Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 10 of 290
Found at i:2865967 original size:44 final size:42
Alignment explanation
Indices: 2865894--2866056 Score: 154
Period size: 44 Copynumber: 3.8 Consensus size: 42
2865884 CCGATATGTG
*
2865894 TTATCGTGTCAGACCACGTCTGGGATGTTGGCATCGACTTATGAT
1 TTAT-GTGTAAGACCACGTCTGGGATGTTGGCATCGA-TT-TGAT
2865939 TTATGTGTAAGACCACGTCTGGGATGTTGGCATCGTATTTG-T
1 TTATGTGTAAGACCACGTCTGGGATGTTGGCATCG-ATTTGAT
* * *
2865981 TTTTGTGTAAGACC-CTGCCTGGGACAG-TGGCATCGATATTTGA-
1 TTATGTGTAAGACCAC-GTCTGGGA-TGTTGGCATCG--ATTTGAT
* ** *
2866024 GTACATGTAAGACCACGTCTAGGATGTTGGCAT
1 TTATGTGTAAGACCACGTCTGGGATGTTGGCAT
2866057 TGCACGAGCT
Statistics
Matches: 100, Mismatches: 11, Indels: 16
0.79 0.09 0.13
Matches are distributed among these distances:
41 1 0.01
42 30 0.30
43 31 0.31
44 33 0.33
45 5 0.05
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (42 bp):
TTATGTGTAAGACCACGTCTGGGATGTTGGCATCGATTTGAT
Found at i:2866055 original size:43 final size:43
Alignment explanation
Indices: 2865885--2866056 Score: 165
Period size: 43 Copynumber: 4.0 Consensus size: 43
2865875 ACATAGGATC
* *
2865885 CGATATGTG-TTATCGTGTCAGACCACGTCTGGGATGTTGGCAT
1 CGATATTTGATTAT-GTGTAAGACCACGTCTGGGATGTTGGCAT
*
2865928 CGACT-TATGATTTATGTGTAAGACCACGTCTGGGATGTTGGCAT
1 CGA-TATTTGA-TTATGTGTAAGACCACGTCTGGGATGTTGGCAT
* * * *
2865972 CG-TATTTGTTTTTGTGTAAGACC-CTGCCTGGGACAG-TGGCAT
1 CGATATTTGATTATGTGTAAGACCAC-GTCTGGGA-TGTTGGCAT
* ** *
2866014 CGATATTTGAGTACATGTAAGACCACGTCTAGGATGTTGGCAT
1 CGATATTTGATTATGTGTAAGACCACGTCTGGGATGTTGGCAT
2866057 TGCACGAGCT
Statistics
Matches: 105, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
41 1 0.01
42 30 0.29
43 38 0.36
44 32 0.30
45 4 0.04
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (43 bp):
CGATATTTGATTATGTGTAAGACCACGTCTGGGATGTTGGCAT
Found at i:2872201 original size:50 final size:50
Alignment explanation
Indices: 2872136--2872425 Score: 305
Period size: 50 Copynumber: 5.8 Consensus size: 50
2872126 ATTGTGAGAA
* * * *
2872136 CACATGTATAGTACTATGTGCAGGCTACTACATGTACCAGATTGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGT
* *
2872186 CGCATGTGTAGTACTAAGTGCAGGCTACTA-GATGTACCGGATTGATAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACG-TGTACCAGATTGATAGGT
* * * * * **
2872236 CACATGTGTAGTACTAAGTGCAGGCCACTATGTGTACCCG-TTAACTTCGAC
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGA--TAGGT
* * * * * *
2872287 CACGTGTGTAGTATTAAGTACAGGCTACTACGTGTATCAGATGGATAAGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGT
* *
2872337 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATTGATAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGT
** * * *
2872387 TGCATGTGTAGTACTAACTGCAGGCTACTATGCGTACCA
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCA
2872426 AACAGCTTTG
Statistics
Matches: 197, Mismatches: 38, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
49 3 0.02
50 156 0.79
51 36 0.18
52 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (50 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGT
Found at i:2872339 original size:101 final size:101
Alignment explanation
Indices: 2872190--2872374 Score: 273
Period size: 101 Copynumber: 1.8 Consensus size: 101
2872180 TTAGGTCGCA
* * * *
2872190 TGTGTAGTACTAAGTGCAGGCTACTAGATGTACCGGATTGATAGGTCACATGTGTAGTACTAAGT
1 TGTGTAGTACTAAGTACAGGCTACTAGATGTACCAGATGGATAAGTCACATGTGTAGTACTAAGT
*
2872255 GCAGGCCACTATGTGTACCCGTTAACTTCGACCACG
66 GCAGGCCACTACGTGTACCCGTTAACTTCGACCACG
* * *
2872291 TGTGTAGTATTAAGTACAGGCTACTACG-TGTATCAGATGGATAAGTCACGTGTGTAGTACTAAG
1 TGTGTAGTACTAAGTACAGGCTACTA-GATGTACCAGATGGATAAGTCACATGTGTAGTACTAAG
*
2872355 TGCAGGCTACTACGTGTACC
65 TGCAGGCCACTACGTGTACC
2872375 AAATTGATAG
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
101 73 0.99
102 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (101 bp):
TGTGTAGTACTAAGTACAGGCTACTAGATGTACCAGATGGATAAGTCACATGTGTAGTACTAAGT
GCAGGCCACTACGTGTACCCGTTAACTTCGACCACG
Found at i:2873717 original size:58 final size:58
Alignment explanation
Indices: 2873647--2873758 Score: 224
Period size: 58 Copynumber: 1.9 Consensus size: 58
2873637 AGTTATTTTG
2873647 TTTTATGTCATAACTAATTTGGCCTAAAATGTTAGCCTTCAATATTTGATAGCTAACA
1 TTTTATGTCATAACTAATTTGGCCTAAAATGTTAGCCTTCAATATTTGATAGCTAACA
2873705 TTTTATGTCATAACTAATTTGGCCTAAAATGTTAGCCTTCAATATTTGATAGCT
1 TTTTATGTCATAACTAATTTGGCCTAAAATGTTAGCCTTCAATATTTGATAGCT
2873759 CATTTTGTAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.41
Consensus pattern (58 bp):
TTTTATGTCATAACTAATTTGGCCTAAAATGTTAGCCTTCAATATTTGATAGCTAACA
Found at i:2880092 original size:50 final size:50
Alignment explanation
Indices: 2879973--2880367 Score: 366
Period size: 50 Copynumber: 7.8 Consensus size: 50
2879963 GTTGTGAGAA
* ** *
2879973 CACATGTGTAGTACTATGTGCAGGCTACTTTGTGTTTAAGACAG-TT-TTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTG--T-A-CCAGATTGTTAGGT
* *
2880025 CACGTGTGTAGTACTAAGTGCAGCCTACTACGTGTACCAGATTGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
* * *** * * * *
2880075 CGCATGTGTAGTACTAAGTGCAGGCTACTATGCAAACCCGATAGTTTTGAT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTG-TTAGGT
* * *
2880126 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATTGATAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
* * * * * * *
2880176 CACATGTGTAGTACTAA-TTCTAGGCTACTATGCGTACCCG-TTAACTTCGAT
1 CACATGTGTAGTACTAAGTGC-AGGCTACTACGTGTACCAGATT--GTTAGGT
* * * * * * *
2880227 TACGTGTGTAGTACTAAGTGCAGGCTACTACCTGTATCAGATGGATAAGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
* *
2880277 CACATGTGTAGTACTAAGTGCAGGCTATTACGTGTACCAGATTGATAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
* *
2880327 CACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGA
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA
2880368 GAGCTTCGGT
Statistics
Matches: 274, Mismatches: 61, Indels: 18
0.78 0.17 0.05
Matches are distributed among these distances:
48 3 0.01
49 7 0.03
50 160 0.58
51 72 0.26
52 32 0.12
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (50 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
Found at i:2880157 original size:101 final size:101
Alignment explanation
Indices: 2879973--2880367 Score: 434
Period size: 101 Copynumber: 3.9 Consensus size: 101
2879963 GTTGTGAGAA
* * * **** * *
2879973 CACATGTGTAGTACTATGTGCAGGCTACTTTGTGTTTAAGACAGTTTTAGGTCACGTGTGTAGTA
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAGTTTT-GATCACGTGTGTAGTA
* *
2880038 CTAAGTGCAGCCTACTACGTGTACCAGATTGTTAGGT
65 CTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGT
* **
2880075 CGCATGTGTAGTACTAAGTGCAGGCTACTATGCAAACCCGATAGTTTTGATCACGTGTGTAGTAC
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAGTTTTGATCACGTGTGTAGTAC
*
2880140 TAAGTGCAGGCTACTACGTGTACCGGATTGATAGGT
66 TAAGTGCAGGCTACTACGTGTACCAGATTGATAGGT
* * ** * *
2880176 CACATGTGTAGTACTAA-TTCTAGGCTACTATGCGTACCCGTTAACTTCGATTACGTGTGTAGTA
1 CACATGTGTAGTACTAAGTGC-AGGCTACTATGCGTACCCGATAGTTTTGATCACGTGTGTAGTA
* * * *
2880240 CTAAGTGCAGGCTACTACCTGTATCAGATGGATAAGT
65 CTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGT
* * * * * * * * *
2880277 CACATGTGTAGTACTAAGTGCAGGCTATTACGTGTACCAGATTG-ATAGGTCACATGTGTAGTAC
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAGTTTTGATCACGTGTGTAGTAC
* *
2880341 TAAGTGCAGGCTACTATGCGTACCAGA
66 TAAGTGCAGGCTACTACGTGTACCAGA
2880368 GAGCTTCGGT
Statistics
Matches: 245, Mismatches: 46, Indels: 6
0.82 0.15 0.02
Matches are distributed among these distances:
100 40 0.16
101 166 0.68
102 39 0.16
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (101 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAGTTTTGATCACGTGTGTAGTAC
TAAGTGCAGGCTACTACGTGTACCAGATTGATAGGT
Found at i:2880375 original size:151 final size:151
Alignment explanation
Indices: 2880020--2880381 Score: 435
Period size: 151 Copynumber: 2.4 Consensus size: 151
2880010 AAGACAGTTT
* * * * * * **
2880020 TAGGTCACGTGTGTAGTACTAAGTGCAGCCTACTACGTGTACCAGATTG-TTAGGTCGCATGTGT
1 TAGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAGCTTCGGTTACATGTGT
* * ** *
2880084 AGTACTAAGTGCAGGCTACTATGCAAACCCGATAGTTTTGATCACGTGTGTAGTACTAAGTGCAG
66 AGTACTAAGTGCAGGCTACTATG-AAACCAGATAGATAAGATCACATGTGTAGTACTAAGTGCAG
*
2880149 GCTACTACGTGTACCGGATTGA
130 GCTACTACGTGTACCAGATTGA
* * * * * *
2880171 TAGGTCACATGTGTAGTACTAA-TTCTAGGCTACTATGCGTACCCGTTAACTTCGATTACGTGTG
1 TAGGTCACATGTGTAGTACTAAGTGC-AGGCTACTATGCGTACCAGATAGCTTCGGTTACATGTG
* * *
2880235 TAGTACTAAGTGCAGGCTACTACCTG-TATCAGATGGATAAG-TCACATGTGTAGTACTAAGTGC
65 TAGTACTAAGTGCAGGCTACTA--TGAAACCAGATAGATAAGATCACATGTGTAGTACTAAGTGC
*
2880298 AGGCTATTACGTGTACCAGATTGA
128 AGGCTACTACGTGTACCAGATTGA
*
2880322 TAGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGAGAGCTTCGGTTACA
1 TAGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAGCTTCGGTTACA
2880382 AGGGTGGTAT
Statistics
Matches: 175, Mismatches: 31, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
150 2 0.01
151 130 0.74
152 41 0.23
154 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (151 bp):
TAGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAGCTTCGGTTACATGTGT
AGTACTAAGTGCAGGCTACTATGAAACCAGATAGATAAGATCACATGTGTAGTACTAAGTGCAGG
CTACTACGTGTACCAGATTGA
Found at i:2882412 original size:12 final size:11
Alignment explanation
Indices: 2882387--2882427 Score: 57
Period size: 12 Copynumber: 3.7 Consensus size: 11
2882377 TATTAACATG
*
2882387 TTAAATTTTAA
1 TTAATTTTTAA
2882398 TTAATTTTATAA
1 TTAATTTT-TAA
2882410 TTAATTTTT-A
1 TTAATTTTTAA
2882420 TTAATTTT
1 TTAATTTT
2882428 GATCATTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 9 0.32
11 8 0.29
12 11 0.39
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TTAATTTTTAA
Found at i:2883307 original size:20 final size:18
Alignment explanation
Indices: 2883274--2883310 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
2883264 TGTGATGTTG
2883274 ATATGTTTAATTTAATTA
1 ATATGTTTAATTTAATTA
2883292 ATATGGTTTAAATTTAATT
1 ATAT-GTTT-AATTTAATT
2883311 CGTGTTAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 4 0.24
20 9 0.53
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (18 bp):
ATATGTTTAATTTAATTA
Found at i:2885322 original size:16 final size:15
Alignment explanation
Indices: 2885295--2885328 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
2885285 ATAACTAGTA
*
2885295 TATAATTATATTTAT
1 TATAATTATATTAAT
2885310 TATAATATATATTAAT
1 TATAAT-TATATTAAT
2885326 TAT
1 TAT
2885329 TATCAAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATAATTATATTAAT
Found at i:2887193 original size:51 final size:51
Alignment explanation
Indices: 2887109--2887231 Score: 133
Period size: 51 Copynumber: 2.4 Consensus size: 51
2887099 AGATGCCCGA
* *
2887109 TGGCCTGCACATAATACCACCCTTGTAGTCAAAGCTACCTTCTT-CACAAAG
1 TGGCCTGCACATAATACCACACTTGTAGCCAAAGCTACCTT-TTACACAAAG
* * * *
2887160 TGGCCTTCACATAGTACCACACTTGT-GACCAAAGCTATCTTTTACACATAG
1 TGGCCTGCACATAATACCACACTTGTAG-CCAAAGCTACCTTTTACACAAAG
* * *
2887211 TGCCCTGCACTTACTACCACA
1 TGGCCTGCACATAATACCACA
2887232 GATGTGATCG
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
50 3 0.05
51 57 0.95
ACGTcount: A:0.28, C:0.32, G:0.13, T:0.27
Consensus pattern (51 bp):
TGGCCTGCACATAATACCACACTTGTAGCCAAAGCTACCTTTTACACAAAG
Found at i:2887238 original size:51 final size:51
Alignment explanation
Indices: 2887112--2887249 Score: 118
Period size: 51 Copynumber: 2.7 Consensus size: 51
2887102 TGCCCGATGG
* * * * * *
2887112 CCTGCACATAATACCACCCTTGT-AGTCAAAGCTACCTTCTTCACAAAGTGG
1 CCTGCACATACTACCACACATGTGA-CCAAAGCTATCTTCTTCACAAAGTGC
* * * *
2887163 CCTTCACATAGTACCACACTTGTGACCAAAGCTATCTT-TTACACATAGTGC
1 CCTGCACATACTACCACACATGTGACCAAAGCTATCTTCTT-CACAAAGTGC
* * * *
