Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 58 of 97
Found at i:23137256 original size:32 final size:33
Alignment explanation
Indices: 23137188--23137275 Score: 135
Period size: 33 Copynumber: 2.7 Consensus size: 33
23137178 TTTTAATATC
23137188 ATATTTTATTTTTATTTTTAATTATAATTTTAT
1 ATATTTTATTTTTATTTTTAATTATAATTTTAT
*
23137221 ATATTTTATTTTTATTTTTAA-TATAATTTTTT
1 ATATTTTATTTTTATTTTTAATTATAATTTTAT
*
23137253 ATATTATATATTTTA-TTTTAATT
1 ATATTTTAT-TTTTATTTTTAATT
23137276 GTAAGTAATT
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
32 24 0.47
33 27 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (33 bp):
ATATTTTATTTTTATTTTTAATTATAATTTTAT
Found at i:23137267 original size:27 final size:25
Alignment explanation
Indices: 23137147--23137267 Score: 69
Period size: 25 Copynumber: 4.8 Consensus size: 25
23137137 TTTATCATTA
*
23137147 ATTTTTATATAATATTATTTTTTAA-AT
1 ATTTTTATAT--TA-TATATTTTAATAT
* * *
23137174 ATGTTTT-TAATATCATATTTTATTTTT
1 AT-TTTTATATTAT-ATATTTTA-ATAT
23137201 ATTTTTA-ATTATA-ATTTT-ATAT
1 ATTTTTATATTATATATTTTAATAT
*
23137223 A-TTTTAT-TTTTAT-TTTTAATAT
1 ATTTTTATATTATATATTTTAATAT
23137245 AATTTTTTATATTATATATTTTA
1 -A-TTTTTATATTATATATTTTA
23137268 TTTTAATTGT
Statistics
Matches: 72, Mismatches: 9, Indels: 26
0.67 0.08 0.24
Matches are distributed among these distances:
21 13 0.18
22 7 0.10
23 1 0.01
24 6 0.08
25 16 0.22
26 13 0.18
27 12 0.17
28 4 0.06
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (25 bp):
ATTTTTATATTATATATTTTAATAT
Found at i:23137285 original size:37 final size:39
Alignment explanation
Indices: 23137217--23137289 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
23137207 AATTATAATT
* *
23137217 TTATATATTTTATTTTTATTTTTAATATAATTTTTTATA
1 TTATATATTTTATTTTTAATTGTAATATAATTTTTTATA
*
23137256 TTATATATTTTA-TTTTAATTGTAA-GTAATTTTTT
1 TTATATATTTTATTTTTAATTGTAATATAATTTTTT
23137290 TAAAAGTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 9 0.29
38 10 0.32
39 12 0.39
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (39 bp):
TTATATATTTTATTTTTAATTGTAATATAATTTTTTATA
Found at i:23142240 original size:17 final size:18
Alignment explanation
Indices: 23142218--23142255 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
23142208 GATGCTATGG
23142218 TAGAAAA-TTATTGAAGA
1 TAGAAAATTTATTGAAGA
*
23142235 TAGAAAATTTTTTGAAGA
1 TAGAAAATTTATTGAAGA
23142253 TAG
1 TAG
23142256 GTTATGATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.34
Consensus pattern (18 bp):
TAGAAAATTTATTGAAGA
Found at i:23144287 original size:30 final size:30
Alignment explanation
Indices: 23144251--23144310 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
23144241 CTTTATATTA
23144251 TAATATAATTAC-AGATAATATGATTACAAG
1 TAATATAATTACAAG-TAATATGATTACAAG
* *
23144281 TAATATAATTGCAAGTAATGTGATTACAAG
1 TAATATAATTACAAGTAATATGATTACAAG
23144311 GAAGATAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (30 bp):
TAATATAATTACAAGTAATATGATTACAAG
Found at i:23144310 original size:15 final size:15
Alignment explanation
Indices: 23144251--23144310 Score: 68
Period size: 15 Copynumber: 4.0 Consensus size: 15
23144241 CTTTATATTA
*
23144251 TAATATAATTAC-AG
1 TAATATGATTACAAG
23144265 ATAATATGATTACAAG
1 -TAATATGATTACAAG
* *
23144281 TAATATAATTGCAAG
1 TAATATGATTACAAG
*
23144296 TAATGTGATTACAAG
1 TAATATGATTACAAG
23144311 GAAGATAACA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
15 36 0.95
16 2 0.05
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (15 bp):
TAATATGATTACAAG
Found at i:23145006 original size:27 final size:27
Alignment explanation
Indices: 23144973--23145028 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
23144963 ATTTTATATA
*
23144973 TTTTAT-TTTTAT-TTTTAATATAATT
1 TTTTATATTATATATTTTAATATAATT
* *
23144998 TTTTATATTATATATTTTATTTTAATT
1 TTTTATATTATATATTTTAATATAATT
23145025 TTTT
1 TTTT
23145029 TACCTATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 6 0.23
26 5 0.19
27 15 0.58
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (27 bp):
TTTTATATTATATATTTTAATATAATT
Found at i:23145023 original size:32 final size:33
Alignment explanation
Indices: 23144935--23145020 Score: 122
Period size: 33 Copynumber: 2.6 Consensus size: 33
23144925 TTTTAATGTC
*
23144935 ATATATTTTATA-TTTATTTCTTATTATAATTTT
1 ATATATTTTATATTTTATTT-TTAATATAATTTT
23144968 ATATATTTTAT-TTTTATTTTTAATATAATTTT
1 ATATATTTTATATTTTATTTTTAATATAATTTT
* *
23145000 TTATATTATATATTTTATTTT
1 ATATATTTTATATTTTATTTT
23145021 AATTTTTTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
32 21 0.44
33 27 0.56
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (33 bp):
ATATATTTTATATTTTATTTTTAATATAATTTT
Found at i:23153690 original size:68 final size:68
Alignment explanation
Indices: 23153581--23153710 Score: 206
Period size: 68 Copynumber: 1.9 Consensus size: 68
23153571 AAATCAATTA
* * *
23153581 GTCGGATAGGGATTTTAAACATTTTATTTAATAAAATTTTTCTTTATCTTTATATCTATAATAAT
1 GTCGGATAGAGACTTTAAACATTTTATTTAATAAAAATTTTCTTTATCTTTATATCTATAATAAT
23153646 TGT
66 TGT
* * *
23153649 GTCGGATAGAGACTTTAAATATTTTATTTAATAAAAATTTTCTTTATTTTTATATTTATAAT
1 GTCGGATAGAGACTTTAAACATTTTATTTAATAAAAATTTTCTTTATCTTTATATCTATAAT
23153711 TGCTATTATT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 56 1.00
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (68 bp):
GTCGGATAGAGACTTTAAACATTTTATTTAATAAAAATTTTCTTTATCTTTATATCTATAATAAT
TGT
Found at i:23166122 original size:314 final size:312
Alignment explanation
Indices: 23165544--23166163 Score: 1057
Period size: 314 Copynumber: 2.0 Consensus size: 312
23165534 TGATGCTTAC
23165544 AATAGATGCACAATCTTAACTTTCCTTTTGGAAATCACTCATCACTTTATGTTTGACGACAAGCA
1 AATAGATGCACAATCTTAACTTTCCTTTTGGAAATCACTCATCACTTTATGTTTGACGACAAGCA
* *
23165609 GCACTGAGATTGTATTCAATATTTATATGCTGCTGCACAAAAACTGCTGGTATCATTTAAGGAAG
66 GCACTGAGATTGTATTCAATATTTATATGCTGCTCCACAAAAACTGCTGGAATCATTTAAGGAAG
* *
23165674 CGTCACTCTGGTTAACTAATGGTCCCACAGAAGGTAACTTAACAAATTCTGTACACTTCTAAAAC
131 CGTCACTCTGGTTAACTAATGGTCCCACACAAGGTAACTTAACAAATTCTGCACACTTCTAAAAC
*
23165739 ACAAAACCATAAAAAGAGCTTCTCAATGAAATTTTAACAAACAAATCACCATTCTAAGTGTAGAA
196 ACAAAACCATAAAAAGAGCTTCTCAATGAAATTTTAACAAACAAATCACCATTCTAAGTGTAAAA
*
23165804 TTAATCATCCCTGTTACCAAACATTTTACGAGAAATTTGTTTTAAAGCATAT
261 TTAATCATCCCTGTTAACAAACATTTTACGAGAAATTTGTTTTAAAGCATAT
*
23165856 AATAGATTCACAATCTTAACTTTCCTTTTGGAAATCACACTCATCACTTTATGTTTGACGACAAG
1 AATAGATGCACAATCTTAACTTTCCTTTTGGAAAT--CACTCATCACTTTATGTTTGACGACAAG
*
23165921 CAGGACTGAGATTGTATTCAATATTTATATGCTGCTCCACAAAAACTGCTGGAATCATTTAAGGA
64 CAGCACTGAGATTGTATTCAATATTTATATGCTGCTCCACAAAAACTGCTGGAATCATTTAAGGA
* * *
23165986 TGTGTCACTGTGGTCT-ACTAATGGTCCCACACAAGGTAA-TGTAACAAATTCTGCACACTTCTA
129 AGCGTCACTCTGGT-TAACTAATGGTCCCACACAAGGTAACT-TAACAAATTCTGCACACTTCTA
*
23166049 AAACACAAAACCATAAAAAGAGCTTCTCAATGAATTTTTAACAAACAAATCACCATTCTAAGAT-
192 AAACACAAAACCATAAAAAGAGCTTCTCAATGAAATTTTAACAAACAAATCACCATTCTAAG-TG
*
23166113 TAAAATTAATCATCCCTGTTAACAAACATTTTATGAGAAATTTGTTTTAAA
256 TAAAATTAATCATCCCTGTTAACAAACATTTTACGAGAAATTTGTTTTAAA
23166164 CTTAATAACT
Statistics
Matches: 290, Mismatches: 13, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
312 34 0.12
313 1 0.00
314 253 0.87
315 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (312 bp):
AATAGATGCACAATCTTAACTTTCCTTTTGGAAATCACTCATCACTTTATGTTTGACGACAAGCA
GCACTGAGATTGTATTCAATATTTATATGCTGCTCCACAAAAACTGCTGGAATCATTTAAGGAAG
CGTCACTCTGGTTAACTAATGGTCCCACACAAGGTAACTTAACAAATTCTGCACACTTCTAAAAC
ACAAAACCATAAAAAGAGCTTCTCAATGAAATTTTAACAAACAAATCACCATTCTAAGTGTAAAA
TTAATCATCCCTGTTAACAAACATTTTACGAGAAATTTGTTTTAAAGCATAT
Found at i:23169644 original size:16 final size:17
Alignment explanation
Indices: 23169612--23169654 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
23169602 GTACCTTCTT
23169612 ATATTATATATCTAATAA
1 ATATTATAT-TCTAATAA
*
23169630 ATATTATATTC-AATAT
1 ATATTATATTCTAATAA
23169646 ATATT-TATT
1 ATATTATATT
23169655 ATATTAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 9 0.38
17 2 0.08
18 9 0.38
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATTATATTCTAATAA
Found at i:23185990 original size:2 final size:2
Alignment explanation
Indices: 23185926--23185972 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
23185916 GTGTATACAG
*
23185926 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AA AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
23185968 AC AC A
1 AC AC A
23185973 AATATGCATG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:23191540 original size:21 final size:20
Alignment explanation
Indices: 23191516--23191559 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
23191506 GACAGATTAG
* *
23191516 TCTTAACCGATTAACACAAAT
1 TCTTAACCAATTAAAAC-AAT
*
23191537 TCTTAATCAATTAAAACAAT
1 TCTTAACCAATTAAAACAAT
23191557 TCT
1 TCT
23191560 GGGCTTTACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.34
Consensus pattern (20 bp):
TCTTAACCAATTAAAACAAT
Found at i:23193152 original size:22 final size:22
Alignment explanation
Indices: 23193092--23193158 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
23193082 AATACTCTTA
* *
23193092 ATTATAAGTAAATAATATTTTT
1 ATTATAATTTAATAATATTTTT
** * * *
23193114 ACCAAAATATAAAAATATTTTT
1 ATTATAATTTAATAATATTTTT
23193136 ATTATAATTTAATAATATCTTTT
1 ATTATAATTTAATAATAT-TTTT
23193159 TAAAGCTGTC
Statistics
Matches: 32, Mismatches: 12, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
22 28 0.88
23 4 0.12
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.48
Consensus pattern (22 bp):
ATTATAATTTAATAATATTTTT
Found at i:23194619 original size:72 final size:73
Alignment explanation
Indices: 23194438--23194635 Score: 228
Period size: 72 Copynumber: 2.7 Consensus size: 73
23194428 AAATTGCAGA
* *
23194438 CAGAGAGC-TCTTAGTCGACTAACTTTCTTCTTGGTCGACTAAGTTGGTTCTGTCTTTTGATCGT
1 CAGAGAGCATCTTAGTCGACTAACTCTCTTCTTGGTCGACTAAGTTGGTTCTGTC-TTTGATAGT
*
23194502 AGATTCTGT
65 AGATTCTGG
* *
23194511 CAGAGAGCAT-TTAGTCTACTAACTCAT-TTCTTGGTCGACTAAGTTGGTTTTGTC-TTGA-AGT
1 CAGAGAGCATCTTAGTCGACTAACTC-TCTTCTTGGTCGACTAAGTTGGTTCTGTCTTTGATAG-
*
23194572 TCAGATTTTGG
64 T-AGATTCTGG
* * * *
23194583 CAG-TAGCTTCTTAGTCGACTAACTCTCATCTTGGTCGACTAAATTGGTTCTGT
