Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397258.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4.1, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 11097736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 71999 characters in sequence are not A, C, G, or T
File 5 of 22
Found at i:2391436 original size:21 final size:22
Alignment explanation
Indices: 2391399--2391450 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
2391389 CACCATTGCG
*
2391399 CATTTTTAACACACTTTTCATA
1 CATTTTTAACACACTTTTCACA
*
2391421 CATTTTTAAC-CTCTTTTCACA
1 CATTTTTAACACACTTTTCACA
*
2391442 CTTTTTTAA
1 CATTTTTAA
2391451 TATGTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (22 bp):
CATTTTTAACACACTTTTCACA
Found at i:2392845 original size:51 final size:51
Alignment explanation
Indices: 2392769--2392868 Score: 182
Period size: 51 Copynumber: 2.0 Consensus size: 51
2392759 TTTTCACACA
*
2392769 TTTTTAGTACATTTTTTTATATGTTTTTAGATTTTTTGACACTTAATTAAG
1 TTTTTAGTACATTTTTTTATATGTTTTTAGATTTTTTGACACGTAATTAAG
*
2392820 TTTTTAGTACATTTTTTTGTATGTTTTTAGATTTTTTGACACGTAATTA
1 TTTTTAGTACATTTTTTTATATGTTTTTAGATTTTTTGACACGTAATTA
2392869 GATGCTAATT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.24, C:0.06, G:0.11, T:0.59
Consensus pattern (51 bp):
TTTTTAGTACATTTTTTTATATGTTTTTAGATTTTTTGACACGTAATTAAG
Found at i:2394736 original size:2 final size:2
Alignment explanation
Indices: 2394731--2394761 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2394721 ATGTGTGTTT
2394731 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2394762 GGCAACGAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2404854 original size:17 final size:17
Alignment explanation
Indices: 2404832--2404866 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2404822 TATCCAAATT
2404832 GTATCAACAGCAAAAAG
1 GTATCAACAGCAAAAAG
2404849 GTATCAACAGCAAAAAG
1 GTATCAACAGCAAAAAG
2404866 G
1 G
2404867 CAAATTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.17, G:0.20, T:0.11
Consensus pattern (17 bp):
GTATCAACAGCAAAAAG
Found at i:2412614 original size:15 final size:15
Alignment explanation
Indices: 2412594--2412628 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2412584 AATATTCTAA
*
2412594 AATTATCTTTTTAAC
1 AATTATATTTTTAAC
*
2412609 AATTATATTTTTAAT
1 AATTATATTTTTAAC
2412624 AATTA
1 AATTA
2412629 CATATATGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (15 bp):
AATTATATTTTTAAC
Found at i:2418301 original size:28 final size:27
Alignment explanation
Indices: 2418265--2418317 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
2418255 ATTGATATAA
2418265 TAAAATTAAAATAAAATAAATATTTTT
1 TAAAATTAAAATAAAATAAATATTTTT
*
2418292 TAAAAGTTAAAATAAAATGAATATTT
1 TAAAA-TTAAAATAAAATAAATATTT
2418318 ATTACACTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (27 bp):
TAAAATTAAAATAAAATAAATATTTTT
Found at i:2418531 original size:13 final size:13
Alignment explanation
Indices: 2418513--2418537 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2418503 ATCGACCCAA
2418513 ATATTTTATTTTC
1 ATATTTTATTTTC
2418526 ATATTTTATTTT
1 ATATTTTATTTT
2418538 ATAAGAAATA
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:0.04, G:0.00, T:0.72
Consensus pattern (13 bp):
ATATTTTATTTTC
Found at i:2419715 original size:23 final size:24
Alignment explanation
Indices: 2419667--2419713 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2419657 TTTTTATCTT
*
2419667 TTAATATAATAATAAATTTTTAAA
1 TTAATATAAAAATAAATTTTTAAA
2419691 TTAATA-AAAAATAAATATTTTAA
1 TTAATATAAAAATAAAT-TTTTAA
2419714 TTTTTTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TTAATATAAAAATAAATTTTTAAA
Found at i:2419786 original size:22 final size:21
Alignment explanation
Indices: 2419769--2419812 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
2419759 GTTTATTTTA
2419769 AAAT-TTAATAATTTTTATAT
1 AAATATTAATAATTTTTATAT
2419789 AAATATTAATAATTTTTTATAT
1 AAATATTAATAA-TTTTTATAT
2419811 AA
1 AA
2419813 TTTTAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 4 0.18
21 7 0.32
22 11 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AAATATTAATAATTTTTATAT
Found at i:2419797 original size:21 final size:21
Alignment explanation
Indices: 2419769--2419819 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
2419759 GTTTATTTTA
2419769 AAATTTAATAA-TTTTTATAT
1 AAATTTAATAATTTTTTATAT
2419789 AAATATTAATAATTTTTTATAT
1 AAAT-TTAATAATTTTTTATAT
*
2419811 AATTTTAAT
1 AAATTTAAT
2419820 TAAAATTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 4 0.14
21 12 0.43
22 12 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
AAATTTAATAATTTTTTATAT
Found at i:2419828 original size:22 final size:22
Alignment explanation
Indices: 2419769--2419829 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 22
2419759 GTTTATTTTA
*
2419769 AAAT-TTAAT-AATTTTTATAT
1 AAATATTAATAAAATTTTATAT
**
2419789 AAATATTAATAATTTTTTATAT
1 AAATATTAATAAAATTTTATAT
*
2419811 -AATTTTAATTAAAATTTTA
1 AAATATTAA-TAAAATTTTA
2419830 AAAAATACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 4 0.12
21 12 0.35
22 18 0.53
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AAATATTAATAAAATTTTATAT
Found at i:2420257 original size:14 final size:14
Alignment explanation
Indices: 2420238--2420267 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2420228 TTTATATCTC
2420238 ATAAATATGTAAAA
1 ATAAATATGTAAAA
*
2420252 ATAAATATTTAAAA
1 ATAAATATGTAAAA
2420266 AT
1 AT
2420268 CATGTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (14 bp):
ATAAATATGTAAAA
Found at i:2420267 original size:24 final size:24
Alignment explanation
Indices: 2420240--2420285 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
2420230 TATATCTCAT
2420240 AAAT-ATGTAAAAATAAATATTTAA
1 AAATCATGT-AAAATAAATATTTAA
2420264 AAATCATGTAAAATAAATATTT
1 AAATCATGTAAAATAAATATTT
2420286 TTTAACAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATCATGTAAAATAAATATTTAA
Found at i:2420387 original size:21 final size:21
Alignment explanation
Indices: 2420363--2420402 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2420353 ATACTTATAC
*
2420363 ATTATCTT-TTAACTAAATATG
1 ATTATATTATTAAC-AAATATG
2420384 ATTATATTATTAACAAATA
1 ATTATATTATTAACAAATA
2420403 AATTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (21 bp):
ATTATATTATTAACAAATATG
Found at i:2420722 original size:2 final size:2
Alignment explanation
Indices: 2420715--2420740 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2420705 TTTATGTGTT
2420715 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2420741 GCACGTAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2420850 original size:126 final size:127
Alignment explanation
Indices: 2420622--2420862 Score: 331
Period size: 126 Copynumber: 1.9 Consensus size: 127
2420612 TAATCAAATA
* * * *
2420622 AAGCTAATCACGCAAAATAGATTATCTGATTACTTATGCTACATTTTTTTATAGATTGAACTCAA
1 AAGCAAATCACGCAAAATACATTATATGATTACTTATGCTACAATTTTTTATAGATTGAACTCAA
*
2420687 ATACCCAATAGACCTCAATTTATGTGTTTATATATATATATATATATATATATAGCACGTAG
66 ATACACAATAGACCTCAATTTATGTGTTTATATATATATATATATATATATATAGCACGTAG
* * * * * *
2420749 AAGCAAATCACGTAAATTACATTATATGATTATTTATGTTA-AATTTTTTATAGATTGAATTTAA
1 AAGCAAATCACGCAAAATACATTATATGATTACTTATGCTACAATTTTTTATAGATTGAACTCAA
* * * * *
2420813 GTACATAATAGATCTTAATTTATGTGTTTTTATATATATATATATATATA
66 ATACACAATAGACCTCAATTTATGTGTTTATATATATATATATATATATA
2420863 GCATGCACAG
Statistics
Matches: 98, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
126 64 0.65
127 34 0.35
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.42
Consensus pattern (127 bp):
AAGCAAATCACGCAAAATACATTATATGATTACTTATGCTACAATTTTTTATAGATTGAACTCAA
ATACACAATAGACCTCAATTTATGTGTTTATATATATATATATATATATATATAGCACGTAG
Found at i:2424353 original size:14 final size:15
Alignment explanation
Indices: 2424334--2424362 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2424324 TAATTAATTA
2424334 TTATTT-ATAAAAAT
1 TTATTTAATAAAAAT
2424348 TTATTTAATAAAAAT
1 TTATTTAATAAAAAT
2424363 AAAATATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTATTTAATAAAAAT
Found at i:2424371 original size:28 final size:32
Alignment explanation
Indices: 2424339--2424399 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
2424329 AATTATTATT
2424339 TATAAAAATTT-ATTT-A-AT-AAAAATAAAA
1 TATAAAAATTTGATTTAACATAAAAAATAAAA
*
2424367 TATAATAATTTGATTTAACATAAAAAATAAAA
1 TATAAAAATTTGATTTAACATAAAAAATAAAA
2424399 T
1 T
2424400 TTGAAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 10 0.36
29 4 0.14
30 1 0.04
31 2 0.07
32 11 0.39
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (32 bp):
TATAAAAATTTGATTTAACATAAAAAATAAAA
Found at i:2448307 original size:31 final size:31
Alignment explanation
Indices: 2448272--2448335 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
2448262 AGAAAGAAAG
2448272 AAGAAATTTATCTTAATACAACTATTTACTT
1 AAGAAATTTATCTTAATACAACTATTTACTT
2448303 AAGAAATTTATCTTAATACAACTATTTACTT
1 AAGAAATTTATCTTAATACAACTATTTACTT
2448334 AA
1 AA
2448336 CTTATATAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.41
Consensus pattern (31 bp):
AAGAAATTTATCTTAATACAACTATTTACTT
Found at i:2452874 original size:2 final size:2
Alignment explanation
Indices: 2452869--2452914 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
2452859 AGGAAAAAAC
2452869 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2452911 -G AG A
1 AG AG A
2452915 CATGGACCCC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2458604 original size:2 final size:2
Alignment explanation
Indices: 2458597--2458627 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2458587 ATGGATAAAT
2458597 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2458628 GAAGCGAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2465960 original size:17 final size:18
Alignment explanation
Indices: 2465930--2465968 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
2465920 TAAAAAAATT
*
2465930 AATATTTTATTTTAAAAA
1 AATATTTTAATTTAAAAA
*
2465948 AATA-TTTAATTTAAAAT
1 AATATTTTAATTTAAAAA
2465965 AATA
1 AATA
2465969 ATATAAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATATTTTAATTTAAAAA
Found at i:2483147 original size:10 final size:10
Alignment explanation
Indices: 2483134--2483158 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2483124 GATTTTTTTA
2483134 ATATTGATTC
1 ATATTGATTC
2483144 ATATTGATTC