2887214 CCTGCACTTACTACCACAGATGTGATCGAAGCTATC
1 CCTGCACATACTACCACACATGTGACCAAAGCTATC
2887250 GGGTACATAG
Statistics
Matches: 71, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
50 2 0.03
51 68 0.96
52 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.14, T:0.27
Consensus pattern (51 bp):
CCTGCACATACTACCACACATGTGACCAAAGCTATCTTCTTCACAAAGTGC
Found at i:2887284 original size:49 final size:49
Alignment explanation
Indices: 2887216--2887330 Score: 124
Period size: 50 Copynumber: 2.3 Consensus size: 49
2887206 CATAGTGCCC
* * * * * *
2887216 TGCACTTACTACCACAGATGTGATCGAAGCTATCGGGTACA-TAGTAGCT
1 TGCACTTAGTACTACAGATGCGACCGAA-CCATCGGATACACTAGTAGCT
* * *
2887265 TGCACTTAGTACTATAGATGCGACCTAACCATCTGATACACGTAGTAGCT
1 TGCACTTAGTACTACAGATGCGACCGAACCATCGGATACAC-TAGTAGCT
2887315 TGCACTTAGTACTACA
1 TGCACTTAGTACTACA
2887331 CACATACCTA
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
48 9 0.17
49 22 0.41
50 23 0.43
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (49 bp):
TGCACTTAGTACTACAGATGCGACCGAACCATCGGATACACTAGTAGCT
Found at i:2887367 original size:51 final size:49
Alignment explanation
Indices: 2887254--2887383 Score: 145
Period size: 51 Copynumber: 2.6 Consensus size: 49
2887244 GCTATCGGGT
* * *
2887254 ACATAGTAGCTTGCACTTAGTACTATAGATGCGACCTAACCATCTGATAC
1 ACATAGTAGCTTGCACTTAGTACTACACA-GCGACCTAACCATCTGAAAC
* * * *
2887304 ACGTAGTAGCTTGCACTTAGTACTACACA-CATACCTAAAACCATTTTAAAC
1 ACATAGTAGCTTGCACTTAGTACTACACAGC-GACCT--AACCATCTGAAAC
*
2887355 ACATAGTAGCTTGCACGTAGTACTACACA
1 ACATAGTAGCTTGCACTTAGTACTACACA
2887384 TGTGTTCTCA
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
48 1 0.01
49 4 0.06
50 26 0.38
51 37 0.54
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.27
Consensus pattern (49 bp):
ACATAGTAGCTTGCACTTAGTACTACACAGCGACCTAACCATCTGAAAC
Found at i:2889213 original size:25 final size:26
Alignment explanation
Indices: 2889156--2889213 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
2889146 ATTTTTCTCC
*
2889156 TAAA-TTTCAAATTTATTTAATTATT
1 TAAATTTTCAAATTTATTGAATTATT
*
2889181 TAAGTTTTC-AATTTATTGAATTA-T
1 TAAATTTTCAAATTTATTGAATTATT
2889205 TAATATTTT
1 TAA-ATTTT
2889214 ATACTAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 4 0.14
25 20 0.71
26 4 0.14
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.57
Consensus pattern (26 bp):
TAAATTTTCAAATTTATTGAATTATT
Found at i:2898340 original size:47 final size:47
Alignment explanation
Indices: 2898289--2898435 Score: 249
Period size: 47 Copynumber: 3.1 Consensus size: 47
2898279 TTAGGATTTT
2898289 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
2898336 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
2898383 ATATGATGAATATGAACATGCATATATGTGATAAGGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
2898430 ATGTGA
1 ATGTGA
2898436 AATATGTATG
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 92 1.00
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:2898474 original size:48 final size:48
Alignment explanation
Indices: 2898405--2898539 Score: 225
Period size: 48 Copynumber: 2.8 Consensus size: 48
2898395 TGAACATGCA
* * *
2898405 TATATGTGATAAGGCCGAATGGCTAATGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATG
* *
2898453 TATATGTGGTAAAGCCGAATGGCTAGTGCGAAATATGTATGAGGTATG
1 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATG
2898501 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
1 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
2898540 GGCGATGTGC
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 81 1.00
ACGTcount: A:0.33, C:0.07, G:0.29, T:0.30
Consensus pattern (48 bp):
TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATG
Found at i:2898736 original size:37 final size:37
Alignment explanation
Indices: 2898686--2898835 Score: 257
Period size: 37 Copynumber: 4.1 Consensus size: 37
2898676 GGAAATATAT
2898686 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTCG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTCG
2898723 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTAT-G
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT-TCG
*
2898760 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTCG
* *
2898797 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTTCG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTCG
2898834 TC
1 TC
2898836 TGAGCTAAAG
Statistics
Matches: 108, Mismatches: 3, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
36 1 0.01
37 106 0.98
38 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.31, T:0.26
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTCG
Found at i:2902083 original size:40 final size:40
Alignment explanation
Indices: 2901979--2902123 Score: 157
Period size: 40 Copynumber: 3.6 Consensus size: 40
2901969 TACTCGAATG
*
2901979 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* * * * *
2902020 ACATCCAGACTATGAT-CCAAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
2902060 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* * *
2902100 ATATACGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
2902124 CTTGTGCGAG
Statistics
Matches: 85, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
39 1 0.01
40 58 0.68
41 25 0.29
42 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:2910060 original size:80 final size:80
Alignment explanation
Indices: 2909908--2910100 Score: 212
Period size: 80 Copynumber: 2.4 Consensus size: 80
2909898 CGGTTTTAGT
* * * *
2909908 AACTCACACAATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTT
1 AACTCGCACAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTT
*
2909973 AACCCGGATTTA-AC
66 AACCCGGATATATAC
** *
2909987 AACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATC
1 AACTCGCAC-AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGA-C
** *
2910051 TTAGTCCGGATATATTC
64 TTAACCCGGATATATAC
* * *
2910068 -ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AAC-TCGCACAATGCCTTCGGGACTTAACCCGGA
2910101 CAGCATTCAA
Statistics
Matches: 96, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
79 11 0.11
80 79 0.82
81 6 0.06
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.23
Consensus pattern (80 bp):
AACTCGCACAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTT
AACCCGGATATATAC
Found at i:2910061 original size:40 final size:40
Alignment explanation
Indices: 2909878--2910047 Score: 225
Period size: 40 Copynumber: 4.3 Consensus size: 40
2909868 TCCTCGTTCA
* * * ** *
2909878 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
2909917 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
2909957 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
2909997 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
2910037 AAGGCCTTCGG
1 AATGCCTTCGG
2910048 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 34 0.29
40 85 0.71
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:2910109 original size:41 final size:41
Alignment explanation
Indices: 2910032--2910109 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
2910022 TTAGTATCTC
* * *
2910032 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
2910073 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
2910110 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:2918236 original size:40 final size:40
Alignment explanation
Indices: 2918053--2918222 Score: 225
Period size: 40 Copynumber: 4.3 Consensus size: 40
2918043 TCCTCGTTCA
* * * * *
2918053 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
2918092 AATGCCTTCGGGACGTAACCCGAATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
2918132 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
2918172 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
2918212 AAGGCCTTCGG
1 AATGCCTTCGG
2918223 ATCTTAGTCC
Statistics
Matches: 116, Mismatches: 14, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
39 32 0.28
40 84 0.72
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:2920475 original size:24 final size:23
Alignment explanation
Indices: 2920421--2920476 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
2920411 GGATAACTAA
* *
2920421 GAAAGGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGATTTGGTAC
***
2920444 GTTTTGGTATTTGGGATTTGGTAC
1 GAAATGGTATTT-GGATTTGGTAC
2920468 GAAATGGTA
1 GAAATGGTA
2920477 ATGGTTCAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.21, C:0.04, G:0.34, T:0.41
Consensus pattern (23 bp):
GAAATGGTATTTGGATTTGGTAC
Found at i:2927698 original size:40 final size:40
Alignment explanation
Indices: 2927514--2927738 Score: 249
Period size: 40 Copynumber: 5.7 Consensus size: 40
2927504 GCTCCTCGTT
* * * * *
2927514 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* * *
2927554 C-AATGCCTTTGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
*
2927593 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
*
2927633 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* ** * * * *
2927673 CAAAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCA
*
2927714 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
2927739 CAGCATTCAA
Statistics
Matches: 163, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
39 36 0.22
40 116 0.71
41 11 0.07
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
Found at i:2927747 original size:41 final size:41
Alignment explanation
Indices: 2927670--2927747 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
2927660 TTAATAACTC
* * *
2927670 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
2927711 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
2927748 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:2928490 original size:74 final size:74
Alignment explanation
Indices: 2928369--2928514 Score: 274
Period size: 74 Copynumber: 2.0 Consensus size: 74
2928359 TGTGCTCACA
*
2928369 CAAAAATGCTAAAAAGGAGGTTCAAGAATCATCAAGCCATCATCACATGCATCATTAACAAGCTT
1 CAAAAATGCTAAAAAGGAGGTTCAAGAATCATCAAGCCACCATCACATGCATCATTAACAAGCTT
2928434 CATATTTCT
66 CATATTTCT
*
2928443 CAAAAATGCTAAAAAGGAGGTTCAAGAATCATCAAGCCACCATCACATGCATCATTAACAAGTTT
1 CAAAAATGCTAAAAAGGAGGTTCAAGAATCATCAAGCCACCATCACATGCATCATTAACAAGCTT
2928508 CATATTT
66 CATATTT
2928515 AGCATGCAAT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.25
Consensus pattern (74 bp):
CAAAAATGCTAAAAAGGAGGTTCAAGAATCATCAAGCCACCATCACATGCATCATTAACAAGCTT
CATATTTCT
Found at i:2929722 original size:14 final size:14
Alignment explanation
Indices: 2929703--2929732 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2929693 CCATATACAA
*
2929703 ATAAACTTATCAAC
1 ATAAACTTATAAAC
2929717 ATAAACTTATAAAC
1 ATAAACTTATAAAC
2929731 AT
1 AT
2929733 CAAGAATACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAAACTTATAAAC
Found at i:2930109 original size:44 final size:42
Alignment explanation
Indices: 2929958--2930116 Score: 123
Period size: 44 Copynumber: 3.7 Consensus size: 42
2929948 AGCATATACA
* * * *
2929958 ATGCCAACATCCGAGACGTGGTTTTACATGTAATCAA-ACATCG
1 ATGCCAACATCCCAGACGTGGTCTTACACGTAA--AACAAATCG
*
2930001 ATGCC-ACTATCCCAGACAG-GGTCTTACAC--AAAATCAAATACC
1 ATGCCAAC-ATCCCAGAC-GTGGTCTTACACGTAAAA-CAAAT-CG
** *
2930043 ATGCCAATGTCTCAGA-GATGGTCTTACACGTAAAACAGAAGTCG
1 ATGCCAACATCCCAGACG-TGGTCTTACACGTAAAACA-AA-TCG
2930087 ATGCCAACATCCCAGACGTGGTCTTACACG
1 ATGCCAACATCCCAGACGTGGTCTTACACG
2930117 ATAACACATA
Statistics
Matches: 91, Mismatches: 12, Indels: 25
0.71 0.09 0.20
Matches are distributed among these distances:
39 2 0.02
40 1 0.01
41 5 0.05
42 24 0.26
43 24 0.26
44 33 0.36
45 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (42 bp):
ATGCCAACATCCCAGACGTGGTCTTACACGTAAAACAAATCG
Found at i:2933698 original size:16 final size:16
Alignment explanation
Indices: 2933677--2933708 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2933667 ACTGTAACGC
