Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 135 of 433
Found at i:41617815 original size:57 final size:57
Alignment explanation
Indices: 41617727--41617845 Score: 166
Period size: 57 Copynumber: 2.1 Consensus size: 57
41617717 ATGTTGTCTT
* * * *
41617727 AATGTAATTTATAGTTGGTGTCAAAATGTCTCCTAATGTGCATATCTATGCTATCCA
1 AATGTAATTTACAGCTGCTGTCAAAATGTCTCCTAATGTGCATATCTATGCTATCAA
* * * *
41617784 AATGTAATTTACAGCTGCTGTCATAATGTCTCTTAATGTGCATATTTATGTTATCAA
1 AATGTAATTTACAGCTGCTGTCAAAATGTCTCCTAATGTGCATATCTATGCTATCAA
41617841 AATGT
1 AATGT
41617846 GAATAATTGC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.40
Consensus pattern (57 bp):
AATGTAATTTACAGCTGCTGTCAAAATGTCTCCTAATGTGCATATCTATGCTATCAA
Found at i:41619925 original size:16 final size:15
Alignment explanation
Indices: 41619901--41619930 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
41619891 AACTATTTTA
41619901 TTACAAATTTCACTC
1 TTACAAATTTCACTC
41619916 TTACATAATTTCACT
1 TTACA-AATTTCACT
41619931 TACTCCATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.43
Consensus pattern (15 bp):
TTACAAATTTCACTC
Found at i:41620307 original size:50 final size:50
Alignment explanation
Indices: 41620128--41620476 Score: 343
Period size: 50 Copynumber: 7.0 Consensus size: 50
41620118 GTAACCAAAG
* * *
41620128 CTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC-AA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAA
* * *
41620177 CAATCTGGTACATGTAGTAGCCTGCACTTAGTACTACAC--GTGA-TTGAA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCT-AA
* * * * *
41620225 GTTGTCGGGTACGCGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAA
1 -CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAA
*
41620276 CTATCTGGTACACGTTGTAGCCTGCACTTAGTACTACACACT-TGACCTAA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACA-TGTGACCTAA
* ** * * * *
41620326 CCAGT-TGACACACTTAGTAGCCTGCACTTTGTACTACACACGTGA-TTAAA
1 CTA-TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCT-AA
* * * * * * *
41620376 GTTGTCGGGTACGCATAGTAGCTTGCACTTAGTACTACACATGCGACCTAA
1 -CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAA
* *
41620427 CTATCTGGTACACGTAGTAGCCTACACTTAGTACTACACACGTGACCTAA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAA
41620477 AACCATCTTA
Statistics
Matches: 237, Mismatches: 50, Indels: 25
0.76 0.16 0.08
Matches are distributed among these distances:
47 3 0.01
48 2 0.01
49 69 0.29
50 121 0.51
51 40 0.17
52 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (50 bp):
CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAA
Found at i:41620403 original size:151 final size:149
Alignment explanation
Indices: 41620128--41620476 Score: 508
Period size: 151 Copynumber: 2.3 Consensus size: 149
41620118 GTAACCAAAG
* * * **
41620128 CTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACA-TGCGACC-AACAATCTGGTACATG
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACT-TGACCTAACAATCTGACACATG
* *
41620191 TAGTAGCCTGCACTTAGTACTACACGTGATTGAAGTTGTCGGGTACGCGTAGTAGCCTGCACTTA
65 TAGTAGCCTGCACTTAGTACTACACGTGATTAAAGTTGTCGGGTACGCATAGTAGCCTGCACTTA
41620256 GTACTACACATGCGACCTAA
130 GTACTACACATGCGACCTAA
* *
41620276 CTATCTGGTACACGTTGTAGCCTGCACTTAGTACTACACACTTGACCTAACCAGT-TGACACACT
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACTTGACCTAA-CAATCTGACACA-T
* *
41620340 -TAGTAGCCTGCACTTTGTACTACACACGTGATTAAAGTTGTCGGGTACGCATAGTAGCTTGCAC
64 GTAGTAGCCTGCACTTAGTACT--ACACGTGATTAAAGTTGTCGGGTACGCATAGTAGCCTGCAC
41620404 TTAGTACTACACATGCGACCTAA
127 TTAGTACTACACATGCGACCTAA
* *
41620427 CTATCTGGTACACGTAGTAGCCTACACTTAGTACTACACACGTGACCTAA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACTTGACCTAA
41620477 AACCATCTTA
Statistics
Matches: 181, Mismatches: 14, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
148 41 0.23
149 28 0.15
150 4 0.02
151 108 0.60
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (149 bp):
CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACTTGACCTAACAATCTGACACATGT
AGTAGCCTGCACTTAGTACTACACGTGATTAAAGTTGTCGGGTACGCATAGTAGCCTGCACTTAG
TACTACACATGCGACCTAA
Found at i:41632706 original size:10 final size:10
Alignment explanation
Indices: 41632691--41632722 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
41632681 TAAATACATT
41632691 TAATTAAAGA
1 TAATTAAAGA
41632701 TAATTAAAGA
1 TAATTAAAGA
41632711 TAATTAAA-A
1 TAATTAAAGA
41632720 TAA
1 TAA
41632723 AATTCTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (10 bp):
TAATTAAAGA
Found at i:41633381 original size:16 final size:15
Alignment explanation
Indices: 41633354--41633397 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
41633344 ATTAGTACTT
41633354 ATTTTTTC-TTTTTC
1 ATTTTTTCTTTTTTC
* *
41633368 TTTTTTTCCTTTTTTG
1 ATTTTTT-CTTTTTTC
41633384 ATTTTTTCTTTTTT
1 ATTTTTTCTTTTTT
41633398 TTATTTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 6 0.24
15 8 0.32
16 11 0.44
ACGTcount: A:0.05, C:0.11, G:0.02, T:0.82
Consensus pattern (15 bp):
ATTTTTTCTTTTTTC
Found at i:41633398 original size:16 final size:15
Alignment explanation
Indices: 41633352--41633403 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
41633342 TTATTAGTAC
41633352 TTATTTTTTCTTTTT
1 TTATTTTTTCTTTTT
*
41633367 CTT-TTTTTCCTTTTT
1 -TTATTTTTTCTTTTT
*
41633382 TGATTTTTTCTTTTTT
1 TTATTTTTTC-TTTTT
41633398 TTATTT
1 TTATTT
41633404 AAATTTTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 1 0.03
15 17 0.57
16 12 0.40
ACGTcount: A:0.06, C:0.10, G:0.02, T:0.83
Consensus pattern (15 bp):
TTATTTTTTCTTTTT
Found at i:41633684 original size:118 final size:118
Alignment explanation
Indices: 41633529--41633758 Score: 354
Period size: 118 Copynumber: 1.9 Consensus size: 118
41633519 TATTTCCGGT
*
41633529 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGTGAAGTAGAATGACAACCCAAGCAC
1 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
* *
41633594 CCTACCCC-AGTTACTCAGTCAGTCACGATTTGAGCTATACTCATAACCTCGGC
66 CCTACCCCGA-TTACTCAGTCAGTCACGATCTAAGCTATACTCATAACCTCGGC
**** * *
41633647 TAGCGGAGTTTTACTTGTCACGTCACACAACGTTTTGACGCGAAGTAGAATGACAACCCAAGCAT
1 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
*
41633712 CCTACCCCGATTACTCAGTCAGTCACGATCTAAGCTGTACTCATAAC
66 CCTACCCCGATTACTCAGTCAGTCACGATCTAAGCTATACTCATAAC
41633759 AATGGAAAAC
Statistics
Matches: 101, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
118 100 0.99
119 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (118 bp):
TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
CCTACCCCGATTACTCAGTCAGTCACGATCTAAGCTATACTCATAACCTCGGC
Found at i:41634688 original size:6 final size:6
Alignment explanation
Indices: 41634672--41634732 Score: 70
Period size: 6 Copynumber: 9.7 Consensus size: 6
41634662 ATATTTAACT
41634672 AAAAT- AAAATA AAAATAA AATAATA ATAAATA ATAAATA AAAATA AAAATA
1 AAAATA AAAATA AAAAT-A AA-AATA A-AAATA A-AAATA AAAATA AAAATA
*
41634723 AAAAGA AAAA
1 AAAATA AAAA
41634733 GAAAGATTGG
Statistics
Matches: 51, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
5 5 0.10
6 25 0.49
7 17 0.33
8 4 0.08
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:41634688 original size:11 final size:11
Alignment explanation
Indices: 41634672--41634725 Score: 74
Period size: 11 Copynumber: 4.8 Consensus size: 11
41634662 ATATTTAACT
41634672 AAAATAAAATA
1 AAAATAAAATA
41634683 AAAATAAAATA
1 AAAATAAAATA
*
41634694 ATAAT-AAATA
1 AAAATAAAATA
41634704 ATAAATAAAAATA
1 A-AAAT-AAAATA
41634717 AAAATAAAA
1 AAAATAAAA
41634726 AGAAAAAGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
10 6 0.16
11 22 0.58
12 4 0.11
13 6 0.16
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:41634726 original size:7 final size:7
Alignment explanation
Indices: 41634677--41634726 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
41634667 TAACTAAAAT
41634677 AAAAT-A
1 AAAATAA
41634683 AAAATAA
1 AAAATAA
41634690 AATAATAA
1 AA-AATAA
*
41634698 TAAATAA
1 AAAATAA
*
41634705 TAAAT-A
1 AAAATAA
41634711 AAAAT-A
1 AAAATAA
41634717 AAAATAA
1 AAAATAA
41634724 AAA
1 AAA
41634727 GAAAAAGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
6 16 0.41
7 17 0.44
8 6 0.15
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (7 bp):
AAAATAA
Found at i:41641094 original size:20 final size:20
Alignment explanation
Indices: 41641069--41641116 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
41641059 TAAATTCTAG
*
41641069 AAAGATAAATACATG-TAATT
1 AAAGATAAATA-AAGATAATT
41641089 AAAGATAAATAAAGATAATT
1 AAAGATAAATAAAGATAATT
41641109 AAA-ATAAA
1 AAAGATAAA
41641117 ATCCTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.25
Consensus pattern (20 bp):
AAAGATAAATAAAGATAATT
Found at i:41642515 original size:49 final size:49
Alignment explanation
Indices: 41642443--41642617 Score: 171
Period size: 49 Copynumber: 3.6 Consensus size: 49
41642433 TGTGCGTGCT
* * *
41642443 AGTGTAAGACCTGTCAGGGACATGGCATCGGCACCTATAGATGAGAGCC
1 AGTGTAAGACCTGACTGGGACATGGCATCGGCACCAATAGATGAGAGCC
* * *
41642492 AGTGTAAGACCTGACTGGGACATGGCATCGACACAAATA-AGTGAAAGCC
1 AGTGTAAGACCTGACTGGGACATGGCATCGGCACCAATAGA-TGAGAGCC
* * * *
41642541 AGTGTAAGACCT-ATCTGAGACACGGCATCGGC-CTCGAT-GTAT-AGAAGTC
1 AGTGTAAGACCTGA-CTGGGACATGGCATCGGCAC-CAATAG-ATGAG-AGCC
*
41642590 AGTGTAAGACCTGTCTGGGACATGGCAT
1 AGTGTAAGACCTGACTGGGACATGGCAT
41642618 TGACTTAGAT
Statistics
Matches: 103, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
48 4 0.04
49 98 0.95
50 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.29, T:0.20
Consensus pattern (49 bp):
AGTGTAAGACCTGACTGGGACATGGCATCGGCACCAATAGATGAGAGCC
Found at i:41642629 original size:49 final size:49
Alignment explanation
Indices: 41642443--41642669 Score: 155
Period size: 49 Copynumber: 4.7 Consensus size: 49
41642433 TGTGCGTGCT
*
41642443 AGTGTAAGACCTGTCAGGGACATGGCATCGGCACCTATAGATG---AG-AGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATC-G-A-CT-TAGATGTATAGAAGCC
* ** * *
41642492 AGTGTAAGACCTGACTGGGACATGGCATCGACACAAAT-AAGT-GAAAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACTTAGATGTA-TAG-AAGCC
* * * * * * *
41642541 AGTGTAAGACCTATCTGAGACACGGCATCGGCCTCGATGTATAGAAGTC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACTTAGATGTATAGAAGCC
* *
41642590 AGTGTAAGACCTGTCTGGGACATGGCATTGACTTAGATGT-GAG-AGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACTTAGATGTATAGAAGCC
* * * * *
41642637 ACTATAAGACCATGTTTGGAACATGACATCGAC
1 AGTGTAAGACC-TGTCTGGGACATGGCATCGAC
41642670 ATCGTACCTT
Statistics
Matches: 138, Mismatches: 31, Indels: 19
0.73 0.16 0.10
Matches are distributed among these distances:
45 3 0.02
46 1 0.01
47 14 0.10
48 20 0.14
49 98 0.71
50 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (49 bp):
AGTGTAAGACCTGTCTGGGACATGGCATCGACTTAGATGTATAGAAGCC
Found at i:41643990 original size:21 final size:22
Alignment explanation
Indices: 41643949--41643990 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
41643939 GTCAAGAAGG
*
41643949 CCACATGGGCGTGTCGCCCCTT
1 CCACACGGGCGTGTCGCCCCTT
*
41643971 CCACACGGGTGTGT-GCCCCT
1 CCACACGGGCGTGTCGCCCCT
41643991 GTTTTAAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.10, C:0.40, G:0.29, T:0.21
Consensus pattern (22 bp):
CCACACGGGCGTGTCGCCCCTT
Found at i:41650132 original size:26 final size:24
Alignment explanation
Indices: 41650102--41650149 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
41650092 AATAAAAAAA
*
41650102 TTAAAAATATAATAAATCAAATATAT
1 TTAAAAACATAA-AAAT-AAATATAT
41650128 TTAAAAACATAAAAATAAATAT
1 TTAAAAACATAAAAATAAATAT
41650150 TAAAACAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 4 0.19
26 11 0.52
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (24 bp):
TTAAAAACATAAAAATAAATATAT
Found at i:41650161 original size:22 final size:22
Alignment explanation
Indices: 41650120--41650178 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
41650110 ATAATAAATC
