Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 4 of 218
Found at i:1250115 original size:31 final size:31
Alignment explanation
Indices: 1250036--1250117 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
1250026 TTTTTTTTGT
* * *
1250036 TTAATTTGGTACCTAAACTTGACACTTTTTTC
1 TTAAATTGGTA-CTAATCTTGACACTTTTCTC
**
1250068 TTATTTTGGTACTAATCTTGACAC-TTTCTC
1 TTAAATTGGTACTAATCTTGACACTTTTCTC
*
1250098 TTAAATTGTTACTTAATCTT
1 TTAAATTGGTAC-TAATCTT
1250118 TTTGGGGTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
30 14 0.33
31 19 0.44
32 10 0.23
ACGTcount: A:0.24, C:0.17, G:0.09, T:0.50
Consensus pattern (31 bp):
TTAAATTGGTACTAATCTTGACACTTTTCTC
Found at i:1250695 original size:59 final size:60
Alignment explanation
Indices: 1250580--1250694 Score: 162
Period size: 59 Copynumber: 1.9 Consensus size: 60
1250570 AGGTATAAAA
* * * *
1250580 TTTAGGCACTAAATTAGGAAAAAATGTCAAGTTCATGTACCAAATTGGGTCCAAAAAGGG
1 TTTAGGCACCAAATTAGGAAAAAATATCAAGTTCAAGTACCAAATTGGGTCAAAAAAGGG
* *
1250640 TTTAGGTACCAAATTAGG-AAAAGTATCAAGTTCAAGTACCAAATTGGG-CAAAAAA
1 TTTAGGCACCAAATTAGGAAAAAATATCAAGTTCAAGTACCAAATTGGGTCAAAAAA
1250695 AAAAGAGTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
58 6 0.12
59 27 0.55
60 16 0.33
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.24
Consensus pattern (60 bp):
TTTAGGCACCAAATTAGGAAAAAATATCAAGTTCAAGTACCAAATTGGGTCAAAAAAGGG
Found at i:1258488 original size:17 final size:17
Alignment explanation
Indices: 1258466--1258499 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1258456 ATCCACTAAT
*
1258466 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1258483 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1258500 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1263127 original size:17 final size:17
Alignment explanation
Indices: 1263105--1263138 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1263095 ATCCACTAAT
*
1263105 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1263122 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1263139 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1265682 original size:5 final size:5
Alignment explanation
Indices: 1265672--1265698 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1265662 CTTAGCTAGA
1265672 ATAAT ATAAT ATAAT ATAAT ATAAT AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT AT
1265699 TATTAGGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:1266955 original size:9 final size:9
Alignment explanation
Indices: 1266941--1266974 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
1266931 TTTGGTTAAA
1266941 AATTACCCG
1 AATTACCCG
1266950 AATTACCCG
1 AATTACCCG
*
1266959 AATTAACCG
1 AATTACCCG
1266968 AATTACC
1 AATTACC
1266975 GAAAAATACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.38, C:0.29, G:0.09, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:1267157 original size:13 final size:13
Alignment explanation
Indices: 1267139--1267168 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1267129 TTTTAGTTTT
1267139 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
1267152 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
1267165 ATTG
1 ATTG
1267169 AGTTTGGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:1273307 original size:18 final size:18
Alignment explanation
Indices: 1273284--1273345 Score: 97
Period size: 18 Copynumber: 3.4 Consensus size: 18
1273274 CCCAACTACT
*
1273284 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
1273302 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
1273320 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
*
1273338 GTAAACGT
1 GTATACGT
1273346 CGTATTCCCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:1278488 original size:49 final size:49
Alignment explanation
Indices: 1278419--1278850 Score: 701
Period size: 47 Copynumber: 9.1 Consensus size: 49
1278409 GAAATGATAG
1278419 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1278468 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1278517 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1278566 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATA-GTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
*
1278612 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGAGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1278659 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGT-A
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1278707 T-AGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1278753 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
* * * * * * *
1278800 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1278847 TAAG
1 TAAG
1278851 TCCCGAAGGG
Statistics
Matches: 365, Mismatches: 11, Indels: 16
0.93 0.03 0.04
Matches are distributed among these distances:
45 9 0.02
46 48 0.13
47 161 0.44
48 3 0.01
49 144 0.39
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (49 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
Found at i:1279024 original size:37 final size:37
Alignment explanation
Indices: 1278968--1279046 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
1278958 CCGAGCTCTA
* * *
1278968 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
1279005 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
1279042 AAGAC
1 AAGAC
1279047 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:1280954 original size:43 final size:43
Alignment explanation
Indices: 1280906--1281008 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
1280896 TTGGTTTTCA
1280906 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1280949 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1280992 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
1281009 TTGAAATGCA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.22, C:0.16, G:0.36, T:0.26
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:1281025 original size:29 final size:29
Alignment explanation
Indices: 1280990--1281062 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 29
1280980 GTTGTGAGAT
* *
1280990 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
1281019 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
1281048 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
1281063 ATGGTTGATT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 35 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:1281469 original size:39 final size:41
Alignment explanation
Indices: 1281373--1281628 Score: 128
Period size: 39 Copynumber: 6.5 Consensus size: 41
1281363 TCGAATGATG
*
1281373 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTGACCATA
* *
1281413 TCCGGACTAAGAT-CCGAAGGCATTTGTGCG-AGAT-ACTA-A
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAAG-TGACCATA
** * **
1281452 TCCGGGCTAAGTCCCGAAGAGCATTCATGC-TAGTGA-TGTA
1 TCCGGGCTAAGTCCCGAAG-GCATTTGTGCGAAGTGACCATA
** * **
1281492 TCCGGGCTAAGT-CCGAAGAGCATTCATGC-TAGTGA-TGTA
1 TCCGGGCTAAGTCCCGAAG-GCATTTGTGCGAAGTGACCATA
** * **
1281531 TCCGGGCTAAGT-CCGAAGAGCATTCATGC-TAGTGA-TGTA
1 TCCGGGCTAAGTCCCGAAG-GCATTTGTGCGAAGTGACCATA
* ** * **
1281570 TCCGGGCTAAGTTCCGAAGAGCATTCATGC-TAGTGA-TGTA
1 TCCGGGCTAAGTCCCGAAG-GCATTTGTGCGAAGTGACCATA
*
1281610 TCCGGGCTAAGTTCCGAAG
1 TCCGGGCTAAGTCCCGAAG
1281629 ATGCTAGTGT
Statistics
Matches: 200, Mismatches: 7, Indels: 18
0.89 0.03 0.08
Matches are distributed among these distances:
38 1 0.00
39 97 0.49
40 93 0.47
41 9 0.05
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTGACCATA
Found at i:1281495 original size:40 final size:40
Alignment explanation
Indices: 1281451--1281717 Score: 347
Period size: 40 Copynumber: 6.9 Consensus size: 40
1281441 CGAGATACTA
1281451 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1281491 ATCCGGGCTAAGT-CCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1281530 ATCCGGGCTAAGT-CCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
*
1281569 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* *
1281609 ATCCGGGCTAAGTTCCG-A-AG-----ATGCTAGTG-TAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* ** * * * *
1281641 ATCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGTGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* * *
1281681 ATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
1281718 CGTGTATTCG
Statistics
Matches: 204, Mismatches: 14, Indels: 18
0.86 0.06 0.08
Matches are distributed among these distances:
32 15 0.07
33 10 0.05
34 2 0.01
38 2 0.01
39 86 0.42
40 89 0.44
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
Found at i:1281515 original size:79 final size:80
Alignment explanation
Indices: 1281373--1281717 Score: 312
Period size: 79 Copynumber: 4.5 Consensus size: 80
1281363 TCGAATGATG
** ** *
1281373 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAG-GCA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGTGA-TGTATCCGGGCTAAGATCCGAAGAGCA
**
1281435 TTTGTGCGAGAT-ACT-AA
64 TTCATGCGAG-TGA-TGAA
1281452 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAG-TCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGATCCGAAGAGCATT
* *
1281516 CATGCTAGTGATGTA
66 CATGCGAGTGATGAA
*
1281531 TCCGGGCTAAGT-CCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGATCCGAAGAGCATT
* *
1281595 CATGCTAGTGATGTA
66 CATGCGAGTGATGAA
* * * *
1281610 TCCGGGCTAAGTTCCG-A-AG-----ATGCTAGTG-TATATCCGTGCTAA-ACCCCGAAGAGCAT
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGA-TCCGAAGAGCAT
* *
1281666 TCGTGCTG-GTG-TTATA
65 TCATGC-GAGTGATGA-A
* * *
1281682 TCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
1281718 CGTGTATTCG
Statistics
Matches: 228, Mismatches: 20, Indels: 35
0.81 0.07 0.12
Matches are distributed among these distances:
71 1 0.00
72 46 0.20
73 10 0.04
74 2 0.01
78 49 0.21
79 104 0.46
80 10 0.04
81 6 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGATCCGAAGAGCATT
CATGCGAGTGATGAA
Found at i:1281659 original size:32 final size:33
Alignment explanation
Indices: 1281596--1281661 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 33
1281586 AAGAGCATTC
* ***
1281596 ATGCTAGTGATGTATCCGGGCTAAGTTCCGAAG
1 ATGCTAGTGATATATCCGGGCTAAACCCCGAAG
*
1281629 ATGCTAGTG-TATATCCGTGCTAAACCCCGAAG
1 ATGCTAGTGATATATCCGGGCTAAACCCCGAAG
1281661 A
1 A
1281662 GCATTCGTGC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 19 0.68
33 9 0.32
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (33 bp):
ATGCTAGTGATATATCCGGGCTAAACCCCGAAG
Found at i:1281684 original size:72 final size:73
Alignment explanation
Indices: 1281478--1281701 Score: 229
Period size: 72 Copynumber: 3.0 Consensus size: 73
1281468 AAGAGCATTC
* ** *
1281478 ATGCTAGTGATGTATCCGGGCT-AAGTCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAG
1 ATGCTAGTGATATATCCGGGCTAAACCCCGAAGAGCATTCATGCTAGTGATATATCCGGGCTAAG
1281542 T-CCGAAGAG
66 TCCCG-A-AG
* *** *
1281551 CATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTATCCGGG
1 -----ATGCTAGTGATATATCCGGGCTAAACCCCGAAGAGCATTCATGCTAGTGATATATCCGGG
*
1281616 CTAAGTTCCGAAG
61 CTAAGTCCCGAAG
* * * * *
1281629 ATGCTAGTG-TATATCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAGG
1 ATGCTAGTGATATATCCGGGCTAAACCCCGAAGAGCATTCATGCTAGTGATATATCCGGGCTAAG
1281693 TCCCGAAG
66 TCCCGAAG
1281701 A
1 A
1281702 GCAATCATGC
Statistics
Matches: 131, Mismatches: 13, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
72 53 0.40
73 9 0.07
78 24 0.18
79 42 0.32
80 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (73 bp):
ATGCTAGTGATATATCCGGGCTAAACCCCGAAGAGCATTCATGCTAGTGATATATCCGGGCTAAG
TCCCGAAG
Found at i:1285245 original size:49 final size:49
Alignment explanation
Indices: 1285176--1285610 Score: 687
Period size: 47 Copynumber: 9.1 Consensus size: 49
1285166 GAAATGATAG
1285176 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1285225 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT-ATATATATGTGA
1285275 T-AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
*
1285323 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
*
1285370 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGAGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1285417 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGT-A
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1285465 TAAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
1 TAA-GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1285513 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
* * * * * * *
1285560 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1285607 TAAG
1 TAAG
1285611 TCCCGAAGGG
Statistics
Matches: 365, Mismatches: 13, Indels: 18
0.92 0.03 0.05
Matches are distributed among these distances:
47 181 0.50
48 22 0.06
49 149 0.41
50 13 0.04
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (49 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
Found at i:1285473 original size:143 final size:143
Alignment explanation
Indices: 1285176--1285610 Score: 707
Period size: 143 Copynumber: 3.0 Consensus size: 143
1285166 GAAATGATAG
1285176 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
1285241 ATGTGATGAATGTGAAAGTGTAATATATATGTGAT-AGGCCTAATGGCCGATGTGATGAATGTGA
64 ATGTGATGAATGTGAAAGTG---TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
1285305 AAGTGTATATATATGTGA
126 AAGTGTATATATATGTGA
*
1285323 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
*
1285388 GTGATGAATGTGAAAGTGTATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
66 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1285453 TATATATATGT-A
131 TATATATATGTGA
1285465 TAAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGA
1 TAA-GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGA
* * * * * * *
1285530 TGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGT
65 TGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT
1285595 GTATA-A-ATGTGA
130 GTATATATATGTGA
1285607 TAAG
1 TAAG
1285611 TCCCGAAGGG
Statistics
Matches: 274, Mismatches: 11, Indels: 12
0.92 0.04 0.04
Matches are distributed among these distances:
141 5 0.02
142 20 0.07
143 167 0.61
145 46 0.17
147 36 0.13
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (143 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
TATATATATGTGA
Found at i:1285785 original size:37 final size:37
Alignment explanation
Indices: 1285729--1285807 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
1285719 CCGAGCTCTA
* * *
1285729 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
1285766 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
1285803 AAGAC
1 AAGAC
1285808 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:1292378 original size:14 final size:15
Alignment explanation
Indices: 1292359--1292388 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1292349 AAAGAAAGTT
1292359 AAAATTT-TAAAATA
1 AAAATTTCTAAAATA
1292373 AAAATTTCTAAAATA
1 AAAATTTCTAAAATA
1292388 A
1 A
1292389 TAGTTGCAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAATTTCTAAAATA
Found at i:1292624 original size:21 final size:21
Alignment explanation
Indices: 1292586--1292625 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1292576 TAACTCGAAC
* *
1292586 AATTTCACTTGACTCGACTTG
1 AATTTCACTTCACCCGACTTG
*
1292607 AATTTCATTTCACCCGACT
1 AATTTCACTTCACCCGACT
1292626 CAATTTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.28, G:0.10, T:0.38
Consensus pattern (21 bp):
AATTTCACTTCACCCGACTTG
Found at i:1293699 original size:9 final size:9
Alignment explanation
Indices: 1293673--1293706 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1293663 TATATATGCC
1293673 TTTTAAAAAA
1 TTTT-AAAAA
1293683 TTTT-AAAA
1 TTTTAAAAA
1293691 TTTTAAAAA
1 TTTTAAAAA
1293700 TTTTAAA
1 TTTTAAA
1293707 TTAGTAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.35
9 11 0.48
10 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:1298793 original size:18 final size:18
Alignment explanation
Indices: 1298770--1298862 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
1298760 CCCAACTACT
*
1298770 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
1298788 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
* *
1298806 ATATACGTGAATAGTACT
1 GTATACGTGAATAGTACC
* *
1298824 GTATACGTAAATAGTGCC
1 GTATACGTGAATAGTACC
1298842 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
1298860 GTA
1 GTA
1298863 AACGGTCGTA
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:1298822 original size:36 final size:36
Alignment explanation
Indices: 1298771--1298862 Score: 148
Period size: 36 Copynumber: 2.6 Consensus size: 36
1298761 CCAACTACTG
* *
1298771 TATACGTGAACAGTACCGTATACGTGAATAGTGCCA
1 TATACGTGAATAGTACCGTATACGTAAATAGTGCCA
* *
1298807 TATACGTGAATAGTACTGTATACGTAAATAGTGCCG
1 TATACGTGAATAGTACCGTATACGTAAATAGTGCCA
1298843 TATACGTGAATAGTACCGTA
1 TATACGTGAATAGTACCGTA
1298863 AACGGTCGTA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (36 bp):
TATACGTGAATAGTACCGTATACGTAAATAGTGCCA
Found at i:1317869 original size:18 final size:20
Alignment explanation
Indices: 1317829--1317870 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
1317819 AAAAATTACA
*
1317829 AAAACTTCAAAATAATTTTT
1 AAAACTTCAAAATAATTTAT
*
1317849 AAAA-TTCAAAA-CATTTAT
1 AAAACTTCAAAATAATTTAT
1317867 AAAA
1 AAAA
1317871 ATTTCAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.45
19 7 0.35
20 4 0.20
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAACTTCAAAATAATTTAT
Found at i:1317920 original size:11 final size:12
Alignment explanation
Indices: 1317897--1317929 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1317887 TTTTTTAAAG
1317897 AATTGTAAAAAA
1 AATTGTAAAAAA
1317909 AATTGTAAAAAA
1 AATTGTAAAAAA
*
1317921 AATTCTAAA
1 AATTGTAAA
1317930 TAATATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27
Consensus pattern (12 bp):
AATTGTAAAAAA
Found at i:1328615 original size:20 final size:20
Alignment explanation
Indices: 1328564--1328617 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
1328554 AATTACAAAA
1328564 ATAAAAATTCAAAATAATTT
1 ATAAAAATTCAAAATAATTT
* *
1328584 -TTAAAATTCAAAAT-GTTT
1 ATAAAAATTCAAAATAATTT
1328602 ATAAAAATTTCAAAAT
1 ATAAAAA-TTCAAAAT
