Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 89 of 97
Found at i:35064114 original size:45 final size:44
Alignment explanation
Indices: 35064027--35064136 Score: 112
Period size: 45 Copynumber: 2.4 Consensus size: 44
35064017 ATCTTCCTTG
* * ** * *
35064027 ATGTAGGATTAATAGCTCTTTGCTAGGTTCATGACATCCTCCCCG
1 ATGT-GGATTAATAGCTCTCTACTAGGACCATAACATCCTCCCCA
* *
35064072 ATGTGAGATTAATAGCTCTCTACTAGGACCATAACATTCTCCCTA
1 ATGTG-GATTAATAGCTCTCTACTAGGACCATAACATCCTCCCCA
*
35064117 ATGTGGAATTAATAACTCTC
1 ATGTGG-ATTAATAGCTCTC
35064137 CGTTAGGATC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
44 2 0.04
45 52 0.96
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (44 bp):
ATGTGGATTAATAGCTCTCTACTAGGACCATAACATCCTCCCCA
Found at i:35066974 original size:23 final size:23
Alignment explanation
Indices: 35066945--35066991 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
35066935 TTTTGAAAAG
35066945 TAAGATTTGCTTTATTATTAAGT
1 TAAGATTTGCTTTATTATTAAGT
35066968 TAAGATTTGCTTTATTATTAAGT
1 TAAGATTTGCTTTATTATTAAGT
35066991 T
1 T
35066992 GCATTTTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.13, T:0.53
Consensus pattern (23 bp):
TAAGATTTGCTTTATTATTAAGT
Found at i:35068281 original size:12 final size:12
Alignment explanation
Indices: 35068266--35068343 Score: 59
Period size: 12 Copynumber: 6.0 Consensus size: 12
35068256 ACAGAAAGAG
35068266 GAAGAAAAGGAA
1 GAAGAAAAGGAA
*
35068278 GAAGAAAAAGAGGAG
1 GAAG--AAA-AGGAA
*
35068293 GAAGAGAA-GAA
1 GAAGAAAAGGAA
*
35068304 GGAAGTAAAGGAA
1 -GAAGAAAAGGAA
35068317 GAAGTAAAAGAGGAA
1 GAAG--AAA-AGGAA
35068332 GAAGAAAAGGAA
1 GAAGAAAAGGAA
35068344 TCGAAAATGG
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
11 2 0.04
12 20 0.38
13 8 0.15
14 5 0.10
15 17 0.33
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.03
Consensus pattern (12 bp):
GAAGAAAAGGAA
Found at i:35068291 original size:15 final size:15
Alignment explanation
Indices: 35068246--35068339 Score: 58
Period size: 15 Copynumber: 6.7 Consensus size: 15
35068236 ATAGGTTCAC
* *
35068246 AAGAAGAAAAACAGA
1 AAGAAGAAAAAGAGG
*
35068261 AAGAGGAAGAAA-AGG
1 AAGAAGAA-AAAGAGG
35068276 AAGAAGAAAAAGAGG
1 AAGAAGAAAAAGAGG
* *
35068291 AGGAAG-AGAAGA--
1 AAGAAGAAAAAGAGG
* *
35068303 AGGAAG--TAA-AGG
1 AAGAAGAAAAAGAGG
*
35068315 AAGAAGTAAAAGAGG
1 AAGAAGAAAAAGAGG
35068330 AAGAAGAAAA
1 AAGAAGAAAA
35068340 GGAATCGAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
10 1 0.02
11 2 0.03
12 11 0.17
14 10 0.16
15 36 0.57
16 3 0.05
ACGTcount: A:0.64, C:0.01, G:0.33, T:0.02
Consensus pattern (15 bp):
AAGAAGAAAAAGAGG
Found at i:35078330 original size:30 final size:30
Alignment explanation
Indices: 35078259--35078343 Score: 109
Period size: 29 Copynumber: 2.8 Consensus size: 30
35078249 AAAAAATTTG
* * *
35078259 AATAAGTTATTATATTTTTATTAT-ATTTA
1 AATAAGTTTTTATATTTTTATTTTAAGTTA
* *
35078288 ATTAAATTTTTATATTTTTATTTTAAGTTA
1 AATAAGTTTTTATATTTTTATTTTAAGTTA
35078318 AATAAGTTTTTATATTTTTTATTTTA
1 AATAAGTTTTTATA-TTTTTATTTTA
35078344 CTCAAATATA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 20 0.43
30 16 0.34
31 11 0.23
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (30 bp):
AATAAGTTTTTATATTTTTATTTTAAGTTA
Found at i:35078351 original size:30 final size:29
Alignment explanation
Indices: 35078259--35078351 Score: 105
Period size: 30 Copynumber: 3.1 Consensus size: 29
35078249 AAAAAATTTG
* * *
35078259 AATAAGTTATTATATTTTTATTATATTTA
1 AATAAGTTTTTATATTTTTATTTTACTTA
* * *
35078288 ATTAAATTTTTATATTTTTATTTTAAGTTA
1 AATAAGTTTTTATATTTTTATTTT-ACTTA
*
35078318 AATAAGTTTTTATATTTTTTATTTTACTCA
1 AATAAGTTTTTATA-TTTTTATTTTACTTA
35078348 AATA
1 AATA
35078352 TACTCTTATC
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
29 20 0.38
30 23 0.43
31 10 0.19
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.59
Consensus pattern (29 bp):
AATAAGTTTTTATATTTTTATTTTACTTA
Found at i:35080117 original size:30 final size:31
Alignment explanation
Indices: 35080072--35080140 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 31
35080062 TTTATTATGT
*
35080072 TCAATTAAATCTTTATACTTTT-ATTTTGAG
1 TCAAATAAATCTTTATACTTTTAATTTTGAG
* * *
35080102 TTAAATAAATTTTTATATTTTTAATTTTGAG
1 TCAAATAAATCTTTATACTTTTAATTTTGAG
35080133 TCAAATAA
1 TCAAATAA
35080141 GCTCTTGTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 18 0.55
31 15 0.45
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (31 bp):
TCAAATAAATCTTTATACTTTTAATTTTGAG
Found at i:35080132 original size:31 final size:30
Alignment explanation
Indices: 35080055--35080140 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 30
35080045 GAATAAGTTA
* * * *
35080055 TTATATTTTTATTATG-TTCAATTAAATCT
1 TTATACTTTTATTTTGAGTCAAATAAATCT
* *
35080084 TTATACTTTTATTTTGAGTTAAATAAATTT
1 TTATACTTTTATTTTGAGTCAAATAAATCT
*
35080114 TTATATTTTTAATTTTGAGTCAAATAA
1 TTATACTTTT-ATTTTGAGTCAAATAA
35080141 GCTCTTGTTA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 14 0.30
30 18 0.38
31 15 0.32
ACGTcount: A:0.34, C:0.05, G:0.06, T:0.56
Consensus pattern (30 bp):
TTATACTTTTATTTTGAGTCAAATAAATCT
Found at i:35082417 original size:29 final size:31
Alignment explanation
Indices: 35082385--35082507 Score: 102
Period size: 32 Copynumber: 4.2 Consensus size: 31
35082375 GAATATATTG
*
35082385 TGTAACAATAATA-T-TTTTTCAACATGACA
1 TGTAACAACAATATTATTTTTCAACATGACA
*
35082414 TGTAACAACAATATTTATTTTTCAACATGACG
1 TGTAACAACAATA-TTATTTTTCAACATGACA
***
35082446 TGTAACAAC----TT-TTTTT-AACCATGGTG
1 TGTAACAACAATATTATTTTTCAA-CATGACA
*
35082472 TGTAACAACAATATGT-TTTTTCAACATGACG
1 TGTAACAACAATAT-TATTTTTCAACATGACA
35082503 TGTAA
1 TGTAA
35082508 TAATCTAACC
Statistics
Matches: 78, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
25 2 0.03
26 19 0.24
27 2 0.03
29 12 0.15
30 1 0.01
31 17 0.22
32 25 0.32
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (31 bp):
TGTAACAACAATATTATTTTTCAACATGACA
Found at i:35082551 original size:45 final size:45
Alignment explanation
Indices: 35082497--35082591 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 45
35082487 TTTTTTCAAC
* * ** *
35082497 ATGACGTGTAATAATCTAACCATGGCTTTTCACAAGTTTTTGTAT
1 ATGACGTGTAACAAGCTAACCATAACTTGTCACAAGTTTTTGTAT
*
35082542 ATGAGGTGTAACAAGCTAACCATAACTTGTCACAAGTTTTTGTAT
1 ATGACGTGTAACAAGCTAACCATAACTTGTCACAAGTTTTTGTAT
35082587 ATGAC
1 ATGAC
35082592 TTATCACATA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36
Consensus pattern (45 bp):
ATGACGTGTAACAAGCTAACCATAACTTGTCACAAGTTTTTGTAT
Found at i:35082666 original size:44 final size:45
Alignment explanation
Indices: 35082586--35082674 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 45
35082576 AGTTTTTGTA
* *
35082586 TATGACTTATCACATATTTTTATACATAGTGTGTAACAAGCTAAC
1 TATGACTTATCACAGATTTTTATACATAGCGTGTAACAAGCTAAC
* * *
35082631 TATGACTTGTTACAGATTTTT-TACATAGCGTGTAACACGCTAAC
1 TATGACTTATCACAGATTTTTATACATAGCGTGTAACAAGCTAAC
35082675 CATGGTTGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 21 0.54
45 18 0.46
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (45 bp):
TATGACTTATCACAGATTTTTATACATAGCGTGTAACAAGCTAAC
Found at i:35091269 original size:68 final size:68
Alignment explanation
Indices: 35091132--35091269 Score: 154
Period size: 68 Copynumber: 2.0 Consensus size: 68
35091122 AAATTTTTAA
* * ** *
35091132 TAAAAAAATATTAACACACTATTTTATATTAACATAATTCTTCATATAATGATCAATAAAGTTTT
1 TAAAAAAATATTAACACACTATTTTATATTAACATAATTCTTAATATAATCATCAATAAAGAATA
35091197 TTT
66 TTT
** * * *
35091200 TAAAAACAA-ATTAACACTTTATTTTATATTAATATAATTCTTAATATAATCATTAGTCAAA-AA
1 TAAAAA-AATATTAACACACTATTTTATATTAACATAATTCTTAATATAATCATCAAT-AAAGAA
35091263 TATTT
64 TATTT
35091268 TA
1 TA
35091270 TAATTACAAG
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
68 53 0.91
69 5 0.09
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (68 bp):
TAAAAAAATATTAACACACTATTTTATATTAACATAATTCTTAATATAATCATCAATAAAGAATA
TTT
Found at i:35093520 original size:90 final size:90
Alignment explanation
Indices: 35093373--35093544 Score: 290
Period size: 90 Copynumber: 1.9 Consensus size: 90
35093363 GTCGAGTCTC
* *
35093373 ATAGACTGGAACTAATGAAATCCAAGTATGGAGAAATTGAGGAAATGGAAGCAATGTTGGATAAA
1 ATAGACTGGAACTAATGAAATCCAAGTATGGAGAAATTGACGAAATCGAAGCAATGTTGGATAAA
35093438 TTCAAGAATATGGAGGCCGAGGCCA
66 TTCAAGAATATGGAGGCCGAGGCCA
* * *
35093463 ATAGCCTGGAACTAATGAAATCCAAGTATGGAGAAATTGACGAAATCGAATCCATGTTGGATAAA
1 ATAGACTGGAACTAATGAAATCCAAGTATGGAGAAATTGACGAAATCGAAGCAATGTTGGATAAA
*
35093528 TTCAAGAATTTGGAGGC
66 TTCAAGAATATGGAGGC
35093545 TGAGTCACAT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 76 1.00
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.22
Consensus pattern (90 bp):
ATAGACTGGAACTAATGAAATCCAAGTATGGAGAAATTGACGAAATCGAAGCAATGTTGGATAAA
TTCAAGAATATGGAGGCCGAGGCCA
Found at i:35105305 original size:32 final size:32
Alignment explanation
Indices: 35105267--35105374 Score: 110
Period size: 32 Copynumber: 3.3 Consensus size: 32
35105257 TGTTAGGTTG
*
35105267 TGGTTGAGCCTTTGAAAAACCACTTTGAGTTT
1 TGGTTGAGCCTTTGAAAAACCACTTTGAGTTA
**
35105299 TGGTTGAGCCCATGAAAAACCA-TTGTGAAAGGTTA
1 TGGTTGAGCCTTTGAAAAACCACTT-TG--A-GTTA
* * *
35105334 TGGTTAAGTCTTTGAAAAACCACTTTGGGTTA
