Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 34 of 295
Found at i:9502611 original size:5 final size:5
Alignment explanation
Indices: 9502603--9502628 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
9502593 AAAATTTGAT
9502603 TTTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC T
9502629 GGGTATTTAG
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:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:9505736 original size:19 final size:21
Alignment explanation
Indices: 9505705--9505750 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
9505695 TAAATTTTAC
*
9505705 AATTTTTATAAA-TATTTTG-
1 AATTTTTATAAATTATATTGT
9505724 AATTTTTGA-AAATTATATTGT
1 AATTTTT-ATAAATTATATTGT
9505745 AATTTT
1 AATTTT
9505751 GGTTAAGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 10 0.43
20 7 0.30
21 6 0.26
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
AATTTTTATAAATTATATTGT
Found at i:9506933 original size:17 final size:17
Alignment explanation
Indices: 9506913--9506945 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9506903 CTTAAATTAA
*
9506913 TAAATTAATTTCTCAAT
1 TAAATAAATTTCTCAAT
9506930 TAAATAAATTTCTCAA
1 TAAATAAATTTCTCAA
9506946 CTCAATTCTA
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:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATAAATTTCTCAAT
Found at i:9509454 original size:46 final size:46
Alignment explanation
Indices: 9509368--9509544 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
9509358 ACATATCCGT
* * * *
9509368 GCCGATGCCGTGTCCCAGACATGGTCTTACACT-GAC--ACATTTTGTA
1 GCCGATG-CATGTCCTAGACAT-GTCTTACACTAG-CTTACATTTCGAA
9509414 GCCGATGCATGTCCTAGACATGTCTTACACTAGCTTACATTTCGAA
1 GCCGATGCATGTCCTAGACATGTCTTACACTAGCTTACATTTCGAA
* * *
9509460 GCCGATGCATGTCTTAGACATGTCTTATACTGGCTTACATTTCGAA
1 GCCGATGCATGTCCTAGACATGTCTTACACTAGCTTACATTTCGAA
* * *
9509506 GCCGATGCATGTCTTAGACATGTTTTACACTAGCATACA
1 GCCGATGCATGTCCTAGACATGTCTTACACTAGCTTACA
9509545 ATTAACTTGA
Statistics
Matches: 117, Mismatches: 11, Indels: 6
0.87 0.08 0.04
Matches are distributed among these distances:
44 11 0.09
45 13 0.11
46 93 0.79
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (46 bp):
GCCGATGCATGTCCTAGACATGTCTTACACTAGCTTACATTTCGAA
Found at i:9517060 original size:46 final size:48
Alignment explanation
Indices: 9516811--9517129 Score: 215
Period size: 46 Copynumber: 6.8 Consensus size: 48
9516801 CATAGGGTAT
* * * * *
9516811 AATGCCAATGCCATATCCCAGACATGGTCTTACATTGGCCCATC-TATC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTC-TCATATC
* * *
9516859 AA-GTCGATGCCATGTCCTAGACATGGTCTTTCACT-GACTCTCACATATC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAG-CTCT--CATATC
** * * *
9516908 CGTGCCGATGCCATGTCCCAGACATGGTCTTACACT-G-ACACATTTTGC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCA-TAT-C
** *
9516956 -A-GCCGATG-CATGTAACAGACAT-GTCTTACACTAGCT-TACATCTC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCT-CATATC
* *
9517000 GA-GACCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCT-TTATC
1 AATG-CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATC
* * *
9517045 AATGCCGATGCCATGTCCCAGACATGGTTTTACACTGGCTCTCGTA--
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATC
* *
9517091 ATGTGGCCAATG-CATGTCCCAGACAT-GTCTTACACTAGC
1 A-AT-GCCGATGCCATGTCCCAGACATGGTCTTACACTAGC
9517130 ACACAATTAA
Statistics
Matches: 219, Mismatches: 33, Indels: 40
0.75 0.11 0.14
Matches are distributed among these distances:
44 11 0.05
45 27 0.12
46 72 0.33
47 61 0.28
48 13 0.06
49 4 0.02
50 31 0.14
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (48 bp):
AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATC
Found at i:9518679 original size:22 final size:21
Alignment explanation
Indices: 9518653--9518696 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
9518643 TTCACCCGTT
9518653 AGGCTTCAGTGTCGCGACACCC
1 AGGCTTCAGTGTCGCGAC-CCC
**
9518675 AGGCTTTGGTGTCGCGACCCC
1 AGGCTTCAGTGTCGCGACCCC
9518696 A
1 A
9518697 CGACAGTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.16, C:0.34, G:0.30, T:0.20
Consensus pattern (21 bp):
AGGCTTCAGTGTCGCGACCCC
Found at i:9522282 original size:47 final size:48
Alignment explanation
Indices: 9522166--9522294 Score: 215
Period size: 48 Copynumber: 2.7 Consensus size: 48
9522156 GTGCGAGCGA
*
9522166 TACCTTGATTTGGCTATGGGCCATGGTATAGGTATTTCGGAGAGGAGT
1 TACCTTGATTTGGCTATGGGCCATGGTATAGGTATTTCGGAGAGAAGT
* *
9522214 TACCTTGATTTGGCTACGGGCCATGGTATAGGTATTTCGG-GATAAGT
1 TACCTTGATTTGGCTATGGGCCATGGTATAGGTATTTCGGAGAGAAGT
*
9522261 TACCTAGATTTGGCTATGGGCCATGGTATAGGTA
1 TACCTTGATTTGGCTATGGGCCATGGTATAGGTA
9522295 CTTATCGATT
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
47 37 0.49
48 39 0.51
ACGTcount: A:0.22, C:0.14, G:0.31, T:0.33
Consensus pattern (48 bp):
TACCTTGATTTGGCTATGGGCCATGGTATAGGTATTTCGGAGAGAAGT
Found at i:9522362 original size:29 final size:29
Alignment explanation
Indices: 9522320--9522377 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
9522310 TATTAAATAT
9522320 CCAATTTCTATTCTGAATGGTTCAACGGG
1 CCAATTTCTATTCTGAATGGTTCAACGGG
9522349 CCAATTTCTATTCTGAATGGTTCAACGGG
1 CCAATTTCTATTCTGAATGGTTCAACGGG
9522378 TCAACGAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (29 bp):
CCAATTTCTATTCTGAATGGTTCAACGGG
Found at i:9523953 original size:104 final size:104
Alignment explanation
Indices: 9523772--9523976 Score: 302
Period size: 104 Copynumber: 2.0 Consensus size: 104
9523762 CTGTCTGTTT
* * * *
9523772 TTGTCCCCTCAAATAGTCCAGATTGCACATGTTATTTCCTTGTACTTATCCTTAGAATGCACAAA
1 TTGTCCCCGCAAATAGCCCAGATTGCACATGTTATTTACTTGCACTTATCCTTAGAATGCACAAA
*
9523837 TAACAACCAGTCCATCCACTGTCTGTATCTCTCATTCAA
66 GAACAACCAGTCCATCCACTGTCTGTATCTCTCATTCAA
* * *
9523876 TTGTCCCCGCAAATAGCCCAGATTGCACATGTTATTTATTTGCACTTATCCTTAGACTGCATAAA
1 TTGTCCCCGCAAATAGCCCAGATTGCACATGTTATTTACTTGCACTTATCCTTAGAATGCACAAA
* * * *
9523941 GAACAGCTAGTCCATCCATTGTTTGTATCTCTCATT
66 GAACAACCAGTCCATCCACTGTCTGTATCTCTCATT
9523977 AAACTAATTT
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
104 89 1.00
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.35
Consensus pattern (104 bp):
TTGTCCCCGCAAATAGCCCAGATTGCACATGTTATTTACTTGCACTTATCCTTAGAATGCACAAA
GAACAACCAGTCCATCCACTGTCTGTATCTCTCATTCAA
Found at i:9528462 original size:23 final size:23
Alignment explanation
Indices: 9528394--9528464 Score: 87
Period size: 21 Copynumber: 3.3 Consensus size: 23
9528384 CCTGATCAGT
** *
9528394 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACGAGGTGCCTGAA
9528416 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACGAGGTGCCTGAA
9528436 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACGAGGTGCCTGAA
9528459 ATACGA
1 ATACGA
9528465 TACATAAAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
20 1 0.02
21 34 0.81
22 1 0.02
23 6 0.14
ACGTcount: A:0.38, C:0.25, G:0.23, T:0.14
Consensus pattern (23 bp):
ATACGACACACGAGGTGCCTGAA
Found at i:9528476 original size:23 final size:23
Alignment explanation
Indices: 9528394--9528480 Score: 83
Period size: 21 Copynumber: 4.0 Consensus size: 23
9528384 CCTGATCAGT
*
9528394 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
9528416 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
9528436 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
* *
9528459 ATACGATACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
9528481 TCGATAAAGC
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.63
22 1 0.02
23 18 0.33
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:9530008 original size:27 final size:30
Alignment explanation
Indices: 9529963--9530017 Score: 71
Period size: 27 Copynumber: 1.9 Consensus size: 30
9529953 GCTCGAATGC
*
9529963 TTTCTGTTCTCTTTTCTCT-ATTCTTTTTG
1 TTTCTGTTCTCTTTACTCTGATTCTTTTTG
*
9529992 TTTCT-TT-TCTTTACTCTGTTTCTTTT
1 TTTCTGTTCTCTTTACTCTGATTCTTTT
9530018 ATTCACTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 9 0.39
28 9 0.39
29 5 0.22
ACGTcount: A:0.04, C:0.20, G:0.05, T:0.71
Consensus pattern (30 bp):
TTTCTGTTCTCTTTACTCTGATTCTTTTTG
Found at i:9530273 original size:20 final size:21
Alignment explanation
Indices: 9530232--9530271 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
9530222 TTTTTATTAA
*
9530232 TCACTCTAATTTAAGCTAAAT
1 TCACTCTAATTTAACCTAAAT
9530253 TCAC-CTAATTTAAACCTAA
1 TCACTCTAATTT-AACCTAA
9530272 TTAAACACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.40, C:0.23, G:0.03, T:0.35
Consensus pattern (21 bp):
TCACTCTAATTTAACCTAAAT
Found at i:9532532 original size:128 final size:127
Alignment explanation
Indices: 9532400--9532640 Score: 419
Period size: 128 Copynumber: 1.9 Consensus size: 127
9532390 AAGTGTGTGC
* * * *
9532400 ACAACTCGAGTTGGATTTTAGGATTCACTCGTTCCAAAGGAATAAAATACTACATCCAGCACGTT
1 ACAACTCAAGTTGGATTTTAAGATTCACTCGTTCCAAAAGAATAAAATACCACATCCAGCACGTT
*
9532465 AGGACACGATATTTTAAGCCTCCAAAAAACTGAGATCACCTCATGATTTCCAAAACATGCAAA
66 AGGACACGATATTTTAAGCCTCC-AAAAACTGAGATCACCACATGATTTCCAAAACATGCAAA
*
9532528 ACAACTCAAGTTGGATTTTAAGATTCACTCGTTCCAAAAGAATAAAATACCAGATCCAGCACGTT
1 ACAACTCAAGTTGGATTTTAAGATTCACTCGTTCCAAAAGAATAAAATACCACATCCAGCACGTT
9532593 AGGACACGATATTTTAAGCCTCCAAAAACTGAGATCACCACATGATTT
66 AGGACACGATATTTTAAGCCTCCAAAAACTGAGATCACCACATGATTT
9532641 TCGAAACACG
Statistics
Matches: 107, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
127 24 0.22
128 83 0.78
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (127 bp):
ACAACTCAAGTTGGATTTTAAGATTCACTCGTTCCAAAAGAATAAAATACCACATCCAGCACGTT
AGGACACGATATTTTAAGCCTCCAAAAACTGAGATCACCACATGATTTCCAAAACATGCAAA
Found at i:9535087 original size:45 final size:45
Alignment explanation
Indices: 9535031--9535128 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 45
9535021 GTGGCTAAAA
* * *
9535031 TCTGCTCCATAGCCGATACATGGAGATAAGACTCT-CCATTTTCAG
1 TCTGCTTCATAGCCGATACATGGAGATAAGA-TCTGCAACTTTCAG
* *
9535076 TCTGCTTCATAGTCGATACATGGAGATAAGATCTGTAACTTTCAG
1 TCTGCTTCATAGCCGATACATGGAGATAAGATCTGCAACTTTCAG
9535121 TCTGCTTC
1 TCTGCTTC
9535129 CTTGCTATCT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 3 0.06
45 44 0.94
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (45 bp):
TCTGCTTCATAGCCGATACATGGAGATAAGATCTGCAACTTTCAG
Found at i:9535159 original size:178 final size:177
Alignment explanation
Indices: 9534835--9535296 Score: 586
Period size: 178 Copynumber: 2.6 Consensus size: 177
9534825 CTGCAACTTT
* * * *
