Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold230
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: 2055625
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 10 of 14
Found at i:1103354 original size:18 final size:19
Alignment explanation
Indices: 1103302--1103355 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 19
1103292 AATTTATATT
*
1103302 TTTTATTATATTTAA-AATA
1 TTTTAATATA-TTAATAATA
* *
1103321 TTTT-ATATTTTTATAA-A
1 TTTTAATATATTAATAATA
1103338 TTTTAATATATTAATAAT
1 TTTTAATATATTAATAAT
1103356 TAATTTCATA
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
17 8 0.30
18 15 0.56
19 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTAATATATTAATAATA
Found at i:1103421 original size:35 final size:35
Alignment explanation
Indices: 1103380--1103468 Score: 146
Period size: 33 Copynumber: 2.6 Consensus size: 35
1103370 TTTTAAAATA
*
1103380 TATATTTATATTATATATTTTTATTTTATATATAT
1 TATATTTATATAATATATTTTTATTTTATATATAT
1103415 TATATTTATATAAT-TA-TTTTATTTTATATATAT
1 TATATTTATATAATATATTTTTATTTTATATATAT
1103448 TATATTTATATAATTATATTT
1 TATATTTATATAA-TATATTT
1103469 AAAACTTATC
Statistics
Matches: 50, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
33 30 0.60
34 3 0.06
35 15 0.30
36 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (35 bp):
TATATTTATATAATATATTTTTATTTTATATATAT
Found at i:1103895 original size:4 final size:4
Alignment explanation
Indices: 1103888--1103922 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
1103878 TTTATTGTAT
* *
1103888 TAGA TAGA TAGA TAGA TAGA TAAA TAAA TAGA TAG
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAG
1103923 GTACAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.54, C:0.00, G:0.20, T:0.26
Consensus pattern (4 bp):
TAGA
Found at i:1104726 original size:302 final size:303
Alignment explanation
Indices: 1104173--1104757 Score: 1075
Period size: 302 Copynumber: 1.9 Consensus size: 303
1104163 GACTTCTTGA
* * *
1104173 AATTTCTGCAGTAACTAATACTTCCCATTCATAAGTCAGAGAATAACAATGGCAGTAACTGAAGT
1 AATTTCTGCAGTAACTAATACTTCCCATTCATAAGTCACAAAATAAAAATGGCAGTAACTGAAGT
1104238 GAGGTTTAGATCAGAAATTGAAGATGAAAAGAAAGAGATAGACCAGAAAAGCAAAGAAGAATAGA
66 GAGGTTTAGATCAGAAATTGAAGATGAAAAGAAAGAGATAGACCAGAAAAGCAAAGAAGAATAGA
1104303 AAGAGAAATTAGAGAATTTTAATAATTTTCATTCATAATTCCCATTCAGTACATGATGATATATA
131 AAGAGAAATTAGAGAATTTTAATAATTTTCATTCATAATTCCCATTCAGTACATGATGATATATA
1104368 TAAGCTCACAATTACAACCTCTCTACCAGATCACTAACTTCTAGAATATCGGAATAACTGACTAA
196 TAAGCTCACAATTACAACCTCTCTACCAGATCACTAACTTCTAGAATATCGGAATAACTGACTAA
1104433 AATGACAAACT-AGTAATTACTAACATGGGAATACCAGATTACT
261 AATGACAAACTGA-TAATTACTAACATGGGAATACCAGATTACT
* *
1104476 AATTTCTGCAGTAAGTAATTCTTCCCATTCATAAGTCACAAAATAAAAATGGCAGTAACTGAAGT
1 AATTTCTGCAGTAACTAATACTTCCCATTCATAAGTCACAAAATAAAAATGGCAGTAACTGAAGT
1104541 GAGGTTTAGATCAGAAATTGAAGATGAAAAGAAAGAGATAGACCAGAAAAG-AAAGAAGAATAGA
66 GAGGTTTAGATCAGAAATTGAAGATGAAAAGAAAGAGATAGACCAGAAAAGCAAAGAAGAATAGA
*
1104605 ACGAGAAATTAGAGAATTTTAATAATTTTCATTCATAATTCCCATTCAGTACATGATGATATATA
131 AAGAGAAATTAGAGAATTTTAATAATTTTCATTCATAATTCCCATTCAGTACATGATGATATATA
* *
1104670 TAAGCTCACAATTACAACCTCTCTACCAGATCACTAACTTCTAGAATATGGGAATAACTGACTCA
196 TAAGCTCACAATTACAACCTCTCTACCAGATCACTAACTTCTAGAATATCGGAATAACTGACTAA
1104735 AATGACAAACTGATAATTACTAA
261 AATGACAAACTGATAATTACTAA
1104758 TATAATTTAT
Statistics
Matches: 273, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
302 161 0.59
303 112 0.41
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.26
Consensus pattern (303 bp):
AATTTCTGCAGTAACTAATACTTCCCATTCATAAGTCACAAAATAAAAATGGCAGTAACTGAAGT
GAGGTTTAGATCAGAAATTGAAGATGAAAAGAAAGAGATAGACCAGAAAAGCAAAGAAGAATAGA
AAGAGAAATTAGAGAATTTTAATAATTTTCATTCATAATTCCCATTCAGTACATGATGATATATA
TAAGCTCACAATTACAACCTCTCTACCAGATCACTAACTTCTAGAATATCGGAATAACTGACTAA
AATGACAAACTGATAATTACTAACATGGGAATACCAGATTACT
Found at i:1108952 original size:12 final size:12
Alignment explanation
Indices: 1108919--1109003 Score: 50
Period size: 12 Copynumber: 7.1 Consensus size: 12
1108909 TTCAATTATT
1108919 AAAATAATA-AA
1 AAAATAATATAA
*
1108930 AAATATTATATAA
1 AAA-ATAATATAA
*
1108943 AAAATAATAT-G
1 AAAATAATATAA
* * *
1108954 AATATGATATTA
1 AAAATAATATAA
1108966 AAAATAATATTAA
1 AAAATAATA-TAA
* *
1108979 TACAAT-ACATAA
1 -AAAATAATATAA
*
1108991 AAAATAACATAA
1 AAAATAATATAA
1109003 A
1 A
1109004 TACGAAATGA
Statistics
Matches: 56, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
11 15 0.27
12 28 0.50
13 9 0.16
14 4 0.07
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:1108957 original size:23 final size:23
Alignment explanation
Indices: 1108931--1109021 Score: 74
Period size: 23 Copynumber: 3.8 Consensus size: 23
1108921 AATAATAAAA
*
1108931 AATATTATATAAAAAATAATATG
1 AATATGATATAAAAAATAATATG
* *
1108954 AATATGATATTAAAAATAATATT
1 AATATGATATAAAAAATAATATG
** * *
1108977 AATACAATACATAAAAAATAACATA
1 AATATGAT--ATAAAAAATAATATG
* *
1109002 AATACGAAATGAAAAAATAA
1 AATATGATAT-AAAAAATAA
1109022 CACAAAACAA
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
23 28 0.51
24 9 0.16
25 18 0.33
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.27
Consensus pattern (23 bp):
AATATGATATAAAAAATAATATG
Found at i:1108993 original size:25 final size:23
Alignment explanation
Indices: 1108919--1109021 Score: 73
Period size: 23 Copynumber: 4.3 Consensus size: 23
1108909 TTCAATTATT
* **
1108919 AAAATAATAAAAAATATTATATAA
1 AAAATAAT-ATAAATACAATATAA
* ** *
1108943 AAAATAATATGAATATGATATTA
1 AAAATAATATAAATACAATATAA
*
1108966 AAAATAATATTAATACAATACATAA
1 AAAATAATATAAATACAAT--ATAA
*
1108991 AAAATAACATAAATACGAA-ATGAA
1 AAAATAATATAAATAC-AATAT-AA
1109015 AAAATAA
1 AAAATAA
1109022 CACAAAACAA
Statistics
Matches: 65, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
23 29 0.45
24 17 0.26
25 17 0.26
26 2 0.03
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (23 bp):
AAAATAATATAAATACAATATAA
Found at i:1109035 original size:24 final size:24
Alignment explanation
Indices: 1108989--1109033 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1108979 TACAATACAT
* *
1108989 AAAAAATAACATAAATACGAAATG
1 AAAAAATAACACAAATACAAAATG
1109013 AAAAAATAACACAAA-ACAAAA
1 AAAAAATAACACAAATACAAAA
1109034 ATTAACATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.73, C:0.11, G:0.04, T:0.11
Consensus pattern (24 bp):
AAAAAATAACACAAATACAAAATG
Found at i:1109265 original size:24 final size:24
Alignment explanation
Indices: 1109217--1109265 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1109207 CATGAATTTG
* *
1109217 TTCATGTTATTTTCTCATATAGTA
1 TTCATGTAATTTTCTCATACAGTA
* *
1109241 TTCATGTAATTTTTTCATACCGTA
1 TTCATGTAATTTTCTCATACAGTA
1109265 T
1 T
1109266 ATTCGTGTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.08, T:0.53
Consensus pattern (24 bp):
TTCATGTAATTTTCTCATACAGTA
Found at i:1109924 original size:29 final size:30
Alignment explanation
Indices: 1109890--1109949 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 30
1109880 AAAAAATAAT
1109890 AATATTTTAATAAATT-ATTTTA-AAACAAA
1 AATATTTTAAT-AATTAATTTTATAAACAAA
1109919 AATATTTTAATAATTAATTTTATAAACAAA
1 AATATTTTAATAATTAATTTTATAAACAAA
1109949 A
1 A
1109950 GTAGTTTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
28 4 0.14
29 17 0.59
30 8 0.28
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (30 bp):
AATATTTTAATAATTAATTTTATAAACAAA
Found at i:1111186 original size:28 final size:30
Alignment explanation
Indices: 1111138--1111196 Score: 86
Period size: 28 Copynumber: 2.0 Consensus size: 30
1111128 AATTATTCAC
*
1111138 TTAATTTTTATTTTTATAAAATAAAAATAT