1 ATATTGATTC
2483154 ATATT
1 ATATT
2483159 ATGTGATAAA
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:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (10 bp):
ATATTGATTC
Found at i:2489436 original size:40 final size:41
Alignment explanation
Indices: 2489375--2489454 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 41
2489365 ATTTGTCATC
* *
2489375 ATCATCTCTTTTTAACTGTCACTTGGGGAGCTGCCCCTGAT
1 ATCATCACTTTTTAACTGTCACTAGGGGAGCTGCCCCTGAT
*
2489416 ATCATCAC-TTTTAATTGTCACTAGGGGAGCTGCCCCTGA
1 ATCATCACTTTTTAACTGTCACTAGGGGAGCTGCCCCTGA
2489455 CAAAAGAACC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
40 29 0.81
41 7 0.19
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.34
Consensus pattern (41 bp):
ATCATCACTTTTTAACTGTCACTAGGGGAGCTGCCCCTGAT
Found at i:2492768 original size:29 final size:29
Alignment explanation
Indices: 2492711--2492781 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
2492701 TTAAAAAATC
*
2492711 AATTAAATTGTT-T-TTTTTATTATATTT
1 AATTAAATTTTTATATTTTTATTATATTT
2492738 AATTAAATTTTTATATTTTTATT-TATATT
1 AATTAAATTTTTATATTTTTATTATAT-TT
* *
2492767 AAATAAACTTTTATA
1 AATTAAATTTTTATA
2492782 ACTAGTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 11 0.29
28 4 0.11
29 23 0.61
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (29 bp):
AATTAAATTTTTATATTTTTATTATATTT
Found at i:2498157 original size:32 final size:33
Alignment explanation
Indices: 2498100--2498161 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
2498090 AGGAAGACAG
* *
2498100 TAAACATCAGATAGTTTTAAGGCAATGTTGTCA
1 TAAACATCAGATAGGTTTAACGCAATGTTGTCA
2498133 TAAACATCAGAT-GGTTTAACGCAATGTTG
1 TAAACATCAGATAGGTTTAACGCAATGTTG
2498162 CCATGACTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 15 0.56
33 12 0.44
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.32
Consensus pattern (33 bp):
TAAACATCAGATAGGTTTAACGCAATGTTGTCA
Found at i:2499530 original size:31 final size:30
Alignment explanation
Indices: 2499428--2499522 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
2499418 TACAAATTTT
* *
2499428 AAATAAATTTTTATATTTTTA--TTATATT
1 AAATAAATTTTTATATTTTTATTTTAAATA
* * *
2499456 GAATCAAGA-TTTTGTATTTTTATTTTTAATA
1 AAAT-AA-ATTTTTATATTTTTATTTTAAATA
2499487 AAATAAATTTTTATATTTTTATTTTAAATTA
1 AAATAAATTTTTATATTTTTATTTTAAA-TA
2499518 AAATA
1 AAATA
2499523 TTTTTTTAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
28 3 0.06
29 15 0.28
30 21 0.40
31 14 0.26
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (30 bp):
AAATAAATTTTTATATTTTTATTTTAAATA
Found at i:2499642 original size:33 final size:33
Alignment explanation
Indices: 2499600--2499673 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 33
2499590 ATGTAATGTA
* *
2499600 ATAACATATCATAATTGATAA-AAAAGTAAGATG
1 ATAATATATCATAATTAATAACAAAA-TAAGATG
* *
2499633 ATAATATATCATAATTAATAACAAAATGATATG
1 ATAATATATCATAATTAATAACAAAATAAGATG
2499666 ATAATATA
1 ATAATATA
2499674 ATCGTACGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
33 32 0.89
34 4 0.11
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.31
Consensus pattern (33 bp):
ATAATATATCATAATTAATAACAAAATAAGATG
Found at i:2500298 original size:3 final size:3
Alignment explanation
Indices: 2500290--2500319 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2500280 ATAGCCTTAT
2500290 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2500320 TACAAAGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2508765 original size:19 final size:19
Alignment explanation
Indices: 2508738--2508774 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2508728 AATTCAATTC
*
2508738 TATTGTTTTATTTTAAAAT
1 TATTGTTTTAATTTAAAAT
*
2508757 TATTTTTTTAATTTAAAA
1 TATTGTTTTAATTTAAAA
2508775 ATTTGAACTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
TATTGTTTTAATTTAAAAT
Found at i:2508775 original size:20 final size:19
Alignment explanation
Indices: 2508738--2508777 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
2508728 AATTCAATTC
*
2508738 TATTGTTTTATTTTAAAAT
1 TATTGTTTTATTTAAAAAT
*
2508757 TATTTTTTTAATTTAAAAAT
1 TATTGTTTT-ATTTAAAAAT
2508777 T
1 T
2508778 TGAACTCTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
TATTGTTTTATTTAAAAAT
Found at i:2508844 original size:16 final size:17
Alignment explanation
Indices: 2508813--2508846 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2508803 CCGAATCATT
2508813 TAATGATAACCCAAAAA
1 TAATGATAACCCAAAAA
2508830 TAATGATAA-CCAAAAA
1 TAATGATAACCCAAAAA
2508846 T
1 T
2508847 CGAAAACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.59, C:0.15, G:0.06, T:0.21
Consensus pattern (17 bp):
TAATGATAACCCAAAAA
Found at i:2509572 original size:17 final size:18
Alignment explanation
Indices: 2509529--2509572 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2509519 TTTGTATTTA
*
2509529 GCATGAAAAATAAAATAT
1 GCATAAAAAATAAAATAT
** *
2509547 ATATAAAAAATAAATTAT
1 GCATAAAAAATAAAATAT
2509565 GCATAAAA
1 GCATAAAA
2509573 TTATAAATAA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.64, C:0.05, G:0.07, T:0.25
Consensus pattern (18 bp):
GCATAAAAAATAAAATAT
Found at i:2509573 original size:12 final size:12
Alignment explanation
Indices: 2509558--2509593 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2509548 TATAAAAAAT
*
2509558 AAATTATGCATA
1 AAATTATGAATA
*
2509570 AAATTATAAATA
1 AAATTATGAATA
2509582 AAATTATGAATA
1 AAATTATGAATA
2509594 GATAACTCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (12 bp):
AAATTATGAATA
Found at i:2515760 original size:76 final size:82
Alignment explanation
Indices: 2515629--2515786 Score: 247
Period size: 76 Copynumber: 2.0 Consensus size: 82
2515619 GTATAATTTC
*
2515629 TCTTTTAACTAGACCTTCTGTATCTTTATATTTTCATACTCTAATTCATCTTTGCATCAC-TTTT
1 TCTTTTAACTAGACC-TCTGTATCTTTACATTTTCATACTCTAATTCATCTTTGCATCACTTTTT
2515693 TT-TTTTTCATGTGGATT
65 TTATTTTTCATGTGGATT
2515710 TCTTTTAACTAGA-C-CT-TATCTTTACA-TTTCATACTCTAATTCATCTTTGCATCACTTTTTT
1 TCTTTTAACTAGACCTCTGTATCTTTACATTTTCATACTCTAATTCATCTTTGCATCACTTTTTT
*
2515771 TATTTTTTATGTGGAT
66 TATTTTTCATGTGGAT
2515787 AGTCTTTCTG
Statistics
Matches: 73, Mismatches: 2, Indels: 7
0.89 0.02 0.09
Matches are distributed among these distances:
76 29 0.40
77 15 0.21
78 15 0.21
80 1 0.01
81 13 0.18
ACGTcount: A:0.21, C:0.18, G:0.07, T:0.54
Consensus pattern (82 bp):
TCTTTTAACTAGACCTCTGTATCTTTACATTTTCATACTCTAATTCATCTTTGCATCACTTTTTT
TATTTTTCATGTGGATT
Found at i:2529838 original size:16 final size:17
Alignment explanation
Indices: 2529804--2529841 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
2529794 TCAAGAAAAT
2529804 TTTTTAATCAAAAAGTA
1 TTTTTAATCAAAAAGTA
* *
2529821 TTTTTAAT-ATAAATTA
1 TTTTTAATCAAAAAGTA
2529837 TTTTT
1 TTTTT
2529842 TATTGTTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTTTAATCAAAAAGTA
Found at i:2529842 original size:17 final size:18
Alignment explanation
Indices: 2529802--2529843 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
2529792 TTTCAAGAAA
2529802 ATTTTTTAATCAAAAAGT
1 ATTTTTTAATCAAAAAGT
* *
2529820 A-TTTTTAAT-ATAAATT
1 ATTTTTTAATCAAAAAGT
2529836 ATTTTTTA
1 ATTTTTTA
2529844 TTGTTTGGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 6 0.29
17 14 0.67
18 1 0.05
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
ATTTTTTAATCAAAAAGT
Found at i:2531987 original size:30 final size:28
Alignment explanation
Indices: 2531906--2531991 Score: 75
Period size: 30 Copynumber: 2.9 Consensus size: 28
2531896 TCAAAAAAAT
* * *
2531906 TCAAATAAATCTTTATTCTTTTATTTTGT
1 TCAAATAAATCTTAAAT-TTTTATTTTGG
* *
2531935 TC-AATCAAATTCTTATACTTTTATTTTGAG
1 TCAAAT-AAA-TCTTAAATTTTTATTTTG-G
2531965 TCAAATAAACTCTTAAATTTTTATTTT
1 TCAAATAAA-TCTTAAATTTTTATTTT
2531992 AAGTTGAATA
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
28 3 0.07
29 15 0.33
30 24 0.53
31 3 0.07
ACGTcount: A:0.31, C:0.12, G:0.03, T:0.53
Consensus pattern (28 bp):
TCAAATAAATCTTAAATTTTTATTTTGG
Found at i:2532664 original size:2 final size:2
Alignment explanation
Indices: 2532657--2532683 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2532647 AATGATAATT
2532657 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2532684 CTTTATGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2534495 original size:13 final size:13
Alignment explanation
Indices: 2534478--2534516 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
2534468 TTTATTATAT
2534478 TTTTAAATTATCA
1 TTTTAAATTATCA
* *
2534491 TTTTATATTATGA
1 TTTTAAATTATCA
*
2534504 TTATAAATTATCA
1 TTTTAAATTATCA
2534517 AAATATATGT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (13 bp):
TTTTAAATTATCA
Found at i:2536977 original size:26 final size:27
Alignment explanation
Indices: 2536948--2537006 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
2536938 TTATTACACT
2536948 ATTTTTAATTTAAAATTA-ATTAATTA
1 ATTTTTAATTTAAAATTATATTAATTA
* * * *
2536974 ATTTATATTTTAAATTTATATTTATTA
1 ATTTTTAATTTAAAATTATATTAATTA
*
2537001 TTTTTT
1 ATTTTT
2537007 TAGTAAAATT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (27 bp):
ATTTTTAATTTAAAATTATATTAATTA
Found at i:2544605 original size:5 final size:5
Alignment explanation
Indices: 2544595--2544619 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2544585 TCGTCTATGA
2544595 TTTGG TTTGG TTTGG TTTGG TTTGG
1 TTTGG TTTGG TTTGG TTTGG TTTGG
2544620 ACTTTTGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.40, T:0.60
Consensus pattern (5 bp):
TTTGG
Found at i:2546021 original size:23 final size:24
Alignment explanation
Indices: 2545978--2546028 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
2545968 TTTAAAAAAC
*
2545978 TTTAAATAAATATTTTTTAATTTA
1 TTTAAATAAATATTTTATAATTTA
* *
2546002 TTTAATTAAAT-TTTTATAATTTT
1 TTTAAATAAATATTTTATAATTTA
2546025 TTTA
1 TTTA
2546029 TTTTAAATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTAAATAAATATTTTATAATTTA
Found at i:2550481 original size:20 final size:19
Alignment explanation
Indices: 2550452--2550491 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
2550442 GCTTTTGGTT
*
2550452 TCTTCTTTTTCTTTTCTTCC
1 TCTTCCTTTTCTTTT-TTCC
*
2550472 TCTTCCTTTTGTTTTTTCC
1 TCTTCCTTTTCTTTTTTCC
2550491 T
1 T
2550492 TGGATTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.00, C:0.28, G:0.03, T:0.70
Consensus pattern (19 bp):
TCTTCCTTTTCTTTTTTCC
Found at i:2550987 original size:20 final size:18
