Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 70 of 135
Found at i:27820452 original size:8 final size:8
Alignment explanation
Indices: 27820439--27820473 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
27820429 AAATGAGAGA
27820439 AAAAGAAG
1 AAAAGAAG
27820447 AAAAGAAG
1 AAAAGAAG
27820455 AAAAGAAG
1 AAAAGAAG
27820463 AAAA-AAG
1 AAAAGAAG
27820470 AAAA
1 AAAA
27820474 ATCTAGATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (8 bp):
AAAAGAAG
Found at i:27820474 original size:16 final size:17
Alignment explanation
Indices: 27820436--27820474 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
27820426 TCAAAATGAG
27820436 AGAAAAAGAAGAAAAGA
1 AGAAAAAGAAGAAAAGA
27820453 AG-AAAAGAAGAAAA-A
1 AGAAAAAGAAGAAAAGA
27820468 AGAAAAA
1 AGAAAAA
27820475 TCTAGATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.14
16 16 0.76
17 2 0.10
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
AGAAAAAGAAGAAAAGA
Found at i:27822868 original size:44 final size:44
Alignment explanation
Indices: 27822802--27823059 Score: 184
Period size: 44 Copynumber: 5.6 Consensus size: 44
27822792 GGAAAAGGTG
27822802 AATCTTATCTCCCTGATG-TTACAGTGGAGCAGATTGAAGCCAGA
1 AATCTTATCTCCCTGA-GATTACAGTGGAGCAGATTGAAGCCAGA
* *** * *
27822846 AATCTTATCTCCCTGAGTTTACAACAGAGCAGATTGAAGCTAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGA
* ***
27822890 AATCCTATCTCCCTGAGATTACAGTGGAGC-GAATT-AAAATA-A
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAG-ATTGAAGCCAGA
** * *
27822932 AGGATCTTATCTCTTTGA-AGTTACAACAGAGTAGATCGCATCAGATTAAAGCCAGA
1 A--ATCTTATCTCCCTGAGA-TT---AC--AGT-G---G-AGCAGATTGAAGCCAGA
* *
27822988 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGA
* *
27823032 AATCTTATTTCCCTGAGATTACGGTGGA
1 AATCTTATCTCCCTGAGATTACAGTGGA
27823060 ATAGACCAAA
Statistics
Matches: 166, Mismatches: 29, Indels: 38
0.71 0.12 0.16
Matches are distributed among these distances:
42 1 0.01
43 7 0.04
44 118 0.71
45 1 0.01
47 2 0.01
48 1 0.01
49 5 0.03
50 1 0.01
51 2 0.01
53 1 0.01
54 20 0.12
55 5 0.03
56 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGA
Found at i:27823167 original size:50 final size:50
Alignment explanation
Indices: 27823108--27823744 Score: 413
Period size: 50 Copynumber: 12.7 Consensus size: 50
27823098 GTAGTGGAAT
* * *
27823108 AGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTACAGTTAAAA
1 AGATTAAAGCCACAACGGCGAATCTTACTTCCCCGGCATTGCAGTTAAAA
* * * *** *
27823158 AGATTAAAGCTACAACAGCGAATCTTACATT-CCAGGCGA-TGCAGCGGAAT
1 AGATTAAAGCCACAACGGCGAATCTTAC-TTCCCCGGC-ATTGCAGTTAAAA
* * * *
27823208 AGATTAAAGCCACAATGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGCGAATCTTACTTCCCCGGCATTGCAGTTAAAA
* * * * ** *
27823258 AGACTAAAGCCACAACGGCGAGTGTTACTTCCCTGGCGA-TGCAGTGGAAC
1 AGATTAAAGCCACAACGGCGAATCTTACTTCCCCGGC-ATTGCAGTTAAAA
* * * * * *
27823308 AGATTAAAGCCACATC-CCTGAATCTTGCTTCCCCGACATTACAGTTAAAG
1 AGATTAAAGCCACAACGGC-GAATCTTACTTCCCCGGCATTGCAGTTAAAA
* * * * ** **
27823358 AGATTAAAGCTACAACAGCGAATCTTACCTCCCAGGCGA-TGCAGTGGAGC
1 AGATTAAAGCCACAACGGCGAATCTTACTTCCCCGGC-ATTGCAGTTAAAA
** * * **
27823408 AGATTAAAGCCACATTGGTGAATCTTGCTTCCCCAACATTGCAGTTCAAAA
1 AGATTAAAGCCACAACGGCGAATCTTACTTCCCCGGCATTGCAGTT-AAAA
* * * * * * ** *
27823459 AGATTAAAGCTACAACAGTGAATCTTACCTCTCAGGCGA-TGCAGTGGAAC
1 AGATTAAAGCCACAACGGCGAATCTTACTTCCCCGGC-ATTGCAGTTAAAA
** * * ** * *
27823509 AGATTAAAGCCACATTGGTGAATCTTGCTTCCCCAACGTTGCAGTTAAAG
1 AGATTAAAGCCACAACGGCGAATCTTACTTCCCCGGCATTGCAGTTAAAA
* * * * ** *
27823559 AGATTAAAGCTACAACAGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
1 AGATTAAAGCCACAACGGCGAATCTTACTTCCCCGGCATTGCAGTTAAAA
* * ** ** *
27823609 AGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGGCATTTTAGCTAAAA
1 AGATTAAAGCCACAACGGCGAATCTTACTTCCCCGGCATTGCAGTTAAAA
* * * * **
27823659 GGATTAAAGCTGCCATAAAGGCGAATCTTACTTCCCTGGCGGTGCAGTTAAAA
1 AGATTAAA---GCCACAACGGCGAATCTTACTTCCCCGGCATTGCAGTTAAAA
* * *
27823712 AGATTGAAGCTACAATGGCGAATCTTACTTCCC
1 AGATTAAAGCCACAACGGCGAATCTTACTTCCC
27823745 AAAAGTTGCG
Statistics
Matches: 428, Mismatches: 143, Indels: 32
0.71 0.24 0.05
Matches are distributed among these distances:
49 6 0.01
50 345 0.81
51 40 0.09
52 1 0.00
53 36 0.08
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (50 bp):
AGATTAAAGCCACAACGGCGAATCTTACTTCCCCGGCATTGCAGTTAAAA
Found at i:27823219 original size:100 final size:99
Alignment explanation
Indices: 27823100--27823693 Score: 760
Period size: 100 Copynumber: 5.9 Consensus size: 99
27823090 CAAGCGGTGT
* * * *
27823100 AGTGGAATAGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTACAGTTAAAAAGATTAA
1 AGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAA
27823165 AGCTACAACAGCGAATCTTACATTCCAGGCGATGC
66 AGCTACAACAGCGAATCTTAC-TTCCAGGCGATGC
* * *
27823200 AGCGGAATAGATTAAAGCCACAAT-GGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGACTA
1 AGTGGAACAGATTAAAGCCAC-ATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTA
* * * * *
27823264 AAGCCACAACGGCGAGTGTTACTTCCCTGGCGATGC
65 AAGCTACAACAGCGAATCTTACTT-CCAGGCGATGC
** * *
27823300 AGTGGAACAGATTAAAGCCACATCCCTGAATCTTGCTTCCCCGACATTACAGTTAAAGAGATTAA
1 AGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAA
*
27823365 AGCTACAACAGCGAATCTTACCTCCCAGGCGATGC
66 AGCTACAACAGCGAATCTTA-CTTCCAGGCGATGC
* * *
27823400 AGTGGAGCAGATTAAAGCCACATTGGTGAATCTTGCTTCCCCAACATTGCAGTTCAAAAAGATTA
1 AGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTT-AAAAAGATTA
* *
27823465 AAGCTACAACAGTGAATCTTACCTCTCAGGCGATGC
65 AAGCTACAACAGCGAATCTTACTTC-CAGGCGATGC
* * * *
27823501 AGTGGAACAGATTAAAGCCACATTGGTGAATCTTGCTTCCCCAACGTTGCAGTTAAAGAGATTAA
1 AGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAA
*
27823566 AGCTACAACAGCGAATCTTACTTCCCTGGC-AGTGC
66 AGCTACAACAGCGAATCTTACTT-CCAGGCGA-TGC
* * ** * *
27823601 AGTGGAACAGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGGCATTTTAGCTAAAAGGATTAA
1 AGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAA
* *
27823666 AGCTGCCATAAAGGCGAATCTTACTTCC
66 AGCT-ACA-ACA-GCGAATCTTACTTCC
27823694 CTGGCGGTGC
Statistics
Matches: 432, Mismatches: 51, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
99 5 0.01
100 313 0.72
101 97 0.22
102 4 0.01
103 13 0.03
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.23
Consensus pattern (99 bp):
AGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAA
AGCTACAACAGCGAATCTTACTTCCAGGCGATGC
Found at i:27826916 original size:24 final size:26
Alignment explanation
Indices: 27826884--27826943 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
27826874 CCTTGTTTTT
* *
27826884 TATTCTTATTTTTA-ATTA-TAATAC
1 TATTATTATTATTACATTATTAATAC
*
27826908 TATTATTATTATTACTATTATTACTAC
1 TATTATTATTATTAC-ATTATTAATAC
27826935 TATTATTAT
1 TATTATTAT
27826944 AGATGTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 12 0.40
26 4 0.13
27 14 0.47
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (26 bp):
TATTATTATTATTACATTATTAATAC
Found at i:27826928 original size:12 final size:12
Alignment explanation
Indices: 27826911--27826943 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
27826901 ATAATACTAT
27826911 TATTATTATTAC
1 TATTATTATTAC
*
27826923 TATTATTACTAC
1 TATTATTATTAC
27826935 TATTATTAT
1 TATTATTAT
27826944 AGATGTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTATTATTAC
Found at i:27827015 original size:20 final size:21
Alignment explanation
Indices: 27826992--27827030 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
27826982 TTTATTTTAT
*
27826992 TTTATTATGTATT-TTATTCC
1 TTTATCATGTATTATTATTCC
27827012 TTTATCATGTATTATTATT
1 TTTATCATGTATTATTATT
27827031 TAATCAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.08, G:0.05, T:0.64
Consensus pattern (21 bp):
TTTATCATGTATTATTATTCC
Found at i:27828234 original size:88 final size:87
Alignment explanation
Indices: 27828033--27828247 Score: 286
Period size: 87 Copynumber: 2.5 Consensus size: 87
27828023 GTGAAAATAG
* * * * *
27828033 CAGACCTTGCCTTCCCGCATTGACAGCGAAGCAGATTGAAAACAAATCCTTGCCTCCATCAGTTG
1 CAGATCTTGCCTTCCTGCATTGACAGTGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCAGTTG
* * *
27828098 TAGTGGAGCTGGTTGAAGATAG
66 CAGTGGAGCTGGTTAAAGATAA
* * * **
27828120 CAGATCTTGCCTTCCTGCGTTAACAGTGAAGCACATCGAAAACAAAGCCTTGCCTCCATTGGTTG
1 CAGATCTTGCCTTCCTGCATTGACAGTGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCAGTTG
27828185 CAGCTGGAGCTGGTTAAAGATAA
66 CAG-TGGAGCTGGTTAAAGATAA
* *
27828208 CAGATCTTGCCTTCCTGCATCGACAGTGAAACAGATCGAA
1 CAGATCTTGCCTTCCTGCATTGACAGTGAAGCAGATCGAA
27828248 GATGGCGAAT
Statistics
Matches: 109, Mismatches: 18, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
87 57 0.52
88 52 0.48
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.24
Consensus pattern (87 bp):
CAGATCTTGCCTTCCTGCATTGACAGTGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCAGTTG
CAGTGGAGCTGGTTAAAGATAA
Found at i:27828478 original size:128 final size:128
Alignment explanation
Indices: 27828239--27828496 Score: 358
Period size: 128 Copynumber: 2.0 Consensus size: 128
27828229 GACAGTGAAA
* ** * *
27828239 CAGATCGAAGATGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTCAAGCCACAAGTCCTATA
1 CAGATCGAAGATGGCAAATCTTATCCCCAAGAGTAAGGAAACAGATTCAAGCCACAAGTCCTATA
** * *
27828304 TCCCTGGTCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAGCAGTAGCGGAG
66 TCCCTGACCAGCAGTGGAATAGGTTGGAAATTACAGATCTTATCTCCCTAAGCAGTAGCGGAG
* *
27828367 CAGATCGAAGATGGCAAATCTTATCCCCAGGAGT-AGAGAAATAGATTCAAGCCACAAGTCCTAT
1 CAGATCGAAGATGGCAAATCTTATCCCCAAGAGTAAG-GAAACAGATTCAAGCCACAAGTCCTAT
* * *
27828431 GTCCTTGACCAGCAGTGGAATAGGTTGGAAATTACA-AGTCTTATCTCCCTAAGCAGTAGTGGAG
65 ATCCCTGACCAGCAGTGGAATAGGTTGGAAATTACAGA-TCTTATCTCCCTAAGCAGTAGCGGAG