2933677 CCCAAAAATCCAGAAA
1 CCCAAAAATCCAGAAA
*
2933693 CCCAAAAATCCTGAAA
1 CCCAAAAATCCAGAAA
2933709 TCTCAAATTT
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:0.53, C:0.31, G:0.06, T:0.09
Consensus pattern (16 bp):
CCCAAAAATCCAGAAA
Found at i:2934935 original size:8 final size:8
Alignment explanation
Indices: 2934922--2934948 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
2934912 ATCGGCCAAA
2934922 GCCGAAAT
1 GCCGAAAT
2934930 GCCGAAAT
1 GCCGAAAT
2934938 GCCGAAAT
1 GCCGAAAT
2934946 GCC
1 GCC
2934949 AAAAAGTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.33, C:0.30, G:0.26, T:0.11
Consensus pattern (8 bp):
GCCGAAAT
Found at i:2934959 original size:16 final size:16
Alignment explanation
Indices: 2934919--2934960 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
2934909 TAGATCGGCC
*
2934919 AAAGCCGAAATGCCGA
1 AAAGCCGAAATGCCAA
*
2934935 AATGCCGAAATGCCAA
1 AAAGCCGAAATGCCAA
*
2934951 AAAGTCGAAA
1 AAAGCCGAAA
2934961 GTTTGGCTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.48, C:0.21, G:0.21, T:0.10
Consensus pattern (16 bp):
AAAGCCGAAATGCCAA
Found at i:2935243 original size:28 final size:27
Alignment explanation
Indices: 2935174--2935286 Score: 100
Period size: 28 Copynumber: 4.0 Consensus size: 27
2935164 AGCATGACTG
* *
2935174 TAAATGTGATTTGGGTCTAATGTCCATA
1 TAAATGTGA-TTGGGCCTAATGGCCATA
* * *
2935202 TGAATGTGGTTTGGGCCTAATGAGCCACA
1 TAAATGT-GATTGGGCCTAATG-GCCATA
*
2935231 TAAATGTGATTGGGCCGAATGGGCCATA
1 TAAATGTGATTGGGCCTAAT-GGCCATA
* * *
2935259 TGAATGAGATTGGGCCTAGTGGGCCATA
1 TAAATGTGATTGGGCCTAAT-GGCCATA
2935287 AGCATGTATG
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
28 57 0.83
29 12 0.17
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.29
Consensus pattern (27 bp):
TAAATGTGATTGGGCCTAATGGCCATA
Found at i:2941409 original size:27 final size:26
Alignment explanation
Indices: 2941357--2941415 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
2941347 CCACATATAT
*
2941357 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
2941383 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
2941410 ATATCT
1 ATATCT
2941416 AGTAGCATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.36
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:2950042 original size:26 final size:27
Alignment explanation
Indices: 2950013--2950066 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
2950003 CCACACAAGT
*
2950013 TAGTCATTT-ACGCACGAGGGGCAAAA
1 TAGTCATTTAACACACGAGGGGCAAAA
* *
2950039 TAGTCATTTAACACCCTAGGGGCAAAA
1 TAGTCATTTAACACACGAGGGGCAAAA
2950066 T
1 T
2950067 GGTAATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (27 bp):
TAGTCATTTAACACACGAGGGGCAAAA
Found at i:2950097 original size:27 final size:27
Alignment explanation
Indices: 2950067--2950239 Score: 204
Period size: 27 Copynumber: 6.4 Consensus size: 27
2950057 GGGGCAAAAT
* * *
2950067 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
2950094 GGTAATTCTACCCTACAGGGGTATTTA
1 GGTAATTCTACCCTACAAGGGTATTTC
** *
2950121 TATATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
2950148 GGCAATTCTATCCTAC-AGAGGTATTTC
1 GGTAATTCTACCCTACAAG-GGTATTTC
2950175 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
** * *
2950202 AATAATTCTACCCTAGAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
2950229 GGTAATTCTAC
1 GGTAATTCTAC
2950240 AACTTATCCA
Statistics
Matches: 121, Mismatches: 23, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
26 2 0.02
27 117 0.97
28 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:2950185 original size:81 final size:81
Alignment explanation
Indices: 2950086--2950238 Score: 236
Period size: 81 Copynumber: 1.9 Consensus size: 81
2950076 ACCCCACAAG
* *
2950086 GGTATCTCGGTAATTCTACCCTACAGGGGTATTT-ATATATTTCTACCCTACAAGGGTATTTCGG
1 GGTATCTCGGTAATTCTACCCTACAAGGGTATTTCA-ATAATTCTACCCTACAAGGGTATTTCGG
2950150 CAATTCTATCCTACAGA
65 CAATTCTATCCTACAGA
* * * *
2950167 GGTATTTCGGTAATTCTACCCTACAAGGGTATTTCAATAATTCTACCCTAGAGGGGTATTTCGGT
1 GGTATCTCGGTAATTCTACCCTACAAGGGTATTTCAATAATTCTACCCTACAAGGGTATTTCGGC
2950232 AATTCTA
66 AATTCTA
2950239 CAACTTATCC
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
81 64 0.98
82 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.35
Consensus pattern (81 bp):
GGTATCTCGGTAATTCTACCCTACAAGGGTATTTCAATAATTCTACCCTACAAGGGTATTTCGGC
AATTCTATCCTACAGA
Found at i:2950225 original size:54 final size:54
Alignment explanation
Indices: 2950067--2950239 Score: 229
Period size: 54 Copynumber: 3.2 Consensus size: 54
2950057 GGGGCAAAAT
* * * *
2950067 GGTAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTA
1 GGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
** * * * *
2950121 TATATTTCTACCCTACAAGGGTATTTCGGCAATTCTATCCTACAGAGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
** *
2950175 GGTAATTCTACCCTACAAGGGTATTTCAATAATTCTACCCTAGAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
2950229 GGTAATTCTAC
1 GGTAATTCTAC
2950240 AACTTATCCA
Statistics
Matches: 100, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 100 1.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (54 bp):
GGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
Found at i:2954925 original size:28 final size:28
Alignment explanation
Indices: 2954854--2954952 Score: 119
Period size: 28 Copynumber: 3.5 Consensus size: 28
2954844 ATAATAAGCC
*
2954854 CGCACACTTAGTGCT-TAATAGTCGAACT
1 CGCACACTTAGTGCTAT-ATAATCGAACT
* *
2954882 CACACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCGAACT
* * *
2954910 CGCACACTTAGTGCTATACAATTTGAACC
1 CGCACACTTAGTGCTATATAA-TCGAACT
2954939 CGCACACTTAGTGC
1 CGCACACTTAGTGC
2954953 CAATCTCATG
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
28 42 0.69
29 19 0.31
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCGAACT
Found at i:2956223 original size:13 final size:13
Alignment explanation
Indices: 2956202--2956237 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
2956192 GATTACGTAC
*
2956202 GACGGGTGAGACG
1 GACGAGTGAGACG
2956215 GACGAGTGAGACG
1 GACGAGTGAGACG
2956228 GACGAGTGAG
1 GACGAGTGAG
2956238 CATTCACCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.28, C:0.14, G:0.50, T:0.08
Consensus pattern (13 bp):
GACGAGTGAGACG
Found at i:2961226 original size:285 final size:285
Alignment explanation
Indices: 2960716--2961233 Score: 1009
Period size: 285 Copynumber: 1.8 Consensus size: 285
2960706 TACCCAAACT
*
2960716 GTGCTATGACTCCTTAGGCATTTCGGCTCGATCTCATACCAAGCCCTACTTTGACAATTCATACA
1 GTGCTATAACTCCTTAGGCATTTCGGCTCGATCTCATACCAAGCCCTACTTTGACAATTCATACA
2960781 TTACACCATATGACATTGGATGCATTTATCTTCAAGTATAATCACCACATAGGTTCAAGACTTAC
66 TTACACCATATGACATTGGATGCATTTATCTTCAAGTATAATCACCACATAGGTTCAAGACTTAC
2960846 CAAGCTCAATCCCAAATATAAATAAAATGTCTATTCCTCATGAGCTCAAGGTGTTTAATCGTACC
131 CAAGCTCAATCCCAAATATAAATAAAATGTCTATTCCTCATGAGCTCAAGGTGTTTAATCGTACC
2960911 GCTGTGAATGATTGACTCGATAAGGCCGCACACTTAGAGCATGTATATTTATTAGAGAATGTATA
196 GCTGTGAATGATTGACTCGATAAGGCCGCACACTTAGAGCATGTATATTTATTAGAGAATGTATA
2960976 ATAAGCCCGCACACTTAGTGCTTAG
261 ATAAGCCCGCACACTTAGTGCTTAG
* *
2961001 GTGCTATAATTCCTTAGGCATTTCGGCTCGATCTCATACCAAGCCCTACTTTGACATTTCATACA
1 GTGCTATAACTCCTTAGGCATTTCGGCTCGATCTCATACCAAGCCCTACTTTGACAATTCATACA
2961066 TTACACCATATGACATTGGATGCATTTATCTTCAAGTATAATCACCACATAGGTTCAAGACTTAC
66 TTACACCATATGACATTGGATGCATTTATCTTCAAGTATAATCACCACATAGGTTCAAGACTTAC
2961131 CAAGCTCAATCCCAAATATAAATAAAATGTCTATTCCTCATGAGCTCAAGGTGTTTAATCGTACC
131 CAAGCTCAATCCCAAATATAAATAAAATGTCTATTCCTCATGAGCTCAAGGTGTTTAATCGTACC
2961196 GCTGTGAATGATTGACTCGATAAGGCCGCACACTTAGA
196 GCTGTGAATGATTGACTCGATAAGGCCGCACACTTAGA
2961234 TCGTACCGCT
Statistics
Matches: 230, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
285 230 1.00
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (285 bp):
GTGCTATAACTCCTTAGGCATTTCGGCTCGATCTCATACCAAGCCCTACTTTGACAATTCATACA
TTACACCATATGACATTGGATGCATTTATCTTCAAGTATAATCACCACATAGGTTCAAGACTTAC
CAAGCTCAATCCCAAATATAAATAAAATGTCTATTCCTCATGAGCTCAAGGTGTTTAATCGTACC
GCTGTGAATGATTGACTCGATAAGGCCGCACACTTAGAGCATGTATATTTATTAGAGAATGTATA
ATAAGCCCGCACACTTAGTGCTTAG
Found at i:2961252 original size:45 final size:45
Alignment explanation
Indices: 2961188--2961278 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
2961178 AAGGTGTTTA
2961188 ATCGTACCGCTGTGAATGATTGACTCGATAAGGCCGCACACTTAG
1 ATCGTACCGCTGTGAATGATTGACTCGATAAGGCCGCACACTTAG
*
2961233 ATCGTACCGCTGTGCATGATTGACTCGATAAGGCCGCACACTTAG
1 ATCGTACCGCTGTGAATGATTGACTCGATAAGGCCGCACACTTAG
2961278 A
1 A
2961279 GCATGTATAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.24
Consensus pattern (45 bp):
ATCGTACCGCTGTGAATGATTGACTCGATAAGGCCGCACACTTAG
Found at i:2961345 original size:28 final size:29
Alignment explanation
Indices: 2961313--2961411 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 29
2961303 ATAATAAGCC
*
2961313 CGCACACTTAGTGCTTA-ATAGTCGAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
* *
2961341 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
* * *
2961369 CGCACACTTAGTGCTATACA-ATTTGAACC
1 CGCACACTTAGTGCT-TACATAATCGAACT
2961398 CGCACACTTAGTGC
1 CGCACACTTAGTGC
2961412 CAATCTCATG
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
27 2 0.03
28 37 0.61
29 19 0.31
30 3 0.05
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCTTACATAATCGAACT
Found at i:2969265 original size:16 final size:15
Alignment explanation
Indices: 2969246--2969297 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
2969236 GTAAATCGGT
2969246 AAAAGCTGAAATGCC
1 AAAAGCTGAAATGCC
* *
2969261 GAAAAGCAGAAATACC
1 -AAAAGCTGAAATGCC
2969277 AAAAAG-TCGAAATGCC
1 -AAAAGCT-GAAATGCC
2969293 AAAAG
1 AAAAG
2969298 TTTGGCTATG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 5 0.17
16 25 0.83
ACGTcount: A:0.54, C:0.17, G:0.19, T:0.10
Consensus pattern (15 bp):
AAAAGCTGAAATGCC
Found at i:2969608 original size:28 final size:28
Alignment explanation
Indices: 2969511--2969613 Score: 91
Period size: 28 Copynumber: 3.7 Consensus size: 28
2969501 TAAATGTGAT
* **
2969511 TTGGACCTAAT-GGCCATTTGAATTTGA
1 TTGGACCTAATGGGCCATATGAATGAGA
* * * * * *
2969538 TTTGGGCCTAATAGACCACATAAATGTGA
1 -TTGGACCTAATGGGCCATATGAATGAGA
2969567 TTGGACCTAATGGGCCATATGAATGAGA
1 TTGGACCTAATGGGCCATATGAATGAGA
* *
2969595 TTGGGCCTAGTGGGCCATA
1 TTGGACCTAATGGGCCATA
2969614 AGCATGTATG
Statistics
Matches: 60, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
28 49 0.82
29 11 0.18
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (28 bp):
TTGGACCTAATGGGCCATATGAATGAGA
Found at i:2973178 original size:104 final size:104
Alignment explanation
Indices: 2972998--2973205 Score: 407
Period size: 104 Copynumber: 2.0 Consensus size: 104
2972988 CATGAAGCTA
2972998 TTGTAAACTGCAAGAGAAAGACTATTGATTTATGATGTCAGAATGATAAGATTATTCGGATTGAA
1 TTGTAAACTGCAAGAGAAAGACTATTGATTTATGATGTCAGAATGATAAGATTATTCGGATTGAA
2973063 TCTAATGATTTGAATGGATTACCAGCAGTGATATCTTCG
66 TCTAATGATTTGAATGGATTACCAGCAGTGATATCTTCG
*
2973102 TTGTAAACTGCAAGAGAAAGACTATTGATTTATGATGTCAGAATGATGAGATTATTCGGATTGAA
1 TTGTAAACTGCAAGAGAAAGACTATTGATTTATGATGTCAGAATGATAAGATTATTCGGATTGAA
2973167 TCTAATGATTTGAATGGATTACCAGCAGTGATATCTTCG
66 TCTAATGATTTGAATGGATTACCAGCAGTGATATCTTCG
2973206 ATGTTAGCTC
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 103 1.00
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.34
Consensus pattern (104 bp):
TTGTAAACTGCAAGAGAAAGACTATTGATTTATGATGTCAGAATGATAAGATTATTCGGATTGAA
TCTAATGATTTGAATGGATTACCAGCAGTGATATCTTCG
Found at i:2979812 original size:28 final size:28
Alignment explanation
Indices: 2979747--2979845 Score: 119
Period size: 28 Copynumber: 3.5 Consensus size: 28
2979737 CATGAGATTG
* * *
2979747 GCACTAAGTGTGCGGGTTCAAATTGTATA