Alignment explanation
Indices: 2550949--2550990 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 18
2550939 TCATTATAAG
2550949 TTATTATTAATTAAAATA
1 TTATTATTAATTAAAATA
*
2550967 TTATGTATTATATTAATATA
1 TTAT-TATTA-ATTAAAATA
2550987 TTAT
1 TTAT
2550991 AATAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.19
19 5 0.24
20 12 0.57
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
TTATTATTAATTAAAATA
Found at i:2551091 original size:17 final size:19
Alignment explanation
Indices: 2551055--2551092 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2551045 CATTCACCTC
*
2551055 ATTTTTTTAATATATAAAA
1 ATTTATTTAATATATAAAA
2551074 ATTTATTTAAT-T-TAAAA
1 ATTTATTTAATATATAAAA
2551091 AT
1 AT
2551093 AAAAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 1 0.06
19 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTATTTAATATATAAAA
Found at i:2555771 original size:16 final size:16
Alignment explanation
Indices: 2555750--2555791 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
2555740 AATATTTTAA
*
2555750 TTAAAATATTATATTT
1 TTAAAATATTATATCT
*
2555766 TTAAAA-ATTTTATCT
1 TTAAAATATTATATCT
*
2555781 TAAAAATATTA
1 TTAAAATATTA
2555792 CTTTTTTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAAATATTATATCT
Found at i:2571192 original size:13 final size:12
Alignment explanation
Indices: 2571173--2571218 Score: 56
Period size: 13 Copynumber: 3.6 Consensus size: 12
2571163 GTTATCATGA
2571173 ATAATATGATAT
1 ATAATATGATAT
2571185 ATTAATATGATAT
1 A-TAATATGATAT
*
2571198 GATAATATAATCAT
1 -ATAATATGAT-AT
2571212 ATAATAT
1 ATAATAT
2571219 ATTAATGTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 1 0.03
13 26 0.87
14 3 0.10
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (12 bp):
ATAATATGATAT
Found at i:2571199 original size:18 final size:17
Alignment explanation
Indices: 2571176--2571242 Score: 59
Period size: 18 Copynumber: 3.8 Consensus size: 17
2571166 ATCATGAATA
2571176 ATATGATATATTAATATG
1 ATAT-ATATATTAATATG
2571194 ATATGATA-ATATAATCAT-
1 ATAT-ATATAT-TAAT-ATG
*
2571212 ATA-ATATATTAATGTG
1 ATATATATATTAATATG
2571228 ATATATATAATTAAT
1 ATATATAT-ATTAAT
2571243 GATATTTTGA
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
15 1 0.02
16 10 0.24
17 8 0.19
18 21 0.50
19 2 0.05
ACGTcount: A:0.48, C:0.01, G:0.07, T:0.43
Consensus pattern (17 bp):
ATATATATATTAATATG
Found at i:2573296 original size:13 final size:13
Alignment explanation
Indices: 2573262--2573325 Score: 50
Period size: 12 Copynumber: 5.3 Consensus size: 13
2573252 TGATGTAGTC
2573262 AAAT-TTATTAAA
1 AAATATTATTAAA
2573274 AAA-A-TA-TAAA
1 AAATATTATTAAA
2573284 AAATATTATT-AA
1 AAATATTATTAAA
*
2573296 AAATATTTTTAACA
1 AAATATTATTAA-A
* *
2573310 ATACATT-TTAAA
1 AAATATTATTAAA
2573322 AAAT
1 AAAT
2573326 GTGCATTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
10 7 0.17
11 3 0.07
12 19 0.46
13 6 0.15
14 6 0.15
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATATTATTAAA
Found at i:2573297 original size:12 final size:12
Alignment explanation
Indices: 2573262--2573312 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
2573252 TGATGTAGTC
2573262 AAAT-TTATTAA
1 AAATATTATTAA
* *
2573273 AAA-AATATAAA
1 AAATATTATTAA
2573284 AAATATTATTAA
1 AAATATTATTAA
*
2573296 AAATATTTTTAA
1 AAATATTATTAA
*
2573308 CAATA
1 AAATA
2573313 CATTTTAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
11 11 0.34
12 21 0.66
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (12 bp):
AAATATTATTAA
Found at i:2581614 original size:18 final size:18
Alignment explanation
Indices: 2581575--2581632 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
2581565 TTATCAATAT
*
2581575 ATATCATATGACGTTGA-C
1 ATATCATATGAC-ATGATC
*
2581593 ATATCATAAT-ACATGATG
1 ATATCAT-ATGACATGATC
*
2581611 ATATGATATGACATGATC
1 ATATCATATGACATGATC
2581629 ATAT
1 ATAT
2581633 GATGTGTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 5 0.15
18 26 0.79
19 2 0.06
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (18 bp):
ATATCATATGACATGATC
Found at i:2590728 original size:6 final size:6
Alignment explanation
Indices: 2590717--2590748 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
2590707 AAACAACAAT
*
2590717 CATCAG CATCAG CATCAG TATCAG CATCAG CA
1 CATCAG CATCAG CATCAG CATCAG CATCAG CA
2590749 ATTAAGCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.34, C:0.31, G:0.16, T:0.19
Consensus pattern (6 bp):
CATCAG
Found at i:2592644 original size:30 final size:30
Alignment explanation
Indices: 2592610--2592668 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
2592600 TCATAAGAGT
*
2592610 TTATTCAATTTAAAATAAAAATATAAAAAC
1 TTATTCAATTCAAAATAAAAATATAAAAAC
*
2592640 TTATTTAATTCAAAATAAAAATATAAAAA
1 TTATTCAATTCAAAATAAAAATATAAAAA
2592669 TTTTTTTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (30 bp):
TTATTCAATTCAAAATAAAAATATAAAAAC
Found at i:2613380 original size:48 final size:49
Alignment explanation
Indices: 2613328--2613437 Score: 129
Period size: 50 Copynumber: 2.2 Consensus size: 49
2613318 AAAAATTTAT
*
2613328 TATTTTAAATATATAAATTAA-A-TTAAAATTTTAATTATAAATT-TGTAA
1 TATTTTAAATA-ATAAAATAAGAGTTAAAATTTTAATTATAAATTAT-TAA
**
2613376 TATTTTAAA-AATAAAATAATGATGTTAATGTTTTAATTATAAATTATTAA
1 TATTTTAAATAATAAAATAA-GA-GTTAAAATTTTAATTATAAATTATTAA
2613426 TATTTTAAATAA
1 TATTTTAAATAA
2613438 AATATAAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
46 8 0.15
47 1 0.02
48 10 0.19
50 31 0.58
51 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (49 bp):
TATTTTAAATAATAAAATAAGAGTTAAAATTTTAATTATAAATTATTAA
Found at i:2613383 original size:22 final size:23
Alignment explanation
Indices: 2613328--2613433 Score: 74
Period size: 22 Copynumber: 4.3 Consensus size: 23
2613318 AAAAATTTAT
2613328 TATTTTAAATATATAAATTAAAT-TAA
1 TATTTT-AAT-TATAAATT--ATGTAA
*
2613354 AATTTTAATTATAAATT-TGTAA
1 TATTTTAATTATAAATTATGTAA
**
2613376 TATTTTAAAAATAAAATAATGATGTTAA
1 TATTTTAATTAT-AAAT--T-ATG-TAA
*
2613404 TGTTTTAATTATAAATTAT-TAA
1 TATTTTAATTATAAATTATGTAA
2613426 TATTTTAA
1 TATTTTAA
2613434 ATAAAATATA
Statistics
Matches: 65, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
21 1 0.02
22 22 0.34
23 4 0.06
24 10 0.15
25 5 0.08
26 5 0.08
27 6 0.09
28 12 0.18
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (23 bp):
TATTTTAATTATAAATTATGTAA
Found at i:2613547 original size:21 final size:22
Alignment explanation
Indices: 2613512--2613554 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2613502 AAATAAATTA
*
2613512 TTAAAATAATAAATATTTTAAT
1 TTAAAATAATAAATATTATAAT
*
2613534 TTAAAA-ATTAAATATTATAAT
1 TTAAAATAATAAATATTATAAT
2613555 AATGAGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TTAAAATAATAAATATTATAAT
Found at i:2620724 original size:47 final size:49
Alignment explanation
Indices: 2620658--2620802 Score: 154
Period size: 50 Copynumber: 3.0 Consensus size: 49
2620648 TTATATGGCT
* * *
2620658 CAAAATTTTTAAAAATTTTTATTATCTATATA-TATTAATGG-CCCTTC
1 CAAAATTTTTAGAATTTTTTATTATCTATATATTTTTAATGGTCCCTTC
* *
2620705 CAAAATTTTTAGAATTTTTTATTTAT-TATATATTTTTTAATGGTCTCTTT
1 CAAAATTTTTAGAATTTTTTA-TTATCTATATA-TTTTTAATGGTCCCTTC
* * *
2620755 CAAAATTTATGGAATTATTTATT-TACTATATATTTTTAATGGTTCCCT
1 CAAAATTTTTAGAATTTTTTATTAT-CTATATATTTTTAATGG-TCCCT
2620803 CAAAATAAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
47 25 0.30
48 5 0.06
49 20 0.24
50 32 0.39
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.52
Consensus pattern (49 bp):
CAAAATTTTTAGAATTTTTTATTATCTATATATTTTTAATGGTCCCTTC
Found at i:2621127 original size:16 final size:17
Alignment explanation
Indices: 2621096--2621129 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2621086 TATTTGTTTT
2621096 CTATTCATATTATTTAA
1 CTATTCATATTATTTAA
*
2621113 CTATTTATA-TATTTAA
1 CTATTCATATTATTTAA
2621129 C
1 C
2621130 CATTGTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (17 bp):
CTATTCATATTATTTAA
Found at i:2621194 original size:7 final size:7
Alignment explanation
Indices: 2621162--2621208 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
2621152 CGTATTTAAC
2621162 TATTTT-
1 TATTTTA
2621168 TATTTTA
1 TATTTTA
*
2621175 TATATTA
1 TATTTTA
2621182 TAATTTTA
1 T-ATTTTA
*
2621190 TATTTAA
1 TATTTTA
2621197 TATTTTA
1 TATTTTA
*
2621204 AATTT
1 TATTT
2621209 AAATAAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
6 6 0.18
7 22 0.65
8 6 0.18
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (7 bp):
TATTTTA
Found at i:2621209 original size:20 final size:20
Alignment explanation
Indices: 2621166--2621209 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2621156 TTTAACTATT
*
2621166 TTTATTTTATATATTATAAT
1 TTTATTTTATATATTATAAA
*
2621186 TTTATATTTA-ATATTTTAAA
1 TTTAT-TTTATATATTATAAA
2621206 TTTA
1 TTTA
2621210 AATAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTATTTTATATATTATAAA
Found at i:2622156 original size:17 final size:16
Alignment explanation
Indices: 2622131--2622164 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2622121 ATCCAAATTT
2622131 TTATAATTAATAACGAA
1 TTATAATTAATAA-GAA
*
2622148 TTATTATTAATAAGAA
1 TTATAATTAATAAGAA
2622164 T
1 T
2622165 GACACTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (16 bp):
TTATAATTAATAAGAA
Found at i:2622518 original size:19 final size:17
Alignment explanation
Indices: 2622485--2622519 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
2622475 TCTATCTCCC
2622485 TTTTTCTTTGTCTTTTT
1 TTTTTCTTTGTCTTTTT
2622502 TTTTTGCTTTAGTCTTTT
1 TTTTT-CTTT-GTCTTTT
2622520 CTTTGTAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 4 0.25
19 7 0.44
ACGTcount: A:0.03, C:0.11, G:0.09, T:0.77
Consensus pattern (17 bp):
TTTTTCTTTGTCTTTTT
Found at i:2622756 original size:7 final size:7
Alignment explanation
Indices: 2622724--2622770 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
2622714 CGTATTTAAT
2622724 TATTTT-
1 TATTTTA
2622730 TATTTTA
1 TATTTTA
*
2622737 TATATTA
1 TATTTTA
2622744 TAATTTTA
1 T-ATTTTA
*
2622752 TATTTAA
1 TATTTTA
2622759 TATTTTA
1 TATTTTA
*
2622766 AATTT
1 TATTT
2622771 AAAATAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
6 6 0.18
7 22 0.65
8 6 0.18
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (7 bp):
TATTTTA
Found at i:2622771 original size:20 final size:20
Alignment explanation
Indices: 2622728--2622771 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2622718 TTTAATTATT
