Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 189 of 214
Found at i:55468375 original size:49 final size:50
Alignment explanation
Indices: 55468312--55468415 Score: 160
Period size: 49 Copynumber: 2.1 Consensus size: 50
55468302 GGTAGGCAAC
55468312 TTTTTTTTTGCGCTGTTTG-TT-TT-TTTTTAAAGATTTTTCTCAACTCTTT
1 TTTTTTTTTGCGCTGTTTGCTTCTTCTTTTT-AAGATTTTTCTCAACT-TTT
*
55468361 TTTTTTTTTGCGCTGTTTGCTTCTTCTTTTTTAGATTTTTCTCAACTTTT
1 TTTTTTTTTGCGCTGTTTGCTTCTTCTTTTTAAGATTTTTCTCAACTTTT
55468411 TTTTT
1 TTTTT
55468416 ACGCTTTTTG
Statistics
Matches: 51, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
49 19 0.37
50 10 0.20
51 17 0.33
52 5 0.10
ACGTcount: A:0.10, C:0.13, G:0.10, T:0.67
Consensus pattern (50 bp):
TTTTTTTTTGCGCTGTTTGCTTCTTCTTTTTAAGATTTTTCTCAACTTTT
Found at i:55468433 original size:23 final size:23
Alignment explanation
Indices: 55468361--55468434 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 23
55468351 TCAACTCTTT
* *
55468361 TTTTTTTTTGCGCTGTTTGCTTC
1 TTTTTTTTTACGCTTTTTGCTTC
* * *
55468384 TTCTTTTTTA-GATTTTT-CTCAAC
1 TTTTTTTTTACGCTTTTTGCT--TC
55468407 TTTTTTTTTACGCTTTTTGCTT-
1 TTTTTTTTTACGCTTTTTGCTTC
55468429 TTTTTT
1 TTTTTT
55468435 ATTAACTATT
Statistics
Matches: 39, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
21 2 0.05
22 11 0.28
23 18 0.46
24 6 0.15
25 2 0.05
ACGTcount: A:0.07, C:0.15, G:0.09, T:0.69
Consensus pattern (23 bp):
TTTTTTTTTACGCTTTTTGCTTC
Found at i:55469014 original size:31 final size:32
Alignment explanation
Indices: 55468955--55469019 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
55468945 GGCAAATTAC
55468955 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
55468987 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
55469018 AA
1 AA
55469020 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:55472973 original size:33 final size:33
Alignment explanation
Indices: 55472936--55472998 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
55472926 TTCATTTATA
55472936 ATTATTTAATA-AT-ATTTTAGTAATTTTTTTCAT
1 ATTA-TTAATATATAATTTTAGT-ATTTTTTTCAT
55472969 ATTATTAATATATAATTTTAGTATTTTTTT
1 ATTATTAATATATAATTTTAGTATTTTTTT
55472999 AACTTAAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 6 0.21
33 14 0.50
34 8 0.29
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (33 bp):
ATTATTAATATATAATTTTAGTATTTTTTTCAT
Found at i:55474225 original size:18 final size:19
Alignment explanation
Indices: 55474175--55474229 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 19
55474165 TAAAACATAA
55474175 AAATTAATTTATAAAAATTC
1 AAATTAATTTATAAAAA-TC
*
55474195 AAA--AA-TAATTAAAAA-C
1 AAATTAATTTA-TAAAAATC
55474211 AAATTAATTTATAAAAATC
1 AAATTAATTTATAAAAATC
55474230 TAAACATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 11
0.68 0.05 0.27
Matches are distributed among these distances:
16 4 0.14
17 2 0.07
18 16 0.57
19 3 0.11
20 3 0.11
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATTAATTTATAAAAATC
Found at i:55474343 original size:20 final size:18
Alignment explanation
Indices: 55474301--55474343 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
55474291 TTGGTTTATA
55474301 TAAATTAAAATAAATAAT
1 TAAATTAAAATAAATAAT
* *
55474319 AAAATCTAAACATATATAAT
1 TAAAT-TAAA-ATAAATAAT
55474339 TAAAT
1 TAAAT
55474344 AGTTAATTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 4 0.20
19 4 0.20
20 12 0.60
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAATTAAAATAAATAAT
Found at i:55474805 original size:26 final size:27
Alignment explanation
Indices: 55474765--55474824 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 27
55474755 ATCATATTTA
*
55474765 AAATAAAATAAAAATTA-ATTTATTGTAT
1 AAATAAAAT-AAAA-TACATCTATTGTAT
*
55474793 AAATAAAAT-AAATACATCTATTTTAT
1 AAATAAAATAAAATACATCTATTGTAT
55474819 AAATAA
1 AAATAA
55474825 CTTTTAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 2 0.07
26 18 0.62
28 9 0.31
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (27 bp):
AAATAAAATAAAATACATCTATTGTAT
Found at i:55475473 original size:9 final size:8
Alignment explanation
Indices: 55475457--55475486 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
55475447 AATGTAAAAA
55475457 TATTTTTT
1 TATTTTTT
55475465 TATTTTTT
1 TATTTTTT
*
55475473 TATTTTTC
1 TATTTTTT
55475481 TATTTT
1 TATTTT
55475487 ATTTGTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.83
Consensus pattern (8 bp):
TATTTTTT
Found at i:55477368 original size:14 final size:14
Alignment explanation
Indices: 55477331--55477368 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
55477321 TTAACATTTA
*
55477331 TTTTTAAAATAAAC
1 TTTTTAATATAAAC
55477345 TTATTT-ATATAAAC
1 TT-TTTAATATAAAC
55477359 TTTTTAATAT
1 TTTTTAATAT
55477369 TTTTTTACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 3 0.14
14 15 0.71
15 3 0.14
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTTTAATATAAAC
Found at i:55482163 original size:18 final size:17
Alignment explanation
Indices: 55482131--55482164 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
55482121 GTAGATATGG
*
55482131 TTTTATTTTACTTTTAC
1 TTTTATTTTAATTTTAC
55482148 TTTTATTTTTAATTTTA
1 TTTTA-TTTTAATTTTA
55482165 GTCATGTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTATTTTAATTTTAC
Found at i:55514624 original size:21 final size:21
Alignment explanation
Indices: 55514598--55514640 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
55514588 GGTTCGCTGT
*
55514598 ATTGGATTAGAGGTGTATTGG
1 ATTGGATTAGAGGTGTAATGG
55514619 ATTGGATTAGAGGTGTAATGG
1 ATTGGATTAGAGGTGTAATGG
55514640 A
1 A
55514641 ATAGAGGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (21 bp):
ATTGGATTAGAGGTGTAATGG
Found at i:55514640 original size:16 final size:16
Alignment explanation
Indices: 55514621--55514653 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
55514611 TGTATTGGAT
*
55514621 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
55514637 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
55514653 T
1 T
55514654 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:55514698 original size:45 final size:44
Alignment explanation
Indices: 55514632--55514726 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
55514622 GGATTAGAGG
* *
55514632 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
55514677 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
55514721 TGTAAT
1 TGTAAT
55514727 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:55514909 original size:18 final size:17
Alignment explanation
Indices: 55514888--55514922 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
55514878 TTATTATTTA
*
55514888 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
55514906 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
55514923 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:55515035 original size:144 final size:146
Alignment explanation
Indices: 55514807--55515077 Score: 467
Period size: 144 Copynumber: 1.9 Consensus size: 146
55514797 ATGATTATTG
55514807 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTA--TATTATCAAAAATAAATAATTTAATCATATTTAA
* *
55514872 ATATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
64 ACATAATTATTATTAAATATA-TTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
55514937 AGAAATTTGTTTTGGTAAA
128 AGAAATTTGTTTTGGTAAA
*
55514956 TTATT-TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAAC
1 TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
55515018 ATAATTATTATTAAATATATTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ATAATTATTATTAAATATATTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
55515078 ATATTCTTAT
Statistics
Matches: 119, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
143 41 0.34
144 49 0.41
145 1 0.01
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (146 bp):
TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAAATATATTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAGA
AATTTGTTTTGGTAAA
Found at i:55515053 original size:17 final size:17
Alignment explanation
Indices: 55515032--55515065 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
55515022 TTATTATTAA
55515032 ATAT-ATTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
55515049 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
55515066 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:55519294 original size:37 final size:37
Alignment explanation
Indices: 55519244--55519316 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
55519234 CTTTCGATTT
**
55519244 TAATTACACAAAATATTATTTAATTATATAAATTATA
1 TAATTACACAAAATATTATCCAATTATATAAATTATA
**
55519281 TAATTACGGAAAATATTATCCAATTATATAAATTAT
1 TAATTACACAAAATATTATCCAATTATATAAATTAT
55519317 TACAGATTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (37 bp):
TAATTACACAAAATATTATCCAATTATATAAATTATA
Found at i:55519317 original size:20 final size:18
Alignment explanation
Indices: 55519258--55519318 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 18
55519248 TACACAAAAT
55519258 ATTATT-TAATTATATAA
1 ATTATTATAATTATATAA
***
55519275 ATTA-TATAATTACGGAA
1 ATTATTATAATTATATAA
*
55519292 AATATTATCCAATTATATAA
1 ATTATTAT--AATTATATAA
55519312 ATTATTA
1 ATTATTA
55519319 CAGATTTCGT
Statistics
Matches: 32, Mismatches: 8, Indels: 5
0.71 0.18 0.11
Matches are distributed among these distances:
16 1 0.03
17 15 0.47
18 3 0.09
20 13 0.41
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (18 bp):
ATTATTATAATTATATAA
Found at i:55519376 original size:20 final size:20
Alignment explanation
Indices: 55519253--55519364 Score: 56
Period size: 20 Copynumber: 5.8 Consensus size: 20
55519243 TTAATTACAC
*
55519253 AAAATATTATTTAATTA--T
1 AAAATATTATATAATTATCT
* *
55519271 ATAA-ATTATATAATTA-CGG
1 AAAATATTATATAATTATC-T
** *
55519290 AAAATATTATCCAATTATAT
