Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 46 of 135
Found at i:11922201 original size:17 final size:17
Alignment explanation
Indices: 11922178--11922247 Score: 79
Period size: 17 Copynumber: 3.9 Consensus size: 17
11922168 ACTTTATTAA
11922178 TTTATAATTTTATAATT
1 TTTATAATTTTATAATT
*
11922195 ATTATAATTTTATATATT
1 TTTATAATTTTATA-ATT
11922213 TTTAATAATATTTATAAGTT
1 TTT-ATAAT-TTTATAA-TT
*
11922233 TTTATTATTTT-TAAT
1 TTTATAATTTTATAAT
11922248 AAATTTATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
16 1 0.02
17 16 0.35
18 8 0.17
19 10 0.22
20 11 0.24
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (17 bp):
TTTATAATTTTATAATT
Found at i:11922229 original size:9 final size:8
Alignment explanation
Indices: 11922178--11922262 Score: 62
Period size: 9 Copynumber: 9.5 Consensus size: 8
11922168 ACTTTATTAA
11922178 TTTATAAT
1 TTTATAAT
11922186 TTTATAAT
1 TTTATAAT
11922194 TATTATAAT
1 T-TTATAAT
11922203 TTTATATATT
1 TTTATA-A-T
11922213 TTTAATAAT
1 TTT-ATAAT
11922222 ATTTATAAGTT
1 -TTTATAA--T
*
11922233 TTTATTATT
1 TTTA-TAAT
*
11922242 TTTAATAAA
1 TTT-ATAAT
*
11922251 TTTATAAG
1 TTTATAAT
11922259 TTTA
1 TTTA
11922263 CATCAATTTT
Statistics
Matches: 64, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
8 22 0.34
9 23 0.36
10 13 0.20
11 6 0.09
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (8 bp):
TTTATAAT
Found at i:11922271 original size:29 final size:29
Alignment explanation
Indices: 11922181--11922276 Score: 87
Period size: 28 Copynumber: 3.4 Consensus size: 29
11922171 TTATTAATTT
* *
11922181 ATAA-TTTT-ATAAT-TATTATAATTTTAT
1 ATAATTTTTAATAATAT-TTATAAGTTTAC
**
11922208 AT-ATTTTTAATAATATTTATAAGTTTTT
1 ATAATTTTTAATAATATTTATAAGTTTAC
*
11922236 ATTATTTTTAATAA-ATTTATAAGTTTAC
1 ATAATTTTTAATAATATTTATAAGTTTAC
11922264 ATCAA-TTTTAATA
1 AT-AATTTTTAATA
11922277 TTTAATATTT
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
26 1 0.02
27 6 0.10
28 39 0.66
29 13 0.22
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (29 bp):
ATAATTTTTAATAATATTTATAAGTTTAC
Found at i:11930471 original size:2 final size:2
Alignment explanation
Indices: 11930464--11930490 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11930454 TGATGTTATT
11930464 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
11930491 GTTTGTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11931135 original size:31 final size:30
Alignment explanation
Indices: 11931100--11931158 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
11931090 TTAGTAAAAG
*
11931100 TAAAATTGT-ACTTTGATCTTCTTAAAAATGA
1 TAAAATTGTGA-TTTAATCTT-TTAAAAATGA
*
11931131 TAAAATTTTGATTTAATCTTTTAAAAAT
1 TAAAATTGTGATTTAATCTTTTAAAAAT
11931159 TACACTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 8 0.32
31 16 0.64
32 1 0.04
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.46
Consensus pattern (30 bp):
TAAAATTGTGATTTAATCTTTTAAAAATGA
Found at i:11931294 original size:3 final size:3
Alignment explanation
Indices: 11931286--11931328 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
11931276 TGCAACACAA
11931286 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
11931329 TGAGCACATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:11941984 original size:20 final size:22
Alignment explanation
Indices: 11941948--11941987 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
11941938 TTAATCTTTT
11941948 ATTTTTATAATAAAAATTATTA
1 ATTTTTATAATAAAAATTATTA
11941970 ATTTTT-TAA-AAAAATTAT
1 ATTTTTATAATAAAAATTAT
11941988 AAAAAATACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 3 0.17
22 6 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTTTTATAATAAAAATTATTA
Found at i:11941993 original size:10 final size:10
Alignment explanation
Indices: 11941978--11942104 Score: 85
Period size: 10 Copynumber: 13.5 Consensus size: 10
11941968 TAATTTTTTA
11941978 AAAAAATTAT
1 AAAAAATTAT
11941988 AAAAAA-TACT
1 AAAAAATTA-T
*
11941998 AAACAATTAT
1 AAAAAATTAT
*
11942008 ---AAACT-T
1 AAAAAATTAT
11942014 -AAAAATTAT
1 AAAAAATTAT
*
11942023 AAAAACTT-T
1 AAAAAATTAT
11942032 AAAAAATTCAT
1 AAAAAATT-AT
11942043 AAAAAATTAT
1 AAAAAATTAT
*
11942053 -AAATATTAT
1 AAAAAATTAT
* *
11942062 AAAATATAAT
1 AAAAAATTAT
11942072 -AAAAA-TAT
1 AAAAAATTAT
*
11942080 AATAAATTAT
1 AAAAAATTAT
* *
11942090 AAAAGACTAT
1 AAAAAATTAT
11942100 AAAAA
1 AAAAA
11942105 TAATAAATAT
Statistics
Matches: 91, Mismatches: 15, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
6 1 0.01
7 3 0.03
8 6 0.07
9 27 0.30
10 43 0.47
11 11 0.12
ACGTcount: A:0.65, C:0.05, G:0.01, T:0.29
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:11942045 original size:35 final size:35
Alignment explanation
Indices: 11941979--11942104 Score: 92
Period size: 38 Copynumber: 3.4 Consensus size: 35
11941969 AATTTTTTAA
*
11941979 AAAAATTATAAAAAATACTAAACAATTATAAACTT
1 AAAAATTATAAAAAATACTAAAAAATTATAAACTT
* * *
11942014 AAAAATTATAAAAACT-TTAAAAAATTCATAAAAAATT
1 AAAAATTATAAAAAATACTAAAAAATT-AT--AAACTT
* * * *
11942051 ATAAATATTATAAAATATAATAAAAATATAATAAATTAT
1 A-AAA-ATTATAAAAAATACTAAAAA-ATTATAAACT-T
*
11942090 AAAAGACTATAAAAA
1 AAAA-ATTATAAAAA
11942105 TAATAAATAT
Statistics
Matches: 71, Mismatches: 12, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
34 8 0.11
35 17 0.24
37 6 0.08
38 18 0.25
39 12 0.17
40 8 0.11
41 2 0.03
ACGTcount: A:0.65, C:0.05, G:0.01, T:0.29
Consensus pattern (35 bp):
AAAAATTATAAAAAATACTAAAAAATTATAAACTT
Found at i:11942066 original size:28 final size:27
Alignment explanation
Indices: 11941980--11942093 Score: 85
Period size: 28 Copynumber: 4.1 Consensus size: 27
11941970 ATTTTTTAAA
*
11941980 AAAATTATAAAAAA-TACTAAACAATTAT
1 AAAATCATAAAAAATTA-TAAA-AATTAT
* *
11942008 -AAA-C-TTAAAAATTATAAAAACTTTAA
1 AAAATCATAAAAAATTATAAAAA--TTAT
*
11942034 AAAATTCATAAAAAATTATAAATATTAT
1 AAAA-TCATAAAAAATTATAAAAATTAT
*
11942062 AAAAT-ATAATAAAAATATAATAAATTAT
1 AAAATCATAA-AAAATTATAA-AAATTAT
11942090 AAAA
1 AAAA
11942094 GACTATAAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
24 2 0.03
25 10 0.14
26 9 0.13
27 16 0.23
28 17 0.25
29 1 0.01
30 14 0.20
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (27 bp):
AAAATCATAAAAAATTATAAAAATTAT
Found at i:11942078 original size:11 final size:11
Alignment explanation
Indices: 11942053--11942085 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
11942043 AAAAAATTAT
*
11942053 AAATATTAT-A
1 AAATATAATAA
11942063 AAATATAATAA
1 AAATATAATAA
11942074 AAATATAATAA
1 AAATATAATAA
11942085 A
1 A
11942086 TTATAAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AAATATAATAA
Found at i:11942101 original size:28 final size:26
Alignment explanation
Indices: 11942057--11942120 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 26
11942047 AATTATAAAT
*
11942057 ATTATAAAATATAATAAAAATATAATAA
1 ATTATAAAAGATAAT-AAAA-ATAATAA
11942085 ATTATAAAAGACT-ATAAAAATAATAA
1 ATTATAAAAGA-TAATAAAAATAATAA
11942111 ATATATAAAA
1 AT-TATAAAA
11942121 AGAGATATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
26 9 0.27
27 11 0.33
28 12 0.36
29 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (26 bp):
ATTATAAAAGATAATAAAAATAATAA
Found at i:11942108 original size:37 final size:37
Alignment explanation
Indices: 11942041--11942121 Score: 110
Period size: 37 Copynumber: 2.2 Consensus size: 37
11942031 TAAAAAATTC
* *
11942041 ATAAAAAATTATAAATATTATAAAATATAATAAAAAT
1 ATAAAAAATTATAAAGACTATAAAATATAATAAAAAT
* *
11942078 ATAATAAATTATAAAAGACTATAAAA-ATAATAAATAT
1 ATAAAAAATTAT-AAAGACTATAAAATATAATAAAAAT
11942115 ATAAAAA
1 ATAAAAA
11942122 GAGATATTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
37 27 0.71
38 11 0.29
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (37 bp):
ATAAAAAATTATAAAGACTATAAAATATAATAAAAAT
Found at i:11942121 original size:28 final size:27
Alignment explanation
Indices: 11942041--11942123 Score: 89
Period size: 26 Copynumber: 3.0 Consensus size: 27
11942031 TAAAAAATTC
* *
11942041 ATAAAAAATTATAAATATTATAAAATATA
1 ATAAAAAATAATAAATA-TATAAAA-AGA
11942070 ATAAAAATATAATAAAT-TAT-AAAAGA
1 ATAAAAA-ATAATAAATATATAAAAAGA
*
11942096 CTATAAAAATAATAAATATATAAAAAGA
1 ATA-AAAAATAATAAATATATAAAAAGA
11942124 GATATTTAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
26 13 0.28
27 10 0.21
28 9 0.19
29 7 0.15
30 8 0.17
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.29
Consensus pattern (27 bp):
ATAAAAAATAATAAATATATAAAAAGA
Found at i:11942222 original size:2 final size:2
Alignment explanation
Indices: 11942215--11942260 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
11942205 AAGATATGGA
11942215 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11942257 AT AT
1 AT AT