1 TTAATTTTAATTTTTATAAAATAAAAATAT
*
1111168 TTAA-TTTAATTTTTA-AAAATTAAAATAT
1 TTAATTTTAATTTTTATAAAATAAAAATAT
1111196 T
1 T
1111197 ATATATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 13 0.48
29 10 0.37
30 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
TTAATTTTAATTTTTATAAAATAAAAATAT
Found at i:1121788 original size:55 final size:56
Alignment explanation
Indices: 1121669--1121773 Score: 153
Period size: 55 Copynumber: 1.9 Consensus size: 56
1121659 AAATAATATA
* *
1121669 AAAATATTTTAATATAATATAAAATATAAATATTTTAAATATAATTATAACATAAT
1 AAAATATATAAATATAATATAAAATATAAATATTTTAAATATAATTATAACATAAT
1121725 AAAATATATAAATATAATAT-AAATAT-AATAATTTT-AATATAAATTATAA
1 AAAATATATAAATATAATATAAAATATAAAT-ATTTTAAATAT-AATTATAA
1121774 ATTATTAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
54 8 0.18
55 19 0.42
56 18 0.40
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (56 bp):
AAAATATATAAATATAATATAAAATATAAATATTTTAAATATAATTATAACATAAT
Found at i:1122005 original size:24 final size:22
Alignment explanation
Indices: 1121962--1122006 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
1121952 ATTTAATATT
*
1121962 ATTTATAAAATTTAAAAATTTA
1 ATTTATAAAATGTAAAAATTTA
*
1121984 ATTTATCATAAATGTAATAATTT
1 ATTTAT-A-AAATGTAAAAATTT
1122007 TTATAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 6 0.32
23 1 0.05
24 12 0.63
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
ATTTATAAAATGTAAAAATTTA
Found at i:1122182 original size:12 final size:12
Alignment explanation
Indices: 1122158--1122190 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1122148 ATAATTTATG
1122158 TATTTTTAT-TA
1 TATTTTTATATA
1122169 TATTTTTATATA
1 TATTTTTATATA
*
1122181 TATTTATATA
1 TATTTTTATA
1122191 AATTTATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TATTTTTATATA
Found at i:1124053 original size:34 final size:34
Alignment explanation
Indices: 1123989--1124171 Score: 242
Period size: 34 Copynumber: 5.4 Consensus size: 34
1123979 CAGCCTTTGG
* *
1123989 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
1124022 TGTTGACTAAATGGGAAATTTGGTAACTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1124056 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * * *
1124090 TATTGATTAAATGAGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
1124124 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1124158 TGTTGATTAAATGG
1 TGTTGATTAAATGG
1124172 TGGTTTTTAC
Statistics
Matches: 128, Mismatches: 21, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
33 11 0.09
34 117 0.91
ACGTcount: A:0.27, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:1124532 original size:19 final size:19
Alignment explanation
Indices: 1124476--1124538 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
1124466 TGGTTGTCGA
**
1124476 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
1124495 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
1124514 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
1124533 GTTACT
1 GGTACT
1124539 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:1128670 original size:34 final size:34
Alignment explanation
Indices: 1128604--1128788 Score: 264
Period size: 34 Copynumber: 5.5 Consensus size: 34
1128594 AAGTGGGAGA
* *
1128604 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
1128637 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1128671 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
1128705 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
1128739 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1128773 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1128789 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 13 0.10
34 121 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:1130194 original size:20 final size:21
Alignment explanation
Indices: 1130158--1130196 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1130148 ATTAAATATA
1130158 ATATTTTTATATGAATATAGG
1 ATATTTTTATATGAATATAGG
*
1130179 ATATTTTTA-ATTAATATA
1 ATATTTTTATATGAATATA
1130197 AATGTAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (21 bp):
ATATTTTTATATGAATATAGG
Found at i:1130246 original size:21 final size:21
Alignment explanation
Indices: 1130217--1130259 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1130207 TAATAATTAT
*
1130217 ATTTTAATAAATAAAT-ATAAA
1 ATTTAAATAAAT-AATGATAAA
1130238 ATTTAAATAAATAATGATAAA
1 ATTTAAATAAATAATGATAAA
1130259 A
1 A
1130260 ATATAAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
ATTTAAATAAATAATGATAAA
Found at i:1130493 original size:87 final size:87
Alignment explanation
Indices: 1130297--1130510 Score: 245
Period size: 87 Copynumber: 2.5 Consensus size: 87
1130287 GGCATGTGTG
* * ** *
1130297 ATGTGTGTAATTCAATTGATAACGTAAGCAAATTAGTAATT-TAAGACTGATAGGAATATAAAAA
1 ATGTATGTAATTCAATTGATAACGTAAGCAAATTAGTAATTATAAGAATGATAAAAAAATAAAAA
1130361 GAAATATAAACTAGACTTAGCC
66 GAAATATAAACTAGACTTAGCC
* * *
1130383 ATGTAAGTAATTCAAATGATAACGTAAGCAAATTAGTAACTTATATA-AATGATAAAAAAATAAG
1 ATGTATGTAATTCAATTGATAACGTAAGCAAATTAGTAA-TTATA-AGAATGATAAAAAAATAAA
* * * * * *
1130447 ATGAAATGTAGACT-TATTTAGGC
64 AAGAAATATAAACTAGACTTAGCC
* *
1130470 ATGTATGTAATTCAATTGATAACGTAAGTAACTTAGTAATT
1 ATGTATGTAATTCAATTGATAACGTAAGCAAATTAGTAATT
1130511 TATGAATATT
Statistics
Matches: 107, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
86 38 0.36
87 43 0.40
88 25 0.23
89 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.31
Consensus pattern (87 bp):
ATGTATGTAATTCAATTGATAACGTAAGCAAATTAGTAATTATAAGAATGATAAAAAAATAAAAA
GAAATATAAACTAGACTTAGCC
Found at i:1130728 original size:10 final size:10
Alignment explanation
Indices: 1130713--1130737 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1130703 AGCAGGTAAC
1130713 ATAATATTAT
1 ATAATATTAT
1130723 ATAATATTAT
1 ATAATATTAT
1130733 ATAAT
1 ATAAT
1130738 TGATAACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
ATAATATTAT
Found at i:1136993 original size:16 final size:17
Alignment explanation
Indices: 1136965--1136997 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1136955 TTCACCTTTT
1136965 AATAACTTTAAATAAAA
1 AATAACTTTAAATAAAA
1136982 AATAAC-TTAAATAAAA
1 AATAACTTTAAATAAAA
1136998 TTAAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
AATAACTTTAAATAAAA
Found at i:1140091 original size:19 final size:18
Alignment explanation
Indices: 1140054--1140108 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 18
1140044 ATTGATGTCG
1140054 TTTTATTATTTATATTAATT
1 TTTTATTATTTA-A-TAATT
1140074 TTTTATTATATTAATAATT
1 TTTTATTAT-TTAATAATT
* *
1140093 ATTTAATATCTTAATA
1 TTTTATTAT-TTAATA
1140109 TAAGAGATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 18 0.58
20 10 0.32
21 3 0.10
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTATTATTTAATAATT
Found at i:1143844 original size:16 final size:16
Alignment explanation
Indices: 1143795--1143849 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1143785 CATATAATAT
* * *
1143795 AAATTATACAATATAT
1 AAATTATATAATAAAA
*
1143811 AAATATAAATAATAAAA
1 AAAT-TATATAATAAAA
*
1143828 AAATTATATAATTAAA
1 AAATTATATAATAAAA
1143844 AAATTA
1 AAATTA
1143850 ACTAAATTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
16 20 0.62
17 12 0.38
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATTATATAATAAAA
Found at i:1143948 original size:19 final size:19
Alignment explanation
Indices: 1143913--1143950 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1143903 TTTATAAAAT
*
1143913 ATTTAATTTTTTTATTTAA
1 ATTTAATTTTTTAATTTAA
1143932 ATTT-ATTTTTTAAATTTAA