1 CAGAGAGCATCTTAGTCGACTAACTCTCTTCTTGGTCGACTAAGTTGGTTCTGT
23194636 TTCTCAATAT
Statistics
Matches: 107, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
70 1 0.01
71 10 0.09
72 47 0.44
73 47 0.44
74 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (73 bp):
CAGAGAGCATCTTAGTCGACTAACTCTCTTCTTGGTCGACTAAGTTGGTTCTGTCTTTGATAGTA
GATTCTGG
Found at i:23198190 original size:3 final size:3
Alignment explanation
Indices: 23198182--23198227 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
23198172 CTTTACAATT
23198182 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
23198228 CCATTTTTGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:23201482 original size:20 final size:20
Alignment explanation
Indices: 23201454--23201501 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
23201444 TTATAATTAG
*
23201454 TTTATTTTTAAGTGAGTTT-T
1 TTTAATTTTAAGTGA-TTTCT
* *
23201474 TTTAATTTTATGTTATTTCT
1 TTTAATTTTAAGTGATTTCT
23201494 TTTAATTT
1 TTTAATTT
23201502 ATTTATTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.21, C:0.02, G:0.08, T:0.69
Consensus pattern (20 bp):
TTTAATTTTAAGTGATTTCT
Found at i:23203805 original size:12 final size:12
Alignment explanation
Indices: 23203788--23203812 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23203778 CTTAACTGCT
23203788 TAAGTGGCTACA
1 TAAGTGGCTACA
23203800 TAAGTGGCTACA
1 TAAGTGGCTACA
23203812 T
1 T
23203813 TATCTAAGAA
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:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (12 bp):
TAAGTGGCTACA
Found at i:23218436 original size:20 final size:20
Alignment explanation
Indices: 23218410--23218455 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
23218400 AATCTTACCT
* *
23218410 TTTTTCACTTGTTTCCTTGAA
1 TTTTACACTT-TTCCCTTGAA
23218431 TTTTCACACTTTTCCCTTGAA
1 TTTT-ACACTTTTCCCTTGAA
23218452 TTTT
1 TTTT
23218456 TCCACCTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.15, C:0.22, G:0.07, T:0.57
Consensus pattern (20 bp):
TTTTACACTTTTCCCTTGAA
Found at i:23218457 original size:22 final size:22
Alignment explanation
Indices: 23218415--23218455 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
23218405 TACCTTTTTT
*
23218415 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
23218437 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
23218456 TCCACCTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:23219291 original size:2 final size:2
Alignment explanation
Indices: 23219284--23219337 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
23219274 GTAATATTTA
23219284 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT -T 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
23219324 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
23219338 CATAAGCATA
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 48 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23219318 original size:30 final size:30
Alignment explanation
Indices: 23219275--23219337 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 30
23219265 TACCTATTCG
23219275 TAATATTTAATATATATATATATATATATA
1 TAATATTTAATATATATATATATATATATA
23219305 TAATATATTATATATATATATATATATATATA
1 TAATAT-TTA-ATATATATATATATATATATA
23219337 T
1 T
23219338 CATAAGCATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 6 0.19
31 3 0.10
32 22 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
TAATATTTAATATATATATATATATATATA
Found at i:23224396 original size:26 final size:26
Alignment explanation
Indices: 23224367--23224425 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
23224357 ATTTTCTAGT
* *
23224367 TTTCCTTTGT-TTTTCTCTTTTCTTCC
1 TTTCCTTTCTATTTTCTCTCTTCTT-C
* *
23224393 TTTCCTCTCTATTTTCTCTCTTGTTC
1 TTTCCTTTCTATTTTCTCTCTTCTTC
23224419 TTTCCTT
1 TTTCCTT
23224426 ATGGCCAGCC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.02, C:0.29, G:0.03, T:0.66
Consensus pattern (26 bp):
TTTCCTTTCTATTTTCTCTCTTCTTC
Found at i:23236058 original size:25 final size:25
Alignment explanation
Indices: 23236030--23236090 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
23236020 ATGGTCGCAA
* * * *
23236030 CCACGTATATCAACTCGTGGCCTAG
1 CCACGTATAACAACCCCTAGCCTAG
*
23236055 CCACGTATAACAACCCCTAGCCTTG
1 CCACGTATAACAACCCCTAGCCTAG
23236080 CCACGTATAAC
1 CCACGTATAAC
23236091 CATAAACCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.28, C:0.36, G:0.15, T:0.21
Consensus pattern (25 bp):
CCACGTATAACAACCCCTAGCCTAG
Found at i:23236509 original size:2 final size:2
Alignment explanation
Indices: 23236497--23236531 Score: 52
Period size: 2 Copynumber: 16.5 Consensus size: 2
23236487 AACACTTTAC
23236497 AT AT AT CAT AT AT AT AT AT AT AT AT AT AT AGT AT A
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT A-T AT A
23236532 CACAAAACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 27 0.87
3 4 0.13
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:23237857 original size:56 final size:55
Alignment explanation
Indices: 23237788--23237915 Score: 134
Period size: 56 Copynumber: 2.3 Consensus size: 55
23237778 TGGAATTTGG
*
23237788 TATT-TATATGGCCACCCACTCAACCAATCA-AATTGCATGCACACTTTCAACTTTT
1 TATTCTATTTGGCCACCCACTCAACCAATCACAATT-CATGCACACTTT-AACTTTT
* * * ** * *
23237843 TATTCTATTTGGCCACCCACTTAGCCAATTACAATTCATGCATTCTTTTATTTTT
1 TATTCTATTTGGCCACCCACTCAACCAATCACAATTCATGCACACTTTAACTTTT
*
23237898 TCATGCTATTTGGCCACC
1 T-ATTCTATTTGGCCACC
23237916 TTGCCAACCT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
55 10 0.16
56 47 0.77
57 4 0.07
ACGTcount: A:0.26, C:0.27, G:0.09, T:0.38
Consensus pattern (55 bp):
TATTCTATTTGGCCACCCACTCAACCAATCACAATTCATGCACACTTTAACTTTT
Found at i:23238524 original size:31 final size:31
Alignment explanation
Indices: 23238489--23238549 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
23238479 AATTTTCCTT
* *
23238489 TTTTACCATTTGACCCTCCAAACTTTTCATC
1 TTTTACAATTTGACCCTCCAAACATTTCATC
** *
23238520 TTTTACAATTTGGTCCTTCAAACATTTCAT
1 TTTTACAATTTGACCCTCCAAACATTTCAT
23238550 AAATTACAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.25, C:0.26, G:0.05, T:0.44
Consensus pattern (31 bp):
TTTTACAATTTGACCCTCCAAACATTTCATC
Found at i:23238587 original size:30 final size:31
Alignment explanation
Indices: 23238522--23238588 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
23238512 TTTTCATCTT
23238522 TTACAATTTGGTCCTTCAAACATTTCATAAA
1 TTACAATTTGGTCCTTCAAACATTTCATAAA
* *
23238553 TTACAGTTTGGTCCTTC-AACTTGTTCAT-AA
1 TTACAATTTGGTCCTTCAAACAT-TTCATAAA
23238583 TTACAA
1 TTACAA
23238589 CTTCACCCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 11 0.34
31 21 0.66
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.40
Consensus pattern (31 bp):
TTACAATTTGGTCCTTCAAACATTTCATAAA
Found at i:23240627 original size:48 final size:48
Alignment explanation
Indices: 23240572--23240719 Score: 217
Period size: 48 Copynumber: 3.1 Consensus size: 48
23240562 GCCAAACAAG
* * *
23240572 GATTTGCCTCTAAGAAATCTGCTTCCCAAATCTTTACCATAATTTTTT
1 GATTTGCCTCTATGAAATCTGCTTCTCAAATCTTCACCATAATTTTTT
*
23240620 GATTTGCCT-TCATGAAATCTGCTTCTCAAATCTTCACCATTATTTTTT
1 GATTTGCCTCT-ATGAAATCTGCTTCTCAAATCTTCACCATAATTTTTT
* * *
23240668 GATTTGCCTCTATGAAATTTTCTTCTCAAATCTTCACCATAATTTTCT
1 GATTTGCCTCTATGAAATCTGCTTCTCAAATCTTCACCATAATTTTTT
23240716 GATT
1 GATT
23240720 ATCACAAATC
Statistics
Matches: 90, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
47 1 0.01
48 88 0.98
49 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.08, T:0.45
Consensus pattern (48 bp):
GATTTGCCTCTATGAAATCTGCTTCTCAAATCTTCACCATAATTTTTT
Found at i:23245078 original size:43 final size:43
Alignment explanation
Indices: 23245031--23245135 Score: 115
Period size: 43 Copynumber: 2.4 Consensus size: 43
23245021 AGCTCTTGCG
* ** * *
23245031 CACTCCCTACTTGCACAT-GGCTGGGTCATCAC-CGGGTTATGCA
1 CACTCCCTACTCGCACATAATC-GGGTCATC-CTCGGCTTATACA
* *
23245074 CACTCCTTACTCGCACATAATCGGGTCATCCTCGGCTTATACG
1 CACTCCCTACTCGCACATAATCGGGTCATCCTCGGCTTATACA
23245117 CACTCCCTACTCGCACATA
1 CACTCCCTACTCGCACATA
23245136 GCCGAGTTAA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
42 1 0.02
43 50 0.96
44 1 0.02
ACGTcount: A:0.21, C:0.36, G:0.17, T:0.26
Consensus pattern (43 bp):
CACTCCCTACTCGCACATAATCGGGTCATCCTCGGCTTATACA
Found at i:23245967 original size:19 final size:19
Alignment explanation
Indices: 23245929--23245967 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
23245919 AAAAGAAGAC
**
23245929 AAGCTGCTGGAAGTTCAAG
1 AAGCTGCTGGAAGGACAAG
*
23245948 AAGCTGCTGGAAGGAGAAG
1 AAGCTGCTGGAAGGACAAG
23245967 A
1 A
23245968 TATTTTATAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.36, C:0.13, G:0.36, T:0.15
Consensus pattern (19 bp):
AAGCTGCTGGAAGGACAAG
Found at i:23247772 original size:48 final size:48
Alignment explanation
Indices: 23247711--23247805 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
23247701 CCAAACAAGG
23247711 ATTTGCTTCCATGAAATCTGCTTCCCAAATCTTCACCATAATTTTCTA
1 ATTTGCTTCCATGAAATCTGCTTCCCAAATCTTCACCATAATTTTCTA
*
23247759 ATTTGCCTT-CATGAAATCTGCTTCTCAAATCTTCACCATAATTTTCT
1 ATTTG-CTTCCATGAAATCTGCTTCCCAAATCTTCACCATAATTTTCT
23247806 GATTATCACA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
48 42 0.93
49 3 0.07
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.41
Consensus pattern (48 bp):
ATTTGCTTCCATGAAATCTGCTTCCCAAATCTTCACCATAATTTTCTA
Found at i:23264293 original size:61 final size:61
Alignment explanation
Indices: 23264198--23264315 Score: 182
Period size: 61 Copynumber: 1.9 Consensus size: 61
23264188 ATAGCATAAT
* * *
23264198 TTAAGACAAATAACACAGTCAATAATTTGCTTCCACATTGTAATACATATGTTTACTAGCC
1 TTAAGACAAATAACACAGTCAAAAATTTGATTCCACATTGCAATACATATGTTTACTAGCC
* * *
23264259 TTAAGACAAATAACATAGTCAAAAATTTGATTCCATATTGCAATACATATTTTTACT
1 TTAAGACAAATAACACAGTCAAAAATTTGATTCCACATTGCAATACATATGTTTACT
23264316 GGCTTGACAG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (61 bp):
TTAAGACAAATAACACAGTCAAAAATTTGATTCCACATTGCAATACATATGTTTACTAGCC
Found at i:23264860 original size:2 final size:2
Alignment explanation
Indices: 23264855--23264889 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
23264845 TGTTTATGTA
