360 CCACAAAGTTAAACTAAATGGAAAACCA
1 CCACAAAGTTAAACTAAATGGAAAACCA
2748388 C
1 C
2748389 TGAATACAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.53, C:0.23, G:0.11, T:0.14
Consensus pattern (28 bp):
CCACAAAGTTAAACTAAATGGAAAACCA
Found at i:2748624 original size:13 final size:14
Alignment explanation
Indices: 2748604--2748636 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2748594 AACAATTTTG
2748604 AATAAAAAGTTACA
1 AATAAAAAGTTACA
*
2748618 AATAAAAAGTTATA
1 AATAAAAAGTTACA
2748632 AATAA
1 AATAA
2748637 CCAAAAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.24
Consensus pattern (14 bp):
AATAAAAAGTTACA
Found at i:2749437 original size:4 final size:4
Alignment explanation
Indices: 2749428--2749452 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2749418 TATATCTTGC
2749428 AAGA AAGA AAGA AAGA AAGA AAGA A
1 AAGA AAGA AAGA AAGA AAGA AAGA A
2749453 GATCGAACGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:2763178 original size:20 final size:20
Alignment explanation
Indices: 2763147--2763222 Score: 67
Period size: 19 Copynumber: 4.2 Consensus size: 20
2763137 AAAATTACAA
2763147 AAAAATTC-AAAATATTTAT
1 AAAAATTCTAAAATATTTAT
*
2763166 AAAAATTCT-AAA-ATCTAT
1 AAAAATTCTAAAATATTTAT
*
2763184 ---ATTTCTAAAATA-TTAT
1 AAAAATTCTAAAATATTTAT
* *
2763200 AAAAATTCTAAAAAATATAT
1 AAAAATTCTAAAATATTTAT
2763220 AAA
1 AAA
2763223 TGAAGTTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 13
0.70 0.10 0.21
Matches are distributed among these distances:
15 5 0.11
16 6 0.14
17 1 0.02
18 5 0.11
19 21 0.48
20 6 0.14
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAATTCTAAAATATTTAT
Found at i:2766396 original size:40 final size:39
Alignment explanation
Indices: 2766352--2766485 Score: 103
Period size: 40 Copynumber: 3.4 Consensus size: 39
2766342 CCAGTTTAGC
*
2766352 ACCCAGTGCCTCATCGGATAATTCGAAGTAATAAGTTGAT
1 ACCCAGTGCCTCATCGGATAATCCGAAGTAATAA-TTGAT
* * ** *
2766392 ACCCAATGTCTCATCGG-CCATGCCGAAGT-A-AATTGGT
1 ACCCAGTGCCTCATCGGATAAT-CCGAAGTAATAATTGAT
* * * * *
2766429 ACCCAGTACCTCATCGAATTTATCCGAAGTAATAATTTAAC
1 ACCCAGTGCCTCATCGGA-TAATCCGAAGTAATAA-TTGAT
*
2766470 ACCCAGTGTCTCATCG
1 ACCCAGTGCCTCATCG
2766486 ACTCGAAGTC
Statistics
Matches: 71, Mismatches: 17, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
37 17 0.24
38 9 0.13
39 6 0.08
40 23 0.32
41 16 0.23
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (39 bp):
ACCCAGTGCCTCATCGGATAATCCGAAGTAATAATTGAT
Found at i:2766631 original size:11 final size:11
Alignment explanation
Indices: 2766615--2766639 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2766605 TTCAATTCAA
2766615 ATAATCAATAT
1 ATAATCAATAT
2766626 ATAATCAATAT
1 ATAATCAATAT
2766637 ATA
1 ATA
2766640 TACAAATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAATCAATAT
Found at i:2767443 original size:30 final size:31
Alignment explanation
Indices: 2767403--2767481 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 31
2767393 TTTTATTTAT
*
2767403 TATATTTACTTATTATAATATATA-ATATAA
1 TATATATACTTATTATAATATATAGATATAA
2767433 TATATATACTTA--ATAAT-TA-AGATATAA
1 TATATATACTTATTATAATATATAGATATAA
*
2767460 TAT-TATA-GTATTATAATATATA
1 TATATATACTTATTATAATATATA
2767482 TTTTTAACTT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
25 2 0.05
26 5 0.12
27 16 0.38
28 7 0.17
29 1 0.02
30 11 0.26
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (31 bp):