1 ATTTAATTTTTT-AATTTAA
1143951 TATATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTTAATTTTTTAATTTAA
Found at i:1146655 original size:2 final size:2
Alignment explanation
Indices: 1146648--1146694 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1146638 CCTTTCCCAA
1146648 AG AG AG AG AG 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 AG AG AG AG AG
1146690 AG AG A
1 AG AG A
1146695 TTAGAACTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1147784 original size:3 final size:3
Alignment explanation
Indices: 1147776--1147803 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1147766 CTGAGAATCG
1147776 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1147804 CGGCTTGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1155937 original size:2 final size:2
Alignment explanation
Indices: 1155930--1155961 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1155920 AACAAATGTG
1155930 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
1155962 AAAGGATAAC
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1156762 original size:44 final size:44
Alignment explanation
Indices: 1156689--1156773 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
1156679 CTTCGTGTTG
* * * * *
1156689 TAATCGTGTCTTGTCGTATTATATTAACATAAACGGATCAAGTC
1 TAATCGTGTCGTGTCATATCATATAAACATAAACAGATCAAGTC
* *
1156733 TAATCGTGTCGTGTCATGTCATATAAACATTAACAGATCAA
1 TAATCGTGTCGTGTCATATCATATAAACATAAACAGATCAA
1156774 TTTTAACTGT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (44 bp):
TAATCGTGTCGTGTCATATCATATAAACATAAACAGATCAAGTC
Found at i:1159416 original size:19 final size:21
Alignment explanation
Indices: 1159378--1159417 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
1159368 TTTTTAATGA
*
1159378 AATAATATCATTCGATTCATT
1 AATAATATCATTCAATTCATT
1159399 AATAATAT-A-TCAATTCATT
1 AATAATATCATTCAATTCATT
1159418 TATGATCAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 1 0.06
21 8 0.44
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (21 bp):
AATAATATCATTCAATTCATT
Found at i:1160160 original size:2 final size:2
Alignment explanation
Indices: 1160153--1160182 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1160143 TATAAGAGCT
1160153 TC TC 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
1160183 ATTTTTTTCA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1163305 original size:25 final size:24
Alignment explanation
Indices: 1163246--1163308 Score: 63
Period size: 26 Copynumber: 2.5 Consensus size: 24
1163236 TATTGTAAAA
* *
1163246 TTTAAAATTTAATTTTAAATTAAT
1 TTTAAATTTTAATTTAAAATTAAT
* *
1163270 TAATTATATTTTTATTTAAAATTATAT
1 T--TTAAATTTTAATTTAAAATTA-AT
1163297 TTTAAATTTTAA
1 TTTAAATTTTAA
1163309 AATAAGTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
24 1 0.03
25 9 0.30
26 17 0.57
27 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTAAATTTTAATTTAAAATTAAT
Found at i:1163307 original size:20 final size:19
Alignment explanation
Indices: 1163243--1163311 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
1163233 TCGTATTGTA
1163243 AAATTTAAAATT-TAATTTT
1 AAATTTAAAATTAT-ATTTT
1163262 AAA-TTAATTAATTATATTTT
1 AAATTTAA--AATTATATTTT
*
1163282 -TATTTAAAATTATATTTT
1 AAATTTAAAATTATATTTT
1163300 AAATTTTAAAAT
1 AAA-TTTAAAAT
1163312 AAGTTTAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
18 15 0.36
19 5 0.12
20 21 0.50
21 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AAATTTAAAATTATATTTT
Found at i:1163403 original size:13 final size:13
Alignment explanation
Indices: 1163387--1163429 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
1163377 TAAAAAATAA
1163387 ATTTAATTTTTAT
1 ATTTAATTTTTAT
1163400 ATTTAA-TTTTA-
1 ATTTAATTTTTAT
1163411 ATTTAATTATTT-T
1 ATTTAATT-TTTAT
1163424 ATTTAA
1 ATTTAA
1163430 ATTAAAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 6 0.22
12 6 0.22
13 15 0.56
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
ATTTAATTTTTAT
Found at i:1163512 original size:21 final size:21
Alignment explanation
Indices: 1163488--1163529 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1163478 GATCAATAAT
1163488 TATTTTAAAAAATTAAAAAAA
1 TATTTTAAAAAATTAAAAAAA
* *
1163509 TATTTTAAAAATTTTAAAAAA
1 TATTTTAAAAAATTAAAAAAA
1163530 GAAATATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TATTTTAAAAAATTAAAAAAA
Found at i:1163627 original size:32 final size:32
Alignment explanation
Indices: 1163565--1163627 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
1163555 AAGAGTTATA
* * *
1163565 AAAATAATATTTATCTTTAATATTATTAAATT
1 AAAATAATATTTATCTTCAATATAACTAAATT
1163597 AAAATAATATTTATCTTCAATATAACTAAAT
1 AAAATAATATTTATCTTCAATATAACTAAAT
1163628 CAATATTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.44
Consensus pattern (32 bp):
AAAATAATATTTATCTTCAATATAACTAAATT
Found at i:1163770 original size:13 final size:14
Alignment explanation
Indices: 1163752--1163785 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1163742 TATAAGTTAA
1163752 TTAAATTAAATA-T
1 TTAAATTAAATAGT
*
1163765 TTAAATTAACTAGT
1 TTAAATTAAATAGT
1163779 TTAAATT
1 TTAAATT
1163786 TAATTCAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (14 bp):
TTAAATTAAATAGT
Found at i:1165632 original size:29 final size:27
Alignment explanation
Indices: 1165600--1165720 Score: 86
Period size: 27 Copynumber: 4.4 Consensus size: 27
1165590 TATTGATTAG
1165600 TATATTTATATAGAATTTATAAAAT-TTAT
1 TATATTTATATA-AATTT-TAAAATATT-T
*
1165629 TATA-TCATAATAATATTTTAAAATATTT
1 TATATTTAT-ATAA-ATTTTAAAATATTT
** * * *
1165657 TATATTTATATAAATTTTTTATTAATA
1 TATATTTATATAAATTTTAAAATATTT
* * **
1165684 GAAATTTATATGTATTTTAAAATA-TT
1 TATATTTATATAAATTTTAAAATATTT
1165710 TATATTTATAT
1 TATATTTATAT
1165721 TATATTTTTA
Statistics
Matches: 71, Mismatches: 17, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
26 10 0.14
27 26 0.37
28 19 0.27
29 16 0.23
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (27 bp):
TATATTTATATAAATTTTAAAATATTT
Found at i:1165676 original size:19 final size:17
Alignment explanation
Indices: 1165641--1165716 Score: 52
Period size: 17 Copynumber: 4.4 Consensus size: 17
1165631 TATCATAATA
1165641 ATATTTTAAAATATTTT
1 ATATTTTAAAATATTTT
1165658 ATATTTATATAAAT-TTTT
1 ATATTT-TA-AAATATTTT
*
1165676 -TATTAATAGAAAT-TTATAT
1 ATATT-TTA-AAATATT-T-T
*
1165695 GTATTTTAAAATA-TTT
1 ATATTTTAAAATATTTT
1165711 ATATTT
1 ATATTT
1165717 ATATTATATT
Statistics
Matches: 48, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
16 6 0.12
17 19 0.40
18 12 0.25
19 7 0.15
20 4 0.08
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
ATATTTTAAAATATTTT
Found at i:1165716 original size:6 final size:6
Alignment explanation
Indices: 1165705--1165739 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
1165695 GTATTTTAAA
*
1165705 ATATTT ATATTT ATA-TT ATATTT TTATTT ATATTT
1 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT
1165740 TTTATATCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
ATATTT
Found at i:1165727 original size:17 final size:17
Alignment explanation
Indices: 1165705--1165781 Score: 65
Period size: 17 Copynumber: 4.7 Consensus size: 17
1165695 GTATTTTAAA
1165705 ATATTTATATTTATATT
1 ATATTTATATTTATATT
*
1165722 ATATTTTTATTTATATT
1 ATATTTATATTTATATT
*
1165739 -T-TTTATATCGTATCA-T
1 ATATTTATAT-TTAT-ATT
1165755 AT-TTTATATTT-TATT
1 ATATTTATATTTATATT
* *
1165770 TTAATTATATTT
1 ATATTTATATTT
1165782 TTCATGGTGT
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
14 1 0.02
15 9 0.18
16 14 0.29
17 25 0.51
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (17 bp):
