Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 85 of 168
Found at i:25020795 original size:17 final size:18
Alignment explanation
Indices: 25020765--25020804 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
25020755 CGTGCTTTTT
25020765 ATATATATTATATATTAA
1 ATATATATTATATATTAA
*
25020783 ATAT-TATTCTATATTAA
1 ATATATATTATATATTAA
*
25020800 TTATA
1 ATATA
25020805 ACTTAATTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATATATTATATATTAA
Found at i:25024476 original size:14 final size:14
Alignment explanation
Indices: 25024457--25024484 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
25024447 TCAATGACTT
25024457 ATATTAATTTATCA
1 ATATTAATTTATCA
25024471 ATATTAATTTATCA
1 ATATTAATTTATCA
25024485 TTCCTTGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATTAATTTATCA
Found at i:25024835 original size:38 final size:38
Alignment explanation
Indices: 25024784--25024861 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
25024774 TGTGGATATA
*
25024784 AAGTAAAAGGAATGGAAGTAAAAGTATCAAGTTGTCAC
1 AAGTAAAAGGAATGAAAGTAAAAGTATCAAGTTGTCAC
25024822 AAGTAAAAGGAATGAAAGTAAAAGTATCAAGTTGTCAC
1 AAGTAAAAGGAATGAAAGTAAAAGTATCAAGTTGTCAC
25024860 AA
1 AA
25024862 TTTATATTGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.50, C:0.08, G:0.22, T:0.21
Consensus pattern (38 bp):
AAGTAAAAGGAATGAAAGTAAAAGTATCAAGTTGTCAC
Found at i:25033963 original size:20 final size:20
Alignment explanation
Indices: 25033940--25033986 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
25033930 GGGTTGAGGT
25033940 TGAGCTGAATTCAACTCGAA
1 TGAGCTGAATTCAACTCGAA
* * * *
25033960 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTCAACTCGAA
25033980 TGAGCTG
1 TGAGCTG
25033987 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTCAACTCGAA
Found at i:25039122 original size:16 final size:15
Alignment explanation
Indices: 25039101--25039130 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
25039091 AGAACGAGTC
25039101 AAAAAGAAAAAGAAAT
1 AAAAAG-AAAAGAAAT
25039117 AAAAAGAAAAGAAA
1 AAAAAGAAAAGAAA
25039131 GACAAGAGAT
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:0.83, C:0.00, G:0.13, T:0.03
Consensus pattern (15 bp):
AAAAAGAAAAGAAAT
Found at i:25051659 original size:25 final size:26
Alignment explanation
Indices: 25051631--25051706 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 26
25051621 TGCTCGTGAA
25051631 AAAAAAAAAGAGAAAAGGAA-AAG-AG
1 AAAAAAAAA-AGAAAAGGAACAAGAAG
*
25051656 AAAAAAGAATA-AAAA-GAACAAGAAG
1 AAAAAA-AAAAGAAAAGGAACAAGAAG
*
25051681 AAAAAAAAAAGAAAA-GAAGAAGAAG
1 AAAAAAAAAAGAAAAGGAACAAGAAG
25051706 A
1 A
25051707 GAATATGCAC
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
23 3 0.07
24 10 0.23
25 29 0.66
26 2 0.05
ACGTcount: A:0.78, C:0.01, G:0.20, T:0.01
Consensus pattern (26 bp):
AAAAAAAAAAGAAAAGGAACAAGAAG
Found at i:25051670 original size:37 final size:37
Alignment explanation
Indices: 25051629--25051701 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
25051619 AATGCTCGTG
*
25051629 AAAAAAAAAAAG-AGAAAAGGAAAAGAGAAAA-AAGAAT
1 AAAAAAAAAAAGAAGAAAA--AAAAAAGAAAAGAAGAAT
* *
25051666 AAAAAGAACAAGAAGAAAAAAAAAAGAAAAGAAGAA
1 AAAAAAAAAAAGAAGAAAAAAAAAAGAAAAGAAGAA
25051702 GAAGAGAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
36 10 0.32
37 15 0.48
38 6 0.19
ACGTcount: A:0.79, C:0.01, G:0.18, T:0.01
Consensus pattern (37 bp):
AAAAAAAAAAAGAAGAAAAAAAAAAGAAAAGAAGAAT
Found at i:25062057 original size:20 final size:20
Alignment explanation
Indices: 25062021--25062059 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
25062011 TGGCGCCAAT
25062021 TCTGTAAGTGTTCTGAAAAA
1 TCTGTAAGTGTTCTGAAAAA
*
25062041 TCTGATAAGT-TTTTGAAAA
1 TCTG-TAAGTGTTCTGAAAA
25062060 TATGAGTAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (20 bp):
TCTGTAAGTGTTCTGAAAAA
Found at i:25066003 original size:198 final size:198
Alignment explanation
Indices: 25065665--25066071 Score: 771
Period size: 198 Copynumber: 2.1 Consensus size: 198
25065655 GTAGGTTAAG
*
25065665 GCTAAGCATCAGTTACCTTTAGGTTTACTGCAATCGGTTAAGATACCGTTATGGAAATGGGAGCG
1 GCTAAGCATCAGTTACCTTCAGGTTTACTGCAATCGGTTAAGATACCGTTATGGAAATGGGAGCG
*
25065730 AGTAACGATGGGCTTCGTTAGTGGGTTGCCTCTAACACTCACTAAGAAAGATTTTGTCTGGGTCA
66 AGTAACGATGGGCTTCGTTAGTGGGTAGCCTCTAACACTCACTAAGAAAGATTTTGTCTGGGTCA
25065795 TCGTGGATTAATTAACCAAGTCTGCTCATTTCATCCTGGTAAGGACAAAGTTTTCTCTTCAGAAA
131 TCGTGGATTAATTAACCAAGTCTGCTCATTTCATCCTGGTAAGGACAAAGTTTTCTCTTCAGAAA
25065860 TTA
196 TTA
*
25065863 GCTAAGCATCAGTTACCTTCAGGTTTACTGCAATTGGTTAAGATACCGTTATGGAAATGGGAGCG
1 GCTAAGCATCAGTTACCTTCAGGTTTACTGCAATCGGTTAAGATACCGTTATGGAAATGGGAGCG
*
25065928 AGTAACGATGGGCTTCGTTAGTGGGTAGCCTCTAACACTCACTAAGAAAGATTTTGTCTGGGTTA
66 AGTAACGATGGGCTTCGTTAGTGGGTAGCCTCTAACACTCACTAAGAAAGATTTTGTCTGGGTCA
25065993 TCGTGGATTAATTAACCAAGTCTGCTCATTTCATCCTGGTAAGGACAAAGTTTTCTCTTCAGAAA
131 TCGTGGATTAATTAACCAAGTCTGCTCATTTCATCCTGGTAAGGACAAAGTTTTCTCTTCAGAAA
25066058 TTA
196 TTA
25066061 GCTAAGC-TCAG
1 GCTAAGCATCAG
25066072 CATATCAAAA
Statistics
Matches: 205, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
197 4 0.02
198 201 0.98
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (198 bp):
GCTAAGCATCAGTTACCTTCAGGTTTACTGCAATCGGTTAAGATACCGTTATGGAAATGGGAGCG
AGTAACGATGGGCTTCGTTAGTGGGTAGCCTCTAACACTCACTAAGAAAGATTTTGTCTGGGTCA
TCGTGGATTAATTAACCAAGTCTGCTCATTTCATCCTGGTAAGGACAAAGTTTTCTCTTCAGAAA
TTA
Found at i:25070394 original size:49 final size:49
Alignment explanation
Indices: 25070259--25070368 Score: 220
Period size: 49 Copynumber: 2.2 Consensus size: 49
25070249 CCATCCGATC
25070259 GTTGTTGGGCCACCTAGGATGGTAAAATGTAAGAATAGTGAAAGTCATT
1 GTTGTTGGGCCACCTAGGATGGTAAAATGTAAGAATAGTGAAAGTCATT
25070308 GTTGTTGGGCCACCTAGGATGGTAAAATGTAAGAATAGTGAAAGTCATT
1 GTTGTTGGGCCACCTAGGATGGTAAAATGTAAGAATAGTGAAAGTCATT
25070357 GTTGTTGGGCCA
1 GTTGTTGGGCCA
25070369 TTCAGGATGG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 61 1.00
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.29
Consensus pattern (49 bp):
GTTGTTGGGCCACCTAGGATGGTAAAATGTAAGAATAGTGAAAGTCATT
Found at i:25073807 original size:21 final size:21
Alignment explanation
Indices: 25073781--25073843 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
25073771 TTGGTATTTG
25073781 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
25073802 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
25073823 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
25073844 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:25081157 original size:20 final size:20
Alignment explanation
Indices: 25081132--25081178 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
25081122 AACTAAAGTA
*
25081132 AGCTAAAAATGAGCTCATTG
1 AGCTAAAAACGAGCTCATTG
*
25081152 AGCTAAGAACGAGCTCATTG
1 AGCTAAAAACGAGCTCATTG
25081172 AGCTAAA
1 AGCTAAA
25081179 GTTGAGCTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (20 bp):
AGCTAAAAACGAGCTCATTG
Found at i:25082907 original size:12 final size:12
Alignment explanation
Indices: 25082890--25082914 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25082880 TTTCACTCGT
25082890 CTCTTTTTCAAA
1 CTCTTTTTCAAA
25082902 CTCTTTTTCAAA
1 CTCTTTTTCAAA
25082914 C
1 C
25082915 CTTCTCTCTT
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:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (12 bp):
CTCTTTTTCAAA
Found at i:25085457 original size:20 final size:20
Alignment explanation
Indices: 25085432--25085505 Score: 91
Period size: 20 Copynumber: 3.8 Consensus size: 20
25085422 CATGTGGTTC
25085432 AGCTCATTCGAGCTCAAGTT
1 AGCTCATTCGAGCTCAAGTT
* *
25085452 AGCTCATTAGAGCTCAAGTC
1 AGCTCATTCGAGCTCAAGTT
25085472 AG-TGCATTCGAGCTCAA-TT
1 AGCT-CATTCGAGCTCAAGTT
25085491 CAGCTCATT-GAGCTC
1 -AGCTCATTCGAGCTC
25085506 GTTATTAGCT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
19 8 0.17
20 38 0.81
21 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (20 bp):
AGCTCATTCGAGCTCAAGTT
Found at i:25088961 original size:25 final size:25
Alignment explanation
Indices: 25088927--25089045 Score: 127
Period size: 25 Copynumber: 4.8 Consensus size: 25
25088917 TCTTGTACAT
25088927 GTATGCTCATACGAGCTGTGAA-TCG
1 GTATGCTCATACGAGCTGT-AAGTCG
*
25088952 GTATGCTCATACGAGCTGT-AGACCG
1 GTATGCTCATACGAGCTGTAAG-TCG
* * *
25088977 ATATGCTC-TCACGAGCTATAAGTTG
1 GTATGCTCAT-ACGAGCTGTAAGTCG
* *
25089002 ATATGCTCACACGAGCTGTAAGTCG
1 GTATGCTCATACGAGCTGTAAGTCG
*
25089027 GTATGCTCACACGAGCTGT
1 GTATGCTCATACGAGCTGT
25089046 GGAGTATCCA
Statistics
Matches: 80, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
23 1 0.01
24 1 0.01
25 76 0.95
26 2 0.03
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (25 bp):
GTATGCTCATACGAGCTGTAAGTCG
Found at i:25095718 original size:27 final size:27
Alignment explanation
Indices: 25095366--25095706 Score: 398
Period size: 27 Copynumber: 12.6 Consensus size: 27
25095356 TAATGGCCCT
*
25095366 AAATTACCGAAATACCCTCAATGGGTA
1 AAATTACCGAAATACCCTCGATGGGTA
* * *
25095393 AACTTACCAAAATACCCTCGATGGGAA
1 AAATTACCGAAATACCCTCGATGGGTA
* * *
25095420 AAATTACTGAAATACCTTTGATGGGTA
1 AAATTACCGAAATACCCTCGATGGGTA
* * *
25095447 AAACTACTGAAATACCCTCGATAGGTA
1 AAATTACCGAAATACCCTCGATGGGTA
*
25095474 AAACTACCGAAATACCCTCGATGGGTA
1 AAATTACCGAAATACCCTCGATGGGTA
* * ** **
25095501 AAATGATCGAAATACCCTTAATACGTA
1 AAATTACCGAAATACCCTCGATGGGTA
* * *
25095528 AAATGACCAAAATACCCTCGATGGATA
1 AAATTACCGAAATACCCTCGATGGGTA
*
25095555 AAATTATCGAAATACCCTCGATGGGTA
1 AAATTACCGAAATACCCTCGATGGGTA
* **
25095582 AAATTACTGAAATACCCTTAATGGGTA
1 AAATTACCGAAATACCCTCGATGGGTA
* *
25095609 AAATTACAGAAATACCCTTGATGGGTA
