Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 16 of 141
Found at i:5307417 original size:44 final size:44
Alignment explanation
Indices: 5307352--5307438 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
5307342 TATGTTTTTA
* * *
5307352 GTTTCTCACTTAAACTCTGATTAGTATAAGTTGTTTTAATATTG
1 GTTTCCCACTTAAACTATGATTAGTATAAGTTATTTTAATATTG
* *
5307396 GTTTCCCACTTAAACTATGATTAGTGTAGGTTATTTTAATATT
1 GTTTCCCACTTAAACTATGATTAGTATAAGTTATTTTAATATT
5307439 ATTTGACCTA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (44 bp):
GTTTCCCACTTAAACTATGATTAGTATAAGTTATTTTAATATTG
Found at i:5309061 original size:56 final size:57
Alignment explanation
Indices: 5308987--5309095 Score: 134
Period size: 56 Copynumber: 1.9 Consensus size: 57
5308977 AATTGAATAG
* *
5308987 TTGGCTGACCATTTTGTAAATTGAT-ATAATTAGG-TGACC-AAAAAAGAAATTTTCTA
1 TTGGATGACCATTTTGTAAATTG-TCATAATT-GGTTAACCAAAAAAAGAAATTTTCTA
* * *
5309043 TTGGATGATCATTTTGTAACTTGTCATAGTTGGTTAACCAAAAAAAGAAATTT
1 TTGGATGACCATTTTGTAAATTGTCATAATTGGTTAACCAAAAAAAGAAATTT
5309096 ACTAATAGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
55 3 0.07
56 29 0.64
57 13 0.29
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (57 bp):
TTGGATGACCATTTTGTAAATTGTCATAATTGGTTAACCAAAAAAAGAAATTTTCTA
Found at i:5319128 original size:15 final size:16
Alignment explanation
Indices: 5319099--5319128 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5319089 GTAATTTAAT
5319099 TAACTAAATTAATTTC
1 TAACTAAATTAATTTC
5319115 TAACTAAA-TAATTT
1 TAACTAAATTAATTT
5319129 TTTCAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (16 bp):
TAACTAAATTAATTTC
Found at i:5332394 original size:21 final size:21
Alignment explanation
Indices: 5332353--5332395 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
5332343 AATAAAGTAG
*
5332353 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
5332374 ATTATATATTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
5332395 A
1 A
5332396 AATTCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
ATTATATATTATATTTATAGT
Found at i:5332651 original size:45 final size:44
Alignment explanation
Indices: 5332560--5332652 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 44
5332550 ATTACAATAT
5332560 CATTCCATTCAACCAAACACAAGAATACTATTACACTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACACTTCTATTC
* * *
5332604 CATTTCATTCAACCAAACA-ATTGATTACTGATTACAGCTT-TATTC
1 CATTCCATTCAACCAAACACA-AGAATACT-ATTACA-CTTCTATTC
5332649 CATT
1 CATT
5332653 ACAGCTCTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
43 1 0.02
44 24 0.56
45 15 0.35
46 3 0.07
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.34
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACACTTCTATTC
Found at i:5332689 original size:16 final size:16
Alignment explanation
Indices: 5332634--5332689 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
5332624 TTGATTACTG
5332634 ATTACAGCTT-TATTCC
1 ATTACAG-TTCTATTCC
* *
5332650 ATTACAGCTCTATTCA
1 ATTACAGTTCTATTCC
5332666 ATTACAGTTCTATTCC
1 ATTACAGTTCTATTCC
5332682 ATTACAGT
1 ATTACAGT
5332690 GAACCAAACG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 1 0.03
16 34 0.97
ACGTcount: A:0.29, C:0.23, G:0.07, T:0.41
Consensus pattern (16 bp):
ATTACAGTTCTATTCC
Found at i:5342153 original size:24 final size:23
Alignment explanation
Indices: 5342124--5342183 Score: 102
Period size: 24 Copynumber: 2.6 Consensus size: 23
5342114 TAATTTGAAA
*
5342124 TATTTTTAAAATACTTTTTTTAT
1 TATTTTTAAAATAATTTTTTTAT
5342147 TATTTTTAAAATAAATTTTTTTAT
1 TATTTTTAAAAT-AATTTTTTTAT
5342171 TATTTTTAAAATA
1 TATTTTTAAAATA
5342184 TTTCGGGCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
23 13 0.37
24 22 0.63
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
TATTTTTAAAATAATTTTTTTAT
Found at i:5342434 original size:17 final size:17
Alignment explanation
Indices: 5342414--5342449 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
5342404 ATACTTTTAT
5342414 TTTTAAAAAAAATTGAA
1 TTTTAAAAAAAATTGAA
*
5342431 TTTTACAAAAAATTGAA
1 TTTTAAAAAAAATTGAA
5342448 TT
1 TT
5342450 ATTCAGTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.39
Consensus pattern (17 bp):
TTTTAAAAAAAATTGAA
Found at i:5344689 original size:22 final size:24
Alignment explanation
Indices: 5344636--5344692 Score: 75
Period size: 22 Copynumber: 2.5 Consensus size: 24
5344626 ATATGATCTA
5344636 AAAAGAAGAAATAAAAAAATTAGT
1 AAAAGAAGAAATAAAAAAATTAGT
* *
5344660 AATA-AAGAAAT-CAAAAA-TAGT
1 AAAAGAAGAAATAAAAAAATTAGT
5344681 AAAAGAAGAAAT
1 AAAAGAAGAAAT
5344693 TTGAAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 7 0.24
22 12 0.41
23 7 0.24
24 3 0.10
ACGTcount: A:0.70, C:0.02, G:0.12, T:0.16
Consensus pattern (24 bp):
AAAAGAAGAAATAAAAAAATTAGT
Found at i:5347582 original size:50 final size:50
Alignment explanation
Indices: 5347469--5347666 Score: 220
Period size: 50 Copynumber: 3.9 Consensus size: 50
5347459 ACATTTGGGT
* * *
5347469 GATGAGA--TCCCATGTAAGACCATGTTTGGAACATGGCATTGGCATCATTGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA
*
5347520 GGTTATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
1 -G--ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
** *
5347573 GATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
* ** * *
5347623 TATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGG
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG
5347667 AAGTACAAGA
Statistics
Matches: 126, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
50 81 0.64
52 2 0.02
53 2 0.02
54 6 0.05
55 1 0.01
56 34 0.27
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (50 bp):
GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
Found at i:5351063 original size:21 final size:22
Alignment explanation
Indices: 5351024--5351086 Score: 85
Period size: 23 Copynumber: 2.9 Consensus size: 22
5351014 CTTGATCAAT
5351024 ATACGACACATAAGTGCCTG-A
1 ATACGACACATAAGTGCCTGAA
*
5351045 A-ACGACACACAAGGTGCCTGAA
1 ATACGACACATAA-GTGCCTGAA
5351067 ATACGACACATAAAGTGCCT
1 ATACGACACAT-AAGTGCCT
5351087 AATCGGTAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
20 10 0.28
21 8 0.22
22 2 0.06
23 14 0.39
24 2 0.06
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.16
Consensus pattern (22 bp):
ATACGACACATAAGTGCCTGAA
Found at i:5352575 original size:25 final size:24
Alignment explanation
Indices: 5352508--5352575 Score: 59
Period size: 25 Copynumber: 2.8 Consensus size: 24
5352498 ATGAAAATGT
*
5352508 TATTGTATAAATAAAATTA-CAAA
1 TATTGTAAAAATAAAATTATCAAA
* * * *
5352531 TA-TATAAAAATGGAATTTATGAATA
1 TATTGTAAAAAT-AAAATTATCAA-A
5352556 TATTGTAAAAATAAAATTAT
1 TATTGTAAAAATAAAATTAT
5352576 AAAAATGTGT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
22 7 0.21
23 7 0.21
24 2 0.06
25 9 0.27
26 8 0.24
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.37
Consensus pattern (24 bp):
TATTGTAAAAATAAAATTATCAAA
Found at i:5352743 original size:12 final size:12
Alignment explanation
Indices: 5352727--5352762 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
5352717 AATAACATCT
5352727 ATAATAATAGTA
1 ATAATAATAGTA
*
5352739 GTAATAATAGTA
1 ATAATAATAGTA
5352751 ATAATAATAGTA
1 ATAATAATAGTA
5352763 TTATAACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (12 bp):
ATAATAATAGTA
Found at i:5352777 original size:24 final size:24
Alignment explanation
Indices: 5352727--5352783 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
5352717 AATAACATCT
**
5352727 ATAATAATAGTAGTAATAATAGTA
1 ATAATAATAGTAGTAATAATAAAA
*
5352751 ATAATAATAGTA-TTATAACTAAAA
1 ATAATAATAGTAGTAATAA-TAAAA
*
5352775 ATAAGAATA
1 ATAATAATA
5352784 AAAAAAAGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 5 0.18
24 23 0.82
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.32
Consensus pattern (24 bp):
ATAATAATAGTAGTAATAATAAAA
Found at i:5353971 original size:22 final size:22
Alignment explanation
Indices: 5353941--5353989 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
5353931 GTTGGGCTGA
* *
5353941 TTTGGGCTAAGTGTAAT-TGGG
1 TTTGGGCTAAATGTAATCTAGG
5353962 TTTGAGGCTAAATGTAATCTAGG
1 TTTG-GGCTAAATGTAATCTAGG
5353985 TTTGG
1 TTTGG
5353990 ATGTAATACT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.17
22 13 0.54
23 7 0.29
ACGTcount: A:0.22, C:0.06, G:0.33, T:0.39
Consensus pattern (22 bp):
TTTGGGCTAAATGTAATCTAGG
Found at i:5354415 original size:44 final size:44
Alignment explanation
Indices: 5354319--5354586 Score: 141
Period size: 44 Copynumber: 6.2 Consensus size: 44
5354309 ACTTGATGTG
* * ** *
5354319 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTACAACTTCA
* * *
5354363 ATCCGCTCCACTACAACTTCAGGGAGATAGGAT-TACCAACTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTA-CAACTTCA
* * * * * **
5354407 ATCTGCTCCACTGCAACCTCAAGGAGATGAGATTTGCTTCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTACAACTTCA
* * ** * * * * *
5354451 GTCTGCCCCACTGTGACTTCAGGGGGATAAGACCT--GA-TGCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTACAACTTCA
** * * * ** *
5354492 ATCCACTCTACTGCAACGTCAGAGAGATAAGATCTATTACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTACAACTTCA
* * * * * *
5354536 ATCCGCTCCACTACAACTTCAGGGAAATAGGAT-TATAGGCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTACA-ACTTCA
5354580 ATCTGCT
1 ATCTGCT
5354587 TCCTTACACT
Statistics
Matches: 161, Mismatches: 57, Indels: 12
0.70 0.25 0.05
Matches are distributed among these distances:
41 26 0.16
43 6 0.04
44 128 0.80
45 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTACAACTTCA
Found at i:5354694 original size:128 final size:128
Alignment explanation
Indices: 5354554--5355212 Score: 1052
Period size: 128 Copynumber: 5.2 Consensus size: 128
5354544 CACTACAACT
* * *
5354554 TCAGGGAAATAGGA-TTATAGGCTTCAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCT
1 TCAGGGACATAGGACTTGT-GGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCT
* * *
5354618 GCAATCTACTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGG
65 TCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGG
* *
5354682 TCAGGGACATAGGACTTGTGGCTTAAATCTGCTTCTTTACACTTGAAGATAAGATTCGCCGTCTT
1 TCAGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTT
*
5354747 CGATCTGCCCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGG
66 CGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGG
* * *
5354810 TCAGGGGCATAGGACCTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTT
1 TCAGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTT
* * *
