Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 71 of 125
Found at i:22304483 original size:63 final size:63
Alignment explanation
Indices: 22304403--22304637 Score: 219
Period size: 63 Copynumber: 3.7 Consensus size: 63
22304393 ATGCATTTCT
* *
22304403 AAGGGCACCGTAA-TGCAAGACAAGGGCATCGTAGTGCAATACAGGGGCACCATAGTGCAATAC
1 AAGGGCACCG-AAGTGCAAGACAAGGGCACCGAAGTGCAATACAGGGGCACCATAGTGCAATAC
* * * * * *
22304466 AAGGGCACCGAAGTGCAAGTCAAGAGCACCGTAGTGTAATATAGGGGCACCGA-AGTACAAGT-C
1 AAGGGCACCGAAGTGCAAGACAAGGGCACCGAAGTGCAATACAGGGGCACC-ATAGTGCAA-TAC
* * * * * * * *
22304529 AAGGGAATCGTAGTGCAATACAGGGGCACGGAAGTGCAAGTA-AGGGGTACCGTAGTGCAATAC
1 AAGGGCACCGAAGTGCAAGACAAGGGCACCGAAGTGCAA-TACAGGGGCACCATAGTGCAATAC
* * *
22304592 AGGGGCACTGAAGTGCAAGTC-AGGAGCACCGAAGTGCAATACAGGG
1 AAGGGCACCGAAGTGCAAGACAAGG-GCACCGAAGTGCAATACAGGG
22304638 CCATTTTTCA
Statistics
Matches: 136, Mismatches: 28, Indels: 16
0.76 0.16 0.09
Matches are distributed among these distances:
62 7 0.05
63 125 0.92
64 4 0.03
ACGTcount: A:0.34, C:0.20, G:0.32, T:0.14
Consensus pattern (63 bp):
AAGGGCACCGAAGTGCAAGACAAGGGCACCGAAGTGCAATACAGGGGCACCATAGTGCAATAC
Found at i:22304495 original size:42 final size:42
Alignment explanation
Indices: 22304383--22304638 Score: 250
Period size: 42 Copynumber: 6.1 Consensus size: 42
22304373 AACATTACTG
* ** * *
22304383 GGGCACCGAAATGCATTTCTAAGGGCACCGTAATGCAAGACAA
1 GGGCACCGAAGTGCAAGTC-AAGGGCACCGTAGTGCAATACAA
* * * *
22304426 GGGCATCGTAGTGCAA-TACAGGGGCACCATAGTGCAATACAA
1 GGGCACCGAAGTGCAAGT-CAAGGGCACCGTAGTGCAATACAA
* * * *
22304468 GGGCACCGAAGTGCAAGTCAAGAGCACCGTAGTGTAATATAG
1 GGGCACCGAAGTGCAAGTCAAGGGCACCGTAGTGCAATACAA
* * * *
22304510 GGGCACCGAAGTACAAGTCAAGGGAATCGTAGTGCAATACAG
1 GGGCACCGAAGTGCAAGTCAAGGGCACCGTAGTGCAATACAA
* * *
22304552 GGGCACGGAAGTGCAAGT-AAGGGGTACCGTAGTGCAATACAG
1 GGGCACCGAAGTGCAAGTCAA-GGGCACCGTAGTGCAATACAA
* *
22304594 GGGCACTGAAGTGCAAGTC-AGGAGCACCGAAGTGCAATAC-A
1 GGGCACCGAAGTGCAAGTCAAGG-GCACCGTAGTGCAATACAA
22304635 GGGC
1 GGGC
22304639 CATTTTTCAC
Statistics
Matches: 178, Mismatches: 30, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
41 8 0.04
42 156 0.88
43 14 0.08
ACGTcount: A:0.33, C:0.20, G:0.32, T:0.15
Consensus pattern (42 bp):
GGGCACCGAAGTGCAAGTCAAGGGCACCGTAGTGCAATACAA
Found at i:22304636 original size:21 final size:21
Alignment explanation
Indices: 22304382--22304637 Score: 191
Period size: 21 Copynumber: 12.1 Consensus size: 21
22304372 GAACATTACT
* * *
22304382 GGGGCACCGAAATGCATTTCTA
1 GGGGCACCGAAGTGCAATAC-A
* *
22304404 AGGGCACCGTAA-TGCAAGACA
1 GGGGCACCG-AAGTGCAATACA
* * *
22304425 AGGGCATCGTAGTGCAATACA
1 GGGGCACCGAAGTGCAATACA
22304446 GGGGCACC-ATAGTGCAATACA
1 GGGGCACCGA-AGTGCAATACA
*
22304467 AGGGCACCGAAGTGCAAGT-CA
1 GGGGCACCGAAGTGCAA-TACA
* * * * *
22304488 AGAGCACCGTAGTGTAATATA
1 GGGGCACCGAAGTGCAATACA
*
22304509 GGGGCACCGAAGTACAAGT-CA
1 GGGGCACCGAAGTGCAA-TACA
* * * *
22304530 AGGGAATCGTAGTGCAATACA
1 GGGGCACCGAAGTGCAATACA
*
22304551 GGGGCACGGAAGTGCAAGTA-A
1 GGGGCACCGAAGTGCAA-TACA
* *
22304572 GGGGTACCGTAGTGCAATACA
1 GGGGCACCGAAGTGCAATACA
*
22304593 GGGGCACTGAAGTGCAAGT-CA
1 GGGGCACCGAAGTGCAA-TACA
*
22304614 GGAGCACCGAAGTGCAATACA
1 GGGGCACCGAAGTGCAATACA
22304635 GGG
1 GGG
22304638 CCATTTTTCA
Statistics
Matches: 182, Mismatches: 40, Indels: 25
0.74 0.16 0.10
Matches are distributed among these distances:
20 6 0.03
21 155 0.85
22 19 0.10
23 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.32, T:0.15
Consensus pattern (21 bp):
GGGGCACCGAAGTGCAATACA
Found at i:22306480 original size:21 final size:21
Alignment explanation
Indices: 22306455--22306504 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
22306445 ATACTTGAAA
*
22306455 TACTTCTATCGATACAAG-TG
1 TACTTCTATCGAAACAAGTTG
*
22306475 TAACTTCTATTGAAACAAGTTG
1 T-ACTTCTATCGAAACAAGTTG
22306497 TACTTCTA
1 TACTTCTA
22306505 CTGATACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 1 0.04
21 22 0.85
22 3 0.12
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (21 bp):
TACTTCTATCGAAACAAGTTG
Found at i:22307304 original size:25 final size:25
Alignment explanation
Indices: 22307210--22307307 Score: 108
Period size: 25 Copynumber: 3.9 Consensus size: 25
22307200 GATAGAGAAT
* *
22307210 CGCTCTTACGAGCAAGACAAAATTA
1 CGCTCTTACGAGCCAGACAGAATTA
* * * *
22307235 CACTCTTGCGAGCCAAACA-AAATA
1 CGCTCTTACGAGCCAGACAGAATTA
*
22307259 CCGCTCTTATGAGCCAGACAGAATTA
1 -CGCTCTTACGAGCCAGACAGAATTA
*
22307285 CGCTCTTGCGAGCCAGACAGAAT
1 CGCTCTTACGAGCCAGACAGAAT
22307308 ATTTCTCTTA
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
24 4 0.07
25 51 0.86
26 4 0.07
ACGTcount: A:0.35, C:0.28, G:0.18, T:0.19
Consensus pattern (25 bp):
CGCTCTTACGAGCCAGACAGAATTA
Found at i:22307316 original size:50 final size:50
Alignment explanation
Indices: 22307210--22307351 Score: 151
Period size: 50 Copynumber: 2.8 Consensus size: 50
22307200 GATAGAGAAT
* * * *
22307210 CGCTCTTACGAGCAAGACAAAATTACACTCTTGCGAGCCAAACAAAATAC
1 CGCTCTTACGAGCCAGACAGAATTACGCTCTTGCGAGCCAGACAAAATAC
* * *
22307260 CGCTCTTATGAGCCAGACAGAATTACGCTCTTGCGAGCCAGACAGAATAT
1 CGCTCTTACGAGCCAGACAGAATTACGCTCTTGCGAGCCAGACAAAATAC
** * * * *
22307310 TTCTCTTACAAGCCAAATAGAATTATGCTCTTGC-ATGCCAGA
1 CGCTCTTACGAGCCAGACAGAATTACGCTCTTGCGA-GCCAGA
22307352 ATCAGAATGT
Statistics
Matches: 77, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
49 1 0.01
50 76 0.99
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (50 bp):
CGCTCTTACGAGCCAGACAGAATTACGCTCTTGCGAGCCAGACAAAATAC
Found at i:22310835 original size:99 final size:99
Alignment explanation
Indices: 22310712--22310934 Score: 263
Period size: 99 Copynumber: 2.3 Consensus size: 99
22310702 TCCCTGTTGT
* * * * *
22310712 GGCCTTAACCTTTCCCTTT-ATATCTTTATGATAGCGGATTCGCTGTTGT-GACCTCAATCCTTC
1 GGCCTCAACCTTT-CCTTTCATATCTTCATGATACCAGATTCGCCGTTGTAG-CCTCAATCCTTC
* *
22310775 CCATCGCATCTTC-AATGGTATCGGGTTTGCCATTGC
64 CCATCACATCTTCTAA-GGTATCGGGTTCGCCATTGC
* * ** *
22310811 GGCTTCAACCTTTCCTTTCATATCTTCATGGTACCAGATTTTCCGTTGTAGCCTCAATTCTTCCC
1 GGCCTCAACCTTTCCTTTCATATCTTCATGATACCAGATTCGCCGTTGTAGCCTCAATCCTTCCC
* *
22310876 ATCACATCTTCTAAGGTATCGGGTTCGCCGTTGT
66 ATCACATCTTCTAAGGTATCGGGTTCGCCATTGC
*
22310910 GGCCTCAACCTTTCCCTTCATATCT
1 GGCCTCAACCTTTCCTTTCATATCT
22310935 CTATATTTCC
Statistics
Matches: 105, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
98 5 0.05
99 97 0.92
100 3 0.03
ACGTcount: A:0.17, C:0.29, G:0.16, T:0.38
Consensus pattern (99 bp):
GGCCTCAACCTTTCCTTTCATATCTTCATGATACCAGATTCGCCGTTGTAGCCTCAATCCTTCCC
ATCACATCTTCTAAGGTATCGGGTTCGCCATTGC
Found at i:22310925 original size:50 final size:49
Alignment explanation
Indices: 22310699--22310934 Score: 163
Period size: 50 Copynumber: 4.8 Consensus size: 49
22310689 TAAGGTACAA
* * * * * *
22310699 GGTTC-CCTGTTGTGGCCTTAACCTTTCCCTTTATATCTTTATGATAGCG
1 GGTTCGCC-GTTGTGGCCTCAACCTTTCCCTTCATATCTTCAAGGTATCG
* * * * **
22310748 GATTCGCTGTTGTGACCTCAATCC-TTCCCATCGCATCTTCAATGGTATCG
1 GGTTCGCCGTTGTGGCCTCAA-CCTTTCCCTTCATATCTTCAA-GGTATCG
* * * * * * * *
22310798 GGTTTGCCATTGCGGCTTCAACCTTTCCTTTCATATCTTCATGGTACCA
1 GGTTCGCCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCAAGGTATCG
* ** * * * *
22310847 GATTTTCCGTTGTAGCCTCAA-TTCTTCCCATCACATCTTCTAAGGTATCG
1 GGTTCGCCGTTGTGGCCTCAACCT-TTCCCTTCATATCTTC-AAGGTATCG
22310897 GGTTCGCCGTTGTGGCCTCAACCTTTCCCTTCATATCT
1 GGTTCGCCGTTGTGGCCTCAACCTTTCCCTTCATATCT
22310935 CTATATTTCC
Statistics
Matches: 134, Mismatches: 46, Indels: 13
0.69 0.24 0.07
Matches are distributed among these distances:
48 1 0.01
49 62 0.46
50 70 0.52
51 1 0.01
ACGTcount: A:0.16, C:0.29, G:0.17, T:0.38
Consensus pattern (49 bp):
GGTTCGCCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCAAGGTATCG
Found at i:22324029 original size:56 final size:56
Alignment explanation
Indices: 22323943--22324055 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
22323933 GATCAATCCT
22323943 CTTTAATTGAGTGATTCTGGATCCCTTTCTCTATATTAGGTTAGGAATAAATTTAA
1 CTTTAATTGAGTGATTCTGGATCCCTTTCTCTATATTAGGTTAGGAATAAATTTAA
22323999 CTTTAATTGAGTGATTCTGGATCCCTTTCTCTATATTAGGTTAGGAATAAATTTAA
1 CTTTAATTGAGTGATTCTGGATCCCTTTCTCTATATTAGGTTAGGAATAAATTTAA
22324055 C
1 C
22324056 CCAATTTTTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.42
Consensus pattern (56 bp):
CTTTAATTGAGTGATTCTGGATCCCTTTCTCTATATTAGGTTAGGAATAAATTTAA
Found at i:22349866 original size:86 final size:87
Alignment explanation
Indices: 22349669--22350275 Score: 565
Period size: 86 Copynumber: 7.1 Consensus size: 87
22349659 CTAGTACGTA
* * ** * ** * * * *
22349669 AGTGCATCATCGGATAAATCGAAGTAGTTATACTGGCACACATAGTATATCATCAGATAAACC-A
1 AGTGCATCATCGAATATATCGAAGTAACTATACTGGCACACACAGTGCATCATCGGACAAGCCTG
*
22349733 AAGCAATTATATTGGCAC--AC
66 AAGCAATTATACTGGCACATAC
*
22349753 AGTGCATCAGC-AGATATATCGAAGTAACTATA-TAGGCACACACAGTGCATCATCGGACAAGCC
1 AGTGCATCATCGA-ATATATCGAAGTAACTATACT-GGCACACACAGTGCATCATCGGACAAGCC
*
22349816 TG-AGCAATTATATTGGCACATAC
64 TGAAGCAATTATACTGGCACATAC
* *
22349839 AGTGCATCATCGAATATATCGAAGTAACTATACTGGCACACACAGTGCGTCATCGGACAAGCC-A
1 AGTGCATCATCGAATATATCGAAGTAACTATACTGGCACACACAGTGCATCATCGGACAAGCCTG
** * *
22349903 AAAAAATTACACTAGCACATAC
66 AAGCAATTATACTGGCACATAC
* * * * * * *
22349925 AATGCATCATCGAATATATCAAAGCAACTATACTGGCACACATAGTGCATTATTGGAAAAG-CTG
1 AGTGCATCATCGAATATATCGAAGTAACTATACTGGCACACACAGTGCATCATCGGACAAGCCTG
*
22349989 AAGCAATTATACTAGCACATAC
66 AAGCAATTATACTGGCACATAC
* ** * ** * * * *
22350011 AATATATCATCGGATATGCCGAAGCAACTATATTGGCACACACAGTGCATCATCGGACATG-TTG
1 AGTGCATCATCGAATATATCGAAGTAACTATACTGGCACACACAGTGCATCATCGGACAAGCCTG
* *
22350075 AAGCAATTATACTGGAACATAT
66 AAGCAATTATACTGGCACATAC
* * * * * ** * * **
22350097 AGTGCATCATCGGATATACCAAAGCAATTATACAAGCACACACAATCCATCATAAGACAAGCC-G
1 AGTGCATCATCGAATATATCGAAGTAACTATACTGGCACACACAGTGCATCATCGGACAAGCCTG
22350161 AAGCAATTATACTGGCACATAC
66 AAGCAATTATACTGGCACATAC
* * * ** *
22350183 AGTGCGTCATC-AGATATA-CTGAAGTAACTATACTGACACACACAATGCATCATCAAACAAGTC
1 AGTGCATCATCGA-ATATATC-GAAGTAACTATACTGGCACACACAGTGCATCATCGGACAAGCC
*
22350246 -GAAGCAATTATACTGACACATAC
64 TGAAGCAATTATACTGGCACATAC
22350269 AGTGCAT
1 AGTGCAT
22350276 TATCAGGTAT
Statistics
Matches: 432, Mismatches: 79, Indels: 22
0.81 0.15 0.04
Matches are distributed among these distances:
83 1 0.00
84 66 0.15
85 2 0.00
86 361 0.84
87 2 0.00
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (87 bp):
AGTGCATCATCGAATATATCGAAGTAACTATACTGGCACACACAGTGCATCATCGGACAAGCCTG
AAGCAATTATACTGGCACATAC
Found at i:22349884 original size:43 final size:43
Alignment explanation
Indices: 22349669--22350275 Score: 324
Period size: 43 Copynumber: 14.2 Consensus size: 43
22349659 CTAGTACGTA
* * * * * *
22349669 AGTGCATCATCGGATAAATCGAAGTAGTTATACTGGCACACAT