ATATTTATATTTATATT
Found at i:1167080 original size:20 final size:19
Alignment explanation
Indices: 1167042--1167080 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1167032 CTATAAAAGG
*
1167042 AAGCTCCCTCCTCCCTCTC
1 AAGCTCCCTCATCCCTCTC
*
1167061 AAGCATCCCTCATCCTTCTC
1 AAGC-TCCCTCATCCCTCTC
1167081 TTGTATCCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.15, C:0.51, G:0.05, T:0.28
Consensus pattern (19 bp):
AAGCTCCCTCATCCCTCTC
Found at i:1169573 original size:21 final size:22
Alignment explanation
Indices: 1169544--1169589 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
1169534 TGTTCAGACA
* *
1169544 AGTAGTACTCCACAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
1169566 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
1169587 AGT
1 AGT
1169590 TTCAACAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:1171599 original size:20 final size:19
Alignment explanation
Indices: 1171561--1171599 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1171551 CTATAAAAGG
*
1171561 AAGCTCCCTCCTCCCTCTC
1 AAGCTCCCTCATCCCTCTC
*
1171580 AAGCATCCCTCATCCTTCTC
1 AAGC-TCCCTCATCCCTCTC
1171600 TTGTATCCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.15, C:0.51, G:0.05, T:0.28
Consensus pattern (19 bp):
AAGCTCCCTCATCCCTCTC
Found at i:1174126 original size:25 final size:25
Alignment explanation
Indices: 1174089--1174154 Score: 60
Period size: 25 Copynumber: 2.5 Consensus size: 25
1174079 GATAAATATT
1174089 AAATATAATTATATTTATAATATAAAA
1 AAATAT-A-TATATTTATAATATAAAA
* * * *
1174116 AAATATATATATATATGATATGAAT
1 AAATATATATATTTATAATATAAAA
*
1174141 ATATAATATATATT
1 AAAT-ATATATATT
1174155 AAAATTTATA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
25 17 0.53
26 9 0.28
27 6 0.19
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (25 bp):
AAATATATATATTTATAATATAAAA
Found at i:1174136 original size:15 final size:13
Alignment explanation
Indices: 1174091--1174186 Score: 57
Period size: 13 Copynumber: 7.9 Consensus size: 13
1174081 TAAATATTAA
1174091 ATATAAT-TATAT
1 ATATAATATATAT
* * *
1174103 TTATAATATAAAA
1 ATATAATATATAT
*
1174116 AAAT-ATATATAT
1 ATATAATATATAT
*
1174128 ATATGATATGA-AT
1 ATATAATAT-ATAT
1174141 ATATAATATATAT
1 ATATAATATATAT
1174154 -TA-AA-AT-T-T
1 ATATAATATATAT
*
1174162 ATATAATATAAAT
1 ATATAATATATAT
1174175 -TATTAATATATA
1 ATA-TAATATATA
1174187 AAATTTTTAT
Statistics
Matches: 63, Mismatches: 11, Indels: 19
0.68 0.12 0.20
Matches are distributed among these distances:
8 1 0.02
9 3 0.05
10 4 0.06
11 4 0.06
12 20 0.32
13 30 0.48
14 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (13 bp):
ATATAATATATAT
Found at i:1174182 original size:34 final size:32
Alignment explanation
Indices: 1174122--1174212 Score: 85
Period size: 34 Copynumber: 2.7 Consensus size: 32
1174112 AAAAAAATAT
* * *
1174122 ATATATATATGATATGAATATATAATATATATTAA
1 ATATTTATATAATATAAATAT-TAATATATA--AA
1174157 A-ATTTATATAATATAAATTATTAATATATAAA
1 ATATTTATATAATATAAA-TATTAATATATAAA
*
1174189 ATTTTTATATAAATATAAAATATT
1 ATATTTATAT-AATAT-AAATATT
1174213 TTAAATACAT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
32 3 0.06
33 7 0.15
34 31 0.65
35 7 0.15
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (32 bp):
ATATTTATATAATATAAATATTAATATATAAA
Found at i:1174198 original size:15 final size:15
Alignment explanation
Indices: 1174147--1174199 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
1174137 GAATATATAA
*
1174147 TATATATTAAAATTTA
1 TATATA-TAAAATTTT
1174163 TATA-ATATAAATTATT
1 TATATATA-AAATT-TT
*
1174179 AATATATAAAATTTT
1 TATATATAAAATTTT
1174194 TATATA
1 TATATA
1174200 AATATAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 2 0.06
15 13 0.42
16 13 0.42
17 3 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATATATAAAATTTT
Found at i:1174224 original size:20 final size:19
Alignment explanation
Indices: 1174182--1174226 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1174172 AATTATTAAT
*
1174182 ATATAAAATTTTTATATAA
1 ATATAAAATTTTTAAATAA
*
1174201 ATATAAAATATTTTAAATAC
1 ATATAAAAT-TTTTAAATAA
1174221 ATATAA
1 ATATAA
1174227 TAATCTCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATAAAATTTTTAAATAA
Found at i:1178772 original size:38 final size:38
Alignment explanation
Indices: 1178730--1178804 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
1178720 AATTATTGTG
* *
1178730 AAAAATATATTTTTATATTTTAT-AATTA-AATTTAAATA
1 AAAAAT-TATTTTT-TATTATATGAATAATAATTTAAATA
1178768 AAAAATTATTTTTTATTATATGAATAATAATTTAAAT
1 AAAAATTATTTTTTATTATATGAATAATAATTTAAAT
1178805 GAAGTAGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 7 0.21
37 11 0.33
38 15 0.45
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (38 bp):
AAAAATTATTTTTTATTATATGAATAATAATTTAAATA
Found at i:1178818 original size:208 final size:207
Alignment explanation
Indices: 1178463--1178863 Score: 581
Period size: 208 Copynumber: 1.9 Consensus size: 207
1178453 ATGTTTATGA
* *
1178463 ATTGAATTAAAACTCGAATTTGATCTAACTTAATTTAATTTGTAAATTCAAATTATTGTGAAAAT
1 ATTGAATTAAAACTCAAATTTAATCTAACTTAATTTAATTTGTAAATTCAAATTATTGTGAAAAT
*
1178528 ATATTTTTATATTTTATAATTAAATATAAATAAAAAATTATTTTTTATTAAATAAATATTAATTT
66 ATATTTTTATATTTTATAATTAAATATAAATAAAAAATTATTTTTTATTAAATAAATAATAATTT
* * * * *
1178593 AAGTTAATCAAAATCTCTAAATATAGTAC-GAGCAACCTAAACTCAAAAGAGTCAACCCAAATTA
131 AAATGAATCAAAATCTCTAAATATAGAACGGA-CAACATAAACCCAAAAGAGTCAACCCAAATTA
1178657 GATATGTTTTTAG
195 GATATGTTTTTAG
* * * * *
1178670 ATTGAATTGAGACTCAAATTTAATTTGACTTAATTTAATTTGTAAGTTCAAATTATTGTGAAAAA
1 ATTGAATTAAAACTCAAATTTAATCTAACTTAATTTAATTTGTAAATTCAAATTATTGTG-AAAA
* * *
1178735 TATATTTTTATATTTTATAATTAAATTTAAATAAAAAATTATTTTTTATTATATGAATAATAATT
65 TATATTTTTATATTTTATAATTAAATATAAATAAAAAATTATTTTTTATTAAATAAATAATAATT
* * * *
1178800 TAAATGAAGT-AGAATCTCTAAATATAGAACGGATAACATAAACCCAAAGGAGTCTACCCAAATT
130 TAAATGAA-TCAAAATCTCTAAATATAGAACGGACAACATAAACCCAAAAGAGTCAACCCAAATT
1178864 GTGATTTCTT
Statistics
Matches: 171, Mismatches: 20, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
207 53 0.31
208 115 0.67
209 3 0.02
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.39
Consensus pattern (207 bp):
ATTGAATTAAAACTCAAATTTAATCTAACTTAATTTAATTTGTAAATTCAAATTATTGTGAAAAT
ATATTTTTATATTTTATAATTAAATATAAATAAAAAATTATTTTTTATTAAATAAATAATAATTT
AAATGAATCAAAATCTCTAAATATAGAACGGACAACATAAACCCAAAAGAGTCAACCCAAATTAG
ATATGTTTTTAG
Found at i:1179232 original size:19 final size:17
Alignment explanation
Indices: 1179198--1179232 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
1179188 CCCAAAAATT
1179198 AAAAAAAGAAAAAAGAA
1 AAAAAAAGAAAAAAGAA
1179215 AAAAAAATGAAAATAAGA
1 AAAAAAA-GAAAA-AAGA
1179233 TTGGTGTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 5 0.31
19 4 0.25
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (17 bp):
AAAAAAAGAAAAAAGAA
Found at i:1181908 original size:15 final size:14
Alignment explanation
Indices: 1181888--1181935 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
1181878 GGTCCATATT
1181888 AATATTTATTGATAA
1 AATATTTATT-ATAA
*
1181903 AATATTT-TTATTTA
1 AATATTTATTA-TAA
1181917 AAT-TTTATTATAA
1 AATATTTATTATAA
1181930 AATATT
1 AATATT
1181936 AATATAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
13 9 0.32
14 12 0.43
15 7 0.25
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (14 bp):
AATATTTATTATAA
Found at i:1182826 original size:20 final size:21
Alignment explanation
Indices: 1182799--1182840 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
1182789 AAAATATATT
1182799 AAAAATA-TA-AAAAATTAAA