*
2622728 TTTATTTTATATATTATAAT
1 TTTATTTTATATATTATAAA
*
2622748 TTTATATTTA-ATATTTTAAA
1 TTTAT-TTTATATATTATAAA
2622768 TTTA
1 TTTA
2622772 AAATAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTATTTTATATATTATAAA
Found at i:2630252 original size:27 final size:27
Alignment explanation
Indices: 2630212--2630265 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
2630202 TGATACAATA
* *
2630212 AAGGTAACATGTAACTGAGCAACTGTT
1 AAGGTAACACGTAACTGAGCAAATGTT
2630239 AAGGTAACACGTAACTGAGCAAATGTT
1 AAGGTAACACGTAACTGAGCAAATGTT
2630266 TTTCTTTCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (27 bp):
AAGGTAACACGTAACTGAGCAAATGTT
Found at i:2647972 original size:24 final size:25
Alignment explanation
Indices: 2647930--2647978 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
2647920 ATTTGTAATA
2647930 TTTAATTTTAAATTTTTAAT-AGAT
1 TTTAATTTTAAATTTTTAATGAGAT
*
2647954 TTTAATTTT-ATTTTATTAATGAGAT
1 TTTAATTTTAAATTT-TTAATGAGAT
2647979 AGCAAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 4 0.18
24 14 0.64
25 4 0.18
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (25 bp):
TTTAATTTTAAATTTTTAATGAGAT
Found at i:2655960 original size:18 final size:18
Alignment explanation
Indices: 2655937--2655971 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2655927 CCGTAGCCAC
2655937 CTTCAC-CAATCACATTCT
1 CTTCACACAATC-CATTCT
2655955 CTTCACACAATCCATTC
1 CTTCACACAATCCATTC
2655972 GTAGCTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.29, C:0.40, G:0.00, T:0.31
Consensus pattern (18 bp):
CTTCACACAATCCATTCT
Found at i:2663669 original size:2 final size:2
Alignment explanation
Indices: 2663662--2663692 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2663652 GAATGCTGGG
2663662 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2663693 GGAGGGAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2675394 original size:2 final size:2
Alignment explanation
Indices: 2675387--2675412 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2675377 TTCCTCTGCT
2675387 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2675413 CATACGTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2676322 original size:7 final size:7
Alignment explanation
Indices: 2676312--2676336 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2676302 TAAAAAAAAA
2676312 AAAGAAG
1 AAAGAAG
2676319 AAAGAAG
1 AAAGAAG
2676326 AAAGAAG
1 AAAGAAG
2676333 AAAG
1 AAAG
2676337 GAAAAAACGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (7 bp):
AAAGAAG
Found at i:2690154 original size:6 final size:6
Alignment explanation
Indices: 2690145--2690181 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
2690135 GAGAAAGTCC
2690145 AAAAA- AAAAA- AAGAAAG AAAAAG AAAAAG AAAAAG AA
1 AAAAAG AAAAAG AA-AAAG AAAAAG AAAAAG AAAAAG AA
2690182 TGTTCTTGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 7 0.23
6 21 0.70
7 2 0.07
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:2690165 original size:16 final size:16
Alignment explanation
Indices: 2690146--2690176 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2690136 AGAAAGTCCA
2690146 AAAAAAAAAAAGAAAG
1 AAAAAAAAAAAGAAAG
*
2690162 AAAAAGAAAAAGAAA
1 AAAAAAAAAAAGAAA
2690177 AAGAATGTTC
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:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAGAAAG
Found at i:2698534 original size:16 final size:17
Alignment explanation
Indices: 2698509--2698542 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2698499 TCTTTTTTTA
*
2698509 TTTTTTTTG-TGTTTGC
1 TTTTTCTTGTTGTTTGC
2698525 TTTTTCTTGTTGTTTGC
1 TTTTTCTTGTTGTTTGC
2698542 T
1 T
2698543 CCCTAGAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.00, C:0.09, G:0.18, T:0.74
Consensus pattern (17 bp):
TTTTTCTTGTTGTTTGC
Found at i:2712156 original size:26 final size:24
Alignment explanation
Indices: 2712098--2712160 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 24
2712088 ATTAAAAAAA
*
2712098 TTTAAA-TAAATTTTTATTTTTAT
1 TTTAAATTAAATTTTTATTTATAT
*
2712121 TAATATAATTAAATTTAATTATTTATAT
1 T-TTA-AATTAAATTT--TTATTTATAT
2712149 TTTAAATTAAAT
1 TTTAAATTAAAT
2712161 AAATATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
23 1 0.03
24 2 0.06
25 2 0.06
26 15 0.47
27 2 0.06
28 10 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTAAATTAAATTTTTATTTATAT
Found at i:2714568 original size:15 final size:15
Alignment explanation
Indices: 2714548--2714669 Score: 75
Period size: 15 Copynumber: 7.7 Consensus size: 15
2714538 AGAGCCAGAG
*
2714548 AAGAAGGAGGAGCCA
1 AAGAAGGAAGAGCCA
2714563 AAGAAGGAAGAGCCCA
1 AAGAAGGAAGAG-CCA
* *
2714579 AGAAAGAGGAGGAAG-CA
1 A-AGA-AGGAAG-AGCCA
* * *
2714596 AAGAAAGAAGAACCC
1 AAGAAGGAAGAGCCA
* *
2714611 AAGAAAGAAGAGGAGCCG
1 AAG-AAG--GAAGAGCCA
* *
2714629 AAGAAAGAAGAGCCT
1 AAGAAGGAAGAGCCA
2714644 AAGAAGGAAGAGCCA
1 AAGAAGGAAGAGCCA
*
2714659 AAGAAAGAAGA
1 AAGAAGGAAGA
2714670 ACCCAAGAAA
Statistics
Matches: 81, Mismatches: 18, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
14 1 0.01
15 49 0.60
16 8 0.10
17 7 0.09
18 14 0.17
19 2 0.02
ACGTcount: A:0.54, C:0.12, G:0.33, T:0.01
Consensus pattern (15 bp):
AAGAAGGAAGAGCCA
Found at i:2714640 original size:18 final size:18
Alignment explanation
Indices: 2714562--2714640 Score: 76
Period size: 18 Copynumber: 4.5 Consensus size: 18
2714552 AGGAGGAGCC
*
2714562 AAAGAAGGAAGAGCCCAAG
1 AAAGAA-GAGGAGCCCAAG
* *
2714581 AAAGAGGAGGAAG-CAAAG
1 AAAGAAGAGG-AGCCCAAG
2714599 AAAGAAGA--A-CCCAAG
1 AAAGAAGAGGAGCCCAAG
*
2714614 AAAGAAGAGGAGCCGAAG
1 AAAGAAGAGGAGCCCAAG
2714632 AAAGAAGAG
1 AAAGAAGAG
2714641 CCTAAGAAGG
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
15 13 0.27
17 1 0.02
18 28 0.57
19 7 0.14
ACGTcount: A:0.56, C:0.11, G:0.33, T:0.00
Consensus pattern (18 bp):
AAAGAAGAGGAGCCCAAG
Found at i:2714672 original size:63 final size:66
Alignment explanation
Indices: 2714548--2714681 Score: 186
Period size: 63 Copynumber: 2.1 Consensus size: 66
2714538 AGAGCCAGAG
* *
2714548 AAGAAGGAGGAGCCAAAGAAGGAAGAGCCCAAGAAAGAGGAGGAAGCAAAGAAAGAAGAACCCAA
1 AAGAAGGAGGAGCCAAAGAAAGAAGAGCCCAAG-AAGAGGAAGAAGCAAAGAAAGAAGAACCCAA
2714613 GA
65 GA
* *
2714615 AAGAA-GAGGAGCCGAAGAAAGAAGAGCCTAAG-A-AGGAAG-AGCCAAAGAAAGAAGAACCCAA
1 AAGAAGGAGGAGCCAAAGAAAGAAGAGCCCAAGAAGAGGAAGAAG-CAAAGAAAGAAGAACCCAA
2714676 GA
65 GA
2714678 AAGA
1 AAGA
2714682 GGAAGAGAAG
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
62 2 0.03
63 30 0.48
64 1 0.02
66 24 0.39
67 5 0.08
ACGTcount: A:0.54, C:0.13, G:0.31, T:0.01
Consensus pattern (66 bp):
AAGAAGGAGGAGCCAAAGAAAGAAGAGCCCAAGAAGAGGAAGAAGCAAAGAAAGAAGAACCCAAG
A
Found at i:2714677 original size:15 final size:15
Alignment explanation
Indices: 2714563--2714681 Score: 94
Period size: 15 Copynumber: 7.5 Consensus size: 15
2714553 GGAGGAGCCA
* *
2714563 AAGAAGGAAGAGCCC
1 AAGAAAGAAGAACCC
* *
2714578 AAGAAAGAGGAGGAAGCA
1 AAGAAAGA--A-GAACCC
2714596 AAGAAAGAAGAACCC
1 AAGAAAGAAGAACCC
*
2714611 AAGAAAGAAGAGGAGCCG
1 AAGAAAGAAGA--A-CCC
* *
2714629 AAGAAAGAAGAGCCT
1 AAGAAAGAAGAACCC
* * *
2714644 AAGAAGGAAGAGCCA
1 AAGAAAGAAGAACCC
2714659 AAGAAAGAAGAACCC
1 AAGAAAGAAGAACCC
2714674 AAGAAAGA
1 AAGAAAGA
2714682 GGAAGAGAAG
Statistics
Matches: 84, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
15 57 0.68
16 1 0.01
17 2 0.02
18 24 0.29
ACGTcount: A:0.55, C:0.13, G:0.30, T:0.01
Consensus pattern (15 bp):
AAGAAAGAAGAACCC
Found at i:2714688 original size:33 final size:33
Alignment explanation
Indices: 2714552--2714684 Score: 166
Period size: 33 Copynumber: 4.1 Consensus size: 33
2714542 CCAGAGAAGA
* *
2714552 AGGAGGAGCCAAAGAAGGAAGAGCCCAAGAAAG
1 AGGAGGAGCCAAAGAAAGAAGAACCCAAGAAAG
2714585 AGGAGGAAG-CAAAGAAAGAAGAACCCAAGAAAG
1 AGGAGG-AGCCAAAGAAAGAAGAACCCAAGAAAG
* * * *
2714618 AAGAGGAGCCGAAGAAAGAAGAGCCTAAG--A-
1 AGGAGGAGCCAAAGAAAGAAGAACCCAAGAAAG
*
2714648 AGGAAGAGCCAAAGAAAGAAGAACCCAAGAAAG
1 AGGAGGAGCCAAAGAAAGAAGAACCCAAGAAAG
2714681 AGGA
1 AGGA
2714685 AGAGAAGAAG
Statistics
Matches: 84, Mismatches: 11, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
30 24 0.29
31 1 0.01
32 3 0.04
33 54 0.64
34 2 0.02
ACGTcount: A:0.53, C:0.14, G:0.32, T:0.01
Consensus pattern (33 bp):
AGGAGGAGCCAAAGAAAGAAGAACCCAAGAAAG
Found at i:2720244 original size:24 final size:24
Alignment explanation
Indices: 2720212--2720265 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
2720202 TCGCCCGAAC
2720212 GAGTGGGGAGTGAGGGGAAAGCAT
1 GAGTGGGGAGTGAGGGGAAAGCAT
2720236 GAGTGGGGAGTGAGGGGAAAGCAT
1 GAGTGGGGAGTGAGGGGAAAGCAT
*
2720260 GCGTGG
1 GAGTGG
2720266 AGACATGAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.26, C:0.06, G:0.56, T:0.13
Consensus pattern (24 bp):
GAGTGGGGAGTGAGGGGAAAGCAT
Found at i:2722047 original size:8 final size:8
Alignment explanation
Indices: 2722012--2722046 Score: 52
Period size: 9 Copynumber: 4.1 Consensus size: 8
2722002 TGAAAATAAG
2722012 AAAAAGAA
1 AAAAAGAA
2722020 AAAAAGGAA
1 AAAAA-GAA
2722029 AAAAAGAA
1 AAAAAGAA
2722037 AAGAAAGAA
1 AA-AAAGAA
2722046 A
1 A
2722047 GTAAGTAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 10 0.40
9 15 0.60
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:2722570 original size:2 final size:2
Alignment explanation
Indices: 2722563--2722604 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
2722553 TGGGTTAGAG
* *
2722563 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2722605 GCCAACCTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2726676 original size:19 final size:18
Alignment explanation
Indices: 2726654--2726689 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2726644 TAATGTTGTT
*
2726654 TTTGTTTTTTTCTTTTTAA
1 TTTGTTTTATT-TTTTTAA
2726673 TTTGTTTTATTTTTTTA
1 TTTGTTTTATTTTTTTA
2726690 TTTTTATTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.11, C:0.03, G:0.06, T:0.81
Consensus pattern (18 bp):
TTTGTTTTATTTTTTTAA
Found at i:2726685 original size:24 final size:26
Alignment explanation
Indices: 2726641--2726695 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 26
2726631 AGTGACTCAA
* *
2726641 TTTTAATGTTGTTTTTGTTTTTTTCT
1 TTTTAATGTTGTTTTTATTTTTTTAT
2726667 TTTTAAT-TTG-TTTTATTTTTTTAT
1 TTTTAATGTTGTTTTTATTTTTTTAT
2726691 TTTTA
1 TTTTA
2726696 TTCTATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 17 0.63
25 3 0.11
26 7 0.26
ACGTcount: A:0.13, C:0.02, G:0.07, T:0.78