27828495 CA
1 CA
27828497 AACAGAAGAA
Statistics
Matches: 114, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
127 3 0.03
128 111 0.97
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (128 bp):
CAGATCGAAGATGGCAAATCTTATCCCCAAGAGTAAGGAAACAGATTCAAGCCACAAGTCCTATA
TCCCTGACCAGCAGTGGAATAGGTTGGAAATTACAGATCTTATCTCCCTAAGCAGTAGCGGAG
Found at i:27828748 original size:44 final size:44
Alignment explanation
Indices: 27828699--27828803 Score: 124
Period size: 44 Copynumber: 2.4 Consensus size: 44
27828689 TCTCCTTGAC
* *
27828699 GTTGTAGTAGAGCAGATTGAATTCAATA-ATCCTATCTCTCTGAA
1 GTTGTAGTAGAGCAGATTAAAGT-AATAGATCCTATCTCTCTGAA
* * *
27828743 TTTGTAGTGGAGC-GAATTAAAGTAATAGATCTTATCTCTCTGAA
1 GTTGTAGTAGAGCAG-ATTAAAGTAATAGATCCTATCTCTCTGAA
*
27828787 GTTGCAGTAGAGCAGAT
1 GTTGTAGTAGAGCAGAT
27828804 AGTATCAAGT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
43 5 0.10
44 44 0.88
45 1 0.02
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.33
Consensus pattern (44 bp):
GTTGTAGTAGAGCAGATTAAAGTAATAGATCCTATCTCTCTGAA
Found at i:27830378 original size:24 final size:26
Alignment explanation
Indices: 27830346--27830405 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
27830336 CTTGTTTTTT
* *
27830346 TATTCTTATTTTTA-ATTA-TAATAC
1 TATTATTATTATTACATTATTAATAC
*
27830370 TATTATTATTATTACTATTATTACTAC
1 TATTATTATTATTAC-ATTATTAATAC
27830397 TATTATTAT
1 TATTATTAT
27830406 AGATGTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 12 0.40
26 4 0.13
27 14 0.47
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (26 bp):
TATTATTATTATTACATTATTAATAC
Found at i:27830390 original size:12 final size:12
Alignment explanation
Indices: 27830373--27830405 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
27830363 ATAATACTAT
27830373 TATTATTATTAC
1 TATTATTATTAC
*
27830385 TATTATTACTAC
1 TATTATTATTAC
27830397 TATTATTAT
1 TATTATTAT
27830406 AGATGTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTATTATTAC
Found at i:27830484 original size:21 final size:21
Alignment explanation
Indices: 27830454--27830493 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27830444 TTTATTTTAT
* *
27830454 TTTATTATGTATTTTTATTCC
1 TTTATCATGTATTATTATTCC
27830475 TTTATCATGTATTATTATT
1 TTTATCATGTATTATTATT
27830494 TATTCAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.07, G:0.05, T:0.65
Consensus pattern (21 bp):
TTTATCATGTATTATTATTCC
Found at i:27840323 original size:7 final size:7
Alignment explanation
Indices: 27840311--27840336 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
27840301 AAAATGTTTC
27840311 AAAATTG
1 AAAATTG
27840318 AAAATTG
1 AAAATTG
27840325 AAAATTG
1 AAAATTG
27840332 AAAAT
1 AAAAT
27840337 GACTTACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.27
Consensus pattern (7 bp):
AAAATTG
Found at i:27843704 original size:22 final size:22
Alignment explanation
Indices: 27843676--27843717 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
27843666 TACAGGAAAA
27843676 TAGACTTTTAGCGGCGCTTTTT
1 TAGACTTTTAGCGGCGCTTTTT
27843698 TAGACTTTTAGCGGCGCTTT
1 TAGACTTTTAGCGGCGCTTT
27843718 AACAAGCACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.14, C:0.19, G:0.24, T:0.43
Consensus pattern (22 bp):
TAGACTTTTAGCGGCGCTTTTT
Found at i:27843835 original size:43 final size:43
Alignment explanation
Indices: 27843788--27843881 Score: 127
Period size: 43 Copynumber: 2.2 Consensus size: 43
27843778 AAAAACGTCG
* * *
27843788 CTAAAGATGATGACCTTTAGC-AGCGCTTATACCACAAACGCCA
1 CTAAAAATCATGACATTTAGCGA-CGCTTATACCACAAACGCCA
*
27843831 CTAAAAATCATGACATTTAGCGACGCTTCTACCACAAACGCCA
1 CTAAAAATCATGACATTTAGCGACGCTTATACCACAAACGCCA
27843874 CTATAAAA
1 CTA-AAAA
27843882 AATTGACTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
43 40 0.89
44 5 0.11
ACGTcount: A:0.38, C:0.28, G:0.13, T:0.21
Consensus pattern (43 bp):
CTAAAAATCATGACATTTAGCGACGCTTATACCACAAACGCCA
Found at i:27843914 original size:43 final size:43
Alignment explanation
Indices: 27843788--27843902 Score: 126
Period size: 43 Copynumber: 2.7 Consensus size: 43
27843778 AAAAACGTCG
* * * *
27843788 CTAAAGATGATGACCTTTAGC-AGCGCTTATACCACAAACGCCA
1 CTAAAAATAATGACATTTAGCGA-CGCTTCTACCACAAACGCCA
*
27843831 CTAAAAATCATGACATTTAGCGACGCTTCTACCACAAACGCCA
1 CTAAAAATAATGACATTTAGCGACGCTTCTACCACAAACGCCA
* *
27843874 CTATAAAA-AATTGACTTTTAGCGATGCTT
1 CTA-AAAATAA-TGACATTTAGCGACGCTT
27843903 TTTCACAAAC
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
43 41 0.66
44 21 0.34
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (43 bp):
CTAAAAATAATGACATTTAGCGACGCTTCTACCACAAACGCCA
Found at i:27847172 original size:30 final size:30
Alignment explanation
Indices: 27847138--27847197 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
27847128 GGAAAACCAC
27847138 TGTCAAACTACCCAATACAAATAAAAACTA
1 TGTCAAACTACCCAATACAAATAAAAACTA
27847168 TGTCAAACTACCCAATACAAATAAAAACTA
1 TGTCAAACTACCCAATACAAATAAAAACTA
27847198 ACACCAGACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.53, C:0.23, G:0.03, T:0.20
Consensus pattern (30 bp):
TGTCAAACTACCCAATACAAATAAAAACTA
Found at i:27848363 original size:21 final size:20
Alignment explanation
Indices: 27848337--27848390 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
27848327 AATAGCGGTG
27848337 GCGGTGAGATTAATTACTGTA
1 GCGGTGAGATTAA-TACTGTA
*
27848358 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATT-AATACTGTA
* *
27848379 ACGGTGATATTA
1 GCGGTGAGATTA
27848391 GAAACAATGG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.28, C:0.09, G:0.31, T:0.31
Consensus pattern (20 bp):
GCGGTGAGATTAATACTGTA
Found at i:27848528 original size:19 final size:18
Alignment explanation
Indices: 27848504--27848549 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
27848494 AGAAGTTTTT
*
27848504 AAAATTATTTAACAATTA
1 AAAATTATTAAACAATTA
* *
27848522 CAAAATTAATAAATAATTA
1 -AAAATTATTAAACAATTA
27848541 AAAATTATT
1 AAAATTATT
27848550 GGGCTCAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAATTATTAAACAATTA
Found at i:27851359 original size:6 final size:6
Alignment explanation
Indices: 27851348--27851386 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
27851338 TTTGCAACCC
*
27851348 AAGGGG AAGGGG AAAGGG AAGGGG AAAGGGG AAAGGGG A
1 AAGGGG AAGGGG AAGGGG AAGGGG -AAGGGG -AAGGGG A
27851387 GAAGAAGGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 17 0.57
7 13 0.43
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (6 bp):
AAGGGG
Found at i:27851376 original size:7 final size:7
Alignment explanation
Indices: 27851348--27851386 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
27851338 TTTGCAACCC
27851348 AAGGGG-
1 AAGGGGA
27851354 AAGGGGA
1 AAGGGGA
27851361 AA-GGG-
1 AAGGGGA
27851366 AAGGGGA
1 AAGGGGA
27851373 AAGGGGA
1 AAGGGGA
27851380 AAGGGGA
1 AAGGGGA
27851387 GAAGAAGGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 2 0.07
6 12 0.40
7 16 0.53
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (7 bp):
AAGGGGA
Found at i:27853008 original size:14 final size:13
Alignment explanation
Indices: 27852991--27853046 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 13
27852981 CCCTAAATCA
*
27852991 CTAACTCTTAACCT
1 CTAACTC-TAACCC
*
27853005 CTAACCCCTAACCC
1 CTAA-CTCTAACCC
27853019 CTAACTACTAACCC
1 CTAACT-CTAACCC
27853033 CTAACTACTAACCC
1 CTAACT-CTAACCC
27853047 TTAAACCTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
13 1 0.03
14 34 0.92
15 2 0.05
ACGTcount: A:0.32, C:0.45, G:0.00, T:0.23
Consensus pattern (13 bp):
CTAACTCTAACCC
Found at i:27853009 original size:7 final size:7
Alignment explanation
Indices: 27852999--27853037 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
27852989 CACTAACTCT
*
27852999 TAACCTC
1 TAACCCC
27853006 TAACCCC
1 TAACCCC
27853013 TAACCCC
1 TAACCCC
**
27853020 TAACTAC
1 TAACCCC
27853027 TAACCCC
1 TAACCCC
27853034 TAAC
1 TAAC
27853038 TACTAACCCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.33, C:0.46, G:0.00, T:0.21
Consensus pattern (7 bp):
TAACCCC
Found at i:27853015 original size:21 final size:21
Alignment explanation
Indices: 27852991--27853044 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
27852981 CCCTAAATCA
*
27852991 CTAACTCTTAACCT-CTAACCC
1 CTAACTCCTAA-CTACTAACCC
*
27853012 CTAACCCCTAACTACTAACCC
1 CTAACTCCTAACTACTAACCC
*
27853033 CTAACTACTAAC
1 CTAACTCCTAAC
27853045 CCTTAAACCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.33, C:0.43, G:0.00, T:0.24
Consensus pattern (21 bp):
CTAACTCCTAACTACTAACCC
Found at i:27853166 original size:14 final size:14
Alignment explanation
Indices: 27853143--27853189 Score: 85
Period size: 14 Copynumber: 3.4 Consensus size: 14
27853133 AATTAATCTA
*
27853143 AACCCTAAACCCAT
1 AACCCCAAACCCAT
27853157 AACCCCAAACCCAT
1 AACCCCAAACCCAT
27853171 AACCCCAAACCCAT
1 AACCCCAAACCCAT
27853185 AACCC
1 AACCC
27853190 TTAAACCTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.43, C:0.49, G:0.00, T:0.09
Consensus pattern (14 bp):
AACCCCAAACCCAT
Found at i:27853166 original size:21 final size:20
Alignment explanation
Indices: 27853142--27853196 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
27853132 CAATTAATCT
27853142 AAACCC-TAAACCCATAACCCC
1 AAACCCATAAACCCA-AA-CCC
*
27853163 AAACCCATAACCCCAAACCC
1 AAACCCATAAACCCAAACCC
*
27853183 ATAACCCTTAAACC
1 A-AACCCATAAACC
27853197 TTAAACGATC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 4 0.14
21 18 0.62
22 7 0.24
ACGTcount: A:0.44, C:0.45, G:0.00, T:0.11
Consensus pattern (20 bp):
AAACCCATAAACCCAAACCC
Found at i:27853280 original size:14 final size:14
Alignment explanation
Indices: 27853270--27853300 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
27853260 TCTTAAATCT
