Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 190 of 216
Found at i:59315934 original size:7 final size:7
Alignment explanation
Indices: 59315924--59315979 Score: 51
Period size: 7 Copynumber: 7.4 Consensus size: 7
59315914 GCATGAGAGC
59315924 TGAGGGA
1 TGAGGGA
59315931 TGA-GGA
1 TGAGGGA
59315937 TGAGAGAGA
1 TGAG-G-GA
59315946 TGAGAGGA
1 TGAG-GGA
*
59315954 TGAGAGA
1 TGAGGGA
59315961 TGAGAGGGA
1 T--GAGGGA
59315970 TGAGGGA
1 TGAGGGA
59315977 TGA
1 TGA
59315980 TTGAAAAAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
6 6 0.14
7 15 0.36
8 7 0.17
9 14 0.33
ACGTcount: A:0.36, C:0.00, G:0.50, T:0.14
Consensus pattern (7 bp):
TGAGGGA
Found at i:59315949 original size:15 final size:16
Alignment explanation
Indices: 59315924--59315979 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
59315914 GCATGAGAGC
* *
59315924 TGAGGGATGAGGATGA
1 TGAGAGATGAGGAGGA
59315940 -GAGAGATGA-GAGGA
1 TGAGAGATGAGGAGGA
59315954 TGAGAGATGA-GAGGGA
1 TGAGAGATGAGGA-GGA
*
59315970 TGAGGGATGA
1 TGAGAGATGA
59315980 TTGAAAAAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
14 4 0.11
15 19 0.54
16 12 0.34
ACGTcount: A:0.36, C:0.00, G:0.50, T:0.14
Consensus pattern (16 bp):
TGAGAGATGAGGAGGA
Found at i:59315952 original size:24 final size:24
Alignment explanation
Indices: 59315918--59315979 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
59315908 TGATAGGCAT
*
59315918 GAGAGCTGAG-GGATGAG-GATGA
1 GAGAGATGAGAGGATGAGAGATGA
59315940 GAGAGATGAGAGGATGAGAGATGA
1 GAGAGATGAGAGGATGAGAGATGA
*
59315964 GAGGGATGAG-GGATGA
1 GAGAGATGAGAGGATGA
59315980 TTGAAAAAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
22 9 0.25
23 13 0.36
24 14 0.39
ACGTcount: A:0.35, C:0.02, G:0.50, T:0.13
Consensus pattern (24 bp):
GAGAGATGAGAGGATGAGAGATGA
Found at i:59315954 original size:17 final size:17
Alignment explanation
Indices: 59315932--59315973 Score: 61
Period size: 15 Copynumber: 2.5 Consensus size: 17
59315922 GCTGAGGGAT
59315932 GAGGATGAGAGAGATGA
1 GAGGATGAGAGAGATGA
59315949 GAGGAT--GAGAGATGA
1 GAGGATGAGAGAGATGA
59315964 GAGGGATGAG
1 GA-GGATGAG
59315974 GGATGATTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 11 0.50
16 4 0.18
17 6 0.27
18 1 0.05
ACGTcount: A:0.38, C:0.00, G:0.50, T:0.12
Consensus pattern (17 bp):
GAGGATGAGAGAGATGA
Found at i:59315972 original size:16 final size:15
Alignment explanation
Indices: 59315940--59315979 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
59315930 ATGAGGATGA
59315940 GAGAGATGAGAGGAT
1 GAGAGATGAGAGGAT
59315955 GAGAGATGAGAGGGAT
1 GAGAGATGAGA-GGAT
*
59315971 GAGGGATGA
1 GAGAGATGA
59315980 TTGAAAAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.38, C:0.00, G:0.50, T:0.12
Consensus pattern (15 bp):
GAGAGATGAGAGGAT
Found at i:59316525 original size:17 final size:18
Alignment explanation
Indices: 59316503--59316538 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
59316493 CCACTTTATA
59316503 GCTTAAA-AATATAAAAT
1 GCTTAAATAATATAAAAT
59316520 GCTTAAATTAATATAAAAT
1 GCTTAAA-TAATATAAAAT
59316539 AAGCCATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
19 10 0.59
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.33
Consensus pattern (18 bp):
GCTTAAATAATATAAAAT
Found at i:59320003 original size:20 final size:20
Alignment explanation
Indices: 59319978--59320015 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
59319968 ACCCCCTTTA
59319978 TTAACATAAA-AATTTAAAAT
1 TTAACA-AAATAATTTAAAAT
59319998 TTAACAAAATAATTTAAA
1 TTAACAAAATAATTTAAA
59320016 CTAGAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
TTAACAAAATAATTTAAAAT
Found at i:59325554 original size:24 final size:23
Alignment explanation
Indices: 59325527--59325602 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 23
59325517 AGATATTTAT
*
59325527 ATTATTTATTTATATAATATATAA
1 ATTAATTATTTATATAATAT-TAA
** *
59325551 ATTAATTATAAAGTATATTATTAA
1 ATTAATTATTTA-TATAATATTAA
*
59325575 ATTAATTATATTATA-AATATTAT
1 ATTAATTAT-TTATATAATATTAA
59325598 ATTAA
1 ATTAA
59325603 GAAATAAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
23 11 0.26
24 23 0.55
25 8 0.19
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (23 bp):
ATTAATTATTTATATAATATTAA
Found at i:59325570 original size:12 final size:11
Alignment explanation
Indices: 59325541--59325584 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
59325531 TTTATTTATA
59325541 TAATATATAAAT
1 TAAT-TATAAAT
*
59325553 TAATTATAAAG
1 TAATTATAAAT
59325564 TATATTATTAAAT
1 TA-ATTA-TAAAT
59325577 TAATTATA
1 TAATTATA
59325585 TTATAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 10 0.36
12 12 0.43
13 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (11 bp):
TAATTATAAAT
Found at i:59325596 original size:14 final size:17
Alignment explanation
Indices: 59325564--59325601 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
59325554 AATTATAAAG
59325564 TATATTATTAAATTAAT
1 TATATTATTAAATTAAT
59325581 TATATTA-TAAA-T-AT
1 TATATTATTAAATTAAT
59325595 TATATTA
1 TATATTA
59325602 AGAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 1 0.05
16 4 0.19
17 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTATTAAATTAAT
Found at i:59326386 original size:12 final size:12
Alignment explanation
Indices: 59326369--59326417 Score: 80
Period size: 12 Copynumber: 4.1 Consensus size: 12
59326359 ATGTGAGGTA
*
59326369 AGTATTAATATT
1 AGTATTATTATT
*
59326381 AGTATTAGTATT
1 AGTATTATTATT
59326393 AGTATTATTATT
1 AGTATTATTATT
59326405 AGTATTATTATT
1 AGTATTATTATT
59326417 A
1 A
59326418 TTAAGATGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (12 bp):
AGTATTATTATT
Found at i:59326420 original size:6 final size:6
Alignment explanation
Indices: 59326369--59326417 Score: 71
Period size: 6 Copynumber: 8.2 Consensus size: 6
59326359 ATGTGAGGTA
* * *
59326369 AGTATT AATATT AGTATT AGTATT AGTATT ATTATT AGTATT ATTATT
1 AGTATT AGTATT AGTATT AGTATT AGTATT AGTATT AGTATT AGTATT
59326417 A
1 A
59326418 TTAAGATGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (6 bp):
AGTATT
Found at i:59329905 original size:17 final size:18
Alignment explanation
Indices: 59329883--59329918 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
59329873 CACTTCATAG
59329883 CTTAAA-AATATAAAATA
1 CTTAAATAATATAAAATA
59329900 CTTAAATTAATATAAAATA
1 CTTAAA-TAATATAAAATA
59329919 AGCCATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
19 11 0.65
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (18 bp):
CTTAAATAATATAAAATA
Found at i:59337854 original size:18 final size:18
Alignment explanation
Indices: 59337833--59337879 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
59337823 GTATAAGTTA
*
59337833 TATTTTTCTTTTTCTTTT
1 TATTTTTCTTTTTCTCTT
* *
59337851 TATTCTTATTTTTCTCTT
1 TATTTTTCTTTTTCTCTT
*
59337869 TATTTTCCTTT
1 TATTTTTCTTT
59337880 CTTTCGAAAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.77
Consensus pattern (18 bp):
TATTTTTCTTTTTCTCTT
Found at i:59338533 original size:3 final size:3
Alignment explanation
Indices: 59338527--59338610 Score: 64
Period size: 3 Copynumber: 27.7 Consensus size: 3
59338517 TTTAGCATTT
* * * * *
59338527 TTA TTA TT- TTC TTCA TTA TTT TTA ATA -TA TTA TCA TCTT TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
* *
59338572 TTA TTT TTG TTA TTA TTA GTTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT
59338611 TCTTCATCTA
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
2 4 0.06
3 55 0.85
4 6 0.09
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:59338597 original size:22 final size:22
Alignment explanation
Indices: 59338569--59338610 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
59338559 TCATCTTTTA
* *
59338569 TTATTATTTTTGTTATTATTAG
1 TTATTATTATTATTATTATTAG
59338591 TTATTATTATTATTATTATT
1 TTATTATTATTATTATTATT
59338611 TCTTCATCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (22 bp):
TTATTATTATTATTATTATTAG
Found at i:59339298 original size:109 final size:109
Alignment explanation
Indices: 59339099--59339497 Score: 554
Period size: 109 Copynumber: 3.7 Consensus size: 109
59339089 AAAAATTTCT
* * * * * *
59339099 AAATGAGGCAATATTTAGCCTTTGGAAATTCGAGAAAACATGCCCTAATGTACTGGGTTTCGATT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAAGGTACTGGGTTTCGATT
59339164 TCTCGTTCGACTAAATAGCTAAATATTCTTTTTAAAACTTTTCAA
65 TCTCGTTCGACTAAATAGCTAAATATTCTTTTTAAAACTTTTCAA
* *
59339209 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCACTAAGGTACTGGGTTTCGATTT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
* * * *
59339274 CTCGTTCCACTAAAT-GACTTAATATCCTTTTTCAAAAATTTTC-A
66 CTCGTTCGACTAAATAG-CTAAATATTCTTTTT-AAAACTTTTCAA
59339318 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACT-GGTTTCGATTT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
* * *
59339382 CTTGTTCGACCAAATAGCTAAATA-TCTTTTAAGAAAACTTTTCAA
66 CTCGTTCGACTAAATAGCTAAATATTCTTTT--TAAAACTTTTCAA
* * * *
59339427 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTACCCTAAGGTGCTGGGTTTTGATTT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
59339492 CTCGTT
66 CTCGTT
59339498 TAACCAAACT
Statistics
Matches: 256, Mismatches: 26, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
107 5 0.02
108 39 0.15
109 158 0.62
110 54 0.21
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (109 bp):
AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
CTCGTTCGACTAAATAGCTAAATATTCTTTTTAAAACTTTTCAA
Found at i:59339476 original size:218 final size:219
Alignment explanation
Indices: 59339088--59339497 Score: 646
Period size: 218 Copynumber: 1.9 Consensus size: 219
59339078 TCAAAAAGCA
* * *
59339088 AAAAAATTTCTAAATGAGGCAATATTTAGCCTTTGGAAATTCGAGAAAACATGCCCTAATGTACT
1 AAAAAATTTCAAAATAAGGCAATATTTAGCCTTTGGAAATTCGAGAAAACATGCCCTAAGGTACT
* *
59339153 GGGTTTCGATTTCTCGTTCGACTAAATAGCTAAATATTCTTTTTAAAACTTTTCAAAAATAAGGC
66 GGGTTTCGATTTCTCGTTCGACCAAATAGCTAAATATTCTTTTGAAAACTTTTCAAAAATAAGGC
*
59339218 AATGTTTTGCGTTTGGAAATTCGAGGAACGTGCACTAAGGTACTGGGTTTCGATTTCTCGTTCCA
131 AATGTTTTGCGTTTGGAAATTCGAGGAACGTACACTAAGGTACTGGGTTTCGATTTCTCGTTCCA
59339283 CTAAATGACTTAATATCCTTTTTC
196 CTAAATGACTTAATATCCTTTTTC
* * * * *
59339307 AAAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAAGGTACT
1 AAAAAATTTCAAAATAAGGCAATATTTAGCCTTTGGAAATTCGAGAAAACATGCCCTAAGGTACT
*
59339371 -GGTTTCGATTTCTTGTTCGACCAAATAGCTAAATA-TCTTTTAAGAAAACTTTTCAAAAATAAG
66 GGGTTTCGATTTCTCGTTCGACCAAATAGCTAAATATTCTTTT--GAAAACTTTTCAAAAATAAG
* * *
59339434 GCAATGTTTTGCGTTTGGAAATTCGAGGAACGTACCCTAAGGTGCTGGGTTTTGATTTCTCGTT
129 GCAATGTTTTGCGTTTGGAAATTCGAGGAACGTACACTAAGGTACTGGGTTTCGATTTCTCGTT
59339498 TAACCAAACT
Statistics
Matches: 174, Mismatches: 15, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
216 6 0.03
217 33 0.19
218 95 0.55
219 40 0.23
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35
Consensus pattern (219 bp):
AAAAAATTTCAAAATAAGGCAATATTTAGCCTTTGGAAATTCGAGAAAACATGCCCTAAGGTACT
GGGTTTCGATTTCTCGTTCGACCAAATAGCTAAATATTCTTTTGAAAACTTTTCAAAAATAAGGC