1 AGTGCATCATCGAATATACCGAAGCAATTATACTGGCACACAC
** * * *
22349712 AGTATATCATC-AGATAAACCAAAGCAATTATATTGG--CACAC
1 AGTGCATCATCGA-ATATACCGAAGCAATTATACTGGCACACAC
* * * *
22349753 AGTGCATCAGC-AGATATATCGAAGTAACTATA-TAGGCACACAC
1 AGTGCATCATCGA-ATATACCGAAGCAATTATACT-GGCACACAC
* * * *
22349796 AGTGCATCATCGGACA-AGCCTG-AGCAATTATATTGGCACATAC
1 AGTGCATCATCGAATATA-CC-GAAGCAATTATACTGGCACACAC
* * *
22349839 AGTGCATCATCGAATATATCGAAGTAACTATACTGGCACACAC
1 AGTGCATCATCGAATATACCGAAGCAATTATACTGGCACACAC
* * * * ** * * *
22349882 AGTGCGTCATCGGACA-AGCCAAAAAAATTACACTAGCACATAC
1 AGTGCATCATCGAATATA-CCGAAGCAATTATACTGGCACACAC
* * * * *
22349925 AATGCATCATCGAATATATCAAAGCAACTATACTGGCACACAT
1 AGTGCATCATCGAATATACCGAAGCAATTATACTGGCACACAC
* * * * *
22349968 AGTGCATTATTGGAA-A-AGCTGAAGCAATTATACTAGCACATAC
1 AGTGCATCA-TCGAATATA-CCGAAGCAATTATACTGGCACACAC
* ** * * * *
22350011 AATATATCATCGGATATGCCGAAGCAACTATATTGGCACACAC
1 AGTGCATCATCGAATATACCGAAGCAATTATACTGGCACACAC
* * *** * * *
22350054 AGTGCATCATCGGACATGTTGAAGCAATTATACTGGAACATAT
1 AGTGCATCATCGAATATACCGAAGCAATTATACTGGCACACAC
* * **
22350097 AGTGCATCATCGGATATACCAAAGCAATTATACAAGCACACAC
1 AGTGCATCATCGAATATACCGAAGCAATTATACTGGCACACAC
* * * * *
22350140 AATCCATCATAAGACA-A-GCCGAAGCAATTATACTGGCACATAC
1 AGTGCATCAT-CGA-ATATACCGAAGCAATTATACTGGCACACAC
* * * * *
22350183 AGTGCGTCATC-AGATATACTGAAGTAACTATACTGACACACAC
1 AGTGCATCATCGA-ATATACCGAAGCAATTATACTGGCACACAC
* * * * * *
22350226 AATGCATCATCAAACA-AGTCGAAGCAATTATACTGACACATAC
1 AGTGCATCATCGAATATA-CCGAAGCAATTATACTGGCACACAC
22350269 AGTGCAT
1 AGTGCAT
22350276 TATCAGGTAT
Statistics
Matches: 416, Mismatches: 126, Indels: 44
0.71 0.22 0.08
Matches are distributed among these distances:
40 1 0.00
41 32 0.08
42 9 0.02
43 362 0.87
44 11 0.03
45 1 0.00
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (43 bp):
AGTGCATCATCGAATATACCGAAGCAATTATACTGGCACACAC
Found at i:22351393 original size:72 final size:72
Alignment explanation
Indices: 22351306--22351505 Score: 258
Period size: 72 Copynumber: 2.8 Consensus size: 72
22351296 TTGCCCTGAC
* *
22351306 CAGTAAAACCGAAAAATGAGTGTGCCCAACACTGATCGATATAACCGAAAAATAAATACACCCTG
1 CAGTAAAACCAAAAAATGAGTGTGCCCAACACTGGTCGATATAACCGAAAAATAAATACACCCTG
*
22351371 CATTGGT
66 CACTGGT
* * * * * * * *
22351378 CAGTAAAATCAAAAAATGAGTGTGCCAAAAATTGGTTGATATAATCGAAAAATAAATGCGCCCTG
1 CAGTAAAACCAAAAAATGAGTGTGCCCAACACTGGTCGATATAACCGAAAAATAAATACACCCTG
22351443 CACTGGT
66 CACTGGT
* * * *
22351450 CCGTAAAACCAACAAATGAGTGTGCCCAACACTGGTCGGTATAACC-ACAAATAAAT
1 CAGTAAAACCAAAAAATGAGTGTGCCCAACACTGGTCGATATAACCGAAAAATAAAT
22351506 GCGTCCCGCG
Statistics
Matches: 107, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
71 9 0.08
72 98 0.92
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.20
Consensus pattern (72 bp):
CAGTAAAACCAAAAAATGAGTGTGCCCAACACTGGTCGATATAACCGAAAAATAAATACACCCTG
CACTGGT
Found at i:22352347 original size:21 final size:21
Alignment explanation
Indices: 22352318--22352371 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
22352308 GTGCAGTTTC
* *
22352318 CTACTGATAGAAGT-GGGTGTT
1 CTACCGATACAAGTAGGG-GTT
*
22352339 CTACCGATACAAGTATGGGTT
1 CTACCGATACAAGTAGGGGTT
*
22352360 CTACCGACACAA
1 CTACCGATACAA
22352372 CTCATACATC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (21 bp):
CTACCGATACAAGTAGGGGTT
Found at i:22353429 original size:158 final size:158
Alignment explanation
Indices: 22353141--22353447 Score: 391
Period size: 158 Copynumber: 1.9 Consensus size: 158
22353131 CTTGTATTGC
* * * * * *
22353141 TCACATGAGCTGTAAAATAGGCCTGCTCACACGAGCTGTGGGTTGAGATGTCGAGCTACACGATG
1 TCACACGAGCTGTAAAATAGGCCTGCTCACAAGAGCTATGGGTCGAGAAGTCGAGCTACACGATA
* * * ** * * *
22353206 CTGCTCACACGAGTTGTGGAGAATTTGGAATAATTGTTCGTTCTCAACCATCGGTAGGACATCTA
66 CTGCTCACACAAGCTATGGAGAATCCGCAATAATTGTACGATCTCAACCATCGGTAGGACATCTA
*
22353271 AGACCAGCACCCATATAACCTGTAATGT
131 AGACAAGCACCCATATAACCTGTAATGT
* * * *
22353299 TCACACGAGCTGTGAAATGGGCCTGCTCACAAGAGCTATGGGTCGAGAAGTTGAGCTACACGGTA
1 TCACACGAGCTGTAAAATAGGCCTGCTCACAAGAGCTATGGGTCGAGAAGTCGAGCTACACGATA
* * * *
22353364 CTGCTCACATAAGCTATGGAGAATCCGCAATAATTG-ACGGATCTTAGCCATCGTTAGGACATCT
66 CTGCTCACACAAGCTATGGAGAATCCGCAATAATTGTAC-GATCTCAACCATCGGTAGGACATCT
22353428 AAGACAAGCACCCATATAAC
130 AAGACAAGCACCCATATAAC
22353448 TTATAATCCT
Statistics
Matches: 125, Mismatches: 23, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
157 1 0.01
158 124 0.99
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.24
Consensus pattern (158 bp):
TCACACGAGCTGTAAAATAGGCCTGCTCACAAGAGCTATGGGTCGAGAAGTCGAGCTACACGATA
CTGCTCACACAAGCTATGGAGAATCCGCAATAATTGTACGATCTCAACCATCGGTAGGACATCTA
AGACAAGCACCCATATAACCTGTAATGT
Found at i:22358516 original size:13 final size:13
Alignment explanation
Indices: 22358500--22358524 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22358490 TTAGATTTAT
22358500 TGATTTTGTAAAG
1 TGATTTTGTAAAG
22358513 TGATTTTGTAAA
1 TGATTTTGTAAA
22358525 ATGGTGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (13 bp):
TGATTTTGTAAAG
Found at i:22368490 original size:17 final size:17
Alignment explanation
Indices: 22368465--22368508 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
22368455 CATGCATTTC
22368465 TTTTAATTGTCAT-TGCA
1 TTTTAATTGTC-TCTGCA
*
22368482 TTTTTATTGTCTCTGCA
1 TTTTAATTGTCTCTGCA
*
22368499 TTTTACTTGT
1 TTTTAATTGT
22368509 TTTAGCATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 1 0.04
17 22 0.96
ACGTcount: A:0.16, C:0.14, G:0.11, T:0.59
Consensus pattern (17 bp):
TTTTAATTGTCTCTGCA
Found at i:22374190 original size:36 final size:36
Alignment explanation
Indices: 22374143--22374231 Score: 133
Period size: 36 Copynumber: 2.5 Consensus size: 36
22374133 TGGTAATAGG
22374143 CATGAACTTTGGGTCAATAAGAAGTAAAATGAGCAT
1 CATGAACTTTGGGTCAATAAGAAGTAAAATGAGCAT
* *
22374179 CATGATCTTTGGGTCAATAAGGAGTAAAATGAGCAT
1 CATGAACTTTGGGTCAATAAGAAGTAAAATGAGCAT
* * *
22374215 TATGACCTTTGAGTCAA
1 CATGAACTTTGGGTCAA
22374232 CAGGGAGTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.28
Consensus pattern (36 bp):
CATGAACTTTGGGTCAATAAGAAGTAAAATGAGCAT
Found at i:22374239 original size:36 final size:36
Alignment explanation
Indices: 22374143--22374243 Score: 121
Period size: 36 Copynumber: 2.8 Consensus size: 36
22374133 TGGTAATAGG
* * * *
22374143 CATGAACTTTGGGTCAATAAGAAGTAAAATGAGCAT
1 CATGACCTTTGAGTCAACAAGGAGTAAAATGAGCAT
* * *
22374179 CATGATCTTTGGGTCAATAAGGAGTAAAATGAGCAT
1 CATGACCTTTGAGTCAACAAGGAGTAAAATGAGCAT
* *
22374215 TATGACCTTTGAGTCAACAGGGAGTAAAA
1 CATGACCTTTGAGTCAACAAGGAGTAAAA
22374244 CGAATAACGA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.26
Consensus pattern (36 bp):
CATGACCTTTGAGTCAACAAGGAGTAAAATGAGCAT
Found at i:22381490 original size:36 final size:37
Alignment explanation
Indices: 22381448--22381551 Score: 140
Period size: 36 Copynumber: 2.9 Consensus size: 37
22381438 TGGTAACAAG
22381448 CATGACCTTTAGGTCAATAGGGAGTAAAACGAGCA-T
1 CATGACCTTTAGGTCAATAGGGAGTAAAACGAGCAGT
* * * *
22381484 CATGACCTCTGGGTCAATAGGGAGTAAAACAAGTAGT
1 CATGACCTTTAGGTCAATAGGGAGTAAAACGAGCAGT
* *
22381521 -ATGACCTTTAGGTCAACAGGCAGTAAAACGA
1 CATGACCTTTAGGTCAATAGGGAGTAAAACGA
22381552 ATAGCAAACG
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
36 57 0.98
37 1 0.02
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (37 bp):
CATGACCTTTAGGTCAATAGGGAGTAAAACGAGCAGT
Found at i:22395857 original size:11 final size:11
Alignment explanation
Indices: 22395832--22395868 Score: 56
Period size: 11 Copynumber: 3.2 Consensus size: 11
22395822 TCACATTTAT
22395832 AAAAAAAGAAGA
1 AAAAAAAGAA-A
22395844 AAAGAAAAGAAA
1 AAA-AAAAGAAA
22395856 AAAAAAAGAAA
1 AAAAAAAGAAA
22395867 AA
1 AA
22395869 TATTTATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 10 0.42
12 7 0.29
13 7 0.29
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:22411161 original size:11 final size:11
Alignment explanation
Indices: 22411136--22411172 Score: 56
Period size: 11 Copynumber: 3.2 Consensus size: 11
22411126 TCACATTTAT
22411136 AAAAAAAGAAGA
1 AAAAAAAGAA-A
22411148 AAAGAAAAGAAA
1 AAA-AAAAGAAA
22411160 AAAAAAAGAAA
1 AAAAAAAGAAA
22411171 AA
1 AA
22411173 TATTTATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 10 0.42
12 7 0.29
13 7 0.29
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:22421902 original size:24 final size:24
Alignment explanation
Indices: 22421870--22421916 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
22421860 TAATTAAACT
22421870 CTATCTGGGCTCATAAGAGCTAAC
1 CTATCTGGGCTCATAAGAGCTAAC
*
22421894 CTATCTGGGCTCGTAAGAGCTAA
1 CTATCTGGGCTCATAAGAGCTAA
22421917 TTTTGTCTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (24 bp):
CTATCTGGGCTCATAAGAGCTAAC
Found at i:22424281 original size:37 final size:36
Alignment explanation
Indices: 22424240--22424335 Score: 138
Period size: 37 Copynumber: 2.6 Consensus size: 36
22424230 ACATCCAAAT
22424240 TTGCGCCTAAAACTATCGCCACATGAGCACCTCTAGA
1 TTGCGCC-AAAACTATCGCCACATGAGCACCTCTAGA
* * *
22424277 TTGCGCCCAAAACTGTCGCCACATGAGCACTTCTAGG
1 TTGCG-CCAAAACTATCGCCACATGAGCACCTCTAGA
*
22424314 TTGCACCAAAACTATCGCCACA
1 TTGCGCCAAAACTATCGCCACA
22424336 GGTATATTTC
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
36 16 0.30
37 35 0.66
38 2 0.04
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (36 bp):
TTGCGCCAAAACTATCGCCACATGAGCACCTCTAGA
Found at i:22424448 original size:37 final size:38
Alignment explanation
Indices: 22424351--22424434 Score: 118
Period size: 38 Copynumber: 2.2 Consensus size: 38
22424341 ATTTCCGAAA
*
22424351 TGCACCCA-AGACTATTACTGCATAAATATTCTTCAAAT
1 TGCACCCAGA-ACTATCACTGCATAAATATTCTTCAAAT
* *
22424389 TGCATCCAGAACTATCACTGCATAAGTATTCTTC-AAT
1 TGCACCCAGAACTATCACTGCATAAATATTCTTCAAAT
22424426 TGCACCCAG
1 TGCACCCAG
22424435 GAATGTCGCT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
37 11 0.27
38 29 0.71
39 1 0.02
ACGTcount: A:0.33, C:0.26, G:0.11, T:0.30
Consensus pattern (38 bp):
TGCACCCAGAACTATCACTGCATAAATATTCTTCAAAT
Found at i:22425614 original size:21 final size:21
Alignment explanation
Indices: 22425580--22425619 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
22425570 TATGAAATTG
* *
22425580 CCTGCTTGTTTCGGTAGAACT
1 CCTGCATGTATCGGTAGAACT
22425601 CCTGCATGTATCGGTAGAA
1 CCTGCATGTATCGGTAGAA
22425620 GTACAGGGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.33
Consensus pattern (21 bp):
CCTGCATGTATCGGTAGAACT
Found at i:22433432 original size:25 final size:25
Alignment explanation
Indices: 22433377--22433449 Score: 103
Period size: 25 Copynumber: 3.0 Consensus size: 25
22433367 TTAAACTCTG
* *
22433377 TCTGGGCTTGTAAGAGCTAA-CCTA
1 TCTGGGCTCGTAAGAGCTAATTCTA
22433401 TCTGGGCTCGTAAGAGCTAATTCTA
1 TCTGGGCTCGTAAGAGCTAATTCTA
* *
22433426 TCTGGGCTCGTATGACCTAATTCT
