Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 41 of 438
Found at i:10273070 original size:126 final size:126
Alignment explanation
Indices: 10272844--10273071 Score: 339
Period size: 126 Copynumber: 1.8 Consensus size: 126
10272834 AATCATTTTT
* * ** * * *
10272844 AAAATAATGGCAATTTTCGGTATTTATGGAACTCAAAGGATCGTGCCCTAACGTACTGGGTTTCG
1 AAAATAAAGGCAATGTTCGGTATTTAAAGAACTCAAAGAATCGTGCCCTAACGTACTGGGCTCCG
*
10272909 CTTTCTTTGTTGGTCTTGAATATTCGAATAACCTCTTCCCAGTGCACTCTCAAAAGATTTC
66 CTTTCTTTGTTGATCTTGAATATTCGAATAACCTCTTCCCAGTGCACTCTCAAAAGATTTC
* *
10272970 AAAATAAAGGCAATGTTCGGTATTTAAAGAATTCGAAGAATCGTGCCCTAACGTACTGGGCTCCG
1 AAAATAAAGGCAATGTTCGGTATTTAAAGAACTCAAAGAATCGTGCCCTAACGTACTGGGCTCCG
* * *
10273035 CTTTCTTTGTTTATTTTGAATATTCGAATATCCTCTT
66 CTTTCTTTGTTGATCTTGAATATTCGAATAACCTCTT
10273072 AAGGCTAAAA
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
126 89 1.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (126 bp):
AAAATAAAGGCAATGTTCGGTATTTAAAGAACTCAAAGAATCGTGCCCTAACGTACTGGGCTCCG
CTTTCTTTGTTGATCTTGAATATTCGAATAACCTCTTCCCAGTGCACTCTCAAAAGATTTC
Found at i:10286913 original size:25 final size:22
Alignment explanation
Indices: 10286885--10286937 Score: 52
Period size: 24 Copynumber: 2.2 Consensus size: 22
10286875 TTTAATGTTT
*
10286885 AAAATTGAATGTATTTTTTTGTTAA
1 AAAATT-AAT-TAATTTTTT-TTAA
*
10286910 AAAACTTAATTAATTTTTTTTAG
1 AAAA-TTAATTAATTTTTTTTAA
10286933 AAAAT
1 AAAAT
10286938 ACAAAAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 1 0.04
23 7 0.28
24 8 0.32
25 7 0.28
26 2 0.08
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.49
Consensus pattern (22 bp):
AAAATTAATTAATTTTTTTTAA
Found at i:10290219 original size:228 final size:228
Alignment explanation
Indices: 10289822--10290277 Score: 912
Period size: 228 Copynumber: 2.0 Consensus size: 228
10289812 GTTCGGTAAG
10289822 ATTTATCGTTTAATACATCAAACTTACTAAGCTTCATTAAACTTACTTGTGTTGTTTAATGTCAT
1 ATTTATCGTTTAATACATCAAACTTACTAAGCTTCATTAAACTTACTTGTGTTGTTTAATGTCAT
10289887 TATAGATTCTTGGAAGGTTGGACGATCGAATCAACACTCAAAGTCACACTATCCAGCTCATCTCG
66 TATAGATTCTTGGAAGGTTGGACGATCGAATCAACACTCAAAGTCACACTATCCAGCTCATCTCG
10289952 GTAGTTTTTGGAATGTTTAATTCAGATTATATGGCATGTATAGACTCTTGTGTGGTTTTGGTTAA
131 GTAGTTTTTGGAATGTTTAATTCAGATTATATGGCATGTATAGACTCTTGTGTGGTTTTGGTTAA
10290017 TGTTTGGCTATGTAAATATTATGAATGATATTT
196 TGTTTGGCTATGTAAATATTATGAATGATATTT
10290050 ATTTATCGTTTAATACATCAAACTTACTAAGCTTCATTAAACTTACTTGTGTTGTTTAATGTCAT
1 ATTTATCGTTTAATACATCAAACTTACTAAGCTTCATTAAACTTACTTGTGTTGTTTAATGTCAT
10290115 TATAGATTCTTGGAAGGTTGGACGATCGAATCAACACTCAAAGTCACACTATCCAGCTCATCTCG
66 TATAGATTCTTGGAAGGTTGGACGATCGAATCAACACTCAAAGTCACACTATCCAGCTCATCTCG
10290180 GTAGTTTTTGGAATGTTTAATTCAGATTATATGGCATGTATAGACTCTTGTGTGGTTTTGGTTAA
131 GTAGTTTTTGGAATGTTTAATTCAGATTATATGGCATGTATAGACTCTTGTGTGGTTTTGGTTAA
10290245 TGTTTGGCTATGTAAATATTATGAATGATATTT
196 TGTTTGGCTATGTAAATATTATGAATGATATTT
10290278 TGTGCAAATA
Statistics
Matches: 228, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
228 228 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.40
Consensus pattern (228 bp):
ATTTATCGTTTAATACATCAAACTTACTAAGCTTCATTAAACTTACTTGTGTTGTTTAATGTCAT
TATAGATTCTTGGAAGGTTGGACGATCGAATCAACACTCAAAGTCACACTATCCAGCTCATCTCG
GTAGTTTTTGGAATGTTTAATTCAGATTATATGGCATGTATAGACTCTTGTGTGGTTTTGGTTAA
TGTTTGGCTATGTAAATATTATGAATGATATTT
Found at i:10290854 original size:20 final size:21
Alignment explanation
Indices: 10290829--10290867 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
10290819 CCTGCAGTCC
*
10290829 AAAATTTTCAAAT-TTTTCTT
1 AAAATTTCCAAATGTTTTCTT
10290849 AAAATTTCCAAATGTTTTC
1 AAAATTTCCAAATGTTTTC
10290868 GATTTAGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.36, C:0.13, G:0.03, T:0.49
Consensus pattern (21 bp):
AAAATTTCCAAATGTTTTCTT
Found at i:10293844 original size:2 final size:2
Alignment explanation
Indices: 10293837--10293866 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10293827 TAATATGTAA
10293837 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10293867 TTCAAATAAT
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):
AT
Found at i:10294712 original size:8 final size:8
Alignment explanation
Indices: 10294701--10294742 Score: 68
Period size: 8 Copynumber: 5.4 Consensus size: 8
10294691 TTTTTTTAAT
10294701 TTTATATA
1 TTTATATA
10294709 TTTATATA
1 TTTATATA
*
10294717 TTTATAAA
1 TTTATATA
10294725 TTTATATA
1 TTTATATA
10294733 -TTATATA
1 TTTATATA
10294740 TTT
1 TTT
10294743 TAAAATAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
7 7 0.23
8 24 0.77
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TTTATATA
Found at i:10298704 original size:22 final size:22
Alignment explanation
Indices: 10298678--10298721 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
10298668 CTTACAAAAT
10298678 TAATTATTTGGATATTAAGCCA
1 TAATTATTTGGATATTAAGCCA
*
10298700 TAATTATTTGGCTATTAAGCCA
1 TAATTATTTGGATATTAAGCCA
10298722 ATCCAATTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (22 bp):
TAATTATTTGGATATTAAGCCA
Found at i:10299919 original size:19 final size:19
Alignment explanation
Indices: 10299897--10299936 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
10299887 GTGATTGAAG
10299897 ATGGGTTTTAGTGACAGGA
1 ATGGGTTTTAGTGACAGGA
*
10299916 ATGGGTTTTGGTGACAGGA
1 ATGGGTTTTAGTGACAGGA
10299935 AT
1 AT
10299937 CAATCAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.25, C:0.05, G:0.38, T:0.33
Consensus pattern (19 bp):
ATGGGTTTTAGTGACAGGA
Found at i:10301770 original size:42 final size:42
Alignment explanation
Indices: 10301711--10301794 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
10301701 GATGGAAAAA
*
10301711 TACCTTTAAAATCTTTAAAATCTGCCCAAATTCCAAATCTAG
1 TACCTTTAAAATCTTTAAAATCCGCCCAAATTCCAAATCTAG
*
10301753 TACCTTTAAAATCTTTAAAATCCGCCCAAATTTCAAATCTAG
1 TACCTTTAAAATCTTTAAAATCCGCCCAAATTCCAAATCTAG
10301795 AAATTTAGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.33
Consensus pattern (42 bp):
TACCTTTAAAATCTTTAAAATCCGCCCAAATTCCAAATCTAG
Found at i:10302938 original size:2 final size:2
Alignment explanation
Indices: 10302931--10302969 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
10302921 CCAATAAGAT
10302931 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10302970 CATCTATTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10305707 original size:19 final size:19
Alignment explanation
Indices: 10305683--10305725 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
10305673 TAATGTGTTA
*
10305683 TAAAAAAATAGAT-AGAGAG
1 TAAAAAAA-AAATGAGAGAG
10305702 TAAAAAAAAAATGAGAGAG
1 TAAAAAAAAAATGAGAGAG
10305721 TAAAA
1 TAAAA
10305726 GAGAGAACGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.14
Consensus pattern (19 bp):
TAAAAAAAAAATGAGAGAG
Found at i:10311379 original size:33 final size:33
Alignment explanation
Indices: 10311327--10311402 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
10311317 TGCAAAAACC
10311327 ATTTTGCTTTACGTACAAAAACCATTAAGGACA
1 ATTTTGCTTTACGTACAAAAACCATTAAGGACA
* * *
10311360 ATTTTTCTTTGCGTCCAAAAACCATTAAGGACA
1 ATTTTGCTTTACGTACAAAAACCATTAAGGACA
10311393 ATATTTGCTT
1 AT-TTTGCTT
10311403 CCATTTTTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
33 32 0.84
34 6 0.16
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (33 bp):
ATTTTGCTTTACGTACAAAAACCATTAAGGACA
Found at i:10317120 original size:50 final size:51
Alignment explanation
Indices: 10317043--10317171 Score: 199
Period size: 50 Copynumber: 2.5 Consensus size: 51
10317033 GACCATGGCA
10317043 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGA-AAAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAA-TG
*
10317094 A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
* * *
10317144 ACAAGTGAAAAGTGGTAGCTTCAGCTAC
1 ACAAGTGATAAGTGATAGCTTCGGCTAC
10317172 CTGATCAGTG
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
50 45 0.62
51 27 0.38
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
Found at i:10317185 original size:31 final size:31
Alignment explanation
Indices: 10317147--10317295 Score: 237
Period size: 31 Copynumber: 4.8 Consensus size: 31
10317137 ACAAATGACA
*
10317147 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
10317178 AGTGAAAAGTGGTAG-TTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTT-CGGCTACCTGATC
*
10317209 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
10317240 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
10317271 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
10317296 AAGTGACAAG
Statistics
Matches: 110, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
30 2 0.02
31 107 0.97
32 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:10317391 original size:46 final size:44
Alignment explanation
Indices: 10317324--10317483 Score: 175
Period size: 46 Copynumber: 3.6 Consensus size: 44
10317314 GATTTCTGTT
* * *
10317324 TAAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTATGTA
1 TAAGACCATAGCTGGGATATGGCATC-GTG-GATATATGATATGTG
* *
10317370 TAAGACCATATCTGGGATATGGCATCAGTGAGATATGTGAT-TCGTG
1 TAAGACCATAGCTGGGATATGGCATC-GTG-GATATATGATAT-GTG
*
10317416 TAAGACCATAGCTGGGCTATGGCATC---GATATATGAATATGTG
1 TAAGACCATAGCTGGGATATGGCATCGTGGATATATG-ATATGTG
*
10317458 TAAGACCATAGCTGGGCTATGGCATC
1 TAAGACCATAGCTGGGATATGGCATC
10317484 ATTATGTGAA
Statistics
Matches: 103, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
41 7 0.07
42 31 0.30
43 1 0.01
45 1 0.01
46 63 0.61
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (44 bp):
TAAGACCATAGCTGGGATATGGCATCGTGGATATATGATATGTG
Found at i:10317471 original size:42 final size:42
Alignment explanation
Indices: 10317355--10317527 Score: 172
Period size: 42 Copynumber: 4.0 Consensus size: 42
10317345 GCATCGGTGT
* * * *
10317355 GATATATG-CTATGTATAAGACCATATCTGGGATATGGCATC
1 GATATATGAATATGTGTAAGACCATAGCTGGGCTATGGCATC
* *
10317396 AGTGAGATATGTGAT-TCGTGTAAGACCATAGCTGGGCTATGGCATC
1 ---GATATATG-AATAT-GTGTAAGACCATAGCTGGGCTATGGCATC
10317442 GATATATGAATATGTGTAAGACCATAGCTGGGCTATGGCATC
1 GATATATGAATATGTGTAAGACCATAGCTGGGCTATGGCATC
* * * **
10317484 -ATTATGTGAAGATGTGTAAGACCATAGTTGAACTATGGCATC
1 GA-TATATGAATATGTGTAAGACCATAGCTGGGCTATGGCATC
10317526 GA
1 GA
10317528 GAAAACGAAA
Statistics