1328618 TTATATTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 3 0.10
19 18 0.62
20 8 0.28
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (20 bp):
ATAAAAATTCAAAATAATTT
Found at i:1332614 original size:21 final size:21
Alignment explanation
Indices: 1332588--1332628 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1332578 AGACGAGCAA
* *
1332588 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
1332609 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
1332629 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:1335309 original size:46 final size:44
Alignment explanation
Indices: 1335242--1335475 Score: 279
Period size: 36 Copynumber: 5.6 Consensus size: 44
1335232 TTTAAGTACT
1335242 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC--TAGCTACACTTA
1335288 TCTGATCAAGTGACAAAGTGAT-A-----AG-T-GCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTAGCTACACTTA
*
1335324 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC--TAGCTACACTTA
1335370 TCTGATCAAGTGACAAAGTGAT-A-----AG-T-GCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTAGCTACACTTA
1335406 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTAGCTACACTTA
*
1335451 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
1335476 ATCATACGTA
Statistics
Matches: 166, Mismatches: 3, Indels: 41
0.79 0.01 0.20
Matches are distributed among these distances:
36 63 0.38
37 4 0.02
40 4 0.02
42 4 0.02
43 12 0.07
44 6 0.04
45 20 0.12
46 53 0.32
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (44 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTAGCTACACTTA
Found at i:1335379 original size:82 final size:82
Alignment explanation
Indices: 1335242--1335475 Score: 420
Period size: 82 Copynumber: 2.9 Consensus size: 82
1335232 TTTAAGTACT
1335242 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
1335307 GATAAGTGCTACACTTA
66 GATAAGTGCTACACTTA
*
1335324 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
1335389 GATAAGTGCTACACTTA
66 GATAAGTGCTACACTTA
* *
1335406 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGATC-AGGGAC-AAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
1335468 GATAAGTG
66 GATAAGTG
1335476 ATCATACGTA
Statistics
Matches: 148, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
79 12 0.08
80 5 0.03
81 19 0.13
82 112 0.76
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (82 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
GATAAGTGCTACACTTA
Found at i:1339763 original size:15 final size:15
Alignment explanation
Indices: 1339743--1339794 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
1339733 TAGTATTTAT
1339743 ATTTTAATTTAATTA
1 ATTTTAATTTAATTA
*
1339758 ATTTTAATATTTA-TA
1 ATTTTAAT-TTAATTA
* *
1339773 TTTTTAAAATTAATTA
1 ATTTT-AATTTAATTA
1339789 ATTTTA
1 ATTTTA
1339795 GTTTTTAGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 18 0.62
16 11 0.38
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTAATTTAATTA
Found at i:1339789 original size:31 final size:31
Alignment explanation
Indices: 1339731--1339814 Score: 118
Period size: 31 Copynumber: 2.8 Consensus size: 31
1339721 AAACTATGGC
*
1339731 TTTAGTATTTATA-TTTT-AATTTAATTAAT
1 TTTAGTATTTATATTTTTAAAATTAATTAAT
*
1339760 TTTAATATTTATATTTTTAAAATTAATTAAT
1 TTTAGTATTTATATTTTTAAAATTAATTAAT
* *
1339791 TTTAGTTTTTAGATTTTTAAAATT
1 TTTAGTATTTATATTTTTAAAATT
1339815 TTGGAACTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 12 0.25
30 4 0.08
31 32 0.67
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.61
Consensus pattern (31 bp):
TTTAGTATTTATATTTTTAAAATTAATTAAT
Found at i:1348502 original size:20 final size:20
Alignment explanation
Indices: 1348477--1348518 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1348467 CCGATACCGT
1348477 AAAGCTTTCTCGTGCAATTA
1 AAAGCTTTCTCGTGCAATTA
1348497 AAAGCTTTCTCGTGCAATTA
1 AAAGCTTTCTCGTGCAATTA
1348517 AA
1 AA
1348519 CCAACATCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (20 bp):
AAAGCTTTCTCGTGCAATTA
Found at i:1349122 original size:18 final size:20
Alignment explanation
Indices: 1349082--1349123 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
1349072 AAAAATTACA
*
1349082 AAAACTTCAAAATAATTTTT
1 AAAACTTCAAAATAATTTAT
*
1349102 AAAA-TTCAAAA-CATTTAT
1 AAAACTTCAAAATAATTTAT
1349120 AAAA
1 AAAA
1349124 ATTTCAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.45
19 7 0.35
20 4 0.20
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAACTTCAAAATAATTTAT
Found at i:1357086 original size:19 final size:20
Alignment explanation
Indices: 1357064--1357101 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
1357054 ATTAATAAAT
1357064 AAACTGAAAA-AA-GCATTAG
1 AAACT-AAAACAATGCATTAG
1357083 AAACTAAAACAATGCATTA
1 AAACTAAAACAATGCATTA
1357102 AAAAATAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.24
19 7 0.41
20 6 0.35
ACGTcount: A:0.58, C:0.13, G:0.11, T:0.18
Consensus pattern (20 bp):
AAACTAAAACAATGCATTAG
Found at i:1359643 original size:79 final size:80
Alignment explanation
Indices: 1359559--1359705 Score: 190
Period size: 79 Copynumber: 1.9 Consensus size: 80
1359549 CTATTAAAAA
** * * *
1359559 TATATTAAAATTTTCAAATTGGTTATACAT-AAAATATT-TTTAATACGTTTAAAATATTAATAT
1 TATATTAAAAAATTAAAATTGGTTATAC-TCAAAATATTCTTTAACACATTTAAAATATTAATAT
1359622 ATTTTAATGTATTAAG
65 ATTTTAATGTATTAAG
* * * *
1359638 TATATTAAAAAATTAAAATTGGTTATACTCAACATTTTCTTTAACATATTTAAAATTTTAATATA
1 TATATTAAAAAATTAAAATTGGTTATACTCAAAATATTCTTTAACACATTTAAAATATTAATATA
1359703 TTT
66 TTT
1359706 AAAAAATTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
78 1 0.02
79 31 0.54
80 25 0.44
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (80 bp):
TATATTAAAAAATTAAAATTGGTTATACTCAAAATATTCTTTAACACATTTAAAATATTAATATA
TTTTAATGTATTAAG
Found at i:1359703 original size:17 final size:17
Alignment explanation
Indices: 1359677--1359741 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 17
1359667 CAACATTTTC
*
1359677 TTTAACATATTTAAAAT
1 TTTAATATATTTAAAAT
1359694 TTTAATATATTTAAAAAAT
1 TTTAATATATTT--AAAAT
* *
1359713 TTTAAGT-TTTTTGAAAT
1 TTTAA-TATATTTAAAAT
1359730 TTTAAATATATT
1 TTT-AATATATT
1359742 AAACTATCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
17 19 0.49
18 5 0.13
19 14 0.36
20 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (17 bp):
TTTAATATATTTAAAAT
Found at i:1363561 original size:20 final size:21
Alignment explanation
Indices: 1363538--1363577 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1363528 TTAGTTTTCT
*
1363538 AAAATTTTAAATAT-ATTAAA
1 AAAATGTTAAATATAATTAAA
*
1363558 AAAATGTTAAGTATAATTAA
1 AAAATGTTAAATATAATTAA
1363578 TTTTAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (21 bp):
AAAATGTTAAATATAATTAAA
Found at i:1363692 original size:17 final size:17
Alignment explanation
Indices: 1363672--1363715 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
1363662 TTTAAAAAAC
1363672 TTAAAAAATTAAATATA
1 TTAAAAAATTAAATATA
* **
1363689 TTAAGATTTTAAATATA
1 TTAAAAAATTAAATATA
*
1363706 ATAAAAAATT
1 TTAAAAAATT
1363716 TTAAATATAA
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
TTAAAAAATTAAATATA
Found at i:1363711 original size:34 final size:35
Alignment explanation
Indices: 1363648--1363724 Score: 88
Period size: 34 Copynumber: 2.2 Consensus size: 35
1363638 AGGTTTTCTT
1363648 AATATATTTAAAATTTTAAAAAACTTAAAAAA-TTA
1 AATATATTTAAAATTTTAAAAAAC-TAAAAAATTTA
*
1363683 AATATA-TTAAGATTTTAAATATAA-TAAAAAATTTTA
1 AATATATTTAAAATTTTAAA-A-AACTAAAAAA-TTTA
1363719 AATATA
1 AATATA
1363725 ACCAATTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
34 19 0.51
35 7 0.19
36 11 0.30
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (35 bp):
AATATATTTAAAATTTTAAAAAACTAAAAAATTTA
Found at i:1363772 original size:18 final size:19
Alignment explanation
Indices: 1363741--1363778 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1363731 TTTAATATAT
*
1363741 TTAATATATTTTAAAAAAA
1 TTAATATATATTAAAAAAA
1363760 TTAA-ATATATTAAAAAAA
1 TTAATATATATTAAAAAAA
1363778 T
1 T
1363779 GTTAAGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAATATATATTAAAAAAA
Found at i:1363913 original size:17 final size:16
Alignment explanation
Indices: 1363891--1363957 Score: 62
Period size: 17 Copynumber: 3.9 Consensus size: 16
1363881 AAAAAAGATT
1363891 TTTTAATATATTTAAAA
1 TTTTAA-ATATTTAAAA
* *
1363908 TTTTAAAAAACTTAAAAA
1 TTTT-AAATA-TTTAAAA
*
1363926 ATTTAAATATATTAAAA
1 TTTTAAATAT-TTAAAA
*
1363943 TTTTAAATATGTAAA
1 TTTTAAATATTTAAA
1363958 GAAAATGTTG
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
16 5 0.12
17 24 0.60
18 11 0.28
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (16 bp):
TTTTAAATATTTAAAA
Found at i:1364006 original size:67 final size:69
Alignment explanation
Indices: 1363931--1364064 Score: 179
Period size: 70 Copynumber: 2.0 Consensus size: 69
1363921 AAAAAATTTA
* *
1363931 AATATATTAAAATTTT-AA-ATATGTAAAGAAAATGTTGAG-T-A-ACCAATTTTAAATTTTTAA
1 AATATATTAAAATTTTAAACATAT-TAAA-AAAAT-TTAAGATAATACCAATTTTAAAATTTTAA
1363991 TATACTT
63 TATACTT