1 TCTGGGCTCGTAAGAGCTAATTCT
22433450 GGAAGACCTA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
24 19 0.43
25 25 0.57
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (25 bp):
TCTGGGCTCGTAAGAGCTAATTCTA
Found at i:22437148 original size:30 final size:29
Alignment explanation
Indices: 22437114--22437236 Score: 102
Period size: 30 Copynumber: 4.1 Consensus size: 29
22437104 CAAATCTCAA
* * *
22437114 ATATACCAAAATAGCCACAAAGGCTTTCAC
1 ATATA-CAAAACAACCACAAAGGCTTCCAC
* * *
22437144 ATATATCAAAACATCCACGAAGGCTTTCAC
1 ATATA-CAAAACAACCACAAAGGCTTCCAC
* * *
22437174 ATATGATAGAACAACCACAACGGCTTCCAC
1 ATAT-ACAAAACAACCACAAAGGCTTCCAC
* * *
22437204 ATATAACAAAATACCCACACAGGCTTCCAC
1 ATAT-ACAAAACAACCACAAAGGCTTCCAC
22437234 ATA
1 ATA
22437237 CCGATAAACT
Statistics
Matches: 75, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
30 74 0.99
31 1 0.01
ACGTcount: A:0.42, C:0.28, G:0.10, T:0.20
Consensus pattern (29 bp):
ATATACAAAACAACCACAAAGGCTTCCAC
Found at i:22437608 original size:13 final size:14
Alignment explanation
Indices: 22437590--22437619 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
22437580 TTCAATACAA
22437590 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
22437603 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
22437617 TCA
1 TCA
22437620 ATGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:22439169 original size:12 final size:12
Alignment explanation
Indices: 22439152--22439185 Score: 61
Period size: 11 Copynumber: 2.9 Consensus size: 12
22439142 GCAAATATAA
22439152 TTTTTTTTCTTC
1 TTTTTTTTCTTC
22439164 TTTTTTTTC-TC
1 TTTTTTTTCTTC
22439175 TTTTTTTTCTT
1 TTTTTTTTCTT
22439186 TTTCAAGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTTTCTTC
Found at i:22440279 original size:12 final size:12
Alignment explanation
Indices: 22440262--22440297 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
22440252 CTTTTGTTTA
22440262 TTCTCTTCTTCC
1 TTCTCTTCTTCC
22440274 TTCTCTTCTT-C
1 TTCTCTTCTTCC
22440285 TTC-CTT-TTCC
1 TTCTCTTCTTCC
22440295 TTC
1 TTC
22440298 AGTTGGTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.09
10 7 0.30
11 4 0.17
12 10 0.43
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (12 bp):
TTCTCTTCTTCC
Found at i:22450411 original size:10 final size:10
Alignment explanation
Indices: 22450378--22450431 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 10
22450368 TCAATCATTT
22450378 GAAAAAGAAA
1 GAAAAAGAAA
* * *
22450388 CAAAATGAGA
1 GAAAAAGAAA
22450398 -AAAAAGAAA
1 GAAAAAGAAA
*
22450407 GAAAAAAAAA
1 GAAAAAGAAA
22450417 GAAAAAAGAAA
1 G-AAAAAGAAA
22450428 GAAA
1 GAAA
22450432 TTTTTGATAA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
9 7 0.20
10 19 0.54
11 9 0.26
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (10 bp):
GAAAAAGAAA
Found at i:22450411 original size:11 final size:11
Alignment explanation
Indices: 22450395--22450431 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
22450385 AAACAAAATG
22450395 AGAAAAAAGAA
1 AGAAAAAAGAA
22450406 AGAAAAAA-AA
1 AGAAAAAAGAA
22450416 AGAAAAAAGAA
1 AGAAAAAAGAA
22450427 AGAAA
1 AGAAA
22450432 TTTTTGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 10 0.40
11 15 0.60
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AGAAAAAAGAA
Found at i:22450419 original size:21 final size:23
Alignment explanation
Indices: 22450381--22450431 Score: 79
Period size: 21 Copynumber: 2.3 Consensus size: 23
22450371 ATCATTTGAA
*
22450381 AAAGAAACAAAATGAGAAAAAAG
1 AAAGAAACAAAATAAGAAAAAAG
22450404 AAAGAAA-AAAA-AAGAAAAAAG
1 AAAGAAACAAAATAAGAAAAAAG
22450425 AAAGAAA
1 AAAGAAA
22450432 TTTTTGATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 16 0.59
22 4 0.15
23 7 0.26
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (23 bp):
AAAGAAACAAAATAAGAAAAAAG
Found at i:22450421 original size:7 final size:7
Alignment explanation
Indices: 22450395--22450427 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
22450385 AAACAAAATG
22450395 AGAAAAA
1 AGAAAAA
22450402 AGAAAGAA
1 AGAAA-AA
22450410 A-AAAAA
1 AGAAAAA
22450416 AGAAAAA
1 AGAAAAA
22450423 AGAAA
1 AGAAA
22450428 GAAATTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 3 0.12
7 18 0.75
8 3 0.12
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AGAAAAA
Found at i:22451986 original size:13 final size:14
Alignment explanation
Indices: 22451957--22451986 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
22451947 TTCAGTACAT
22451957 TGACATTTAACCTC
1 TGACATTTAACCTC
22451971 TGACATTTAA-CTC
1 TGACATTTAACCTC
22451984 TGA
1 TGA
22451987 TTGCATTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (14 bp):
TGACATTTAACCTC
Found at i:22458121 original size:6 final size:6
Alignment explanation
Indices: 22458112--22458152 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
22458102 TTTTATTTAT
* * *
22458112 ATTTTC ATTTTC ATTTTC ATCTTC ATCTTC ATCTTC ATTTT
1 ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTTT
22458153 ATTATGCATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.17, C:0.22, G:0.00, T:0.61
Consensus pattern (6 bp):
ATTTTC
Found at i:22458127 original size:12 final size:12
Alignment explanation
Indices: 22458112--22458152 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
22458102 TTTTATTTAT
*
22458112 ATTTTCATTTTC
1 ATTTTCATCTTC
22458124 ATTTTCATCTTC
1 ATTTTCATCTTC
*
22458136 ATCTTCATCTTC
1 ATTTTCATCTTC
22458148 ATTTT
1 ATTTT
22458153 ATTATGCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.17, C:0.22, G:0.00, T:0.61
Consensus pattern (12 bp):
ATTTTCATCTTC
Found at i:22462699 original size:23 final size:22
Alignment explanation
Indices: 22462651--22462695 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
22462641 CTTTGCCTAC
*
22462651 TAAAGGTGGTAAAAAAATCACT
1 TAAAGGTGGTAAAAAAAGCACT
*
22462673 TAAAGGTGAGT-AAAGAAGCACT
1 TAAAGGTG-GTAAAAAAAGCACT
22462695 T
1 T
22462696 TAAAATTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.47, C:0.09, G:0.22, T:0.22
Consensus pattern (22 bp):
TAAAGGTGGTAAAAAAAGCACT
Found at i:22464273 original size:28 final size:28
Alignment explanation
Indices: 22464217--22464275 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
22464207 AAATGGGAAG
* **
22464217 AGAGTAAAAGTTTTGGGGAAAGTGAAAA
1 AGAGTAAAAATTTTGGGGAAAGAAAAAA
*
22464245 AGAGTAAAAATTTTGGGGAAAAAATAAAA
1 AGAGTAAAAATTTTGGGGAAAGAA-AAAA
22464274 AG
1 AG
22464276 GTTTGAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 20 0.77
29 6 0.23
ACGTcount: A:0.53, C:0.00, G:0.27, T:0.20
Consensus pattern (28 bp):
AGAGTAAAAATTTTGGGGAAAGAAAAAA
Found at i:22477495 original size:20 final size:20
Alignment explanation
Indices: 22477470--22477510 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
22477460 TTTGGAATCT
22477470 GGTCACTGATTTCTGTTTGA
1 GGTCACTGATTTCTGTTTGA
22477490 GGTCACTGATTTCTGTTTGA
1 GGTCACTGATTTCTGTTTGA
22477510 G
1 G
22477511 TCCTTCCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.27, T:0.44
Consensus pattern (20 bp):
GGTCACTGATTTCTGTTTGA
Found at i:22486488 original size:24 final size:24
Alignment explanation
Indices: 22486456--22486548 Score: 105
Period size: 24 Copynumber: 3.8 Consensus size: 24
22486446 GCGCATAAAT
*
22486456 AAGCTGACGAGCGTAAATGTGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
* **
22486480 AAGCTGACGAGCGTAAACGCGATAAAT
1 AAGCTGACGAGCGTAAACGTG-T--GC
*
22486507 AAGCTGACGAACGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
*
22486531 AAGCTGACGAGCATAAAC
1 AAGCTGACGAGCGTAAAC
22486549 ACAATAAATA
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
24 35 0.62
25 1 0.02
26 1 0.02
27 19 0.34
ACGTcount: A:0.37, C:0.19, G:0.28, T:0.16
Consensus pattern (24 bp):
AAGCTGACGAGCGTAAACGTGTGC
Found at i:22486510 original size:51 final size:51
Alignment explanation
Indices: 22486450--22486558 Score: 173
Period size: 51 Copynumber: 2.1 Consensus size: 51
22486440 TTATATGCGC
* * * * *
22486450 ATAAATAAGCTGACGAGCGTAAATGTGTGCAAGCTGACGAGCGTAAACGCG
1 ATAAATAAGCTGACGAACGTAAACGTGTGCAAGCTGACGAGCATAAACACA
22486501 ATAAATAAGCTGACGAACGTAAACGTGTGCAAGCTGACGAGCATAAACACA
1 ATAAATAAGCTGACGAACGTAAACGTGTGCAAGCTGACGAGCATAAACACA
22486552 ATAAATA
1 ATAAATA
22486559 TCTTGATATG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.17
Consensus pattern (51 bp):
ATAAATAAGCTGACGAACGTAAACGTGTGCAAGCTGACGAGCATAAACACA
Found at i:22493054 original size:42 final size:42
Alignment explanation
Indices: 22493008--22493117 Score: 141
Period size: 42 Copynumber: 2.6 Consensus size: 42
22492998 TAATCCCACG
* * *
22493008 CTCATTCCGGGTCATGAGTCTTCCTTTAATCATAATATCGTT
1 CTCATTCCGAGACATGAGTCTTCCTTTAATCATAATATCATT
* * * *
22493050 CTCATCCCAAGACATGAGTCTTCCTTTAATCATATTCTCATT
1 CTCATTCCGAGACATGAGTCTTCCTTTAATCATAATATCATT
22493092 CTCA-TCCTGAGACATGAGTCTTCCTT
1 CTCATTCC-GAGACATGAGTCTTCCTT
22493118 AAATATATCC
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 2 0.03
42 56 0.97
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.38
Consensus pattern (42 bp):
CTCATTCCGAGACATGAGTCTTCCTTTAATCATAATATCATT
Found at i:22493196 original size:43 final size:40
Alignment explanation
Indices: 22493050--22493197 Score: 116
Period size: 42 Copynumber: 3.5 Consensus size: 40
22493040 TAATATCGTT
* * * * *
22493050 CTCATCCCAAGACATGAGTCTTCCTTTAATCATATTCTCATT
1 CTCAT-CCGAGACACGAGTCTTCCTTAAAT-AAATTCTCATG
* * *
22493092 CTCATCCTGAGACATGAGTCTTCCTTAAATATATCCTCATG
1 CTCATCC-GAGACACGAGTCTTCCTTAAATAAATTCTCATG
* * * *
22493133 CTCATTTCGAGTCACAAGTCTTCCATTCATATAAATTCTCATG
1 CTCA-TCCGAGACACGAGTCTTCC-TT-AAATAAATTCTCATG
*
22493176 CTCAGACCGAGACACGAGTCTT
1 CTCA-TCCGAGACACGAGTCTT
22493198 TGATTTATAT
Statistics
Matches: 86, Mismatches: 16, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
41 28 0.33
42 29 0.34
43 29 0.34
ACGTcount: A:0.27, C:0.28, G:0.11, T:0.34
Consensus pattern (40 bp):
CTCATCCGAGACACGAGTCTTCCTTAAATAAATTCTCATG
Found at i:22496787 original size:6 final size:6
Alignment explanation
Indices: 22496776--22496814 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
22496766 TGATCAAAAT
* * *
22496776 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
22496815 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:22498604 original size:48 final size:48
Alignment explanation
Indices: 22498484--22498714 Score: 194
Period size: 50 Copynumber: 4.7 Consensus size: 48
22498474 GTGCATAAAT
* * * * * * ** *
22498484 AAGCTGACGAGCGTAAACATGTGTAAGTTGGCGAGTGTAAATGCATAAAA
1 AAGCTGACGAGCATAAACGTGTGCAAGCTGACAAGTGTAAA--CATGTAC
* * * * *
22498534 AAGTTGACGAGCGTAAACGTGTGCAAACCGACGAGTGTAAACATGTAC
1 AAGCTGACGAGCATAAACGTGTGCAAGCTGACAAGTGTAAACATGTAC
* * * * *
22498582 AAGATGGCGAGCATAAATGTGTGCAAGCTGACAAGCT-TAAATGCATGAAT
1 AAGCTGACGAGCATAAACGTGTGCAAGCTGACAAG-TGTAAA--CATGTAC
