Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 22 of 185
Found at i:6292801 original size:88 final size:88
Alignment explanation
Indices: 6292627--6292898 Score: 431
Period size: 88 Copynumber: 3.1 Consensus size: 88
6292617 AAGCTTTGTT
* ** *
6292627 TTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCA-CTACA
1 TTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTTAACCAGCTCTATC-ACA
* *
6292690 ATCGAGAGAGGCAAGGTTTGTGTC
65 ACCGAAAGAGGCAAGGTTTGTGTC
* * * *
6292714 TTCGACCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAA
1 TTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTTAACCAGCTCTATCACAA
6292779 CCGAAAGAGGCAAGGTTTGTGTC
66 CCGAAAGAGGCAAGGTTTGTGTC
6292802 TTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTTAACCAGCTCTATCACAA
1 TTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTTAACCAGCTCTATCACAA
6292867 CCGAAAGAGGCAAGGTTTGTGTC
66 CCGAAAGAGGCAAGGTTTGTGTC
6292890 TTCGATCTG
1 TTCGATCTG
6292899 TCCCTTGGGG
Statistics
Matches: 169, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
87 36 0.21
88 132 0.78
89 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (88 bp):
TTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTTAACCAGCTCTATCACAA
CCGAAAGAGGCAAGGTTTGTGTC
Found at i:6299354 original size:20 final size:20
Alignment explanation
Indices: 6299329--6299375 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
6299319 AATAAGAAAG
6299329 ATATAAATAATA-TCAATAT-A
1 ATATAAAT-ATAGT-AATATCA
6299349 ATATAAATATAGTAATATCA
1 ATATAAATATAGTAATATCA
6299369 ATATAAA
1 ATATAAA
6299376 AACAAATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (20 bp):
ATATAAATATAGTAATATCA
Found at i:6305047 original size:10 final size:10
Alignment explanation
Indices: 6305017--6305058 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
6305007 ATCACAAGTC
6305017 TTGTGATATA
1 TTGTGATATA
*
6305027 GTGTGATATA
1 TTGTGATATA
6305037 TTGTGATATA
1 TTGTGATATA
*
6305047 TATATGATATA
1 T-TGTGATATA
6305058 T
1 T
6305059 GTAGAAATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 19 0.68
11 9 0.32
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (10 bp):
TTGTGATATA
Found at i:6313851 original size:21 final size:21
Alignment explanation
Indices: 6313827--6313897 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
6313817 TGTTGATGAG
*
6313827 TTGGGGCAGCTTTTTGCTGAA
1 TTGGGGCAGCTTATTGCTGAA
* * *
6313848 TTGGAGTAGCTTATTGCTGAG
1 TTGGGGCAGCTTATTGCTGAA
*
6313869 TTGGGGCAGCTTCTTGCTGAA
1 TTGGGGCAGCTTATTGCTGAA
6313890 TTGGGGCA
1 TTGGGGCA
6313898 ACCTTGATTA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.15, C:0.14, G:0.35, T:0.35
Consensus pattern (21 bp):
TTGGGGCAGCTTATTGCTGAA
Found at i:6316395 original size:26 final size:27
Alignment explanation
Indices: 6316360--6316474 Score: 90
Period size: 27 Copynumber: 4.3 Consensus size: 27
6316350 CAAAAGGGCA
* **
6316360 TTCTCTTCATAAATCGCC-CAAAGGCT
1 TTCTTTTCATAAATAACCACAAAGGCT
* * * *
6316386 TTCTTTTCATAGATAGCTATAAAGGCT
1 TTCTTTTCATAAATAACCACAAAGGCT
* *
6316413 GTCTTTTCA-AAGATAACCATAAAGGCT
1 TTCTTTTCATAA-ATAACCACAAAGGCT
* * *
6316440 TCCTTTTCATAGATCACCACAAAGGCT
1 TTCTTTTCATAAATAACCACAAAGGCT
*
6316467 TCCTTTTC
1 TTCTTTTC
6316475 TAGTGTGTTT
Statistics
Matches: 72, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
26 15 0.21
27 56 0.78
28 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (27 bp):
TTCTTTTCATAAATAACCACAAAGGCT
Found at i:6316409 original size:27 final size:27
Alignment explanation
Indices: 6316379--6316474 Score: 120
Period size: 27 Copynumber: 3.6 Consensus size: 27
6316369 TAAATCGCCC
* *
6316379 AAAGGCTTTCTTTTCATAGATAGCTAT
1 AAAGGCTTTCTTTTCATAGATAACCAT
* *
6316406 AAAGGCTGTCTTTTCAAAGATAACCAT
