Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 59 of 255
Found at i:16939778 original size:5 final size:5
Alignment explanation
Indices: 16939768--16939796 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
16939758 CAAGTAATTT
16939768 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
16939797 TATATGCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:16940716 original size:18 final size:18
Alignment explanation
Indices: 16940693--16940728 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
16940683 CATAGCATCA
16940693 ATAGGCATTCAAACCAAT
1 ATAGGCATTCAAACCAAT
16940711 ATAGGCATTCAAACCAAT
1 ATAGGCATTCAAACCAAT
16940729 CTCATCTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.22, G:0.11, T:0.22
Consensus pattern (18 bp):
ATAGGCATTCAAACCAAT
Found at i:16943626 original size:29 final size:29
Alignment explanation
Indices: 16943563--16943630 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
16943553 TAATCAACCG
16943563 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
16943592 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
16943621 CGCACACTTA
1 CGCACACTTA
16943631 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:16943743 original size:174 final size:174
Alignment explanation
Indices: 16943452--16943779 Score: 602
Period size: 174 Copynumber: 1.9 Consensus size: 174
16943442 AACTCAAGGT
* *
16943452 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
16943517 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
16943582 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
16943626 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
16943691 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
*
16943756 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
16943780 TGTACAATTT
Statistics
Matches: 148, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
174 148 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:16943771 original size:29 final size:30
Alignment explanation
Indices: 16943732--16943810 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
16943722 CTTAATAATC
16943732 AACCACGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
16943762 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
16943791 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
16943811 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:16945867 original size:19 final size:19
Alignment explanation
Indices: 16945843--16945882 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
16945833 TGTGTTATCA
*
16945843 TAAATTCATAGGCATAACT
1 TAAATTCATAGACATAACT
**
16945862 TAAATTTGTAGACATAACT
1 TAAATTCATAGACATAACT
16945881 TA
1 TA
16945883 CACAATTTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (19 bp):
TAAATTCATAGACATAACT
Found at i:16946653 original size:16 final size:18
Alignment explanation
Indices: 16946632--16946665 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
16946622 CAAATTCACC
16946632 TTATTC-AATCA-TCAAA
1 TTATTCAAATCAGTCAAA
16946648 TTATTCAAATCAGTCAAA
1 TTATTCAAATCAGTCAAA
16946666 AAAATTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 5 0.31
18 5 0.31
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.35
Consensus pattern (18 bp):
TTATTCAAATCAGTCAAA
Found at i:16948922 original size:22 final size:22
Alignment explanation
Indices: 16948897--16948938 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
16948887 ATAGGTTACG
*
16948897 GTACTATTTTCTCATAGCTTCT
1 GTACCATTTTCTCATAGCTTCT
16948919 GTACCATTTTCTCATAGCTT
1 GTACCATTTTCTCATAGCTT
16948939 TTTTGGGTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.24, G:0.10, T:0.48
Consensus pattern (22 bp):
GTACCATTTTCTCATAGCTTCT
Found at i:16951077 original size:42 final size:41
Alignment explanation
Indices: 16951018--16951172 Score: 175
Period size: 42 Copynumber: 3.7 Consensus size: 41
16951008 CTAAGTCTAT
* * * *
16951018 GTGTAAGACCGTATCTGGGATATGGCATCAATATGGGACTTC
1 GTGTAAGACCATATCTGGGATATGGCATCGATAAGAGA-TTC
*
16951060 GTGTAAGACCATATCTGGGATATGGCATCGATAAGACATTTC
1 GTGTAAGACCATATCTGGGATATGGCATCGATAAGAGA-TTC
* * * * *
16951102 GTGTAAGACAATAGCTAGGCTATTGGCATCGATACGAGATTAC
1 GTGTAAGACCATATCTGGGATA-TGGCATCGATAAGAGATT-C
*
16951145 ATGTAAGACCATATCTGGGATATGGCAT
1 GTGTAAGACCATATCTGGGATATGGCAT
16951173 TGGCATGGTA
Statistics
Matches: 94, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
42 62 0.66
43 32 0.34
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (41 bp):
GTGTAAGACCATATCTGGGATATGGCATCGATAAGAGATTC
Found at i:16955270 original size:40 final size:40
Alignment explanation
Indices: 16955215--16955461 Score: 422
Period size: 40 Copynumber: 6.2 Consensus size: 40
16955205 AACCCAAGTA
*
16955215 CCTTCGGGATTTAGCCCGGATATAGCAACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATG
*
16955255 CCTTCGGGATTTAGCCCGGATATAGCAACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATG
* *
16955295 CCTTCGGGACTTAGCTCGGATATAGTAACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATG
*
16955335 CCTTTGGGACTTAGCCCGGATATAGCAACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATG
*
16955375 CCTTCGGGATTTAGCCCGGATATAGCAACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATG
* *
16955415 CCTTCGGGACTTAGCCCGGATATAGTAACTAGGACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATG
16955455 CCTTCGG
1 CCTTCGG
16955462 ATCTTAGTTC
Statistics
Matches: 196, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 196 1.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATG
Found at i:16956275 original size:19 final size:19
Alignment explanation
Indices: 16956223--16956278 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
16956213 ATAAGTATAA
*
16956223 GTTCAATATAAACTCACAT
1 GTTCAATATAAATTCACAT
* *
16956242 G-T-AA-CTAAATACACAT
1 GTTCAATATAAATTCACAT
16956258 GTTCAATATAAATTCACAT
1 GTTCAATATAAATTCACAT
16956277 GT
1 GT
16956279 AATCGAATAC
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
16 10 0.34
17 3 0.10
18 3 0.10
19 13 0.45
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (19 bp):
GTTCAATATAAATTCACAT
Found at i:16957770 original size:28 final size:25
Alignment explanation
Indices: 16957746--16957797 Score: 68
Period size: 28 Copynumber: 2.0 Consensus size: 25
16957736 AGTACTGTGT
16957746 TAGTGGCTTTGCCACGTAATTACTGCTC
1 TAGTGGCTTTGCCACGT--TTACTG-TC
*
16957774 TGGTGGCTTTGCCACGTTTACTGT
1 TAGTGGCTTTGCCACGTTTACTGT
16957798 TATTAGTAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 1 0.04
26 6 0.26
28 16 0.70
ACGTcount: A:0.13, C:0.23, G:0.25, T:0.38
Consensus pattern (25 bp):
TAGTGGCTTTGCCACGTTTACTGTC
Found at i:16957976 original size:28 final size:27
Alignment explanation
Indices: 16957945--16957997 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
16957935 ATACTAAATT
* *
16957945 GGGCTTAGGCCCATACTGTTACTGTATA
1 GGGCTAAGGCCCAGACTG-TACTGTATA
*
16957973 GGGCTAAGGCCGAGACTGTACTGTA
1 GGGCTAAGGCCCAGACTGTACTGTA
16957998 CTGAATAGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 7 0.32
28 15 0.68
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (27 bp):
GGGCTAAGGCCCAGACTGTACTGTATA
Found at i:16958006 original size:32 final size:33
Alignment explanation
Indices: 16957958--16958021 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
16957948 CTTAGGCCCA
*
16957958 TACTGTTACTGTATAGGGCTAAGGCCGAGACTG
1 TACTGTTACTGAATAGGGCTAAGGCCGAGACTG
* *
16957991 TACTG-TACTGAATAGGGCTCAGGCCTAGACT
1 TACTGTTACTGAATAGGGCTAAGGCCGAGACT
16958022 ATTACTGCGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 23 0.82
33 5 0.18
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (33 bp):
TACTGTTACTGAATAGGGCTAAGGCCGAGACTG
Found at i:16963541 original size:43 final size:42
Alignment explanation
Indices: 16963419--16963569 Score: 187
Period size: 42 Copynumber: 3.6 Consensus size: 42
16963409 TAAGTCTATG
** * * *
16963419 TGTAAGACCATATCTGGGATATGATATCAATATGAGACTTCA
1 TGTAAGACCATATCTGGGATATGGCATCGATAAGAGATTTCA
*
16963461 TGTAAGACCATATCTGGGATATGGCATCGATAAGAGATTTCG