* *
41650120 AAATATAT-TTAAAA-ACATAA
1 AAATAAATATTAAAACAAATAA
41650140 AAATAAATATTAAAACAAATAA
1 AAATAAATATTAAAACAAATAA
*
41650162 AAAT-AATACTAAAACAA
1 AAATAAATATTAAAACAA
41650179 TTCTTAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 18 0.53
22 9 0.26
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (22 bp):
AAATAAATATTAAAACAAATAA
Found at i:41652235 original size:40 final size:40
Alignment explanation
Indices: 41652191--41652371 Score: 197
Period size: 40 Copynumber: 4.5 Consensus size: 40
41652181 GCTCGATTGT
* * *
41652191 CTTCGGGACATAGCCCGG-TTATAGTGATTCGCACAATTGC
1 CTTCGGGACATAGCCCGGATT-TAGTAACTCGCACAAATGC
41652231 CTTCGGGA-ATTAGCCCGGATTTAGTAACTCGCACAAATGC
1 CTTCGGGACA-TAGCCCGGATTTAGTAACTCGCACAAATGC
* * * *
41652271 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGACATAGCCCGGATTTAGTAACTCGCACAAATGC
* * * *
41652311 CTTCGGGA-ATTGACCCGGATTTAGTCACTTAGCACAAAAGC
1 CTTCGGGACATAG-CCCGGATTTAGTAAC-TCGCACAAATGC
*
41652352 CTTCGGGACTTAGCCCGGAT
1 CTTCGGGACATAGCCCGGAT
41652372 ACCATTCGAA
Statistics
Matches: 118, Mismatches: 17, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
39 2 0.02
40 87 0.74
41 27 0.23
42 2 0.02
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
CTTCGGGACATAGCCCGGATTTAGTAACTCGCACAAATGC
Found at i:41652289 original size:80 final size:81
Alignment explanation
Indices: 41652191--41652369 Score: 245
Period size: 80 Copynumber: 2.2 Consensus size: 81
41652181 GCTCGATTGT
* * * *
41652191 CTTCGGGACATAGCCCGGTTATAGTGATTCGCACAATTGCCTTCGGGAATT-AGCCCGGATTTAG
1 CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAATTGA-CCCGGATTTAG
* *
41652255 TAAC-TCGCACAAATGC
65 TAACTTAGCACAAAAGC
* * *
41652271 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGCCTTCGGGAATTGACCCGGATTTAGT
1 CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAATTGACCCGGATTTAGT
*
41652336 CACTTAGCACAAAAGC
66 AACTTAGCACAAAAGC
41652352 CTTCGGGACTTAGCCCGG
1 CTTCGGGACTTAGCCCGG
41652370 ATACCATTCG
Statistics
Matches: 86, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
80 58 0.67
81 28 0.33
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (81 bp):
CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAATTGACCCGGATTTAGT
AACTTAGCACAAAAGC
Found at i:41653084 original size:2 final size:2
Alignment explanation
Indices: 41653077--41653112 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
41653067 ATGTGCAAAC
41653077 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
41653113 GCTAGAGCCG
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:41660351 original size:39 final size:40
Alignment explanation
Indices: 41660255--41660434 Score: 204
Period size: 40 Copynumber: 4.5 Consensus size: 40
41660245 GCTCGATTGT
* * * *
41660255 CTTCGGGACATAGCCCGG-TTATAGTGATTCGCACAATTGC
1 CTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACAAATGC
*
41660295 CTTCGGGAATTAGCCCGGATTTAGTAACTCGCAC-AATGC
1 CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
* * *
41660334 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
* * * *
41660374 CTTCGGGAATT-GACCCGGATTTAGTCACTTAGCACAAAAGC
1 CTTCGGGACTTAG-CCCGGATTTAGTAAC-TCGCACAAATGC
41660415 CTTCGGGACTTAGCCCGGAT
1 CTTCGGGACTTAGCCCGGAT
41660435 ACCATTCGAA
Statistics
Matches: 118, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
39 34 0.29
40 54 0.46
41 29 0.25
42 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
Found at i:41660351 original size:79 final size:81
Alignment explanation
Indices: 41660255--41660432 Score: 236
Period size: 79 Copynumber: 2.2 Consensus size: 81
41660245 GCTCGATTGT
* * * *
41660255 CTTCGGGACATAGCCCGGTTATAGTGATTCGCACAATTGCCTTCGGGAATT-AGCCCGGATTTAG
1 CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAATTGA-CCCGGATTTAG
* *
41660319 TAAC-TCGCAC-AATGC
65 TAACTTAGCACAAAAGC
* * *
41660334 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGCCTTCGGGAATTGACCCGGATTTAGT
1 CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAATTGACCCGGATTTAGT
*
41660399 CACTTAGCACAAAAGC
66 AACTTAGCACAAAAGC
41660415 CTTCGGGACTTAGCCCGG
1 CTTCGGGACTTAGCCCGG
41660433 ATACCATTCG
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
79 58 0.68
80 6 0.07
81 21 0.25
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (81 bp):
CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAATTGACCCGGATTTAGT
AACTTAGCACAAAAGC
Found at i:41666406 original size:40 final size:40
Alignment explanation
Indices: 41666322--41666471 Score: 139
Period size: 40 Copynumber: 3.8 Consensus size: 40
41666312 AAATTGAATG
* * *
41666322 ATATCCGGGCTAAG-CCCGAAGACAATATGCTG-GA--AATT
1 ATATCCGGGCTAAGACCCGAAGGCAAT-TG-TGCGAGTGACT
* * *
41666360 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGACT
* * *
41666400 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTGACT
* *
41666440 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
41666472 ACGTGATTAA
Statistics
Matches: 91, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
37 2 0.02
38 16 0.18
39 14 0.15
40 57 0.63
41 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGACT
Found at i:41666486 original size:40 final size:40
Alignment explanation
Indices: 41666357--41666487 Score: 156
Period size: 40 Copynumber: 3.3 Consensus size: 40
41666347 TATGCTGGAA
* * *
41666357 ATTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG
** * * *
41666397 GCTATATCCGGGCTAAGGCCCGAAGGCATTCGTGCGAGTT
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG
*
41666437 ATTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTG
*
41666477 ATTAAATCCGG
1 ATTATATCCGG
41666488 TTATATTCCG
Statistics
Matches: 74, Mismatches: 16, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
39 1 0.01
40 73 0.99
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG
Found at i:41668731 original size:50 final size:50
Alignment explanation
Indices: 41668665--41668824 Score: 166
Period size: 50 Copynumber: 3.2 Consensus size: 50
41668655 CATGTCTTAG
* * *
41668665 ACATGGTCTTGCACTAGCTCTCAAATATCGGTGCTGATGCCATGTTCTAA
1 ACATGGTCTTACACTAGCTCTCAAATATAGGTGCTGATGCCATGTTCCAA
* * * * *
41668715 ACATGGTCCTAAACTAGC-CT-ACATGTTAAGT-CTGATGCCATGTTCCAA
1 ACATGGTCTTACACTAGCTCTCAAAT-ATAGGTGCTGATGCCATGTTCCAA
* * * *
41668763 ACATGGTCTTACACAAGCTCTCATATATTGAG-GCCGATGCCATGTTCCAA
1 ACATGGTCTTACACTAGCTCTCAAATATAG-GTGCTGATGCCATGTTCCAA
41668813 ACATGGTCTTAC
1 ACATGGTCTTAC
41668825 GCTGGTTCAC
Statistics
Matches: 89, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
48 34 0.38
49 8 0.09
50 47 0.53
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (50 bp):
ACATGGTCTTACACTAGCTCTCAAATATAGGTGCTGATGCCATGTTCCAA
Found at i:41668759 original size:48 final size:50
Alignment explanation
Indices: 41668697--41668820 Score: 153
Period size: 48 Copynumber: 2.5 Consensus size: 50
41668687 AAATATCGGT
* * *
41668697 GCTGATGCCATGTTCTAAACATGGTCCTAAACTAGC-CT-ACATGTTAAG
1 GCTGATGCCATGTTCCAAACATGGTCCTAAACAAGCTCTCACATATTAAG
* * * * *
41668745 TCTGATGCCATGTTCCAAACATGGTCTTACACAAGCTCTCATATATTGAG
1 GCTGATGCCATGTTCCAAACATGGTCCTAAACAAGCTCTCACATATTAAG
*
41668795 GCCGATGCCATGTTCCAAACATGGTC
1 GCTGATGCCATGTTCCAAACATGGTC
41668821 TTACGCTGGT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
48 31 0.48
49 2 0.03
50 31 0.48
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (50 bp):
GCTGATGCCATGTTCCAAACATGGTCCTAAACAAGCTCTCACATATTAAG
Found at i:41676705 original size:46 final size:46
Alignment explanation
Indices: 41676655--41676827 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
41676645 TGGTTGAGCA
*
41676655 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
41676701 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
*
41676748 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
41676794 -CTCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTA
1 TC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
41676828 GGGGTGGTTT
Statistics
Matches: 107, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
43 6 0.06
45 4 0.04
46 60 0.56
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:41676811 original size:93 final size:93
Alignment explanation
Indices: 41676652--41676822 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
41676642 GGATGGTTGA
*
41676652 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAACTCGTTGAGT
41676717 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
41676745 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CTCGAGCTTGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTC-CGAACTCGTTGAG
41676809 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
41676823 ACTTAGGGGT
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
92 1 0.01
93 72 0.99
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:41678429 original size:48 final size:48
Alignment explanation
Indices: 41678328--41678524 Score: 189
Period size: 48 Copynumber: 4.1 Consensus size: 48
41678318 TTAAACGAAG
** * * * * * *
41678328 TCTCATAACGGTGCTGATGCCATGTCCCAGACATGGTCTTATACGAGA
1 TCTCATAACAATGCCGATGCCATATCCCAGATATGATCTTACACGGGA
* * * * * *
41678376 CCTCATAACGATGCCAATGTCATATCCTAGATATGATCTTACATGGGA
1 TCTCATAACAATGCCGATGCCATATCCCAGATATGATCTTACACGGGA
* * * *
41678424 TCTCAT-ACTAATGCTGATGCCATATCCCATATATGGTCTTATACGGGA
1 TCTCATAAC-AATGCCGATGCCATATCCCAGATATGATCTTACACGGGA
* * *
41678472 TCTCTTATCAATGCCGATGCCATTTCCCAGATATGATCTTACACGGGA
1 TCTCATAACAATGCCGATGCCATATCCCAGATATGATCTTACACGGGA
41678520 TCTCA
1 TCTCA
41678525 ATACTCACAT
Statistics
Matches: 117, Mismatches: 30, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
47 2 0.02
48 114 0.97
49 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (48 bp):
TCTCATAACAATGCCGATGCCATATCCCAGATATGATCTTACACGGGA
Found at i:41678486 original size:96 final size:97
Alignment explanation
Indices: 41678339--41678529 Score: 258
Period size: 96 Copynumber: 2.0 Consensus size: 97
41678329 CTCATAACGG
* * * *
41678339 TGCTGATGCCATGTCCCAGACATGGTCTTATACGAGACCTCATAACGATGCCAATGTCATATCCT
1 TGCTGATGCCATATCCCAGACATGGTCTTATACGAGACCTCATAACAATGCCAATGCCATATCCC
*
41678404 AGATATGATCTTACATGGGATCTC-ATACTAA
66 AGATATGATCTTACACGGGATCTCAATACTAA
* * * * * * * *
41678435 TGCTGATGCCATATCCCATATATGGTCTTATACGGGATCTCTTATCAATGCCGATGCCATTTCCC
1 TGCTGATGCCATATCCCAGACATGGTCTTATACGAGACCTCATAACAATGCCAATGCCATATCCC
41678500 AGATATGATCTTACACGGGATCTCAATACT
66 AGATATGATCTTACACGGGATCTCAATACT
41678530 CACATGTCGT
Statistics
Matches: 81, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
96 76 0.94
97 5 0.06
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (97 bp):
TGCTGATGCCATATCCCAGACATGGTCTTATACGAGACCTCATAACAATGCCAATGCCATATCCC
AGATATGATCTTACACGGGATCTCAATACTAA
Found at i:41682120 original size:50 final size:50
Alignment explanation
Indices: 41682045--41682221 Score: 209
Period size: 50 Copynumber: 3.6 Consensus size: 50
41682035 TAAGATGCCT
* * *
41682045 ATGCCATTTTCCAGACATGGTCTTACACTGGATCTCATGTATC-AGTGCTG
1 ATGCCATGTTCCAAACATGGTCTTACACTAGATCTCATGTATCGAG-GCTG
** * *
41682095 ATGCCATGTTCCAAACATGGTCTTACACTAGCCCACATG--TCGAGGCCG
1 ATGCCATGTTCCAAACATGGTCTTACACTAGATCTCATGTATCGAGGCTG
* * * *
41682143 ATGCCATGTTCTAAACATGGCCTTACACTAGATCTTATATATCGAGG-TCG
1 ATGCCATGTTCCAAACATGGTCTTACACTAGATCTCATGTATCGAGGCT-G
41682193 ATGCCATGTTCCAAACATGGTCTTACACT
1 ATGCCATGTTCCAAACATGGTCTTACACT
41682222 GGCTCACATA
Statistics
Matches: 106, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
48 37 0.35
49 2 0.02
50 67 0.63
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (50 bp):
ATGCCATGTTCCAAACATGGTCTTACACTAGATCTCATGTATCGAGGCTG
Found at i:41682214 original size:98 final size:98
Alignment explanation
Indices: 41682045--41682230 Score: 259
Period size: 98 Copynumber: 1.9 Consensus size: 98
41682035 TAAGATGCCT
* * * * *
41682045 ATGCCATTTTCCAGACATGGTCTTACACTGGATCTCATGTATCAGTGCTGATGCCATGTTCCAAA