11942261 TATTAGTTCC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11942518 original size:10 final size:9
Alignment explanation
Indices: 11942503--11942580 Score: 57
Period size: 10 Copynumber: 7.9 Consensus size: 9
11942493 ATTTATTAAG
11942503 TTTTTATGAA
1 TTTTTAT-AA
11942513 TTTTTATAA
1 TTTTTATAA
*
11942522 GTTTATATAAA
1 -TTTTTAT-AA
*
11942533 TTTTTAATATT
1 TTTTT-ATA-A
11942544 TTTTTATAA
1 TTTTTATAA
*
11942553 TTTATTAGAA
1 TTT-TTATAA
*
11942563 TTTCTATAA
1 TTTTTATAA
11942572 GTTTTTATA
1 -TTTTTATA
11942581 TTAGTTATAT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
9 9 0.17
10 36 0.67
11 9 0.17
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:11942554 original size:20 final size:20
Alignment explanation
Indices: 11942490--11942580 Score: 71
Period size: 20 Copynumber: 4.6 Consensus size: 20
11942480 TTATAAAATT
*
11942490 TAAATTTAT-TAAGTTTTTA
1 TAAATTTTTATAAGTTTTTA
* *
11942509 TGAATTTTTATAAGTTTATA
1 TAAATTTTTATAAGTTTTTA
**
11942529 TAAATTTTTAATATTTTTTTA
1 TAAATTTTT-ATAAGTTTTTA
* *
11942550 T-AATTTATTAGAA-TTTCTA
1 TAAATTT-TTATAAGTTTTTA
*
11942569 TAAGTTTTTATA
1 TAAATTTTTATA
11942581 TTAGTTATAT
Statistics
Matches: 56, Mismatches: 12, Indels: 8
0.74 0.16 0.11
Matches are distributed among these distances:
19 17 0.30
20 28 0.50
21 11 0.20
ACGTcount: A:0.35, C:0.01, G:0.05, T:0.58
Consensus pattern (20 bp):
TAAATTTTTATAAGTTTTTA
Found at i:11942577 original size:30 final size:31
Alignment explanation
Indices: 11942513--11942590 Score: 74
Period size: 30 Copynumber: 2.5 Consensus size: 31
11942503 TTTTTATGAA
* *
11942513 TTTTTATAAGTTTATATAAATTTTTAATATT
1 TTTTTATAAGTTTATATAAATTTCTAATAGT
11942544 TTTTTATAA-TTTAT-TAGAATTTCT-ATAAGT
1 TTTTTATAAGTTTATATA-AATTTCTAAT-AGT
*
11942574 TTTTATATTAG-TTATAT
1 TTTT-TATAAGTTTATAT
11942591 GTTTTCTACA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
29 4 0.10
30 17 0.44
31 17 0.44
32 1 0.03
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.60
Consensus pattern (31 bp):
TTTTTATAAGTTTATATAAATTTCTAATAGT
Found at i:11944264 original size:29 final size:29
Alignment explanation
Indices: 11944192--11944277 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 29
11944182 GTACCTGAAT
* *
11944192 TTGACATTTTTTTAATTTGGTAC-CTAA-
1 TTGACTTTTTTTTAATTTGGTACTCAAAC
*
11944219 TT---TTTTTGTTCAATTTGGTACTCAAAC
1 TTGACTTTTT-TTTAATTTGGTACTCAAAC
11944246 TTGACTTTTTTTTAATTTGGTACT-AAAC
1 TTGACTTTTTTTTAATTTGGTACTCAAAC
11944274 TTGA
1 TTGA
11944278 TACTTTTCCT
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
24 4 0.08
25 12 0.24
26 3 0.06
27 4 0.08
28 8 0.16
29 13 0.27
30 5 0.10
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.52
Consensus pattern (29 bp):
TTGACTTTTTTTTAATTTGGTACTCAAAC
Found at i:11944290 original size:29 final size:28
Alignment explanation
Indices: 11944230--11944305 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 28
11944220 TTTTTTGTTC
**
11944230 AATTTGGTACTCAAACTTGACTTTTTTTT
1 AATTTGGTACT-AAACTTGACTTTTTCCT
11944259 AATTTGGTACTAAACTTGA-TACTTTTCCT
1 AATTTGGTACTAAACTTGACT--TTTTCCT
*
11944288 AATTTGATACCTAAACTT
1 AATTTGGTA-CTAAACTT
11944306 TTTTTTGACC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 1 0.02
28 8 0.20
29 24 0.59
30 8 0.20
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.46
Consensus pattern (28 bp):
AATTTGGTACTAAACTTGACTTTTTCCT
Found at i:11944697 original size:58 final size:57
Alignment explanation
Indices: 11944513--11944697 Score: 149
Period size: 58 Copynumber: 3.1 Consensus size: 57
11944503 TAAATTTAAG
* * * * ** * *
11944513 TACCAAATTGAATCTAAAAAAAGCTTAGGTACCAAATTAAGAAAAATGCCAAGTTCAGG
1 TACCAAATTGAGTC-AAAAAAA-TTTAGGTATCAAATTAAAAAAAATATCAAATTCAGA
* * * *
11944572 TACCAAATTG-GATAACAAAAAAGTTTAGGTATTAAATTAGGAAAAAATATCAAATACATG-
1 TACCAAATTGAG-T--CAAAAAAATTTAGGTATCAAATTA-AAAAAAATATCAAATTCA-GA
* * *
11944632 TATCAAATTGAGTCAAAAAAATTTAAGTATCAAATTAATAAAAAATATCAAATTTAGA
1 TACCAAATTGAGTCAAAAAAATTTAGGTATCAAATTAA-AAAAAATATCAAATTCAGA
11944690 TACCAAAT
1 TACCAAAT
11944698 ATTATATTAA
Statistics
Matches: 99, Mismatches: 19, Indels: 17
0.73 0.14 0.13
Matches are distributed among these distances:
57 1 0.01
58 43 0.43
59 24 0.24
60 28 0.28
61 3 0.03
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.26
Consensus pattern (57 bp):
TACCAAATTGAGTCAAAAAAATTTAGGTATCAAATTAAAAAAAATATCAAATTCAGA
Found at i:11945240 original size:80 final size:82
Alignment explanation
Indices: 11945152--11945319 Score: 259
Period size: 81 Copynumber: 2.1 Consensus size: 82
11945142 TTTGGCTCAT
* * ** *
11945152 CTAAAAATGATAAAACTTTGATTTATTCCTTT-AAAATTGTATTTTTACTATCATAAAAATTACA
1 CTAAAAATGATAAAACTTTAATTTAATCCTTTAAAAATTACATTGTTACTATCATAAAAATTACA
11945216 ATTTAACTTCGAT-CCC
66 ATTTAACTTCGATCCCC
*
11945232 CTAAAAATGATAAAATTTTAATTTAATCCTTTAAAAATTACATTGTTACTATCATAAAAATTACA
1 CTAAAAATGATAAAACTTTAATTTAATCCTTTAAAAATTACATTGTTACTATCATAAAAATTACA
*
11945297 ATTTAACTTCGTTCCCC
66 ATTTAACTTCGATCCCC
11945314 CTAAAA
1 CTAAAA
11945320 TTTTTTTTTG
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
80 29 0.37
81 41 0.52
82 9 0.11
ACGTcount: A:0.41, C:0.15, G:0.04, T:0.39
Consensus pattern (82 bp):
CTAAAAATGATAAAACTTTAATTTAATCCTTTAAAAATTACATTGTTACTATCATAAAAATTACA
ATTTAACTTCGATCCCC
Found at i:11946105 original size:21 final size:21
Alignment explanation
Indices: 11946080--11946119 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
11946070 TTTAAAATAG
11946080 TGAAAATAA-TTCAAAATTTCT
1 TGAAAA-AAGTTCAAAATTTCT
*
11946101 TGAAAAAAGTTTAAAATTT
1 TGAAAAAAGTTCAAAATTT
11946120 TAAAATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (21 bp):
TGAAAAAAGTTCAAAATTTCT
Found at i:11949788 original size:54 final size:54
Alignment explanation
Indices: 11949730--11949844 Score: 142
Period size: 54 Copynumber: 2.1 Consensus size: 54
11949720 AGCTGTGTAC
* * *
11949730 AGAGTATTAG-TAATTCGGGCCAGAAATAGAGTATTGCTCATTCAAGCCAAAATT
1 AGAGTATT-GCTAATTCGAGCCAGAAACAGAGTATTGCTCATTCAAGCCAAAAAT
** * * *
11949784 AGAGTATTGCTCTTTCGAGCTAGAAACAGAGTATTGCTCTTTCGAGCCAAAAAT
1 AGAGTATTGCTAATTCGAGCCAGAAACAGAGTATTGCTCATTCAAGCCAAAAAT
11949838 AGAGTAT
1 AGAGTAT
11949845 CGCTCTTTGC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
53 1 0.02
54 51 0.98
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.29
Consensus pattern (54 bp):
AGAGTATTGCTAATTCGAGCCAGAAACAGAGTATTGCTCATTCAAGCCAAAAAT
Found at i:11949850 original size:27 final size:27
Alignment explanation
Indices: 11949743--11949852 Score: 139
Period size: 27 Copynumber: 4.1 Consensus size: 27
11949733 GTATTAGTAA
* * *
11949743 TTCGGGCCAGAAATAGAGTATTGCTCA
1 TTCGAGCCAAAAATAGAGTATTGCTCT
* *
11949770 TTCAAGCCAAAATTAGAGTATTGCTCT
1 TTCGAGCCAAAAATAGAGTATTGCTCT
* * *
11949797 TTCGAGCTAGAAACAGAGTATTGCTCT
1 TTCGAGCCAAAAATAGAGTATTGCTCT
*
11949824 TTCGAGCCAAAAATAGAGTATCGCTCT
1 TTCGAGCCAAAAATAGAGTATTGCTCT
11949851 TT
1 TT
11949853 GCTCAAACTT
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 69 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (27 bp):
TTCGAGCCAAAAATAGAGTATTGCTCT
Found at i:11979374 original size:12 final size:12
Alignment explanation
Indices: 11979342--11979374 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
11979332 TTTCGAAGGT
*
11979342 ACACACGGCCTG
1 ACACACGGGCTG
11979354 ACACACGGGCTG
1 ACACACGGGCTG
11979366 ACACACGGG
1 ACACACGGG
11979375 TGTGTGCCCT
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:0.27, C:0.36, G:0.30, T:0.06
Consensus pattern (12 bp):
ACACACGGGCTG
Found at i:11985216 original size:12 final size:12
Alignment explanation
Indices: 11985199--11985223 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11985189 AAAAACTGGG
11985199 TAACTAGAATCA
1 TAACTAGAATCA
11985211 TAACTAGAATCA
1 TAACTAGAATCA
11985223 T
1 T
11985224 TGTCTAAAAA
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:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (12 bp):
TAACTAGAATCA
Found at i:11987280 original size:41 final size:42
Alignment explanation
Indices: 11987205--11987437 Score: 150
Period size: 41 Copynumber: 5.5 Consensus size: 42
11987195 CTTGATGCAT
* * *
11987205 ATTAAAGGAAGACTCATGTCTCGGGATAAACATGAGAATAT-
1 ATTAAAGGAAGACTCATGTCTCGAGATGAGCATGAGAATATA
*
11987246 ATTAAAGGAAGACTCATGTCTCAAGATGAGCATGAGATTATATA
1 ATTAAAGGAAGACTCATGTCTCGAGATGAGCATGAGA--ATATA
** ** * * * *
11987290 AAAAAAGGAAGACTGTTGACTCGAGAGGAGCATGAGATTATG
1 ATTAAAGGAAGACTCATGTCTCGAGATGAGCATGAGAATATA
* * ** *
11987332 ATT-AAGGAAGACTCATGACTCG-GAAAGAG-ATGAGGTTATGT
1 ATTAAAGGAAGACTCATGTCTCGAG-ATGAGCATGAGAATAT-A
* * * * * * **
11987373 TTTAAAGGACGACTCGTGACTCGAAATGAGCATGAGATTCCA
1 ATTAAAGGAAGACTCATGTCTCGAGATGAGCATGAGAATATA
* * *
11987415 TTTAAAGGAAGACTTATGACTCG
1 ATTAAAGGAAGACTCATGTCTCG
11987438 GTTGATTACG
Statistics
