Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 131 of 221
Found at i:40434442 original size:26 final size:26
Alignment explanation
Indices: 40434413--40434474 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
40434403 TACCCCCAGC
* *
40434413 AAAATTTTGATAATTTTATCCT-TGGT
1 AAAATTTTGACAATTTT-GCCTCTGGT
*
40434439 AAAATTTTGACGATTTTGCCTCTGGT
1 AAAATTTTGACAATTTTGCCTCTGGT
40434465 AAAATTTTGA
1 AAAATTTTGA
40434475 GAAAATATGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
25 3 0.09
26 29 0.91
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.45
Consensus pattern (26 bp):
AAAATTTTGACAATTTTGCCTCTGGT
Found at i:40475185 original size:26 final size:27
Alignment explanation
Indices: 40475132--40475185 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
40475122 ATTTTGGTTC
* *
40475132 ATATGTGTATATGTGTGTAAACTATGA
1 ATATGTGTATATGAGTGCAAACTATGA
40475159 ATATG-GTATATGAGTAGCAAACT-TGA
1 ATATGTGTATATGAGT-GCAAACTATGA
40475185 A
1 A
40475186 AGTGAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (27 bp):
ATATGTGTATATGAGTGCAAACTATGA
Found at i:40477907 original size:12 final size:12
Alignment explanation
Indices: 40477890--40477916 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
40477880 CACACGCCCG
40477890 TGTGCTAGGCCA
1 TGTGCTAGGCCA
40477902 TGTGCTAGGCCA
1 TGTGCTAGGCCA
40477914 TGT
1 TGT
40477917 AACAGCCTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.22, G:0.33, T:0.30
Consensus pattern (12 bp):
TGTGCTAGGCCA
Found at i:40479164 original size:25 final size:25
Alignment explanation
Indices: 40479136--40479212 Score: 109
Period size: 25 Copynumber: 3.1 Consensus size: 25
40479126 ATTCGAGTTG
* *
40479136 TAAATCGATATGCTCTCACAAGCTA
1 TAAATCGGTATGCTCTCACGAGCTA
* * *
40479161 TAAATTGGTTTGCTCTTACGAGCTA
1 TAAATCGGTATGCTCTCACGAGCTA
40479186 TAAATCGGTATGCTCTCACGAGCTA
1 TAAATCGGTATGCTCTCACGAGCTA
40479211 TA
1 TA
40479213 GAGTATCCGT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (25 bp):
TAAATCGGTATGCTCTCACGAGCTA
Found at i:40490630 original size:25 final size:25
Alignment explanation
Indices: 40490602--40490650 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
40490592 TACATTGATC
40490602 CATTCACATTGTG-ATAACA-TAATAA
1 CATTCA-ATT-TGAATAACATTAATAA
40490627 CATTCAATTTGAATAACATTAATA
1 CATTCAATTTGAATAACATTAATA
40490651 CAATAACTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 2 0.09
24 9 0.41
25 11 0.50
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.35
Consensus pattern (25 bp):
CATTCAATTTGAATAACATTAATAA
Found at i:40495231 original size:40 final size:40
Alignment explanation
Indices: 40495187--40495448 Score: 363
Period size: 40 Copynumber: 6.6 Consensus size: 40
40495177 TCCTCGTTCG
* *
40495187 AATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACA
*
40495227 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACA
*
40495267 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACA
*
40495307 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACA
* *
40495347 AATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACA
* * * *
40495386 AATGCCTTCGGAACTTAGTCCGGATATT-GTCACTTAGCAC-
1 AATGCCTTCGGGACTTAGCCCGGAT-TTAGTAAC-TCGCACA
40495426 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
40495449 CAGCATTCAA
Statistics
Matches: 204, Mismatches: 14, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
39 54 0.26
40 141 0.69
41 9 0.04
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACA
Found at i:40503300 original size:79 final size:80
Alignment explanation
Indices: 40503200--40503381 Score: 216
Period size: 79 Copynumber: 2.3 Consensus size: 80
40503190 TCCTCGTTCG
* *
40503200 AATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAACCCG
1 AATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTC-GGATCTTAACCCG
*
40503262 GAT-TTAGTAAC-TCGCAC
63 GATATT-GTAACTTAGCAC
**
40503279 AAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAACCCGGA
*
40503343 TATTGTCACTTAGCAC
65 TATTGTAACTTAGCAC
40503359 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
40503382 CAGCATTCAA
Statistics
Matches: 90, Mismatches: 6, Indels: 13
0.83 0.06 0.12
Matches are distributed among these distances:
78 14 0.16
79 56 0.62
80 20 0.22
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.26
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAACCCGGAT
ATTGTAACTTAGCAC
Found at i:40503315 original size:39 final size:41
Alignment explanation
Indices: 40503200--40503381 Score: 195
Period size: 40 Copynumber: 4.6 Consensus size: 41
40503190 TCCTCGTTCG
* *
40503200 AATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACA
1 AATGCCTTCGGGACTTAGCCCGGAAT-TAGTAATCTCGCACA
* *
40503240 AATGCCTTCGGGACTTAACCCGGATTTAGTAA-CTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCACA
40503280 AATGCCTTCGGG-CTTAGCCCGGAATTAGT-ATCTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCACA
* * *
40503319 AATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCAC-
1 AATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAATC-TCGCACA
40503359 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
40503382 CAGCATTCAA
Statistics
Matches: 126, Mismatches: 7, Indels: 19
0.83 0.05 0.12
Matches are distributed among these distances:
38 3 0.02
39 48 0.38
40 64 0.51
41 11 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.26
Consensus pattern (41 bp):
AATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCACA
Found at i:40511915 original size:15 final size:14
Alignment explanation
Indices: 40511867--40511904 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
40511857 ATATATTCAA
40511867 ATATATTTT-AAAT
1 ATATATTTTAAAAT
40511880 A-AT-TTTTAAAAT
1 ATATATTTTAAAAT
40511892 ATATATTTTAAAA
1 ATATATTTTAAAA
40511905 CTGATTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 4 0.18
12 7 0.32
13 3 0.14
14 8 0.36
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATATTTTAAAAT
Found at i:40512040 original size:8 final size:8
Alignment explanation
Indices: 40512027--40512051 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
40512017 TTTTCTATAA
40512027 TACATTTT
1 TACATTTT
40512035 TACATTTT
1 TACATTTT
40512043 TACATTTT
1 TACATTTT
40512051 T
1 T
40512052 GATAGTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (8 bp):
TACATTTT
Found at i:40513872 original size:17 final size:18
Alignment explanation
Indices: 40513839--40513872 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40513829 ACAAGATAGA
*
40513839 AAATAAAAAAGGAAAAAC
1 AAATAAAAAAGAAAAAAC
40513857 AAAT-AAAAAGAAAAAA
1 AAATAAAAAAGAAAAAA
40513873 ATGAACAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.82, C:0.03, G:0.09, T:0.06
Consensus pattern (18 bp):
AAATAAAAAAGAAAAAAC
Found at i:40514815 original size:50 final size:50
Alignment explanation
Indices: 40514761--40515027 Score: 205
Period size: 50 Copynumber: 5.3 Consensus size: 50
40514751 ACCGCCGTGA
*
40514761 CTTCAATCTATTCCACTACACCTCCAGGGAAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTTTTCCACTACACCTCCAGGGAAGTAAGATCCGCCGTTGTGG
** * * * *** * * *
40514811 CTTCAATCTTTTAAATTACA-ATGCCGGGGAAACCAGAGCTGCCGTCGTGG
1 CTTCAATCTTTTCCACTACACCT-CCAGGGAAGTAAGATCCGCCGTTGTGG
** * * ** * *
40514861 CTTCAATCTGCTCCACTACACCGCTAGGGAAGTAAGATATGCCATTGTTG
1 CTTCAATCTTTTCCACTACACCTCCAGGGAAGTAAGATCCGCCGTTGTGG
** * * * * * *** *
40514911 CTTCAATCTTTTTAATTGCA-ATGTCGGGGAAACCAGATCCGCCGTTATGG
1 CTTCAATCTTTTCCACTACACCT-CCAGGGAAGTAAGATCCGCCGTTGTGG
* *
40514961 CTTCAATCTGTTCCACTACACCACCAGGGAAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTTTTCCACTACACCTCCAGGGAAGTAAGATCCGCCGTTGTGG
40515011 CTTCAATCTTTTCCACT
1 CTTCAATCTTTTCCACT
40515028 GTAATGCTAA
Statistics
Matches: 151, Mismatches: 62, Indels: 8
0.68 0.28 0.04
Matches are distributed among these distances:
49 1 0.01
50 150 0.99
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.28
Consensus pattern (50 bp):
CTTCAATCTTTTCCACTACACCTCCAGGGAAGTAAGATCCGCCGTTGTGG
Found at i:40514867 original size:100 final size:100
Alignment explanation
Indices: 40514756--40515022 Score: 381
Period size: 100 Copynumber: 2.7 Consensus size: 100
40514746 GATTCACCGC
* * *
40514756 CGTGACTTCAATCTATTCCACTACACCTCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTT
1 CGTGGCTTCAATCTGTTCCACTACACCACCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTT
*
40514821 TTAAATTACAATGCCGGGGAAACCAGAGCTGCCGT
66 TTAAATTACAATGCCGGGGAAACCAGAGCCGCCGT
* * * ** * *
40514856 CGTGGCTTCAATCTGCTCCACTACACCGCTAGGGAAGTAAGATATGCCATTGTTGCTTCAATCTT
1 CGTGGCTTCAATCTGTTCCACTACACCACCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTT
* * * *
40514921 TTTAATTGCAATGTCGGGGAAACCAGATCCGCCGT
66 TTAAATTACAATGCCGGGGAAACCAGAGCCGCCGT
**
40514956 TATGGCTTCAATCTGTTCCACTACACCACCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTT
1 CGTGGCTTCAATCTGTTCCACTACACCACCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTT
40515021 TT
66 TT
40515023 CCACTGTAAT
Statistics
Matches: 144, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
100 144 1.00
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.28
Consensus pattern (100 bp):
CGTGGCTTCAATCTGTTCCACTACACCACCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTT
TTAAATTACAATGCCGGGGAAACCAGAGCCGCCGT
Found at i:40515364 original size:88 final size:88
Alignment explanation
Indices: 40515215--40515535 Score: 464
Period size: 88 Copynumber: 3.6 Consensus size: 88
40515205 GGCGATAGGA
* * * * *
40515215 CTGATGTCTTCGATCTACTTCGCTGCCAGTACAGGAAGGCAAGATCTG-TCATTTTCGACCTACT
1 CTGATATCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCT-ATTTTCAACCTACT
40515279 CCACTACTGCCCAGGGAGACAAGG
65 CCACTACTGCCCAGGGAGACAAGG
40515303 CTGATATCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTACTC
1 CTGATATCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTACTC
*
40515368 CACTACTGCCTAGGGAGACAAGG
66 CACTACTGCCCAGGGAGACAAGG
* * * * **
40515391 TTGGTATCTTCGATCTGCTTCTCTGTCAGTACAGGAATGCAAGATCTACTATTTTCAACCCGCTC
1 CTGATATCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTACTC
40515456 CACTACTGCCCAGGGAGACAAGG
66 CACTACTGCCCAGGGAGACAAGG
* ** * * *
40515479 CTGGTATCTTTTATCTGCTTCTCTATCAGTACAGGAAGGCAAGATCAGCTATCTTCA
1 CTGATATCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCA
40515536 GTCTGCTCTG
Statistics
Matches: 211, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
88 210 1.00
89 1 0.00
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (88 bp):
CTGATATCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTACTC
CACTACTGCCCAGGGAGACAAGG
Found at i:40520351 original size:27 final size:27
Alignment explanation
Indices: 40520295--40520351 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
40520285 AATGATGTAG
* *
40520295 AAAAAGAATAAAAGAATAATTACTCGA
1 AAAAAGAATAAAAGAATAACTACTCAA
*
40520322 AAAAATAATAAAAGAAT-ACTAGCTCAA
1 AAAAAGAATAAAAGAATAACTA-CTCAA
40520349 AAA
1 AAA
40520352 TGCATACGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 3 0.12
27 23 0.88
ACGTcount: A:0.65, C:0.09, G:0.09, T:0.18
Consensus pattern (27 bp):
AAAAAGAATAAAAGAATAACTACTCAA
Found at i:40527532 original size:24 final size:24
Alignment explanation
Indices: 40527474--40527532 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 24
40527464 ATTATTACCT
* *
40527474 TAATTTAAATTATACATATATATG
1 TAATTTAAAATATACATATATAAG
40527498 T-ATTTACAAAATATA-ATATATAAG
1 TAATTT--AAAATATACATATATAAG
40527522 TAAATTTAAAA
1 T-AATTTAAAA
40527533 AAAATGTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
23 4 0.14
24 14 0.48
25 7 0.24
26 4 0.14
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (24 bp):
TAATTTAAAATATACATATATAAG
Found at i:40528455 original size:17 final size:16
Alignment explanation
Indices: 40528427--40528464 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
40528417 AACAAGATAG
40528427 AAAATAAAAAAGGAAAA
1 AAAATAAAAAA-GAAAA
40528444 ACAAAT-AAAAAGAAAA
1 A-AAATAAAAAAGAAAA
40528460 AAAAT
1 AAAAT
40528465 GAACAGAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.20
16 6 0.30
17 6 0.30
18 4 0.20
ACGTcount: A:0.82, C:0.03, G:0.08, T:0.08
