Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 60 of 136
Found at i:19790787 original size:16 final size:15
Alignment explanation
Indices: 19790766--19790795 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
19790756 AGAACGAGTC
19790766 AAAAAGAAAAAGAAAT
1 AAAAAG-AAAAGAAAT
19790782 AAAAAGAAAAGAAA
1 AAAAAGAAAAGAAA
19790796 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:19803323 original size:25 final size:26
Alignment explanation
Indices: 19803295--19803370 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 26
19803285 ATGCTCGTGA
19803295 AAAAAAAAAGAGAAAAGGAA-AAG-AG
1 AAAAAAAAA-AGAAAAGGAACAAGAAG
*
19803320 AAAAAAGAATA-AAAA-GAACAAGAAG
1 AAAAAA-AAAAGAAAAGGAACAAGAAG
*
19803345 AAAAAAAAAAGAAAA-GAAGAAGAAG
1 AAAAAAAAAAGAAAAGGAACAAGAAG
19803370 A
1 A
19803371 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:19807949 original size:21 final size:21
Alignment explanation
Indices: 19807925--19807968 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
19807915 GAATCTTTAG
*
19807925 TATTTATTGTATCATTT-TATT
1 TATTTAAT-TATCATTTCTATT
*
19807946 TATTTAATTATCCTTTCTATT
1 TATTTAATTATCATTTCTATT
19807967 TA
1 TA
19807969 ATTAGGTCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (21 bp):
TATTTAATTATCATTTCTATT
Found at i:19808321 original size:21 final size:21
Alignment explanation
Indices: 19808297--19808340 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
19808287 GAATCTTTAG
*
19808297 TATTTATTGTATCATTT-TATT
1 TATTTAAT-TATCATTTCTATT
*
19808318 TATTTAATTATCCTTTCTATT
1 TATTTAATTATCATTTCTATT
19808339 TA
1 TA
19808341 ATTAGGTCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (21 bp):
TATTTAATTATCATTTCTATT
Found at i:19808371 original size:372 final size:372
Alignment explanation
Indices: 19807686--19808429 Score: 1425
Period size: 372 Copynumber: 2.0 Consensus size: 372
19807676 ATACTATGCC
* * * *
19807686 GCCACTCGGACTCGAACCGAGATGCTCTAGCACTGCTTCCTAAGAGCAGCGTGTCTACCGATTTC
1 GCCACTCAGACTCGAACCGAGATGCTCTAGCACTACTTCCTAAGAGCAACATGTCTACCGATTTC
*
19807751 ACCATAGCGGCTTGCTCGAAATCATAATAACCCATTTTTTAGTCAATCGTCGAGATTGAAGGTGA
66 ACCATAGCGGCTTGCTCGAAATCATAATAACCCATTTTTGAGTCAATCGTCGAGATTGAAGGTGA
19807816 AGGGGTCAATTCAATGTAAAATGTCAAATTTGTTAGGAAGCATTTAATTTTTATTGATAAATAAC
131 AGGGGTCAATTCAATGTAAAATGTCAAATTTGTTAGGAAGCATTTAATTTTTATTGATAAATAAC
*
19807881 AACTCGTTGAAATAGCAATTTGAAGGTTCAAAAGGAATCTTTAGTATTTATTGTATCATTTTATT
196 AACTCGTTGAAATAGCAATTTGAAGGTCCAAAAGGAATCTTTAGTATTTATTGTATCATTTTATT
19807946 TATTTAATTATCCTTTCTATTTAATTAGGTCGTCAATAGAGATTTTTTAGTTTGTGTTTTCCTAA
261 TATTTAATTATCCTTTCTATTTAATTAGGTCGTCAATAGAGATTTTTTAGTTTGTGTTTTCCTAA
19808011 AAGAGAACTCCTTTATTGTAACTAAACTAACTAGTTGTAACTTCAAT
326 AAGAGAACTCCTTTATTGTAACTAAACTAACTAGTTGTAACTTCAAT
19808058 GCCACTCAGACTCGAACCGAGATGCTCTAGCACTACTTCCTAAGAGCAACATGTCTACCGATTTC
1 GCCACTCAGACTCGAACCGAGATGCTCTAGCACTACTTCCTAAGAGCAACATGTCTACCGATTTC
19808123 ACCATAGCGGCTTGCTCGAAATCATAATAACCCATTTTTGAGTCAATCGTCGAGATTGAAGGTGA
66 ACCATAGCGGCTTGCTCGAAATCATAATAACCCATTTTTGAGTCAATCGTCGAGATTGAAGGTGA
*
19808188 AGGGGTCAATTCAATGTAAAATGTCAAATTTGTTAGGAAGCATTTCATTTTTATTGATAAATAAC
131 AGGGGTCAATTCAATGTAAAATGTCAAATTTGTTAGGAAGCATTTAATTTTTATTGATAAATAAC
19808253 AACTCGTTGAAATAGCAATTTGAAGGTCCAAAAGGAATCTTTAGTATTTATTGTATCATTTTATT
196 AACTCGTTGAAATAGCAATTTGAAGGTCCAAAAGGAATCTTTAGTATTTATTGTATCATTTTATT
19808318 TATTTAATTATCCTTTCTATTTAATTAGGTCGTCAATAGAGATTTTTTAGTTTGTGTTTTCCTAA
261 TATTTAATTATCCTTTCTATTTAATTAGGTCGTCAATAGAGATTTTTTAGTTTGTGTTTTCCTAA
19808383 AAGAGAACTCCTTTATTGTAACTAAACTAACTAGTTGTAACTTCAAT
326 AAGAGAACTCCTTTATTGTAACTAAACTAACTAGTTGTAACTTCAAT
19808430 TCATAGATAA
Statistics
Matches: 365, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
372 365 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Consensus pattern (372 bp):
GCCACTCAGACTCGAACCGAGATGCTCTAGCACTACTTCCTAAGAGCAACATGTCTACCGATTTC
ACCATAGCGGCTTGCTCGAAATCATAATAACCCATTTTTGAGTCAATCGTCGAGATTGAAGGTGA
AGGGGTCAATTCAATGTAAAATGTCAAATTTGTTAGGAAGCATTTAATTTTTATTGATAAATAAC
AACTCGTTGAAATAGCAATTTGAAGGTCCAAAAGGAATCTTTAGTATTTATTGTATCATTTTATT
TATTTAATTATCCTTTCTATTTAATTAGGTCGTCAATAGAGATTTTTTAGTTTGTGTTTTCCTAA
AAGAGAACTCCTTTATTGTAACTAAACTAACTAGTTGTAACTTCAAT
Found at i:19812751 original size:21 final size:20
Alignment explanation
Indices: 19812725--19812765 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
19812715 TCGCATCTCG
*
19812725 TTTTATCTATTATTGTTTTTA
1 TTTTATCTATTAGT-TTTTTA
*
19812746 TTTTATGTATTAGTTTTTTA
1 TTTTATCTATTAGTTTTTTA
19812766 GTAATTTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.20, C:0.02, G:0.07, T:0.71
Consensus pattern (20 bp):
TTTTATCTATTAGTTTTTTA
Found at i:19814775 original size:20 final size:20
Alignment explanation
Indices: 19814739--19814777 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
19814729 TGGCGCCAAT
19814739 TCTGTAAGTGTTCTGAAAAA
1 TCTGTAAGTGTTCTGAAAAA
*
19814759 TCTGATAAGT-TTTTGAAAA
1 TCTG-TAAGTGTTCTGAAAA
19814778 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:19818721 original size:198 final size:198
Alignment explanation
Indices: 19818383--19818789 Score: 789
Period size: 198 Copynumber: 2.1 Consensus size: 198
19818373 GTAGGTTAAG
*
19818383 GCTAAGCATCAGTTACCTTTAGGTTTACTGCAATCGGTTAAGATACCGTTATGGAAATGGGAGCG
1 GCTAAGCATCAGTTACCTTCAGGTTTACTGCAATCGGTTAAGATACCGTTATGGAAATGGGAGCG
19818448 AGTAACGATGGGCTTCGTTAGTGGGTAGCCTCTAACACTCACTAAGAAAGATTTTGTCTGGGTTA
66 AGTAACGATGGGCTTCGTTAGTGGGTAGCCTCTAACACTCACTAAGAAAGATTTTGTCTGGGTTA
19818513 TCGTGGATTAATTAACCAAGTCTGCTCATTTCATCCTGGTAAGGACAAAGTTTTCTCTTCAGAAA
131 TCGTGGATTAATTAACCAAGTCTGCTCATTTCATCCTGGTAAGGACAAAGTTTTCTCTTCAGAAA
19818578 TTA
196 TTA
*
19818581 GCTAAGCATCAGTTACCTTCAGGTTTACTGCAATTGGTTAAGATACCGTTATGGAAATGGGAGCG
1 GCTAAGCATCAGTTACCTTCAGGTTTACTGCAATCGGTTAAGATACCGTTATGGAAATGGGAGCG
19818646 AGTAACGATGGGCTTCGTTAGTGGGTAGCCTCTAACACTCACTAAGAAAGATTTTGTCTGGGTTA
66 AGTAACGATGGGCTTCGTTAGTGGGTAGCCTCTAACACTCACTAAGAAAGATTTTGTCTGGGTTA
19818711 TCGTGGATTAATTAACCAAGTCTGCTCATTTCATCCTGGTAAGGACAAAGTTTTCTCTTCAGAAA
131 TCGTGGATTAATTAACCAAGTCTGCTCATTTCATCCTGGTAAGGACAAAGTTTTCTCTTCAGAAA
19818776 TTA
196 TTA
19818779 GCTAAGC-TCAG
1 GCTAAGCATCAG
19818790 CATATCAAAA
Statistics
Matches: 207, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
197 4 0.02
198 203 0.98
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (198 bp):
GCTAAGCATCAGTTACCTTCAGGTTTACTGCAATCGGTTAAGATACCGTTATGGAAATGGGAGCG
AGTAACGATGGGCTTCGTTAGTGGGTAGCCTCTAACACTCACTAAGAAAGATTTTGTCTGGGTTA
TCGTGGATTAATTAACCAAGTCTGCTCATTTCATCCTGGTAAGGACAAAGTTTTCTCTTCAGAAA
TTA
Found at i:19823112 original size:49 final size:49
Alignment explanation
Indices: 19822977--19823086 Score: 220
Period size: 49 Copynumber: 2.2 Consensus size: 49
19822967 CCATCCGATC
19822977 GTTGTTGGGCCACCTAGGATGGTAAAATGTAAGAATAGTGAAAGTCATT
1 GTTGTTGGGCCACCTAGGATGGTAAAATGTAAGAATAGTGAAAGTCATT
19823026 GTTGTTGGGCCACCTAGGATGGTAAAATGTAAGAATAGTGAAAGTCATT
1 GTTGTTGGGCCACCTAGGATGGTAAAATGTAAGAATAGTGAAAGTCATT
19823075 GTTGTTGGGCCA
1 GTTGTTGGGCCA
19823087 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:19826525 original size:21 final size:21
Alignment explanation
Indices: 19826499--19826561 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
19826489 TTGGTATTTG
19826499 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
19826520 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
19826541 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
19826562 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:19835361 original size:12 final size:12
Alignment explanation
Indices: 19835344--19835368 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19835334 TTTCACTCGT
19835344 CTCTTTTTCAAA
1 CTCTTTTTCAAA
19835356 CTCTTTTTCAAA
1 CTCTTTTTCAAA
19835368 C
1 C
19835369 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:19837911 original size:20 final size:20
Alignment explanation
Indices: 19837886--19837959 Score: 91
Period size: 20 Copynumber: 3.8 Consensus size: 20
19837876 CATGTGGTTC
19837886 AGCTCATTCGAGCTCAAGTT
1 AGCTCATTCGAGCTCAAGTT
* *
19837906 AGCTCATTAGAGCTCAAGTC
1 AGCTCATTCGAGCTCAAGTT
19837926 AG-TGCATTCGAGCTCAA-TT
1 AGCT-CATTCGAGCTCAAGTT
19837945 CAGCTCATT-GAGCTC