27853270 TAAACCCTAAACCA
1 TAAACCCTAAACCA
*
27853284 TAAACCCTAAACTA
1 TAAACCCTAAACCA
27853298 TAA
1 TAA
27853301 TGATAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:27853467 original size:39 final size:40
Alignment explanation
Indices: 27853424--27853510 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
27853414 CATTTGTAAT
*
27853424 GGCATTTTCCT-AAAAGCGC-GCTAATGCTCGATCTTTAGC
1 GGCATTTT-CTGAAAAGCGCTACTAATGCTCGATCTTTAGC
* * * *
27853463 GGCATTTTTTGAAAAGCGCTACTAATGCTTGATTTTTAGT
1 GGCATTTTCTGAAAAGCGCTACTAATGCTCGATCTTTAGC
*
27853503 GGCGTTTT
1 GGCATTTT
27853511 TTATTCAAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
38 1 0.03
39 16 0.40
40 23 0.57
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (40 bp):
GGCATTTTCTGAAAAGCGCTACTAATGCTCGATCTTTAGC
Found at i:27853501 original size:40 final size:39
Alignment explanation
Indices: 27853435--27853512 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
27853425 GCATTTTCCT
*
27853435 AAAAGCGCGCTAATGCTCGATCTTTAGCGGCATTTTTTG
1 AAAAGCGCACTAATGCTCGATCTTTAGCGGCATTTTTTG
* * * *
27853474 AAAAGCGCTACTAATGCTTGATTTTTAGTGGCGTTTTTT
1 AAAAGCGC-ACTAATGCTCGATCTTTAGCGGCATTTTTT
27853513 ATTCAAACGC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 8 0.24
40 25 0.76
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (39 bp):
AAAAGCGCACTAATGCTCGATCTTTAGCGGCATTTTTTG
Found at i:27860183 original size:50 final size:50
Alignment explanation
Indices: 27860077--27860215 Score: 208
Period size: 50 Copynumber: 2.8 Consensus size: 50
27860067 ACATGCCAAA
* ** *
27860077 GCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGGTGCCCAT
*
27860128 GCCATGTCCCAAACATGGTCTTAC-GGAGGACCTCTCATCTCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACAGG-GGACCTCTCATCTCGGTGCCCAT
27860178 GCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCAT
1 GCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCAT
27860216 GATCTCAAGG
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
50 52 0.65
51 28 0.35
ACGTcount: A:0.19, C:0.31, G:0.24, T:0.26
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCCAT
Found at i:27868966 original size:18 final size:18
Alignment explanation
Indices: 27868943--27868982 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
27868933 AGTGAAGAAT
27868943 AGCCTAGAGAACCTGAGC
1 AGCCTAGAGAACCTGAGC
27868961 AGCCTAGAGAACCTGAGC
1 AGCCTAGAGAACCTGAGC
27868979 AGCC
1 AGCC
27868983 GAAACCCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.30, G:0.28, T:0.10
Consensus pattern (18 bp):
AGCCTAGAGAACCTGAGC
Found at i:27876580 original size:23 final size:22
Alignment explanation
Indices: 27876537--27876580 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
27876527 TTCTAAGTCG
27876537 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
27876560 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
27876581 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:27876689 original size:45 final size:45
Alignment explanation
Indices: 27876625--27876718 Score: 161
Period size: 45 Copynumber: 2.1 Consensus size: 45
27876615 AACAGATACT
* *
27876625 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
*
27876670 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
27876715 CGGT
1 CGGT
27876719 TCACATAGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:27876782 original size:51 final size:50
Alignment explanation
Indices: 27876724--27876910 Score: 207
Period size: 51 Copynumber: 3.7 Consensus size: 50
27876714 TCGGTTCACA
* *
27876724 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACG
1 TAGTAGCCTACACATAGTACTACACACGTGACCA-TACCATCCGATACACG
* * * * * *
27876775 TAGTAGCCTACACATAGTACTACACACGTGATCGAAACTATCTGGTACACA
1 TAGTAGCCTACACATAGTACTACACACGTGA-CCATACCATCCGATACACG
* * * * *
27876826 TAGTAGCCTGCACATAGTACTAGACATGCGACC-TATCATTCC-AGTACACG
1 TAGTAGCCTACACATAGTACTACACACGTGACCATACCA-TCCGA-TACACG
27876876 TAGTAGCCTACACATAGTACTACACACGTGACCAT
1 TAGTAGCCTACACATAGTACTACACACGTGACCAT
27876911 CAGTTTCACT
Statistics
Matches: 109, Mismatches: 23, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
49 2 0.02
50 37 0.34
51 68 0.62
52 2 0.02
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.24
Consensus pattern (50 bp):
TAGTAGCCTACACATAGTACTACACACGTGACCATACCATCCGATACACG
Found at i:27876900 original size:101 final size:101
Alignment explanation
Indices: 27876720--27876906 Score: 306
Period size: 101 Copynumber: 1.8 Consensus size: 101
27876710 ATGTTCGGTT
*
27876720 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACGTAGTAGCCTA
1 CACATAGTAGCCTGCACATAGTACTACACATGCGACCA-TACCATCCGATACACGTAGTAGCCTA
27876785 CACATAGTACTACACACGTGATCGAAACTATCTGGTA
65 CACATAGTACTACACACGTGATCGAAACTATCTGGTA
* *
27876822 CACATAGTAGCCTGCACATAGTACTAGACATGCGACC-TATCATTCC-AGTACACGTAGTAGCCT
1 CACATAGTAGCCTGCACATAGTACTACACATGCGACCATACCA-TCCGA-TACACGTAGTAGCCT
27876885 ACACATAGTACTACACACGTGA
64 ACACATAGTACTACACACGTGA
27876907 CCATCAGTTT
Statistics
Matches: 80, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
100 5 0.06
101 40 0.50
102 35 0.44
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (101 bp):
CACATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATCCGATACACGTAGTAGCCTAC
ACATAGTACTACACACGTGATCGAAACTATCTGGTA
Found at i:27888136 original size:20 final size:20
Alignment explanation
Indices: 27888111--27888150 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
27888101 AAGGATAATT
27888111 TTTGTAGGCTTTATCGACTA
1 TTTGTAGGCTTTATCGACTA
27888131 TTTGTAGGCTTTATCGACTA
1 TTTGTAGGCTTTATCGACTA
27888151 ACACATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (20 bp):
TTTGTAGGCTTTATCGACTA
Found at i:27901758 original size:22 final size:22
Alignment explanation
Indices: 27901733--27901776 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
27901723 ACACCAAAAC
*
27901733 AGGCTTTTAGCGGCACTTTTTT
1 AGGCCTTTAGCGGCACTTTTTT
*
27901755 AGGCCTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCACTTTTTT
27901777 GCGCCGCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.11, C:0.20, G:0.25, T:0.43
Consensus pattern (22 bp):
AGGCCTTTAGCGGCACTTTTTT
Found at i:27901930 original size:43 final size:43
Alignment explanation
Indices: 27901869--27902111 Score: 272
Period size: 43 Copynumber: 5.6 Consensus size: 43
27901859 TTTTAGAAAA
* *
27901869 AAACGCCGCTAAAGACCAAGACCTTTAGCAGCGCTTTTACCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * * **
27901912 AAATGCCGCTAAAAACCAATATCTTTAGCGGCGCTACTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * * *
27901955 AAACGCCGCTAAAGACTAATATCTTTAGCGACGCTTTTCCCAA
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
27901998 AAACGCCACTAAAGACCAAGACATTTAGCGGCGCTTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC-TTTTCCCAC
* * * *
27902042 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTCTCACAA
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
27902085 AAACGCCACTAAAAACCATA-ACCTTTA
1 AAACGCCGCTAAAGACCA-AGACCTTTA
27902112 AAAATATATA
Statistics
Matches: 167, Mismatches: 31, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
43 128 0.77
44 39 0.23
ACGTcount: A:0.34, C:0.31, G:0.14, T:0.21
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:27904838 original size:2 final size:2
Alignment explanation
Indices: 27904831--27904856 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27904821 CCAACAAAAC
27904831 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
27904857 GAAATACCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27907671 original size:7 final size:7
Alignment explanation
Indices: 27907661--27907685 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
27907651 ACTAACTCTT
27907661 AACCCCA
1 AACCCCA
27907668 AACCCCA
1 AACCCCA
27907675 AACCCCA
1 AACCCCA
27907682 AACC
1 AACC
27907686 ACTAACCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.56, G:0.00, T:0.00
Consensus pattern (7 bp):
AACCCCA
Found at i:27907780 original size:89 final size:89
Alignment explanation
Indices: 27907669--27907843 Score: 269
Period size: 89 Copynumber: 2.0 Consensus size: 89
27907659 TTAACCCCAA
* *
27907669 ACCCCAAACCCCAAACCACTAACCTCTAAACCTTATTTAATATAGAAATTAAAAAACACTAATTA
1 ACCCCAAACCCCAAACCACTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTA
*
27907734 ATCTAAATCATAAACCCTAACCCG
66 ATCTAAACCATAAACCCTAACCCG
* * * * *
27907758 ACCCCAAATCCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAACACACTAATTA
1 ACCCCAAACCCCAAACCACTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTA
*
27907823 ATCTAAACCCTAAACCCTAAC
66 ATCTAAACCATAAACCCTAAC
27907844 TATATAAATT
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
89 77 1.00
ACGTcount: A:0.45, C:0.30, G:0.01, T:0.23
Consensus pattern (89 bp):
ACCCCAAACCCCAAACCACTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTA
ATCTAAACCATAAACCCTAACCCG
Found at i:27907851 original size:46 final size:46
Alignment explanation
Indices: 27907798--27907888 Score: 164
Period size: 46 Copynumber: 2.0 Consensus size: 46
27907788 CATTATTTAA
27907798 TATATAAATTAAAACACACTAATTAATCTAAACCCTAAACCCTAAC
1 TATATAAATTAAAACACACTAATTAATCTAAACCCTAAACCCTAAC
* *
27907844 TATATAAATTAAAACACACTAATTAATCTAAACTCTAAACTCTAA
1 TATATAAATTAAAACACACTAATTAATCTAAACCCTAAACCCTAA
27907889 AACCCTAAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.29
Consensus pattern (46 bp):
TATATAAATTAAAACACACTAATTAATCTAAACCCTAAACCCTAAC
Found at i:27907865 original size:23 final size:23
Alignment explanation
Indices: 27907798--27907865 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
27907788 CATTATTTAA
*
27907798 TATATAAATTAAAACACACTAAT
1 TATATAAATTAAAACACACTAAC
* *
27907821 TAATCTAAACCCT-AAAC-C-CTAAC