1 AAATTACCGAAATACCCTCGATGGGTA
*
25095636 AAATTACCAAAATACCCTCG-TAGGGTA
1 AAATTACCGAAATACCCTCGAT-GGGTA
*
25095663 AAATTACTGAAATACCC-CTGATGGGTA
1 AAATTACCGAAATACCCTC-GATGGGTA
25095690 AAATTACCGAAATACCC
1 AAATTACCGAAATACCC
25095707 CCATAGGTTA
Statistics
Matches: 265, Mismatches: 46, Indels: 6
0.84 0.15 0.02
Matches are distributed among these distances:
26 2 0.01
27 262 0.99
28 1 0.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (27 bp):
AAATTACCGAAATACCCTCGATGGGTA
Found at i:25099726 original size:50 final size:50
Alignment explanation
Indices: 25099598--25100041 Score: 595
Period size: 50 Copynumber: 8.9 Consensus size: 50
25099588 GATAATAACA
* * ** * * *
25099598 TGCCAAAGCCATGTCCCAGACATGGTTTTACATGGGATGTTTCCTGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * * * * ** * *
25099647 TGCCAATGCCATATCCTAGATATGCTCTTACATGGGAGTTCTCATATTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * **
25099697 TGCCCATGCCATGTCCCATACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
25099747 TGCCAACGCCATGCCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
25099797 TGCCAACGGCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
25099847 TGCCAACGCCATGTCCCAGACATGGTCTTATATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
25099897 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
25099947 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
25099997 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCAT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT
25100042 AATTTTAGTA
Statistics
Matches: 348, Mismatches: 45, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
49 36 0.10
50 312 0.90
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:25107295 original size:25 final size:25
Alignment explanation
Indices: 25107231--25107299 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
25107221 TCTTGCACAT
25107231 GTATGCTCAT-ACGAGCTATGAATCG
1 GTATGCTC-TCACGAGCTATGAATCG
* *
25107256 GTATGCT-TACTCGAGCTGT-AGATCG
1 GTATGCTCT-CACGAGCTATGA-ATCG
25107281 GTATGCTCTCACGAGCTAT
1 GTATGCTCTCACGAGCTAT
25107300 AAGTTCGTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
23 1 0.03
24 1 0.03
25 33 0.92
26 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (25 bp):
GTATGCTCTCACGAGCTATGAATCG
Found at i:25107349 original size:25 final size:25
Alignment explanation
Indices: 25107281--25107339 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
25107271 CTGTAGATCG
* * * *
25107281 GTATGCTCTCACGAGCTATAAGTTC
1 GTATGCTCACACAAGTTGTAAGTTC
*
25107306 GTATGCTCACACAAGTTGTAAGTTG
1 GTATGCTCACACAAGTTGTAAGTTC
25107331 GTATGCTCA
1 GTATGCTCA
25107340 GATGAGTTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.32
Consensus pattern (25 bp):
GTATGCTCACACAAGTTGTAAGTTC
Found at i:25113102 original size:40 final size:40
Alignment explanation
Indices: 25113016--25113120 Score: 133
Period size: 40 Copynumber: 2.7 Consensus size: 40
25113006 TTACCGAAAT
*
25113016 CATTGTTATAATTATTGTAATTAT-A-ATTTACGATCAAA
1 CATTATTATAATTATTGTAATTATAATATTTACGATCAAA
* * * * *
25113054 TATTATTATAACTATTGTAATTGTAATATTTTCGGTCAAA
1 CATTATTATAATTATTGTAATTATAATATTTACGATCAAA
*
25113094 CATTATTATAATTATGGTAATTATAAT
1 CATTATTATAATTATTGTAATTATAAT
25113121 TATAATATTT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 20 0.36
39 1 0.02
40 34 0.62
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (40 bp):
CATTATTATAATTATTGTAATTATAATATTTACGATCAAA
Found at i:25116607 original size:16 final size:16
Alignment explanation
Indices: 25116586--25116617 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
25116576 ATTTATTGGG
25116586 CCTAATACATACTGAT
1 CCTAATACATACTGAT
25116602 CCTAATACATACTGAT
1 CCTAATACATACTGAT
25116618 ATATGTGGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (16 bp):
CCTAATACATACTGAT
Found at i:25126874 original size:15 final size:15
Alignment explanation
Indices: 25126851--25126888 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
25126841 TACCATCTCA
*
25126851 TTCTTTTTTTTTCTT
1 TTCTCTTTTTTTCTT
25126866 TTCTC-TTTTTTCTT
1 TTCTCTTTTTTTCTT
25126880 TT-TCTTTTT
1 TTCTCTTTTT
25126889 GCCACAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 15 0.71
15 4 0.19
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTCTCTTTTTTTCTT
Found at i:25126876 original size:14 final size:13
Alignment explanation
Indices: 25126857--25126888 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
25126847 CTCATTCTTT
25126857 TTTTTTCTTTTCTC
1 TTTTTTCTTTT-TC
25126871 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
25126884 TTTTT
1 TTTTT
25126889 GCCACAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:25129109 original size:11 final size:11
Alignment explanation
Indices: 25129093--25129118 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
25129083 AGAAGATTGT
25129093 AAAAAAATCAA
1 AAAAAAATCAA
25129104 AAAAAAATCAA
1 AAAAAAATCAA
25129115 AAAA
1 AAAA
25129119 CAGGGTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.08, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAAAATCAA
Found at i:25166839 original size:18 final size:19
Alignment explanation
Indices: 25166794--25166842 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
25166784 GAATATTTAC
*
25166794 ATAAAAATTAAACTAAGTAA
1 ATAAAAA-TAAACTAAATAA
25166814 A-AATAAATAAA-TAAATAA
1 ATAA-AAATAAACTAAATAA
25166832 ATAAAAATAAA
1 ATAAAAATAAA
25166843 AATAAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 8 0.31
20 4 0.15
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (19 bp):
ATAAAAATAAACTAAATAA
Found at i:25168041 original size:13 final size:13
Alignment explanation
Indices: 25168023--25168047 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25168013 ATATAATCAG
25168023 ATAAATTGTAAAA
1 ATAAATTGTAAAA
25168036 ATAAATTGTAAA
1 ATAAATTGTAAA
25168048 TCTATTAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (13 bp):
ATAAATTGTAAAA
Found at i:25172454 original size:41 final size:41
Alignment explanation
Indices: 25172409--25172521 Score: 127
Period size: 41 Copynumber: 2.8 Consensus size: 41
25172399 AATAATGACG
* * * * *
25172409 AATTGTACATAAGTGTCCCTGTTTGTACTTCGATACCCTTC
1 AATTGTACATACGTGCCCCTGTTTATACTTCGATACCCCTA
* * *
25172450 AATTGTACATACGTGCCCCTATGTATACTTCGGTACCCCTA
1 AATTGTACATACGTGCCCCTGTTTATACTTCGATACCCCTA
** *
25172491 AATTACACATACGTGCCCCTGTTTAGACTTC
1 AATTGTACATACGTGCCCCTGTTTATACTTC
25172522 AATAATTCTG
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.35
Consensus pattern (41 bp):
AATTGTACATACGTGCCCCTGTTTATACTTCGATACCCCTA
Found at i:25176874 original size:30 final size:30
Alignment explanation
Indices: 25176818--25176876 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
25176808 ATGCGAGCTG
* *
25176818 AATTAGCTCATTTCCATTTCATTGAACTCC
1 AATTAGCTCATTTCCACTCCATTGAACTCC
25176848 AATTAGCTCATTTCCAGCTCCA-TGAACTC
1 AATTAGCTCATTTCCA-CTCCATTGAACTC
25176877 ATTTCAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 23 0.88
31 3 0.12
ACGTcount: A:0.27, C:0.29, G:0.08, T:0.36
Consensus pattern (30 bp):
AATTAGCTCATTTCCACTCCATTGAACTCC
Found at i:25177158 original size:25 final size:25
Alignment explanation
Indices: 25177124--25177173 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
25177114 AATTTAATAC
25177124 TTAGTTAATTAATTTGTCTAGTTAT
1 TTAGTTAATTAATTTGTCTAGTTAT
25177149 TTAGTTAATTAATTTGTCTAGTTAT
1 TTAGTTAATTAATTTGTCTAGTTAT
25177174 ATTACATCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.12, T:0.56
Consensus pattern (25 bp):
TTAGTTAATTAATTTGTCTAGTTAT
Found at i:25182227 original size:41 final size:41
Alignment explanation
Indices: 25182182--25182384 Score: 253
Period size: 41 Copynumber: 5.0 Consensus size: 41
25182172 CATTATTTCG
*
25182182 ACTTCGGTACCCCTGAAATGCACATACGTGCCCCTGTTTGT
1 ACTTCGGTACCCCTGAATTGCACATACGTGCCCCTGTTTGT
* * *
25182223 ACTTCAGTACCCCTGAATTGTACATACATGCCCCTGTTTGT
1 ACTTCGGTACCCCTGAATTGCACATACGTGCCCCTGTTTGT
* * * * *
25182264 ACTTTGGTACCACTAAATTGCACATACGTGCCCCTATTTTT
1 ACTTCGGTACCCCTGAATTGCACATACGTGCCCCTGTTTGT
* * * *
25182305 ACTTCGGTACACGTGAATTGGACATACATGCCCCTGTTTGT
1 ACTTCGGTACCCCTGAATTGCACATACGTGCCCCTGTTTGT
* * * *
25182346 ACTTTGTTACCCCTGAATTGCACATATGTGCCCTTGTTT
1 ACTTCGGTACCCCTGAATTGCACATACGTGCCCCTGTTT
25182385 AGACTTTGGT
Statistics
Matches: 133, Mismatches: 29, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 133 1.00
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (41 bp):
ACTTCGGTACCCCTGAATTGCACATACGTGCCCCTGTTTGT
Found at i:25182237 original size:20 final size:19
Alignment explanation
Indices: 25182212--25182267 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 19
25182202 CACATACGTG
25182212 CCCCTGTTTGTACTTCAGTA
1 CCCCTGTTTGTACTTCA-TA
* * *
25182232 CCCCTGAATTGTACATACATG
1 CCCCTG-TTTGTAC-TTCATA
25182253 CCCCTGTTTGTACTT
1 CCCCTGTTTGTACTT
25182268 TGGTACCACT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
19 1 0.03
20 12 0.41
21 13 0.45
22 3 0.10
ACGTcount: A:0.18, C:0.30, G:0.14, T:0.38
Consensus pattern (19 bp):
CCCCTGTTTGTACTTCATA
Found at i:25182248 original size:82 final size:82
Alignment explanation
Indices: 25182182--25182384 Score: 282
Period size: 82 Copynumber: 2.5 Consensus size: 82
25182172 CATTATTTCG
* *
25182182 ACTTCGGTACCCCTGAAATGCACATACGTGCCCCTGTTTGTACTTCAGTACCCCTGAATTGTACA
1 ACTTTGGTACCCCTGAAATGCACATACGTGCCCCTGTTTGTACTTCAGTACACCTGAATTGTACA
25182247 TACATGCCCCTGTTTGT
66 TACATGCCCCTGTTTGT
* * * * * *
25182264 ACTTTGGTACCACT-AAATTGCACATACGTGCCCCTATTTTTACTTCGGTACACGTGAATTGGAC
1 ACTTTGGTACCCCTGAAA-TGCACATACGTGCCCCTGTTTGTACTTCAGTACACCTGAATTGTAC
