Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold329
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: 4121247
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 5938 characters in sequence are not A, C, G, or T
File 22 of 25
Found at i:3486413 original size:120 final size:116
Alignment explanation
Indices: 3486289--3486523 Score: 278
Period size: 120 Copynumber: 2.0 Consensus size: 116
3486279 TTTTCCTTCT
* *
3486289 AAGCCCACAGCTCCGTGGCACTC-TTTTCCCGTT-TAAGCCCACAACTCCGTGGCACCATTTTAA
1 AAGCCCACAACTCCGTGGCACTCATTTT-CC-TTCTAAGCCCACAACTCCGTGGCACCAGTTTAA
* *
3486352 GTCCACAACTCAGTGGCA-CCTTCTCATCAAAGTCCACAACTTCGTGGCACCCTTTTA
64 GCCCACAACTCAGTGGCACCCTT-T--T--AAGTCCACAACTCCGTGGCACCCTTTTA
** * * * *
3486409 AAGCCCACAACTTTGTGGTACTCATTTTTCTTCTAAGTCCACAACTCCGTGGCACCCGTTTAAGC
1 AAGCCCACAACTCCGTGGCACTCATTTTCCTTCTAAGCCCACAACTCCGTGGCACCAGTTTAAGC
* *
3486474 CCACAACTCCGTGGCACCCTTTTAAGTCCACGACTCCGTGGCACCCTTTT
66 CCACAACTCAGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
3486524 TTCCTTTAAA
Statistics
Matches: 100, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
116 25 0.25
118 1 0.01
119 2 0.02
120 64 0.64
121 8 0.08
ACGTcount: A:0.22, C:0.35, G:0.15, T:0.27
Consensus pattern (116 bp):
AAGCCCACAACTCCGTGGCACTCATTTTCCTTCTAAGCCCACAACTCCGTGGCACCAGTTTAAGC
CCACAACTCAGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTA
Found at i:3486460 original size:62 final size:58
Alignment explanation
Indices: 3486322--3486523 Score: 214
Period size: 62 Copynumber: 3.5 Consensus size: 58
3486312 TTTTCCCGTT
* * *
3486322 TAAGCCCACAACTCCGTGGCACCATTTTAAGTCCACAACTCAGTGGCACCTTCTCATC
1 TAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCAGTGGCACCTTCTCATC
* * ** * * *
3486380 AAAGTCCACAACTTCGTGGCACCCTTTTAAAGCCCACAACTTTGTGGTACTCATTTTTCTTC
1 TAAGTCCACAACTCCGTGGCACCCTTTT-AAGCCCACAACTCAGTGGCAC-C--TTCTCATC
* * *
3486442 TAAGTCCACAACTCCGTGGCACCCGTTTAAGCCCACAACTCCGTGGCACC--CT--TT
1 TAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCAGTGGCACCTTCTCATC
*
3486496 TAAGTCCACGACTCCGTGGCACCCTTTT
1 TAAGTCCACAACTCCGTGGCACCCTTTT
3486524 TTCCTTTAAA
Statistics
Matches: 120, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
54 27 0.22
56 1 0.01
58 24 0.20
59 17 0.14
60 2 0.02
61 18 0.15
62 31 0.26
ACGTcount: A:0.23, C:0.35, G:0.15, T:0.27
Consensus pattern (58 bp):
TAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCAGTGGCACCTTCTCATC
Found at i:3486540 original size:89 final size:89
Alignment explanation
Indices: 3486385--3486552 Score: 205
Period size: 89 Copynumber: 1.9 Consensus size: 89
3486375 TCATCAAAGT
* ** * * *
3486385 CCACAACTTCGTGGCACCCTTTTAAAGCCCACAACTTTGTGGTACTCATTTTTCTTCTAAGTCCA
1 CCACAACTCCGTGGCACCCTTTTAAAGCCCACAACTCCGTGGCACCCATTTTTCTTCTAAGCCCA
*
3486450 CAACTCCGTGGCACCCGTTTAAGC
66 CAACTACGTGGCACCCGTTTAAGC
* * *
3486474 CCACAACTCCGTGGCACCCTTTT-AAGTCCACGACTCCGTGGCACCCTTTTTTCCTT-TAAAGCC
1 CCACAACTCCGTGGCACCCTTTTAAAGCCCACAACTCCGTGGCACCCATTTTT-CTTCT-AAGCC
*
3486537 CACAACTATGTGGCAC
64 CACAACTACGTGGCAC
3486553 TCTTTTCCTT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
88 23 0.35
89 43 0.65
ACGTcount: A:0.22, C:0.35, G:0.15, T:0.29
Consensus pattern (89 bp):
CCACAACTCCGTGGCACCCTTTTAAAGCCCACAACTCCGTGGCACCCATTTTTCTTCTAAGCCCA
CAACTACGTGGCACCCGTTTAAGC
Found at i:3486583 original size:33 final size:34
Alignment explanation
Indices: 3486491--3486584 Score: 100
Period size: 33 Copynumber: 2.8 Consensus size: 34
3486481 TCCGTGGCAC
* *
3486491 CCTTTTAAGTCCACGACTCCGTGGCACCCTTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCA-CCTCTTTT
* * **
3486526 CCTTTAAAGCCCACAACTATGTGGCA-CTCTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTCTTTT
* *
3486559 CCTTTTAAGTCCACAAGTCGGTGGCA
1 CCTTTTAAGTCCACAACTCCGTGGCA
3486585 ACCTTCTTCT
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
33 27 0.56
35 21 0.44
ACGTcount: A:0.20, C:0.31, G:0.16, T:0.33
Consensus pattern (34 bp):
CCTTTTAAGTCCACAACTCCGTGGCACCTCTTTT
Found at i:3486607 original size:33 final size:33
Alignment explanation
Indices: 3486570--3486756 Score: 342
Period size: 33 Copynumber: 5.7 Consensus size: 33
3486560 CTTTTAAGTC
3486570 CACAAGTCGGTGGCAACC-TTCTTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCATTC-TCTAAAGCCCA
3486603 CACAAGTCGGTGGCAACCATTCTC-AAAGCCCA
1 CACAAGTCGGTGGCAACCATTCTCTAAAGCCCA
3486635 CACAAGTCGGTGGCAACCATTCTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCATTCTCTAAAGCCCA
3486668 CACAAGTCGGTGGCAACCATTCTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCATTCTCTAAAGCCCA
3486701 CACAAGTCGGTGGCAACCATTCTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCATTCTCTAAAGCCCA
*
3486734 CACAAGTCGGTGGCAACCCTTCT
1 CACAAGTCGGTGGCAACCATTCT
3486757 AACCCCAATA
Statistics
Matches: 151, Mismatches: 1, Indels: 4
0.97 0.01 0.03
Matches are distributed among these distances:
32 32 0.21
33 116 0.77
34 3 0.02
ACGTcount: A:0.29, C:0.34, G:0.19, T:0.19
Consensus pattern (33 bp):
CACAAGTCGGTGGCAACCATTCTCTAAAGCCCA
Found at i:3486672 original size:98 final size:99
Alignment explanation
Indices: 3486570--3486756 Score: 342
Period size: 98 Copynumber: 1.9 Consensus size: 99
3486560 CTTTTAAGTC
3486570 CACAAGTCGGTGGCAACC-TTCTTCTAAAGCCCACACAAGTCGGTGGCAACCATTCTC-AAAGCC
1 CACAAGTCGGTGGCAACCATTC-TCTAAAGCCCACACAAGTCGGTGGCAACCATTCTCTAAAGCC
3486633 CACACAAGTCGGTGGCAACCATTCTCTAAAGCCCA
65 CACACAAGTCGGTGGCAACCATTCTCTAAAGCCCA
3486668 CACAAGTCGGTGGCAACCATTCTCTAAAGCCCACACAAGTCGGTGGCAACCATTCTCTAAAGCCC
1 CACAAGTCGGTGGCAACCATTCTCTAAAGCCCACACAAGTCGGTGGCAACCATTCTCTAAAGCCC
*
3486733 ACACAAGTCGGTGGCAACCCTTCT
66 ACACAAGTCGGTGGCAACCATTCT
3486757 AACCCCAATA
Statistics
Matches: 86, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
98 53 0.62
99 33 0.38
ACGTcount: A:0.29, C:0.34, G:0.19, T:0.19
Consensus pattern (99 bp):
CACAAGTCGGTGGCAACCATTCTCTAAAGCCCACACAAGTCGGTGGCAACCATTCTCTAAAGCCC
ACACAAGTCGGTGGCAACCATTCTCTAAAGCCCA
Found at i:3486814 original size:49 final size:49
Alignment explanation
Indices: 3486761--3487352 Score: 688
Period size: 49 Copynumber: 12.6 Consensus size: 49
3486751 CCTTCTAACC
* *
3486761 CCAATATAGTTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
*
3486810 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* *
3486853 CCAATATCGCTGGCCTTGAATCAGCATATTGGCA----C--CTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* *
3486896 CTAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* **
3486939 CCAATATCGCTGGCCTTGAATCAGCATGTTGGCACCTTCATCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
3486988 CCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * *
3487031 CCAATATCGCTGGCCTTGACTCAGCATATTGGCACCTTCATCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * *
3487080 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTACGT
1 CCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* *
3487129 CCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * *
3487178 CAAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
*
3487226 CCAAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGT
1 CC-AATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * *
3487270 CCAATATAGCTGGCCTTGAATCGGCATATTGGCACCTTTTCCATATTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTTTAAGT
* *
3487322 TCAATGTAGCTGGCCTTGAATCAGCACATTG
1 CCAATATAGCTGGCCTTGAATCAGCACATTG
3487353 ACATCCTTTT
Statistics
Matches: 479, Mismatches: 42, Indels: 41
0.85 0.07 0.07
Matches are distributed among these distances:
43 184 0.38
44 10 0.02
45 2 0.00
46 1 0.00
47 2 0.00
48 12 0.03
49 233 0.49
50 1 0.00
52 34 0.07
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (49 bp):
CCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
Found at i:3486865 original size:43 final size:43
Alignment explanation
Indices: 3486802--3487308 Score: 573
Period size: 43 Copynumber: 11.1 Consensus size: 43
3486792 GCACCTTCAT
*
3486802 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* *
3486845 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* *
3486888 CTTTAAGTCTAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* **
3486931 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATGTTGGCACCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C
3486978 ATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
3487023 CTTTAAGTCCAATATCGCTGGCCTTGACTCAGCATATTGGCACCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C
*
3487070 ATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* *
3487115 CTTTATCTTTACGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTC
1 CTTTA-----A-GTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C
* *
3487168 ATCTTTAAGTCAAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG-----CAC
*
3487218 CTTTAAGTCCAAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCC-AATATAGCTGGCCTTGAATCAGCACATTGGCAC
* *
3487262 CTTTAAGTCCAATATAGCTGGCCTTGAATCGGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
3487305 CTTT
1 CTTT
3487309 TCCATATTTA
Statistics
Matches: 405, Mismatches: 29, Indels: 60
0.82 0.06 0.12
Matches are distributed among these distances:
43 194 0.48
44 13 0.03
45 2 0.00
47 2 0.00
48 10 0.02
49 174 0.43
50 2 0.00
53 1 0.00
54 2 0.00
55 5 0.01
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:3487045 original size:92 final size:92
Alignment explanation
Indices: 3486761--3487308 Score: 733
Period size: 92 Copynumber: 6.0 Consensus size: 92
3486751 CCTTCTAACC
* *
3486761 CCAATATAGTTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCT
3486826 TGAATCAGCACATTGGCACCTTTAAGT
66 TGAATCAGCACATTGGCACCTTTAAGT
* * *
3486853 CCAATATCGCTGGCCTTGAATCAGCATATTGGCA----C--CTTTAAGTCTAATGTAGCTGGCCT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCT
3486912 TGAATCAGCACATTGGCACCTTTAAGT
66 TGAATCAGCACATTGGCACCTTTAAGT
* *
3486939 CCAATATCGCTGGCCTTGAATCAGCATGTTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCT
3487004 TGAATCAGCACATTGGCACCTTTAAGT
66 TGAATCAGCACATTGGCACCTTTAAGT
* *
3487031 CCAATATCGCTGGCCTTGACTCAGCATATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCT
*
3487096 TGAATCAGCATATTGGCACCTTTATCTTTACGT
66 TGAATCAGCACATTGGCACCTTTA-----A-GT
* * * * *
3487129 CCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCAAATGTAGCTGGCCT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCT
3487194 TGAATCAGCACATTGGCACCTCACCTTTAAGT
66 TGAATCAGCACATTGG-----CACCTTTAAGT
* *
3487226 CCAAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATAGCTGGCC
1 CC-AATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCC
* *
3487285 TTGAATCGGCATATTGGCACCTTT
65 TTGAATCAGCACATTGGCACCTTT
3487309 TCCATATTTA
Statistics
Matches: 418, Mismatches: 20, Indels: 41
0.87 0.04 0.09
Matches are distributed among these distances:
86 83 0.20
87 7 0.02
88 1 0.00
90 1 0.00
92 203 0.49
94 1 0.00
97 5 0.01
98 109 0.26
103 8 0.02
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.31
Consensus pattern (92 bp):
CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCT
TGAATCAGCACATTGGCACCTTTAAGT
Found at i:3487341 original size:52 final size:53
Alignment explanation
Indices: 3487263--3487383 Score: 154
Period size: 52 Copynumber: 2.3 Consensus size: 53
3487253 CATTGGCACC
* * *
3487263 TTTAAGTCCAATATAGCTGGCCTTGAATCGGCATATTGGCA-CCTTTTCCATA
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTCCATA
* * *
3487315 TTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCC-TTTTC-CATA
*
3487370 TTTAAGCCCAATAT
1 TTTAAGTCCAATAT
3487384 CGTTGCCCGT
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
52 36 0.63
53 2 0.04
54 5 0.09
55 14 0.25
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (53 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTCCATA
Found at i:3487473 original size:67 final size:68
Alignment explanation
Indices: 3487365--3487491 Score: 168
Period size: 67 Copynumber: 1.9 Consensus size: 68
3487355 ATCCTTTTTC
* * *
3487365 TCATCTTTAAGCCCAATATCGTTGCCCGTGAATCAACATATTGGCATCTTTATCA-CTTTTCTCA
1 TCATCTTTAAGCCCAATATCGTAGCCCGTGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
3487429 TCT
66 TCT
* * * *
3487432 TCATCTTTAAGTCCAATATTGCTAG-CCTTGAATCAGCATATTGGCACCTTCATCATCTTT
1 TCATCTTTAAGCCCAATATCG-TAGCCCGTGAATCAACATATTGGCACCTTCATCATCTTT
3487492 AAAACCCAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
67 45 0.88
68 6 0.12
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (68 bp):
TCATCTTTAAGCCCAATATCGTAGCCCGTGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
TCT
Found at i:3487874 original size:52 final size:52
Alignment explanation
Indices: 3487796--3487915 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
3487786 CACCGATCTT
* *
3487796 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
3487848 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATAAAA
3487900 TGTATCGATACATGCA
1 TGTATCGATACATGCA
3487916 GATAAATTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:3497372 original size:10 final size:10
Alignment explanation
Indices: 3497359--3497386 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
3497349 TGTTTCTTTT
3497359 GGGAGCTATA
1 GGGAGCTATA
3497369 GGGAGCTATA
1 GGGAGCTATA
3497379 GGGAGCTA
1 GGGAGCTA
3497387 CGGGAATGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.43, T:0.18
Consensus pattern (10 bp):
GGGAGCTATA
Found at i:3497874 original size:20 final size:20
Alignment explanation
Indices: 3497849--3497973 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
3497839 TTTTAACTAG
*
3497849 ATGTATCGATATATTGAAAA
1 ATGTATCGATACATTGAAAA
3497869 ATGTATCGATACATCTGGGCAAAA
1 ATGTATCGATACAT-T--G-AAAA
*
3497893 GGATAGAATGTATCGATACATTGAAGA
1 --AT-G--T--ATCGATACATTGAAAA
* * *
3497920 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTGAAAA
3497940 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
3497960 ATGTATCGATACAT
1 ATGTATCGATACAT
3497974 CTGGGTACTT
Statistics
Matches: 85, Mismatches: 9, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
20 56 0.66
21 1 0.01
22 1 0.01
23 1 0.01
24 5 0.06
25 2 0.02
26 2 0.02
27 4 0.05
28 1 0.01
29 1 0.01
30 1 0.01
31 10 0.12
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:3503822 original size:36 final size:35
Alignment explanation
Indices: 3503739--3503836 Score: 125
Period size: 36 Copynumber: 2.9 Consensus size: 35
3503729 CCTTACAACA
*
3503739 CTATC-TTTC-AAGGCTAAGATAGAA--AC-CTCC
1 CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCC
**
3503769 CTATCTTTTCACGGGCTAAGATAGAACCTCTCTCC
1 CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCC
3503804 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
3503837 AATCACTTCG
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
30 5 0.09
31 4 0.07
32 13 0.23
34 1 0.02
35 9 0.16
36 25 0.44
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.31
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCC
Found at i:3504298 original size:20 final size:20
Alignment explanation
Indices: 3504273--3504347 Score: 80
Period size: 20 Copynumber: 3.6 Consensus size: 20
3504263 CGTTGGACTC
3504273 AATGTATCGATACTATTCAT
1 AATGTATCGATACTATTCAT
* *
3504293 AATGTATCGAAAC-ATGAACAGT
1 AATGTATCGATACTAT--TCA-T
* *
3504315 GATGTATCGATACTATTCAC
1 AATGTATCGATACTATTCAT
3504335 AATGTATCGATAC
1 AATGTATCGATAC
3504348 ATGAACAGTG
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
19 2 0.05
20 24 0.55
21 4 0.09
22 12 0.27
23 2 0.05
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACTATTCAT
Found at i:3504321 original size:42 final size:42
Alignment explanation
Indices: 3504274--3504358 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
3504264 GTTGGACTCA
*
3504274 ATGTATCGATACTATTCATAATGTATCGAAACATGAACAGTG
1 ATGTATCGATACTATTCACAATGTATCGAAACATGAACAGTG
*
3504316 ATGTATCGATACTATTCACAATGTATCGATACATGAACAGTG
1 ATGTATCGATACTATTCACAATGTATCGAAACATGAACAGTG
3504358 A
1 A
3504359 AAATGAGATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (42 bp):
ATGTATCGATACTATTCACAATGTATCGAAACATGAACAGTG
Found at i:3504322 original size:22 final size:22
Alignment explanation
Indices: 3504294--3504358 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 22
3504284 ACTATTCATA
*
3504294 ATGTATCGAAACATGAACAGTG
1 ATGTATCGATACATGAACAGTG
**
3504316 ATGTATCGATACTATTCACA---
1 ATGTATCGATAC-ATGAACAGTG
3504336 ATGTATCGATACATGAACAGTG
1 ATGTATCGATACATGAACAGTG
3504358 A
1 A
3504359 AAATGAGATT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
19 5 0.15
20 12 0.35
22 12 0.35
23 5 0.15
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (22 bp):
ATGTATCGATACATGAACAGTG
Found at i:3504402 original size:13 final size:13
Alignment explanation
Indices: 3504386--3504410 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3504376 TATCAGTTTT
3504386 ATGTATCGATACA
1 ATGTATCGATACA
3504399 ATGTATCGATAC
1 ATGTATCGATAC
3504411 TAAGCAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3507765 original size:21 final size:21
Alignment explanation
Indices: 3507724--3507783 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
3507714 TTTTTATTAG
*
3507724 CTAACTCA-TCATATTCATTTT
1 CTAACTCATTCATTTTC-TTTT
3507745 GC-AACTCATTTC-TTTTCTTTT
1 -CTAACTCA-TTCATTTTCTTTT
3507766 CTAACTCATTCATTTTCT
1 CTAACTCATTCATTTTCT
3507784 CCTCTAATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
20 4 0.12
21 22 0.67
22 5 0.15
23 2 0.06
ACGTcount: A:0.22, C:0.25, G:0.02, T:0.52
Consensus pattern (21 bp):
CTAACTCATTCATTTTCTTTT
Found at i:3507789 original size:21 final size:21
Alignment explanation
Indices: 3507747--3507790 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3507737 TTCATTTTGC
**
3507747 AACTCATTTCTTTTCTTTTCT
1 AACTCATTTCTTTTCTCCTCT
3507768 AACTCA-TTCATTTTCTCCTCT
1 AACTCATTTC-TTTTCTCCTCT
3507789 AA
1 AA
3507791 TTCACTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.20, C:0.27, G:0.00, T:0.52
Consensus pattern (21 bp):
AACTCATTTCTTTTCTCCTCT
Found at i:3509435 original size:35 final size:36
Alignment explanation
Indices: 3509368--3509460 Score: 126
Period size: 36 Copynumber: 2.7 Consensus size: 36
3509358 CAACACTATC
3509368 TTTC-AAGGCTAAGATAGAA-A-C-CTCCCTATC-T
1 TTTCAAAGGCTAAGATAGAACATCTCTCCCTATCTT
*
3509399 TTTCACAA-GCTAAGATAGAACCTCTCTCCCTATCTT
1 TTTCA-AAGGCTAAGATAGAACATCTCTCCCTATCTT
3509435 TTTCAAAGGCTAAGATAGAACATCTC
1 TTTCAAAGGCTAAGATAGAACATCTC
3509461 AATCACTTCG
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
31 4 0.08
32 12 0.23
33 2 0.04
34 1 0.02
35 11 0.21
36 23 0.43
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (36 bp):
TTTCAAAGGCTAAGATAGAACATCTCTCCCTATCTT
Found at i:3512686 original size:13 final size:13
Alignment explanation
Indices: 3512670--3512699 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3512660 AGAGGAGAGT
*
3512670 AAAACACAAAACA
1 AAAACAAAAAACA
3512683 AAAACAAAAAACA
1 AAAACAAAAAACA
3512696 AAAA
1 AAAA
3512700 ATTATATCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAACAAAAAACA
Found at i:3513433 original size:13 final size:13
Alignment explanation
Indices: 3513415--3513439 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3513405 CATTACGCTT
3513415 TGTATCGATACAA
1 TGTATCGATACAA
3513428 TGTATCGATACA
1 TGTATCGATACA
3513440 TGTTCATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3513537 original size:20 final size:20
Alignment explanation
Indices: 3513512--3513562 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
3513502 CCACTGTTTA
* *
3513512 TATCGATACATGGCATAA-TG
1 TATCGATACAT-GAAGAATTG
3513532 TATCGATACATGAAGAATTG
1 TATCGATACATGAAGAATTG
3513552 TATCGATACAT
1 TATCGATACAT
3513563 TGCCTCAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (20 bp):
TATCGATACATGAAGAATTG
Found at i:3518104 original size:10 final size:10
Alignment explanation
Indices: 3518089--3518117 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
3518079 TGTTTTTATG
3518089 ATTTCAAATT
1 ATTTCAAATT
3518099 ATTTCAAATT
1 ATTTCAAATT
3518109 ATTTCAAAT
1 ATTTCAAAT
3518118 GGATGTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.48
Consensus pattern (10 bp):
ATTTCAAATT
Found at i:3519727 original size:13 final size:13
Alignment explanation
Indices: 3519709--3519748 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
3519699 ATAATATTCT
*
3519709 TTGTATTGATACA
1 TTGTATCGATACA
*
3519722 TTGTATCGATGCA
1 TTGTATCGATACA
*
3519735 ATGTATCGATACA
1 TTGTATCGATACA
3519748 T
1 T
3519749 GGGTTACTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3519868 original size:21 final size:22
Alignment explanation
Indices: 3519835--3519878 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
3519825 AAACCCTAAC
3519835 AATTTTTCATCAAATTTCTTCA
1 AATTTTTCATCAAATTTCTTCA
3519857 AATTTTTC-TCAAATTTCTTCA
1 AATTTTTCATCAAATTTCTTCA
3519878 A
1 A
3519879 TTTCATAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (22 bp):
AATTTTTCATCAAATTTCTTCA
Found at i:3519870 original size:11 final size:11
Alignment explanation
Indices: 3519835--3519872 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
3519825 AAACCCTAAC
3519835 AATTTTTCATCA
1 AATTTTTC-TCA
*
3519847 AATTTCT-TCA
1 AATTTTTCTCA
3519857 AATTTTTCTCA
1 AATTTTTCTCA
3519868 AATTT
1 AATTT
3519873 CTTCAATTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 9 0.39
11 8 0.35
12 6 0.26
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.53
Consensus pattern (11 bp):
AATTTTTCTCA
Found at i:3519880 original size:9 final size:10
Alignment explanation
Indices: 3519839--3519882 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