1 AAAATATTATATAATTATCT
* * *
55519310 AAATTATTACA-GATT-TCGT
1 AAAATATTATATAATTATC-T
* * *
55519329 AATATTTTGTATAATTATCT
1 AAAATATTATATAATTATCT
55519349 AAAATATTATATAATT
1 AAAATATTATATAATT
55519365 TCCTAAACTA
Statistics
Matches: 65, Mismatches: 22, Indels: 12
0.66 0.22 0.12
Matches are distributed among these distances:
17 11 0.17
18 4 0.06
19 13 0.20
20 35 0.54
21 2 0.03
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (20 bp):
AAAATATTATATAATTATCT
Found at i:55519580 original size:8 final size:7
Alignment explanation
Indices: 55519546--55519585 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
55519536 AATATGTTTG
55519546 AATTT-A
1 AATTTAA
55519552 AATTTAA
1 AATTTAA
55519559 AATTTAA
1 AATTTAA
55519566 AATTTAA
1 AATTTAA
55519573 AGATTT-A
1 A-ATTTAA
55519580 AATTTA
1 AATTTA
55519586 TATTAATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 9 0.29
7 18 0.58
8 4 0.13
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (7 bp):
AATTTAA
Found at i:55522430 original size:51 final size:52
Alignment explanation
Indices: 55522342--55522444 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 52
55522332 ACAAGAAGAG
55522342 AATGAGAATCTACTTGACAAGGTGAGCCTTTATCATTACTGTTGTGTTATCT
1 AATGAGAATCTACTTGACAAGGTGAGCCTTTATCATTACTGTTGTGTTATCT
55522394 AATGAGAATCTACTTGAC-AGGTGAGCCTTTATCATTACTGTTGTGTTATCT
1 AATGAGAATCTACTTGACAAGGTGAGCCTTTATCATTACTGTTGTGTTATCT
55522445 GCAACATGTA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 33 0.65
52 18 0.35
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (52 bp):
AATGAGAATCTACTTGACAAGGTGAGCCTTTATCATTACTGTTGTGTTATCT
Found at i:55530714 original size:20 final size:20
Alignment explanation
Indices: 55530689--55530726 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
55530679 ATATGAAAAT
* *
55530689 TAAATTAATTCATTTAATAA
1 TAAATTAACTAATTTAATAA
55530709 TAAATTAACTAATTTAAT
1 TAAATTAACTAATTTAAT
55530727 CTAACCCCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAATTAACTAATTTAATAA
Found at i:55531420 original size:30 final size:27
Alignment explanation
Indices: 55531375--55531436 Score: 79
Period size: 30 Copynumber: 2.2 Consensus size: 27
55531365 TGCATAGAAT
*
55531375 AATATTATAATATATAATTATTACTTAA
1 AATATTATAATATATAACTATTA-TTAA
*
55531403 AATATTAATACATATATAACTATTATTAT
1 AATATT-ATA-ATATATAACTATTATTAA
55531432 AATAT
1 AATAT
55531437 AAATTATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 6 0.20
29 11 0.37
30 13 0.43
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (27 bp):
AATATTATAATATATAACTATTATTAA
Found at i:55531704 original size:264 final size:257
Alignment explanation
Indices: 55531415--55532238 Score: 926
Period size: 264 Copynumber: 3.2 Consensus size: 257
55531405 TATTAATACA
* * *
55531415 TATATAACTATTATTATAATATAAATTATAATAAAAGATATAATATTACATGATATTAAAATATT
1 TATATAACTATTATTATATTATAAATTATAATAAAAGATATAATATTACATGATATTATAATGTT
*
55531480 TAATCATTGATTCATATATATAAACTATTAATATATCATGTGATATCATATAACATTATATAATA
66 TAATCATTGATACATATATATAAACTATTAATATAT-AT-T-ATATCATAT-ACATTATATAATA
* *
55531545 TACATACATATCATACAATATAGTAGGAGGGCTAACTTTTAAATGTACGAAAAGTATAGAGACTT
127 TA-ATGCAT-T-ATACAATATAGTAGGAGGGCTAACTTTCAAATGTACGAAAAGTATAGAGACTT
*
55531610 AGAGCATATTTCAACTAGTATAATAACAAATAATAACATTATAATAATTAATATATAATGTACTA
189 AGAGCATATTTCAACTAGTATAATAACAAATAATAATATTATAATAATTAATATATAATGTACTA
55531675 CTAT
254 CTAT
* *
55531679 TATATAACTATTATTATATTATAAATTATAATAAAAGATATAATATTGCATAATATTATAATGTT
1 TATATAACTATTATTATATTATAAATTATAATAAAAGATATAATATTACATGATATTATAATGTT
* *
55531744 TAATCATTGATACATATTATATATAAACTATTAATATAT-TATATATTATATTATATTATATTAT
66 TAATCATTGATAC--A-TATATATAAACTATTAATATATAT-TATATCATA-TACATTATA-TA-
* * * * * * *
55531808 ATTATATTGCATTATATAATATAATAAGAAGGTTAACTTTCAAATGTACGTAAAA-TATAGAGAT
124 A-TATAATGCATTATACAATATAGTAGGAGGGCTAACTTTCAAATGTACG-AAAAGTATAGAGAC
* * *
55531872 TTAGAGCATATTTTAACTAGTACAATAACAAATAATAATATTATAATAATTAATATATAATATAC
187 TTAGAGCATATTTCAACTAGTATAATAACAAATAATAATATTATAATAATTAATATATAATGTAC
55531937 TACTAT
252 TACTAT
* * * * *
55531943 TATATAACTATTATTTTATTATAGATTACAATAAAATATATAGT-TTACATGATATTATAATGTT
1 TATATAACTATTATTATATTATAAATTATAATAAAAGATATAATATTACATGATATTATAATGTT
* * * * * * *
55532007 TGATCATTGATGC--ATGTATAAACCATT-A-ATATATTATA-CA-CTACATGGA-ATGATAT-A
66 TAATCATTGATACATATATATAAACTATTAATATATATTATATCATATACAT-TATATAATATAA
* * * *
55532064 -GCATTATACAATATAGTAGGAGAGCTAACTTTCAAATATACGAAAAGTATA-AGGGCTTAGAAC
130 TGCATTATACAATATAGTAGGAGGGCTAACTTTCAAATGTACGAAAAGTATAGA-GACTTAGAGC
* ** * * * *
55532127 ATATTTCAACAAGTATAATATTAAACAATAATA-TATAATAAGTAATATAAAATGCACTACTAT
194 ATATTTCAACTAGTATAATAACAAATAATAATATTATAATAATTAATATATAATGTACTACTAT
* * *
55532190 TATAT-A-TAATTATTATATTATAGGA-TATAATAAAATATATAGTATTACA
1 TATATAACT-ATTATTATATTATA-AATTATAATAAAAGATATAATATTACA
55532239 CACAGTGGTA
Statistics
Matches: 484, Mismatches: 61, Indels: 47
0.82 0.10 0.08
Matches are distributed among these distances:
245 1 0.00
246 31 0.06
247 43 0.09
248 73 0.15
250 3 0.01
251 1 0.00
252 1 0.00
253 5 0.01
254 1 0.00
255 1 0.00
256 8 0.02
257 2 0.00
258 12 0.02
263 29 0.06
264 231 0.48
265 10 0.02
266 6 0.01
267 26 0.05
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (257 bp):
TATATAACTATTATTATATTATAAATTATAATAAAAGATATAATATTACATGATATTATAATGTT
TAATCATTGATACATATATATAAACTATTAATATATATTATATCATATACATTATATAATATAAT
GCATTATACAATATAGTAGGAGGGCTAACTTTCAAATGTACGAAAAGTATAGAGACTTAGAGCAT
ATTTCAACTAGTATAATAACAAATAATAATATTATAATAATTAATATATAATGTACTACTAT
Found at i:55531793 original size:5 final size:5
Alignment explanation
Indices: 55531785--55531829 Score: 63
Period size: 5 Copynumber: 9.0 Consensus size: 5
55531775 TAATATATTA
** *
55531785 TATAT TATAT TATAT TATAT TATAT TATAT TGCAT TATAT AATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
55531830 AATAAGAAGG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (5 bp):
TATAT
Found at i:55539538 original size:5 final size:5
Alignment explanation
Indices: 55539523--55539552 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
55539513 AATACTTACA
55539523 TATTT TA-TT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT TATTT T
55539553 TAAATAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:55541533 original size:21 final size:20
Alignment explanation
Indices: 55541509--55541555 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
55541499 ATAAGTGTCT
55541509 GTTAGTAGTTAGCAGTTAGTA
1 GTTAGTAGTTAGCAGTT-GTA
* *
55541530 GTTAGTAGTTATCAGTTGTG
1 GTTAGTAGTTAGCAGTTGTA
55541550 GTTAGT
1 GTTAGT
55541556 TACAACAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.23, C:0.04, G:0.30, T:0.43
Consensus pattern (20 bp):
GTTAGTAGTTAGCAGTTGTA
Found at i:55541546 original size:7 final size:7
Alignment explanation
Indices: 55541509--55541540 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
55541499 ATAAGTGTCT
55541509 GTTAGTA
1 GTTAGTA
*
55541516 GTTAGCA
1 GTTAGTA
55541523 GTTAGTA
1 GTTAGTA
55541530 GTTAGTA
1 GTTAGTA
55541537 GTTA
1 GTTA
55541541 TCAGTTGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.28, C:0.03, G:0.28, T:0.41
Consensus pattern (7 bp):
GTTAGTA
Found at i:55546132 original size:21 final size:20
Alignment explanation
Indices: 55546108--55546154 Score: 76
Period size: 21 Copynumber: 2.3 Consensus size: 20
55546098 AGAAGTGTCT
55546108 GTTAGTAGTTAACAGTTAGTG
1 GTTAGTAGTTAACAGTT-GTG
*
55546129 GTTAGTAGTTATCAGTTGTG
1 GTTAGTAGTTAACAGTTGTG
55546149 GTTAGT
1 GTTAGT
55546155 TATAACAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.23, C:0.04, G:0.30, T:0.43
Consensus pattern (20 bp):
GTTAGTAGTTAACAGTTGTG
Found at i:55546964 original size:15 final size:15
Alignment explanation
Indices: 55546944--55546993 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
55546934 AACAATTAAT
*
55546944 TTTTTTTAATGTTTA
1 TTTTTTTAATATTTA
55546959 TTTTTTTAATATTTA
1 TTTTTTTAATATTTA
* * * *
55546974 TATTTTCAACACTTA
1 TTTTTTTAATATTTA
55546989 TTTTT
1 TTTTT
55546994 AAAATTTATT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.68
Consensus pattern (15 bp):
TTTTTTTAATATTTA
Found at i:55555664 original size:18 final size:17
Alignment explanation
Indices: 55555636--55555670 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
55555626 ATTATTAAGA
*
55555636 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
55555653 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
55555671 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:55555808 original size:18 final size:17
Alignment explanation
Indices: 55555780--55555814 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
55555770 ATTATTAACC
*
55555780 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
55555797 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
55555815 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:55556029 original size:44 final size:45
Alignment explanation
Indices: 55555980--55556067 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 45
55555970 ACCTCTATTA
* *
55555980 CATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCCATTC
1 CATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCCATTC
** *
55556024 CATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCCATT
1 CATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCCATT
55556068 ACACCTCTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
44 14 0.37
45 24 0.63
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.35
Consensus pattern (45 bp):
CATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCCATTC
Found at i:55556061 original size:45 final size:43
Alignment explanation
Indices: 55555961--55556067 Score: 123
Period size: 45 Copynumber: 2.5 Consensus size: 43
55555951 TTCTCCATTA
*
55555961 TGCTATTACACCTCTATT--A--CATTCAACCAAACACAGTTT