AATGTTTTGCGTTTGGAAATTCGAGGAACGTACACTAAGGTACTGGGTTTCGATTTCTCGTTCCA
CTAAATGACTTAATATCCTTTTTC
Found at i:59342842 original size:17 final size:18
Alignment explanation
Indices: 59342820--59342856 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
59342810 TTATTCTTTT
59342820 ATTCTTTCATCCA-AATC
1 ATTCTTTCATCCATAATC
*
59342837 ATTCTTTCATTCATAATC
1 ATTCTTTCATCCATAATC
59342855 AT
1 AT
59342857 ACTGTGCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTCTTTCATCCATAATC
Found at i:59343599 original size:7 final size:7
Alignment explanation
Indices: 59343584--59343638 Score: 67
Period size: 7 Copynumber: 7.6 Consensus size: 7
59343574 AAAATAGGAG
59343584 AAAAAGA
1 AAAAAGA
*
59343591 AAGAAGA
1 AAAAAGA
59343598 AAAAAGAA
1 AAAAAG-A
59343606 AAAAAGA
1 AAAAAGA
59343613 AAAAAGA
1 AAAAAGA
59343620 AAAAA-A
1 AAAAAGA
59343626 AGAAAATGA
1 A-AAAA-GA
59343635 AAAA
1 AAAA
59343639 GGAGAGGTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
6 2 0.05
7 28 0.67
8 10 0.24
9 2 0.05
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.02
Consensus pattern (7 bp):
AAAAAGA
Found at i:59343612 original size:15 final size:15
Alignment explanation
Indices: 59343584--59343631 Score: 71
Period size: 15 Copynumber: 3.2 Consensus size: 15
59343574 AAAATAGGAG
*
59343584 AAAAAG-AAAGAAGA
1 AAAAAGAAAAAAAGA
59343598 AAAAAGAAAAAAAGA
1 AAAAAGAAAAAAAGA
59343613 AAAAAGAAAAAAAAGA
1 AAAAAG-AAAAAAAGA
59343629 AAA
1 AAA
59343632 TGAAAAAGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 6 0.19
15 13 0.42
16 12 0.39
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAGA
Found at i:59343631 original size:22 final size:23
Alignment explanation
Indices: 59343573--59343638 Score: 82
Period size: 22 Copynumber: 2.9 Consensus size: 23
59343563 AATCAAAGTC
* *
59343573 AAAAATAGGAGAAAAAGAAAGAAG
1 AAAAA-AGAAGAAAAAGAAAAAAG
59343597 AAAAAAGAA-AAAAAGAAAAAAG
1 AAAAAAGAAGAAAAAGAAAAAAG
*
59343619 AAAAAA-AAGAAAATGAAAAA
1 AAAAAAGAAGAAAAAGAAAAA
59343639 GGAGAGGTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 2 0.05
22 28 0.74
23 3 0.08
24 5 0.13
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (23 bp):
AAAAAAGAAGAAAAAGAAAAAAG
Found at i:59343638 original size:16 final size:16
Alignment explanation
Indices: 59343594--59343631 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
59343584 AAAAAGAAAG
59343594 AAGAAAAAAG-AAAAA
1 AAGAAAAAAGAAAAAA
59343609 AAGAAAAAAGAAAAAA
1 AAGAAAAAAGAAAAAA
59343625 AAGAAAA
1 AAGAAAA
59343632 TGAAAAAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAGAAAAAA
Found at i:59345766 original size:44 final size:44
Alignment explanation
Indices: 59345716--59346030 Score: 150
Period size: 44 Copynumber: 7.2 Consensus size: 44
59345706 AGTTATAGAG
* *
59345716 CTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGATACAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGAAACAAAC
* * * * *
59345760 CTTGCC-TCTCT-CGATTG-TAGCGGAGCTGGTTC-AAGACAACAGAT
1 CTTGCCTTC-CTGC-ATTGACAGCGAAGCAGG-TCGAAGA-AACAAAC
* *
59345804 CTTGCCTTCCTGCATTGACAGCAAAGCAGGTCGAAGACACAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGAAACAAAC
** * * * * *
59345848 CTTGCC-TCTCTCGGTTGTGA-TG-G-AGCTGGTTGAAGACAACATAT
1 CTTGCCTTC-CT-GCAT-TGACAGCGAAGCAGGTCGAAGA-AACAAAC
* * * *
59345892 CTTGCCTTCCTGCATTGACAGCAAAGTAGATCGAAGACACAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGAAACAAAC
* ** * * * * *
59345936 CTTGCC-TCTCT-CGGTTG-TGGTGGAGCTGGTTGAAGACAA-AAGAT
1 CTTGCCTTC-CTGC-ATTGACAGCGAAGCAGGTCGAAGA-AACAA-AC
* * * *
59345980 CTTGCCTTCCTTCATTGACAACGAAGCAGATCGAAGACACAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGAAACAAAC
59346024 CTTGCCT
1 CTTGCCT
59346031 CCCTCGGTTG
Statistics
Matches: 190, Mismatches: 57, Indels: 48
0.64 0.19 0.16
Matches are distributed among these distances:
42 3 0.02
43 46 0.24
44 93 0.49
45 45 0.24
46 3 0.02
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (44 bp):
CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGAAACAAAC
Found at i:59345873 original size:88 final size:88
Alignment explanation
Indices: 59345716--59346049 Score: 508
Period size: 88 Copynumber: 3.8 Consensus size: 88
59345706 AGTTATAGAG
* * * * * *
59345716 CTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGATACAAACCTTGCCTCTCTCGATTGTAGC
1 CTTGCCTTCCTGCATTGACAGCAAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGTTGTAGT
*
59345781 GGAGCTGGTTCAAGACAACAGAT
66 GGAGCTGGTTGAAGACAACAGAT
*
59345804 CTTGCCTTCCTGCATTGACAGCAAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGT-GA
1 CTTGCCTTCCTGCATTGACAGCAAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGTTGTAG-
*
59345868 TGGAGCTGGTTGAAGACAACATAT
65 TGGAGCTGGTTGAAGACAACAGAT
* *
59345892 CTTGCCTTCCTGCATTGACAGCAAAGTAGATCGAAGACACAAACCTTGCCTCTCTCGGTTGTGGT
1 CTTGCCTTCCTGCATTGACAGCAAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGTTGTAGT
*
59345957 GGAGCTGGTTGAAGACAAAAGAT
66 GGAGCTGGTTGAAGACAACAGAT
* * * *
59345980 CTTGCCTTCCTTCATTGACAACGAAGCAGATCGAAGACACAAACCTTGCCTCCCTCGGTTGTAGT
1 CTTGCCTTCCTGCATTGACAGCAAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGTTGTAGT
59346045 GGAGC
66 GGAGC
59346050 AGATCAAAGA
Statistics
Matches: 227, Mismatches: 17, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
87 1 0.00
88 225 0.99
89 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.25
Consensus pattern (88 bp):
CTTGCCTTCCTGCATTGACAGCAAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGTTGTAGT
GGAGCTGGTTGAAGACAACAGAT
Found at i:59346897 original size:18 final size:18
Alignment explanation
Indices: 59346876--59346922 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
59346866 GTATAAGTTA
*
59346876 TATTTTTCTTTTTCTTTT
1 TATTTTTCTTTTTCTCTT
* *
59346894 TATTCTTATTTTTCTCTT
1 TATTTTTCTTTTTCTCTT
*
59346912 TATTTTCCTTT
1 TATTTTTCTTT
59346923 CTTTCGAAAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.77
Consensus pattern (18 bp):
TATTTTTCTTTTTCTCTT
Found at i:59347596 original size:3 final size:3
Alignment explanation
Indices: 59347551--59347631 Score: 67
Period size: 3 Copynumber: 26.7 Consensus size: 3
59347541 TTTAGCATTT
* * * *
59347551 TTA TTA TT- TTC TTCA TTA TTT TTA ATA -TA TTA TCA TCTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
* *
59347596 TTA TTG TTG TTA TTA TTA GTTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TT
59347632 TCTTCATCTA
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
2 4 0.06
3 54 0.83
4 7 0.11
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:59347965 original size:22 final size:22
Alignment explanation
Indices: 59347929--59348006 Score: 72
Period size: 22 Copynumber: 3.5 Consensus size: 22
59347919 TCTATTTTTC
*
59347929 TTTATTGTTTTTATGTTCATTTA
1 TTTATT-TATTTATGTTCATTTA
*
59347952 TGTATTTATTTATGTGTTC-TTT-
1 TTTATTTATTTA--TGTTCATTTA
*
59347974 TTTATTTACTTTA-GTTTATTTA
1 TTTATTTA-TTTATGTTCATTTA
59347996 TTTATTTATTT
1 TTTATTTATTT
59348007 GCTATGATTG
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
20 3 0.07
21 6 0.13
22 20 0.43
23 12 0.26
24 5 0.11
ACGTcount: A:0.18, C:0.04, G:0.08, T:0.71
Consensus pattern (22 bp):
TTTATTTATTTATGTTCATTTA
Found at i:59348024 original size:4 final size:4
Alignment explanation
Indices: 59347947--59348006 Score: 52
Period size: 4 Copynumber: 15.0 Consensus size: 4
59347937 TTTTATGTTC
* * * *
59347947 ATTT ATGT ATTT ATTT ATGT -GTT CTTT -TTT ATTT ACTTT AGTTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A-TTT A-TTT ATTT
59347995 ATTT ATTT ATTT
1 ATTT ATTT ATTT
59348007 GCTATGATTG
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
3 4 0.09
4 34 0.74
5 8 0.17
ACGTcount: A:0.20, C:0.03, G:0.07, T:0.70
Consensus pattern (4 bp):
ATTT
Found at i:59348324 original size:109 final size:109
Alignment explanation
Indices: 59348125--59348533 Score: 545
Period size: 109 Copynumber: 3.7 Consensus size: 109
59348115 AAATTTTTCT
* * * * *
59348125 AAATGAGGCAATATTTAGCCTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTGGGTTTCGATT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAAGGTACTGGGTTTCGATT
*
59348190 TCTCGTTCGACTAAATAGCTAAATATTCTTTTTAAAACTTTTCAA
65 TCTCGTTCGACCAAATAGCTAAATATTCTTTTTAAAACTTTTCAA
* *
59348235 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCACTAAGGTACTGGGTTTCGATTT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
* * * * *
59348300 CTCGTTCCACCAAAT-GACTTAATATCCTTTTTCAAAAATTTT-TA
66 CTCGTTCGACCAAATAG-CTAAATATTCTTTTT-AAAACTTTTCAA
*
59348344 AAATAAGGTAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACT-GGTTTCGATTT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
* * **
59348408 CTCATTCGACCAAATAGCTAAATATCTTTTTTTTTTAACTTTTCAA
66 CTCGTTCGACCAAATAGCTAAATA--TTCTTTTTAAAACTTTTCAA
* * *
59348454 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTGCTGGGTTTTGATTT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
**
59348519 CTCGTTTAACCAAAT
66 CTCGTTCGACCAAAT
59348534 TGCCAAATGT
Statistics
Matches: 260, Mismatches: 32, Indels: 13
0.85 0.10 0.04
Matches are distributed among these distances:
108 31 0.12
109 112 0.43
110 95 0.37
111 22 0.08
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.36
Consensus pattern (109 bp):
AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
CTCGTTCGACCAAATAGCTAAATATTCTTTTTAAAACTTTTCAA
Found at i:59348520 original size:219 final size:220
Alignment explanation
Indices: 59348113--59348533 Score: 650
Period size: 219 Copynumber: 1.9 Consensus size: 220
59348103 TTCAAAAAAG
* *
59348113 AAAAATTTTTCTAAATGAGGCAATATTTAGCCTTTGGAAATTCGAGAAAACATGCCCTAAGGTAC
1 AAAAATTTTTCAAAATAAGGCAATATTTAGCCTTTGGAAATTCGAGAAAACATGCCCTAAGGTAC
* *
59348178 TGGGTTTCGATTTCTCGTTCGACTAAATAGCTAAATATTCTTTTTAAAACTTTTCAAAAATAAGG
66 TGGGTTTCGATTTCTCATTCGACCAAATAGCTAAATATTCTTTTTAAAACTTTTCAAAAATAAGG
*
59348243 CAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCACTAAGGTACTGGGTTTCGATTTCTCGTTCC
131 CAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCACTAAGGTACTGGGTTTCGATTTCTCGTTCA
59348308 ACCAAATGACTTAATATCCTTTTTC
196 ACCAAATGACTTAATATCCTTTTTC
* * * * *
59348333 AAAAATTTTT-AAAATAAGGTAATATTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAAGGTAC
1 AAAAATTTTTCAAAATAAGGCAATATTTAGCCTTTGGAAATTCGAGAAAACATGCCCTAAGGTAC
* **
59348396 T-GGTTTCGATTTCTCATTCGACCAAATAGCTAAATATCTTTTTTTTTTAACTTTTCAAAAATAA
66 TGGGTTTCGATTTCTCATTCGACCAAATAGCTAAATA--TTCTTTTTAAAACTTTTCAAAAATAA
* * *
59348460 GGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTGCTGGGTTTTGATTTCTCGTT
129 GGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCACTAAGGTACTGGGTTTCGATTTCTCGTT
*
59348525 TAACCAAAT
194 CAACCAAAT
59348534 TGCCAAATGT
Statistics
Matches: 182, Mismatches: 17, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
217 33 0.18
218 17 0.09
219 122 0.67
220 10 0.05
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (220 bp):
AAAAATTTTTCAAAATAAGGCAATATTTAGCCTTTGGAAATTCGAGAAAACATGCCCTAAGGTAC
TGGGTTTCGATTTCTCATTCGACCAAATAGCTAAATATTCTTTTTAAAACTTTTCAAAAATAAGG
CAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCACTAAGGTACTGGGTTTCGATTTCTCGTTCA
