Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold36
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: 4808052
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18886 characters in sequence are not A, C, G, or T
File 7 of 28
Found at i:1069249 original size:17 final size:18
Alignment explanation
Indices: 1069185--1069250 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 18
1069175 ATAATGCTAT
1069185 TTAT-TATTAAAATATTAA
1 TTATATATTAAAATA-TAA
* * *
1069203 TTATATAATAAAATTTTA
1 TTATATATTAAAATATAA
1069221 TT-TATATT--AATATAA
1 TTATATATTAAAATATAA
1069236 TTAT-TATTAAAATAT
1 TTATATATTAAAATAT
1069251 TCTTTTTAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
15 11 0.29
16 1 0.03
17 10 0.26
18 8 0.21
19 8 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTATATATTAAAATATAA
Found at i:1070085 original size:2 final size:2
Alignment explanation
Indices: 1070080--1070111 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1070070 ATATATATAT
1070080 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1070112 GATAAATCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1072450 original size:2 final size:2
Alignment explanation
Indices: 1072443--1072478 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1072433 AGCAGCAAAG
1072443 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1072479 TACATGTCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1073942 original size:11 final size:11
Alignment explanation
Indices: 1073926--1073967 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
1073916 GATATGTATT
1073926 TTATTTATTTA
1 TTATTTATTTA
1073937 TTATTTATTTA
1 TTATTTATTTA
1073948 -TA-TTATTTTA
1 TTATTTA-TTTA
*
1073958 TGATTTATTT
1 TTATTTATTT
1073968 GTGATAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
9 3 0.11
10 6 0.22
11 15 0.56
12 3 0.11
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (11 bp):
TTATTTATTTA
Found at i:1073957 original size:21 final size:19
Alignment explanation
Indices: 1073925--1073967 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
1073915 TGATATGTAT
*
1073925 TTTATTTATTTATTATTTA
1 TTTATTTATTTATGATTTA
1073944 TTTATATTATTTTATGATTTA
1 TTTAT-TTA-TTTATGATTTA
1073965 TTT
1 TTT
1073968 GTGATAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 3 0.14
21 13 0.62
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (19 bp):
TTTATTTATTTATGATTTA
Found at i:1075833 original size:8 final size:8
Alignment explanation
Indices: 1075820--1075846 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1075810 CTTTGTCCCT
1075820 AAAGATGA
1 AAAGATGA
1075828 AAAGATGA
1 AAAGATGA
1075836 AAAGATGA
1 AAAGATGA
1075844 AAA
1 AAA
1075847 CTGTGATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.22, T:0.11
Consensus pattern (8 bp):
AAAGATGA
Found at i:1076134 original size:31 final size:31
Alignment explanation
Indices: 1076092--1076154 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
1076082 TGGACAAGAG
* *
1076092 AACATTCTGGTAGCTGCAATCTCTAAGCCAT
1 AACATTCTGGTAGCTACAATCTATAAGCCAT
* *
1076123 AACATTTTGGTAGCTACAATCTATAAGGCAT
1 AACATTCTGGTAGCTACAATCTATAAGCCAT
1076154 A
1 A
1076155 GGTCCAATCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (31 bp):
AACATTCTGGTAGCTACAATCTATAAGCCAT
Found at i:1087339 original size:20 final size:20
Alignment explanation
Indices: 1087311--1087381 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
1087301 TTTTACCTAG
1087311 ATGTATCGATATATTTTTCA
1 ATGTATCGATATATTTTTCA
* * * * *
1087331 ATATATCGATACATGTATGA
1 ATGTATCGATATATTTTTCA
*
1087351 ATGTATCGATATATTCTTCA
1 ATGTATCGATATATTTTTCA
1087371 ATGTATCGATA
1 ATGTATCGATA
1087382 CATTATGTCT
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (20 bp):
ATGTATCGATATATTTTTCA
Found at i:1087371 original size:40 final size:39
Alignment explanation
Indices: 1087311--1087388 Score: 129
Period size: 40 Copynumber: 2.0 Consensus size: 39
1087301 TTTTACCTAG
*
1087311 ATGTATCGATATATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATATATTCTTCAATATATCGATACAT-TATGA
*
1087351 ATGTATCGATATATTCTTCAATGTATCGATACATTATG
1 ATGTATCGATATATTCTTCAATATATCGATACATTATG
1087389 TCTTTTTACC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 4 0.11
40 32 0.89
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (39 bp):
ATGTATCGATATATTCTTCAATATATCGATACATTATGA
Found at i:1087896 original size:13 final size:13
Alignment explanation
Indices: 1087878--1087903 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1087868 TACAGCAAGT
1087878 ATGTATCGATACA
1 ATGTATCGATACA
1087891 ATGTATCGATACA
1 ATGTATCGATACA
1087904 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1090154 original size:21 final size:21
Alignment explanation
Indices: 1090121--1090165 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1090111 TTGCAAGTTG
*
1090121 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1090143 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1090163 AAA
1 AAA
1090166 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1094095 original size:13 final size:13
Alignment explanation
Indices: 1094077--1094115 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
1094067 ACATTTTTCT
1094077 TTGTATCGATACA
1 TTGTATCGATACA
1094090 TTGTATCGATACA
1 TTGTATCGATACA
1094103 TTGTATCGATACA
1 TTGTATCGATACA
1094116 GGGTGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1094279 original size:20 final size:20
Alignment explanation
Indices: 1094236--1094282 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
1094226 AAATCTTTTG
1094236 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1094257 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1094277 CAAAAT
1 CAAAAT
1094283 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.45
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1098258 original size:20 final size:19
Alignment explanation
Indices: 1098226--1098271 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1098216 AGCCTTTGAC
*
1098226 CATGCATTTTTTATTATGTTT
1 CATGCA-TTTTTAATAT-TTT
1098247 CATGCATTTTTAATATTTT
1 CATGCATTTTTAATATTTT
1098266 CA-GCAT
1 CATGCAT
1098272 CTCATTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 5 0.21
20 9 0.38
21 6 0.25
ACGTcount: A:0.24, C:0.13, G:0.09, T:0.54
Consensus pattern (19 bp):
CATGCATTTTTAATATTTT
Found at i:1111312 original size:9 final size:9
Alignment explanation
Indices: 1111298--1111358 Score: 65
Period size: 8 Copynumber: 7.0 Consensus size: 9
1111288 CCTTTACACC
1111298 CAAAAAAAA
1 CAAAAAAAA
1111307 C-AAAAAAA
1 CAAAAAAAA
*
1111315 -AATAAAAA
1 CAAAAAAAA
*
1111323 -AAACAAAA
1 CAAAAAAAA
1111331 CAAAAAAAA
1 CAAAAAAAA
*
1111340 CAAAAAAAC
1 CAAAAAAAA
1111349 CAAGAAAAAA
1 CAA-AAAAAA
1111359 TAGCAAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
8 19 0.44
9 19 0.44
10 5 0.12
ACGTcount: A:0.85, C:0.11, G:0.02, T:0.02
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:1111332 original size:24 final size:22
Alignment explanation
Indices: 1111299--1111347 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 22
1111289 CTTTACACCC
*
1111299 AAAAAAAACAAAAAAAAATAAAA
1 AAAAAAAAC-AAAAAAAACAAAA
1111322 AAAACAAAACAAAAAAAACAAAA
1 AAAA-AAAACAAAAAAAACAAAA
1111345 AAA
1 AAA
1111348 CCAAGAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.90, C:0.08, G:0.00, T:0.02
Consensus pattern (22 bp):
AAAAAAAACAAAAAAAACAAAA
Found at i:1111367 original size:1 final size:1
Alignment explanation
Indices: 1111299--1111347 Score: 53
Period size: 1 Copynumber: 49.0 Consensus size: 1
1111289 CTTTACACCC
* * * * *
1111299 AAAAAAAACAAAAAAAAATAAAAAAAACAAAACAAAAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1111348 CCAAGAAAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.90, C:0.08, G:0.00, T:0.02