9534835 AGAGAGACAAGG-TCGGTGGCTAAAATCTACTCCATAGCCGATACATGGAGATAAGACTCGCTAT
1 AGAGAGATAAGGCT-GGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCTCCA-
* * * *
9534899 TTTTTA-TCTG-TTC----C-ATACATGGATATAAGCTCTGTAACTTTCAATTTGCTTCCTTGCT
64 TTTTCAGTCTGCTTCATAGCGATACATGGAGATAAGATCTGTAACTTTCAATCTGCTTCCTTGCT
*
9534957 ACCTCAGGAAGACAATACTTGTATCTCCAACCTACTCTCTTGCTACCTC
129 ACCTCAGGAAGACAAGACTTGTATCTCCAACCTACTCTCTTGCTACCTC
9535006 AGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCTCCATT
1 AGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCTCCATT
*
9535071 TTCAGTCTGCTTCATAGTCGATACATGGAGATAAGATCTGTAACTTTCAGTCTGCTTCCTTGCTA
66 TTCAGTCTGCTTCATAG-CGATACATGGAGATAAGATCTGTAACTTTCAATCTGCTTCCTTGCTA
* * * * *
9535136 TCTGAGGAAGATAAGACTTGTATCTTCAACCTGCTCTCTTGCTACCTC
130 CCTCAGGAAGACAAGACTTGTATCTCCAACCTACTCTCTTGCTACCTC
* * * *
9535184 AGAGAGATAAGGCTGGTGGCTCAAATTTGCTCCATAGCTGATACATGGAGATAAGA-TTTGCCAT
1 AGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCT-CCAT
* * * *
9535248 CTTC-GATCTGCTCCATAGCCGATACATAGAGATAAGATCTGCAA-TTTCA
65 TTTCAG-TCTGCTTCATAG-CGATACATGGAGATAAGATCTGTAACTTTCA
9535297 CTGATGTCGC
Statistics
Matches: 256, Mismatches: 24, Indels: 16
0.86 0.08 0.05
Matches are distributed among these distances:
170 5 0.02
171 61 0.24
172 4 0.02
177 9 0.04
178 177 0.69
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (177 bp):
AGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCTCCATT
TTCAGTCTGCTTCATAGCGATACATGGAGATAAGATCTGTAACTTTCAATCTGCTTCCTTGCTAC
CTCAGGAAGACAAGACTTGTATCTCCAACCTACTCTCTTGCTACCTC
Found at i:9539961 original size:21 final size:21
Alignment explanation
Indices: 9539936--9539979 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
9539926 GAAATGCAAG
*
9539936 AAAAGAAAATTTGCTCAAGAT
1 AAAAGAAAATTTGCTCAAAAT
*
9539957 AAAAGAATATTTGCTCAAAAT
1 AAAAGAAAATTTGCTCAAAAT
9539978 AA
1 AA
9539980 GACATAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.55, C:0.09, G:0.11, T:0.25
Consensus pattern (21 bp):
AAAAGAAAATTTGCTCAAAAT
Found at i:9548436 original size:88 final size:87
Alignment explanation
Indices: 9548327--9548487 Score: 216
Period size: 88 Copynumber: 1.8 Consensus size: 87
9548317 ACCGTCTTTT
* * * *
9548327 GATCTGCTTCCCTACTTCTTAGGGTGATAAGATTTATAAACTTC-AGCTTGTTACCCTACTACTT
1 GATCTGCTTCCCTACTACTTAGGGGGATAAGATCTATAAAC-TCGA-CCTGTTACCCTACTACTT
9548391 AGGGGGTTAAAGCTCGTTGCCTTC
64 AGGGGGTTAAAGCTCGTTGCCTTC
* * * *
9548415 GATCTGTTTCCCTACTACTTAGGGGGTTAAGATCTGTAAACTCGACCTGTTACCCTACTGCTTAG
1 GATCTGCTTCCCTACTACTTAGGGGGATAAGATCTATAAACTCGACCTGTTACCCTACTACTTAG
*
9548480 GGGTTTAA
66 GGGGTTAA
9548488 GGTCTACAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
87 27 0.43
88 36 0.57
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.35
Consensus pattern (87 bp):
GATCTGCTTCCCTACTACTTAGGGGGATAAGATCTATAAACTCGACCTGTTACCCTACTACTTAG
GGGGTTAAAGCTCGTTGCCTTC
Found at i:9548479 original size:43 final size:43
Alignment explanation
Indices: 9548375--9548531 Score: 136
Period size: 43 Copynumber: 3.6 Consensus size: 43
9548365 AACTTCAGCT
* *** *
9548375 TGTTACCCTACTACTTAGGGGGTTAA-AGCTCGTTGCCTTCGATC
1 TGTTACCCTACTACTTAGGGGGTTAAGATCT-GTAAAC-TCGACC
*
9548419 TGTTTCCCTACTACTTAGGGGGTTAAGATCTGTAAACTCGACC
1 TGTTACCCTACTACTTAGGGGGTTAAGATCTGTAAACTCGACC
* * * ** * * * *
9548462 TGTTACCCTACTGCTTAGGGGTTTAAGGTCTACAAATTTGGCT
1 TGTTACCCTACTACTTAGGGGGTTAAGATCTGTAAACTCGACC
* *
9548505 TGCTACCCTACTGCTTAGGGGGTTAAG
1 TGTTACCCTACTACTTAGGGGGTTAAG
9548532 GCCTGTGAAT
Statistics
Matches: 94, Mismatches: 18, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
43 63 0.67
44 28 0.30
45 3 0.03
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (43 bp):
TGTTACCCTACTACTTAGGGGGTTAAGATCTGTAAACTCGACC
Found at i:9560450 original size:3 final size:3
Alignment explanation
Indices: 9560442--9560500 Score: 50
Period size: 3 Copynumber: 20.0 Consensus size: 3
9560432 ATAAAAGATG
* * * * *
9560442 ATA ATA ATA ATG ATA ATA ATA AT- GTA GTA CCT- ATA ATA CTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
9560486 ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA
9560501 CTATTAATGA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
2 2 0.04
3 43 0.93
4 1 0.02
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:9560456 original size:12 final size:12
Alignment explanation
Indices: 9560439--9560500 Score: 56
Period size: 12 Copynumber: 5.0 Consensus size: 12
9560429 AACATAAAAG
9560439 ATGATAATAATA
1 ATGATAATAATA
9560451 ATGATAATAATA
1 ATGATAATAATA
*
9560463 ATG-TAGTACCTATA
1 ATGATAATA---ATA
9560477 AT-ACTAATAATA
1 ATGA-TAATAATA
*
9560489 ATAATAATAATA
1 ATGATAATAATA
9560501 CTATTAATGA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
11 4 0.10
12 28 0.67
13 1 0.02
14 5 0.12
15 4 0.10
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (12 bp):
ATGATAATAATA
Found at i:9560771 original size:14 final size:14
Alignment explanation
Indices: 9560729--9560772 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
9560719 AACAACTATA
9560729 AGTATATACATAAAT
1 AGTATATACAT-AAT
*
9560744 AGATATATA-GTAAT
1 AG-TATATACATAAT
9560758 AGTATATACATAAT
1 AGTATATACATAAT
9560772 A
1 A
9560773 TAGTTATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
13 6 0.24
14 10 0.40
15 3 0.12
16 6 0.24
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.34
Consensus pattern (14 bp):
AGTATATACATAAT
Found at i:9560801 original size:26 final size:25
Alignment explanation
Indices: 9560728--9560817 Score: 74
Period size: 26 Copynumber: 3.4 Consensus size: 25
9560718 AAACAACTAT
9560728 AAGTATATACATAA-ATAGATATATAGTA
1 AAGTATATACATAAGATAG-TATA-A--A
* *
9560756 ATAGTATATACATAATATAGTTATTAA
1 A-AGTATATACATAAGATAG-TATAAA
**
9560783 AAGTATATATGTAAGATAGTATAAA
1 AAGTATATACATAAGATAGTATAAA
9560808 AATGTATATA
1 AA-GTATATA
9560818 ATATAGTATC
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
25 7 0.13
26 22 0.42
27 2 0.04
28 1 0.02
29 14 0.26
30 7 0.13
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.36
Consensus pattern (25 bp):
AAGTATATACATAAGATAGTATAAA
Found at i:9562920 original size:13 final size:13
Alignment explanation
Indices: 9562902--9562926 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9562892 AACTTGGCTT
9562902 GTATTTTGGGCCA
1 GTATTTTGGGCCA
9562915 GTATTTTGGGCC
1 GTATTTTGGGCC
9562927 GGGTTTTGTA
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:0.12, C:0.16, G:0.32, T:0.40
Consensus pattern (13 bp):
GTATTTTGGGCCA
Found at i:9571299 original size:20 final size:20
Alignment explanation
Indices: 9571274--9571317 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
9571264 TTAGTTTTGA
*
9571274 ATTTTTTTAAATTTTAAAAT
1 ATTTTTATAAATTTTAAAAT
* *
9571294 ATTTTTATAATTTTTAAATT
1 ATTTTTATAAATTTTAAAAT
9571314 ATTT
1 ATTT
9571318 GTTGATATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTTTTATAAATTTTAAAAT
Found at i:9572770 original size:8 final size:8
Alignment explanation
Indices: 9572759--9572785 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
9572749 AAAATACAAA
9572759 AAAAATAT
1 AAAAATAT
9572767 AAAAATAT
1 AAAAATAT
9572775 AAAAATAT
1 AAAAATAT
9572783 AAA
1 AAA
9572786 TTTTTACCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAAATAT
Found at i:9572908 original size:11 final size:12
Alignment explanation
Indices: 9572878--9572909 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
9572868 TCCCCCTCCT
9572878 TTCTCTC-TCCC
1 TTCTCTCTTCCC
9572889 TTCTCTCTTCCC
1 TTCTCTCTTCCC
9572901 -TCTCTCTTC
1 TTCTCTCTTC
9572910 TTTTTTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (12 bp):
TTCTCTCTTCCC
Found at i:9573308 original size:3 final size:3
Alignment explanation
Indices: 9573300--9573336 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
9573290 TGTATTTCAA
9573300 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
9573337 GTACATTAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:9573492 original size:127 final size:129
Alignment explanation
Indices: 9573309--9573546 Score: 315
Period size: 127 Copynumber: 1.9 Consensus size: 129
9573299 ATATTATTAT
* * * * *
9573309 TATTATTATTATTATTATTATTATTATTGTACATTAGTGTATATCTTCATGTATGTATATATATA
1 TATTATTATTATTATTATTATTATCATTGAACATTACTATATATCTTCATGTATGTATATATACA
* * *
9573374 TGTAGTAATGTTTTT-ATTACTTTATTTTAATAT-TTTTTATTATAATAGCTTTTGTATTTCAA
66 TATAGTAATGTTTTTAATGACTTTATTTTAATATCATTTTATTATAATAGCTTTTGTATTTCAA
*
9573436 TATTATTATTATTGTTATTATTATCATT-AACATTACTATATATTCTT-AT-TAGATGTATATAT
1 TATTATTATTATTATTATTATTATCATTGAACATTACTATATA-TCTTCATGT--ATGTATATAT
* *
9573498 ACATATATTACTGTTTTTAATGACTTTATTTTAATATCATTTTATTATA
63 ACATATAGTAATGTTTTTAATGACTTTATTTTAATATCATTTTATTATA
9573547 TTTACTTTTT
Statistics
Matches: 95, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
125 1 0.01
126 13 0.14
127 54 0.57
128 17 0.18
129 10 0.11
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (129 bp):
TATTATTATTATTATTATTATTATCATTGAACATTACTATATATCTTCATGTATGTATATATACA
TATAGTAATGTTTTTAATGACTTTATTTTAATATCATTTTATTATAATAGCTTTTGTATTTCAA
Found at i:9581731 original size:29 final size:29
Alignment explanation
Indices: 9581689--9581747 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
9581679 TCCCCTGGGT
9581689 TTCATGTTGAACAATTGGACTGCCGAGGA
1 TTCATGTTGAACAATTGGACTGCCGAGGA
9581718 TTCATGTTGAACAATTGGACTGCCGAGGA
1 TTCATGTTGAACAATTGGACTGCCGAGGA
9581747 T
1 T
9581748 CTTCTTGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (29 bp):
TTCATGTTGAACAATTGGACTGCCGAGGA
Found at i:9586529 original size:75 final size:75
Alignment explanation
Indices: 9586422--9586643 Score: 354
Period size: 75 Copynumber: 2.9 Consensus size: 75
9586412 TATGTTTTCC
* * *
9586422 AAAAATCAGCTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTTAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTT
9586487 TGCTTTTCAA
66 TGCTTTTCAA
* * *
9586497 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTT
**
9586562 TGCTGGTCAA
66 TGCTTTTCAA
*
9586572 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCGATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT-
9586637 TTGCTTT
65 TTGCTTT
9586644 CCAATTTCTG
Statistics
Matches: 132, Mismatches: 14, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
75 128 0.97
76 4 0.03
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (75 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTT
TGCTTTTCAA
Found at i:9586906 original size:73 final size:72
Alignment explanation
Indices: 9586750--9587053 Score: 313