1 T-ATATAAA--TTAAAACACACTAAC
27907844 TATATAAATTAAAACACACTAA
1 TATATAAATTAAAACACACTAA
27907866 TTAATCTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 12
0.67 0.10 0.24
Matches are distributed among these distances:
20 1 0.03
21 4 0.12
22 7 0.21
23 10 0.29
24 7 0.21
25 4 0.12
26 1 0.03
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (23 bp):
TATATAAATTAAAACACACTAAC
Found at i:27907882 original size:7 final size:7
Alignment explanation
Indices: 27907870--27907920 Score: 66
Period size: 7 Copynumber: 7.0 Consensus size: 7
27907860 CACTAATTAA
27907870 TCTAAAC
1 TCTAAAC
27907877 TCTAAAC
1 TCTAAAC
27907884 TCTAAAAC
1 TCT-AAAC
*
27907892 CCTAAAC
1 TCTAAAC
*
27907899 CCTAAACC
1 TCTAAA-C
27907907 TCTAAAC
1 TCTAAAC
27907914 TCTAAAC
1 TCTAAAC
27907921 CTTAAATCCC
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
7 28 0.70
8 12 0.30
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.24
Consensus pattern (7 bp):
TCTAAAC
Found at i:27907888 original size:23 final size:23
Alignment explanation
Indices: 27907813--27907888 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 23
27907803 AAATTAAAAC
*
27907813 ACACTAATTAATCTAAACCCTAA
1 ACACTAATTAATCTAAACTCTAA
* * * * **
27907836 ACCCTAACT-ATATAAATTAAAA
1 ACACTAATTAATCTAAACTCTAA
27907858 CACACTAATTAATCTAAACTCTAA
1 -ACACTAATTAATCTAAACTCTAA
*
27907882 ACTCTAA
1 ACACTAA
27907889 AACCCTAAAC
Statistics
Matches: 37, Mismatches: 14, Indels: 4
0.67 0.25 0.07
Matches are distributed among these distances:
22 8 0.22
23 20 0.54
24 9 0.24
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.28
Consensus pattern (23 bp):
ACACTAATTAATCTAAACTCTAA
Found at i:27907896 original size:22 final size:22
Alignment explanation
Indices: 27907871--27907926 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
27907861 ACTAATTAAT
*
27907871 CTAAACTCTAAA-CTCTAAAACC
1 CTAAACCCTAAACCTCT-AAACC
*
27907893 CTAAACCCTAAACCTCTAAACT
1 CTAAACCCTAAACCTCTAAACC
*
27907915 CTAAACCTTAAA
1 CTAAACCCTAAA
27907927 TCCCTAACTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 26 0.87
23 4 0.13
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (22 bp):
CTAAACCCTAAACCTCTAAACC
Found at i:27907920 original size:15 final size:15
Alignment explanation
Indices: 27907870--27907926 Score: 75
Period size: 15 Copynumber: 3.9 Consensus size: 15
27907860 CACTAATTAA
27907870 TCTAAA-CTCTAAAC
1 TCTAAACCTCTAAAC
27907884 TCTAAAACC-CTAAAC
1 TCT-AAACCTCTAAAC
*
27907899 CCTAAACCTCTAAAC
1 TCTAAACCTCTAAAC
27907914 TCTAAACCT-TAAA
1 TCTAAACCTCTAAA
27907927 TCCCTAACTC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
14 12 0.32
15 25 0.66
16 1 0.03
ACGTcount: A:0.44, C:0.32, G:0.00, T:0.25
Consensus pattern (15 bp):
TCTAAACCTCTAAAC
Found at i:27907948 original size:7 final size:7
Alignment explanation
Indices: 27907928--27907961 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
27907918 AACCTTAAAT
27907928 CCCTAAC
1 CCCTAAC
* *
27907935 TCTTAAC
1 CCCTAAC
27907942 CCCTAAC
1 CCCTAAC
27907949 CCCTAAC
1 CCCTAAC
27907956 CCCTAA
1 CCCTAA
27907962 ACATTAAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.29, C:0.50, G:0.00, T:0.21
Consensus pattern (7 bp):
CCCTAAC
Found at i:27908005 original size:14 final size:15
Alignment explanation
Indices: 27907988--27908020 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
27907978 CTTAAATCAG
27907988 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
27908002 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
27908017 AATC
1 AATC
27908021 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:27908537 original size:14 final size:14
Alignment explanation
Indices: 27908520--27908571 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
27908510 TCTTGACTTC
*
27908520 TAACCCTTAACCCT
1 TAACCCTTAACCCA
*
27908534 TAACCCCTAACCCA
1 TAACCCTTAACCCA
* **
27908548 TAAACCTTAAATCA
1 TAACCCTTAACCCA
*
27908562 CAACCCTTAA
1 TAACCCTTAA
27908572 ATCTGAATCC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.23
Consensus pattern (14 bp):
TAACCCTTAACCCA
Found at i:27908600 original size:14 final size:15
Alignment explanation
Indices: 27908577--27908609 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
27908567 CTTAAATCTG
27908577 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
*
27908591 AATCCTTAATTCCAT
1 AATCCCTAATTCCAT
27908606 AATC
1 AATC
27908610 TATAAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.33
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:27908822 original size:40 final size:41
Alignment explanation
Indices: 27908740--27908850 Score: 138
Period size: 40 Copynumber: 2.8 Consensus size: 41
27908730 TTCCAAAAAA
* *
27908740 CGCCGCTAATGCTC-ATTTTTAGCGGCG-CTTCCAGGAAAG
1 CGCCGCTAATGCTCGATTTTTAGCGGCGTTTTACAGGAAAG
* * *
27908779 CGCCGCTAATGCTCGATCTTTAGCGGCGTTTTAC-GTAAGG
1 CGCCGCTAATGCTCGATTTTTAGCGGCGTTTTACAGGAAAG
* *
27908819 CGCCGCTAATGCTCGATTTTTAGTGACGTTTT
1 CGCCGCTAATGCTCGATTTTTAGCGGCGTTTT
27908851 TTGTCCAAAC
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
39 14 0.23
40 45 0.73
41 3 0.05
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (41 bp):
CGCCGCTAATGCTCGATTTTTAGCGGCGTTTTACAGGAAAG
Found at i:27917411 original size:39 final size:39
Alignment explanation
Indices: 27917337--27917513 Score: 187
Period size: 39 Copynumber: 4.5 Consensus size: 39
27917327 ATTCACTTTT
* * * *
27917337 AAGCATATACCA-AATTACACATATAATCACCTAACATAC
1 AAGCATATATCACAA-TACTCATATAATCACATAACATTC
*
27917376 AAGCATATATCACAATACTCATA-AAGTCACATAACATTT
1 AAGCATATATCACAATACTCATATAA-TCACATAACATTC
* * * * *
27917415 AAGTATATGTTAGAATACTCGTATAATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* * * *
27917454 AATCATATATCACCATACTCATATAATCGCATAACATTT
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
*
27917493 AAGCATATATGACAATACTCA
1 AAGCATATATCACAATACTCA
27917514 AAAACACCTT
Statistics
Matches: 112, Mismatches: 23, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
38 2 0.02
39 106 0.95
40 4 0.04
ACGTcount: A:0.45, C:0.21, G:0.06, T:0.29
Consensus pattern (39 bp):
AAGCATATATCACAATACTCATATAATCACATAACATTC
Found at i:27917510 original size:78 final size:78
Alignment explanation
Indices: 27917358--27917512 Score: 213
Period size: 78 Copynumber: 2.0 Consensus size: 78
27917348 AAATTACACA
* *
27917358 TATAATCACCTAACATACAAGCATATATCACAATACTCATAAAGTCACATAACATTTAAGTATAT
1 TATAATCACATAACATACAAGCATATATCACAATACTCATAAAGTCACATAACATTTAAGCATAT
* * *
27917423 GTTAGAATACTCG
66 ATGACAATACTCG
* * * *
27917436 TATAATCACATAACATTCAATCATATATCACCATACTCATATAA-TCGCATAACATTTAAGCATA
1 TATAATCACATAACATACAAGCATATATCACAATACTCATA-AAGTCACATAACATTTAAGCATA
27917500 TATGACAATACTC
65 TATGACAATACTC
27917513 AAAAACACCT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
78 65 0.97
79 2 0.03
ACGTcount: A:0.43, C:0.21, G:0.06, T:0.30
Consensus pattern (78 bp):
TATAATCACATAACATACAAGCATATATCACAATACTCATAAAGTCACATAACATTTAAGCATAT
ATGACAATACTCG
Found at i:27922521 original size:24 final size:26
Alignment explanation
Indices: 27922493--27922550 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 26
27922483 AATATGGAAA
* *
27922493 TTAAAATAATAACA-TAA-GATAAAT
1 TTAAAATAATAAAATTAATAATAAAT
27922517 TTAAAA-AA-AAAATTAATAATAAAT
1 TTAAAATAATAAAATTAATAATAAAT
27922541 TTAAAATAAT
1 TTAAAATAAT
27922551 GATTGAGCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 3 0.11
23 5 0.18
24 18 0.64
25 2 0.07
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (26 bp):
TTAAAATAATAAAATTAATAATAAAT
Found at i:27929684 original size:38 final size:38
Alignment explanation
Indices: 27929620--27929699 Score: 124
Period size: 38 Copynumber: 2.1 Consensus size: 38
27929610 GCAAATCCAT
* *
27929620 TTTTGTGATTTTGTAGGTTTTGTTGTTAATTGATTACG
1 TTTTGTGATTTCGTAGATTTTGTTGTTAATTGATTACG
* *
27929658 TTTTGTGATTTCGTAGATTTTTTTGTTAATTGATTATG
1 TTTTGTGATTTCGTAGATTTTGTTGTTAATTGATTACG
27929696 TTTT
1 TTTT
27929700 AGGAATAAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.16, C:0.03, G:0.20, T:0.61
Consensus pattern (38 bp):
TTTTGTGATTTCGTAGATTTTGTTGTTAATTGATTACG
Found at i:27932295 original size:38 final size:39
Alignment explanation
Indices: 27932221--27932297 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 39
27932211 AAAGGCTAGT
* *
27932221 TTGAATGTTATGTGATTATATGAGTATTATGGTATATGC
1 TTGAATGTTATGTGATTATATGAGTAATATGATATATGC
* *
27932260 TTGAATGTTATGT-ATTATATGTGTAATGTGATATATGC
1 TTGAATGTTATGTGATTATATGAGTAATATGATATATGC
27932298 CTAAAAGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
38 21 0.62
39 13 0.38
ACGTcount: A:0.29, C:0.03, G:0.22, T:0.47
Consensus pattern (39 bp):
TTGAATGTTATGTGATTATATGAGTAATATGATATATGC
Found at i:27935160 original size:36 final size:36
Alignment explanation
Indices: 27935122--27935204 Score: 134
Period size: 36 Copynumber: 2.4 Consensus size: 36
27935112 GCCACACCTA
*
27935122 TATATTATATATAT-ATAAAA-AATGCACTCATATT
1 TATATTATATATATAATAAAACAATGCACACATATT
*
27935156 TATATTATATATATAATAAAACCATGCACACATATT
1 TATATTATATATATAATAAAACAATGCACACATATT
27935192 TATATTATATATA
1 TATATTATATATA
27935205 CACGTACCTA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
34 14 0.31
35 6 0.13
36 25 0.56
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.41
Consensus pattern (36 bp):
TATATTATATATATAATAAAACAATGCACACATATT
Found at i:27937869 original size:7 final size:7
Alignment explanation
Indices: 27937857--27937881 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
27937847 TCAAGTAATT
27937857 CATTGAA
1 CATTGAA
27937864 CATTGAA
1 CATTGAA
27937871 CATTGAA
1 CATTGAA
27937878 CATT
1 CATT
27937882 TAATAATTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (7 bp):
CATTGAA