1 AAAAATATTACAAAAATTAAA
*
1182818 AAAATATATTACAAATATTAAA
1 AAAA-ATATTACAAAAATTAAA
1182840 A
1 A
1182841 TATTTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 4 0.21
20 3 0.16
21 2 0.11
22 10 0.53
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAAATATTACAAAAATTAAA
Found at i:1182855 original size:20 final size:20
Alignment explanation
Indices: 1182832--1182870 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1182822 TATATTACAA
1182832 ATATTAAAATATTTATATTT
1 ATATTAAAATATTTATATTT
* *
1182852 ATATTTATATATTTATATT
1 ATATTAAAATATTTATATT
1182871 ATTTAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATATTAAAATATTTATATTT
Found at i:1182892 original size:21 final size:20
Alignment explanation
Indices: 1182862--1182914 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
1182852 ATATTTATAT
*
1182862 ATTTATATTATTTAAATAATA
1 ATTTAAATTATTTAAATAA-A
* *
1182883 ATTTAAATTAAATTAAATTAA
1 ATTTAAATT-ATTTAAATAAA
1182904 ATTTAAATTAT
1 ATTTAAATTAT
1182915 AAAACCTACA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 18 0.67
22 8 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTAAATTATTTAAATAAA
Found at i:1182909 original size:11 final size:11
Alignment explanation
Indices: 1182871--1182913 Score: 61
Period size: 10 Copynumber: 3.9 Consensus size: 11
1182861 TATTTATATT
*
1182871 ATTTAAATAATA
1 ATTTAAATTA-A
1182883 ATTTAAATTAA
1 ATTTAAATTAA
1182894 A-TTAAATTAA
1 ATTTAAATTAA
1182904 ATTTAAATTA
1 ATTTAAATTA
1182914 TAAAACCTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 10 0.34
11 10 0.34
12 9 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATTTAAATTAA
Found at i:1186384 original size:14 final size:14
Alignment explanation
Indices: 1186367--1186393 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1186357 TATGTAATTT
1186367 TTATTATGTCATGA
1 TTATTATGTCATGA
1186381 TTATTATGTCATG
1 TTATTATGTCATG
1186394 TAACAATCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.07, G:0.15, T:0.52
Consensus pattern (14 bp):
TTATTATGTCATGA
Found at i:1187477 original size:9 final size:9
Alignment explanation
Indices: 1187465--1187498 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
1187455 TGATTCTATG
*
1187465 AAATGAAAT
1 AAATAAAAT
1187474 AAATAAAAT
1 AAATAAAAT
1187483 AAAATAAAAT
1 -AAATAAAAT
1187493 AAATAA
1 AAATAA
1187499 TATGTAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:1187586 original size:8 final size:8
Alignment explanation
Indices: 1187522--1187616 Score: 66
Period size: 8 Copynumber: 10.8 Consensus size: 8
1187512 TATTAATGTA
1187522 ATATAAAT
1 ATATAAAT
*
1187530 ATGTAAAT
1 ATATAAAT
*
1187538 ATTTAAAT
1 ATATAAAT
1187546 AATATAAAT
1 -ATATAAAT
1187555 -TATTAATAT
1 ATA-TAA-AT
*
1187564 ATAAAAATTT
1 ATATAAA--T
1187574 ATATAAAT
1 ATATAAAT
1187582 ATATAAAT
1 ATATAAAT
1187590 ATAATTATAAT
1 AT-A-TA-AAT
1187601 ATAATAAAAT
1 AT-AT-AAAT
1187611 ATATAA
1 ATATAA
1187617 CTTCAACTAT
Statistics
Matches: 72, Mismatches: 5, Indels: 20
0.74 0.05 0.21
Matches are distributed among these distances:
7 2 0.03
8 31 0.43
9 14 0.19
10 17 0.24
11 8 0.11
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (8 bp):
ATATAAAT
Found at i:1187598 original size:20 final size:19
Alignment explanation
Indices: 1187546--1187613 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 19
1187536 ATATTTAAAT
1187546 AATATAAATTATTAATATATA
1 AATAT-AATTA-TAATATATA
* *
1187567 AAAAT-TTATATAAATATATA
1 AATATAAT-TAT-AATATATA
1187587 AATATAATTATAATATAATAA
1 AATATAATTATAATAT-AT-A
1187608 AATATA
1 AATATA
1187614 TAACTTCAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
19 7 0.18
20 19 0.50
21 12 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AATATAATTATAATATATA
Found at i:1187614 original size:37 final size:35
Alignment explanation
Indices: 1187534--1187616 Score: 89
Period size: 37 Copynumber: 2.3 Consensus size: 35
1187524 ATAAATATGT
*
1187534 AAATATTTAAATAATATAAATTATTAATATATAAA
1 AAATATATAAATAATATAAATTATTAATATATAAA
*
1187569 AATTTATATAAAT-ATATAAATATAATT-ATAATATAATA
1 AA-ATATATAAATAATATAAAT-T-ATTAAT-ATATAA-A
1187607 AAATATATAA
1 AAATATATAA
1187617 CTTCAACTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
35 10 0.25
36 11 0.28
37 16 0.40
38 3 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (35 bp):
AAATATATAAATAATATAAATTATTAATATATAAA
Found at i:1188373 original size:6 final size:6
Alignment explanation
Indices: 1188362--1188394 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
1188352 GGCTTTGAAG
1188362 GAAAAA GAAAAA -AAAAA GAAAAA GAAAAA GAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAA
1188395 GAAAGATCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:1188379 original size:11 final size:12
Alignment explanation
Indices: 1188362--1188394 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
1188352 GGCTTTGAAG
1188362 GAAAAAGAAAAA
1 GAAAAAGAAAAA
1188374 -AAAAAGAAAAA
1 GAAAAAGAAAAA
1188385 GAAAAAGAAA
1 GAAAAAGAAA
1188395 GAAAGATCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
GAAAAAGAAAAA
Found at i:1189385 original size:13 final size:13
Alignment explanation
Indices: 1189343--1189385 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1189333 TATGCATCTA
1189343 TATATATATATAAT
1 TATA-ATATATAAT
***
1189357 TATAATATAGGCT
1 TATAATATATAAT
1189370 TATAATATATAAT
1 TATAATATATAAT
1189383 TAT
1 TAT
1189386 CATAATAAAC
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (13 bp):
TATAATATATAAT
Found at i:1189766 original size:91 final size:91
Alignment explanation
Indices: 1189636--1189806 Score: 297
Period size: 91 Copynumber: 1.9 Consensus size: 91
1189626 AAAAGCATGC
* *
1189636 CTAGGCGCACTAGACATGTGCCTGATCAAATGCGCCTTGCCTGAAAGGGTTTGAGGCGCTTTTGT
1 CTAGGCGCACTAGAAACGTGCCTGATCAAATGCGCCTTGCCTGAAAGGGTTTGAGGCGCTTTTGT
1189701 TGTCTAACACTAAGGTGCAGGCACTT
66 TGTCTAACACTAAGGTGCAGGCACTT
* * *
1189727 CTAGGCGCACTGGAAACGTGCTTGATCAAATGCGCCTTGCCTGAAAGGGTTTGAGGTGCTTTTGT
1 CTAGGCGCACTAGAAACGTGCCTGATCAAATGCGCCTTGCCTGAAAGGGTTTGAGGCGCTTTTGT
1189792 TGTCTAACACTAAGG
66 TGTCTAACACTAAGG
1189807 CGCAAGGCGC
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
91 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (91 bp):
CTAGGCGCACTAGAAACGTGCCTGATCAAATGCGCCTTGCCTGAAAGGGTTTGAGGCGCTTTTGT
TGTCTAACACTAAGGTGCAGGCACTT
Found at i:1193961 original size:2 final size:2
Alignment explanation
Indices: 1193954--1193998 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1193944 TTTGTAAAAG
*
1193954 AT AT AT AT AT AT AT AT 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 AT AT AT AT
1193996 AT A
1 AT A
1193999 AGGACATCCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1194261 original size:2 final size:2
Alignment explanation
Indices: 1194254--1194280 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1194244 TATGCTTTTC
1194254 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
1194281 GCTTTTTTTT
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:1194352 original size:37 final size:35
Alignment explanation
Indices: 1194311--1194390 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 35
1194301 ATCATCATTT
* * *
1194311 TTTTAAATATTAA-TATTTAAATTTATTAAATATTATA
1 TTTTAAATA-TAATTATATAAATTAATT-AA-ATTAAA
1194348 TTTTAAATATAATTATATAAATTAATTAAATTAAA
1 TTTTAAATATAATTATATAAATTAATTAAATTAAA
1194383 TTTTAAAT
1 TTTTAAAT
1194391 TTTTGATCCA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
35 13 0.33
36 5 0.13
37 21 0.54
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (35 bp):
TTTTAAATATAATTATATAAATTAATTAAATTAAA
Found at i:1194384 original size:23 final size:21
