Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold8
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: 6381039
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 22487 characters in sequence are not A, C, G, or T
File 25 of 33
Found at i:4303329 original size:21 final size:22
Alignment explanation
Indices: 4303283--4303331 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
4303273 ATTATTTATT
4303283 TATAA-AA-TTTAAATTATTAA
1 TATAATAATTTTAAATTATTAA
4303303 TATAATAATTTTAATATT-TTAA
1 TATAATAATTTTAA-ATTATTAA
4303325 T-TAATAA
1 TATAATAA
4303332 AATAAACAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.19
21 8 0.31
22 10 0.38
23 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TATAATAATTTTAAATTATTAA
Found at i:4305177 original size:16 final size:16
Alignment explanation
Indices: 4305158--4305188 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4305148 ATATATATAA
4305158 ATATAATTATTTTAAT
1 ATATAATTATTTTAAT
*
4305174 ATATAATTTTTTTAA
1 ATATAATTATTTTAA
4305189 AAAAATAAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATAATTATTTTAAT
Found at i:4306368 original size:18 final size:16
Alignment explanation
Indices: 4306328--4306365 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
4306318 GATTATTCTA
4306328 ATTATTATTTTAAAAT
1 ATTATTATTTTAAAAT
*
4306344 -TTATTATATTTAATAT
1 ATTATTAT-TTTAAAAT
4306360 ATTATT
1 ATTATT
4306366 TATTGATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 7 0.37
16 7 0.37
17 5 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTATTATTTTAAAAT
Found at i:4313929 original size:19 final size:22
Alignment explanation
Indices: 4313891--4313931 Score: 61
Period size: 19 Copynumber: 2.0 Consensus size: 22
4313881 AGCCACGTGG
4313891 CTTTTTCTTCTTTCTCATTTTT
1 CTTTTTCTTCTTTCTCATTTTT
4313913 CTTTTT-TT-TTT-TCATTTTT
1 CTTTTTCTTCTTTCTCATTTTT
4313932 TTCTAGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
20 3 0.16
21 2 0.11
22 6 0.32
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (22 bp):
CTTTTTCTTCTTTCTCATTTTT
Found at i:4324518 original size:2 final size:2
Alignment explanation
Indices: 4324511--4324563 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
4324501 CTCTCGACAT
4324511 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4324553 GA GA GA GA GA G
1 GA GA GA GA GA G
4324564 GGTTCAAGCA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4327226 original size:3 final size:3
Alignment explanation
Indices: 4327220--4327263 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
4327210 TCGCGCTTGC
4327220 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
4327264 AACTTGTTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:4327982 original size:30 final size:29
Alignment explanation
Indices: 4327948--4328004 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
4327938 CATTTATTTT
4327948 TATAAATTTATATATTATGTATTGATAATA
1 TATAAATTTATATATTAT-TATTGATAATA
* * *
4327978 TATAATTTTATGTATTATTATTTATAA
1 TATAAATTTATATATTATTATTGATAA
4328005 ATCAGTTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.54
Consensus pattern (29 bp):
TATAAATTTATATATTATTATTGATAATA
Found at i:4329209 original size:28 final size:28
Alignment explanation
Indices: 4329178--4329251 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 28
4329168 ATTAATTAAA
*
4329178 AAATAT-GTAAATAATAAATATATAATTT
1 AAATATAGTAAATAATAAATA-AAAATTT
* * *
4329206 AAATATATTAAATATTTAATAAAAATTT
1 AAATATAGTAAATAATAAATAAAAATTT
* *
4329234 AAATTTAATTAAATAATA
1 AAATAT-AGTAAATAATA
4329252 TAAATTTTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
28 17 0.46
29 20 0.54
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (28 bp):
AAATATAGTAAATAATAAATAAAAATTT
Found at i:4329237 original size:19 final size:19
Alignment explanation
Indices: 4329213--4329270 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
4329203 TTTAAATATA
4329213 TTAAATATTTAATAAAAAT
1 TTAAATATTTAATAAAAAT
4329232 TT-AA-ATTTAATTAAATAAT
1 TTAAATATTTAA-TAAA-AAT
*
4329251 ATAAAT-TTTAATATAAAAT
1 TTAAATATTTAATA-AAAAT
4329270 T
1 T
4329271 AAAGTTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
17 6 0.19
18 6 0.19
19 11 0.34
20 9 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAAATATTTAATAAAAAT
Found at i:4329288 original size:37 final size:37
Alignment explanation
Indices: 4329204--4329282 Score: 94
Period size: 38 Copynumber: 2.2 Consensus size: 37
4329194 AATATATAAT
*
4329204 TTAAAT-ATATTAAATATTTAATAAAAATTTAAATTTAA
1 TTAAATAATA-TAAATATTTAATAAAAATTTAAAGTT-A
4329242 TTAAATAATATAAAT-TTTAATATAAAA-TTAAAGTT-
1 TTAAATAATATAAATATTTAATA-AAAATTTAAAGTTA
4329277 TTAAAT
1 TTAAAT
4329283 TTAATAATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
35 6 0.16
37 14 0.37
38 15 0.39
39 3 0.08
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (37 bp):
TTAAATAATATAAATATTTAATAAAAATTTAAAGTTA
Found at i:4329334 original size:22 final size:21
Alignment explanation
Indices: 4329311--4329352 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
4329301 ATTAAATAAA
4329311 TTTTATATTGATATATTATTAAT
1 TTTTATA-TGATATA-TATTAAT
*
4329334 TTTTGTATGATATATATTA
1 TTTTATATGATATATATTA
4329353 TGAAATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 7 0.39
23 6 0.33
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (21 bp):
TTTTATATGATATATATTAAT
Found at i:4330250 original size:21 final size:24
Alignment explanation
Indices: 4330227--4330280 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 24
4330217 TAAAAAATAA
*
4330227 ATTATTATTATT-T-TATTT-TTA
1 ATTATAATTATTATATATTTATTA
*
4330248 ATTATAATTTTTATATATTTATTA
1 ATTATAATTATTATATATTTATTA
4330272 ATTA-AATTA
1 ATTATAATTA
4330281 ATTTCATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 10 0.37
22 1 0.04
23 9 0.33
24 7 0.26
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
ATTATAATTATTATATATTTATTA
Found at i:4331087 original size:17 final size:18
Alignment explanation
Indices: 4331065--4331098 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4331055 TTCTATTTAT
*
4331065 TAAATAATATCT-AAAAC
1 TAAATAAAATCTGAAAAC
4331082 TAAATAAAATCTGAAAA
1 TAAATAAAATCTGAAAA
4331099 ATGAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.62, C:0.09, G:0.03, T:0.26
Consensus pattern (18 bp):
TAAATAAAATCTGAAAAC
Found at i:4340601 original size:14 final size:15
Alignment explanation
Indices: 4340576--4340606 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
4340566 AATGTCTGAT
4340576 ATAAATATATATTTA
1 ATAAATATATATTTA
4340591 ATAAA-ATATATTTA
1 ATAAATATATATTTA
4340605 AT
1 AT
4340607 TTTTTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAAATATATATTTA
Found at i:4342969 original size:4 final size:4
Alignment explanation
Indices: 4342962--4342995 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
4342952 TATATATATA
4342962 TATG TATG TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TA
4342996 CTGAAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:4343467 original size:23 final size:23
Alignment explanation
Indices: 4343412--4343479 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
4343402 AAGTTATTCT
4343412 ATTTAATTTATTCAATCAATTTTAAA
1 ATTTAATTT-TT-AAT-AATTTTAAA
**
4343438 AAATAATTTTTAATAATTTTAAA
1 ATTTAATTTTTAATAATTTTAAA
* *
4343461 TTTTAATATTT-ATAATTTT
1 ATTTAATTTTTAATAATTTT
4343480 TTATTAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
22 8 0.22
23 16 0.44
24 3 0.08
25 2 0.06
