Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 57 of 120
Found at i:16895488 original size:2 final size:2
Alignment explanation
Indices: 16895483--16895518 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
16895473 TATTAAAACA
16895483 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
16895519 TGTGATGCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16895641 original size:32 final size:30
Alignment explanation
Indices: 16895605--16895669 Score: 76
Period size: 32 Copynumber: 2.1 Consensus size: 30
16895595 TAAATAAATG
* * *
16895605 AAAAATATGTTTCTATTATATTAAAATTTTTA
1 AAAAATATATTTCTA-AATATTAAAA-ATTTA
*
16895637 AAAAATATATTTTTAAATATTAAAAATTTA
1 AAAAATATATTTCTAAATATTAAAAATTTA
16895667 AAA
1 AAA
16895670 TAAAAAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 7 0.24
31 9 0.31
32 13 0.45
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (30 bp):
AAAAATATATTTCTAAATATTAAAAATTTA
Found at i:16897626 original size:6 final size:6
Alignment explanation
Indices: 16897615--16897644 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
16897605 TTCAGCTGCT
*
16897615 TGAGCC TGAGCC TGAGCC TGAGCT TGAGCC
1 TGAGCC TGAGCC TGAGCC TGAGCC TGAGCC
16897645 GCAACACTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.30, G:0.33, T:0.20
Consensus pattern (6 bp):
TGAGCC
Found at i:16898221 original size:26 final size:26
Alignment explanation
Indices: 16898166--16898241 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
16898156 GCTAAACCTC
**
16898166 ATTAAATAAATTCAAACATAAAAATT
1 ATTAAATAAATTCAAACATAAAAAGA
** *
16898192 ATTAAATAAATTCAAATTTAAACAGA
1 ATTAAATAAATTCAAACATAAAAAGA
* *
16898218 ATTAATTCTAAATTCAATCATAAA
1 ATTAA--ATAAATTCAAACATAAA
16898242 CTTAATTAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
26 26 0.67
28 13 0.33
ACGTcount: A:0.57, C:0.09, G:0.01, T:0.33
Consensus pattern (26 bp):
ATTAAATAAATTCAAACATAAAAAGA
Found at i:16901561 original size:14 final size:14
Alignment explanation
Indices: 16901518--16901561 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
16901508 ATTAATTTTA
16901518 TTTTTTGTATTATAT
1 TTTTTTGTATTAT-T
** *
16901533 TTTGGTGTATAATT
1 TTTTTTGTATTATT
16901547 TTTTTTGTATTATT
1 TTTTTTGTATTATT
16901561 T
1 T
16901562 ATGTAAAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.18, C:0.00, G:0.11, T:0.70
Consensus pattern (14 bp):
TTTTTTGTATTATT
Found at i:16901651 original size:27 final size:27
Alignment explanation
Indices: 16901610--16901688 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
16901600 TGTGGGGTTG
*
16901610 GTGCAGCCTGCCAGGTAGGCACTACTA
1 GTGCAGCCTGCCAGGTAGGCACCACTA
* *
16901637 GTGCCGCCTGGCAGGTAGGCACCACTA
1 GTGCAGCCTGCCAGGTAGGCACCACTA
* * *
16901664 GTGCTGCCTGTCAGATAGGCACCAC
1 GTGCAGCCTGCCAGGTAGGCACCAC
16901689 CCCTTGTACC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.20, C:0.32, G:0.30, T:0.18
Consensus pattern (27 bp):
GTGCAGCCTGCCAGGTAGGCACCACTA
Found at i:16913554 original size:17 final size:17
Alignment explanation
Indices: 16913532--16913564 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16913522 TGTTAGTGCA
*
16913532 CATTGTCATTGCATTTC
1 CATTGTCACTGCATTTC
16913549 CATTGTCACTGCATTT
1 CATTGTCACTGCATTT
16913565 TAGTGTCAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.24, G:0.12, T:0.45
Consensus pattern (17 bp):
CATTGTCACTGCATTTC
Found at i:16916956 original size:28 final size:27
Alignment explanation
Indices: 16916927--16916980 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
16916917 GTTAAAACTC
16916927 TTCTT-AAAAG-AAAACTC-AAGAGCAA
1 TTCTTGAAAAGAAAAACTCAAAGAG-AA
16916952 TTCTTGAAAAGAAAAACTCAAAGAGAA
1 TTCTTGAAAAGAAAAACTCAAAGAGAA
16916979 TT
1 TT
16916981 TGAATAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 5 0.19
26 5 0.19
27 11 0.42
28 5 0.19
ACGTcount: A:0.52, C:0.13, G:0.13, T:0.22
Consensus pattern (27 bp):
TTCTTGAAAAGAAAAACTCAAAGAGAA
Found at i:16920661 original size:24 final size:25
Alignment explanation
Indices: 16920628--16920714 Score: 87
Period size: 24 Copynumber: 3.7 Consensus size: 25
16920618 TCAGTAGTCG
16920628 CATAACAAGTATCGGTAGTACTATT
1 CATAACAAGTATCGGTAGTACTATT
* * *
16920653 CATAA-AAGTAT-TG-A-TAATCTT
1 CATAACAAGTATCGGTAGTACTATT
*
16920674 -ATAACAAGTATCGGTAGTACTGTT
1 CATAACAAGTATCGGTAGTACTATT
*
16920698 CAT-AGAAGTATCGGTAG
1 CATAACAAGTATCGGTAG
16920715 CCTGAGTACT
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
20 4 0.08
21 11 0.22
22 2 0.04
23 2 0.04
24 24 0.48
25 7 0.14
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (25 bp):
CATAACAAGTATCGGTAGTACTATT
Found at i:16926687 original size:18 final size:18
Alignment explanation
Indices: 16926661--16926707 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
16926651 CCTGATTAGT
*
16926661 TGCAATCACATACCCAGA
1 TGCAATCACATAACCAGA
* *
16926679 TGCAGTCACATAATCAGA
1 TGCAATCACATAACCAGA
*
16926697 TGCAACCACAT
1 TGCAATCACAT
16926708 GTTCGAATAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.38, C:0.30, G:0.13, T:0.19
Consensus pattern (18 bp):
TGCAATCACATAACCAGA
Found at i:16935442 original size:17 final size:18
Alignment explanation
Indices: 16935405--16935444 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
16935395 TAACAAAATG
16935405 ATGCAGTGACAAAATAAA
1 ATGCAGTGACAAAATAAA
* *
16935423 ATGCAGTGATAATA-AAA
1 ATGCAGTGACAAAATAAA
16935440 ATGCA
1 ATGCA
16935445 TTAAAACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.53, C:0.10, G:0.17, T:0.20
Consensus pattern (18 bp):
ATGCAGTGACAAAATAAA
Found at i:16943236 original size:27 final size:27
Alignment explanation
Indices: 16943206--16943273 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
16943196 GTAGTGGTAA
* *
16943206 ATCTTGTGGCAGTATTGGAGGAATATT
1 ATCTTGTGGCAGCACTGGAGGAATATT
16943233 ATCTTGTGGCAGCACTGGAGGAATATT
1 ATCTTGTGGCAGCACTGGAGGAATATT
*
16943260 ATCCTGTGGCAGCA
1 ATCTTGTGGCAGCA
16943274 ATGGTGGTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.31
Consensus pattern (27 bp):
ATCTTGTGGCAGCACTGGAGGAATATT
Found at i:16943287 original size:27 final size:27
Alignment explanation
Indices: 16943210--16943288 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
16943200 TGGTAAATCT
* * * *
16943210 TGTGGCAGTATTGGAGGAATATTATCT
1 TGTGGCAGCAATGGAGGAAGATTATCC
* *
16943237 TGTGGCAGCACTGGAGGAATATTATCC
1 TGTGGCAGCAATGGAGGAAGATTATCC
* *
16943264 TGTGGCAGCAATGGTGGTAGATTAT
1 TGTGGCAGCAATGGAGGAAGATTAT
16943289 TATTTTTGTT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.25, C:0.11, G:0.32, T:0.32
Consensus pattern (27 bp):
TGTGGCAGCAATGGAGGAAGATTATCC
Found at i:16955147 original size:24 final size:24
Alignment explanation
Indices: 16955119--16955164 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
16955109 GCGATCAAGA
16955119 AAAGGATA-AAGAAAAAGAAGAAGG
1 AAAGGA-AGAAGAAAAAGAAGAAGG
*
16955143 AAAGGAAGAAGAGAAAGAAGAA
1 AAAGGAAGAAGAAAAAGAAGAA
16955165 ACAGAACCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.02
Consensus pattern (24 bp):
AAAGGAAGAAGAAAAAGAAGAAGG
Found at i:16955150 original size:12 final size:12
Alignment explanation
Indices: 16955127--16955164 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
16955117 GAAAAGGATA
*
16955127 AAGAAAAAGAAG
1 AAGAGAAAGAAG
16955139 AAG-GAAAGGAAG
1 AAGAGAAA-GAAG
16955151 AAGAGAAAGAAG
1 AAGAGAAAGAAG
16955163 AA
1 AA
16955165 ACAGAACCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
11 3 0.13
12 16 0.70
13 4 0.17
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (12 bp):
AAGAGAAAGAAG
Found at i:16956860 original size:18 final size:15
Alignment explanation
Indices: 16956847--16956875 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16956837 GAAGAATGAG
16956847 AGAAGGAAGAAGAAA
1 AGAAGGAAGAAGAAA
16956862 AGAAGGAAGAAGAA
1 AGAAGGAAGAAGAA
16956876 GAAAAAGAGG
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:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (15 bp):
AGAAGGAAGAAGAAA
Found at i:16956876 original size:18 final size:18
Alignment explanation
Indices: 16956852--16956889 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
16956842 ATGAGAGAAG
16956852 GAAGAAG-AAAAGAAGGAA
1 GAAGAAGAAAAAG-AGGAA
16956870 GAAGAAGAAAAAGAGGAA
1 GAAGAAGAAAAAGAGGAA
16956888 GA
1 GA
16956890 CATTGTAGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (18 bp):
GAAGAAGAAAAAGAGGAA
Found at i:16966655 original size:23 final size:23
Alignment explanation
Indices: 16966613--16966658 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
16966603 TTTTCTAAGT
16966613 GGAGAAAAAAGAAAGGTGAGAGAA
1 GGAGAAAAAAG-AAGGTGAGAGAA
16966637 GGAGAAATAAAG-AGGTGAGAGA
1 GGAGAAA-AAAGAAGGTGAGAGA
16966659 GAATGGGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 10 0.48
24 7 0.33
25 4 0.19
ACGTcount: A:0.54, C:0.00, G:0.39, T:0.07
Consensus pattern (23 bp):
GGAGAAAAAAGAAGGTGAGAGAA
Found at i:16981376 original size:18 final size:17
Alignment explanation
Indices: 16981348--16981381 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
16981338 ACTTTTCTGC
16981348 TTTTCTCTTCTTCTTTG
1 TTTTCTCTTCTTCTTTG
16981365 TTTTCTTCTTCTTCTTT
1 TTTTC-TCTTCTTCTTT
16981382 TCTATTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.00, C:0.24, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTCTCTTCTTCTTTG
Found at i:16982433 original size:15 final size:15
Alignment explanation
Indices: 16982413--16982442 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16982403 CATCTTCCTT
*
16982413 CTCTTCTTTCTTCTC
1 CTCTTCTTCCTTCTC
16982428 CTCTTCTTCCTTCTC
1 CTCTTCTTCCTTCTC
16982443 TTCATTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (15 bp):
CTCTTCTTCCTTCTC
Found at i:16982456 original size:27 final size:28
Alignment explanation
Indices: 16982405--16982462 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
16982395 TTTCAGGGCA
* *
16982405 TCTTCCTTCTCTTCTTTCTTCTCC-TCT
1 TCTTCCTTCTCTTCATTATTCTCCTTCT
*
16982432 TCTTCCTTCTCTTCATTATTTTCCTTCT
1 TCTTCCTTCTCTTCATTATTCTCCTTCT
16982460 TCT
1 TCT
16982463 CCTCAAGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.03, C:0.36, G:0.00, T:0.60
Consensus pattern (28 bp):
TCTTCCTTCTCTTCATTATTCTCCTTCT
Found at i:16997676 original size:17 final size:18
Alignment explanation
Indices: 16997654--16997693 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
16997644 TCAACGCGGG
16997654 GAGAAAAG-GAAAATTTT
1 GAGAAAAGAGAAAATTTT
*
16997671 GAG-AAAGAGAGAATTTT
1 GAGAAAAGAGAAAATTTT
16997688 GAGAAA
1 GAGAAA
16997694 GGGATAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 4 0.20
17 14 0.70
18 2 0.10
ACGTcount: A:0.53, C:0.00, G:0.28, T:0.20
Consensus pattern (18 bp):
GAGAAAAGAGAAAATTTT
Found at i:17011109 original size:24 final size:23
Alignment explanation
Indices: 17011081--17011135 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
17011071 ACACAAGTGG
*
17011081 AAGAAGTGGAAGAAGAAGAAGGAA
1 AAGAAGTGAAAGAA-AAGAAGGAA
* *
17011105 AAGAAGAAGAAAGAAAGGAAGGAA
1 AAGAAG-TGAAAGAAAAGAAGGAA
17011129 AAGAAGT
1 AAGAAGT