1363998 AATATATTAAAATTTTAAACATATTAAAAAAATTTAAGTATAATACCAATTTTAAAATTTTAATA
1 AATATATTAAAATTTTAAACATATTAAAAAAATTTAAG-ATAATACCAATTTTAAAATTTTAATA
1364063 TA
65 TA
1364065 TTTTTTAATA
Statistics
Matches: 59, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
66 4 0.07
67 21 0.36
68 7 0.12
69 5 0.08
70 22 0.37
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (69 bp):
AATATATTAAAATTTTAAACATATTAAAAAAATTTAAGATAATACCAATTTTAAAATTTTAATAT
ACTT
Found at i:1367080 original size:17 final size:17
Alignment explanation
Indices: 1367058--1367118 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
1367048 TTTTTAAATG
1367058 ATATTTTATAATTTTTA
1 ATATTTTATAATTTTTA
* *
1367075 ATATTTTTTATATGTTT-
1 ATATTTTATA-ATTTTTA
*
1367092 AGATTTTATTAATATTTTA
1 ATATTTTA-TAAT-TTTTA
*
1367111 ATTTTTTA
1 ATATTTTA
1367119 AGAGACGAAG
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
17 17 0.52
18 10 0.30
19 6 0.18
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (17 bp):
ATATTTTATAATTTTTA
Found at i:1367092 original size:18 final size:16
Alignment explanation
Indices: 1367070--1367117 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
1367060 ATTTTATAAT
1367070 TTTTAATATTTTTTATA
1 TTTTAAT-TTTTTTATA
*
1367087 TGTTTAGATTTTATTAATA
1 T-TTTA-ATTTT-TTTATA
1367106 TTTTAATTTTTT
1 TTTTAATTTTTT
1367118 AAGAGACGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
16 2 0.07
17 6 0.22
18 11 0.41
19 8 0.30
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (16 bp):
TTTTAATTTTTTTATA
Found at i:1367962 original size:22 final size:22
Alignment explanation
Indices: 1367928--1367969 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1367918 AGTTTTGATA
* *
1367928 TTCACTTTGATACTTAAATTCT
1 TTCAATTTAATACTTAAATTCT
*
1367950 TTCAATTTAATACTTGAATT
1 TTCAATTTAATACTTAAATT
1367970 TTTTTTTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.14, G:0.05, T:0.50
Consensus pattern (22 bp):
TTCAATTTAATACTTAAATTCT
Found at i:1370888 original size:29 final size:30
Alignment explanation
Indices: 1370837--1370901 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
1370827 TCACATATTT
*
1370837 AGAATTTAGTCGTTGTACATTT-ATTTTTA
1 AGAATTTAGTCATTGTACATTTAATTTTTA
*
1370866 AGAATTTAGTCCATT-TACTTTTAAATTTTTA
1 AGAATTTAGT-CATTGTACATTT-AATTTTTA
1370897 A-AATT
1 AGAATT
1370902 CAAGTCCAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 16 0.52
30 7 0.23
31 8 0.26
ACGTcount: A:0.32, C:0.08, G:0.09, T:0.51
Consensus pattern (30 bp):
AGAATTTAGTCATTGTACATTTAATTTTTA
Found at i:1382086 original size:14 final size:14
Alignment explanation
Indices: 1382067--1382113 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
1382057 AAGGTGCAGA
1382067 TTTAATTTTTGTAT
1 TTTAATTTTTGTAT
*
1382081 TTTAATTTGAT-TATT
1 TTTAATTT-TTGTA-T
1382096 TTTAATTTTTAGTAT
1 TTTAATTTTT-GTAT
1382111 TTT
1 TTT
1382114 TTTAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
14 11 0.41
15 14 0.52
16 2 0.07
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.70
Consensus pattern (14 bp):
TTTAATTTTTGTAT
Found at i:1382869 original size:26 final size:23
Alignment explanation
Indices: 1382823--1382869 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 23
1382813 ATAAAGTATA
1382823 TAATATATATATATAAAATAACC
1 TAATATATATATATAAAATAACC
1382846 TAATATACTATATTATAAACATAA
1 TAATATA-TATA-TATAAA-ATAA
1382870 AAAATGGGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 4 0.19
25 6 0.29
26 4 0.19
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (23 bp):
TAATATATATATATAAAATAACC
Found at i:1383398 original size:19 final size:19
Alignment explanation
Indices: 1383370--1383409 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1383360 TGTAGATTAA
1383370 ATACACTAAATCAAAATTT
1 ATACACTAAATCAAAATTT
* *
1383389 ATACATTAAATTAAAATTT
1 ATACACTAAATCAAAATTT
1383408 AT
1 AT
1383410 TTATAATTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.38
Consensus pattern (19 bp):
ATACACTAAATCAAAATTT
Found at i:1399317 original size:44 final size:44
Alignment explanation
Indices: 1399233--1399407 Score: 181
Period size: 44 Copynumber: 4.0 Consensus size: 44
1399223 CGACTACTGT
* * * *
1399233 TACTGTTACTGATTTGACACTTTGTGTATCGAATACTGTTACCG
1 TACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGTTACCG
* * * * *
1399277 TATTATTATAGATTCGGCACTTTGTGTGTCGAATATTGTTATCG
1 TACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGTTACCG
* * * *
1399321 TTACTGTTACCA-ATTTGACACTTTGTATGTCGAATACTATTACCG
1 -TACTGTTA-CAGATTCGGCACTTTGTGTGTCGAATACTGTTACCG
* * *
1399366 TACTGTTACAGATTCGGCACTTTATCTGTTGAATACTGTTAC
1 TACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGTTAC
1399408 TGTTACTATT
Statistics
Matches: 104, Mismatches: 24, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
43 2 0.02
44 68 0.65
45 33 0.32
46 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.42
Consensus pattern (44 bp):
TACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGTTACCG
Found at i:1399354 original size:89 final size:89
Alignment explanation
Indices: 1399227--1399419 Score: 253
Period size: 89 Copynumber: 2.2 Consensus size: 89
1399217 ATGTGCCGAC
** * * * *
1399227 TACTGTTACTGTTACTGATTTGACACTTTGTGTATCGAATACTGTTACCGTATTATTATAGATTC
1 TACTGTTACTGTTACCAATTTGACACTTTGTATATCGAATACTATTACCGTACTATTACAGATTC
* * *
1399292 GGCACTTTGTGTGTCGAATATTGT
66 GGCACTTTATCTGTCGAATACTGT
* *
1399316 TA-TCGTTACTGTTACCAATTTGACACTTTGTATGTCGAATACTATTACCGTACTGTTACAGATT
1 TACT-GTTACTGTTACCAATTTGACACTTTGTATATCGAATACTATTACCGTACTATTACAGATT
*
1399380 CGGCACTTTATCTGTTGAATACTGT
65 CGGCACTTTATCTGTCGAATACTGT
*
1399405 TACTGTTACTATTAC
1 TACTGTTACTGTTAC
1399420 TGCTACCGTT
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
88 1 0.01
89 87 0.98
90 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.42
Consensus pattern (89 bp):
TACTGTTACTGTTACCAATTTGACACTTTGTATATCGAATACTATTACCGTACTATTACAGATTC
GGCACTTTATCTGTCGAATACTGT
Found at i:1402532 original size:50 final size:50
Alignment explanation
Indices: 1402454--1402576 Score: 210
Period size: 50 Copynumber: 2.5 Consensus size: 50
1402444 TTGGGTAAAT
*
1402454 AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAG
1 AGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGATGAG
*
1402504 AGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATGAG
1 AGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGATGAG
**
1402554 AGGTCCCCCGTAAGACCATGTCT
1 AGGTCCCATGTAAGACCATGTCT
1402577 GGGATGTAAC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 69 1.00
ACGTcount: A:0.25, C:0.24, G:0.30, T:0.20
Consensus pattern (50 bp):
AGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGATGAG
Found at i:1403032 original size:5 final size:5
Alignment explanation
Indices: 1403022--1403088 Score: 77
Period size: 5 Copynumber: 13.2 Consensus size: 5
1403012 AATTATGTTT
1403022 TTATA TTATA TTATTA TTA-A -TATA TTATA TTATA TTATA TTATA TTAT-
1 TTATA TTATA TTA-TA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1403070 TATATTA TTATA TATATA T
1 T-TA-TA TTATA T-TATA T
1403089 GACAAAGAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 13
0.81 0.00 0.19
Matches are distributed among these distances:
3 2 0.04
4 3 0.05
5 36 0.65
6 13 0.24
7 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:1403036 original size:8 final size:8
Alignment explanation
Indices: 1403022--1403082 Score: 67
Period size: 8 Copynumber: 7.8 Consensus size: 8
1403012 AATTATGTTT
1403022 TTATATTA
1 TTATATTA
1403030 -TATTATTA
1 TTA-TATTA
1403038 TTA-ATATA
1 TTATAT-TA
1403046 TTATATTA
1 TTATATTA
1403054 -TAT-TATA
1 TTATAT-TA
1403061 TTATATTA
1 TTATATTA
1403069 TTATATTA
1 TTATATTA
1403077 TTATAT
1 TTATAT
1403083 ATATATGACA
Statistics
Matches: 46, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
6 1 0.02
7 9 0.20
8 31 0.67
9 5 0.11
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TTATATTA
Found at i:1403038 original size:3 final size:3
Alignment explanation
Indices: 1403025--1403080 Score: 54
Period size: 3 Copynumber: 21.0 Consensus size: 3
1403015 TATGTTTTTA
*
1403025 TAT TA- TAT TAT TAT TAA TA- TAT TA- TAT TA- TAT TA- TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1403067 TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT
1403081 ATATATATGA
Statistics
Matches: 45, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
2 14 0.31
3 31 0.69
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1403154 original size:40 final size:41
Alignment explanation
Indices: 1403098--1403177 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 41
1403088 TGACAAAGAA
1403098 AGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGGG
1 AGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGGG
*
1403139 AGAAAG-AAAGAAACAGAGAGCAAAACGAAACAGAGAAGG
1 AGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
1403178 AAAGAAGGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 32 0.84
41 6 0.16
ACGTcount: A:0.62, C:0.10, G:0.28, T:0.00
Consensus pattern (41 bp):
AGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGGG
Found at i:1404600 original size:41 final size:39