1 TGTAAGACCATATCTGGGATATGGCATCGATAAGAGATTTCA
* * *
16963503 TGTAAGACCATAGCT-GGACTATTGGCATCGATACGAGATTACA
1 TGTAAGACCATATCTGGGA-TA-TGGCATCGATAAGAGATTTCA
*
16963546 TGTAAGACCATATCTGGTATATGG
1 TGTAAGACCATATCTGGGATATGG
16963570 TATTGGTATG
Statistics
Matches: 94, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
41 3 0.03
42 55 0.59
43 34 0.36
44 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.29
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGATATGGCATCGATAAGAGATTTCA
Found at i:16969613 original size:19 final size:19
Alignment explanation
Indices: 16969569--16969615 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
16969559 AAAACTTTGG
*
16969569 AAAAATATTAGAATACATA
1 AAAAATTTTAGAATACATA
16969588 AAAAATTTTAGCAA-ACATA
1 AAAAATTTTAG-AATACATA
16969607 AAAAATTTT
1 AAAAATTTT
16969616 TAAAATACAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 24 0.92
20 2 0.08
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (19 bp):
AAAAATTTTAGAATACATA
Found at i:16981118 original size:23 final size:22
Alignment explanation
Indices: 16981076--16981120 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
16981066 TATTTATTTA
16981076 TTTTTATATTAAATAAATATAAT
1 TTTTTATATTAAAT-AATATAAT
16981099 TTTTTATATATACAAT-ATATAA
1 TTTTTATAT-TA-AATAATATAA
16981121 ATATAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 15 0.75
24 2 0.10
25 3 0.15
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTTATATTAAATAATATAAT
Found at i:16981148 original size:12 final size:12
Alignment explanation
Indices: 16981133--16981158 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16981123 ATAAAATTTG
16981133 TTATATTAATAA
1 TTATATTAATAA
16981145 TTATATTAATAA
1 TTATATTAATAA
16981157 TT
1 TT
16981159 TTAAAAAATT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TTATATTAATAA
Found at i:16981231 original size:29 final size:27
Alignment explanation
Indices: 16981178--16981254 Score: 73
Period size: 29 Copynumber: 2.7 Consensus size: 27
16981168 TTAATCAAAT
16981178 TAAAATTTTATATATAAAATTATATAAAAA
1 TAAAA-TTTATATAT--AATTATATAAAAA
* *
16981208 TAAAATTTATATATAATTAGATATTAAAT
1 TAAAATTTATATATAATT--ATATAAAAA
* *
16981237 TATAATTCATATATAATT
1 TAAAATTTATATATAATT
16981255 TTAATATTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 4 0.10
29 32 0.78
30 5 0.12
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (27 bp):
TAAAATTTATATATAATTATATAAAAA
Found at i:16982189 original size:17 final size:17
Alignment explanation
Indices: 16982169--16982210 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
16982159 TTTGAAGAGT
16982169 TTTTATTTTTTTCATAA
1 TTTTATTTTTTTCATAA
*
16982186 TTTT-TTATTTTTCATAT
1 TTTTATT-TTTTTCATAA
16982203 TTTTATTT
1 TTTTATTT
16982211 AAAATATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 2 0.09
17 18 0.82
18 2 0.09
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTATTTTTTTCATAA
Found at i:16982207 original size:15 final size:17
Alignment explanation
Indices: 16982176--16982210 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
16982166 AGTTTTTATT
16982176 TTTTTCATAATTTTTTA
1 TTTTTCATAATTTTTTA
16982193 TTTTTCAT-A-TTTTTA
1 TTTTTCATAATTTTTTA
16982208 TTT
1 TTT
16982211 AAAATATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 1 0.06
17 8 0.44
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTCATAATTTTTTA
Found at i:16983010 original size:64 final size:64
Alignment explanation
Indices: 16982909--16983042 Score: 259
Period size: 64 Copynumber: 2.1 Consensus size: 64
16982899 TTTCTCACCA
*
16982909 AAATTTTTGTGAGGCAAATTTTGGTGCCAAGCATATAATGACGTAAATTTATACACATTTGTTG
1 AAATTATTGTGAGGCAAATTTTGGTGCCAAGCATATAATGACGTAAATTTATACACATTTGTTG
16982973 AAATTATTGTGAGGCAAATTTTGGTGCCAAGCATATAATGACGTAAATTTATACACATTTGTTG
1 AAATTATTGTGAGGCAAATTTTGGTGCCAAGCATATAATGACGTAAATTTATACACATTTGTTG
16983037 AAATTA
1 AAATTA
16983043 ATGTATATTA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 69 1.00
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (64 bp):
AAATTATTGTGAGGCAAATTTTGGTGCCAAGCATATAATGACGTAAATTTATACACATTTGTTG
Found at i:16987652 original size:20 final size:20
Alignment explanation
Indices: 16987627--16987664 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
16987617 GAAACATATA
16987627 TCATGAACTCAGACCACAAC
1 TCATGAACTCAGACCACAAC
* *
16987647 TCATGAGCTCAGATCACA
1 TCATGAACTCAGACCACA
16987665 TAGTTCCTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.32, G:0.13, T:0.18
Consensus pattern (20 bp):
TCATGAACTCAGACCACAAC
Found at i:16987906 original size:9 final size:9
Alignment explanation
Indices: 16987892--16987918 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
16987882 ACATGCAATA
16987892 TTAAAGTAT
1 TTAAAGTAT
16987901 TTAAAGTAT
1 TTAAAGTAT
16987910 TTAAAGTAT
1 TTAAAGTAT
16987919 GGTACATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (9 bp):
TTAAAGTAT
Found at i:16991379 original size:40 final size:40
Alignment explanation
Indices: 16991335--16991410 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
16991325 CGGCTAAGAA
* *
16991335 TGGCACTTAGTGTGCGGTTTGAAATAGCTTCGGCTAAATG
1 TGGCACTTAGTGTACGATTTGAAATAGCTTCGGCTAAATG
* *
16991375 TGGCACTTGGTGTACGATTTGAGATAGCTTCGGCTA
1 TGGCACTTAGTGTACGATTTGAAATAGCTTCGGCTA
16991411 TATATGCGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.33
Consensus pattern (40 bp):
TGGCACTTAGTGTACGATTTGAAATAGCTTCGGCTAAATG
Found at i:16991452 original size:28 final size:28
Alignment explanation
Indices: 16991415--16991483 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
16991405 CGGCTATATA
* * *
16991415 TGCGAAATATTGAGAATGGCACTTGGTG
1 TGCGAGATATTGAGAATGGAACTTAGTG
* *
16991443 TGCGAGATATTTAGTATGGAACTTAGTG
1 TGCGAGATATTGAGAATGGAACTTAGTG
*
16991471 TGTGAGATATTGA
1 TGCGAGATATTGA
16991484 AGATGCAACG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.29, C:0.07, G:0.30, T:0.33
Consensus pattern (28 bp):
TGCGAGATATTGAGAATGGAACTTAGTG
Found at i:17001218 original size:47 final size:47
Alignment explanation
Indices: 17001167--17001342 Score: 246
Period size: 47 Copynumber: 3.7 Consensus size: 47
17001157 TTAGGATTCT
* * *
17001167 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
17001214 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
17001261 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCTAATGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * *
17001308 ACGTGATGGATGTGAATGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
17001343 TCCCGAAGGG
Statistics
Matches: 116, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
46 1 0.01
47 115 0.99
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:17001516 original size:37 final size:37
Alignment explanation
Indices: 17001460--17001538 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
17001450 CCGAGCTCTA
* * * *
17001460 AAGACCCGATGAGTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
17001497 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
17001534 AAGAC
1 AAGAC
17001539 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:17003476 original size:40 final size:39
Alignment explanation
Indices: 17003392--17003575 Score: 158
Period size: 40 Copynumber: 4.6 Consensus size: 39
17003382 TTGAATGATG
* * * * *
17003392 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGACTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
*
17003432 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGACTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
17003472 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGACTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
17003511 TCC-GAGTTAAGTCCCGAAGGCATTTGTTCAAGTTACTATAA
1 TCCGGA-CTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
17003552 -CCGGGCTAAGTCCCGAAGAGCATT
1 TCCGGACTAAGT-CCGAAG-GCATT
17003576 CATGCTAGTG
Statistics
Matches: 119, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
38 1 0.01
39 32 0.27
40 70 0.59
41 16 0.13
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (39 bp):
TCCGGACTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:17003597 original size:40 final size:40
Alignment explanation
Indices: 17003552--17003786 Score: 326
Period size: 40 Copynumber: 5.9 Consensus size: 40
17003542 GTTACTATAA
17003552 CCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTAT
1 CCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTAT
* * *
17003592 TCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTAT
17003632 CCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTAT
1 CCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTAT
* * *
17003672 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATAT
1 CCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTAT
* ** * * * *
17003712 CCGTGCTAAACCCCGAAGAGCATTCGTGCTGGTGTTATAT
1 CCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTAT
* * *
17003752 CCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 CCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
17003787 CGTGTATTCG
Statistics
Matches: 173, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 173 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTAT
Found at i:17003636 original size:80 final size:80
Alignment explanation
Indices: 17003392--17003773 Score: 355
Period size: 80 Copynumber: 4.8 Consensus size: 80
17003382 TTGAATGATG
** ** * *
17003392 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAG-GCA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGTGA-TGTATCCGGGCTAAGTTCCGAAGAGCA
* * *
17003454 TTTGTGCGAGTTACTA-A
64 TTCGTGCTAGTGA-TATA
** * * ** * * *
17003471 TTCCGGGCTAAG-CCCGAAG-GCATTGGTGCGAGTTACTAAATCCGAGTTAAGTCCCGAAG-GCA
1 -TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA-TGTATCCGGGCTAAGTTCCGAAGAGCA
* * * *
17003533 TTTGTTCAAGTTACTATA
64 TTCGTGCTAGTGA-TATA
* *
17003551 ACCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATTCGGGCTAAGTTCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATT
*
17003616 CGTGCTAGTGATGTA
66 CGTGCTAGTGATATA
17003631 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATT
17003696 CGTGCTAGTGATATA
66 CGTGCTAGTGATATA
* ** * * * * * *
17003711 TCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAGGTCCCGAAGAGCA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCA
17003774 ATCATGCTGG
Statistics
Matches: 257, Mismatches: 40, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
79 57 0.22
80 176 0.68
81 24 0.09
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATT
CGTGCTAGTGATATA
Found at i:17016078 original size:11 final size:10
Alignment explanation
Indices: 17016053--17016113 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
17016043 ACCAATAAAA
17016053 TAAA-TGAGC
1 TAAATTGAGC
*
17016062 TGAATTGTAGC
1 TAAATTG-AGC
17016073 TAAATTGAGC
1 TAAATTGAGC
**
17016083 TCGATTGAGC
1 TAAATTGAGC
17016093 TGAAA-TGAGC
1 T-AAATTGAGC
*
17016103 TCAATTGAGC
1 TAAATTGAGC
17016113 T
1 T
17016114 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:17016114 original size:20 final size:20
Alignment explanation
Indices: 17016054--17016114 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
17016044 CCAATAAAAT
*
17016054 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
17016074 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
17016095 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
17016115 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:17017200 original size:15 final size:13
Alignment explanation
Indices: 17017180--17017241 Score: 72
Period size: 13 Copynumber: 4.5 Consensus size: 13
17017170 CCGTATGCAA
17017180 TTTTTTTTTCAAAAT
1 TTTTTTTTTC--AAT
17017195 TTTTTTTTTCAAT
1 TTTTTTTTTCAAT
*
17017208 TTTTTTTTCTCGA-
1 TTTTTTTT-TCAAT
17017221 TTTTTTTTTCTAAT
1 TTTTTTTTTC-AAT
17017235 TTTTTTT
1 TTTTTTT
17017242 GAATCTACAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
12 2 0.05
13 20 0.48
14 10 0.24
15 10 0.24
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTCAAT
Found at i:17017207 original size:27 final size:26
Alignment explanation
Indices: 17017177--17017241 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 26
17017167 AGACCGTATG
17017177 CAATTTTTTTTTCAAAATTTTTTTTTT
1 CAATTTTTTTTTCAAAA-TTTTTTTTT
***
17017204 CAATTTTTTTTTCTCGATTTTTTTTT
1 CAATTTTTTTTTCAAAATTTTTTTTT
17017230 CTAATTTTTTTT
1 C-AATTTTTTTT
17017242 GAATCTACAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 10 0.29
27 24 0.71
ACGTcount: A:0.17, C:0.09, G:0.02, T:0.72
Consensus pattern (26 bp):
CAATTTTTTTTTCAAAATTTTTTTTT
Found at i:17023656 original size:24 final size:25
Alignment explanation
Indices: 17023603--17023656 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
17023593 AACAAATTCT
* *
17023603 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
17023628 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
17023651 TTTTTT
1 TTTTTT
17023657 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:17029031 original size:19 final size:19
Alignment explanation
Indices: 17029009--17029052 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
17028999 TTCTCTCTCA
17029009 TTTTTACCTGA-TTCTTTTC
1 TTTTT-CCTGATTTCTTTTC
* *
17029028 TTTTTTCTGATTTGTTTTC
1 TTTTTCCTGATTTCTTTTC
17029047 TTTTTC
1 TTTTTC
17029053 TTGCTCACTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.07, C:0.16, G:0.07, T:0.70
Consensus pattern (19 bp):
TTTTTCCTGATTTCTTTTC
Found at i:17029037 original size:18 final size:19
Alignment explanation
Indices: 17029016--17029051 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
17029006 TCATTTTTAC
17029016 CTGA-TTCTTTTCTTTTTT
1 CTGATTTCTTTTCTTTTTT
*
17029034 CTGATTTGTTTTCTTTTT
1 CTGATTTCTTTTCTTTTT
17029052 CTTGCTCACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.06, C:0.14, G:0.08, T:0.72
Consensus pattern (19 bp):
CTGATTTCTTTTCTTTTTT
Found at i:17032939 original size:20 final size:20
Alignment explanation
Indices: 17032916--17032969 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
17032906 AGTTTTTCCC
*
17032916 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
17032936 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
17032956 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
17032970 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:17032951 original size:30 final size:30
Alignment explanation
Indices: 17032916--17032989 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
17032906 AGTTTTTCCC
17032916 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
17032946 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
17032976 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
17032990 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:17032979 original size:20 final size:20
Alignment explanation
Indices: 17032916--17032980 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
17032906 AGTTTTTCCC
* * * *
17032916 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
17032936 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
17032955 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
17032976 AGCTC
1 AGCTC
17032981 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:17034593 original size:10 final size:10
Alignment explanation
Indices: 17034578--17034643 Score: 60
Period size: 10 Copynumber: 6.1 Consensus size: 10
17034568 ATTGGAGTAA
17034578 CAAAAAAAAT
1 CAAAAAAAAT
*
17034588 CAAAAAAATT
1 CAAAAAAAAT
17034598 CAAAAAAAAAT
1 C-AAAAAAAAT
*
17034609 CGAAAAAAAAG
1 C-AAAAAAAAT
*
17034620 GAAAAAAAAGT
1 CAAAAAAAA-T
17034631 GACAAAAAAAAT
1 --CAAAAAAAAT
17034643 C
1 C
17034644 GAGTTAAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
10 19 0.42
11 17 0.38
12 1 0.02
13 8 0.18
ACGTcount: A:0.74, C:0.09, G:0.08, T:0.09
Consensus pattern (10 bp):
CAAAAAAAAT
Found at i:17034604 original size:12 final size:12
Alignment explanation
Indices: 17034579--17034666 Score: 57
Period size: 11 Copynumber: 7.7 Consensus size: 12
17034569 TTGGAGTAAC
17034579 AAAAAAAATC--
1 AAAAAAAATCGA
*
17034589 AAAAAAATTC-A
1 AAAAAAAATCGA
17034600 AAAAAAAATCG-