17011136 CGAGGCAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 20 0.77
25 6 0.23
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.04
Consensus pattern (23 bp):
AAGAAGTGAAAGAAAAGAAGGAA
Found at i:17011114 original size:15 final size:15
Alignment explanation
Indices: 17011090--17011125 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
17011080 GAAGAAGTGG
*
17011090 AAGAAGAAGAAGGAA
1 AAGAAGAAGAAAGAA
17011105 AAGAAGAAGAAAGAA
1 AAGAAGAAGAAAGAA
*
17011120 AGGAAG
1 AAGAAG
17011126 GAAAAGAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
AAGAAGAAGAAAGAA
Found at i:17012202 original size:15 final size:14
Alignment explanation
Indices: 17012182--17012222 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
17012172 CACATATAAA
17012182 AAAAAGAGAAAAGAG
1 AAAAAGAGAAAA-AG
17012197 AAAAAG-GAAAAAG
1 AAAAAGAGAAAAAG
17012210 AAGAAA-AGAAAAA
1 AA-AAAGAGAAAAA
17012223 TATATATTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.17
14 14 0.58
15 6 0.25
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (14 bp):
AAAAAGAGAAAAAG
Found at i:17023947 original size:21 final size:21
Alignment explanation
Indices: 17023922--17023998 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 21
17023912 CGCATTGATC
17023922 AAAATTATTTTCATAAACTGA
1 AAAATTATTTTCATAAACTGA
*
17023943 AAAATTA--TTCATAAATACCTTCA
1 AAAATTATTTTCAT-AA-A-C-TGA
17023966 AATATTATTATTTTCATAAACTGA
1 AA-A--ATTATTTTCATAAACTGA
17023990 AAAATTATT
1 AAAATTATT
17023999 CATAAATACC
Statistics
Matches: 45, Mismatches: 2, Indels: 18
0.69 0.03 0.28
Matches are distributed among these distances:
19 5 0.11
20 2 0.04
21 14 0.31
22 1 0.02
23 5 0.11
24 5 0.11
25 1 0.02
26 5 0.11
27 2 0.04
28 5 0.11
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (21 bp):
AAAATTATTTTCATAAACTGA
Found at i:17023955 original size:19 final size:19
Alignment explanation
Indices: 17023931--17024004 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
17023921 CAAAATTATT
17023931 TTCATAAACTGAAAAATTA
1 TTCATAAACTGAAAAATTA
*
17023950 TTCATAAATACCTTCAAATATTATTA
1 TTCAT-AA-A-C-TGAAA-A--ATTA
17023976 TTTTCATAAACTGAAAAATTA
1 --TTCATAAACTGAAAAATTA
17023997 TTCATAAA
1 TTCATAAA
17024005 TACCTTCAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 18
0.69 0.03 0.28
Matches are distributed among these distances:
19 13 0.30
20 2 0.05
21 5 0.11
22 1 0.02
23 5 0.11
24 5 0.11
25 1 0.02
26 5 0.11
27 2 0.05
28 5 0.11
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (19 bp):
TTCATAAACTGAAAAATTA
Found at i:17023972 original size:23 final size:23
Alignment explanation
Indices: 17023946--17024018 Score: 60
Period size: 23 Copynumber: 3.1 Consensus size: 23
17023936 AAACTGAAAA
17023946 ATTATTCATAAATACCTTCAAAT
1 ATTATTCATAAATACCTTCAAAT
** * * *
17023969 ATTATT-ATTTTCATAAAC-TGAAAA
1 ATTATTCA--TAAAT-ACCTTCAAAT
17023993 ATTATTCATAAATACCTTCAAAT
1 ATTATTCATAAATACCTTCAAAT
17024016 ATT
1 ATT
17024019 CCTTGATCAT
Statistics
Matches: 35, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
22 3 0.09
23 16 0.46
24 13 0.37
25 3 0.09
ACGTcount: A:0.44, C:0.14, G:0.01, T:0.41
Consensus pattern (23 bp):
ATTATTCATAAATACCTTCAAAT
Found at i:17023985 original size:47 final size:47
Alignment explanation
Indices: 17023925--17024018 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
17023915 ATTGATCAAA
17023925 ATTATTTTCATAAACTGAAAAATTATTCATAAATACCTTCAAATATT
1 ATTATTTTCATAAACTGAAAAATTATTCATAAATACCTTCAAATATT
17023972 ATTATTTTCATAAACTGAAAAATTATTCATAAATACCTTCAAATATT
1 ATTATTTTCATAAACTGAAAAATTATTCATAAATACCTTCAAATATT
17024019 CCTTGATCAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.45, C:0.13, G:0.02, T:0.40
Consensus pattern (47 bp):
ATTATTTTCATAAACTGAAAAATTATTCATAAATACCTTCAAATATT
Found at i:17074893 original size:18 final size:18
Alignment explanation
Indices: 17074860--17074900 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
17074850 ACATGAAAAG
17074860 AAGAAGGAAAATGAGGAA
1 AAGAAGGAAAATGAGGAA
*
17074878 GAGAAGGAAGAA-GAGGAA
1 AAGAAGGAA-AATGAGGAA
17074896 AAGAA
1 AAGAA
17074901 TAAAGAGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.02
Consensus pattern (18 bp):
AAGAAGGAAAATGAGGAA
Found at i:17074897 original size:27 final size:28
Alignment explanation
Indices: 17074857--17074915 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
17074847 AAAACATGAA
*
17074857 AAGAAGAAGGAAAATG-AGGAAGAGAAGG
1 AAGAAGAAGGAAAA-GAAGAAAGAGAAGG
*
17074885 AAGAAG-AGGAAAAGAATAAAGAGAAGG
1 AAGAAGAAGGAAAAGAAGAAAGAGAAGG
17074912 AAGA
1 AAGA
17074916 TGCCCCGACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 1 0.04
27 21 0.75
28 6 0.21
ACGTcount: A:0.61, C:0.00, G:0.36, T:0.03
Consensus pattern (28 bp):
AAGAAGAAGGAAAAGAAGAAAGAGAAGG
Found at i:17083937 original size:17 final size:17
Alignment explanation
Indices: 17083912--17083951 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
17083902 AATGCAAGCT
*
17083912 TTTTCTTTTAT-TTATTA
1 TTTTATTTTATCTT-TTA
17083929 TTTTATTTTATCTTTTA
1 TTTTATTTTATCTTTTA
17083946 TTTTAT
1 TTTTAT
17083952 GTCTTCTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 19 0.90
18 2 0.10
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTATTTTATCTTTTA
Found at i:17083944 original size:12 final size:12
Alignment explanation
Indices: 17083911--17083951 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
17083901 CAATGCAAGC
17083911 TTTT-TCTTTTA
1 TTTTATCTTTTA
*
17083922 -TTTATTATTTTA
1 TTTTA-TCTTTTA
17083934 TTTTATCTTTTA
1 TTTTATCTTTTA
17083946 TTTTAT
1 TTTTAT
17083952 GTCTTCTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
10 3 0.12
12 18 0.72
13 4 0.16
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTATCTTTTA
Found at i:17086901 original size:28 final size:30
Alignment explanation
Indices: 17086847--17086903 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 30
17086837 GTTGAAATTT
17086847 TCAACTTAATCCTTAAAACAAAATCAAAAC
1 TCAACTTAATCCTTAAAACAAAATCAAAAC
* *
17086877 TCAATTTAAT-CTTGAAA-AAAATCAAAA
1 TCAACTTAATCCTTAAAACAAAATCAAAA
17086904 ATTCAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 10 0.40
29 6 0.24
30 9 0.36
ACGTcount: A:0.54, C:0.18, G:0.02, T:0.26
Consensus pattern (30 bp):
TCAACTTAATCCTTAAAACAAAATCAAAAC
Found at i:17093782 original size:28 final size:29
Alignment explanation
Indices: 17093727--17093782 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
17093717 AAAATAATTG
**
17093727 GTTCTGAAAAAATAAATTTGACCTAATGT
1 GTTCTGAAAAAATAAATTTGACAAAATGT
17093756 GTTCTGAAAAAAT-AATTTGACAAAATG
1 GTTCTGAAAAAATAAATTTGACAAAATG
17093783 GATTTTGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 12 0.48
29 13 0.52
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.32
Consensus pattern (29 bp):
GTTCTGAAAAAATAAATTTGACAAAATGT
Found at i:17094084 original size:155 final size:155
Alignment explanation
Indices: 17093731--17094226 Score: 646
Period size: 155 Copynumber: 3.2 Consensus size: 155
17093721 TAATTGGTTC
** * * * *
17093731 TGAAAAAATAAATTTGACCTAATGTGTTCTGAAAAAATAA-TTTGACAAAATGGATTTTGTTTTG
1 TGAAAAAATAAATTTGAGATGATGTGTTCTGAAAAAATAATTTTGACGAGATGAATTTTGTTTTG
* *
17093795 TTCTGAAAAAA-GCTCTAAGTAGGATGCACAGTCAGTAATACT--ATAGAAAAAAGCTTCCAACT
66 TTCTGAAAAAACGCTCTAAGTAGGATGCACAGTCAGTAATAGTACATA-AAAAAAGCTTCCAGCT
* ** *
17093857 GGATACTTTTTTTGTACTGATGCTTT
130 AGACGCTTTTTTTGTATTGATGCTTT
* *
17093883 TGACAAAA-AAATTTGAGATGATGTGTTCTGAAAAAATAATTTTGACGAGATGAAATTTGTTTTG
1 TGAAAAAATAAATTTGAGATGATGTGTTCTGAAAAAATAATTTTGACGAGATGAATTTTGTTTTG
* * * *
17093947 TTCTGAAAAAACGCTTTAAGTAAGATGCACAGTTAGTAATAGTACATAAAAAAAGCTTCCAGCTC
66 TTCTGAAAAAACGCTCTAAGTAGGATGCACAGTCAGTAATAGTACATAAAAAAAGCTTCCAGCTA
* *
17094012 GACGCTTTTTTTGTTTTAATGCTTT
131 GACGCTTTTTTTGTATTGATGCTTT
* * *
17094037 TGAAAAAATAAACTTGAGGTGATGTGTTCTGAAAAAATAATTTTGACGAGATGAATTTTATTTTG
1 TGAAAAAATAAATTTGAGATGATGTGTTCTGAAAAAATAATTTTGACGAGATGAATTTTGTTTTG
* * * *
17094102 TTCTGAAAAAAACGCTCTAAGTAGGATCCATAGTCAGTAATTGTACATAAAAAAAGCTTTCAGCT
66 TTCTG-AAAAAACGCTCTAAGTAGGATGCACAGTCAGTAATAGTACATAAAAAAAGCTTCCAGCT
*
17094167 AGACGC-TTTTTTGTATTGATGCTTC
130 AGACGCTTTTTTTGTATTGATGCTTT
* * *
17094192 TAAAAAAATAAATTTGAGAAGAAG-GTTCTGAAAAA
1 TGAAAAAATAAATTTGAGATGATGTGTTCTGAAAAA
17094227 TATCTCAAGA
Statistics
Matches: 298, Mismatches: 40, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
151 28 0.09
152 38 0.13
153 27 0.09
154 53 0.18
155 95 0.32
156 57 0.19
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (155 bp):
TGAAAAAATAAATTTGAGATGATGTGTTCTGAAAAAATAATTTTGACGAGATGAATTTTGTTTTG
TTCTGAAAAAACGCTCTAAGTAGGATGCACAGTCAGTAATAGTACATAAAAAAAGCTTCCAGCTA
GACGCTTTTTTTGTATTGATGCTTT
Found at i:17101631 original size:26 final size:26
Alignment explanation
Indices: 17101601--17101681 Score: 101
Period size: 26 Copynumber: 3.1 Consensus size: 26
17101591 AGACTTGAAG
17101601 ATATTGTACTAGCTC-ATAAGAGTGAT
1 ATATTGTACTAGCTCGA-AAGAGTGAT
* * * *
17101627 ATATTGTACTGGCTCGAAAAAATGCT
1 ATATTGTACTAGCTCGAAAGAGTGAT
*
17101653 ATATTGTACTAGCTCGAAAGAGCGAT
1 ATATTGTACTAGCTCGAAAGAGTGAT
17101679 ATA
1 ATA
17101682 CTGAACTGGG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 44 0.98
27 1 0.02
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.31
Consensus pattern (26 bp):
ATATTGTACTAGCTCGAAAGAGTGAT
Found at i:17105369 original size:19 final size:19
Alignment explanation
Indices: 17105345--17105383 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
17105335 AAATTACTTA
17105345 ACTGGCTCATAAGAGCGAT
1 ACTGGCTCATAAGAGCGAT
* *
17105364 ACTGGCTCGTAAGAGTGAT
1 ACTGGCTCATAAGAGCGAT
17105383 A
1 A
17105384 TTCTATATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.23
Consensus pattern (19 bp):
ACTGGCTCATAAGAGCGAT
Found at i:17105493 original size:26 final size:26
Alignment explanation
Indices: 17105470--17105532 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
17105460 ACTGGCTCAT
*
17105470 AAGAGCGATATATTGTATTAGCTCGA
1 AAGAGCGATATACTGTATTAGCTCGA
17105496 AAGAGCGATATACTGTATTAGCTCGA
1 AAGAGCGATATACTGTATTAGCTCGA
17105522 AAGAGCGATAT
1 AAGAGCGATAT
17105533 GCTGAACTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.27
Consensus pattern (26 bp):
AAGAGCGATATACTGTATTAGCTCGA
Found at i:17107989 original size:27 final size:27
Alignment explanation
Indices: 17107957--17108070 Score: 75
Period size: 27 Copynumber: 4.2 Consensus size: 27
17107947 TGATTCGTGT
* *
17107957 ACAGAGTATTATTAATTCAGGCCAGAA
1 ACAGAGTATTACTAATTCAAGCCAGAA
* * * *
17107984 ATAGAGTATCACTCATTCAAGCGAGAA
1 ACAGAGTATTACTAATTCAAGCCAGAA
* ** ** *
17108011 ACAGAGTATTGCTCTTTTGAGCGAGAA
1 ACAGAGTATTACTAATTCAAGCCAGAA
* ** * *
17108038 ACAGAGTATTGCTCTTTCGAGCGAGAA
1 ACAGAGTATTACTAATTCAAGCCAGAA
17108065 ACAGAG
1 ACAGAG
17108071 CATTGTTCTT
Statistics
Matches: 74, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 74 1.00
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.25
Consensus pattern (27 bp):
ACAGAGTATTACTAATTCAAGCCAGAA
Found at i:17108042 original size:81 final size:81
Alignment explanation