Matches: 152, Mismatches: 32, Indels: 15
0.76 0.16 0.08
Matches are distributed among these distances:
40 10 0.07
41 56 0.37
42 45 0.30
43 11 0.07
44 30 0.20
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.24
Consensus pattern (42 bp):
ATTAAAGGAAGACTCATGTCTCGAGATGAGCATGAGAATATA
Found at i:11988071 original size:20 final size:21
Alignment explanation
Indices: 11988032--11988084 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
11988022 TGGAGTTTTA
11988032 GTATCGATAGAAGCATGACTT
1 GTATCGATAGAAGCATGACTT
* *
11988053 GTATCGGTA-AAGTATGACTT
1 GTATCGATAGAAGCATGACTT
*
11988073 GTATCGCTAGAA
1 GTATCGATAGAA
11988085 CTATCACAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (21 bp):
GTATCGATAGAAGCATGACTT
Found at i:11994566 original size:21 final size:21
Alignment explanation
Indices: 11994542--11994581 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11994532 TGTTTAGGTG
*
11994542 TTGTTTTGGTATTGTTTTTTA
1 TTGTTTTGGTATTCTTTTTTA
*
11994563 TTGTTTTGGTGTTCTTTTT
1 TTGTTTTGGTATTCTTTTT
11994582 ACTGTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.05, C:0.03, G:0.20, T:0.72
Consensus pattern (21 bp):
TTGTTTTGGTATTCTTTTTTA
Found at i:11994568 original size:32 final size:33
Alignment explanation
Indices: 11994507--11994580 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 33
11994497 AAATTTATAT
*
11994507 TGTTGTTTTGGTTCTATTTTTTTACTGTTTAGG
1 TGTTGTTTTGGTTCTAGTTTTTTACTGTTTAGG
* *
11994540 TGTTGTTTTGGTAT-T-GTTTTTTATTGTTTTGG
1 TGTTGTTTTGGT-TCTAGTTTTTTACTGTTTAGG
*
11994572 TGTTCTTTT
1 TGTTGTTTT
11994581 TACTGTTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 22 0.61
33 13 0.36
34 1 0.03
ACGTcount: A:0.07, C:0.04, G:0.22, T:0.68
Consensus pattern (33 bp):
TGTTGTTTTGGTTCTAGTTTTTTACTGTTTAGG
Found at i:11994582 original size:20 final size:21
Alignment explanation
Indices: 11994542--11994587 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
11994532 TGTTTAGGTG
*
11994542 TTGTTTTGGTATTGTTTTTTA
1 TTGTTTTGGTATTGCTTTTTA
*
11994563 TTGTTTTGGTGTT-CTTTTTA
1 TTGTTTTGGTATTGCTTTTTA
*
11994583 CTGTT
1 TTGTT
11994588 ATTTTTGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.07, C:0.04, G:0.20, T:0.70
Consensus pattern (21 bp):
TTGTTTTGGTATTGCTTTTTA
Found at i:11994604 original size:23 final size:23
Alignment explanation
Indices: 11994578--11994692 Score: 115
Period size: 23 Copynumber: 5.0 Consensus size: 23
11994568 TTGGTGTTCT
11994578 TTTTACTGTTATTTTTGTTGTTG
1 TTTTACTGTTATTTTTGTTGTTG
* ** *
11994601 TTTTACTGCTACATTTGTTGCTG
1 TTTTACTGTTATTTTTGTTGTTG
* *
11994624 TTTTAGTTGTTA-TTTTGTTATTG
1 TTTTA-CTGTTATTTTTGTTGTTG
* * *
11994647 TTTTACTGCTATATTTGTTGCTG
1 TTTTACTGTTATTTTTGTTGTTG
*
11994670 TTTTAGTTGTTATTTTTGTTGTT
1 TTTTA-CTGTTATTTTTGTTGTT
11994693 TTGATGTTAT
Statistics
Matches: 71, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
22 4 0.06
23 50 0.70
24 17 0.24
ACGTcount: A:0.11, C:0.07, G:0.17, T:0.64
Consensus pattern (23 bp):
TTTTACTGTTATTTTTGTTGTTG
Found at i:11994640 original size:46 final size:47
Alignment explanation
Indices: 11994584--11994692 Score: 193
Period size: 46 Copynumber: 2.3 Consensus size: 47
11994574 TTCTTTTTAC
11994584 TGTTATTTTTGTTGTTGTTTTACTGCTACATTTGTTGCTGTTTTAGT
1 TGTTATTTTTGTTGTTGTTTTACTGCTACATTTGTTGCTGTTTTAGT
* *
11994631 TGTTA-TTTTGTTATTGTTTTACTGCTATATTTGTTGCTGTTTTAGT
1 TGTTATTTTTGTTGTTGTTTTACTGCTACATTTGTTGCTGTTTTAGT
11994677 TGTTATTTTTGTTGTT
1 TGTTATTTTTGTTGTT
11994693 TTGATGTTAT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
46 44 0.76
47 14 0.24
ACGTcount: A:0.11, C:0.06, G:0.18, T:0.64
Consensus pattern (47 bp):
TGTTATTTTTGTTGTTGTTTTACTGCTACATTTGTTGCTGTTTTAGT
Found at i:11994702 original size:20 final size:21
Alignment explanation
Indices: 11994613--11994706 Score: 66
Period size: 23 Copynumber: 4.3 Consensus size: 21
11994603 TTACTGCTAC
*
11994613 ATTTGTTGCTGTTTTAGTTGTT
1 ATTT-TTGCTGTTTTAGATGTT
** *
11994635 ATTTTGTTATTGTTTTA-CTGCTAT
1 A-TTT-TTGCTGTTTTAGATG-T-T
*
11994659 ATTTGTTGCTGTTTTAGTTGTT
1 ATTT-TTGCTGTTTTAGATGTT
*
11994681 ATTTTTGTTGTTTT-GATGTT
1 ATTTTTGCTGTTTTAGATGTT
11994701 ATTTTT
1 ATTTTT
11994707 TTTATGCGTT
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
20 11 0.18
21 9 0.15
22 8 0.13
23 28 0.47
24 4 0.07
ACGTcount: A:0.12, C:0.04, G:0.18, T:0.66
Consensus pattern (21 bp):
ATTTTTGCTGTTTTAGATGTT
Found at i:12003160 original size:29 final size:29
Alignment explanation
Indices: 12003115--12003172 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
12003105 ATCAACATGC
* *
12003115 GATATCACAACACAGAATAAAATCACACA
1 GATAACACAACAAAGAATAAAATCACACA
* *
12003144 GATAACACAACAAAGAATAATATTACACA
1 GATAACACAACAAAGAATAAAATCACACA
12003173 AGGTGTGGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.57, C:0.21, G:0.07, T:0.16
Consensus pattern (29 bp):
GATAACACAACAAAGAATAAAATCACACA
Found at i:12004798 original size:22 final size:22
Alignment explanation
Indices: 12004773--12004815 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
12004763 TCTCGTTAAA
*
12004773 ATTGGATTGATTTTTGGAAAAG
1 ATTGGATTGAATTTTGGAAAAG
12004795 ATTGGATTGAATTTTGGAAAA
1 ATTGGATTGAATTTTGGAAAA
12004816 AAATCGTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.40
Consensus pattern (22 bp):
ATTGGATTGAATTTTGGAAAAG
Found at i:12005686 original size:22 final size:21
Alignment explanation
Indices: 12005654--12005713 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
12005644 TTAATTTGAA
12005654 TATATAATTTAAAATATAGATAT
1 TATA-AATTTAAAATATA-ATAT
*
12005677 TATAAATTTAAATATATAATTT
1 TATAAATTTAAA-ATATAATAT
* *
12005699 TATATATTTGAAATA
1 TATAAATTTAAAATA
12005714 AATTTTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 3 0.09
22 21 0.64
23 9 0.27
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (21 bp):
TATAAATTTAAAATATAATAT
Found at i:12011373 original size:18 final size:18
Alignment explanation
Indices: 12011347--12011381 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12011337 AATGTATTCT
* *
12011347 AAATTACATAATTTAAAA
1 AAATAACATAATATAAAA
12011365 AAATAACATAATATAAA
1 AAATAACATAATATAAA
12011382 GTATTATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATAACATAATATAAAA
Found at i:12020437 original size:10 final size:10
Alignment explanation
Indices: 12020422--12020447 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
12020412 CAAAAAGGAA
12020422 AAAATTATTT
1 AAAATTATTT
12020432 AAAATTATTT
1 AAAATTATTT
12020442 AAAATT
1 AAAATT
12020448 TGTAATGCTT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
AAAATTATTT
Found at i:12029226 original size:17 final size:18
Alignment explanation
Indices: 12029206--12029242 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
12029196 TTGTTTCTAC
*
12029206 TTTTT-TATTT-TTTCTT
1 TTTTTCTATTTCTGTCTT
12029222 TTTTTCTATTTCTGTCTT
1 TTTTTCTATTTCTGTCTT
12029240 TTT
1 TTT
12029243 GGCTAAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 5 0.28
17 5 0.28
18 8 0.44
ACGTcount: A:0.05, C:0.11, G:0.03, T:0.81
Consensus pattern (18 bp):
TTTTTCTATTTCTGTCTT
Found at i:12035643 original size:12 final size:12
Alignment explanation
Indices: 12035628--12035666 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
12035618 TTTAAAGCAT
12035628 AAAATAAAAGAA
1 AAAATAAAAGAA
* *
12035640 AAAATAAAATAG
1 AAAATAAAAGAA
12035652 AAAATAAAAGCAA
1 AAAATAAAAG-AA
12035665 AA
1 AA
12035667 GTTGAGATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 19 0.86
13 3 0.14
ACGTcount: A:0.79, C:0.03, G:0.08, T:0.10
Consensus pattern (12 bp):
AAAATAAAAGAA
Found at i:12042359 original size:52 final size:52
Alignment explanation
Indices: 12042289--12042523 Score: 303
Period size: 52 Copynumber: 4.5 Consensus size: 52
12042279 AGGTTTGATG
*
12042289 ACTAAGTGTCATCGTGAGTATATGAATCCTTTAAGGATTAAGAGGTCCGATA
1 ACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAGAGGTCCGATA
* * *
12042341 ACTAAGTGTCATCATGAGTATATGAATCCTTTACGGATTAAGAGATCCGATG
1 ACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAGAGGTCCGATA
* * *
12042393 ACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTGAGAGGTTCGATC
1 ACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAGAGGTCCGATA
** * * *
12042445 ACTCTGTGTCATCGTGAGTATATGAATCCCTTGCGGATTATA-AGGTCC-AGTG
1 ACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTA-AGAGGTCCGA-TA
* * *
12042497 GCTATGTGTCATTGTGAGTATATGAAT
1 ACTAAGTGTCATCGTGAGTATATGAAT
12042524 AAAGTGAAAT
Statistics
Matches: 162, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
51 1 0.01
52 160 0.99
53 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.33
Consensus pattern (52 bp):
ACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAGAGGTCCGATA
Found at i:12043502 original size:14 final size:15
