Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167882.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_15, 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: 22478863
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 61000 characters in sequence are not A, C, G, or T
File 15 of 106
Found at i:2454521 original size:16 final size:17
Alignment explanation
Indices: 2454491--2454522 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2454481 AAATTAGTTT
2454491 TGATAAAATTTAAATAA
1 TGATAAAATTTAAATAA
2454508 TGATAAAA-TTAAATA
1 TGATAAAATTTAAATA
2454523 TTAAAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.34
Consensus pattern (17 bp):
TGATAAAATTTAAATAA
Found at i:2454692 original size:19 final size:19
Alignment explanation
Indices: 2454648--2454702 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 19
2454638 AATTTATATA
*
2454648 TAATAAAAATTT-T-AAAT
1 TAATAAATATTTATAAAAT
* *
2454665 TATTTAATATTTATAAAAT
1 TAATAAATATTTATAAAAT
* *
2454684 TAATAAATAATTAAAAAAT
1 TAATAAATATTTATAAAAT
2454703 ATTAAATTAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
17 9 0.31
18 1 0.03
19 19 0.66
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATAAATATTTATAAAAT
Found at i:2460250 original size:43 final size:43
Alignment explanation
Indices: 2460189--2460273 Score: 170
Period size: 43 Copynumber: 2.0 Consensus size: 43
2460179 GTGGCTATAT
2460189 ATATAATTAGAACATGAACTTTTAAGAATAATTTTAGGATAAC
1 ATATAATTAGAACATGAACTTTTAAGAATAATTTTAGGATAAC
2460232 ATATAATTAGAACATGAACTTTTAAGAATAATTTTAGGATAA
1 ATATAATTAGAACATGAACTTTTAAGAATAATTTTAGGATAA
2460274 ATTCTTTTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (43 bp):
ATATAATTAGAACATGAACTTTTAAGAATAATTTTAGGATAAC
Found at i:2465139 original size:2 final size:2
Alignment explanation
Indices: 2465132--2465168 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2465122 CATTATTGTG
2465132 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2465169 GAAGAGATAT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2467921 original size:29 final size:30
Alignment explanation
Indices: 2467883--2467956 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
2467873 TAATAGGTAC
* *
2467883 AAATTAAAAGGTTAA-GGTTCATTTGGGTGT
1 AAATT-AAAGATTAAGGGTTCATTTGAGTGT
*
2467913 AAATTAAAGATTAAGGGTTTATTTGAGTGT
1 AAATTAAAGATTAAGGGTTCATTTGAGTGT
*
2467943 AAATTAAAGTTTAA
1 AAATTAAAGATTAA
2467957 AGGCTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 8 0.21
30 31 0.79
ACGTcount: A:0.39, C:0.01, G:0.22, T:0.38
Consensus pattern (30 bp):
AAATTAAAGATTAAGGGTTCATTTGAGTGT
Found at i:2468853 original size:10 final size:10
Alignment explanation
Indices: 2468838--2468900 Score: 58
Period size: 11 Copynumber: 6.3 Consensus size: 10
2468828 TGAAAGTTTT
*
2468838 AAAATTTTAA
1 AAAATTCTAA
*
2468848 AAAATTCAAA
1 AAAATTCTAA
*
2468858 AATAATTCAAA
1 AA-AATTCTAA
2468869 ACAAATTCTAA
1 A-AAATTCTAA
*
2468880 AAAATT-TTA
1 AAAATTCTAA
2468889 AAAATTC-AA
1 AAAATTCTAA
2468898 AAA
1 AAA
2468901 TTTTTGAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
9 12 0.27
10 15 0.33
11 17 0.38
12 1 0.02
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (10 bp):
AAAATTCTAA
Found at i:2469281 original size:17 final size:17
Alignment explanation
Indices: 2469258--2469305 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
2469248 AAAAATTTAG
2469258 AAATTTTTAATATTTC-
1 AAATTTTTAATATTTCT
*
2469274 ATATTTTTTAAT-TTTCT
1 A-AATTTTTAATATTTCT
2469291 AAATTTTTAATATTT
1 AAATTTTTAATATTT
2469306 AACTTTTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 14 0.52
17 13 0.48
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (17 bp):
AAATTTTTAATATTTCT
Found at i:2469313 original size:16 final size:15
Alignment explanation
Indices: 2469261--2469313 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
2469251 AATTTAGAAA
2469261 TTTTTAATATTTCATAT
1 TTTTTAATATTT-A-AT
* *
2469278 TTTTTAATTTTCTAAA
1 TTTTTAATATT-TAAT
*
2469294 TTTTTAATATTTAAC
1 TTTTTAATATTTAAT
2469309 TTTTT
1 TTTTT
2469314 GAAATTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 8 0.26
16 11 0.35
17 11 0.35
18 1 0.03
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTTAATATTTAAT
Found at i:2469320 original size:33 final size:32
Alignment explanation
Indices: 2469258--2469368 Score: 98
Period size: 34 Copynumber: 3.3 Consensus size: 32
2469248 AAAAATTTAG
* *
2469258 AAATTTTTAATATTTCATA-TTTTTTAATTTTCT
1 AAATTTTTAATATTT-A-ACTTTTTAAATTTTTT
2469291 AAATTTTTAATATTTAACTTTTTGAAATTTTTTT
1 AAATTTTTAATATTTAACTTTTT-AAA-TTTTTT
* * * *
2469325 GAATTTTTCATATTTTACATTTTAAAAATTTTTT
1 AAATTTTTAATATTTAAC-TTTT-TAAATTTTTT
*
2469359 AGATTTTTAA
1 AAATTTTTAA
2469369 AAAAAATTCA
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
31 1 0.02
32 6 0.09
33 17 0.27
34 33 0.52
35 7 0.11
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.60
Consensus pattern (32 bp):
AAATTTTTAATATTTAACTTTTTAAATTTTTT
Found at i:2473863 original size:2 final size:2
Alignment explanation
Indices: 2473858--2473900 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
2473848 ATAACAATCA
*
2473858 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2473900 A
1 A
2473901 AAAGTTAACT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2475481 original size:18 final size:18
Alignment explanation
Indices: 2475458--2475519 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 18
2475448 TAAATAATAG
2475458 AATAAAATGATAATAAAA
1 AATAAAATGATAATAAAA
*
2475476 AAT-AAA-GATAAAACTAAA
1 AATAAAATGATAATA--AAA
* *
2475494 AATAAAGATAAAAATAAAA
1 AATAAA-ATGATAATAAAA
2475513 AATAAAA
1 AATAAAA
2475520 ATAGAACTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
16 6 0.17
17 3 0.09
18 10 0.29
19 11 0.31
20 1 0.03
21 4 0.11
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.18
Consensus pattern (18 bp):
AATAAAATGATAATAAAA
Found at i:2475488 original size:12 final size:11
Alignment explanation
Indices: 2475428--2475522 Score: 54
Period size: 12 Copynumber: 8.5 Consensus size: 11
2475418 ATATATAAAT
2475428 AAATAAAATAA
1 AAATAAAATAA
* *
2475439 TTAATTAAATAA
1 -AAATAAAATAA
*
2475451 ATAATAGAAT-A
1 A-AATAAAATAA
*
2475462 AAAT--GATAA
1 AAATAAAATAA
*
2475471 TAA-AAAATAA
1 AAATAAAATAA
*
2475481 AGATAAAACTAA
1 AAATAAAA-TAA
2475493 AAATAAAGATAA
1 AAATAAA-ATAA
2475505 AAATAAAAAATAA
1 AAAT--AAAATAA
2475518 AAATA
1 AAATA
2475523 GAACTAGAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 19
0.68 0.12 0.20
Matches are distributed among these distances:
8 2 0.03
9 3 0.05
10 8 0.13
11 7 0.11
12 31 0.49
13 9 0.14
14 3 0.05
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.22
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:2475493 original size:6 final size:6
Alignment explanation
Indices: 2475473--2475522 Score: 64
Period size: 6 Copynumber: 8.2 Consensus size: 6
2475463 AATGATAATA
* * *
2475473 AAAAAT AAAGAT AAAACT AAAAAT AAAGAT AAAAAT AAAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT -AAAAAT AAAAAT
2475522 A
1 A
2475523 GAACTAGAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
6 31 0.84
7 6 0.16
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:2476824 original size:66 final size:65
Alignment explanation
Indices: 2476671--2476835 Score: 147
Period size: 66 Copynumber: 2.5 Consensus size: 65
2476661 TGAATAATTG
* * * * * * *
2476671 GGATTGAACTGTAAGTCAGAAAAATAAAATGACCTGGATTAAGCTAAGGTCAAAAATTAGTGACC
1 GGATTGAACTGTAAGTAAAAAAAATAAAATGACCTGGATTAAGCCAAGATCAAAAATGAATCACC
* * * * *
2476736 GAAATTGAACTG-CAGATAAAAAAAATAAAATGATCTGGATTGAA-CCAAGATCGAAGATGAATC
1 G-GATTGAACTGTAAG-TAAAAAAAATAAAATGACCTGGATT-AAGCCAAGATCAAAAATGAATC
2476799 ACC
63 ACC
* *
2476802 AGGATTGAACTGTAAGT-TAAAAAATAAAGTGACC
1 -GGATTGAACTGTAAGTAAAAAAAATAAAATGACC
2476836 AAGACCAAGT
Statistics
Matches: 78, Mismatches: 17, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
65 17 0.22
66 56 0.72
67 5 0.06
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.22
Consensus pattern (65 bp):
GGATTGAACTGTAAGTAAAAAAAATAAAATGACCTGGATTAAGCCAAGATCAAAAATGAATCACC
Found at i:2476978 original size:22 final size:22
Alignment explanation
Indices: 2476937--2476978 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2476927 TTTTTTTTAA
* *
2476937 AAATCATGTTTAGAAGTCTTAT
1 AAATCATGTTTAAAAATCTTAT
2476959 AAATCATGTTTAAAAATCTT
1 AAATCATGTTTAAAAATCTT
2476979 CAAAAATGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (22 bp):
AAATCATGTTTAAAAATCTTAT
Found at i:2478995 original size:21 final size:21
Alignment explanation
Indices: 2478966--2479010 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
2478956 ATGGCTAATC
2478966 TCTTCAGGACTTTCTTATCAT
1 TCTTCAGGACTTTCTTATCAT
*
2478987 TCTTTAGGACTTTCTTATCAT
1 TCTTCAGGACTTTCTTATCAT
2479008 TCT
1 TCT
2479011 CTATTGCCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.22, G:0.09, T:0.51
Consensus pattern (21 bp):
TCTTCAGGACTTTCTTATCAT
Found at i:2484882 original size:12 final size:11
Alignment explanation
Indices: 2484861--2484890 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2484851 ATTCTCTCTT
*
2484861 AATTTCTTCCC
1 AATTTCTTTCC
2484872 AATTTCTTTCC
1 AATTTCTTTCC
2484883 AATTTCTT
1 AATTTCTT
2484891 AACACAGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.20, C:0.27, G:0.00, T:0.53
Consensus pattern (11 bp):
AATTTCTTTCC
Found at i:2485026 original size:5 final size:5
Alignment explanation
Indices: 2485016--2485046 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
2485006 AACTAACATG
*
2485016 AATGC AATGC AATGC AATGC AATGT AATGC A
1 AATGC AATGC AATGC AATGC AATGC AATGC A
2485047 TGAAATACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (5 bp):
AATGC
Found at i:2488657 original size:15 final size:17
Alignment explanation
Indices: 2488622--2488659 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
2488612 TTATTTAAAC
2488622 ATATTTTTTATAAAAAT
1 ATATTTTTTATAAAAAT
2488639 ATATTTTTTA-AAATAAT
1 ATATTTTTTATAAA-AAT
2488656 ATAT
1 ATAT
2488660 GCATAACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATTTTTTATAAAAAT
Found at i:2489581 original size:3 final size:3
Alignment explanation
Indices: 2489575--2489603 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2489565 ATTAAATAAT
2489575 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
2489604 TAATAATAAT
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:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:2490633 original size:18 final size:17
Alignment explanation
Indices: 2490599--2490631 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2490589 ATTTCATTTA