Matches: 111, Mismatches: 12, Indels: 13
0.82 0.09 0.10
Matches are distributed among these distances:
41 1 0.01
42 66 0.59
43 9 0.08
44 7 0.06
45 1 0.01
46 27 0.24
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (42 bp):
GATATATGAATATGTGTAAGACCATAGCTGGGCTATGGCATC
Found at i:10321474 original size:3 final size:3
Alignment explanation
Indices: 10321466--10321508 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
10321456 TTTTGTTTTC
*
10321466 ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
10321509 GTAGTAGTAG
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):
ATT
Found at i:10321513 original size:3 final size:3
Alignment explanation
Indices: 10321507--10321531 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
10321497 TTATTATTAT
10321507 TAG TAG TAG TAG TAG TAG TAG TAG T
1 TAG TAG TAG TAG TAG TAG TAG TAG T
10321532 TTAGTTAATA
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:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TAG
Found at i:10333147 original size:17 final size:17
Alignment explanation
Indices: 10333121--10333160 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
10333111 TTCCCCTTTT
* *
10333121 AAAAATAAAATAATAT-
1 AAAAACAAAAAAATATC
10333137 AAAAACAAAAAAATATC
1 AAAAACAAAAAAATATC
10333154 AAAAACA
1 AAAAACA
10333161 CTCGTAGGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAAACAAAAAAATATC
Found at i:10336395 original size:14 final size:14
Alignment explanation
Indices: 10336376--10336408 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
10336366 AAATAACATA
10336376 CGAGTTAGGTAAAT
1 CGAGTTAGGTAAAT
10336390 CGAGTTAGGTAAAT
1 CGAGTTAGGTAAAT
10336404 C-AGTT
1 CGAGTT
10336409 TGAACTTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.30
Consensus pattern (14 bp):
CGAGTTAGGTAAAT
Found at i:10340290 original size:21 final size:21
Alignment explanation
Indices: 10340264--10340305 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
10340254 TGGCAGTGGG
10340264 GTGATGAATAATAAAAAAAAA
1 GTGATGAATAATAAAAAAAAA
10340285 GTGATGAATAATAAAAAAAAA
1 GTGATGAATAATAAAAAAAAA
10340306 AATATTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.14, T:0.19
Consensus pattern (21 bp):
GTGATGAATAATAAAAAAAAA
Found at i:10348962 original size:20 final size:20
Alignment explanation
Indices: 10348924--10348960 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
10348914 TTTCGAAAAT
10348924 AAATCTATATTTATATTTTG
1 AAATCTATATTTATATTTTG
10348944 AAATC-ATATTTAT-TTTT
1 AAATCTATATTTATATTTT
10348961 TTATTTCGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 8 0.47
20 5 0.29
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (20 bp):
AAATCTATATTTATATTTTG
Found at i:10349033 original size:13 final size:13
Alignment explanation
Indices: 10349010--10349043 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
10349000 TTTTTTTAAA
10349010 TATAA-TATATTT
1 TATAATTATATTT
*
10349022 TATTATTATATTT
1 TATAATTATATTT
10349035 TATAATTAT
1 TATAATTAT
10349044 TTATAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATAATTATATTT
Found at i:10349038 original size:20 final size:20
Alignment explanation
Indices: 10349015--10349060 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
10349005 TTAAATATAA
*
10349015 TATATTTTA-TTATTATATT
1 TATATTTTATTTATAATATT
*
10349034 T-TATAATTATTTATAATATT
1 TATAT-TTTATTTATAATATT
10349054 TATATTT
1 TATATTT
10349061 AAATTTAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 5
0.72 0.10 0.17
Matches are distributed among these distances:
18 3 0.14
19 4 0.19
20 11 0.52
21 3 0.14
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TATATTTTATTTATAATATT
Found at i:10349632 original size:25 final size:25
Alignment explanation
Indices: 10349604--10349651 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
10349594 TATGAAAAAC
*
10349604 AATTATAATTAACAATAACAAAAGG
1 AATTATAATTAAAAATAACAAAAGG
* * *
10349629 AATTTTATTTAAAAATAATAAAA
1 AATTATAATTAAAAATAACAAAA
10349652 ATAAAATTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (25 bp):
AATTATAATTAAAAATAACAAAAGG
Found at i:10350164 original size:30 final size:30
Alignment explanation
Indices: 10350130--10350192 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
10350120 ATTTATTTTA
10350130 TTGTTAATTTTCTTATTATTTTA-AAGGCAT
1 TTGTTAATTTTCTTATTATTTTAGAA-GCAT
*
10350160 TTGTTAATTTTTTTATTATTTTAGAAGCAT
1 TTGTTAATTTTCTTATTATTTTAGAAGCAT
10350190 TTG
1 TTG
10350193 CTTCTTAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 29 0.94
31 2 0.06
ACGTcount: A:0.25, C:0.05, G:0.11, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTCTTATTATTTTAGAAGCAT
Found at i:10350961 original size:2 final size:2
Alignment explanation
Indices: 10350954--10350986 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
10350944 TCCAATCTTT
10350954 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10350987 GATGTTGCGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10352199 original size:16 final size:16
Alignment explanation
Indices: 10352178--10352216 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
10352168 TATAGAATCT
10352178 AAAAT-AATAATAATTA
1 AAAATAAATAA-AATTA
10352194 AAAATAAATAAAATT-
1 AAAATAAATAAAATTA
10352209 AAAATAAA
1 AAAATAAA
10352217 CTTAAAATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.36
16 9 0.41
17 5 0.23
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATAAATAAAATTA
Found at i:10353696 original size:16 final size:16
Alignment explanation
Indices: 10353675--10353745 Score: 115
Period size: 16 Copynumber: 4.4 Consensus size: 16
10353665 GTTTGGTTCA
*
10353675 CTGTAATGGAATAGGG
1 CTGTAATGGAATAGAG
*
10353691 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
10353707 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
*
10353723 CTGTAATAGAATAGAG
1 CTGTAATGGAATAGAG
10353739 CTGTAAT
1 CTGTAAT
10353746 CAGTAATTCA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.37, C:0.07, G:0.28, T:0.28
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:10353811 original size:44 final size:46
Alignment explanation
Indices: 10353731--10353820 Score: 141
Period size: 44 Copynumber: 2.0 Consensus size: 46
10353721 AGCTGTAATA
10353731 GAATAGAGCTGTAATCAGTAATTCAACTGTTTGGTTGAATGGAATG
1 GAATAGAGCTGTAATCAGTAATTCAACTGTTTGGTTGAATGGAATG
*
10353777 GAATAGAGCTGTAAT-AG-AATTCTTA-TGTTTGGTTGAATGGAATG
1 GAATAGAGCTGTAATCAGTAATTC-AACTGTTTGGTTGAATGGAATG
10353821 ATGTTGTAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
44 24 0.57
45 3 0.07
46 15 0.36
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.34
Consensus pattern (46 bp):
GAATAGAGCTGTAATCAGTAATTCAACTGTTTGGTTGAATGGAATG
Found at i:10353983 original size:61 final size:55
Alignment explanation
Indices: 10353901--10354049 Score: 140
Period size: 61 Copynumber: 2.5 Consensus size: 55
10353891 GATTATTGTT
*
10353901 ATTAAATTTTAATA-AGATTATTGATACATATATTTTAATAAAAATAAAAATAAATAATTTA
1 ATTAAATTTTAATATA-ATTATT-ATA-ATATAATTTAAT-AAAAT---AATAAATAATTTA
* * *
10353962 ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAATAATATATATTTTA
1 ATTAAATTTTAATATAATTATTA-T-AATATAATTTAATAAAATAATAAATAATTTA
10354019 A-TAACATTATTAATATAATTATTAATAATAT
1 ATTAA-ATT-TTAATATAATTATT-ATAATAT
10354050 TTAATAATAA
Statistics
Matches: 77, Mismatches: 5, Indels: 16
0.79 0.05 0.16
Matches are distributed among these distances:
56 2 0.03
57 20 0.26
58 15 0.19
59 1 0.01
60 6 0.08
61 31 0.40
62 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (55 bp):
ATTAAATTTTAATATAATTATTATAATATAATTTAATAAAATAATAAATAATTTA
Found at i:10354069 original size:10 final size:10
Alignment explanation
Indices: 10353954--10354069 Score: 59
Period size: 12 Copynumber: 11.4 Consensus size: 10
10353944 ATAAAAATAA
10353954 ATAATTTAATT
1 ATAATTTAA-T
*
10353965 ATATTTTAAT
1 ATAATTTAAT
10353975 ATAA-TT-AT
1 ATAATTTAAT
*
10353983 -T-ATTAAAT
1 ATAATTTAAT
10353991 ATAATTTAAT
1 ATAATTTAAT
*
10354001 A-AA-ATAAT
1 ATAATTTAAT
10354009 ATATATTTTAAT
1 ATA-A-TTTAAT
10354021 A-ACATTATTAAT
1 ATA-A-T-TTAAT
10354033 ATAATTATTAAT
1 ATAA-T-TTAAT
10354045 A-ATATTTAAT
1 ATA-ATTTAAT
10354055 AATAATTTAAT
1 -ATAATTTAAT
10354066 ATAA
1 ATAA
10354070 AATTATTATT
Statistics
Matches: 85, Mismatches: 7, Indels: 27
0.71 0.06 0.23
Matches are distributed among these distances:
6 1 0.01
7 2 0.02
8 9 0.11
9 6 0.07
10 21 0.25
11 22 0.26
12 23 0.27
13 1 0.01
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (10 bp):
ATAATTTAAT
Found at i:10354074 original size:35 final size:33
Alignment explanation
Indices: 10353983--10354096 Score: 87
Period size: 35 Copynumber: 3.5 Consensus size: 33
10353973 ATATAATTAT
*
10353983 TATTAAAT-ATAATTTAATA-AA--A-TAATATA
1 TATTTAATAATAATTTAATATAATTATTAATA-A
* *
10354012 TATTTTAATAACATTATTAATATAATTATTAATAA
1 TA-TTTAATAATAAT-TTAATATAATTATTAATAA
*
10354047 TATTTAATAATAATTTAATATAAAATTATTATTAA
1 TATTTAATAATAATTTAATAT--AATTATTAATAA
*
10354082 -ATATTATTAATAATT
1 TAT-TTAATAATAATT
10354097 ATATTAATAA
Statistics
Matches: 68, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
29 2 0.03
30 5 0.07
31 3 0.04
32 6 0.09
33 9 0.13
34 12 0.18
35 26 0.38
36 5 0.07
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (33 bp):
TATTTAATAATAATTTAATATAATTATTAATAA
Found at i:10370146 original size:14 final size:14
Alignment explanation
Indices: 10370127--10370164 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
10370117 CTCAGCTCGG
10370127 TGAAGGATTTAAAA
1 TGAAGGATTTAAAA
10370141 TGAAGGATTTAAAA
1 TGAAGGATTTAAAA
10370155 TGAAGGATTT
1 TGAAGGATTT
10370165 GGGAGCAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.32
Consensus pattern (14 bp):
TGAAGGATTTAAAA
Found at i:10371747 original size:41 final size:41
Alignment explanation
Indices: 10371694--10371821 Score: 202
Period size: 41 Copynumber: 3.1 Consensus size: 41
10371684 GCAAAAATTG
* *
10371694 AAAAACACAGAGCAATAGCGGCGCTTTTGGCAAAACGCCGCT
1 AAAAAC-CAGAGCATTAGCGGCGCTTTTGGAAAAACGCCGCT
* *
10371736 AAAAACCAGAGCATTAGCGGTGCTTTTGGAAAAACACCGCT
1 AAAAACCAGAGCATTAGCGGCGCTTTTGGAAAAACGCCGCT
*
10371777 AAAAACCAGAGCATTAGCGGCGCTTTTAGAAAAACGCCGCT
1 AAAAACCAGAGCATTAGCGGCGCTTTTGGAAAAACGCCGCT
10371818 AAAA
1 AAAA
10371822 GTCATATAAC
Statistics
Matches: 79, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