1 -AGCTCATTCGAGCTC
19837960 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:19841415 original size:25 final size:25
Alignment explanation
Indices: 19841381--19841499 Score: 127
Period size: 25 Copynumber: 4.8 Consensus size: 25
19841371 TCTTGTACAT
19841381 GTATGCTCATACGAGCTGTGAA-TCG
1 GTATGCTCATACGAGCTGT-AAGTCG
*
19841406 GTATGCTCATACGAGCTGT-AGACCG
1 GTATGCTCATACGAGCTGTAAG-TCG
* * *
19841431 ATATGCTC-TCACGAGCTATAAGTTG
1 GTATGCTCAT-ACGAGCTGTAAGTCG
* *
19841456 ATATGCTCACACGAGCTGTAAGTCG
1 GTATGCTCATACGAGCTGTAAGTCG
*
19841481 GTATGCTCACACGAGCTGT
1 GTATGCTCATACGAGCTGT
19841500 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:19848172 original size:27 final size:27
Alignment explanation
Indices: 19847820--19848160 Score: 398
Period size: 27 Copynumber: 12.6 Consensus size: 27
19847810 TAATGGCCCT
*
19847820 AAATTACCGAAATACCCTCAATGGGTA
1 AAATTACCGAAATACCCTCGATGGGTA
* * *
19847847 AACTTACCAAAATACCCTCGATGGGAA
1 AAATTACCGAAATACCCTCGATGGGTA
* * *
19847874 AAATTACTGAAATACCTTTGATGGGTA
1 AAATTACCGAAATACCCTCGATGGGTA
* * *
19847901 AAACTACTGAAATACCCTCGATAGGTA
1 AAATTACCGAAATACCCTCGATGGGTA
*
19847928 AAACTACCGAAATACCCTCGATGGGTA
1 AAATTACCGAAATACCCTCGATGGGTA
* * ** **
19847955 AAATGATCGAAATACCCTTAATACGTA
1 AAATTACCGAAATACCCTCGATGGGTA
* * *
19847982 AAATGACCAAAATACCCTCGATGGATA
1 AAATTACCGAAATACCCTCGATGGGTA
*
19848009 AAATTATCGAAATACCCTCGATGGGTA
1 AAATTACCGAAATACCCTCGATGGGTA
* **
19848036 AAATTACTGAAATACCCTTAATGGGTA
1 AAATTACCGAAATACCCTCGATGGGTA
* *
19848063 AAATTACAGAAATACCCTTGATGGGTA
1 AAATTACCGAAATACCCTCGATGGGTA
*
19848090 AAATTACCAAAATACCCTCG-TAGGGTA
1 AAATTACCGAAATACCCTCGAT-GGGTA
*
19848117 AAATTACTGAAATACCC-CTGATGGGTA
1 AAATTACCGAAATACCCTC-GATGGGTA
19848144 AAATTACCGAAATACCC
1 AAATTACCGAAATACCC
19848161 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:19852308 original size:56 final size:50
Alignment explanation
Indices: 19852191--19852326 Score: 182
Period size: 50 Copynumber: 2.6 Consensus size: 50
19852181 NNNNNNNNNN
19852191 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCAG
* * *
19852241 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATAATTTTAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT--T-ATCTCAG
*
19852294 TAATGCCAATGCCATGTCCCAGACATGGTCTTA
1 ---TGCCAACGCCATGTCCCAGACATGGTCTTA
19852327 ACTGGCTCAC
Statistics
Matches: 75, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
50 41 0.55
52 1 0.01
53 5 0.07
56 28 0.37
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCAG
Found at i:19857550 original size:22 final size:22
Alignment explanation
Indices: 19857522--19857585 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
19857512 CCTTTTTGAA
19857522 CCATTACCATTTCGTACCAAAT
1 CCATTACCATTTCGTACCAAAT
* **
19857544 CCATTACCATTTTGTGTCAAAT
1 CCATTACCATTTCGTACCAAAT
*
19857566 CCTTTACCATTTCGTACCAA
1 CCATTACCATTTCGTACCAA
19857586 TTCCCAAATA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.28, C:0.30, G:0.06, T:0.36
Consensus pattern (22 bp):
CCATTACCATTTCGTACCAAAT
Found at i:19859535 original size:25 final size:25
Alignment explanation
Indices: 19859471--19859539 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
19859461 TCTTGCACAT
19859471 GTATGCTCAT-ACGAGCTATGAATCG
1 GTATGCTC-TCACGAGCTATGAATCG
* *
19859496 GTATGCT-TACTCGAGCTGT-AGATCG
1 GTATGCTCT-CACGAGCTATGA-ATCG
19859521 GTATGCTCTCACGAGCTAT
1 GTATGCTCTCACGAGCTAT
19859540 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:19859589 original size:25 final size:25
Alignment explanation
Indices: 19859521--19859579 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
19859511 CTGTAGATCG
* * * *
19859521 GTATGCTCTCACGAGCTATAAGTTC
1 GTATGCTCACACAAGTTGTAAGTTC
*
19859546 GTATGCTCACACAAGTTGTAAGTTG
1 GTATGCTCACACAAGTTGTAAGTTC
19859571 GTATGCTCA
1 GTATGCTCA
19859580 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:19865323 original size:40 final size:40
Alignment explanation
Indices: 19865237--19865341 Score: 133
Period size: 40 Copynumber: 2.7 Consensus size: 40
19865227 TTACCGAAAT
*
19865237 CATTGTTATAATTATTGTAATTAT-A-ATTTACGATCAAA
1 CATTATTATAATTATTGTAATTATAATATTTACGATCAAA
* * * * *
19865275 TATTATTATAACTATTGTAATTGTAATATTTTCGGTCAAA
1 CATTATTATAATTATTGTAATTATAATATTTACGATCAAA
*
19865315 CATTATTATAATTATGGTAATTATAAT
1 CATTATTATAATTATTGTAATTATAAT
19865342 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:19868828 original size:16 final size:16
Alignment explanation
Indices: 19868807--19868838 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
19868797 ATTTATTGGG
19868807 CCTAATACATACTGAT
1 CCTAATACATACTGAT
19868823 CCTAATACATACTGAT
1 CCTAATACATACTGAT
19868839 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:19879096 original size:15 final size:15
Alignment explanation
Indices: 19879073--19879110 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
19879063 TACCATCTCA
*
19879073 TTCTTTTTTTTTCTT
1 TTCTCTTTTTTTCTT
19879088 TTCTC-TTTTTTCTT
1 TTCTCTTTTTTTCTT
19879102 TT-TCTTTTT
1 TTCTCTTTTT
19879111 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:19879098 original size:14 final size:13
Alignment explanation
Indices: 19879079--19879110 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
19879069 CTCATTCTTT
19879079 TTTTTTCTTTTCTC
1 TTTTTTCTTTT-TC
19879093 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
19879106 TTTTT
1 TTTTT
19879111 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:19881331 original size:11 final size:11
Alignment explanation
Indices: 19881315--19881340 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19881305 AGAAGATTGT
19881315 AAAAAAATCAA
1 AAAAAAATCAA
19881326 AAAAAAATCAA
1 AAAAAAATCAA
19881337 AAAA
1 AAAA
19881341 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:19920866 original size:13 final size:13
Alignment explanation
Indices: 19920848--19920872 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19920838 ATATAATCAG
19920848 ATAAATTGTAAAA
1 ATAAATTGTAAAA
19920861 ATAAATTGTAAA
1 ATAAATTGTAAA
19920873 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:19925096 original size:41 final size:41
Alignment explanation
Indices: 19925051--19925163 Score: 127
Period size: 41 Copynumber: 2.8 Consensus size: 41
19925041 AATAATGACG
* * * * *
19925051 AATTGTACATAAGTGTCCCTGTTTGTACTTCGATACCCTTC
1 AATTGTACATACGTGCCCCTGTTTATACTTCGATACCCCTA
* * *
19925092 AATTGTACATACGTGCCCCTATGTATACTTCGGTACCCCTA
1 AATTGTACATACGTGCCCCTGTTTATACTTCGATACCCCTA
** *
19925133 AATTACACATACGTGCCCCTGTTTAGACTTC
1 AATTGTACATACGTGCCCCTGTTTATACTTC
19925164 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:19929516 original size:30 final size:30
Alignment explanation
Indices: 19929460--19929518 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
19929450 ATGCGAGCTG
* *
19929460 AATTAGCTCATTTCCATTTCATTGAACTCC
1 AATTAGCTCATTTCCACTCCATTGAACTCC
19929490 AATTAGCTCATTTCCAGCTCCA-TGAACTC
1 AATTAGCTCATTTCCA-CTCCATTGAACTC
19929519 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:19929800 original size:25 final size:25
Alignment explanation
Indices: 19929766--19929815 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
19929756 AATTTAATAC
19929766 TTAGTTAATTAATTTGTCTAGTTAT
1 TTAGTTAATTAATTTGTCTAGTTAT
19929791 TTAGTTAATTAATTTGTCTAGTTAT
1 TTAGTTAATTAATTTGTCTAGTTAT
19929816 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:19934716 original size:41 final size:41
Alignment explanation
Indices: 19934671--19934873 Score: 253
Period size: 41 Copynumber: 5.0 Consensus size: 41
19934661 CATTATTTCG
*
19934671 ACTTCGGTACCCCTGAAATGCACATACGTGCCCCTGTTTGT
1 ACTTCGGTACCCCTGAATTGCACATACGTGCCCCTGTTTGT
* * *
19934712 ACTTCAGTACCCCTGAATTGTACATACATGCCCCTGTTTGT
1 ACTTCGGTACCCCTGAATTGCACATACGTGCCCCTGTTTGT
* * * * *
19934753 ACTTTGGTACCACTAAATTGCACATACGTGCCCCTATTTTT
1 ACTTCGGTACCCCTGAATTGCACATACGTGCCCCTGTTTGT
* * * *
19934794 ACTTCGGTACACGTGAATTGGACATACATGCCCCTGTTTGT
1 ACTTCGGTACCCCTGAATTGCACATACGTGCCCCTGTTTGT
* * * *
19934835 ACTTTGTTACCCCTGAATTGCACATATGTGCCCTTGTTT
1 ACTTCGGTACCCCTGAATTGCACATACGTGCCCCTGTTT
19934874 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:19934726 original size:20 final size:19
Alignment explanation
