Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 159 of 433
Found at i:49548701 original size:28 final size:28
Alignment explanation
Indices: 49548654--49548718 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
49548644 AAATTAACCC
* *
49548654 TAGGGGTATAAAGGTCATTTTGCATATA
1 TAGGGGTATAAAGGTAATTTTGCATACA
* *
49548682 TAGGGGTATAATGGTAATTTTTCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
49548710 TAGGGGTAT
1 TAGGGGTAT
49548719 TCTAGTACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.37
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTTGCATACA
Found at i:49550533 original size:2 final size:2
Alignment explanation
Indices: 49550526--49550555 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
49550516 GAATCATCTC
49550526 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49550556 CACAATTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49558461 original size:37 final size:37
Alignment explanation
Indices: 49558411--49558484 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
49558401 ACCCTCAAAG
49558411 ATAGCGCCCTAAATCTAGACCCTCCCCTATCGTTAGC
1 ATAGCGCCCTAAATCTAGACCCTCCCCTATCGTTAGC
49558448 ATAGCGCCCTAAATCTAGACCCTCCCCTATCGTTAGC
1 ATAGCGCCCTAAATCTAGACCCTCCCCTATCGTTAGC
49558485 CTAAAATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.38, G:0.14, T:0.24
Consensus pattern (37 bp):
ATAGCGCCCTAAATCTAGACCCTCCCCTATCGTTAGC
Found at i:49559531 original size:5 final size:5
Alignment explanation
Indices: 49559521--49559546 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
49559511 GAAGAAGATA
49559521 TTAAT TTAAT TTAAT TTAAT TTAAT T
1 TTAAT TTAAT TTAAT TTAAT TTAAT T
49559547 ACCAACTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTAAT
Found at i:49566480 original size:39 final size:40
Alignment explanation
Indices: 49566433--49566576 Score: 175
Period size: 39 Copynumber: 3.6 Consensus size: 40
49566423 AATGTTCGAG
49566433 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA
* * *
49566472 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCAAATTG
1 TGATATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA
* ** *
49566511 TGATATCCGGGTTAAGTCCCGAAGGCCTTTGTGCGGGTTA
1 TGATATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA
** * *
49566551 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAGTCCCGAAGGC
49566577 GTTTGAACGA
Statistics
Matches: 89, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
39 51 0.57
40 38 0.43
ACGTcount: A:0.24, C:0.23, G:0.30, T:0.24
Consensus pattern (40 bp):
TGATATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA
Found at i:49569611 original size:43 final size:43
Alignment explanation
Indices: 49569550--49569634 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
49569540 TGTACAACAA
*
49569550 GTACATAACCAATGACTTTTCATACATAGTTTTCTCTCTTGCG
1 GTACATAACCAATGACTTTTCATACATAATTTTCTCTCTTGCG
*
49569593 GTACATAACCAATTACTTTTCATACATAATTTTCTCTCTTGC
1 GTACATAACCAATGACTTTTCATACATAATTTTCTCTCTTGC
49569635 AAGTTCTCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.27, C:0.24, G:0.08, T:0.41
Consensus pattern (43 bp):
GTACATAACCAATGACTTTTCATACATAATTTTCTCTCTTGCG
Found at i:49570854 original size:6 final size:6
Alignment explanation
Indices: 49570836--49570865 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
49570826 GATTTTTCGT
49570836 ATACAG A-ACAG ATACAG ATACAG ATACAG A
1 ATACAG ATACAG ATACAG ATACAG ATACAG A
49570866 CATAAATTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.53, C:0.17, G:0.17, T:0.13
Consensus pattern (6 bp):
ATACAG
Found at i:49574483 original size:44 final size:44
Alignment explanation
Indices: 49574435--49574523 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
49574425 TTTGAATAAA
49574435 TAATAGGTTTTATTAAGTTTTGAAACATAATTTCTTGTATGACT
1 TAATAGGTTTTATTAAGTTTTGAAACATAATTTCTTGTATGACT
49574479 TAATAGGTTTTATTAAGTTTTGAAACATAATTTCTTGTATGACT
1 TAATAGGTTTTATTAAGTTTTGAAACATAATTTCTTGTATGACT
49574523 T
1 T
49574524 GTCTTTTAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.48
Consensus pattern (44 bp):
TAATAGGTTTTATTAAGTTTTGAAACATAATTTCTTGTATGACT
Found at i:49575418 original size:11 final size:11
Alignment explanation
Indices: 49575402--49575431 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
49575392 TTTAATGAGA
49575402 TATTTTATTAT
1 TATTTTATTAT
49575413 TATTTTATTAT
1 TATTTTATTAT
49575424 TATTTTAT
1 TATTTTAT
49575432 CTAGTATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:49577467 original size:33 final size:33
Alignment explanation
Indices: 49577399--49577470 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
49577389 TTATATGTAG
* *
49577399 GACCATAACTGGGCTATGGCATTTTAATGAAAA
1 GACCATAACTGGGCTATGGCATTTGAACGAAAA
* *
49577432 GACCATAACTGGGTTATGGCACTTTGAACG-TAA
1 GACCATAACTGGGCTATGGCA-TTTGAACGAAAA
49577465 GACCAT
1 GACCAT
49577471 GGTTGGACCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 28 0.82
34 6 0.18
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.26
Consensus pattern (33 bp):
GACCATAACTGGGCTATGGCATTTGAACGAAAA
Found at i:49577551 original size:103 final size:102
Alignment explanation
Indices: 49577327--49577588 Score: 303
Period size: 103 Copynumber: 2.6 Consensus size: 102
49577317 GAATTGACGG
* * * * * *
49577327 ATAAGACCATAACTGGGTTATGGAACTATGAACATAATACCATGATTGGACCATGGTAGTGTTTA
1 ATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAGTATTTA
* * * *
49577392 TATGTAGGACCATAACTGGGCTATGGCATTTTAATGA
66 TATGTAAGACCATAACTAGGCTATGACATTCTAATGA
*
49577429 A-AAGACCATAACTGGGTTATGGCACTTTGAACGTAAGACCATGGTTGGACCATGGCAGTATATA
1 ATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAGTAT-T-
* * *
49577493 TATGTGTAAGACCATAGCTAGGCTATGACATTCTGAT-A
64 TATATGTAAGACCATAACTAGGCTATGACATTCTAATGA
* * * * * * *
49577531 ATAAGACCATAATTGAGTTATGGCGCTACGAATGTAAGACCATGGTAGGGCCATGGCA
1 ATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCA
49577589 TAGCATGTGT
Statistics
Matches: 135, Mismatches: 22, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
101 53 0.39
102 4 0.03
103 78 0.58
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (102 bp):
ATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAGTATTTA
TATGTAAGACCATAACTAGGCTATGACATTCTAATGA
Found at i:49577757 original size:2 final size:2
Alignment explanation
Indices: 49577750--49577775 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
49577740 CATGAAATGA
49577750 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
49577776 CTTGATATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49580002 original size:25 final size:25
Alignment explanation
Indices: 49579949--49580052 Score: 95
Period size: 25 Copynumber: 4.2 Consensus size: 25
49579939 GACACACCAT
***
49579949 AGCTTGT-ATGAGCTTACCGATTTGT
1 AGCTTGTGA-GAGCTTACCGATTCAC
* * *
49579974 AGCTCGTGAGAGCTTACCTATTCTC
1 AGCTTGTGAGAGCTTACCGATTCAC
49579999 AGCTTGT-ATGAGCTTACCGATTCAC
1 AGCTTGTGA-GAGCTTACCGATTCAC
* * *
49580024 AGCTTGTGAGAGCATACTGATTCAT
1 AGCTTGTGAGAGCTTACCGATTCAC
49580049 AGCT
1 AGCT
49580053 CGAATGAGCA
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
24 1 0.02
25 62 0.95
26 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (25 bp):
AGCTTGTGAGAGCTTACCGATTCAC
Found at i:49580060 original size:50 final size:50
Alignment explanation
Indices: 49579946--49580061 Score: 137
Period size: 50 Copynumber: 2.3 Consensus size: 50
49579936 GCGGACACAC
*** *
49579946 CATAGCTTGTATGAGCTTACCGATTTGTAGCTCGTGAGAGCTTACCTATT
1 CATAGCTTGTATGAGCTTACCGATTCACAGCTCGTGAGAGCATACCTATT
*
49579996 C-TCAGCTTGTATGAGCTTACCGATTCACAGCTTGTGAGAGCATA-CTGATT
1 CAT-AGCTTGTATGAGCTTACCGATTCACAGCTCGTGAGAGCATACCT-ATT
* *
49580046 CATAGCTCGAATGAGC
1 CATAGCTTGTATGAGC
49580062 ATACATGTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
49 3 0.05
50 52 0.93
51 1 0.02
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (50 bp):
CATAGCTTGTATGAGCTTACCGATTCACAGCTCGTGAGAGCATACCTATT
Found at i:49585811 original size:32 final size:32
Alignment explanation
Indices: 49585770--49585833 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
49585760 TGTCCCGAGA
49585770 TCCTGCATGTGTTGCAGAAAAGGATTTAGCCC
1 TCCTGCATGTGTTGCAGAAAAGGATTTAGCCC
49585802 TCCTGCATGTGTTGCAGAAAAGGATTTAGCCC
1 TCCTGCATGTGTTGCAGAAAAGGATTTAGCCC
49585834 GAACGGGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (32 bp):
TCCTGCATGTGTTGCAGAAAAGGATTTAGCCC
Found at i:49599321 original size:46 final size:44
Alignment explanation
Indices: 49599218--49599525 Score: 296
Period size: 46 Copynumber: 6.7 Consensus size: 44
49599208 ACATAATCGT
* *
49599218 GCCGATGTCATGTCCCAGACATGGTCTTACACTGACACATCTCGTA-
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCATATCTCG-AG
* * *
49599264 GCTGATGCATGTCCCAAACATGTCTTACACTGGCTTATGTCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGC--ATATCTCGAG
* *
49599310 GCCGATGCATGTCCCAGACATGGTCTTACACTGACACATCTCGCA-
1 GCCGATGCATGTCCCAGACAT-GTCTTACACTGGCATATCTCG-AG
* * *
49599355 GCTGATGCATGTCCCAAACATGTCTTACACTGGCTTATGTCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGC--ATATCTCGAG
* * *
49599401 GCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCGAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCA-T-ATCTCGAG
* * * * *
49599447 GCCGATGCCACGTCCCAGACATGGTCTTACACTGGCTCTCATATTGTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGC-AT-ATCTCGAG
*
49599495 GCCGATGCATGTCCCAGACATGTTTTACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
49599526 AGCTCACACA
Statistics
Matches: 220, Mismatches: 29, Indels: 26
0.80 0.11 0.09
Matches are distributed among these distances:
44 25 0.11
45 41 0.19
46 92 0.42
47 38 0.17
48 24 0.11
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (44 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCATATCTCGAG
Found at i:49599328 original size:91 final size:89
Alignment explanation
Indices: 49599218--49599525 Score: 422
Period size: 91 Copynumber: 3.3 Consensus size: 89
49599208 ACATAATCGT
49599218 GCCGATGTCATGTCCCAGACATGGTCTTACACTGACACATCTCGTAGCTGATGCATGTCCCAAAC
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGACACATCTCG-AGCTGATGCATGTCCCAAAC