3519829 CCTAACAATT
*
3519839 TTTCATCAAA
1 TTTCTTCAAA
3519849 TTTCTTCAAA
1 TTTCTTCAAA
*
3519859 TTTTTCTCAAA
1 TTTCT-TCAAA
3519870 TTTCTTC-AA
1 TTTCTTCAAA
3519879 TTTC
1 TTTC
3519883 ATAACAAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
9 6 0.20
10 15 0.50
11 9 0.30
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.52
Consensus pattern (10 bp):
TTTCTTCAAA
Found at i:3521954 original size:20 final size:20
Alignment explanation
Indices: 3521929--3522022 Score: 124
Period size: 20 Copynumber: 4.7 Consensus size: 20
3521919 GTTTGAAGCA
3521929 ATGTATCGATACAAT-T-CATC
1 ATGTATCGATACAATGTGC--C
3521949 ATGTATCGATACAATGTGCC
1 ATGTATCGATACAATGTGCC
3521969 ATGTATCGATACAAT-T-CATC
1 ATGTATCGATACAATGTGC--C
3521989 ATGTATCGATACAATGTGCC
1 ATGTATCGATACAATGTGCC
3522009 ATGTATCGATACAA
1 ATGTATCGATACAA
3522023 ACAGTGGTAG
Statistics
Matches: 68, Mismatches: 0, Indels: 12
0.85 0.00 0.15
Matches are distributed among these distances:
18 1 0.01
19 1 0.01
20 62 0.91
21 2 0.03
22 2 0.03
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACAATGTGCC
Found at i:3521979 original size:40 final size:40
Alignment explanation
Indices: 3521929--3522022 Score: 188
Period size: 40 Copynumber: 2.4 Consensus size: 40
3521919 GTTTGAAGCA
3521929 ATGTATCGATACAATTCATCATGTATCGATACAATGTGCC
1 ATGTATCGATACAATTCATCATGTATCGATACAATGTGCC
3521969 ATGTATCGATACAATTCATCATGTATCGATACAATGTGCC
1 ATGTATCGATACAATTCATCATGTATCGATACAATGTGCC
3522009 ATGTATCGATACAA
1 ATGTATCGATACAA
3522023 ACAGTGGTAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (40 bp):
ATGTATCGATACAATTCATCATGTATCGATACAATGTGCC
Found at i:3522095 original size:19 final size:19
Alignment explanation
Indices: 3522052--3522106 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
3522042 TGCTAGTTTT
**
3522052 ATGTATCGATACAATTGTCC
1 ATGTATCGATACAA-TGAAC
*
3522072 ATGTATTGATACAATGAAC
1 ATGTATCGATACAATGAAC
3522091 ATGTATCGATACAATG
1 ATGTATCGATACAATG
3522107 TATCGATACA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.58
20 13 0.42
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (19 bp):
ATGTATCGATACAATGAAC
Found at i:3522109 original size:13 final size:13
Alignment explanation
Indices: 3522091--3522117 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3522081 TACAATGAAC
3522091 ATGTATCGATACA
1 ATGTATCGATACA
3522104 ATGTATCGATACA
1 ATGTATCGATACA
3522117 A
1 A
3522118 AACATAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3523415 original size:13 final size:13
Alignment explanation
Indices: 3523397--3523421 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3523387 CATTATGCTT
3523397 TGTATCGATACAA
1 TGTATCGATACAA
3523410 TGTATCGATACA
1 TGTATCGATACA
3523422 TGTTCATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3523418 original size:33 final size:32
Alignment explanation
Indices: 3523376--3523440 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
3523366 ACATTTTCAG
*
3523376 ATGTATCGATACAT-TATGCTTTGTATCGATACA
1 ATGTATCGATACATGT-T-CATTGTATCGATACA
3523409 ATGTATCGATACATGTTCATTGTATCGATACA
1 ATGTATCGATACATGTTCATTGTATCGATACA
3523441 TGAACAAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.47
33 15 0.50
34 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (32 bp):
ATGTATCGATACATGTTCATTGTATCGATACA
Found at i:3523442 original size:19 final size:18
Alignment explanation
Indices: 3523358--3523441 Score: 70
Period size: 20 Copynumber: 4.7 Consensus size: 18
3523348 ACCTTTGTAA
*
3523358 GTATCGATACATTTTCAGAT
1 GTATCGATACA-TTTCA-TT
*
3523378 GTATCGATACATTATGCTTT
1 GTATCGATACATT-T-CATT
3523398 GTATCGATACA----A-T
1 GTATCGATACATTTCATT
3523411 GTATCGATACATGTTCATT
1 GTATCGATACAT-TTCATT
3523430 GTATCGATACAT
1 GTATCGATACAT
3523442 GAACAAATGT
Statistics
Matches: 53, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
13 12 0.23
18 1 0.02
19 15 0.28
20 24 0.45
21 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (18 bp):
GTATCGATACATTTCATT
Found at i:3523454 original size:20 final size:19
Alignment explanation
Indices: 3523406--3523464 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
3523396 TTGTATCGAT
*
3523406 ACAATGTATCGATACATGT
1 ACAATGTATCGATACATGA
* *
3523425 TCATTGTATCGATACATGA
1 ACAATGTATCGATACATGA
*
3523444 ACAAATGTATCAATACATGA
1 AC-AATGTATCGATACATGA
3523464 A
1 A
3523465 ACTGGCAGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.31
Consensus pattern (19 bp):
ACAATGTATCGATACATGA
Found at i:3526455 original size:20 final size:19
Alignment explanation
Indices: 3526400--3526458 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 19
3526390 CATGTTGGGC
*
3526400 TTTTTATAATATAGATTTTA
1 TTTTTA-AATATATATTTTA
* *
3526420 -TTTTAAATTTTTTATTTTA
1 TTTTTAAA-TATATATTTTA
3526439 TTTTTAAATAATATATTTTA
1 TTTTTAAAT-ATATATTTTA
3526459 AAAGATTAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
18 2 0.06
19 14 0.45
20 15 0.48
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTTAAATATATATTTTA
Found at i:3536898 original size:22 final size:22
Alignment explanation
Indices: 3536848--3536920 Score: 85
Period size: 22 Copynumber: 3.3 Consensus size: 22
3536838 AAAAAATGCT
* *
3536848 AAAATAAAATAA-ACATGAAGAGA
1 AAAATAAAATAATAAAT-AATA-A
* *
3536871 AAAATAAAATAATAATTAATTA
1 AAAATAAAATAATAAATAATAA
3536893 AAAATAAAATAATAAATAATAA
1 AAAATAAAATAATAAATAATAA
3536915 AAAATA
1 AAAATA
3536921 TATAAACAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
22 27 0.63
23 14 0.33
24 2 0.05
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.22
Consensus pattern (22 bp):
AAAATAAAATAATAAATAATAA
Found at i:3536909 original size:7 final size:7
Alignment explanation
Indices: 3536877--3536936 Score: 50
Period size: 7 Copynumber: 8.3 Consensus size: 7
3536867 GAGAAAAATA
3536877 AAATAAT
1 AAATAAT
*
3536884 AATTAATT
1 AAATAA-T
3536892 AAA-AAT
1 AAATAAT
3536898 AAAATAAT
1 -AAATAAT
3536906 AAATAAT
1 AAATAAT
*
3536913 AAAAAAT
1 AAATAAT
* *
3536920 ATATAAAC
1 AAAT-AAT
3536928 AAATAAT
1 AAATAAT
3536935 AA
1 AA
3536937 TCTAAATGAA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
6 1 0.02
7 29 0.71
8 11 0.27
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.27
Consensus pattern (7 bp):
AAATAAT
Found at i:3536925 original size:14 final size:15
Alignment explanation
Indices: 3536877--3536936 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
3536867 GAGAAAAATA
*
3536877 AAATAAT-AATTAATT
1 AAATAATAAAATAA-T
3536892 AAA-AATAAAATAAT
1 AAATAATAAAATAAT
3536906 AAATAATAAAA-AAT
1 AAATAATAAAATAAT
*
3536920 ATATAA-ACAAATAAT
1 AAATAATA-AAATAAT
3536935 AA
1 AA
3536937 TCTAAATGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
13 1 0.03
14 18 0.47
15 19 0.50
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.27
Consensus pattern (15 bp):
AAATAATAAAATAAT
Found at i:3538234 original size:221 final size:221
Alignment explanation
Indices: 3537846--3538286 Score: 720
Period size: 221 Copynumber: 2.0 Consensus size: 221
3537836 GGAAAAAAAA
*
3537846 AGTAAAATTCATAGTTGATGTATCGCTTGAAAACGATGAAGGCATGACATTGTGTGTAAAATGTA
1 AGTAAAATTCATAGTTGATGTATCACTTGAAAACGATGAAGGCATGACATTGTGTGTAAAATGTA
* *
3537911 GAGGAATAGAGCCACAAGGTGTATCATTGATAAAAAGCATAAGTATGGTAAATGGTAAACATAAG
66 GAAGAATAGAGCCACAAGGTGTATCATTGATAAAAAGCATAAGTATGGTAAATGGTAAACATAAA
*
3537976 GTCCATAACTAGAACTTTGTCCAAAGTACGATGGATACAATACCTCTAGGTGTTAAAAGTGATTA
131 GTCCATAACTAGAACTTTGTCCAAAGTACGATGGATACAATACCTCTAGGTGGTAAAAGTGATTA
*
3538041 GTTTGAGATGAATACTCACTGATTTT
196 GTTTAAGATGAATACTCACTGATTTT
* * *
3538067 AGTAAAATTCATGGTTGATGTATCACTTGAAAGCGATGAAGGCATTACATTGTGTGTAAAATGTA
1 AGTAAAATTCATAGTTGATGTATCACTTGAAAACGATGAAGGCATGACATTGTGTGTAAAATGTA
* * **
3538132 GAAGAATGGAGCCACAAGGTGTATCATTGGTAAAAAGCATGGGTATGGTAAATGGTAAACATAAA
66 GAAGAATAGAGCCACAAGGTGTATCATTGATAAAAAGCATAAGTATGGTAAATGGTAAACATAAA
* * * *
3538197 GTCCATAATTAGAACTTTGTCCAAAGTATGGTGGATACAATACCTCTATGTGGTAAAAGTGATTA
131 GTCCATAACTAGAACTTTGTCCAAAGTACGATGGATACAATACCTCTAGGTGGTAAAAGTGATTA
* *
3538262 GTTTAAGATGATTACTCATTGATTT
196 GTTTAAGATGAATACTCACTGATTT
3538287 CATTCTTATC
Statistics
Matches: 202, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
221 202 1.00
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (221 bp):
AGTAAAATTCATAGTTGATGTATCACTTGAAAACGATGAAGGCATGACATTGTGTGTAAAATGTA
GAAGAATAGAGCCACAAGGTGTATCATTGATAAAAAGCATAAGTATGGTAAATGGTAAACATAAA
GTCCATAACTAGAACTTTGTCCAAAGTACGATGGATACAATACCTCTAGGTGGTAAAAGTGATTA
GTTTAAGATGAATACTCACTGATTTT
Found at i:3540918 original size:18 final size:18
Alignment explanation
Indices: 3540895--3540929 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3540885 ATCTTCGTGG
3540895 TCTTTAATCTTAT-TCTTT
1 TCTTTAAT-TTATCTCTTT
3540913 TCTTTAATTTATCTCTT
1 TCTTTAATTTATCTCTT
3540930 CTCCTTTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.66
Consensus pattern (18 bp):
TCTTTAATTTATCTCTTT
Found at i:3543353 original size:22 final size:21
Alignment explanation
Indices: 3543316--3543367 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
3543306 GTAAAACCTA
* *
3543316 ATTTTTGAATATTTGATTTTTT
1 ATTTTT-ATTATTTGACTTTTT
*
3543338 TTGTTTTATTATTTGACTTTTT
1 AT-TTTTATTATTTGACTTTTT
3543360 ATTTTTAT
1 ATTTTTAT
3543368 AAAATTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 6 0.24
22 15 0.60
23 4 0.16
ACGTcount: A:0.19, C:0.02, G:0.08, T:0.71
Consensus pattern (21 bp):
ATTTTTATTATTTGACTTTTT
Found at i:3544061 original size:13 final size:13
Alignment explanation
Indices: 3544030--3544055 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3544020 TGAATTAGAG
3544030 GAAAGAATAAAGA
1 GAAAGAATAAAGA
3544043 GAAAGAATAAAGA
1 GAAAGAATAAAGA
3544056 TTAAGAGACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.23, T:0.08
Consensus pattern (13 bp):
GAAAGAATAAAGA
Found at i:3547317 original size:52 final size:53
Alignment explanation
Indices: 3547243--3547382 Score: 169
Period size: 53 Copynumber: 2.7 Consensus size: 53
3547233 TCTAGAAAGA
* *
3547243 AAATGTATCGATA-AATTTTCATTGCATTGATACATTCTGGG-TTTTAGAACC
1 AAATGTATCGATACATTTTTCATTGTATTGATACATTCTGGGTTTTTAGAACC
* * * * *
3547294 AAATGTATTGATACATTTTTCATTGTA-TCATTGCATTCTGGGTTTTTTGACCC
1 AAATGTATCGATACATTTTTCATTGTATTGA-TACATTCTGGGTTTTTAGAACC
* *
3547347 AAATGTATCGATACATTTTTCAATGTATCGATACAT
1 AAATGTATCGATACATTTTTCATTGTATTGATACAT
3547383 ACAGGCTATT
Statistics
Matches: 73, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
51 14 0.19
52 21 0.29
53 37 0.51
54 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.42
Consensus pattern (53 bp):
AAATGTATCGATACATTTTTCATTGTATTGATACATTCTGGGTTTTTAGAACC
Found at i:3548846 original size:19 final size:19
Alignment explanation
Indices: 3548804--3548887 Score: 99
Period size: 19 Copynumber: 4.7 Consensus size: 19