2490599 TTTCCAAACAAAAAAAT
1 TTTCCAAACAAAAAAAT
2490616 TTTCCAAACAAAAAAA
1 TTTCCAAACAAAAAAA
2490632 ATAAATGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.61, C:0.18, G:0.00, T:0.21
Consensus pattern (17 bp):
TTTCCAAACAAAAAAAT
Found at i:2490738 original size:6 final size:6
Alignment explanation
Indices: 2490707--2490765 Score: 68
Period size: 6 Copynumber: 9.8 Consensus size: 6
2490697 AAAAGATAAC
* *
2490707 AAAAT- AAAAT- AAAATAA AAAATTG AAAATG AAAATA AAAATA AAAATA
1 AAAATA AAAATA AAAAT-A AAAA-TA AAAATA AAAATA AAAATA AAAATA
2490755 AAAATA AAAAT
1 AAAATA AAAAT
2490766 TTGTTCGATA
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
5 10 0.20
6 30 0.61
7 8 0.16
8 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:2491028 original size:16 final size:16
Alignment explanation
Indices: 2491003--2491035 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2490993 AAAGTAATAG
2491003 AAAATATTAAA-AAAT
1 AAAATATTAAATAAAT
2491018 AAAATTATTAAATAAAT
1 AAAA-TATTAAATAAAT
2491035 A
1 A
2491036 TTTATATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 7 0.44
17 5 0.31
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATATTAAATAAAT
Found at i:2491801 original size:12 final size:11
Alignment explanation
Indices: 2491749--2491841 Score: 60
Period size: 12 Copynumber: 7.5 Consensus size: 11
2491739 TGATCATAGG
2491749 TTTTTCTTTTTCA
1 TTTTT-TTTTT-A
*
2491762 TTTTCTTTTTTG
1 TTTT-TTTTTTA
**
2491774 TTTTTGTTTTGG
1 TTTTT-TTTTTA
*
2491786 TTTTGTTTTTA
1 TTTTTTTTTTA
2491797 TTTTTTGTTTTA
1 TTTTTT-TTTTA
2491809 TTTTATTTTTCTAA
1 TTTT-TTTTT-T-A
2491823 GTTTTTATTTTTA
1 -TTTTT-TTTTTA
2491836 TTTTTT
1 TTTTTT
2491842 AATTGTGATT
Statistics
Matches: 66, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
11 11 0.17
12 30 0.45
13 13 0.20
14 4 0.06
15 8 0.12
ACGTcount: A:0.09, C:0.04, G:0.08, T:0.80
Consensus pattern (11 bp):
TTTTTTTTTTA
Found at i:2491974 original size:13 final size:14
Alignment explanation
Indices: 2491937--2491974 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
2491927 TGATTTTATT
2491937 ATGATA-TTTTTGC
1 ATGATATTTTTTGC
*
2491950 ATGATGTTTTTTGC
1 ATGATATTTTTTGC
2491964 ATGA-ATTTTTT
1 ATGATATTTTTT
2491975 ATTTTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.21, C:0.05, G:0.16, T:0.58
Consensus pattern (14 bp):
ATGATATTTTTTGC
Found at i:2493291 original size:19 final size:20
Alignment explanation
Indices: 2493267--2493315 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2493257 ATATAAATAT
2493267 AAAATTAAATA-A-ACATGAA
1 AAAATTAAATACATACAT-AA
*
2493286 AAAATTAAATACATATATAA
1 AAAATTAAATACATACATAA
2493306 AAAATTAAAT
1 AAAATTAAAT
2493316 TTAAATAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 11 0.41
20 13 0.48
21 3 0.11
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (20 bp):
AAAATTAAATACATACATAA
Found at i:2494847 original size:22 final size:21
Alignment explanation
Indices: 2494817--2494858 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2494807 TGCATTTTTA
2494817 ATGGAAGTTTAAAAATTAGTTC
1 ATGGAAG-TTAAAAATTAGTTC
* *
2494839 ATGGCAGTTAAAAGTTAGTT
1 ATGGAAGTTAAAAATTAGTT
2494859 ACTTTCAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (21 bp):
ATGGAAGTTAAAAATTAGTTC
Found at i:2497222 original size:20 final size:20
Alignment explanation
Indices: 2497190--2497227 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2497180 AGTTCTCCTA
2497190 TTTTTCATTATAA-AAACAT
1 TTTTTCATTATAATAAACAT
*
2497209 TTTTTTATTGATAATAAAC
1 TTTTTCATT-ATAATAAAC
2497228 TTTAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 8 0.50
20 4 0.25
21 4 0.25
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.50
Consensus pattern (20 bp):
TTTTTCATTATAATAAACAT
Found at i:2498854 original size:24 final size:24
Alignment explanation
Indices: 2498827--2498875 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
2498817 AGTTCCTATA
* *
2498827 CTTAATTAAATGTATCATAAGACT
1 CTTAATCAAATCTATCATAAGACT
2498851 CTTAATCAAATCTATCATAAGACT
1 CTTAATCAAATCTATCATAAGACT
2498875 C
1 C
2498876 ATTATTCTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (24 bp):
CTTAATCAAATCTATCATAAGACT
Found at i:2505886 original size:16 final size:15
Alignment explanation
Indices: 2505819--2506010 Score: 96
Period size: 16 Copynumber: 12.7 Consensus size: 15
2505809 ATTTTAATAT
2505819 TTAA-TAATATTTAA
1 TTAATTAATATTTAA
* *
2505833 TTAATTAATAAATAATA
1 TTAATTAAT-ATTTA-A
2505850 TTAATTATAATATTTAA
1 TTAA-T-TAATATTTAA
2505867 -TAA-T-A-ATTTAA
1 TTAATTAATATTTAA
2505878 TTAATTAAT-TTTAA
1 TTAATTAATATTTAA
* *
2505892 TACTAATCAATATTAATA
1 T--TAATTAATATTTA-A
*
2505910 TTAATTAA-AATTAA
1 TTAATTAATATTTAA
*
2505924 TTAAATAATATTATAA
1 TTAATTAATATT-TAA
*
2505940 TTAAATAATATTTAA
1 TTAATTAATATTTAA
* * *
2505955 TATTATT-AGATTAATA
1 T-TAATTAATATTTA-A
**
2505971 TTAATTAATATTTTG
1 TTAATTAATATTTAA
*
2505986 TTAAATTATTATTT-A
1 TT-AATTAATATTTAA
*
2506001 TTATTTAATA
1 TTAATTAATA
2506011 ATTTTTATAA
Statistics
Matches: 135, Mismatches: 24, Indels: 38
0.69 0.12 0.19
Matches are distributed among these distances:
11 6 0.04
12 4 0.03
13 2 0.01
14 25 0.19
15 26 0.19
16 53 0.39
17 9 0.07
18 6 0.04
19 4 0.03
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (15 bp):
TTAATTAATATTTAA
Found at i:2505916 original size:10 final size:10
Alignment explanation
Indices: 2505812--2505982 Score: 95
Period size: 10 Copynumber: 16.8 Consensus size: 10
2505802 TAAAAATATT
2505812 TTAATATTTAA
1 TTAATA-TTAA
2505823 -TAATATTTAA
1 TTAATA-TTAA
*
2505833 TTAATTAATAA
1 TTAA-TATTAA
*
2505844 ATAATATTAA
1 TTAATATTAA
* *
2505854 TT-ATAATAT
1 TTAATATTAA
*
2505863 TTAATAATAA
1 TTAATATTAA
*
2505873 TTTA-ATTAA
1 TTAATATTAA
*
2505882 TTAATTTTAA
1 TTAATATTAA
*
2505892 TACTAATCAAT-A
1 T--TAAT-ATTAA
2505904 TTAATATTAA
1 TTAATATTAA
*
2505914 TTAAAATTAA
1 TTAATATTAA
2505924 TTAA-A-TAA
1 TTAATATTAA
*
2505932 TATTATAATTAA
1 T-TAAT-ATTAA
*
2505944 ATAATATTTAA
1 TTAATA-TTAA
*
2505955 -TATTATTAGA
1 TTAATATTA-A
2505965 TTAATATTAA
1 TTAATATTAA
2505975 TTAATATT
1 TTAATATT
2505983 TTGTTAAATT
Statistics
Matches: 125, Mismatches: 20, Indels: 31
0.71 0.11 0.18
Matches are distributed among these distances:
8 4 0.03
9 22 0.18
10 63 0.50
11 24 0.19
12 11 0.09
13 1 0.01
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (10 bp):
TTAATATTAA
Found at i:2505974 original size:47 final size:44
Alignment explanation
Indices: 2505813--2505983 Score: 119
Period size: 47 Copynumber: 3.8 Consensus size: 44
2505803 AAAAATATTT
* *
2505813 TAATATTTAATAATATTTAATTAATTAATAAATAATA-TTAATT--A
1 TAATATTTAATATTA-TTAATTAA--ATTAAATAATATTTAATTAAA
* *
2505857 TAATATTTAATA--A-TAATTTAATTAATTAAT-TTTAA-TACTAA
1 TAATATTTAATATTATTAATTAAATTAAATAATATTTAATTA--AA
2505898 TCAATA-TTAATATTAATTAAAATT-AATTAAATAATATTATAATTAAA
1 T-AATATTTAATATT-ATT--AATTAAATTAAATAATATT-TAATTAAA
*
2505945 TAATATTTAATATTATTAGATTAATATTAATTAATATTT
1 TAATATTTAATATTATTA-ATTAA-ATTAAATAATATTT
2505984 TGTTAAATTA
Statistics
Matches: 103, Mismatches: 5, Indels: 36
0.72 0.03 0.25
Matches are distributed among these distances:
37 1 0.01
38 12 0.12
40 6 0.06
41 8 0.08
42 5 0.05
44 14 0.14
45 4 0.04
46 19 0.18
47 29 0.28
48 3 0.03
49 2 0.02
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (44 bp):
TAATATTTAATATTATTAATTAAATTAAATAATATTTAATTAAA
Found at i:2507447 original size:15 final size:15
Alignment explanation
Indices: 2507424--2507454 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2507414 TTTAAATACA
*
2507424 AAATCATAAATTAAT
1 AAATAATAAATTAAT
2507439 AAATAATAAATTAAT
1 AAATAATAAATTAAT
2507454 A
1 A
2507455 TTTTAACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATAATAAATTAAT
Found at i:2508737 original size:18 final size:17
Alignment explanation
Indices: 2508703--2508735 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2508693 ATTTCATTTA
2508703 TTTCCAAACAAAAAAAT
1 TTTCCAAACAAAAAAAT
2508720 TTTCCAAACAAAAAAA
1 TTTCCAAACAAAAAAA
2508736 ATAAATGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.61, C:0.18, G:0.00, T:0.21
Consensus pattern (17 bp):
TTTCCAAACAAAAAAAT
Found at i:2508842 original size:6 final size:6
Alignment explanation
Indices: 2508811--2508863 Score: 56
Period size: 6 Copynumber: 8.8 Consensus size: 6
2508801 AAAAGACAAT
* *
2508811 AAAAT- AAAAT- AAAATAA AAAATTG AAAATG AAAATA AAAATA AAAATA
1 AAAATA AAAATA AAAAT-A AAAA-TA AAAATA AAAATA AAAATA AAAATA
2508859 AAAAT
1 AAAAT
2508864 TTGTTTGGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
5 10 0.23
6 24 0.56
7 8 0.19
8 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:2509128 original size:16 final size:16
Alignment explanation
Indices: 2509103--2509135 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2509093 AAAGTAATAG
2509103 AAAATATTAAA-AAAT
1 AAAATATTAAATAAAT
2509118 AAAATTATTAAATAAAT
1 AAAA-TATTAAATAAAT
2509135 A
1 A
2509136 TTTATATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 7 0.44
17 5 0.31
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATATTAAATAAAT
Found at i:2509884 original size:11 final size:11
Alignment explanation
Indices: 2509870--2509906 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
2509860 TCATTTTTCT
2509870 TTTTGTTTTTG
1 TTTTGTTTTTG
*
2509881 TTTTGGTTTTG
1 TTTTGTTTTTG
*
2509892 TTTTATTTTTG
1 TTTTGTTTTTG
2509903 TTTT
1 TTTT
2509907 ATTTATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.03, C:0.00, G:0.16, T:0.81
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:2511421 original size:20 final size:20
Alignment explanation
Indices: 2511375--2511424 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2511365 ATATAAATAT
2511375 AAAATTAAATAAACATGATA
1 AAAATTAAATAAACATGATA
* * *
2511395 AATATTAAATACATAT-ATAA
1 AAAATTAAATAAACATGAT-A
2511415 AAAATTAAAT
1 AAAATTAAAT
2511425 TTAAATAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (20 bp):
AAAATTAAATAAACATGATA
Found at i:2512956 original size:22 final size:21
Alignment explanation
Indices: 2512926--2512967 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2512916 TGCATTTTTA
2512926 ATGGAAGTTTAAAAATTAGTTC
1 ATGGAAG-TTAAAAATTAGTTC
* *
2512948 ATGGCAGTTAAAAGTTAGTT
1 ATGGAAGTTAAAAATTAGTT
2512968 ACTTTCAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (21 bp):
ATGGAAGTTAAAAATTAGTTC
Found at i:2515321 original size:20 final size:21
Alignment explanation
Indices: 2515295--2515334 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
2515285 AAAGTTCTCT
*
2515295 ATTTTTTCATT-ATAA-AAAC
1 ATTTTTTTATTGATAATAAAC
2515314 ATTTTTTTATTGATAATAAAC