Consensus pattern (26 bp):
TTTTAATGTTGTTTTTATTTTTTTAT
Found at i:2727531 original size:2 final size:2
Alignment explanation
Indices: 2727524--2727550 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2727514 CCATTCAATC
2727524 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2727551 ACACCATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2728702 original size:29 final size:29
Alignment explanation
Indices: 2728634--2728704 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 29
2728624 TCTAAAATTT
* *
2728634 AAATAAATTTTTAT-TTTTTATTATATTC
1 AAATAAATTTTTATACTTTTATTATAATC
*
2728662 -AATCAAA-TTTTATACTTTTATTCTAATC
1 AAAT-AAATTTTTATACTTTTATTATAATC
2728690 AAATAAATTTTTATA
1 AAATAAATTTTTATA
2728705 ATTAATAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
27 9 0.25
28 17 0.47
29 10 0.28
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (29 bp):
AAATAAATTTTTATACTTTTATTATAATC
Found at i:2728880 original size:18 final size:18
Alignment explanation
Indices: 2728845--2728896 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
2728835 CTAGGTATTA
**
2728845 TAATAAGTAATATTTTAAC
1 TAATAA-TAATAAATTAAC
*
2728864 TAATAATAATAAATTAAT
1 TAATAATAATAAATTAAC
*
2728882 TATTAATAATAAATT
1 TAATAATAATAAATT
2728897 CTTAAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 23 0.79
19 6 0.21
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (18 bp):
TAATAATAATAAATTAAC
Found at i:2744489 original size:20 final size:20
Alignment explanation
Indices: 2744464--2744528 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
2744454 TGAAGTGTAT
2744464 ATATTTTTTTATTAAATTAA
1 ATATTTTTTTATTAAATTAA
* *
2744484 ATA-TTTTTAAATAAA-TAA
1 ATATTTTTTTATTAAATTAA
* *
2744502 ACATATTTATTATTAAATTAA
1 ATAT-TTTTTTATTAAATTAA
2744523 A-ATTTT
1 ATATTTT
2744529 AATTACAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
18 5 0.14
19 13 0.36
20 14 0.39
21 4 0.11
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
ATATTTTTTTATTAAATTAA
Found at i:2744492 original size:18 final size:18
Alignment explanation
Indices: 2744469--2744544 Score: 73
Period size: 18 Copynumber: 4.1 Consensus size: 18
2744459 TGTATATATT
2744469 TTTTTATTAAATTAAATA
1 TTTTTATTAAATTAAATA
* *
2744487 TTTTTAAATAAATAAACATA
1 TTTTT-ATTAAATTAA-ATA
2744507 TTTATTATTAAATTAAA-A
1 TTT-TTATTAAATTAAATA
* *
2744525 TTTTAATTACAATTAGATA
1 TTTTTATTA-AATTAAATA
2744544 T
1 T
2744545 AATACTAGTA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
17 5 0.11
18 15 0.32
19 11 0.23
20 14 0.30
21 2 0.04
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (18 bp):
TTTTTATTAAATTAAATA
Found at i:2785550 original size:194 final size:194
Alignment explanation
Indices: 2785212--2785597 Score: 673
Period size: 194 Copynumber: 2.0 Consensus size: 194
2785202 GGTGGCGCTG
* * * * *
2785212 AAATCGACGGTAATTATGATGCTAATAATGAAGTGGAAATGGGGTTCGATTTTTAATGCAGATAT
1 AAATCGACAGTAATTATGATGCTAATAATGAAGTGGAAATGGGGCTAGATTTTTAACGCACATAT
2785277 CCTTTTCTCTTTCATTTCTACATCCATCAATTCCAAGTGCAGAAAATTTAGTTGAAAAGCAATTG
66 CCTTTTCTCTTTCATTTCTACATCCATCAATTCCAAGTGCAGAAAATTTAGTTGAAAAGCAATTG
*
2785342 AAATAATGCATCAAGTATAGAAACATTCATGATTAATGAAGAGCATTGCAGAAAAAGCTTGCCA
131 AAATAATGCATCAAGTATAGAAACATTAATGATTAATGAAGAGCATTGCAGAAAAAGCTTGCCA
* *
2785406 AAATTGACAGTAATTATGATGCTAATAATGAAGTGGAAATGGGGCTAGATTTTTAACGCCCATAT
1 AAATCGACAGTAATTATGATGCTAATAATGAAGTGGAAATGGGGCTAGATTTTTAACGCACATAT
* * *
2785471 CCTTTTCTCTTTCATTTCTACATCCATCAATTCCAAGTGCGGAAAATTTTGTTGAAATGCAATTG
66 CCTTTTCTCTTTCATTTCTACATCCATCAATTCCAAGTGCAGAAAATTTAGTTGAAAAGCAATTG
2785536 AAATAATGCATCAAGTATAGAAACATTAATGATTAATGAAGAGCATTGCAGAAAAAGCTTGC
131 AAATAATGCATCAAGTATAGAAACATTAATGATTAATGAAGAGCATTGCAGAAAAAGCTTGC
2785598 TATCCTACCT
Statistics
Matches: 181, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
194 181 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (194 bp):
AAATCGACAGTAATTATGATGCTAATAATGAAGTGGAAATGGGGCTAGATTTTTAACGCACATAT
CCTTTTCTCTTTCATTTCTACATCCATCAATTCCAAGTGCAGAAAATTTAGTTGAAAAGCAATTG
AAATAATGCATCAAGTATAGAAACATTAATGATTAATGAAGAGCATTGCAGAAAAAGCTTGCCA
Found at i:2800572 original size:295 final size:296
Alignment explanation
Indices: 2800042--2801162 Score: 1049
Period size: 295 Copynumber: 3.9 Consensus size: 296
2800032 TCATCCCTAC
* *
2800042 ATAGGAATGCCACATATACCAAGATGTTAGATTTACATATTGGCAACATTATACCTTAATGGATA
1 ATAGGAATGCCACATATACCAAGATGTTAGATTTATATATTGGCAACATTATACCTTAATGTATA
* * * * * * * * * *
2800107 ATAGGTATGCCACATACCCACAACATTACACTATTCTCAACTGACACCATTGTATCTTAATGTAC
66 ATAGGAATGCCACATGCCCACAATATTATACCATTATTAATTGACATCATTGTACCTTAATGTAC
* *
2800172 AATCGAAATGTCAAATTAACACATCAAGCTATGTATTCACATATGCA-CAAT-TGCATCTTTATT
131 AATCGAAATGTCAAATTAACACATCAAGCTATGTGTTCACATATGCACCATTGTGCATCTTTATT
** * * *
2800235 GTATAATAGGAATGTCATACCAAATATATTAAATATCTA-TTT-TACATCATTACACCTTAATGT
196 ACACAATAGGAATGCCATACCAAATATATTAAATATCTATTTTGTAC-T-ATTACACCTTAATAT
* *
2800298 ATAATAGAAATGTTAACATGCCAAACACCATAGAGTATA
259 ATAATAGAAATG-CAACATGCCAAACACCATAAAGTATA
*
2800337 ATAGGAATGCCACATATACCAAGATGTTAGATTTATATATTGGCATCATTATACCTTAATGTATA
1 ATAGGAATGCCACATATACCAAGATGTTAGATTTATATATTGGCAACATTATACCTTAATGTATA
* * *
2800402 ATAAGAATGCCACATGCCCACATTATTATACCATTATTAATTAACATCATTGTACCTTAATGTAC
66 ATAGGAATGCCACATGCCCACAATATTATACCATTATTAATTGACATCATTGTACCTTAATGTAC
* *
2800467 AATCGGAATGCCAAATTAACACATCAAGCTATGTGTTCACATATGCACCATTGTGC-T-TTTATT
131 AATCGAAATGTCAAATTAACACATCAAGCTATGTGTTCACATATGCACCATTGTGCATCTTTATT
** * * *
2800530 ACACAATAGGAATGCCATTTCAAATATATTTAATGTCTATTTTGTACTATTATACCTTAATATAT
196 ACACAATAGGAATGCCATACCAAATATATTAAATATCTATTTTGTACTATTACACCTTAATATAT
* * * **** *
2800595 AGTAGGAATGCCACATGCCAATTGTCATAAAGTATT
261 AATAGAAATGCAACATGCCAAACACCATAAAGTATA
* * * *
2800631 ATAGGAATGTCACATACACTAAGATGTTAGATTTATATATTGGCACCATTATACCTTAATGTATA
1 ATAGGAATGCCACATATACCAAGATGTTAGATTTATATATTGGCAACATTATACCTTAATGTATA
* * * * * *
2800696 ATAGGAATACCACATGCCTACACTATTATACCATTATTAATTGACATCTTTATACCTTAATATAC
66 ATAGGAATGCCACATGCCCACAATATTATACCATTATTAATTGACATCATTGTACCTTAATGTAC
* * * *
2800761 AATCGAAATATCAAATTAACACATCAAGTTATATGTTCACATATGCACCATTGT--A-C---CTT
131 AATCGAAATGTCAAATTAACACATCAAGCTATGTGTTCACATATGCACCATTGTGCATCTTTATT
* ********** *
2800820 ------T--G--T--CATGCCAAATATATTAAATATCTATTTTNNNNNNNNNNACCTTAATGTAT
196 ACACAATAGGAATGCCATACCAAATATATTAAATATCTATTTTGTACTATTACACCTTAATATAT
* * * *
2800873 AATAGGAATGCCACATGCCAAATC-CCACAAAATATA
261 AATAGAAATGCAACATGCCAAA-CACCATAAAGTATA
* * * * * * * *
2800909 ATCGGAATGTCACATATACCAAAATGTTATATTTACATATTGACACCATTATACCTTAATATATA
1 ATAGGAATGCCACATATACCAAGATGTTAGATTTATATATTGGCAACATTATACCTTAATGTATA
* * ** ** * * * *
2800974 ATAGGAATACCAGACACCCACACCATTATACCATT-TTCAATAGACACCATTGTACTTTAATATA
66 ATAGGAATGCCACATGCCCACAATATTATACCATTATT-AATTGACATCATTGTACCTTAATGTA
* * * * * * *
2801038 CAATC-AACATGTCAAATTAACTCATCAAACTATTTGTTTACATATGCACCATTATGC--CCTCA
130 CAATCGAA-ATGTCAAATTAACACATCAAGCTATGTGTTCACATATGCACCATTGTGCATCTTTA
* * * * * * * * *
2801100 TTGCACATTAGAAATGCCATATCAAATTTATTGAATATCTATTTTGCACCATTATACCTTAAT
194 TTACACAATAGGAATGCCATACCAAATATATTAAATATCTATTTTGTACTATTACACCTTAAT
2801163 TTTTAAAAGG
Statistics
Matches: 679, Mismatches: 121, Indels: 53
0.80 0.14 0.06
Matches are distributed among these distances:
277 4 0.01
278 216 0.32
279 1 0.00
280 1 0.00
282 3 0.00
284 1 0.00
288 1 0.00
290 2 0.00
292 1 0.00
294 217 0.32
295 218 0.32
296 8 0.01
297 6 0.01
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.33
Consensus pattern (296 bp):
ATAGGAATGCCACATATACCAAGATGTTAGATTTATATATTGGCAACATTATACCTTAATGTATA
ATAGGAATGCCACATGCCCACAATATTATACCATTATTAATTGACATCATTGTACCTTAATGTAC
AATCGAAATGTCAAATTAACACATCAAGCTATGTGTTCACATATGCACCATTGTGCATCTTTATT
ACACAATAGGAATGCCATACCAAATATATTAAATATCTATTTTGTACTATTACACCTTAATATAT
AATAGAAATGCAACATGCCAAACACCATAAAGTATA
Found at i:2800754 original size:294 final size:297
Alignment explanation
Indices: 2800042--2801162 Score: 1055
Period size: 294 Copynumber: 3.9 Consensus size: 297
2800032 TCATCCCTAC
* *
2800042 ATAGGAATGCCACATATACCAAGATGTTAGATTTACATATTGGCAACATTATACCTTAATGGATA
1 ATAGGAATGCCACATATACCAAGATGTTAGATTTATATATTGGCAACATTATACCTTAATGTATA
* * * * * * * * *
2800107 ATAGGTATGCCACATACCCACAAC-ATTACACTATTCTCAACTGACACCATTGTATCTTAATGTA
66 ATAGGAATGCCACATGCCCAC-ACTATTATACCATTATTAATTGACATCATTGTACCTTAATGTA
* *
2800171 CAATCGAAATGTCAAATTAACACATCAAGCTATGTATTCACATATGCA-CAAT-TGCATCTTTAT
130 CAATCGAAATGTCAAATTAACACATCAAGCTATGTGTTCACATATGCACCATTGTGCATCTTTAT
** * * *
2800234 TGTATAATAGGAATGTCATACCAAATATATTAAATATCTATTTTACATCATTACACCTTAATGTA
195 TACACAATAGGAATGCCATACCAAATATATTAAATATCTATTTTACATCATTACACCTTAATATA
* *
2800299 TAATAGAAATGTTAACATGCCAAACACCATAGAGTATA
260 TAATAGAAATGTCAACATGCCAAACACCATAAAGTATA
*
2800337 ATAGGAATGCCACATATACCAAGATGTTAGATTTATATATTGGCATCATTATACCTTAATGTATA
1 ATAGGAATGCCACATATACCAAGATGTTAGATTTATATATTGGCAACATTATACCTTAATGTATA
* * *
2800402 ATAAGAATGCCACATGCCCACATTATTATACCATTATTAATTAACATCATTGTACCTTAATGTAC
66 ATAGGAATGCCACATGCCCACACTATTATACCATTATTAATTGACATCATTGTACCTTAATGTAC
* *
2800467 AATCGGAATGCCAAATTAACACATCAAGCTATGTGTTCACATATGCACCATTGTGC-T-TTTATT
131 AATCGAAATGTCAAATTAACACATCAAGCTATGTGTTCACATATGCACCATTGTGCATCTTTATT
** * * *
2800530 ACACAATAGGAATGCCATTTCAAATATATTTAATGTCTATTTTGTAC-T-ATTATACCTTAATAT
196 ACACAATAGGAATGCCATACCAAATATATTAAATATCTA-TTT-TACATCATTACACCTTAATAT
* * * **** *
2800593 ATAGTAGGAATG-CCACATGCCAATTGTCATAAAGTATT
259 ATAATAGAAATGTCAACATGCCAAACACCATAAAGTATA
* * * *
2800631 ATAGGAATGTCACATACACTAAGATGTTAGATTTATATATTGGCACCATTATACCTTAATGTATA
1 ATAGGAATGCCACATATACCAAGATGTTAGATTTATATATTGGCAACATTATACCTTAATGTATA
* * * * *
2800696 ATAGGAATACCACATGCCTACACTATTATACCATTATTAATTGACATCTTTATACCTTAATATAC
66 ATAGGAATGCCACATGCCCACACTATTATACCATTATTAATTGACATCATTGTACCTTAATGTAC
* * * *
2800761 AATCGAAATATCAAATTAACACATCAAGTTATATGTTCACATATGCACCATTGT--A-C---CTT
131 AATCGAAATGTCAAATTAACACATCAAGCTATGTGTTCACATATGCACCATTGTGCATCTTTATT
* ********** *
2800820 ------T--G--T--CATGCCAAATATATTAAATATCTATTTTNNNNNNNNNNACCTTAATGTAT
196 ACACAATAGGAATGCCATACCAAATATATTAAATATCTATTTTACATCATTACACCTTAATATAT
* * * *
2800873 AATAGGAATG-CCACATGCCAAATC-CCACAAAATATA
261 AATAGAAATGTCAACATGCCAAA-CACCATAAAGTATA
* * * * * * * *
2800909 ATCGGAATGTCACATATACCAAAATGTTATATTTACATATTGACACCATTATACCTTAATATATA
1 ATAGGAATGCCACATATACCAAGATGTTAGATTTATATATTGGCAACATTATACCTTAATGTATA
* * ** * * * * *