Found at i:27938052 original size:20 final size:20
Alignment explanation
Indices: 27938021--27938127 Score: 81
Period size: 20 Copynumber: 5.3 Consensus size: 20
27938011 GCATCATAGA
27938021 TGCATAACAGGGGCACCGATG
1 TGCA-AACAGGGGCACCGATG
* * **
27938042 TGTAGACAGGGGCACAAATG
1 TGCAAACAGGGGCACCGATG
27938062 TGCAAACAGGGGCACCG-TAG
1 TGCAAACAGGGGCACCGAT-G
* * * * *
27938082 TGCGAATAGAGGCACCAAAG
1 TGCAAACAGGGGCACCGATG
* * *
27938102 TGTATACAGGGGCACCGAAG
1 TGCAAACAGGGGCACCGATG
27938122 TGCAAA
1 TGCAAA
27938128 TCCCGTACAA
Statistics
Matches: 63, Mismatches: 21, Indels: 5
0.71 0.24 0.06
Matches are distributed among these distances:
19 1 0.02
20 59 0.94
21 3 0.05
ACGTcount: A:0.34, C:0.21, G:0.33, T:0.13
Consensus pattern (20 bp):
TGCAAACAGGGGCACCGATG
Found at i:27944832 original size:5 final size:5
Alignment explanation
Indices: 27944824--27944848 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
27944814 TACCTTTTGT
27944824 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
27944849 CCAAATTACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:27954275 original size:29 final size:29
Alignment explanation
Indices: 27954242--27954313 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 29
27954232 TTCCTTTAAG
* *
27954242 AGAGATAGCCACAAAAATTTTCTTATAAA
1 AGAGATCGCCACAAAAACTTTCTTATAAA
* * *
27954271 AGAGATCGCCAGAAAGACTTTCTTATAAT
1 AGAGATCGCCACAAAAACTTTCTTATAAA
*
27954300 AGAGACCGCCACAA
1 AGAGATCGCCACAA
27954314 GGATTTCTTA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.22
Consensus pattern (29 bp):
AGAGATCGCCACAAAAACTTTCTTATAAA
Found at i:27958428 original size:30 final size:29
Alignment explanation
Indices: 27958384--27958478 Score: 110
Period size: 30 Copynumber: 3.3 Consensus size: 29
27958374 TATACAGTAT
27958384 CAGT-ACAG-TGTGGGCCTTAGCCCAATA
1 CAGTAACAGTTGTGGGCCTTAGCCCAATA
* *
27958411 TAGTAACAGTCTGTGGGCCTTTGCCCAATA
1 CAGTAACAGT-TGTGGGCCTTAGCCCAATA
27958441 CAGTAACA--TG-GGGCCCTTAGCCCAATA
1 CAGTAACAGTTGTGGG-CCTTAGCCCAATA
27958468 CAGTAATCAGT
1 CAGTAA-CAGT
27958479 GCAATGCAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
26 3 0.05
27 23 0.40
28 6 0.11
30 25 0.44
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.24
Consensus pattern (29 bp):
CAGTAACAGTTGTGGGCCTTAGCCCAATA
Found at i:27958863 original size:27 final size:26
Alignment explanation
Indices: 27958833--27959242 Score: 231
Period size: 27 Copynumber: 15.2 Consensus size: 26
27958823 GGTTTAACAA
* *
27958833 TCATTTTATCTTATGAGGGTATTTCAT
1 TCATTTTACCTT-TGAGGGTATTTCAG
* * *
27958860 TCATTTTACCCTTCGAGGGCATTTCAA
1 TCATTTTA-CCTTTGAGGGTATTTCAG
*
27958887 TCATTTTACCCTTGAAGGGTATTTCAG
1 TCATTTTACCTTTG-AGGGTATTTCAG
*
27958914 TCATTTTACCTTTCAAGGGTATTTCAG
1 TCATTTTACCTTT-GAGGGTATTTCAG
*
27958941 TCATTTTACCCTTCGA-GGTCATTTC-G
1 TCATTTTA-CCTTTGAGGGT-ATTTCAG
*** **
27958967 ATCATTTTACCCTCCAAGGGTATTTTTG
1 -TCATTTTA-CCTTTGAGGGTATTTCAG
* *
27958995 TCATTTTACCCTTCAGGGGTATTTCTA-
1 TCATTTTACCTTTGA-GGGTATTTC-AG
* *
27959022 TCATTTTACTCTTCGAGGGAATTTC-G
1 TCATTTTAC-CTTTGAGGGTATTTCAG
* * *
27959048 ATCATTTTAGCCTTCGAGGGCATTTCGG
1 -TCATTTTA-CCTTTGAGGGTATTTCAG
* *
27959076 TCATTTTAACCTTTAAGGGTATTTCTG
1 TCATTTT-ACCTTTGAGGGTATTTCAG
* * * *
27959103 TCATTTTACCCTTCGAGGGCATTTTAA
1 TCATTTTA-CCTTTGAGGGTATTTCAG
* ** *
27959130 TAATTTTACCCTTTGAAAGT-TTTCGG
1 TCATTTTA-CCTTTGAGGGTATTTCAG
** *
27959156 TCATTTTACCCTTCAAGGGTATTT-TG
1 TCATTTTA-CCTTTGAGGGTATTTCAG
* ** *
27959182 ATCAATTTACCCTTCAAGGGTATTTCGG
1 -TCATTTTA-CCTTTGAGGGTATTTCAG
* *
27959210 TCATTTTATCCTTCGAAGGTATTTC-G
1 TCATTTTA-CCTTTGAGGGTATTTCAG
27959236 ATCATTT
1 -TCATTT
27959243 GCCCATGAGT
Statistics
Matches: 306, Mismatches: 56, Indels: 42
0.76 0.14 0.10
Matches are distributed among these distances:
26 32 0.10
27 256 0.84
28 18 0.06
ACGTcount: A:0.21, C:0.20, G:0.16, T:0.43
Consensus pattern (26 bp):
TCATTTTACCTTTGAGGGTATTTCAG
Found at i:27958888 original size:54 final size:54
Alignment explanation
Indices: 27958830--27959242 Score: 288
Period size: 54 Copynumber: 7.7 Consensus size: 54
27958820 AGGGGTTTAA
* * *
27958830 CAATCATTTTA-TCTTATGAGGGTATTTCATTCATTTTACCCTTCGAGGGCATTT
1 CAATCATTTTACCCTT-TGAGGGTATTTCATTCATTTTACCCTTCAAGGGTATTT
* *
27958884 CAATCATTTTACCC-TTGAAGGGTATTTCAGTCATTTTACCTTTCAAGGGTATTT
1 CAATCATTTTACCCTTTG-AGGGTATTTCATTCATTTTACCCTTCAAGGGTATTT
* * *
27958938 CAGTCATTTTACCCTTCGA-GGTCATTTCGA-TCATTTTACCCTCCAAGGGTATTT
1 CAATCATTTTACCCTTTGAGGGT-ATTTC-ATTCATTTTACCCTTCAAGGGTATTT
*** * * * *
27958992 TTGTCATTTTACCC-TTCAGGGGTATTTC-TATCATTTTACTCTTCGAGGGAATTT
1 CAATCATTTTACCCTTTGA-GGGTATTTCAT-TCATTTTACCCTTCAAGGGTATTT
* * * * ** * *
27959046 CGATCATTTTAGCCTTCGAGGGCATTTCGGTCATTTTAACCTTTAAGGGTATTT
1 CAATCATTTTACCCTTTGAGGGTATTTCATTCATTTTACCCTTCAAGGGTATTT
** * * * * * * *
27959100 CTGTCATTTTACCCTTCGAGGGCATTTTAATAATTTTACCCTTTGAA-AGT-TTT
1 CAATCATTTTACCCTTTGAGGGTATTTCATTCATTTTACCC-TTCAAGGGTATTT
** ** * *
27959153 CGGTCATTTTACCCTTCAAGGGTATTTTGA-TCAATTTACCCTTCAAGGGTATTT
1 CAATCATTTTACCCTTTGAGGGTA-TTTCATTCATTTTACCCTTCAAGGGTATTT
** * * *
27959207 CGGTCATTTTATCCTTCGAAGGTATTTCGA-TCATTT
1 CAATCATTTTACCCTTTGAGGGTATTTC-ATTCATTT
27959243 GCCCATGAGT
Statistics
Matches: 290, Mismatches: 53, Indels: 32
0.77 0.14 0.09
Matches are distributed among these distances:
52 4 0.01
53 45 0.16
54 228 0.79
55 13 0.04
ACGTcount: A:0.21, C:0.20, G:0.16, T:0.43
Consensus pattern (54 bp):
CAATCATTTTACCCTTTGAGGGTATTTCATTCATTTTACCCTTCAAGGGTATTT
Found at i:27958945 original size:81 final size:81
Alignment explanation
Indices: 27958848--27959242 Score: 451
Period size: 81 Copynumber: 4.9 Consensus size: 81
27958838 TTATCTTATG
* * *
27958848 AGGGTATTTCATTCATTTTACCCTTCGAGGGCATTTCAATCATTTTACCCTTGAAGGGTATTTCA
1 AGGGTATTTCAGTCATTTTACCCTTCGAGGGCATTTCGATCATTTTACCCTTGAAGGGTATTTCG
*
27958913 GTCATTTTACCTTTCA
66 GTCATTTTACCCTTCA
* ** **
27958929 AGGGTATTTCAGTCATTTTACCCTTCGAGGTCATTTCGATCATTTTACCCTCCAAGGGTATTTTT
1 AGGGTATTTCAGTCATTTTACCCTTCGAGGGCATTTCGATCATTTTACCCTTGAAGGGTATTTCG
27958994 GTCATTTTACCCTTCA
66 GTCATTTTACCCTTCA
* * * * *
27959010 GGGGTATTTCTA-TCATTTTACTCTTCGAGGGAATTTCGATCATTTTAGCCTTCG-AGGGCATTT
1 AGGGTATTTC-AGTCATTTTACCCTTCGAGGGCATTTCGATCATTTTACCCTT-GAAGGGTATTT
* *
27959073 CGGTCATTTTAACCTTTA
64 CGGTCATTTTACCCTTCA
* ** * *
27959091 AGGGTATTTCTGTCATTTTACCCTTCGAGGGCATTTTAATAATTTTACCCTTTGAA-AGT-TTTC
1 AGGGTATTTCAGTCATTTTACCCTTCGAGGGCATTTCGATCATTTTACCC-TTGAAGGGTATTTC
27959154 GGTCATTTTACCCTTCA
65 GGTCATTTTACCCTTCA
* * * * * *
27959171 AGGGTATTT-TGATCAATTTACCCTTCAAGGGTATTTCGGTCATTTTATCCTTCGAA-GGTATTT
1 AGGGTATTTCAG-TCATTTTACCCTTCGAGGGCATTTCGATCATTTTACCCTT-GAAGGGTATTT
*
27959234 CGATCATTT
64 CGGTCATTT
27959243 GCCCATGAGT
Statistics
Matches: 264, Mismatches: 42, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
79 4 0.02
80 63 0.24
81 193 0.73
82 4 0.02
ACGTcount: A:0.21, C:0.20, G:0.16, T:0.43
Consensus pattern (81 bp):
AGGGTATTTCAGTCATTTTACCCTTCGAGGGCATTTCGATCATTTTACCCTTGAAGGGTATTTCG
GTCATTTTACCCTTCA
Found at i:27968120 original size:30 final size:28
Alignment explanation
Indices: 27968072--27968164 Score: 123
Period size: 28 Copynumber: 3.2 Consensus size: 28
27968062 TAGTATCAGT
* *
27968072 ACAGTGTGGGCTTTAGCCCATTATAGTA
1 ACAGTGTGGGCCTTAGCCCAATATAGTA
*
27968100 ACAGTGTGTAGGCCTTAGCCCAATACAGTA
1 ACAGTGTG--GGCCTTAGCCCAATATAGTA
*
27968130 ACAGTGGGGGCCTTAGCCCAATATAGTA
1 ACAGTGTGGGCCTTAGCCCAATATAGTA
27968158 ATCAGTG
1 A-CAGTG
27968165 CAATGCAGTA
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
28 28 0.49
29 5 0.09
30 24 0.42
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (28 bp):
ACAGTGTGGGCCTTAGCCCAATATAGTA
Found at i:27968261 original size:26 final size:26
Alignment explanation
Indices: 27968232--27968308 Score: 100
Period size: 26 Copynumber: 3.0 Consensus size: 26
27968222 ACACCAATAT
* *
27968232 CGCAGCCAAGCTGCCAGTAATAGTGA
1 CGCAGCAAAGCTGCCAGTAATAGTAA
* *
27968258 CGCAGCAAAGCTACCAGTAACAGTAA
1 CGCAGCAAAGCTGCCAGTAATAGTAA
* *
27968284 CACAGCAAAGCTGCCAGTAGTAGTA
1 CGCAGCAAAGCTGCCAGTAATAGTA
27968309 TATGTGGCAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.36, C:0.26, G:0.23, T:0.14
Consensus pattern (26 bp):
CGCAGCAAAGCTGCCAGTAATAGTAA
Found at i:27968528 original size:27 final size:26
Alignment explanation
Indices: 27968499--27968945 Score: 400
Period size: 27 Copynumber: 16.6 Consensus size: 26
27968489 TAACTTATGG
* * *
27968499 GGGTATTTCAGTCATTTCACTCTTCAG
1 GGGTATTTC-GTCATTTTACCCTTCAA
* *
27968526 GGGTATTTCGTTCCTTTTACCCTAT-GA
1 GGGTATTTCG-TCATTTTACCCT-TCAA
* *
27968553 GGGTATTTCGATCATTTTACCGTTCAG
1 GGGTATTTCG-TCATTTTACCCTTCAA
* *
27968580 GGGTATCTCGATCATTTTACCTTTCAA
1 GGGTATTTCG-TCATTTTACCCTTCAA
* * *
27968607 GGGCATTTTAGTCATTTTACCCTTTAA
1 GGGTA-TTTCGTCATTTTACCCTTCAA
* * *
27968634 AGGTATTTTGGTCATTTTACCCTTTAA
1 GGGTA-TTTCGTCATTTTACCCTTCAA
* * *
27968661 AGGTATTTCAGTTATTTTACCCTTCGA
1 GGGTATTTC-GTCATTTTACCCTTCAA
* *
27968688 GGGCATTTCGGTCATTTGACCCTTCAA
1 GGGTATTTC-GTCATTTTACCCTTCAA
* **
27968715 GGTTATTTCAGTCATTTTA-CCTTTTA
1 GGGTATTTC-GTCATTTTACCCTTCAA
27968741 GGGTATTTCGATCATTTTACCCTTCGAA
1 GGGTATTTCG-TCATTTTACCCTTC-AA
*
27968769 -GGCATTTCGATCATTTTACCCTTCAA
1 GGGTATTTCG-TCATTTTACCCTTCAA
*
27968795 GGGTATTTCGATCATTTTACCCTTCGA
1 GGGTATTTCG-TCATTTTACCCTTCAA
*
27968822 GGGCATTTCGATCATTTTACCCTTCAA
1 GGGTATTTCG-TCATTTTACCCTTCAA
*
27968849 GGGTATTTCAGTCA-TTTACCCTTCGA
1 GGGTATTTC-GTCATTTTACCCTTCAA
* *
27968875 GGGTATTTTGGTCATTTTACCGTTCAA
1 GGGTA-TTTCGTCATTTTACCCTTCAA
* *
27968902 AGGTATTTCGGT-AGTTTTACTCTTCAA
1 GGGTATTTC-GTCA-TTTTACCCTTCAA
27968929 GGGTATTTCAGTCATTT
1 GGGTATTTC-GTCATTT
27968946 GCCTATAAGT
Statistics
Matches: 349, Mismatches: 56, Indels: 30
