Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 125 of 345
Found at i:33477497 original size:78 final size:79
Alignment explanation
Indices: 33477352--33477503 Score: 270
Period size: 78 Copynumber: 1.9 Consensus size: 79
33477342 AAATTGAAAG
*
33477352 AACAGAAATTGAAAATACCTCAGCATGTCCTGAGGTTCAACTCACCTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
33477417 TTTTGAAAAGCAGA
66 TTTTGAAAAGCAGA
* *
33477431 AACAGAAATTGAAATTACCTCAGCGTGTCCTGA-GCTCAACTCACCTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
33477495 TTTTGAAAA
66 TTTTGAAAA
33477504 CATGAATTAA
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
78 39 0.56
79 31 0.44
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (79 bp):
AACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTTGAAAAGCAGA
Found at i:33477534 original size:15 final size:15
Alignment explanation
Indices: 33477514--33477542 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
33477504 CATGAATTAA
33477514 AACAGAAATTGAAAG
1 AACAGAAATTGAAAG
33477529 AACAGAAATTGAAA
1 AACAGAAATTGAAA
33477543 ATACCTCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.07, G:0.17, T:0.14
Consensus pattern (15 bp):
AACAGAAATTGAAAG
Found at i:33477560 original size:177 final size:178
Alignment explanation
Indices: 33477023--33477708 Score: 1045
Period size: 178 Copynumber: 3.8 Consensus size: 178
33477013 AAATTAAAAA
* * *
33477023 GCTCAACTCACCTCTCGCAGTATGAGTTGATTTTTGAAAAACATAAATTAAAAACAGAAATTGAA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGC-------AGAAACAGAAATTGAA
* * * *
33477088 GATGT--CTCAGCATGTCCTAAAGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAATCA
59 -AT-TACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACA
* * * *
33477151 TGAATTAAAATAGAAATTGGAAGAATAGAATTTGAAAATACCTCAGCGTGTCCTGAG
122 TGAATTAAAACAGAAATTGAAAGAACAGAAATTGAAAATACCTCAGCGTGTCCTGAG
*
33477208 GCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAGCAGAAACAGAAATTGAAATTACCT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGCAGAAACAGAAATTGAAATTACCT
*
33477273 CAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACATGAATTAAA
66 CAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACATGAATTAAA
* *
33477338 ACATAAATTGAAAGAACAGAAATTGAAAATACCTCAGCATGTCCTGAG
131 ACAGAAATTGAAAGAACAGAAATTGAAAATACCTCAGCGTGTCCTGAG
*
33477386 GTTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGCAGAAACAGAAATTGAAATTACCT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGCAGAAACAGAAATTGAAATTACCT
*
33477451 CAGCGTGTCCTGA-GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACATGAATTAAA
66 CAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACATGAATTAAA
*
33477515 ACAGAAATTGAAAGAACAGAAATTGAAAATACCTCATCGTGTCCTGAG
131 ACAGAAATTGAAAGAACAGAAATTGAAAATACCTCAGCGTGTCCTGAG
33477563 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGCAGAAACAGAAATTGAAATTACCT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGCAGAAACAGAAATTGAAATTACCT
* * * *
33477628 CAGAATGTCCTGAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTGAAAAGTATAAATTAA
66 CAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA-CATGAATT-A
*
33477693 AAACAGAAATTAAAAG
129 AAACAGAAATTGAAAG
33477709 GCTCAACTCA
Statistics
Matches: 469, Mismatches: 27, Indels: 15
0.92 0.05 0.03
Matches are distributed among these distances:
176 1 0.00
177 173 0.37
178 234 0.50
179 6 0.01
180 16 0.03
185 39 0.08
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (178 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGCAGAAACAGAAATTGAAATTACCT
CAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACATGAATTAAA
ACAGAAATTGAAAGAACAGAAATTGAAAATACCTCAGCGTGTCCTGAG
Found at i:33477660 original size:79 final size:79
Alignment explanation
Indices: 33477529--33477682 Score: 263
Period size: 79 Copynumber: 1.9 Consensus size: 79
33477519 AAATTGAAAG
***
33477529 AACAGAAATTGAAAATACCTCATCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGAATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
33477594 TTTTGAAAAGCAGA
66 TTTTGAAAAGCAGA
* *
33477608 AACAGAAATTGAAATTACCTCAGAATGTCCTGAGGCTCAACTCACCTTTCGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGAATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
33477673 TTTTGAAAAG
66 TTTTGAAAAG
33477683 TATAAATTAA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 70 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (79 bp):
AACAGAAATTGAAAATACCTCAGAATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTTGAAAAGCAGA
Found at i:33480322 original size:29 final size:29
Alignment explanation
Indices: 33480288--33480419 Score: 149
Period size: 29 Copynumber: 4.6 Consensus size: 29
33480278 TACTCGATTT
** *
33480288 CGCACACTTAGTGCCATGCGATTT-AAGCC
1 CGCACACTTAGTGCCAT-ATATTTCAAGCA
* *** * *
33480317 CGCACACATAGTGCCATACCCTTCGAGCT
1 CGCACACTTAGTGCCATATATTTCAAGCA
*
33480346 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCAAGCA
*
33480375 TGCACACTTAGTGCCATATATTTCAAGCA
1 CGCACACTTAGTGCCATATATTTCAAGCA
33480404 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
33480420 ATCTCGTCAC
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
28 2 0.02
29 84 0.98
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.25
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCAAGCA
Found at i:33482476 original size:40 final size:40
Alignment explanation
Indices: 33482431--33482561 Score: 174
Period size: 40 Copynumber: 3.3 Consensus size: 40
33482421 CGGAATATAA
33482431 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
33482471 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
33482511 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
33482551 CCGGATATAAT
1 CCGGATATAAT
33482562 TTCCAGCATA
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
39 1 0.01
40 76 0.99
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:33482575 original size:40 final size:40
Alignment explanation
Indices: 33482431--33482598 Score: 153
Period size: 40 Copynumber: 4.2 Consensus size: 40
33482421 CGGAATATAA
* ** *
33482431 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATAACCAGCACAATTGCCTTCGGGTCTTAGC
*
33482471 CCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGTCTTAGC
1 CCGGATATAATAAC-CAGCAC-AATTGCCTTCGGGTCTTAGC
*** * *
33482511 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATAACCAGCACAATTGCCTTCGGGTCTTAGC
** * *
33482551 CCGGATATAATTTCCAGCATAATTGTCC-TCGGGGCTTAGC
1 CCGGATATAATAACCAGCACAATTG-CCTTCGGGTCTTAGC
*
33482591 CCAGATAT
1 CCGGATAT
33482599 CATTCAATTT
Statistics
Matches: 105, Mismatches: 18, Indels: 10
0.79 0.14 0.08
Matches are distributed among these distances:
39 2 0.02
40 99 0.94
41 4 0.04
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATAACCAGCACAATTGCCTTCGGGTCTTAGC
Found at i:33492840 original size:40 final size:40
Alignment explanation
Indices: 33492713--33492840 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 40
33492703 ATGCTGGAAA
* *
33492713 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * * **
33492753 CTACATCCGGGCTAAGACCCGAAGGTATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
33492793 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
33492833 TTATATCC
1 TTATATCC
33492841 AGTTGTATTC
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
39 4 0.06
40 68 0.94
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.25
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:33499643 original size:24 final size:24
Alignment explanation
Indices: 33499598--33499644 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
33499588 AGTATGGTAT
*
33499598 TGGAAATATATACATGGGATAATA
1 TGGAAATATATACATAGGATAATA
* *
33499622 TGGAAATATGTACATAGTATAAT
1 TGGAAATATATACATAGGATAAT
33499645 GTTAAAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32
Consensus pattern (24 bp):
TGGAAATATATACATAGGATAATA
Found at i:33500363 original size:3 final size:3
Alignment explanation
Indices: 33500357--33500421 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
33500347 AAACATAAGC
33500357 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
33500405 TAA TAA TAA TAC TAA TA
1 TAA TAA TAA TAA TAA TA
33500422 TTATAAAAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:33503420 original size:80 final size:80
Alignment explanation
Indices: 33503336--33503484 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
33503326 TATGGTAACC
* * * *
33503336 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
33503400 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
33503416 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
33503481 CCGG
66 CCGG
33503485 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:33503426 original size:40 final size:38
Alignment explanation
Indices: 33503377--33503484 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
33503367 ATCACGATTT
*
33503377 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
33503417 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
33503457 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
33503485 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:33511500 original size:80 final size:80
Alignment explanation
Indices: 33511416--33511564 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
33511406 TATGGTAACC
* * * *
33511416 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
33511480 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
33511496 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
33511561 CCGG
66 CCGG
33511565 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:33511506 original size:40 final size:38
Alignment explanation
Indices: 33511457--33511564 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
33511447 ATCACGATTT
*
33511457 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