1 ATGCCATGTTCCAAACATGGCCTTACACTAGATCTCATATATCAGTGCTGATGCCATGTTCCAAA
41682110 CATGGTCTTACACTAGCCCACATGTCGAGGCCG
66 CATGGTCTTACACTAGCCCACATGTCGAGGCCG
* *
41682143 ATGCCATGTTCTAAACATGGCCTTACACTAGATCTTATATATCGAG-G-TCGATGCCATGTTCCA
1 ATGCCATGTTCCAAACATGGCCTTACACTAGATCTCATATATC-AGTGCT-GATGCCATGTTCCA
* *
41682206 AACATGGTCTTACACTGGCTCACAT
64 AACATGGTCTTACACTAGCCCACAT
41682231 ATCCCTAGTA
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
97 1 0.01
98 74 0.96
99 2 0.03
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (98 bp):
ATGCCATGTTCCAAACATGGCCTTACACTAGATCTCATATATCAGTGCTGATGCCATGTTCCAAA
CATGGTCTTACACTAGCCCACATGTCGAGGCCG
Found at i:41684232 original size:46 final size:46
Alignment explanation
Indices: 41684182--41684357 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
41684172 TGGTTGAGCA
41684182 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
41684228 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
41684273 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
41684321 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
41684358 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:41684338 original size:93 final size:93
Alignment explanation
Indices: 41684179--41684350 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
41684169 GGATGGTTGA
* *
41684179 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
41684244 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
41684272 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
41684337 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
41684351 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:41687553 original size:30 final size:30
Alignment explanation
Indices: 41687519--41687577 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
41687509 GATTTTCGAG
*
41687519 TCTAGGGGCAAAATGGTCATTTTGTCAAAT
1 TCTAGGGGCAAAATGGTCATTTTGCCAAAT
*
41687549 TCTAGGGGCAAAATGGTCGTTTTGCCAAA
1 TCTAGGGGCAAAATGGTCATTTTGCCAAA
41687578 GATATGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TCTAGGGGCAAAATGGTCATTTTGCCAAAT
Found at i:41688032 original size:46 final size:45
Alignment explanation
Indices: 41687909--41688032 Score: 135
Period size: 46 Copynumber: 2.7 Consensus size: 45
41687899 CACTTAAGTG
*
41687909 AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGT
1 AGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGACGT
* ** *
41687954 AAGCTCGTGTAAGACATGAATGGGACATGCATCAG-CTACGAGATGT
1 -AGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCT-CGAGACGT
* *
41688000 -GTTAGTGTAAGACCATGTCTGGGGCATGGCATC
1 AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATC
41688033 GGCACAGATT
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
44 10 0.15
45 13 0.20
46 42 0.65
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (45 bp):
AGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGACGT
Found at i:41693345 original size:39 final size:39
Alignment explanation
Indices: 41693230--41693346 Score: 162
Period size: 39 Copynumber: 3.0 Consensus size: 39
41693220 AAGACACTGC
* ** *
41693230 AAATGTATCCGGGCTAAAGTCCCGTAGGCTTTTTGCTAG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCATGCTGG
** *
41693269 AAATGTATCCGGGCTAAAGTTTCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCATGCTGG
*
41693308 AAATGTATCCGAGCTAAAGTCCCGCAGGCTTCATGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCATGCTGG
41693347 TAATATAATT
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 68 1.00
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.27
Consensus pattern (39 bp):
AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCATGCTGG
Found at i:41695783 original size:32 final size:34
Alignment explanation
Indices: 41695742--41695804 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 34
41695732 AAATATTAAA
*
41695742 AATTATTTAAAATA-A-AAAATTGTAAAAAAGTG
1 AATTATTTAAAATATAGAAAAGTGTAAAAAAGTG
*
41695774 AATTTTTTAAAATATAGAAAAGTGTAAAAAA
1 AATTATTTAAAATATAGAAAAGTGTAAAAAA
41695805 TTATAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 13 0.48
33 1 0.04
34 13 0.48
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.32
Consensus pattern (34 bp):
AATTATTTAAAATATAGAAAAGTGTAAAAAAGTG
Found at i:41695885 original size:17 final size:16
Alignment explanation
Indices: 41695858--41695910 Score: 61
Period size: 17 Copynumber: 3.2 Consensus size: 16
41695848 ATTCAAAAAT
*
41695858 AAAATAGAATTATAAA
1 AAAATAAAATTATAAA
41695874 AAGAATAAAATTATATAA
1 AA-AATAAAATTATA-AA
* *
41695892 AATATAAAAATATAAA
1 AAAATAAAATTATAAA
41695908 AAA
1 AAA
41695911 TGTTTAGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
16 6 0.19
17 21 0.68
18 4 0.13
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.25
Consensus pattern (16 bp):
AAAATAAAATTATAAA
Found at i:41696367 original size:8 final size:9
Alignment explanation
Indices: 41696352--41696378 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
41696342 ATTTTTTAAA
41696352 TATAAAAAT
1 TATAAAAAT
41696361 TATAAAAAT
1 TATAAAAAT
41696370 TATAAAAAT
1 TATAAAAAT
41696379 ATTTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
TATAAAAAT
Found at i:41699451 original size:177 final size:177
Alignment explanation
Indices: 41699246--41700847 Score: 2388
Period size: 177 Copynumber: 9.1 Consensus size: 177
41699236 CGATACGTGA
*
41699246 AGATAAGATCTGTAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAAATAAGACTTGTATCTTCA
1 AGATAAGATCTGTAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTGTATCTTCA
* * * * * * *
41699311 ACCTGCTTTCTTGCTACCTCAGAGGGACAAGGATGATGGCTAAAATCTGCTCCATTGCCGATACG
66 ACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACA
* * *
41699376 TGGAGATAAGACTCGTCATCTTCGATCTGCTTCACTACTGCTTAGGG
131 TGGAGATAAGACTCGCCATTTTCGATCTGCTCCACTACTGCTTAGGG
* *
41699423 AGATAAGATTTGTAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGGTAAGACTTGTATCTTCA
1 AGATAAGATCTGTAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTGTATCTTCA
* * *
41699488 ACCTGCTCTCTTGCTACCTCAGATAGATAAGGCTGGTGGCTAAAATTTGCTCCATAGCTGATACA
66 ACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACA
* *
41699553 TAGAGATAAGACTCGCCATTTTCGATCTGCTCCACTACTGCTTAGGA
131 TGGAGATAAGACTCGCCATTTTCGATCTGCTCCACTACTGCTTAGGG
* *
41699600 AGATAAGATCTGTAATTTTTAGTTTGCTTCCTTGCTACCTCAGGAAGATAAGACTTG-----T--
1 AGATAAGATCTGTAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTGTATCTTCA
* * *
41699658 A--T--TCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTTCTCCATAACCGATATA
66 ACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACA
** * * *
41699719 -GGAGATAAGACTCGCCATTTTTTATCTTCTCTACTATTGCTTAGGG
131 TGGAGATAAGACTCGCCATTTTCGATCTGCTCCACTACTGCTTAGGG
*
41699765 AGATAAGATCTGTAATTTTTAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTGTATCTTCA
1 AGATAAGATCTGTAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTGTATCTTCA
* *
41699830 ACCTGCTCTCTTGCTACCTCGGAGAGATAAGGCTGGTGGCTAAAATCTACTCCATAGCCGATACA
66 ACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACA
*
41699895 TGGAGATAAGACTCGCCATTTTCGATCTGCTCCACCACTGCTTAGGG
131 TGGAGATAAGACTCGCCATTTTCGATCTGCTCCACTACTGCTTAGGG
*
41699942 AGATAAGATCTGTAATTTTCAGTCTGCTTCATTGCTACCTCAGGAAGATAAGACTTGTATCTTCA
1 AGATAAGATCTGTAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTGTATCTTCA
* * * * * *
41700007 ACCTGCTCTCTTGCTACTTTATAGAGATAAGACTGGTGGCTAAAATTTGTTCCATAGCCGATACA
66 ACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACA
* * * * *
41700072 TGGAGATAAGACTCACCATTTTCAATCAGCTCCACCACTACTTAGGG
131 TGGAGATAAGACTCGCCATTTTCGATCTGCTCCACTACTGCTTAGGG
41700119 AGATAAGATCTGTAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTGTATCTTCA
1 AGATAAGATCTGTAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTGTATCTTCA
* * * *
41700184 ACTTGCTCTCTTGCTACCTTAGAGAAATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCAATACA
66 ACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACA
* * ** * *
41700249 TGAAGATAAGACTCACCATTTTTTATATGC-CACACTACTGCTTAAGG
131 TGGAGATAAGACTCGCCATTTTCGATCTGCTC-CACTACTGCTTAGGG
* *
41700296 AGATAAGATCTGTAATTTTCAGTCTGCTTCCTTGCTACCTGAGGAAGACAAGACTTGTATCTTCA
1 AGATAAGATCTGTAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTGTATCTTCA
**
41700361 ACCTGCTCTCTTGCTACCTTGGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACA
66 ACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACA
* *
41700426 TGGAGATAAGACTCGCCATTTTCGATTTGCTCCACTACTACTTAGGG
131 TGGAGATAAGACTCGCCATTTTCGATCTGCTCCACTACTGCTTAGGG
* * *
41700473 AGATAAGATCTGTAATTTTCAGTCTACTTCCTTTCTACCTTAGGAAGATAAGACTTGTATCTTCA
1 AGATAAGATCTGTAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTGTATCTTCA
*
41700538 ACCTGCTCTCTTGCTACCTCGGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACA
66 ACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACA
* * * **
41700603 TGGAGATAAGACCCGCTA-TTTCTGATCTTCTCCACTACTGCTTAGAA
131 TGGAGATAAGACTCGCCATTTTC-GATCTGCTCCACTACTGCTTAGGG
* * *
41700650 AGATAAGATCTGTAATTTTCAGTCTGCTTCCTTGCTATCTTAGGAAGATAAGACTTGTATCTTTA
1 AGATAAGATCTGTAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTGTATCTTCA
*
41700715 ACCTGCTCTCTTGCTACCTC-GAAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGTCGATAC
66 ACCTGCTCTCTTGCTACCTCAG-AGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATAC
* * *
41700779 ATAGAGATAAGACTCGCCATTTTTGATCTGTTCCACTACTGCTTAGGG
130 ATGGAGATAAGACTCGCCATTTTCGATCTGCTCCACTACTGCTTAGGG
41700827 AGATAAGATCTGTAATTTTCA
1 AGATAAGATCTGTAATTTTCA
41700848 CCGATGTCGC
Statistics
Matches: 1293, Mismatches: 115, Indels: 34
0.90 0.08 0.02
Matches are distributed among these distances:
165 95 0.07
166 53 0.04
168 1 0.00
170 2 0.00
172 2 0.00
174 1 0.00
176 61 0.05
177 1074 0.83
178 4 0.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (177 bp):
AGATAAGATCTGTAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTGTATCTTCA
ACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACA
TGGAGATAAGACTCGCCATTTTCGATCTGCTCCACTACTGCTTAGGG
Found at i:41699457 original size:133 final size:134
Alignment explanation
Indices: 41699205--41699465 Score: 316
Period size: 133 Copynumber: 2.0 Consensus size: 134
41699195 TCAGGGAGAA
* *
41699205 AAGGTTGATAGCTAAAATCTGCTCCTATTGCCGATACGTGAAGATAAGATCTGTAATTTTCAGTC
1 AAGGATGATAGCTAAAATCTGCTCCTATTGCCGATACGTGAAGATAAGATCTGTAATCTTCAGTC
* *
41699270 TGCTTCCTTGCTACCTCAGGAAAATAAGACTTGTATCTTCAACCTGCTTTCTTGCTACCTCAGAG
66 TGCTTCCTTACTACCTCAGGAAAATAAGACTTGTATCTTCAACCTGCTTCCTTGCTACCTCAGAG
41699335 GGAC
131 GGAC
* * *
41699339 AAGGATGATGGCTAAAATCTGCTCC-ATTGCCGATACGTGGAGATAAGA-CTCGTCATCTTC-GA
1 AAGGATGATAGCTAAAATCTGCTCCTATTGCCGATACGTGAAGATAAGATCT-GTAATCTTCAG-
* * * * * * **
41699401 TCTGCTTCAC-TACT-GCTTAGGGAGATAAGATTTGTAATTTTCAGTCTGCTTCCTTGCTACCTC
64 TCTGCTTC-CTTACTACCTCAGGAAAATAAGACTTGT-ATCTTCAACCTGCTTCCTTGCTACCTC
41699464 AG
127 AG
41699466 GAAGGTAAGA
Statistics
Matches: 108, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
132 19 0.18
133 65 0.60
134 24 0.22
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (134 bp):
AAGGATGATAGCTAAAATCTGCTCCTATTGCCGATACGTGAAGATAAGATCTGTAATCTTCAGTC
TGCTTCCTTACTACCTCAGGAAAATAAGACTTGTATCTTCAACCTGCTTCCTTGCTACCTCAGAG
GGAC
Found at i:41711172 original size:12 final size:12
Alignment explanation
Indices: 41711155--41711181 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
41711145 TAACTCAATC
41711155 TATGGATCCCCT
1 TATGGATCCCCT
41711167 TATGGATCCCCT
1 TATGGATCCCCT
41711179 TAT
1 TAT
41711182 TAGGTTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.19, C:0.30, G:0.15, T:0.37
Consensus pattern (12 bp):
TATGGATCCCCT
Found at i:41719222 original size:28 final size:28
Alignment explanation
Indices: 41719189--41719306 Score: 123
Period size: 28 Copynumber: 4.2 Consensus size: 28
41719179 CTGTATAATG
*
41719189 CATATGGCCCA-CTAGGCCCAATCTCATT
1 CATATGGCCCATC-AGGCCCAATCACATT
* * *
41719217 TATATGGCCCATCCGGCCCAATTCACGTT