49599283 ATGTCTTACACTGGCTTATGTCTCGAG
63 ATGTCTTACACTGGCTTATGTCTCGAG
49599310 GCCGATGCATGTCCCAGACATGGTCTTACACTGACACATCTCGCAGCTGATGCATGTCCCAAACA
1 GCCGATGCATGTCCCAGACAT-GTCTTACACTGACACATCTCG-AGCTGATGCATGTCCCAAACA
49599375 TGTCTTACACTGGCTTATGTCTCGAG
64 TGTCTTACACTGGCTTATGTCTCGAG
* * * * *
49599401 GCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCGATGCCGATGCCACGTCCCAGA
1 GCCGATGCATGTCCCAGACATGTCTTACACT-G-ACACATCTCGA-GCTGATG-CATGTCCCAAA
* *
49599466 CATGGTCTTACACTGGCTCTCATAT-T-GTG
62 CAT-GTCTTACACTGGCT-T-ATGTCTCGAG
*
49599495 GCCGATGCATGTCCCAGACATGTTTTACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
49599526 AGCTCACACA
Statistics
Matches: 200, Mismatches: 9, Indels: 12
0.90 0.04 0.05
Matches are distributed among these distances:
90 10 0.05
91 106 0.53
92 21 0.10
93 12 0.06
94 46 0.23
95 2 0.01
96 3 0.01
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (89 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGACACATCTCGAGCTGATGCATGTCCCAAACATG
TCTTACACTGGCTTATGTCTCGAG
Found at i:49599422 original size:137 final size:140
Alignment explanation
Indices: 49599121--49599480 Score: 380
Period size: 137 Copynumber: 2.6 Consensus size: 140
49599111 GGTAAGGTGT
* * * * **
49599121 CGATGCCATGTCCTAGACATGGTCTTACACTGG-TTATCATCTTCAAGGTCGATGCCATGTCCTG
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTATCGTC-TCGAGGCCGATGCCATGTCCCA
* * *
49599185 GACATGGTCTTACACTAGCTTTCACATAATCGTGCCGATGTCATGTCCCAGACATGGTCTTACAC
63 GACATGGTCTTACACT-G--TACACATAATCGAGCCGATGTCATGTCCCAAACATGGTCTTACAC
49599250 TGACACATCTCGTAGC
125 TGACACATCTCGTAGC
* *
49599266 TGATGCATGTCCCAAACATGTCTTACACTGGCTTAT-GTCTCGAGGCCGATG-CATGTCCCAGAC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTTATCGTCTCGAGGCCGATGCCATGTCCCAGAC
* * *
49599329 ATGGTCTTACACTG-ACACAT-CTCGCAGCTGATG-CATGTCCCAAACAT-GTCTTACACTGGCT
66 ATGGTCTTACACTGTACACATAATCG-AGCCGATGTCATGTCCCAAACATGGTCTTACACTGAC-
**
49599390 TATGTCTCG-AGGC
129 -ACATCTCGTA-GC
* * *
49599403 CGATGCATGTCCCAGACATGTCTTACACTAGC--ACTCGTCTCGATGCCGATGCCACGTCCCAGA
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTTA-TCGTCTCGAGGCCGATGCCATGTCCCAGA
49599466 CATGGTCTTACACTG
65 CATGGTCTTACACTG
49599481 GCTCTCATAT
Statistics
Matches: 186, Mismatches: 21, Indels: 23
0.81 0.09 0.10
Matches are distributed among these distances:
135 13 0.07
136 18 0.10
137 62 0.33
138 25 0.13
140 1 0.01
141 23 0.12
142 10 0.05
143 14 0.08
144 16 0.09
145 4 0.02
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.28
Consensus pattern (140 bp):
CGATGCATGTCCCAGACATGTCTTACACTGGCTTATCGTCTCGAGGCCGATGCCATGTCCCAGAC
ATGGTCTTACACTGTACACATAATCGAGCCGATGTCATGTCCCAAACATGGTCTTACACTGACAC
ATCTCGTAGC
Found at i:49599886 original size:30 final size:30
Alignment explanation
Indices: 49599850--49599907 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
49599840 AAATTTACAC
*
49599850 CTTTGGTAAAATGACCATTTTGCCCCTAGA
1 CTTTGGTAAAATGACAATTTTGCCCCTAGA
49599880 CTTTGGTAAAATGACAATTTTGCCCCTA
1 CTTTGGTAAAATGACAATTTTGCCCCTA
49599908 TGCTCGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (30 bp):
CTTTGGTAAAATGACAATTTTGCCCCTAGA
Found at i:49601621 original size:108 final size:109
Alignment explanation
Indices: 49601392--49601621 Score: 318
Period size: 108 Copynumber: 2.1 Consensus size: 109
49601382 GGCGTGTGGT
**
49601392 TTGGCCGTGTGACCCAAGTTAGGGAGTTACACGGGCACAGACACAGTCTAGGACACGACCGTGTG
1 TTGGCCGTGTGACCCAAGTTAGGGAGTTACAAAGGCACAGA-ACAGTCTAGGACACGACCGTGTG
* ** *
49601457 TCTCAATTTTGAATGTCCATATTGCCTAAGACACGAGCATGTGGC
65 TCTCAATTTTGAATGTCCACACGGCCTAAGACACGAGCATGTCGC
* * * * *
49601502 TCGGCCATGTGACCCAAGTTAGGGAGTTACAAAGGCACAG-ACAGTCTGGGACATGGCCGTGTGT
1 TTGGCCGTGTGACCCAAGTTAGGGAGTTACAAAGGCACAGAACAGTCTAGGACACGACCGTGTGT
* * *
49601566 CTCTATTTTGAATGTCCACACGGCCTAAGACACGAGCGTGTCTC
66 CTCAATTTTGAATGTCCACACGGCCTAAGACACGAGCATGTCGC
49601610 TTGGCCGTGTGA
1 TTGGCCGTGTGA
49601622 GTCACACGGC
Statistics
Matches: 104, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
108 68 0.65
110 36 0.35
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (109 bp):
TTGGCCGTGTGACCCAAGTTAGGGAGTTACAAAGGCACAGAACAGTCTAGGACACGACCGTGTGT
CTCAATTTTGAATGTCCACACGGCCTAAGACACGAGCATGTCGC
Found at i:49603255 original size:9 final size:9
Alignment explanation
Indices: 49603230--49603355 Score: 58
Period size: 9 Copynumber: 13.3 Consensus size: 9
49603220 ATTATGATAT
49603230 AATTTTTTAA
1 AATTTTTT-A
*
49603240 AAATTTTTA
1 AATTTTTTA
*
49603249 ACTTTTTTA
1 AATTTTTTA
49603258 TATATTTTTTA
1 -A-ATTTTTTA
49603269 AATTTTTTGA
1 AATTTTTT-A
**
49603279 AA-AATTTA
1 AATTTTTTA
49603287 TAATATTTTTA
1 -AAT-TTTTTA
*** *
49603298 AAAAATATA
1 AATTTTTTA
*
49603307 AA-TTTTGA
1 AATTTTTTA
49603315 AATTTTTATA
1 AATTTTT-TA
*
49603325 AATATTTTA
1 AATTTTTTA
**
49603334 AATTTTAAA
1 AATTTTTTA
49603343 AATTATTTTA
1 AATT-TTTTA
49603353 AAT
1 AAT
49603356 ATTTGAAAAT
Statistics
Matches: 84, Mismatches: 23, Indels: 18
0.67 0.18 0.14
Matches are distributed among these distances:
8 5 0.06
9 41 0.49
10 27 0.32
11 11 0.13
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.55
Consensus pattern (9 bp):
AATTTTTTA
Found at i:49603256 original size:19 final size:18
Alignment explanation
Indices: 49603229--49603301 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 18
49603219 TATTATGATA
49603229 TAATTTTTTAAAAATTTT
1 TAATTTTTTAAAAATTTT
* *
49603247 TAACTTTTTTATATATTTTT
1 TAA-TTTTTTA-AAAATTTT
*
49603267 TAAATTTTTTGAAAAATTTA
1 T-AATTTTTT-AAAAATTTT
49603287 TAATATTTTTAAAAA
1 TAAT-TTTTTAAAAA
49603302 ATATAAATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
18 3 0.07
19 15 0.33
20 24 0.53
21 3 0.07
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (18 bp):
TAATTTTTTAAAAATTTT
Found at i:49603286 original size:18 final size:18
Alignment explanation
Indices: 49603265--49603312 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 18
49603255 TTATATATTT
*
49603265 TTTAAATTTTTTGAAAAA
1 TTTAAATTTTTTAAAAAA
49603283 TTTATAATATTTTTAAAAAA
1 TTTA-AAT-TTTTTAAAAAA
*
49603303 TATAAATTTT
1 TTTAAATTTT
49603313 GAAATTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 7 0.27
19 6 0.23
20 13 0.50
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TTTAAATTTTTTAAAAAA
Found at i:49603338 original size:19 final size:19
Alignment explanation
Indices: 49603303--49603355 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
49603293 TTTTAAAAAA
*
49603303 TATAAAT-TTTGAAATTTT
1 TATAAATATTTTAAATTTT
49603321 TATAAATATTTTAAA-TTT
1 TATAAATATTTTAAATTTT
*
49603339 TAAAAATTATTTTAAAT
1 TATAAA-TATTTTAAAT
49603356 ATTTGAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 15 0.50
19 15 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TATAAATATTTTAAATTTT
Found at i:49603340 original size:18 final size:18
Alignment explanation
Indices: 49603303--49603355 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
49603293 TTTTAAAAAA
*
49603303 TATAAAT-TTTGAAATTTT
1 TATAAATATTTTAAA-TTT
49603321 TATAAATATTTTAAATTT
1 TATAAATATTTTAAATTT
*
49603339 TAAAAATTATTTTAAAT
1 TATAAA-TATTTTAAAT
49603356 ATTTGAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 15 0.48
19 16 0.52
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
TATAAATATTTTAAATTT
Found at i:49603354 original size:28 final size:27
Alignment explanation
Indices: 49603305--49603359 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
49603295 TTAAAAAATA
* *
49603305 TAAATTTTGAAATTTTTATAAATATTT
1 TAAATTTTAAAATTATTATAAATATTT
*
49603332 TAAATTTTAAAAATTATTTTAAATATTT
1 TAAATTTT-AAAATTATTATAAATATTT
49603360 GAAAATTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (27 bp):
TAAATTTTAAAATTATTATAAATATTT
Found at i:49603366 original size:20 final size:19
Alignment explanation
Indices: 49603308--49603371 Score: 76
Period size: 20 Copynumber: 3.3 Consensus size: 19
49603298 AAAAATATAA
*
49603308 ATTTTGAAATTTTTATAAA-T
1 ATTTT-AAA-TTTTAAAAATT
49603328 ATTTTAAATTTTAAAAATT
1 ATTTTAAATTTTAAAAATT
*
49603347 ATTTTAAATATTTGAAAATT
1 ATTTTAAAT-TTTAAAAATT
49603367 ATTTT
1 ATTTT
49603372 GAACTTTGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.20
19 13 0.32
20 19 0.47
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
ATTTTAAATTTTAAAAATT
Found at i:49603628 original size:3 final size:3
Alignment explanation
Indices: 49603620--49603659 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
49603610 ACTTTTAAAA
*
49603620 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAA AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
49603660 CCAAGTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:49614168 original size:22 final size:22
Alignment explanation
Indices: 49614143--49614190 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
49614133 AAATCTATAA
49614143 AATTAAAAAAGAA-AAACGAATC
1 AATTAAAAAAGAATAAA-GAATC
* **
49614165 AATTCAAAATTAATAAAGAATC
1 AATTAAAAAAGAATAAAGAATC
49614187 AATT
1 AATT
49614191 CATTATCAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.62, C:0.08, G:0.06, T:0.23
Consensus pattern (22 bp):
AATTAAAAAAGAATAAAGAATC
Found at i:49614201 original size:22 final size:22
Alignment explanation
Indices: 49614160--49614202 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
49614150 AAAGAAAAAC
*
49614160 GAATCAATTCAAAATTAATAAA
1 GAATCAATTCAAAATCAATAAA
**
49614182 GAATCAATTCATTATCAATAA
1 GAATCAATTCAAAATCAATAA
49614203 TTCAACATGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.30
Consensus pattern (22 bp):
GAATCAATTCAAAATCAATAAA
Found at i:49615495 original size:4 final size:4
Alignment explanation
Indices: 49615488--49615519 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
49615478 TATATATATA
49615488 TATT TATT TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT
49615520 CAAAGATCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:49616446 original size:16 final size:16
Alignment explanation
Indices: 49616425--49616461 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
49616415 CGCCCTCAAC
*
49616425 CTCCATCGACTTGGAG
1 CTCCATCGACCTGGAG
49616441 CTCCATCGACCTGGAG
1 CTCCATCGACCTGGAG
49616457 C-CCAT