1 TGCTATTACACCTCTATTCCATTCATTCAACCAAACACAGATT
* * **
55556000 TACTATTACGCCTCTATTCCATTCCATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATT-CATTCAACCAAACA-CAGATT
55556045 TGCTATTACACCTCTATTCCATT
1 TGCTATTACACCTCTATTCCATT
55556068 ACACCTCTAA
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
39 16 0.29
41 1 0.02
44 14 0.25
45 24 0.44
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.36
Consensus pattern (43 bp):
TGCTATTACACCTCTATTCCATTCATTCAACCAAACACAGATT
Found at i:55556070 original size:16 final size:16
Alignment explanation
Indices: 55556049--55556081 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
55556039 TTGATTTGCT
*
55556049 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
55556065 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
55556081 A
1 A
55556082 ATCCAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.36, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:55556091 original size:21 final size:21
Alignment explanation
Indices: 55556062--55556104 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
55556052 ACACCTCTAT
*
55556062 TCCATTACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
55556083 TCCAATACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
55556104 T
1 T
55556105 ACAGCGAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (21 bp):
TCCAATACACCTCTAATCCAA
Found at i:55559784 original size:18 final size:18
Alignment explanation
Indices: 55559761--55559797 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
55559751 TTTTAAACTC
*
55559761 ACCAAAAGTAAACACAAG
1 ACCAAAAATAAACACAAG
55559779 ACCAAAAATAAACACAAG
1 ACCAAAAATAAACACAAG
55559797 A
1 A
55559798 TGCATTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.65, C:0.22, G:0.08, T:0.05
Consensus pattern (18 bp):
ACCAAAAATAAACACAAG
Found at i:55560670 original size:11 final size:11
Alignment explanation
Indices: 55560654--55560679 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
55560644 GTCGCCTCTT
55560654 CCTTCGTTCTA
1 CCTTCGTTCTA
55560665 CCTTCGTTCTA
1 CCTTCGTTCTA
55560676 CCTT
1 CCTT
55560680 TGCCTCCCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.38, G:0.08, T:0.46
Consensus pattern (11 bp):
CCTTCGTTCTA
Found at i:55563855 original size:16 final size:16
Alignment explanation
Indices: 55563834--55563875 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
55563824 TTATTAAATT
*
55563834 ATATATTTTAATTATA
1 ATATATTTTAATAATA
55563850 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
55563865 AT-TATGTTTAA
1 ATATAT-TTTAA
55563876 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:55563860 original size:15 final size:15
Alignment explanation
Indices: 55563825--55563866 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
55563815 TTAAGAATTT
*
55563825 TATTAAATTAT-ATA
1 TATTTAATTATAATA
55563839 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
55563853 TATTTAATAATAAT
1 TATTTAATTATAAT
55563867 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:55564006 original size:18 final size:17
Alignment explanation
Indices: 55563978--55564012 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
55563968 ATTATTAAGA
*
55563978 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
55563995 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
55564013 TTAAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:55564095 original size:157 final size:157
Alignment explanation
Indices: 55563809--55564125 Score: 562
Period size: 157 Copynumber: 2.0 Consensus size: 157
55563799 ATAAGAATAT
* *
55563809 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAAAAATAATTATGTTT
*
55563874 AAATATGATTAAAATATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
55563939 TAATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
*
55563966 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAAAAATAATTATTTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAAAAATAATTATGTTT
* *
55564031 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAATAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
55564096 TAATCATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
55564123 TAA
1 TAA
55564126 GGGTATTCTA
Statistics
Matches: 152, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
157 152 1.00
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAAAAATAATTATGTTT
AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:55564269 original size:16 final size:16
Alignment explanation
Indices: 55564248--55564283 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
55564238 GATTTGCTAT
55564248 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
55564264 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
55564280 TACA
1 TACA
55564284 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:55564782 original size:27 final size:27
Alignment explanation
Indices: 55564752--55564805 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
55564742 AAAAAACTTA
*
55564752 TATATAATTATCATT-TTTTTAATTTTT
1 TATATAATTATAATTATTTTT-ATTTTT
*
55564779 TATATTATTATAATTATTTTTATTTTT
1 TATATAATTATAATTATTTTTATTTTT
55564806 ATCTGAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (27 bp):
TATATAATTATAATTATTTTTATTTTT
Found at i:55566080 original size:7 final size:7
Alignment explanation
Indices: 55566068--55566093 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
55566058 GATTTTTTTG
55566068 TTATTAA
1 TTATTAA
55566075 TTATTAA
1 TTATTAA
55566082 TTATTAA
1 TTATTAA
55566089 TTATT
1 TTATT
55566094 TATGTTTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TTATTAA
Found at i:55572726 original size:51 final size:50
Alignment explanation
Indices: 55572667--55572775 Score: 148
Period size: 51 Copynumber: 2.2 Consensus size: 50
55572657 ATGATATTTT
* * * *
55572667 ATTAAAAAATTTAATATAAAATATTGATTGGCGCCTGTC-AGATAGACGCC
1 ATTAAAAAAATTAATATAAAATATTCATTGACGCCTCTCAAG-TAGACGCC
*
55572717 ATTTAAAAAAATTAATATAAAATATTCATTGACGCCTCTCAAGTAGGCGCC
1 A-TTAAAAAAATTAATATAAAATATTCATTGACGCCTCTCAAGTAGACGCC
55572768 ATTAAAAA
1 ATTAAAAA
55572776 CATACTATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
50 8 0.15
51 42 0.81
52 2 0.04
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (50 bp):
ATTAAAAAAATTAATATAAAATATTCATTGACGCCTCTCAAGTAGACGCC
Found at i:55574339 original size:105 final size:105
Alignment explanation
Indices: 55574157--55574345 Score: 326
Period size: 105 Copynumber: 1.8 Consensus size: 105
55574147 AAATTATTAT
*
55574157 GGAAATAATGTTGGTCAAAATTGTTTTGGGGTTGGTCAAAATAATGGTGTTTCTGGTCAAAATGT
1 GGAAATAATGTTGGTCAAAATTGTTTAGGGGTTGGTCAAAATAATGGTGTTTCTGGTCAAAATGT
*
55574222 GTGTGCTGATGGCTATAATGGTTTTCTAGAACAACGTGCA
66 GTGTGCTCATGGCTATAATGGTTTTCTAGAACAACGTGCA
* *
55574262 GGAAATAATGTTGGTCAAAATTGGTTTAGGGG-TGGTCAAACTAATTGTGTTTCTGGTCAAAATG
1 GGAAATAATGTTGGTCAAAATT-GTTTAGGGGTTGGTCAAAATAATGGTGTTTCTGGTCAAAATG
55574326 TGTGTGCTCATGGCTATAAT
65 TGTGTGCTCATGGCTATAAT
55574346 TGTGCAGGAC
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
105 71 0.90
106 8 0.10
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.35
Consensus pattern (105 bp):
GGAAATAATGTTGGTCAAAATTGTTTAGGGGTTGGTCAAAATAATGGTGTTTCTGGTCAAAATGT
GTGTGCTCATGGCTATAATGGTTTTCTAGAACAACGTGCA
Found at i:55579709 original size:7 final size:7
Alignment explanation
Indices: 55579697--55579728 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
55579687 CATCTATTTG
55579697 AAATTCT
1 AAATTCT
55579704 AAATTCT
1 AAATTCT
55579711 AAATTCT
1 AAATTCT
*
55579718 AAATTTT
1 AAATTCT
55579725 AAAT
1 AAAT
55579729 ATTTTAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (7 bp):
AAATTCT
Found at i:55580687 original size:14 final size:14
Alignment explanation
Indices: 55580658--55580703 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
55580648 AATTTACAAC
* *
55580658 ATATACGAATAAAT
1 ATATACAAATACAT
*
55580672 ATTTACAAATACAT
1 ATATACAAATACAT
55580686 ATATACAAATACA-
1 ATATACAAATACAT
55580699 ATATA
1 ATATA
55580704 ACAGTAAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 5 0.18
14 23 0.82
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (14 bp):
ATATACAAATACAT
Found at i:55582986 original size:50 final size:50
Alignment explanation
Indices: 55582894--55583485 Score: 397
Period size: 50 Copynumber: 11.9 Consensus size: 50
55582884 TTTGTTCAAC
* *** * * * * *
55582894 TGCAATGTCGGGGAAACCAGATCCGCTGTCGTAGCTTTAATCTGTTCCAC
1 TGCAATGTCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTGTTCCAT
* ** * * **
55582944 CGCACCGTCAGGGAAGTAAGATCTGCCGTTGTGGCTTCAATCTTTTAAAT
1 TGCAATGTCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTGTTCCAT
* * * * *
55582994 TGCAATGTCAGGAAAACT-AGATCCGCCGTCGTAGCTTCAATCTATTCCAT
1 TGCAATGTCAGG-GAAGTAAGATCCGCCGTTGTGGCTTCAATCTGTTCCAT
* * * * * **
55583044 TGTACTG-CTAAGGAAGTAAGATCCGCCGTTGTGGTTTCAATCTTTTTTAT
1 TGCAATGTC-AGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTGTTCCAT
* *** * * *
55583094 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCAC
1 TGCAATGTCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTGTTCCAT
* * * **
55583144 TGCACTG-CTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
1 TGCAATGTC-AGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTGTTCCAT
* * *** * * * *
55583194 TGTAATATCAGGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCAC
1 TGCAATGTCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTGTTCCAT
* * * * **
55583244 TGCACTGTTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
1 TGCAATGTCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTGTTCCAT
* *** * *
55583294 TGCAATATCAGGGAAACCAGATCCGCCGTTGTAGCTTCAATCTGTTCCAC
1 TGCAATGTCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTGTTCCAT
* * * * **
55583344 TGCACTG-CTAAGGAAGTAAGATCTGCCGCTGTGGCTTCAATCT-TTTGAT