ACCAAATGACTTAATATCCTTTTTC
Found at i:59365166 original size:15 final size:15
Alignment explanation
Indices: 59365148--59365199 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
59365138 AATAATGACA
59365148 ATAATAATAAATAAT
1 ATAATAATAAATAAT
*
59365163 ATAATAATACATAAT
1 ATAATAATAAATAAT
*
59365178 GAT-ATAATTTAATAAT
1 -ATAATAA-TAAATAAT
59365194 A-AATAA
1 ATAATAA
59365200 ATAATTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 23 0.74
16 8 0.26
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (15 bp):
ATAATAATAAATAAT
Found at i:59367069 original size:44 final size:44
Alignment explanation
Indices: 59367014--59367262 Score: 178
Period size: 44 Copynumber: 5.6 Consensus size: 44
59367004 TCGCTACCGA
* * *
59367014 TATAGGAAGACAGGACCTGCTATCTTTGATCTACTTCACGCCAG
1 TATATGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAG
* * * * * *
59367058 TATATGAAGACAAGATCTGTTTTCTTCGATCTGCTT--TGCCAC
1 TATATGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAG
* * * *
59367100 TAGTATGGGAAGGCAAGATCTGGTATCTATGACCTACTTCACGCCAG
1 TA-TAT--GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAG
* * * * ** * * *
59367147 TACATAAAGACAAGATCTACTTTCTTCAATCTGCTTCGCCACCAG
1 TATATGAAGACAAGATCTGCTATCTTTGATCTACTTC-ACGCCAG
** * * * *
59367192 TATGGGAAGGCAAGATCTGGTATCTATGGTCTACTTCACGCCAG
1 TATATGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAG
* *
59367236 TACATGAAGACAAGATCTGTTATCTTT
1 TATATGAAGACAAGATCTGCTATCTTT
59367263 CAACCTGCTC
Statistics
Matches: 147, Mismatches: 52, Indels: 12
0.70 0.25 0.06
Matches are distributed among these distances:
42 6 0.04
43 3 0.02
44 77 0.52
45 53 0.36
46 2 0.01
47 6 0.04
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (44 bp):
TATATGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAG
Found at i:59367111 original size:89 final size:89
Alignment explanation
Indices: 59367034--59367271 Score: 359
Period size: 89 Copynumber: 2.7 Consensus size: 89
59367024 CAGGACCTGC
* * * *
59367034 TATCTTTGATCTACTTCACGCCAGTATATGAAGACAAGATCTGTTTTCTTCGATCTGCTTTGCCA
1 TATCTATGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCAATCTGCTTCGCCA
*
59367099 CTAGTATGGGAAGGCAAGATCTGG
66 CCAGTATGGGAAGGCAAGATCTGG
* * **
59367123 TATCTATGACCTACTTCACGCCAGTACATAAAGACAAGATCTACTTTCTTCAATCTGCTTCGCCA
1 TATCTATGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCAATCTGCTTCGCCA
59367188 CCAGTATGGGAAGGCAAGATCTGG
66 CCAGTATGGGAAGGCAAGATCTGG
* * *
59367212 TATCTATGGTCTACTTCACGCCAGTACATGAAGACAAGATCTGTTATCTTTCAACCTGCT
1 TATCTATGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTC-TTCAATCTGCT
59367272 CCACTGTTGC
Statistics
Matches: 132, Mismatches: 16, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
89 122 0.92
90 10 0.08
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (89 bp):
TATCTATGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCAATCTGCTTCGCCA
CCAGTATGGGAAGGCAAGATCTGG
Found at i:59379185 original size:3 final size:3
Alignment explanation
Indices: 59379165--59379227 Score: 53
Period size: 3 Copynumber: 21.7 Consensus size: 3
59379155 CGTATGTACA
*
59379165 AAT AA- AAT AAT AAC AAT AAT AAT AAAT AAT -AT AAT AAT ACAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT A-AT AAT
* *
59379210 GAT -AT AAT -GT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
59379228 ATAAATAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
2 7 0.14
3 36 0.73
4 6 0.12
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:59381478 original size:19 final size:19
Alignment explanation
Indices: 59381434--59381494 Score: 70
Period size: 20 Copynumber: 3.2 Consensus size: 19
59381424 CTTTCAACAA
* *
59381434 AAAATACAAAATAATTTTCA
1 AAAATTCAAAATAATTTT-T
59381454 AAAATTCAAAATAATTTTT
1 AAAATTCAAAATAATTTTT
* *
59381473 AAAATTTAAAAT-ATTTAT
1 AAAATTCAAAATAATTTTT
59381491 AAAA
1 AAAA
59381495 ATTCTAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.24
19 11 0.30
20 17 0.46
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTT
Found at i:59381495 original size:19 final size:19
Alignment explanation
Indices: 59381453--59381514 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
59381443 AATAATTTTC
*
59381453 AAAAATTCAAAATAATTT-T
1 AAAAATTTAAAAT-ATTTAT
*
59381472 TAAAATTTAAAATATTTAT
1 AAAAATTTAAAATATTTAT
59381491 AAAAATTCT-AAAT-TTTAT
1 AAAAATT-TAAAATATTTAT
59381509 ATAAAA
1 A-AAAA
59381515 AAAATTTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 10 0.27
19 26 0.70
20 1 0.03
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAAATTTAAAATATTTAT
Found at i:59381545 original size:35 final size:35
Alignment explanation
Indices: 59381480--59381548 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
59381470 TTTAAAATTT
* ***
59381480 AAAATATTTATAAAAATTCTAAATTTTATATAAAA
1 AAAATATTTAAAAAAATTCTAAAGAATATATAAAA
59381515 AAAAT-TTTAAAAAAATTTCTAAAGAATATATAAA
1 AAAATATTTAAAAAAA-TTCTAAAGAATATATAAA
59381549 GAAAGTTCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 9 0.31
35 20 0.69
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.36
Consensus pattern (35 bp):
AAAATATTTAAAAAAATTCTAAAGAATATATAAAA
Found at i:59383636 original size:31 final size:32
Alignment explanation
Indices: 59383601--59383668 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 32
59383591 AATGAAGATT
* *
59383601 AAAATTTTAAAATATGTG-AATAGTTAAACTA
1 AAAATTTTAAAATATGAGAAATAATTAAACTA
59383632 AAAATTTTAAAATATGAGAAATAATTAAACTA
1 AAAATTTTAAAATATGAGAAATAATTAAACTA
59383664 AAAAT
1 AAAAT
59383669 AATCAAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 17 0.50
32 17 0.50
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.32
Consensus pattern (32 bp):
AAAATTTTAAAATATGAGAAATAATTAAACTA
Found at i:59386472 original size:50 final size:51
Alignment explanation
Indices: 59386366--59386577 Score: 329
Period size: 51 Copynumber: 4.2 Consensus size: 51
59386356 ATCACATTTA
* *
59386366 TCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCACTTATCACTTG
1 TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
* * *
59386417 TCACTTGTAACCGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTG
1 TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
*
59386467 TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCAGTTATCACTTG
1 TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
*
59386518 TCACTTATCACTGATCAGATAAGTGTAACTAAA-CTACCACTTATCACTTG
1 TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
* *
59386568 TTACTGATCA
1 TCACTTATCA
59386578 GAAGTACTCA
Statistics
Matches: 149, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
50 71 0.48
51 78 0.52
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (51 bp):
TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
Found at i:59386481 original size:101 final size:101
Alignment explanation
Indices: 59386366--59386577 Score: 334
Period size: 101 Copynumber: 2.1 Consensus size: 101
59386356 ATCACATTTA
* *
59386366 TCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTGTAACCGA
1 TCACTTATCACTGATCAAATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTATAACCGA
* *
59386431 TCAGATAAGTGTAGCTAAGCTACCACTTATCACTTG
66 TCAGATAAGTGTAACTAAACTACCACTTATCACTTG
* * * *
59386467 TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCAGTTATCACTTGTCACTTATCACTGA
1 TCACTTATCACTGATCAAATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTATAACCGA
59386532 TCAGATAAGTGTAACTAAACTACCACTTATCACTTG
66 TCAGATAAGTGTAACTAAACTACCACTTATCACTTG
* *
59386568 TTACTGATCA
1 TCACTTATCA
59386578 GAAGTACTCA
Statistics
Matches: 101, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (101 bp):
TCACTTATCACTGATCAAATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTATAACCGA
TCAGATAAGTGTAACTAAACTACCACTTATCACTTG
Found at i:59386673 original size:17 final size:17
Alignment explanation
Indices: 59386651--59386683 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
59386641 TATTCTCAAT
59386651 TCATCA-ACAAATATATC
1 TCATCATAC-AATATATC
59386668 TCATCATACAATATAT
1 TCATCATACAATATAT
59386684 AATTCATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
TCATCATACAATATATC
Found at i:59389337 original size:15 final size:15
Alignment explanation
Indices: 59389317--59389347 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
59389307 ATTAGAATGA
*
59389317 GGTGGGGTAGGGTGG
1 GGTGGGGTAAGGTGG
59389332 GGTGGGGTAAGGTGG
1 GGTGGGGTAAGGTGG
59389347 G
1 G
59389348 TCGTGAAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.00, G:0.71, T:0.19
Consensus pattern (15 bp):
GGTGGGGTAAGGTGG
Found at i:59398400 original size:22 final size:23
Alignment explanation
Indices: 59398368--59398416 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
59398358 ACATAAATAT
*
59398368 TTTAAATAATATATAATAATAAA
1 TTTAAATAATATATAAAAATAAA
*
59398391 TTTAAA-AATATATAAAAATAAT
1 TTTAAATAATATATAAAAATAAA
59398413 TTTA
1 TTTA
59398417 TTAATATTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TTTAAATAATATATAAAAATAAA
Found at i:59398406 original size:10 final size:10
Alignment explanation
Indices: 59398344--59398410 Score: 55
Period size: 10 Copynumber: 6.5 Consensus size: 10
59398334 AATTTCAAAG
59398344 AAATATATAA
1 AAATATATAA
*
59398354 AAATACATAA
1 AAATATATAA
* *
59398364 ATAT-TTTAA
1 AAATATATAA
59398373 ATAATATATAA
1 A-AATATATAA
* *
59398384 TAATAAATTTAA
1 -AA-ATATATAA
59398396 AAATATATAA
1 AAATATATAA
59398406 AAATA
1 AAATA
59398411 ATTTTATTAA
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
9 4 0.09
10 25 0.58
11 7 0.16
12 7 0.16
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (10 bp):
AAATATATAA
Found at i:59398422 original size:22 final size:22
Alignment explanation
Indices: 59398372--59398423 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
59398362 AAATATTTTA
*
59398372 AATAATATATAATAATAAATTT
1 AATAATATATAAAAATAAATTT
* *
59398394 AAAAATATATAAAAATAATTTT
1 AATAATATATAAAAATAAATTT
*
59398416 ATTAATAT
1 AATAATAT
59398424 TGAATAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AATAATATATAAAAATAAATTT
Found at i:59400703 original size:16 final size:17
Alignment explanation
Indices: 59400682--59400725 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
59400672 ATTAAGGGTT
59400682 AAATTGTGAAATATG-A
1 AAATTGTGAAATATGTA
*
59400698 AAATTGT-AAATGTGTA
1 AAATTGTGAAATATGTA
59400714 AAATTGTGAAAT
1 AAATTGTGAAAT
59400726 GTATGGACTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 6 0.24
16 15 0.60
17 4 0.16
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.34
Consensus pattern (17 bp):
AAATTGTGAAATATGTA
Found at i:59412511 original size:29 final size:28
Alignment explanation
Indices: 59412478--59412540 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 28
59412468 TATTTTTCTC
59412478 ATAAAATGATTAAAAATCAGAAAAA-AATT
1 ATAAAATGA-TAAAAATCAGAAAAATAA-T
*
59412507 ATAAAAATTATAAAAATCAGAAAAATAAT
1 AT-AAAATGATAAAAATCAGAAAAATAAT
59412536 ATAAA
1 ATAAA
59412541 TAATATTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 3 0.10
29 20 0.65
30 8 0.26