1 CATATGGCCCATCAGGCCCAA-TCACATT
41719246 CATAT-GCCCATCAGGCCCAATTCACATT
1 CATATGGCCCATCAGGCCCAA-TCACATT
* * *
41719274 CATATTGCCTATTAGGCCCAATCACATT
1 CATATGGCCCATCAGGCCCAATCACATT
*
41719302 TATAT
1 CATAT
41719307 TCATGCTCAC
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
28 54 0.70
29 23 0.30
ACGTcount: A:0.26, C:0.32, G:0.13, T:0.29
Consensus pattern (28 bp):
CATATGGCCCATCAGGCCCAATCACATT
Found at i:41736255 original size:2 final size:2
Alignment explanation
Indices: 41736248--41736282 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
41736238 TACACCTATT
41736248 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41736283 TTACAATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41736402 original size:18 final size:18
Alignment explanation
Indices: 41736379--41736434 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
41736369 TTTTTAAATC
41736379 ATATTTTTTATAATTTTT
1 ATATTTTTTATAATTTTT
*
41736397 ATATTTTTCTGGTAA--TTT
1 ATATTTTT-T-ATAATTTTT
*
41736415 ATA-TTTTTATAATTTAT
1 ATATTTTTTATAATTTTT
41736432 ATA
1 ATA
41736435 AAATCATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
15 3 0.10
16 1 0.03
17 9 0.29
18 14 0.45
19 1 0.03
20 3 0.10
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (18 bp):
ATATTTTTTATAATTTTT
Found at i:41736482 original size:20 final size:20
Alignment explanation
Indices: 41736437--41736523 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
41736427 TTTATATAAA
41736437 ATCATTTTTAATAAA-TTTT
1 ATCATTTTTAATAAATTTTT
* *
41736456 -GCAATTTTTACTAAATTTTT
1 ATC-ATTTTTAATAAATTTTT
*
41736476 ATCATTTAT-ATAAATTTTTT
1 ATCATTTTTAATAAA-TTTTT
* *
41736496 GTCATTTATAAT-AATTTTT
1 ATCATTTTTAATAAATTTTT
41736515 AT-ATTTTTA
1 ATCATTTTTA
41736524 TTTTTCTTGC
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
18 7 0.13
19 21 0.38
20 24 0.44
21 3 0.05
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (20 bp):
ATCATTTTTAATAAATTTTT
Found at i:41737443 original size:20 final size:20
Alignment explanation
Indices: 41737392--41737448 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
41737382 TTAATAATAT
* *
41737392 ATAAGCCTAATATATTATAG
1 ATAAGTCTAATATATTAGAG
*
41737412 AT-AGATCCAATATATTAGAG
1 ATAAG-TCTAATATATTAGAG
*
41737432 ATAAGTCTAATACATTA
1 ATAAGTCTAATATATTA
41737449 CATAAGCCCA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.07
20 26 0.87
21 2 0.07
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (20 bp):
ATAAGTCTAATATATTAGAG
Found at i:41737654 original size:21 final size:22
Alignment explanation
Indices: 41737608--41737654 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
41737598 AATGTAAGGT
*
41737608 TTGTTATTATGTTTTAATTTAG
1 TTGTTATTATGTGTTAATTTAG
41737630 -TGTTATTATCGTGTT-ATTT-G
1 TTGTTATTAT-GTGTTAATTTAG
41737650 TTGTT
1 TTGTT
41737655 TTTAAATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
20 1 0.05
21 17 0.77
22 4 0.18
ACGTcount: A:0.17, C:0.02, G:0.17, T:0.64
Consensus pattern (22 bp):
TTGTTATTATGTGTTAATTTAG
Found at i:41741157 original size:18 final size:18
Alignment explanation
Indices: 41741109--41741159 Score: 50
Period size: 21 Copynumber: 2.7 Consensus size: 18
41741099 ATCCAAAACT
*
41741109 AATT-AAAATAATATAAA
1 AATTAAAAATAAAATAAA
*
41741126 ATATTATAATAATAAAATTAA
1 A-ATTA-AA-AATAAAATAAA
41741147 AATTAAAAATAAA
1 AATTAAAAATAAA
41741160 TAATATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
17 1 0.04
18 9 0.32
19 2 0.07
20 6 0.21
21 10 0.36
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AATTAAAAATAAAATAAA
Found at i:41742656 original size:16 final size:16
Alignment explanation
Indices: 41742635--41742677 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
41742625 GTGAGATTTA
41742635 AATATTTTATTAAAAT
1 AATATTTTATTAAAAT
*
41742651 AATATTTTAATTAAGAT
1 AATATTTT-ATTAAAAT
*
41742668 CAT-TTTTATT
1 AATATTTTATT
41742678 TAATAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 3 0.12
16 12 0.50
17 9 0.38
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (16 bp):
AATATTTTATTAAAAT
Found at i:41743457 original size:18 final size:18
Alignment explanation
Indices: 41743412--41743482 Score: 74
Period size: 18 Copynumber: 4.0 Consensus size: 18
41743402 GAGATAGTAT
41743412 AAACTTATAAAAATATAA
1 AAACTTATAAAAATATAA
* *
41743430 AAAATCATAAAAATATAA
1 AAACTTATAAAAATATAA
*
41743448 ACACTTATAAAAA-ATAA
1 AAACTTATAAAAATATAA
* *
41743465 TAAATTTA-AAAAAAATAA
1 -AAACTTATAAAAATATAA
41743483 TTACAAAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
17 9 0.20
18 35 0.80
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (18 bp):
AAACTTATAAAAATATAA
Found at i:41743478 original size:36 final size:35
Alignment explanation
Indices: 41743414--41743482 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 35
41743404 GATAGTATAA
*
41743414 ACTTATAAAAATATAAAAAATCATAAAAATATAAAC
1 ACTTATAAAAATATAAAAAATCA-AAAAAAATAAAC
* *
41743450 ACTTATAAAAA-ATAATAAATTTAAAAAAAATAA
1 ACTTATAAAAATATAA-AAAATCAAAAAAAATAA
41743483 TTACAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 13 0.45
36 16 0.55
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (35 bp):
ACTTATAAAAATATAAAAAATCAAAAAAAATAAAC
Found at i:41743499 original size:9 final size:9
Alignment explanation
Indices: 41743416--41743500 Score: 51
Period size: 9 Copynumber: 10.0 Consensus size: 9
41743406 TAGTATAAAC
41743416 TTATAAAAA
1 TTATAAAAA
41743425 -TATAAAAAA
1 TTAT-AAAAA
*
41743434 TCATAAAAA
1 TTATAAAAA
*
41743443 -TATAAACAC
1 TTATAAA-AA
41743452 TTATAAAAA
1 TTATAAAAA
41743461 --ATAATAAA
1 TTATAA-AAA
41743469 TT-TAAAAA
1 TTATAAAAA
*
41743477 --A-AATAA
1 TTATAAAAA
*
41743483 TTACAAAAA
1 TTATAAAAA
41743492 TTATAAAAA
1 TTATAAAAA
41743501 AGTCATTTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 22
0.67 0.08 0.25
Matches are distributed among these distances:
6 4 0.07
7 4 0.07
8 15 0.26
9 27 0.47
10 8 0.14
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (9 bp):
TTATAAAAA
Found at i:41746435 original size:15 final size:15
Alignment explanation
Indices: 41746412--41746446 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
41746402 TGTAAAACTA
*
41746412 ATGTATGGTATTTTT
1 ATGTTTGGTATTTTT
41746427 ATGTTTGGTATTTTT
1 ATGTTTGGTATTTTT
41746442 ATGTT
1 ATGTT
41746447 ATGCTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.20, T:0.63
Consensus pattern (15 bp):
ATGTTTGGTATTTTT
Found at i:41748445 original size:21 final size:21
Alignment explanation
Indices: 41748419--41748471 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
41748409 TGTTGTTTCT
* *
41748419 AATCTCACCGCTATAGTATCC
1 AATCTCACCGCTACAGTAACC
* *
41748440 AATCTCACTGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
41748461 AATCTCACCGC
1 AATCTCACCGC
41748472 CACCGTTGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.34, G:0.09, T:0.26
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:41748803 original size:20 final size:18
Alignment explanation
Indices: 41748780--41748830 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 18
41748770 TTTTAAAATT
*
41748780 ATTTTTATCAGTTTTTATGA
1 ATTTTTATAAG-TTTTAT-A
41748800 ATTTTCTATAAGTTTTATA
1 ATTTT-TATAAGTTTTATA
41748819 ATTTTTATAAGT
1 ATTTTTATAAGT
41748831 ATACATAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 7 0.24
19 6 0.21
20 11 0.38
21 5 0.17
ACGTcount: A:0.29, C:0.04, G:0.08, T:0.59
Consensus pattern (18 bp):
ATTTTTATAAGTTTTATA
Found at i:41748900 original size:22 final size:20
Alignment explanation
Indices: 41748839--41748912 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
41748829 GTATACATAA
* *
41748839 AATTTTAATATTTTTTTATA
1 AATTTTAATAATTTTTTATT
41748859 AATTTT-ATAATATTTTTATT
1 AATTTTAATAAT-TTTTTATT
41748879 AATTTTAAATAA-TTTTTA-T
1 AATTTT-AATAATTTTTTATT
41748898 -ATTTTAATGAATTTT
1 AATTTTAAT-AATTTT
41748913 ATTGAAAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
17 3 0.06
18 7 0.15
19 8 0.17
20 25 0.53
22 4 0.09
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (20 bp):
AATTTTAATAATTTTTTATT
Found at i:41757455 original size:27 final size:27
Alignment explanation
Indices: 41757398--41757456 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
41757388 ATACATCTCA
* *
41757398 TAGGGGCATATTAGTCATTTTACCATG
1 TAGGGGCATATTAATCATTTTACAATG
41757425 TAGGGGCAT-TTCAATCATTTTATCAAT-
1 TAGGGGCATATT-AATCATTTTA-CAATG
41757452 TAGGG
1 TAGGG
41757457 AGTCTAGGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 2 0.07
27 23 0.82
28 3 0.11
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (27 bp):
TAGGGGCATATTAATCATTTTACAATG
Found at i:41761009 original size:23 final size:23
Alignment explanation
Indices: 41760980--41761042 Score: 81
Period size: 24 Copynumber: 2.7 Consensus size: 23
41760970 TATCAACTCA
41760980 TAAGAGCTTACTGTTTCAGCACG
1 TAAGAGCTTACTGTTTCAGCACG
*
41761003 TAAGAGCTTACTGTTTTCAGCTCG
1 TAAGAGCTTACTG-TTTCAGCACG
** *
41761027 CCAGAGCTTACCGTTT
1 TAAGAGCTTACTGTTT
41761043 TAGCTCAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 16 0.46
24 19 0.54
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (23 bp):
TAAGAGCTTACTGTTTCAGCACG
Found at i:41761032 original size:24 final size:24
Alignment explanation
Indices: 41760981--41761063 Score: 91
Period size: 23 Copynumber: 3.5 Consensus size: 24
41760971 ATCAACTCAT
* *
41760981 AAGAGCTTACTG-TTTCAGCACGT
1 AAGAGCTTACTGTTTTCAGCTCGA
*
41761004 AAGAGCTTACTGTTTTCAGCTCGC
1 AAGAGCTTACTGTTTTCAGCTCGA
* *
41761028 CAGAGCTTACCGTTTT-AGCTC-A
1 AAGAGCTTACTGTTTTCAGCTCGA
41761050 ATAGAGCTTACTGT
1 A-AGAGCTTACTGT
41761064 CCATCAGCTT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
23 28 0.55
24 23 0.45
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (24 bp):
AAGAGCTTACTGTTTTCAGCTCGA
Found at i:41761211 original size:19 final size:19
Alignment explanation
Indices: 41761187--41761321 Score: 91
Period size: 19 Copynumber: 7.1 Consensus size: 19
41761177 AAGCTATGTC
*
41761187 TTATATGAATGAATTACTG
1 TTATACGAATGAATTACTG
* * *
41761206 TTATATGGATGAAATACTG
1 TTATACGAATGAATTACTG
*
41761225 TT-TAGGCGAATGAGTTACTG
1 TTATA--CGAATGAATTACTG
*
41761245 TTA-ACGAATGAATTACTA
1 TTATACGAATGAATTACTG
* * *
41761263 TTATATGGAT-ACAGTACTG
1 TTATACGAATGA-ATTACTG
* *
41761282 TTTAGACAAAT-AAGTTACTG
1 -TTATACGAATGAA-TTACTG
41761302 TTAT-CGAATGAATTACTG
1 TTATACGAATGAATTACTG
41761320 TT
1 TT
41761322 TATATGATTG
Statistics
Matches: 89, Mismatches: 19, Indels: 17
0.71 0.15 0.14
Matches are distributed among these distances:
18 30 0.34
19 34 0.38
20 25 0.28
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.38
Consensus pattern (19 bp):
TTATACGAATGAATTACTG
Found at i:41761254 original size:18 final size:19
Alignment explanation
Indices: 41761220--41761321 Score: 57
Period size: 18 Copynumber: 5.4 Consensus size: 19
41761210 ATGGATGAAA
*
41761220 TACTGTTTAGGCGAATGAGT
1 TACTG-TTAGACGAATGAGT
*
41761240 TACTGTTA-ACGAATGAAT
1 TACTGTTAGACGAATGAGT
* * * * *
41761258 TACTATTATATGGATACAG-
1 TACTGTTAGACGAAT-GAGT
* *
41761277 TACTGTTTAGACAAATAAGT
1 TACTG-TTAGACGAATGAGT
* *
41761297 TACTGTTA-TCGAATGAAT
1 TACTGTTAGACGAATGAGT
41761315 TACTGTT
1 TACTGTT
41761322 TATATGATTG
Statistics
Matches: 61, Mismatches: 17, Indels: 10
0.69 0.19 0.11
Matches are distributed among these distances:
18 28 0.46
19 16 0.26
20 17 0.28
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (19 bp):
TACTGTTAGACGAATGAGT
Found at i:41761281 original size:57 final size:57
Alignment explanation
Indices: 41761193--41761327 Score: 182
Period size: 57 Copynumber: 2.4 Consensus size: 57
41761183 TGTCTTATAT
* * * *
41761193 GAATGAATTACTGTTATATGGATGAAATACTGTTTAGGCGAATGAGTTACTGTTAAC
1 GAATGAATTACTATTATATGGATGAAATACTGTTTAGACAAATAAGTTACTGTTAAC
* *
41761250 GAATGAATTACTATTATATGGAT-ACAGTACTGTTTAGACAAATAAGTTACTGTTATC
1 GAATGAATTACTATTATATGGATGA-AATACTGTTTAGACAAATAAGTTACTGTTAAC