Alignment explanation
Indices: 1404552--1404663 Score: 111
Period size: 37 Copynumber: 2.9 Consensus size: 39
1404542 TCGACCTTGA
1404552 GTCGATGAGACACTGGGTGTCATACTATTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCA-ACTATTACTTCGGATAG
* ** ** * *
1404592 ATTCGATGAGGTACTGGGTACCAAC--TTACTTCGGCTTG
1 -GTCGATGAGACACTGGGTGTCAACTATTACTTCGGATAG
* *
1404630 GCCGATGAGACACTGGGTGTCAACTATTGCTTCG
1 GTCGATGAGACACTGGGTGTCAACTATTACTTCG
1404664 AACTATCCGA
Statistics
Matches: 55, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
37 18 0.33
38 11 0.20
39 7 0.13
40 2 0.04
41 17 0.31
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (39 bp):
GTCGATGAGACACTGGGTGTCAACTATTACTTCGGATAG
Found at i:1405388 original size:17 final size:17
Alignment explanation
Indices: 1405344--1405391 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
1405334 TGGCATGTAT
*
1405344 CTAAGTAATGTACATAC
1 CTAAGTAATGTATATAC
*
1405361 CTAGGTAATGTATATAC
1 CTAAGTAATGTATATAC
*
1405378 CTAAGTGATGTATA
1 CTAAGTAATGTATA
1405392 GGGATTAGTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (17 bp):
CTAAGTAATGTATATAC
Found at i:1408565 original size:56 final size:56
Alignment explanation
Indices: 1408481--1408589 Score: 182
Period size: 56 Copynumber: 1.9 Consensus size: 56
1408471 TGTATTTTGG
*
1408481 AGGAGGTGTAGTCCATATACATGTGTAAGTTACAACATTCATTAGCCTATAAATTC
1 AGGAGGTGTAGTCCATATACATGGGTAAGTTACAACATTCATTAGCCTATAAATTC
* * *
1408537 AGGATGTGTGGTCCATATACGTGGGTAAGTTACAACATTCATTAGCCTATAAA
1 AGGAGGTGTAGTCCATATACATGGGTAAGTTACAACATTCATTAGCCTATAAA
1408590 ATCCATTAGC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (56 bp):
AGGAGGTGTAGTCCATATACATGGGTAAGTTACAACATTCATTAGCCTATAAATTC
Found at i:1409733 original size:4 final size:4
Alignment explanation
Indices: 1409724--1409749 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1409714 GGAACTTATA
1409724 TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TA
1409750 CGCATGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:1413151 original size:21 final size:21
Alignment explanation
Indices: 1413072--1413179 Score: 110
Period size: 21 Copynumber: 5.1 Consensus size: 21
1413062 CCTCATCAGT
1413072 ATACGACACAT-AAGTGCCTG
1 ATACGACACATAAAGTGCCTG
* ** * *
1413092 AAACGACACACGAGGTGTCTG
1 ATACGACACATAAAGTGCCTG
** *
1413113 ATACGACACACGAGGTGCCTG
1 ATACGACACATAAAGTGCCTG
1413134 ATACGACACATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCT--G
*
1413157 ATACGACACGTAAAGTGCCTG
1 ATACGACACATAAAGTGCCTG
1413178 AT
1 AT
1413180 GGGCAAAGCC
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.12
21 46 0.61
23 20 0.27
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (21 bp):
ATACGACACATAAAGTGCCTG
Found at i:1413416 original size:36 final size:36
Alignment explanation
Indices: 1413369--1413459 Score: 105
Period size: 36 Copynumber: 2.5 Consensus size: 36
1413359 CTTTTCAAAT
* *
1413369 TCACATTTCAATTCAATTTCACTTTTTTACTTTCAA-
1 TCACAATTCAATTCAATTT-ACTTTTCTACTTTCAAG
*
1413405 TCACAATTCAATTCAAATTTACTTTTCTATTTTCAAG
1 TCACAATTCAATTC-AATTTACTTTTCTACTTTCAAG
*
1413442 TCA-ATATTCATTTCAATT
1 TCACA-ATTCAATTCAATT
1413460 CCACACATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
36 32 0.67
37 16 0.33
ACGTcount: A:0.31, C:0.20, G:0.01, T:0.48
Consensus pattern (36 bp):
TCACAATTCAATTCAATTTACTTTTCTACTTTCAAG
Found at i:1413531 original size:16 final size:16
Alignment explanation
Indices: 1413509--1413548 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
1413499 TTAATAATAA
1413509 TACTTACCTTA-TATT
1 TACTTACCTTATTATT
1413524 TCACTTACCTTATTATT
1 T-ACTTACCTTATTATT
1413541 TACTTACC
1 TACTTACC
1413549 ATACACATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.04
16 17 0.74
17 5 0.22
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (16 bp):
TACTTACCTTATTATT
Found at i:1414752 original size:25 final size:27
Alignment explanation
Indices: 1414715--1414774 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
1414705 ATAATATAGT
*
1414715 TATTTTGAATTAATTTAATATAATTTATAA
1 TATTTT-AATTAA-ATAATAT-ATTTATAA
*
1414745 TATTTTAATTAAATAATATTTTTATAA
1 TATTTTAATTAAATAATATATTTATAA
1414772 TAT
1 TAT
1414775 AAATCAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 10 0.36
28 6 0.21
29 6 0.21
30 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (27 bp):
TATTTTAATTAAATAATATATTTATAA
Found at i:1414776 original size:16 final size:17
Alignment explanation
Indices: 1414740--1414776 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1414730 TAATATAATT
1414740 TATAATATTTTAATTAA
1 TATAATATTTTAATTAA
*
1414757 -ATAATATTTTTA-TAA
1 TATAATATTTTAATTAA
1414772 TATAA
1 TATAA
1414777 ATCAAGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 3 0.17
16 15 0.83
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATAATATTTTAATTAA
Found at i:1416828 original size:20 final size:21
Alignment explanation
Indices: 1416774--1416819 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1416764 TTGATATGTT
1416774 AGTGAAGAAAAATAAGAGAAA
1 AGTGAAGAAAAATAAGAGAAA
1416795 AGTGAAGAAAAATAAGAG-AA
1 AGTGAAGAAAAATAAGAGAAA
1416815 AGTGA
1 AGTGA
1416820 TGGGAAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.11
Consensus pattern (21 bp):
AGTGAAGAAAAATAAGAGAAA
Found at i:1440203 original size:58 final size:56
Alignment explanation
Indices: 1440116--1440299 Score: 215
Period size: 58 Copynumber: 3.1 Consensus size: 56
1440106 GGTTCGAACT
* *
1440116 TTTTTTTGTTCAAGTTAGGCCATAAACTTGGAAATTGTTCCCACATTAGGGTCTAAAC
1 TTTTTTTGTTCAAGTTAGGCC-TGAACTTGGCAATTGTTCCCACATTAGGG-CTAAAC
* *
1440174 TTTTTTTATTCAAGTTAGGTCCTGAACTTGGCAATTGTTCCCACATTGGGGCCTAAAC
1 TTTTTTTGTTCAAGTTAGG-CCTGAACTTGGCAATTGTTCCCACATTAGGG-CTAAAC
* * * *
1440232 TTTTTTTTTTGTTTAAGTTAGACTCTGAATTTGGCAATTGTTCCCACATTAGGGCTTGAAC
1 ---TTTTTTTGTTCAAGTTAGGC-CTGAACTTGGCAATTGTTCCCACATTAGGGC-TAAAC
1440293 TTTTTTT
1 TTTTTTT
1440300 TTAGTCCAAG
Statistics
Matches: 109, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
58 57 0.52
59 2 0.02
60 2 0.02
61 48 0.44
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (56 bp):
TTTTTTTGTTCAAGTTAGGCCTGAACTTGGCAATTGTTCCCACATTAGGGCTAAAC
Found at i:1440269 original size:61 final size:60
Alignment explanation
Indices: 1440115--1440313 Score: 226
Period size: 61 Copynumber: 3.3 Consensus size: 60
1440105 GGGTTCGAAC
* * *
1440115 TTTTTTTTGTTCAAGTTAGGC-CATAAACTTGGAAATTGTTCCCACATTAGGGTCTAAAC--
1 TTTTTTTTGTTCAAGTTA-GCTC-TGAACTTGGCAATTGTTCCCACATTAGGGCCTAAACTT
* * *
1440174 -TTTTTTTATTCAAGTTAGGTCCTGAACTTGGCAATTGTTCCCACATTGGGGCCTAAACTT
1 TTTTTTTTGTTCAAGTTAGCT-CTGAACTTGGCAATTGTTCCCACATTAGGGCCTAAACTT
* * * *
1440234 TTTTTTTTGTTTAAGTTAGACTCTGAATTTGGCAATTGTTCCCACATTAGGGCTTGAACTT
1 TTTTTTTTGTTCAAGTTAG-CTCTGAACTTGGCAATTGTTCCCACATTAGGGCCTAAACTT
* *
1440295 TTTTTTTAGTCCAAGTTAG
1 TTTTTTTTGTTCAAGTTAG
1440314 TCCTTGAAAA
Statistics
Matches: 118, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
57 1 0.01
58 48 0.41
59 1 0.01
61 67 0.57
62 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.43
Consensus pattern (60 bp):
TTTTTTTTGTTCAAGTTAGCTCTGAACTTGGCAATTGTTCCCACATTAGGGCCTAAACTT
Found at i:1453829 original size:34 final size:34
Alignment explanation
Indices: 1453798--1453867 Score: 85
Period size: 32 Copynumber: 2.1 Consensus size: 34
1453788 ACGTATTTGA
1453798 TAAATTAAATAT-AA-A-GTATTCTATTTATATTT
1 TAAATTAAATATAAATATGTATT-TATTTATATTT
* *
1453830 TACATTATATATAAATATGTATTTATTTATA-TT
1 TAAATTAAATATAAATATGTATTTATTTATATTT
1453863 TAAAT
1 TAAAT
1453868 ATTTTGTTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
32 10 0.31
33 8 0.25
34 9 0.28
35 5 0.16
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (34 bp):
TAAATTAAATATAAATATGTATTTATTTATATTT
Found at i:1454226 original size:30 final size:30
Alignment explanation
Indices: 1454196--1454252 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
1454186 AATAAGATAT
1454196 TATTTTTTATA--TTT-AATTTAAATAAAA
1 TATTTTTTATAGTTTTAAATTTAAATAAAA
1454223 TATTTTTTATAGTTTTAAAATTTAAATAAA
1 TATTTTTTATAGTTTT-AAATTTAAATAAA
1454253 CGAAAAAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 11 0.42
29 3 0.12
31 12 0.46
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (30 bp):
TATTTTTTATAGTTTTAAATTTAAATAAAA
Found at i:1481329 original size:31 final size:32
Alignment explanation
Indices: 1481291--1481364 Score: 89
Period size: 34 Copynumber: 2.3 Consensus size: 32
1481281 TCTCAATACC
* *
1481291 ATACATGAA-TTATGGTTTAA-TGTGCAATTGT
1 ATACATGAACTT-TGATTTAATTGTGCAATTAT
1481322 ATACATGAACTTTGATTTAATTTTGTGCAATTAT
1 ATACATGAACTTTGATTTAA--TTGTGCAATTAT
1481356 ATACATGAA
1 ATACATGAA
1481365 GTTTTAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
31 16 0.43
32 2 0.05
34 19 0.51
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (32 bp):
ATACATGAACTTTGATTTAATTGTGCAATTAT
Found at i:1484513 original size:18 final size:18
Alignment explanation
Indices: 1484475--1484513 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1484465 TGTGTGTTCT
* *
1484475 AGTCAAATTAAACATTGA
1 AGTCAAATCAAACATTAA
*
1484493 AGTCAAATCAAATATTAA