Alignment explanation
Indices: 12043476--12043505 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
12043466 TATAATATAA
12043476 TGATAAGATGAACAG
1 TGATAAGATGAACAG
12043491 TGATAA-ATGAACAG
1 TGATAAGATGAACAG
12043505 T
1 T
12043506 AAAACACCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.47, C:0.07, G:0.23, T:0.23
Consensus pattern (15 bp):
TGATAAGATGAACAG
Found at i:12044238 original size:19 final size:19
Alignment explanation
Indices: 12044214--12044250 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12044204 TCATTTTCGC
*
12044214 TTTGTTTATTTAATTTTAT
1 TTTGTTTATTTAAGTTTAT
*
12044233 TTTGTTTCTTTAAGTTTA
1 TTTGTTTATTTAAGTTTA
12044251 ATATTTTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.19, C:0.03, G:0.08, T:0.70
Consensus pattern (19 bp):
TTTGTTTATTTAAGTTTAT
Found at i:12044477 original size:6 final size:6
Alignment explanation
Indices: 12044466--12044494 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
12044456 CCTTTCTTAA
12044466 TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
12044495 TATCATGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
TTTTTG
Found at i:12047223 original size:44 final size:44
Alignment explanation
Indices: 12047160--12047247 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
12047150 TTTTTGAAAG
12047160 TAAGTACGCCTTCATGGAGCAATTTGAAGAATGACCTTTGTGGT
1 TAAGTACGCCTTCATGGAGCAATTTGAAGAATGACCTTTGTGGT
*
12047204 TAAGTACGCCTTCATGGAGCAGTTTGAAGAATGACCTTTGTGGT
1 TAAGTACGCCTTCATGGAGCAATTTGAAGAATGACCTTTGTGGT
12047248 AATGATCTGA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (44 bp):
TAAGTACGCCTTCATGGAGCAATTTGAAGAATGACCTTTGTGGT
Found at i:12050732 original size:24 final size:25
Alignment explanation
Indices: 12050684--12050747 Score: 94
Period size: 24 Copynumber: 2.6 Consensus size: 25
12050674 AATTGAATTT
12050684 AAATTAAAATTTTTTCAAATCAAATC
1 AAATTAAAA-TTTTTCAAATCAAATC
*
12050710 AAATTAAAAATTTT-AAATCAAATC
1 AAATTAAAATTTTTCAAATCAAATC
*
12050734 GAATTAAAATTTTT
1 AAATTAAAATTTTT
12050748 TATTATTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
24 22 0.63
25 4 0.11
26 9 0.26
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.39
Consensus pattern (25 bp):
AAATTAAAATTTTTCAAATCAAATC
Found at i:12055474 original size:6 final size:6
Alignment explanation
Indices: 12055437--12055513 Score: 62
Period size: 6 Copynumber: 14.0 Consensus size: 6
12055427 AGCTTTTGAT
* *
12055437 TTTAAA -TTAAT TTTAAA TTT-TA TTTAAA TTTAAA TTT--A TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
12055481 TTT--A TCTTCAA TTTAAA TTT-AA -TTAAA TTTAAA
1 TTTAAA T-TTAAA TTTAAA TTTAAA TTTAAA TTTAAA
12055514 AGGATATTAA
Statistics
Matches: 57, Mismatches: 5, Indels: 18
0.71 0.06 0.22
Matches are distributed among these distances:
4 8 0.14
5 14 0.25
6 33 0.58
7 2 0.04
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:12055476 original size:16 final size:17
Alignment explanation
Indices: 12055443--12055484 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
12055433 TGATTTTAAA
*
12055443 TTAATTTTAAATTTTAT
1 TTAAATTTAAATTTTAT
12055460 TTAAATTTAAA-TTTAT
1 TTAAATTTAAATTTTAT
12055476 TTAAATTTA
1 TTAAATTTA
12055485 TCTTCAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTAAATTTAAATTTTAT
Found at i:12055493 original size:27 final size:26
Alignment explanation
Indices: 12055437--12055511 Score: 96
Period size: 27 Copynumber: 2.8 Consensus size: 26
12055427 AGCTTTTGAT
*
12055437 TTTAAATTAATTTTAAATTTTATTTAAA
1 TTTAAATTTA-TTTAAA-TTTATTTAAA
*
12055465 TTTAAATTTATTTAAATTTATCTTCAA
1 TTTAAATTTATTTAAATTTAT-TTAAA
*
12055492 TTTAAATTTAATTAAATTTA
1 TTTAAATTTATTTAAATTTA
12055512 AAAGGATATT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 5 0.12
27 29 0.67
28 9 0.21
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (26 bp):
TTTAAATTTATTTAAATTTATTTAAA
Found at i:12055504 original size:11 final size:11
Alignment explanation
Indices: 12055437--12055512 Score: 61
Period size: 11 Copynumber: 7.0 Consensus size: 11
12055427 AGCTTTTGAT
12055437 TTTAAA-TTAA
1 TTTAAATTTAA
*
12055447 TTTTAAATTTTA
1 -TTTAAATTTAA
12055459 TTTAAATTTAAA
1 TTTAAATTT-AA
12055471 TTT--ATTTAAA
1 TTTAAATTT-AA
** *
12055481 TTTATCTTCAA
1 TTTAAATTTAA
12055492 TTTAAATTTAA
1 TTTAAATTTAA
12055503 -TTAAATTTAA
1 TTTAAATTTAA
12055513 AAGGATATTA
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
10 20 0.37
11 25 0.46
12 9 0.17
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:12055511 original size:16 final size:15
Alignment explanation
Indices: 12055458--12055513 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
12055448 TTTAAATTTT
*
12055458 ATTTAAATTTAAATTT
1 ATTTAAATTT-AATTA
*
12055474 ATTTAAATTTATCTTCA
1 ATTTAAATTTA-ATT-A
12055491 ATTTAAATTTAATTAA
1 ATTTAAATTTAATT-A
12055507 ATTTAAA
1 ATTTAAA
12055514 AGGATATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
15 1 0.03
16 22 0.65
17 11 0.32
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTTAAATTTAATTA
Found at i:12056232 original size:15 final size:15
Alignment explanation
Indices: 12056212--12056241 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12056202 ATAATTTCAT
12056212 AAATATCATTAATAA
1 AAATATCATTAATAA
*
12056227 AAATATTATTAATAA
1 AAATATCATTAATAA
12056242 TCATAATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATATCATTAATAA
Found at i:12056242 original size:3 final size:3
Alignment explanation
Indices: 12056221--12056304 Score: 51
Period size: 3 Copynumber: 26.7 Consensus size: 3
12056211 TAAATATCAT
* * * * *
12056221 TAA TAA AAA TAT TAT TAA TAA TCA TAA TAA TTAA TAA TAG TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA T-AA
* * * *
12056268 TAT TTA TAA TTA TAA TTAA TAT TAA TAA TTAA TAA TA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA -TAA TAA TA
12056305 TCAACCATTA
Statistics
Matches: 61, Mismatches: 16, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
3 49 0.80
4 12 0.20
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:12056255 original size:16 final size:15
Alignment explanation
Indices: 12056234--12056305 Score: 67
Period size: 16 Copynumber: 4.7 Consensus size: 15
12056224 TAAAAATATT
12056234 ATTAATAATCATAATA
1 ATTAATAAT-ATAATA
12056250 ATTAATAATAGTAATA
1 ATTAATAATA-TAATA
* * * *
12056266 AATATTTATAATTATA
1 ATTAATAAT-ATAATA
12056282 ATTAAT-AT-TAATA
1 ATTAATAATATAATA
12056295 ATTAATAATAT
1 ATTAATAATAT
12056306 CAACCATTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
13 10 0.22
14 2 0.04
15 4 0.09
16 28 0.62
17 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (15 bp):
ATTAATAATATAATA
Found at i:12056266 original size:19 final size:18
Alignment explanation
Indices: 12056244--12056304 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 18
12056234 ATTAATAATC
12056244 ATAATAATTAATAATAGTA
1 ATAATAATTAATAATA-TA
*
12056263 ATAA-ATATTTATAATTATA
1 ATAATA-ATTAATAA-TATA
12056282 ATTAAT-ATTAATAAT-TA
1 A-TAATAATTAATAATATA
12056299 ATAATA
1 ATAATA
12056305 TCAACCATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
16 4 0.11
17 3 0.09
18 2 0.06
19 21 0.60
20 5 0.14
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
ATAATAATTAATAATATA
Found at i:12056384 original size:22 final size:22
Alignment explanation
Indices: 12056356--12056406 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
12056346 TTGCTTCCCT
* *
12056356 GTCTCGCACCGCCATCGCCGGA
1 GTCTCGCACCACCACCGCCGGA
12056378 GTCTCGCACCACCACCGCCGGA
1 GTCTCGCACCACCACCGCCGGA
*
12056400 GTTTCGC
1 GTCTCGC
12056407 TCGTACGTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.14, C:0.45, G:0.25, T:0.16
Consensus pattern (22 bp):
GTCTCGCACCACCACCGCCGGA
Found at i:12057406 original size:29 final size:29
Alignment explanation
Indices: 12057374--12057466 Score: 93
Period size: 29 Copynumber: 3.2 Consensus size: 29
12057364 GATTTCACCA
12057374 AAAATTACCATTTTACCCCCAAACTTTCC
1 AAAATTACCATTTTACCCCCAAACTTTCC
* * *
12057403 AAAATT-CCATTTTAACCTC-GA-TTTCACC
1 AAAATTACCATTTTACCCCCAAACTTT--CC
* *
12057431 AAAAATTACCATTTTACCCCCAAACCTTCT
1 -AAAATTACCATTTTACCCCCAAACTTTCC
12057461 AAAATT
1 AAAATT
12057467 CTATTTTTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
26 3 0.06
27 1 0.02
28 13 0.26
29 18 0.36
30 12 0.24
31 1 0.02
32 2 0.04
ACGTcount: A:0.37, C:0.30, G:0.01, T:0.32
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCAAACTTTCC
Found at i:12057444 original size:58 final size:59
Alignment explanation
Indices: 12057312--12057508 Score: 308
Period size: 58 Copynumber: 3.4 Consensus size: 59
12057302 CCCAAATAGT
* * * *
12057312 CCAAAAATTACCATTTTACCCCTAAACTTTTTAGAATTCTATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCTAAAATTCTATTTTTAACCTCGATTTCA
* *