1 TGCAATGTC-AGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTGTTCCAT
* * * * *
55583393 TGCAATATCAGGGAAACT-AGATCCGCCGTCGTAGCTTCAATCTGTTCCAC
1 TGCAATGTCAGGG-AAGTAAGATCCGCCGTTGTGGCTTCAATCTGTTCCAT
* * * *
55583443 TACACT-ACTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCT
1 TGCAATGTC-AGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCT
55583486 TTTCAACCCG
Statistics
Matches: 395, Mismatches: 135, Indels: 24
0.71 0.24 0.04
Matches are distributed among these distances:
49 42 0.11
50 348 0.88
51 5 0.01
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (50 bp):
TGCAATGTCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTGTTCCAT
Found at i:55583072 original size:100 final size:100
Alignment explanation
Indices: 55582894--55583488 Score: 924
Period size: 100 Copynumber: 6.0 Consensus size: 100
55582884 TTTGTTCAAC
* * * * * * *
55582894 TGCAATGTCGGGGAAACCAGATCCGCTGTCGTAGCTTTAATCTGTTCCACCGCACCG-TCAGGGA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCT-AAGGA
* **
55582958 AGTAAGATCTGCCGTTGTGGCTTCAATCTTTTAAAT
65 AGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
* * * * * *
55582994 TGCAATGTCAGGAAAACTAGATCCGCCGTCGTAGCTTCAATCTATTCCATTGTACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
* *
55583059 GTAAGATCCGCCGTTGTGGTTTCAATCTTTTTTAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
55583094 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
55583159 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
* * *
55583194 TGTAATATCAGGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGTTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
55583259 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
*
55583294 TGCAATATCAGGGAAACCAGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
* *
55583359 GTAAGATCTGCCGCTGTGGCTTCAATC-TTTTGAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
* * *
55583393 TGCAATATCAGGGAAACTAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTACACTACTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
55583458 GTAAGATCCGCCGTTGTGGCTTCAATCTTTT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTT
55583489 CAACCCGCTC
Statistics
Matches: 455, Mismatches: 38, Indels: 4
0.92 0.08 0.01
Matches are distributed among these distances:
99 93 0.20
100 361 0.79
101 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (100 bp):
TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
Found at i:55588871 original size:14 final size:14
Alignment explanation
Indices: 55588842--55588887 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
55588832 AATTTACAAC
* *
55588842 ATATACGAATAAAT
1 ATATACAAATACAT
*
55588856 ATTTACAAATACAT
1 ATATACAAATACAT
55588870 ATATACAAATACA-
1 ATATACAAATACAT
55588883 ATATA
1 ATATA
55588888 ACAGTAAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 5 0.18
14 23 0.82
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (14 bp):
ATATACAAATACAT
Found at i:55599873 original size:28 final size:28
Alignment explanation
Indices: 55599840--55599897 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
55599830 TACGTGAACT
* *
55599840 CTAGCTTGGTGAACATATACCTGCAAGC
1 CTAGCTTGGCGAACATATACCTACAAGC
*
55599868 CTAGCTTGGCGAACATATGCCTACAAGC
1 CTAGCTTGGCGAACATATACCTACAAGC
55599896 CT
1 CT
55599898 TACTTACGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (28 bp):
CTAGCTTGGCGAACATATACCTACAAGC
Found at i:55601566 original size:20 final size:18
Alignment explanation
Indices: 55601518--55601567 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
55601508 TTTATCTTGT
55601518 TATTAAATTAA-ATTTAA
1 TATTAAATTAATATTTAA
55601535 TATTAAGA-TAATCACTTTAA
1 TATTAA-ATTAAT-A-TTTAA
55601555 TATTAAATTAATA
1 TATTAAATTAATA
55601568 AAATACTACC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
17 9 0.32
18 1 0.04
19 3 0.11
20 15 0.54
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (18 bp):
TATTAAATTAATATTTAA
Found at i:55601637 original size:17 final size:17
Alignment explanation
Indices: 55601586--55601643 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
55601576 CCAAGATAAG
* *
55601586 TATTAAATTAAATTAAA
1 TATTAAATTTATTTAAA
*
55601603 TATTAAATTTATTAAAA
1 TATTAAATTTATTTAAA
*
55601620 TATTATTATTT-TTTAAA
1 TATTA-AATTTATTTAAA
55601637 TAATTAA
1 T-ATTAA
55601644 TCTAAAATCA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
17 25 0.76
18 8 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTAAATTTATTTAAA
Found at i:55605600 original size:19 final size:19
Alignment explanation
Indices: 55605576--55605623 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
55605566 GTAATTTGTA
55605576 TGAAATTAAACTT-TCAAAT
1 TGAAATTAAACTTAT-AAAT
55605595 TGAAATTAAACTTATAAAT
1 TGAAATTAAACTTATAAAT
*
55605614 TAAAATTAAA
1 TGAAATTAAA
55605624 AGAGAAATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 26 0.96
20 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.35
Consensus pattern (19 bp):
TGAAATTAAACTTATAAAT
Found at i:55608255 original size:42 final size:42
Alignment explanation
Indices: 55608198--55608355 Score: 133
Period size: 42 Copynumber: 3.8 Consensus size: 42
55608188 TCAACTCATA
* * *
55608198 TGAGTTTTAGATTAACCCTTCTGGGTTTCAGTTAAGCTCTTT
1 TGAGCTTTAGATTAACCCTTATGGGTTTCCGTTAAGCTCTTT
* * * *
55608240 TGAGCTTTAGTTTAACTCTAATGGGTTTCCGTTTAGCT-TTT
1 TGAGCTTTAGATTAACCCTTATGGGTTTCCGTTAAGCTCTTT
* * * * *
55608281 CCGAGCTTCAGATTAACCCTTATGAGTTTCCGTTCAGCTCCTAT
1 -TGAGCTTTAGATTAACCCTTATGGGTTTCCGTTAAGCT-CTTT
* * **
55608325 T-AGC-TTCGTTTAACCCTTACAGGTTTCCGTT
1 TGAGCTTTAGATTAACCCTTATGGGTTTCCGTT
55608356 TAGCATTTAT
Statistics
Matches: 91, Mismatches: 22, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
41 24 0.26
42 65 0.71
44 2 0.02
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (42 bp):
TGAGCTTTAGATTAACCCTTATGGGTTTCCGTTAAGCTCTTT
Found at i:55611293 original size:59 final size:59
Alignment explanation
Indices: 55611230--55611399 Score: 313
Period size: 59 Copynumber: 2.9 Consensus size: 59
55611220 TCAAGTTTAT
* *
55611230 TTTACTAATCAAATATTAGATTTTGTTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
55611289 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
*
55611348 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATT
55611400 AATAATTTAA
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 108 1.00
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (59 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
Found at i:55611435 original size:22 final size:23
Alignment explanation
Indices: 55611400--55611462 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
55611390 ATTAACAATT
*
55611400 AATAATTTAATAATTTTACT-AACA
1 AATAATTT--TAATTTTACTAAAAA
* * *
55611424 ATTAGTTTTAATTTTATTAAAAA
1 AATAATTTTAATTTTACTAAAAA
55611447 AATAATTTTAATTTTA
1 AATAATTTTAATTTTA
55611463 ATTAAAAACG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
22 9 0.28
23 17 0.53
24 6 0.19
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (23 bp):
AATAATTTTAATTTTACTAAAAA
Found at i:55612706 original size:25 final size:25
Alignment explanation
Indices: 55612626--55612743 Score: 71
Period size: 25 Copynumber: 4.8 Consensus size: 25
55612616 GCCCTCTCTT
* * **
55612626 GAGCCATATAACGGGAATCTCATGT
1 GAGCCATATAACGGGAAGCTTATAA
* * **
55612651 GAGCCATGTAGCGGGAAGCTTATCC
1 GAGCCATATAACGGGAAGCTTATAA
* *
55612676 GGGCTATATAACGGGAAGCTTATAA
1 GAGCCATATAACGGGAAGCTTATAA
* * **
55612701 GAG-C-TATAATCAGGAAGCTCATGC
1 GAGCCATATAA-CGGGAAGCTTATAA
*
55612725 GAGCCA-ATAACGGGTAGCT
1 GAGCCATATAACGGGAAGCT
55612744 CCGGATAGCC
Statistics
Matches: 70, Mismatches: 20, Indels: 7
0.72 0.21 0.07
Matches are distributed among these distances:
23 5 0.07
24 20 0.29
25 45 0.64
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.21
Consensus pattern (25 bp):
GAGCCATATAACGGGAAGCTTATAA
Found at i:55612959 original size:24 final size:24
Alignment explanation
Indices: 55612913--55612975 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
55612903 ATCACAACCA
* *
55612913 AACGGGATGCTCCGTAGAGCTAT-T
1 AACGGGAAGCT-CGTAGAACTATAT
55612937 AACGGGAAGCTCGTAGGAACTATAT
1 AACGGGAAGCTCGTA-GAACTATAT
*
55612962 AACGAGAAGCTCGT
1 AACGGGAAGCTCGT
55612976 GAGGGCTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 4 0.12
24 16 0.47
25 14 0.41
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.21
Consensus pattern (24 bp):
AACGGGAAGCTCGTAGAACTATAT
Found at i:55621817 original size:71 final size:71
Alignment explanation
Indices: 55621701--55621842 Score: 266
Period size: 71 Copynumber: 2.0 Consensus size: 71
55621691 TTGTCTTGTC
* *
55621701 TAATTTGTTGATGCTTCTTTATGTGAAACATTGCTGTTTTGTTCATTTTGATTTTATGACCTCTG
1 TAATTTGTTGATGCTTCTTTATGTGAAACATTGCTGTTTTATTCATTTTGATTTTATGACCTCAG
55621766 GACAAT
66 GACAAT
55621772 TAATTTGTTGATGCTTCTTTATGTGAAACATTGCTGTTTTATTCATTTTGATTTTATGACCTCAG
1 TAATTTGTTGATGCTTCTTTATGTGAAACATTGCTGTTTTATTCATTTTGATTTTATGACCTCAG
55621837 GACAAT
66 GACAAT
55621843 GCATCTGAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.23, C:0.13, G:0.16, T:0.49
Consensus pattern (71 bp):
TAATTTGTTGATGCTTCTTTATGTGAAACATTGCTGTTTTATTCATTTTGATTTTATGACCTCAG
GACAAT
Found at i:55626165 original size:19 final size:19
Alignment explanation
Indices: 55626141--55626199 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
55626131 AAGAAAAAAA
55626141 TTGAAAATAATCCCACAAT
1 TTGAAAATAATCCCACAAT
* *
55626160 TTGAAAA-GAT---A-AAA
1 TTGAAAATAATCCCACAAT
55626174 TTGAAAATAATCCCACAAT
1 TTGAAAATAATCCCACAAT
55626193 TTGAAAA
1 TTGAAAA
55626200 GATTACTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 9 0.29
15 3 0.10
18 3 0.10
19 16 0.52
ACGTcount: A:0.53, C:0.14, G:0.08, T:0.25
Consensus pattern (19 bp):
TTGAAAATAATCCCACAAT
Found at i:55626176 original size:33 final size:33
Alignment explanation