* * *
22498632 AAGCTGACGAGCATAAACGTGTGCAAGCTAACAAGTGTAAACGTGTGC
1 AAGCTGACGAGCATAAACGTGTGCAAGCTGACAAGTGTAAACATGTAC
* *
22498680 AAGCTGACGAGCATAAATGTGTGCAAGCTGGCAAG
1 AAGCTGACGAGCATAAACGTGTGCAAGCTGACAAG
22498715 CATAAACGTA
Statistics
Matches: 147, Mismatches: 30, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
48 71 0.48
49 2 0.01
50 74 0.50
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.20
Consensus pattern (48 bp):
AAGCTGACGAGCATAAACGTGTGCAAGCTGACAAGTGTAAACATGTAC
Found at i:22498608 original size:24 final size:24
Alignment explanation
Indices: 22498591--22498720 Score: 134
Period size: 24 Copynumber: 5.3 Consensus size: 24
22498581 CAAGATGGCG
22498591 AGCATAAATGTGTGCAAGCTGACA
1 AGCATAAATGTGTGCAAGCTGACA
* *** *
22498615 AGCTTAAATGCATGAATAAGCTGACG
1 AGCATAAATG--TGTGCAAGCTGACA
* *
22498641 AGCATAAACGTGTGCAAGCTAACA
1 AGCATAAATGTGTGCAAGCTGACA
** * *
22498665 AGTGTAAACGTGTGCAAGCTGACG
1 AGCATAAATGTGTGCAAGCTGACA
*
22498689 AGCATAAATGTGTGCAAGCTGGCA
1 AGCATAAATGTGTGCAAGCTGACA
22498713 AGCATAAA
1 AGCATAAA
22498721 CGTAATAAAT
Statistics
Matches: 83, Mismatches: 21, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
24 65 0.78
26 18 0.22
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (24 bp):
AGCATAAATGTGTGCAAGCTGACA
Found at i:22498669 original size:98 final size:98
Alignment explanation
Indices: 22498521--22498720 Score: 274
Period size: 98 Copynumber: 2.0 Consensus size: 98
22498511 TTGGCGAGTG
* * * *
22498521 TAAATGCATAAAAAAGTTGACGAGCGTAAACGTGTGCAAACCGACGAGTGTAAACATGTACAAGA
1 TAAATGCATAAAAAAGCTGACGAGCATAAACGTGTGCAAACCAACAAGTGTAAACATGTACAAGA
* *
22498586 TGGCGAGCATAAATGTGTGCAAGCTGACAAGCT
66 TGACGAGCATAAATGTGTGCAAGCTGACAAGCA
* * * * * * *
22498619 TAAATGCATGAATAAGCTGACGAGCATAAACGTGTGCAAGCTAACAAGTGTAAACGTGTGCAAGC
1 TAAATGCATAAAAAAGCTGACGAGCATAAACGTGTGCAAACCAACAAGTGTAAACATGTACAAGA
*
22498684 TGACGAGCATAAATGTGTGCAAGCTGGCAAGCA
66 TGACGAGCATAAATGTGTGCAAGCTGACAAGCA
22498717 TAAA
1 TAAA
22498721 CGTAATAAAT
Statistics
Matches: 88, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
98 88 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.20
Consensus pattern (98 bp):
TAAATGCATAAAAAAGCTGACGAGCATAAACGTGTGCAAACCAACAAGTGTAAACATGTACAAGA
TGACGAGCATAAATGTGTGCAAGCTGACAAGCA
Found at i:22498723 original size:48 final size:48
Alignment explanation
Indices: 22498538--22498721 Score: 179
Period size: 48 Copynumber: 3.8 Consensus size: 48
22498528 ATAAAAAAGT
* * * * * ** *
22498538 TGACGAGCGTAAACGTGTGCAAACCGACGAGTGTAAACATGTACAAGA
1 TGACGAGCATAAATGTGTGCAAGCTGACAAGCATAAACATGTACAAGC
* * * *
22498586 TGGCGAGCATAAATGTGTGCAAGCTGACAAGCTTAAATGCATGAATAAGC
1 TGACGAGCATAAATGTGTGCAAGCTGACAAGCATAAA--CATGTACAAGC
* * ** * *
22498636 TGACGAGCATAAACGTGTGCAAGCTAACAAGTGTAAACGTGTGCAAGC
1 TGACGAGCATAAATGTGTGCAAGCTGACAAGCATAAACATGTACAAGC
*
22498684 TGACGAGCATAAATGTGTGCAAGCTGGCAAGCATAAAC
1 TGACGAGCATAAATGTGTGCAAGCTGACAAGCATAAAC
22498722 GTAATAAATA
Statistics
Matches: 109, Mismatches: 25, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
48 69 0.63
50 40 0.37
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.19
Consensus pattern (48 bp):
TGACGAGCATAAATGTGTGCAAGCTGACAAGCATAAACATGTACAAGC
Found at i:22504717 original size:22 final size:22
Alignment explanation
Indices: 22504692--22504734 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
22504682 ATTTTTAAGT
*
22504692 AATTAATATTA-ATTATTTAAAA
1 AATTAA-ATTAGATTATATAAAA
*
22504714 AATTTAATTAGATTATATAAA
1 AATTAAATTAGATTATATAAA
22504735 CTAGATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
AATTAAATTAGATTATATAAAA
Found at i:22505098 original size:12 final size:12
Alignment explanation
Indices: 22505081--22505108 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
22505071 ATTGTTTGAT
22505081 TCACCATCATCA
1 TCACCATCATCA
22505093 TCACCATCATCA
1 TCACCATCATCA
22505105 TCAC
1 TCAC
22505109 TTTCTCCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.43, G:0.00, T:0.25
Consensus pattern (12 bp):
TCACCATCATCA
Found at i:22506677 original size:73 final size:72
Alignment explanation
Indices: 22506476--22506732 Score: 383
Period size: 72 Copynumber: 3.6 Consensus size: 72
22506466 AGCAAATTTT
* * * * *
22506476 ATATCC-AAAATCAAATATAAACAACTATTGATAAAACTAAATTACACATAAATAAGTAAAACAT
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTGCACATAAATAAGTAGAACAT
22506540 AAATTCA
66 AAATTCA
*
22506547 ATATCCAAAAACCAAACATAAACAATTATTGATAAAACTAGATTGCACATAAATAAGTAGAACAT
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTGCACATAAATAAGTAGAACAT
22506612 AAATTCA
66 AAATTCA
* * * * *
22506619 ATATCCAAAAACCATAC-TCATCATAACTATTGATAAAGCTAGATTGGACATAAATAAGTAGAAC
1 ATATCCAAAAACCAAACAT-A-AACAACTATTGATAAAACTAGATTGCACATAAATAAGTAGAAC
22506683 ATAAATTCA
64 ATAAATTCA
22506692 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAG
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAG
22506733 TTTAACATTG
Statistics
Matches: 166, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
71 7 0.04
72 94 0.57
73 64 0.39
74 1 0.01
ACGTcount: A:0.54, C:0.16, G:0.06, T:0.24
Consensus pattern (72 bp):
ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTGCACATAAATAAGTAGAACAT
AAATTCA
Found at i:22507192 original size:18 final size:18
Alignment explanation
Indices: 22507163--22507214 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
22507153 CGTTTCCATC
22507163 AATGTTAACATCATTTGA
1 AATGTTAACATCATTTGA
22507181 AAT-TTGAACATCATTTGA
1 AATGTT-AACATCATTTGA
22507199 AATGTTAACATCATTT
1 AATGTTAACATCATTT
22507215 CTTGCATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.06
18 28 0.88
19 2 0.06
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (18 bp):
AATGTTAACATCATTTGA
Found at i:22514421 original size:19 final size:18
Alignment explanation
Indices: 22514374--22514421 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
22514364 AACGAAATTT
*
22514374 AAAGGAAAAAAGAAAGAA
1 AAAGGAAGAAAGAAAGAA
*
22514392 AAAAGACAGAAAGAAAGGAA
1 AAAGGA-AGAAAGAAA-GAA
*
22514412 GAAGGAAGAA
1 AAAGGAAGAA
22514422 GGAGAAGAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.21
19 12 0.50
20 7 0.29
ACGTcount: A:0.71, C:0.02, G:0.27, T:0.00
Consensus pattern (18 bp):
AAAGGAAGAAAGAAAGAA
Found at i:22514603 original size:18 final size:18
Alignment explanation
Indices: 22514580--22514614 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
22514570 GGAAAAAAGG
22514580 TAAGTTTAATTAATTTTT
1 TAAGTTTAATTAATTTTT
**
22514598 TAAGTTTGGTTAATTTT
1 TAAGTTTAATTAATTTT
22514615 AAATTTAATT
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:0.29, C:0.00, G:0.11, T:0.60
Consensus pattern (18 bp):
TAAGTTTAATTAATTTTT
Found at i:22514897 original size:17 final size:18
Alignment explanation
Indices: 22514860--22514893 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
22514850 TGTTCATATT
22514860 TATTGATTTAAAATTTAA
1 TATTGATTTAAAATTTAA
22514878 TATTG-TTT-AAATTTAA
1 TATTGATTTAAAATTTAA
22514894 ATATAATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 3 0.19
18 5 0.31
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
TATTGATTTAAAATTTAA
Found at i:22515390 original size:14 final size:15
Alignment explanation
Indices: 22515371--22515416 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
22515361 AACCTAACTA
22515371 ATTAATTACCAAAAT
1 ATTAATTACCAAAAT
*
22515386 A-TAATATA-AAAAAT
1 ATTAAT-TACCAAAAT
22515400 AATTAATTACCAAAAT
1 -ATTAATTACCAAAAT
22515416 A
1 A
22515417 ATATCCCCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
14 9 0.36
15 7 0.28
16 9 0.36
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (15 bp):
ATTAATTACCAAAAT
Found at i:22515414 original size:16 final size:16
Alignment explanation
Indices: 22515369--22515418 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
22515359 TAAACCTAAC
22515369 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
*
22515385 T-A-TAATATA-AAAAA
1 TAATTAAT-TACCAAAA
22515399 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
22515415 TAAT
1 TAAT
22515419 ATCCCCATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (16 bp):
TAATTAATTACCAAAA
Found at i:22515485 original size:30 final size:30
Alignment explanation
Indices: 22515451--22515545 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 30
22515441 AAATGGTACA
*
22515451 AAATAAATATTTGTTTTGTACCATTTTAGT
1 AAATAAATATATGTTTTGTACCATTTTAGT
** * * *
22515481 AAAT-AAT-GGTGTGTGGATACCATTTTGGT
1 AAATAAATATATGTTTTG-TACCATTTTAGT
* *
22515510 ATATAAATATATATTTTGTACCATTTTAGT
1 AAATAAATATATGTTTTGTACCATTTTAGT
22515540 AAATAA
1 AAATAA
22515546 CTCATTTTGA
Statistics
Matches: 49, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
28 5 0.10
29 17 0.35
30 23 0.47
31 4 0.08
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (30 bp):
AAATAAATATATGTTTTGTACCATTTTAGT
Found at i:22517434 original size:45 final size:45
Alignment explanation
Indices: 22517346--22517437 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
22517336 GCACAGCTCA
* * *
22517346 TCAAGCCAAGGATATCAGCCTCAATTTGACGACCCATCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAATTTAACGACCCACCACAATAC
* * **
22517391 TCAAGCTAAGGATATCAGCCTCAGTTTAACGAGTCACCACAATAC
1 TCAAGCCAAGGATATCAGCCTCAATTTAACGACCCACCACAATAC
22517436 TC
1 TC
22517438 TACTCCTCCG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.22
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAATTTAACGACCCACCACAATAC
Found at i:22517456 original size:21 final size:21
Alignment explanation
Indices: 22517430--22517474 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
22517420 CGAGTCACCA
*
22517430 CAATACTCTACTCCTCCGGGG
1 CAATACTCTACTCCTCCGAGG
22517451 CAATACTCTACTCCTCCGAGG
1 CAATACTCTACTCCTCCGAGG
22517472 CAA
1 CAA
22517475 ATGGACCCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.38, G:0.16, T:0.22
Consensus pattern (21 bp):
CAATACTCTACTCCTCCGAGG
Found at i:22517726 original size:28 final size:28
Alignment explanation
Indices: 22517695--22517817 Score: 106
Period size: 28 Copynumber: 4.4 Consensus size: 28
22517685 TTCATATCAT
*
22517695 TAAACCCTAAAACCTAAACCAT-AAACCC
1 TAAACCCTAAAACCTAAA-CTTGAAACCC
* * *
22517723 TAAACCTTAAATCCTAAACTTGAAACCT
1 TAAACCCTAAAACCTAAACTTGAAACCC
* *
22517751 TAAACCAT-AAACACTAAACTTGAAGCCC
1 TAAACCCTAAAAC-CTAAACTTGAAACCC
* * * * *
22517779 TAAACCCTAAATCTTAAACTTAAAAACT
1 TAAACCCTAAAACCTAAACTTGAAACCC
*
22517807 TAAACCTTAAA
1 TAAACCCTAAA
22517818 CCTTAAATCT
Statistics
Matches: 76, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
27 5 0.07
28 68 0.89
29 3 0.04
ACGTcount: A:0.48, C:0.27, G:0.02, T:0.23
Consensus pattern (28 bp):
TAAACCCTAAAACCTAAACTTGAAACCC
Found at i:22517755 original size:7 final size:7
Alignment explanation