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (28 bp):
ATAAAATGATAAAAATCAGAAAAATAAT
Found at i:59412512 original size:8 final size:9
Alignment explanation
Indices: 59412500--59412751 Score: 90
Period size: 9 Copynumber: 27.6 Consensus size: 9
59412490 AAAATCAGAA
59412500 AAAAATTAT
1 AAAAATTAT
59412509 AAAAATTAT
1 AAAAATTAT
* *
59412518 AAAAATCAG
1 AAAAATTAT
*
59412527 AAAAATAAT
1 AAAAATTAT
* *
59412536 ATAAATAAT
1 AAAAATTAT
*
59412545 ATTAAA-TAT
1 A-AAAATTAT
* **
59412554 TAAAACCATT
1 AAAAATTA-T
*
59412564 AAAATTTAT
1 AAAAATTAT
* *
59412573 ATGAACTTAT
1 A-AAAATTAT
*
59412583 TAAAATTAT
1 AAAAATTAT
*
59412592 AAAAAAATAT
1 -AAAAATTAT
59412602 AAAAACTTAT
1 AAAAA-TTAT
*
59412612 AAATATTAT
1 AAAAATTAT
59412621 AAAAA-TAT
1 AAAAATTAT
59412629 AATAAATCTA-
1 AA-AAAT-TAT
*
59412639 ATAAATTAT
1 AAAAATTAT
*
59412648 AAAAA-AAT
1 AAAAATTAT
**
59412656 AATTATTATTT
1 AAAAATTA--T
59412667 AAAATATT-T
1 AAAA-ATTAT
*
59412676 AAAATTTA-
1 AAAAATTAT
*
59412684 AAAAAGTAT
1 AAAAATTAT
* *
59412693 TAGAATTATT
1 AAAAATTA-T
59412703 AAAAAATTA-
1 -AAAAATTAT
59412712 AAAAA-T-T
1 AAAAATTAT
*
59412719 AAAATTTAT
1 AAAAATTAT
* *
59412728 ATAGACTTAT
1 A-AAAATTAT
59412738 AAAAATTAT
1 AAAAATTAT
59412747 AAAAA
1 AAAAA
59412752 AAATCAAAAA
Statistics
Matches: 177, Mismatches: 44, Indels: 44
0.67 0.17 0.17
Matches are distributed among these distances:
7 5 0.03
8 29 0.16
9 91 0.51
10 38 0.21
11 11 0.06
12 3 0.02
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (9 bp):
AAAAATTAT
Found at i:59412657 original size:27 final size:29
Alignment explanation
Indices: 59412583--59412658 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
59412573 ATGAACTTAT
*
59412583 TAAAATTATAAAAAAAT-ATAAAAACTTA
1 TAAAATTATAAAAAAATAATAAAAACTAA
* *
59412611 TAAATATTATAAAAATATAAT-AAATCTAA
1 TAAA-ATTATAAAAAAATAATAAAAACTAA
59412640 T-AAATTATAAAAAAATAAT
1 TAAAATTATAAAAAAATAAT
59412659 TATTATTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 15 0.36
28 6 0.14
29 19 0.45
30 2 0.05
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (29 bp):
TAAAATTATAAAAAAATAATAAAAACTAA
Found at i:59413800 original size:16 final size:17
Alignment explanation
Indices: 59413774--59413806 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
59413764 TATTATAATC
59413774 TATATTATAATAATAGT
1 TATATTATAATAATAGT
*
59413791 TATA-TATAATAGTAGT
1 TATATTATAATAATAGT
59413807 ACATTATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (17 bp):
TATATTATAATAATAGT
Found at i:59414090 original size:28 final size:28
Alignment explanation
Indices: 59414024--59414096 Score: 69
Period size: 30 Copynumber: 2.6 Consensus size: 28
59414014 TTATATCTTT
* * *
59414024 TATTATAATTTATATTATAATAGTTGTA
1 TATTATAATATATATTATAATAGCTATA
*
59414052 TATGTATTAATATGT-TTAGTAATAGCTATA
1 TAT-TA-TAATATATATTA-TAATAGCTATA
59414082 TATTATAATAT-TATT
1 TATTATAATATATATT
59414097 TTATGTACTA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
27 1 0.03
28 11 0.30
29 7 0.19
30 18 0.49
ACGTcount: A:0.38, C:0.01, G:0.08, T:0.52
Consensus pattern (28 bp):
TATTATAATATATATTATAATAGCTATA
Found at i:59414226 original size:16 final size:17
Alignment explanation
Indices: 59414178--59414239 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
59414168 TAATATATTA
* *
59414178 TTATATTATCATTAATT
1 TTATATAATTATTAATT
*
59414195 TT-TA-ATTTA-TAGATT
1 TTATATAATTATTA-ATT
59414210 TTA-ATAATTATTAATT
1 TTATATAATTATTAATT
*
59414226 TTATATATTTATTA
1 TTATATAATTATTA
59414240 TACATGTATA
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
14 2 0.06
15 8 0.23
16 12 0.34
17 13 0.37
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (17 bp):
TTATATAATTATTAATT
Found at i:59414237 original size:17 final size:17
Alignment explanation
Indices: 59414188--59414239 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
59414178 TTATATTATC
59414188 ATTAATTTT-TA-ATTT
1 ATTAATTTTATATATTT
*
59414203 A-TAGATTTTA-ATAATT
1 ATTA-ATTTTATATATTT
59414219 ATTAATTTTATATATTT
1 ATTAATTTTATATATTT
59414236 ATTA
1 ATTA
59414240 TACATGTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 2 0.07
15 7 0.23
16 10 0.33
17 11 0.37
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
ATTAATTTTATATATTT
Found at i:59414818 original size:9 final size:9
Alignment explanation
Indices: 59414785--59414810 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
59414775 AAAAATCTTT
59414785 TTTTTTTTG
1 TTTTTTTTG
59414794 TTTTTTTTG
1 TTTTTTTTG
59414803 TTTTTTTT
1 TTTTTTTT
59414811 ATTGTTTTCT
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:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:59419289 original size:13 final size:13
Alignment explanation
Indices: 59419271--59419295 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59419261 TAACTCGTTT
59419271 TATATTTTTATAA
1 TATATTTTTATAA
59419284 TATATTTTTATA
1 TATATTTTTATA
59419296 TTTTGTGTAA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATATTTTTATAA
Found at i:59425946 original size:21 final size:21
Alignment explanation
Indices: 59425920--59425972 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
59425910 CGCTGTTTCT
*
59425920 AATCTCACCGCTACAATATCC
1 AATCTCACCGCTACAATAACC
** * *
59425941 AATCTCACTACTTCAATAACT
1 AATCTCACCGCTACAATAACC
59425962 AATCTCACCGC
1 AATCTCACCGC
59425973 CACCGTTGTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.36, G:0.04, T:0.26
Consensus pattern (21 bp):
AATCTCACCGCTACAATAACC
Found at i:59431319 original size:84 final size:84
Alignment explanation
Indices: 59431178--59431333 Score: 201
Period size: 84 Copynumber: 1.9 Consensus size: 84
59431168 ATGTGTTTTC
* * *
59431178 GTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGCGTAAGACCATGTCTGGGACA
1 GTGTAAGACCACGTCTAGGACGTTGGCATCGACTTGTGATTACACGTAAGACCATGTCTGGGACA
59431243 TTGGCATCGTATTTGATTT
66 TTGGCATCGTATTTGATTT
* *
59431262 GTGTAAGACC-CTGTCTAGGACAG-TGGCATCGA-TATGTGATTACATGTAAGATCATGTCTGGG
1 GTGTAAGACCAC-GTCTAGGAC-GTTGGCATCGACT-TGTGATTACACGTAAGACCATGTCTGGG
**
59431324 ATGTTGGCAT
63 ACATTGGCAT
59431334 TGTACGAGTC
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
83 2 0.03
84 59 0.95
85 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.31
Consensus pattern (84 bp):
GTGTAAGACCACGTCTAGGACGTTGGCATCGACTTGTGATTACACGTAAGACCATGTCTGGGACA
TTGGCATCGTATTTGATTT
Found at i:59431332 original size:43 final size:43
Alignment explanation
Indices: 59431163--59431333 Score: 179
Period size: 43 Copynumber: 4.0 Consensus size: 43
59431153 ACATAGGATT
* * *
59431163 TCGATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCA
1 TCGATATGTGATTACGTGTAAGACCATGTCTGGGACGTTGGCA
* * *
59431206 TCGACT-TGTGTTTACGCGTAAGACCATGTCTGGGACATTGGCA
1 TCGA-TATGTGATTACGTGTAAGACCATGTCTGGGACGTTGGCA
* * * *
59431249 TCG-TATTTGATT-TGTGTAAGACCCTGTCTAGGACAG-TGGCA
1 TCGATATGTGATTACGTGTAAGACCATGTCTGGGAC-GTTGGCA
* * *
59431290 TCGATATGTGATTACATGTAAGATCATGTCTGGGATGTTGGCA
1 TCGATATGTGATTACGTGTAAGACCATGTCTGGGACGTTGGCA
59431333 T
1 T
59431334 TGTACGAGTC
Statistics
Matches: 104, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
41 27 0.26
42 14 0.13
43 62 0.60
44 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (43 bp):
TCGATATGTGATTACGTGTAAGACCATGTCTGGGACGTTGGCA
Found at i:59439270 original size:15 final size:15
Alignment explanation
Indices: 59439250--59439280 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
59439240 TGAAACCTAC
*
59439250 CTTAACCAATGAGAT
1 CTTAACCAATAAGAT
59439265 CTTAACCAATAAGAT
1 CTTAACCAATAAGAT
59439280 C
1 C
59439281 AAGGCTAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.26
Consensus pattern (15 bp):
CTTAACCAATAAGAT
Found at i:59476083 original size:23 final size:21
Alignment explanation
Indices: 59476057--59476100 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
59476047 TTTCTACCTT
*
59476057 AAAATCATACATTATATTTTTCA
1 AAAATCATA-ATT-TACTTTTCA
*
59476080 AAAATTATAATTTACTTTTCA
1 AAAATCATAATTTACTTTTCA
59476101 GATTTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.42
22 3 0.16
23 8 0.42
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.45
Consensus pattern (21 bp):
AAAATCATAATTTACTTTTCA
Found at i:59482920 original size:15 final size:16
Alignment explanation
Indices: 59482880--59482924 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
59482870 AATAAATAAA
*
59482880 AAATATTTTAAATTATT
1 AAATAATTTAAA-TATT
59482897 AAAT-A-TTAAAT-TT
1 AAATAATTTAAATATT
59482910 AAATAATTTAAATAT
1 AAATAATTTAAATAT
59482925 ATTTTTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
13 6 0.25
14 2 0.08
15 11 0.46
16 1 0.04
17 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATAATTTAAATATT
Found at i:59482931 original size:21 final size:21
Alignment explanation
Indices: 59482884--59482932 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
59482874 AATAAAAAAT
*
59482884 ATTTTAAATTATTAAATATTA
1 ATTTTAAATAATTAAATATTA
*
59482905 AATTTAAATAATTTAAATA-TA
1 ATTTTAAATAA-TTAAATATTA
*
59482926 TTTTTAA
1 ATTTTAA
59482933 TTTTTTTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTTAAATAATTAAATATTA
Found at i:59483504 original size:2 final size:2
Alignment explanation
Indices: 59483497--59483521 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
59483487 ATTAACACAA
59483497 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
59483522 TGCATACCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:59490043 original size:24 final size:24
Alignment explanation
Indices: 59490016--59490062 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
59490006 ATTGAAATGA
59490016 ATTGA-TTTAGTATGTGA-TGAATTT
1 ATTGAGTTTA-TAT-TGATTGAATTT
59490040 ATTGAGTTTATATTGATTGAATT
1 ATTGAGTTTATATTGATTGAATT
59490063 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 14 0.67
25 4 0.19
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (24 bp):
ATTGAGTTTATATTGATTGAATTT
Found at i:59490341 original size:40 final size:39
Alignment explanation
Indices: 59490218--59490358 Score: 117
Period size: 40 Copynumber: 3.6 Consensus size: 39
59490208 CGACTTCGAG
* * * *
59490218 TCGATGAGACACTAGGTGTCAATTTACTACTTCAAATATA
1 TCGATGAGACACTGGGTGTCAAATTATTACTTCGAAT-TA
* * * **
59490258 TTTGATGAGGCACTGGGTG-CCAA-T-TTACTTCGGTTTA
1 -TCGATGAGACACTGGGTGTCAAATTATTACTTCGAATTA
59490295 GTCGATGAGACACTGGGTGTCAAATTATTACTTCGAATTA
1 -TCGATGAGACACTGGGTGTCAAATTATTACTTCGAATTA
* * *
59490335 TCCGATGAGGCATTGGGTGCCAAA
1 T-CGATGAGACACTGGGTGTCAAA
59490359 CTGTGTGTTT
Statistics
Matches: 78, Mismatches: 18, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
37 18 0.23
38 10 0.13
39 3 0.04
40 32 0.41
41 15 0.19
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (39 bp):
TCGATGAGACACTGGGTGTCAAATTATTACTTCGAATTA
Found at i:59494736 original size:266 final size:267
Alignment explanation
Indices: 59494262--59494798 Score: 988
Period size: 266 Copynumber: 2.0 Consensus size: 267
59494252 ACTAGTGAGT
59494262 AATTTTCTCTTTTCCATAATTTTCTATCGGTTCTTGATCTATACGATAATTTATTTCAATTATCA
1 AATTTTCTCTTTTCCATAATTTTCTATCGGTTCTTGATCTATACGATAATTTATTTCAATTATCA