Consensus pattern (16 bp):
AAAATAAAAAAGAAAA
Found at i:40530909 original size:28 final size:28
Alignment explanation
Indices: 40530871--40530946 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
40530861 AGAATTTTTT
* *
40530871 ATTTTTTATTTTTATTACCTTTTTA-TTA
1 ATTTTATATTTTTATTA-ATTTTTATTTA
40530899 ATTTTATA-TTTTATTAATTTTTATTTTA
1 ATTTTATATTTTTATTAATTTTTA-TTTA
40530927 ATTTTA-ATTTTCTA-TAATTT
1 ATTTTATATTTT-TATTAATTT
40530947 ATTTTATATT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
26 6 0.14
27 9 0.21
28 25 0.60
29 2 0.05
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (28 bp):
ATTTTATATTTTTATTAATTTTTATTTA
Found at i:40530925 original size:15 final size:16
Alignment explanation
Indices: 40530891--40530926 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
40530881 TTTATTACCT
40530891 TTTTATTAATTTTATA
1 TTTTATTAATTTTATA
40530907 TTTTATTAATTTT-TA
1 TTTTATTAATTTTATA
40530922 TTTTA
1 TTTTA
40530927 ATTTTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTATTAATTTTATA
Found at i:40530936 original size:27 final size:27
Alignment explanation
Indices: 40530874--40530958 Score: 79
Period size: 26 Copynumber: 3.1 Consensus size: 27
40530864 ATTTTTTATT
* *
40530874 TTTTATTTTTATTACCTTTTTA--TTAA
1 TTTTAATTTTATTA-ATTTTTATTTTAA
40530900 TTTTATATTTTATTAATTTTTATTTTAA
1 TTTTA-ATTTTATTAATTTTTATTTTAA
*
40530928 TTTTAATTTTCTATAA--TTTATTTTATA
1 TTTTAATTTTAT-TAATTTTTATTTTA-A
40530955 TTTT
1 TTTT
40530959 TTACTTTTCT
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
26 20 0.39
27 19 0.37
28 12 0.24
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.71
Consensus pattern (27 bp):
TTTTAATTTTATTAATTTTTATTTTAA
Found at i:40531010 original size:8 final size:8
Alignment explanation
Indices: 40530997--40531049 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
40530987 GGAAAATAAA
40530997 AATTTTTT
1 AATTTTTT
40531005 AATTTTTTT
1 AA-TTTTTT
*
40531014 AATTTTCT
1 AATTTTTT
*
40531022 -ATATTTCT
1 AAT-TTTTT
40531030 AATTTTTT
1 AATTTTTT
*
40531038 ATTTTTTT
1 AATTTTTT
40531046 AATT
1 AATT
40531050 ATTATCATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
7 2 0.05
8 26 0.68
9 10 0.26
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (8 bp):
AATTTTTT
Found at i:40531141 original size:9 final size:10
Alignment explanation
Indices: 40531098--40531143 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
40531088 TTCTATAAAT
40531098 TTTTTTATAA
1 TTTTTTATAA
***
40531108 TTTTAGGTAA
1 TTTTTTATAA
40531118 TTTTTTATAA
1 TTTTTTATAA
*
40531128 TTTTTTATGA
1 TTTTTTATAA
40531138 TTTTTT
1 TTTTTT
40531144 TATTAAATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.70
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:40531154 original size:21 final size:21
Alignment explanation
Indices: 40531096--40531155 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
40531086 GTTTCTATAA
40531096 ATTTTTTTAT-AATTTTAGGT
1 ATTTTTTTATAAATTTTAGGT
* * *
40531116 AATTTTTTATAATTTTTTATG-
1 ATTTTTTTATAA-ATTTTAGGT
40531137 ATTTTTTTATTAAATTTTA
1 ATTTTTTTA-TAAATTTTA
40531156 ATAATCATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 9 0.28
21 14 0.44
22 9 0.28
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (21 bp):
ATTTTTTTATAAATTTTAGGT
Found at i:40554638 original size:16 final size:16
Alignment explanation
Indices: 40554617--40554685 Score: 104
Period size: 16 Copynumber: 4.3 Consensus size: 16
40554607 TTGGTTCGCT
40554617 GTAATGGAATAGAGAC
1 GTAATGGAATAGAGAC
*
40554633 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGAC
40554649 GTAATGGAATAGA-AGC
1 GTAATGGAATAGAGA-C
*
40554665 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGAC
40554681 GTAAT
1 GTAAT
40554686 AGCAATTCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.41, C:0.06, G:0.33, T:0.20
Consensus pattern (16 bp):
GTAATGGAATAGAGAC
Found at i:40554653 original size:32 final size:32
Alignment explanation
Indices: 40554617--40554685 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
40554607 TTGGTTCGCT
40554617 GTAATGGAATAG-AGACGTAATGGAATAGAGGC
1 GTAATGGAATAGAAG-CGTAATGGAATAGAGGC
40554649 GTAATGGAATAGAAGCGTAATGGAATAGAGGC
1 GTAATGGAATAGAAGCGTAATGGAATAGAGGC
40554681 GTAAT
1 GTAAT
40554686 AGCAATTCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
32 34 0.94
33 2 0.06
ACGTcount: A:0.41, C:0.06, G:0.33, T:0.20
Consensus pattern (32 bp):
GTAATGGAATAGAAGCGTAATGGAATAGAGGC
Found at i:40554726 original size:45 final size:45
Alignment explanation
Indices: 40554665--40554778 Score: 151
Period size: 44 Copynumber: 2.6 Consensus size: 45
40554655 GAATAGAAGC
40554665 GTAATGGAATAGAGGCGTAATAGCAATTCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGCAATTC-ATGTGTTTGGTTGAAT
* *
40554710 GTAATGGAATAGAGGCGTAATAG-TATTCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGCAATTCATGTGTTTGGTTGAAT
* * * *
40554754 GGAATGGAGTGGAGGTGTAATAGCA
1 GTAATGGAATAGAGGCGTAATAGCA
40554779 TAAGGGAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
43 1 0.02
44 36 0.60
45 23 0.38
ACGTcount: A:0.31, C:0.05, G:0.32, T:0.32
Consensus pattern (45 bp):
GTAATGGAATAGAGGCGTAATAGCAATTCATGTGTTTGGTTGAAT
Found at i:40554961 original size:17 final size:18
Alignment explanation
Indices: 40554920--40554954 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
40554910 TAATTATTAA
*
40554920 ATATATTTTAATTAAAAT
1 ATATAATTTAATTAAAAT
40554938 ATATAATTTAA-TAAAAT
1 ATATAATTTAATTAAAAT
40554955 TTTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATAATTTAATTAAAAT
Found at i:40555047 original size:16 final size:14
Alignment explanation
Indices: 40555017--40555068 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
40555007 CTATAAAATA
40555017 TAATTTAAAATAAT
1 TAATTTAAAATAAT
40555031 TAATATTAAATATAAT
1 TAAT-TTAAA-ATAAT
* *
40555047 TTAGTTAAAAT-AT
1 TAATTTAAAATAAT
40555060 ATAATTTAA
1 -TAATTTAA
40555069 TAAAATTCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
13 2 0.06
14 12 0.39
15 10 0.32
16 7 0.23
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (14 bp):
TAATTTAAAATAAT
Found at i:40555120 original size:117 final size:120
Alignment explanation
Indices: 40554914--40555134 Score: 360
Period size: 117 Copynumber: 1.9 Consensus size: 120
40554904 TTAACATAAT
* *
40554914 TATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTTTTAATAATCAATATTCTTATAT
1 TATTAAATATAATTTAATTAAAATATATAATTTAATAAAA-TTTCAATAATCAATATTCTTATAT
40554979 GAATTTACTAAAATCATAATATATAATACTAT-AAAATATAATTTAAAATAATTAA
65 GAATTTACTAAAATCATAATATATAATACTATGAAAATATAATTTAAAATAATTAA
*
40555034 TATTAAATATAATTTAGTTAAAATATATAATTTAATAAAA-TTCAAT-AT-AATTATTCTTATAT
1 TATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTTCAATAATCAA-TATTCTTATAT
*
40555096 GAATTTACTAAAATCATATTATATAATACTATGAAAATA
65 GAATTTACTAAAATCATAATATATAATACTATGAAAATA
40555135 ATATATAATC
Statistics
Matches: 95, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
116 2 0.02
117 44 0.46
118 11 0.12
120 38 0.40
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
TATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTTCAATAATCAATATTCTTATATG
AATTTACTAAAATCATAATATATAATACTATGAAAATATAATTTAAAATAATTAA
Found at i:40556812 original size:4 final size:4
Alignment explanation
Indices: 40556803--40556833 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
40556793 GATGTTTATA
*
40556803 TATG TATG TATG TATG TATG CATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
40556834 TTGGTTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:40557870 original size:46 final size:46
Alignment explanation
Indices: 40557804--40557894 Score: 155
Period size: 46 Copynumber: 2.0 Consensus size: 46
40557794 TCAAAGAAAG
*
40557804 AAGACTTGCAATCAGAAACTATTAGGCTTCACAGAATAAACTTTCA
1 AAGACTTGCAATCAGAAACTATGAGGCTTCACAGAATAAACTTTCA
* *
40557850 AAGACTTGCAATCAGAAACTATGATGCTTCATAGAATAAACTTTC
1 AAGACTTGCAATCAGAAACTATGAGGCTTCACAGAATAAACTTTC
40557895 TCGGATACAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (46 bp):
AAGACTTGCAATCAGAAACTATGAGGCTTCACAGAATAAACTTTCA
Found at i:40558932 original size:17 final size:17
Alignment explanation
Indices: 40558891--40558940 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
40558881 AAATTAAAAA
*
40558891 ACAAAATTTATAAACATT
1 ACAAAATTTAT-AATATT
* *
40558909 TCAAAATATATAATATT
1 ACAAAATTTATAATATT
40558926 ACAAAATTTATAATA
1 ACAAAATTTATAATA
40558941 AGATTGTTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 18 0.67
18 9 0.33
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (17 bp):
ACAAAATTTATAATATT
Found at i:40564111 original size:43 final size:43
Alignment explanation
Indices: 40564046--40564315 Score: 400
Period size: 43 Copynumber: 6.3 Consensus size: 43
40564036 TTATGTAAAA
* **
40564046 AAACGTCGCTAAAGAACATGACCTTTAGCGGCATTTTACCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCAC
* * *
40564089 AAACGCCGCTAAAGAACTTGACCTTTAGCAGCGCTTCACCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCAC
40564132 AAACGCCGCTAAAGAACATGACCTTTAGCGGCG-TTTCACCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTT-ACCCAC
*
40564175 AAACGCCGCTAAAGAACATCACCTTTAGCGGCGCTTTACCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTA-CCCAC
* *
40564219 AAACGCCGCTAAAGAATATGACATTTAGCGGCGCTTTACCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCAC
* * *
40564262 AAATGCCGCTAAAGAACATGATCTTTAGCGGTGCTTTA-CCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCAC
40564304 AAACGCCGCTAA
1 AAACGCCGCTAA
40564316 TTTTGACAAA
Statistics
Matches: 205, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
42 17 0.08
43 145 0.71
44 43 0.21
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.20
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCAC
Found at i:40564260 original size:87 final size:85
Alignment explanation
Indices: 40564046--40564315 Score: 398
Period size: 87 Copynumber: 3.1 Consensus size: 85
40564036 TTATGTAAAA
* * *
40564046 AAACGTCGCTAAAGAACATGACCTTTAGCGGCATTTTACCCACAAACGCCGCTAAAGAACTTGAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGC-GTTTACCCACAAACGCCGCTAAAGAACATGAC
* *
40564111 CTTTAGCAGCGCTTCACCCAC
65 CTTTAGCGGCGCTTTACCCAC
*
40564132 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGTTTCACCCACAAACGCCGCTAAAGAACATCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGTTT-ACCCACAAACGCCGCTAAAGAACATGAC
40564197 CTTTAGCGGCGCTTTACCCCAC
65 CTTTAGCGGCGCTTTA-CCCAC
* * * *
40564219 AAACGCCGCTAAAGAATATGACATTTAGCGGCGCTTTACCCACAAATGCCGCTAAAGAACATGAT
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCG-TTTACCCACAAACGCCGCTAAAGAACATGAC
*
40564284 CTTTAGCGGTGCTTTA-CCAC
65 CTTTAGCGGCGCTTTACCCAC
40564304 AAACGCCGCTAA
1 AAACGCCGCTAA
40564316 TTTTGACAAA
Statistics
Matches: 169, Mismatches: 12, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
85 19 0.11
86 71 0.42
87 76 0.45
88 3 0.02
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.20
Consensus pattern (85 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGTTTACCCACAAACGCCGCTAAAGAACATGACC
TTTAGCGGCGCTTTACCCAC
Found at i:40569654 original size:42 final size:42
Alignment explanation
Indices: 40569595--40569681 Score: 156
Period size: 42 Copynumber: 2.1 Consensus size: 42
40569585 GTTTAGGAGA
* *
40569595 TCTGCAGTACTCTGTCAATGCTCTAAGATGTCGTATACTCTT
1 TCTGCAGTACTCTGTCAATGCTCCAAGATGTCGCATACTCTT
40569637 TCTGCAGTACTCTGTCAATGCTCCAAGATGTCGCATACTCTT
1 TCTGCAGTACTCTGTCAATGCTCCAAGATGTCGCATACTCTT
40569679 TCT
1 TCT
40569682 TGTTGATTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (42 bp):
TCTGCAGTACTCTGTCAATGCTCCAAGATGTCGCATACTCTT
Found at i:40578329 original size:22 final size:22
Alignment explanation
Indices: 40578304--40578353 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
40578294 GGTGCATACC
40578304 CGACGGCTCCTCAAATCCCAAG
1 CGACGGCTCCTCAAATCCCAAG
40578326 CGACGGCTCCTCAAATCCCAAG
1 CGACGGCTCCTCAAATCCCAAG
*
40578348 CAACGG
1 CGACGG
40578354 AACCCAATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.28, C:0.40, G:0.20, T:0.12
Consensus pattern (22 bp):
CGACGGCTCCTCAAATCCCAAG
Found at i:40584523 original size:16 final size:16