1 AAAAAAAATCGA
*
17034611 AAAAAAAA-GGA
1 AAAAAAAATCGA
*
17034622 AAAAAAAGT-GA
1 AAAAAAAATCGA
17034633 CAAAAAAAATCGA
1 -AAAAAAAATCGA
17034646 GTTAAAAAAAA--GA
1 ---AAAAAAAATCGA
17034659 AAAAAAAA
1 AAAAAAAA
17034667 GTAAAAGAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
10 18 0.28
11 26 0.41
12 8 0.12
13 4 0.06
15 8 0.12
ACGTcount: A:0.76, C:0.06, G:0.09, T:0.09
Consensus pattern (12 bp):
AAAAAAAATCGA
Found at i:17034627 original size:34 final size:33
Alignment explanation
Indices: 17034589--17034697 Score: 94
Period size: 37 Copynumber: 3.1 Consensus size: 33
17034579 AAAAAAAATC
*
17034589 AAAAAAATTCAAAAAAAAATCGAAAAAAAAGG-A
1 AAAAAAAGT-AAAAAAAAATCGAAAAAAAAGGAA
*
17034622 AAAAAAAGTGACAAAAAAAATCGAGTTAAAAAAAAGAA
1 AAAAAAAGT-A-AAAAAAAATCGA---AAAAAAAGGAA
* *
17034660 AAAAAAAGTAAAAGAAAAGAACAAAAAAAAAGTGAA
1 AAAAAAAGTAAAA-AAAA-ATCGAAAAAAAAG-GAA
17034696 AA
1 AA
17034698 GTATTGTGAG
Statistics
Matches: 62, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
33 9 0.15
34 12 0.19
35 7 0.11
36 8 0.13
37 13 0.21
38 13 0.21
ACGTcount: A:0.75, C:0.05, G:0.12, T:0.08
Consensus pattern (33 bp):
AAAAAAAGTAAAAAAAAATCGAAAAAAAAGGAA
Found at i:17034663 original size:11 final size:10
Alignment explanation
Indices: 17034649--17034688 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
17034639 AAATCGAGTT
17034649 AAAAAAAAGA
1 AAAAAAAAGA
17034659 AAAAAAAAGTA
1 AAAAAAAAG-A
*
17034670 AAAGAAAAGA
1 AAAAAAAAGA
17034680 ACAAAAAAA
1 A-AAAAAAA
17034689 AAGTGAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 11 0.42
11 15 0.58
ACGTcount: A:0.85, C:0.03, G:0.10, T:0.03
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:17034677 original size:21 final size:21
Alignment explanation
Indices: 17034648--17034688 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
17034638 AAAATCGAGT
17034648 TAAAAAAAAGAA-AAAAAAAG
1 TAAAAAAAAGAACAAAAAAAG
17034668 TAAAAGAAAAGAACAAAAAAA
1 TAAAA-AAAAGAACAAAAAAA
17034689 AAGTGAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 7 0.37
22 7 0.37
ACGTcount: A:0.83, C:0.02, G:0.10, T:0.05
Consensus pattern (21 bp):
TAAAAAAAAGAACAAAAAAAG
Found at i:17034677 original size:25 final size:25
Alignment explanation
Indices: 17034650--17034698 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
17034640 AATCGAGTTA
* *
17034650 AAAAAAAGAAAAAAAAAGTA-AAAG
1 AAAAAAACAAAAAAAAAGTGAAAAG
*
17034674 AAAAGAACAAAAAAAAAGTGAAAAG
1 AAAAAAACAAAAAAAAAGTGAAAAG
17034699 TATTGTGAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.04
Consensus pattern (25 bp):
AAAAAAACAAAAAAAAAGTGAAAAG
Found at i:17034697 original size:11 final size:11
Alignment explanation
Indices: 17034589--17034640 Score: 52
Period size: 12 Copynumber: 4.6 Consensus size: 11
17034579 AAAAAAAATC
* *
17034589 AAAAAAATTCA
1 AAAAAAAGTGA
*
17034600 AAAAAAAATCGA
1 AAAAAAAGT-GA
17034612 AAAAAAAG-GA
1 AAAAAAAGTGA
17034622 AAAAAAAGTGA
1 AAAAAAAGTGA
17034633 CAAAAAAA
1 -AAAAAAA
17034641 ATCGAGTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
10 10 0.29
11 10 0.29
12 15 0.43
ACGTcount: A:0.77, C:0.06, G:0.10, T:0.08
Consensus pattern (11 bp):
AAAAAAAGTGA
Found at i:17035745 original size:17 final size:18
Alignment explanation
Indices: 17035713--17035746 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17035703 AAAAGAGAGT
*
17035713 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
17035731 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
17035747 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:17037035 original size:20 final size:20
Alignment explanation
Indices: 17037012--17037065 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
17037002 AGTTTTTCCC
*
17037012 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
17037032 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
17037052 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
17037066 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:17037047 original size:30 final size:30
Alignment explanation
Indices: 17037012--17037085 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
17037002 AGTTTTTCCC
17037012 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
17037042 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
17037072 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
17037086 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:17037075 original size:20 final size:20
Alignment explanation
Indices: 17037012--17037076 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
17037002 AGTTTTTCCC
* * * *
17037012 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
17037032 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
17037051 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
17037072 AGCTC
1 AGCTC
17037077 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:17045624 original size:27 final size:26
Alignment explanation
Indices: 17045577--17045632 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 26
17045567 GCAGCAACTA
17045577 ATTAAATTTGTCTCTAAACTAGACAC
1 ATTAAATTTGTCTCTAAACTAGACAC
17045603 ATTAAATTGATGTC-CTAAACTAGACAC
1 ATTAAATT--TGTCTCTAAACTAGACAC
17045630 ATT
1 ATT
17045633 TAAGCTATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 8 0.29
27 16 0.57
28 4 0.14
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (26 bp):
ATTAAATTTGTCTCTAAACTAGACAC
Found at i:17051570 original size:15 final size:14
Alignment explanation
Indices: 17051534--17051588 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
17051524 TCTATTGGTC
17051534 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
17051548 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
17051562 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
17051577 GAAAGAAAAGAA
1 GAGA-AAAAGAA
17051589 TGAGGAGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 16 0.47
15 18 0.53
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:17053616 original size:40 final size:40
Alignment explanation
Indices: 17053572--17053919 Score: 633
Period size: 40 Copynumber: 8.7 Consensus size: 40
17053562 GCAAACACAT
* *
17053572 TTGCCTTCGGGTCTTAGCCCGAACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
17053612 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
17053652 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
17053692 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
17053732 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
17053772 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
17053812 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
17053852 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
17053892 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
17053920 TCCAATGCTC
Statistics
Matches: 300, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 300 1.00
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:17069002 original size:11 final size:11
Alignment explanation
Indices: 17068986--17069051 Score: 87
Period size: 12 Copynumber: 5.6 Consensus size: 11
17068976 ATACAAGTAT
17068986 AAAAAAATTCA
1 AAAAAAATTCA
17068997 AAAAAAATTCGA
1 AAAAAAATTC-A
17069009 AAAAAAATTCGA
1 AAAAAAATTC-A
*
17069021 AAAAAAGTTCA
1 AAAAAAATTCA
17069032 AAAAAAAGTTTCA
1 AAAAAAA--TTCA
17069045 AAAAAAA
1 AAAAAAA
17069052 AGATTTGTAC
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
11 17 0.34
12 22 0.44
13 11 0.22
ACGTcount: A:0.70, C:0.08, G:0.06, T:0.17
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:17069917 original size:5 final size:5
Alignment explanation
Indices: 17069907--17069963 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
17069897 AACAGAAAAC
*
17069907 AAAGA AAAGA AAAGAA AAAGA AAA-A GAAGAA AAAGAA AAAGA AATA-A
1 AAAGA AAAGA AAAG-A AAAGA AAAGA AAAG-A AAAG-A AAAGA AA-AGA
17069954 AAAGA AAAGA
1 AAAGA AAAGA
17069964 GAGGCAAGAG
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.56
6 16 0.36
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:17069936 original size:25 final size:25