26 7 0.19
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (23 bp):
ATTTAATTTTTAATAATTTTAAA
Found at i:4343480 original size:16 final size:17
Alignment explanation
Indices: 4343440--4343480 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
4343430 ATTTTAAAAA
4343440 ATAATTTTTAATAATTT
1 ATAATTTTTAATAATTT
*
4343457 -TAAATTTTAAT-ATTT
1 ATAATTTTTAATAATTT
4343472 ATAATTTTT
1 ATAATTTTT
4343481 TATTAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATAATTTTTAATAATTT
Found at i:4345000 original size:2 final size:2
Alignment explanation
Indices: 4344993--4345033 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
4344983 CCAAAGACAA
4344993 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4345034 TGATCTCCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:4347241 original size:22 final size:23
Alignment explanation
Indices: 4347199--4347242 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
4347189 ATTTTTACAA
4347199 GTATTCTTGAAAGAAATGAAAGG
1 GTATTCTTGAAAGAAATGAAAGG
*
4347222 GTATTCTTGAATG-AATGAAAG
1 GTATTCTTGAAAGAAATGAAAG
4347243 ATGATGTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.41, C:0.05, G:0.25, T:0.30
Consensus pattern (23 bp):
GTATTCTTGAAAGAAATGAAAGG
Found at i:4351656 original size:20 final size:20
Alignment explanation
Indices: 4351628--4351666 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4351618 ATCGAAATGT
4351628 TTTTCTTATTTATTTATTTA
1 TTTTCTTATTTATTTATTTA
* *
4351648 TTTTGTTATTTCTTTATTT
1 TTTTCTTATTTATTTATTT
4351667 GAAATGCAGT
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:0.15, C:0.05, G:0.03, T:0.77
Consensus pattern (20 bp):
TTTTCTTATTTATTTATTTA
Found at i:4352988 original size:32 final size:31
Alignment explanation
Indices: 4352903--4352990 Score: 122
Period size: 32 Copynumber: 2.7 Consensus size: 31
4352893 GTTGAAACTT
* *
4352903 TTTAATAATTATTAAATTTATAAGTAATTATA
1 TTTAAT-ATTATCAAATTTATGAGTAATTATA
*
4352935 TTTAATATTTATCAAATTTATGAGTAATTTTA
1 TTTAATA-TTATCAAATTTATGAGTAATTATA
4352967 TTTAATATTAATCAAATTTATGAG
1 TTTAATATT-ATCAAATTTATGAG
4352991 AGATTATGTC
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
31 3 0.06
32 48 0.94
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (31 bp):
TTTAATATTATCAAATTTATGAGTAATTATA
Found at i:4354147 original size:11 final size:11
Alignment explanation
Indices: 4354131--4354203 Score: 57
Period size: 11 Copynumber: 7.0 Consensus size: 11
4354121 TCGAGACACG
4354131 ATATAAATATA
1 ATATAAATATA
4354142 ATATAAA-A-A
1 ATATAAATATA
*
4354151 AT-TAATTA-A
1 ATATAAATATA
* *
4354160 AGTATAACT-CA
1 A-TATAAATATA
* *
4354171 ATACAAAAATA
1 ATATAAATATA
4354182 ATATAAATATA
1 ATATAAATATA
4354193 ATATAAATATA
1 ATATAAATATA
4354204 TGAATGTAAC
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
8 3 0.06
9 6 0.12
10 6 0.12
11 34 0.69
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.32
Consensus pattern (11 bp):
ATATAAATATA
Found at i:4354517 original size:18 final size:18
Alignment explanation
Indices: 4354478--4354521 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
4354468 AAATTACATA
* *
4354478 AAAAAATATGAATATGAT
1 AAAATATATGAACATGAT
4354496 AAAATATATGAACATG-T
1 AAAATATATGAACATGAT
4354513 CAAAATATA
1 -AAAATATA
4354522 CATAATACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.59, C:0.05, G:0.09, T:0.27
Consensus pattern (18 bp):
AAAATATATGAACATGAT
Found at i:4354935 original size:17 final size:17
Alignment explanation
Indices: 4354913--4354963 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
4354903 AATTTAATTA
4354913 AAATATAATAAAAAAAT
1 AAATATAATAAAAAAAT
* * *
4354930 AAATATGATACAAATAT
1 AAATATAATAAAAAAAT
4354947 AAA-A-ACATAAAAAAAT
1 AAATATA-ATAAAAAAAT
4354963 A
1 A
4354964 TATGTCAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
16 10 0.37
17 17 0.63
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.22
Consensus pattern (17 bp):
AAATATAATAAAAAAAT
Found at i:4357019 original size:42 final size:42
Alignment explanation
Indices: 4356960--4357042 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
4356950 CCCGACCCTT
4356960 GTCTGCTGCTTTGATAAGGTACTAATTCCTGCGAGTTGTTAG
1 GTCTGCTGCTTTGATAAGGTACTAATTCCTGCGAGTTGTTAG
4357002 GTCTGCTGCTTTGATAAGGTACTAATTCCTGCGAGTTGTTA
1 GTCTGCTGCTTTGATAAGGTACTAATTCCTGCGAGTTGTTA
4357043 TTGCTTCTGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (42 bp):
GTCTGCTGCTTTGATAAGGTACTAATTCCTGCGAGTTGTTAG
Found at i:4357402 original size:132 final size:132
Alignment explanation
Indices: 4357165--4357423 Score: 455
Period size: 132 Copynumber: 2.0 Consensus size: 132
4357155 GAGAAATTCG
4357165 AGCACCACCTGGAAGCCTTTTGGGAGGTGAACTATTCACTATCTGCTGGTCATCTGAGCTGGTAA
1 AGCACCACCTGGAAGCCTTTTGGGAGGTGAACTATTCACTATCTGCTGGTCATCTGAGCTGGTAA
** * *
4357230 ACTGATTTGATATGCATGTCAGCTTTTTCCCAATCTCAGGGAGCCTAGGGGATTGAACTTCAATG
66 ACTGATTTGATACACATATCAGCTTTTTCCCAATCTCAGGGAGCCTAGGGGAATGAACTTCAATG
4357295 CA
131 CA
* *
4357297 AGCACCACCTGGAAGCCTTTTGGGAGGTGACCTATTCACTATCTGCTGGTCATTTGAGCTGGTAA
1 AGCACCACCTGGAAGCCTTTTGGGAGGTGAACTATTCACTATCTGCTGGTCATCTGAGCTGGTAA
*
4357362 ACTGATTTGATGCACATATCAGCTTTTTCCCAATCTCAGGGAGCCTAGGGGAATGAACTTCA
66 ACTGATTTGATACACATATCAGCTTTTTCCCAATCTCAGGGAGCCTAGGGGAATGAACTTCA
4357424 GTATCCGATT
Statistics
Matches: 120, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 120 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (132 bp):
AGCACCACCTGGAAGCCTTTTGGGAGGTGAACTATTCACTATCTGCTGGTCATCTGAGCTGGTAA
ACTGATTTGATACACATATCAGCTTTTTCCCAATCTCAGGGAGCCTAGGGGAATGAACTTCAATG
CA
Found at i:4360774 original size:17 final size:17
Alignment explanation
Indices: 4360723--4360790 Score: 54
Period size: 16 Copynumber: 4.1 Consensus size: 17
4360713 TATTTAATGA
4360723 ATATAATT-TTATAA-AT
1 ATATAATTATTA-AATAT
* *
4360739 ATATAA-TATT-TATAA
1 ATATAATTATTAAATAT
4360754 ATATAATTATTAAATAT
1 ATATAATTATTAAATAT
*
4360771 ATATAAATACTATAAATAT
1 ATATAATTA-T-TAAATAT
4360790 A
1 A
4360791 AAGCGAATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
14 1 0.02
15 8 0.20
16 12 0.29
17 11 0.27
18 1 0.02
19 8 0.20
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATAATTATTAAATAT
Found at i:4360774 original size:32 final size:31
Alignment explanation
Indices: 4360713--4360791 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 31
4360703 CTTTTAATGT
*
4360713 TATTTAATGAATATAATTTTATAAATATATAA
1 TATTT-ATAAATATAATTTTATAAATATATAA
4360745 TATTTATAAATATAATTATTA-AATATATATAA
1 TATTTATAAATATAATT-TTATAA-ATATATAA
*
4360777 -ATACTATAAATATAA
1 TAT-TTATAAATATAA
4360792 AGCGAATAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
31 15 0.36
32 27 0.64
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (31 bp):
TATTTATAAATATAATTTTATAAATATATAA
Found at i:4360792 original size:15 final size:15
Alignment explanation
Indices: 4360722--4360792 Score: 63
Period size: 17 Copynumber: 4.5 Consensus size: 15
4360712 TTATTTAATG
*
4360722 AATAT-AATTTTATA
1 AATATAAATATTATA
4360736 AATATATAATATTTATA
1 AATATA-AATA-TTATA
*
4360753 AATATAATTATTAAATA
1 AATATAAATATT--ATA
* *
4360770 TATATAAATACTATA
1 AATATAAATATTATA
4360785 AATATAAA
1 AATATAAA
4360793 GCGAATAATG
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
14 5 0.11
15 12 0.26
16 6 0.13
17 23 0.50
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (15 bp):
AATATAAATATTATA
Found at i:4368672 original size:19 final size:20
Alignment explanation