Indices: 22517694--22517829 Score: 86
Period size: 7 Copynumber: 19.4 Consensus size: 7
22517684 TTTCATATCA
22517694 TTAAACCC
1 TTAAA-CC
*
22517702 TAAAACC
1 TTAAACC
22517709 -TAAACC
1 TTAAACC
*
22517715 ATAAACC
1 TTAAACC
*
22517722 CTAAACC
1 TTAAACC
22517729 TTAAATCC
1 TTAAA-CC
22517737 -TAAA-C
1 TTAAACC
22517742 TTGAAACC
1 TT-AAACC
22517750 TTAAACC
1 TTAAACC
*
22517757 ATAAACAC
1 TTAAAC-C
22517765 -TAAA-C
1 TTAAACC
*
22517770 TTGAAGCC
1 TT-AAACC
*
22517778 CTAAACC
1 TTAAACC
* *
22517785 CTAAATC
1 TTAAACC
22517792 TTAAA-C
1 TTAAACC
*
22517798 TTAAAAAC
1 TT-AAACC
22517806 TTAAACC
1 TTAAACC
22517813 TTAAACC
1 TTAAACC
*
22517820 TTAAATC
1 TTAAACC
22517827 TTA
1 TTA
22517830 TACATTAAAT
Statistics
Matches: 105, Mismatches: 12, Indels: 23
0.75 0.09 0.16
Matches are distributed among these distances:
5 2 0.02
6 10 0.10
7 78 0.74
8 15 0.14
ACGTcount: A:0.46, C:0.26, G:0.02, T:0.25
Consensus pattern (7 bp):
TTAAACC
Found at i:22523544 original size:11 final size:10
Alignment explanation
Indices: 22523526--22523592 Score: 50
Period size: 10 Copynumber: 6.7 Consensus size: 10
22523516 AAGTCAAAAA
*
22523526 AATTTTTAAT
1 AATTTTTTAT
22523536 AATTTTTTA-
1 AATTTTTTAT
*
22523545 ACTTTTTTTAT
1 A-ATTTTTTAT
*
22523556 ATATTCTTTA-
1 A-ATTTTTTAT
*
22523566 GATTTTTT-T
1 AATTTTTTAT
22523575 AATTTTTTAAT
1 AATTTTTT-AT
22523586 AATTTTT
1 AATTTTT
22523593 GTTAATATAA
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
9 14 0.32
10 15 0.34
11 15 0.34
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.67
Consensus pattern (10 bp):
AATTTTTTAT
Found at i:22523553 original size:21 final size:22
Alignment explanation
Indices: 22523528--22523577 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
22523518 GTCAAAAAAA
*
22523528 TTTTTAATA-ATTTTTTA-ACTT
1 TTTTTAATATATTCTTTAGA-TT
22523549 TTTTT-ATATATTCTTTAGATT
1 TTTTTAATATATTCTTTAGATT
22523570 TTTTTAAT
1 TTTTTAAT
22523578 TTTTTAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 3 0.12
21 19 0.76
22 3 0.12
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (22 bp):
TTTTTAATATATTCTTTAGATT
Found at i:22523598 original size:10 final size:9
Alignment explanation
Indices: 22523528--22523598 Score: 52
Period size: 11 Copynumber: 6.9 Consensus size: 9
22523518 GTCAAAAAAA
22523528 TTTTTAATAAT
1 TTTTTAAT--T
22523539 TTTTTAACTT
1 TTTTTAA-TT
22523549 TTTTTATATAT
1 TTTTTA-AT-T
*
22523560 TCTTTAGATT
1 TTTTTA-ATT
22523570 TTTTTAATT
1 TTTTTAATT
22523579 TTTTAATAATT
1 TTTT--TAATT
22523590 TTTGTTAAT
1 TTT-TTAAT
22523599 ATAAATTTTG
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
9 7 0.14
10 18 0.35
11 24 0.47
12 2 0.04
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.68
Consensus pattern (9 bp):
TTTTTAATT
Found at i:22524983 original size:26 final size:24
Alignment explanation
Indices: 22524946--22524997 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
22524936 GATTATATAA
22524946 AAAATTTTAATAAATAAAA-AATAT
1 AAAATTTTAAT-AATAAAATAATAT
*
22524970 AAAATTGTTAAATATTAAAATAATAT
1 AAAATT-TT-AATAATAAAATAATAT
22524996 AA
1 AA
22524998 TATAATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 6 0.25
25 8 0.33
26 10 0.42
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
AAAATTTTAATAATAAAATAATAT
Found at i:22524999 original size:42 final size:40
Alignment explanation
Indices: 22524953--22525040 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 40
22524943 TAAAAAATTT
22524953 TAATA-AATAAAAAATATAAAATTGTT-AAATATTAAAATAATA
1 TAATATAAT-AAAAATAT-AAATTGTTAAAATATTAAAA-AA-A
* * *
22524995 TAATATAATATAAATATATATTTTTAAAATATTAAAAAAA
1 TAATATAATAAAAATATAAATTGTTAAAATATTAAAAAAA
22525035 TAATAT
1 TAATAT
22525041 GGACAGACTT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
40 7 0.17
41 8 0.20
42 23 0.56
43 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (40 bp):
TAATATAATAAAAATATAAATTGTTAAAATATTAAAAAAA
Found at i:22527956 original size:2 final size:2
Alignment explanation
Indices: 22527949--22527977 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
22527939 GCTTTTCCTA
22527949 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22527978 AACGGATTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22529232 original size:18 final size:18
Alignment explanation
Indices: 22529193--22529248 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 18
22529183 AATTATAAAA
* *
22529193 AAAATTTAAAATAATTTTT
1 AAAATTCAAAAT-ATTTAT
22529212 AAAATTCAAAATATTTAT
1 AAAATTCAAAATATTTAT
22529230 AAAAATTCAAAAT-TTTAT
1 -AAAATTCAAAATATTTAT
22529248 A
1 A
22529249 TATTTTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 1 0.03
18 10 0.29
19 23 0.68
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATTCAAAATATTTAT
Found at i:22529256 original size:45 final size:45
Alignment explanation
Indices: 22529193--22529279 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 45
22529183 AATTATAAAA
22529193 AAAATTTAAAATAATTTTTAAAATTCAAAAT-ATTTATAAAAATTC
1 AAAATTTAAAATAATTTTTAAAATT-AAAATAATTTATAAAAATTC
* * * * *
22529238 AAAATTTTATATATTTTTTAAAATTATAATAATTTTTAAAAA
1 AAAATTTAAAATAATTTTTAAAATTAAAATAATTTATAAAAA
22529280 AATCCTAAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
44 4 0.11
45 32 0.89
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (45 bp):
AAAATTTAAAATAATTTTTAAAATTAAAATAATTTATAAAAATTC
Found at i:22529275 original size:18 final size:19
Alignment explanation
Indices: 22529238--22529278 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
22529228 ATAAAAATTC
* *
22529238 AAAATTTTATATATTTTTT
1 AAAATTATATATAATTTTT
22529257 AAAATTATA-ATAATTTTT
1 AAAATTATATATAATTTTT
22529275 AAAA
1 AAAA
22529279 AAATCCTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAAATTATATATAATTTTT
Found at i:22529952 original size:30 final size:31
Alignment explanation
Indices: 22529918--22529980 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
22529908 CATTTAACAC
22529918 AATAGTCACTCAAC-TT-T-GAAAATGTGACAA
1 AATAGTCA-TCAACGTTATCGAAAA-GTGACAA
*
22529948 AATAGTCATTAACGTTATCGAAAAGTGACAA
1 AATAGTCATCAACGTTATCGAAAAGTGACAA
22529979 AA
1 AA
22529981 CAATCACTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 4 0.14
30 10 0.34
31 10 0.34
32 5 0.17
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.25
Consensus pattern (31 bp):
AATAGTCATCAACGTTATCGAAAAGTGACAA
Found at i:22530364 original size:6 final size:6
Alignment explanation
Indices: 22530345--22530383 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
22530335 TTAGGGTTTA
* *
22530345 TTTGAT TTTAAT TTGGAT TTTGAT TTTGATT TTTGAT TT
1 TTTGAT TTTGAT TTTGAT TTTGAT TTTGA-T TTTGAT TT
22530384 AGGGTTATGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.18, C:0.00, G:0.15, T:0.67
Consensus pattern (6 bp):
TTTGAT
Found at i:22532496 original size:23 final size:23
Alignment explanation
Indices: 22532462--22532586 Score: 146
Period size: 23 Copynumber: 5.4 Consensus size: 23
22532452 ACACTAGCGC
22532462 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGTCT-GT
*
22532485 GCTTTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGTCT-GT
*
22532508 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTCTGT
* *
22532531 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTCTGT
* * *
22532554 GCTCTCTGTTCAGCACTATGTGT
1 GCTCTCTGTTTAGCACTGTCTGT
*
22532577 GCTCTATGTT
1 GCTCTCTGTT
22532587 GCCCAGCACT
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
23 90 0.97
24 3 0.03
ACGTcount: A:0.10, C:0.25, G:0.23, T:0.42
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTCTGT
Found at i:22534871 original size:13 final size:13
Alignment explanation
Indices: 22534853--22534890 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
22534843 TTTATAAATA
*
22534853 TAAATATCATATT
1 TAAATATTATATT
22534866 TAAATATTATATT
1 TAAATATTATATT
22534879 TAAATATTATAT
1 TAAATATTATAT
22534891 ATACATTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (13 bp):
TAAATATTATATT
Found at i:22539200 original size:15 final size:15
Alignment explanation
Indices: 22539163--22539203 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
22539153 TTTTCTTTTA
22539163 TTTCACAATTTGAAGC
1 TTTCACAATTT-AAGC
22539179 --T-ACAATTTAAGC
1 TTTCACAATTTAAGC
22539191 TTTCACAATTTAA
1 TTTCACAATTTAA
22539204 AGCCACAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
12 4 0.18
13 7 0.32
14 2 0.09
15 9 0.41
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (15 bp):
TTTCACAATTTAAGC
Found at i:22539945 original size:6 final size:6
Alignment explanation
Indices: 22539934--22539991 Score: 107
Period size: 6 Copynumber: 9.7 Consensus size: 6
22539924 TAGCGAACAC
22539934 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
*
22539982 ATACAA ATAT
1 ATATAA ATAT
22539992 TTAGATTAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAA
Found at i:22543289 original size:22 final size:22
Alignment explanation
Indices: 22543262--22543312 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
22543252 CAACAAAATA
22543262 ATATAAACAAATATTTATATTT
1 ATATAAACAAATATTTATATTT
*
22543284 ATATAAATAAATATTTATATTT
1 ATATAAACAAATATTTATATTT
*
22543306 ATTTAAA
1 ATATAAA
22543313 AACATCAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATAAACAAATATTTATATTT
Found at i:22545922 original size:19 final size:19
Alignment explanation
Indices: 22545807--22545924 Score: 110
Period size: 19 Copynumber: 6.2 Consensus size: 19
22545797 CAATACAGTA
*
22545807 TATTGCTCTTATGAGCCAG
1 TATTGCTCTTACGAGCCAG
** *
22545826 TATCACTATTACGAGCCAG
1 TATTGCTCTTACGAGCCAG
* * *
22545845 TAATGCTCTTTCGAGCTAG
1 TATTGCTCTTACGAGCCAG
*
22545864 TATTGCTCTCACGAGCCAG
1 TATTGCTCTTACGAGCCAG
* * * *
22545883 TAATGCTCATACGGGCTAG
1 TATTGCTCTTACGAGCCAG
* *
22545902 TATTGCTCTTAGGAGTCAG
1 TATTGCTCTTACGAGCCAG
22545921 TATT
1 TATT
22545925 TATATTCCTT
Statistics
Matches: 74, Mismatches: 25, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
19 74 1.00
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (19 bp):
TATTGCTCTTACGAGCCAG
Found at i:22545922 original size:38 final size:38
Alignment explanation
Indices: 22545836--22545910 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
22545826 TATCACTATT
* *
22545836 ACGAGCCAGTAATGCTCTTTCGAGCTAGTATTGCTCTC
1 ACGAGCCAGTAATGCTCATACGAGCTAGTATTGCTCTC
*
22545874 ACGAGCCAGTAATGCTCATACGGGCTAGTATTGCTCT
1 ACGAGCCAGTAATGCTCATACGAGCTAGTATTGCTCT
22545911 TAGGAGTCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (38 bp):
ACGAGCCAGTAATGCTCATACGAGCTAGTATTGCTCTC
Found at i:22549272 original size:165 final size:164
Alignment explanation
Indices: 22548976--22549273 Score: 358
Period size: 165 Copynumber: 1.8 Consensus size: 164
22548966 TAATTATTAT
* * *
22548976 AAAATTCAAATATAGAATATAATCTATTAATCGGCGAGAATAAATCCGAAAACATATCTAGTAAA