TATATATACTTATTATAATATATAGATATAA
Found at i:2769145 original size:7 final size:7
Alignment explanation
Indices: 2769133--2769174 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
2769123 ATCTCGAACC
2769133 CTAAACT
1 CTAAACT
*
2769140 CTAAACC
1 CTAAACT
2769147 CTAAA-T
1 CTAAACT
2769153 CTAAACT
1 CTAAACT
2769160 CTAAAC-
1 CTAAACT
2769166 CTCAAACT
1 CT-AAACT
2769174 C
1 C
2769175 AGACCTTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
6 7 0.23
7 22 0.73
8 1 0.03
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.24
Consensus pattern (7 bp):
CTAAACT
Found at i:2769157 original size:13 final size:14
Alignment explanation
Indices: 2769129--2769165 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
2769119 CTGAATCTCG
2769129 AACCCTAAACTCTA
1 AACCCTAAACTCTA
2769143 AACCCTAAA-TCTA
1 AACCCTAAACTCTA
*
2769156 AACTCTAAAC
1 AACCCTAAAC
2769166 CTCAAACTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.22
Consensus pattern (14 bp):
AACCCTAAACTCTA
Found at i:2772737 original size:44 final size:44
Alignment explanation
Indices: 2772687--2772782 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 44
2772677 GGTTCGTATA
*
2772687 AAGGGTTCACATACATATTCAC-TAAGGGATTGCCTA-CATGCACT
1 AAGGGTTCACATA-A-ATTCACTTAAGGGATTGCATATCATGCACT
* * * *
2772731 AAGGGTTCGCATAAATTCCCTTAAGGGTTTGCATATCATGCTCT
1 AAGGGTTCACATAAATTCACTTAAGGGATTGCATATCATGCACT
*
2772775 AGGGGTTC
1 AAGGGTTC
2772783 GCAATATAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
42 5 0.11
43 13 0.30
44 26 0.59
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (44 bp):
AAGGGTTCACATAAATTCACTTAAGGGATTGCATATCATGCACT
Found at i:2772842 original size:22 final size:22
Alignment explanation
Indices: 2772817--2772892 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
2772807 GCATAAAAAC
* *
2772817 TCATATAGGTTCGCATAGTACT
1 TCATATAGGTTTGCATAATACT
* *
2772839 TCATCTAGGATTTGCATAATAAT
1 TCATATAGG-TTTGCATAATACT
* *
2772862 TCTTATAGGTTTGTATAATACT
1 TCATATAGGTTTGCATAATACT
*
2772884 TCATCTAGG
1 TCATATAGG
2772893 GTTTACACAT
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
22 26 0.60
23 17 0.40
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (22 bp):
TCATATAGGTTTGCATAATACT
Found at i:2773111 original size:16 final size:16
Alignment explanation
Indices: 2773092--2773127 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2773082 CTAGGGTTTG
2773092 CATACATAAGGGTTCA
1 CATACATAAGGGTTCA
**
2773108 CATACATGGGGGTTCA
1 CATACATAAGGGTTCA
2773124 CATA
1 CATA
2773128 ACAAATTACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (16 bp):
CATACATAAGGGTTCA
Found at i:2775398 original size:8 final size:8
Alignment explanation
Indices: 2775380--2775421 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
2775370 ATTACTCTTC
2775380 TTTTTTCT
1 TTTTTTCT
*
2775388 TTTTCT-T
1 TTTTTTCT
2775395 TTTTTTCT
1 TTTTTTCT
2775403 TTTTTTCT
1 TTTTTTCT
2775411 TTTTTT-T
1 TTTTTTCT
2775418 TTTT
1 TTTT
2775422 GCGTCTGACA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
7 11 0.35
8 20 0.65
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTCT
Found at i:2775401 original size:9 final size:9
Alignment explanation
Indices: 2775387--2775421 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
2775377 TTCTTTTTTC
2775387 TTTTTCTTT
1 TTTTTCTTT
2775396 TTTTTC-TT
1 TTTTTCTTT
2775404 TTTTTCTTT
1 TTTTTCTTT
2775413 TTTTT-TTT
1 TTTTTCTTT