25182328 ATACATGCCCCTGTTTGT
65 ATACATGCCCCTGTTTGT
* * * *
25182346 ACTTTGTTACCCCTGAATTGCACATATGTGCCCTTGTTT
1 ACTTTGGTACCCCTGAAATGCACATACGTGCCCCTGTTT
25182385 AGACTTTGGT
Statistics
Matches: 105, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
81 3 0.03
82 100 0.95
83 2 0.02
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (82 bp):
ACTTTGGTACCCCTGAAATGCACATACGTGCCCCTGTTTGTACTTCAGTACACCTGAATTGTACA
TACATGCCCCTGTTTGT
Found at i:25182256 original size:21 final size:21
Alignment explanation
Indices: 25182191--25182258 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
25182181 GACTTCGGTA
* * *
25182191 CCCCTGAAATGCACATACGTG
1 CCCCTGAATTGTACATACATG
* * *
25182212 CCCCTG-TTTGTAC-TTCAGTA
1 CCCCTGAATTGTACATACA-TG
25182232 CCCCTGAATTGTACATACATG
1 CCCCTGAATTGTACATACATG
25182253 CCCCTG
1 CCCCTG
25182259 TTTGTACTTT
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
19 2 0.06
20 11 0.31
21 19 0.54
22 3 0.09
ACGTcount: A:0.22, C:0.34, G:0.16, T:0.28
Consensus pattern (21 bp):
CCCCTGAATTGTACATACATG
Found at i:25184127 original size:15 final size:16
Alignment explanation
Indices: 25184100--25184129 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25184090 TGTCACATCC
25184100 AAAAAATTCGGGTTAG
1 AAAAAATTCGGGTTAG
25184116 AAAAAATT-GGGTTA
1 AAAAAATTCGGGTTA
25184130 ATGAATCGAG
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:0.47, C:0.03, G:0.23, T:0.27
Consensus pattern (16 bp):
AAAAAATTCGGGTTAG
Found at i:25187038 original size:41 final size:41
Alignment explanation
Indices: 25186992--25187078 Score: 174
Period size: 41 Copynumber: 2.1 Consensus size: 41
25186982 TGTGTAGTAC
25186992 TGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACA
1 TGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACA
25187033 TGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACA
1 TGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACA
25187074 TGTGT
1 TGTGT
25187079 AGTACTAAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.29
Consensus pattern (41 bp):
TGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACA
Found at i:25187209 original size:102 final size:101
Alignment explanation
Indices: 25187035--25187362 Score: 464
Period size: 102 Copynumber: 3.2 Consensus size: 101
25187025 TGGTCACATG
*
25187035 TGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAGTGAAGGCTACAA
1 TGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAGTGAAGGCTACTA
*
25187100 TGTGTACCGAGAAGCTTTGGTCACGTGTGTAGTACTG
66 TGTGTACCGA-AAGCTTTGGTCACGTGTGTAGTACTA
* *
25187137 TGTGAAGGCTACTACGTGAATTGATAAATGATGGTCACATGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAGTGAAGGCTACTA
25187202 TGTGTACCGAAAAGCTTTGGTCACGTGTGTAGTACTA
66 TGTGTACCG-AAAGCTTTGGTCACGTGTGTAGTACTA
* * * * *
25187239 TGTGAAGGCTACTACGTGAACCG-TAAA-GCTTGATCACGTGTGTAGTACTATGTGAAGGCTACT
1 TGTGAAGGCTACTACGTGAATCGATAAATG-ATGGTCACATGTGTAGTACTAAGTGAAGGCTACT
* * * *
25187302 ACGTGAACCGTAAAAC-TTGATCACGTGTGTAGTACTA
65 ATGTGTACCG-AAAGCTTTGGTCACGTGTGTAGTACTA
* *
25187339 TGTGAAGGCTACTATGTGTATCGA
1 TGTGAAGGCTACTACGTGAATCGA
25187363 ATGATAAAAC
Statistics
Matches: 204, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
100 41 0.20
101 45 0.22
102 117 0.57
103 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (101 bp):
TGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAGTGAAGGCTACTA
TGTGTACCGAAAGCTTTGGTCACGTGTGTAGTACTA
Found at i:25187289 original size:50 final size:50
Alignment explanation
Indices: 25187035--25187352 Score: 372
Period size: 51 Copynumber: 6.3 Consensus size: 50
25187025 TGGTCACATG
* * *
25187035 TGTGAAGGCTACTACGTGAATCGATAAATG-ATGGTCACATGTGTAGTACTA
1 TGTGAAGGCTACTACGTGAACCG-TAAA-GCTTGGTCACGTGTGTAGTACTA
* * * * *
25187086 AGTGAAGGCTACAATGTGTACCG-AGAAGCTTTGGTCACGTGTGTAGTACTG
1 TGTGAAGGCTACTACGTGAACCGTA-AAGC-TTGGTCACGTGTGTAGTACTA
** * *
25187137 TGTGAAGGCTACTACGTGAATTGATAAATG-ATGGTCACATGTGTAGTACTA
1 TGTGAAGGCTACTACGTGAACCG-TAAA-GCTTGGTCACGTGTGTAGTACTA
* * * * *
25187188 AGTGCAGGCTACTATGTGTACCGAAAAGCTTTGGTCACGTGTGTAGTACTA
1 TGTGAAGGCTACTACGTGAACCGTAAAGC-TTGGTCACGTGTGTAGTACTA
*
25187239 TGTGAAGGCTACTACGTGAACCGTAAAGCTTGATCACGTGTGTAGTACTA
1 TGTGAAGGCTACTACGTGAACCGTAAAGCTTGGTCACGTGTGTAGTACTA
* *
25187289 TGTGAAGGCTACTACGTGAACCGTAAAACTTGATCACGTGTGTAGTACTA
1 TGTGAAGGCTACTACGTGAACCGTAAAGCTTGGTCACGTGTGTAGTACTA
25187339 TGTGAAGGCTACTA
1 TGTGAAGGCTACTA
25187353 TGTGTATCGA
Statistics
Matches: 226, Mismatches: 33, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
49 3 0.01
50 88 0.39
51 131 0.58
52 2 0.01
53 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (50 bp):
TGTGAAGGCTACTACGTGAACCGTAAAGCTTGGTCACGTGTGTAGTACTA
Found at i:25189257 original size:22 final size:22
Alignment explanation
Indices: 25189229--25189272 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
25189219 TTATGATGAA
25189229 TGATATG-ATGAGATTGATATTT
1 TGATATGTATGAGATT-ATATTT
*
25189251 TGATATGTATGTGATTATATTT
1 TGATATGTATGAGATTATATTT
25189273 GTGTTGATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (22 bp):
TGATATGTATGAGATTATATTT
Found at i:25194644 original size:21 final size:21
Alignment explanation
Indices: 25194581--25194644 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
25194571 TTCAGGTGGA
* *
25194581 TTAGCTTTTATGAGCTTCTAT
1 TTAGCTCTTATGAGCTTCTGT
*
25194602 TAAGCTCTTATGAGCTTCTGT
1 TTAGCTCTTATGAGCTTCTGT
*
25194623 TTAGCTCTTATGAGCTTTTGT
1 TTAGCTCTTATGAGCTTCTGT
25194644 T
1 T
25194645 GGCGTGTTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.17, C:0.16, G:0.17, T:0.50
Consensus pattern (21 bp):
TTAGCTCTTATGAGCTTCTGT
Found at i:25203786 original size:22 final size:22
Alignment explanation
Indices: 25203743--25203807 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
25203733 CCTTTTTGAA
*
25203743 CCATTTCCATTTTCGTACCAAAT
1 CCATTACCA-TTTCGTACCAAAT
**
25203766 CCATTACCATTTCGTTTCAAAT
1 CCATTACCATTTCGTACCAAAT
* * *
25203788 CCCTTACCGTTTCATACCAA
1 CCATTACCATTTCGTACCAA
25203808 TTCCTAAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
22 26 0.76
23 8 0.24
ACGTcount: A:0.26, C:0.32, G:0.05, T:0.37
Consensus pattern (22 bp):
CCATTACCATTTCGTACCAAAT
Found at i:25212871 original size:40 final size:40
Alignment explanation
Indices: 25212782--25212881 Score: 130
Period size: 40 Copynumber: 2.5 Consensus size: 40
25212772 GAGCTTCTAT
* ***
25212782 TCAGCTCTTATGAGCTTCT-ATTGGCGTGTTTCAGGTGGA
1 TCAGCTCTTATGAGCTTCTGTTTGGCGTACATCAGGTGGA
* * *
25212821 CCAGCACTTATGAGCTTCTGTTTGGCGTACATCAGTTGGA
1 TCAGCTCTTATGAGCTTCTGTTTGGCGTACATCAGGTGGA
25212861 TCAGCTCTTATGAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
25212882 CTGGTGTGTT
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
39 17 0.33
40 34 0.67
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.37
Consensus pattern (40 bp):
TCAGCTCTTATGAGCTTCTGTTTGGCGTACATCAGGTGGA
Found at i:25215704 original size:11 final size:11
Alignment explanation
Indices: 25215665--25215706 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
25215655 AGTTTTAGCA
25215665 TTAG-TTTCTT
1 TTAGTTTTCTT
* *
25215675 TTAGGTTTCTC
1 TTAGTTTTCTT
25215686 TTAGTTTTCTT
1 TTAGTTTTCTT
*
25215697 TTACTTTTCT
1 TTAGTTTTCT
25215707 AGTGTTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
10 4 0.15
11 23 0.85
ACGTcount: A:0.10, C:0.14, G:0.10, T:0.67
Consensus pattern (11 bp):
TTAGTTTTCTT
Found at i:25215705 original size:22 final size:21
Alignment explanation
Indices: 25215665--25215706 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
25215655 AGTTTTAGCA
*
25215665 TTAGTTTCTTTTAGGTTTCTC
1 TTAGTTTCTTTTACGTTTCTC
*
25215686 TTAGTTTTCTTTTACTTTTCT
1 TTAG-TTTCTTTTACGTTTCT
25215707 AGTGTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.10, C:0.14, G:0.10, T:0.67
Consensus pattern (21 bp):
TTAGTTTCTTTTACGTTTCTC
Found at i:25216967 original size:40 final size:40
Alignment explanation
Indices: 25216915--25217004 Score: 153
Period size: 40 Copynumber: 2.2 Consensus size: 40
25216905 GTAAATTATA
* * *
25216915 CCCTGATTGCACTTACGTGCCCTTGTTTGTACTTCGGTAC
1 CCCTGATTGCACTTACATGCCCCTGTTTGTACTTCGATAC
25216955 CCCTGATTGCACTTACATGCCCCTGTTTGTACTTCGATAC
1 CCCTGATTGCACTTACATGCCCCTGTTTGTACTTCGATAC
25216995 CCCTGATTGC
1 CCCTGATTGC
25217005 TCATCGGTGC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.14, C:0.32, G:0.18, T:0.36
Consensus pattern (40 bp):
CCCTGATTGCACTTACATGCCCCTGTTTGTACTTCGATAC
Found at i:25216977 original size:20 final size:20
Alignment explanation
Indices: 25216915--25217004 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
25216905 GTAAATTATA
*
25216915 CCCTGATTGCACTTACG-TGC
1 CCCTGATTGCACTT-CGATAC
* * * *
25216935 CCTTGTTTGTACTTCGGTAC
1 CCCTGATTGCACTTCGATAC
*
25216955 CCCTGATTGCACTTAC-ATGC
1 CCCTGATTGCACTT-CGATAC
* *
25216975 CCCTGTTTGTACTTCGATAC
1 CCCTGATTGCACTTCGATAC
25216995 CCCTGATTGC
1 CCCTGATTGC
25217005 TCATCGGTGC
Statistics
Matches: 53, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
19 3 0.06
20 49 0.92
21 1 0.02
ACGTcount: A:0.14, C:0.32, G:0.18, T:0.36
Consensus pattern (20 bp):
CCCTGATTGCACTTCGATAC
Found at i:25217016 original size:40 final size:40
Alignment explanation
Indices: 25216915--25217025 Score: 152
Period size: 40 Copynumber: 2.8 Consensus size: 40
25216905 GTAAATTATA
* * *
25216915 CCCTGATTGCACTTACGTGCCCTTGTTTGTACTTCGGTAC
1 CCCTGATTGCACATACGTGCCCCTGTTTGTACTTCGATAC
* *
25216955 CCCTGATTGCACTTACATGCCCCTGTTTGTACTTCGATAC
1 CCCTGATTGCACATACGTGCCCCTGTTTGTACTTCGATAC
*
25216995 CCCTGATTGCTCAT-CGGTGCCCCTGTTTGTA
1 CCCTGATTGCACATAC-GTGCCCCTGTTTGTA
25217026 GTTCAGTGCT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