1 AAAATCCAAATATAAAATATAATCTATTAATCGGCGAGAATAAATCCGAAAACAGATCTAGTAAA
* * *
22549041 CTTATTCTTGTTTTGGAAAAAAATCAAACTGGAATAGAATCTTTTAAACAGTGGGAAAATTTTCG
66 CTTATTCTCGTTTTGGAAAAAAATCAAAAT-GAATAGAATCTTTTAAACAGTGGGAAAAATTTCG
22549106 AAAGAGATTTATTTACTTAATTATTATTTGGAACC
130 AAAGAGATTTATTTACTTAATTATTATTTGGAACC
* * * *
22549141 AAAATCCAAATATAAAAT-TAAATCTGTTAAAT-GGCGGGAATAAATCCCG-AAACAGATGTATT
1 AAAATCCAAATATAAAATAT-AATCTATT-AATCGGCGAGAATAAAT-CCGAAAACAGATCTAGT
* *
22549203 CAACTTATTCTCGTTTTGGAAATAAAATCAAAAT-AA-A-ATAT-TTGTTAAACGGTGGGAAATA
63 AAACTTATTCTCGTTTTGGAAA-AAAATCAAAATGAATAGA-ATCTT-TTAAACAGTGGG-AA-A
22549264 AATTTCGAAA
123 AATTTCGAAA
22549274 CAAATTATTT
Statistics
Matches: 113, Mismatches: 12, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
162 3 0.03
163 14 0.12
164 5 0.04
165 75 0.66
166 16 0.14
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.32
Consensus pattern (164 bp):
AAAATCCAAATATAAAATATAATCTATTAATCGGCGAGAATAAATCCGAAAACAGATCTAGTAAA
CTTATTCTCGTTTTGGAAAAAAATCAAAATGAATAGAATCTTTTAAACAGTGGGAAAAATTTCGA
AAGAGATTTATTTACTTAATTATTATTTGGAACC
Found at i:22551311 original size:28 final size:30
Alignment explanation
Indices: 22551269--22551354 Score: 124
Period size: 28 Copynumber: 3.0 Consensus size: 30
22551259 ACGTTAGCAA
22551269 GACAC-CCCCACATTTTCAAGTGGTTGTA-
1 GACACACCCCACATTTTCAAGTGGTTGTAG
*
22551297 GA-ACACCCCACATTTCCAAGTGGTTGTAG
1 GACACACCCCACATTTTCAAGTGGTTGTAG
* *
22551326 GACACCCCCCACATTTTCAAGTGATTGTA
1 GACACACCCCACATTTTCAAGTGGTTGTA
22551355 AGATTGTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.04
28 24 0.47
29 2 0.04
30 23 0.45
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (30 bp):
GACACACCCCACATTTTCAAGTGGTTGTAG
Found at i:22555213 original size:83 final size:82
Alignment explanation
Indices: 22555096--22555381 Score: 245
Period size: 83 Copynumber: 3.5 Consensus size: 82
22555086 TAAATCGTTG
* * * * * * *
22555096 TTTGAAAACTAAATCAAACTTA-AATCAAATCTGTTAATTGACGGGAATAAATCCCAAAACAGAT
1 TTTGGAAACAAAATCAAA-ATAGAATAAAATCTGTTAA-CGACGGGAATAAATCCAAAAACAAAT
* *
22555160 TTAGTCAACTTATTCTTGT
64 TTATTTAACTTATTCTTGT
* * * *
22555179 TTTGGAAACAAAATTAAACTAGAATAAAATCTGTTAAACAACAGGAA-AAATCCAAAAACAAATT
1 TTTGGAAACAAAATCAAAATAGAATAAAATCTGTT-AACGACGGGAATAAATCCAAAAACAAATT
* * * *
22555243 TATTTACCTAATTATT-A
65 TATTTAACTTATTCTTGT
* * ** ** *
22555260 TTTGGAACCAAAATCCAAATATAGAATTAAATCTGTTGAACGGTGGGAATAAATCCTGAAACATA
1 TTTGGAAACAAAAT-CAAA-ATAGAATAAAATCTGTT-AACGACGGGAATAAATCCAAAAACAAA
*
22555325 TTTATTTAACTTATTCTCGT
63 TTTATTTAACTTATTCTTGT
* * *
22555345 TTTGGGAATAAAATCAAAATAGAATAAAATTTGTTAA
1 TTTGGAAACAAAATCAAAATAGAATAAAATCTGTTAA
22555382 ACGGTGGTAA
Statistics
Matches: 159, Mismatches: 38, Indels: 13
0.76 0.18 0.06
Matches are distributed among these distances:
81 13 0.08
82 33 0.21
83 70 0.44
84 32 0.20
85 11 0.07
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.32
Consensus pattern (82 bp):
TTTGGAAACAAAATCAAAATAGAATAAAATCTGTTAACGACGGGAATAAATCCAAAAACAAATTT
ATTTAACTTATTCTTGT
Found at i:22556829 original size:83 final size:82
Alignment explanation
Indices: 22556742--22557003 Score: 264
Period size: 84 Copynumber: 3.1 Consensus size: 82
22556732 CGGGGGGAAT
* * * *
22556742 AAATCCCAAAACAGATTTAGTCATCTTATTCTTATTTTGGAAACAAAATCAAATTGGAATAAAAT
1 AAATCCCGAAACAGATTTATTAATCTTATTCTTATTTTGGAAACAAAATCAAATTAGAATAAAAT
22556807 CTGTTAAATAGCGAGAAA
66 CTGTTAAAT-GCGAGAAA
* * * * *
22556825 AAATCTCGAAACATATTTAATTAAT-TAATTATTA-TTTGGAACCAAAATTCAAATATAGAA-AT
1 AAATCCCGAAACAGATTT-ATTAATCTTATTCTTATTTTGGAAACAAAA-TCAAAT-TAGAATA-
* *
22556887 AAATCTGTTGAATGGCGCA-AAT
62 AAATCTGTTAAAT-GCG-AGAAA
* * *
22556909 AAATCCCGAAACAGATTTATTAAACTTATTCTCT-TTTTGGAAATAAAATCAAAATAGAATAAAA
1 AAATCCCGAAACAGATTTATTAATCTTATTCT-TATTTTGGAAACAAAATCAAATTAGAATAAAA
*
22556973 TCTGTTAAATGACAAGAAA
65 TCTGTTAAATG-CGAGAAA
22556992 TAAATCCCGAAA
1 -AAATCCCGAAA
22557004 TAAATTATTT
Statistics
Matches: 144, Mismatches: 23, Indels: 23
0.76 0.12 0.12
Matches are distributed among these distances:
82 14 0.10
83 54 0.38
84 63 0.44
85 13 0.09
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.31
Consensus pattern (82 bp):
AAATCCCGAAACAGATTTATTAATCTTATTCTTATTTTGGAAACAAAATCAAATTAGAATAAAAT
CTGTTAAATGCGAGAAA
Found at i:22556920 original size:84 final size:83
Alignment explanation
Indices: 22556701--22557003 Score: 262
Period size: 84 Copynumber: 3.6 Consensus size: 83
22556691 TAATTATTAT
* * * * * * *
22556701 AAAATCCAAATATAGAATATAATCTGCT-AATCGGGGGGAATAAATCCCAAAACAGATTTAGTCA
1 AAAAT-CAAATATAGAATAAAATCTGTTAAAT--GGCGAAATAAATCCCGAAACAGATTTATTAA
* *
22556765 TCTTATTCT-TATTTTGGAAAC
63 ACTTATTATCTA-TTTGGAAAC
* * * * *
22556786 AAAATCAAAT-TGGAATAAAATCTGTTAAATAGCGAGAAAAAATCTCGAAACATATTTAATT-AA
1 AAAATCAAATATAGAATAAAATCTGTTAAATGGCGA-AATAAATCCCGAAACAGATTT-ATTAAA
*
22556849 -TTAATTAT-TATTTGGAACC
64 CTT-ATTATCTATTTGGAAAC
*
22556868 AAAATTCAAATATAGAA-ATAAATCTGTTGAATGGCGCAAATAAATCCCGAAACAGATTTATTAA
1 AAAA-TCAAATATAGAATA-AAATCTGTTAAATGGCG-AAATAAATCCCGAAACAGATTTATTAA
* * *
22556932 ACTTATTCTCTTTTTGGAAAT
63 ACTTATTATCTATTTGGAAAC
*
22556953 AAAATCAAA-ATAGAATAAAATCTGTTAAATGACAAGAAATAAATCCCGAAA
1 AAAATCAAATATAGAATAAAATCTGTTAAATGGC--GAAATAAATCCCGAAA
22557004 TAAATTATTT
Statistics
Matches: 178, Mismatches: 26, Indels: 29
0.76 0.11 0.12
Matches are distributed among these distances:
82 16 0.09
83 67 0.38
84 74 0.42
85 21 0.12
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.30
Consensus pattern (83 bp):
AAAATCAAATATAGAATAAAATCTGTTAAATGGCGAAATAAATCCCGAAACAGATTTATTAAACT
TATTATCTATTTGGAAAC
Found at i:22558545 original size:95 final size:95
Alignment explanation
Indices: 22558380--22558563 Score: 305
Period size: 95 Copynumber: 1.9 Consensus size: 95
22558370 TTTTGTTGAA
* * *
22558380 TTTTTCCTTAAGAATGTATTAGCCCTTTTGACGCGAAGTGGAATGACAACCCAAGCACCCCATCC
1 TTTTTACTTAAGAATGTATTAGCCCTTTTGACACGAAATGGAATGACAACCCAAGCACCCCATCC
22558445 CGGTTACTCAGCCCAACACACTCCCAAAAT
66 CGGTTACTCAGCCCAACACACTCCCAAAAT
* *
22558475 TTTTTACTTAAGAATGTATTGGCCCTTTTGACACGAAATGGAATGACAACCCAAGCATCCCATCC
1 TTTTTACTTAAGAATGTATTAGCCCTTTTGACACGAAATGGAATGACAACCCAAGCACCCCATCC
* *
22558540 TGGTTACTTAGCCCAACACACTCC
66 CGGTTACTCAGCCCAACACACTCC
22558564 TATTTTATTT
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
95 82 1.00
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.26
Consensus pattern (95 bp):
TTTTTACTTAAGAATGTATTAGCCCTTTTGACACGAAATGGAATGACAACCCAAGCACCCCATCC
CGGTTACTCAGCCCAACACACTCCCAAAAT
Found at i:22558801 original size:225 final size:225
Alignment explanation
Indices: 22558423--22558904 Score: 903
Period size: 225 Copynumber: 2.1 Consensus size: 225
22558413 CGAAGTGGAA
*
22558423 TGACAACCCAAGCACCCCATCCCGGTTACTCAGCCCAACACACTCCCAAAATTTTTTACTTAAGA
1 TGACAACCCAAGCACCCCATCCCGATTACTCAGCCCAACACACTCCCAAAATTTTTTACTTAAGA
22558488 ATGTATTGGCCCTTTTGACACGAAATGGAATGACAACCCAAGCATCCCATCCTGGTTACTTAGCC
66 ATGTATTGGCCCTTTTGACACGAAATGGAATGACAACCCAAGCATCCCATCCTGGTTACTTAGCC
22558553 CAACACACTCCTATTTTATTTTTTATTTTTATCCATAATTTCAGTTAGAGGAGATTTACCTAACA
131 CAACACACTCCTATTTTATTTTTTATTTTTATCCATAATTTCAGTTAGAGGAGATTTACCTAACA
22558618 TATCACAAAACCTTTTTACGCGAAATAGGG
196 TATCACAAAACCTTTTTACGCGAAATAGGG
*
22558648 TGACAACCCAAGCATCCCATCCCGATTACTCAGCCCAACACACTCCCAAAATTTTTTACTTAAGA
1 TGACAACCCAAGCACCCCATCCCGATTACTCAGCCCAACACACTCCCAAAATTTTTTACTTAAGA
22558713 ATGTATTGGCCCTTTTGACACGAAATGGAATGACAACCCAAGCATCCCATCCTGGTTACTTAGCC
66 ATGTATTGGCCCTTTTGACACGAAATGGAATGACAACCCAAGCATCCCATCCTGGTTACTTAGCC
22558778 CAACACACTCCTATTTTATTTTTTATTTTTATCCATAATTTCAGTTAGAGGAGATTTACCTAACA
131 CAACACACTCCTATTTTATTTTTTATTTTTATCCATAATTTCAGTTAGAGGAGATTTACCTAACA
*
22558843 TATCACAAAACTTTTTTACGCGAAATAGGG
196 TATCACAAAACCTTTTTACGCGAAATAGGG
* *
22558873 TGACAACCCAAGTACCCTA-CCTCGATTACTCA
1 TGACAACCCAAGCACCCCATCC-CGATTACTCA
22558905 ATCAGTCACG
Statistics
Matches: 250, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
224 2 0.01
225 248 0.99
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.30
Consensus pattern (225 bp):
TGACAACCCAAGCACCCCATCCCGATTACTCAGCCCAACACACTCCCAAAATTTTTTACTTAAGA
ATGTATTGGCCCTTTTGACACGAAATGGAATGACAACCCAAGCATCCCATCCTGGTTACTTAGCC
CAACACACTCCTATTTTATTTTTTATTTTTATCCATAATTTCAGTTAGAGGAGATTTACCTAACA
TATCACAAAACCTTTTTACGCGAAATAGGG
Found at i:22562179 original size:83 final size:84
Alignment explanation
Indices: 22561868--22562176 Score: 263
Period size: 83 Copynumber: 3.7 Consensus size: 84
22561858 TAATTATTAT
* ** * * * * * *
22561868 AAAATCTAAATATAGAATATAATCTGTTAATTGACGAGAATAAATCCCAAAATAGATTTAGTCAA
1 AAAATC-AAATATAGAATAAAATCTGTTAAACGGCGGGAATAAATCTCGAAACAGATTTATTCAA
* *
22561933 CTTATTCTTGTTTTAGAAAC
65 CTTATTCTTATTTTGGAAAC
* * * * *
22561953 AAAATCAAA-CT-GAAATAAAATCTGTTAAACGGCAGGAAAAAATCTAGAAACAGATTTATT-TA
1 AAAATCAAATATAG-AATAAAATCTGTTAAACGGCGGGAATAAATCTCGAAACAGATTTATTCAA
* *
22562015 CTTAATTATTA-TTTGGAACC
65 CTT-ATTCTTATTTTGGAAAC
* * * * *
22562035 AAAATCCAAATATAGAATTAAATCTTTTGAAA-GGTGGGAATAAAACTCGAAACAAATTTATTCA
1 AAAAT-CAAATATAGAATAAAATCTGTT-AAACGGCGGGAATAAATCTCGAAACAGATTTATTCA
* *
22562099 ACTTATTCTCATTTTGGAAAT
64 ACTTATTCTTATTTTGGAAAC
* *
22562120 AAAATCAAA-ATAGAATAAAATCTTTTAAACTGCGGGAAATAAAT-TCCGAAACAGATT
1 AAAATCAAATATAGAATAAAATCTGTTAAACGGCGGG-AATAAATCT-CGAAACAGATT
22562177 ATTTTCCAAT
Statistics
Matches: 176, Mismatches: 37, Indels: 23
0.75 0.16 0.10
Matches are distributed among these distances:
82 20 0.11
83 66 0.38
84 64 0.36
85 26 0.15
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.31
Consensus pattern (84 bp):
AAAATCAAATATAGAATAAAATCTGTTAAACGGCGGGAATAAATCTCGAAACAGATTTATTCAAC
TTATTCTTATTTTGGAAAC
Found at i:22563941 original size:16 final size:17
Alignment explanation
Indices: 22563917--22563965 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 17
22563907 AATTTTACCA
*
22563917 TTATTAATT-TAAAATT
1 TTATAAATTATAAAATT
*
22563933 TTATAAATTATAAAATG
1 TTATAAATTATAAAATT
*
22563950 CT-TAAATTA-AAAATT
1 TTATAAATTATAAAATT
22563965 T
1 T
22563966 ATTATTTTAG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
15 5 0.19
16 15 0.56
17 7 0.26
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (17 bp):
TTATAAATTATAAAATT
Found at i:22565239 original size:19 final size:19
Alignment explanation
Indices: 22565217--22565260 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
22565207 TAGTCACCGA
*
22565217 GTGTTAATTTTCGTTAACG
1 GTGTAAATTTTCGTTAACG
22565236 GTGTAAATTTTCGTTAACG
1 GTGTAAATTTTCGTTAACG
22565255 GTGTAA
1 GTGTAA
22565261 TAGTAAGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.25, C:0.09, G:0.23, T:0.43
Consensus pattern (19 bp):
GTGTAAATTTTCGTTAACG
Found at i:22565969 original size:9 final size:9
Alignment explanation