1 TGGTTGAGCCTTTGAAAAACCACTTTGAGTTA
*
35105366 TAGTTGAGC
1 TGGTTGAGC
35105375 TTGGGAAAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
31 2 0.03
32 32 0.53
34 1 0.02
35 23 0.38
36 2 0.03
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (32 bp):
TGGTTGAGCCTTTGAAAAACCACTTTGAGTTA
Found at i:35105372 original size:67 final size:67
Alignment explanation
Indices: 35105261--35105411 Score: 185
Period size: 67 Copynumber: 2.3 Consensus size: 67
35105251 GTTAGGTGTT
* * * * *
35105261 AGGTTGTGGTTGAGCCTTTGAAAAACCACTTTGAGTTTTGGTTGAGCCCATGAAAAACCATTGTG
1 AGGTTATGGTTAAGCCTTTGAAAAACCACTTTGAGTTATAGTTGAGCCCAGGAAAAACCATTGTG
35105326 AA
66 AA
* * *** *
35105328 AGGTTATGGTTAAGTCTTTGAAAAACCACTTTGGGTTATAGTTGAGCTTGGGAAAAACTATTGTG
1 AGGTTATGGTTAAGCCTTTGAAAAACCACTTTGAGTTATAGTTGAGCCCAGGAAAAACCATTGTG
35105393 AA
66 AA
* *
35105395 AGGTTTTGGCTAAGCCT
1 AGGTTATGGTTAAGCCT
35105412 GATAGAAGCT
Statistics
Matches: 70, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
67 70 1.00
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (67 bp):
AGGTTATGGTTAAGCCTTTGAAAAACCACTTTGAGTTATAGTTGAGCCCAGGAAAAACCATTGTG
AA
Found at i:35110853 original size:23 final size:22
Alignment explanation
Indices: 35110817--35111051 Score: 211
Period size: 23 Copynumber: 10.2 Consensus size: 22
35110807 CCAAGCAATG
*
35110817 CCATATCAAATAGTCACCTGATT
1 CCATATCAACTAGTCACC-GATT
* *
35110840 CTATATTAACTAGTCACGCGATT
1 CCATATCAACTAGTCAC-CGATT
*
35110863 CCAAATCATA-TAGTCACGCGATT
1 CCATATCA-ACTAGTCAC-CGATT
*
35110886 CCATATCAACTAGTCACATGATT
1 CCATATCAACTAGTCAC-CGATT
* **
35110909 CTATATTTACTAGTCACGCGATT
1 CCATATCAACTAGTCAC-CGATT
*
35110932 CCATATCAACTAGTCATGCGATT
1 CCATATCAACTAGTCA-CCGATT
* *
35110955 CCATATCAAATAGTCATGCGATT
1 CCATATCAACTAGTCA-CCGATT
* * *
35110978 CCATATTAACTAGTGACGTGATT
1 CCATATCAACTAGTCAC-CGATT
* *
35111001 CCATATCAATTAGTCACTTGATT
1 CCATATCAACTAGTCAC-CGATT
*
35111024 CAATATCAACTAGTCACGCGATT
1 CCATATCAACTAGTCAC-CGATT
35111047 CCATA
1 CCATA
35111052 CACGCCATTC
Statistics
Matches: 174, Mismatches: 33, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
22 1 0.01
23 171 0.98
24 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (22 bp):
CCATATCAACTAGTCACCGATT
Found at i:35110897 original size:46 final size:46
Alignment explanation
Indices: 35110817--35111051 Score: 283
Period size: 46 Copynumber: 5.1 Consensus size: 46
35110807 CCAAGCAATG
* *
35110817 CCATATCAAATAGTCAC-CTGATTCTATATTAACTAGTCACGCGATT
1 CCATATCAAATAGTCACGC-GATTCCATATCAACTAGTCACGCGATT
* * **
35110863 CCAAATCATATAGTCACGCGATTCCATATCAACTAGTCACATGATT
1 CCATATCAAATAGTCACGCGATTCCATATCAACTAGTCACGCGATT
* ** * *
35110909 CTATATTTACTAGTCACGCGATTCCATATCAACTAGTCATGCGATT
1 CCATATCAAATAGTCACGCGATTCCATATCAACTAGTCACGCGATT
* * * *
35110955 CCATATCAAATAGTCATGCGATTCCATATTAACTAGTGACGTGATT
1 CCATATCAAATAGTCACGCGATTCCATATCAACTAGTCACGCGATT
* ** *
35111001 CCATATCAATTAGTCACTTGATTCAATATCAACTAGTCACGCGATT
1 CCATATCAAATAGTCACGCGATTCCATATCAACTAGTCACGCGATT
35111047 CCATA
1 CCATA
35111052 CACGCCATTC
Statistics
Matches: 156, Mismatches: 32, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
46 155 0.99
47 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (46 bp):
CCATATCAAATAGTCACGCGATTCCATATCAACTAGTCACGCGATT
Found at i:35110928 original size:69 final size:69
Alignment explanation
Indices: 35110817--35111040 Score: 288
Period size: 69 Copynumber: 3.2 Consensus size: 69
35110807 CCAAGCAATG
* *
35110817 CCATATCAAATAGTCACCTGATTCTATATTAACTAGTCACGCGATTCCAAATCATA-TAGTCACG
1 CCATATCAAATAGTCACATGATTCTATATTAACTAGTCACGCGATTCCATATCA-ACTAGTCACG
35110881 CGATT
65 CGATT
* * *
35110886 CCATATCAACTAGTCACATGATTCTATATTTACTAGTCACGCGATTCCATATCAACTAGTCATGC
1 CCATATCAAATAGTCACATGATTCTATATTAACTAGTCACGCGATTCCATATCAACTAGTCACGC
35110951 GATT
66 GATT
*** * * * * **
35110955 CCATATCAAATAGTCATGCGATTCCATATTAACTAGTGACGTGATTCCATATCAATTAGTCACTT
1 CCATATCAAATAGTCACATGATTCTATATTAACTAGTCACGCGATTCCATATCAACTAGTCACGC
35111020 GATT
66 GATT
* *
35111024 CAATATCAACTAGTCAC
1 CCATATCAAATAGTCAC
35111041 GCGATTCCAT
Statistics
Matches: 134, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
68 1 0.01
69 133 0.99
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.32
Consensus pattern (69 bp):
CCATATCAAATAGTCACATGATTCTATATTAACTAGTCACGCGATTCCATATCAACTAGTCACGC
GATT
Found at i:35111391 original size:26 final size:27
Alignment explanation
Indices: 35111354--35111410 Score: 98
Period size: 26 Copynumber: 2.1 Consensus size: 27
35111344 TGCCTTTCTC
35111354 TTTGTTAAATGATACAAAAAAGAATAA
1 TTTGTTAAATGATACAAAAAAGAATAA
*
35111381 TTTG-TAAATGATACAACAAAGAATAA
1 TTTGTTAAATGATACAAAAAAGAATAA
35111407 TTTG
1 TTTG
35111411 GAGATTATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 25 0.86
27 4 0.14
ACGTcount: A:0.51, C:0.05, G:0.12, T:0.32
Consensus pattern (27 bp):
TTTGTTAAATGATACAAAAAAGAATAA
Found at i:35111420 original size:26 final size:26
Alignment explanation
Indices: 35111360--35111421 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
35111350 TCTCTTTGTT
*
35111360 AAATGATACAAAAAAGAATAATTTGT
1 AAATGATACAAAAAAGAATAATTTGG
*
35111386 AAATGATACAACAAAGAATAATTTGG
1 AAATGATACAAAAAAGAATAATTTGG
* *
35111412 AGATTATACA
1 AAATGATACA
35111422 CAACAATGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.55, C:0.06, G:0.13, T:0.26
Consensus pattern (26 bp):
AAATGATACAAAAAAGAATAATTTGG
Found at i:35113467 original size:27 final size:27
Alignment explanation
Indices: 35113435--35113502 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
35113425 CAACATAAGA
35113435 AGCAGTTAGAAAAACAACATCATGAGG
1 AGCAGTTAGAAAAACAACATCATGAGG
* * *
35113462 AGCAGTTGGAAAAGCAGCATCATGAGG
1 AGCAGTTAGAAAAACAACATCATGAGG
*
35113489 AGCAGCTAGAAAAA
1 AGCAGTTAGAAAAA
35113503 AAGCATTGGG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.46, C:0.15, G:0.26, T:0.13
Consensus pattern (27 bp):
AGCAGTTAGAAAAACAACATCATGAGG
Found at i:35113553 original size:12 final size:12
Alignment explanation
Indices: 35113536--35113561 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35113526 GAAGCAACAT
35113536 GAAAAGTAGTAG
1 GAAAAGTAGTAG
35113548 GAAAAGTAGTAG
1 GAAAAGTAGTAG
35113560 GA
1 GA
35113562 GAAACAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.35, T:0.15
Consensus pattern (12 bp):
GAAAAGTAGTAG
Found at i:35115423 original size:23 final size:23
Alignment explanation
Indices: 35115397--35115452 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
35115387 TGAATCATAT
*
35115397 TCACGCAATGACCTATCAACCAA
1 TCACGCAATGACATATCAACCAA
* * *
35115420 TCACGTAATCACATATCAACCAG
1 TCACGCAATGACATATCAACCAA
35115443 TCACGCAATG
1 TCACGCAATG
35115453 TTAAACCTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.38, C:0.32, G:0.11, T:0.20
Consensus pattern (23 bp):
TCACGCAATGACATATCAACCAA
Found at i:35118092 original size:2 final size:2
Alignment explanation
Indices: 35118081--35118130 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
35118071 GCAACAATGT
35118081 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35118122 TA TA TA TA T
1 TA TA TA TA T
35118131 GGCTCTTATT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35119972 original size:35 final size:35
Alignment explanation
Indices: 35119901--35119983 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 35
35119891 GAATAATGAG
* *
35119901 AACAATTAGAACAAGTGAAGTACTATTTCGCATAA
1 AACAATTAGAACAAGTGAAGTACTACTTCGAATAA
* * *
35119936 AACAACTAGAGCAAGTGAAGTATTACTTC-AAGTAA
1 AACAATTAGAACAAGTGAAGTACTACTTCGAA-TAA
35119971 AACAATTAGAACA
1 AACAATTAGAACA
35119984 GTAAAGCACT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
34 1 0.03
35 39 0.98
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.23
Consensus pattern (35 bp):
AACAATTAGAACAAGTGAAGTACTACTTCGAATAA
Found at i:35121641 original size:2 final size:2
Alignment explanation
Indices: 35121634--35121709 Score: 110
Period size: 2 Copynumber: 41.0 Consensus size: 2
35121624 GCAAAGAATA
35121634 AG AG AG AG AG AG AG A- AG AG -G AG AG AG AG AG AG AG AG AG -G
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
35121673 AG AG AG AG -G AG AG AG -G AG AG AG -G AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
35121710 NNNNNNNNNN
Statistics
Matches: 68, Mismatches: 0, Indels: 12
0.85 0.00 0.15
Matches are distributed among these distances:
1 6 0.09
2 62 0.91
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35121747 original size:2 final size:2
Alignment explanation
Indices: 35121740--35121785 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
35121730 NNNNNNNNNN
35121740 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
35121782 GA GA
1 GA GA
35121786 ATATATAATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:35123525 original size:105 final size:105
Alignment explanation
Indices: 35123343--35123560 Score: 418
Period size: 105 Copynumber: 2.1 Consensus size: 105
35123333 TCTAGTTTCT
35123343 GGTTTCTGGCTTTATCTTTAGCAAGTCCAAGTTGCTGCCATTCTTGTTCCTTGATCCTTCACCTT
1 GGTTTCTGGCTTTATCTTTAGCAAGTCCAAGTTGCTGCCATTCTTGTTCCTTGATCCTTCACCTT
35123408 TTTGGGCCTTCCCTCATCAAGTGACTAGTAAGTTTTTTTG
66 TTTGGGCCTTCCCTCATCAAGTGACTAGTAAGTTTTTTTG