1 AGTCAAATCAAACATTAA
1484511 AGT
1 AGT
1484514 ATCAAATAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.28
Consensus pattern (18 bp):
AGTCAAATCAAACATTAA
Found at i:1500715 original size:21 final size:20
Alignment explanation
Indices: 1500691--1500729 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1500681 TTAAGTTCAA
1500691 ATTATTTGAATTTAAAATTCG
1 ATTATTT-AATTTAAAATTCG
*
1500712 ATTATTTTATTTAAAATT
1 ATTATTTAATTTAAAATT
1500730 TTAAGATTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTATTTAATTTAAAATTCG
Found at i:1506788 original size:4 final size:4
Alignment explanation
Indices: 1506781--1506805 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1506771 TATCAATCAC
1506781 AATT AATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AATT AATT A
1506806 GAATAAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:1510191 original size:25 final size:26
Alignment explanation
Indices: 1510163--1510211 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
1510153 TATGTGTACT
1510163 AGTTT-AATTTAAATTAAAT-AAAATA
1 AGTTTGAATTTAAA-TAAATCAAAATA
1510188 AGTTTGAATTTAAATAAATCAAAA
1 AGTTTGAATTTAAATAAATCAAAA
1510212 ATTAAATACC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (26 bp):
AGTTTGAATTTAAATAAATCAAAATA
Found at i:1517309 original size:8 final size:8
Alignment explanation
Indices: 1517298--1517325 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
1517288 TGTTATATAC
1517298 ATATAATA
1 ATATAATA
1517306 ATATAATA
1 ATATAATA
1517314 ATATAATA
1 ATATAATA
1517322 ATAT
1 ATAT
1517326 TTTTTAACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATAATA
Found at i:1527792 original size:10 final size:11
Alignment explanation
Indices: 1527765--1527792 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1527755 TGCAATTAAC
1527765 TGAAAAATTTA
1 TGAAAAATTTA
1527776 TGAAAAATTTA
1 TGAAAAATTTA
1527787 TGAAAA
1 TGAAAA
1527793 GAGATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (11 bp):
TGAAAAATTTA
Found at i:1528258 original size:2 final size:2
Alignment explanation
Indices: 1528251--1528289 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1528241 AATCACATTT
1528251 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1528290 TTTTGCAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1534357 original size:31 final size:31
Alignment explanation
Indices: 1534322--1534394 Score: 146
Period size: 31 Copynumber: 2.4 Consensus size: 31
1534312 TCAAATTTAG
1534322 ACATGAACTTTGGCCCAATGTGGAATTTGAT
1 ACATGAACTTTGGCCCAATGTGGAATTTGAT
1534353 ACATGAACTTTGGCCCAATGTGGAATTTGAT
1 ACATGAACTTTGGCCCAATGTGGAATTTGAT
1534384 ACATGAACTTT
1 ACATGAACTTT
1534395 AATTATACAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (31 bp):
ACATGAACTTTGGCCCAATGTGGAATTTGAT
Found at i:1549746 original size:3 final size:3
Alignment explanation
Indices: 1549732--1549772 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
1549722 AAATTGTTAT
* *
1549732 TTA TTA TCA TTA TTA TTA TTAA TTA TTA TTA TTA TTT TTA T
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA T
1549773 ATTCATGCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1549750 original size:19 final size:19
Alignment explanation
Indices: 1549728--1549772 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1549718 AAGAAAATTG
1549728 TTATTTATTATCATTATTA
1 TTATTTATTATCATTATTA
* *
1549747 TTATTAATTATTATTATTA
1 TTATTTATTATCATTATTA
1549766 TT-TTTAT
1 TTATTTAT
1549773 ATTCATGCGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTTATTATCATTATTA
Found at i:1549756 original size:13 final size:13
Alignment explanation
Indices: 1549740--1549765 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1549730 ATTTATTATC
1549740 ATTATTATTATTA
1 ATTATTATTATTA
1549753 ATTATTATTATTA
1 ATTATTATTATTA
1549766 TTTTTATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTATTATTATTA
Found at i:1550644 original size:98 final size:98
Alignment explanation
Indices: 1550532--1550728 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
1550522 TTAAAAATAA
* * *
1550532 TAAAGGAAATATTCTGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACATATTGGGTGTGATTTC
1 TAAAGGAAATATTCTGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACATATTGGGTGTGATTTC
1550597 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
* *
1550630 TAAAGGAAATATTCTGAGTTTGAGATTCTAAAGGAATCGTGGCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCTGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACATATTGGGTGTGATTTC
1550695 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
1550728 T
1 T
1550729 TTTATTGTAC
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCTGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACATATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:1553934 original size:104 final size:103
Alignment explanation
Indices: 1553754--1553976 Score: 367
Period size: 104 Copynumber: 2.2 Consensus size: 103
1553744 TGTATATAAA
** * *
1553754 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
1553819 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCCG
* *
1553858 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
1553922 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
1553961 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
1553977 GATATCCATT
Statistics
Matches: 112, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
103 21 0.19
104 90 0.80
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
Found at i:1554028 original size:70 final size:72
Alignment explanation
Indices: 1553896--1554046 Score: 243
Period size: 71 Copynumber: 2.1 Consensus size: 72
1553886 TCATTGGTGG
* *
1553896 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
1553960 GAGGGGT
66 GAGGGGT
***
1553967 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
1554031 GAGGGGT
66 GAGGGGT
1554038 TGCTAAGTG
1 TGCTAAGTG
1554047 ATGATTCCCC
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 24 0.32
71 50 0.68
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:1564192 original size:3 final size:3
Alignment explanation
Indices: 1564178--1564217 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
1564168 AAATTGTTAT
*
1564178 TTA TTA TCA TTA TTA TTA TTAA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA T
1564218 AATTCATCGC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1564202 original size:13 final size:13
Alignment explanation
Indices: 1564186--1564211 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1564176 ATTTATTATC
1564186 ATTATTATTATTA
1 ATTATTATTATTA
1564199 ATTATTATTATTA
1 ATTATTATTATTA
1564212 TTTTATAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTATTATTATTA
Found at i:1564202 original size:19 final size:19
Alignment explanation
Indices: 1564174--1564213 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1564164 TAAGAAATTG
*
1564174 TTATTTATTATCATTATTA
1 TTATTAATTATCATTATTA
*
1564193 TTATTAATTATTATTATTA
1 TTATTAATTATCATTATTA
1564212 TT
1 TT
1564214 TTATAATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATTAATTATCATTATTA
Found at i:1565068 original size:95 final size:96
Alignment explanation
Indices: 1564956--1565134 Score: 290
Period size: 96 Copynumber: 1.9 Consensus size: 96
1564946 TAAAAATAAT
* * *
1564956 AGGAAATATTTCTGAGTTTGGGATTTTAAAGGAATTGTGC-CTAACATATTGGGTGTGATTTCTT
1 AGGAAATATTTCTGAGTTTGAGATTCTAAAGGAATCG-GCGCTAACATATTGGGTGTGATTTCTT
1565020 AAATCTTGGATAAGTGGATTGTTTTTAAGTAA
65 AAATCTTGGATAAGTGGATTGTTTTTAAGTAA
*
1565052 AGGAAATA-TTCTGAGTTTGAGATTCTAAAGGAATCGGCGGCTAACGTATTGGGTGTGATTTCTT
1 AGGAAATATTTCTGAGTTTGAGATTCTAAAGGAATCGGC-GCTAACATATTGGGTGTGATTTCTT
1565116 AAATCTTGGATAAGTGGAT
65 AAATCTTGGATAAGTGGAT
1565135 GTTCTTTTAA
Statistics
Matches: 77, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
94 2 0.03
95 25 0.32
96 50 0.65
ACGTcount: A:0.29, C:0.08, G:0.26, T:0.37
Consensus pattern (96 bp):
AGGAAATATTTCTGAGTTTGAGATTCTAAAGGAATCGGCGCTAACATATTGGGTGTGATTTCTTA
AATCTTGGATAAGTGGATTGTTTTTAAGTAA
Found at i:1568210 original size:105 final size:100
Alignment explanation
Indices: 1568081--1568281 Score: 280
Period size: 105 Copynumber: 2.0 Consensus size: 100
1568071 GGTTGCTGTG
* *
1568081 TGCTGATTCCCCGATTTATGGGTGGTGCTATGTG-G-TGATCCACCATATCTTTGACAATGTGAA
1 TGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGAT-AT-CA-CATATCTTTGA-AATGTGAA
*
1568144 GGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAAGAA
62 AGGGGTT-CTATGTGCTGATT--CCCGAGGGGTTGCTAAGAA
* *
1568186 TGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCACATATCTTTGAAATGTGAAAGGG
1 TGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGATATCACATATCTTTGAAATGTGAAAGGG
1568251 GTTCTATGTGCTGATTCCCGAGGGGTTGCTA
66 GTTCTATGTGCTGATTCCCGAGGGGTTGCTA
1568282 GGTGCGTATA
Statistics
Matches: 89, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
100 15 0.17
102 13 0.15
103 14 0.16
104 11 0.12
105 32 0.36
106 3 0.03
107 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.30, T:0.32
Consensus pattern (100 bp):
TGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGATATCACATATCTTTGAAATGTGAAAGGG