23264855 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23264890 GCACCTTCCG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23271244 original size:13 final size:13
Alignment explanation
Indices: 23271226--23271250 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23271216 GGAAAATGAG
23271226 ATTTTATAAAATA
1 ATTTTATAAAATA
23271239 ATTTTATAAAAT
1 ATTTTATAAAAT
23271251 TTTTAAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:23274521 original size:18 final size:18
Alignment explanation
Indices: 23274498--23274580 Score: 60
Period size: 18 Copynumber: 4.6 Consensus size: 18
23274488 GTTTCTACAC
23274498 ACATAACCT-TTTGAACAA
1 ACATAA-CTATTTGAACAA
*
23274516 ACATAATTATTTGAACAA
1 ACATAACTATTTGAACAA
** * *
23274534 ATGTAATTATTTGAATAA
1 ACATAACTATTTGAACAA
** * * *
23274552 ACATAGTTACTTGAATAG
1 ACATAACTATTTGAACAA
23274570 ACATAACTATT
1 ACATAACTATT
23274581 CAAAGGACTA
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
17 1 0.02
18 51 0.98
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.35
Consensus pattern (18 bp):
ACATAACTATTTGAACAA
Found at i:23275695 original size:67 final size:66
Alignment explanation
Indices: 23275572--23275765 Score: 169
Period size: 67 Copynumber: 2.9 Consensus size: 66
23275562 TTACAATGGC
* * ** * * *
23275572 TTTTACAAGGCTCAGCCAAAACCTTTTTCACTAGTTTTTCACAGGCTAAACTAAAACCTAAAGTG
1 TTTTA-AAGGCTCAACCATAACCTTTCACAATAGTTTTTCACAGGCTAAACCAAAACCCAAAGTG
23275637 AT
65 AT
* * * * *
23275639 TATTTAAAGGCTCAACCATAACCTTTCACAATGGTTTTTTACGGGCTCAACCAAAACCCAAGGTG
1 T-TTTAAAGGCTCAACCATAACCTTTCACAATAGTTTTTCACAGGCTAAACCAAAACCCAAAGTG
*
23275704 GT
65 AT
* * * *
23275706 TTTTCAAAGGCTCAACCATAA-CTTACA-AATATGGTTTT-ACCAGGATCAACCAAAACCCAA
1 TTTT-AAAGGCTCAACCATAACCTTTCACAATA-GTTTTTCA-CAGGCTAAACCAAAACCCAA
23275766 CAATCAACTT
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
65 4 0.04
66 31 0.30
67 66 0.63
68 4 0.04
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28
Consensus pattern (66 bp):
TTTTAAAGGCTCAACCATAACCTTTCACAATAGTTTTTCACAGGCTAAACCAAAACCCAAAGTGA
T
Found at i:23283157 original size:41 final size:41
Alignment explanation
Indices: 23283112--23283194 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
23283102 TGTTGGACTT
*
23283112 TCCTTCATCCATTTCTCGAGCATTTGACTTTGAGTCTTTTG
1 TCCTTCATCCATCTCTCGAGCATTTGACTTTGAGTCTTTTG
23283153 TCCTTCATCCATCTCTCGAGCATTTGACTTTGAGTCTTTTG
1 TCCTTCATCCATCTCTCGAGCATTTGACTTTGAGTCTTTTG
23283194 T
1 T
23283195 TCTTTCTCAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.14, C:0.25, G:0.14, T:0.46
Consensus pattern (41 bp):
TCCTTCATCCATCTCTCGAGCATTTGACTTTGAGTCTTTTG
Found at i:23284533 original size:37 final size:37
Alignment explanation
Indices: 23284477--23284581 Score: 158
Period size: 37 Copynumber: 2.8 Consensus size: 37
23284467 GTAATGTTGA
*
23284477 AGTGTGCGAGTA-GAGAGTGCACACATGATGATGATAG
1 AGTGTGCGAGTAGGA-AGTGCACACATGATGATAATAG
*
23284514 AGTGTGCGTGTAGGAAGTGCACACATGATGATAATAG
1 AGTGTGCGAGTAGGAAGTGCACACATGATGATAATAG
* *
23284551 AGTGTGCAAGTAGGGAGTGCACACATGATGA
1 AGTGTGCGAGTAGGAAGTGCACACATGATGA
23284582 CGATGTATGT
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
37 60 0.97
38 2 0.03
ACGTcount: A:0.32, C:0.11, G:0.34, T:0.22
Consensus pattern (37 bp):
AGTGTGCGAGTAGGAAGTGCACACATGATGATAATAG
Found at i:23290730 original size:2 final size:2
Alignment explanation
Indices: 23290723--23290802 Score: 137
Period size: 2 Copynumber: 40.5 Consensus size: 2
23290713 AGATAACATA
23290723 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23290763 NAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23290803 ATTTTTCATT
Statistics
Matches: 75, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.03
2 72 0.96
3 1 0.01
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23296194 original size:43 final size:43
Alignment explanation
Indices: 23296147--23296251 Score: 115
Period size: 43 Copynumber: 2.5 Consensus size: 43
23296137 AGACATGTCC
* *
23296147 TTTGCATTCAATGTGGGAATC-CCTTCCTCTATAAGCCACATTA
1 TTTGCATTCAATGTGGGAATCACCTTCCTCTATAAGACACA-CA
** * * *
23296190 TTTGCATTCAATG-GATAAACATCTTCCTCTATAAGACACACC
1 TTTGCATTCAATGTGGGAATCACCTTCCTCTATAAGACACACA
*
23296232 TTTGCATTTAATGTGGGAAT
1 TTTGCATTCAATGTGGGAAT
23296252 TACTTGCTTT
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
42 16 0.33
43 33 0.67
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (43 bp):
TTTGCATTCAATGTGGGAATCACCTTCCTCTATAAGACACACA
Found at i:23300157 original size:41 final size:42
Alignment explanation
Indices: 23300070--23300157 Score: 142
Period size: 43 Copynumber: 2.1 Consensus size: 42
23300060 CAATCAACAT
23300070 TCAAGGTATGTCTACAATTACAGCTTGAGAGAAGTTTACTAGA
1 TCAAGGTATGTCTACAATTACAGCTT-AGAGAAGTTTACTAGA
* *
23300113 TCAAGGTATTTCTACAATTACAGCTT-GAGAAGTTTACTATA
1 TCAAGGTATGTCTACAATTACAGCTTAGAGAAGTTTACTAGA
23300154 TCAA
1 TCAA
23300158 TATTGTACTA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
41 18 0.42
43 25 0.58
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (42 bp):
TCAAGGTATGTCTACAATTACAGCTTAGAGAAGTTTACTAGA
Found at i:23304775 original size:17 final size:17
Alignment explanation
Indices: 23304753--23304788 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
23304743 TGCCTCATTG
* *
23304753 AAACCTTATTAGAAAAA
1 AAACCTCATGAGAAAAA
23304770 AAACCTCATGAGAAAAA
1 AAACCTCATGAGAAAAA
23304787 AA
1 AA
23304789 TTCGAGTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.61, C:0.14, G:0.08, T:0.17
Consensus pattern (17 bp):
AAACCTCATGAGAAAAA
Found at i:23308458 original size:11 final size:13
Alignment explanation
Indices: 23308434--23308463 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
23308424 TATAATTTAT
23308434 TAATAAAAACACA
1 TAATAAAAACACA
*
23308447 TAATAAAAACATA
1 TAATAAAAACACA
23308460 TAAT
1 TAAT
23308464 TTAAATATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (13 bp):
TAATAAAAACACA
Found at i:23315785 original size:32 final size:32
Alignment explanation
Indices: 23315723--23315786 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
23315713 ATGGCATTCC
* **
23315723 ATGTGGCATCAATGTGATGATGTGGCAATGCT
1 ATGTGGCATCAATATGATGACATGGCAATGCT
* *
23315755 ATGTGGCATTAATATGATGACATGGTAATGCT
1 ATGTGGCATCAATATGATGACATGGCAATGCT
23315787 GACATGGTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.33
Consensus pattern (32 bp):
ATGTGGCATCAATATGATGACATGGCAATGCT
Found at i:23329397 original size:279 final size:278
Alignment explanation
Indices: 23328897--23329447 Score: 1084
Period size: 279 Copynumber: 2.0 Consensus size: 278
23328887 GATTTGATAA
23328897 GGATGACATGATAATGACATAAGCATATTTGATAACTTGCTCTCACATGCATTCTTGTAGTCTAA
1 GGATGACATGATAATGACATAAGCATATTTGATAACTTGCTCTCACATGCATTCTTGTAGTCTAA
23328962 ACAAGGAAACTAAACCTAAAAGTTAATATTTTTAATTTCCTTATGTCTAAAATGCATTAACCTTA
66 ACAAGGAAACTAAACCTAAAAGTTAATATTTTTAATTTCCTTATGTCTAAAATGCATTAACCTTA
23329027 TGAACAACCTTGTTTTAGAATCAAATGTATAAGTTCAAATTGTTTGACTACTTAAATTGAATTCT
131 TGAACAACCTTGTTTTAGAATCAAATGTATAAGTTCAAATTGTTTGACTACTTAAATTGAATTCT
23329092 TCAATATAGGCTTACATGAATACATAGCTTGAACAAGTTGTCACATGTTGAAAATGCTATTATTA
196 TCAATATAGGCTTACATGAATACATAGCTTGAACAAGTTGTCACATGTTGAAAATGCTATTATTA
23329157 CTTATTCTTGATAAATAT
261 CTTATTCTTGATAAATAT
23329175 NGGATGACATGATAATGACATAAGCATATTTGATAACTTGCTCTCACATGCATTCTTGTAGTCTA
1 -GGATGACATGATAATGACATAAGCATATTTGATAACTTGCTCTCACATGCATTCTTGTAGTCTA
23329240 AACAAGGAAACTAAACCTAAAAGTTAATATTTTTAATTTCCTTATGTCTAAAATGCATTAACCTT
65 AACAAGGAAACTAAACCTAAAAGTTAATATTTTTAATTTCCTTATGTCTAAAATGCATTAACCTT
23329305 ATGAACAACCTTGTTTTAGAATCAAATGTATAAGTTCAAATTGTTTGACTACTTAAATTGAATTC
130 ATGAACAACCTTGTTTTAGAATCAAATGTATAAGTTCAAATTGTTTGACTACTTAAATTGAATTC
23329370 TTCAATATAGGCTTACATGAATACATAGCTTGAACAAGTTGTCACATGTTGAAAATGCTATTATT
195 TTCAATATAGGCTTACATGAATACATAGCTTGAACAAGTTGTCACATGTTGAAAATGCTATTATT
*
23329435 ACTTGTTCTTGAT
260 ACTTATTCTTGAT
23329448 GAAAATGATT
Statistics
Matches: 271, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
279 271 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.37
Consensus pattern (278 bp):
GGATGACATGATAATGACATAAGCATATTTGATAACTTGCTCTCACATGCATTCTTGTAGTCTAA
ACAAGGAAACTAAACCTAAAAGTTAATATTTTTAATTTCCTTATGTCTAAAATGCATTAACCTTA
TGAACAACCTTGTTTTAGAATCAAATGTATAAGTTCAAATTGTTTGACTACTTAAATTGAATTCT
TCAATATAGGCTTACATGAATACATAGCTTGAACAAGTTGTCACATGTTGAAAATGCTATTATTA
CTTATTCTTGATAAATAT
Found at i:23333026 original size:21 final size:21
Alignment explanation
Indices: 23332997--23333047 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
23332987 AAGAATAATC
* * *
23332997 ATAGCCGACTACAGAGGAAGT
1 ATAGTCGACTACAAAGGAAAT
*
23333018 ATAGTCGACTATAAAGGAAAT
1 ATAGTCGACTACAAAGGAAAT
23333039 ATAGTCGAC
1 ATAGTCGAC
23333048 CTTGTTCTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.20
Consensus pattern (21 bp):
ATAGTCGACTACAAAGGAAAT
Found at i:23333187 original size:21 final size:22
Alignment explanation
Indices: 23333155--23333196 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
23333145 GTCAACTTTA
*
23333155 AGAAGCCATAGTCAATTATAAG
1 AGAAGCCATAGTCAAGTATAAG
23333177 AGAAG-CATAGTCAAGTATAA
1 AGAAGCCATAGTCAAGTATAA
23333197 AAGGCTAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.21
Consensus pattern (22 bp):
AGAAGCCATAGTCAAGTATAAG
Found at i:23333753 original size:49 final size:49
Alignment explanation
Indices: 23333693--23333806 Score: 147
Period size: 50 Copynumber: 2.3 Consensus size: 49
23333683 GCTTCTTATC
* ** *
23333693 AAAAAGCAAGAATCCTTTGTGGATTATTTGGGTTATCGATTGATCTCGT
1 AAAAAGCAAGAATCCTTTATGGATTATAAGGGTTATCGATTGATCCCGT
* * * *
23333742 AAAAAGTAAGAATTCCTTTATGGATTGTAAGGGTTATTGCTTGATCCCGT
1 AAAAAGCAAGAA-TCCTTTATGGATTATAAGGGTTATCGATTGATCCCGT
23333792 AAAAAGCAAGAATCC
1 AAAAAGCAAGAATCC
23333807 CATGTGAATT
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
49 14 0.25
50 41 0.75
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.32
Consensus pattern (49 bp):
AAAAAGCAAGAATCCTTTATGGATTATAAGGGTTATCGATTGATCCCGT
Found at i:23336237 original size:8 final size:8
Alignment explanation
Indices: 23336226--23336265 Score: 64
Period size: 8 Copynumber: 5.1 Consensus size: 8
23336216 TTTCTTATTT
23336226 CTTTCTTC
1 CTTTCTTC
*
23336234 CTTTCCTC
1 CTTTCTTC
23336242 CTTTCTTC
1 CTTTCTTC
23336250 CTTTC-TC
1 CTTTCTTC
23336257 CTTTCTTC
1 CTTTCTTC