*
41761307 GAATGAATTACTGTTTATATG
1 GAATGAATTACT-ATTATATG
41761328 ATTGATAGTC
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
56 1 0.01
57 61 0.88
58 7 0.10
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (57 bp):
GAATGAATTACTATTATATGGATGAAATACTGTTTAGACAAATAAGTTACTGTTAAC
Found at i:41765141 original size:27 final size:28
Alignment explanation
Indices: 41765111--41765180 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
41765101 ATAGTGAATC
*
41765111 CGCACACTTAGTGCTATAAAATC-AGCT
1 CGCACACTTAGTGCTATAAAATCAAACT
* * *
41765138 CGCACACATAGTGCTATATAATCAAATT
1 CGCACACTTAGTGCTATAAAATCAAACT
41765166 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41765181 GTACAATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATAAAATCAAACT
Found at i:41765252 original size:42 final size:42
Alignment explanation
Indices: 41765188--41765294 Score: 187
Period size: 42 Copynumber: 2.5 Consensus size: 42
41765178 GCTGTACAAT
* * *
41765188 TTTAAACCCGCACACGTAGTGCCAATCTTGTCACCGTGTCCA
1 TTTATACCCGCACACTTAGTGCCAATCTTGTCACCATGTCCA
41765230 TTTATACCCGCACACTTAGTGCCAATCTTGTCACCATGTCCA
1 TTTATACCCGCACACTTAGTGCCAATCTTGTCACCATGTCCA
41765272 TTTATACCCGCACACTTAGTGCC
1 TTTATACCCGCACACTTAGTGCC
41765295 GAGACCAATA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.29
Consensus pattern (42 bp):
TTTATACCCGCACACTTAGTGCCAATCTTGTCACCATGTCCA
Found at i:41770461 original size:56 final size:58
Alignment explanation
Indices: 41770372--41770500 Score: 163
Period size: 56 Copynumber: 2.2 Consensus size: 58
41770362 GACAAGATTG
* * * * ***
41770372 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAG-T-TTTTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTAAAATATATA
*
41770428 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCT-AAAATATATA
41770487 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
41770501 GATTCACTAT
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
56 41 0.66
57 1 0.02
59 20 0.32
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.29
Consensus pattern (58 bp):
GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTAAAATATATA
Found at i:41770494 original size:29 final size:30
Alignment explanation
Indices: 41770372--41770500 Score: 160
Period size: 30 Copynumber: 4.5 Consensus size: 30
41770362 GACAAGATTG
* * * * *
41770372 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
**
41770402 GCACTAAGTGTGCGAG-T---TTTTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
41770428 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
41770458 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
41770487 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
41770501 GATTCACTAT
Statistics
Matches: 88, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
26 21 0.24
27 1 0.01
29 21 0.24
30 45 0.51
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.29
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:41772982 original size:27 final size:28
Alignment explanation
Indices: 41772952--41773021 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
41772942 ATAGTGAATC
*
41772952 CGCACACTTAGTGCTATAAAATC-AGCT
1 CGCACACTTAGTGCTATAAAATCAAACT
* * *
41772979 CGCACACATAGTGCTATATAATCAAATT
1 CGCACACTTAGTGCTATAAAATCAAACT
41773007 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41773022 GTACAATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATAAAATCAAACT
Found at i:41773093 original size:42 final size:42
Alignment explanation
Indices: 41773029--41773135 Score: 196
Period size: 42 Copynumber: 2.5 Consensus size: 42
41773019 GCTGTACAAT
* *
41773029 TTTAAACCCGCACACGTAGTGCCAATCTTGTCACCGTGTCCA
1 TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
41773071 TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
1 TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
41773113 TTTATACCCGCACACTTAGTGCC
1 TTTATACCCGCACACTTAGTGCC
41773136 GAGACCAATA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.22, C:0.34, G:0.15, T:0.29
Consensus pattern (42 bp):
TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
Found at i:41780453 original size:12 final size:12
Alignment explanation
Indices: 41780436--41780460 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41780426 TTTTGTCCAT
41780436 CATGTGTTGCGG
1 CATGTGTTGCGG
41780448 CATGTGTTGCGG
1 CATGTGTTGCGG
41780460 C
1 C
41780461 TGGGTAGTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.20, G:0.40, T:0.32
Consensus pattern (12 bp):
CATGTGTTGCGG
Found at i:41784037 original size:22 final size:22
Alignment explanation
Indices: 41784009--41784051 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
41783999 TTTACACTTA
*
41784009 AATTATTAATATATTGAATTTT
1 AATTATTAATATAATGAATTTT
**
41784031 AATTATTTTTATAATGAATTT
1 AATTATTAATATAATGAATTT
41784052 ACACAAACTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (22 bp):
AATTATTAATATAATGAATTTT
Found at i:41787514 original size:26 final size:26
Alignment explanation
Indices: 41787485--41787561 Score: 64
Period size: 28 Copynumber: 2.8 Consensus size: 26
41787475 GCCCTTTGAA
* * *
41787485 TCATTTGATATTTTGCACACTAAGTG
1 TCATTTAATATCTCGCACACTAAGTG
41787511 TCATTCTTAATATCTCGCACACTAAGTG
1 TCA-T-TTAATATCTCGCACACTAAGTG
* * *
41787539 CCATTCTCAATATTTCGTACACT
1 TCATT-T-AATATCTCGCACACT
41787562 GAGTACCATA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
26 4 0.10
27 3 0.07
28 34 0.83
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.39
Consensus pattern (26 bp):
TCATTTAATATCTCGCACACTAAGTG
Found at i:41787530 original size:28 final size:28
Alignment explanation
Indices: 41787499--41787570 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
41787489 TTGATATTTT
* *
41787499 GCACACTAAGTGTCATTCTTAATATCTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
41787527 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGTGCCATTCTCAATATCTC
* * *
41787555 GTACACTGAGTACCAT
1 GCACACTAAGTGCCAT
41787571 ATTTGATTGC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (28 bp):
GCACACTAAGTGCCATTCTCAATATCTC
Found at i:41816819 original size:33 final size:34
Alignment explanation
Indices: 41816776--41816844 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 34
41816766 ACACTTGTTA
*
41816776 ACCCTAAAATCATTACTTTTAGTCATTCGCTTTT
1 ACCCTAAAATCATTACTTCTAGTCATTCGCTTTT
*
41816810 ACCC-AAAATCGTTACTTCTAGTCATTCGCTTTT
1 ACCCTAAAATCATTACTTCTAGTCATTCGCTTTT
41816843 AC
1 AC
41816845 ACATTTCATT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
33 29 0.88
34 4 0.12
ACGTcount: A:0.26, C:0.26, G:0.07, T:0.41
Consensus pattern (34 bp):
ACCCTAAAATCATTACTTCTAGTCATTCGCTTTT
Found at i:41822877 original size:28 final size:28
Alignment explanation
Indices: 41822829--41822884 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
41822819 ACAAAGTGCA
*
41822829 AATAACGATAAGCACCGAAGTGCAAATT
1 AATAACGATAAGCACCAAAGTGCAAATT
* *
41822857 AATAACGATATGCATCAAAGTGCAAATT
1 AATAACGATAAGCACCAAAGTGCAAATT
41822885 TTTACAGCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.21
Consensus pattern (28 bp):
AATAACGATAAGCACCAAAGTGCAAATT
Found at i:41825605 original size:15 final size:16
Alignment explanation
Indices: 41825585--41825614 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
41825575 TAACAACTAA
41825585 TATATAAT-TATATTT
1 TATATAATATATATTT
41825600 TATATAATATATATT
1 TATATAATATATATT
41825615 AATTGTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATAATATATATTT
Found at i:41831756 original size:53 final size:53
Alignment explanation
Indices: 41831578--41831784 Score: 189
Period size: 53 Copynumber: 3.8 Consensus size: 53
41831568 ATTAGGGTTT
* * * * * * *
41831578 AAGGATACCAAGTAAGACCATGCCATGGCATGCCATTGGTAAGTTTTACAAGGC
1 AAGGATACCACGTAAGACCATGCCAAGACATGGCAATGGTAAG-TTCATAAGGC
* * * * * * * *
41831632 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAACTACTATAAGGC
1 AAGGATACCACGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAGGC
* * * *
41831687 AAAGATCCCACGTAAGACCATGCCAAGGCATGGCAATGGTAAGTTCCTAAGGC
1 AAGGATACCACGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
* * *
41831740 AAGGATACCACGTAAGACCACGTCAAGACATGGAAATGGTAAGTT
1 AAGGATACCACGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
41831785 TAAAAAGGAA
Statistics
Matches: 121, Mismatches: 30, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
53 45 0.37
54 37 0.31
55 39 0.32
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (53 bp):
AAGGATACCACGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
Found at i:41837041 original size:48 final size:48
Alignment explanation
Indices: 41836989--41837174 Score: 212
Period size: 48 Copynumber: 3.9 Consensus size: 48
41836979 TACGAAGTCT
*
41836989 CATATCAGTGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACA
1 CATATCAGTGCCAATGCCATGTCCCAGACATGGTCTTACACTAGCACA
* *
41837037 CATATCA-TCGCCAATGCCATGTCCCAAACATGGTCTTACACTGGCACA
1 CATATCAGT-GCCAATGCCATGTCCCAGACATGGTCTTACACTAGCACA
*** ** * * *
41837085 CATATCAACACTGATGCCATGTTCCAGACATGGTCTTACACTAGCTCT
1 CATATCAGTGCCAATGCCATGTCCCAGACATGGTCTTACACTAGCACA
* * * *
41837133 CATCTCTGATGCCAATGTCATGTCCCTGACATGGTCTTACAC
1 CATATCAG-TGCCAATGCCATGTCCCAGACATGGTCTTACAC
41837175 GAGATCTCAT
Statistics
Matches: 113, Mismatches: 22, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
47 1 0.01
48 86 0.76
49 26 0.23
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.26
Consensus pattern (48 bp):
CATATCAGTGCCAATGCCATGTCCCAGACATGGTCTTACACTAGCACA
Found at i:41840460 original size:80 final size:80
Alignment explanation
Indices: 41840376--41840529 Score: 200
Period size: 80 Copynumber: 1.9 Consensus size: 80
41840366 TTATAGTGAT
* * ** * *
41840376 TCGCACGATTGCCTTCAGGTCTTAACCCGGATTTGGTAACTTGCACAAATGCCTTCAGGTCTTAG
1 TCGCACGAATGCCTTCAGGTCTTAACCCGGATATAATAACTAGCACAAATGCCTTCAGGACTTAG
41840441 CCCGGATATAACAAC
66 CCCGGATATAACAAC
* * * * * *
41840456 TCGCACGAATGCCTTCGGGTCTTAGCCCGGATATAATTACTAGCATAATTGCCTTCGGGACTTAG
1 TCGCACGAATGCCTTCAGGTCTTAACCCGGATATAATAACTAGCACAAATGCCTTCAGGACTTAG
41840521 CCCGGATAT
66 CCCGGATAT
41840530 CATTCCAATG
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
80 62 1.00
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (80 bp):
TCGCACGAATGCCTTCAGGTCTTAACCCGGATATAATAACTAGCACAAATGCCTTCAGGACTTAG
CCCGGATATAACAAC
Found at i:41840491 original size:40 final size:40
Alignment explanation
Indices: 41840322--41840529 Score: 175
Period size: 40 Copynumber: 5.2 Consensus size: 40
41840312 CGGGATTTAA
** * * * * *
41840322 CCGGATATAGCGACTCGCTCGATTGTCTTCGGGACCTAGC
1 CCGGATATAGTAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
41840362 CCGGTTATAGTGATTCGCACGATTGCCTTCAGGTCTTAAC
1 CCGGATATAGTAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * *
41840402 CCGGATTTGGTAACTTGCACAAATGCCTTCAGGTCTTAGC
1 CCGGATATAGTAACTCGCACGAATGCCTTCGGGTCTTAGC
**
41840442 CCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAGTAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * *
41840482 CCGGATATAATTACTAGCA-TAATTGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACGAA-TGCCTTCGGGTCTTAGC
41840522 CCGGATAT
1 CCGGATAT
41840530 CATTCCAATG
Statistics
Matches: 137, Mismatches: 30, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
39 2 0.01
40 135 0.99
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:41846944 original size:48 final size:48
Alignment explanation
Indices: 41846889--41847109 Score: 253
Period size: 48 Copynumber: 4.6 Consensus size: 48
41846879 ATCAGTGCCG
* *
41846889 ATGCCATGTCCCAGACATGGTCTTACATTGGAACACATATCAACGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACGCCA
* *
41846937 ATTCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACGCCT
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACGCCA
* * ** * *
41846985 ATGCTATGTCGCAGACATGGTCTTACACTACCACACATGTCAACGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACGCCA
* * * ** * * *
41847033 ATGCCATGTTCCAGACATGGTCTTACACTAGCTCTTATCTCGAATGCCT
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATC-AACGCCA
* *
41847082 ATGCCATGTCCTAGACATGGTCCTACAC
1 ATGCCATGTCCCAGACATGGTCTTACAC
41847110 AGGATCTCAT
Statistics
Matches: 148, Mismatches: 24, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
48 118 0.80
49 30 0.20
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.26
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACGCCA
Found at i:41848926 original size:10 final size:9
Alignment explanation
Indices: 41848910--41848960 Score: 57
Period size: 10 Copynumber: 5.2 Consensus size: 9
41848900 ATCACTTTTT
41848910 AAAAAAGAA
1 AAAAAAGAA
41848919 AGAAAAAGAA
1 A-AAAAAGAA
*
41848929 GCAAAAAGAA
1 -AAAAAAGAA
41848939 AACAAAAGAA
1 AA-AAAAGAA
41848949 AAAACAAGAA
1 AAAA-AAGAA
41848959 AA
1 AA
41848961 GCACGTCCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
9 4 0.11
10 32 0.89
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:41848998 original size:9 final size:9
Alignment explanation
Indices: 41848983--41849031 Score: 57
Period size: 9 Copynumber: 5.7 Consensus size: 9
41848973 AAAGAGTAAA
41848983 AAATAAAAT
1 AAATAAAAT
*
41848992 CAATAAAAT
1 AAATAAAAT
41849001 AAAT-AAAT
1 AAATAAAAT
*
41849009 AAAT-AAAC
1 AAATAAAAT
41849017 AAATAAAAT
1 AAATAAAAT
*
41849026 ATATAA
1 AAATAA
41849032 CAAAATAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
8 15 0.44
9 19 0.56
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (9 bp):
AAATAAAAT
Found at i:41849007 original size:25 final size:25
Alignment explanation
Indices: 41848979--41849039 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
41848969 ATAGAAAGAG
41848979 TAAAAAATAAAATC-AATAAAATAAA
1 TAAAAAATAAAA-CAAATAAAATAAA
*
41849004 TAAATAAAT-AAACAAATAAAATATA
1 TAAA-AAATAAAACAAATAAAATAAA
41849029 TAACAAAATAA
1 TAA-AAAATAA
41849040 TTATAATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
24 1 0.03
25 24 0.77
26 6 0.19
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (25 bp):
TAAAAAATAAAACAAATAAAATAAA
Found at i:41852772 original size:13 final size:13
Alignment explanation
Indices: 41852756--41852781 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41852746 ATGATTCAGG
41852756 TAGGAGATTAGCA
1 TAGGAGATTAGCA
41852769 TAGGAGATTAGCA
1 TAGGAGATTAGCA
41852782 AGAAAATCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.31, T:0.23
Consensus pattern (13 bp):
TAGGAGATTAGCA
Found at i:41859504 original size:96 final size:96
Alignment explanation
Indices: 41859333--41859979 Score: 900
Period size: 96 Copynumber: 6.6 Consensus size: 96
41859323 GCTGAAATTG
*
41859333 ATGTATAAGATATGTATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAGATATGTAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAGATATGTAT
* * *
41859398 ATGTGGTAAAGCCGAATGGCTAGTGTCAAAA
66 ATGTGGTAAAGCCGAATGGCTAATGTGAAAT
* *
41859429 ATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAGATATGTAT
41859494 ATGTGGTAAAGCCGAATGGCTAATGTGAAAT
66 ATGTGGTAAAGCCGAATGGCTAATGTGAAAT
* *
41859525 ATGTATGAGATATGTATATGTGGTATAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAGATATGTAT
41859590 ATGTGGTAAAGCCGAATGGCTAATGTGAAAT
66 ATGTGGTAAAGCCGAATGGCTAATGTGAAAT
*
41859621 ATGTATGAGATATGTATATGTGGTATAGCCAAATGGCTAATGTGAAATATGTATGAGATATGTAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAGATATGTAT
*
41859686 ATGTGGTAAAGCCGAATGGCTAATGCGAAATATATATATATAT
66 ATGTGGTAAAGCCGAATGGCTAAT--G-------T-GA-A-AT
* * *** * *
41859729 ATATATGAGATATGTGTATGTGGTAAAGCTGGATGGTTAATGTGAAATATATATATATGAGATAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCAAATGGCTAATGTG--A-A-ATATGTATGAGATAT
41859794 GTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
62 GTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
* * *
41859829 ATGTATGAGATATGCATATGTGGTAAAGCCGAATGG-TCAATGTGAAATATATATATGAGATATG
1 ATGTATGAGATATGTATATGTGGTAAAGCCAAATGGCT-AATGTG-AA-ATATGTATGAGATATG
* *
41859893 TATATGTGGTAAAGCCGAATAGCTAGTGTGAAAT
63 TATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
* *
41859927 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
1 ATGTATGAGATATGTATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTA
41859980 GGCGATGTGT
Statistics
Matches: 504, Mismatches: 29, Indels: 36
0.89 0.05 0.06
Matches are distributed among these distances:
96 278 0.55
97 2 0.00
98 91 0.18
99 4 0.01
100 39 0.08
101 1 0.00
102 1 0.00
103 1 0.00
105 1 0.00
106 1 0.00
107 1 0.00
108 39 0.08
110 2 0.00
111 1 0.00
112 42 0.08
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.32
Consensus pattern (96 bp):
ATGTATGAGATATGTATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAGATATGTAT
ATGTGGTAAAGCCGAATGGCTAATGTGAAAT
Found at i:41859593 original size:144 final size:145
Alignment explanation
Indices: 41859333--41859979 Score: 949
Period size: 144 Copynumber: 4.4 Consensus size: 145
41859323 GCTGAAATTG
* *
41859333 ATGTATAAGATATGTATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAGATATGTAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTAT
* * *
41859398 ATGTGGTAAAGCCGAATGGCTAGTGTCAA-AAATATATGAGATATGTATATGTGGTAAAGCCGAA
66 ATGTGGTAAAGCCGAATGGCTAATGTGAATATATATATGAGATATGTATATGTGGTAAAGCCGAA
41859462 TGGCTAATGTGAAAT
131 TGGCTAATGTGAAAT
41859477 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTAT
* *
41859542 ATGTGGTATAGCCGAATGGCTAATGTGAA-ATATGTATGAGATATGTATATGTGGTAAAGCCGAA
66 ATGTGGTAAAGCCGAATGGCTAATGTGAATATATATATGAGATATGTATATGTGGTAAAGCCGAA
41859606 TGGCTAATGTGAAAT
131 TGGCTAATGTGAAAT
* *
41859621 ATGTATGAGATATGTATATGTGGTATAGCCAAATGGCTAATGTGAAATATGTATGAGATATGTAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTAT
* *
41859686 ATGTGGTAAAGCCGAATGGCTAATGCGAAATATATATATATATATATATGAGATATGTGTATGTG
66 ATGTGGTAAAGCCGAATGGCTAAT--G-------T-GA-ATATATATATGAGATATGTATATGTG
* * *
41859751 GTAAAGCTGGATGGTTAATGTGAAATATAT
120 GTAAAGCCGAATGGCTAATGTG--A-A-AT
* *
41859781 ATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGCAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTAT
41859846 ATGTGGTAAAGCCGAATGG-TCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCCG
66 ATGTGGTAAAGCCGAATGGCT-AATGTG-AATATATATATGAGATATGTATATGTGGTAAAGCCG
* *
41859910 AATAGCTAGTGTGAAAT
129 AATGGCTAATGTGAAAT
*
41859927 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTA
41859980 GGCGATGTGT
Statistics
Matches: 456, Mismatches: 29, Indels: 34
0.88 0.06 0.07
Matches are distributed among these distances:
144 223 0.49
146 54 0.12
147 1 0.00
148 1 0.00
150 42 0.09
151 2 0.00
153 1 0.00
154 1 0.00
155 1 0.00
156 41 0.09
158 2 0.00
159 2 0.00
160 85 0.19
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.32
Consensus pattern (145 bp):
ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTAT
ATGTGGTAAAGCCGAATGGCTAATGTGAATATATATATGAGATATGTATATGTGGTAAAGCCGAA
TGGCTAATGTGAAAT
Found at i:41859739 original size:60 final size:57
Alignment explanation
Indices: 41859667--41859830 Score: 203
Period size: 52 Copynumber: 2.9 Consensus size: 57
41859657 CTAATGTGAA
*
41859667 ATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGCGAAATATATATATAT
1 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATG-GAAATATA-A-ATAT
* * * * *
41859727 ATATATATGAGATATGTGTATGTGGTAAAGCTGGATGGTTAAT-G---T-GAAATAT
1 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGGAAATATAAATAT
41859779 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATAT
1 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATG-GAAATAT
41859831 GTATGAGATA
Statistics
Matches: 87, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
52 43 0.49
53 1 0.01
54 2 0.02
55 1 0.01
57 1 0.01
58 1 0.01
60 38 0.44
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (57 bp):
ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGGAAATATAAATAT
Found at i:41859816 original size:112 final size:108
Alignment explanation
Indices: 41859619--41859830 Score: 307
Period size: 112 Copynumber: 1.9 Consensus size: 108
41859609 CTAATGTGAA
* * *
41859619 ATATGTATGAGATATGTATATGTGGTATAGCCAAATGGCTAATGTGAAATATGTATGAGATATGT
1 ATATATATGAGATATGTATATGTGGTAAAGCCAAATGGCTAATGTGAAATATATATGAGATATGT
41859684 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATATATATATAT
66 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATATATATATAT
* *** *
41859727 ATATATATGAGATATGTGTATGTGGTAAAGCTGGATGGTTAATGTGAAATATATATATATGAGAT
1 ATATATATGAGATATGTATATGTGGTAAAGCCAAATGGCTAATGTG--A-A-ATATATATGAGAT
*
41859792 ATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATAT
62 ATGTATATGTGGTAAAGCCGAATGGCTAATGCGAAATAT
41859831 GTATGAGATA
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
108 39 0.43
110 1 0.01
111 1 0.01
112 50 0.55
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (108 bp):
ATATATATGAGATATGTATATGTGGTAAAGCCAAATGGCTAATGTGAAATATATATGAGATATGT
ATATGTGGTAAAGCCGAATGGCTAATGCGAAATATATATATAT
Found at i:41859891 original size:50 final size:50
Alignment explanation
Indices: 41859340--41859976 Score: 817
Period size: 48 Copynumber: 12.9 Consensus size: 50
41859330 TTGATGTATA
* *
41859340 AGATATGTATATGTGGTAAAGCCAAATGGCTAATGTG-AA-ATATGTATG
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATG
* *
41859388 AGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTCAAA-A-ATATATG
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATG
*
41859436 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG-AA-ATATGTATG
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATG
*
41859484 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG-AA-ATATGTATG
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATG
* *
41859532 AGATATGTATATGTGGTATAGCCGAATGGCTAATGTG-AA-ATATGTATG
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATG
*
41859580 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG-AA-ATATGTATG
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATG
* * *
41859628 AGATATGTATATGTGGTATAGCCAAATGGCTAATGTG-AA-ATATGTATG
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATG
*
41859676 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGCGAAATATATATATATATATATATG
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAAT--G-----T-GA-A-ATATATATATG
* * * *
41859736 AGATATGTGTATGTGGTAAAGCTGGATGGTTAATGTGAAATATATATATATG
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG-AA-ATATATATATG
*
41859788 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG-AA-ATATGTATG
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATG
*
41859836 AGATATGCATATGTGGTAAAGCCGAATGG-TCAATGTGAAATATATATATG
1 AGATATGTATATGTGGTAAAGCCGAATGGCT-AATGTGAAATATATATATG
* * *
41859886 AGATATGTATATGTGGTAAAGCCGAATAGCTAGTGTG-AA-ATATGTATG
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATG
*
41859934 AGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATAT
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATAT
41859977 GTAGGCGATG
Statistics
Matches: 536, Mismatches: 32, Indels: 40
0.88 0.05 0.07
Matches are distributed among these distances:
47 4 0.01
48 387 0.72
49 10 0.02
50 44 0.08
51 1 0.00
52 46 0.09
53 2 0.00
55 1 0.00
58 2 0.00
59 1 0.00
60 38 0.07
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.32
Consensus pattern (50 bp):
AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATG
Found at i:41860186 original size:37 final size:37
Alignment explanation
Indices: 41860131--41860239 Score: 182
Period size: 37 Copynumber: 2.9 Consensus size: 37
41860121 GGAAATATAT
*
41860131 TCCGGGTAAGACCTGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
41860168 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* * *
41860205 TTCGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
41860240 CATCTGAGCT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.29
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:41863208 original size:30 final size:30