GTTCTATGTGCTGATTCCCGAGGGGTTGCTAAGAA
Found at i:1581767 original size:26 final size:26
Alignment explanation
Indices: 1581738--1581793 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
1581728 AGTGGTTGAA
1581738 AATGGCAGTTGGAATTTGGTATTACT
1 AATGGCAGTTGGAATTTGGTATTACT
* * *
1581764 AATGGCGGTTGGAATTTTGTATTAGT
1 AATGGCAGTTGGAATTTGGTATTACT
1581790 AATG
1 AATG
1581794 CTCCCATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.27, C:0.05, G:0.29, T:0.39
Consensus pattern (26 bp):
AATGGCAGTTGGAATTTGGTATTACT
Found at i:1587701 original size:21 final size:22
Alignment explanation
Indices: 1587675--1587721 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
1587665 CTCTGCTCAA
*
1587675 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
1587696 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
1587718 ACTC
1 ACTC
1587722 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:1591515 original size:13 final size:13
Alignment explanation
Indices: 1591497--1591521 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1591487 TTATAAACAA
1591497 AGAATACCTCTTT
1 AGAATACCTCTTT
1591510 AGAATACCTCTT
1 AGAATACCTCTT
1591522 AAAGACTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (13 bp):
AGAATACCTCTTT
Found at i:1592046 original size:18 final size:17
Alignment explanation
Indices: 1591998--1592046 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
1591988 GTGTCGTTCG
1591998 TTTCCAAAACATTACTCA
1 TTTCC-AAACATTACTCA
* *
1592016 TTTACAAATCATTATTCAA
1 TTTCCAAA-CATTACTC-A
1592035 TTTCCAAACATT
1 TTTCCAAACATT
1592047 TTTTTATTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 3 0.12
18 15 0.58
19 8 0.31
ACGTcount: A:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (17 bp):
TTTCCAAACATTACTCA
Found at i:1595833 original size:17 final size:17
Alignment explanation
Indices: 1595803--1595850 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
1595793 AATTTAGCCA
*
1595803 TTTATTTTTATTTCA-T
1 TTTATTTTTTTTTCAGT
1595819 TTTATTTTTCTTTTCAGT
1 TTTATTTTT-TTTTCAGT
*
1595837 TTAATTTTTTTTTC
1 TTTATTTTTTTTTC
1595851 TAATTTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 9 0.32
17 10 0.36
18 9 0.32
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTATTTTTTTTTCAGT
Found at i:1602241 original size:12 final size:12
Alignment explanation
Indices: 1602224--1602248 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1602214 CGCCAACTTG
1602224 TTGTTCTTGCTT
1 TTGTTCTTGCTT
1602236 TTGTTCTTGCTT
1 TTGTTCTTGCTT
1602248 T
1 T
1602249 GGTTTTGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.16, G:0.16, T:0.68
Consensus pattern (12 bp):
TTGTTCTTGCTT
Found at i:1612459 original size:18 final size:18
Alignment explanation
Indices: 1612436--1612523 Score: 115
Period size: 18 Copynumber: 4.9 Consensus size: 18
1612426 CCCAACTACT
*
1612436 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
1612454 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
1612472 GTATACGTAAATAGTACC
1 GTATACGTGAATAGTACC
* * *
1612490 GTA-ATGTGAATAGTGCT
1 GTATACGTGAATAGTACC
1612507 GTATACGTGAATAGTAC
1 GTATACGTGAATAGTAC
1612524 AGTAAACGGT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
17 13 0.22
18 46 0.78
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:1612511 original size:35 final size:35
Alignment explanation
Indices: 1612434--1612528 Score: 136
Period size: 35 Copynumber: 2.7 Consensus size: 35
1612424 ATCCCAACTA
*
1612434 CTGTATACGTGAACAGTACCGTATACGTGAATAGTG
1 CTGTATACGTGAATAGTACCGTA-ACGTGAATAGTG
* * *
1612470 CCGTATACGTAAATAGTACCGTAATGTGAATAGTG
1 CTGTATACGTGAATAGTACCGTAACGTGAATAGTG
*
1612505 CTGTATACGTGAATAGTACAGTAA
1 CTGTATACGTGAATAGTACCGTAA
1612529 ACGGTCGTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
35 32 0.62
36 20 0.38
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (35 bp):
CTGTATACGTGAATAGTACCGTAACGTGAATAGTG
Found at i:1620533 original size:6 final size:6
Alignment explanation
Indices: 1620522--1620549 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1620512 AAATTATGTT
1620522 AAATAA AAATAA AAATAA AAATAA AAAT
1 AAATAA AAATAA AAATAA AAATAA AAAT
1620550 TAAAGCCAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
AAATAA
Found at i:1623999 original size:50 final size:52
Alignment explanation
Indices: 1623875--1624118 Score: 248
Period size: 50 Copynumber: 4.7 Consensus size: 52
1623865 GATAATAACA
* * ** *
1623875 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGT-TC-TCGTGATGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTATCATCGT-ACGG
* *
1623926 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTATCATC-T-CGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTATCATCGTACGG
* * * * *
1623976 TGCCAACGCCATGTCCCAGACATGGTCTGACATGGGACCTCTCGTC-T-CGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTATCATCGTACGG
* * * *
1624026 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-C-CT-ATCATCGTACGG
*
1624081 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA
1624119 TCTCTTTACC
Statistics
Matches: 161, Mismatches: 24, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
50 78 0.48
51 35 0.22
52 5 0.03
53 5 0.03
54 1 0.01
55 2 0.01
56 35 0.22
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.25
Consensus pattern (52 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTATCATCGTACGG
Found at i:1624052 original size:100 final size:106
Alignment explanation
Indices: 1623874--1624123 Score: 343
Period size: 100 Copynumber: 2.4 Consensus size: 106
1623864 TGATAATAAC
**
1623874 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
1623939 TCCCAGACATGGTCTTATAGGGGA-C-CT-ATCATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCATCATCTTAAGG
* * *
1623976 -TGCCAACGCCATGTCCCAGACATGGTCTGACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
*
1624039 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCATCATCTTAAGG
* *
1624081 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1624124 TTACCCAAAT
Statistics
Matches: 130, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
99 1 0.01
100 44 0.34
101 36 0.28
102 2 0.02
103 5 0.04
104 1 0.01
105 2 0.02
106 39 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (106 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCATCATCTTAAGG
Found at i:1624239 original size:13 final size:13
Alignment explanation
Indices: 1624218--1624249 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1624208 GCTTGGATCA
*
1624218 TCATCAAATAAAT
1 TCATAAAATAAAT
1624231 TCATAAAATAAAT
1 TCATAAAATAAAT
1624244 TCATAA
1 TCATAA
1624250 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:1624495 original size:30 final size:30
Alignment explanation
Indices: 1624461--1624518 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1624451 CCTCGACTCT
*
1624461 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
1624491 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
1624519 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:1625789 original size:37 final size:37
Alignment explanation
Indices: 1625728--1625873 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
1625718 TACGTATGAT
* *
1625728 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
1625763 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1625800 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
1625837 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1625874 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:1625890 original size:46 final size:46
Alignment explanation
Indices: 1625837--1626045 Score: 249
Period size: 46 Copynumber: 4.3 Consensus size: 46
1625827 TAAGTGTAGC
* **
1625837 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
1625883 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1625929 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGT-GCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
1625980 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1626032 CACTTATCACTTTG
1 CACTTATCACTTTG
1626046 ATCAGAAGTA
Statistics
Matches: 149, Mismatches: 6, Indels: 16
0.87 0.04 0.09
Matches are distributed among these distances:
46 56 0.38
49 1 0.01
50 4 0.03
51 47 0.32
52 41 0.28
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:1625988 original size:51 final size:52
Alignment explanation
Indices: 1625880--1626044 Score: 269
Period size: 51 Copynumber: 3.2 Consensus size: 52
1625870 TAGCTAAAGC
* * *
1625880 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1625933 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGT-GCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
* *
1625984 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1626036 TATCACTTT
1 TATCACTTT
1626045 GATCAGAAGT
Statistics
Matches: 106, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
51 50 0.47
52 44 0.42
53 12 0.11
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
Found at i:1626014 original size:103 final size:99
Alignment explanation
Indices: 1625837--1626044 Score: 285