23336265 C
1 C
23336266 ATTCCCTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 7 0.24
8 22 0.76
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.57
Consensus pattern (8 bp):
CTTTCTTC
Found at i:23336259 original size:15 final size:16
Alignment explanation
Indices: 23336226--23336270 Score: 74
Period size: 15 Copynumber: 2.9 Consensus size: 16
23336216 TTTCTTATTT
23336226 CTTTCTTCCTTTCCTC
1 CTTTCTTCCTTTCCTC
23336242 CTTTCTTCCTTT-CTC
1 CTTTCTTCCTTTCCTC
*
23336257 CTTTCTTCCATTCC
1 CTTTCTTCCTTTCC
23336271 CTCTTTGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.02, C:0.42, G:0.00, T:0.56
Consensus pattern (16 bp):
CTTTCTTCCTTTCCTC
Found at i:23341005 original size:19 final size:18
Alignment explanation
Indices: 23340978--23341020 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
23340968 TTAATATTTT
*
23340978 AATACTATTCTATTAGTAA
1 AATATTATTCTATT-GTAA
* *
23340997 AATATTATTTTATTTTAA
1 AATATTATTCTATTGTAA
23341015 AATATT
1 AATATT
23341021 CTTTTCACCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (18 bp):
AATATTATTCTATTGTAA
Found at i:23357749 original size:27 final size:27
Alignment explanation
Indices: 23357701--23357756 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
23357691 AATCAATACT
* *
23357701 AACTAAACTAAAAGAAATTTAAAATAA
1 AACTAAAATAAAAGAAACTTAAAATAA
*
23357728 AACTAAAAT-AAAGAAAACTTAAATTAA
1 AACTAAAATAAAAG-AAACTTAAAATAA
23357755 AA
1 AA
23357757 TAACTCAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.68, C:0.07, G:0.04, T:0.21
Consensus pattern (27 bp):
AACTAAAATAAAAGAAACTTAAAATAA
Found at i:23365514 original size:50 final size:50
Alignment explanation
Indices: 23365417--23365544 Score: 136
Period size: 50 Copynumber: 2.6 Consensus size: 50
23365407 AATAACTTTT
* * *
23365417 ACACAATCCAC-ACAAGATTCTTACTTTTTCATGGGACCAAGCATAACCC
1 ACACAATCCACAAAAAGATTCTTGCTTTTTCATGGGACCAAACATAACCC
** * * *
23365466 TTATAATCCACAAAAAGATTCTTGCTTTTT-ATGGGATCAAACGGTAACCC
1 ACACAATCCACAAAAAGATTCTTGCTTTTTCATGGGACCAAAC-ATAACCC
* *
23365516 ACACAATCCACAAAGA-ACTCTTGCTTTTT
1 ACACAATCCACAAAAAGATTCTTGCTTTTT
23365545 GATAGGAAGT
Statistics
Matches: 64, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
49 30 0.47
50 34 0.53
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (50 bp):
ACACAATCCACAAAAAGATTCTTGCTTTTTCATGGGACCAAACATAACCC
Found at i:23365541 original size:49 final size:49
Alignment explanation
Indices: 23365417--23365544 Score: 134
Period size: 49 Copynumber: 2.6 Consensus size: 49
23365407 AATAACTTTT
* *
23365417 ACACAATCCACACAAG-ATTCTTACTTTTTCATGGGACCAAGCATAACCC
1 ACACAATCCACA-AAGAATTCTTGCTTTTTCATGGGACCAAACATAACCC
** * * * *
23365466 TTATAATCCACAAAAAGATTCTTGCTTTTT-ATGGGATCAAACGGTAACCC
1 ACACAATCCACAAAGA-ATTCTTGCTTTTTCATGGGACCAAAC-ATAACCC
*
23365516 ACACAATCCACAAAGAACTCTTGCTTTTT
1 ACACAATCCACAAAGAATTCTTGCTTTTT
23365545 GATAGGAAGT
Statistics
Matches: 63, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
48 2 0.03
49 31 0.49
50 30 0.48
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (49 bp):
ACACAATCCACAAAGAATTCTTGCTTTTTCATGGGACCAAACATAACCC
Found at i:23365927 original size:20 final size:21
Alignment explanation
Indices: 23365902--23365941 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
23365892 AGCTATTATT
23365902 AAAGCT-TGAAGGTCAACTAC
1 AAAGCTCTGAAGGTCAACTAC
* *
23365922 AAAGCTCTTAGGGTCAACTA
1 AAAGCTCTGAAGGTCAACTA
23365942 TGTTATTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (21 bp):
AAAGCTCTGAAGGTCAACTAC
Found at i:23367243 original size:2 final size:2
Alignment explanation
Indices: 23367236--23367285 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
23367226 TTATGCACTC
* *
23367236 TA TA TA TA TA -A TA TA TA TA TG TA TA TA TA TT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23367277 TA TA TA TA T
1 TA TA TA TA T
23367286 TCAATCAAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23458913 original size:129 final size:128
Alignment explanation
Indices: 23458682--23458939 Score: 507
Period size: 129 Copynumber: 2.0 Consensus size: 128
23458672 AACGTAAATT
23458682 ATAAAGAAATGAAAGCTTGCCACTTGTCACCATTCCATTGGTCCATGTTTAACACTTAACAACTA
1 ATAAAGAAATGAAAGCTTGCCACTTGTCACCATTCCATTGGTCCATGTTTAACACTTAACAACTA
23458747 AGCTTTCTTTCACCACCACATAAATTATCTCAATTATCCATAATATAAAATGTTAATGGATGA
66 AGCTTTCTTTCACCACCACATAAATTATCTCAATTATCCATAATATAAAATGTTAATGGATGA
23458810 ANTAAAGAAATGAAAGCTTGCCACTTGTCACCATTCCATTGGTCCATGTTTAACACTTAACAACT
1 A-TAAAGAAATGAAAGCTTGCCACTTGTCACCATTCCATTGGTCCATGTTTAACACTTAACAACT
23458875 AAGCTTTCTTTCACCACCACATAAATTATCTCAATTATCCATAATATAAAATGTTAATGGATGA
65 AAGCTTTCTTTCACCACCACATAAATTATCTCAATTATCCATAATATAAAATGTTAATGGATGA
23458939 A
1 A
23458940 ATCCTTAGGC
Statistics
Matches: 129, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
128 1 0.01
129 128 0.99
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.32
Consensus pattern (128 bp):
ATAAAGAAATGAAAGCTTGCCACTTGTCACCATTCCATTGGTCCATGTTTAACACTTAACAACTA
AGCTTTCTTTCACCACCACATAAATTATCTCAATTATCCATAATATAAAATGTTAATGGATGA
Found at i:23469021 original size:20 final size:20
Alignment explanation
Indices: 23468996--23469041 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
23468986 TTTTGATCCC
*
23468996 ATTTGACTTATTGGAGTATA
1 ATTTGACATATTGGAGTATA
*
23469016 ATTTGACATATTGGAGTATG
1 ATTTGACATATTGGAGTATA
23469036 ATTTGA
1 ATTTGA
23469042 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.22, T:0.43
Consensus pattern (20 bp):
ATTTGACATATTGGAGTATA
Found at i:23477146 original size:34 final size:35
Alignment explanation
Indices: 23477087--23477158 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 35
23477077 GGCAATGTTG
* *
23477087 AAAAATATTTTCTACAAGATGATCCACATAACAAA
1 AAAAATATTTTCAACAAGATGATCCAAATAACAAA
* * *
23477122 AAAAATATTTTCAACAA-TTTATCCAAATAACATA
1 AAAAATATTTTCAACAAGATGATCCAAATAACAAA
23477156 AAA
1 AAA
23477159 TGTTAAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
34 16 0.50
35 16 0.50
ACGTcount: A:0.54, C:0.15, G:0.03, T:0.28
Consensus pattern (35 bp):
AAAAATATTTTCAACAAGATGATCCAAATAACAAA
Found at i:23496314 original size:42 final size:42
Alignment explanation
Indices: 23496243--23496497 Score: 269
Period size: 42 Copynumber: 6.0 Consensus size: 42
23496233 CACCTTCCCA
* * * * *
23496243 TCATCATCAGCTCATGTGCACTCCCCACTCGCACATGGCTGGG
1 TCATCATCGGCTTATGCGCACT-CCCACTCGCACATAGCTAGG
* * * * *
23496286 TCATCATCGGCTTATGCGTACCCCCACTCTCATATAGCCAGG
1 TCATCATCGGCTTATGCGCACTCCCACTCGCACATAGCTAGG
* *
23496328 TCATCATCGGCTTATGTGCACTCCCACTCGCACATAGCCAGG
1 TCATCATCGGCTTATGCGCACTCCCACTCGCACATAGCTAGG
* * * * *
23496370 TCATCATCGGCTTATGCACACTTCTACTCGCACAAAG-TCGGG
1 TCATCATCGGCTTATGCGCACTCCCACTCGCACATAGCT-AGG
* * * *
23496412 TCATCATCGACGTATGCGCACTCCTACTCGCACATAACTAGG
1 TCATCATCGGCTTATGCGCACTCCCACTCGCACATAGCTAGG
* * *
23496454 TCATCATCGGCTTATGCGCACTCCTACTCCCACATAGCTGGG
1 TCATCATCGGCTTATGCGCACTCCCACTCGCACATAGCTAGG
23496496 TC
1 TC
23496498 CACATCAACA
Statistics
Matches: 176, Mismatches: 34, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
42 158 0.90
43 18 0.10
ACGTcount: A:0.22, C:0.35, G:0.18, T:0.25
Consensus pattern (42 bp):
TCATCATCGGCTTATGCGCACTCCCACTCGCACATAGCTAGG
Found at i:23503310 original size:42 final size:42
Alignment explanation
Indices: 23503189--23503436 Score: 246
Period size: 42 Copynumber: 5.9 Consensus size: 42
23503179 CACCATCTCA
* * * * *
23503189 TCATCATCAGCTCATGTGCACTCCCCACTCGCACATGGCTGGG
1 TCATCATCGGCTTATGCGCACT-CCCACTCGCACATAGCCGGG
* * * *
23503232 TCATCATCGGC-TATGCGTACCCCCACTCTCATATAGCCGGG
1 TCATCATCGGCTTATGCGCACTCCCACTCGCACATAGCCGGG
*
23503273 TCATCATCGGCTTATGCGCACTCCCACTCGCACATAGCCAGG
1 TCATCATCGGCTTATGCGCACTCCCACTCGCACATAGCCGGG
* *** *
23503315 TCATCATCGGCTTATGCACACTTTTACTCGCACATAGTCGGG
1 TCATCATCGGCTTATGCGCACTCCCACTCGCACATAGCCGGG
* * * * *
23503357 TCATCATCGGCGTATGTGCACTCCTACTCGTACATAGTCGGG
1 TCATCATCGGCTTATGCGCACTCCCACTCGCACATAGCCGGG
** * * **
23503399 TCATCATCGGAGTATGCGCGCTCCTACTTACACATAGC
1 TCATCATCGGCTTATGCGCACTCCCACTCGCACATAGC
23503437 TAGGTCCACA
Statistics
Matches: 171, Mismatches: 33, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
41 27 0.16
42 134 0.78
43 10 0.06
ACGTcount: A:0.21, C:0.33, G:0.20, T:0.26
Consensus pattern (42 bp):
TCATCATCGGCTTATGCGCACTCCCACTCGCACATAGCCGGG
Found at i:23503415 original size:126 final size:125
Alignment explanation
Indices: 23503215--23503442 Score: 289
Period size: 126 Copynumber: 1.8 Consensus size: 125
23503205 TGCACTCCCC
* *
23503215 ACTCGCACATGGCTGGGTCATCATCGGCTATGCGTACCCCCACTCTCATATAGCCGGGTCATCAT
1 ACTCGCACATGGCTGGGTCATCATCGGCTATGCGCACCCCCACTCTCACATAGCCGGGTCATCAT
** *
23503280 CGGCTTATGCGCACTCCCACTCGCACATAGCCAGGTCATCATCGGCTTATGCACACTTTT
66 CGGAGTATGCGCACTCCCACTCACACATAGCCAGGTCATCATCGGCTTATGCACACTTTT
* * * * *
23503340 ACTCGCACATAG-TCGGGTCATCATCGGCGTATGTGCACTCCTACTCGT-ACATAGTCGGGTCAT
1 ACTCGCACATGGCT-GGGTCATCATCGGC-TATGCGCACCCCCACTC-TCACATAGCCGGGTCAT
* * * *
23503403 CATCGGAGTATGCGCGCTCCTACTTACACATAGCTAGGTC
63 CATCGGAGTATGCGCACTCCCACTCACACATAGCCAGGTC
23503443 CACATCAACA
Statistics
Matches: 86, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
124 1 0.01
125 25 0.29
126 59 0.69
127 1 0.01
ACGTcount: A:0.21, C:0.32, G:0.21, T:0.26
Consensus pattern (125 bp):
ACTCGCACATGGCTGGGTCATCATCGGCTATGCGCACCCCCACTCTCACATAGCCGGGTCATCAT
CGGAGTATGCGCACTCCCACTCACACATAGCCAGGTCATCATCGGCTTATGCACACTTTT
Found at i:23507968 original size:20 final size:20
Alignment explanation
Indices: 23507943--23507988 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
23507933 TTTTGACCCC
23507943 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
*
23507963 ATTTGACTTATTGGAGTATG
1 ATTTGACTTATTGGAGTATA
23507983 ATTTGA
1 ATTTGA
23507989 GGTTTAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:23516327 original size:45 final size:44
Alignment explanation
Indices: 23516278--23516365 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 44
23516268 TCGTTGGAAA
23516278 TTTCCAA-TGGAATTTTTCTGTTGGAAACAAATTTCCAACGAAAAT
1 TTTCCAACT-GAATTTTTC-GTTGGAAACAAATTTCCAACGAAAAT
* * *
23516323 TTTCCAACTGATTTTTTCGTTGGAAAGATATTTCCAACGAAAA
1 TTTCCAACTGAATTTTTCGTTGGAAACAAATTTCCAACGAAAA
