Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 82 of 106
Found at i:31112178 original size:17 final size:16
Alignment explanation
Indices: 31112152--31112216 Score: 57
Period size: 17 Copynumber: 4.1 Consensus size: 16
31112142 CCTATATATA
*
31112152 TAATAATAATATTTTG
1 TAATAATAATATTATG
31112168 TAATAAATAATATTATG
1 TAAT-AATAATATTATG
31112185 T-A-AATATATATTACTG
1 TAATAATA-ATATTA-TG
*
31112201 T-ATAATTAT-TTATG
1 TAATAATAATATTATG
31112215 TA
1 TA
31112217 TTAGTTAAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
14 7 0.17
15 9 0.21
16 11 0.26
17 15 0.36
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.48
Consensus pattern (16 bp):
TAATAATAATATTATG
Found at i:31112217 original size:14 final size:16
Alignment explanation
Indices: 31112154--31112217 Score: 57
Period size: 16 Copynumber: 4.1 Consensus size: 16
31112144 TATATATATA
*
31112154 ATAATA-ATATTTTGT
1 ATAATATATATTATGT
31112169 AATAA-ATAATATTATGT
1 -ATAATAT-ATATTATGT
31112186 A-AATATATATTACTGT
1 ATAATATATATTA-TGT
31112202 ATAAT-TAT-TTATGT
1 ATAATATATATTATGT
31112216 AT
1 AT
31112218 TAGTTAAGTG
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
14 5 0.12
15 12 0.29
16 14 0.33
17 11 0.26
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (16 bp):
ATAATATATATTATGT
Found at i:31112888 original size:22 final size:21
Alignment explanation
Indices: 31112860--31112915 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
31112850 TTTAGGGTTA
*
31112860 AACTTATAATATA-CATATATTT
1 AACTTATAATA-AGCAT-TACTT
*
31112882 AATTTATACATAAGCATTACTT
1 AACTTATA-ATAAGCATTACTT
31112904 AACTTATAATAA
1 AACTTATAATAA
31112916 ACTTCAAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 4 0.14
22 19 0.66
23 6 0.21
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (21 bp):
AACTTATAATAAGCATTACTT
Found at i:31120933 original size:30 final size:30
Alignment explanation
Indices: 31120845--31120933 Score: 80
Period size: 28 Copynumber: 3.0 Consensus size: 30
31120835 CAAACGATTC
31120845 AAAATATAACGTGACGTGTAACAACTTTTTT
1 AAAATATAACGTGACGTGTAACAAC-TTTTT
* * *
31120876 AATATAGTATA--TAACAAT-TAA-AA-TTTTT
1 AAAATA-TA-ACGTGAC-GTGTAACAACTTTTT
31120904 AAAATATAACGTGACGTGTAACAACTTTTT
1 AAAATATAACGTGACGTGTAACAACTTTTT
31120934 TAATATGGTG
Statistics
Matches: 44, Mismatches: 6, Indels: 17
0.66 0.09 0.25
Matches are distributed among these distances:
26 1 0.02
27 3 0.07
28 16 0.36
29 2 0.05
30 7 0.16
31 11 0.25
32 3 0.07
33 1 0.02
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (30 bp):
AAAATATAACGTGACGTGTAACAACTTTTT
Found at i:31120937 original size:59 final size:59
Alignment explanation
Indices: 31120845--31120961 Score: 216
Period size: 59 Copynumber: 2.0 Consensus size: 59
31120835 CAAACGATTC
31120845 AAAATATAACGTGACGTGTAACAACTTTTTTAATATAGTATATAACAATTAAAATTTTT
1 AAAATATAACGTGACGTGTAACAACTTTTTTAATATAGTATATAACAATTAAAATTTTT
* *
31120904 AAAATATAACGTGACGTGTAACAACTTTTTTAATATGGTGTATAACAATTAAAATTTT
1 AAAATATAACGTGACGTGTAACAACTTTTTTAATATAGTATATAACAATTAAAATTTT
31120962 CAATATGACG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.38
Consensus pattern (59 bp):
AAAATATAACGTGACGTGTAACAACTTTTTTAATATAGTATATAACAATTAAAATTTTT
Found at i:31120985 original size:27 final size:27
Alignment explanation
Indices: 31120946--31121215 Score: 229
Period size: 27 Copynumber: 9.9 Consensus size: 27
31120936 ATATGGTGTA
* *
31120946 TAACAATTAAAATTTTCAATATGACGTG
1 TAACAACT-AAATTTTCAACATGACGTG
* * * *
31120974 TAATAATTAAATTTTTAACATGGCGTG
1 TAACAACTAAATTTTCAACATGACGTG
*
31121001 TAACAACTAAATCTTCAACATGACGTG
1 TAACAACTAAATTTTCAACATGACGTG
* *
31121028 TAACAACTATATTTTTTAACATGACGTG
1 TAACAACTA-AATTTTCAACATGACGTG
* * * **
31121056 TAACAACTATATTTTTTAACATAATATG
1 TAACAACTA-AATTTTCAACATGACGTG
*
31121084 TAACAACTAAATTTTCAACA-AAGCGTG
1 TAACAACTAAATTTTCAACATGA-CGTG
* * *
31121111 TAACTACTAAATCTTCAACAT-AGTGTG
1 TAACAACTAAATTTTCAACATGA-CGTG
* * * *
31121138 TAACTACTAAACTTTCAATATAACGTG
1 TAACAACTAAATTTTCAACATGACGTG
* * * *
31121165 TAACTACTACATTTTTTAACATGACATG
1 TAACAACTA-AATTTTCAACATGACGTG
*
31121193 TAACAACTAAATTTTCAATATGA
1 TAACAACTAAATTTTCAACATGA
31121216 TTTATAACAA
Statistics
Matches: 201, Mismatches: 36, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
26 2 0.01
27 122 0.61
28 77 0.38
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.35
Consensus pattern (27 bp):
TAACAACTAAATTTTCAACATGACGTG
Found at i:31121223 original size:27 final size:27
Alignment explanation
Indices: 31121193--31121245 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
31121183 ACATGACATG
31121193 TAACAACTAAATTTTCAATATGATTTA
1 TAACAACTAAATTTTCAATATGATTTA
** *
31121220 TAACAACTGCATTTTCAATGTGATTT
1 TAACAACTAAATTTTCAATATGATTT
31121246 TTTGTCGCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.42
Consensus pattern (27 bp):
TAACAACTAAATTTTCAATATGATTTA
Found at i:31122765 original size:2 final size:2
Alignment explanation
Indices: 31122758--31122786 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31122748 TATTTATCTT
31122758 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
31122787 CATGAATAAA
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:31123196 original size:3 final size:3
Alignment explanation
Indices: 31123188--31123221 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
31123178 CCCTCTTCTA
31123188 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
31123222 GTAGTAGTAG
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:31123226 original size:3 final size:3
Alignment explanation
Indices: 31123220--31123290 Score: 79
Period size: 3 Copynumber: 23.7 Consensus size: 3
31123210 TTATTATTAT
* * * * *
31123220 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TTG TTG TTG TTG TTG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
* *
31123268 TTG TAG TCG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TA
31123291 TTATTACTTC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.24, C:0.01, G:0.32, T:0.42
Consensus pattern (3 bp):
TAG
Found at i:31124476 original size:23 final size:24
Alignment explanation
Indices: 31124420--31124477 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
31124410 GTTCTATTTT
31124420 TTAATAAATCAATACTACAAAAATA
1 TTAATAAAT-AATACTACAAAAATA
31124445 TTAA-AAATAATACTA-AAAAAT-
1 TTAATAAATAATACTACAAAAATA
31124466 TATAATAAATAA
1 T-TAATAAATAA
31124478 GATGGATACT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
21 1 0.03
22 9 0.29
23 13 0.42
24 4 0.13
25 4 0.13
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (24 bp):
TTAATAAATAATACTACAAAAATA
Found at i:31126092 original size:8 final size:8
Alignment explanation
Indices: 31126079--31126120 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
31126069 TTTTAATAAA
31126079 AAAAAAAG
1 AAAAAAAG
31126087 AAAAAAAG
1 AAAAAAAG
* *
31126095 TAAGAAAG
1 AAAAAAAG
31126103 AAAAAAA-
1 AAAAAAAG
*
31126110 AAGAAAAG
1 AAAAAAAG
31126118 AAA
1 AAA
31126121 TTCAAGCAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (8 bp):
AAAAAAAG
Found at i:31134315 original size:33 final size:33
Alignment explanation
Indices: 31134278--31134340 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
31134268 TTACATTTAA
*
31134278 CATGTCATG-CTATCATTGATTATAATATGTTAG
1 CATGTCATGTC-ATCATTAATTATAATATGTTAG
* *
31134311 CATGTTATGTCATCATTAATTATGATATGT
1 CATGTCATGTCATCATTAATTATAATATGT
31134341 CCACATATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 25 0.96
34 1 0.04
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.44
Consensus pattern (33 bp):
CATGTCATGTCATCATTAATTATAATATGTTAG
Found at i:31137948 original size:20 final size:20
Alignment explanation
Indices: 31137923--31137960 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31137913 GGTTATTAGA
31137923 TATCTAAAA-CTGAACTAATC
1 TATCTAAAATC-GAACTAATC
31137943 TATCTAAAATCGAACTAA
1 TATCTAAAATCGAACTAA
31137961 CCGAAATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.47, C:0.18, G:0.05, T:0.29
Consensus pattern (20 bp):
TATCTAAAATCGAACTAATC
Found at i:31142309 original size:13 final size:13
Alignment explanation
Indices: 31142291--31142316 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31142281 TTCTAGAAAA
31142291 TTTATAAAATCAT
1 TTTATAAAATCAT
31142304 TTTATAAAATCAT
1 TTTATAAAATCAT
31142317 AATTTCTCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:31151245 original size:22 final size:22