Period size: 103 Copynumber: 2.1 Consensus size: 99
1625827 TAAGTGTAGC
* * * *
1625837 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCACT
1625902 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
66 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
*
1625936 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGT-GCCGAAGCTATCACTTATCACTTTCCACTT
1 CACTTTTCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCAC--T----TT
* *
1625999 GTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTAT
60 GTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
1626039 CACTTT
1 CACTTT
1626045 GATCAGAAGT
Statistics
Matches: 96, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
97 19 0.20
98 22 0.23
99 10 0.10
103 45 0.47
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (99 bp):
CACTTTTCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCACT
TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:1644234 original size:15 final size:14
Alignment explanation
Indices: 1644209--1644241 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1644199 GTGGGTTACA
1644209 TTTTTCCTTTTTTT
1 TTTTTCCTTTTTTT
1644223 TCTTTT-CTTTTTTT
1 T-TTTTCCTTTTTTT
1644237 TTTTT
1 TTTTT
1644242 TAACATGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.22
14 10 0.56
15 4 0.22
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTCCTTTTTTT
Found at i:1651591 original size:17 final size:18
Alignment explanation
Indices: 1651561--1651597 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1651551 AATATATCAT
*
1651561 TAAAAATTTAATTAAAAA
1 TAAAAAATTAATTAAAAA
1651579 TAAAAAATT-ATTAAAAA
1 TAAAAAATTAATTAAAAA
1651596 TA
1 TA
1651598 GATTTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAAAATTAATTAAAAA
Found at i:1656881 original size:32 final size:35
Alignment explanation
Indices: 1656842--1656933 Score: 118
Period size: 32 Copynumber: 2.6 Consensus size: 35
1656832 CCTATATAAA
1656842 AAATAGTTTGATACCCTGTGCATTTGG-ATA-TAT
1 AAATAGTTTGATACCCTGTGCATTTGGTATATTAT
*
1656875 -AATAGTTTGATACCTTGTGCAATTTGGTTATATTAT
1 AAATAGTTTGATACCCTGTGC-ATTTGG-TATATTAT
*
1656911 AAACTAGTTCGATACCCTGTGCA
1 AAA-TAGTTTGATACCCTGTGCA
1656934 CTGCTCAGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
32 19 0.38
33 6 0.12
35 3 0.06
36 3 0.06
37 3 0.06
38 16 0.32
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.39
Consensus pattern (35 bp):
AAATAGTTTGATACCCTGTGCATTTGGTATATTAT
Found at i:1657361 original size:22 final size:22
Alignment explanation
Indices: 1657336--1657403 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 22
1657326 TTGACAATAT
*
1657336 AATATGCTTTATTACTGCACAC
1 AATATGCTTTATTAATGCACAC
* *
1657358 AATA--C-TTATAAAATCCACAC
1 AATATGCTTTAT-TAATGCACAC
*
1657378 AATATGCTTTATTATTGCACATC
1 AATATGCTTTATTAATGCACA-C
1657401 AAT
1 AAT
1657404 GGATTTTATT
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
19 4 0.11
20 12 0.34
22 11 0.31
23 8 0.23
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (22 bp):
AATATGCTTTATTAATGCACAC
Found at i:1659323 original size:21 final size:21
Alignment explanation
Indices: 1659299--1659342 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1659289 AGTACTCGAT
1659299 TCAAACAACTCATGACCCTAA
1 TCAAACAACTCATGACCCTAA
* ***
1659320 TCAAGCTTTTCATGACCCTAA
1 TCAAACAACTCATGACCCTAA
1659341 TC
1 TC
1659343 TTGAGTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.32, G:0.07, T:0.27
Consensus pattern (21 bp):
TCAAACAACTCATGACCCTAA
Found at i:1661045 original size:23 final size:23
Alignment explanation
Indices: 1661015--1661062 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1661005 CTAAGCCTAT
1661015 TTAAAGGGGTCATTATATCACTG
1 TTAAAGGGGTCATTATATCACTG
1661038 TTAAAGGGGTCATTATATCACTG
1 TTAAAGGGGTCATTATATCACTG
1661061 TT
1 TT
1661063 TAGTTATGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (23 bp):
TTAAAGGGGTCATTATATCACTG
Found at i:1661856 original size:15 final size:15
Alignment explanation
Indices: 1661833--1661867 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1661823 ATGTGCTTAA
*
1661833 TTCAATGGAGCTGTT
1 TTCAGTGGAGCTGTT
1661848 TTCAGTGGAGCTGTT
1 TTCAGTGGAGCTGTT
1661863 TTCAG
1 TTCAG
1661868 GATCCACACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.14, G:0.29, T:0.40
Consensus pattern (15 bp):
TTCAGTGGAGCTGTT
Found at i:1662335 original size:535 final size:535
Alignment explanation
Indices: 1661320--1662378 Score: 1951
Period size: 535 Copynumber: 2.0 Consensus size: 535
1661310 CGGATAAAAA
1661320 GAGCTATTTTCAGGATCCACACGGCCTGGGGCCAGGGCATTTCCACATGGGCTGGCCACACGCCC
1 GAGCTATTTTCAGGATCCACACGGCCTGGGGCCAGGGCATTTCCACATGGGCTGGCCACACGCCC
*
1661385 ATGTGCCAGCCCATGTCGATTTCGCACCCTGATTCCCAAACACGCAGAAAAACTCAATTTTTAGG
66 ATGTGCCAGCCCATGTCAATTTCGCACCCTGATTCCCAAACACGCAGAAAAACTCAATTTTTAGG
* *
1661450 CTTTTTGAGCATTCTAAAGTTTATAAATACATATTAGGAGAGGACCTAAGGGAGCACACGAAGAA
131 CTTTCTGAGCATTCTAAAGTCTATAAATACATATTAGGAGAGGACCTAAGGGAGCACACGAAGAA
1661515 GAACAAAGAAAAGACTCGAAGAACGCCACCGAATTCAACTCAGAAGCGAATCTCCTCCAAGATTG
196 GAACAAAGAAAAGACTCGAAGAACGCCACCGAATTCAACTCAGAAGCGAATCTCCTCCAAGATTG
1661580 GAGATCTCCATTCAATTTCCTTAGAAGTTTTATTGAGTTTCTTTATGTCTTGATGTTATCCTAAC
261 GAGATCTCCATTCAATTTCCTTAGAAGTTTTATTGAGTTTCTTTATGTCTTGATGTTATCCTAAC
*
1661645 TTTGAGATGATTTTATTTCAGATTATGAACTAAATTCCCTAGATACCTAGGGAAGATGAAACCTA
326 TTTGAGATGATTTTATTTCAGATTATGAACTAAATTCCCTAGATACCTAAGGAAGATGAAACCTA
*
1661710 AGATGAATCTTATTATTTGATTTTTGAATTACATGATAAATACTTGATTCTTGTTCTCAGTTATG
391 AGATGAATCTTATTATTTGATTTCTGAATTACATGATAAATACTTGATTCTTGTTCTCAGTTATG
1661775 TATGCTTATTTCGTGTTTTAATATTTTCAAGATATTAATTCATGTTTAATGTGCTTAATTCAATG
456 TATGCTTATTTCGTGTTTTAATATTTTCAAGATATTAATTCATGTTTAATGTGCTTAATTCAATG
1661840 GAGCTGTTTTCAGTG
521 GAGCTGTTTTCAGTG
*
1661855 GAGCTGTTTTCAGGATCCACACGGCCTGGGGCCTA-GGCATTTCCACATGGGCTGGCCACACGCC
1 GAGCTATTTTCAGGATCCACACGGCCTGGGGCC-AGGGCATTTCCACATGGGCTGGCCACACGCC
* *
1661919 CATGTGCCAGCCCGTGTCAATTTCGCACCCTGATTCCCAAACACGTAGAAAAACTCAATTTTTAG
65 CATGTGCCAGCCCATGTCAATTTCGCACCCTGATTCCCAAACACGCAGAAAAACTCAATTTTTAG
*
1661984 GCTTTCTGAGCATTCTAAAGTCTATAAATACATATTAGGAGAGGACCTAAGGGAGCACGC-AGAG
130 GCTTTCTGAGCATTCTAAAGTCTATAAATACATATTAGGAGAGGACCTAAGGGAGCACACGA-AG
* * *
1662048 AAGAACGAAGAAAATACTCGAAGAACGCCATCGAATTCAACTCAGAAGCGAATCTCCTCCAAGAT
194 AAGAACAAAGAAAAGACTCGAAGAACGCCACCGAATTCAACTCAGAAGCGAATCTCCTCCAAGAT
*
1662113 TGGAGATCTCCATTCAATTTCCTTAGAAGTTTTATTGAGTTTCTTTATGTCTTGTTGTTATCCTA
259 TGGAGATCTCCATTCAATTTCCTTAGAAGTTTTATTGAGTTTCTTTATGTCTTGATGTTATCCTA
1662178 ACTTTGAGATGATTTTATTTCAGATTATGAACTAAATTCCCTAGATACCTAAGGAAGATGAAACC
324 ACTTTGAGATGATTTTATTTCAGATTATGAACTAAATTCCCTAGATACCTAAGGAAGATGAAACC
1662243 TAAGATGAATCTTATTATTTGATTTCTGAATTACATGATAAATACTTGATTCTTGTTCTCAGTTA
389 TAAGATGAATCTTATTATTTGATTTCTGAATTACATGATAAATACTTGATTCTTGTTCTCAGTTA
* *
1662308 TGTATGCTTATTTCGTGTTTTAATATTTTCAAGATATTAATTCATGTTTAATGTGCTTATTTCAG
454 TGTATGCTTATTTCGTGTTTTAATATTTTCAAGATATTAATTCATGTTTAATGTGCTTAATTCAA
1662373 TGGAGC
519 TGGAGC
1662379 AAAAGTCCCT
Statistics
Matches: 507, Mismatches: 15, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
534 1 0.00
535 505 1.00
536 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (535 bp):
GAGCTATTTTCAGGATCCACACGGCCTGGGGCCAGGGCATTTCCACATGGGCTGGCCACACGCCC
ATGTGCCAGCCCATGTCAATTTCGCACCCTGATTCCCAAACACGCAGAAAAACTCAATTTTTAGG
CTTTCTGAGCATTCTAAAGTCTATAAATACATATTAGGAGAGGACCTAAGGGAGCACACGAAGAA
GAACAAAGAAAAGACTCGAAGAACGCCACCGAATTCAACTCAGAAGCGAATCTCCTCCAAGATTG
GAGATCTCCATTCAATTTCCTTAGAAGTTTTATTGAGTTTCTTTATGTCTTGATGTTATCCTAAC
TTTGAGATGATTTTATTTCAGATTATGAACTAAATTCCCTAGATACCTAAGGAAGATGAAACCTA
AGATGAATCTTATTATTTGATTTCTGAATTACATGATAAATACTTGATTCTTGTTCTCAGTTATG
TATGCTTATTTCGTGTTTTAATATTTTCAAGATATTAATTCATGTTTAATGTGCTTAATTCAATG
GAGCTGTTTTCAGTG
Found at i:1669598 original size:20 final size:20
Alignment explanation
Indices: 1669563--1669602 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1669553 ACCAAAAATT
1669563 TATTTTAAAAAATAAAAAAA
1 TATTTTAAAAAATAAAAAAA
**
1669583 TATTTTAAAATTTAAAAAAA
1 TATTTTAAAAAATAAAAAAA
1669603 AAAAAAGTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TATTTTAAAAAATAAAAAAA
Found at i:1681369 original size:13 final size:13
Alignment explanation
Indices: 1681336--1681369 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1681326 AATTATAAAC
*
1681336 ACATGTACTTTTT
1 ACATGTATTTTTT
*
1681349 GCATGTATTTTTT
1 ACATGTATTTTTT
1681362 ACATGTAT
1 ACATGTAT
1681370 ACTTAAACCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53
Consensus pattern (13 bp):
ACATGTATTTTTT
Found at i:1682822 original size:31 final size:32
Alignment explanation
Indices: 1682763--1682822 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
1682753 TCCGAAATCA
*
1682763 AAATTGAACCAAACCTTAAATAACTTGAATTC
1 AAATTGAACCAAACCTAAAATAACTTGAATTC
*
1682795 AAATTG-ACCATAACC-AAAATGACTTGAA
1 AAATTGAACCA-AACCTAAAATAACTTGAA
1682823 ATTTTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 15 0.60
32 10 0.40
ACGTcount: A:0.48, C:0.18, G:0.08, T:0.25
Consensus pattern (32 bp):
AAATTGAACCAAACCTAAAATAACTTGAATTC
Done.