33511497 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
33511537 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
33511565 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:33516448 original size:19 final size:19
Alignment explanation
Indices: 33516424--33516463 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
33516414 TTTTCCTTGC
*
33516424 TATTTTTT-ACTTCTTTTGT
1 TATTTTTTCAC-TATTTTGT
33516443 TATTTTTTCACTATTTTGT
1 TATTTTTTCACTATTTTGT
33516462 TA
1 TA
33516464 CCATTTCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.70
Consensus pattern (19 bp):
TATTTTTTCACTATTTTGT
Found at i:33518369 original size:46 final size:48
Alignment explanation
Indices: 33518301--33518423 Score: 146
Period size: 48 Copynumber: 2.6 Consensus size: 48
33518291 TTTGTGTGCT
* *
33518301 AGTGTAAGACATGTTTGGGACATGCATCGGCCAC-A-ATA-TGAGAGCC
1 AGTGTAAGACATGTATGAGACATGCATCGGCCACGAGATATTGA-AGCC
* * *
33518347 AGTGTAAGACATGTATGAGACATGCTTCGGCCTCGAGATATTTAAGCC
1 AGTGTAAGACATGTATGAGACATGCATCGGCCACGAGATATTGAAGCC
*
33518395 AGTGTAAGACATGTCT-AGGACATGCATCG
1 AGTGTAAGACATGTATGA-GACATGCATCG
33518424 ACATTGAGAC
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
46 30 0.45
47 2 0.03
48 32 0.48
49 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACATGTATGAGACATGCATCGGCCACGAGATATTGAAGCC
Found at i:33518631 original size:49 final size:48
Alignment explanation
Indices: 33518532--33518664 Score: 142
Period size: 49 Copynumber: 2.7 Consensus size: 48
33518522 TGTTGTGTGT
* * * *
33518532 CAGTGTAAGACCTGTTTGGGATATGGCATCGACACCGATAGGTGAGAGC
1 CAGTGTAAGACCTGTCT-GGATATGGCATCGGCACCGATAGATGAAAGC
* *
33518581 CAGTGTAAGACCTGTCTAGGATATGGCATCGGC-CTCGCTATATGAAAGC
1 CAGTGTAAGACCTGTCT-GGATATGGCATCGGCAC-CGATAGATGAAAGC
* *
33518630 CAGTGTAAGACCATGTCCTGGACATGGCGTCGGCA
1 CAGTGTAAGACC-TGT-CTGGATATGGCATCGGCA
33518665 TCTTAACCCA
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
48 1 0.01
49 52 0.73
50 16 0.23
51 2 0.03
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.23
Consensus pattern (48 bp):
CAGTGTAAGACCTGTCTGGATATGGCATCGGCACCGATAGATGAAAGC
Found at i:33520233 original size:24 final size:24
Alignment explanation
Indices: 33520206--33520253 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
33520196 TGATAGTGTG
*
33520206 ACGACTCTTGATGAGATAAATTAT
1 ACGACTCCTGATGAGATAAATTAT
33520230 ACGACTCCTGATGAGATAAATTAT
1 ACGACTCCTGATGAGATAAATTAT
33520254 GTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.31
Consensus pattern (24 bp):
ACGACTCCTGATGAGATAAATTAT
Found at i:33520736 original size:26 final size:27
Alignment explanation
Indices: 33520707--33520762 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
33520697 GGGGATTGTT
**
33520707 TTAG-GAAGAGTTTTGAAAGAAGTACA
1 TTAGTGAAGAGTTTCAAAAGAAGTACA
33520733 TTAGTGAAGAGTTTCAAAAGAAGTACA
1 TTAGTGAAGAGTTTCAAAAGAAGTACA
33520760 TTA
1 TTA
33520763 ATTAGAGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.43, C:0.05, G:0.23, T:0.29
Consensus pattern (27 bp):
TTAGTGAAGAGTTTCAAAAGAAGTACA
Found at i:33525801 original size:46 final size:46
Alignment explanation
Indices: 33525734--33525899 Score: 199
Period size: 46 Copynumber: 3.6 Consensus size: 46
33525724 TTTGTGTGAT
* *
33525734 AGTGTAAGACATGTTTAGGACATGCATCCGCCATAATATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCCGCCATAATATGAGAGCC
33525780 AGTGTAAGACATGTCTGGGACATGCATCCGCCATAATATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCCGCCATAATATGAGAGCC
* * * * * * ** * *
33525826 AGTGCAAGACATGTCTGAGACATGTAT-CGGCATTGAGACAAAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCCGCCA-TAATATGAGAGCC
*
33525872 AATGTAAGACATGTCTGGGACATGCATC
1 AGTGTAAGACATGTCTGGGACATGCATC
33525900 AACCTCGCGA
Statistics
Matches: 102, Mismatches: 16, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
45 4 0.04
46 98 0.96
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCCGCCATAATATGAGAGCC
Found at i:33526036 original size:49 final size:49
Alignment explanation
Indices: 33525964--33526072 Score: 148
Period size: 49 Copynumber: 2.2 Consensus size: 49
33525954 GTTGTGTGTT
* * *
33525964 AGTGTAAGACCTGTCTGGGACATGGCATTGACAC-CGATAGATGAAAGCC
1 AGTGTAAGACCTATCTAGGACATGGCATCGAC-CTCGATAGATGAAAGCC
* *
33526013 AGTGTAAGACCTATCTAGGACATGGCATCGACCTCGCTATATGAAAGCC
1 AGTGTAAGACCTATCTAGGACATGGCATCGACCTCGATAGATGAAAGCC
*
33526062 AGTGTACGACC
1 AGTGTAAGACC
33526073 ATGTCGGGGA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
48 1 0.02
49 52 0.98
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (49 bp):
AGTGTAAGACCTATCTAGGACATGGCATCGACCTCGATAGATGAAAGCC
Found at i:33528373 original size:12 final size:12
Alignment explanation
Indices: 33528356--33528380 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33528346 TACACCGTAT
33528356 CGGTAACAGTAA
1 CGGTAACAGTAA
33528368 CGGTAACAGTAA
1 CGGTAACAGTAA
33528380 C
1 C
33528381 AGTAGTGATA
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:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTAACAGTAA
Found at i:33529933 original size:13 final size:13
Alignment explanation
Indices: 33529915--33529940 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33529905 GACACATGGG
33529915 CGTGTGTCTAGGC
1 CGTGTGTCTAGGC
33529928 CGTGTGTCTAGGC
1 CGTGTGTCTAGGC
33529941 ACATTAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.23, G:0.38, T:0.31
Consensus pattern (13 bp):
CGTGTGTCTAGGC
Found at i:33533215 original size:13 final size:13
Alignment explanation
Indices: 33533199--33533231 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
33533189 TGATGCATTC
33533199 TAGTCTTATTTCG
1 TAGTCTTATTTCG
33533212 TAGTCTTATTTCG
1 TAGTCTTATTTCG
33533225 TAGTCTT
1 TAGTCTT
33533232 TCAAATGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.55
Consensus pattern (13 bp):
TAGTCTTATTTCG
Found at i:33534918 original size:23 final size:22
Alignment explanation
Indices: 33534852--33534943 Score: 114
Period size: 23 Copynumber: 4.0 Consensus size: 22
33534842 TTAGCTCGTA
33534852 AGAGCTTACTGTTCTCAGCTCAT
1 AGAGCTTACTGTT-TCAGCTCAT
33534875 ATGAGCTTACTG-TTCAGCTCAT
1 A-GAGCTTACTGTTTCAGCTCAT
*
33534897 CAGAGCTTACTGTTTCAACTCAGT
1 -AGAGCTTACTGTTTCAGCTCA-T
33534921 AGAGCTTACTGTCTATCAGCTCA
1 AGAGCTTACTGT-T-TCAGCTCA
33534944 GGAGGAGTTT
Statistics
Matches: 61, Mismatches: 2, Indels: 10
0.84 0.03 0.14
Matches are distributed among these distances:
22 19 0.31
23 23 0.38
24 12 0.20
25 7 0.11
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (22 bp):
AGAGCTTACTGTTTCAGCTCAT
Found at i:33541690 original size:48 final size:48
Alignment explanation
Indices: 33541604--33541826 Score: 219
Period size: 48 Copynumber: 4.7 Consensus size: 48
33541594 GATAAGTTGT
* *
33541604 CGATGCCATGTCTTAGACATGGTCTTACACTGGCTATCATCAT-TAAGGC
1 CGATGCCATGCCCTAGACAT-GTCTTACACTGGCTATCATCATCT-AGGC
* *
33541653 CGATGCCATGCCCTAGACATGTCTTACACTGGCTATCATCATCGAGAC
1 CGATGCCATGCCCTAGACATGTCTTACACTGGCTATCATCATCTAGGC
* * *
33541701 CGATG-CATGTCCC-AGACATGTCTTACATTGGC-ACTCGTC-TCTACGC
1 CGATGCCATG-CCCTAGACATGTCTTACACTGGCTA-TCATCATCTAGGC
* * * * * *
33541747 CGATGCCATGTCCTAGACATCGTCTTATACTGGCTCTCATAATGT-GTC
1 CGATGCCATGCCCTAGACAT-GTCTTACACTGGCTATCATCATCTAGGC
33541795 CGATG-CATGTCCC-AGACATGTCTTACACTGGC
1 CGATGCCATG-CCCTAGACATGTCTTACACTGGC
33541827 ACACAATCAC
Statistics
Matches: 145, Mismatches: 20, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
46 24 0.17
47 46 0.32
48 55 0.38
49 20 0.14
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (48 bp):
CGATGCCATGCCCTAGACATGTCTTACACTGGCTATCATCATCTAGGC
Found at i:33541798 original size:94 final size:94
Alignment explanation
Indices: 33541651--33541828 Score: 277
Period size: 94 Copynumber: 1.9 Consensus size: 94
33541641 CATCATTAAG
*
33541651 GCCGATGCCATGCCCTAGACATGTCTTACACTGGCTATCATCATCGAGACCGATGCATGTCCCAG
1 GCCGATGCCATGCCCTAGACATGTCTTACACTGGCTATCATAATCGAGACCGATGCATGTCCCAG
*
33541716 ACATGTCTTACATTGGCACTCGTCTCTAC
66 ACATGTCTTACACTGGCACTCGTCTCTAC
* * * * *
33541745 GCCGATGCCATGTCCTAGACATCGTCTTATACTGGCTCTCATAAT-GTGTCCGATGCATGTCCCA
1 GCCGATGCCATGCCCTAGACAT-GTCTTACACTGGCTATCATAATCGAGACCGATGCATGTCCCA
33541809 GACATGTCTTACACTGGCAC
65 GACATGTCTTACACTGGCAC
33541829 ACAATCACCC
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
94 57 0.75
95 19 0.25
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.28
Consensus pattern (94 bp):
GCCGATGCCATGCCCTAGACATGTCTTACACTGGCTATCATAATCGAGACCGATGCATGTCCCAG
ACATGTCTTACACTGGCACTCGTCTCTAC
Found at i:33544827 original size:40 final size:40
Alignment explanation
Indices: 33544726--33544904 Score: 189
Period size: 40 Copynumber: 4.5 Consensus size: 40
33544716 CGAATGGTGT
* * * *
33544726 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAAA
* *
33544767 CTGGG-TCAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
1 CCGGGCT-AAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
* * * *
33544807 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
* * * * *
33544847 CCGGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
*
33544887 CCGGGCTATGTCCCGAAG
1 CCGGGCTAAGTCCCGAAG
33544905 ACAATCGAGC
Statistics
Matches: 114, Mismatches: 22, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
40 89 0.78
41 25 0.22
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
Found at i:33544873 original size:80 final size:80
Alignment explanation
Indices: 33544726--33544918 Score: 208
Period size: 80 Copynumber: 2.4 Consensus size: 80
33544716 CGAATGGTGT
* * * * *
33544726 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAATCTGGGTCAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTGACTAAATCCGGGTCAAGTCCCGAAGGCAATT
* *
33544791 GTGCGAGTTACCAAAA
65 GTGCGAATCACCAAAA
* * * *
33544807 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGG-CTAATTCCCGAAGGCAATT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTGACTAAATCCGGGTC-AAGTCCCGAAGGCAATT