* * *
59494327 ATCCTAAGTACATTATAAACGTCCATTTGATGCATATGACTTTTTTATTGACATTTTTCATAATT
66 ATCCCAAGTACATTATAAAAGTCCATTTGATGCATATGAATTTTTTATTGACATTTTTCATAATT
59494392 GCCCTAAAATTTTACATTTTATTCAATTTAGTCCCTAAAACCGAAACAAGCTCATTTTTTTCTTA
131 GCCCTAAAATTTTACATTTTATTCAATTTAGTCCCTAAAACCGAAACAAGCTCATTTTTTTCTTA
*
59494457 ATTAAGCCC-AAAAATATTATGCCTAATTCATTATTATCCTAAAAAACCCTCAAGTCACAAAATT
196 ATTAAGCCCAAAAAATATTATGCCTAATTCATTATCATCCTAAAAAACCCTCAAGTCACAAAATT
59494521 TACAAGA
261 TACAAGA
*
59494528 AATTTTCTTTTTTCCATAATTTTCTATCGGTTCTTGATCTATACGATAATTTATTTCAATTATCA
1 AATTTTCTCTTTTCCATAATTTTCTATCGGTTCTTGATCTATACGATAATTTATTTCAATTATCA
*
59494593 GTCCCAAGTACATTATAAAAGTCCATTTGATGCATATGAATTTTTTATTGACATTTTTCATAATT
66 ATCCCAAGTACATTATAAAAGTCCATTTGATGCATATGAATTTTTTATTGACATTTTTCATAATT
*
59494658 TCCCTAAAATTTTACATTTTATTCAATTTAGTCCCTAAAACCGAAACAAGCTCATTTTTTTTCTT
131 GCCCTAAAATTTTACATTTTATTCAATTTAGTCCCTAAAACCGAAACAAGCTCA-TTTTTTTCTT
59494723 AATTAAG-CCAAAAAATATTATGCCTAATTCATTATCATCCTAAAAAACCCTCAAGTCACAAAAT
195 AATTAAGCCCAAAAAATATTATGCCTAATTCATTATCATCCTAAAAAACCCTCAAGTCACAAAAT
59494787 TTACAAGA
260 TTACAAGA
59494795 AATT
1 AATT
59494799 AATTCCATTC
Statistics
Matches: 262, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
266 180 0.69
267 82 0.31
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.41
Consensus pattern (267 bp):
AATTTTCTCTTTTCCATAATTTTCTATCGGTTCTTGATCTATACGATAATTTATTTCAATTATCA
ATCCCAAGTACATTATAAAAGTCCATTTGATGCATATGAATTTTTTATTGACATTTTTCATAATT
GCCCTAAAATTTTACATTTTATTCAATTTAGTCCCTAAAACCGAAACAAGCTCATTTTTTTCTTA
ATTAAGCCCAAAAAATATTATGCCTAATTCATTATCATCCTAAAAAACCCTCAAGTCACAAAATT
TACAAGA
Found at i:59498278 original size:21 final size:22
Alignment explanation
Indices: 59498230--59498303 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 22
59498220 ATTGATAAGA
* *
59498230 TGCACTGAAGTGCCACTATTC-TT
1 TGCACCGAAGTGCCAC--TTCACT
*
59498253 TGCACCGAAGTGTCAC-TCACT
1 TGCACCGAAGTGCCACTTCACT
* *
59498274 TGCACAGTAGTGCCACTTTCACT
1 TGCACCGAAGTGCCAC-TTCACT
59498297 TGCACCG
1 TGCACCG
59498304 TAGTACCATT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
20 2 0.05
21 14 0.34
23 25 0.61
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.28
Consensus pattern (22 bp):
TGCACCGAAGTGCCACTTCACT
Found at i:59502382 original size:35 final size:35
Alignment explanation
Indices: 59502343--59502412 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
59502333 TATTTTATTA
59502343 CATACATCTGAATAAGATGTTTTGTAATGTTATGG
1 CATACATCTGAATAAGATGTTTTGTAATGTTATGG
59502378 CATACATCTGAATAAGATGTTTTGTAATGTTATGG
1 CATACATCTGAATAAGATGTTTTGTAATGTTATGG
59502413 AACTACTACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (35 bp):
CATACATCTGAATAAGATGTTTTGTAATGTTATGG
Found at i:59504526 original size:13 final size:13
Alignment explanation
Indices: 59504487--59504526 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
59504477 TAATTTATGT
59504487 AAAAATAATTTTTC
1 AAAAA-AATTTTTC
*
59504501 CAAAAAATATTTTC
1 AAAAAAAT-TTTTC
59504515 AAAAAAATTTTT
1 AAAAAAATTTTT
59504527 AAACAGCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 7 0.30
14 16 0.70
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAAAAATTTTTC
Found at i:59504541 original size:32 final size:33
Alignment explanation
Indices: 59504500--59504580 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 33
59504490 AATAATTTTT
**
59504500 CCAAAAAATATTTTCAAAAAAATT-TTTAAACA
1 CCAAAAAATATTTTCAAAAAAATTATCCAAACA
* * *
59504532 GCAAAAAATATTTT-ACACAAATTCATCCAAACA
1 CCAAAAAATATTTTCAAAAAAATT-ATCCAAACA
59504565 CCAAAAAATATTTTCA
1 CCAAAAAATATTTTCA
59504581 GTAAATTATT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
31 7 0.17
32 13 0.32
33 19 0.47
34 1 0.03
ACGTcount: A:0.53, C:0.17, G:0.01, T:0.28
Consensus pattern (33 bp):
CCAAAAAATATTTTCAAAAAAATTATCCAAACA
Found at i:59504619 original size:19 final size:20
Alignment explanation
Indices: 59504582--59504619 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
59504572 ATATTTTCAG
*
59504582 TAAATTATTTTTCAGAAAAA
1 TAAATTATTTTCCAGAAAAA
59504602 TAAATTATTTTCCA-AAAA
1 TAAATTATTTTCCAGAAAA
59504620 TTATTTTCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (20 bp):
TAAATTATTTTCCAGAAAAA
Found at i:59507390 original size:2 final size:2
Alignment explanation
Indices: 59507378--59507407 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
59507368 TTTCCATCCT
*
59507378 TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
59507408 AGCATGGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:59514175 original size:22 final size:22
Alignment explanation
Indices: 59514140--59514193 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
59514130 ATTTAGTCAT
* *
59514140 ATAATAAATCATTAATATAATAA
1 ATAATAATTTATTAATATAA-AA
* *
59514163 AT-ATAATTTATTATTTTAAAA
1 ATAATAATTTATTAATATAAAA
59514184 ATAATAATTT
1 ATAATAATTT
59514194 TAAATAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 4 0.15
22 20 0.77
23 2 0.08
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
ATAATAATTTATTAATATAAAA
Found at i:59517849 original size:13 final size:13
Alignment explanation
Indices: 59517831--59517855 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59517821 TAACTCGTTT
59517831 TATATTTTTATAA
1 TATATTTTTATAA
59517844 TATATTTTTATA
1 TATATTTTTATA
59517856 TTTTGTGTAA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATATTTTTATAA
Found at i:59524506 original size:21 final size:21
Alignment explanation
Indices: 59524480--59524532 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
59524470 CGCTGTTTCT
*
59524480 AATCTCACCGCTACAATATCC
1 AATCTCACCGCTACAATAACC
** * *
59524501 AATCTCACTACTTCAATAACT
1 AATCTCACCGCTACAATAACC
59524522 AATCTCACCGC
1 AATCTCACCGC
59524533 CACCGTTGTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.36, G:0.04, T:0.26
Consensus pattern (21 bp):
AATCTCACCGCTACAATAACC
Found at i:59529877 original size:84 final size:84
Alignment explanation
Indices: 59529736--59529891 Score: 201
Period size: 84 Copynumber: 1.9 Consensus size: 84
59529726 ATGTGTTTTC
* * *
59529736 GTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGCGTAAGACCATGTCTGGGACA
1 GTGTAAGACCACGTCTAGGACGTTGGCATCGACTTGTGATTACACGTAAGACCATGTCTGGGACA
59529801 TTGGCATCGTATTTGATTT
66 TTGGCATCGTATTTGATTT
* *
59529820 GTGTAAGACC-CTGTCTAGGACAG-TGGCATCGA-TATGTGATTACATGTAAGATCATGTCTGGG
1 GTGTAAGACCAC-GTCTAGGAC-GTTGGCATCGACT-TGTGATTACACGTAAGACCATGTCTGGG
**
59529882 ATGTTGGCAT
63 ACATTGGCAT
59529892 TGTACGAGTC
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
83 2 0.03
84 59 0.95
85 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.31
Consensus pattern (84 bp):
GTGTAAGACCACGTCTAGGACGTTGGCATCGACTTGTGATTACACGTAAGACCATGTCTGGGACA
TTGGCATCGTATTTGATTT
Found at i:59529890 original size:43 final size:43
Alignment explanation
Indices: 59529721--59529891 Score: 179
Period size: 43 Copynumber: 4.0 Consensus size: 43
59529711 ACATAGGATT
* * *
59529721 TCGATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCA
1 TCGATATGTGATTACGTGTAAGACCATGTCTGGGACGTTGGCA
* * *
59529764 TCGACT-TGTGTTTACGCGTAAGACCATGTCTGGGACATTGGCA
1 TCGA-TATGTGATTACGTGTAAGACCATGTCTGGGACGTTGGCA
* * * *
59529807 TCG-TATTTGATT-TGTGTAAGACCCTGTCTAGGACAG-TGGCA
1 TCGATATGTGATTACGTGTAAGACCATGTCTGGGAC-GTTGGCA
* * *
59529848 TCGATATGTGATTACATGTAAGATCATGTCTGGGATGTTGGCA
1 TCGATATGTGATTACGTGTAAGACCATGTCTGGGACGTTGGCA
59529891 T
1 T
59529892 TGTACGAGTC
Statistics
Matches: 104, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
41 27 0.26
42 14 0.13
43 62 0.60
44 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (43 bp):
TCGATATGTGATTACGTGTAAGACCATGTCTGGGACGTTGGCA
Found at i:59537827 original size:15 final size:15
Alignment explanation
Indices: 59537807--59537837 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
59537797 TGAAACCTAC
*
59537807 CTTAACCAATGAGAT
1 CTTAACCAATAAGAT
59537822 CTTAACCAATAAGAT
1 CTTAACCAATAAGAT
59537837 C
1 C
59537838 AAGGCTAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.26
Consensus pattern (15 bp):
CTTAACCAATAAGAT
Found at i:59547703 original size:22 final size:22
Alignment explanation
Indices: 59547668--59547721 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
59547658 ATTTAGTCAT
* *
59547668 ATAATAAATCATTAATATAATAA
1 ATAATAATTTATTAATATAA-AA
* *
59547691 AT-ATAATTTATTATTTTAAAA
1 ATAATAATTTATTAATATAAAA
59547712 ATAATAATTT
1 ATAATAATTT
59547722 TAAATAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 4 0.15
22 20 0.77
23 2 0.08
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
ATAATAATTTATTAATATAAAA
Found at i:59560818 original size:12 final size:11
Alignment explanation
Indices: 59560783--59560814 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
59560773 ATTAAGTAAA
59560783 TAAATAAATAT
1 TAAATAAATAT
59560794 TAAATGAAATAT
1 TAAAT-AAATAT
59560806 TAAATAAAT
1 TAAATAAAT
59560815 TATTTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (11 bp):
TAAATAAATAT
Found at i:59562601 original size:50 final size:50
Alignment explanation
Indices: 59562542--59563085 Score: 294
Period size: 50 Copynumber: 10.9 Consensus size: 50
59562532 CCCACTACAC
* *
59562542 TGCCAGGGAAGTAAGATTCATCGTTGTGGCTTCAATCTTTTCAATTGCAA
1 TGCCGGGGAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTCAATTGCAA
* ** * * * * * * *
59562592 TACCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCAC
1 TGCCGGGGAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTCAATTGCAA
* * * * *
59562642 CGCCAGTGG-AGTAAGATTCGCCGTTGCGGCTTTAATCTTTT-AATTGCAA
1 TGCC-GGGGAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTCAATTGCAA
* ** * * * * * *
59562691 TGTCGGGGAAACAAGATTCGTCGTCGTAGCTTCAATCTATTCCACTGCAC
1 TGCCGGGGAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTCAATTGCAA
* * *
59562741 CGCCATGGG-AGTAAGATTCGCCGTTGTGGCTTCAATCTTTT-AATTGCAA
1 TGCC-GGGGAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTCAATTGCAA
* ** * * * * ** * * * *
59562790 TGTCGGGGAAACAAGATTCATCGTCGTAGCTTTAATCTGCTCCACTACAC
1 TGCCGGGGAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTCAATTGCAA
* ** ** * *
59562840 TGCCAGAAAAGTAAGATTCGTCGTTACGGCTTCAATCTTTTTAATTACAA
1 TGCCGGGGAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTCAATTGCAA
* * * * ** * *
59562890 TGTCGGGGAACG--AGATTTGCCGTTGTAGCTTCAATCTGATCCACTGC-A
1 TGCCGGGGAA-GTAAGATTCGTCGTTGTGGCTTCAATCTTTTCAATTGCAA
* ** * *
59562938 T-CACGAAGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAA
1 TGC-CG-GGGAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTCAATTGCAA
* * * * * ** * * *
59562989 TGTCGGGGAAGCAAGATTCGTCGTCGTAGCTTTAATCTGCTCCACTGCAC
1 TGCCGGGGAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTCAATTGCAA
* * * * *
59563039 TGTCAGGAAAGTAAGATTCGTCGTTGCGGCTTCAATCTTTTTAATTG
1 TGCCGGGGAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTCAATTG
59563086 TAAACTATGG
Statistics
Matches: 343, Mismatches: 138, Indels: 26
0.68 0.27 0.05
Matches are distributed among these distances:
48 11 0.03