1 ATTTTTTTATTGATAATAAAC
2515335 TTTAAATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 4 0.22
21 4 0.22
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (21 bp):
ATTTTTTTATTGATAATAAAC
Found at i:2516965 original size:24 final size:24
Alignment explanation
Indices: 2516938--2516986 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
2516928 AGTTCCTATA
* *
2516938 CTTAATTAAATGTATCATAAGACT
1 CTTAATCAAATCTATCATAAGACT
2516962 CTTAATCAAATCTATCATAAGACT
1 CTTAATCAAATCTATCATAAGACT
2516986 C
1 C
2516987 ATTATTCTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (24 bp):
CTTAATCAAATCTATCATAAGACT
Found at i:2524012 original size:16 final size:15
Alignment explanation
Indices: 2523961--2524136 Score: 86
Period size: 16 Copynumber: 12.0 Consensus size: 15
2523951 TCATTATTAT
* *
2523961 TTTAAGTAAATAATA
1 TTTAATTAATTAATA
2523976 -TTAATT-A-TAATA
1 TTTAATTAATTAATA
2523988 TTTAA-TAA-T-A-A
1 TTTAATTAATTAATA
2523999 TTTAATTAATTAAT-
1 TTTAATTAATTAATA
*
2524013 TTTAATACTAATCAATA
1 TTTAAT--TAATTAATA
*
2524030 TTAATATTAATTAA-A
1 TTTA-ATTAATTAATA
* *
2524045 ATTAATTAAATAATA
1 TTTAATTAATTAATA
*
2524060 TTATAATTAAATAATA
1 TT-TAATTAATTAATA
* *
2524076 TTTAATATTATT-AGA
1 TTTAAT-TAATTAATA
*
2524091 TTAATATTAATTAATA
1 TTTA-ATTAATTAATA
** *
2524107 TTTTGTTAAATTATTA
1 TTTAATT-AATTAATA
*
2524123 TTT-ATTATTTAATA
1 TTTAATTAATTAATA
2524137 ATTTTTATAA
Statistics
Matches: 124, Mismatches: 21, Indels: 33
0.70 0.12 0.19
Matches are distributed among these distances:
11 6 0.05
12 10 0.08
13 8 0.06
14 26 0.21
15 22 0.18
16 47 0.38
17 3 0.02
18 2 0.02
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (15 bp):
TTTAATTAATTAATA
Found at i:2524042 original size:10 final size:10
Alignment explanation
Indices: 2523971--2524108 Score: 81
Period size: 10 Copynumber: 13.7 Consensus size: 10
2523961 TTTAAGTAAA
2523971 TAATATTAAT
1 TAATATTAAT
* *
2523981 T-ATAATATT
1 TAATATTAAT
*
2523990 TAATAATAAT
1 TAATATTAAT
*
2524000 TTA-ATTAAT
1 TAATATTAAT
*
2524009 TAATTTTAAT
1 TAATATTAAT
*
2524019 ACTAATCAAT-AT
1 --TAAT-ATTAAT
2524031 TAATATTAAT
1 TAATATTAAT
*
2524041 TAAAATTAAT
1 TAATATTAAT
2524051 TAA-A-TAAT
1 TAATATTAAT
* *
2524059 ATTATAATTAAA
1 -TAAT-ATTAAT
2524071 TAATATTTAA-
1 TAATA-TTAAT
*
2524081 TATTATTAGAT
1 TAATATTA-AT
2524092 TAATATTAAT
1 TAATATTAAT
2524102 TAATATT
1 TAATATT
2524109 TTGTTAAATT
Statistics
Matches: 99, Mismatches: 16, Indels: 26
0.70 0.11 0.18
Matches are distributed among these distances:
8 4 0.04
9 22 0.22
10 48 0.48
11 15 0.15
12 9 0.09
13 1 0.01
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (10 bp):
TAATATTAAT
Found at i:2525575 original size:15 final size:15
Alignment explanation
Indices: 2525552--2525582 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2525542 TTTAAATACA
*
2525552 AAATCATAAATTAAT
1 AAATAATAAATTAAT
2525567 AAATAATAAATTAAT
1 AAATAATAAATTAAT
2525582 A
1 A
2525583 TTTTAACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATAATAAATTAAT
Found at i:2528874 original size:14 final size:15
Alignment explanation
Indices: 2528847--2528883 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
2528837 GAAAGGCAAG
2528847 CAAAA-TAAGCAAAA
1 CAAAAGTAAGCAAAA
*
2528861 GAAAAGTAAG-AAAA
1 CAAAAGTAAGCAAAA
2528875 CAAAAGTAA
1 CAAAAGTAA
2528884 AAACCTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.70, C:0.08, G:0.14, T:0.08
Consensus pattern (15 bp):
CAAAAGTAAGCAAAA
Found at i:2537250 original size:14 final size:15
Alignment explanation
Indices: 2537223--2537259 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
2537213 GAAAGGCAAG
2537223 CAAAA-TAAGCAAAA
1 CAAAAGTAAGCAAAA
*
2537237 GAAAAGTAAG-AAAA
1 CAAAAGTAAGCAAAA
2537251 CAAAAGTAA
1 CAAAAGTAA
2537260 AAACCTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.70, C:0.08, G:0.14, T:0.08
Consensus pattern (15 bp):
CAAAAGTAAGCAAAA
Found at i:2548006 original size:39 final size:39
Alignment explanation
Indices: 2547925--2548012 Score: 104
Period size: 39 Copynumber: 2.3 Consensus size: 39
2547915 AATGAACCCA
** * * * *
2547925 TTAGTGCAATGGGATAGAACAAAGATCGCAATAACTCTT
1 TTAGTGCAATGAAACAGAACAAAGATCACAATAACCCCT
* *
2547964 TTAGTGCAATGAAACAGAACAAAGATCATAGTAACCCCT
1 TTAGTGCAATGAAACAGAACAAAGATCACAATAACCCCT
2548003 TTAGTGCAAT
1 TTAGTGCAAT
2548013 AGGTCAGAAG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (39 bp):
TTAGTGCAATGAAACAGAACAAAGATCACAATAACCCCT
Found at i:2554089 original size:4 final size:4
Alignment explanation
Indices: 2554063--2554157 Score: 57
Period size: 4 Copynumber: 21.5 Consensus size: 4
2554053 TTGAATTTCC
2554063 TTTA TTT- TTTA TTTTA TTTTA TTTA TTTA TTTTA TTTA TATTGAA TTTA
1 TTTA TTTA TTTA -TTTA -TTTA TTTA TTTA -TTTA TTTA T-TT--A TTTA
* * **
2554112 TATAAA TTTA TCTCA TTTA CCCTA TTTA TTTA TTTA TTTA TTTA TT
1 T-T-TA TTTA T-TTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TT
2554158 CTTTCCTTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
3 3 0.04
4 42 0.58
5 22 0.30
6 4 0.05
7 2 0.03
ACGTcount: A:0.26, C:0.05, G:0.01, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:2558376 original size:19 final size:19
Alignment explanation
Indices: 2558349--2558387 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2558339 AAAATAGATG
2558349 TTTTTCATTATGA-TTTTT
1 TTTTTCATTATGACTTTTT
*
2558367 TTTTTACATTTTGACTTTTT
1 TTTTT-CATTATGACTTTTT
2558387 T
1 T
2558388 CTCTTGTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 7 0.39
20 6 0.33
ACGTcount: A:0.15, C:0.08, G:0.05, T:0.72
Consensus pattern (19 bp):
TTTTTCATTATGACTTTTT
Found at i:2558548 original size:15 final size:16
Alignment explanation
Indices: 2558517--2558551 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2558507 CAATGAATTG
2558517 AATAAATAAATATTCA
1 AATAAATAAATATTCA
*
2558533 AATAAATAGA-ATTCA
1 AATAAATAAATATTCA
2558548 AATA
1 AATA
2558552 TCGAGCAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.63, C:0.06, G:0.03, T:0.29
Consensus pattern (16 bp):
AATAAATAAATATTCA
Found at i:2561170 original size:63 final size:63
Alignment explanation
Indices: 2561103--2561245 Score: 164
Period size: 62 Copynumber: 2.3 Consensus size: 63
2561093 TTTTTTGGTA
* * *
2561103 AAAAATGCTTTAAATAATACTTTTCAATTTTTTAAAAGATATTATTTAAGGCATTTTTTTACC
1 AAAAACGCTTTAAATAATAATCTTCAATTTTTTAAAAGATATTATTTAAGGCATTTTTTTACC
* * ** ** *
2561166 AAAAACG-TCTTAAATAA-AATCTTCACTTTTTTTAACTATATTATTTAAGGTGTTTTTTTACT
1 AAAAACGCT-TTAAATAATAATCTTCAATTTTTTAAAAGATATTATTTAAGGCATTTTTTTACC
*
2561228 AAAAACACTTTAAATAAT
1 AAAAACGCTTTAAATAAT
2561246 CCCTTTAATT
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
62 51 0.77
63 15 0.23
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (63 bp):
AAAAACGCTTTAAATAATAATCTTCAATTTTTTAAAAGATATTATTTAAGGCATTTTTTTACC
Found at i:2561449 original size:60 final size:60
Alignment explanation
Indices: 2561385--2561501 Score: 141
Period size: 61 Copynumber: 1.9 Consensus size: 60
2561375 TTTAGGAAGA
* *
2561385 TTATTTAATAAG-TTTTTAGTCAAAAATACCTTAAATAATAC-CTTTCAATT-TTTATACTAT
1 TTATTTAAGAAGTTTTTTA-TCAAAAATACCATAAATAAT-CTCTTTC-ATTATTTATACTAT
* *
2561445 TTATTTAAGACGTTTTTTTATTAAAAATACCATAAATAATCTCTTTCATTATTTATA
1 TTATTTAAGAAG-TTTTTTATCAAAAATACCATAAATAATCTCTTTCATTATTTATA
2561502 AGATTTAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
60 14 0.29
61 29 0.59
62 6 0.12
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.48
Consensus pattern (60 bp):
TTATTTAAGAAGTTTTTTATCAAAAATACCATAAATAATCTCTTTCATTATTTATACTAT
Found at i:2561937 original size:42 final size:43
Alignment explanation
Indices: 2561855--2561937 Score: 98
Period size: 41 Copynumber: 2.0 Consensus size: 43
2561845 ACATAATTTT
* *
2561855 TTTTCAAAATCTTAAAATATGATAAAAAAATTATGATTTTTGA
1 TTTTAAAAATCTTAAAATATGATAAAAAAATTATCATTTTTGA
* * *
2561898 TTTTAAAAAT-TT-AAATATTATTAAAAATTTATCACTTTTT
1 TTTTAAAAATCTTAAAATATGATAAAAAAATTATCA-TTTTT
2561938 TTTAAATCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
41 18 0.53
42 7 0.21
43 9 0.26
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.47
Consensus pattern (43 bp):
TTTTAAAAATCTTAAAATATGATAAAAAAATTATCATTTTTGA
Found at i:2562667 original size:2 final size:2
Alignment explanation
Indices: 2562660--2562690 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2562650 TTTGTAAGAT
2562660 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2562691 TAACACAATT
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2573918 original size:14 final size:14
Alignment explanation
Indices: 2573862--2573922 Score: 53
Period size: 14 Copynumber: 4.7 Consensus size: 14
2573852 TAATTGCAAG
2573862 TTTAATTTTATACA
1 TTTAATTTTATACA
*
2573876 -TT--TTTTATGCA
1 TTTAATTTTATACA
*
2573887 TAT-ATTTT-TA-A
1 TTTAATTTTATACA
2573898 GTTTAATTTTATACA
1 -TTTAATTTTATACA
2573913 TTTAATTTTA
1 TTTAATTTTA
2573923 AATATATTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
11 9 0.24
12 4 0.11
13 11 0.30
14 12 0.32
15 1 0.03
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (14 bp):
TTTAATTTTATACA
Found at i:2575280 original size:3 final size:3
Alignment explanation
Indices: 2575272--2575304 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2575262 TTAATTGCCT
2575272 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2575305 AAGGAAAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2579591 original size:28 final size:28
Alignment explanation
Indices: 2579551--2579606 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
2579541 TGGCAATATA
* *
2579551 ATGAAAAATTTTGTTGATATGGTAATTT
1 ATGAAAAAGTTTGCTGATATGGTAATTT
2579579 ATGAAAAAGTTTGCTGATATGGTAATTT
1 ATGAAAAAGTTTGCTGATATGGTAATTT
2579607 CCAATGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.36, C:0.02, G:0.20, T:0.43
Consensus pattern (28 bp):
ATGAAAAAGTTTGCTGATATGGTAATTT
Found at i:2579873 original size:111 final size:111
Alignment explanation
Indices: 2579733--2579936 Score: 293
Period size: 111 Copynumber: 1.8 Consensus size: 111
2579723 TCTACCACCC
* * * *
2579733 AGAAATTTCATCCCATATCACCCTTATCCATCCTAC-CTACTTTATTACCCCACCACAAATAACG
1 AGAAATTTCATCCCATATCACCCCTATCCAACCTACTC-ACCTTATTACCCCACCACAAATAACA
2579797 TTCTCTAAGGTCCATACCCATATCAATCGGTATCAAATCAAAAACCT
65 TTCTCTAAGGTCCATACCCATATCAATCGGTATCAAATCAAAAACCT
* * *
2579844 AGAAATTTCATCCCATATCACCCCTATCCAACCTACTCGCCTTATTACCCCACCATAAATAATAT
1 AGAAATTTCATCCCATATCACCCCTATCCAACCTACTCACCTTATTACCCCACCACAAATAACAT
* * **
2579909 TTTTTAAGGTTTATACCCATATCAATCG
66 TCTCTAAGGTCCATACCCATATCAATCG
2579937 ATAACACCAC
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
111 80 0.99
112 1 0.01