* *
33544871 GTGCGAATCACTATAA
65 GTGCGAATCACCAAAA
* * * *
33544887 CCGGGCTATGTCCCGAAGACAATCGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGT
33544919 CGCTATATCC
Statistics
Matches: 93, Mismatches: 18, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
79 1 0.01
80 67 0.72
81 25 0.27
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.23
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTGACTAAATCCGGGTCAAGTCCCGAAGGCAATTG
TGCGAATCACCAAAA
Found at i:33544925 original size:40 final size:40
Alignment explanation
Indices: 33544847--33544930 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
33544837 GTTATTAAAT
* * *
33544847 CCGGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATAA
1 CCGGGCTAATTCCCGAAGACAATCGAGCGAATCACTATAA
* * *
33544887 CCGGGCT-ATGTCCCGAAGACAATCGAGCGAGTCGCTATAT
1 CCGGGCTAAT-TCCCGAAGACAATCGAGCGAATCACTATAA
33544927 CCGG
1 CCGG
33544931 TTAAATTCCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
39 2 0.05
40 35 0.95
ACGTcount: A:0.26, C:0.27, G:0.26, T:0.20
Consensus pattern (40 bp):
CCGGGCTAATTCCCGAAGACAATCGAGCGAATCACTATAA
Found at i:33547527 original size:15 final size:16
Alignment explanation
Indices: 33547492--33547526 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
33547482 GTACTTTATG
33547492 TTTTT-TTTTTTGAAA
1 TTTTTATTTTTTGAAA
33547507 TTTTTATTTTTTGAAA
1 TTTTTATTTTTTGAAA
33547523 TTTT
1 TTTT
33547527 AAATATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.74
Consensus pattern (16 bp):
TTTTTATTTTTTGAAA
Found at i:33547533 original size:19 final size:19
Alignment explanation
Indices: 33547497--33547557 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
33547487 TTATGTTTTT
33547497 TTTTTTGAAATTTT---TA
1 TTTTTTGAAATTTTAAATA
33547513 TTTTTTGAAATTTTAAATA
1 TTTTTTGAAATTTTAAATA
*
33547532 TTTTTAT-AATTTTTAAATTA
1 TTTTT-TGAAATTTTAAA-TA
33547552 TTTTTT
1 TTTTTT
33547558 TATATAATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
16 14 0.36
19 17 0.44
20 8 0.21
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTTTTGAAATTTTAAATA
Found at i:33547759 original size:20 final size:20
Alignment explanation
Indices: 33547734--33547780 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
33547724 TAAAAAGTAG
33547734 AATAAATATAAA-ATTAACAA
1 AATAAATATAAATATTAA-AA
33547754 AATAAATATAAATATTAAAA
1 AATAAATATAAATATTAAAA
33547774 AATAAAT
1 AATAAAT
33547781 TTATCATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (20 bp):
AATAAATATAAATATTAAAA
Found at i:33547928 original size:2 final size:2
Alignment explanation
Indices: 33547921--33547953 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
33547911 TCACATTTCA
33547921 AT AT 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 AT AT A
33547954 AAAAAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33560835 original size:30 final size:30
Alignment explanation
Indices: 33560801--33560858 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
33560791 CATGGACATG
33560801 ACACACGGGCGTGTAG-TCTACCCGTGTGTC
1 ACACACGGGCGTGTAGAT-TACCCGTGTGTC
*
33560831 ACACACGGGCGTGTGGATTACCCGTGTG
1 ACACACGGGCGTGTAGATTACCCGTGTG
33560859 GAAGTGCCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.17, C:0.28, G:0.33, T:0.22
Consensus pattern (30 bp):
ACACACGGGCGTGTAGATTACCCGTGTGTC
Found at i:33576433 original size:66 final size:68
Alignment explanation
Indices: 33576357--33576543 Score: 281
Period size: 71 Copynumber: 2.7 Consensus size: 68
33576347 TAGTACCACT
*
33576357 CATGCGACCTAGC-CGATTTGTC-T-CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
1 CATGCGACCTAGCAC-ATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
33576419 CACG
65 CACG
33576423 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
33576488 ATCACG
63 ATCACG
33576494 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGG
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGG
33576544 GATACATCTC
Statistics
Matches: 114, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
66 13 0.11
67 6 0.05
68 1 0.01
69 1 0.01
71 93 0.82
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (68 bp):
CATGCGACCTAGCACATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATC
ACG
Found at i:33576468 original size:71 final size:71
Alignment explanation
Indices: 33576380--33576543 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
33576370 CGATTTGTCT
33576380 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
33576445 CTTTCA
66 CTTTCA
33576451 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
33576516 CTTTCA
66 CTTTCA
33576522 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
33576544 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:33576581 original size:71 final size:70
Alignment explanation
Indices: 33576380--33576577 Score: 276
Period size: 71 Copynumber: 2.8 Consensus size: 70
33576370 CGATTTGTCT
* * *
33576380 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
33576445 CTTTCA
65 CTTTCA
* * *
33576451 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
33576516 CTTTCA
65 CTTTCA
* *
33576522 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACGCATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACGCATGCGACCTAGCTAC
33576578 TACAGGGTGT
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 23 0.19
69 1 0.01
70 1 0.01
71 96 0.79
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACGCATGCGACCTAGCTACATTTATC
TTTCA
Found at i:33592074 original size:17 final size:17
Alignment explanation
Indices: 33592049--33592092 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
33592039 TTTATGTCTT
33592049 AAAACACTACTTAATTA
1 AAAACACTACTTAATTA
*
33592066 AAAATACTACTTAATTA
1 AAAACACTACTTAATTA
33592083 AAAACACTAC
1 AAAACACTAC
33592093 ATAAGTCTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAACACTACTTAATTA
Found at i:33593458 original size:20 final size:20
Alignment explanation
Indices: 33593412--33593459 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
33593402 ATTAAATAAA
* *
33593412 TAATTAAAAATTCTTAAAAT
1 TAATAAAAAATTCTAAAAAT
33593432 TAATAAAAAATT-TAAAAAGT
1 TAATAAAAAATTCTAAAAA-T
*
33593452 TATTAAAA
1 TAATAAAA
33593460 TTTTAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (20 bp):
TAATAAAAAATTCTAAAAAT
Found at i:33594159 original size:2 final size:2
Alignment explanation
Indices: 33594152--33594218 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
33594142 TCTAATTATC
33594152 AT AT AT 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
33594194 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 A
33594219 GGAAGTTAGT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33599456 original size:17 final size:16
Alignment explanation
Indices: 33599419--33599459 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
33599409 AAATAACTAG
*
33599419 AATCTAAAATTATCAA
1 AATCTAAAATTACCAA
*
33599435 AATCTAAAATTAACCGA
1 AATCTAAAATT-ACCAA
33599452 AATCTAAA
1 AATCTAAA
33599460 GTCAACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.56, C:0.15, G:0.02, T:0.27
Consensus pattern (16 bp):
AATCTAAAATTACCAA
Found at i:33600388 original size:32 final size:31
Alignment explanation
Indices: 33600328--33600397 Score: 88
Period size: 32 Copynumber: 2.3 Consensus size: 31
33600318 TTTAATAGTT
*
33600328 GGTGATCAAAAAAGAAAAAATCGTATAATTA
1 GGTGATCAAAAAAGAAAAAATCGAATAATTA
** *
33600359 GGTGACTCAAAAAAGAAAATTTTGAATAATTA
1 GGTGA-TCAAAAAAGAAAAAATCGAATAATTA
33600391 -GTGATCA
1 GGTGATCA
33600398 TTTTGTAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 3 0.09
31 9 0.26
32 22 0.65
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.26
Consensus pattern (31 bp):
GGTGATCAAAAAAGAAAAAATCGAATAATTA
Found at i:33601832 original size:6 final size:6
Alignment explanation
Indices: 33601821--33601880 Score: 84
Period size: 6 Copynumber: 10.0 Consensus size: 6
33601811 CCATAACACG
* * * *
33601821 CATACA CATACA CATACA CATACA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
33601869 CATATA CATATA
1 CATATA CATATA
33601881 TATAGGTATA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (6 bp):
CATATA
Found at i:33602127 original size:10 final size:11
Alignment explanation
Indices: 33602099--33602127 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
33602089 TCTTTCAATA
33602099 ATTTTTTTCAT
1 ATTTTTTTCAT
33602110 ATTTTTTT-AT
1 ATTTTTTTCAT
33602120 ATTTTTTT
1 ATTTTTTT
33602128 TCCATCCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.79
Consensus pattern (11 bp):
ATTTTTTTCAT
Found at i:33605864 original size:28 final size:28
Alignment explanation
Indices: 33605808--33605865 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
33605798 ATTTACCACA
*
33605808 TTATTCATTTTTTAAATTGTTTTGCTAT
1 TTATTCATTTTTTAAATTGTTTTGATAT
*
33605836 TTATTCAAGTTTTTTTAA-TGTTTT-ATAT
1 TTATTC-A-TTTTTTAAATTGTTTTGATAT
33605864 TT
1 TT
33605866 TATATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 11 0.42
29 7 0.27
30 8 0.31
ACGTcount: A:0.22, C:0.05, G:0.07, T:0.66
Consensus pattern (28 bp):
TTATTCATTTTTTAAATTGTTTTGATAT
Found at i:33606037 original size:2 final size:2
Alignment explanation
Indices: 33606030--33606072 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
33606020 ACTTTTATTT
33606030 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33606072 T
1 T
33606073 CTAACTGTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:33608280 original size:46 final size:44
Alignment explanation
Indices: 33608176--33608283 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
33608166 TGTCTTTGAC
** * * *
33608176 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
33608220 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
33608266 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