0.80 0.13 0.07
Matches are distributed among these distances:
25 1 0.00
26 52 0.15
27 289 0.83
28 7 0.02
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.42
Consensus pattern (26 bp):
GGGTATTTCGTCATTTTACCCTTCAA
Found at i:27968812 original size:134 final size:133
Alignment explanation
Indices: 27968500--27968945 Score: 508
Period size: 134 Copynumber: 3.3 Consensus size: 133
27968490 AACTTATGGG
* * * * * *
27968500 GGTATTTCAGTCATTTCACTCTTCAGGGGTATTTC-GTTCCTTTTACCCTAT-GAGGGTATTTCG
1 GGTATTTCGGTCATTTTACCCTTCAAGGGTATTTCAG-TCATTTTACCCT-TCGAGGGCATTTCG
* * * * *
27968563 ATCATTTTACCGTTCAGGGGTATCTC-GATCATTTTACCTTTCAAGGGCATTTTAGTCATTTTAC
64 ATCATTTTACCCTTCAAGGGTATTTCAG-TCATTTTACCTTT-AAGGGTATTTGA-TCATTTTAC
*
27968627 CCTTTAAA
126 CCTTCAAA
* * * * *
27968635 GGTATTTTGGTCATTTTACCCTTTAAAGGTATTTCAGTTATTTTACCCTTCGAGGGCATTTCGGT
1 GGTATTTCGGTCATTTTACCCTTCAAGGGTATTTCAGTCATTTTACCCTTCGAGGGCATTTCGAT
* * *
27968700 CATTTGACCCTTCAAGGTTATTTCAGTCATTTTACCTTTTAGGGTATTTCGATCATTTTACCCTT
66 CATTTTACCCTTCAAGGGTATTTCAGTCATTTTACCTTTAAGGGTATTT-GATCATTTTACCCTT
*
27968765 CGAA
130 CAAA
* *
27968769 GGCATTTCGATCATTTTACCCTTCAAGGGTATTTC-GATCATTTTACCCTTCGAGGGCATTTCGA
1 GGTATTTCGGTCATTTTACCCTTCAAGGGTATTTCAG-TCATTTTACCCTTCGAGGGCATTTCGA
** * *
27968833 TCATTTTACCCTTCAAGGGTATTTCAGTCA-TTTACCCTTCGAGGGTATTTTGGTCATTTTACCG
65 TCATTTTACCCTTCAAGGGTATTTCAGTCATTTTA-CCTTTAAGGGTA-TTTGATCATTTTACCC
27968897 TTCAAA
128 TTCAAA
*
27968903 GGTATTTCGGT-AGTTTTACTCTTCAAGGGTATTTCAGTCATTT
1 GGTATTTCGGTCA-TTTTACCCTTCAAGGGTATTTCAGTCATTT
27968946 GCCTATAAGT
Statistics
Matches: 264, Mismatches: 38, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
133 6 0.02
134 169 0.64
135 87 0.33
136 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.42
Consensus pattern (133 bp):
GGTATTTCGGTCATTTTACCCTTCAAGGGTATTTCAGTCATTTTACCCTTCGAGGGCATTTCGAT
CATTTTACCCTTCAAGGGTATTTCAGTCATTTTACCTTTAAGGGTATTTGATCATTTTACCCTTC
AAA
Found at i:27976706 original size:17 final size:18
Alignment explanation
Indices: 27976676--27976710 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
27976666 TAATATACCT
*
27976676 GAAAAAGAGGGAAAAATA
1 GAAAAAGAGAGAAAAATA
27976694 GAAAAA-AGAGAAAAATA
1 GAAAAAGAGAGAAAAATA
27976711 ACACAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.06
Consensus pattern (18 bp):
GAAAAAGAGAGAAAAATA
Found at i:27981584 original size:23 final size:23
Alignment explanation
Indices: 27981558--27981656 Score: 144
Period size: 23 Copynumber: 4.3 Consensus size: 23
27981548 ATAAGTGCCA
27981558 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
27981581 CACTGATACGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
27981604 CACTAAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
27981627 AACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
27981650 CACTGAT
1 CACTGAT
27981657 CAATAACACT
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 65 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:27981632 original size:46 final size:46
Alignment explanation
Indices: 27981565--27981653 Score: 160
Period size: 46 Copynumber: 1.9 Consensus size: 46
27981555 CCACACTGAT
*
27981565 ATGTAGCCGAAGCTACCACTGATACGTAGCCGTAGCTACCACTAAA
1 ATGTAGCCGAAGCTACAACTGATACGTAGCCGTAGCTACCACTAAA
*
27981611 ATGTAGCCGAAGCTACAACTGATATGTAGCCGTAGCTACCACT
1 ATGTAGCCGAAGCTACAACTGATACGTAGCCGTAGCTACCACT
27981654 GATCAATAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.21
Consensus pattern (46 bp):
ATGTAGCCGAAGCTACAACTGATACGTAGCCGTAGCTACCACTAAA
Found at i:27983535 original size:12 final size:12
Alignment explanation
Indices: 27983518--27983543 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27983508 CCAGCCTTCC
27983518 ATGTGTTTTTAA
1 ATGTGTTTTTAA
27983530 ATGTGTTTTTAA
1 ATGTGTTTTTAA
27983542 AT
1 AT
27983544 CAGCCCCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (12 bp):
ATGTGTTTTTAA
Found at i:27986421 original size:14 final size:14
Alignment explanation
Indices: 27986402--27986428 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
27986392 AGTTTAACTA
27986402 GGAGATTATTTCTG
1 GGAGATTATTTCTG
27986416 GGAGATTATTTCT
1 GGAGATTATTTCT
27986429 CAAATTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.07, G:0.26, T:0.44
Consensus pattern (14 bp):
GGAGATTATTTCTG
Found at i:27988301 original size:23 final size:22
Alignment explanation
Indices: 27988275--27988321 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
27988265 TACTTTGAGT
27988275 GAAAA-CTAGAAAGAAAATGAAAA
1 GAAAACCTA-AAAGAAAAT-AAAA
*
27988298 GAAAACCTAAAAGGAAATAAAA
1 GAAAACCTAAAAGAAAATAAAA
27988320 GA
1 GA
27988322 TAATGTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 6 0.27
23 13 0.59
24 3 0.14
ACGTcount: A:0.68, C:0.06, G:0.17, T:0.09
Consensus pattern (22 bp):
GAAAACCTAAAAGAAAATAAAA
Found at i:27989067 original size:10 final size:10
Alignment explanation
Indices: 27989054--27989082 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
27989044 GTCCTCAGGG
27989054 GTCAAAACAA
1 GTCAAAACAA
27989064 GTCAAAACAA
1 GTCAAAACAA
27989074 GTCAAAACA
1 GTCAAAACA
27989083 GGGGAAGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.59, C:0.21, G:0.10, T:0.10
Consensus pattern (10 bp):
GTCAAAACAA
Found at i:27990061 original size:49 final size:49
Alignment explanation
Indices: 27990001--27990095 Score: 156
Period size: 49 Copynumber: 1.9 Consensus size: 49
27989991 CGTAGAGAAG
* *
27990001 TACACTTCTTCTATTTGATATTAATTAGAATAA-GTTGTTTCAACCTTAC
1 TACACTACTTCTATTTGACATTAATTAGAATAAGGTT-TTTCAACCTTAC
27990050 TACACTACTTCTATTTGACATTAATTAGAATAAGGTTTTTCAACCT
1 TACACTACTTCTATTTGACATTAATTAGAATAAGGTTTTTCAACCT
27990096 ATAAATAGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
49 40 0.93
50 3 0.07
ACGTcount: A:0.32, C:0.17, G:0.08, T:0.43
Consensus pattern (49 bp):
TACACTACTTCTATTTGACATTAATTAGAATAAGGTTTTTCAACCTTAC
Found at i:27997184 original size:17 final size:17
Alignment explanation
Indices: 27997158--27997195 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
27997148 TTATAGTTTT
27997158 AAATAATA-TTTGGGTA
1 AAATAATATTTTGGGTA
*
27997174 AAATAAATATTTTGGGTC
1 AAAT-AATATTTTGGGTA
27997192 AAAT
1 AAAT
27997196 TAGAATTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 4 0.21
18 11 0.58
ACGTcount: A:0.45, C:0.03, G:0.16, T:0.37
Consensus pattern (17 bp):
AAATAATATTTTGGGTA
Found at i:28013680 original size:21 final size:22
Alignment explanation
Indices: 28013639--28013687 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
28013629 ATTAATACCT
*
28013639 ATTTATAGTGTAATAAATAAAA
1 ATTTATAGTCTAATAAATAAAA
*
28013661 ATTTTTAGTCTAAT-AATAAAAA
1 ATTTATAGTCTAATAAAT-AAAA
28013683 ATTTA
1 ATTTA
28013688 AAATCACTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (22 bp):
ATTTATAGTCTAATAAATAAAA
Found at i:28024365 original size:17 final size:17
Alignment explanation
Indices: 28024343--28024375 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28024333 GTTAGTGCAC
*
28024343 ATTGTCATTGCATTTTT
1 ATTGTCATTGAATTTTT
28024360 ATTGTCATTGAATTTT
1 ATTGTCATTGAATTTT
28024376 AATGTTAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.09, G:0.12, T:0.58
Consensus pattern (17 bp):
ATTGTCATTGAATTTTT
Found at i:28024426 original size:23 final size:23
Alignment explanation
Indices: 28024388--28024447 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
28024378 TGTTAGTGCA
*
28024388 TTGGGGGCAATACAAACTTTAAGT
1 TTGGGGG-AATGCAAACTTTAAGT
28024412 TTGGGGGAATGCAAACTTTAAGT
1 TTGGGGGAATGCAAACTTTAAGT
28024435 TTGGGGGAATGCA
1 TTGGGGGAATGCA
28024448 TATGGGTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 28 0.80
24 7 0.20
ACGTcount: A:0.30, C:0.10, G:0.32, T:0.28
Consensus pattern (23 bp):
TTGGGGGAATGCAAACTTTAAGT
Found at i:28026927 original size:50 final size:51
Alignment explanation
Indices: 28026803--28027044 Score: 204
Period size: 50 Copynumber: 4.7 Consensus size: 51
28026793 GATAATAACA
* ** * * *
28026803 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTC-T-TGTAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATATAG
* * ** *
28026852 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATAT-TGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATATAG
* * ** * * **
28026902 TGCCCATGCCATGTCCCAAACATGGTCTTACGGGGGACCTATCATCT-CGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATATAG
* * * *
28026952 TGCCAACGCCATGTCCCAAACATGGTCTTACGTGGGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--T--ATAG
28027008 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
28027045 TCTCATTCCC
Statistics
Matches: 155, Mismatches: 30, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
49 37 0.24
50 82 0.53
51 1 0.01
53 1 0.01
56 34 0.22
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (51 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATATAG
Found at i:28028600 original size:51 final size:50
Alignment explanation
Indices: 28028475--28028617 Score: 189
Period size: 50 Copynumber: 2.8 Consensus size: 50
28028465 GAAAATGATG
*
28028475 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAA
1 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATAATAA
* * * * * **
28028525 GTCGCATGTGTAGTACTATGTGCAGGATACTATGCGTACCGG-ATAATTTC
1 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATAA-TAA
28028575 GATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG
1 G-TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG
28028618 TCATATGCTC
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
49 3 0.04
50 39 0.50
51 36 0.46
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (50 bp):
GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATAATAA
Found at i:28035724 original size:25 final size:25