Alignment explanation
Indices: 1194350--1194391 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
1194340 ATATTATATT
1194350 TTAAATATAATTATATAAATTAA
1 TTAAATATAATT-T-TAAATTAA
1194373 TTAAAT-TAAATTTTAAATT
1 TTAAATAT-AATTTTAAATT
1194392 TTTGATCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
21 6 0.33
22 2 0.11
23 10 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAAATATAATTTTAAATTAA
Found at i:1194575 original size:20 final size:21
Alignment explanation
Indices: 1194550--1194597 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
1194540 ATTTTTATAT
1194550 TTATAAAAGT-TATTTATAAA
1 TTATAAAAGTATATTTATAAA
*
1194570 TTATAAAAATTATATTTATAAA
1 TTAT-AAAAGTATATTTATAAA
*
1194592 TAATAA
1 TTATAA
1194598 TTAAATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 4 0.17
21 7 0.29
22 13 0.54
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TTATAAAAGTATATTTATAAA
Found at i:1194599 original size:19 final size:19
Alignment explanation
Indices: 1194572--1194613 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1194562 TTTATAAATT
*
1194572 ATAAAAATTATATTTATAA
1 ATAAAAATTAAATTTATAA
*
1194591 ATAATAATTAAATTTAT-A
1 ATAAAAATTAAATTTATAA
1194609 ATAAA
1 ATAAA
1194614 TACTAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAAAAATTAAATTTATAA
Found at i:1196032 original size:5 final size:5
Alignment explanation
Indices: 1196024--1196107 Score: 55
Period size: 5 Copynumber: 16.2 Consensus size: 5
1196014 AATTAAATAA
* * *
1196024 TTAAT TTAAT TTAAT TTAA- TTGAG TTAAT TTAAAT AATAAT TTGAA-
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TT-AAT -TTAAT TT-AAT
* * *
1196070 TTAAT TTAAA TTAAT TTGATT TTTAT TTAAAT TTAAT T
1 TTAAT TTAAT TTAAT TT-AAT TTAAT TT-AAT TTAAT T
1196108 ATAAAAATAT
Statistics
Matches: 61, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
4 5 0.08
5 39 0.64
6 16 0.26
7 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (5 bp):
TTAAT
Found at i:1196073 original size:22 final size:20
Alignment explanation
Indices: 1196029--1196107 Score: 79
Period size: 22 Copynumber: 3.8 Consensus size: 20
1196019 AATAATTAAT
* *
1196029 TTAATTTAATTTAA-TTGAG
1 TTAATTTAAATTAATTTGAA
1196048 TTAATTTAAATAATAATTTGAA
1 TTAATTTAAAT--TAATTTGAA
*
1196070 TTAATTTAAATTAATTTGATT
1 TTAATTTAAATTAATTTGA-A
*
1196091 TTTATTTAAATTTAATT
1 TTAATTTAAA-TTAATT
1196108 ATAAAAATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
19 10 0.20
20 8 0.16
21 12 0.24
22 21 0.41
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
TTAATTTAAATTAATTTGAA
Found at i:1198257 original size:2 final size:2
Alignment explanation
Indices: 1198252--1198278 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1198242 GAGAGGTAGG
1198252 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
1198279 TAAAAATGAG
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:1198367 original size:19 final size:20
Alignment explanation
Indices: 1198343--1198381 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1198333 ATTTTATATA
1198343 TAATTAATATATT-AATAAT
1 TAATTAATATATTAAATAAT
*
1198362 TAATTATTATATTAAATAAT
1 TAATTAATATATTAAATAAT
1198382 ATTGTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAATTAATATATTAAATAAT
Found at i:1198941 original size:2 final size:2
Alignment explanation
Indices: 1198934--1198958 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1198924 CTACTTCAGC
1198934 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 T
1198959 TGAAGCCTTT
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1199260 original size:22 final size:22
Alignment explanation
Indices: 1199233--1199309 Score: 60
Period size: 22 Copynumber: 3.7 Consensus size: 22
1199223 TATATAAAAA
1199233 AATATATATAATATAATTTAT-T
1 AATATATATAATA-AATTTATAT
1199255 AATATAT-T-A-AAATTTATAT
1 AATATATATAATAAATTTATAT
**
1199274 AA-ATATATAATTTA-TTATA-
1 AATATATATAATAAATTTATAT
1199293 AATATAATTATAATAAA
1 AATAT-A-TATAATAAA
1199310 AAATAACATA
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
18 11 0.25
19 7 0.16
20 9 0.20
21 3 0.07
22 14 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AATATATATAATAAATTTATAT
Found at i:1199261 original size:20 final size:19
Alignment explanation
Indices: 1199236--1199301 Score: 63
Period size: 16 Copynumber: 3.7 Consensus size: 19
1199226 ATAAAAAAAT
1199236 ATATATAATATAATTTATTA
1 ATATAT-ATATAATTTATTA
*
1199256 ATATAT-TAAAATTTA-T-
1 ATATATATATAATTTATTA
*
1199272 ATAAATATATAATTTATT-
1 ATATATATATAATTTATTA
1199290 ATA-A-ATATAATT
1 ATATATATATAATT
1199302 ATAATAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
16 13 0.32
17 10 0.24
18 12 0.29
20 6 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATATATATATAATTTATTA
Found at i:1199292 original size:18 final size:18
Alignment explanation
Indices: 1199243--1199298 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
1199233 AATATATATA
*
1199243 ATATAATTTATTA-ATAT
1 ATATAATTTATTATAAAT
*
1199260 ATTAAAATTTA-TATAAAT
1 A-TATAATTTATTATAAAT
1199278 ATATAATTTATTATAAAT
1 ATATAATTTATTATAAAT
1199296 ATA
1 ATA
1199299 ATTATAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
17 11 0.33
18 22 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATATAATTTATTATAAAT
Found at i:1199304 original size:32 final size:36
Alignment explanation
Indices: 1199234--1199314 Score: 89
Period size: 35 Copynumber: 2.3 Consensus size: 36
1199224 ATATAAAAAA
* *
1199234 ATATATATAATATAATTTATTAATATATTAAAATTT
1 ATATAAATAATATAATTTATTAATATAATAAAATTT
*
1199270 ATATAAAT-ATATAATTTATT-ATA-AATATAA-TT
1 ATATAAATAATATAATTTATTAATATAATAAAATTT
*
1199302 ATAATAAAAAATA
1 AT-ATAAATAATA
1199315 ACATAAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
32 4 0.10
33 10 0.26
34 6 0.15
35 12 0.31
36 7 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (36 bp):
ATATAAATAATATAATTTATTAATATAATAAAATTT
Found at i:1199308 original size:15 final size:16
Alignment explanation
Indices: 1199242--1199309 Score: 59
Period size: 17 Copynumber: 4.1 Consensus size: 16
1199232 AAATATATAT
1199242 AATATAATTTATTAATA
1 AATATAATTTA-TAATA
* *
1199259 TATTAAAATTTAT-ATAA
1 -AATATAATTTATAAT-A
*
1199276 ATATATAATTTATTATA
1 A-ATATAATTTATAATA
1199293 AATATAA-TTATAATA
1 AATATAATTTATAATA
1199308 AA
1 AA
1199310 AAATAACATA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
15 9 0.21
16 9 0.21
17 13 0.31
18 11 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AATATAATTTATAATA
Found at i:1199584 original size:11 final size:11
Alignment explanation
Indices: 1199561--1199594 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1199551 TTATTTTATT
1199561 TTAAATT-AAA
1 TTAAATTAAAA
1199571 TTAAATTAAAA
1 TTAAATTAAAA
*
1199582 TTAATTTAAAA
1 TTAAATTAAAA
1199593 TT
1 TT
1199595 TTATTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 7 0.32
11 15 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TTAAATTAAAA
Found at i:1199634 original size:29 final size:30
Alignment explanation
Indices: 1199575--1199634 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 30
1199565 ATTAAATTAA
* * *
1199575 ATTAAAATTAATTTAAAATTTTATTTAATT
1 ATTAAAATTAATATAAAAATATATTTAATT
1199605 ATTAAAA-TAATATAAAAATAT-TTTATATT
1 ATTAAAATTAATATAAAAATATATTTA-ATT
1199634 A
1 A
1199635 ATATTTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 4 0.15
29 15 0.58
30 7 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
ATTAAAATTAATATAAAAATATATTTAATT
Found at i:1199655 original size:34 final size:32
Alignment explanation
Indices: 1199592--1199657 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 32