Alignment explanation
Indices: 40584494--40584532 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
40584484 TTTCGGGTAT
40584494 GGGAA-AAA-TTTGAG
1 GGGAATAAATTTTGAG
*
40584508 GGGACTAAATTTTGAG
1 GGGAATAAATTTTGAG
40584524 GGGAATAAA
1 GGGAATAAA
40584533 ACGATAGCGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 4 0.19
15 3 0.14
16 14 0.67
ACGTcount: A:0.41, C:0.03, G:0.33, T:0.23
Consensus pattern (16 bp):
GGGAATAAATTTTGAG
Found at i:40584839 original size:47 final size:48
Alignment explanation
Indices: 40584781--40584879 Score: 182
Period size: 47 Copynumber: 2.1 Consensus size: 48
40584771 CATAGTTTTG
*
40584781 TTTAAGTAATATTTATAAAAATTAGATAAAATTATAAATTTTAGT-TT
1 TTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAATTTTAGTGTT
40584828 TTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAATTTTAGTGTT
1 TTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAATTTTAGTGTT
40584876 TTTA
1 TTTA
40584880 TTTTTTTTAT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 44 0.88
48 6 0.12
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (48 bp):
TTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAATTTTAGTGTT
Found at i:40585325 original size:15 final size:15
Alignment explanation
Indices: 40585305--40585333 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40585295 CCACTAACGT
40585305 CTAACCCCTAAACCC
1 CTAACCCCTAAACCC
40585320 CTAACCCCTAAACC
1 CTAACCCCTAAACC
40585334 TTAAATCCCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.52, G:0.00, T:0.14
Consensus pattern (15 bp):
CTAACCCCTAAACCC
Found at i:40585641 original size:22 final size:21
Alignment explanation
Indices: 40585602--40585642 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
40585592 CCCTAAATCC
*
40585602 CTAACTCTTAACCACTAACAT
1 CTAACTCTAAACCACTAACAT
*
40585623 CTAACTCCTAAACCCCTAAC
1 CTAACT-CTAAACCACTAAC
40585643 CCCTAAACCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.37, C:0.39, G:0.00, T:0.24
Consensus pattern (21 bp):
CTAACTCTAAACCACTAACAT
Found at i:40585801 original size:318 final size:317
Alignment explanation
Indices: 40585183--40585888 Score: 1100
Period size: 318 Copynumber: 2.2 Consensus size: 317
40585173 TAAATTATAC
* *
40585183 ATCTTTTACAATTACATAAGAACATATTTAAAATATAAATAAAAAAATTAATCTAAACCCAAAAC
1 ATCTTTTACAACTACATAATAACATATTTAAAATATAAATAAAAAAATTAATCTAAACCCAAAAC
* * *
40585248 CTTAACCCGACTCTTGAAACCCTAAACCCTAAATCCCTAACTCTTAACCACTAACGTCTAACCCC
66 CCTAACCCGACCCTTGAAACCCTAAACCCTAAATCCCTAACTCTTAACCACTAACATCTAACCCC
* *
40585313 TAAACCCCTAACCCCTAAACCTTAAATCCCGACCAACCCTTAATTAAACCATAATCCCTAATCTA
131 TAAACCCCTAACCCCTAAACCTTAAATCCAGACCAACCCTTAATTAAACCATAATCCCTAATCCA
* * * *
40585378 TAATCCCTAAATCCATATATATATAGTACTCCCTAAACCTTTAAATATGAACTCCTAAACCAGCC
196 TAATCCCT-AAGCCAAATATATATAGTACTACCTAAACCTTAAAATATGAACTCCTAAACCAGCC
*
40585443 TTAAATCTTAATTATCATATACCCTAATCTAATTAAAACCCTAAACAATTTTATTATT
260 TTAAATCTTAATTATCATATACCCTAAACTAATTAAAACCCTAAACAATTTTATTATT
*
40585501 ATCTTCTACAACTACATAATAACATATTTAAAATATAAATAAAAAAATTAATCTAAACCCAAAAC
1 ATCTTTTACAACTACATAATAACATATTTAAAATATAAATAAAAAAATTAATCTAAACCCAAAAC
* *
40585566 CCTAACCCGACCCTTGAAACCTTAAACCCTAAATCCCTAACTCTTAACCACTAACATCTAACTCC
66 CCTAACCCGACCCTTGAAACCCTAAACCCTAAATCCCTAACTCTTAACCACTAACATCTAACCCC
*
40585631 TAAACCCCTAACCCCTAAACCTTAAATCCAGGCCAACCCTTAATTAAACCATAATCCCTAATCCA
131 TAAACCCCTAACCCCTAAACCTTAAATCCAGACCAACCCTTAATTAAACCATAATCCCTAATCCA
* * *
40585696 TAATCCCT-AGCTAAATCTATAT-GTACTACCTAAACCTTAAAATATGAACTCCTAAACCGGCCT
196 TAATCCCTAAGCCAAATATATATAGTACTACCTAAACCTTAAAATATGAACTCCTAAACCAGCCT
40585759 TAAATCTTAAATTTATCATATACCCTAAACTAATTAAAAACCCTAAACAATTTTATTATT
261 TAAATCTT-AA-TTATCATATACCCTAAACTAATT-AAAACCCTAAACAATTTTATTATT
*
40585819 ATCTCTTTTACGATTACATATATAATAACATATTTAAAATATAAAT--AAAAA--AATCTAAACC
1 A--TCTTTTAC-A--AC-TACATAATAACATATTTAAAATATAAATAAAAAAATTAATCTAAACC
40585880 CAAAACCCT
60 CAAAACCCT
40585889 GACCTTAAAC
Statistics
Matches: 358, Mismatches: 21, Indels: 16
0.91 0.05 0.04
Matches are distributed among these distances:
315 46 0.13
316 12 0.03
317 22 0.06
318 217 0.61
320 26 0.07
321 1 0.00
322 5 0.01
323 2 0.01
324 27 0.08
ACGTcount: A:0.42, C:0.26, G:0.03, T:0.29
Consensus pattern (317 bp):
ATCTTTTACAACTACATAATAACATATTTAAAATATAAATAAAAAAATTAATCTAAACCCAAAAC
CCTAACCCGACCCTTGAAACCCTAAACCCTAAATCCCTAACTCTTAACCACTAACATCTAACCCC
TAAACCCCTAACCCCTAAACCTTAAATCCAGACCAACCCTTAATTAAACCATAATCCCTAATCCA
TAATCCCTAAGCCAAATATATATAGTACTACCTAAACCTTAAAATATGAACTCCTAAACCAGCCT
TAAATCTTAATTATCATATACCCTAAACTAATTAAAACCCTAAACAATTTTATTATT
Found at i:40585904 original size:7 final size:7
Alignment explanation
Indices: 40585873--40585939 Score: 82
Period size: 7 Copynumber: 9.7 Consensus size: 7
40585863 ATAAAAAAAT
40585873 CTAAACC
1 CTAAACC
*
40585880 CAAAACC
1 CTAAACC
*
40585887 CT-GACC
1 CTAAACC
*
40585893 TTAAACC
1 CTAAACC
40585900 CTAAACC
1 CTAAACC
*
40585907 ATAAACC
1 CTAAACC
40585914 CTAAACC
1 CTAAACC
*
40585921 ATAAACC
1 CTAAACC
40585928 CTAAACC
1 CTAAACC
40585935 CTAAA
1 CTAAA
40585940 TTCATAAACC
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
6 4 0.08
7 45 0.92
ACGTcount: A:0.46, C:0.37, G:0.01, T:0.15
Consensus pattern (7 bp):
CTAAACC
Found at i:40585920 original size:21 final size:21
Alignment explanation
Indices: 40585895--40585949 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
40585885 CCCTGACCTT
*
40585895 AAACCCTAAACCATAAACCCT
1 AAACCATAAACCATAAACCCT
*
40585916 AAACCATAAACCCTAAACCCT
1 AAACCATAAACCATAAACCCT
*
40585937 AAATTCATAAACC
1 AAA-CCATAAACC
40585950 TCAAATCCCT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 22 0.73
22 8 0.27
ACGTcount: A:0.49, C:0.35, G:0.00, T:0.16
Consensus pattern (21 bp):
AAACCATAAACCATAAACCCT
Found at i:40585982 original size:37 final size:37
Alignment explanation
Indices: 40585933--40586012 Score: 151
Period size: 37 Copynumber: 2.2 Consensus size: 37
40585923 AAACCCTAAA
40585933 CCCTAAATTCATAAACCTCAAATCCCTAACTCTTAAC
1 CCCTAAATTCATAAACCTCAAATCCCTAACTCTTAAC
*
40585970 CCCTAAATTCATAAACCTTAAATCCCTAACTCTTAAC
1 CCCTAAATTCATAAACCTCAAATCCCTAACTCTTAAC
40586007 CCCTAA
1 CCCTAA
40586013 CATCTAACCC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.28
Consensus pattern (37 bp):
CCCTAAATTCATAAACCTCAAATCCCTAACTCTTAAC
Found at i:40586013 original size:7 final size:7
Alignment explanation
Indices: 40585993--40586041 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
40585983 AACCTTAAAT
40585993 CCCTAAC
1 CCCTAAC
* *
40586000 TCTTAAC
1 CCCTAAC
40586007 CCCTAAC
1 CCCTAAC
**
40586014 ATCTAAC
1 CCCTAAC
40586021 CCCTAAAC
1 CCCT-AAC
40586029 CCCTAAC
1 CCCTAAC
40586036 CCCTAA
1 CCCTAA
40586042 ACTTTAAATC
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
7 26 0.79
8 7 0.21
ACGTcount: A:0.33, C:0.47, G:0.00, T:0.20
Consensus pattern (7 bp):
CCCTAAC
Found at i:40586036 original size:15 final size:15
Alignment explanation
Indices: 40586003--40586043 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
40585993 CCCTAACTCT
*
40586003 TAACCCCT-AACATC
1 TAACCCCTAAACACC
*
40586017 TAACCCCTAAACCCC
1 TAACCCCTAAACACC
40586032 TAACCCCTAAAC
1 TAACCCCTAAAC
40586044 TTTAAATCCC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.37, C:0.46, G:0.00, T:0.17
Consensus pattern (15 bp):
TAACCCCTAAACACC
Found at i:40586099 original size:15 final size:15
Alignment explanation
Indices: 40586064--40586101 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
40586054 AACCCTTAAT
40586064 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
40586078 T-AATCCATAATCCC
1 TAAATCCATAATCCC
40586092 TAAATCCATA
1 TAAATCCATA
40586102 TATATATACT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.09
14 12 0.55
15 8 0.36
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:40587270 original size:41 final size:40
Alignment explanation
Indices: 40587225--40587693 Score: 501
Period size: 41 Copynumber: 11.4 Consensus size: 40
40587215 GTGTTTTAAC
* *
40587225 AAAAACGACGCTAAAACCTCA-AGCATTAGCGGCTCTTCTTA
1 AAAAACGCCGCTAAAACC-CAGAGCATTAGCGGCGCTT-TTA
* * *
40587266 AAAAACGCCGCTAAAACCCCGAGAATTAGCAGCGCTTTTCA
1 AAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTTTT-A
* ** *
40587307 GAAAATTCCGCTAAAACCCCGAGCATTAGCGGCGCTTCTTA
1 AAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTT-TTA
* *
40587348 GAAAACGCCGCTAAAACCCAGAGCATTAGTGGCGCTTTTTA
1 AAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGC-TTTTA
* *
40587389 GAAAACGCCGCTAAAACCTAGAGCATTAGCGGCGCTTCTTA
1 AAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTT-TTA
*
40587430 TTAGAAAACACCGCTAAAACCCAGAGCATTAGCGGCGCTTATTA
1 --A-AAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTT-TTA
* * *
40587474 ATAAACGCCGCTAAAACCCTGAGCATTAGCGGCGCTTTCA
1 AAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTTTTA
* **
40587514 CAAAAACGCCGCTAAAACCAAGAGCATTAGCGATGCTTCTTA
1 -AAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTT-TTA
* * *
40587556 AAAAACGCCGCTAAAACCCCGAGCATTAGTGGCGCTTTCA
1 AAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTTTTA
*
40587596 CAAAAACGCCGCTAAAACCCAGAGCATTAGCGGTGCTTTCTA
1 -AAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTTT-TA
** * * * *
40587638 AAAAACATCGCTAAAACTCTGAGCATTAGTGGCGATTTCTCA
1 AAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTTT-T-A
*
40587680 AAAAA-GCCACTAAA
1 AAAAACGCCGCTAAA
40587694 GCCACCGAAG
Statistics
Matches: 365, Mismatches: 50, Indels: 26
0.83 0.11 0.06
Matches are distributed among these distances:
40 9 0.02
41 305 0.84
42 14 0.04
44 37 0.10
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (40 bp):
AAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTTTTA
Found at i:40587591 original size:208 final size:205
Alignment explanation
Indices: 40587225--40587671 Score: 580
Period size: 208 Copynumber: 2.2 Consensus size: 205
40587215 GTGTTTTAAC
* *
40587225 AAAAACGA-CGCTAAAACCTCA-AGCATTAGCGGCTCTTCTTAAAAAACGCCGCTAAAACCCCGA
1 AAAAAC-ACCGCTAAAACC-CAGAGCATTAGCGGCGCTTATTAAAAAACGCCGCTAAAACCCCGA
* ** ** * *
40587288 GAATTAGCAGCGCTTTTCAGAAAATTCCGCTAAAACCCCGAGCATTAGCGGCGCTTCTTAGAAAA
64 GAATTAGCAGCGCTTTTCAAAAAACGCCGCTAAAACCAAGAGCATTAGCGACGCTTCTTAAAAAA
* * *
40587353 CGCCGCTAAAACCCAGAGCATTAGTGGCGCTTTTTA-GAAAACGCCGCTAAAACCTAGAGCATTA
129 CGCCGCTAAAACCCAGAGCATTAGTGGCGC-TTTCACAAAAACGCCGCTAAAACCCAGAGCATTA
40587417 GCGGCGC-TTCTTA
193 GCGGCGCTTTC-TA
* *
40587430 TTAGAAAACACCGCTAAAACCCAGAGCATTAGCGGCGCTTATTAATAAACGCCGCTAAAACCCTG
1 --A-AAAACACCGCTAAAACCCAGAGCATTAGCGGCGCTTATTAAAAAACGCCGCTAAAACCCCG
* * *
40587495 AGCATTAGCGGCGC-TTTCACAAAAACGCCGCTAAAACCAAGAGCATTAGCGATGCTTCTTAAAA
63 AGAATTAGCAGCGCTTTTCA-AAAAACGCCGCTAAAACCAAGAGCATTAGCGACGCTTCTTAAAA
*
40587559 AACGCCGCTAAAACCCCGAGCATTAGTGGCGCTTTCACAAAAACGCCGCTAAAACCCAGAGCATT
127 AACGCCGCTAAAACCCAGAGCATTAGTGGCGCTTTCACAAAAACGCCGCTAAAACCCAGAGCATT
*
40587624 AGCGGTGCTTTCTA
192 AGCGGCGCTTTCTA
* * * *
40587638 AAAAACATCGCTAAAACTCTGAGCATTAGTGGCG
1 AAAAACACCGCTAAAACCCAGAGCATTAGCGGCG
40587672 ATTTCTCAAA
Statistics
Matches: 211, Mismatches: 23, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
205 29 0.14
206 1 0.00
207 13 0.06
208 165 0.78
209 3 0.01
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (205 bp):
AAAAACACCGCTAAAACCCAGAGCATTAGCGGCGCTTATTAAAAAACGCCGCTAAAACCCCGAGA
ATTAGCAGCGCTTTTCAAAAAACGCCGCTAAAACCAAGAGCATTAGCGACGCTTCTTAAAAAACG
CCGCTAAAACCCAGAGCATTAGTGGCGCTTTCACAAAAACGCCGCTAAAACCCAGAGCATTAGCG
GCGCTTTCTA
Found at i:40591333 original size:8 final size:8
Alignment explanation
Indices: 40591320--40591353 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
40591310 CAAAATTCAG
40591320 AATAATAA
1 AATAATAA
40591328 AATAATAA
1 AATAATAA
40591336 AATAATAA
1 AATAATAA
40591344 AATAATAA
1 AATAATAA
40591352 AA
1 AA
40591354 CTTAATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAATAA
Found at i:40593652 original size:17 final size:17
Alignment explanation
Indices: 40593630--40593667 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
40593620 CACACTGCCT
*
40593630 TGTGAGCCATACGGGCG
1 TGTGAGCCATACGAGCG