3548794 TTTCAACGAT
*
3548804 TTGTATCGATACATAAAATG
1 TTGTATCGATACAT-AAGTG
3548824 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
3548843 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
*
3548857 -TGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
3548875 TTGTATCGATACA
1 TTGTATCGATACA
3548888 ATGTAAGCTA
Statistics
Matches: 57, Mismatches: 1, Indels: 13
0.80 0.01 0.18
Matches are distributed among these distances:
13 11 0.19
15 2 0.04
17 2 0.04
19 28 0.49
20 14 0.25
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:3548862 original size:13 final size:13
Alignment explanation
Indices: 3548844--3548868 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3548834 ACATAAGTGT
3548844 TGTATCGATACAA
1 TGTATCGATACAA
3548857 TGTATCGATACA
1 TGTATCGATACA
3548869 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3548864 original size:32 final size:32
Alignment explanation
Indices: 3548825--3548892 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
3548815 CATAAAATGT
3548825 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
3548857 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
3548889 TGTA
1 TGTA
3548893 AGCTACTGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:3548992 original size:52 final size:52
Alignment explanation
Indices: 3548950--3549078 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
3548940 CACTGATCTT
3548950 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
3549002 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
3549054 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
3549079 TCATATATCG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:3555994 original size:8 final size:8
Alignment explanation
Indices: 3555981--3556024 Score: 72
Period size: 8 Copynumber: 5.5 Consensus size: 8
3555971 AAGTGATGAA
3555981 AAAAAAAC
1 AAAAAAAC
3555989 AAAAAAAC
1 AAAAAAAC
3555997 AAAAAAAAC
1 -AAAAAAAC
3556006 AAAAAAAC
1 AAAAAAAC
3556014 AAAAAAA-
1 AAAAAAAC
3556021 AAAA
1 AAAA
3556025 CACAGAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
7 4 0.11
8 23 0.66
9 8 0.23
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:3556000 original size:17 final size:17
Alignment explanation
Indices: 3555980--3556021 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
3555970 AAAGTGATGA
3555980 AAAAAAAACAAAAAAAC
1 AAAAAAAACAAAAAAAC
3555997 AAAAAAAACAAAAAAAC
1 AAAAAAAACAAAAAAAC
3556014 AAAAAAAA
1 AAAAAAAA
3556022 AAACACAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAAACAAAAAAAC
Found at i:3556035 original size:1 final size:1
Alignment explanation
Indices: 3555979--3556024 Score: 56
Period size: 1 Copynumber: 46.0 Consensus size: 1
3555969 AAAAGTGATG
* * * *
3555979 AAAAAAAAACAAAAAAACAAAAAAAACAAAAAAACAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3556025 CACAGAAAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3556035 original size:12 final size:12
Alignment explanation
Indices: 3555979--3556026 Score: 71
Period size: 12 Copynumber: 3.9 Consensus size: 12
3555969 AAAAGTGATG
3555979 AAAAAAAAACAA
1 AAAAAAAAACAA
3555991 AAAAACAAAA-AA
1 AAAAA-AAAACAA
3556003 AACAAAAAAACAA
1 AA-AAAAAAACAA
3556016 AAAAAAAAACA
1 AAAAAAAAACA
3556027 CAGAAAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
12 22 0.67
13 11 0.33
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAACAA
Found at i:3556306 original size:17 final size:17
Alignment explanation
Indices: 3556273--3556306 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3556263 TGTTCTTTTC
*
3556273 CAAAAAAAGAAACAAAA
1 CAAAAAAAGAAAAAAAA
*
3556290 CAAAAAAGGAAAAAAAA
1 CAAAAAAAGAAAAAAAA
3556307 AGAACAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.82, C:0.09, G:0.09, T:0.00
Consensus pattern (17 bp):
CAAAAAAAGAAAAAAAA
Found at i:3557389 original size:60 final size:61
Alignment explanation
Indices: 3557312--3557426 Score: 196
Period size: 61 Copynumber: 1.9 Consensus size: 61
3557302 CTTTTCTACA
* *
3557312 AAGCCCACAACTACGTGGCACTC-TTTTCCTTTTAAGTCCACAACTCTGTGGCACCATTTT
1 AAGCCCACAACTACGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCTGTGGCACCATTTT
*
3557372 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCTGTGGCAC
1 AAGCCCACAACTACGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCTGTGGCAC
3557427 TCTTTTTCCT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
60 22 0.43
61 29 0.57
ACGTcount: A:0.23, C:0.35, G:0.14, T:0.29
Consensus pattern (61 bp):
AAGCCCACAACTACGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCTGTGGCACCATTTT
Found at i:3557409 original size:34 final size:33
Alignment explanation
Indices: 3557316--3558125 Score: 543
Period size: 34 Copynumber: 24.6 Consensus size: 33
3557306 TCTACAAAGC
*
3557316 CCACAACTACGTGGCA-CTCTTTTCCTTTTAAGT
1 CCACAACTCCGTGGCACCT-TTTTCCTTTTAAGT
* * *
3557349 CCACAACTCTGTGGCA-C-----CATTTTAAGC
1 CCACAACTCCGTGGCACCTTTTTCCTTTTAAGT
* *
3557376 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGC
1 CCACAACTCCGTGGCAC-CTTTTTCCTTTTAAGT
* *
3557410 CCACAACTCTGTGGCACTCTTTTTCCTTCTAAGT
1 CCACAACTCCGTGGCAC-CTTTTTCCTTTTAAGT
* * * *
3557444 CCACAACTCTGTGGTA-C-----CCGTTTAAGC
1 CCACAACTCCGTGGCACCTTTTTCCTTTTAAGT
*
3557471 CCATAACTCCGTGGCACTCTTTTT-CTTTCTAAGT
1 CCACAACTCCGTGGCAC-CTTTTTCCTTT-TAAGT
* *
3557505 CCACAACTTCGTGGCA-C-----CCTTTTAAGC
1 CCACAACTCCGTGGCACCTTTTTCCTTTTAAGT
*
3557532 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGT
1 CCACAACTCCGTGGCAC-CTTTTTCCTTTTAAGT
* * *
3557566 CCACAACTCCGTGGCACATTTTTCTTTTTAAAGC
1 CCACAACTCCGTGGCACCTTTTTCCTTTT-AAGT
3557600 CCACAACTCCGTGGCACTCTTTTTCCCTTTTTAAAGT
1 CCACAACTCCGTGGCAC-CTTTTT-CC-TTTT-AAGT
* * *
3557637 CCACAACCCCGTGACACCTTGTTCCTTTTAAGT
1 CCACAACTCCGTGGCACCTTTTTCCTTTTAAGT
* * * ** *
3557670 CCACGACTCCGTGACACCTTCTT--TTCAAAGC
1 CCACAACTCCGTGGCACCTTTTTCCTTTTAAGT
3557701 CCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGT
1 CCACAACTCCGTGGCAC-CTTTTT-CCTTTT-AAGT
* *
3557737 CCACAACTTCGTGGCACTCTTTTCCCCTTTTAAAGT
1 CCACAACTCCGTGGCAC-CTTTT-TCCTTTT-AAGT
* * *
3557773 CCACAAC-CCTGTGACACCTTGTTCCATTTAAGT
1 CCACAACTCC-GTGGCACCTTTTTCCTTTTAAGT
* * * ** *
3557806 CCACTGACTCCGTGACACCTTCTT--TTCAAAGC
1 CCAC-AACTCCGTGGCACCTTTTTCCTTTTAAGT
*
3557838 CCACAACTCCGTGGCACTTTTTTTCTCTTTTAAAGT
1 CCACAACTCCGTGGCAC-CTTTTTC-CTTTT-AAGT
** * *
3557874 CCACAACTTTGTGGCACCTTGTTCCTTCTAAGT
1 CCACAACTCCGTGGCACCTTTTTCCTTTTAAGT
* * * *
3557907 CCACAACTCTGCGGC-GC-----CCTTTTAAAGC
1 CCACAACTCCGTGGCACCTTTTTCCTTTT-AAGT
* *
3557935 CCACAACTTCGTGGCACTCTTTTCCCCTTTTAAAGT
1 CCACAACTCCGTGGCAC-CTTTT-TCCTTTT-AAGT
* * *
3557971 CCACAACCCCGTGACACCTTGTTCCTTTTAAGT
1 CCACAACTCCGTGGCACCTTTTTCCTTTTAAGT
* * * ** *
3558004 CCACTGACTCCGTGACACCTTCTT--TTCAAAGC
1 CCAC-AACTCCGTGGCACCTTTTTCCTTTTAAGT
3558036 CCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGT
1 CCACAACTCCGTGGCAC-CTTTTT-CCTTTT-AAGT
* * *
3558072 CCATAACTTCGTGGCACCTTGTTCCTTTTAAGT
1 CCACAACTCCGTGGCACCTTTTTCCTTTTAAGT
* *
3558105 CCACAACTTCGTGGCATCTTT
1 CCACAACTCCGTGGCACCTTT
3558126 CACCTTTTTC
Statistics
Matches: 617, Mismatches: 104, Indels: 112
0.74 0.12 0.13
Matches are distributed among these distances:
27 67 0.11
28 19 0.03
29 3 0.00
30 1 0.00
31 42 0.07
32 34 0.06
33 106 0.17
34 173 0.28
35 34 0.06
36 115 0.19
37 23 0.04
ACGTcount: A:0.20, C:0.34, G:0.13, T:0.33
Consensus pattern (33 bp):
CCACAACTCCGTGGCACCTTTTTCCTTTTAAGT
Found at i:3557455 original size:95 final size:95
Alignment explanation
Indices: 3557312--3557759 Score: 402
Period size: 95 Copynumber: 4.7 Consensus size: 95
3557302 CTTTTCTACA
* *
3557312 AAGCCCACAACTACGTGGCACTC-TTTTCCTTTTAAGTCCACAACTCTGTGGCAC-CATTTTAAG
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACTCCTTTTAAG
*
3557375 CCCACAACTCCGTGGCACTCTTTTTCCTTCT
66 CCCACAACTCCGTGGCAC-CTTTTTCTTTCT
* * * *
3557406 AAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGTAC-CCGTTTAAG
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACTCCTTTTAAG
*
3557470 CCCATAACTCCGTGGCACTCTTTTTCTTTCT
66 CCCACAACTCCGTGGCAC-CTTTTTCTTTCT
* * * *
3557501 AAGTCCACAACTTCGTGGCA--C-----CCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCA--C----TCCT
* * * *
3557559 TCTAAGTCCACAACTCCGTGGCACATTTTTCTTTTT
60 TTTAAGCCCACAACTCCGTGGCACCTTTTTCTTTCT
* * *
3557595 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTTAAAGTCCACAACCCCGTGACACCTTGTT
1 -AAGCCCACAACTCCGTGGCACTCTTTTT-CC-TTTT-AAGTCCACAACTCTGTGGCA-C----T
* * * * *
3557660 CCTTTTAAGTCCACGACTCCGTGACACC-TTCT-TTTCA
57 CCTTTTAAGCCCACAACTCCGTGGCACCTTTTTCTTTCT
3557697 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGTCCACAACT-TCGTGGCACT-CTTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTT-CCTTTT-AAGTCCACAACTCT-GTGGCACTCCTTTT
3557760 CCCCTTTTAA
Statistics
Matches: 296, Mismatches: 38, Indels: 40
0.79 0.10 0.11
Matches are distributed among these distances:
88 22 0.07
90 1 0.00
93 1 0.00
94 36 0.12
95 124 0.42
97 1 0.00
99 1 0.00
100 21 0.07
101 31 0.10
102 3 0.01
103 5 0.02
104 33 0.11
105 17 0.06
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.33
Consensus pattern (95 bp):
AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACTCCTTTTAAG
CCCACAACTCCGTGGCACCTTTTTCTTTCT
Found at i:3557470 original size:61 final size:61
Alignment explanation
Indices: 3557405--3557643 Score: 291
Period size: 61 Copynumber: 3.8 Consensus size: 61
3557395 TTTTTCCTTC
* *
3557405 TAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGTACCCGTT
1 TAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCACCCGTT
* * *
3557466 TAAGCCCATAACTCCGTGGCACTCTTTTTCTTTCTAAGTCCACAACT-TCGTGGCACCCTTT
1 TAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCT-GTGGCACCCGTT
* **
3557527 TAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACATTTTTCTT
1 TAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCAC------CCG
3557592 TT
60 TT
*
3557594 TAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTTAAAGTCCACAAC
1 T-AAGCCCACAACTCCGTGGCACTCTTTTT-CC-TTCT-AAGTCCACAAC
3557644 CCCGTGACAC
Statistics
Matches: 156, Mismatches: 10, Indels: 14
0.87 0.06 0.08
Matches are distributed among these distances:
60 1 0.01
61 106 0.68
67 5 0.03
68 28 0.18
69 2 0.01
70 3 0.02
71 11 0.07
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (61 bp):
TAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCACCCGTT
Found at i:3557744 original size:137 final size:136
Alignment explanation
Indices: 3557522--3557913 Score: 542
Period size: 137 Copynumber: 2.9 Consensus size: 136
3557512 TTCGTGGCAC
* * * * * *
3557522 CCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCAC-ATT
1 CCTTTTAAGTCCACGACTCCGTGACAC-CTTCTT--TTCAAAGCCCACAACTCCGTGGCACTATT
* * *