1 AAAGGCTTTCTTTTCATAGATAACCAT
* * *
6316433 AAAGGCTTCCTTTTCATAGATCACCAC
1 AAAGGCTTTCTTTTCATAGATAACCAT
*
6316460 AAAGGCTTCCTTTTC
1 AAAGGCTTTCTTTTC
6316475 TAGTGTGTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (27 bp):
AAAGGCTTTCTTTTCATAGATAACCAT
Found at i:6319895 original size:11 final size:11
Alignment explanation
Indices: 6319856--6319893 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
6319846 ATAATACGTG
6319856 AAACACATGTT
1 AAACACATGTT
6319867 AAACACATGTT
1 AAACACATGTT
*
6319878 AAACATATGTT
1 AAACACATGTT
6319889 AAACA
1 AAACA
6319894 TACCTTACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.50, C:0.16, G:0.08, T:0.26
Consensus pattern (11 bp):
AAACACATGTT
Found at i:6320113 original size:45 final size:45
Alignment explanation
Indices: 6320045--6320174 Score: 151
Period size: 45 Copynumber: 2.9 Consensus size: 45
6320035 GGAAGGAAGA
* *
6320045 ATTAGTGGCTTCGTCCACGACCTACATGATAGCTTGTCTATGAAT
1 ATTAGTGGCTTCATCCACAACCTACATGATAGCTTGTCTATGAAT
* *
6320090 ATTAGTGGCTTCATCCACAACCTACATAGCA-A-CTTGTTTGTGAAT
1 ATTAGTGGCTTCATCCACAACCTACAT-G-ATAGCTTGTCTATGAAT
* *
6320135 ATTAGTGG-TTTATCCACAACCTACAT-AGTAGCTTATCTAT
1 ATTAGTGGCTTCATCCACAACCTACATGA-TAGCTTGTCTAT
6320175 AAATTTGGAG
Statistics
Matches: 72, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
41 1 0.01
43 1 0.01
44 23 0.32
45 44 0.61
46 2 0.03
47 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.35
Consensus pattern (45 bp):
ATTAGTGGCTTCATCCACAACCTACATGATAGCTTGTCTATGAAT
Found at i:6321105 original size:92 final size:92
Alignment explanation
Indices: 6320948--6321135 Score: 331
Period size: 92 Copynumber: 2.0 Consensus size: 92
6320938 CAAAATTACT
* * *
6320948 AATATTTACAAATGAGATTTCTTAATACATTTAATTTTGAAGTTAATGTGTTTTTCCTGAATAAC
1 AATATTTACAAATGAAATTTCTTAATACATTTAATTCTAAAGTTAATGTGTTTTTCCTGAATAAC
*
6321013 GACGAATAACCAAGGTATTTAGTTTTG
66 GACGAATAACCAAGGTATTTAATTTTG
6321040 AATATTTACAAATGAAATTTCTTAATACATTTAATTCTAAAGTTAATGTGTTTTTCCTGAATAAC
1 AATATTTACAAATGAAATTTCTTAATACATTTAATTCTAAAGTTAATGTGTTTTTCCTGAATAAC
*
6321105 GATGAATAACCAAGGTATTTAATTTTG
66 GACGAATAACCAAGGTATTTAATTTTG
6321132 AATA
1 AATA
6321136 AATAAACGAA
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 91 1.00
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (92 bp):
AATATTTACAAATGAAATTTCTTAATACATTTAATTCTAAAGTTAATGTGTTTTTCCTGAATAAC
GACGAATAACCAAGGTATTTAATTTTG
Found at i:6324415 original size:14 final size:15
Alignment explanation
Indices: 6324398--6324427 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
6324388 ATTTATATAA
6324398 TAACAATA-AAATAT
1 TAACAATATAAATAT
6324412 TAACAATATAAATAT
1 TAACAATATAAATAT
6324427 T
1 T
6324428 TTTACCCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (15 bp):
TAACAATATAAATAT
Found at i:6326795 original size:2 final size:2
Alignment explanation
Indices: 6326788--6326814 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6326778 ATTTAATTAA
6326788 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
6326815 ACAGATGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6331625 original size:39 final size:41
Alignment explanation
Indices: 6331565--6331652 Score: 101
Period size: 41 Copynumber: 2.2 Consensus size: 41
6331555 ATAGGAGCGA
*
6331565 AAATGGG-GAGAAAGAATGAGGAAAG-AGAAAAAAAAAAAG
1 AAATGGGAGAGAAAGAAGGAGGAAAGAAGAAAAAAAAAAAG
* ***
6331604 AAATGGGAGAGAAA-AGGGAGGAAAGATAGAGGGAAAAAAAG
1 AAATGGGAGAGAAAGAAGGAGGAAAGA-AGAAAAAAAAAAAG
6331645 AAATGGGA
1 AAATGGGA
6331653 AGGAAAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.39
40 6 0.15
41 19 0.46
ACGTcount: A:0.59, C:0.00, G:0.35, T:0.06
Consensus pattern (41 bp):
AAATGGGAGAGAAAGAAGGAGGAAAGAAGAAAAAAAAAAAG
