Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 96 of 206
Found at i:28000824 original size:16 final size:17
Alignment explanation
Indices: 28000793--28000826 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
28000783 CAATTCATTC
28000793 CAAAATTCAAACTTTTG
1 CAAAATTCAAACTTTTG
*
28000810 CAAAATT-ACACTTTTG
1 CAAAATTCAAACTTTTG
28000826 C
1 C
28000827 CCCTAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (17 bp):
CAAAATTCAAACTTTTG
Found at i:28000950 original size:29 final size:29
Alignment explanation
Indices: 28000908--28000965 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
28000898 ATATCATGCT
28000908 AGCTAAATGCACTAGGGACCTATACCAAC
1 AGCTAAATGCACTAGGGACCTATACCAAC
*
28000937 AGCTAAATTCACTAGGGACCTATACCAAC
1 AGCTAAATGCACTAGGGACCTATACCAAC
28000966 TCATACAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.38, C:0.28, G:0.16, T:0.19
Consensus pattern (29 bp):
AGCTAAATGCACTAGGGACCTATACCAAC
Found at i:28005075 original size:2 final size:2
Alignment explanation
Indices: 28005068--28005101 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
28005058 AGCTAAAATA
*
28005068 AG AG AG AG AG AG AG AG AG AG AG AG AG AG CG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
28005102 TCTGGTAGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28006515 original size:35 final size:35
Alignment explanation
Indices: 28006467--28006535 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
28006457 TTAATTAATC
* *
28006467 AGCTTTGAGAATTGGAGTTCCCGAACAGTCATTGG
1 AGCTTTGACAATTGGAGTTCCCGAACAGCCATTGG
*
28006502 AGCTTTGTCAATTGGAGTTCCCGAACAGCCATTG
1 AGCTTTGACAATTGGAGTTCCCGAACAGCCATTG
28006536 AGGTAGACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (35 bp):
AGCTTTGACAATTGGAGTTCCCGAACAGCCATTGG
Found at i:28042676 original size:16 final size:16
Alignment explanation
Indices: 28042655--28042685 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28042645 AATTCAATCC
28042655 ATTTCAATCAACTATA
1 ATTTCAATCAACTATA
*
28042671 ATTTCAATCCACTAT
1 ATTTCAATCAACTAT
28042686 CAAAGTGCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTTCAATCAACTATA
Found at i:28044312 original size:22 final size:21
Alignment explanation
Indices: 28044284--28044334 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
28044274 AAGGTGGAAG
* *
28044284 TTATGTGGCAGTTTATTTGCAA
1 TTATGTGGCAG-GTATTAGCAA
*
28044306 TTATGTGGCCGGTATTAGCAA
1 TTATGTGGCAGGTATTAGCAA
28044327 TTATGTGG
1 TTATGTGG
28044335 TGGCTTGTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.22, C:0.10, G:0.27, T:0.41
Consensus pattern (21 bp):
TTATGTGGCAGGTATTAGCAA
Found at i:28044803 original size:22 final size:22
Alignment explanation
Indices: 28044777--28044821 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
28044767 TGGACTTTAA
*
28044777 TTTGGG-TTTGTTTTAATAAATT
1 TTTGGGATTTATTTTAA-AAATT
28044799 TTTGGGACTTTATTTTAAAAATT
1 TTTGGGA-TTTATTTTAAAAATT
28044822 GGACTGTGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 6 0.30
23 5 0.25
24 9 0.45
ACGTcount: A:0.27, C:0.02, G:0.16, T:0.56
Consensus pattern (22 bp):
TTTGGGATTTATTTTAAAAATT
Found at i:28054202 original size:22 final size:24
Alignment explanation
Indices: 28054152--28054202 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
28054142 TTACAATGCT
28054152 TTTATATTTTAATAATTGAGTATTA
1 TTTATATTTTAAT-ATTGAGTATTA
28054177 -TTATATATTTAAT-TTGA-T-TTA
1 TTTATAT-TTTAATATTGAGTATTA
28054198 TTTAT
1 TTTAT
28054203 TTATAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
21 3 0.12
22 5 0.21
23 4 0.17
24 6 0.25
25 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (24 bp):
TTTATATTTTAATATTGAGTATTA
Found at i:28070759 original size:27 final size:27
Alignment explanation
Indices: 28070721--28070776 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
28070711 TTTAATCAAC
28070721 CAAACAAACACAAATTCAATCATTTAT
1 CAAACAAACACAAATTCAATCATTTAT
28070748 CAAACAAACACAAATTCAATCATTTAT
1 CAAACAAACACAAATTCAATCATTTAT
28070775 CA
1 CA
28070777 TTCATACTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.25
Consensus pattern (27 bp):
CAAACAAACACAAATTCAATCATTTAT
Found at i:28073286 original size:25 final size:25
Alignment explanation
Indices: 28073258--28073307 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
28073248 TAATTATTGG
28073258 TGATTGATGAAACCATATGCCCACA
1 TGATTGATGAAACCATATGCCCACA
28073283 TGATTGATGAAACCATATGCCCACA
1 TGATTGATGAAACCATATGCCCACA
28073308 CAAATGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (25 bp):
TGATTGATGAAACCATATGCCCACA
Found at i:28079454 original size:27 final size:27
Alignment explanation
Indices: 28079413--28080800 Score: 1434
Period size: 27 Copynumber: 51.3 Consensus size: 27
28079403 AATGGGCCTC
* *
28079413 TAAAATTATCGAAATACCCTCGATGGG
1 TAAAATTACCAAAATACCCTCGATGGG
*
28079440 TAAAATTACCAAAATACCCTCGATAGG
1 TAAAATTACCAAAATACCCTCGATGGG
*
28079467 TAAAATTACCGAAATACCCTCGATGGG
1 TAAAATTACCAAAATACCCTCGATGGG
28079494 TAAAATTACCAAAATACCC-CTGATGGG
1 TAAAATTACCAAAATACCCTC-GATGGG
*
28079521 TAAAATTACCGAAATACCC-CTGATGGG
1 TAAAATTACCAAAATACCCTC-GATGGG
* *
28079548 TAAAATTA-TAGAAATACCC-CTGATCGG
1 TAAAATTACCA-AAATACCCTC-GATGGG
*
28079575 TAAAATTACCAAAAGACCCTCGATGGG
1 TAAAATTACCAAAATACCCTCGATGGG
28079602 TAAAATTACCAAAATA-CCTCTGATGGG
1 TAAAATTACCAAAATACCCTC-GATGGG
** *
28079629 TAAAATTACTGAAATACCCTTGATGGG
1 TAAAATTACCAAAATACCCTCGATGGG
*
28079656 TAAAATTACCAAAATACCTTCGATGGG
1 TAAAATTACCAAAATACCCTCGATGGG
* * *
28079683 TAAAATTACTAAAATACCCCCAATGGG
1 TAAAATTACCAAAATACCCTCGATGGG
*
28079710 TCAAATTA-CAAAATACCCTCGATGGG
1 TAAAATTACCAAAATACCCTCGATGGG
* *
28079736 TAAAATTACCAAAATACCCCCGATGTG
1 TAAAATTACCAAAATACCCTCGATGGG
* * *
28079763 TAAAATTATCGAAATACCCTCGATAGG
1 TAAAATTACCAAAATACCCTCGATGGG
*
28079790 TAAAATTACCAAAATACCCTTGATGGG
1 TAAAATTACCAAAATACCCTCGATGGG
* * *
28079817 TAAAATTACTAAAATACCCTCAAAGGG
1 TAAAATTACCAAAATACCCTCGATGGG
* * *
28079844 TAAAATTATCGAAATACCC-CTGATAGG
1 TAAAATTACCAAAATACCCTC-GATGGG
** *
28079871 TAAAATTACTGAAATACCC-CTAATGGG
1 TAAAATTACCAAAATACCCTC-GATGGG
* * *
28079898 TACAATTATCAAAATACCC-CTAATGGG
1 TAAAATTACCAAAATACCCTC-GATGGG
**
28079925 TAAAATTACTGAAATACCCTCGATGGG
1 TAAAATTACCAAAATACCCTCGATGGG
*
28079952 TAAAATTATCAAAATACCCTCGATGGG
1 TAAAATTACCAAAATACCCTCGATGGG
* *
28079979 TAAAATTACCGAAATACCCTCGATTGG
1 TAAAATTACCAAAATACCCTCGATGGG
28080006 TAAAATTACCAAAATACCC-CTGATGGG
1 TAAAATTACCAAAATACCCTC-GATGGG
* *
28080033 TAAAATTACCGAAATGCCC-CTGATGGG
1 TAAAATTACCAAAATACCCTC-GATGGG
* *
28080060 TAAAATTA-CAGAAATACCCTTGATCGG
1 TAAAATTACCA-AAATACCCTCGATGGG
*** *
28080087 TAAAATTATTGAAAGACCCTCGATGGG
1 TAAAATTACCAAAATACCCTCGATGGG
28080114 TAAAATTACCAAAATA-CCTCTGATGGG
1 TAAAATTACCAAAATACCCTC-GATGGG
** *
28080141 TAAAATTACTGAAATACCCTTGATGGG
1 TAAAATTACCAAAATACCCTCGATGGG
* * * *
28080168 TAAAATTATCGAAATACCATTGATGGG
1 TAAAATTACCAAAATACCCTCGATGGG
* *
28080195 TAAAATTACTAAAATACCCCCGATGGG
1 TAAAATTACCAAAATACCCTCGATGGG
*
28080222 TCAAATTA-CAAAATACCCTCGATGGG
1 TAAAATTACCAAAATACCCTCGATGGG
28080248 TAAAATTACCAAAATACCC-CTGATGGG
1 TAAAATTACCAAAATACCCTC-GATGGG
* * *
28080275 TAAAATTATCGAAATACCCTCGATAGG
1 TAAAATTACCAAAATACCCTCGATGGG
*
28080302 TAAAATTACAAAAATACCCTCGATGGG
1 TAAAATTACCAAAATACCCTCGATGGG
* * * *
28080329 TAAACTTACTAAAATACCCTCAAAGGG
1 TAAAATTACCAAAATACCCTCGATGGG
* * *
28080356 TAAAATTATCGAAATACCC-CTGATAGG
1 TAAAATTACCAAAATACCCTC-GATGGG
* * *
28080383 TAAAATTACCGAAATACCCCCAATGGG
1 TAAAATTACCAAAATACCCTCGATGGG
* * *
28080410 TAAAATTATCGAAATACCC-CTAATGGG
1 TAAAATTACCAAAATACCCTC-GATGGG
** *
28080437 TAAAATTACTGAAATACCCTCGATGTG
1 TAAAATTACCAAAATACCCTCGATGGG
* *
28080464 TAAAATTATCGAAATACCCTCGATGGGTCGAGGG
1 TAAAATTACCAAAATACCCTCGA----T---GGG
*
28080498 TAAAATTACTAAAATA-CC-CGATGGG
1 TAAAATTACCAAAATACCCTCGATGGG
** *
28080523 TAAAATTACTGAAATACCCTCGATAGG
1 TAAAATTACCAAAATACCCTCGATGGG
* *
28080550 TAAAATTATCGAAATACCC-CTGATGGG
1 TAAAATTACCAAAATACCCTC-GATGGG
* * *
28080577 TAAAATTATCGAAATACCCTCGAAGGG
1 TAAAATTACCAAAATACCCTCGATGGG
** * *
28080604 TAAAATTACTGAAATACCTTTGATGGG
1 TAAAATTACCAAAATACCCTCGATGGG
** ** *
28080631 TAAAATTACTGAAATACCCTAAAAGGG
1 TAAAATTACCAAAATACCCTCGATGGG
* *
28080658 TAAAATTACCAAAATACCTTCAATGGG
1 TAAAATTACCAAAATACCCTCGATGGG
* * *
28080685 TAAAATTACTAAAATATCGTCGATGGG
1 TAAAATTACCAAAATACCCTCGATGGG
*
28080712 TAAAATTACAAAAATACCCTCGATGGG
1 TAAAATTACCAAAATACCCTCGATGGG
* * *
28080739 TAAAATTACGAAAATACCC-CTAAAGGG
1 TAAAATTACCAAAATACCCTC-GATGGG
*
28080766 T-AAATTGACCGAAATACCCTCGATGGG
1 TAAAATT-ACCAAAATACCCTCGATGGG
28080793 TAAAATTA
1 TAAAATTA
28080801 TTGAAATACC
Statistics
Matches: 1155, Mismatches: 169, Indels: 74
0.83 0.12 0.05
Matches are distributed among these distances:
25 18 0.02
26 69 0.06
27 1027 0.89
28 20 0.02
31 1 0.00
32 3 0.00
33 2 0.00
34 15 0.01
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (27 bp):
TAAAATTACCAAAATACCCTCGATGGG
Found at i:28081021 original size:26 final size:26
Alignment explanation
Indices: 28080992--28081068 Score: 102
Period size: 26 Copynumber: 3.0 Consensus size: 26
28080982 TTGCCACAAA
* *
28080992 TACTGTTATTGGTAGCTTTGATGCGT
1 TACTGTTATTGGAAGCTTTGCTGCGT
*
28081018 TACTGATATTGGAAGCTCTT-CTGCGT
1 TACTGTTATTGGAAGCT-TTGCTGCGT
*
28081044 TACTGTTATTGGCAGCTTTGCTGCG
1 TACTGTTATTGGAAGCTTTGCTGCG
28081069 ATATTGATGT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
25 2 0.05
26 40 0.91
27 2 0.05
ACGTcount: A:0.16, C:0.17, G:0.26, T:0.42
Consensus pattern (26 bp):
TACTGTTATTGGAAGCTTTGCTGCGT
Found at i:28082328 original size:35 final size:35
Alignment explanation
Indices: 28082289--28082413 Score: 142
Period size: 35 Copynumber: 3.5 Consensus size: 35
28082279 TAGTCTTTGT
*
28082289 TTGGTGTGTTTTGGTTGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCA
**
28082324 TTGGTGTGTTTCGGAAGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCA
* * * * * * *
28082359 CTGGTGTGTTTCAGTTGGATTGGATCTGATGAGAA
1 TTGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCA
*
28082394 TCTGGTGTGTTTTGGTTGGA
1 T-TGGTGTGTTTCGGTTGGA
28082414 TTGACGATGT
Statistics
Matches: 74, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
35 58 0.78
36 16 0.22
ACGTcount: A:0.16, C:0.10, G:0.34, T:0.40
Consensus pattern (35 bp):
TTGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCA
Found at i:28086233 original size:25 final size:25
Alignment explanation
Indices: 28086204--28086252 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
28086194 TATAAAATAT
*
28086204 TAATTCAAT-AAATTGAAAATTTAAA
1 TAATTAAATAAAATTG-AAATTTAAA
28086229 TAATTAAATAAAATTGAAATTTAA
1 TAATTAAATAAAATTGAAATTTAA
28086253 GAGAAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (25 bp):
TAATTAAATAAAATTGAAATTTAAA
Found at i:28086960 original size:29 final size:30
Alignment explanation
Indices: 28086902--28086960 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
28086892 TGCCTTTGAA
* *
28086902 AATATTTACAAAAAGAGACATCTAATTTTT
1 AATATTTACAAAAAGAGACAACTAAATTTT
*
28086932 AATATTTACAAAAAG-GGCAACTAAATTTT
1 AATATTTACAAAAAGAGACAACTAAATTTT
28086961 GAAAATAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.34
Consensus pattern (30 bp):
AATATTTACAAAAAGAGACAACTAAATTTT
Found at i:28093901 original size:22 final size:22
Alignment explanation
Indices: 28093868--28093919 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
28093858 TATTTAACCC
28093868 AAATT-AAATTAAATTAGATTA-
1 AAATTAAAATT-AATTAGATTAT
*
28093889 AAATTAAAATTAATTATATTAT
1 AAATTAAAATTAATTAGATTAT
28093911 AAATTAAAA
1 AAATTAAAA
28093920 CACATAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
AAATTAAAATTAATTAGATTAT
Found at i:28093904 original size:16 final size:15
Alignment explanation
Indices: 28093869--28093917 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
28093859 ATTTAACCCA
28093869 AATTAAATT-AAATT
1 AATTAAATTAAAATT
28093883 AGATTAAAATTAAAATT
1 A-ATT-AAATTAAAATT
*
28093900 AATTATATTATAAATT
1 AATTAAATTA-AAATT
28093916 AA
1 AA
28093918 AACACATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
14 1 0.03
15 8 0.27
16 15 0.50
17 6 0.20
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
AATTAAATTAAAATT
Found at i:28094068 original size:11 final size:11
Alignment explanation
Indices: 28094052--28094091 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
28094042 AAAAATGATC
*
28094052 AAAATTAATAA
1 AAAATTAATAT
*
28094063 AAAATTATTAT
1 AAAATTAATAT
28094074 AAAATTAA-AT
1 AAAATTAATAT
28094084 AAAATTAA
1 AAAATTAA
28094092 ACATATTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AAAATTAATAT