Alignment explanation
Indices: 17069911--17069959 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
17069901 GAAAACAAAG
17069911 AAAAGAAAAGAAAAAGAAAAAGAAGA
1 AAAAGAAAA-AAAAAGAAAAAGAAGA
* *
17069937 AAAAGAAAAAGAAATAAAAAGAA
1 AAAAGAAAAAAAAAGAAAAAGAA
17069960 AAGAGAGGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (25 bp):
AAAAGAAAAAAAAAGAAAAAGAAGA
Found at i:17069938 original size:15 final size:15
Alignment explanation
Indices: 17069907--17069961 Score: 74
Period size: 16 Copynumber: 3.5 Consensus size: 15
17069897 AACAGAAAAC
*
17069907 AAAGAAAAGAAAAGAA
1 AAAGAAAA-AGAAGAA
17069923 AAAGAAAAAGAAGAA
1 AAAGAAAAAGAAGAA
*
17069938 AAAGAAAAAGAAATAA
1 AAAGAAAAAG-AAGAA
17069954 AAAGAAAA
1 AAAGAAAA
17069962 GAGAGGCAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
15 16 0.44
16 20 0.56
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (15 bp):
AAAGAAAAAGAAGAA
Found at i:17069961 original size:6 final size:6
Alignment explanation
Indices: 17069907--17069950 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
17069897 AACAGAAAAC
17069907 AAAG-A AAAG-A AAAGAA AAAGAA AAAG-- -AAGAA AAAGAA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
17069950 A
1 A
17069951 TAAAAAGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
3 3 0.09
5 9 0.26
6 23 0.66
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:17069962 original size:21 final size:20
Alignment explanation
Indices: 17069911--17069963 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 20
17069901 GAAAACAAAG
17069911 AAAAGAAAAGAAAAAGAAAA
1 AAAAGAAAAGAAAAAGAAAA
*
17069931 AGAAGAAAAAGAAAAAGAAATA
1 AAAAG-AAAAGAAAAAGAAA-A
17069953 AAAAGAAAAGA
1 AAAAGAAAAGA
17069964 GAGGCAAGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 4 0.14
21 20 0.69
22 5 0.17
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (20 bp):
AAAAGAAAAGAAAAAGAAAA
Found at i:17070070 original size:12 final size:12
Alignment explanation
Indices: 17070044--17070088 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
17070034 AAAACAAAAA
*
17070044 GAAAAAGAAAAT
1 GAAAAAGAGAAT
* *
17070056 GAAAATGAGATT
1 GAAAAAGAGAAT
17070068 GAAAAAGAGAAT
1 GAAAAAGAGAAT
17070080 GAAAAAGAG
1 GAAAAAGAG
17070089 TTTGAGAGAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.11
Consensus pattern (12 bp):
GAAAAAGAGAAT
Found at i:17070071 original size:24 final size:24
Alignment explanation
Indices: 17070044--17070102 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
17070034 AAAACAAAAA
*
17070044 GAAAAAGAAAATGAAAATGAGATT
1 GAAAAAGAAAATGAAAAAGAGATT
* *
17070068 GAAAAAGAGAATGAAAAAGAGTTT
1 GAAAAAGAAAATGAAAAAGAGATT
* *
17070092 GAGAGAGAAAA
1 GAAAAAGAAAA
17070103 AGAATGTGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.61, C:0.00, G:0.25, T:0.14
Consensus pattern (24 bp):
GAAAAAGAAAATGAAAAAGAGATT
Found at i:17078599 original size:23 final size:22
Alignment explanation
Indices: 17078547--17078599 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
17078537 TCCACGCCTT
*
17078547 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
17078569 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
17078592 TTTCTTTT
1 TTTCTTTT
17078600 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:17082078 original size:30 final size:30
Alignment explanation
Indices: 17082044--17082140 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
17082034 AGCTCACTCC
17082044 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
17082074 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
17082104 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
17082134 TAGCTCA
1 TAGCTCA
17082141 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:17084714 original size:13 final size:13
Alignment explanation
Indices: 17084696--17084720 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17084686 TGGTCATCAT
17084696 GGTGTGAACACAA
1 GGTGTGAACACAA
17084709 GGTGTGAACACA
1 GGTGTGAACACA
17084721 TGATCAATAC
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:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:17085988 original size:47 final size:47
Alignment explanation
Indices: 17085910--17086014 Score: 133
Period size: 47 Copynumber: 2.2 Consensus size: 47
17085900 GAGTGTCATG
* *
17085910 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAA-AAATC
* *
17085957 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
17086005 GAAAAAGAAA
1 GAAAAAGAAA
17086015 GAAAAGACAA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
47 26 0.51
48 18 0.35
49 7 0.14
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:17087730 original size:20 final size:20
Alignment explanation
Indices: 17087684--17087730 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
17087674 AGCTCGTTTC
*
17087684 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
17087704 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
17087724 CAGCTCA
1 CAGCTCA
17087731 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:17089996 original size:30 final size:30
Alignment explanation
Indices: 17089962--17090058 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
17089952 AGCTCACTCC
17089962 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
17089992 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
17090022 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
17090052 TAGCTCA
1 TAGCTCA
17090059 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:17092631 original size:13 final size:13
Alignment explanation
Indices: 17092613--17092637 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17092603 TGGTCATCAT
17092613 GGTGTGAACACAA
1 GGTGTGAACACAA
17092626 GGTGTGAACACA
1 GGTGTGAACACA
17092638 TGATCAATAC
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:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:17093906 original size:48 final size:47
Alignment explanation
Indices: 17093827--17093932 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
17093817 GAGTGTCATG
*
17093827 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
17093875 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
17093923 GAAAAAGAAA
1 GAAAAAGAAA
17093933 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:17095515 original size:24 final size:23
Alignment explanation
Indices: 17095461--17095516 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
17095451 GGATAACTAA
* *
17095461 GAAAGGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGATTTGGTAC
***
17095484 GTTTTGGTATTTGGGATTTGGTAC
1 GAAATGGTATTT-GGATTTGGTAC
17095508 GAAATGGTA
1 GAAATGGTA
17095517 ATGGTTCAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.21, C:0.04, G:0.34, T:0.41
Consensus pattern (23 bp):
GAAATGGTATTTGGATTTGGTAC
Found at i:17100086 original size:15 final size:15
Alignment explanation
Indices: 17100052--17100090 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
17100042 TTTTTTCCTT
* *
17100052 CTTTTTTTTTCGGAT
1 CTTTTTTTTTCGAAA
*
17100067 TTTTTTTTTTCGAAA
1 CTTTTTTTTTCGAAA
17100082 CTTTTTTTT
1 CTTTTTTTT
17100091 AACTTTTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.10, C:0.10, G:0.08, T:0.72
Consensus pattern (15 bp):
CTTTTTTTTTCGAAA
Found at i:17100086 original size:27 final size:27
Alignment explanation
Indices: 17100056--17100107 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
17100046 TTCCTTCTTT
* *
17100056 TTTTTTCGGATTTTTTTTTTTCGAAAC
1 TTTTTTCGAACTTTTTTTTTTCGAAAC
**
17100083 TTTTTTTTAACTTTTTTTTTTCGAA
1 TTTTTTCGAACTTTTTTTTTTCGAA
17100108 GCTACGATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.15, C:0.10, G:0.08, T:0.67
Consensus pattern (27 bp):
TTTTTTCGAACTTTTTTTTTTCGAAAC
Found at i:17103069 original size:11 final size:11
Alignment explanation
Indices: 17103053--17103096 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 11
17103043 GTTCGTAATG
17103053 AAAAAAATCAAAA
1 AAAAAAATC--AA
17103066 AAAAAGAAGTCAA
1 AAAAA-AA-TCAA
17103079 AAAAAAATCAA
1 AAAAAAATCAA
17103090 AAAAAAA
1 AAAAAAA