Indices: 55626137--55626202 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
55626127 AGACAAGAAA
55626137 AAAATTGAAAATAATCCCACAATTTGAAAAGAT
1 AAAATTGAAAATAATCCCACAATTTGAAAAGAT
55626170 AAAATTGAAAATAATCCCACAATTTGAAAAGAT
1 AAAATTGAAAATAATCCCACAATTTGAAAAGAT
55626203 TACTAAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.55, C:0.12, G:0.09, T:0.24
Consensus pattern (33 bp):
AAAATTGAAAATAATCCCACAATTTGAAAAGAT
Found at i:55628961 original size:34 final size:34
Alignment explanation
Indices: 55628897--55628965 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
55628887 AGATTTCAAT
* * * * *
55628897 AAATCAATGAATTGATATACTCTTCTGCATTTAG
1 AAATCAATAAATTCAGATACACTTCCGCATTTAG
55628931 AAATCAATAAATTCAGATACACTTCCGCATTTAG
1 AAATCAATAAATTCAGATACACTTCCGCATTTAG
55628965 A
1 A
55628966 TTTATTCTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.33
Consensus pattern (34 bp):
AAATCAATAAATTCAGATACACTTCCGCATTTAG
Found at i:55640435 original size:26 final size:26
Alignment explanation
Indices: 55640382--55640436 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
55640372 GTGGATTTAG
***
55640382 GTGTAATTGCTTGTAATTGAATTTGA
1 GTGTAATTGCTTGTAATTGAACAAGA
55640408 GTGTAATTGCTTGTAATT-ACACAAGA
1 GTGTAATTGCTTGTAATTGA-ACAAGA
55640434 GTG
1 GTG
55640437 GCTTGTTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 1 0.04
26 24 0.96
ACGTcount: A:0.29, C:0.07, G:0.24, T:0.40
Consensus pattern (26 bp):
GTGTAATTGCTTGTAATTGAACAAGA
Found at i:55641883 original size:12 final size:12
Alignment explanation
Indices: 55641866--55641899 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
55641856 GGCCCACTAT
55641866 TAAAATAA-ATAA
1 TAAAATAACA-AA
55641878 TAAAATAACAAA
1 TAAAATAACAAA
55641890 TAAAATAACA
1 TAAAATAACA
55641900 CCCCAAATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 20 0.95
13 1 0.05
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.21
Consensus pattern (12 bp):
TAAAATAACAAA
Found at i:55654200 original size:18 final size:20
Alignment explanation
Indices: 55654173--55654210 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
55654163 TTCAGCTTAA
*
55654173 AATTTTAATT-TTAA-TTTT
1 AATTTGAATTCTTAACTTTT
55654191 AATTTGAATTCTTAACTTTT
1 AATTTGAATTCTTAACTTTT
55654211 GAACTGTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 4 0.24
20 4 0.24
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (20 bp):
AATTTGAATTCTTAACTTTT
Found at i:55654827 original size:79 final size:79
Alignment explanation
Indices: 55654624--55655065 Score: 404
Period size: 79 Copynumber: 5.6 Consensus size: 79
55654614 CATATATGTT
** * * *
55654624 TTTTTTATTACAATATGGAGAATATTAACTGATAAAATTTGTTAATTTCGTTAGTGACGTGTGAG
1 TTTTTTATTACAATAAAGAGAATATTAACTAATAAAATTCGTTAATTTCGTTAGTGACATGTGAG
* *
55654689 CAATCATCAAATAAAA
66 CGATCATC-AA-AGAA
*
55654705 TTTTTTTATTACAATAAAGAGAATATTAACTAATAAAATTCGTTAATTTCGTTAGTGGCATGTGA
1 -TTTTTTATTACAATAAAGAGAATATTAACTAATAAAATTCGTTAATTTCGTTAGTGACATGTGA
55654770 GCGATCATCAAAGAA
65 GCGATCATCAAAGAA
** * * * *
55654785 TTTTTTATTACAATAAAGAGAATATTAACTAATAAAGCTCGTTAATTGCGTTAGTTACGTGTTAG
1 TTTTTTATTACAATAAAGAGAATATTAACTAATAAAATTCGTTAATTTCGTTAGTGACATGTGAG
*
55654850 CGATCATTAAAG-A
66 CGATCATCAAAGAA
* * * * *
55654863 TGTCATTTATTATAATAAA-AAAATATTAACTGATAAAATTCGCTAATTTCGTT-GATGACAT-T
1 T-T-TTTTATTACAATAAAGAGAATATTAACTAATAAAATTCGTTAATTTCGTTAG-TGACATGT
* *
55654925 GAGAGATCATTAAAGAAA
63 GAGCGATCATCAAAG-AA
** * * *
55654943 TTTTTTATTATGACAAA-A-AA-ATTAACTGATAAAATTCGCTAATTTCGTT-GATGACAT-TGA
1 TTTTTTATTACAATAAAGAGAATATTAACTAATAAAATTCGTTAATTTCGTTAG-TGACATGTGA
* * *
55655003 GAGATCATTAAAAAAAAA
65 GCGATCA-T--CAAAGAA
* *
55655021 TTTTATTATGACAA-AAA-A-AATACTAACTAATAAAATTCGTTAATT
1 TTTT-TTATTACAATAAAGAGAATATTAACTAATAAAATTCGTTAATT
55655066 GATTAGTGAT
Statistics
Matches: 311, Mismatches: 39, Indels: 23
0.83 0.10 0.06
Matches are distributed among these distances:
76 47 0.15
77 3 0.01
78 42 0.14
79 133 0.43
80 18 0.06
81 2 0.01
82 66 0.21
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.36
Consensus pattern (79 bp):
TTTTTTATTACAATAAAGAGAATATTAACTAATAAAATTCGTTAATTTCGTTAGTGACATGTGAG
CGATCATCAAAGAA
Found at i:55656788 original size:22 final size:22
Alignment explanation
Indices: 55656760--55656804 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
55656750 TTGGCACACC
55656760 TGCCCATCACCACAAGATAATA
1 TGCCCATCACCACAAGATAATA
55656782 TGCCCATCACCACAAGATAATA
1 TGCCCATCACCACAAGATAATA
55656804 T
1 T
55656805 AAACTCATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.31, G:0.09, T:0.20
Consensus pattern (22 bp):
TGCCCATCACCACAAGATAATA
Found at i:55659432 original size:81 final size:79
Alignment explanation
Indices: 55659092--55659729 Score: 684
Period size: 78 Copynumber: 8.2 Consensus size: 79
55659082 AATTTGTGAC
* * * *
55659092 GATCGTTCATACGTCACTAACG-AATTAACAAATTTTATTAGTTAATATTTATTTTATTGTAATA
1 GATCGCTCACACGTCACTAACGAAATTAACGAATTTTATTAGTTAATATTT-CTTTATTGTAATA
*
55659156 AAAAAAAT-TTTAAT
65 AAAAAAATCTTTGAT
* ** *
55659170 GATCGCTCA-ACGT-ACCTAATGAAATTAAAAAATTTTATTAGTTAATATTTTTTTATTGTAATA
1 GATCGCTCACACGTCA-CTAACGAAATTAACGAATTTTATTAGTTAATATTTCTTTATTGTAATA
* * *
55659233 AAAGACATCTTTAAT
65 AAAAAAATCTTTGAT
** *
55659248 GATCATTCA-ACGTCACTAACGAAATTAACGAATTTTATTAGTTAA-ATTTTTTTATTGTAATAA
1 GATCGCTCACACGTCACTAACGAAATTAACGAATTTTATTAGTTAATATTTCTTTATTGTAATAA
* * *
55659311 AAGACATCTTTAAT
66 AAAAAATCTTTGAT
* * * *
55659325 GACCGCTCACACGTCACTACCGAAATTAACGAGTTTTATTAGTTAACATTCTCTTTATTGTAATA
1 GATCGCTCACACGTCACTAACGAAATTAACGAATTTTATTAGTTAATATT-TCTTTATTGTAATA
55659390 AAAAAAATTCTTTGAT
65 AAAAAAA-TCTTTGAT
* * * *
55659406 GATCACTCACACATCACTAACGAAATTAACGAATTTTATTAGTTAATGTTCACTTTATTGTAATA
1 GATCGCTCACACGTCACTAACGAAATTAACGAATTTTATTAGTTAATATT-TCTTTATTGTAATA
*
55659471 AAAAAATTAC-TTGAT
65 AAAAAAAT-CTTTGAT
* * *
55659486 GATCGCTCACACGTCACTACCGAAATTAACGAGTTTTATTAGTTAACATTCTCTTTATTGTAAT-
1 GATCGCTCACACGTCACTAACGAAATTAACGAATTTTATTAGTTAATATT-TCTTTATTGTAATA
*
55659550 AAAAAATTCTTTGAT
65 AAAAAAATCTTTGAT
* *
55659565 GATCACTCACACATCACTAACGAAATTAACGAATTTTATTA-TT--TA-------A-TGTAATAA
1 GATCGCTCACACGTCACTAACGAAATTAACGAATTTTATTAGTTAATATTTCTTTATTGTAATAA
* *
55659619 AAAAATTTTATTTGAT
66 AAAAA--ATCTTTGAT
* * * *
55659635 GATTGCTCACACGTCACTAACGAAATTAACGAATTTTATCAGTTAATATTCTCCTTATTGTAAGA
1 GATCGCTCACACGTCACTAACGAAATTAACGAATTTTATTAGTTAATATT-TCTTTATTGTAATA
*
55659700 AAAAAACATATTTGAT
65 AAAAAA-ATCTTTGAT
55659716 GATCGCTCACACGT
1 GATCGCTCACACGT
55659730 GTTGATGTTT
Statistics
Matches: 486, Mismatches: 49, Indels: 47
0.84 0.08 0.08
Matches are distributed among these distances:
67 6 0.01
68 7 0.01
70 45 0.09
71 2 0.00
73 2 0.00
76 2 0.00
77 66 0.14
78 116 0.24
79 54 0.11
80 81 0.17
81 93 0.19
82 12 0.02
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (79 bp):
GATCGCTCACACGTCACTAACGAAATTAACGAATTTTATTAGTTAATATTTCTTTATTGTAATAA
AAAAAATCTTTGAT
Found at i:55659448 original size:159 final size:157
Alignment explanation
Indices: 55659105--55659727 Score: 735
Period size: 161 Copynumber: 4.0 Consensus size: 157
55659095 CGTTCATACG
*
55659105 TCACTAACG-AATTAACAAATTTTATTAGTTAATATTTATTTTATTGTAATAAAAAAAATTTTAA
1 TCACTAACGAAATTAACGAATTTTATTAGTTAA-ATTTATTTTATTGTAAT-AAAAAAATTTTAA
* ** * *
55659169 TGATCGCTCA-ACGT-ACCTAATGAAATTAAAAAATTTTATTAGTTAATATT-TTTTTATTGTAA
64 TGATCGCTCACACGTCA-CTAACGAAATTAACGAATTTTATTAGTTAACATTCTCTTTATTGTAA
* * * * *
55659231 TAAAAGACATCTTTAATGATCATTCA-ACG
128 TAAAAAAAATCTTTGATGATCACTCACACA
*
55659260 TCACTAACGAAATTAACGAATTTTATTAGTTAAATTT-TTTTATTGTAATAAAAGACATCTTTAA
1 TCACTAACGAAATTAACGAATTTTATTAGTTAAATTTATTTTATTGTAATAAAA-AAAT-TTTAA
* * *
55659324 TGACCGCTCACACGTCACTACCGAAATTAACGAGTTTTATTAGTTAACATTCTCTTTATTGTAAT
64 TGATCGCTCACACGTCACTAACGAAATTAACGAATTTTATTAGTTAACATTCTCTTTATTGTAAT
55659389 AAAAAAAATTCTTTGATGATCACTCACACA
129 AAAAAAAA-TCTTTGATGATCACTCACACA
*
55659419 TCACTAACGAAATTAACGAATTTTATTAGTT-AATGTTCACTTTATTGTAATAAAAAAATTACTT
1 TCACTAACGAAATTAACGAATTTTATTAGTTAAAT-TT-ATTTTATTGTAATAAAAAAATT--TT
* * *
55659483 GATGATCGCTCACACGTCACTACCGAAATTAACGAGTTTTATTAGTTAACATTCTCTTTATTGTA
62 AATGATCGCTCACACGTCACTAACGAAATTAACGAATTTTATTAGTTAACATTCTCTTTATTGTA
*
55659548 AT-AAAAAATTCTTTGATGATCACTCACACA
127 ATAAAAAAAATCTTTGATGATCACTCACACA
55659578 TCACTAACGAAATTAACGAA--TT-TTA-TT--ATTTA----A-TGTAATAAAAAAATTTTATTT
1 TCACTAACGAAATTAACGAATTTTATTAGTTAAATTTATTTTATTGTAATAAAAAAATTTTA---
* * * *
55659632 GATGATTGCTCACACGTCACTAACGAAATTAACGAATTTTATCAGTTAATATTCTCCTTATTGTA
63 -ATGATCGCTCACACGTCACTAACGAAATTAACGAATTTTATTAGTTAACATTCTCTTTATTGTA
* * *
55659697 AGAAAAAAACATATTTGATGATCGCTCACAC
127 ATAAAAAAA-ATCTTTGATGATCACTCACAC
55659728 GTGTTGATGT
Statistics
Matches: 418, Mismatches: 31, Indels: 42
0.85 0.06 0.09
Matches are distributed among these distances:
145 2 0.00
147 15 0.04
148 1 0.00
149 59 0.14
150 6 0.01
151 18 0.04
152 1 0.00
153 6 0.01
154 17 0.04
155 29 0.07
156 57 0.14
157 21 0.05
158 18 0.04
159 77 0.18
160 9 0.02
161 82 0.20
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (157 bp):
TCACTAACGAAATTAACGAATTTTATTAGTTAAATTTATTTTATTGTAATAAAAAAATTTTAATG
ATCGCTCACACGTCACTAACGAAATTAACGAATTTTATTAGTTAACATTCTCTTTATTGTAATAA
AAAAAATCTTTGATGATCACTCACACA
Found at i:55659621 original size:67 final size:69
Alignment explanation
Indices: 55659539--55659673 Score: 202
Period size: 70 Copynumber: 2.0 Consensus size: 69
55659529 TAACATTCTC
* *
55659539 TTTATTGTAAT-AAAAAA-TTCTTTGATGATCACTCACACATCACTAACGAAATTAACGAATTTT
1 TTTAATGTAATAAAAAAATTTATTTGATGATCACTCACACATCACTAACGAAATTAACGAATTTT
55659602 ATTA
66 ATTA
** *
55659606 TTTAATGTAATAAAAAAATTTTATTTGATGATTGCTCACACGTCACTAACGAAATTAACGAATTT
1 TTTAATGTAATAAAAAAA-TTTATTTGATGATCACTCACACATCACTAACGAAATTAACGAATTT
55659671 TAT
65 TAT
55659674 CAGTTAATAT
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