1 GCACTAAGTGTGCGAGTT-AGATTATATA
*
2979776 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTAGATTATATA
* *
2979804 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCGAGTTAGATTATAT-A
2979832 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
2979846 GGCTTATTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
27 1 0.02
28 45 0.71
29 17 0.27
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTAGATTATATA
Found at i:2983852 original size:26 final size:26
Alignment explanation
Indices: 2983802--2983852 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
2983792 TTGATAATTT
* *
2983802 AATGTTATAATTACATGCTGTTATGA
1 AATGTTATAATTAAATGCTGCTATGA
2983828 AATGTTATAATTAAATTG-TGCTATG
1 AATGTTATAATTAAA-TGCTGCTATG
2983853 GCCGAATATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (26 bp):
AATGTTATAATTAAATGCTGCTATGA
Found at i:2986938 original size:28 final size:29
Alignment explanation
Indices: 2986901--2986996 Score: 122
Period size: 29 Copynumber: 3.3 Consensus size: 29
2986891 AAGTCTACAT
* * * *
2986901 ACATGCATATGGCCCACTAGG-TCGAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
* *
2986929 TCATTCATATGACCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
*
2986958 ACATTCGTATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
2986987 ACATTCATAT
1 ACATTCATAT
2986997 ACATGCTTTC
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
28 17 0.30
29 40 0.70
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAGGCCCAAATC
Found at i:2991746 original size:93 final size:93
Alignment explanation
Indices: 2991639--2991809 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
2991629 GCCCATAAGT
* *
2991639 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
2991704 TGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
*
2991732 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
2991797 CGAGTTCGGATGC
66 CGAGTTCGGATGC
2991810 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:2991806 original size:46 final size:46
Alignment explanation
Indices: 2991631--2991806 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
2991621 TGTAACCCGC
* * *
2991631 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
2991677 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* * *
2991727 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
2991770 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
2991807 TGCTCAACCA
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 63 0.58
47 28 0.26
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:2992263 original size:30 final size:30
Alignment explanation
Indices: 2992229--2992288 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
2992219 ATTTAATACG
2992229 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
2992259 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
2992289 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:2993755 original size:29 final size:29
Alignment explanation
Indices: 2993688--2993812 Score: 144
Period size: 29 Copynumber: 4.3 Consensus size: 29
2993678 AAGTCTACAT
* *
2993688 ACATGCATATGGCCCACTAAGCCC-AATC
1 ACATTCATATGGCCCATTAAGCCCAAATC
* *
2993716 TCATTCATATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAAGCCCAAATC
** *
2993745 ACATTTGTATGGACCATTAAGCCCAAATC
1 ACATTCATATGGCCCATTAAGCCCAAATC
* * * *
2993774 ACATCCATATGTCCCATTAGGCCTAAATC
1 ACATTCATATGGCCCATTAAGCCCAAATC
2993803 ACATTCATAT
1 ACATTCATAT
2993813 ACATGCTTTC
Statistics
Matches: 79, Mismatches: 17, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
28 20 0.25
29 59 0.75
ACGTcount: A:0.32, C:0.30, G:0.12, T:0.26
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAAGCCCAAATC
Found at i:2993766 original size:57 final size:58
Alignment explanation
Indices: 2993695--2993807 Score: 165
Period size: 58 Copynumber: 2.0 Consensus size: 58
2993685 CATACATGCA
* * *
2993695 TATGGCCCACTAAGCCC-AATCTCATTCATATGGCCCATTAGGCCCAAATCACATTTG
1 TATGGACCACTAAGCCCAAATCACATCCATATGGCCCATTAGGCCCAAATCACATTTG
* * *
2993752 TATGGACCATTAAGCCCAAATCACATCCATATGTCCCATTAGGCCTAAATCACATT
1 TATGGACCACTAAGCCCAAATCACATCCATATGGCCCATTAGGCCCAAATCACATT
2993808 CATATACATG
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
57 15 0.31
58 34 0.69
ACGTcount: A:0.31, C:0.30, G:0.12, T:0.27
Consensus pattern (58 bp):
TATGGACCACTAAGCCCAAATCACATCCATATGGCCCATTAGGCCCAAATCACATTTG
Found at i:2993892 original size:17 final size:18
Alignment explanation
Indices: 2993870--2993904 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2993860 TGCCTATTAT
2993870 GGGCCCA-ATAGCCCATC
1 GGGCCCACATAGCCCATC
*
2993887 GGGCCCACTTAGCCCATC
1 GGGCCCACATAGCCCATC
2993905 CTGACCTGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.20, C:0.43, G:0.23, T:0.14
Consensus pattern (18 bp):
GGGCCCACATAGCCCATC
Found at i:2997431 original size:8 final size:7
Alignment explanation
Indices: 2997392--2997463 Score: 108
Period size: 7 Copynumber: 9.7 Consensus size: 7
2997382 GTGATGCATC
2997392 ACCCTAA
1 ACCCTAA
2997399 ACCCTAA
1 ACCCTAA
2997406 ACCCTAA
1 ACCCTAA
2997413 ACCCTAA
1 ACCCTAA
2997420 ACCCTAAA
1 ACCCT-AA
2997428 ACCCTAAA
1 ACCCT-AA
2997436 ACCCTAAA
1 ACCCT-AA
2997444 ACCCTAA
1 ACCCTAA
2997451 ACCCTAAA
1 ACCCT-AA
2997459 ACCCT
1 ACCCT
2997464 TCATGATTGA
Statistics
Matches: 63, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
7 33 0.52
8 30 0.48
ACGTcount: A:0.44, C:0.42, G:0.00, T:0.14
Consensus pattern (7 bp):
ACCCTAA
Found at i:2997431 original size:15 final size:15
Alignment explanation
Indices: 2997392--2997463 Score: 121
Period size: 15 Copynumber: 4.9 Consensus size: 15
2997382 GTGATGCATC
2997392 ACCCT-AAACCCTAA
1 ACCCTAAAACCCTAA
2997406 ACCCT-AAACCCTAA
1 ACCCTAAAACCCTAA
2997420 ACCCTAAAACCCTAAA
1 ACCCTAAAACCCT-AA
2997436 ACCCTAAAACCCTAA
1 ACCCTAAAACCCTAA
2997451 ACCCTAAAACCCT
1 ACCCTAAAACCCT
2997464 TCATGATTGA
Statistics
Matches: 56, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
14 19 0.34
15 22 0.39
16 15 0.27
ACGTcount: A:0.44, C:0.42, G:0.00, T:0.14
Consensus pattern (15 bp):
ACCCTAAAACCCTAA
Found at i:2998649 original size:50 final size:49
Alignment explanation
Indices: 2998583--2998808 Score: 215
Period size: 50 Copynumber: 4.5 Consensus size: 49
2998573 TGAATACACG
* * *
2998583 TGTGTAGTACTGAGTGCAGGCTACTACGTGTACCATATTGTTAAGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTT-AGTCACA
* * * *
2998633 TGTGTAGTACTAAGTGCAGGCTACTATGCGAACTCCATGACTTCG--A-TCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTA--CCA-GA-TT-GTTAGTCACA
* * * *
2998684 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTGCAGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGT-TAGTCACA
* ** * *
2998734 TGTGTAGTACTAAGTGTAGGCTACTACGTGTACTGGATTGTTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGTCACA
*
2998783 TGTGTAGTACTAAGTGCAAGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
2998809 TGCATATCAG
Statistics
Matches: 144, Mismatches: 23, Indels: 19
0.77 0.12 0.10
Matches are distributed among these distances:
46 1 0.01
47 1 0.01
48 2 0.01
49 31 0.22
50 69 0.48
51 32 0.22
52 4 0.03
53 1 0.01
54 2 0.01
55 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGTCACA
Found at i:2998938 original size:27 final size:26
Alignment explanation
Indices: 2998908--2998959 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
2998898 GGGAAAATCG
2998908 ATAAAGTGGTAATATGTG-AAAGTTATT
1 ATAAAGTGG--ATATGTGCAAAGTTATT
* *
2998935 ATAAGGTGGATATGTGCAAATTTAT
1 ATAAAGTGGATATGTGCAAAGTTAT
2998960 GTTTATGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 7 0.32
26 7 0.32
27 8 0.36
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (26 bp):
ATAAAGTGGATATGTGCAAAGTTATT
Found at i:3012359 original size:448 final size:448
Alignment explanation
Indices: 3011751--3012593 Score: 1650
Period size: 448 Copynumber: 1.9 Consensus size: 448
3011741 TCATGCTTTT
3011751 ATTTGTATTAAAAGTTTTATGCCAATCAATTTATTGTTTCAATATTTGTTACAGATGTCTTATGC
1 ATTTGTATTAAAAGTTTTATGCCAATCAATTTATTGTTTCAATATTTGTTACAGATGTCTTATGC
*
3011816 ACAATATTATCTCAGAGTTTGTTTTCGCAGTTCGCAGCCTCACTACGGTTCGTAGTTTACTCTAA
66 ACAATATTATCTCAGAGTTTGTTTTCGCAATTCGCAGCCTCACTACGGTTCGTAGTTTACTCTAA
*
3011881 AGAGTTTCAGCACAGTTTTACTAGCTAAGTAGTCTCAGCATGTAACACCCCTTACCCGTATCCAA
131 AGAGTTTCAGCACAGTTTTACTACCTAAGTAGTCTCAGCATGTAACACCCCTTACCCGTATCCAA
* *
3011946 GGCCGGAACAGAGTACGAGGCATTACCAGACTTAATAATACACATAGATGAAAACGGGGCCATAA
196 GGCCGGAACAGAGTACGAGGCATTACCAGACTTAACAATACACATAGACGAAAACGGGGCCATAA
3012011 AATTTCATTTAATTCAAAACTTTTCGAACACATGCATAACAAACAAAGCTAACTATATCATCACA
261 AATTTCATTTAATTCAAAACTTTTCGAACACATGCATAACAAACAAAGCTAACTATATCATCACA
3012076 TCAAAACGTAGGACATGCCACGATTAATTAAACTTATAAACCATAATGGATAAGGACCACATCTC
326 TCAAAACGTAGGACATGCCACGATTAATTAAACTTATAAACCATAATGGATAAGGACCACATCTC
3012141 ATGATCATATACGATAACTCAATGCAGACTGATACGTAAGGTCAAAATCATAATAAAA
391 ATGATCATATACGATAACTCAATGCAGACTGATACGTAAGGTCAAAATCATAATAAAA
3012199 ATTTGTATTAAAAGTTTTATGCCAATCAATTTATTGTTTCAATATTTGTTACAGATGTCTTATGC
1 ATTTGTATTAAAAGTTTTATGCCAATCAATTTATTGTTTCAATATTTGTTACAGATGTCTTATGC
3012264 ACAATATTATCTCAGAGTTTGTTTTCGCAATTCGCAGCCTCACTACGGTTCGTAGTTTACTCTAA
66 ACAATATTATCTCAGAGTTTGTTTTCGCAATTCGCAGCCTCACTACGGTTCGTAGTTTACTCTAA
3012329 AGAGTTTCAGCACAGTTTTACTACCTAAGTAGTCTCAGCATGTAACACCCCTTACCCGTATCCAA
131 AGAGTTTCAGCACAGTTTTACTACCTAAGTAGTCTCAGCATGTAACACCCCTTACCCGTATCCAA
3012394 GGCCGGAACAGAGTACGAGGCATTACCAGACTTAACAATACACATAGACGAAAACGGGGCCATAA
196 GGCCGGAACAGAGTACGAGGCATTACCAGACTTAACAATACACATAGACGAAAACGGGGCCATAA
3012459 AATTTCATTTAATTCAAAACTTTTCGAACACATGCATAACAAACAAAGCTAACTATATCATCACA
261 AATTTCATTTAATTCAAAACTTTTCGAACACATGCATAACAAACAAAGCTAACTATATCATCACA
3012524 TCAAAACGTAGGACATGCCACGATTAATTAAACTTATAAACCATAATGGATAAGGACCACATCTC
326 TCAAAACGTAGGACATGCCACGATTAATTAAACTTATAAACCATAATGGATAAGGACCACATCTC
3012589 ATGAT
391 ATGAT
3012594 NNNNNNNNNN
Statistics
Matches: 391, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
448 391 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (448 bp):
ATTTGTATTAAAAGTTTTATGCCAATCAATTTATTGTTTCAATATTTGTTACAGATGTCTTATGC
ACAATATTATCTCAGAGTTTGTTTTCGCAATTCGCAGCCTCACTACGGTTCGTAGTTTACTCTAA
AGAGTTTCAGCACAGTTTTACTACCTAAGTAGTCTCAGCATGTAACACCCCTTACCCGTATCCAA
GGCCGGAACAGAGTACGAGGCATTACCAGACTTAACAATACACATAGACGAAAACGGGGCCATAA
AATTTCATTTAATTCAAAACTTTTCGAACACATGCATAACAAACAAAGCTAACTATATCATCACA
TCAAAACGTAGGACATGCCACGATTAATTAAACTTATAAACCATAATGGATAAGGACCACATCTC
ATGATCATATACGATAACTCAATGCAGACTGATACGTAAGGTCAAAATCATAATAAAA
Found at i:3013172 original size:50 final size:49
Alignment explanation
Indices: 3013035--3013374 Score: 308
Period size: 50 Copynumber: 6.9 Consensus size: 49
3013025 TATGTAGCCA
* * * *
3013035 AACTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 AACTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
* * **
3013084 AATTATCCGGTGTACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
1 AACTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
**
3013133 TAACTATCTAATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCAC
1 -AACTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-C-C
** * * * * * *
3013185 AGTTTTCGGGTACGCATAGTAGCCTGCACTTAGTACT--ACATGCGACC
1 AACTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
* *
3013232 AAC-AGTCTGGTACACGTAGTAGGCTGCACTTAGTACTACACACGTGTCC
1 AACTA-TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
* * ** * *
3013281 TCACCATCTAATACAAGTAGTAGCCTGCACTTATTACTACACACGTGATCAC
1 -AACTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-C-C
** * * * *
3013333 AGTTTTCGGGTACGCATAGTAGCCTGCACTTAGTACTACACA
1 AACTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACA
3013375 TGCGACCTCA
Statistics
Matches: 228, Mismatches: 53, Indels: 18
0.76 0.18 0.06