Consensus pattern (1 bp):
A
Found at i:1112625 original size:28 final size:28
Alignment explanation
Indices: 1112586--1113130 Score: 669
Period size: 28 Copynumber: 19.0 Consensus size: 28
1112576 GTTCATCCCT
*
1112586 TTTCAAAGCCCACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
* * **
1112614 TTTCAAAACCCACAAGTCAGTTGCATTC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
* **
1112642 TTTCAAAGCCCACAAGTCAGTTGCATTC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
*
1112670 TTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
*
1112698 TTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
1112726 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
*
1112754 TTTCAAAGCCCATACAAGTTAGTGGCACCC
1 TTTCAAAGCCC--ACAAGTCAGTGGCACCC
* * *
1112784 TTTCAAAGCCCACAAATCAGTGACACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
*
1112813 TTTCAAAGCCCACAAGTCAGTGGCACCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
* **
1112841 TTTCAAAGCCCATAAGTCAGTGGCACTTT
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
* *
1112870 TTTCAAAGCCCACAAGTTAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
*
1112898 TTTCAAAGCCCACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
* *
1112926 TTTCAAAGCCCAAGTAATTCAGTGGCACCC
1 TTTCAAAGCCC-A-CAAGTCAGTGGCACCC
*
1112956 TTTCAAAGCCCACAAGTTC-GTGGCACTCT
1 TTTCAAAGCCCACAAG-TCAGTGGCAC-CC
**
1112985 TTTCAAAGCCCACAAGTCAGTGGCACAT
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
1113013 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
*
1113041 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
** *
1113070 TTTCAAAGCCCACACGAGTTGGTGGCAACTCT
1 TTTCAAAGCCCACA--AGTCAGTGGC-AC-CC
*
1113102 TTTCAAAGCTCACACAAGTTAGTGGCACC
1 TTTCAAAGC-C-CACAAGTCAGTGGCACC
1113131 ATTTTTTTTA
Statistics
Matches: 465, Mismatches: 37, Indels: 28
0.88 0.07 0.05
Matches are distributed among these distances:
28 283 0.61
29 92 0.20
30 52 0.11
31 10 0.02
32 23 0.05
33 1 0.00
34 4 0.01
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCACCC
Found at i:1112922 original size:172 final size:170
Alignment explanation
Indices: 1112586--1113130 Score: 762
Period size: 172 Copynumber: 3.2 Consensus size: 170
1112576 GTTCATCCCT
* * *
1112586 TTTCAAAGCCC-ACAAGTTAGTGGCACCCTTTCAAAACCCACAAGTCAGTTGCATTC-TTTCAAA
1 TTTCAAAGCCCAACAAGTTAGTGGCACCCTTTCAAAGCCCACAAATCAG-TGCACTCTTTTCAAA
* *
1112649 GCCCACAAGTCAGTTGCA-TTCTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACA
65 GCCCACAAGTCAGTGGCACAT-TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACA
*
1112712 AGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCC
129 AGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCC
1112754 TTTCAAAGCCCATACAAGTTAGTGGCACCCTTTCAAAGCCCACAAATCAGTGACACTCTTTTCAA
1 TTTCAAAGCCCA-ACAAGTTAGTGGCACCCTTTCAAAGCCCACAAATCAGTG-CACTCTTTTCAA
* * **
1112819 AGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCATAAGTCAGTGGCACTTTTTTCAAAGCCCACA
64 AGCCCACAAGTCAGTGGCACATTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACA
*
1112884 AGTTAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCC
129 AGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCC
* *
1112926 TTTCAAAGCCCAAGTAA-TTCAGTGGCACCCTTTCAAAGCCCACAAGTTC-GTGGCACTCTTTTC
1 TTTCAAAGCCCAA-CAAGTT-AGTGGCACCCTTTCAAAGCCCACAA-ATCAGT-GCACTCTTTTC
1112989 AAAGCCCACAAGTCAGTGGCACATTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCA
62 AAAGCCCACAAGTCAGTGGCACATTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCA
* * *
1113053 CAAGTCAGTGGCACTCTTTTCAAAGCCCACACGAGTTGGTGGCAACTCT
127 CAAGTCAGTGGCA-TCCTTTCAAAGCCCACA--AGTTAGTGGC-AC-CC
*
1113102 TTTCAAAGCTCACACAAGTTAGTGGCACC
1 TTTCAAAGCCCA-ACAAGTTAGTGGCACC
1113131 ATTTTTTTTA
Statistics
Matches: 338, Mismatches: 22, Indels: 26
0.88 0.06 0.07
Matches are distributed among these distances:
168 11 0.03
169 2 0.01
170 39 0.12
171 75 0.22
172 171 0.51
173 3 0.01
174 9 0.03
175 2 0.01
176 23 0.07
177 3 0.01
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (170 bp):
TTTCAAAGCCCAACAAGTTAGTGGCACCCTTTCAAAGCCCACAAATCAGTGCACTCTTTTCAAAG
CCCACAAGTCAGTGGCACATTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAG
TCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCC
Found at i:1113723 original size:20 final size:20
Alignment explanation
Indices: 1113691--1113765 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
1113681 TTTTACCCAG
*
1113691 ATGTATTGATACATTTTTTA
1 ATGTATCGATACATTTTTTA
* * * *
1113711 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTTA
* *
1113731 ATGTATCGATATATTCTTTA
1 ATGTATCGATACATTTTTTA
1113751 ATGTATCGATACATT
1 ATGTATCGATACATT
1113766 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.45
Consensus pattern (20 bp):
ATGTATCGATACATTTTTTA
Found at i:1113751 original size:40 final size:39
Alignment explanation
Indices: 1113691--1113768 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1113681 TTTTACCCAG
* *
1113691 ATGTATTGATACATTTTTTAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTTTAATATATCGATACAT-TATGA
* *
1113731 ATGTATCGATATATTCTTTAATGTATCGATACATTATG
1 ATGTATCGATACATTCTTTAATATATCGATACATTATG
1113769 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (39 bp):
ATGTATCGATACATTCTTTAATATATCGATACATTATGA
Found at i:1114684 original size:20 final size:19
Alignment explanation
Indices: 1114652--1114697 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1114642 AGCCTTTGAC
*
1114652 CATGCATTTTTTATTATGTTT
1 CATGCA-TTTTTAATAT-TTT
1114673 CATGCATTTTTAATATTTT
1 CATGCATTTTTAATATTTT
1114692 CA-GCAT
1 CATGCAT
1114698 CTCATTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 5 0.21
20 9 0.38
21 6 0.25
ACGTcount: A:0.24, C:0.13, G:0.09, T:0.54
Consensus pattern (19 bp):
CATGCATTTTTAATATTTT
Found at i:1125618 original size:21 final size:20
Alignment explanation
Indices: 1125570--1125624 Score: 92
Period size: 20 Copynumber: 2.7 Consensus size: 20
1125560 ATATTTTGGA
1125570 TATGTATCGATACATTAACT
1 TATGTATCGATACATTAACT
1125590 TATGTATCGATACATTAACT
1 TATGTATCGATACATTAACT
*
1125610 TATTGTATCAATACA
1 TA-TGTATCGATACA
1125625 AATTGTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 22 0.67
21 11 0.33
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (20 bp):
TATGTATCGATACATTAACT
Found at i:1128214 original size:15 final size:16
Alignment explanation
Indices: 1128178--1128217 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
1128168 TTTAATATCT
*
1128178 ATAAAATTTTTAATTAA
1 ATAAAA-TTATAATTAA
1128195 ATAAAATTATAATT-A
1 ATAAAATTATAATTAA
1128210 ATAAAATT
1 ATAAAATT
1128218 TATTTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 7 0.32
17 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAATTATAATTAA
Found at i:1128220 original size:16 final size:17
Alignment explanation
Indices: 1128178--1128220 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
1128168 TTTAATATCT
*
1128178 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
1128195 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
1128210 ATAAAATTTAT
1 ATAAAATTTAT
1128221 TTAAAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 11 0.46
17 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:1134291 original size:2 final size:2
Alignment explanation
Indices: 1134284--1134311 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1134274 CACAAAATTC
1134284 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
1134312 GAATGTGTTT
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:1136416 original size:32 final size:33
Alignment explanation
Indices: 1136371--1136456 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 33
1136361 AATAAATATG
* **
1136371 ATATAGATATATTAATATTTTAAAATTTAAATA
1 ATATAAATATATTAATATACTAAAATTTAAATA
*