1199582 TTAATTTAAA
1199592 ATTTTATTTAATTATTAAAATAATATAAAAAT
1 ATTTTATTTAATTATTAAAATAATATAAAAAT
*
1199624 ATTTTATATTAA-TATTTATAAATAA-ATTAAAAT
1 ATTTTAT-TTAATTA-TTA-AAATAATATAAAAAT
1199657 A
1 A
1199658 AAAAAGTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
32 9 0.30
33 15 0.50
34 6 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (32 bp):
ATTTTATTTAATTATTAAAATAATATAAAAAT
Found at i:1203765 original size:3 final size:3
Alignment explanation
Indices: 1203759--1203785 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1203749 AAGAAGAGAC
1203759 TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA
1203786 CTTCTTTTTT
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:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:1203997 original size:2 final size:2
Alignment explanation
Indices: 1203990--1204015 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1203980 GGGAAGAGGG
1203990 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
1204016 TGGTTGGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1204168 original size:22 final size:21
Alignment explanation
Indices: 1204115--1204172 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
1204105 ATTTTTATTA
1204115 TATTTTATAAAATAAAAAATTTT
1 TATTTT-T-AAATAAAAAATTTT
* * * *
1204138 AAATATTAATATAAAATATTTT
1 TATTTTTAA-ATAAAAAATTTT
1204160 TATTTTTAAATAA
1 TATTTTTAAATAA
1204173 TAGTATATTT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
21 6 0.22
22 18 0.67
23 3 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TATTTTTAAATAAAAAATTTT
Found at i:1205428 original size:15 final size:15
Alignment explanation
Indices: 1205408--1205437 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1205398 GTTTCCTGTC
*
1205408 TGGCTTCATTGCCAT
1 TGGCTTCATCGCCAT
1205423 TGGCTTCATCGCCAT
1 TGGCTTCATCGCCAT
1205438 GTGCCTCTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.30, G:0.20, T:0.37
Consensus pattern (15 bp):
TGGCTTCATCGCCAT
Found at i:1214182 original size:25 final size:24
Alignment explanation
Indices: 1214152--1214214 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 24
1214142 TAATTACTAG
1214152 TAAAATAAAATTATAATTATTCTTA
1 TAAAATAAAATTATAATTATT-TTA
*
1214177 TAAAAT-ATATATATAATTATTTTA
1 TAAAATAAAAT-TATAATTATTTTA
1214201 TAAAAATATAAATT
1 T-AAAATA-AAATT
1214215 TTATAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
24 7 0.22
25 21 0.66
26 1 0.03
27 3 0.09
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
TAAAATAAAATTATAATTATTTTA
Found at i:1214956 original size:20 final size:20
Alignment explanation
Indices: 1214924--1214962 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
1214914 ATAATAAGTT
1214924 TAAAAAGGTAATGA-AAAGC
1 TAAAAAGGTAATGACAAAGC
1214943 TAAAAAGGTAAATGACAAAG
1 TAAAAAGGT-AATGACAAAG
1214963 TATCTAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 5 0.28
21 4 0.22
ACGTcount: A:0.59, C:0.05, G:0.21, T:0.15
Consensus pattern (20 bp):
TAAAAAGGTAATGACAAAGC
Found at i:1215366 original size:20 final size:19
Alignment explanation
Indices: 1215321--1215367 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1215311 AGCGAGGTGT
*
1215321 TTGAAAAGGTAATAAAAAC
1 TTGAAAAGGTAAGAAAAAC
* *
1215340 TTAAAAAGGTAAGATAGAAC
1 TTGAAAAGGTAAGA-AAAAC
1215360 TTGAAAAG
1 TTGAAAAG
1215368 ATTAAGTATC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.55, C:0.04, G:0.19, T:0.21
Consensus pattern (19 bp):
TTGAAAAGGTAAGAAAAAC
Found at i:1215963 original size:17 final size:18
Alignment explanation
Indices: 1215936--1215969 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1215926 ACTTTGTCGC
1215936 ATGTGTTTGACTTGAAAG
1 ATGTGTTTGACTTGAAAG
1215954 ATGT-TTTGACTTGAAA
1 ATGTGTTTGACTTGAAA
1215970 AAGCTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.29, C:0.06, G:0.24, T:0.41
Consensus pattern (18 bp):
ATGTGTTTGACTTGAAAG
Found at i:1216045 original size:21 final size:21
Alignment explanation
Indices: 1216021--1216072 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
1216011 AAAACATATG
*
1216021 AAAAGATAAATGAA-AATTTTA
1 AAAAGATAAATGAAGAA-CTTA
1216042 AAAAGAT-AATGAAGAACTTA
1 AAAAGATAAATGAAGAACTTA
1216062 AAAAGATAAAT
1 AAAAGATAAAT
1216073 AGCAAGGTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.23
Consensus pattern (21 bp):
AAAAGATAAATGAAGAACTTA
Found at i:1216642 original size:2 final size:2
Alignment explanation
Indices: 1216635--1216663 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1216625 GCAATCCATC
1216635 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1216664 TAGATATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1216725 original size:22 final size:22
Alignment explanation
Indices: 1216691--1216736 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1216681 ATATAATAGA
1216691 ATATGAATAAAATT-TTAAATTT
1 ATATGAATAAAATTATT-AATTT
1216713 ATAT-AATATAAATTATTAATTT
1 ATATGAATA-AAATTATTAATTT
1216735 AT
1 AT
1216737 TAAAATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.18
22 16 0.73
23 2 0.09
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
ATATGAATAAAATTATTAATTT
Found at i:1216971 original size:20 final size:19
Alignment explanation
Indices: 1216939--1216994 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 19
1216929 CAATTAAATC
1216939 ATATTGAAAGTTA-AAATATT
1 ATATT-AAAGTTATAAAT-TT
1216959 ATATTAAATGTTATTAAATTT
1 ATATTAAA-GTTA-TAAATTT
1216980 ATATTAAAGATTATA
1 ATATTAAAG-TTATA
1216995 TTGTATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
19 3 0.09
20 12 0.38
21 13 0.41
22 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (19 bp):
ATATTAAAGTTATAAATTT
Found at i:1217031 original size:26 final size:25
Alignment explanation
Indices: 1216978--1217058 Score: 74
Period size: 26 Copynumber: 3.2 Consensus size: 25
1216968 GTTATTAAAT
* *
1216978 TTATATTAAAGATTATATTGTATATA
1 TTATATAAAAGATTATATTTTAT-TA
1217004 TTATATAAAAGATTATATATTTATTA
1 TTATATAAAAGATTATAT-TTTATTA
* * * *
1217030 TT-TTTAAAAAATTATGTGTTTATTG
1 TTATATAAAAGATTATAT-TTTATTA
1217055 TTAT
1 TTAT
1217059 TTATTATATA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
25 20 0.43
26 22 0.48
27 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (25 bp):
TTATATAAAAGATTATATTTTATTA
Found at i:1217378 original size:3 final size:3
Alignment explanation
Indices: 1217370--1217400 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1217360 AAATTAGAAT
1217370 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1217401 AACTCCTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1218010 original size:12 final size:13
Alignment explanation
Indices: 1217987--1218018 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
1217977 AAATTAAAGA
1217987 TTATTTTAATTTT
1 TTATTTTAATTTT
1218000 TTATTTT-ATTTT
1 TTATTTTAATTTT
1218012 TTATTTT
1 TTATTTT
1218019 TTATATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (13 bp):
TTATTTTAATTTT
Found at i:1218019 original size:13 final size:13
Alignment explanation
Indices: 1217987--1218029 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
1217977 AAATTAAAGA
*
1217987 TTATTTTAATTTT
1 TTATTTTTATTTT
1218000 TTA-TTTTATTTT
1 TTATTTTTATTTT
*
1218012 TTATTTTTTATATT
1 TTA-TTTTTATTTT
1218026 TTAT
1 TTAT
1218030 AAATATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 11 0.42
13 4 0.15
14 11 0.42
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTATTTTTATTTT
Found at i:1218025 original size:21 final size:20
Alignment explanation
Indices: 1217990--1218029 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1217980 TTAAAGATTA