Matches are distributed among these distances:
47 30 0.13
48 1 0.00
49 54 0.24
50 79 0.35
51 62 0.27
52 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (49 bp):
AACTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
Found at i:3013290 original size:148 final size:149
Alignment explanation
Indices: 3013043--3013381 Score: 547
Period size: 148 Copynumber: 2.3 Consensus size: 149
3013033 CAAACTATCT
* **
3013043 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTGTACGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTA-ACATGCGACCAATCATCCGGTACACGTAGTAGCC
* *
3013108 TGCACTTAGTACTACACACGTGACCTAACTATCTAATACACGTAGTAGCCTGCACTTAGTACTAC
65 TGCACTTAGTACTACACACGTGACCTAACCATCTAATACAAGTAGTAGCCTGCACTTAGTACTAC
3013173 ACACGTGATCACAGTTTTCG
130 ACACGTGATCACAGTTTTCG
* *
3013193 GGTACGCATAGTAGCCTGCACTTAGTACT-ACATGCGACCAA-CAGTCTGGTACACGTAGTAGGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTAACATGCGACCAATCA-TCCGGTACACGTAGTAGCC
* * *
3013256 TGCACTTAGTACTACACACGTGTCCTCACCATCTAATACAAGTAGTAGCCTGCACTTATTACTAC
65 TGCACTTAGTACTACACACGTGACCTAACCATCTAATACAAGTAGTAGCCTGCACTTAGTACTAC
3013321 ACACGTGATCACAGTTTTCG
130 ACACGTGATCACAGTTTTCG
3013341 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 GGTACGCATAGTAGCCTGCACTTAGTACTA-ACATGCGACC
3013382 TCACAATAGA
Statistics
Matches: 176, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
147 1 0.01
148 136 0.77
150 39 0.22
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (149 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTAACATGCGACCAATCATCCGGTACACGTAGTAGCCT
GCACTTAGTACTACACACGTGACCTAACCATCTAATACAAGTAGTAGCCTGCACTTAGTACTACA
CACGTGATCACAGTTTTCG
Found at i:3019581 original size:95 final size:96
Alignment explanation
Indices: 3019418--3019612 Score: 374
Period size: 95 Copynumber: 2.0 Consensus size: 96
3019408 TGAAAATTTT
*
3019418 TTTAAGTTAAGCCTTACAATCCCGTGTCGAGGCAATGCAGACGTCCGTGTGCTTTGGGACACGCC
1 TTTAAGTTAAGCCTTACAATCCCGTGTCGAGGCAATGCACACGTCCGTGTGCTTTGGGACACGCC
3019483 CATGTCCCCTACCCGTGTGAAATTAATTG-A
66 CATGTCCCCTACCCGTGTGAAATTAATTGAA
3019513 TTTAAGTTAAGCCTTACAATCCCGTGTCGAGGCAATGCACACGTCCGTGTGCTTTGGGACACGCC
1 TTTAAGTTAAGCCTTACAATCCCGTGTCGAGGCAATGCACACGTCCGTGTGCTTTGGGACACGCC
3019578 CATGTCCCCTACCCGTGTGAAATTAATTGAA
66 CATGTCCCCTACCCGTGTGAAATTAATTGAA
3019609 TTTA
1 TTTA
3019613 TTTTCTATTT
Statistics
Matches: 98, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
95 93 0.95
96 5 0.05
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (96 bp):
TTTAAGTTAAGCCTTACAATCCCGTGTCGAGGCAATGCACACGTCCGTGTGCTTTGGGACACGCC
CATGTCCCCTACCCGTGTGAAATTAATTGAA
Found at i:3024581 original size:43 final size:43
Alignment explanation
Indices: 3024515--3024600 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
3024505 GCCATCACCC
3024515 AAAACAATATGACCCAAGAACCCTACTTCTTGGAGCCAAAATT
1 AAAACAATATGACCCAAGAACCCTACTTCTTGGAGCCAAAATT
*
3024558 AAAATAATATGACCCAAGAACCCTACTTCTTGGAGCCAAAATT
1 AAAACAATATGACCCAAGAACCCTACTTCTTGGAGCCAAAATT
3024601 CACTCTTGCT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.42, C:0.24, G:0.12, T:0.22
Consensus pattern (43 bp):
AAAACAATATGACCCAAGAACCCTACTTCTTGGAGCCAAAATT
Found at i:3038030 original size:37 final size:37
Alignment explanation
Indices: 3037952--3038022 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
3037942 TTATTACGAA
* *
3037952 GTCTTACCCGGACATAATCTCCACACGAAGTTATCAG
1 GTCTTACCCGGACAAAATCTCCACACGAAGTCATCAG
*
3037989 GTCTTACCCGGACAAAATCTCCACACGTAGTCAT
1 GTCTTACCCGGACAAAATCTCCACACGAAGTCAT
3038023 TGGGTCTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.30, C:0.31, G:0.15, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCTCCACACGAAGTCATCAG
Found at i:3038218 original size:47 final size:47
Alignment explanation
Indices: 3038149--3038598 Score: 873
Period size: 47 Copynumber: 9.6 Consensus size: 47
3038139 CCCTTCGGGA
* *
3038149 CTTATCACATTTATACACTTTCACATCCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
3038196 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
3038243 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
3038290 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
3038337 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
3038384 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
3038431 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
3038478 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
3038525 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
3038572 CTTATCACATATATAAACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
3038599 TATTCAAATA
Statistics
Matches: 400, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 400 1.00
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:3044681 original size:55 final size:55
Alignment explanation
Indices: 3044596--3044704 Score: 173
Period size: 55 Copynumber: 2.0 Consensus size: 55
3044586 GTCCATGCCC
* * *
3044596 GTGTTAATCTGACAGGTTCGACCACAGTTTCTTGGCACGGGTGTGTCGCACGCCA
1 GTGTTAATCTGACAGGTTCGACCACAGTTTCTAGGCACAGGCGTGTCGCACGCCA
* *
3044651 GTGTTAATTTGACAGGTTCGACCACGGTTTCTAGGCACAGGCGTGTCGCACGCC
1 GTGTTAATCTGACAGGTTCGACCACAGTTTCTAGGCACAGGCGTGTCGCACGCC
3044705 CATATTGTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.27
Consensus pattern (55 bp):
GTGTTAATCTGACAGGTTCGACCACAGTTTCTAGGCACAGGCGTGTCGCACGCCA
Found at i:3045047 original size:26 final size:25
Alignment explanation
Indices: 3045007--3045057 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
3044997 TACTCCTCAT
**
3045007 TCCTGCTATTTATCTCATCAAAATA
1 TCCTGCTATGAATCTCATCAAAATA
*
3045032 NTCCTGCTATGAATCTCATTAAAATA
1 -TCCTGCTATGAATCTCATCAAAATA
3045058 AGGTTTTAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.37
Consensus pattern (25 bp):
TCCTGCTATGAATCTCATCAAAATA
Found at i:3049419 original size:20 final size:19
Alignment explanation
Indices: 3049380--3049423 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
3049370 GTTTAGTCTA
3049380 TGATTGTGAAGTGAATATTT
1 TGATTGTGAAGTGAATA-TT
*
3049400 TGATTGTGAA-TTAATGATT
1 TGATTGTGAAGTGAAT-ATT
3049419 TGATT
1 TGATT
3049424 TAGCGTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.48
Consensus pattern (19 bp):
TGATTGTGAAGTGAATATT
Found at i:3053885 original size:13 final size:13
Alignment explanation
Indices: 3053867--3053894 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3053857 ACGGAAAGAC
3053867 CCTATACCTTCAA
1 CCTATACCTTCAA
3053880 CCTATACCTTCAA
1 CCTATACCTTCAA
3053893 CC
1 CC
3053895 ATTTTCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.43, G:0.00, T:0.29
Consensus pattern (13 bp):
CCTATACCTTCAA
Found at i:3057388 original size:21 final size:21
Alignment explanation
Indices: 3057364--3057405 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3057354 GCTAGGTAAG
3057364 CTTCATATTCTTTTCCCAAAT
1 CTTCATATTCTTTTCCCAAAT
3057385 CTTCATATTCTTTTCCCAAAT
1 CTTCATATTCTTTTCCCAAAT
3057406 ATTTCTCAGC
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:0.24, C:0.29, G:0.00, T:0.48
Consensus pattern (21 bp):
CTTCATATTCTTTTCCCAAAT
Found at i:3060108 original size:23 final size:23
Alignment explanation
Indices: 3060078--3060125 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
3060068 ATATGAGATG
3060078 TTAATGGCCTAATTTCATACTTT
1 TTAATGGCCTAATTTCATACTTT
3060101 TTAATGGCCTAATTTCATACTTT
1 TTAATGGCCTAATTTCATACTTT
3060124 TT
1 TT
3060126 TTTAATTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (23 bp):
TTAATGGCCTAATTTCATACTTT
Found at i:3074538 original size:28 final size:29
Alignment explanation
Indices: 3074507--3074569 Score: 101
Period size: 28 Copynumber: 2.2 Consensus size: 29
3074497 ACTATAATTA
3074507 AAGTGTGCAAGTTTGATTATAT-AGCACT
1 AAGTGTGCAAGTTTGATTATATAAGCACT
* *
3074535 AAGTGTGCGAGTTTGATTATGTAAGCACT
1 AAGTGTGCAAGTTTGATTATATAAGCACT
3074564 AAGTGT
1 AAGTGT
3074570 AAAAAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 20 0.62
29 12 0.38
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.35
Consensus pattern (29 bp):
AAGTGTGCAAGTTTGATTATATAAGCACT
Found at i:3074679 original size:20 final size:20
Alignment explanation
Indices: 3074654--3074696 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
3074644 CCAACGCACT
*
3074654 AATAAAGAAAATGTAATGAC
1 AATAAAGAAAATGCAATGAC
3074674 AATAAAGAAAATGCAATGAC
1 AATAAAGAAAATGCAATGAC
3074694 AAT
1 AAT
3074697 GTATATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.60, C:0.07, G:0.14, T:0.19
Consensus pattern (20 bp):
AATAAAGAAAATGCAATGAC
Found at i:3074871 original size:5 final size:5
Alignment explanation
Indices: 3074861--3074887 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
3074851 ATTGGAGCAC
3074861 TTTCT TTTCT TTTCT TTTCT TTTCT TT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TT
3074888 GGGCTTTGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:3077512 original size:48 final size:48
Alignment explanation
Indices: 3077450--3078756 Score: 2184
Period size: 48 Copynumber: 27.1 Consensus size: 48
3077440 AATTCTAAAT
*
3077450 TGTG-ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
3077497 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
3077545 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
3077593 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
3077641 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
3077689 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
3077737 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
3077785 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
3077833 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
3077881 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
3077929 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
3077977 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
3078025 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
3078073 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
3078121 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
3078169 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
3078217 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
3078265 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATA
* *
3078315 TGTG-ATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATA
* *
3078364 TGTG-ATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATA
* *
3078413 TGTG-ATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATA
* *
3078462 TGTG-ATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATA
* *
3078511 TGTG-ATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATA
* *
3078560 TGTG-ATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATA
* *
3078609 TGTG-ATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATA
* *
3078658 TGTG-ATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* * * * * * *
3078705 TGTG-ACAGGGCCGAGTGGCCAATGTGATGGATGTGAAAGTGCATAAA
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
3078752 TGTGA
1 TGTGA
3078757 TAAGTCCCGA
Statistics
Matches: 1244, Mismatches: 12, Indels: 7
0.98 0.01 0.01
Matches are distributed among these distances:
47 52 0.04
48 804 0.65
49 378 0.30
50 10 0.01
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.30
Consensus pattern (48 bp):
TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
Found at i:3078934 original size:37 final size:37
Alignment explanation
Indices: 3078878--3078956 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
3078868 TCGAGCTCTA
* * *
3078878 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
3078915 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
3078952 AAGAC
1 AAGAC
3078957 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:3091890 original size:75 final size:74
Alignment explanation
Indices: 3091764--3091913 Score: 219