Alignment explanation
Indices: 31151217--31151267 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
31151207 AAGCTTTGTA
*
31151217 CTATGATCTTTAAAACCAAAGG
1 CTATGATCTTTAAAACCAAAAG
*
31151239 CTTTGATCTTTAAAACCAAAAG
1 CTATGATCTTTAAAACCAAAAG
31151261 CTATGAT
1 CTATGAT
31151268 ACCAATCTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (22 bp):
CTATGATCTTTAAAACCAAAAG
Found at i:31153360 original size:16 final size:16
Alignment explanation
Indices: 31153339--31153371 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
31153329 TTACCATTTT
31153339 ACCCTTGGATAGTGAA
1 ACCCTTGGATAGTGAA
31153355 ACCCTTGGATAGTGAA
1 ACCCTTGGATAGTGAA
31153371 A
1 A
31153372 TTTTCGGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (16 bp):
ACCCTTGGATAGTGAA
Found at i:31155264 original size:2 final size:2
Alignment explanation
Indices: 31155251--31155284 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
31155241 TTACATCGAA
* *
31155251 AT AT AT AC AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31155285 TGAATGAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:31160495 original size:39 final size:39
Alignment explanation
Indices: 31160452--31160530 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
31160442 TTTTCTGAAG
* *
31160452 ATTAAAATTTTTAATATTATTTGTAGTTGTGATTGCTGA
1 ATTAAAATTTTTAATAGTATTTGTAGTTATGATTGCTGA
31160491 ATTAAAATTTTTAATAGTATTTGTAGTTATGATTGCTGA
1 ATTAAAATTTTTAATAGTATTTGTAGTTATGATTGCTGA
31160530 A
1 A
31160531 AGCTAGTTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.33, C:0.03, G:0.15, T:0.49
Consensus pattern (39 bp):
ATTAAAATTTTTAATAGTATTTGTAGTTATGATTGCTGA
Found at i:31171194 original size:24 final size:24
Alignment explanation
Indices: 31171148--31171194 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
31171138 TTTTGTATAT
*
31171148 GTATAAAATAATATTTATAAATAC
1 GTATAAAATAATATATATAAATAC
* * *
31171172 GTATAATATATTATATATTAATA
1 GTATAAAATAATATATATAAATA
31171195 TAATAATATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (24 bp):
GTATAAAATAATATATATAAATAC
Found at i:31172053 original size:19 final size:19
Alignment explanation
Indices: 31172027--31172067 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 19
31172017 CTTCTCCTCA
31172027 TTCTTTG-TG-CTTCTTT-
1 TTCTTTGTTGTCTTCTTTC
*
31172043 TTCTTTGTTGTTTTCTTTC
1 TTCTTTGTTGTCTTCTTTC
31172062 TTCTTT
1 TTCTTT
31172068 CTACTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 7 0.33
17 2 0.10
18 6 0.29
19 6 0.29
ACGTcount: A:0.00, C:0.17, G:0.10, T:0.73
Consensus pattern (19 bp):
TTCTTTGTTGTCTTCTTTC
Found at i:31172107 original size:17 final size:19
Alignment explanation
Indices: 31172053--31172107 Score: 51
Period size: 21 Copynumber: 2.8 Consensus size: 19
31172043 TTCTTTGTTG
31172053 TTTTCTTTCTTCTTTCTACTA
1 TTTTC-TTCTT-TTTCTACTA
*
31172074 TTTTCTTCAGATTTTCT-CT-
1 TTTTCTTC--TTTTTCTACTA
31172093 TTTTCTTCTTTTTCT
1 TTTTCTTCTTTTTCT
31172108 TTGGTTTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
17 6 0.20
19 8 0.27
20 5 0.17
21 10 0.33
22 1 0.03
ACGTcount: A:0.07, C:0.22, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTTCTTCTTTTTCTACTA
Found at i:31173377 original size:21 final size:20
Alignment explanation
Indices: 31173352--31173391 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
31173342 AATATTAGTA
31173352 AAAAAGGAATATTAATAAAATG
1 AAAAA-GAATA-TAATAAAATG
*
31173374 AAAAAGCATATAATAAAA
1 AAAAAGAATATAATAAAA
31173392 ATAAAATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 4 0.24
22 5 0.29
ACGTcount: A:0.68, C:0.03, G:0.10, T:0.20
Consensus pattern (20 bp):
AAAAAGAATATAATAAAATG
Found at i:31173394 original size:26 final size:24
Alignment explanation
Indices: 31173365--31173414 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
31173355 AAGGAATATT
*
31173365 AATAAAATGAAAAAGCATATAATAAA
1 AATAAAAT-AAAAAG-AAATAATAAA
*
31173391 AATAAAATACAAAGAAATAATAAA
1 AATAAAATAAAAAGAAATAATAAA
31173415 GTGGTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 9 0.41
25 5 0.23
26 8 0.36
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.18
Consensus pattern (24 bp):
AATAAAATAAAAAGAAATAATAAA
Found at i:31180875 original size:2 final size:2
Alignment explanation
Indices: 31180868--31180920 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
31180858 NNNNNNNNNN
31180868 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31180910 AT AT AT AT AT A
1 AT AT AT AT AT A
31180921 CACACACATG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31181224 original size:21 final size:21
Alignment explanation
Indices: 31181181--31181224 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
31181171 ACTGTAGCTC
* **
31181181 CTCGTTGTAGCGAGATTCATT
1 CTCGTTGCAGCGAGAAACATT
*
31181202 CTCGTTGCAGCGAGAAACTTT
1 CTCGTTGCAGCGAGAAACATT
31181223 CT
1 CT
31181225 GTTTTGTGAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (21 bp):
CTCGTTGCAGCGAGAAACATT
Found at i:31187182 original size:36 final size:35
Alignment explanation
Indices: 31187149--31187217 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
31187139 GTTAAAAACT
31187149 ATTCTTGAAGGGTTCTGCTTGCGCTCGTGAAAAAGC
1 ATTCTTGAA-GGTTCTGCTTGCGCTCGTGAAAAAGC
* * * *
31187185 GTTGTTGAAGGTTTTGCTTGCTCTCGTGAAAAA
1 ATTCTTGAAGGTTCTGCTTGCGCTCGTGAAAAA
31187218 AATATTGTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 22 0.76
36 7 0.24
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.35
Consensus pattern (35 bp):
ATTCTTGAAGGTTCTGCTTGCGCTCGTGAAAAAGC
Found at i:31187233 original size:35 final size:35
Alignment explanation
Indices: 31187142--31187233 Score: 87
Period size: 35 Copynumber: 2.6 Consensus size: 35
31187132 GGAGTCCGTT
* *
31187142 AAAAACTATTCTTGAAGGGTTCTGCTTGCGCTCGTGA
1 AAAAAC-ATTGTTG-AGGGTTTTGCTTGCGCTCGTGA
* * * *
31187179 AAAAGCGTTGTTGAAGGTTTTGCTTGCTCTCGTGAA
1 AAAAACATTGTTGAGGGTTTTGCTTGCGCTCGTG-A
*
31187215 AAAAATATTG-TGAGGGTTT
1 AAAAACATTGTTGAGGGTTT
31187234 AATGCTTGTT
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
35 26 0.59
36 13 0.30
37 5 0.11
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (35 bp):
AAAAACATTGTTGAGGGTTTTGCTTGCGCTCGTGA
Found at i:31189762 original size:22 final size:22
Alignment explanation
Indices: 31189723--31189771 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
31189713 TCAATATTAT
31189723 AATA-TTCCGAGTCCAAGCATC
1 AATATTTCCGAGTCCAAGCATC
* *
31189744 AATATTTCTGAGTCTAAGCATC
1 AATATTTCCGAGTCCAAGCATC
31189766 AATATT
1 AATATT
31189772 GACCCAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (22 bp):
AATATTTCCGAGTCCAAGCATC
Found at i:31193137 original size:2 final size:2
Alignment explanation
Indices: 31193132--31193174 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
31193122 ATTGTGTGGC
* * *
31193132 CT CT CT CT CT CT GT TT CT CT CT CT GT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
31193174 C
1 C
31193175 AGAGTAACAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.44, G:0.05, T:0.51
Consensus pattern (2 bp):
CT
Found at i:31193152 original size:12 final size:12
Alignment explanation
Indices: 31193133--31193174 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
31193123 TTGTGTGGCC
31193133 TCTCTCTCTCTG
1 TCTCTCTCTCTG
*
31193145 TTTCTCTCTCTG
1 TCTCTCTCTCTG
*
31193157 TCTCTCTCTCTC
1 TCTCTCTCTCTG
31193169 TCTCTC
1 TCTCTC
31193175 AGAGTAACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.00, C:0.43, G:0.05, T:0.52
Consensus pattern (12 bp):
TCTCTCTCTCTG
Found at i:31206029 original size:39 final size:39
Alignment explanation
Indices: 31205975--31206054 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
31205965 AATTTTACTT
31205975 AAAATAATAAACCTTTATCAAATTTATTCATATAATAGA
1 AAAATAATAAACCTTTATCAAATTTATTCATATAATAGA
*
31206014 AAAATAATAAGCCTTTATCAAATTTATTCATATAATAGA
1 AAAATAATAAACCTTTATCAAATTTATTCATATAATAGA
31206053 AA
1 AA
31206055 CCTAGTTGGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.51, C:0.10, G:0.04, T:0.35
Consensus pattern (39 bp):
AAAATAATAAACCTTTATCAAATTTATTCATATAATAGA
Found at i:31211159 original size:41 final size:42
Alignment explanation
Indices: 31211067--31211324 Score: 156
Period size: 41 Copynumber: 5.9 Consensus size: 42
31211057 NNNNNNNNNN
*
31211067 AAATAAAATATTAATATTTTAAAATATTAATGATTAAGTTAT
1 AAATAAAATATTAATATTTTAAAATATTAATGATTAAATTAT
* *
31211109 AAATAAAATATTAATA-TTTAAATTATCT-ATTATTAATATTTTAAAT