Indices: 17107957--17108127 Score: 193
Period size: 81 Copynumber: 2.1 Consensus size: 81
17107947 TGATTCGTGT
* * * *
17107957 ACAGAGTATTATTAATTC-AGGCCAGAAATAGAGTATCACTCATTCAAGCGAGAAACAGAGTATT
1 ACAGAGTATTACTAATTCGA-GCCAGAAACAGAGCATCACTCATTCAAGCGAGAAACAGAGTATC
17108021 GCTCTTTTGAG-CGAGAA
65 GCTCTTTTGAGTC-AGAA
* ** * *** * *
17108038 ACAGAGTATTGCTCTTTCGAGCGAGAAACAGAGCATTGTTCTTTCGAGCGAGAAACAGAGTATCG
1 ACAGAGTATTACTAATTCGAGCCAGAAACAGAGCATCACTCATTCAAGCGAGAAACAGAGTATCG
17108103 CTCTTTTGAGTCAGAA
66 CTCTTTTGAGTCAGAA
17108119 ACAGAGTAT
1 ACAGAGTAT
17108128 CGCTCTTTCC
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
81 73 0.97
82 2 0.03
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (81 bp):
ACAGAGTATTACTAATTCGAGCCAGAAACAGAGCATCACTCATTCAAGCGAGAAACAGAGTATCG
CTCTTTTGAGTCAGAA
Found at i:17108075 original size:27 final size:27
Alignment explanation
Indices: 17107980--17108136 Score: 199
Period size: 27 Copynumber: 5.8 Consensus size: 27
17107970 AATTCAGGCC
* ** * *
17107980 AGAAATAGAGTATCACTCATTCAAGCG
1 AGAAACAGAGTATTGCTCTTTCGAGCG
*
17108007 AGAAACAGAGTATTGCTCTTTTGAGCG
1 AGAAACAGAGTATTGCTCTTTCGAGCG
17108034 AGAAACAGAGTATTGCTCTTTCGAGCG
1 AGAAACAGAGTATTGCTCTTTCGAGCG
* *
17108061 AGAAACAGAGCATTGTTCTTTCGAGCG
1 AGAAACAGAGTATTGCTCTTTCGAGCG
* *
17108088 AGAAACAGAGTATCGCTCTTTTGAGTC-
1 AGAAACAGAGTATTGCTCTTTCGAG-CG
*
17108115 AGAAACAGAGTATCGCTCTTTC
1 AGAAACAGAGTATTGCTCTTTC
17108137 CTCAGACTTT
Statistics
Matches: 115, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
27 114 0.99
28 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (27 bp):
AGAAACAGAGTATTGCTCTTTCGAGCG
Found at i:17110922 original size:20 final size:20
Alignment explanation
Indices: 17110897--17110967 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
17110887 AAAATATAAA
17110897 TTTGAATTTTTTATAAA-TAT
1 TTTGAATTTTTTA-AAACTAT
* *
17110917 TTTGAA-TTTTAAAAATTAT
1 TTTGAATTTTTTAAAACTAT
**
17110936 TTTGAATTTTAGAAAACTAT
1 TTTGAATTTTTTAAAACTAT
17110956 TTTGAATTTTTT
1 TTTGAATTTTTT
17110968 TTGCAATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
18 3 0.07
19 14 0.33
20 26 0.60
ACGTcount: A:0.35, C:0.01, G:0.07, T:0.56
Consensus pattern (20 bp):
TTTGAATTTTTTAAAACTAT
Found at i:17110936 original size:19 final size:18
Alignment explanation
Indices: 17110905--17110965 Score: 86
Period size: 20 Copynumber: 3.2 Consensus size: 18
17110895 AATTTGAATT
*
17110905 TTTTATAAATATTTTGAA
1 TTTTAAAAATATTTTGAA
17110923 TTTTAAAAATTATTTTGAA
1 TTTTAAAAA-TATTTTGAA
17110942 TTTTAGAAAACTATTTTGAA
1 TTTTA-AAAA-TATTTTGAA
17110962 TTTT
1 TTTT
17110966 TTTTGCAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.21
19 14 0.36
20 17 0.44
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.54
Consensus pattern (18 bp):
TTTTAAAAATATTTTGAA
Found at i:17112473 original size:12 final size:13
Alignment explanation
Indices: 17112445--17112473 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
17112435 ATCTCTTATT
17112445 AAATTGTAAAGAA
1 AAATTGTAAAGAA
17112458 AAATTGTAAA-AA
1 AAATTGTAAAGAA
17112470 AAAT
1 AAAT
17112474 AAAATAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (13 bp):
AAATTGTAAAGAA
Found at i:17112504 original size:13 final size:14
Alignment explanation
Indices: 17112486--17112520 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
17112476 AATAATTAAA
17112486 GTTAAAATAAA-TT
1 GTTAAAATAAAGTT
17112499 GTTAAAATAAAGTT
1 GTTAAAATAAAGTT
*
17112513 TTTAAAAT
1 GTTAAAAT
17112521 TTAATTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (14 bp):
GTTAAAATAAAGTT
Found at i:17118989 original size:18 final size:18
Alignment explanation
Indices: 17118947--17119033 Score: 97
Period size: 18 Copynumber: 4.8 Consensus size: 18
17118937 CGGGAGGAAT
*
17118947 AGCATACTAGCTCGTTTG-
1 AGCATACTGGCTCG-TTGA
* *
17118965 AGTATACTGGCTTGTTGA
1 AGCATACTGGCTCGTTGA
*
17118983 AGCATACTGACTCGTTTG-
1 AGCATACTGGCTCG-TTGA
*
17119001 AGCATATTGGCTCGTTGA
1 AGCATACTGGCTCGTTGA
17119019 AGCATACTGGCTCGT
1 AGCATACTGGCTCGT
17119034 AAGAGCATAT
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
17 6 0.11
18 48 0.84
19 3 0.05
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (18 bp):
AGCATACTGGCTCGTTGA
Found at i:17118997 original size:36 final size:36
Alignment explanation
Indices: 17118947--17119047 Score: 123
Period size: 36 Copynumber: 2.8 Consensus size: 36
17118937 CGGGAGGAAT
* *
17118947 AGCATACT-AGCTCGTTTGAGTATACTGGCTTGTTGA
1 AGCATACTGA-CTCGTTTGAGCATACTGGCTCGTTGA
*
17118983 AGCATACTGACTCGTTTGAGCATATTGGCTCGTTGA
1 AGCATACTGACTCGTTTGAGCATACTGGCTCGTTGA
* **
17119019 AGCATACTGGCTCGTAAGAGCATATCTGG
1 AGCATACTGACTCGTTTGAGCATA-CTGG
17119048 ACTGCATGAA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
36 52 0.93
37 4 0.07
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.32
Consensus pattern (36 bp):
AGCATACTGACTCGTTTGAGCATACTGGCTCGTTGA
Found at i:17119040 original size:18 final size:17
Alignment explanation
Indices: 17118947--17119047 Score: 94
Period size: 18 Copynumber: 5.6 Consensus size: 17
17118937 CGGGAGGAAT
*
17118947 AGCATACTAGCTCGTTTG
1 AGCATACTGGCTCG-TTG
* *
17118965 AGTATACTGGCTTGTTG
1 AGCATACTGGCTCGTTG
*
17118982 AAGCATACTGACTCGTTTG
1 -AGCATACTGGCTCG-TTG
*
17119001 AGCATATTGGCTCGTTG
1 AGCATACTGGCTCGTTG
*
17119018 AAGCATACTGGCTCGTAAG
1 -AGCATACTGGCTCGT-TG
17119037 AGCATATCTGG
1 AGCATA-CTGG
17119048 ACTGCATGAA
Statistics
Matches: 68, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
17 6 0.09
18 54 0.79
19 8 0.12
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.32
Consensus pattern (17 bp):
AGCATACTGGCTCGTTG
Found at i:17121227 original size:20 final size:21
Alignment explanation
Indices: 17121197--17121246 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
17121187 ATTAGAATGA
17121197 TTTATATTAAG-TGTAAAT-AGG
1 TTTA-ATTAAGAT-TAAATGAGG
17121218 TTTAATTAAGATTAAATGAGG
1 TTTAATTAAGATTAAATGAGG
17121239 -TTAATTAA
1 TTTAATTAA
17121247 AGCTTAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (21 bp):
TTTAATTAAGATTAAATGAGG
Found at i:17123103 original size:21 final size:21
Alignment explanation
Indices: 17123055--17123106 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
17123045 GGAGGTTTTA
*
17123055 GTATCGGTAGAAGCATGACAT
1 GTATCGGTAGAAGCATCACAT
* *
17123076 GTTTCGGTAGAAGTC-TCACTT
1 GTATCGGTAGAAG-CATCACAT
17123097 GTATCGGTAG
1 GTATCGGTAG
17123107 TACTGCCTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGCATCACAT
Found at i:17123684 original size:3 final size:3
Alignment explanation
Indices: 17123676--17123726 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
17123666 CAATGGCCAC
17123676 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17123724 ATA
1 ATA
17123727 TCATCTTATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:17128013 original size:114 final size:113
Alignment explanation
Indices: 17127843--17128262 Score: 407
Period size: 114 Copynumber: 3.8 Consensus size: 113
17127833 GATTCGCTAC
* * *
17127843 TTGTTTTAACCGACTTCTCTGTATCTTACCA-AGAAGATGGAATTTGAAGTCTCACTCCACTCTA
1 TTGTTTTAACCCACTTCTCTGTACCTCACCAGA-AAGATGG-ATTTGAAGTCTCACTCCACTCTA
* *
17127907 CTGTATCCTTAGGGACATTGAGCTCGGTTTCGTTGTTTTGATTCAACATA
64 CTGTATCCTTAGGGACGTTGAGCTCGGCTTCGTTGTTTTGATTCAACATA
* * * * *
17127957 TTGTTTTGACCCACTTCTCTGTACCTCACCAGAAAGATAGGATTTGAAGCCTCACTCTACTCCAT
1 TTGTTTTAACCCACTTCTCTGTACCTCACCAGAAAGAT-GGATTTGAAGTCTCACTCCACTCTAC
* *
17128022 TGTATCCTTAGGGATGTTGAGCTTGGCTTCGTTGTTTTGATTCAACATA
65 TGTATCCTTAGGGACGTTGAGCTCGGCTTCGTTGTTTTGATTCAACATA
* * * * *
17128071 TAGTTTTGACCC-CTTTCTTTGTACCCCACTC-GAAAGATGGGTTTTGAAG--T--CT-CA---T
1 TTGTTTTAACCCAC-TTCTCTGTACCTCAC-CAGAAAGAT-GGATTTGAAGTCTCACTCCACTCT
* * * * ** ** * *
17128126 --TGTATTCTAAGAGACGTTGAGTTCTACTTCGTCATTTTGATTAAACACA
63 ACTGTATCCTTAGGGACGTTGAGCTCGGCTTCGTTGTTTTGATTCAACATA
* *
17128175 CTGTTTTAACCCACTTCTCTGTACCTCACCAGGAAGATGAGATTTGAAGTCTCACTCCACTCTAC
1 TTGTTTTAACCCACTTCTCTGTACCTCACCAGAAAGATG-GATTTGAAGTCTCACTCCACTCTAC
* *
17128240 TGTATCCTCAGGGACGTTAAGCT
65 TGTATCCTTAGGGACGTTGAGCT
17128263 TTGCTTAATT
Statistics
Matches: 246, Mismatches: 43, Indels: 34
0.76 0.13 0.11
Matches are distributed among these distances:
103 2 0.01
104 73 0.30
105 1 0.00
106 1 0.00
108 2 0.01
109 3 0.01
110 2 0.01
112 2 0.01
113 1 0.00
114 155 0.63
115 4 0.02
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (113 bp):
TTGTTTTAACCCACTTCTCTGTACCTCACCAGAAAGATGGATTTGAAGTCTCACTCCACTCTACT
GTATCCTTAGGGACGTTGAGCTCGGCTTCGTTGTTTTGATTCAACATA
Found at i:17128345 original size:96 final size:95
Alignment explanation
Indices: 17128178--17128480 Score: 435
Period size: 96 Copynumber: 3.2 Consensus size: 95
17128168 AAACACACTG
*
17128178 TTTTAACCCACTTCTCTGTACCTCACCAGGAAGATGAGATTTGAAGTCTCACTCCACTCTACTGT
1 TTTTAACCCACTTCTCTGTACCTCACCAGGAAGATG-GATTTGAAGTCTCACTCCACTCTATTGT
* * * * *
17128243 ATCCTCAGGGACGTTAAGCTTTGCTTAATTG
65 ATCCTCAGGGATGTTGAGCTCTGCTTCATTA
* * * *
17128274 TTTTGACCCACTTCTCTGTACCTCACTAGAAAGATAGGATTTGAAGTCTCACTCCACTCCATTGT
1 TTTTAACCCACTTCTCTGTACCTCACCAGGAAGAT-GGATTTGAAGTCTCACTCCACTCTATTGT
*
17128339 AACCTCAGGGATGTTGAGCTCTGCTTCATTA
65 ATCCTCAGGGATGTTGAGCTCTGCTTCATTA
*
17128370 TTTTAACCCACTTCTCTATACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACTCTATTGT
1 TTTTAACCCACTTCTCTGTACCTCACCAGGAAGAT-GGATTTGAAGTCTCACTCCACTCTATTGT
* *
17128435 ATCCTTAGGGATGTTGAGCTCTACTTCATTA
65 ATCCTCAGGGATGTTGAGCTCTGCTTCATTA
* *
17128466 TATTGACCCACTTCT
1 TTTTAACCCACTTCT
17128481 TTGCAATTTT
Statistics
Matches: 184, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
96 183 0.99
97 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (95 bp):
TTTTAACCCACTTCTCTGTACCTCACCAGGAAGATGGATTTGAAGTCTCACTCCACTCTATTGTA
TCCTCAGGGATGTTGAGCTCTGCTTCATTA
Found at i:17128641 original size:49 final size:50
Alignment explanation
Indices: 17128548--17129522 Score: 423
Period size: 49 Copynumber: 19.8 Consensus size: 50
17128538 GCGTATAAGA
* * * * * *
17128548 TTCACCATTGTGGCTTCAATCTTTCCCGTCATGT-TTCTAAGGTACTAGG
1 TTCACCGTTGCGGCCTCAACCTTTCCCATCATATCTTCTAAGGTACTAGG
* ** * * * *
17128597 TTCACCGTTACGGCCTCAACCTTTCCTTTTATAT-TTCCATGGTACTAGA
1 TTCACCGTTGCGGCCTCAACCTTTCCCATCATATCTTCTAAGGTACTAGG
* ** * * * * *** * * *
17128646 TCCGTCGTTACGGCCTCGATCATTCTTGTCACATCTTTTAAGGGA-TAAGG
1 TTCACCGTTGCGGCCTCAACCTTTCCCATCATATCTTCTAAGGTACT-AGG
** * * * * * *
17128696 TTCGTCGTTGCGGCCTCGACCTTTCCCTTTATATTTTC-ATGGTACTAGA
1 TTCACCGTTGCGGCCTCAACCTTTCCCATCATATCTTCTAAGGTACTAGG
* * * * *
17128745 TTCACCGTTGCAGCCTCAATCTTTCCCATCATGT-TTCTAAGGTACCAAG
1 TTCACCGTTGCGGCCTCAACCTTTCCCATCATATCTTCTAAGGTACTAGG
*** * * * * * * *
17128794 TTCGTTGTTGTGACCTCAACCTTTCCCTTTATAT-TTCCATGGTACTAGA
1 TTCACCGTTGCGGCCTCAACCTTTCCCATCATATCTTCTAAGGTACTAGG
** * * * *
17128843 TAT-ACCGTTGCAACCTCGATCTTTCCCATCATGTCTTTTAAGGTA-TAGGG
1 T-TCACCGTTGCGGCCTCAACCTTTCCCATCATATCTTCTAAGGTACTA-GG
** * ** *
17128893 TTCGTCATTGCGGCCTCAACCTTTCCTTTCATATCTTC-ATGGTAC--GG
1 TTCACCGTTGCGGCCTCAACCTTTCCCATCATATCTTCTAAGGTACTAGG
* * * * * *