Alignment explanation
Indices: 41863164--41863238 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
41863154 ACAGCCTAAG
*
41863164 ACACGGGCGTGTGTCTCAGCCATGTGTGAC
1 ACACGGGCGTGTGTCTCAACCATGTGTGAC
41863194 ACACAGGG-GTGTGTCTCAACCATGTGTGAC
1 ACAC-GGGCGTGTGTCTCAACCATGTGTGAC
* *
41863224 ACACGGTCTTGTGTC
1 ACACGGGCGTGTGTC
41863239 CTCTATAGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
29 2 0.05
30 35 0.88
31 3 0.08
ACGTcount: A:0.19, C:0.25, G:0.31, T:0.25
Consensus pattern (30 bp):
ACACGGGCGTGTGTCTCAACCATGTGTGAC
Found at i:41868965 original size:48 final size:46
Alignment explanation
Indices: 41868758--41868972 Score: 209
Period size: 46 Copynumber: 4.6 Consensus size: 46
41868748 TGATATGTGT
* *
41868758 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCAC-AGTATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGTA-GAAA
* **
41868804 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATTTAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAG-TA-GAAA
* * * * * * *
41868852 GCCAGTGTAAGACATGTTTAGGACATGCATCGGCATTGAG-ACAAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGTAGAA-A
* * *
41868898 GATAGCGTAAGACACGTCTGGGACATGCATCAGCCTCGCAGTAGACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCG-AGTAGA-AA
* *
41868946 GCTAGTGTAAGACTTGTCTGAGACATG
1 GCTAGTGTAAGACATGTCTGGGACATG
41868973 GCGTCAACTT
Statistics
Matches: 136, Mismatches: 27, Indels: 10
0.79 0.16 0.06
Matches are distributed among these distances:
45 1 0.01
46 66 0.49
47 4 0.03
48 64 0.47
49 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.22
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGTAGAAA
Found at i:41869057 original size:49 final size:49
Alignment explanation
Indices: 41868997--41869114 Score: 148
Period size: 49 Copynumber: 2.4 Consensus size: 49
41868987 TGTGTTAGTG
* * *
41868997 TAAGACTTGTCTGGGACATGGCATCGACAC-CGATAGATGAAAGCCAGTA
1 TAAGACCTGTCTGGGACATGGCATCGAC-CTCGATACATAAAAGCCAGTA
* * *
41869046 TAAGACCTGTCTGGGACATGGCATCGGCCTCGCTACATAAAAGCCAGTG
1 TAAGACCTGTCTGGGACATGGCATCGACCTCGATACATAAAAGCCAGTA
*
41869095 TAAGACCATGTCTAGGACAT
1 TAAGACC-TGTCTGGGACAT
41869115 AGCGTTGGCA
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
48 1 0.02
49 48 0.80
50 11 0.18
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.21
Consensus pattern (49 bp):
TAAGACCTGTCTGGGACATGGCATCGACCTCGATACATAAAAGCCAGTA
Found at i:41872094 original size:28 final size:28
Alignment explanation
Indices: 41872052--41872142 Score: 123
Period size: 28 Copynumber: 3.2 Consensus size: 28
41872042 ATGACAGAGT
41872052 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATATTTTGTGGCAGTGC
* *
41872081 CACCAGAACAGATAATTTGTGGCAGGGC
1 CACCAGAACAGATATTTTGTGGCAGTGC
41872109 CACCAGAACAGAT-TATTTGTGGCA-TAGC
1 CACCAGAACAGATAT-TTTGTGGCAGT-GC
41872137 CACCAG
1 CACCAG
41872143 GACGCTTCCT
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
28 49 0.88
29 7 0.12
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.22
Consensus pattern (28 bp):
CACCAGAACAGATATTTTGTGGCAGTGC
Found at i:41872295 original size:28 final size:28
Alignment explanation
Indices: 41872248--41872312 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
41872238 AAATTAACCC
*
41872248 TAGGGGTATAAAGGTCATTTTACATACA
1 TAGGGGTATAAAGGTAATTTTACATACA
* *
41872276 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTACATACA
41872304 TAGGGGTAT
1 TAGGGGTAT
41872313 TCTTATAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.34
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTTACATACA
Found at i:41880986 original size:49 final size:49
Alignment explanation
Indices: 41880866--41881037 Score: 167
Period size: 49 Copynumber: 3.6 Consensus size: 49
41880856 CACGGTAGAT
* * * *
41880866 AAGCTAGTGTAAGACCTGTCTGGGACATGGCGTCAA-CTC-GT-CGTG-
1 AAGCCAGTGTAAGACCTGTCTGGGACATGGCATCAACCTCAATACATGA
* * *
41880911 -TGCTAGTGTAAGACCTGTCTGGGACATGGCATCAACAC-CAATAGATGA
1 AAGCCAGTGTAAGACCTGTCTGGGACATGGCATCAAC-CTCAATACATGA
* * * * **
41880959 GAGCCAGTGTAAGACCTATCTGAGACATGGCATCATCCTCGCTACATGA
1 AAGCCAGTGTAAGACCTGTCTGGGACATGGCATCAACCTCAATACATGA
41881008 AAGCCAGTGTAAGACCATGTCTGGGACATG
1 AAGCCAGTGTAAGACC-TGTCTGGGACATG
41881038 ACGTTGGCAT
Statistics
Matches: 103, Mismatches: 16, Indels: 11
0.79 0.12 0.08
Matches are distributed among these distances:
44 33 0.32
45 1 0.01
46 2 0.02
47 2 0.02
48 1 0.01
49 53 0.51
50 11 0.11
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.23
Consensus pattern (49 bp):
AAGCCAGTGTAAGACCTGTCTGGGACATGGCATCAACCTCAATACATGA
Found at i:41886819 original size:37 final size:37
Alignment explanation
Indices: 41886766--41886837 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
41886756 TGTCGTGGCA
*
41886766 TGTTATCGGTTAGATTAGCTCTTATAAGCGATTGGTG
1 TGTTATCGGGTAGATTAGCTCTTATAAGCGATTGGTG
*
41886803 TGTTATCGGGTGGATTAGCTCTTATAAGCGATTGG
1 TGTTATCGGGTAGATTAGCTCTTATAAGCGATTGG
41886838 CATGTTTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (37 bp):
TGTTATCGGGTAGATTAGCTCTTATAAGCGATTGGTG
Found at i:41892846 original size:216 final size:216
Alignment explanation
Indices: 41892472--41892874 Score: 680
Period size: 216 Copynumber: 1.9 Consensus size: 216
41892462 ACCTTAGTTT
* *
41892472 CATATTACTCTTAGTCTTGTAATTGTGATAGATTTACCCTAACTTTATTTTATACTTGGATTAAG
1 CATATTACTCTTAGTCTTGTAATTATGATAGATATACCCTAACTTTATTTTATACTTGGATTAAG
41892537 GGTAAGGGTCATTGGCGATCATGACATCTATCGATGAACATATATGCTCATAGTTTTACTTTACC
66 GGTAAGGGTCATTGGCGATCATGACATCTATCGATGAACATATATGCTCATAGTTTTACTTTACC
* * *
41892602 TAGAGCATTGATTTGGTTGAGTATGAAACTCATAGTGATTGGCATTATAAGTGTTTTATCATGCT
131 TAGAGCATTGATTTAGTTGAGTATGAAACTCATAGTGATTAGCAATATAAGTGTTTTATCATGCT
41892667 AAGCATGGTTTTTGATTATTC
196 AAGCATGGTTTTTGATTATTC
* * ** *
41892688 CATATTACTTTTAGTCTTGTAATTATGATGGATATGTCCTAACTTTATTTTATACTTGGCTTAAG
1 CATATTACTCTTAGTCTTGTAATTATGATAGATATACCCTAACTTTATTTTATACTTGGATTAAG
* * * *
41892753 GTTAAGGGTCATTGGTGATCATGACATCTATCGATGAACATTTATGCTCATAGTTTTGCTTTACC
66 GGTAAGGGTCATTGGCGATCATGACATCTATCGATGAACATATATGCTCATAGTTTTACTTTACC
41892818 TAGAGCATTGATTTAGTTGAGTATGAAACTCATAGTGATTAGCAATATAAGTGTTTT
131 TAGAGCATTGATTTAGTTGAGTATGAAACTCATAGTGATTAGCAATATAAGTGTTTT
41892875 GCTATTCTAA
Statistics
Matches: 173, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
216 173 1.00
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (216 bp):
CATATTACTCTTAGTCTTGTAATTATGATAGATATACCCTAACTTTATTTTATACTTGGATTAAG
GGTAAGGGTCATTGGCGATCATGACATCTATCGATGAACATATATGCTCATAGTTTTACTTTACC
TAGAGCATTGATTTAGTTGAGTATGAAACTCATAGTGATTAGCAATATAAGTGTTTTATCATGCT
AAGCATGGTTTTTGATTATTC
Found at i:41894279 original size:46 final size:46
Alignment explanation
Indices: 41894229--41894401 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
41894219 TTGAGCATCT
*
41894229 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC
* * * *
41894275 GAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CGTCC
* * *
41894322 GAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC
* *
41894368 GAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
41894402 GTGGGTTACA
Statistics
Matches: 106, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 60 0.57
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.28
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC
Found at i:41894382 original size:93 final size:93
Alignment explanation
Indices: 41894223--41894394 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
41894213 GGATGGTTGA
* * * *
41894223 GCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGT
41894288 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
41894316 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGT
41894381 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
41894395 CTTATGGGTG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:41897189 original size:6 final size:6
Alignment explanation
Indices: 41897178--41897357 Score: 149
Period size: 6 Copynumber: 29.8 Consensus size: 6
41897168 AACCAAAATG
*
41897178 AGAATC AGAATC AGAATC AGTAA-C AGAATC AGAATC AGAATC A-ATATT
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGA-ATC
* * *
41897226 AGTAA-C AGAATC AGAATT AG-GTGAC AGAATT AGAATC AGAATC AGTAA-C
1 AG-AATC AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAATC AG-AATC
* * *
41897275 AGAATC AGAATC AGAATT AGTATT AGTAA-C AGAATC AGAATC AGAATC
1 AGAATC AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC
* * *
41897323 AGTATT AGTAA-C AGAATC AAAATC AGAATC AGAAT
1 AGAATC AG-AATC AGAATC AGAATC AGAATC AGAAT
41897358 TACGTGACAG
Statistics
Matches: 141, Mismatches: 18, Indels: 30
0.75 0.10 0.16
Matches are distributed among these distances:
5 12 0.09
6 118 0.84
7 9 0.06
8 2 0.01
ACGTcount: A:0.49, C:0.13, G:0.17, T:0.22
Consensus pattern (6 bp):
AGAATC
Found at i:41897265 original size:73 final size:73
Alignment explanation
Indices: 41897178--41897315 Score: 249
Period size: 73 Copynumber: 1.9 Consensus size: 73
41897168 AACCAAAATG
41897178 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAAT
1 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAAT
41897243 TAGGTGAC
66 TAGGTGAC
* * *
41897251 AGAATTAGAATCAGAATCAGTAACAGAATCAGAATCAGAATTAGTATTAGTAACAGAATCAGAAT
1 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAAT
41897316 CAGAATCAGT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 62 1.00
ACGTcount: A:0.49, C:0.12, G:0.17, T:0.22
Consensus pattern (73 bp):
AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAAT
TAGGTGAC
Found at i:41897554 original size:27 final size:26
Alignment explanation
Indices: 41897515--41897613 Score: 117
Period size: 27 Copynumber: 3.7 Consensus size: 26
41897505 CAGTTATCAT
* *
41897515 ATATTGTGACAGAGTCACCAGATACAG
1 ATATTGTGGCAGAGCCACCAGA-ACAG
41897542 ATATTGTGGCAGAGCCACCAGAACAG
1 ATATTGTGGCAGAGCCACCAGAACAG
* *
41897568 ATATTTGTGGCATAGCCACCAGAAACAT
1 ATA-TTGTGGCAGAGCCACCAG-AACAG
* *
41897596 ATAATGTGGCAAAGCCAC
1 ATATTGTGGCAGAGCCAC
41897614 TTAACAGAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
26 7 0.11
27 50 0.78
28 7 0.11
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.20
Consensus pattern (26 bp):
ATATTGTGGCAGAGCCACCAGAACAG
Found at i:41897799 original size:22 final size:22
Alignment explanation
Indices: 41897771--41897835 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
41897761 GCAAATACTT
*
41897771 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
*
41897793 TTGGCACAAAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
*
41897815 TTGACACAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
41897836 AAGGCTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.05
22 33 0.89
23 2 0.05
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:41898318 original size:27 final size:27
Alignment explanation
Indices: 41898260--41898544 Score: 311
Period size: 27 Copynumber: 10.3 Consensus size: 27
41898250 AAGGGCAAAA
* * * *
41898260 TGGTAATTTTACCCCACA-AGGTATCT
1 TGGTAATTCTACCCTACAGGGGTATTT
*
41898286 TGGTAATTCCACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* * *
41898313 TAGTAATTCTACCTTATAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
*
41898340 TAGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
*
41898367 CGGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
*
41898394 CTGTATTTCTGTATTTCTACCCTACAGGGGTATTT
1 -TG-------GTAATTCTACCCTACAGGGGTATTT
* *
41898429 CGGTAATTCTACCCTACAGGGGTATTG
1 TGGTAATTCTACCCTACAGGGGTATTT
* *
41898456 CGATAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* *
41898483 CGGTAATTCTACCCTACAAGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* * *
41898510 CGATAATTCTACCCTGCAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
41898537 TGGTAATT
1 TGGTAATT
41898545 TTATTGATCG
Statistics