1 CTCCAT
49616462 ATCGAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.19, C:0.38, G:0.22, T:0.22
Consensus pattern (16 bp):
CTCCATCGACCTGGAG
Found at i:49617067 original size:38 final size:40
Alignment explanation
Indices: 49616997--49617072 Score: 129
Period size: 38 Copynumber: 1.9 Consensus size: 40
49616987 TAAAAATATT
*
49616997 TATATTAAAAAACATTAACATAAATATAATAAATATTTAG
1 TATATTAAAAAACATCAACATAAATATAATAAATATTTAG
49617037 TATATTAAAAAACA-CAA-ATAAATATAATAAATATTT
1 TATATTAAAAAACATCAACATAAATATAATAAATATTT
49617073 CATTGTATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 19 0.54
39 2 0.06
40 14 0.40
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.34
Consensus pattern (40 bp):
TATATTAAAAAACATCAACATAAATATAATAAATATTTAG
Found at i:49618581 original size:3 final size:3
Alignment explanation
Indices: 49618573--49618630 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
49618563 TTTAGGGTTT
49618573 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
49618621 AAG AAG AAG A
1 AAG AAG AAG A
49618631 GAAAAAATGA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:49621430 original size:26 final size:26
Alignment explanation
Indices: 49621399--49621506 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
49621389 TGAAATTCCC
*
49621399 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
49621425 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
49621451 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
49621477 ATCATAGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
49621503 ATCA
1 ATCA
49621507 ATTTGTATCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:49621517 original size:10 final size:10
Alignment explanation
Indices: 49621502--49621526 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
49621492 CCTAACCCAT
49621502 TATCAATTTG
1 TATCAATTTG
49621512 TATCAATTTG
1 TATCAATTTG
49621522 TATCA
1 TATCA
49621527 TAAATTATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (10 bp):
TATCAATTTG
Found at i:49622260 original size:3 final size:3
Alignment explanation
Indices: 49622252--49622296 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
49622242 GAGAGCCAAT
49622252 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
49622297 GTGAAGACAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:49622507 original size:20 final size:20
Alignment explanation
Indices: 49622470--49622509 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
49622460 CAACGTGGTA
*
49622470 AGTTAACTGACCACATCAAC
1 AGTTAACTGACCAAATCAAC
49622490 AGTTAACTTG-CCAAATCAAC
1 AGTTAAC-TGACCAAATCAAC
49622510 GCTCTCGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.40, C:0.28, G:0.10, T:0.23
Consensus pattern (20 bp):
AGTTAACTGACCAAATCAAC
Found at i:49624388 original size:41 final size:40
Alignment explanation
Indices: 49624185--49624393 Score: 226
Period size: 41 Copynumber: 5.1 Consensus size: 40
49624175 TCAAAAATTT
* * * *
49624185 TAAAATACAGAGCAATAGCAGCG-TTTTAAGAAAAACGCCGC
1 TAAAA-ACAGAGCATTAGCGGCGCTTTT-GGTAAAACGCCGC
** * *
49624226 TAAAAACAGAGCAACAGCGGCG-TTTTAGTAAAAAACGTCGC
1 TAAAAACAGAGCATTAGCGGCGCTTTTGGT--AAAACGCCGC
*
49624267 TAAAAACAGAGCATTAGCTGCGCTTTCT-GTAAAACGCCGC
1 TAAAAACAGAGCATTAGCGGCGCTTT-TGGTAAAACGCCGC
* *
49624307 TAAAAACCAGAGCATTAGCGGCACTTTTGATAAAACGCCGC
1 TAAAAA-CAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGC
*
49624348 TAAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAATGCCGC
1 TAAAAA-CAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGC
49624389 TAAAA
1 TAAAA
49624394 GTCATATAAC
Statistics
Matches: 148, Mismatches: 14, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
39 2 0.01
40 35 0.24
41 105 0.71
42 5 0.03
43 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.20
Consensus pattern (40 bp):
TAAAAACAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGC
Found at i:49624830 original size:25 final size:25
Alignment explanation
Indices: 49624801--49624854 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
49624791 GTGATTTTGA
*
49624801 ATGTGGAATTAGCATTTGTTGAACT
1 ATGTGGAATTAGCAATTGTTGAACT
49624826 ATGTGGAATTAGCAATTGTTGAACT
1 ATGTGGAATTAGCAATTGTTGAACT
49624851 ATGT
1 ATGT
49624855 ATAATTTCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.30, C:0.07, G:0.24, T:0.39
Consensus pattern (25 bp):
ATGTGGAATTAGCAATTGTTGAACT
Found at i:49625195 original size:2 final size:2
Alignment explanation
Indices: 49625190--49625216 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
49625180 TATATATATA
49625190 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
49625217 TTTAATTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:49625501 original size:15 final size:15
Alignment explanation
Indices: 49625481--49625512 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
49625471 TTTAATTTAG
*
49625481 AAGATAAATGTATAT
1 AAGATAAATATATAT
49625496 AAGATAAATATATAT
1 AAGATAAATATATAT
49625511 AA
1 AA
49625513 ATTATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.31
Consensus pattern (15 bp):
AAGATAAATATATAT
Found at i:49631009 original size:9 final size:9
Alignment explanation
Indices: 49630995--49631029 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
49630985 AAAGTTCAAA
49630995 TTACATAAC
1 TTACATAAC
49631004 TTACATAA-
1 TTACATAAC
49631012 TCTACATAAC
1 T-TACATAAC
49631022 TTACATAA
1 TTACATAA
49631030 AACATAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 1 0.04
9 22 0.92
10 1 0.04
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (9 bp):
TTACATAAC
Found at i:49632331 original size:22 final size:22
Alignment explanation
Indices: 49632303--49632346 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
49632293 TCCCCGGAGA
49632303 GAAAGGCCCCGGAAATGATATT
1 GAAAGGCCCCGGAAATGATATT
49632325 GAAAGGCCCCGGAAATGATATT
1 GAAAGGCCCCGGAAATGATATT
49632347 AACATATATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.18
Consensus pattern (22 bp):
GAAAGGCCCCGGAAATGATATT
Found at i:49632450 original size:35 final size:35
Alignment explanation
Indices: 49632404--49632477 Score: 130
Period size: 35 Copynumber: 2.1 Consensus size: 35
49632394 GGGTGTTGAG
*
49632404 ACGTATAATGTATTGAGAAAGGATAACTTTTACCT
1 ACGTATAATGTATTGAGAAAGGAGAACTTTTACCT
*
49632439 ACGTATGATGTATTGAGAAAGGAGAACTTTTACCT
1 ACGTATAATGTATTGAGAAAGGAGAACTTTTACCT
49632474 ACGT
1 ACGT
49632478 GCTGCTTTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.32
Consensus pattern (35 bp):
ACGTATAATGTATTGAGAAAGGAGAACTTTTACCT
Found at i:49636546 original size:21 final size:21
Alignment explanation
Indices: 49636522--49636569 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
49636512 TCAATTTGGA
49636522 GCGGAGGCAGCAGCGAGGGAG
1 GCGGAGGCAGCAGCGAGGGAG
49636543 GCGGAGGCAGCAGCGAGGGAG
1 GCGGAGGCAGCAGCGAGGGAG
*
49636564 GTGGAG
1 GCGGAG
49636570 CAGAACAGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.17, G:0.58, T:0.02
Consensus pattern (21 bp):
GCGGAGGCAGCAGCGAGGGAG
Found at i:49636942 original size:43 final size:43
Alignment explanation
Indices: 49636862--49637063 Score: 223
Period size: 43 Copynumber: 4.7 Consensus size: 43
49636852 ACTGGGCAAA
*
49636862 TTAGCGGCATTTTTTAAAAAAGCGCCGCTAAAA-TACATGTCT
1 TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTACATGTCT
* *
49636904 TTAGCAGCGTTTTTTAAAAAAGCACCGCTAAAAGTACATGTCT
1 TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTACATGTCT
* * * * * *
49636947 CTAGCAGCGTTTTTTATAGAAGCGCCGCTAAAGGT-CCTGGTCT
1 TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTACAT-GTCT
* * **
49636990 ATAGCGGCACTTTTTT-AAAAAGCGCTACTAAAAGTACATGTCT
1 TTAGCGGC-GTTTTTTAAAAAAGCGCCGCTAAAAGTACATGTCT
**
49637033 TTAGCGGCG-TTTTTATGAAAGCGCCGCTAAA
1 TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAA
49637064 GGTCCTGGTC
Statistics
Matches: 131, Mismatches: 24, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
41 5 0.04
42 44 0.34
43 74 0.56
44 8 0.06
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (43 bp):
TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTACATGTCT
Found at i:49637021 original size:86 final size:86
Alignment explanation
Indices: 49636913--49637074 Score: 247
Period size: 86 Copynumber: 1.9 Consensus size: 86
49636903 TTTAGCAGCG
*
49636913 TTTTTTAAAAAAGCACCGCTAAAAGTACATGTCTCTAGCAGCGTTTTTTAT-AGAAGCGCCGCTA
1 TTTTTTAAAAAAGCACCACTAAAAGTACATGTCTCTAGCAGCG-TTTTTATGA-AAGCGCCGCTA
49636977 AAGGTCCTGGTCTATAGCGGCAC
64 AAGGTCCTGGTCTATAGCGGCAC
* * * *
49637000 TTTTTT-AAAAAGCGCTACTAAAAGTACATGTCTTTAGCGGCGTTTTTATGAAAGCGCCGCTAAA
1 TTTTTTAAAAAAGCACCACTAAAAGTACATGTCTCTAGCAGCGTTTTTATGAAAGCGCCGCTAAA
49637064 GGTCCTGGTCT
66 GGTCCTGGTCT
49637075 TTAACGGCGC
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
85 31 0.45
86 32 0.46
87 6 0.09
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (86 bp):
TTTTTTAAAAAAGCACCACTAAAAGTACATGTCTCTAGCAGCGTTTTTATGAAAGCGCCGCTAAA
GGTCCTGGTCTATAGCGGCAC
Found at i:49639642 original size:33 final size:33
Alignment explanation
Indices: 49639603--49639672 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
49639593 ACAAACATAC
*
49639603 AAAGTAATACTTAAATAATGCATGATATACAAA
1 AAAGTAATAATTAAATAATGCATGATATACAAA
49639636 AAAGTAATAATTAAATAATGCATGATATACAAA
1 AAAGTAATAATTAAATAATGCATGATATACAAA
49639669 AAAG
1 AAAG
49639673 AGTAATACAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.57, C:0.07, G:0.10, T:0.26
Consensus pattern (33 bp):
AAAGTAATAATTAAATAATGCATGATATACAAA
Found at i:49639894 original size:21 final size:21
Alignment explanation
Indices: 49639856--49639910 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
49639846 TTTGCTATAC
*
49639856 AATATATA-AAACATAATAACA
1 AATATATATAAA-AGAATAACA
* *
49639877 AATATTTATAAAAGAATAATA
1 AATATATATAAAAGAATAACA
*
49639898 ATTATATATAAAA
1 AATATATATAAAA
49639911 TATATGGGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.31
Consensus pattern (21 bp):
AATATATATAAAAGAATAACA
Found at i:49640347 original size:19 final size:19
Alignment explanation
Indices: 49640289--49640351 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 19
49640279 ATGTAAAAAC