33608284 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:33619413 original size:6 final size:6
Alignment explanation
Indices: 33619402--33619433 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
33619392 ACAACATGAT
33619402 GAGCAA GAGCAA GAGCAA GAGCAA GAGCAA GA
1 GAGCAA GAGCAA GAGCAA GAGCAA GAGCAA GA
33619434 TGATGAATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.16, G:0.34, T:0.00
Consensus pattern (6 bp):
GAGCAA
Found at i:33626684 original size:26 final size:26
Alignment explanation
Indices: 33626645--33626726 Score: 137
Period size: 26 Copynumber: 3.2 Consensus size: 26
33626635 TGATACAAAT
** *
33626645 TGATAATGAATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
33626671 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
33626697 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
33626723 TGAT
1 TGAT
33626727 GGGCATTTCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:33628243 original size:26 final size:26
Alignment explanation
Indices: 33628214--33628266 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
33628204 TTTACAGTTT
*
33628214 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCATAGG-GATAAATTGACCGAAA
* *
33628240 TACCCATAGGGTTAAATTGACCTAAA
1 TACCCATAGGGATAAATTGACCGAAA
33628266 T
1 T
33628267 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCATAGGGATAAATTGACCGAAA
Found at i:33630701 original size:16 final size:16
Alignment explanation
Indices: 33630682--33630716 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
33630672 GAAATGAATA
* *
33630682 AATGTGTAAATGTGAT
1 AATGTGCAAATATGAT
33630698 AATGTGCAAATATGAT
1 AATGTGCAAATATGAT
33630714 AAT
1 AAT
33630717 TAGATATTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.03, G:0.20, T:0.34
Consensus pattern (16 bp):
AATGTGCAAATATGAT
Found at i:33632281 original size:50 final size:46
Alignment explanation
Indices: 33632171--33632324 Score: 156
Period size: 44 Copynumber: 3.4 Consensus size: 46
33632161 ACTAATTATG
* *
33632171 TGCACTTAGTGTGCGAAATCAAGATAGCTTCAGC--TATATATATT
1 TGCACTTAGTGTGCGAGATCGAGATAGCTTCAGCTATATATATATT
*
33632215 TGCACTTAGTGCGCGAGATCGAGATAGCTTCAGCTATATATATGTATAT
1 TGCACTTAGTGTGCGAGATCGAGATAGCTTCAGCTATATATA--TAT-T
* * * *
33632264 TGGCACTTAGTGTGCGAGATTGATACAGCTTTAGCTAT-T-TAT-TT
1 T-GCACTTAGTGTGCGAGATCGAGATAGCTTCAGCTATATATATATT
* *
33632308 GGCACTAAGTGTGCGAG
1 TGCACTTAGTGTGCGAG
33632325 TTTCCCGAGT
Statistics
Matches: 94, Mismatches: 10, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
43 15 0.16
44 32 0.34
45 1 0.01
46 7 0.07
48 5 0.05
49 3 0.03
50 31 0.33
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (46 bp):
TGCACTTAGTGTGCGAGATCGAGATAGCTTCAGCTATATATATATT
Found at i:33637126 original size:25 final size:25
Alignment explanation
Indices: 33637098--33637163 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 25
33637088 TCTAATTATA
33637098 AGATTAATAAAAATAATAAAAAAAT
1 AGATTAATAAAAATAATAAAAAAAT
* *
33637123 AGATTACT-AAAATAA-AAATAAAT
1 AGATTAATAAAAATAATAAAAAAAT
33637146 A-A-T-ATAACAAATAATAAA
1 AGATTAATAA-AAATAATAAA
33637164 GAAAGAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
20 1 0.03
21 2 0.06
22 7 0.20
23 11 0.31
24 7 0.20
25 7 0.20
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (25 bp):
AGATTAATAAAAATAATAAAAAAAT
Found at i:33638078 original size:20 final size:20
Alignment explanation
Indices: 33638053--33638100 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
33638043 CTGAAGGAAA
33638053 TTGAAGGAAGATCTTCAGTC
1 TTGAAGGAAGATCTTCAGTC
*
33638073 TTGAAGGGAGATCTTCAGTC
1 TTGAAGGAAGATCTTCAGTC
33638093 TTGAAGGA
1 TTGAAGGA
33638101 GAATCCAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (20 bp):
TTGAAGGAAGATCTTCAGTC
Found at i:33639446 original size:64 final size:64
Alignment explanation
Indices: 33639331--33639551 Score: 169
Period size: 64 Copynumber: 3.5 Consensus size: 64
33639321 GTTTTTCTTT
* * * * * * * *
33639331 ACTTCTCCCACGCCCATGTAAGATTCCATACACTCGTGTGGCTTGGT-CGTGTGTAATCTCCTTC
1 ACTTCTCCCAAGCCCATGTGAGATCCCACACGCCCGTGTGGC-TCGTCCGTGTGTGATCTCCTTC
* * * *
33639395 ACTTCTCCCAAGCCCATGTGAGATCCCACACGCCCGTGTGGCTCATCCGTGTATGATCCCCTTT
1 ACTTCTCCCAAGCCCATGTGAGATCCCACACGCCCGTGTGGCTCGTCCGTGTGTGATCTCCTTC
* * * * * * * * * * *
33639459 GCTTCTCCTATGCCCGTGTG-GAATCGCACACGACCGTGTGGCTTGGCCGTGTAG-GGTTTCTTT
1 ACTTCTCCCAAGCCCATGTGAG-ATCCCACACGCCCGTGTGGCTCGTCCGTGT-GTGATCTCCTT
33639522 C
64 C
* *
33639523 GCTTCTCCCAGGCCCATGTGAGATCCCAC
1 ACTTCTCCCAAGCCCATGTGAGATCCCAC
33639552 TCACTCATGT
Statistics
Matches: 122, Mismatches: 31, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
63 3 0.02
64 118 0.97
65 1 0.01
ACGTcount: A:0.15, C:0.33, G:0.22, T:0.29
Consensus pattern (64 bp):
ACTTCTCCCAAGCCCATGTGAGATCCCACACGCCCGTGTGGCTCGTCCGTGTGTGATCTCCTTC
Found at i:33642712 original size:13 final size:14
Alignment explanation
Indices: 33642688--33642721 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
33642678 TCTTCTTGTC
33642688 ATAAACTAAAATAAA
1 ATAAA-TAAAATAAA
33642703 A-AAATAAAATAAA
1 ATAAATAAAATAAA
33642716 ATAAAT
1 ATAAAT
33642722 TAGAATGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 10 0.56
14 7 0.39
15 1 0.06
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (14 bp):
ATAAATAAAATAAA
Found at i:33644461 original size:15 final size:15
Alignment explanation
Indices: 33644440--33644505 Score: 60
Period size: 15 Copynumber: 4.4 Consensus size: 15
33644430 TGCTTGATAA
33644440 ACTGAAAAATTAAAT
1 ACTGAAAAATTAAAT
* * *
33644455 GCTGAAAAAATAAGT
1 ACTGAAAAATTAAAT
** *
33644470 GTTGAAAAATTAAGT
1 ACTGAAAAATTAAAT
* *
33644485 ATTGAAAACTTAAAT
1 ACTGAAAAATTAAAT
33644500 ACTGAA
1 ACTGAA
33644506 TTGAAGTTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.53, C:0.06, G:0.14, T:0.27
Consensus pattern (15 bp):
ACTGAAAAATTAAAT
Found at i:33645616 original size:38 final size:38
Alignment explanation
Indices: 33645565--33645640 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
33645555 GCCAATTAAG
*
33645565 TTAAAATTCAATTGACTTCTTGTGAACAGTTTAATACT
1 TTAAAATTCAATTGACTTCTTGCGAACAGTTTAATACT
*
33645603 TTAAAATTCAATTGACTTCTTGCGAATAGTTTAATACT
1 TTAAAATTCAATTGACTTCTTGCGAACAGTTTAATACT
33645641 CTCTTCAACT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (38 bp):
TTAAAATTCAATTGACTTCTTGCGAACAGTTTAATACT
Found at i:33647129 original size:14 final size:14
Alignment explanation
Indices: 33647110--33647141 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
33647100 AATCAGCGAC
33647110 TTTATTTGATACTT
1 TTTATTTGATACTT
33647124 TTTATTTGATACTT
1 TTTATTTGATACTT
33647138 TTTA
1 TTTA
33647142 ATGATATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.66
Consensus pattern (14 bp):
TTTATTTGATACTT
Found at i:33647146 original size:13 final size:14
Alignment explanation
Indices: 33647110--33647147 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
33647100 AATCAGCGAC
*
33647110 TTTATTTGATACTT
1 TTTATATGATACTT
*
33647124 TTTATTTGATACTT
1 TTTATATGATACTT
33647138 TTTA-ATGATA
1 TTTATATGATA
33647148 TAAAGACTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 5 0.22
14 18 0.78
ACGTcount: A:0.26, C:0.05, G:0.08, T:0.61
Consensus pattern (14 bp):
TTTATATGATACTT
Found at i:33650182 original size:5 final size:5
Alignment explanation
Indices: 33650172--33650196 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
33650162 CATTCACCAA
33650172 GTATT GTATT GTATT GTATT GTATT
1 GTATT GTATT GTATT GTATT GTATT
33650197 ATCCCATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (5 bp):
GTATT
Found at i:33651991 original size:27 final size:27
Alignment explanation
Indices: 33651961--33652100 Score: 124
Period size: 27 Copynumber: 5.2 Consensus size: 27
33651951 ATTACTGTTT
* * *
33651961 TACCCTCAATTTACAGAATTACCAAAA
1 TACCCTCAGTTTATAAAATTACCAAAA
** *
33651988 TACCCTTGGTTTATAAAATCACCAAAA
1 TACCCTCAGTTTATAAAATTACCAAAA
* *
33652015 TACCC-CTAGTTTGTAAAATTACTAAAA
1 TACCCTC-AGTTTATAAAATTACCAAAA
**
33652042 TACCCTTTGTTTATAAAATTACCAAAA
1 TACCCTCAGTTTATAAAATTACCAAAA
* *
33652069 TACCCAT-GGTTTGA-AAAATTACTAAAA
1 TACCC-TCAGTTT-ATAAAATTACCAAAA
33652096 TACCC
1 TACCC
33652101 CTGTAGGGTA
Statistics
Matches: 92, Mismatches: 17, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
27 90 0.98
28 2 0.02
ACGTcount: A:0.41, C:0.21, G:0.06, T:0.31
Consensus pattern (27 bp):
TACCCTCAGTTTATAAAATTACCAAAA
Found at i:33652019 original size:54 final size:54
Alignment explanation
Indices: 33651963--33652100 Score: 152
Period size: 54 Copynumber: 2.5 Consensus size: 54
33651953 TACTGTTTTA
*
33651963 CCCTCAATTTACAGAATTACCAAAATACCCTTGGTTTATAAAATCACCAAAATAC
1 CCCT-AATTTACAAAATTACCAAAATACCCTTGGTTTATAAAATCACCAAAATAC
* ** * * *
33652018 CCCTAGTTTGTAAAATTACTAAAATACCCTTTGTTTATAAAATTACCAAAATAC
1 CCCTAATTTACAAAATTACCAAAATACCCTTGGTTTATAAAATCACCAAAATAC
* ** *
33652072 CCATGGTTTGA-AAAATTACTAAAATACCC
1 CCCTAATTT-ACAAAATTACCAAAATACCC
33652101 CTGTAGGGTA
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
54 68 0.94
55 4 0.06
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (54 bp):
CCCTAATTTACAAAATTACCAAAATACCCTTGGTTTATAAAATCACCAAAATAC
Found at i:33652113 original size:27 final size:27
Alignment explanation
Indices: 33652083--33652144 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
33652073 CATGGTTTGA
33652083 AAAATTACTAAAATACCCCTGTAGGGT
1 AAAATTACTAAAATACCCCTGTAGGGT
* *
33652110 AAAATTACTGAAATACCCTTGTAGGGT
1 AAAATTACTAAAATACCCCTGTAGGGT
33652137 AAAATTAC
1 AAAATTAC
33652145 CATTTTGCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (27 bp):
AAAATTACTAAAATACCCCTGTAGGGT
Found at i:33652113 original size:54 final size:54
Alignment explanation
Indices: 33651977--33652127 Score: 153
Period size: 54 Copynumber: 2.8 Consensus size: 54
33651967 CAATTTACAG
* ** * * *