23516366 ATTCCATTGG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
44 23 0.59
45 15 0.38
46 1 0.03
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (44 bp):
TTTCCAACTGAATTTTTCGTTGGAAACAAATTTCCAACGAAAAT
Found at i:23516347 original size:71 final size:69
Alignment explanation
Indices: 23516148--23516348 Score: 181
Period size: 73 Copynumber: 2.8 Consensus size: 69
23516138 TTTTAGGTTT
* ** * * * * *
23516148 TTTCGTTGGAAACTCATTTCCAATGGAATAATTATCTACCAAATTTTCCATTGGAAATGAATTTC
1 TTTCTTTGGAAACAAATTTCCAACGGAATAATTATCAACCGAATTTTTCGTTGG--A--AATTTC
23516213 CAACGGAA
62 CAACGGAA
** * *
23516221 TTTCTTTGGAAACCTATTTCCAACGGAATAATTATCTACCGAATTTTTCGTTGGAAATTTCCAAT
1 TTTCTTTGGAAACAAATTTCCAACGGAATAATTATCAACCGAATTTTTCGTTGGAAATTTCCAAC
23516286 GGAA
66 GGAA
* * *
23516290 TTTTTCTGTTGGAAACAAATTTCCAAC-GAA-AATTTTCCAACTGATTTTTTCGTTGGAAA
1 --TTTCT-TTGGAAACAAATTTCCAACGGAATAATTAT-CAACCGAATTTTTCGTTGGAAA
23516349 GATATTTCCA
Statistics
Matches: 110, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
69 13 0.12
70 5 0.05
71 28 0.25
72 17 0.15
73 47 0.43
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (69 bp):
TTTCTTTGGAAACAAATTTCCAACGGAATAATTATCAACCGAATTTTTCGTTGGAAATTTCCAAC
GGAA
Found at i:23517094 original size:19 final size:19
Alignment explanation
Indices: 23517070--23517107 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
23517060 CCATTTAACT
*
23517070 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
23517089 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
23517108 GGTTTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:23518376 original size:13 final size:13
Alignment explanation
Indices: 23518358--23518382 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23518348 AGAGAAATTG
23518358 TGATTTTATAAAA
1 TGATTTTATAAAA
23518371 TGATTTTATAAA
1 TGATTTTATAAA
23518383 TTTTCTAGAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:23522264 original size:22 final size:22
Alignment explanation
Indices: 23522239--23522315 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
23522229 TGTGTGACTA
*
23522239 GTTTTTAGGCATTACGTGATTG
1 GTTTTTAGGCATTGCGTGATTG
* *
23522261 GTTTCTGATAAGGCATTGCGTGACTA
1 GTTT-T--T-AGGCATTGCGTGATTG
* *
23522287 GTTTTTAGACATTGTGTGATTG
1 GTTTTTAGGCATTGCGTGATTG
*
23522309 ATTTTTA
1 GTTTTTA
23522316 AGCAATGCCT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
22 22 0.51
23 2 0.05
25 2 0.05
26 17 0.40
ACGTcount: A:0.21, C:0.09, G:0.25, T:0.45
Consensus pattern (22 bp):
GTTTTTAGGCATTGCGTGATTG
Found at i:23522374 original size:22 final size:23
Alignment explanation
Indices: 23522335--23522417 Score: 89
Period size: 26 Copynumber: 3.5 Consensus size: 23
23522325 TAAGTCAGTT
*
23522335 ATGCCTTA-CTAACAAGTCACGCA
1 ATGCCTTATC-AACTAGTCACGCA
23522358 ATGCC-TATCAACTAGTCACGCA
1 ATGCCTTATCAACTAGTCACGCA
*
23522380 ATGCCTTATCAGAAACTAGTCACGTA
1 ATGCCTTATC---AACTAGTCACGCA
*
23522406 ATACCTTATCAA
1 ATGCCTTATCAA
23522418 AAACTAGTCA
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
22 19 0.37
23 12 0.23
26 21 0.40
ACGTcount: A:0.35, C:0.28, G:0.12, T:0.25
Consensus pattern (23 bp):
ATGCCTTATCAACTAGTCACGCA
Found at i:23522396 original size:26 final size:25
Alignment explanation
Indices: 23522349--23522429 Score: 105
Period size: 26 Copynumber: 3.3 Consensus size: 25
23522339 CTTACTAACA
23522349 AGTCACGCAATGCC-TATC--AACT
1 AGTCACGCAATGCCTTATCAAAACT
23522371 AGTCACGCAATGCCTTATCAGAAACT
1 AGTCACGCAATGCCTTATCA-AAACT
* *
23522397 AGTCACGTAATACCTTATCAAAAACT
1 AGTCACGCAATGCCTTATC-AAAACT
23522423 AGTCACG
1 AGTCACG
23522430 TAATTTTCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
22 14 0.27
23 4 0.08
26 33 0.63
27 1 0.02
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (25 bp):
AGTCACGCAATGCCTTATCAAAACT
Found at i:23522430 original size:26 final size:26
Alignment explanation
Indices: 23522367--23522433 Score: 107
Period size: 26 Copynumber: 2.6 Consensus size: 26
23522357 AATGCCTATC
* * *
23522367 AACTAGTCACGCAATGCCTTATCAGA
1 AACTAGTCACGTAATACCTTATCAAA
23522393 AACTAGTCACGTAATACCTTATCAAA
1 AACTAGTCACGTAATACCTTATCAAA
23522419 AACTAGTCACGTAAT
1 AACTAGTCACGTAAT
23522434 TTTCAAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.25
Consensus pattern (26 bp):
AACTAGTCACGTAATACCTTATCAAA
Found at i:23522442 original size:22 final size:24
Alignment explanation
Indices: 23522367--23522442 Score: 84
Period size: 26 Copynumber: 3.1 Consensus size: 24
23522357 AATGCCTATC
* *
23522367 AACTAGTCACGCAATGCCTTATCAGA
1 AACTAGTCACGTAAT--CTTATCAAA
23522393 AACTAGTCACGTAATACCTTATCAAA
1 AACTAGTCACGTAAT--CTTATCAAA
23522419 AACTAGTCACGTAAT-TT-TCAAA
1 AACTAGTCACGTAATCTTATCAAA
23522441 AA
1 AA
23522443 TCACCAAAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
22 7 0.15
23 2 0.04
26 38 0.81
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.26
Consensus pattern (24 bp):
AACTAGTCACGTAATCTTATCAAA
Found at i:23525892 original size:31 final size:31
Alignment explanation
Indices: 23525872--23526261 Score: 296
Period size: 31 Copynumber: 12.6 Consensus size: 31
23525862 GTGTTTATGT
*
23525872 TGGCGTGTAACAAAATTTGACTTGATATGCA
1 TGGCGTGTAACAAAATTTGACGTGATATGCA
* * *
23525903 TGGCGTGTAACAACATTTTACTTGATATGCA
1 TGGCGTGTAACAAAATTTGACGTGATATGCA
* * * * * *
23525934 TGGAGTGTAACAACATTTAACTTGATACGTA
1 TGGCGTGTAACAAAATTTGACGTGATATGCA
* * * * **
23525965 TGGCGTGTTACAACATTTTACGTTATATATA
1 TGGCGTGTAACAAAATTTGACGTGATATGCA
* * * *
23525996 TGGCATGTAACAATATTTTACGTTATATGCA
1 TGGCGTGTAACAAAATTTGACGTGATATGCA
* * *
23526027 TGGCGTGTAACAACATTTTACTTGATATGCA
1 TGGCGTGTAACAAAATTTGACGTGATATGCA
* *
23526058 TGGCGTGTAACAACA-TTGTACTTGATATGCA
1 TGGCGTGTAACAAAATTTG-ACGTGATATGCA
** * ***
23526089 TGGCGTGTAACAATTTTTGACTTGATACAAA
1 TGGCGTGTAACAAAATTTGACGTGATATGCA
* * * * *
23526120 TAGCGTGTAACAACATTTTACATTATATGCA
1 TGGCGTGTAACAAAATTTGACGTGATATGCA
* * * *
23526151 TGGCGTGTAACAAAATTTTATGTTATGTGCA
1 TGGCGTGTAACAAAATTTGACGTGATATGCA
* * *
23526182 TGGCGTGTAACAACATTTTACTTGATATGCA
1 TGGCGTGTAACAAAATTTGACGTGATATGCA
** * * *
23526213 CAGCGTGTAACAACATTTTACTTGATATGCA
1 TGGCGTGTAACAAAATTTGACGTGATATGCA
*** *
23526244 CAACGTGTAACAACATTT
1 TGGCGTGTAACAAAATTT
23526262 ATTTCTTTCT
Statistics
Matches: 307, Mismatches: 50, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
30 2 0.01
31 302 0.98
32 3 0.01
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (31 bp):
TGGCGTGTAACAAAATTTGACGTGATATGCA
Found at i:23525978 original size:62 final size:62
Alignment explanation
Indices: 23525876--23526261 Score: 435
Period size: 62 Copynumber: 6.2 Consensus size: 62
23525866 TTATGTTGGC
* *
23525876 GTGTAACAAAATTTGACTTGATATGCATGGCGTGTAACAACATTTTACTTGATATGCATGGA
1 GTGTAACAACATTTTACTTGATATGCATGGCGTGTAACAACATTTTACTTGATATGCATGGA
* * * * **
23525938 GTGTAACAACATTTAACTTGATACGTATGGCGTGTTACAACATTTTACGTT-ATATATATGGCA
1 GTGTAACAACATTTTACTTGATATGCATGGCGTGTAACAACATTTTAC-TTGATATGCATGG-A
* *
23526001 -TGTAACAATATTTTACGTT-ATATGCATGGCGTGTAACAACATTTTACTTGATATGCATGGC
1 GTGTAACAACATTTTAC-TTGATATGCATGGCGTGTAACAACATTTTACTTGATATGCATGGA
* * *** * *
23526062 GTGTAACAACATTGTACTTGATATGCATGGCGTGTAACAA-TTTTTGACTTGATACAAATAGC
1 GTGTAACAACATTTTACTTGATATGCATGGCGTGTAACAACATTTT-ACTTGATATGCATGGA
* * * *
23526124 GTGTAACAACATTTTACATT-ATATGCATGGCGTGTAACAAAATTTTA-TGTTATGTGCATGGC
1 GTGTAACAACATTTTAC-TTGATATGCATGGCGTGTAACAACATTTTACT-TGATATGCATGGA
** **
23526186 GTGTAACAACATTTTACTTGATATGCACAGCGTGTAACAACATTTTACTTGATATGCA-CAA
1 GTGTAACAACATTTTACTTGATATGCATGGCGTGTAACAACATTTTACTTGATATGCATGGA
23526247 CGTGTAACAACATTT
1 -GTGTAACAACATTT
23526262 ATTTCTTTCT
Statistics
Matches: 273, Mismatches: 38, Indels: 26
0.81 0.11 0.08
Matches are distributed among these distances:
61 11 0.04
62 250 0.92
63 12 0.04
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (62 bp):
GTGTAACAACATTTTACTTGATATGCATGGCGTGTAACAACATTTTACTTGATATGCATGGA
Found at i:23526035 original size:93 final size:93
Alignment explanation
Indices: 23525872--23526261 Score: 475
Period size: 93 Copynumber: 4.2 Consensus size: 93
23525862 GTGTTTATGT
* * *
23525872 TGGCGTGTAACAAAATTTGAC-TTGATATGCATGGCGTGTAACAACATTTTACTTGATATGCATG
1 TGGCGTGTAACAACATTTTACGTT-ATATGCATGGCGTGTAACAACATTTTACTTGATATGCATA
* * * *
23525936 GAGTGTAACAACATTTAACTTGATACGTA
65 GCGTGTAACAACATTTTACTTGATATGCA
* ** * * *
23525965 TGGCGTGTTACAACATTTTACGTTATATATATGGCATGTAACAATATTTTACGTT-ATATGCATG
1 TGGCGTGTAACAACATTTTACGTTATATGCATGGCGTGTAACAACATTTTAC-TTGATATGCATA
23526029 GCGTGTAACAACATTTTACTTGATATGCA
65 GCGTGTAACAACATTTTACTTGATATGCA
* * ***
23526058 TGGCGTGTAACAACATTGTAC-TTGATATGCATGGCGTGTAACAA-TTTTTGACTTGATACAAAT
1 TGGCGTGTAACAACATTTTACGTT-ATATGCATGGCGTGTAACAACATTTT-ACTTGATATGCAT
23526121 AGCGTGTAACAACATTTTACATT-ATATGCA
64 AGCGTGTAACAACATTTTAC-TTGATATGCA
* * * *
23526151 TGGCGTGTAACAAAATTTTATGTTATGTGCATGGCGTGTAACAACATTTTACTTGATATGCACAG
1 TGGCGTGTAACAACATTTTACGTTATATGCATGGCGTGTAACAACATTTTACTTGATATGCATAG
23526216 CGTGTAACAACATTTTACTTGATATGCA
66 CGTGTAACAACATTTTACTTGATATGCA
***
23526244 CAACGTGTAACAACATTT
1 TGGCGTGTAACAACATTT
23526262 ATTTCTTTCT
Statistics
Matches: 254, Mismatches: 34, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
92 10 0.04
93 232 0.91
94 12 0.05
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (93 bp):
TGGCGTGTAACAACATTTTACGTTATATGCATGGCGTGTAACAACATTTTACTTGATATGCATAG
CGTGTAACAACATTTTACTTGATATGCA
Found at i:23528019 original size:145 final size:142
Alignment explanation
Indices: 23527699--23528025 Score: 366
Period size: 145 Copynumber: 2.3 Consensus size: 142
23527689 GTAAGGACAG
* ** * *
23527699 TTCTAACGATTTGTGTTCAACAATTCCATATGTGATTATGGAATAATATATTTGTGTTTGCAGTT
1 TTCTAACGGTTTGTGTTCAACAATTCCATATGTGATTATCAAATAACATATCTGTGTTTGCAGTT
* * * * * * * *
23527764 GGACCATGCGACAGCTCCACAACCACCGAGAGGTCTTTCACAGACTCACAGTGCCAACAAACCAT
66 GGACCATACGACAACTCCACAACCACCGAAAGGTCATCCACAAACGCACAATGCCAACAAACCAT
*** * *
23527829 TGGTAAGATTGG
131 CAATAAGATCGA
* *
23527841 TTCTAACAGTTTGTGTTCAACAATTCCATATGTGATTATCAAATAACATATCTGTGTTTGTAGTT
1 TTCTAACGGTTTGTGTTCAACAATTCCATATGTGATTATCAAATAACATATCTGTGTTTGCAGTT
* *** * * * *
23527906 GGACCACGTAATGACAACTTTTCAACCACCGAAAGGTCATCCTCAAACGCACAATGCTAACGAGC
66 GGACCA--T-ACGACAACTCCACAACCACCGAAAGGTCATCCACAAACGCACAATGCCAACAAAC