Period size: 72 Copynumber: 4.0 Consensus size: 72
9586740 TGTTTTTTTT
** * *
9586750 AAATCAACTCATAATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTTGACCTCC
1 AAATCAACTCAT-ATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATCTCT
*
9586815 GTTTTCGA
65 GTTTTCAA
*
9586823 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATCTCTG
9586888 TTTGTCAA
66 TTT-TCAA
** *
9586896 AAATCAACTCATATCACGAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGTCTTTTCAATTT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGG-----T-AA---
* *
9586960 TTTTTTAATTTCTGTTTTTCAA
54 --TTTCAATCTCTG-TTTTCAA
* *
9586982 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATCTC
1 A--AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATCTC
9587047 TGTTTTC
64 TGTTTTC
9587054 TCCAATTTAT
Statistics
Matches: 197, Mismatches: 15, Indels: 37
0.79 0.06 0.15
Matches are distributed among these distances:
72 53 0.27
73 49 0.25
74 5 0.03
75 20 0.10
80 3 0.02
81 3 0.02
86 27 0.14
87 3 0.02
88 32 0.16
89 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (72 bp):
AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATCTCTG
TTTTCAA
Found at i:9587009 original size:161 final size:157
Alignment explanation
Indices: 9586822--9587369 Score: 457
Period size: 161 Copynumber: 3.4 Consensus size: 157
9586812 TCCGTTTTCG
*
9586822 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
** *
9586887 GTTTGTCAAAAATCAACTCATATCACGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTCTT
66 GTTT-TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG-TCACA-GCTGAGGTATT
9586952 TTCAATTTTTTTTTAATTTCTGTTTTTCAAA
128 TTCAATTTTTTTTTAATTT-TGTTTTTCAAA
*
9586983 AAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATCTCT
1 AAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAA-----
* * *
9587048 GTTTTCTCCAATTTATGTTTTTCAAAAATTAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGG
61 ---TT-T-C------TG-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGT
* * *
9587113 CAC-GCTGAGGTATTCTCGATTTCTGTTTTTCAATTTATG--TTTC-CA
113 CACAGCTGAGGTATTTTCAATTT-T-TTTTT-AATTT-TGTTTTTCAAA
* * * * * * * *
9587158 AAAATCAATTCATAGC-ACTAAAGGTGAATTGAGCCTCGGGTCACATAGC-GAGGTATTTTCAAT
1 AAAATCAACTCATA-CTGCGAGAGGTGAGTTGAGCCTCAGG--ACA-CGCTGAGGTAATTTCAAT
*
9587221 TTATG-TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGT
62 TTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTCACA-GCTGAGGT
*
9587285 GTTTTCAA------TTT-A---TGTTTTTCAAA
125 ATTTTCAATTTTTTTTTAATTTTGTTTTTCAAA
* * *
9587308 AAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTC-GGAGCACGCTGAGGTATTTTCAATT
1 AAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGA-CACGCTGAGGTAATTTCAATT
9587370 AATGTTTTTT
Statistics
Matches: 317, Mismatches: 37, Indels: 79
0.73 0.09 0.18
Matches are distributed among these distances:
147 5 0.02
148 17 0.05
149 6 0.02
150 30 0.09
151 1 0.00
153 3 0.01
159 45 0.14
161 73 0.23
168 1 0.00
169 4 0.01
170 1 0.00
171 1 0.00
175 49 0.15
176 6 0.02
177 61 0.19
178 14 0.04
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (157 bp):
AAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
GTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTCACAGCTGAGGTATTTTC
AATTTTTTTTTAATTTTGTTTTTCAAA
Found at i:9587094 original size:89 final size:85
Alignment explanation
Indices: 9586876--9587171 Score: 321
Period size: 89 Copynumber: 3.4 Consensus size: 85
9586866 GCTGAGGTAA
* * **
9586876 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATCACGAGAGGTGAGTTGAGCCTC-GGCTCACA
1 TTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACA
*
9586940 TGCTGAGGTCTTTTCAATT-T-TT
63 TGCTGAGGT-ATTTCAATTCTGTT
* * *
9586962 TTTTAATTTCTGTTTTTCAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACAT
1 TTTCAATTTATGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAT
9587027 GCTGAGGTAATTTCAATCTCTGTT
64 GCTGAGGT-ATTTCAAT-TCTGTT
* * * *
9587051 TTCTCCAATTTATGTTTTTCAAAAATTAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCAC
1 TT-T-CAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAT
*
9587116 GCTGAGGTATTCTCGATTTCTGTT
64 GCTGAGGTATT-TC-AATTCTGTT
* *
9587140 TTTCAATTTATG-TTTCCAAAAATCAATTCATA
1 TTTCAATTTATGTTTTTCAAAAATCAACTCATA
9587172 GCACTAAAGG
Statistics
Matches: 181, Mismatches: 19, Indels: 20
0.82 0.09 0.09
Matches are distributed among these distances:
86 51 0.28
87 10 0.06
88 40 0.22
89 64 0.35
90 3 0.02
91 13 0.07
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (85 bp):
TTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGC
TGAGGTATTTCAATTCTGTT
Found at i:9587220 original size:177 final size:175
Alignment explanation
Indices: 9586879--9587220 Score: 381
Period size: 177 Copynumber: 1.9 Consensus size: 175
9586869 GAGGTAATTT
* *
9586879 CAATTTCTGTTTGTCAAAAATCAACTCATATCACGAGAGGTGAGTTGAGCCTCGGCTCACATGCT
1 CAATTTATGTTTGTCAAAAATCAACTCATATCACGAGAGGTGAGTTGAGCCTCGGCGCACA-GCT
* * * * *
9586944 GAGGTCTTTTCAATTTTTTTTTAATTTCTGTTTTTCAAAAAAATCAACTCATACTGCGAGAGGTG
65 GAGGTATTCTCAATTTTTTTTTAATTTATG-TTTTCAAAAAAATCAACTCATACTACGAAAGGTG
*
9587009 AGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATCTCTGTTTTCTC
129 AATTGAGCCTCAGGACATGCTGAGGTAATTTCAATCTCTGTTTTCTC
* * * **
9587056 CAATTTATGTTTTTCAAAAATTAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-GCAC-GCT
1 CAATTTATGTTTGTCAAAAATCAACTCATATCACGAGAGGTGAGTTGAGCCTC-GGCGCACAGCT
* * * *
9587119 GAGGTATTCTCGATTTCTGTTTTTCAATTTATG-TTTC-CAAAAATCAATTCATAGC-ACTAAAG
65 GAGGTATTCTCAATTT-T-TTTTT-AATTTATGTTTTCAAAAAAATCAACTCATA-CTACGAAAG
* *
9587181 GTGAATTGAGCCTCGGGTCACATAGC-GAGGTATTTTCAAT
126 GTGAATTGAGCCTCAGG--ACAT-GCTGAGGTAATTTCAAT
9587221 TTATGTTTCA
Statistics
Matches: 138, Mismatches: 19, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
175 49 0.36
176 6 0.04
177 72 0.52
178 11 0.08
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (175 bp):
CAATTTATGTTTGTCAAAAATCAACTCATATCACGAGAGGTGAGTTGAGCCTCGGCGCACAGCTG
AGGTATTCTCAATTTTTTTTTAATTTATGTTTTCAAAAAAATCAACTCATACTACGAAAGGTGAA
TTGAGCCTCAGGACATGCTGAGGTAATTTCAATCTCTGTTTTCTC
Found at i:9587263 original size:73 final size:72
Alignment explanation
Indices: 9587139--9587376 Score: 284
Period size: 73 Copynumber: 3.2 Consensus size: 72
9587129 CGATTTCTGT
* *** * * *
9587139 TTTTCAATTTATGTTTCCAAAAATCAATTCATAGCACTAAAGGTGAATTGAGCCTCGGGTCACAT
1 TTTTCAATTTATGTTT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC--
9587204 AGC-GAGGTA
63 AGCTGAGGTA
9587213 TTTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACG
1 TTTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACA-G
*
9587278 CTGAGGTG
65 CTGAGGTA
*
9587286 TTTTCAATTTATGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGAG-C
1 TTTTCAATTTATG--TTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG-GTC
9587350 AC-GCTGAGGTA
61 ACAGCTGAGGTA
*
9587361 TTTTCAATTAATGTTT
1 TTTTCAATTTATGTTT
9587377 TTTCAATTCA
Statistics
Matches: 146, Mismatches: 11, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
71 1 0.01
72 2 0.01
73 60 0.41
74 16 0.11
75 24 0.16
77 42 0.29
78 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (72 bp):
TTTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACAGC
TGAGGTA
Found at i:9587426 original size:165 final size:165
Alignment explanation
Indices: 9587213--9587621 Score: 416
Period size: 165 Copynumber: 2.4 Consensus size: 165
9587203 TAGCGAGGTA
* **
9587213 TTTTCAATTTATG-TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACAC
1 TTTTCAATTCATGTTTTC-AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGTCACAC
* * * ** * *
9587277 GCTGAGGTGTTTTCAATTTATGTTTTTC-AA-AAAAATCAACTCATATTGCGAGAGGTAAGTTGA
65 ACCGAGGTATTTTCAAAATATGTTTTACAAATAAAAATCAACTCATATTGCGAGAAGTAAGTTGA
*
9587340 GCCTCGGAGCAC-GCTGAGGTATTTTCAATTAATGTT
130 GCCTCGGAGCACGGCTGAGCTATTTTCAATTAATG-T
* *
9587376 TTTTCAATTCATGCTTTTCAAGAATCAACTCATATTACGAGAAATGAGTTGAGCCTTGGGTCACA
1 TTTTCAATTCATG-TTTTCAA-AATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGTCACA
*
9587441 TACCGAGGTATTTTCAAAATATGTTTTACAAATTTTGTTTTAAAAATCAACTCATATTGCGAGAA
64 CACCGAGGTATTTTCAAAATATGTTTTACAAA--------TAAAAATCAACTCATATTGCGAGAA
* * ** **
9587506 GTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAATTTTTGT
121 GTAAGTTGAGCCTCGGAGCACG-GCTGAGCTATTTTCAATTAATGT
* * * * *
9587552 TTTTGATTTC-TGTTTTTAAAAGTCAATTCATATTGCGAGAAATGAGTTGAG-CTCAGGATCACA
1 TTTTCAATTCATGTTTTCAAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTC-GGGTCACA
9587615 CACCGAG
64 CACCGAG
9587622 TAAAGAATAA
Statistics
Matches: 201, Mismatches: 28, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
163 12 0.06
164 2 0.01
165 65 0.32
166 2 0.01
173 4 0.02
174 46 0.23
175 42 0.21
176 9 0.04
177 19 0.09
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.36
Consensus pattern (165 bp):
TTTTCAATTCATGTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGTCACACA
CCGAGGTATTTTCAAAATATGTTTTACAAATAAAAATCAACTCATATTGCGAGAAGTAAGTTGAG
CCTCGGAGCACGGCTGAGCTATTTTCAATTAATGT
Found at i:9587505 original size:87 final size:85
Alignment explanation
Indices: 9587284--9587603 Score: 288
Period size: 87 Copynumber: 3.6 Consensus size: 85
9587274 CACGCTGAGG
* ** * *
9587284 TGTTTTCAATTTATGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGGAG
1 TGTTTTCAATTT-TGCTTTT---AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTTGG-G
9587349 -CAC-GCTGAGGTATTTTC-AATTAA
61 TCACTGCTGAGGTATTTTCAAATT-A
* * *
9587372 TGTTTTTTCAATTCATGCTTTTCAAGAATCAACTCATATTACGAGAAATGAGTTGAGCCTTGGGT
1 TG--TTTTCAATT-TTGCTTTT-AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTTGGGT
* * *
9587437 CACATACCGAGGTATTTTCAAAATA
62 CAC-TGCTGAGGTATTTTCAAATTA
* *
9587462 TGTTTTACAAATTTTG-TTTTAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCA
1 TGTTTT-C-AATTTTGCTTTTAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTTGGGTCA
* * *
9587526 CGTGCTGAGCTATTTTCAATTTT
64 C-TGCTGAGGTATTTTCAAATTA
** * * *
9587549 TGTTTTTGATTTCTGTTTTTAAAAGTCAATTCATATTGCGAGAAATGAGTTGAGC
1 TGTTTTCAATTT-TGCTTTTAAAAATCAACTCATATTGCGAGAAATGAGTTGAGC
9587604 TCAGGATCAC
Statistics
Matches: 192, Mismatches: 29, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
85 4 0.02
86 2 0.01
87 99 0.52
88 47 0.24
89 3 0.02
90 34 0.18
91 3 0.02
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.38
Consensus pattern (85 bp):
TGTTTTCAATTTTGCTTTTAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTTGGGTCACT
GCTGAGGTATTTTCAAATTA