2800974 ATAGGAATACCAGACACCCACACCATTATACCATT-TTCAATAGACACCATTGTACTTTAATATA
66 ATAGGAATGCCACATGCCCACACTATTATACCATTATT-AATTGACATCATTGTACCTTAATGTA
* * * * * * *
2801038 CAATC-AACATGTCAAATTAACTCATCAAACTATTTGTTTACATATGCACCATTATGC--CCTCA
130 CAATCGAA-ATGTCAAATTAACACATCAAGCTATGTGTTCACATATGCACCATTGTGCATCTTTA
* * * * * * * * *
2801100 TTGCACATTAGAAATGCCATATCAAATTTATTGAATATCTATTTTGCACCATTATACCTTAAT
194 TTACACAATAGGAATGCCATACCAAATATATTAAATATCTATTTTACATCATTACACCTTAAT
2801163 TTTTAAAAGG
Statistics
Matches: 679, Mismatches: 118, Indels: 59
0.79 0.14 0.07
Matches are distributed among these distances:
276 1 0.00
277 7 0.01
278 212 0.31
279 1 0.00
280 1 0.00
282 3 0.00
284 1 0.00
288 1 0.00
290 2 0.00
292 1 0.00
294 218 0.32
295 217 0.32
296 8 0.01
297 6 0.01
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.33
Consensus pattern (297 bp):
ATAGGAATGCCACATATACCAAGATGTTAGATTTATATATTGGCAACATTATACCTTAATGTATA
ATAGGAATGCCACATGCCCACACTATTATACCATTATTAATTGACATCATTGTACCTTAATGTAC
AATCGAAATGTCAAATTAACACATCAAGCTATGTGTTCACATATGCACCATTGTGCATCTTTATT
ACACAATAGGAATGCCATACCAAATATATTAAATATCTATTTTACATCATTACACCTTAATATAT
AATAGAAATGTCAACATGCCAAACACCATAAAGTATA
Found at i:2801055 original size:278 final size:268
Alignment explanation
Indices: 2800576--2801090 Score: 611
Period size: 278 Copynumber: 1.9 Consensus size: 268
2800566 CTATTTTGTA
* * * ** * * *
2800576 CTATTATACCTTAATATATAGTAGGAATGCCACATGCCAATTGTCATAAAGTATTATAGGAATGT
1 CTATTTTACCTTAATATATAATAGGAATGCCACATGCCAAATCCCACAAAATATAATAGGAATGT
* * * * *
2800641 CACATACACTAAGATGTTAGATTTATATATTGGCACCATTATACCTTAATGTATAATAGGAATAC
66 CACATACACCAAAATGTTAGATTTACATATTGACACCATTATACCTTAATATATAATAGGAATAC
** * * * * *
2800706 CACATGCCTACACTATTATACCATTATTAATTGACATCTTTATACCTTAATATACAATCGAAATA
131 CACACACCCACACCATTATACCATTATTAATAGACACCATTATACCTTAATATACAATCGAAATA
**
2800771 TCAAATTAACACATCAAGTTATATGTTCACATATGCACCATTGTACCTTTGTCATGCCAAATATA
196 TCAAATTAACACATCAAACTATATGTTCACATATGCACCATTGTACCTTTGTCATGCCAAATATA
2800836 TTAAATAT
261 TTAAATAT
*
2800844 CTATTTTNNNNNNNNNNACCTTAATGTATAATAGGAATGCCACATGCCAAATCCCACAAAATATA
1 CTATTTT----------ACCTTAATATATAATAGGAATGCCACATGCCAAATCCCACAAAATATA
* * *
2800909 ATCGGAATGTCACATATACCAAAATGTTATATTTACATATTGACACCATTATACCTTAATATATA
56 ATAGGAATGTCACATACACCAAAATGTTAGATTTACATATTGACACCATTATACCTTAATATATA
* * *
2800974 ATAGGAATACCAGACACCCACACCATTATACCATT-TTCAATAGACACCATTGTACTTTAATATA
121 ATAGGAATACCACACACCCACACCATTATACCATTATT-AATAGACACCATTATACCTTAATATA
* * * *
2801038 CAATC-AACATGTCAAATTAACTCATCAAACTATTTGTTTACATATGCACCATT
185 CAATCGAA-ATATCAAATTAACACATCAAACTATATGTTCACATATGCACCATT
2801091 ATGCCCTCAT
Statistics
Matches: 202, Mismatches: 33, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
268 6 0.03
277 4 0.02
278 192 0.95
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.33
Consensus pattern (268 bp):
CTATTTTACCTTAATATATAATAGGAATGCCACATGCCAAATCCCACAAAATATAATAGGAATGT
CACATACACCAAAATGTTAGATTTACATATTGACACCATTATACCTTAATATATAATAGGAATAC
CACACACCCACACCATTATACCATTATTAATAGACACCATTATACCTTAATATACAATCGAAATA
TCAAATTAACACATCAAACTATATGTTCACATATGCACCATTGTACCTTTGTCATGCCAAATATA
TTAAATAT
Found at i:2801329 original size:98 final size:99
Alignment explanation
Indices: 2801175--2801406 Score: 286
Period size: 98 Copynumber: 2.4 Consensus size: 99
2801165 TTAAAAGGCC
* * *** * *
2801175 ACTATTGTACCTTAATGTATAATAGGAATACCATATGTAAACACCACAAAGTATAATAGGAATGT
1 ACTATTATACCTTAATGTATAATAGGAATACCACAAACAAACACCACAAAGGATAATAGAAATGT
* ** *
2801240 CA-ATGTATGAAGATGTTAAATTTACATATTAAA
66 CACATATACCAAAATGTTAAATTTACATATTAAA
* *
2801273 ACTATTATACCTTAATGTATAATAAGAATGCCACAAACAAACACCACAAAGGATAATAGAAATGT
1 ACTATTATACCTTAATGTATAATAGGAATACCACAAACAAACACCACAAAGGATAATAGAAATGT
* * *
2801338 CACATATACCAAAATGTTAGATTTACATATTGAC
66 CACATATACCAAAATGTTAAATTTACATATTAAA
* * *
2801372 ACTAGTATACTTTAATGTATAATAGGAATTCCACA
1 ACTATTATACCTTAATGTATAATAGGAATACCACA
2801407 TGCCCACACC
Statistics
Matches: 113, Mismatches: 20, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
98 58 0.51
99 55 0.49
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (99 bp):
ACTATTATACCTTAATGTATAATAGGAATACCACAAACAAACACCACAAAGGATAATAGAAATGT
CACATATACCAAAATGTTAAATTTACATATTAAA
Found at i:2801417 original size:99 final size:98
Alignment explanation
Indices: 2801182--2801409 Score: 285
Period size: 99 Copynumber: 2.3 Consensus size: 98
2801172 GCCACTATTG
* * * * *
2801182 TACCTTAATGTATAATAGGAATACCATATGTAAACACCACAAAGTATAATAGGAATGTCAATGTA
1 TACCTTAATGTATAATAGGAATACCACATGCAAACACCACAAAGGATAATAGAAATGTCAATATA
** * *
2801247 TGAAGATGTTAAATTTACATATTAAAACTATTA
66 CCAAAATGTTAAATTTACATATTAAAACTAGTA
* * **
2801280 TACCTTAATGTATAATAAGAATGCCACAAACAAACACCACAAAGGATAATAGAAATGTCACATAT
1 TACCTTAATGTATAATAGGAATACCACATGCAAACACCACAAAGGATAATAGAAATGTCA-ATAT
* * *
2801345 ACCAAAATGTTAGATTTACATATTGACACTAGTA
65 ACCAAAATGTTAAATTTACATATTAAAACTAGTA
* *
2801379 TACTTTAATGTATAATAGGAATTCCACATGC
1 TACCTTAATGTATAATAGGAATACCACATGC
2801410 CCACACCATT
Statistics
Matches: 108, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
98 52 0.48
99 56 0.52
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.29
Consensus pattern (98 bp):
TACCTTAATGTATAATAGGAATACCACATGCAAACACCACAAAGGATAATAGAAATGTCAATATA
CCAAAATGTTAAATTTACATATTAAAACTAGTA
Found at i:2802232 original size:264 final size:264
Alignment explanation
Indices: 2801818--2802793 Score: 902
Period size: 264 Copynumber: 3.6 Consensus size: 264
2801808 ACAATGTATA
* * ** * * * *
2801818 ATAGGGATGTCACATATACTAGGATGTTAGATTTATATATTGGAATCATTATACCTTAATGTATA
1 ATAGGAATGTCACATATACCAAAATGTTATATTTACATATTGGCACCATTATACCTTAATGTATA
* * ** * * * * *
2801883 ATAAGAATGTCGGATG-TCCATACCATTATACCATTCTTAATTGACACCATTGTACCTTAGTGTA
66 ATAGGAATGCCACATGCT-CACACCATTATACCACTCTCAATAGACACCATTGTACCTTAATGTA
2801947 CAATCGAAATGTCAAATTAACACATCAAGCCACCATTGTGCCTTTATTGCACACTAGAAATGCCA
130 CAATCGAAATGTCAAATTAACACATCAAGCCACCATTGTGCCTTTATTGCACACTAGAAATGCCA
*
2802012 AATATCTCATTTGCACCATTACCCATTAATGTATAATAGGAATGCCACATGTACAACACGACAAA
195 AATATCTCATTTGCACCATTACCCATTAATGTATAATAGGAATGCCACATGTACAACACCACAAA
2802077 ATATT
260 ATATT
* * *
2802082 ATAAGAATGTCACATATACCAAAATATTATATTTACATATTGGCACCATTATACCTTAATGTATG
1 ATAGGAATGTCACATATACCAAAATGTTATATTTACATATTGGCACCATTATACCTTAATGTATA
* * ** * ** *
2802147 ATAGGAATACCACATGCACACACCATTATACCACAATGAACGGACACCATTGTACCTTAATGTAT
66 ATAGGAATGCCACATGCTCACACCATTATACCACTCTCAATAGACACCATTGTACCTTAATGTAC
* * * * * ***
2802212 AATCGAAATGCCAAATTAACACATTAAGCTA-TA-TGTTCACACGCACCAAATTAACACATCAAG
131 AATCGAAATGTCAAATTAACACATCAAGCCACCATTG-T-----G--CC--TTTATTGCA-C-A-
* * * * * ** *
2802275 CTATAATCGGAATGTCAAATATATTAAATATT-TA-TTTTGCACCATTATACCTTAATGTATAAT
183 C--T-A--GAAATGCCAAATAT-CT-CAT-TTGCACCATT--ACC---C-A--TTAATGTATAAT
* * * ** *
2802338 AGAAATGTCACATG-CCAAACACCACAATGTATA
232 AGGAATGCCACATGTAC-AACACCACAAAATATT
* * * *
2802371 ATAGGGATGTCACATATACTAAAATGTTATATTTACATAATGGCATCATTATACCTTAATGTATA
1 ATAGGAATGTCACATATACCAAAATGTTATATTTACATATTGGCACCATTATACCTTAATGTATA
* ** * * * * * *
2802436 ATAGGAATGTCGTATGTTCACACAATTATACCATTCTCAATTGACACCATTGTACCTTAGTATAC
66 ATAGGAATGCCACATGCTCACACCATTATACCACTCTCAATAGACACCATTGTACCTTAATGTAC
* *
2802501 AATCGGAATGTCAAATTAACACATCAAGCCACCATTGTGCCTTTATTGCACACTAAAAATGCCAA
131 AATCGAAATGTCAAATTAACACATCAAGCCACCATTGTGCCTTTATTGCACACTAGAAATGCCAA
** *
2802566 ATATCTCATTTGCACCATTATACATTAATGTATAATAAGAATGCCACATGTACAACACCACAAAA
196 ATATCTCATTTGCACCATTACCCATTAATGTATAATAGGAATGCCACATGTACAACACCACAAAA
2802631 TATT
261 TATT
* * * * * * *
2802635 ATAGGAACGTCACATATGCCAAGATGTTAGATTTACATATTGACACTATTATACCTTAATGTTTA
1 ATAGGAATGTCACATATACCAAAATGTTATATTTACATATTGGCACCATTATACCTTAATGTATA
* * * *
2802700 ATAGGAATGCCACATGCTCACACCATTATATCACTCTCAATAGACGCCATTGTACATTAATGTAT
66 ATAGGAATGCCACATGCTCACACCATTATACCACTCTCAATAGACACCATTGTACCTTAATGTAC
*
2802765 AATCAAAATGTCAAATTAACACATCAAGC
131 AATCGAAATGTCAAATTAACACATCAAGC
2802794 TATATGTTCA
Statistics
Matches: 551, Mismatches: 125, Indels: 72
0.74 0.17 0.10
Matches are distributed among these distances:
262 2 0.00
263 2 0.00
264 300 0.54
265 1 0.00
266 1 0.00
268 1 0.00
270 5 0.01
271 3 0.01
272 8 0.01
273 12 0.02
274 1 0.00
275 2 0.00
276 1 0.00
277 1 0.00
278 2 0.00
279 1 0.00
280 13 0.02
281 8 0.01
282 3 0.01
283 7 0.01
285 1 0.00
287 1 0.00
288 1 0.00
289 170 0.31
290 2 0.00
291 2 0.00
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (264 bp):
ATAGGAATGTCACATATACCAAAATGTTATATTTACATATTGGCACCATTATACCTTAATGTATA
ATAGGAATGCCACATGCTCACACCATTATACCACTCTCAATAGACACCATTGTACCTTAATGTAC
AATCGAAATGTCAAATTAACACATCAAGCCACCATTGTGCCTTTATTGCACACTAGAAATGCCAA
ATATCTCATTTGCACCATTACCCATTAATGTATAATAGGAATGCCACATGTACAACACCACAAAA
TATT
Found at i:2802782 original size:553 final size:553
Alignment explanation
Indices: 2801733--2802812 Score: 1719
Period size: 553 Copynumber: 2.0 Consensus size: 553
2801723 TAAGAATGCT
*
2801733 ATGTCAAATATATTAAAAATCTATTTTGTACCATTATACCTTAATGTATAAAAGAAATATCACAT
1 ATGTCAAATATATTAAAAATCTATTTTGCACCATTATACCTTAATGTATAAAAGAAATATCACAT
* ** * *
2801798 GCCAAACTCCACAATGTATAATAGGGATGTCACATATACTAGGATGTTAGATTTATATATTGGAA
66 GCCAAACACCACAATGTATAATAGGGATGTCACATATACTAAAATGTTAGATTTACATAATGGAA
* * *
2801863 TCATTATACCTTAATGTATAATAAGAATGTCGGATGTCCATACCATTATACCATTCTTAATTGAC
131 TCATTATACCTTAATGTATAATAAGAATGTCGGATGTCCACACAATTATACCATTCTCAATTGAC
*
2801928 ACCATTGTACCTTAGTGTACAATCGAAATGTCAAATTAACACATCAAGCCACCATTGTGCCTTTA
196 ACCATTGTACCTTAGTATACAATCGAAATGTCAAATTAACACATCAAGCCACCATTGTGCCTTTA
* * *
2801993 TTGCACACTAGAAATGCCAAATATCTCATTTGCACCATTACCCATTAATGTATAATAGGAATGCC
261 TTGCACACTAAAAATGCCAAATATCTCATTTGCACCATTACACATTAATGTATAATAAGAATGCC
* * *
2802058 ACATGTACAACACGACAAAATATTATAAGAATGTCACATATACCAAAATATTATATTTACATATT
326 ACATGTACAACACCACAAAATATTATAAGAACGTCACATATACCAAAATATTAGATTTACATATT
* * *
2802123 GGCACCATTATACCTTAATGTATGATAGGAATACCACATGCACACACCATTATACCACAATGAAC
391 GACACCATTATACCTTAATGTATAATAGGAATACCACATGCACACACCATTATACCACAATCAAC
* * * *
2802188 GGACACCATTGTACCTTAATGTATAATCGAAATGCCAAATTAACACATTAAGCTATATGTTCACA
456 AGACACCATTGTACATTAATGTATAATCAAAATGCCAAATTAACACATCAAGCTATATGTTCACA
2802253 CGCACCAAATTAACACATCAAGCTATAATCGGA
521 CGCACCAAATTAACACATCAAGCTATAATCGGA
* * * *
2802286 ATGTCAAATATATTAAATATTTATTTTGCACCATTATACCTTAATGTATAATAGAAATGTCACAT
1 ATGTCAAATATATTAAAAATCTATTTTGCACCATTATACCTTAATGTATAAAAGAAATATCACAT
* *