41 73 0.92
42 6 0.08
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.16
Consensus pattern (41 bp):
AAAAACCAGAGCATTAGCGGCGCTTTTGGAAAAACGCCGCT
Found at i:10371966 original size:14 final size:14
Alignment explanation
Indices: 10371947--10371994 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
10371937 AAAGAGATAG
10371947 TATCGAATTTAAAA
1 TATCGAATTTAAAA
10371961 TATCGAA-TT--AA
1 TATCGAATTTAAAA
* *
10371972 TTTTGAATTTAAAA
1 TATCGAATTTAAAA
10371986 TATCGAATT
1 TATCGAATT
10371995 AATTATCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
11 7 0.26
12 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (14 bp):
TATCGAATTTAAAA
Found at i:10371985 original size:25 final size:25
Alignment explanation
Indices: 10371951--10371998 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
10371941 AGATAGTATC
10371951 GAATTTAAAATATCGAATTAATTTT
1 GAATTTAAAATATCGAATTAATTTT
10371976 GAATTTAAAATATCGAATTAATT
1 GAATTTAAAATATCGAATTAATT
10371999 ATCATTATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (25 bp):
GAATTTAAAATATCGAATTAATTTT
Found at i:10372025 original size:14 final size:14
Alignment explanation
Indices: 10372003--10372100 Score: 61
Period size: 14 Copynumber: 6.7 Consensus size: 14
10371993 TTAATTATCA
*
10372003 TTATAGTTTAAGGT
1 TTATGGTTTAAGGT
*
10372017 TTATGGTTTAAGAT
1 TTATGGTTTAAGGT
* *
10372031 ATATGGTTTAGGGT
1 TTATGGTTTAAGGT
* *
10372045 TTAAGGTTTATGAGT
1 TTATGGTTTAAG-GT
*
10372060 TAACTATGGTTTAAGAT
1 T---TATGGTTTAAGGT
* * *
10372077 ATATAGTTTAGGGT
1 TTATGGTTTAAGGT
*
10372091 TTAAGGTTTA
1 TTATGGTTTA
10372101 GGAGTTAACT
Statistics
Matches: 62, Mismatches: 18, Indels: 8
0.70 0.20 0.09
Matches are distributed among these distances:
14 49 0.79
15 3 0.05
17 1 0.02
18 9 0.15
ACGTcount: A:0.29, C:0.01, G:0.24, T:0.46
Consensus pattern (14 bp):
TTATGGTTTAAGGT
Found at i:10372038 original size:21 final size:21
Alignment explanation
Indices: 10372014--10372095 Score: 83
Period size: 21 Copynumber: 3.7 Consensus size: 21
10372004 TATAGTTTAA
*
10372014 GGTTTATGGTTTAAGATATAT
1 GGTTTAGGGTTTAAGATATAT
* *
10372035 GGTTTAGGGTTTAAGGTTTAT
1 GGTTTAGGGTTTAAGATATAT
*
10372056 GAGTTAACTATGGTTTAAGATATAT
1 G-GTT---TAGGGTTTAAGATATAT
*
10372081 AGTTTAGGGTTTAAG
1 GGTTTAGGGTTTAAG
10372096 GTTTAGGAGT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
21 29 0.59
22 3 0.06
24 3 0.06
25 14 0.29
ACGTcount: A:0.28, C:0.01, G:0.27, T:0.44
Consensus pattern (21 bp):
GGTTTAGGGTTTAAGATATAT
Found at i:10372068 original size:46 final size:46
Alignment explanation
Indices: 10372018--10372111 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
10372008 GTTTAAGGTT
* *
10372018 TATGGTTTAAGATATATGGTTTAGGGTTTAAGGTTTATGAGTTAAC
1 TATGGTTTAAGATATATAGTTTAGGGTTTAAGGTTTAGGAGTTAAC
10372064 TATGGTTTAAGATATATAGTTTAGGGTTTAAGGTTTAGGAGTTAAC
1 TATGGTTTAAGATATATAGTTTAGGGTTTAAGGTTTAGGAGTTAAC
10372110 TA
1 TA
10372112 GTATTTGAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.30, C:0.02, G:0.26, T:0.43
Consensus pattern (46 bp):
TATGGTTTAAGATATATAGTTTAGGGTTTAAGGTTTAGGAGTTAAC
Found at i:10372197 original size:15 final size:15
Alignment explanation
Indices: 10372170--10372238 Score: 70
Period size: 15 Copynumber: 4.7 Consensus size: 15
10372160 GTTTAAGGTG
10372170 TAAGGGTTT-GGGGT
1 TAAGGGTTTAGGGGT
10372184 TAAGGGTTTAGGGGT
1 TAAGGGTTTAGGGGT
* * *
10372199 T-AGTGTTTATGGGA
1 TAAGGGTTTAGGGGT
* *
10372213 TAAGGGTTAAGAGGT
1 TAAGGGTTTAGGGGT
*
10372228 TTAGGGTTTAG
1 TAAGGGTTTAG
10372239 ATTAATTAGT
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
14 20 0.47
15 23 0.53
ACGTcount: A:0.22, C:0.00, G:0.42, T:0.36
Consensus pattern (15 bp):
TAAGGGTTTAGGGGT
Found at i:10372235 original size:7 final size:7
Alignment explanation
Indices: 10372140--10372238 Score: 58
Period size: 7 Copynumber: 13.9 Consensus size: 7
10372130 TGAATTATGA
10372140 GTTTAGG
1 GTTTAGG
*
10372147 GGTTAGG
1 GTTTAGG
10372154 G-TT-GG
1 GTTTAGG
*
10372159 AGTTTAAG
1 -GTTTAGG
*
10372167 GTGTAAGG
1 GT-TTAGG
*
10372175 GTTTGGG
1 GTTTAGG
*
10372182 GTTAAGG
1 GTTTAGG
10372189 GTTTAGG
1 GTTTAGG
* *
10372196 GGTTAGT
1 GTTTAGG
10372203 GTTTATGG
1 GTTTA-GG
* *
10372211 GATAAGG
1 GTTTAGG
*
10372218 GTTAAGAG
1 GTTTAG-G
10372226 GTTTAGG
1 GTTTAGG
10372233 GTTTAG
1 GTTTAG
10372239 ATTAATTAGT
Statistics
Matches: 69, Mismatches: 17, Indels: 12
0.70 0.17 0.12
Matches are distributed among these distances:
5 2 0.03
6 3 0.04
7 48 0.70
8 16 0.23
ACGTcount: A:0.20, C:0.00, G:0.43, T:0.36
Consensus pattern (7 bp):
GTTTAGG
Found at i:10377094 original size:22 final size:23
Alignment explanation
Indices: 10377052--10377094 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
10377042 TTTCAAAAAT
*
10377052 TAAACATAATATAATATTTAACA
1 TAAAAATAATATAATATTTAACA
*
10377075 TAAAAATAA-ATATTATTTAA
1 TAAAAATAATATAATATTTAA
10377095 TTAAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (23 bp):
TAAAAATAATATAATATTTAACA
Found at i:10377115 original size:22 final size:22
Alignment explanation
Indices: 10377049--10377116 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
10377039 AAATTTCAAA
* * *
10377049 AATTAAACATAATATAATATTTA
1 AATTAAA-ATAAAATAATTTTTT
* *
10377072 ACATAAAAAT-AAAT-ATTATTT
1 A-ATTAAAATAAAATAATTTTTT
10377093 AATTAAAATAAAATAATTTTTT
1 AATTAAAATAAAATAATTTTTT
10377115 AA
1 AA
10377117 AGTTCATGAT
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
20 7 0.20
21 9 0.26
22 11 0.31
23 3 0.09
24 5 0.14
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (22 bp):
AATTAAAATAAAATAATTTTTT
Found at i:10377181 original size:43 final size:43
Alignment explanation
Indices: 10377114--10377249 Score: 186
Period size: 43 Copynumber: 3.2 Consensus size: 43
10377104 AATAATTTTT
* * * *
10377114 TAAAGTTCATGAT-TTCTAGTGGCG-TTTGTGAGAAAAGCGCTGC
1 TAAAGGTCATGATCTT-TAGCGGCGTTTTTTG-GAAAAGCGCCGC
10377157 TAAAGGTCATGATCTTTAGCGGCGTTTTTTGGAAAAGCGCCGC
1 TAAAGGTCATGATCTTTAGCGGCGTTTTTTGGAAAAGCGCCGC
* *
10377200 TAAAGGTCATGGTCTTTATCGGCGTTTTTTGGAAAAGCGCCGC
1 TAAAGGTCATGATCTTTAGCGGCGTTTTTTGGAAAAGCGCCGC
10377243 TAAAGGT
1 TAAAGGT
10377250 AACGGCGTTT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
43 78 0.92
44 7 0.08
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (43 bp):
TAAAGGTCATGATCTTTAGCGGCGTTTTTTGGAAAAGCGCCGC
Found at i:10378343 original size:30 final size:31
Alignment explanation
Indices: 10378309--10378373 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
10378299 AGAAAAATTT
*
10378309 AATAGCTCAGTGACTT-AATAAAAACTTTTG
1 AATAGCTCAGTGACTTAAATAAAAACTTTCG
* * *
10378339 AATAGTTTAGTGACTTAAATGAAAACTTTCG
1 AATAGCTCAGTGACTTAAATAAAAACTTTCG
10378370 AATA
1 AATA
10378374 ATTTTGTGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 14 0.47
31 16 0.53
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.34
Consensus pattern (31 bp):
AATAGCTCAGTGACTTAAATAAAAACTTTCG
Found at i:10378367 original size:31 final size:30
Alignment explanation
Indices: 10378317--10378383 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 30
10378307 TTAATAGCTC
* *
10378317 AGTGACTTAATAAAAACTTTTGAATAGTTT
1 AGTGACTTAATAAAAACTTTCGAATAATTT
*
10378347 AGTGACTTAAATGAAAACTTTCGAATAATTT
1 AGTGACTT-AATAAAAACTTTCGAATAATTT
*
10378378 TGTGAC
1 AGTGAC
10378384 CAAATTATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 8 0.25
31 24 0.75
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (30 bp):
AGTGACTTAATAAAAACTTTCGAATAATTT
Found at i:10384172 original size:14 final size:14
Alignment explanation
Indices: 10384153--10384180 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10384143 TAACAACCTT
10384153 TTATTACCATAGTA
1 TTATTACCATAGTA
10384167 TTATTACCATAGTA
1 TTATTACCATAGTA
10384181 AAGAGAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
TTATTACCATAGTA
Found at i:10384426 original size:9 final size:9
Alignment explanation
Indices: 10384412--10384436 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
10384402 CTCATAGCCT
10384412 CCTCCTCTC
1 CCTCCTCTC
10384421 CCTCCTCTC
1 CCTCCTCTC
10384430 CCTCCTC
1 CCTCCTC
10384437 ACTTACTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (9 bp):
CCTCCTCTC
Found at i:10384731 original size:43 final size:43
Alignment explanation
Indices: 10384676--10384853 Score: 259
Period size: 43 Copynumber: 4.2 Consensus size: 43
10384666 TTAAAAAAAA
*
10384676 GCCGCTAAAAGTCATGGCTTTTAGCGGCATTTGTTGGAAAAGC
1 GCCGCTAAAAGTCATGGCTTTTAGCGGCGTTTGTTGGAAAAGC
* * * *
10384719 GCCGCTAAAAGTCATGGCTTTTAACAGTGTTTGTTTGAAAAGC
1 GCCGCTAAAAGTCATGGCTTTTAGCGGCGTTTGTTGGAAAAGC
* *
10384762 GCCGCTAAAAGTCATGGCCTTTAGCTGCGTTTGTTGGAAAAGC
1 GCCGCTAAAAGTCATGGCTTTTAGCGGCGTTTGTTGGAAAAGC
* **
10384805 GCCGCTAAAAGCCATAACTTTTAGCGGCGTTTGTTGGAAAA-C
1 GCCGCTAAAAGTCATGGCTTTTAGCGGCGTTTGTTGGAAAAGC
10384847 GCCGCTA
1 GCCGCTA
10384854 GTTTTGACAG
Statistics
Matches: 120, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 8 0.07
43 112 0.93
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (43 bp):
GCCGCTAAAAGTCATGGCTTTTAGCGGCGTTTGTTGGAAAAGC
Found at i:10385246 original size:21 final size:21
Alignment explanation
Indices: 10385222--10385318 Score: 90
Period size: 21 Copynumber: 4.6 Consensus size: 21
10385212 TCTGCTGCCA
* *
10385222 TCGCTGTTGCCTCTGCCTCCT
1 TCGCTGCTGCCTCTGCCTCCC
*
10385243 TCGCT-CGTGCCTCTACCTCCC
1 TCGCTGC-TGCCTCTGCCTCCC
* * *
10385264 TCACTACTGCCGCTGCCTCCC
1 TCGCTGCTGCCTCTGCCTCCC
*
10385285 TCGCTGCTG-CTGCTGCCTCCT
1 TCGCTGCTGCCT-CTGCCTCCC
*
10385306 TCTCTGCTGCCTC
1 TCGCTGCTGCCTC
10385319 CGCTCTAAGT
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.02
21 57 0.93
22 3 0.05
ACGTcount: A:0.03, C:0.47, G:0.18, T:0.32
Consensus pattern (21 bp):
TCGCTGCTGCCTCTGCCTCCC
Found at i:10390899 original size:9 final size:9
Alignment explanation
Indices: 10390878--10390998 Score: 63
Period size: 9 Copynumber: 13.6 Consensus size: 9
10390868 TATATATTAC
*
10390878 GTAAGTTAA
1 GTAAGTTAT
10390887 GTAAGCTT-T
1 GTAAG-TTAT
10390896 GTAAGTTAT
1 GTAAGTTAT
10390905 GTAAGTTAT
1 GTAAGTTAT
* *
10390914 GTTA-TGAT
1 GTAAGTTAT
* *
10390922 ATACATTTAT
1 GTA-AGTTAT
**
10390932 GTAAGGCAT
1 GTAAGTTAT
10390941 GTAAGTTAT
1 GTAAGTTAT
* *
10390950 GATATGATAT
1 G-TAAGTTAT
* *
10390960 AT-ATTTAT