1 AAATAAAATATTAATATTTTAAAATAT-TAATGATTAA-A--TT--AT
* * *
31211155 AAATAATCAATTATTAATATTTTAAATAAATAATCAATTATTAATATTTAA
1 AAATAA--AA-TATTAATATTTT--A-AAAT-ATTAATGATTAA-A-TTAT
* ** *
31211206 AAATAAAATA-AAATAAAAATTAATCAT-TATAAT-ATTTAAA-T-T
1 AAATAAAATATTAAT--ATTTTAA-AATAT-TAATGA-TTAAATTAT
*
31211248 AAATAAATTATTAATATTTT-AAATATTAATGATTAAATTAT
1 AAATAAAATATTAATATTTTAAAATATTAATGATTAAATTAT
* *
31211289 AAGTAAAATATTAATA-TTTAAAATATTAATTATTAA
1 AAATAAAATATTAATATTTTAAAATATTAATGATTAA
31211325 TATTTTTATT
Statistics
Matches: 170, Mismatches: 20, Indels: 53
0.70 0.08 0.22
Matches are distributed among these distances:
39 11 0.06
40 7 0.04
41 49 0.29
42 26 0.15
43 4 0.02
44 2 0.01
45 3 0.02
46 16 0.09
47 6 0.04
48 4 0.02
49 13 0.08
50 3 0.02
51 7 0.04
52 1 0.01
53 6 0.04
54 12 0.07
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (42 bp):
AAATAAAATATTAATATTTTAAAATATTAATGATTAAATTAT
Found at i:31211167 original size:27 final size:27
Alignment explanation
Indices: 31211127--31211212 Score: 136
Period size: 27 Copynumber: 3.1 Consensus size: 27
31211117 TATTAATATT
* *
31211127 TAAATTATCTATTATTAATATTTTAAA
1 TAAATAATCAATTATTAATATTTTAAA
31211154 TAAATAATCAATTATTAATATTTTAAA
1 TAAATAATCAATTATTAATATTTTAAA
*
31211181 TAAATAATCAATTATTAATATTTAAAAA
1 TAAATAATCAATTATTAATATTT-TAAA
31211209 TAAA
1 TAAA
31211213 ATAAAATAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 48 0.87
28 7 0.13
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (27 bp):
TAAATAATCAATTATTAATATTTTAAA
Found at i:31211276 original size:48 final size:44
Alignment explanation
Indices: 31211067--31211356 Score: 145
Period size: 41 Copynumber: 6.4 Consensus size: 44
31211057 NNNNNNNNNN
* * *
31211067 AAATAAAATATTAATATTTTAAAATATTAATGATT-A-AGTTA-T
1 AAATAAATTATTAATATTTT-AAATATTAATCATTAATATTTATT
* * *
31211109 AAATAAAATATTAATA-TTTAAATTATCT-ATTATTAATATTTTAAAT
1 AAATAAATTATTAATATTTTAAA-TAT-TAATCATTAATA-TTT-ATT
* * *
31211155 AAATAATCAATTATTAATATTTTAAATAAATAATCAATTATTA-ATATT
1 AAAT-A--AATTATTAATATTTTAAAT-ATTAATC-ATTAATATTTATT
* * *** *
31211203 TAA-AAA-TA-AAATAAAATAAAAATTAATCATTATAATATTTAAATT
1 AAATAAATTATTAATATTTTAAATATTAATCA-T-TAATATTT--ATT
*
31211248 AAATAAATTATTAATATTTTAAATATTAATGATTAA-A-TTA-T
1 AAATAAATTATTAATATTTTAAATATTAATCATTAATATTTATT
* * * *
31211289 AAGTAAAATATTAATATTTAAAATATTAATTATTAATATTTTTATT
1 AAATAAATTATTAATATTTTAAATATTAATCATTAATA--TTTATT
31211335 AAATTATAAATTATTAATATTT
1 -AA--ATAAATTATTAATATTT
31211357 AAAAAATCTA
Statistics
Matches: 188, Mismatches: 30, Indels: 53
0.69 0.11 0.20
Matches are distributed among these distances:
40 4 0.02
41 51 0.27
42 32 0.17
43 4 0.02
44 6 0.03
45 10 0.05
46 13 0.07
47 6 0.03
48 19 0.10
49 28 0.15
50 9 0.05
51 6 0.03
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (44 bp):
AAATAAATTATTAATATTTTAAATATTAATCATTAATATTTATT
Found at i:31211359 original size:15 final size:15
Alignment explanation
Indices: 31211251--31211359 Score: 65
Period size: 15 Copynumber: 7.3 Consensus size: 15
31211241 TTAAATTAAA
31211251 TAAATTATTAATATTT
1 TAAATTATTAATA-TT
31211267 TAAA-TATTAATGA-T
1 TAAATTATTAAT-ATT
31211281 TAAATTA-TAAGTA--
1 TAAATTATTAA-TATT
31211294 -AAA-TATTAATATT
1 TAAATTATTAATATT
*
31211307 TAAAATATTAAT-TAT
1 TAAATTATTAATAT-T
31211322 TAATATTTTTATTAA-ATT
1 TAA-A---TTATTAATATT
31211340 ATAAATTATTAATATT
1 -TAAATTATTAATATT
31211356 TAAA
1 TAAA
31211360 AAATCTAATA
Statistics
Matches: 76, Mismatches: 1, Indels: 33
0.69 0.01 0.30
Matches are distributed among these distances:
11 4 0.05
12 6 0.08
14 13 0.17
15 32 0.42
16 9 0.12
18 2 0.03
19 10 0.13
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
TAAATTATTAATATT
Found at i:31214778 original size:28 final size:29
Alignment explanation
Indices: 31214714--31214779 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
31214704 AACCCTAAAA
*
31214714 CCCTAATTTCCATATCCCTAACCTTAATT
1 CCCTAATTTCCATAACCCTAACCTTAATT
*
31214743 CTCTAATTTCCATAACCCTAACC-TAATT
1 CCCTAATTTCCATAACCCTAACCTTAATT
31214771 CCCTAATTT
1 CCCTAATTT
31214780 AAGACTTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 13 0.38
29 21 0.62
ACGTcount: A:0.29, C:0.33, G:0.00, T:0.38
Consensus pattern (29 bp):
CCCTAATTTCCATAACCCTAACCTTAATT
Found at i:31218279 original size:31 final size:31
Alignment explanation
Indices: 31218244--31218305 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
31218234 ATTTCAATAA
**
31218244 TTTTGCATTTAATATTTCAACAACTTACAAC
1 TTTTGCATCCAATATTTCAACAACTTACAAC
* *
31218275 TTTTGCATCCAATATTTCAATAACTTCCAAC
1 TTTTGCATCCAATATTTCAACAACTTACAAC
31218306 AACTTTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (31 bp):
TTTTGCATCCAATATTTCAACAACTTACAAC
Found at i:31220291 original size:7 final size:7
Alignment explanation
Indices: 31220279--31220321 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
31220269 CTCTGAATTT
31220279 TTTTTTA
1 TTTTTTA
31220286 TTTTTT-
1 TTTTTTA
*
31220292 TCTTTTA
1 TTTTTTA
31220299 TTATTATTA
1 TT-TT-TTA
31220308 TTTTTTA
1 TTTTTTA
31220315 TTTTTTA
1 TTTTTTA
31220322 AGGAATTACA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
6 5 0.16
7 17 0.55
8 4 0.13
9 5 0.16
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTTA
Found at i:31220963 original size:72 final size:73
Alignment explanation
Indices: 31220839--31220999 Score: 207
Period size: 72 Copynumber: 2.2 Consensus size: 73
31220829 AATAGAACTG
* ** * *** *
31220839 ACTTAGTCGACCAAGATGTGAGTTAGTCGACTAAATGCTCTCTGCCAAAATCT-GGACTTTAAGA
1 ACTTAGTCGACCAAAAAATGAGTTAGTCGACTAAATGCTCTCTGCCAAAATCTACGACCAGAAAA
*
31220903 CAAAGCCA
66 CAAAACCA
* *
31220911 ACTTAGTCGACCAAAAAATGAGTTAGTCGACTAAATGCTCTCTGTCAGAATCTACGACCAGAAAA
1 ACTTAGTCGACCAAAAAATGAGTTAGTCGACTAAATGCTCTCTGCCAAAATCTACGACCAGAAAA
31220976 CAAAACCA
66 CAAAACCA
*
31220984 ACTTAGTCGACTAAAA
1 ACTTAGTCGACCAAAA
31221000 GCTCTTTGTC
Statistics
Matches: 76, Mismatches: 12, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
72 48 0.63
73 28 0.37
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (73 bp):
ACTTAGTCGACCAAAAAATGAGTTAGTCGACTAAATGCTCTCTGCCAAAATCTACGACCAGAAAA
CAAAACCA
Found at i:31228707 original size:2 final size:2
Alignment explanation
Indices: 31228700--31228763 Score: 92
Period size: 2 Copynumber: 32.0 Consensus size: 2
31228690 TGTGCTATTA
* * * *
31228700 AT AT AT AT AT AT AC AT AT AT AT AT AC AT AT AT AC AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31228742 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
31228764 GTAAGAGTAT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:31240399 original size:2 final size:2
Alignment explanation
Indices: 31240392--31240420 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31240382 AAAGAGAATT
31240392 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
31240421 TTAAGTAGAT
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:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:31240839 original size:25 final size:25
Alignment explanation
Indices: 31240811--31240858 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
31240801 AGAGAAACAT
31240811 TAGAATGAAAGAAATAAATAAAAAC
1 TAGAATGAAAGAAATAAATAAAAAC
* *
31240836 TAGAGTGAAAGAAGTAAATAAAA
1 TAGAATGAAAGAAATAAATAAAA
31240859 GTTGGCCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.17, T:0.17
Consensus pattern (25 bp):
TAGAATGAAAGAAATAAATAAAAAC
Found at i:31246006 original size:42 final size:42
Alignment explanation
Indices: 31245941--31246021 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
31245931 GTTGATTTGA
31245941 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
1 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
* *
31245983 ACCCGGCTATGTGTGAGTGGGAGTGCACATAAGCCGTTG
1 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTG
31246022 TTGCCTCCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.21, C:0.22, G:0.35, T:0.22
Consensus pattern (42 bp):
ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
Found at i:31246317 original size:26 final size:26
Alignment explanation
Indices: 31246256--31246317 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
31246246 TTGCATATGA
*
31246256 GATGATGATAATGGGATGATGTGCAT
1 GATGATGATGATGGGATGATGTGCAT
*
31246282 GATGATGATGATGGGATGGTGTGCAT
1 GATGATGATGATGGGATGATGTGCAT
*
31246308 GTTGATGATG
1 GATGATGATG
31246318 GGTATATGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.26, C:0.03, G:0.39, T:0.32