17128940 ATTCACCGTTACGACCGT-AATCTTTCCCATCACATCTTTTAAGGTACAAGG
1 -TTCACCGTTGCGGCC-TCAACCTTTCCCATCATATCTTCTAAGGTACTAGG
* *
17128991 TTCACCGTTGCGGCCTCAATCTTTCCCATCACATCTTCTAAGGTAC-AGGG
1 TTCACCGTTGCGGCCTCAACCTTTCCCATCATATCTTCTAAGGTACTA-GG
* * *
17129041 TTCACCGTTACGGCCTCAA-CTTTCCCATCACATCTTCTAAGGTACAAGG
1 TTCACCGTTGCGGCCTCAACCTTTCCCATCATATCTTCTAAGGTACTAGG
* * *
17129090 TTCACCGTTGCGGCCTCAACCTTTCCCTTCATATCTTC-ATA-GTA-TCGAA
1 TTCACCGTTGCGGCCTCAACCTTTCCCATCATATCTTCTA-AGGTACTAG-G
* * * * *
17129139 TTCGCCGTTGCAGCCTCAA-TTCTTCCCATCACAACTTCTAAGGTAC-AGGG
1 TTCACCGTTGCGGCCTCAACCT-TTCCCATCATATCTTCTAAGGTACTA-GG
* * * ** * * *
17129189 TTCGCTGTTGCGGCCTCAACCTTT--CTTTTTAT-TTCCATGGTACTAGA
1 TTCACCGTTGCGGCCTCAACCTTTCCCATCATATCTTCTAAGGTACTAGG
* * * * *
17129236 TTCGCCATTACGGCCTCAATCC-TTCCCATCACATCTTCTAAGATA-TAGGG
1 TTCACCGTTGCGGCCTCAA-CCTTTCCCATCATATCTTCTAAGGTACTA-GG
** * ** * * *
17129286 TTCGTCGTTGCAGCCTCAACCTTTCCTTTTATTTCTTCATAA--TAC-AGAA
1 TTCACCGTTGCGGCCTCAACCTTTCCCATCATATCTTC-TAAGGTACTAG-G
* * * * * * *
17129335 TCCACCATTGCAGCTTCGATCC-TTCCCATCACATCTTCTAAGGTGC-AGGG
1 TTCACCGTTGCGGCCTC-AACCTTTCCCATCATATCTTCTAAGGTACTA-GG
* * * * * *
17129385 TTCGCCGTTGCGGCCTCAACCTTTCCCTTTATTTCCATC-ATGGTACT-GG
1 TTCACCGTTGCGGCCTCAACCTTTCCCATCATAT-CTTCTAAGGTACTAGG
*** * * *
17129434 ATTTGTCGTTGCGGGCTCAATCC-TTCCCATCACATCTTCTAAAGTAC-AGGG
1 -TTCACCGTTGCGGCCTCAA-CCTTTCCCATCATATCTTCTAAGGTACTA-GG
* * * *
17129485 TTCGCCGTTGTGACCTCAACCTTTCCCTTCATATCTTC
1 TTCACCGTTGCGGCCTCAACCTTTCCCATCATATCTTC
17129523 ATGGTTCCTC
Statistics
Matches: 679, Mismatches: 198, Indels: 97
0.70 0.20 0.10
Matches are distributed among these distances:
47 30 0.04
48 41 0.06
49 299 0.44
50 294 0.43
51 15 0.02
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.35
Consensus pattern (50 bp):
TTCACCGTTGCGGCCTCAACCTTTCCCATCATATCTTCTAAGGTACTAGG
Found at i:17128761 original size:99 final size:99
Alignment explanation
Indices: 17128563--17129527 Score: 787
Period size: 99 Copynumber: 9.8 Consensus size: 99
17128553 CATTGTGGCT
* ** * ** * *
17128563 TCAATCTTTCCCGTCATGT-TTCTAAGGTACTAGGTTCACCGTTACGGCCTCAACCTTTCCTTTT
1 TCAATCTTTCCCATCACATCTTCTAAGGTACAAGGTTCGTCGTTGCGGCCTCAACCTTTCCCTTT
* * ** *
17128627 ATATTTCCATGGTACTAGATCCGTCGTTACGGCC
66 ATATTTTCATGGTACTAGATTCACCGTTACAGCC
* * *** * * * *
17128661 TCGATCATTCTTGTCACATCTTTTAAGGGATAAGGTTCGTCGTTGCGGCCTCGACCTTTCCCTTT
1 TCAATCTTTCCCATCACATCTTCTAAGGTACAAGGTTCGTCGTTGCGGCCTCAACCTTTCCCTTT
*
17128726 ATATTTTCATGGTACTAGATTCACCGTTGCAGCC
66 ATATTTTCATGGTACTAGATTCACCGTTACAGCC
** * * *
17128760 TCAATCTTTCCCATCATGT-TTCTAAGGTACCAA-GTTCGTTGTTGTGACCTCAACCTTTCCCTT
1 TCAATCTTTCCCATCACATCTTCTAAGGTA-CAAGGTTCGTCGTTGCGGCCTCAACCTTTCCCTT
* * *
17128823 TATATTTCCATGGTACTAGATAT-ACCGTTGCAACC
65 TATATTTTCATGGTACTAGAT-TCACCGTTACAGCC
* ** * * * *
17128858 TCGATCTTTCCCATCATGTCTTTTAAGGTATAGGGTTCGTCATTGCGGCCTCAACCTTT-CCTTT
1 TCAATCTTTCCCATCACATCTTCTAAGGTACAAGGTTCGTCGTTGCGGCCTCAACCTTTCCCTTT
* *
17128922 CATATCTTCATGGTAC-GGATTCACCGTTAC-GACC
66 -ATATTTTCATGGTACTAGATTCACCGTTACAG-CC
* ** * *
17128956 GT-AATCTTTCCCATCACATCTTTTAAGGTACAAGGTTCACCGTTGCGGCCTCAATCTTTCCCAT
1 -TCAATCTTTCCCATCACATCTTCTAAGGTACAAGGTTCGTCGTTGCGGCCTCAACCTTTCCCTT
* * * * * *
17129020 CACATCTTCTAAGGTAC-AGGGTTCACCGTTACGGCC
65 TATATTTTC-ATGGTACTA-GATTCACCGTTACAGCC
** *
17129056 TCAA-CTTTCCCATCACATCTTCTAAGGTACAAGGTTCACCGTTGCGGCCTCAACCTTTCCCTTC
1 TCAATCTTTCCCATCACATCTTCTAAGGTACAAGGTTCGTCGTTGCGGCCTCAACCTTTCCCTTT
* * * * *
17129120 ATATCTTCATAGTA-TCGAATTCGCCGTTGCAGCC
66 ATATTTTCATGGTACTAG-ATTCACCGTTACAGCC
* *
17129154 TCAAT-TCTTCCCATCACAACTTCTAAGGTACAGGGTTCG-CTGTTGCGGCCTCAACCTTT--CT
1 TCAATCT-TTCCCATCACATCTTCTAAGGTACAAGGTTCGTC-GTTGCGGCCTCAACCTTTCCCT
* * * * *
17129215 TTTTATTTCCATGGTACTAGATTCGCCATTACGGCC
64 TTATATTTTCATGGTACTAGATTCACCGTTACAGCC
* * * * * *
17129251 TCAATCCTTCCCATCACATCTTCTAAGATATAGGGTTCGTCGTTGCAGCCTCAACCTTTCCTTTT
1 TCAATCTTTCCCATCACATCTTCTAAGGTACAAGGTTCGTCGTTGCGGCCTCAACCTTTCCCTTT
** * * * *
17129316 AT-TTCTTCATAATAC-AGAATCCACCATTGCAGCT
66 ATATT-TTCATGGTACTAG-ATTCACCGTTACAGCC
* * * * *
17129350 TCGATCCTTCCCATCACATCTTCTAAGGTGCAGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTT
1 TCAATCTTTCCCATCACATCTTCTAAGGTACAAGGTTCGTCGTTGCGGCCTCAACCTTTCCCTTT
* * *** * * *
17129415 AT-TTCCATCATGGTACTGGATTTGTCGTTGCGGGC
66 ATATT--TTCATGGTACTAGATTCACCGTTACAGCC
* * * * * * *
17129450 TCAATCCTTCCCATCACATCTTCTAAAGTACAGGGTTCGCCGTTGTGACCTCAACCTTTCCCTTC
1 TCAATCTTTCCCATCACATCTTCTAAGGTACAAGGTTCGTCGTTGCGGCCTCAACCTTTCCCTTT
*
17129515 ATATCTTCATGGT
66 ATATTTTCATGGT
17129528 TCCTCGGTTC
Statistics
Matches: 708, Mismatches: 130, Indels: 57
0.79 0.15 0.06
Matches are distributed among these distances:
97 79 0.11
98 198 0.28
99 335 0.47
100 93 0.13
101 3 0.00
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.35
Consensus pattern (99 bp):
TCAATCTTTCCCATCACATCTTCTAAGGTACAAGGTTCGTCGTTGCGGCCTCAACCTTTCCCTTT
ATATTTTCATGGTACTAGATTCACCGTTACAGCC
Found at i:17128882 original size:197 final size:195
Alignment explanation
Indices: 17128545--17129524 Score: 875
Period size: 197 Copynumber: 5.0 Consensus size: 195
17128535 TCGGCGTATA
* ** * * * * *
17128545 AGATTCACCATTGTGGCTTCAATCTTTCCCGTCATGTTTCTAAGGTACTAGGTTCACCGTTACGG
1 AGATTCACCGTTGCAGCCTCAATCTTTCCCATCATATTTCTAAGGTAC-AGGTTCGCCGTTGCGG
* * ** * ***
17128610 CCTCAACCTTTCCTTTTATATTTCCATGGTACTAGATCCGTCGTTACGGCCTCGATCATTCTTGT
65 CCTCAACCTTTCCCTTTATATTTCCATGGTACTAGATTCACCGTTACGGCCTCGATCTTTCCCAT
* * * * *
17128675 CACATCTTTTAAGGGATAAGGTTCGTCGTTGCGGCCTCGACCTTTCCCTTTATATTTTCATGGTA
130 CACATCTTCTAAGGTATAAGGTTCGTCGTTGCGGCCTCAACCTTTCCCTTTATATCTTCATAGTA
17128740 C
195 C
* * ** *
17128741 TAGATTCACCGTTGCAGCCTCAATCTTTCCCATCATGTTTCTAAGGTACCAAGTTCGTTGTTGTG
1 -AGATTCACCGTTGCAGCCTCAATCTTTCCCATCATATTTCTAAGGTA-CAGGTTCGCCGTTGCG
* * **
17128806 ACCTCAACCTTTCCCTTTATATTTCCATGGTACTAGATAT-ACCGTTGCAACCTCGATCTTTCCC
64 GCCTCAACCTTTCCCTTTATATTTCCATGGTACTAGAT-TCACCGTTACGGCCTCGATCTTTCCC
** * * * *
17128870 ATCATGTCTTTTAAGGTATAGGGTTCGTCATTGCGGCCTCAACCTTT-CCTTTCATATCTTCATG
128 ATCACATCTTCTAAGGTATAAGGTTCGTCGTTGCGGCCTCAACCTTTCCCTTT-ATATCTTCATA
17128934 GTAC
192 GTAC
* * * * *
17128938 GGATTCACCGTTAC-GACCGT-AATCTTTCCCATCACATCTTTTAAGGTACAAGGTTCACCGTTG
1 AGATTCACCGTTGCAG-CC-TCAATCTTTCCCATCATAT-TTCTAAGGTAC-AGGTTCGCCGTTG
* * * * * * * *
17129001 CGGCCTCAATCTTTCCCATCACATCTTCTAAGGTAC-AGGGTTCACCGTTACGGCCTC-AACTTT
62 CGGCCTCAACCTTTCCCTTTATAT-TTCCATGGTACTA-GATTCACCGTTACGGCCTCGATCTTT
* ** *
17129064 CCCATCACATCTTCTAAGGTACAAGGTTCACCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCA
125 CCCATCACATCTTCTAAGGTATAAGGTTCGTCGTTGCGGCCTCAACCTTTCCCTTTATATCTTCA
17129129 TAGTATC
190 TAGTA-C
* * * *
17129136 -GAATTCGCCGTTGCAGCCTCAAT-TCTTCCCATCACAACTTCTAAGGTACAGGGTTCGCTGTTG
1 AG-ATTCACCGTTGCAGCCTCAATCT-TTCCCATCA-TATTTCTAAGGTACA-GGTTCGCCGTTG
* * * * *
17129199 CGGCCTCAACCTTT--CTTTTTATTTCCATGGTACTAGATTCGCCATTACGGCCTCAATCCTTCC
62 CGGCCTCAACCTTTCCCTTTATATTTCCATGGTACTAGATTCACCGTTACGGCCTCGATCTTTCC
* * * * *
17129262 CATCACATCTTCTAAGATATAGGGTTCGTCGTTGCAGCCTCAACCTTTCCTTTTATTTCTTCATA
127 CATCACATCTTCTAAGGTATAAGGTTCGTCGTTGCGGCCTCAACCTTTCCCTTTATATCTTCATA
*
17129327 ATAC
192 GTAC
* * * * * * *
17129331 AGAATCCACCATTGCAGCTTCGATCCTTCCCATCACATCTTCTAAGGTGCAGGGTTCGCCGTTGC
1 AG-ATTCACCGTTGCAGCCTCAATCTTTCCCATCATAT-TTCTAAGGTACA-GGTTCGCCGTTGC
* * *** * * * *
17129396 GGCCTCAACCTTTCCCTTTAT-TTCCATCATGGTACTGGATTTGTCGTTGCGGGCTCAATCCTTC
63 GGCCTCAACCTTTCCCTTTATATTTC--CATGGTACTAGATTCACCGTTACGGCCTCGATCTTTC
* * * * * * *
17129460 CCATCACATCTTCTAAAGTACAGGGTTCGCCGTTGTGACCTCAACCTTTCCCTTCATATCTTCAT
126 CCATCACATCTTCTAAGGTATAAGGTTCGTCGTTGCGGCCTCAACCTTTCCCTTTATATCTTCAT
17129525 GGTTCCTCGG
Statistics
Matches: 637, Mismatches: 119, Indels: 52
0.79 0.15 0.06
Matches are distributed among these distances:
195 28 0.04
196 168 0.26
197 263 0.41
198 90 0.14
199 88 0.14
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.35
Consensus pattern (195 bp):
AGATTCACCGTTGCAGCCTCAATCTTTCCCATCATATTTCTAAGGTACAGGTTCGCCGTTGCGGC
CTCAACCTTTCCCTTTATATTTCCATGGTACTAGATTCACCGTTACGGCCTCGATCTTTCCCATC
ACATCTTCTAAGGTATAAGGTTCGTCGTTGCGGCCTCAACCTTTCCCTTTATATCTTCATAGTAC
Found at i:17129035 original size:148 final size:148
Alignment explanation
Indices: 17128846--17129311 Score: 436
Period size: 148 Copynumber: 3.2 Consensus size: 148
17128836 TACTAGATAT
* * ** * * *
17128846 ACCGTTGCAACCTCGATCTTTCCCATCATGTCTTTTAAGGTATAGGGTTCGTCATTGCGGCCTCA
1 ACCGTTGCAGCCTCAATCTTTCCCATCACATCTTCTAAGGTACAGGGTTCG-CGTTGCGGCCTCA
*
17128911 ACCTTTCCTTTCATATCTTCATGGTAC-GGATTCACCGTTACGACCGT-AATCTTTCCCATCACA
65 ACCTTTCCTTTCATATCTTCATGGTACAGGATTCACCGTTACGGCC-TCAATCTTTCCCATCACA
17128974 TCTTTTAAGGTACAAGGTTC
129 TCTTTTAAGGTACAAGGTTC
* * *
17128994 ACCGTTGCGGCCTCAATCTTTCCCATCACATCTTCTAAGGTACAGGGTTCACCGTTACGGCCTCA
1 ACCGTTGCAGCCTCAATCTTTCCCATCACATCTTCTAAGGTACAGGGTTC-GCGTTGCGGCCTCA
** * * * * * *
17129059 A-CTTTCCCATCACATCTTCTAAGGTACAAGG-TTCACCGTTGCGGCCTCAACCTTTCCCTTCAT
65 ACCTTTCCTTTCATATCTTC-ATGGTAC-AGGATTCACCGTTACGGCCTCAATCTTTCCCATCAC
*
17129122 ATC-TTCATA-GTATCGAA--TTC
128 ATCTTTTA-AGGTA-C-AAGGTTC
* *
17129142 GCCGTTGCAGCCTCAAT-TCTTCCCATCACAACTTCTAAGGTACAGGGTTCGCTGTTGCGGCCTC
1 ACCGTTGCAGCCTCAATCT-TTCCCATCACATCTTCTAAGGTACAGGGTTCGC-GTTGCGGCCTC
* * * *
17129206 AACCTTT-CTTT-TTAT-TTCCATGGTACTA-GATTCGCCATTACGGCCTCAATCCTTCCCATCA
64 AACCTTTCCTTTCATATCTT-CATGGTAC-AGGATTCACCGTTACGGCCTCAATCTTTCCCATCA
* * * *
17129267 CATCTTCTAAGATATAGGGTTC
127 CATCTTTTAAGGTACAAGGTTC
** *
17129289 GTCGTTGCAGCCTCAACCTTTCC
1 ACCGTTGCAGCCTCAATCTTTCC
17129312 TTTTATTTCT
Statistics
Matches: 255, Mismatches: 45, Indels: 37
0.76 0.13 0.11
Matches are distributed among these distances:
145 2 0.01
146 38 0.15
147 46 0.18
148 131 0.51
149 34 0.13
150 4 0.02
ACGTcount: A:0.21, C:0.30, G:0.16, T:0.33
Consensus pattern (148 bp):
ACCGTTGCAGCCTCAATCTTTCCCATCACATCTTCTAAGGTACAGGGTTCGCGTTGCGGCCTCAA
CCTTTCCTTTCATATCTTCATGGTACAGGATTCACCGTTACGGCCTCAATCTTTCCCATCACATC
TTTTAAGGTACAAGGTTC
Found at i:17129109 original size:296 final size:296
Alignment explanation
Indices: 17128563--17129527 Score: 906
Period size: 296 Copynumber: 3.3 Consensus size: 296
17128553 CATTGTGGCT
* ** * *
17128563 TCAATCTTTCCCGTCATGT-TTCTAAGGTACTA-GGTTCACCGTTACGGCCTCAACCTTTCCTTT
1 TCAATCTTTCCCATCACATCTTCTAAGGTAC-AGGGTTC-GCGTTGCGGCCTCAACCTTTCCTTT
* * ** * * * * *** *
17128626 TATAT-TTCCATGGTACTAGATCCGTCGTTACGGCCTCGATCATTCTTGTCACATCTTTTAAGGG
64 CATATCTT-CATGGTACTAGATTCACCATTACGACCTCAATCCTTCCCATCACATCTTTTAAGGT
* * *
17128690 ATAAGGTTCGTCGTTGCGGCCTCGACCTTTCCCTTTATATTTTC-ATGGTACTA-GATTCACCGT
128 ATAAGGTTCGTCGTTGCGGCCTCAACCTTTCCCTTTATATCTTCTAAGGTAC-AGGATTCACCGT
** ** * *
17128753 TGCAGCCTCAATCTTTCCCATCATGT-TTCTAAGGTACCAA-GTTCGTTGTTGTGACCTCAACCT
192 TGCAGCCTCAA-CTTTCCCATCACATCTTCTAAGGTA-CAAGGTTCGCCGTTGCGGCCTCAACCT
* *
17128816 TTCCCTTTATATTTCCATGGTACTAGATATACCGTTGCAACC
255 TTCCCTTTATATTTCCATGGTACTAGATATGCCGTTGCAGCC
* ** * * *
17128858 TCGATCTTTCCCATCATGTCTTTTAAGGTATAGGGTTCGTCATTGCGGCCTCAACCTTTCCTTTC