Found at i:6335265 original size:139 final size:139
Alignment explanation
Indices: 6334993--6335265 Score: 361
Period size: 139 Copynumber: 2.0 Consensus size: 139
6334983 AAACTTAGGC
* * *
6334993 TTAATATATAGATTGGCTCCTAAACTTGGCAACTTTTCTCAAATTAGCTCCTAAACTTTTTTTTG
1 TTAATATACAGATTGGCCCCTAAACTTGGCAACTTTTCTCAAATTAGCCCCTAAACTTTTTTTTG
* * * * * * *
6335058 GATCACATTGGTCCCTAAGGTTGGCATCCGTTTCACAAATTGGTCCCTATAGTTAAAACCGTTAG
66 GATCACAGTGGTCCCTAAGGTTGGCATCCATTGCACAAATTAGTCCCTACAGCTAAAACAGTTAG
6335123 TTTTAAGGT
131 TTTTAAGGT
* *
6335132 TTAATATACAGATTGGCCCCTAAACTTGGCAGCTTTTCTCACATT-GTCCCCTAAACTCTTTTTT
1 TTAATATACAGATTGGCCCCTAAACTTGGCAACTTTTCTCAAATTAG-CCCCTAAACT-TTTTTT
* * * *
6335196 TGGGTCATAGTGGTCCCTAAGGTTGGCATCCATTGCATAAATTAGTCCCTACA-CTAACACAGTT
64 TGGATCACAGTGGTCCCTAAGGTTGGCATCCATTGCACAAATTAGTCCCTACAGCTAAAACAGTT
*
6335260 TGTTTT
129 AGTTTT
6335266 TGAAGATTTT
Statistics
Matches: 115, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
138 1 0.01
139 63 0.55
140 51 0.44
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (139 bp):
TTAATATACAGATTGGCCCCTAAACTTGGCAACTTTTCTCAAATTAGCCCCTAAACTTTTTTTTG
GATCACAGTGGTCCCTAAGGTTGGCATCCATTGCACAAATTAGTCCCTACAGCTAAAACAGTTAG
TTTTAAGGT
Found at i:6335448 original size:16 final size:16
Alignment explanation
Indices: 6335421--6335474 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
6335411 TTATAAATTA
*
6335421 TAAAAATTCAAAAAAG
1 TAAAAATACAAAAAAG
* *
6335437 TAAATATACAAAAAAA
1 TAAAAATACAAAAAAG
6335453 TAAAAATA-AAAAAAG
1 TAAAAATACAAAAAAG
*
6335468 TTAAAAT
1 TAAAAAT
6335475 TTAACATTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 12 0.38
16 20 0.62
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.20
Consensus pattern (16 bp):
TAAAAATACAAAAAAG
Found at i:6335547 original size:23 final size:19
Alignment explanation
Indices: 6335534--6335572 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
6335524 ATCTAAAACT
6335534 ATATAACAAATAAAATTAAAA
1 ATAT-ACAAAT-AAATTAAAA
6335555 ATATACAAATAAA-TAAAA
1 ATATACAAATAAATTAAAA
6335573 GTCAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 3 0.17
20 6 0.33
21 4 0.22
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (19 bp):
ATATACAAATAAATTAAAA
Found at i:6335902 original size:35 final size:35
Alignment explanation
Indices: 6335830--6335902 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 35
6335820 AAATTTGATA
* * *
6335830 TTTTTATTTTCAATTTATACATATTCTTTTTTATT
1 TTTTTATTTTCAATTTATACATATTATATTCTATT
6335865 TTTTTATTTTCAATTTATATACATA-TATATTCT-TT
1 TTTTTATTTTCAA-TT-TATACATATTATATTCTATT
6335900 TTT
1 TTT
6335903 AAAAGTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 18 0.55
36 7 0.21
37 8 0.24
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (35 bp):
TTTTTATTTTCAATTTATACATATTATATTCTATT
Found at i:6336323 original size:19 final size:18
Alignment explanation
Indices: 6336301--6336359 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 18
6336291 ATTACAAAAT
6336301 AATTCAAAATAATTTTCAA
1 AATTCAAAATAATTTT-AA
6336320 AATTTCAAAATAAGTTTTAA
1 AA-TTCAAAATAA-TTTTAA
6336340 AATTCAAAAT-ATTTATAA
1 AATTCAAAATAATTT-TAA
6336358 AA
1 AA
6336360 ATTCTAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
17 3 0.08
18 6 0.16
19 10 0.27
20 14 0.38
21 4 0.11
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (18 bp):
AATTCAAAATAATTTTAA
Found at i:6336360 original size:19 final size:19
Alignment explanation
Indices: 6336301--6336368 Score: 77
Period size: 19 Copynumber: 3.5 Consensus size: 19
6336291 ATTACAAAAT
6336301 AATTCAAAATAATTTTCAAA
1 AATTCAAAATAATTTT-AAA
*
6336321 ATTTCAAAATAAGTTTT-AA
1 AATTCAAAATAA-TTTTAAA
6336340 AATTCAAAAT-ATTTATAAA
1 AATTCAAAATAATTT-TAAA
6336359 AATTCTAAAA
1 AATTC-AAAA