5354875 CGATCTGGTCCGCTACTGCTTAAGGAGACAAGATCTACAATTTCCAACCTATTCCACTGCTGG
66 CGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGG
* *
5354938 TCAGGGGCATAGGACCTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTT
1 TCAGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTT
*
5355003 CGATCTGCTCCGCTACTGC-TAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTACTGG
66 CGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGG
* * * **
5355065 TCAGGGACATAGGAATTGTGGCTTAAATCTACTTCTTTACACTTGAAGATAAGATTTTCCGTCTT
1 TCAGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTT
* *
5355130 CGATCTTCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTAG
66 CGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGG
* *
5355193 CCAGGGATATAGGACTTGTG
1 TCAGGGACATAGGACTTGTG
5355213 ATTTCACCGA
Statistics
Matches: 495, Mismatches: 34, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
127 116 0.23
128 376 0.76
129 3 0.01
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (128 bp):
TCAGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTT
CGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGG
Found at i:5356391 original size:6 final size:7
Alignment explanation
Indices: 5356375--5356415 Score: 66
Period size: 7 Copynumber: 6.0 Consensus size: 7
5356365 CCGTCATTAC
5356375 TTTTCAT
1 TTTTCAT
5356382 TTTTCAT
1 TTTTCAT
5356389 TTTTCA-
1 TTTTCAT
5356395 TTTTCAT
1 TTTTCAT
*
5356402 TTTTAAT
1 TTTTCAT
5356409 TTTTCAT
1 TTTTCAT
5356416 CCCCCCCCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 6 0.19
7 25 0.81
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTCAT
Found at i:5356398 original size:13 final size:13
Alignment explanation
Indices: 5356375--5356411 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
5356365 CCGTCATTAC
5356375 TTTTCATTTTTCAT
1 TTTTCA-TTTTCAT
5356389 TTTTCATTTTCAT
1 TTTTCATTTTCAT
*
5356402 TTTTAATTTT
1 TTTTCATTTT
5356412 TCATCCCCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTCATTTTCAT
Found at i:5356400 original size:20 final size:20
Alignment explanation
Indices: 5356375--5356415 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
5356365 CCGTCATTAC
*
5356375 TTTTCATTTTTCATTTTTCA
1 TTTTCATTTTTAATTTTTCA
5356395 TTTTCATTTTTAATTTTTCA
1 TTTTCATTTTTAATTTTTCA
5356415 T
1 T
5356416 CCCCCCCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTCATTTTTAATTTTTCA
Found at i:5357329 original size:30 final size:28
Alignment explanation
Indices: 5357280--5357358 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 28
5357270 CTTTTTTCTC
* *
5357280 TTTTTCATATTTTTATTTTGACTTTAAT
1 TTTTTCTTTTTTTTATTTTGACTTTAAT
* *
5357308 TTATTTCTCTTTTTTTCTTTTGACTTTGAT
1 TT-TTTCT-TTTTTTTATTTTGACTTTAAT
*
5357338 TTTTTCTTTTTTCTTTTTTTG
1 TTTTTCTTTTTT-TTATTTTG
5357359 TTTTTGATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
28 7 0.16
29 16 0.37
30 20 0.47
ACGTcount: A:0.11, C:0.10, G:0.05, T:0.73
Consensus pattern (28 bp):
TTTTTCTTTTTTTTATTTTGACTTTAAT
Found at i:5357349 original size:29 final size:28
Alignment explanation
Indices: 5357289--5357369 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 28
5357279 CTTTTTCATA
* *
5357289 TTTTTATTTTGACTTTAATTTATTTCTCT
1 TTTTTTTTTTGACTTTGATTT-TTTCTCT
*
5357318 TTTTTTCTTTTGACTTTGATTTTTTCTTT
1 TTTTTT-TTTTGACTTTGATTTTTTCTCT
**
5357347 TTTCTTTTTTTGTTTTTGATTTT
1 TTT-TTTTTTTGACTTTGATTTT
5357370 GATTTGATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
29 28 0.62
30 17 0.38
ACGTcount: A:0.10, C:0.09, G:0.06, T:0.75
Consensus pattern (28 bp):
TTTTTTTTTTGACTTTGATTTTTTCTCT
Found at i:5362284 original size:25 final size:24
Alignment explanation
Indices: 5362217--5362284 Score: 59
Period size: 25 Copynumber: 2.8 Consensus size: 24
5362207 ATGAAAATGT
*
5362217 TATTGTATAAATAAAATTA-CAAA
1 TATTGTAAAAATAAAATTATCAAA
* * * *
5362240 TA-TATAAAAATGGAATTTATGAATA
1 TATTGTAAAAAT-AAAATTATCAA-A
5362265 TATTGTAAAAATAAAATTAT
1 TATTGTAAAAATAAAATTAT
5362285 AAAAATGTGT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
22 7 0.21
23 7 0.21
24 2 0.06
25 9 0.27
26 8 0.24
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.37
Consensus pattern (24 bp):
TATTGTAAAAATAAAATTATCAAA
Found at i:5362375 original size:21 final size:21
Alignment explanation
Indices: 5362345--5362384 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5362335 TAATTGAATA
* *
5362345 AATAATAATACATGATAAAGG
1 AATAAAAATACATAATAAAGG
5362366 AATAAAAATACATAATAAA
1 AATAAAAATACATAATAAA
5362385 ATAAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.65, C:0.05, G:0.07, T:0.23
Consensus pattern (21 bp):
AATAAAAATACATAATAAAGG
Found at i:5362449 original size:12 final size:12
Alignment explanation
Indices: 5362433--5362468 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
5362423 AATAACATCT
5362433 ATAATAATAGTA
1 ATAATAATAGTA
*
5362445 GTAATAATAGTA
1 ATAATAATAGTA
5362457 ATAATAATAGTA
1 ATAATAATAGTA
5362469 TTATAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (12 bp):
ATAATAATAGTA
Found at i:5362740 original size:16 final size:16
Alignment explanation
Indices: 5362719--5362754 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
5362709 GAAGAAAACT
5362719 GAATCAAAACGACACC
1 GAATCAAAACGACACC
5362735 GAATCAAAACGACACC
1 GAATCAAAACGACACC
5362751 GAAT
1 GAAT
5362755 GCACAGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.28, G:0.14, T:0.08
Consensus pattern (16 bp):
GAATCAAAACGACACC
Found at i:5367858 original size:17 final size:18
Alignment explanation
Indices: 5367836--5367885 Score: 70
Period size: 17 Copynumber: 2.9 Consensus size: 18
5367826 ACCCACATAA
5367836 TATTTTT-TATTTTTCTT
1 TATTTTTGTATTTTTCTT
5367853 TATTTTTCGTA-TTTTCTT
1 TATTTTT-GTATTTTTCTT
5367871 T-TTTTTGTATTTTTC
1 TATTTTTGTATTTTTC
5367886 GATCAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 3 0.10
17 17 0.57
18 8 0.27
19 2 0.07
ACGTcount: A:0.10, C:0.08, G:0.04, T:0.78
Consensus pattern (18 bp):
TATTTTTGTATTTTTCTT
Found at i:5367867 original size:18 final size:16
Alignment explanation
Indices: 5367846--5367883 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 16
5367836 TATTTTTTAT
5367846 TTTTCTTTATTTTTCGTA
1 TTTTCTTT-TTTTT-GTA
5367864 TTTTCTTTTTTTTGTA
1 TTTTCTTTTTTTTGTA
5367880 TTTT
1 TTTT
5367884 TCGATCAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.35
17 5 0.25
18 8 0.40
ACGTcount: A:0.08, C:0.08, G:0.05, T:0.79
Consensus pattern (16 bp):
TTTTCTTTTTTTTGTA
Found at i:5367873 original size:25 final size:26
Alignment explanation
Indices: 5367836--5367886 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
5367826 ACCCACATAA
*
5367836 TATTTTTTATTTTTCTT-TATTTTTCG
1 TATTTTCTATTTTT-TTGTATTTTTCG
5367862 TATTTTCT-TTTTTTTGTATTTTTCG
1 TATTTTCTATTTTTTTGTATTTTTCG
5367887 ATCAATTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 2 0.09
25 14 0.61
26 7 0.30
ACGTcount: A:0.10, C:0.08, G:0.06, T:0.76
Consensus pattern (26 bp):
TATTTTCTATTTTTTTGTATTTTTCG
Found at i:5368763 original size:8 final size:8
Alignment explanation
Indices: 5368752--5368777 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
5368742 AAAGAAATTT
5368752 AATAATAA
1 AATAATAA
5368760 AATAATAA
1 AATAATAA
5368768 AATAATAA
1 AATAATAA
5368776 AA
1 AA
5368778 GTTGATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AATAATAA
Found at i:5376522 original size:24 final size:24
Alignment explanation
Indices: 5376478--5376524 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5376468 ATTGAAATGG
* *
5376478 ATTGATTTTGTATGTGATGAATTT
1 ATTGAATTTATATGTGATGAATTT
5376502 ATTGAATTTATAT-TGATTGAATT
1 ATTGAATTTATATGTGA-TGAATT
5376525 GGATAGGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (24 bp):
ATTGAATTTATATGTGATGAATTT
Found at i:5377479 original size:2 final size:2
Alignment explanation
Indices: 5377472--5377504 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5377462 TTAGTTTGGC
5377472 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5377505 CACATGTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5385757 original size:28 final size:26
Alignment explanation
Indices: 5385699--5385775 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 26
5385689 TAATTCAAAA
*
5385699 TAATAATTTTGAATATTTTTTGTAATTT
1 TAATAATTTT-AAT-TTTTTTATAATTT
*
5385727 TAAATAAATTTAATTTTTTTATAATTCT
1 T-AATAATTTTAATTTTTTTATAATT-T
5385755 TAATAATTGTTAATTATTTTT
1 TAATAATT-TTAATT-TTTTT
5385776 TCATAATTAC
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
27 17 0.40
28 12 0.29
29 13 0.31
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60
Consensus pattern (26 bp):
TAATAATTTTAATTTTTTTATAATTT
Found at i:5388488 original size:19 final size:19
Alignment explanation
Indices: 5388464--5388503 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
5388454 TTAATACTAG
5388464 TTGCATTGCTATTAAGGCA
1 TTGCATTGCTATTAAGGCA
5388483 TTGCATTGCTATTAAGGCA
1 TTGCATTGCTATTAAGGCA
5388502 TT
1 TT
5388504 AGCTTGATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (19 bp):
TTGCATTGCTATTAAGGCA
Found at i:5394974 original size:10 final size:10
Alignment explanation
Indices: 5394959--5394993 Score: 70
Period size: 10 Copynumber: 3.5 Consensus size: 10
5394949 AAAGTTGCCA
5394959 TATGTATGTG
1 TATGTATGTG
5394969 TATGTATGTG
1 TATGTATGTG
5394979 TATGTATGTG
1 TATGTATGTG
5394989 TATGT
1 TATGT
5394994 GTGTATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (10 bp):
TATGTATGTG
Found at i:5394982 original size:16 final size:16
Alignment explanation
Indices: 5394961--5394995 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5394951 AGTTGCCATA
*
5394961 TGTATGTGTATGTATG
1 TGTATGTATATGTATG
*
5394977 TGTATGTATGTGTATG
1 TGTATGTATATGTATG
5394993 TGT
1 TGT
5394996 GTATAAATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.51
Consensus pattern (16 bp):
TGTATGTATATGTATG
Found at i:5396957 original size:15 final size:15
Alignment explanation
Indices: 5396937--5396969 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5396927 GGTACATAAA
5396937 TAAAACAACATGAAG
1 TAAAACAACATGAAG
*
5396952 TAAAACTACATGAAG
1 TAAAACAACATGAAG
5396967 TAA
1 TAA
5396970 GTAATAGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.18
Consensus pattern (15 bp):
TAAAACAACATGAAG
Found at i:5397339 original size:24 final size:24
Alignment explanation
Indices: 5397301--5397552 Score: 152
Period size: 24 Copynumber: 10.8 Consensus size: 24
5397291 TGAATTGGAT
* *
5397301 AATTTACAATAAATAATATATAATA
1 AATTTAAAAT-AATAATATATGATA
* *
5397326 AATTTGAAATAATAATACAT-ATAA
1 AATTTAAAATAATAATATATGAT-A
*