39 1 0.02
40 63 0.98
ACGTcount: A:0.14, C:0.32, G:0.19, T:0.36
Consensus pattern (40 bp):
CCCTGATTGCACATACGTGCCCCTGTTTGTACTTCGATAC
Found at i:25222458 original size:40 final size:39
Alignment explanation
Indices: 25222395--25222568 Score: 197
Period size: 40 Copynumber: 4.4 Consensus size: 39
25222385 ACGTAAATTA
* * *
25222395 TACCCTAATTGCACTTAC-GTGCCCCTGTTTGTACTTCGG
1 TACCCTGATTGCACAT-CGGTGCCCCTGTTTGCACTTCGG
* * *
25222434 TACCCTTGATTGCAAATCGATGCCCCTGTTTGTACTTCGG
1 TACCC-TGATTGCACATCGGTGCCCCTGTTTGCACTTCGG
* *
25222474 TACCCCTGATTGCACATTGGTGCCCCTGTTTGCACTTCAG
1 TA-CCCTGATTGCACATCGGTGCCCCTGTTTGCACTTCGG
* *
25222514 TGCTCCTGATTGCACATCGGTGCCCCTGTTTGCACTTCAG
1 TAC-CCTGATTGCACATCGGTGCCCCTGTTTGCACTTCGG
*
25222554 TGCTCCTGATTGCAC
1 TAC-CCTGATTGCAC
25222569 TTTGGTTCCC
Statistics
Matches: 120, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
39 7 0.06
40 110 0.92
41 3 0.03
ACGTcount: A:0.15, C:0.31, G:0.20, T:0.34
Consensus pattern (39 bp):
TACCCTGATTGCACATCGGTGCCCCTGTTTGCACTTCGG
Found at i:25222481 original size:20 final size:20
Alignment explanation
Indices: 25222403--25222570 Score: 151
Period size: 20 Copynumber: 8.4 Consensus size: 20
25222393 TATACCCTAA
25222403 TTGCACTTAC-GTGCCCCTGT
1 TTGCACTT-CGGTGCCCCTGT
* * * *
25222423 TTGTACTTCGGTACCCTTGA
1 TTGCACTTCGGTGCCCCTGT
** *
25222443 TTGCAAATCGATGCCCCTGT
1 TTGCACTTCGGTGCCCCTGT
* * *
25222463 TTGTACTTCGGTACCCCTGA
1 TTGCACTTCGGTGCCCCTGT
25222483 TTGCACATT-GGTGCCCCTGT
1 TTGCAC-TTCGGTGCCCCTGT
* * *
25222503 TTGCACTTCAGTGCTCCTGA
1 TTGCACTTCGGTGCCCCTGT
*
25222523 TTGCACATCGGTGCCCCTGT
1 TTGCACTTCGGTGCCCCTGT
* * *
25222543 TTGCACTTCAGTGCTCCTGA
1 TTGCACTTCGGTGCCCCTGT
25222563 TTGCACTT
1 TTGCACTT
25222571 TGGTTCCCTT
Statistics
Matches: 114, Mismatches: 31, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
19 3 0.03
20 109 0.96
21 2 0.02
ACGTcount: A:0.14, C:0.30, G:0.21, T:0.35
Consensus pattern (20 bp):
TTGCACTTCGGTGCCCCTGT
Found at i:25222538 original size:80 final size:80
Alignment explanation
Indices: 25222413--25222574 Score: 218
Period size: 80 Copynumber: 2.0 Consensus size: 80
25222403 TTGCACTTAC
* * * *
25222413 GTGCCCCTGTTTGTACTTCGGTACCCTTGATTGCAAATCGATGCCCCTGTTTGTACTTCGGTACC
1 GTGCCCCTGTTTGCACTTCAGTACCCTTGATTGCAAATCGATGCCCCTGTTTGCACTTCAGTACC
25222478 CCTGATTGCACATTG
66 CCTGATTGCACATTG
* * * *
25222493 GTGCCCCTGTTTGCACTTCAGTGCTCC-TGATTGCACATCGGTGCCCCTGTTTGCACTTCAGTGC
1 GTGCCCCTGTTTGCACTTCAGTAC-CCTTGATTGCAAATCGATGCCCCTGTTTGCACTTCAGTAC
* *
25222557 TCCTGATTGCACTTTG
65 CCCTGATTGCACATTG
25222573 GT
1 GT
25222575 TCCCTTATCT
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
80 69 0.97
81 2 0.03
ACGTcount: A:0.13, C:0.30, G:0.22, T:0.35
Consensus pattern (80 bp):
GTGCCCCTGTTTGCACTTCAGTACCCTTGATTGCAAATCGATGCCCCTGTTTGCACTTCAGTACC
CCTGATTGCACATTG
Found at i:25224448 original size:20 final size:20
Alignment explanation
Indices: 25224423--25224467 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
25224413 ACCCCTGTAG
*
25224423 TTTGAAAATTT-TCATCTTTT
1 TTTGAAAATTTCT-ATATTTT
25224443 TTTGAAAATTTCTATATTTT
1 TTTGAAAATTTCTATATTTT
25224463 TTTGA
1 TTTGA
25224468 TTTAGTCCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.60
Consensus pattern (20 bp):
TTTGAAAATTTCTATATTTT
Found at i:25235898 original size:51 final size:50
Alignment explanation
Indices: 25235759--25235938 Score: 177
Period size: 51 Copynumber: 3.6 Consensus size: 50
25235749 AAAGTGATGG
* * * * *
25235759 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCCGA-A-TGATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTAATACGCGTATCAGATAGT-AT-GA
* * * *
25235809 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGGATAGCT-TCGA
1 TCACATGTGTAGTACTATGTGCAGGCTAATACGCGTATCAGATAG-TAT-GA
* * * *
25235860 TCACGTGTGTAGTACTATGCGCAGGCTAATACGTGTATCAGATAGTGATGG
1 TCACATGTGTAGTACTATGTGCAGGCTAATACGCGTATCAGATAGT-ATGA
25235911 TCACATGTGTAGTACTATGTGCAGGCTA
1 TCACATGTGTAGTACTATGTGCAGGCTA
25235939 CTATGTGAAC
Statistics
Matches: 108, Mismatches: 17, Indels: 9
0.81 0.13 0.07
Matches are distributed among these distances:
50 38 0.35
51 68 0.63
52 1 0.01
53 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.30
Consensus pattern (50 bp):
TCACATGTGTAGTACTATGTGCAGGCTAATACGCGTATCAGATAGTATGA
Found at i:25235943 original size:102 final size:101
Alignment explanation
Indices: 25235759--25235943 Score: 291
Period size: 101 Copynumber: 1.8 Consensus size: 101
25235749 AAAGTGATGG
* * * *
25235759 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCCGAATGATAGGTCGCATGTGTAGTAC
1 TCACATGTGTAGTACTATGCGCAGGCTAATACGTGTACCAGAATGATAGGTCACATGTGTAGTAC
25235824 TATGTGCAGGCTACTATGCGTATCGGATAGCTTCGA
66 TATGTGCAGGCTACTATGCGTATCGGATAGCTTCGA
* *
25235860 TCACGTGTGTAGTACTATGCGCAGGCTAATACGTGTATCAGATAGTGAT-GGTCACATGTGTAGT
1 TCACATGTGTAGTACTATGCGCAGGCTAATACGTGTACCAGA-A-TGATAGGTCACATGTGTAGT
25235924 ACTATGTGCAGGCTACTATG
64 ACTATGTGCAGGCTACTATG
25235944 TGAACCGGTA
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
101 37 0.49
102 35 0.46
103 4 0.05
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.30
Consensus pattern (101 bp):
TCACATGTGTAGTACTATGCGCAGGCTAATACGTGTACCAGAATGATAGGTCACATGTGTAGTAC
TATGTGCAGGCTACTATGCGTATCGGATAGCTTCGA
Found at i:25238530 original size:6 final size:6
Alignment explanation
Indices: 25238516--25238555 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
25238506 TTTTGCTTTC
* **
25238516 TTTCAT TTTCTT TTTCTT TTTCAA TTTCTT TTTCTT TTTC
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTC
25238556 ACATGCTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.75
Consensus pattern (6 bp):
TTTCTT
Found at i:25238543 original size:18 final size:18
Alignment explanation
Indices: 25238516--25238556 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
25238506 TTTTGCTTTC
*
25238516 TTTCATTTTCTTTTTCTT
1 TTTCAATTTCTTTTTCTT
25238534 TTTCAATTTCTTTTTCTT
1 TTTCAATTTCTTTTTCTT
25238552 TTTCA
1 TTTCA
25238557 CATGCTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTCAATTTCTTTTTCTT
Found at i:25238564 original size:18 final size:18
Alignment explanation
Indices: 25238525--25238567 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
25238515 CTTTCATTTT
*
25238525 CTTTTTCTTTTTCAATTT
1 CTTTTTCTTTTTCAATTG
25238543 CTTTTTCTTTTTCACA-TG
1 CTTTTTCTTTTTCA-ATTG
25238561 CTTTTTC
1 CTTTTTC
25238568 GATTTCATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.09, C:0.21, G:0.02, T:0.67
Consensus pattern (18 bp):
CTTTTTCTTTTTCAATTG
Found at i:25240558 original size:3 final size:3
Alignment explanation
Indices: 25240550--25240622 Score: 74
Period size: 3 Copynumber: 24.3 Consensus size: 3
25240540 TTCTTTTAAA
* * * * *
25240550 TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT CAT TAT TAA TGT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
25240598 TGT TAT AAT TAT TAG TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
25240623 TGTATTAGTA
Statistics
Matches: 54, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:25240840 original size:25 final size:25
Alignment explanation
Indices: 25240801--25240849 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
25240791 TATTATATGT
*
25240801 TTGTTTTAAAATTCATTGTGTATTA
1 TTGTTTTAAAATTCATTATGTATTA
**
25240826 TTGTTTTAATCTTCATTATGTATT
1 TTGTTTTAAAATTCATTATGTATT
25240850 CTTTACACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.24, C:0.06, G:0.10, T:0.59
Consensus pattern (25 bp):
TTGTTTTAAAATTCATTATGTATTA
Found at i:25256361 original size:6 final size:6
Alignment explanation
Indices: 25256352--25256383 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
25256342 AAACTAAAGT
25256352 AATATA AATATA AATATA AATATA AATA-A AAT
1 AATATA AATATA AATATA AATATA AATATA AAT
25256384 CAATATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AATATA
Found at i:25257778 original size:27 final size:27
Alignment explanation
Indices: 25257719--25257785 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
25257709 TGGACCACCC
*
25257719 CATGTTTATTGTCCAAACAAACTACCT
1 CATGTTTACTGTCCAAACAAACTACCT
* *
25257746 CATGTTTACTGTCCCATCAAACTATCC-
1 CATGTTTACTGTCCAAACAAACTA-CCT
*
25257773 CGTGTTTACTGTC
1 CATGTTTACTGTC
25257786 TCAATAGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 33 0.94
28 2 0.06
ACGTcount: A:0.25, C:0.28, G:0.10, T:0.36
Consensus pattern (27 bp):
CATGTTTACTGTCCAAACAAACTACCT
Found at i:25258810 original size:21 final size:21
Alignment explanation
Indices: 25258784--25258827 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
25258774 CGAAGAAGAC
25258784 CTATACATACTCTTTAAGCAG
1 CTATACATACTCTTTAAGCAG
25258805 CTATACATACTCTTTAAGCAG
1 CTATACATACTCTTTAAGCAG
25258826 CT
1 CT
25258828 TTCACTGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.25, G:0.09, T:0.34
Consensus pattern (21 bp):
CTATACATACTCTTTAAGCAG
Found at i:25271664 original size:15 final size:14
Alignment explanation
Indices: 25271644--25271674 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
25271634 TATTCTTACA
25271644 ATAATGTTAAAAGAT
1 ATAATGTTAAAA-AT
25271659 ATAATGTTAAAAAT
1 ATAATGTTAAAAAT
25271673 AT
1 AT
25271675 TCTTACAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (14 bp):
ATAATGTTAAAAAT
Found at i:25274592 original size:9 final size:9
Alignment explanation
Indices: 25274578--25274880 Score: 218
Period size: 9 Copynumber: 34.0 Consensus size: 9
25274568 TAAGTATAAT
25274578 TAAGTTATG
1 TAAGTTATG
25274587 TAAGTTATG
1 TAAGTTATG
* * *
25274596 ATATGATATA
1 -TAAGTTATG
*
25274606 T-ATTTATG
1 TAAGTTATG