Found at i:28104128 original size:27 final size:27
Alignment explanation
Indices: 28104071--28104153 Score: 103
Period size: 27 Copynumber: 3.1 Consensus size: 27
28104061 ACACTCCAGA
* *
28104071 AAAAAGAAGTCTTTGTGGCTATATATG
1 AAAAAGAAGTCTTTGTGGCGATCTATG
* *
28104098 AAAAGGAAGTCTTTGTGGCGATCTATT
1 AAAAAGAAGTCTTTGTGGCGATCTATG
* * *
28104125 AAAAAGAAGCCTTCGTGGAGATCTATG
1 AAAAAGAAGTCTTTGTGGCGATCTATG
28104152 AA
1 AA
28104154 GGGAATGCCC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (27 bp):
AAAAAGAAGTCTTTGTGGCGATCTATG
Found at i:28107485 original size:18 final size:17
Alignment explanation
Indices: 28107448--28107494 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
28107438 ACTTAATCAT
28107448 TTTAATA-TTAAATTAA
1 TTTAATATTTAAATTAA
*
28107464 TTTAATATTTAGATTAAA
1 TTTAATATTTAAATT-AA
28107482 TTTAATA-TTAAAT
1 TTTAATATTTAAAT
28107495 CTATTAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 7 0.26
17 11 0.41
18 9 0.33
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
TTTAATATTTAAATTAA
Found at i:28107491 original size:12 final size:12
Alignment explanation
Indices: 28107448--28107494 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
28107438 ACTTAATCAT
28107448 TTTAATATTAAA
1 TTTAATATTAAA
28107460 -TTAAT-TTAATA
1 TTTAATATTAA-A
*
28107471 TTT-AGATTAAA
1 TTTAATATTAAA
28107482 TTTAATATTAAA
1 TTTAATATTAAA
28107494 T
1 T
28107495 CTATTAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
10 4 0.14
11 11 0.38
12 14 0.48
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (12 bp):
TTTAATATTAAA
Found at i:28107579 original size:20 final size:18
Alignment explanation
Indices: 28107529--28107580 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
28107519 CTACAAGATA
28107529 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
28107546 AATATTAAGA-TAATCAGTTT
1 AATATTAA-ATTAAT-A-TTT
28107566 AATATTAAATTAATA
1 AATATTAAATTAATA
28107581 AAATAGTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 3 0.10
20 15 0.50
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:28108922 original size:11 final size:12
Alignment explanation
Indices: 28108892--28108924 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
28108882 GTCACAAGTG
28108892 AATTAATTCACA
1 AATTAATTCACA
*
28108904 AATGAATTCA-A
1 AATTAATTCACA
28108915 AATTAATTCA
1 AATTAATTCA
28108925 TCTTGGGTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.52, C:0.12, G:0.03, T:0.33
Consensus pattern (12 bp):
AATTAATTCACA
Found at i:28110043 original size:28 final size:28
Alignment explanation
Indices: 28110012--28110067 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
28110002 CAGTAATAGT
28110012 ACAATGTGGGCCTTAGCCCAATACAGTA
1 ACAATGTGGGCCTTAGCCCAATACAGTA
28110040 ACAATGTGGGCCTTAGCCCAATACAGTA
1 ACAATGTGGGCCTTAGCCCAATACAGTA
28110068 TCGGTATAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.21
Consensus pattern (28 bp):
ACAATGTGGGCCTTAGCCCAATACAGTA
Found at i:28110464 original size:27 final size:27
Alignment explanation
Indices: 28110431--28110761 Score: 367
Period size: 27 Copynumber: 12.3 Consensus size: 27
28110421 GGGTATAACA
* * *
28110431 GTCATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTAATTCG
* *
28110458 GTTATTTTACCCTATGGGGGTAATTTG
1 GTCATTTTACCCTATGGGGGTAATTCG
* * *
28110485 GTCATTTTACCTTGTGGGGGGAATTCG
1 GTCATTTTACCCTATGGGGGTAATTCG
* **
28110512 ATCATTTTACCCTATGGGGGGTAATTTA
1 GTCATTTTACCCTAT-GGGGGTAATTCG
* * *
28110540 GTTAGTTTACCCTATGGGGGTAATTCA
1 GTCATTTTACCCTATGGGGGTAATTCG
* * *
28110567 ATCATGTTACCTTAT-GGGGTAATTCG
1 GTCATTTTACCCTATGGGGGTAATTCG
*
28110593 GTCATTTTACCCTGTGGGGGTAATTCG
1 GTCATTTTACCCTATGGGGGTAATTCG
* *
28110620 GTCATTTTACCCTATGAGGGTAATTGG
1 GTCATTTTACCCTATGGGGGTAATTCG
* * *
28110647 GTTATTTTACCCTGTAGGGGTAATTCG
1 GTCATTTTACCCTATGGGGGTAATTCG
* *
28110674 ATCATTTTACCCTATGGGGGTAATTTG
1 GTCATTTTACCCTATGGGGGTAATTCG
* *
28110701 GTCATTTTACCCTGTGGGAGTAATTCG
1 GTCATTTTACCCTATGGGGGTAATTCG
** * *
28110728 GTCATTTTACCCTGCGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTAATTCG
28110755 GTCATTT
1 GTCATTT
28110762 ATCGACCTCT
Statistics
Matches: 253, Mismatches: 49, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
26 21 0.08
27 211 0.83
28 21 0.08
ACGTcount: A:0.19, C:0.15, G:0.26, T:0.40
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTAATTCG
Found at i:28110489 original size:54 final size:54
Alignment explanation
Indices: 28110431--28110761 Score: 412
Period size: 54 Copynumber: 6.1 Consensus size: 54
28110421 GGGTATAACA
* * * * * *
28110431 GTCATTTTACCCTATGAGGGTATTTTGGTTATTTTACCCTATGGGGGTAATTTG
1 GTCATTTTACCCTGTGGGGGTAATTCGATCATTTTACCCTATGGGGGTAATTTG
* * *
28110485 GTCATTTTACCTTGTGGGGGGAATTCGATCATTTTACCCTATGGGGGGTAATTTA
1 GTCATTTTACCCTGTGGGGGTAATTCGATCATTTTACCCTAT-GGGGGTAATTTG
* * * * * * *
28110540 GTTAGTTTACCCTATGGGGGTAATTCAATCATGTTACCTTAT-GGGGTAATTCG
1 GTCATTTTACCCTGTGGGGGTAATTCGATCATTTTACCCTATGGGGGTAATTTG
* * *
28110593 GTCATTTTACCCTGTGGGGGTAATTCGGTCATTTTACCCTATGAGGGTAATTGG
1 GTCATTTTACCCTGTGGGGGTAATTCGATCATTTTACCCTATGGGGGTAATTTG
* *
28110647 GTTATTTTACCCTGTAGGGGTAATTCGATCATTTTACCCTATGGGGGTAATTTG
1 GTCATTTTACCCTGTGGGGGTAATTCGATCATTTTACCCTATGGGGGTAATTTG
* * ** *
28110701 GTCATTTTACCCTGTGGGAGTAATTCGGTCATTTTACCCTGCGGGGGTATTTTG
1 GTCATTTTACCCTGTGGGGGTAATTCGATCATTTTACCCTATGGGGGTAATTTG
28110755 GTCATTT
1 GTCATTT
28110762 ATCGACCTCT
Statistics
Matches: 235, Mismatches: 40, Indels: 4
0.84 0.14 0.01
Matches are distributed among these distances:
53 44 0.19
54 146 0.62
55 45 0.19
ACGTcount: A:0.19, C:0.15, G:0.26, T:0.40
Consensus pattern (54 bp):
GTCATTTTACCCTGTGGGGGTAATTCGATCATTTTACCCTATGGGGGTAATTTG
Found at i:28110748 original size:81 final size:81
Alignment explanation
Indices: 28110432--28110749 Score: 404
Period size: 81 Copynumber: 3.9 Consensus size: 81
28110422 GGTATAACAG
* * * * *
28110432 TCATTTTACCCTATGAGGGTATTTTGGTTATTTTACCCTATGGGGGTAATTTGGTCATTTTACCT
1 TCATTTTACCCTATGGGGGTAATTTGGTCATTTTACCCTATGGGGGTAATTCGGTCATTTTACCC
*
28110497 TGTGGGGGGAATTCGA
66 TGTGGGGGTAATTCGA
* * * ** *
28110513 TCATTTTACCCTATGGGGGGTAATTTAGTTAGTTTACCCTATGGGGGTAATTCAATCATGTTACC
1 TCATTTTACCCTAT-GGGGGTAATTTGGTCATTTTACCCTATGGGGGTAATTCGGTCATTTTACC
* * *
28110578 TTAT-GGGGTAATTCGG
65 CTGTGGGGGTAATTCGA
* * * * *
28110594 TCATTTTACCCTGTGGGGGTAATTCGGTCATTTTACCCTATGAGGGTAATTGGGTTATTTTACCC
1 TCATTTTACCCTATGGGGGTAATTTGGTCATTTTACCCTATGGGGGTAATTCGGTCATTTTACCC
*
28110659 TGTAGGGGTAATTCGA
66 TGTGGGGGTAATTCGA
* *
28110675 TCATTTTACCCTATGGGGGTAATTTGGTCATTTTACCCTGTGGGAGTAATTCGGTCATTTTACCC
1 TCATTTTACCCTATGGGGGTAATTTGGTCATTTTACCCTATGGGGGTAATTCGGTCATTTTACCC
*
28110740 TGCGGGGGTA
66 TGTGGGGGTA
28110750 TTTTGGTCAT
Statistics
Matches: 201, Mismatches: 34, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
80 42 0.21
81 114 0.57
82 45 0.22
ACGTcount: A:0.19, C:0.16, G:0.26, T:0.39
Consensus pattern (81 bp):
TCATTTTACCCTATGGGGGTAATTTGGTCATTTTACCCTATGGGGGTAATTCGGTCATTTTACCC
TGTGGGGGTAATTCGA
Found at i:28110997 original size:19 final size:19
Alignment explanation
Indices: 28110973--28111021 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
28110963 GTGTAGGGCC
*
28110973 CACGAGCCCATTGAGCCCA
1 CACGAGCCCATTGAACCCA
28110992 CACGAGCCCATTGAACCCA
1 CACGAGCCCATTGAACCCA
28111011 CACGA-CCCATT
1 CACGAGCCCATT
28111022 TCGGCCCAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 6 0.21
19 23 0.79
ACGTcount: A:0.29, C:0.43, G:0.16, T:0.12
Consensus pattern (19 bp):
CACGAGCCCATTGAACCCA
Found at i:28114007 original size:60 final size:59
Alignment explanation
Indices: 28113933--28114062 Score: 161
Period size: 60 Copynumber: 2.2 Consensus size: 59
28113923 TTGATCGTAA
* ** * *
28113933 TATAAAAAGTTCAATAAATTTAGCTCTCAATGTTTACAAAATTTGTCATTTTACTTCAAAT
1 TATAAAAA--TCAATAAATTTAGCTATCAACATTTACAAAATGTATCATTTTACTTCAAAT
* * *
28113994 TCTTAAAAATCAATAAATTTAGCTATCAACATTTACAAAATGTATCATTTTAGTTCTAAT
1 T-ATAAAAATCAATAAATTTAGCTATCAACATTTACAAAATGTATCATTTTACTTCAAAT
28114054 TATAAAAAT
1 TATAAAAAT
28114063 TTCAAAAAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
59 7 0.12
60 45 0.76
61 1 0.02
62 6 0.10
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.40
Consensus pattern (59 bp):
TATAAAAATCAATAAATTTAGCTATCAACATTTACAAAATGTATCATTTTACTTCAAAT
Found at i:28114775 original size:61 final size:61
Alignment explanation
Indices: 28114671--28114797 Score: 157
Period size: 61 Copynumber: 2.1 Consensus size: 61
28114661 CTTTTTTTAA
* *
28114671 TTTTTAGAATTAGAACTAAATTGATAAATTTTGCAAACGTTGAGAGCTAAATTTATAGAAC
1 TTTTTAGAATTAGAACTAAATTGACAAATTTTGCAAACATTGAGAGCTAAATTTATAGAAC
** * * * * *
28114732 TTTTTAGAATTCTAACTAAAATT-ACAAATTTTGTAAACATTGAGGGCTAAGTTTATTGAAT
1 TTTTTAGAATTAGAACT-AAATTGACAAATTTTGCAAACATTGAGAGCTAAATTTATAGAAC
28114793 TTTTT
1 TTTTT
28114798 TATATTTAGG
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
61 51 0.91
62 5 0.09
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (61 bp):
TTTTTAGAATTAGAACTAAATTGACAAATTTTGCAAACATTGAGAGCTAAATTTATAGAAC
Found at i:28117757 original size:18 final size:19
Alignment explanation
Indices: 28117736--28117778 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
28117726 ATTAAATGTA
*
28117736 AAAATGTAATTTTTAA-AT
1 AAAATGTAATTTTAAAGAT
*
28117754 AAAA-GTTATTTTAAAGAT
1 AAAATGTAATTTTAAAGAT
28117772 AAAATGT
1 AAAATGT
28117779 GAAATTGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 9 0.43
18 10 0.48
19 2 0.10
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (19 bp):
AAAATGTAATTTTAAAGAT
Found at i:28118045 original size:19 final size:21
Alignment explanation
Indices: 28118010--28118057 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
28118000 ATGGGGGTAA
*
28118010 AGGGTGAGAAGTAAAA-GTTT
1 AGGGGGAGAAGTAAAAGGTTT
28118030 AGGGGGAGAA-TAAAAGGTTT
1 AGGGGGAGAAGTAAAAGGTTT
*
28118050 TGGGGGAG
1 AGGGGGAG
28118058 TAAAATTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.35, C:0.00, G:0.44, T:0.21
Consensus pattern (21 bp):
AGGGGGAGAAGTAAAAGGTTT
Found at i:28118342 original size:18 final size:18
Alignment explanation
Indices: 28118319--28118353 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28118309 AATCAAGTTG
*
28118319 ACTCGAATAACTCGATTA
1 ACTCGAACAACTCGATTA
28118337 ACTCGAACAACTCGATT
1 ACTCGAACAACTCGATT
28118354 CGTTTAACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.26
Consensus pattern (18 bp):
ACTCGAACAACTCGATTA
Found at i:28119359 original size:21 final size:21
Alignment explanation
Indices: 28119330--28119372 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
28119320 TCGAAAGTTG
*
28119330 AACAAAAGCTTGTAAGAGCTT
1 AACAAAAGCTCGTAAGAGCTT
*
28119351 AACAGAAGCTCGTAAGAGCTT
1 AACAAAAGCTCGTAAGAGCTT
28119372 A
1 A
28119373 TCCACCGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (21 bp):
AACAAAAGCTCGTAAGAGCTT
Found at i:28123134 original size:27 final size:26
Alignment explanation
Indices: 28123096--28123167 Score: 119
Period size: 27 Copynumber: 2.7 Consensus size: 26
28123086 AAAAATAAAA
28123096 ATTTACCAAAATATTATAACTTTTTTT
1 ATTTACCAAAATATTATAA-TTTTTTT
28123123 ATTTACCAAAATATATATAATTTTTTT
1 ATTTACCAAAATAT-TATAATTTTTTT
28123150 ATTTACCAAAATA-TATAA
1 ATTTACCAAAATATTATAA
28123168 AAAAACAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
25 5 0.11
27 34 0.77
28 5 0.11
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (26 bp):
ATTTACCAAAATATTATAATTTTTTT
Found at i:28123265 original size:27 final size:27
Alignment explanation
Indices: 28123235--28123311 Score: 136
Period size: 27 Copynumber: 2.9 Consensus size: 27
28123225 ACGCCAATTG
*
28123235 CATTGGCGGCACCAAAGGTGCCAAAAC
1 CATTGGCGGCACCAATGGTGCCAAAAC
*
28123262 CATTGGCGGCACCAATGGTGCCAATAC
1 CATTGGCGGCACCAATGGTGCCAAAAC
28123289 CATTGGCGGCACCAATGGTGCCA
1 CATTGGCGGCACCAATGGTGCCA
28123312 TATTGTTTGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (27 bp):
CATTGGCGGCACCAATGGTGCCAAAAC
Found at i:28123501 original size:19 final size:21
Alignment explanation
Indices: 28123463--28123501 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
28123453 ATTTTTTGCT
*
28123463 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
28123484 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
28123502 TTGTTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:28123577 original size:3 final size:3
Alignment explanation
Indices: 28123571--28123611 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
28123561 ATTATTATTA