Indices: 19934701--19934756 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 19
19934691 CACATACGTG
19934701 CCCCTGTTTGTACTTCAGTA
1 CCCCTGTTTGTACTTCA-TA
* * *
19934721 CCCCTGAATTGTACATACATG
1 CCCCTG-TTTGTAC-TTCATA
19934742 CCCCTGTTTGTACTT
1 CCCCTGTTTGTACTT
19934757 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:19934737 original size:82 final size:82
Alignment explanation
Indices: 19934671--19934873 Score: 282
Period size: 82 Copynumber: 2.5 Consensus size: 82
19934661 CATTATTTCG
* *
19934671 ACTTCGGTACCCCTGAAATGCACATACGTGCCCCTGTTTGTACTTCAGTACCCCTGAATTGTACA
1 ACTTTGGTACCCCTGAAATGCACATACGTGCCCCTGTTTGTACTTCAGTACACCTGAATTGTACA
19934736 TACATGCCCCTGTTTGT
66 TACATGCCCCTGTTTGT
* * * * * *
19934753 ACTTTGGTACCACT-AAATTGCACATACGTGCCCCTATTTTTACTTCGGTACACGTGAATTGGAC
1 ACTTTGGTACCCCTGAAA-TGCACATACGTGCCCCTGTTTGTACTTCAGTACACCTGAATTGTAC
19934817 ATACATGCCCCTGTTTGT
65 ATACATGCCCCTGTTTGT
* * * *
19934835 ACTTTGTTACCCCTGAATTGCACATATGTGCCCTTGTTT
1 ACTTTGGTACCCCTGAAATGCACATACGTGCCCCTGTTT
19934874 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:19934745 original size:21 final size:21
Alignment explanation
Indices: 19934680--19934747 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
19934670 GACTTCGGTA
* * *
19934680 CCCCTGAAATGCACATACGTG
1 CCCCTGAATTGTACATACATG
* * *
19934701 CCCCTG-TTTGTAC-TTCAGTA
1 CCCCTGAATTGTACATACA-TG
19934721 CCCCTGAATTGTACATACATG
1 CCCCTGAATTGTACATACATG
19934742 CCCCTG
1 CCCCTG
19934748 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:19936616 original size:15 final size:16
Alignment explanation
Indices: 19936589--19936618 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19936579 TGTCACATCC
19936589 AAAAAATTCGGGTTAG
1 AAAAAATTCGGGTTAG
19936605 AAAAAATT-GGGTTA
1 AAAAAATTCGGGTTA
19936619 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:19939643 original size:102 final size:102
Alignment explanation
Indices: 19939467--19939906 Score: 417
Period size: 102 Copynumber: 4.4 Consensus size: 102
19939457 TATCGATGAA
* * *
19939467 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATAGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGACTACTACGTGAATCGATAAATGATGGTCACATGTATAGTAC
* *
19939532 TAAGTGAAGGCTACAATATGTACCGAGAAGCTTCGGT
66 TAAGTGAAGGCTACAATATGTACCGAAAAGCTTCAGT
* *
19939569 CACGTGTGTAGTACTGTGTGAAGACTACTACTTGAATTGATAAATGATGGTCACATGTATAGTAC
1 CACGTGTGTAGTACTGTGTGAAGACTACTACGTGAATCGATAAATGATGGTCACATGTATAGTAC
* * *
19939634 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTAGT
66 TAAGTGAAGGCTACAATATGTACCGAAAAGCTTCAGT
* * *** * *
19939671 CACGTATGTAGTACTATGTGAAGACTACTACGTGAATCG-TAAAACTTGATCACGTGTATAGTAC
1 CACGTGTGTAGTACTGTGTGAAGACTACTACGTGAATCGATAAATGATGGTCACATGTATAGTAC
* ** ** * * *
19939735 TATGTGAAGGCTATTACGTGAACCGTAAAA-ATTGA-T
66 TAAGTGAAGGCTACAATATGTACCG-AAAAGCTTCAGT
* * * *** ** * *
19939771 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTTATCACGTGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGACTACTACGTGAATCGATAAATGATGGTCACATGTATAGTAC
** ** * *
19939835 TACA-TGAAGGCTATTACGTGAACCGTAAAA-CTTTA-T
66 TA-AGTGAAGGCTACAATATGTACCG-AAAAGCTTCAGT
* *
19939871 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAA
1 CACGTGTGTAGTACTGTGTGAAGACTACTACGTGAA
19939907 CCGTAAAACT
Statistics
Matches: 303, Mismatches: 33, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
100 128 0.42
101 44 0.15
102 131 0.43
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (102 bp):
CACGTGTGTAGTACTGTGTGAAGACTACTACGTGAATCGATAAATGATGGTCACATGTATAGTAC
TAAGTGAAGGCTACAATATGTACCGAAAAGCTTCAGT
Found at i:19939737 original size:50 final size:50
Alignment explanation
Indices: 19939467--19939946 Score: 500
Period size: 50 Copynumber: 9.5 Consensus size: 50
19939457 TATCGATGAA
* * *
19939467 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGA-TAG-T
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA--ACTTGAT
* * * ** * * *
19939518 CACATGTGTAGTACTAAGTGAAGGCTACAATATGTACCG-AGAAGCTTCGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTA-AAACTT-GAT
* * * ** *** *
19939569 CACGTGTGTAGTACTGTGTGAAGACTACTACTTGAATTGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGAT
* * * * * *
19939620 CACATGTATAGTACTAAGTGAAGGCTACTATGTGTACCG-AAAAGCTTTAGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAA-CTTGA-T
* * *
19939671 CACGTATGTAGTACTATGTGAAGACTACTACGTGAATCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
* * *
19939721 CACGTGTATAGTACTATGTGAAGGCTATTACGTGAACCGTAAAAATTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
*
19939771 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTTAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
** * *
19939821 CACGTGTGTAGTACTACATGAAGGCTATTACGTGAACCGTAAAACTTTAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
*
19939871 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTTAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
**
19939921 CACGTGTGTAGTACTACATGAAGGCT
1 CACGTGTGTAGTACTATGTGAAGGCT
19939947 GTAAAATAGA
Statistics
Matches: 355, Mismatches: 65, Indels: 19
0.81 0.15 0.04
Matches are distributed among these distances:
49 5 0.01
50 213 0.60
51 129 0.36
52 7 0.02
53 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
Found at i:19941535 original size:22 final size:22
Alignment explanation
Indices: 19941507--19941550 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
19941497 TTATGATGAA
19941507 TGATATG-ATGAGATTGATATTT
1 TGATATGTATGAGATT-ATATTT
*
19941529 TGATATGTATGTGATTATATTT
1 TGATATGTATGAGATTATATTT
19941551 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:19946933 original size:21 final size:21
Alignment explanation
Indices: 19946870--19946933 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
19946860 TTCAGGTGGA
* *
19946870 TTAGCTTTTATGAGCTTCTAT
1 TTAGCTCTTATGAGCTTCTGT
*
19946891 TAAGCTCTTATGAGCTTCTGT
1 TTAGCTCTTATGAGCTTCTGT
*
19946912 TTAGCTCTTATGAGCTTTTGT
1 TTAGCTCTTATGAGCTTCTGT
19946933 T
1 T
19946934 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:19965279 original size:40 final size:40
Alignment explanation
Indices: 19965190--19965289 Score: 130
Period size: 40 Copynumber: 2.5 Consensus size: 40
19965180 GAGCTTCTAT
* ***
19965190 TCAGCTCTTATGAGCTTCT-ATTGGCGTGTTTCAGGTGGA
1 TCAGCTCTTATGAGCTTCTGTTTGGCGTACATCAGGTGGA
* * *
19965229 CCAGCACTTATGAGCTTCTGTTTGGCGTACATCAGTTGGA
1 TCAGCTCTTATGAGCTTCTGTTTGGCGTACATCAGGTGGA
19965269 TCAGCTCTTATGAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
19965290 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:19968112 original size:11 final size:11
Alignment explanation
Indices: 19968073--19968114 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
19968063 AGTTTTAGCA
19968073 TTAG-TTTCTT
1 TTAGTTTTCTT
* *
19968083 TTAGGTTTCTC
1 TTAGTTTTCTT
19968094 TTAGTTTTCTT
1 TTAGTTTTCTT
*
19968105 TTACTTTTCT
1 TTAGTTTTCT
19968115 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:19968113 original size:22 final size:21
Alignment explanation
Indices: 19968073--19968114 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
19968063 AGTTTTAGCA
*
19968073 TTAGTTTCTTTTAGGTTTCTC
1 TTAGTTTCTTTTACGTTTCTC
*
19968094 TTAGTTTTCTTTTACTTTTCT
1 TTAG-TTTCTTTTACGTTTCT
19968115 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:19969375 original size:40 final size:40
Alignment explanation
Indices: 19969323--19969412 Score: 153
Period size: 40 Copynumber: 2.2 Consensus size: 40
19969313 GTAAATTATA
* * *
19969323 CCCTGATTGCACTTACGTGCCCTTGTTTGTACTTCGGTAC
1 CCCTGATTGCACTTACATGCCCCTGTTTGTACTTCGATAC
19969363 CCCTGATTGCACTTACATGCCCCTGTTTGTACTTCGATAC
1 CCCTGATTGCACTTACATGCCCCTGTTTGTACTTCGATAC
19969403 CCCTGATTGC
1 CCCTGATTGC
19969413 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:19969385 original size:20 final size:20
Alignment explanation
Indices: 19969323--19969412 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
19969313 GTAAATTATA
*
19969323 CCCTGATTGCACTTACG-TGC
1 CCCTGATTGCACTT-CGATAC
* * * *
19969343 CCTTGTTTGTACTTCGGTAC
1 CCCTGATTGCACTTCGATAC
*
19969363 CCCTGATTGCACTTAC-ATGC
1 CCCTGATTGCACTT-CGATAC
* *
19969383 CCCTGTTTGTACTTCGATAC
1 CCCTGATTGCACTTCGATAC
19969403 CCCTGATTGC
1 CCCTGATTGC