6336369 ATTATATTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
17 3 0.07
18 2 0.05
19 18 0.43
20 15 0.36
21 4 0.10
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.37
Consensus pattern (19 bp):
AATTCAAAATAATTTTAAA
Found at i:6336373 original size:18 final size:18
Alignment explanation
Indices: 6336338--6336405 Score: 50
Period size: 18 Copynumber: 3.8 Consensus size: 18
6336328 AATAAGTTTT
6336338 AAAATTC-AAAATATTTATA
1 AAAATTCTAAAA-A-TTATA
6336357 AAAATTCTAAAAATTATA
1 AAAATTCTAAAAATTATA
**** **
6336375 TTTTTTAAAAAAATTATA
1 AAAATTCTAAAAATTATA
6336393 AAAATT-TAAAAAT
1 AAAATTCTAAAAAT
6336406 AAATTCTAAA
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
17 6 0.16
18 19 0.51
19 8 0.22
20 4 0.11
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATTCTAAAAATTATA
Found at i:6337685 original size:15 final size:17
Alignment explanation
Indices: 6337659--6337696 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
6337649 AGCTCAAAGC
6337659 ATAAGTAGAAAAGAAAT
1 ATAAGTAGAAAAGAAAT
*
6337676 A-AAGTA-AAAATAAAT
1 ATAAGTAGAAAAGAAAT
6337691 ATAAGT
1 ATAAGT
6337697 TGTAGTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 9 0.47
16 9 0.47
17 1 0.05
ACGTcount: A:0.66, C:0.00, G:0.13, T:0.21
Consensus pattern (17 bp):
ATAAGTAGAAAAGAAAT
Found at i:6341149 original size:29 final size:30
Alignment explanation
Indices: 6341108--6341188 Score: 105
Period size: 29 Copynumber: 2.8 Consensus size: 30
6341098 ATTTAATAAT
*
6341108 TATATTTAAATATTTAA-AAT-ATATTTTA
1 TATATTAAAATATTTAATAATAATATTTTA
*
6341136 TATATTAGAAATATTTAATATTAATATTTTA
1 TATATTA-AAATATTTAATAATAATATTTTA
*
6341167 TATATTAAAATA-TTAACAATAA
1 TATATTAAAATATTTAATAATAA
6341189 GTTATAATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
28 6 0.13
29 18 0.39
30 7 0.15
31 15 0.33
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (30 bp):
TATATTAAAATATTTAATAATAATATTTTA
Found at i:6341163 original size:13 final size:15
Alignment explanation
Indices: 6341128--6341174 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
6341118 TATTTAAAAT
6341128 ATATTTTATATATTA
1 ATATTTTATATATTA
*
6341143 GAAATATTTA-ATATTA
1 -ATAT-TTTATATATTA
6341159 ATATTTTATATATTA
1 ATATTTTATATATTA
6341174 A
1 A
6341175 AATATTAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 4 0.15
15 10 0.37
16 9 0.33
17 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
ATATTTTATATATTA
Found at i:6341166 original size:31 final size:28
Alignment explanation
Indices: 6341108--6341180 Score: 101
Period size: 31 Copynumber: 2.5 Consensus size: 28
6341098 ATTTAATAAT
*
6341108 TATATTTAAATATTTAAAATATATTTTA
1 TATATTAAAATATTTAAAATATATTTTA
*
6341136 TATATTAGAAATATTTAATATTAATATTTTA
1 TATATTA-AAATATTTAA-AAT-ATATTTTA
6341167 TATATTAAAATATT
1 TATATTAAAATATT
6341181 AACAATAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 6 0.15
29 10 0.25
30 9 0.22
31 15 0.38
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (28 bp):
TATATTAAAATATTTAAAATATATTTTA
Found at i:6344736 original size:13 final size:13
Alignment explanation
Indices: 6344713--6344754 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
6344703 TTGGTTTTTT
*
6344713 TACACAAATAATA
1 TACAAAAATAATA
*
6344726 TATAAAAATAAT-
1 TACAAAAATAATA
6344738 TACAAAAATAAGTA
1 TACAAAAATAA-TA
6344752 TAC
1 TAC
6344755 TGAACAATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 10 0.42
13 11 0.46
14 3 0.12
ACGTcount: A:0.62, C:0.10, G:0.02, T:0.26
Consensus pattern (13 bp):
TACAAAAATAATA
Found at i:6345523 original size:30 final size:30
Alignment explanation
Indices: 6345475--6345540 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
6345465 TTAAACCTTA
6345475 AATTAAATTTTTTATTATTAATAATAAATT