1 TCAATCTTTCCCATCACATCTTCTAAGGTACAGGGTTCG-CGTTGCGGCCTCAACCTTTCCTTTC
* * *
17128923 ATATCTTCATGGTAC-GGATTCACCGTTACGACCGT-AATCTTTCCCATCACATCTTTTAAGGTA
65 ATATCTTCATGGTACTAGATTCACCATTACGACC-TCAATCCTTCCCATCACATCTTTTAAGGTA
* ** * * * * * *
17128986 CAAGGTTCACCGTTGCGGCCTCAATCTTTCCCATCACATCTTCTAAGGTACAGGGTTCACCGTTA
129 TAAGGTTCGTCGTTGCGGCCTCAACCTTTCCCTTTATATCTTCTAAGGTACAGGATTCACCGTTG
* *
17129051 CGGCCTCAACTTTCCCATCACATCTTCTAAGGTACAAGGTTCACCGTTGCGGCCTCAACCTTTCC
194 CAGCCTCAACTTTCCCATCACATCTTCTAAGGTACAAGGTTCGCCGTTGCGGCCTCAACCTTTCC
* * *
17129116 CTTCATATCTT-CATAGTA-TCGA-ATTCGCCGTTGCAGCC
259 CTTTATAT-TTCCATGGTACTAGATA-T-GCCGTTGCAGCC
*
17129154 TCAAT-TCTTCCCATCACAACTTCTAAGGTACAGGGTTCGCTGTTGCGGCCTCAACCTTT-CTTT
1 TCAATCT-TTCCCATCACATCTTCTAAGGTACAGGGTTCGC-GTTGCGGCCTCAACCTTTCCTTT
* * * * *
17129217 -TTAT-TTCCATGGTACTAGATTCGCCATTACGGCCTCAATCCTTCCCATCACATCTTCTAAGAT
64 CATATCTT-CATGGTACTAGATTCACCATTACGACCTCAATCCTTCCCATCACATCTTTTAAGGT
* * * * * * *
17129280 ATAGGGTTCGTCGTTGCAGCCTCAACCTTTCCTTTTATTTCTTCATAA--TACAGAATCCACCAT
128 ATAAGGTTCGTCGTTGCGGCCTCAACCTTTCCCTTTATATCTTC-TAAGGTACAGGATTCACCGT
* * * * *
17129343 TGCAGCTTCGATCCTTCCCATCACATCTTCTAAGGTGCAGGGTTCGCCGTTGCGGCCTCAACCTT
192 TGCAGCCTC-AACTTTCCCATCACATCTTCTAAGGTACAAGGTTCGCCGTTGCGGCCTCAACCTT
* * * * * *
17129408 TCCCTTTAT-TTCCATCATGGTACTGGATTTGTCGTTGCGGGC
256 TCCCTTTATATTTC--CATGGTACTAGATATGCCGTTGCAGCC
* * * * *
17129450 TCAATCCTTCCCATCACATCTTCTAAAGTACAGGGTTCGCCGTTGTGACCTCAACCTTTCCCTTC
1 TCAATCTTTCCCATCACATCTTCTAAGGTACAGGGTTCG-CGTTGCGGCCTCAACCTTTCCTTTC
17129515 ATATCTTCATGGT
65 ATATCTTCATGGT
17129528 TCCTCGGTTC
Statistics
Matches: 544, Mismatches: 97, Indels: 55
0.78 0.14 0.08
Matches are distributed among these distances:
293 3 0.01
294 31 0.06
295 242 0.44
296 245 0.45
297 12 0.02
298 9 0.02
299 2 0.00
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.35
Consensus pattern (296 bp):
TCAATCTTTCCCATCACATCTTCTAAGGTACAGGGTTCGCGTTGCGGCCTCAACCTTTCCTTTCA
TATCTTCATGGTACTAGATTCACCATTACGACCTCAATCCTTCCCATCACATCTTTTAAGGTATA
AGGTTCGTCGTTGCGGCCTCAACCTTTCCCTTTATATCTTCTAAGGTACAGGATTCACCGTTGCA
GCCTCAACTTTCCCATCACATCTTCTAAGGTACAAGGTTCGCCGTTGCGGCCTCAACCTTTCCCT
TTATATTTCCATGGTACTAGATATGCCGTTGCAGCC
Found at i:17129494 original size:50 final size:50
Alignment explanation
Indices: 17128847--17129522 Score: 400
Period size: 50 Copynumber: 13.7 Consensus size: 50
17128837 ACTAGATATA
** * * ** * *
17128847 CCGTTGCAACCTCGATCTTTCCCATCATGTCTTTTAAGGTATAGGGTTCG
1 CCGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAGGGTTCG
* * ** * * * *
17128897 TCATTGCGGCCTCAA-CCTTTCCTTTCATATCTTC-ATGGTAC-GGATTCA
1 CCGTTGCGGCCTCAATCC-TTCCCATCACATCTTCTAAGGTACAGGGTTCG
* * * * * *
17128945 CCGTTACGACCGT-AATCTTTCCCATCACATCTTTTAAGGTACAAGGTTCA
1 CCGTTGCGGCC-TCAATCCTTCCCATCACATCTTCTAAGGTACAGGGTTCG
* *
17128995 CCGTTGCGGCCTCAATCTTTCCCATCACATCTTCTAAGGTACAGGGTTCA
1 CCGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAGGGTTCG
* * * *
17129045 CCGTTACGGCCTCAA-CTTTCCCATCACATCTTCTAAGGTACAAGGTTCA
1 CCGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAGGGTTCG
* * **
17129094 CCGTTGCGGCCTCAA-CCTTTCCCTTCATATCTTC-ATA-GTATC-GAATTCG
1 CCGTTGCGGCCTCAATCC-TTCCCATCACATCTTCTA-AGGTA-CAGGGTTCG
* * *
17129143 CCGTTGCAGCCTCAATTCTTCCCATCACAACTTCTAAGGTACAGGGTTCG
1 CCGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAGGGTTCG
* * * *** * * *
17129193 CTGTTGCGGCCTCAA-CCTT-TCTTTTTAT-TTCCATGGTACTA-GATTCG
1 CCGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTAC-AGGGTTCG
* * * *
17129240 CCATTACGGCCTCAATCCTTCCCATCACATCTTCTAAGATATAGGGTTCG
1 CCGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAGGGTTCG
* * ** * ** ** * *
17129290 TCGTTGCAGCCTCAA-CCTTTCCTTTTATTTCTTCATAA--TACAGAATCCA
1 CCGTTGCGGCCTCAATCC-TTCCCATCACATCTTC-TAAGGTACAGGGTTCG
* * * * *
17129339 CCATTGCAGCTTCGATCCTTCCCATCACATCTTCTAAGGTGCAGGGTTCG
1 CCGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAGGGTTCG
* * ** * * * * *
17129389 CCGTTGCGGCCTCAA-CCTTTCCCTTTATTTCCATC-ATGGTACTGGATTTG
1 CCGTTGCGGCCTCAATCC-TTCCCATCACAT-CTTCTAAGGTACAGGGTTCG
* * *
17129439 TCGTTGCGGGCTCAATCCTTCCCATCACATCTTCTAAAGTACAGGGTTCG
1 CCGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAGGGTTCG
* * * *
17129489 CCGTTGTGACCTCAA-CCTTTCCCTTCATATCTTC
1 CCGTTGCGGCCTCAATCC-TTCCCATCACATCTTC
17129523 ATGGTTCCTC
Statistics
Matches: 466, Mismatches: 132, Indels: 56
0.71 0.20 0.09
Matches are distributed among these distances:
47 26 0.06
48 37 0.08
49 144 0.31
50 251 0.54
51 8 0.02
ACGTcount: A:0.20, C:0.30, G:0.16, T:0.34
Consensus pattern (50 bp):
CCGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAGGGTTCG
Found at i:17130517 original size:13 final size:14
Alignment explanation
Indices: 17130485--17130518 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
17130475 TTTTTAATTT
*
17130485 TTTTCTTCTTTTCTC
1 TTTT-TTCTTTCCTC
17130500 TTTTTTCTTTCCTC
1 TTTTTTCTTTCCTC
17130514 TTTTT
1 TTTTT
17130519 AGGTGGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTTTCTTTCCTC
Found at i:17149849 original size:18 final size:18
Alignment explanation
Indices: 17149802--17149851 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
17149792 ATCACACTTG
*
17149802 CAATGCTTTTAACCCTAC
1 CAATGCTTTTATCCCTAC
17149820 CAATGCTTTTATCCCTAC
1 CAATGCTTTTATCCCTAC
17149838 CAATGCTTTTATCC
1 CAATGCTTTTATCC
17149852 ACACAATCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.24, C:0.32, G:0.06, T:0.38
Consensus pattern (18 bp):
CAATGCTTTTATCCCTAC
Found at i:17152778 original size:4 final size:4
Alignment explanation
Indices: 17152765--17152807 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
17152755 AAATGATTGT
**
17152765 AAAG -AAG AAAG AAATG TGAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAA-G AAAG AAAG AAAG AAAG AAAG AAAG AAA
17152808 AAGGAAAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
3 3 0.09
4 28 0.85
5 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.26, T:0.05
Consensus pattern (4 bp):
AAAG
Found at i:17155997 original size:1 final size:1
Alignment explanation
Indices: 17155993--17156024 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
17155983 CTATTTTTAG
*
17155993 TTTTTTTTATTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
17156025 CTTTCTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:17156001 original size:10 final size:9
Alignment explanation
Indices: 17155986--17156024 Score: 55
Period size: 8 Copynumber: 4.4 Consensus size: 9
17155976 CTCCCCTCTA
17155986 TTTTTAGTTT
1 TTTTTA-TTT
17155996 TTTTTATTT
1 TTTTTATTT
17156005 TTTTT-TTT
1 TTTTTATTT
17156013 TTTTT-TTT
1 TTTTTATTT
17156021 TTTT
1 TTTT
17156025 CTTTCTCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 15 0.52
9 8 0.28
10 6 0.21
ACGTcount: A:0.05, C:0.00, G:0.03, T:0.92
Consensus pattern (9 bp):
TTTTTATTT
Found at i:17160488 original size:23 final size:23
Alignment explanation
Indices: 17160455--17160500 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
17160445 TTGACTAGAC
*
17160455 CTTCTAAAAGCTGCTGATTGGAT
1 CTTCTAAAAGCTGCTAATTGGAT
*
17160478 CTTCTAGAAGCTGCTAATTGGAT
1 CTTCTAAAAGCTGCTAATTGGAT
17160501 GTCACGTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (23 bp):
CTTCTAAAAGCTGCTAATTGGAT
Found at i:17161262 original size:9 final size:9
Alignment explanation
Indices: 17161234--17161263 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
17161224 AGCAACTATG
17161234 TTTTTTTCT
1 TTTTTTTCT
*
17161243 TCTTTTTCT
1 TTTTTTTCT
17161252 TTTTTTTCT
1 TTTTTTTCT
17161261 TTT
1 TTT
17161264 CGAACCTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:17171241 original size:21 final size:21
Alignment explanation
Indices: 17171201--17171241 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
17171191 ATCTACAGTC
17171201 AATGAGAAAGAAAACTAAAAA
1 AATGAGAAAGAAAACTAAAAA
17171222 AATGA-AAAGAAAACTAAAAA
1 AATGAGAAAGAAAACTAAAAA
17171242 CAGAGGGGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.73, C:0.05, G:0.12, T:0.10
Consensus pattern (21 bp):
AATGAGAAAGAAAACTAAAAA
Found at i:17173639 original size:20 final size:20
Alignment explanation
Indices: 17173577--17173640 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
17173567 GTATAAAAAA
*
17173577 ATTTTAATGTATTTTCAATTT
1 ATTTTAATGT-TTTTAAATTT
*
17173598 ATTTT-TTG-TTTTAATATTT
1 ATTTTAATGTTTTTAA-ATTT
*
17173617 ATTTTAATGTTTTTAAATAT
1 ATTTTAATGTTTTTAAATTT
17173637 ATTT
1 ATTT
17173641 GATATATTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
18 5 0.14
19 9 0.25
20 11 0.31
21 11 0.31
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.66
Consensus pattern (20 bp):
ATTTTAATGTTTTTAAATTT
Found at i:17182151 original size:28 final size:27
Alignment explanation
Indices: 17182088--17182147 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
17182078 AATATTAATT
*
17182088 AAACTAATTAAATTAATTATCCTGAAAT
1 AAACTAATTAAATTAATTATCCT-AAAA
*
17182116 AACCTAATTAAATTAATTAAT-CTAAAA
1 AAACTAATTAAATTAATT-ATCCTAAAA
17182143 AAACT
1 AAACT
17182148 TAATGGAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 7 0.25
28 19 0.68
29 2 0.07
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (27 bp):
AAACTAATTAAATTAATTATCCTAAAA
Found at i:17190160 original size:145 final size:143
Alignment explanation
Indices: 17189671--17190247 Score: 726
Period size: 142 Copynumber: 4.0 Consensus size: 143
17189661 CGAAGTTTTC
* * *
17189671 TTTTTTTAACAAAATCACTATTTTTCTTAAAAATCAAAATTTTTATTTTGAAATAGTTAAATAAT
1 TTTTTTTAAAAAAATCACTATTTTTCTTAAAAATCAAAATTTTTATTTCGAAATAGTTAAAAAAT
* * * *
17189736 C-AAATTTTGTTTAAAAATTTAAA-TTTTTCTCTTTAAAATGATTAAAAAATAGATTTTTA-TTT
66 CAAAATTTTATTTAAAAATTTAAACTTTTTC-CTTTAAAATGACTAAAAAACATATTTTTATTTT
*
17189798 TTAAAATTTTAAACT
130 TTAAAA-TCTAAACT
* *
17189813 TTTTTGTTAAAAAAATCATTATTTTT-TTAAAAATCAAAGTTTTTATTTCGAAATAGTTAAAAAA
1 TTTTT-TTAAAAAAATCACTATTTTTCTTAAAAATCAAAATTTTTATTTCGAAATAGTTAAAAAA
* *
17189877 --AACTAACTTTATTTAAAAATTTAAACTTTTTCCTTTAAATTGACTTAAAAAACATATTTTTAT
65 TCAA--AATTTTATTTAAAAATTTAAACTTTTTCCTTTAAAATGAC-TAAAAAACATATTTTTAT
* *
17189940 TTGTAAAAATCTAAACT
127 TTTTTAAAATCTAAACT
** *
17189957 TTTTTTT--TTAAATCACTATTTTTCATAAAAATCAAAATTTTTATTTCGAAATAGTTAAAAAAT
1 TTTTTTTAAAAAAATCACTATTTTTCTTAAAAATCAAAATTTTTATTTCGAAATAGTTAAAAAAT
* *
17190020 CAAAATTTTATTTAAAAATTTAAATTTTTTCCTTTAAAAGGACT-AAAAACATATTTTTATTTTT
66 CAAAATTTTATTTAAAAATTTAAACTTTTTCCTTTAAAATGACTAAAAAACATATTTTTA-TTTT
*
17190084 TTAAAATCTAAAAT
130 TTAAAATCTAAACT
* * *
17190098 TTCTTTTTAAAAAAACTCATTATTTTTCTTAAAAATCAAAACTTTTATTTCAAAATAGTTAAAAA
1 TT-TTTTTAAAAAAA-TCACTATTTTTCTTAAAAATCAAAATTTTTATTTCGAAATAGTT--AAA
* *
17190163 AAATTAAACTTTT-TTT-AAAATTTAAACTTTTTCCTTTAAAATGACTAAAAAACATATTTTTAT
62 AAATCAAAATTTTATTTAAAAATTTAAACTTTTTCCTTTAAAATGACTAAAAAACATATTTTTA-
17190226 TTTTTTAAAAAATCTAAACT
126 TTTTTT--AAAATCTAAACT
17190246 TT
1 TT
17190248 CTCTCTCTTT
Statistics
Matches: 378, Mismatches: 37, Indels: 34
0.84 0.08 0.08
Matches are distributed among these distances:
140 15 0.04