19969413 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:19969424 original size:40 final size:40
Alignment explanation
Indices: 19969323--19969433 Score: 152
Period size: 40 Copynumber: 2.8 Consensus size: 40
19969313 GTAAATTATA
* * *
19969323 CCCTGATTGCACTTACGTGCCCTTGTTTGTACTTCGGTAC
1 CCCTGATTGCACATACGTGCCCCTGTTTGTACTTCGATAC
* *
19969363 CCCTGATTGCACTTACATGCCCCTGTTTGTACTTCGATAC
1 CCCTGATTGCACATACGTGCCCCTGTTTGTACTTCGATAC
*
19969403 CCCTGATTGCTCAT-CGGTGCCCCTGTTTGTA
1 CCCTGATTGCACATAC-GTGCCCCTGTTTGTA
19969434 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:19974866 original size:40 final size:39
Alignment explanation
Indices: 19974803--19974976 Score: 197
Period size: 40 Copynumber: 4.4 Consensus size: 39
19974793 ACGTAAATTA
* * *
19974803 TACCCTAATTGCACTTAC-GTGCCCCTGTTTGTACTTCGG
1 TACCCTGATTGCACAT-CGGTGCCCCTGTTTGCACTTCGG
* * *
19974842 TACCCTTGATTGCAAATCGATGCCCCTGTTTGTACTTCGG
1 TACCC-TGATTGCACATCGGTGCCCCTGTTTGCACTTCGG
* *
19974882 TACCCCTGATTGCACATTGGTGCCCCTGTTTGCACTTCAG
1 TA-CCCTGATTGCACATCGGTGCCCCTGTTTGCACTTCGG
* *
19974922 TGCTCCTGATTGCACATCGGTGCCCCTGTTTGCACTTCAG
1 TAC-CCTGATTGCACATCGGTGCCCCTGTTTGCACTTCGG
*
19974962 TGCTCCTGATTGCAC
1 TAC-CCTGATTGCAC
19974977 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:19974889 original size:20 final size:20
Alignment explanation
Indices: 19974811--19974978 Score: 151
Period size: 20 Copynumber: 8.4 Consensus size: 20
19974801 TATACCCTAA
19974811 TTGCACTTAC-GTGCCCCTGT
1 TTGCACTT-CGGTGCCCCTGT
* * * *
19974831 TTGTACTTCGGTACCCTTGA
1 TTGCACTTCGGTGCCCCTGT
** *
19974851 TTGCAAATCGATGCCCCTGT
1 TTGCACTTCGGTGCCCCTGT
* * *
19974871 TTGTACTTCGGTACCCCTGA
1 TTGCACTTCGGTGCCCCTGT
19974891 TTGCACATT-GGTGCCCCTGT
1 TTGCAC-TTCGGTGCCCCTGT
* * *
19974911 TTGCACTTCAGTGCTCCTGA
1 TTGCACTTCGGTGCCCCTGT
*
19974931 TTGCACATCGGTGCCCCTGT
1 TTGCACTTCGGTGCCCCTGT
* * *
19974951 TTGCACTTCAGTGCTCCTGA
1 TTGCACTTCGGTGCCCCTGT
19974971 TTGCACTT
1 TTGCACTT
19974979 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:19974946 original size:80 final size:80
Alignment explanation
Indices: 19974821--19974982 Score: 218
Period size: 80 Copynumber: 2.0 Consensus size: 80
19974811 TTGCACTTAC
* * * *
19974821 GTGCCCCTGTTTGTACTTCGGTACCCTTGATTGCAAATCGATGCCCCTGTTTGTACTTCGGTACC
1 GTGCCCCTGTTTGCACTTCAGTACCCTTGATTGCAAATCGATGCCCCTGTTTGCACTTCAGTACC
19974886 CCTGATTGCACATTG
66 CCTGATTGCACATTG
* * * *
19974901 GTGCCCCTGTTTGCACTTCAGTGCTCC-TGATTGCACATCGGTGCCCCTGTTTGCACTTCAGTGC
1 GTGCCCCTGTTTGCACTTCAGTAC-CCTTGATTGCAAATCGATGCCCCTGTTTGCACTTCAGTAC
* *
19974965 TCCTGATTGCACTTTG
65 CCCTGATTGCACATTG
19974981 GT
1 GT
19974983 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:19976856 original size:20 final size:20
Alignment explanation
Indices: 19976831--19976875 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
19976821 ACCCCTGTAG
*
19976831 TTTGAAAATTT-TCATCTTTT
1 TTTGAAAATTTCT-ATATTTT
19976851 TTTGAAAATTTCTATATTTT
1 TTTGAAAATTTCTATATTTT
19976871 TTTGA
1 TTTGA
19976876 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:19988315 original size:51 final size:50
Alignment explanation
Indices: 19988229--19988355 Score: 157
Period size: 51 Copynumber: 2.5 Consensus size: 50
19988219 NNNTAGGTCG
* * *
19988229 CATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGGATAGCT-TCGATCA
1 CATGTGTAGTACTATGTGCAGGCTAATACGCGTATCAGATAG-TAT-GATCA
* * * *
19988280 CGTGTGTAGTACTATGCGCAGGCTAATACGTGTATCAGATAGTGATGGTCA
1 CATGTGTAGTACTATGTGCAGGCTAATACGCGTATCAGATAGT-ATGATCA
19988331 CATGTGTAGTACTATGTGCAGGCTA
1 CATGTGTAGTACTATGTGCAGGCTA
19988356 CTATGTGAAC
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
50 1 0.02
51 63 0.97
52 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (50 bp):
CATGTGTAGTACTATGTGCAGGCTAATACGCGTATCAGATAGTATGATCA
Found at i:19990953 original size:6 final size:6
Alignment explanation
Indices: 19990939--19990978 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
19990929 TTTTGCTTTC
* **
19990939 TTTCAT TTTCTT TTTCTT TTTCAA TTTCTT TTTCTT TTTC
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTC
19990979 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:19990966 original size:18 final size:18
Alignment explanation
Indices: 19990939--19990979 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
19990929 TTTTGCTTTC
*
19990939 TTTCATTTTCTTTTTCTT
1 TTTCAATTTCTTTTTCTT
19990957 TTTCAATTTCTTTTTCTT
1 TTTCAATTTCTTTTTCTT
19990975 TTTCA
1 TTTCA
19990980 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:19990987 original size:18 final size:18
Alignment explanation
Indices: 19990948--19990990 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
19990938 CTTTCATTTT
*
19990948 CTTTTTCTTTTTCAATTT
1 CTTTTTCTTTTTCAATTG
19990966 CTTTTTCTTTTTCACA-TG
1 CTTTTTCTTTTTCA-ATTG
19990984 CTTTTTC
1 CTTTTTC
19990991 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:19992981 original size:3 final size:3
Alignment explanation
Indices: 19992973--19993045 Score: 74
Period size: 3 Copynumber: 24.3 Consensus size: 3
19992963 TTCTTTTAAA
* * * * *
19992973 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
* * *
19993021 TGT TAT AAT TAT TAG TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
19993046 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:19993263 original size:25 final size:25
Alignment explanation
Indices: 19993224--19993272 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
19993214 TATTATATGT
*
19993224 TTGTTTTAAAATTCATTGTGTATTA
1 TTGTTTTAAAATTCATTATGTATTA
**
19993249 TTGTTTTAATCTTCATTATGTATT
1 TTGTTTTAAAATTCATTATGTATT
19993273 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:20008783 original size:6 final size:6
Alignment explanation
Indices: 20008774--20008805 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
20008764 AAACTAAAGT
20008774 AATATA AATATA AATATA AATATA AATA-A AAT
1 AATATA AATATA AATATA AATATA AATATA AAT
20008806 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:20010200 original size:27 final size:27
Alignment explanation
Indices: 20010141--20010207 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
20010131 TGGACCACCC
*
20010141 CATGTTTATTGTCCAAACAAACTACCT
1 CATGTTTACTGTCCAAACAAACTACCT
* *
20010168 CATGTTTACTGTCCCATCAAACTATCC-
1 CATGTTTACTGTCCAAACAAACTA-CCT
*
20010195 CGTGTTTACTGTC
1 CATGTTTACTGTC
20010208 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:20011232 original size:21 final size:21
Alignment explanation
Indices: 20011206--20011249 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
20011196 CGAAGAAGAC
20011206 CTATACATACTCTTTAAGCAG
1 CTATACATACTCTTTAAGCAG
20011227 CTATACATACTCTTTAAGCAG
1 CTATACATACTCTTTAAGCAG
20011248 CT
1 CT
20011250 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:20023989 original size:15 final size:14
Alignment explanation
Indices: 20023969--20023999 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
20023959 TATTCTTACA
20023969 ATAATGTTAAAAGAT
1 ATAATGTTAAAA-AT
20023984 ATAATGTTAAAAAT
1 ATAATGTTAAAAAT
20023998 AT
1 AT
20024000 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:20026917 original size:9 final size:9
Alignment explanation
Indices: 20026903--20027205 Score: 218
Period size: 9 Copynumber: 34.0 Consensus size: 9
20026893 TAAGTATAAT
20026903 TAAGTTATG
1 TAAGTTATG
20026912 TAAGTTATG
1 TAAGTTATG
* * *
20026921 ATATGATATA
1 -TAAGTTATG
*
20026931 T-ATTTATG
1 TAAGTTATG
20026939 T-A-TTATG
1 TAAGTTATG
20026946 TAAGTTATG
1 TAAGTTATG
20026955 TAAGTTATG
1 TAAGTTATG
*
20026964 TGAGTTATG
1 TAAGTTATG
20026973 TAAGTTATG
1 TAAGTTATG
* *
20026982 ATATGATATATA
1 -TAAG-T-TATG
*
20026994 TACGTTAT-
1 TAAGTTATG
20027002 TAAGTTATG
1 TAAGTTATG
20027011 TAAGTTATG
1 TAAGTTATG
*
20027020 TGAGTTATG
1 TAAGTTATG
*
20027029 TAAGTTACG
1 TAAGTTATG
* *
20027038 ATATGATATATA
1 -TAAG-T-TATG
20027050 TAAGTTAT-
1 TAAGTTATG
20027058 TAAGTTATG
1 TAAGTTATG
*
20027067 TATG-TATG
1 TAAGTTATG
*
20027075 TGAGTTATG
1 TAAGTTATG
20027084 TAAGTTATG
1 TAAGTTATG
*
20027093 -ATA-TTATA
1 TA-AGTTATG
*
20027101 TATATTTATG
1 TA-AGTTATG
20027111 T-A-TTATG
1 TAAGTTATG
20027118 TAAGTTATG
1 TAAGTTATG
*
20027127 TGAGTTATG
1 TAAGTTATG
20027136 TAAGTTATG