49640289 AATATATATAAATAAT-TAATA
1 AATATA-AT-AATAATATAA-A
49640310 AATAT-ATAATACA-AGTAAA
1 AATATAATAATA-ATA-TAAA
49640329 AATATAATAATAATATAAA
1 AATATAATAATAATATAAA
49640348 AATA
1 AATA
49640352 ATGATGTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
18 4 0.11
19 18 0.49
20 10 0.27
21 5 0.14
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (19 bp):
AATATAATAATAATATAAA
Found at i:49640372 original size:21 final size:20
Alignment explanation
Indices: 49640343--49640396 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
49640333 TAATAATAAT
*
49640343 ATAAAAATAATGATGT-AAATA
1 ATAATAATAAT-ATGTGAAA-A
*
49640364 ATAATAATAATTTGTGAAAA
1 ATAATAATAATATGTGAAAA
49640384 ATAATAAATAATA
1 ATAAT-AATAATA
49640397 AATAATATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.31
Consensus pattern (20 bp):
ATAATAATAATATGTGAAAA
Found at i:49640483 original size:2 final size:2
Alignment explanation
Indices: 49640478--49640522 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
49640468 AATATATGAA
* *
49640478 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT A- AT AA AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49640518 AT AT A
1 AT AT A
49640523 GGGCTAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:49642453 original size:205 final size:205
Alignment explanation
Indices: 49642101--49642604 Score: 855
Period size: 205 Copynumber: 2.5 Consensus size: 205
49642091 AAATCTGCTT
* * * *
49642101 CTTCGATTTGTTCTCTAACAATACAGAGATGACAAATCATCTTAGATTTGCTTCAGCATAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACAC
* * *
49642166 GTGAAAGCCAAATCAACTATGTCTTCGATTTGCTCTTTGTAAGCACAAGGATGACAAATCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGACAAACCATCTT
*
49642231 GGATATGCTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTCTGCCATCCGTCGAAGTGA
131 GGATATACTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTCTGCCATCCGTCGAAGTGA
49642296 AGATGCCAGA
196 AGATGCCAGA
* *
49642306 CTTCGATTTGTTCTCTGACAATATAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACAC
* * *
49642371 ATGAAAGCCAAATCAGCTATGTCTTTGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGACAAACCATCTT
* * * *
49642436 GGATCTACTTCAGTATAAACATCTGAAGTTTGGATCTGCTATGTGTCTGCCCTCCGTCGAAGTGG
131 GGATATACTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTCTGCCATCCGTCGAAGTGA
49642501 AGATGCCAGA
196 AGATGCCAGA
49642511 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACAC
49642576 GTGAAAGCCAAATCAGCTATGTCTTCGAT
66 GTGAAAGCCAAATCAGCTATGTCTTCGAT
49642605 CTACAGAGAT
Statistics
Matches: 278, Mismatches: 21, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
205 278 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (205 bp):
CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACAC
GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGACAAACCATCTT
GGATATACTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTCTGCCATCCGTCGAAGTGA
AGATGCCAGA
Found at i:49642787 original size:44 final size:43
Alignment explanation
Indices: 49642758--49642932 Score: 129
Period size: 44 Copynumber: 4.0 Consensus size: 43
49642748 TCAGATCTGT
49642758 TATCTTTGATCTGTTCCCTATAAACACAGGGATGCCAAATCTTC
1 TATC-TTGATCTGTTCCCTATAAACACAGGGATGCCAAATCTTC
* * **
49642802 TATCTTCAACTTGTTCCCTATAAACACAGGGATGCC--ATGCTGA
1 TATCTTGATC-TGTTCCCTATAAACACAGGGATGCCAAAT-CTTC
* ** * * * * * * * *
49642845 AATCCTCAATCTGGTTCGCTGTAAGCAGAGGAATGTCAGATCTGC
1 TAT-CTTGATCT-GTTCCCTATAAACACAGGGATGCCAAATCTTC
* *
49642890 TATCTCCGATCTGTTCCCTATAAACAAAGGGATGCCAAATCTT
1 TATCT-TGATCTGTTCCCTATAAACACAGGGATGCCAAATCTT
49642933 GTTTCTTTGA
Statistics
Matches: 99, Mismatches: 25, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
42 2 0.02
43 9 0.09
44 76 0.77
45 10 0.10
46 2 0.02
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (43 bp):
TATCTTGATCTGTTCCCTATAAACACAGGGATGCCAAATCTTC
Found at i:49642863 original size:132 final size:132
Alignment explanation
Indices: 49642656--49642932 Score: 437
Period size: 132 Copynumber: 2.1 Consensus size: 132
49642646 ACAATACAAA
* * * *
49642656 GATGTCAAATCTGCTATCTTCAACTTGTTCCCTATAAACACAAGGACGCCATGTTGAAATCCTCG
1 GATGCCAAATCTTCTATCTTCAACTTGTTCCCTATAAACACAAGGACGCCATGCTGAAATCCTCA
* * ** *
49642721 ATCTGCTTCGCTGTAAGCACAGGAGTGTCAGATCTGTTATCTTTGATCTGTTCCCTATAAACACA
66 ATCTGCTTCGCTGTAAGCACAGGAATGTCAGATCTGCTATCTCCGATCTGTTCCCTATAAACAAA
49642786 GG
131 GG
* *
49642788 GATGCCAAATCTTCTATCTTCAACTTGTTCCCTATAAACACAGGGATGCCATGCTGAAATCCTCA
1 GATGCCAAATCTTCTATCTTCAACTTGTTCCCTATAAACACAAGGACGCCATGCTGAAATCCTCA
* *
49642853 ATCTGGTTCGCTGTAAGCAGAGGAATGTCAGATCTGCTATCTCCGATCTGTTCCCTATAAACAAA
66 ATCTGCTTCGCTGTAAGCACAGGAATGTCAGATCTGCTATCTCCGATCTGTTCCCTATAAACAAA
49642918 GG
131 GG
49642920 GATGCCAAATCTT
1 GATGCCAAATCTT
49642933 GTTTCTTTGA
Statistics
Matches: 132, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
132 132 1.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (132 bp):
GATGCCAAATCTTCTATCTTCAACTTGTTCCCTATAAACACAAGGACGCCATGCTGAAATCCTCA
ATCTGCTTCGCTGTAAGCACAGGAATGTCAGATCTGCTATCTCCGATCTGTTCCCTATAAACAAA
GG
Found at i:49654560 original size:33 final size:33
Alignment explanation
Indices: 49654521--49654590 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
49654511 ACAAACATAC
*
49654521 AAAGTAATACTTAAATAATGCATGATATACAAA
1 AAAGTAATAATTAAATAATGCATGATATACAAA
49654554 AAAGTAATAATTAAATAATGCATGATATACAAA
1 AAAGTAATAATTAAATAATGCATGATATACAAA
49654587 AAAG
1 AAAG
49654591 AGTAATACAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.57, C:0.07, G:0.10, T:0.26
Consensus pattern (33 bp):
AAAGTAATAATTAAATAATGCATGATATACAAA
Found at i:49655734 original size:17 final size:19
Alignment explanation
Indices: 49655692--49655735 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
49655682 ATGAAATTTT
*
49655692 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
49655711 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
49655729 AA-TATTA
1 AATTATTA
49655736 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:49657558 original size:28 final size:28
Alignment explanation
Indices: 49657525--49657593 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
49657515 GCGTAGATCA
49657525 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
49657553 TGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
49657581 CGATA-TACCCCTA
1 CGAAATTACCCCTA
49657594 GGTTTTAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 8 0.21
28 30 0.79
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.20
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:49659998 original size:17 final size:19
Alignment explanation
Indices: 49659956--49659999 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
49659946 ATGAAATTTT
*
49659956 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
49659975 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
49659993 AA-TATTA
1 AATTATTA
49660000 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:49661823 original size:28 final size:28
Alignment explanation
Indices: 49661790--49661858 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
49661780 GCGTAGATCA
49661790 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
49661818 TGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
49661846 CGATA-TACCCCTA
1 CGAAATTACCCCTA
49661859 GGTTTTAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 8 0.21
28 30 0.79
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.20
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:49664455 original size:14 final size:14
Alignment explanation
Indices: 49664436--49664522 Score: 70
Period size: 14 Copynumber: 6.1 Consensus size: 14
49664426 TGAATGACTC
49664436 AAGGTTTAAGGTCT
1 AAGGTTTAAGGTCT
**
49664450 AAGG-TTCGGGAT-T
1 AAGGTTTAAGG-TCT
*
49664463 AATGGTTTCAAGGTCC
1 AA-GGTTT-AAGGTCT
*
49664479 AAGGTTTAAGATCTT
1 AAGGTTTAAGGTC-T
* *
49664494 AAAGTCTAAGGTCT
1 AAGGTTTAAGGTCT
49664508 AAGGTTTAAGGTCT
1 AAGGTTTAAGGTCT
49664522 A
1 A
49664523 GTGTATAAAT
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
13 7 0.13
14 26 0.47
15 18 0.33
16 4 0.07
ACGTcount: A:0.30, C:0.10, G:0.26, T:0.33
Consensus pattern (14 bp):
AAGGTTTAAGGTCT
Found at i:49676923 original size:97 final size:98
Alignment explanation
Indices: 49676817--49677216 Score: 297
Period size: 97 Copynumber: 4.1 Consensus size: 98
49676807 TTTGTTCCAA
* * *
49676817 GTTTAAATGTTGTAATGTATCTAATTTATGATCACAAATTTTGTTCC-AA-GTTTTAATGTATCT
1 GTTTTAATGTTGTAATGTATCTAATTTATGATCACAAAGTTTGTTCCTAATGTTGTAATGTATCT
*
49676880 AATTTATATTACAAAGTTTGTTCC-------AA-
66 AATTTATACTACAAA-TTTGTTCCAAGTTTTAAT
49676906 GTTTTAATGTTGTAATGTATCTAATTTATGATCACAAAGTTTGTTCCAAATTTTAATGTTGTAAT
1 GTTTTAATGTTGTAATGTATCTAATTTATGATCACAAAGTTTGTTCC------TAATGTTGTAAT
* *
49676971 GTATCTAATTTATATTACAAA-TT-TT----GTTCTAA-
60 GTATCTAATTTATACTACAAATTTGTTCCAAGTTTTAAT
* * *
49677003 GTTTTAATGTTGTAATGTATCTAATTTATGATAACAAAGTTTGTTCC-AA-GTTTTAATGT-TGT
1 GTTTTAATGTTGTAATGTATCTAATTTATGATCACAAAGTTTGTTCCTAATGTTGTAATGTATCT
* * *
49677065 AATGTAT-CT--AAATTATGATCACAAAGTTTGTTCAAA
66 AATTTATACTACAAATT-TGTTC-C-AAG-TT-TT-AAT
* * *
49677101 GTTTTAATGCTGTAGTGTATCTAATTTATGACCACAAAGTTTGTTCCAGGTTTTAATGTTGTAAT
1 GTTTTAATGTTGTAATGTATCTAATTTATGATCACAAAGTTTGTTCC------TAATGTTGTAAT
*
49677166 GTATCTAATTTATGACCACAAAGTTTGTTCCAAGTTTTAAT
60 GTATCTAATTTAT-ACTACAAA-TTTGTTCCAAGTTTTAAT
*
49677207 GTTGTAATGT
1 GTTTTAATGT
49677217 ATCTAATTTA
Statistics
Matches: 249, Mismatches: 22, Indels: 63
0.75 0.07 0.19
Matches are distributed among these distances:
85 3 0.01
86 1 0.00
87 2 0.01
88 9 0.04
89 54 0.22
90 2 0.01
94 3 0.01
95 4 0.02
96 3 0.01
97 78 0.31
98 43 0.17
105 2 0.01
106 19 0.08
107 10 0.04
108 2 0.01
109 4 0.02
110 1 0.00
111 7 0.03
112 2 0.01
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.46
Consensus pattern (98 bp):
GTTTTAATGTTGTAATGTATCTAATTTATGATCACAAAGTTTGTTCCTAATGTTGTAATGTATCT
AATTTATACTACAAATTTGTTCCAAGTTTTAAT
Found at i:49676960 original size:49 final size:49
Alignment explanation
Indices: 49676870--49677272 Score: 607
Period size: 49 Copynumber: 8.3 Consensus size: 49