2802351 GCCAAACACCACAATGTATAATAGGGATGTCACATATACTAAAATGTTATATTTACATAATGGCA
66 GCCAAACACCACAATGTATAATAGGGATGTCACATATACTAAAATGTTAGATTTACATAATGGAA
* * *
2802416 TCATTATACCTTAATGTATAATAGGAATGTCGTATGTTCACACAATTATACCATTCTCAATTGAC
131 TCATTATACCTTAATGTATAATAAGAATGTCGGATGTCCACACAATTATACCATTCTCAATTGAC
*
2802481 ACCATTGTACCTTAGTATACAATCGGAATGTCAAATTAACACATCAAGCCACCATTGTGCCTTTA
196 ACCATTGTACCTTAGTATACAATCGAAATGTCAAATTAACACATCAAGCCACCATTGTGCCTTTA
*
2802546 TTGCACACTAAAAATGCCAAATATCTCATTTGCACCATTATACATTAATGTATAATAAGAATGCC
261 TTGCACACTAAAAATGCCAAATATCTCATTTGCACCATTACACATTAATGTATAATAAGAATGCC
* * * *
2802611 ACATGTACAACACCACAAAATATTATAGGAACGTCACATATGCCAAGATGTTAGATTTACATATT
326 ACATGTACAACACCACAAAATATTATAAGAACGTCACATATACCAAAATATTAGATTTACATATT
* * * * * ** *
2802676 GACACTATTATACCTTAATGTTTAATAGGAATGCCACATGCTCACACCATTATATCACTCTCAAT
391 GACACCATTATACCTTAATGTATAATAGGAATACCACATGCACACACCATTATACCACAATCAAC
* *
2802741 AGACGCCATTGTACATTAATGTATAATCAAAATGTCAAATTAACACATCAAGCTATATGTTCACA
456 AGACACCATTGTACATTAATGTATAATCAAAATGCCAAATTAACACATCAAGCTATATGTTCACA
*
2802806 TGCACCA
521 CGCACCA
2802813 TTTTGCCTTT
Statistics
Matches: 478, Mismatches: 49, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
553 478 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.31
Consensus pattern (553 bp):
ATGTCAAATATATTAAAAATCTATTTTGCACCATTATACCTTAATGTATAAAAGAAATATCACAT
GCCAAACACCACAATGTATAATAGGGATGTCACATATACTAAAATGTTAGATTTACATAATGGAA
TCATTATACCTTAATGTATAATAAGAATGTCGGATGTCCACACAATTATACCATTCTCAATTGAC
ACCATTGTACCTTAGTATACAATCGAAATGTCAAATTAACACATCAAGCCACCATTGTGCCTTTA
TTGCACACTAAAAATGCCAAATATCTCATTTGCACCATTACACATTAATGTATAATAAGAATGCC
ACATGTACAACACCACAAAATATTATAAGAACGTCACATATACCAAAATATTAGATTTACATATT
GACACCATTATACCTTAATGTATAATAGGAATACCACATGCACACACCATTATACCACAATCAAC
AGACACCATTGTACATTAATGTATAATCAAAATGCCAAATTAACACATCAAGCTATATGTTCACA
CGCACCAAATTAACACATCAAGCTATAATCGGA
Found at i:2803047 original size:553 final size:551
Alignment explanation
Indices: 2801733--2803004 Score: 1579
Period size: 553 Copynumber: 2.3 Consensus size: 551
2801723 TAAGAATGCT
* ** * * * **
2801733 ATGTCAAATATATTAAAAATCTATTTTGTACCATTATACCTTAATGTATAAAAGAAATATCACAT
1 ATGTCAAATATATTAAATATCTATTTTACACCATCATACCTTAATATATAATAGAAATGCCACAT
* * * * ** * * * * *
2801798 GCCAAACTCCACAATGTATAATAGGGATGTCACATATACTAGGATGTTAGATTTATATATTGGAA
66 GCCAAACACCACAAAGTATAATAGGAATGTCAAATATACTAAAATGCTATATTTACATAATGGCA
* * * * * *
2801863 TCATTATACCTTAATGTATAATAAGAATGTCGGATGTCCATACCATTATACCATTCTTAATTGAC
131 TCATTATACCTTAATGCATAATAGGAATGTC-GATGT-CACACAATTATACAATTCTCAATTGAC
*
2801928 ACCATTGTACCTTAGTGTACAATCGAAATGTCAAATTAACACATCAAGCCACCATTGTGCCTTTA
194 ACCATTGTACCTTAGTATACAATCGAAATGTCAAATTAACACATCAAGCCACCATTGTGCCTTTA
* * *
2801993 TTGCACACTAGAAATGCCAAATATCTCATTTGCACCATTACCCATTAATGTATAATAGGAATGCC
259 TTGCACACTAAAAATGCCAAATATCTCATTTGCACCATTACACATTAATGTATAATAAGAATGCC
* * *
2802058 ACATGTACAACACGACAAAATATTATAAGAATGTCACATATACCAAAATATTATATTTACATATT
324 ACATGTACAACACCACAAAATATTATAAGAACGTCACATATACCAAAATATTAGATTTACATATT
* * *
2802123 GGCACCATTATACCTTAATGTATGATAGGAATACCACATGCACACACCATTATACCACAATGAAC
389 GACACCATTATACCTTAATGTATAATAGGAATACCACATGCACACACCATTATACCACAATCAAC
* * * *
2802188 GGACACCATTGTACCTTAATGTATAATCGAAATGCCAAATTAACACATTAAGCTATATGTTCACA
454 AGACACCATTGTACATTAATGTATAATCAAAATGCCAAATTAACACATCAAGCTATATGTTCACA
* *
2802253 CGCACCAAATTAACACATCAAGCTATAATCGGA
519 CGCACCAAATTAACACATCAAACTAGAATCGGA
* * * * *
2802286 ATGTCAAATATATTAAATATTTATTTTGCACCATTATACCTTAATGTATAATAGAAATGTCACAT
1 ATGTCAAATATATTAAATATCTATTTTACACCATCATACCTTAATATATAATAGAAATGCCACAT
* * * *
2802351 GCCAAACACCACAATGTATAATAGGGATGTCACATATACTAAAATGTTATATTTACATAATGGCA
66 GCCAAACACCACAAAGTATAATAGGAATGTCAAATATACTAAAATGCTATATTTACATAATGGCA
* *
2802416 TCATTATACCTTAATGTATAATAGGAATGTCGTATGTTCACACAATTATACCATTCTCAATTGAC
131 TCATTATACCTTAATGCATAATAGGAATGTCG-ATG-TCACACAATTATACAATTCTCAATTGAC
*
2802481 ACCATTGTACCTTAGTATACAATCGGAATGTCAAATTAACACATCAAGCCACCATTGTGCCTTTA
194 ACCATTGTACCTTAGTATACAATCGAAATGTCAAATTAACACATCAAGCCACCATTGTGCCTTTA
*
2802546 TTGCACACTAAAAATGCCAAATATCTCATTTGCACCATTATACATTAATGTATAATAAGAATGCC
259 TTGCACACTAAAAATGCCAAATATCTCATTTGCACCATTACACATTAATGTATAATAAGAATGCC
* * * *
2802611 ACATGTACAACACCACAAAATATTATAGGAACGTCACATATGCCAAGATGTTAGATTTACATATT
324 ACATGTACAACACCACAAAATATTATAAGAACGTCACATATACCAAAATATTAGATTTACATATT
* * * * * ** *
2802676 GACACTATTATACCTTAATGTTTAATAGGAATGCCACATGCTCACACCATTATATCACTCTCAAT
389 GACACCATTATACCTTAATGTATAATAGGAATACCACATGCACACACCATTATACCACAATCAAC
* *
2802741 AGACGCCATTGTACATTAATGTATAATCAAAATGTCAAATTAACACATCAAGCTATATGTTCACA
454 AGACACCATTGTACATTAATGTATAATCAAAATGCCAAATTAACACATCAAGCTATATGTTCACA
* ** ** ** **
2802806 TGCACCATTTTGCCTTTATTGCACAAC-AGGAA-CGTC
519 CGCACCAAATTAAC-ACA-T-CA-AACTA-GAATCGGA
*
2802842 ATGTCAAATATATTAAATATCTATTTTACACCATCATACCTTAATATATAATAGGAATGCCACAT
1 ATGTCAAATATATTAAATATCTATTTTACACCATCATACCTTAATATATAATAGAAATGCCACAT
* * * **
2802907 GCCTAATATCACAAAGTATAATCA-GAATGTCAAAT-TAAC-ACATCTAGCTATATGTTCACAT-
66 GCCAAACACCACAAAGTATAAT-AGGAATGTCAAATAT-ACTA-AAAT-GCTATAT-TT-ACATA
*
2802968 AT-GCA-CTATTATGCCTTAATTGCATAATAGGAATGTC
125 ATGGCATC-ATTATACCTTAA-TGCATAATAGGAATGTC
2803005 ATGCCAAATA
Statistics
Matches: 630, Mismatches: 74, Indels: 25
0.86 0.10 0.03
Matches are distributed among these distances:
552 1 0.00
553 479 0.76
554 2 0.00
555 3 0.00
556 96 0.15
557 25 0.04
558 20 0.03
559 4 0.01
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.31
Consensus pattern (551 bp):
ATGTCAAATATATTAAATATCTATTTTACACCATCATACCTTAATATATAATAGAAATGCCACAT
GCCAAACACCACAAAGTATAATAGGAATGTCAAATATACTAAAATGCTATATTTACATAATGGCA
TCATTATACCTTAATGCATAATAGGAATGTCGATGTCACACAATTATACAATTCTCAATTGACAC
CATTGTACCTTAGTATACAATCGAAATGTCAAATTAACACATCAAGCCACCATTGTGCCTTTATT
GCACACTAAAAATGCCAAATATCTCATTTGCACCATTACACATTAATGTATAATAAGAATGCCAC
ATGTACAACACCACAAAATATTATAAGAACGTCACATATACCAAAATATTAGATTTACATATTGA
CACCATTATACCTTAATGTATAATAGGAATACCACATGCACACACCATTATACCACAATCAACAG
ACACCATTGTACATTAATGTATAATCAAAATGCCAAATTAACACATCAAGCTATATGTTCACACG
CACCAAATTAACACATCAAACTAGAATCGGA
Found at i:2803061 original size:163 final size:161
Alignment explanation
Indices: 2802761--2803101 Score: 486
Period size: 163 Copynumber: 2.1 Consensus size: 161
2802751 GTACATTAAT
* * *
2802761 GTATAATCAAAATGTCAAATTAACACATCAAGCTATATGTTCACATGCACCATTTTGCCTTTATT
1 GTATAATCAGAATGTCAAATTAACACATCAAGCTATATGTTCACATGCACCATTATGCCTTAATT
*
2802826 GCACAACAGGAACGTCATGTCAAATATATTAAATATCTATTTTACACCATCATACCTTAATATAT
66 GCACAACAGGAACGTCATGCCAAATATATTAAATATCTATTTTACACCATCATACCTTAATATAT
** * *
2802891 AATAGGAATGCCACATGCCTAATATCACAAA
131 AATAGGAATGCCACATGCAAAACACCACAAA
* *
2802922 GTATAATCAGAATGTCAAATTAACACATCTAGCTATATGTTCACATATGCACTATTATGCCTTAA
1 GTATAATCAGAATGTCAAATTAACACATCAAGCTATATGTTCAC--ATGCACCATTATGCCTTAA
* * * * * *
2802987 TTGCATAATAGGAATGTCATGCCAAATATATTAAATATCTATTTTGCACCATTATACCTTAATGT
64 TTGCACAACAGGAACGTCATGCCAAATATATTAAATATCTATTTTACACCATCATACCTTAATAT
* *
2803052 ATAATAGGAATGCTACATGTAAAACACCACAAA
129 ATAATAGGAATGCCACATGCAAAACACCACAAA
2803085 GTATAAT-AGGAATGTCA
1 GTATAATCA-GAATGTCA
2803102 CATATACCAA
Statistics
Matches: 159, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
161 42 0.26
162 1 0.01
163 116 0.73
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (161 bp):
GTATAATCAGAATGTCAAATTAACACATCAAGCTATATGTTCACATGCACCATTATGCCTTAATT
GCACAACAGGAACGTCATGCCAAATATATTAAATATCTATTTTACACCATCATACCTTAATATAT
AATAGGAATGCCACATGCAAAACACCACAAA
Found at i:2804059 original size:290 final size:290
Alignment explanation
Indices: 2803510--2804157 Score: 868
Period size: 290 Copynumber: 2.2 Consensus size: 290
2803500 GTACCATTAC
* ** * * * *
2803510 ACCTTAATATATAATAAAAATATCACATACCCACACCATTATATCATTCTCAATGGACACCATTG
1 ACCTTAATGTATAATAGGAATACCACATGCCCACACCATTATACCATTCTCAATTGACACCATTG
* **
2803575 TACCTTAATATATAATCGGAATGTCAAATCAACACAGCAAGCTATATGTTTGCATATGCACCATC
66 TACCTTAATATACAATCGGAATGTCAAATCAACACAGCAAGCTATAAATTTG-ATATGCACCATC
* * *
2803640 GACCCTTTATTGTATAATAGGAATGTCATGTTAAATATATTAAATATCTATTTTGCACCATTATA
130 GACCCTTTATCG---AATAGGAATGTCATCTCAAATATATTAAATATCTATTTTGCACCATTATA
*
2803705 CCTTAATGTACAATAAGAATGCCACATGCCTAATACCACAAAATATAATCGGATTATTACATATA
192 CCTTAATGTACAATAAGAATGCCACATGCCTAATACCACAAAATATAATCGGAGTATTACATATA
*
2803770 TCAAAATGTTAAATTTACATATTGGCATCATCAT
257 TCAAAATATTAAATTTACATATTGGCATCATCAT
* *
2803804 ACCTTAATGTATAATAGGAATGCCACATGCCCACACCATTATACCACTCTCAATTGACACCATTG
1 ACCTTAATGTATAATAGGAATACCACATGCCCACACCATTATACCATTCTCAATTGACACCATTG
* * *
2803869 TACCTTAATGTACAATCGGAATGTCAAATTAACACATCAAGCTATAAATTCATG-TATGCACCAT
66 TACCTTAATATACAATCGGAATGTCAAATCAACACAGCAAGCTATAAATT--TGATATGCACCAT
* ** **********
2803933 TGTGCCTTTATCG-ATAGGAATGTCATCTCAAATATATTAAATATCTATTTTGNNNNNNNNNNCC
129 CGACCCTTTATCGAATAGGAATGTCATCTCAAATATATTAAATATCTATTTTGCACCATTATACC
* * *
2803997 TTAATGTACAATAAGAATGCCGCATGCCTAATGCCACAAAGTATAATCGGAGTATTACATATATC
194 TTAATGTACAATAAGAATGCCACATGCCTAATACCACAAAATATAATCGGAGTATTACATATATC
* *
2804062 AAGATATTAAATTTACATATTGGTATCATCAT
259 AAAATATTAAATTTACATATTGGCATCATCAT
* *
2804094 ACCTTAATGTACAATAGGAATACCACATGCCCACACCATTACACCATTCTCAATTGACACCATT
1 ACCTTAATGTATAATAGGAATACCACATGCCCACACCATTATACCATTCTCAATTGACACCATT
2804158 NNNNNNNNNN
Statistics
Matches: 310, Mismatches: 42, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
290 189 0.61
294 119 0.38
296 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.31
Consensus pattern (290 bp):
ACCTTAATGTATAATAGGAATACCACATGCCCACACCATTATACCATTCTCAATTGACACCATTG
TACCTTAATATACAATCGGAATGTCAAATCAACACAGCAAGCTATAAATTTGATATGCACCATCG
ACCCTTTATCGAATAGGAATGTCATCTCAAATATATTAAATATCTATTTTGCACCATTATACCTT
AATGTACAATAAGAATGCCACATGCCTAATACCACAAAATATAATCGGAGTATTACATATATCAA
AATATTAAATTTACATATTGGCATCATCAT
Found at i:2804199 original size:290 final size:281
Alignment explanation
Indices: 2803510--2804231 Score: 746
Period size: 290 Copynumber: 2.5 Consensus size: 281
2803500 GTACCATTAC
* * ** * * * * * *
2803510 ACCTTAATATATAATAAAAATATCACATACCCACACCATTATATCATTCTCAATGGACACCATTG
1 ACCTTAATGTACAATAGGAATACCACATGCCCACACCATTACACCACTCTCAATTGACACCATTG
* * * * ** ** *
2803575 TACCTTAATATATAATCGGAATGTCAAATCAACACAGCAAGCTATATGTTTGCATATGCACCATC
66 TACCTTAATGTACAATCGGAATGTCAAATTAACACATCAAGCTATAAATTCACATATGCACCATT
** * * *
2803640 G-ACCCTTTATTGTATAATAGGAATGTCATGTTAAATATATTAAATATCTATTTTGCACCATTAT