1 TAAGTTATG
* * *
20027145 ATATGATATA
1 -TAAGTTATG
*
20027155 T-ATTTATG
1 TAAGTTATG
20027163 T-A-TTATG
1 TAAGTTATG
20027170 TAAGTTATG
1 TAAGTTATG
20027179 TAAGTTATG
1 TAAGTTATG
*
20027188 TGAGTTATG
1 TAAGTTATG
*
20027197 CAAGTTATG
1 TAAGTTATG
20027206 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:20026960 original size:52 final size:52
Alignment explanation
Indices: 20026903--20027196 Score: 333
Period size: 52 Copynumber: 5.3 Consensus size: 52
20026893 TAAGTATAAT
20026903 TAAGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATGTAAG
1 TAAGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTA--T--G
20026959 TTATGTGAGTTATGTAAGTTATGATATGATATATATACGTTAT-TAAGTTATGTAAGTTATG
1 -TA----AGTTATGTAAGTTATGATATGATATATAT---TTATGT-A-TTATGTAAGTTATG
* * *
20027020 TGAGTTATGTAAGTTACGATATGATATATATAAGTTAT-TAAGTTATGTATG-TATG
1 TAAGTTATGTAAGTTATGATATGATATATAT---TTATGT-A-TTATGTAAGTTATG
* *
20027075 TGAGTTATGTAAGTTATGATATTATATATATTTATGTATTATGTAAGTTATG
1 TAAGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATG
*
20027127 TGAGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATG
1 TAAGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATG
*
20027179 TAAGTTATGTGAGTTATG
1 TAAGTTATGTAAGTTATG
20027197 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:20027433 original size:24 final size:24
Alignment explanation
Indices: 20027406--20027467 Score: 61
Period size: 28 Copynumber: 2.4 Consensus size: 24
20027396 AATCAATTAA
*
20027406 TCAAATATAAAATCGATAATTTAT
1 TCAAATAAAAAATCGATAATTTAT
*
20027430 TCAATTAAATAAAAAATTGATAATTTAT
1 TC----AAATAAAAAATCGATAATTTAT
*
20027458 TCACATAAAA
1 TCAAATAAAA
20027468 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:20027493 original size:38 final size:37
Alignment explanation
Indices: 20027449--20027642 Score: 165
Period size: 38 Copynumber: 5.7 Consensus size: 37
20027439 TAAAAAATTG
*
20027449 ATAATTTATTCACATAAAATCAAATAAACTAATCAAAC
1 ATAATTTATTCA-ATTAAATCAAATAAACTAATCAAAC
*
20027487 ATAATTTATTCAATTAAAT---A-AAA--AATC---G
1 ATAATTTATTCAATTAAATCAAATAAACTAATCAAAC
*
20027515 ATAATTTATTCACATTAAATCGAATAAACTAATCAAAC
1 ATAATTTATTCA-ATTAAATCAAATAAACTAATCAAAC
*
20027553 ATAATTTATTCAATTAAATC----AAA--AATC---G
1 ATAATTTATTCAATTAAATCAAATAAACTAATCAAAC
* * *
20027581 ATAATTTATTCACATTAAACCTAGTAAACTAATCAAAC
1 ATAATTTATTCA-ATTAAATCAAATAAACTAATCAAAC
20027619 ATAATTTATTCAATT-AATCAAATA
1 ATAATTTATTCAATTAAATCAAATA
20027643 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:20027496 original size:66 final size:66
Alignment explanation
Indices: 20027421--20027635 Score: 367
Period size: 66 Copynumber: 3.3 Consensus size: 66
20027411 TATAAAATCG
* *
20027421 ATAATTTATTCAATTAAATAAAAAATTGATAATTTATTCACATAAAATCAAATAAACTAATCAAA
1 ATAATTTATTCAATTAAATAAAAAATCGATAATTTATTCACATTAAATCAAATAAACTAATCAAA
20027486 C
66 C
*
20027487 ATAATTTATTCAATTAAATAAAAAATCGATAATTTATTCACATTAAATCGAATAAACTAATCAAA
1 ATAATTTATTCAATTAAATAAAAAATCGATAATTTATTCACATTAAATCAAATAAACTAATCAAA
20027552 C
66 C
* * * *
20027553 ATAATTTATTCAATTAAATCAAAAATCGATAATTTATTCACATTAAACCTAGTAAACTAATCAAA
1 ATAATTTATTCAATTAAATAAAAAATCGATAATTTATTCACATTAAATCAAATAAACTAATCAAA
20027618 C
66 C
20027619 ATAATTTATTCAATTAA
1 ATAATTTATTCAATTAA
20027636 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:20027499 original size:28 final size:28
Alignment explanation
Indices: 20027487--20027592 Score: 77
Period size: 28 Copynumber: 3.4 Consensus size: 28
20027477 CTAATCAAAC
*
20027487 ATAATTTATTCAATTAAATAAAAAATCG
1 ATAATTTATTCAAATAAATAAAAAATCG
* *
20027515 ATAATTTATTCACATTAAATCGAATAAACTAATCAAAC
1 ATAATTTATTCA-AATAAAT---A-AAA--AATC---G
* *
20027553 ATAATTTATTCAATTAAATCAAAAATCG
1 ATAATTTATTCAAATAAATAAAAAATCG
20027581 ATAATTTATTCA
1 ATAATTTATTCA
20027593 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:20030200 original size:21 final size:22
Alignment explanation
Indices: 20030165--20030210 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
20030155 TGATTGCAAA
*
20030165 TTAAGATTTTAAAATTTAA-AT
1 TTAAGATTTTAAAATATAATAT
20030186 TTAA-ATTTTAGAAATATAATAT
1 TTAAGATTTTA-AAATATAATAT
20030208 TTA
1 TTA
20030211 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:20030809 original size:7 final size:7
Alignment explanation
Indices: 20030764--20030862 Score: 74
Period size: 7 Copynumber: 13.9 Consensus size: 7
20030754 TTAAAATCGG
20030764 ACCCTAA
1 ACCCTAA
*
20030771 ACACTAA
1 ACCCTAA
*
20030778 ACCATAA
1 ACCCTAA
20030785 ACCCTAA
1 ACCCTAA
* *
20030792 GCACGTAA
1 AC-CCTAA
20030800 ACCCTAA
1 ACCCTAA
*
20030807 ACCATAA
1 ACCCTAA
**
20030814 ACTTTAA
1 ACCCTAA
*
20030821 ATCCTAA
1 ACCCTAA
20030828 ACCCTAA
1 ACCCTAA
*
20030835 ACCTTAA
1 ACCCTAA
*
20030842 GCCC-ATA
1 ACCCTA-A
20030849 ACCCTTAA
1 ACCC-TAA
20030857 ACCCTA
1 ACCCTA
20030863 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:20031018 original size:7 final size:7
Alignment explanation
Indices: 20031008--20031074 Score: 53
Period size: 7 Copynumber: 9.6 Consensus size: 7
20030998 ATCTTAAATA
20031008 CTAAACT
1 CTAAACT
*
20031015 CTAAACC
1 CTAAACT
*
20031022 CTAAACC
1 CTAAACT
* *
20031029 CCAAACC
1 CTAAACT
*
20031036 CCAAACT
1 CTAAACT
* *
20031043 TTAAACC
1 CTAAACT
20031050 CTAAACT
1 CTAAACT
20031057 CTAAACT
1 CTAAACT
* *
20031064 CAAAAAT
1 CTAAACT
20031071 CTAA
1 CTAA
20031075 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:20031025 original size:14 final size:14
Alignment explanation
Indices: 20031008--20031062 Score: 74
Period size: 14 Copynumber: 3.9 Consensus size: 14
20030998 ATCTTAAATA
20031008 CTAAACTCTAAACC
1 CTAAACTCTAAACC
* *
20031022 CTAAACCCCAAACC
1 CTAAACTCTAAACC
* *
20031036 CCAAACTTTAAACC
1 CTAAACTCTAAACC
20031050 CTAAACTCTAAAC
1 CTAAACTCTAAAC
20031063 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:20031167 original size:14 final size:14
Alignment explanation
Indices: 20031109--20031174 Score: 53
Period size: 14 Copynumber: 4.7 Consensus size: 14
20031099 ATAAGCCCTA
20031109 AAACCCTAAACCAT
1 AAACCCTAAACCAT
**
20031123 AAACATTAAA-CATT
1 AAACCCTAAACCA-T
** *
20031137 AAATACTAAACCCT
1 AAACCCTAAACCAT
*
20031151 AAACCCTAAACTAT
1 AAACCCTAAACCAT
*
20031165 AAAACCTAAA
1 AAACCCTAAA
20031175 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:20031472 original size:156 final size:156
Alignment explanation
Indices: 20031189--20031638 Score: 465
Period size: 156 Copynumber: 2.9 Consensus size: 156
20031179 GTTCAGCAAA
* * * ** * *
20031189 AAATGACGTCATTTTGCTCAACTTTTTTACGGCATTTTACAAAAAGCGTTGTTATTGCTTGATCT
1 AAATAACGTCATTTTGCTCAACTTTTTTGCGGCATTTTCCAAAAAGCGCCGCTAATGCTTGATCT
* * * *
20031254 TCAGCGGCGTTTATCAAAAAGCGCCGCTAATTCTCTATCTATCGCGGTATTTGTTAGAAAGTGCC
66 TCAGCGGCGTTTAACAAAAAGCGCCGCTAATTCTCAATCTATCGCGGCATTTGTTAAAAAGTGCC
*
20031319 TCTAATGCCACTAAAGCTC-AAAAGG
131 ACTAATGCCACTAAAGCTCAAAAAGG
* * * *
20031344 AAAATAATGTCATTTTGCTTAACTTTTTTGCGGCGTTTTCCAAAAAACGCCGCTAATGCTTGATC
1 -AAATAACGTCATTTTGCTCAACTTTTTTGCGGCATTTTCCAAAAAGCGCCGCTAATGCTTGATC
** ** ** * * *
20031409 TTTTGCGTTGTTTAACAAAAAGCGTTGTTAATTCTCAATCTATTGCGGCGTTTGTTAAAAAGTGC
65 TTCAGCGGCGTTTAACAAAAAGCGCCGCTAATTCTCAATCTATCGCGGCATTTGTTAAAAAGTGC
20031474 CACTAATGCCACTAAAGCTCAAAAAGG
130 CACTAATGCCACTAAAGCTCAAAAAGG
* * * * * *
20031501 AAATGACGTCGTTTTGCTCAACTTTTTTGCTGCATTTTCCAAAAAGCACCGCAAATGATTGATCT
1 AAATAACGTCATTTTGCTCAACTTTTTTGCGGCATTTTCCAAAAAGCGCCGCTAATGCTTGATCT
* * * * * * * * * * * *
20031566 ACAGTGGCATTTTACAAGAAGCGCCACT-ATTGCT-TACCTATTGTGGCATTTTGTTAAGAAGCG
66 TCAGCGGCGTTTAACAAAAAGCGCCGCTAATT-CTCAATCTATCGCGGCA-TTTGTTAAAAAGTG
20031629 CCACTAATGC
129 CCACTAATGC
20031639 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:20032179 original size:9 final size:9
Alignment explanation
Indices: 20032165--20032190 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
20032155 ATTCATTATT
20032165 TTTTAGTTA
1 TTTTAGTTA
20032174 TTTTAGTTA
1 TTTTAGTTA
20032183 TTTTAGTT
1 TTTTAGTT
20032191 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:20046896 original size:10 final size:10
Alignment explanation
Indices: 20046882--20046910 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
20046872 ATATAAATTA
20046882 TAAAAAATAT
1 TAAAAAATAT
20046892 TAAAAAA-AT
1 TAAAAAATAT