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.30
Consensus pattern (111 bp):
AGAAATTTCATCCCATATCACCCCTATCCAACCTACTCACCTTATTACCCCACCACAAATAACAT
TCTCTAAGGTCCATACCCATATCAATCGGTATCAAATCAAAAACCT
Found at i:2585804 original size:7 final size:7
Alignment explanation
Indices: 2585786--2585877 Score: 55
Period size: 7 Copynumber: 12.9 Consensus size: 7
2585776 TGAAGAGGGT
2585786 TAAAAAA
1 TAAAAAA
2585793 TTAAAAAA
1 -TAAAAAA
*
2585801 TAAATACA
1 TAAA-AAA
2585809 -AAAAAA
1 TAAAAAA
2585815 TAAAAAA
1 TAAAAAA
2585822 TAAAAAA
1 TAAAAAA
*
2585829 CAATAAACA
1 TAA-AAA-A
2585838 -AAAAAA
1 TAAAAAA
** *
2585844 CCAACAA
1 TAAAAAA
*
2585851 CAAACAAA
1 TAAA-AAA
*
2585859 AAAAAAA
1 TAAAAAA
2585866 T-AAAAA
1 TAAAAAA
2585872 TAAAAA
1 TAAAAA
2585878 GAAAAAGCTC
Statistics
Matches: 68, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
6 9 0.13
7 39 0.57
8 19 0.28
9 1 0.01
ACGTcount: A:0.80, C:0.09, G:0.00, T:0.11
Consensus pattern (7 bp):
TAAAAAA
Found at i:2585831 original size:22 final size:21
Alignment explanation
Indices: 2585795--2585871 Score: 75
Period size: 22 Copynumber: 3.6 Consensus size: 21
2585785 TTAAAAAATT
*
2585795 AAAAAAT-AAATACAAAAAAA
1 AAAAAATAAAAAACAAAAAAA
*
2585815 TAAAAAATAAAAAACAATAAACA
1 -AAAAAATAAAAAACAA-AAAAA
** *
2585838 AAAAAACCAACAACAAACAAAA
1 AAAAAATAAAAAACAAA-AAAA
2585860 AAAAAATAAAAA
1 AAAAAATAAAAA
2585872 TAAAAAGAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
21 8 0.18
22 32 0.73
23 4 0.09
ACGTcount: A:0.82, C:0.10, G:0.00, T:0.08
Consensus pattern (21 bp):
AAAAAATAAAAAACAAAAAAA
Found at i:2589806 original size:21 final size:21
Alignment explanation
Indices: 2589776--2589828 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
2589766 TAATGATGAA
*
2589776 GCTTCTTCAAATGAACAAATG
1 GCTTTTTCAAATGAACAAATG
*
2589797 GTTTTTTCAAATGAACAAATG
1 GCTTTTTCAAATGAACAAATG
2589818 GCTTTTTCAAA
1 GCTTTTTCAAA
2589829 CTATGTTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (21 bp):
GCTTTTTCAAATGAACAAATG
Found at i:2594091 original size:18 final size:18
Alignment explanation
Indices: 2594058--2594093 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2594048 GATAAATGCA
*
2594058 AAAAGAAAAGAAAAAAAT
1 AAAAGAAAACAAAAAAAT
*
2594076 AAAAGAAAACATAAAAAT
1 AAAAGAAAACAAAAAAAT
2594094 CAAGAAGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.81, C:0.03, G:0.08, T:0.08
Consensus pattern (18 bp):
AAAAGAAAACAAAAAAAT
Found at i:2606366 original size:16 final size:16
Alignment explanation
Indices: 2606347--2606377 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2606337 AAATATAAAT
2606347 GAAAAATGAAAAAAAG
1 GAAAAATGAAAAAAAG
*
2606363 GAAAAATTAAAAAAA
1 GAAAAATGAAAAAAA
2606378 TCCAAGAAAA
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:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (16 bp):
GAAAAATGAAAAAAAG
Found at i:2606369 original size:23 final size:23
Alignment explanation
Indices: 2606325--2606375 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
2606315 TAAGGATAAC
* *
2606325 AAAAATGAAAGAAAATATAAATG
1 AAAAATGAAAGAAAAGAAAAATG
*
2606348 AAAAATGAAA-AAAAGGAAAAATT
1 AAAAATGAAAGAAAA-GAAAAATG
2606371 AAAAA
1 AAAAA
2606376 AATCCAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.14
Consensus pattern (23 bp):
AAAAATGAAAGAAAAGAAAAATG
Found at i:2607075 original size:46 final size:44
Alignment explanation
Indices: 2607025--2607394 Score: 192
Period size: 46 Copynumber: 8.0 Consensus size: 44
2607015 TGAGATTTTT
* *
2607025 AAAGTCATTGAAACCTTGTTTAAAAGAGTTTTCAAATTTATTTTCA
1 AAAGTCATTG-AGCCTTGCTTAAAAGAGTTTT-AAATTTATTTTCA
* * *
2607071 AAAGTTATTGAGCCTTTGCTTAAAAAAGCTTTTAAATATATTTTCA
1 AAAGTCATTGAGCC-TTGCTTAAAAGAG-TTTTAAATTTATTTTCA
* ** * ** * *
2607117 AAAATCATTTTGCTTTTGCTTAACGGAGCTTTTAAATTTCTCTTCA
1 AAAGTCATTGAGC-CTTGCTTAAAAGAG-TTTTAAATTTATTTTCA
* *
2607163 AAAGTCATTGAGCCTTTACTTAAAATAGTTTTTAAATTTATTTTCA
1 AAAGTCATTGAGCC-TTGCTTAAAAGAG-TTTTAAATTTATTTTCA
** ** * *
2607209 AATTTGGTTAAGCCTTTGCTTAAAAGAGTTTTTAAATTTATTTTCC
1 AAAGTCATTGAGCC-TTGCTTAAAAGAG-TTTTAAATTTATTTTCA
* ** * * * * * *
2607255 AAATTTGTTAAGCCTTTACTTAAATGTGTTTTTAAATTTACTTTAA
1 AAAGTCATTGAGCC-TTGCTTAAAAGAG-TTTTAAATTTATTTTCA
* ** * *
2607301 AAAATTGTTAAGTCTTTGCTT-AAAGAAGTTTTTAAATTTACTTTT-A
1 AAAGTCATTGAG-CCTTGCTTAAAAG-AG-TTTTAAATTTA-TTTTCA
*
2607347 AAAGT--TGTGCAGCCTTTAC-TAAAAGGAGTTTTTAAATTTATTTTCA
1 AAAGTCAT-TG-AGCC-TTGCTTAAAA-GAG-TTTTAAATTTATTTTCA
2607393 AA
1 AA
2607395 TGGTCAAGTC
Statistics
Matches: 258, Mismatches: 53, Indels: 26
0.77 0.16 0.08
Matches are distributed among these distances:
44 1 0.00
45 13 0.05
46 235 0.91
47 9 0.03
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (44 bp):
AAAGTCATTGAGCCTTGCTTAAAAGAGTTTTAAATTTATTTTCA
Found at i:2607227 original size:92 final size:91
Alignment explanation
Indices: 2607044--2607394 Score: 350
Period size: 92 Copynumber: 3.8 Consensus size: 91
2607034 GAAACCTTGT
* * * * * *
2607044 TTAAAAGAGTTTTCAAATTTATTTTCAAAAGTTATTGAGCCTTTGCTTAAAAAAGCTTTTAAATA
1 TTAAAGGAGTTTTTAAATTTATTTTCAAAAGTTATTGAGCCTTTACTTAAAATAGTTTTTAAATT
** ** *
2607109 TATTTTCAAAAATCATTTTGCTTTTGC
66 TATTTTC-AAAATTGTTAAGCCTTTGC
* * * * *
2607136 TTAACGGAGCTTTTAAATTTCTCTTCAAAAGTCATTGAGCCTTTACTTAAAATAGTTTTTAAATT
1 TTAAAGGAGTTTTTAAATTTATTTTCAAAAGTTATTGAGCCTTTACTTAAAATAGTTTTTAAATT
*
2607201 TATTTTCAAATTTGGTTAAGCCTTTGC
66 TATTTTCAAAATT-GTTAAGCCTTTGC
* * * * * *
2607228 TTAAAAGAGTTTTTAAATTTATTTTCCAAATTTGTTAAGCCTTTACTT-AAATGTGTTTTTAAAT
1 TTAAAGGAGTTTTTAAATTTATTTTCAAAAGTTATTGAGCCTTTACTTAAAAT-AGTTTTTAAAT
** *
2607292 TTACTTTAAAAAATTGTTAAGTCTTTGC
65 TTA-TTTTCAAAATTGTTAAGCCTTTGC
* * *
2607320 TTAAAGAAGTTTTTAAATTTACTTTT-AAAAGTT-GTGCAGCCTTTAC-TAAAAGGAGTTTTTAA
1 TTAAAGGAGTTTTTAAATTTA-TTTTCAAAAGTTATTG-AGCCTTTACTTAAAA-TAGTTTTTAA
2607382 ATTTATTTTCAAA
63 ATTTATTTTCAAA
2607395 TGGTCAAGTC
Statistics
Matches: 210, Mismatches: 42, Indels: 15
0.79 0.16 0.06
Matches are distributed among these distances:
91 16 0.08
92 182 0.87
93 12 0.06
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.46
Consensus pattern (91 bp):
TTAAAGGAGTTTTTAAATTTATTTTCAAAAGTTATTGAGCCTTTACTTAAAATAGTTTTTAAATT
TATTTTCAAAATTGTTAAGCCTTTGC
Found at i:2607277 original size:138 final size:136
Alignment explanation
Indices: 2607044--2607395 Score: 341
Period size: 138 Copynumber: 2.6 Consensus size: 136
2607034 GAAACCTTGT
* * * * * *
2607044 TTAAAAGAGTTTTCAAATTTATTTTCAAAAGTTATTGAGCCTTTGCTTAAAAAAGCTTTTAAATA
1 TTAAAA-AGTTTTTAAATTTATTTTC-AAAGTTGTTAAGCCTTTGCTTAAAAGAGTTTTTAAATT
* * ** * * * * * *
2607109 TATTTTCAAAAATCATTTTGCTTTTGCTTAACGGAGCTTTTAAATTT-CTCTTCAAAAGTCATTG
64 TATTTTCCAAATTCATTAAGCCTTTACTTAAAGGAGCTTTTAAATTTACT-TTAAAAAATCATTA
2607173 AGCCTTTAC
128 AGCCTTTAC
*
2607182 TTAAAATAGTTTTTAAATTTATTTTCAAATTTGGTTAAGCCTTTGCTTAAAAGAGTTTTTAAATT
1 TTAAAA-AGTTTTTAAATTTATTTTCAAAGTT-GTTAAGCCTTTGCTTAAAAGAGTTTTTAAATT
** * * * **
2607247 TATTTTCCAAATTTGTTAAGCCTTTACTTAAATGTGTTTTTAAATTTACTTTAAAAAATTGTTAA
64 TATTTTCCAAATTCATTAAGCCTTTACTTAAAGGAGCTTTTAAATTTACTTTAAAAAATCATTAA
* *
2607312 GTCTTTGC
129 GCCTTTAC
* ** *
2607320 TTAAAGAAGTTTTTAAATTTACTTTTAAAAGTTGTGCAGCCTTTAC-TAAAAGGAGTTTTTAAAT
1 TTAAA-AAGTTTTTAAATTTA-TTTTCAAAGTTGTTAAGCCTTTGCTTAAAA-GAGTTTTTAAAT
2607384 TTATTTT-CAAAT
63 TTATTTTCCAAAT
2607396 GGTCAAGTCC
Statistics
Matches: 177, Mismatches: 32, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
137 15 0.08
138 150 0.85
139 12 0.07
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.46
Consensus pattern (136 bp):
TTAAAAAGTTTTTAAATTTATTTTCAAAGTTGTTAAGCCTTTGCTTAAAAGAGTTTTTAAATTTA
TTTTCCAAATTCATTAAGCCTTTACTTAAAGGAGCTTTTAAATTTACTTTAAAAAATCATTAAGC
CTTTAC
Found at i:2608270 original size:16 final size:16
Alignment explanation
Indices: 2608249--2608279 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2608239 CTATCATATC
2608249 CATTATTATTTATTAT
1 CATTATTATTTATTAT
*
2608265 CATTATTTTTTATTA
1 CATTATTATTTATTA
2608280 GGAAATTAAG
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:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (16 bp):
CATTATTATTTATTAT
Found at i:2612508 original size:13 final size:12
Alignment explanation
Indices: 2612490--2612524 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
2612480 TTTTTTTTTT
2612490 ATAAAATAATTTA
1 ATAAAA-AATTTA
*
2612503 ATAAAAATTTTA
1 ATAAAAAATTTA
2612515 ATAAAAAATT
1 ATAAAAAATT
2612525 AAAATTGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
ATAAAAAATTTA
Found at i:2617532 original size:48 final size:48
Alignment explanation
Indices: 2617422--2617606 Score: 198
Period size: 49 Copynumber: 3.8 Consensus size: 48
2617412 GCTAAACAAC
* * *
2617422 TAATGAGAGTGTTTCTCTAAAAAATAACAAAA--ATTAAAGGGAATAGG
1 TAATG-GAGTGTTTCCCTTAAAAATAACAAAACTATTAAAAGGAATAGG
*
2617469 TAATGGTAGTGTTTCCCTGAAAAATAGA-AAAACTATTAAAAGGAATAGG
1 TAATGG-AGTGTTTCCCTTAAAAATA-ACAAAACTATTAAAAGGAATAGG
* * * *
2617518 TAAAGGAGTGTTTCCCTTAAAAAT-ACAAAAATTATGAAAAAGAATAGG
1 TAATGGAGTGTTTCCCTTAAAAATAAC-AAAACTATTAAAAGGAATAGG
* * *
2617566 TAATGAGAATGTTTCCCTTAAAAATAAGAAAACCATTAAAA
1 TAATG-GAGTGTTTCCCTTAAAAATAACAAAACTATTAAAA
2617607 TAAATAGATA
Statistics
Matches: 116, Mismatches: 14, Indels: 14
0.81 0.10 0.10
Matches are distributed among these distances:
46 2 0.02
47 26 0.22
48 40 0.34
49 47 0.41
50 1 0.01
ACGTcount: A:0.49, C:0.09, G:0.17, T:0.26
Consensus pattern (48 bp):
TAATGGAGTGTTTCCCTTAAAAATAACAAAACTATTAAAAGGAATAGG
Found at i:2617579 original size:97 final size:95
Alignment explanation
Indices: 2617428--2617606 Score: 229
Period size: 97 Copynumber: 1.9 Consensus size: 95
2617418 CAACTAATGA
* ** *
2617428 GAGTGTTTCTCTAAAAAATAACAAAAATTAAAGGGAATAGGTAATGGTAGTGTTTCCCTGAAAAA
1 GAGTGTTTCCCTAAAAAATAACAAAAATTAAAAAGAATAGGTAATGGTAATGTTTCCCTGAAAAA
*
2617493 T-AGAAAAACTATTAAAAGGAATAGGTAAAG
66 TAAG-AAAACCATTAAAAGGAATAGGTAAAG
* *
2617523 GAGTGTTTCCCTTAAAAAT-ACAAAAATTATGAAAAAGAATAGGTAATGAG-AATGTTTCCCTTA
1 GAGTGTTTCCCTAAAAAATAACAAAAA-T-T-AAAAAGAATAGGTAATG-GTAATGTTTCCCTGA
2617586 AAAATAAGAAAACCATTAAAA
62 AAAATAAGAAAACCATTAAAA
2617607 TAAATAGATA
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
94 7 0.10
95 18 0.25
96 1 0.01
97 43 0.60
98 3 0.04
ACGTcount: A:0.49, C:0.09, G:0.17, T:0.26
Consensus pattern (95 bp):
GAGTGTTTCCCTAAAAAATAACAAAAATTAAAAAGAATAGGTAATGGTAATGTTTCCCTGAAAAA
TAAGAAAACCATTAAAAGGAATAGGTAAAG
Found at i:2639909 original size:12 final size:12
Alignment explanation
Indices: 2639876--2639910 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2639866 TTCTAACGTC
2639876 TTTTAGTTTTAT
1 TTTTAGTTTTAT
*
2639888 TTTTAATTTTAT
1 TTTTAGTTTTAT
*
2639900 TTTTTGTTTTA