49676860 TTCCAAGTTT
*
49676870 TAATGTATCTAATTTAT-ATTACAAAGTTTGTTCCAAGTTTTAATGTTG
1 TAATGTATCTAATTTATGATCACAAAGTTTGTTCCAAGTTTTAATGTTG
*
49676918 TAATGTATCTAATTTATGATCACAAAGTTTGTTCCAAATTTTAATGTTG
1 TAATGTATCTAATTTATGATCACAAAGTTTGTTCCAAGTTTTAATGTTG
* * *
49676967 TAATGTATCTAATTTAT-ATTACAAATTTTGTTCTAAGTTTTAATGTTG
1 TAATGTATCTAATTTATGATCACAAAGTTTGTTCCAAGTTTTAATGTTG
*
49677015 TAATGTATCTAATTTATGATAACAAAGTTTGTTCCAAGTTTTAATGTTG
1 TAATGTATCTAATTTATGATCACAAAGTTTGTTCCAAGTTTTAATGTTG
* * *
49677064 TAATGTATCTAAATTATGATCACAAAGTTTGTTCAAAGTTTTAATGCTG
1 TAATGTATCTAATTTATGATCACAAAGTTTGTTCCAAGTTTTAATGTTG
* * *
49677113 TAGTGTATCTAATTTATGACCACAAAGTTTGTTCCAGGTTTTAATGTTG
1 TAATGTATCTAATTTATGATCACAAAGTTTGTTCCAAGTTTTAATGTTG
*
49677162 TAATGTATCTAATTTATGACCACAAAGTTTGTTCCAAGTTTTAATGTTG
1 TAATGTATCTAATTTATGATCACAAAGTTTGTTCCAAGTTTTAATGTTG
* * * *
49677211 TAATGTATCTAATTTA-CAGCACAAAGTTTGTTCCAATTTTTAATATTG
1 TAATGTATCTAATTTATGATCACAAAGTTTGTTCCAAGTTTTAATGTTG
*
49677259 CAAT-TAATCTAATT
1 TAATGT-ATCTAATT
49677273 AAATAAATAC
Statistics
Matches: 326, Mismatches: 26, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
47 1 0.00
48 100 0.31
49 225 0.69
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (49 bp):
TAATGTATCTAATTTATGATCACAAAGTTTGTTCCAAGTTTTAATGTTG
Found at i:49677131 original size:98 final size:97
Alignment explanation
Indices: 49676870--49677272 Score: 603
Period size: 97 Copynumber: 4.1 Consensus size: 97
49676860 TTCCAAGTTT
*
49676870 TAATGTATCTAATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTAT
1 TAATGTATCTAATTTATATCACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTAT
*
49676935 GATCACAAAGTTTGTTCCAAATTTTAATGTTG
66 GATCACAAAGTTTGTTCCAAGTTTTAATGTTG
* * *
49676967 TAATGTATCTAATTTATATTACAAATTTTGTTCTAAGTTTTAATGTTGTAATGTATCTAATTTAT
1 TAATGTATCTAATTTATATCACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTAT
*
49677032 GATAACAAAGTTTGTTCCAAGTTTTAATGTTG
66 GATCACAAAGTTTGTTCCAAGTTTTAATGTTG
* * * *
49677064 TAATGTATCTAAATTATGATCACAAAGTTTGTTCAAAGTTTTAATGCTGTAGTGTATCTAATTTA
1 TAATGTATCTAATTTAT-ATCACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTA
* *
49677129 TGACCACAAAGTTTGTTCCAGGTTTTAATGTTG
65 TGATCACAAAGTTTGTTCCAAGTTTTAATGTTG
*
49677162 TAATGTATCTAATTTATGACCACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTA
1 TAATGTATCTAATTTAT-ATCACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTA
* * * *
49677227 -CAGCACAAAGTTTGTTCCAATTTTTAATATTG
65 TGATCACAAAGTTTGTTCCAAGTTTTAATGTTG
*
49677259 CAAT-TAATCTAATT
1 TAATGT-ATCTAATT
49677273 AAATAAATAC
Statistics
Matches: 280, Mismatches: 24, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
96 1 0.00
97 147 0.52
98 132 0.47
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (97 bp):
TAATGTATCTAATTTATATCACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTAT
GATCACAAAGTTTGTTCCAAGTTTTAATGTTG
Found at i:49678403 original size:14 final size:14
Alignment explanation
Indices: 49678384--49678418 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
49678374 CAAATTACAT
49678384 GTTAGAATAGTATC
1 GTTAGAATAGTATC
49678398 GTTAGAATAGTATC
1 GTTAGAATAGTATC
*
49678412 ATTAGAA
1 GTTAGAA
49678419 AAAAATATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (14 bp):
GTTAGAATAGTATC
Found at i:49680150 original size:48 final size:48
Alignment explanation
Indices: 49680008--49680177 Score: 238
Period size: 48 Copynumber: 3.5 Consensus size: 48
49679998 AATAAAAATA
* * *
49680008 ACATGCCAACTAAATTACATAAAAAATAAATCTCCATAAACCTAAAACAC
1 ACATGACAAATAAATTACAT-AAAAATAAATCT-AATAAACCTAAAACAC
49680058 ACATG-CAAATAAATTACATAAAAA-AAATCTAATAAACCTAAAACAC
1 ACATGACAAATAAATTACATAAAAATAAATCTAATAAACCTAAAACAC
* *
49680104 ATATGACAAAT-AATTACATAAAAATTAAATCTAATAAACATAAAACAC
1 ACATGACAAATAAATTACATAAAAA-TAAATCTAATAAACCTAAAACAC
49680152 ACATGACAAATAAATTACATCAAAAA
1 ACATGACAAATAAATTACAT-AAAAA
49680178 ACAAAACATT
Statistics
Matches: 110, Mismatches: 5, Indels: 10
0.88 0.04 0.08
Matches are distributed among these distances:
46 32 0.29
47 11 0.10
48 36 0.33
49 21 0.19
50 10 0.09
ACGTcount: A:0.59, C:0.18, G:0.02, T:0.21
Consensus pattern (48 bp):
ACATGACAAATAAATTACATAAAAATAAATCTAATAAACCTAAAACAC
Found at i:49681265 original size:16 final size:18
Alignment explanation
Indices: 49681238--49681270 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
49681228 TAGAATTGGG
49681238 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
49681255 TTGAG-AAATTAATTTA
1 TTGAGAAAATTAATTTA
49681271 GCTAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:49683171 original size:17 final size:18
Alignment explanation
Indices: 49683151--49683192 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
49683141 TCAAAAATAA
49683151 TAATATTTTAATA-AATT
1 TAATATTTTAATATAATT
49683168 TAATA-TTTAATATAATT
1 TAATATTTTAATATAATT
49683185 TAATATTT
1 TAATATTT
49683193 ATCTTGCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.30
17 14 0.61
18 2 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAATATTTTAATATAATT
Found at i:49687526 original size:24 final size:24
Alignment explanation
Indices: 49687423--49687587 Score: 248
Period size: 23 Copynumber: 7.0 Consensus size: 24
49687413 GCTTTATCAT
*
49687423 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
49687448 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
49687471 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
49687494 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
49687518 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
49687542 ATAATTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
49687565 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
49687588 GCACTTCCTC
Statistics
Matches: 132, Mismatches: 5, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
23 67 0.51
24 53 0.40
25 12 0.09
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:49687562 original size:71 final size:70
Alignment explanation
Indices: 49687423--49687588 Score: 262
Period size: 71 Copynumber: 2.3 Consensus size: 70
49687413 GCTTTATCAT
* *
49687423 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAG
1 ATAACTGG-GGCATAAGCC-CTTTTGATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAG
49687487 CCCTTTA
64 CCCTTTA
* *
49687494 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAATTGGGGCATAAGC
1 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGC
49687559 CCTTTA
65 CCTTTA
49687565 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
49687589 CACTTCCTCC
Statistics
Matches: 89, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
70 28 0.31
71 61 0.69
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (70 bp):
ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
CTTTA
Found at i:49687661 original size:20 final size:20
Alignment explanation
Indices: 49687633--49687703 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
49687623 GCATTTATGA
* *
49687633 ACATCTCATGTGTATATCAT
1 ACATATCATGTGCATATCAT
49687653 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
49687673 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
49687693 ACATATCATGT
1 ACATATCATGT
49687704 TTATCAAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:49687768 original size:25 final size:25
Alignment explanation
Indices: 49687740--49687787 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
49687730 ATATATAAAC
* *
49687740 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAATGGTCATTTTTA
49687765 CCTAGGGGCAAAATGGTCATTTT
1 CCTAGGGGCAAAATGGTCATTTT
49687788 CATATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAATGGTCATTTTTA
Found at i:49692870 original size:40 final size:39
Alignment explanation
Indices: 49692825--49692988 Score: 154
Period size: 40 Copynumber: 4.2 Consensus size: 39
49692815 CGGAATATAA
49692825 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGG-CTTAGC
* * * *
49692865 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGCTTAGC
** * *
49692904 CCGG--ATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGG-CTTAGC
** * * * *
49692942 CCGGATATAATTTCCAGCATAATTGTCTTCGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGCTTAGC
49692981 CCGGATAT
1 CCGGATAT
49692989 CATTCAATTT
Statistics
Matches: 101, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
37 20 0.20
38 9 0.09
39 24 0.24
40 48 0.48
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (39 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGCTTAGC
Found at i:49692945 original size:77 final size:77
Alignment explanation
Indices: 49692841--49692987 Score: 199
Period size: 77 Copynumber: 1.9 Consensus size: 77
49692831 ATAATCACGT
*
49692841 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAAC-CAGCA-GAATTGCCTTCGGGCTTAGC
49692904 CCGGATAGCCACTA
64 CCGGATAGCCACTA
* * ** * *
49692918 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCAGCATAATTGTCTTCGGGCTTAGCCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACCAGCAGAATTGCCTTCGGGCTTAGCCC
49692983 GGATA
66 GGATA
49692988 TCATTCAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
76 3 0.05
77 58 0.95
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (77 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACCAGCAGAATTGCCTTCGGGCTTAGCCC
GGATAGCCACTA
Found at i:49700962 original size:40 final size:39
Alignment explanation
Indices: 49700851--49700964 Score: 138
Period size: 40 Copynumber: 2.8 Consensus size: 39
49700841 TTAATCACGT
* * *
49700851 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATATAACAACTA
* * *
49700891 GCACGAATGCCTTCGGGCCTTAGCCCGGATATAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATATAACAACTA
*
49700931 GCACAATTGCCTTCGGGTCTTAACCCGGATATAA
1 GCACAA-TGCCTTCGGGTCTTAGCCCGGATATAA
49700965 TTTCCAGCAT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
39 2 0.03
40 61 0.97
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (39 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATATAACAACTA
Found at i:49702996 original size:17 final size:17
Alignment explanation
Indices: 49702974--49703006 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