* *
35123448 GGTTTTTGGCTTTATCTTTAGTAAGTCCAAGTTGCTGCCATTCTTGTTCCTTGATCCTTCACCTT
1 GGTTTCTGGCTTTATCTTTAGCAAGTCCAAGTTGCTGCCATTCTTGTTCCTTGATCCTTCACCTT
35123513 TTTGGGCCTTCCCTCATCAAGTGACTAGTAAGTTTTTTTG
66 TTTGGGCCTTCCCTCATCAAGTGACTAGTAAGTTTTTTTG
35123553 GGTTTCTG
1 GGTTTCTG
35123561 CCATCGTTCA
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 110 1.00
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (105 bp):
GGTTTCTGGCTTTATCTTTAGCAAGTCCAAGTTGCTGCCATTCTTGTTCCTTGATCCTTCACCTT
TTTGGGCCTTCCCTCATCAAGTGACTAGTAAGTTTTTTTG
Found at i:35128346 original size:14 final size:16
Alignment explanation
Indices: 35128331--35128372 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
35128321 TATTTTATAT
35128331 TAATATTATAAAATT-A
1 TAAT-TTATAAAATTAA
35128347 TAATTTATAAAATTATA
1 TAATTTATAAAATTA-A
*
35128364 AAATTTATA
1 TAATTTATA
35128373 TAACAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 10 0.43
16 4 0.17
17 9 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATTTATAAAATTAA
Found at i:35128348 original size:8 final size:8
Alignment explanation
Indices: 35128335--35128368 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
35128325 TTATATTAAT
35128335 ATTATAAA
1 ATTATAAA
35128343 ATTAT-AA
1 ATTATAAA
*
35128350 TTTATAAA
1 ATTATAAA
35128358 ATTATAAA
1 ATTATAAA
35128366 ATT
1 ATT
35128369 TATATAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
ATTATAAA
Found at i:35128356 original size:15 final size:16
Alignment explanation
Indices: 35128331--35128364 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
35128321 TATTTTATAT
35128331 TAATATTATAAAATTA
1 TAATATTATAAAATTA
35128347 TAAT-TTATAAAATTA
1 TAATATTATAAAATTA
35128362 TAA
1 TAA
35128365 AATTTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATATTATAAAATTA
Found at i:35128757 original size:133 final size:132
Alignment explanation
Indices: 35128612--35129063 Score: 566
Period size: 133 Copynumber: 3.4 Consensus size: 132
35128602 CCAACTGCCA
* * * *
35128612 GCCTACCACGCCACGCTCGGCTCTTTCATCAGTTCATCTTTTTTTTCTCCTCAGTCGTCCAGCCA
1 GCCTACCACGCCACGCTCGGCTCCTTCATCAGTTCATCTTTCTTTTCTCCCCAGTCGCCCAGCCA
* * * * *
35128677 CAGCCACGCCCTGCCAACTACCTCAGTGTCGCCCCAAGCCCCACACCCTTGTTCTTCCCCAGTTG
66 CAGCCACGCCCTGCCGACTGCCTC-GTGTCGCCCCAAGCCCCACGCCCTTGTTTTTCCCCAGCTG
35128742 TCG
130 TCG
* * **
35128745 GCTTACCACGCCATGCTCGGCTCCTTCATCAGTTCATCTTTCTTTTCTCCCCAGTAACCCAGCCA
1 GCCTACCACGCCACGCTCGGCTCCTTCATCAGTTCATCTTTCTTTTCTCCCCAGTCGCCCAGCCA
* *
35128810 CAGCTACGCCCTGCCGACTGCCTCG-GAATCGCCCCAAGCCCCACGCCCTTGTTTTTCCCCAACT
66 CAGCCACGCCCTGCCGACTGCCTCGTG--TCGCCCCAAGCCCCACGCCCTTGTTTTTCCCCAGCT
35128874 GTCG
129 GTCG
* * * *
35128878 GCCTACCACACCACGCTCGGCTCTTTCATCATTTCATCTTTCTTTTCTCCCCAG-CTGCCCAACC
1 GCCTACCACGCCACGCTCGGCTCCTTCATCAGTTCATCTTTCTTTTCTCCCCAGTC-GCCCAGCC
* * * * * * * *
35128942 ATAGCCACGCCTTACTGGCTGCCTCGTTGTCACCCCAAGCCCTACGCCCTTGTTTTTCCCTAGCT
65 ACAGCCACGCCCTGCCGACTGCCTCG-TGTCGCCCCAAGCCCCACGCCCTTGTTTTTCCCCAGCT
*
35129007 GTTG
129 GTCG
** *
35129011 GCCTACCACGCCACTTTCAGCTCCTTCATCAGTTCATCTTTCTTTTCTCCCCA
1 GCCTACCACGCCACGCTCGGCTCCTTCATCAGTTCATCTTTCTTTTCTCCCCA
35129064 CCCACCATTA
Statistics
Matches: 274, Mismatches: 40, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
131 1 0.00
132 1 0.00
133 271 0.99
135 1 0.00
ACGTcount: A:0.15, C:0.42, G:0.14, T:0.29
Consensus pattern (132 bp):
GCCTACCACGCCACGCTCGGCTCCTTCATCAGTTCATCTTTCTTTTCTCCCCAGTCGCCCAGCCA
CAGCCACGCCCTGCCGACTGCCTCGTGTCGCCCCAAGCCCCACGCCCTTGTTTTTCCCCAGCTGT
CG
Found at i:35129802 original size:16 final size:16
Alignment explanation
Indices: 35129783--35129813 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
35129773 CATAAATATA
35129783 AAAGTAAAAAAAAAGT
1 AAAGTAAAAAAAAAGT
35129799 AAAGTAAAAAAAAAG
1 AAAGTAAAAAAAAAG
35129814 GGAGCTGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (16 bp):
AAAGTAAAAAAAAAGT
Found at i:35130407 original size:8 final size:7
Alignment explanation
Indices: 35130391--35130448 Score: 56
Period size: 6 Copynumber: 8.9 Consensus size: 7
35130381 GGTGTCGGGG
35130391 AGAAGAA
1 AGAAGAA
35130398 AGAGAGAA
1 AGA-AGAA
35130406 AGAAG-A
1 AGAAGAA
35130412 AGAAGAA
1 AGAAGAA
35130419 A-AAGAA
1 AGAAGAA
35130425 A-AA-ACA
1 AGAAGA-A
35130431 A-AAGAA
1 AGAAGAA
35130437 AGAA-AA
1 AGAAGAA
35130443 AGAAGA
1 AGAAGA
35130449 GTTGCGGGCT
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
5 1 0.02
6 26 0.58
7 11 0.24
8 7 0.16
ACGTcount: A:0.74, C:0.02, G:0.24, T:0.00
Consensus pattern (7 bp):
AGAAGAA
Found at i:35130415 original size:21 final size:20
Alignment explanation
Indices: 35130391--35130448 Score: 68
Period size: 18 Copynumber: 3.0 Consensus size: 20
35130381 GGTGTCGGGG
35130391 AGAAGAAAGAGAGAAAGAAGA
1 AGAAGAAAGA-AGAAAGAAGA
* *
35130412 AGAAGAAA-AAGAAAAAACA
1 AGAAGAAAGAAGAAAGAAGA
35130431 A-AAGAAAGAA-AAAGAAGA
1 AGAAGAAAGAAGAAAGAAGA
35130449 GTTGCGGGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 12 0.38
19 11 0.34
20 1 0.03
21 8 0.25
ACGTcount: A:0.74, C:0.02, G:0.24, T:0.00
Consensus pattern (20 bp):
AGAAGAAAGAAGAAAGAAGA
Found at i:35130510 original size:18 final size:17
Alignment explanation
Indices: 35130479--35130528 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
35130469 AAAGAGAAGC
*
35130479 AAAGAAGAGGAAAAAAG
1 AAAGAAGAGAAAAAAAG
*
35130496 AAAGAGAGAGAAAAAGAG
1 AAAGA-AGAGAAAAAAAG
35130514 AAAGAAGA-AAAAAAA
1 AAAGAAGAGAAAAAAA
35130529 AAGGATAGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 6 0.21
17 8 0.28
18 15 0.52
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (17 bp):
AAAGAAGAGAAAAAAAG
Found at i:35130526 original size:16 final size:16
Alignment explanation
Indices: 35130479--35130531 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 16
35130469 AAAGAGAAGC
35130479 AAAGAAGAGGAAAAAAG
1 AAAGAAGA-GAAAAAAG
35130496 AAAGAGAGAGAAAAAGAG
1 AAAGA-AGAGAAAAA-AG
35130514 AAAGAAGA-AAAAAA-
1 AAAGAAGAGAAAAAAG
35130528 AAAG
1 AAAG
35130532 GATAGCAGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.12
15 1 0.03
16 5 0.15
17 14 0.41
18 10 0.29
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (16 bp):
AAAGAAGAGAAAAAAG
Found at i:35131571 original size:14 final size:15
Alignment explanation
Indices: 35131525--35131573 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 15
35131515 ATAATGGTTG
35131525 TTAAAAAATAATATACA
1 TTAAAAAATAA-ATA-A
35131542 TTAGAAAAAATAAATAA
1 TT--AAAAAATAAATAA
35131559 TTAAAAAAT-AATAA
1 TTAAAAAATAAATAA
35131573 T
1 T
35131574 AAATAGGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 6 0.20
15 7 0.23
17 5 0.17
18 3 0.10
19 9 0.30
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (15 bp):
TTAAAAAATAAATAA
Found at i:35131574 original size:17 final size:17
Alignment explanation
Indices: 35131525--35131575 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
35131515 ATAATGGTTG
35131525 TTAAAAAATAAT-ATACA
1 TTAAAAAATAATAATA-A
*
35131542 TTAGAAAA-AATAAATAA
1 TTAAAAAATAAT-AATAA
35131559 TTAAAAAATAATAATAA
1 TTAAAAAATAATAATAA
35131576 ATAGGTAAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 3 0.10
17 20 0.69
18 6 0.21
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (17 bp):
TTAAAAAATAATAATAA
Found at i:35135141 original size:34 final size:35
Alignment explanation
Indices: 35135078--35135146 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
35135068 TATGTGCTTG
* *
35135078 GTTATTTAAGTTTATGTTATTTGTTTGGATCTTTA
1 GTTATTTAAGTTTATGTTAGTTGTTTGGATATTTA
35135113 GTTATTTAAGTTTATGTT-GTTGTTTGGATATTTA
1 GTTATTTAAGTTTATGTTAGTTGTTTGGATATTTA
35135147 TGTATAGTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 14 0.44
35 18 0.56
ACGTcount: A:0.20, C:0.01, G:0.19, T:0.59
Consensus pattern (35 bp):
GTTATTTAAGTTTATGTTAGTTGTTTGGATATTTA
Found at i:35135175 original size:40 final size:40
Alignment explanation
Indices: 35135111--35135209 Score: 144
Period size: 40 Copynumber: 2.5 Consensus size: 40
35135101 TTTGGATCTT
* * *
35135111 TAGTTATTTAAGTTTATGTTGTTGTTTGGATATTTATGTA
1 TAGTTATTTAAGTTTATATCGTTGTATGGATATTTATGTA
* * *
35135151 TAGTTATTTAAGCTTATATCGTTGTATGGATATTTATTTT
1 TAGTTATTTAAGTTTATATCGTTGTATGGATATTTATGTA
35135191 TAGTTATTTAAGTTTATAT
1 TAGTTATTTAAGTTTATAT
35135210 TTAAGATCTT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.25, C:0.02, G:0.16, T:0.57
Consensus pattern (40 bp):
TAGTTATTTAAGTTTATATCGTTGTATGGATATTTATGTA
Found at i:35139144 original size:618 final size:618
Alignment explanation
Indices: 35137968--35139212 Score: 2382
Period size: 618 Copynumber: 2.0 Consensus size: 618
35137958 TTTTGTTGTG
35137968 GGAAATCACTTTGATATTCGGACTGCCATGTCGTTTCCAAGTCAAGAAAGTCAGAGCGAGTTCAA
1 GGAAATCACTTTGATATTCGGACTGCCATGTCGTTTCCAAGTCAAGAAAGTCAGAGCGAGTTCAA
35138033 CCACTGCCCAGATTTAACCGCTATGGTTCATAATGTAGATCAGACTCCTTTAGCCATTTCTCCGG
66 CCACTGCCCAGATTTAACCGCTATGGTTCATAATGTAGATCAGACTCCTTTAGCCATTTCTCCGG
* *
35138098 ACGACTTGACCCAGAGGTCCATGAACTCTCAGTTTCATCCTGACGTTGAAGTGGAGACCGGTTCT
131 ACGACTTGACCCAGAGGTCCATGAACTCTCAGTTTCAACCTCACGTTGAAGTGGAGACCGGTTCT
*
35138163 GTGGCACAGAATGGAGATGGGAGTAGTAGCTGGGGATTATCTTTCTCAGACATGCCGTTGGATTC
196 GTGGCACAGAATGGAGATGGGAGTAGTAGCTGGGGATTACCTTTCTCAGACATGCCGTTGGATTC