28123571 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
28123612 AGTATTAAGA
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:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:28130213 original size:4 final size:4
Alignment explanation
Indices: 28130197--28130322 Score: 77
Period size: 4 Copynumber: 31.0 Consensus size: 4
28130187 CTCATTTCCT
*
28130197 TTTC TTTC CTTC TTTC TTTC TTT- TTTC TTCTC TTTTCC TTT- TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-TC -TTT-C TTTC T-TTC
* * *
28130243 -TTC -TTC TTTC TTTC TTTT TTTC TCTTC -TCC TTTCC TTTTC TTTC CTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTT-C -TTTC TTTC TTTC
*
28130291 -TT- TTTC TTTC TTTCC TCTC ATTTC TTTC TTTC
1 TTTC TTTC TTTC TTT-C TTTC -TTTC TTTC TTTC
28130323 CCTCTCCTTC
Statistics
Matches: 98, Mismatches: 9, Indels: 30
0.72 0.07 0.22
Matches are distributed among these distances:
3 16 0.16
4 59 0.60
5 17 0.17
6 6 0.06
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (4 bp):
TTTC
Found at i:28130254 original size:44 final size:44
Alignment explanation
Indices: 28130171--28130304 Score: 159
Period size: 44 Copynumber: 3.1 Consensus size: 44
28130161 NNNNNNNNNC
* * * *
28130171 TTCTTTTTT-TTCTCTTCTCATTTCCTT-TTCTTTCCTTCTTTCT
1 TTCTTTTTTCTTCTCTTTTCCTTTTCTTCTTC-TTCTTTCTTTCT
28130214 TTCTTTTTTCTTCTCTTTTCCTTTTCTTCTTCTTCTTTCTTTCT
1 TTCTTTTTTCTTCTCTTTTCCTTTTCTTCTTCTTCTTTCTTTCT
* *
28130258 TT-TTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTT-TTTCTTTCT
1 TTCTTTTTTCTTCTCTTTTCCTTTTC-TT-CTTCTTCTTTCTTTCT
28130302 TTC
1 TTC
28130305 CTCTCATTTC
Statistics
Matches: 80, Mismatches: 6, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
43 30 0.38
44 41 0.51
45 9 0.11
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (44 bp):
TTCTTTTTTCTTCTCTTTTCCTTTTCTTCTTCTTCTTTCTTTCT
Found at i:28130255 original size:18 final size:18
Alignment explanation
Indices: 28130170--28130321 Score: 74
Period size: 18 Copynumber: 8.6 Consensus size: 18
28130160 NNNNNNNNNN
*
28130170 CTTCTTTTTTTTC-TCTT
1 CTTCTTTCTTTTCTTCTT
28130187 C-TCATTTCCTTTTCTTTCCTT
1 CTTC-TTT-CTTTTC-TT-CTT
28130208 CTTTCTTTCTTTT-TTCTT
1 C-TTCTTTCTTTTCTTCTT
28130226 C-TCTTTTCCTTTTCTTCTT
1 CTTC-TTT-CTTTTCTTCTT
28130245 CTTCTTTC-TTTCTT-TT
1 CTTCTTTCTTTTCTTCTT
* * *
28130261 -TT-TCTCTTCTCCT-TT
1 CTTCTTTCTTTTCTTCTT
* *
28130276 CCT-TTTCTTTCCTTCTT
1 CTTCTTTCTTTTCTTCTT
* * *
28130293 TTTCTTTCTTTCCTCTCAT
1 CTTCTTTCTTTTCT-TCTT
28130312 -TTCTTTCTTT
1 CTTCTTTCTTT
28130322 CCCTCTCCTT
Statistics
Matches: 107, Mismatches: 12, Indels: 31
0.71 0.08 0.21
Matches are distributed among these distances:
14 3 0.03
15 8 0.07
16 14 0.13
17 16 0.15
18 35 0.33
19 14 0.13
20 3 0.03
21 9 0.08
22 3 0.03
23 2 0.02
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (18 bp):
CTTCTTTCTTTTCTTCTT
Found at i:28130291 original size:48 final size:45
Alignment explanation
Indices: 28130171--28130304 Score: 151
Period size: 39 Copynumber: 3.2 Consensus size: 45
28130161 NNNNNNNNNC
* *
28130171 TTCTTTTTTTTCTCTTCTCATTTCCTTTT-C-T-TTC--C-TTCT
1 TTCTTTCTTTTCTCTTCTCCTTTCCTTTTCCTTCTTCTTCTTTCT
* *
28130210 TTCTTTCTTTTTTCTTCTCTTTTCCTTTT-CTTCTTCTTCTTTCT
1 TTCTTTCTTTTCTCTTCTCCTTTCCTTTTCCTTCTTCTTCTTTCT
*
28130254 TTCTTT-TTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTT-TTTCT
1 TTCTTTCTTTTCTCTTCTCCTTTCCTTTTCCTT-CTTCTTCTTTCT
28130298 TTCTTTC
1 TTCTTTC
28130305 CTCTCATTTC
Statistics
Matches: 81, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
39 27 0.33
40 1 0.01
41 3 0.04
43 21 0.26
44 23 0.28
45 6 0.07
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (45 bp):
TTCTTTCTTTTCTCTTCTCCTTTCCTTTTCCTTCTTCTTCTTTCT
Found at i:28130333 original size:18 final size:18
Alignment explanation
Indices: 28130251--28130333 Score: 69
Period size: 18 Copynumber: 4.4 Consensus size: 18
28130241 TCTTCTTCTT
* *
28130251 TCTTTCTTTTTTTCTCTTC
1 TCTTTCTTTCTTTC-CCTC
*
28130270 TCCTTTCCTTTTCTTTCCTTC
1 T-CTTT-C-TTTCTTTCCCTC
*
28130291 TTTTTCTTTCTTT-CCTC
1 TCTTTCTTTCTTTCCCTC
28130308 TCATTTCTTTCTTTCCCTC
1 TC-TTTCTTTCTTTCCCTC
*
28130327 TCCTTCT
1 TCTTTCT
28130334 GCCCCCCCAC
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
17 4 0.07
18 22 0.41
19 8 0.15
20 7 0.13
21 6 0.11
22 7 0.13
ACGTcount: A:0.01, C:0.34, G:0.00, T:0.65
Consensus pattern (18 bp):
TCTTTCTTTCTTTCCCTC
Found at i:28130440 original size:27 final size:27
Alignment explanation
Indices: 28130366--28130432 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
28130356 TATTATTAAG
28130366 TGGTGCCGCCAATGGTATTGGCACCAT
1 TGGTGCCGCCAATGGTATTGGCACCAT
* * *
28130393 TGGTGCAGCCAATGGTTTTGGCACCTT
1 TGGTGCCGCCAATGGTATTGGCACCAT
28130420 TGGTGCCGCCAAT
1 TGGTGCCGCCAAT
28130433 CCCATTGGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.16, C:0.25, G:0.30, T:0.28
Consensus pattern (27 bp):
TGGTGCCGCCAATGGTATTGGCACCAT
Found at i:28130540 original size:27 final size:28
Alignment explanation
Indices: 28130510--28130579 Score: 126
Period size: 27 Copynumber: 2.6 Consensus size: 28
28130500 TGTTTTTTTG
28130510 ATATATTTTGGTAAATAAAAAAA-TTAT
1 ATATATTTTGGTAAATAAAAAAAGTTAT
28130537 ATATATTTTGGTAAATAAAAAAAGTTAT
1 ATATATTTTGGTAAATAAAAAAAGTTAT
28130565 A-ATATTTTGGTAAAT
1 ATATATTTTGGTAAAT
28130580 TTTTATTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 37 0.88
28 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (28 bp):
ATATATTTTGGTAAATAAAAAAAGTTAT
Found at i:28135110 original size:73 final size:73
Alignment explanation
Indices: 28134986--28135138 Score: 261
Period size: 73 Copynumber: 2.1 Consensus size: 73
28134976 ATCACATTTT
*
28134986 AATGAATGAAATACATGCATGAGTTTAATTGAAAGCATGAACGATGAAGGTATAGACATCATAAA
1 AATG-ATGAAATACATGCATGAGTTGAATTGAAAGCATGAACGATGAAGGTATAGACATCATAAA
28135051 CATGAATCA
65 CATGAATCA
* *
28135060 AATGATGAAATACGTGCATGAGTTGAATTGAAAGCATGAACGATTAAGGTATAGACATCATAAAC
1 AATGATGAAATACATGCATGAGTTGAATTGAAAGCATGAACGATGAAGGTATAGACATCATAAAC
28135125 ATGAATCA
66 ATGAATCA
*
28135133 GATGAT
1 AATGAT
28135139 CTTTGTCAAA
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
73 71 0.95
74 4 0.05
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.25
Consensus pattern (73 bp):
AATGATGAAATACATGCATGAGTTGAATTGAAAGCATGAACGATGAAGGTATAGACATCATAAAC
ATGAATCA
Found at i:28135469 original size:18 final size:16
Alignment explanation
Indices: 28135430--28135461 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
28135420 AGGAAATAAC
28135430 AAGTGAAGAATGAA-G
1 AAGTGAAGAATGAATG
28135445 AAG-GAAGAATGAATG
1 AAGTGAAGAATGAATG
28135460 AA
1 AA
28135462 TGATGAAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.31, T:0.12
Consensus pattern (16 bp):
AAGTGAAGAATGAATG
Found at i:28141515 original size:32 final size:33
Alignment explanation
Indices: 28141453--28141518 Score: 82
Period size: 32 Copynumber: 2.0 Consensus size: 33
28141443 AGCTCAATGG
* *
28141453 TCTTGTGGTGTGAAAACTAGAATAGAAATAGCC
1 TCTTGTGGTGTGAAAACCAGAACAGAAATAGCC
*
28141486 TCTTGT-GTGTGAACAACCAGAACCG-AATAGCC
1 TCTTGTGGTGTGAA-AACCAGAACAGAAATAGCC
28141518 T
1 T
28141519 TAGCATGTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (33 bp):
TCTTGTGGTGTGAAAACCAGAACAGAAATAGCC
Found at i:28142002 original size:15 final size:15
Alignment explanation
Indices: 28141979--28142008 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28141969 CCAGATTTTA
28141979 TTAAATTAATTAATT
1 TTAAATTAATTAATT
*
28141994 TTAAGTTAATTAATT
1 TTAAATTAATTAATT
28142009 AATTTAACTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
TTAAATTAATTAATT
Found at i:28148072 original size:10 final size:11
Alignment explanation
Indices: 28148051--28148084 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
28148041 AGCTAGCAAT
28148051 TGAGCTTTAAA
1 TGAGCTTTAAA
28148062 TGAGC-TTAAA
1 TGAGCTTTAAA
28148072 TGAGCTTTAAA
1 TGAGCTTTAAA
28148083 TG
1 TG
28148085 TGCTGCTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (11 bp):
TGAGCTTTAAA
Found at i:28154118 original size:84 final size:84
Alignment explanation
Indices: 28154010--28154297 Score: 421
Period size: 84 Copynumber: 3.5 Consensus size: 84
28154000 CAAAGGATCC
*
28154010 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATAAGGGGAATCAGCACATAGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
*
28154075 CCTTTCGCAATCAAGGATA
66 CCTTTCACAATCAAGGATA
* * * * *
28154094 TGGTGGAATCAACACTTAGTAACCACCTTATAATCAATCATACGGGGAATCAGCACATAACAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
28154159 CCTTTCACAATCAAGGATA
66 CCTTTCACAATCAAGGATA
* * *
28154178 CGAT-G-A--A--A-TCA-CAACCACCTTATAATCAATGATACGGGGAATCAGCACATGGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
28154235 CCTTTCACAATCAAGGATA
66 CCTTTCACAATCAAGGATA
*
28154254 CGGTGGAATCAGCACTTACCAACCACCTTATAATCAATGATACG
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACG
28154298 AGTTCACATA
Statistics
Matches: 180, Mismatches: 16, Indels: 16
0.85 0.08 0.08
Matches are distributed among these distances:
76 64 0.36
77 3 0.02
78 2 0.01
80 2 0.01
82 2 0.01
83 3 0.02
84 104 0.58
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (84 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
CCTTTCACAATCAAGGATA
Found at i:28154240 original size:76 final size:76
Alignment explanation
Indices: 28154114--28154264 Score: 257
Period size: 76 Copynumber: 2.0 Consensus size: 76
28154104 AACACTTAGT
28154114 AACCACCTTATAATCAATCATACGGGGAATCAGCACATAACAACCCCTTTCACAATCAAGGATAC
1 AACCACCTTATAATCAATCATACGGGGAATCAGCACATAACAACCCCTTTCACAATCAAGGATAC
28154179 GATGAAATCAC
66 GATGAAATCAC
* **
28154190 AACCACCTTATAATCAATGATACGGGGAATCAGCACATGGCAACCCCTTTCACAATCAAGGATAC
1 AACCACCTTATAATCAATCATACGGGGAATCAGCACATAACAACCCCTTTCACAATCAAGGATAC
* *
28154255 GGTGGAATCA
66 GATGAAATCA
28154265 GCACTTACCA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
76 70 1.00
ACGTcount: A:0.38, C:0.26, G:0.15, T:0.20
Consensus pattern (76 bp):
AACCACCTTATAATCAATCATACGGGGAATCAGCACATAACAACCCCTTTCACAATCAAGGATAC
GATGAAATCAC
Found at i:28154277 original size:43 final size:43
Alignment explanation
Indices: 28154189--28154282 Score: 113
Period size: 43 Copynumber: 2.2 Consensus size: 43
28154179 GATGAAATCA
* * **
28154189 CAACCACC-TT-ATAATCAATGATACGGGGAATCAGCACATGG
1 CAACCACCTTTCACAATCAAGGATACGGGGAATCAGCACATAC
*
28154230 CAACC-CCTTTCACAATCAAGGATACGGTGGAATCAGCACTTAC
1 CAACCACCTTTCACAATCAAGGATACGG-GGAATCAGCACATAC
28154273 CAACCACCTT
1 CAACCACCTT
28154283 ATAATCAATG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
40 2 0.05
41 7 0.16
42 14 0.32
43 17 0.39
44 4 0.09
ACGTcount: A:0.34, C:0.30, G:0.16, T:0.20
Consensus pattern (43 bp):
CAACCACCTTTCACAATCAAGGATACGGGGAATCAGCACATAC
Found at i:28154289 original size:42 final size:41
Alignment explanation
Indices: 28154014--28154297 Score: 214
Period size: 42 Copynumber: 7.0 Consensus size: 41
28154004 GGATCCCGGT
* * *
28154014 GGAATCAGCACTTAGCAACCACCTTATAATCAATGATAAGG
1 GGAATCAGCACATACCAACCACCTTATAATCAATGATACGG
* * *
28154055 GGAATCAGCACATAGCAACC-CCTT-TCGCAATCAAGGATATGG
1 GGAATCAGCACATACCAACCACCTTAT---AATCAATGATACGG
* * ** *
28154097 TGGAATCAACACTTAGTAACCACCTTATAATCAATCATACGG
1 -GGAATCAGCACATACCAACCACCTTATAATCAATGATACGG
* * *
28154139 GGAATCAGCACATAACAACC-CCTTTCACAATCAAGGATAC--
1 GGAATCAGCACATACCAACCACC-TT-ATAATCAATGATACGG
*
28154179 -G-AT--G-AAAT-CACAACCACCTTATAATCAATGATACGG
1 GGAATCAGCACATAC-CAACCACCTTATAATCAATGATACGG
** * *
28154215 GGAATCAGCACATGGCAACC-CCTTTCACAATCAAGGATACGG
1 GGAATCAGCACATACCAACCACC-TT-ATAATCAATGATACGG
*
28154257 TGGAATCAGCACTTACCAACCACCTTATAATCAATGATACG
1 -GGAATCAGCACATACCAACCACCTTATAATCAATGATACG
28154298 AGTTCACATA
Statistics
Matches: 192, Mismatches: 29, Indels: 43
0.73 0.11 0.16
Matches are distributed among these distances:
34 12 0.06
35 10 0.05
36 3 0.02
37 1 0.01
38 4 0.02
39 2 0.01
40 9 0.05
41 47 0.24
42 61 0.32
43 36 0.19
44 6 0.03
45 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (41 bp):
GGAATCAGCACATACCAACCACCTTATAATCAATGATACGG
Found at i:28154382 original size:51 final size:52
Alignment explanation
Indices: 28154302--28154494 Score: 223
Period size: 51 Copynumber: 3.8 Consensus size: 52
28154292 GATACGAGTT
* * *
28154302 CACATAGTAGCCTACACATAGTACTACACATGTGACCATCA-CTATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCAGCTATCCGGTA
* * * *
28154353 CACGTAGTAGCCTGCAAATAGTACTACACACGTGATCA-AAGCTATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCAGCTATCCGGTA
* * * * * * *