67 10 0.17
68 6 0.10
70 44 0.73
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (69 bp):
TTTAATGTAATAAAAAAATTTATTTGATGATCACTCACACATCACTAACGAAATTAACGAATTTT
ATTA
Found at i:55662792 original size:21 final size:22
Alignment explanation
Indices: 55662768--55662814 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
55662758 TGTTTAGAAC
*
55662768 AATAATA-TGTTAT-AATATTAA
1 AATAATATTGTAATAAAT-TTAA
55662789 AATAATATTGTAATAAATTTAA
1 AATAATATTGTAATAAATTTAA
55662811 AATA
1 AATA
55662815 TACTAACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 7 0.30
22 13 0.57
23 3 0.13
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (22 bp):
AATAATATTGTAATAAATTTAA
Found at i:55666843 original size:21 final size:21
Alignment explanation
Indices: 55666796--55666848 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
55666786 ACCATTGTTT
* * *
55666796 CTAATCTCACTACTACAGTAT
1 CTAATCTCACCACTACAATAA
* *
55666817 CCAATCTCACCACTATAATAA
1 CTAATCTCACCACTACAATAA
55666838 CTAATCTCACC
1 CTAATCTCACC
55666849 GCCACCGCTG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.36, C:0.34, G:0.02, T:0.28
Consensus pattern (21 bp):
CTAATCTCACCACTACAATAA
Found at i:55667671 original size:20 final size:21
Alignment explanation
Indices: 55667637--55667678 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
55667627 CCCGCTATCC
55667637 AATAAAAACCTAAAATT-CCT
1 AATAAAAACCTAAAATTGCCT
55667657 AATAATAAACC-AAAATTGCCT
1 AATAA-AAACCTAAAATTGCCT
55667678 A
1 A
55667679 TCCGATTAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.55, C:0.19, G:0.02, T:0.24
Consensus pattern (21 bp):
AATAAAAACCTAAAATTGCCT
Found at i:55667807 original size:32 final size:32
Alignment explanation
Indices: 55667766--55667831 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
55667756 GAACACAAAA
*
55667766 TATAAATTTATATCAAATT-TGATTATTTAGCT
1 TATAAATTTATATCAAATTCAG-TTATTTAGCT
55667798 TATAAATTTATATCAAATTCAGTTATTTAGCT
1 TATAAATTTATATCAAATTCAGTTATTTAGCT
55667830 TA
1 TA
55667832 GGTAAAAACT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 31 0.97
33 1 0.03
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (32 bp):
TATAAATTTATATCAAATTCAGTTATTTAGCT
Found at i:55670259 original size:36 final size:36
Alignment explanation
Indices: 55670203--55670390 Score: 232
Period size: 36 Copynumber: 4.9 Consensus size: 36
55670193 AAGCTATCAT
55670203 TTATCACTTTGTCACTTGATCAGATAAGTATAGCAC
1 TTATCACTTTGTCACTTGATCAGATAAGTATAGCAC
* *
55670239 TTATCACTTTTTCACATGATCAGATAAGTATAGCAC
1 TTATCACTTTGTCACTTGATCAGATAAGTATAGCAC
*
55670275 TTATCACTTTTTCACTTGATCAGATAAGTGTAGATAAAGCTACCAC
1 TTATCACTTTGTCACTTGATCAGATAA--GT--AT--AG----CAC
* *
55670321 TTATCACTTTGTCTCTTGATCAGATAAGTGTAGCAC
1 TTATCACTTTGTCACTTGATCAGATAAGTATAGCAC
*
55670357 TTATCACTTTGTCACTTGATCAGATAAGTGTAGC
1 TTATCACTTTGTCACTTGATCAGATAAGTATAGC
55670391 TAAAGCTACC
Statistics
Matches: 135, Mismatches: 7, Indels: 20
0.83 0.04 0.12
Matches are distributed among these distances:
36 96 0.71
38 2 0.01
40 4 0.03
42 3 0.02
44 2 0.01
46 28 0.21
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (36 bp):
TTATCACTTTGTCACTTGATCAGATAAGTATAGCAC
Found at i:55670311 original size:46 final size:46
Alignment explanation
Indices: 55670272--55670426 Score: 168
Period size: 46 Copynumber: 3.6 Consensus size: 46
55670262 ATAAGTATAG
* *
55670272 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGATAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGATAAAGATAC
*
55670318 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T--AG----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGATAAAGATAC
* *
55670354 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGATAAAGATAC
* **
55670400 CACTTATCACTTTATCTTTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
55670427 AGTACTCAAA
Statistics
Matches: 93, Mismatches: 6, Indels: 20
0.78 0.05 0.17
Matches are distributed among these distances:
36 29 0.31
38 2 0.02
39 1 0.01
40 3 0.03
42 3 0.03
43 1 0.01
44 2 0.02
46 52 0.56
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.37
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGATAAAGATAC
Found at i:55670331 original size:118 final size:115
Alignment explanation
Indices: 55670157--55670390 Score: 351
Period size: 118 Copynumber: 2.0 Consensus size: 115
55670147 TATGTATGAT
* * *
55670157 CACTTATCATTTGTCCCTGATCAGATAAGTGTAGCTAAGCTATCATTTATCACTTTGTCACTTGA
1 CACTTATCATTTGTCCCTGATCAGATAAGTGTAGATAAGCTACCACTTATCACTTTGTCACTTGA
*
55670222 TCAGATAAGTATAGCACTTATCACTTTTTCACATGATCAGATAAGTATAG
66 TCAGATAAGTATAGCACTTATCACTTTGTCACATGATCAGATAAGTATAG
* * *
55670272 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGATAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCA-TTTGTC-CCTGATCAGATAAGTGTAGAT-AAGCTACCACTTATCACTTTGTCACT
* * *
55670337 TGATCAGATAAGTGTAGCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
63 TGATCAGATAAGTATAGCACTTATCACTTTGTCACATGATCAGATAAGTATAG
55670390 C
1 C
55670391 TAAAGCTACC
Statistics
Matches: 106, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
115 9 0.08
116 5 0.05
117 19 0.18
118 73 0.69
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (115 bp):
CACTTATCATTTGTCCCTGATCAGATAAGTGTAGATAAGCTACCACTTATCACTTTGTCACTTGA
TCAGATAAGTATAGCACTTATCACTTTGTCACATGATCAGATAAGTATAG
Found at i:55670422 original size:82 final size:82
Alignment explanation
Indices: 55670236--55670426 Score: 310
Period size: 82 Copynumber: 2.3 Consensus size: 82
55670226 ATAAGTATAG
* * * *
55670236 CACTTATCACTTTTTCACATGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATA
1 CACTTATCACTTTATCTCTTGATCAGATAAGTATAGCACTTATCACTTTGTCACTTGATCAGATA
55670301 AGTGTAGATAAAGCTAC
66 AGTGTAGATAAAGCTAC
* *
55670318 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCACTTATCACTTTGTCACTTGATCAGATA
1 CACTTATCACTTTATCTCTTGATCAGATAAGTATAGCACTTATCACTTTGTCACTTGATCAGATA
*
55670383 AGTGTAGCTAAAGCTAC
66 AGTGTAGATAAAGCTAC
*
55670400 CACTTATCACTTTATCTTTTGATCAGA
1 CACTTATCACTTTATCTCTTGATCAGA
55670427 AGTACTCAAA
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 101 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (82 bp):
CACTTATCACTTTATCTCTTGATCAGATAAGTATAGCACTTATCACTTTGTCACTTGATCAGATA
AGTGTAGATAAAGCTAC
Found at i:55682846 original size:10 final size:9
Alignment explanation
Indices: 55682816--55682875 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
55682806 TATTATTATG
*
55682816 ATTTTTATA
1 ATTTTAATA
* *
55682825 GTTTTGATA
1 ATTTTAATA
55682834 ATTTTATATA
1 ATTTTA-ATA
55682844 ATTTTAATA
1 ATTTTAATA
* *
55682853 CTTGTAATA
1 ATTTTAATA
55682862 GATTTT-ATA
1 -ATTTTAATA
55682871 ATTTT
1 ATTTT
55682876 TATGAGTTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
8 5 0.12
9 24 0.59
10 12 0.29
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (9 bp):
ATTTTAATA
Found at i:55682886 original size:19 final size:18
Alignment explanation
Indices: 55682811--55682911 Score: 69
Period size: 19 Copynumber: 5.3 Consensus size: 18
55682801 TTTTTTATTA
*
55682811 TTATGATTTTTATAGTTT
1 TTATAATTTTTATAGTTT
* *
55682829 TGATAATTTTATATAATTT
1 TTATAATTTT-TATAGTTT
* * * * *
55682848 TAATACTTGTAATAGATT
1 TTATAATTTTTATAGTTT
55682866 TTATAATTTTTATGAGTTT
1 TTATAATTTTTAT-AGTTT
55682885 TTATAGAATTTTGT-TATGTTT
1 TTAT--AATTTT-TATA-GTTT
55682906 TTATAA
1 TTATAA
55682912 AAATTTAAAT
Statistics
Matches: 63, Mismatches: 14, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
18 22 0.35
19 24 0.38
20 1 0.02
21 15 0.24
22 1 0.02
ACGTcount: A:0.31, C:0.01, G:0.10, T:0.58
Consensus pattern (18 bp):
TTATAATTTTTATAGTTT
Found at i:55682890 original size:28 final size:27
Alignment explanation
Indices: 55682811--55682896 Score: 75
Period size: 28 Copynumber: 3.1 Consensus size: 27
55682801 TTTTTTATTA
* *
55682811 TTATGATTTTTATAGTTTTGATA-ATTT
1 TTATAATTTTTATAGTTTTAATAGA-TT
* * *
55682838 TATATAATTTTAATACTTGTAATAGATT
1 T-TATAATTTTTATAGTTTTAATAGATT
*
55682866 TTATAATTTTTATGAGTTTTTATAGAATT
1 TTATAATTTTTAT-AGTTTTAATAG-ATT
55682895 TT
1 TT
55682897 GTTATGTTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
27 12 0.26
28 28 0.61
29 6 0.13
ACGTcount: A:0.31, C:0.01, G:0.09, T:0.58
Consensus pattern (27 bp):
TTATAATTTTTATAGTTTTAATAGATT
Found at i:55682905 original size:21 final size:20
Alignment explanation
Indices: 55682864--55682939 Score: 66
Period size: 22 Copynumber: 3.7 Consensus size: 20
55682854 TTGTAATAGA
*
55682864 TTTTAT-AATTTTTATGA-GT
1 TTTTATAAATTTTAAT-ATGT
**
55682883 TTTTATAGAATTTTGTTATGT
1 TTTTATA-AATTTTAATATGT
*
55682904 TTTTATAAAAATTTAAATATGT
1 TTTTAT--AAATTTTAATATGT
55682926 TTTTATAAATTTTA
1 TTTTATAAATTTTA
55682940 TTTTTATTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
19 6 0.13
20 8 0.17
21 15 0.33
22 16 0.35
23 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (20 bp):
TTTTATAAATTTTAATATGT
Found at i:55682973 original size:28 final size:28
Alignment explanation
Indices: 55682920--55682974 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
55682910 AAAAATTTAA
*
55682920 ATATGTTTTTATAAATTTTATTTTTATT
1 ATATGTTTTTATAAATTTTATCTTTATT
55682948 ATAT-TTTTTAT-AATATTTATACTTTAT
1 ATATGTTTTTATAAAT-TTTAT-CTTTAT
55682975 ATCTATTTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 3 0.12
27 12 0.50
28 9 0.38
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (28 bp):
ATATGTTTTTATAAATTTTATCTTTATT
Found at i:55685016 original size:19 final size:19
Alignment explanation
Indices: 55684992--55685083 Score: 157
Period size: 19 Copynumber: 4.8 Consensus size: 19
55684982 AATCATATAT
55684992 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
55685011 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
55685030 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
55685049 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