49702964 ATAAGTATAC
*
49702974 ATTGTCATTGCATTTTT
1 ATTGTCATTACATTTTT
49702991 ATTGTCATTACATTTT
1 ATTGTCATTACATTTT
49703007 CACATTAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (17 bp):
ATTGTCATTACATTTTT
Found at i:49704997 original size:31 final size:32
Alignment explanation
Indices: 49704948--49705009 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
49704938 ACGAAGTCAT
* *
49704948 CAGATACAGATATTGTGGCTAGGCCACCAGAA
1 CAGATACAGATATTGTGGCGAAGCCACCAGAA
49704980 CAGATA-A-ATATATGTGGCGAAGCCACCAGA
1 CAGATACAGATAT-TGTGGCGAAGCCACCAGA
49705010 TTGCAGCGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 4 0.15
31 17 0.63
32 6 0.22
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (32 bp):
CAGATACAGATATTGTGGCGAAGCCACCAGAA
Found at i:49705741 original size:27 final size:27
Alignment explanation
Indices: 49705710--49706103 Score: 513
Period size: 27 Copynumber: 14.6 Consensus size: 27
49705700 TTACCCCATG
*
49705710 AGGGTATCTCGGTAATTCTACCCTACA
1 AGGGTATTTCGGTAATTCTACCCTACA
* * *
49705737 GGGGTATTTTGGTATTTCTACCCTACA
1 AGGGTATTTCGGTAATTCTACCCTACA
* *
49705764 AAGGTATTTCGGTAATTCTATCCTACA
1 AGGGTATTTCGGTAATTCTACCCTACA
* ** *
49705791 GGGGTATTTTAGTACTTCTACCCTACA
1 AGGGTATTTCGGTAATTCTACCCTACA
* * *
49705818 GGGGTATTTCGATATTTCTACCCTACA
1 AGGGTATTTCGGTAATTCTACCCTACA
* *
49705845 AGGGTATTTCGATATTTCTACCCTACA
1 AGGGTATTTCGGTAATTCTACCCTACA
49705872 AGGGTATTTCGGTAATTCTACCCTACA
1 AGGGTATTTCGGTAATTCTACCCTACA
* *
49705899 GGGGTATTTCAGTAATTCTACCCTAC-
1 AGGGTATTTCGGTAATTCTACCCTACA
* *
49705925 AGGGCTATTTTGGTATTTCTACCCTACA
1 AGGG-TATTTCGGTAATTCTACCCTACA
*
49705953 AGGGTATTTCGGTATTTCTACCCTACA
1 AGGGTATTTCGGTAATTCTACCCTACA
*
49705980 AGGGTATTTTGGTAATTCTACCCTACA
1 AGGGTATTTCGGTAATTCTACCCTACA
* *
49706007 GGGGTATTTCAGTAATT-TACCCTACA
1 AGGGTATTTCGGTAATTCTACCCTACA
* * *
49706033 GGGGTATTTTGGTATTTCTACCCTACA
1 AGGGTATTTCGGTAATTCTACCCTACA
*
49706060 AGGGTATTTTGGTAATTCTACCCTACA
1 AGGGTATTTCGGTAATTCTACCCTACA
*
49706087 AGGGTATTTCGATAATT
1 AGGGTATTTCGGTAATT
49706104 TCACAAATCT
Statistics
Matches: 323, Mismatches: 41, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
26 26 0.08
27 293 0.91
28 4 0.01
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (27 bp):
AGGGTATTTCGGTAATTCTACCCTACA
Found at i:49706119 original size:54 final size:55
Alignment explanation
Indices: 49705692--49706238 Score: 498
Period size: 54 Copynumber: 10.1 Consensus size: 55
49705682 AGGGGAAAAA
* * ** * *
49705692 TGGTAATTTTACCCCATGAGGGTATCTCGGTAA-TTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAAGGGTATTTTGGTAATTTCTACCCTACAGGGGTATTT
* * * *
49705746 TGGTATTTCTACCCTACAAAGGTATTTCGGTAA-TTCTATCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAAGGGTATTTTGGTAATTTCTACCCTACAGGGGTATTT
* * * * * *
49705800 TAGTACTTCTACCCTACAGGGGTATTTCGAT-ATTTCTACCCTACAAGGGTATTT
1 TGGTAATTCTACCCTACAAGGGTATTTTGGTAATTTCTACCCTACAGGGGTATTT
* * * *
49705854 CGATATTTCTACCCTACAAGGGTATTTCGGTAA-TTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAAGGGTATTTTGGTAATTTCTACCCTACAGGGGTATTT
** *
49705908 CAGTAATTCTACCCTAC-AGGGCTATTTTGGT-ATTTCTACCCTACAAGGGTATTT
1 TGGTAATTCTACCCTACAAGGG-TATTTTGGTAATTTCTACCCTACAGGGGTATTT
* *
49705962 CGGTATTTCTACCCTACAAGGGTATTTTGGTAA-TTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAAGGGTATTTTGGTAATTTCTACCCTACAGGGGTATTT
** * *
49706016 CAGTAATT-TACCCTACAGGGGTATTTTGGT-ATTTCTACCCTACAAGGGTATTT
1 TGGTAATTCTACCCTACAAGGGTATTTTGGTAATTTCTACCCTACAGGGGTATTT
* * ** *
49706069 TGGTAATTCTACCCTACAAGGGTATTTCGATAATTTC-A-CAAATCTGGGGTATTT
1 TGGTAATTCTACCCTACAAGGGTATTTTGGTAATTTCTACCCTA-CAGGGGTATTT
* ** * ** *
49706123 TGGTAATTTTA-CAAACCAAAGGTATTTTGGTAATTT-TA-CAAACCAGGAGTATTT
1 TGGTAATTCTACCCTA-CAAGGGTATTTTGGTAATTTCTACCCTA-CAGGGGTATTT
* ** **
49706177 TGGTAATTTTA-CAAACCAAGGGTATTTTGGTAATTT-TA-CAAACCAGGGGTATTT
1 TGGTAATTCTACCCTA-CAAGGGTATTTTGGTAATTTCTACCCTA-CAGGGGTATTT
*
49706231 TAGTAATT
1 TGGTAATT
49706239 TGGTAAACTA
Statistics
Matches: 426, Mismatches: 55, Indels: 24
0.84 0.11 0.05
Matches are distributed among these distances:
52 1 0.00
53 57 0.13
54 357 0.84
55 11 0.03
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (55 bp):
TGGTAATTCTACCCTACAAGGGTATTTTGGTAATTTCTACCCTACAGGGGTATTT
Found at i:49706146 original size:27 final size:27
Alignment explanation
Indices: 49706058--49706239 Score: 224
Period size: 27 Copynumber: 6.7 Consensus size: 27
49706048 TTCTACCCTA
* **
49706058 CAAGGGTATTTTGGTAATTCTACCCTA-
1 CAAGGGTATTTTGGTAATTTTA-CAAAC
* * * *
49706085 CAAGGGTATTTCGATAATTTCACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAC
**
49706112 CTGGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
*
49706139 CAAAGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
49706166 C-AGGAGTATTTTGGTAATTTTACAAAC
1 CAAGG-GTATTTTGGTAATTTTACAAAC
49706193 CAAGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
* *
49706220 CAGGGGTATTTTAGTAATTT
1 CAAGGGTATTTTGGTAATTT
49706240 GGTAAACTAA
Statistics
Matches: 134, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
26 4 0.03
27 127 0.95
28 3 0.02
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAC
Found at i:49706246 original size:27 final size:27
Alignment explanation
Indices: 49706031--49706239 Score: 217
Period size: 27 Copynumber: 7.7 Consensus size: 27
49706021 ATTTACCCTA
**
49706031 CAGGGGTATTTTGGT-ATTTCTACCCTA-
1 CAGGGGTATTTTGGTAATTT-TA-CAAAC
* * **
49706058 CAAGGGTATTTTGGTAATTCTACCCTA-
1 CAGGGGTATTTTGGTAATTTTA-CAAAC
* * * * *
49706085 CAAGGGTATTTCGATAATTTCACAAAT
1 CAGGGGTATTTTGGTAATTTTACAAAC
*
49706112 CTGGGGTATTTTGGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
**
49706139 CAAAGGTATTTTGGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
*
49706166 CAGGAGTATTTTGGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
*
49706193 CAAGGGTATTTTGGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
*
49706220 CAGGGGTATTTTAGTAATTT
1 CAGGGGTATTTTGGTAATTT
49706240 GGTAAACTAA
Statistics
Matches: 156, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
26 2 0.01
27 151 0.97
28 3 0.02
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (27 bp):
CAGGGGTATTTTGGTAATTTTACAAAC
Found at i:49708427 original size:33 final size:33
Alignment explanation
Indices: 49708353--49708442 Score: 94
Period size: 33 Copynumber: 2.8 Consensus size: 33
49708343 CTGATTGCAT
* * * *
49708353 ACTG-TACTGTTACTGTAATGGGCTTAGGCCCC
1 ACTGATACTGTTACTGAAATGGGCTCAAGCCAC
*
49708385 ACTGATACTGTTACTGAAATGGGCTCAAGCCAG
1 ACTGATACTGTTACTGAAATGGGCTCAAGCCAC
* *
49708418 ACT-ACTACTGCTACTGATATGGGCT
1 ACTGA-TACTGTTACTGAAATGGGCT
49708443 AAGGCCCTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
32 5 0.10
33 44 0.90
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.29
Consensus pattern (33 bp):
ACTGATACTGTTACTGAAATGGGCTCAAGCCAC
Found at i:49708633 original size:20 final size:20
Alignment explanation
Indices: 49708608--49708647 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
49708598 ACTCAGTGGT
49708608 GGCCACTCGACTTAGTTAAC
1 GGCCACTCGACTTAGTTAAC
49708628 GGCCACTCGACTTAGTTAAC
1 GGCCACTCGACTTAGTTAAC
49708648 TTTTAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (20 bp):
GGCCACTCGACTTAGTTAAC
Found at i:49713548 original size:40 final size:40
Alignment explanation
Indices: 49713421--49713550 Score: 158
Period size: 40 Copynumber: 3.2 Consensus size: 40
49713411 ATGCTGGAAA
* *
49713421 TTATATCC-GGCTTAAGACCTGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGC-TAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * *
49713461 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
49713501 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
49713541 TTATATCCGG
1 TTATATCCGG
49713551 TTGTATTCCG
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
39 4 0.05
40 70 0.91
41 3 0.04
ACGTcount: A:0.22, C:0.25, G:0.28, T:0.25
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:49716680 original size:93 final size:93
Alignment explanation
Indices: 49716572--49716743 Score: 274
Period size: 93 Copynumber: 1.8 Consensus size: 93
49716562 GCCCATAAGT
* *
49716572 GAACTCAGACTCAACTCAATGAGCTC-GAGCGTTCGCATCCATAAGTGAACTCGGACTCAAATCA
1 GAACTCAGACTCAACTCAATGAGCTCGGA-CATTCGCATCCATAACTGAACTCGGACTCAAATCA
49716636 ACGAGCTCGGATGCCTAGTTACATCTCTC
65 ACGAGCTCGGATGCCTAGTTACATCTCTC
* * *
49716665 GAACTCAGACTCAACTCAATGAGTTCGGACATTTGCATCCATAACTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAATGAGCTCGGACATTCGCATCCATAACTGAACTCGGACTCAAATCAA
*
49716730 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
49716744 CAAACATCCT
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
93 70 0.97
94 2 0.03
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAATGAGCTCGGACATTCGCATCCATAACTGAACTCGGACTCAAATCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:49716735 original size:46 final size:47
Alignment explanation
Indices: 49716564--49716739 Score: 157
Period size: 46 Copynumber: 3.8 Consensus size: 47
49716554 TGTAACCCGC
* * * *
49716564 CCATAAGTGAACTCAGACTCAACTCAATGAGCTC-GAGCGTTCGCAT
1 CCATAACTGAACTCAGACTCAACTCAACGAGCTCGGAGCATTTGCAT
* * * * *
49716610 CCATAAGTGAACTCGGACTCAAATCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAACTGAACTCAGACTCAACTCAACGAGCTCGGA-G-C-ATTTGCAT
* *
49716660 -C-T--CTCGAACTCAGACTCAACTCAATGAGTTCGGA-CATTTGCAT
1 CCATAACT-GAACTCAGACTCAACTCAACGAGCTCGGAGCATTTGCAT
* *
49716703 CCATAACTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAACTGAACTCAGACTCAACTCAACGAGCTCGGA
49716740 TGCCCAAACA
Statistics
Matches: 105, Mismatches: 16, Indels: 18
0.76 0.12 0.13
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 1 0.01
46 59 0.56
47 29 0.28
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.23
Consensus pattern (47 bp):
CCATAACTGAACTCAGACTCAACTCAACGAGCTCGGAGCATTTGCAT
Found at i:49720801 original size:14 final size:15
Alignment explanation
Indices: 49720782--49720814 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
49720772 ATTGTTAAAA
49720782 TTATTAAAATT-ATT
1 TTATTAAAATTAATT
*
49720796 TTATTAAATTTAATT
1 TTATTAAAATTAATT
49720811 TTAT
1 TTAT