3557586 TTT-CTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTTAAAGTCCACAACCCCGTG
63 TTTCCCTTTTAAAGTCCACAACTTCGTGGCACTCTTTTTCCC-TTTTAAAGTCCACAACCCCGTG
3557650 ACACCTTGTT
127 ACACCTTGTT
*
3557660 CCTTTTAAGTCCACGACTCCGTGACACCTTCTTTTCAAAGCCCACAACTCCGTGGCACTCTTTTT
1 CCTTTTAAGTCCACGACTCCGTGACACCTTCTTTTCAAAGCCCACAACTCCGTGGCACTATTTTT
* *
3557725 CCCTTTTAAAGTCCACAACTTCGTGGCACTCTTTTCCCCTTTTAAAGTCCACAACCCTGTGACAC
66 CCCTTTTAAAGTCCACAACTTCGTGGCACTCTTTTTCCCTTTTAAAGTCCACAACCCCGTGACAC
3557790 CTTGTT
131 CTTGTT
* *
3557796 CCATTTAAGTCCACTGACTCCGTGACACCTTCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTT
1 CCTTTTAAGTCCAC-GACTCCGTGACACCTTCTTTTCAAAGCCCACAACTCCGTGGCACTATTTT
* * * *
3557861 TCTCTTTTAAAGTCCACAACTTTGTGGCAC-CTTGTT-CCTTCT-AAGTCCACAAC
65 TCCCTTTTAAAGTCCACAACTTCGTGGCACTCTTTTTCCCTTTTAAAGTCCACAAC
3557914 TCTGCGGCGC
Statistics
Matches: 232, Mismatches: 19, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
134 11 0.05
135 28 0.12
136 53 0.23
137 116 0.50
138 24 0.10
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.34
Consensus pattern (136 bp):
CCTTTTAAGTCCACGACTCCGTGACACCTTCTTTTCAAAGCCCACAACTCCGTGGCACTATTTTT
CCCTTTTAAAGTCCACAACTTCGTGGCACTCTTTTTCCCTTTTAAAGTCCACAACCCCGTGACAC
CTTGTT
Found at i:3557945 original size:198 final size:198
Alignment explanation
Indices: 3557725--3558112 Score: 704
Period size: 198 Copynumber: 2.0 Consensus size: 198
3557715 CACTCTTTTT
* *
3557725 CCCTTTTAAAGTCCACAACTTCGTGGCACTCTTTTCCCCTTTTAAAGTCCACAACCCTGTGACAC
1 CCCTTTTAAAGCCCACAACTTCGTGGCACTCTTTTCCCCTTTTAAAGTCCACAACCCCGTGACAC
3557790 CTTGTTCCATTTAAGTCCACTGACTCCGTGACACCTTCTTTTCAAAGCCCACAACTCCGTGGCAC
66 CTTGTTCCATTTAAGTCCACTGACTCCGTGACACCTTCTTTTCAAAGCCCACAACTCCGTGGCAC
* * *
3557855 TTTTTTTCTCTTTTAAAGTCCACAACTTTGTGGCACCTTGTTCCTTCTAAGTCCACAACTCTGCG
131 TCTTTTTCCCTTTTAAAGTCCACAACTTCGTGGCACCTTGTTCCTTCTAAGTCCACAACTCTGCG
3557920 GCG
196 GCG
3557923 CCCTTTTAAAGCCCACAACTTCGTGGCACTCTTTTCCCCTTTTAAAGTCCACAACCCCGTGACAC
1 CCCTTTTAAAGCCCACAACTTCGTGGCACTCTTTTCCCCTTTTAAAGTCCACAACCCCGTGACAC
*
3557988 CTTGTTCCTTTTAAGTCCACTGACTCCGTGACACCTTCTTTTCAAAGCCCACAACTCCGTGGCAC
66 CTTGTTCCATTTAAGTCCACTGACTCCGTGACACCTTCTTTTCAAAGCCCACAACTCCGTGGCAC
* *
3558053 TCTTTTTCCCTTTTAAAGTCCATAACTTCGTGGCACCTTGTTCCTTTTAAGTCCACAACT
131 TCTTTTTCCCTTTTAAAGTCCACAACTTCGTGGCACCTTGTTCCTTCTAAGTCCACAACT
3558113 TCGTGGCATC
Statistics
Matches: 182, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
198 182 1.00
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.33
Consensus pattern (198 bp):
CCCTTTTAAAGCCCACAACTTCGTGGCACTCTTTTCCCCTTTTAAAGTCCACAACCCCGTGACAC
CTTGTTCCATTTAAGTCCACTGACTCCGTGACACCTTCTTTTCAAAGCCCACAACTCCGTGGCAC
TCTTTTTCCCTTTTAAAGTCCACAACTTCGTGGCACCTTGTTCCTTCTAAGTCCACAACTCTGCG
GCG
Found at i:3558092 original size:101 final size:99
Alignment explanation
Indices: 3557475--3558120 Score: 636
Period size: 101 Copynumber: 6.5 Consensus size: 99
3557465 TTAAGCCCAT
* *
3557475 AACTCCGTGGCACTCTT-TTTCTTTCTAAGTCCACAACTTCGTGGCACC--CTTTT-AAGCCCAC
1 AACTCCGTGGCAC-CTTGTTCCTTT-TAAGTCCACAACTCCGTGGCACCTTCTTTTAAAGCCCAC
*
3557536 AACTCCGTGGCACTCTTTTT-CCTTCT-AAGTCCAC
64 AACTCCGTGGCACTCTTTTTCCCTTTTAAAGTCCAC
* * * *
3557570 AACTCCGTGGCACATTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTTAAA
1 AACTCCGTGGCACCTTGTTCCTTTT-AAGTCCACAACTCCGTGGCAC-C---TT--C-TTTTAAA
* * * *
3557635 GTCCACAACCCCGTGACAC-CTTGTT-CCTTTT-AAGTCCAC
58 GCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGTCCAC
* * * ** * *
3557674 GACTCCGTGACACCTTCTT--TTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGT
1 AACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCAC-C---TT--CTTTTAAAGC
* *
3557737 CCACAACTTCGTGGCACTCTTTTCCCCTTTTAAAGTCCAC
60 CCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGTCCAC
* * * *
3557777 AAC-CCTGTGACACCTTGTTCCATTTAAGTCCACTGACTCCGTGACACCTTCTTTTCAAAGCCCA
1 AACTCC-GTGGCACCTTGTTCCTTTTAAGTCCAC-AACTCCGTGGCACCTTCTTTT-AAAGCCCA
* *
3557841 CAACTCCGTGGCACTTTTTTTCTCTTTTAAAGTCCAC
63 CAACTCCGTGGCACTCTTTTTCCCTTTTAAAGTCCAC
** * * * *
3557878 AACTTTGTGGCACCTTGTTCCTTCTAAGTCCACAACTCTGCGGCGCC--CTTTTAAAGCCCACAA
1 AACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTTCTTTTAAAGCCCACAA
* *
3557941 CTTCGTGGCACTCTTTTCCCCTTTTAAAGTCCAC
66 CTCCGTGGCACTCTTTTTCCCTTTTAAAGTCCAC
* * * *
3557975 AACCCCGTGACACCTTGTTCCTTTTAAGTCCACTGACTCCGTGACACCTTCTTTTCAAAGCCCAC
1 AACTCCGTGGCACCTTGTTCCTTTTAAGTCCAC-AACTCCGTGGCACCTTCTTTT-AAAGCCCAC
*
3558040 AACTCCGTGGCACTCTTTTTCCCTTTTAAAGTCCAT
64 AACTCCGTGGCACTCTTTTTCCCTTTTAAAGTCCAC
* *
3558076 AACTTCGTGGCACCTTGTTCCTTTTAAGTCCACAACTTCGTGGCA
1 AACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCA
3558121 TCTTTCACCT
Statistics
Matches: 459, Mismatches: 67, Indels: 45
0.80 0.12 0.08
Matches are distributed among these distances:
94 3 0.01
95 37 0.08
96 1 0.00
97 69 0.15
98 14 0.03
100 51 0.11
101 174 0.38
102 12 0.03
103 23 0.05
104 37 0.08
105 27 0.06
106 11 0.02
ACGTcount: A:0.20, C:0.34, G:0.13, T:0.33
Consensus pattern (99 bp):
AACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTTCTTTTAAAGCCCACAA
CTCCGTGGCACTCTTTTTCCCTTTTAAAGTCCAC
Found at i:3558271 original size:32 final size:33
Alignment explanation
Indices: 3558134--3558389 Score: 368
Period size: 32 Copynumber: 8.0 Consensus size: 33
3558124 TTCACCTTTT
3558134 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
3558167 TCTAAAGCCCACACAAGTCGGT-GCAA--CTT-
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
*
3558196 TCTAAAGCCCACACAAGTCGGTGGCAAACC-T-
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
* *
3558227 TCTAAAGCCCACATAAGTCGGTGGCAACCCTTT
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
** *
3558260 TC-AAAGCCCACACAAGTCGGTGGCAACATTTT
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
*
3558292 TC-AAAGCCCACACAAGTCGGTAGCAACCC-TC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
* *
3558323 TCTAAAGCCCACACAAGTTGGTGGCAACCATTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
3558356 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
3558389 T
1 T
3558390 AAGCCCAATA
Statistics
Matches: 202, Mismatches: 14, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
29 22 0.11
30 7 0.03
31 32 0.16
32 83 0.41
33 58 0.29
ACGTcount: A:0.30, C:0.33, G:0.18, T:0.20
Consensus pattern (33 bp):
TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
Found at i:3558453 original size:49 final size:48
Alignment explanation
Indices: 3558389--3558661 Score: 305
Period size: 43 Copynumber: 5.8 Consensus size: 48
3558379 GCAACCCTTC
* * *
3558389 TAAGCCCAATATAGCTGGCCTTGAAACAGCATATTGGCACCTTCTTCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTC-TCTT
*
3558438 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C-CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCTCTT
* * *
3558481 TAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTC-TCTT
*
3558530 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C-CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCTCTT
* *
3558573 TAAGTCCAATATAACTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC--TT-C-TCTT
* *
3558625 TAAGTTCAATGTAGCTAGGCCTTGAATCAGCACATTG
1 TAAGTCCAATATAGCT-GGCCTTGAATCAGCACATTG
3558662 ACATCCTTTT
Statistics
Matches: 189, Mismatches: 19, Indels: 28
0.80 0.08 0.12
Matches are distributed among these distances:
43 77 0.41
45 2 0.01
47 1 0.01
49 73 0.39
50 1 0.01
52 16 0.08
53 19 0.10
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.31
Consensus pattern (48 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCTCTT
Found at i:3558551 original size:92 final size:92
Alignment explanation
Indices: 3558384--3558670 Score: 448
Period size: 92 Copynumber: 3.1 Consensus size: 92
3558374 CGGTGGCAAC
* * *
3558384 CCTTCTAAGCCCAATATAGCTGGCCTTGAAACAGCATATTGGCACCTTCTTCTTTAAGTCCAATG
1 CCTT-TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
3558449 TAGCTGGCCTTGAATCAGCACATTGGCA
65 TAGCTGGCCTTGAATCAGCACATTGGCA
* *
3558477 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
3558542 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* *
3558569 CCTTTAAGTCCAATATAACTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGTCCAA
*
3558634 TGTAGCTAGGCCTTGAATCAGCACATTGACA
63 TGTAGCT-GGCCTTGAATCAGCACATTGGCA
3558665 TCCTTT
1 -CCTTT
3558671 TTCTCATCTT
Statistics
Matches: 179, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
92 125 0.70
93 4 0.02
94 2 0.01
95 21 0.12
96 22 0.12
97 5 0.03
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (92 bp):
CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGGCA
Found at i:3558649 original size:53 final size:53
Alignment explanation
Indices: 3558570--3558724 Score: 177
Period size: 53 Copynumber: 2.9 Consensus size: 53
3558560 ACATTGGCAC
*
3558570 CTTTAAGTCCAATATAACTGGCCTTGAATCAGCATATTGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
* * * *
3558622 CTTTAAGTTCAATGTAGCTAGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCT-GGCCTTGAATCAGCATATTGGCA-CC-TTTTCTCAT
* * * * * *
3558678 CTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT
3558725 ATCACTTTTC
Statistics
Matches: 84, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
52 16 0.19
53 24 0.29
54 3 0.04
55 24 0.29
56 17 0.20
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
Found at i:3559577 original size:19 final size:19
Alignment explanation
Indices: 3559538--3559621 Score: 108
Period size: 19 Copynumber: 4.7 Consensus size: 19
3559528 TTTCAACGAT
3559538 TTGTATCGATACATAAAGTG
1 TTGTATCGATACAT-AAGTG
3559558 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
3559577 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
*
3559591 -TGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
3559609 TTGTATCGATACA
1 TTGTATCGATACA
3559622 ATGTAAGCTA
Statistics
Matches: 58, Mismatches: 0, Indels: 13
0.82 0.00 0.18
Matches are distributed among these distances:
13 11 0.19
15 2 0.03
17 2 0.03
19 29 0.50
20 14 0.24
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:3559596 original size:13 final size:13
Alignment explanation
Indices: 3559578--3559602 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3559568 ACATAAGTGT
3559578 TGTATCGATACAA
1 TGTATCGATACAA
3559591 TGTATCGATACA
1 TGTATCGATACA
3559603 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3559600 original size:32 final size:32
Alignment explanation
Indices: 3559559--3559626 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
3559549 CATAAAGTGT
3559559 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
3559591 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
3559623 TGTA
1 TGTA
3559627 AGCTACTACC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:3559682 original size:13 final size:13