55685068 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
55685084 CTAAAAAATT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 67 1.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:55685039 original size:38 final size:38
Alignment explanation
Indices: 55684969--55685083 Score: 158
Period size: 38 Copynumber: 2.9 Consensus size: 38
55684959 AAATTAAATC
*
55684969 TCTAAGATTACAAAATCATATATTCTAAGATTGCATATCATA
1 TCTAAGATTAC-ATATC--ATA-TCTAAGATTGCATATCATA
*
55685011 TCTAAGATTATATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
* *
55685049 TCTAGGATTGCATATCATATCTAAGATTGCATATC
1 TCTAAGATTACATATCATATCTAAGATTGCATATC
55685084 CTAAAAAATT
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
38 51 0.75
39 3 0.04
41 4 0.06
42 10 0.15
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:55687780 original size:3 final size:3
Alignment explanation
Indices: 55687772--55687857 Score: 102
Period size: 3 Copynumber: 28.7 Consensus size: 3
55687762 TTTAGCAATT
* *
55687772 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TCT- TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
* * **
55687817 TTA TTA TTA TTA TTA TTA TTA TCA ATA TTA TGG TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
55687858 GTGATGTTTT
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
2 1 0.01
3 67 0.97
4 1 0.01
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:55688149 original size:18 final size:18
Alignment explanation
Indices: 55688112--55688148 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
55688102 TTTTAAAATG
55688112 TATTTCATATATTTTATA
1 TATTTCATATATTTTATA
*
55688130 TATTTCGTA-A-TTTATA
1 TATTTCATATATTTTATA
55688146 TAT
1 TAT
55688149 ACACACATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 9 0.50
17 1 0.06
18 8 0.44
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.59
Consensus pattern (18 bp):
TATTTCATATATTTTATA
Found at i:55696446 original size:6 final size:6
Alignment explanation
Indices: 55696435--55696461 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
55696425 ATAAATAATA
55696435 AAATTT AAATTT AAATTT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAA
55696462 ATACATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (6 bp):
AAATTT
Found at i:55697135 original size:41 final size:41
Alignment explanation
Indices: 55697090--55697179 Score: 119
Period size: 41 Copynumber: 2.2 Consensus size: 41
55697080 GCTTAGCACG
* *
55697090 CCCGTGTGCTAG-TCATGTGTCTCACATGACCTAGTCACACT
1 CCCGTGTGCTAGCT-ATGTGTCTCACACGACCTAGTCACACA
* *
55697131 CCCGTGTGCTAGCTGTGTGTCTCACACGGCCTAGTCACACA
1 CCCGTGTGCTAGCTATGTGTCTCACACGACCTAGTCACACA
*
55697172 CCCATGTG
1 CCCGTGTG
55697180 TCTGGCCATG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 42 0.98
42 1 0.02
ACGTcount: A:0.18, C:0.33, G:0.22, T:0.27
Consensus pattern (41 bp):
CCCGTGTGCTAGCTATGTGTCTCACACGACCTAGTCACACA
Found at i:55698202 original size:40 final size:40
Alignment explanation
Indices: 55698158--55698287 Score: 124
Period size: 40 Copynumber: 3.3 Consensus size: 40
55698148 ATACACCAGT
**
55698158 TTGACACCCAGTGCCTCATCAGATAATTCGAAGTAATAAA
1 TTGACACCCAGTGCCTCATCAGATAAACCGAAGTAATAAA
* *
55698198 TTGACACCCAGTGTCTCATCAGTTAAACCGAAG---TAAA
1 TTGACACCCAGTGCCTCATCAGATAAACCGAAGTAATAAA
* * * * *
55698235 TTGGCATCCAGTACCTCATC-GAACAAATCCGAAGTGATAAA
1 TTGACACCCAGTGCCTCATCAG-ATAAA-CCGAAGTAATAAA
*
55698276 TTGGCACCCAGT
1 TTGACACCCAGT
55698288 CATCAACTCA
Statistics
Matches: 74, Mismatches: 11, Indels: 9
0.79 0.12 0.10
Matches are distributed among these distances:
36 1 0.01
37 23 0.31
38 6 0.08
40 29 0.39
41 15 0.20
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.24
Consensus pattern (40 bp):
TTGACACCCAGTGCCTCATCAGATAAACCGAAGTAATAAA
Found at i:55704199 original size:19 final size:19
Alignment explanation
Indices: 55704148--55704205 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
55704138 ATATACTTAA
*
55704148 ATATTAAATAAACATAT-T
1 ATATTAAATATACATATGT
*
55704166 TTATTAATATATACATATGT
1 ATATTAA-ATATACATATGT
* *
55704186 ATATTAAATTTACACATGT
1 ATATTAAATATACATATGT
55704205 A
1 A
55704206 ATCACTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
18 6 0.18
19 20 0.61
20 7 0.21
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (19 bp):
ATATTAAATATACATATGT
Found at i:55714438 original size:34 final size:34
Alignment explanation
Indices: 55714395--55714463 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
55714385 TGTATTATAA
55714395 TTTAGTATATATACACACGCATATTCATGCATGC
1 TTTAGTATATATACACACGCATATTCATGCATGC
55714429 TTTAGTATATATACACACGCATATTCATGCATGC
1 TTTAGTATATATACACACGCATATTCATGCATGC
55714463 T
1 T
55714464 ATCTGATGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (34 bp):
TTTAGTATATATACACACGCATATTCATGCATGC
Found at i:55716439 original size:22 final size:18
Alignment explanation
Indices: 55716387--55716444 Score: 77
Period size: 17 Copynumber: 3.4 Consensus size: 18
55716377 TTTTTATGTT
55716387 TTATA-AATATTATTTTA
1 TTATATAATATTATTTTA
55716404 TTATATAATA-TATTTTA
1 TTATATAATATTATTTTA
* *
55716421 TTATATTA-ATTATATTA
1 TTATATAATATTATTTTA
55716438 TTATATA
1 TTATATA
55716445 TTAAATAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
16 1 0.03
17 31 0.86
18 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTATATAATATTATTTTA
Found at i:55719555 original size:22 final size:21
Alignment explanation
Indices: 55719530--55719589 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 21
55719520 CTATACAAAT
55719530 AGCATAAATGTGCTAAACGGAG
1 AGCAT-AATGTGCTAAACGGAG
*
55719552 AGCATTAATGTGCTAAACTGAG
1 AGCA-TAATGTGCTAAACGGAG
55719574 AGCACTAATGTGCTAA
1 AGCA-TAATGTGCTAA
55719590 TAATCGGAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 34 0.97
23 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (21 bp):
AGCATAATGTGCTAAACGGAG
Found at i:55720841 original size:70 final size:70
Alignment explanation
Indices: 55720728--55720867 Score: 217
Period size: 70 Copynumber: 2.0 Consensus size: 70
55720718 CTCAGATATA
* * * *
55720728 AAAAAGAGATCATACCCAGTAAATTAGGACACGATCTTTTCTTACTTCCCGAGATCTTTTAAAAC
1 AAAAAGAGATCATACCCAGTAAATTAGGACACAATCTCTTCTTAATTCCCGAGATCGTTTAAAAC
55720793 TTGAG
66 TTGAG
* * *
55720798 AAAAAGAGATCATGCCCAGTAAGTTAGGACACAATCTCTTCTTAATTCTCGAGATCGTTTAAAAC
1 AAAAAGAGATCATACCCAGTAAATTAGGACACAATCTCTTCTTAATTCCCGAGATCGTTTAAAAC
55720863 TTGAG
66 TTGAG
55720868 TTTGAAAAGA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
70 63 1.00
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (70 bp):
AAAAAGAGATCATACCCAGTAAATTAGGACACAATCTCTTCTTAATTCCCGAGATCGTTTAAAAC
TTGAG
Found at i:55721520 original size:26 final size:27
Alignment explanation
Indices: 55721483--55721534 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
55721473 ATATATACAC
*
55721483 AAATTTACAATAAATAATATATAAAAG
1 AAATTTACAATAAATAATACATAAAAG
*
55721510 AAATTTA-AATAAATTATACATAAAA
1 AAATTTACAATAAATAATACATAAAA
55721535 CAGTTCAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (27 bp):
AAATTTACAATAAATAATACATAAAAG
Found at i:55722465 original size:15 final size:15
Alignment explanation
Indices: 55722430--55722466 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 15
55722420 GTACAAAAAC
55722430 AAAAATAAAAGAGAT
1 AAAAATAAAAGAGAT
55722445 AAAAAATAAAAAGAGAT
1 -AAAAAT-AAAAGAGAT
55722462 AAAAA
1 AAAAA
55722467 CAATAAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (15 bp):
AAAAATAAAAGAGAT
Found at i:55722474 original size:19 final size:17
Alignment explanation
Indices: 55722430--55722466 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
55722420 GTACAAAAAC
55722430 AAAAAT-AAAAGAGATA
1 AAAAATAAAAAGAGATA
55722446 AAAAATAAAAAGAGATA
1 AAAAATAAAAAGAGATA
55722463 AAAA
1 AAAA
55722467 CAATAAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (17 bp):
AAAAATAAAAAGAGATA
Found at i:55723020 original size:21 final size:22
Alignment explanation
Indices: 55722996--55723050 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 22
55722986 AACAACGGTG
55722996 GCGGTGAGATTAGG-TACTGTA
1 GCGGTGAGATTAGGATACTGTA
55723017 GCGGTGAGATT-GGATACTGTA
1 GCGGTGAGATTAGGATACTGTA
**
55723038 GCAATGAGATTAG
1 GCGGTGAGATTAG
55723051 AAACAACGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 2 0.07
21 27 0.90
22 1 0.03
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.27
Consensus pattern (22 bp):
GCGGTGAGATTAGGATACTGTA
Found at i:55723237 original size:18 final size:18
Alignment explanation
Indices: 55723214--55723347 Score: 90
Period size: 18 Copynumber: 7.9 Consensus size: 18
55723204 TTATTATTAA
55723214 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
55723232 ATATAATTTAAT-AAAAT
1 ATATAATTTAATAAAAAT
*
55723249 ATATGAATTTACT-AAAAT
1 ATAT-AATTTAATAAAAAT
* * *
55723267 -TATAATAT-ATAATATT
1 ATATAATTTAATAAAAAT
* * *
55723283 ATAAAATATAATTTAAAAT
1 ATATAATTTAA-TAAAAAT
* *
55723302 A-ATTA-TT-AT--CAA-
1 ATATAATTTAATAAAAAT
*
55723314 ATATAATTTAACAAAAAT
1 ATATAATTTAATAAAAAT
55723332 ATATAATTTAATAAAA
1 ATATAATTTAATAAAA
55723348 TTCTTAGTAT
Statistics
Matches: 88, Mismatches: 17, Indels: 22
0.69 0.13 0.17
Matches are distributed among these distances:
12 1 0.01
13 5 0.06
14 2 0.02
15 3 0.03
16 8 0.09
17 22 0.25
18 42 0.48
19 5 0.06
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:55723285 original size:15 final size:15
Alignment explanation
Indices: 55723265--55723320 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 15
55723255 ATTTACTAAA
*
55723265 ATTATAATATATAAT
1 ATTATAAAATATAAT
55723280 ATTATAAAATAT-A-
1 ATTATAAAATATAAT
*
55723293 ATT-TAAAATA-ATT
1 ATTATAAAATATAAT
*
55723306 ATTATCAAATATAAT
1 ATTATAAAATATAAT
55723321 TTAACAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
12 7 0.21
13 6 0.18
14 7 0.21
15 13 0.39