12057371 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCA-TTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCTAAAATTCTATTTTTAACCTCGATTTCA
*
12057429 CCAAAAATTACCATTTTACCCCCAAACCTTCTAAAATTCTATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCTAAAATTCTATTTTTAACCTCGATTTCA
*
12057488 CC-AAAATTACCATTTTGCCCC
1 CCAAAAATTACCATTTTACCCC
12057509 TGGTATCCAA
Statistics
Matches: 127, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
58 72 0.57
59 55 0.43
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCAAACTTTCTAAAATTCTATTTTTAACCTCGATTTCA
Found at i:12059868 original size:24 final size:24
Alignment explanation
Indices: 12059807--12059869 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
12059797 TAGAGTAATA
* *
12059807 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
12059831 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
12059855 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
12059870 GATTATTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.24
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:12061860 original size:24 final size:24
Alignment explanation
Indices: 12061799--12061861 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
12061789 TAGAGTAATA
* * *
12061799 AGAGTTTGACTCAAATAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
12061823 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
12061847 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
12061862 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:12066920 original size:36 final size:36
Alignment explanation
Indices: 12066880--12067045 Score: 136
Period size: 36 Copynumber: 4.4 Consensus size: 36
12066870 AACGATCACT
* *
12066880 TAGCATTACGCTCTAACCGAGACGTAAGCAA-ATTCA
1 TAGCAATACGCTCTAACCGAGACGTATGCAACA-TCA
* * * *
12066916 TAGCAATACACTTTAACCGGGATGTAGACGTACGCAACTTCA
1 TAGCAATACGCTCTAACC-----G-AGACGTATGCAACATCA
* * *
12066958 TAGTAATACGCTCTAACCGAGATGTATGCAACATCT
1 TAGCAATACGCTCTAACCGAGACGTATGCAACATCA
* ** *
12066994 TTGCAATACATTCTTACCGAGACGTATGCAACATCA
1 TAGCAATACGCTCTAACCGAGACGTATGCAACATCA
*
12067030 TAGTAATACGCTCTAA
1 TAGCAATACGCTCTAA
12067046 TCTTTACATC
Statistics
Matches: 99, Mismatches: 24, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
36 68 0.69
37 1 0.01
41 1 0.01
42 29 0.29
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.26
Consensus pattern (36 bp):
TAGCAATACGCTCTAACCGAGACGTATGCAACATCA
Found at i:12066958 original size:42 final size:42
Alignment explanation
Indices: 12066899--12066983 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
12066889 GCTCTAACCG
* *
12066899 AGACGTAAGCAAATTCATAGCAATACACTTTAACCGGGATGT
1 AGACGTAAGCAAATTCATAGCAATACACTCTAACCGAGATGT
* * * *
12066941 AGACGTACGCAACTTCATAGTAATACGCTCTAACCGAGATGT
1 AGACGTAAGCAAATTCATAGCAATACACTCTAACCGAGATGT
12066983 A
1 A
12066984 TGCAACATCT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (42 bp):
AGACGTAAGCAAATTCATAGCAATACACTCTAACCGAGATGT
Found at i:12081822 original size:26 final size:26
Alignment explanation
Indices: 12081793--12081861 Score: 102
Period size: 26 Copynumber: 2.7 Consensus size: 26
12081783 TATCATGTAT
*
12081793 TGCTCACACGAGCTGTGAATTAGGCC
1 TGCTCACACGAGCTGTGAAATAGGCC
* * *
12081819 TGCTTACACAAGCTGTGAAATGGGCC
1 TGCTCACACGAGCTGTGAAATAGGCC
12081845 TGCTCACACGAGCTGTG
1 TGCTCACACGAGCTGTG
12081862 GGTCAAGATG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.23
Consensus pattern (26 bp):
TGCTCACACGAGCTGTGAAATAGGCC
Found at i:12083489 original size:36 final size:36
Alignment explanation
Indices: 12083434--12083689 Score: 183
Period size: 36 Copynumber: 7.3 Consensus size: 36
12083424 ATGCTTTAAC
* * * *
12083434 CGAGACATAAGCAAATTCATAGAAATATGCTCTAAT
1 CGAGACGTATGCAACTTCATAGAAATACGCTCTAAT
*
12083470 CGATACGTATGCAACTTCATA-ATAATACGCTCTAAT
1 CGAGACGTATGCAACTTCATAGA-AATACGCTCTAAT
** * * * *
12083506 TAAGACGTATG------CA-AGTAATACACTATAAC
1 CGAGACGTATGCAACTTCATAGAAATACGCTCTAAT
* * *
12083535 CAAGACGTATGCAACATT-ATAGCAATACGCTCTAAC
1 CGAGACGTATGCAAC-TTCATAGAAATACGCTCTAAT
* * *
12083571 CGAGACGTATGCAACGTCATAGTAAA-ACACTTTAAT
1 CGAGACGTATGCAACTTCATAG-AAATACGCTCTAAT
* *
12083607 CGAGACGTATGCAA-ATCATAGCAATACGCTCTAAT
1 CGAGACGTATGCAACTTCATAGAAATACGCTCTAAT
* ** * *
12083642 TGAGACGTATGCAACTTCATATCAATACACTCCAAT
1 CGAGACGTATGCAACTTCATAGAAATACGCTCTAAT
*
12083678 CGAGACATATGC
1 CGAGACGTATGC
12083690 TTTCTTTGAA
Statistics
Matches: 173, Mismatches: 33, Indels: 28
0.74 0.14 0.12
Matches are distributed among these distances:
29 21 0.12
30 2 0.01
34 2 0.01
35 30 0.17
36 116 0.67
37 2 0.01
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.25
Consensus pattern (36 bp):
CGAGACGTATGCAACTTCATAGAAATACGCTCTAAT
Found at i:12083578 original size:65 final size:70
Alignment explanation
Indices: 12083474--12083662 Score: 212
Period size: 65 Copynumber: 2.8 Consensus size: 70
12083464 TCTAATCGAT
** *
12083474 ACGTATGCAAC-TTCATAATAATACGCTCTAATTAAGACGTATGCAA-GT-A-A-T-ACACTATA
1 ACGTATGCAACATT-ATAGCAATACGCTCTAATTGAGACGTATGCAACGTCATAGTAACACTATA
12083533 ACCAAG
65 ACCAAG
** *
12083539 ACGTATGCAACATTATAGCAATACGCTCTAACCGAGACGTATGCAACGTCATAGTAAAACACTTT
1 ACGTATGCAACATTATAGCAATACGCTCTAATTGAGACGTATGCAACGTCATAGT--AACACTAT
* *
12083604 AATCGAG
64 AACCAAG
* *
12083611 ACGTATGCAA-ATCATAGCAATACGCTCTAATTGAGACGTATGCAACTTCATA
1 ACGTATGCAACATTATAGCAATACGCTCTAATTGAGACGTATGCAACGTCATA
12083663 TCAATACACT
Statistics
Matches: 104, Mismatches: 12, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
65 38 0.37
66 4 0.04
67 1 0.01
68 1 0.01
69 1 0.01
71 38 0.37
72 21 0.20
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.25
Consensus pattern (70 bp):
ACGTATGCAACATTATAGCAATACGCTCTAATTGAGACGTATGCAACGTCATAGTAACACTATAA
CCAAG
Found at i:12083619 original size:101 final size:101
Alignment explanation
Indices: 12083430--12083620 Score: 240
Period size: 101 Copynumber: 1.9 Consensus size: 101
12083420 CATTATGCTT
* * * * *
12083430 TAACCGAGACATAAGCAAATTCATAGAAATATGCTCTAATCGATACGTATGCAACTTCATAATAA
1 TAACCAAGACATAAGCAAATTCATAGAAATACGCTCTAACCGAGACGTATGCAACGTCATAATAA
* * *
12083495 TACGCTCTAATTAAGACGTATGCAAGTAATACACTA
66 AACACTCTAATCAAGACGTATGCAAGTAATACACTA
* * * *
12083531 TAACCAAGACGTATGCAACATT-ATAGCAATACGCTCTAACCGAGACGTATGCAACGTCATAGTA
1 TAACCAAGACATAAGCAA-ATTCATAGAAATACGCTCTAACCGAGACGTATGCAACGTCATAATA
* *
12083595 AAACACTTTAATCGAGACGTATGCAA
65 AAACACTCTAATCAAGACGTATGCAA
12083621 ATCATAGCAA
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
101 72 0.96
102 3 0.04
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (101 bp):
TAACCAAGACATAAGCAAATTCATAGAAATACGCTCTAACCGAGACGTATGCAACGTCATAATAA
AACACTCTAATCAAGACGTATGCAAGTAATACACTA
Found at i:12083647 original size:71 final size:72
Alignment explanation
Indices: 12083519--12083689 Score: 220
Period size: 71 Copynumber: 2.4 Consensus size: 72
12083509 GACGTATGCA
* * *
12083519 AGTAATACACTATAACCAAGACGTATGCAACATTATAGCAATACGCTCTAACCGAGACGTATGCA
1 AGTAATACACTATAATCGAGACGTATGCAACATCATAGCAATACGCTCTAACCGAGACGTATGCA
12083584 ACGTCAT
66 ACGTCAT
* * **
12083591 AGTAAAACACTTTAATCGAGACGTATGCAA-ATCATAGCAATACGCTCTAATTGAGACGTATGCA
1 AGTAATACACTATAATCGAGACGTATGCAACATCATAGCAATACGCTCTAACCGAGACGTATGCA
*
12083655 ACTTCAT
66 ACGTCAT
** *
12083662 A-TCAATACACTCCAATCGAGACATATGC
1 AGT-AATACACTATAATCGAGACGTATGC
12083690 TTTCTTTGAA
Statistics
Matches: 86, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
70 1 0.01
71 59 0.69
72 26 0.30
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.24
Consensus pattern (72 bp):
AGTAATACACTATAATCGAGACGTATGCAACATCATAGCAATACGCTCTAACCGAGACGTATGCA
ACGTCAT
Found at i:12085064 original size:3 final size:3
Alignment explanation
Indices: 12085056--12085097 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
12085046 CCTTCCATTT
12085056 TTA TTA TTA TTA TTTA TTA TTA TTA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12085098 AATAATAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:12085110 original size:27 final size:27
Alignment explanation
Indices: 12085057--12085113 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
12085047 CTTCCATTTT
* * * **
12085057 TATTATTATTATTTATTATTATTATTA
1 TATTATTATTATTAAATAATAAAATTA
12085084 TATTATTATTATTAAATAATAAAATTA
1 TATTATTATTATTAAATAATAAAATTA
12085111 TAT
1 TAT
12085114 AAATATATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TATTATTATTATTAAATAATAAAATTA
Found at i:12085126 original size:17 final size:16
Alignment explanation
Indices: 12085091--12085124 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 16
12085081 TTATATTATT
12085091 ATTATTAAATAATAAA
1 ATTATTAAATAATAAA
12085107 ATTATATAAATATATAAA
1 ATTAT-TAAATA-ATAAA
12085125 TTTCTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 6 0.38