Consensus pattern (26 bp):
GATGATGATGATGGGATGATGTGCAT
Found at i:31254658 original size:35 final size:35
Alignment explanation
Indices: 31254587--31254658 Score: 81
Period size: 35 Copynumber: 2.1 Consensus size: 35
31254577 CTATGCGAAA
* *
31254587 TAGTTATTCCATATGGAGTAGCATTTCACTTATTT
1 TAGTTATTCCATATGAAGTAGCACTTCACTTATTT
* * * * *
31254622 TAGTTGTTCCATTTGAAGTAGTACTTCATTTGTTT
1 TAGTTATTCCATATGAAGTAGCACTTCACTTATTT
31254657 TA
1 TA
31254659 ATCATTCTAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.49
Consensus pattern (35 bp):
TAGTTATTCCATATGAAGTAGCACTTCACTTATTT
Found at i:31262483 original size:28 final size:28
Alignment explanation
Indices: 31262452--31262593 Score: 185
Period size: 29 Copynumber: 4.9 Consensus size: 28
31262442 AAATATTTTA
* *
31262452 TCTTGTCTAAATTGAGACAAATATGTTT
1 TCTTGTCTAAATTAAGACAAACATGTTT
* * *
31262480 TCTTGACTAAATTAAGACAAAAAATATTTT
1 TCTTGTCTAAATTAAGAC-AAACAT-GTTT
* *
31262510 TCTTGTCTTAAATTAAGGCAAACATATTT
1 TCTTGTC-TAAATTAAGACAAACATGTTT
31262539 TCTTGTCTAAATTAAGACCAAACATGTTT
1 TCTTGTCTAAATTAAGA-CAAACATGTTT
31262568 TCTTGTCTAAATTAAGACAAACATGT
1 TCTTGTCTAAATTAAGACAAACATGT
31262594 CAAAGCTGCC
Statistics
Matches: 100, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
28 34 0.34
29 42 0.42
30 14 0.14
31 10 0.10
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATGTTT
Found at i:31262522 original size:59 final size:58
Alignment explanation
Indices: 31262429--31262593 Score: 224
Period size: 59 Copynumber: 2.8 Consensus size: 58
31262419 TCTTGTCTGT
* *
31262429 AATTAAGACAAAAAAATATTTTATCTTGTCTAAATTGAGACAAATATGTTTTCTTGACTA
1 AATTAAGAC-AAAAAATATTTT-TCTTGTCTAAATTAAGACAAACATGTTTTCTTGACTA
* * *
31262489 AATTAAGACAAAAAATATTTTTCTTGTCTTAAATTAAGGCAAACATATTTTCTTGTCTA
1 AATTAAGACAAAAAATATTTTTCTTGTC-TAAATTAAGACAAACATGTTTTCTTGACTA
* * *
31262548 AATTAAGACCAAACAT-GTTTTCTTGTCTAAATTAAGACAAACATGT
1 AATTAAGACAAAAAATATTTTTCTTGTCTAAATTAAGACAAACATGT
31262594 CAAAGCTGCC
Statistics
Matches: 94, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
57 17 0.18
58 17 0.18
59 51 0.54
60 9 0.10
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.38
Consensus pattern (58 bp):
AATTAAGACAAAAAATATTTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTGACTA
Found at i:31262544 original size:29 final size:28
Alignment explanation
Indices: 31262419--31262591 Score: 184
Period size: 29 Copynumber: 5.9 Consensus size: 28
31262409 TTAAGACAAC
* *
31262419 TCTTGTCTGTAATTAAGACAAAAAAATATTTT
1 TCTTGTCT-AAATTAAGAC--AAACATA-TTT
* * *
31262451 ATCTTGTCTAAATTGAGACAAATATGTTT
1 -TCTTGTCTAAATTAAGACAAACATATTT
* *
31262480 TCTTGACTAAATTAAGACAAAAAATATTTT
1 TCTTGTCTAAATTAAGAC-AAACATA-TTT
*
31262510 TCTTGTCTTAAATTAAGGCAAACATATTT
1 TCTTGTC-TAAATTAAGACAAACATATTT
*
31262539 TCTTGTCTAAATTAAGACCAAACATGTTT
1 TCTTGTCTAAATTAAGA-CAAACATATTT
31262568 TCTTGTCTAAATTAAGACAAACAT
1 TCTTGTCTAAATTAAGACAAACAT
31262592 GTCAAAGCTG
Statistics
Matches: 123, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
28 32 0.26
29 45 0.37
30 20 0.16
31 10 0.08
32 8 0.07
33 8 0.07
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.39
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATATTT
Found at i:31266574 original size:4 final size:4
Alignment explanation
Indices: 31266564--31266631 Score: 50
Period size: 4 Copynumber: 16.8 Consensus size: 4
31266554 TCCTTGTCTT
* * * *
31266564 TTTC TTCC TTCTC CTTTC TTTC TTTC TTTC TTCC TTTC TTCC TTTC -TCC
1 TTTC TTTC TT-TC -TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
*
31266613 TTT- TTTCC TTTC TCTC TTT
1 TTTC TTT-C TTTC TTTC TTT
31266632 GCTTCCAAGC
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
3 5 0.10
4 36 0.73
5 6 0.12
6 2 0.04
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (4 bp):
TTTC
Found at i:31266590 original size:15 final size:15
Alignment explanation
Indices: 31266581--31266631 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
31266571 CTTCTCCTTT
31266581 CTTTCTTTCTTTCTTC
1 CTTTCTTTCTTTC-TC
*
31266597 CTTTCTTCCTTTCTC
1 CTTTCTTTCTTTCTC
31266612 CTTT-TTTCCTTTCTC
1 CTTTCTTT-CTTTCTC
31266627 TCTTT
1 -CTTT
31266632 GCTTCCAAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 2 0.06
15 13 0.42
16 16 0.52
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (15 bp):
CTTTCTTTCTTTCTC
Found at i:31305090 original size:55 final size:55
Alignment explanation
Indices: 31305031--31305141 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
31305021 ATATATGAAT
31305031 AAAAATAAAACGTTTCCTGGTCTCACTTTGCTTTGTTGAGTAGAGGATGTCGGCC
1 AAAAATAAAACGTTTCCTGGTCTCACTTTGCTTTGTTGAGTAGAGGATGTCGGCC
31305086 AAAAATAAAACGTTTCCTGGTCTCACTTTGCTTTGTTGAGTAGAGGATGTCGGCC
1 AAAAATAAAACGTTTCCTGGTCTCACTTTGCTTTGTTGAGTAGAGGATGTCGGCC
31305141 A
1 A
31305142 CACCATCGAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.32
Consensus pattern (55 bp):
AAAAATAAAACGTTTCCTGGTCTCACTTTGCTTTGTTGAGTAGAGGATGTCGGCC
Found at i:31306727 original size:2 final size:2
Alignment explanation
Indices: 31306720--31306784 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
31306710 CAATTATTAN
31306720 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31306762 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
31306785 ACACCAATGT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31310059 original size:27 final size:27
Alignment explanation
Indices: 31310029--31310085 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
31310019 CCGAAAGTGT
*
31310029 CCAAAAGTGTT-TCAAGTGCAGAAGCGC
1 CCAAAAGTATTCT-AAGTGCAGAAGCGC
* *
31310056 CCAAGAGTATTCTAAGTGCATAAGCGC
1 CCAAAAGTATTCTAAGTGCAGAAGCGC
31310083 CCA
1 CCA
31310086 GAAGCGTTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (27 bp):
CCAAAAGTATTCTAAGTGCAGAAGCGC
Found at i:31313469 original size:52 final size:52
Alignment explanation
Indices: 31313407--31313506 Score: 123
Period size: 52 Copynumber: 1.9 Consensus size: 52
31313397 AATATATTTT
** * *
31313407 TATATATTATAT-TATTAATA-TTTTTAAATATACTTCGAAAATACCTCAAAAA
1 TATATATTATATATAAAAATAGTTTTAAAATATA-TT-AAAAATACCTCAAAAA
*
31313459 TATATTTTATATATAAAAATAGTTTTAAAATATATTAAAAATACCTCA
1 TATATATTATATATAAAAATAGTTTTAAAATATATTAAAAATACCTCA
31313507 CATTCAAATC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
52 22 0.54
53 8 0.20
54 11 0.27
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (52 bp):
TATATATTATATATAAAAATAGTTTTAAAATATATTAAAAATACCTCAAAAA
Found at i:31325497 original size:2 final size:2
Alignment explanation
Indices: 31325486--31325527 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
31325476 TGCAGTCTTT
*
31325486 TC TC -C TC TC TC TC TT TC 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
31325527 T
1 T
31325528 TGCTCTCATA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:31325533 original size:10 final size:9
Alignment explanation
Indices: 31325486--31325534 Score: 55
Period size: 10 Copynumber: 5.2 Consensus size: 9
31325476 TGCAGTCTTT
*
31325486 TCTCCTCTC
1 TCTCTTCTC
31325495 TCTCTT-TC
1 TCTCTTCTC
31325503 TCTCTCTCTC
1 TCTCT-TCTC
31325513 TCTCTCTCTC
1 TCTCT-TCTC
31325523 TCTCTTGCTC
1 TCTCTT-CTC
31325533 TC
1 TC
31325535 ATATCAGTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
8 7 0.19
9 7 0.19
10 22 0.61
ACGTcount: A:0.00, C:0.47, G:0.02, T:0.51
Consensus pattern (9 bp):
TCTCTTCTC
Found at i:31326144 original size:2 final size:2
Alignment explanation
Indices: 31326137--31326167 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
31326127 TAACAATCTA
31326137 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
31326168 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:31329228 original size:2 final size:2
Alignment explanation
Indices: 31329221--31329245 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31329211 AGATAAATAA
31329221 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
31329246 AAGAAATGGC
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:31336011 original size:2 final size:2
Alignment explanation
Indices: 31336004--31336042 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
31335994 TACCTAAATT
31336004 TA TA TA TA TA TA T- 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 TA TA TA TA TA
31336043 GTTTGTTTAG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31343245 original size:2 final size:2
Alignment explanation