*
35138228 ATATTGGAAAGACCTTGATGTAGACCTCAGTTCTGTGGCACAGACTGAAGATTTGAGTCCGATGT
261 ATATTGGAAAGACCTTGATGTAGACCTCAGTTCTGTGGCACAGACTGAAGATTTGAGTCCGATAT
35138293 CGACATCTAAAACAGACACGCCGCGGCCAGGAGGAGGCAATGCTAATGAGTTACCCCAGCAGTTC
326 CGACATCTAAAACAGACACGCCGCGGCCAGGAGGAGGCAATGCTAATGAGTTACCCCAGCAGTTC
35138358 AATTCCTCTGACCAGCCATTGAATTCACTTGCTGGGAATTTAACTGCTGATCAGCTGGTGAACTC
391 AATTCCTCTGACCAGCCATTGAATTCACTTGCTGGGAATTTAACTGCTGATCAGCTGGTGAACTC
35138423 TCACGGAGACGTTGAAACGGAGGTACGGTGTTCTGAACCAAACCAAAGCCACCTGGATCATGAAG
456 TCACGGAGACGTTGAAACGGAGGTACGGTGTTCTGAACCAAACCAAAGCCACCTGGATCATGAAG
35138488 AAAGACCATCTGATCAAGCTTCAAATGGACAAAAACAAAGGGGTCGTAAACCAAGGGTAACACCA
521 AAAGACCATCTGATCAAGCTTCAAATGGACAAAAACAAAGGGGTCGTAAACCAAGGGTAACACCA
35138553 GTGGAAAAAGCAAAGAACCAACTTGATCAAGCA
586 GTGGAAAAAGCAAAGAACCAACTTGATCAAGCA
*
35138586 GGAAATCACTTTGATGTTCGGACTGCCATGTCGTTTCCAAGTCAAGAAAGTCAGAGCGAGTTCAA
1 GGAAATCACTTTGATATTCGGACTGCCATGTCGTTTCCAAGTCAAGAAAGTCAGAGCGAGTTCAA
35138651 CCACTGCCCAGATTTAACCGCTATGGTTCATAATGTAGATCAGACTCCTTTAGCCATTTCTCCGG
66 CCACTGCCCAGATTTAACCGCTATGGTTCATAATGTAGATCAGACTCCTTTAGCCATTTCTCCGG
* *
35138716 ACGACTTGACCCAGAGGTCCTTGAACTCTCAGTTTCAACCTCACGTTGAAGTGGAGACTGGTTCT
131 ACGACTTGACCCAGAGGTCCATGAACTCTCAGTTTCAACCTCACGTTGAAGTGGAGACCGGTTCT
*
35138781 GTGGCACAGAATGGAGATGGGAGTAGTAGTTGGGGATTACCTTTCTCAGACATGCCGTTGGATTC
196 GTGGCACAGAATGGAGATGGGAGTAGTAGCTGGGGATTACCTTTCTCAGACATGCCGTTGGATTC
35138846 ATATTGGAAAGACCTTGATGTAGACCTCAGTTCTGTGGCACAGACTGAAGATTTGAGTCCGATAT
261 ATATTGGAAAGACCTTGATGTAGACCTCAGTTCTGTGGCACAGACTGAAGATTTGAGTCCGATAT
* *
35138911 CGACATCTAAAACAGACATGCCGGGGCCAGGAGGAGGCAATGCTAATGAGTTACCCCAGCAGTTC
326 CGACATCTAAAACAGACACGCCGCGGCCAGGAGGAGGCAATGCTAATGAGTTACCCCAGCAGTTC
35138976 AATTCCTCTGACCAGCCATTGAATTCACTTGCTGGGAATTTAACTGCTGATCAGCTGGTGAACTC
391 AATTCCTCTGACCAGCCATTGAATTCACTTGCTGGGAATTTAACTGCTGATCAGCTGGTGAACTC
*
35139041 TCACGGAGACGTTGAAACGGGGGTACGGTGTTCTGAACCAAACCAAAGCCACCTGGATCATGAAG
456 TCACGGAGACGTTGAAACGGAGGTACGGTGTTCTGAACCAAACCAAAGCCACCTGGATCATGAAG
35139106 AAAGACCATCTGATCAAGCTTCAAATGGACAAAAACAAAGGGGTCGTAAACCAAGGGTAACACCA
521 AAAGACCATCTGATCAAGCTTCAAATGGACAAAAACAAAGGGGTCGTAAACCAAGGGTAACACCA
35139171 GTGGAAAAAGCAAAGAACCAACTTGATCAAGCA
586 GTGGAAAAAGCAAAGAACCAACTTGATCAAGCA
35139204 GGAACATCA
1 GGAA-ATCA
35139213 GCTAAAGCTC
Statistics
Matches: 615, Mismatches: 11, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
618 611 0.99
619 4 0.01
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.23
Consensus pattern (618 bp):
GGAAATCACTTTGATATTCGGACTGCCATGTCGTTTCCAAGTCAAGAAAGTCAGAGCGAGTTCAA
CCACTGCCCAGATTTAACCGCTATGGTTCATAATGTAGATCAGACTCCTTTAGCCATTTCTCCGG
ACGACTTGACCCAGAGGTCCATGAACTCTCAGTTTCAACCTCACGTTGAAGTGGAGACCGGTTCT
GTGGCACAGAATGGAGATGGGAGTAGTAGCTGGGGATTACCTTTCTCAGACATGCCGTTGGATTC
ATATTGGAAAGACCTTGATGTAGACCTCAGTTCTGTGGCACAGACTGAAGATTTGAGTCCGATAT
CGACATCTAAAACAGACACGCCGCGGCCAGGAGGAGGCAATGCTAATGAGTTACCCCAGCAGTTC
AATTCCTCTGACCAGCCATTGAATTCACTTGCTGGGAATTTAACTGCTGATCAGCTGGTGAACTC
TCACGGAGACGTTGAAACGGAGGTACGGTGTTCTGAACCAAACCAAAGCCACCTGGATCATGAAG
AAAGACCATCTGATCAAGCTTCAAATGGACAAAAACAAAGGGGTCGTAAACCAAGGGTAACACCA
GTGGAAAAAGCAAAGAACCAACTTGATCAAGCA
Found at i:35144965 original size:20 final size:20
Alignment explanation
Indices: 35144915--35145064 Score: 66
Period size: 20 Copynumber: 7.5 Consensus size: 20
35144905 CATATCTTAA
35144915 ATATATTTTATTTTTAT-TT
1 ATATATTTTATTTTTATATT
* * *
35144934 TTA-ATATAATTTTTATATT
1 ATATATTTTATTTTTATATT
35144953 ATATATTTTA-TTTTA-A-T
1 ATATATTTTATTTTTATATT
* **
35144970 -T-TCTTTTA--CCTATATT
1 ATATATTTTATTTTTATATT
35144986 ATATAAATTTTAATTTCTTATATTTT
1 ATAT--ATTTT-ATTT-TTATA--TT
*
35145012 ATTTTAATTTTGATTTTTATATT
1 A-TAT-ATTTT-ATTTTTATATT
*
35145035 ATATATTTTATTTTAATATT
1 ATATATTTTATTTTTATATT
* *
35145055 TTTTATTTTA
1 ATATATTTTA
35145065 ATTATAATGT
Statistics
Matches: 98, Mismatches: 18, Indels: 29
0.68 0.12 0.20
Matches are distributed among these distances:
14 2 0.02
15 7 0.07
16 2 0.02
17 2 0.02
18 13 0.13
19 11 0.11
20 26 0.27
21 6 0.06
22 2 0.02
23 3 0.03
24 4 0.04
25 5 0.05
26 13 0.13
27 2 0.02
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.67
Consensus pattern (20 bp):
ATATATTTTATTTTTATATT
Found at i:35146531 original size:2 final size:2
Alignment explanation
Indices: 35146524--35146617 Score: 95
Period size: 2 Copynumber: 48.5 Consensus size: 2
35146514 AAATGTTTTC
35146524 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * * *
35146565 T- TA TN TG CA AA AA TG T- TT TC TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35146605 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
35146618 TAATATTATG
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
1 3 0.04
2 77 0.96
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:35146970 original size:35 final size:35
Alignment explanation
Indices: 35146893--35146970 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 35
35146883 TGCAGAATAG
* * *
35146893 AACAATTACAGCAAGTGAAGTATTATTTCATACAA
1 AACAATTAAAACAAGTGAAGTATTATTTCACACAA
* **
35146928 AATAATTAAAACAAGT-AATGTATTATTTCACGTAA
1 AACAATTAAAACAAGTGAA-GTATTATTTCACACAA
35146963 AACAATTA
1 AACAATTA
35146971 GAGTAAATAG
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
34 2 0.06
35 33 0.94
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.31
Consensus pattern (35 bp):
AACAATTAAAACAAGTGAAGTATTATTTCACACAA
Found at i:35147161 original size:15 final size:15
Alignment explanation
Indices: 35147123--35147162 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
35147113 TATATTACTT
*
35147123 ATTAAAAAATAAAAT
1 ATTAAAAAATAAAAA
*
35147138 ACTAAAAAATAAAAA
1 ATTAAAAAATAAAAA
35147153 ATTATAAAAA
1 ATTA-AAAAA
35147163 AAGAATATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (15 bp):
ATTAAAAAATAAAAA
Found at i:35148438 original size:35 final size:35
Alignment explanation
Indices: 35148353--35148440 Score: 104
Period size: 35 Copynumber: 2.5 Consensus size: 35
35148343 AAACAATGAG
* *
35148353 AACAATTAGAACAAGTGAAGTACTAATTCACGCAA
1 AACAATTAGAACAAGTAAAGTACTAATTCAAGCAA
* * * * * *
35148388 AATAACTAGAGCAAGTAAAGTATTACTTCAAGTAA
1 AACAATTAGAACAAGTAAAGTACTAATTCAAGCAA
35148423 AACAATTAGAACAAGTAA
1 AACAATTAGAACAAGTAA
35148441 CGCACTGCTT
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.51, C:0.14, G:0.14, T:0.22
Consensus pattern (35 bp):
AACAATTAGAACAAGTAAAGTACTAATTCAAGCAA
Found at i:35148485 original size:70 final size:70
Alignment explanation
Indices: 35148353--35148487 Score: 182
Period size: 70 Copynumber: 1.9 Consensus size: 70
35148343 AAACAATGAG
* * * *
35148353 AACAATTAGAACAAGTGAAGTACTAATTCACGCAAAATAACTAGAGCAAGTAAAGTATTACTTCA
1 AACAATTAGAACAAGTGAAGCACTAATTCACACAAAATAACTAGAGCAAGTAAAGCACTACTTCA
35148418 AGTAA
66 AGTAA
** * *
35148423 AACAATTAGAACAAGT-AACGCACTGCTTCACACCAAATAACTAGAGCAAGTAGAGCACTACTTC
1 AACAATTAGAACAAGTGAA-GCACTAATTCACACAAAATAACTAGAGCAAGTAAAGCACTACTTC
35148487 A
65 A
35148488 TACGATATAA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
69 2 0.04
70 54 0.96
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.21
Consensus pattern (70 bp):
AACAATTAGAACAAGTGAAGCACTAATTCACACAAAATAACTAGAGCAAGTAAAGCACTACTTCA
AGTAA
Found at i:35151528 original size:4 final size:4
Alignment explanation
Indices: 35151514--35151543 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
35151504 TATTGACTAT
*
35151514 TTTA GTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
35151544 GTCATGAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:35153051 original size:99 final size:100
Alignment explanation
Indices: 35152919--35153145 Score: 321
Period size: 101 Copynumber: 2.3 Consensus size: 100
35152909 CCACTCAAAC
* * **
35152919 CAGCTCTCCCTTCACCCCCCCAAATCGGGCTTCTCTCTC-TGTCATTGATCTGCAAATGGCTCCC
1 CAGCTCTCCCTTCA-CCGCCCAAATCGAGCTTCTCTCTCTTGTCACCGATCTGCAAATGGCTCCC
*
35152983 CGTGAAACCTCTAGATCTTTCCCAAAAACTATAGAT
65 CATGAAACCTCTAGATCTTTCCCAAAAACTATAGAT
* * *
35153019 CGGCTCTCCTTTCACCGCCCAAATCGAGCTTCTCTCTCTTTGTCGCCGATCTGCAAATGGCTCCC
1 CAGCTCTCCCTTCACCGCCCAAATCGAGCTTCTCTCTC-TTGTCACCGATCTGCAAATGGCTCCC
* *
35153084 CATGAAACCTCTAGATCTTTCCCAAAAACTGTCGAT
65 CATGAAACCTCTAGATCTTTCCCAAAAACTATAGAT
* *
35153120 CAGCTCTCCCTTCACTGTCCAAATCG
1 CAGCTCTCCCTTCACCGCCCAAATCG
35153146 GCTCTCCCTT
Statistics
Matches: 111, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
99 22 0.20
100 12 0.11
101 77 0.69
ACGTcount: A:0.22, C:0.37, G:0.14, T:0.28
Consensus pattern (100 bp):
CAGCTCTCCCTTCACCGCCCAAATCGAGCTTCTCTCTCTTGTCACCGATCTGCAAATGGCTCCCC
ATGAAACCTCTAGATCTTTCCCAAAAACTATAGAT
Found at i:35153165 original size:24 final size:24
Alignment explanation
Indices: 35153122--35153167 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
35153112 CTGTCGATCA
***
35153122 GCTCTCCCTTCACTGTCCAAATCG
1 GCTCTCCCTTCACCACCCAAATCG
35153146 GCTCTCCCTTCACCACCCAAAT
1 GCTCTCCCTTCACCACCCAAAT
35153168 TGAGCTTCCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.20, C:0.46, G:0.09, T:0.26
Consensus pattern (24 bp):
GCTCTCCCTTCACCACCCAAATCG
Found at i:35154318 original size:2 final size:2
Alignment explanation