Alignment explanation
Indices: 3559664--3559688 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3559654 ATTACTCAAA
3559664 TGTATCGATACAT
1 TGTATCGATACAT
3559677 TGTATCGATACA
1 TGTATCGATACA
3559689 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3562866 original size:52 final size:52
Alignment explanation
Indices: 3562775--3562905 Score: 226
Period size: 52 Copynumber: 2.5 Consensus size: 52
3562765 CCCGAAATAT
* *
3562775 GAAAAGTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGG
* *
3562827 GCAAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGG
3562879 GAAAATTTGCCTGCATGTATCGATACA
1 GAAAATTTGCCTGCATGTATCGATACA
3562906 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (52 bp):
GAAAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGG
Found at i:3562918 original size:52 final size:51
Alignment explanation
Indices: 3562775--3562925 Score: 214
Period size: 52 Copynumber: 2.9 Consensus size: 51
3562765 CCCGAAATAT
*
3562775 GAAAAGTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGG
* * *
3562827 GCAAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGG
*
3562879 GAAAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 GAAAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
3562926 ATGTATCGAT
Statistics
Matches: 89, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 87 0.98
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (51 bp):
GAAAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGG
Found at i:3562932 original size:13 final size:13
Alignment explanation
Indices: 3562914--3562938 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3562904 CAAAGATCAG
3562914 TGTATCGATACAA
1 TGTATCGATACAA
3562927 TGTATCGATACA
1 TGTATCGATACA
3562939 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3563005 original size:19 final size:18
Alignment explanation
Indices: 3562981--3563078 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
3562971 TAGCTTAAAT
3562981 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
3563000 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
3563013 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
3563032 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
3563045 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
3563065 TGTATCGATACAAA
1 TGTATCGATACAAA
3563079 TCGTTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 24 0.36
20 13 0.20
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:3563018 original size:13 final size:13
Alignment explanation
Indices: 3563000--3563056 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
3562990 ACAAAACTTA
3563000 TGTATCGATACAT
1 TGTATCGATACAT
3563013 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
3563031 ATGTATCGATACAT
1 -TGTATCGATACAT
3563045 TGTATCGATACA
1 TGTATCGATACA
3563057 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3563020 original size:32 final size:32
Alignment explanation
Indices: 3562979--3563076 Score: 178
Period size: 32 Copynumber: 3.0 Consensus size: 32
3562969 AGTAGCTTAA
*
3562979 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
3563011 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
3563043 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAC-TTATGTATCGATAC
3563076 A
1 A
3563077 AATCGTTGAA
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 49 0.77
33 15 0.23
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATGTATCGATAC
Found at i:3563445 original size:52 final size:52
Alignment explanation
Indices: 3563380--3563502 Score: 210
Period size: 52 Copynumber: 2.4 Consensus size: 52
3563370 AGTGTCTACA
3563380 GATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTACAAAATGTATC
1 GATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTACAAAATGTATC
* * **
3563432 GATACATGAAGGCAAATTTGCCTAGATGTATCGATACACTATGAAATGTATC
1 GATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTACAAAATGTATC
3563484 GATACATGCAGGCAAATTT
1 GATACATGCAGGCAAATTT
3563503 TCATATATCG
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.27
Consensus pattern (52 bp):
GATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTACAAAATGTATC
Found at i:3569575 original size:15 final size:15
Alignment explanation
Indices: 3569536--3569580 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
3569526 TAAATATTTT
3569536 AATATATTATTTAAA
1 AATATATTATTTAAA
*
3569551 AATACATTATTTAAA
1 AATATATTATTTAAA
*
3569566 AATATTTTATATTAA
1 AATATATTAT-TTAA
3569581 TATTTATATC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 22 0.85
16 4 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATATTATTTAAA
Found at i:3569713 original size:13 final size:12
Alignment explanation
Indices: 3569648--3569714 Score: 59
Period size: 12 Copynumber: 5.7 Consensus size: 12
3569638 ATAACATTTG
*
3569648 AAAT-TATTTTT
1 AAATATATTTTA
*
3569659 AAATTTATTTTA
1 AAATATATTTTA
*
3569671 AAATAAATTTTA
1 AAATATATTTTA
3569683 AAA-A-ATTTTA
1 AAATATATTTTA
*
3569693 ATATTATATTTTCA
1 A-AATATATTTT-A
3569707 AAATATAT
1 AAATATAT
3569715 AAAAGTTAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
10 7 0.15
11 6 0.13
12 20 0.43
13 11 0.24
14 2 0.04
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (12 bp):
AAATATATTTTA
Found at i:3571269 original size:28 final size:28
Alignment explanation
Indices: 3571229--3571300 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
3571219 AAAAAAAAAT
* ** *
3571229 CGGGATTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
3571257 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
3571285 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
3571301 TCGATTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:3571429 original size:52 final size:51
Alignment explanation
Indices: 3571290--3571458 Score: 153
Period size: 52 Copynumber: 3.3 Consensus size: 51
3571280 AATAACGAGG
* * * * * * *
3571290 TTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAGAATC-GGA
1 TTGGAGTATCCCCGATTGAGGAAAATTGGT-GTTTTGAAAATAAAACCGGGA
* * *
3571341 GTTGGAATATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCGGGA
1 -TTGGAGTATCCCCGATT-GAGGAAAATTGGTGTTTTGAAAATAAAACCGGGA
* ** *
3571394 TTGGAGTATCCCCGATTGAGGAAATATTAGTGTTTT-AGCGATAAAACCGGGG
1 TTGGAGTATCCCCGATTGAGGAAA-ATTGGTGTTTTGA-AAATAAAACCGGGA
3571446 TTGGAGTATCCCC
1 TTGGAGTATCCCC
3571459 TCGAAAATAA
Statistics
Matches: 96, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
51 7 0.07
52 77 0.80
53 12 0.12
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (51 bp):
TTGGAGTATCCCCGATTGAGGAAAATTGGTGTTTTGAAAATAAAACCGGGA
Found at i:3571504 original size:27 final size:27
Alignment explanation
Indices: 3571432--3571516 Score: 111
Period size: 27 Copynumber: 3.1 Consensus size: 27
3571422 AGTGTTTTAG
*
3571432 CGATAAA-ACCGGGGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTAT-CCC
3571459 TCGA-AAATAACGGGGTTGGAGTATCCC
1 -CGATAAATAACGGGGTTGGAGTATCCC
* *
3571486 CGATGATTAACGGGGTTGGAGTATCCC
1 CGATAAATAACGGGGTTGGAGTATCCC
3571513 CGAT
1 CGAT
3571517 TGTGAAGAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
26 3 0.06
27 31 0.60
28 18 0.35
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (27 bp):
CGATAAATAACGGGGTTGGAGTATCCC
Found at i:3571530 original size:212 final size:212
Alignment explanation
Indices: 3571224--3571623 Score: 599
Period size: 212 Copynumber: 1.9 Consensus size: 212
3571214 AGAAGAAAAA
* * *
3571224 AAAATCGGGATTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAG
1 AAAACCGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAG
* * *
3571289 GTTGGAGTATCCTCGATTGTGAAAAATTGGT-ATTTTTGGAAATAGAATCGGAGTTGGAATATCC
66 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGATTTTTGGAAATAAAATCGGAGTTAGAATATCC
* * *
3571353 CCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCGG-GATTGGAGTATCCCCGATTGAGGAA
131 CCAATTAAA-GAAAATTAGCGTTTTGAAAATAAAACCGGAG-TTGGAATATCCCCGATTGAGGAA
3571417 ATATTAGTGTTTTAGCGAT
194 ATATTAGTGTTTTAGCGAT
* * *
3571436 AAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGG
1 AAAACCGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAG
* *
3571500 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTATC
66 GTTGGAGTATCCCCGATTGTGAA-AAATTGGTGATTTTTGGAAATAAAATCGGAGTTAGAATATC
* * *
3571565 CCCAATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTG
130 CCCAATTAAAGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTG
3571624 TGGAGAATTG
Statistics
Matches: 168, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
211 29 0.17
212 102 0.61
213 37 0.22
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.28
Consensus pattern (212 bp):
AAAACCGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAG
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGATTTTTGGAAATAAAATCGGAGTTAGAATATCC
CCAATTAAAGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGAGGAAAT
ATTAGTGTTTTAGCGAT
Found at i:3574006 original size:13 final size:13
Alignment explanation
Indices: 3573988--3574013 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3573978 ACAAAGATCC
3573988 ATGTATCGATACA
1 ATGTATCGATACA
3574001 ATGTATCGATACA
1 ATGTATCGATACA
3574014 CAGAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3574077 original size:19 final size:18
Alignment explanation
Indices: 3574053--3574120 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
3574043 CAGTAGCTAA
3574053 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
3574072 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
3574087 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
*
3574104 TTATGTATCTATACAAA
1 TTATGTATCGATACAAA
3574121 TCGTTGAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.10
19 24 0.57
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:3574093 original size:13 final size:13
Alignment explanation
Indices: 3574075--3574099 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3574065 ACAATACTTA
3574075 TGTATCGATACAT
1 TGTATCGATACAT
3574088 TGTATCGATACA
1 TGTATCGATACA
3574100 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3574097 original size:32 final size:32
Alignment explanation
Indices: 3574056--3574118 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
3574046 TAGCTAATTA
*
3574056 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
*
3574088 TGTATCGATACAAAACTTATGTATCTATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
3574119 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:3574182 original size:21 final size:21
Alignment explanation
Indices: 3574156--3574233 Score: 115
Period size: 21 Copynumber: 3.8 Consensus size: 21
3574146 GTTGGGACCC
3574156 TGTATCGATACATTTGTAGAA
1 TGTATCGATACATTTGTAGAA
3574177 TGTATCGATACATTTGT-GAA