1 TTTTAGTTTTA
2639911 GGAGATTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (12 bp):
TTTTAGTTTTAT
Found at i:2639989 original size:21 final size:20
Alignment explanation
Indices: 2639945--2640002 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 20
2639935 AAATTCTAGC
2639945 TTTGTTAATTTTTTAAAGAATTT
1 TTTGTT-ATTTTTT-AAG-ATTT
2639968 TTTGTTATTTTTTAAG-TTT
1 TTTGTTATTTTTTAAGATTT
2639987 TTTGGTTTATTTTTTA
1 TTT-G-TTATTTTTTA
2640003 TGTAAGTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.18
20 1 0.03
21 13 0.39
22 7 0.21
23 6 0.18
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (20 bp):
TTTGTTATTTTTTAAGATTT
Found at i:2643805 original size:17 final size:18
Alignment explanation
Indices: 2643775--2643834 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 18
2643765 TGTAAATGAC
* *
2643775 TCAAGATTCTCAAAGGTT
1 TCAAGATTCACAAAGATT
2643793 TCAA-ATTCACAAAGATT
1 TCAAGATTCACAAAGATT
* * *
2643810 TCATGTTTCACAGAGA-T
1 TCAAGATTCACAAAGATT
2643827 TCAAGATT
1 TCAAGATT
2643835 TGCAAGATCA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
17 21 0.62
18 13 0.38
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (18 bp):
TCAAGATTCACAAAGATT
Found at i:2644176 original size:34 final size:34
Alignment explanation
Indices: 2644121--2644252 Score: 124
Period size: 34 Copynumber: 3.9 Consensus size: 34
2644111 AAGGTTCCAA
* * * *
2644121 ATTCACAAGAATTTCATATTCACAACAATCCAAAG
1 ATTCATAAGAA-TTCAAATTCACAAGAATTCAAAG
*
2644156 ATTCATAAGAATTCAAATTCATAAGAATTTTC-AA-
1 ATTCATAAGAATTCAAATTCACAAGAA--TTCAAAG
*
2644190 ATTCATAAGAATTCAAATTCACAAGACTTCAAAG
1 ATTCATAAGAATTCAAATTCACAAGAATTCAAAG
* * * **
2644224 ATTCGTAAGGATTTAGTTTCACAAGAATT
1 ATTCATAAGAATTCAAATTCACAAGAATT
2644253 TTAGATTCGT
Statistics
Matches: 80, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
32 3 0.04
33 2 0.03
34 61 0.76
35 12 0.15
36 2 0.03
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (34 bp):
ATTCATAAGAATTCAAATTCACAAGAATTCAAAG
Found at i:2644177 original size:16 final size:16
Alignment explanation
Indices: 2644118--2644222 Score: 102
Period size: 16 Copynumber: 6.2 Consensus size: 16
2644108 ACAAAGGTTC
2644118 CAAATTCACAAGAATTT
1 CAAATTCACAAGAA-TT
* * *
2644135 CATATTCACAACAATC
1 CAAATTCACAAGAATT
*
2644151 CAAAGATTCATAAGAATT
1 C-AA-ATTCACAAGAATT
*
2644169 CAAATTCATAAGAATTTT
1 CAAATTCACAAGAA--TT
*
2644187 CAAATTCATAAGAATT
1 CAAATTCACAAGAATT
*
2644203 CAAATTCACAAGACTT
1 CAAATTCACAAGAATT
2644219 CAAA
1 CAAA
2644223 GATTCGTAAG
Statistics
Matches: 75, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
16 33 0.44
17 15 0.20
18 27 0.36
ACGTcount: A:0.48, C:0.18, G:0.06, T:0.29
Consensus pattern (16 bp):
CAAATTCACAAGAATT
Found at i:2644250 original size:68 final size:69
Alignment explanation
Indices: 2644118--2644254 Score: 168
Period size: 68 Copynumber: 2.0 Consensus size: 69
2644108 ACAAAGGTTC
* *
2644118 CAAATTCACAAGAATTTCATATTCACAACAATCCAAAGATTCATAAGAATTCAAATTCATAAGAA
1 CAAATTCACAAGAATTTCAAATTCACAACAATCCAAAGATTCATAAGAATTCAAATTCACAAGAA
2644183 TTTT
66 TTTT
* * * * * * * **
2644187 CAAATTCATAAGAA-TTCAAATTCACAAGACTTCAAAGATTCGTAAGGATTTAGTTTCACAAGAA
1 CAAATTCACAAGAATTTCAAATTCACAACAATCCAAAGATTCATAAGAATTCAAATTCACAAGAA
2644251 TTTT
66 TTTT
2644255 AGATTCGTAA
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
68 44 0.77
69 13 0.23
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (69 bp):
CAAATTCACAAGAATTTCAAATTCACAACAATCCAAAGATTCATAAGAATTCAAATTCACAAGAA
TTTT
Found at i:2644289 original size:17 final size:17
Alignment explanation
Indices: 2644222--2644307 Score: 77
Period size: 17 Copynumber: 5.1 Consensus size: 17
2644212 AAGACTTCAA
*
2644222 AGATTCGTAAGGA-TTT
1 AGATTCGTAAGAATTTT
* **
2644238 AGTTTCACAAGAATTTT
1 AGATTCGTAAGAATTTT
* *
2644255 AGATTCGTAAAAACTTT
1 AGATTCGTAAGAATTTT
* *
2644272 AGGTTCGTAAGAGTTTT
1 AGATTCGTAAGAATTTT
2644289 AGATTC-TCAAGAATTTT
1 AGATTCGT-AAGAATTTT
2644306 AG
1 AG
2644308 GTTTGCAAGA
Statistics
Matches: 53, Mismatches: 15, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
16 10 0.19
17 43 0.81
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (17 bp):
AGATTCGTAAGAATTTT
Found at i:2644316 original size:17 final size:17
Alignment explanation
Indices: 2644222--2644318 Score: 70
Period size: 17 Copynumber: 5.8 Consensus size: 17
2644212 AAGACTTCAA
* *
2644222 AGATTCGTAAGGA-TTT
1 AGATTCGCAAGAATTTT
* *
2644238 AGTTTCACAAGAATTTT
1 AGATTCGCAAGAATTTT
* * *
2644255 AGATTCGTAAAAACTTT
1 AGATTCGCAAGAATTTT
* * *
2644272 AGGTTCGTAAGAGTTTT
1 AGATTCGCAAGAATTTT
*
2644289 AGATTCTCAAGAATTTT
1 AGATTCGCAAGAATTTT
* *
2644306 AGGTTTGCAAGAA
1 AGATTCGCAAGAA
2644319 CTTTCATCAT
Statistics
Matches: 60, Mismatches: 20, Indels: 1
0.74 0.25 0.01
Matches are distributed among these distances:
16 9 0.15
17 51 0.85
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (17 bp):
AGATTCGCAAGAATTTT
Found at i:2644321 original size:51 final size:50
Alignment explanation
Indices: 2644225--2644322 Score: 124
Period size: 51 Copynumber: 1.9 Consensus size: 50
2644215 ACTTCAAAGA
* *
2644225 TTCGTAAGGATTTAGTTTCACAAGAATTTTAGATTCGTAAAAACTTTAGG
1 TTCGTAAGGATTTAGATTCACAAGAATTTTAGATTCGCAAAAACTTTAGG
* * * * *
2644275 TTCGTAAGAGTTTTAGATTCTCAAGAATTTTAGGTTTGCAAGAACTTT
1 TTCGTAAG-GATTTAGATTCACAAGAATTTTAGATTCGCAAAAACTTT
2644323 CATCATTGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
50 8 0.20
51 32 0.80
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (50 bp):
TTCGTAAGGATTTAGATTCACAAGAATTTTAGATTCGCAAAAACTTTAGG
Found at i:2644468 original size:23 final size:22
Alignment explanation
Indices: 2644441--2644592 Score: 67
Period size: 22 Copynumber: 6.8 Consensus size: 22
2644431 CCAGAATTCA
2644441 AAGATTCTCATTCAAAAATTTT
1 AAGATTCTCATTCAAAAATTTT
** * *
2644463 AGAGATTAACATTC-AAAAGTTA
1 A-AGATTCTCATTCAAAAATTTT
* * **
2644485 AAGATTTTTATTCAAAAAACTT
1 AAGATTCTCATTCAAAAATTTT
* **
2644507 AGAGATTCACA-TCGAAAGTTTTT
1 A-AGATTCTCATTC-AAAAATTTT
* * * *
2644530 AAAATTCACATTAAAAAACTTT
1 AAGATTCTCATTCAAAAATTTT
* * *
2644552 AACATT-TCATAACAAAAATTTCA
1 AAGATTCTCAT-TCAAAAATTT-T
*
2644575 AAGATTCTCATCCAAAAA
1 AAGATTCTCATTCAAAAA
2644593 ATTTCAAGGT
Statistics
Matches: 92, Mismatches: 30, Indels: 15
0.67 0.22 0.11
Matches are distributed among these distances:
21 12 0.13
22 42 0.46
23 34 0.37
24 4 0.04
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.33
Consensus pattern (22 bp):
AAGATTCTCATTCAAAAATTTT
Found at i:2644488 original size:44 final size:43
Alignment explanation
Indices: 2644440--2644526 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 43
2644430 TCCAGAATTC
**
2644440 AAAGATTCTCATTCAAAAATTTTAGAGATTAACATTCAAAAGTT
1 AAAGATTCTCATTCAAAAAACTTAGAGATTAACA-TCAAAAGTT
* * * *
2644484 AAAGATTTTTATTCAAAAAACTTAGAGATTCACATCGAAAGTT
1 AAAGATTCTCATTCAAAAAACTTAGAGATTAACATCAAAAGTT
2644527 TTTAAAATTC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 8 0.22
44 29 0.78
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.33
Consensus pattern (43 bp):
AAAGATTCTCATTCAAAAAACTTAGAGATTAACATCAAAAGTT
Found at i:2644618 original size:22 final size:23
Alignment explanation
Indices: 2644564--2644631 Score: 93
Period size: 24 Copynumber: 3.0 Consensus size: 23
2644554 CATTTCATAA
*
2644564 CAAAAATTTCAAAGATTCTCATC
1 CAAAAATTTCAAAGATTCACATC
* *
2644587 CAAAAAATTTCAAGGTTTCACATC
1 C-AAAAATTTCAAAGATTCACATC
2644611 C-AAAATTTCAAAGATTCACAT
1 CAAAAATTTCAAAGATTCACAT
2644632 TTGAAAAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
22 18 0.46
23 1 0.03
24 20 0.51
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.29
Consensus pattern (23 bp):
CAAAAATTTCAAAGATTCACATC
Found at i:2644673 original size:22 final size:22
Alignment explanation
Indices: 2644566--2644674 Score: 71
Period size: 22 Copynumber: 4.8 Consensus size: 22
2644556 TTTCATAACA
*
2644566 AAAATTTCAAAGATT-CTCATCC
1 AAAATTTCAAGGATTCCT-ATCC
*
2644588 AAAAAATTTCAAGGTTTCAC-ATCC
1 --AAAATTTCAAGGATTC-CTATCC
* * **
2644612 AAAATTTCAAAGATTCACATTTGA
1 AAAATTTCAAGGATTC-C-TATCC
*
2644636 AAAATTT-TAGGAATTCCTATCC
1 AAAATTTCAAGG-ATTCCTATCC
2644658 AAAATTTCAAGGATTCC
1 AAAATTTCAAGGATTCC
2644675 CCTTTGAAAA
Statistics
Matches: 66, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
22 30 0.45
23 6 0.09
24 29 0.44
26 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.32
Consensus pattern (22 bp):
AAAATTTCAAGGATTCCTATCC
Found at i:2644712 original size:46 final size:46
Alignment explanation
Indices: 2644566--2644768 Score: 150
Period size: 46 Copynumber: 4.5 Consensus size: 46
2644556 TTTCATAACA
* *** * *
2644566 AAAATTTCAAAGATTCTCATCCAAAAAATTTCAAGG-TTTCACATCC
1 AAAATTTCAAAGATTCACATTTGAAAAATTT-TAGGAATTCACATCC
2644612 AAAATTTCAAAGATTCACATTTGAAAAATTTTAGGAATTC-CTATCC
1 AAAATTTCAAAGATTCACATTTGAAAAATTTTAGGAATTCAC-ATCC
* * * *
2644658 AAAATTTCAAGGATTCCCCTTTG-AAAATTGTTA-GAGATTCACATCT
1 AAAATTTCAAAGATTCACATTTGAAAAATT-TTAGGA-ATTCACATCC
* * * * * **
2644704 AAAGTTTCAAAGACTCATA-TTCAAAAA-ATTA-GAGATTCACATTT
1 AAAATTTCAAAGATTCACATTTGAAAAATTTTAGGA-ATTCACATCC
*
2644748 AAAGTTTCAAAGATTCACATT
1 AAAATTTCAAAGATTCACATT
2644769 CAAAGTTTCA
Statistics
Matches: 129, Mismatches: 21, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
44 32 0.25
45 15 0.12
46 81 0.63
47 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (46 bp):
AAAATTTCAAAGATTCACATTTGAAAAATTTTAGGAATTCACATCC
Found at i:2644737 original size:44 final size:44
Alignment explanation
Indices: 2644688--2644772 Score: 143
Period size: 44 Copynumber: 1.9 Consensus size: 44
2644678 TTGAAAATTG
*
2644688 TTAGAGATTCACATCTAAAGTTTCAAAGACTCATATTCAAAAAA
1 TTAGAGATTCACATCTAAAGTTTCAAAGACTCACATTCAAAAAA
* *
2644732 TTAGAGATTCACATTTAAAGTTTCAAAGATTCACATTCAAA
1 TTAGAGATTCACATCTAAAGTTTCAAAGACTCACATTCAAA
2644773 GTTTCAAAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (44 bp):
TTAGAGATTCACATCTAAAGTTTCAAAGACTCACATTCAAAAAA
Found at i:2644794 original size:22 final size:22
Alignment explanation
Indices: 2644692--2644781 Score: 94
Period size: 22 Copynumber: 4.1 Consensus size: 22
2644682 AAATTGTTAG
2644692 AGATTCACA-TCTAAAGTTTCAA
1 AGATTCACATTC-AAAGTTTCAA
* * ** *
2644714 AGACTCATATTCAAAAAATT-AG
1 AGATTCACATTC-AAAGTTTCAA
*
2644736 AGATTCACATTTAAAGTTTCAA
1 AGATTCACATTCAAAGTTTCAA
2644758 AGATTCACATTCAAAGTTTCAA
1 AGATTCACATTCAAAGTTTCAA
2644780 AG
1 AG
2644782 GTTCTTTTTC
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
21 5 0.09
22 41 0.77
23 7 0.13
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (22 bp):
AGATTCACATTCAAAGTTTCAA
Found at i:2647779 original size:132 final size:132