Indices: 35154311--35154345 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
35154301 AAATATAAGA
*
35154311 AT AT AT AT AT AT AA AT AT AT AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35154346 TTTGATTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35155007 original size:15 final size:15
Alignment explanation
Indices: 35154983--35155067 Score: 61
Period size: 15 Copynumber: 5.5 Consensus size: 15
35154973 AAAATCATTC
35154983 AAAA-AATAAATAAT
1 AAAATAATAAATAAT
35154997 AAAATAATAAATAA-
1 AAAATAATAAATAAT
**
35155011 ACAAATAATAGGTAAAT
1 A-AAATAATAAAT-AAT
35155028 ATATATATAATAAATAA-
1 A-A-A-ATAATAAATAAT
*
35155045 AAAATAA-AAATGAT
1 AAAATAATAAATAAT
35155059 AATAATAAT
1 AA-AATAAT
35155068 TCAAATGTAT
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
13 5 0.09
14 11 0.20
15 24 0.43
16 3 0.05
17 3 0.05
18 3 0.05
19 7 0.12
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.26
Consensus pattern (15 bp):
AAAATAATAAATAAT
Found at i:35155339 original size:14 final size:14
Alignment explanation
Indices: 35155322--35155399 Score: 51
Period size: 14 Copynumber: 5.7 Consensus size: 14
35155312 TTGCTTACAA
35155322 AAAATAATAATAAG
1 AAAATAATAATAAG
35155336 -AAA-AA-AAT-AG
1 AAAATAATAATAAG
35155346 AAAAATAAGATAATAA-
1 -AAAAT-A-ATAATAAG
*
35155362 AAAATAATAA-AAT
1 AAAATAATAATAAG
*
35155375 AATAATAATAATTAG
1 AA-AATAATAATAAG
*
35155390 ATAATAATAA
1 AAAATAATAA
35155400 ATGACCAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 20
0.69 0.04 0.27
Matches are distributed among these distances:
10 2 0.04
11 3 0.06
12 7 0.14
13 9 0.18
14 18 0.35
15 8 0.16
16 3 0.06
17 1 0.02
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (14 bp):
AAAATAATAATAAG
Found at i:35155349 original size:24 final size:24
Alignment explanation
Indices: 35155320--35155385 Score: 78
Period size: 26 Copynumber: 2.6 Consensus size: 24
35155310 GATTGCTTAC
35155320 AAAAAATAATAATAAGAAAAAAATA
1 AAAAAATAATAATAA-AAAAAAATA
* *
35155345 GAAAAATAAGATAATAAAAAATAATA
1 AAAAAAT-A-ATAATAAAAAAAAATA
*
35155371 AAATAATAATAATAA
1 AAAAAATAATAATAA
35155386 TTAGATAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 7 0.20
25 7 0.20
26 14 0.40
27 7 0.20
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (24 bp):
AAAAAATAATAATAAAAAAAAATA
Found at i:35155361 original size:3 final size:3
Alignment explanation
Indices: 35155355--35155399 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
35155345 GAAAAATAAG
35155355 ATA ATA A-A A-A ATA ATA A-A ATA ATA ATA ATA ATTA GATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA -ATA ATA ATA
35155399 A
1 A
35155400 ATGACCAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 6 0.16
3 27 0.71
4 4 0.11
5 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:35155367 original size:23 final size:24
Alignment explanation
Indices: 35155322--35155385 Score: 78
Period size: 23 Copynumber: 2.7 Consensus size: 24
35155312 TTGCTTACAA
*
35155322 AAAATAATAATAAGAAAAAAATAGA-
1 AAAATAATAATAA-TAAAAAATA-AT
*
35155347 AAAATAA-GATAATAAAAAATAAT
1 AAAATAATAATAATAAAAAATAAT
35155370 AAAATAATAATAATAA
1 AAAATAATAATAATAA
35155386 TTAGATAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 1 0.03
23 15 0.44
24 11 0.32
25 7 0.21
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (24 bp):
AAAATAATAATAATAAAAAATAAT
Found at i:35155380 original size:11 final size:11
Alignment explanation
Indices: 35155327--35155396 Score: 54
Period size: 11 Copynumber: 6.0 Consensus size: 11
35155317 TACAAAAAAT
*
35155327 AATAATAAGAA
1 AATAATAATAA
*
35155338 AAAAATAGA-AA
1 AATAATA-ATAA
35155349 AATAAGATAATAA
1 AAT-A-ATAATAA
35155362 AA-AATAATAA
1 AATAATAATAA
35155372 AATAATAATAA
1 AATAATAATAA
35155383 TAATTAGATAATAA
1 -AA-TA-ATAATAA
35155397 TAAATGACCA
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
10 9 0.18
11 19 0.39
12 5 0.10
13 9 0.18
14 7 0.14
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (11 bp):
AATAATAATAA
Found at i:35155393 original size:17 final size:17
Alignment explanation
Indices: 35155324--35155399 Score: 71
Period size: 17 Copynumber: 4.3 Consensus size: 17
35155314 GCTTACAAAA
* *
35155324 AATAATAATAAGAAAAA
1 AATAATAATAAGATAAT
*
35155341 AATAGAAAAATAAGATAAT
1 AAT--AATAATAAGATAAT
* *
35155360 AAAAAATAATAAAATAAT
1 -AATAATAATAAGATAAT
*
35155378 AATAATAATTAGATAAT
1 AATAATAATAAGATAAT
35155395 AATAA
1 AATAA
35155400 ATGACCAAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
17 22 0.47
18 12 0.26
19 11 0.23
20 2 0.04
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (17 bp):
AATAATAATAAGATAAT
Found at i:35156777 original size:27 final size:26
Alignment explanation
Indices: 35156739--35156824 Score: 95
Period size: 27 Copynumber: 3.2 Consensus size: 26
35156729 CAGTCTTACA
*
35156739 TTTTTTC-TTTTCATTTTTTTGTTAT
1 TTTTTTCATTTTCATTTTTTTATTAT
*
35156764 TTTTTTCATTTTTCATTCATTTTTTTTA-
1 TTTTTTCA-TTTTCATT--TTTTTATTAT
35156792 TTTTTTCATTTTCATTTTTGTTATTAT
1 TTTTTTCATTTTCATTTTT-TTATTAT
*
35156819 TATTTT
1 TTTTTT
35156825 GTCTTCTGTA
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
25 10 0.19
26 5 0.10
27 21 0.40
28 8 0.15
29 8 0.15
ACGTcount: A:0.13, C:0.08, G:0.02, T:0.77
Consensus pattern (26 bp):
TTTTTTCATTTTCATTTTTTTATTAT
Found at i:35156785 original size:20 final size:21
Alignment explanation
Indices: 35156746--35156810 Score: 71
Period size: 20 Copynumber: 3.1 Consensus size: 21
35156736 ACATTTTTTC
**
35156746 TTTTCATTTTTTTGTT-ATTT
1 TTTTCATTTTTTCATTCATTT
35156766 TTTTCA-TTTTTCATTCATTT
1 TTTTCATTTTTTCATTCATTT
*
35156786 TTTTTATTTTTTCATTTTCATTT
1 TTTTCATTTTTTCA--TTCATTT
35156809 TT
1 TT
35156811 GTTATTATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
19 7 0.18
20 15 0.39
21 7 0.18
23 9 0.24
ACGTcount: A:0.12, C:0.09, G:0.02, T:0.77
Consensus pattern (21 bp):
TTTTCATTTTTTCATTCATTT
Found at i:35156787 original size:21 final size:22
Alignment explanation
Indices: 35156762--35156816 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
35156752 TTTTTTTGTT
*
35156762 ATTTTTTTCA-TTTTTCA-TTC
1 ATTTTTTTTATTTTTTCATTTC
35156782 ATTTTTTTTATTTTTTCATTTTC
1 ATTTTTTTTATTTTTTCA-TTTC
*
35156805 ATTTTTGTTATT
1 ATTTTTTTTATT
35156817 ATTATTTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 9 0.30
21 7 0.23
23 14 0.47
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.75
Consensus pattern (22 bp):
ATTTTTTTTATTTTTTCATTTC
Found at i:35158610 original size:4 final size:4
Alignment explanation
Indices: 35158593--35158640 Score: 60
Period size: 4 Copynumber: 12.0 Consensus size: 4
35158583 ATATTTAGTT
* * * *
35158593 TATA TATT TATA TATA TATA TATA CATA TATA CATA CATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
35158641 ATTAATGATG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (4 bp):
TATA
Found at i:35158624 original size:12 final size:12
Alignment explanation
Indices: 35158594--35158640 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
35158584 TATTTAGTTT
* *
35158594 ATATATTTATAT
1 ATATATATATAC
35158606 ATATATATATAC
1 ATATATATATAC
*
35158618 ATATATACATAC
1 ATATATATATAC
35158630 ATATATATATA
1 ATATATATATA
35158641 ATTAATGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (12 bp):
ATATATATATAC
Found at i:35159732 original size:15 final size:14
Alignment explanation
Indices: 35159712--35159793 Score: 78
Period size: 15 Copynumber: 5.6 Consensus size: 14
35159702 TATTATATAA
*
35159712 ATTTTAATTTCTTAT
1 ATTTTAATTT-TTTT
*
35159727 ATTTTATTTTATTTT
1 ATTTTAATTT-TTTT
*
35159742 AATTTT--TTATTTT
1 -ATTTTAATTTTTTT
35159755 ATTTTAATATTTTTT
1 ATTTTAAT-TTTTTT
35159770 ATTTTAATATTTTTT
1 ATTTTAAT-TTTTTT
35159785 ATTTTAATT
1 ATTTTAATT
35159794 ATAACGTTAC
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
12 5 0.09
13 4 0.07
14 4 0.07
15 40 0.69
16 5 0.09
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.73
Consensus pattern (14 bp):
ATTTTAATTTTTTT
Found at i:35159751 original size:18 final size:20
Alignment explanation
Indices: 35159728--35159775 Score: 82
Period size: 18 Copynumber: 2.5 Consensus size: 20
35159718 ATTTCTTATA
35159728 TTTTATTTTATTTT-A-ATT
1 TTTTATTTTATTTTAATATT
35159746 TTTTATTTTATTTTAATATT
1 TTTTATTTTATTTTAATATT
35159766 TTTTATTTTA
1 TTTTATTTTA
35159776 ATATTTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 14 0.50
19 1 0.04
20 13 0.46
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTATTTTATTTTAATATT
Found at i:35161869 original size:90 final size:89
Alignment explanation
Indices: 35161590--35161861 Score: 366
Period size: 90 Copynumber: 3.0 Consensus size: 89
35161580 TAGATTTCAT
* * *
35161590 CTAATGAAATCCAAGTATGGAAAAATTGAGGAAGTTGAATCCATGTT-AGATAAATTCAAGAATT
1 CTAATGAAATCCAAGTATAGAGAAATTGAGGAAATTGAATCCATGTTGA-ATAAATTCAAGAATT
*
35161654 TGGAGGCCGAGTCACATAGACTGAAA
65 TGGAGGCCGAGTCA-ATAGACTGGAA
* * * *
35161680 CTAATGAAATCTAAGTATAGAGAAATTGAGGAAATTGAATCCAGGTTGGATAAATTCAAAAATTT
1 CTAATGAAATCCAAGTATAGAGAAATTGAGGAAATTGAATCCATGTTGAATAAATTCAAGAATTT
*
35161745 GGAGGCCGAGTTCAATAGATTGGAA
66 GGAGGCCGAG-TCAATAGACTGGAA
* *
35161770 CTAATGAAATCCAATTATAGAGAAATTGAGGAAATTGAATCCATGTTGAATAAATTCAAGAGTTT
1 CTAATGAAATCCAAGTATAGAGAAATTGAGGAAATTGAATCCATGTTGAATAAATTCAAGAATTT
* * * *