18 5 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTATTAAATAATAAA
Found at i:12085235 original size:12 final size:12
Alignment explanation
Indices: 12085218--12085250 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
12085208 AAAATGTTTG
12085218 AATAAGAATTCA
1 AATAAGAATTCA
*
12085230 AATAAGAATTTA
1 AATAAGAATTCA
12085242 AATAAGAAT
1 AATAAGAAT
12085251 ATATTTGAGT
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:0.61, C:0.03, G:0.09, T:0.27
Consensus pattern (12 bp):
AATAAGAATTCA
Found at i:12085312 original size:3 final size:3
Alignment explanation
Indices: 12085304--12085368 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
12085294 TTTTATTGTT
12085304 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12085351 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
12085369 ATGGGAGGTT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 59 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:12089185 original size:15 final size:15
Alignment explanation
Indices: 12089165--12089202 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
12089155 GTCAATTTTT
12089165 TAATTTA-ACTCATAC
1 TAATTTACACTCA-AC
12089180 TAATTTACGACTCAAC
1 TAATTTAC-ACTCAAC
12089196 TAATTTA
1 TAATTTA
12089203 GTACCGATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 9 0.43
17 5 0.24
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.39
Consensus pattern (15 bp):
TAATTTACACTCAAC
Found at i:12089540 original size:22 final size:22
Alignment explanation
Indices: 12089495--12089549 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
12089485 AAAATATATT
*
12089495 TTTATATT-TTTATTTTTAAGA
1 TTTAAATTATTTATTTTTAAGA
* *
12089516 TTTTAATTTATTTATTTTTTA-A
1 -TTTAAATTATTTATTTTTAAGA
12089538 TTTAAATTATTT
1 TTTAAATTATTT
12089550 TAGATGTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 11 0.39
22 7 0.25
23 10 0.36
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTAAATTATTTATTTTTAAGA
Found at i:12089550 original size:16 final size:16
Alignment explanation
Indices: 12089516--12089550 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
12089506 ATTTTTAAGA
*
12089516 TTTTAATTTATTTATT
1 TTTTAATTTAATTATT
12089532 TTTTAATTTAAATTATT
1 TTTTAATTT-AATTATT
12089549 TT
1 TT
12089551 AGATGTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTAATTTAATTATT
Found at i:12089551 original size:22 final size:22
Alignment explanation
Indices: 12089501--12089551 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
12089491 TATTTTTATA
*
12089501 TTTTTATTTTTAAGATTTTAAT
1 TTTTTATTTTTAAGATTTAAAT
*
12089523 TTATTTATTTTTTA-ATTTAAAT
1 TT-TTTATTTTTAAGATTTAAAT
12089545 TATTTTA
1 T-TTTTA
12089552 GATGTAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTTATTTTTAAGATTTAAAT
Found at i:12090162 original size:26 final size:25
Alignment explanation
Indices: 12090133--12090181 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
12090123 TATAATGTAA
*
12090133 ATATAAAAAAATTTATTAAGATAATT
1 ATATAAAAAAATTTAATAA-ATAATT
* *
12090159 ATATATAAAACTTTAATAAATAA
1 ATATAAAAAAATTTAATAAATAA
12090182 AAACATATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (25 bp):
ATATAAAAAAATTTAATAAATAATT
Found at i:12098127 original size:158 final size:158
Alignment explanation
Indices: 12097839--12098142 Score: 448
Period size: 158 Copynumber: 1.9 Consensus size: 158
12097829 ATTTTGGGAT
* * * **
12097839 TTACAGGTTATATGGGTGCTGGTCTTACATGTCCTACAGATGGCTGAGATTCGGTATTTGTTACA
1 TTACAGATTATATGAGTGCTGGTCTTACATGTCCTACAGATGGCTGAGATCCGACATTTGTTACA
* * *
12097904 GATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCTTTATATCTCGACCCACAGCTCGTGTGAG
66 GATTCTCCACAGCTCGTGTGAGCAGCATCATGTAGCTTTACATCTCGACCCACAGCTCATGTGAG
12097969 CAGACCCACTTCACAGCTCATATGATCA
131 CAGACCCACTTCACAGCTCATATGATCA
* * *
12097997 TTACAGATTATATGAGTGCTGGTCTTAGATGTCCTACCA-ATGGCTGAGATCCGACATTTTTTGC
1 TTACAGATTATATGAGTGCTGGTCTTACATGTCCTA-CAGATGGCTGAGATCCGACATTTGTTAC
* * *
12098061 GGATTCTCCACAGTTCGTGTGAGCAGCATCATGTAGCTTTACATCTCGACCCATAGCTCATGTGA
65 AGATTCTCCACAGCTCGTGTGAGCAGCATCATGTAGCTTTACATCTCGACCCACAGCTCATGTGA
* *
12098126 GCAGGCCCATTTCACAG
130 GCAGACCCACTTCACAG
12098143 AGATTTTATA
Statistics
Matches: 129, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
158 127 0.98
159 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (158 bp):
TTACAGATTATATGAGTGCTGGTCTTACATGTCCTACAGATGGCTGAGATCCGACATTTGTTACA
GATTCTCCACAGCTCGTGTGAGCAGCATCATGTAGCTTTACATCTCGACCCACAGCTCATGTGAG
CAGACCCACTTCACAGCTCATATGATCA
Found at i:12099626 original size:16 final size:16
Alignment explanation
Indices: 12099590--12099619 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12099580 ATTATGTAAA
12099590 ATTAATTAATATAATT
1 ATTAATTAATATAATT
12099606 ATTAATTAAT-TAAT
1 ATTAATTAATATAAT
12099620 ATTTTAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTAATTAATATAATT
Found at i:12102252 original size:24 final size:24
Alignment explanation
Indices: 12102219--12102269 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
12102209 AGAAATAATC
*
12102219 TTTCAGTTAAACTCTGTTCATTTG
1 TTTCAATTAAACTCTGTTCATTTG
* *
12102243 TTTCAATTAAACTTTGTTTATTTG
1 TTTCAATTAAACTCTGTTCATTTG
12102267 TTT
1 TTT
12102270 GAGTCAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.12, G:0.10, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTCATTTG
Found at i:12102278 original size:24 final size:24
Alignment explanation
Indices: 12102227--12102281 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
12102217 TCTTTCAGTT
*
12102227 AAACTCTGTTCATTTGTTTCAATT
1 AAACTCTGTTCATTTGTTTCAATC
* * * *
12102251 AAACTTTGTTTATTTGTTTGAGTC
1 AAACTCTGTTCATTTGTTTCAATC
12102275 AAACTCT
1 AAACTCT
12102282 TATTACTCTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.49
Consensus pattern (24 bp):
AAACTCTGTTCATTTGTTTCAATC
Found at i:12108432 original size:23 final size:23
Alignment explanation
Indices: 12108405--12108455 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
12108395 CATATTTTTA
*
12108405 ATTTTAGGAAT-TTAATGTCTTT
1 ATTTTTGGAATATTAATGTCTTT
** *
12108427 ATTTTTTTAATATTAATGTTTTT
1 ATTTTTGGAATATTAATGTCTTT
12108450 ATTTTT
1 ATTTTT
12108456 TTAATTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.25, C:0.02, G:0.08, T:0.65
Consensus pattern (23 bp):
ATTTTTGGAATATTAATGTCTTT
Found at i:12108464 original size:22 final size:22
Alignment explanation
Indices: 12108413--12108464 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 22
12108403 TAATTTTAGG
12108413 AATTTAATGTCTTTATTTTTTT
1 AATTTAATGTCTTTATTTTTTT
*
12108435 AATATTAATGTTTTTATTTTTTT
1 AAT-TTAATGTCTTTATTTTTTT
12108458 AATTTAA
1 AATTTAA
12108465 AATTTTAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 7 0.25
23 21 0.75
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (22 bp):
AATTTAATGTCTTTATTTTTTT
Found at i:12108470 original size:22 final size:23
Alignment explanation
Indices: 12108424--12108475 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
12108414 ATTTAATGTC
**
12108424 TTTATTTTTTTAATATTAATGTT
1 TTTATTTTTTTAATATTAAAATT
12108447 TTTATTTTTTTAAT-TTAAAATT
1 TTTATTTTTTTAATATTAAAATT
*
12108469 TTAATTT
1 TTTATTT
12108476 CATTTGTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 12 0.46
23 14 0.54
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTATTTTTTTAATATTAAAATT
Found at i:12114505 original size:29 final size:30
Alignment explanation
Indices: 12114433--12114514 Score: 95
Period size: 28 Copynumber: 2.9 Consensus size: 30
12114423 TCACTTAATT
*
12114433 TAAAAAATA-TTAAGTTAATT-TTATTTTA
1 TAAAAAATATTTAAATTAATTATTATTTTA
* *
12114461 TTAAAAAT-TTGAAATTAATTATT-TTTTA
1 TAAAAAATATTTAAATTAATTATTATTTTA
12114489 TAAAAAATATTTAAATT-ATTA-TATTT
1 TAAAAAATATTTAAATTAATTATTATTT
12114515 ATCTTCCATC
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
27 1 0.02
28 35 0.78
29 9 0.20
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (30 bp):
TAAAAAATATTTAAATTAATTATTATTTTA
Found at i:12114545 original size:10 final size:10
Alignment explanation
Indices: 12114532--12114556 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12114522 ATCCAAAACT
12114532 ATATAAAATA
1 ATATAAAATA
12114542 ATATAAAATA
1 ATATAAAATA
12114552 ATATA
1 ATATA
12114557 TTAATAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
ATATAAAATA
Found at i:12115082 original size:23 final size:21
Alignment explanation
Indices: 12115052--12115117 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 21
12115042 GTATGTGTAT
12115052 TTAAAATATTTCACATATAAA
1 TTAAAATATTTCACATATAAA
* * *
12115073 TATAATAATATTTGAAATAATTAA
1 T-TAA-AATATTTCACAT-ATAAA
12115097 TTAAAATATTTCACATATAAA
1 TTAAAATATTTCACATATAAA
12115118 AATATTTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