1 GTAAGTTAT
10390968 GT-A-TTAT
1 GTAAGTTAT
*
10390975 GTAAGTTGT
1 GTAAGTTAT
10390984 GTAAGTTAT
1 GTAAGTTAT
10390993 GATAAG
1 G-TAAG
10390999 ATATATATTT
Statistics
Matches: 83, Mismatches: 21, Indels: 15
0.70 0.18 0.13
Matches are distributed among these distances:
7 6 0.07
8 12 0.14
9 48 0.58
10 17 0.20
ACGTcount: A:0.34, C:0.02, G:0.21, T:0.43
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:10391019 original size:56 final size:56
Alignment explanation
Indices: 10390952--10391183 Score: 348
Period size: 56 Copynumber: 4.2 Consensus size: 56
10390942 TAAGTTATGA
10390952 TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATT
1 TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATT
* *
10391008 TATGATATATATTTGGA-GTATTATGTAAGTTGTGTAAGTTATGATATGATACATATT
1 TATGATATATATTT--ATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATT
* * *
10391065 TATGAAATATATTTATGTATTATGTTAGTTGTGTAAGTTATGATATGATATATATT
1 TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATT
* *
10391121 TATGATATATATTTATGTATTATGTAAGTTTTGTAAGTTATG-TAAG-T-TAT-TA
1 TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATT
10391173 TATGATATATA
1 TATGATATATA
10391184 ATAAATATTA
Statistics
Matches: 163, Mismatches: 10, Indels: 10
0.89 0.05 0.05
Matches are distributed among these distances:
52 12 0.07
53 3 0.02
54 1 0.01
55 4 0.02
56 91 0.56
57 51 0.31
58 1 0.01
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.49
Consensus pattern (56 bp):
TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATT
Found at i:10391081 original size:113 final size:112
Alignment explanation
Indices: 10390952--10391162 Score: 361
Period size: 113 Copynumber: 1.9 Consensus size: 112
10390942 TAAGTTATGA
*
10390952 TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATTTATGATATA
1 TATGAAATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATTTATGATATA
10391017 TATTTGGA-GTATTATGTAAGTTGTGTAAGTTATGATATGATACATATT
66 TATTT--ATGTATTATGTAAGTTGTGTAAGTTATGATATGATACATATT
* *
10391065 TATGAAATATATTTATGTATTATGTTAGTTGTGTAAGTTATGATATGATATATATTTATGATATA
1 TATGAAATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATTTATGATATA
*
10391130 TATTTATGTATTATGTAAGTTTTGTAAGTTATG
66 TATTTATGTATTATGTAAGTTGTGTAAGTTATG
10391163 TAAGTTATTA
Statistics
Matches: 93, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
111 1 0.01
112 25 0.27
113 67 0.72
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (112 bp):
TATGAAATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATTTATGATATA
TATTTATGTATTATGTAAGTTGTGTAAGTTATGATATGATACATATT
Found at i:10391126 original size:13 final size:13
Alignment explanation
Indices: 10391108--10391137 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
10391098 TAAGTTATGA
10391108 TATGATATATATT
1 TATGATATATATT
10391121 TATGATATATATT
1 TATGATATATATT
10391134 TATG
1 TATG
10391138 TATTATGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (13 bp):
TATGATATATATT
Found at i:10391157 original size:9 final size:9
Alignment explanation
Indices: 10391140--10391170 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
10391130 TATTTATGTA
10391140 TTATGTAAG
1 TTATGTAAG
*
10391149 TTTTGTAAG
1 TTATGTAAG
10391158 TTATGTAAG
1 TTATGTAAG
10391167 TTAT
1 TTAT
10391171 TATATGATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (9 bp):
TTATGTAAG
Found at i:10391621 original size:37 final size:37
Alignment explanation
Indices: 10391577--10391667 Score: 104
Period size: 36 Copynumber: 2.5 Consensus size: 37
10391567 AAATTATATT
*
10391577 AATTGATAAATATTGAAATAT-TG-AAAT-ATATTTAA
1 AATTGATAAATATTGAAATATAAGCAAATCAT-TTTAA
10391612 AATGTTGAT-AA-A-TGAAATATAAGCAAATCATTTTAA
1 AA--TTGATAAATATTGAAATATAAGCAAATCATTTTAA
10391648 AATTGATAAATATTGAAATA
1 AATTGATAAATATTGAAATA
10391668 CATTAAAGCA
Statistics
Matches: 47, Mismatches: 1, Indels: 14
0.76 0.02 0.23
Matches are distributed among these distances:
34 13 0.28
35 6 0.13
36 14 0.30
37 14 0.30
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (37 bp):
AATTGATAAATATTGAAATATAAGCAAATCATTTTAA
Found at i:10393665 original size:59 final size:59
Alignment explanation
Indices: 10393567--10393696 Score: 183
Period size: 59 Copynumber: 2.2 Consensus size: 59
10393557 TTTCAAATTG
* * ** *
10393567 GGGAGAAAGGGGTGATTATTTTAGGGTTTCGAATTAGGGAAAATTGG-GGGAATAAA-CTA
1 GGGAGAAGGGGGTGATTATTTTAGGGATTCGAAGAAGGGAAAA-TGGAGGAAATAAATC-A
10393626 GGGAGAAGGGGGTGATTATTTTAGGGATTCGAAGAAGGGAAAATGGAGGAAATAAATCA
1 GGGAGAAGGGGGTGATTATTTTAGGGATTCGAAGAAGGGAAAATGGAGGAAATAAATCA
10393685 GGGAGAAGGGGG
1 GGGAGAAGGGGG
10393697 AACTCGGTGT
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
58 3 0.05
59 60 0.94
60 1 0.02
ACGTcount: A:0.35, C:0.03, G:0.40, T:0.22
Consensus pattern (59 bp):
GGGAGAAGGGGGTGATTATTTTAGGGATTCGAAGAAGGGAAAATGGAGGAAATAAATCA
Found at i:10394154 original size:230 final size:228
Alignment explanation
Indices: 10393808--10394292 Score: 498
Period size: 230 Copynumber: 2.1 Consensus size: 228
10393798 AATTGCGGCA
* * * * *
10393808 TTTTAACAT-AAACGCCACTAAAAAAACAAACAAAACGACACCGTTTTGATATAGACAGAATAAA
1 TTTTAACCTAAAACGCCACT-AAAAATCGAATAAAACGACACCGTTTTGATATAAACAGAATAAA
* * * * *
10393872 CTTTAATGGCGTTTTTCTGTAGCGCCGCTAAAGGCAAATCAATTGCGGCGTTTCACCCTA-AAAT
65 CATTAATGGCGTTTTCCTGTAGCGCCGCTAAAGGCAAACCAATTGCGGCGTTTCAACC-ACAAAC
* * *
10393936 GCCACTAAAAATCCAAAAAAACGACGA-CGTTTTCATATGAACAGAATAACATTTAGTGGCGTTT
129 GCCACTAAAAATCCAAAAAAACGAC-ACCGTTTTCATATAAACAAAATAACACTTAGTGGC-TTT
* *
10394000 TATCACCAAGCGTCGCTAAAGGCGAA-ACTATTCTGACG
192 TATAACCAAGCGCCGCTAAA-GC-AACACTATTCTGACG
* * * * *
10394038 TTTTACCCTAAAACGCCACTAATAATCGAATAAAACTACATCGTTTTGATATAAACA-AATTAAC
1 TTTTAACCTAAAACGCCACTAAAAATCGAATAAAACGACACCGTTTTGATATAAACAGAA-TAAA
* * * * *
10394102 CATTAGTGGCGTTTATACCT-TAGCGCCGCTAAA-TCAAACCTATTGTGGCGTTTGAACCACAAA
65 CATTAATGGCGTTT-T-CCTGTAGCGCCGCTAAAGGCAAACCAATTGCGGCGTTTCAACCACAAA
* * * * * * *
10394165 CGCCACTAAAAATCTATAAAAACTACACCTTTTTTATCTAAACAAAATAACCCTTAGTGGCTTTT
128 CGCCACTAAAAATCCAAAAAAACGACACCGTTTTCATATAAACAAAATAACACTTAGTGGCTTTT
** * * * *
10394230 ATAACCTTGCGCCGCTAAATCAACCCTATTGTGGCG
193 ATAACCAAGCGCCGCTAAAGCAACACTATTCTGACG
10394266 TTTTAACCTAAAACGCCACTAAAAATC
1 TTTTAACCTAAAACGCCACTAAAAATC
10394293 CAAAGAAAAC
Statistics
Matches: 208, Mismatches: 40, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
227 2 0.01
228 35 0.17
229 23 0.11
230 122 0.59
231 24 0.12
232 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (228 bp):
TTTTAACCTAAAACGCCACTAAAAATCGAATAAAACGACACCGTTTTGATATAAACAGAATAAAC
ATTAATGGCGTTTTCCTGTAGCGCCGCTAAAGGCAAACCAATTGCGGCGTTTCAACCACAAACGC
CACTAAAAATCCAAAAAAACGACACCGTTTTCATATAAACAAAATAACACTTAGTGGCTTTTATA
ACCAAGCGCCGCTAAAGCAACACTATTCTGACG
Found at i:10394187 original size:114 final size:114
Alignment explanation
Indices: 10393755--10394303 Score: 455
Period size: 114 Copynumber: 4.8 Consensus size: 114
10393745 CAAAATAAAT
* * * * * *
10393755 TAACATTTGCGGCGTTT-TCACC-TAGCGCCGCTAAAGGCAAACCAATTGCGGCATTTTAACAT-
1 TAACATTAGTGGCGTTTATCACCTTAGCGCCGCTAAAGGCAAACCTATTGTGGCGTTTTAACCTA
* *
10393817 AAACGCCACTAAAAAAACAAACAAAACGACACCGTTTTGATATAGACAGAA
66 AAACGCCACT-AAAAATCAAACAAAACGACACCGTTTTGATATAAACA-AA
* * * * * * * *
10393868 TAAACTTTAATGGCGTTT-T--TCTGTAGCGCCGCTAAAGGCAAATCAATTGCGGCGTTTCACCC
1 T-AACATTAGTGGCGTTTATCACCT-TAGCGCCGCTAAAGGCAAACCTATTGTGGCGTTTTAACC
* * *
10393930 TAAAATGCCACTAAAAATCCAAA-AAAACGACGA-CGTTTTCATATGAACAGAA
64 TAAAACGCCACTAAAAAT-CAAACAAAACGAC-ACCGTTTTGATATAAACA-AA
* * * * *
10393982 TAACATTTAGTGGCGTTTTATCACC-AAGCGTCGCTAAAGGCGAAA-CTATTCTGACGTTTTACC
1 TAACA-TTAGTGGCG-TTTATCACCTTAGCGCCGCTAAAGGC-AAACCTATTGTGGCGTTTTAAC
* * * * *
10394045 CTAAAACGCCACTAATAATCGAATAAAACTACATCGTTTTGATATAAACAAA
63 CTAAAACGCCACTAAAAATCAAACAAAACGACACCGTTTTGATATAAACAAA
* *
10394097 TTAACCATTAGTGGCGTTTAT-ACCTTAGCGCCGCTAAA-TCAAACCTATTGTGGCGTTTGAACC
1 -TAA-CATTAGTGGCGTTTATCACCTTAGCGCCGCTAAAGGCAAACCTATTGTGGCGTTTTAACC
* * * * *
10394160 -ACAAACGCCACTAAAAATCTATA-AAAACTACACCTTTTTTATCTAAACAAAA
64 TA-AAACGCCACTAAAAATC-AAACAAAACGACACCGTTTTGATATAAAC-AAA
* * * * *
10394212 TAACCCTTAGTGGCTTTTATAACCTT-GCGCCGCTAAA-TCAACCCTATTGTGGCGTTTTAACCT
1 TAA-CATTAGTGGCGTTTATCACCTTAGCGCCGCTAAAGGCAAACCTATTGTGGCGTTTTAACCT
*
10394275 AAAACGCCACTAAAAATCCAAAGAAAACG
65 AAAACGCCACTAAAAAT-CAAACAAAACG
10394304 GTGTCGTCTT
Statistics
Matches: 360, Mismatches: 51, Indels: 48
0.78 0.11 0.10
Matches are distributed among these distances:
112 1 0.00
113 8 0.02
114 212 0.59
115 55 0.15
116 78 0.22
117 5 0.01
118 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.26
Consensus pattern (114 bp):
TAACATTAGTGGCGTTTATCACCTTAGCGCCGCTAAAGGCAAACCTATTGTGGCGTTTTAACCTA
AAACGCCACTAAAAATCAAACAAAACGACACCGTTTTGATATAAACAAA
Found at i:10395206 original size:45 final size:44
Alignment explanation
Indices: 10395149--10395252 Score: 129
Period size: 45 Copynumber: 2.3 Consensus size: 44
10395139 GTTTAATTAG
* *
10395149 GGTTTTAAAGGTTATAGTTTAGTGTTTA-GTGTTTAGGGGGTTTA
1 GGTTTTAGAGGTTATAGATTAGTGTTTATGT-TTTAGGGGGTTTA
**
10395193 GTGTTTTAGAGGTTATAGATTAGTGTTTATGTTTTTTGGGGTTTAA
1 G-GTTTTAGAGGTTATAGATTAGTGTTTATGTTTTAGGGGGTTT-A
*
10395239 GGTTTTAGGGGTTA
1 GGTTTTAGAGGTTA
10395253 AATGACTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
44 1 0.02
45 47 0.90
46 4 0.08
ACGTcount: A:0.19, C:0.00, G:0.32, T:0.49
Consensus pattern (44 bp):
GGTTTTAGAGGTTATAGATTAGTGTTTATGTTTTAGGGGGTTTA
Found at i:10395316 original size:41 final size:41
Alignment explanation
Indices: 10395259--10395549 Score: 257
Period size: 41 Copynumber: 7.1 Consensus size: 41
10395249 GTTAAATGAC
*
10395259 TTTTAGCGGCGTTTTACCAAAAACGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCTGGT
* * * *
10395300 TTTTAGTGGCGTTTTA-CACAAAGCGCCGCAAATT-CTTTGGT
1 TTTTAGCGGCGTTTTACCA-AAAACGCCGC-TATTGCTCTGGT
* * * * *
10395341 TTTTAGTGGCGTTTTACCAAAAGCGCCACTAATGCTCTGGC
1 TTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCTGGT
* **** * * *
10395382 TTTTAGCGGTGTTTTTGGTAAAACGCCACTATTGCTATGTT
1 TTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCTGGT
* ** * * **
10395423 TTTTGGCGGCGTTTT-CTGTAAAACGCCGCTATTTCTATAAT
1 TTTTAGCGGCGTTTTAC-CAAAAACGCCGCTATTGCTCTGGT
* * *
10395464 TTTTAGCGTCGTTTTAACTAAAAATGCCGCTATTGCTCT-GT