17103097 AATTTGAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 11 0.38
12 2 0.07
13 12 0.41
14 2 0.07
15 2 0.07
ACGTcount: A:0.82, C:0.07, G:0.05, T:0.07
Consensus pattern (11 bp):
AAAAAAATCAA
Found at i:17103197 original size:14 final size:13
Alignment explanation
Indices: 17103178--17103217 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
17103168 AAAGGAGAAG
17103178 AAATTCAGAAAAAA
1 AAATTC-GAAAAAA
17103192 AAATTC-AAAAAA
1 AAATTCGAAAAAA
17103204 AAA-TCGAAAAAA
1 AAATTCGAAAAAA
17103216 AA
1 AA
17103218 GGAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 17 0.68
14 6 0.24
ACGTcount: A:0.75, C:0.07, G:0.05, T:0.12
Consensus pattern (13 bp):
AAATTCGAAAAAA
Found at i:17103203 original size:12 final size:12
Alignment explanation
Indices: 17103185--17103244 Score: 56
Period size: 11 Copynumber: 5.2 Consensus size: 12
17103175 AAGAAATTCA
17103185 GAAAAAAAAATTC
1 GAAAAAAAAA-TC
17103198 -AAAAAAAAATC
1 GAAAAAAAAATC
*
17103209 G-AAAAAAAA-G
1 GAAAAAAAAATC
*
17103219 GAAAAAAAAGT-
1 GAAAAAAAAATC
17103230 GACAAAAAAAATC
1 GA-AAAAAAAATC
17103243 GA
1 GA
17103245 GTTAAAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
10 1 0.03
11 19 0.49
12 17 0.44
13 2 0.05
ACGTcount: A:0.73, C:0.07, G:0.12, T:0.08
Consensus pattern (12 bp):
GAAAAAAAAATC
Found at i:17104206 original size:37 final size:37
Alignment explanation
Indices: 17104155--17104225 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
17104145 CATTCTTGTA
17104155 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
17104192 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
17104226 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:17104225 original size:6 final size:6
Alignment explanation
Indices: 17104165--17104214 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
17104155 AAGAGAAAAC
*
17104165 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
17104214 A
1 A
17104215 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:17104307 original size:11 final size:12
Alignment explanation
Indices: 17104275--17104305 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
17104265 TTGAGAGAAC
17104275 TTGAAAAAGCCT
1 TTGAAAAAGCCT
17104287 TTGAAAAAGCCT
1 TTGAAAAAGCCT
17104299 TTGAAAA
1 TTGAAAA
17104306 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:17106603 original size:12 final size:12
Alignment explanation
Indices: 17106586--17106655 Score: 50
Period size: 12 Copynumber: 5.4 Consensus size: 12
17106576 ATGGAGTAAC
17106586 AAAAAAAATCAA
1 AAAAAAAATCAA
*
17106598 AAAAAAATTCGAA
1 AAAAAAAATC-AA
*
17106611 AAAAAAATTGATTGAA
1 AAAAAAA---A-TCAA
*
17106627 AAAAAAATTCAA
1 AAAAAAAATCAA
* *
17106639 AAAAAAAGTGAA
1 AAAAAAAATCAA
17106651 AAAAA
1 AAAAA
17106656 TCGAGCAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
12 27 0.59
13 9 0.20
16 9 0.20
17 1 0.02
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAAAAAATCAA
Found at i:17107753 original size:6 final size:6
Alignment explanation
Indices: 17107744--17107841 Score: 54
Period size: 6 Copynumber: 16.0 Consensus size: 6
17107734 TGAAAGAAAC
* * ** * **
17107744 AAAAAG AAAACG AAGAAG -AAAAG AAATTG CAAAAG AAAAAG AAATCG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
** * * *
17107791 AAAAAG TGAGAG AAAAAG AAAATG AAGAAAAG AAAATTG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG -A-AAAAG AAAA-AG AAAAAG AAAAAG
17107842 CGAAAAAAGA
Statistics
Matches: 64, Mismatches: 24, Indels: 8
0.67 0.25 0.08
Matches are distributed among these distances:
5 4 0.06
6 49 0.77
7 7 0.11
8 4 0.06
ACGTcount: A:0.69, C:0.03, G:0.20, T:0.07
Consensus pattern (6 bp):
AAAAAG
Found at i:17107794 original size:17 final size:17
Alignment explanation
Indices: 17107744--17107794 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
17107734 TGAAAGAAAC
*
17107744 AAAAAGAAAACGAAGAAG
1 AAAAAGAAATCGAA-AAG
*
17107762 -AAAAGAAATTGCAAAAG
1 AAAAAGAAATCG-AAAAG
17107779 AAAAAGAAATCGAAAA
1 AAAAAGAAATCGAAAA
17107795 AGTGAGAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 16 0.57
18 12 0.43
ACGTcount: A:0.71, C:0.06, G:0.18, T:0.06
Consensus pattern (17 bp):
AAAAAGAAATCGAAAAG
Found at i:17107823 original size:14 final size:13
Alignment explanation
Indices: 17107802--17107839 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
17107792 AAAAGTGAGA
17107802 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
17107814 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
17107829 GAAAAAGAAAA
1 GAAAAAGAAAA
17107840 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:17107853 original size:21 final size:21
Alignment explanation
Indices: 17107803--17107853 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
17107793 AAAGTGAGAG
*
17107803 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
17107824 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
17107845 AAAAAGAAA
1 AAAAAGAAA
17107854 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:17108001 original size:48 final size:47
Alignment explanation
Indices: 17107922--17108027 Score: 126
Period size: 48 Copynumber: 2.2 Consensus size: 47
17107912 GAGTGTCATG
* *
17107922 GAAAATGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
17107970 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
17108018 GAAAAAGAAA
1 GAAAAAGAAA
17108028 GAAAAGACAA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
48 39 0.76
49 8 0.16
50 4 0.08
ACGTcount: A:0.58, C:0.02, G:0.25, T:0.15
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:17109746 original size:20 final size:20
Alignment explanation
Indices: 17109700--17109746 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
17109690 AGCTCGTTTC
*
17109700 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
17109720 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
17109740 CAGCTCA
1 CAGCTCA
17109747 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:17111225 original size:11 final size:13
Alignment explanation
Indices: 17111209--17111278 Score: 58
Period size: 12 Copynumber: 5.4 Consensus size: 13
17111199 ATGGAGTAAC
17111209 AAAAAAAA-TC-A
1 AAAAAAAATTCGA
17111220 AAAAAAAATTCGAA
1 AAAAAAAATTCG-A
*
17111234 AAAAAAAATTAATTGA
1 AAAAAAAA-T--TCGA
17111250 AAAAAAAATTC-A
1 AAAAAAAATTCGA
*
17111262 AAAAAAAAGT-GA
1 AAAAAAAATTCGA
17111274 AAAAA
1 AAAAA
17111279 CTCGAGCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
11 8 0.16
12 18 0.37
13 1 0.02
14 9 0.18
15 2 0.04
16 9 0.18
17 2 0.04
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.14
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:17111226 original size:12 final size:13
Alignment explanation
Indices: 17111209--17111242 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
17111199 ATGGAGTAAC
17111209 AAAAAAAATC-AA
1 AAAAAAAATCGAA
*
17111221 AAAAAAATTCGAA
1 AAAAAAAATCGAA
17111234 AAAAAAAAT
1 AAAAAAAAT
17111243 TAATTGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.79, C:0.06, G:0.03, T:0.12
Consensus pattern (13 bp):
AAAAAAAATCGAA
Found at i:17112391 original size:6 final size:6
Alignment explanation
Indices: 17112358--17112465 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
17112348 AAAGAAATTG
* * * ** *
17112358 AAAG-A AAACAA AAAGAA AACGAA GAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
17112405 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
17112456 AAAGAA AAAG
1 AAAGAA AAAG
17112466 CGAAAAAAGA
Statistics
Matches: 73, Mismatches: 26, Indels: 7
0.69 0.25 0.07
Matches are distributed among these distances:
5 3 0.04
6 59 0.81
7 7 0.10
8 4 0.05
ACGTcount: A:0.70, C:0.04, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:17112419 original size:18 final size:18
Alignment explanation
Indices: 17112362--17112420 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
17112352 AAATTGAAAG
* *
17112362 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAATCGA
* * *
17112380 AGAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAATCGA
17112398 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAATCGA
17112416 AAAAG
1 AAAAG
17112421 TGAGAGAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.71, C:0.07, G:0.17, T:0.05
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCGA
Found at i:17112447 original size:14 final size:13
Alignment explanation
Indices: 17112426--17112463 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
17112416 AAAAGTGAGA
17112426 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
17112438 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
17112453 GAAAAAGAAAA
1 GAAAAAGAAAA
17112464 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:17112477 original size:21 final size:21
Alignment explanation
Indices: 17112427--17112477 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
17112417 AAAGTGAGAG
*
17112427 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
17112448 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
17112469 AAAAAGAAA
1 AAAAAGAAA
17112478 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:17112481 original size:27 final size:27
Alignment explanation
Indices: 17112379--17112483 Score: 77
Period size: 27 Copynumber: 3.8 Consensus size: 27
17112369 AAAGAAAACG
* *
17112379 AAGAAGAAAAAGAAATTGCAAAAGAAA
1 AAGAAGAAAAAAAAATTGAAAAAGAAA
*** **
17112406 AAGAAATCGAAAAAGTGAGAGAAAAAGAAA
1 AAG-AA--GAAAAAAAAATTGAAAAAGAAA
* *
17112436 ATGAAGAAAAGAAAATTGAAAAAGAAA
1 AAGAAGAAAAAAAAATTGAAAAAGAAA
*
17112463 AAG-CGAAAAAAGAAATTGAAA
1 AAGAAGAAAAAA-AAATTGAAA
17112484 GAGAGCTTGA
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
26 6 0.10
27 30 0.51
28 2 0.03
29 2 0.03
30 19 0.32
ACGTcount: A:0.69, C:0.03, G:0.20, T:0.09
Consensus pattern (27 bp):
AAGAAGAAAAAAAAATTGAAAAAGAAA
Found at i:17114366 original size:20 final size:20
Alignment explanation
Indices: 17114320--17114366 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
17114310 AGCTCGTTTC
*
17114320 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
17114340 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
17114360 CAGCTCA
1 CAGCTCA
17114367 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:17115883 original size:14 final size:14
Alignment explanation
Indices: 17115836--17115884 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
17115826 CAAAAAAATC
*
17115836 AAAAAAAAATTCGA
1 AAAAAAAAATTCAA
17115850 AAAAAAAAATT-AA
1 AAAAAAAAATTCAA
*
17115863 TTGAAAAAAAATTCAA
1 --AAAAAAAAATTCAA
17115879 AAAAAA
1 AAAAAA
17115885 GTGAAAAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 1 0.03
14 16 0.55
15 10 0.34
16 2 0.07
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (14 bp):
AAAAAAAAATTCAA
Found at i:17117019 original size:16 final size:16
Alignment explanation
Indices: 17116971--17117019 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
17116961 TGAAAGAAAC
*
17116971 AAAAGAAAACGAAGAAG
1 AAAAGAAATCGAA-AAG
* *
17116988 AAAAGAAATTGCAAAG
1 AAAAGAAATCGAAAAG
17117004 AAAAGAAATCGAAAAG
1 AAAAGAAATCGAAAAG
17117020 TGAGAGAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 17 0.63
17 10 0.37
ACGTcount: A:0.67, C:0.06, G:0.20, T:0.06
Consensus pattern (16 bp):
AAAAGAAATCGAAAAG
Found at i:17117042 original size:13 final size:14
Alignment explanation
Indices: 17117014--17117059 Score: 53
Period size: 12 Copynumber: 3.4 Consensus size: 14
17117004 AAAAGAAATC
17117014 GAAAAGTGAGAGAAAA
1 GAAAA-TGA-AGAAAA
17117030 G-AAATGAAGAAAA
1 GAAAATGAAGAAAA
17117043 GAAAATG-A-AAAA
1 GAAAATGAAGAAAA
17117055 GAAAA
1 GAAAA
17117060 AGCGAAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 9 0.31
13 8 0.28
14 8 0.28
15 3 0.10
16 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.24, T:0.07
Consensus pattern (14 bp):
GAAAATGAAGAAAA
Found at i:17118961 original size:20 final size:20
Alignment explanation
Indices: 17118915--17118961 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
17118905 AGCTCGTTTC
*
17118915 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
17118935 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
17118955 CAGCTCA
1 CAGCTCA
17118962 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:17120457 original size:13 final size:12
Alignment explanation
Indices: 17120425--17120482 Score: 64
Period size: 13 Copynumber: 4.6 Consensus size: 12
17120415 ATGGAGTAAC
17120425 AAAAAAAA-TCA
1 AAAAAAAATTCA
17120436 AAAAAAAATTCGA
1 AAAAAAAATTC-A
*
17120449 AAAAAAAATTAA
1 AAAAAAAATTCA
17120461 TTGAAAAAAAATTCA
1 ---AAAAAAAATTCA
17120476 AAAAAAA
1 AAAAAAA
17120483 GTGAAAAAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
11 8 0.20
12 10 0.25
13 11 0.28
15 11 0.28
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:17121584 original size:11 final size:12
Alignment explanation
Indices: 17121568--17121627 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
17121558 AAAGAAATTG
17121568 AAAGAAAAC-AA
1 AAAGAAAACGAA
17121579 AAAGAAAACGAA
1 AAAGAAAACGAA
*
17121591 GAAGAAAA-GAA
1 AAAGAAAACGAA
**
17121602 ATTGCAAAA-GAA
1 AAAG-AAAACGAA
*
17121614 AAAGAAATCGAA
1 AAAGAAAACGAA
17121626 AA
1 AA
17121628 GTGAGAGAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
11 16 0.41
12 23 0.59
ACGTcount: A:0.72, C:0.07, G:0.17, T:0.05
Consensus pattern (12 bp):
AAAGAAAACGAA
Found at i:17121627 original size:17 final size:17
Alignment explanation
Indices: 17121571--17121628 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
17121561 GAAATTGAAA
* *
17121571 GAAAACAAAAAGAAAAC
1 GAAAAGAAAAAGAAATC
*
17121588 GAAGAAG-AAAAGAAATT
1 GAA-AAGAAAAAGAAATC
17121605 GCAAAAGAAAAAGAAATC
1 G-AAAAGAAAAAGAAATC
17121623 GAAAAG
1 GAAAAG
17121629 TGAGAGAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 20 0.59
18 14 0.41
ACGTcount: A:0.69, C:0.07, G:0.19, T:0.05
Consensus pattern (17 bp):
GAAAAGAAAAAGAAATC
Found at i:17121652 original size:14 final size:15
Alignment explanation
Indices: 17121623--17121684 Score: 60
Period size: 14 Copynumber: 4.3 Consensus size: 15
17121613 AAAAGAAATC
17121623 GAAAAGTGAGAGAAAA
1 GAAAAGTGA-AGAAAA
17121639 GAAAA-TGAAGAAAA
1 GAAAAGTGAAGAAAA
*
17121653 GAAAATTG-A-AAAA
1 GAAAAGTGAAGAAAA
*
17121666 GAAAAAGCGAA-AAAA
1 G-AAAAGTGAAGAAAA
17121681 GAAA
1 GAAA
17121685 TTGAAAGAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
13 5 0.12
14 20 0.49
15 11 0.27
16 5 0.12
ACGTcount: A:0.69, C:0.02, G:0.23, T:0.06
Consensus pattern (15 bp):
GAAAAGTGAAGAAAA
Found at i:17121831 original size:48 final size:47
Alignment explanation
Indices: 17121752--17121857 Score: 126
Period size: 48 Copynumber: 2.2 Consensus size: 47
17121742 GAGTGTCATG
* *
17121752 GAAAATGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
17121800 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
17121848 GAAAAAGAAA
1 GAAAAAGAAA
17121858 GAAAAGACAA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
48 39 0.76
49 8 0.16
50 4 0.08
ACGTcount: A:0.58, C:0.02, G:0.25, T:0.15
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:17123576 original size:20 final size:20
Alignment explanation
Indices: 17123530--17123576 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
17123520 AGCTCGTTTC
*
17123530 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
17123550 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
17123570 CAGCTCA
1 CAGCTCA
17123577 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:17132360 original size:23 final size:22
Alignment explanation
Indices: 17132309--17132360 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
17132299 TCCTCGTCTT
*
17132309 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
17132331 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
17132354 TTCTTTT
1 TTCTTTT
17132361 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:17132375 original size:18 final size:18
Alignment explanation
Indices: 17132354--17132392 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
17132344 TTTCTTCAAC
* *
17132354 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