1217990 TTTTAATTTTTTATTTTATT
1 TTTTAATTTTTTATTTTATT
*
1218010 TTTTATTTTTTATATTTTAT
1 TTTTAATTTTT-TATTTTAT
1218030 AAATATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTAATTTTTTATTTTATT
Found at i:1218028 original size:7 final size:7
Alignment explanation
Indices: 1217988--1218030 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
1217978 AATTAAAGAT
1217988 TATTTTA
1 TATTTTA
*
1217995 -ATTTTT
1 TATTTTA
1218001 TATTTTA
1 TATTTTA
*
1218008 TTTTTTA
1 TATTTTA
*
1218015 TTTTTTA
1 TATTTTA
1218022 TATTTTA
1 TATTTTA
1218029 TA
1 TA
1218031 AATATATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 5 0.16
7 26 0.84
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TATTTTA
Found at i:1220444 original size:5 final size:6
Alignment explanation
Indices: 1220377--1220443 Score: 59
Period size: 6 Copynumber: 10.8 Consensus size: 6
1220367 AGTTTTAAGT
*
1220377 TTTAAGA TTTAAAA TTTAAA ATTAAA -TTAAA -TTAAA TTATTAAAA TTTAAA
1 TTTAA-A TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA -T-TT-AAA TTTAAA
1220428 TTTAAA TTT-AA TTTAA
1 TTTAAA TTTAAA TTTAA
1220444 TACGTTCATC
Statistics
Matches: 53, Mismatches: 1, Indels: 13
0.79 0.01 0.19
Matches are distributed among these distances:
5 15 0.28
6 21 0.40
7 9 0.17
8 5 0.09
9 3 0.06
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:1220781 original size:20 final size:18
Alignment explanation
Indices: 1220755--1220801 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 18
1220745 ATAATATAAT
1220755 ATAAAAATAT-ATTAAATTA
1 ATAAAAAT-TGATT-AATTA
1220774 ATAGAAAATTGATTAATTA
1 ATA-AAAATTGATTAATTA
1220793 ATAAAAATT
1 ATAAAAATT
1220802 AAAACTGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 6 0.23
19 12 0.46
20 8 0.31
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (18 bp):
ATAAAAATTGATTAATTA
Found at i:1227025 original size:12 final size:11
Alignment explanation
Indices: 1227008--1227039 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
1226998 ACTGGTGATG
1227008 TTCTTCTTCTTT
1 TTCTTCTTC-TT
1227020 TTCTTCTTCTT
1 TTCTTCTTCTT
1227031 TTCTTCTTC
1 TTCTTCTTC
1227040 CCTTCTGTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (11 bp):
TTCTTCTTCTT
Found at i:1229639 original size:2 final size:2
Alignment explanation
Indices: 1229632--1229663 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1229622 GAAATGGCCC
1229632 CT CT CT CT CT CT CT CT 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
1229664 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1229668 original size:2 final size:2
Alignment explanation
Indices: 1229663--1229711 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1229653 TCTCTCTCTC
1229663 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
1229705 TA TA TA T
1 TA TA TA T
1229712 CCTGCTTTGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1232089 original size:18 final size:17
Alignment explanation
Indices: 1232036--1232089 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
1232026 TAATAAAAAT
1232036 ATATCAAAATTTATGT-A
1 ATATCAAAATTTAT-TAA
1232053 ATAT--AAA-TTATTAA
1 ATATCAAAATTTATTAA
1232067 TATATCAAAATTTATATAA
1 -ATATCAAAATTTAT-TAA
1232086 ATAT
1 ATAT
1232090 ATAATATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
13 1 0.03
14 5 0.16
15 7 0.23
17 7 0.23
18 8 0.26
19 3 0.10
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (17 bp):
ATATCAAAATTTATTAA
Found at i:1232283 original size:3 final size:3
Alignment explanation
Indices: 1232275--1232299 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1232265 GATTTTTCTC
1232275 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
1232300 AATGAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1233386 original size:2 final size:2
Alignment explanation
Indices: 1233381--1233407 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1233371 ACACACACAC
1233381 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
1233408 AAAGATAAGA
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:1233633 original size:20 final size:20
Alignment explanation
Indices: 1233585--1233635 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1233575 TTTATAAATA
*
1233585 TAATTT-TAATTAATGTTAT
1 TAATTTATAATTAATATTAT
*
1233604 TAATTAATAATTAATATT-T
1 TAATTTATAATTAATATTAT
1233623 TATATTTATAATT
1 TA-ATTTATAATT
1233636 TATGGGACGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 8 0.30
20 19 0.70
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
TAATTTATAATTAATATTAT
Found at i:1233684 original size:14 final size:15
Alignment explanation
Indices: 1233658--1233686 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1233648 ATAAATTTTA
1233658 ATGATATTAATTAAG
1 ATGATATTAATTAAG
1233673 ATGATA-TAATTAAG
1 ATGATATTAATTAAG
1233687 TATAATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (15 bp):
ATGATATTAATTAAG
Found at i:1236165 original size:2 final size:2
Alignment explanation
Indices: 1236160--1236188 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1236150 ATTAAGCACC
1236160 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1236189 AATGGGAAGA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1242065 original size:20 final size:20
Alignment explanation
Indices: 1242040--1242078 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1242030 ATGATTTTTA
*
1242040 TATTTAATTTTAAGTTTAAT
1 TATTTAATTTTAAATTTAAT
*
1242060 TATTTATTTTTAAATTTAA
1 TATTTAATTTTAAATTTAA
1242079 ATTAATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
TATTTAATTTTAAATTTAAT
Found at i:1242227 original size:31 final size:30
Alignment explanation
Indices: 1242149--1242228 Score: 74
Period size: 31 Copynumber: 2.6 Consensus size: 30
1242139 GTGTTATGAT
*
1242149 TTTTAAATTTTATTT-ATTTAATAATTTAAA
1 TTTTAAATTTT-TTTAATATAATAATTTAAA
* *
1242179 TTATTTAATTTAATTTAATAATAATAAATTTAAA
1 TT-TTAAATTT-TTTTAAT-ATAAT-AATTTAAA
1242213 -TTTAAATTTTTTTAAT
1 TTTTAAATTTTTTTAAT
1242229 TTAAACTTGA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
30 2 0.05
31 16 0.40
32 9 0.22
33 5 0.12
34 8 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
TTTTAAATTTTTTTAATATAATAATTTAAA
Found at i:1244410 original size:2 final size:2
Alignment explanation
Indices: 1244403--1244436 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1244393 AGTAGTTGGC
1244403 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1244437 GTGTGAGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1250014 original size:14 final size:15
Alignment explanation
Indices: 1249997--1250025 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1249987 TTTATATTTC
1249997 TATATTAT-TTTTAT
1 TATATTATATTTTAT
1250011 TATATTATATTTTAT
1 TATATTATATTTTAT
1250026 ATTACAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TATATTATATTTTAT
Found at i:1254661 original size:7 final size:7
Alignment explanation
Indices: 1254645--1254677 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
1254635 CCTGTAAGCA
1254645 TAAAAA-
1 TAAAAAT
1254651 TAAAAAT
1 TAAAAAT
1254658 TAAAAAT
1 TAAAAAT
1254665 TAAAAAT
1 TAAAAAT
1254672 TAAAAA
1 TAAAAA
1254678 AAAAAAGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
TAAAAAT
Found at i:1254683 original size:14 final size:14
Alignment explanation
Indices: 1254646--1254683 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
1254636 CTGTAAGCAT
1254646 AAAAATAAAAATTA
1 AAAAATAAAAATTA
*
1254660 AAAATTAAAAATTA
1 AAAAATAAAAATTA
1254674 AAAAA-AAAAA
1 AAAAATAAAAA
1254684 GAAGCCACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (14 bp):
AAAAATAAAAATTA
Done.