5397350 AATTT-AAA-AAT--TTTGATGAT-
1 AATTTAAAATAATAATAT-ATGATA
* * **
5397370 AATTCTAGAATAATCATACGTGATA
1 AATT-TAAAATAATAATATATGATA
** * *
5397395 AATCCAAAATAATAGTATATAATA
1 AATTTAAAATAATAATATATGATA
*
5397419 AATTT-AAA-AATATTA-ATGATA
1 AATTTAAAATAATAATATATGATA
* *
5397440 AATTTGAAATAGAT-ATACATGATA
1 AATTTAAAATA-ATAATATATGATA
** * *
5397464 AATTTAAAATAATGTTA-ACGATG
1 AATTTAAAATAATAATATATGATA
5397487 AATTTAAAATAATAATAT-TGATA
1 AATTTAAAATAATAATATATGATA
* *
5397510 AA-TTACAAATAATAAAACATGATA
1 AATTTA-AAATAATAATATATGATA
*
5397534 AATCTAAAATAATAATATA
1 AATTTAAAATAATAATATA
5397553 CAAATAAACT
Statistics
Matches: 174, Mismatches: 35, Indels: 37
0.71 0.14 0.15
Matches are distributed among these distances:
20 5 0.03
21 13 0.07
22 19 0.11
23 50 0.29
24 73 0.42
25 14 0.08
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (24 bp):
AATTTAAAATAATAATATATGATA
Found at i:5397397 original size:69 final size:69
Alignment explanation
Indices: 5397323--5397584 Score: 196
Period size: 69 Copynumber: 3.8 Consensus size: 69
5397313 ATAATATATA
* * *
5397323 ATAAATTTGAAATAATAATACAT-ATAAAATTTAAAAATTTTGATGAT-AATTCT-AGAATA-AT
1 ATAAATTTAAAATAATAATACATAAT-AAATTTAAAAATATTAATGATAAATT-TGA-AATAGAT
*
5397384 CATACGTG
63 -ATACATG
** * *
5397392 ATAAATCCAAAATAATAGTATATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGATATA
1 ATAAATTTAAAATAATAATACATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGATATA
5397457 CATG
66 CATG
** ** * * * **
5397461 ATAAATTTAAAATAATGTTA-ACGATGAATTTAAAATAATAATATTGATAAATTACAAATA-ATA
1 ATAAATTTAAAATAATAATACATAATAAATTT-AAA-AATATTAATGATAAATTTGAAATAGAT-
*
5397524 AAACATG
63 ATACATG
* * * *
5397531 ATAAATCTAAAATAATAATATACA-AATAAACTTAATAATATTAATGATTAATTT
1 ATAAATTTAAAATAAT-A-ATACATAATAAATTTAAAAATATTAATGATAAATTT
5397585 AATGATAATA
Statistics
Matches: 152, Mismatches: 31, Indels: 19
0.75 0.15 0.09
Matches are distributed among these distances:
68 8 0.05
69 69 0.45
70 64 0.42
71 2 0.01
72 8 0.05
73 1 0.01
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.35
Consensus pattern (69 bp):
ATAAATTTAAAATAATAATACATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGATATA
CATG
Found at i:5397568 original size:70 final size:69
Alignment explanation
Indices: 5397390--5397583 Score: 185
Period size: 70 Copynumber: 2.8 Consensus size: 69
5397380 TAATCATACG
* * * * * **
5397390 TGATAAATCCAAAATAATAGTATATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGATA
1 TGATAAATCTAAAATAATAATATACAATAAATTTAATAATAATAATGATAAATTACAAATAGATA
*
5397455 TACA
66 AACA
* ** * * *
5397459 TGATAAATTTAAAATAATGTTA-ACGATGAATTTAAAATAATAATATTGATAAATTACAAATA-A
1 TGATAAATCTAAAATAATAATATACAATAAATTT--AATAATAATAATGATAAATTACAAATAGA
5397522 TAAAACA
64 T-AAACA
* * *
5397529 TGATAAATCTAAAATAATAATATACAAATAAACTTAATAATATTAATGATTAATT
1 TGATAAATCTAAAATAATAATATAC-AATAAATTTAATAATAATAATGATAAATT
5397584 TAATGATAAT
Statistics
Matches: 98, Mismatches: 22, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
68 8 0.08
69 20 0.20
70 62 0.63
71 2 0.02
72 6 0.06
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (69 bp):
TGATAAATCTAAAATAATAATATACAATAAATTTAATAATAATAATGATAAATTACAAATAGATA
AACA
Found at i:5398416 original size:18 final size:20
Alignment explanation
Indices: 5398355--5398424 Score: 92
Period size: 19 Copynumber: 3.6 Consensus size: 20
5398345 TTTATTTCTT
*
5398355 TTTTCCTCCCTTTACACTAA
1 TTTTCCTCCCTTTACACTGA
* *
5398375 TTTT-TTCTCTTTACACTGA
1 TTTTCCTCCCTTTACACTGA
5398394 TTTTCC-CCCTTTACACTGA
1 TTTTCCTCCCTTTACACTGA
5398413 -TTTCCTCCCTTT
1 TTTTCCTCCCTTT
5398425 TTTATGAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
18 5 0.12
19 34 0.79
20 4 0.09
ACGTcount: A:0.14, C:0.33, G:0.03, T:0.50
Consensus pattern (20 bp):
TTTTCCTCCCTTTACACTGA
Found at i:5406062 original size:18 final size:18
Alignment explanation
Indices: 5406004--5406063 Score: 52
Period size: 20 Copynumber: 3.3 Consensus size: 18
5405994 AAATATAAAG
5406004 TATTCTATTTATATTT-TA
1 TATT-TATTTATATTTATA
* **
5406022 T-TTTATATATATAAATAA
1 TATTTATTTATATTTAT-A
5406040 TTATTTATTTATATTTATA
1 -TATTTATTTATATTTATA
5406059 TATTT
1 TATTT
5406064 TCTTCACTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
16 8 0.25
17 3 0.09
18 7 0.22
19 2 0.06
20 12 0.38
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTTATTTATATTTATA
Found at i:5406678 original size:30 final size:30
Alignment explanation
Indices: 5406642--5406703 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
5406632 ACCCACAAGA
5406642 TTATGATTGTCTTGTGACTGAAGATAATGT
1 TTATGATTGTCTTGTGACTGAAGATAATGT
5406672 TTATGATTGTCTTGTGACTGAAGATAATGT
1 TTATGATTGTCTTGTGACTGAAGATAATGT
5406702 TT
1 TT
5406704 TTTTACTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.45
Consensus pattern (30 bp):
TTATGATTGTCTTGTGACTGAAGATAATGT
Found at i:5411018 original size:142 final size:143
Alignment explanation
Indices: 5410837--5411124 Score: 569
Period size: 142 Copynumber: 2.0 Consensus size: 143
5410827 AACCTATTAA
5410837 ATTTAAAAATAATTTAAAGAATAAAATCATATTTTAAAAATAATTAAATAAAATATAATCTGTAG
1 ATTTAAAAATAATTTAAAGAATAAAATCATATTTTAAAAATAATTAAATAAAATATAATCTGTAG
5410902 TAAAATATTATTTTAATACTCCATTACTTTTCACATATATAGTATTTCGAAACAAAATAGCAAAC
66 TAAAATATTATTTTAATACTCCATTACTTTTCACATATATAGTATTTCGAAACAAAATAGCAAAC
5410967 AAGTTGTGCAAGT
131 AAGTTGTGCAAGT
5410980 ATTTAAAAAT-ATTTAAAGAATAAAATCATATTTTAAAAATAATTAAATAAAATATAATCTGTAG
1 ATTTAAAAATAATTTAAAGAATAAAATCATATTTTAAAAATAATTAAATAAAATATAATCTGTAG
5411044 TAAAATATTATTTTAATACTCCATTACTTTTCACATATATAGTATTTCGAAACAAAATAGCAAAC
66 TAAAATATTATTTTAATACTCCATTACTTTTCACATATATAGTATTTCGAAACAAAATAGCAAAC
5411109 AAGTTGTGCAAGT
131 AAGTTGTGCAAGT
5411122 ATT
1 ATT
5411125 ATTAAAATTA
Statistics
Matches: 145, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
142 135 0.93
143 10 0.07
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (143 bp):
ATTTAAAAATAATTTAAAGAATAAAATCATATTTTAAAAATAATTAAATAAAATATAATCTGTAG
TAAAATATTATTTTAATACTCCATTACTTTTCACATATATAGTATTTCGAAACAAAATAGCAAAC
AAGTTGTGCAAGT
Found at i:5413448 original size:9 final size:9
Alignment explanation
Indices: 5413436--5413473 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
5413426 ATAACTTTTG
5413436 TTTATAATT
1 TTTATAATT
*
5413445 TTTATGATT
1 TTTATAATT
5413454 TTTAATAATT
1 TTT-ATAATT
5413464 TTTA-AATT
1 TTTATAATT
5413472 TT
1 TT
5413474 AAAAGTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
8 6 0.23
9 12 0.46
10 8 0.31
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTATAATT
Found at i:5415468 original size:14 final size:14
Alignment explanation
Indices: 5415449--5415488 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
5415439 TTTTTTAAAA
* *
5415449 ATATATATATGTGT
1 ATATATATATATCT
*
5415463 ATATATCTATATCT
1 ATATATATATATCT
5415477 ATATATATATAT
1 ATATATATATAT
5415489 ATGTTAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (14 bp):
ATATATATATATCT
Found at i:5417239 original size:44 final size:44
Alignment explanation
Indices: 5417161--5417503 Score: 190
Period size: 44 Copynumber: 7.8 Consensus size: 44
5417151 TTGTGGTAGA
* * * *
5417161 TTTAATCCGAC-CTACTGCAACTTCAGAGG-TATAGGATCCATCAT
1 TTTAATCCG-CTCCACTGCAACTTCAG-GGAGATAGGATCTATGAT
*
5417205 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGAT-TA-GTAGC
1 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATCTATG-A-T
* * *
5417249 TTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGG-T-T-TGAT
1 TTTAATCCGCTCCACTGCAACTTCAGGGAGAT-AGGATCTATGAT
* * * * * * *
5417291 ATCTTCAGTCTGCTCCACTACAACTTCAGAGAGATAAGATCTGTGGT
1 -T-TT-AATCCGCTCCACTGCAACTTCAGGGAGATAGGATCTATGAT
* *
5417338 TTTAATCCGCTCCGCTGCAACTTTAGGGAGATAGGA--T-TGACT
1 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATCTATGA-T
** * * * *
5417380 TCTTCTGTCTGCTCCACTGCAACTTCAGAGAGATAAGA-CT-GGA-
1 T-TT-AATCCGCTCCACTGCAACTTCAGGGAGATAGGATCTATGAT
** * * * * * *
5417423 TGCAATCTGCTCTACTGCAACTTCAGAGACATAAGATCTATGGT
1 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATCTATGAT
* * *
5417467 TTTAATCCGTTCCACTGCAACTCCAGGGAGATTGGAT
1 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGAT
5417504 TGACTTCTTC
Statistics
Matches: 230, Mismatches: 50, Indels: 38
0.72 0.16 0.12
Matches are distributed among these distances:
41 31 0.13
42 5 0.02
43 11 0.05
44 144 0.63
45 34 0.15
46 2 0.01
47 3 0.01
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (44 bp):
TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATCTATGAT
Found at i:5417443 original size:41 final size:41
Alignment explanation
Indices: 5417387--5417587 Score: 127
Period size: 41 Copynumber: 4.8 Consensus size: 41
5417377 ACTTCTTCTG
*
5417387 TCTGCTCCACTGCAACTTCAGAGAGATAAGACTGGATGCAA
1 TCTGCTCTACTGCAACTTCAGAGAGATAAGACTGGATGCAA
* * **
5417428 TCTGCTCTACTGCAACTTCAGAGACATAAGATCTATGGTTTTAA
1 TCTGCTCTACTGCAACTTCAGAGAGATAAGA-C--TGGATGCAA
* * * * * ** * * *
5417472 TCCGTTCCACTGCAACTCCAGGGAGATTGGA-TTGACTTC-T
1 TCTGCTCTACTGCAACTTCAGAGAGATAAGACTGGA-TGCAA
* * * **
5417512 TCTGTCTGCTCCACTGTAACTTCAGGGAGATAAGATTGGATGCGG
1 TCTG-CT-CT--ACTGCAACTTCAGAGAGATAAGACTGGATGCAA
*
5417557 TCTACTCTACTGCAACTTCAGAGAGATAAGA
1 TCTGCTCTACTGCAACTTCAGAGAGATAAGA
5417588 TCTGTGGTTT
Statistics
Matches: 120, Mismatches: 30, Indels: 20
0.71 0.18 0.12
Matches are distributed among these distances:
40 5 0.04
41 53 0.44
42 2 0.02
43 2 0.02
44 52 0.43
45 6 0.05
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Consensus pattern (41 bp):
TCTGCTCTACTGCAACTTCAGAGAGATAAGACTGGATGCAA
Found at i:5417495 original size:129 final size:129
Alignment explanation
Indices: 5417172--5417600 Score: 547
Period size: 129 Copynumber: 3.3 Consensus size: 129
5417162 TTAATCCGAC
* * **
5417172 CTACTGCAACTTCAGAG-GTATAGGATCCATCATTTTAATCCGCTCCACTGCAACTTCAGGGAGA
1 CTACTGCAACTTCAGAGAG-ATAAGATCTATGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGA
* * ** * * *
5417236 TAGGATT-AGTAGCTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGGTTTGATATCTTCAGT
65 TAGGATTGACT-TCTTCTGTCTGCTCCACTGTAACTTCAGGGAGATAA-GATTG-GA--TGCAGT
5417300 CTGCT
125 CTGCT
* * * * *
5417305 CCACTACAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCGCTGCAACTTTAGGGAGAT
1 CTACTGCAACTTCAGAGAGATAAGATCTATGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGAT
* * * *
5417370 AGGATTGACTTCTTCTGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTGGATGCAATCTGCT
66 AGGATTGACTTCTTCTGTCTGCTCCACTGTAACTTCAGGGAGATAAGATTGGATGCAGTCTGCT
* * *
5417434 CTACTGCAACTTCAGAGACATAAGATCTATGGTTTTAATCCGTTCCACTGCAACTCCAGGGAGAT