1136404 ATATAAAT-TATTAATATACTAAAATTTATATAA
1 ATATAAATATATTAATATACTAAAATTTAAAT-A
* *
1136437 ATTTAAATAATTTTAATATA
1 ATATAAAT-ATATTAATATA
1136457 ATTATAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
32 20 0.45
33 15 0.34
35 9 0.20
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (33 bp):
ATATAAATATATTAATATACTAAAATTTAAATA
Found at i:1136809 original size:17 final size:17
Alignment explanation
Indices: 1136774--1136878 Score: 65
Period size: 17 Copynumber: 5.8 Consensus size: 17
1136764 AATATAAAAA
1136774 ATAAT-TAAAATATAA-T
1 ATAATATAAAA-ATAATT
1136790 ATAATATAAAAATAATT
1 ATAATATAAAAATAATT
*
1136807 ATATAAATAAAATATGAATAT
1 ATA-ATATAAAA-AT-AAT-T
*
1136828 ATAAAATTATAAAAAT-TTAT
1 AT--AA-TATAAAAATAAT-T
1136848 ATAATATAAAAATAA-T
1 ATAATATAAAAATAATT
1136864 ATAAATATACAAAAT
1 AT-AATATA-AAAAT
1136879 TTAAAAACTA
Statistics
Matches: 73, Mismatches: 4, Indels: 22
0.74 0.04 0.22
Matches are distributed among these distances:
16 12 0.16
17 24 0.33
18 14 0.19
19 2 0.03
20 8 0.11
21 3 0.04
22 3 0.04
23 7 0.10
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (17 bp):
ATAATATAAAAATAATT
Found at i:1137997 original size:15 final size:17
Alignment explanation
Indices: 1137964--1138082 Score: 65
Period size: 18 Copynumber: 7.2 Consensus size: 17
1137954 AATATTTACA
*
1137964 TTATATTTATATTATTT
1 TTATATATATATTATTT
1137981 TTATATATA-ATTATTT
1 TTATATATATATTATTT
*
1137997 TTA-A-A-ATATTATATA
1 TTATATATATATTAT-TT
*
1138012 TT-TACATA-A--ATTT
1 TTATATATATATTATTT
* *
1138025 TAATATATCTATATATTT
1 TTATATATATAT-TATTT
* *
1138043 ATATTATATTTATTATTT
1 TTA-TATATATATTATTT
*
1138061 TTACATATCATATTATATT
1 TTATATAT-ATATTAT-TT
1138080 TTA
1 TTA
1138083 ATTATTTTTA
Statistics
Matches: 77, Mismatches: 12, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
13 3 0.04
14 12 0.16
15 6 0.08
16 12 0.16
17 13 0.17
18 18 0.23
19 13 0.17
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATATATATATTATTT
Found at i:1138054 original size:28 final size:28
Alignment explanation
Indices: 1137955--1138089 Score: 93
Period size: 28 Copynumber: 4.9 Consensus size: 28
1137945 TCGCTTTCAA
*
1137955 ATATTTACATTATATTT-ATATTATTTTT
1 ATATTTACATTATATTTAATA-TATTTAT
* * *
1137983 ATATATA-ATTATTTTTAAAATA-TTAT
1 ATATTTACATTATATTTAATATATTTAT
* *
1138009 ATATTTACA-TAAATTTTAATATATCTAT
1 ATATTTACATTATA-TTTAATATATTTAT
* * * *
1138037 ATATTTATATTATATTTATTATTTTTAC
1 ATATTTACATTATATTTAATATATTTAT
* *
1138065 ATA-TCATATTATATTTTAAT-TATTT
1 ATATTTACATTATA-TTTAATATATTT
1138090 TTATTATAAT
Statistics
Matches: 83, Mismatches: 18, Indels: 13
0.73 0.16 0.11
Matches are distributed among these distances:
26 11 0.13
27 32 0.39
28 37 0.45
29 3 0.04
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.59
Consensus pattern (28 bp):
ATATTTACATTATATTTAATATATTTAT
Found at i:1138102 original size:11 final size:10
Alignment explanation
Indices: 1138036--1138102 Score: 52
Period size: 9 Copynumber: 6.8 Consensus size: 10
1138026 AATATATCTA
1138036 TATATTTATAT
1 TATATTT-TAT
1138047 TATA-TTTAT
1 TATATTTTAT
1138056 TAT-TTTTA-
1 TATATTTTAT
* **
1138064 CATATCATAT
1 TATATTTTAT
1138074 TATATTTTAAT
1 TATATTTT-AT
1138085 TAT-TTTTAT
1 TATATTTTAT
1138094 TATAATTTT
1 TAT-ATTTT
1138103 GTGTATACAC
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
8 2 0.05
9 18 0.41
10 11 0.25
11 13 0.30
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (10 bp):
TATATTTTAT
Found at i:1150424 original size:13 final size:13
Alignment explanation
Indices: 1150403--1150435 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1150393 AATGAATTCC
1150403 AAGAAAAAAGGAAA
1 AAGAAAAAA-GAAA
1150417 AA-AAAAAAGAAA
1 AAGAAAAAAGAAA
1150429 AAGAAAA
1 AAGAAAA
1150436 TCAAATGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.33
13 10 0.56
14 2 0.11
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAGAAA
Found at i:1155396 original size:25 final size:25
Alignment explanation
Indices: 1155362--1155412 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
1155352 ACATACCATT
1155362 CCACACCACTTAAATCACTACAAGG
1 CCACACCACTTAAATCACTACAAGG
* * *
1155387 CCACACCACTTGAATTATTACAAGG
1 CCACACCACTTAAATCACTACAAGG
1155412 C
1 C
1155413 TACTTGCCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.33, G:0.10, T:0.20
Consensus pattern (25 bp):
CCACACCACTTAAATCACTACAAGG
Found at i:1159838 original size:18 final size:18
Alignment explanation
Indices: 1159815--1159853 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1159805 AGGTCGGACA
1159815 TAGCTTATGCTGTTAGTG
1 TAGCTTATGCTGTTAGTG
*
1159833 TAGCTTATGTTGTTAGTG
1 TAGCTTATGCTGTTAGTG
1159851 TAG
1 TAG
1159854 TAAGTCAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.18, C:0.08, G:0.28, T:0.46
Consensus pattern (18 bp):
TAGCTTATGCTGTTAGTG
Found at i:1163750 original size:2 final size:2
Alignment explanation
Indices: 1163745--1163769 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1163735 TAAACGGGGG
1163745 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
1163770 CATGTGACAG
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1168481 original size:25 final size:25
Alignment explanation
Indices: 1168453--1168501 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
1168443 ATATATAGGC
*
1168453 TTGATTGTAGGAGATTTGATTAGAT
1 TTGATTATAGGAGATTTGATTAGAT
1168478 TTGATTATAGGAGATTTGATTAGA
1 TTGATTATAGGAGATTTGATTAGA
1168502 AGTGATTAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.27, T:0.43
Consensus pattern (25 bp):
TTGATTATAGGAGATTTGATTAGAT
Found at i:1168507 original size:25 final size:25
Alignment explanation
Indices: 1168454--1168509 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
1168444 TATATAGGCT
* **
1168454 TGATTGTAGGAGATTTGATTAGATT
1 TGATTATAGGAGATTTGATTAGAAG
1168479 TGATTATAGGAGATTTGATTAGAAG
1 TGATTATAGGAGATTTGATTAGAAG
1168504 TGATTA
1 TGATTA
1168510 GATTTTAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.27, T:0.41
Consensus pattern (25 bp):
TGATTATAGGAGATTTGATTAGAAG
Found at i:1173365 original size:14 final size:13
Alignment explanation
Indices: 1173327--1173365 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1173317 GTTACTAATT
1173327 ATGTTAGAAGATA
1 ATGTTAGAAGATA
* *
1173340 TTGCTAGAAGATA
1 ATGTTAGAAGATA
1173353 ATGTTAGGAAGAT
1 ATGTTA-GAAGAT
1173366 GATTCAGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.41, C:0.03, G:0.26, T:0.31
Consensus pattern (13 bp):
ATGTTAGAAGATA
Found at i:1173470 original size:25 final size:25
Alignment explanation
Indices: 1173442--1173494 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 25
1173432 GATTTGTTAG
1173442 TTTTAAATATTT-AATTTATTT-AATT
1 TTTTAAAT-TTTAAATTT-TTTGAATT
1173467 TTTTAAATTTTAAATTTTTTGAATT
1 TTTTAAATTTTAAATTTTTTGAATT
1173492 TTT
1 TTT
1173495 AATTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 6 0.23
25 20 0.77
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (25 bp):
TTTTAAATTTTAAATTTTTTGAATT
Found at i:1173503 original size:9 final size:8
Alignment explanation
Indices: 1173451--1173502 Score: 61
Period size: 8 Copynumber: 6.4 Consensus size: 8
1173441 GTTTTAAATA
1173451 TTTAATTT
1 TTTAATTT
1173459 ATTTAATTT
1 -TTTAATTT
*
1173468 TTTAAATT
1 TTTAATTT
*
1173476 TTAAATTT
1 TTTAATTT
1173484 TTTGAA-TT
1 TTT-AATTT
1173492 TTTAATTT
1 TTTAATTT
1173500 TTT
1 TTT
1173503 TTGTTATCTA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
7 2 0.05
8 25 0.68
9 10 0.27
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (8 bp):
TTTAATTT
Found at i:1173680 original size:3 final size:3
Alignment explanation
Indices: 1173672--1173714 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
1173662 ATTACAATTC
*
1173672 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1173715 TGGCCTTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1182218 original size:27 final size:28