131 GTGTCCTTTATCG----ATAGGAATGTCATCTCAAATATATTAAATATCTATTTTG---------
*
2803704 ACCTTAATGTACAATAAGAATGCCACATGCCTAATACCACAAAATATAATCGGATTATTACATAT
183 -CCTTAATGTACAATAAGAATGCCACATGCCTAATACCACAAAATATAATCGGAGTATTACATAT
*
2803769 ATCAAAATGTTAAATTTACATATTGGCATCATCAT
247 ATCAAAATATTAAATTTACATATTGGCATCATCAT
* * *
2803804 ACCTTAATGTATAATAGGAATGCCACATGCCCACACCATTATACCACTCTCAATTGACACCATTG
1 ACCTTAATGTACAATAGGAATACCACATGCCCACACCATTACACCACTCTCAATTGACACCATTG
**
2803869 TACCTTAATGTACAATCGGAATGTCAAATTAACACATCAAGCTATAAATTCATGTATGCACCATT
66 TACCTTAATGTACAATCGGAATGTCAAATTAACACATCAAGCTATAAATTCACATATGCACCATT
2803934 GTG-CCTTTATCGATAGGAATGTCATCTCAAATATATTAAATATCTATTTTGNNNNNNNNNNCCT
131 GTGTCCTTTATCGATAGGAATGTCATCTCAAATATATTAAATATCTATTTTG----------CCT
* * *
2803998 TAATGTACAATAAGAATGCCGCATGCCTAATGCCACAAAGTATAATCGGAGTATTACATATATCA
186 TAATGTACAATAAGAATGCCACATGCCTAATACCACAAAATATAATCGGAGTATTACATATATCA
* *
2804063 AGATATTAAATTTACATATTGGTATCATCAT
251 AAATATTAAATTTACATATTGGCATCATCAT
* *
2804094 ACCTTAATGTACAATAGGAATACCACATGCCCACACCATTACACCATTCTCAATTGACACCATTN
1 ACCTTAATGTACAATAGGAATACCACATGCCCACACCATTACACCACTCTCAATTGACACCATTG
********* ** ***
2804159 NNNNNNNNNGTACAATCGGAATGTCAAATTAATTCATCAAGCTATTTGTTCACATATGCACCATT
66 TACCTTAATGTACAATCGGAATGTCAAATTAACACATCAAGCTATAAATTCACATATGCACCATT
2804224 GTGTCCTT
131 GTGTCCTT
2804232 ATTGCACAAT
Statistics
Matches: 364, Mismatches: 62, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
290 241 0.66
291 4 0.01
294 119 0.33
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.31
Consensus pattern (281 bp):
ACCTTAATGTACAATAGGAATACCACATGCCCACACCATTACACCACTCTCAATTGACACCATTG
TACCTTAATGTACAATCGGAATGTCAAATTAACACATCAAGCTATAAATTCACATATGCACCATT
GTGTCCTTTATCGATAGGAATGTCATCTCAAATATATTAAATATCTATTTTGCCTTAATGTACAA
TAAGAATGCCACATGCCTAATACCACAAAATATAATCGGAGTATTACATATATCAAAATATTAAA
TTTACATATTGGCATCATCAT
Found at i:2821212 original size:6 final size:6
Alignment explanation
Indices: 2821201--2821233 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
2821191 TCTCCTTACT
2821201 CTTTCC CTTTCC CTTTCC CTTTCC CTTTCC CTT
1 CTTTCC CTTTCC CTTTCC CTTTCC CTTTCC CTT
2821234 ATTTTCTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (6 bp):
CTTTCC
Found at i:2829315 original size:31 final size:29
Alignment explanation
Indices: 2829265--2829329 Score: 76
Period size: 31 Copynumber: 2.2 Consensus size: 29
2829255 CTTAATTATA
** * *
2829265 AAAATTTATTTGATTCAAAATAAAAATATT
1 AAAATTTATTAAATACAAAAAAAAAAT-TT
2829295 ATAAATTTATTAAATACAAAAAAAAAATTT
1 A-AAATTTATTAAATACAAAAAAAAAATTT
2829325 AAAAT
1 AAAAT
2829330 AATTTAAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 4 0.13
30 4 0.13
31 22 0.73
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (29 bp):
AAAATTTATTAAATACAAAAAAAAAATTT
Found at i:2832338 original size:2 final size:2
Alignment explanation
Indices: 2832331--2832367 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2832321 CACAGTCATC
2832331 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2832368 CGCTTTGCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2854270 original size:30 final size:28
Alignment explanation
Indices: 2854234--2854296 Score: 90
Period size: 30 Copynumber: 2.2 Consensus size: 28
2854224 TTGTTAATTG
* *
2854234 TAAAAATTTATTTAATTTAAAATAAAAATA
1 TAAAAATTTAATTAA-ATAAAATAAAAA-A
2854264 TAAAAATTTAATTAAATAAAATAAAAAA
1 TAAAAATTTAATTAAATAAAATAAAAAA
2854292 TAAAA
1 TAAAA
2854297 GTAACGTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 6 0.19
29 11 0.35
30 14 0.45
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (28 bp):
TAAAAATTTAATTAAATAAAATAAAAAA
Found at i:2860167 original size:60 final size:60
Alignment explanation
Indices: 2860074--2860192 Score: 193
Period size: 60 Copynumber: 2.0 Consensus size: 60
2860064 CCCTCCTCAA
* *
2860074 GGTAAAACATAAGGACCTTGTGATTTTTGTTATTTAACGTTTTCACATCAAGGTAATTCT
1 GGTAAAACATAAGGACCTTCTGATTTTTGTTATTTAAAGTTTTCACATCAAGGTAATTCT
* * *
2860134 GGTAAAACATGAGGACCTTCTGTTTTTTGTTATTTAAAGTTTTCACATCATGGTAATTC
1 GGTAAAACATAAGGACCTTCTGATTTTTGTTATTTAAAGTTTTCACATCAAGGTAATTC
2860193 CGTCATCTGA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (60 bp):
GGTAAAACATAAGGACCTTCTGATTTTTGTTATTTAAAGTTTTCACATCAAGGTAATTCT
Found at i:2862417 original size:145 final size:145
Alignment explanation
Indices: 2862251--2862519 Score: 396
Period size: 145 Copynumber: 1.9 Consensus size: 145
2862241 TATTTTGACC
* * * *
2862251 AATTTAATATTCATATTCTATTCAAATTCAATTATAATATTTTATTAGAATTTAAATAATACTTA
1 AATTTAATATTCATATTCTATTCAAATTCAATTATAATATTCTATTAGAACTTAAATAAGACTCA
* * *
2862316 AATATATTTATTTAATTAGAAATAATATAAACACTTACTATA-AAACCCGACTCAATCTATATTT
66 AATACATTTATTTAATTAGAAATAATACAAACACTCACTATACAAA-CCGACTCAATCTATATTT
2862380 AATAATTGAATTAAAA
130 AATAATTGAATTAAAA
** *
2862396 AATTTAATATTCATATTCTATTCAAATTTGATTATAATATTCTATTAGAACTTAAATAAGACTCG
1 AATTTAATATTCATATTCTATTCAAATTCAATTATAATATTCTATTAGAACTTAAATAAGACTCA
* * * *
2862461 AATCCGTTTATTTAGTTAGAAATAATACAAACACTCACTATACAAACCGACTCGATCTA
66 AATACATTTATTTAATTAGAAATAATACAAACACTCACTATACAAACCGACTCAATCTA
2862520 AATTAAGTAT
Statistics
Matches: 109, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
145 106 0.97
146 3 0.03
ACGTcount: A:0.43, C:0.13, G:0.05, T:0.39
Consensus pattern (145 bp):
AATTTAATATTCATATTCTATTCAAATTCAATTATAATATTCTATTAGAACTTAAATAAGACTCA
AATACATTTATTTAATTAGAAATAATACAAACACTCACTATACAAACCGACTCAATCTATATTTA
ATAATTGAATTAAAA
Found at i:2866768 original size:2 final size:2
Alignment explanation
Indices: 2866755--2866789 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2866745 CACAACTTAC
*
2866755 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2866790 AAAAAACTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2880524 original size:21 final size:21
Alignment explanation
Indices: 2880499--2880549 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
2880489 TATATTTCTT
* *
2880499 TATCATTTTATATAATAATAC
1 TATCATTTTACATAATAACAC
*
2880520 TATCACTTTTTACATAATAACAG
1 TATCA--TTTTACATAATAACAC
2880543 TATCATT
1 TATCATT
2880550 CAAAGTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 7 0.28
23 18 0.72
ACGTcount: A:0.39, C:0.14, G:0.02, T:0.45
Consensus pattern (21 bp):
TATCATTTTACATAATAACAC
Found at i:2880546 original size:23 final size:23
Alignment explanation
Indices: 2880504--2880547 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2880494 TTCTTTATCA
* *
2880504 TTTTATATAATAATACTATCACT
1 TTTTACATAATAACACTATCACT
*
2880527 TTTTACATAATAACAGTATCA
1 TTTTACATAATAACACTATCA
2880548 TTCAAAGTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (23 bp):
TTTTACATAATAACACTATCACT
Found at i:2891711 original size:20 final size:19
Alignment explanation
Indices: 2891655--2891712 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
2891645 TTAATTAAAA
*
2891655 TTTTAAATAAATTTATTAAT
1 TTTTAAATAAATTT-TTTAT
*
2891675 TTTTAAATAAATATTTTAT
1 TTTTAAATAAATTTTTTAT
*
2891694 TTTTAAAATATATTTTTTA
1 TTTT-AAATAAATTTTTTA
2891713 ATAAATATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.24
20 25 0.76
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTAAATAAATTTTTTAT
Found at i:2891718 original size:16 final size:16
Alignment explanation
Indices: 2891673--2891722 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
2891663 AAATTTATTA
*
2891673 ATTTTTAAATAAATAT
1 ATTTTTTAATAAATAT
* *
2891689 TTTATTTTTA-AAATAT
1 ATT-TTTTAATAAATAT
2891705 ATTTTTTAATAAATAT
1 ATTTTTTAATAAATAT
2891721 AT
1 AT
2891723 AAATTCAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
15 5 0.19
16 18 0.67
17 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTTTTAATAAATAT
Found at i:2891722 original size:18 final size:19
Alignment explanation
Indices: 2891678--2891723 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
2891668 TATTAATTTT
* **
2891678 TAAATAAATATTTTATTTT
1 TAAATATATATTTTATTAA
2891697 TAAA-ATATATTTT-TTAA
1 TAAATATATATTTTATTAA
2891714 TAAATATATA
1 TAAATATATA
2891724 AATTCAATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 6 0.26
18 13 0.57
19 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TAAATATATATTTTATTAA
Found at i:2904199 original size:3 final size:3
Alignment explanation
Indices: 2904191--2904219 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2904181 TATATAGAAT
2904191 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2904220 TATAGCTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2910547 original size:2 final size:2
Alignment explanation
Indices: 2910540--2910564 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2910530 TTATGTCTTT
2910540 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2910565 GTGTGTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2910569 original size:2 final size:2
Alignment explanation
Indices: 2910564--2910588 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2910554 TATATATATA
2910564 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
2910589 AGTATTGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2914267 original size:13 final size:14
Alignment explanation
Indices: 2914239--2914271 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2914229 AATCTGTTTG
2914239 ATAAATTTACTTTT
1 ATAAATTTACTTTT
*
2914253 ATAAATTT-TTTTT
1 ATAAATTTACTTTT
2914266 ATAAAT
1 ATAAAT
2914272 AAGTTATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (14 bp):
ATAAATTTACTTTT
Found at i:2915321 original size:26 final size:25
Alignment explanation
Indices: 2915271--2915321 Score: 59
Period size: 28 Copynumber: 2.0 Consensus size: 25
2915261 TAATATAAAA
*
2915271 AATTATTAATTTTATATATCATATTT
1 AATTATTAATTTTATACAT-ATATTT
2915297 AATTATTTATATTTTATACAT-TATT
1 AATTA-TTA-ATTTTATACATATATT
2915322 CTTTTTCATC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 9 0.41
27 3 0.14
28 10 0.45
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (25 bp):
AATTATTAATTTTATACATATATTT
Found at i:2923876 original size:19 final size:17
Alignment explanation
Indices: 2923852--2923886 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
2923842 TTTGATTTTA
2923852 GAAAAATGACAAAAAAAAG
1 GAAAAA-GA-AAAAAAAAG
2923871 GAAAAAGAAAAAAAAA
1 GAAAAAGAAAAAAAAA
2923887 ACCACGAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.80, C:0.03, G:0.14, T:0.03
Consensus pattern (17 bp):
GAAAAAGAAAAAAAAAG
Done.