20046901 TAAAAAATAT
1 TAAAAAATAT
20046911 ATACAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
TAAAAAATAT
Found at i:20047076 original size:9 final size:9
Alignment explanation
Indices: 20047024--20047121 Score: 55
Period size: 9 Copynumber: 11.0 Consensus size: 9
20047014 AAAACAAATG
*
20047024 AAAAATTGT
1 AAAAATTAT
20047033 AAAAATTAT
1 AAAAATTAT
*
20047042 GAAAAGATATTT
1 -AAAA-AT-TAT
20047054 AAAAA-TAT
1 AAAAATTAT
20047062 AGAAAATTAT
1 A-AAAATTAT
*
20047072 AAAAAATAT
1 AAAAATTAT
*
20047081 AAAAA-AAT
1 AAAAATTAT
* *
20047089 AGAAAAGT-G
1 A-AAAATTAT
20047098 AAAAA-TAT
1 AAAAATTAT
20047106 AAAAA-T-T
1 AAAAATTAT
20047113 AAAAATTAT
1 AAAAATTAT
20047122 TCAAATTTAT
Statistics
Matches: 71, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
7 7 0.10
8 17 0.24
9 30 0.42
10 9 0.13
11 6 0.08
12 2 0.03
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (9 bp):
AAAAATTAT
Found at i:20047084 original size:8 final size:8
Alignment explanation
Indices: 20047053--20047118 Score: 55
Period size: 8 Copynumber: 7.9 Consensus size: 8
20047043 AAAAGATATT
20047053 TAAAAATA
1 TAAAAATA
20047061 TAGAAAATTA
1 TA-AAAA-TA
20047071 TAAAAAATA
1 T-AAAAATA
*
20047080 TAAAAAAA
1 TAAAAATA
20047088 TAGAAAAGT-
1 TA-AAAA-TA
*
20047097 GAAAAATA
1 TAAAAATA
20047105 TAAAAAT-
1 TAAAAATA
20047112 TAAAAAT
1 TAAAAAT
20047119 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:20047094 original size:19 final size:19
Alignment explanation
Indices: 20047054--20047094 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
20047044 AAAGATATTT
* * *
20047054 AAAAATATAGAAAATTATA
1 AAAAATATAAAAAAATAGA
20047073 AAAAATATAAAAAAATAGA
1 AAAAATATAAAAAAATAGA
20047092 AAA
1 AAA
20047095 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:20047493 original size:19 final size:18
Alignment explanation
Indices: 20047453--20047503 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
20047443 TTAAATTTGC
*
20047453 TTTATAATTTTTATGTTA
1 TTTATAATTTTTATGTAA
20047471 TTTATAATATTTTAT-TAA
1 TTTATAAT-TTTTATGTAA
20047489 TTTTATTAATTTTTA
1 -TTTA-TAATTTTTA
20047504 AAANNNNNNN
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:20047790 original size:25 final size:25
Alignment explanation
Indices: 20047737--20047783 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
20047727 TATTTTTTAA
*
20047737 ATATTTAAATATTTTTTAATTATCT
1 ATATTTAAATATTTTTTAATGATCT
*
20047762 ATATTTTAA-ATTTTTTAATGAT
1 ATATTTAAATATTTTTTAATGAT
20047784 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:20047857 original size:5 final size:5
Alignment explanation
Indices: 20047847--20047872 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
20047837 TGAGCATTCG
20047847 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
20047873 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:20048768 original size:9 final size:9
Alignment explanation
Indices: 20048754--20048790 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
20048744 TATAGTTTGA
20048754 TATTCGAAT
1 TATTCGAAT
20048763 TATTCGAAT
1 TATTCGAAT
*
20048772 TATTCGAGT
1 TATTCGAAT
20048781 TATTCGAAT
1 TATTCGAAT
20048790 T
1 T
20048791 CAAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:20050511 original size:31 final size:29
Alignment explanation
Indices: 20050453--20050555 Score: 80
Period size: 31 Copynumber: 3.4 Consensus size: 29
20050443 ATTCCTTTAA
* * * *
20050453 ATGTGTACAATTGAATCAAAATTAAAGTTTC
1 ATGTATACATTTGAA-CCAAATCAAAG-TTC
*
20050484 ATGTATACATTTGAACCATGATCAAAGTTC
1 ATGTATACATTTGAACCA-AATCAAAGTTC
* * *
20050514 TATGTATATAATTGCACCAAATCAAAGTTC
1 -ATGTATACATTTGAACCAAATCAAAGTTC
*
20050544 ATGAATCACATT
1 ATGTAT-ACATT
20050556 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:20053417 original size:21 final size:23
Alignment explanation
Indices: 20053388--20053433 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
20053378 CCAACTAAAG
*
20053388 CCTCCATTTCC-TAA-AATTCAA
1 CCTCCATTTCCAGAACAATTCAA
*
20053409 CCTCTATTTCCAGAACAATTCAA
1 CCTCCATTTCCAGAACAATTCAA
20053432 CC
1 CC
20053434 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:20055611 original size:12 final size:11
Alignment explanation
Indices: 20055594--20055661 Score: 57
Period size: 12 Copynumber: 5.8 Consensus size: 11
20055584 AGGCAACCCA
20055594 ATTTTTATTTTT
1 ATTTTTA-TTTT
*
20055606 ATTTTTTATTATC
1 A-TTTTTATT-TT
*
20055619 ATTTTTACTTT
1 ATTTTTATTTT
*
20055630 ATTTATTACTTT
1 ATTT-TTATTTT
20055642 A-TTTTATTTT
1 ATTTTTATTTT
20055652 ATTATTTATT
1 ATT-TTTATT
20055662 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:20055660 original size:17 final size:17
Alignment explanation
Indices: 20055596--20055661 Score: 57
Period size: 17 Copynumber: 3.8 Consensus size: 17
20055586 GCAACCCAAT
20055596 TTTTATT-TTTATTTT-
1 TTTTATTATTTATTTTA
* *
20055611 TTATTATCATTTTTACTTTA
1 TT-TTAT--TATTTATTTTA
20055631 -TTTATTACTTTATTTTA
1 TTTTATTA-TTTATTTTA
20055648 TTTTATTATTTATT
1 TTTTATTATTTATT
20055662 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:20056694 original size:102 final size:102
Alignment explanation
Indices: 20056503--20056695 Score: 216
Period size: 102 Copynumber: 1.9 Consensus size: 102
20056493 AAGAACATGT
* * * *
20056503 TGGGCTGAGTAACTGGGGTAGGGTGCTTGGGTTGTCATCCTATTTCGCGTCAAAAGGTTCGATGT
1 TGGGCTGAGTAACCGGGGTAGGGTGCTTGGGCTGTCATCCTATTTCGCGCCAAAAGGTTCGATAT
* * *
20056568 GTTCTTAAGAAAAAATTATAATAAATTAGGAGTCTAC
66 GTCCTAAAGAAAAAATAATAATAAATTAGGAGTCTAC
* * *
20056605 TGGGCTGAGTAACCGGGGTGGGGTGCTT-GGCTGTTATCTCTCTTT-GCGCCAAAAGGTTCAGTA
1 TGGGCTGAGTAACCGGGGTAGGGTGCTTGGGCTGTCATC-CTATTTCGCGCCAAAAGGTTC-G-A
20056668 TAT-TCCTAAAGCATAAAAA-AAT-ATAAAT
63 TATGTCCTAAAG-A-AAAAATAATAATAAAT
20056696 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:20056710 original size:10 final size:9
Alignment explanation
Indices: 20056680--20056749 Score: 59
Period size: 10 Copynumber: 7.0 Consensus size: 9
20056670 TTCCTAAAGC
20056680 ATAAAAAAA
1 ATAAAAAAA
20056689 TATAAATAAAAA
1 -AT-AA-AAAAA
20056701 ATAAATAAAA
1 ATAAA-AAAA
*
20056711 ATCAAAATAA
1 AT-AAAAAAA
20056721 ATAAAAATAA
1 ATAAAAA-AA
20056731 ATAAAGAAAA
1 ATAAA-AAAA
*
20056741 AGAAAAAAA
1 ATAAAAAAA
20056750 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:20056717 original size:16 final size:15
Alignment explanation
Indices: 20056680--20056752 Score: 71
Period size: 16 Copynumber: 4.9 Consensus size: 15
20056670 TTCCTAAAGC
20056680 ATAAAA-AAATATAAA
1 ATAAAATAAATA-AAA
*
20056695 TAAAAAATAAATAAAA
1 -ATAAAATAAATAAAA
20056711 ATCAAAATAAATAAAA
1 AT-AAAATAAATAAAA
*
20056727 AT-AAATAAAGAAAA
1 ATAAAATAAATAAAA
*
20056741 AGAAAA-AAATAA
1 ATAAAATAAATAA
20056753 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:20060231 original size:24 final size:24
Alignment explanation
Indices: 20060198--20060244 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
20060188 TAAAAGTGTG
*
20060198 ACTCTCACACCCTCCTAAGGGTCT
1 ACTCTCACACCCTCATAAGGGTCT
* *
20060222 ACTCTTACACCCTCATGAGGGTC
1 ACTCTCACACCCTCATAAGGGTC
20060245 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:20066389 original size:18 final size:18
Alignment explanation
Indices: 20066366--20066403 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
20066356 ATTAACTCAC
*
20066366 CTGAACTTTTCTATTAGG
1 CTGAACTTGTCTATTAGG
20066384 CTGAACTTGTCTATTAGG
1 CTGAACTTGTCTATTAGG
20066402 CT
1 CT
20066404 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:20072414 original size:13 final size:14
Alignment explanation
Indices: 20072396--20072429 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
20072386 ATAATAAATA
20072396 TATTTTTT-ATTTT
1 TATTTTTTAATTTT
20072409 TATTTTTTAATTTT
1 TATTTTTTAATTTT
*
20072423 TAATTTT
1 TATTTTT
20072430 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:20072421 original size:14 final size:13
Alignment explanation
Indices: 20072396--20072429 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
20072386 ATAATAAATA
20072396 TATTTTTTATTTT
1 TATTTTTTATTTT
20072409 TATTTTTTAATTTT
1 TATTTTTT-ATTTT
20072423 TAATTTT
1 T-ATTTT
20072430 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:20073427 original size:17 final size:18
Alignment explanation