28154404 CGCATAGTAGCCTGCACATAATACTACACATGCGACC-T-ATCTTTCTGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCAGCTATCCGGTA
*
28154454 CACATAGTAGGCTGCACATAGTACTACACACGTGACCATCA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCA
28154495 ATTTCACTTT
Statistics
Matches: 116, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
50 42 0.36
51 73 0.63
52 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (52 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCAGCTATCCGGTA
Found at i:28154477 original size:101 final size:101
Alignment explanation
Indices: 28154304--28154488 Score: 264
Period size: 101 Copynumber: 1.8 Consensus size: 101
28154294 TACGAGTTCA
* * *
28154304 CATAGTAGCCTACACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTACACATAATACTACACATGCGACCAT-ACTATCCGATACACATAGTAGCCTGCA
28154369 AATAGTACTACACACGTGATCAAAGCTATCCGGTACG
65 AATAGTACTACACACGTGATCAAAGCTATCCGGTACG
* * * * *
28154406 CATAGTAGCCTGCACATAATACTACACATGCGACC-TATCTTTCTGGTACACATAGTAGGCTGCA
1 CATAGTAGCCTACACATAATACTACACATGCGACCATA-CTATCCGATACACATAGTAGCCTGCA
*
28154470 CATAGTACTACACACGTGA
65 AATAGTACTACACACGTGA
28154489 CCATCAATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
100 1 0.01
101 40 0.55
102 32 0.44
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (101 bp):
CATAGTAGCCTACACATAATACTACACATGCGACCATACTATCCGATACACATAGTAGCCTGCAA
ATAGTACTACACACGTGATCAAAGCTATCCGGTACG
Found at i:28159948 original size:42 final size:42
Alignment explanation
Indices: 28159868--28160138 Score: 211
Period size: 42 Copynumber: 6.5 Consensus size: 42
28159858 GGATCCCGGT
* *
28159868 GGAATCAGCACTTAGCAACCACC-TT-ATAATCAATGATACGA
1 GGAATCAGCACATAGCAA-CACCTTTCACAATCAATGATACGA
* * *
28159909 GGAATGAACACATAGCAACACCTTTCACAATCAATGATACGGT
1 GGAATCAGCACATAGCAACACCTTTCACAATCAATGATAC-GA
* * * *
28159952 GGAATCAGCACTTAACAACCACC-TT-ATAATCAATGATA-TA
1 GGAATCAGCACATAGCAA-CACCTTTCACAATCAATGATACGA
* *
28159992 GGGAATCAGCACATAGCAACCCCTTTCACAATCAAGGATACG-
1 -GGAATCAGCACATAGCAACACCTTTCACAATCAATGATACGA
* * *
28160034 GTAGAATCAGCACTTAGCAACCACC-TT-ATAATCAATGATA-TA
1 G--GAATCAGCACATAGCAA-CACCTTTCACAATCAATGATACGA
* * *
28160076 GGGAATCAGCACATAGCAAC-CCATTTCACAATCAAGGATATGGT
1 -GGAATCAGCACATAGCAACACC-TTTCACAATCAATGATA-CGA
* *
28160120 GGAATCAACACTTAGCAAC
1 GGAATCAGCACATAGCAAC
28160139 CATCTTATAA
Statistics
Matches: 182, Mismatches: 30, Indels: 34
0.74 0.12 0.14
Matches are distributed among these distances:
39 2 0.01
40 8 0.04
41 54 0.30
42 58 0.32
43 53 0.29
44 7 0.04
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.21
Consensus pattern (42 bp):
GGAATCAGCACATAGCAACACCTTTCACAATCAATGATACGA
Found at i:28159984 original size:84 final size:83
Alignment explanation
Indices: 28159864--28160157 Score: 446
Period size: 84 Copynumber: 3.5 Consensus size: 83
28159854 CAAAGGATCC
* *
28159864 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGA-GGAATGAACACATAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATA-GAGGGAATCAGCACATAGCAAC
*
28159928 ACCTTTCACAATCAATGATA
65 -CCTTTCACAATCAAGGATA
* *
28159948 CGGTGGAATCAGCACTTAACAACCACCTTATAATCAATGATATAGGGAATCAGCACATAGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATAGAGGGAATCAGCACATAGCAA-C
28160013 CCTTTCACAATCAAGGATA
65 CCTTTCACAATCAAGGATA
* *
28160032 CGGTAGAATCAGCACTTAGCAACCACCTTATAATCAATGATATAGGGAATCAGCACATAGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATAGAGGGAATCAGCACATAGCAACC
28160097 CATTTCACAATCAAGGATA
66 C-TTTCACAATCAAGGATA
* * * *
28160116 TGGTGGAATCAACACTTAGCAACCATCTTATAATTAATGATA
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATA
28160158 CGGGTTCACA
Statistics
Matches: 195, Mismatches: 12, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
83 4 0.02
84 190 0.97
85 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.23
Consensus pattern (83 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATAGAGGGAATCAGCACATAGCAACC
CTTTCACAATCAAGGATA
Found at i:28160224 original size:51 final size:51
Alignment explanation
Indices: 28160164--28160340 Score: 171
Period size: 51 Copynumber: 3.5 Consensus size: 51
28160154 GATACGGGTT
* * *
28160164 CACATAGTACTACACATGTGACCATCA-CTATCCGATACACGTAGTAGCCTG
1 CACATAGTACTACACACGTGACCAT-AGCTATCCGGTACACATAGTAGCCTG
* * * *
28160215 TACATAGTACTACACACGTGATCGA-AGCTATCCGGTACGCATAATAGCCTG
1 CACATAGTACTACACACGTGA-CCATAGCTATCCGGTACACATAGTAGCCTG
* * * * * ** *
28160266 CACATAATACTACACATGCGACC-TATCTTTTTGGTTCACATAGTAGCCTG
1 CACATAGTACTACACACGTGACCATAGCTATCCGGTACACATAGTAGCCTG
*
28160316 CATATAGTACTACACACGTGACCAT
1 CACATAGTACTACACACGTGACCAT
28160341 CACTTTCACT
Statistics
Matches: 99, Mismatches: 23, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
50 40 0.40
51 57 0.58
52 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (51 bp):
CACATAGTACTACACACGTGACCATAGCTATCCGGTACACATAGTAGCCTG
Found at i:28175931 original size:35 final size:34
Alignment explanation
Indices: 28175864--28176015 Score: 144
Period size: 35 Copynumber: 4.3 Consensus size: 34
28175854 ACTTTTTGTT
* * *
28175864 TTGGTGTGTTTCGATTGGACTAGCT-TTCATGAGCA
1 TTGGTGTATTTCGA-GGGATTAGCTCTT-ATGAGCA
*
28175899 TTGTTGTATTTCAGAGGGATTAGCTCTTATGAGCA
1 TTGGTGTATTTC-GAGGGATTAGCTCTTATGAGCA
* * *
28175934 TTGATGTGTTTCGAAGGGATTAGTTCTTATGAGCA
1 TTGGTGTATTTCG-AGGGATTAGCTCTTATGAGCA
* * * *
28175969 TTGGTGTATTTTGGATGGATTGGCTCTTGTGAGCA
1 TTGGTGTA-TTTCGAGGGATTAGCTCTTATGAGCA
28176004 TCTGGTGTATTT
1 T-TGGTGTATTT
28176016 TGGTTGGATT
Statistics
Matches: 98, Mismatches: 14, Indels: 10
0.80 0.11 0.08
Matches are distributed among these distances:
34 1 0.01
35 82 0.84
36 15 0.15
ACGTcount: A:0.18, C:0.11, G:0.29, T:0.42
Consensus pattern (34 bp):
TTGGTGTATTTCGAGGGATTAGCTCTTATGAGCA
Found at i:28186055 original size:11 final size:11
Alignment explanation
Indices: 28186039--28186067 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
28186029 TCCAAAATCA
28186039 ATACTTGTACC
1 ATACTTGTACC
28186050 ATACTTGTACC
1 ATACTTGTACC
28186061 ATACTTG
1 ATACTTG
28186068 CTCAAGGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.38
Consensus pattern (11 bp):
ATACTTGTACC
Found at i:28188563 original size:28 final size:28
Alignment explanation
Indices: 28188531--28188587 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
28188521 TCAAAAGGAG
*
28188531 TATAGCTAGGTTTTGGTCAAGCCATTTT
1 TATAGCTAGGTTTCGGTCAAGCCATTTT
28188559 TATAGCTAGGTTTCGGTCAAGCCATTTT
1 TATAGCTAGGTTTCGGTCAAGCCATTTT
28188587 T
1 T
28188588 GCTTGCATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (28 bp):
TATAGCTAGGTTTCGGTCAAGCCATTTT
Found at i:28189205 original size:17 final size:17
Alignment explanation
Indices: 28189183--28189218 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
28189173 TAACGTTTTA
*
28189183 ATGTTATTTTGATATTT
1 ATGTTATTGTGATATTT
*
28189200 ATGTTATTGTGCTATTT
1 ATGTTATTGTGATATTT
28189217 AT
1 AT
28189219 CATGTAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.22, C:0.03, G:0.14, T:0.61
Consensus pattern (17 bp):
ATGTTATTGTGATATTT
Found at i:28191284 original size:12 final size:11
Alignment explanation
Indices: 28191248--28191289 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
28191238 GTTTTTGGAT
*
28191248 AAATGATAAGA
1 AAATAATAAGA
28191259 AAATAATAAGA
1 AAATAATAAGA
*
28191270 AAATAAATAACA
1 AAAT-AATAAGA
28191282 AAA-AATAA
1 AAATAATAA
28191290 ACAAAAAGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 5 0.18
11 14 0.50
12 9 0.32
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.17
Consensus pattern (11 bp):
AAATAATAAGA
Found at i:28193384 original size:35 final size:35
Alignment explanation
Indices: 28193338--28193405 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
28193328 GAGACTACGT
*
28193338 ACTTGTAACATCCCGATTTTAGGCCTAGTCGGAAC
1 ACTTGTAACATCCCGATTTTAGGCCTAATCGGAAC
*
28193373 ACTTGTAACATCCCGATTTTGGGCCTAATCGGA
1 ACTTGTAACATCCCGATTTTAGGCCTAATCGGA
28193406 GCAGTGGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (35 bp):
ACTTGTAACATCCCGATTTTAGGCCTAATCGGAAC
Found at i:28194711 original size:50 final size:50
Alignment explanation
Indices: 28194590--28194822 Score: 177
Period size: 50 Copynumber: 4.6 Consensus size: 50
28194580 GTAAAGAGAT
* * * *
28194590 CCCATGTAAGACCATGTCT-GGACATGACATTGGCATCATTGAGATTATGAGAGGT
1 CCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-C--CGAG---ATGAGAGGC
* *
28194645 CCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGC
1 CCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAGGC
** * * *
28194695 CCCCCGTAAGACCATGTCTGGGATATGGCATGGGCACCGATATGAGA-AC
1 CCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAGGC
* * * * * * * ***
28194744 TCCCATGTAAGACCATATCTGGGATATGACATTGGCA--GTACAAGAAACAT
1 -CCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCG-AGATGAGAGGC
28194794 CCCATGTAAGACCATGTCTGGGACATGGC
1 CCCATGTAAGACCATGTCTGGGACATGGC
28194823 TTTGGCATGT
Statistics
Matches: 151, Mismatches: 23, Indels: 14
0.80 0.12 0.07
Matches are distributed among these distances:
48 1 0.01
49 32 0.21
50 81 0.54
53 3 0.02
55 20 0.13
56 14 0.09
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (50 bp):
CCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAGGC
Found at i:28194828 original size:49 final size:48
Alignment explanation
Indices: 28194644--28194829 Score: 178
Period size: 50 Copynumber: 3.8 Consensus size: 48
28194634 TTATGAGAGG
* * *
28194644 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CGACATGA-A-AC
** * * *
28194695 -CCCCCGTAAGACCATGTCTGGGATATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CGACATGA-AAC
* * * *
28194744 TCCCATGTAAGACCATATCTGGGATATGACATTGGCA-GTACAAGAAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACG-ACATGAAAC
*
28194792 ATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 -TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
28194830 TGTTATTATC
Statistics
Matches: 114, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
48 4 0.04
49 38 0.33
50 72 0.63
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (48 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACGACATGAAAC
Found at i:28198232 original size:36 final size:36
Alignment explanation
Indices: 28198187--28198263 Score: 154
Period size: 36 Copynumber: 2.1 Consensus size: 36
28198177 TTAAACATTT
28198187 CAACATCACAAATATTCATAGACATGTTCATAACAA
1 CAACATCACAAATATTCATAGACATGTTCATAACAA
28198223 CAACATCACAAATATTCATAGACATGTTCATAACAA
1 CAACATCACAAATATTCATAGACATGTTCATAACAA
28198259 CAACA
1 CAACA
28198264 ATAAAATTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.48, C:0.23, G:0.05, T:0.23
Consensus pattern (36 bp):
CAACATCACAAATATTCATAGACATGTTCATAACAA
Found at i:28201426 original size:12 final size:13
Alignment explanation
Indices: 28201402--28201426 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28201392 TGTTGTAGTT
28201402 AAAATTTTAAAAA
1 AAAATTTTAAAAA
28201415 AAAATTTTAAAA
1 AAAATTTTAAAA
28201427 TTTTGGGAGC
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAATTTTAAAAA
Found at i:28216545 original size:48 final size:49
Alignment explanation
Indices: 28216484--28216724 Score: 188
Period size: 48 Copynumber: 4.8 Consensus size: 49
28216474 CTGATAATAA
*
28216484 CATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTT-TC-T-T
1 CATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATAT
* * *
28216531 TACTGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATAT
1 CA-TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATAT
* * * ** *
28216581 CGATGCCCATGCCATGTCCTAGACATGGTTTTACGGGGGA-TCTCTCATCT
1 C-ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGT-TCTCATAT
* * * **
28216631 CGGTGCCAACGCCATGT--CAGACATGGTCTTACATAGGACCTCTCATAATCT
1 C-ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCAT-A--T
*
28216682 CAATGATACCAATTCCATGTCCCAGACATGGTCTTACATGGGA
1 C-ATG---CCAATGCCATGTCCCAGACATGGTCTTACATGGGA
28216725 TCTCTTTACC
Statistics
Matches: 151, Mismatches: 28, Indels: 21
0.75 0.14 0.10
Matches are distributed among these distances:
47 4 0.03
48 58 0.38
49 2 0.01
50 52 0.34
51 5 0.03
54 10 0.07
56 20 0.13
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (49 bp):
CATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATAT
Found at i:28222980 original size:41 final size:41
Alignment explanation
Indices: 28222845--28223085 Score: 238
Period size: 41 Copynumber: 5.8 Consensus size: 41
28222835 TGGGATTCAT
* *
28222845 TTGATGAA-AAAGGGGTTGCTAAGTGCAGATTCCCCGAATTA
1 TTGAT-AATAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCA
** * *
28222886 CCGATAAAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCA
1 TTGATAATAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCA
* * *
28222927 CTGATGAA-AAAGGGGTTGCTAAGTGCTGATTCCCTGAATTA
1 TTGAT-AATAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCA
** * * *
28222968 TTGATTCTAAAGGTGGTTGCTAGGTGCTGATTCCACCGTATCC
1 TTGATAATAAAGG-GGTTGCTAAGTGCTGATTCC-CCGAATCA
* * *
28223011 TTGATAGTGAAAGGGGTTGCTATGTGCTGATTCCCCGTATCA
1 TTGATAAT-AAAGGGGTTGCTAAGTGCTGATTCCCCGAATCA
28223053 TTG--AATATAAGGTGGTTGCTAAGTGCTGATTCC
1 TTGATAATA-AAGG-GGTTGCTAAGTGCTGATTCC
28223086 AACGAGTGAT
Statistics
Matches: 171, Mismatches: 21, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
39 1 0.01
40 8 0.05
41 97 0.57
42 31 0.18
43 29 0.17
44 5 0.03
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.30
Consensus pattern (41 bp):
TTGATAATAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCA
Found at i:28231044 original size:13 final size:13
Alignment explanation
Indices: 28231026--28231055 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28231016 AAACTAGATT
*
28231026 TTAACTAAGTAAA
1 TTAACTAAGAAAA
28231039 TTAACTAAGAAAA
1 TTAACTAAGAAAA
28231052 TTAA
1 TTAA
28231056 AAGATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (13 bp):
TTAACTAAGAAAA
Found at i:28243539 original size:21 final size:21
Alignment explanation
Indices: 28243513--28243575 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
28243503 CGAACACGCC
28243513 AACAGAAGCTCATAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
* * *
28243534 AACAGAAGCACAAAAGAGCTA
1 AACAGAAGCTCATAAGAGCTG
*
28243555 AACAAAAGCTC-TAAAGAGCTG
1 AACAGAAGCTCAT-AAGAGCTG
28243576 TCCACCCGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.49, C:0.19, G:0.21, T:0.11
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTG
Found at i:28258334 original size:42 final size:42
Alignment explanation
Indices: 28258254--28258335 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
28258244 CATTTTCTCT
* **
28258254 ATGCCATAGTCCAACTATGGTCTTACACATATTTACATATTG
1 ATGCCATAGCCCAACTATGGTCTTACACATATGCACATATTG
28258296 ATGCCATAGCCCAGA-TATGGTCTTACACAGTA-GCACATAT
1 ATGCCATAGCCCA-ACTATGGTCTTACACA-TATGCACATAT
28258336 CACACCAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 32 0.91
43 3 0.09
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (42 bp):
ATGCCATAGCCCAACTATGGTCTTACACATATGCACATATTG
Found at i:28260934 original size:42 final size:43
Alignment explanation
Indices: 28260887--28261044 Score: 196
Period size: 43 Copynumber: 3.7 Consensus size: 43
28260877 TAAATTTAGT
* *
28260887 GATACGG-GGAATTAGCACATAGCAACCCCTTTCACAATCAAA
1 GATACGGTGGAATCAACACATAGCAACCCCTTTCACAATCAAA
* * * * **
28260929 GATACGGTGGAATCAGCACTTAGCAACCACCTTT-ATATTCAGT
1 GATACGGTGGAATCAACACATAGCAACC-CCTTTCACAATCAAA
28260972 GATACGG-GGAATCAACACATAGCAACCCCTTTCACAATCAAA
1 GATACGGTGGAATCAACACATAGCAACCCCTTTCACAATCAAA
* *
28261014 TATACGGTGGAATCAACACTTAGCAACCCCT
1 GATACGGTGGAATCAACACATAGCAACCCCT
28261045 CGGGGAATCT
Statistics
Matches: 98, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
41 5 0.05
42 36 0.37
43 52 0.53
44 5 0.05
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (43 bp):
GATACGGTGGAATCAACACATAGCAACCCCTTTCACAATCAAA
Found at i:28260998 original size:85 final size:84
Alignment explanation
Indices: 28260849--28261041 Score: 305
Period size: 85 Copynumber: 2.3 Consensus size: 84
28260839 ATCCATTACT
* * * * *
28260849 CGGTGGATTCAGCACTTAGTAACCACCTTAAATTTAGTGATACGGGGAATTAGCACATAGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTAAATTCAGTGATACGGGGAATCAACACATAGCAACC
28260914 CCTTTCACAATCAAAGATA
66 CCTTTCACAATCAAAGATA
*
28260933 CGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCAACACATAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCACC-TTAAATTCAGTGATACGGGGAATCAACACATAGCAAC
*
28260998 CCCTTTCACAATCAAATATA
65 CCCTTTCACAATCAAAGATA
*
28261018 CGGTGGAATCAACACTTAGCAACC
1 CGGTGGAATCAGCACTTAGCAACC
28261042 CCTCGGGGAA
Statistics
Matches: 100, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
84 25 0.25
85 75 0.75
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (84 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTAAATTCAGTGATACGGGGAATCAACACATAGCAACC
CCTTTCACAATCAAAGATA
Found at i:28261662 original size:12 final size:12
Alignment explanation
Indices: 28261645--28261677 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
28261635 TCTTTTTTCC
28261645 AAATAAACATCA
1 AAATAAACATCA
28261657 AAATAAACATCA
1 AAATAAACATCA
28261669 AAATAAACA
1 AAATAAACA
28261678 CATTTCACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (12 bp):
AAATAAACATCA
Found at i:28269412 original size:22 final size:22
Alignment explanation
Indices: 28269377--28269425 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 22
28269367 TAATCGTAGA
28269377 TTTATTATTCTATTTTAATTAT
1 TTTATTATTCTATTTTAATTAT
28269399 TTTAGTTATT-TATTTTAATTAT
1 TTTA-TTATTCTATTTTAATTAT
28269421 TTTAT
1 TTTAT
28269426 ATAACTTGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 1 0.04
22 20 0.77
23 5 0.19
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTATTATTCTATTTTAATTAT
Found at i:28273063 original size:23 final size:22
Alignment explanation
Indices: 28273036--28273081 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
28273026 CATCTTTAAC
*
28273036 TATTTTGATTAAAAACATTTTAT
1 TATTTTGATTAAAAA-ATATTAT
**
28273059 TATTTTTTTTAAAAAATATTAT
1 TATTTTGATTAAAAAATATTAT
28273081 T
1 T
28273082 TTAACAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TATTTTGATTAAAAAATATTAT
Found at i:28275590 original size:107 final size:107
Alignment explanation
Indices: 28275404--28275625 Score: 392
Period size: 107 Copynumber: 2.1 Consensus size: 107
28275394 TGAAGTTTTA
28275404 AAAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTC
1 AAAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTC
* *
28275469 GAATTTCCTAACGCAAAACATTGCCTCGTTTTGAAATTATTG
66 AAATTTCCGAACGCAAAACATTGCCTCGTTTTGAAATTATTG
*
28275511 AAAGGATATTTGG-TCATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCT
1 AAAGGATATTTGGCT-ATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCT
*
28275575 CAAATTTTCGAACGCAAAACATTGCCTCGTTTTGAAATTATTG
65 CAAATTTCCGAACGCAAAACATTGCCTCGTTTTGAAATTATTG
28275618 AAAGGATA
1 AAAGGATA
28275626 AAATACAATG
Statistics
Matches: 110, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
106 1 0.01
107 109 0.99
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (107 bp):
AAAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTC
AAATTTCCGAACGCAAAACATTGCCTCGTTTTGAAATTATTG
Found at i:28277811 original size:132 final size:132
Alignment explanation
Indices: 28277565--28278057 Score: 713
Period size: 132 Copynumber: 3.7 Consensus size: 132
28277555 TTTCGTCTGC
* * *
28277565 TCTTCAATCTATTCCACTGTTGTCCAGGGA-AGTAGAACTACTGGCTTCAATGTACTCTACTGTA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGA-TAGAACTACTGGCTTCAATGTACTCCACTGTA
* * * * *
28277629 ATCTCAGAGAGGTAAAATCCGCCATCTTCGATCTGCTCTACTATTGCTTAGGGAGATAAGATCTA
65 ATCTCAGGGAGGTAAAATCCGCCATCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
28277694 TAA
130 TAA
* * * * * *
28277697 TCTTCAATCTATTCCACAGTTGCTCAGGGA-AGTAGAATTTCTGGCTTCAATGTACTCCACTATA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGA-TAGAACTACTGGCTTCAATGTACTCCACTGTA
* * * * *
28277761 ACCACAGGGAGGTAAAATTCGCCATCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTG
65 ATCTCAGGGAGGTAAAATCCGCCATCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
**
28277826 TGG
130 TAA
*
28277829 T-TTTAATCTATTCCACTGCTGCCCAGGGAGATAGAACTACTGGCTTCAATGTACTCCACTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAACTACTGGCTTCAATGTACTCCACTGTAA
28277893 TCTCAGGGAGGTAAAATCCGCCATCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
66 TCTCAGGGAGGTAAAATCCGCCATCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
28277958 AA
131 AA
* *
28277960 TATTCAATCTATTCCACTGCTGCCCAGGGAGATAGAACTACCGGCTTCAATGTACTCCACTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAACTACTGGCTTCAATGTACTCCACTGTAA
* *
28278025 TCTTAGGGAGGTAAAATCTGCCATCTTCAATCT
66 TCTCAGGGAGGTAAAATCCGCCATCTTCAATCT
28278058 TCAATCTTCA
Statistics
Matches: 324, Mismatches: 35, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
131 115 0.35
132 209 0.65
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (132 bp):
TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAACTACTGGCTTCAATGTACTCCACTGTAA
TCTCAGGGAGGTAAAATCCGCCATCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
AA
Found at i:28277945 original size:44 final size:44
Alignment explanation
Indices: 28277766--28278057 Score: 146
Period size: 44 Copynumber: 6.7 Consensus size: 44
28277756 CTATAACCAC
* * * *
28277766 AGGGAGGTAAAAT-TCGCCATCTTCGATCTGCTCCACTACTACTT
1 AGGGAGATAAAATCT-GCCATCTTCAATCTACTCCACTACTGCTT
* *** * * * **
28277810 AGGGAGATAAGATCTGTGGT-TTTAATCTATTCCACTGCTGCCC
1 AGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTGCTT
* * *** * * *
28277853 AGGGAGATAGAA-CTACTGGCTTCAATGTACTCCACTGTAAT-CTC
1 AGGGAGATAAAATCTGCCATCTTCAATCTACTCCAC--TACTGCTT
* * *
28277897 AGGGAGGTAAAATCCGCCATCTTCAATCTGCTCCACTACTGCTT
1 AGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTGCTT
* ** * * * **
28277941 AGGGAGATAAGATCTGTAATATTCAATCTATTCCACTGCTGCCC
1 AGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTGCTT
* * ** * *
28277985 AGGGAGATAGAA-CTACCGGCTTCAATGTACTCCACTGTAAT-CTT
1 AGGGAGATAAAATCTGCCATCTTCAATCTACTCCAC--TACTGCTT
*
28278029 AGGGAGGTAAAATCTGCCATCTTCAATCT
1 AGGGAGATAAAATCTGCCATCTTCAATCT
28278058 TCAATCTTCA
Statistics
Matches: 172, Mismatches: 67, Indels: 17
0.67 0.26 0.07
Matches are distributed among these distances:
42 3 0.02
43 55 0.32
44 81 0.47
45 33 0.19
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (44 bp):
AGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTGCTT
Found at i:28278037 original size:263 final size:263
Alignment explanation
Indices: 28277570--28278057 Score: 748
Period size: 263 Copynumber: 1.9 Consensus size: 263
28277560 TCTGCTCTTC
* * *
28277570 AATCTATTCCACTGTTGTCCAGGGAAGTAGAACTACTGGCTTCAATGTACTCTACTGTAATCTCA
1 AATCTATTCCACTGCTGCCCAGGGAAGTAGAACTACTGGCTTCAATGTACTCCACTGTAATCTCA
* * * *
28277635 GAGAGGTAAAATCCGCCATCTTCGATCTGCTCTACTATTGCTTAGGGAGATAAGATCTATAATCT
66 GAGAGGTAAAATCCGCCATCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATAT
* * * * *
28277700 TCAATCTATTCCACAGTTGCTCAGGGAAGTAGAATTTCTGGCTTCAATGTACTCCACTATAACCA
131 TCAATCTATTCCACAGCTGCCCAGGGAAGTAGAACTACCGGCTTCAATGTACTCCACTATAACCA
*
28277765 CAGGGAGGTAAAAT-TCGCCATCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTGG
196 CAGGGAGGTAAAATCT-GCCATCTTCAATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTGG
28277829 TTTT
260 TTTT
28277833 AATCTATTCCACTGCTGCCCAGGG-AGATAGAACTACTGGCTTCAATGTACTCCACTGTAATCTC
1 AATCTATTCCACTGCTGCCCAGGGAAG-TAGAACTACTGGCTTCAATGTACTCCACTGTAATCTC
* *
28277897 AGGGAGGTAAAATCCGCCATCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATA
65 AGAGAGGTAAAATCCGCCATCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATA
* * *
28277962 TTCAATCTATTCCACTGCTGCCCAGGG-AGATAGAACTACCGGCTTCAATGTACTCCACTGTAAT
130 TTCAATCTATTCCACAGCTGCCCAGGGAAG-TAGAACTACCGGCTTCAATGTACTCCACTATAAC
**
28278026 CTTAGGGAGGTAAAATCTGCCATCTTCAATCT
194 CACAGGGAGGTAAAATCTGCCATCTTCAATCT
28278058 TCAATCTTCA
Statistics
Matches: 202, Mismatches: 20, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
262 4 0.02
263 197 0.98
264 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (263 bp):
AATCTATTCCACTGCTGCCCAGGGAAGTAGAACTACTGGCTTCAATGTACTCCACTGTAATCTCA
GAGAGGTAAAATCCGCCATCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATAT
TCAATCTATTCCACAGCTGCCCAGGGAAGTAGAACTACCGGCTTCAATGTACTCCACTATAACCA
CAGGGAGGTAAAATCTGCCATCTTCAATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTGGT
TTT
Found at i:28278057 original size:7 final size:7
Alignment explanation
Indices: 28278047--28278071 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28278037 AAAATCTGCC
28278047 ATCTTCA
1 ATCTTCA
28278054 ATCTTCA
1 ATCTTCA
28278061 ATCTTCA
1 ATCTTCA
28278068 ATCT
1 ATCT
28278072 ATTCCACTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (7 bp):
ATCTTCA
Found at i:28278115 original size:103 final size:102
Alignment explanation
Indices: 28277962--28278160 Score: 299
Period size: 103 Copynumber: 1.9 Consensus size: 102
28277952 ATCTGTAATA
** *
28277962 TTCAATCTATTCCACTGCTGCCCAGGGAGATAGAACTACCGGCTTCAATGTACTCCACTGTAATC