40593647 TGTGAGCCATACGAGCG
1 TGTGAGCCATACGAGCG
40593664 TGTG
1 TGTG
40593668 CTAGACCGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.21, G:0.39, T:0.21
Consensus pattern (17 bp):
TGTGAGCCATACGAGCG
Found at i:40595512 original size:29 final size:29
Alignment explanation
Indices: 40595447--40595515 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 29
40595437 TACAGAGATG
* *
40595447 CATTGAAGTGCAATAAGAAAACAAAGTGA
1 CATTGAAGTGCAATAACAAAACAAAATGA
** * *
40595476 TGTCGAAGTGCAATACCAAAACAAAATGA
1 CATTGAAGTGCAATAACAAAACAAAATGA
40595505 CATTGAAGTGC
1 CATTGAAGTGC
40595516 TTAGCAGAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.46, C:0.14, G:0.20, T:0.19
Consensus pattern (29 bp):
CATTGAAGTGCAATAACAAAACAAAATGA
Found at i:40596903 original size:43 final size:42
Alignment explanation
Indices: 40596835--40597104 Score: 305
Period size: 42 Copynumber: 6.4 Consensus size: 42
40596825 ACGTCGCTAA
* * *
40596835 CTTTTGCGGCGCTTACAGAAAAAACGCTGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTA-GGAAAAAACGCCGCTAAAGATCATGTT
* * *
40596878 CTTTAGCGGCACTAAGGAAATAAACGCCACTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAA-AAACGCCGCTAAAGATCATGTT
* * *
40596921 CTTTAGCGGCGCTTATGAAAAAATGCTGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
40596963 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
* * *
40597005 CTTTACCGGCGCTTTGGAAGAAAACGCCGCTAAA-AGTAATGTT
1 CTTTAGCGGCGCTTAGGAA-AAAACGCCGCTAAAGA-TCATGTT
* ** *
40597048 CTATAGCGGCGCTT-GTTCAAAAACACCGCTAACAG-T-AGTGTT
1 CTTTAGCGGCGCTTAG-GAAAAAACGCCGCTAA-AGATCA-TGTT
40597090 CTTTAGCGGCGCTTA
1 CTTTAGCGGCGCTTA
40597105 TTTCACAAAT
Statistics
Matches: 195, Mismatches: 24, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
41 1 0.01
42 111 0.57
43 83 0.43
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
Found at i:40596994 original size:127 final size:128
Alignment explanation
Indices: 40596835--40597104 Score: 325
Period size: 127 Copynumber: 2.1 Consensus size: 128
40596825 ACGTCGCTAA
* * *
40596835 CTTTTGCGGCGCTTACAGAAAAAACGCTGCTAAAGATCATGTTCTTTAGCGGCACTAAGGAA-AT
1 CTTTAGCGGCGCTTACAGAAAAAACGCCGCTAAAGATCATGTTCTTTACCGGCACTAAGGAAGA-
* * ** *
40596899 AAACGCCACT-AAAGATCATGTTCTTTAGCGGCGCTTATGAAAAAATGCTGCTAA-AGATCA-TG
65 AAACGCCACTAAAAG-TAATGTTCTATAGCGGCGCTTATGAAAAAACACCGCTAACAG-T-AGTG
40596961 TT
127 TT
* * **
40596963 CTTTAGCGGCGCTTA-GGAAAAAACGCCGCTAAAGATCATGTTCTTTACCGGCGCTTTGGAAGAA
1 CTTTAGCGGCGCTTACAGAAAAAACGCCGCTAAAGATCATGTTCTTTACCGGCACTAAGGAAGAA
* * **
40597027 AACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTGTTCAAAAACACCGCTAACAGTAGTGTT
66 AACGCCACTAAAAGTAATGTTCTATAGCGGCGCTTATGAAAAAACACCGCTAACAGTAGTGTT
40597090 CTTTAGCGGCGCTTA
1 CTTTAGCGGCGCTTA
40597105 TTTCACAAAT
Statistics
Matches: 122, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
126 1 0.01
127 100 0.82
128 21 0.17
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (128 bp):
CTTTAGCGGCGCTTACAGAAAAAACGCCGCTAAAGATCATGTTCTTTACCGGCACTAAGGAAGAA
AACGCCACTAAAAGTAATGTTCTATAGCGGCGCTTATGAAAAAACACCGCTAACAGTAGTGTT
Found at i:40597037 original size:85 final size:84
Alignment explanation
Indices: 40596835--40597105 Score: 318
Period size: 85 Copynumber: 3.2 Consensus size: 84
40596825 ACGTCGCTAA
* * * *
40596835 CTTTTGCGGCGCTTACAGAAAAAACGCTGCTAAAGATCATGTTCTTTAGCGGCACTAAGGAAATA
1 CTTTAGCGGCGCTTA-TGAAAAAACGCTGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAA-A
*
40596900 AACGCCACTAAAGATCATGTT
64 AACGCCGCTAAAGATCATGTT
*
40596921 CTTTAGCGGCGCTTATGAAAAAATGCTGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAA
1 CTTTAGCGGCGCTTATGAAAAAACGCTGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAA
40596986 CGCCGCTAAAGATCATGTT
66 CGCCGCTAAAGATCATGTT
* * * * **
40597005 CTTTACCGGCGCTT-TGGAAGAAAACGCCGCTAAA-AGTAATGTTCTATAGCGGCGCTT-GTTCA
1 CTTTAGCGGCGCTTAT-GAA-AAAACGCTGCTAAAGA-TCATGTTCTTTAGCGGCGCTTAG-GAA
*
40597067 AAAACACCGCTAACAG-T-AGTGTT
62 AAAACGCCGCTAA-AGATCA-TGTT
40597090 CTTTAGCGGCGCTTAT
1 CTTTAGCGGCGCTTAT
40597106 TTCACAAATG
Statistics
Matches: 163, Mismatches: 15, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
83 1 0.01
84 40 0.25
85 105 0.64
86 17 0.10
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (84 bp):
CTTTAGCGGCGCTTATGAAAAAACGCTGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAA
CGCCGCTAAAGATCATGTT
Found at i:40597556 original size:12 final size:12
Alignment explanation
Indices: 40597539--40597577 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
40597529 TTTTGAACCT
*
40597539 CTGCTTCTATCG
1 CTGCTTCTCTCG
*
40597551 CTGCTTCTCTCA
1 CTGCTTCTCTCG
40597563 CTGCTTCTCTCG
1 CTGCTTCTCTCG
40597575 CTG
1 CTG
40597578 TGGGCTCTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.05, C:0.38, G:0.15, T:0.41
Consensus pattern (12 bp):
CTGCTTCTCTCG
Found at i:40597625 original size:21 final size:21
Alignment explanation
Indices: 40597563--40597631 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
40597553 GCTTCTCTCA
* *
40597563 CTGCTTCTCTCGCTGTGGGCT
1 CTGCTTCTCTCGCTGTAGCCT
*
40597584 CTACTTCTCTCGCTGTAGCCT
1 CTGCTTCTCTCGCTGTAGCCT
* **
40597605 CTGCTTCCCTCGCTGCCGCCT
1 CTGCTTCTCTCGCTGTAGCCT
40597626 CTGCTT
1 CTGCTT
40597632 TAAGTTGTTG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.03, C:0.41, G:0.20, T:0.36
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGTAGCCT
Found at i:40603137 original size:7 final size:7
Alignment explanation
Indices: 40603127--40603179 Score: 70
Period size: 7 Copynumber: 7.0 Consensus size: 7
40603117 TGATATATTT
40603127 TTATGTA
1 TTATGTA
40603134 TTATGTAA
1 TTATGT-A
40603142 GTTATGTAA
1 -TTATGT-A
40603151 GTTATGTA
1 -TTATGTA
40603159 TTATGTA
1 TTATGTA
40603166 TTATGTA
1 TTATGTA
40603173 TTATGTA
1 TTATGTA
40603180 AGTACTGTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
7 27 0.61
8 2 0.05
9 15 0.34
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (7 bp):
TTATGTA
Found at i:40603148 original size:9 final size:9
Alignment explanation
Indices: 40603134--40603528 Score: 358
Period size: 9 Copynumber: 43.8 Consensus size: 9
40603124 TTTTTATGTA
40603134 TTATGTAAG
1 TTATGTAAG
40603143 TTATGTAAG
1 TTATGTAAG
40603152 TTATGT-A-
1 TTATGTAAG
40603159 TTATGT-A-
1 TTATGTAAG
40603166 TTATGT-A-
1 TTATGTAAG
40603173 TTATGTAAG
1 TTATGTAAG
40603182 -TACTGTAAG
1 TTA-TGTAAG
* *
40603191 TAATGTACG
1 TTATGTAAG
* *
40603200 TTATTTAAT
1 TTATGTAAG
*
40603209 TTATGTAGG
1 TTATGTAAG
40603218 TTATGTAAG
1 TTATGTAAG
* * * *
40603227 TCCACGGAAT
1 T-TATGTAAG
40603237 TTATGTAAG
1 TTATGTAAG
40603246 TTATGTAAG
1 TTATGTAAG
* *
40603255 TTATTTAAT
1 TTATGTAAG
40603264 TTATGTAAG
1 TTATGTAAG
40603273 TTATGTAAG
1 TTATGTAAG
* *
40603282 TTATTTAAT
1 TTATGTAAG
*
40603291 TTATGTAGG
1 TTATGTAAG
40603300 TTATGTAAG
1 TTATGTAAG
40603309 TTATGTAAG
1 TTATGTAAG
* *
40603318 TTATTTAAT
1 TTATGTAAG
*
40603327 TTATGCAAG
1 TTATGTAAG
40603336 TTTATGTAAG
1 -TTATGTAAG
40603346 TTATGTAAG
1 TTATGTAAG
* *
40603355 TTATTTAAT
1 TTATGTAAG
*
40603364 TTATGTAGG
1 TTATGTAAG
40603373 TTATGTAAG
1 TTATGTAAG
40603382 TTATGTAAG
1 TTATGTAAG
* *
40603391 TTATTTAAT
1 TTATGTAAG
*
40603400 TTATGCAAG
1 TTATGTAAG
40603409 TTTATGTAAG
1 -TTATGTAAG
*
40603419 TCATGTAAG
1 TTATGTAAG
*
40603428 TTAAT-TAAT
1 TT-ATGTAAG
*
40603437 TTATGCAAG
1 TTATGTAAG
40603446 TTTATGTAAG
1 -TTATGTAAG
40603456 TTATGTAAG
1 TTATGTAAG
*
40603465 TTACT-TAAT
1 TTA-TGTAAG
40603474 TTATGTAAG
1 TTATGTAAG
* *
40603483 TTATTTAAT
1 TTATGTAAG
40603492 TTATGTAAG
1 TTATGTAAG
*
40603501 TTATGCAAG
1 TTATGTAAG
*
40603510 CTTATATACAAG
1 -TTATGT--AAG
40603522 TTATGTA
1 TTATGTA
40603529 TTATAACATA
Statistics
Matches: 309, Mismatches: 62, Indels: 30
0.77 0.15 0.07
Matches are distributed among these distances:
7 20 0.06
8 7 0.02
9 237 0.77
10 37 0.12
11 5 0.02
12 3 0.01
ACGTcount: A:0.32, C:0.03, G:0.17, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:40603276 original size:73 final size:73
Alignment explanation
Indices: 40603237--40603504 Score: 405
Period size: 73 Copynumber: 3.7 Consensus size: 73
40603227 TCCACGGAAT
* * **
40603237 TTATGTAAGTTATGTAAGTTATTTAA-TTTATGTAAGTTATGTAAGTTATTTAATTTATGTAGGT
1 TTATGTAAGTTATTTAATTTATGCAAGTTTATGTAAGTTATGTAAGTTATTTAATTTATGTAGGT
40603301 TATGTAAG
66 TATGTAAG
40603309 TTATGTAAGTTATTTAATTTATGCAAGTTTATGTAAGTTATGTAAGTTATTTAATTTATGTAGGT
1 TTATGTAAGTTATTTAATTTATGCAAGTTTATGTAAGTTATGTAAGTTATTTAATTTATGTAGGT
40603374 TATGTAAG
66 TATGTAAG
* * * *
40603382 TTATGTAAGTTATTTAATTTATGCAAGTTTATGTAAGTCATGTAAGTTAATTAATTTATGCAAGT
1 TTATGTAAGTTATTTAATTTATGCAAGTTTATGTAAGTTATGTAAGTTATTTAATTTATG-TAGG
40603447 TTATGTAAG
65 TTATGTAAG
* * * *
40603456 TTATGTAAGTTACTTAATTTATGTAAG-TTATTTAATTTATGTAAGTTAT
1 TTATGTAAGTTATTTAATTTATGCAAGTTTATGTAAGTTATGTAAGTTAT
40603505 GCAAGCTTAT
Statistics
Matches: 180, Mismatches: 14, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
72 22 0.12
73 122 0.68
74 36 0.20
ACGTcount: A:0.32, C:0.02, G:0.16, T:0.49
Consensus pattern (73 bp):
TTATGTAAGTTATTTAATTTATGCAAGTTTATGTAAGTTATGTAAGTTATTTAATTTATGTAGGT
TATGTAAG
Found at i:40603715 original size:16 final size:16
Alignment explanation
Indices: 40603690--40603727 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
40603680 GAAAACGAAG
*
40603690 TAAA-TTTAATACTAA
1 TAAATTTTAATACAAA
40603705 TAAATTTTAATACAAA
1 TAAATTTTAATACAAA
40603721 TAAATTT
1 TAAATTT
40603728 AGAAAACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTTTAATACAAA
Found at i:40603742 original size:13 final size:13
Alignment explanation
Indices: 40603724--40603751 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
40603714 ATACAAATAA
40603724 ATTTAGAAAACTT
1 ATTTAGAAAACTT
40603737 ATTTAGAAAACTT
1 ATTTAGAAAACTT
40603750 AT
1 AT
40603752 AAATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (13 bp):
ATTTAGAAAACTT
Found at i:40603759 original size:17 final size:17
Alignment explanation
Indices: 40603720--40603769 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
40603710 TTTAATACAA
40603720 ATAAATTTAGAAAAC-T
1 ATAAATTTAGAAAACTT
40603736 -T--ATTTAGAAAACTT
1 ATAAATTTAGAAAACTT
40603750 ATAAATTTAGAAAACTT
1 ATAAATTTAGAAAACTT
40603767 ATA
1 ATA
40603770 TAGATATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 11 0.37
14 1 0.03
15 2 0.07
17 16 0.53
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (17 bp):
ATAAATTTAGAAAACTT
Found at i:40605377 original size:191 final size:191
Alignment explanation
Indices: 40605053--40605432 Score: 598
Period size: 191 Copynumber: 2.0 Consensus size: 191
40605043 AAGCAACACA
* *
40605053 GAATTTAAAGTGAAAGGAAAAACAAAGCGAGCATTAGAGAAAGAAAAAATCAAACAGAAAAATGA
1 GAATTTAAAGAGAAAGGAAAAACAAAGCGAGCATTACAGAAAGAAAAAATCAAACAGAAAAATGA
* * * *
40605118 ATAGCCATATACGTATTCAACGAAGAAATTAAGGATTTGGAAAGATTTTTACCAGTCAGCCCAGA
66 ACAGCCATATACGGAGTCAACGAAGAAATTAAGGATTTGGAAAGATTTTTACCAATCAGCCCAGA
* ** *
40605183 CGAGAAGCAATATTCGATCGAAAAGAGGGGAAATCATCGTTGAAGGGGTGAATGGTCTATG
131 CGAGAAGCAATATTCGACCGAAAAGAGGGGAAATCATCGTTGAAAAGGTGAAAGGTCTATG
* *
40605244 GAATTTAAAGAGAAAGGAAAAACAAAGCGGGCATTACAGAAAGAAAAAATCAAACATAAAAATGA
1 GAATTTAAAGAGAAAGGAAAAACAAAGCGAGCATTACAGAAAGAAAAAATCAAACAGAAAAATGA
* * * *
40605309 ACAGCCATATACGGAGTCAACGGAGAAATTAGGGATTTGGAAAGTTTTTTACCAATCAGCCTAGA
66 ACAGCCATATACGGAGTCAACGAAGAAATTAAGGATTTGGAAAGATTTTTACCAATCAGCCCAGA
* *
40605374 CGAGAAGCGATATTCGACCGAGAAGAGGGGAAATCATCGTTGAAAAGGTGAAAGGTCTA
131 CGAGAAGCAATATTCGACCGAAAAGAGGGGAAATCATCGTTGAAAAGGTGAAAGGTCTA
40605433 GGGATTTGCA
Statistics
Matches: 171, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
191 171 1.00
ACGTcount: A:0.44, C:0.13, G:0.24, T:0.19
Consensus pattern (191 bp):
GAATTTAAAGAGAAAGGAAAAACAAAGCGAGCATTACAGAAAGAAAAAATCAAACAGAAAAATGA
ACAGCCATATACGGAGTCAACGAAGAAATTAAGGATTTGGAAAGATTTTTACCAATCAGCCCAGA
CGAGAAGCAATATTCGACCGAAAAGAGGGGAAATCATCGTTGAAAAGGTGAAAGGTCTATG
Found at i:40606041 original size:15 final size:14
Alignment explanation
Indices: 40606003--40606043 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
40605993 TAAACCTTAG
*
40606003 CCCCAACCCCTAAA
1 CCCCAATCCCTAAA
40606017 CCCCAATCCCTAAA