1 AATTAAATTTTTTATTATTAATAATAAATT
* *
6345505 AATTGAATTTATTT-TTATTAATAATTAATT
1 AATTAAATTT-TTTATTATTAATAATAAATT
6345535 AATTAA
1 AATTAA
6345541 TAAAAATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 29 0.91
31 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (30 bp):
AATTAAATTTTTTATTATTAATAATAAATT
Found at i:6346192 original size:25 final size:26
Alignment explanation
Indices: 6346139--6346194 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
6346129 AATTTTAAAA
* *
6346139 TATTTTTAAAATACTTTTTTTATTTTT
1 TATTTTTAAAATAC-TTTTTTAGTGTT
*
6346166 TATTTTTAAAATA-TTTTTTGGTGTT
1 TATTTTTAAAATACTTTTTTAGTGTT
6346191 TATT
1 TATT
6346195 AAAAAAATGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 13 0.50
27 13 0.50
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (26 bp):
TATTTTTAAAATACTTTTTTAGTGTT
Found at i:6348750 original size:20 final size:19
Alignment explanation
Indices: 6348712--6348754 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
6348702 AATAATAATT
6348712 TAATATTTTACTAAAAATAA
1 TAATATTTTACTAAAAAT-A
*
6348732 TAATATTTTA-TAAGTAATA
1 TAATATTTTACTAA-AAATA
6348751 TAAT
1 TAAT
6348755 GTATATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (19 bp):
TAATATTTTACTAAAAATA
Found at i:6349426 original size:26 final size:27
Alignment explanation
Indices: 6349387--6349457 Score: 108
Period size: 27 Copynumber: 2.6 Consensus size: 27
6349377 AATATAATAA
6349387 ATATTTTTA-TTTTTTATTTTTAAAAT
1 ATATTTTTATTTTTTTATTTTTAAAAT
*
6349413 ATTTTTTTATTTTTTTATTTTTAAAAT
1 ATATTTTTATTTTTTTATTTTTAAAAT
6349440 ATATTTTTAAATTTTTTT
1 ATATTTTT--ATTTTTTT
6349458 GGTGTTTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 8 0.20
27 24 0.60
29 8 0.20
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (27 bp):
ATATTTTTATTTTTTTATTTTTAAAAT
Found at i:6349727 original size:34 final size:34
Alignment explanation
Indices: 6349666--6349730 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
6349656 TGTATGTTTA
* * *
6349666 AATCGATTGTCATGTTGTAATACTGCTTCTTTTG
1 AATCAATTGTCATGGTGGAATACTGCTTCTTTTG
* *
6349700 AATCAATTGTTATGGTGGAATATTGCTTCTT
1 AATCAATTGTCATGGTGGAATACTGCTTCTT
6349731 CTTCTTTTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.46
Consensus pattern (34 bp):
AATCAATTGTCATGGTGGAATACTGCTTCTTTTG
Found at i:6351960 original size:21 final size:20
Alignment explanation
Indices: 6351934--6351979 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
6351924 AATAAATACC
*
6351934 AAAAAATTATTTTAAAAATTA
1 AAAAAAGTATTTT-AAAATTA
6351955 AAAAAAGTATTTTAAAATTA
1 AAAAAAGTATTTTAAAATTA
6351975 AAAAA
1 AAAAA
6351980 TAAATATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
AAAAAAGTATTTTAAAATTA
Found at i:6360282 original size:20 final size:20
Alignment explanation
Indices: 6360257--6360361 Score: 79
Period size: 20 Copynumber: 5.3 Consensus size: 20
6360247 CAGTAATAAG
*
6360257 AAATCAAAGGATTGAGAATC
1 AAATCAAAGGAATGAGAATC
* * **
6360277 AAATCAATGTAATG-GAAAG
1 AAATCAAAGGAATGAGAATC
* *
6360296 AAATCAAAAGATTGAGAATC
1 AAATCAAAGGAATGAGAATC
* * **
6360316 AAATCAATGTAATG-GAAAG
1 AAATCAAAGGAATGAGAATC
* *
6360335 AAATCAAAAGACTGAGAATC
1 AAATCAAAGGAATGAGAATC
6360355 AAATCAA
1 AAATCAA
6360362 TGTAAACAAG
Statistics
Matches: 60, Mismatches: 23, Indels: 4
0.69 0.26 0.05
Matches are distributed among these distances:
19 26 0.43
20 34 0.57
ACGTcount: A:0.54, C:0.10, G:0.17, T:0.19
Consensus pattern (20 bp):
AAATCAAAGGAATGAGAATC
Found at i:6360300 original size:39 final size:39
Alignment explanation
Indices: 6360254--6360366 Score: 208
Period size: 39 Copynumber: 2.9 Consensus size: 39
6360244 AAACAGTAAT
*
6360254 AAGAAATCAAAGGATTGAGAATCAAATCAATGTAATGGA
1 AAGAAATCAAAAGATTGAGAATCAAATCAATGTAATGGA