1 TTCAATCTATTCCACTGCAACCCAGGGAGATAGAACTACCGGATTCAATGTACTCCACTGTAATC
* **
28278027 TTAGGGAGGTAAAATCTGCCATCTTCAATCTTCAATC
66 TCAGGGAGGTAAAATCCACCATCTTCAATCTTCAATC
* * *
28278064 TTCAATCTATTCCACTGCCAACCCAGGGAGATAGAATTATCGGATTCAATGTACTCCACTGTAGT
1 TTCAATCTATTCCACTG-CAACCCAGGGAGATAGAACTACCGGATTCAATGTACTCCACTGTAAT
*
28278129 CTCAGGGAGGTAAAATCCACCATCTTCGATCT
65 CTCAGGGAGGTAAAATCCACCATCTTCAATCT
28278161 GCTCCACTAC
Statistics
Matches: 86, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
102 17 0.20
103 69 0.80
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (102 bp):
TTCAATCTATTCCACTGCAACCCAGGGAGATAGAACTACCGGATTCAATGTACTCCACTGTAATC
TCAGGGAGGTAAAATCCACCATCTTCAATCTTCAATC
Found at i:28278270 original size:235 final size:234
Alignment explanation
Indices: 28277833--28278292 Score: 726
Period size: 235 Copynumber: 2.0 Consensus size: 234
28277823 CTGTGGTTTT
** *
28277833 AATCTATTCCACTGCTGCCCAGGGAGATAGAACTACTGGCTTCAATGTACTCCACTGTAATCTCA
1 AATCTATTCCACTGCAACCCAGGGAGATAGAACTACTGGATTCAATGTACTCCACTGTAATCTCA
*
28277898 GGGAGGTAAAATCCGCCATCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATAT
66 GGGAGGTAAAATCCACCATCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATAT
* * *
28277963 TCAATCTATTCCACTGCTGCCCAGGGAGATAGAACTACCGGCTTCAATGTACTCCACTGTAATCT
131 TCAATCTATTCCACTACTGCCCAGGGAGATAGAACTACCGGCTTCAATGTACTCCACTGTAACCA
*
28278028 TAGGGAGGTAAAATCTGCCATCTTCAATCTTCAATCTTC
196 CAGGGAGGTAAAATCTGCCATCTTCAATCTTCAATCTTC
* *
28278067 AATCTATTCCACTGCCAACCCAGGGAGATAGAATTA-TCGGATTCAATGTACTCCACTGTAGTCT
1 AATCTATTCCACTG-CAACCCAGGGAGATAGAACTACT-GGATTCAATGTACTCCACTGTAATCT
*
28278131 CAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAAT
64 CAGGGAGGTAAAATCCACCATCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAAT
* * * * *
28278196 TTTCAATCTATTCCACTATTGCCCAGGGA-AGTAGAATTTCTGGCTTCAATGTACTCCACTGTAA
129 ATTCAATCTATTCCACTACTGCCCAGGGAGA-TAGAACTACCGGCTTCAATGTACTCCACTGTAA
*
28278260 CCACAGGGAGGTAAAATCTGCCATCTTCGATCT
193 CCACAGGGAGGTAAAATCTGCCATCTTCAATCT
28278293 GCTCCACTAC
Statistics
Matches: 206, Mismatches: 17, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
234 16 0.08
235 190 0.92
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (234 bp):
AATCTATTCCACTGCAACCCAGGGAGATAGAACTACTGGATTCAATGTACTCCACTGTAATCTCA
GGGAGGTAAAATCCACCATCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATAT
TCAATCTATTCCACTACTGCCCAGGGAGATAGAACTACCGGCTTCAATGTACTCCACTGTAACCA
CAGGGAGGTAAAATCTGCCATCTTCAATCTTCAATCTTC
Found at i:28278322 original size:132 final size:132
Alignment explanation
Indices: 28278064--28278555 Score: 747
Period size: 132 Copynumber: 3.7 Consensus size: 132
28278054 ATCTTCAATC
* ** * *
28278064 TTCAATCTATTCCACTGCCAACCCAGGGAGATAGAATTA-TCGGATTCAATGTACTCCACTGTAG
1 TTCAATCTATTCCACT-ACTGCCCAGGGAGATAGAATTACT-GGCTTCAATGTACTCCACTGTAA
*
28278128 TCTCAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
64 TCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
28278193 AATT
129 AATT
* * *
28278197 TTCAATCTATTCCACTATTGCCCAGGGA-AGTAGAATTTCTGGCTTCAATGTACTCCACTGTAAC
1 TTCAATCTATTCCACTACTGCCCAGGGAGA-TAGAATTACTGGCTTCAATGTACTCCACTGTAAT
* * *
28278261 CACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTG
65 CTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTA
*
28278326 GTT
130 ATT
* *
28278329 TT-AATCTATTCCACTGCTGCCCAGGGAGATAGAAGTACTGGCTTCAATGTACTCCACTGTAATC
1 TTCAATCTATTCCACTACTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAATC
*
28278393 TCAAGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA
66 TCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA
*
28278458 TC
131 TT
* * *
28278460 TTCAATCTATTCCACTACTGCTCAGGGAGATAGAACTACCGGCTTCAATGTACTCCACTGTAATC
1 TTCAATCTATTCCACTACTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAATC
*
28278525 TCAGGGAGGTAAAATCCGCCATCTTCAATCT
66 TCAGGGAGGTAAAATCCGCCATCTTCGATCT
28278556 TCAATCTATT
Statistics
Matches: 325, Mismatches: 30, Indels: 9
0.89 0.08 0.02
Matches are distributed among these distances:
131 119 0.37
132 189 0.58
133 17 0.05
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (132 bp):
TTCAATCTATTCCACTACTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAATC
TCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA
TT
Found at i:28278323 original size:44 final size:44
Alignment explanation
Indices: 28278129--28278783 Score: 188
Period size: 44 Copynumber: 14.7 Consensus size: 44
28278119 CCACTGTAGT
* * ** * *
28278129 CTCAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTG
1 CTCAGGGAGATAAGATCTGCCATCTTCAATCTACTCCACTACTG
* ** * * *
28278173 CTTAGGGAGATAAGATCTGTAATTTTCAATCTATTCCACTATTG
1 CTCAGGGAGATAAGATCTGCCATCTTCAATCTACTCCACTACTG
* * *** *
28278217 CCCAGGGA-AGT-AGAAT-TTCTGGCTTCAATGTACTCCACTGTAAC--
1 CTCAGGGAGA-TAAG-ATCTGCCATCTTCAATCTACTCCAC--T-ACTG
* * * * *
28278261 CACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTG
1 CTCAGGGAGATAAGATCTGCCATCTTCAATCTACTCCACTACTG
* *** * * *
28278305 CTTAGGGAGATAAGATCTGTGGT-TTTAATCTATTCCACTGCTG
1 CTCAGGGAGATAAGATCTGCCATCTTCAATCTACTCCACTACTG
* ** * *** * *
28278348 CCCAGGGAGAT-AGAAGTACTGGCTTCAATGTACTCCACTGTAAT-
1 CTCAGGGAGATAAGATCTGCCATCTTCAATCTACTCCAC--TACTG
* * * * * *
28278392 CTCAAGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTG
1 CTCAGGGAGATAAGATCTGCCATCTTCAATCTACTCCACTACTG
* ** *
28278436 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTACTG
1 CTCAGGGAGATAAGATCTGCCATCTTCAATCTACTCCACTACTG
* * ** * *
28278480 CTCAGGGAGAT-AGAACTACCGGCTTCAATGTACTCCACTGTAAT-
1 CTCAGGGAGATAAGATCTGCCATCTTCAATCTACTCCAC--TACTG
* * * * **
28278524 CTCAGGGAGGTAAAATCCGCCATCTTCAATCTTCAATCTATTCCACTGCCAA
1 CTCAGGGAGATAAGATCTGCCATCTTCAATC-T--A-C---TCCACT-ACTG
* ** ** * *
28278576 CCCAGGGAGAT-AGAAT-TATCGGCTTCAATGTACTCCACT-GTAG
1 CTCAGGGAGATAAG-ATCTGCCATCTTCAATCTACTCCACTACT-G
* * * * * *
28278619 TCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCTACTACTG
1 -CTCAGGGAGATAAGATCTGCCATCTTCAATCTACTCCACTACTG
* ** * * *
28278664 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCAATGCTG
1 CTCAGGGAGATAAGATCTGCCATCTTCAATCTACTCCACTACTG
* * * ** * *
28278708 CCCAGGGAGAT-AGAACTACCGGCTTCAATGTACTCCACTGTAAT-
1 CTCAGGGAGATAAGATCTGCCATCTTCAATCTACTCCAC--TACTG
* * **
28278752 CTCAGGGAGGTAAAATCCACCATCTTCAATCT
1 CTCAGGGAGATAAGATCTGCCATCTTCAATCT
28278784 TCAATCTATT
Statistics
Matches: 413, Mismatches: 162, Indels: 71
0.64 0.25 0.11
Matches are distributed among these distances:
42 7 0.02
43 94 0.23
44 196 0.47
45 82 0.20
46 3 0.01
47 1 0.00
48 2 0.00
49 1 0.00
50 2 0.00
51 9 0.02
52 16 0.04
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.28
Consensus pattern (44 bp):
CTCAGGGAGATAAGATCTGCCATCTTCAATCTACTCCACTACTG
Found at i:28278525 original size:498 final size:491
Alignment explanation
Indices: 28277610--28278783 Score: 1958
Period size: 498 Copynumber: 2.4 Consensus size: 491
28277600 AACTACTGGC
* * * *
28277610 TTCAATGTACTCTACTGTAATCTCAGAGAGGTAAAATCCGCCATCTTCGATCTGCTCTACTATTG
1 TTCAATGTACTCCACTGTAGTCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCTACTACTG
* *
28277675 CTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCAC-AGTTGCTCAGGGAAGTAGAATTTCT
66 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTA-TTGCCCAGGGAAGTAGAATTTCT
*
28277739 GGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAAT-TCGCCATCTTCGATCTGCTCCACT
130 GGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCT-GCCATCTTCGATCTGCTCCACT
28277803 ACTACTTAGGGAGATAAGATCTGTGGTTTTAATCTATTCCACTGCTGCCCAGGGAGATAGAACTA
194 ACTACTTAGGGAGATAAGATCTGTGGTTTTAATCTATTCCACTGCTGCCCAGGGAGATAGAACTA
*
28277868 CTGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATCTTCAATCTGCTCCAC
259 CTGGCTTCAATGTACTCCACTGTAATCTCAAGGAGGTAAAATCCGCCATCTTCAATCTGCTCCAC
*
28277933 TACTGCTTAGGGAGATAAGATCTGTAATATTCAATCTATTCCACTGCTGCCCAGGGAGATAGAAC
324 TACTGCTTAGGGAGATAAGATCTGTAATATTCAATCTATTCCACTACTGCCCAGGGAGATAGAAC
* *
28277998 TACCGGCTTCAATGTACTCCACTGTAATCTTAGGGAGGTAAAATCTGCCATCTTCAATCTTCAAT
389 TACCGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAA--T-CC-GC--C-ATCTTCAAT
28278063 CTTCAATCTATTCCACTGCCAACCCAGGGAGATAGAATTATCGGA
447 CTTCAATCTATTCCACTGCCAACCCAGGGAGATAGAATTATCGGA
* *
28278108 TTCAATGTACTCCACTGTAGTCTCAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTG
1 TTCAATGTACTCCACTGTAGTCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCTACTACTG
*
28278173 CTTAGGGAGATAAGATCTGTAATTTTCAATCTATTCCACTATTGCCCAGGGAAGTAGAATTTCTG
66 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTATTGCCCAGGGAAGTAGAATTTCTG
28278238 GCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTAC
131 GCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTAC
* *
28278303 TGCTTAGGGAGATAAGATCTGTGGTTTTAATCTATTCCACTGCTGCCCAGGGAGATAGAAGTACT
196 TACTTAGGGAGATAAGATCTGTGGTTTTAATCTATTCCACTGCTGCCCAGGGAGATAGAACTACT
*
28278368 GGCTTCAATGTACTCCACTGTAATCTCAAGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTA
261 GGCTTCAATGTACTCCACTGTAATCTCAAGGAGGTAAAATCCGCCATCTTCAATCTGCTCCACTA
* *
28278433 CTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTACTGCTCAGGGAGATAGAACTA
326 CTGCTTAGGGAGATAAGATCTGTAATATTCAATCTATTCCACTACTGCCCAGGGAGATAGAACTA
28278498 CCGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATCTTCAATCTTCAATCT
391 CCGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATCTTCAATCTTCAATCT
*
28278563 ATTCCACTGCCAACCCAGGGAGATAGAATTATCGGC
456 ATTCCACTGCCAACCCAGGGAGATAGAATTATCGGA
28278599 TTCAATGTACTCCACTGTAGTCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCTACTACTG
1 TTCAATGTACTCCACTGTAGTCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCTACTACTG
* ** * * *
28278664 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCAATGCTGCCCAGGG-AGATAGAACTACC
66 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTATTGCCCAGGGAAG-TAGAATTTCT
* * ** *
28278728 GGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCACCATCTTCAATCT
130 GGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCT
28278784 TCAATCTATT
Statistics
Matches: 639, Mismatches: 34, Indels: 13
0.93 0.05 0.02
Matches are distributed among these distances:
490 2 0.00
491 221 0.35
492 1 0.00
494 1 0.00
495 2 0.00
496 1 0.00
498 409 0.64
499 2 0.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29
Consensus pattern (491 bp):
TTCAATGTACTCCACTGTAGTCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCTACTACTG
CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTATTGCCCAGGGAAGTAGAATTTCTG
GCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTAC
TACTTAGGGAGATAAGATCTGTGGTTTTAATCTATTCCACTGCTGCCCAGGGAGATAGAACTACT
GGCTTCAATGTACTCCACTGTAATCTCAAGGAGGTAAAATCCGCCATCTTCAATCTGCTCCACTA
CTGCTTAGGGAGATAAGATCTGTAATATTCAATCTATTCCACTACTGCCCAGGGAGATAGAACTA
CCGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATCTTCAATCTTCAATCT
ATTCCACTGCCAACCCAGGGAGATAGAATTATCGGA
Found at i:28278602 original size:228 final size:228
Alignment explanation
Indices: 28278331--28278881 Score: 953
Period size: 228 Copynumber: 2.4 Consensus size: 228
28278321 CTGTGGTTTT
** * *
28278331 AATCTATTCCACTG-CTGCCCAGGGAGATAGAAGTA-CTGGCTTCAATGTACTCCACTGTAATCT
1 AATCTATTCCACTGCCAACCCAGGGAGATAGAATTATC-GGCTTCAATGTACTCCACTGTAGTCT
*
28278394 CAAGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAAT
65 CAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAAT
* *
28278459 CTTCAATCTATTCCACTACTGCTCAGGGAGATAGAACTACCGGCTTCAATGTACTCCACTGTAAT
130 CTTCAATCTATTCCAATACTGCCCAGGGAGATAGAACTACCGGCTTCAATGTACTCCACTGTAAT
*
28278524 CTCAGGGAGGTAAAATCCGCCATCTTCAATCTTC
195 CTCAGGGAGGTAAAATCCACCATCTTCAATCTTC
28278558 AATCTATTCCACTGCCAACCCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAGTCTC
1 AATCTATTCCACTGCCAACCCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAGTCTC
*
28278623 AGGGAGGTAAAATCCGCCATCTTCGATCTGCTCTACTACTGCTTAGGGAGATAAGATCTGTAATC
66 AGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATC
*
28278688 TTCAATCTATTCCAATGCTGCCCAGGGAGATAGAACTACCGGCTTCAATGTACTCCACTGTAATC
131 TTCAATCTATTCCAATACTGCCCAGGGAGATAGAACTACCGGCTTCAATGTACTCCACTGTAATC
28278753 TCAGGGAGGTAAAATCCACCATCTTCAATCTTC
196 TCAGGGAGGTAAAATCCACCATCTTCAATCTTC
*
28278786 AATCTATTCCACTGCCAACCCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAGTCTT
1 AATCTATTCCACTGCCAACCCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAGTCTC
* * *
28278851 AGGGAGGTAAAATCTGCCATATTTGATCTGC
66 AGGGAGGTAAAATCCGCCATCTTCGATCTGC
28278882 CCCGCTGTCG
Statistics
Matches: 308, Mismatches: 14, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