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
ATTATAAAATATAAT
Found at i:55723333 original size:59 final size:57
Alignment explanation
Indices: 55723270--55723468 Score: 181
Period size: 59 Copynumber: 3.4 Consensus size: 57
55723260 CTAAAATTAT
55723270 AATATATAATATT-ATAAAATATAATTTAAAATAATTATTATCAAATATAATTTAACAAA
1 AATATATAAT-TTAATAAAATATAATTT-AAATAATTATTAT-AAATATAATTTAACAAA
* * * * * ** *
55723329 AATATATAATTTAATAAAATTCTTAGTATTAAAT-ATTCTTATATGAATTTACTAAAATC-AT
1 AATATATAATTTAATAAAA-T-ATAAT-TTAAATAATTATTATA--AATATAATTTAA-CAAA
*
55723390 AATATATAATACT-ATAAAATATAATTTTAAATAATTATTATTAAATATAATTTAACAAA
1 AATATATAAT-TTAATAAAATATAA-TTTAAATAATTATTA-TAAATATAATTTAACAAA
55723449 AATATATAATTTAATAAAAT
1 AATATATAATTTAATAAAAT
55723469 TCTTAGTATT
Statistics
Matches: 109, Mismatches: 18, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
58 4 0.04
59 51 0.47
60 16 0.15
61 34 0.31
62 4 0.04
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (57 bp):
AATATATAATTTAATAAAATATAATTTAAATAATTATTATAAATATAATTTAACAAA
Found at i:55723381 original size:120 final size:120
Alignment explanation
Indices: 55723248--55723490 Score: 450
Period size: 120 Copynumber: 2.0 Consensus size: 120
55723238 TTTAATAAAA
* *
55723248 TATATGAATTTACTAAAATTATAATATATAATATTATAAAATATAATTTAAAATAATTATTATCA
1 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATCA
55723313 AATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
66 AATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
* *
55723368 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTTAAATAATTATTATTA
1 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATCA
55723433 AATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
66 AATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
55723488 TAT
1 TAT
55723491 GATTGTATCA
Statistics
Matches: 119, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 119 1.00
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATCA
AATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
Found at i:55723397 original size:61 final size:60
Alignment explanation
Indices: 55723298--55723490 Score: 178
Period size: 61 Copynumber: 3.2 Consensus size: 60
55723288 ATATAATTTA
* * **
55723298 AAATAATTATTATCAAATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATT
1 AAAT-ATTCTTATTAAATATAATAAAACAAAAATATATAATTTAATAAAATTCTTAGTATT
* * * * * * * *
55723359 AAATATTCTTATATGAATTTACTAAAATC-ATAATATATAATACT-ATAAAA-T-ATAATTTT
1 AAATATTCTTAT-TAAATATAATAAAA-CAAAAATATATAAT-TTAATAAAATTCTTAGTATT
* **
55723418 AAATAATTATTATTAAATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATT
1 AAAT-ATTCTTATTAAATATAATAAAACAAAAATATATAATTTAATAAAATTCTTAGTATT
55723479 AAATATTCTTAT
1 AAATATTCTTAT
55723491 GATTGTATCA
Statistics
Matches: 100, Mismatches: 24, Indels: 17
0.71 0.17 0.12
Matches are distributed among these distances:
58 2 0.02
59 35 0.35
60 23 0.23
61 38 0.38
62 2 0.02
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (60 bp):
AAATATTCTTATTAAATATAATAAAACAAAAATATATAATTTAATAAAATTCTTAGTATT
Found at i:55726561 original size:6 final size:6
Alignment explanation
Indices: 55726550--55726587 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
55726540 TTTGCAAACC
*
55726550 AAGGGG AAGGGG AAAGGG AAGGGG AAGGGG AAAGGGG A
1 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG -AAGGGG A
55726588 GAAGAAGGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (6 bp):
AAGGGG
Found at i:55726573 original size:18 final size:18
Alignment explanation
Indices: 55726550--55726585 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
55726540 TTTGCAAACC
55726550 AAGGGGAAGGGGAAAGGG
1 AAGGGGAAGGGGAAAGGG
55726568 AAGGGGAAGGGGAAAGGG
1 AAGGGGAAGGGGAAAGGG
55726586 GAGAAGAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (18 bp):
AAGGGGAAGGGGAAAGGG
Found at i:55726594 original size:18 final size:18
Alignment explanation
Indices: 55726555--55726596 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
55726545 AAACCAAGGG
**
55726555 GAAGGGGAAAGGGAAGGG
1 GAAGGGGAAAGGGAAGAA
*
55726573 GAAGGGGAAAGGGGAGAA
1 GAAGGGGAAAGGGAAGAA
55726591 GAAGGG
1 GAAGGG
55726597 TAACCAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (18 bp):
GAAGGGGAAAGGGAAGAA
Found at i:55728264 original size:13 final size:13
Alignment explanation
Indices: 55728246--55728270 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55728236 AAATTATTCA
55728246 ACCCAACCCAATT
1 ACCCAACCCAATT
55728259 ACCCAACCCAAT
1 ACCCAACCCAAT
55728271 AAAACTAAAA
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:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:55728318 original size:38 final size:39
Alignment explanation
Indices: 55728251--55728325 Score: 116
Period size: 38 Copynumber: 1.9 Consensus size: 39
55728241 ATTCAACCCA
*
55728251 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
1 ACCCAATTACCCAACCCAATAAAAATAAAACTAAAGTCT
* *
55728290 ACCCAATTA-TCAACTCAATAAAAATAAAACTAAAGT
1 ACCCAATTACCCAACCCAATAAAAATAAAACTAAAGT
55728326 TTAACTCTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 24 0.73
39 9 0.27
ACGTcount: A:0.52, C:0.25, G:0.03, T:0.20
Consensus pattern (39 bp):
ACCCAATTACCCAACCCAATAAAAATAAAACTAAAGTCT
Found at i:55733930 original size:10 final size:11
Alignment explanation
Indices: 55733915--55733961 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
55733905 CAACTAAATC
55733915 ATTTCTCTC-A
1 ATTTCTCTCAA
*
55733925 ATTTCTCTCTA
1 ATTTCTCTCAA
55733936 ATATTCTCTCAA
1 AT-TTCTCTCAA
*
55733948 ATTCCTCTCAA
1 ATTTCTCTCAA
55733959 ATT
1 ATT
55733962 CCTATTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
10 9 0.27
11 14 0.42
12 10 0.30
ACGTcount: A:0.26, C:0.28, G:0.00, T:0.47
Consensus pattern (11 bp):
ATTTCTCTCAA
Found at i:55733942 original size:12 final size:10
Alignment explanation
Indices: 55733915--55733958 Score: 52
Period size: 10 Copynumber: 4.1 Consensus size: 10
55733905 CAACTAAATC
55733915 ATTTCTCTCA
1 ATTTCTCTCA
55733925 ATTTCTCTCTA
1 ATTTCTCTC-A
55733936 ATATTCTCTCAA
1 AT-TTCTCTC-A
*
55733948 ATTCCTCTCA
1 ATTTCTCTCA
55733958 A
1 A
55733959 ATTCCTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 11 0.37
11 9 0.30
12 10 0.33
ACGTcount: A:0.25, C:0.30, G:0.00, T:0.45
Consensus pattern (10 bp):
ATTTCTCTCA
Found at i:55735787 original size:18 final size:18
Alignment explanation
Indices: 55735764--55735806 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
55735754 TGCCAGGTGC
*
55735764 GTATCCTAACCCTTTTAT
1 GTATCCTAACCCTTATAT
*
55735782 GTATCCTAACTCTTATAT
1 GTATCCTAACCCTTATAT
*
55735800 GTTTCCT
1 GTATCCT
55735807 TTTCCTAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.26, G:0.07, T:0.47
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:55736284 original size:49 final size:49
Alignment explanation
Indices: 55736229--55736347 Score: 202
Period size: 49 Copynumber: 2.4 Consensus size: 49
55736219 TTATATTAAT
* *
55736229 GTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTGAA
1 GTAATAAAATACAAAATAGTTTATTTTGAATATTTTAATATTATTTCAA
*
55736278 GTAATAAAATACAAAATAGTTTATTTTGAATATTTTAATATTATTTCAT
1 GTAATAAAATACAAAATAGTTTATTTTGAATATTTTAATATTATTTCAA
*
55736327 TTAATAAAATACAAAATAGTT
1 GTAATAAAATACAAAATAGTT
55736348 AATATTCTTA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 66 1.00
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (49 bp):
GTAATAAAATACAAAATAGTTTATTTTGAATATTTTAATATTATTTCAA
Found at i:55739664 original size:124 final size:125
Alignment explanation
Indices: 55739444--55739730 Score: 459
Period size: 124 Copynumber: 2.3 Consensus size: 125
55739434 CCCAAACATG
* * *
55739444 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCAATTTCAAAAATTCTTCTGATAAAGCATCTTAC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTTAAAAATTCTTCTGATAAAGCATCCTAC
* * *
55739509 TTGAGGCATTTTTTATACTATTTGCTCAGAAATGTCAACTCGAAATTA-TTTTTCAGGAC
66 TTGAAGCATTTTTTATACTATTTGCTCAGAAACGTCAAATCGAAATTATTTTTTCAGGAC
* * *
55739568 CTACTGTAGCAAAAGCGCGTCCACGTGAGAGCGATTTTAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTTAAAAATTCTTCTGATAAAGCATCCTAC
*
55739633 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAAATCGAAATTATTTTTTCAGGAC
66 TTGAAGCATTTTTTATACTATTTGCTCAGAAACGTCAAATCGAAATTATTTTTTCAGGAC
* *
55739693 CTACTGTATCAAAAACGCGTCCACGTGGGAGCGATTTT
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTT
55739731 CTTAATAAAT
Statistics
Matches: 149, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
124 103 0.69
125 46 0.31
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTTAAAAATTCTTCTGATAAAGCATCCTAC
TTGAAGCATTTTTTATACTATTTGCTCAGAAACGTCAAATCGAAATTATTTTTTCAGGAC
Found at i:55739937 original size:21 final size:21
Alignment explanation
Indices: 55739911--55739951 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
55739901 CCTAAAAATC
* *
55739911 CTAAAAACCCTAATCCTAACT
1 CTAAAAACCCAAAACCTAACT
55739932 CTAAAAACCCAAAACCTAAC
1 CTAAAAACCCAAAACCTAAC
55739952 GTGGAAGAAA
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:0.49, C:0.34, G:0.00, T:0.17
Consensus pattern (21 bp):
CTAAAAACCCAAAACCTAACT
Found at i:55744918 original size:3 final size:3
Alignment explanation
Indices: 55744912--55744943 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
55744902 GGTTGCAGTG
55744912 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
55744944 TCTCCACATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:55761652 original size:15 final size:16
Alignment explanation
Indices: 55761624--55761662 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
55761614 TTTTATTTTT
55761624 TAATTTATATTTAA-AA
1 TAATTTA-ATTTAATAA
55761640 TAATTTAATTTAATAA
1 TAATTTAATTTAATAA
55761656 -AATTTAA
1 TAATTTAA
55761663 CAAAATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATTTAATTTAATAA
Done.