6360293 AAGAAATCAAAAGATTGAGAATCAAATCAATGTAATGGA
1 AAGAAATCAAAAGATTGAGAATCAAATCAATGTAATGGA
*
6360332 AAGAAATCAAAAGACTGAGAATCAAATCAATGTAA
1 AAGAAATCAAAAGATTGAGAATCAAATCAATGTAA
6360367 ACAAGATTTT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 72 1.00
ACGTcount: A:0.54, C:0.09, G:0.18, T:0.19
Consensus pattern (39 bp):
AAGAAATCAAAAGATTGAGAATCAAATCAATGTAATGGA
Found at i:6360301 original size:19 final size:19
Alignment explanation
Indices: 6360277--6360341 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
6360267 ATTGAGAATC
6360277 AAATCAATGTAATGGAAAG
1 AAATCAATGTAATGGAAAG
* * **
6360296 AAATCAAAAG-ATTGAGAATC
1 AAATC-AATGTAATG-GAAAG
6360316 AAATCAATGTAATGGAAAG
1 AAATCAATGTAATGGAAAG
6360335 AAATCAA
1 AAATCAA
6360342 AAGACTGAGA
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
19 21 0.60
20 14 0.40
ACGTcount: A:0.55, C:0.08, G:0.17, T:0.20
Consensus pattern (19 bp):
AAATCAATGTAATGGAAAG
Found at i:6361278 original size:20 final size:20
Alignment explanation
Indices: 6361255--6361299 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
6361245 ATGTACGTAT
*
6361255 ATATATAATACTTTCTATAC
1 ATATATAATAATTTCTATAC
* * *
6361275 ATATTTTATAATTTCTATAT
1 ATATATAATAATTTCTATAC
6361295 ATATA
1 ATATA
6361300 ATCATTATCT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATATAATAATTTCTATAC
Found at i:6361307 original size:98 final size:99
Alignment explanation
Indices: 6361192--6361396 Score: 313
Period size: 98 Copynumber: 2.1 Consensus size: 99
6361182 TTTTTAAGTT
* * * * * *
6361192 TATATATGTAATTATTATTTTTATGATTTATATATTTATTACCTTATATATATATGTACGTATAT
1 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATATACGTATAT
*
6361257 A-TATAATACTTTCTATACATATTTTATAATTTC
66 AGTATAATACTTTCTATACACATTTTATAATTTC
6361290 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATATACGTATAT
1 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATATACGTATAT
* *
6361355 ATGTATTATACTTTCTATCCACATTTTATAATTTC
66 A-GTATAATACTTTCTATACACATTTTATAATTTC
6361390 TATATAT
1 TATATAT
6361397 GTATATTTTC
Statistics
Matches: 96, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
98 60 0.62
100 36 0.38
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.53
Consensus pattern (99 bp):
TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATATACGTATAT
AGTATAATACTTTCTATACACATTTTATAATTTC
Found at i:6361330 original size:24 final size:24
Alignment explanation
Indices: 6361290--6361347 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
6361280 TTATAATTTC
*
6361290 TATATATATAATCATTATCTT-TA
1 TATATATATAATCATTAACTTATA
* * *
6361313 TGATCTATATATTTATTAACTTATA
1 T-ATATATATAATCATTAACTTATA
6361338 TATATATATA
1 TATATATATA
6361348 CGTATATATG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 1 0.04
24 24 0.86
25 3 0.11
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.52
Consensus pattern (24 bp):
TATATATATAATCATTAACTTATA
Found at i:6361339 original size:16 final size:17
Alignment explanation
Indices: 6361318--6361367 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 17
6361308 CTTTATGATC
*
6361318 TATATATTTATTA-ACT
1 TATATATATATTATACT
*
6361334 TATATATATA-TATACG
1 TATATATATATTATACT
*
6361350 TATATATGTATTATACT
1 TATATATATATTATACT
6361367 T
1 T
6361368 TCTATCCACA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
15 2 0.07
16 20 0.71
17 6 0.21
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (17 bp):
TATATATATATTATACT
Found at i:6363047 original size:9 final size:9
Alignment explanation
Indices: 6363032--6363117 Score: 102
Period size: 9 Copynumber: 9.6 Consensus size: 9
6363022 TTTTGGTTAA
6363032 GAATTAACC
1 GAATTAACC
*
6363041 AAATTAACC
1 GAATTAACC
6363050 GAATT-ACC
1 GAATTAACC