Alignment explanation
Indices: 2647623--2647881 Score: 355
Period size: 132 Copynumber: 2.0 Consensus size: 132
2647613 TACAAAAATG
* * * * * *
2647623 TATATGTAAATACATGTATGCAATACAT-AGT-AACAATAAGAATTCATATTCAAAACTATGTAC
1 TATATGCAAATACATGTATACAATACATAAATGAA-AACAAAAATTCATATCCAAAACTATGTAC
*
2647686 GAAATTGAAATGGAAAAGATTTTTCC-AAACAAATGAAAT-ACTATACATACAAAGATGTTTACA
65 AAAATTGAAA-GGAAAAGA-TTTTCCTAAACAAATGAAATAAC-ATACATACAAAGATGTTTACA
2647749 TTAATC
127 TTAATC
* *
2647755 TATATGCAAATACATGTATACAATATATAAATGAAAACAAAAATTCATATCCAAACCTATGTACA
1 TATATGCAAATACATGTATACAATACATAAATGAAAACAAAAATTCATATCCAAAACTATGTACA
* *
2647820 AAATTGAAAGGCAAAGATTTTCCTAAACAAATGAAATAACATATATACAAAGATGTTTACAT
66 AAATTGAAAGGAAAAGATTTTCCTAAACAAATGAAATAACATACATACAAAGATGTTTACAT
2647882 GGATGCATGT
Statistics
Matches: 112, Mismatches: 11, Indels: 8
0.85 0.08 0.06
Matches are distributed among these distances:
131 6 0.05
132 66 0.59
133 38 0.34
134 2 0.02
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.29
Consensus pattern (132 bp):
TATATGCAAATACATGTATACAATACATAAATGAAAACAAAAATTCATATCCAAAACTATGTACA
AAATTGAAAGGAAAAGATTTTCCTAAACAAATGAAATAACATACATACAAAGATGTTTACATTAA
TC
Found at i:2648127 original size:21 final size:21
Alignment explanation
Indices: 2648102--2648150 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
2648092 AGGGGTAGTA
*
2648102 AACATGATATATACAAAAAAC
1 AACATAATATATACAAAAAAC
*
2648123 AACATAATATATACAAAGAAC
1 AACATAATATATACAAAAAAC
2648144 AACATAA
1 AACATAA
2648151 AGGGTTAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.63, C:0.14, G:0.04, T:0.18
Consensus pattern (21 bp):
AACATAATATATACAAAAAAC
Found at i:2651810 original size:160 final size:160
Alignment explanation
Indices: 2651610--2652092 Score: 567
Period size: 160 Copynumber: 3.0 Consensus size: 160
2651600 AATATCATCA
* * * * *
2651610 AAACTGTTAAAATAGAATAATAATAGCATATTTGCATTTTTTCCTTTTAACGACACAAAAATCTT
1 AAACTATTAAAATAGAATAATAACAACAAATTTGCATTTTTGCCTTTTAACGACACAAAAATCTT
* * * *
2651675 AAACAGAGGTAAACAACAACTTTTTCACATATATCAACTGTGAAAATCAAGTTTAATCATTCAAA
66 AAACAGAGGTAAACAACAACTTTTTCACACATATCAACTGTGAAAACCAAGTTCAATCATTCAGA
*
2651740 CAAGTTTAATATCGTGTATTGAAGCTATCT
131 CAAGTTTAATATCGTGTATTGAAGCTATCC
* * * *
2651770 AAACTATTAAAATAGCATAACAACAACAAATTTGCATTTTTGCCTTTTAACGGCATAAAAAGTCT
1 AAACTATTAAAATAGAATAATAACAACAAATTTGCATTTTTGCCTTTTAACGACACAAAAA-TCT
* ** * * * * * * **
2651835 TAAACTGACATAAACAATAACTTTTTTATACATTTCAATTGTGGAAACCAA-ACCAATCATTCAG
65 TAAACAGAGGTAAACAACAACTTTTTCACACATATCAACTGTGAAAACCAAGTTCAATCATTCAG
* *
2651899 ACAAGTTTACTATCATGTATTGAAGC-ATCC
130 ACAAGTTTAATATCGTGTATTGAAGCTATCC
* * * * *
2651929 AAACTATTAAAACAGAACAATAACAACAATTTTCCATTTTTGCCTTTTAACAACACAAAAAAATC
1 AAACTATTAAAATAGAATAATAACAACAAATTTGCATTTTTGCCTTTTAACGACAC--AAAAATC
* * * * *
2651994 TTAAATAGAGGTAAACAACAACCTTTTCACACATATCAACTATGAAAACCAAGTTCAGTCATTCT
64 TTAAACAGAGGTAAACAACAACTTTTTCACACATATCAACTGTGAAAACCAAGTTCAATCATTCA
*
2652059 GACAAGTTTAATAT-GATGCATTGAAGCTATCC
129 GACAAGTTTAATATCG-TGTATTGAAGCTATCC
2652091 AA
1 AA
2652093 GTTGTTAAAA
Statistics
Matches: 262, Mismatches: 55, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
159 50 0.19
160 127 0.48
161 79 0.30
162 6 0.02
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (160 bp):
AAACTATTAAAATAGAATAATAACAACAAATTTGCATTTTTGCCTTTTAACGACACAAAAATCTT
AAACAGAGGTAAACAACAACTTTTTCACACATATCAACTGTGAAAACCAAGTTCAATCATTCAGA
CAAGTTTAATATCGTGTATTGAAGCTATCC
Found at i:2652182 original size:111 final size:111
Alignment explanation
Indices: 2651988--2652200 Score: 302
Period size: 111 Copynumber: 1.9 Consensus size: 111
2651978 ACAACACAAA
** *
2651988 AAAATCTTAAATAGAGGTAAACAACAACCTTTTCACACATATCAACTATGAAAACCAAGTTCAGT
1 AAAATCTTAAATAGACATAAACAACAACCTTTTCACACATATCAACTATGAAAACCAAGTTCAAT
*
2652053 CATTCTGACAAGTTTAATATGATGCATTGAAGCTATCCAAGTTGTT
66 CATTCTGACAAGTTTAATATGATGCATTGAAACTATCCAAGTTGTT
* * * * * *
2652099 AAAATCTTAAATAGACATAAACGATAACTTTTTCATACATATCAACTGTGGAAACCAAGTTCAAT
1 AAAATCTTAAATAGACATAAACAACAACCTTTTCACACATATCAACTATGAAAACCAAGTTCAAT
* *
2652164 CATT-TGAACAAGTTTAATATTATGTATTGAAACTATC
66 CATTCTG-ACAAGTTTAATATGATGCATTGAAACTATC
2652201 AAAACTATTA
Statistics
Matches: 89, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
110 2 0.02
111 87 0.98
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.31
Consensus pattern (111 bp):
AAAATCTTAAATAGACATAAACAACAACCTTTTCACACATATCAACTATGAAAACCAAGTTCAAT
CATTCTGACAAGTTTAATATGATGCATTGAAACTATCCAAGTTGTT
Found at i:2652312 original size:161 final size:162
Alignment explanation
Indices: 2652106--2652829 Score: 847
Period size: 161 Copynumber: 4.5 Consensus size: 162
2652096 GTTAAAATCT
* * * *
2652106 TAAATAGACATAAACGATAACTTTTTCATACATATCAACTGTGGAAACCAAGTTCAATCATTTGA
1 TAAACAGACATAAACAACAACTTTTTCATACATATCAACTGTGGAAACCAAGTTCAATCATTTCA
*
2652171 -ACAAGTTTAATATTATGTATTGAAACTATCAAAACTATTAAAATAGAACAATAATAGCAAATTT
66 GACAAGTTTAATATCATGTATTGAAACTATCAAAACTATTAAAATAGAACAATAATAGCAAATTT
* *
2652235 GCATTTTTGCCTTTTAATGGCATAAAAAGTCC
131 GCATTTTTGCCTTTTAACGGCACAAAAAGTCC
* *
2652267 TAAACAGATATAAACAACAACTTTTTCATACATATCAATTGTGGAAACCAAGTTCAATCA-TTCA
1 TAAACAGACATAAACAACAACTTTTTCATACATATCAACTGTGGAAACCAAGTTCAATCATTTCA
* * * * *
2652331 GACAAGTTTAATATCATGTATTGAAGCTATCCAAACTGTTAAAATAGCACAATAATAGCAATTTT
66 GACAAGTTTAATATCATGTATTGAAACTATCAAAACTATTAAAATAGAACAATAATAGCAAATTT
* * *
2652396 GTATTTTTTCCTTTTAACGGCACAAAAAGTCT
131 GCATTTTTGCCTTTTAACGGCACAAAAAGTCC
* * ** **** * *
2652428 TAAATAGACGTAAATGGTAGTTTTTTTTTATACATATCAACTGTGAAAACCAAGTTCAATCATTT
1 TAAACAGACATAAA--CAACAACTTTTTCATACATATCAACTGTGGAAACCAAGTTCAATCATTT
* * * * * *
2652493 -AGACAAATTTAATATCATGTATTTAATCTATCCAAACTATTAAAATAGAACAACAATAGCAATT
64 CAGACAAGTTTAATATCATGTATTGAAACTATCAAAACTATTAAAATAGAACAATAATAGCAAAT
* * *
2652557 TTGTATTTTTGCCTTTTAACAGCATAAAAAGTCC
129 TTGCATTTTTGCCTTTTAACGGCACAAAAAGTCC
* * * *
2652591 TCAACAGACAT--A-AACAACTTTTTCACACATATCAA-TCATGGAAACCAAGTTCAATTA-TTC
1 TAAACAGACATAAACAACAACTTTTTCATACATATCAACT-GTGGAAACCAAGTTCAATCATTTC
* * * *
2652651 AGACAACTTTAATATCATGTATTGAAACTATCAAAACTGTTAAAATAGAACAATAATTGTAAATT
65 AGACAAGTTTAATATCATGTATTGAAACTATCAAAACTATTAAAATAGAACAATAATAGCAAATT
* *
2652716 TGCATTTTTGCCTTTTAATGGCACAAAAAGTCT
130 TGCATTTTTGCCTTTTAACGGCACAAAAAGTCC
**** * **
2652749 TAAACA-ACCATAAATTGTAACTTTTTCACACATATCAACAATGGAAACCAAGTTCAATCA-TTC
1 TAAACAGA-CATAAACAACAACTTTTTCATACATATCAACTGTGGAAACCAAGTTCAATCATTTC
* *
2652812 GGATAAGTTTAATATCAT
65 AGACAAGTTTAATATCAT
2652830 AAACTTTTTT
Statistics
Matches: 477, Mismatches: 75, Indels: 22
0.83 0.13 0.04
Matches are distributed among these distances:
157 4 0.01
158 125 0.26
160 4 0.01
161 209 0.44
163 133 0.28
164 2 0.00
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (162 bp):
TAAACAGACATAAACAACAACTTTTTCATACATATCAACTGTGGAAACCAAGTTCAATCATTTCA
GACAAGTTTAATATCATGTATTGAAACTATCAAAACTATTAAAATAGAACAATAATAGCAAATTT
GCATTTTTGCCTTTTAACGGCACAAAAAGTCC
Found at i:2652317 original size:272 final size:271
Alignment explanation
Indices: 2651827--2652375 Score: 708
Period size: 272 Copynumber: 2.0 Consensus size: 271
2651817 TAACGGCATA
* * *
2651827 AAAAGTCTTAAACTGACATAAACAATAACTTTTTTATACATTTCAATTGTGGAAACCAAACCAAT
1 AAAA-TCTTAAACTGACATAAACAATAACTTTTTCATACATATCAACTGTGGAAACCAAACCAAT
* * *
2651892 CATTCAGACAAGTTTACTATCATGTATTGAAGCATCCAAACTATTAAAACAGAACAATAACAACA
65 CATTCAGACAAGTTTAATATCATGTATTGAAACATCAAAACTATTAAAACAGAACAATAACAACA
* * * *
2651957 ATTTTCCATTTTTGCCTTTTAACAACACAAAAAAATCTTAAATAGAGGTAAACAACAACCTTTTC
130 AATTTCCATTTTTGCCTTTTAACAACACAAAAAAATCCTAAACAGAGATAAACAACAACCTTTTC
* * *
2652022 ACACATATCAACTATGAAAACCAAGTTCAGTCATTCTGACAAGTTTAATATGATGCATTGAAGCT
195 ACACATATCAACTATGAAAACCAAGTTCAATCATTCAGACAAGTTTAATATCATGCATTGAAGCT
**
2652087 ATCCAAGTTGTT
260 ATCCAAACTGTT
* **
2652099 AAAATCTTAAA-TAGACATAAACGATAACTTTTTCATACATATCAACTGTGGAAACCAAGTTCAA
1 AAAATCTTAAACT-GACATAAACAATAACTTTTTCATACATATCAACTGTGGAAACCAA-ACCAA
* * * *
2652163 TCATT-TGAACAAGTTTAATATTATGTATTGAAACTATCAAAACTATTAAAATAGAACAATAATA
64 TCATTCAG-ACAAGTTTAATATCATGTATTGAAAC-ATCAAAACTATTAAAACAGAACAATAACA
* * *** * * * *
2652227 GCAAATTTGCATTTTTGCCTTTTAATGGCA-TAAAAAGTCCTAAACAGATATAAACAACAACTTT
127 ACAAATTTCCATTTTTGCCTTTTAACAACACAAAAAAATCCTAAACAGAGATAAACAACAACCTT
* * * * *
2652291 TTCATACATATCAATTGTGGAAACCAAGTTCAATCATTCAGACAAGTTTAATATCATGTATTGAA
192 TTCACACATATCAACTATGAAAACCAAGTTCAATCATTCAGACAAGTTTAATATCATGCATTGAA
2652356 GCTATCCAAACTGTT
257 GCTATCCAAACTGTT
2652371 AAAAT
1 AAAAT
2652376 AGCACAATAA
Statistics
Matches: 237, Mismatches: 36, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
270 1 0.00
271 49 0.21
272 137 0.58
273 50 0.21
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (271 bp):
AAAATCTTAAACTGACATAAACAATAACTTTTTCATACATATCAACTGTGGAAACCAAACCAATC
ATTCAGACAAGTTTAATATCATGTATTGAAACATCAAAACTATTAAAACAGAACAATAACAACAA
ATTTCCATTTTTGCCTTTTAACAACACAAAAAAATCCTAAACAGAGATAAACAACAACCTTTTCA
CACATATCAACTATGAAAACCAAGTTCAATCATTCAGACAAGTTTAATATCATGCATTGAAGCTA
TCCAAACTGTT
Found at i:2652750 original size:321 final size:323
Alignment explanation
Indices: 2652127--2652829 Score: 968
Period size: 321 Copynumber: 2.2 Consensus size: 323
2652117 AAACGATAAC
* * *
2652127 TTTTTCATACATATCAACTGTGGAAACCAAGTTCAATCATTTGAACAAGTTTAATATTATGTATT
1 TTTTTCATACATATCAACTGTGAAAACCAAGTTCAATCATTTGAACAAATTTAATATCATGTATT
* **
2652192 GAAACTATCAAAACTATTAAAATAGAACAATAATAGCAAATTTGCATTTTTGCCTTTTAATGGCA
66 GAAACTATCAAAACTATTAAAATAGAACAACAATAGCAAATTTGCATTTTTGCCTTTTAACAGCA
* * **
2652257 TAAAAAGTCCTAAACAGATATAAACAACAACTTTTTCATACATATCAATTGTGGAAACCAAGTTC
131 TAAAAAGTCCTAAACAGACAT-AACAACAACTTTTTCACACATATCAATCATGGAAACCAAGTTC
* * * *
2652322 AATCATTCAGACAAGTTTAATATCATGTATTGAAGCTATCCAAACTGTTAAAATAGCACAATAAT
195 AATCATTCAGACAACTTTAATATCATGTATTGAAACTATCAAAACTGTTAAAATAGAACAATAAT
* * *
2652387 AGCAATTTTGTATTTTTTCCTTTTAACGGCACAAAAAGTCTTAAATAGACGTAAATGGTAGTTT
260 AGCAAATTTGCATTTTTGCCTTTTAACGGCACAAAAAGTCTTAAATAGACGTAAATGGTAGTTT
*
2652451 TTTTTTATACATATCAACTGTGAAAACCAAGTTCAATCATTT-AGACAAATTTAATATCATGTAT
1 TTTTTCATACATATCAACTGTGAAAACCAAGTTCAATCATTTGA-ACAAATTTAATATCATGTAT
* * * * *
2652515 TTAATCTATCCAAACTATTAAAATAGAACAACAATAGCAATTTTGTATTTTTGCCTTTTAACAGC
65 TGAAACTATCAAAACTATTAAAATAGAACAACAATAGCAAATTTGCATTTTTGCCTTTTAACAGC
*
2652580 ATAAAAAGTCCTCAACAGACAT-A-AACAACTTTTTCACACATATCAATCATGGAAACCAAGTTC
130 ATAAAAAGTCCTAAACAGACATAACAACAACTTTTTCACACATATCAATCATGGAAACCAAGTTC
*
2652643 AATTATTCAGACAACTTTAATATCATGTATTGAAACTATCAAAACTGTTAAAATAGAACAATAAT
195 AATCATTCAGACAACTTTAATATCATGTATTGAAACTATCAAAACTGTTAAAATAGAACAATAAT