Matches: 223, Mismatches: 27, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
26 15 0.07
27 182 0.82
28 1 0.00
34 1 0.00
35 24 0.11
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (27 bp):
TGGTAATTCTACCCTACAGGGGTATTT
Found at i:41898412 original size:35 final size:35
Alignment explanation
Indices: 41898360--41898438 Score: 122
Period size: 35 Copynumber: 2.3 Consensus size: 35
41898350 ACCCTACAGG
*
41898360 GGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
1 GGTATTTCTGTAATTCTACCCTACAGGGGTATTTC
* *
41898395 TGTATTTCTGTATTTCTACCCTACAGGGGTATTTC
1 GGTATTTCTGTAATTCTACCCTACAGGGGTATTTC
*
41898430 GGTAATTCT
1 GGTATTTCT
41898439 ACCCTACAGG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (35 bp):
GGTATTTCTGTAATTCTACCCTACAGGGGTATTTC
Found at i:41898500 original size:116 final size:116
Alignment explanation
Indices: 41898296--41898510 Score: 351
Period size: 116 Copynumber: 1.9 Consensus size: 116
41898286 TGGTAATTCC
* * * **
41898296 ACCCTACAGGGGTATTTTAGTAATTCTACCTTATAGGGGTATTTTAGTAATTCTACCCTACAGGG
1 ACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTCGAGTAATTCTACCCTACAGGG
*
41898361 GTATTTCGGTAATTCTACCCTACAGGGGTATTTCTGTATTTCTGTATTTCT
66 GTATTTCGGTAATTCTACCCTACAAGGGTATTTCTGTATTTCTGTATTTCT
*
41898412 ACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTGCGA-TAATTCTACCCTACAGG
1 ACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATT-CGAGTAATTCTACCCTACAGG
41898476 GGTATTTCGGTAATTCTACCCTACAAGGGTATTTC
65 GGTATTTCGGTAATTCTACCCTACAAGGGTATTTC
41898511 GATAATTCTA
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
116 90 0.99
117 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.36
Consensus pattern (116 bp):
ACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTCGAGTAATTCTACCCTACAGGG
GTATTTCGGTAATTCTACCCTACAAGGGTATTTCTGTATTTCTGTATTTCT
Found at i:41898559 original size:27 final size:27
Alignment explanation
Indices: 41898529--41898959 Score: 204
Period size: 27 Copynumber: 16.1 Consensus size: 27
41898519 TACCCTGCAG
* **
41898529 GGGTATTTTGGTAATTTTATTGATCGA
1 GGGTATTTCGGTAATTTTATAAATCGA
* **
41898556 GGGTATTTCAGTAATTTTGCAAA-CTGA
1 GGGTATTTCGGTAATTTTATAAATC-GA
* *
41898583 AGGTATTTCGGTAATTTTACAAATCGA
1 GGGTATTTCGGTAATTTTATAAATCGA
* * *
41898610 GGATATTTGGGTAATTTTATAAACCG-
1 GGGTATTTCGGTAATTTTATAAATCGA
* * *
41898636 GGGTACTTT-GGTAATTTTACAACTGGA
1 GGGTA-TTTCGGTAATTTTATAAATCGA
** *
41898663 -GGTATTTTAGTAATTTCAT-AATCGA
1 GGGTATTTCGGTAATTTTATAAATCGA
** * *
41898688 GGGTAAAAT-GGTAATTTTGTAAATTGA
1 GGGT-ATTTCGGTAATTTTATAAATCGA
** *
41898715 GGGTAAAAT-GGTAATTTTGTAAATCGA
1 GGGT-ATTTCGGTAATTTTATAAATCGA
*** * * *
41898742 GGGTAAAACAGTAATTCTGTAAATCGA
1 GGGTATTTCGGTAATTTTATAAATCGA
** *
41898769 GGGTAAAAT-GGTAATTCTATAAATCGA
1 GGGT-ATTTCGGTAATTTTATAAATCGA
** *
41898796 GGGTAAAAT-GGTAATTTTGTAAATCGA
1 GGGT-ATTTCGGTAATTTTATAAATCGA
*** * * *
41898823 GGGTAAAACAGTAATTCTGTAAATCGA
1 GGGTATTTCGGTAATTTTATAAATCGA
** *
41898850 GGGTAAAAT-GGTAATTCTATAAATCGA
1 GGGT-ATTTCGGTAATTTTATAAATCGA
** *
41898877 GGGTAAAAT-GGTAATTTTGTAAATCGA
1 GGGT-ATTTCGGTAATTTTATAAATCGA
** *
41898904 GGGTGA-AACGGTAATTTTGTAAATCGA
1 GGGT-ATTTCGGTAATTTTATAAATCGA
* *
41898931 GGGTACTTT-GGTAATTTTACAAATTGA
1 GGGTA-TTTCGGTAATTTTATAAATCGA
41898958 GG
1 GG
41898960 ACATTTTAGT
Statistics
Matches: 335, Mismatches: 54, Indels: 30
0.80 0.13 0.07
Matches are distributed among these distances:
25 7 0.02
26 49 0.15
27 272 0.81
28 7 0.02
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.35
Consensus pattern (27 bp):
GGGTATTTCGGTAATTTTATAAATCGA
Found at i:41898948 original size:54 final size:54
Alignment explanation
Indices: 41898682--41898935 Score: 391
Period size: 54 Copynumber: 4.7 Consensus size: 54
41898672 GTAATTTCAT
*
41898682 AATCGAGGGTAAAATGGTAATTTTGTAAATTGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTTTGTA
** * * *
41898736 AATCGAGGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTTTGTA
** *
41898790 AATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTTTGTA
* *
41898844 AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTTTGTA
* *
41898898 AATCGAGGGTGAAACGGTAATTTTGTAAATCGAGGGTA
1 AATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTA
41898936 CTTTGGTAAT
Statistics
Matches: 179, Mismatches: 21, Indels: 0
0.89 0.10 0.00
Matches are distributed among these distances:
54 179 1.00
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.30
Consensus pattern (54 bp):
AATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTTTGTA
Found at i:41898980 original size:81 final size:81
Alignment explanation
Indices: 41898682--41898935 Score: 454
Period size: 81 Copynumber: 3.1 Consensus size: 81
41898672 GTAATTTCAT
* * *
41898682 AATCGAGGGTAAAATGGTAATTTTGTAAATTGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTA
1 AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTA
41898747 AAACAGTAATTCTGTA
66 AAACAGTAATTCTGTA
41898763 AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTA
1 AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTA
41898828 AAACAGTAATTCTGTA
66 AAACAGTAATTCTGTA
*
41898844 AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTG
1 AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTA
* *
41898909 AAACGGTAATTTTGTA
66 AAACAGTAATTCTGTA
41898925 AATCGAGGGTA
1 AATCGAGGGTA
41898936 CTTTGGTAAT
Statistics
Matches: 167, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 167 1.00
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.30
Consensus pattern (81 bp):
AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTA
AAACAGTAATTCTGTA
Found at i:41901636 original size:40 final size:39
Alignment explanation
Indices: 41901432--41901621 Score: 274
Period size: 39 Copynumber: 4.8 Consensus size: 39
41901422 GGACTAAGAT
* * *
41901432 CCGAAGGCGTTCGTGTGAGTTAATAAATCCGGGTTAAGC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGC
* *
41901471 CTGAAGGCATTCGTGCGAGTTAATAAATCCGGGTTAAGC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGC
*
41901510 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGC
* * *
41901549 CTGAAGGCATTTGTGCGAGTTACTAAACCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAG-C
41901589 CCGAAGGCATTCGTGCGAGTTACTATAA-CCGGG
1 CCGAAGGCATTCGTGCGAGTTACTA-AATCCGGG
41901622 GTTTGTCCCG
Statistics
Matches: 139, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
39 108 0.78
40 29 0.21
41 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGC
Found at i:41901663 original size:79 final size:79
Alignment explanation
Indices: 41901432--41901674 Score: 244
Period size: 78 Copynumber: 3.1 Consensus size: 79
41901422 GGACTAAGAT
* * * * * * * *
41901432 CCGAAGGCGTTCGTGTGAGTTAATAAATCCGGGTTAAGCCTGAAGGCATTCGTGCGAGTTAATAA
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGCCCGAAGGCATTTGAGCGAGTGACTAA
41901497 ATCCGGGTTAAG-C
66 ATCCGGGTTAAGTC
* * * *
41901510 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGCCTGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGCCCGAAGGCATTTGAGCGAGTGACTAA
*
41901575 ACCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* * *
41901589 CCGAAGGCATTCGTGCGAGTTACTATAA-CCGGGGTT-TGTCCCGAAGGCTTTTGAGCTAGTCGA
1 CCGAAGGCATTCGTGCGAGTTACTA-AATCC-GGGTTAAG-CCCGAAGGCATTTGAGCGAGT-GA
* * *
41901652 -TATATCC-GGTTAAATT
62 CTAAATCCGGGTTAAGTC
41901668 CCGAAGG
1 CCGAAGG
41901675 TACGTGATTC
Statistics
Matches: 142, Mismatches: 18, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
78 70 0.49
79 42 0.30
80 29 0.20
81 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (79 bp):
CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGCCCGAAGGCATTTGAGCGAGTGACTAA
ATCCGGGTTAAGTC
Found at i:41903488 original size:93 final size:93
Alignment explanation
Indices: 41903376--41903547 Score: 283
Period size: 93 Copynumber: 1.8 Consensus size: 93
41903366 GCCCATAAGT
* *
41903376 GAACTCGGACTCAACTCAACGAGCTT-GGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAG-TTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
* *
41903440 ATGAGCTCGGATGCCTAGTTACATCTCTC
65 ACGAGCTCGAATGCCTAGTTACATCTCTC
41903469 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
41903534 CGAGTTCGAATGCC
66 CGAGCTCGAATGCC
41903548 CAAATATCCT
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGAATGCCTAGTTACATCTCTC
Found at i:41903538 original size:46 final size:45
Alignment explanation
Indices: 41903368--41903541 Score: 199
Period size: 46 Copynumber: 3.8 Consensus size: 45
41903358 TGTAACCCGC
* *
41903368 CCATAAGTGAACTCGGACTCAACTCAACGAGCTTGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAG-TTCGGCATTCGCAT
* * *
41903414 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGG-ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGC-A--T
* ***
41903460 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTTCGG-CATTCGCAT
41903507 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG
41903542 AATGCCCAAA
Statistics
Matches: 105, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 3 0.03
46 62 0.59
47 31 0.30
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGCAT
Found at i:41903975 original size:15 final size:15
Alignment explanation
Indices: 41903927--41904006 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
41903917 TAAAGATAAT
*
41903927 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
41903941 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
41903956 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
41903971 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
41903986 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
41904001 AAGAAA
1 AAGAAA
41904007 CCCAATATAT
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:41905033 original size:14 final size:15
Alignment explanation
Indices: 41904984--41905033 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
41904974 ATATCTTGGG
*
41904984 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
41904999 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
41905014 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
41905028 TTTCTT
1 TTTCTT
41905034 GTTATATTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 8 0.26
15 23 0.74
ACGTcount: A:0.10, C:0.18, G:0.12, T:0.60
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:41907461 original size:46 final size:46
Alignment explanation
Indices: 41907411--41907582 Score: 188
Period size: 46 Copynumber: 3.7 Consensus size: 46
41907401 TTGAGCATCC
*
41907411 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCG
* * * *
41907457 AACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CGTCCG
* * * *
41907504 AACTCGTTGAGTTGAGTCTGAGTTCACTCATGGATGCGAACGCCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCG
* *
41907550 AGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
41907583 GGGGTTACAT
Statistics
Matches: 103, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 58 0.56
47 28 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCG
Found at i:41907570 original size:93 final size:92
Alignment explanation
Indices: 41907405--41907575 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 92
41907395 GGATGGTTGA
* * *
41907405 GCATCCAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGTT
1 GCATCCAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGTT
41907470 GAGTCCGAGTTCGTGAGATGTAACTAG
66 GAGTCCGAGTTCGTGAGATGTAACTAG
* * *
41907497 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTCATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCC-AACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGT
41907562 TGAGTCCGAGTTCG
65 TGAGTCCGAGTTCG
41907576 CTTATGGGGG
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
92 6 0.08
93 66 0.92
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (92 bp):
GCATCCAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGTT
GAGTCCGAGTTCGTGAGATGTAACTAG
Done.