21 5 0.14
22 13 0.36
23 13 0.36
24 5 0.14
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (21 bp):
TTAAAATATTTCACATATAAA
Found at i:12116922 original size:16 final size:17
Alignment explanation
Indices: 12116898--12116946 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 17
12116888 AATATTACCA
*
12116898 TTATTAATT-TAAAATT
1 TTATAAATTATAAAATT
*
12116914 TTATAAATTATAAAATA
1 TTATAAATTATAAAATT
*
12116931 CT-TAAATTA-AAAATT
1 TTATAAATTATAAAATT
12116946 T
1 T
12116947 ACAATTTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
15 5 0.19
16 15 0.56
17 7 0.26
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
TTATAAATTATAAAATT
Found at i:12118413 original size:79 final size:78
Alignment explanation
Indices: 12118316--12118534 Score: 287
Period size: 79 Copynumber: 2.8 Consensus size: 78
12118306 TCGTAAATGG
* *
12118316 AAATTGAATAATTTTGTTTCAGGATTTATTCCTGCCGTTCAACAAAATTCATTCGAGTTTCTATT
1 AAATTAAATAATTTTGTTTCAGGATTTATTCCTGCCGTTCAACAAAATTAATTCGAGTTTCTATT
12118381 TCCAAACAAAAAT
66 TCCAAACAAAAAT
* * * * * * *
12118394 AAATTCAAATAATTCTGTTTTAGGATTTATTCTTGCCGTTCAATAGAATTAATTTGAGTTTCTGT
1 AAATT-AAATAATTTTGTTTCAGGATTTATTCCTGCCGTTCAACAAAATTAATTCGAGTTTCTAT
*
12118459 TTGCAAACAAAAAT
65 TTCCAAACAAAAAT
* * * *
12118473 AAATTAAAGTAATTTTGTTTGAGGATGTATTCCTGTCGTTCAACAAAATTTATTCGA-TTTCT
1 AAATTAAA-TAATTTTGTTTCAGGATTTATTCCTGCCGTTCAACAAAATTAATTCGAGTTTCT
12118535 GTTGTTAACA
Statistics
Matches: 120, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
78 13 0.11
79 107 0.89
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (78 bp):
AAATTAAATAATTTTGTTTCAGGATTTATTCCTGCCGTTCAACAAAATTAATTCGAGTTTCTATT
TCCAAACAAAAAT
Found at i:12118830 original size:25 final size:26
Alignment explanation
Indices: 12118799--12118858 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
12118789 TGACAAAAGC
*
12118799 TTAAATTTTAACCTTAAA-TGTGGCT
1 TTAAATTGTAACCTTAAATTGTGGCT
**
12118824 TTAAATTGTGGCCTTAAATTGTGGCT
1 TTAAATTGTAACCTTAAATTGTGGCT
12118850 TTAAATTGT
1 TTAAATTGT
12118859 GACAAATGCT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
25 15 0.48
26 16 0.52
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.45
Consensus pattern (26 bp):
TTAAATTGTAACCTTAAATTGTGGCT
Found at i:12118833 original size:13 final size:13
Alignment explanation
Indices: 12118812--12118859 Score: 80
Period size: 13 Copynumber: 3.8 Consensus size: 13
12118802 AATTTTAACC
12118812 TTAAA-TGTGGCT
1 TTAAATTGTGGCT
*
12118824 TTAAATTGTGGCC
1 TTAAATTGTGGCT
12118837 TTAAATTGTGGCT
1 TTAAATTGTGGCT
12118850 TTAAATTGTG
1 TTAAATTGTG
12118860 ACAAATGCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
12 5 0.15
13 28 0.85
ACGTcount: A:0.25, C:0.08, G:0.23, T:0.44
Consensus pattern (13 bp):
TTAAATTGTGGCT
Found at i:12118853 original size:26 final size:25
Alignment explanation
Indices: 12118810--12118859 Score: 91
Period size: 26 Copynumber: 2.0 Consensus size: 25
12118800 TAAATTTTAA
12118810 CCTTAAATGTGGCTTTAAATTGTGG
1 CCTTAAATGTGGCTTTAAATTGTGG
12118835 CCTTAAATTGTGGCTTTAAATTGTG
1 CCTTAAA-TGTGGCTTTAAATTGTG
12118860 ACAAATGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.42
Consensus pattern (25 bp):
CCTTAAATGTGGCTTTAAATTGTGG
Found at i:12121020 original size:6 final size:6
Alignment explanation
Indices: 12120997--12121059 Score: 51
Period size: 6 Copynumber: 10.7 Consensus size: 6
12120987 TTTATTTTTG
* **
12120997 AATTT- AATTT- ATTTTA AATTTA AATTTA TCCTTTTA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA --AATTTA AATTTA AATTTA
*
12121044 ACTTTA AATTTA AATT
1 AATTTA AATTTA AATT
12121060 CAATCAAATT
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
5 13 0.28
6 29 0.63
8 4 0.09
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (6 bp):
AATTTA
Found at i:12121033 original size:20 final size:18
Alignment explanation
Indices: 12120984--12121059 Score: 95
Period size: 17 Copynumber: 4.3 Consensus size: 18
12120974 AAATTGATTC
* *
12120984 AAATTTATTTTTGAATTT
1 AAATTTACTTTTAAATTT
12121002 -AATTTA-TTTTAAATTT
1 AAATTTACTTTTAAATTT
12121018 AAATTTATCCTTTTAAATTT
1 AAATTTA--CTTTTAAATTT
12121038 AAATTTAC-TTTAAATTT
1 AAATTTACTTTTAAATTT
12121055 AAATT
1 AAATT
12121060 CAATCAAATT
Statistics
Matches: 53, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
16 9 0.17
17 26 0.49
18 1 0.02
20 17 0.32
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (18 bp):
AAATTTACTTTTAAATTT
Found at i:12121050 original size:37 final size:34
Alignment explanation
Indices: 12120984--12121059 Score: 107
Period size: 37 Copynumber: 2.1 Consensus size: 34
12120974 AAATTGATTC
* *
12120984 AAATTTATTTTTGAATTTAATTTATTTTAAATTT
1 AAATTTATTTTTAAATTTAATTTACTTTAAATTT
12121018 AAATTTATCCTTTTAAATTTAAATTTACTTTAAATTT
1 AAATTTAT--TTTTAAATTT-AATTTACTTTAAATTT
12121055 AAATT
1 AAATT
12121060 CAATCAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
34 8 0.22
36 9 0.24
37 20 0.54
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (34 bp):
AAATTTATTTTTAAATTTAATTTACTTTAAATTT
Found at i:12121297 original size:25 final size:25
Alignment explanation
Indices: 12121269--12121330 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
12121259 CTGCTGATTG
*
12121269 CTGCCACCACCAGCTCTAACC-T-CT
1 CTGCCACCACCAACTC-AACCTTACT
*
12121293 CCTGCCACCACCAACTCCACCTTACT
1 -CTGCCACCACCAACTCAACCTTACT
12121319 CTGCCACCACCA
1 CTGCCACCACCA
12121331 TTACCTGCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 3 0.09
25 28 0.85
26 2 0.06
ACGTcount: A:0.23, C:0.53, G:0.06, T:0.18
Consensus pattern (25 bp):
CTGCCACCACCAACTCAACCTTACT
Found at i:12121984 original size:15 final size:15
Alignment explanation
Indices: 12121972--12122000 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12121962 ATTAATAATT
12121972 AATAATAATATAAAA
1 AATAATAATATAAAA
12121987 AATAATAATA-AAAA
1 AATAATAATATAAAA
12122001 GAAAGTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAATAATATAAAA
Found at i:12123367 original size:30 final size:30
Alignment explanation
Indices: 12123043--12123384 Score: 308
Period size: 30 Copynumber: 11.6 Consensus size: 30
12123033 CCCTAAATTG
** * *
12123043 TCCAAAAATTGTA-TTTTAACCCCTAAACT
1 TCCAAAAATTACATTTTTGACCCCGAAACT
* *
12123072 TCTCTAAAATTACA-TTTTGACCCCAAAACT
1 TC-CAAAAATTACATTTTTGACCCCGAAACT
* *
12123102 TCTCCAAAATTACATTTTTGCCCCCG-AACT
1 TC-CAAAAATTACATTTTTGACCCCGAAACT
*
12123132 TCCAAAAATTACATTTTTGACCTCGAAACT
1 TCCAAAAATTACATTTTTGACCCCGAAACT
* *
12123162 TCCAAAAATTTCATTTTTGACCCCAAAACT
1 TCCAAAAATTACATTTTTGACCCCGAAACT
* *
12123192 TCCAAAAATTACATTTTT-ACCCCCAAAAT
1 TCCAAAAATTACATTTTTGACCCCGAAACT
* *
12123221 TCCAAAAAATACAATTTT-ACTCCCG-AACT
1 TCCAAAAATTACATTTTTGAC-CCCGAAACT
* **
12123250 TCCAAAAATTTCATTTTTGACTTCGAAACT
1 TCCAAAAATTACATTTTTGACCCCGAAACT
** *
12123280 TCCAAATTTTATA-TTTTGACCCC-AAACT
1 TCCAAAAATTACATTTTTGACCCCGAAACT
* * *
12123308 TCTCCAAAATTACA-TTTTAACCCCAAAACT
1 TC-CAAAAATTACATTTTTGACCCCGAAACT
* * *
12123338 TTCAAAAATTCCATTTTTGACTCCGAAAC-
1 TCCAAAAATTACATTTTTGACCCCGAAACT
**
12123367 TCCCGAAATTACCATTTT
1 TCCAAAAATTA-CATTTT
12123385 GCCCCCCGGA
Statistics
Matches: 256, Mismatches: 47, Indels: 19
0.80 0.15 0.06
Matches are distributed among these distances:
28 7 0.03
29 109 0.43
30 131 0.51
31 9 0.04
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (30 bp):
TCCAAAAATTACATTTTTGACCCCGAAACT
Found at i:12123385 original size:88 final size:86
Alignment explanation
Indices: 12123043--12123390 Score: 326
Period size: 88 Copynumber: 3.9 Consensus size: 86
12123033 CCCTAAATTG
** * *
12123043 TCCAAAAATTGTATTTTAACCCCTAAACTTCTCTAAAATTACA-TTTTGACCCCAAAACTTCTCC
1 TCCAAAAATTACATTTTAACCCC-AAACTTC-CAAAAATTTCATTTTTGACCCCAAAACTTC-CC
* *
12123107 AAAATTACATTTTTGCCCCCGAACT
63 AAAATTACA-TTTTGACCCCAAACT
* * *
12123132 TCCAAAAATTACATTTTTGACCTCGAAACTTCCAAAAATTTCATTTTTGACCCCAAAACTTCCAA
1 TCCAAAAATTACA-TTTTAACC-CCAAACTTCCAAAAATTTCATTTTTGACCCCAAAACTTCCCA
* *
12123197 AAATTACATTTTTACCCCCAAAAT
64 AAATTACATTTTGA-CCCCAAACT
* * ** *
12123221 TCCAAAAAATACAATTTT-ACTCCCGAACTTCCAAAAATTTCATTTTTGACTTCGAAACTT-CCA
1 TCCAAAAATTAC-ATTTTAAC-CCCAAACTTCCAAAAATTTCATTTTTGACCCCAAAACTTCCCA
* *
12123284 AATTTTATATTTTGACCCCAAACT
64 AA-ATTACATTTTGACCCCAAACT
* * * * * *
12123308 TCTCCAAAATTACATTTTAACCCCAAAACTTTCAAAAATTCCATTTTTGACTCCGAAAC-TCCCG
1 TC-CAAAAATTACATTTTAACCCC-AAACTTCCAAAAATTTCATTTTTGACCCCAAAACTTCCCA
*
12123372 AAATTACCATTTTGCCCCC
64 AAATTA-CATTTTGACCCC
12123391 CGGATGCCCA
Statistics
Matches: 215, Mismatches: 32, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
87 26 0.12
88 102 0.47
89 53 0.25
90 33 0.15
91 1 0.00
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.33
Consensus pattern (86 bp):