1 CCCCAATCCCTAAA
*
40606031 CCCATAATCCCTA
1 CCC-CAATCCCTA
40606044 GTCCACAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.34, C:0.51, G:0.00, T:0.15
Consensus pattern (14 bp):
CCCCAATCCCTAAA
Found at i:40606119 original size:21 final size:21
Alignment explanation
Indices: 40606095--40606138 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
40606085 AACATCTATC
* *
40606095 CCTTAATCTCCAACC-TCTAAA
1 CCTTAAACTCAAACCAT-TAAA
40606116 CCTTAAACTCAAACCATTAAA
1 CCTTAAACTCAAACCATTAAA
40606137 CC
1 CC
40606139 AAGTACCCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (21 bp):
CCTTAAACTCAAACCATTAAA
Found at i:40606288 original size:22 final size:22
Alignment explanation
Indices: 40606272--40606391 Score: 76
Period size: 21 Copynumber: 5.6 Consensus size: 22
40606262 CCATAATCTT
40606272 TAAACCTTAAACCCATAAACCC
1 TAAACCTTAAACCCATAAACCC
* * *
40606294 TAAACCTT-AACTCATAAAACA
1 TAAACCTTAAACCCATAAACCC
40606315 TAAA-CTATAAACCC-TAAACCCC
1 TAAACCT-TAAACCCATAAA-CCC
* *
40606337 TAACCCTT-AA-CCATTAACCC
1 TAAACCTTAAACCCATAAACCC
*
40606357 GTAACACC-TATA--CATTAAACCC
1 -TAA-ACCTTAAACCCA-TAAACCC
*
40606379 TAACCCTTAAACC
1 TAAACCTTAAACC
40606392 ATGGCCCATA
Statistics
Matches: 73, Mismatches: 13, Indels: 23
0.67 0.12 0.21
Matches are distributed among these distances:
20 9 0.12
21 36 0.49
22 26 0.36
23 2 0.03
ACGTcount: A:0.43, C:0.34, G:0.01, T:0.22
Consensus pattern (22 bp):
TAAACCTTAAACCCATAAACCC
Found at i:40606965 original size:114 final size:114
Alignment explanation
Indices: 40606804--40607400 Score: 810
Period size: 114 Copynumber: 5.2 Consensus size: 114
40606794 GTTTCGGTTT
* * *
40606804 AAAACGATGCGTTTTGGTTAAGATTTGTTTGCGGTGCTTTGTATAATGCGCCGCTAATGATGTAC
1 AAAACGATGCGTTTTGGTTAAGATTT-TTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGC
* * *
40606869 TTTAGCGGCGTTTTACTAT-AGCACCACTAATTCTAAAAATACCTCAACCA
65 TTTAGCGGCATTTTACTATAAGCGCCACTAATTCT-AAAATACCTCAACCC
* ** *
40606919 AAAATGATGCGTTTTGGTTATTATTTTTTGCGGCACTTTGTATAATGCGCCGCTAATGGTGTGCT
1 AAAACGATGCGTTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
* *
40606984 TTAGCGGCATTTATCCT-TAAGCGCCACTAAATCTAAAATACCTCAACCC
66 TTAGCGGCATTT-TACTATAAGCGCCACTAATTCTAAAATACCTCAACCC
* *
40607033 AAAACGATGCATTTTGGTTAAGATTTTTTGCGGCGCTTTGAATAATGCGCCGCTAATGGTGTGCT
1 AAAACGATGCGTTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
* *
40607098 TTAGTGGCA-TTTA-TCAGTAAGCGCCACTAATTCTAATATACCTCAACCC
66 TTAGCGGCATTTTACT-A-TAAGCGCCACTAATTCTAAAATACCTCAACCC
* * *
40607147 AAAACGATGCGTTTCGATTAAGATTTTTTGCGGCGCTTTGTATGATGCGCCGCTAATGGTGTGCT
1 AAAACGATGCGTTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
* * *
40607212 TTAGCGGCGTTTTTACT-TAAGCACCACTAGTTCTAAAATACCTCAACCC
66 TTAGCGGC-ATTTTACTATAAGCGCCACTAATTCTAAAATACCTCAACCC
* * * *
40607261 AGAACGATGCGTTTTGGTTATGATTTTTTGCGACGCTTTGTATAATGCGCTGCTAATGGTGTGCT
1 AAAACGATGCGTTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
* * *
40607326 TTAGCGGCA-TTTATCCATAAGCGCCACTAATTCTAATATACCTTAACCC
66 TTAGCGGCATTTTA-CTATAAGCGCCACTAATTCTAAAATACCTCAACCC
* *
40607375 AAAACGATGCATTTCGGTTAAGATTT
1 AAAACGATGCGTTTTGGTTAAGATTT
40607401 CTGAAATCAT
Statistics
Matches: 423, Mismatches: 49, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
111 1 0.00
112 5 0.01
113 3 0.01
114 370 0.87
115 39 0.09
116 4 0.01
117 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (114 bp):
AAAACGATGCGTTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
TTAGCGGCATTTTACTATAAGCGCCACTAATTCTAAAATACCTCAACCC
Found at i:40608956 original size:124 final size:124
Alignment explanation
Indices: 40608793--40609040 Score: 406
Period size: 124 Copynumber: 2.0 Consensus size: 124
40608783 AACTTAAAAC
40608793 GGGTCGGGTCAAGCTTGAGCCTTAAATGTTCAAACCCGAGCCTAACCCATATTTTAAACAAGCTT
1 GGGTCGGGTCAAGCTTGAGCCTTAAATGTTCAAACCCGAGCCTAACCCATATTTTAAACAAGCTT
*
40608858 AATTTTTTTGTCCAAGCTCATTTTTCGAGCCTAACATTTTTGCTCAAACCCTCTCAAAT
66 AATTTTTTTGTCCAAGCTCATTTTTCGAGCCTAACATTTTTACTCAAACCCTCTCAAAT
* * * *
40608917 GGGTCGGGTTAAGCTTGAGTCTTGAATGTTCAAACCCGAGCCTAACCCATATTTTAAACGAGCTT
1 GGGTCGGGTCAAGCTTGAGCCTTAAATGTTCAAACCCGAGCCTAACCCATATTTTAAACAAGCTT
* * * * *
40608982 AATTTTTTTGTCCAAGCTCATTTTTTGAGGCTAATATTTTTACTCAAAGCTTCTCAAAT
66 AATTTTTTTGTCCAAGCTCATTTTTCGAGCCTAACATTTTTACTCAAACCCTCTCAAAT
40609041 TTTGAATAGG
Statistics
Matches: 114, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
124 114 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (124 bp):
GGGTCGGGTCAAGCTTGAGCCTTAAATGTTCAAACCCGAGCCTAACCCATATTTTAAACAAGCTT
AATTTTTTTGTCCAAGCTCATTTTTCGAGCCTAACATTTTTACTCAAACCCTCTCAAAT
Found at i:40617242 original size:19 final size:19
Alignment explanation
Indices: 40617214--40617250 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
40617204 ATGACTACTT
40617214 TTCATATTTTTCTCCACTC
1 TTCATATTTTTCTCCACTC
*
40617233 TTCATCTTTTTCTCCACT
1 TTCATATTTTTCTCCACT
40617251 TTTCTACACA
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:0.14, C:0.32, G:0.00, T:0.54
Consensus pattern (19 bp):
TTCATATTTTTCTCCACTC
Found at i:40619040 original size:12 final size:12
Alignment explanation
Indices: 40619023--40619049 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
40619013 TATCCTTAAA
40619023 ATTTTACATTTT
1 ATTTTACATTTT
40619035 ATTTTACATTTT
1 ATTTTACATTTT
40619047 ATT
1 ATT
40619050 CAATTTAGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (12 bp):
ATTTTACATTTT
Found at i:40622172 original size:55 final size:55
Alignment explanation
Indices: 40622107--40622216 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
40622097 TCAAACCTCT
40622107 TATACCACTGTCGTGGTGACTATTTCAAACCGTAAAGGGACTTTTTCAGCAAGCA
1 TATACCACTGTCGTGGTGACTATTTCAAACCGTAAAGGGACTTTTTCAGCAAGCA
* *
40622162 TATACCACTGTCGTGGTGACTGTTTTAAACCGTAAAGGGACTTTTTCAGCAAGCA
1 TATACCACTGTCGTGGTGACTATTTCAAACCGTAAAGGGACTTTTTCAGCAAGCA
40622217 AACATAGTCA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (55 bp):
TATACCACTGTCGTGGTGACTATTTCAAACCGTAAAGGGACTTTTTCAGCAAGCA
Found at i:40631972 original size:28 final size:28
Alignment explanation
Indices: 40631913--40631979 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
40631903 GTATCATGTT
* * *
40631913 TTAACATAAATATAAATTTAGTAATTAT
1 TTAACATAAATATAAATTTAGCAACTAA
*
40631941 TTAACATAAATATAATTTTA-CAACTACA
1 TTAACATAAATATAAATTTAGCAACTA-A
40631969 TTAAC-TAAATA
1 TTAACATAAATA
40631980 GTTTAATCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 10 0.29
28 24 0.71
ACGTcount: A:0.51, C:0.09, G:0.01, T:0.39
Consensus pattern (28 bp):
TTAACATAAATATAAATTTAGCAACTAA
Found at i:40633605 original size:42 final size:42
Alignment explanation
Indices: 40633554--40633840 Score: 434
Period size: 42 Copynumber: 6.8 Consensus size: 42
40633544 GTTTACAAAC
* *
40633554 AAAAACGCCGTTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
40633596 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
40633638 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
* * *
40633680 AAATACGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTGTAA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG-AA
* * * *
40633722 AAAAATGCCACTAAAGACCATGTTCTTTAGCGGCGCTTAGGA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
* *
40633764 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTA-ATG
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGA-A
*
40633806 GAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG
40633841 TTTTTTTTCT
Statistics
Matches: 224, Mismatches: 18, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
41 3 0.01
42 218 0.97
43 3 0.01
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.24
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
Found at i:40633896 original size:84 final size:82
Alignment explanation
Indices: 40633554--40633930 Score: 348
Period size: 84 Copynumber: 4.5 Consensus size: 82
40633544 GTTTACAAAC
* * * * *
40633554 AAAAACGCCGTTAAAGACCATGTTCTTTAGCGGCG-CTTAGAAAAAAACGCCGCTAAAGATCATG
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTTAG-AAAAATCGCCGCTAAAGAACATG
* **
40633618 TTCTTTAGCGGCGCTTAGAA
65 TTCTTTAGCGGC-ATT-TTA
*
40633638 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG-CTTAGAAAAATACGCCGCTAAAGAACATG
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTTAGAAAAAT-CGCCGCTAAAGAACATG
*
40633702 TTCTTTAGCGGCGTTTGTAA
65 TTCTTTAGCGGCATTT-T-A
* * * * *
40633722 AAAAATGCCACTAAAGACCATGTTCTTTAGCGGCG-CTTAGGAAAAAACGCCGCTAAAGAACATG
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTTA-GAAAAATCGCCGCTAAAGAACATG
**
40633786 TTCTTTAGCGGC-GCTTA
65 TTCTTTAGCGGCATTTTA
******
40633803 ATGGAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTTTTTTCTGATCGCCGCTAAAGAAC
1 A---AAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG-TTTTAGAAAAATCGCCGCTAAAGAAC
* *
40633868 ATGTTCTTTAGTGGCATTTTTT
62 ATGTTCTTTAGCGGCA-TTTTA
* * * *
40633890 ACAAACGCCGCAAAAGAACATGTTCTTTAGTGGCGCTTTTA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG-TTTTA
40633931 TACAAAAACG
Statistics
Matches: 248, Mismatches: 34, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
81 2 0.01
82 1 0.00
83 8 0.03
84 197 0.79
85 35 0.14
86 2 0.01
87 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (82 bp):
AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTTAGAAAAATCGCCGCTAAAGAACATGT
TCTTTAGCGGCATTTTA
Found at i:40633896 original size:126 final size:126
Alignment explanation
Indices: 40633554--40633927 Score: 416
Period size: 126 Copynumber: 3.0 Consensus size: 126
40633544 GTTTACAAAC
* * * * * *
40633554 AAAA-ACGCCGTTAAAGACCATGTTCTTTAGCGGCGCTTAG-AAAAAAACGCCGCTAAAGATCAT
1 AAAATACGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTGTAAAAAAATGCCACTAAAGAACAT
* * *
40633617 GTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGA
65 GTTCTTTAGCGGCGATTAGGAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGA
*
40633679 AAAATACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTAAAAAAATGCCACTAAAGACCATG
1 AAAATACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTAAAAAAATGCCACTAAAGAACATG
*
40633744 TTCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTA-A
66 TTCTTTAGCGGCGATTAGGAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGA
* * * ****** *
40633804 TGGAAA-ACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTTTTTTCTGATCGCCGCTAAAGAAC
1 --AAAATACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTAAAAAAAT-GCCACTAAAGAAC
* **** * * *
40633868 ATGTTCTTTAGTGGC-ATTTTTTACAAACGCCGCAAAAGAACATGTTCTTTAGTGGCGCTT
63 ATGTTCTTTAGCGGCGATTAGGAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTT
40633928 TTATACAAAA
Statistics
Matches: 216, Mismatches: 28, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
125 8 0.04
126 180 0.83
127 28 0.13
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (126 bp):
AAAATACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTAAAAAAATGCCACTAAAGAACATG
TTCTTTAGCGGCGATTAGGAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGA
Found at i:40634018 original size:14 final size:14
Alignment explanation
Indices: 40633995--40634028 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
40633985 GCCCTCCTGT
*
40633995 AGCAAAATTTCAAA
1 AGCAACATTTCAAA
40634009 AGCAACATTTCAAA
1 AGCAACATTTCAAA
40634023 AGCAAC
1 AGCAAC
40634029 CAATAGCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.53, C:0.21, G:0.09, T:0.18
Consensus pattern (14 bp):
AGCAACATTTCAAA
Found at i:40634320 original size:21 final size:21
Alignment explanation
Indices: 40634252--40634322 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
40634242 TTTTGCTCTG
* *
40634252 CTCTGCTTCTCTTGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
40634273 CTCCGCTTCCCTCGCTGCAGT
1 CTCTGCTTCCCTCGCTGCAGC
* * *
40634294 CGCTGCTTCCCTCGCTTCCGC
1 CTCTGCTTCCCTCGCTGCAGC
40634315 CTCTGCTT
1 CTCTGCTT
40634323 TAAGTTGTAG
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.03, C:0.45, G:0.18, T:0.34
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:40639818 original size:11 final size:9
Alignment explanation
Indices: 40639770--40639934 Score: 69