Indices: 4368648--4368688 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
4368638 AATTTACATT
*
4368648 AAAATAAAT-TTTATTTTTA
1 AAAATAAATATTTAATTTTA
4368667 AAAATAAATATTTAATTTTA
1 AAAATAAATATTTAATTTTA
4368687 AA
1 AA
4368689 TTTATATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AAAATAAATATTTAATTTTA
Found at i:4370181 original size:33 final size:33
Alignment explanation
Indices: 4370139--4370204 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
4370129 AATAGACTAA
*
4370139 GGTGTGGACTTTTGAGCTGTTGTAATTCCGAAT
1 GGTGTGGACTTTTGAGCTGTTGTAATTACGAAT
4370172 GGTGTGGACTTTTGAGCTGTTGTAATTACGAAT
1 GGTGTGGACTTTTGAGCTGTTGTAATTACGAAT
4370205 ACGATGATGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.11, G:0.30, T:0.39
Consensus pattern (33 bp):
GGTGTGGACTTTTGAGCTGTTGTAATTACGAAT
Found at i:4370245 original size:22 final size:22
Alignment explanation
Indices: 4370217--4370278 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
4370207 GATGATGCCG
4370217 TAAAATATATAAAAATAAAATA
1 TAAAATATATAAAAATAAAATA
* *
4370239 TAAAATATA-ATATAATATAATA
1 TAAAATATATA-AAAATAAAATA
*
4370261 TAATAT-TATAAATAATAA
1 TAAAATATATAAA-AATAA
4370279 TATGAGTAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
21 4 0.12
22 28 0.88
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
TAAAATATATAAAAATAAAATA
Found at i:4370250 original size:5 final size:5
Alignment explanation
Indices: 4370242--4370281 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
4370232 TAAAATATAA
*
4370242 AATAT AATAT AATAT AATAT AATAT TATA- AATAAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AAT-AT AATAT
4370282 GAGTAGAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 2 0.06
5 26 0.84
6 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:4370255 original size:17 final size:17
Alignment explanation
Indices: 4370230--4370299 Score: 54
Period size: 17 Copynumber: 4.1 Consensus size: 17
4370220 AATATATAAA
*
4370230 AATAAAATATAAAATAT
1 AATATAATATAAAATAT
*
4370247 AATATAATATAATATAAT
1 AATATAATATAAAAT-AT
*
4370265 ATTATAA-ATAATAATAT
1 AATATAATATAA-AATAT
* *
4370282 GAGTAGAATAT-AAATAT
1 -AATATAATATAAAATAT
4370299 A
1 A
4370300 TTTAAAATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
16 1 0.02
17 24 0.56
18 16 0.37
19 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.34
Consensus pattern (17 bp):
AATATAATATAAAATAT
Found at i:4370262 original size:15 final size:14
Alignment explanation
Indices: 4370223--4370281 Score: 61
Period size: 15 Copynumber: 4.3 Consensus size: 14
4370213 GCCGTAAAAT
*
4370223 ATATAA-AAATAAA
1 ATATAATAAATATA
4370236 ATAT-A-AAATATA
1 ATATAATAAATATA
4370248 ATATAATATAATATA
1 ATATAATA-AATATA
*
4370263 ATATTATAAATAATA
1 ATATAATAAAT-ATA
4370278 ATAT
1 ATAT
4370282 GAGTAGAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
12 11 0.28
13 5 0.12
14 4 0.10
15 20 0.50
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
ATATAATAAATATA
Found at i:4373195 original size:2 final size:2
Alignment explanation
Indices: 4373188--4373217 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4373178 AAGATGAATG
4373188 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4373218 GAAGCTTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4373603 original size:20 final size:22
Alignment explanation
Indices: 4373578--4373620 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
4373568 TTTAATGAGG
4373578 TAAAAT-GATAAGATTTT-GAA
1 TAAAATCGATAAGATTTTAGAA
*
4373598 TAAAATCGATAATATTTTAGAA
1 TAAAATCGATAAGATTTTAGAA
4373620 T
1 T
4373621 TATAAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 10 0.50
22 4 0.20
ACGTcount: A:0.49, C:0.02, G:0.12, T:0.37
Consensus pattern (22 bp):
TAAAATCGATAAGATTTTAGAA
Found at i:4374314 original size:16 final size:18
Alignment explanation
Indices: 4374293--4374354 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 18
4374283 TATATATAAA
4374293 ATATAAT-TAAA-ATATG
1 ATATAATATAAATATATG
4374309 ATATAATATAAATATAT-
1 ATATAATATAAATATATG
* * * *
4374326 AAATATTTTAAA-ATA-A
1 ATATAATATAAATATATG
4374342 ATATAATATAAAT
1 ATATAATATAAAT
4374355 TATTATTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
16 19 0.53
17 13 0.36
18 4 0.11
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
ATATAATATAAATATATG
Found at i:4374372 original size:29 final size:31
Alignment explanation
Indices: 4374280--4374372 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 31
4374270 CACGATGAAT
*
4374280 ATATATATATAAA-ATATA-A--TTAAAATATG
1 ATATA-ATATAAATATATATATTTTAAAATA-A
4374309 ATATAATATAAATATATAAATATTTTAAAATAA
1 ATATAATATAAATATAT--ATATTTTAAAATAA
4374342 ATATAATATAAAT-TAT-TATTTTATAAA-AA
1 ATATAATATAAATATATATATTTTA-AAATAA
4374371 AT
1 AT
4374373 TAAATCAAGA
Statistics
Matches: 56, Mismatches: 1, Indels: 14
0.79 0.01 0.20
Matches are distributed among these distances:
28 7 0.12
29 20 0.36
30 3 0.05
31 1 0.02
32 4 0.07
33 13 0.23
34 8 0.14
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (31 bp):
ATATAATATAAATATATATATTTTAAAATAA
Found at i:4374386 original size:29 final size:29
Alignment explanation
Indices: 4374299--4374372 Score: 78
Period size: 33 Copynumber: 2.4 Consensus size: 29
4374289 TAAAATATAA
*
4374299 TTAAAATATGATATAATATAAATATATAAATATT
1 TTAAAATA-AATATAATATAAAT-TAT---TATT
4374333 TTAAAATAAATATAATATAAATTATTATT
1 TTAAAATAAATATAATATAAATTATTATT
4374362 TTATAAA-AAAT
1 TTA-AAATAAAT
4374373 TAAATCAAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
29 11 0.29
30 3 0.08
32 3 0.08
33 13 0.34
34 8 0.21
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (29 bp):
TTAAAATAAATATAATATAAATTATTATT
Found at i:4374485 original size:3 final size:3
Alignment explanation
Indices: 4374477--4374510 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
4374467 ATCCCTTTTC
4374477 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
4374511 AGAAATCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:4375540 original size:22 final size:22
Alignment explanation
Indices: 4375505--4375587 Score: 66
Period size: 22 Copynumber: 3.7 Consensus size: 22
4375495 CAATTAGAGG
*
4375505 ATAAAATGTAATATAAA-A-ATA
1 ATAAAAT-TTATATAAATATATA
4375526 ATTAAAATATTATATTAAATATATA
1 A-TAAAAT-TTATA-TAAATATATA
*
4375551 ATAAAATTTATAT-AATATAAA
1 ATAAAATTTATATAAATATATA
*
4375572 ATATTAATTTAT-TAAA
1 ATA-AAATTTATATAAA
4375588 ATTTATATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
21 12 0.23
22 20 0.38
23 9 0.17
24 7 0.13
25 4 0.08
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (22 bp):
ATAAAATTTATATAAATATATA
Found at i:4375562 original size:14 final size:14
Alignment explanation
Indices: 4375545--4375597 Score: 52
Period size: 16 Copynumber: 3.5 Consensus size: 14
4375535 TTATATTAAA
4375545 TATATAATAAAATT
1 TATATAATAAAATT
4375559 TATATAATATAAAATAT
1 TATAT-A-ATAAAAT-T
* *
4375576 TAATTTATTAAAATT
1 T-ATATAATAAAATT
4375591 TATATAA
1 TATATAA
4375598 ATATATAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 9 0.29
15 3 0.10
16 13 0.42
17 3 0.10
18 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAATAAAATT
Found at i:4375570 original size:16 final size:16
Alignment explanation
Indices: 4375551--4375602 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
4375541 TAAATATATA
4375551 ATAAAATTTATATAAT
1 ATAAAATTTATATAAT
*
4375567 ATAAAATATTA-AT-TT
1 ATAAAAT-TTATATAAT
4375582 ATTAAAATTTATATAAAT
1 A-TAAAATTTATAT-AAT
4375600 ATA
1 ATA