1 CTACTGCAACTTCAGAGAGATAAGATCTATGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGAT
* * *
5417499 TGGATTGACTTCTTCTGTCTGCTCCACTGTAACTTCAGGGAGATAAGATTGGATGCGGTCTACT
66 AGGATTGACTTCTTCTGTCTGCTCCACTGTAACTTCAGGGAGATAAGATTGGATGCAGTCTGCT
*
5417563 CTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAA
1 CTACTGCAACTTCAGAGAGATAAGATCTATGGTTTTAA
5417601 ATCCACTCAC
Statistics
Matches: 257, Mismatches: 37, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
129 159 0.62
131 1 0.00
132 3 0.01
133 91 0.35
134 3 0.01
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.30
Consensus pattern (129 bp):
CTACTGCAACTTCAGAGAGATAAGATCTATGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGAT
AGGATTGACTTCTTCTGTCTGCTCCACTGTAACTTCAGGGAGATAAGATTGGATGCAGTCTGCT
Found at i:5417549 original size:44 final size:43
Alignment explanation
Indices: 5417213--5417588 Score: 223
Period size: 44 Copynumber: 8.7 Consensus size: 43
5417203 ATTTTAATCC
* * **
5417213 GCTCCACTGCAACTTCAGGGAGATAGGATT-AGTAGCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGA-T-TCTTCTGTCT
* * *
5417257 GCTCCACTGTAACTTCAGGGAGATAAGGTTTGATATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAA-GATTGAT-TCTTCTGTCT
* * ** * * *
5417302 GCTCCACTACAACTTCAGAGAGATAAGATCTG-TGGTTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGAT-TGATTCTTCT-GTCT
* * *
5417346 GCTCCGCTGCAACTTTAGGGAGATAGGATTGACTTCTTCTGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGA-TTCTTCTGTCT
* * * *
5417390 GCTCCACTGCAACTTCAGAGAGATAAGACTGGATGCAATCTG-CT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TTGATTC-TTCTGTCT
* * ** * * *
5417434 -CT--ACTGCAACTTCAGAGACATAAGATCT-ATGGTTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGAT-TGATTCTTCT-GTCT
* * **
5417475 GTTCCACTGCAACTCCAGGGAGATTGGATTGACTTCTTCTGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGA-TTCTTCTGTCT
* * *
5417519 GCTCCACTGTAACTTCAGGGAGATAAGATTGGA---TGCGGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATT-GATTCTTCTGTCT
* * *
5417560 ACTCTACTGCAACTTCAGAGAGATAAGAT
1 GCTCCACTGCAACTTCAGGGAGATAAGAT
5417589 CTGTGGTTTT
Statistics
Matches: 254, Mismatches: 61, Indels: 37
0.72 0.17 0.11
Matches are distributed among these distances:
39 2 0.01
40 4 0.02
41 54 0.21
42 1 0.00
43 7 0.03
44 130 0.51
45 55 0.22
46 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (43 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATTGATTCTTCTGTCT
Found at i:5417786 original size:100 final size:100
Alignment explanation
Indices: 5417610--5418727 Score: 1477
Period size: 100 Copynumber: 11.2 Consensus size: 100
5417600 AATCCACTCA
* * ** * * *
5417610 CCAGGGAAGTAAGATT-AGCTGTTGTAGCTTCAATCTACTTAACTGCAATGTCAGGGAAACAAGA
1 CCAGGGAAGTAAGATTCA-CCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGA
* * ** *
5417674 TTCGCTGTTGTAGCTTCAATCTATTTAACTGCAACG
65 TTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCG
*
5417710 CCTGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGAT
1 CCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGAT
* * ** *
5417775 TCGCTGTTGTAGCTTCAATCTATTTAACTGCAACG
66 TCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCG
*
5417810 CCTGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGAT
1 CCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGAT
* *
5417875 TCGCTGTTGTAGCTTCAATCTGTTCCACTGTA-CG
66 TCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCG
* * * * *
5417909 CCAGAGAAGTAAGATTTACCATTGTGGCTTCAATCTTTTTAATTACAATGTCGGGGAAACAAGAT
1 CCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGAT
*
5417974 TCGCCGTTGTAGCTTCAATCTGTTCTACTGCACCG
66 TCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCG
* * *
5418009 CCAGAGAAGTAAGATT-AGCCGTTGTGGCTTCAATTTTTTTAATTACAATGTCGGGGAAGCAAGA
1 CCAGGGAAGTAAGATTCA-CCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGA
* *
5418073 TTCGCCGTTATAGTTTCAATCTGTTCCACTGCACCG
65 TTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCG
* * *
5418109 CCAGAGAAGTAAGATTTACCATTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGAT
1 CCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGAT
** *
5418174 TTACCGTTGTAGCTTCAATCTGTTCCACTGCACCA
66 TCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCG
* ** *
5418209 CCAGGAAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACAAGAT
1 CCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGAT
*
5418274 TCGCCGTTGTAGCTTCAATCTGTTCCACTACACCG
66 TCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCG
* ** * * * **
5418309 CAAGGGAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTTAATTGCGATGTTGGGAAAATAAGAT
1 CCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGAT
* * *
5418374 TCGTCGTTGTAGCTTCAATATGTTCCACTGCACTG
66 TCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCG
* * * * *
5418409 CAAGGGAAGTAAGATTCGCCATTGTGGCTTCAATCTTTTTAATTGCGATGTCGGGGAAACAAGAT
1 CCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGAT
* *
5418474 TCGCCGTTGTAGCTTCAATCTGTTCTACTGCACTG
66 TCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCG
** ** * * *
5418509 TAAGGGAAGTAAGATTCGTCGTTATGGCTTCAATCTTTTTAATTGTAATGTCGGGGAAGTAAGAT
1 CCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGAT
* *
5418574 TCGCCGCTGTAGCTTCAATCTATTCCACTGCACCG
66 TCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCG
** * * * * *
5418609 CTTGGGAAGTAAGATTCGCTGTTGTGGCTTCAATTTTTTTAATTGCGATGTCGAGGAAGCAAGAT
1 CCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGAT
* *
5418674 TCGCTGTTGTAGCTTCAATCTGTTCCACTACACCG
66 TCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCG
*
5418709 CCTGGGAAGTAAGATTCAC
1 CCAGGGAAGTAAGATTCAC
5418728 TGTCTTTGAT
Statistics
Matches: 921, Mismatches: 93, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
99 91 0.10
100 828 0.90
101 2 0.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (100 bp):
CCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGAT
TCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCG
Found at i:5418725 original size:50 final size:50
Alignment explanation
Indices: 5417611--5418694 Score: 834
Period size: 50 Copynumber: 21.7 Consensus size: 50
5417601 ATCCACTCAC
* * **
5417611 CAGGGAAGTAAGATTAGCTGTTGTAGCTTCAATCTACTTAACTGCAATGT
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAACTGCAATGT
** * * * *
5417661 CAGGGAAACAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAACGC
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAACTGCAATGT
* * * *
5417711 CTGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGT
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAACTGCAATGT
* * * * * *
5417761 CGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAACGC
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAACTGCAATGT
* * * *
5417811 CTGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGT
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAACTGCAATGT
* * * * ** * * *
5417861 CGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTG-TACGC
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAACTGCAATGT
* ** * * * *
5417910 CAGAGAAGTAAGATTTACCATTGTGGCTTCAATCTTTTTAATTACAATGT
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAACTGCAATGT
* ** * ** *
5417960 CGGGGAAACAAGATTCGCCGTTGTAGCTTCAATCTGTTCT-ACTGCACCGC
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCT-TTTTAACTGCAATGT
* * * * * *
5418010 CAGAGAAGTAAGATTAGCCGTTGTGGCTTCAATTTTTTTAATTACAATGT
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAACTGCAATGT
* * * * * ** ** *
5418060 CGGGGAAGCAAGATTCGCCGTTATAGTTTCAATCTGTTCCACTGCACCGC
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAACTGCAATGT
* ** * * *
5418110 CAGAGAAGTAAGATTTACCATTGTGGCTTCAATCTTTTTAATTGCAATGT
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAACTGCAATGT
* * ** * ** ****
5418160 CGGGGAAGCAAGATTTACCGTTGTAGCTTCAATCTGTTCCACTGCACCAC
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAACTGCAATGT
* * * *
5418210 CAGGAAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTTAATTGCAATGT
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAACTGCAATGT
* ** * ** * **
5418260 CGGGGAAACAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTACACCG-
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAACTGCAATGT
* * * *
5418309 CAAGGGAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTTAATTGCGATGT
1 C-AGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAACTGCAATGT
* * * * * ** *
5418360 -TGGGAAAATAAGATTCGTCGTTGTAGCTTCAATATGTTCCACTGCACTG-
1 CAGGG-AAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAACTGCAATGT
* * * *
5418409 CAAGGGAAGTAAGATTCGCCATTGTGGCTTCAATCTTTTTAATTGCGATGT
1 C-AGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAACTGCAATGT
* ** * *
5418460 CGGGGAAACAAGATTCGCCGTTGTAGCTTCAATCTGTTCT-ACTGCACTGT
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCT-TTTTAACTGCAATGT
* * * * * *
5418510 AAGGGAAGTAAGATTCGTCGTTATGGCTTCAATCTTTTTAATTGTAATGT
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAACTGCAATGT
* * * ** **
5418560 CGGGGAAGTAAGATTCGCCGCTGTAGCTTCAATCTATTCCACTGCACCG-
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAACTGCAATGT
* * * * * *
5418609 CTTGGGAAGTAAGATTCGCTGTTGTGGCTTCAATTTTTTTAATTGCGATGT
1 C-AGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAACTGCAATGT
* *
5418660 C-GAGGAAGCAAGATTCGCTGTTGTAGCTTCAATCT
1 CAG-GGAAGTAAGATTCGCCGTTGTAGCTTCAATCT
5418695 GTTCCACTAC
Statistics
Matches: 775, Mismatches: 245, Indels: 28
0.74 0.23 0.03
Matches are distributed among these distances:
49 45 0.06
50 719 0.93
51 11 0.01
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (50 bp):
CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAACTGCAATGT
Found at i:5418915 original size:44 final size:43
Alignment explanation
Indices: 5418867--5419066 Score: 144
Period size: 44 Copynumber: 4.6 Consensus size: 43
5418857 CATATTCGAT
5418867 ATGCTCCACTACTGCTTAGGGAGACAAGATCTGCAATCTTCAAC
1 ATGCTCCACTACTGCTTAGGGAGACAAGATCT-CAATCTTCAAC
* * *
5418911 ATGCTCCACTACTGCTTAGGGAGATAGGA-CT-AATGGCTTAAATC
1 ATGCTCCACTACTGCTTAGGGAGACAAGATCTCAAT--CTTCAA-C
* * ** *
5418955 TACTTCTCCACTA-T-CTT-GGGAAGATAAGAT-TCACTATCTTTGAT
1 -A-TGCTCCACTACTGCTTAGGG-AGACAAGATCTCA--ATCTTCAAC
*
5418999 TTGCTCCACTACTGCTTAGGGAGAC-AGAATCTGCAATCTTCAAC
1 ATGCTCCACTACTGCTTAGGGAGACAAG-ATCT-CAATCTTCAAC
* * *
5419043 CTACTCCACTACGGCTTAGGGAGA
1 ATGCTCCACTACTGCTTAGGGAGA
5419067 TAGGACTAAT
Statistics
Matches: 123, Mismatches: 17, Indels: 32
0.72 0.10 0.19
Matches are distributed among these distances:
41 3 0.02
42 9 0.07