Indices: 20073393--20073431 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
20073383 ATTAATTAAG
20073393 TTTATATATTTTTAAAAT
1 TTTATATATTTTTAAAAT
*
20073411 TTTATCTATTTTT-AAAT
1 TTTATATATTTTTAAAAT
20073428 TTTA
1 TTTA
20073432 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:20073738 original size:22 final size:23
Alignment explanation
Indices: 20073710--20073761 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
20073700 CATGTTAGCG
20073710 AACAAATATATAAATATA-AATA
1 AACAAATATATAAATATATAATA
* *
20073732 AACAAATATTTATATATATAATA
1 AACAAATATATAAATATATAATA
20073755 AA-AAATA
1 AACAAATA
20073762 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:20075343 original size:33 final size:35
Alignment explanation
Indices: 20075290--20075361 Score: 130
Period size: 33 Copynumber: 2.1 Consensus size: 35
20075280 TTAAAATTGA
20075290 ATTTTGAAACATTCAAATCATTATTTTCCTTA-TT
1 ATTTTGAAACATTCAAATCATTATTTTCCTTATTT
20075324 ATTTTGAAAC-TTCAAATCATTATTTTCCTTATTT
1 ATTTTGAAACATTCAAATCATTATTTTCCTTATTT
20075358 ATTT
1 ATTT
20075362 GAAGTAAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 21 0.57
34 16 0.43
ACGTcount: A:0.31, C:0.14, G:0.03, T:0.53
Consensus pattern (35 bp):
ATTTTGAAACATTCAAATCATTATTTTCCTTATTT
Found at i:20076551 original size:40 final size:40
Alignment explanation
Indices: 20076479--20076554 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
20076469 ATTGTTCATG
*
20076479 CCACGTCAGCAAATCGCGTCCTAGGGGGCGCGATTTGTGT
1 CCACGTCAGCAAATCGCGTCCTAGGGGACGCGATTTGTGT
* *
20076519 CCACGTCAGCAAATCGCG-CTTACGTGGACGCGATTT
1 CCACGTCAGCAAATCGCGTCCTA-GGGGACGCGATTT
20076555 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:20077477 original size:15 final size:15
Alignment explanation
Indices: 20077442--20077483 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
20077432 ATAAATCATT
20077442 ATATTTA-TTTAATA
1 ATATTTATTTTAATA
* *
20077456 CTTTTTATTTTAATA
1 ATATTTATTTTAATA
20077471 ATATTTAATTTTA
1 ATATTT-ATTTTA
20077484 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:20077743 original size:21 final size:21
Alignment explanation
Indices: 20077712--20077761 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
20077702 TCGTTGTTTC
*
20077712 TAATGTCACCATTACAGT-AT
1 TAATCTCACCATTACAGTAAT
*
20077732 TCAATCTCACCATTATAGTAAT
1 T-AATCTCACCATTACAGTAAT
20077754 TAATCTCA
1 TAATCTCA
20077762 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:20078391 original size:19 final size:19
Alignment explanation
Indices: 20078367--20078407 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
20078357 CATCATTATC
20078367 ATCACCATTTATTCAATCA
1 ATCACCATTTATTCAATCA
20078386 ATCACCATTTATTCAATCA
1 ATCACCATTTATTCAATCA
20078405 ATC
1 ATC
20078408 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:20080980 original size:63 final size:61
Alignment explanation
Indices: 20080875--20081013 Score: 158
Period size: 63 Copynumber: 2.2 Consensus size: 61
20080865 ATTTATTCAC
* * *
20080875 ATGTGGTTCGAATGTATGTTCAAATTATTTGAGCTGAAATTTAA-G-TATGAATCTTATACAT
1 ATGTGGTTCGAATATAGGTTCAAATTACTTGAGCTGAAATTTAATGTTATGAA--TTATACAT
* * *
20080936 ATAAGTGGTTCGAATATAGGTTACAAATTCCTTGAGCTG-TATTTAATGTTGTGAATTATACAT
1 AT--GTGGTTCGAATATAGGTT-CAAATTACTTGAGCTGAAATTTAATGTTATGAATTATACAT
20080999 ATGTGGTTCGAATAT
1 ATGTGGTTCGAATAT
20081014 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:20081175 original size:41 final size:41
Alignment explanation
Indices: 20081128--20081282 Score: 238
Period size: 41 Copynumber: 3.8 Consensus size: 41
20081118 ATCTAAGTTA
* *
20081128 TTCAGACTTTATGTCTAGCAGGCTTAATGCTGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
* * *
20081169 TCCAGACTTTAAGTCTAGCTGGCTTAATGCCGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
*
20081210 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGATGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
* *
20081251 TTCAGACTTTACATCTAGCAAGCTTAATGCCG
1 TTCAGACTTTACGTCTAGCAGGCTTAATGCCG
20081283 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:20081310 original size:82 final size:82
Alignment explanation
Indices: 20081142--20081328 Score: 200
Period size: 82 Copynumber: 2.3 Consensus size: 82
20081132 GACTTTATGT
* ** *
20081142 CTAGCAGGCTTAATGCTGGTGAAATATTCCAGACTTTAAGTCTAGCTGGCTTAATGCCGGTGAAA
1 CTAGCAGGCTTAATGCCGGTGAAATATTCCAGACTTTAAGTCTAGCAAGCTTAATGCCGATGAAA
* * * *
20081207 TATTTCAGACTTTACGT
66 TATATCAGACTTCAAGC
* * **
20081224 CTAGCAGGCTTAATGCCGATGAAATATTTCAGACTTTACA-TCTAGCAAGCTTAATGCCGATGTT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCCAGACTTTA-AGTCTAGCAAGCTTAATGCCGATGAA
* *
20081288 CTGA-ATCAGGCTTCAAGC
65 AT-ATATCAGACTTCAAGC
20081306 CTAGCAGGC-TACATGCCGGTGAA
1 CTAGCAGGCTTA-ATGCCGGTGAA
20081329 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:20099570 original size:50 final size:50
Alignment explanation
Indices: 20099489--20099598 Score: 139
Period size: 50 Copynumber: 2.2 Consensus size: 50
20099479 GATATCCTAT
* * * ** *
20099489 GTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCC
1 GTAAGACCATGTCTGGGACATGACATGGGCACCGAGATGAGAACTCCCAC
* * *
20099539 GTAAGACCATGTCTGGGACATGACATGGGCACCTATATGAGAACTCCCAT
1 GTAAGACCATGTCTGGGACATGACATGGGCACCGAGATGAGAACTCCCAC
20099589 GTAAGACCAT
1 GTAAGACCAT
20099599 ATCTNNNNNN
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGACATGACATGGGCACCGAGATGAGAACTCCCAC
Found at i:20107975 original size:13 final size:13
Alignment explanation
Indices: 20107957--20107983 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20107947 TTTCCAGCAA
20107957 TTATGAATTTATT
1 TTATGAATTTATT
20107970 TTATGAATTTATT
1 TTATGAATTTATT
20107983 T
1 T
20107984 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:20108148 original size:42 final size:43
Alignment explanation
Indices: 20108101--20108276 Score: 165
Period size: 50 Copynumber: 3.8 Consensus size: 43
20108091 ATGTAAGATG
**
20108101 ATGTCTGGGACATGGCGTTCTCACCGAGATGAGAGGTC-GACC
1 ATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCAGACC
20108143 ATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCTCATGTAAGACC
1 ATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG--TC-----AGACC
*
20108193 ATGTCTTGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACC
1 ATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGT----C---AGACC
* * *
20108243 ATGTCTGGGACATGGCATGGGCACCGATATGAGA
1 ATGTCTGGGACATGGCGTTGGCACCGAGATGAGA
20108277 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:20108197 original size:50 final size:50
Alignment explanation
Indices: 20108139--20108316 Score: 230
Period size: 50 Copynumber: 3.5 Consensus size: 50
20108129 ATGAGAGGTC
*
20108139 GACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCTCATGTAA
1 GACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAA
* **
20108189 GACCATGTCTTGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAA
1 GACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAA
* * * **
20108239 GACCATGTCTGGGACATGGCATGGGCACCGATATGAGAATATCCCATGTAA
1 GACCATGTCTGGGACATGGCGTTGGCACCGAGATGAG-AGGTCCCATGTAA
* * * *
20108290 GAACAGGTTTGGGACATGGCTTTGGCA
1 GACCATGTCTGGGACATGGCGTTGGCA
20108317 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:20111959 original size:50 final size:50
Alignment explanation
Indices: 20111884--20112068 Score: 237
Period size: 50 Copynumber: 3.7 Consensus size: 50
20111874 TTGGGTAAAG
*
20111884 CATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATGAGAGGTCT
1 CATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATGAGAGGTCC
*
20111934 CATGTAAGACCATGTCTT-GGACATGGTGTTGGCACCGAGATGAGAGGTCC
1 CATGTAAGACCATGT-TTGGGACATGGCGTTGGCACCGAGATGAGAGGTCC
** * * * * * **
20111984 CCCGTAAGACCATGTCTGGGACATGGCATGGGCACCAATATGAGAATATCC
1 CATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATGAG-AGGTCC
*
20112035 CATGTAAGACCATGTTTGGGACATGGCTTTGGCA
1 CATGTAAGACCATGTTTGGGACATGGCGTTGGCA
20112069 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:20119982 original size:33 final size:34
Alignment explanation
Indices: 20119931--20120005 Score: 125
Period size: 33 Copynumber: 2.2 Consensus size: 34
20119921 AGATTTAAAC
20119931 AAATTAATTACTAACACTTATTTAAGCTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