33651977 AATTACCAAAATACCCT-TGGTTTATAAAATCACCAAAATACCCCTAGTTTGTAA
1 AATTACTAAAATACCCTCT-GTGGATAAAATTACCAAAATACCCATAGTTTGAAA
* ** *
33652031 AATTACTAAAATACCCTTTGTTTATAAAATTACCAAAATACCCATGGTTTGAAA
1 AATTACTAAAATACCCTCTGTGGATAAAATTACCAAAATACCCATAGTTTGAAA
* **
33652085 AATTACTAAAATACCC-CTGTAGGGTAAAATTACTGAAATACCC
1 AATTACTAAAATACCCTCTGT-GGATAAAATTACCAAAATACCC
33652128 TTGTAGGGTA
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
53 3 0.04
54 80 0.95
55 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.30
Consensus pattern (54 bp):
AATTACTAAAATACCCTCTGTGGATAAAATTACCAAAATACCCATAGTTTGAAA
Found at i:33652129 original size:81 final size:81
Alignment explanation
Indices: 33651977--33652129 Score: 220
Period size: 81 Copynumber: 1.9 Consensus size: 81
33651967 CAATTTACAG
* **
33651977 AATTACCAAAATACCCTTGGTTTATAAAATCACCAAAATACCCCTAGTTTGTAAAATTACTAAAA
1 AATTACCAAAATACCCATGGTTTATAAAATCACCAAAATACCCCTAGTGGGTAAAATTACTAAAA
33652042 TACCCTTTGTTTATAA
66 TACCCTTTGTTTATAA
* * *
33652058 AATTACCAAAATACCCATGGTTTGA-AAAATTACTAAAATACCCCT-GTAGGGTAAAATTACTGA
1 AATTACCAAAATACCCATGGTTT-ATAAAATCACCAAAATACCCCTAGT-GGGTAAAATTACTAA
33652121 AATACCCTT
64 AATACCCTT
33652130 GTAGGGTAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
80 2 0.03
81 61 0.95
82 1 0.02
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (81 bp):
AATTACCAAAATACCCATGGTTTATAAAATCACCAAAATACCCCTAGTGGGTAAAATTACTAAAA
TACCCTTTGTTTATAA
Found at i:33652798 original size:28 final size:28
Alignment explanation
Indices: 33652765--33652860 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
33652755 GCTTAGATCA
33652765 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
33652793 TGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
* *
33652821 CG-AATTACCCCTAAATAGTAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
33652848 C--AATATACCCCTA
1 CGAAAT-TACCCCTA
33652861 GGGTTTAAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
26 3 0.05
27 32 0.51
28 28 0.44
ACGTcount: A:0.45, C:0.25, G:0.08, T:0.22
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:33656533 original size:115 final size:115
Alignment explanation
Indices: 33656328--33656555 Score: 447
Period size: 115 Copynumber: 2.0 Consensus size: 115
33656318 TATAAAGTTA
33656328 TATTACCCTTTTGATTACTATGTAAAAATTCTGCTTGTTTCCCGGGAATATATTTAAGATACCAA
1 TATTACCCTTTTGATTACTATGTAAAAATTCTGCTTGTTTCCCGGGAATATATTTAAGATACCAA
33656393 AGAAAACTGATAATCCCATAGGGTCAAGCATGTATTTTCAATTAACCTCC
66 AGAAAACTGATAATCCCATAGGGTCAAGCATGTATTTTCAATTAACCTCC
33656443 TATTACCCTTTTGATTACTATGTAAAAATTCTGCTTGTTTCCCGGGAATATATTTAAGATACCAA
1 TATTACCCTTTTGATTACTATGTAAAAATTCTGCTTGTTTCCCGGGAATATATTTAAGATACCAA
*
33656508 AGAAAACTGATAATCCCATATGGTCAAGCATGTATTTTCAATTAACCT
66 AGAAAACTGATAATCCCATAGGGTCAAGCATGTATTTTCAATTAACCT
33656556 TCCCCCCCCC
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
115 112 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (115 bp):
TATTACCCTTTTGATTACTATGTAAAAATTCTGCTTGTTTCCCGGGAATATATTTAAGATACCAA
AGAAAACTGATAATCCCATAGGGTCAAGCATGTATTTTCAATTAACCTCC
Found at i:33656585 original size:115 final size:115
Alignment explanation
Indices: 33656351--33656585 Score: 301
Period size: 115 Copynumber: 2.0 Consensus size: 115
33656341 ATTACTATGT
33656351 AAAAATTCTGCTTGTTTCCCGGGAATATATTTAAGATACCAAAGAAAACTGATAATCCCATAGGG
1 AAAAATTCTGCTTGTTTCCCGGGAATATATTTAAGATACCAAAGAAAACTGATAATCCCATAGGG
* ** ***** * ** ***
33656416 TCAAGCATGTATTTTCAATTAACCTCCTATTACCCTTTTGATTACTATGT
66 TCAAGCATGTATTTTCAATTAACCTCCCACCACCCCCCCCATAAAAAAAA
*
33656466 AAAAATTCTGCTTGTTTCCCGGGAATATATTTAAGATACCAAAGAAAACTGATAATCCCATATGG
1 AAAAATTCTGCTTGTTTCCCGGGAATATATTTAAGATACCAAAGAAAACTGATAATCCCATAGGG
* *
33656531 TCAAGCATGTATTTTCAATTAACCTTCCCCCCCCCCCCCCCA-AAAAAAAA
66 TCAAGCATGTATTTTCAATTAACC-TCCCACCACCCCCCCCATAAAAAAAA
33656581 AAAAA
1 AAAAA
33656586 GAAGGGTTTT
Statistics
Matches: 102, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
115 95 0.93
116 7 0.07
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (115 bp):
AAAAATTCTGCTTGTTTCCCGGGAATATATTTAAGATACCAAAGAAAACTGATAATCCCATAGGG
TCAAGCATGTATTTTCAATTAACCTCCCACCACCCCCCCCATAAAAAAAA
Found at i:33659842 original size:29 final size:30
Alignment explanation
Indices: 33659791--33659856 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
33659781 ATAGGTATCT
* * *
33659791 AATCAAATTAATCCTTCTGCTATTAAATGG
1 AATCAAATTAATCCCTCTACTATTAAAAGG
* *
33659821 -ATCAATTTAGTCCCTCTACTATTAAAAGG
1 AATCAAATTAATCCCTCTACTATTAAAAGG
33659850 AATCAAA
1 AATCAAA
33659857 CAAGGCTAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.33
Consensus pattern (30 bp):
AATCAAATTAATCCCTCTACTATTAAAAGG
Found at i:33662661 original size:3 final size:3
Alignment explanation
Indices: 33662655--33662689 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
33662645 CTTATACCTC
33662655 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
33662690 TTTTTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:33677091 original size:23 final size:23
Alignment explanation
Indices: 33677065--33677109 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
33677055 CCTTAATCTT
*
33677065 TTAGAACCAAATCTTGAAATCCC
1 TTAGAACCAAATCGTGAAATCCC
*
33677088 TTAGACCCAAATCGTGAAATCC
1 TTAGAACCAAATCGTGAAATCC
33677110 TTAATCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.24
Consensus pattern (23 bp):
TTAGAACCAAATCGTGAAATCCC
Found at i:33677947 original size:30 final size:30
Alignment explanation
Indices: 33677893--33677950 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
33677883 CTGGGCATTC
**
33677893 CCACACAGGCTGAGCACATGCCCATGTGAG
1 CCACACAGGCTGAGCACACACCCATGTGAG
33677923 CCACACAGGCTG-GCAACACACCCATGTG
1 CCACACAGGCTGAGC-ACACACCCATGTG
33677951 CCAGCCTGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.28, C:0.36, G:0.24, T:0.12
Consensus pattern (30 bp):
CCACACAGGCTGAGCACACACCCATGTGAG
Found at i:33680834 original size:47 final size:46
Alignment explanation
Indices: 33680716--33680889 Score: 189
Period size: 45 Copynumber: 3.8 Consensus size: 46
33680706 TGGATATTTG
*
33680716 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCGA
* * *
33680763 TG--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATGTAACTA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATG---CGA
*
33680808 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCG-A
* *
33680856 CGC--CCGAGCTCGTTGAGTTGAGTCCGAGTTCACT
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT
33680890 TATGGGCGGG
Statistics
Matches: 108, Mismatches: 10, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
42 4 0.04
44 2 0.02
45 32 0.30
46 30 0.28
47 31 0.29
48 5 0.05
50 4 0.04
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (46 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCGA
Found at i:33680885 original size:46 final size:46
Alignment explanation
Indices: 33680721--33680894 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
33680711 ATTTGGGCAT
* *
33680721 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG-ATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* * *
33680766 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC
33680811 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
*
33680859 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
33680895 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 9, Indels: 19
0.80 0.07 0.14
Matches are distributed among these distances:
42 5 0.05
44 2 0.02
45 29 0.26
46 35 0.32
47 28 0.25
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:33683862 original size:15 final size:15
Alignment explanation
Indices: 33683842--33683910 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
33683832 GTATCTTGGG
33683842 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
33683857 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
33683872 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
33683887 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
33683902 TTTCTTTAT
1 TTTCTTTAT
33683911 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:33683911 original size:30 final size:30
Alignment explanation
Indices: 33683833--33683920 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
33683823 CATAGTATCG
* * * *
33683833 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
33683863 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
33683893 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
33683921 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:33686351 original size:46 final size:46
Alignment explanation
Indices: 33686301--33686476 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
33686291 TATTTGGGCA
33686301 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
33686347 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
33686392 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
33686440 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
33686477 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 3 0.03
46 64 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:33686456 original size:93 final size:93
Alignment explanation
Indices: 33686297--33686468 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
33686287 TGGATATTTG
* *
33686297 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
33686362 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
33686390 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
33686455 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
33686469 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:33691235 original size:4 final size:4
Alignment explanation
Indices: 33691220--33691274 Score: 60
Period size: 4 Copynumber: 13.8 Consensus size: 4
33691210 ACCCTTATCT
* *
33691220 TTTA TATTA TTTA TTTA TTTA TTTTA TTTC TTTA TTTC TTTA -TTA TTTA