4375603 TAAGATCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
15 5 0.17
16 17 0.59
17 5 0.17
18 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAAAATTTATATAAT
Found at i:4375575 original size:12 final size:12
Alignment explanation
Indices: 4375505--4375575 Score: 58
Period size: 14 Copynumber: 5.8 Consensus size: 12
4375495 CAATTAGAGG
*
4375505 ATAAAATGTAAT
1 ATAAAATATAAT
4375517 ATAAAA-ATAAT
1 ATAAAATATAAT
*
4375528 -TAAAATATTAT
1 ATAAAATATAAT
4375539 ATTAAATATATAAT
1 A-TAAA-ATATAAT
4375553 A-AAATTTATATAAT
1 ATAAA---ATATAAT
4375567 ATAAAATAT
1 ATAAAATAT
4375576 TAATTTATTA
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
10 5 0.10
11 8 0.16
12 13 0.27
13 4 0.08
14 16 0.33
15 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (12 bp):
ATAAAATATAAT
Found at i:4377538 original size:50 final size:49
Alignment explanation
Indices: 4377440--4377556 Score: 114
Period size: 50 Copynumber: 2.4 Consensus size: 49
4377430 TTGTATTATT
*
4377440 TATGTTGTAATCGTGTCGTATCATATTAAGATAAACAGATCAAGTTTAA
1 TATGTAGTAATCGTGTCGTATCATATTAAGATAAACAGATCAAGTTTAA
* * * * * *
4377489 CTATGTCGTAATCGTGTCTTATCGTATTAA-ATTTAAA-ATATTAATTTTAA
1 -TATGTAGTAATCGTGTCGTATCATATTAAGA--TAAACAGATCAAGTTTAA
*
4377539 -ATGTATTAATCGTGTCGT
1 TATGTAGTAATCGTGTCGT
4377557 GTCGCGCACA
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
48 15 0.27
49 1 0.02
50 36 0.64
51 4 0.07
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (49 bp):
TATGTAGTAATCGTGTCGTATCATATTAAGATAAACAGATCAAGTTTAA
Found at i:4382979 original size:2 final size:2
Alignment explanation
Indices: 4382972--4383000 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4382962 CTAGAAGCCC
4382972 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
4383001 AATGGCTCCA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:4384013 original size:18 final size:18
Alignment explanation
Indices: 4383986--4384027 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
4383976 TATCAGCAAT
*
4383986 AGCCAAAGCCAAAGCCAC
1 AGCCACAGCCAAAGCCAC
* *
4384004 AGCCACAGCCATAGCCAT
1 AGCCACAGCCAAAGCCAC
4384022 AGCCAC
1 AGCCAC
4384028 CAGCATCGAC
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:0.38, C:0.40, G:0.17, T:0.05
Consensus pattern (18 bp):
AGCCACAGCCAAAGCCAC
Found at i:4385330 original size:127 final size:129
Alignment explanation
Indices: 4385156--4385423 Score: 461
Period size: 129 Copynumber: 2.1 Consensus size: 129
4385146 TAAATATATA
* ** *
4385156 AATAATTAATACCATCCAAATGGATAAAAGAGGTTAATTTTATTATATATTGAACATTA-A-ATA
1 AATATTTAATACCATCCAAAAAGATAAAAGAGGTTAATTCTATTATATATTGAACATTATATATA
4385219 TATATATATTT-GTAATGAATCAGATTTTGATTCTAAGGTGATTGTGAAATGATGCTGCCCTTGG
66 TATATATATTTGGT-ATGAATCAGATTTTGATTCTAAGGTGATTGTGAAATGATGCTGCCCTTGG
*
4385283 AATATTTAATACCATCCAAAAAGATAAGAGAGGTTAATTCTATTATATATTGAACATTATATATA
1 AATATTTAATACCATCCAAAAAGATAAAAGAGGTTAATTCTATTATATATTGAACATTATATATA
4385348 TATATATATTTGGTATGAATCAGATTTTGATTCTAAGGTGATTGTGAAATGATGCTGCCCTTGG
66 TATATATATTTGGTATGAATCAGATTTTGATTCTAAGGTGATTGTGAAATGATGCTGCCCTTGG
4385412 AATATTTAATAC
1 AATATTTAATAC
4385424 TCCTTTATCG
Statistics
Matches: 133, Mismatches: 5, Indels: 4
0.94 0.04 0.03
Matches are distributed among these distances:
127 54 0.41
128 1 0.01
129 76 0.57
130 2 0.02
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (129 bp):
AATATTTAATACCATCCAAAAAGATAAAAGAGGTTAATTCTATTATATATTGAACATTATATATA
TATATATATTTGGTATGAATCAGATTTTGATTCTAAGGTGATTGTGAAATGATGCTGCCCTTGG
Found at i:4387033 original size:17 final size:17
Alignment explanation
Indices: 4387011--4387043 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
4387001 TTCTTGAACA
4387011 AATTTAGTATCATATTC
1 AATTTAGTATCATATTC
4387028 AATTTAGTATCATATT
1 AATTTAGTATCATATT
4387044 AATCCCATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (17 bp):
AATTTAGTATCATATTC
Found at i:4397447 original size:2 final size:2
Alignment explanation
Indices: 4397440--4397465 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4397430 ATAAAGTTGC
4397440 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
4397466 CTCCCCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4398485 original size:3 final size:3
Alignment explanation
Indices: 4398479--4398519 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
4398469 AAAAAGTGTT
4398479 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4398520 TTGCATGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4400088 original size:19 final size:18
Alignment explanation
Indices: 4400055--4400095 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
4400045 AAATTGAATT
4400055 ATTTAATATATTTAATAA
1 ATTTAATATATTTAATAA
* *
4400073 ATTTAATTTGATTTAATTA
1 ATTTAATAT-ATTTAATAA
4400092 ATTT
1 ATTT
4400096 TAAATATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
ATTTAATATATTTAATAA
Found at i:4400099 original size:26 final size:25
Alignment explanation
Indices: 4400037--4400112 Score: 66
Period size: 26 Copynumber: 2.9 Consensus size: 25
4400027 TTATATATAT
* *
4400037 TTAATTATAAATTGAA-TTATTTAA
1 TTAATTTTAAATTTAATTTATTTAA
4400061 -TATATTTAATAAATTTAATTTGATTTAA
1 TTA-ATTT--TAAATTTAATTT-ATTTAA
*
4400089 TTAATTTTAAATATAATTTTATTT
1 TTAATTTTAAATTTAA-TTTATTT
4400113 TATTTTAAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
23 2 0.05
24 3 0.07
26 20 0.48
27 5 0.12
28 10 0.24
29 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (25 bp):
TTAATTTTAAATTTAATTTATTTAA
Found at i:4401614 original size:28 final size:28
Alignment explanation
Indices: 4401562--4401615 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
4401552 AAAACTATTA
**
4401562 TTGCATGTAGAGTAGTAAATTTTTTTTT
1 TTGCATGTAGAGTAGTAAAAGTTTTTTT
*
4401590 TTGCATGTAGAGTGGTAAAAGTTTTT
1 TTGCATGTAGAGTAGTAAAAGTTTTT
4401616 ATAACTACCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.26, C:0.04, G:0.22, T:0.48
Consensus pattern (28 bp):
TTGCATGTAGAGTAGTAAAAGTTTTTTT
Found at i:4402639 original size:2 final size:2
Alignment explanation
Indices: 4402632--4402658 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4402622 TTCAAAGACC
4402632 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 A
4402659 GTTTTAACGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4403256 original size:12 final size:12
Alignment explanation
Indices: 4403232--4403264 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4403222 CTCCTTCCCC
*
4403232 TTTC-TTTTCTT
1 TTTCTTTTTTTT
4403243 TTTCTTTTTTTT
1 TTTCTTTTTTTT
4403255 TTTCTTTTTT
1 TTTCTTTTTT
4403265 CACTTCTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (12 bp):
TTTCTTTTTTTT
Found at i:4406486 original size:2 final size:2
Alignment explanation
Indices: 4406479--4406523 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
4406469 ATGTAGTGTT
*
4406479 TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
4406521 TC T
1 TC T
4406524 ATATATATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:4406545 original size:2 final size:2
Alignment explanation
Indices: 4406540--4406570 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4406530 ATATATATAT
*
4406540 AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4406571 ATGAGCATCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4410598 original size:3 final size:3
Alignment explanation
Indices: 4410590--4410620 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
4410580 ATGTCCTCAC
4410590 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