141 32 0.08
142 117 0.31
143 49 0.13
144 38 0.10
145 75 0.20
146 25 0.07
147 14 0.04
148 13 0.03
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (143 bp):
TTTTTTTAAAAAAATCACTATTTTTCTTAAAAATCAAAATTTTTATTTCGAAATAGTTAAAAAAT
CAAAATTTTATTTAAAAATTTAAACTTTTTCCTTTAAAATGACTAAAAAACATATTTTTATTTTT
TAAAATCTAAACT
Found at i:17190259 original size:29 final size:28
Alignment explanation
Indices: 17190226--17190280 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
17190216 ATATTTTTAT
* *
17190226 TTTTTTAAAAAATCTAAACTTTCTCTCTC
1 TTTTTAAAAAAATCAAAACTTT-TCTCTC
17190255 TTTTTAAAAAAATCAAAACTTTTCTC
1 TTTTTAAAAAAATCAAAACTTTTCTC
17190281 AATATCAAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.45
Consensus pattern (28 bp):
TTTTTAAAAAAATCAAAACTTTTCTCTC
Found at i:17193809 original size:43 final size:43
Alignment explanation
Indices: 17193748--17193829 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
17193738 GAAAAATCCC
*
17193748 GCTATAAAACATGATCTTTAGCAACGCTTTTCTCACAAAAGCT
1 GCTATAAAACATGATCTTTAGCAACGCTTTTCCCACAAAAGCT
* * * *
17193791 GCTATAGAACATGTTCTTTAGCAGCGTTTTTCCCACAAA
1 GCTATAAAACATGATCTTTAGCAACGCTTTTCCCACAAA
17193830 CGCCGCTAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (43 bp):
GCTATAAAACATGATCTTTAGCAACGCTTTTCCCACAAAAGCT
Found at i:17202274 original size:18 final size:18
Alignment explanation
Indices: 17202225--17202265 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
17202215 AATTTTATAC
*
17202225 TTCA-TTATTAAT-TTAT
1 TTCATTTATTTATATTAT
17202241 TTCATTTATTTATATTAT
1 TTCATTTATTTATATTAT
*
17202259 TTTATTT
1 TTCATTT
17202266 CTTTTTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 4 0.19
17 7 0.33
18 10 0.48
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (18 bp):
TTCATTTATTTATATTAT
Found at i:17205235 original size:10 final size:10
Alignment explanation
Indices: 17205210--17205252 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
17205200 TCGAATAAAG
*
17205210 AAGAAAAAATA
1 AAGAACAAA-A
17205221 AAGAACAAAA
1 AAGAACAAAA
17205231 AAGAACAAAA
1 AAGAACAAAA
*
17205241 AA-AAGAAAA
1 AAGAACAAAA
17205250 AAG
1 AAG
17205253 CAAAAGGTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 8 0.28
10 13 0.45
11 8 0.28
ACGTcount: A:0.81, C:0.05, G:0.12, T:0.02
Consensus pattern (10 bp):
AAGAACAAAA
Found at i:17205244 original size:14 final size:14
Alignment explanation
Indices: 17205203--17205232 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17205193 AAGGAGTTCG
*
17205203 AATAAAGAAGAAAA
1 AATAAAGAACAAAA
17205217 AATAAAGAACAAAA
1 AATAAAGAACAAAA
17205231 AA
1 AA
17205233 GAACAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.80, C:0.03, G:0.10, T:0.07
Consensus pattern (14 bp):
AATAAAGAACAAAA
Found at i:17205280 original size:11 final size:11
Alignment explanation
Indices: 17205264--17205289 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
17205254 AAAAGGTTCG
17205264 AAAAGAAAATA
1 AAAAGAAAATA
17205275 AAAAGAAAATA
1 AAAAGAAAATA
17205286 AAAA
1 AAAA
17205290 AAATGATTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAAGAAAATA
Found at i:17206073 original size:23 final size:23
Alignment explanation
Indices: 17206018--17206076 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
17206008 CTTATGTGGT
17206018 ATCTAGTCAGCAACTTCTAAAAG
1 ATCTAGTCAGCAACTTCTAAAAG
* * *
17206041 ATCCAATCAGCAACTTCTAGAAG
1 ATCTAGTCAGCAACTTCTAAAAG
*
17206064 GTCTAGTCAGCAA
1 ATCTAGTCAGCAA
17206077 GGATGGATGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (23 bp):
ATCTAGTCAGCAACTTCTAAAAG
Found at i:17211433 original size:8 final size:8
Alignment explanation
Indices: 17211420--17211506 Score: 53
Period size: 8 Copynumber: 11.6 Consensus size: 8
17211410 ACATAGTTGC
17211420 AAATAATT
1 AAATAATT
17211428 AAATAATT
1 AAATAATT
17211436 AAATAATT
1 AAATAATT
* *
17211444 AATTATTT
1 AAATAATT
*
17211452 AATTAAGTT
1 AAATAA-TT
*
17211461 -ACT--TT
1 AAATAATT
*
17211466 TAATAATT
1 AAATAATT
17211474 AAAT-ATT
1 AAATAATT
17211481 ---TAATT
1 AAATAATT
*
17211486 TAATAATT
1 AAATAATT
*
17211494 TAATAATT
1 AAATAATT
17211502 AAATA
1 AAATA
17211507 TTTGTATTGT
Statistics
Matches: 64, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
4 1 0.02
5 5 0.08
6 2 0.03
7 3 0.05
8 51 0.80
9 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (8 bp):
AAATAATT
Found at i:17211448 original size:20 final size:20
Alignment explanation
Indices: 17211423--17211503 Score: 69
Period size: 20 Copynumber: 4.2 Consensus size: 20
17211413 TAGTTGCAAA
17211423 TAATTAAATAATTAAATAAT
1 TAATTAAATAATTAAATAAT
** * *
17211443 TAATTATTTAATTAAGTTACT
1 TAATTAAATAATTAA-ATAAT
*
17211464 T--TT-AATAATTAAATATT
1 TAATTAAATAATTAAATAAT
* *
17211481 TAATTTAATAATTTAATAAT
1 TAATTAAATAATTAAATAAT
17211501 TAA
1 TAA
17211504 ATATTTGTAT
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
17 4 0.09
18 7 0.15
19 4 0.09
20 28 0.60
21 4 0.09
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (20 bp):
TAATTAAATAATTAAATAAT
Found at i:17211473 original size:30 final size:28
Alignment explanation
Indices: 17211423--17211509 Score: 104
Period size: 28 Copynumber: 3.0 Consensus size: 28
17211413 TAGTTGCAAA
* * *
17211423 TAATTAAATAATTAAATAATTAATTATT
1 TAATTTAATAATTTAATAATTAAATATT
*
17211451 TAA-TTAAGTTACTTTTAATAATTAAATATT
1 TAATTTAA--TA-ATTTAATAATTAAATATT
17211481 TAATTTAATAATTTAATAATTAAATATT
1 TAATTTAATAATTTAATAATTAAATATT
17211509 T
1 T
17211510 GTATTGTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
27 3 0.06
28 21 0.42
29 4 0.08
30 18 0.36
31 4 0.08
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (28 bp):
TAATTTAATAATTTAATAATTAAATATT
Found at i:17211542 original size:26 final size:26
Alignment explanation
Indices: 17211492--17211542 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
17211482 AATTTAATAA
* **
17211492 TTTAATAATTAAATATTTGTATTGTT
1 TTTAATAATTAAATAATCATATTGTT
*
17211518 TTTAATAATTAAATAATCATTTTGT
1 TTTAATAATTAAATAATCATATTGT
17211543 AGAATCAACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (26 bp):
TTTAATAATTAAATAATCATATTGTT
Found at i:17215784 original size:31 final size:29
Alignment explanation
Indices: 17215748--17215817 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
17215738 ATCTCAATAT
* *
17215748 TATACATGAACATTGATTTAATGTGCAATTA
1 TATACATGAACATTAATTT--GGTGCAATTA
*
17215779 TATACATGAACTTTAATTTGGTGCAATTA
1 TATACATGAACATTAATTTGGTGCAATTA
*
17215808 TATACGTGAA
1 TATACATGAA
17215818 TTTTTAATTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.51
31 17 0.49
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (29 bp):
TATACATGAACATTAATTTGGTGCAATTA
Found at i:17215795 original size:26 final size:28
Alignment explanation
Indices: 17215770--17215827 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
17215760 TTGATTTAAT
17215770 GTGCAATTATATACATGAACTTTAATTTG
1 GTGCAATTATATACATGAACTTTAA-TTG
* *
17215799 GTGCAATTATATACGTGAATTTTTAATTG
1 GTGCAATTATATACATGAA-CTTTAATTG
17215828 TGGTTCACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.43
Consensus pattern (28 bp):
GTGCAATTATATACATGAACTTTAATTG
Found at i:17215855 original size:31 final size:30
Alignment explanation
Indices: 17215770--17215858 Score: 101
Period size: 31 Copynumber: 3.0 Consensus size: 30
17215760 TTGATTTAAT
17215770 GTGCAATTATATACATG-AACTTTAATTTG
1 GTGCAATTATATACATGAAACTTTAATTTG
* **
17215799 GTGCAATTATATACGTGAATTTTTAATTGTG
1 GTGCAATTATATACATGAAACTTTAATT-TG
* *
17215830 GTTCACA-TGTATACATGAAACTTTAATTT
1 GTGCA-ATTATATACATGAAACTTTAATTT
17215859 TGATTTAATC
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
29 16 0.33
30 9 0.18
31 23 0.47
32 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.43
Consensus pattern (30 bp):
GTGCAATTATATACATGAAACTTTAATTTG
Found at i:17216226 original size:41 final size:41
Alignment explanation
Indices: 17216159--17216306 Score: 165
Period size: 41 Copynumber: 3.6 Consensus size: 41
17216149 AAACGACACA
*
17216159 ATTGCTTAACCTTTAGCGGCGTTTTTCCTATAAACGTCGCT
1 ATTGCTTAACCTTTAGCAGCGTTTTTCCTATAAACGTCGCT
* *
17216200 AATGCTCTAACCTTTAGCAGCG-TTTT-CTCATAAACGCCGCT
1 ATTGCT-TAACCTTTAGCAGCGTTTTTCCT-ATAAACGTCGCT
* * **
17216241 ATTGCTCTAACTTTTAGCGGCGTTTTTCCTATAAATATCGCT
1 ATTGCT-TAACCTTTAGCAGCGTTTTTCCTATAAACGTCGCT
* * *
17216283 ATTGCTTTACCTTTTGCAGTGTTT
1 ATTGCTTAACCTTTAGCAGCGTTT
17216307 AAGAAAAAAC
Statistics
Matches: 89, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
40 2 0.02
41 52 0.58
42 33 0.37
43 2 0.02
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.41
Consensus pattern (41 bp):
ATTGCTTAACCTTTAGCAGCGTTTTTCCTATAAACGTCGCT
Found at i:17220254 original size:58 final size:60
Alignment explanation
Indices: 17220192--17220339 Score: 171
Period size: 63 Copynumber: 2.5 Consensus size: 60
17220182 TAATAGGATC
*
17220192 ATTATTAAATATAATTTAA-TAAAGAT-AAT-AAATAATTTAAT-CATATTTTAATATAATT
1 ATTATTAAATATAATTTAATTAAA-ATAAATAAAATAATATAATACAT-TTTTAATATAATT
17220250 ATTATTAAATATAATTTAATTAAAATAAAATAAAAATAATATAATAACATTTTTAATATAATT
1 ATTATTAAATATAATTTAATTAAAAT-AAAT-AAAATAATATAAT-ACATTTTTAATATAATT
* * *
17220313 ATTTTTATAT-TAAATTATATTAAAATA
1 ATTATTAAATATAATTTA-ATTAAAATA
17220340 CTTTATATTA
Statistics
Matches: 78, Mismatches: 4, Indels: 12
0.83 0.04 0.13
Matches are distributed among these distances:
58 21 0.27
59 4 0.05
60 3 0.04
62 18 0.23
63 29 0.37
64 3 0.04
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (60 bp):
ATTATTAAATATAATTTAATTAAAATAAATAAAATAATATAATACATTTTTAATATAATT
Found at i:17220398 original size:40 final size:44
Alignment explanation
Indices: 17220315--17220408 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 44
17220305 ATATAATTAT
* *
17220315 TTTTATATTAAATTATATTAAAATACTTTATATTAATTTTTTTAG
1 TTTTATATTAAATTATATTAAAATACTTTACA-TAATTATTTTAG
* *
17220360 TTTTATATTAAATTATATTCAAATA-TTT-CA-AA-TATTTTAT
1 TTTTATATTAAATTATATTAAAATACTTTACATAATTATTTTAG
17220400 TTTTATATT
1 TTTTATATT
17220409 TTTTGAGTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
40 15 0.33
41 2 0.04
43 1 0.02
44 3 0.07
45 24 0.53
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (44 bp):
TTTTATATTAAATTATATTAAAATACTTTACATAATTATTTTAG
Found at i:17220913 original size:59 final size:59
Alignment explanation
Indices: 17220797--17220933 Score: 179
Period size: 58 Copynumber: 2.3 Consensus size: 59
17220787 GGACTTGACA
* *
17220797 CTTAATTTGGTA-CTTAAACTTTTTTGACCCAATTTGGTATCTGAATTTGA-TACTTTTT
1 CTTAATTTGGTATC-TAAACTTTTTTGACCCAATTTAGTATCTGAATTGGATTACTTTTT
* **
17220855 CTTAATTTGGTATCTAAACTTTTTTGAACCCAATTTAGTATCTGAACTTGGCTTTTTTTTT
1 CTTAATTTGGTATCTAAACTTTTTTG-ACCCAATTTAGTATCTGAA-TTGGATTACTTTTT
*
17220916 CCTAATTTGGTATCTAAA
1 CTTAATTTGGTATCTAAA
17220934 TTTATTAAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
58 24 0.35
59 19 0.28
60 3 0.04
61 23 0.33
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.49
Consensus pattern (59 bp):
CTTAATTTGGTATCTAAACTTTTTTGACCCAATTTAGTATCTGAATTGGATTACTTTTT
Found at i:17221246 original size:31 final size:29