1 TTTTAGCGGCGTTTT-ACCAAAAACGCCGCTATTGCTCTGGT
10395505 TTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCTGCGT
1 TTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCTG-GT
10395547 TTT
1 TTT
10395550 ACAATTTTTG
Statistics
Matches: 202, Mismatches: 39, Indels: 17
0.78 0.15 0.07
Matches are distributed among these distances:
40 25 0.12
41 151 0.75
42 25 0.12
43 1 0.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCTGGT
Found at i:10395528 original size:123 final size:123
Alignment explanation
Indices: 10395258--10395549 Score: 291
Period size: 123 Copynumber: 2.4 Consensus size: 123
10395248 GGTTAAATGA
* * * *
10395258 CTTTTAGCGGCGTTTTACCAAAAACGCCGCTAATGCTCTGGTTTTTAGTGGCGTTTTACACAAAG
1 CTTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTATGGTTTTTAGCGGCGTTTTACACAAAA
* ** * *
10395323 CGCCGCAAATTCTTTGGTTTTTAGTGGCGTTTTACCAAAAGCGCCACTAATGCTCTGG
66 CGCCGCAAATTCTATAATTTTTAGCGGCGTTTTACCAAAAACGCCACTAATGCTCTGG
* **** * * * **
10395381 CTTTTAGCGGTGTTTTTGGTAAAACGCCACTATTGCTATGTTTTTTGGCGGCGTTTT-CTGTAAA
1 CTTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTATGGTTTTTAGCGGCGTTTTAC-ACAAA
* * * * * * *
10395445 ACGCCGCTATTTCTATAATTTTTAGCGTCGTTTTAACTAAAAATGCCGCTATTGCTCT-G
65 ACGCCGCAAATTCTATAATTTTTAGCGGCGTTTT-ACCAAAAACGCCACTAATGCTCTGG
* *
10395504 TTTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCTGCGTTTT
1 CTTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTATG-GTTTT
10395550 ACAATTTTTG
Statistics
Matches: 131, Mismatches: 35, Indels: 5
0.77 0.20 0.03
Matches are distributed among these distances:
122 1 0.01
123 108 0.82
124 22 0.17
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (123 bp):
CTTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTATGGTTTTTAGCGGCGTTTTACACAAAA
CGCCGCAAATTCTATAATTTTTAGCGGCGTTTTACCAAAAACGCCACTAATGCTCTGG
Found at i:10408610 original size:21 final size:23
Alignment explanation
Indices: 10408586--10408643 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 23
10408576 TTCCTAACTT
* *
10408586 AACTTTCTTTTGA-T-ATCTTGC
1 AACTTTCTTTTCATTGATCTTAC
*
10408607 AACTTTCGTTTTCATTGATCTTAT
1 AACTTTC-TTTTCATTGATCTTAC
10408631 AACTTTCTTTTCA
1 AACTTTCTTTTCA
10408644 CTAAGATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 7 0.23
22 5 0.16
23 7 0.23
24 12 0.39
ACGTcount: A:0.21, C:0.19, G:0.07, T:0.53
Consensus pattern (23 bp):
AACTTTCTTTTCATTGATCTTAC
Found at i:10410560 original size:41 final size:41
Alignment explanation
Indices: 10410503--10410585 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
10410493 TAGTAATTCT
*
10410503 TAATAGCAGCAGCACTCTGGCGTAGTCCTTCTAGCAAACAG
1 TAATAGCAGCAGCACTCTGGCGTAGTCCTTCTAACAAACAG
*
10410544 TAATAGCAGCAGCACTCTGGCGTAGTCCTTCTAATAAACAG
1 TAATAGCAGCAGCACTCTGGCGTAGTCCTTCTAACAAACAG
10410585 T
1 T
10410586 CTTTTCAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24
Consensus pattern (41 bp):
TAATAGCAGCAGCACTCTGGCGTAGTCCTTCTAACAAACAG
Found at i:10411727 original size:20 final size:18
Alignment explanation
Indices: 10411680--10411728 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
10411670 GTAGATAAAC
10411680 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
10411697 ATTAAGA-TAATCATTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
10411717 ATTAAATTAATA
1 ATTAAATTAATA
10411729 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:10411774 original size:37 final size:38
Alignment explanation
Indices: 10411680--10411777 Score: 100
Period size: 37 Copynumber: 2.6 Consensus size: 38
10411670 GTAGATAAAC
*
10411680 ATTAAATTAA-ATTTAA-TATTAAGATAATCATTTTAAT
1 ATTAAATTAATATTAAACTATTAAGATAATCA-TTTAAT
*
10411717 ATTAAATTAATA-AAATACTATTAAGATAAGT-A-TTAA-
1 ATTAAATTAATATTAA-ACTATTAAGATAA-TCATTTAAT
10411753 ATTAAATTTAATATTAAACTATTAA
1 ATTAAA-TTAATATTAAACTATTAA
10411778 AAATAATATT
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
36 6 0.12
37 29 0.56
38 4 0.08
39 12 0.23
40 1 0.02
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (38 bp):
ATTAAATTAATATTAAACTATTAAGATAATCATTTAAT
Found at i:10411788 original size:37 final size:37
Alignment explanation
Indices: 10411712--10411788 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 37
10411702 GATAATCATT
*
10411712 TTAATATTAAATTAATAAAATACTATTAAGATAAGTA
1 TTAATATTAAATTAATAAAATACTATTAAAATAAGTA
*
10411749 TTAA-ATTAAATTTAATATTAA-ACTATTAAAAATAA-TA
1 TTAATATTAAA-TTAATA-AAATACTATT-AAAATAAGTA
10411786 TTA
1 TTA
10411789 TTTTTGGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
36 6 0.17
37 21 0.60
38 8 0.23
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (37 bp):
TTAATATTAAATTAATAAAATACTATTAAAATAAGTA
Found at i:10418734 original size:12 final size:12
Alignment explanation
Indices: 10418717--10418748 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
10418707 CATGTTATGG
10418717 CACACGGCTTAC
1 CACACGGCTTAC
*
10418729 CACACGGCTTAT
1 CACACGGCTTAC
10418741 CACACGGC
1 CACACGGC
10418749 CATGTAGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.25, C:0.41, G:0.19, T:0.16
Consensus pattern (12 bp):
CACACGGCTTAC
Found at i:10436557 original size:2 final size:2
Alignment explanation
Indices: 10436550--10436583 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
10436540 TGTGTAATGG
10436550 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10436584 GTGTGTGTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10439488 original size:17 final size:17
Alignment explanation
Indices: 10439466--10439500 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
10439456 CCTGTCAGAA
10439466 AATTCAATCGACGAAAT
1 AATTCAATCGACGAAAT
*
10439483 AATTCAATCGATGAAAT
1 AATTCAATCGACGAAAT
10439500 A
1 A
10439501 TCGTTTACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (17 bp):
AATTCAATCGACGAAAT
Found at i:10440907 original size:10 final size:9
Alignment explanation
Indices: 10440890--10440933 Score: 61
Period size: 10 Copynumber: 4.7 Consensus size: 9
10440880 TCAAAAGAAT
10440890 TATTAAAAA
1 TATTAAAAA
10440899 TATTAAAAA
1 TATTAAAAA
10440908 TATTTAAAAA
1 TA-TTAAAAA
10440918 TATTTAAAAA
1 TA-TTAAAAA
*
10440928 TTTTAA
1 TATTAA
10440934 TTTTTTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
9 15 0.45
10 18 0.55
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
TATTAAAAA
Found at i:10440916 original size:19 final size:19
Alignment explanation
Indices: 10440887--10440933 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 19
10440877 AATTCAAAAG
10440887 AATTATTAAAAATA-TTAAA
1 AATT-TTAAAAATATTTAAA
10440906 AATATTTAAAAATATTTAAA
1 AAT-TTTAAAAATATTTAAA
10440926 AATTTTAA
1 AATTTTAA
10440934 TTTTTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AATTTTAAAAATATTTAAA
Found at i:10442526 original size:24 final size:24
Alignment explanation
Indices: 10442497--10442543 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
10442487 TTGTTGGTGT
*
10442497 TTTGTGGTCTC-TTGTGATAGGTCA
1 TTTGTGGCCTCTTTG-GATAGGTCA
10442521 TTTGTGGCCTCTTTGGATAGGTC
1 TTTGTGGCCTCTTTGGATAGGTC
10442544 GGTGGTGCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.11, C:0.15, G:0.30, T:0.45
Consensus pattern (24 bp):
TTTGTGGCCTCTTTGGATAGGTCA
Found at i:10443442 original size:27 final size:28
Alignment explanation
Indices: 10443369--10443425 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
10443359 ATTATATCAG
10443369 AATAAGAGAGGAGAGTGTTTGGTGGTTT
1 AATAAGAGAGGAGAGTGTTTGGTGGTTT
10443397 AATAAGAGAGGAGAGTGTTTGGTGGTTT
1 AATAAGAGAGGAGAGTGTTTGGTGGTTT
10443425 A
1 A
10443426 TAAATTGATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.39, T:0.32
Consensus pattern (28 bp):
AATAAGAGAGGAGAGTGTTTGGTGGTTT
Found at i:10444513 original size:3 final size:3
Alignment explanation
Indices: 10444505--10444538 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
10444495 TTCTATTCTG
10444505 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
10444539 TTCTGTGTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:10446286 original size:29 final size:28
Alignment explanation
Indices: 10446220--10446306 Score: 133
Period size: 28 Copynumber: 3.1 Consensus size: 28
10446210 TATTTTGGAG
10446220 AGAAGAGA--TTTTTTTTTTGAGATTCA
1 AGAAGAGATTTTTTTTTTTTGAGATTCA
10446246 AGAAGAGATTTTTTTTTTTTGAGATTCA
1 AGAAGAGATTTTTTTTTTTTGAGATTCA
* *
10446274 AGAGGGGATTTTTCTTTTTTTGAGATTCA
1 AGAAGAGATTTTT-TTTTTTTGAGATTCA
10446303 AGAA
1 AGAA
10446307 CAAAAAATCA
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
26 8 0.15
28 29 0.53
29 18 0.33
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.46
Consensus pattern (28 bp):
AGAAGAGATTTTTTTTTTTTGAGATTCA
Found at i:10446770 original size:3 final size:3
Alignment explanation
Indices: 10446762--10446806 Score: 81
Period size: 3 Copynumber: 14.7 Consensus size: 3
10446752 TGCATTTTAA
10446762 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA
10446807 GTGTATATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:10446909 original size:3 final size:3
Alignment explanation
Indices: 10446901--10446933 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
10446891 TGTATTTCTA
10446901 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
10446934 ATGGTAGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:10447059 original size:16 final size:15
Alignment explanation
Indices: 10447028--10447070 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
10447018 CCTTCATTCC
*
10447028 ATTATTATTATTACT
1 ATTATTATTTTTACT
10447043 ATTATTATATTTTACT
1 ATTATTAT-TTTTACT
*
10447059 ATCATTATTTTT
1 ATTATTATTTTT
10447071 CATACGTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTATTATTTTTACT
Found at i:10447196 original size:16 final size:16
Alignment explanation
Indices: 10447175--10447206 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
10447165 CTATTGTTAC
10447175 TGTTATTATCATCACT
1 TGTTATTATCATCACT
*
10447191 TGTTATTCTCATCACT
1 TGTTATTATCATCACT
10447207 ATTATTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (16 bp):
TGTTATTATCATCACT
Found at i:10447248 original size:11 final size:13
Alignment explanation
Indices: 10447218--10447249 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
10447208 TTATTATAAT
10447218 TTATTATTGTTAC
1 TTATTATTGTTAC
10447231 TTATTATT-TTAC
1 TTATTATTGTTAC