43 13 0.11
44 74 0.60
45 11 0.09
46 11 0.09
47 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (43 bp):
ATGCTCCACTACTGCTTAGGGAGACAAGATCTCAATCTTCAAC
Found at i:5419021 original size:132 final size:132
Alignment explanation
Indices: 5418711--5419345 Score: 967
Period size: 132 Copynumber: 4.8 Consensus size: 132
5418701 CTACACCGCC
**
5418711 TGGGAAG-TAAGATTCACTGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTGCAAT
1 TGGGAAGATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTGCAAT
* * * *
5418775 CTTCGACCTACTCCATTACTGCTTAGGGAGATAGG---AGTGGTTTAAATCTGCTTCTCCACTAT
66 CTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTAT
5418837 CT
131 CT
* * *
5418839 TGGGAAGATAAGATTCACCATATTCGATATGCTCCACTACTGCTTAGGGAGACA-AGATCTGCAA
1 TGGGAAGATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGA-ATCTGCAA
* * *
5418903 TCTTCAACATGCTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTACTTCTCCACTA
65 TCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTA
5418968 TCT
130 TCT
* *
5418971 TGGGAAGATAAGATTCACTATCTTTGATTTGCTCCACTACTGCTTAGGGAGACAGAATCTGCAAT
1 TGGGAAGATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTGCAAT
* *
5419036 CTTCAACCTACTCCACTACGGCTTAGGGAGATAGGACTAATGACTTAAATCTGCTTCTCCACTAT
66 CTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTAT
5419101 CT
131 CT
* * * * *
5419103 TGGAAAGATAATATTCACCATCTTCGATCTACTCCACTACTGCTTAGGGAGACAGAATATGCAAT
1 TGGGAAGATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTGCAAT
*
5419168 CTTCAGCCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTAT
66 CTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTAT
5419233 CT
131 CT
* * * *
5419235 TGGGAAGATAAGATTCACCGTCTTTGATCTGCTCTACTACTGCTTAGAGAGACA-ATATCTGTAA
1 TGGGAAGATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGA-ATCTGCAA
*
5419299 TCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAGTGGCTT
65 TCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTT
5419346 CATCGATCTA
Statistics
Matches: 458, Mismatches: 42, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
128 8 0.02
129 81 0.18
131 1 0.00
132 367 0.80
133 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (132 bp):
TGGGAAGATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTGCAAT
CTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTAT
CT
Found at i:5419179 original size:44 final size:43
Alignment explanation
Indices: 5419002--5419198 Score: 147
Period size: 44 Copynumber: 4.5 Consensus size: 43
5418992 CTTTGATTTG
* *
5419002 CTCCACTACTGCTTAGGGAGACAGAATCTGCAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGACAGAATATGCAATCTTC-GCCTA
* * * *
5419046 CTCCACTACGGCTTAGGGAGATAGGACTAATGACTTAAATC-T-G-CTT
1 CTCCACTACTGCTTAGGGAGACA-GAAT-ATG-C---AATCTTCGCCTA
* * * * *
5419092 CTCCACTA-T-CTT--GGAAAGATAATATTCACCATCTTCGATCTA
1 CTCCACTACTGCTTAGGGAGACAGAATATGCA--ATCTTCG-CCTA
5419134 CTCCACTACTGCTTAGGGAGACAGAATATGCAATCTTCAGCCTA
1 CTCCACTACTGCTTAGGGAGACAGAATATGCAATCTTC-GCCTA
5419178 CTCCACTACTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGA
5419199 TAGGACTAAT
Statistics
Matches: 118, Mismatches: 18, Indels: 34
0.69 0.11 0.20
Matches are distributed among these distances:
36 1 0.01
38 3 0.03
39 2 0.02
40 3 0.03
41 2 0.02
42 15 0.13
43 1 0.01
44 57 0.48
45 4 0.03
46 24 0.20
47 1 0.01
49 1 0.01
50 4 0.03
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.27
Consensus pattern (43 bp):
CTCCACTACTGCTTAGGGAGACAGAATATGCAATCTTCGCCTA
Found at i:5420588 original size:6 final size:6
Alignment explanation
Indices: 5420577--5420639 Score: 56
Period size: 6 Copynumber: 10.3 Consensus size: 6
5420567 CATTGGCCTC
* ** *
5420577 TTCTTT TTCTTT TTCTTT TTCTTA TGGTCT TTCTTT CTTCTTT TT-TTT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT -TTCTTT TTCTTT
*
5420625 CTTTTTT TTCTTT TT
1 -TTCTTT TTCTTT TT
5420640 TAAATATTTT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
5 3 0.07
6 33 0.73
7 9 0.20
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.79
Consensus pattern (6 bp):
TTCTTT
Found at i:5420629 original size:8 final size:9
Alignment explanation
Indices: 5420604--5420640 Score: 56
Period size: 9 Copynumber: 3.9 Consensus size: 9
5420594 TTTCTTATGG
5420604 TCTTTCTTTCT
1 TCTTT-TTT-T
5420615 TCTTTTTTT
1 TCTTTTTTT
5420624 TCTTTTTTT
1 TCTTTTTTT
5420633 TCTTTTTT
1 TCTTTTTT
5420641 AAATATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 18 0.69
10 3 0.12
11 5 0.19
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:5422939 original size:12 final size:12
Alignment explanation
Indices: 5422908--5422941 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5422898 ATTTTCTAGT
5422908 TGTTCTTGCATC
1 TGTTCTTGCATC
**
5422920 TGGGCTTGCATC
1 TGTTCTTGCATC
5422932 TGTTCTTGCA
1 TGTTCTTGCA
5422942 ATTGCTCTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.09, C:0.24, G:0.24, T:0.44
Consensus pattern (12 bp):
TGTTCTTGCATC
Found at i:5427485 original size:12 final size:12
Alignment explanation
Indices: 5427465--5427494 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5427455 AAACAAGAAC
*
5427465 AGAACAAAATAA
1 AGAAGAAAATAA
5427477 AGAAGAAAATAA
1 AGAAGAAAATAA
5427489 AGAAGA
1 AGAAGA
5427495 TATATGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.73, C:0.03, G:0.17, T:0.07
Consensus pattern (12 bp):
AGAAGAAAATAA
Found at i:5427715 original size:25 final size:26
Alignment explanation
Indices: 5427666--5427716 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
5427656 AACTTTTTCT
*
5427666 AAAAGAAAACACAAGAGAAATTTTTA
1 AAAAGAAAACACAAGAGAAAATTTTA
* *
5427692 AAAAGAAAACTCAA-ATAAAATTTTA
1 AAAAGAAAACACAAGAGAAAATTTTA
5427717 TTAATTCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.63, C:0.08, G:0.08, T:0.22
Consensus pattern (26 bp):
AAAAGAAAACACAAGAGAAAATTTTA
Found at i:5429139 original size:14 final size:14
Alignment explanation
Indices: 5429120--5429149 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5429110 TTTATTTTGG
5429120 TTTAACCCCTATTC
1 TTTAACCCCTATTC
5429134 TTTAACCCCTATTC
1 TTTAACCCCTATTC
5429148 TT
1 TT
5429150 GAACTTTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.33, G:0.00, T:0.47
Consensus pattern (14 bp):
TTTAACCCCTATTC
Found at i:5429973 original size:17 final size:17
Alignment explanation
Indices: 5429948--5429981 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5429938 AACTCACCAT
*
5429948 TTTGGAATTAGAGTCAC
1 TTTGAAATTAGAGTCAC
5429965 TTTGAAATTAGAGTCAC
1 TTTGAAATTAGAGTCAC
5429982 ACGGGCCAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (17 bp):
TTTGAAATTAGAGTCAC
Found at i:5430030 original size:80 final size:80
Alignment explanation
Indices: 5429892--5430040 Score: 235
Period size: 80 Copynumber: 1.9 Consensus size: 80
5429882 TGTTTTAAAG
* * * *
5429892 TTAGAGTTACACGGGCCAGGGACACGGGCGTGTGTCCAGGCTGTGTAACTCACCATTTTGGAATT
1 TTAGAGTCACACGGGCCAAGGACACAGGCGTGTGTCCAGGCCGTGTAACTCACCATTTTGGAATT
5429957 AGAGTCACTTTGAAA
66 AGAGTCACTTTGAAA
** *
5429972 TTAGAGTCACACGGGCCAAGGACACAGGCGTGTGTTTAGGCCGTGTAACTCACTATTTTGGAATT
1 TTAGAGTCACACGGGCCAAGGACACAGGCGTGTGTCCAGGCCGTGTAACTCACCATTTTGGAATT
5430037 AGAG
66 AGAG
5430041 ACACACAGAC
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 62 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (80 bp):
TTAGAGTCACACGGGCCAAGGACACAGGCGTGTGTCCAGGCCGTGTAACTCACCATTTTGGAATT
AGAGTCACTTTGAAA
Found at i:5430262 original size:108 final size:108
Alignment explanation
Indices: 5430126--5430336 Score: 298
Period size: 108 Copynumber: 2.0 Consensus size: 108
5430116 TGTTGGGTTG
* *
5430126 TGTGCTAGACCGTGCAACTTACTGTTTTGAGCCACATGGGCGTGTGTTAAGAC-ATGTGATAGGC
1 TGTGCTAGACCGTGCAACTCACTGTTTTGAGCCACATGGGCGTGTGTTAAGACGA-GTGACAGGC
* * *
5430190 CGTGTGCGACATTGAGGTAGGCCACGCAGGTGTGTGCTATGCCT
65 CATGTGCGACATTGAGGTAGGCCACACAGGTGCGTGCTATGCCT
* * * * * *
5430234 TGTGCTAGACCGTGTAACTCATTGTTTTGAGCCACATGGGTGTGTGTTAGGCCGAGTGACAGGTC
1 TGTGCTAGACCGTGCAACTCACTGTTTTGAGCCACATGGGCGTGTGTTAAGACGAGTGACAGGCC
*
5430299 ATGTGCGACATTGAGGTAGGCCACACGGGTGCGTGCTA
66 ATGTGCGACATTGAGGTAGGCCACACAGGTGCGTGCTA
5430337 GGCCGTGTAG
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
108 89 0.99
109 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.33, T:0.27
Consensus pattern (108 bp):
TGTGCTAGACCGTGCAACTCACTGTTTTGAGCCACATGGGCGTGTGTTAAGACGAGTGACAGGCC
ATGTGCGACATTGAGGTAGGCCACACAGGTGCGTGCTATGCCT
Found at i:5430904 original size:22 final size:22
Alignment explanation
Indices: 5430858--5430905 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
5430848 GGGGTAGGAC
* *
5430858 TCTGCATCTGAATCTGAAATGT
1 TCTGCAACTGAATCTGAAATCT
* *
5430880 TCTGCAACTGTATCTGAAGTCT
1 TCTGCAACTGAATCTGAAATCT
5430902 TCTG
1 TCTG
5430906 TTTCTATTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.38
Consensus pattern (22 bp):
TCTGCAACTGAATCTGAAATCT
Found at i:5431604 original size:7 final size:7
Alignment explanation
Indices: 5431588--5431630 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
5431578 ACTAAATCAG
5431588 AAAA-AA
1 AAAAGAA
5431594 AAAAGAA
1 AAAAGAA
5431601 AAAAGAA
1 AAAAGAA
5431608 AAAAG-A
1 AAAAGAA
5431614 AAAAGAA
1 AAAAGAA
5431621 GAAGAAGAA
1 -AA-AAGAA
5431630 A
1 A
5431631 GTGTTTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 10 0.30
7 15 0.45
8 3 0.09
9 5 0.15
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:5431617 original size:52 final size:50
Alignment explanation
Indices: 5431510--5431609 Score: 112
Period size: 52 Copynumber: 2.0 Consensus size: 50
5431500 TAATTTTTTA
* * * ** *
5431510 AAAAAATGAATAAAAAATTAAATCAGAAAAAAAACCAATAAAAACGATTAT
1 AAAAAATGAATAAAAAACTAAATCAGAAAAAAAA-CAAGAAAAAAGAAAAG
*
5431561 AAAAAATTAATAGAAAAACTAAATCAGAAAAAAAA-AAGAAAAAAGAAAA
1 AAAAAATGAATA-AAAAACTAAATCAGAAAAAAAACAAGAAAAAAGAAAA
5431610 AAGAAAAAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
50 10 0.24
51 11 0.26
52 21 0.50
ACGTcount: A:0.73, C:0.06, G:0.07, T:0.14
Consensus pattern (50 bp):
AAAAAATGAATAAAAAACTAAATCAGAAAAAAAACAAGAAAAAAGAAAAG
Found at i:5443017 original size:19 final size:20
Alignment explanation
Indices: 5442981--5443019 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5442971 GTGTGTTTTG
*
5442981 GTAAAATTAATTTTGATCAA
1 GTAAAATTAATATTGATCAA
5443001 GTAAAATTAA-ATTGATCAA
1 GTAAAATTAATATTGATCAA
5443020 ATCAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (20 bp):
GTAAAATTAATATTGATCAA
Found at i:5447823 original size:20 final size:20
Alignment explanation
Indices: 5447786--5447823 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5447776 CTTGGTTAGT