Indices: 31343238--31343262 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31343228 TCATATTGAT
31343238 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
31343263 TACTCTCACT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:31350445 original size:2 final size:2
Alignment explanation
Indices: 31350432--31350491 Score: 102
Period size: 2 Copynumber: 30.0 Consensus size: 2
31350422 AAAATTTTAA
* *
31350432 AT AT AC AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31350474 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
31350492 TAAAGAAAAC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:31353205 original size:31 final size:29
Alignment explanation
Indices: 31353170--31353239 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
31353160 TAGTTATTAT
*
31353170 AGATATTCAATATATCTTACTTAGTTACTGC
1 AGATATT--ATATATCTTACTTAGCTACTGC
* * *
31353201 AGATATTGTATATCTTATTTAGCTACTGT
1 AGATATTATATATCTTACTTAGCTACTGC
31353230 AGATATTATA
1 AGATATTATA
31353240 AATATTTCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 27 0.79
31 7 0.21
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (29 bp):
AGATATTATATATCTTACTTAGCTACTGC
Found at i:31353222 original size:29 final size:29
Alignment explanation
Indices: 31353180--31353236 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
31353170 AGATATTCAA
*
31353180 TATATCTTACTTAGTTACTGCAGATATTG
1 TATATCTTACTTAGCTACTGCAGATATTG
* *
31353209 TATATCTTATTTAGCTACTGTAGATATT
1 TATATCTTACTTAGCTACTGCAGATATT
31353237 ATAAATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (29 bp):
TATATCTTACTTAGCTACTGCAGATATTG
Found at i:31358285 original size:4 final size:4
Alignment explanation
Indices: 31358276--31358301 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
31358266 AGTCTTAAAC
31358276 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
31358302 AGAGGAAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:31376853 original size:15 final size:14
Alignment explanation
Indices: 31376826--31376867 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 14
31376816 AATAAAATGA
31376826 TAAAATT-AAAATT
1 TAAAATTGAAAATT
31376839 TACAAATTGAAAATT
1 TA-AAATTGAAAATT
31376854 TAATAATTGAAAAT
1 TAA-AATTGAAAAT
31376868 AATAGTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.08
14 6 0.23
15 18 0.69
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (14 bp):
TAAAATTGAAAATT
Found at i:31377234 original size:28 final size:28
Alignment explanation
Indices: 31377193--31377254 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
31377183 GGAAAATTAA
*
31377193 AAAATTTATAAGTGACAATTTTTTTTTT
1 AAAATTTATAAGTGACAAATTTTTTTTT
* * *
31377221 GAAATTTTTAAGTGAGAAATTTTTTTTT
1 AAAATTTATAAGTGACAAATTTTTTTTT
31377249 AAAATT
1 AAAATT
31377255 CTATCAAAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.52
Consensus pattern (28 bp):
AAAATTTATAAGTGACAAATTTTTTTTT
Found at i:31379252 original size:72 final size:71
Alignment explanation
Indices: 31379186--31379324 Score: 197
Period size: 72 Copynumber: 1.9 Consensus size: 71
31379176 TAGATGCTAC
*
31379186 ACATCTATCGATAAATAGCCACCCAAGAACACTTTAAAGGGACCCTGACTTGCATTTATTGATAG
1 ACATCTATCGATAAATAGCCACCCAAGAACACTTCAAAGGGACCCTGACTTGCATTTATTGATAG
31379251 ATGTCG
66 ATGTCG
* * * * * * *
31379257 TGCATTTATCGATAGATAGCCACCCGATAACACTTCAAAGGGACCTTGACTTGCATCTATTGATA
1 -ACATCTATCGATAAATAGCCACCCAAGAACACTTCAAAGGGACCCTGACTTGCATTTATTGATA
31379322 GAT
65 GAT
31379325 ACTTATATCT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 59 1.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.28
Consensus pattern (71 bp):
ACATCTATCGATAAATAGCCACCCAAGAACACTTCAAAGGGACCCTGACTTGCATTTATTGATAG
ATGTCG
Found at i:31385858 original size:161 final size:161
Alignment explanation
Indices: 31385586--31385887 Score: 498
Period size: 161 Copynumber: 1.9 Consensus size: 161
31385576 AAATAGGTTT
*
31385586 CTCACTTCATTCGTAAATACACACTTGAATAAGATTTTCTTACTCCCTCTAAATACTTTCTCTTA
1 CTCACTTCATTCGTAAATACACACTTGAATAAGATCTTCTTACTCCCTCTAAATACTTTCTCTTA
* *
31385651 TAGTTGTTTTTTCAAGTTATATTTCATAACATGTTAGCAACACGATT-TTCTAATCTCTTAAGCT
66 TAGTTGTTTTTTCAAGTTATATTTCATAACACGTTAGCAACACGATTCTT-TAATCTCTCAAGCT
*
31385715 TTGATATCATTTGTAGCCTATAAAAAGGCCCC
130 TTGAGATCATTTGTAGCCTATAAAAAGGCCCC
* ** *
31385747 CTCACTTCATTTGTAAATACACACTTGAATAAGATCTTCTTACTTTCTCTAAATACTTTTTCTTA
1 CTCACTTCATTCGTAAATACACACTTGAATAAGATCTTCTTACTCCCTCTAAATACTTTCTCTTA
* *
31385812 TAGTTGTTTTTTCAAGTTATATTTCATAACACGTTAGCAGCACGATTCTTTAATCTCTCAAGTTT
66 TAGTTGTTTTTTCAAGTTATATTTCATAACACGTTAGCAACACGATTCTTTAATCTCTCAAGCTT
31385877 TGAGATCATTT
131 TGAGATCATTT
31385888 AGTTTTCATC
Statistics
Matches: 130, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
161 128 0.98
162 2 0.02
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.42
Consensus pattern (161 bp):
CTCACTTCATTCGTAAATACACACTTGAATAAGATCTTCTTACTCCCTCTAAATACTTTCTCTTA
TAGTTGTTTTTTCAAGTTATATTTCATAACACGTTAGCAACACGATTCTTTAATCTCTCAAGCTT
TGAGATCATTTGTAGCCTATAAAAAGGCCCC
Found at i:31387327 original size:19 final size:20
Alignment explanation
Indices: 31387303--31387342 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
31387293 CCATTTGACT
31387303 TATTGGAGTATGATTT-AAG
1 TATTGGAGTATGATTTGAAG
31387322 TATTGGAGTATGATTTGAAG
1 TATTGGAGTATGATTTGAAG
31387342 T
1 T
31387343 TTAGAATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (20 bp):
TATTGGAGTATGATTTGAAG
Found at i:31389750 original size:32 final size:32
Alignment explanation
Indices: 31389709--31389790 Score: 164
Period size: 32 Copynumber: 2.6 Consensus size: 32
31389699 TGTTGATGTG
31389709 TTTTAGTATAACTTTATTAGGAACTTAGTATA
1 TTTTAGTATAACTTTATTAGGAACTTAGTATA
31389741 TTTTAGTATAACTTTATTAGGAACTTAGTATA
1 TTTTAGTATAACTTTATTAGGAACTTAGTATA
31389773 TTTTAGTATAACTTTATT
1 TTTTAGTATAACTTTATT
31389791 GGCATAAGTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (32 bp):
TTTTAGTATAACTTTATTAGGAACTTAGTATA
Found at i:31393909 original size:20 final size:20
Alignment explanation
Indices: 31393852--31393909 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
31393842 CTCTTACAAA
*
31393852 AACATAAAAATAAACATAAAT
1 AACAT-AAAATAAACATTAAT
*
31393873 AACATAAAACT-AACATTATT
1 AACATAAAA-TAAACATTAAT
*
31393893 AACTTAAAATAAACATT
1 AACATAAAATAAACATT
31393910 TAAATATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 1 0.03
20 25 0.78
21 6 0.19
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.26
Consensus pattern (20 bp):
AACATAAAATAAACATTAAT
Found at i:31395304 original size:2 final size:2
Alignment explanation
Indices: 31395297--31395324 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31395287 ATGTAAAACA
31395297 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
31395325 TANNNNNNNN
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:31403735 original size:29 final size:28
Alignment explanation
Indices: 31403678--31403739 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
31403668 TAAGGAATAT
* *
31403678 AGGAAAATCTGACACAAAAGATCTCTGA
1 AGGAAAATCTGACAAAAAAGATCTATGA
*
31403706 AGGAAAATCTCTACAAAAAAGA-CTTATGA
1 AGGAAAATCT-GACAAAAAAGATC-TATGA
31403735 AGGAA
1 AGGAA
31403740 GATTTTTAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 11 0.38
29 18 0.62
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (28 bp):
AGGAAAATCTGACAAAAAAGATCTATGA
Found at i:31412129 original size:24 final size:25
Alignment explanation
Indices: 31412101--31412148 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
31412091 TCAATTTATC
* *
31412101 AAAAAGTTGCTACGTGCCATGTTCT
1 AAAATGTTGCTACATGCCATGTTCT
*
31412126 AAAATTTTGCTACATGCCATGTT
1 AAAATGTTGCTACATGCCATGTT
31412149 GAAAACATGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (25 bp):
AAAATGTTGCTACATGCCATGTTCT
Found at i:31429921 original size:2 final size:2
Alignment explanation
Indices: 31429914--31429940 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31429904 ATCAGTGTAG
31429914 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
31429941 GTAAATACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31432666 original size:2 final size:2
Alignment explanation
Indices: 31432659--31432709 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
31432649 GATTTGTAAG
31432659 TA TA TA TA TA TA 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 TA TA TA TA TA TA
31432701 TA TA TA TA T
1 TA TA TA TA T
31432710 NNNNNNNNNN