* * * * * * **
2652708 TGTAAATTTGCATTTTTGCCTTTTAATGGCACAAAAAGTCTTAAACA-ACCATAAATTGTA--AC
260 AGCAAATTTGCATTTTTGCCTTTTAACGGCACAAAAAGTCTTAAATAGA-CGTAAATGGTAGTTT
* ** * * * * *
2652770 TTTTTCACACATATCAACAATGGAAACCAAGTTCAATCATTCGGATAAGTTTAATATCAT
1 TTTTTCATACATATCAACTGTGAAAACCAAGTTCAATCATTTGAACAAATTTAATATCAT
2652830 AAACTTTTTT
Statistics
Matches: 334, Mismatches: 42, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
319 50 0.15
320 1 0.00
321 146 0.44
322 1 0.00
323 1 0.00
324 135 0.40
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (323 bp):
TTTTTCATACATATCAACTGTGAAAACCAAGTTCAATCATTTGAACAAATTTAATATCATGTATT
GAAACTATCAAAACTATTAAAATAGAACAACAATAGCAAATTTGCATTTTTGCCTTTTAACAGCA
TAAAAAGTCCTAAACAGACATAACAACAACTTTTTCACACATATCAATCATGGAAACCAAGTTCA
ATCATTCAGACAACTTTAATATCATGTATTGAAACTATCAAAACTGTTAAAATAGAACAATAATA
GCAAATTTGCATTTTTGCCTTTTAACGGCACAAAAAGTCTTAAATAGACGTAAATGGTAGTTT
Found at i:2653901 original size:13 final size:13
Alignment explanation
Indices: 2653880--2653916 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
2653870 ATAAAAGCGA
2653880 ATATATAAAAAAC
1 ATATATAAAAAAC
* *
2653893 ATATGTAAAGAAC
1 ATATATAAAAAAC
2653906 ATATATAAAAA
1 ATATATAAAAA
2653917 CATTAAGAGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.24
Consensus pattern (13 bp):
ATATATAAAAAAC
Found at i:2658708 original size:34 final size:34
Alignment explanation
Indices: 2658665--2658731 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
2658655 ACAAAAATGT
* *
2658665 AACAAATCAGACAGGAAGTTTAGGGATTTGACCA
1 AACAAATCAGACAAGAAATTTAGGGATTTGACCA
*
2658699 AACAAATCAGATAAGAAATTTAGGGATTTGACC
1 AACAAATCAGACAAGAAATTTAGGGATTTGACC
2658732 CAAAATGTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.22
Consensus pattern (34 bp):
AACAAATCAGACAAGAAATTTAGGGATTTGACCA
Found at i:2661715 original size:29 final size:30
Alignment explanation
Indices: 2661652--2661715 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
2661642 AACTTAAAGA
* *
2661652 CTTATTTGAATGTAAATTAAAGTTTAAGGG
1 CTTATTTGAATGTAAATAAAAGTATAAGGG
* *
2661682 TTTATTTGGATGT-AATAAAAGTATAAGGG
1 CTTATTTGAATGTAAATAAAAGTATAAGGG
2661711 CTTAT
1 CTTAT
2661716 CTGAGTTAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 18 0.62
30 11 0.38
ACGTcount: A:0.36, C:0.03, G:0.20, T:0.41
Consensus pattern (30 bp):
CTTATTTGAATGTAAATAAAAGTATAAGGG
Found at i:2663573 original size:72 final size:71
Alignment explanation
Indices: 2663450--2663704 Score: 229
Period size: 72 Copynumber: 3.7 Consensus size: 71
2663440 TTCAATAAGT
* * * * * * * **
2663450 ATTGCATTTTTAAAATAAAAAACGTAATGGATGTTGAAGCTATATTATCAAAATTTTGGAATTTT
1 ATTGCATTTTTAAGAT-AAAAACATAGTAGATGTTGAAACTTTATTTTCAAAATTTTAAAATTTT
2663515 AATAAAAG
65 AAT-AAAG
* * **
2663523 CTTGCATTTTTAAGATAAAAACATAGTATATGTTGAAACTTTATTTTCAAAATCCTAAAATTTTA
1 ATTGCATTTTTAAGATAAAAACATAGTAGATGTTGAAACTTTATTTTCAAAATTTTAAAATTTTA
2663588 ATAAAG
66 ATAAAG
* * * *
2663594 ATCGCATTTTCAAGATAAAAAAATAGTAGATGTTGAAA--TTA---T---ATTTTTAAAATTTTA
1 ATTGCATTTTTAAGATAAAAACATAGTAGATGTTGAAACTTTATTTTCAAAATTTTAAAATTTTA
2663651 ATAAAG
66 ATAAAG
** * * *
2663657 ATCACTTTTTTAAGATAAAAAATATAGTGGATGTTGAAACTTTATTTT
1 ATTGCATTTTTAAGAT-AAAAACATAGTAGATGTTGAAACTTTATTTT
2663705 TGAAATTATG
Statistics
Matches: 150, Mismatches: 26, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
63 31 0.21
64 20 0.13
66 4 0.03
69 4 0.03
71 37 0.25
72 40 0.27
73 14 0.09
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (71 bp):
ATTGCATTTTTAAGATAAAAACATAGTAGATGTTGAAACTTTATTTTCAAAATTTTAAAATTTTA
ATAAAG
Found at i:2663677 original size:63 final size:64
Alignment explanation
Indices: 2663578--2663711 Score: 200
Period size: 63 Copynumber: 2.1 Consensus size: 64
2663568 TTCAAAATCC
*
2663578 TAAAATTTTAATAAAGATCGCATTTTCAAGATAAAAAA-ATAGTAGATGTTGAAA-TTATATTTT
1 TAAAATTTTAATAAAGATCACATTTTCAAGATAAAAAATATAGTAGATGTTGAAACTT-TATTTT
* * *
2663641 TAAAATTTTAATAAAGATCACTTTTTTAAGATAAAAAATATAGTGGATGTTGAAACTTTATTTT
1 TAAAATTTTAATAAAGATCACATTTTCAAGATAAAAAATATAGTAGATGTTGAAACTTTATTTT
*
2663705 TGAAATT
1 TAAAATT
2663712 ATGAAACTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
63 35 0.55
64 27 0.42
65 2 0.03
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.40
Consensus pattern (64 bp):
TAAAATTTTAATAAAGATCACATTTTCAAGATAAAAAATATAGTAGATGTTGAAACTTTATTTT
Found at i:2664169 original size:16 final size:18
Alignment explanation
Indices: 2664145--2664181 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
2664135 CTCTTTTAAT
*
2664145 ATCACTTTT-CTCC-AAA
1 ATCAATTTTCCTCCTAAA
2664161 ATCAATTTTCCTCCTAAA
1 ATCAATTTTCCTCCTAAA
2664179 ATC
1 ATC
2664182 TAAGAAACCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 4 0.22
18 6 0.33
ACGTcount: A:0.32, C:0.30, G:0.00, T:0.38
Consensus pattern (18 bp):
ATCAATTTTCCTCCTAAA
Found at i:2666752 original size:9 final size:8
Alignment explanation
Indices: 2666738--2666776 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
2666728 CATCACAAGT
2666738 AGAAAAGAA
1 AGAAAA-AA
2666747 AGAAAAAA
1 AGAAAAAA
*
2666755 AGGAAAAA
1 AGAAAAAA
2666763 AGAAAAAA
1 AGAAAAAA
*
2666771 GGAAAA
1 AGAAAA
2666777 TGAAAAGGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
8 21 0.78
9 6 0.22
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (8 bp):
AGAAAAAA
Found at i:2666770 original size:15 final size:16
Alignment explanation
Indices: 2666745--2666776 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2666735 AGTAGAAAAG
2666745 AAAGAAAAAAAGGAAA
1 AAAGAAAAAAAGGAAA
2666761 AAAG-AAAAAAGGAAA
1 AAAGAAAAAAAGGAAA
2666776 A
1 A
2666777 TGAAAAGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAAAGGAAA
Found at i:2667616 original size:1 final size:1
Alignment explanation
Indices: 2667605--2667638 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
2667595 TTAGAATGAA
* *
2667605 CCCCACCCCCCCTCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
2667639 AAAAAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.03, C:0.94, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:2675812 original size:20 final size:19
Alignment explanation
Indices: 2675787--2675870 Score: 72
Period size: 20 Copynumber: 4.5 Consensus size: 19
2675777 ATCTTTGAAC
2675787 TTAGCATACTAATTAATTAA
1 TTAGCATACTAATT-ATTAA
2675807 TTAGCATACTAACATTATCT--
1 TTAGCATACT-A-ATTAT-TAA
*
2675827 TTTG-AT--TAA-TATTAA
1 TTAGCATACTAATTATTAA
2675842 TTAGCATACTAATTAATTAA
1 TTAGCATACTAATT-ATTAA
2675862 TTAGCATAC
1 TTAGCATAC
2675871 AAACTTTGCC
Statistics
Matches: 52, Mismatches: 2, Indels: 20
0.70 0.03 0.27
Matches are distributed among these distances:
13 1 0.02
14 3 0.06
15 4 0.08
16 3 0.06
17 1 0.02
18 3 0.06
19 3 0.06
20 27 0.52
21 3 0.06
22 4 0.08
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (19 bp):
TTAGCATACTAATTATTAA
Found at i:2676870 original size:56 final size:55
Alignment explanation
Indices: 2676735--2676952 Score: 195
Period size: 56 Copynumber: 3.8 Consensus size: 55
2676725 CAAATTCTTG
* * * * * *
2676735 AAAATTTTTGTTTAAGAAAAGATTGATATTTCAACTCTTTTCTTAAATCTTTTTGAA
1 AAAATTTTTTTTTAAAAAAAAATTGATACTTCAACT-TTTTCTCAAATATTTTT-AA
* * ** *
2676792 ATTAATTTTGTTTT-AAGGAAAATTAATACTTCAACTTTTTCTCAAATATTTTTAA
1 A-AAATTTTTTTTTAAAAAAAAATTGATACTTCAACTTTTTCTCAAATATTTTTAA
* *
2676847 AAAATTTTTATTTTAAAAAAAAATTGATACTTCATCTTTTTCTCAAAACATTTTGTAGA
1 AAAATTTTT-TTTTAAAAAAAAATTGATACTTCAACTTTTTCTC-AAATATTTT-TA-A
* * * * *
2676906 AATATTTTTTTATTTAAAGAAAATTGATACTTTAGCTTTTTCTCAAA
1 AAAATTTTTTT-TTAAAAAAAAATTGATACTTCAACTTTTTCTCAAA
2676953 AAAAAGTTTT
Statistics
Matches: 131, Mismatches: 23, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
54 6 0.05
55 7 0.05
56 40 0.31
57 25 0.19
58 16 0.12
59 37 0.28
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.47
Consensus pattern (55 bp):
AAAATTTTTTTTTAAAAAAAAATTGATACTTCAACTTTTTCTCAAATATTTTTAA
Found at i:2676936 original size:59 final size:57
Alignment explanation
Indices: 2676802--2676953 Score: 182
Period size: 59 Copynumber: 2.6 Consensus size: 57
2676792 ATTAATTTTG
* * *
2676802 TTTTAAGGAAAATTAATACTTCAACTTTTTCTC-AAATATTTTTAAAAAATTTTTAT
1 TTTTAAAGAAAATTGATACTTCAACTTTTTCTCAAAACATTTTTAAAAAATTTTTAT
* * * *
2676858 TTTAAAAAAAAATTGATACTTCATCTTTTTCTCAAAACATTTTGTAGAAATATTTTT-T
1 TTTTAAAGAAAATTGATACTTCAACTTTTTCTCAAAACATTTT-TA-AAAAATTTTTAT
* *
2676916 TATTTAAAGAAAATTGATACTTTAGCTTTTTCTCAAAA
1 T-TTTAAAGAAAATTGATACTTCAACTTTTTCTCAAAA
2676954 AAAAGTTTTA
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
56 28 0.35
57 8 0.10
58 4 0.05
59 41 0.51
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (57 bp):
TTTTAAAGAAAATTGATACTTCAACTTTTTCTCAAAACATTTTTAAAAAATTTTTAT
Found at i:2676975 original size:59 final size:59
Alignment explanation
Indices: 2676810--2676981 Score: 144
Period size: 59 Copynumber: 2.9 Consensus size: 59
2676800 TGTTTTAAGG
* * * *
2676810 AAAATTAATACTTCAACTTTTTCTC-AAATA-TTTTTAAAA-A--ATTTTTATTTTAAAAA
1 AAAATTGATACTTCAGCTTTTTCTCAAAAAAGTTTGTAAAATATTATTTTTA-TTT-AAAA
* * * *
2676866 AAAATTGATACTTCATCTTTTTCTCAAAACATTTTGTAGAAATATT-TTTTTATTTAAAG
1 AAAATTGATACTTCAGCTTTTTCTCAAAAAAGTTTGTA-AAATATTATTTTTATTTAAAA
* *
2676925 AAAATTGATACTTTAGCTTTTTCTCAAAAAAAAGTTT-T-AATTATTATTTTTTATTTA
1 AAAATTGATACTTCAGCTTTTTCTC--AAAAAAGTTTGTAAAATATTA-TTTTTATTTA
2676982 GGGAAACATT
Statistics
Matches: 96, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
56 23 0.24
57 4 0.04
58 11 0.11
59 29 0.30
60 15 0.16
61 14 0.15
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48
Consensus pattern (59 bp):
AAAATTGATACTTCAGCTTTTTCTCAAAAAAGTTTGTAAAATATTATTTTTATTTAAAA
Found at i:2678686 original size:77 final size:77
Alignment explanation
Indices: 2678578--2678722 Score: 186
Period size: 77 Copynumber: 1.9 Consensus size: 77
2678568 GACTTAATAT
* * * * * *
2678578 GAAAGATTCTAATAAATAAAATCTTTGATTTAGTGAGATA-CCT-TTTAATTGTATATATTGTAA
1 GAAAGATTCTAACAAATAAAATATTTAATTTA-AGA-ATATACTATTTAATTGTATATATTGCAA
2678641 TCTTTAGATATTAG
64 TCTTTAGATATTAG
* *
2678655 GAAAGATTCTAACAAATCAAATATTTAATTTAAGAATATATTATTTAATTGTATATATTGCAATC
1 GAAAGATTCTAACAAATAAAATATTTAATTTAAGAATATACTATTTAATTGTATATATTGCAATC
2678720 TTT
66 TTT
2678723 TAGGTAGATT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
75 3 0.05
76 3 0.05
77 52 0.90
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (77 bp):
GAAAGATTCTAACAAATAAAATATTTAATTTAAGAATATACTATTTAATTGTATATATTGCAATC
TTTAGATATTAG
Found at i:2683170 original size:3 final size:3
Alignment explanation
Indices: 2683111--2683158 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
2683101 GACTAAGTAA
* * * *