Period size: 7 Copynumber: 19.0 Consensus size: 9
40639760 AATTGCAATG
40639770 GTAAGTTAT
1 GTAAGTTAT
40639779 GTAAGTTAT
1 GTAAGTTAT
40639788 GTAAGTTAAAT
1 GTAAGTT--AT
40639799 GT-A-TTAT
1 GTAAGTTAT
40639806 GTAAGTTAAAT
1 GTAAGTT--AT
40639817 GTAAG-T-T
1 GTAAGTTAT
40639824 GTAAGTTAT
1 GTAAGTTAT
*
40639833 -TATGTATTAT
1 GTAAG--TTAT
40639843 GTAAG-T-T
1 GTAAGTTAT
40639850 GTAAGTTAAAT
1 GTAAGTT--AT
*
40639861 GT-A-TTGT
1 GTAAGTTAT
40639868 GTAAG-T-T
1 GTAAGTTAT
40639875 GTAAGTTAAAT
1 GTAAGTT--AT
40639886 GT-A-TTAT
1 GTAAGTTAT
40639893 GTAAG-T-T
1 GTAAGTTAT
40639900 GTAAGTTAT
1 GTAAGTTAT
*
40639909 -TATGTATTAT
1 GTAAG--TTAT
40639919 GTAAG-T-T
1 GTAAGTTAT
40639926 GTAAGTTAT
1 GTAAGTTAT
40639935 TATGTATTGT
Statistics
Matches: 121, Mismatches: 5, Indels: 60
0.65 0.03 0.32
Matches are distributed among these distances:
7 41 0.34
8 18 0.15
9 27 0.22
10 12 0.10
11 23 0.19
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:40639845 original size:19 final size:19
Alignment explanation
Indices: 40639784--40640201 Score: 82
Period size: 18 Copynumber: 21.6 Consensus size: 19
40639774 GTTATGTAAG
*
40639784 TTATGTAAGTTA-AATGTA
1 TTATGTAAGTTATTATGTA
*
40639802 TTATGTAAGTTA-AATGTAA
1 TTATGTAAGTTATTATGT-A
*
40639821 GT-TGTAAGTTATTATGTA
1 TTATGTAAGTTATTATGTA
40639839 TTATGTAAGTTGTAAGTTAAATGTA
1 TTATGTAAG-T-T-A-TT--ATGTA
*
40639864 TTGTGTAAGTTGTAAGTTAAATGTA
1 TTATGTAAG-T-T-A-TT--ATGTA
* *
40639889 TTATGTAAGTT-GTAAG--
1 TTATGTAAGTTATTATGTA
*
40639905 TTAT-TATG-TATTATGTAA
1 TTATGTAAGTTATTATGT-A
*
40639923 GT-TGTAAGTTATTATGTA
1 TTATGTAAGTTATTATGTA
*
40639941 TTGTGTAAGTTGCAAGTTAAATGTA
1 TTATGTAAGTT---A-TT--ATGTA
* *
40639966 TTATGTAAGTT-GTAAG--
1 TTATGTAAGTTATTATGTA
*
40639982 TTAT-TATG-TATTATGTAA
1 TTATGTAAGTTATTATGT-A
*
40640000 GT-TGTAAGTTATTATGTA
1 TTATGTAAGTTATTATGTA
* * *
40640018 TTGTGTAAGTT-GTAAG--
1 TTATGTAAGTTATTATGTA
*
40640034 TTAT-TATG-TATTATGTAA
1 TTATGTAAGTTATTATGT-A
*
40640052 GT-TGTAAGTTATTATGTA
1 TTATGTAAGTTATTATGTA
*
40640070 TTGTGTAAGTTGTAAGTTAAATGTA
1 TTATGTAAG-T-T-A-TT--ATGTA
* * *
40640095 TTATGTCAGTCA-AATGTA
1 TTATGTAAGTTATTATGTA
40640113 TTATGTAAGTTGTAAGTTAAATGTA
1 TTATGTAAG-T-T-A-TT--ATGTA
* *
40640138 TTATGTAAGTT-GTAAGTTA
1 TTATGTAAGTTATTATG-TA
*
40640157 TTATGT-A-TTATGTAAGTA
1 TTATGTAAGTTAT-TATGTA
*
40640175 --ATGTAAGTTA-AATGTA
1 TTATGTAAGTTATTATGTA
40640191 TTATGTAAGTT
1 TTATGTAAGTT
40640202 GTAAGTTATT
Statistics
Matches: 301, Mismatches: 43, Indels: 112
0.66 0.09 0.25
Matches are distributed among these distances:
14 3 0.01
15 18 0.06
16 19 0.06
17 6 0.02
18 83 0.28
19 71 0.24
20 5 0.02
21 3 0.01
22 4 0.01
23 8 0.03
24 3 0.01
25 78 0.26
ACGTcount: A:0.33, C:0.01, G:0.20, T:0.46
Consensus pattern (19 bp):
TTATGTAAGTTATTATGTA
Found at i:40639849 original size:26 final size:26
Alignment explanation
Indices: 40639815--40640220 Score: 579
Period size: 26 Copynumber: 16.1 Consensus size: 26
40639805 TGTAAGTTAA
40639815 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
40639841 ATGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* *
40639866 GTGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
40639891 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
40639917 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* * *
40639943 GTGTAAGTTGCAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
40639968 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
40639994 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
40640020 GTGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
40640046 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* *
40640072 GTGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* *
40640097 ATGTCA---GTCA---A--ATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
40640115 ATGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
40640140 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
40640166 ATGTAAGTAATGTAAGTTA-AATGTATT
1 ATGTAAGT--TGTAAGTTATTATGTATT
40640193 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
40640219 AT
1 AT
40640221 TTAATAAAAT
Statistics
Matches: 345, Mismatches: 22, Indels: 26
0.88 0.06 0.07
Matches are distributed among these distances:
18 12 0.03
19 1 0.00
21 3 0.01
22 3 0.01
24 1 0.00
25 113 0.33
26 188 0.54
27 15 0.04
28 9 0.03
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (26 bp):
ATGTAAGTTGTAAGTTATTATGTATT
Found at i:40640190 original size:53 final size:51
Alignment explanation
Indices: 40639815--40640220 Score: 571
Period size: 51 Copynumber: 8.0 Consensus size: 51
40639805 TGTAAGTTAA
* *
40639815 ATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTA-AATGTATTATGTAAGTTGTAAGTTATTATGTATT
*
40639866 GTGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
* * * *
40639917 ATGTAAGTTGTAAGTTATTATGTATTGTGTAAGTTGCAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTA-AATGTATTATGTAAGTTGTAAGTTATTATGTATT
*
40639968 ATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-AATGTATTATGTAAGTTGTAAGTTATTATGTATT
* *
40640020 GTGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-AATGTATTATGTAAGTTGTAAGTTATTATGTATT
* * *
40640072 GTGTAAGTTGTAAGTTAAATGTATTATGTCA---GTCA---A--ATGTATT
1 ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
40640115 ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
40640166 ATGTAAGTAATGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGT--TGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
40640219 AT
1 AT
40640221 TTAATAAAAT
Statistics
Matches: 324, Mismatches: 18, Indels: 24
0.89 0.05 0.07
Matches are distributed among these distances:
43 36 0.11
45 1 0.00
46 3 0.01
48 3 0.01
49 1 0.00
50 24 0.07
51 114 0.35
52 97 0.30
53 45 0.14
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (51 bp):
ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
Found at i:40640213 original size:19 final size:19
Alignment explanation
Indices: 40639990--40640216 Score: 100
Period size: 19 Copynumber: 12.5 Consensus size: 19
40639980 AGTTATTATG
40639990 TATTATGTAAGTTGTAAGT
1 TATTATGTAAGTTGTAAGT
40640009 TATTATGT-A-TTGT--GT
1 TATTATGTAAGTTGTAAGT
* * * *
40640024 AAGT-TGTAAGTTATTA-T
1 TATTATGTAAGTTGTAAGT
40640041 GTATTATGTAAGTTGTAAGT
1 -TATTATGTAAGTTGTAAGT
40640061 TATTATGT-A-TTGT--GT
1 TATTATGTAAGTTGTAAGT
* * *
40640076 AAGT-TGTAAG-T-TAAAT
1 TATTATGTAAGTTGTAAGT
* * *
40640092 GTATTATGTCAG-T-CAAAT
1 -TATTATGTAAGTTGTAAGT
40640110 GTATTATGTAAGTTGTAAGTTAAAT
1 -TATTATGTAAGTTGTAAG-----T
40640135 GTATTATGTAAGTTGTAAGT
1 -TATTATGTAAGTTGTAAGT
*
40640155 TATTATGT-ATTATGTAAG-
1 TATTATGTAAGT-TGTAAGT
*
40640173 TA--ATGTAAG-T-TAAAT
1 TATTATGTAAGTTGTAAGT
40640188 GTATTATGTAAGTTGTAAGT
1 -TATTATGTAAGTTGTAAGT
40640208 TATTATGTA
1 TATTATGTA
40640217 TTATTTAATA
Statistics
Matches: 159, Mismatches: 21, Indels: 56
0.67 0.09 0.24
Matches are distributed among these distances:
14 10 0.06
15 12 0.08
16 10 0.06
17 12 0.08
18 36 0.23
19 51 0.32
20 8 0.05
25 20 0.13
ACGTcount: A:0.33, C:0.01, G:0.20, T:0.47
Consensus pattern (19 bp):
TATTATGTAAGTTGTAAGT
Found at i:40640414 original size:74 final size:74
Alignment explanation
Indices: 40640257--40640404 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
40640247 ACATTACTAA
40640257 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
1 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
40640322 TATTTTTTT
66 TATTTTTTT
40640331 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
1 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
40640396 TATTTTTTT
66 TATTTTTTT
40640405 ATATTTTATT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.51
Consensus pattern (74 bp):
TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
TATTTTTTT
Found at i:40640571 original size:13 final size:13
Alignment explanation
Indices: 40640553--40640623 Score: 106
Period size: 13 Copynumber: 5.5 Consensus size: 13
40640543 ATTTATAATT
40640553 ATTTAAGTAATAA
1 ATTTAAGTAATAA
* *
40640566 ATTTAAGTAACAT
1 ATTTAAGTAATAA
40640579 ATTTAAGTAATAA
1 ATTTAAGTAATAA
* *
40640592 ATTTAAGTAACAT
1 ATTTAAGTAATAA
40640605 ATTTAAGTAATAA
1 ATTTAAGTAATAA
40640618 ATTTAA
1 ATTTAA
40640624 ACAAATTTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 50 1.00
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (13 bp):
ATTTAAGTAATAA
Found at i:40640582 original size:26 final size:26
Alignment explanation
Indices: 40640552--40640623 Score: 144
Period size: 26 Copynumber: 2.8 Consensus size: 26
40640542 TATTTATAAT
40640552 TATTTAAGTAATAAATTTAAGTAACA
1 TATTTAAGTAATAAATTTAAGTAACA
40640578 TATTTAAGTAATAAATTTAAGTAACA
1 TATTTAAGTAATAAATTTAAGTAACA
40640604 TATTTAAGTAATAAATTTAA
1 TATTTAAGTAATAAATTTAA
40640624 ACAAATTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (26 bp):
TATTTAAGTAATAAATTTAAGTAACA
Found at i:40640650 original size:17 final size:17
Alignment explanation
Indices: 40640628--40640926 Score: 161
Period size: 17 Copynumber: 16.6 Consensus size: 17
40640618 ATTTAAACAA
40640628 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
40640645 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
*
40640662 ATTTTAGTAA-TAAATTT
1 ATTTTAGTAAGT-AATGT
40640679 AAACAAATTTTAGTAAGTAATGT
1 ------ATTTTAGTAAGTAATGT
* * *
40640702 ATTTAAGTAATTAAT-A
1 ATTTTAGTAAGTAATGT
* *
40640718 AATTTA--AA-CAA---
1 ATTTTAGTAAGTAATGT
40640729 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
40640746 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
*
40640763 ATTTTAGTAA-TAAATTT
1 ATTTTAGTAAGT-AATGT
40640780 AAACAAATTTTAGTAAGTAATGT
1 ------ATTTTAGTAAGTAATGT
* *
40640803 ATTTTAG-AAATAAATTT
1 ATTTTAGTAAGT-AATGT
*
40640820 AAACAAATTTATGTAAGTAATGT
1 -----ATTTTA-GTAAGTAATGT
40640843 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
*
40640860 ATTTTAGTAA-TAAATTT
1 ATTTTAGTAAGT-AATGT
*
40640877 AAACAAATTTTAGTAAGTAATTT
1 ------ATTTTAGTAAGTAATGT
40640900 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
40640917 ATTTTAGTAA
1 ATTTTAGTAA
40640927 TAAATTTAAC
Statistics
Matches: 224, Mismatches: 20, Indels: 76
0.70 0.06 0.24
Matches are distributed among these distances:
11 5 0.02
13 4 0.02
14 4 0.02
16 10 0.04
17 137 0.61
18 5 0.02
22 5 0.02
23 48 0.21
24 6 0.03
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.44
Consensus pattern (17 bp):
ATTTTAGTAAGTAATGT
Found at i:40640674 original size:57 final size:57
Alignment explanation
Indices: 40640595--40640935 Score: 375
Period size: 57 Copynumber: 6.5 Consensus size: 57
40640585 GTAATAAATT
** *
40640595 TAAGTAACATATTTAAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
1 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
40640652 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTA--TT--
1 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
* * *
40640705 TAAGTAAT-TA----A-T-A-AATTTAAACA-AATTTT-AGTAAGTAATGTATTTTAG
1 TAAGTAATGTATTTTAGTAATAAATTTAA-ACAAATTTTAGTAAGTAATGTATTTTAG
40640753 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
1 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
* *
40640810 -AAATAA---A-TTTA--AACAAATTT-----A----T-GTAAGTAATGTATTTTAG
1 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
*
40640850 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATTTATTTTAG
1 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
40640907 TAAGTAATGTATTTTAGTAATAAATTTAA
1 TAAGTAATGTATTTTAGTAATAAATTTAA
40640936 CATTCAATCG
Statistics
Matches: 238, Mismatches: 14, Indels: 64
0.75 0.04 0.20
Matches are distributed among these distances:
40 18 0.08
41 6 0.03
44 14 0.06
45 16 0.07
46 4 0.02
47 9 0.04
48 9 0.04
49 2 0.01
50 8 0.03
52 7 0.03
53 10 0.04
54 1 0.00
55 4 0.02
56 17 0.07
57 113 0.47
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.43
Consensus pattern (57 bp):
TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
Found at i:40640689 original size:40 final size:40
Alignment explanation
Indices: 40640645--40640755 Score: 177
Period size: 44 Copynumber: 2.7 Consensus size: 40
40640635 TAAGTAATGT
40640645 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAA
1 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAA
*
40640685 ATTTTAGTAAGTAATGTATTTAAGTAATTAATAAATTTAAACAA
1 ATTTTAGTAAGTAATGTATTT---T-AGTAATAAATTTAAACAA
40640729 ATTTTAGTAAGTAATGTATTTTAGTAA
1 ATTTTAGTAAGTAATGTATTTTAGTAA
40640756 GTAATGTATT
Statistics
Matches: 65, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
40 25 0.38
41 1 0.02
43 1 0.02
44 38 0.58
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.43
Consensus pattern (40 bp):
ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAA
Found at i:40640731 original size:101 final size:100
Alignment explanation
Indices: 40640612--40640914 Score: 533
Period size: 101 Copynumber: 3.0 Consensus size: 100
40640602 CATATTTAAG
40640612 TAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAAGTAATGTATTTTAGTAATAAAT
1 TAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAAGTAATGTATTTTAGTAATAAAT
*
40640677 TTAAACAAATTTTAGTAAGTAATGTATTTAAGTAA
66 TTAAACAAATTTTAGTAAGTAATGTATTTTAGTAA
40640712 TTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAAGTAATGTATTTTAGTAATAAA
1 -TAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAAGTAATGTATTTTAGTAATAAA
40640777 TTTAAACAAATTTTAGTAAGTAATGTATTTTAG--A
65 TTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAA
40640811 -AATAAATTTAAACAAA-TTTATGTAAGTAATGTATTTTAGTAAGTAATGTATTTTAGTAATAAA
1 TAATAAATTTAAACAAATTTTA-GTAAGTAATGTATTTTAGTAAGTAATGTATTTTAGTAATAAA
*
40640874 TTTAAACAAATTTTAGTAAGTAATTTATTTTAGTAA
65 TTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAA
40640910 GTAAT
1 -TAAT
40640915 GTATTTTAGT
Statistics
Matches: 195, Mismatches: 2, Indels: 10
0.94 0.01 0.05
Matches are distributed among these distances:
96 4 0.02
97 90 0.46
99 2 0.01
101 99 0.51
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.43
Consensus pattern (100 bp):
TAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAAGTAATGTATTTTAGTAATAAAT
TTAAACAAATTTTAGTAAGTAATGTATTTTAGTAA
Found at i:40640793 original size:40 final size:40
Alignment explanation
Indices: 40640746--40640852 Score: 189
Period size: 40 Copynumber: 2.7 Consensus size: 40
40640736 TAAGTAATGT
40640746 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAA
1 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAA
*
40640786 ATTTTAGTAAGTAATGTATTTTAGAAATAAATTTAAACAA
1 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAA
40640826 A-TTTATGTAAGTAATGTATTTTAGTAA
1 ATTTTA-GTAAGTAATGTATTTTAGTAA
40640853 GTAATGTATT
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
39 4 0.06
40 60 0.94
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.43
Consensus pattern (40 bp):
ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAA
Found at i:40640906 original size:97 final size:97
Alignment explanation
Indices: 40640595--40640903 Score: 521
Period size: 97 Copynumber: 3.1 Consensus size: 97
40640585 GTAATAAATT
** *
40640595 TAAGTAACATATTTAAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAAGTAAT
1 TAAGTAATGTATTTAAGAAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAAGTAAT
40640660 GTATTTTAGTAATAAATTTAAACAAATTTTAG
66 GTATTTTAGTAATAAATTTAAACAAATTTTAG
40640692 TAAGTAATGTATTTAAGTAATTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAAG
1 TAAGTAATGTATTTAAG--A--AATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAAG
40640757 TAATGTATTTTAGTAATAAATTTAAACAAATTTTAG
62 TAATGTATTTTAGTAATAAATTTAAACAAATTTTAG
*
40640793 TAAGTAATGTATTTTAGAAATAAATTTAAACAAA-TTTATGTAAGTAATGTATTTTAGTAAGTAA
1 TAAGTAATGTATTTAAGAAATAAATTTAAACAAATTTTA-GTAAGTAATGTATTTTAGTAAGTAA
40640857 TGTATTTTAGTAATAAATTTAAACAAATTTTAG
65 TGTATTTTAGTAATAAATTTAAACAAATTTTAG
*
40640890 TAAGTAATTTATTT
1 TAAGTAATGTATTT
40640904 TAGTAAGTAA
Statistics
Matches: 202, Mismatches: 5, Indels: 10
0.93 0.02 0.05
Matches are distributed among these distances:
96 4 0.02
97 102 0.50
99 1 0.00
101 95 0.47
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.43
Consensus pattern (97 bp):
TAAGTAATGTATTTAAGAAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAAGTAAT
GTATTTTAGTAATAAATTTAAACAAATTTTAG
Found at i:40642282 original size:11 final size:11
Alignment explanation
Indices: 40642266--40642305 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
40642256 GATGATAATA
40642266 CATTAGTTACC
1 CATTAGTTACC
40642277 CATTAGTTACC
1 CATTAGTTACC
*
40642288 CACTAGTTACC
1 CATTAGTTACC
40642299 CA-TAGTT
1 CATTAGTT
40642306 TGAGATATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
10 5 0.18
11 23 0.82
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.35
Consensus pattern (11 bp):
CATTAGTTACC
Found at i:40644283 original size:7 final size:7
Alignment explanation
Indices: 40644230--40644305 Score: 64
Period size: 7 Copynumber: 10.9 Consensus size: 7
40644220 ACCTTAATCA
*
40644230 CTAAACT
1 CTAAACC
40644237 CTCAAACC
1 CT-AAACC
40644245 CTAAACC
1 CTAAACC
** *
40644252 AAAAACA
1 CTAAACC
40644259 CTAAA-C
1 CTAAACC
* *
40644265 CTACATC
1 CTAAACC
*
40644272 GTAAACC
1 CTAAACC
40644279 CTAAACC
1 CTAAACC
*
40644286 CTAAACT
1 CTAAACC
40644293 CTAAACC
1 CTAAACC
40644300 CTAAAC
1 CTAAAC
40644306 TAGAATTCAA
Statistics
Matches: 53, Mismatches: 14, Indels: 4
0.75 0.20 0.06
Matches are distributed among these distances:
6 4 0.08
7 43 0.81
8 6 0.11
ACGTcount: A:0.46, C:0.36, G:0.01, T:0.17
Consensus pattern (7 bp):
CTAAACC
Found at i:40644367 original size:17 final size:17
Alignment explanation
Indices: 40644345--40644394 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 17
40644335 TATCCTATTT
40644345 CCTACATTATATAATAA
1 CCTACATTATATAATAA
40644362 CCTACATTATATAATAA
1 CCTACATTATATAATAA
*
40644379 ACTACA-TATATAATAA
1 CCTACATTATATAATAA
40644395 TCTAGCGGCG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 10 0.31
17 22 0.69
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (17 bp):
CCTACATTATATAATAA
Found at i:40644597 original size:113 final size:111
Alignment explanation
Indices: 40644416--40644766 Score: 402
Period size: 113 Copynumber: 3.1 Consensus size: 111
40644406 TTCCCACAAC
* * * *
40644416 GCGCCGCTAATAATATGTTTTACCGGCGTTTTACCATAAGCGCCAC-AACTGGTAGTATACATCA
1 GCGCCGCTAATACTATGATTTAGCGGCGTTTTA-AATAAGCGCCACTAA-T-GTAGTATACATCA
40644480 AGACCAAAGCGCTGCGTTTTGGTTAATGTTTTGCGGCGCTTTACAATAA
63 AGACCAAAGCGCTGCGTTTTGGTTAATGTTTTGCGGCGCTTTACAATAA
* * *
40644529 GCGCCGCTAATACTATGATTTAGCGGCGTTTTCAAATAAGCGCCACTAATCGTAATGTACCTCAA
1 GCGCCGCTAATACTATGATTTAGCGGCGTTTT-AAATAAGCGCCACTAAT-GTAGTATACATCAA
* * * * *
40644594 GACCAAA-CTCTGCGTTTTGGTTAA-GAAATATTGCGGCGCTTTTCACTAC
64 GACCAAAGCGCTGCGTTTTGGTTAATG---TTTTGCGGCGCTTTACAATAA
* ** * *
40644643 TCGCCGCTAATACTATTCTTTAGCAGCGTTTTAATATAAGCGCCACTACTGCTAGTATACATCAA
1 GCGCCGCTAATACTATGATTTAGCGGCGTTTTAA-ATAAGCGCCACTAATG-TAGTATACATCAA
* * *
40644708 GACCAAAGCGCTGCGTTTTGGTTAATATTTTGCGGCGTTTTCCAATAA
64 GACCAAAGCGCTGCGTTTTGGTTAATGTTTTGCGGCGCTTTACAATAA
*
40644756 GCGCCACTAAT
1 GCGCCGCTAAT
40644767 CCTAATATAC
Statistics
Matches: 199, Mismatches: 30, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
111 1 0.01
112 16 0.08
113 87 0.44
114 79 0.40
115 16 0.08
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (111 bp):
GCGCCGCTAATACTATGATTTAGCGGCGTTTTAAATAAGCGCCACTAATGTAGTATACATCAAGA
CCAAAGCGCTGCGTTTTGGTTAATGTTTTGCGGCGCTTTACAATAA
Found at i:40644868 original size:188 final size:188
Alignment explanation
Indices: 40644546--40644948 Score: 689
Period size: 188 Copynumber: 2.1 Consensus size: 188
40644536 TAATACTATG
* * * * *
40644546 ATTTAGCGGCGTTTTCAAATAAGCGCCACTAATCGTAATGTACCTCAAGACCAAACTCTGCGTTT
1 ATTTTGCGGCGTTTTCCAATAAGCGCCACTAATCCTAATATACCGCAAGACCAAACTCTGCGTTT
40644611 TGGTTAAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTA
66 TGGTTAAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTA
40644676 ATATAAGCGCCACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAAT
131 ATATAAGCGCCACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAAT
40644734 ATTTTGCGGCGTTTTCCAATAAGCGCCACTAATCCTAATATACCGCAAGACCAAACTCTGCGTTT
1 ATTTTGCGGCGTTTTCCAATAAGCGCCACTAATCCTAATATACCGCAAGACCAAACTCTGCGTTT
* * *
40644799 TGGTTAAGAAATCTTGCGGCGCTTTTCACTACTCGCTGCTAATACTATTCTTTAGTAGCGTTTTA
66 TGGTTAAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTA
* *
40644864 ATATAAGTGCCACTACTGGTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAAT
131 ATATAAGCGCCACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAAT
* * *
40644922 ATTTTGCGACGCTTTACAATAAGCGCC
1 ATTTTGCGGCGTTTTCCAATAAGCGCC
40644949 GCTACTACTA
Statistics
Matches: 202, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
188 202 1.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (188 bp):
ATTTTGCGGCGTTTTCCAATAAGCGCCACTAATCCTAATATACCGCAAGACCAAACTCTGCGTTT
TGGTTAAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTA
ATATAAGCGCCACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAAT
Found at i:40644989 original size:113 final size:114
Alignment explanation
Indices: 40644739--40645164 Score: 464
Period size: 114 Copynumber: 3.7 Consensus size: 114
40644729 TTAATATTTT
* ** *
40644739 GCGGCGTTTTCCA-ATAAGCGCCACTAATCCTAATATACCGCAAGACCAAACTCTGCGTTTTGGT
1 GCGGCGTTTT-AATATAAGCGCCACTAATCCTAATATACATCAAGACCAAACGCTGCGTTTTGGT
* * * *
40644803 TAAGAAATCTTGCGGCGCTTTTCACTACTCGCTGCTAATACTATTCTTTA
65 TAAGAAATATTGCGGCGCTTTTCAATACTCGCCGCTAATACTATACTTTA
** * * ** *
40644853 GTAGCGTTTTAATATAAGTGCCACTACTGGTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGT
1 GCGGCGTTTTAATATAAGCGCCACTAATCCTAATATACATCAAGACCAAA-CGCTGCGTTTTGGT
* * * * ** * * *
40644918 T-A-ATATTTTGCGACGCTTTACAATAAGCGCCGCTACTACTATGCGTTA
65 TAAGAAATATTGCGGCGCTTTTCAATACTCGCCGCTAATACTATACTTTA
* * *
40644966 GCGGCGTTTTTAA-ATAAGCGCCACTAATCCTAATGTACCTCAAGACCAAACTCTGCGTTTTGGT
1 GCGGCG-TTTTAATATAAGCGCCACTAATCCTAATATACATCAAGACCAAACGCTGCGTTTTGGT
*
40645030 TAAGAAATATTGCGGCGCTTTTCAGTACTCGCCGCTAATACTATACTTTA
65 TAAGAAATATTGCGGCGCTTTTCAATACTCGCCGCTAATACTATACTTTA
* ** * *
40645080 GCGGCGTTTGAATATAAGCGCCACTAAGGCTACTATACATCAAGACCAAAGCGCTGCGTTTTGGA
1 GCGGCGTTTTAATATAAGCGCCACTAATCCTAATATACATCAAGACCAAA-CGCTGCGTTTTGGT
** *
40645145 TAAGAGCTTTTGCGGCGCTT
65 TAAGAAATATTGCGGCGCTT
40645165 GGTAGTAAAC
Statistics
Matches: 252, Mismatches: 53, Indels: 13
0.79 0.17 0.04
Matches are distributed among these distances:
112 14 0.06
113 76 0.30
114 119 0.47
115 43 0.17
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.31
Consensus pattern (114 bp):
GCGGCGTTTTAATATAAGCGCCACTAATCCTAATATACATCAAGACCAAACGCTGCGTTTTGGTT
AAGAAATATTGCGGCGCTTTTCAATACTCGCCGCTAATACTATACTTTA
Found at i:40648191 original size:41 final size:41
Alignment explanation
Indices: 40648127--40648246 Score: 98
Period size: 41 Copynumber: 2.9 Consensus size: 41
40648117 GTTAGCGACG
* ** * *
40648127 TTTTTCCCATAAACGTTGTAAAAGATAAAGCAATAATGGCA
1 TTTTTCGCATAAACGCCGCAAAAGATAAAGCAATAACGGCA
* * * **
40648168 TTTTT-GCATAAACGCCGCAAAAAGTTAAAAACAATAGCGGTG
1 TTTTTCGCATAAACGCCGC-AAAAGAT-AAAGCAATAACGGCA
* * *
40648210 TTTTTCTCATAAACGCCGCTAAAGGTAAAGCAATAAC
1 TTTTTCGCATAAACGCCGCAAAAGATAAAGCAATAAC
40648247 AACATTTTGC
Statistics
Matches: 61, Mismatches: 15, Indels: 6
0.74 0.18 0.07
Matches are distributed among these distances:
40 9 0.15
41 20 0.33
42 20 0.33
43 12 0.20
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (41 bp):
TTTTTCGCATAAACGCCGCAAAAGATAAAGCAATAACGGCA
Found at i:40648368 original size:24 final size:24
Alignment explanation
Indices: 40648340--40648392 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
40648330 CCCTTAAATC
* *
40648340 ATTTTCCCCAAATT-CCTAATTTA
1 ATTTTTCCCAAATTCCCTAACTTA
*
40648363 ATTTTTCCCTAATTCCCTAACTTA
1 ATTTTTCCCAAATTCCCTAACTTA
40648387 ATTTTT
1 ATTTTT
40648393 TTTCCCATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 12 0.46
24 14 0.54
ACGTcount: A:0.26, C:0.25, G:0.00, T:0.49
Consensus pattern (24 bp):
ATTTTTCCCAAATTCCCTAACTTA
Found at i:40659277 original size:18 final size:20
Alignment explanation
Indices: 40659256--40659294 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
40659246 AAATAAAAAC
*
40659256 ATAAAAA-AGAAA-TTCATA
1 ATAAAAACAAAAAGTTCATA
40659274 ATAAAAACAAAAAGTTCATA