Alignment explanation
Indices: 17221206--17221264 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 29
17221196 ATCTCAAAAT
* *
17221206 TATACATGAACTTTGATTTAATGTGCAATTG
1 TATACATGAAATTTAATTT--TGTGCAATTG
*
17221237 TATATATGAAATTTAATTTTGTGCAATT
1 TATACATGAAATTTAATTTTGTGCAATT
17221265 ATACACGTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.36
31 16 0.64
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.46
Consensus pattern (29 bp):
TATACATGAAATTTAATTTTGTGCAATTG
Found at i:17221792 original size:21 final size:21
Alignment explanation
Indices: 17221765--17221813 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
17221755 ATTTTTACTT
*
17221765 TAAAAAAATTCCTT-AAAATA
1 TAAAAAAATTCATTAAAAATA
*
17221785 TAAAAAAATTCATTAAAAATG
1 TAAAAAAATTCATTAAAAATA
17221806 TAAAAAAA
1 TAAAAAAA
17221814 ATATATCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (21 bp):
TAAAAAAATTCATTAAAAATA
Found at i:17222054 original size:20 final size:21
Alignment explanation
Indices: 17222031--17222069 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
17222021 GGGTTTTCAT
*
17222031 ATTTTTTATGAATT-TTTTGA
1 ATTTTTAATGAATTGTTTTGA
17222051 ATTTTTAATGAATTGTTTT
1 ATTTTTAATGAATTGTTTT
17222070 AGAAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (21 bp):
ATTTTTAATGAATTGTTTTGA
Found at i:17222629 original size:18 final size:18
Alignment explanation
Indices: 17222597--17222648 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
17222587 CTGTGATGAG
17222597 AATAAATTT--TTAATTA
1 AATAAATTTAATTAATTA
17222613 AATAAATTTAATTAATTA
1 AATAAATTTAATTAATTA
*
17222631 AA-AATTTTAAATTAATTA
1 AATAAATTT-AATTAATTA
17222649 CAATTGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 9 0.28
17 5 0.16
18 18 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATAAATTTAATTAATTA
Found at i:17233692 original size:111 final size:112
Alignment explanation
Indices: 17233478--17233707 Score: 446
Period size: 111 Copynumber: 2.1 Consensus size: 112
17233468 AATAACAGCA
17233478 GTTCGC-ATACCTTTTAAGTTTGCATTTAAACATTTAACTAGGTCCACATACAAAACAAGCTTCA
1 GTTCGCTATACCTTTTAAGTTTGCATTTAAACATTTAACTAGGTCCACATACAAAACAAGCTTCA
17233542 CAAAAAAAAAAAAGATCGTTCACACAAGGGTTCACATACTTTATAGG
66 CAAAAAAAAAAAAGATCGTTCACACAAGGGTTCACATACTTTATAGG
17233589 GTTCGCTATACCTTTTAAGTTTGCATTTAAACATTTAACTAGGTCCACATACAAAACAAGCTTCA
1 GTTCGCTATACCTTTTAAGTTTGCATTTAAACATTTAACTAGGTCCACATACAAAACAAGCTTCA
17233654 C-AAAAAAAAAAAGATCGTTCACACAAGGGTTCACATACTTTATAGG
66 CAAAAAAAAAAAAGATCGTTCACACAAGGGTTCACATACTTTATAGG
17233700 GTTCGCTA
1 GTTCGCTA
17233708 AATGGTATGG
Statistics
Matches: 118, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
111 59 0.50
112 59 0.50
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (112 bp):
GTTCGCTATACCTTTTAAGTTTGCATTTAAACATTTAACTAGGTCCACATACAAAACAAGCTTCA
CAAAAAAAAAAAAGATCGTTCACACAAGGGTTCACATACTTTATAGG
Found at i:17235318 original size:24 final size:25
Alignment explanation
Indices: 17235286--17235337 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
17235276 TAATGGCCGT
17235286 ATAGTTTTTGCAG-ATAAACTGCCAC
1 ATAGTTTTTGCAGTA-AAACTGCCAC
*
17235311 ATAG-TTTTGCAGTAAAACTGTCAC
1 ATAGTTTTTGCAGTAAAACTGCCAC
17235335 ATA
1 ATA
17235338 TTTGCCAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (25 bp):
ATAGTTTTTGCAGTAAAACTGCCAC
Found at i:17236492 original size:13 final size:15
Alignment explanation
Indices: 17236473--17236509 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
17236463 ATTCTAGAGG
17236473 GAAAAGAGAA-G-AA
1 GAAAAGAGAATGAAA
*
17236486 TAAAAGAGAATGAAA
1 GAAAAGAGAATGAAA
17236501 GAAAAGAGA
1 GAAAAGAGA
17236510 GCTATTCGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 9 0.45
14 1 0.05
15 10 0.50
ACGTcount: A:0.68, C:0.00, G:0.27, T:0.05
Consensus pattern (15 bp):
GAAAAGAGAATGAAA
Found at i:17241677 original size:120 final size:119
Alignment explanation
Indices: 17241453--17241807 Score: 629
Period size: 120 Copynumber: 3.0 Consensus size: 119
17241443 TAGATACTCT
*
17241453 TAAGATTAAAGTTGTCTTCTTGGAATTATGGTTGGGAGGAAATTTTGATATTTTAGAGTATGTTT
1 TAAGATTAAAGTTGTCTTCTTGGAACTATGGTTGGGAGGAAATTTTGATATTTTAGAGTATGTTT
* *
17241518 CAATCCGGGTAAAGCCTTAGAGAAAGAGTGAACCAACCTTCCATATCTTTTATA
66 CAATCCGGGTAAAACCTTAGAGAAAGAGTGAACTAACCTTCCATATCTTTTATA
* *
17241572 TAAGATTAAAGTTGTCTTCTTGGAACTATGGTTGGAAGGAAATTTTGATATCTTAAGAGTATGTT
1 TAAGATTAAAGTTGTCTTCTTGGAACTATGGTTGGGAGGAAATTTTGATAT-TTTAGAGTATGTT
17241637 TCAATCCGGGTAAAACCTTAGAGAAAGAGTGAACTAACCTTCCATATCTTTTATA
65 TCAATCCGGGTAAAACCTTAGAGAAAGAGTGAACTAACCTTCCATATCTTTTATA
17241692 TAAGATTAAAGTTGTCTTCTTGGAACTATGGTTGGGAGGAAATTTTGATATTTTAGAGTATGTTT
1 TAAGATTAAAGTTGTCTTCTTGGAACTATGGTTGGGAGGAAATTTTGATATTTTAGAGTATGTTT
* * *
17241757 CAATCTGGGTAAAACCTTCGAGAAAGAGTGAAATAACCTTCCATATCTTTT
66 CAATCCGGGTAAAACCTTAGAGAAAGAGTGAACTAACCTTCCATATCTTTT
17241808 TTTATTATAT
Statistics
Matches: 225, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
119 110 0.49
120 115 0.51
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (119 bp):
TAAGATTAAAGTTGTCTTCTTGGAACTATGGTTGGGAGGAAATTTTGATATTTTAGAGTATGTTT
CAATCCGGGTAAAACCTTAGAGAAAGAGTGAACTAACCTTCCATATCTTTTATA
Found at i:17249457 original size:411 final size:404
Alignment explanation
Indices: 17248653--17249468 Score: 1373
Period size: 411 Copynumber: 2.0 Consensus size: 404
17248643 TATTTGTTTT
17248653 GTTGTTTTGAGGTGCCATTGAAGGCATATCGGTATGATTGAATTTTGGTTGGTTTTGAATTATTG
1 GTTGTTTTGAGGTGCCATTGAAGGCATATCGGTATGATTGAATTTTGGTTGGTTTTGAATTATTG
*
17248718 ATTGAGGTGGAAATAGTGGCATATTGGTTAGGCATTTAGGATGATTGTTATAAATGATATTTTTG
66 ATTAAGGTGGAAATAGTGGCATATTGGTTAGGCATTTAGGATGATTGTTATAAATGATATTTTTG
* *
17248783 GTGTGATTTTGATGTTTTTAAAATGGTTGAGATATGGTTTAATGGTTACTCGAGAGCTAAGTGAT
131 GTATGATTTTGATGTTTTTAAAATGGTTGAGATATGGTTTAATGGTTACTCGAGACCTAAGTGAT
* * *
17248848 TTAAGGTTAGATAACTTGTATTGAAAGGCATTTTCAGGTACGCACGGTCGTGGGCCTTACACGGC
196 TTAAGGTTAGAAAACTTGTATTGAAAGGCATTTTCAAGTACACACGGTCGTGGGCCTTACACGGC
* *
17248913 ATAAGACACAACTGTGTGGTTTGTAGGTTTTGGATGATTTTTAGTGCACACGACCACAATCTGTT
261 ATAAGACACAACAGTGTGGTTTGTAAGTTTTGGATGATTTTTAGTGCACACGACCACAATCTGTT
* * *
17248978 ACACGATCCAGCGACATGGTCGTGTGACATATTTTTGAATATTTACACTTTTGACCCACACGACA
326 ACACGATCCAGCGACACGGTCGTATGACATATTTTTGAATATTTACAATTTTGACCCACACGACA
17249043 TCAGTGAGTTACAC
391 TCAGTGAGTTACAC
17249057 GTTGTTTTGAGGTGCCATTGAAGGCATATCGGTATGATTGAATATAGTCTTTTGGTTGGTTTTGA
1 GTTGTTTTGAGGTGCCATTGAAGGCATATCGGTATGATTG---A-A---TTTTGGTTGGTTTTGA
* *
17249122 ATTATTGATTAAGGTGGCAATTGTGGCATATTGGTTAGGCATTTAGGATGATTGTTATAAATGAT
59 ATTATTGATTAAGGTGGAAATAGTGGCATATTGGTTAGGCATTTAGGATGATTGTTATAAATGAT
*
17249187 ATTTTTGGTATGATTTTGATGTTTTTAAATTGGTTGAGATATGGTTTAATGGTTACTCGAGACCT
124 ATTTTTGGTATGATTTTGATGTTTTTAAAATGGTTGAGATATGGTTTAATGGTTACTCGAGACCT
* *
17249252 AAGTGATTTAAGGTTAGAAAACTTGTATTGAAAGGCATTTTCAAGTACACGCGGTCGTGTGCCTT
189 AAGTGATTTAAGGTTAGAAAACTTGTATTGAAAGGCATTTTCAAGTACACACGGTCGTGGGCCTT
*
17249317 ACACGGCATAAGACACAACAGTGTGGTTTGTAAGTTTTGGATGATTTTTAGTGCACAC-AGCCAT
254 ACACGGCATAAGACACAACAGTGTGGTTTGTAAGTTTTGGATGATTTTTAGTGCACACGA-CCAC
* * *
17249381 AATCTGTTACACGATCTAGGGACACGGTTGTATGACATATTTTTGAATATTTACAATTTTGACCC
318 AATCTGTTACACGATCCAGCGACACGGTCGTATGACATATTTTTGAATATTTACAATTTTGACCC
17249446 ACACGACATCAGTGAGTTACAC
383 ACACGACATCAGTGAGTTACAC
17249468 G
1 G
17249469 ATTTGTTCGC
Statistics
Matches: 384, Mismatches: 20, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
404 40 0.10
407 1 0.00
408 1 0.00
410 1 0.00
411 341 0.89
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.37
Consensus pattern (404 bp):
GTTGTTTTGAGGTGCCATTGAAGGCATATCGGTATGATTGAATTTTGGTTGGTTTTGAATTATTG
ATTAAGGTGGAAATAGTGGCATATTGGTTAGGCATTTAGGATGATTGTTATAAATGATATTTTTG
GTATGATTTTGATGTTTTTAAAATGGTTGAGATATGGTTTAATGGTTACTCGAGACCTAAGTGAT
TTAAGGTTAGAAAACTTGTATTGAAAGGCATTTTCAAGTACACACGGTCGTGGGCCTTACACGGC
ATAAGACACAACAGTGTGGTTTGTAAGTTTTGGATGATTTTTAGTGCACACGACCACAATCTGTT
ACACGATCCAGCGACACGGTCGTATGACATATTTTTGAATATTTACAATTTTGACCCACACGACA
TCAGTGAGTTACAC
Found at i:17250475 original size:68 final size:67
Alignment explanation
Indices: 17250354--17250561 Score: 272
Period size: 68 Copynumber: 3.1 Consensus size: 67
17250344 CAACTTCTTG
* ** * *
17250354 GTTTACTGTCCTGGCGGACTTCATATGTTGTTATAGTCCAACTATGGTCTTACACTATATGATGT
1 GTTTACTGTCCTGGC-GACTTCATATGTTGTCATAACCCAACTATGGTCTTACACAATATGGTGT
17250419 CAT
65 CAT
* * * * * *
17250422 GTTTATTGTCTTGGCGTACTTCATATGTTGTCATAACCCAGCTCTGGTTTTACACAATATGGTGC
1 GTTTACTGTCCTGGCG-ACTTCATATGTTGTCATAACCCAACTATGGTCTTACACAATATGGTGT
17250487 CAT
65 CAT
* *
17250490 GTTTACTGTCCTAGCAGACTTCATATGTTGCCATAACCCAACTATGGTCTTACACAATATGGTGT
1 GTTTACTGTCCTGGC-GACTTCATATGTTGTCATAACCCAACTATGGTCTTACACAATATGGTGT
17250555 CAT
65 CAT
17250558 GTTT
1 GTTT
17250562 TCCCATGAAC
Statistics
Matches: 119, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
67 1 0.01
68 117 0.98
69 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (67 bp):
GTTTACTGTCCTGGCGACTTCATATGTTGTCATAACCCAACTATGGTCTTACACAATATGGTGTC
AT
Found at i:17250822 original size:38 final size:38
Alignment explanation
Indices: 17250772--17250858 Score: 104
Period size: 38 Copynumber: 2.3 Consensus size: 38
17250762 GAGTCTGTAG
* * ** * * *
17250772 ACCATTTTCATGGTGTTGCTCTGTAGAGCTAGTAGGTA
1 ACCATTCTCATGGCGTTGCTCCATAAAGCCAGTAGATA
17250810 ACCATTCTCATGGCGTTGCTCCATAAAGCCAGTAGATA
1 ACCATTCTCATGGCGTTGCTCCATAAAGCCAGTAGATA
17250848 ACCATTC-CATG
1 ACCATTCTCATG
17250859 ATGCCACCAA
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 4 0.10
38 38 0.90
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (38 bp):
ACCATTCTCATGGCGTTGCTCCATAAAGCCAGTAGATA
Found at i:17253116 original size:2 final size:2
Alignment explanation
Indices: 17253111--17253148 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
17253101 CTTTTGAGTC
17253111 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
17253149 TATTTCTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17254547 original size:19 final size:18
Alignment explanation
Indices: 17254520--17254572 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 18
17254510 TGAACTTTAG
17254520 TTAAT-ATTTTTATAAAAT
1 TTAATAATTTTT-TAAAAT
17254538 TTAATAATTTTTTACAAAT
1 TTAATAATTTTTTA-AAAT
17254557 TT-ATAATTTTTTAAAA
1 TTAATAATTTTTTAAAA
17254573 AACATATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
17 3 0.09
18 18 0.55
19 12 0.36
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAATAATTTTTTAAAAT
Found at i:17261811 original size:21 final size:21
Alignment explanation
Indices: 17261787--17261838 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
17261777 AATAACTATT
*
17261787 AATTTTAAATG-TAATATAGAA
1 AATTTTAAATGATAA-ATAAAA
*
17261808 AATTTAAAATGATTAAATAAAA
1 AATTTTAAATGA-TAAATAAAA
17261830 AATTTTAAA
1 AATTTTAAA
17261839 AATTAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 10 0.38
22 13 0.50
23 3 0.12
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.37
Consensus pattern (21 bp):
AATTTTAAATGATAAATAAAA
Found at i:17262431 original size:19 final size:19