1 TGTATCGATACATTTGTAGAA
* *
3574197 TGTATCGATACA-TTCTACAAA
1 TGTATCGATACATTTGTA-GAA
3574218 TGTATCGATACATTTG
1 TGTATCGATACATTTG
3574234 GAATTTTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
19 3 0.06
20 15 0.29
21 31 0.61
22 2 0.04
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTGTAGAA
Found at i:3574220 original size:41 final size:40
Alignment explanation
Indices: 3574156--3574237 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 40
3574146 GTTGGGACCC
* *
3574156 TGTATCGATACATTTGTAGAATGTATCGATACATTTGTGAA
1 TGTATCGATACATTTCTAAAATGTATCGATACATTTG-GAA
3574197 TGTATCGATACA-TTCTACAAATGTATCGATACATTTGGAA
1 TGTATCGATACATTTCTA-AAATGTATCGATACATTTGGAA
3574237 T
1 T
3574238 TTTTTTTTCC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 8 0.21
41 30 0.79
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (40 bp):
TGTATCGATACATTTCTAAAATGTATCGATACATTTGGAA
Found at i:3574921 original size:55 final size:55
Alignment explanation
Indices: 3574826--3576328 Score: 2304
Period size: 55 Copynumber: 27.3 Consensus size: 55
3574816 ATAAACTGTA
* * * * * *
3574826 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
3574881 TCCAGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-ATGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* * *
3574936 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTAGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
3574991 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
3575046 TCCTGTTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
3575101 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
3575156 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
3575211 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
3575266 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
3575321 TCCTACTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
3575376 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
3575431 TCCTGCTCTTTG-GAGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAG-GACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
3575486 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
3575541 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
3575596 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
3575651 TCCTACTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
3575706 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
3575761 TCCTGTTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
3575816 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
3575871 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
3575926 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
3575981 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
3576036 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
3576091 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
3576146 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
3576201 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
3576256 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
3576311 TCTTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
3576329 AAAAAGCGGA
Statistics
Matches: 1346, Mismatches: 75, Indels: 54
0.91 0.05 0.04
Matches are distributed among these distances:
54 37 0.03
55 1272 0.95
56 37 0.03
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:3575235 original size:26 final size:26
Alignment explanation
Indices: 3575206--3575676 Score: 83
Period size: 26 Copynumber: 17.2 Consensus size: 26
3575196 GGGCTTTAAG
*
3575206 AGGTGTCCTGCTCTTTGGGGACTGAA
1 AGGTGTCCTCCTCTTTGGGGACTGAA
* * *
3575232 AGGTG-CCACCAACTTGTGTGGG-CTTTAA
1 AGGTGTCCTCC-TCTT-TG-GGGAC-TGAA
*
3575260 GAGGTGTCCTGCTCTTTGGGGACTGAA
1 -AGGTGTCCTCCTCTTTGGGGACTGAA
* * *
3575287 AGGTG-CCACCAACTTGTGTGGG-CTTTAA
1 AGGTGTCCTCC-TCTT-TG-GGGAC-TGAA
*
3575315 GAGGTGTCCTACTCTTTGGGGACTGAA
1 -AGGTGTCCTCCTCTTTGGGGACTGAA
* * *
3575342 AGGTG-CCACCAACTTGTGTGGG-CTTTAA
1 AGGTGTCCTCC-TCTT-TG-GGGAC-TGAA
* *
3575370 GAGGTGTCCTGCTCTTTGAGGACTGGAA
1 -AGGTGTCCTCCTCTTTGGGGACT-GAA
* * * * *
3575398 A-ATG-CCACCAACTTGGGTGGGCTTTGAA
1 AGGTGTCCTCC-TCTTTGG-GGAC--TGAA
* *
3575426 AGGTGTCCTGCTCTTTGGAGACTGAA
1 AGGTGTCCTCCTCTTTGGGGACTGAA
* * *
3575452 AGGTG-CCACCAACTTGTGTGGG-CTTTAA
1 AGGTGTCCTCC-TCTT-TG-GGGAC-TGAA
* *
3575480 GAGGTGTCCTGCTCTTTGAGGACTGGAA
1 -AGGTGTCCTCCTCTTTGGGGACT-GAA
* * * * *
3575508 A-ATG-CCACCAACTTGGGTGGGCTTTGAA
1 AGGTGTCCTCC-TCTTTGG-GGAC--TGAA
*
3575536 AGGTGTCCTGCTCTTTGGGGACTGAA
1 AGGTGTCCTCCTCTTTGGGGACTGAA
* * *
3575562 AGGTG-CCACCAACTTGTGTGGG-CTTTAA
1 AGGTGTCCTCC-TCTT-TG-GGGAC-TGAA
* * *
3575590 GAGGTGTCCTGCTCTTTGAGGACTGGA
1 -AGGTGTCCTCCTCTTTGGGGACTGAA
* * * *
3575617 AGGCG-CCACCAACTTGTGTGGG-CTTTAA
1 AGGTGTCCTCC-TCTT-TG-GGGAC-TGAA
*
3575645 GAGGTGTCCTACTCTTTGGGGACTGAA
1 -AGGTGTCCTCCTCTTTGGGGACTGAA
3575672 AGGTG
1 AGGTG
3575677 CCACCAACTT
Statistics
Matches: 305, Mismatches: 84, Indels: 112
0.61 0.17 0.22
Matches are distributed among these distances:
25 24 0.08
26 72 0.24
27 54 0.18
28 68 0.22
29 63 0.21
30 24 0.08
ACGTcount: A:0.20, C:0.20, G:0.32, T:0.28
Consensus pattern (26 bp):
AGGTGTCCTCCTCTTTGGGGACTGAA
Found at i:3576113 original size:27 final size:27
Alignment explanation
Indices: 3575973--3576113 Score: 65
Period size: 28 Copynumber: 5.1 Consensus size: 27
3575963 GGTGGGCTTT
*
3575973 GAAAGGTGTCCTGCTCTTTGGGGACT-
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
** * * * *
3575999 GAAAGGTG-CCACCAACTTGTGTGGGCTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGACTG
*
3576027 TAAGAGGTGTCCTGCTCTTTGAGGACTG
1 GAA-AGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
3576055 GAAA-ATG-CCACCAACTTGTGTGGGCTTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGAC-TG
3576083 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
3576110 GAAA
1 GAAA
3576114 ATGCCACCAA
Statistics
Matches: 78, Mismatches: 27, Indels: 19
0.63 0.22 0.15
Matches are distributed among these distances:
25 6 0.08
26 16 0.21
27 17 0.22
28 20 0.26
29 13 0.17
30 6 0.08
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.28
Consensus pattern (27 bp):
GAAAGGTGTCCTGCTCTTTGAGGACTG
Found at i:3576225 original size:26 final size:26
Alignment explanation
Indices: 3576196--3576281 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
3576186 GGGCTTTAAG
3576196 AGGTGTCCTGCTCTTTGGGGACTGAA
1 AGGTGTCCTGCTCTTTGGGGACTGAA
** * *
3576222 AGGTG-CCACCAACTTGTGTGGG-CTTTAA
1 AGGTGTCCTGC-TCTT-TG-GGGAC-TGAA
*
3576250 GAGGTGTCCTGCTCTTTGAGGACTGAA
1 -AGGTGTCCTGCTCTTTGGGGACTGAA
3576277 AGGTG
1 AGGTG
3576282 CCACCAACTT
Statistics
Matches: 44, Mismatches: 9, Indels: 14
0.66 0.13 0.21
Matches are distributed among these distances:
25 3 0.07
26 13 0.30
27 8 0.18
28 9 0.20
29 8 0.18
30 3 0.07
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.29
Consensus pattern (26 bp):
AGGTGTCCTGCTCTTTGGGGACTGAA
Found at i:3577315 original size:1 final size:1
Alignment explanation
Indices: 3577311--3577367 Score: 60
Period size: 1 Copynumber: 57.0 Consensus size: 1
3577301 CTTTTCTCTC
* * * * * *
3577311 TTTTTCTTTGTTTTGTTTTTTTTTGTTTTTTTTTCTTTTTTTTTTCTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3577368 GAAGAGAAGG
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.00, C:0.05, G:0.05, T:0.89
Consensus pattern (1 bp):
T
Found at i:3577324 original size:10 final size:9
Alignment explanation
Indices: 3577295--3577364 Score: 56
Period size: 9 Copynumber: 7.7 Consensus size: 9
3577285 CTTAAGTAGG
3577295 TTTTTTCTT
1 TTTTTTCTT
* *
3577304 TTCTCTCTT
1 TTTTTTCTT
*
3577313 TTTCTTTGTT
1 TTT-TTTCTT
3577323 TTGTTTT-TT
1 TT-TTTTCTT
3577332 TTTGTTT-TT
1 TTT-TTTCTT
3577341 TTTTCTT-TT
1 TTTT-TTCTT
3577350 TTTTTTCTT
1 TTTTTTCTT
3577359 TTTTTT
1 TTTTTT
3577365 TTTGAAGAGA
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
8 4 0.08
9 37 0.73
10 9 0.18
11 1 0.02
ACGTcount: A:0.00, C:0.10, G:0.04, T:0.86
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:3577329 original size:15 final size:14
Alignment explanation
Indices: 3577311--3577367 Score: 68
Period size: 15 Copynumber: 4.3 Consensus size: 14
3577301 CTTTTCTCTC
3577311 TTTTTCTTTGTTTT
1 TTTTTCTTTGTTTT
*
3577325 GTTTTTTTTTGTTTT
1 -TTTTTCTTTGTTTT
3577340 TTTTTC--T-TTTT
1 TTTTTCTTTGTTTT
3577351 TTTTTCTTT-TTTT
1 TTTTTCTTTGTTTT
3577364 TTTT
1 TTTT
3577368 GAAGAGAAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
11 10 0.26
12 1 0.03
13 9 0.24
14 5 0.13
15 13 0.34
ACGTcount: A:0.00, C:0.05, G:0.05, T:0.89
Consensus pattern (14 bp):
TTTTTCTTTGTTTT
Found at i:3577352 original size:21 final size:21
Alignment explanation
Indices: 3577326--3577365 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3577316 CTTTGTTTTG
*
3577326 TTTTTTTTTGTTTTTTTTTCT
1 TTTTTTTTTCTTTTTTTTTCT
3577347 TTTTTTTTTCTTTTTTTTT
1 TTTTTTTTTCTTTTTTTTT
3577366 TTGAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.00, C:0.05, G:0.03, T:0.93
Consensus pattern (21 bp):
TTTTTTTTTCTTTTTTTTTCT
Found at i:3577365 original size:10 final size:10
Alignment explanation
Indices: 3577296--3577365 Score: 70
Period size: 10 Copynumber: 6.9 Consensus size: 10
3577286 TTAAGTAGGT
3577296 TTTTTCTTTTC
1 TTTTT-TTTTC
* *
3577307 TCTCTTTTTC
1 TTTTTTTTTC
* *
3577317 -TTTGTTTTG
1 TTTTTTTTTC
*
3577326 TTTTTTTTTG
1 TTTTTTTTTC
3577336 TTTTTTTTTC
1 TTTTTTTTTC
3577346 TTTTTTTTTTC
1 -TTTTTTTTTC
3577357 TTTTTTTTT
1 TTTTTTTTT
3577366 TTGAAGAGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
9 5 0.10
10 31 0.63
11 13 0.27
ACGTcount: A:0.00, C:0.10, G:0.04, T:0.86
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:3589887 original size:28 final size:28
Alignment explanation
Indices: 3589847--3589918 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
3589837 AAAAAAAAAT
* ** *
3589847 CGGGATTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
3589875 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
3589903 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
3589919 TCGATTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:3590047 original size:52 final size:52
Alignment explanation
Indices: 3589960--3590076 Score: 130
Period size: 52 Copynumber: 2.2 Consensus size: 52
3589950 AGAATCGGAG
* *
3589960 TTGGAATATCCCCGATTAAAGGAAAATTGGCGTTTT-GAAAATAAAACCGGGA
1 TTGGAGTATCCCCGATTAAAGGAAAATTAGCGTTTTAG-AAATAAAACCGGGA
* * * ** *
3590012 TTGGAGTATCTCCGATT-GAGGAAATATTAGTGTTTTAGCGATAAAACCGGGG
1 TTGGAGTATCCCCGATTAAAGGAAA-ATTAGCGTTTTAGAAATAAAACCGGGA
3590064 TTGGAGTATCCCC
1 TTGGAGTATCCCC
3590077 TCGGAAATAA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
51 6 0.11
52 47 0.87
53 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.28
Consensus pattern (52 bp):