49 89 0.26
50 232 0.68
51 11 0.03
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (50 bp):
TGCCGGGGAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTCAATTGCAA
Found at i:59562734 original size:99 final size:99
Alignment explanation
Indices: 59562482--59563085 Score: 730
Period size: 99 Copynumber: 6.1 Consensus size: 99
59562472 TTCTGTCAAA
* * * * * * * *
59562482 TTAACTGCAATGTTGGGGAAGCAAGATTCGCCATTGTAGCTTCAATCTGCCCCACTACACTGCCA
1 TTAATTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGCTCCACTGCACCGCCA
** *
59562547 GGGAAGTAAGATTCATCGTTGTGGCTTCAATCTTT
66 -GGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTT
* ** *
59562582 TCAATTGCAATACCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCCA
1 TTAATTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGCTCCACTGCACCGCCA
* *
59562647 GTGGAGTAAGATTCGCCGTTGCGGCTTTAATC-TT
66 G-GAAGTAAGATTCGCCGTTGCGGCTTCAATCTTT
* **
59562681 TTAATTGCAATGTCGGGGAAACAAGATTCGTCGTCGTAGCTTCAATCTATTCCACTGCACCGCCA
1 TTAATTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGCTCCACTGCACCGCCA
* *
59562746 TGGGAGTAAGATTCGCCGTTGTGGCTTCAATC-TT
66 -GGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTT
** * * *
59562780 TTAATTGCAATGTCGGGGAAACAAGATTCATCGTCGTAGCTTTAATCTGCTCCACTACACTGCCA
1 TTAATTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGCTCCACTGCACCGCCA
* * *
59562845 GAAAAGTAAGATTCGTCGTTACGGCTTCAATCTTT
66 G-GAAGTAAGATTCGCCGTTGCGGCTTCAATCTTT
* * * * *
59562880 TTAATTACAATGTCGGGG-AACGAGATTTGCCGTTGTAGCTTCAATCTGATCCACTGCATCACG-
1 TTAATTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGCTCCACTGCA-C-CGC
* *
59562943 AAGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTT
64 CAGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTT
* * * * *
59562979 TTAATTGCAATGTCGGGGAAGCAAGATTCGTCGTCGTAGCTTTAATCTGCTCCACTGCACTGTCA
1 TTAATTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGCTCCACTGCACCGCCA
*
59563044 GGAAAGTAAGATTCGTCGTTGCGGCTTCAATCTTT
66 GG-AAGTAAGATTCGCCGTTGCGGCTTCAATCTTT
59563079 TTAATTG
1 TTAATTG
59563086 TAAACTATGG
Statistics
Matches: 433, Mismatches: 62, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
98 2 0.00
99 259 0.60
100 171 0.39
101 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (99 bp):
TTAATTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGCTCCACTGCACCGCCA
GGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTT
Found at i:59562884 original size:199 final size:197
Alignment explanation
Indices: 59562482--59563085 Score: 791
Period size: 199 Copynumber: 3.0 Consensus size: 197
59562472 TTCTGTCAAA
* * * * ** * *
59562482 TTAACTGCAATGTTGGGGAAGCAAGATTCGCCATTGTAGCTTCAATCTGCCCCACTACACTGCCA
1 TTAATTGCAATGTCGGGGAAACAAGATTCGCCGTTGTAGCTTCAATCT-ATCCACTGCACCGCCA
* **
59562547 GGGAAGTAAGATTCATCGTTGTGGCTTCAATCTTTTCAATTGCAATACCGGGGAAACAAGATTCG
65 GGG-AGTAAGATTCACCGTTGTGGCTTCAATCTTTT-AATTGCAATGTCGGGGAAACAAGATTCG
* * * * *** * *
59562612 CCGTCGTAGCTTCAATCTGTTCCACTGCACCGCCAGTGGAGTAAGATTCGCCGTTGCGGCTTTAA
128 TCGTCGTAGCTTTAATCTGCTCCACTGCACTGCCAGAAAAGTAAGATTCGTCGTTGCGGCTTCAA
59562677 TC-TT
193 TCTTT
* *
59562681 TTAATTGCAATGTCGGGGAAACAAGATTCGTCGTCGTAGCTTCAATCTATTCCACTGCACCGCCA
1 TTAATTGCAATGTCGGGGAAACAAGATTCGCCGTTGTAGCTTCAATCTA-TCCACTGCACCGCCA
* *
59562746 TGGGAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAATTGCAATGTCGGGGAAACAAGATTCAT
65 -GGGAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAATTGCAATGTCGGGGAAACAAGATTCGT
* *
59562811 CGTCGTAGCTTTAATCTGCTCCACTACACTGCCAGAAAAGTAAGATTCGTCGTTACGGCTTCAAT
129 CGTCGTAGCTTTAATCTGCTCCACTGCACTGCCAGAAAAGTAAGATTCGTCGTTGCGGCTTCAAT
59562876 CTTT
194 CTTT
* * *
59562880 TTAATTACAATGTCGGGG-AACGAGATTTGCCGTTGTAGCTTCAATCTGATCCACTGCATCACG-
1 TTAATTGCAATGTCGGGGAAACAAGATTCGCCGTTGTAGCTTCAATCT-ATCCACTGCA-C-CGC
* * * *
59562943 AAGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTC
63 CAGGGAGTAAGATTCACCGTTGTGGCTTCAATC-TTTTAATTGCAATGTCGGGGAAACAAGATTC
* *
59563008 GTCGTCGTAGCTTTAATCTGCTCCACTGCACTGTCAGGAAAGTAAGATTCGTCGTTGCGGCTTCA
127 GTCGTCGTAGCTTTAATCTGCTCCACTGCACTGCCAGAAAAGTAAGATTCGTCGTTGCGGCTTCA
59563073 ATCTTT
192 ATCTTT
59563079 TTAATTG
1 TTAATTG
59563086 TAAACTATGG
Statistics
Matches: 356, Mismatches: 42, Indels: 14
0.86 0.10 0.03
Matches are distributed among these distances:
198 143 0.40
199 208 0.58
200 5 0.01
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (197 bp):
TTAATTGCAATGTCGGGGAAACAAGATTCGCCGTTGTAGCTTCAATCTATCCACTGCACCGCCAG
GGAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAATTGCAATGTCGGGGAAACAAGATTCGTCG
TCGTAGCTTTAATCTGCTCCACTGCACTGCCAGAAAAGTAAGATTCGTCGTTGCGGCTTCAATCT
TT
Found at i:59563167 original size:45 final size:45
Alignment explanation
Indices: 59563118--59563225 Score: 171
Period size: 45 Copynumber: 2.4 Consensus size: 45
59563108 GCTTCGTCAT
* * *
59563118 CAATACAGGAAGGCAAGATCTGCTATTTTCAGTCTACTTCGCTAC
1 CAATACAGGAAGACAAGATCTACTATATTCAGTCTACTTCGCTAC
* *
59563163 CAATACAAGAAGACAAGATCTACTATATTCAGTCTACTTCGCTGC
1 CAATACAGGAAGACAAGATCTACTATATTCAGTCTACTTCGCTAC
59563208 CAATACAGGAAGACAAGA
1 CAATACAGGAAGACAAGA
59563226 CTTTCTATCT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 57 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (45 bp):
CAATACAGGAAGACAAGATCTACTATATTCAGTCTACTTCGCTAC
Found at i:59563487 original size:127 final size:127
Alignment explanation
Indices: 59563256--59563527 Score: 454
Period size: 127 Copynumber: 2.1 Consensus size: 127
59563246 CTGCTTCAAT
* *
59563256 TTCAGGGAGATAGGATTAATTTCTTCTGTCTGCTCCACTACTACTTAGGGAGATAAGACTGAATG
1 TTCAGGGAGATAGTATTGATTTCTTCTGTCTGCTCCACTACTACTTAGGGAGATAAGACTGAATG
*
59563321 CGATCTGCTCCACTACTGCTTAGGGAGATAAGACCTGTGGTTTTAATCCGCTCCACTACAAC
66 CGATCTGCTCCACTACTGCTTAAGGAGATAAGACCTGTGGTTTTAATCCGCTCCACTACAAC
* * * *
59563383 TTCAGGAAGATAGTATTGATTTTTTCTGTCTGCTCCGCTACTGCTTAGGGAGATAAGACTGAATG
1 TTCAGGGAGATAGTATTGATTTCTTCTGTCTGCTCCACTACTACTTAGGGAGATAAGACTGAATG
** *
59563448 CGATCTGCTCCACTACTGCTTAAGGAGATAAGATTTGTGGTTTTAATCCGCTCCACTGCAAC
66 CGATCTGCTCCACTACTGCTTAAGGAGATAAGACCTGTGGTTTTAATCCGCTCCACTACAAC
59563510 TTCAGGGAGATAGTATTG
1 TTCAGGGAGATAGTATTG
59563528 GATGCGATCT
Statistics
Matches: 134, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
127 134 1.00
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (127 bp):
TTCAGGGAGATAGTATTGATTTCTTCTGTCTGCTCCACTACTACTTAGGGAGATAAGACTGAATG
CGATCTGCTCCACTACTGCTTAAGGAGATAAGACCTGTGGTTTTAATCCGCTCCACTACAAC
Found at i:59563597 original size:44 final size:44
Alignment explanation
Indices: 59563472--59563599 Score: 120
Period size: 41 Copynumber: 3.0 Consensus size: 44
59563462 ACTGCTTAAG
* * *
59563472 GAGATAAGATTTGTGGTTTTAATCCGCTCCACTGCAACTTCAGG
1 GAGATAAGATATGTGGTTTTAATTCGCTCCACTGCAACTTCAGA
* *** * *
59563516 GAGAT-AG-TAT-TGGATGCGA-TCTGCTCTACTGTAACTTCAGA
1 GAGATAAGATATGTGGTTTTAATTC-GCTCCACTGCAACTTCAGA
* *
59563557 GAGATAAGATCTGTGGTTTTAATTCACTCCACTGCAACTTCAG
1 GAGATAAGATATGTGGTTTTAATTCGCTCCACTGCAACTTCAG
59563600 TGATATAGGA
Statistics
Matches: 62, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
40 1 0.02
41 26 0.42
42 4 0.06
43 4 0.06
44 25 0.40
45 2 0.03
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (44 bp):
GAGATAAGATATGTGGTTTTAATTCGCTCCACTGCAACTTCAGA
Found at i:59563668 original size:212 final size:212
Alignment explanation
Indices: 59563345--59563733 Score: 645
Period size: 212 Copynumber: 1.8 Consensus size: 212
59563335 ACTGCTTAGG
* * *
59563345 GAGATAAGACCTGTGGTTTTAATCCGCTCCACTACAACTTCAGGAAGATAGTATTGATTTTTTCT
1 GAGATAAGACCTGTGGTTTTAATCCACTCCACTACAACTTCAGGAAGATAGGATTGATTTCTTCT
*
59563410 GTCTGCTCCGCTACTGCTTAGGGAGATAAGACTGAATGCGATCTGCTCCACTACTGCTTAAGGAG
66 GTCAGCTCCGCTACTGCTTAGGGAGATAAGACTGAATGCGATCTGCTCCACTACTGCTTAAGGAG
*
59563475 ATAAGATTTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGTATTGGATGCGATCTGC
131 ATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGTATTGGATGCGATCTGC
59563540 TCTACTGTAACTTCAGA
196 TCTACTGTAACTTCAGA
* * * *
59563557 GAGATAAGATCTGTGGTTTTAATTCACTCCACTGCAACTTCAGTG-ATATAGGATTGATTTCTTC
1 GAGATAAGACCTGTGGTTTTAATCCACTCCACTACAACTTCAG-GAAGATAGGATTGATTTCTTC
* *
59563621 TGTCAGCTCCGCTACTGCTTAGGGAGATAAGACTGAATGTGATCTGCTCCACTACTGCTTAGGGA
65 TGTCAGCTCCGCTACTGCTTAGGGAGATAAGACTGAATGCGATCTGCTCCACTACTGCTTAAGGA
* *
59563686 GATAAGATCTGTGGTTTTAATCCGCTCCACTGTAACTTTAGGGAGATA
130 GATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATA
59563734 AGATTGATTT
Statistics
Matches: 163, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
212 162 0.99
213 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.32
Consensus pattern (212 bp):
GAGATAAGACCTGTGGTTTTAATCCACTCCACTACAACTTCAGGAAGATAGGATTGATTTCTTCT
GTCAGCTCCGCTACTGCTTAGGGAGATAAGACTGAATGCGATCTGCTCCACTACTGCTTAAGGAG
ATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGTATTGGATGCGATCTGC
TCTACTGTAACTTCAGA
Found at i:59563859 original size:44 final size:41
Alignment explanation
Indices: 59563638--59563860 Score: 110
Period size: 43 Copynumber: 5.3 Consensus size: 41
59563628 TCCGCTACTG
** * * * * **
59563638 CTTAGGGAGATAAGAC-TGAATGTGATCTGCTCCACTACTG
1 CTTAGGGAGATAAGACTTGGTTTTAATCCGCTCCACTGCAA
*
59563678 CTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGTAA
1 CTTAGGGAGATAAGA-CT-TGGTTTTAATCCGCTCCACTGCAA
* ** * * * **
59563721 CTTTAGGGAGATAAGA-TTGATTTCTTCTGTCTGCTCCGCTACTG
1 C-TTAGGGAGATAAGACTTG-GTT-TT-AATCCGCTCCACTGCAA
** *** * * **
59563765 CTTAGGGAGATAAGAC-TGAATACGATCTGCTCCACTACTG
1 CTTAGGGAGATAAGACTTGGTTTTAATCCGCTCCACTGCAA
59563805 CTTAGGGAGATAAGACCTGTGGTTTTAATCCGCTCCACTGCAA
1 CTTAGGGAGATAAGA-CT-TGGTTTTAATCCGCTCCACTGCAA
59563848 CTTCAGGGAGATA
1 CTT-AGGGAGATA
59563861 GGATTGATTT
Statistics
Matches: 137, Mismatches: 34, Indels: 20
0.72 0.18 0.10
Matches are distributed among these distances:
40 44 0.32
41 4 0.03
42 4 0.03
43 52 0.38
44 33 0.24
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.30
Consensus pattern (41 bp):
CTTAGGGAGATAAGACTTGGTTTTAATCCGCTCCACTGCAA
Found at i:59563972 original size:40 final size:39
Alignment explanation
Indices: 59563674--59563972 Score: 101
Period size: 40 Copynumber: 7.1 Consensus size: 39
59563664 CTGCTCCACT
* *
59563674 ACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTCC
1 ACTGCTTAGGGAGATAAGATCTGTGGCTTT-ATCTGCTCC
** *
59563714 ACTGTAACTTTAGGGAGATAAGAT-TGATTTCTTCTGTCTGCTCCGC
1 ACTG---C-TTAGGGAGATAAGATCTG-TGGCTT-TATCTGCT-C-C
* *
59563760 TACTGCTTAGGGAGATAAGA-CTGAAT-AC--GATCTGCTCCAC
1 -ACTGCTTAGGGAGATAAGATCTG--TGGCTTTATCTGCT-C-C
* * *
59563800 TACTGCTTAGGGAGATAAGACCTGTGGTTTTAATCCGCTCC
1 -ACTGCTTAGGGAGATAAGATCTGTGGCTTT-ATCTGCTCC
* ** *
59563841 ACTGCAACTTCAGGGAGATAGGAT-TGATTTCTTCTGTCTGCTCCGC
1 ACTG---CTT-AGGGAGATAAGATCTG-TGGCTT-TATCTGCT-C-C
* ** * * *
59563887 TATTGCTTAGGGAGATAAGA-CTGAAT-GCGATATGCTCCACT
1 -ACTGCTTAGGGAGATAAGATCTG--TGGCTTTAT-CTGCTCC
59563928 ACTGCTTAGGGAGATAAGATCTGTGGCTTTAATCTGCTCC
1 ACTGCTTAGGGAGATAAGATCTGTGGCTTT-ATCTGCTCC
59563968 ACTGC
1 ACTGC
59563973 AACTTCAGAG
Statistics
Matches: 193, Mismatches: 35, Indels: 62
0.67 0.12 0.21