1 TTTA T-TTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA
33691269 -TTA TTT
1 TTTA TTT
33691275 GCTATTTTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
3 6 0.14
4 29 0.67
5 8 0.19
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:33691246 original size:17 final size:17
Alignment explanation
Indices: 33691220--33691307 Score: 67
Period size: 17 Copynumber: 5.1 Consensus size: 17
33691210 ACCCTTATCT
*
33691220 TTTATATTATTTATTTA
1 TTTATTTTATTTATTTA
*
33691237 TTTATTTTATTTCTTTA
1 TTTATTTTATTTATTTA
*
33691254 TTT-CTTTA-TTATTTA
1 TTTATTTTATTTATTTA
33691269 -TTATTTGCTATTTTATTTTA
1 TTTATTT--TA-TTTA-TTTA
*
33691289 TTT-TTATTATTTTTTTA
1 TTTATT-TTATTTATTTA
33691306 TT
1 TT
33691308 CTGTTTTTGT
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
14 2 0.04
15 8 0.14
16 4 0.07
17 26 0.46
18 3 0.05
19 5 0.09
20 6 0.11
21 3 0.05
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.75
Consensus pattern (17 bp):
TTTATTTTATTTATTTA
Found at i:33691306 original size:8 final size:8
Alignment explanation
Indices: 33691226--33691307 Score: 58
Period size: 8 Copynumber: 9.6 Consensus size: 8
33691216 ATCTTTTATA
*
33691226 TTATTTAT
1 TTATTTTT
33691234 TTATTTATT
1 TTATTT-TT
*
33691243 TTATTTCT
1 TTATTTTT
*
33691251 TTATTTCT
1 TTATTTTT
33691259 TTATTATTT
1 TTATT-TTT
*
33691268 ATTATTTGCTA
1 -TTATTT--TT
*
33691279 TT-TTATT
1 TTATTTTT
33691286 TTATTTTT
1 TTATTTTT
33691294 ATTATTTTT
1 -TTATTTTT
33691303 TTATT
1 TTATT
33691308 CTGTTTTTGT
Statistics
Matches: 60, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
7 3 0.05
8 29 0.48
9 20 0.33
10 7 0.12
11 1 0.02
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.76
Consensus pattern (8 bp):
TTATTTTT
Found at i:33694345 original size:15 final size:14
Alignment explanation
Indices: 33694325--33694361 Score: 58
Period size: 13 Copynumber: 2.6 Consensus size: 14
33694315 TTTTGCTTCT
33694325 TCTTCCTTCACATCA
1 TCTTCCTTC-CATCA
33694340 TCTTCCTT-CATCA
1 TCTTCCTTCCATCA
33694353 TCTTCCTTC
1 TCTTCCTTC
33694362 TTCTTCATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 13 0.62
15 8 0.38
ACGTcount: A:0.14, C:0.41, G:0.00, T:0.46
Consensus pattern (14 bp):
TCTTCCTTCCATCA
Found at i:33695899 original size:19 final size:17
Alignment explanation
Indices: 33695861--33695900 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
33695851 ATTACAATGA
*
33695861 AAATATTTGAATTTATT
1 AAATATTTGAATTTAGT
33695878 AAATATTTGAAATTTTAGT
1 AAATATTTG-AA-TTTAGT
33695897 AAAT
1 AAAT
33695901 TTTTATAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 2 0.10
19 9 0.45
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (17 bp):
AAATATTTGAATTTAGT
Found at i:33695941 original size:27 final size:28
Alignment explanation
Indices: 33695911--33695970 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
33695901 TTTTATAGTT
33695911 TTTTTGTAA-TTTTAT-ATTTTTAATATA
1 TTTTTGTAATTTTTATCATTTTTAA-ATA
*
33695938 TTTTTGTAATTTTTTTCATTTTTAAATA
1 TTTTTGTAATTTTTATCATTTTTAAATA
33695966 TTTTT
1 TTTTT
33695971 ATTAGAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 9 0.30
28 13 0.43
29 8 0.27
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.70
Consensus pattern (28 bp):
TTTTTGTAATTTTTATCATTTTTAAATA
Found at i:33695942 original size:28 final size:29
Alignment explanation
Indices: 33695910--33695970 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
33695900 TTTTTATAGT
33695910 TTTTTTGTAA-TTTTAT-ATTTTT-AATA
1 TTTTTTGTAATTTTTATCATTTTTAAATA
*
33695936 TATTTTTGTAATTTTTTTCATTTTTAAATA
1 T-TTTTTGTAATTTTTATCATTTTTAAATA
33695966 TTTTT
1 TTTTT
33695971 ATTAGAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 1 0.03
27 9 0.30
28 5 0.17
29 10 0.33
30 5 0.17
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.70
Consensus pattern (29 bp):
TTTTTTGTAATTTTTATCATTTTTAAATA
Found at i:33700536 original size:46 final size:44
Alignment explanation
Indices: 33700444--33700537 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 44
33700434 ATTACAACAT
*
33700444 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTC
* ***
33700488 CATTCCATTTAACCAAACAGTTGAATTACTTATTACAGCTCTATTC
1 CATTCCATTCAACCAAACACAAGAA-TAC-TATTACAGCTCTATTC
33700534 CATT
1 CATT
33700538 GCAGCTCTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 21 0.49
45 3 0.07
46 19 0.44
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTC
Found at i:33700878 original size:49 final size:49
Alignment explanation
Indices: 33700805--33700935 Score: 131
Period size: 49 Copynumber: 2.7 Consensus size: 49
33700795 CACCTTAAGT
* * * * *
33700805 CGATGCCATGTCTCGGACAGGTCTTACACTAGCT-TGCATATCTTGAG-GC
1 CGATGCCGTGTCCCAGACAGGTCTTACACTAGCTCT-CATATATCG-GTGC
* * * *
33700854 CGATGCCGTGTCCTAGATAGGTCTTACACTGGCTCTCATCTATCGGTGC
1 CGATGCCGTGTCCCAGACAGGTCTTACACTAGCTCTCATATATCGGTGC
* *
33700903 CGATGCCGTGTCCCAGACAGATATTACACTAGC
1 CGATGCCGTGTCCCAGACAGGTCTTACACTAGC
33700936 ACACATATCA
Statistics
Matches: 66, Mismatches: 14, Indels: 4
0.79 0.17 0.05
Matches are distributed among these distances:
48 1 0.02
49 64 0.97
50 1 0.02
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.27
Consensus pattern (49 bp):
CGATGCCGTGTCCCAGACAGGTCTTACACTAGCTCTCATATATCGGTGC
Found at i:33700879 original size:142 final size:141
Alignment explanation
Indices: 33700665--33700919 Score: 343
Period size: 142 Copynumber: 1.8 Consensus size: 141
33700655 CATCTAACTA
*
33700665 GATGCCATGTCCCAGAAAGGTCTTACACGACTTCCATACATCGAGGCCTATGCCATGTCCTAGAC
1 GATGCCATGTCCCAGAAAGGTCTTACACGACTTCCATACATCGAGGCCGATGCCATGTCCTAGAC
* *
33700730 AGCTCTTACACTGGCTCTCA-CTTATCTGTGTCGATGCCATATCCCAGATAGGTCTTACATTGAC
66 AGCTCTTACACTGGCTCTCATC-TATCGGTGCCGATGCCATATCCCAGATAGGTCTTACATTGAC
33700794 ACACCTTAAGTC
130 ACACCTTAAGTC
* * * * * * *
33700806 GATGCCATGTCTCGGACAGGTCTTACACTAGCTTGCATATC-TTGAGGCCGATGCCGTGTCCTAG
1 GATGCCATGTCCCAGAAAGGTCTTACACGA-CTTCCATA-CATCGAGGCCGATGCCATGTCCTAG
* * * *
33700870 ATAGGTCTTACACTGGCTCTCATCTATCGGTGCCGATGCCGTGTCCCAGA
64 ACAGCTCTTACACTGGCTCTCATCTATCGGTGCCGATGCCATATCCCAGA
33700920 CAGATATTAC
Statistics
Matches: 97, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
141 26 0.27
142 69 0.71
143 2 0.02
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (141 bp):
GATGCCATGTCCCAGAAAGGTCTTACACGACTTCCATACATCGAGGCCGATGCCATGTCCTAGAC
AGCTCTTACACTGGCTCTCATCTATCGGTGCCGATGCCATATCCCAGATAGGTCTTACATTGACA
CACCTTAAGTC
Found at i:33708250 original size:45 final size:44
Alignment explanation
Indices: 33708110--33708265 Score: 160
Period size: 41 Copynumber: 3.6 Consensus size: 44
33708100 TGTCGTATAG
* * * *
33708110 TGCCAATGTCTCAGACGTGGTCTTACATGTAATCACAT-ATCGA
1 TGCCAACGTCCCAGACATGGTCTTACACGTAATCACATAATCGA
* * *
33708153 TGCC-ACTTCCCAGACAGGGTCTTACACG-AATCAAAT-A-CGA
1 TGCCAACGTCCCAGACATGGTCTTACACGTAATCACATAATCGA
* * * *
33708193 TGCCGATGTCCCAGACATGTTCTTACACGTAACCACATAAATCGA
1 TGCCAACGTCCCAGACATGGTCTTACACGTAATCACAT-AATCGA
*
33708238 TGCCAACGTCCCAGACGTGGTCTTACAC
1 TGCCAACGTCCCAGACATGGTCTTACAC
33708266 AAGAACACAT
Statistics
Matches: 91, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
40 7 0.08
41 28 0.31
42 24 0.26
43 4 0.04
44 1 0.01
45 27 0.30
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (44 bp):
TGCCAACGTCCCAGACATGGTCTTACACGTAATCACATAATCGA
Found at i:33708278 original size:45 final size:45
Alignment explanation
Indices: 33708110--33708265 Score: 148
Period size: 45 Copynumber: 3.6 Consensus size: 45
33708100 TGTCGTATAG
* * * *
33708110 TGCCAATGTCTCAGACGTGGTCTTACATGTAATCACAT--ATCGA
1 TGCCAACGTCCCAGACGTGGTCTTACACGTAACCACATAAATCGA
* * *
33708153 TGCC-ACTTCCCAGACAG-GGTCTTACACG-AATCA-A-ATA-CGA
1 TGCCAACGTCCCAGAC-GTGGTCTTACACGTAACCACATAAATCGA
* * * *
33708193 TGCCGATGTCCCAGACATGTTCTTACACGTAACCACATAAATCGA
1 TGCCAACGTCCCAGACGTGGTCTTACACGTAACCACATAAATCGA
33708238 TGCCAACGTCCCAGACGTGGTCTTACAC
1 TGCCAACGTCCCAGACGTGGTCTTACAC
33708266 AAGAACACAT
Statistics
Matches: 90, Mismatches: 14, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
40 8 0.09
41 25 0.28
42 22 0.24
43 6 0.07
44 2 0.02
45 27 0.30
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (45 bp):
TGCCAACGTCCCAGACGTGGTCTTACACGTAACCACATAAATCGA
Found at i:33710406 original size:21 final size:22
Alignment explanation
Indices: 33710380--33710420 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
33710370 CTCTTGAAAC
33710380 AGGGGC-ACACGCCAGTGTGGA
1 AGGGGCGACACGCCAGTGTGGA
*
33710401 AGGGGCGACACGCCCGTGTG
1 AGGGGCGACACGCCAGTGTG
33710421 CCCTTCTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.20, C:0.27, G:0.44, T:0.10
Consensus pattern (22 bp):
AGGGGCGACACGCCAGTGTGGA
Found at i:33710881 original size:14 final size:14
Alignment explanation
Indices: 33710864--33710890 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
33710854 AAATATTCTC
33710864 TGGAAAATGATTTT
1 TGGAAAATGATTTT
33710878 TGGAAAATGATTT
1 TGGAAAATGATTT
33710891 ACTTTTCTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (14 bp):
TGGAAAATGATTTT
Found at i:33711063 original size:12 final size:12
Alignment explanation
Indices: 33711048--33711076 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
33711038 TTTTAATTTT
33711048 TTTATTAATAAA
1 TTTATTAATAAA
33711060 TTTATTAATAAA
1 TTTATTAATAAA
33711072 TTTAT
1 TTTAT
33711077 ATTTTAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTTATTAATAAA
Found at i:33712466 original size:32 final size:32
Alignment explanation
Indices: 33712420--33712489 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
33712410 TGTCAATCAT
33712420 TTCAATATCGAACAAGCTTAAAACATAATAAA
1 TTCAATATCGAACAAGCTTAAAACATAATAAA
* *
33712452 TTCAATATCTAACAAGCTTAAAACATAATCAA
1 TTCAATATCGAACAAGCTTAAAACATAATAAA
33712484 TATCAA
1 T-TCAA
33712490 ACAAATTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 31 0.89
33 4 0.11