TTGGAGTATCCCCGATTAAAGGAAAATTAGCGTTTTAGAAATAAAACCGGGA
Found at i:3590122 original size:27 final size:28
Alignment explanation
Indices: 3590059--3590134 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 28
3590049 GCGATAAAAC
***
3590059 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
3590087 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
3590114 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
3590135 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:3590148 original size:212 final size:212
Alignment explanation
Indices: 3589842--3590241 Score: 608
Period size: 212 Copynumber: 1.9 Consensus size: 212
3589832 AGAAGAAAAA
* *
3589842 AAAATCGGGATTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAG
1 AAAACCGGGATTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAG
* * *
3589907 GTTGGAGTATCCTCGATTGTGAAAAATTGGT-ATTTTTGGAAATAGAATCGGAGTTGGAATATCC
66 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGATTTTTGGAAATAAAATCGGAGTTAGAATATCC
* * *
3589971 CCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCGG-GATTGGAGTATCTCCGATTGAGGAA
131 CCGATTAAA-GAAAATTAGCGTTTTGAAAATAAAACCGGAG-TTGGAATATCCCCGATTGAGGAA
3590035 ATATTAGTGTTTTAGCGAT
194 ATATTAGTGTTTTAGCGAT
* * *
3590054 AAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGG
1 AAAACCGGGATTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAG
* *
3590118 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTATC
66 GTTGGAGTATCCCCGATTGTGAA-AAATTGGTGATTTTTGGAAATAAAATCGGAGTTAGAATATC
* * *
3590183 CCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTG
130 CCCGATTAAAGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTG
3590242 TGGAGAATTG
Statistics
Matches: 169, Mismatches: 16, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
211 29 0.17
212 102 0.60
213 38 0.22
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (212 bp):
AAAACCGGGATTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAG
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGATTTTTGGAAATAAAATCGGAGTTAGAATATCC
CCGATTAAAGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGAGGAAAT
ATTAGTGTTTTAGCGAT
Found at i:3590218 original size:51 final size:53
Alignment explanation
Indices: 3590122--3590240 Score: 154
Period size: 51 Copynumber: 2.3 Consensus size: 53
3590112 AACGGGGTTG
* * *
3590122 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
*
3590176 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
*
3590227 GAATATCCCCGATT
1 GAGTATCCCCGATT
3590241 GTGGAGAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
51 34 0.58
52 2 0.03
53 8 0.14
54 15 0.25
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.32
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:3592625 original size:13 final size:13
Alignment explanation
Indices: 3592607--3592632 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3592597 ACAAAGATCC
3592607 ATGTATCGATACA
1 ATGTATCGATACA
3592620 ATGTATCGATACA
1 ATGTATCGATACA
3592633 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3592628 original size:33 final size:33
Alignment explanation
Indices: 3592586--3592652 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3592576 AAAATTTCCA
***
3592586 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
3592619 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
3592652 A
1 A
3592653 TTTCCATGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:3592696 original size:19 final size:18
Alignment explanation
Indices: 3592672--3592739 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
3592662 CAGTAGCTAA
3592672 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
3592691 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
3592706 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
*
3592723 TTATGTATTGATACAAA
1 TTATGTATCGATACAAA
3592740 TCGTTGAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.10
19 24 0.57
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:3592712 original size:13 final size:13
Alignment explanation
Indices: 3592694--3592718 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3592684 ACAATACTTA
3592694 TGTATCGATACAT
1 TGTATCGATACAT
3592707 TGTATCGATACA
1 TGTATCGATACA
3592719 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3592716 original size:32 final size:32
Alignment explanation
Indices: 3592675--3592737 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
3592665 TAGCTAATTA
*
3592675 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
*
3592707 TGTATCGATACAAAACTTATGTATTGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
3592738 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:3592801 original size:21 final size:21
Alignment explanation
Indices: 3592775--3592852 Score: 115
Period size: 21 Copynumber: 3.8 Consensus size: 21
3592765 GTTGGGACCC
3592775 TGTATCGATACATTTGTAGAA
1 TGTATCGATACATTTGTAGAA
3592796 TGTATCGATACATTTGT-GAA
1 TGTATCGATACATTTGTAGAA
* *
3592816 TGTATCGATACA-TTCTACAAA
1 TGTATCGATACATTTGTA-GAA
3592837 TGTATCGATACATTTG
1 TGTATCGATACATTTG
3592853 GAATTTTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
19 3 0.06
20 15 0.29
21 31 0.61
22 2 0.04
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTGTAGAA
Found at i:3592839 original size:41 final size:40
Alignment explanation
Indices: 3592775--3592856 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 40
3592765 GTTGGGACCC
* *
3592775 TGTATCGATACATTTGTAGAATGTATCGATACATTTGTGAA
1 TGTATCGATACATTTCTAAAATGTATCGATACATTTG-GAA
3592816 TGTATCGATACA-TTCTACAAATGTATCGATACATTTGGAA
1 TGTATCGATACATTTCTA-AAATGTATCGATACATTTGGAA
3592856 T
1 T
3592857 TTTTTTTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 8 0.21
41 30 0.79
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (40 bp):
TGTATCGATACATTTCTAAAATGTATCGATACATTTGGAA
Found at i:3606421 original size:52 final size:53
Alignment explanation
Indices: 3606329--3606594 Score: 226
Period size: 52 Copynumber: 5.1 Consensus size: 53
3606319 TTGGTATAAT
* * * * * * *
3606329 TGATAATGATAATGCCATGGTGGTGAGTA-GAGCCA-TAGTGACTTGTTTTCAC
1 TGATAATGATAAAGCCATGGTGGCGATTAGGA-TCAGAAGTGACTTGGTGTCAC
* * * * *
3606381 TGGTAATGATAATGCCATGGTGGCAATCAGGAT-AGAAGTGACTTGGTGTCAT
1 TGATAATGATAAAGCCATGGTGGCGATTAGGATCAGAAGTGACTTGGTGTCAC
* *
3606433 TGATAGTGATAAAGCCATGATGGCGATTAGGATCAG-AGTGACTTGGTGTCAC
1 TGATAATGATAAAGCCATGGTGGCGATTAGGATCAGAAGTGACTTGGTGTCAC
**
3606485 TGATAATGATGGCA-CCATGGTGGCGATTAGGATCA-AAGTGACTTGGTGTCAC
1 TGATAATGAT-AAAGCCATGGTGGCGATTAGGATCAGAAGTGACTTGGTGTCAC
* * * * * * *
3606537 TAATAATGATGACA-CTATAGTGACAATTAAGG-TC-GAAGTGACTTGGTATCAC
1 TGATAATGAT-AAAGCCATGGTGGCGATT-AGGATCAGAAGTGACTTGGTGTCAC
3606589 TGATAA
1 TGATAA
3606595 CGTCGTTATG
Statistics
Matches: 178, Mismatches: 29, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
51 1 0.01
52 169 0.95
53 8 0.04
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.29
Consensus pattern (53 bp):
TGATAATGATAAAGCCATGGTGGCGATTAGGATCAGAAGTGACTTGGTGTCAC
Found at i:3608116 original size:19 final size:19
Alignment explanation
Indices: 3608092--3608130 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3608082 ATCGAATGCC
3608092 CTGCACAACTCTGAAATCA
1 CTGCACAACTCTGAAATCA
3608111 CTGCACAACTCTGAAATCA
1 CTGCACAACTCTGAAATCA
3608130 C
1 C
3608131 ATGATGATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.33, G:0.10, T:0.21
Consensus pattern (19 bp):
CTGCACAACTCTGAAATCA
Found at i:3616166 original size:40 final size:40
Alignment explanation
Indices: 3616088--3616166 Score: 90
Period size: 40 Copynumber: 2.0 Consensus size: 40
3616078 TAATTATCAT
* *
3616088 TTTAAAAAAAATTATGTATTTAATATATTATTTTACTAAA
1 TTTAAAAAAAATTATGTATTTAATATATCATTTAACTAAA
* *
3616128 TTTAAAAATATATTAT-T-TTTTATATATCACTTTAACTAA
1 TTTAAAAA-AAATTATGTATTTAATATATCA-TTTAACTAA
3616167 TACTTAATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
39 10 0.30
40 17 0.52
41 6 0.18
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.49
Consensus pattern (40 bp):
TTTAAAAAAAATTATGTATTTAATATATCATTTAACTAAA
Found at i:3617100 original size:26 final size:25
Alignment explanation
Indices: 3617069--3617118 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
3617059 TTTAACATAC
3617069 ATAATTTAAA-TAAATAAAATATAAAA
1 ATAA-TTAAATTAAAT-AAATATAAAA
3617095 ATAATTAAATTAAATAAATATAAA
1 ATAATTAAATTAAATAAATATAAA
3617119 TTAGGCTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (25 bp):
ATAATTAAATTAAATAAATATAAAA
Found at i:3617877 original size:15 final size:15
Alignment explanation
Indices: 3617857--3617969 Score: 54
Period size: 16 Copynumber: 7.3 Consensus size: 15
3617847 GGAATTGTTT
3617857 TTTTTATTTGAATTA
1 TTTTTATTTGAATTA
*
3617872 TTTTTATTTAAATATA
1 TTTTTATTTGAAT-TA
* * *
3617888 TTTTAGATTT-AGGTAA
1 TTTT-TATTTGA-ATTA
3617904 TTTTTATTGTG-A-TA
1 TTTTTATT-TGAATTA
*
3617918 TTTTTAAATTTG-ATTT
1 TTTTT--ATTTGAATTA
*
3617934 TTTTTATTTTAAGTTA
1 TTTTTATTTGAA-TTA
* *
3617950 TTTTGACTTTAAATTA
1 TTTTTA-TTTGAATTA
3617966 TTTT
1 TTTT
3617970 AGATATAAAT
Statistics
Matches: 75, Mismatches: 12, Indels: 21
0.69 0.11 0.19
Matches are distributed among these distances:
14 10 0.13
15 19 0.25
16 36 0.48
17 10 0.13
ACGTcount: A:0.27, C:0.01, G:0.08, T:0.64
Consensus pattern (15 bp):
TTTTTATTTGAATTA
Found at i:3617889 original size:16 final size:15
Alignment explanation
Indices: 3617857--3617891 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3617847 GGAATTGTTT
*
3617857 TTTTTATTTGAATTA
1 TTTTTATTTAAATTA
3617872 TTTTTATTTAAATATA
1 TTTTTATTTAAAT-TA
3617888 TTTT
1 TTTT
3617892 AGATTTAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
TTTTTATTTAAATTA
Found at i:3618178 original size:16 final size:16
Alignment explanation
Indices: 3618150--3618183 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3618140 TTTAAAAATT
3618150 AATAAATATTTATATA
1 AATAAATATTTATATA
3618166 AATATAATA-TTATATA
1 AATA-AATATTTATATA
3618182 AA
1 AA
3618184 ATTTTATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATAAATATTTATATA
Found at i:3618558 original size:2 final size:2
Alignment explanation
Indices: 3618551--3618584 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3618541 AAACATTTAC
3618551 AT AT 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 AT AT
3618585 TCTAATCTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3618734 original size:19 final size:19
Alignment explanation
Indices: 3618710--3618746 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3618700 TTGCATTAAA
*
3618710 AATTTGGATTTTAAAAATG
1 AATTTGGATTTAAAAAATG
3618729 AATTTGGATTTAAAAAAT
1 AATTTGGATTTAAAAAAT
3618747 CATGTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.41
Consensus pattern (19 bp):
AATTTGGATTTAAAAAATG
Done.