17132372 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
17132390 TTC
1 TTC
17132393 ACTCTCAATC
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:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:17133879 original size:47 final size:47
Alignment explanation
Indices: 17133802--17133906 Score: 133
Period size: 47 Copynumber: 2.2 Consensus size: 47
17133792 TTGTCTTCTC
* *
17133802 TTTCTTTTTCAATTTTCTCTTTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTTCTCTCTTT-CTCACATCCTTT-TTCAATCTCAA
* *
17133850 TTTCTTTTTCGATTTCTTTCTCTTT-TCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTT-TCTCTCTTTCTCACATCCTTTTTCAATCTCAA
17133897 TTTCTTTTTC
1 TTTCTTTTTC
17133907 CATGACACTC
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
47 26 0.51
48 18 0.35
49 7 0.14
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (47 bp):
TTTCTTTTTCAATTTTCTCTCTTTCTCACATCCTTTTTCAATCTCAA
Found at i:17134947 original size:11 final size:10
Alignment explanation
Indices: 17134933--17134970 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
17134923 ACTTTTCACT
17134933 TTTTTTTGTTC
1 TTTTTTT-TTC
*
17134944 TTTTTTTTAC
1 TTTTTTTTTC
17134954 TTTTTTTTTC
1 TTTTTTTTTC
17134964 TTTTTTT
1 TTTTTTT
17134971 GCTCACTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 18 0.72
11 7 0.28
ACGTcount: A:0.03, C:0.08, G:0.03, T:0.87
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:17134978 original size:23 final size:21
Alignment explanation
Indices: 17134925--17134986 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 21
17134915 CTCGCAAGAC
17134925 TTTTCACTTTTTTTTGTTCTTTT
1 TTTTCAC-TTTTTTT-TTCTTTT
17134948 TTTT-ACTTTTTTTTTCTTTT
1 TTTTCACTTTTTTTTTCTTTT
17134968 TTTGCTCACTTCTTTTTTT
1 TTT--TCACTT-TTTTTTT
17134987 TGAATTTCGA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
20 10 0.29
21 7 0.20
22 3 0.09
23 8 0.23
24 7 0.20
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.77
Consensus pattern (21 bp):
TTTTCACTTTTTTTTTCTTTT
Found at i:17135106 original size:12 final size:11
Alignment explanation
Indices: 17135071--17135105 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
17135061 AAATTACAAC
*
17135071 TTGAGATTTTT
1 TTGAAATTTTT
*
17135082 TTGATATTTTT
1 TTGAAATTTTT
17135093 TTGAAATTTTT
1 TTGAAATTTTT
17135104 TT
1 TT
17135106 TACCAACCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.20, C:0.00, G:0.11, T:0.69
Consensus pattern (11 bp):
TTGAAATTTTT
Found at i:17139282 original size:30 final size:30
Alignment explanation
Indices: 17139248--17139344 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
17139238 TAAACTAAAA
17139248 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* ** * * * *
17139278 TGAGCTGAGGC-CAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
17139308 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
17139338 TGAGCTA
1 TGAGCTA
17139345 GGAGTGAGCT
Statistics
Matches: 48, Mismatches: 16, Indels: 6
0.69 0.23 0.09
Matches are distributed among these distances:
29 2 0.04
30 40 0.83
31 6 0.12
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.27
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:17140018 original size:77 final size:77
Alignment explanation
Indices: 17139900--17140054 Score: 310
Period size: 77 Copynumber: 2.0 Consensus size: 77
17139890 AAATAAACAA
17139900 AATGATACGAGTCATAAAGGCCCAATCCAAGTTCAAGAACGTGATGGGCTCAAATTGCCACAAGG
1 AATGATACGAGTCATAAAGGCCCAATCCAAGTTCAAGAACGTGATGGGCTCAAATTGCCACAAGG
17139965 CCCAATAACGAG
66 CCCAATAACGAG
17139977 AATGATACGAGTCATAAAGGCCCAATCCAAGTTCAAGAACGTGATGGGCTCAAATTGCCACAAGG
1 AATGATACGAGTCATAAAGGCCCAATCCAAGTTCAAGAACGTGATGGGCTCAAATTGCCACAAGG
17140042 CCCAATAACGAG
66 CCCAATAACGAG
17140054 A
1 A
17140055 TCAAAGGCCC
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (77 bp):
AATGATACGAGTCATAAAGGCCCAATCCAAGTTCAAGAACGTGATGGGCTCAAATTGCCACAAGG
CCCAATAACGAG
Found at i:17141774 original size:18 final size:20
Alignment explanation
Indices: 17141743--17141784 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
17141733 AAAATCAGTC
*
17141743 AAAAAAGTCAAAA-T-AATA
1 AAAAAAGACAAAATTCAATA
*
17141761 AAAAAAGACGAAATTCAATA
1 AAAAAAGACAAAATTCAATA
17141781 AAAA
1 AAAA
17141785 TTTTAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 11 0.55
19 1 0.05
20 8 0.40
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.14
Consensus pattern (20 bp):
AAAAAAGACAAAATTCAATA
Found at i:17147757 original size:51 final size:49
Alignment explanation
Indices: 17147593--17147775 Score: 222
Period size: 50 Copynumber: 3.7 Consensus size: 49
17147583 CTGGTACTCA
* *
17147593 TAGTAGCCTGTACTTAGTACTACACATGTGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
* * ** * *
17147642 TAGTAGCATGCACTTTGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCCGGTACACG
* * * * *
17147692 TAGTAGCCTACACTTAGCACTACACACGTGATCGAAGTTATCGGGTACGCG
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCCGGTACACG
17147743 TAGTAGCCTGCACTTAGTACTACACACGTGACC
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC
17147776 TCACAATAGA
Statistics
Matches: 110, Mismatches: 21, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
49 29 0.26
50 42 0.38
51 39 0.35
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
Found at i:17147763 original size:101 final size:99
Alignment explanation
Indices: 17147593--17147776 Score: 269
Period size: 101 Copynumber: 1.8 Consensus size: 99
17147583 CTGGTACTCA
** * * *
17147593 TAGTAGCCTGTACTTAGTACTACACATGTGACCAATTATCCGGTACACGTAGTAGCATGCACTTT
1 TAGTAGCCTACACTTAGCACTACACACGTGACCAATTATCCGGTACACGTAGTAGCATGCACTTA
17147658 GTACTACACACGTGACCTAACCATCTGATACACG
66 GTACTACACACGTGACCTAACCATCTGATACACG
* * * *
17147692 TAGTAGCCTACACTTAGCACTACACACGTGATCGAAGTTATCGGGTACGCGTAGTAGCCTGCACT
1 TAGTAGCCTACACTTAGCACTACACACGTGA-CCAA-TTATCCGGTACACGTAGTAGCATGCACT
17147757 TAGTACTACACACGTGACCT
64 TAGTACTACACACGTGACCT
17147777 CACAATAGAT
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 27 0.36
100 3 0.04
101 44 0.59
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (99 bp):
TAGTAGCCTACACTTAGCACTACACACGTGACCAATTATCCGGTACACGTAGTAGCATGCACTTA
GTACTACACACGTGACCTAACCATCTGATACACG
Found at i:17150547 original size:20 final size:20
Alignment explanation
Indices: 17150524--17150570 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
17150514 GGGTTAAGAT
*
17150524 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
17150544 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
17150564 TGAGCTG
1 TGAGCTG
17150571 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:17152641 original size:27 final size:26
Alignment explanation
Indices: 17152611--17152666 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 26
17152601 ACATAACTTA
*
17152611 AATGTGTCTAGTTTAG-GACATCAATTT
1 AATGTGTCTAGCTTAGAGACA--AATTT
17152638 AATGTGTCTAGCTTAGAGACAAATTT
1 AATGTGTCTAGCTTAGAGACAAATTT
17152664 AAT
1 AAT
17152667 TAGTTGCTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 8 0.30
27 15 0.56
28 4 0.15
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.38
Consensus pattern (26 bp):
AATGTGTCTAGCTTAGAGACAAATTT
Found at i:17156513 original size:12 final size:12
Alignment explanation
Indices: 17156498--17156539 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 12
17156488 CAACTTCTAA
17156498 AGAAAACTCAAG
1 AGAAAACTCAAG
**
17156510 AGAAAACTCTTGG
1 AGAAAACTC-AAG
17156523 AGAAAACTCAA-
1 AGAAAACTCAAG
17156534 AGAAAA
1 AGAAAA
17156540 TTCTGCTCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
11 6 0.24
12 9 0.36
13 10 0.40
ACGTcount: A:0.57, C:0.14, G:0.17, T:0.12
Consensus pattern (12 bp):
AGAAAACTCAAG
Found at i:17159866 original size:15 final size:16
Alignment explanation
Indices: 17159841--17159872 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
17159831 TATCTCACAC
17159841 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
17159857 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
17159872 T
1 T
17159873 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Done.