227 14 0.05
228 293 0.95
229 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (228 bp):
AATCTATTCCACTGCCAACCCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAGTCTC
AGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATC
TTCAATCTATTCCAATACTGCCCAGGGAGATAGAACTACCGGCTTCAATGTACTCCACTGTAATC
TCAGGGAGGTAAAATCCACCATCTTCAATCTTC
Found at i:28278623 original size:96 final size:95
Alignment explanation
Indices: 28278456--28278651 Score: 311
Period size: 96 Copynumber: 2.1 Consensus size: 95
28278446 TAAGATCTGT
** *
28278456 AATCTTCAATCTATTCCACTACTGCTCAGGGAGATAGAACTACCGGCTTCAATGTACTCCACTGT
1 AATCTTCAATCTATTCCACTACAACCCAGGGAGATAGAACTACCGGCTTCAATGTACTCCACTGT
28278521 AATCTCAGGGAGGTAAAATCCGCCATCTTC
66 AATCTCAGGGAGGTAAAATCCGCCATCTTC
* * *
28278551 AATCTTCAATCTATTCCACTGCCAACCCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTG
1 AATCTTCAATCTATTCCACT-ACAACCCAGGGAGATAGAACTACCGGCTTCAATGTACTCCACTG
*
28278616 TAGTCTCAGGGAGGTAAAATCCGCCATCTTC
65 TAATCTCAGGGAGGTAAAATCCGCCATCTTC
*
28278647 GATCT
1 AATCT
28278652 GCTCTACTAC
Statistics
Matches: 92, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
95 20 0.22
96 72 0.78
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (95 bp):
AATCTTCAATCTATTCCACTACAACCCAGGGAGATAGAACTACCGGCTTCAATGTACTCCACTGT
AATCTCAGGGAGGTAAAATCCGCCATCTTC
Found at i:28278855 original size:96 final size:95
Alignment explanation
Indices: 28278684--28278864 Score: 290
Period size: 96 Copynumber: 1.9 Consensus size: 95
28278674 TAAGATCTGT
**
28278684 AATCTTCAATCTATTCCAATGCTGCCCAGGGAGATAGAACTACCGGCTTCAATGTACTCCACTGT
1 AATCTTCAATCTATTCCAATGCAACCCAGGGAGATAGAACTACCGGCTTCAATGTACTCCACTGT
28278749 AATCTCAGGGAGGTAAAATCCACCATCTTC
66 AATCTCAGGGAGGTAAAATCCACCATCTTC
* * *
28278779 AATCTTCAATCTATTCCACTGCCAACCCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTG
1 AATCTTCAATCTATTCCAATG-CAACCCAGGGAGATAGAACTACCGGCTTCAATGTACTCCACTG
* *
28278844 TAGTCTTAGGGAGGTAAAATC
65 TAATCTCAGGGAGGTAAAATC
28278865 TGCCATATTT
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
95 20 0.26
96 58 0.74
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (95 bp):
AATCTTCAATCTATTCCAATGCAACCCAGGGAGATAGAACTACCGGCTTCAATGTACTCCACTGT
AATCTCAGGGAGGTAAAATCCACCATCTTC
Found at i:28278950 original size:45 final size:46
Alignment explanation
Indices: 28278901--28279009 Score: 145
Period size: 44 Copynumber: 2.4 Consensus size: 46
28278891 GATGCAAGAG
* *
28278901 GGCAAGATCTGCTATCTTTAG-TCTGCTCCACTGTTAGTACAGGAA
1 GGCAAGATCTGCTATCTTTAGATCTGCTCCACCGTCAGTACAGGAA
* *
28278946 GGCAAGA-CTGGCT-TCTTT-GATCTGCTTCGCCGTCAGTACAGGAA
1 GGCAAGATCT-GCTATCTTTAGATCTGCTCCACCGTCAGTACAGGAA
28278990 GGCAAGATCTGCTATCTTTA
1 GGCAAGATCTGCTATCTTTA
28279010 ACCAGCTCTA
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
43 1 0.02
44 37 0.67
45 17 0.31
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (46 bp):
GGCAAGATCTGCTATCTTTAGATCTGCTCCACCGTCAGTACAGGAA
Found at i:28279078 original size:87 final size:87
Alignment explanation
Indices: 28278964--28279349 Score: 596
Period size: 87 Copynumber: 4.4 Consensus size: 87
28278954 TGGCTTCTTT
* * * * * *
28278964 GATCTGCTTCGCCGTCAGTACAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCTACTGCAACCG
1 GATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCG
28279029 ATGGAGGCAAGGTTTTGTTTTC
66 ATGGAGGCAAGGTTTTGTTTTC
*
28279051 GATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCG
1 GATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCG
* *
28279116 ATGAAGGCAAGGTTTTATTTTC
66 ATGGAGGCAAGGTTTTGTTTTC
*
28279138 GATTTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCG
1 GATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCG
*
28279203 AT-GAGGCAAGGTTTTGTTTTT
66 ATGGAGGCAAGGTTTTGTTTTC
* * * *
28279224 TATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTGTCTTCAACCAGCTCTACTACAACCG
1 GATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCG
*
28279289 A-GAGAGGCAAGGTTTGTGTCTTC
66 ATG-GAGGCAAGGTTT-TGTTTTC
28279312 GATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGC
1 GATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGC
28279350 AACTTCATCG
Statistics
Matches: 276, Mismatches: 20, Indels: 5
0.92 0.07 0.02
Matches are distributed among these distances:
86 77 0.28
87 157 0.57
88 42 0.15
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.30
Consensus pattern (87 bp):
GATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCG
ATGGAGGCAAGGTTTTGTTTTC
Found at i:28279082 original size:43 final size:43
Alignment explanation
Indices: 28279033--28279169 Score: 100
Period size: 43 Copynumber: 3.2 Consensus size: 43
28279023 CAACCGATGG
28279033 AGGCAAGGTTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGA
1 AGGCAAGGTTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGA
* * ** * * * * * * *
28279076 AGGCAA-GATCTGCTATCTTTAACCAGCTCCACTG-CAA-CCGATGA
1 AGGCAAGGTTTTG-T-T-TTCGATCTGCTTCGCTGTTAATGC-AGGA
* *
28279120 AGGCAAGGTTTTATTTTCGATTTGCTTCGCTGTTAATGCAGGA
1 AGGCAAGGTTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGA
28279163 AGGCAAG
1 AGGCAAG
28279170 ATCTGCTATC
Statistics
Matches: 63, Mismatches: 24, Indels: 14
0.62 0.24 0.14
Matches are distributed among these distances:
42 14 0.22
43 21 0.33
44 14 0.22
45 14 0.22
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (43 bp):
AGGCAAGGTTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGA
Found at i:28279581 original size:22 final size:22
Alignment explanation
Indices: 28279556--28279627 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
28279546 GTTCTAAACC
28279556 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
28279578 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
** *
28279600 CTCATGTTTCACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
28279622 CTCATG
1 CTCATG
28279628 TTTGAACATT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.31
Consensus pattern (22 bp):
CTCATGGCTAACGTACTAAGCT
Found at i:28279969 original size:108 final size:108
Alignment explanation
Indices: 28279780--28279975 Score: 313
Period size: 108 Copynumber: 1.8 Consensus size: 108
28279770 GAAAAATGCT
*
28279780 TGAAAAAGATTATCAAAATGGACAAAATGAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAAT
1 TGAAAAAGATTATCAAAATGGACAAAATGAAATTTTGTTGAGAGCAAAACTCTAAACAAACAAAT
28279845 TAATCAAGACAGCAAATTTTGCTGAGATACGAGATGTATAAGA
66 TAATCAAGACAGCAAATTTTGCTGAGATACGAGATGTATAAGA
* * * **
28279888 TGAAAAAGATTATCACAATGGATAAGATGGAAA-TTTGTTGAGAGCAAAACTCTAAATGAACAAA
1 TGAAAAAGATTATCAAAATGGACAAAAT-GAAATTTTGTTGAGAGCAAAACTCTAAACAAACAAA
*
28279952 TTAATCAAGATAGCAAATTTTGCT
65 TTAATCAAGACAGCAAATTTTGCT
28279976 AGAATACAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
108 76 0.95
109 4 0.05
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.26
Consensus pattern (108 bp):
TGAAAAAGATTATCAAAATGGACAAAATGAAATTTTGTTGAGAGCAAAACTCTAAACAAACAAAT
TAATCAAGACAGCAAATTTTGCTGAGATACGAGATGTATAAGA
Found at i:28280017 original size:45 final size:47
Alignment explanation
Indices: 28279949--28280036 Score: 117
Period size: 45 Copynumber: 1.9 Consensus size: 47
28279939 CTAAATGAAC
* *
28279949 AAATTAATCAAGATAGCAAATTTTG-CTAGAATACAAA-ATGAGAAT
1 AAATTAATCAAGATAGCAAATTTTGTCAAAAATACAAAGATGAGAAT
* **
28279994 AAATTAATCAAGATGGCGTATTTTGTCAAAAATACAAAGATGA
1 AAATTAATCAAGATAGCAAATTTTGTCAAAAATACAAAGATGA
28280037 ATAAAATGGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
45 22 0.61
46 10 0.28
47 4 0.11
ACGTcount: A:0.49, C:0.09, G:0.15, T:0.27
Consensus pattern (47 bp):
AAATTAATCAAGATAGCAAATTTTGTCAAAAATACAAAGATGAGAAT
Found at i:28280039 original size:45 final size:43
Alignment explanation
Indices: 28279941--28280041 Score: 112
Period size: 45 Copynumber: 2.3 Consensus size: 43
28279931 GCAAAACTCT
* * *
28279941 AAATGAACAAATTAATCAAGATAGCAAATTTTGCTAGAATACA
1 AAATGAATAAATTAATCAAGATAGCAAATTTTGCAAAAATACA
* **
28279984 AAATGAGAATAAATTAATCAAGATGGCGTATTTTGTCAAAAATACA
1 AAAT--GAATAAATTAATCAAGATAGCAAATTTTG-CAAAAATACA
28280030 AAGATGAATAAA
1 AA-ATGAATAAA
28280042 ATGGAAATAG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
43 4 0.08
45 32 0.67
46 10 0.21
47 2 0.04
ACGTcount: A:0.51, C:0.09, G:0.14, T:0.26
Consensus pattern (43 bp):
AAATGAATAAATTAATCAAGATAGCAAATTTTGCAAAAATACA
Found at i:28280340 original size:18 final size:18
Alignment explanation
Indices: 28280312--28280365 Score: 56
Period size: 20 Copynumber: 2.9 Consensus size: 18
28280302 GGCCTCTCCT
*
28280312 TTTTATCTTTTCTTTTTCG
1 TTTT-TCTTTTCTTTTTCC
28280331 TTTTTCTTTTCCTTTTTTCC
1 TTTTTCTTTT-C-TTTTTCC
*
28280351 TTTTT-GTTTCTTTTT
1 TTTTTCTTTTCTTTTT
28280366 TTTTCAAGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 5 0.16
18 7 0.23
19 8 0.26
20 11 0.35
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.78
Consensus pattern (18 bp):
TTTTTCTTTTCTTTTTCC
Found at i:28280354 original size:32 final size:29
Alignment explanation
Indices: 28280308--28280370 Score: 74
Period size: 32 Copynumber: 2.1 Consensus size: 29
28280298 CCTTGGCCTC
*
28280308 TCCTTTTTATCTTTTCTTTTTCGTTTTTCTTT
1 TCCTTTTTATCTTTT-TGTTTC-TTTTT-TTT
28280340 TCCTTTTT-TCCTTTTTGTTTCTTTTTTTT
1 TCCTTTTTAT-CTTTTTGTTTCTTTTTTTT
28280369 TC
1 TC
28280371 AAGTGAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 5 0.17
30 5 0.17
31 6 0.21
32 13 0.45
ACGTcount: A:0.02, C:0.19, G:0.03, T:0.76
Consensus pattern (29 bp):
TCCTTTTTATCTTTTTGTTTCTTTTTTTT
Found at i:28280821 original size:1 final size:1
Alignment explanation
Indices: 28280805--28280879 Score: 51
Period size: 1 Copynumber: 75.0 Consensus size: 1
28280795 CCAGTAGAGG
* * * * * * * * * *
28280805 TTTTTTCTTTTGTTTTTATTTTTGTTTTTTTGTTGTTTTTTTGTTTTTGTTGTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
28280870 TGTTTTTTTT
1 TTTTTTTTTT
28280880 GCCTCCACTG
Statistics
Matches: 52, Mismatches: 22, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.01, C:0.01, G:0.12, T:0.85
Consensus pattern (1 bp):
T
Found at i:28280821 original size:12 final size:11
Alignment explanation
Indices: 28280804--28280879 Score: 77
Period size: 11 Copynumber: 6.8 Consensus size: 11
28280794 CCCAGTAGAG
28280804 GTTTTTTCTTTT
1 GTTTTTT-TTTT
28280816 GTTTTTATTTTT
1 GTTTTT-TTTTT
*
28280828 GTTTTTTTGTT
1 GTTTTTTTTTT
28280839 GTTTTTTTGTTT
1 GTTTTTTT-TTT
*
28280851 -TTGTTGTTTTT
1 GTT-TTTTTTTT
28280862 G--TTTTTTTT
1 GTTTTTTTTTT
28280871 GTTTTTTTT
1 GTTTTTTTT
28280880 GCCTCCACTG
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
9 8 0.15
11 23 0.43
12 22 0.41
13 1 0.02
ACGTcount: A:0.01, C:0.01, G:0.13, T:0.84
Consensus pattern (11 bp):
GTTTTTTTTTT
Found at i:28280832 original size:17 final size:17
Alignment explanation
Indices: 28280805--28280880 Score: 68
Period size: 17 Copynumber: 4.4 Consensus size: 17
28280795 CCAGTAGAGG
*
28280805 TTTTTTCTTTTGTT-TT
1 TTTTTTGTTTTGTTGTT
*
28280821 TATTTTTGTTTTTTTGTTGT
1 T-TTTTTGTTTTGTTG-T-T
28280841 TTTTTTGTTTTTGTTGTT
1 TTTTTTG-TTTTGTTGTT
*
28280859 TTTGTT-TTTT-TTGTT
1 TTTTTTGTTTTGTTGTT
28280874 TTTTTTG
1 TTTTTTG
28280881 CCTCCACTGA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
15 10 0.20
16 5 0.10
17 11 0.22
18 6 0.12
19 8 0.16
20 9 0.18
ACGTcount: A:0.01, C:0.01, G:0.13, T:0.84
Consensus pattern (17 bp):
TTTTTTGTTTTGTTGTT
Found at i:28280843 original size:9 final size:9
Alignment explanation
Indices: 28280823--28280880 Score: 84
Period size: 9 Copynumber: 6.7 Consensus size: 9
28280813 TTTGTTTTTA
28280823 TTTTTGTT-
1 TTTTTGTTG
28280831 TTTTTGTTG
1 TTTTTGTTG
28280840 TTTTT-TTG
1 TTTTTGTTG
28280848 TTTTTGTTG
1 TTTTTGTTG
*
28280857 TTTTTGTTT
1 TTTTTGTTG
*
28280866 TTTTTGTTT
1 TTTTTGTTG
28280875 TTTTTG
1 TTTTTG
28280881 CCTCCACTGA
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
8 16 0.34
9 31 0.66
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (9 bp):
TTTTTGTTG
Found at i:28280844 original size:24 final size:24
Alignment explanation
Indices: 28280804--28280876 Score: 87
Period size: 24 Copynumber: 3.0 Consensus size: 24
28280794 CCCAGTAGAG
* *
28280804 GTTTTTTCTTTTG-TTTTTATTTTT
1 GTTTTTT-TGTTGTTTTTTGTTTTT
28280828 GTTTTTTTGTTGTTTTTTTGTTTTT
1 GTTTTTTTGTTG-TTTTTTGTTTTT
28280853 GTTGTTTTTGTT-TTTTTTGTTTTT
1 GTT-TTTTTGTTGTTTTTTGTTTTT
28280877 TTTGCCTCCA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
23 4 0.09
24 19 0.43
25 13 0.30
26 8 0.18
ACGTcount: A:0.01, C:0.01, G:0.14, T:0.84
Consensus pattern (24 bp):
GTTTTTTTGTTGTTTTTTGTTTTT
Found at i:28280862 original size:15 final size:15