Found at i:9587517 original size:325 final size:328
Alignment explanation
Indices: 9586822--9587553 Score: 806
Period size: 325 Copynumber: 2.2 Consensus size: 328
9586812 TCCGTTTTCG
* * * *
9586822 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACGCTGAGGTAATTTCAATTT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCACATGCTGAGGTATTTTCAATTT
* *
9586885 CTGTTTGTCAAAAATCAACTCATATCACGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTC
66 ATG-TT-TCAAAAATCAACTCATATCACGAGAGGTGAGTTGAGCCTCGGCTCACACGCTGAGGTC
*
9586950 TTTTCAATTTTTTTTTAATTTCTGTTTTTCAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGA
129 TTTTCAA-----TTTTAA--T-TGTTTTTCAAAAAAATCAACTCATACTGCGAGAGGTAAGTTGA
* * * * * *
9587015 GCCTCAGGACATGCTGAGGTAATTTCAATCTCTGTTTTCTCCAATTTATGTTTTTCAAAAATTAG
186 GCCTCAGGACACGCTGAGGTAATTTCAATCTATGTTTTCTCCAATTCATGCTTTTCAAAAATCAA
* ** * * * ** * *
9587080 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTCTCGATTTCTGTTTTTCA
251 CTCATATTACGAGAAATGAGTTGAGCCTCAGGGCACACCGAGGTATTCTCAAAATATGTTTTACA
9587145 ATTTATGTTTCCA
316 ATTTATGTTTCCA
* *** * *
9587158 AAAATCAATTCATAGCACTA-AAGGTGAATTGAGCCTCGGGTCACATAGC-GAGGTATTTTCAAT
1 AAAATCAACTCATATTGCGAGAA-GTGAGTTGAGCCTCGGGTCACAT-GCTGAGGTATTTTCAAT
** * *
9587221 TTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTG
64 TTATGTTTCAAAAATCAACTCATATCACGAGAGGTGAGTTGAGCCTCGGCTCACACGCTGAGGTC
*
9587286 TTTTCAA-TTT-A-TGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTC-GG
129 TTTTCAATTTTAATTGTTTTTCAAAAAAATCAACTCATACTGCGAGAGGTAAGTTGAGCCTCAGG
* * *
9587347 AGCACGCTGAGGTATTTTCAAT-TAATGTTTT-TTCAATTCATGCTTTTCAAGAATCAACTCATA
194 A-CACGCTGAGGTAATTTCAATCT-ATGTTTTCTCCAATTCATGCTTTTCAAAAATCAACTCATA
* *
9587410 TTACGAGAAATGAGTTGAGCCT-TGGGTCACATACCGAGGTATTTTCAAAATATGTTTTACAAAT
257 TTACGAGAAATGAGTTGAGCCTCAGGG-CAC--ACCGAGGTATTCTCAAAATATGTTTTAC-AAT
*
9587474 TT-TGTTT-TA
318 TTATGTTTCCA
* * * *
9587483 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAATTT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCACATGCTGAGGTATTTTCAATTT
*
9587548 TTGTTT
66 ATGTTT
9587554 TTGATTTCTG
Statistics
Matches: 333, Mismatches: 51, Indels: 35
0.79 0.12 0.08
Matches are distributed among these distances:
323 3 0.01
324 54 0.16
325 125 0.38
326 27 0.08
327 5 0.02
329 1 0.00
330 3 0.01
335 1 0.00
336 90 0.27
337 2 0.01
338 20 0.06
339 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (328 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCACATGCTGAGGTATTTTCAATTT
ATGTTTCAAAAATCAACTCATATCACGAGAGGTGAGTTGAGCCTCGGCTCACACGCTGAGGTCTT
TTCAATTTTAATTGTTTTTCAAAAAAATCAACTCATACTGCGAGAGGTAAGTTGAGCCTCAGGAC
ACGCTGAGGTAATTTCAATCTATGTTTTCTCCAATTCATGCTTTTCAAAAATCAACTCATATTAC
GAGAAATGAGTTGAGCCTCAGGGCACACCGAGGTATTCTCAAAATATGTTTTACAATTTATGTTT
CCA
Found at i:9588629 original size:11 final size:11
Alignment explanation
Indices: 9588613--9588647 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
9588603 CCCTTCCCCC
9588613 CTCCCTTCTCT
1 CTCCCTTCTCT
9588624 CTCCCTTCTCT
1 CTCCCTTCTCT
9588635 CTTCCC-TCTCT
1 C-TCCCTTCTCT
9588646 CT
1 CT
9588648 TTTTTTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.04
11 18 0.78
12 4 0.17
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCCCTTCTCT
Found at i:9595251 original size:32 final size:32
Alignment explanation
Indices: 9595185--9595252 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 32
9595175 TTTTTGTTAA
* * *
9595185 TGTTGGATTCTGAAATTTTAGTTTATTATGTT
1 TGTTGGATTCTAAAATTTTAGTCTATGATGTT
9595217 TGTTGGATTCTAAAATTATTATGTCT-TGAT-TT
1 TGTTGGATTCTAAAATT-TTA-GTCTATGATGTT
9595249 TGTT
1 TGTT
9595253 AGATATTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
32 22 0.71
33 6 0.19
34 3 0.10
ACGTcount: A:0.22, C:0.04, G:0.18, T:0.56
Consensus pattern (32 bp):
TGTTGGATTCTAAAATTTTAGTCTATGATGTT
Found at i:9595278 original size:27 final size:27
Alignment explanation
Indices: 9595248--9595320 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 27
9595238 TGTCTTGATT
9595248 TTGTTAGATATTGATTATGTTTCAAGC
1 TTGTTAGATATTGATTATGTTTCAAGC
*
9595275 TTGTTAGATATTGAATTTATTATGTTTTAAGC
1 TTGTTAGATATTG-----ATTATGTTTCAAGC
*
9595307 TTGTTGGATATTGA
1 TTGTTAGATATTGA
9595321 AATGATTGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
27 14 0.36
32 25 0.64
ACGTcount: A:0.26, C:0.04, G:0.19, T:0.51
Consensus pattern (27 bp):
TTGTTAGATATTGATTATGTTTCAAGC
Found at i:9595300 original size:32 final size:32
Alignment explanation
Indices: 9595261--9595321 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
9595251 TTAGATATTG
9595261 ATTATGTTTCAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTCAAGCTTGTTAGATATTGAATTT
* *
9595293 ATTATGTTTTAAGCTTGTTGGATATTGAA
1 ATTATGTTTCAAGCTTGTTAGATATTGAA
9595322 ATGATTGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.28, C:0.05, G:0.18, T:0.49
Consensus pattern (32 bp):
ATTATGTTTCAAGCTTGTTAGATATTGAATTT
Found at i:9596334 original size:22 final size:22
Alignment explanation
Indices: 9596303--9596351 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
9596293 GGACAATGTT
9596303 GTTATAATGTGCTGTAATATTA
1 GTTATAATGTGCTGTAATATTA
* *
9596325 GTTATCATGTGGTGTAATATTA
1 GTTATAATGTGCTGTAATATTA
9596347 GTTAT
1 GTTAT
9596352 GCACTTGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.04, G:0.20, T:0.47
Consensus pattern (22 bp):
GTTATAATGTGCTGTAATATTA
Found at i:9596364 original size:22 final size:22
Alignment explanation
Indices: 9596274--9596364 Score: 59
Period size: 22 Copynumber: 4.2 Consensus size: 22
9596264 TAATGTGGTG
9596274 TAATATTAGTTATGCACT-TGGA
1 TAATATTAGTTAT-CACTGTGGA
* * *
9596296 CAATGTT-GTTAT-AATGTGCTG-
1 TAATATTAGTTATCACTGTG--GA
*
9596317 TAATATTAGTTATCA-TGTGGTG
1 TAATATTAGTTATCACTGTGG-A
9596339 TAATATTAGTTATGCACT-TGGA
1 TAATATTAGTTAT-CACTGTGGA
9596361 TAAT
1 TAAT
9596365 GTTGTTGTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 18
0.69 0.08 0.23
Matches are distributed among these distances:
19 2 0.04
20 3 0.06
21 10 0.19
22 32 0.59
23 6 0.11
24 1 0.02
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.43
Consensus pattern (22 bp):
TAATATTAGTTATCACTGTGGA
Found at i:9596855 original size:29 final size:29
Alignment explanation
Indices: 9596794--9596853 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
9596784 CCAGAAAAGT
*
9596794 AAATCATTTTCCAGAAATTATTTTCCAGG
1 AAATCATTTTCCAGAAATCATTTTCCAGG
9596823 AAATCATTTTCCAGAAATCATTTTCC-GG
1 AAATCATTTTCCAGAAATCATTTTCCAGG
9596851 AAA
1 AAA
9596854 ATATTTTACC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 5 0.17
29 25 0.83
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (29 bp):
AAATCATTTTCCAGAAATCATTTTCCAGG
Found at i:9596860 original size:14 final size:14
Alignment explanation
Indices: 9596794--9596853 Score: 93
Period size: 14 Copynumber: 4.2 Consensus size: 14
9596784 CCAGAAAAGT
9596794 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
9596808 AAATTATTTTCCAGG
1 AAATCATTTTCCA-G
9596823 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
9596837 AAATCATTTTCCGG
1 AAATCATTTTCCAG
9596851 AAA
1 AAA
9596854 ATATTTTACC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
14 29 0.69
15 13 0.31
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:9599322 original size:20 final size:20
Alignment explanation
Indices: 9599279--9599322 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
9599269 ATATATATAA
* *
9599279 TTTTGTTAAAATATGAGTAT
1 TTTTCTTAAAATATGAGTAC
* *
9599299 TTTTCTTAAAATTTGATTAC
1 TTTTCTTAAAATATGAGTAC
9599319 TTTT
1 TTTT
9599323 AAAATTTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.57
Consensus pattern (20 bp):
TTTTCTTAAAATATGAGTAC
Found at i:9599533 original size:30 final size:31
Alignment explanation
Indices: 9599490--9599550 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
9599480 AATGCTAAAC
* *
9599490 TTTAAAATTTAAAAAATA-AATGAATTAAATT
1 TTTAAAATATAAAAAATATAAAG-ATTAAATT
9599521 TTTAAAA-ATAAAAAATATAAAGATTAAATT
1 TTTAAAATATAAAAAATATAAAGATTAAATT
9599551 CTATTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (31 bp):
TTTAAAATATAAAAAATATAAAGATTAAATT
Found at i:9599541 original size:23 final size:23
Alignment explanation
Indices: 9599491--9599541 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
9599481 ATGCTAAACT
*
9599491 TTAAAATTTAAAAAATAAATGAA
1 TTAAAATTTAAAAAATAAATAAA
* *
9599514 TTAAATTTTTAAAAATAAA-AAA
1 TTAAAATTTAAAAAATAAATAAA
9599536 TATAAA
1 T-TAAA
9599542 GATTAAATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 3 0.12
23 21 0.88
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
TTAAAATTTAAAAAATAAATAAA
Found at i:9603006 original size:20 final size:20
Alignment explanation
Indices: 9602981--9603020 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
9602971 TTAAGAACAA
9602981 AGATAATTAAAAATTAGCAG
1 AGATAATTAAAAATTAGCAG
9603001 AGATAATTAAAAATTAGCAG
1 AGATAATTAAAAATTAGCAG
9603021 TTAAGGAATA
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:0.55, C:0.05, G:0.15, T:0.25
Consensus pattern (20 bp):
AGATAATTAAAAATTAGCAG
Found at i:9610275 original size:186 final size:187
Alignment explanation
Indices: 9610045--9610409 Score: 484
Period size: 186 Copynumber: 1.9 Consensus size: 187
9610035 CGATGATTAT
* * *
9610045 GATGATAATGATGATCATGATCATGAAGCAGCGGCAACTACGACTCTTACTGTACTTACACTTAT
1 GATGATAATGATGA--ATGATCATGAAGCAGCGACAACTACGACTCTCACTGTACTTACACTTAC
** * * * *
9610110 ATGCTTTTTTTTCCTTTCT-TATTTCAATTAATGGTTTTGTCATTTGTGTTCTTTTGTTACATAT
64 ACACTTTTTTTTCCTTT-TGTATTTCAATTAATGGTTTTGTCATTTCTGTTCTTCTGTGACACAT
* * * * *
9610174 ATGTACACATTCGCATTTACTTTTTCATTTTA-CCATGAACATGTAAAAGTGTGGAAATTC
128 AAGTAAACACTCACACTTACTTTTTC-TTTTATCCATGAACATGTAAAAGTGTGGAAATTC
* * * *
9610234 GATGATAATGATG-ATGATTATGAAGCAGCGACAGCTACGACTCTCACTTTGCTTACACTTACAC
1 GATGATAATGATGAATGATCATGAAGCAGCGACAACTACGACTCTCACTGTACTTACACTTACAC
* *
9610298 ACTTTTTTTTCCTTTTGTATTTCAATTAATGGTTTTGTCGTTTCTTTTCTTCTGTGACACATAAG
66 ACTTTTTTTTCCTTTTGTATTTCAATTAATGGTTTTGTCATTTCTGTTCTTCTGTGACACATAAG
*
9610363 TAAACACTCACACTTACTTTTTCTTTTATCCGTGAACATGTAAAAGT
131 TAAACACTCACACTTACTTTTTCTTTTATCCATGAACATGTAAAAGT
9610410 ATAAAACCCC
Statistics
Matches: 153, Mismatches: 21, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
185 6 0.04
186 134 0.88
189 13 0.08
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (187 bp):
GATGATAATGATGAATGATCATGAAGCAGCGACAACTACGACTCTCACTGTACTTACACTTACAC
ACTTTTTTTTCCTTTTGTATTTCAATTAATGGTTTTGTCATTTCTGTTCTTCTGTGACACATAAG