10447243 -TATTATT
1 TTATTATT
10447250 ATCTAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.37
12 4 0.21
13 8 0.42
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.66
Consensus pattern (13 bp):
TTATTATTGTTAC
Found at i:10447450 original size:22 final size:22
Alignment explanation
Indices: 10447420--10447480 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
10447410 TTATTATATC
*
10447420 TTTTACTATTATTATTGTTGTA
1 TTTTACTATTATTATTGTTATA
* * *
10447442 TTTTTCTATTATTGTTATTATA
1 TTTTACTATTATTATTGTTATA
* *
10447464 TTTTCCT-TTATTTTTGT
1 TTTTACTATTATTATTGT
10447481 ATTTACTTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 8 0.25
22 24 0.75
ACGTcount: A:0.18, C:0.07, G:0.07, T:0.69
Consensus pattern (22 bp):
TTTTACTATTATTATTGTTATA
Found at i:10447454 original size:3 final size:3
Alignment explanation
Indices: 10447206--10447435 Score: 75
Period size: 3 Copynumber: 77.3 Consensus size: 3
10447196 TTCTCATCAC
* * *
10447206 TAT TAT TAT AATT TAT TAT TGT TACT TAT TAT T-T TAC TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
* * * * * * * *
10447252 CTAA TA- TAT CAT CAT CAT CAT TAT T-T TCAT TAT AACT TAA TA- GAT
1 -TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TA-T TAT TAT TAT
* * *
10447297 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG CAC TACT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
* * * * ** * *
10447342 TAC TAT TAT T-T AAT ATAT TAT TTT TAC TAT TAT CGT CA- TAT TGT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
10447386 TAC TAT TAC TAT TA- TAT TAT TA- TGT TAT TA- TAT CTTT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT
10447429 TAT TAT T
1 TAT TAT T
10447436 GTTGTATTTT
Statistics
Matches: 166, Mismatches: 43, Indels: 36
0.68 0.18 0.15
Matches are distributed among these distances:
2 16 0.10
3 134 0.81
4 16 0.10
ACGTcount: A:0.32, C:0.09, G:0.03, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:10460024 original size:206 final size:205
Alignment explanation
Indices: 10459268--10460194 Score: 1448
Period size: 205 Copynumber: 4.5 Consensus size: 205
10459258 TAGGCCGCAG
* * * * *
10459268 CATAACAGATCTGGCCTACAGATG-TTATACTGAAGCAGATCCAAGATGGTTTGGCGTTCTTGTG
1 CATAGCAGATCTGACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTG
*
10459332 TTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGATGAAGCAAATCT
66 TTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGATGAAGCAAATCT
* * * * **
10459397 AAGATGATTTGTCGTCTTTGTATTGTCAGAGAACAAATCGAAGTTTGGTATCTTCACTTTGATGG
131 AAGATGATTTGTCGTCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTCAATGG
10459462 AGAGCAGACA
196 AGAGCAGACA
* *
10459472 CATAGCAGATCTCACCTTCAGATGATTT-CACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGT
1 CATAGCAGATCTGACCTTCAGATG-TTTATACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGT
*
10459536 GTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTTATTACGATGAAGCAAATC
65 GTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGATGAAGCAAATC
* * * * **
10459601 TAAGATGATTTGTCATCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGATG
130 TAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTCAATG
10459666 GAGAGCAGACA
195 GAGAGCAGACA
* *
10459677 CGTAGCAGATCTCG-CCTTCAGATGATTT-CACTGAAGCAGATCCAAGATGGTTTGGCATCCTTG
1 CATAGCAGATCT-GACCTTCAGATG-TTTATACTGAAGCAGATCCAAGATGGTTTGGCATCCTTG
10459740 TGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGATGAAGCAAAT
64 TGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGATGAAGCAAAT
10459805 CTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTCAAT
129 CTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTCAAT
*
10459870 GGAGAGCAGATA
194 GGAGAGCAGACA
*
10459882 CATAGCAGATCTGACCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGGCATCCTTGT
1 CATAGCAGATCTGACCTTCAGATGTTTATACTGAAGC-AGATCCAAGATGGTTTGGCATCCTTGT
** * *
10459947 ACTTATAAGGAACAAATCGAAGACATAGTTGATTTGGCTTTCACGTGATTACGATGAAGCAAATC
65 GTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGATGAAGCAAATC
* *
10460012 AAAGATGATTTGTGGTCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTCAATG
130 TAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTCAATG
*
10460077 GAGAGCAGATA
195 GAGAGCAGACA
* *
10460088 CATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGGCATCCTTGT
1 CATAGCAGATCTGACCTTCAGATGTTTATACTGAAGC-AGATCCAAGATGGTTTGGCATCCTTGT
* * *
10460153 GCTTACAAGGAACAAATCGAAGACATAGCAGATTTGACTTTC
65 GTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTC
10460195 GGATGTTCCC
Statistics
Matches: 679, Mismatches: 38, Indels: 10
0.93 0.05 0.01
Matches are distributed among these distances:
204 24 0.04
205 391 0.58
206 264 0.39
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (205 bp):
CATAGCAGATCTGACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTG
TTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGATGAAGCAAATCT
AAGATGATTTGTCGTCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTCAATGG
AGAGCAGACA
Found at i:10460382 original size:44 final size:44
Alignment explanation
Indices: 10460334--10460621 Score: 286
Period size: 44 Copynumber: 6.6 Consensus size: 44
10460324 CCGTATTGTC
* *
10460334 AGGGAACAAGTTGAAAATAGTAGATTTGGCATCCCTGTGCTTAT
1 AGGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTGTGCTTAT
* * * * *
10460378 AGGGAGC-AGATCGAAGATAGCAGATCTGACATTCCTGTGCTTA-
1 AGGGAACAAG-TTGAAGATAGCAGATTTGGCATCCCTGTGCTTAT
* ** *
10460421 CGGTGAAGC-AGATTGAAGATTTCAGCA--TGGAATCCCTGTGCTTAT
1 AGG-GAA-CAAG-TTGAAGATAGCAG-ATTTGGCATCCCTGTGCTTAT
* *
10460466 AGGGATCAAGTTGAAGATAGCAGATTTGGCATCCCTGTGTTTAT
1 AGGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTGTGCTTAT
* * *
10460510 AGGGAATAAGTTGAAGACAGCAGATTTGGCATCCCTGTGTTTAT
1 AGGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTGTGCTTAT
* * *
10460554 AGGGAATAAGTTGAAGACAGCAGATTTGGCATCCCTGTGTTTAT
1 AGGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTGTGCTTAT
10460598 -GAGGAAC-AGATTGAAGA-AGCAGAT
1 AG-GGAACAAG-TTGAAGATAGCAGAT
10460622 CAAGAACTCA
Statistics
Matches: 209, Mismatches: 25, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
42 1 0.00
43 26 0.12
44 165 0.79
45 16 0.08
46 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (44 bp):
AGGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTGTGCTTAT
Found at i:10461118 original size:29 final size:28
Alignment explanation
Indices: 10461061--10461138 Score: 129
Period size: 28 Copynumber: 2.8 Consensus size: 28
10461051 AGAGAAGAGA
10461061 TTTTTTTTTGAGATTCAAGAAGAGATTT
1 TTTTTTTTTGAGATTCAAGAAGAGATTT
* *
10461089 TTTTTTTTTGAGATTCAAGAGGGGATTT
1 TTTTTTTTTGAGATTCAAGAAGAGATTT
10461117 TTCTTTTTTTGAGATTCAAGAA
1 TT-TTTTTTTGAGATTCAAGAA
10461139 CAAAAAATCA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
28 28 0.61
29 18 0.39
ACGTcount: A:0.26, C:0.05, G:0.19, T:0.50
Consensus pattern (28 bp):
TTTTTTTTTGAGATTCAAGAAGAGATTT
Found at i:10461601 original size:3 final size:3
Alignment explanation
Indices: 10461593--10461634 Score: 75
Period size: 3 Copynumber: 13.7 Consensus size: 3
10461583 TGCATTTTAA
10461593 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA
10461635 GTGTATATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:10461737 original size:3 final size:3
Alignment explanation
Indices: 10461729--10461761 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
10461719 TGTATTTCTA
10461729 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
10461762 ATGGTAGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:10461887 original size:16 final size:15
Alignment explanation
Indices: 10461856--10461898 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
10461846 CCTTCATTCC
*
10461856 ATTATTATTATTACT
1 ATTATTATTTTTACT
10461871 ATTATTATATTTTACT
1 ATTATTAT-TTTTACT
*
10461887 ATCATTATTTTT
1 ATTATTATTTTT
10461899 CATACGTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTATTATTTTTACT
Found at i:10462024 original size:16 final size:16
Alignment explanation
Indices: 10462003--10462034 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
10461993 CTATTGTTAC
10462003 TGTTATTATCATCACT
1 TGTTATTATCATCACT
*
10462019 TGTTATTCTCATCACT
1 TGTTATTATCATCACT
10462035 ATTATTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (16 bp):
TGTTATTATCATCACT
Found at i:10462076 original size:11 final size:13
Alignment explanation
Indices: 10462046--10462077 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
10462036 TTATTATAAT
10462046 TTATTATTGTTAC
1 TTATTATTGTTAC
10462059 TTATTATT-TTAC
1 TTATTATTGTTAC
10462071 -TATTATT
1 TTATTATT
10462078 ATCTAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.37
12 4 0.21
13 8 0.42
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.66
Consensus pattern (13 bp):
TTATTATTGTTAC
Found at i:10462287 original size:22 final size:22
Alignment explanation
Indices: 10462250--10462317 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
10462240 TATTATGTTA
10462250 TTATATCTTTTACTATTATTATTG
1 TTATAT-TTTT-CTATTATTATTG
* * *
10462274 TTGTATTTTTCTATTATTGTTA
1 TTATATTTTTCTATTATTATTG
*
10462296 TTATATTTTTCT-TTATTTTTG
1 TTATATTTTTCTATTATTATTG
10462317 T
1 T
10462318 ATTTACTTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
21 8 0.21
22 21 0.55
23 4 0.11
24 5 0.13
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (22 bp):
TTATATTTTTCTATTATTATTG
Found at i:10462291 original size:3 final size:3
Alignment explanation
Indices: 10462034--10462272 Score: 93
Period size: 3 Copynumber: 80.3 Consensus size: 3
10462024 TTCTCATCAC
* * *
10462034 TAT TAT TAT AATT TAT TAT TGT TACT TAT TAT T-T TAC TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
* * * * * * * *
10462080 CTAA TA- TAT CAT CAT CAT CAT TAT T-T TCAT TAT AACT TAA TA- GAT
1 -TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TA-T TAT TAT TAT
* * *
10462125 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG CAC TACT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
* * * * ** *
10462174 T-T TAT TAC TAT TAT T-T AAT ATAT TAT TTT TAC TAT TAT CGT CA-
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
10462217 TAT TGT TAC TAT TAC TAT TA- TAT TAT TA- TGT TAT TA- TAT CTTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