Alignment explanation
Indices: 1182188--1182240 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
1182178 TAAATATATT
1182188 ATTAAAA-AATAAAATAAAA-AATTTTAA
1 ATTAAAATAAT-AAATAAAATAATTTTAA
*
1182215 ATTAAAATAATTAATAAAATAATTTT
1 ATTAAAATAATAAATAAAATAATTTT
1182241 TTTAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (28 bp):
ATTAAAATAATAAATAAAATAATTTTAA
Found at i:1182479 original size:12 final size:12
Alignment explanation
Indices: 1182449--1182484 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
1182439 ATACATAATT
1182449 TAAA-AATAAAA
1 TAAATAATAAAA
1182460 TAAAATAATAAAA
1 T-AAATAATAAAA
1182473 TAAATAATAAAA
1 TAAATAATAAAA
1182485 ATTAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.04
12 14 0.61
13 8 0.35
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (12 bp):
TAAATAATAAAA
Found at i:1182481 original size:25 final size:25
Alignment explanation
Indices: 1182435--1182484 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1182425 ATTAATTTTT
**
1182435 TAAAATACATAATTTAAAAATAAAA
1 TAAAATACATAAAATAAAAATAAAA
1182460 TAAAATA-ATAAAATAAATAATAAAA
1 TAAAATACATAAAATAAA-AATAAAA
1182485 ATTAAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (25 bp):
TAAAATACATAAAATAAAAATAAAA
Found at i:1183576 original size:13 final size:14
Alignment explanation
Indices: 1183553--1183583 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
1183543 CATATTTAAA
1183553 AATTAAATAAAATT
1 AATTAAATAAAATT
1183567 AATT-AATAAAATT
1 AATTAAATAAAATT
1183580 AATT
1 AATT
1183584 TATTATTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTAAATAAAATT
Found at i:1183693 original size:18 final size:18
Alignment explanation
Indices: 1183670--1183707 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1183660 TTTTAAATAC
*
1183670 ATAATTTAAAAAATAAAA
1 ATAATTCAAAAAATAAAA
*
1183688 ATAATTCATAAAATAAAA
1 ATAATTCAAAAAATAAAA
1183706 AT
1 AT
1183708 TTTAAGGGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAATTCAAAAAATAAAA
Found at i:1183793 original size:15 final size:14
Alignment explanation
Indices: 1183775--1183809 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
1183765 TATGTCATTA
1183775 AAAAATAAAATAAAT
1 AAAAATAAAA-AAAT
1183790 AAAAATAAAAAAAT
1 AAAAATAAAAAAAT
1183804 AGAAAA
1 A-AAAA
1183810 AAAGGTCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (14 bp):
AAAAATAAAAAAAT
Found at i:1192668 original size:20 final size:20
Alignment explanation
Indices: 1192635--1192696 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
1192625 TCTTAGAGGG
*
1192635 TTTTTAATTATATTTA-ATTAA
1 TTTTT-ATTTTATTTATATT-A
1192656 TTTTTATTTTATTTCATATTA
1 TTTTTATTTTATTT-ATATTA
* *
1192677 GTTTTA-TTTATTTATTTTA
1 TTTTTATTTTATTTATATTA
1192696 T
1 T
1192697 AATTAAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 5 0.14
20 15 0.43
21 12 0.34
22 3 0.09
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTTTATTTTATTTATATTA
Found at i:1193037 original size:16 final size:17
Alignment explanation
Indices: 1193016--1193052 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
1193006 GATTTGATAA
*
1193016 CTTTTAGTTTTTTTT-T
1 CTTTTAATTTTTTTTAT
1193032 CTTTTAATTTTTTTTAT
1 CTTTTAATTTTTTTTAT
1193049 CTTT
1 CTTT
1193053 ATTATAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.11, C:0.08, G:0.03, T:0.78
Consensus pattern (17 bp):
CTTTTAATTTTTTTTAT
Found at i:1194142 original size:8 final size:8
Alignment explanation
Indices: 1194129--1194166 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
1194119 ATCATAATTT
1194129 AAATTTTA
1 AAATTTTA
1194137 AAATTTTA
1 AAATTTTA
*
1194145 ATTATTTTA
1 A-AATTTTA
1194154 AAA-TTTA
1 AAATTTTA
1194161 AAATTT
1 AAATTT
1194167 AAATAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
7 7 0.27
8 12 0.46
9 7 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
AAATTTTA
Found at i:1194699 original size:32 final size:34
Alignment explanation
Indices: 1194663--1194725 Score: 103
Period size: 32 Copynumber: 1.9 Consensus size: 34
1194653 GGACGAGTAT
*
1194663 TATTTAATTTTTTTAAAT-TTTTA-ATATAAATA
1 TATTTAATTTTTTAAAATCTTTTATATATAAATA
1194695 TATTTAATTTTTTAAAATCTTTTATATATAA
1 TATTTAATTTTTTAAAATCTTTTATATATAA
1194726 TAAAATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 17 0.61
33 5 0.18
34 6 0.21
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (34 bp):
TATTTAATTTTTTAAAATCTTTTATATATAAATA
Found at i:1197107 original size:15 final size:17
Alignment explanation
Indices: 1197088--1197128 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1197078 ATGTTTAATA
*
1197088 ATATAATTTAATTAAAT
1 ATATATTTTAATTAAAT
*
1197105 ATATATTTTTATTAAAT
1 ATATATTTTAATTAAAT
*
1197122 ATTTATT
1 ATATATT
1197129 ATTTTTAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATATATTTTAATTAAAT
Found at i:1197128 original size:17 final size:18
Alignment explanation
Indices: 1197093--1197162 Score: 65
Period size: 17 Copynumber: 3.9 Consensus size: 18
1197083 TAATAATATA
*
1197093 ATTTAATTAAATATATATT
1 ATTT-ATTAAATATTTATT
1197112 -TTTATTAAATATTTATT
1 ATTTATTAAATATTTATT
*
1197129 ATTT-TT-AATATTAAAATT
1 ATTTATTAAATATT--TATT
*
1197147 ATTTATTTAATATTTA
1 ATTTATTAAATATTTA
1197163 AATTTTTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
16 6 0.14
17 15 0.35
18 14 0.33
19 2 0.05
20 6 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTATTAAATATTTATT
Found at i:1197134 original size:21 final size:24
Alignment explanation
Indices: 1197110--1197153 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
1197100 TAAATATATA
1197110 TTTT-TATT-AAA-TATTTATTAT
1 TTTTATATTAAAATTATTTATTAT
1197131 TTTTAATATTAAAATTATTTATT
1 TTTT-ATATTAAAATTATTTATT
1197154 TAATATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.21
23 4 0.21
24 3 0.16
25 8 0.42
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TTTTATATTAAAATTATTTATTAT
Found at i:1197174 original size:20 final size:20
Alignment explanation
Indices: 1197132--1197170 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1197122 ATTTATTATT
1197132 TTTAATATTAAAATTATTTA
1 TTTAATATTAAAATTATTTA
*
1197152 TTTAATATTTAAATT-TTTA
1 TTTAATATTAAAATTATTTA
1197171 ATTTTATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTAATATTAAAATTATTTA
Found at i:1198971 original size:40 final size:39
Alignment explanation
Indices: 1198901--1198976 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 39
1198891 ACAATTATAG
1198901 TTAAAAATATTATATTAAAACTGTATAAATAATAAATGAT
1 TTAAAAATATTATATTAAAACTGTATAAAT-ATAAATGAT
1198941 TTAAAATATATTTATATT-AAA-TG-ATGAAATATAAAT
1 TTAAAA-ATA-TTATATTAAAACTGTAT-AAATATAAAT
1198977 AAAATTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
39 8 0.24
40 12 0.36
41 6 0.18
42 7 0.21
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.39
Consensus pattern (39 bp):
TTAAAAATATTATATTAAAACTGTATAAATATAAATGAT
Found at i:1199485 original size:28 final size:29
Alignment explanation
Indices: 1199431--1199485 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 29
1199421 TATAACTCAA
* * *
1199431 TTTAAATCATAATATATTTTAATAATATG
1 TTTAAATCATAATATAATTGAAAAATATG
*
1199460 TTTAAAT-ATAATTTAATTGAAAAATA
1 TTTAAATCATAATATAATTGAAAAATA
1199486 AATATTATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 15 0.68
29 7 0.32
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (29 bp):
TTTAAATCATAATATAATTGAAAAATATG
Found at i:1200570 original size:20 final size:20
Alignment explanation
Indices: 1200525--1200571 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1200515 TAATTTTTTG
*
1200525 TATAATTAATATTTTAATAA
1 TATAATTAATAATTTAATAA
*
1200545 -ATTAATTAATAATTTATTAA
1 TA-TAATTAATAATTTAATAA
1200565 TATAATT
1 TATAATT