4410621 CCAATCTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:4413646 original size:48 final size:48
Alignment explanation
Indices: 4413570--4413662 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 48
4413560 AGAATCAGAA
**
4413570 TCTGAAAATGATATCGAATGCCGTACAAAACGAGAAGTGGAGCAGTGT
1 TCTGAAAATGATATCGAATGCCAAACAAAACGAGAAGTGGAGCAGTGT
* * * * *
4413618 TCTGAAAATGATGTTGAGTGCCAAACAAAATGGGAAGTGGAGCAG
1 TCTGAAAATGATATCGAATGCCAAACAAAACGAGAAGTGGAGCAG
4413663 AACGATGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.38, C:0.13, G:0.29, T:0.20
Consensus pattern (48 bp):
TCTGAAAATGATATCGAATGCCAAACAAAACGAGAAGTGGAGCAGTGT
Found at i:4420067 original size:16 final size:16
Alignment explanation
Indices: 4420018--4420069 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
4420008 TTTATTTTTA
4420018 TTATATTTATATAAATT
1 TTATA-TTATATAAATT
* **
4420035 TTAAAAAAT-TAATATT
1 TTATATTATATAA-ATT
4420051 TTATATTATATAAATT
1 TTATATTATATAAATT
4420067 TTA
1 TTA
4420070 AGTGTACAGT
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
15 3 0.11
16 17 0.63
17 7 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATATTATATAAATT
Found at i:4420184 original size:2 final size:2
Alignment explanation
Indices: 4420177--4420201 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4420167 TCTCCTCCCC
4420177 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 A
4420202 ACCACTCTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4421906 original size:2 final size:2
Alignment explanation
Indices: 4421899--4421927 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4421889 TTCATACTTT
4421899 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
4421928 GCAAATGTTA
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:4426361 original size:19 final size:20
Alignment explanation
Indices: 4426337--4426378 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
4426327 TATAAATTAT
4426337 AATTTAAAAATATGATAA-A
1 AATTTAAAAATATGATAATA
* *
4426356 AATTTATAAATATTATAATA
1 AATTTAAAAATATGATAATA
4426376 AAT
1 AAT
4426379 ATGAATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
AATTTAAAAATATGATAATA
Found at i:4430563 original size:13 final size:13
Alignment explanation
Indices: 4430545--4430609 Score: 51
Period size: 13 Copynumber: 4.8 Consensus size: 13
4430535 ATAAAAAAAA
4430545 TTTTTAATTATAT
1 TTTTTAATTATAT
4430558 TTTTTATTATTATAT
1 TTTTTA--ATTATAT
* *
4430573 TTTATAATAATA-
1 TTTTTAATTATAT
* * *
4430585 GTTATAATTTTAT
1 TTTTTAATTATAT
4430598 TTTATTAATTAT
1 TTT-TTAATTAT
4430610 TGATTCGTTG
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
12 9 0.22
13 13 0.32
14 6 0.15
15 12 0.30
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (13 bp):
TTTTTAATTATAT
Found at i:4433880 original size:18 final size:19
Alignment explanation
Indices: 4433859--4433895 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
4433849 AATTTAATTA
*
4433859 TAAATTTTAA-ATAAAAAT
1 TAAATATTAATATAAAAAT
4433877 TAAATATTAATATAAAAAT
1 TAAATATTAATATAAAAAT
4433896 ATTTTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAATATTAATATAAAAAT
Found at i:4433980 original size:18 final size:17
Alignment explanation
Indices: 4433953--4433986 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
4433943 TGGGCAAATG
*
4433953 AATTTTTTTTCTTATCTC
1 AATTTATTTTC-TATCTC
4433971 AATTTATTTTCTATCT
1 AATTTATTTTCTATCT
4433987 TTAGCCTACC
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:0.15, G:0.00, T:0.65
Consensus pattern (17 bp):
AATTTATTTTCTATCTC
Found at i:4434737 original size:3 final size:3
Alignment explanation
Indices: 4434729--4434769 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
4434719 AACTTTTTCC
4434729 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
4434770 CCTCTGTCAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:4435217 original size:2 final size:2
Alignment explanation
Indices: 4435210--4435240 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4435200 CTGGCTCGTA
4435210 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 A
4435241 ACCAACAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4437750 original size:22 final size:22
Alignment explanation
Indices: 4437690--4437750 Score: 54
Period size: 22 Copynumber: 2.7 Consensus size: 22
4437680 CATAACAATA
* *
4437690 ATATTTATTTAATATTTCTATTAT
1 ATATTTATATAA-A-TTATATTAT
4437714 -T-TTTATATTATAATTATATTAT
1 ATATTTATA-TA-AATTATATTAT
4437736 ATATTTATATAAATT
1 ATATTTATATAAATT
4437751 TAAAATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
22 17 0.55
23 7 0.23
24 7 0.23
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
ATATTTATATAAATTATATTAT
Found at i:4438121 original size:20 final size:20
Alignment explanation
Indices: 4438082--4438145 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
4438072 TAGAAAAAAT
*
4438082 AAATTATATATAATATATTTTA
1 AAATTAAATA-AATA-ATTTTA
4438104 AAATTAAATAAATAATTTTA
1 AAATTAAATAAATAATTTTA
* * *
4438124 AAAATAAATAATTGATTTTA
1 AAATTAAATAAATAATTTTA
4438144 AA
1 AA
4438146 TAAAAATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
20 25 0.66
21 4 0.11
22 9 0.24
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
AAATTAAATAAATAATTTTA
Found at i:4438162 original size:20 final size:20
Alignment explanation
Indices: 4438091--4438162 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
4438081 TAAATTATAT
* *
4438091 ATAATATATTTTAAAAT-TAA
1 ATAA-ATATTTTTAAATAAAA
*
4438111 ATAAATAATTTTAAA-AATAA
1 ATAAATATTTTTAAATAA-AA
*
4438131 ATAATTGA-TTTTAAATAAAA
1 ATAAAT-ATTTTTAAATAAAA
4438151 ATAAATATTTTT
1 ATAAATATTTTT
4438163 TTAAAAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
19 10 0.24
20 29 0.69
21 3 0.07
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (20 bp):
ATAAATATTTTTAAATAAAA
Found at i:4438173 original size:20 final size:23
Alignment explanation
Indices: 4438122--4438171 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
4438112 TAAATAATTT
4438122 TAAAAATAAATAATTGATTTTAAA
1 TAAAAATAAATAATT-ATTTTAAA
*
4438146 TAAAAATAAAT-ATTTTTTTAAA
1 TAAAAATAAATAATTATTTTAAA
4438168 -AAAA
1 TAAAA
4438172 TATTTTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 4 0.16
22 7 0.28
23 3 0.12
24 11 0.44
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
TAAAAATAAATAATTATTTTAAA
Found at i:4444020 original size:1 final size:1
Alignment explanation
Indices: 4444014--4444039 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
4444004 GGCCAATCAC
4444014 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
4444040 GGTGGAAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4448336 original size:22 final size:22
Alignment explanation
Indices: 4448311--4448352 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
4448301 AATAAAATAA
4448311 AATATTAA-ATTAATTTAAATTC
1 AATA-TAATATTAATTTAAATTC
*
4448333 AATATAATTTTAATTTAAAT
1 AATATAATATTAATTTAAAT
4448353 AAAAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
AATATAATATTAATTTAAATTC
Found at i:4449768 original size:17 final size:18
Alignment explanation
Indices: 4449746--4449784 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
4449736 ATCTACCGAT
4449746 AAATATTTTAC-TTTAAC
1 AAATATTTTACATTTAAC
*
4449763 AAATATTTTACATTTATC
1 AAATATTTTACATTTAAC
4449781 AAAT
1 AAAT
4449785 TTGAAAACTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATATTTTACATTTAAC
Found at i:4450083 original size:10 final size:10
Alignment explanation