35161835 GAAGACCAAGTCATATAGACCGGAA
66 GGAGGCCGAGTCA-ATAGACTGGAA
35161860 CT
1 CT
35161862 GGAGAAATTG
Statistics
Matches: 159, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
89 3 0.02
90 153 0.96
91 3 0.02
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (89 bp):
CTAATGAAATCCAAGTATAGAGAAATTGAGGAAATTGAATCCATGTTGAATAAATTCAAGAATTT
GGAGGCCGAGTCAATAGACTGGAA
Found at i:35161921 original size:74 final size:74
Alignment explanation
Indices: 35161789--35161926 Score: 224
Period size: 74 Copynumber: 1.9 Consensus size: 74
35161779 TCCAATTATA
* *
35161789 GAGAAATTGAGGAAATTGAATCCATGTTGAATAAATTCAAGAGTTTGAAGACCAAGTCATATAGA
1 GAGAAATTGAGGAAATTGAATCCATGTTGAATAAATTCAAGAATTTGAAGACCAAGTCACATAGA
35161854 CCGGAACTG
66 CCGGAACTG
* *
35161863 GAGAAATTGAGGAAATTGAATCCATGTTGGATAAATTCAAGAATTTGGAAG-CCGAGTCACATAG
1 GAGAAATTGAGGAAATTGAATCCATGTTGAATAAATTCAAGAATTT-GAAGACCAAGTCACATAG
35161927 GTTCGAGCAA
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
74 55 0.93
75 4 0.07
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.25
Consensus pattern (74 bp):
GAGAAATTGAGGAAATTGAATCCATGTTGAATAAATTCAAGAATTTGAAGACCAAGTCACATAGA
CCGGAACTG
Found at i:35165923 original size:23 final size:23
Alignment explanation
Indices: 35165911--35165953 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
35165901 CCCAAACCGT
35165911 TTAAA-CCCTTAAACCCAAAATC
1 TTAAATCCCTTAAACCCAAAATC
35165933 TTAAATCCCTTAAACCCAAAA
1 TTAAATCCCTTAAACCCAAAA
35165954 CCCTAAACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (23 bp):
TTAAATCCCTTAAACCCAAAATC
Found at i:35165924 original size:8 final size:8
Alignment explanation
Indices: 35165911--35166016 Score: 62
Period size: 8 Copynumber: 13.8 Consensus size: 8
35165901 CCCAAACCGT
35165911 TTAAACCC
1 TTAAACCC
35165919 TTAAACCC
1 TTAAACCC
**
35165927 --AAAATC
1 TTAAACCC
35165933 TTAAATCCC
1 TTAAA-CCC
35165942 TTAAACCC
1 TTAAACCC
*
35165950 -AAAACCC
1 TTAAACCC
*
35165957 -TAAACAC
1 TTAAACCC
*
35165964 --AAAACC
1 TTAAACCC
35165970 TTAAACCC
1 TTAAACCC
35165978 TTAAACCAC
1 TTAAACC-C
**
35165987 CCAAACCC
1 TTAAACCC
** *
35165995 AAAAAACC
1 TTAAACCC
35166003 TTAAACCC
1 TTAAACCC
35166011 TTAAAC
1 TTAAAC
35166017 TAGCCAAACC
Statistics
Matches: 74, Mismatches: 18, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
6 8 0.11
7 11 0.15
8 43 0.58
9 12 0.16
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.18
Consensus pattern (8 bp):
TTAAACCC
Found at i:35165960 original size:23 final size:22
Alignment explanation
Indices: 35165912--35166035 Score: 81
Period size: 24 Copynumber: 5.4 Consensus size: 22
35165902 CCAAACCGTT
* *
35165912 TAAACCCTTAAACCCAAAATCT
1 TAAACCCTTAAACCCAAAACCC
35165934 TAAATCCCTTAAACCCAAAACCC
1 TAAA-CCCTTAAACCCAAAACCC
* * **
35165957 TAAACAC-AAAACCTTAAACCC
1 TAAACCCTTAAACCCAAAACCC
** *
35165978 TTAAACCACCCAAACCCAAAAAACCT
1 -TAAACC-CTTAAACCC--AAAACCC
35166004 TAAACCCTTAAACTAGCC-AAACCC
1 TAAACCCTTAAAC---CCAAAACCC
35166028 TAAACCCT
1 TAAACCCT
35166036 AAATACTTAA
Statistics
Matches: 79, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
21 11 0.14
22 11 0.14
23 21 0.27
24 23 0.29
25 6 0.08
26 5 0.06
27 2 0.03
ACGTcount: A:0.46, C:0.36, G:0.01, T:0.17
Consensus pattern (22 bp):
TAAACCCTTAAACCCAAAACCC
Found at i:35166006 original size:33 final size:33
Alignment explanation
Indices: 35165964--35166027 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
35165954 CCCTAAACAC
35165964 AAAACCTTAAACCCTTAAACCACCCAAACCCAA
1 AAAACCTTAAACCCTTAAACCACCCAAACCCAA
* *
35165997 AAAACCTTAAACCCTTAAACTAGCCAAACCC
1 AAAACCTTAAACCCTTAAACCACCCAAACCC
35166028 TAAACCCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.47, C:0.38, G:0.02, T:0.14
Consensus pattern (33 bp):
AAAACCTTAAACCCTTAAACCACCCAAACCCAA
Found at i:35177507 original size:2 final size:2
Alignment explanation
Indices: 35177500--35177531 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
35177490 GTGAAAGAAT
*
35177500 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35177532 CAAGTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35181101 original size:27 final size:27
Alignment explanation
Indices: 35181065--35181204 Score: 112
Period size: 27 Copynumber: 5.1 Consensus size: 27
35181055 ATTAATATTA
35181065 AAATTATCAATTATTAATATTTTAAAT
1 AAATTATCAATTATTAATATTTTAAAT
35181092 AAATTATCAATTATTAATATTTTAAAAAT
1 AAATTATCAATTATTAATATTTT--AAAT
* * *
35181121 AAAATA-AAATTAATCGTAATAATATT---T
1 AAATTATCAATT-AT--TAAT-ATTTTAAAT
* *
35181148 AAATTATTAATTATTAATATTTTAATT
1 AAATTATCAATTATTAATATTTTAAAT
* *
35181175 AAATTCT-AGATTATTAATA-TTTAAAA
1 AAATTATCA-ATTATTAATATTTTAAAT
35181201 AAAT
1 AAAT
35181205 CTAATAAAAA
Statistics
Matches: 93, Mismatches: 9, Indels: 23
0.74 0.07 0.18
Matches are distributed among these distances:
24 4 0.04
25 4 0.04
26 10 0.11
27 48 0.52
28 8 0.09
29 11 0.12
31 4 0.04
32 4 0.04
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (27 bp):
AAATTATCAATTATTAATATTTTAAAT
Found at i:35196215 original size:19 final size:19
Alignment explanation
Indices: 35196180--35196221 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
35196170 GAATACTAAA
* *
35196180 CTTTTCTCAAATTTGGGGT
1 CTTTTCTCAAATCTGGGCT
35196199 CTTTTC-CAAACTCTGGGCT
1 CTTTTCTCAAA-TCTGGGCT
35196218 CTTT
1 CTTT
35196222 GTTGAGAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.45
Consensus pattern (19 bp):
CTTTTCTCAAATCTGGGCT
Found at i:35204079 original size:30 final size:30
Alignment explanation
Indices: 35204038--35204141 Score: 115
Period size: 29 Copynumber: 3.5 Consensus size: 30
35204028 ATTATTAATC
* *
35204038 ATAAAAGTTTATTTAACTTAAAATAAAAAT
1 ATAAAAATTTATTTAAATTAAAATAAAAAT
*
35204068 ATAAAAATTTATTT-AGTTCAAAAATAAAAAT
1 ATAAAAATTTATTTAAATT--AAAATAAAAAT
*
35204099 ATAAAAATTTAATTAAATGT--AATAAAAAT
1 ATAAAAATTTATTTAAAT-TAAAATAAAAAT
*
35204128 ATAAAAACTTATTT
1 ATAAAAATTTATTT
35204142 TTAAAAAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
29 24 0.38
30 13 0.20
31 24 0.38
32 2 0.03
33 1 0.02
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (30 bp):
ATAAAAATTTATTTAAATTAAAATAAAAAT
Found at i:35215995 original size:2 final size:2
Alignment explanation
Indices: 35215983--35216034 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
35215973 ATATCTTTAG
35215983 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35216024 AT AT AT AT AT A
1 AT AT AT AT AT A
35216035 AACTCTTACA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35217721 original size:19 final size:18
Alignment explanation
Indices: 35217692--35217728 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
35217682 ATCTAAATTG
35217692 TATATTATAATATATATA
1 TATATTATAATATATATA
*
35217710 TATATATATAATTTATATA
1 TATAT-TATAATATATATA
35217729 AATTAATGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATATTATAATATATATA
Found at i:35221077 original size:2 final size:2
Alignment explanation
Indices: 35221070--35221103 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
35221060 ATAGTACAGA
*
35221070 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35221104 TTAATAGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35230009 original size:50 final size:50
Alignment explanation
Indices: 35229934--35230034 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
35229924 AGGAGTTAGG
35229934 ATAGATGGATATAACCAAAACTGGTCTGTTTTGATACTTTTATGTAGATC
1 ATAGATGGATATAACCAAAACTGGTCTGTTTTGATACTTTTATGTAGATC
35229984 ATAGATGGATATAACCAAAACTGGTCTGTTTTGATACTTTTATGTAGATC
1 ATAGATGGATATAACCAAAACTGGTCTGTTTTGATACTTTTATGTAGATC
35230034 A
1 A
35230035 AGGCCCTCCA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.38
Consensus pattern (50 bp):
ATAGATGGATATAACCAAAACTGGTCTGTTTTGATACTTTTATGTAGATC
Found at i:35233707 original size:38 final size:38
Alignment explanation
Indices: 35233656--35233742 Score: 174
Period size: 38 Copynumber: 2.3 Consensus size: 38
35233646 CAGTTCCAAA
35233656 CACACAATTATTATTAATCAAAGCCTAGAGCTCCACTC
1 CACACAATTATTATTAATCAAAGCCTAGAGCTCCACTC
35233694 CACACAATTATTATTAATCAAAGCCTAGAGCTCCACTC
1 CACACAATTATTATTAATCAAAGCCTAGAGCTCCACTC
35233732 CACACAATTAT
1 CACACAATTAT
35233743 ATGAGAGAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.38, C:0.29, G:0.07, T:0.26
Consensus pattern (38 bp):
CACACAATTATTATTAATCAAAGCCTAGAGCTCCACTC
Found at i:35254919 original size:12 final size:12
Alignment explanation
Indices: 35254902--35254926 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35254892 TGTTTTGACG
35254902 TAAAATATATTT
1 TAAAATATATTT
35254914 TAAAATATATTT
1 TAAAATATATTT
35254926 T
1 T
35254927 CAGAATTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAAATATATTT
Found at i:35255130 original size:14 final size:14
Alignment explanation
Indices: 35255111--35255173 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
35255101 AATGGATATT
35255111 AATATTTAACTTAA
1 AATATTTAACTTAA
* ** *
35255125 AATATTAAAAATATT
1 AATATTTAACTTA-A
35255140 AATATTTAA-TTAAA
1 AATATTTAACTT-AA
*
35255154 AATTTTTAACTTAA
1 AATATTTAACTTAA
35255168 AATATT
1 AATATT
35255174 AATATTTAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
14 26 0.70
15 11 0.30