20119965 AAATTAATT-CTAACACTTATTTGAGCTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
20119998 AATTTAAT
1 AAATTAAT
20120006 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:20126516 original size:20 final size:19
Alignment explanation
Indices: 20126491--20126528 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
20126481 TTTCACTTTC
20126491 CATTCTCTTTTTCTCTTTTT
1 CATTCTCTTTTTCT-TTTTT
20126511 CATTCTCTTTTTCTTTTT
1 CATTCTCTTTTTCTTTTT
20126529 CGATTTCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.71
Consensus pattern (19 bp):
CATTCTCTTTTTCTTTTTT
Found at i:20131985 original size:17 final size:17
Alignment explanation
Indices: 20131963--20131999 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
20131953 ATGCACTAAC
*
20131963 ATGAAAATGTAATGACA
1 ATGAAAATGTAATGAAA
20131980 ATGAAAATGTAATGAAA
1 ATGAAAATGTAATGAAA
20131997 ATG
1 ATG
20132000 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:20134674 original size:183 final size:184
Alignment explanation
Indices: 20134355--20134721 Score: 727
Period size: 183 Copynumber: 2.0 Consensus size: 184
20134345 CAACGTGAAT
20134355 GCAATTTACCTGGGTGCAATTTGAGTCGAGAATTGAATAATAAAACCTATTGATCCGCAATTAAT
1 GCAATTTACCTGGGTGCAATTTGAGTCGAGAATTGAATAATAAAACCTATTGATCCGCAATTAAT
20134420 TACCACTGTAAAATAATCTTGTCAAGCCATCGTTTGGTCTTTTCCTTGTAAATTGTAGCATTTTT
66 TACCACTGTAAAATAATCTTGTCAAGCCATCGTTTGGTCTTTTCCTTGTAAATTGTAGCATTTTT
20134485 ATAAACATTTCTCCTAATCTCTAGTTCAATGATATCCAATAGTCTTTTCTTTCC
131 ATAAACATTTCTCCTAATCTCTAGTTCAATGATATCCAATAGTCTTTTCTTTCC
20134539 GCAATTTACC-GGGTGCAATTTGAGTCGAGAATTGAATAATAAAACCTATTGATCCGCAATTAAT
1 GCAATTTACCTGGGTGCAATTTGAGTCGAGAATTGAATAATAAAACCTATTGATCCGCAATTAAT
20134603 TACCACTGTAAAATAATCTTGTCAAGCCATCGTTTGGTCTTTTCCTTGTAAATTGTAGCATTTTT
66 TACCACTGTAAAATAATCTTGTCAAGCCATCGTTTGGTCTTTTCCTTGTAAATTGTAGCATTTTT
20134668 ATAAACATTTCTCCTAATCTCTAGTTCAATGATATCCAATAGTCTTTTCTTTCC
131 ATAAACATTTCTCCTAATCTCTAGTTCAATGATATCCAATAGTCTTTTCTTTCC
20134722 AACTGCTTTA
Statistics
Matches: 183, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
183 173 0.95
184 10 0.05
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (184 bp):
GCAATTTACCTGGGTGCAATTTGAGTCGAGAATTGAATAATAAAACCTATTGATCCGCAATTAAT
TACCACTGTAAAATAATCTTGTCAAGCCATCGTTTGGTCTTTTCCTTGTAAATTGTAGCATTTTT
ATAAACATTTCTCCTAATCTCTAGTTCAATGATATCCAATAGTCTTTTCTTTCC
Found at i:20152324 original size:35 final size:36
Alignment explanation
Indices: 20152269--20152338 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 36
20152259 GTTTCCCTAT
20152269 CCATCTCCTAAACAACTTTAGAACCTATAAGTTTCC
1 CCATCTCCTAAACAACTTTAGAACCTATAAGTTTCC
20152305 CCATCTCCT-AACAACTTTAGAACCTATAAGTTTC
1 CCATCTCCTAAACAACTTTAGAACCTATAAGTTTC
20152339 GGGTCAACCT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 25 0.74
36 9 0.26
ACGTcount: A:0.33, C:0.30, G:0.06, T:0.31
Consensus pattern (36 bp):
CCATCTCCTAAACAACTTTAGAACCTATAAGTTTCC
Found at i:20155336 original size:20 final size:21
Alignment explanation
Indices: 20155313--20155358 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
20155303 TCTCATTTTC
20155313 TTTTCACTTTC-TTTTTCTAT
1 TTTTCACTTTCTTTTTTCTAT
* *
20155333 TTTT-GCTTTCTTTTTTTTAT
1 TTTTCACTTTCTTTTTTCTAT
20155353 TTTTCA
1 TTTTCA
20155359 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:20155370 original size:23 final size:22
Alignment explanation
Indices: 20155321--20155383 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
20155311 TCTTTTCACT
*
20155321 TTCTTTTTCTATTTTTGC-TTTC
1 TTCTTTTTTTATTTTT-CATTTC
20155343 -T-TTTTTTTATTTTTCATGTTC
1 TTCTTTTTTTATTTTTCAT-TTC
*
20155364 TTCTTTTTTTCTTTTTCATT
1 TTCTTTTTTTATTTTTCATT
20155384 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:20156307 original size:18 final size:20
Alignment explanation
Indices: 20156284--20156330 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
20156274 CTTCACTTCA
20156284 TTTTTTTTATAC-T-CAAAC
1 TTTTTTTTATACTTCCAAAC
*
20156302 TTTTTTTTATACTTCCAAAT
1 TTTTTTTTATACTTCCAAAC
20156322 TTTTTTTTA
1 TTTTTTTTA
20156331 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:20156309 original size:20 final size:19
Alignment explanation
Indices: 20156283--20156328 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
20156273 ACTTCACTTC
20156283 ATTTTTTTTATAC-T-CAA
1 ATTTTTTTTATACTTCCAA
20156300 ACTTTTTTTTATACTTCCAA
1 A-TTTTTTTTATACTTCCAA
20156320 ATTTTTTTT
1 ATTTTTTTT
20156329 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:20157596 original size:17 final size:19
Alignment explanation
Indices: 20157576--20157610 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
20157566 TCAAACACAT
20157576 TAATTT-AAC-AAATTAAC
1 TAATTTAAACTAAATTAAC
20157593 TAATTTAAACTAAATTAA
1 TAATTTAAACTAAATTAA
20157611 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:20158626 original size:27 final size:28
Alignment explanation
Indices: 20158564--20158626 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
20158554 AAACACAATA
20158564 AAATG-ATGTAATAAGCTAAGACAAATT
1 AAATGCATGTAATAAGCTAAGACAAATT
* *
20158591 -AATGTCATGTACTAA-CTAAGACATATT
1 AAATG-CATGTAATAAGCTAAGACAAATT
20158618 AAATGCATG
1 AAATGCATG
20158627 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:20159151 original size:11 final size:11
Alignment explanation
Indices: 20159119--20159177 Score: 50
Period size: 11 Copynumber: 5.2 Consensus size: 11
20159109 AGAAAAGAGC
*
20159119 GAATGATGAAT
1 GAATGAGGAAT
20159130 G-ATGA-GAAT
1 GAATGAGGAAT
20159139 GAATGAGGAAT
1 GAATGAGGAAT
*
20159150 GATTGAGGGATGAT
1 GAATGA-GGA--AT
20159164 GAATGAAGGAAT
1 GAATG-AGGAAT
20159176 GA
1 GA
20159178 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:20162139 original size:13 final size:13
Alignment explanation
Indices: 20162123--20162156 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
20162113 AAACAACTCG
20162123 AAAAAAAATTTGA
1 AAAAAAAATTTGA
20162136 AAAAAAAATTTGA
1 AAAAAAAATTTGA
20162149 AAAAAAAA
1 AAAAAAAA
20162157 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
Found at i:20162218 original size:14 final size:13
Alignment explanation
Indices: 20162199--20162243 Score: 81
Period size: 13 Copynumber: 3.5 Consensus size: 13
20162189 CCAAGTTGTG
*
20162199 AAAAAAAATTTGA
1 AAAAAAAAATTGA
20162212 AAAAAAAAATTGA
1 AAAAAAAAATTGA
20162225 AAAAAAAAATTGA
1 AAAAAAAAATTGA
20162238 AAAAAA
1 AAAAAA
20162244 GAGAGTTAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.16
Consensus pattern (13 bp):
AAAAAAAAATTGA
Found at i:20179796 original size:21 final size:23
Alignment explanation
Indices: 20179749--20179798 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
20179739 TCATCTGCAA
*
20179749 TAAACACATTAAAATAAGTTAAT
1 TAAACACATGAAAATAAGTTAAT
*
20179772 TAAACACATGAAAA-CAGTT-AT
1 TAAACACATGAAAATAAGTTAAT
20179793 TAAACA
1 TAAACA
20179799 TAACACACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 8 0.32
22 4 0.16
23 13 0.52
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (23 bp):
TAAACACATGAAAATAAGTTAAT
Found at i:20180100 original size:29 final size:30
Alignment explanation
Indices: 20180066--20180146 Score: 80
Period size: 28 Copynumber: 2.8 Consensus size: 30
20180056 AAATGCAAAT
*
20180066 TTAACTAACATGAAAGTTACATATTTAAAC
1 TTAACTAACATGAAAGTTACATATGTAAAC
* * *
20180096 -TAACTTGAC-T-TAATTTA-ATGATGTAAAC
1 TTAAC-TAACATGAAAGTTACAT-ATGTAAAC
20180124 TTAACTAACATGAAAGTTACATA
1 TTAACTAACATGAAAGTTACATA
20180147 ATGCATGAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
27 2 0.05
28 15 0.39
29 10 0.26
30 9 0.24
31 2 0.05
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (30 bp):
TTAACTAACATGAAAGTTACATATGTAAAC
Found at i:20182939 original size:15 final size:15
Alignment explanation
Indices: 20182910--20182967 Score: 71
Period size: 15 Copynumber: 3.8 Consensus size: 15
20182900 TCCATTGAGC
*
20182910 GAGAAAAAGAAAAAAA
1 GAGAAAAA-AGAAAAA
20182926 GAGAAAAAAGAAAAA
1 GAGAAAAAAGAAAAA
**
20182941 GATTAAAAAGAAAAA
1 GAGAAAAAAGAAAAA
*
20182956 GAGAGAAAAGAA
1 GAGAAAAAAGAA
20182968 TGATGAGAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
15 28 0.78
16 8 0.22
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (15 bp):
GAGAAAAAAGAAAAA
Done.