*
10462260 TAC TAT TAT TAT T
1 TAT TAT TAT TAT T
10462273 GTTGTATTTT
Statistics
Matches: 175, Mismatches: 43, Indels: 36
0.69 0.17 0.14
Matches are distributed among these distances:
2 16 0.09
3 143 0.82
4 16 0.09
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:10464145 original size:10 final size:10
Alignment explanation
Indices: 10464130--10464163 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
10464120 TTTTTATTAT
10464130 AAAAATTTTA
1 AAAAATTTTA
*
10464140 AAAAATTATAA
1 AAAAATT-TTA
10464151 AAAAATTTTA
1 AAAAATTTTA
10464161 AAA
1 AAA
10464164 TATATATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
AAAAATTTTA
Found at i:10464388 original size:20 final size:22
Alignment explanation
Indices: 10464363--10464408 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
10464353 ATTTTTATAC
10464363 TAAAAAATATT-AAATTTAA-A
1 TAAAAAATATTAAAATTTAAGA
*
10464383 T-AAAAATCTTAAAATTTAAGA
1 TAAAAAATATTAAAATTTAAGA
10464404 TAAAA
1 TAAAA
10464409 TTAGTGATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 8 0.36
20 9 0.41
21 2 0.09
22 3 0.14
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
TAAAAAATATTAAAATTTAAGA
Found at i:10464389 original size:19 final size:21
Alignment explanation
Indices: 10464365--10464408 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
10464355 TTTTATACTA
10464365 AAAAATATT-AAATTTAA-AT
1 AAAAATATTAAAATTTAAGAT
*
10464384 AAAAATCTTAAAATTTAAGAT
1 AAAAATATTAAAATTTAAGAT
10464405 AAAA
1 AAAA
10464409 TTAGTGATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.36
20 8 0.36
21 6 0.27
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (21 bp):
AAAAATATTAAAATTTAAGAT
Found at i:10472136 original size:20 final size:20
Alignment explanation
Indices: 10472107--10472158 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
10472097 AAAAAAATTA
10472107 AAAAAT-ATTTTTATACTTTT
1 AAAAATAATTTTTA-ACTTTT
*
10472127 -AAAATAATTTTTAATTTTT
1 AAAAATAATTTTTAACTTTT
10472146 AAAAATAATTTTT
1 AAAAATAATTTTT
10472159 TGATTTTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 10 0.34
20 19 0.66
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
AAAAATAATTTTTAACTTTT
Found at i:10472165 original size:20 final size:19
Alignment explanation
Indices: 10472108--10472187 Score: 72
Period size: 21 Copynumber: 4.0 Consensus size: 19
10472098 AAAAAATTAA
*
10472108 AAAAT-ATTTTTATACTTTT
1 AAAATAATTTTTA-ATTTTT
10472127 AAAATAATTTTTAATTTTT
1 AAAATAATTTTTAATTTTT
*
10472146 AAAAATAATTTTTTGATTTTT
1 -AAAATAA-TTTTTAATTTTT
* *
10472167 ATAAAAAATTAATTAATTTTT
1 A-AAATAATT-TTTAATTTTT
10472188 GATGTGGCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
19 10 0.20
20 17 0.33
21 24 0.47
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (19 bp):
AAAATAATTTTTAATTTTT
Found at i:10472176 original size:21 final size:19
Alignment explanation
Indices: 10472104--10472176 Score: 74
Period size: 21 Copynumber: 3.6 Consensus size: 19
10472094 TTTAAAAAAA
*
10472104 TTAAAAAATATTTTTATACTT
1 TTAAAAAA-ATTTTT-TATTT
* *
10472125 TTAAAATAATTTTTAATTT
1 TTAAAAAAATTTTTTATTT
10472144 TTAAAAATAATTTTTTGATTT
1 TTAAAAA-AATTTTTT-ATTT
10472165 TTATAAAAAATT
1 TTA-AAAAAATT
10472177 AATTAATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
19 9 0.20
20 13 0.30
21 18 0.41
22 4 0.09
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (19 bp):
TTAAAAAAATTTTTTATTT
Found at i:10484176 original size:31 final size:32
Alignment explanation
Indices: 10484135--10484239 Score: 94
Period size: 31 Copynumber: 3.4 Consensus size: 32
10484125 TTTTAATAAC
*
10484135 TTAATGTAATATTTATCTAGTTAGA-ATTTTA
1 TTAATTTAATATTTATCTAGTTAGATATTTTA
* * **
10484166 TTAATTTAATA-TTA-ATA-TGAGATATTAAA
1 TTAATTTAATATTTATCTAGTTAGATATTTTA
* * *
10484195 TTTAATTTAATATTTATCTTGATA-ATATTTTG
1 -TTAATTTAATATTTATCTAGTTAGATATTTTA
10484227 TTAATTTAATATT
1 TTAATTTAATATT
10484240 AATGTCATTA
Statistics
Matches: 57, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
28 4 0.07
29 6 0.11
30 14 0.25
31 26 0.46
32 6 0.11
33 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (32 bp):
TTAATTTAATATTTATCTAGTTAGATATTTTA
Found at i:10491899 original size:46 final size:46
Alignment explanation
Indices: 10491847--10491938 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
10491837 TCGTATGCAA
*
10491847 ATTTTAAGTGTAAGGAGATTGAGTATTCTGTAGGGGACTTCATTTT
1 ATTTTAAGTGTAAGGAGATTGAGTATTCTATAGGGGACTTCATTTT
*
10491893 ATTTTAAGTGTAAGGAGATTGAGTATTCTATGGGGGACTTCATTTT
1 ATTTTAAGTGTAAGGAGATTGAGTATTCTATAGGGGACTTCATTTT
10491939 TCTCAAGGTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (46 bp):
ATTTTAAGTGTAAGGAGATTGAGTATTCTATAGGGGACTTCATTTT
Found at i:10502328 original size:42 final size:42
Alignment explanation
Indices: 10502267--10502352 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
10502257 AAATGAAGGT
*
10502267 AGCAGAATAGCTATTGGCCTCACTAATACGACCATTTTGTTA
1 AGCAGAATAGCTATCGGCCTCACTAATACGACCATTTTGTTA
*
10502309 AGCAGAATAGCTATCGGCCTCACTAATACGTCCATTTTGTTA
1 AGCAGAATAGCTATCGGCCTCACTAATACGACCATTTTGTTA
10502351 AG
1 AG
10502353 TTAAGTTCGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (42 bp):
AGCAGAATAGCTATCGGCCTCACTAATACGACCATTTTGTTA
Found at i:10502730 original size:92 final size:92
Alignment explanation
Indices: 10502564--10502744 Score: 292
Period size: 92 Copynumber: 2.0 Consensus size: 92
10502554 TAAGCTCATA
* * *
10502564 ATTATTATCGTCGGTTAACCTGACTAGTACTGGGTGCAATTATTGTTGGTTTATCCAACTAGAGT
1 ATTATTATCGTCGATTAACCTGACTAGCACTGGGTGCAATTATTGTTGGTTTATCCAACTAGAGC
* *
10502629 TGGGCTCACAATT-ATTATCGTCGGGTT
66 TAGGATCAC-ATTCATTATCGTCGGGTT
*
10502656 ATTATTATCGTCGATTAACCTGACTGGCACTGGGTGCAATTATTGTTGGTTTATCCAACTAGAGC
1 ATTATTATCGTCGATTAACCTGACTAGCACTGGGTGCAATTATTGTTGGTTTATCCAACTAGAGC
10502721 TAGGATCACATTCATTATCGTCGG
66 TAGGATCACATTCATTATCGTCGG
10502745 TTAATCTGAC
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
91 3 0.04
92 79 0.96
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (92 bp):
ATTATTATCGTCGATTAACCTGACTAGCACTGGGTGCAATTATTGTTGGTTTATCCAACTAGAGC
TAGGATCACATTCATTATCGTCGGGTT
Found at i:10508470 original size:46 final size:46
Alignment explanation
Indices: 10508418--10508772 Score: 421
Period size: 46 Copynumber: 7.7 Consensus size: 46
10508408 AGTGTGCTCT
10508418 CTGATATGAAATGTGTAAGACTC-TGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGAC-CATGGTTGAAAGATACCATGGCAAC
*
10508464 CTGATATGAAATGTGTAAAACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
10508510 CTAATATGAAATGTGTAGGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
10508556 AC-GATATGAAATGTGTAGGACTATGGTTGAAAGATACCATGGCAAC
1 -CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* ** *
10508602 ATGATA-GAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * **
10508648 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *** ** *
10508694 ATGACGGGAAAATGAATAAGAACATGGTTGAAAGATACCATGGCAAC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * *
10508741 ATGACA-GAAAATGAGTAAGACCATAGTTGAAA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAA
10508773 AACACTATGG
Statistics
Matches: 280, Mismatches: 23, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
45 2 0.01
46 234 0.84
47 44 0.16
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:10508670 original size:138 final size:138
Alignment explanation
Indices: 10508420--10508772 Score: 467
Period size: 138 Copynumber: 2.6 Consensus size: 138
10508410 TGTGCTCTCT
* * * * *
10508420 GATATGAAATGTGTAAGACTCTGGTTGAAAGATACCATGGCAACCTGATATG-AAATGTGTAAAA
1 GATATGAAATGTGTAGGACTATGGTTGAAAGATACCATGGCAACATGATA-GAAAATGAGTAAGA
* ** *
10508484 CCATGGTTGAAAGATACCATGGCAACCTAATATGAAATGTGTAGGACCATGGTTGAAAGATACCA
65 CCATGGTTGAAAGATACCATGGCAACCTAACATGAAATGAATAAGACCATGGTTGAAAGATACCA
10508549 TGGCAACAC
130 TGGCAACAC
*
10508558 GATATGAAATGTGTAGGACTATGGTTGAAAGATACCATGGCAACATGATAGAAAATGAATAAGAC
1 GATATGAAATGTGTAGGACTATGGTTGAAAGATACCATGGCAACATGATAGAAAATGAGTAAGAC
* * *
10508623 CATGGTTGAAAGATACCATGGCAGCGTGACATGAAATGAATAAGACCATGGTTGAAAGATACCAT
66 CATGGTTGAAAGATACCATGGCAACCTAACATGAAATGAATAAGACCATGGTTGAAAGATACCAT
*
10508688 GGCAACAT
131 GGCAACAC
*** ** * *
10508696 GACGGGAAAATGAATAAGAAC-ATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAG
1 GATATG-AAATGTGT-AGGACTATGGTTGAAAGATACCATGGCAACATGATAGAAAATGAGTAAG
*
10508760 ACCATAGTTGAAA
64 ACCATGGTTGAAA
10508773 AACACTATGG
Statistics
Matches: 189, Mismatches: 23, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
137 1 0.01
138 125 0.66
139 59 0.31
140 4 0.02
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.22
Consensus pattern (138 bp):
GATATGAAATGTGTAGGACTATGGTTGAAAGATACCATGGCAACATGATAGAAAATGAGTAAGAC
CATGGTTGAAAGATACCATGGCAACCTAACATGAAATGAATAAGACCATGGTTGAAAGATACCAT
GGCAACAC
Found at i:10508742 original size:24 final size:24
Alignment explanation
Indices: 10508669--10508743 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
10508659 TGAATAAGAC
10508669 CATGGTTGAAAGATACCATGGCAA
1 CATGGTTGAAAGATACCATGGCAA
* *
10508693 CATGACG-GGAAA-ATGA--ATAAG-AA
1 CATG--GTTGAAAGAT-ACCAT-GGCAA
10508716 CATGGTTGAAAGATACCATGGCAA
1 CATGGTTGAAAGATACCATGGCAA
10508740 CATG
1 CATG
10508744 ACAGAAAATG
Statistics
Matches: 38, Mismatches: 4, Indels: 18
0.63 0.07 0.30
Matches are distributed among these distances:
21 1 0.03
22 5 0.13
23 11 0.29
24 15 0.39
25 5 0.13
26 1 0.03
ACGTcount: A:0.41, C:0.15, G:0.25, T:0.19
Consensus pattern (24 bp):
CATGGTTGAAAGATACCATGGCAA
Found at i:10508891 original size:13 final size:13
Alignment explanation
Indices: 10508873--10508902 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
10508863 CCGGATGACG
10508873 AATGGTTATATGA
1 AATGGTTATATGA
*
10508886 AATGGTTATGTGA
1 AATGGTTATATGA
10508899 AATG
1 AATG
10508903 CTTACAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.37
Consensus pattern (13 bp):
AATGGTTATATGA
Found at i:10509091 original size:16 final size:17
Alignment explanation
Indices: 10509070--10509102 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
10509060 ATTATGGAGC
10509070 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
10509086 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
10509103 TATAGTTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:10514852 original size:26 final size:26