*
5447786 TAAATTAATTACTGTTTTGA
1 TAAATTAATTACTATTTTGA
5447806 TAAATT-ATTATCTATTTT
1 TAAATTAATTA-CTATTTT
5447824 TGTATATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.55
Consensus pattern (20 bp):
TAAATTAATTACTATTTTGA
Found at i:5451953 original size:17 final size:17
Alignment explanation
Indices: 5451931--5451970 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
5451921 TCATAATTTA
5451931 TTTTTCTATTTCACTTT
1 TTTTTCTATTTCACTTT
* *
5451948 TTTTTCTTTTTCCCTTT
1 TTTTTCTATTTCACTTT
5451965 TATTTT
1 T-TTTT
5451971 ATTCTTTCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTCTATTTCACTTT
Found at i:5451978 original size:19 final size:17
Alignment explanation
Indices: 5451939--5451983 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
5451929 TATTTTTCTA
* *
5451939 TTTCACTTTTTTTTCTT
1 TTTCCCTTTTTTTTATT
5451956 TTTCCCTTTTATTTTATT
1 TTTCCCTTTT-TTTTATT
5451974 CTTTCCCTTT
1 -TTTCCCTTT
5451984 CCCTTTCCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.38
18 6 0.25
19 9 0.38
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTCCCTTTTTTTTATT
Found at i:5451999 original size:7 final size:7
Alignment explanation
Indices: 5451987--5452046 Score: 102
Period size: 7 Copynumber: 8.6 Consensus size: 7
5451977 TCCCTTTCCC
5451987 TTTCCAG
1 TTTCCAG
5451994 TTTCCAG
1 TTTCCAG
5452001 TTTCCAG
1 TTTCCAG
5452008 TTTCCAG
1 TTTCCAG
5452015 TTTCCAG
1 TTTCCAG
*
5452022 TTTCTAG
1 TTTCCAG
5452029 TTTCCAG
1 TTTCCAG
*
5452036 TTTCCAT
1 TTTCCAG
5452043 TTTC
1 TTTC
5452047 TTTTCTCTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.13, C:0.27, G:0.12, T:0.48
Consensus pattern (7 bp):
TTTCCAG
Found at i:5452055 original size:7 final size:7
Alignment explanation
Indices: 5452045--5452078 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
5452035 GTTTCCATTT
5452045 TCTTTTC
1 TCTTTTC
5452052 TCTTTTC
1 TCTTTTC
5452059 TCTTTTC
1 TCTTTTC
5452066 T-TTTT-
1 TCTTTTC
5452071 TCTTTTC
1 TCTTTTC
5452078 T
1 T
5452079 TCTAATTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 1 0.04
6 8 0.32
7 16 0.64
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
TCTTTTC
Found at i:5452057 original size:12 final size:12
Alignment explanation
Indices: 5452042--5452079 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5452032 CCAGTTTCCA
5452042 TTTTCT-TTTCTC
1 TTTTCTCTTT-TC
5452054 TTTTCTCTTTTC
1 TTTTCTCTTTTC
*
5452066 TTTTTTCTTTTC
1 TTTTCTCTTTTC
5452078 TT
1 TT
5452080 CTAATTCTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 21 0.88
13 3 0.12
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTCTCTTTTC
Found at i:5452058 original size:19 final size:19
Alignment explanation
Indices: 5452042--5452078 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5452032 CCAGTTTCCA
5452042 TTTTCTTTTCTCTTTTCTC
1 TTTTCTTTTCTCTTTTCTC
*
5452061 TTTTCTTTTTTCTTTTCT
1 TTTTCTTTTCTCTTTTCT
5452079 TCTAATTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTCTTTTCTCTTTTCTC
Found at i:5452655 original size:30 final size:31
Alignment explanation
Indices: 5452613--5452670 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
5452603 TTATAGATTG
*
5452613 ATGGATTTTTGTTTGTTATGTTAATTTTTTA
1 ATGGATTTTTGTTTGTGATGTTAATTTTTTA
5452644 ATGGA-TTTTGTTTGTGATGTTAATTTT
1 ATGGATTTTTGTTTGTGATGTTAATTTT
5452671 CTTGATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.62
Consensus pattern (31 bp):
ATGGATTTTTGTTTGTGATGTTAATTTTTTA
Found at i:5454452 original size:21 final size:23
Alignment explanation
Indices: 5454419--5454464 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
5454409 GAGAAAAAGT
*
5454419 TTTGAGGGAAAAAGTA-AAAATA
1 TTTGAGGGAAAAAATATAAAATA
*
5454441 TTTG-GGGTAAAAATATAAAATA
1 TTTGAGGGAAAAAATATAAAATA
5454463 TT
1 TT
5454465 ATAGTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (23 bp):
TTTGAGGGAAAAAATATAAAATA
Found at i:5456745 original size:84 final size:85
Alignment explanation
Indices: 5456623--5456799 Score: 338
Period size: 84 Copynumber: 2.1 Consensus size: 85
5456613 AATTTAAATA
5456623 AAAAAATTAAATCTTTAATATATAATAATATAATATAAATATTAAAAAAATATGTTAAGTTGTAT
1 AAAAAATTAAATC-TTAATATATAATAATATAATATAAATATTAAAAAAATATGTTAAGTTGTAT
5456688 ATGTTAAAATTTTAATAACAG
65 ATGTTAAAATTTTAATAACAG
5456709 AAAAAATTAAATC-TAATATATAATAATATAATATAAATATTAAAAAAATATGTTAAGTTGTATA
1 AAAAAATTAAATCTTAATATATAATAATATAATATAAATATTAAAAAAATATGTTAAGTTGTATA
5456773 TGTTAAAATTTTAATAACAG
66 TGTTAAAATTTTAATAACAG
5456793 AAAAAAT
1 AAAAAAT
5456800 ATATAATAAT
Statistics
Matches: 91, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
84 78 0.86
86 13 0.14
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (85 bp):
AAAAAATTAAATCTTAATATATAATAATATAATATAAATATTAAAAAAATATGTTAAGTTGTATA
TGTTAAAATTTTAATAACAG
Found at i:5456797 original size:42 final size:42
Alignment explanation
Indices: 5456667--5456801 Score: 132
Period size: 42 Copynumber: 3.2 Consensus size: 42
5456657 ATAAATATTA
5456667 AAAAAATATGTTAAGTTGTATATGTTAAAATTTTAATAACAG
1 AAAAAATATGTTAAGTTGTATATGTTAAAATTTTAATAACAG
** * ** * * * **
5456709 AAAAAATTAAATCTAA--TATATAATAATATAATATAAATATTA-
1 AAAAAA-TATGT-TAAGTTGTAT-ATGTTAAAATTTTAATAACAG
5456751 AAAAAATATGTTAAGTTGTATATGTTAAAATTTTAATAACAG
1 AAAAAATATGTTAAGTTGTATATGTTAAAATTTTAATAACAG
5456793 AAAAAATAT
1 AAAAAATAT
5456802 ATAATAATCA
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
40 3 0.04
41 16 0.24
42 29 0.43
43 16 0.24
44 3 0.04
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.36
Consensus pattern (42 bp):
AAAAAATATGTTAAGTTGTATATGTTAAAATTTTAATAACAG
Found at i:5458427 original size:53 final size:53
Alignment explanation
Indices: 5458357--5458544 Score: 376
Period size: 53 Copynumber: 3.5 Consensus size: 53
5458347 TTTGTTACAC
5458357 CAATTAATACAATTAACAATTAATAATTTGATATAATTTGATAATTTTAGTAA
1 CAATTAATACAATTAACAATTAATAATTTGATATAATTTGATAATTTTAGTAA
5458410 CAATTAATACAATTAACAATTAATAATTTGATATAATTTGATAATTTTAGTAA
1 CAATTAATACAATTAACAATTAATAATTTGATATAATTTGATAATTTTAGTAA
5458463 CAATTAATACAATTAACAATTAATAATTTGATATAATTTGATAATTTTAGTAA
1 CAATTAATACAATTAACAATTAATAATTTGATATAATTTGATAATTTTAGTAA
5458516 CAATTAATACAATTAACAATTAATAATTT
1 CAATTAATACAATTAACAATTAATAATTT
5458545 TACTAGCAAA
Statistics
Matches: 135, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 135 1.00
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (53 bp):
CAATTAATACAATTAACAATTAATAATTTGATATAATTTGATAATTTTAGTAA
Found at i:5461592 original size:11 final size:11
Alignment explanation
Indices: 5461576--5461600 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5461566 TTATACTAGG
5461576 AATAATCAGAC
1 AATAATCAGAC
5461587 AATAATCAGAC
1 AATAATCAGAC
5461598 AAT
1 AAT
5461601 GCTTGATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.16, G:0.08, T:0.20
Consensus pattern (11 bp):
AATAATCAGAC
Found at i:5468314 original size:40 final size:38
Alignment explanation
Indices: 5468261--5468337 Score: 118
Period size: 40 Copynumber: 2.0 Consensus size: 38
5468251 TCCCTTATTC
*
5468261 TTTTTTTTAATGAAAAAGAAATTACATGACACAACCTT
1 TTTTTTTTAATGAAAAAGAAATTACAAGACACAACCTT
*
5468299 TTTTTTTTATGATGAAAAAGAAATTATAAGACACAACCT
1 TTTTTTTTA--ATGAAAAAGAAATTACAAGACACAACCT
5468338 ACATAGGTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 9 0.26
40 26 0.74
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (38 bp):
TTTTTTTTAATGAAAAAGAAATTACAAGACACAACCTT
Found at i:5476681 original size:34 final size:35
Alignment explanation
Indices: 5476637--5476703 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
5476627 CAGTAAAATA
*
5476637 TTTTCCGTAAAATGATTT-CTAGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
* *
5476671 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTT
5476704 CTAGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
Found at i:5477501 original size:12 final size:12
Alignment explanation
Indices: 5477465--5477503 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5477455 ATGAGTTATT
5477465 TAAGTGAGCAAG
1 TAAGTGAGCAAG
* *
5477477 TAAGTAAACAAG
1 TAAGTGAGCAAG
*
5477489 TAAGTGAGTAAG
1 TAAGTGAGCAAG
5477501 TAA
1 TAA
5477504 AGAAGCGAGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.49, C:0.05, G:0.26, T:0.21
Consensus pattern (12 bp):
TAAGTGAGCAAG
Found at i:5487460 original size:21 final size:21
Alignment explanation
Indices: 5487431--5487487 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
5487421 TTCGACACTT
* *
5487431 AGTATGATCTATGATAAGATA
1 AGTAAGATCTATAATAAGATA
* *
5487452 AGTACGATCTATAATATGATA
1 AGTAAGATCTATAATAAGATA
*
5487473 AGTAAGATCCATAAT
1 AGTAAGATCTATAAT
5487488 TATTAAGCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.32
Consensus pattern (21 bp):
AGTAAGATCTATAATAAGATA
Found at i:5499606 original size:13 final size:12
Alignment explanation
Indices: 5499585--5499640 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
5499575 AAAACCTGCA
5499585 GTTTTTTTATTT
1 GTTTTTTTATTT
*
5499597 GTTGTTTTTA-CT
1 GTT-TTTTTATTT
* *
5499609 GTTTTTTTGTGT
1 GTTTTTTTATTT
5499621 GTTTTTTT-TTT
1 GTTTTTTTATTT
5499632 GTTTTTTTA
1 GTTTTTTTA
5499641 CTATTTTGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
11 15 0.41
12 16 0.43
13 6 0.16
ACGTcount: A:0.05, C:0.02, G:0.14, T:0.79
Consensus pattern (12 bp):
GTTTTTTTATTT
Found at i:5499623 original size:24 final size:23
Alignment explanation
Indices: 5499585--5499640 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
5499575 AAAACCTGCA
*
5499585 GTTTTTTTATTTGTTGTTTTTACT
1 GTTTTTTTATGTGTT-TTTTTACT
* **
5499609 GTTTTTTTGTGTGTTTTTTTTTT
1 GTTTTTTTATGTGTTTTTTTACT
5499632 GTTTTTTTA
1 GTTTTTTTA
5499641 CTATTTTGCT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.05, C:0.02, G:0.14, T:0.79
Consensus pattern (23 bp):
GTTTTTTTATGTGTTTTTTTACT
Found at i:5499896 original size:13 final size:13
Alignment explanation
Indices: 5499862--5499898 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
5499852 TATATTTTTT
5499862 TAAAAAATT-ATA
1 TAAAAAATTAATA
*
5499874 -AAAAATTTAATA
1 TAAAAAATTAATA
5499886 TAAAAAATTAATA
1 TAAAAAATTAATA
5499899 CGGGTTGGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
11 7 0.33
12 3 0.14
13 11 0.52
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAAAAATTAATA
Found at i:5500544 original size:35 final size:35
Alignment explanation
Indices: 5500505--5500605 Score: 123
Period size: 35 Copynumber: 2.9 Consensus size: 35
5500495 GACAAAAGTG
*
5500505 ACCTTAAAGAGGTTGAGG-CAGACCCGTCTAAGACA
1 ACCTTAAAAAGGTTG-GGACAGACCCGTCTAAGACA
* * * *