TAAACACTCACACTTACTTTTTCTTTTATCCATGAACATGTAAAAGTGTGGAAATTC
Found at i:9611052 original size:410 final size:413
Alignment explanation
Indices: 9610277--9611059 Score: 1049
Period size: 410 Copynumber: 1.9 Consensus size: 413
9610267 GCTACGACTC
* * *
9610277 TCACTTTGCTTACACTTACACACTTTTTTTTCCTTTTGTATTTCAATTAATGGTTTTGTCGTTTC
1 TCACTTTACTTACACTTACACACATTTTTTTCCTTATGTATTTCAATTAATGGTTTTGTCGTTTC
* *
9610342 TTTTCTTCTGTGACACATAAGTAAACACTCACACTTACTTTTTCTTTTATCCGTGAACATGTAAA
66 TTTTCTTCTATGACACATAAGTAAACACTCACACTTACTTTTTCTTTTATCCGTAAACATGTAAA
* * ** * * *
9610407 AGTATAAAACCCCTTTATGACTCACATGTGCACGCGTATACTCTATCTTACTTACCTTTCCCCCT
131 ACTATAAAACCCCCTTATGACTCACACATGCACACGTATACTCTACCTTACTTACCCTTCCCCCT
* * * ** **
9610472 ACCCCATTTATTTTTCGTTATTGTTTAGTTTTATTCTATGAACCGAAATTAATTTCTAAATAGTA
196 ACCCCATTTATTTTTCATTATTCTTCAGTTTTATTCTACAAACAAAAATTAATTTCTAAATAGTA
* * * * * *
9610537 TTATAATTATGGCGTAAAGAAAAACAAAGCATTGGAGAGGTTGATATTGTTTGGAAGTGGCAGGA
261 TTATAATAATGGCGTAAAGAAAAACAAAGCATTGGAGAGGTTGATACTATTTGGAAATGGAAAGA
* * *
9610602 AATGATCTACTTCAAAAGGCAAGCATTAAAACTGTTATGTGCATGATTTGTGAATGATTCATGTA
326 AATGATCTACTTCAAAAGGCAAGAATCAAAACTATTATGTGCATGATTTGTGAATGATTCATGTA
9610667 TTATGATGCATCAAGAGCAACTT
391 TTATGATGCATCAAGAGCAACTT
* * *
9610690 TCACTTTACTTACACTTATACACATTTTTTTCCTTATGTA-TTCAAATTAGTGGTTTT-TCTTTT
1 TCACTTTACTTACACTTACACACATTTTTTTCCTTATGTATTTC-AATTAATGGTTTTGTCGTTT
* * * ** *
9610753 GTTTTCTTCTATTACACATACA-TATACACTTGCACTTATTTTTTCTTTT-TACCGTAAACATGT
65 CTTTTCTTCTATGACACATA-AGTAAACACTCACACTTACTTTTTCTTTTAT-CCGTAAACATGT
* * * *
9610816 AAAACTATAAAACCCCCTTATGGCTCCCACATGCATACGTATACTCTGCCTTACTTACCCTTCCC
128 AAAACTATAAAACCCCCTTATGACTCACACATGCACACGTATACTCTACCTTACTTACCCTTCCC
* *
9610881 CC-ACCCCCTTTATTTTTCATTA-TCTTCAGTTTTATTCTACAAACAAAAATT-ATTTCCTAGAT
193 CCTACCCCATTTATTTTTCATTATTCTTCAGTTTTATTCTACAAACAAAAATTAATTT-CTAAAT
* * *
9610943 AGTATTATGATAATGGCGTAAAGAAAAATAAAGCATTGGTGAGGTTGATACTATTTGGAAATGGA
257 AGTATTATAATAATGGCGTAAAGAAAAACAAAGCATTGGAGAGGTTGATACTATTTGGAAATGGA
* *
9611008 AAGAAATGATCTATTTCAAAAGGCAAGAATCAGAACTATTATGTGCATGATT
322 AAGAAATGATCTACTTCAAAAGGCAAGAATCAAAACTATTATGTGCATGATT
9611060 CGTGCATTAT
Statistics
Matches: 318, Mismatches: 48, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
409 4 0.01
410 131 0.41
411 19 0.06
412 115 0.36
413 49 0.15
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (413 bp):
TCACTTTACTTACACTTACACACATTTTTTTCCTTATGTATTTCAATTAATGGTTTTGTCGTTTC
TTTTCTTCTATGACACATAAGTAAACACTCACACTTACTTTTTCTTTTATCCGTAAACATGTAAA
ACTATAAAACCCCCTTATGACTCACACATGCACACGTATACTCTACCTTACTTACCCTTCCCCCT
ACCCCATTTATTTTTCATTATTCTTCAGTTTTATTCTACAAACAAAAATTAATTTCTAAATAGTA
TTATAATAATGGCGTAAAGAAAAACAAAGCATTGGAGAGGTTGATACTATTTGGAAATGGAAAGA
AATGATCTACTTCAAAAGGCAAGAATCAAAACTATTATGTGCATGATTTGTGAATGATTCATGTA
TTATGATGCATCAAGAGCAACTT
Found at i:9613728 original size:29 final size:29
Alignment explanation
Indices: 9613696--9613791 Score: 80
Period size: 29 Copynumber: 3.5 Consensus size: 29
9613686 TGTGTGTGTG
9613696 TGATTCGTGCATTATGTTTTGTGCATTAA
1 TGATTCGTGCATTATGTTTTGTGCATTAA
* ** *
9613725 TGA-TC-T---TT-TGTATGTGTGTGTGT-G
1 TGATTCGTGCATTATGT-TTTGTGCAT-TAA
9613749 TGATTCGTGCATTATGTTTTGTGCATTAA
1 TGATTCGTGCATTATGTTTTGTGCATTAA
*
9613778 TGATTCATGCATTA
1 TGATTCGTGCATTA
9613792 ATTGTTTGTG
Statistics
Matches: 49, Mismatches: 9, Indels: 18
0.64 0.12 0.24
Matches are distributed among these distances:
23 3 0.06
24 11 0.22
25 3 0.06
26 1 0.02
27 1 0.02
28 3 0.06
29 24 0.49
30 3 0.06
ACGTcount: A:0.19, C:0.09, G:0.23, T:0.49
Consensus pattern (29 bp):
TGATTCGTGCATTATGTTTTGTGCATTAA
Found at i:9613758 original size:53 final size:53
Alignment explanation
Indices: 9613678--9613781 Score: 208
Period size: 53 Copynumber: 2.0 Consensus size: 53
9613668 CCTTATTGCC
9613678 TTTGTATGTGTGTGTGTGTGATTCGTGCATTATGTTTTGTGCATTAATGATCT
1 TTTGTATGTGTGTGTGTGTGATTCGTGCATTATGTTTTGTGCATTAATGATCT
9613731 TTTGTATGTGTGTGTGTGTGATTCGTGCATTATGTTTTGTGCATTAATGAT
1 TTTGTATGTGTGTGTGTGTGATTCGTGCATTATGTTTTGTGCATTAATGAT
9613782 TCATGCATTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.15, C:0.07, G:0.27, T:0.51
Consensus pattern (53 bp):
TTTGTATGTGTGTGTGTGTGATTCGTGCATTATGTTTTGTGCATTAATGATCT
Found at i:9620484 original size:6 final size:6
Alignment explanation
Indices: 9620473--9620502 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
9620463 TCCTCTTGAG
9620473 CATTCA CATTCA CATTCA CATTCA CATTCA
1 CATTCA CATTCA CATTCA CATTCA CATTCA
9620503 TGCGTCTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (6 bp):
CATTCA
Found at i:9630390 original size:19 final size:19
Alignment explanation
Indices: 9630353--9630390 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
9630343 CAAGTAAGAA
*
9630353 TTGCACACAGCTTGAGCAC
1 TTGCACACAGCGTGAGCAC
9630372 TTGCACACGAGCGTG-GCAC
1 TTGCACAC-AGCGTGAGCAC
9630391 ACGGCAGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.24, C:0.32, G:0.26, T:0.18
Consensus pattern (19 bp):
TTGCACACAGCGTGAGCAC
Found at i:9634578 original size:30 final size:29
Alignment explanation
Indices: 9634535--9634595 Score: 113
Period size: 30 Copynumber: 2.1 Consensus size: 29
9634525 CAAATAGGCG
9634535 AAGCTAGTTAAATCGCACACTTAGTGCCA
1 AAGCTAGTTAAATCGCACACTTAGTGCCA
9634564 AAGCTAGTTTAAATCGCACACTTAGTGCCA
1 AAGCTAG-TTAAATCGCACACTTAGTGCCA
9634594 AA
1 AA
9634596 ACTTTCGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 7 0.23
30 24 0.77
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (29 bp):
AAGCTAGTTAAATCGCACACTTAGTGCCA
Found at i:9652904 original size:18 final size:18
Alignment explanation
Indices: 9652881--9652924 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
9652871 TGTGGTAAGC
**
9652881 CGTGTGATGGAACACGGG
1 CGTGTGATGGAACACGAA
9652899 CGTGTGATGGAACACGAA
1 CGTGTGATGGAACACGAA
9652917 CGTGTGAT
1 CGTGTGAT
9652925 CGACGAGCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.25, C:0.16, G:0.39, T:0.20
Consensus pattern (18 bp):
CGTGTGATGGAACACGAA
Found at i:9653536 original size:18 final size:19
Alignment explanation
Indices: 9653499--9653537 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
9653489 TAGGATTTGA
* *
9653499 TACTGTATATTTGTTACTG
1 TACTGAATATTTGATACTG
9653518 TACTGAATA-TTGATACTG
1 TACTGAATATTTGATACTG
9653536 TA
1 TA
9653538 ATGGGCCAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.46
Consensus pattern (19 bp):
TACTGAATATTTGATACTG
Found at i:9654361 original size:11 final size:11
Alignment explanation
Indices: 9654345--9654369 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9654335 GTGTGTTTAA
9654345 AATGGTTAATT
1 AATGGTTAATT
9654356 AATGGTTAATT
1 AATGGTTAATT
9654367 AAT
1 AAT
9654370 AGGTATAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (11 bp):
AATGGTTAATT
Found at i:9662607 original size:24 final size:24
Alignment explanation
Indices: 9662580--9662636 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
9662570 TAGCGATTAA
9662580 CTTTCATTATTTTATAATTTAGTT
1 CTTTCATTATTTTATAATTTAGTT
9662604 CTTTCATTATTTTATAATTTAGTT
1 CTTTCATTATTTTATAATTTAGTT
*
9662628 CTTCCATTA
1 CTTTCATTA
9662637 GAATTAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.25, C:0.12, G:0.04, T:0.60
Consensus pattern (24 bp):
CTTTCATTATTTTATAATTTAGTT
Found at i:9662670 original size:17 final size:18
Alignment explanation
Indices: 9662650--9662688 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
9662640 TTAATTACTA
9662650 ATTTAAAA-AAATTATCT
1 ATTTAAAATAAATTATCT
9662667 ATTTAAAATTCAAATTATCT
1 ATTTAAAA-T-AAATTATCT
9662687 AT
1 AT
9662689 ATAATAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
20 11 0.58
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTTAAAATAAATTATCT
Found at i:9663217 original size:19 final size:18
Alignment explanation
Indices: 9663166--9663219 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
9663156 TATTAAATAT
9663166 TATAATATTATGTTAT-AC
1 TATAATATTA-GTTATAAC
*
9663184 TATATATTTTA-TTATAATC
1 TATA-ATATTAGTTATAA-C
9663203 TATAATATTAGTTATAA
1 TATAATATTAGTTATAA
9663220 ATAGGCATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
17 4 0.13
18 10 0.33
19 16 0.53
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (18 bp):
TATAATATTAGTTATAAC
Found at i:9679401 original size:73 final size:72
Alignment explanation
Indices: 9679094--9679403 Score: 330
Period size: 73 Copynumber: 4.3 Consensus size: 72
9679084 TATGTGGATG
* *
9679094 TTTC-ATTTCTGTTTTCAAAAAAATCAACTCATAATTGCGAAAGGTGAGTTGAGCCTCGGGGCAC
1 TTTCAATTTCTGTTTTC--AAAAATCAACTCAT-ATTGCGAGAGGTGAGTTGAGCCTCAGGGCAC
*
9679158 GCCGAGGTAT
63 GCTGAGGTAT
* * ** *
9679168 TTTCAAATTCTACTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT--TGGCTTAC
1 TTTCAATTTCT-GTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGC--AC
* *
9679231 G-TGTTGAGTCAC
63 GCTG-AG-GT-AT
* *
9679243 TTTCAATTTCTGTTTT----TATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGGCACGCT
1 TTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCT
*
9679304 GAGGCAT
66 GAGGTAT
* *
9679311 TTTCAATTTATGTTTTTCAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
1 TTTCAATTTCTG-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
9679376 TGAGGTAT
65 TGAGGTAT
9679384 TTTCAATTTCTGCTTTTCAA
1 TTTCAATTTCTG-TTTTCAA
9679404 TTTCTGCTTT
Statistics
Matches: 197, Mismatches: 24, Indels: 31
0.78 0.10 0.12
Matches are distributed among these distances:
68 12 0.06
69 5 0.03
70 37 0.19
71 5 0.03
72 4 0.02
73 92 0.47
74 23 0.12
75 16 0.08
76 3 0.02
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (72 bp):
TTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCT
GAGGTAT
Found at i:9679402 original size:14 final size:14
Alignment explanation
Indices: 9679383--9679413 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
9679373 CGCTGAGGTA
9679383 TTTTCAATTTCTGC
1 TTTTCAATTTCTGC
9679397 TTTTCAATTTCTGC
1 TTTTCAATTTCTGC
9679411 TTT
1 TTT
9679414 CCAAAAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.13, C:0.19, G:0.06, T:0.61
Consensus pattern (14 bp):
TTTTCAATTTCTGC
Found at i:9679442 original size:161 final size:162
Alignment explanation
Indices: 9679260--9679959 Score: 779
Period size: 161 Copynumber: 4.2 Consensus size: 162
9679250 TTCTGTTTTT
9679260 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGG-CACGCTGAGG-CATTTTCAATTTATG
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGACACGCTGAGGTCATTTTCAATTTATG
* *