23527971 CATCAATAAGATCGA
128 CATCAATAAGATCGA
*
23527986 TTCTAACGGTTTGTGTTCAATAATTCCATATGTGATTATC
1 TTCTAACGGTTTGTGTTCAACAATTCCATATGTGATTATC
23528026 GAATCTGTGT
Statistics
Matches: 152, Mismatches: 30, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
142 64 0.42
144 1 0.01
145 87 0.57
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (142 bp):
TTCTAACGGTTTGTGTTCAACAATTCCATATGTGATTATCAAATAACATATCTGTGTTTGCAGTT
GGACCATACGACAACTCCACAACCACCGAAAGGTCATCCACAAACGCACAATGCCAACAAACCAT
CAATAAGATCGA
Found at i:23528101 original size:138 final size:140
Alignment explanation
Indices: 23527699--23528145 Score: 348
Period size: 138 Copynumber: 3.2 Consensus size: 140
23527689 GTAAGGACAG
* * * * *
23527699 TTCTAACGATTTGTGTTCAACAATTCCATATGTGATTATGGAATAATATATTTGTGTTTGCAGTT
1 TTCTAACGGTTTGTGTTCAACAATTCCATATGTGA-T-T---ATCACATATCTGTGTTTGTAGTT
* * * * * * * * * * * *
23527764 GGACCATG---CGACAGCTCCACAACCACCGAGAGGTCTTTCACAGACTCACAGTGCCAACAAAC
61 GGACCACGCAACGACAACTCCTCAACCACCGAAAGGTCATCCTCAAACGCACAATGCTAACAACC
*** * *
23527826 CATTGGTAAGATTGG
126 CATCAATAAGATCGA
*
23527841 TTCTAACAGTTTGTGTTCAACAATTCCATATGTGATTATCAAATAACATATCTGTGTTTGTAGTT
1 TTCTAACGGTTTGTGTTCAACAATTCCATATGTGATTATC-----ACATATCTGTGTTTGTAGTT
* * ** * *
23527906 GGACCACGTAATGACAACTTTTCAACCACCGAAAGGTCATCCTCAAACGCACAATGCTAACGAGC
61 GGACCACGCAACGACAACTCCTCAACCACCGAAAGGTCATCCTCAAACGCACAATGCTAACAACC
23527971 CATCAATAAGATCGA
126 CATCAATAAGATCGA
* * *
23527986 TTCTAACGGTTTGTGTTCAATAATTCCATATGTGATTATC-GA-ATCTGTGTTTTTAGTTGGACC
1 TTCTAACGGTTTGTGTTCAACAATTCCATATGTGATTATCACATATCTGTGTTTGTAGTTGGACC
* * * * * * * * *
23528049 ATGCGACGATAGCTCCTCAACCACCGAGAGGTTC-TCCTCAGATGCATAATGCTAACAACCCGTC
66 ACGCAACGACAACTCCTCAACCACCGAAAGG-TCATCCTCAAACGCACAATGCTAACAACCCATC
*
23528113 AGTAAGATCGA
130 AATAAGATCGA
* * *
23528124 TTCTAATGATTTGTGTTTAACA
1 TTCTAACGGTTTGTGTTCAACA
23528146 TTTTCACATA
Statistics
Matches: 245, Mismatches: 51, Indels: 22
0.77 0.16 0.07
Matches are distributed among these distances:
137 2 0.01
138 94 0.38
139 3 0.01
140 1 0.00
141 1 0.00
142 57 0.23
145 87 0.36
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (140 bp):
TTCTAACGGTTTGTGTTCAACAATTCCATATGTGATTATCACATATCTGTGTTTGTAGTTGGACC
ACGCAACGACAACTCCTCAACCACCGAAAGGTCATCCTCAAACGCACAATGCTAACAACCCATCA
ATAAGATCGA
Found at i:23536148 original size:21 final size:21
Alignment explanation
Indices: 23536106--23536148 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
23536096 CTTGTACCGG
*
23536106 TGGTGGAACTAAAGGAGTAAC
1 TGGTGGAACTAAAGGAGGAAC
* * *
23536127 TGGTGGTACTATAGGTGGAAC
1 TGGTGGAACTAAAGGAGGAAC
23536148 T
1 T
23536149 TGACCAGTCG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.09, G:0.35, T:0.26
Consensus pattern (21 bp):
TGGTGGAACTAAAGGAGGAAC
Found at i:23538854 original size:20 final size:20
Alignment explanation
Indices: 23538826--23538864 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
23538816 AAACCGTAAA
23538826 TTTCCCTTTGAATTTTCTTG
1 TTTCCCTTTGAATTTTCTTG
* *
23538846 TTTCTCTTTGATTTTTCTT
1 TTTCCCTTTGAATTTTCTT
23538865 TCTTTCTTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.18, G:0.08, T:0.67
Consensus pattern (20 bp):
TTTCCCTTTGAATTTTCTTG
Found at i:23541621 original size:31 final size:31
Alignment explanation
Indices: 23541583--23541682 Score: 103
Period size: 31 Copynumber: 3.2 Consensus size: 31
23541573 TTGGGGCATG
*
23541583 GCGTGTCACCCTTGAATACTACAACAAGTCA
1 GCGTGTCACCCCTGAATACTACAACAAGTCA
* ** * *
23541614 GCGTGTCACGCCCTGTAT-CTACTTCCACTCA
1 GCGTGTCAC-CCCTGAATACTACAACAAGTCA
**
23541645 GCGTGTCACCCCACAATACTACAACAAGTCA
1 GCGTGTCACCCCTGAATACTACAACAAGTCA
*
23541676 GTGTGTC
1 GCGTGTC
23541683 GCGCCATAAA
Statistics
Matches: 53, Mismatches: 14, Indels: 4
0.75 0.20 0.06
Matches are distributed among these distances:
30 5 0.09
31 42 0.79
32 6 0.11
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.24
Consensus pattern (31 bp):
GCGTGTCACCCCTGAATACTACAACAAGTCA
Found at i:23541682 original size:62 final size:62
Alignment explanation
Indices: 23541583--23541716 Score: 178
Period size: 62 Copynumber: 2.2 Consensus size: 62
23541573 TTGGGGCATG
*** * **
23541583 GCGTGTCACCCTTGAATACTACAACAAGTCAGCGTGTCACGCCCTGTATCTACTTCCACTCA
1 GCGTGTCACCCCACAATACTACAACAAGTCAGCGTGTCACGCCATAAATCTACTTCCACTCA
* * * *
23541645 GCGTGTCACCCCACAATACTACAACAAGTCAGTGTGTCGCGCCATAAATCTGCTTCCACTTA
1 GCGTGTCACCCCACAATACTACAACAAGTCAGCGTGTCACGCCATAAATCTACTTCCACTCA
23541707 GCGTGTCACC
1 GCGTGTCACC
23541717 ACAATTGGGG
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.25, C:0.34, G:0.17, T:0.25
Consensus pattern (62 bp):
GCGTGTCACCCCACAATACTACAACAAGTCAGCGTGTCACGCCATAAATCTACTTCCACTCA
Found at i:23541790 original size:86 final size:86
Alignment explanation
Indices: 23541645--23541889 Score: 339
Period size: 86 Copynumber: 2.8 Consensus size: 86
23541635 CTTCCACTCA
* * *
23541645 GCGTGTCACCCCACAATACTACAACAAGTCAGTGTGTC-GCGCCATAAATCTGCTTCCACTTAGC
1 GCGTGTCACCCCACAATACTGCAACAAGTCAGTGTGTCATC-CCATAAATCTGCTTCCACTCAGC
* *
23541709 GTGTCACCACAATTGGGGTGTG
65 GTGTCACCACAATTGGAGAGTG
*
23541731 GCGTGTCACCCCACAATACTGCAACAAGTCAGTGTGTCATCCCATAAATCTGCTTCCACTCAACG
1 GCGTGTCACCCCACAATACTGCAACAAGTCAGTGTGTCATCCCATAAATCTGCTTCCACTCAGCG
* *
23541796 TGCCAACACAATTGGAGAGTG
66 TGTCACCACAATTGGAGAGTG
* * * * * * *
23541817 ACGTGTCACCCCACAATATTGCAACAAGTCAGCGTGTTATGCCATAAATCTGTTTCCACTCAGTG
1 GCGTGTCACCCCACAATACTGCAACAAGTCAGTGTGTCATCCCATAAATCTGCTTCCACTCAGCG
23541882 TGTCACCA
66 TGTCACCA
23541890 GAAGATGTCA
Statistics
Matches: 140, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
86 139 0.99
87 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.24
Consensus pattern (86 bp):
GCGTGTCACCCCACAATACTGCAACAAGTCAGTGTGTCATCCCATAAATCTGCTTCCACTCAGCG
TGTCACCACAATTGGAGAGTG
Found at i:23542194 original size:23 final size:23
Alignment explanation
Indices: 23542168--23542217 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
23542158 ATTTTATATT
23542168 ATTTTTGCAAAAATGATAAATTA
1 ATTTTTGCAAAAATGATAAATTA
*
23542191 ATTTTTGTAAAAATGATAAATTA
1 ATTTTTGCAAAAATGATAAATTA
23542214 ATTT
1 ATTT
23542218 ATTAATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (23 bp):
ATTTTTGCAAAAATGATAAATTA
Found at i:23549272 original size:31 final size:30
Alignment explanation
Indices: 23549234--23549373 Score: 174
Period size: 31 Copynumber: 4.5 Consensus size: 30
23549224 TTTATAAGTC
*
23549234 ATGTTGTTACATGCCATGCATAT-AACGTAA
1 ATGTTGTTACACGCCATGCATATCAA-GTAA
*
23549264 GATGTTGTTACACGCCATGCGTATCAAGTCAA
1 -ATGTTGTTACACGCCATGCATATCAAGT-AA
* *
23549296 ATGTTGTTACACACCATGTATATCAAGTAAA
1 ATGTTGTTACACGCCATGCATATCAAGT-AA
*
23549327 ATGTTGTTACATGCCATGCATATCAAGTCAA
1 ATGTTGTTACACGCCATGCATATCAAGT-AA
*
23549358 ATCTTGTTACACGCCA
1 ATGTTGTTACACGCCA
23549374 ACACTTACAC
Statistics
Matches: 95, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
31 91 0.96
32 4 0.04
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Consensus pattern (30 bp):
ATGTTGTTACACGCCATGCATATCAAGTAA
Found at i:23549313 original size:62 final size:62
Alignment explanation
Indices: 23549234--23549369 Score: 193
Period size: 62 Copynumber: 2.2 Consensus size: 62
23549224 TTTATAAGTC
** * *
23549234 ATGTTGTTACATGCCATGCATAT-AACGTAAGATGTTGTTACACGCCATGCGTATCAAGTCAA
1 ATGTTGTTACACACCATGCATATCAA-GTAAAATGTTGTTACACGCCATGCATATCAAGTCAA
* *
23549296 ATGTTGTTACACACCATGTATATCAAGTAAAATGTTGTTACATGCCATGCATATCAAGTCAA
1 ATGTTGTTACACACCATGCATATCAAGTAAAATGTTGTTACACGCCATGCATATCAAGTCAA
*
23549358 ATCTTGTTACAC
1 ATGTTGTTACAC
23549370 GCCAACACTT
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
62 64 0.97
63 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (62 bp):
ATGTTGTTACACACCATGCATATCAAGTAAAATGTTGTTACACGCCATGCATATCAAGTCAA
Found at i:23550368 original size:2 final size:2
Alignment explanation
Indices: 23550361--23550389 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23550351 TTTTTATTAT
23550361 TA 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 TA T
23550390 GTCACAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23551573 original size:72 final size:72
Alignment explanation
Indices: 23551414--23551574 Score: 187
Period size: 72 Copynumber: 2.2 Consensus size: 72
23551404 AAGATCATAA
* * * *
23551414 AACCCTAGTTGACTAGAGAGGAAGCAAAGTTGACCTTGTTCCAAAAAGATCAAGAAAATCAAGAT
1 AACCATAGTTGACTACAGAGGAAGCAAACTCGACCTTGTTCCAAAAAGATCAAGAAAATCAAGAT
*
23551479 GAAGAAC
66 AAAGAAC
* ** * * * * *
23551486 AATCATAGTCAACTACAGAGGAAGTATACTCGACCTTGTTCTAGAAAGATCAAGAAAATCAAGCT
1 AACCATAGTTGACTACAGAGGAAGCAAACTCGACCTTGTTCCAAAAAGATCAAGAAAATCAAGAT
*
23551551 AAAGAAT
66 AAAGAAC
*
23551558 AACCATATTTGACTACA
1 AACCATAGTTGACTACA
23551575 TAAAAGATAT
Statistics
Matches: 71, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.21
Consensus pattern (72 bp):
AACCATAGTTGACTACAGAGGAAGCAAACTCGACCTTGTTCCAAAAAGATCAAGAAAATCAAGAT
AAAGAAC
Found at i:23551594 original size:72 final size:72
Alignment explanation
Indices: 23551446--23551595 Score: 167
Period size: 72 Copynumber: 2.1 Consensus size: 72
23551436 AGCAAAGTTG
* * *
23551446 ACCTTGTTCCAAAAAGATCAAGAAAATCAAGATGAAGAACAATCATAGTCAACTACAGAGGAAGT
1 ACCTTGTTCCAAAAAGATCAAGAAAATCAAGATAAAGAACAACCATAGTCAACTACAGAGAAAGT
*
23551511 ATACTCG
66 ATACTCA
* * * * * ** *
23551518 ACCTTGTTCTAGAAAGATCAAGAAAATCAAGCTAAAGAATAACCATATTTGACTACATA-AAAGA
1 ACCTTGTTCCAAAAAGATCAAGAAAATCAAGATAAAGAACAACCATAGTCAACTACAGAGAAAG-
*
23551582 TATAGTCA
65 TATACTCA
23551590 ACCTTG
1 ACCTTG
23551596 ATAAGTCAAA
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
71 3 0.05
72 61 0.95
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.23
Consensus pattern (72 bp):
ACCTTGTTCCAAAAAGATCAAGAAAATCAAGATAAAGAACAACCATAGTCAACTACAGAGAAAGT
ATACTCA
Found at i:23551643 original size:20 final size:21
Alignment explanation
Indices: 23551614--23551667 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
23551604 AAAGCCATAA
* *
23551614 ATAGTTAACTTTAAG-AAGCC
1 ATAGTCAACTATAAGAAAGCC
*
23551634 ATAGTCAACTATAAGAAAGGC
1 ATAGTCAACTATAAGAAAGCC
*
23551655 ATAGTCGACTATA
1 ATAGTCAACTATA
23551668 GAAGGGTAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.26
Consensus pattern (21 bp):
ATAGTCAACTATAAGAAAGCC