1200572 TTATTTGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATAATTAATAATTTAATAA
Found at i:1201528 original size:23 final size:24
Alignment explanation
Indices: 1201502--1201547 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
1201492 ATTTTTTTAT
*
1201502 AGAAT-TTTCATTGAAA-AATTTTC
1 AGAATATTTC-TTAAAAGAATTTTC
1201525 AGAATATTTCTTAAAAGAATTTT
1 AGAATATTTCTTAAAAGAATTTT
1201548 ATTGAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (24 bp):
AGAATATTTCTTAAAAGAATTTTC
Found at i:1202300 original size:25 final size:24
Alignment explanation
Indices: 1202261--1202315 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 24
1202251 CCATTGACAT
1202261 AAATA-TTAAATTATTAATTATTA
1 AAATATTTAAATTATTAATTATTA
* *
1202284 AAATATTTAAAATTATTTATTTTTA
1 AAATATTT-AAATTATTAATTATTA
1202309 AAATATT
1 AAATATT
1202316 AATATTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.18
24 2 0.07
25 21 0.75
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
AAATATTTAAATTATTAATTATTA
Found at i:1202327 original size:15 final size:15
Alignment explanation
Indices: 1202285--1202337 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
1202275 TAATTATTAA
1202285 AATATTTAAAATTATT
1 AATATTTAAAA-TATT
* *
1202301 TATTTTTAAAATATT
1 AATATTTAAAATATT
* *
1202316 AATATTTCAAATAAT
1 AATATTTAAAATATT
1202331 AATATTT
1 AATATTT
1202338 TAATCATAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
15 22 0.71
16 9 0.29
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
AATATTTAAAATATT
Found at i:1202348 original size:14 final size:15
Alignment explanation
Indices: 1202309--1202351 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1202299 TTTATTTTTA
*
1202309 AAATATTAATATTTC
1 AAATAATAATATTTC
1202324 AAATAATAATATTT-
1 AAATAATAATATTTC
* *
1202338 TAATCATAATATTT
1 AAATAATAATATTT
1202352 ATATTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (15 bp):
AAATAATAATATTTC
Found at i:1203456 original size:30 final size:30
Alignment explanation
Indices: 1203335--1203456 Score: 90
Period size: 30 Copynumber: 4.1 Consensus size: 30
1203325 TAAAATATTG
* * *
1203335 ATTTAAAGGCTTATTTAAGTACAAATTAAA
1 ATTTAAAGACTTATTTAAGTATAAAATAAA
* ** *
1203365 GA-TTAAGGGTTTATTTGA-T-TAAAAGTTAAA
1 -ATTTAAAGACTTATTTAAGTATAAAA--TAAA
*
1203395 AGTTAAAGACTTATTTAAGTATAAAATAAA
1 ATTTAAAGACTTATTTAAGTATAAAATAAA
* *
1203425 ATTTAATGACTTATTTGAGTATAATAA-AAA
1 ATTTAAAGACTTATTTAAGTATAA-AATAAA
1203455 AT
1 AT
1203457 ATAAGGGATT
Statistics
Matches: 73, Mismatches: 12, Indels: 13
0.74 0.12 0.13
Matches are distributed among these distances:
28 3 0.04
29 2 0.03
30 59 0.81
31 4 0.05
32 5 0.07
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (30 bp):
ATTTAAAGACTTATTTAAGTATAAAATAAA
Found at i:1203854 original size:2 final size:2
Alignment explanation
Indices: 1203849--1203891 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
1203839 ATATAATTTA
*
1203849 AT AT AT AT AT AT AT A- AA AT A- 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
1203889 AT A
1 AT A
1203892 AAAGAATTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1204270 original size:16 final size:16
Alignment explanation
Indices: 1204231--1204271 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
1204221 AAATAACTTA
1204231 TTATTTCACAAAAAAAT
1 TTATTT-ACAAAAAAAT
*
1204248 TTAATTTACATAAAAAT
1 TT-ATTTACAAAAAAAT
1204265 TTATTTA
1 TTATTTA
1204272 AATATAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 5 0.23
17 13 0.59
18 4 0.18
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (16 bp):
TTATTTACAAAAAAAT
Found at i:1205267 original size:20 final size:20
Alignment explanation
Indices: 1205228--1205273 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1205218 TTTAATATAA
*
1205228 TATATATTTATATATATTAT
1 TATATATTAATATATATTAT
* * *
1205248 TGTATATTAATATTTTTTAT
1 TATATATTAATATATATTAT
1205268 TATATA
1 TATATA
1205274 AATTTTTAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TATATATTAATATATATTAT
Found at i:1207463 original size:15 final size:15
Alignment explanation
Indices: 1207443--1207475 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1207433 AATAATTTTA
1207443 TTAAA-TATTTTAAAT
1 TTAAATTATTTT-AAT
1207458 TTAAATTATTTTAAT
1 TTAAATTATTTTAAT
1207473 TTA
1 TTA
1207476 TTTTAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAAATTATTTTAAT
Found at i:1207510 original size:11 final size:11
Alignment explanation
Indices: 1207494--1207528 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1207484 GATAATTTAT
1207494 TTATTATTCAA
1 TTATTATTCAA
1207505 TTATTATTCAA
1 TTATTATTCAA
*
1207516 ATATTATT-AA
1 TTATTATTCAA
1207526 TTA
1 TTA
1207529 AATTTATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 4 0.18
11 18 0.82
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (11 bp):
TTATTATTCAA
Found at i:1208267 original size:22 final size:25
Alignment explanation
Indices: 1208213--1208267 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 25
1208203 AAGTTTGTTC
1208213 AAACAAATATATGAATAATTTTATT
1 AAACAAATATATGAATAATTTTATT
* *
1208238 AAAAAAAT-TATTAA-AA-TTTATT
1 AAACAAATATATGAATAATTTTATT
*
1208260 TAACAAAT
1 AAACAAAT
1208268 GGAAATAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 12 0.46
23 2 0.08
24 5 0.19
25 7 0.27
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (25 bp):
AAACAAATATATGAATAATTTTATT
Found at i:1210216 original size:2 final size:2
Alignment explanation
Indices: 1210178--1210204 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1210168 TGTATGTGTG
1210178 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
1210205 TTTAAAATAT
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:1210310 original size:11 final size:11
Alignment explanation
Indices: 1210294--1210340 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
1210284 TTTTAAAATA
1210294 TATATTTTTAT
1 TATATTTTTAT
*
1210305 TATATTTATAT
1 TATATTTTTAT
1210316 TAT-TTTTTAT
1 TATATTTTTAT
1210326 ATCATATTTTATAT
1 -T-ATATTTT-TAT
1210340 T
1 T
1210341 TTTTATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
10 6 0.20
11 14 0.47
12 2 0.07
13 5 0.17
14 3 0.10
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (11 bp):
TATATTTTTAT
Found at i:1210322 original size:21 final size:21
Alignment explanation
Indices: 1210292--1210348 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
1210282 AATTTTAAAA
1210292 TATATATTTTTAT-T-ATATTT
1 TATAT-TTTTTATATCATATTT
1210312 ATATTATTTTTTATATCATATTT
1 -TA-TATTTTTTATATCATATTT
1210335 TATATTTTTTATAT
1 TATATTTTTTATAT
1210349 AACATTCATA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
21 21 0.64
22 6 0.18
23 6 0.18
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (21 bp):
TATATTTTTTATATCATATTT
Found at i:1210344 original size:23 final size:22
Alignment explanation
Indices: 1210298--1210349 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
1210288 AAAATATATA
1210298 TTTTTAT-TATATTTATATTAT
1 TTTTTATATATATTTATATTAT
1210319 TTTTTATATCATATTT-TA-TAT
1 TTTTTATAT-ATATTTATATTAT
1210340 TTTTTATATA
1 TTTTTATATA
1210350 ACATTCATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 1 0.03
21 19 0.66
22 3 0.10
23 6 0.21
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTTTATATATATTTATATTAT
Found at i:1210611 original size:2 final size:2
Alignment explanation
Indices: 1210606--1210630 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1210596 AGTGATGAAC
1210606 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
1210631 ATAAAGAAAA
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:1211521 original size:13 final size:13
Alignment explanation
Indices: 1211503--1211528 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1211493 AAAGATTAAG
1211503 TAAAAGAAAGAAA
1 TAAAAGAAAGAAA
1211516 TAAAAGAAAGAAA
1 TAAAAGAAAGAAA
1211529 CATACAAATT