25274614 T-A-TTATG
1 TAAGTTATG
25274621 TAAGTTATG
1 TAAGTTATG
25274630 TAAGTTATG
1 TAAGTTATG
*
25274639 TGAGTTATG
1 TAAGTTATG
25274648 TAAGTTATG
1 TAAGTTATG
* *
25274657 ATATGATATATA
1 -TAAG-T-TATG
*
25274669 TACGTTAT-
1 TAAGTTATG
25274677 TAAGTTATG
1 TAAGTTATG
25274686 TAAGTTATG
1 TAAGTTATG
*
25274695 TGAGTTATG
1 TAAGTTATG
*
25274704 TAAGTTACG
1 TAAGTTATG
* *
25274713 ATATGATATATA
1 -TAAG-T-TATG
25274725 TAAGTTAT-
1 TAAGTTATG
25274733 TAAGTTATG
1 TAAGTTATG
*
25274742 TATG-TATG
1 TAAGTTATG
*
25274750 TGAGTTATG
1 TAAGTTATG
25274759 TAAGTTATG
1 TAAGTTATG
*
25274768 -ATA-TTATA
1 TA-AGTTATG
*
25274776 TATATTTATG
1 TA-AGTTATG
25274786 T-A-TTATG
1 TAAGTTATG
25274793 TAAGTTATG
1 TAAGTTATG
*
25274802 TGAGTTATG
1 TAAGTTATG
25274811 TAAGTTATG
1 TAAGTTATG
* * *
25274820 ATATGATATA
1 -TAAGTTATG
*
25274830 T-ATTTATG
1 TAAGTTATG
25274838 T-A-TTATG
1 TAAGTTATG
25274845 TAAGTTATG
1 TAAGTTATG
25274854 TAAGTTATG
1 TAAGTTATG
*
25274863 TGAGTTATG
1 TAAGTTATG
*
25274872 CAAGTTATG
1 TAAGTTATG
25274881 ATATGAGATA
Statistics
Matches: 236, Mismatches: 38, Indels: 40
0.75 0.12 0.13
Matches are distributed among these distances:
7 18 0.08
8 40 0.17
9 140 0.59
10 25 0.11
11 8 0.03
12 5 0.02
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:25274635 original size:52 final size:52
Alignment explanation
Indices: 25274578--25274871 Score: 333
Period size: 52 Copynumber: 5.3 Consensus size: 52
25274568 TAAGTATAAT
25274578 TAAGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATGTAAG
1 TAAGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTA--T--G
25274634 TTATGTGAGTTATGTAAGTTATGATATGATATATATACGTTAT-TAAGTTATGTAAGTTATG
1 -TA----AGTTATGTAAGTTATGATATGATATATAT---TTATGT-A-TTATGTAAGTTATG
* * *
25274695 TGAGTTATGTAAGTTACGATATGATATATATAAGTTAT-TAAGTTATGTATG-TATG
1 TAAGTTATGTAAGTTATGATATGATATATAT---TTATGT-A-TTATGTAAGTTATG
* *
25274750 TGAGTTATGTAAGTTATGATATTATATATATTTATGTATTATGTAAGTTATG
1 TAAGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATG
*
25274802 TGAGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATG
1 TAAGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATG
*
25274854 TAAGTTATGTGAGTTATG
1 TAAGTTATGTAAGTTATG
25274872 CAAGTTATGA
Statistics
Matches: 216, Mismatches: 10, Indels: 27
0.85 0.04 0.11
Matches are distributed among these distances:
51 8 0.04
52 76 0.35
53 1 0.00
55 33 0.15
56 46 0.21
57 2 0.01
60 1 0.00
61 30 0.14
63 2 0.01
64 5 0.02
65 12 0.06
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.47
Consensus pattern (52 bp):
TAAGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATG
Found at i:25275108 original size:24 final size:24
Alignment explanation
Indices: 25275081--25275142 Score: 61
Period size: 28 Copynumber: 2.4 Consensus size: 24
25275071 AATCAATTAA
*
25275081 TCAAATATAAAATCGATAATTTAT
1 TCAAATAAAAAATCGATAATTTAT
*
25275105 TCAATTAAATAAAAAATTGATAATTTAT
1 TC----AAATAAAAAATCGATAATTTAT
*
25275133 TCACATAAAA
1 TCAAATAAAA
25275143 TCAAATAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
24 9 0.29
28 22 0.71
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.35
Consensus pattern (24 bp):
TCAAATAAAAAATCGATAATTTAT
Found at i:25275168 original size:38 final size:37
Alignment explanation
Indices: 25275124--25275317 Score: 165
Period size: 38 Copynumber: 5.7 Consensus size: 37
25275114 TAAAAAATTG
*
25275124 ATAATTTATTCACATAAAATCAAATAAACTAATCAAAC
1 ATAATTTATTCA-ATTAAATCAAATAAACTAATCAAAC
*
25275162 ATAATTTATTCAATTAAAT---A-AAA--AATC---G
1 ATAATTTATTCAATTAAATCAAATAAACTAATCAAAC
*
25275190 ATAATTTATTCACATTAAATCGAATAAACTAATCAAAC
1 ATAATTTATTCA-ATTAAATCAAATAAACTAATCAAAC
*
25275228 ATAATTTATTCAATTAAATC----AAA--AATC---G
1 ATAATTTATTCAATTAAATCAAATAAACTAATCAAAC
* * *
25275256 ATAATTTATTCACATTAAACCTAGTAAACTAATCAAAC
1 ATAATTTATTCA-ATTAAATCAAATAAACTAATCAAAC
25275294 ATAATTTATTCAATT-AATCAAATA
1 ATAATTTATTCAATTAAATCAAATA
25275318 TATAAAGTAA
Statistics
Matches: 127, Mismatches: 9, Indels: 42
0.71 0.05 0.24
Matches are distributed among these distances:
28 24 0.19
29 14 0.11
31 8 0.06
32 1 0.01
33 12 0.09
34 1 0.01
35 8 0.06
36 6 0.05
37 17 0.13
38 36 0.28
ACGTcount: A:0.51, C:0.13, G:0.02, T:0.34
Consensus pattern (37 bp):
ATAATTTATTCAATTAAATCAAATAAACTAATCAAAC
Found at i:25275171 original size:66 final size:66
Alignment explanation
Indices: 25275096--25275310 Score: 367
Period size: 66 Copynumber: 3.3 Consensus size: 66
25275086 TATAAAATCG
* *
25275096 ATAATTTATTCAATTAAATAAAAAATTGATAATTTATTCACATAAAATCAAATAAACTAATCAAA
1 ATAATTTATTCAATTAAATAAAAAATCGATAATTTATTCACATTAAATCAAATAAACTAATCAAA
25275161 C
66 C
*
25275162 ATAATTTATTCAATTAAATAAAAAATCGATAATTTATTCACATTAAATCGAATAAACTAATCAAA
1 ATAATTTATTCAATTAAATAAAAAATCGATAATTTATTCACATTAAATCAAATAAACTAATCAAA
25275227 C
66 C
* * * *
25275228 ATAATTTATTCAATTAAATCAAAAATCGATAATTTATTCACATTAAACCTAGTAAACTAATCAAA
1 ATAATTTATTCAATTAAATAAAAAATCGATAATTTATTCACATTAAATCAAATAAACTAATCAAA
25275293 C
66 C
25275294 ATAATTTATTCAATTAA
1 ATAATTTATTCAATTAA
25275311 TCAAATATAT
Statistics
Matches: 142, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 142 1.00
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.34
Consensus pattern (66 bp):
ATAATTTATTCAATTAAATAAAAAATCGATAATTTATTCACATTAAATCAAATAAACTAATCAAA
C
Found at i:25275174 original size:28 final size:28
Alignment explanation
Indices: 25275162--25275267 Score: 77
Period size: 28 Copynumber: 3.4 Consensus size: 28
25275152 CTAATCAAAC
*
25275162 ATAATTTATTCAATTAAATAAAAAATCG
1 ATAATTTATTCAAATAAATAAAAAATCG
* *
25275190 ATAATTTATTCACATTAAATCGAATAAACTAATCAAAC
1 ATAATTTATTCA-AATAAAT---A-AAA--AATC---G
* *
25275228 ATAATTTATTCAATTAAATCAAAAATCG
1 ATAATTTATTCAAATAAATAAAAAATCG
25275256 ATAATTTATTCA
1 ATAATTTATTCA
25275268 CATTAAACCT
Statistics
Matches: 65, Mismatches: 3, Indels: 20
0.74 0.03 0.23
Matches are distributed among these distances:
28 24 0.37
29 7 0.11
31 4 0.06
32 1 0.02
33 6 0.09
35 4 0.06
37 7 0.11
38 12 0.18
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.36
Consensus pattern (28 bp):
ATAATTTATTCAAATAAATAAAAAATCG
Found at i:25276140 original size:2 final size:2
Alignment explanation
Indices: 25276133--25276170 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
25276123 ATGCATTACC
25276133 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25276171 GCATAGACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25277858 original size:21 final size:22
Alignment explanation
Indices: 25277823--25277868 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
25277813 TGATTGCAAA
*
25277823 TTAAGATTTTAAAATTTAA-AT
1 TTAAGATTTTAAAATATAATAT
25277844 TTAA-ATTTTAGAAATATAATAT
1 TTAAGATTTTA-AAATATAATAT
25277866 TTA
1 TTA
25277869 TGATAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 11 0.50
22 5 0.23
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (22 bp):
TTAAGATTTTAAAATATAATAT
Found at i:25278467 original size:7 final size:7
Alignment explanation
Indices: 25278422--25278520 Score: 74
Period size: 7 Copynumber: 13.9 Consensus size: 7
25278412 TTAAAATCGG
25278422 ACCCTAA
1 ACCCTAA
*
25278429 ACACTAA
1 ACCCTAA
*
25278436 ACCATAA
1 ACCCTAA
25278443 ACCCTAA
1 ACCCTAA
* *
25278450 GCACGTAA
1 AC-CCTAA
25278458 ACCCTAA
1 ACCCTAA
*
25278465 ACCATAA
1 ACCCTAA
**
25278472 ACTTTAA
1 ACCCTAA
*
25278479 ATCCTAA
1 ACCCTAA
25278486 ACCCTAA
1 ACCCTAA
*
25278493 ACCTTAA
1 ACCCTAA
*
25278500 GCCC-ATA
1 ACCCTA-A
25278507 ACCCTTAA
1 ACCC-TAA
25278515 ACCCTA
1 ACCCTA
25278521 TACCTACACA
Statistics
Matches: 69, Mismatches: 19, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
6 1 0.01
7 57 0.83
8 10 0.14
9 1 0.01
ACGTcount: A:0.43, C:0.34, G:0.03, T:0.19
Consensus pattern (7 bp):
ACCCTAA
Found at i:25278676 original size:7 final size:7
Alignment explanation
Indices: 25278666--25278732 Score: 53
Period size: 7 Copynumber: 9.6 Consensus size: 7
25278656 ATCTTAAATA
25278666 CTAAACT
1 CTAAACT
*
25278673 CTAAACC
1 CTAAACT
*
25278680 CTAAACC
1 CTAAACT
* *
25278687 CCAAACC
1 CTAAACT
*
25278694 CCAAACT
1 CTAAACT
* *
25278701 TTAAACC
1 CTAAACT
25278708 CTAAACT
1 CTAAACT
25278715 CTAAACT
1 CTAAACT
* *
25278722 CAAAAAT
1 CTAAACT
25278729 CTAA
1 CTAA
25278733 TCCAAAAATA
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 49 1.00
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.19
Consensus pattern (7 bp):
CTAAACT
Found at i:25278683 original size:14 final size:14
Alignment explanation
Indices: 25278666--25278720 Score: 74
Period size: 14 Copynumber: 3.9 Consensus size: 14
25278656 ATCTTAAATA
25278666 CTAAACTCTAAACC
1 CTAAACTCTAAACC
* *
25278680 CTAAACCCCAAACC
1 CTAAACTCTAAACC
* *
25278694 CCAAACTTTAAACC
1 CTAAACTCTAAACC
25278708 CTAAACTCTAAAC
1 CTAAACTCTAAAC
25278721 TCAAAAATCT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.18
Consensus pattern (14 bp):
CTAAACTCTAAACC
Found at i:25278825 original size:14 final size:14
Alignment explanation
Indices: 25278767--25278832 Score: 53
Period size: 14 Copynumber: 4.7 Consensus size: 14
25278757 ATAAGCCCTA
25278767 AAACCCTAAACCAT
1 AAACCCTAAACCAT
**
25278781 AAACATTAAA-CATT
1 AAACCCTAAACCA-T
** *
25278795 AAATACTAAACCCT
1 AAACCCTAAACCAT
*
25278809 AAACCCTAAACTAT
1 AAACCCTAAACCAT
*
25278823 AAAACCTAAA
1 AAACCCTAAA
25278833 AAAAGTTCAG
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
13 2 0.05
14 37 0.93
15 1 0.03
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.20
Consensus pattern (14 bp):
AAACCCTAAACCAT
Found at i:25279130 original size:156 final size:156
Alignment explanation
Indices: 25278847--25279296 Score: 465