Found at i:23551659 original size:21 final size:20
Alignment explanation
Indices: 23551614--23551671 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
23551604 AAAGCCATAA
* *
23551614 ATAGTTAACTTTAAGAAGCC
1 ATAGTCAACTATAAGAAGCC
*
23551634 ATAGTCAACTATAAGAAAGGC
1 ATAGTCAACTATAAG-AAGCC
*
23551655 ATAGTCGACTAT-AGAAG
1 ATAGTCAACTATAAGAAG
23551672 GGTAGATTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 3 0.09
20 15 0.45
21 15 0.45
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (20 bp):
ATAGTCAACTATAAGAAGCC
Found at i:23552396 original size:51 final size:51
Alignment explanation
Indices: 23552322--23552428 Score: 198
Period size: 51 Copynumber: 2.1 Consensus size: 51
23552312 AAAATTAAAT
23552322 TTTTA-TTACAAATTACAAATTAAAACATTTTTAATTTGTGCGCCTAAACA
1 TTTTACTTACAAATTACAAATTAAAACATTTTTAATTTGTGCGCCTAAACA
*
23552372 TTTTACTTACAAATTACAAATTAAAACATTTTTAATTTGTGCTCCTAAACA
1 TTTTACTTACAAATTACAAATTAAAACATTTTTAATTTGTGCGCCTAAACA
23552423 TTTTAC
1 TTTTAC
23552429 ACAACCTATT
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 5 0.09
51 50 0.91
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (51 bp):
TTTTACTTACAAATTACAAATTAAAACATTTTTAATTTGTGCGCCTAAACA
Found at i:23553360 original size:179 final size:178
Alignment explanation
Indices: 23553039--23553477 Score: 614
Period size: 179 Copynumber: 2.5 Consensus size: 178
23553029 TGGTGTATCT
* *
23553039 TTAGGAATTTAATTTCAATAAAATTTATCATGATAGATAACTCATGGAACTGTTCCAGAATAAAT
1 TTAGGAATTTAATTCCAATAAAATTTATCATGATAGATAACTCATGGAACTATTCCAGAATAAAT
* ** * * *
23553104 TTTCAGGATTTTATGATTTGATTTAGCTATTCAAAAAATCAAAAACCGTGACCTTTATCTGTAGG
66 TTTCAGGATTTTAGGAGGTGATTTAGCCATTCAAAAAATCAAAAACCGAGACCTTTATCTGCAGG
* * *
23553169 AGGCGGAATTGGTTTTTGAGAACTTTTGAAATTCTTTGTGACTAAAAC
131 AGGCAGAATTGGTTTTTGAGAACTTTTGAAATTCTTTGGGACAAAAAC
* * *
23553217 TTAGGAATTTAATTCCTAATAAAATTTATCTTCATATAT-ACTCATGGAACTATTCCAGAATAAA
1 TTAGGAATTTAATTCC-AATAAAATTTATCATGATAGATAACTCATGGAACTATTCCAGAATAAA
*
23553281 TTTTCAGGATTTTAGGAGGTGA-TTGGCCCATTCAAAAAATTCAAAAACCGAGACCTTTATCTGC
65 TTTTCAGGATTTTAGGAGGTGATTTAG-CCATTCAAAAAA-TCAAAAACCGAGACCTTTATCTGC
*
23553345 AGGAGGCAGAATTGGTTTTTGAGAACTTTTGAAATTTTTTGGGACAAAAAC
128 AGGAGGCAGAATTGGTTTTTGAGAACTTTTGAAATTCTTTGGGACAAAAAC
* * * * * *
23553396 TTAGGAATTTAATTCCAAATAAAATTTATCCTGATAGATAATTTATGGAACAATTCCATAGT-AA
1 TTAGGAATTTAATTCC-AATAAAATTTATCATGATAGATAACTCATGGAACTATTCCAGAATAAA
23553460 TTTTCCAGGATTTTAGGA
65 TTTT-CAGGATTTTAGGA
23553478 AATGATTTTG
Statistics
Matches: 231, Mismatches: 25, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
177 3 0.01
178 69 0.30
179 129 0.56
180 30 0.13
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.36
Consensus pattern (178 bp):
TTAGGAATTTAATTCCAATAAAATTTATCATGATAGATAACTCATGGAACTATTCCAGAATAAAT
TTTCAGGATTTTAGGAGGTGATTTAGCCATTCAAAAAATCAAAAACCGAGACCTTTATCTGCAGG
AGGCAGAATTGGTTTTTGAGAACTTTTGAAATTCTTTGGGACAAAAAC
Found at i:23576573 original size:3 final size:3
Alignment explanation
Indices: 23576565--23576602 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
23576555 TGTCAACTGA
23576565 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
23576603 ATTAATGTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:23624068 original size:79 final size:77
Alignment explanation
Indices: 23623909--23624069 Score: 198
Period size: 79 Copynumber: 2.1 Consensus size: 77
23623899 TGATTGGTTG
* * * *
23623909 AAATTTAGTTTTATCTCTAAATTATCTTAATTATTTATAGATAAATTGGATGACTAATAAGTGAA
1 AAATTTAGATTTATCTCTAAAATATCTTAATTATTTAAAAATAAATTGGATGACTAATAAGTGAA
*
23623974 TCTTAATTGATC
66 TCTTAATTGACC
* * *
23623986 AAATTTAAGATTTATCTTTAAAATATCTTAATTTATTTAAAAATAAATTGGATGATTCATGAA-T
1 AAATTT-AGATTTATCTCTAAAATATCTTAA-TTATTTAAAAATAAATTGGATGACTAAT-AAGT
* *
23624050 GAATTTTAATTGGCC
63 GAATCTTAATTGACC
23624065 AAATT
1 AAATT
23624070 ATGTTATTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
77 6 0.08
78 21 0.30
79 42 0.59
80 2 0.03
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (77 bp):
AAATTTAGATTTATCTCTAAAATATCTTAATTATTTAAAAATAAATTGGATGACTAATAAGTGAA
TCTTAATTGACC
Found at i:23624080 original size:23 final size:23
Alignment explanation
Indices: 23624052--23624096 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
23624042 TCATGAATGA
* *
23624052 ATTTTAATTGGCCAAATTATGTT
1 ATTTTAAATGGCCAAATAATGTT
23624075 ATTTTAAATGGCCAAATAATGT
1 ATTTTAAATGGCCAAATAATGT
23624097 GTAATTGGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (23 bp):
ATTTTAAATGGCCAAATAATGTT
Found at i:23625643 original size:38 final size:38
Alignment explanation
Indices: 23625546--23625635 Score: 162
Period size: 38 Copynumber: 2.4 Consensus size: 38
23625536 ACACACAAGG
*
23625546 CAATATCATCATCATGTGCACTCCCTACTCGCACATTT
1 CAATATCATCATCATGTGCACTCCCTACTCGAACATTT
*
23625584 CAATATCATCATCATGTGCACTCCTTACTCGAACATTT
1 CAATATCATCATCATGTGCACTCCCTACTCGAACATTT
23625622 CAATATCATCATCA
1 CAATATCATCATCA
23625636 CACGCACTTC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.30, C:0.31, G:0.07, T:0.32
Consensus pattern (38 bp):
CAATATCATCATCATGTGCACTCCCTACTCGAACATTT
Found at i:23626552 original size:21 final size:23
Alignment explanation
Indices: 23626505--23626558 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
23626495 TGAGATGGGA
23626505 GGAAAAA-GATGAAGAAGCTACT
1 GGAAAAATGATGAAGAAGCTACT
* *
23626527 GGAAAAATGA-GAAGAAGTTGCT
1 GGAAAAATGATGAAGAAGCTACT
23626549 -GAAAAATGAT
1 GGAAAAATGAT
23626559 ATTTATAGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 9 0.32
22 17 0.61
23 2 0.07
ACGTcount: A:0.50, C:0.06, G:0.28, T:0.17
Consensus pattern (23 bp):
GGAAAAATGATGAAGAAGCTACT
Found at i:23627738 original size:95 final size:95
Alignment explanation
Indices: 23627566--23627741 Score: 280
Period size: 95 Copynumber: 1.9 Consensus size: 95
23627556 TGCAGCCTGG
* *
23627566 AGATGACTTCAAAATACCTCAAAATCCTATTAGCATTTAAAAGAGAATTGAACTCAAGTCTAGAG
1 AGATGACATCAAAATACCTCAAAATCCTATTAGCATTTAAAAGAGAATTGAACTCAAGTCTAGAA
*
23627631 AAAAGTACCGTATCATTAGTGAATTCTTGA
66 AAAAATACCGTATCATTAGTGAATTCTTGA
* * * *
23627661 AGATGACATGAAAATACCTCAAAATCCTTTTAGCATTTAAAAGAGAATTGAACTTAGGTCTAGAA
1 AGATGACATCAAAATACCTCAAAATCCTATTAGCATTTAAAAGAGAATTGAACTCAAGTCTAGAA
*
23627726 AAAAATATCGTATCAT
66 AAAAATACCGTATCAT
23627742 CAAATACTTG
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
95 73 1.00
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (95 bp):
AGATGACATCAAAATACCTCAAAATCCTATTAGCATTTAAAAGAGAATTGAACTCAAGTCTAGAA
AAAAATACCGTATCATTAGTGAATTCTTGA
Found at i:23634420 original size:27 final size:28
Alignment explanation
Indices: 23634390--23634443 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
23634380 ATGTCCTGGT
*
23634390 GGTGG-AAAATTACAATTTTGCCCCTAG
1 GGTGGCAAAATTACAATTTTACCCCTAG
*
23634417 GGTGGCAAAATTACCATTTTACCCCTA
1 GGTGGCAAAATTACAATTTTACCCCTA
23634444 TACTTCAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (28 bp):
GGTGGCAAAATTACAATTTTACCCCTAG
Found at i:23634510 original size:19 final size:19
Alignment explanation
Indices: 23634486--23634523 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
23634476 ACTTCTAAAC
23634486 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
23634505 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
23634524 AGTCCAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:23636435 original size:263 final size:259
Alignment explanation
Indices: 23635969--23636485 Score: 901
Period size: 263 Copynumber: 2.0 Consensus size: 259
23635959 GTATAAGAGG
* *
23635969 GAAATGGTAATTTTGCCACCTCGGGGGCAAATTTGTAAATTTTCACCCCGACACTTGTCAAGACC
1 GAAATGGTAATTTAGCCACCTCGGGGGCAAATCTGTAAATTTTCACCCCGACACTTGTCAAGACC
23636034 AAGGGATTTTATTTATCATGGAAATGGATAAACATGAGAAATGTGTGGCGGAGAATTAAAGAATT
66 AAGGGATTTTATTTATCATGGAAATGGATAAACATGAGAAATGTGTGGCGGAGAATTAAAGAATT
*
23636099 AAAAATCAAATATTTAAAATTTGAACCAATAAGGAAATGCCATGTGTCATGTTTTTATTATTTTA
131 AAAAATCAAATATTTAAAATTTGAACCAATAAGGAAATGCCATGTGTCATGTTTTTATTATGTTA
*
23636164 TTATTTCTTTCTAAAAAGGCAAAAAATCAGCCCATTTCTCCCATAGTGATCAGCCAAACCACNGG
196 TTATTTCTTTAT-AAAAGGCAAAAAATCAG-CCATTTCTCCCATAGTGATCAGCCAAACCAC-GG
23636229 GT
258 GT
23636231 GAAATGGTAATTTAGCCACCTCGGGGGCAAATCTGTAAATTTTCACCCTCGACACTTGTCAAGAC
1 GAAATGGTAATTTAGCCACCTCGGGGGCAAATCTGTAAATTTTCACCC-CGACACTTGTCAAGAC
* *
23636296 TAAGGGGTTTTATTTATCATGGAAATGGATAAACATGAGAAATGTGT-GCTGGAGAATTAAAGAA
65 CAAGGGATTTTATTTATCATGGAAATGGATAAACATGAGAAATGTGTGGC-GGAGAATTAAAGAA
* *
23636360 TTAAAAGTCCAATATTTAAAATTTGAACCAATAAGGAAATGCCATGTGTCATGTTTTTATTATGT
129 TTAAAAATCAAATATTTAAAATTTGAACCAATAAGGAAATGCCATGTGTCATGTTTTTATTATGT
*
23636425 TATTATTTCTTTATAAAAGGCAAAAAATCAGCCATTTCTTCCATAGTGATCAGCCAAACCA
194 TATTATTTCTTTATAAAAGGCAAAAAATCAGCCATTTCTCCCATAGTGATCAGCCAAACCA
23636486 GCAGAGAAGA
Statistics
Matches: 244, Mismatches: 9, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
261 29 0.12
262 65 0.27
263 150 0.61
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.31
Consensus pattern (259 bp):
GAAATGGTAATTTAGCCACCTCGGGGGCAAATCTGTAAATTTTCACCCCGACACTTGTCAAGACC
AAGGGATTTTATTTATCATGGAAATGGATAAACATGAGAAATGTGTGGCGGAGAATTAAAGAATT
AAAAATCAAATATTTAAAATTTGAACCAATAAGGAAATGCCATGTGTCATGTTTTTATTATGTTA
TTATTTCTTTATAAAAGGCAAAAAATCAGCCATTTCTCCCATAGTGATCAGCCAAACCACGGGT
Found at i:23637440 original size:13 final size:13
Alignment explanation
Indices: 23637422--23637446 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23637412 GGAGAAATTG
23637422 TGATTTTATAAAA
1 TGATTTTATAAAA
23637435 TGATTTTATAAA
1 TGATTTTATAAA
23637447 TTTTCTGGAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:23638680 original size:15 final size:15
Alignment explanation
Indices: 23638660--23638698 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
23638650 CAAAGATTTT
*
23638660 GATTTTAAAACTTTG
1 GATTTTAAAACTTTC
**
23638675 GATTTTAAAGTTTTC
1 GATTTTAAAACTTTC
23638690 GATTTTAAA
1 GATTTTAAA
23638699 TTTTAAGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (15 bp):
GATTTTAAAACTTTC
Found at i:23641532 original size:17 final size:17
Alignment explanation
Indices: 23641510--23641545 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
23641500 CACATACCAG
23641510 AATAACAAAC-AAACTTA
1 AATAAC-AACTAAACTTA
23641527 AATAACAACTAAACTTA