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31432809 original size:2 final size:2
Alignment explanation
Indices: 31432793--31432858 Score: 107
Period size: 2 Copynumber: 33.5 Consensus size: 2
31432783 NNNNNNNNNN
*
31432793 TA TA T- TA TC TA 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 TA TA TA TA TA TA
*
31432834 TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
31432859 GCTTTGGCAT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
1 1 0.02
2 58 0.98
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31443978 original size:53 final size:53
Alignment explanation
Indices: 31443898--31444066 Score: 223
Period size: 53 Copynumber: 3.2 Consensus size: 53
31443888 GAAAAGCTGT
*
31443898 TGTAAGGGTTATCACTTGATCTTGTCAAAAAGTAAAAATCCCTTTGTGGATTG
1 TGTAAGGGTTATCACTTGATCTTGTCAAAAAGTAAGAATCCCTTTGTGGATTG
** * *
31443951 TGTAAGGGTTATCGTTTGATCTTGTCAAAAAGTAAGAATCTCTTTATGGATTG
1 TGTAAGGGTTATCACTTGATCTTGTCAAAAAGTAAGAATCCCTTTGTGGATTG
*** * * *
31444004 TGTAAGGGTTATCACTTGATCCCATTAAAACGTAAGAATCCTTTTGTGGATTG
1 TGTAAGGGTTATCACTTGATCTTGTCAAAAAGTAAGAATCCCTTTGTGGATTG
31444057 TG-AGAGGGTT
1 TGTA-AGGGTT
31444067 TTCGCTTTGT
Statistics
Matches: 100, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
52 1 0.01
53 99 0.99
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (53 bp):
TGTAAGGGTTATCACTTGATCTTGTCAAAAAGTAAGAATCCCTTTGTGGATTG
Found at i:31444085 original size:53 final size:54
Alignment explanation
Indices: 31443898--31444095 Score: 194
Period size: 53 Copynumber: 3.7 Consensus size: 54
31443888 GAAAAGCTGT
* ** * * *
31443898 TGTAAGGGTTATCAC-TTGATCTTGTCAAAAAGTAAAAATCCCTTTGTGGATTG
1 TGTAAGGGTTATCGCTTTGATCCCGTTAAAAAGTAAGAATCCTTTTGTGGATTG
** * *
31443951 TGTAAGGGTTATCG-TTTGATCTTGTCAAAAAGTAAGAAT-CTCTTTATGGATTG
1 TGTAAGGGTTATCGCTTTGATCCCGTTAAAAAGTAAGAATCCT-TTTGTGGATTG
* * *
31444004 TGTAAGGGTTATCAC-TTGATCCCATTAAAACGTAAGAATCCTTTTGTGGATTG
1 TGTAAGGGTTATCGCTTTGATCCCGTTAAAAAGTAAGAATCCTTTTGTGGATTG
*
31444057 TG-AGAGGGTTTTCGCTTTG-TCCCGTTAAAAA-TCAAGAAT
1 TGTA-AGGGTTATCGCTTTGATCCCGTTAAAAAGT-AAGAAT
31444096 TCTTGATAGT
Statistics
Matches: 123, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
52 3 0.02
53 115 0.93
54 5 0.04
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (54 bp):
TGTAAGGGTTATCGCTTTGATCCCGTTAAAAAGTAAGAATCCTTTTGTGGATTG
Found at i:31444087 original size:106 final size:105
Alignment explanation
Indices: 31443898--31444099 Score: 248
Period size: 106 Copynumber: 1.9 Consensus size: 105
31443888 GAAAAGCTGT
***
31443898 TGTAAGGGTTATCACTTGATCTTGTCAAAAAGTAAAAATCCCTTTGTGGATTGTGTAAGGGTTAT
1 TGTAAGGGTTATCACTTGATCCCATCAAAAAGTAAAAATCCCTTTGTGGATTGTGTAAGGGTTAT
**
31443963 CGTTTGATCTTGTCAAAAAGT-AAGAATCTCTTTATGGATTG
66 CGTTTGATCCCGTCAAAAA-TCAAGAAT-TCTTTATGGATTG
* * * * *
31444004 TGTAAGGGTTATCACTTGATCCCATTAAAACGTAAGAATCCTTTTGTGGATTGTG-AGAGGGTTT
1 TGTAAGGGTTATCACTTGATCCCATCAAAAAGTAAAAATCCCTTTGTGGATTGTGTA-AGGGTTA
*
31444068 TCGCTTTG-TCCCGTTAAAAATCAAGAATTCTT
65 TCG-TTTGATCCCGTCAAAAATCAAGAATTCTT
31444100 GATAGTTGAT
Statistics
Matches: 82, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
105 6 0.07
106 72 0.88
107 4 0.05
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.37
Consensus pattern (105 bp):
TGTAAGGGTTATCACTTGATCCCATCAAAAAGTAAAAATCCCTTTGTGGATTGTGTAAGGGTTAT
CGTTTGATCCCGTCAAAAATCAAGAATTCTTTATGGATTG
Found at i:31446907 original size:19 final size:19
Alignment explanation
Indices: 31446883--31446928 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
31446873 GAATTTTCAT
*
31446883 TTTCTTTTCTTTGTTTTCC
1 TTTCTTTTCTTTATTTTCC
*
31446902 TTTCTTTTCTTTATTTTTC
1 TTTCTTTTCTTTATTTTCC
*
31446921 TTGCTTTT
1 TTTCTTTT
31446929 TCCTTCTCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.76
Consensus pattern (19 bp):
TTTCTTTTCTTTATTTTCC
Found at i:31451681 original size:29 final size:29
Alignment explanation
Indices: 31451625--31451681 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
31451615 CCTTGTTTTA
* * *
31451625 TTGTACCTGTTTACGTATAGCTTATTCTT
1 TTGTACCTATTTACGTACACCTTATTCTT
*
31451654 TTGTACCTATTTACGTACACCTTTTTCT
1 TTGTACCTATTTACGTACACCTTATTCT
31451682 CTTAACTTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.18, C:0.21, G:0.11, T:0.51
Consensus pattern (29 bp):
TTGTACCTATTTACGTACACCTTATTCTT
Found at i:31452119 original size:64 final size:64
Alignment explanation
Indices: 31452051--31452186 Score: 175
Period size: 64 Copynumber: 2.1 Consensus size: 64
31452041 CTACCGCTCA
*** * *
31452051 CCTATTCTCTATCTACTT-TTTGTCTTACTCTATTACTTTGGTAATACAGTTATTCTACCACTTG
1 CCTATTCTCTATCTA-TTCTCAATCTTACTCTACTACTTTGGCAATACAGTTATTCTACCACTTG
* * *
31452115 CCTATTTTCTATCTATTCTCAATCTTACTCTACTATTTTGGCAATACAGTTATTTTACCACTTG
1 CCTATTCTCTATCTATTCTCAATCTTACTCTACTACTTTGGCAATACAGTTATTCTACCACTTG
*
31452179 CATATTCT
1 CCTATTCT
31452187 TTACTTATCC
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
63 2 0.03
64 59 0.97
ACGTcount: A:0.22, C:0.24, G:0.07, T:0.48
Consensus pattern (64 bp):
CCTATTCTCTATCTATTCTCAATCTTACTCTACTACTTTGGCAATACAGTTATTCTACCACTTG
Found at i:31452200 original size:64 final size:64
Alignment explanation
Indices: 31452073--31452202 Score: 174
Period size: 64 Copynumber: 2.0 Consensus size: 64
31452063 CTACTTTTTG
* * * *
31452073 TCTTACTCTATTACTTTGGTAATACAGTTATTCTACCACTTGCCTATTTTCTATCTATTCTCAA
1 TCTTACTCTACTACTTTGGCAATACAGTTATTCTACCACTTGCATATTTTCTATCTATCCTCAA
* *
31452137 TCTTACTCTACTATTTTGGCAATACAGTTATTTTACCACTTGCATATTCTT-TA-CTTATCCTCA
1 TCTTACTCTACTACTTTGGCAATACAGTTATTCTACCACTTGCATATT-TTCTATC-TATCCTCA
31452200 A
64 A
31452201 TC
1 TC
31452203 ATTATTTAAC
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
63 1 0.02
64 55 0.95
65 2 0.03
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.46
Consensus pattern (64 bp):
TCTTACTCTACTACTTTGGCAATACAGTTATTCTACCACTTGCATATTTTCTATCTATCCTCAA
Found at i:31452618 original size:17 final size:17
Alignment explanation
Indices: 31452596--31452631 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
31452586 ACAGGTTACT
*
31452596 TTAAAATTGATTTTGGG
1 TTAAAATTGATCTTGGG
31452613 TTAAAATTGATCTTGGG
1 TTAAAATTGATCTTGGG
31452630 TT
1 TT
31452632 TTGGGTGGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.03, G:0.22, T:0.47
Consensus pattern (17 bp):
TTAAAATTGATCTTGGG
Found at i:31453254 original size:47 final size:46
Alignment explanation
Indices: 31453175--31453310 Score: 143
Period size: 47 Copynumber: 3.0 Consensus size: 46
31453165 ATTCTCATGA
* * *
31453175 AAATAT-T-ATTAAAATATAGTCAATGATAATTTTGTCTTTTGGTAT
1 AAATATGTGATTAAATTATAGTCAAGGGTAATTTTGTC-TTTGGTAT
* *
31453220 AAATATGTGATTAAATTATAATCAAGGGTAATTTTATCTTTGAGTAT
1 AAATATGTGATTAAATTATAGTCAAGGGTAATTTTGTCTTTG-GTAT
* * * *
31453267 AAATCTGTGATTAAATTGTAGTGAAGGGT-ATTTGGTCATTTGGT
1 AAATATGTGATTAAATTATAGTCAAGGGTAATTTTGTC-TTTGGT
31453311 GTAAGTGTTT
Statistics
Matches: 76, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
45 6 0.08
46 13 0.17
47 57 0.75
ACGTcount: A:0.35, C:0.04, G:0.18, T:0.43
Consensus pattern (46 bp):
AAATATGTGATTAAATTATAGTCAAGGGTAATTTTGTCTTTGGTAT
Found at i:31454522 original size:15 final size:16
Alignment explanation
Indices: 31454491--31454529 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
31454481 TTATAAATAC
*
31454491 AATATTAATATTTTAA
1 AATATTAATAGTTTAA
31454507 AATATTAAT-GTTTAA
1 AATATTAATAGTTTAA
*
31454522 ATTATTAA
1 AATATTAA
31454530 ATGAAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (16 bp):
AATATTAATAGTTTAA
Found at i:31454619 original size:8 final size:8
Alignment explanation
Indices: 31454596--31454629 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
31454586 TTTTAAAAAT
31454596 AAATTATTA
1 AAATT-TTA
*
31454605 AATTTTTA
1 AAATTTTA
31454613 AAATTTTA
1 AAATTTTA
31454621 AAATTTTA
1 AAATTTTA
31454629 A
1 A
31454630 TGAAAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 19 0.83
9 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
AAATTTTA
Found at i:31454847 original size:43 final size:41
Alignment explanation
Indices: 31454800--31454907 Score: 112
Period size: 41 Copynumber: 2.6 Consensus size: 41
31454790 AATATTTTAA
31454800 ATTTAAAATTAATTAAAATTATTAATATTTTTANAA-TAATAAT
1 ATTTAAAATTAATTAAAATTATTAATA--TTTA-AATTAATAAT
* * *
31454843 ATTTAAATTATAAATAAAA-TATTAATATTTAAATTATTAAT
1 ATTTAAAAT-TAATTAAAATTATTAATATTTAAATTAATAAT
* *
31454884 ATTTTAAATAAATTATAAATTATT