2775421 T
1 T
2775422 GCGTCTGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 12 0.48
9 13 0.52
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:2775421 original size:15 final size:16
Alignment explanation
Indices: 2775380--2775421 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
2775370 ATTACTCTTC
2775380 TTTTTTCTTTTTCT-T
1 TTTTTTCTTTTTCTCT
*
2775395 TTTTTTCTTTTTTTCT
1 TTTTTTCTTTTTCTCT
2775411 TTTTTT-TTTTT
1 TTTTTTCTTTTT
2775422 GCGTCTGACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 18 0.72
16 7 0.28
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (16 bp):
TTTTTTCTTTTTCTCT
Found at i:2783974 original size:9 final size:9
Alignment explanation
Indices: 2783960--2784053 Score: 125
Period size: 9 Copynumber: 10.4 Consensus size: 9
2783950 TTTGGTTAAA
2783960 AATTAACCG
1 AATTAACCG
2783969 AATTAACCG
1 AATTAACCG
*
2783978 AATTACCCG
1 AATTAACCG
2783987 AATTAACCG
1 AATTAACCG
*
2783996 AATTACCCG
1 AATTAACCG
* *
2784005 AATTACCCA
1 AATTAACCG
2784014 AATTAACCG
1 AATTAACCG
*
2784023 AATTACCCG
1 AATTAACCG
*
2784032 AATTAACCA
1 AATTAACCG
*
2784041 AATTAACCA
1 AATTAACCG
2784050 AATT
1 AATT
2784054 GAATCACTAC
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 76 1.00
ACGTcount: A:0.44, C:0.26, G:0.07, T:0.23
Consensus pattern (9 bp):
AATTAACCG
Found at i:2783998 original size:27 final size:27
Alignment explanation
Indices: 2783959--2784053 Score: 154
Period size: 27 Copynumber: 3.5 Consensus size: 27
2783949 TTTTGGTTAA
*
2783959 AAATTAACCGAATTAACCGAATTACCC
1 AAATTAACCGAATTACCCGAATTACCC
*
2783986 GAATTAACCGAATTACCCGAATTACCC
1 AAATTAACCGAATTACCCGAATTACCC
*
2784013 AAATTAACCGAATTACCCGAATTAACC
1 AAATTAACCGAATTACCCGAATTACCC
*
2784040 AAATTAACCAAATT
1 AAATTAACCGAATT
2784054 GAATCACTAC
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 63 1.00
ACGTcount: A:0.44, C:0.25, G:0.07, T:0.23
Consensus pattern (27 bp):
AAATTAACCGAATTACCCGAATTACCC
Found at i:2784205 original size:18 final size:18
Alignment explanation
Indices: 2784166--2784208 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
2784156 TATGATTGGG
**
2784166 TTGGGTTGGGTTGGGTAA
1 TTGGGTTGGGTTGAATAA
*
2784184 TTGGGTTGGGTTGAATAC
1 TTGGGTTGGGTTGAATAA
2784202 TTGGGTT
1 TTGGGTT
2784209 TAGATTGGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.12, C:0.02, G:0.44, T:0.42
Consensus pattern (18 bp):
TTGGGTTGGGTTGAATAA
Found at i:2785578 original size:13 final size:13
Alignment explanation
Indices: 2785562--2785587 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2785552 TTTGCATATT
2785562 GTCTTCAACAGGC
1 GTCTTCAACAGGC
2785575 GTCTTCAACAGGC
1 GTCTTCAACAGGC
2785588 TCGTACTTTG
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:0.23, C:0.31, G:0.23, T:0.23
Consensus pattern (13 bp):
GTCTTCAACAGGC
Found at i:2792627 original size:16 final size:18
Alignment explanation
Indices: 2792592--2792629 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
2792582 GATACTGATA
*
2792592 ATTCATTCCAAGTATTTT
1 ATTCATTCCAACTATTTT
2792610 ATTCA-TCCAACT-TTTT
1 ATTCATTCCAACTATTTT
2792626 ATTC
1 ATTC
2792630 TCTCTCCTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.26, C:0.21, G:0.03, T:0.50
Consensus pattern (18 bp):
ATTCATTCCAACTATTTT
Found at i:2796232 original size:42 final size:42
Alignment explanation
Indices: 2796168--2796264 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
2796158 TATATGAACA