Indices: 4450064--4450172 Score: 59
Period size: 10 Copynumber: 10.9 Consensus size: 10
4450054 TAGTATGAAA
4450064 AAAATA-ATT
1 AAAATATATT
4450073 AAAATATATT
1 AAAATATATT
*
4450083 AAAATAAAAATTT
1 AAAAT--ATA-TT
*
4450096 AAAAT-TAAT
1 AAAATATATT
*
4450105 ATAATATA--
1 AAAATATATT
4450113 AAAATATATT
1 AAAATATATT
*
4450123 AAAATTTATAT
1 AAAATATAT-T
*
4450134 AAAATAAATT
1 AAAATATATT
*
4450144 ATTAAT-TATT
1 A-AAATATATT
*
4450154 AAAATTTA-T
1 AAAATATATT
4450163 ATAAATATAT
1 A-AAATATAT
4450173 AATATTTTAA
Statistics
Matches: 76, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
8 7 0.09
9 16 0.21
10 33 0.43
11 11 0.14
12 2 0.03
13 7 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
AAAATATATT
Found at i:4450094 original size:22 final size:23
Alignment explanation
Indices: 4450061--4450141 Score: 60
Period size: 27 Copynumber: 3.3 Consensus size: 23
4450051 GTATAGTATG
4450061 AAAA-AAATAATTAAAA-T-ATATT
1 AAAATAAA-AATTAAAATTAATA-T
4450083 AAAATAAAAATTTAAAATTAATAT
1 AAAATAAAAA-TTAAAATTAATAT
* *
4450107 AATATAAAAATATATTAAAATTTATAT
1 AA-A-ATAAA-A-ATTAAAATTAATAT
4450134 AAAATAAA
1 AAAATAAA
4450142 TTATTAATTA
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
22 6 0.12
23 9 0.19
24 4 0.08
25 8 0.17
26 5 0.10
27 15 0.31
28 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAATAAAAATTAAAATTAATAT
Found at i:4450105 original size:27 final size:27
Alignment explanation
Indices: 4450063--4450141 Score: 73
Period size: 25 Copynumber: 3.1 Consensus size: 27
4450053 ATAGTATGAA
4450063 AAAAATAATTAAAA-T-ATAT-TAAAAT
1 AAAAAT-ATTAAAATTAATATATAAAAT
*
4450088 AAAAAT-TTAAAATTAATATAATATAA-
1 AAAAATATTAAAATTAATAT-ATAAAAT
*
4450114 AAATATATTAAAATT--TATATAAAAT
1 AAAAATATTAAAATTAATATATAAAAT
4450139 AAA
1 AAA
4450142 TTATTAATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
23 6 0.13
24 6 0.13
25 16 0.36
26 5 0.11
27 12 0.27
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (27 bp):
AAAAATATTAAAATTAATATATAAAAT
Found at i:4450115 original size:23 final size:23
Alignment explanation
Indices: 4450071--4450141 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 23
4450061 AAAAAAATAA
*
4450071 TTAAAATATATTAAAATAAAAAT
1 TTAAAATATAATAAAATAAAAAT
4450094 TTAAAAT-TAATATAATATAAAAATAT
1 TTAAAATATAATA-AA-AT-AAAA-AT
*
4450120 ATTAAAATTTATATAAAATAAA
1 -TTAAAATATA-ATAAAATAAA
4450142 TTATTAATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
22 4 0.10
23 9 0.22
24 2 0.05
25 4 0.10
26 5 0.12
27 9 0.22
28 4 0.10
29 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
TTAAAATATAATAAAATAAAAAT
Found at i:4450168 original size:26 final size:28
Alignment explanation
Indices: 4450137--4450198 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 28
4450127 TTTATATAAA
4450137 ATAAATTAT-TAAT-TATT-AAAATTTAT
1 ATAAATTATATAATATATTAAAAATTT-T
*
4450163 ATAAA-TATATAATATTTTAAAAATTTT
1 ATAAATTATATAATATATTAAAAATTTT
4450190 ATAATATTA
1 ATAA-ATTA
4450199 AAAATATCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
25 3 0.10
26 9 0.30
27 8 0.27
28 8 0.27
29 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
ATAAATTATATAATATATTAAAAATTTT
Found at i:4450609 original size:17 final size:17
Alignment explanation
Indices: 4450584--4450619 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4450574 ATTTTTTTAA
*
4450584 ATATTTATATTTAATAT
1 ATATATATATTTAATAT
*
4450601 ATATATATATTTGATAT
1 ATATATATATTTAATAT
4450618 AT
1 AT
4450620 TTTTTAATAT
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:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
ATATATATATTTAATAT
Found at i:4453363 original size:2 final size:2
Alignment explanation
Indices: 4453356--4453383 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4453346 AGTTTCTTTA
4453356 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4453384 GAAATCTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4455220 original size:18 final size:18
Alignment explanation
Indices: 4455197--4455248 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 18
4455187 ATATTTTATA
4455197 TAAATTAATTTAATTTTT
1 TAAATTAATTTAATTTTT
* *
4455215 TAAATTTATAT-ATTTTT
1 TAAATTAATTTAATTTTT
*
4455232 AAAATTTTAATTTAATT
1 TAAA--TTAATTTAATT
4455249 ATTATTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 9 0.35
18 9 0.35
19 5 0.19
20 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TAAATTAATTTAATTTTT
Found at i:4455409 original size:2 final size:2
Alignment explanation
Indices: 4455404--4455437 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4455394 TTATATAGTC
4455404 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4455438 GGATAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4460199 original size:20 final size:20
Alignment explanation
Indices: 4460136--4460199 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
4460126 AAATTAAGTA
4460136 ATTAATTTATACTATTAACT
1 ATTAATTTATACTATTAACT
** *
4460156 ATTAA---ATACCTCATCCAGT
1 ATTAATTTATA-CT-ATTAACT
4460175 AATTAATTTATACTATTAACT
1 -ATTAATTTATACTATTAACT
4460196 ATTA
1 ATTA
4460200 TATATCTCAT
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
17 3 0.09
18 2 0.06
19 4 0.12
20 14 0.44
21 4 0.12
22 2 0.06
23 3 0.09
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.44
Consensus pattern (20 bp):
ATTAATTTATACTATTAACT
Found at i:4460209 original size:40 final size:40
Alignment explanation
Indices: 4460132--4460212 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
4460122 TACTAAATTA
4460132 AGTAATTAATTTATACTATTAACTATTAAATACCTCATCC
1 AGTAATTAATTTATACTATTAACTATTAAATACCTCATCC
* *
4460172 AGTAATTAATTTATACTATTAACTATTATATATCTCATCC
1 AGTAATTAATTTATACTATTAACTATTAAATACCTCATCC
4460212 A
1 A
4460213 AAAACTGGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.40, C:0.16, G:0.02, T:0.42
Consensus pattern (40 bp):
AGTAATTAATTTATACTATTAACTATTAAATACCTCATCC
Found at i:4463369 original size:81 final size:83
Alignment explanation
Indices: 4463223--4463404 Score: 242
Period size: 81 Copynumber: 2.2 Consensus size: 83
4463213 CCCCTTCGGA
* * * *
4463223 GGCGGTGGAGGAGGTGGCGGAGCAACGGCTTTTACAGGCGGTGGTGGTGGAGGAGGAGGTGCAAG
1 GGCGCTGGAGGAGGTGGCGCAGCAAC-GCTTTTACAGGCGGTGGAGGTGGAGGAGGAGGTACAAG
*
4463288 TTGTTTGGCCGCTGCTACT
65 TTGTTTGGCCGCTGCCACT
* *
4463307 GGCGCTGGAGGCGGTGGCGCAG-AA-GCTTTTGCAGGCGGTGGAGGTGGAGGAGGAGGTACAAGT
1 GGCGCTGGAGGAGGTGGCGCAGCAACGCTTTTACAGGCGGTGGAGGTGGAGGAGGAGGTACAAGT
*
4463370 TGTTTGGCTGCTGCCACT
66 TGTTTGGCCGCTGCCACT
* * *
4463388 GGCTCCGGAGGTGGTGG
1 GGCGCTGGAGGAGGTGG
4463405 AGGAGGAGGT
Statistics
Matches: 87, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
81 66 0.76
83 2 0.02
84 19 0.22
ACGTcount: A:0.15, C:0.16, G:0.48, T:0.21
Consensus pattern (83 bp):
GGCGCTGGAGGAGGTGGCGCAGCAACGCTTTTACAGGCGGTGGAGGTGGAGGAGGAGGTACAAGT
TGTTTGGCCGCTGCCACT
Found at i:4463461 original size:51 final size:51
Alignment explanation
Indices: 4463352--4463461 Score: 150
Period size: 51 Copynumber: 2.2 Consensus size: 51
4463342 CGGTGGAGGT
* * *
4463352 GGAGGAGGAGGTACAAGTTGTTTGGCTGCTGCCACTGGCTCCGGAGGTGGT
1 GGAGGAGGAGGTACAAGTTGTTTGGCTGCTGACACTGGCTCCGGAGGCGGC
* *
4463403 GGAGGAGGAGGTGCAAGTTGTTTGGCTGCTGACACTGG-TGCTGGAGGCGGC
1 GGAGGAGGAGGTACAAGTTGTTTGGCTGCTGACACTGGCT-CCGGAGGCGGC
*
4463454 GGCGGAGG
1 GGAGGAGG
4463462 CGGAGGCGGT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 1 0.02
51 51 0.98
ACGTcount: A:0.15, C:0.16, G:0.47, T:0.21
Consensus pattern (51 bp):