1 ATTTAAAATTAATTA-AAATTATT
31454908 GTCAATTAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
40 6 0.11
41 20 0.37
42 4 0.07
43 16 0.30
44 8 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.47
Consensus pattern (41 bp):
ATTTAAAATTAATTAAAATTATTAATATTTAAATTAATAAT
Found at i:31454858 original size:15 final size:15
Alignment explanation
Indices: 31454815--31454892 Score: 67
Period size: 15 Copynumber: 5.3 Consensus size: 15
31454805 AAATTAATTA
31454815 AAATTATTAATATTTTT
1 AAATTATTAATA--TTT
*
31454832 ANAA-TAATAATATTT
1 A-AATTATTAATATTT
31454847 AAATTA-TAA-A--T
1 AAATTATTAATATTT
*
31454858 AAAATATTAATATTT
1 AAATTATTAATATTT
31454873 AAATTATTAATATTTT
1 AAATTATTAATA-TTT
31454889 AAAT
1 AAAT
31454893 AAATTATAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
11 6 0.12
12 3 0.06
13 2 0.04
14 5 0.10
15 18 0.35
16 7 0.14
17 8 0.16
18 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AAATTATTAATATTT
Found at i:31454868 original size:26 final size:26
Alignment explanation
Indices: 31454834--31454884 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
31454824 ATATTTTTAN
31454834 AATAATAATATTTAAATTATAAATAA
1 AATAATAATATTTAAATTATAAATAA
* *
31454860 AATATTAATATTTAAATTATTAATA
1 AATAATAATATTTAAATTATAAATA
31454885 TTTTAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
AATAATAATATTTAAATTATAAATAA
Found at i:31456487 original size:21 final size:22
Alignment explanation
Indices: 31456452--31456495 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
31456442 CTTTTAAAGT
31456452 AATTTAAAATAAAATAACATAA
1 AATTTAAAATAAAATAACATAA
* *
31456474 AATTT-AATTAAAATAACTTAA
1 AATTTAAAATAAAATAACATAA
31456495 A
1 A
31456496 TTAACTACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (22 bp):
AATTTAAAATAAAATAACATAA
Found at i:31457263 original size:22 final size:23
Alignment explanation
Indices: 31457237--31457283 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
31457227 TTGACAAAAA
31457237 CCCTTCAAAATGTTT-CTTTTTT
1 CCCTTCAAAATGTTTCCTTTTTT
*
31457259 CCCTTCAAATTGTTTCCCTTTTTT
1 CCCTTCAAAATGTTT-CCTTTTTT
31457283 C
1 C
31457284 TTTCTTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.64
24 8 0.36
ACGTcount: A:0.15, C:0.28, G:0.04, T:0.53
Consensus pattern (23 bp):
CCCTTCAAAATGTTTCCTTTTTT
Found at i:31461710 original size:64 final size:64
Alignment explanation
Indices: 31461582--31461829 Score: 406
Period size: 64 Copynumber: 3.9 Consensus size: 64
31461572 TTAATGGCTA
** * *
31461582 GTGATTGATTCAGCATCATTCATCTGTGTATCTGTGTATATCGTTTCCTCACCCTTTAATGGCCG
1 GTGATTGATTCAGCATCATTCATCTGTG-ATCTGTCCATATCGTTTCCTCACCCTTCAACGGCCG
31461647 GTGATTGATTCAGCATCATTCATCTGTGATCTGTCCATATCGTTTCCTCACCCTTCAACGGCCG
1 GTGATTGATTCAGCATCATTCATCTGTGATCTGTCCATATCGTTTCCTCACCCTTCAACGGCCG
31461711 GTGATTGATTCAGCATCATTCATCTGTGATCTGTCCATATCGTTTCCTCACCCTTCAACGGCCG
1 GTGATTGATTCAGCATCATTCATCTGTGATCTGTCCATATCGTTTCCTCACCCTTCAACGGCCG
* * * * *
31461775 GTGATTGATTCAGCATCATTCATCTGTGATATCTCTACATCATTTCCTCACCCTT
1 GTGATTGATTCAGCATCATTCATCTGTGATCTGTCCATATCGTTTCCTCACCCTT
31461830 TGGCCACTAG
Statistics
Matches: 174, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
64 146 0.84
65 28 0.16
ACGTcount: A:0.19, C:0.27, G:0.16, T:0.37
Consensus pattern (64 bp):
GTGATTGATTCAGCATCATTCATCTGTGATCTGTCCATATCGTTTCCTCACCCTTCAACGGCCG
Found at i:31462892 original size:9 final size:8
Alignment explanation
Indices: 31462875--31462900 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
31462865 AATTCTATTA
31462875 TTATTTTT
1 TTATTTTT
31462883 TTATTTTT
1 TTATTTTT
31462891 TTATTTTT
1 TTATTTTT
31462899 TT
1 TT
31462901 CAATTATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTATTTTT
Found at i:31466150 original size:64 final size:64
Alignment explanation
Indices: 31466070--31466209 Score: 271
Period size: 64 Copynumber: 2.2 Consensus size: 64
31466060 AACTTTATCG
*
31466070 TGGAAATCAGTTGAAGGAACAGGTTGTCTCTTTTGAACTGCAAAATTATGTAAATATATACGGT
1 TGGAAAACAGTTGAAGGAACAGGTTGTCTCTTTTGAACTGCAAAATTATGTAAATATATACGGT
31466134 TGGAAAACAGTTGAAGGAACAGGTTGTCTCTTTTGAACTGCAAAATTATGTAAATATATACGGT
1 TGGAAAACAGTTGAAGGAACAGGTTGTCTCTTTTGAACTGCAAAATTATGTAAATATATACGGT
31466198 TGGAAAACAGTT
1 TGGAAAACAGTT
31466210 CAAGCATTTT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 75 1.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (64 bp):
TGGAAAACAGTTGAAGGAACAGGTTGTCTCTTTTGAACTGCAAAATTATGTAAATATATACGGT
Found at i:31472571 original size:15 final size:15
Alignment explanation
Indices: 31472533--31472572 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
31472523 TGACACCTAC
31472533 TGTTGTAACACCTTG
1 TGTTGTAACACCTTG
* * *
31472548 TGCTATAACACTTTG
1 TGTTGTAACACCTTG
31472563 TGTTGTAACA
1 TGTTGTAACA
31472573 TCTTATACTG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.40
Consensus pattern (15 bp):
TGTTGTAACACCTTG
Found at i:31475307 original size:60 final size:60
Alignment explanation
Indices: 31475163--31475310 Score: 181
Period size: 60 Copynumber: 2.5 Consensus size: 60
31475153 GAGTTTTTTG
* * *
31475163 CTGCAGCAAGATTCAATTTCGCTGCAGCGAAATTGTAACCTAGAAACAGAAAGTTTCTCA
1 CTGCAGCAAGATTCAATTTCGCTGCAGCAAAATTGTAACCCAGAAACAAAAAGTTTCTCA
** * **
31475223 CTGCAGTGAGATTGAAACTCGCTGCAGCAAAATT-TCAACCCAGAAACAAAAAGTTTCTCA
1 CTGCAGCAAGATTCAATTTCGCTGCAGCAAAATTGT-AACCCAGAAACAAAAAGTTTCTCA
* * *
31475283 CTGCAGCAAAATTCATTTTTGCTGCAGC
1 CTGCAGCAAGATTCAATTTCGCTGCAGC
31475311 GAGAAGCTAC
Statistics
Matches: 71, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
59 1 0.01
60 70 0.99
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (60 bp):
CTGCAGCAAGATTCAATTTCGCTGCAGCAAAATTGTAACCCAGAAACAAAAAGTTTCTCA
Found at i:31496862 original size:34 final size:35
Alignment explanation
Indices: 31496791--31496863 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 35
31496781 TTTAACAAAC
** *
31496791 TCAACCACTAACCCATACAATGGCCTTTTTTGAGA
1 TCAACCACTAACCCATACAACAGCCTTTTTTCAGA
*
31496826 TCAACCA-TAACCCTTACAACAG-CTTTTTTCAGGA
1 TCAACCACTAACCCATACAACAGCCTTTTTTCA-GA
31496860 TCAA
1 TCAA
31496864 GTGAACCCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 8 0.24
34 18 0.55
35 7 0.21
ACGTcount: A:0.33, C:0.29, G:0.10, T:0.29
Consensus pattern (35 bp):
TCAACCACTAACCCATACAACAGCCTTTTTTCAGA
Found at i:31497699 original size:101 final size:102
Alignment explanation
Indices: 31497515--31497719 Score: 292
Period size: 101 Copynumber: 2.0 Consensus size: 102
31497505 ATTCCTTTAA
* *
31497515 ATTTTAGCACATAGCTTTGGCCATATCTTCCTTGTGATCAAATGTTGAGTTGAGAATGAACTTCA
1 ATTTTAGCACATAGCTTTGGCCATAACTTCCTTATGATCAAATGTTGAGTTGAGAATGAACTTCA
* * *
31497580 TGGCTTGAAACTACCCTTGGTGTTGTGAAGATCAACC
66 TGACTTGAAACTAACCTTGGTGTTGTGAAAATCAACC
* *
31497617 ATTTTAGCACATAGC-TTGGCCATAACTTCCTTATGGTCAAATGTTGAGTT-A-AAGGTGAGCTT
1 ATTTTAGCACATAGCTTTGGCCATAACTTCCTTATGATCAAATGTTGAGTTGAGAA--TGAACTT
31497679 CATGACTTGAAAAC-AACCTTGGTGTTGTGAAAATCAACC
64 CATGACTTG-AAACTAACCTTGGTGTTGTGAAAATCAACC
31497718 AT
1 AT
31497720 CTTTGAATGC
Statistics
Matches: 93, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
99 2 0.02
100 1 0.01
101 71 0.76
102 19 0.20
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (102 bp):
ATTTTAGCACATAGCTTTGGCCATAACTTCCTTATGATCAAATGTTGAGTTGAGAATGAACTTCA
TGACTTGAAACTAACCTTGGTGTTGTGAAAATCAACC
Found at i:31498365 original size:2 final size:2
Alignment explanation
Indices: 31498358--31498395 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
31498348 AAGTATGTCT
31498358 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
31498396 TATATATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:31499499 original size:25 final size:26
Alignment explanation
Indices: 31499449--31499502 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
31499439 ATCATTAAGC
31499449 ATTTTTAGCAAGCATTCTTCAAAAAT
1 ATTTTTAGCAAGCATTCTTCAAAAAT
*
31499475 ATTTTTCGCAAGCA-T-TTCAAGAAAT
1 ATTTTTAGCAAGCATTCTTCAA-AAAT
31499500 ATT
1 ATT
31499503 CTCCAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 8 0.31
26 13 0.50
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (26 bp):
ATTTTTAGCAAGCATTCTTCAAAAAT
Found at i:31503740 original size:101 final size:101
Alignment explanation
Indices: 31503554--31503753 Score: 287
Period size: 101 Copynumber: 2.0 Consensus size: 101
31503544 CCTTGACATT
* * * *
31503554 TTAGCACGTAACTTTGGCTATATCTTCCTTGTGATCAAATGTTGAGTTGCAAGTAAACTTTATGG