Matches are distributed among these distances:
39 2 0.01
40 67 0.35
41 9 0.05
42 4 0.02
43 48 0.25
44 50 0.26
45 4 0.02
46 2 0.01
47 7 0.04
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (39 bp):
ACTGCTTAGGGAGATAAGATCTGTGGCTTTATCTGCTCC
Found at i:59564009 original size:127 final size:127
Alignment explanation
Indices: 59563557--59563993 Score: 730
Period size: 127 Copynumber: 3.4 Consensus size: 127
59563547 TAACTTCAGA
* * * *
59563557 GAGATAAGATCTGTGGTTTTAATTCACTCCACTGCAACTTCAGTGATATAGGATTGATTTCTTCT
1 GAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
* *
59563622 GTCAGCTCCGCTACTGCTTAGGGAGATAAGACTGAATGTGATCTGCTCCACTACTGCTTAGG
66 GTCTGCTCCGCTACTGCTTAGGGAGATAAGACTGAATGCGATCTGCTCCACTACTGCTTAGG
* * *
59563684 GAGATAAGATCTGTGGTTTTAATCCGCTCCACTGTAACTTTAGGGAGATAAGATTGATTTCTTCT
1 GAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
*
59563749 GTCTGCTCCGCTACTGCTTAGGGAGATAAGACTGAATACGATCTGCTCCACTACTGCTTAGG
66 GTCTGCTCCGCTACTGCTTAGGGAGATAAGACTGAATGCGATCTGCTCCACTACTGCTTAGG
*
59563811 GAGATAAGACCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
1 GAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
* *
59563876 GTCTGCTCCGCTATTGCTTAGGGAGATAAGACTGAATGCGATATGCTCCACTACTGCTTAGG
66 GTCTGCTCCGCTACTGCTTAGGGAGATAAGACTGAATGCGATCTGCTCCACTACTGCTTAGG
* * *
59563938 GAGATAAGATCTGTGGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAGGATTG
1 GAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTG
59563994 GTGCTTCCGA
Statistics
Matches: 289, Mismatches: 21, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
127 289 1.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (127 bp):
GAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
GTCTGCTCCGCTACTGCTTAGGGAGATAAGACTGAATGCGATCTGCTCCACTACTGCTTAGG
Found at i:59564074 original size:45 final size:45
Alignment explanation
Indices: 59564001--59564664 Score: 864
Period size: 45 Copynumber: 14.8 Consensus size: 45
59563991 TTGGTGCTTC
* * * * * *
59564001 CGATCTGCTTCACTGCCAGTACAAGAAGATAAGATCTACTATCTT
1 CGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTT
59564046 C-AGTCTACTTCGCTGCCAATACAGGAAGACAAGA-CTTGCTATCTT
1 CGA-TCTACTTCGCTGCCAATACAGGAAGACAAGATC-TGCTATCTT
* *
59564091 CGACCAACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTT
1 CGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTT
* * * *
59564136 CGATCCACTTCACTACCAATACAGGAAGATAAGATCTGCTATCTT
1 CGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTT
* * **
59564181 CGATCCACTTTGCTGCCAATACAGGAAGGTAAGATCTGCTATCTT
1 CGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTT
*
59564226 C-AGTCTACTTCGCTGCCAATACAGGAAGATAAGATCTGCTATCTT
1 CGA-TCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTT
*
59564271 C-AGTCTACTTCGTTGCCAATACAGGAAGACAAGA-CTTGCTATCTT
1 CGA-TCTACTTCGCTGCCAATACAGGAAGACAAGATC-TGCTATCTT
59564316 CGATCTACTTCGCTGCCAATACAGGAAGACAAGA-CTTGCTATCTT
1 CGATCTACTTCGCTGCCAATACAGGAAGACAAGATC-TGCTATCTT
* * *
59564361 CAATCTACTTCACTGCCAATACAGGAAAACAAGA-CTTGCTATCTT
1 CGATCTACTTCGCTGCCAATACAGGAAGACAAGATC-TGCTATCTT
*
59564406 CGATCTACTTCGCTGCCAATATAGGAAGACAAGATCTGCTATCTT
1 CGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTT
*
59564451 C-AGTCTACTTCGCTGCCAATATAGGAATG-CAAGA-CTTGCTATCTT
1 CGA-TCTACTTCGCTGCCAATACAGGAA-GACAAGATC-TGCTATCTT
* * *
59564496 CGATCTACTTCGCTGTCAATATAGGAAGATAAGATCTGCTATCTT
1 CGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTT
* *
59564541 CAATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATCTT
1 CGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTT
* *
59564586 CGATCTACTTTGCTGCCAATACAGGAAGACAAGATCTGTTATCTT
1 CGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTT
* *
59564631 C-AGTCTACTTCGCTGCCAATACAGGGAGATAAGA
1 CGA-TCTACTTCGCTGCCAATACAGGAAGACAAGA
59564665 CTTGATTTGA
Statistics
Matches: 562, Mismatches: 42, Indels: 30
0.89 0.07 0.05
Matches are distributed among these distances:
44 8 0.01
45 547 0.97
46 7 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (45 bp):
CGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTT
Found at i:59565718 original size:17 final size:18
Alignment explanation
Indices: 59565686--59565724 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
59565676 GGCCTCTCCT
*
59565686 TTTTCTTTTTTATTTTTC
1 TTTTCTTTTATATTTTTC
59565704 TTTTCTTTTAT-TTTTTC
1 TTTTCTTTTATATTTTTC
59565721 TTTT
1 TTTT
59565725 AGTTTCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTCTTTTATATTTTTC
Found at i:59565868 original size:12 final size:12
Alignment explanation
Indices: 59565851--59565878 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
59565841 TAAGGTCCTT
59565851 TCTAGTTTGACA
1 TCTAGTTTGACA
59565863 TCTAGTTTGACA
1 TCTAGTTTGACA
59565875 TCTA
1 TCTA
59565879 CTTTCTTCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (12 bp):
TCTAGTTTGACA
Found at i:59566221 original size:21 final size:21
Alignment explanation
Indices: 59566194--59566243 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
59566184 TTTTTTTCTA
*
59566194 TTTTTTTATTTTCCTTATTTTC
1 TTTTTTT-TTCTCCTTATTTTC
* *
59566216 TTTTTTTTTGCTCTTTCTTTTC
1 TTTTTTTTT-CTCCTTATTTTC
59566238 TTTTTT
1 TTTTTT
59566244 GCCTCCACTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.04, C:0.14, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTTTTTTTCTCCTTATTTTC
Found at i:59571830 original size:22 final size:21
Alignment explanation
Indices: 59571795--59571871 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 21
59571785 AAAGGGTATC
* * *
59571795 TACAAATTAAATCTCTAATAT
1 TACAAATCATATCTCTAAGAT
59571816 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
59571839 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
59571858 TACATATCATATCT
1 TACAAATCATATCT
59571872 AAGATTGCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
19 18 0.39
21 4 0.09
22 15 0.33
23 9 0.20
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.38
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:59571855 original size:19 final size:19
Alignment explanation
Indices: 59571831--59571884 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
59571821 AATCATATCT
59571831 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
59571850 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
59571869 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
59571885 CTTGAAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:59575417 original size:28 final size:28
Alignment explanation
Indices: 59575386--59575460 Score: 107
Period size: 28 Copynumber: 2.7 Consensus size: 28
59575376 AAAAAATAAA
* *
59575386 ATTTACCAAAATACTA-CAAGTTTTTTTT
1 ATTTACCAAAATA-TATAAACTTTTTTTT
*
59575414 ATTTACTAAAATATATAAACTTTTTTTT
1 ATTTACCAAAATATATAAACTTTTTTTT
59575442 ATTTACCAAAATATATAAA
1 ATTTACCAAAATATATAAA
59575461 AAAACCAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 2 0.05
28 40 0.95
ACGTcount: A:0.43, C:0.11, G:0.01, T:0.45
Consensus pattern (28 bp):
ATTTACCAAAATATATAAACTTTTTTTT
Found at i:59575480 original size:17 final size:18
Alignment explanation
Indices: 59575446--59575483 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
59575436 TTTTTTATTT
*
59575446 ACCAAAATATATAAAAAA
1 ACCAAAATATAAAAAAAA
59575464 ACCAAAAT-TAAAAAAAA
1 ACCAAAATATAAAAAAAA
59575481 ACC
1 ACC
59575484 TGACAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.71, C:0.16, G:0.00, T:0.13
Consensus pattern (18 bp):
ACCAAAATATAAAAAAAA
Found at i:59575573 original size:27 final size:27
Alignment explanation
Indices: 59575535--59575601 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
59575525 CGCTAATGGT
59575535 ATTGGCGGCACCAAAGGTGCCAAAACC
1 ATTGGCGGCACCAAAGGTGCCAAAACC
* **
59575562 ATTGGCGGCACCAATGGTGCCAATGCC
1 ATTGGCGGCACCAAAGGTGCCAAAACC
59575589 ATTGGCGGCACCA
1 ATTGGCGGCACCA
59575602 GTTGGTGTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.27, C:0.30, G:0.28, T:0.15
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAACC
Found at i:59575654 original size:4 final size:4
Alignment explanation
Indices: 59575645--59575769 Score: 80
Period size: 4 Copynumber: 30.5 Consensus size: 4
59575635 GCAGAAGGAG
* *
59575645 AGAA AGAA AGAA AGAA AGGAGA GGAA AGAA AGAA AGAA AGAA AGGGGA
1 AGAA AGAA AGAA AGAA A-GA-A AGAA AGAA AGAA AGAA AGAA A--GAA
* * *
59575693 GGAA AGAA AGAAA AGGAA AG-G AGAA GAGAA A-AA AGGAA AGAA A-CA
1 AGAA AGAA AG-AA A-GAA AGAA AGAA -AGAA AGAA A-GAA AGAA AGAA
* *
59575738 AG-A AGAA A-AA AGAA AGAA GGAA GGAA AGAA AG
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AG
59575770 GGAAATGAGA
Statistics
Matches: 97, Mismatches: 11, Indels: 26
0.72 0.08 0.19
Matches are distributed among these distances:
3 13 0.13
4 63 0.65
5 17 0.18
6 4 0.04
ACGTcount: A:0.66, C:0.01, G:0.33, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:59575674 original size:22 final size:22
Alignment explanation
Indices: 59575639--59575769 Score: 110
Period size: 26 Copynumber: 5.8 Consensus size: 22
59575629 GTGGGGGCAG
59575639 AAGGAGA-GAAAGAAAGAAAGA
1 AAGGAGAGGAAAGAAAGAAAGA
59575660 AAGGAGAGGAAAGAAAGAAAGAAAGA
1 AAGGAGA-G---GAAAGAAAGAAAGA
*
59575686 AAGGGGAGGAAAGAAAGAAAAGGA
1 AAGGAGAGGAAAGAAAG-AAA-GA
59575710 AAGGAGAAGAGAAA-AAAGGAAAGA
1 AAGGAG-AG-GAAAGAAA-GAAAGA
** *
59575734 AACAAGAAGAAA-AAAGAAAG-
1 AAGGAGAGGAAAGAAAGAAAGA
59575754 AAGGA-AGGAAAGAAAG
1 AAGGAGAGGAAAGAAAG
59575770 GGAAATGAGA
Statistics
Matches: 91, Mismatches: 8, Indels: 23
0.75 0.07 0.19
Matches are distributed among these distances:
19 5 0.05
20 7 0.08
21 12 0.13
22 16 0.18
23 4 0.04
24 13 0.14
25 9 0.10
26 25 0.27
ACGTcount: A:0.66, C:0.01, G:0.34, T:0.00
Consensus pattern (22 bp):
AAGGAGAGGAAAGAAAGAAAGA
Found at i:59575676 original size:26 final size:26
Alignment explanation
Indices: 59575640--59575755 Score: 118
Period size: 26 Copynumber: 4.7 Consensus size: 26
59575630 TGGGGGCAGA
*
59575640 AGGAGAGAAAGAAAGAAAGAAAGGAG
1 AGGAAAGAAAGAAAGAAAGAAAGGAG
*
59575666 AGGAAAGAAAGAAAGAAAGAAAGGGG
1 AGGAAAGAAAGAAAGAAAGAAAGGAG
*
59575692 AGGAAAGAAAG-AA-AAGGAAAGGAG
1 AGGAAAGAAAGAAAGAAAGAAAGGAG
* **
59575716 A--AGAGAAA-AAAGGAAAGAAACAAG
1 AGGAAAGAAAGAAA-GAAAGAAAGGAG
*
59575740 AAGAAA-AAAGAAAGAA
1 AGGAAAGAAAGAAAGAA
59575756 GGAAGGAAAG
Statistics
Matches: 75, Mismatches: 9, Indels: 13
0.77 0.09 0.13
Matches are distributed among these distances:
22 8 0.11
24 19 0.25
25 8 0.11
26 40 0.53
ACGTcount: A:0.66, C:0.01, G:0.33, T:0.00
Consensus pattern (26 bp):
AGGAAAGAAAGAAAGAAAGAAAGGAG
Found at i:59575735 original size:34 final size:33
Alignment explanation
Indices: 59575692--59575820 Score: 103
Period size: 34 Copynumber: 4.0 Consensus size: 33
59575682 AAGAAAGGGG
59575692 AGGAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAA
1 AGGAAAGAAAGAAAAGGAAA-GAGAAGAGAAAAA
* *
59575726 AGGAAAGAAACAAGAA-G-AA-A-AA-AGAAAGA
1 AGGAAAGAAAGAA-AAGGAAAGAGAAGAGAAAAA
* *
59575755 AGGAAGGAAAGAAAGGGAAATGAGAAGAGAAAAA
1 AGGAAAGAAAGAAAAGGAAA-GAGAAGAGAAAAA
* * *
59575789 AGAAGAAG-AAGAAGAGGGAAGA-AAG-GAAAAA