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:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (13 bp):
TAAAAGAAAGAAA
Found at i:1211794 original size:28 final size:28
Alignment explanation
Indices: 1211737--1211795 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1211727 TTTAATAAAA
*
1211737 ATATATTTATAATTAATACATTAATAAT
1 ATATATTTATAATTAATACATAAATAAT
* *
1211765 ATATATTTATATATTATTA-ATAAATTAT
1 ATATATTTATA-ATTAATACATAAATAAT
1211793 ATA
1 ATA
1211796 GTATGATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 21 0.78
29 6 0.22
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (28 bp):
ATATATTTATAATTAATACATAAATAAT
Found at i:1211875 original size:6 final size:6
Alignment explanation
Indices: 1211864--1211894 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1211854 AATATAAAGC
1211864 CAATAA CAATAA CAATAA CAATAA CAATAA C
1 CAATAA CAATAA CAATAA CAATAA CAATAA C
1211895 GTACGTAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.65, C:0.19, G:0.00, T:0.16
Consensus pattern (6 bp):
CAATAA
Found at i:1212400 original size:23 final size:22
Alignment explanation
Indices: 1212360--1212405 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
1212350 TATCTATTAA
1212360 TATTAAAATAAAAATAATATATT
1 TATTAAAATAAAAATAAT-TATT
* * *
1212383 TATTAATATAATATTAATTATT
1 TATTAAAATAAAAATAATTATT
1212405 T
1 T
1212406 TAATTTTGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TATTAAAATAAAAATAATTATT
Found at i:1214329 original size:17 final size:18
Alignment explanation
Indices: 1214303--1214341 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1214293 ATTCATGTTA
*
1214303 TATTACTATTATTTTTTC
1 TATTACTATTATGTTTTC
*
1214321 TATTA-TATTATGTTTTG
1 TATTACTATTATGTTTTC
1214338 TATT
1 TATT
1214342 GGTATTACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (18 bp):
TATTACTATTATGTTTTC
Found at i:1214564 original size:32 final size:33
Alignment explanation
Indices: 1214523--1214587 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1214513 GAGATTTTAG
*
1214523 ATATAAATTTTAATATATTAATAG-TTCATATT
1 ATATAAATTTTAATACATTAATAGATTCATATT
* *
1214555 ATATAAATTTTGATACATTAATGGATTCATATT
1 ATATAAATTTTAATACATTAATAGATTCATATT
1214588 GTATTGTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 21 0.72
33 8 0.28
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.48
Consensus pattern (33 bp):
ATATAAATTTTAATACATTAATAGATTCATATT
Found at i:1215852 original size:14 final size:13
Alignment explanation
Indices: 1215826--1215867 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
1215816 ATAATGTTAC
1215826 ATTTTTTT-TATT
1 ATTTTTTTATATT
1215838 ATTTTTTTATAATT
1 ATTTTTTTAT-ATT
*
1215852 ATTTATTTAT-TT
1 ATTTTTTTATATT
1215864 ATTT
1 ATTT
1215868 ATAATTTACC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 14 0.52
13 1 0.04
14 12 0.44
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTTTTTATATT
Found at i:1215863 original size:22 final size:21
Alignment explanation
Indices: 1215832--1215873 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
1215822 TTACATTTTT
*
1215832 TTTATTATTTTTTTATAATTA
1 TTTATTATTTATTTATAATTA
1215853 TTTATTTATTTATTTATAATT
1 TTTA-TTATTTATTTATAATT
1215874 TACCTAACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTATTATTTATTTATAATTA
Found at i:1215909 original size:3 final size:3
Alignment explanation
Indices: 1215901--1215941 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1215891 TGATAGATCA
1215901 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1215942 ATTAAGTAAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1217544 original size:2 final size:2
Alignment explanation
Indices: 1217537--1217575 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1217527 CTCTTCCTTA
*
1217537 AT AT AT AT CT 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
1217576 ATTATTTCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1219857 original size:19 final size:19
Alignment explanation
Indices: 1219835--1219898 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
1219825 TAAAGTAGTT
*
1219835 GTTTTCAAATAAATGAATA
1 GTTTTAAAATAAATGAATA
1219854 GTTTTAAGAAT-AATCG-ATA
1 GTTTTAA-AATAAAT-GAATA
1219873 GTTTTTAAAAATAAATGAATA
1 G-TTTT-AAAATAAATGAATA
*
1219894 ATTTT
1 GTTTT
1219899 TTAAAAACTT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
19 13 0.35
20 16 0.43
21 8 0.22
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.41
Consensus pattern (19 bp):
GTTTTAAAATAAATGAATA
Found at i:1220060 original size:20 final size:20
Alignment explanation
Indices: 1220035--1220073 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1220025 AAATCATTAA
1220035 TTAAATTAATATCACTATTC
1 TTAAATTAATATCACTATTC
*
1220055 TTAAATTAATATTACTATT
1 TTAAATTAATATCACTATT
1220074 TCGTAACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAAATTAATATCACTATTC
Found at i:1237242 original size:23 final size:23
Alignment explanation
Indices: 1237173--1237244 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 23
1237163 TCTATATGTT
*
1237173 TAAT-TAATTATATATATAAAAATA
1 TAATATAA-TATATAT-TAAATATA
*
1237197 TAATA-AA-AT-T-TTAAATTTA
1 TAATATAATATATATTAAATATA
1237216 -AATATAATATATATTAAATATA
1 TAATATAATATATATTAAATATA
1237238 TAATATA
1 TAATATA
1237245 TATTTAATGT
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
18 4 0.10
19 8 0.21
20 3 0.08
21 2 0.05
22 10 0.26
23 6 0.15
24 6 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TAATATAATATATATTAAATATA
Found at i:1237266 original size:23 final size:24
Alignment explanation
Indices: 1237240--1237300 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 24
1237230 TAAATATATA
**
1237240 ATATATATTTAATGTATTA-TTTT
1 ATATATATTTAAAATATTACTTTT
*
1237263 ATATTTA-TTAAAATATTACTTTT
1 ATATATATTTAAAATATTACTTTT
*
1237286 AATATATTTTTAAAA
1 -ATATATATTTAAAA
1237301 AATATTTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
22 9 0.30
23 10 0.33
24 5 0.17
25 6 0.20
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (24 bp):
ATATATATTTAAAATATTACTTTT
Found at i:1237279 original size:22 final size:25
Alignment explanation
Indices: 1237254--1237300 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1237244 ATATTTAATG
1237254 TATTA-TTTT-ATAT-TTATTAAAA
1 TATTACTTTTAATATATTATTAAAA
*
1237276 TATTACTTTTAATATATTTTTAAAA
1 TATTACTTTTAATATATTATTAAAA
1237301 AATATTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 4 0.19
24 4 0.19
25 8 0.38
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
TATTACTTTTAATATATTATTAAAA
Found at i:1238019 original size:24 final size:24
Alignment explanation
Indices: 1237990--1238035 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1237980 TAGTTATAGT
1237990 ATTTATATTTAT-GATATTTTAATA
1 ATTTAT-TTTATAGATATTTTAATA
*
1238014 ATTTATTTTATATATATTTTAA
1 ATTTATTTTATAGATATTTTAA
1238036 CATGTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
ATTTATTTTATAGATATTTTAATA
Found at i:1238097 original size:27 final size:28
Alignment explanation
Indices: 1237991--1238111 Score: 87
Period size: 27 Copynumber: 4.4 Consensus size: 28
1237981 AGTTATAGTA
* *
1237991 TTTATATT-TATGATATTTTA-A-TA-A
1 TTTATATTATATCATATTTTACATTATT
*
1238015 TTTATTTTATAT-ATATTTTAACATGTTATT
1 TTTATATTATATCATATTTT-ACA--TTATT
* *
1238045 TATT-TATTAATATCATA-TTAAGATTATT
1 T-TTATATT-ATATCATATTTTACATTATT
1238073 TTTATATTATATCATATTTTA-ATTATT
1 TTTATATTATATCATATTTTACATTATT
*
1238100 TTTATGTTATAT
1 TTTATATTATAT
1238112 TAATAACATA
Statistics
Matches: 78, Mismatches: 7, Indels: 21
0.74 0.07 0.20
Matches are distributed among these distances:
24 14 0.18
25 4 0.05
26 1 0.01
27 27 0.35
28 13 0.17
29 2 0.03
30 6 0.08
31 8 0.10
32 3 0.04
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.60
Consensus pattern (28 bp):