Period size: 75 Copynumber: 2.0 Consensus size: 74
3091754 CGCTCTTCAC
* *
3091764 TCGGCATTGTCCGTAGTGAAATTTTTTGCAACTCTTACACTTCAGCCTTTGATCATCTACACTCC
1 TCGGCATTCTCCGTAGTGAAATTTATTGCAACTCTTACACTTCAGCCTTTGATCATCTACACTCC
3091829 CCACACTAG
66 CCACACTAG
* * * * *
3091838 NTCGGCATTCTCCGTAGTGAAATTTATTGCAACTCTTATACTTCGGCTTTTGATCATCTATACTT
1 -TCGGCATTCTCCGTAGTGAAATTTATTGCAACTCTTACACTTCAGCCTTTGATCATCTACACTC
*
3091903 TCCACACTAG
65 CCCACACTAG
3091913 T
1 T
3091914 TACCATTAGG
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
74 1 0.01
75 66 0.99
ACGTcount: A:0.23, C:0.27, G:0.13, T:0.37
Consensus pattern (74 bp):
TCGGCATTCTCCGTAGTGAAATTTATTGCAACTCTTACACTTCAGCCTTTGATCATCTACACTCC
CCACACTAG
Found at i:3098066 original size:36 final size:36
Alignment explanation
Indices: 3098019--3098091 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
3098009 GAGTAAAGAG
*
3098019 AATGATGCAAATGAACAAATGAAAAGGACAAATTCT
1 AATGATGCAAATGAACAAATGAAAAAGACAAATTCT
*
3098055 AATGATGCAAATGAACAAATGAAAAAGACTAATTCT
1 AATGATGCAAATGAACAAATGAAAAAGACAAATTCT
3098091 A
1 A
3098092 CCTCAGATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.53, C:0.11, G:0.15, T:0.21
Consensus pattern (36 bp):
AATGATGCAAATGAACAAATGAAAAAGACAAATTCT
Found at i:3106269 original size:35 final size:35
Alignment explanation
Indices: 3106230--3106299 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
3106220 CAATATGGTG
3106230 GTTTACCTACTACCTCAGAAAATTCATTTTCCCTA
1 GTTTACCTACTACCTCAGAAAATTCATTTTCCCTA
*
3106265 GTTTACCTACTACCTCAGGAAATTCATTTTCCCTA
1 GTTTACCTACTACCTCAGAAAATTCATTTTCCCTA
3106300 CGGATTCGGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.27, C:0.29, G:0.07, T:0.37
Consensus pattern (35 bp):
GTTTACCTACTACCTCAGAAAATTCATTTTCCCTA
Found at i:3109676 original size:27 final size:27
Alignment explanation
Indices: 3109645--3109822 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
3109635 TAAATTGTAC
3109645 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * ** *
3109672 TGCACTAAGTGTGCAAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
3109698 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
3109726 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
3109754 AGCACTAAGTGTGCGATTTGATTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
3109781 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
3109808 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
3109823 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:3109759 original size:82 final size:81
Alignment explanation
Indices: 3109646--3109801 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
3109636 AAATTGTACA
*
3109646 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCAAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCAAAATGAATATGTA-GCACTAAGTG
3109710 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
3109727 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTATGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCAAAATGAATATGTAGCACTAAGTG
*
3109792 TGCGAGTTGA
65 TGCGAATTGA
3109802 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCAAAATGAATATGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:3109813 original size:82 final size:81
Alignment explanation
Indices: 3109642--3109822 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
3109632 GATTAAATTG
*
3109642 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCAAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCAAAATGAATATGATGCACTAA
3109707 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * * ** *
3109723 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTATG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCAAAATGAATATGAT-GCACT
* **
3109787 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
3109805 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
3109823 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCAAAATGAATATGATGCACTAA
GTGTGCGAATTGACCA
Found at i:3112515 original size:21 final size:21
Alignment explanation
Indices: 3112491--3112534 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3112481 CCTTTATGTC
* *
3112491 TTATTCTGAGTAAATATTCTT
1 TTATTCTAAGCAAATATTCTT
*
3112512 TTATTTTAAGCAAATATTCTT
1 TTATTCTAAGCAAATATTCTT
3112533 TT
1 TT
3112535 CTTGCATTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.55
Consensus pattern (21 bp):
TTATTCTAAGCAAATATTCTT
Found at i:3117186 original size:64 final size:64
Alignment explanation
Indices: 3117112--3117239 Score: 220
Period size: 64 Copynumber: 2.0 Consensus size: 64
3117102 TCATTCATAA
**
3117112 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGTATCCTAATTATTTGACATAAGCAT
1 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAACATCCTAATTATTTGACATAAGCAT
* *
3117176 CACATCTAGTTAGGAGTATTTGATTCATTTCGATCATAACATCCTAATTATTTGGCATAAGCAT
1 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAACATCCTAATTATTTGACATAAGCAT
3117240 AAATATATGA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (64 bp):
CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAACATCCTAATTATTTGACATAAGCAT
Found at i:3117409 original size:44 final size:45
Alignment explanation
Indices: 3117306--3117477 Score: 147
Period size: 45 Copynumber: 3.8 Consensus size: 45
3117296 GTGAAGTCAG
* ** * ** *
3117306 ATCTTATCTCCCTGAAGTTACAGCAGAATAGATCAAAGATTA-CAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGA-TAGCGA
* * *
3117351 ACCTTATCTTCCTGAAGTTGCAGTGGAGTAGGTTGAAG-T-GAC-A
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGATAG-CGA
* *
3117394 AGTCTTATCTCCCTGAAGTTGC-GATGGAGCAGACTGAAGATAGCGA
1 A-TCTTATCTCCCTGAAGTTGCAG-TGGAGTAGATTGAAGATAGCGA
* *
3117440 ATCTTATTTCCCTGAAGTTGCAGTGGAATAGATTGAAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAG
3117478 CTATAAATAA
Statistics
Matches: 101, Mismatches: 18, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
43 4 0.04
44 31 0.31
45 62 0.61
46 4 0.04
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.28
Consensus pattern (45 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGATAGCGA
Found at i:3117789 original size:177 final size:177
Alignment explanation
Indices: 3117561--3117893 Score: 459
Period size: 177 Copynumber: 1.9 Consensus size: 177
3117551 TGTAGTGGAG
* * ** *
3117561 CAGGCTCAAGATACAAGTCTTATCTTCCTGGAGTTGTAGTGGAGGAGACTAAAAATTACAGATCT
1 CAGGCTCAAGATACAAGTCTTATCTTCCTGGAGTAGCAAAGAAGGAGACTAAAAATTACAGATCT
* * * * *
3117626 TATCTCCTTAAGCAGTAGTGGAGTAGATCGAAGACGACGAATCTTATCTCCATGTATCAGCAATG
66 TAGCTCCCTAAGCAGTAGTGGAGCAGATCAAAAACGACGAATCTTATCTCCATGTATCAGCAATG
* * *
3117691 GAGCAGATTTTAGCCACTAGCCTTATTTCTCTGAGGTAGCAAGAGAA
131 GAACAGATTTAAGCCACTACCCTTATTTCTCTGAGGTAGCAAGAGAA
* * * * *
3117738 CAGGCTGAAGATACTAGTTTTATCTTCCTGGGGTAGCAAAGAAGTAGACTAAAAATTACAGATCT
1 CAGGCTCAAGATACAAGTCTTATCTTCCTGGAGTAGCAAAGAAGGAGACTAAAAATTACAGATCT
* ** *
3117803 TAGCTCCCTAAGCAGTAGTGGAGCAGATCAAAAATGGTGAATCTTATCTCCATGTATCGGCAATG
66 TAGCTCCCTAAGCAGTAGTGGAGCAGATCAAAAACGACGAATCTTATCTCCATGTATCAGCAATG
*
3117868 GAACAGATTTAAGCTACTACCCTTAT
131 GAACAGATTTAAGCCACTACCCTTAT
3117894 CTCCCTAAGG
Statistics
Matches: 133, Mismatches: 23, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
177 133 1.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.28
Consensus pattern (177 bp):
CAGGCTCAAGATACAAGTCTTATCTTCCTGGAGTAGCAAAGAAGGAGACTAAAAATTACAGATCT
TAGCTCCCTAAGCAGTAGTGGAGCAGATCAAAAACGACGAATCTTATCTCCATGTATCAGCAATG
GAACAGATTTAAGCCACTACCCTTATTTCTCTGAGGTAGCAAGAGAA
Found at i:3121699 original size:3 final size:3
Alignment explanation
Indices: 3121691--3121723 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3121681 CACTCTGCTC
3121691 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3121724 AAATTTAACT
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):
TTA
Found at i:3124711 original size:28 final size:29
Alignment explanation
Indices: 3124679--3124752 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 29
3124669 TAAAAATTAA
3124679 AAAATGTTTTTTATATTTTTA-TACTTTT
1 AAAATGTTTTTTATATTTTTAGTACTTTT
** * * **
3124707 AAAATAATTTTAATA-ATTTAGTTTTTTT
1 AAAATGTTTTTTATATTTTTAGTACTTTT
3124735 AAAATGTTTTTTATATTT
1 AAAATGTTTTTTATATTT
3124753 ATTTAGATTT
Statistics
Matches: 34, Mismatches: 10, Indels: 3
0.72 0.21 0.06
Matches are distributed among these distances:
27 4 0.12
28 29 0.85
29 1 0.03
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (29 bp):
AAAATGTTTTTTATATTTTTAGTACTTTT
Found at i:3134351 original size:56 final size:56
Alignment explanation
Indices: 3134263--3134374 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
3134253 GACAAGGAGC
*
3134263 GGTTCAGGTTGGATCCACACAAAAGGTAAGTACATATGAAAATGAATGATATAATA
1 GGTTCAGGTTGGATCCACACAAAAGGTAAGTACATATGAAAATGAAAGATATAATA
*
3134319 GGTTCAGGTTGGATCCACACAAAAGGTTAGTACATATGAAAATGAAAGATATAATA
1 GGTTCAGGTTGGATCCACACAAAAGGTAAGTACATATGAAAATGAAAGATATAATA
3134375 TATTCTTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.25
Consensus pattern (56 bp):
GGTTCAGGTTGGATCCACACAAAAGGTAAGTACATATGAAAATGAAAGATATAATA
Found at i:3143108 original size:50 final size:50
Alignment explanation
Indices: 3143033--3143127 Score: 190
Period size: 50 Copynumber: 1.9 Consensus size: 50
3143023 AAAAAAATAT
3143033 ATATTTATGCCGTTATGCTCTTACCTTCCTATCATTGTAACATGTGTATG
1 ATATTTATGCCGTTATGCTCTTACCTTCCTATCATTGTAACATGTGTATG
3143083 ATATTTATGCCGTTATGCTCTTACCTTCCTATCATTGTAACATGT
1 ATATTTATGCCGTTATGCTCTTACCTTCCTATCATTGTAACATGT
3143128 TATCTCGTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.22, C:0.21, G:0.13, T:0.44
Consensus pattern (50 bp):
ATATTTATGCCGTTATGCTCTTACCTTCCTATCATTGTAACATGTGTATG
Found at i:3143354 original size:165 final size:163
Alignment explanation
Indices: 3143082--3143409 Score: 613
Period size: 165 Copynumber: 2.0 Consensus size: 163
3143072 ACATGTGTAT
3143082 GATATTTATGCCGTTATGCTCTTACCTTCCTATCATTGTAACATGTTATCTCGTATGTTATGTTA
1 GATATTTATGCCGTTATGCTCTTACCTTCCTATCATTGTAACATGTTATCTCGTATGTTATGTTA
*
3143147 ATATGCTCCTTCATGCATCGATTTTTTTCTTTTTTTTTAAAAAAAAACGAGACTTCAAATTTTTC
66 ATATGCTCATTCATGCATCGATTTTTTTCTTTTTTTTT--AAAAAAACGAGACTTCAAATTTTTC
3143212 AAAAAAATAAAAAGGCAATGCTTGGTGTTTGGAAG
129 AAAAAAATAAAAAGGCAATGCTTGGTGTTTGGAAG
3143247 GATATTTATGCCGTTATGCTCTTACCTTCCTATCATTGTAACATGTTATCTCGTATGTTATGTTA
1 GATATTTATGCCGTTATGCTCTTACCTTCCTATCATTGTAACATGTTATCTCGTATGTTATGTTA
3143312 ATATGCTCATTCATGCATCGATTTTTTT-TCTTTTTTTTAAAAAAACGAGACTTCAAATTTTTCA
66 ATATGCTCATTCATGCATCGATTTTTTTCT-TTTTTTTTAAAAAAACGAGACTTCAAATTTTTCA
3143376 AAAAAATAAAAAGGCAATGCTTGGTGTTTGGAAG
130 AAAAAATAAAAAGGCAATGCTTGGTGTTTGGAAG
3143410 CTTCGAGAAA
Statistics
Matches: 161, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
163 60 0.37
164 1 0.01
165 100 0.62
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (163 bp):
GATATTTATGCCGTTATGCTCTTACCTTCCTATCATTGTAACATGTTATCTCGTATGTTATGTTA
ATATGCTCATTCATGCATCGATTTTTTTCTTTTTTTTTAAAAAAACGAGACTTCAAATTTTTCAA
AAAAATAAAAAGGCAATGCTTGGTGTTTGGAAG
Found at i:3143662 original size:56 final size:56
Alignment explanation
Indices: 3143590--3143700 Score: 213
Period size: 56 Copynumber: 2.0 Consensus size: 56
3143580 AGGAATTTCT
*
3143590 AAAAAAAGGGTTAACTTAATGTCAATACTTTGATACGAGTGAATCCCAATTTTCAC
1 AAAAAAAAGGTTAACTTAATGTCAATACTTTGATACGAGTGAATCCCAATTTTCAC
3143646 AAAAAAAAGGTTAACTTAATGTCAATACTTTGATACGAGTGAATCCCAATTTTCA
1 AAAAAAAAGGTTAACTTAATGTCAATACTTTGATACGAGTGAATCCCAATTTTCA
3143701 AAATTAAAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.31
Consensus pattern (56 bp):
AAAAAAAAGGTTAACTTAATGTCAATACTTTGATACGAGTGAATCCCAATTTTCAC
Found at i:3146994 original size:15 final size:15
Alignment explanation
Indices: 3146958--3147007 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
3146948 CGATATCCTT
3146958 TTTGCAT-TCATGCA