5500540 ACCTTAAAAAGGTTGGGATATACTCGTCTAAGGCA
1 ACCTTAAAAAGGTTGGGACAGACCCGTCTAAGACA
* *
5500575 ACCTTAAAAAGGTTGGGATAGACACGTCTAA
1 ACCTTAAAAAGGTTGGGACAGACCCGTCTAA
5500606 TAGGGTAGAC
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
34 2 0.03
35 56 0.97
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.22
Consensus pattern (35 bp):
ACCTTAAAAAGGTTGGGACAGACCCGTCTAAGACA
Found at i:5502679 original size:20 final size:22
Alignment explanation
Indices: 5502650--5502694 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5502640 GTGTGTATTA
*
5502650 TTTTAATTT-AT-ATTTATTTT
1 TTTTAATTTAATCATTGATTTT
*
5502670 TTTTATTTTAATCATTGATTTT
1 TTTTAATTTAATCATTGATTTT
5502692 TTT
1 TTT
5502695 ACCCTAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
21 2 0.10
22 11 0.52
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTTAATTTAATCATTGATTTT
Found at i:5502748 original size:15 final size:15
Alignment explanation
Indices: 5502728--5502776 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
5502718 TATTTTTAGG
5502728 GTGACCAAAATGAAA
1 GTGACCAAAATGAAA
* **
5502743 GTGACCAAAAAGTTGA
1 GTGACCAAAATG-AAA
*
5502759 GTGACCAAAATAAAA
1 GTGACCAAAATGAAA
5502774 GTG
1 GTG
5502777 TAAACATGAA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.49, C:0.12, G:0.22, T:0.16
Consensus pattern (15 bp):
GTGACCAAAATGAAA
Found at i:5504222 original size:20 final size:20
Alignment explanation
Indices: 5504197--5504259 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
5504187 ATTATAAAAT
5504197 AATTCAAAATAATTTTTAAA
1 AATTCAAAATAATTTTTAAA
*
5504217 AATTCAAAAT-ATTTATAAA
1 AATTCAAAATAATTTTTAAA
* * *
5504236 AATTACAATATATTTTTTTAA
1 AATT-CAAAATAATTTTTAAA
5504257 AAT
1 AAT
5504260 AAAAAAATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
19 12 0.33
20 15 0.42
21 9 0.25
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (20 bp):
AATTCAAAATAATTTTTAAA
Found at i:5504225 original size:39 final size:40
Alignment explanation
Indices: 5504181--5504280 Score: 98
Period size: 40 Copynumber: 2.5 Consensus size: 40
5504171 GTCTCTCTCA
5504181 ACAAAAATTATAAAATAATT-CAAAATAATTTTTAAAAAT
1 ACAAAAATTATAAAATAATTACAAAATAATTTTTAAAAAT
* * * *
5504220 TCAAAATATT-TATAAA-AATTACAATATATTTTTTTAAAAT
1 ACAAAA-ATTATA-AAATAATTACAAAATAATTTTTAAAAAT
* *
5504260 AAAAAAATTAGAATAATAATT
1 ACAAAAATTATAA-AATAATT
5504281 TTGGGACTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
39 15 0.31
40 29 0.60
41 4 0.08
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (40 bp):
ACAAAAATTATAAAATAATTACAAAATAATTTTTAAAAAT
Found at i:5504508 original size:21 final size:21
Alignment explanation
Indices: 5504475--5504532 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
5504465 ATTTCACTCG
* *
5504475 ATTCGACTTGACTCGAATTTC
1 ATTCCACTCGACTCGAATTTC
* *
5504496 ATTCTACTCGACTCAAATTTC
1 ATTCCACTCGACTCGAATTTC
*
5504517 ACTCCACTCGACTCGA
1 ATTCCACTCGACTCGA
5504533 TTCGAAAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.26, C:0.31, G:0.10, T:0.33
Consensus pattern (21 bp):
ATTCCACTCGACTCGAATTTC
Found at i:5505393 original size:43 final size:43
Alignment explanation
Indices: 5505322--5505699 Score: 479
Period size: 43 Copynumber: 8.8 Consensus size: 43
5505312 GCGTCGCTAA
* ***
5505322 CTTTAGCGGCGTTTTTAGAAAAGAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCAAA-AACGCCGCTAAAGACCAAGAC
* ** **
5505366 CTTTAGTGGCGCTTTAACGGAAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGACCAAGAC
* * *
5505409 CTTTAGCGGCGCTTTTCCGAAAAACGTCGCTAAAGAACAAGAC
1 CTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGACCAAGAC
*
5505452 CGTTAGCGGCGCTTTT-CCAAAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGACCAAGAC
* * *
5505494 CTTTAGCGGCGATTTTCCGAAAAACACCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGACCAAGAC
* *
5505537 CTTTAGCGGCGCTTTTCCCAAAAACGCTGCTATAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGACCAAGAC
* **
5505580 CTTTAGCGGCGCTTTTCCCAAAAACGCCGCTATAGACCACTAC
1 CTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGACCAAGAC
* * * * *
5505623 CTTTAGCGGCGCTTTTCCCACAATCGTCGCTAAAGATCATGAC
1 CTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGACCAAGAC
** *
5505666 CTTTAGCGGCGCTTTTATCACAAACGCCGCTAAA
1 CTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAA
5505700 AATATAACCT
Statistics
Matches: 294, Mismatches: 39, Indels: 3
0.88 0.12 0.01
Matches are distributed among these distances:
42 37 0.13
43 241 0.82
44 16 0.05
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGACCAAGAC
Found at i:5505489 original size:128 final size:128
Alignment explanation
Indices: 5505345--5505699 Score: 453
Period size: 128 Copynumber: 2.8 Consensus size: 128
5505335 TTTAGAAAAG
* *
5505345 AACGCCGCTAAAGACCAAGACCTTTAGTGGCGCTTTAACGGAAAACGCCGCTAAAGACCAAGACC
1 AACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTT-ACGAAAAACGCCGCTAAAGACCAAGACC
*
5505410 TTTAGCGGCGCTTTTCCGAAAAACG-TCGCTAAAGAACAAGACCGTTAGCGGCGCTTTT-CCAAA
65 TTTAGCGGCGCTTTTCCCAAAAACGCT-GCTAAAGAACAAGACCGTTAGCGGCGCTTTTCCCAAA
* * *
5505473 AACGCCGCTAAAGACCAAGACCTTTAGCGGCGATTTTCCGAAAAACACCGCTAAAGACCAAGACC
1 AACGCCGCTAAAGACCAAGACCTTTAGCGGCG-CTTTACGAAAAACGCCGCTAAAGACCAAGACC
* * *
5505538 TTTAGCGGCGCTTTTCCCAAAAACGCTGCTATAGACCAAGACCTTTAGCGGCGCTTTTCCCAAA
65 TTTAGCGGCGCTTTTCCCAAAAACGCTGCTAAAGAACAAGACCGTTAGCGGCGCTTTTCCCAAA
* ** * * * * * * *
5505602 AACGCCGCTATAGACCACTACCTTTAGCGGCGCTTTTCCCACAATCGTCGCTAAAGATCATGACC
1 AACGCCGCTAAAGACCAAGACCTTTAGCGGCGC-TTTACGAAAAACGCCGCTAAAGACCAAGACC
** * *
5505667 TTTAGCGGCGCTTTTATCACAAACGCCGCTAAA
65 TTTAGCGGCGCTTTTCCCAAAAACGCTGCTAAA
5505700 AATATAACCT
Statistics
Matches: 198, Mismatches: 25, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
128 108 0.55
129 90 0.45
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (128 bp):
AACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTACGAAAAACGCCGCTAAAGACCAAGACCT
TTAGCGGCGCTTTTCCCAAAAACGCTGCTAAAGAACAAGACCGTTAGCGGCGCTTTTCCCAAA
Found at i:5506063 original size:19 final size:19
Alignment explanation
Indices: 5506040--5506102 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
5506030 GACAGTAACG
5506040 AAAAATTAAACACCACACA
1 AAAAATTAAACACCACACA
* * * *
5506059 TAAAATTACACAGACAGTAACA
1 AAAAATTAAACA-CCA--CACA
5506081 AAAAATTAAACACCACACA
1 AAAAATTAAACACCACACA
5506100 AAA
1 AAA
5506103 TTTATCAAAC
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
19 16 0.48
20 2 0.06
21 2 0.06
22 13 0.39
ACGTcount: A:0.62, C:0.22, G:0.03, T:0.13
Consensus pattern (19 bp):
AAAAATTAAACACCACACA
Found at i:5506086 original size:22 final size:22
Alignment explanation
Indices: 5506025--5506088 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
5506015 AAAAATTAAA
*
5506025 ACACAGACAGTAACGAAAAATT
1 ACACAGACAGTAACAAAAAATT
* * * *
5506047 AAACA-CCA--CACATAAAATT
1 ACACAGACAGTAACAAAAAATT
5506066 ACACAGACAGTAACAAAAAATT
1 ACACAGACAGTAACAAAAAATT
5506088 A
1 A
5506089 AACACCACAC
Statistics
Matches: 30, Mismatches: 9, Indels: 6
0.67 0.20 0.13
Matches are distributed among these distances:
19 12 0.40
20 2 0.07
21 2 0.07
22 14 0.47
ACGTcount: A:0.58, C:0.20, G:0.08, T:0.14
Consensus pattern (22 bp):
ACACAGACAGTAACAAAAAATT
Found at i:5506649 original size:25 final size:25
Alignment explanation
Indices: 5506621--5506713 Score: 186
Period size: 25 Copynumber: 3.7 Consensus size: 25
5506611 CCTAAGGAAA
5506621 AAGAACACGGTAAATATAAGAACAT
1 AAGAACACGGTAAATATAAGAACAT
5506646 AAGAACACGGTAAATATAAGAACAT
1 AAGAACACGGTAAATATAAGAACAT
5506671 AAGAACACGGTAAATATAAGAACAT
1 AAGAACACGGTAAATATAAGAACAT
5506696 AAGAACACGGTAAATATA
1 AAGAACACGGTAAATATA
5506714 GTAAATTACG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 68 1.00
ACGTcount: A:0.56, C:0.12, G:0.16, T:0.16
Consensus pattern (25 bp):
AAGAACACGGTAAATATAAGAACAT
Found at i:5509356 original size:7 final size:7
Alignment explanation
Indices: 5509344--5509374 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
5509334 TAACTCTTAG
5509344 CCCCAAA
1 CCCCAAA
5509351 CCCCAAA
1 CCCCAAA
5509358 CCCCAAA
1 CCCCAAA
*
5509365 CGCCAAA
1 CCCCAAA
5509372 CCC
1 CCC
5509375 ATAACCACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.39, C:0.58, G:0.03, T:0.00
Consensus pattern (7 bp):
CCCCAAA
Found at i:5509490 original size:39 final size:40
Alignment explanation
Indices: 5509430--5509506 Score: 111
Period size: 39 Copynumber: 1.9 Consensus size: 40
5509420 CACTAATTAA
* * *
5509430 TTTAAATCCTAAACCCTAACCCGACCCTAAATCCCTAATC
1 TTTAAACCCTAAACCCTAACCCAACCCCAAATCCCTAATC
*
5509470 TTTAAACCCT-AACCCTAACCCAACCCCGAATCCCTAA
1 TTTAAACCCTAAACCCTAACCCAACCCCAAATCCCTAA
5509507 CCCCTAAACA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
39 24 0.73
40 9 0.27
ACGTcount: A:0.35, C:0.40, G:0.03, T:0.22
Consensus pattern (40 bp):
TTTAAACCCTAAACCCTAACCCAACCCCAAATCCCTAATC
Found at i:5509515 original size:39 final size:40
Alignment explanation
Indices: 5509432--5509515 Score: 98
Period size: 39 Copynumber: 2.1 Consensus size: 40
5509422 CTAATTAATT
* * * * **
5509432 TAAATCCTAAACCCTAACCCGACCCTAAATCCCTAATCTT
1 TAAACCCTAAACCCTAACCCAACCCCAAATCCCTAACCCC
*
5509472 TAAACCCT-AACCCTAACCCAACCCCGAATCCCTAACCCC
1 TAAACCCTAAACCCTAACCCAACCCCAAATCCCTAACCCC
5509511 TAAAC
1 TAAAC
5509516 ATTATTTAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
39 30 0.81
40 7 0.19
ACGTcount: A:0.36, C:0.43, G:0.02, T:0.19
Consensus pattern (40 bp):
TAAACCCTAAACCCTAACCCAACCCCAAATCCCTAACCCC
Found at i:5510688 original size:41 final size:41
Alignment explanation
Indices: 5510587--5510901 Score: 386
Period size: 41 Copynumber: 7.7 Consensus size: 41
5510577 TTATTAGTGA
* *
5510587 CGCTTTTTTAAAAACGACGCTAAAGGCCCGAGCATTAGCGG
1 CGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGG
*
5510628 CGC-TTTTCAAAAACGCCGCTAAAGGCCAGAGCATTAGCGG
1 CGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGG
* *
5510668 CGCTTTTTCAAAAATGCCGCTAAAGGCCCGAGCGTTAGCGG
1 CGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGG
** * * *
5510709 CGCCTTAAT-AAAAACGCCGCTAAATGCCAGAGCATTAGCAG
1 CG-CTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGG
5510750 CGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGG
1 CGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGG
* * * ** *
5510791 TGCTTTAAT-AAAAACGCCGCTAAAAGCCATAGTATTAGCGG
1 CGCTTT-TTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGG
* * *
5510832 CGCTTTTTCCAAAACGCCACTAAAGTCCCGAGCATTAGCGG
1 CGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGG
* *
5510873 CGCTTTAAT-AAAAACGCCGCTAAATGCCC