2683111 AAT ATT AAT AAT ACAT AAT ATT AAT ACT AAT ACT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2683157 AA
1 AA
2683159 ATATGAATAA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:2683802 original size:16 final size:16
Alignment explanation
Indices: 2683766--2683802 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2683756 ATTAAAACAC
*
2683766 TAAAAGAAACCCTAGG
1 TAAAAGAAACCCTAAG
*
2683782 AAAAAGAAACCCTAAG
1 TAAAAGAAACCCTAAG
2683798 TAAAA
1 TAAAA
2683803 ATCAAAACCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.59, C:0.16, G:0.14, T:0.11
Consensus pattern (16 bp):
TAAAAGAAACCCTAAG
Found at i:2684794 original size:22 final size:22
Alignment explanation
Indices: 2684769--2684810 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2684759 TTGTAGACCT
2684769 AAATTATCTTTTTAATAAAATA
1 AAATTATCTTTTTAATAAAATA
* *
2684791 AAATTATTTTTTTATTAAAA
1 AAATTATCTTTTTAATAAAA
2684811 AGATAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
AAATTATCTTTTTAATAAAATA
Found at i:2685768 original size:35 final size:35
Alignment explanation
Indices: 2685729--2686055 Score: 148
Period size: 35 Copynumber: 9.6 Consensus size: 35
2685719 ACCAATTCTC
**
2685729 AAGATTTAAGCTTAATTTAGTTAG-CACTCATGAAA
1 AAGATTTAAGCCCAATTTAGTTAGCCACTCATG-AA
* * *
2685764 AAGATGTAAGCCCAATTTAGTTGGCCCCTCATGAA
1 AAGATTTAAGCCCAATTTAGTTAGCCACTCATGAA
* * * *
2685799 AAGATTTAAGACCAACTTAGCT-GACA-TCCAATG-A
1 AAGATTTAAGCCCAATTTAGTTAGCCACT-C-ATGAA
* * * *
2685833 AA-CTTTAAGCTCAGTTTAGCTAG-CACTCATGAA
1 AAGATTTAAGCCCAATTTAGTTAGCCACTCATGAA
** * * *
2685866 AAGATTTAAGCCCAGCTTAGCT-GGCACCTAATG--
1 AAGATTTAAGCCCAATTTAGTTAGCCA-CTCATGAA
* *
2685899 AAGATTTAAGTCCAATTTAGTT-GACACTTCATGAA
1 AAGATTTAAGCCCAATTTAGTTAGCCAC-TCATGAA
* * ** **
2685934 AAAATTTAAGCACAGCTTAGTT-GGTACT--T-AA
1 AAGATTTAAGCCCAATTTAGTTAGCCACTCATGAA
*
2685965 CGAAGATTTAAGCCCAATTTAGTT-GGCACTCATGAA
1 --AAGATTTAAGCCCAATTTAGTTAGCCACTCATGAA
* * * * * * *
2686001 AAAATGTAAACCTAGTTTA-TCT-GGCACCCCATGAA
1 AAGATTTAAGCCCAATTTAGT-TAGCCA-CTCATGAA
2686036 AAGATTTAAGCCCAATTTAG
1 AAGATTTAAGCCCAATTTAG
2686056 CTAAAACCAG
Statistics
Matches: 223, Mismatches: 49, Indels: 39
0.72 0.16 0.13
Matches are distributed among these distances:
31 2 0.01
32 5 0.02
33 71 0.32
34 46 0.21
35 90 0.40
36 9 0.04
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.29
Consensus pattern (35 bp):
AAGATTTAAGCCCAATTTAGTTAGCCACTCATGAA
Found at i:2685867 original size:67 final size:67
Alignment explanation
Indices: 2685764--2686002 Score: 200
Period size: 68 Copynumber: 3.5 Consensus size: 67
2685754 ACTCATGAAA
* * * * *
2685764 AAGATGTAAGCCCAATTTAGTTGGCCCCTCATGAAAAGATTTAAGACCAACTTAGCTGACATCC-
1 AAGATTTAAGTCCAATTTAG-TAGACACTCATGAAAAGATTTAAGACCAACTTAGCTGACA-CCT
2685828 AATG
64 AATG
* * * *
2685832 AA-ACTTTAAG-CTCAGTTTAGCTAG-CACTCATGAAAAGATTTAAGCCCAGCTTAGCTGGCACC
1 AAGA-TTTAAGTC-CAATTTAG-TAGACACTCATGAAAAGATTTAAGACCAACTTAGCTGACACC
2685894 TAATG
63 TAATG
* * * * ** *
2685899 AAGATTTAAGTCCAATTTAGTTGACACTTCATGAAAAAATTTAAG-CACAGCTTAGTTGGTACTT
1 AAGATTTAAGTCCAATTTAGTAGACAC-TCATGAAAAGATTTAAGAC-CAACTTAGCTGACACCT
*
2685963 AACG
64 AATG
* * *
2685967 AAGATTTAAGCCCAATTTAGTTGGCACTCATGAAAA
1 AAGATTTAAGTCCAATTTAGTAGACACTCATGAAAA
2686003 AATGTAAACC
Statistics
Matches: 146, Mismatches: 17, Indels: 17
0.81 0.09 0.09
Matches are distributed among these distances:
66 4 0.03
67 66 0.45
68 76 0.52
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (67 bp):
AAGATTTAAGTCCAATTTAGTAGACACTCATGAAAAGATTTAAGACCAACTTAGCTGACACCTAA
TG
Found at i:2685908 original size:33 final size:33
Alignment explanation
Indices: 2685799--2685980 Score: 109
Period size: 33 Copynumber: 5.4 Consensus size: 33
2685789 CCCTCATGAA
* * *
2685799 AAGATTTAAGACCAACTTAGCTGACATCC-AATG
1 AAGATTTAAGCCCAGCTTAGCTGGCA-CCTAATG
* * * *
2685832 AA-ACTTTAAGCTCAGTTTAGCTAGCA-CTCATG
1 AAGA-TTTAAGCCCAGCTTAGCTGGCACCTAATG
2685864 AAAAGATTTAAGCCCAGCTTAGCTGGCACCTAATG
1 --AAGATTTAAGCCCAGCTTAGCTGGCACCTAATG
* ** * * * *
2685899 AAGATTTAAGTCCAATTTAGTTGACACTTCATG
1 AAGATTTAAGCCCAGCTTAGCTGGCACCTAATG
* * * * * *
2685932 AAAAAATTTAAGCACAGCTTAGTTGGTACTTAACG
1 --AAGATTTAAGCCCAGCTTAGCTGGCACCTAATG
2685967 AAGATTTAAGCCCA
1 AAGATTTAAGCCCA
2685981 ATTTAGTTGG
Statistics
Matches: 112, Mismatches: 29, Indels: 16
0.71 0.18 0.10
Matches are distributed among these distances:
31 1 0.01
32 4 0.04
33 56 0.50
34 21 0.19
35 30 0.27
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.28
Consensus pattern (33 bp):
AAGATTTAAGCCCAGCTTAGCTGGCACCTAATG
Found at i:2685953 original size:68 final size:67
Alignment explanation
Indices: 2685764--2686055 Score: 261
Period size: 67 Copynumber: 4.3 Consensus size: 67
2685754 ACTCATGAAA
* * * * * *
2685764 AAGATGTAAGCCCAATTTAGTTGGCCCCTCATGAAAAGATTTAAG-ACCAACTTAGCTGACATCC
1 AAGATTTAAGCCCAATTTAGTT-GACACTCATGAAAAAATTTAAGCA-CAGCTTAGCTGGCA-CC
2685828 -AATG
63 TAATG
* * * * *
2685832 AA-ACTTTAAGCTCAGTTTAGCT-AGCACTCATGAAAAGATTTAAGCCCAGCTTAGCTGGCACCT
1 AAGA-TTTAAGCCCAATTTAGTTGA-CACTCATGAAAAAATTTAAGCACAGCTTAGCTGGCACCT
2685895 AATG
64 AATG
* * * *
2685899 AAGATTTAAGTCCAATTTAGTTGACACTTCATGAAAAAATTTAAGCACAGCTTAGTTGGTACTTA
1 AAGATTTAAGCCCAATTTAGTTGACAC-TCATGAAAAAATTTAAGCACAGCTTAGCTGGCACCTA
*
2685964 ACG
65 ATG
* * * * * **
2685967 AAGATTTAAGCCCAATTTAGTTGGCACTCATGAAAAAATGTAAAC-CTAGTTTATCTGGCACCCC
1 AAGATTTAAGCCCAATTTAGTTGACACTCATGAAAAAATTTAAGCAC-AGCTTAGCTGGCACCTA
2686031 ATG
65 ATG
2686034 AAAAGATTTAAGCCCAATTTAG
1 --AAGATTTAAGCCCAATTTAG
2686056 CTAAAACCAG
Statistics
Matches: 183, Mismatches: 31, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
66 3 0.02
67 83 0.45
68 77 0.42
69 20 0.11
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (67 bp):
AAGATTTAAGCCCAATTTAGTTGACACTCATGAAAAAATTTAAGCACAGCTTAGCTGGCACCTAA
TG
Found at i:2685987 original size:33 final size:33
Alignment explanation
Indices: 2685866--2685994 Score: 123
Period size: 33 Copynumber: 3.8 Consensus size: 33
2685856 CACTCATGAA
* * *
2685866 AAGATTTAAGCCCAGCTTAGCTGGCACCTAATG
1 AAGATTTAAGCCCAACTTAGTTGGCACTTAATG
* * * *
2685899 AAGATTTAAGTCCAATTTAGTTGACACTTCATG
1 AAGATTTAAGCCCAACTTAGTTGGCACTTAATG
* * * * *
2685932 AAAAAATTTAAGCACAGCTTAGTTGGTACTTAACG
1 --AAGATTTAAGCCCAACTTAGTTGGCACTTAATG
*
2685967 AAGATTTAAGCCCAATTTAGTTGGCACT
1 AAGATTTAAGCCCAACTTAGTTGGCACT
2685995 CATGAAAAAA
Statistics
Matches: 73, Mismatches: 21, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
33 49 0.67
35 24 0.33
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (33 bp):
AAGATTTAAGCCCAACTTAGTTGGCACTTAATG
Found at i:2686424 original size:29 final size:29
Alignment explanation
Indices: 2686372--2686427 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
2686362 ACATCATGAT
*
2686372 AAGATTTAAGCCCAGTTTAATTGACACTC
1 AAGATTTAAGCCCAGATTAATTGACACTC
* **
2686401 AAGATTTAAGCCTAGATTGTTTGACAC
1 AAGATTTAAGCCCAGATTAATTGACAC
2686428 CCTGATTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (29 bp):
AAGATTTAAGCCCAGATTAATTGACACTC
Found at i:2686698 original size:34 final size:34
Alignment explanation
Indices: 2686640--2686744 Score: 103
Period size: 34 Copynumber: 3.2 Consensus size: 34
2686630 ATGAAGTTTC
* * * * *
2686640 AAGCCTAGTTTACTTAGCCTTTATGGAAATATTT
1 AAGCCCAGTTTACCTGGCCCTTATGGAAAGATTT
*
2686674 AAGCTCAGTTTACCTGGCCCTTATGGAAAGATTT
1 AAGCCCAGTTTACCTGGCCCTTATGGAAAGATTT
* *
2686708 AAGCCCAG--TACCTGG-CCTAAT-G-AAGTTTT
1 AAGCCCAGTTTACCTGGCCCTTATGGAAAGATTT
2686737 AAGCCCAG
1 AAGCCCAG
2686745 ATTATATGAC
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
29 14 0.23
30 1 0.02
31 5 0.08
32 7 0.11
34 35 0.56
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (34 bp):
AAGCCCAGTTTACCTGGCCCTTATGGAAAGATTT
Found at i:2686770 original size:32 final size:32
Alignment explanation
Indices: 2686701--2687068 Score: 169
Period size: 32 Copynumber: 11.3 Consensus size: 32
2686691 CCCTTATGGA
* *
2686701 AAGATTTAAGCCCAG--TACCTGGC-CTAATG
1 AAGATTTAAGCCCAGATTATCTGACACTAATG
* * *
2686730 AAGTTTTAAGCCCAGATTATATGACACCAATG
1 AAGATTTAAGCCCAGATTATCTGACACTAATG
* ** *
2686762 AAGATTTAAGCCCAGTTTATCCAACACTAGTG
1 AAGATTTAAGCCCAGATTATCTGACACTAATG
* * * * *
2686794 AAAATTTAAACCCAGCTTAGCTGGCACTAATG
1 AAGATTTAAGCCCAGATTATCTGACACTAATG
* * *
2686826 AAGATTTAAGCCTA-ATGTATTTGGCACTTAATG
1 AAGATTTAAGCCCAGAT-TATCTGACAC-TAATG
* * * * * **
2686859 AAGATTTAAGTCTA-ATTTAACTGGCTCTTATAAA
1 AAGATTTAAGCCCAGA-TTATCTGACAC-TA-ATG
* * * *
2686893 AAGATTTAAGCCTAGGTTATCTGTCACCCCAATG
1 AAGATTTAAGCCCAGATTATCTG--ACACTAATG
* * *
2686927 AA-ATTCCAAGCCTAAATTATCTTG-CACTCCAATG
1 AAGATT-TAAGCCCAGATTATC-TGACACT--AATG
* * *
2686961 AAGATTTAAGCCCAGTTTACCTGGCCCAC-AATGG
1 AAGATTTAAGCCCAGATTATCT-G-ACACTAAT-G
* * *
2686995 AA-ATTTAAGCCCAGATTATTTGGCCCTAATG
1 AAGATTTAAGCCCAGATTATCTGACACTAATG
* * *
2687026 AAGATTTAAGCCCAAATTAGCTGGCACTCAATG
1 AAGATTTAAGCCCAGATTATCTGACACT-AATG
*
2687059 AAAATTTAAG
1 AAGATTTAAG
2687069 TCCAATTTAG
Statistics
Matches: 257, Mismatches: 60, Indels: 40
0.72 0.17 0.11
Matches are distributed among these distances:
29 14 0.05
31 11 0.04
32 100 0.39
33 65 0.25
34 56 0.22
35 6 0.02
36 5 0.02
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (32 bp):
AAGATTTAAGCCCAGATTATCTGACACTAATG
Found at i:2687079 original size:33 final size:33
Alignment explanation
Indices: 2686757--2687080 Score: 138
Period size: 33 Copynumber: 9.8 Consensus size: 33
2686747 TATATGACAC
* * * ***
2686757 CAATGAAGATTTAAGCCCAGTTTATCCAACACT
1 CAATGAAAATTTAAGCCCAATTTAGCTGGCACT
* * **
2686790 -AGTGAAAATTTAAACCCAGCTTAGCTGGCACT
1 CAATGAAAATTTAAGCCCAATTTAGCTGGCACT
* * * **
2686822 -AATGAAGATTTAAGCCTAATGTATTTGGCACT
1 CAATGAAAATTTAAGCCCAATTTAGCTGGCACT
* * * * * *
2686854 TAATGAAGATTTAAGTCTAATTTAACTGGCTCT
1 CAATGAAAATTTAAGCCCAATTTAGCTGGCACT
* * * ** * * *
2686887 -TATAAAAAGATTTAAGCCTAGGTTATCTGTCACCC
1 CAAT-GAAA-ATTTAAGCCCAATTTAGCTGGCA-CT
* * * * *
2686922 CAATG-AAATTCCAAGCCTAAATTATCTTGCACT
1 CAATGAAAATT-TAAGCCCAATTTAGCTGGCACT
* * * * *
2686955 CCAATGAAGATTTAAGCCCAGTTTACCTGGCCCA
1 -CAATGAAAATTTAAGCCCAATTTAGCTGGCACT
* ** *
2686989 CAATGGAAATTTAAGCCCAGA-TTATTTGGCCCT
1 CAATGAAAATTTAAGCCCA-ATTTAGCTGGCACT
* *
2687022 -AATGAAGATTTAAGCCCAAATTAGCTGGCACT
1 CAATGAAAATTTAAGCCCAATTTAGCTGGCACT
*
2687054 CAATGAAAATTTAAGTCCAATTTAGCT
1 CAATGAAAATTTAAGCCCAATTTAGCT
2687081 AACATCGAGA
Statistics
Matches: 217, Mismatches: 63, Indels: 22
0.72 0.21 0.07
Matches are distributed among these distances:
31 1 0.00
32 74 0.34
33 82 0.38
34 53 0.24
35 5 0.02
36 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (33 bp):
CAATGAAAATTTAAGCCCAATTTAGCTGGCACT
Done.