TTTATATTATATCATATTTTACATTATT
Found at i:1240384 original size:18 final size:19
Alignment explanation
Indices: 1240359--1240398 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
1240349 TTAAATGAGT
1240359 TTTATTTTTT-ACTTAA-A
1 TTTATTTTTTAACTTAATA
1240376 TTTATTTTTTTAACTTAATA
1 TTTA-TTTTTTAACTTAATA
1240396 TTT
1 TTT
1240399 GTGTTCACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 6 0.30
19 6 0.30
20 4 0.20
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATTTTTTAACTTAATA
Found at i:1241325 original size:23 final size:24
Alignment explanation
Indices: 1241278--1241340 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 24
1241268 AAAATAAAAA
* *
1241278 ATAT-TAAAAAACTT-AAAATGTT
1 ATATATAAAAAAATTAAAAATGAT
1241300 ATATATAAAAAAATTAAAAAT-AT
1 ATATATAAAAAAATTAAAAATGAT
*
1241323 ATA-ATTAAAAAA-TAAAAA
1 ATATATAAAAAAATTAAAAA
1241341 CTTAAAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 6 0.17
22 12 0.33
23 13 0.36
24 5 0.14
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
ATATATAAAAAAATTAAAAATGAT
Found at i:1241335 original size:15 final size:14
Alignment explanation
Indices: 1241311--1241364 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
1241301 TATATAAAAA
1241311 AATTAAAAATATAT
1 AATTAAAAATATAT
*
1241325 AATTAAAAA-ATAAA
1 AATTAAAAATAT-AT
1241339 AACTT-AAAATATAT
1 AA-TTAAAAATATAT
*
1241353 AAATAAAAATAT
1 AATTAAAAATAT
1241365 CAAAAATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
13 3 0.09
14 26 0.79
15 4 0.12
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (14 bp):
AATTAAAAATATAT
Found at i:1241345 original size:29 final size:27
Alignment explanation
Indices: 1241308--1241396 Score: 101
Period size: 28 Copynumber: 3.1 Consensus size: 27
1241298 TTATATATAA
1241308 AAAAATTAAAAATATATAATTAAAAAAT
1 AAAAATTAAAAATATATAA-TAAAAAAT
1241336 AAAAACTT-AAAATATATAAATAAAAATAT
1 AAAAA-TTAAAAATATAT-AATAAAAA-AT
*
1241365 CAAAAATTAATAAAAAT-TAATAAAAAAT
1 -AAAAATTAA-AAATATATAATAAAAAAT
1241393 AAAA
1 AAAA
1241397 TAAAAAAAGA
Statistics
Matches: 54, Mismatches: 1, Indels: 13
0.79 0.01 0.19
Matches are distributed among these distances:
27 4 0.07
28 22 0.41
29 16 0.30
30 7 0.13
31 5 0.09
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (27 bp):
AAAAATTAAAAATATATAATAAAAAAT
Found at i:1241983 original size:22 final size:20
Alignment explanation
Indices: 1241958--1242048 Score: 72
Period size: 18 Copynumber: 4.7 Consensus size: 20
1241948 TAATTGAAAT
1241958 TATAAAAATAATTAAAATATAA
1 TATAAAAATAA-TAAAA-ATAA
*
1241980 TAT--AAAT-AT-AAAACAA
1 TATAAAAATAATAAAAATAA
1241996 TATAAAAATAATACAAACATAA
1 TATAAAAATAATA-AAA-ATAA
1242018 TAT--AAAT-ATAAAAAT-A
1 TATAAAAATAATAAAAATAA
1242034 TATAAAAATATATAA
1 TATAAAAATA-ATAA
1242049 TATAAATTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 22
0.70 0.02 0.27
Matches are distributed among these distances:
16 10 0.18
17 5 0.09
18 12 0.21
19 6 0.11
20 12 0.21
21 3 0.05
22 9 0.16
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (20 bp):
TATAAAAATAATAAAAATAA
Found at i:1241997 original size:16 final size:16
Alignment explanation
Indices: 1241978--1242039 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 16
1241968 ATTAAAATAT
1241978 AATATAAATATAAAAC
1 AATATAAATATAAAAC
1241994 AATATAAAAATAATACAAAC
1 AATAT--AAAT-ATA-AAAC
1242014 ATAATATAAATATAAAA-
1 --AATATAAATATAAAAC
1242031 ATATATAAA
1 A-ATATAAA
1242040 AATATATAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
15 1 0.03
16 12 0.31
18 7 0.18
19 6 0.15
20 8 0.21
22 5 0.13
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (16 bp):
AATATAAATATAAAAC
Found at i:1242002 original size:38 final size:38
Alignment explanation
Indices: 1241954--1242043 Score: 132
Period size: 38 Copynumber: 2.4 Consensus size: 38
1241944 AATCTAATTG
*
1241954 AAAT-TATAAAAATAATTA-AAATATAATATAAATATAA
1 AAATATATAAAAATAA-TACAAACATAATATAAATATAA
1241991 AACA-ATATAAAAATAATACAAACATAATATAAATATAA
1 AA-ATATATAAAAATAATACAAACATAATATAAATATAA
1242029 AAATATATAAAAATA
1 AAATATATAAAAATA
1242044 TATAATATAA
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
37 5 0.10
38 43 0.90
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (38 bp):
AAATATATAAAAATAATACAAACATAATATAAATATAA
Found at i:1242102 original size:22 final size:21
Alignment explanation
Indices: 1242072--1242113 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1242062 CGTATCTAAA
1242072 TTTATATAAATATATAATATT
1 TTTATATAAATATATAATATT
* *
1242093 TTTATTATAATTATATCATAT
1 TTTA-TATAAATATATAATAT
1242114 ATATAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTATATAAATATATAATATT
Found at i:1242733 original size:3 final size:3
Alignment explanation
Indices: 1242725--1242751 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1242715 AAGTTTATAT
1242725 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1242752 AAACCTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1243143 original size:3 final size:3
Alignment explanation
Indices: 1243135--1243181 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1243125 AGATAACCTA
1243135 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1243182 AGCAAGGTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1243668 original size:16 final size:16
Alignment explanation
Indices: 1243647--1243692 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
1243637 AATTTATTTA
1243647 TTTAAATTTAAATAAT
1 TTTAAATTTAAATAAT
*
1243663 TTTAAATTAAAAT-AT
1 TTTAAATTTAAATAAT
1243678 TTT-AATATTAAATAA
1 TTTAAAT-TTAAATAA
1243693 ATAATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 3 0.12
15 10 0.38
16 13 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTAAATTTAAATAAT
Found at i:1243707 original size:16 final size:16
Alignment explanation
Indices: 1243688--1243718 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1243678 TTTAATATTA
1243688 AATAAATAATAAATAT
1 AATAAATAATAAATAT
*
1243704 AATAAATAATTAATA
1 AATAAATAATAAATA
1243719 AAATTATATA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AATAAATAATAAATAT
Found at i:1244119 original size:3 final size:3
Alignment explanation
Indices: 1244113--1244147 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1244103 TGTTGAGTGC
1244113 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1244148 GTATTAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1244256 original size:14 final size:15
Alignment explanation
Indices: 1244227--1244258 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1244217 AACTTTTATA
1244227 TTAATATTTATATTT
1 TTAATATTTATATTT
1244242 TTAATATTT-TATTT
1 TTAATATTTATATTT
1244256 TTA
1 TTA
1244259 TTAAAAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTAATATTTATATTT
Found at i:1245737 original size:28 final size:28
Alignment explanation
Indices: 1245703--1245758 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
1245693 TATTTTTAAA
1245703 TTTTTTTACTAATT-TAAAAA-TAAAATAT
1 TTTTTTTA-T-ATTATAAAAATTAAAATAT
1245731 TTATTTTTATATTATAAAAATTAAAATA
1 TT-TTTTTATATTATAAAAATTAAAATA
1245759 AAATTTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 3 0.12
28 9 0.36
29 13 0.52
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (28 bp):
TTTTTTTATATTATAAAAATTAAAATAT
Found at i:1246233 original size:20 final size:20
Alignment explanation
Indices: 1246210--1246247 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1246200 TTTATTATAG
1246210 TTTTAAAGTT-TTATTTATCA
1 TTTTAAA-TTATTATTTATCA
1246230 TTTTAAATTATTATTTAT
1 TTTTAAATTATTATTTAT
1246248 AAAAAAATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTAAATTATTATTTATCA
Found at i:1246332 original size:26 final size:25
Alignment explanation
Indices: 1246300--1246349 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
1246290 ATTTTTAATT
*