Period size: 156 Copynumber: 2.9 Consensus size: 156
25278837 GTTCAGCAAA
* * * ** * *
25278847 AAATGACGTCATTTTGCTCAACTTTTTTACGGCATTTTACAAAAAGCGTTGTTATTGCTTGATCT
1 AAATAACGTCATTTTGCTCAACTTTTTTGCGGCATTTTCCAAAAAGCGCCGCTAATGCTTGATCT
* * * *
25278912 TCAGCGGCGTTTATCAAAAAGCGCCGCTAATTCTCTATCTATCGCGGTATTTGTTAGAAAGTGCC
66 TCAGCGGCGTTTAACAAAAAGCGCCGCTAATTCTCAATCTATCGCGGCATTTGTTAAAAAGTGCC
*
25278977 TCTAATGCCACTAAAGCTC-AAAAGG
131 ACTAATGCCACTAAAGCTCAAAAAGG
* * * *
25279002 AAAATAATGTCATTTTGCTTAACTTTTTTGCGGCGTTTTCCAAAAAACGCCGCTAATGCTTGATC
1 -AAATAACGTCATTTTGCTCAACTTTTTTGCGGCATTTTCCAAAAAGCGCCGCTAATGCTTGATC
** ** ** * * *
25279067 TTTTGCGTTGTTTAACAAAAAGCGTTGTTAATTCTCAATCTATTGCGGCGTTTGTTAAAAAGTGC
65 TTCAGCGGCGTTTAACAAAAAGCGCCGCTAATTCTCAATCTATCGCGGCATTTGTTAAAAAGTGC
25279132 CACTAATGCCACTAAAGCTCAAAAAGG
130 CACTAATGCCACTAAAGCTCAAAAAGG
* * * * * *
25279159 AAATGACGTCGTTTTGCTCAACTTTTTTGCTGCATTTTCCAAAAAGCACCGCAAATGATTGATCT
1 AAATAACGTCATTTTGCTCAACTTTTTTGCGGCATTTTCCAAAAAGCGCCGCTAATGCTTGATCT
* * * * * * * * * * * *
25279224 ACAGTGGCATTTTACAAGAAGCGCCACT-ATTGCT-TACCTATTGTGGCATTTTGTTAAGAAGCG
66 TCAGCGGCGTTTAACAAAAAGCGCCGCTAATT-CTCAATCTATCGCGGCA-TTTGTTAAAAAGTG
25279287 CCACTAATGC
129 CCACTAATGC
25279297 TCAATTTATT
Statistics
Matches: 237, Mismatches: 54, Indels: 6
0.80 0.18 0.02
Matches are distributed among these distances:
155 13 0.05
156 218 0.92
157 6 0.03
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (156 bp):
AAATAACGTCATTTTGCTCAACTTTTTTGCGGCATTTTCCAAAAAGCGCCGCTAATGCTTGATCT
TCAGCGGCGTTTAACAAAAAGCGCCGCTAATTCTCAATCTATCGCGGCATTTGTTAAAAAGTGCC
ACTAATGCCACTAAAGCTCAAAAAGG
Found at i:25279837 original size:9 final size:9
Alignment explanation
Indices: 25279823--25279848 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
25279813 ATTCATTATT
25279823 TTTTAGTTA
1 TTTTAGTTA
25279832 TTTTAGTTA
1 TTTTAGTTA
25279841 TTTTAGTT
1 TTTTAGTT
25279849 TGTGTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.12, T:0.69
Consensus pattern (9 bp):
TTTTAGTTA
Found at i:25294799 original size:10 final size:9
Alignment explanation
Indices: 25294741--25294817 Score: 66
Period size: 9 Copynumber: 8.2 Consensus size: 9
25294731 TAGTATAAAT
*
25294741 ATATATAAA
1 ATATAAAAA
*
25294750 TTATAAAAA
1 ATATAAAAA
25294759 ATATTAAAAA
1 ATA-TAAAAA
25294769 A-ATTAAAAA
1 ATA-TAAAAA
*
25294778 ATATATACAA
1 ATATA-AAAA
25294788 ATATACAAAA
1 ATATA-AAAA
**
25294798 ATGCAAAAA
1 ATATAAAAA
25294807 ATATAAAAA
1 ATATAAAAA
25294816 AT
1 AT
25294818 TATTGAAATT
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
9 33 0.60
10 22 0.40
ACGTcount: A:0.69, C:0.04, G:0.01, T:0.26
Consensus pattern (9 bp):
ATATAAAAA
Found at i:25295039 original size:28 final size:28
Alignment explanation
Indices: 25294980--25295045 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
25294970 TAAAATATAG
* *
25294980 AAAATTAT-AAAATTATTAGGAATGACA
1 AAAAATATAAAAATTATTAGGAATAACA
* *
25295007 TAAAAGTATAAAAATTATTA-GAATAATA
1 -AAAAATATAAAAATTATTAGGAATAACA
25295035 AAAAATATAAA
1 AAAAATATAAA
25295046 TTAAAAACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 10 0.30
28 13 0.39
29 10 0.30
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.29
Consensus pattern (28 bp):
AAAAATATAAAAATTATTAGGAATAACA
Found at i:25295111 original size:9 final size:9
Alignment explanation
Indices: 25295008--25295156 Score: 57
Period size: 9 Copynumber: 16.9 Consensus size: 9
25294998 GGAATGACAT
*
25295008 AAAAGTATA
1 AAAATTATA
*
25295017 AAAATTATT
1 AAAATTATA
* *
25295026 AGAATAATA
1 AAAATTATA
25295035 AAAA--ATA
1 AAAATTATA
*
25295042 TAAATTA-A
1 AAAATTATA
*
25295050 AAACA-AATGA
1 AAA-ATTAT-A
*
25295060 AAAATTGTA
1 AAAATTATA
25295069 AAAATTATGA
1 AAAATTAT-A
*
25295079 AAAGATATTTA
1 AAA-AT-TATA
25295090 AAAA-TATA
1 AAAATTATA
25295098 GAAAATTATA
1 -AAAATTATA
*
25295108 AAAAATATA
1 AAAATTATA
*
25295117 AAAA-AATA
1 AAAATTATA
* *
25295125 GAAAAGT-GA
1 -AAAATTATA
25295134 AAAA-TATA
1 AAAATTATA
25295142 AAAA-T-TA
1 AAAATTATA
25295149 AAAATTAT
1 AAAATTAT
25295157 TCAAATTTAT
Statistics
Matches: 105, Mismatches: 19, Indels: 32
0.67 0.12 0.21
Matches are distributed among these distances:
7 13 0.12
8 21 0.20
9 49 0.47
10 14 0.13
11 6 0.06
12 2 0.02
ACGTcount: A:0.66, C:0.01, G:0.07, T:0.26
Consensus pattern (9 bp):
AAAATTATA
Found at i:25295119 original size:8 final size:8
Alignment explanation
Indices: 25295088--25295153 Score: 55
Period size: 8 Copynumber: 7.9 Consensus size: 8
25295078 AAAAGATATT
25295088 TAAAAATA
1 TAAAAATA
25295096 TAGAAAATTA
1 TA-AAAA-TA
25295106 TAAAAAATA
1 T-AAAAATA
*
25295115 TAAAAAAA
1 TAAAAATA
25295123 TAGAAAAGT-
1 TA-AAAA-TA
*
25295132 GAAAAATA
1 TAAAAATA
25295140 TAAAAAT-
1 TAAAAATA
25295147 TAAAAAT
1 TAAAAAT
25295154 TATTCAAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
7 8 0.17
8 20 0.42
9 12 0.25
10 7 0.15
11 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (8 bp):
TAAAAATA
Found at i:25295129 original size:19 final size:19
Alignment explanation
Indices: 25295089--25295129 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
25295079 AAAGATATTT
* * *
25295089 AAAAATATAGAAAATTATA
1 AAAAATATAAAAAAATAGA
25295108 AAAAATATAAAAAAATAGA
1 AAAAATATAAAAAAATAGA
25295127 AAA
1 AAA
25295130 GTGAAAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (19 bp):
AAAAATATAAAAAAATAGA
Found at i:25295528 original size:19 final size:18
Alignment explanation
Indices: 25295488--25295538 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
25295478 TTAAATTTGC
*
25295488 TTTATAATTTTTATGTTA
1 TTTATAATTTTTATGTAA
25295506 TTTATAATATTTTAT-TAA
1 TTTATAAT-TTTTATGTAA
25295524 TTTTATTAATTTTTA
1 -TTTA-TAATTTTTA
25295539 AATATTATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 10 0.34
19 15 0.52
20 4 0.14
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTATAATTTTTATGTAA
Found at i:25295605 original size:24 final size:23
Alignment explanation
Indices: 25295578--25295623 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
25295568 AATTTACCTA
*
25295578 TTTTTTATAA-TTTATATATATTTC
1 TTTTTAATAAGTTTA-ATA-ATTTC
25295602 TTTTTAATAAGTTTAATAATTT
1 TTTTTAATAAGTTTAATAATTT
25295624 TATATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 12 0.60
25 4 0.20
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (23 bp):
TTTTTAATAAGTTTAATAATTTC
Found at i:25295732 original size:25 final size:25
Alignment explanation
Indices: 25295679--25295725 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
25295669 TATTTTTTAA
*
25295679 ATATTTAAATATTTTTTAATTATCT
1 ATATTTAAATATTTTTTAATGATCT
*
25295704 ATATTTTAA-ATTTTTTAATGAT
1 ATATTTAAATATTTTTTAATGAT
25295726 TTTATATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (25 bp):
ATATTTAAATATTTTTTAATGATCT
Found at i:25295799 original size:5 final size:5
Alignment explanation
Indices: 25295789--25295814 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
25295779 TGAGCATTCG
25295789 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
25295815 AATTTTTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:25298001 original size:31 final size:29
Alignment explanation
Indices: 25297943--25298045 Score: 80
Period size: 31 Copynumber: 3.4 Consensus size: 29
25297933 ATTCCTTTAA
* * * *
25297943 ATGTGTACAATTGAATCAAAATTAAAGTTTC
1 ATGTATACATTTGAA-CCAAATCAAAG-TTC
*
25297974 ATGTATACATTTGAACCATGATCAAAGTTC
1 ATGTATACATTTGAACCA-AATCAAAGTTC
* * *
25298004 TATGTATATAATTGCACCAAATCAAAGTTC
1 -ATGTATACATTTGAACCAAATCAAAGTTC
*
25298034 ATGAATCACATT
1 ATGTAT-ACATT
25298046 GCATATTGGA
Statistics
Matches: 57, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
29 5 0.09
30 18 0.32
31 34 0.60
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.34
Consensus pattern (29 bp):
ATGTATACATTTGAACCAAATCAAAGTTC
Found at i:25301127 original size:21 final size:23
Alignment explanation
Indices: 25301098--25301143 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
25301088 CCAACTAAAG
*
25301098 CCTCCATTTCC-TAA-AATTCAA
1 CCTCCATTTCCAGAACAATTCAA
*
25301119 CCTCTATTTCCAGAACAATTCAA
1 CCTCCATTTCCAGAACAATTCAA
25301142 CC
1 CC
25301144 AGTGTCGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 2 0.10
23 9 0.43
ACGTcount: A:0.33, C:0.35, G:0.02, T:0.30
Consensus pattern (23 bp):
CCTCCATTTCCAGAACAATTCAA
Found at i:25303321 original size:12 final size:11
Alignment explanation
Indices: 25303304--25303371 Score: 57
Period size: 12 Copynumber: 5.8 Consensus size: 11
25303294 AGGCAACCCA
25303304 ATTTTTATTTTT
1 ATTTTTA-TTTT
*
25303316 ATTTTTTATTATC
1 A-TTTTTATT-TT
*
25303329 ATTTTTACTTT
1 ATTTTTATTTT
*
25303340 ATTTATTACTTT
1 ATTT-TTATTTT
25303352 A-TTTTATTTT
1 ATTTTTATTTT
25303362 ATTATTTATT
1 ATT-TTTATT
25303372 ACTTATTTGG
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
10 7 0.15
11 8 0.17
12 24 0.51
13 8 0.17
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (11 bp):
ATTTTTATTTT
Found at i:25303370 original size:17 final size:17
Alignment explanation
Indices: 25303306--25303371 Score: 57
Period size: 17 Copynumber: 3.8 Consensus size: 17
25303296 GCAACCCAAT
25303306 TTTTATT-TTTATTTT-
1 TTTTATTATTTATTTTA
* *
25303321 TTATTATCATTTTTACTTTA
1 TT-TTAT--TATTTATTTTA
25303341 -TTTATTACTTTATTTTA
1 TTTTATTA-TTTATTTTA
25303358 TTTTATTATTTATT
1 TTTTATTATTTATT
25303372 ACTTATTTGG
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
15 2 0.05
16 5 0.12
17 14 0.34
18 12 0.29
19 8 0.20
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTATTATTTATTTTA
Found at i:25304404 original size:102 final size:102
Alignment explanation
Indices: 25304213--25304405 Score: 216