Alignment explanation
Indices: 28035709--28035777 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
28035699 ACTCTTATGC
28035709 GCTTACCGTTATTCAACTCGGAAGA
1 GCTTACCGTTATTCAACTCGGAAGA
* **
28035734 GCTTACCGTTATACATTTC-GAAGGA
1 GCTTACCGTTATTCAACTCGGAA-GA
*
28035759 GCTTACCGTT-TACAACTCG
1 GCTTACCGTTATTCAACTCG
28035778 TATGAGAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 9 0.24
25 28 0.76
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (25 bp):
GCTTACCGTTATTCAACTCGGAAGA
Found at i:28038042 original size:24 final size:24
Alignment explanation
Indices: 28038015--28038094 Score: 81
Period size: 25 Copynumber: 3.2 Consensus size: 24
28038005 GGTATGCTTT
28038015 TACGAGTT-GTAATCAGTAAGCTCA
1 TACGAGTTAGTAA-CAGTAAGCTCA
*
28038039 TACGAGTTGAGTAACGGTAAGCTCA
1 TACGAGTT-AGTAACAGTAAGCTCA
* * * *
28038064 TACGAGATGAATAACGGTAAGCTTA
1 TACGAG-TTAGTAACAGTAAGCTCA
28038089 TACGAG
1 TACGAG
28038095 CTAAGAATTG
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
24 8 0.16
25 36 0.73
26 5 0.10
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (24 bp):
TACGAGTTAGTAACAGTAAGCTCA
Found at i:28038063 original size:25 final size:25
Alignment explanation
Indices: 28038030--28038094 Score: 103
Period size: 25 Copynumber: 2.6 Consensus size: 25
28038020 GTTGTAATCA
* *
28038030 GTAAGCTCATACGAGTTGAGTAACG
1 GTAAGCTCATACGAGATGAATAACG
28038055 GTAAGCTCATACGAGATGAATAACG
1 GTAAGCTCATACGAGATGAATAACG
*
28038080 GTAAGCTTATACGAG
1 GTAAGCTCATACGAG
28038095 CTAAGAATTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.23
Consensus pattern (25 bp):
GTAAGCTCATACGAGATGAATAACG
Found at i:28038981 original size:15 final size:16
Alignment explanation
Indices: 28038955--28038985 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
28038945 AGATGAAAAC
28038955 TTTAATTTTTTATTTA
1 TTTAATTTTTTATTTA
28038971 TTTAA-TTTTTATTTA
1 TTTAATTTTTTATTTA
28038986 CTAATTTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTAATTTTTTATTTA
Found at i:28039972 original size:17 final size:17
Alignment explanation
Indices: 28039950--28039983 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28039940 TAACGGAGTT
28039950 TGACATTTACGAATATA
1 TGACATTTACGAATATA
28039967 TGACATTTACGAATATA
1 TGACATTTACGAATATA
28039984 CAAAGCCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
TGACATTTACGAATATA
Found at i:28045805 original size:25 final size:24
Alignment explanation
Indices: 28045777--28045843 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
28045767 TTAATGTACA
28045777 TGTATGCTCATACGAGCTCTAAATC
1 TGTATGCTCATACGAGCTCT-AATC
* * *
28045802 TGTATGCTCTTACTAGCTGTAATC
1 TGTATGCTCATACGAGCTCTAATC
* *
28045826 GGTAAGCTCATACGAGCT
1 TGTATGCTCATACGAGCT
28045844 AAGTAACGGT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
24 18 0.51
25 17 0.49
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.33
Consensus pattern (24 bp):
TGTATGCTCATACGAGCTCTAATC
Found at i:28045834 original size:24 final size:25
Alignment explanation
Indices: 28045782--28045887 Score: 85
Period size: 25 Copynumber: 4.3 Consensus size: 25
28045772 GTACATGTAT
* * *
28045782 GCTCATACGAGCT-CTAAATCTGTAT
1 GCTCATACGAGCTAGT-AATCGGTAA
* *
28045807 GCTCTTACTAGCT-GTAATCGGTAA
1 GCTCATACGAGCTAGTAATCGGTAA
28045831 GCTCATACGAGCTAAGTAA-CGGTAA
1 GCTCATACGAGCT-AGTAATCGGTAA
* * *
28045856 GCTCATGCGAGTTGAATAA-CGGTAA
1 GCTCATACGAGCT-AGTAATCGGTAA
28045881 GCTCATA
1 GCTCATA
28045888 TGAGTTGAGA
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
24 18 0.27
25 45 0.67
26 4 0.06
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (25 bp):
GCTCATACGAGCTAGTAATCGGTAA
Found at i:28045892 original size:25 final size:26
Alignment explanation
Indices: 28045820--28045895 Score: 102
Period size: 25 Copynumber: 3.0 Consensus size: 26
28045810 CTTACTAGCT
*
28045820 GTAATCGGTAAGCTCATACGAGCT-AA
1 GTAA-CGGTAAGCTCATACGAGTTGAA
*
28045846 GTAACGGTAAGCTCATGCGAGTTGAA
1 GTAACGGTAAGCTCATACGAGTTGAA
*
28045872 -TAACGGTAAGCTCATATGAGTTGA
1 GTAACGGTAAGCTCATACGAGTTGA
28045896 GAATCAGTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
25 39 0.87
26 6 0.13
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (26 bp):
GTAACGGTAAGCTCATACGAGTTGAA
Found at i:28047887 original size:55 final size:55
Alignment explanation
Indices: 28047820--28047931 Score: 170
Period size: 55 Copynumber: 2.0 Consensus size: 55
28047810 ACGAAACAAT
* *
28047820 AAGGGATTAAATTGAAAGAGACCGCAAGTTAGCAGCGTAAATTAGGAGAAGCGGG
1 AAGGGATAAAATTGAAAGAGACCGCAAGTTAGCAGCCTAAATTAGGAGAAGCGGG
* * * *
28047875 AAGGGATAAAATTGAAAGAGACTGCAAGTTAGTATCCTAAATTAGGAGAAGTGGG
1 AAGGGATAAAATTGAAAGAGACCGCAAGTTAGCAGCCTAAATTAGGAGAAGCGGG
28047930 AA
1 AA
28047932 AGCTAGAAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.42, C:0.09, G:0.30, T:0.19
Consensus pattern (55 bp):
AAGGGATAAAATTGAAAGAGACCGCAAGTTAGCAGCCTAAATTAGGAGAAGCGGG
Found at i:28049076 original size:23 final size:23
Alignment explanation
Indices: 28049046--28049094 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
28049036 ACATCATAAA
*
28049046 CTTGATTTATTCTTTCTGCCAAT
1 CTTGATTTATTCTTTATGCCAAT
*
28049069 CTTGATTTATTCTTTATGTCAAT
1 CTTGATTTATTCTTTATGCCAAT
28049092 CTT
1 CTT
28049095 TATTGTCAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.18, C:0.18, G:0.08, T:0.55
Consensus pattern (23 bp):
CTTGATTTATTCTTTATGCCAAT
Found at i:28051652 original size:15 final size:16
Alignment explanation
Indices: 28051622--28051655 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
28051612 TATTGTCCTC
28051622 AAGCAAGAAAACATAA
1 AAGCAAGAAAACATAA
*
28051638 AAGCAA-AAAATATAA
1 AAGCAAGAAAACATAA
28051653 AAG
1 AAG
28051656 ACAACCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.71, C:0.09, G:0.12, T:0.09
Consensus pattern (16 bp):
AAGCAAGAAAACATAA
Found at i:28058568 original size:37 final size:37
Alignment explanation
Indices: 28058518--28058592 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
28058508 ACGTTTAGAG
28058518 TGTGAATACTACAATCAAATATAAGAGTAGGTGGTTT
1 TGTGAATACTACAATCAAATATAAGAGTAGGTGGTTT
28058555 TGTGAATACTACAATCAAATATAAGAGTAGGTGGTTT
1 TGTGAATACTACAATCAAATATAAGAGTAGGTGGTTT
28058592 T
1 T
28058593 CACAAGTATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.33
Consensus pattern (37 bp):
TGTGAATACTACAATCAAATATAAGAGTAGGTGGTTT
Found at i:28065615 original size:43 final size:43
Alignment explanation
Indices: 28065554--28065714 Score: 182
Period size: 43 Copynumber: 3.7 Consensus size: 43
28065544 GCGTCGCTAA
*
28065554 CTTTAGCGGCGCTTTTCCCAGAAACGCCGCTAAAGACCAATAC
1 CTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGACCAATAC
* * * *
28065597 CTTTAACGGCGCTTTTCCCAAAAATGCCGCTAAAGAACAAGAC
1 CTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGACCAATAC
* * * *
28065640 CTTTAGCGACGCTTTTCCTACAAACGTCGCTAAAG-CTC-ATGAC
1 CTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGAC-CAAT-AC
* * *
28065683 CTTTAGCGGCGCTTCTACTAAAAACGCCGCTA
1 CTTTAGCGGCGCTTTTCCCAAAAACGCCGCTA
28065715 TAACATTGAC
Statistics
Matches: 98, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
42 1 0.01
43 97 0.99
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGACCAATAC
Found at i:28065685 original size:86 final size:86
Alignment explanation
Indices: 28065554--28065714 Score: 209
Period size: 86 Copynumber: 1.9 Consensus size: 86
28065544 GCGTCGCTAA
* * * *
28065554 CTTTAGCGGCGCTTTTCCCAGAAACGCCGCTAAAGACCAATACCTTTAACGGCGCTTTTCCCAAA
1 CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGACCAATACCTTTAACGGCGCTTCTACCAAA
*
28065619 AATGCCGCTAAAGAACAAGAC
66 AACGCCGCTAAAGAACAAGAC
* * * *
28065640 CTTTAGCGACGCTTTTCCTACAAACGTCGCTAAAG-CTC-ATGACCTTTAGCGGCGCTTCTACTA
1 CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGAC-CAAT-ACCTTTAACGGCGCTTCTACCA
28065703 AAAACGCCGCTA
64 AAAACGCCGCTA
28065715 TAACATTGAC
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
85 3 0.05
86 61 0.95
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (86 bp):
CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGACCAATACCTTTAACGGCGCTTCTACCAAA
AACGCCGCTAAAGAACAAGAC
Found at i:28066740 original size:20 final size:22
Alignment explanation
Indices: 28066701--28066740 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
28066691 TCTTATATTA
*
28066701 ATTTTCTTTTATGTCATTTAAT
1 ATTTTCTTTTATATCATTTAAT
28066723 ATTTT-TTTTATATC-TTTA
1 ATTTTCTTTTATATCATTTA
28066741 CAAGTTGTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 8 0.47
22 5 0.29
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.68
Consensus pattern (22 bp):
ATTTTCTTTTATATCATTTAAT
Found at i:28071810 original size:7 final size:7
Alignment explanation
Indices: 28071800--28071867 Score: 68
Period size: 7 Copynumber: 9.4 Consensus size: 7
28071790 TCGTGAAATA
28071800 TAAACCC
1 TAAACCC
28071807 TAAACCAC
1 TAAACC-C
28071815 T-AACCAC
1 TAAACC-C
*
28071822 TAAATCC
1 TAAACCC
28071829 TAAACCCC
1 TAAA-CCC
*
28071837 TAAACCT
1 TAAACCC
28071844 TAAACCC
1 TAAACCC
28071851 T-AACCC
1 TAAACCC
28071857 TTAAACCC
1 -TAAACCC
28071865 TAA
1 TAA
28071868 CACCTAACTG
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
6 5 0.10
7 31 0.60
8 16 0.31
ACGTcount: A:0.43, C:0.38, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:28071847 original size:22 final size:23
Alignment explanation
Indices: 28071800--28071867 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 23
28071790 TCGTGAAATA
*
28071800 TAAACCCTAAACCACT-AACCAC
1 TAAACCCTAAACCCCTAAACCAC
* *
28071822 TAAATCCTAAACCCCTAAACC-T
1 TAAACCCTAAACCCCTAAACCAC
*
28071844 TAAACCCT-AACCCTTAAACC-C
1 TAAACCCTAAACCCCTAAACCAC
28071865 TAA
1 TAA
28071868 CACCTAACTG
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