Indices: 22565955--22565986 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
22565945 TAACACGTTA
22565955 TTTTTTAATT
1 TTTTTTAA-T
22565965 TTTTTTAAT
1 TTTTTTAAT
22565974 TTTTTTAAT
1 TTTTTTAAT
22565983 TTTT
1 TTTT
22565987 ATATATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTAAT
Found at i:22565970 original size:10 final size:10
Alignment explanation
Indices: 22565955--22565986 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
22565945 TAACACGTTA
22565955 TTTTTTAATT
1 TTTTTTAATT
22565965 TTTTTTAA-T
1 TTTTTTAATT
22565974 TTTTTTAATT
1 TTTTTTAATT
22565984 TTT
1 TTT
22565987 ATATATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTTAATT
Found at i:22566365 original size:7 final size:7
Alignment explanation
Indices: 22566337--22566397 Score: 52
Period size: 7 Copynumber: 8.3 Consensus size: 7
22566327 AAGGAAAAAA
*
22566337 AAAGAAA
1 AAAGAAG
22566344 AAAG-AG
1 AAAGAAG
22566350 AAAGAAAG
1 AAAG-AAG
22566358 AAAGAAG
1 AAAGAAG
*
22566365 AAGGAAG
1 AAAGAAG
22566372 AAGGAGAAG
1 AA--AGAAG
22566381 AAAGAAAG
1 AAAG-AAG
*
22566389 AAGGAAG
1 AAAGAAG
22566396 AA
1 AA
22566398 GGAGAAGGAG
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
6 5 0.11
7 22 0.49
8 12 0.27
9 6 0.13
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (7 bp):
AAAGAAG
Found at i:22566372 original size:24 final size:24
Alignment explanation
Indices: 22566348--22566413 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
22566338 AAGAAAAAAG
22566348 AGAA-AGAAAGAAAG-AAGAAGGA
1 AGAAGAGAAAGAAAGAAAGAAGGA
22566370 AGAAG-GAGAAGAAAGAAAGAAGGA
1 AGAAGAGA-AAGAAAGAAAGAAGGA
*
22566394 AGAAGGAGAAGGAGAAGAAA
1 AGAA-GAGAAAGA-AAGAAA
22566414 AAAAAAGTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
22 6 0.16
23 7 0.19
24 12 0.32
25 4 0.11
26 8 0.22
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (24 bp):
AGAAGAGAAAGAAAGAAAGAAGGA
Found at i:22566373 original size:31 final size:31
Alignment explanation
Indices: 22566342--22566420 Score: 85
Period size: 31 Copynumber: 2.7 Consensus size: 31
22566332 AAAAAAAAGA
22566342 AAAAAG-AGAAAGAAAGAAAGAAGAAGGAAG
1 AAAAAGAAGAAAGAAAGAAAGAAGAAGGAAG
** *
22566372 AAGGAGAAGAAAGAAAGAAGGAAGAAGG-AG
1 AAAAAGAAGAAAGAAAGAAAGAAGAAGGAAG
**
22566402 AAGGAGAAGAAA-AAA-AAAG
1 AAAAAGAAGAAAGAAAGAAAG
22566421 TAATGTGTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
28 3 0.07
29 3 0.07
30 18 0.41
31 20 0.45
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (31 bp):
AAAAAGAAGAAAGAAAGAAAGAAGAAGGAAG
Found at i:22566381 original size:27 final size:29
Alignment explanation
Indices: 22566351--22566413 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 29
22566341 AAAAAAGAGA
22566351 AAGAAAGAAAGAA-GAAG-GAAGAAGGAG
1 AAGAAAGAAAGAAGGAAGAGAAGAAGGAG
*
22566378 AAGAAAGAAAGAAGGAAGAAGGAGAAGGAG
1 AAGAAAGAAAGAAGGAAG-AGAAGAAGGAG
22566408 AAGAAA
1 AAGAAA
22566414 AAAAAAGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
27 13 0.41
28 4 0.12
30 15 0.47
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (29 bp):
AAGAAAGAAAGAAGGAAGAGAAGAAGGAG
Found at i:22566398 original size:7 final size:7
Alignment explanation
Indices: 22566355--22566410 Score: 53
Period size: 7 Copynumber: 7.9 Consensus size: 7
22566345 AAGAGAAAGA
*
22566355 AAGAAAG
1 AAGAAGG
22566362 AAGAAGG
1 AAGAAGG
22566369 AAGAAGGAG
1 AAGAA-G-G
*
22566378 AAGAAAGA
1 AAG-AAGG
22566386 AAGAAGG
1 AAGAAGG
22566393 AAGAAGG
1 AAGAAGG
22566400 -AGAAGG
1 AAGAAGG
22566406 -AGAAG
1 AAGAAG
22566411 AAAAAAAAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
6 11 0.26
7 21 0.49
8 4 0.09
9 5 0.12
10 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (7 bp):
AAGAAGG
Found at i:22590292 original size:3 final size:3
Alignment explanation
Indices: 22590286--22590316 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
22590276 CTCCTCCTCC
*
22590286 TCA TCA TCA TCA TCA TCA TCA TCC TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
22590317 TATTTTTAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:22590961 original size:146 final size:146
Alignment explanation
Indices: 22590753--22591135 Score: 488
Period size: 146 Copynumber: 2.6 Consensus size: 146
22590743 AAGTTTTGGT
* *
22590753 TTTTTTTTAAATAATTTTGAAATAAAAGTTTTGATTTTGAAGTAAAGTAGTGATTTTC-TTTAAA
1 TTTTTTTTAACT-ATTTCGAAATAAAA-TTTTGATTTTGAAGTAAAGTAGTGATTTTCTTTTAAA
* * * * *
22590817 AAA-AAA-TTTATATTTTAAAAAATAAAAATCTGTTTTTTAGTTATTTTAAGGAAAAAATTTAAA
64 AAAGAAAGTTTAGATTTTAAAAAATAAAAATCT-ATTTTTAATGATTTTAAAGAAAAAATTTAAA
22590880 TTTTTAAACAAAATTTTGA
128 TTTTTAAACAAAATTTTGA
* * * *
22590899 TTTTTTTTCAACTATTTCGAAATAAAATTTGGATTTTTAGGTAAAATAGTGATTTTCTTTTAAAA
1 TTTTTTTT-AACTATTTCGAAATAAAATTTTGATTTTGAAGTAAAGTAGTGATTTTCTTTTAAAA
* *
22590964 AAGGGAAAGTTTAGATTTTTAAAAATAAAAATCTATTTTTAATGATTTTAAAGAAAAATTTTAAA
65 AA--GAAAGTTTAGATTTTAAAAAATAAAAATCTATTTTTAATGATTTTAAAGAAAAAATTTAAA
*
22591029 TTTTTAAACAAAGTTTTGA
128 TTTTTAAACAAAATTTTGA
* *
22591048 --TTTTTTAGCTATTTCGAAATAAAATTTTGATTTTGAAGTAAAGTAGTGATTTTGTTTTAATCA
1 TTTTTTTTAACTATTTCGAAATAAAATTTTGATTTTGAAGTAAAGTAGTGATTTTCTTTTAA--A
* *
22591111 AAAGAAAACTTTTGATTTTAAAAAA
64 AAAG-AAAGTTTAGATTTTAAAAAA
22591136 AAAGAAAAAG
Statistics
Matches: 205, Mismatches: 23, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
145 26 0.13
146 79 0.39
147 26 0.13
148 4 0.02
149 47 0.23
150 23 0.11
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.45
Consensus pattern (146 bp):
TTTTTTTTAACTATTTCGAAATAAAATTTTGATTTTGAAGTAAAGTAGTGATTTTCTTTTAAAAA
AGAAAGTTTAGATTTTAAAAAATAAAAATCTATTTTTAATGATTTTAAAGAAAAAATTTAAATTT
TTAAACAAAATTTTGA
Found at i:22591137 original size:24 final size:24
Alignment explanation
Indices: 22591097--22591143 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
22591087 AAAGTAGTGA
**
22591097 TTTTGTTTT-AATCAAAAGAAAAC
1 TTTTGTTTTAAAAAAAAAGAAAAC
22591120 TTTTGATTTTAAAAAAAAAGAAAA
1 TTTTG-TTTTAAAAAAAAAGAAAA
22591144 AGAAGAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 4 0.20
25 11 0.55
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (24 bp):
TTTTGTTTTAAAAAAAAAGAAAAC
Found at i:22591589 original size:25 final size:24
Alignment explanation
Indices: 22591561--22591607 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
22591551 CTTTTTTCAT
*
22591561 TTATGC-TTTCTATGTTTGATGTTAA
1 TTATGCATTT-TAT-TTTAATGTTAA
22591586 TTATGCATTTTATTTTAATGTT
1 TTATGCATTTTATTTTAATGTT
22591608 TTTTAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 8 0.40
25 9 0.45
26 3 0.15
ACGTcount: A:0.21, C:0.06, G:0.13, T:0.60
Consensus pattern (24 bp):
TTATGCATTTTATTTTAATGTTAA
Found at i:22592808 original size:20 final size:22
Alignment explanation
Indices: 22592767--22592816 Score: 68
Period size: 20 Copynumber: 2.3 Consensus size: 22
22592757 TTTTTTTTAG
22592767 TATTTGTGCATATTAGATTTATT
1 TATTTGTGCA-ATTAGATTTATT
22592790 TATTTGTGC-ATTA-ATTTATT
1 TATTTGTGCAATTAGATTTATT
*
22592810 TAATTGT
1 TATTTGT
22592817 CTAATGTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 13 0.50
21 4 0.15
23 9 0.35
ACGTcount: A:0.26, C:0.04, G:0.12, T:0.58
Consensus pattern (22 bp):
TATTTGTGCAATTAGATTTATT
Found at i:22595669 original size:20 final size:20
Alignment explanation
Indices: 22595630--22595675 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
22595620 GTGCCCTAAT
** *
22595630 TTCATTCATTCGTTCGTTCG
1 TTCATTCATTCACTCATTCG
22595650 TTCATTCATTCACTCATTCG
1 TTCATTCATTCACTCATTCG
*
22595670 CTCATT
1 TTCATT
22595676 TGTTTATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.15, C:0.28, G:0.09, T:0.48
Consensus pattern (20 bp):
TTCATTCATTCACTCATTCG
Found at i:22599511 original size:21 final size:21
Alignment explanation
Indices: 22599487--22599557 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
22599477 GTTTTAAATC
22599487 AAGAAAAAAATACAAAAAAG-G
1 AAGAAAAAAA-ACAAAAAAGAG
22599508 AAG-AAAAAAA-AAAAAAGAG
1 AAGAAAAAAAACAAAAAAGAG
22599527 AA-AAAAAAAACAACAAAAGAG
1 AAGAAAAAAAACAA-AAAAGAG
22599548 AAGAAAAAAA
1 AAGAAAAAAA
22599558 TAGAAAGAGG
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
18 7 0.16
19 11 0.24
20 8 0.18
21 12 0.27
22 7 0.16
ACGTcount: A:0.82, C:0.04, G:0.13, T:0.01
Consensus pattern (21 bp):
AAGAAAAAAAACAAAAAAGAG
Found at i:22599521 original size:16 final size:15
Alignment explanation
Indices: 22599508--22599536 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
22599498 ACAAAAAAGG
22599508 AAGA-AAAAAAAAAA
1 AAGAGAAAAAAAAAA
22599522 AAGAGAAAAAAAAAA
1 AAGAGAAAAAAAAAA
22599537 CAACAAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAGAGAAAAAAAAAA
Found at i:22599551 original size:40 final size:38
Alignment explanation
Indices: 22599490--22599566 Score: 109
Period size: 40 Copynumber: 2.0 Consensus size: 38
22599480 TTAAATCAAG
*
22599490 AAAAAAATACAAAAAAGGAAGAAAAAAAAAAAAAGAGA
1 AAAAAAAAACAAAAAAGGAAGAAAAAAAAAAAAAGAGA
* *
22599528 AAAAAAAAACAACAAAAGAGAAGAAAAAAATAGAAAGAG
1 AAAAAAAAACAA-AAAAG-GAAGAAAAAAAAAAAAAGAG
22599567 GGAGGAAGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 11 0.32
39 5 0.15
40 18 0.53
ACGTcount: A:0.79, C:0.04, G:0.14, T:0.03
Consensus pattern (38 bp):
AAAAAAAAACAAAAAAGGAAGAAAAAAAAAAAAAGAGA
Found at i:22600024 original size:42 final size:42
Alignment explanation
Indices: 22599965--22600465 Score: 592
Period size: 42 Copynumber: 11.9 Consensus size: 42
22599955 AAGGAAAGCA
* *
22599965 TTCATTGCATTTAGAGGCCCAAGTGTGGATGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * *
22600007 TTCATCGCATTCAGAGGCCCAAGTGTGAAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
22600049 TTCATTGCATTTAGAGGCCCACGTGTAGAAG-CTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTC-CATTTACTT
** * *
22600091 TTCATCACATTTAGAGGCCAAGGTGTGGAGTTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
22600133 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
22600175 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
22600217 TTAATCGAATTTAGAGGCCTAGGTGTGGAGG-CCTATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCC-ATTTACTT
* *
22600259 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * *
22600301 TTCATCGCATTTAGAGACCTAGGTGTGGAGATCCATTTGCTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * *
22600343 TTCATGGCATTTAGAGACCCCGGTGTGGAGATCCATTCACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* ** *
22600385 TTCATTACATTCGGAGGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * * *
22600427 TTGATTGCAATTAGAGGCCTAAGTGTAGAAGTCCATTTA
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTA
22600466 TTTATTTATT
Statistics
Matches: 397, Mismatches: 58, Indels: 8
0.86 0.13 0.02
Matches are distributed among these distances:
41 3 0.01
42 391 0.98
43 3 0.01
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.35