1 AATAACAACTAAACTTA
23641544 AA
1 AA
23641546 ACAAATTGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 3 0.17
17 15 0.83
ACGTcount: A:0.64, C:0.17, G:0.00, T:0.19
Consensus pattern (17 bp):
AATAACAACTAAACTTA
Found at i:23642321 original size:35 final size:35
Alignment explanation
Indices: 23642281--23642429 Score: 128
Period size: 35 Copynumber: 4.3 Consensus size: 35
23642271 TTAAACCATC
* *
23642281 ACAATGCTTTTTCACGGGAGCAAGCAGAACCCTCA
1 ACAATGCTTTTTCATGAGAGCAAGCAGAACCCTCA
* * * * *
23642316 ACAATGCTTTATCATGAAAGTAAGCAGCACCCTTA
1 ACAATGCTTTTTCATGAGAGCAAGCAGAACCCTCA
* *
23642351 ACAA--CGTTTTCATGAGAGCAATG--GAACCCT-T
1 ACAATGCTTTTTCATGAGAGCAA-GCAGAACCCTCA
* *
23642382 ACAATGCTTTTTCATGAGAGCAAACGGAACCCTTCA
1 ACAATGCTTTTTCATGAGAGCAAGCAGAACCC-TCA
* *
23642418 TCAATGGTTTTT
1 ACAATGCTTTTT
23642430 AACCGGTTCA
Statistics
Matches: 89, Mismatches: 18, Indels: 13
0.74 0.15 0.11
Matches are distributed among these distances:
31 4 0.04
32 6 0.07
33 29 0.33
34 7 0.08
35 33 0.37
36 10 0.11
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.27
Consensus pattern (35 bp):
ACAATGCTTTTTCATGAGAGCAAGCAGAACCCTCA
Found at i:23644069 original size:40 final size:42
Alignment explanation
Indices: 23643993--23644079 Score: 106
Period size: 40 Copynumber: 2.1 Consensus size: 42
23643983 ATAGATCAAG
* *
23643993 ATATATTTCCAACTAATACATATTCAAGGAAAGCATAAGGAA
1 ATATATTTCCAACTAATACATATTCAAGCAAAGCATAACGAA
* * * *
23644035 ATATATTTCC-ATTAA-ACATATTTAATCAAGGCATAACGAA
1 ATATATTTCCAACTAATACATATTCAAGCAAAGCATAACGAA
23644075 ATATA
1 ATATA
23644080 CGTGTGAGAC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 25 0.64
41 4 0.10
42 10 0.26
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.30
Consensus pattern (42 bp):
ATATATTTCCAACTAATACATATTCAAGCAAAGCATAACGAA
Found at i:23645351 original size:43 final size:43
Alignment explanation
Indices: 23645303--23645421 Score: 177
Period size: 43 Copynumber: 2.8 Consensus size: 43
23645293 GTAATTATAT
*
23645303 TGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GA
1 TGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCG-GTGA
*
23645346 TGACTCGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
1 TGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
* * *
23645389 TGACCCAGCCATGTGCGAGTAGGGAGTGCGCAT
1 TGACTCGGCTATGTGCGAGTAGGGAGTGCGCAT
23645422 GAGCTGGTGA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
42 1 0.01
43 68 0.99
ACGTcount: A:0.22, C:0.20, G:0.38, T:0.20
Consensus pattern (43 bp):
TGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
Found at i:23645431 original size:43 final size:43
Alignment explanation
Indices: 23645313--23645434 Score: 165
Period size: 43 Copynumber: 2.8 Consensus size: 43
23645303 TGACTCGGCT
* * **
23645313 ATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GATGACTCGGTT
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCG-GTGATGACCCAGCC
*
23645356 ATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAGCC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
* *
23645399 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGA
23645435 TGATGATGGG
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
42 1 0.01
43 69 0.99
ACGTcount: A:0.23, C:0.18, G:0.39, T:0.20
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
Found at i:23651916 original size:25 final size:25
Alignment explanation
Indices: 23651865--23651916 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
23651855 TTTTAGTGAG
*
23651865 TTATTTTAATTTTATGTTATTCCTT
1 TTATTTTAATTTTATGTTATTACTT
* *
23651890 TTATTTTAGTTATTAT-TTATTAGTT
1 TTATTTTAATT-TTATGTTATTACTT
23651915 TT
1 TT
23651917 TATATTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.21, C:0.04, G:0.06, T:0.69
Consensus pattern (25 bp):
TTATTTTAATTTTATGTTATTACTT
Found at i:23653033 original size:14 final size:14
Alignment explanation
Indices: 23652998--23653033 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
23652988 CTTGTTGGTT
23652998 TTAATTTTAGTTAA
1 TTAATTTTAGTTAA
* *
23653012 TCATTTTTAGTTAA
1 TTAATTTTAGTTAA
23653026 TTAATTTT
1 TTAATTTT
23653034 GATTATTTGG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.61
Consensus pattern (14 bp):
TTAATTTTAGTTAA
Found at i:23675393 original size:17 final size:17
Alignment explanation
Indices: 23675371--23675431 Score: 59
Period size: 17 Copynumber: 3.3 Consensus size: 17
23675361 TTTCTTTATT
23675371 TTTTTCTCTTTTTCTTA
1 TTTTTCTCTTTTTCTTA
* *
23675388 TTTTTCCCTTTTTTTTCCTTT
1 TTTTT--C-TCTTTTT-CTTA
23675409 TCTTTTCTCTTTTTCTTA
1 T-TTTTCTCTTTTTCTTA
23675427 TTTTT
1 TTTTT
23675432 TGCTTTCCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
17 9 0.26
18 4 0.11
19 7 0.20
20 7 0.20
21 4 0.11
22 4 0.11
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTCTCTTTTTCTTA
Found at i:23677084 original size:13 final size:13
Alignment explanation
Indices: 23677068--23677097 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
23677058 TTTTTTTATA
*
23677068 AATTTTGGATGTC
1 AATTATGGATGTC
23677081 AATTATGGATGTC
1 AATTATGGATGTC
23677094 AATT
1 AATT
23677098 GTTAAGTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (13 bp):
AATTATGGATGTC
Found at i:23680909 original size:2 final size:2
Alignment explanation
Indices: 23680902--23680936 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
23680892 TGTTATGTTG
*
23680902 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23680937 GTATTAATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23684423 original size:76 final size:76
Alignment explanation
Indices: 23684297--23684451 Score: 222
Period size: 76 Copynumber: 2.0 Consensus size: 76
23684287 TTGATACATG
* * * * * *
23684297 TTCATTTTTTGACCAAATCTATTGATACATCCTTAAATATATCAATAGAATT-CTTCTAGAACAT
1 TTCATCTTTTGACCAAATCTATCGATACATCCTCAAATAGATCAATAGAATTAC-TATAGAACAC
23684361 CTCATATTGTTC
65 CTCATATTGTTC
*
23684373 TTCATCTTTTGACCAAATCTATCGATACATCCTCAAATAGATCGATAGAATTACTATAGAACACC
1 TTCATCTTTTGACCAAATCTATCGATACATCCTCAAATAGATCAATAGAATTACTATAGAACACC
*
23684438 TTATATTGTTC
66 TCATATTGTTC
23684449 TTC
1 TTC
23684452 TTGCCAAGAA
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
76 69 0.99
77 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (76 bp):
TTCATCTTTTGACCAAATCTATCGATACATCCTCAAATAGATCAATAGAATTACTATAGAACACC
TCATATTGTTC
Found at i:23684839 original size:22 final size:21
Alignment explanation
Indices: 23684814--23684862 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
23684804 AGTGTTAGCC
23684814 AAAGAATCAATTTCTTAAAAGA
1 AAAGAATCAATTT-TTAAAAGA
* ** *
23684836 AAAGACTTGATTTTTAAATGA
1 AAAGAATCAATTTTTAAAAGA
23684857 AAAGAA
1 AAAGAA
23684863 AGTGAAATCT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (21 bp):
AAAGAATCAATTTTTAAAAGA
Found at i:23685951 original size:35 final size:35
Alignment explanation
Indices: 23685912--23685979 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
23685902 AGGTTATGCT
* * *
23685912 TAATCCTAT-AAAAGGTATGTTGTAGAGGTTACATC
1 TAATCCT-TCAAAAGGCATGTTGCAAAGGTTACATC
23685947 TAATCCTTCAAAAGGCATGTTGCAAAGGTTACA
1 TAATCCTTCAAAAGGCATGTTGCAAAGGTTACA
23685980 CCTGACCCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 1 0.03
35 28 0.97
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (35 bp):
TAATCCTTCAAAAGGCATGTTGCAAAGGTTACATC
Found at i:23708650 original size:17 final size:17
Alignment explanation
Indices: 23708617--23708651 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
23708607 AGTAAAATAT
*
23708617 GCACACACTAAGGGGGA
1 GCACACACTAAGAGGGA
*
23708634 GCACACACTTAGAGGGA
1 GCACACACTAAGAGGGA
23708651 G
1 G
23708652 GAAATCCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.23, G:0.34, T:0.09
Consensus pattern (17 bp):
GCACACACTAAGAGGGA
Found at i:23709728 original size:35 final size:35
Alignment explanation
Indices: 23709675--23709745 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
23709665 AGTTTGTTTG
* *
23709675 GGTTTTGGTTGACACTGGTAAAAACCATTGTGAAA
1 GGTTTTGGCTGACACTGGTAAAAACCATTGTAAAA
*
23709710 GGTTTTGGCTGAGC-CTGGTAAAAGCCATTGTAAAA
1 GGTTTTGGCTGA-CACTGGTAAAAACCATTGTAAAA
23709745 G
1 G
23709746 CTTGGTGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 31 0.97
36 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.30
Consensus pattern (35 bp):
GGTTTTGGCTGACACTGGTAAAAACCATTGTAAAA
Found at i:23716547 original size:192 final size:190
Alignment explanation
Indices: 23716190--23716697 Score: 684
Period size: 192 Copynumber: 2.7 Consensus size: 190
23716180 GTATATTTTC
* * *
23716190 AAATAAAAATTCT-TGATA-TTGAAATTTTCCAAAATCTCCCAAATGCTCATGGTAAAATTTTAG
1 AAATAAAAATCCTCT-ATATTTAAAATTTTCCAAAATCTCCCAAACGCTCATGGTAAAATTTTAG
* * * ***
23716253 AAAATTCTCTCACCTAGAAATTCCCAATAAGCTACCTTTGGTTTTCTTGAGATTTCATCATTGGC
65 AAAATTCTCTCA-CTAGAAATTCCCAAAAAGCTACTTTTGGTTTTTTTGAGATTTCATCATTAAA
* *
23716318 GAACTTATTTATTTAATTCTATTCTAGTTCCATATTCAATTTTTATTTTCCTTATATATTAAA
129 GAACTTATTTATTTAATTCTATTCTAGTTCAATATTCAATATTTATTTTCCTTATATATT-AA
* *
23716381 AAATAAAAATCCTCTATATTTAAAATATTT-CAAAATCTCCTAAACACTCATGGTAAAATTTTAG
1 AAATAAAAATCCTCTATATTTAAAAT-TTTCCAAAATCTCCCAAACGCTCATGGTAAAATTTTAG
* * *
23716445 AAAATTCTCTTAGCTAGAAATTCACAACAAGCTACTTTTGGTTTTTTTGAGATTTCATCATTAAA
65 AAAATTCTCTCA-CTAGAAATTCCCAAAAAGCTACTTTTGGTTTTTTTGAGATTTCATCATTAAA
* *
23716510 GAACTTATTTATTTAATTTTATTCTAGTTCAATATTCAATATTTATTTTCCTTATATATTAT
129 GAACTTATTTATTTAATTCTATTCTAGTTCAATATTCAATATTTATTTTCCTTATATATTAA
* * ** *
23716572 AAATAGAAATCCTCAATATAAAAAATTTTCCAAAATCTCCCAAACGCTTC-TAGTAAAATTTT-G
1 AAATAAAAATCCTCTATATTTAAAATTTTCCAAAATCTCCCAAACGC-TCATGGTAAAATTTTAG
* *
23716635 AAAAATTCTCTCACGTAGAAATTCCCAAAAAGCCACTTTTGGTTTTTTTTAGATTTCATCATT
65 -AAAATTCTCTCAC-TAGAAATTCCCAAAAAGCTACTTTTGGTTTTTTTGAGATTTCATCATT
23716698 GGAAAAATTA
Statistics
Matches: 280, Mismatches: 30, Indels: 14
0.86 0.09 0.04
Matches are distributed among these distances:
190 5 0.02
191 119 0.43
192 153 0.55
193 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.41
Consensus pattern (190 bp):
AAATAAAAATCCTCTATATTTAAAATTTTCCAAAATCTCCCAAACGCTCATGGTAAAATTTTAGA
AAATTCTCTCACTAGAAATTCCCAAAAAGCTACTTTTGGTTTTTTTGAGATTTCATCATTAAAGA
ACTTATTTATTTAATTCTATTCTAGTTCAATATTCAATATTTATTTTCCTTATATATTAA
Done.