49720815 CACAATATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTATTAAAATTAATT
Found at i:49720936 original size:34 final size:34
Alignment explanation
Indices: 49720872--49720936 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
49720862 TATTACATAA
*
49720872 AAGTAGCAATTATTATAATACAATACAATTAATG
1 AAGTAGCAATTATTATAATAAAATACAATTAATG
49720906 AAGTAGCAATTATTATAATAAAAGTA-AATTA
1 AAGTAGCAATTATTATAATAAAA-TACAATTA
49720937 TATCGCATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 27 0.93
35 2 0.07
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.32
Consensus pattern (34 bp):
AAGTAGCAATTATTATAATAAAATACAATTAATG
Found at i:49730164 original size:12 final size:12
Alignment explanation
Indices: 49730147--49730176 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
49730137 TCAAAGAGTT
*
49730147 ACACGGGTTCAG
1 ACACGGGCTCAG
49730159 ACACGGGCTCAG
1 ACACGGGCTCAG
49730171 ACACGG
1 ACACGG
49730177 CCATGTGATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.30, G:0.33, T:0.10
Consensus pattern (12 bp):
ACACGGGCTCAG
Found at i:49737349 original size:10 final size:10
Alignment explanation
Indices: 49737303--49737350 Score: 60
Period size: 10 Copynumber: 4.6 Consensus size: 10
49737293 CTATCGAAAC
*
49737303 TAATCAAAAT
1 TAATTAAAAT
*
49737313 TAATCAAAAT
1 TAATTAAAAT
49737323 TAATTATAAAAT
1 TAA-T-TAAAAT
49737335 TAATTAAAAT
1 TAATTAAAAT
49737345 TAATTA
1 TAATTA
49737351 TGTTAATAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
10 25 0.71
11 2 0.06
12 8 0.23
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (10 bp):
TAATTAAAAT
Found at i:49737361 original size:22 final size:22
Alignment explanation
Indices: 49737308--49737351 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
49737298 GAAACTAATC
*
49737308 AAAATTAATCAAAATTAATTAT
1 AAAATTAATTAAAATTAATTAT
49737330 AAAATTAATTAAAATTAATTAT
1 AAAATTAATTAAAATTAATTAT
49737352 GTTAATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATTAATTAAAATTAATTAT
Found at i:49741032 original size:29 final size:29
Alignment explanation
Indices: 49740975--49741032 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
49740965 GCCTTTTGAA
* *
49740975 AATATTTACAAAAAAAGCATCTAATTTTT
1 AATATTTACAAAAAAAGCACCCAATTTTT
*
49741004 AATATTTACAAAAAGAGCAACCCAATTTT
1 AATATTTACAAAAAAAGC-ACCCAATTTT
49741033 GAAAATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.33
Consensus pattern (29 bp):
AATATTTACAAAAAAAGCACCCAATTTTT
Found at i:49742140 original size:17 final size:17
Alignment explanation
Indices: 49742118--49742153 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
49742108 AACCCACTTG
*
49742118 ACACATGGTCTACTCCT
1 ACACATAGTCTACTCCT
*
49742135 ACACATAGTCTACTGCT
1 ACACATAGTCTACTCCT
49742152 AC
1 AC
49742154 CAATATGTAC
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:0.28, C:0.33, G:0.11, T:0.28
Consensus pattern (17 bp):
ACACATAGTCTACTCCT
Found at i:49748500 original size:42 final size:42
Alignment explanation
Indices: 49748447--49748539 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
49748437 TAGCCCAACT
* * * *
49748447 ATGGTCTTACACGAAGTCTCTTATCGGTGCCATATCCCAGAA
1 ATGGTCTTACACGAAGTCTCATATAGATGCCATAACCCAGAA
*
49748489 ATGGTCTTACACGAAGTCTCATATAGATGCCATAACCCAGAT
1 ATGGTCTTACACGAAGTCTCATATAGATGCCATAACCCAGAA
49748531 ATGGTCTTA
1 ATGGTCTTA
49748540 AGCATAGTCT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (42 bp):
ATGGTCTTACACGAAGTCTCATATAGATGCCATAACCCAGAA
Found at i:49750169 original size:40 final size:40
Alignment explanation
Indices: 49750125--49750350 Score: 237
Period size: 40 Copynumber: 5.7 Consensus size: 40
49750115 GCTACTCGTT
* * *
49750125 CAAATACCTTCGGGACATAGCCCGG-TTATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
49750165 CAAATGCCTTCGGGACTTATCTCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
49750205 CACATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * *
49750245 CAAATGCCTTC-GGATATTAGTCCAGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* ** *
49750285 CAATTGCCTTC-GGATCTTAGTTCGGATTTAGTAACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
*
49750326 CAAA-GCCTTCAGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
49750351 CATCATTCGA
Statistics
Matches: 162, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
39 3 0.02
40 147 0.91
41 12 0.07
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.28
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:49750237 original size:80 final size:79
Alignment explanation
Indices: 49750153--49750344 Score: 264
Period size: 80 Copynumber: 2.4 Consensus size: 79
49750143 AGCCCGGTTA
* *
49750153 TAGTAGCTCGCACAAATGCCTTCGGGACTTA-TCTCGGATTTAGTAACTCGCACACA-TGCCTTC
1 TAGTAACTCGCACAAATGCCTTC-GGACTTAGTC-CAGATTTAGTAACTCGCACA-ATTGCCTTC
49750216 GGATCTTAGTCCGGATT
63 GGATCTTAGTCCGGATT
*
49750233 TAGTAACTCGCACAAATGCCTTCGGATATTAGTCCAGATTTAGTAACTCGCACAATTGCCTTCGG
1 TAGTAACTCGCACAAATGCCTTCGGA-CTTAGTCCAGATTTAGTAACTCGCACAATTGCCTTCGG
*
49750298 ATCTTAGTTCGGATT
65 ATCTTAGTCCGGATT
*
49750313 TAGTAACTTAGCACAAA-GCCTTCAGGACTTAG
1 TAGTAAC-TCGCACAAATGCCTTC-GGACTTAG
49750345 CCCGGACATC
Statistics
Matches: 101, Mismatches: 6, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
79 4 0.04
80 84 0.83
81 13 0.13
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (79 bp):
TAGTAACTCGCACAAATGCCTTCGGACTTAGTCCAGATTTAGTAACTCGCACAATTGCCTTCGGA
TCTTAGTCCGGATT
Found at i:49756430 original size:2 final size:2
Alignment explanation
Indices: 49756423--49756463 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
49756413 GTTGTAAGCT
49756423 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
49756463 T
1 T
49756464 GCATGCATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:49762346 original size:25 final size:24
Alignment explanation
Indices: 49762292--49762347 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 24
49762282 AATCAGCAAG
* *
49762292 AGAATAAAGAAAAATGGATAGGAA
1 AGAAGAAAGAAAAATGGAGAGGAA
49762316 ATGAAGAAAGAAAAAT-GAGAGAGAA
1 A-GAAGAAAGAAAAATGGAGAG-GAA
49762341 CAGAAGA
1 -AGAAGA
49762348 GATGAGAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 5 0.19
25 21 0.78
26 1 0.04
ACGTcount: A:0.62, C:0.02, G:0.27, T:0.09
Consensus pattern (24 bp):
AGAAGAAAGAAAAATGGAGAGGAA
Found at i:49764392 original size:40 final size:40
Alignment explanation
Indices: 49764265--49764394 Score: 174
Period size: 40 Copynumber: 3.2 Consensus size: 40
49764255 ATGCTGGAAA
* *
49764265 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * *
49764305 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
49764345 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
49764385 TTATATCCGG
1 TTATATCCGG
49764395 TTGTATTCCG
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
39 4 0.05
40 74 0.95
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:49766106 original size:22 final size:22
Alignment explanation
Indices: 49766081--49766124 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
49766071 CAAATCTGTC
*
49766081 AAAATTAATCAAAATTAATTAT
1 AAAAATAATCAAAATTAATTAT
* * *
49766103 AAAAATATTTAAAATTCATTAT
1 AAAAATAATCAAAATTAATTAT
49766125 GTTAATAATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAAATAATCAAAATTAATTAT
Found at i:49768301 original size:15 final size:15
Alignment explanation
Indices: 49768281--49768311 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
49768271 GTCGTGTATA
49768281 ACACACAGTTTGGTG
1 ACACACAGTTTGGTG
*
49768296 ACACACGGTTTGGTG
1 ACACACAGTTTGGTG
49768311 A
1 A
49768312 TACAGCCGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (15 bp):
ACACACAGTTTGGTG
Found at i:49772718 original size:46 final size:46
Alignment explanation
Indices: 49772668--49772933 Score: 258
Period size: 46 Copynumber: 5.7 Consensus size: 46
49772658 TGGTTGAGCA
* *
49772668 TCCGAACTCGTTGAGTTAAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAGG
* * *
49772714 TCCGAACTCGTTGAGTTGAGTCCGAGTTCA-TGA--AATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--AGG
* *
49772759 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAGG
* * * *
49772807 -CTCGAGCTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--AGG
* * *
49772852 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAGG
* *
49772900 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
49772934 GGGGCGGGTT
Statistics
Matches: 179, Mismatches: 25, Indels: 32
0.76 0.11 0.14
Matches are distributed among these distances:
43 10 0.06
45 9 0.05
46 86 0.48
47 56 0.31
48 9 0.05
50 9 0.05
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAGG
Found at i:49772776 original size:47 final size:47
Alignment explanation
Indices: 49772665--49772884 Score: 233
Period size: 47 Copynumber: 4.7 Consensus size: 47
49772655 GGATGGTTGA
* * * *
49772665 GCATCCGAACTCGTTGAGTTAAGTCCGAGTTCACTTATGGATGCAA--AT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCA-TGA--GATGTAACTAG
*
49772713 G--TCCGAACTCGTTGAGTTGAGTCCGAGTTCATGAAATGTAACTAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATGAGATGTAACTAG
* *
49772758 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCA-TGA--GATG-TAACTAG
* *
49772806 GC-T-CGAGCTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATGAGATGTAACTAG
49772851 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAT
49772885 TTATGGATGC
Statistics
Matches: 145, Mismatches: 14, Indels: 27
0.78 0.08 0.15
Matches are distributed among these distances:
42 3 0.02
43 9 0.06
45 8 0.06
46 56 0.39
47 58 0.40
48 5 0.03
50 3 0.02
51 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (47 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATGAGATGTAACTAG
Found at i:49772824 original size:93 final size:93
Alignment explanation
Indices: 49772665--49772929 Score: 442
Period size: 93 Copynumber: 2.8 Consensus size: 93
49772655 GGATGGTTGA
* * *
49772665 GCATCCGAACTCGTTGAGTTAAGTCCGAGTTCACTTATGGATGCAAATG-TCCGAACTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCT-CGAGCTCGTTGAG
49772729 TTGAGTCCGAGTTCATGAAATGTAACTAG
65 TTGAGTCCGAGTTCATGAAATGTAACTAG
*
49772758 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCTCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCTCGAGCTCGTTGAGT
* *
49772823 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCATGAAATGTAACTAG
* *
49772851 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAATGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCTCGAGCTCGTTGAGT
49772916 TGAGTCCGAGTTCA
66 TGAGTCCGAGTTCA
49772930 CTTAGGGGCG
Statistics
Matches: 161, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
93 160 0.99
94 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCTCGAGCTCGTTGAGT
TGAGTCCGAGTTCATGAAATGTAACTAG
Found at i:49773195 original size:19 final size:20
Alignment explanation
Indices: 49773158--49773195 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
49773148 ATAAGGTGGT
49773158 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
49773178 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
49773196 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:49778081 original size:328 final size:328
Alignment explanation
Indices: 49777485--49778136 Score: 1252
Period size: 328 Copynumber: 2.0 Consensus size: 328
49777475 GATGCTTTAA
49777485 GCAGAAAGTTGTTGTTTGCTTTGAGAGTTATGAACACTCAGTTGAAAATTTCAGATGACGGTTCG
1 GCAGAAAGTTGTTGTTTGCTTTGAGAGTTATGAACACTCAGTTGAAAATTTCAGATGACGGTTCG
*
49777550 ATTCTAGCAGAGTTAAGAGCAAGACCGATGTTTTTACAAGAGATTTCTGAAGCTCAAAAAATGAT
66 ATTCTAGCAGAGTTAAGAGCAAGACCAATGTTTTTACAAGAGATTTCTGAAGCTCAAAAAATGAT
49777615 CAAGATTTGCTAGCCAAAAGAAAACAGTGTGAAGCTGATACGGGATCAGATTTCAGAATCGGTTC
131 CAAGATTTGCTAGCCAAAAGAAAACAGTGTGAAGCTGATACGGGATCAGATTTCAGAATCGGTTC
49777680 TGATGGTTGTTTGATGTTTAAAAATCAGATTTGTGTACCGAAAAATGATGAGTTGATTCAAAAGA
196 TGATGGTTGTTTGATGTTTAAAAATCAGATTTGTGTACCGAAAAATGATGAGTTGATTCAAAAGA
*
49777745 TTTTGCATGAAGCACATAATGGTTGTTTAGCGGTTCATCCGGGCA-TAGGAAGATGTATAATGAT
261 TTTTGCATGAAGCACATAATGGTTGTTTAGCGGTTCATCCGGGCAGTACGAAGATGTATAATGAT
49777809 TTT
326 TTT
49777812 GCAGAAAGTTGTTGTTTGCTTTGAGAGTTATGAACACTCAGTTGAAAATTTCAGATGACGGTTCG
1 GCAGAAAGTTGTTGTTTGCTTTGAGAGTTATGAACACTCAGTTGAAAATTTCAGATGACGGTTCG
* *
49777877 ATTCTAGCAGAGTTAAGAGCAAGACCAATGTTTTTAGAAGATATTTCTGAAGCTCAAAAAAATGA
66 ATTCTAGCAGAGTTAAGAGCAAGACCAATGTTTTTACAAGAGATTTCTGAAGCTC-AAAAAATGA
49777942 TCAAGATTTGCTAGCCAAAAGAAAACAGTGTGAAGCTGATACGGGATCAGATTTCAGAATCGGTT
130 TCAAGATTTGCTAGCCAAAAGAAAACAGTGTGAAGCTGATACGGGATCAGATTTCAGAATCGGTT
49778007 CTGATGGTTGTTTGATGTTTAAAAATCAGATTTGTGTACCGAAAAATGATGAGTTGATTCAAAAG
195 CTGATGGTTGTTTGATGTTTAAAAATCAGATTTGTGTACCGAAAAATGATGAGTTGATTCAAAAG
49778072 ATTTTGCATGAAGCACATAATGGTTGTTTAGCGGTTCATCCGGGCAGTACGAAGATGTATAATGA
260 ATTTTGCATGAAGCACATAATGGTTGTTTAGCGGTTCATCCGGGCAGTACGAAGATGTATAATGA
49778137 CTTGAAGAAA
Statistics
Matches: 319, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
327 117 0.37
328 185 0.58
329 17 0.05
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (328 bp):
GCAGAAAGTTGTTGTTTGCTTTGAGAGTTATGAACACTCAGTTGAAAATTTCAGATGACGGTTCG
ATTCTAGCAGAGTTAAGAGCAAGACCAATGTTTTTACAAGAGATTTCTGAAGCTCAAAAAATGAT
CAAGATTTGCTAGCCAAAAGAAAACAGTGTGAAGCTGATACGGGATCAGATTTCAGAATCGGTTC
TGATGGTTGTTTGATGTTTAAAAATCAGATTTGTGTACCGAAAAATGATGAGTTGATTCAAAAGA
TTTTGCATGAAGCACATAATGGTTGTTTAGCGGTTCATCCGGGCAGTACGAAGATGTATAATGAT
TTT
Found at i:49780696 original size:46 final size:44
Alignment explanation
Indices: 49780646--49780856 Score: 222
Period size: 46 Copynumber: 4.8 Consensus size: 44
49780636 TGGTTGAGCA
49780646 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAT-GATG-GAATG
49780692 TCCGAACTCGTTGAGTTGAGTCCGAGTTCAC-T-T-ATGG-A--
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGATGGAATG
* * * *
49780730 TCCGAGCTCATTGAGTTGAGTCCGAGTTCA-TGA-GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGATGGAA-T--G
*
49780775 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAT-GATG-GAATG
* *
49780823 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
49780857 GGGGCGGGTT
Statistics
Matches: 139, Mismatches: 11, Indels: 30
0.77 0.06 0.17
Matches are distributed among these distances:
38 28 0.20
39 3 0.02
40 2 0.01
41 1 0.01
42 3 0.02
44 1 0.01
45 1 0.01
46 62 0.45
47 28 0.20
48 3 0.02
50 5 0.04
51 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.30
Consensus pattern (44 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGATGGAATG
Found at i:49780755 original size:20 final size:20
Alignment explanation
Indices: 49780691--49780760 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
49780681 GGATGCGAAT
* *
49780691 GTCCGAACTCGTTGAGTTGA
1 GTCCGAGCTCATTGAGTTGA
* *
49780711 GTCCGAGTTCACTT-A-TGGA
1 GTCCGAGCTCA-TTGAGTTGA
49780730 -TCCGAGCTCATTGAGTTGA
1 GTCCGAGCTCATTGAGTTGA
*
49780749 GTCCGAGTTCAT
1 GTCCGAGCTCAT
49780761 GAGATGTAAC
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
17 2 0.05
18 10 0.26
19 6 0.15
20 19 0.49
21 2 0.05
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.31
Consensus pattern (20 bp):
GTCCGAGCTCATTGAGTTGA
Found at i:49781118 original size:19 final size:20
Alignment explanation
Indices: 49781081--49781118 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
49781071 ATAAGGTGGT
49781081 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
49781101 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
49781119 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:49789164 original size:23 final size:22
Alignment explanation
Indices: 49789113--49789165 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
49789103 TAACAATAGC
*
49789113 AGAAAAACATGTCATAAGATAA
1 AGAAAAACATGTCATAAAATAA
*
49789135 AGGAAAAGCATGTCATAAAATAGA
1 A-GAAAAACATGTCATAAAATA-A
*
49789159 AAAAAAA
1 AGAAAAA
49789166 AGCTTTAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 1 0.04
23 22 0.88
24 2 0.08
ACGTcount: A:0.62, C:0.08, G:0.15, T:0.15
Consensus pattern (22 bp):
AGAAAAACATGTCATAAAATAA
Found at i:49789446 original size:3 final size:3
Alignment explanation
Indices: 49789438--49789564 Score: 254
Period size: 3 Copynumber: 42.3 Consensus size: 3
49789428 CATTAAAAAG
49789438 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
49789486 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
49789534 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
49789565 AAAAAGTAGA
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 124 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:49790230 original size:13 final size:12
Alignment explanation
Indices: 49790208--49790232 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49790198 TATATGCAAT
49790208 TTATCCAAAAAA
1 TTATCCAAAAAA
49790220 TTATCCAAAAAA
1 TTATCCAAAAAA
49790232 T
1 T
49790233 AAACACAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (12 bp):
TTATCCAAAAAA
Found at i:49798971 original size:22 final size:21
Alignment explanation
Indices: 49798935--49798980 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
49798925 TCGGTCCTTG
49798935 TAGTCTTTAGACTTTTGAAATT
1 TAGTCTTTAGACTTTT-AAATT
** *
49798957 TAGTCTTTATTCTTTTAATTT
1 TAGTCTTTAGACTTTTAAATT
49798978 TAG
1 TAG
49798981 GATTTGAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.24, C:0.09, G:0.11, T:0.57
Consensus pattern (21 bp):
TAGTCTTTAGACTTTTAAATT
Found at i:49806729 original size:19 final size:19
Alignment explanation
Indices: 49806692--49806729 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
49806682 AATTGTTAAA
*
49806692 TATAATTAAAATATAATAT
1 TATAATTAAAAAATAATAT
49806711 TATAA-TAAAAAATACATAT
1 TATAATTAAAAAATA-ATAT
49806730 ACTTTGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
TATAATTAAAAAATAATAT
Found at i:49806843 original size:41 final size:41
Alignment explanation
Indices: 49806757--49806843 Score: 95
Period size: 41 Copynumber: 2.1 Consensus size: 41
49806747 AATTTGATAC
* * * *
49806757 ATAAAACTTTTATTATGGTTCAAATATATATATATATATAT
1 ATAAAACTTTTATTATGATTCAAATATACATATATAAATAA
* * *
49806798 ATAAAAC-TTTACTTTTGATTCAATTATACATATTTAAATAA
1 ATAAAACTTTTA-TTATGATTCAAATATACATATATAAATAA
49806839 ATAAA
1 ATAAA
49806844 TACATTAATT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 4 0.11
41 34 0.89
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (41 bp):
ATAAAACTTTTATTATGATTCAAATATACATATATAAATAA
Found at i:49807023 original size:30 final size:32
Alignment explanation
Indices: 49806964--49807025 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
49806954 ACACAAAATC
*
49806964 AAATTTCATATATAATCTTATACATTTATCCA
1 AAATTTCATATATAATCTTATAAATTTATCCA
*
49806996 AAATTT-ATATATAATTTTA-AAATTTATCCA
1 AAATTTCATATATAATCTTATAAATTTATCCA
49807026 TGATAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 10 0.36
31 12 0.43
32 6 0.21
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.45
Consensus pattern (32 bp):
AAATTTCATATATAATCTTATAAATTTATCCA
Found at i:49807607 original size:10 final size:10
Alignment explanation
Indices: 49807594--49807627 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
49807584 TAATTTTTTT
49807594 AAATTATAAA
1 AAATTATAAA
**
49807604 AAATTGCAAA
1 AAATTATAAA
49807614 AAATTATAAA
1 AAATTATAAA
49807624 AAAT
1 AAAT
49807628 AGTATAATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (10 bp):
AAATTATAAA
Found at i:49818335 original size:25 final size:26
Alignment explanation
Indices: 49818299--49818363 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 26
49818289 TATTTTACGT
* *
49818299 TTAGTAACATTTTGACGA-TTTTCCC
1 TTAGTAAAATTTTGACAATTTTTCCC
* *
49818324 TTGGTAAAATTTTAACAATTTTTCCC
1 TTAGTAAAATTTTGACAATTTTTCCC
49818350 TTAGT-AAATTTTGA
1 TTAGTAAAATTTTGA
49818364 GAAAATATGT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
25 22 0.67
26 11 0.33
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (26 bp):
TTAGTAAAATTTTGACAATTTTTCCC
Found at i:49822387 original size:28 final size:27
Alignment explanation
Indices: 49822324--49822393 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
49822314 ATAGTGAGTC
49822324 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
49822351 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
49822379 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
49822394 GTACAAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Done.