Alignment explanation
Indices: 10514816--10514925 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
10514806 TGATACAAAT
10514816 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
10514842 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
10514868 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
10514894 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
10514920 TGATAA
1 TGATAA
10514926 GAATTTCATG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:10537772 original size:12 final size:10
Alignment explanation
Indices: 10537716--10537765 Score: 50
Period size: 9 Copynumber: 5.0 Consensus size: 10
10537706 ATAATTCAAC
*
10537716 ATTTTATATAT
1 ATTTT-TATAA
10537727 ATTTTT-TAA
1 ATTTTTATAA
*
10537736 TTTTTTAT-A
1 ATTTTTATAA
10537745 ATTTTTATAA
1 ATTTTTATAA
10537755 AGTTTTTATAA
1 A-TTTTTATAA
10537766 CTATTTTGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 15 0.45
10 4 0.12
11 14 0.42
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (10 bp):
ATTTTTATAA
Found at i:10538416 original size:146 final size:145
Alignment explanation
Indices: 10538144--10538875 Score: 799
Period size: 146 Copynumber: 5.0 Consensus size: 145
10538134 ATTTAAGTAA
** * * * *
10538144 AGTTTCTTTTTATTTGGTAAAAGATTAATTTTGGAGAACTGACGGTTATAGTGTCACTGATCATG
1 AGTTTCTTTTTATTTATTAAAAAATTAATTTTGGAGAATTGACAGTTATAGTGTCACTGATCACG
* * * ** *
10538209 TAACGATTGAGAGAGAGAGT-GGACCACACCCAGTCGAGAGTAAAAAGACAATAATCGCCCTAGC
66 TAACGACTGAGAGAGAGACTAGG-CGACAGACAGTCGAGAGTAAAAAGACCATAATCGCCCTAGC
10538273 AAAAAGGGTCACATTAG
130 AAAAAGGG-CACATTAG
* * *
10538290 CA-TTGCTTTTTATTTATTAAAAAAATAATTTTAGAGAATTG-CTAGTTATAGTGTCACTGATCA
1 -AGTTTCTTTTTATTTATTAAAAAATTAATTTTGGAGAATTGAC-AGTTATAGTGTCACTGATCA
* * * * * *
10538353 CATAACGACTGAGAGAGAGTCTAGGCGACAGAGAGTCAAGAGTAAAAAGACCGTAATCACCCTAG
64 CGTAACGACTGAGAGAGAGACTAGGCGACAGACAGTCGAGAGTAAAAAGACCATAATCGCCCTAG
* *
10538418 CAAAAAGGGTCACGTTAA
129 CAAAAAGGG-CACATTAG
* *
10538436 AGTTTCTTTTTATTTGTTAAAAAATTAATTTTGGAGAATTGACCGTTATAGTGTCACTGATCACG
1 AGTTTCTTTTTATTTATTAAAAAATTAATTTTGGAGAATTGACAGTTATAGTGTCACTGATCACG
* * * * * * * * * * *
10538501 TAACGACTGAGAAATAGTCTGGGTGATAGAGAATCAAGAGTAAAAAGATCATAATCGCGCTAGCG
66 TAACGACTGAGAGAGAGACTAGGCGACAGACAGTCGAGAGTAAAAAGACCATAATCGCCCTAGC-
*
10538566 AAAAA-GGCCCATTAG
130 AAAAAGGGCACATTAG
*
10538581 AGTTTCTTTTTATTTATTAAAAAATTAATTTTGGAGAATTGATAGTTATAGTGTCACT-ACTCAC
1 AGTTTCTTTTTATTTATTAAAAAATTAATTTTGGAGAATTGACAGTTATAGTGTCACTGA-TCAC
* * * * * *
10538645 GTAACGACTGAGAGAGAGAGAGATTGAGAGACAGAAAGTCGAGAGTAAAACGACCATAATTGCCC
65 GTAACGACT--GAGAGAGAGA-CTAG-GCGACAGACAGTCGAGAGTAAAAAGACCATAATCGCCC
10538710 TAGCAAAAAGGGCCACATTAG
126 TAGCAAAAAGGG-CACATTAG
* * * * *
10538731 AGTTTCTTTTTAGTTATTAGAAAATTAATTTTGGAGAATTGACAGTTATAGTATCAGTGATCACA
1 AGTTTCTTTTTATTTATTAAAAAATTAATTTTGGAGAATTGACAGTTATAGTGTCACTGATCACG
* * * * * * * *
10538796 TAACGAATGAGAGAGAGACTAAGCAATAGACACTCGAGCGTAAAAAGACCATAATCACCCTAGCG
66 TAACGACTGAGAGAGAGACTAGGCGACAGACAGTCGAGAGTAAAAAGACCATAATCGCCCTAGCA
10538861 AAAAGGGCTACATTA
131 AAAAGGGC-ACATTA
10538876 CATCCCTTTC
Statistics
Matches: 491, Mismatches: 80, Indels: 29
0.82 0.13 0.05
Matches are distributed among these distances:
144 1 0.00
145 76 0.15
146 273 0.56
147 17 0.03
148 17 0.03
149 35 0.07
150 71 0.14
151 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.27
Consensus pattern (145 bp):
AGTTTCTTTTTATTTATTAAAAAATTAATTTTGGAGAATTGACAGTTATAGTGTCACTGATCACG
TAACGACTGAGAGAGAGACTAGGCGACAGACAGTCGAGAGTAAAAAGACCATAATCGCCCTAGCA
AAAAGGGCACATTAG
Found at i:10538841 original size:295 final size:290
Alignment explanation
Indices: 10538141--10538864 Score: 837
Period size: 295 Copynumber: 2.5 Consensus size: 290
10538131 TACATTTAAG
* * *
10538141 TAAAGTTTCTTTTTATTTGGTAAAAGATTAATTTTGGAGAACTGACGGTTATAGTGTCACTGATC
1 TAAAGTTTCTTTTTATTTGTTAAAA-ATTAATTTTGGAGAATTGACAGTTATAGTGTCACTGATC
* * * * * ** *
10538206 ATGTAACGATTGAGAGAGAGAGTGGACCACACCCAGTCGAGAGTAAAAAGACAATAATCGCCCTA
65 ACGTAACGAATGAGAGAGAGACTGG-CAATAGACAATCGAGAGTAAAAAGAC-ATAATCGCCCTA
*
10538271 GC-AAAAAGGGTCACATTAGCATTGCTTTTTATTTATTAAAAAAATAATTTTAGAGAATTGCTAG
128 GCGAAAAAGGGTCACATTAGCATTGCTTTTTATTTATTAAAAAAATAATTTTAGAGAATTGATAG
** * *
10538335 TTATAGTGTCACTGATCACATAACGACTGAGAGAGAGTCTAGGCGACAGAGAGTCAAGAGTAAAA
193 TTATAGTGTCACTGATCACATAACGACTGAGAGAGAGGATAGGAGACAGAAAGTCAAGAGTAAAA
* * *
10538400 AGACCGTAATCACCCTAGCAAAAAGGGTCACGT
258 AGACCATAATCACCCTAGCAAAAAGGGCCACAT
*
10538433 TAAAGTTTCTTTTTATTTGTTAAAAAATTAATTTTGGAGAATTGACCGTTATAGTGTCACTGATC
1 TAAAGTTTCTTTTTATTTGTT-AAAAATTAATTTTGGAGAATTGACAGTTATAGTGTCACTGATC
* * * * ** * * *
10538498 ACGTAACGACTGAGAAATAGTCTGGGTGATAGAGAATCAAGAGTAAAAAGATCATAATCGCGCTA
65 ACGTAACGAATGAGAGAGAGACT-GGCAATAGACAATCGAGAGTAAAAAGA-CATAATCGCCCTA
* * * *
10538563 GCGAAAAA-GG-CCCATTAG-AGTTTCTTTTTATTTATTAAAAAATTAATTTTGGAGAATTGATA
128 GCGAAAAAGGGTCACATTAGCA-TTGCTTTTTATTTATTAAAAAAATAATTTTAGAGAATTGATA
* * *
10538625 GTTATAGTGTCACT-ACTCACGTAACGACTGAGAGAGAGAGAGATTGAGAGACAGAAAGTCGAGA
192 GTTATAGTGTCACTGA-TCACATAACGACT--GAGAGAGAG-GATAG-GAGACAGAAAGTCAAGA
* **
10538689 GTAAAACGACCATAATTGCCCTAGCAAAAAGGGCCACAT
252 GTAAAAAGACCATAATCACCCTAGCAAAAAGGGCCACAT
* * * * *
10538728 TAGAGTTTCTTTTTAGTTATTAGAAAATTAATTTTGGAGAATTGACAGTTATAGTATCAGTGATC
1 TAAAGTTTCTTTTTATTTGTTA-AAAATTAATTTTGGAGAATTGACAGTTATAGTGTCACTGATC
* * * * *
10538793 ACATAACGAATGAGAGAGAGACTAAGCAATAGACACTCGAGCGTAAAAAGACCATAATCACCCTA
65 ACGTAACGAATGAGAGAGAGACT-GGCAATAGACAATCGAGAGTAAAAAGA-CATAATCGCCCTA
10538858 GCGAAAA
128 GCGAAAA
10538865 GGGCTACATT
Statistics
Matches: 363, Mismatches: 58, Indels: 19
0.82 0.13 0.04
Matches are distributed among these distances:
290 2 0.01
291 71 0.20
292 106 0.29
293 21 0.06
294 3 0.01
295 160 0.44
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (290 bp):
TAAAGTTTCTTTTTATTTGTTAAAAATTAATTTTGGAGAATTGACAGTTATAGTGTCACTGATCA
CGTAACGAATGAGAGAGAGACTGGCAATAGACAATCGAGAGTAAAAAGACATAATCGCCCTAGCG
AAAAAGGGTCACATTAGCATTGCTTTTTATTTATTAAAAAAATAATTTTAGAGAATTGATAGTTA
TAGTGTCACTGATCACATAACGACTGAGAGAGAGGATAGGAGACAGAAAGTCAAGAGTAAAAAGA
CCATAATCACCCTAGCAAAAAGGGCCACAT
Found at i:10539492 original size:23 final size:23
Alignment explanation
Indices: 10539466--10539510 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
10539456 TACTTTTAGC
10539466 CTTTAATAGCTTTTGTGATAATG
1 CTTTAATAGCTTTTGTGATAATG
10539489 CTTTAATAGCTTTTGTGATAAT
1 CTTTAATAGCTTTTGTGATAAT
10539511 AGTACCATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.27, C:0.09, G:0.16, T:0.49
Consensus pattern (23 bp):
CTTTAATAGCTTTTGTGATAATG
Found at i:10543055 original size:12 final size:12
Alignment explanation
Indices: 10543034--10543063 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
10543024 GAATACGCTG
10543034 AATTAAATTTAA
1 AATTAAATTTAA
*
10543046 AATTACATTTAA
1 AATTAAATTTAA
10543058 AATTAA
1 AATTAA
10543064 CTTGAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (12 bp):
AATTAAATTTAA
Found at i:10543108 original size:15 final size:15
Alignment explanation
Indices: 10543057--10543110 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
10543047 ATTACATTTA
*
10543057 AAATTAACTTG-AAT
1 AAATTAAATTGAAAT
* *
10543071 AAATTAGAATTTTAAAA
1 AAATTA-AA-TTGAAAT
10543088 AAATTAAATTGAAAT
1 AAATTAAATTGAAAT
10543103 AAATTAAA
1 AAATTAAA
10543111 AAATTAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
14 6 0.19
15 14 0.44
16 4 0.12
17 8 0.25
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (15 bp):
AAATTAAATTGAAAT
Found at i:10543118 original size:32 final size:31
Alignment explanation
Indices: 10543056--10543119 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 31
10543046 AATTACATTT
* * **
10543056 AAAATTAACTTGAATAAATTAGAATTTTAAA
1 AAAATTAAATTGAATAAATTAAAAAATTAAA
10543087 AAAATTAAATTGAAATAAATTAAAAAATTAAA
1 AAAATTAAATTG-AATAAATTAAAAAATTAAA
10543119 A
1 A
10543120 TGAAAATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 11 0.39
32 17 0.61
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (31 bp):
AAAATTAAATTGAATAAATTAAAAAATTAAA
Found at i:10544242 original size:87 final size:90
Alignment explanation
Indices: 10544135--10544370 Score: 245
Period size: 90 Copynumber: 2.7 Consensus size: 90
10544125 AGCCTTACTT
* * * *
10544135 CTTTTTTTTTTTTTCACTCAATTGAGTACTTAAACTTTTAAAATGCATAAAAAAGGCCCTCAAAC
1 CTTTTTTCTTTTGTCACTCAATTGAGTACTTAAAC-TTCAAAATGCATAAAAAAGACCCTCAAAC
10544200 -TT-AAAAAAA-AAAATAAGCCCCTA
65 TTTCAAAAAAATAAAATAAGCCCCTA
* * *
10544223 CTTTTTTCTTTTGT-ACTCAATTGGGTACTTGAACTTCAAAATGCATAAAAAAGACTCTCAAACT
1 CTTTTTTCTTTTGTCACTCAATTGAGTACTTAAACTTCAAAATGCATAAAAAAGACCCTCAAAC-
* *
10544287 TTTTCAAAAAAATTAATTAAGCCCCTA
65 -TTTCAAAAAAATAAAATAAGCCCCTA
* * * * *
10544314 C-TTTTT-TTTT-ACACCCAATT-AGGTACTTGAACTGTCAAAATACATCAAAAAGACCCT
1 CTTTTTTCTTTTGTCACTCAATTGA-GTACTTAAACT-TCAAAATGCATAAAAAAGACCCT
10544371 TTGACCATTA
Statistics
Matches: 125, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
86 26 0.21
87 18 0.14
88 12 0.10
89 24 0.19
90 32 0.26
91 13 0.10
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (90 bp):
CTTTTTTCTTTTGTCACTCAATTGAGTACTTAAACTTCAAAATGCATAAAAAAGACCCTCAAACT
TTCAAAAAAATAAAATAAGCCCCTA
Found at i:10544535 original size:20 final size:20
Alignment explanation
Indices: 10544501--10544586 Score: 79
Period size: 20 Copynumber: 4.3 Consensus size: 20
10544491 TTTAATAAAA
*
10544501 ATAAAAAAATA-AAAAATTT
1 ATAAAAAATTAGAAAAATTT
* * *
10544520 ATTAAAAATTAGAAAAAATG
1 ATAAAAAATTAGAAAAATTT
*
10544540 ATAAAAAATGTA-AAAGATTT
1 ATAAAAAAT-TAGAAAAATTT
*
10544560 ATAAAAAATT-GTAAAATTTT
1 ATAAAAAATTAG-AAAAATTT
10544580 ATAAAAA
1 ATAAAAA
10544587 TCATAAAATG
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
19 10 0.19
20 41 0.77
21 2 0.04
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (20 bp):
ATAAAAAATTAGAAAAATTT
Found at i:10544593 original size:19 final size:20
Alignment explanation
Indices: 10544557--10544595 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
10544547 ATGTAAAAGA
**
10544557 TTTATAAAAAATTGTAAAAT
1 TTTATAAAAAATCATAAAAT
10544577 TTTAT-AAAAATCATAAAAT
1 TTTATAAAAAATCATAAAAT
10544596 GCATCAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (20 bp):
TTTATAAAAAATCATAAAAT
Done.