9679323 TTTTTCAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-GCAC-GCTGAGGTATTT
65 TTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCGCACAGCTGAGGTATTT
9679386 TCAATTTCTGCTTTTCAATTTCTGCTTTCCAAAAA
129 TCAATTTCTGCTTTTCAATTTCTGCTTTCC-AAAA
* *
9679421 ATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTGA-TTTCAATTTATGT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTCATTTTCAATTTATGT
9679485 TTGTCAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-GCAC-GCTGAGGT
66 TTGTC-----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCGCACAGCTGAGGT
* * *
9679548 ATTTTCGATTTCTGCTTTCCAATTTCTGCTCTTCAAAAAA
125 ATTTTCAATTTCTGCTTTTCAATTTCTGCT-TTC-CAAAA
* * *
9679588 ATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT-AATTTCAATTTCTGT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTCATTTTCAATTTATGT
* * * *
9679652 TTGTCAAAAATCAACTCATATCGCGAGAGGTGAGTTAAGCCTCGGCTCACATGCTGAGGTCTTTT
66 TTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCGCACA-GCTGAGGTATTTT
* * * *
9679717 CAATTTCT-ATTTTTAATTTCTGTTTTTCAAAA
130 CAATTTCTGCTTTTCAATTTCTGCTTTCCAAAA
* * *
9679749 ATCAACTCATACTGCAAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATTTCTGTT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG-----TC-A-------T
* ** *
9679814 TTCTCCAATTTATGTTTTTCAAAAATCAGTTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCAC
53 TT-T-CAATTTATGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCGCAC
* * * * ** * *
9679879 ATGCTTAGGTATTTTCAATTTATGTTTTTTCAATTTATATTTTTCAAAG
116 A-GCTGAGGTATTTTCAATTTCTG-CTTTTCAATTTCTGCTTTCCAAAA
9679928 ATCAACTCATATTGCGAGAGGTGAGTTGAGCC
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCC
9679960 GTGGGTTCAC
Statistics
Matches: 468, Mismatches: 40, Indels: 44
0.85 0.07 0.08
Matches are distributed among these distances:
160 3 0.01
161 112 0.24
162 42 0.09
163 12 0.03
164 19 0.04
166 82 0.18
167 71 0.15
168 1 0.00
175 2 0.00
176 1 0.00
177 74 0.16
179 49 0.10
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (162 bp):
ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTCATTTTCAATTTATGT
TTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCGCACAGCTGAGGTATTTTC
AATTTCTGCTTTTCAATTTCTGCTTTCCAAAA
Found at i:9679509 original size:78 final size:74
Alignment explanation
Indices: 9679398--9679561 Score: 222
Period size: 78 Copynumber: 2.2 Consensus size: 74
9679388 AATTTCTGCT
* * *
9679398 TTTCAATTTCTGCTT-TCCAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACAC
1 TTTCAATTTCTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
9679462 GCTGAGGTGA
66 GCTGAGGT-A
* *
9679472 TTTCAATTTATGTTTGTCAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGG
1 TTTCAATTTCTGTTTGTC---AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
9679537 CACGCTGAGGTA
63 CACGCTGAGGTA
*
9679549 TTTTCGATTTCTG
1 -TTTCAATTTCTG
9679562 CTTTCCAATT
Statistics
Matches: 78, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
74 13 0.17
75 2 0.03
77 1 0.01
78 62 0.79
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.32
Consensus pattern (74 bp):
TTTCAATTTCTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
GCTGAGGTA
Found at i:9679910 original size:15 final size:15
Alignment explanation
Indices: 9679890--9679922 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
9679880 TGCTTAGGTA
*
9679890 TTTTCAATTTATGTT
1 TTTTCAATTTATATT
9679905 TTTTCAATTTATATT
1 TTTTCAATTTATATT
9679920 TTT
1 TTT
9679923 CAAAGATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTTCAATTTATATT
Found at i:9679943 original size:90 final size:90
Alignment explanation
Indices: 9679639--9679959 Score: 436
Period size: 89 Copynumber: 3.6 Consensus size: 90
9679629 GCTGAGGTAA
* * * *
9679639 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATCGCGAGAGGTGAGTTAAGCCTCGGCTCACAT
1 TTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACAT
* *
9679704 GCTGAGGTCTTTTCAATTTCT-ATT
66 GCTGAGGTATTTTCAATTTCTGTTT
* * *
9679728 TTT-AATTTCTGTTTTTCAAAAATCAACTCATACTGCAAGAGGTGAGTTGAGCCTCAGG---ACA
1 TTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTCACA
*
9679789 TGCTGAGGTAATTTCAATTTCTGTTT
65 TGCTGAGGTATTTTCAATTTCTGTTT
* **
9679815 TCTCCAATTTATGTTTTTCAAAAATCAGTTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACA
1 T-TTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACA
* *
9679880 TGCTTAGGTATTTTCAATTTATGTTT
65 TGCTGAGGTATTTTCAATTTCTGTTT
* *
9679906 TTTCAATTTATATTTTTCAAAGATCAACTCATATTGCGAGAGGTGAGTTGAGCC
1 TTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
9679960 GTGGGTTCAC
Statistics
Matches: 203, Mismatches: 22, Indels: 13
0.85 0.09 0.05
Matches are distributed among these distances:
86 23 0.11
87 3 0.01
88 50 0.25
89 52 0.26
90 48 0.24
91 27 0.13
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.38
Consensus pattern (90 bp):
TTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACAT
GCTGAGGTATTTTCAATTTCTGTTT
Found at i:9681616 original size:11 final size:11
Alignment explanation
Indices: 9681602--9681626 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9681592 ATTTTCAAAC
9681602 TATTTTGTTAT
1 TATTTTGTTAT
9681613 TATTTTGTTAT
1 TATTTTGTTAT
9681624 TAT
1 TAT
9681627 ATATTATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (11 bp):
TATTTTGTTAT
Found at i:9681755 original size:21 final size:21
Alignment explanation
Indices: 9681729--9681775 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
9681719 ACTTGGGTAT
*
9681729 TATATTATATATATATTTTTA
1 TATATTATATATATACTTTTA
9681750 TATATTATATATATACTTTTA
1 TATATTATATATATACTTTTA
9681771 -ATATT
1 TATATT
9681776 GTATTTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TATATTATATATATACTTTTA
Found at i:9681796 original size:32 final size:32
Alignment explanation
Indices: 9681750--9681819 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
9681740 TATATTTTTA
9681750 TATATTATATATATACTTTTAATATTGTATT-T
1 TATA-TATATATATACTTTTAATATTGTATTAT
* *
9681782 TATATATATCATATATTTTTAATGTTGTATTAT
1 TATATATAT-ATATACTTTTAATATTGTATTAT
9681815 TATAT
1 TATAT
9681820 TTAATATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 5 0.15
32 23 0.68
33 6 0.18
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.59
Consensus pattern (32 bp):
TATATATATATATACTTTTAATATTGTATTAT
Found at i:9682266 original size:37 final size:38
Alignment explanation
Indices: 9682208--9682279 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 38
9682198 CATGTTTTAT
**
9682208 TATACATATATATACACTTTTTATTTTTATTATTTCCG
1 TATACATATATATACACTTTTTATACTTATTATTTCCG
*
9682246 TATATCATAT-TATTCA-TTTTTATACTTATTATTT
1 TATA-CATATATATACACTTTTTATACTTATTATTT
9682280 TCATTATTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
37 16 0.53
38 9 0.30
39 5 0.17
ACGTcount: A:0.29, C:0.11, G:0.01, T:0.58
Consensus pattern (38 bp):
TATACATATATATACACTTTTTATACTTATTATTTCCG
Found at i:9683789 original size:21 final size:22
Alignment explanation
Indices: 9683753--9683809 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
9683743 ATATCAAATA
* **
9683753 ATATATAATATATTAAT-ATTTT
1 ATATAT-ATGTATTAATGATTAG
9683775 ATATATATGTATTAATGATTAG
1 ATATATATGTATTAATGATTAG
9683797 ATAT-TATGTATTA
1 ATATATATGTATTA
9683810 TGTGATATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.58
22 13 0.42
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (22 bp):
ATATATATGTATTAATGATTAG
Found at i:9684920 original size:18 final size:20
Alignment explanation
Indices: 9684897--9684936 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
9684887 ATGATTAGAC
9684897 ATTATAT-TATTATT-TAAT
1 ATTATATCTATTATTATAAT
*
9684915 ATTATATCTTTTATTATAAT
1 ATTATATCTATTATTATAAT
9684935 AT
1 AT
9684937 ATAATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 6 0.32
20 6 0.32
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTATATCTATTATTATAAT
Found at i:9684967 original size:32 final size:31
Alignment explanation
Indices: 9684931--9685001 Score: 74
Period size: 32 Copynumber: 2.3 Consensus size: 31
9684921 TCTTTTATTA
*
9684931 TAATATATAATA-TAATAGTTATATATATGTAT
1 TAATATAT-ATAGTAATAGTTATATAT-TATAT
*
9684963 TAATAGT-TTTAGTAATAGTTATATATTATAT
1 TAATA-TATATAGTAATAGTTATATATTATAT
*
9684994 TATTATAT
1 TAATATAT
9685002 TATTATATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
30 1 0.03
31 11 0.33
32 20 0.61
33 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (31 bp):
TAATATATATAGTAATAGTTATATATTATAT
Found at i:9684999 original size:8 final size:8
Alignment explanation
Indices: 9684897--9685009 Score: 58
Period size: 8 Copynumber: 13.9 Consensus size: 8
9684887 ATGATTAGAC
9684897 ATTATATT
1 ATTATATT
9684905 ATTAT-TT
1 ATTATATT
9684912 A--ATATT
1 ATTATATT
* *
9684918 ATATCTTTT
1 AT-TATATT
*
9684927 ATTATAAT
1 ATTATATT
*
9684935 A-TATAAT
1 ATTATATT
*
9684942 ATAATAGTT
1 ATTATA-TT
9684951 ATATATATGT
1 AT-TATAT-T
9684961 ATTAATAGTT
1 ATT-ATA-TT
*
9684971 -TTAGTAAT
1 ATTA-TATT
9684979 AGTTATA-T
1 A-TTATATT
9684987 ATTATATT
1 ATTATATT
9684995 ATTATATT
1 ATTATATT
9685003 ATTATAT
1 ATTATAT
9685010 GATATAATAA
Statistics
Matches: 82, Mismatches: 9, Indels: 28
0.69 0.08 0.24
Matches are distributed among these distances:
5 2 0.02
6 3 0.04
7 15 0.18
8 32 0.39
9 16 0.20
10 13 0.16
11 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (8 bp):
ATTATATT
Found at i:9688030 original size:17 final size:17
Alignment explanation
Indices: 9687947--9688030 Score: 50
Period size: 16 Copynumber: 4.8 Consensus size: 17
9687937 ATTACATTAA
9687947 TATATTATTTCATTATATGTT
1 TATA-TATTT-ATTA-AT-TT
*
9687968 T-TATATTATCATTAAATT
1 TATATATT-T-ATTAATTT
* *
9687986 TAAATA-TTATAAATTT
1 TATATATTTATTAATTT
9688002 TGATA-A-TTATTAATTT
1 T-ATATATTTATTAATTT
9688018 TATATATTTATTA
1 TATATATTTATTA
9688031 TACATATATA
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
15 3 0.06
16 19 0.37
17 9 0.17
18 4 0.08
19 8 0.15
20 8 0.15
21 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (17 bp):
TATATATTTATTAATTT
Found at i:9697089 original size:31 final size:31
Alignment explanation
Indices: 9697054--9697115 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
9697044 AAAATTATAA
9697054 TTCATGGTCTAAATGCATGATGTCATATCTG
1 TTCATGGTCTAAATGCATGATGTCATATCTG
*
9697085 TTCATGGTCTAAATGCATGATGTCGTATCTG
1 TTCATGGTCTAAATGCATGATGTCATATCTG
9697116 CAAGGCCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (31 bp):
TTCATGGTCTAAATGCATGATGTCATATCTG
Found at i:9704295 original size:48 final size:47