6363058 TGAATTAACC
1 -GAATTAACC
*
6363068 GAATTACCC
1 GAATTAACC
*
6363077 GAATTAACT
1 GAATTAACC
6363086 GAATTAACC
1 GAATTAACC
* *
6363095 GTATTACCC
1 GAATTAACC
6363104 GAATTAACC
1 GAATTAACC
*
6363113 TAATT
1 GAATT
6363118 GAATCATACA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
8 3 0.05
9 58 0.91
10 3 0.05
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (9 bp):
GAATTAACC
Found at i:6363063 original size:27 final size:27
Alignment explanation
Indices: 6363032--6363117 Score: 120
Period size: 27 Copynumber: 3.2 Consensus size: 27
6363022 TTTTGGTTAA
* *
6363032 GAATTAACCAAATTAACCGAATTACCT
1 GAATTAACCGAATTACCCGAATTACCT
*
6363059 GAATTAACCGAATTACCCGAATTAACT
1 GAATTAACCGAATTACCCGAATTACCT
*
6363086 GAATTAACCGTATTACCCGAATTAACCT
1 GAATTAACCGAATTACCCGAATT-ACCT
6363114 -AATT
1 GAATT
6363118 GAATCATACA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
27 50 0.94
28 3 0.06
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (27 bp):
GAATTAACCGAATTACCCGAATTACCT
Found at i:6369179 original size:49 final size:49
Alignment explanation
Indices: 6369126--6369224 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
6369116 AGCTTATCAG
6369126 TTATATATCAGGAAGAGAAAGGGGCCATCTAAATAATGATGAATTTGAC
1 TTATATATCAGGAAGAGAAAGGGGCCATCTAAATAATGATGAATTTGAC
6369175 TTATATATCAGGAAGAGAAAGGGGCCATCTAAATAATGATGAATTTGAC
1 TTATATATCAGGAAGAGAAAGGGGCCATCTAAATAATGATGAATTTGAC
6369224 T
1 T
6369225 CTTTGTCCTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.27
Consensus pattern (49 bp):
TTATATATCAGGAAGAGAAAGGGGCCATCTAAATAATGATGAATTTGAC
Found at i:6389870 original size:7 final size:7
Alignment explanation
Indices: 6389827--6389851 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6389817 AATAAATAAA
6389827 TAAATAT
1 TAAATAT
6389834 TAAATAT
1 TAAATAT
6389841 TAAATAT
1 TAAATAT
6389848 TAAA
1 TAAA
6389852 ATAAATACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
TAAATAT
Found at i:6391484 original size:15 final size:16
Alignment explanation
Indices: 6391458--6391489 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
6391448 AAAAATATGT
6391458 GGCCCGAGCCCGGCCC
1 GGCCCGAGCCCGGCCC
6391474 GGCCC-AGCCCGGCCC
1 GGCCCGAGCCCGGCCC
6391489 G
1 G
6391490 TTTTTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.06, C:0.56, G:0.38, T:0.00
Consensus pattern (16 bp):
GGCCCGAGCCCGGCCC
Found at i:6391524 original size:23 final size:22
Alignment explanation
Indices: 6391490--6391550 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 22
6391480 GCCCGGCCCG
6391490 TTTTTAATTAAAATTAAAATTATT
1 TTTTTAA-TAAAATTAAAATTA-T
6391514 TTTTTAATAAAATTAAAATTAT
1 TTTTTAATAAAATTAAAATTAT
* *
6391536 TTGTTATTAAAATTA
1 TTTTTAATAAAATTA
6391551 TTTGTTAGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.40
23 14 0.40
24 7 0.20
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTTTAATAAAATTAAAATTAT
Found at i:6391546 original size:16 final size:16
Alignment explanation
Indices: 6391525--6391567 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
6391515 TTTTAATAAA
6391525 ATTAAAATTATTTGTT
1 ATTAAAATTATTTGTT
6391541 ATTAAAATTATTTGTT
1 ATTAAAATTATTTGTT
*
6391557 AGTAAAATTAT
1 ATTAAAATTAT
6391568 CAAATTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (16 bp):
ATTAAAATTATTTGTT
Found at i:6391549 original size:22 final size:23
Alignment explanation
Indices: 6391496--6391550 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
6391486 CCCGTTTTTA
*
6391496 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAATTATTTTGTT
*
6391519 AATAAAATTAAAATTA-TTTGTT
1 ATTAAAATTAAAATTATTTTGTT
6391541 ATTAAAATTA
1 ATTAAAATTA
6391551 TTTGTTAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 14 0.48
23 15 0.52