1 TTTGCATCTCATGCA
3146972 TTTGCATCTCATAGCA
1 TTTGCATCTCAT-GCA
3146988 TTT-CATCAT-AT-CA
1 TTTGCATC-TCATGCA
3147001 TTTGCAT
1 TTTGCAT
3147008 TAAAAGTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
13 5 0.16
14 10 0.31
15 10 0.31
16 7 0.22
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (15 bp):
TTTGCATCTCATGCA
Found at i:3155375 original size:210 final size:210
Alignment explanation
Indices: 3155007--3155775 Score: 1034
Period size: 210 Copynumber: 3.7 Consensus size: 210
3154997 CTTCATCAGG
* * * *
3155007 GCAGATCCAAGATGAAAGATCTTATCTCTCTGTATTTAGCGGGGAGCAGATTGAAGATATAGCTG
1 GCAGATCCAAGATGACAGATCTTATCTCTCTGTATTCAGCGGGGAGCAGATCGAAGACATAGCTG
* *
3155072 ATTTGGCTTTCACGTGTTTACGATAAAACAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGA
66 ATTTGGCTTTCACGTGTTTACGATAAAGCAAATCTAAGATGATTTGTCATCTCTGTATTGTCAGA
* ** * *
3155137 GAACAAATCGAAGTCTGGCATTTCCACTTTGATGGA-AGGCAGACACATAGTAGATCTTACCTTC
131 GAACAAATCGAAGTCTGGCATCTCCACTTCAATGGAGA-GCAGACACATAGCAGATCTCACCTTC
3155201 AGATGTTTACGCTGAA
195 AGATGTTTACGCTGAA
* * *
3155217 GCAGATCTAAGATGACAGATCTTATCTCTCTGTATTCGGCGGGGAGCAGATCGAAGATATAGCTG
1 GCAGATCCAAGATGACAGATCTTATCTCTCTGTATTCAGCGGGGAGCAGATCGAAGACATAGCTG
* * *
3155282 GTTTGGCTTTCACGCGTTTACGATGAAGCAAATCTAAGATGATTTGTCATCTCTGTATTGTCAGA
66 ATTTGGCTTTCACGTGTTTACGATAAAGCAAATCTAAGATGATTTGTCATCTCTGTATTGTCAGA
* * *
3155347 GAACAAATCAAAGTCTGGCATCTCCACTTCAATGGAGAACAGACACATAGCAGATCTCACCTTTA
131 GAACAAATCGAAGTCTGGCATCTCCACTTCAATGGAGAGCAGACACATAGCAGATCTCACCTTCA
3155412 GATGTTTACGCTGAA
196 GATGTTTACGCTGAA
* *
3155427 GCAGATCCAAGATGACAGATCTTATCTCTCTGTACTCAGCGGGGAGGAGATCGAAGACATAGCTG
1 GCAGATCCAAGATGACAGATCTTATCTCTCTGTATTCAGCGGGGAGCAGATCGAAGACATAGCTG
*
3155492 ATTTGGCTTTCACGTGTTTACGATAAAGCAAATCTAAGATGATTTGTCATCTCTGCATTGTCAGA
66 ATTTGGCTTTCACGTGTTTACGATAAAGCAAATCTAAGATGATTTGTCATCTCTGTATTGTCAGA
* * * * *
3155557 GAACAAATCGAAGTCTGGTATCTCCACTTCAATGGAGAGTAGATACACAGCAGATCTGACCTTCA
131 GAACAAATCGAAGTCTGGCATCTCCACTTCAATGGAGAGCAGACACATAGCAGATCTCACCTTCA
* *
3155622 GACGATTA-GACTGAA
196 GATGTTTACG-CTGAA
*** * * ** * *
3155637 GCAAGATCCAAGATGATTTAGC--ATC-CT-TGTGCTT-A-CAAGGAACAAATCGAAGACATAGC
1 GC-AGATCCAAGATGACAGATCTTATCTCTCTGT-ATTCAGCGGGGAGCAGATCGAAGACATAGC
* * * * *
3155696 TGATTTGGCTTTCACATGCTTACGATGAAGCAAATCTAAGAT-AGTTTGGCATCTCTGTATTATC
64 TGATTTGGCTTTCACGTGTTTACGATAAAGCAAATCTAAGATGA-TTTGTCATCTCTGTATTGTC
3155760 AGAGAACAAATCGAAG
128 AGAGAACAAATCGAAG
3155776 AAGCAGATTT
Statistics
Matches: 500, Mismatches: 54, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
205 1 0.00
206 91 0.18
207 4 0.01
208 3 0.01
209 4 0.01
210 381 0.76
211 16 0.03
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (210 bp):
GCAGATCCAAGATGACAGATCTTATCTCTCTGTATTCAGCGGGGAGCAGATCGAAGACATAGCTG
ATTTGGCTTTCACGTGTTTACGATAAAGCAAATCTAAGATGATTTGTCATCTCTGTATTGTCAGA
GAACAAATCGAAGTCTGGCATCTCCACTTCAATGGAGAGCAGACACATAGCAGATCTCACCTTCA
GATGTTTACGCTGAA
Found at i:3156997 original size:567 final size:566
Alignment explanation
Indices: 3155924--3157012 Score: 1944
Period size: 567 Copynumber: 1.9 Consensus size: 566
3155914 GAGGGGCAGC
* * *
3155924 TGTAATAGCCTAAATTTGACCGAGCTGAAAGCAGAATATAAAAATTAAAATTTCCATTTAAAAAG
1 TGTAATAGCCCAAATTTAACCGAGCTGAAAGCAGAATATAAAAATTAAAATGTCCATTTAAAAAG
*
3155989 TCCAATTACAAGACCCTACCTAGCAGGCCCACTGTTACTACCCAGCAACCCAAATAAACCCAATA
66 TCCAATTACAAGACCCTACCCAGCAGGCCCACTGTTACTACCCAGCAACCCAAATAAACCCAATA
*
3156054 ACCCCATAGCTCGTTACAGTAACCCAATACACCAATACAGTCATGACCCAAATTCTTAGCAGGCC
131 ACCCCATAGCCCGTTACAGTAACCCAATACACCAATACAGTCATGACCCAAATTCTTAGCAGGCC
* * *
3156119 CAATGAGCCCCAAACACACATCAAACCTTAGTGTTTCTTCCTAACTTTTTTTCCTCGCGCTGTAA
196 CAATGAGCCCCAAACACACATCAAACCCTAGGGTTTCTTCCTAACTTTTTTTCCTCGCGCCGTAA
* * * *
3156184 GGGATTCTGGAAGCTTCGGGGAGCGTCTGTCCAGCTCTCTGAATCGAGGCCATCAATGCAGTCAA
261 GGGATTCTGGAAGCTTCGGGGAGCGTCTGTCCAGCTCCCCGAATCAAAGCCATCAATGCAGTCAA
* * * *
3156249 GGTCGGGACCGTCACCGTCATCATCGAAGCCTTCATCATCGCCACCATCAACGCGCAAGACACGC
326 GGCCGGGACCGTCACCGCCATCATCGAAGCCTTCATCACCACCACCATCAACGCGCAAGACACGC
*
3156314 CAGAATCTGGCGTTGGCTCCATTAGCGTGCAAACATTAGTGATTGAGCAAGATTCTCGTGGGTTA
391 CAGAATCTGGCGTTGGCTCCATTAGCGTGCAAACATCAGTGATTGAGCAAGATTCTCGTGGGTTA
*
3156379 CCTGCGAACAAAAAGGAAACTAAAATAAAGAGATTTCAGCAGATCACAATCAAAGATATGATACA
456 CCTGCGAACAAAAAGGAAACTAAAATAAAAAGATTTCAGCAGATCACAATCAAAGATATGATACA
3156444 ACCGTAATATAATTTTTAATTTTCTAATAATTTATTTTTGTAAGTG
521 ACCGTAATATAATTTTTAATTTTCTAATAATTTATTTTTGTAAGTG
*
3156490 TGTAATAGCCCAAATTTAACCGGGCTGAAAGCAGAATATAAAAATTAAAATGTCCATTTAAAAAG
1 TGTAATAGCCCAAATTTAACCGAGCTGAAAGCAGAATATAAAAATTAAAATGTCCATTTAAAAAG
* *
3156555 TCTAATTACAAGACCCTACCCAGCAGGCCCACTGTTACTACCCAGCAACCCAAATAAACCTAATA
66 TCCAATTACAAGACCCTACCCAGCAGGCCCACTGTTACTACCCAGCAACCCAAATAAACCCAATA
* *
3156620 ACCCCATAGCCCGTTACAGTAACTCAATACACCAATACAGTCATGGCCCAAATTCTTAGCAGGCC
131 ACCCCATAGCCCGTTACAGTAACCCAATACACCAATACAGTCATGACCCAAATTCTTAGCAGGCC
*
3156685 CAATGAGCCCCAAACACACATCGAACCCTAGGGTTTCTTCCTAACTTTTTTTTCCTCGCGCCGTA
196 CAATGAGCCCCAAACACACATCAAACCCTAGGGTTTCTTCCTAAC-TTTTTTTCCTCGCGCCGTA
3156750 AGGGATTCTGGAAGCTTCGGGGAGCGTCTGTCCAGCTCCCCGAATCAAAGCCATCAATGCAGTCA
260 AGGGATTCTGGAAGCTTCGGGGAGCGTCTGTCCAGCTCCCCGAATCAAAGCCATCAATGCAGTCA
*
3156815 AGGCCGGGACCGTCATCGCCATCATCGAAGCCTTCATCACCACCACCATCAACGCGCAAGACACG
325 AGGCCGGGACCGTCACCGCCATCATCGAAGCCTTCATCACCACCACCATCAACGCGCAAGACACG
3156880 CCAGAATCTGGCGTTGGCTCCATTAGCGTGCAAACATCAGTGATTGAGCAAGATTCTCGTGGGTT
390 CCAGAATCTGGCGTTGGCTCCATTAGCGTGCAAACATCAGTGATTGAGCAAGATTCTCGTGGGTT
3156945 ACCTGCGAACAAAAAGGAAACTAAAATAAAAAGATTTCAGCAGATCACAATCAAAGATATGATAC
455 ACCTGCGAACAAAAAGGAAACTAAAATAAAAAGATTTCAGCAGATCACAATCAAAGATATGATAC
3157010 AAC
520 AAC
3157013 AGATAAGAAA
Statistics
Matches: 497, Mismatches: 25, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
566 227 0.46
567 270 0.54
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.23
Consensus pattern (566 bp):
TGTAATAGCCCAAATTTAACCGAGCTGAAAGCAGAATATAAAAATTAAAATGTCCATTTAAAAAG
TCCAATTACAAGACCCTACCCAGCAGGCCCACTGTTACTACCCAGCAACCCAAATAAACCCAATA
ACCCCATAGCCCGTTACAGTAACCCAATACACCAATACAGTCATGACCCAAATTCTTAGCAGGCC
CAATGAGCCCCAAACACACATCAAACCCTAGGGTTTCTTCCTAACTTTTTTTCCTCGCGCCGTAA
GGGATTCTGGAAGCTTCGGGGAGCGTCTGTCCAGCTCCCCGAATCAAAGCCATCAATGCAGTCAA
GGCCGGGACCGTCACCGCCATCATCGAAGCCTTCATCACCACCACCATCAACGCGCAAGACACGC
CAGAATCTGGCGTTGGCTCCATTAGCGTGCAAACATCAGTGATTGAGCAAGATTCTCGTGGGTTA
CCTGCGAACAAAAAGGAAACTAAAATAAAAAGATTTCAGCAGATCACAATCAAAGATATGATACA
ACCGTAATATAATTTTTAATTTTCTAATAATTTATTTTTGTAAGTG
Found at i:3157498 original size:140 final size:140
Alignment explanation
Indices: 3157246--3157524 Score: 513
Period size: 140 Copynumber: 2.0 Consensus size: 140
3157236 GCATGAGTAA
3157246 GGATCTAAGGGAAGAGAGATTACCCATGGAAGGACGAAGGTTTTTAAGCCTTCAGACCACCGTGT
1 GGATCTAAGGGAAGAGAGATTACCCATGGAAGGACGAAGGTTTTTAAGCCTTCAGACCACCGTGT
* *
3157311 ACGACCGCGCGTGTGCAAACACTGCATCGTGGCCGGAGGTCGGAGCTGGGACCTCACTCTTCCCC
66 ACAACCGCGCGTGTGCAAACACTGCACCGTGGCCGGAGGTCGGAGCTGGGACCTCACTCTTCCCC
*
3157376 TCTGTAGAGT
131 TCTGCAGAGT
*
3157386 GGATCTAAGGGAAGAGAGATTACCCATGGAAGGACGAAGGTTTTTAAGCCTTCAGACCACTGTGT
1 GGATCTAAGGGAAGAGAGATTACCCATGGAAGGACGAAGGTTTTTAAGCCTTCAGACCACCGTGT
*
3157451 ACAACGGCGCGTGTGCAAACACTGCACCGTGGCCGGAGGTCGGAGCTGGGACCTCACTCTTCCCC
66 ACAACCGCGCGTGTGCAAACACTGCACCGTGGCCGGAGGTCGGAGCTGGGACCTCACTCTTCCCC
3157516 TCTGCAGAG
131 TCTGCAGAG
3157525 ATCGTTTTTT
Statistics
Matches: 134, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 134 1.00
ACGTcount: A:0.24, C:0.26, G:0.30, T:0.20
Consensus pattern (140 bp):
GGATCTAAGGGAAGAGAGATTACCCATGGAAGGACGAAGGTTTTTAAGCCTTCAGACCACCGTGT
ACAACCGCGCGTGTGCAAACACTGCACCGTGGCCGGAGGTCGGAGCTGGGACCTCACTCTTCCCC
TCTGCAGAGT
Found at i:3159057 original size:18 final size:18
Alignment explanation
Indices: 3159031--3159065 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3159021 CAAGATATCC
* *
3159031 CAAATTAAAATCCAAATT
1 CAAAATAAAACCCAAATT
3159049 CAAAATAAAACCCAAAT
1 CAAAATAAAACCCAAAT
3159066 GTCTAGAGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (18 bp):
CAAAATAAAACCCAAATT
Found at i:3159925 original size:29 final size:29
Alignment explanation
Indices: 3159883--3159943 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
3159873 ACACCCTATT
* *
3159883 ACAAGACCTGTTACACGGACGTGTGTCGC
1 ACAAGACCTATTACACGGACGTGTGTCAC
* *
3159912 ACAAGGCCTATTACACGGCCGTGTGTCAC
1 ACAAGACCTATTACACGGACGTGTGTCAC
3159941 ACA
1 ACA
3159944 CGACATACCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.26, C:0.30, G:0.25, T:0.20
Consensus pattern (29 bp):
ACAAGACCTATTACACGGACGTGTGTCAC
Found at i:3175355 original size:44 final size:44
Alignment explanation
Indices: 3175204--3175406 Score: 222
Period size: 44 Copynumber: 4.7 Consensus size: 44
3175194 AGCTCGTTCA
* *
3175204 ATGCCAACGTCCCAGACGTGGTCTTACATGT-AAT-CAAATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAATACCAA-ATCG
**
3175247 ATGCC-ACTGTCCCAGACAG-GGTCTTACAC--AAA-ATTAAATACG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAAATACCAAAT-CG
* * *
3175289 ATGTCAACGTCCTAGACATGGTCTTACACGTAAATACCAAATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAATACCAAATCG
*
3175333 ATGCCAACGTCCCAGACGTGGTCTTACACATAAATACCAAATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAATACCAAATCG
* * *
3175377 ATGCCAACGTCCTAGACATAGTCTTACACG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG
3175407 ATTTCACATA
Statistics
Matches: 134, Mismatches: 16, Indels: 19
0.79 0.09 0.11
Matches are distributed among these distances:
41 2 0.01
42 30 0.22
43 25 0.19
44 72 0.54
45 5 0.04
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (44 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAATACCAAATCG
Found at i:3175356 original size:86 final size:86
Alignment explanation
Indices: 3175204--3175406 Score: 254
Period size: 86 Copynumber: 2.3 Consensus size: 86
3175194 AGCTCGTTCA
* * *
3175204 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAGACAGGGT
1 ATGCCAACGTCCTAGACATGGTCTTACACGTAATCAAATATCGATGCCACTGTCCCAGACAGGGT
*
3175269 CTTACACA-AAAT-TAAATACG
66 CTTACACATAAATACAAAT-CG
* *
3175289 ATGTCAACGTCCTAGACATGGTCTTACACGTAAATACCAA-ATCGATGCCAAC-GTCCCAGAC-G
1 ATGCCAACGTCCTAGACATGGTCTTACACGT-AAT-CAAATATCGATGCC-ACTGTCCCAGACAG
3175351 TGGTCTTACACATAAATACCAAATCG
63 -GGTCTTACACATAAATA-CAAATCG
*
3175377 ATGCCAACGTCCTAGACATAGTCTTACACG
1 ATGCCAACGTCCTAGACATGGTCTTACACG
3175407 ATTTCACATA
Statistics
Matches: 103, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
85 28 0.27
86 32 0.31
87 9 0.09
88 30 0.29
89 4 0.04
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (86 bp):
ATGCCAACGTCCTAGACATGGTCTTACACGTAATCAAATATCGATGCCACTGTCCCAGACAGGGT
CTTACACATAAATACAAATCG
Found at i:3178583 original size:40 final size:39
Alignment explanation
Indices: 3178499--3178683 Score: 194
Period size: 40 Copynumber: 4.6 Consensus size: 39
3178489 TTGAATGATG
* * * * *
3178499 TCCGGGCTAATTCCTGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCC-GAAGGCATTTGTGC-GAGTTACTAAA
* * *
3178539 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
3178579 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
* *
3178618 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
3178659 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
3178684 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
39 35 0.28
40 76 0.62
41 12 0.10
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:3178705 original size:79 final size:79
Alignment explanation
Indices: 3178552--3178716 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
3178542 GGACTAAGAT
* * **
3178552 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
3178617 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
3178631 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