1 CGCTTT-TTCAAAAACGCCGCTAAAGGCCC
5510902 CCAAAACTCA
Statistics
Matches: 230, Mismatches: 38, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
40 42 0.18
41 182 0.79
42 6 0.03
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.21
Consensus pattern (41 bp):
CGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGG
Found at i:5510756 original size:82 final size:82
Alignment explanation
Indices: 5510587--5510900 Score: 461
Period size: 82 Copynumber: 3.8 Consensus size: 82
5510577 TTATTAGTGA
* * *
5510587 CGCTTTTTTAAAAACGACGCTAAAGGCCCGAGCATTAGCGGCG-CTT-TTCAAAAACGCCGCTAA
1 CGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCCTTAAT-AAAAACGCCGCTAA
*
5510650 AGGCCAGAGCATTAGCGG
65 ATGCCAGAGCATTAGCGG
* *
5510668 CGCTTTTTCAAAAATGCCGCTAAAGGCCCGAGCGTTAGCGGCGCCTTAATAAAAACGCCGCTAAA
1 CGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCCTTAATAAAAACGCCGCTAAA
*
5510733 TGCCAGAGCATTAGCAG
66 TGCCAGAGCATTAGCGG
* *
5510750 CGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGTGCTTTAATAAAAACGCCGCTAAA
1 CGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCCTTAATAAAAACGCCGCTAAA
* * *
5510815 AGCCATAGTATTAGCGG
66 TGCCAGAGCATTAGCGG
* * * *
5510832 CGCTTTTTCCAAAACGCCACTAAAGTCCCGAGCATTAGCGGCGCTTTAATAAAAACGCCGCTAAA
1 CGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCCTTAATAAAAACGCCGCTAAA
5510897 TGCC
66 TGCC
5510901 CCCAAAACTC
Statistics
Matches: 211, Mismatches: 20, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
81 39 0.18
82 171 0.81
83 1 0.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.21
Consensus pattern (82 bp):
CGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCCTTAATAAAAACGCCGCTAAA
TGCCAGAGCATTAGCGG
Found at i:5510997 original size:38 final size:37
Alignment explanation
Indices: 5510937--5511068 Score: 149
Period size: 38 Copynumber: 3.4 Consensus size: 37
5510927 GGGCTTAGGC
*
5510937 TTTTT-GCGGCGCTTTCCAAAAAACGCCGCTAATGCTTA
1 TTTTTAGCGGCG-TTTTC-AAAAACGCCGCTAATGCTTA
*
5510975 TTTTTAGCGGCGTTTTGCAAAAAGCGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTT-CAAAAA-CGCCGCTAATGCT-TA
** *
5511015 CCTTTAGCGGCGTTTTTAAAAACGCCGCTAATGCTTGA
1 TTTTTAGCGGCGTTTTCAAAAACGCCGCTAATGCTT-A
*
5511053 TTTTTAGTGGCGTTTT
1 TTTTTAGCGGCGTTTT
5511069 TTGTCCAAAC
Statistics
Matches: 80, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
38 40 0.50
39 25 0.31
40 15 0.19
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (37 bp):
TTTTTAGCGGCGTTTTCAAAAACGCCGCTAATGCTTA
Found at i:5511069 original size:38 final size:38
Alignment explanation
Indices: 5510955--5511069 Score: 160
Period size: 38 Copynumber: 3.0 Consensus size: 38
5510945 GCGCTTTCCA
*
5510955 AAAAACGCCGCTAATGCTT-ATTTTTAGCGGCGTTTTGC
1 AAAAACGCCGCTAATGCTTGATTTTTAGCGGCGTTTT-T
* **
5510993 AAAAAGCGCCGCTAATGCTCGACCTTTAGCGGCGTTTTT
1 AAAAA-CGCCGCTAATGCTTGATTTTTAGCGGCGTTTTT
*
5511032 AAAAACGCCGCTAATGCTTGATTTTTAGTGGCGTTTTT
1 AAAAACGCCGCTAATGCTTGATTTTTAGCGGCGTTTTT
5511070 TGTCCAAACG
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
38 34 0.51
39 18 0.27
40 15 0.22
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (38 bp):
AAAAACGCCGCTAATGCTTGATTTTTAGCGGCGTTTTT
Found at i:5511092 original size:12 final size:12
Alignment explanation
Indices: 5511075--5511100 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5511065 TTTTTTGTCC
5511075 AAACGCCGCTAA
1 AAACGCCGCTAA
5511087 AAACGCCGCTAA
1 AAACGCCGCTAA
5511099 AA
1 AA
5511101 GCCTGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:5511389 original size:22 final size:20
Alignment explanation
Indices: 5511334--5511394 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
5511324 TTTCTCTCCA
5511334 CTTTTCAATCGATTGTTTCT
1 CTTTTCAATCGATTGTTTCT
*
5511354 CTTTTCAATTGATTGCTTCTCT
1 CTTTTCAATCGATTG-TT-TCT
* *
5511376 TTTTTTAATCGATTGTTTC
1 CTTTTCAATCGATTGTTTC
5511395 GTTATCTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 16 0.46
21 4 0.11
22 15 0.43
ACGTcount: A:0.15, C:0.18, G:0.10, T:0.57
Consensus pattern (20 bp):
CTTTTCAATCGATTGTTTCT
Found at i:5520452 original size:21 final size:21
Alignment explanation
Indices: 5520419--5520467 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
5520409 ACACTCTCTA
* *
5520419 AACTGCTCTTGCAGACTCC-AG
1 AACTGTTCCTGCA-ACTCCAAG
*
5520440 AATTGTTCCTGCAACTCCAAG
1 AACTGTTCCTGCAACTCCAAG
5520461 AACTGTT
1 AACTGTT
5520468 GAGAGCTGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.29
Consensus pattern (21 bp):
AACTGTTCCTGCAACTCCAAG
Found at i:5522141 original size:21 final size:20
Alignment explanation
Indices: 5522107--5522145 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
5522097 TAAAAAATTA
5522107 TAAAAAATTCATTTAGAAATG
1 TAAAAAATTCATTT-GAAATG
* *
5522128 TAAAAATTTTATTTGAAA
1 TAAAAAATTCATTTGAAA
5522146 ACTAAACTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (20 bp):
TAAAAAATTCATTTGAAATG
Found at i:5522240 original size:17 final size:16
Alignment explanation
Indices: 5522204--5522266 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
5522194 AATTCTAACT
*
5522204 AATTATAAAAAAATAA
1 AATTATTAAAAAATAA
* *
5522220 AATTTTTAAAAAATATC
1 AATTATTAAAAAATA-A
* *
5522237 AATTATTAATATATATA
1 AATTATTAAAAAATA-A
5522254 AATTA-TAAAAAAT
1 AATTATTAAAAAAT
5522267 TATTTATTGA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
16 19 0.51
17 18 0.49
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
AATTATTAAAAAATAA
Found at i:5522729 original size:22 final size:23
Alignment explanation
Indices: 5522703--5522751 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
5522693 AATTTGATAA
5522703 TTTATTAGAATTTTTAT-A-AATT
1 TTTATT-GAATTTTTATAACAATT
*
5522725 TTTA-TGAATTTTTTTAACAATT
1 TTTATTGAATTTTTATAACAATT
5522747 TTTAT
1 TTTAT
5522752 AAGTTTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 9 0.39
21 2 0.09
22 12 0.52
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (23 bp):
TTTATTGAATTTTTATAACAATT
Found at i:5522736 original size:9 final size:10
Alignment explanation
Indices: 5522711--5522764 Score: 54
Period size: 10 Copynumber: 5.2 Consensus size: 10
5522701 AATTTATTAG
5522711 AATTTTTATA
1 AATTTTTATA
*
5522721 AATTTTTATG
1 AATTTTTATA
*
5522731 AATTTTTTTAA
1 AATTTTTAT-A
5522742 CAATTTTTATA
1 -AATTTTTATA
* *
5522753 AGTTTATATA
1 AATTTTTATA
5522763 AA
1 AA
5522765 AATTTAAATA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
10 26 0.74
11 1 0.03
12 8 0.23
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (10 bp):
AATTTTTATA
Found at i:5522768 original size:22 final size:22
Alignment explanation
Indices: 5522720--5522769 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
5522710 GAATTTTTAT
* *
5522720 AAATTTTTATGAATTTTTTTAA
1 AAATTTTTATGAATTTATATAA
*
5522742 CAATTTTTAT-AAGTTTATATAA
1 AAATTTTTATGAA-TTTATATAA
5522764 AAATTT
1 AAATTT
5522770 AAATATTCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (22 bp):
AAATTTTTATGAATTTATATAA
Found at i:5525309 original size:13 final size:13
Alignment explanation
Indices: 5525293--5525317 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5525283 TTAATTAAAA
5525293 TTTTAAAAAATAT
1 TTTTAAAAAATAT
5525306 TTTTAAAAAATA
1 TTTTAAAAAATA
5525318 CTAATTATTA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTTAAAAAATAT
Found at i:5529471 original size:9 final size:9
Alignment explanation
Indices: 5529458--5529553 Score: 122
Period size: 9 Copynumber: 10.7 Consensus size: 9
5529448 TTTGGTTAAA
*
5529458 AATTAACCA
1 AATTAACCG
5529467 AATTAACCG
1 AATTAACCG
*
5529476 AAATAACCG
1 AATTAACCG
5529485 AATTAACCG
1 AATTAACCG
*
5529494 AATTACCCG
1 AATTAACCG
5529503 AATT-ACTCG
1 AATTAAC-CG
*
5529512 AATTACCCG
1 AATTAACCG
5529521 AATTAACCG
1 AATTAACCG
*
5529530 AATTACCCG
1 AATTAACCG
*
5529539 AATTAACCA
1 AATTAACCG
5529548 AATTAA
1 AATTAA
5529554 GCAAATTGAA
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
8 1 0.01
9 73 0.97
10 1 0.01
ACGTcount: A:0.45, C:0.24, G:0.08, T:0.23
Consensus pattern (9 bp):
AATTAACCG
Found at i:5529880 original size:83 final size:83
Alignment explanation
Indices: 5529783--5529971 Score: 378
Period size: 83 Copynumber: 2.3 Consensus size: 83
5529773 CGGTTAAACT
5529783 GAAAAAATTCGGTTAACCGACCGGTTTCGAACCGAATTAACCGTTAACCTAAAAATTAAAAAATA
1 GAAAAAATTCGGTTAACCGACCGGTTTCGAACCGAATTAACCGTTAACCTAAAAATTAAAAAATA
5529848 ATTAACCGACCCCCGACC
66 ATTAACCGACCCCCGACC
5529866 GAAAAAATTCGGTTAACCGACCGGTTTCGAACCGAATTAACCGTTAACCTAAAAATTAAAAAATA
1 GAAAAAATTCGGTTAACCGACCGGTTTCGAACCGAATTAACCGTTAACCTAAAAATTAAAAAATA
5529931 ATTAACCGACCCCCGACC
66 ATTAACCGACCCCCGACC
5529949 GAAAAAATTCGGTTAACCGACCG
1 GAAAAAATTCGGTTAACCGACCG
5529972 ATTAACCGAA
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 106 1.00
ACGTcount: A:0.41, C:0.25, G:0.14, T:0.20
Consensus pattern (83 bp):
GAAAAAATTCGGTTAACCGACCGGTTTCGAACCGAATTAACCGTTAACCTAAAAATTAAAAAATA
ATTAACCGACCCCCGACC
Found at i:5533700 original size:11 final size:11
Alignment explanation
Indices: 5533678--5533710 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
5533668 ATTTAATAAT
5533678 AATTAT-TTTA
1 AATTATATTTA
5533688 AATTATATTTA
1 AATTATATTTA
5533699 AATTATATTTA
1 AATTATATTTA
5533710 A
1 A
5533711 TAATAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.27
11 16 0.73
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
AATTATATTTA
Found at i:5533702 original size:21 final size:19
Alignment explanation
Indices: 5533677--5533737 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 19
5533667 TATTTAATAA
5533677 TAATTATTTTAAATTATATT
1 TAATTATTTTAAATTATA-T
5533697 TAAATTATATTT-AA-TA-A-
1 T-AATTAT-TTTAAATTATAT
5533714 TAATTATTTTAAATTATAT
1 TAATTATTTTAAATTATAT
*
5533733 AAATT
1 TAATT
5533738 CATATAAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 13
0.71 0.02 0.27
Matches are distributed among these distances:
15 3 0.09
16 8 0.24
17 3 0.09
18 1 0.03
19 5 0.15
20 3 0.09
21 8 0.24
22 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TAATTATTTTAAATTATAT
Found at i:5533720 original size:16 final size:15
Alignment explanation
Indices: 5533669--5533725 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 15
5533659 TTGAATGTTA
5533669 TTTAATAATAATTAT
1 TTTAATAATAATTAT
5533684 TTTAAATTATATTTAAATTAT
1 TTT-AA-TA-A--T-AATTAT
5533705 ATTTAATAATAATTAT
1 -TTTAATAATAATTAT
5533721 TTTAA
1 TTTAA
5533726 ATTATATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
15 8 0.23
16 8 0.23
17 3 0.09
18 1 0.03
19 1 0.03
20 3 0.09
21 8 0.23
22 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTAATAATAATTAT
Done.