ACGTcount: A:0.51, C:0.17, G:0.04, T:0.27
Consensus pattern (32 bp):
TTCAATATCGAACAAGCTTAAAACATAATAAA
Found at i:33714031 original size:15 final size:15
Alignment explanation
Indices: 33714011--33714042 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
33714001 TTCTCAAGCA
33714011 ATGACTAAAGTTACC
1 ATGACTAAAGTTACC
33714026 ATGACTAAAGTTACC
1 ATGACTAAAGTTACC
33714041 AT
1 AT
33714043 CATTTAAGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (15 bp):
ATGACTAAAGTTACC
Found at i:33717035 original size:448 final size:448
Alignment explanation
Indices: 33716200--33717545 Score: 2638
Period size: 448 Copynumber: 3.0 Consensus size: 448
33716190 GCATAGGAAC
33716200 CAACAAAAGATAATTGAGAACAATATAATTAAGGCAACAACAATAGGCATTCACATCTCTTTCCC
1 CAACAAAAGATAATTGAGAACAATATAATTAAGGCAACAACAATAGGCATTCACATCTCTTTCCC
33716265 CCTTCAAATGGTTCTCTAAACGTAGTTAGCACAATGCAGTACAACTAGGTTATGAAGTATTACTA
66 CCTTCAAATGGTTCTCTAAACGTAGTTAGCACAATGCAGTACAACTAGGTTATGAAGTATTACTA
33716330 AGGTTTAAAAAGTATGGTCAAACTCTAGGCAAAATAAGCGGCTTATTCAGGTTCCATTCCACCAA
131 AGGTTTAAAAAGTATGGTCAAACTCTAGGCAAAATAAGCGGCTTATTCAGGTTCCATTCCACCAA
*
33716395 AAACCTACTATTTTTAGGTCTTTTTCTGATACCTTGAGACCAATATACTTATTCCCTAGTGCTGA
196 AAACCTACTATTTTTAGGTCTTTTTCTGATACCTTGAGACCAATGTACTTATTCCCTAGTGCTGA
*
33716460 TAGGATTCCTTGGTCTTTATCCTATCCAAATTTGACTTGTTGCATCAAATATCACTTACCACAAT
261 TAGAATTCCTTGGTCTTTATCCTATCCAAATTTGACTTGTTGCATCAAATATCACTTACCACAAT
33716525 TGGTCATGCCTCCAAATTTTTTTAACAATGAAGTAATTAAAAAAGGTATTCAAACTTGATTCCAA
326 TGGTCATGCCTCCAAATTTTTTTAACAATGAAGTAATTAAAAAAGGTATTCAAACTTGATTCCAA
33716590 ACTTAAAACCAAATCTAAAGCTTCTCTATCCTAGTAGATTTCATAAGGTAGGAGGGGG
391 ACTTAAAACCAAATCTAAAGCTTCTCTATCCTAGTAGATTTCATAAGGTAGGAGGGGG
33716648 CAACAAAAGATAATTGAGAACAATATAATTAAGGCAACAACAATAGGCATTCACATCTCTTTCCC
1 CAACAAAAGATAATTGAGAACAATATAATTAAGGCAACAACAATAGGCATTCACATCTCTTTCCC
*
33716713 CCTTCAAATGGTTCTCTAAACGTAGTTAGCACAATGCAGTACAATTAGGTTATGAAGTATTACTA
66 CCTTCAAATGGTTCTCTAAACGTAGTTAGCACAATGCAGTACAACTAGGTTATGAAGTATTACTA
*
33716778 AGGTTTAAAAAGTATGGTCAAACTCTAGGCAAAATAAACGGCTTATTCAGGTTCCATTCCACCAA
131 AGGTTTAAAAAGTATGGTCAAACTCTAGGCAAAATAAGCGGCTTATTCAGGTTCCATTCCACCAA
33716843 AAACCTACTATTTTTAGGTCTTTTTCTGATACCTTGAGACCAATGTACTTATTCCCTAGTGCTGA
196 AAACCTACTATTTTTAGGTCTTTTTCTGATACCTTGAGACCAATGTACTTATTCCCTAGTGCTGA
33716908 TAGAATTCCTTGGTCTTTATCCTATCCAAATTTGACTTGTTGCATCAAATATCACTTACCACAAT
261 TAGAATTCCTTGGTCTTTATCCTATCCAAATTTGACTTGTTGCATCAAATATCACTTACCACAAT
33716973 TGGTCATGCCTCCAAATTTTTTTAACAATGAAGTAATTAAAAAAGGTATTCAAACTTGATTCCAA
326 TGGTCATGCCTCCAAATTTTTTTAACAATGAAGTAATTAAAAAAGGTATTCAAACTTGATTCCAA
*
33717038 ACTTAAAACCAAATCTAAAGCTTCTCTATCCTAGTAGATTTCATAAGTTAGGAGGGGG
391 ACTTAAAACCAAATCTAAAGCTTCTCTATCCTAGTAGATTTCATAAGGTAGGAGGGGG
33717096 CAACAAAAGATAATTGAGAACAATATAATTAAGGCAACAACAATAGGCATTCACATCTCTTTCCC
1 CAACAAAAGATAATTGAGAACAATATAATTAAGGCAACAACAATAGGCATTCACATCTCTTTCCC
33717161 CCTTCAAATGGTTCTCTAAACGTAGTTAGCACAATGCAGTACAACTAGGTTATGAAGTATTACTA
66 CCTTCAAATGGTTCTCTAAACGTAGTTAGCACAATGCAGTACAACTAGGTTATGAAGTATTACTA
33717226 AGGTTTAAAAAGTATGGTCAAACTCTAGGCAAAATAAGCGGCTTATTCAGGTTCCATTCCACCAA
131 AGGTTTAAAAAGTATGGTCAAACTCTAGGCAAAATAAGCGGCTTATTCAGGTTCCATTCCACCAA
33717291 AAACCTACTATTTTTAGGTCTTTTTCTGATACCTTGAGACCAATGTACTTATTCCCTAGTGCTGA
196 AAACCTACTATTTTTAGGTCTTTTTCTGATACCTTGAGACCAATGTACTTATTCCCTAGTGCTGA
33717356 TAGAATTCCTTGGTCTTTATCCTATCCAAATTTGACTTGTTGCATCAAATATCACTTACCACAAT
261 TAGAATTCCTTGGTCTTTATCCTATCCAAATTTGACTTGTTGCATCAAATATCACTTACCACAAT
33717421 TGGTCATGCCTCCAAATTTTTTTAACAATGAAGTAATTAAAAAAGGTATTCAAACTTGATTCCAA
326 TGGTCATGCCTCCAAATTTTTTTAACAATGAAGTAATTAAAAAAGGTATTCAAACTTGATTCCAA
*
33717486 ACTTAAAACCAAATCTAAAGCTTCTCTATCTTAGTAGATTTCATAAGGTAGGAGGGGG
391 ACTTAAAACCAAATCTAAAGCTTCTCTATCCTAGTAGATTTCATAAGGTAGGAGGGGG
33717544 CA
1 CA
33717546 GTGGAATAAA
Statistics
Matches: 889, Mismatches: 9, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
448 889 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (448 bp):
CAACAAAAGATAATTGAGAACAATATAATTAAGGCAACAACAATAGGCATTCACATCTCTTTCCC
CCTTCAAATGGTTCTCTAAACGTAGTTAGCACAATGCAGTACAACTAGGTTATGAAGTATTACTA
AGGTTTAAAAAGTATGGTCAAACTCTAGGCAAAATAAGCGGCTTATTCAGGTTCCATTCCACCAA
AAACCTACTATTTTTAGGTCTTTTTCTGATACCTTGAGACCAATGTACTTATTCCCTAGTGCTGA
TAGAATTCCTTGGTCTTTATCCTATCCAAATTTGACTTGTTGCATCAAATATCACTTACCACAAT
TGGTCATGCCTCCAAATTTTTTTAACAATGAAGTAATTAAAAAAGGTATTCAAACTTGATTCCAA
ACTTAAAACCAAATCTAAAGCTTCTCTATCCTAGTAGATTTCATAAGGTAGGAGGGGG
Found at i:33718801 original size:3 final size:3
Alignment explanation
Indices: 33718724--33718783 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
33718714 GTTGAAGAAT
33718724 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
33718772 AGA AGA AGA AGA
1 AGA AGA AGA AGA
33718784 CTTACCTGGA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:33720067 original size:49 final size:49
Alignment explanation
Indices: 33719850--33720122 Score: 181
Period size: 49 Copynumber: 5.7 Consensus size: 49
33719840 ACATCTAAGT
* * * *
33719850 CGATGCCATGTCCCAAATAGGTCTTACACT-GACATCT-ATACATCGAGGC
1 CGATGCCATGTCCCAGACAGGTCTTACACTAG-C-TCTCATATATCGAGAC
* * * * *
33719899 CTATGCCATGTCCCAGACAGGTTTTACACTGGCTCTCACT-TATCTGTG-T
1 CGATGCCATGTCCCAGACAGGTCTTACACTAGCTCTCA-TATATC-GAGAC
** * * ** *
33719948 CGATGTTATGTCCCAGACAGGTCTTACACTA----ACACACCTCAAG-C
1 CGATGCCATGTCCCAGACAGGTCTTACACTAGCTCTCATATATCGAGAC
* * * * **
33719992 CGATACCATGTCCCAAACAGGTCTTACACTAGCT-TACATATCTTGAGGT
1 CGATGCCATGTCCCAGACAGGTCTTACACTAGCTCT-CATATATCGAGAC
* * * *
33720041 TGATGCCATGTCTCAGACAGGACTTACAC-AGGCTCTCATATATCGATAC
1 CGATGCCATGTCCCAGACAGGTCTTACACTA-GCTCTCATATATCGAGAC
33720090 CGATGCCATGTCCCAGACAGGTCTTACACTAGC
1 CGATGCCATGTCCCAGACAGGTCTTACACTAGC
33720123 ACACACATCA
Statistics
Matches: 169, Mismatches: 42, Indels: 26
0.71 0.18 0.11
Matches are distributed among these distances:
44 28 0.17
45 4 0.02
48 11 0.07
49 120 0.71
50 6 0.04
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (49 bp):
CGATGCCATGTCCCAGACAGGTCTTACACTAGCTCTCATATATCGAGAC
Found at i:33736557 original size:40 final size:39
Alignment explanation
Indices: 33736513--33736697 Score: 187
Period size: 40 Copynumber: 4.6 Consensus size: 39
33736503 GCTACTCGTT
* *
33736513 CAAATGCCTTCGGGACATAGCCCGGTTAAAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTT-TAGTAACTCGCA
* *
33736553 CAAATGCCTTCGGGACTTAACCCGAATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCG-GTTTAGTAACTCGCA
*
33736593 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGG-TTTAGTAACTCGCA
* * * * * *
33736633 CGAATGCCTTC-GGATCTTAGTCCTGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAG-CCCGGTTTAGTAAC-TCGCA
33736674 CAAA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
33736698 ACATCATTCG
Statistics
Matches: 122, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
39 6 0.05
40 102 0.84
41 14 0.11
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTTAGTAACTCGCA
Found at i:33736598 original size:80 final size:81
Alignment explanation
Indices: 33736513--33736698 Score: 213
Period size: 80 Copynumber: 2.3 Consensus size: 81
33736503 GCTACTCGTT
*
33736513 CAAATGCCTTCGGGACATAGCCCGG-TTAAAGTAACTCGCACAAATGCCTTCGGGA-CTTA-ACC
1 CAAATGCCTTCGGGACTTAGCCCGGATT-AAGTAACTCGCACAAATGCCTTC-GGATCTTAGACC
* *
33736575 CGAATTTAGTAAC-TCGCA
64 CG-ATATAGTAACTTAGCA
* * * * *
33736593 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCTTAGTCCT
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTAAGTAACTCGCACAAATGCCTTCGGATCTTAGACCC
*
33736657 GATATAGTCACTTAGCA
65 GATATAGTAACTTAGCA
33736674 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
33736699 CATCATTCGA
Statistics
Matches: 90, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
79 6 0.07
80 68 0.76
81 16 0.18
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTAAGTAACTCGCACAAATGCCTTCGGATCTTAGACCCG
ATATAGTAACTTAGCA
Found at i:33752293 original size:18 final size:19
Alignment explanation
Indices: 33752258--33752295 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
33752248 ATGTATATGG
* *
33752258 TCATCTTTAAATAGATATT
1 TCATCTTTAAAAAAATATT
33752277 TCAT-TTTAAAAAAATATT
1 TCATCTTTAAAAAAATATT
33752295 T
1 T
33752296 TGTACATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (19 bp):
TCATCTTTAAAAAAATATT
Found at i:33752368 original size:2 final size:2
Alignment explanation
Indices: 33752363--33752391 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
33752353 TGTATATACT
33752363 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 T
33752392 TATTTCAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33752631 original size:13 final size:13
Alignment explanation
Indices: 33752613--33752637 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33752603 CTGTTGTTTG
33752613 CTTTGATATGTTC
1 CTTTGATATGTTC
33752626 CTTTGATATGTT
1 CTTTGATATGTT
33752638 TTTGGTGTAT
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:0.16, C:0.12, G:0.16, T:0.56
Consensus pattern (13 bp):
CTTTGATATGTTC
Found at i:33756085 original size:42 final size:42
Alignment explanation
Indices: 33756038--33756117 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
33756028 GTTACTGAGA
* *
33756038 TGTGATTACCTGTAAGACCATGTCTGGGACATTGGCATGTAT
1 TGTGATTACCTGTAAGACCATATCTAGGACATTGGCATGTAT
*
33756080 TGTGATTACGTGTAAGACCATATCTAGGACATTGGCAT
1 TGTGATTACCTGTAAGACCATATCTAGGACATTGGCAT
33756118 CGTTATTCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (42 bp):
TGTGATTACCTGTAAGACCATATCTAGGACATTGGCATGTAT
Found at i:33760897 original size:12 final size:12
Alignment explanation
Indices: 33760880--33760904 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33760870 CCCAGCCATT
33760880 TTTTCTTCACTA
1 TTTTCTTCACTA
33760892 TTTTCTTCACTA
1 TTTTCTTCACTA
33760904 T
1 T
33760905 ATAACAACAT