Alignment explanation
Indices: 28280814--28280876 Score: 73
Period size: 15 Copynumber: 4.5 Consensus size: 15
28280804 GTTTTTTCTT
*
28280814 TTGTTTTTATTTTTG
1 TTGTTTTTGTTTTTG
28280829 TT-TTTTTG---TTG
1 TTGTTTTTGTTTTTG
28280840 TT-TTTTTGTTTTTG
1 TTGTTTTTGTTTTTG
*
28280854 TTGTTTTTGTTTTTT
1 TTGTTTTTGTTTTTG
28280869 TTGTTTTT
1 TTGTTTTT
28280877 TTTGCCTCCA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
11 11 0.26
14 10 0.24
15 21 0.50
ACGTcount: A:0.02, C:0.00, G:0.14, T:0.84
Consensus pattern (15 bp):
TTGTTTTTGTTTTTG
Found at i:28283888 original size:107 final size:107
Alignment explanation
Indices: 28283702--28283921 Score: 395
Period size: 107 Copynumber: 2.1 Consensus size: 107
28283692 AAGTTTTAAG
*
28283702 AGGATATTTAGCTATTTAGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACGTTTTCTCGA
1 AGGATATTTAGCCATTTAGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACGTTTTCTCGA
*
28283767 ATTTCCTAACGCAAAACATTGCCTCGTTTTGAAATTATTGAA
66 ATTTCCAAACGCAAAACATTGCCTCGTTTTGAAATTATTGAA
* *
28283809 AGGATATTTGGCCATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACGTTTTCTCGA
1 AGGATATTTAGCCATTTAGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACGTTTTCTCGA
*
28283874 ATTTCCAAACGCAAAATATTGCCTCGTTTTGAAATTATTGAA
66 ATTTCCAAACGCAAAACATTGCCTCGTTTTGAAATTATTGAA
28283916 AGGATA
1 AGGATA
28283922 AAATACAATG
Statistics
Matches: 108, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
107 108 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (107 bp):
AGGATATTTAGCCATTTAGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACGTTTTCTCGA
ATTTCCAAACGCAAAACATTGCCTCGTTTTGAAATTATTGAA
Found at i:28286398 original size:16 final size:17
Alignment explanation
Indices: 28286361--28286398 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
28286351 CCATCGAGCG
*
28286361 AGAAAAAGAAAAAGAGA
1 AGAAAAACAAAAAGAGA
28286378 A-AAAAACAAAAAGA-A
1 AGAAAAACAAAAAGAGA
28286393 AGAAAA
1 AGAAAA
28286399 GAATGACGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 2 0.11
16 16 0.84
17 1 0.05
ACGTcount: A:0.82, C:0.03, G:0.16, T:0.00
Consensus pattern (17 bp):
AGAAAAACAAAAAGAGA
Found at i:28292041 original size:74 final size:75
Alignment explanation
Indices: 28291920--28292068 Score: 266
Period size: 74 Copynumber: 2.0 Consensus size: 75
28291910 AAGGAAAACC
28291920 AGGATTATTCCCTTATTAATAGAGAATGCAAATGGAAAGTTAGAAAAATGAATTAT-TTCTTTCC
1 AGGATTATTCCCTTATTAATAGAGAATGCAAATGGAAAGTTAGAAAAATGAATTATATTCTTTCC
28291984 AAAAGAATAT
66 AAAAGAATAT
*
28291994 AGGATTATTCTCTTATTAATAGAGAA-GACAAATGGAAAGTTAGAAAAATGAATTATATTCTTTC
1 AGGATTATTCCCTTATTAATAGAGAATG-CAAATGGAAAGTTAGAAAAATGAATTATATTCTTTC
28292058 CAAAAGAATAT
65 CAAAAGAATAT
28292069 TAATTTTCAT
Statistics
Matches: 72, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
73 1 0.01
74 53 0.74
75 18 0.25
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.32
Consensus pattern (75 bp):
AGGATTATTCCCTTATTAATAGAGAATGCAAATGGAAAGTTAGAAAAATGAATTATATTCTTTCC
AAAAGAATAT
Found at i:28292297 original size:138 final size:138
Alignment explanation
Indices: 28292044--28292600 Score: 804
Period size: 138 Copynumber: 4.1 Consensus size: 138
28292034 TAGAAAAATG
*
28292044 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCATTTATATTTTGA-CTGAAATTAATTA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCATTTATATTTTGATC-GAAATTAATTA
* ** * *
28292108 ATATAATTGTTTATATTAATAAATTTAGCAAAATATATACAATTAATATTTTGTACGAATCAAAT
65 ATATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
28292173 TCATATATT
130 TCATATATT
* * *
28292182 AATTGTATTCTTTCCAAAA-ATATATTAATTTCCATGTCTTTTATATTTTGATCAAAATTAATTA
1 AATTATATTCTTTCCAAAAGA-ATATTAATTTCCATGTCATTTATATTTTGATCGAAATTAATTA
* * *
28292246 ATAAAACTGGTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAA
65 ATATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
28292311 TCATATATT
130 TCATATATT
* * *
28292320 AAGTATATTCTTCCCAAAAGAATATTAATTTCCATGT-ATTTAACATTTTGATCGAAATTAATTA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCATTT-ATATTTTGATCGAAATTAATTA
* **
28292384 ATATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTAAATGAATCAAAT
65 ATATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
28292449 TCATATATT
130 TCATATATT
*
28292458 AATTATATTCTTAT-CAAAAGAATATTAATTTCCATGTCATTTATATTTTGACCGAAATTAATTA
1 AATTATATTCTT-TCCAAAAGAATATTAATTTCCATGTCATTTATATTTTGATCGAAATTAATTA
* * * * *
28292522 ATATAACTGTTTCTATTCATAAATTTGATAAAATATAT--AATTAATA-TTTGTAAGAATCAAAT
65 ATATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
28292584 TCATATATT
130 TCATATATT
*
28292593 CATTATAT
1 AATTATAT
28292601 CTATGTTCTC
Statistics
Matches: 376, Mismatches: 37, Indels: 15
0.88 0.09 0.04
Matches are distributed among these distances:
135 29 0.08
136 8 0.02
137 4 0.01
138 329 0.88
139 6 0.02
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.44
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCATTTATATTTTGATCGAAATTAATTAA
TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:28299763 original size:23 final size:22
Alignment explanation
Indices: 28299737--28299784 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
28299727 GTTAAAAATT
28299737 TAAACAAC-TAGGTTTAATTTTCG
1 TAAA-AACATAGGTTTAATTTT-G
* *
28299760 TAAAAACATATGTTTGATTTTG
1 TAAAAACATAGGTTTAATTTTG
28299782 TAA
1 TAA
28299785 TACAGTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (22 bp):
TAAAAACATAGGTTTAATTTTG
Found at i:28304478 original size:25 final size:25
Alignment explanation
Indices: 28304450--28304508 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
28304440 TCACTGATAG
28304450 TGTGAGCATTCTAATTCACAGCTCC
1 TGTGAGCATTCTAATTCACAGCTCC
* * * *
28304475 TGTGAGCATTTTGATTTACAGCTCG
1 TGTGAGCATTCTAATTCACAGCTCC
28304500 TGTGAGCAT
1 TGTGAGCAT
28304509 ACATGTACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (25 bp):
TGTGAGCATTCTAATTCACAGCTCC
Found at i:28305198 original size:20 final size:20
Alignment explanation
Indices: 28305151--28305198 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
28305141 AAGTTAAAGA
*
28305151 AAGAAAATGCAATAGAAAGT
1 AAGAAAATGCAATAGAAAAT
28305171 AATG-AAATGCAAATA-AAAAT
1 AA-GAAAATGC-AATAGAAAAT
28305191 AAGAAAAT
1 AAGAAAAT
28305199 TTGAAAGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 1 0.04
20 18 0.75
21 5 0.21
ACGTcount: A:0.65, C:0.04, G:0.15, T:0.17
Consensus pattern (20 bp):
AAGAAAATGCAATAGAAAAT
Found at i:28310365 original size:25 final size:26
Alignment explanation
Indices: 28310337--28310409 Score: 80
Period size: 25 Copynumber: 2.9 Consensus size: 26
28310327 TATCAATTGT
*
28310337 AGCTCATGAGAGCTTACCGATTCT-C
1 AGCTCGTGAGAGCTTACCGATTCTAC
*
28310362 AGCTCGT-ATGAGCTTACTGATT-TAC
1 AGCTCGTGA-GAGCTTACCGATTCTAC
* *
28310387 AGCTCGTGAAAGCATACCGATTC
1 AGCTCGTGAGAGCTTACCGATTC
28310410 AAAGCTTGTG
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
24 2 0.05
25 36 0.92
26 1 0.03
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.29
Consensus pattern (26 bp):
AGCTCGTGAGAGCTTACCGATTCTAC
Found at i:28314533 original size:50 final size:50
Alignment explanation
Indices: 28314333--28314663 Score: 307
Period size: 50 Copynumber: 6.6 Consensus size: 50
28314323 CGATGAACAT
* * * *
28314333 GTGTGTAGTACTGTGTGAAGGCTACTATGTGAATCGATAAA-TGATGGTCAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGA-AAACT-TTGGTCAC
* * * * *
28314384 ATGTGTAGTACTAAGTGAAGGCTAC-A-ATGAATACTGAGAAGCTTTGGTCAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTG-A-ACCGA-AAACTTTGGTCAC
* * ** * *
28314435 GTGTGTAGTACTGTGTGAAGGCTACTACGTAAATTGATAAA-TGATGGTCAT
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGA-AAACT-TTGGTCAC
* * * *
28314486 ATGT-TAGTACTAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAAAA-CTTTGGTCAC
*
28314536 GTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAAC-TTGATCAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-AAAACTTTGGTCAC
* * *
28314586 GTGTGTAGTACTATGTGAAGGCTACTACGTGAACTGTAAAAC-TTGATCAT
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-AAAACTTTGGTCAC
*
28314636 GTGTGTAGTACTATGTAAAGGCTACTAC
1 GTGTGTAGTACTATGTGAAGGCTACTAC
28314664 ATGTATCGAA
Statistics
Matches: 233, Mismatches: 37, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
49 5 0.02
50 119 0.51
51 101 0.43
52 7 0.03
53 1 0.00
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.31
Consensus pattern (50 bp):
GTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAAAACTTTGGTCAC
Found at i:28314544 original size:101 final size:102
Alignment explanation
Indices: 28314333--28314672 Score: 418
Period size: 101 Copynumber: 3.4 Consensus size: 102
28314323 CGATGAACAT
* *
28314333 GTGTGTAGTACTGTGTGAAGGCTACTATGTGAATCGATAAATGATGGTCACATGTGTAGTACTAA
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAA
* ** *
28314398 GTGAAGGCTACAATGAATACTGAGAAGCTTTGGTCAC
66 GTGAAGGCTACTATGTGTACTGAAAAGCTTTGGTCAC
* * * *
28314435 GTGTGTAGTACTGTGTGAAGGCTACTACGTAAATTGATAAATGATGGTCATATGT-TAGTACTAA
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAA
*
28314499 GTGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCAC
66 GTGAAGGCTACTATGTGTACTGAAAAGCTTTGGTCAC
* *** * * *
28314536 GTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGATCACGTGTGTAGTACTAT
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAA
* * * *
28314600 GTGAAGGCTACTACGTGAACTGTAAAA-C-TTGATCAT
66 GTGAAGGCTACTATGTGTACTG-AAAAGCTTTGGTCAC
* * *
28314636 GTGTGTAGTACTATGTAAAGGCTACTACATGTATCGA
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
28314673 ATGATAAAAG
Statistics
Matches: 206, Mismatches: 29, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
100 50 0.24
101 101 0.49
102 55 0.27
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.31
Consensus pattern (102 bp):
GTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAA
GTGAAGGCTACTATGTGTACTGAAAAGCTTTGGTCAC
Found at i:28329625 original size:52 final size:52
Alignment explanation
Indices: 28329474--28329626 Score: 270
Period size: 52 Copynumber: 2.9 Consensus size: 52
28329464 TGAATAATTA
* * *
28329474 TCTTTCACTTTATAAAAGCAGATTCCCTCTTATCTGCTCGTTTAGCTGTATG
1 TCTTTCAATTTGTAAAAGCAGATTCCCTCTTATCTGCTCGTTTAGCTTTATG
28329526 TCTTTCAATTTGTAAAAGCAGATTCCCTCTTATCTGCTCGTTTAGCTTTATG
1 TCTTTCAATTTGTAAAAGCAGATTCCCTCTTATCTGCTCGTTTAGCTTTATG
*
28329578 TCTTTCATTTTGTAAAAGCAGATTCCCTCTTATCTGCTCGTTTAGCTTT
1 TCTTTCAATTTGTAAAAGCAGATTCCCTCTTATCTGCTCGTTTAGCTTT
28329627 TATCCCCTAT
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 97 1.00
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.44
Consensus pattern (52 bp):
TCTTTCAATTTGTAAAAGCAGATTCCCTCTTATCTGCTCGTTTAGCTTTATG
Found at i:28339170 original size:50 final size:50
Alignment explanation
Indices: 28339048--28339286 Score: 268
Period size: 50 Copynumber: 4.8 Consensus size: 50
28339038 TAATAACATA
* ** * * *
28339048 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGATTTTTCTTGTAC--TG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGGTG
* * ** *
28339097 CCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* ** *
28339147 CCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGATG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* * *
28339197 CCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTTATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
*
28339247 CCAACT-CCATGTCCTAGACATGGTCTTACATGGGACCTCT
1 CCAA-TGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
28339287 TTACCCAAAT
Statistics
Matches: 161, Mismatches: 26, Indels: 5
0.84 0.14 0.03
Matches are distributed among these distances:
48 1 0.01
49 38 0.24
50 122 0.76
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
Found at i:28347784 original size:75 final size:75
Alignment explanation
Indices: 28347704--28347845 Score: 225
Period size: 75 Copynumber: 1.9 Consensus size: 75
28347694 GGAAAATCAT
* * *
28347704 GATTATTCCCTTATTAATAGAGAA-GGCAAATGGAAAGTTA-GAAAAGTGAATTATATTCTTTCC
1 GATTATTCCCTTATTAATAGAAAATAG-AAATGAAAAGTTAGGAAAAG-GAATTATATTCTTTCC
28347767 AAAAGAATATAG
64 AAAAGAATATAG
28347779 GATTATTCCCTTATTAATAGAAAATAGAAATGAAAAGTTAGGAAAAGGAATTATATTCTTTCCAA
1 GATTATTCCCTTATTAATAGAAAATAGAAATGAAAAGTTAGGAAAAGGAATTATATTCTTTCCAA
28347844 AA
66 AA
28347846 AAATTAATTT
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
75 55 0.89
76 7 0.11
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.31
Consensus pattern (75 bp):
GATTATTCCCTTATTAATAGAAAATAGAAATGAAAAGTTAGGAAAAGGAATTATATTCTTTCCAA
AAGAATATAG
Done.