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (14 bp):
AATATTTAACTTAA
Found at i:35255131 original size:20 final size:20
Alignment explanation
Indices: 35255106--35255182 Score: 64
Period size: 20 Copynumber: 3.7 Consensus size: 20
35255096 AGTTTAATGG
35255106 ATATTAATATTTAACTTAAA
1 ATATTAATATTTAACTTAAA
* * *
35255126 ATATTAAAAATATTAATATTTAA
1 ATATT-AATAT-TTAA-CTTAAA
* ** *
35255149 TTAAAAATTTTTAACTTAAA
1 ATATTAATATTTAACTTAAA
35255169 ATATTAATATTTAA
1 ATATTAATATTTAA
35255183 ATTATTCAAT
Statistics
Matches: 40, Mismatches: 14, Indels: 6
0.67 0.23 0.10
Matches are distributed among these distances:
20 19 0.47
21 8 0.20
22 7 0.17
23 6 0.15
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATTAATATTTAACTTAAA
Found at i:35255528 original size:2 final size:2
Alignment explanation
Indices: 35255521--35255557 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
35255511 TTGTATATGT
35255521 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35255558 TTGGAGTGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35263697 original size:13 final size:13
Alignment explanation
Indices: 35263681--35263716 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
35263671 CTATAATTAT
35263681 AAAATATATAATG
1 AAAATATATAATG
35263694 AAAAT-TAGTAATG
1 AAAATATA-TAATG
35263707 AAAATATATA
1 AAAATATATA
35263717 TTTTATATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 2 0.10
13 17 0.81
14 2 0.10
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (13 bp):
AAAATATATAATG
Found at i:35263826 original size:17 final size:17
Alignment explanation
Indices: 35263804--35263836 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
35263794 AATTTGACCA
35263804 AATAAA-CCAATTAAACC
1 AATAAATCCAA-TAAACC
35263821 AATAAATCCAATAAAC
1 AATAAATCCAATAAAC
35263837 TAATTAGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.61, C:0.21, G:0.00, T:0.18
Consensus pattern (17 bp):
AATAAATCCAATAAACC
Found at i:35266424 original size:18 final size:16
Alignment explanation
Indices: 35266374--35266426 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 16
35266364 AAAACTTATA
35266374 TAATTTTCTTAAATAATT
1 TAATTTT-TTAAA-AATT
35266392 TAATTTTTTAAAAAAATAT
1 TAATTTTTT--AAAAAT-T
35266411 TATATTTTTTAAAAAT
1 TA-ATTTTTTAAAAAT
35266427 CAAAACCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 2 0.06
18 16 0.52
19 6 0.19
20 7 0.23
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
TAATTTTTTAAAAATT
Found at i:35280135 original size:18 final size:19
Alignment explanation
Indices: 35280108--35280153 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
35280098 CGATATGATT
*
35280108 AATAATTTTTTTTAAATTA
1 AATAATTTTTTATAAATTA
*
35280127 AATAATTTTTTATAATTTA
1 AATAATTTTTTATAAATTA
*
35280146 AAAAATTT
1 AATAATTT
35280154 AATCATCATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AATAATTTTTTATAAATTA
Found at i:35285508 original size:2 final size:2
Alignment explanation
Indices: 35285503--35285528 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35285493 GAAAAAACAA
35285503 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
35285529 TCTTTCAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35287913 original size:14 final size:14
Alignment explanation
Indices: 35287894--35287923 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
35287884 TGTTGGTAAA
35287894 TTTTTTTTTATAAG
1 TTTTTTTTTATAAG
35287908 TTTTTTTTTATAAG
1 TTTTTTTTTATAAG
35287922 TT
1 TT
35287924 ATAATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (14 bp):
TTTTTTTTTATAAG
Found at i:35288105 original size:18 final size:18
Alignment explanation
Indices: 35288084--35288131 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 18
35288074 TTTTTAACTC
35288084 TTTTTTTAAAAA-TT-TT
1 TTTTTTTAAAAAGTTATT
35288100 GTTTTTTTAAAAAAAGTTATT
1 -TTTTTTT--AAAAAGTTATT
35288121 TTTTTTTAAAA
1 TTTTTTTAAAA
35288132 GTTTCTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 7 0.26
18 4 0.15
19 5 0.19
20 9 0.33
21 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (18 bp):
TTTTTTTAAAAAGTTATT
Found at i:35288114 original size:20 final size:20
Alignment explanation
Indices: 35288091--35288131 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
35288081 CTCTTTTTTT
35288091 AAAAATT-TTGTTTTTTTAAA
1 AAAAATTATT-TTTTTTTAAA
*
35288111 AAAAGTTATTTTTTTTTAAA
1 AAAAATTATTTTTTTTTAAA
35288131 A
1 A
35288132 GTTTCTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
AAAAATTATTTTTTTTTAAA
Found at i:35288131 original size:17 final size:17
Alignment explanation
Indices: 35288084--35288135 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
35288074 TTTTTAACTC
*
35288084 TTTTTTTAAAAATTTTG
1 TTTTTTTAAAAGTTTTG
35288101 TTTTTTTAAAAAAAGTTATT-
1 TTTTTTT---AAAAGTT-TTG
35288121 TTTTTTTAAAAGTTT
1 TTTTTTTAAAAGTTT
35288136 CTCAAAAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
16 1 0.03
17 14 0.47
20 13 0.43
21 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
TTTTTTTAAAAGTTTTG
Found at i:35289873 original size:22 final size:22
Alignment explanation
Indices: 35289848--35289902 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
35289838 AGTTATTAGA
*
35289848 TATTGCATTACTGATTTTTAAG
1 TATTGCATGACTGATTTTTAAG
* * *
35289870 TATTACGA-GATTGATTTTTAGG
1 TATTGC-ATGACTGATTTTTAAG
35289892 TATTGCATGAC
1 TATTGCATGAC
35289903 GTAATCATTG
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
21 1 0.04
22 23 0.92
23 1 0.04
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.45
Consensus pattern (22 bp):
TATTGCATGACTGATTTTTAAG
Found at i:35290080 original size:23 final size:23
Alignment explanation
Indices: 35290054--35290101 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
35290044 AATGCCTATA
35290054 AACTAGTCACGCAATACCATATC
1 AACTAGTCACGCAATACCATATC
* *
35290077 AACTAGTCACGTAATACTATATC
1 AACTAGTCACGCAATACCATATC
35290100 AA
1 AA
35290102 TCAGTTACGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.25
Consensus pattern (23 bp):
AACTAGTCACGCAATACCATATC
Found at i:35290115 original size:23 final size:23
Alignment explanation
Indices: 35290054--35290117 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
35290044 AATGCCTATA
* *
35290054 AACTAGTCACGCAATACCATATC
1 AACTAGTCACGGAATACTATATC
*
35290077 AACTAGTCACGTAATACTATATC
1 AACTAGTCACGGAATACTATATC
*
35290100 AA-TCAGTTACGGAATACT
1 AACT-AGTCACGGAATACT
35290118 TAAAAATCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
22 1 0.03
23 35 0.97
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (23 bp):
AACTAGTCACGGAATACTATATC
Found at i:35290603 original size:35 final size:35
Alignment explanation
Indices: 35290564--35290646 Score: 157
Period size: 35 Copynumber: 2.4 Consensus size: 35
35290554 GATTGATTTC
*
35290564 ATTAAAGATAATTTTATTTAAAATTATTTTTTAAA
1 ATTAAAAATAATTTTATTTAAAATTATTTTTTAAA
35290599 ATTAAAAATAATTTTATTTAAAATTATTTTTTAAA
1 ATTAAAAATAATTTTATTTAAAATTATTTTTTAAA
35290634 ATTAAAAATAATT
1 ATTAAAAATAATT
35290647 AAAATTATAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (35 bp):
ATTAAAAATAATTTTATTTAAAATTATTTTTTAAA
Found at i:35290612 original size:20 final size:20
Alignment explanation
Indices: 35290583--35290646 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 20
35290573 AATTTTATTT
*
35290583 AAAATTATTTTTTAAAATTA
1 AAAATAATTTTTTAAAATTA
*
35290603 AAAATAA--TTTT---ATTT
1 AAAATAATTTTTTAAAATTA
*
35290618 AAAATTATTTTTTAAAATTA
1 AAAATAATTTTTTAAAATTA
35290638 AAAATAATT
1 AAAATAATT
35290647 AAAATTATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
15 9 0.26
17 4 0.12
18 4 0.12
20 17 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AAAATAATTTTTTAAAATTA
Found at i:35290648 original size:16 final size:16
Alignment explanation
Indices: 35290629--35290660 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
35290619 AAATTATTTT
35290629 TTAAAATTAAAAATAA
1 TTAAAATTAAAAATAA
*
35290645 TTAAAATTATAAATAA
1 TTAAAATTAAAAATAA
35290661 GATTATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TTAAAATTAAAAATAA
Found at i:35295587 original size:29 final size:29
Alignment explanation
Indices: 35295554--35295613 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
35295544 TTCCAAAGGG
35295554 AGAAAAAGCAACAGATTTGGGTCGGAAGT
1 AGAAAAAGCAACAGATTTGGGTCGGAAGT
35295583 AGAAAAAGCAACAGATTTGGGTCGGAAGT
1 AGAAAAAGCAACAGATTTGGGTCGGAAGT
35295612 AG
1 AG
35295614 TGGCCAAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.42, C:0.10, G:0.32, T:0.17
Consensus pattern (29 bp):
AGAAAAAGCAACAGATTTGGGTCGGAAGT
Found at i:35296013 original size:21 final size:20
Alignment explanation
Indices: 35295987--35296039 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
35295977 ACGTAGGTGA
*
35295987 ATAATTTAATATATAAATATC
1 ATAATTTAATA-ATAAAAATC
*
35296008 ATAATTATAATAATAAAAATG
1 ATAATT-TAATAATAAAAATC
*
35296029 ATAAATTAATA
1 ATAATTTAATA
35296040 GATTATGATG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 18 0.64
22 5 0.18
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
ATAATTTAATAATAAAAATC
Found at i:35297007 original size:3 final size:3
Alignment explanation
Indices: 35296999--35297024 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