Alignment explanation
Indices: 17262391--17262432 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
17262381 TAATACATGA
*
17262391 AATTTAAAAAATAATTCTT
1 AATTTAAAAAATAATTCGT
17262410 AATTTAAAAAAATAATT-GT
1 AATTT-AAAAAATAATTCGT
17262429 AATT
1 AATT
17262433 ATCTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
AATTTAAAAAATAATTCGT
Found at i:17266261 original size:18 final size:18
Alignment explanation
Indices: 17266234--17266268 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17266224 AGCACCACCA
*
17266234 CCAAAGCCACCATAATCC
1 CCAAAGCCACCAAAATCC
*
17266252 CCAAATCCACCAAAATC
1 CCAAAGCCACCAAAATC
17266269 ATCATGATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.43, G:0.03, T:0.11
Consensus pattern (18 bp):
CCAAAGCCACCAAAATCC
Found at i:17268511 original size:21 final size:21
Alignment explanation
Indices: 17268485--17268538 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
17268475 TACATGTTAC
*
17268485 CACTATTCATGGATTTGACCA
1 CACTATTCATGGACTTGACCA
* **
17268506 GACTATTCATGGACTTGACTT
1 CACTATTCATGGACTTGACCA
17268527 CACTATTCATGG
1 CACTATTCATGG
17268539 GACTGACATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (21 bp):
CACTATTCATGGACTTGACCA
Found at i:17282164 original size:20 final size:20
Alignment explanation
Indices: 17282123--17282186 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
17282113 TATGATTATT
** *
17282123 ACTATGGACGTTGATTTTGG
1 ACTATGGATTTTGATTTGGG
* *
17282143 ACTATGGTTTTTGCTTTGGG
1 ACTATGGATTTTGATTTGGG
*
17282163 ACTTTTGGATTTTGATTTGGG
1 AC-TATGGATTTTGATTTGGG
17282184 ACT
1 ACT
17282187 TTTTCTGCAT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 18 0.51
21 17 0.49
ACGTcount: A:0.16, C:0.09, G:0.28, T:0.47
Consensus pattern (20 bp):
ACTATGGATTTTGATTTGGG
Found at i:17282702 original size:147 final size:146
Alignment explanation
Indices: 17282430--17282724 Score: 464
Period size: 147 Copynumber: 2.0 Consensus size: 146
17282420 TACAGACTTA
* * *
17282430 GGCGAGATGGCGTGGCAAGAGCTCAGCCATTTCTTCCTTATGAATACATTTTACTGTTTGATAAT
1 GGCGAGATGGCATGACAAGAGCTCAGCCATTTCTTCCTTATGAATACAATTTACTGTTTGATAAT
*
17282495 GTACACCCTAAAATTGGACCTAGAAGTTTTGAGGGTATTTTAGGAATTTTAGCCTATATGAGTTC
66 GTACACCCCAAAATTGGACCTAGAAGTTTTGAGGGTATTTTAGGAATTTTAGCCTATATGAGTTC
*
17282560 AGAATTTCATAAGTTT
131 AAAATTTCATAAGTTT
* * * * *
17282576 GGCGAGATGGCATGACAAGAGCTCGGTCATTTCTTCCTTTTGAATATAATTTATTGTTTGATAAT
1 GGCGAGATGGCATGACAAGAGCTCAGCCATTTCTTCCTTATGAATACAATTTACTGTTTGATAAT
* * *
17282641 GTCACACCCCAAAATTGGGCCTAGAATTTTTTAGGGTATTTTAGGAATTTTAGCCTATATGAGTT
66 GT-ACACCCCAAAATTGGACCTAGAAGTTTTGAGGGTATTTTAGGAATTTTAGCCTATATGAGTT
17282706 CAAAATTTCATAAGTTT
130 CAAAATTTCATAAGTTT
17282723 GG
1 GG
17282725 TAACCGATAA
Statistics
Matches: 135, Mismatches: 13, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
146 59 0.44
147 76 0.56
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.37
Consensus pattern (146 bp):
GGCGAGATGGCATGACAAGAGCTCAGCCATTTCTTCCTTATGAATACAATTTACTGTTTGATAAT
GTACACCCCAAAATTGGACCTAGAAGTTTTGAGGGTATTTTAGGAATTTTAGCCTATATGAGTTC
AAAATTTCATAAGTTT
Found at i:17290537 original size:52 final size:52
Alignment explanation
Indices: 17290460--17290646 Score: 257
Period size: 52 Copynumber: 3.6 Consensus size: 52
17290450 AAGGGATTCG
* ** ** *
17290460 TATACTCACGATGACACAGAGTCATCGGACCACTTAATCCATAAAGGATCCA
1 TATACTCACAATGACACTTAGTCATCGGACCGTTTAATCCGTAAAGGATCCA
* * * *
17290512 TATACTCACAATGACACTTATTCATCTGACTGTTTAATCCGTAAAGGATTCA
1 TATACTCACAATGACACTTAGTCATCGGACCGTTTAATCCGTAAAGGATCCA
17290564 TATACTCACAATGACACTTAGTCATCGGACCGTTTAATCCGTAAAGGATCCA
1 TATACTCACAATGACACTTAGTCATCGGACCGTTTAATCCGTAAAGGATCCA
* * *
17290616 TATACTCACGATGACACTTTGTCATCAGACC
1 TATACTCACAATGACACTTAGTCATCGGACC
17290647 TCCTCGTTTA
Statistics
Matches: 118, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 118 1.00
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (52 bp):
TATACTCACAATGACACTTAGTCATCGGACCGTTTAATCCGTAAAGGATCCA
Found at i:17297791 original size:52 final size:51
Alignment explanation
Indices: 17297670--17297913 Score: 263
Period size: 52 Copynumber: 4.7 Consensus size: 51
17297660 TCACTTCATT
* * * * * ** *
17297670 CATATACTCATGATGACACATAGCCACCCGGACCTTTATAATCCGCAAGGGATT
1 CATATACTCACGATGACACTTAGTCA-TCGGACC-TT-TAATCCGTAAAAGATC
* * **
17297724 CGTATACTCATGATGACACAGAGTCATCGGACCTCTTAATCCGTAAAAGATC
1 CATATACTCACGATGACACTTAGTCATCGGACCT-TTAATCCGTAAAAGATC
* * * *
17297776 CAAATACTCACGATGACACTTAGTCATCGGACAGTTTAATCCGTAAAGGATT
1 CATATACTCACGATGACACTTAGTCATCGGAC-CTTTAATCCGTAAAAGATC
* * *
17297828 CATATACTCACGATGACACTTAGTCATCAGACCGTTTAATCTGTAAATGATC
1 CATATACTCACGATGACACTTAGTCATCGGACC-TTTAATCCGTAAAAGATC
17297880 CATATACTCACGATGACACTTAGTCATCGGACCT
1 CATATACTCACGATGACACTTAGTCATCGGACCT
17297914 CTTCGTTTAT
Statistics
Matches: 164, Mismatches: 23, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
51 1 0.01
52 132 0.80
53 8 0.05
54 23 0.14
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (51 bp):
CATATACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAAGATC
Found at i:17297855 original size:104 final size:104
Alignment explanation
Indices: 17297708--17297911 Score: 302
Period size: 104 Copynumber: 2.0 Consensus size: 104
17297698 CGGACCTTTA
* * * *
17297708 TAATCCGCAAGGGATTCGTATACTCATGATGACACAGAGTCATCGGACC-TCTTAATCCGTAAAA
1 TAATCCGCAAAGGATTCATATACTCACGATGACACAGAGTCATCAGACCGT-TTAATCCGTAAAA
17297772 GATCCAAATACTCACGATGACACTTAGTCATCGGACAGTT
65 GATCCAAATACTCACGATGACACTTAGTCATCGGACAGTT
* ** * *
17297812 TAATCCGTAAAGGATTCATATACTCACGATGACACTTAGTCATCAGACCGTTTAATCTGTAAATG
1 TAATCCGCAAAGGATTCATATACTCACGATGACACAGAGTCATCAGACCGTTTAATCCGTAAAAG
*
17297877 ATCCATATACTCACGATGACACTTAGTCATCGGAC
66 ATCCAAATACTCACGATGACACTTAGTCATCGGAC
17297912 CTCTTCGTTT
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
104 88 0.99
105 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.27
Consensus pattern (104 bp):
TAATCCGCAAAGGATTCATATACTCACGATGACACAGAGTCATCAGACCGTTTAATCCGTAAAAG
ATCCAAATACTCACGATGACACTTAGTCATCGGACAGTT
Found at i:17305122 original size:29 final size:29
Alignment explanation
Indices: 17305052--17305162 Score: 109
Period size: 29 Copynumber: 3.8 Consensus size: 29
17305042 GAGTCTTGTG
* * * *
17305052 TTAT-TATATTATATAGGCAT-GACTTCA
1 TTATATATAATATATATGCATGGGCTTTA
* *
17305079 TTATATAGATAATATATATGTATGGGTTTTA
1 TTATAT--ATAATATATATGCATGGGCTTTA
*
17305110 TTTTATATAATATATATGCATGGGCTTTA
1 TTATATATAATATATATGCATGGGCTTTA
17305139 TTATATATAGTATATATATGCATG
1 TTATATATA--ATATATATGCATG
17305163 AGATTTGGTG
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
27 4 0.06
28 1 0.01
29 29 0.43
30 12 0.18
31 22 0.32
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47
Consensus pattern (29 bp):
TTATATATAATATATATGCATGGGCTTTA
Found at i:17305422 original size:20 final size:21
Alignment explanation
Indices: 17305381--17305422 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
17305371 TCAAATGTTC
*
17305381 ATTACAAATCCAAAGTCCAAA
1 ATTACAAATCCAAAGTCAAAA
17305402 ATTA-AAATCCAAA-TCTAAAA
1 ATTACAAATCCAAAGTC-AAAA
17305422 A
1 A
17305423 ACCCTAGCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 2 0.11
20 13 0.68
21 4 0.21
ACGTcount: A:0.57, C:0.19, G:0.02, T:0.21
Consensus pattern (21 bp):
ATTACAAATCCAAAGTCAAAA
Found at i:17307108 original size:24 final size:24
Alignment explanation
Indices: 17307091--17307141 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 24
17307081 TTTACTTGTT
17307091 ATTTTTACTTCTTATTTAATTATTC
1 ATTTTTA-TTCTTATTTAATTATTC
17307116 ATTTTTATTCTCCT-TTTAATTATTC
1 ATTTTTATTCT--TATTTAATTATTC
17307141 A
1 A
17307142 CGTTTGATCG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 4 0.17
25 19 0.79
26 1 0.04
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.63
Consensus pattern (24 bp):
ATTTTTATTCTTATTTAATTATTC
Found at i:17318926 original size:16 final size:17
Alignment explanation
Indices: 17318899--17318932 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
17318889 TAGACCAATA
17318899 TATTAGAGTTTAAAGTT
1 TATTAGAGTTTAAAGTT
*
17318916 TATTA-AGTTTAAGGTT
1 TATTAGAGTTTAAAGTT
17318932 T
1 T
17318933 CAGTTTAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (17 bp):
TATTAGAGTTTAAAGTT
Found at i:17319392 original size:36 final size:36
Alignment explanation
Indices: 17319352--17319454 Score: 181
Period size: 36 Copynumber: 2.9 Consensus size: 36
17319342 TGTGAAAGTG
*
17319352 AATATGTGAGTATGATT-TTCATGCCATGTGACAGAA
1 AATATGTGGGTAT-ATTCTTCATGCCATGTGACAGAA
17319388 AATATGTGGGTATATTCTTCATGCCATGTGACAGAA
1 AATATGTGGGTATATTCTTCATGCCATGTGACAGAA
17319424 AATATGTGGGTATATTCTTCATGCCATGTGA
1 AATATGTGGGTATATTCTTCATGCCATGTGA
17319455 TTGATTATAT
Statistics
Matches: 65, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
35 3 0.05
36 62 0.95
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (36 bp):
AATATGTGGGTATATTCTTCATGCCATGTGACAGAA
Found at i:17321254 original size:16 final size:16
Alignment explanation
Indices: 17321218--17321263 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
17321208 TAGAATGGAA
17321218 AGAAAATTGAAAAGATT
1 AGAAAATTG-AAAGATT
17321235 -GAAAATTGAAAG-TGT
1 AGAAAATTGAAAGAT-T
*
17321250 AGAAAATAGAAAGA
1 AGAAAATTGAAAGA
17321264 AGAAATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
14 1 0.04
15 5 0.20
16 19 0.76
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.20
Consensus pattern (16 bp):
AGAAAATTGAAAGATT
Found at i:17324789 original size:28 final size:28
Alignment explanation
Indices: 17324748--17324837 Score: 112
Period size: 28 Copynumber: 3.2 Consensus size: 28
17324738 AAGCCAAACC
* * *
17324748 CAAAGTAATGCTCTTTCGAGCCAGACTA
1 CAAAATAACGCTCTTTCGAGCCAGAATA
*
17324776 CAGAATAACGCTCTTTCGAGCCAGAATA
1 CAAAATAACGCTCTTTCGAGCCAGAATA
*
17324804 CAAAATAACGCTCCTTT-GAGCCA-AATT
1 CAAAATAACGCT-CTTTCGAGCCAGAATA
17324831 CAAAATA
1 CAAAATA
17324838 TAAATTGTGT
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
27 10 0.18
28 41 0.75
29 4 0.07
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.23
Consensus pattern (28 bp):
CAAAATAACGCTCTTTCGAGCCAGAATA
Found at i:17332418 original size:15 final size:13
Alignment explanation
Indices: 17332387--17332413 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17332377 ATGATTGATC
17332387 GAATCATATTGGT
1 GAATCATATTGGT
17332400 GAATCATATTGGT
1 GAATCATATTGGT
17332413 G
1 G
17332414 TGAATTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.26, T:0.37
Consensus pattern (13 bp):
GAATCATATTGGT
Found at i:17332899 original size:20 final size:20
Alignment explanation
Indices: 17332874--17332927 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
17332864 TTGGCATGGG
*
17332874 ACTTCTACCGATAGAACTTC
1 ACTTCTACCGATACAACTTC
* *
17332894 ACTTCTACCTATACAACTTT
1 ACTTCTACCGATACAACTTC
*
17332914 AGTTCTACCGATAC
1 ACTTCTACCGATAC
17332928 CTTGAAGACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.33
Consensus pattern (20 bp):
ACTTCTACCGATACAACTTC
Done.