Alignment explanation
Indices: 9704095--9704411 Score: 202
Period size: 46 Copynumber: 6.7 Consensus size: 47
9704085 ATTTGTATGC
* * * * * *
9704095 TAGTGTAAGACCATGTCTGGGACATGGCATCAGTATTGAGACGA-GAGC
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGGCA-CGATA-GAGGTGT
* * * * *
9704143 TAGTGTAAGA-CATGTCTAGGACAT-GCATCAGC-C-TTCAGATGTAAGC
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGAT-AGAGGT--GT
* *
9704189 CAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACG--AGATGTGT
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGGC-ACGATAGAGGTGT
* *
9704233 TAGTGTAAGGCCATGTCAGGGACATGGCATCGGCACGTATAGAGGTGT
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGGCACG-ATAGAGGTGT
* ** * * *
9704281 TAGTGTAAGACCATGTCTTGGACATGGCATCAACACGGATATGTGAGAGC
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-GATA-GAG-GTGT
* * *** *
9704331 TAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTCGATTTTGATAGT
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGG-CACGATAGAGGT-GT
* *
9704380 CAGTGTAAGACCATGCCTGGGACATGGCATCG
1 TAGTGTAAGACCATGTCTGGGACATGGCATCG
9704412 ACAACATACC
Statistics
Matches: 217, Mismatches: 35, Indels: 33
0.76 0.12 0.12
Matches are distributed among these distances:
43 2 0.01
44 11 0.05
45 16 0.07
46 52 0.24
47 13 0.06
48 52 0.24
49 35 0.16
50 34 0.16
51 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (47 bp):
TAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGATAGAGGTGT
Found at i:9711730 original size:10 final size:10
Alignment explanation
Indices: 9711711--9711747 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
9711701 AATTTTAGCT
*
9711711 TTTATTTCTA
1 TTTATCTCTA
9711721 TTTATCTCTA
1 TTTATCTCTA
*
9711731 TTTATCTTTA
1 TTTATCTCTA
9711741 TTTATCT
1 TTTATCT
9711748 TTTAGAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTATCTCTA
Found at i:9716843 original size:21 final size:21
Alignment explanation
Indices: 9716818--9716858 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
9716808 ATACAAAGTC
9716818 AGTCTATACATATCATGCCAG
1 AGTCTATACATATCATGCCAG
9716839 AGTCTATACATATCATGCCA
1 AGTCTATACATATCATGCCA
9716859 TTAAATTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.29
Consensus pattern (21 bp):
AGTCTATACATATCATGCCAG
Found at i:9717025 original size:20 final size:21
Alignment explanation
Indices: 9717000--9717042 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
9716990 ATTGAGAATC
9717000 ATCTTCATATGATTATA-ATT
1 ATCTTCATATGATTATAGATT
*
9717020 ATCTTCGTATGATTATAGATT
1 ATCTTCATATGATTATAGATT
9717041 AT
1 AT
9717043 TCAAACACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (21 bp):
ATCTTCATATGATTATAGATT
Found at i:9723891 original size:25 final size:26
Alignment explanation
Indices: 9723863--9723913 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
9723853 ATTTGTAATT
* *
9723863 TAATACATTT-AAAATATTAAATATA
1 TAATAAATTTAAAAAAATTAAATATA
9723888 TAATAAATTTAAAAAAATTAAATATA
1 TAATAAATTTAAAAAAATTAAATATA
9723914 ATTATCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (26 bp):
TAATAAATTTAAAAAAATTAAATATA
Found at i:9730394 original size:16 final size:16
Alignment explanation
Indices: 9730373--9730405 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
9730363 ATTGTGCATA
9730373 AAAAGAAAGAAAATAT
1 AAAAGAAAGAAAATAT
*
9730389 AAAAGAATGAAAATAT
1 AAAAGAAAGAAAATAT
9730405 A
1 A
9730406 GTGAGGATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (16 bp):
AAAAGAAAGAAAATAT
Found at i:9735648 original size:20 final size:21
Alignment explanation
Indices: 9735620--9735659 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
9735610 CTTTTATACC
9735620 AATAAATAC-ATAAAATAAAA
1 AATAAATACTATAAAATAAAA
*
9735640 AATATATACTATAAAATAAA
1 AATAAATACTATAAAATAAA
9735660 TTAATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (21 bp):
AATAAATACTATAAAATAAAA
Found at i:9736539 original size:36 final size:37
Alignment explanation
Indices: 9736499--9736573 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 37
9736489 TATAGAATGC
* *
9736499 TTTTTAGTTCTTATATATATTTGTA-ATTTTATAAAT
1 TTTTTAGTTCTTATATATATTTATATATTCTATAAAT
* *
9736535 TTTTTATTTCTTTTATATATTTATATATTCTATAAAT
1 TTTTTAGTTCTTATATATATTTATATATTCTATAAAT
9736572 TT
1 TT
9736574 ATATATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
36 22 0.65
37 12 0.35
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (37 bp):
TTTTTAGTTCTTATATATATTTATATATTCTATAAAT
Found at i:9736559 original size:8 final size:8
Alignment explanation
Indices: 9736546--9736604 Score: 68
Period size: 8 Copynumber: 7.4 Consensus size: 8
9736536 TTTTATTTCT
9736546 TTTATATA
1 TTTATATA
9736554 TTTATATA
1 TTTATATA
*
9736562 TTCTATAAA
1 TT-TATATA
9736571 TTTATATA
1 TTTATATA
*
9736579 TTT-TTTAA
1 TTTATAT-A
9736587 TTTATATA
1 TTTATATA
9736595 -TTATATA
1 TTTATATA
9736602 TTT
1 TTT
9736605 TTCAAAATAG
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
7 9 0.21
8 25 0.58
9 9 0.21
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (8 bp):
TTTATATA
Found at i:9736568 original size:17 final size:17
Alignment explanation
Indices: 9736548--9736602 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 17
9736538 TTATTTCTTT
*
9736548 TATATATTTATATATTC
1 TATATATTTATATATTA
* *
9736565 TATAAATTTATATATTT
1 TATATATTTATATATTA
*
9736582 TTTA-ATTTATATATTA
1 TATATATTTATATATTA
9736598 TATAT
1 TATAT
9736603 TTTTCAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 14 0.44
17 18 0.56
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
TATATATTTATATATTA
Found at i:9739156 original size:2 final size:2
Alignment explanation
Indices: 9739149--9739176 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9739139 AAATCCCACA
9739149 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
9739177 TAAATTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9741286 original size:16 final size:15
Alignment explanation
Indices: 9741265--9741302 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
9741255 ATAGACATGC
9741265 ATAATATCAAATAATA
1 ATAATATCAAA-AATA
9741281 ATAATATTCAAAAATA
1 ATAATA-TCAAAAATA
9741297 A-AATAT
1 ATAATAT
9741303 ATTATTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 1 0.05
15 4 0.19
16 11 0.52
17 5 0.24
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (15 bp):
ATAATATCAAAAATA
Found at i:9742774 original size:31 final size:31
Alignment explanation
Indices: 9742709--9742777 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
9742699 AATTTTTACT
*
9742709 TAAATAATTAATTAAGTCCTTAGTAAAATAA
1 TAAAAAATTAATTAAGTCCTTAGTAAAATAA
* *
9742740 TAAAAAATTCAATTAAGTCC-TCGTAAAATGA
1 TAAAAAATT-AATTAAGTCCTTAGTAAAATAA
9742771 TAAAAAA
1 TAAAAAA
9742778 AATTTAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 24 0.71
32 10 0.29
ACGTcount: A:0.54, C:0.09, G:0.07, T:0.30
Consensus pattern (31 bp):
TAAAAAATTAATTAAGTCCTTAGTAAAATAA
Found at i:9742778 original size:32 final size:32
Alignment explanation
Indices: 9742714--9742789 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 32
9742704 TTACTTAAAT
9742714 AATTAATTAAGTCCTTAGTAAAATAAT-AAAA
1 AATTAATTAAGTCCTTAGTAAAATAATAAAAA
* *
9742745 AATTCAATTAAGTCC-TCGTAAAATGATAAAAAA
1 AATT-AATTAAGTCCTTAGTAAAATAAT-AAAAA
9742778 AATTTAATTAAG
1 AA-TTAATTAAG
9742790 CTCTCTAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
31 14 0.36
32 10 0.26
33 13 0.33
34 2 0.05
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.32
Consensus pattern (32 bp):
AATTAATTAAGTCCTTAGTAAAATAATAAAAA
Found at i:9742787 original size:33 final size:32
Alignment explanation
Indices: 9742716--9742789 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 32
9742706 ACTTAAATAA
*
9742716 TTAATTAAGTCCTTAGTAAAATAATAAAAAAT
1 TTAATTAAGTCCTTAGTAAAATAAAAAAAAAT
* *
9742748 TCAATTAAGTCC-TCGTAAAATGATAAAAAAAAT
1 TTAATTAAGTCCTTAGTAAAAT-A-AAAAAAAAT
9742781 TTAATTAAG
1 TTAATTAAG
9742790 CTCTCTAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 8 0.22
32 12 0.33
33 16 0.44
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.32
Consensus pattern (32 bp):
TTAATTAAGTCCTTAGTAAAATAAAAAAAAAT
Found at i:9761787 original size:13 final size:13
Alignment explanation
Indices: 9761757--9761792 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
9761747 ATTGGTTGAG
*
9761757 AAATTAATTTAGTT
1 AAATTAA-TTAATT
9761771 AAATTAATTAATT
1 AAATTAATTAATT
9761784 AAATTAATT
1 AAATTAATT
9761793 GATTGAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (13 bp):
AAATTAATTAATT
Found at i:9764088 original size:3 final size:3
Alignment explanation
Indices: 9764080--9764109 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
9764070 TTTAATTGTA
9764080 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
9764110 TGATAGTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:9765956 original size:31 final size:33
Alignment explanation
Indices: 9765903--9766006 Score: 88
Period size: 31 Copynumber: 3.2 Consensus size: 33
9765893 TTTTGCATTA
* *
9765903 ATTTATATTTTATGTATCATTATA-TT-AAATT
1 ATTTAAATATTATGTATCATTATATTTAAAATT
* *
9765934 ATTTAAATATTATTTATTATTATATTTAAAATT
1 ATTTAAATATTATGTATCATTATATTTAAAATT
* * * *
9765967 -TTAAAATATTTCATGTATAATTAAATTTACAAATA
1 ATTTAAATA-TT-ATGTATCATTATATTTA-AAATT
9766002 ATTTA
1 ATTTA
9766007 CTAATTATTA
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
31 20 0.35
32 9 0.16
33 7 0.12
34 14 0.25
35 4 0.07
36 3 0.05
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (33 bp):
ATTTAAATATTATGTATCATTATATTTAAAATT
Found at i:9771357 original size:13 final size:13
Alignment explanation
Indices: 9771339--9771388 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
9771329 AAAAGTTTGT
9771339 AAAAAGAAAAGAA
1 AAAAAGAAAAGAA
*
9771352 AAAAAGAAAACAA
1 AAAAAGAAAAGAA
9771365 ACAAAA-AAAA-AA
1 A-AAAAGAAAAGAA
*
9771377 CGAAAAGAAAAG
1 -AAAAAGAAAAG
9771389 TAGAGAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
12 6 0.19
13 21 0.68
14 4 0.13
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAGAA
Found at i:9772129 original size:17 final size:18
Alignment explanation
Indices: 9772098--9772131 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9772088 AAAAATAAAC
*
9772098 TTTTAAATTTCTTTTTAT
1 TTTTAAAGTTCTTTTTAT
9772116 TTTTAAAGTT-TTTTTA
1 TTTTAAAGTTCTTTTTA
9772132 AAATTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTTAAAGTTCTTTTTAT
Found at i:9773076 original size:2 final size:2
Alignment explanation