1 TTAGCACATAACTTTGGCCATATCTTCCTTATGATCAAATGTTGAGTTGCAAGTAAACTTCATGG
* *
31503619 CTTGAAACAATCTTGGTGTTGTGAAGATCAACCATC
66 CTTGAAACAACCTTGGTGTTGTGAACATCAACCATC
* *
31503655 TTAGCACATAGCTTTGGCCATATCTTCCTTATGATCAAATGTTGAGTTG-AGAGTGAACTTCATG
1 TTAGCACATAACTTTGGCCATATCTTCCTTATGATCAAATGTTGAGTTGCA-AGTAAACTTCATG
*
31503719 GCTTGAAA-ACACCTTGTTGTTGTGAACATCAACCA
65 GCTTGAAACA-ACCTTGGTGTTGTGAACATCAACCA
31503754 GCTTTGAATG
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
100 2 0.02
101 86 0.98
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (101 bp):
TTAGCACATAACTTTGGCCATATCTTCCTTATGATCAAATGTTGAGTTGCAAGTAAACTTCATGG
CTTGAAACAACCTTGGTGTTGTGAACATCAACCATC
Found at i:31505069 original size:2 final size:2
Alignment explanation
Indices: 31505012--31505056 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
31505002 CCATTATGTG
31505012 TA TA TA TA TA TA 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 TA TA TA TA TA TA
31505054 TA T
1 TA T
31505057 TATGCAAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31505069 original size:15 final size:15
Alignment explanation
Indices: 31505049--31505079 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31505039 ATATATATAT
31505049 ATATATATTATGCAA
1 ATATATATTATGCAA
*
31505064 ATATATTTTATGCAA
1 ATATATATTATGCAA
31505079 A
1 A
31505080 ATGACAACAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (15 bp):
ATATATATTATGCAA
Found at i:31511174 original size:38 final size:38
Alignment explanation
Indices: 31511131--31511222 Score: 116
Period size: 38 Copynumber: 2.4 Consensus size: 38
31511121 AAGGCTAAAG
*
31511131 GGGAAGAAAAGAAAGAAAATAAGTAAGAACAGTAAAAA
1 GGGAAGAAAAGAAAGAAAATAACTAAGAACAGTAAAAA
* * *
31511169 GGGAAGAAAAGAGAA-AAAGTAACTAGGAACAGTTAAAA
1 GGGAAGAAAAGA-AAGAAAATAACTAAGAACAGTAAAAA
*
31511207 GAGAAGAAAA-AAAGAA
1 GGGAAGAAAAGAAAGAA
31511223 GAAGCAAGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
36 2 0.04
37 3 0.06
38 40 0.85
39 2 0.04
ACGTcount: A:0.64, C:0.03, G:0.25, T:0.08
Consensus pattern (38 bp):
GGGAAGAAAAGAAAGAAAATAACTAAGAACAGTAAAAA
Found at i:31511595 original size:11 final size:13
Alignment explanation
Indices: 31511561--31511595 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
31511551 ATAAACAAAG
31511561 TATATATATTATA
1 TATATATATTATA
31511574 TATATATATTATA
1 TATATATATTATA
31511587 T-TATA-ATTA
1 TATATATATTA
31511596 ATAATTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 4 0.18
12 4 0.18
13 14 0.64
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATTATA
Found at i:31511715 original size:20 final size:20
Alignment explanation
Indices: 31511665--31511705 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
31511655 TTACTAAAAG
* *
31511665 TATATATNTATATATATTAA
1 TATATATATATATATAATAA
31511685 TATATATATATATATAATAA
1 TATATATATATATATAATAA
31511705 T
1 T
31511706 GTAATTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TATATATATATATATAATAA
Found at i:31513145 original size:30 final size:30
Alignment explanation
Indices: 31513109--31513173 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
31513099 AATGTTGGTG
* *
31513109 TGGGTTT-ATGGTTGAGCTCATTAAAAACCA
1 TGGGTTTGA-GGTTGAACCCATTAAAAACCA
31513139 TGGGTTTGAGGTTGAACCCATTAAAAACCA
1 TGGGTTTGAGGTTGAACCCATTAAAAACCA
31513169 TGGGT
1 TGGGT
31513174 GTCGCTCTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (30 bp):
TGGGTTTGAGGTTGAACCCATTAAAAACCA
Found at i:31513228 original size:34 final size:35
Alignment explanation
Indices: 31513190--31513262 Score: 89
Period size: 34 Copynumber: 2.1 Consensus size: 35
31513180 CTATCCCAGT
* * *
31513190 AAAAGGCT-TTGTG-AGGTTTTCGCTTGATCTTGTA
1 AAAAGGCTACTGTGAAGG-TTTCGCTTAATCTCGTA
31513224 AAAA-GCTACTGTGAAGGTTTCGCTTAATCTCGTA
1 AAAAGGCTACTGTGAAGGTTTCGCTTAATCTCGTA
31513258 AAAAG
1 AAAAG
31513263 CTCAATTCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
33 3 0.09
34 27 0.82
35 3 0.09
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (35 bp):
AAAAGGCTACTGTGAAGGTTTCGCTTAATCTCGTA
Found at i:31513263 original size:34 final size:34
Alignment explanation
Indices: 31513199--31513264 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
31513189 TAAAAGGCTT
* *
31513199 TGTGAGGTTTTCGCTTGATCTTGTAAAAAGCTAC
1 TGTGAGGTTTTCGCTTAATCTCGTAAAAAGCTAC
31513233 TGTGAAGG-TTTCGCTTAATCTCGTAAAAAGCT
1 TGTG-AGGTTTTCGCTTAATCTCGTAAAAAGCT
31513265 CAATTCCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 26 0.90
35 3 0.10
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (34 bp):
TGTGAGGTTTTCGCTTAATCTCGTAAAAAGCTAC
Found at i:31518831 original size:30 final size:30
Alignment explanation
Indices: 31518795--31518859 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
31518785 AAAGTTAGTG
*
31518795 TGGGTTTGTGGTTGAGCCCATTAAAAACCA
1 TGGGTTTGTGGTTGAACCCATTAAAAACCA
*
31518825 TGGGTTTGTGGTTGAACCCTTTAAAAACCA
1 TGGGTTTGTGGTTGAACCCATTAAAAACCA
31518855 TGGGT
1 TGGGT
31518860 GTCGCTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (30 bp):
TGGGTTTGTGGTTGAACCCATTAAAAACCA
Found at i:31518963 original size:33 final size:34
Alignment explanation
Indices: 31518910--31519015 Score: 101
Period size: 33 Copynumber: 3.1 Consensus size: 34
31518900 TGCTTTCATG
*
31518910 AAAAGCCATTGTGA-AGGTTTCACTTGATCTCGTA
1 AAAAGCAATTGTGAGA-GTTTCACTTGATCTCGTA
*
31518944 AAAAG-AATTGTGAGAGTTTCACTTGAT-TCTGAAA
1 AAAAGCAATTGTGAGAGTTTCACTTGATCTC-G-TA
* * * * *
31518978 AAAAGCTATTATGAGGGTTCCGCTTGATCTCGTA
1 AAAAGCAATTGTGAGAGTTTCACTTGATCTCGTA
31519012 AAAA
1 AAAA
31519016 ACCCATTTCT
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
32 2 0.03
33 20 0.34
34 17 0.29
35 18 0.31
36 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (34 bp):
AAAAGCAATTGTGAGAGTTTCACTTGATCTCGTA
Found at i:31519015 original size:35 final size:34
Alignment explanation
Indices: 31518930--31519016 Score: 88
Period size: 35 Copynumber: 2.6 Consensus size: 34
31518920 GTGAAGGTTT
* *
31518930 CACTTGATCTCGT-AAAAAGAATTGTGAGAGTTT
1 CACTTGATCTCGTAAAAAAGAATTATGAGAGTTC
* * *
31518963 CACTTGAT-TCTGAAAAAAAGCTATTATGAGGGTTC
1 CACTTGATCTC-GTAAAAAAG-AATTATGAGAGTTC
*
31518998 CGCTTGATCTCGTAAAAAA
1 CACTTGATCTCGTAAAAAA
31519017 CCCATTTCTC
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
32 2 0.05
33 9 0.21
34 6 0.14
35 24 0.56
36 2 0.05
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (34 bp):
CACTTGATCTCGTAAAAAAGAATTATGAGAGTTC
Found at i:31519501 original size:21 final size:21
Alignment explanation
Indices: 31519475--31519528 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
31519465 TCTTCACAAG
* *
31519475 TATAGTCAATTAGAAATTCTT
1 TATAGTCAACTAGAAAGTCTT
31519496 TATAGTCAACTAGAAAGTCTT
1 TATAGTCAACTAGAAAGTCTT
*
31519517 TCTAGTCAACTA
1 TATAGTCAACTA
31519529 CTTTAGTTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (21 bp):
TATAGTCAACTAGAAAGTCTT
Found at i:31528604 original size:2 final size:2
Alignment explanation
Indices: 31528597--31528623 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31528587 GATATGACAA
31528597 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
31528624 ACAATCATGT
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:31534625 original size:13 final size:13
Alignment explanation
Indices: 31534607--31534631 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31534597 TTTCAGAAAA
31534607 TTTATAAAATCAT
1 TTTATAAAATCAT
31534620 TTTATAAAATCA
1 TTTATAAAATCA
31534632 CAATTTCTCT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:31535856 original size:20 final size:20
Alignment explanation
Indices: 31535839--31535876 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31535829 CCTCAAATCT
31535839 TACTCCAATAAATCAAATTA
1 TACTCCAATAAATCAAATTA
* *
31535859 TACTCTAATAAGTCAAAT
1 TACTCCAATAAATCAAAT
31535877 GGGGCAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.18, G:0.03, T:0.32
Consensus pattern (20 bp):
TACTCCAATAAATCAAATTA
Found at i:31544594 original size:19 final size:20
Alignment explanation
Indices: 31544570--31544617 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
31544560 TCATATTTTG
*
31544570 ATTTAATAAGAAAGTAATTA
1 ATTTAATAAGAAAATAATTA
*
31544590 A-TTAA-AGATAAAATAATTA
1 ATTTAATA-AGAAAATAATTA
31544609 ATTTAATAA
1 ATTTAATAA
31544618 ATTATTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
18 1 0.04
19 15 0.65
20 6 0.26
21 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (20 bp):
ATTTAATAAGAAAATAATTA
Done.