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:22601619 original size:149 final size:147
Alignment explanation
Indices: 22601253--22601764 Score: 708
Period size: 146 Copynumber: 3.4 Consensus size: 147
22601243 GATTTTGGGA
* *
22601253 AAAGTTTTGATTTTTTAAACAATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGATTTT
1 AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGATTTT
* * * *
22601318 CTTTAAAAAAGAGAAAATTTATATTTTTAAAAATAAAAATATATTTTTTAGTTATTTTAA-AAAA
66 CTTTAAAAAAAAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAGAAAA
22601382 AGTTTAAATTTTTAAAC
131 AGTTTAAATTTTTAAAC
* * *
22601399 AACGTTTTGATTTTTTTAACTATTTCGAAATAAAAG-TTTGAATTTTTAAGTAAAATAATAATTT
1 AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTG-ATTTTTAAGTAAAATAGTGATTT
* * *
22601463 TCTTTAAAAAATAGAAAGTTTATATTTTTGAAAATAAAAGTCTGTTTTTTAGTTATTTTAAGGAA
65 TCTTTAAAAAAAAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAA-GAA
* *
22601528 AAATTTTAAATTTTTAAAG
129 AAAGTTTAAATTTTTAAAC
*
22601547 AAAGTTTTGATTTTTTTTCAACTATTTCGAAAT-AAAG-TTTGAATTTTTAGGTAAAATAGTGAT
1 AAAGTTTTGA-TTTTTTT-AACTATTTCGAAATAAAAGTTTTG-ATTTTTAAGTAAAATAGTGAT
* * * *
22601610 TTTCTTTAAAAAAAAAAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTTAATGATTTTAAAG
63 TTTCTTTAAAAAAAAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTT-AAG
22601675 AAAAAAGTTTAAATTTTTAAAC
127 -AAAAAGTTTAAATTTTTAAAC
* * *
22601697 AAAGTTTTGATTTTTTTTTTAGCTATTTCGAAATAAAAGTTTTGATTTTGAAGTAAATTAGTGAT
1 AAAGTTTTGA---TTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGAT
22601762 TTT
63 TTT
22601765 GTTTTAATCA
Statistics
Matches: 325, Mismatches: 30, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
145 4 0.01
146 109 0.34
148 28 0.09
149 89 0.27
150 45 0.14
151 13 0.04
152 33 0.10
153 4 0.01
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (147 bp):
AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGATTTT
CTTTAAAAAAAAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAGAAAA
AGTTTAAATTTTTAAAC
Found at i:22602362 original size:27 final size:27
Alignment explanation
Indices: 22602301--22602366 Score: 71
Period size: 27 Copynumber: 2.3 Consensus size: 27
22602291 GTCAATTATG
22602301 CATTTTATTAATTTTTTTTAAATTTATTCA
1 CATTTTA-TAA-TTTTTTT-AATTTATTCA
*
22602331 CATTTGTATAATTTTTTT-ATTTATTCT
1 CATTT-TATAATTTTTTTAATTTATTCA
*
22602358 TATTTTATA
1 CATTTTATA
22602367 TTTATTCATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 4 0.12
27 12 0.36
29 7 0.21
30 8 0.24
31 2 0.06
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (27 bp):
CATTTTATAATTTTTTTAATTTATTCA
Found at i:22610848 original size:10 final size:10
Alignment explanation
Indices: 22610830--22610895 Score: 51
Period size: 12 Copynumber: 6.0 Consensus size: 10
22610820 TTCTCTTACT
22610830 ATATTATATA
1 ATATTATATA
* *
22610840 ATGTTATATC
1 ATATTATATA
22610850 ATATTATATA
1 ATATTATATA
*
22610860 GTATTTAATATA
1 ATA-TT-ATATA
22610872 TATATATATATA
1 -ATAT-TATATA
22610884 TATATATATATA
1 -ATAT-TATATA
22610896 TATCAATGAT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
10 18 0.39
11 2 0.04
12 23 0.50
13 3 0.07
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (10 bp):
ATATTATATA
Found at i:22610872 original size:2 final size:2
Alignment explanation
Indices: 22610844--22610898 Score: 69
Period size: 2 Copynumber: 27.5 Consensus size: 2
22610834 TATATAATGT
*
22610844 TA TA TCA TA T- TA TA TA GTA TT TA -A TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
22610886 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
22610899 CAATGATTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
1 2 0.04
2 41 0.87
3 4 0.09
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22610969 original size:24 final size:24
Alignment explanation
Indices: 22610942--22610998 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
22610932 ATATATTTTA
* *
22610942 TTATGATATATA-ATATAATAATAG
1 TTAT-ATATATATATAAAAAAATAG
*
22610966 TTATATATATATTTAAAAAAATAG
1 TTATATATATATATAAAAAAATAG
22610990 TTATATATA
1 TTATATATA
22610999 ATAGTAGTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 7 0.24
24 22 0.76
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (24 bp):
TTATATATATATATAAAAAAATAG
Found at i:22611513 original size:17 final size:17
Alignment explanation
Indices: 22611491--22611523 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
22611481 AGTAGTACAT
22611491 TATATATTACATATTAC
1 TATATATTACATATTAC
*
22611508 TATATATTATATATTA
1 TATATATTACATATTA
22611524 TTGTTTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATATTACATATTAC
Found at i:22611670 original size:504 final size:478
Alignment explanation
Indices: 22610985--22611986 Score: 1115
Period size: 504 Copynumber: 2.0 Consensus size: 478
22610975 TATTTAAAAA
*
22610985 AATAGTTATATATAATAGTAGTACATTATACATTAACTATTATAATATATTATTGTTTATTATTA
1 AATAGTTATATAAAATAGTAGTACATTATACATTAACTATTATAATATATTATTGTTTATTATTA
* * * * *
22611050 TACTAGTTGAAATATGCTTTAAGCCTCTATATTTGTCGTACATTTGAAAATTAACTCTCTTATTA
66 TACTAGTTGAAATATGCTCTAAGCCTCTACATTTGTCATACATTTGAAAAGTAACCCTCTTATTA
*
22611115 TACTATAAATGCTATATCATTTCATATATTAATAGTTTATATATGCATAAATGATTAAACATTAT
131 TACTATAAATGCTATATCATATCATATATTAATAGTTTATATATGCATAAATGATTAAACATTAT
* * * *
22611180 AATACCATGTAATATTATATATTTGATTATAATATATATTATAATAATAGTTGTATATAATAGTA
196 AATACCATATAATAATATACATTTGATTATAATATATATTATAATAATAGTTATATATAATAGTA
* * *
22611245 GTAAATTATATATTA-GTTAT-TA-TA-TATTATTATACTAATTGAAATATGTTCTAAGTCTTTT
261 GTAAATTATATATTATATTATATATTATTATTATTATACTAATTGAAATATGTTCTAAGTCTCTA
** * *
22611306 TACTTTTCGTACATTTGAAAATTAGTCATTCTACTATATTATATTATATCATATAATGT-ATAAT
326 TACTTTTCGTACATTAAAAAATTAG---TTCT-CT-TATTATATTATATAATATAATATCATAAT
* ** * * *
22611370 ATATAATATATTAATAGCGTATGTATATGCATCAATAATTAAACATTATAGTATTATGTAATATT
386 ATATAATATATTAATA--GTATATATAAACATCAATAATTAAAAATTATAATATCATGTAATATT
*
22611435 ATATCTTTTTATTATAACTTATAATA-TA-A-T
449 ATATC-TTTTATTATAA--TAGAATATTATAGT
* *
22611465 AATAGTTATATAAAATAGTAGTACATTATATATTACATATTACTATATATTATATATTATTGTTT
1 AATAGTTATATAAAATAGTAGTAC---AT-TA-TACAT-TAACTAT-TATAATATATTATTGTTT
** * *
22611530 ATTATTATACTAGTTGAAATATGTGCTCTAAGTTTCTACATTTTTCATATATTTG-AAAGTAAGC
59 ATTATTATACTAGTTGAAATA--TGCTCTAAGCCTCTACATTTGTCATACATTTGAAAAGTAA-C
* *
22611594 CCTTTTATTATA-TAATATAATGCTATATCATATCATATGTTAATAGTTTATATATGTCTGTGTG
121 CCTCTTATTATACT-ATA-AATGCTATATCATATCATATATTAATAGTTTATATA----------
* * * * *
22611658 TGAGCGCATAAATGATTAAACATTATAATATCATATAATAATATACCTTTTATTGTAATCTATAT
174 T----GCATAAATGATTAAACATTATAATACCATATAATAATATACATTTGATTATAATATATAT
**
22611723 TATAATAATAGTTATATATAATAGTAGTTCATTATATATTACTTATTATATATTATTTTTTTTAT
235 TATAATAATAGTTATATATAATAGTAGTAAATTATATATTA--TATTATATATTA------TTAT
* *
22611788 TATTATACTAGTTGAAATATGTTCTAAGTCTCTATATTTTTCGTACATTAAAAAATTAGTTCTCT
292 TATTATACTAATTGAAATATGTTCTAAGTCTCTATACTTTTCGTACATTAAAAAATTAGTTCTCT
* * * * *
22611853 TATTATATTATATAATATTATATCATATTATATAATATATTAATAGTTTATATAAACATCGATGA
357 TATTATATTATATAATATAATATCATAATATATAATATATTAATAGTATATATAAACATCAATAA
22611918 TTAAAAATTATAATATCATGTAATATTATATCTTTTATTATAATAGAATATTATAGT
422 TTAAAAATTATAATATCATGTAATATTATATCTTTTATTATAATAGAATATTATAGT
22611975 AATAGTTATATA
1 AATAGTTATATA
22611987 TATATTAATA
Statistics
Matches: 433, Mismatches: 47, Indels: 54
0.81 0.09 0.10
Matches are distributed among these distances:
480 23 0.05
483 2 0.00
484 2 0.00
485 5 0.01
486 6 0.01
487 38 0.09
488 7 0.02
489 39 0.09
490 34 0.08
500 1 0.00
504 90 0.21
507 10 0.02
508 4 0.01
509 14 0.03
510 56 0.13
511 20 0.05
512 22 0.05
513 4 0.01
516 56 0.13
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (478 bp):
AATAGTTATATAAAATAGTAGTACATTATACATTAACTATTATAATATATTATTGTTTATTATTA
TACTAGTTGAAATATGCTCTAAGCCTCTACATTTGTCATACATTTGAAAAGTAACCCTCTTATTA
TACTATAAATGCTATATCATATCATATATTAATAGTTTATATATGCATAAATGATTAAACATTAT
AATACCATATAATAATATACATTTGATTATAATATATATTATAATAATAGTTATATATAATAGTA
GTAAATTATATATTATATTATATATTATTATTATTATACTAATTGAAATATGTTCTAAGTCTCTA
TACTTTTCGTACATTAAAAAATTAGTTCTCTTATTATATTATATAATATAATATCATAATATATA
ATATATTAATAGTATATATAAACATCAATAATTAAAAATTATAATATCATGTAATATTATATCTT
TTATTATAATAGAATATTATAGT
Found at i:22611758 original size:16 final size:15
Alignment explanation
Indices: 22611720--22611772 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
22611710 TTGTAATCTA
22611720 TATTATAATAATAGT
1 TATTATAATAATAGT
*
22611735 TATATATAATAGTAGT
1 TAT-TATAATAATAGT
* *
22611751 TCATTAT-ATATTACT
1 T-ATTATAATAATAGT
22611766 TATTATA
1 TATTATA
22611773 TATTATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
14 5 0.16
15 10 0.31
16 15 0.47
17 2 0.06
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.49
Consensus pattern (15 bp):
TATTATAATAATAGT
Found at i:22611872 original size:10 final size:10
Alignment explanation
Indices: 22611857--22611907 Score: 61
Period size: 10 Copynumber: 5.1 Consensus size: 10
22611847 TTCTCTTATT
22611857 ATATTATATA
1 ATATTATATA
*
22611867 ATATTATATC
1 ATATTATATA
22611877 ATATTATATA
1 ATATTATATA
22611887 ATA-TAT-TA
1 ATATTATATA
22611895 ATAGTTTATATA
1 ATA--TTATATA
22611907 A
1 A
22611908 ACATCGATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 5 0.14
9 3 0.09
10 21 0.60
11 3 0.09
12 3 0.09
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (10 bp):
ATATTATATA
Found at i:22612023 original size:28 final size:30
Alignment explanation
Indices: 22611971--22612026 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
22611961 TAGAATATTA
22611971 TAGTAATAGTTATATATATATTAATATTTT
1 TAGTAATAGTTATATATATATTAATATTTT
22612001 TAGTAATAGTTATATAT-TA-TAATATT
1 TAGTAATAGTTATATATATATTAATATT
22612027 ATTTTATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 7 0.27
29 2 0.08
30 17 0.65
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (30 bp):
TAGTAATAGTTATATATATATTAATATTTT
Found at i:22612032 original size:30 final size:31
Alignment explanation
Indices: 22611965--22612032 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 31
22611955 TTATAATAGA
*
22611965 ATATTATAGTAATAGTTATATATATATTAAT
1 ATATTTTAGTAATAGTTATATATATATTAAT
22611996 AT-TTTTAGTAATAGTTATATAT-TA-TAAT
1 ATATTTTAGTAATAGTTATATATATATTAAT
22612024 ATTATTTTA
1 A-TATTTTA
22612033 TGTATTAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
28 5 0.15
29 3 0.09
30 24 0.71
31 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (31 bp):
ATATTTTAGTAATAGTTATATATATATTAAT
Found at i:22612177 original size:16 final size:17
Alignment explanation
Indices: 22612158--22612190 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
22612148 AATTTTATAG
22612158 ATTTTA-ATAATTATTA
1 ATTTTATATAATTATTA
*
22612174 ATTTTATATATTTATTA
1 ATTTTATATAATTATTA
22612191 TATATATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTATATAATTATTA
Done.