Indices: 9773071--9773095 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9773061 ATTAGATGTG
9773071 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
9773096 AGTTTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9773501 original size:21 final size:22
Alignment explanation
Indices: 9773460--9773518 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 22
9773450 AATTTTTTAA
*
9773460 ATTTTAAAAAATTATAGAATTT
1 ATTTTAAAAAATTATAAAATTT
*
9773482 ATTTTGAAAAATTA-AAAA-TT
1 ATTTTAAAAAATTATAAAATTT
*
9773502 A--TTATAAAATTATAAAA
1 ATTTTAAAAAATTATAAAA
9773519 AATATTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 9 0.28
19 4 0.12
20 3 0.09
21 3 0.09
22 13 0.41
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (22 bp):
ATTTTAAAAAATTATAAAATTT
Found at i:9773517 original size:20 final size:20
Alignment explanation
Indices: 9773458--9773524 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
9773448 TTAATTTTTT
* *
9773458 AAATT-TTAAAAAATTATAG
1 AAATTATTATAAAATTATAA
* * *
9773477 AATTTATTTTGAAAAAT-TAA
1 AAATTATTAT-AAAATTATAA
9773497 AAATTATTATAAAATTATAA
1 AAATTATTATAAAATTATAA
*
9773517 AAAATATT
1 AAATTATT
9773525 TTTTAAAATT
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
19 9 0.25
20 22 0.61
21 5 0.14
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (20 bp):
AAATTATTATAAAATTATAA
Found at i:9777878 original size:38 final size:38
Alignment explanation
Indices: 9777821--9777957 Score: 177
Period size: 38 Copynumber: 3.6 Consensus size: 38
9777811 TGTAATAGAA
* ** *
9777821 CAATTCAACACTAGTAGTAGACATGTATAACAAGTACT
1 CAATTCATCACTAACAGTAGACATGTTTAACAAGTACT
* *
9777859 CAATTCAGCACTAACAGTAGAAATGTTTAAC-AGTACT
1 CAATTCATCACTAACAGTAGACATGTTTAACAAGTACT
* * *
9777896 CAATTTATCATTAACAGTAGACATGTTTAACATGTACT
1 CAATTCATCACTAACAGTAGACATGTTTAACAAGTACT
*
9777934 CAATTCATCATTAACAGTAGACAT
1 CAATTCATCACTAACAGTAGACAT
9777958 ACTTATCATG
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
37 33 0.38
38 54 0.62
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (38 bp):
CAATTCATCACTAACAGTAGACATGTTTAACAAGTACT
Found at i:9777968 original size:38 final size:38
Alignment explanation
Indices: 9777836--9777957 Score: 183
Period size: 38 Copynumber: 3.2 Consensus size: 38
9777826 CAACACTAGT
* * * *
9777836 AGTAGACATGTATAACAAGTACTCAATTCAGCACTAAC
1 AGTAGACATGTTTAACATGTACTCAATTCATCATTAAC
* *
9777874 AGTAGAAATGTTTAACA-GTACTCAATTTATCATTAAC
1 AGTAGACATGTTTAACATGTACTCAATTCATCATTAAC
9777911 AGTAGACATGTTTAACATGTACTCAATTCATCATTAAC
1 AGTAGACATGTTTAACATGTACTCAATTCATCATTAAC
9777949 AGTAGACAT
1 AGTAGACAT
9777958 ACTTATCATG
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
37 33 0.43
38 43 0.57
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.30
Consensus pattern (38 bp):
AGTAGACATGTTTAACATGTACTCAATTCATCATTAAC
Found at i:9779386 original size:20 final size:21
Alignment explanation
Indices: 9779332--9779386 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
9779322 TTTGCCTAAG
* * *
9779332 ATGTGAATTGGATTGAATTGA
1 ATGTAAATTGTATTAAATTGA
9779353 ATGTAAATTGTATTAAATTG-
1 ATGTAAATTGTATTAAATTGA
9779373 ATGTTAAATT-TATT
1 ATG-TAAATTGTATT
9779387 CGTATAGATC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.23
21 23 0.77
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (21 bp):
ATGTAAATTGTATTAAATTGA
Found at i:9779727 original size:24 final size:25
Alignment explanation
Indices: 9779689--9779741 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
9779679 CAACTCGAAA
* * *
9779689 GAGCATTCCGTTA-TTAGCTTTCAT
1 GAGCATCCCGATATTTAGCTCTCAT
*
9779713 GAGCATCCCGATATTTGGCTCTCAT
1 GAGCATCCCGATATTTAGCTCTCAT
9779738 GAGC
1 GAGC
9779742 TTCCTGTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34
Consensus pattern (25 bp):
GAGCATCCCGATATTTAGCTCTCAT
Found at i:9780020 original size:25 final size:25
Alignment explanation
Indices: 9779991--9780053 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 25
9779981 ATGGCTTTCT
*
9779991 AGAGCTTCCCGTTGCATGGCTC-ACA
1 AGAGCTTCCCGTTACATGGCTCGA-A
* *
9780016 TGAGCTTCCCGTTATATGGCTCGAA
1 AGAGCTTCCCGTTACATGGCTCGAA
9780041 AGAGCTTCCCGTT
1 AGAGCTTCCCGTT
9780054 TATGTACTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 32 0.97
26 1 0.03
ACGTcount: A:0.19, C:0.29, G:0.24, T:0.29
Consensus pattern (25 bp):
AGAGCTTCCCGTTACATGGCTCGAA
Found at i:9780063 original size:25 final size:25
Alignment explanation
Indices: 9779991--9780070 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
9779981 ATGGCTTTCT
** *
9779991 AGAGCTTCCCGTTGCATGGCTC-ACA
1 AGAGCTTCCCGTTATATGACTCGA-A
* *
9780016 TGAGCTTCCCGTTATATGGCTCGAA
1 AGAGCTTCCCGTTATATGACTCGAA
*
9780041 AGAGCTTCCCGTT-TATGTACTCGTA
1 AGAGCTTCCCGTTATATG-ACTCGAA
9780066 AGAGC
1 AGAGC
9780071 ATTATTGAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
24 4 0.09
25 42 0.89
26 1 0.02
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (25 bp):
AGAGCTTCCCGTTATATGACTCGAA
Found at i:9784046 original size:21 final size:21
Alignment explanation
Indices: 9784021--9784061 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
9784011 AAATTTTATG
*
9784021 ATTTTTAAATTTTTTTAATAT
1 ATTTTTAAAGTTTTTTAATAT
**
9784042 ATTTTTTTAGTTTTTTAATA
1 ATTTTTAAAGTTTTTTAATA
9784062 CCTCACATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (21 bp):
ATTTTTAAAGTTTTTTAATAT
Found at i:9789869 original size:32 final size:32
Alignment explanation
Indices: 9789817--9789955 Score: 221
Period size: 32 Copynumber: 4.4 Consensus size: 32
9789807 AAAATACCAA
9789817 ATATAAAAAA-T--ATCATACATTAGTTTTAC
1 ATATAAAAAAGTAGATCATACATTAGTTTTAC
9789846 ATATAAAAAAGTAGATCATACATTAGTTTTAC
1 ATATAAAAAAGTAGATCATACATTAGTTTTAC
* *
9789878 ATATAAAAAAGTTGATCATACATTAGTTTTGC
1 ATATAAAAAAGTAGATCATACATTAGTTTTAC
* *
9789910 ATATAAAAAAATAGAGCATACATTAGTTTTAC
1 ATATAAAAAAGTAGATCATACATTAGTTTTAC
9789942 ATATAAAAAAGTAG
1 ATATAAAAAAGTAG
9789956 TATAGTTATA
Statistics
Matches: 100, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
29 10 0.10
30 1 0.01
32 89 0.89
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (32 bp):
ATATAAAAAAGTAGATCATACATTAGTTTTAC
Found at i:9792700 original size:5 final size:5
Alignment explanation
Indices: 9792690--9792741 Score: 86
Period size: 5 Copynumber: 10.4 Consensus size: 5
9792680 AGCTACAATC
* *
9792690 ATTAG ATTAG ATTAG ATTAG ACTAG ATTAG ATTAG ATTAG AATAG ATTAG
1 ATTAG ATTAG ATTAG ATTAG ATTAG ATTAG ATTAG ATTAG ATTAG ATTAG
9792740 AT
1 AT
9792742 GTTTATCTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 43 1.00
ACGTcount: A:0.42, C:0.02, G:0.19, T:0.37
Consensus pattern (5 bp):
ATTAG
Found at i:9795487 original size:30 final size:30
Alignment explanation
Indices: 9795451--9795512 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
9795441 ACTTATTTTA
9795451 TTATTAATTTTGTTATTATTTTAAAGGAAT
1 TTATTAATTTTGTTATTATTTTAAAGGAAT
* *
9795481 TTATTAATTTTGTTATTATTTTAGAGGCAT
1 TTATTAATTTTGTTATTATTTTAAAGGAAT
9795511 TT
1 TT
9795513 GCTTGTTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.29, C:0.02, G:0.11, T:0.58
Consensus pattern (30 bp):
TTATTAATTTTGTTATTATTTTAAAGGAAT
Found at i:9797373 original size:21 final size:21
Alignment explanation
Indices: 9797348--9797388 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
9797338 AATATATTTG
* *
9797348 ACATATAATTTTTATTTTTAA
1 ACATATAATGTTTAATTTTAA
9797369 ACATATAATGTTTAATTTTA
1 ACATATAATGTTTAATTTTA
9797389 GATAAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (21 bp):
ACATATAATGTTTAATTTTAA
Found at i:9802939 original size:17 final size:18
Alignment explanation
Indices: 9802909--9802942 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
9802899 TCAAAAATGG
*
9802909 TAAAAATTATTAAAAATA
1 TAAAAATTAATAAAAATA
9802927 TAAAAA-TAATAAAAAT
1 TAAAAATTAATAAAAAT
9802943 GAACCCCAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAAATTAATAAAAATA
Found at i:9806418 original size:93 final size:93
Alignment explanation
Indices: 9806306--9806477 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
9806296 CGCCCATAAG
* *
9806306 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
9806371 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
9806399 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
9806464 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
9806478 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:9806474 original size:46 final size:46
Alignment explanation
Indices: 9806299--9806474 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
9806289 TGTAACCCGC
* * *
9806299 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
9806345 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
9806395 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
9806438 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
9806475 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:9813501 original size:46 final size:42
Alignment explanation
Indices: 9813399--9813521 Score: 192
Period size: 46 Copynumber: 2.8 Consensus size: 42
9813389 TGTAACCCGC
* *
9813399 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGTTCGCAT
9813441 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-G---TTCGCAT
9813487 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG
9813522 GATGCTCAAC
Statistics
Matches: 75, Mismatches: 2, Indels: 5
0.91 0.02 0.06
Matches are distributed among these distances:
42 32 0.43
43 1 0.01
45 1 0.01
46 41 0.55
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.20
Consensus pattern (42 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGTTCGCAT
Found at i:9815300 original size:14 final size:14
Alignment explanation
Indices: 9815281--9815310 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
9815271 AAGATATTCT
9815281 TTTTCTAAATAAAG
1 TTTTCTAAATAAAG
*
9815295 TTTTCTAAATGAAG
1 TTTTCTAAATAAAG
9815309 TT
1 TT
9815311 GAACCAGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.47
Consensus pattern (14 bp):
TTTTCTAAATAAAG
Found at i:9815349 original size:14 final size:16
Alignment explanation
Indices: 9815330--9815366 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
9815320 TCGATATCCT
9815330 TTTGCAT-TCAT-GCA
1 TTTGCATCTCATAGCA
9815344 TTTGCATCTCATAGCA
1 TTTGCATCTCATAGCA
9815360 TTT-CATC
1 TTTGCATC
9815367 ACATCGTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 8 0.38
16 6 0.29
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (16 bp):
TTTGCATCTCATAGCA
Done.