GGAGGAGGAGGTACAAGTTGTTTGGCTGCTGACACTGGCTCCGGAGGCGGC
Found at i:4465044 original size:22 final size:24
Alignment explanation
Indices: 4464995--4465047 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 24
4464985 ATATTTTATC
*
4464995 AAAAAATTTTATTTATTTACTTTT
1 AAAAAATTTTATTTATCTACTTTT
4465019 --AAAATTTTATTT-TCT-CTTTT
1 AAAAAATTTTATTTATCTACTTTT
4465039 AAAAAATTT
1 AAAAAATTT
4465048 ACTCTCTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 5 0.19
21 2 0.08
22 19 0.73
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.57
Consensus pattern (24 bp):
AAAAAATTTTATTTATCTACTTTT
Found at i:4465052 original size:17 final size:17
Alignment explanation
Indices: 4465027--4465063 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
4465017 TTAAAATTTT
* *
4465027 ATTTTCTCTTTTAAAAA
1 ATTTACTCTCTTAAAAA
4465044 ATTTACTCTCTTAAAAA
1 ATTTACTCTCTTAAAAA
4465061 ATT
1 ATT
4465064 ATTTATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTACTCTCTTAAAAA
Found at i:4468484 original size:22 final size:22
Alignment explanation
Indices: 4468450--4468491 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
4468440 AATTTTTTTA
4468450 AAATTTAATTATAAAAATATAT
1 AAATTTAATTATAAAAATATAT
4468472 AAATATTAA-TATAAAAATAT
1 AAAT-TTAATTATAAAAATAT
4468492 TTTTATTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATTTAATTATAAAAATATAT
Found at i:4469120 original size:18 final size:19
Alignment explanation
Indices: 4469097--4469151 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 19
4469087 GATTTTAAAT
4469097 TATTAAAATATTA-TTTTA
1 TATTAAAATATTATTTTTA
* *
4469115 TATTAATATTTATATTTTTA
1 TATTAAAATAT-TATTTTTA
4469135 TAATTAAAA-A-TATTTTT
1 T-ATTAAAATATTATTTTT
4469152 CATTTTTTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
18 16 0.53
19 2 0.07
20 6 0.20
21 6 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTAAAATATTATTTTTA
Found at i:4469132 original size:40 final size:39
Alignment explanation
Indices: 4469071--4469156 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 39
4469061 ATTTAAAAAT
4469071 TTTTATTTAAATTTATGA-TTTTA-AATTATTAAAATATTA
1 TTTTATTTAAATTTATGATTTTTATAATTA--AAAATATTA
4469110 TTTTATATTAATATTTAT-ATTTTTATAATTAAAAATATT-
1 TTTTAT-TTAA-ATTTATGATTTTTATAATTAAAAATATTA
*
4469149 TTTCATTT
1 TTTTATTT
4469157 TTTGAATAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
38 2 0.05
39 11 0.26
40 13 0.31
41 11 0.26
42 5 0.12
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (39 bp):
TTTTATTTAAATTTATGATTTTTATAATTAAAAATATTA
Found at i:4470322 original size:2 final size:2
Alignment explanation
Indices: 4470315--4470353 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4470305 CTTCTGGTAC
4470315 AT 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
4470354 AATCAAACGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4472628 original size:14 final size:15
Alignment explanation
Indices: 4472597--4472630 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
4472587 ATATAATTTT
*
4472597 TATAATTATATATTA
1 TATAATTATATATCA
4472612 TATAATT-TATATCA
1 TATAATTATATATCA
4472626 TATAA
1 TATAA
4472631 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TATAATTATATATCA
Found at i:4472829 original size:11 final size:11
Alignment explanation
Indices: 4472803--4472874 Score: 56
Period size: 11 Copynumber: 6.3 Consensus size: 11
4472793 TTATTTATTT
*
4472803 TAAAATATAAA
1 TAAAATTTAAA
4472814 T-AAATTTAAA
1 TAAAATTTAAA
4472824 TAAAATTTAAA
1 TAAAATTTAAA
* *
4472835 TTTTATATTTTAAA
1 ---TAAAATTTAAA
*
4472849 TTAAATTTAAA
1 TAAAATTTAAA
*
4472860 TAAATATATAAA
1 TAAA-ATTTAAA
4472872 TAA
1 TAA
4472875 TATTAATATC
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
10 9 0.19
11 21 0.44
12 9 0.19
14 9 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TAAAATTTAAA
Found at i:4475056 original size:158 final size:154
Alignment explanation
Indices: 4474770--4475057 Score: 429
Period size: 158 Copynumber: 1.9 Consensus size: 154
4474760 ATTAATTAAT
* * *
4474770 AAAATTAATAATTAATTAATAATTTAAATAAAAACGTGAATGATAATGTCTTTCTTTTTTGGTTA
1 AAAATCAATAATTAAATAATAATTTAAACAAAAACGTGAATGATAATGTCTTTCTTTTTTGGTTA
* * *
4474835 AGATAAGTCGTGCTTGGTATTGGTGATTTTGTAATTTACTTTTTTTATCTTTAAAAATTAAAAAA
66 AGATAAGTCGTGCTCGGTATTGGTAATTTTGTAATTTACTTATTTTATCTTTAAAAATTAAAAAA
4474900 AAAAATTGGATCTATAAAGTAAAC
131 AAAAATTGGATCTATAAAGTAAAC
*
4474924 AAAATCAATAATTAAATGATAATTTTAAACAAAAACGTGACATGATAATGTCTTTCCTTTTTTTT
1 AAAATCAATAATTAAATAATAA-TTTAAACAAAAACGTGA-ATGATAATGTCTTT-C--TTTTTT
*
4474989 GG-TAAGATAAGTCAG-GCTCGGTATTGGTAATTTTGTAATTTA-TTATTTTATCTTTCAAAATT
61 GGTTAAGATAAGTC-GTGCTCGGTATTGGTAATTTTGTAATTTACTTATTTTATCTTTAAAAATT
4475051 AAAAAAA
125 AAAAAAA
4475058 CATTTGAATT
Statistics
Matches: 120, Mismatches: 8, Indels: 9
0.88 0.06 0.07
Matches are distributed among these distances:
154 19 0.16
155 16 0.13
156 14 0.12
157 26 0.22
158 36 0.30
159 9 0.08
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.41
Consensus pattern (154 bp):
AAAATCAATAATTAAATAATAATTTAAACAAAAACGTGAATGATAATGTCTTTCTTTTTTGGTTA
AGATAAGTCGTGCTCGGTATTGGTAATTTTGTAATTTACTTATTTTATCTTTAAAAATTAAAAAA
AAAAATTGGATCTATAAAGTAAAC
Found at i:4476529 original size:2 final size:2
Alignment explanation
Indices: 4476519--4476557 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
4476509 AAAACTCTTG
4476519 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4476558 GAATACGTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4477854 original size:17 final size:19
Alignment explanation
Indices: 4477829--4477867 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
4477819 ACATATTCCA
4477829 TTTTATTA-TTTATTTTTC
1 TTTTATTATTTTATTTTTC
4477847 TTTT-TTATTTTATTTTTC
1 TTTTATTATTTTATTTTTC
4477865 TTT
1 TTT
4477868 CTAAATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.13, C:0.05, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTATTATTTTATTTTTC
Found at i:4477876 original size:18 final size:18
Alignment explanation
Indices: 4477836--4477876 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
4477826 CCATTTTATT
* *
4477836 ATTTATTTTTCTTTTTTA
1 ATTTATTTTTCTTTCTAA
*
4477854 TTTTATTTTTCTTTCTAA
1 ATTTATTTTTCTTTCTAA
4477872 ATTTA
1 ATTTA
4477877 AATTTTTTCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (18 bp):
ATTTATTTTTCTTTCTAA
Found at i:4477913 original size:24 final size:24
Alignment explanation
Indices: 4477886--4477939 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
4477876 AAATTTTTTC
* *
4477886 AAATAATTGTTATAATTATTTAAA
1 AAATAATTGTTATAATCATATAAA
* *
4477910 AAATAATTTTTATAATCATATAAT
1 AAATAATTGTTATAATCATATAAA
4477934 AAATAA
1 AAATAA
4477940 ATAGTTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (24 bp):
AAATAATTGTTATAATCATATAAA
Found at i:4483569 original size:21 final size:23
Alignment explanation
Indices: 4483539--4483580 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
4483529 ACATCATAAA
*
4483539 AAAATTTTA-TTTAT-ATTTAAT
1 AAAATATTATTTTATAATTTAAT
4483560 AAAATATTATTTTATAATTTA
1 AAAATATTATTTTATAATTTA
4483581 TTGAGATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 5 0.28
23 5 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
AAAATATTATTTTATAATTTAAT
Found at i:4484077 original size:9 final size:9
Alignment explanation
Indices: 4484063--4484103 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
4484053 TTATTAATAA
4484063 ATTTAATTT
1 ATTTAATTT
*
4484072 AATTAATTT
1 ATTTAATTT