3178694 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
3178710 CCGAAGG
1 CCGAAGG
3178717 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:3180660 original size:23 final size:23
Alignment explanation
Indices: 3180626--3180699 Score: 89
Period size: 23 Copynumber: 3.2 Consensus size: 23
3180616 CTCCTGAGCT
3180626 GCTG-AACAGTAAGCTCTATTGA
1 GCTGAAACAGTAAGCTCTATTGA
**
3180648 GCTGAAACAGTAAGCTCTATCAA
1 GCTGAAACAGTAAGCTCTATTGA
*
3180671 GCTGAAAATAGTAAGCTCT-TTCGA
1 GCTG-AAACAGTAAGCTCTATT-GA
3180695 GCTGA
1 GCTGA
3180700 TATATTGGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
22 4 0.09
23 22 0.50
24 18 0.41
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.26
Consensus pattern (23 bp):
GCTGAAACAGTAAGCTCTATTGA
Found at i:3180688 original size:24 final size:24
Alignment explanation
Indices: 3180630--3180699 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
3180620 TGAGCTGCTG
*
3180630 AACAGTAAGCTCTATTGAGCTG-A
1 AACAGTAAGCTCTATCGAGCTGAA
*
3180653 AACAGTAAGCTCTATCAAGCTGAA
1 AACAGTAAGCTCTATCGAGCTGAA
* *
3180677 AATAGTAAGCTCTTTCGAGCTGA
1 AACAGTAAGCTCTATCGAGCTGA
3180700 TATATTGGTA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 20 0.49
24 21 0.51
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.26
Consensus pattern (24 bp):
AACAGTAAGCTCTATCGAGCTGAA
Found at i:3182947 original size:21 final size:21
Alignment explanation
Indices: 3182923--3182964 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3182913 TATATGCTTA
3182923 GTAAGTTCGTATAACAGGAAT
1 GTAAGTTCGTATAACAGGAAT
*
3182944 GTAAGTTCGTATAATAGGAAT
1 GTAAGTTCGTATAACAGGAAT
3182965 TAAAACTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.07, G:0.24, T:0.31
Consensus pattern (21 bp):
GTAAGTTCGTATAACAGGAAT
Found at i:3186289 original size:37 final size:35
Alignment explanation
Indices: 3186238--3186308 Score: 90
Period size: 37 Copynumber: 2.0 Consensus size: 35
3186228 TCAGATTAAA
*
3186238 TAATATTATTTTAATAGT-TTAATATTAAATTTAATT
1 TAATATTATCTTAATAGTATT-ATATT-AATTTAATT
*
3186274 TAATACTTATCTTAATAGTATTTTATTAATTTAAT
1 TAATA-TTATCTTAATAGTATTATATTAATTTAAT
3186309 GCTAAAGTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 13 0.42
37 16 0.52
38 2 0.06
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (35 bp):
TAATATTATCTTAATAGTATTATATTAATTTAATT
Found at i:3194655 original size:49 final size:50
Alignment explanation
Indices: 3194589--3194718 Score: 158
Period size: 49 Copynumber: 2.6 Consensus size: 50
3194579 ATTGAAGTTT
*
3194589 ATGACGTGTCCCAGACAGGTCTTACACTGACAT-TCATATATCGAG-GCCA
1 ATGACATGTCCCAGACAGGTCTTACACTGACATCTCATATATCG-GTGCCA
* * * * * *
3194638 ATGCCATGTCCCAGACAGGTCTTAGACTGGC-TCTCATCTATTGGTGTCA
1 ATGACATGTCCCAGACAGGTCTTACACTGACATCTCATATATCGGTGCCA
*
3194687 ATGACATGTCCCAGACAGGACTTACACTGACA
1 ATGACATGTCCCAGACAGGTCTTACACTGACA
3194719 CACAACAAGC
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
48 2 0.03
49 65 0.97
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (50 bp):
ATGACATGTCCCAGACAGGTCTTACACTGACATCTCATATATCGGTGCCA
Found at i:3196448 original size:48 final size:47
Alignment explanation
Indices: 3196389--3196658 Score: 270
Period size: 48 Copynumber: 5.6 Consensus size: 47
3196379 TATGTGTGCT
* *
3196389 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCACGATATGAGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATCGG-CACGATATGAGAGCC
* ***
3196437 AGTGTAAGACCATGTTTGGAACATGGCATCGGCAATTTAATGAGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCACGAT-ATGAGAGCC
* * * * * * *
3196485 AGAGTAAGACCATGTCTGGGACATGGCATCGACATTGATATGTGTGCT
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCA-CGATATGAGAGCC
* * * * * *
3196533 AGTGTAAGACCATGTTTGGGACATGACATCAGCATTGAGACGAGAGCT
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCA-CGATATGAGAGCC
* * * *
3196581 AGTGTAAGACTATGTTTGGGACATGGCATCGGCCTCGACATGTGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATCGG-CACGATATGAGAGCC
* *
3196629 AGTGTAAGACCATATTTGGAACATGGCATC
1 AGTGTAAGACCATGTTTGGGACATGGCATC
3196659 AACAATTCAC
Statistics
Matches: 182, Mismatches: 37, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
47 3 0.02
48 177 0.97
49 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.24
Consensus pattern (47 bp):
AGTGTAAGACCATGTTTGGGACATGGCATCGGCACGATATGAGAGCC
Found at i:3196557 original size:96 final size:96
Alignment explanation
Indices: 3196392--3196659 Score: 333
Period size: 96 Copynumber: 2.8 Consensus size: 96
3196382 GTGTGCTAGT
* * *
3196392 GTAAGACCATGTCTGGGACATAGCATCGGCCA-CGATATGAGAGCCAGTGTAAGACCATGTTTGG
1 GTAAGACCATGTCTGGGACATGGCATC-GACATCGATATGTGAGCCAGTGTAAGACCATGTTTGG
* * *
3196456 AACATGGCATCGGCAATTTA-ATGAGAGCCAGA
65 AACATGGCATCAGC-ATTGAGACGAGAGCCAGA
* * * *
3196488 GTAAGACCATGTCTGGGACATGGCATCGACATTGATATGTGTGCTAGTGTAAGACCATGTTTGGG
1 GTAAGACCATGTCTGGGACATGGCATCGACATCGATATGTGAGCCAGTGTAAGACCATGTTTGGA
* * *
3196553 ACATGACATCAGCATTGAGACGAGAGCTAGT
66 ACATGGCATCAGCATTGAGACGAGAGCCAGA
* * * * * *
3196584 GTAAGACTATGTTTGGGACATGGCATCGGCCTCGACATGTGAGCCAGTGTAAGACCATATTTGGA
1 GTAAGACCATGTCTGGGACATGGCATCGACATCGATATGTGAGCCAGTGTAAGACCATGTTTGGA
3196649 ACATGGCATCA
66 ACATGGCATCA
3196660 ACAATTCACC
Statistics
Matches: 146, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
95 7 0.05
96 139 0.95
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (96 bp):
GTAAGACCATGTCTGGGACATGGCATCGACATCGATATGTGAGCCAGTGTAAGACCATGTTTGGA
ACATGGCATCAGCATTGAGACGAGAGCCAGA
Found at i:3196589 original size:144 final size:144
Alignment explanation
Indices: 3196376--3196658 Score: 374
Period size: 144 Copynumber: 2.0 Consensus size: 144
3196366 TGACATTTAG
* * *
3196376 TGATATGTGTGCTAGTGTAAGACCATGTCTGGGACATAGCATCGGCCACGATATGAGAGCCAGTG
1 TGATATGTGTGCTAGTGTAAGACCATGTCTGGGACATAGCATCAGCCACGAGACGAGAGCCAGTG
** * *
3196441 TAAGACCATGTTTGGAACATGGCATCGGCAATTTA-ATGAGAGCCAGAGTAAGACCATGTCTGGG
66 TAAGACCATGTTTGGAACATGGCATCGGC-ATCGACATGAGAGCCAGAGTAAGACCATATCTGGA
3196505 ACATGGCATCGACAT
130 ACATGGCATCGACAT
* * *
3196520 TGATATGTGTGCTAGTGTAAGACCATGTTTGGGACAT-GACATCAG-CATTGAGACGAGAGCTAG
1 TGATATGTGTGCTAGTGTAAGACCATGTCTGGGACATAG-CATCAGCCA-CGAGACGAGAGCCAG
* * * * * *
3196583 TGTAAGACTATGTTTGGGACATGGCATCGGCCTCGACATGTGAGCCAGTGTAAGACCATATTTGG
64 TGTAAGACCATGTTTGGAACATGGCATCGGCATCGACATGAGAGCCAGAGTAAGACCATATCTGG
3196648 AACATGGCATC
129 AACATGGCATC
3196659 AACAATTCAC
Statistics
Matches: 120, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
143 5 0.04
144 115 0.96
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (144 bp):
TGATATGTGTGCTAGTGTAAGACCATGTCTGGGACATAGCATCAGCCACGAGACGAGAGCCAGTG
TAAGACCATGTTTGGAACATGGCATCGGCATCGACATGAGAGCCAGAGTAAGACCATATCTGGAA
CATGGCATCGACAT
Found at i:3201627 original size:40 final size:40
Alignment explanation
Indices: 3201574--3201929 Score: 541
Period size: 40 Copynumber: 8.9 Consensus size: 40
3201564 GAATACACAT
*
3201574 CACCAGCATGAATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* * *
3201614 CACCAGTACGAATGCTCTTCGGGACTTAACCCTGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* *
3201654 CTCCAGCACGAATGCTCTTCGAGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* *
3201694 CACCAACACGTATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* *
3201734 CACCAGCATGTATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* * **
3201774 CTCTAGCACGAATGCTCTTCGGGACTTAGCCCCAATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
*
3201814 CACCAGCACGTATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* **
3201854 CTCTTGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
*
3201894 CACCAGCACGTATGCTCTTCGGGACTTAGCCCGGAT
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
3201930 CATCGGCGAG
Statistics
Matches: 282, Mismatches: 34, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 282 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
Found at i:3205277 original size:66 final size:66
Alignment explanation
Indices: 3205200--3205331 Score: 264
Period size: 66 Copynumber: 2.0 Consensus size: 66
3205190 TTCAACCATT
3205200 CAAAGCCTATCTAATTTCTCAAATAGATTTCTAATACAAGAATTAAGCCAACCTACTAACCTTGA
1 CAAAGCCTATCTAATTTCTCAAATAGATTTCTAATACAAGAATTAAGCCAACCTACTAACCTTGA
3205265 C
66 C
3205266 CAAAGCCTATCTAATTTCTCAAATAGATTTCTAATACAAGAATTAAGCCAACCTACTAACCTTGA
1 CAAAGCCTATCTAATTTCTCAAATAGATTTCTAATACAAGAATTAAGCCAACCTACTAACCTTGA
3205331 C
66 C
3205332 ACCCACATTC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.39, C:0.24, G:0.08, T:0.29
Consensus pattern (66 bp):
CAAAGCCTATCTAATTTCTCAAATAGATTTCTAATACAAGAATTAAGCCAACCTACTAACCTTGA
C
Found at i:3205662 original size:69 final size:69
Alignment explanation
Indices: 3205576--3205710 Score: 270
Period size: 69 Copynumber: 2.0 Consensus size: 69
3205566 TAAAATCTCA
3205576 AAGAATTTACCTAAAACTTACCTTAATTAAGCAAGTAGAAGACCGAATGCCTAGCTTCTTCCCCC
1 AAGAATTTACCTAAAACTTACCTTAATTAAGCAAGTAGAAGACCGAATGCCTAGCTTCTTCCCCC
3205641 CTCC
66 CTCC
3205645 AAGAATTTACCTAAAACTTACCTTAATTAAGCAAGTAGAAGACCGAATGCCTAGCTTCTTCCCCC
1 AAGAATTTACCTAAAACTTACCTTAATTAAGCAAGTAGAAGACCGAATGCCTAGCTTCTTCCCCC
3205710 C
66 C
3205711 CCCTTTTTTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (69 bp):
AAGAATTTACCTAAAACTTACCTTAATTAAGCAAGTAGAAGACCGAATGCCTAGCTTCTTCCCCC
CTCC
Found at i:3208518 original size:21 final size:21
Alignment explanation
Indices: 3208470--3208519 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
3208460 TTTTGACTCA
*
3208470 TTTTTCACCCAAATTGAGAGT
1 TTTTTCTCCCAAATTGAGAGT
*
3208491 TTTTTCTCCCGAATTGAGAGT
1 TTTTTCTCCCAAATTGAGAGT
3208512 TTTTTCTC
1 TTTTTCTC
3208520 TCTTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (21 bp):
TTTTTCTCCCAAATTGAGAGT
Found at i:3212451 original size:28 final size:28
Alignment explanation
Indices: 3212388--3212538 Score: 214
Period size: 28 Copynumber: 5.4 Consensus size: 28
3212378 ATATTAAGTC
*
3212388 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
3212415 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
3212443 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTATATAATCAAACT
*
3212471 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
3212499 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
3212528 CGCACACTTAG
1 CGCACACTTAG
3212539 CGCCAATCTC
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.19
28 75 0.66
29 16 0.14
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:3214841 original size:26 final size:26
Alignment explanation
Indices: 3214812--3214865 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
3214802 TAATAAATGA
3214812 TAGTTAATTAGTCATAAATGAGGTGT
1 TAGTTAATTAGTCATAAATGAGGTGT
3214838 TAGTTAATTAGTCATAAATGAGGTGT
1 TAGTTAATTAGTCATAAATGAGGTGT
3214864 TA
1 TA
3214866 TAAGGTTGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.39
Consensus pattern (26 bp):
TAGTTAATTAGTCATAAATGAGGTGT
Found at i:3216636 original size:25 final size:25
Alignment explanation
Indices: 3216603--3216656 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 25
3216593 ATTAAACTAG
*
3216603 TTTTCTTT-ATTTTTTTAAATATTTA
1 TTTTATTTAATTTTTTTAAA-ATTTA
*
3216628 TTTTATTTACATTTTTTTATAATTTA
1 TTTTATTTA-ATTTTTTTAAAATTTA
3216654 TTT
1 TTT
3216657 GATCGAATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.28
26 8 0.32
27 10 0.40
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (25 bp):
TTTTATTTAATTTTTTTAAAATTTA
Found at i:3220630 original size:6 final size:6
Alignment explanation
Indices: 3220616--3220651 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
3220606 CCAAAATCTG
*
3220616 CTATTC CTATGC CTATGC CTATGC CTATGC CTATGC
1 CTATGC CTATGC CTATGC CTATGC CTATGC CTATGC
3220652 ATTTGACCGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.33, G:0.14, T:0.36
Consensus pattern (6 bp):
CTATGC
Done.