1 ATAAAAACAAAAAGTTCATA
40659294 A
1 A
40659295 AAATATGGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 4 0.22
20 7 0.39
ACGTcount: A:0.67, C:0.08, G:0.05, T:0.21
Consensus pattern (20 bp):
ATAAAAACAAAAAGTTCATA
Found at i:40659455 original size:86 final size:86
Alignment explanation
Indices: 40659364--40659523 Score: 313
Period size: 86 Copynumber: 1.9 Consensus size: 86
40659354 AAACAAAACG
40659364 TAAAAAATAGAAACTAAAAATCAAAC-AAAAAAACCCATAAATCATTCAATAATTTTCACATTGA
1 TAAAAAATAGAAACTAAAAATCAAACAAAAAAAACCCATAAATCATTCAATAATTTTCACATTGA
40659428 AAAAAATGAAGTCGTTTTGTT
66 AAAAAATGAAGTCGTTTTGTT
40659449 TAAAAAATAGAAACTAAAAATCAAACAAAAAAAACCCATAAATCATTCAATAATTTTCACATTGA
1 TAAAAAATAGAAACTAAAAATCAAACAAAAAAAACCCATAAATCATTCAATAATTTTCACATTGA
40659514 AAAAAATGAA
66 AAAAAATGAA
40659524 TTCAACGAAC
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
85 26 0.35
86 48 0.65
ACGTcount: A:0.57, C:0.13, G:0.06, T:0.24
Consensus pattern (86 bp):
TAAAAAATAGAAACTAAAAATCAAACAAAAAAAACCCATAAATCATTCAATAATTTTCACATTGA
AAAAAATGAAGTCGTTTTGTT
Found at i:40660689 original size:38 final size:39
Alignment explanation
Indices: 40660647--40660751 Score: 119
Period size: 38 Copynumber: 2.7 Consensus size: 39
40660637 AAGAAGATGA
* *
40660647 ATAAAATTATAAAAATGTAAAAAGATATAT-A-TATGTAT
1 ATAAAATTAT-AAAATATAAAAAAATATATAAGTATGTAT
40660685 ATAAAAATTATAAAATATAAAAAAATATATAAGTATGTAT
1 AT-AAAATTATAAAATATAAAAAAATATATAAGTATGTAT
*
40660725 AT-ATATTCATGAAAATA-AAAAAAATAT
1 ATAAAATT-AT-AAAATATAAAAAAATAT
40660752 GAATATAGAT
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
38 23 0.39
39 21 0.36
40 15 0.25
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.32
Consensus pattern (39 bp):
ATAAAATTATAAAATATAAAAAAATATATAAGTATGTAT
Found at i:40660765 original size:2 final size:2
Alignment explanation
Indices: 40660754--40660824 Score: 56
Period size: 2 Copynumber: 35.5 Consensus size: 2
40660744 AAAAATATGA
* * * * *
40660754 AT AT AG AT AT AT AT AT AT AG AT AT GT AT AT A- AA AT AT A- AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
40660794 AT AT AT AT AT GAGT AT AT AT GT AT AT AT AT A
1 AT AT AT AT AT -A-T AT AT AT AT AT AT AT AT A
40660825 AATAAGTTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
1 2 0.04
2 50 0.91
3 2 0.04
4 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (2 bp):
AT
Found at i:40660799 original size:9 final size:10
Alignment explanation
Indices: 40660671--40660828 Score: 55
Period size: 10 Copynumber: 16.1 Consensus size: 10
40660661 ATGTAAAAAG
*
40660671 ATATATATAT
1 ATATATAAAT
* *
40660681 GTATATAAAA
1 ATATATAAAT
40660691 AT-TATAAA-
1 ATATATAAAT
* *
40660699 ATATAAAAAA
1 ATATATAAAT
*
40660709 ATATATAAGT
1 ATATATAAAT
* *
40660719 ATGTATATAT
1 ATATATAAAT
40660729 AT-TCATGAAA-
1 ATAT-AT-AAAT
40660739 ATA-A-AAA-
1 ATATATAAAT
* *
40660746 AAATATGAAT
1 ATATATAAAT
* *
40660756 ATAGATATAT
1 ATATATAAAT
40660766 ATATATAGATAT
1 ATATATA-A-AT
*
40660778 GTATATAAA-
1 ATATATAAAT
40660787 ATATA-AAAT
1 ATATATAAAT
*
40660796 ATATATATGAGT
1 ATATATA--AAT
**
40660808 ATATATGTAT
1 ATATATAAAT
40660818 ATATATAAAT
1 ATATATAAAT
40660828 A
1 A
40660829 AGTTTTTTAA
Statistics
Matches: 106, Mismatches: 28, Indels: 28
0.65 0.17 0.17
Matches are distributed among these distances:
7 5 0.05
8 6 0.06
9 24 0.23
10 52 0.49
11 3 0.03
12 16 0.15
ACGTcount: A:0.56, C:0.01, G:0.07, T:0.37
Consensus pattern (10 bp):
ATATATAAAT
Found at i:40660938 original size:3 final size:3
Alignment explanation
Indices: 40660923--40661009 Score: 50
Period size: 3 Copynumber: 28.0 Consensus size: 3
40660913 TGAATGAGTA
* * * **
40660923 AAT AAT TAT AAT AAT AAGT AAGT AAT AAA AAT AA- ATAC AAT AAT AGC
1 AAT AAT AAT AAT AAT AA-T AA-T AAT AAT AAT AAT A-AT AAT AAT AAT
* * * *
40660970 AAT AAT AAT ATTT AAA AAT AAT AAT AAT AGT AAA AAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
40661010 GATATTGTTA
Statistics
Matches: 63, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
2 1 0.02
3 52 0.83
4 10 0.16
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:40661021 original size:18 final size:19
Alignment explanation
Indices: 40660970--40661022 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 19
40660960 CAATAATAGC
*
40660970 AATAATAATATTTAAAAAT
1 AATAATAATAGTTAAAAAT
40660989 AATAATAATAG-TAAAAAT
1 AATAATAATAGTTAAAAAT
* *
40661007 AATGAT-ATTGTTAAAA
1 AATAATAATAGTTAAAA
40661023 TTAGTTAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 3 0.10
18 17 0.57
19 10 0.33
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (19 bp):
AATAATAATAGTTAAAAAT
Found at i:40661790 original size:11 final size:11
Alignment explanation
Indices: 40661749--40661782 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
40661739 TTTAGTATGC
40661749 GAAAACAAAAA
1 GAAAACAAAAA
40661760 GAAAACAAAAA
1 GAAAACAAAAA
40661771 GAAAACAAAAA
1 GAAAACAAAAA
40661782 G
1 G
40661783 GAATCAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.79, C:0.09, G:0.12, T:0.00
Consensus pattern (11 bp):
GAAAACAAAAA
Found at i:40664513 original size:20 final size:21
Alignment explanation
Indices: 40664468--40664513 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
40664458 AGAAAACTAT
40664468 TAAACTTATTAAAAATTAATAA
1 TAAA-TTATTAAAAATTAATAA
*
40664490 -AAATTATTTAAAATTAA-AA
1 TAAATTATTAAAAATTAATAA
40664509 TAAAT
1 TAAAT
40664514 ATTCAAATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 2 0.09
20 17 0.77
21 3 0.14
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAATTATTAAAAATTAATAA
Found at i:40667013 original size:10 final size:10
Alignment explanation
Indices: 40666998--40667023 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
40666988 CTTACTGATC
40666998 TGTTAGTATT
1 TGTTAGTATT
40667008 TGTTAGTATT
1 TGTTAGTATT
40667018 TGTTAG
1 TGTTAG
40667024 CACTTAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.23, T:0.58
Consensus pattern (10 bp):
TGTTAGTATT
Found at i:40669099 original size:14 final size:15
Alignment explanation
Indices: 40669046--40669101 Score: 57
Period size: 14 Copynumber: 4.0 Consensus size: 15
40669036 ATCCAAACAC
40669046 CAGAAAAT-ATTTT-
1 CAGAAAATCATTTTA
* * *
40669059 CCGTAAATCATTTTC
1 CAGAAAATCATTTTA
40669074 CAG-AAATCATTTTA
1 CAGAAAATCATTTTA
40669088 CAGAAAAT-ATTTTA
1 CAGAAAATCATTTTA
40669102 TTGGCAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
13 6 0.17
14 24 0.67
15 6 0.17
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (15 bp):
CAGAAAATCATTTTA
Found at i:40674847 original size:11 final size:10
Alignment explanation
Indices: 40674829--40674854 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
40674819 TTTGTTATTT
40674829 ACAAAAAAAA
1 ACAAAAAAAA
40674839 ACAAAAAAAA
1 ACAAAAAAAA
40674849 ACAAAA
1 ACAAAA
40674855 TAGATTTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (10 bp):
ACAAAAAAAA
Found at i:40675280 original size:11 final size:11
Alignment explanation
Indices: 40675252--40675339 Score: 93
Period size: 11 Copynumber: 8.6 Consensus size: 11
40675242 TAAATATATT
*
40675252 TATTTTTTAAA
1 TATTTTTAAAA
40675263 -A-TTTTAAAA
1 TATTTTTAAAA
40675272 TATTTTTAAAA
1 TATTTTTAAAA
*
40675283 TAATTTTT-TAA
1 T-ATTTTTAAAA
40675294 T-TTTTT--AA
1 TATTTTTAAAA
40675302 -A-TTTTAAAA
1 TATTTTTAAAA
40675311 TATTTTTAAAA
1 TATTTTTAAAA
40675322 TATTTTTAAAA
1 TATTTTTAAAA
40675333 TATTTTT
1 TATTTTT
40675340 TTTTAATTTT
Statistics
Matches: 67, Mismatches: 2, Indels: 16
0.79 0.02 0.19
Matches are distributed among these distances:
7 4 0.06
8 2 0.03
9 14 0.21
10 3 0.04
11 38 0.57
12 6 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:40675298 original size:39 final size:38
Alignment explanation
Indices: 40675250--40675328 Score: 131
Period size: 39 Copynumber: 2.1 Consensus size: 38
40675240 AATAAATATA
*
40675250 TTTATTTTTTAAAATTTTAAAATATTTTTAAAATAATTT
1 TTTAATTTTTAAAATTTTAAAATATTTTTAAAAT-ATTT
*
40675289 TTTAATTTTTTAAATTTTAAAATATTTTTAAAATATTT
1 TTTAATTTTTAAAATTTTAAAATATTTTTAAAATATTT
40675327 TT
1 TT
40675329 AAAATATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 6 0.16
39 32 0.84
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (38 bp):
TTTAATTTTTAAAATTTTAAAATATTTTTAAAATATTT
Found at i:40675308 original size:28 final size:29
Alignment explanation
Indices: 40675275--40675331 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
40675265 TTTAAAATAT
*
40675275 TTTTAAAATAATTTTT-TAAT-TTTTTAAA
1 TTTTAAAAT-ATTTTTAAAATATTTTTAAA
40675303 TTTTAAAATATTTTTAAAATATTTTTAAA
1 TTTTAAAATATTTTTAAAATATTTTTAAA
40675332 ATATTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 6 0.23
28 12 0.46
29 8 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TTTTAAAATATTTTTAAAATATTTTTAAA
Found at i:40675357 original size:10 final size:10
Alignment explanation
Indices: 40675253--40675365 Score: 78
Period size: 11 Copynumber: 11.2 Consensus size: 10
40675243 AAATATATTT
40675253 ATTTTTTAAA
1 ATTTTTTAAA
40675263 A--TTTTAAA
1 ATTTTTTAAA
40675271 ATATTTTTAAA
1 AT-TTTTTAAA
*
40675282 ATAATTTTT-TA
1 AT--TTTTTAAA
40675293 ATTTTTT-AA
1 ATTTTTTAAA
40675302 A--TTTTAAA
1 ATTTTTTAAA
40675310 ATATTTTTAAA
1 AT-TTTTTAAA
40675321 ATATTTTTAAAA
1 AT-TTTTT-AAA
**
40675333 TATTTTTTTTTA
1 -A-TTTTTTAAA
40675345 ATTTTTTAAA
1 ATTTTTTAAA
40675355 A-TTTTTAAA
1 ATTTTTTAAA
40675364 AT
1 AT
40675366 AAAAATGGGC
Statistics
Matches: 85, Mismatches: 6, Indels: 24
0.74 0.05 0.21
Matches are distributed among these distances:
7 4 0.05
8 11 0.13
9 16 0.19
10 9 0.11
11 28 0.33
12 10 0.12
13 6 0.07
14 1 0.01
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATTTTTTAAA
Found at i:40675359 original size:8 final size:9
Alignment explanation
Indices: 40675255--40675365 Score: 70
Period size: 9 Copynumber: 12.1 Consensus size: 9
40675245 ATATATTTAT
40675255 TTTTTAAAA
1 TTTTTAAAA
*
40675264 TTTTAAAATA
1 TTTTTAAA-A
40675274 TTTTTAAAA
1 TTTTTAAAA
**
40675283 TAATTTTTTAA
1 T--TTTTAAAA
*
40675294 TTTTTTAAA
1 TTTTTAAAA
*
40675303 TTTTAAAATA
1 TTTTTAAA-A
40675313 TTTTTAAAATA
1 TTTTT-AAA-A
40675324 TTTTTAAAA
1 TTTTTAAAA
40675333 TATTTT----
1 T-TTTTAAAA
*
40675339 TTTTT-AAT
1 TTTTTAAAA
40675347 TTTTTAAAA
1 TTTTTAAAA
40675356 TTTTTAAAA
1 TTTTTAAAA
40675365 T
1 T
40675366 AAAAATGGGC
Statistics
Matches: 83, Mismatches: 9, Indels: 20
0.74 0.08 0.18
Matches are distributed among these distances:
5 4 0.05
6 1 0.01
8 5 0.06
9 36 0.43
10 20 0.24
11 17 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:40679781 original size:28 final size:28
Alignment explanation
Indices: 40679749--40679807 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
40679739 AAACTCAATA
40679749 TCTTTCCGTTTCAAATCTACGTATGATT
1 TCTTTCCGTTTCAAATCTACGTATGATT
40679777 TCTTTCCGTTTCAAATCTACGTATGATT
1 TCTTTCCGTTTCAAATCTACGTATGATT
40679805 TCT
1 TCT
40679808 AACGATCTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.20, C:0.22, G:0.10, T:0.47
Consensus pattern (28 bp):
TCTTTCCGTTTCAAATCTACGTATGATT
Found at i:40681508 original size:33 final size:34
Alignment explanation
Indices: 40681466--40681532 Score: 127
Period size: 33 Copynumber: 2.0 Consensus size: 34
40681456 CAGATCAACT
40681466 CTTATACCCGATGCTGACACTAT-TGTCCTAGAA
1 CTTATACCCGATGCTGACACTATATGTCCTAGAA
40681499 CTTATACCCGATGCTGACACTATATGTCCTAGAA
1 CTTATACCCGATGCTGACACTATATGTCCTAGAA
40681533 AACCAACTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 23 0.70
34 10 0.30
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (34 bp):
CTTATACCCGATGCTGACACTATATGTCCTAGAA
Found at i:40685476 original size:23 final size:25
Alignment explanation
Indices: 40685423--40685483 Score: 83
Period size: 23 Copynumber: 2.5 Consensus size: 25
40685413 AAGCCATGAT
40685423 CGGTAAGCTCATTCTGAGCTGAAAAA
1 CGGTAAGCTCATTCTGAGCTG-AAAA
40685449 CGGTAAGCTC-TATC-GAGCTG-AAA
1 CGGTAAGCTCAT-TCTGAGCTGAAAA
40685472 CGGTAAGCTCAT
1 CGGTAAGCTCAT
40685484 AAGAGCGGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
23 13 0.39
24 1 0.03
25 7 0.21
26 12 0.36
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (25 bp):
CGGTAAGCTCATTCTGAGCTGAAAA
Done.