TCCAAAAATTACATTTTAACCCCAAACTTCCAAAAATTTCATTTTTGACCCCAAAACTTCCCAAA
ATTACATTTTGACCCCAAACT
Found at i:12127589 original size:15 final size:14
Alignment explanation
Indices: 12127568--12127607 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
12127558 TTTGTTTTAG
*
12127568 ATTATATTTTAATT
1 ATTATATTTTAAAT
*
12127582 ATTTATATTTAAAAT
1 A-TTATATTTTAAAT
12127597 ATTATATTTTA
1 ATTATATTTTA
12127608 GTCATTTACG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATTATATTTTAAAT
Found at i:12127771 original size:18 final size:18
Alignment explanation
Indices: 12127748--12127790 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
12127738 TTTTCAGTTG
12127748 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
12127766 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
12127784 TAATTAA
1 TAATTAA
12127791 AAATTTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:12131282 original size:21 final size:21
Alignment explanation
Indices: 12131257--12131298 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
12131247 TGTGACCCTA
12131257 CACATGACTATGTGGCTACCC
1 CACATGACTATGTGGCTACCC
* *
12131278 CACATGCCTGTGTGGCTACCC
1 CACATGACTATGTGGCTACCC
12131299 TACACGCCCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.36, G:0.21, T:0.24
Consensus pattern (21 bp):
CACATGACTATGTGGCTACCC
Found at i:12131311 original size:21 final size:21
Alignment explanation
Indices: 12131267--12131311 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
12131257 CACATGACTA
* *
12131267 TGTGGCTACCCCACATGCCTG
1 TGTGGCTACCCCACACGCCCG
*
12131288 TGTGGCTACCCTACACGCCCG
1 TGTGGCTACCCCACACGCCCG
12131309 TGT
1 TGT
12131312 CCCAAATTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.13, C:0.38, G:0.24, T:0.24
Consensus pattern (21 bp):
TGTGGCTACCCCACACGCCCG
Found at i:12138361 original size:41 final size:41
Alignment explanation
Indices: 12138300--12138395 Score: 156
Period size: 41 Copynumber: 2.3 Consensus size: 41
12138290 GAATTTTATT
*
12138300 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAATCACCCAATTCTAACAATCTCCACC
*
12138341 TTAACAAGAATTCTAATCACCTAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAATCACCCAATTCTAACAATCTCCACC
* *
12138382 TTGACAAAAATTCT
1 TTAACAAGAATTCT
12138396 CTATGAACAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.39, C:0.28, G:0.04, T:0.29
Consensus pattern (41 bp):
TTAACAAGAATTCTAATCACCCAATTCTAACAATCTCCACC
Found at i:12144447 original size:15 final size:16
Alignment explanation
Indices: 12144429--12144458 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12144419 CTTCTCTATT
12144429 TTCTA-TTTCTTTTAG
1 TTCTATTTTCTTTTAG
12144444 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
12144459 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.13, G:0.03, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAG
Found at i:12144474 original size:21 final size:21
Alignment explanation
Indices: 12144450--12144504 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
12144440 TTAGTTCTAT
12144450 TTTCTTTTATTTTTAATTCTG
1 TTTCTTTTATTTTTAATTCTG
12144471 TTTCTTTTATTTTTAATTCTG
1 TTTCTTTTATTTTTAATTCTG
12144492 TTTCTTTTATTTT
1 TTTCTTTTATTTT
12144505 CCATATCACG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.13, C:0.09, G:0.04, T:0.75
Consensus pattern (21 bp):
TTTCTTTTATTTTTAATTCTG
Found at i:12145206 original size:17 final size:17
Alignment explanation
Indices: 12145184--12145218 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
12145174 GGTTGGATGG
12145184 TAAAGAGAACACGAGAA
1 TAAAGAGAACACGAGAA
12145201 TAAAGAGAACACGAGAA
1 TAAAGAGAACACGAGAA
12145218 T
1 T
12145219 GAGAATGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.11, G:0.23, T:0.09
Consensus pattern (17 bp):
TAAAGAGAACACGAGAA
Found at i:12145250 original size:2 final size:2
Alignment explanation
Indices: 12145243--12145283 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
12145233 GACCATTTTA
12145243 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
12145284 CCACTTTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:12146392 original size:18 final size:20
Alignment explanation
Indices: 12146360--12146396 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
12146350 TACTTTTTTC
12146360 ATAAATATTTCTTAAAAACA
1 ATAAATATTTCTTAAAAACA
12146380 ATAAAT-TTT-TTAAAAAC
1 ATAAATATTTCTTAAAAAC
12146397 TTTTAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 3 0.18
20 6 0.35
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (20 bp):
ATAAATATTTCTTAAAAACA
Found at i:12146433 original size:19 final size:19
Alignment explanation
Indices: 12146411--12146449 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
12146401 AAATTATTTT
12146411 TATTATTTTAAAT-ATAAAA
1 TATT-TTTTAAATCATAAAA
*
12146430 TATTTTTTATATCATAAAA
1 TATTTTTTAAATCATAAAA
12146449 T
1 T
12146450 CTAAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTTTTTAAATCATAAAA
Found at i:12151217 original size:23 final size:23
Alignment explanation
Indices: 12151197--12151244 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
12151187 AGATATTGTC
12151197 ATTGAAATGTTAAAATCATTGAA
1 ATTGAAATGTTAAAATCATTGAA
*
12151220 ATTGAAATGTTAAAATCTTTGAA
1 ATTGAAATGTTAAAATCATTGAA
12151243 AT
1 AT
12151245 GTTAAAACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.38
Consensus pattern (23 bp):
ATTGAAATGTTAAAATCATTGAA
Found at i:12152614 original size:25 final size:25
Alignment explanation
Indices: 12152533--12152617 Score: 80
Period size: 25 Copynumber: 3.4 Consensus size: 25
12152523 GACGGTTTTG
* * * * *
12152533 CAGAGAGTTCACCATAAAAGCCTTA
1 CAGAGAATTCACCACAAAGGCTTTC
**
12152558 CAGAGAATTTGCCACAAAGGCTTTC
1 CAGAGAATTCACCACAAAGGCTTTC
* *
12152583 CAAAGAATTCACCACAAAGGCTTTT
1 CAGAGAATTCACCACAAAGGCTTTC
*
12152608 TAGAGAATTC
1 CAGAGAATTC
12152618 GTGTTTACTG
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (25 bp):
CAGAGAATTCACCACAAAGGCTTTC
Found at i:12164607 original size:24 final size:24
Alignment explanation
Indices: 12164575--12164625 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
12164565 GCAAGTTCAT
**
12164575 TACGTTTATGCTCGTCAGTATGAA
1 TACGTTTATGCTCGTCAACATGAA
12164599 TACGTTTATGCTCGTCAACATGAA
1 TACGTTTATGCTCGTCAACATGAA
12164623 TAC
1 TAC
12164626 AAGAAACATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (24 bp):
TACGTTTATGCTCGTCAACATGAA
Found at i:12167919 original size:16 final size:16
Alignment explanation
Indices: 12167898--12167936 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
12167888 TTTTAACATT
*
12167898 TATTTTTATTTTAAAC
1 TATTTTTATTTAAAAC
*
12167914 TATTTTGATTTAAAAC
1 TATTTTTATTTAAAAC
12167930 T-TTTTTA
1 TATTTTTA
12167937 AAATTGATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (16 bp):
TATTTTTATTTAAAAC
Found at i:12168618 original size:26 final size:26
Alignment explanation
Indices: 12168584--12168635 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
12168574 AATATTAAGA
*
12168584 TAAATAATATTTAT-TTTAATGATAAT
1 TAAAAAATATTTATATTT-ATGATAAT
12168610 TAAAAAATATTTATATTTATGATAAT
1 TAAAAAATATTTATATTTATGATAAT
12168636 ATTATTCATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 21 0.88
27 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (26 bp):
TAAAAAATATTTATATTTATGATAAT
Found at i:12169757 original size:13 final size:13
Alignment explanation
Indices: 12169701--12169764 Score: 65
Period size: 13 Copynumber: 4.9 Consensus size: 13
12169691 TTTAGTATTG
12169701 CTTTTGAAAAGTA
1 CTTTTGAAAAGTA
* *
12169714 CTTTTAAAAAGTG
1 CTTTTGAAAAGTA
* * *
12169727 CGTTAGAAAAATA
1 CTTTTGAAAAGTA
* *
12169740 ATTTTGAAAAGTC
1 CTTTTGAAAAGTA
12169753 CTTTTGAAAAGT
1 CTTTTGAAAAGT
12169765 TTGGTTTAAG
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.36
Consensus pattern (13 bp):
CTTTTGAAAAGTA
Found at i:12172269 original size:16 final size:16
Alignment explanation
Indices: 12172248--12172279 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12172238 AAAGTTAACA
12172248 CACTTATAGCACCTAT
1 CACTTATAGCACCTAT
12172264 CACTTATAGCACCTAT
1 CACTTATAGCACCTAT
12172280 GTACATGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.06, T:0.31
Consensus pattern (16 bp):
CACTTATAGCACCTAT
Found at i:12175719 original size:34 final size:34
Alignment explanation
Indices: 12175681--12175745 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
12175671 TTCATCTCAT
* *
12175681 TTGACTTTTAACCTT-TCATCTTTCTTAACCTCCC
1 TTGACCTTTAACCTTCT-ATCTTCCTTAACCTCCC
*
12175715 TTGACCTTTAATCTTCTATCTTCCTTAACCT
1 TTGACCTTTAACCTTCTATCTTCCTTAACCT
12175746 TTCATATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
34 26 0.96
35 1 0.04
ACGTcount: A:0.18, C:0.31, G:0.03, T:0.48
Consensus pattern (34 bp):
TTGACCTTTAACCTTCTATCTTCCTTAACCTCCC
Done.