1246300 TAATTTTATTCATCATTTAAATGATA
1 TAATTTTATTAATCA-TTAAATGATA
* *
1246326 TAATTTTTTTAATTATTAAATGAT
1 TAATTTTATTAATCATTAAATGAT
1246350 TCTGTACATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (25 bp):
TAATTTTATTAATCATTAAATGATA
Found at i:1246468 original size:15 final size:16
Alignment explanation
Indices: 1246448--1246483 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1246438 AGGTCTCAAA
1246448 TTTGAG-ATAGATTAT
1 TTTGAGTATAGATTAT
*
1246463 TTTGAGTTTAGATTAT
1 TTTGAGTATAGATTAT
1246479 TTTGA
1 TTTGA
1246484 ATAAATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (16 bp):
TTTGAGTATAGATTAT
Found at i:1247562 original size:28 final size:28
Alignment explanation
Indices: 1247531--1247638 Score: 64
Period size: 26 Copynumber: 3.9 Consensus size: 28
1247521 TATTAAATCT
1247531 ATTATAATATTATTATTTTTTATTTTAA
1 ATTATAATATTATTATTTTTTATTTTAA
* **
1247559 A-T-TAATTTTA-TATTATTTATAAGTTAA
1 ATTATAATATTATTATT-TTT-TATTTTAA
* * * * *
1247586 TATTTTTATATTATTATTATTAATTTTAT
1 -ATTATAATATTATTATTTTTTATTTTAA
*
1247615 ATTAT--TATTGTTATTTTTTTATTT
1 ATTATAATATTATTA-TTTTTTATTT
1247639 ATATTATCAA
Statistics
Matches: 59, Mismatches: 14, Indels: 15
0.67 0.16 0.17
Matches are distributed among these distances:
25 4 0.07
26 17 0.29
27 15 0.25
28 6 0.10
29 5 0.08
30 8 0.14
31 4 0.07
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (28 bp):
ATTATAATATTATTATTTTTTATTTTAA
Found at i:1247597 original size:22 final size:21
Alignment explanation
Indices: 1247530--1247597 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
1247520 TTATTAAATC
* *
1247530 TATTATAATATTATTATTTTT-
1 TATTTTAA-ATTAATATTTTTA
*
1247551 TATTTTAAATTAAT-TTTATA
1 TATTTTAAATTAATATTTTTA
*
1247571 TTATTTATAAGTTAATATTTTTA
1 -TATTT-TAAATTAATATTTTTA
1247594 TATT
1 TATT
1247598 ATTATTATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 4 0.11
20 5 0.13
21 12 0.32
22 12 0.32
23 5 0.13
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (21 bp):
TATTTTAAATTAATATTTTTA
Found at i:1247621 original size:20 final size:20
Alignment explanation
Indices: 1247538--1247670 Score: 85
Period size: 20 Copynumber: 6.5 Consensus size: 20
1247528 TCTATTATAA
*
1247538 TATTATT-ATTTTTTATT-T
1 TATTATTAATTTTATATTAT
*
1247556 TA-AATTAATTTTATATTATT
1 TATTATTAATTTTATATTA-T
*
1247576 TATAAGTTAATATTTTTATATTAT
1 TATTA-TT-A-A-TTTTATATTAT
1247600 TATTATTAATTTTATATTAT
1 TATTATTAATTTTATATTAT
* * *
1247620 TATTGTTATTTTTTTATT-T
1 TATTATTAATTTTATATTAT
* *
1247639 ATATTATCAAATTTATTATTAT
1 -TATTATTAATTTTA-TATTAT
*
1247661 ATATTTTTAA
1 -TATTATTAA
1247671 AAAAATTAGT
Statistics
Matches: 91, Mismatches: 13, Indels: 18
0.75 0.11 0.15
Matches are distributed among these distances:
17 3 0.03
18 11 0.12
19 1 0.01
20 38 0.42
21 7 0.08
22 12 0.13
23 3 0.03
24 6 0.07
25 10 0.11
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.65
Consensus pattern (20 bp):
TATTATTAATTTTATATTAT
Found at i:1248203 original size:49 final size:49
Alignment explanation
Indices: 1248142--1248290 Score: 289
Period size: 49 Copynumber: 3.0 Consensus size: 49
1248132 TCAGGGTAAG
1248142 ATATGATAGATATGAAGGTTAGTCAGGATATTGTAGTTGGTAAAAAAAA
1 ATATGATAGATATGAAGGTTAGTCAGGATATTGTAGTTGGTAAAAAAAA
1248191 ATATGATAGATATGAAGGTTAGTCAGGATATTGTAGTTGGTAAAAAAAAA
1 ATATGATAGATATGAAGGTTAGTCAGGATATTGTAGTTGGT-AAAAAAAA
1248241 ATATGATAGATATGAAGGTTAGTCAGGATATTGTAGTTGGTAAAAAAAA
1 ATATGATAGATATGAAGGTTAGTCAGGATATTGTAGTTGGTAAAAAAAA
1248290 A
1 A
1248291 GAATGGGTAA
Statistics
Matches: 99, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
49 50 0.51
50 49 0.49
ACGTcount: A:0.44, C:0.02, G:0.24, T:0.30
Consensus pattern (49 bp):
ATATGATAGATATGAAGGTTAGTCAGGATATTGTAGTTGGTAAAAAAAA
Found at i:1248258 original size:50 final size:50
Alignment explanation
Indices: 1248142--1248290 Score: 291
Period size: 50 Copynumber: 3.0 Consensus size: 50
1248132 TCAGGGTAAG
1248142 ATATGATAGATATGAAGGTTAGTCAGGATATTGTAGTTGGT-AAAAAAAA
1 ATATGATAGATATGAAGGTTAGTCAGGATATTGTAGTTGGTAAAAAAAAA
1248191 ATATGATAGATATGAAGGTTAGTCAGGATATTGTAGTTGGTAAAAAAAAA
1 ATATGATAGATATGAAGGTTAGTCAGGATATTGTAGTTGGTAAAAAAAAA
1248241 ATATGATAGATATGAAGGTTAGTCAGGATATTGTAGTTGGTAAAAAAAAA
1 ATATGATAGATATGAAGGTTAGTCAGGATATTGTAGTTGGTAAAAAAAAA
1248291 GAATGGGTAA
Statistics
Matches: 99, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
49 41 0.41
50 58 0.59
ACGTcount: A:0.44, C:0.02, G:0.24, T:0.30
Consensus pattern (50 bp):
ATATGATAGATATGAAGGTTAGTCAGGATATTGTAGTTGGTAAAAAAAAA
Found at i:1251061 original size:44 final size:44
Alignment explanation
Indices: 1251007--1251095 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
1250997 GTAGATCATT
1251007 GATCATATTGATGCACACAATGATTGCTTACCTGTTCATTGTTA
1 GATCATATTGATGCACACAATGATTGCTTACCTGTTCATTGTTA
1251051 GATCATATTGATGCACACAATGATTGCTTACCTGTTCATTGTTA
1 GATCATATTGATGCACACAATGATTGCTTACCTGTTCATTGTTA
1251095 G
1 G
1251096 CATGTAGGCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (44 bp):
GATCATATTGATGCACACAATGATTGCTTACCTGTTCATTGTTA
Found at i:1255087 original size:40 final size:34
Alignment explanation
Indices: 1255043--1255166 Score: 99
Period size: 35 Copynumber: 3.4 Consensus size: 34
1255033 TCATACCATA
*
1255043 TTTATATATATTTATATTATAATTATTATATTTAAATTTT
1 TTTATATA-ATTT-TAATA-AATT-TT-TATTT-AATTTT
1255083 TTTATATAATTTTAATAAATTTTTATTTAA-TTT
1 TTTATATAATTTTAATAAATTTTTATTTAATTTT
* *
1255116 TATATA-AATTTTAATATATTTATATTATTTATATTTT
1 TTTATATAATTTTAATA-AATT-T-TTATTTA-ATTTT
*
1255153 ATTTATATCATTTT
1 -TTTATATAATTTT
1255167 CCCTATCTTA
Statistics
Matches: 72, Mismatches: 5, Indels: 15
0.78 0.05 0.16
Matches are distributed among these distances:
32 10 0.14
33 11 0.15
34 3 0.04
35 12 0.17
36 3 0.04
37 7 0.10
38 9 0.12
39 9 0.12
40 8 0.11
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (34 bp):
TTTATATAATTTTAATAAATTTTTATTTAATTTT
Found at i:1255107 original size:21 final size:22
Alignment explanation
Indices: 1255043--1255140 Score: 85
Period size: 21 Copynumber: 4.3 Consensus size: 22
1255033 TCATACCATA
* *
1255043 TTTATATATATTTATATTATAAT
1 TTTATATAAATTTTTA-TATAAT
1255066 TATTATATTTAAATTTTTTTATATAAT
1 T-TTATA--TAAA--TTTTTATATAAT
*
1255093 TTTA-ATAAATTTTTATTTAAT
1 TTTATATAAATTTTTATATAAT
*
1255114 TTTATATAAATTTTAATAT-A-
1 TTTATATAAATTTTTATATAAT
1255134 TTTATAT
1 TTTATAT
1255141 TATTTATATT
Statistics
Matches: 64, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
20 7 0.11
21 16 0.25
22 12 0.19
23 5 0.08
24 5 0.08
25 1 0.02
26 6 0.09
27 7 0.11
28 5 0.08
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTATATAAATTTTTATATAAT
Found at i:1255131 original size:32 final size:31
Alignment explanation
Indices: 1255082--1255141 Score: 93
Period size: 32 Copynumber: 1.9 Consensus size: 31
1255072 ATTTAAATTT
*
1255082 TTTTATATAATTTTAATAAATTTTTATTTAA
1 TTTTATATAATTTTAATAAATTTATATTTAA
*
1255113 TTTTATATAAATTTTAATATATTTATATT
1 TTTTATAT-AATTTTAATAAATTTATATT
1255142 ATTTATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 8 0.31
32 18 0.69
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (31 bp):
TTTTATATAATTTTAATAAATTTATATTTAA
Found at i:1265551 original size:2 final size:2
Alignment explanation
Indices: 1265544--1265573 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1265534 TGCGTTGGTG
1265544 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
1265574 ATTTTTTTTA
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:1265779 original size:13 final size:14
Alignment explanation
Indices: 1265756--1265788 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1265746 AATTTTATTC
*
1265756 ATAAAAAAAATAAA
1 ATAATAAAAATAAA
1265770 A-AATAAAAATAAA
1 ATAATAAAAATAAA
1265783 ATAATA
1 ATAATA
1265789 TTATGATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (14 bp):
ATAATAAAAATAAA
Done.