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:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTTCTTCACTA
Found at i:33762410 original size:117 final size:117
Alignment explanation
Indices: 33762238--33762448 Score: 368
Period size: 117 Copynumber: 1.8 Consensus size: 117
33762228 GGTAACAGAA
* *
33762238 ATCAACAACATCGAGACCACTGTCGCATCACAAATTGATAAAACAAACCCTATATTGTGGCACTG
1 ATCAACAACATCGAGACCACTGTCGCATCACAAATCGACAAAACAAACCCTATATTGTGGCACTG
33762303 AAATTGCAATAATAAATCACAAATAACCATAAACAATTTTAATAACAGCTTT
66 AAATTGCAATAATAAATCACAAATAACCATAAACAATTTTAATAACAGCTTT
* * * *
33762355 ATCAATAACATCGGGACCATTGTCGCATCACAAATCGACAAAACAAGCCCTATATTGTGGCACTG
1 ATCAACAACATCGAGACCACTGTCGCATCACAAATCGACAAAACAAACCCTATATTGTGGCACTG
33762420 AAATTGCAATAATAAATCACAAATAACCA
66 AAATTGCAATAATAAATCACAAATAACCA
33762449 ACAAACCAAA
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
117 88 1.00
ACGTcount: A:0.44, C:0.22, G:0.11, T:0.23
Consensus pattern (117 bp):
ATCAACAACATCGAGACCACTGTCGCATCACAAATCGACAAAACAAACCCTATATTGTGGCACTG
AAATTGCAATAATAAATCACAAATAACCATAAACAATTTTAATAACAGCTTT
Found at i:33762687 original size:16 final size:16
Alignment explanation
Indices: 33762635--33762687 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
33762625 GAATACTAAT
33762635 GATTTAGGGATTTCAA
1 GATTTAGGGATTTCAA
* * *
33762651 AATTT-GAAGATTTTAA
1 GATTTAG-GGATTTCAA
*
33762667 TATTTAGGGATTTCAA
1 GATTTAGGGATTTCAA
33762683 GATTT
1 GATTT
33762688 TAGGAATTCA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
15 1 0.04
16 26 0.93
17 1 0.04
ACGTcount: A:0.34, C:0.04, G:0.19, T:0.43
Consensus pattern (16 bp):
GATTTAGGGATTTCAA
Found at i:33763737 original size:20 final size:21
Alignment explanation
Indices: 33763712--33763750 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
33763702 TCCAAGCTTT
33763712 AAAAAA-TAAACTTTTTTTAA
1 AAAAAATTAAACTTTTTTTAA
*
33763732 AAAAAATTTAACTTTTTTT
1 AAAAAATTAAACTTTTTTT
33763751 TGTTGCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (21 bp):
AAAAAATTAAACTTTTTTTAA
Found at i:33764870 original size:29 final size:29
Alignment explanation
Indices: 33764828--33764886 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
33764818 CAATGCAAAG
33764828 ATAAGTTTTTACTTCAAAGTGTGGTCACT
1 ATAAGTTTTTACTTCAAAGTGTGGTCACT
*
33764857 ATAAGTTTTTACTTCAACGTGTGGTCACT
1 ATAAGTTTTTACTTCAAAGTGTGGTCACT
33764886 A
1 A
33764887 GTCCCGGAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (29 bp):
ATAAGTTTTTACTTCAAAGTGTGGTCACT
Found at i:33772243 original size:13 final size:13
Alignment explanation
Indices: 33772227--33772300 Score: 51
Period size: 13 Copynumber: 5.7 Consensus size: 13
33772217 GATGAAACAA
*
33772227 TTATATGAATTGG
1 TTATATGAAATGG
*
33772240 TTATACGAAATGG
1 TTATATGAAATGG
* * * *
33772253 TTACAGGGAATGA
1 TTATATGAAATGG
*
33772266 TTACATGAAATGG
1 TTATATGAAATGG
*
33772279 TTATGA-GAATTGG
1 TTAT-ATGAAATGG
*
33772292 TTATGTGAA
1 TTATATGAA
33772301 GATATATGTA
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
13 46 0.98
14 1 0.02
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (13 bp):
TTATATGAAATGG
Found at i:33774031 original size:4 final size:4
Alignment explanation
Indices: 33773990--33774486 Score: 644
Period size: 4 Copynumber: 127.8 Consensus size: 4
33773980 TAACGGACAC
* * * * *
33773990 ACAT ACAC ACAT ACAC ACAT ACAC ACAT ACAC ACAT ACAT ACAT ACAC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * *
33774038 ACAT ACAT ACAT AC-- ACAC ACAT ACAC ACAT ACAT AC-- ACAC ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * *
33774082 ACAC ACAT AC-- ACAT ACAT ACAT ACAT ACAT ACAC ACAT ACAC ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
33774128 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
33774176 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * *
33774224 ACAT ACAC ACAT GCAT ACAC ACAT ACAT ACAC ACAT AC-- ACAC ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * *
33774270 ACAC ACAT ACAT ACAC ACAT ACAT ACAC ACAT AC-- ACAT ACAC ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * *
33774316 ACAT ACAC ACAT ACAT AC-- ACAC ACAT ACAC ACAT AC-- ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * *
33774360 ACAT ACAT ATAT ACAC ACAT ACAC ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
33774408 ACAT ACAC ACAT ACAC ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
33774456 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
33774487 ACTCCTCAAG
Statistics
Matches: 427, Mismatches: 52, Indels: 28
0.84 0.10 0.06
Matches are distributed among these distances:
2 14 0.03
4 413 0.97
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (4 bp):
ACAT
Found at i:33776247 original size:44 final size:42
Alignment explanation
Indices: 33776183--33776347 Score: 163
Period size: 43 Copynumber: 3.9 Consensus size: 42
33776173 ATATGTGTTA
* *
33776183 TCGTGTAAGACCACGTCTGGGACGTTGGCATTG-ACTTATGATT
1 TCGTGTAAGACCATGTCTGGGACGTTGGCATCGTA-TT-TGATT
* *
33776226 TACGTGTAAGTCCATGTCTGGGATGTTGGCATCGTATTTGATT
1 T-CGTGTAAGACCATGTCTGGGACGTTGGCATCGTATTTGATT
*
33776269 TCGTGTAAGACCCTGTCTGGGACAG-TGGCATCGATATTTGATT
1 TCGTGTAAGACCATGTCTGGGAC-GTTGGCATCG-TATTTGATT
* *** * * *
33776312 ACAAATTAGACCACGTCTGGGACGTTGGCATTGTAT
1 TCGTGTAAGACCATGTCTGGGACGTTGGCATCGTAT
33776348 GAGGTTTCTG
Statistics
Matches: 102, Mismatches: 15, Indels: 11
0.80 0.12 0.09
Matches are distributed among these distances:
42 31 0.30
43 40 0.39
44 30 0.29
45 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (42 bp):
TCGTGTAAGACCATGTCTGGGACGTTGGCATCGTATTTGATT
Found at i:33776287 original size:42 final size:42
Alignment explanation
Indices: 33776183--33776311 Score: 138
Period size: 44 Copynumber: 3.0 Consensus size: 42
33776173 ATATGTGTTA
* *
33776183 TCGTGTAAGACCAC-GTCTGGGACGTTGGCATTG-ACTTATGATT
1 TCGTGTAAGACC-CTGTCTGGGAAGTTGGCATCGTA-TT-TGATT
* * *
33776226 TACGTGTAAGTCCATGTCTGGGATGTTGGCATCGTATTTGATT
1 T-CGTGTAAGACCCTGTCTGGGAAGTTGGCATCGTATTTGATT
33776269 TCGTGTAAGACCCTGTCTGGGACAG-TGGCATCGATATTTGATT
1 TCGTGTAAGACCCTGTCTGGGA-AGTTGGCATCG-TATTTGATT
33776312 ACAAATTAGA
Statistics
Matches: 74, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
42 27 0.36
43 17 0.23
44 29 0.39
45 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.35
Consensus pattern (42 bp):
TCGTGTAAGACCCTGTCTGGGAAGTTGGCATCGTATTTGATT
Found at i:33778948 original size:18 final size:18
Alignment explanation
Indices: 33778910--33778948 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
33778900 AACTTACTGA
*
33778910 GCTTTATGCCTACTTTAT
1 GCTTTATGCCTACTATAT
* *
33778928 GCTTTATGCTTACTATGT
1 GCTTTATGCCTACTATAT
33778946 GCT
1 GCT
33778949 CATGTCTTGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.15, C:0.21, G:0.15, T:0.49
Consensus pattern (18 bp):
GCTTTATGCCTACTATAT
Found at i:33785715 original size:46 final size:47
Alignment explanation
Indices: 33785623--33785799 Score: 173
Period size: 47 Copynumber: 3.8 Consensus size: 47
33785613 TGGGTAAAGT
* * * *
33785623 GCCGATGCCATGTCCCAGACATGGTCTTACTCTGGCTCACATCTCAA
1 GCCGATGTCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAA
** *
33785670 GTAGATGTCATGTCCCAGACAT-GTCTTACACTAGCTCTCGTCTCAA
1 GCCGATGTCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAA
* * * * **
33785716 TGCCGATG-CTATATCCCAGGCATGGTCTTACACTGGCTCTCATAATGTA
1 -GCCGATGTC-ATGTCCCAGACATGGTCTTACACTAGCTCTCAT-CTCAA
*
33785765 GCCGAT-TCATGTCTCAGACAT-GTCTTACACTAGCT
1 GCCGATGTCATGTCCCAGACATGGTCTTACACTAGCT
33785800 TACACACAAA
Statistics
Matches: 105, Mismatches: 20, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
46 34 0.32
47 45 0.43
48 24 0.23
49 2 0.02
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (47 bp):
GCCGATGTCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAA
Found at i:33785783 original size:94 final size:94
Alignment explanation
Indices: 33785622--33785799 Score: 241
Period size: 94 Copynumber: 1.9 Consensus size: 94
33785612 ATGGGTAAAG
* * * *
33785622 TGCCGATGCCATGTCCCAGACATGGTCTTACTCTGGCTCACATCTCAAGTAGATGTCATGTCCCA
1 TGCCGATGCCATATCCCAGACATGGTCTTACACTGGCTCACATATCAAGCAGATGTCATGTCCCA
33785687 GACATGTCTTACACTAGCTCTCGTCTCAA
66 GACATGTCTTACACTAGCTCTCGTCTCAA
* * * ** * *
33785716 TGCCGATGCTATATCCCAGGCATGGTCTTACACTGGCTCTCATAATGTAGCCGAT-TCATGTCTC
1 TGCCGATGCCATATCCCAGACATGGTCTTACACTGGCTCACAT-ATCAAGCAGATGTCATGTCCC
33785780 AGACATGTCTTACACTAGCT
65 AGACATGTCTTACACTAGCT
33785800 TACACACAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
94 66 0.92
95 6 0.08
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.30
Consensus pattern (94 bp):
TGCCGATGCCATATCCCAGACATGGTCTTACACTGGCTCACATATCAAGCAGATGTCATGTCCCA
GACATGTCTTACACTAGCTCTCGTCTCAA
Found at i:33793112 original size:21 final size:19
Alignment explanation
Indices: 33793078--33793118 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
33793068 TTTAACCTTA
*
33793078 TTTATAATTTATATTATTT
1 TTTATAATTTATATAATTT
33793097 TTTATAATTGTTATATAATTT
1 TTTATAA-T-TTATATAATTT
33793118 T
1 T
33793119 GTTTTTCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 1 0.05
21 11 0.58
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTATAATTTATATAATTT
Found at i:33799078 original size:60 final size:60
Alignment explanation
Indices: 33799014--33799127 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
33799004 ATTTAATACA
* *
33799014 TGAGTTTGGCTTCAATATTCAAATTGGTATTTAAGTTTTCTTTTA-TTCCAATTAGGCACT
1 TGAGTTTAGCTTCAATATTCAAATTGGTATTTAAGTTTT-TTCTAGTTCCAATTAGGCACT
** * *
33799074 TGAGTTTAGCTTTGATGTTCAATTTGGTATTTAAGTTTTTTCTAGTTCCAATTA
1 TGAGTTTAGCTTCAATATTCAAATTGGTATTTAAGTTTTTTCTAGTTCCAATTA
33799128 AAGTACTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 4 0.09
60 43 0.91
ACGTcount: A:0.24, C:0.11, G:0.16, T:0.49
Consensus pattern (60 bp):
TGAGTTTAGCTTCAATATTCAAATTGGTATTTAAGTTTTTTCTAGTTCCAATTAGGCACT
Done.