21 14 0.36
22 21 0.54
23 4 0.10
ACGTcount: A:0.43, C:0.38, G:0.00, T:0.19
Consensus pattern (23 bp):
TAAACCCTAAACCCCTAAACCAC
Found at i:28071875 original size:7 final size:7
Alignment explanation
Indices: 28071831--28071900 Score: 68
Period size: 7 Copynumber: 10.0 Consensus size: 7
28071821 CTAAATCCTA
28071831 AACCCCT
1 AACCCCT
* *
28071838 AAACCTT
1 AACCCCT
*
28071845 AAACCCT
1 AACCCCT
*
28071852 AACCCTT
1 AACCCCT
*
28071859 AAACCCT
1 AACCCCT
*
28071866 AACACCT
1 AACCCCT
**
28071873 AACTGCT
1 AACCCCT
28071880 AACCCCT
1 AACCCCT
28071887 AACCCCT
1 AACCCCT
28071894 AACCCCT
1 AACCCCT
28071901 CTTTTACAAT
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.34, C:0.46, G:0.01, T:0.19
Consensus pattern (7 bp):
AACCCCT
Found at i:28072109 original size:14 final size:14
Alignment explanation
Indices: 28072090--28072123 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28072080 CTAATTAATC
*
28072090 TAAACCCTAAACTA
1 TAAACCCTAAACCA
*
28072104 TAAACCCTAACCCA
1 TAAACCCTAAACCA
28072118 TAAACC
1 TAAACC
28072124 TTATTTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.18
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:28072164 original size:68 final size:70
Alignment explanation
Indices: 28072040--28072169 Score: 219
Period size: 68 Copynumber: 1.9 Consensus size: 70
28072030 CCCTTAACTA
* *
28072040 CTAACCCCTAAACCTTATTTAATATATAAATTAAAAAATACTAATTAATCTAAACCCTAAACTAT
1 CTAACCCATAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACTAT
28072105 AAACC
66 AAACC
*
28072110 CTAACCCATAAACCTTATTT-A-ATATAAATTAAAATACACTAATTAATCTAAACCCTAAAC
1 CTAACCCATAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAAC
28072170 CTTAACCTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
68 37 0.65
69 1 0.02
70 19 0.33
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (70 bp):
CTAACCCATAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACTAT
AAACC
Found at i:28072583 original size:41 final size:41
Alignment explanation
Indices: 28072526--28072708 Score: 267
Period size: 41 Copynumber: 4.5 Consensus size: 41
28072516 GCACTTTTTT
28072526 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTCC
1 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTCC
* *
28072567 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTTTC
1 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTCC
* * *
28072608 AAAAACGCCGTTAAAGCCCTAAGCATTAGTGGCGCTTCTCC
1 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTCC
* * * **
28072649 AAAAACACCGCTAAATCCCTGAGCATTAGCGGCGCTTTTTT
1 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTCC
*
28072690 AAAAACGCCACTAAAGCCC
1 AAAAACGCCGCTAAAGCCC
28072709 CGAAAGGTCA
Statistics
Matches: 124, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 124 1.00
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.20
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTCC
Found at i:28072660 original size:82 final size:82
Alignment explanation
Indices: 28072519--28072708 Score: 317
Period size: 82 Copynumber: 2.3 Consensus size: 82
28072509 TTTTGTGGCA
* *
28072519 CTTTTTTAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGC
1 CTTTTTTAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTCTCCAAAAACACCGCTAAAGC
28072584 CCTGAGCATTAGCGGCG
66 CCTGAGCATTAGCGGCG
* * * *
28072601 CTTTTTCAAAAACGCCGTTAAAGCCCTAAGCATTAGTGGCGCTTCTCCAAAAACACCGCTAAATC
1 CTTTTTTAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTCTCCAAAAACACCGCTAAAGC
28072666 CCTGAGCATTAGCGGCG
66 CCTGAGCATTAGCGGCG
*
28072683 CTTTTTTAAAAACGCCACTAAAGCCC
1 CTTTTTTAAAAACGCCGCTAAAGCCC
28072709 CGAAAGGTCA
Statistics
Matches: 99, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 99 1.00
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (82 bp):
CTTTTTTAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTCTCCAAAAACACCGCTAAAGC
CCTGAGCATTAGCGGCG
Found at i:28072810 original size:20 final size:19
Alignment explanation
Indices: 28072771--28072811 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
28072761 GTAAAAACGC
* *
28072771 CGCTAATGCTCTTTTTTAG
1 CGCTAATGCTCATCTTTAG
28072790 CGCTAATGCTCGATCTTTAG
1 CGCTAATGCTC-ATCTTTAG
28072810 CG
1 CG
28072812 GCGTTTTGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (19 bp):
CGCTAATGCTCATCTTTAG
Found at i:28074663 original size:56 final size:50
Alignment explanation
Indices: 28074542--28074678 Score: 157
Period size: 50 Copynumber: 2.6 Consensus size: 50
28074532 ATCGGTTCTT
* **
28074542 ATGCCATGTCCCAGACATGGTCTTACGAGGGACCTCTCATCTTGGTACCA
1 ATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATCTTAATACCA
** *
28074592 GCGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATAACCTCAATAATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCAT---CT---TAATACCA
*
28074648 ATGCCATGTCCCAGACATGGTCTTACATGGG
1 ATGCCATGTCCCAGACATGGTCTTACGTGGG
28074679 GTCTCATCCC
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
50 37 0.51
53 2 0.03
56 33 0.46
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.25
Consensus pattern (50 bp):
ATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATCTTAATACCA
Found at i:28077777 original size:19 final size:19
Alignment explanation
Indices: 28077753--28077800 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
28077743 ATCAAATGAT
28077753 CTTTTGCTGGAGTGTTTGG
1 CTTTTGCTGGAGTGTTTGG
28077772 CTTTTGCTGGAGTGTTTGG
1 CTTTTGCTGGAGTGTTTGG
28077791 CTTTTGCTGG
1 CTTTTGCTGG
28077801 GCATTCATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.04, C:0.12, G:0.35, T:0.48
Consensus pattern (19 bp):
CTTTTGCTGGAGTGTTTGG
Found at i:28080583 original size:25 final size:24
Alignment explanation
Indices: 28080532--28080583 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
28080522 CTACTCAAAT
28080532 TCCTCAAATCTCTCTTAAAATCAC
1 TCCTCAAATCTCTCTTAAAATCAC
* *
28080556 TCCTCCAATCCTCTCCTTGAAATC-C
1 TCCTCAAAT-CTCT-CTTAAAATCAC
28080581 TCC
1 TCC
28080584 ATGATCCACT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.33
25 8 0.33
26 8 0.33
ACGTcount: A:0.25, C:0.40, G:0.02, T:0.33
Consensus pattern (24 bp):
TCCTCAAATCTCTCTTAAAATCAC
Found at i:28081287 original size:18 final size:19
Alignment explanation
Indices: 28081247--28081288 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
28081237 TAAAAAGGAT
* *
28081247 TAAAAATAAATAACTAACA
1 TAAAAATAAAGAAATAACA
28081266 -AAAAATAAAGAAATAA-A
1 TAAAAATAAAGAAATAACA
28081283 TAAAAA
1 TAAAAA
28081289 ATGAATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.17
Consensus pattern (19 bp):
TAAAAATAAAGAAATAACA
Found at i:28086575 original size:15 final size:16
Alignment explanation
Indices: 28086546--28086575 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28086536 CAAACATGAT
28086546 TTAACACATTATCAAA
1 TTAACACATTATCAAA
28086562 TTAACACA-TATCAA
1 TTAACACATTATCAA
28086576 CAAGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:28087740 original size:25 final size:25
Alignment explanation
Indices: 28087712--28087781 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
28087702 CTGTACATGT
* *
28087712 ATGCTCACACGAGCTGTGACTCAGA
1 ATGCTCACATGAGCTGTGAATCAGA
*
28087737 ATGCTCACATGAGCTATGAATCAGA
1 ATGCTCACATGAGCTGTGAATCAGA
*
28087762 ATGCTTACATGAGCTGTGAA
1 ATGCTCACATGAGCTGTGAA
28087782 AATGGGCCTA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.24
Consensus pattern (25 bp):
ATGCTCACATGAGCTGTGAATCAGA
Found at i:28089625 original size:6 final size:6
Alignment explanation
Indices: 28089614--28089656 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
28089604 AGTGCAATTA
28089614 GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG G
1 GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG G
28089657 TGCTATCAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (6 bp):
GGAGAG
Found at i:28097332 original size:8 final size:8
Alignment explanation
Indices: 28097288--28097339 Score: 51
Period size: 8 Copynumber: 7.0 Consensus size: 8
28097278 NAAAATTTAG
28097288 AATATAT-
1 AATATATA
28097295 AATATATA
1 AATATATA
28097303 AATA-A-A
1 AATATATA
28097309 AATGATA-A
1 AAT-ATATA
*
28097317 AAT-GATA
1 AATATATA
28097324 AATATATA
1 AATATATA
28097332 AATATATA
1 AATATATA
28097340 TAAAAGAACT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
6 5 0.13
7 13 0.34
8 20 0.53
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (8 bp):
AATATATA
Found at i:28097462 original size:17 final size:17
Alignment explanation
Indices: 28097440--28097483 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
28097430 TAAAAACTTC
*
28097440 TTTATATTTTTTATTAA
1 TTTATAATTTTTATTAA
*
28097457 TTTATAATTTTTATTTA
1 TTTATAATTTTTATTAA
*
28097474 TTTTTAATTT
1 TTTATAATTT
28097484 CATAATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTATAATTTTTATTAA
Found at i:28097643 original size:18 final size:18
Alignment explanation
Indices: 28097620--28097671 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
28097610 AAATTTACAC
28097620 TTTTTATTAATTTATATA
1 TTTTTATTAATTTATATA
***
28097638 TTTTTAAGGATTT-T-TA
1 TTTTTATTAATTTATATA
28097654 TTTTT-TTAATTTATATA
1 TTTTTATTAATTTATATA
28097671 T
1 T
28097672 GCTACGTGTC
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
15 4 0.15
16 8 0.31
17 4 0.15
18 10 0.38
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (18 bp):
TTTTTATTAATTTATATA
Found at i:28099778 original size:11 final size:11
Alignment explanation
Indices: 28099762--28099786 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28099752 TAGTATTATA
28099762 ATTAGTGCATC
1 ATTAGTGCATC
28099773 ATTAGTGCATC
1 ATTAGTGCATC
28099784 ATT
1 ATT
28099787 TTTCACAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (11 bp):
ATTAGTGCATC
Done.