35296989 GAAGTTGTTA
35296999 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
35297025 AACTGTCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:35299717 original size:36 final size:34
Alignment explanation
Indices: 35299645--35299712 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
35299635 ACCCCCGTTA
35299645 GGAGTTTCTCTCCATAACCATAACATCTTTGATG
1 GGAGTTTCTCTCCATAACCATAACATCTTTGATG
* *
35299679 GGAGTTTCTCTCTATGACCATAACATCTTTGATG
1 GGAGTTTCTCTCCATAACCATAACATCTTTGATG
35299713 TGGGACTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (34 bp):
GGAGTTTCTCTCCATAACCATAACATCTTTGATG
Found at i:35317278 original size:20 final size:21
Alignment explanation
Indices: 35317250--35317305 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
35317240 CATGTATCCA
35317250 AATTATAATCATA-ATAATTT
1 AATTATAATCATATATAATTT
* *
35317270 AATTTTAATTATATATAATTT
1 AATTATAATCATATATAATTT
35317291 -ATTATAAATC-TATAT
1 AATTAT-AATCATATAT
35317306 TAATATGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 20 0.67
21 10 0.33
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (21 bp):
AATTATAATCATATATAATTT
Found at i:35317689 original size:2 final size:2
Alignment explanation
Indices: 35317677--35317720 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
35317667 TAAAGTAATG
*
35317677 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35317718 TA T
1 TA T
35317721 TTAATTTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35317734 original size:240 final size:239
Alignment explanation
Indices: 35317475--35317932 Score: 652
Period size: 240 Copynumber: 1.9 Consensus size: 239
35317465 TAAACATTAT
**
35317475 ATATATTTAATTTATACATAAACATTAATATAACTTATAATAAACTTTAGTTATATAATTGTACT
1 ATATATTTAATTTATACATAAACATTAATATAACTTATAATAAACTTTAGTTATATAATTACACT
* *
35317540 TAATAACCTTATTAATTATCACCTTAGTTTTTGTAACATATTGTTCATAATTAGTTATTATTTAT
66 TAATAACCTTATTAATTATCACCTTAATTTTTATAACATATTGTTCATAATTAGTTATTATTTAT
* *
35317605 ACAAATTTTGATAT-AAAA-C-ATTATAACATATAAGTTGTGTTATTAATTTCATATATACATAA
131 ACAAAATTTGATATAAAAATCAATTATAACATATAAGTTGTGTCATTAATTTCATATAT--ATAA
35317667 TAAAGTAATGTATATTATATATATATATATATATATATATATATATAC
194 TAAAGTAA--TATATTATATATATATATATATATATATATATATATAC
** * * * * *
35317715 ATATATTTAATTTATACATAAGTATTACTGTAACTTATAATAGACTTTATTTATATGATTACACT
1 ATATATTTAATTTATACATAAACATTAATATAACTTATAATAAACTTTAGTTATATAATTACACT
** * * *
35317780 TAATAATTTTTTTAATTATCGCCTTAATTTTTATAACATATTGTTTATAATTAGTTATTATTTAT
66 TAATAACCTTATTAATTATCACCTTAATTTTTATAACATATTGTTCATAATTAGTTATTATTTAT
*
35317845 ACAAAATTTGATATAAAAATCAAAATATTGTAACATATAAGTTGTGTCATTAATTTCATATATAT
131 ACAAAATTTGATATAAAAATC---A-ATTATAACATATAAGTTGTGTCATTAATTTCATATATAT
35317910 AATAAAGTAATATATTATATATA
192 AATAAAGTAATATATTATATATA
35317933 CGTATATTTA
Statistics
Matches: 192, Mismatches: 19, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
240 127 0.66
241 4 0.02
242 1 0.01
243 13 0.07
245 12 0.06
247 35 0.18
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (239 bp):
ATATATTTAATTTATACATAAACATTAATATAACTTATAATAAACTTTAGTTATATAATTACACT
TAATAACCTTATTAATTATCACCTTAATTTTTATAACATATTGTTCATAATTAGTTATTATTTAT
ACAAAATTTGATATAAAAATCAATTATAACATATAAGTTGTGTCATTAATTTCATATATATAATA
AAGTAATATATTATATATATATATATATATATATATATATATAC
Found at i:35318659 original size:30 final size:30
Alignment explanation
Indices: 35318624--35318682 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
35318614 TCATAAGATC
*
35318624 ATAAAAACTTATTTAATTTAAAATAAAAAT
1 ATAAAAACTTATTTAATTCAAAATAAAAAT
** *
35318654 ATAAAATTTTATTTTATTCAAAATAAAAA
1 ATAAAAACTTATTTAATTCAAAATAAAAA
35318683 AAATAAGAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (30 bp):
ATAAAAACTTATTTAATTCAAAATAAAAAT
Found at i:35341826 original size:2 final size:2
Alignment explanation
Indices: 35341819--35341916 Score: 189
Period size: 2 Copynumber: 49.5 Consensus size: 2
35341809 GAATGAAGAC
35341819 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
35341861 GA GA GA GA GA G- GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
35341902 GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA G
35341917 GAAGGATAAC
Statistics
Matches: 95, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 94 0.99
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:35343270 original size:14 final size:14
Alignment explanation
Indices: 35343253--35343290 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
35343243 AGAGATTAAG
*
35343253 ATTTAGGGTTTACA
1 ATTTAGGATTTACA
*
35343267 ATTTAGAATTTACA
1 ATTTAGGATTTACA
35343281 ATTTAGGATT
1 ATTTAGGATT
35343291 CTGAATTTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (14 bp):
ATTTAGGATTTACA
Found at i:35343303 original size:7 final size:7
Alignment explanation
Indices: 35343238--35343306 Score: 52
Period size: 7 Copynumber: 9.9 Consensus size: 7
35343228 TTAGTATGAA
35343238 AATTTAG
1 AATTTAG
*
35343245 AGATTAAG
1 A-ATTTAG
35343253 -ATTTAG
1 AATTTAG
** *
35343259 GGTTTAC
1 AATTTAG
35343266 AATTTAG
1 AATTTAG
*
35343273 AATTTAC
1 AATTTAG
35343280 AATTTAG
1 AATTTAG
*
35343287 GATTCT-G
1 AATT-TAG
35343294 AATTTAG
1 AATTTAG
35343301 AATTTA
1 AATTTA
35343307 AGAGTTAAGA
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
6 6 0.13
7 35 0.74
8 6 0.13
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (7 bp):
AATTTAG
Found at i:35374245 original size:21 final size:20
Alignment explanation
Indices: 35374221--35374270 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 20
35374211 CAGAATAATA
*
35374221 AAAATATATTTAAATTTTTTT
1 AAAATAT-TTTAAAGTTTTTT
35374242 AAAATAGTTTTAAAGTTTTTT
1 AAAATA-TTTTAAAGTTTTTT
35374263 AAAATATT
1 AAAATATT
35374271 AAGATTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 2 0.07
21 24 0.89
22 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (20 bp):
AAAATATTTTAAAGTTTTTT
Found at i:35375103 original size:24 final size:24
Alignment explanation
Indices: 35375071--35375116 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
35375061 AATTACTTAA
35375071 GTGAACTGATTCTATATAGTGTAT
1 GTGAACTGATTCTATATAGTGTAT
35375095 GTGAACTGATTCTATATAGTGT
1 GTGAACTGATTCTATATAGTGT
35375117 TTATAAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41
Consensus pattern (24 bp):
GTGAACTGATTCTATATAGTGTAT
Found at i:35405928 original size:29 final size:30
Alignment explanation
Indices: 35405894--35405956 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
35405884 TATACATCAA
*
35405894 TGTTGAATTTTATCATTATACTTTCA-TTT
1 TGTTGAATTTTATAATTATACTTTCACTTT
* * *
35405923 TGTTGAATTTTGTAATTGTATTTTCACTTT
1 TGTTGAATTTTATAATTATACTTTCACTTT
35405953 TGTT
1 TGTT
35405957 TATTTTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.21, C:0.08, G:0.11, T:0.60
Consensus pattern (30 bp):
TGTTGAATTTTATAATTATACTTTCACTTT
Found at i:35432039 original size:3 final size:3
Alignment explanation
Indices: 35432031--35432064 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
35432021 GGTGGGCCTC
35432031 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
35432065 CTCTGAAGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:35432658 original size:18 final size:18
Alignment explanation
Indices: 35432632--35432666 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35432622 TTTAAAAAAA
*
35432632 TTTTAAAAATATAATTTT
1 TTTTAAAAATAAAATTTT
*
35432650 TTTTTAAAATAAAATTT
1 TTTTAAAAATAAAATTT
35432667 AAAAAAAAAA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTTAAAAATAAAATTTT
Found at i:35433260 original size:15 final size:16
Alignment explanation
Indices: 35433231--35433261 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
35433221 TAAGTGCCCG
35433231 TTTAACTTAATTTATT
1 TTTAACTTAATTTATT
35433247 TTTAACTT-ATTTATT
1 TTTAACTTAATTTATT
35433262 ACTTAAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTAACTTAATTTATT
Found at i:35433602 original size:17 final size:17
Alignment explanation
Indices: 35433580--35433612 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
35433570 GTATTTCTTC
35433580 TTTTTC-TTTCTATTTTG
1 TTTTTCATTT-TATTTTG
35433597 TTTTTCATTTTATTTT
1 TTTTTCATTTTATTTT
35433613 CTATCATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTTCATTTTATTTTG
Found at i:35442790 original size:18 final size:18
Alignment explanation
Indices: 35442767--35442803 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
35442757 TAACTGAGAA
35442767 TGGGTTTAAAATGTCTAG
1 TGGGTTTAAAATGTCTAG
35442785 TGGGTTTAAAATGTCTAG
1 TGGGTTTAAAATGTCTAG
35442803 T
1 T
35442804 CAAACTCTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.05, G:0.27, T:0.41
Consensus pattern (18 bp):
TGGGTTTAAAATGTCTAG
Found at i:35455024 original size:15 final size:15
Alignment explanation
Indices: 35455006--35455054 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
35454996 AAGTATGTGA
35455006 AATATATGATTAACT
1 AATATATGATTAACT
*
35455021 AATATATG--TGA--
1 AATATATGATTAACT
*
35455032 AATATATGATTAGCT
1 AATATATGATTAACT
35455047 AATATATG
1 AATATATG
35455055 TGAAATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
11 8 0.30
13 3 0.11
15 16 0.59
ACGTcount: A:0.45, C:0.04, G:0.12, T:0.39
Consensus pattern (15 bp):
AATATATGATTAACT
Done.