1 AGGA-AAGAAAGAAAAGGAAAGAGAAGAGAAAAA
59575820 A
1 A
59575821 AAGGGAAAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
28 1 0.01
29 18 0.24
30 4 0.05
31 8 0.11
32 4 0.05
33 6 0.08
34 31 0.41
35 4 0.05
ACGTcount: A:0.67, C:0.01, G:0.32, T:0.01
Consensus pattern (33 bp):
AGGAAAGAAAGAAAAGGAAAGAGAAGAGAAAAA
Found at i:59575790 original size:21 final size:20
Alignment explanation
Indices: 59575703--59575833 Score: 99
Period size: 21 Copynumber: 6.3 Consensus size: 20
59575693 GGAAAGAAAG
*
59575703 AAAAGGAAAGGAGAAGAGAA
1 AAAAGGAAAGAAGAAGAGAA
*
59575723 AAAAGGAAAGAAACAAGAAGAA
1 AAAAGGAAAG-AAGAAG-AGAA
59575745 AAAA-GAAAGAAGGAAG-GAA
1 AAAAGGAAAGAA-GAAGAGAA
59575764 AGAAAGGGAAATG-AGAAGAGAA
1 A-AAA-GGAAA-GAAGAAGAGAA
*
59575786 AAAAGAAGAAGAAGAAGAGGGAA
1 AAAAGGA-AAGAAGAAGA--GAA
* * *
59575809 GAAAGGAAA-AAAAAGGGAA
1 AAAAGGAAAGAAGAAGAGAA
59575828 AAAAGG
1 AAAAGG
59575834 TAATTTTATT
Statistics
Matches: 90, Mismatches: 9, Indels: 25
0.73 0.07 0.20
Matches are distributed among these distances:
19 12 0.13
20 18 0.20
21 32 0.36
22 19 0.21
23 9 0.10
ACGTcount: A:0.66, C:0.01, G:0.32, T:0.01
Consensus pattern (20 bp):
AAAAGGAAAGAAGAAGAGAA
Found at i:59582186 original size:36 final size:36
Alignment explanation
Indices: 59582142--59582247 Score: 101
Period size: 26 Copynumber: 3.3 Consensus size: 36
59582132 AAATAATAAA
59582142 CAAAATAATACACACTAAAATTATTAATTTTATACT
1 CAAAATAATACACACTAAAATTATTAATTTTATACT
**
59582178 ---ACGAAT--A-A-T---ATTATTAATTTTATACT
1 CAAAATAATACACACTAAAATTATTAATTTTATACT
59582204 CAAAATAATACACACTAAAATTATTAA-TTT-TACT
1 CAAAATAATACACACTAAAATTATTAATTTTATACT
*
59582238 AAAAATAATA
1 CAAAATAATA
59582248 ACTAACTATA
Statistics
Matches: 55, Mismatches: 5, Indels: 22
0.67 0.06 0.27
Matches are distributed among these distances:
26 17 0.31
29 5 0.09
30 1 0.02
31 2 0.04
32 1 0.02
33 5 0.09
34 13 0.24
35 3 0.05
36 8 0.15
ACGTcount: A:0.51, C:0.11, G:0.01, T:0.37
Consensus pattern (36 bp):
CAAAATAATACACACTAAAATTATTAATTTTATACT
Found at i:59582403 original size:3 final size:3
Alignment explanation
Indices: 59582395--59582435 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
59582385 TCTTCATACT
59582395 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
59582436 TAATAATAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:59582721 original size:27 final size:27
Alignment explanation
Indices: 59582683--59582758 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
59582673 ATAATACGAG
59582683 TGGTGCCGCCAATGGCATTGGCACCAT
1 TGGTGCCGCCAATGGCATTGGCACCAT
** *
59582710 TGGTGCCGCCAATGGTTTTGGCACCTT
1 TGGTGCCGCCAATGGCATTGGCACCAT
**
59582737 TGGTGCCGCCAATACCATTGGC
1 TGGTGCCGCCAATGGCATTGGC
59582759 GTGACCAGTG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (27 bp):
TGGTGCCGCCAATGGCATTGGCACCAT
Found at i:59582892 original size:29 final size:28
Alignment explanation
Indices: 59582829--59582901 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
59582819 GTTTTTTTTG
**
59582829 ATATATTTTGGTAAATAAAAAAAAGTTT
1 ATATATTTTGGTAAATAAAAAAAAACTT
*
59582857 ATATATTTTGATAAATAAAAAAAAACTT
1 ATATATTTTGGTAAATAAAAAAAAACTT
*
59582885 GTAGTATTTTGGTAAAT
1 ATA-TATTTTGGTAAAT
59582902 TTTTATTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
28 27 0.69
29 12 0.31
ACGTcount: A:0.48, C:0.01, G:0.11, T:0.40
Consensus pattern (28 bp):
ATATATTTTGGTAAATAAAAAAAAACTT
Found at i:59598696 original size:15 final size:15
Alignment explanation
Indices: 59598676--59598727 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 15
59598666 ACTACTAAAC
59598676 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
59598691 ATTTATAATTATAATAAAT
1 ATTTATTA-T-TAAT--AT
59598710 ATTTATTATTAATAT
1 ATTTATTATTAATAT
59598725 ATT
1 ATT
59598728 AATATTGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 12 0.39
16 1 0.03
17 8 0.26
18 1 0.03
19 9 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:59598733 original size:17 final size:16
Alignment explanation
Indices: 59598679--59598733 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 16
59598669 ACTAAACATT
59598679 TATTATTAATATATTTA
1 TATTATTAATATA-TTA
59598696 TAATTA-TAATAAATATT-
1 T-ATTATTAAT--ATATTA
59598713 TATTATTAATATATTAA
1 TATTATTAATATATT-A
59598730 TATT
1 TATT
59598734 GAATATTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
15 5 0.16
16 4 0.12
17 14 0.44
18 6 0.19
19 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTATTAATATATTA
Found at i:59601384 original size:37 final size:37
Alignment explanation
Indices: 59601319--59601468 Score: 187
Period size: 37 Copynumber: 3.9 Consensus size: 37
59601309 TACATATGAT
*
59601319 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
*
59601354 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
59601391 CACTTATCACTTTGTCTCTTGATCAGATAAATGTAGCTAAAGC
1 CACTTATCACTTTGTCTCTTGATCAGAT-AA-GT-G-T--AGC
59601434 TATCACTTATCACTTTGTCTCTTGATCAGATAAGT
1 ---CACTTATCACTTTGTCTCTTGATCAGATAAGT
59601469 ATATCCGAAG
Statistics
Matches: 101, Mismatches: 3, Indels: 13
0.86 0.03 0.11
Matches are distributed among these distances:
35 10 0.10
36 4 0.04
37 46 0.46
38 2 0.02
39 2 0.02
40 1 0.01
41 1 0.01
43 3 0.03
44 2 0.02
45 2 0.02
46 28 0.28
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
Found at i:59601444 original size:46 final size:46
Alignment explanation
Indices: 59601391--59601659 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
59601381 TAAGTGTAGC
* * **
59601391 CACTTATCACTTTGTCTCTTGATCAGATAAATGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* * *
59601437 CACTTATCACTTTGTCTCTTGATCAGATAAGTATATCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
59601483 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAACCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
59601535 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
59601587 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
59601633 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
59601660 AGTACTCAAA
Statistics
Matches: 204, Mismatches: 12, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
46 111 0.54
49 1 0.00
50 1 0.00
51 3 0.01
52 88 0.43
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:59601510 original size:52 final size:52
Alignment explanation
Indices: 59601434--59601653 Score: 308
Period size: 52 Copynumber: 4.3 Consensus size: 52
59601424 TAGCTAAAGC
* * *
59601434 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATATCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* *
59601487 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAACCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * *
59601539 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
59601591 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
59601637 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
59601654 ATCAGAAGTA
Statistics
Matches: 150, Mismatches: 10, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
46 43 0.29
50 1 0.01
52 91 0.61
53 15 0.10
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.36
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:59603787 original size:68 final size:68
Alignment explanation
Indices: 59603670--59603819 Score: 187
Period size: 68 Copynumber: 2.2 Consensus size: 68
59603660 CTATTACAAA
* * * * *
59603670 GGTCTTACACAGTATGATCCCATGTTTAATGTCCCAGTGGACTCTCTTTGTTGCCACAGTCGAGC
1 GGTCTTACACAATAGGAACCCATATTTAATGTCCCAGTGGACTCCCTTTGTTGCCACAGTCGAGC
59603735 TAT
66 TAT
* * *
59603738 GGTCTTACACAATAGGAACCCATATTTAATGTCCTGACG-GG-CTCCCTTTGTTGCCATAGTTGA
1 GGTCTTACACAATAGGAACCCATATTTAATGTCC-CA-GTGGACTCCCTTTGTTGCCACAGTCGA
*
59603801 GTTAT
64 GCTAT
59603806 GGTCTTACACAATA
1 GGTCTTACACAATA
59603820 TAACCTCTTT
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
68 67 0.94
69 3 0.04
70 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.33
Consensus pattern (68 bp):
GGTCTTACACAATAGGAACCCATATTTAATGTCCCAGTGGACTCCCTTTGTTGCCACAGTCGAGC
TAT
Found at i:59603984 original size:38 final size:39
Alignment explanation
Indices: 59603923--59604033 Score: 101
Period size: 35 Copynumber: 3.0 Consensus size: 39
59603913 AGAGTCGAGG
* **
59603923 GACCCTCGTCACAATGTCACTCTAGCGAGCCAGTTGATA
1 GACCGTCGTCACGGTGTCACTCTAGCGAGCCAGTTGATA
* * *
59603962 -ATCAC-T-GTCACGGTGTCGCTCTA--TAG--AGTCGATA
1 GA-C-CGTCGTCACGGTGTCACTCTAGCGAGCCAGTTGATA
59603996 GACCGTCGTCACGGTGTCACTCTAGCGAGCCAGTTGAT
1 GACCGTCGTCACGGTGTCACTCTAGCGAGCCAGTTGAT
59604034 GACATTCCAT
Statistics
Matches: 55, Mismatches: 8, Indels: 18
0.68 0.10 0.22
Matches are distributed among these distances:
33 1 0.02
34 9 0.16
35 17 0.31
36 2 0.04
37 2 0.04
38 15 0.27
39 8 0.15
40 1 0.02
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (39 bp):
GACCGTCGTCACGGTGTCACTCTAGCGAGCCAGTTGATA
Found at i:59603988 original size:73 final size:73
Alignment explanation
Indices: 59603896--59604033 Score: 213
Period size: 73 Copynumber: 1.9 Consensus size: 73
59603886 CTTACTGCCA
*
59603896 TCACGGTATCGCTCCATAGAGTCGAGGGACCCTCGTCACAATGTCACTCTAGCGAGCCAGTTGAT
1 TCACGGTATCGCTCCATAGAGTCGAGAGACCCTCGTCACAATGTCACTCTAGCGAGCCAGTTGAT
59603961 AATCACTG
66 AATCACTG
* * * * **
59603969 TCACGGTGTCGCTCTATAGAGTCGATAGACCGTCGTCACGGTGTCACTCTAGCGAGCCAGTTGAT
1 TCACGGTATCGCTCCATAGAGTCGAGAGACCCTCGTCACAATGTCACTCTAGCGAGCCAGTTGAT
59604034 GACATTCCAT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 58 1.00
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (73 bp):
TCACGGTATCGCTCCATAGAGTCGAGAGACCCTCGTCACAATGTCACTCTAGCGAGCCAGTTGAT
AATCACTG
Found at i:59610417 original size:16 final size:16
Alignment explanation
Indices: 59610396--59610447 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
59610386 TTTGGTTCGC
59610396 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
59610412 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* * *
59610428 TGTAATGGAATAGATG
1 TGTATTGGATTAGAGG
59610444 TGTA
1 TGTA
59610448 ATAGCAAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:59610494 original size:45 final size:44
Alignment explanation
Indices: 59610428--59610522 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 44
59610418 GGATTAGAGG
* * * *
59610428 TGTAATGGAATAGATGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAAAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
59610473 TGTAATGGAATAAAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAAAGGCGTAATAGCAAAACACTGTTTGGTTGAA
59610517 TGTAAT
1 TGTAAT
59610523 AGAGGTGTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 18 0.42
45 25 0.58
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAAAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:59610704 original size:17 final size:17
Alignment explanation
Indices: 59610684--59610717 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
59610674 TTATTATTTA
59610684 ATAT-ATTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
59610701 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
59610718 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Done.