Period size: 102 Copynumber: 1.9 Consensus size: 102
25304203 AAGAACATGT
* * * *
25304213 TGGGCTGAGTAACTGGGGTAGGGTGCTTGGGTTGTCATCCTATTTCGCGTCAAAAGGTTCGATGT
1 TGGGCTGAGTAACCGGGGTAGGGTGCTTGGGCTGTCATCCTATTTCGCGCCAAAAGGTTCGATAT
* * *
25304278 GTTCTTAAGAAAAAATTATAATAAATTAGGAGTCTAC
66 GTCCTAAAGAAAAAATAATAATAAATTAGGAGTCTAC
* * *
25304315 TGGGCTGAGTAACCGGGGTGGGGTGCTT-GGCTGTTATCTCTCTTT-GCGCCAAAAGGTTCAGTA
1 TGGGCTGAGTAACCGGGGTAGGGTGCTTGGGCTGTCATC-CTATTTCGCGCCAAAAGGTTC-G-A
25304378 TAT-TCCTAAAGCATAAAAA-AAT-ATAAAT
63 TATGTCCTAAAG-A-AAAAATAATAATAAAT
25304406 AAAAAATAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
101 21 0.28
102 44 0.58
103 6 0.08
104 5 0.07
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (102 bp):
TGGGCTGAGTAACCGGGGTAGGGTGCTTGGGCTGTCATCCTATTTCGCGCCAAAAGGTTCGATAT
GTCCTAAAGAAAAAATAATAATAAATTAGGAGTCTAC
Found at i:25304420 original size:10 final size:9
Alignment explanation
Indices: 25304390--25304459 Score: 59
Period size: 10 Copynumber: 7.0 Consensus size: 9
25304380 TTCCTAAAGC
25304390 ATAAAAAAA
1 ATAAAAAAA
25304399 TATAAATAAAAA
1 -AT-AA-AAAAA
25304411 ATAAATAAAA
1 ATAAA-AAAA
*
25304421 ATCAAAATAA
1 AT-AAAAAAA
25304431 ATAAAAATAA
1 ATAAAAA-AA
25304441 ATAAAGAAAA
1 ATAAA-AAAA
*
25304451 AGAAAAAAA
1 ATAAAAAAA
25304460 TAATTTGGGG
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
9 9 0.18
10 28 0.55
11 9 0.18
12 5 0.10
ACGTcount: A:0.80, C:0.01, G:0.03, T:0.16
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:25304427 original size:16 final size:15
Alignment explanation
Indices: 25304390--25304462 Score: 71
Period size: 16 Copynumber: 4.9 Consensus size: 15
25304380 TTCCTAAAGC
25304390 ATAAAA-AAATATAAA
1 ATAAAATAAATA-AAA
*
25304405 TAAAAAATAAATAAAA
1 -ATAAAATAAATAAAA
25304421 ATCAAAATAAATAAAA
1 AT-AAAATAAATAAAA
*
25304437 AT-AAATAAAGAAAA
1 ATAAAATAAATAAAA
*
25304451 AGAAAA-AAATAA
1 ATAAAATAAATAA
25304463 TTTGGGGACT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
14 17 0.35
15 4 0.08
16 23 0.47
17 5 0.10
ACGTcount: A:0.79, C:0.01, G:0.03, T:0.16
Consensus pattern (15 bp):
ATAAAATAAATAAAA
Found at i:25308103 original size:24 final size:24
Alignment explanation
Indices: 25308070--25308116 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
25308060 TAAAAGTGTG
*
25308070 ACTCTCACACCCTCCTAAGGGTCT
1 ACTCTCACACCCTCATAAGGGTCT
* *
25308094 ACTCTTACACCCTCATGAGGGTC
1 ACTCTCACACCCTCATAAGGGTC
25308117 CCTTCAAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (24 bp):
ACTCTCACACCCTCATAAGGGTCT
Found at i:25314260 original size:18 final size:18
Alignment explanation
Indices: 25314237--25314274 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
25314227 ATTAACTCAC
*
25314237 CTGAACTTTTCTATTAGG
1 CTGAACTTGTCTATTAGG
25314255 CTGAACTTGTCTATTAGG
1 CTGAACTTGTCTATTAGG
25314273 CT
1 CT
25314275 TTTACCTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.42
Consensus pattern (18 bp):
CTGAACTTGTCTATTAGG
Found at i:25320163 original size:13 final size:14
Alignment explanation
Indices: 25320145--25320178 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
25320135 ATAATAAATA
25320145 TATTTTTT-ATTTT
1 TATTTTTTAATTTT
25320158 TATTTTTTAATTTT
1 TATTTTTTAATTTT
*
25320172 TAATTTT
1 TATTTTT
25320179 AAAATACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TATTTTTTAATTTT
Found at i:25320170 original size:14 final size:13
Alignment explanation
Indices: 25320145--25320178 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
25320135 ATAATAAATA
25320145 TATTTTTTATTTT
1 TATTTTTTATTTT
25320158 TATTTTTTAATTTT
1 TATTTTTT-ATTTT
25320172 TAATTTT
1 T-ATTTT
25320179 AAAATACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
14 6 0.32
15 5 0.26
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TATTTTTTATTTT
Found at i:25321176 original size:17 final size:18
Alignment explanation
Indices: 25321142--25321180 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
25321132 ATTAATTAAG
25321142 TTTATATATTTTTAAAAT
1 TTTATATATTTTTAAAAT
*
25321160 TTTATCTATTTTT-AAAT
1 TTTATATATTTTTAAAAT
25321177 TTTA
1 TTTA
25321181 ATTATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTATATATTTTTAAAAT
Found at i:25321487 original size:22 final size:23
Alignment explanation
Indices: 25321459--25321510 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
25321449 CATGTTAGCG
25321459 AACAAATATATAAATATA-AATA
1 AACAAATATATAAATATATAATA
* *
25321481 AACAAATATTTATATATATAATA
1 AACAAATATATAAATATATAATA
25321504 AA-AAATA
1 AACAAATA
25321511 AATTGAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 21 0.78
23 6 0.22
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (23 bp):
AACAAATATATAAATATATAATA
Found at i:25323893 original size:40 final size:40
Alignment explanation
Indices: 25323821--25323896 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
25323811 ATTGTTCATG
*
25323821 CCACGTCAGCAAATCGCGTCCTAGGGGGCGCGATTTGTGT
1 CCACGTCAGCAAATCGCGTCCTAGGGGACGCGATTTGTGT
* *
25323861 CCACGTCAGCAAATCGCG-CTTACGTGGACGCGATTT
1 CCACGTCAGCAAATCGCGTCCTA-GGGGACGCGATTT
25323897 CCTGGCGCGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 3 0.09
40 29 0.91
ACGTcount: A:0.20, C:0.29, G:0.29, T:0.22
Consensus pattern (40 bp):
CCACGTCAGCAAATCGCGTCCTAGGGGACGCGATTTGTGT
Found at i:25324816 original size:15 final size:15
Alignment explanation
Indices: 25324781--25324822 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
25324771 ATAAATCATT
25324781 ATATTTA-TTTAATA
1 ATATTTATTTTAATA
* *
25324795 CTTTTTATTTTAATA
1 ATATTTATTTTAATA
25324810 ATATTTAATTTTA
1 ATATTT-ATTTTA
25324823 TATAGTTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 5 0.23
15 11 0.50
16 6 0.27
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
ATATTTATTTTAATA
Found at i:25325082 original size:21 final size:21
Alignment explanation
Indices: 25325051--25325100 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
25325041 TCGTTGTTTC
*
25325051 TAATGTCACCATTACAGT-AT
1 TAATCTCACCATTACAGTAAT
*
25325071 TCAATCTCACCATTATAGTAAT
1 T-AATCTCACCATTACAGTAAT
25325093 TAATCTCA
1 TAATCTCA
25325101 TTGCCACCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 1 0.04
21 22 0.85
22 3 0.12
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (21 bp):
TAATCTCACCATTACAGTAAT
Found at i:25325730 original size:19 final size:19
Alignment explanation
Indices: 25325706--25325746 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
25325696 CATCATTATC
25325706 ATCACCATTTATTCAATCA
1 ATCACCATTTATTCAATCA
25325725 ATCACCATTTATTCAATCA
1 ATCACCATTTATTCAATCA
25325744 ATC
1 ATC
25325747 TTATTTTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.37, C:0.27, G:0.00, T:0.37
Consensus pattern (19 bp):
ATCACCATTTATTCAATCA
Found at i:25328319 original size:63 final size:61
Alignment explanation
Indices: 25328214--25328352 Score: 158
Period size: 63 Copynumber: 2.2 Consensus size: 61
25328204 ATTTATTCAC
* * *
25328214 ATGTGGTTCGAATGTATGTTCAAATTATTTGAGCTGAAATTTAA-G-TATGAATCTTATACAT
1 ATGTGGTTCGAATATAGGTTCAAATTACTTGAGCTGAAATTTAATGTTATGAA--TTATACAT
* * *
25328275 ATAAGTGGTTCGAATATAGGTTACAAATTCCTTGAGCTG-TATTTAATGTTGTGAATTATACAT
1 AT--GTGGTTCGAATATAGGTT-CAAATTACTTGAGCTGAAATTTAATGTTATGAATTATACAT
25328338 ATGTGGTTCGAATAT
1 ATGTGGTTCGAATAT
25328353 GTGTTTACTA
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
61 15 0.22
63 32 0.48
64 15 0.22
65 5 0.07
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (61 bp):
ATGTGGTTCGAATATAGGTTCAAATTACTTGAGCTGAAATTTAATGTTATGAATTATACAT
Found at i:25328514 original size:41 final size:41
Alignment explanation
Indices: 25328467--25328621 Score: 238
Period size: 41 Copynumber: 3.8 Consensus size: 41
25328457 ATCTAAGTTA
* *
25328467 TTCAGACTTTATGTCTAGCAGGCTTAATGCTGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
* * *
25328508 TCCAGACTTTAAGTCTAGCTGGCTTAATGCCGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
*
25328549 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGATGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
* *
25328590 TTCAGACTTTACATCTAGCAAGCTTAATGCCG
1 TTCAGACTTTACGTCTAGCAGGCTTAATGCCG
25328622 ATGTTCTGAA
Statistics
Matches: 104, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 104 1.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (41 bp):
TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
Found at i:25328649 original size:82 final size:82
Alignment explanation
Indices: 25328481--25328667 Score: 200
Period size: 82 Copynumber: 2.3 Consensus size: 82
25328471 GACTTTATGT
* ** *
25328481 CTAGCAGGCTTAATGCTGGTGAAATATTCCAGACTTTAAGTCTAGCTGGCTTAATGCCGGTGAAA
1 CTAGCAGGCTTAATGCCGGTGAAATATTCCAGACTTTAAGTCTAGCAAGCTTAATGCCGATGAAA
* * * *
25328546 TATTTCAGACTTTACGT
66 TATATCAGACTTCAAGC
* * **
25328563 CTAGCAGGCTTAATGCCGATGAAATATTTCAGACTTTACA-TCTAGCAAGCTTAATGCCGATGTT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCCAGACTTTA-AGTCTAGCAAGCTTAATGCCGATGAA
* *
25328627 CTGA-ATCAGGCTTCAAGC
65 AT-ATATCAGACTTCAAGC
25328645 CTAGCAGGC-TACATGCCGGTGAA
1 CTAGCAGGCTTA-ATGCCGGTGAA
25328668 TCATTTTAAA
Statistics
Matches: 87, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
81 2 0.02
82 83 0.95
83 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (82 bp):
CTAGCAGGCTTAATGCCGGTGAAATATTCCAGACTTTAAGTCTAGCAAGCTTAATGCCGATGAAA
TATATCAGACTTCAAGC
Found at i:25345728 original size:49 final size:50
Alignment explanation
Indices: 25345562--25345733 Score: 159
Period size: 50 Copynumber: 3.5 Consensus size: 50
25345552 AAGATATCCT
* * * * * * **
25345562 ATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCC
1 ATGTAAGACCATGTCTGGGACATGACATGGGCACCTACAAGAGAACTCCC
** * *
25345612 CCGTAAGACCATGTCTGGGACATGACATGGGCACCTATATGAGAACTCCC
1 ATGTAAGACCATGTCTGGGACATGACATGGGCACCTACAAGAGAACTCCC
* * * * *
25345662 ATGTAAGACCATATCTGGGATATGGCATTGGCA-GTACAAGA-AACATCCC
1 ATGTAAGACCATGTCTGGGACATGACATGGGCACCTACAAGAGAAC-TCCC
*
25345711 ATGTAAGACTATGTCTGGGACAT
1 ATGTAAGACCATGTCTGGGACAT
25345734 AGCTTTGACA
Statistics
Matches: 100, Mismatches: 21, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
48 3 0.03
49 29 0.29
50 68 0.68
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (50 bp):
ATGTAAGACCATGTCTGGGACATGACATGGGCACCTACAAGAGAACTCCC
Found at i:25354069 original size:13 final size:13
Alignment explanation
Indices: 25354051--25354077 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
25354041 TTTCCAGCAA
25354051 TTATGAATTTATT
1 TTATGAATTTATT
25354064 TTATGAATTTATT
1 TTATGAATTTATT
25354077 T
1 T
25354078 AATGTTGACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:25354242 original size:42 final size:43
Alignment explanation
Indices: 25354195--25354370 Score: 165
Period size: 50 Copynumber: 3.8 Consensus size: 43
25354185 ATGTAAGATG
**
25354195 ATGTCTGGGACATGGCGTTCTCACCGAGATGAGAGGTC-GACC
1 ATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCAGACC
25354237 ATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCTCATGTAAGACC
1 ATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG--TC-----AGACC
*
25354287 ATGTCTTGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACC
1 ATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGT----C---AGACC
* * *
25354337 ATGTCTGGGACATGGCATGGGCACCGATATGAGA
1 ATGTCTGGGACATGGCGTTGGCACCGAGATGAGA
25354371 ATATCCCATG
Statistics
Matches: 115, Mismatches: 7, Indels: 16
0.83 0.05 0.12
Matches are distributed among these distances:
42 34 0.30
44 2 0.02
48 1 0.01
50 77 0.67
52 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.34, T:0.21
Consensus pattern (43 bp):
ATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCAGACC
Found at i:25354291 original size:50 final size:50
Alignment explanation
Indices: 25354233--25354410 Score: 230
Period size: 50 Copynumber: 3.5 Consensus size: 50
25354223 ATGAGAGGTC
*
25354233 GACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCTCATGTAA
1 GACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAA
* **
25354283 GACCATGTCTTGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAA
1 GACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAA
* * * **
25354333 GACCATGTCTGGGACATGGCATGGGCACCGATATGAGAATATCCCATGTAA
1 GACCATGTCTGGGACATGGCGTTGGCACCGAGATGAG-AGGTCCCATGTAA
* * * *
25354384 GAACAGGTTTGGGACATGGCTTTGGCA
1 GACCATGTCTGGGACATGGCGTTGGCA
25354411 TGTTATTATC
Statistics
Matches: 110, Mismatches: 17, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
50 79 0.72
51 31 0.28
ACGTcount: A:0.25, C:0.21, G:0.32, T:0.22
Consensus pattern (50 bp):
GACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAA
Found at i:25358053 original size:50 final size:50
Alignment explanation
Indices: 25357978--25358162 Score: 237
Period size: 50 Copynumber: 3.7 Consensus size: 50
25357968 TTGGGTAAAG
*
25357978 CATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATGAGAGGTCT
1 CATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATGAGAGGTCC
*
25358028 CATGTAAGACCATGTCTT-GGACATGGTGTTGGCACCGAGATGAGAGGTCC
1 CATGTAAGACCATGT-TTGGGACATGGCGTTGGCACCGAGATGAGAGGTCC
** * * * * * **
25358078 CCCGTAAGACCATGTCTGGGACATGGCATGGGCACCAATATGAGAATATCC
1 CATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATGAG-AGGTCC
*
25358129 CATGTAAGACCATGTTTGGGACATGGCTTTGGCA
1 CATGTAAGACCATGTTTGGGACATGGCGTTGGCA
25358163 TGTTATTATC
Statistics
Matches: 115, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
49 1 0.01
50 79 0.69
51 35 0.30
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.24
Consensus pattern (50 bp):
CATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATGAGAGGTCC
Found at i:25365692 original size:33 final size:34
Alignment explanation
Indices: 25365641--25365715 Score: 125
Period size: 33 Copynumber: 2.2 Consensus size: 34
25365631 AGATTTAAAC
25365641 AAATTAATTACTAACACTTATTTAAGCTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
25365675 AAATTAATT-CTAACACTTATTTGAGCTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
25365708 AATTTAAT
1 AAATTAAT
25365716 AAACCAACTC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 30 0.77
34 9 0.23
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (34 bp):
AAATTAATTACTAACACTTATTTAAGCTGAACTA
Found at i:25372850 original size:18 final size:18
Alignment explanation
Indices: 25372822--25372865 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
25372812 TCAATCTCTT
25372822 TTTTCTCTTTTTC-ATTCTC
1 TTTT-TCTTTTTCGATT-TC
25372841 TTTTTCTTTTTCGATTTC
1 TTTTTCTTTTTCGATTTC
*
25372859 CTTTTCT
1 TTTTTCT
25372866 GTCTTCCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.05, C:0.23, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTTTCTTTTTCGATTTC
Found at i:25378305 original size:17 final size:17
Alignment explanation
Indices: 25378283--25378319 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
25378273 ATGCACTAAC
*
25378283 ATGAAAATGTAATGACA
1 ATGAAAATGTAATGAAA
25378300 ATGAAAATGTAATGAAA
1 ATGAAAATGTAATGAAA
25378317 ATG
1 ATG
25378320 TATACTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.54, C:0.03, G:0.19, T:0.24
Consensus pattern (17 bp):
ATGAAAATGTAATGAAA
Found at i:25402004 original size:20 final size:21
Alignment explanation
Indices: 25401981--25402026 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
25401971 TCTCATTTTC
25401981 TTTTCACTTTC-TTTTTCTAT
1 TTTTCACTTTCTTTTTTCTAT
* *
25402001 TTTT-GCTTTCTTTTTTTTAT
1 TTTTCACTTTCTTTTTTCTAT
25402021 TTTTCA
1 TTTTCA
25402027 TGTTCTTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.09, C:0.15, G:0.02, T:0.74
Consensus pattern (21 bp):
TTTTCACTTTCTTTTTTCTAT
Found at i:25402038 original size:23 final size:22
Alignment explanation
Indices: 25401989--25402051 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
25401979 TCTTTTCACT
*
25401989 TTCTTTTTCTATTTTTGC-TTTC
1 TTCTTTTTTTATTTTT-CATTTC
25402011 -T-TTTTTTTATTTTTCATGTTC
1 TTCTTTTTTTATTTTTCAT-TTC
*
25402032 TTCTTTTTTTCTTTTTCATT
1 TTCTTTTTTTATTTTTCATT
25402052 CAATTGAGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
19 1 0.03
20 13 0.37
21 4 0.11
22 2 0.06
23 15 0.43
ACGTcount: A:0.06, C:0.14, G:0.03, T:0.76
Consensus pattern (22 bp):
TTCTTTTTTTATTTTTCATTTC
Found at i:25402975 original size:18 final size:20
Alignment explanation
Indices: 25402952--25402998 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
25402942 CTTCACTTCA
25402952 TTTTTTTTATAC-T-CAAAC
1 TTTTTTTTATACTTCCAAAC
*
25402970 TTTTTTTTATACTTCCAAAT
1 TTTTTTTTATACTTCCAAAC
25402990 TTTTTTTTA
1 TTTTTTTTA
25402999 ATTACAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 12 0.46
19 1 0.04
20 13 0.50
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTTTTTATACTTCCAAAC
Found at i:25402977 original size:20 final size:19
Alignment explanation
Indices: 25402951--25402996 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
25402941 ACTTCACTTC
25402951 ATTTTTTTTATAC-T-CAA
1 ATTTTTTTTATACTTCCAA
25402968 ACTTTTTTTTATACTTCCAA
1 A-TTTTTTTTATACTTCCAA
25402988 ATTTTTTTT
1 ATTTTTTTT
25402997 TAATTACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 1 0.04
18 12 0.46
19 9 0.35
20 4 0.15
ACGTcount: A:0.24, C:0.13, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTTTTTATACTTCCAA
Found at i:25404264 original size:17 final size:19
Alignment explanation
Indices: 25404244--25404278 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
25404234 TCAAACACAT
25404244 TAATTT-AAC-AAATTAAC
1 TAATTTAAACTAAATTAAC
25404261 TAATTTAAACTAAATTAA
1 TAATTTAAACTAAATTAA
25404279 ATGGAGCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 3 0.19
19 7 0.44
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (19 bp):
TAATTTAAACTAAATTAAC
Found at i:25405294 original size:27 final size:28
Alignment explanation
Indices: 25405232--25405294 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
25405222 AAACACAATA
25405232 AAATG-ATGTAATAAGCTAAGACAAATT
1 AAATGCATGTAATAAGCTAAGACAAATT
* *
25405259 -AATGTCATGTACTAA-CTAAGACATATT
1 AAATG-CATGTAATAAGCTAAGACAAATT
25405286 AAATGCATG
1 AAATGCATG
25405295 CATGAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
26 4 0.13
27 15 0.48
28 12 0.39
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (28 bp):
AAATGCATGTAATAAGCTAAGACAAATT
Found at i:25405819 original size:11 final size:11
Alignment explanation
Indices: 25405787--25405845 Score: 50
Period size: 11 Copynumber: 5.2 Consensus size: 11
25405777 AGAAAAGAGC
*
25405787 GAATGATGAAT
1 GAATGAGGAAT
25405798 G-ATGA-GAAT
1 GAATGAGGAAT
25405807 GAATGAGGAAT
1 GAATGAGGAAT
*
25405818 GATTGAGGGATGAT
1 GAATGA-GGA--AT
25405832 GAATGAAGGAAT
1 GAATG-AGGAAT
25405844 GA
1 GA
25405846 GAGGGTCTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 10 0.25
12 7 0.17
14 9 0.22
15 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.36, T:0.22
Consensus pattern (11 bp):
GAATGAGGAAT
Found at i:25408952 original size:13 final size:13
Alignment explanation
Indices: 25408936--25408969 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
25408926 AAACAACTCG
25408936 AAAAAAAATTTGA
1 AAAAAAAATTTGA
25408949 AAAAAAAATTTGA
1 AAAAAAAATTTGA
25408962 AAAAAAAA
1 AAAAAAAA
25408970 CTAGTTTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (13 bp):
AAAAAAAATTTGA
Done.