4484081 -TTTAAATTT
1 ATTT-AATTT
4484090 ATTTAATTT
1 ATTTAATTT
4484099 -TTTAA
1 ATTTAA
4484104 ATTTTTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
8 7 0.25
9 18 0.64
10 3 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
ATTTAATTT
Found at i:4484088 original size:18 final size:18
Alignment explanation
Indices: 4484067--4484107 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
4484057 TAATAAATTT
4484067 AATTTAATTAATTTTTTA
1 AATTTAATTAATTTTTTA
*
4484085 AATTTATTTAATTTTTTA
1 AATTTAATTAATTTTTTA
4484103 AATTT
1 AATTT
4484108 TTAAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
AATTTAATTAATTTTTTA
Found at i:4484093 original size:27 final size:26
Alignment explanation
Indices: 4484063--4484114 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
4484053 TTATTAATAA
*
4484063 ATTTAATTTAATTAATTTTTTAAATTT
1 ATTTAATTT-ATTAAATTTTTAAATTT
*
4484090 ATTTAATTTTTTAAATTTTTAAATT
1 ATTTAATTTATTAAATTTTTAAATT
4484115 AAACTGTTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
ATTTAATTTATTAAATTTTTAAATTT
Found at i:4484106 original size:9 final size:9
Alignment explanation
Indices: 4484076--4484114 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
4484066 TAATTTAATT
4484076 AATTTTTTA
1 AATTTTTTA
4484085 AATTTATTT-
1 AATTT-TTTA
4484094 AATTTTTTA
1 AATTTTTTA
4484103 AA-TTTTTA
1 AATTTTTTA
4484111 AATT
1 AATT
4484115 AAACTGTTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 11 0.41
9 13 0.48
10 3 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
AATTTTTTA
Found at i:4485072 original size:20 final size:21
Alignment explanation
Indices: 4485049--4485092 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4485039 TAAAATTTAA
* *
4485049 ATAATTATAA-AATTTTAAAT
1 ATAATTATAATAAATTAAAAT
4485069 ATAATTATAATAAATTAAAAT
1 ATAATTATAATAAATTAAAAT
4485090 ATA
1 ATA
4485093 TAAATATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAATTATAATAAATTAAAAT
Found at i:4485074 original size:29 final size:30
Alignment explanation
Indices: 4485042--4485102 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
4485032 AATATATTAA
* *
4485042 AATTTA-AATAATTATAAAAT-TTTAAATAT
1 AATTTATAATAAAT-TAAAATATATAAATAT
4485071 AA-TTATAATAAATTAAAATATATAAATAT
1 AATTTATAATAAATTAAAATATATAAATAT
4485100 AAT
1 AAT
4485103 AGGAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
AATTTATAATAAATTAAAATATATAAATAT
Found at i:4485093 original size:23 final size:23
Alignment explanation
Indices: 4485019--4485103 Score: 70
Period size: 23 Copynumber: 3.7 Consensus size: 23
4485009 ATAGATATAT
*
4485019 AATAT-TAATTATTAATATATTAA
1 AATATATAATTA-TAATAAATTAA
* **
4485042 AATTTAAATAATTAT-A-AAATTTT
1 AA--TATATAATTATAATAAATTAA
4485065 AA-ATATAATTATAATAAATTAA
1 AATATATAATTATAATAAATTAA
*
4485087 AATATATAAATATAATA
1 AATATATAATTATAATA
4485104 GGAATATAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
20 9 0.19
21 1 0.02
22 7 0.15
23 21 0.44
24 1 0.02
25 3 0.06
26 6 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
AATATATAATTATAATAAATTAA
Found at i:4488777 original size:20 final size:22
Alignment explanation
Indices: 4488738--4488782 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
4488728 TAATTAAAAA
*
4488738 TAAAATTATTTATAATTTTT-T
1 TAAAATTATATATAATTTTTAT
*
4488759 TAAAA-TATATATCATTTTTAT
1 TAAAATTATATATAATTTTTAT
4488780 TAA
1 TAA
4488783 TTATAAACTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TAAAATTATATATAATTTTTAT
Found at i:4488787 original size:20 final size:20
Alignment explanation
Indices: 4488740--4488787 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
4488730 ATTAAAAATA
*
4488740 AAATTATTTATAATTTTTTT
1 AAATTATATATAATTTTTTT
* *
4488760 AAAATATATATCATTTTTATT
1 AAATTATATATAATTTTT-TT
4488781 -AATTATA
1 AAATTATA
4488788 AACTCATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
AAATTATATATAATTTTTTT
Found at i:4492665 original size:17 final size:17
Alignment explanation
Indices: 4492605--4492671 Score: 54
Period size: 16 Copynumber: 4.2 Consensus size: 17
4492595 CGTTCGAATT
*
4492605 TTTAAAT-TCTAATTAA
1 TTTAAATATTTAATTAA
* *
4492621 TTT-TATATTTTATT--
1 TTTAAATATTTAATTAA
*
4492635 TTAAAATAATTTAATTAA
1 TTTAAAT-ATTTAATTAA
4492653 TTTAAATATTTAA-TAA
1 TTTAAATATTTAATTAA
4492669 TTT
1 TTT
4492672 GTTATTCGAC
Statistics
Matches: 39, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
14 2 0.05
15 4 0.10
16 21 0.54
17 6 0.15
18 6 0.15
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAAATATTTAATTAA
Found at i:4492905 original size:27 final size:27
Alignment explanation
Indices: 4492849--4492910 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 27
4492839 TATAGATCAA
*
4492849 TAAA-TTTTAAAAATAATATAAATTAT
1 TAAAGTTTTAAAAATAATATAAATTAC
*
4492875 TAAAGTTTTAAAAAATAATATATATT-C
1 TAAAGTTTT-AAAAATAATATAAATTAC
4492902 TAAAGTTTT
1 TAAAGTTTT
4492911 CTTTCTCCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
26 4 0.12
27 13 0.41
28 15 0.47
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (27 bp):
TAAAGTTTTAAAAATAATATAAATTAC
Found at i:4496337 original size:46 final size:46
Alignment explanation
Indices: 4496232--4496339 Score: 116
Period size: 46 Copynumber: 2.3 Consensus size: 46
4496222 TATAAATAAA
4496232 TTTA-TTTATTATTTAATTATAATATAATTAATAATATTATTATTTG
1 TTTATTTTA-TATTTAATTATAATATAATTAATAATATTATTATTTG
* * * *
4496278 TGTT-TGATT-TATTTATTTATAATATATTTAATAATATTTATTGTTT-
1 T-TTAT-TTTATATTTAATTATAATATAATTAATAATA-TTATTATTTG
4496324 TTTATTTTATATTTAA
1 TTTATTTTATATTTAA
4496340 AATTAAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
45 4 0.08
46 34 0.68
47 10 0.20
48 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (46 bp):
TTTATTTTATATTTAATTATAATATAATTAATAATATTATTATTTG
Found at i:4496390 original size:25 final size:23
Alignment explanation
Indices: 4496354--4496402 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
4496344 AAAAAATATT
4496354 TTTTTATCTATTATTTATGAACATA
1 TTTTTA-C-ATTATTTATGAACATA
4496379 TTTTTA-ATTATTTATGAACATA
1 TTTTTACATTATTTATGAACATA
4496401 TT
1 TT
4496403 CAATTTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 18 0.75
25 6 0.25
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (23 bp):
TTTTTACATTATTTATGAACATA
Found at i:4496439 original size:23 final size:23
Alignment explanation
Indices: 4496413--4496457 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
4496403 CAATTTTATA
* *
4496413 TTCATAAACATATTTATTTAGTG
1 TTCACAAACAAATTTATTTAGTG
*
4496436 TTCACAAATAAATTTATTTAGT
1 TTCACAAACAAATTTATTTAGT
4496458 ATAAAACTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.47
Consensus pattern (23 bp):
TTCACAAACAAATTTATTTAGTG
Found at i:4496783 original size:17 final size:17
Alignment explanation
Indices: 4496761--4496794 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4496751 TAATTTTCAT
*
4496761 AAAAATTGAAAGAATTA
1 AAAAATTAAAAGAATTA
4496778 AAAAATTAAAAGAATTA
1 AAAAATTAAAAGAATTA
4496795 CTACATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.24
Consensus pattern (17 bp):
AAAAATTAAAAGAATTA
Found at i:4499707 original size:1 final size:1
Alignment explanation
Indices: 4499701--4499760 Score: 57
Period size: 1 Copynumber: 60.0 Consensus size: 1
4499691 AAATCTTCAC
* * ** * * *
4499701 TTTTTTTTTTGTTTTTTTTTTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4499761 CCAATTGCCA
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.00, C:0.07, G:0.05, T:0.88
Consensus pattern (1 bp):
T
Done.