2796168 GCACTAAGTGTGCGAAACTAAAAT-GACGAGGTTGAATAAAGG
1 GCACTAAGTGTGCGAAACTAAAATGGA-GAGGTTGAATAAAGG
* * *
2796210 GCACTAAGTGTGCGAAATTAAAATGGAGATGTTGAATAACGG
1 GCACTAAGTGTGCGAAACTAAAATGGAGAGGTTGAATAAAGG
2796252 GCACTAAGTGTGC
1 GCACTAAGTGTGC
2796265 AATACCGAGA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
42 49 0.96
43 2 0.04
ACGTcount: A:0.37, C:0.12, G:0.29, T:0.22
Consensus pattern (42 bp):
GCACTAAGTGTGCGAAACTAAAATGGAGAGGTTGAATAAAGG
Found at i:2800054 original size:15 final size:15
Alignment explanation
Indices: 2800006--2800048 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
2799996 ATGACCTTGC
*
2800006 GAGGTCGATGAGCAA
1 GAGGTCAATGAGCAA
**
2800021 CCGGTCAATGAGCAA
1 GAGGTCAATGAGCAA
2800036 GAGGTCAATGAGC
1 GAGGTCAATGAGC
2800049 CGGAGGATGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.33, C:0.19, G:0.35, T:0.14
Consensus pattern (15 bp):
GAGGTCAATGAGCAA
Found at i:2801042 original size:3 final size:3
Alignment explanation
Indices: 2801034--2801071 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2801024 ATTATGTAGT
2801034 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2801072 GTTTATTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2818939 original size:20 final size:19
Alignment explanation
Indices: 2818914--2818954 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
2818904 ATAGAAATTA
*
2818914 TTATTCCCAGAAAATATAAT
1 TTATTCCAAGAAAATA-AAT
2818934 TTATTCCAAGAAAATAAAT
1 TTATTCCAAGAAAATAAAT
2818953 TT
1 TT
2818955 CCACTACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (19 bp):
TTATTCCAAGAAAATAAAT
Found at i:2820771 original size:15 final size:13
Alignment explanation
Indices: 2820745--2820788 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 13
2820735 TGTATGCCAT
2820745 ATGATTTATGATAC
1 ATGA-TTATGATAC
*
2820759 ATGTATATATGATTC
1 ATG-AT-TATGATAC
2820774 ATGATTATGATAC
1 ATGATTATGATAC
2820787 AT
1 AT
2820789 TTGTGTTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 9 0.35
14 6 0.23
15 11 0.42
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (13 bp):
ATGATTATGATAC
Found at i:2823648 original size:18 final size:19
Alignment explanation
Indices: 2823617--2823653 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2823607 ATTGTAGTTC
*
2823617 AAAATTACTAAACATTTAA
1 AAAATCACTAAACATTTAA
2823636 AAAATCACT-AACATTTAA
1 AAAATCACTAAACATTTAA
2823654 CTATCTAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAATCACTAAACATTTAA
Found at i:2823755 original size:51 final size:51
Alignment explanation
Indices: 2823679--2823780 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
2823669 AACTAATTAT
2823679 ATTAAAAAAGTCAGAAAATACAACTTAAAGGAAAGCGCGTCCTGCTGGGTG
1 ATTAAAAAAGTCAGAAAATACAACTTAAAGGAAAGCGCGTCCTGCTGGGTG
2823730 ATTAAAAAAGTCAGAAAATACAACTTAAAGGAAAGCGCGTCCTGCTGGGTG
1 ATTAAAAAAGTCAGAAAATACAACTTAAAGGAAAGCGCGTCCTGCTGGGTG
2823781 CGCTTTCCCA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.20
Consensus pattern (51 bp):
ATTAAAAAAGTCAGAAAATACAACTTAAAGGAAAGCGCGTCCTGCTGGGTG
Found at i:2825117 original size:4 final size:4
Alignment explanation
Indices: 2825108--2825139 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
2825098 CAAACTCGTA
2825108 TATG TATG TATG TATG TATG TATG TATG -ATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG T
2825140 GAAGTTGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Done.