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
ATTAAAATTAAAATTATTTTGTT
Found at i:6391641 original size:66 final size:59
Alignment explanation
Indices: 6391569--6391688 Score: 188
Period size: 59 Copynumber: 2.1 Consensus size: 59
6391559 TAAAATTATC
* * * *
6391569 AAATTAT-TAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTATAACAAAATCTAACATTTGATTAGTA
*
6391627 AATTTATCAAATTATTAATTGTATTAATTGTTATAACAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTATAACAAAATCTAACATTTGATTAGTA
6391686 AAA
1 AAA
6391689 CAAACTTGAT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
58 6 0.11
59 49 0.89
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.44
Consensus pattern (59 bp):
AAATTATCAAATTATTAATTGTATTAATTGTTATAACAAAATCTAACATTTGATTAGTA
Found at i:6391793 original size:21 final size:23
Alignment explanation
Indices: 6391752--6391796 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
6391742 GTAAATAAAC
6391752 TTAAAATAAAAAACTATTATATT
1 TTAAAATAAAAAACTATTATATT
6391775 TTAAAATAAAAAA-TA-TATATT
1 TTAAAATAAAAAACTATTATATT
6391796 T
1 T
6391797 AATATTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 7 0.32
22 2 0.09
23 13 0.59
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
TTAAAATAAAAAACTATTATATT
Found at i:6400704 original size:23 final size:22
Alignment explanation
Indices: 6400652--6400704 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
6400642 TCCACGTCTT
*
6400652 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
6400674 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
6400697 TTTCTTTT
1 TTTCTTTT
6400705 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:6404645 original size:23 final size:23
Alignment explanation
Indices: 6404612--6404660 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
6404602 AACACAGTTT
*
6404612 GGATTCTTCAATCCTATATCTAC
1 GGATTCCTCAATCCTATATCTAC
6404635 GGATTCCTCAATCCTATATCTAC
1 GGATTCCTCAATCCTATATCTAC
6404658 GGA
1 GGA
6404661 GCCTTGCTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (23 bp):
GGATTCCTCAATCCTATATCTAC
Found at i:6407229 original size:23 final size:23
Alignment explanation
Indices: 6407211--6407254 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
6407201 AATGTTTTTT
6407211 TGCTGTTTTTTTCATTGTTTTAC
1 TGCTGTTTTTTTCATTGTTTTAC
*
6407234 TGCTGTTTTTTTTATTGTTTT
1 TGCTGTTTTTTTCATTGTTTT
6407255 GTTATCATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.07, C:0.09, G:0.14, T:0.70
Consensus pattern (23 bp):
TGCTGTTTTTTTCATTGTTTTAC
Found at i:6408347 original size:9 final size:9
Alignment explanation
Indices: 6408322--6408351 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
6408312 ATTATCAATC
6408322 AAATTTTAA
1 AAATTTTAA
6408331 ATAATTTTAA
1 A-AATTTTAA
6408341 AAATTTTAA
1 AAATTTTAA
6408350 AA
1 AA
6408352 TGATATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
AAATTTTAA
Found at i:6417637 original size:31 final size:29
Alignment explanation
Indices: 6417602--6417660 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 29
6417592 ATCTTAAAAT
*
6417602 TATACATGAATATTGATTTAATGTGCAATTG
1 TATACATGAATATTAATTT-A-GTGCAATTG
* *
6417633 TATACATTAATTTTAATTTAGTGCAATT
1 TATACATGAATATTAATTTAGTGCAATT
6417661 ATACATATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.32
30 1 0.04
31 16 0.64
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.46
Consensus pattern (29 bp):
TATACATGAATATTAATTTAGTGCAATTG
Found at i:6424238 original size:26 final size:26
Alignment explanation
Indices: 6424202--6424256 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
6424192 GAAGCTCCGG
*
6424202 AGAGCCTTTAATCAGGAAGCTCACAA
1 AGAGCCCTTAATCAGGAAGCTCACAA
* *
6424228 AGAGCCCTTAATCATGAAGCTCACGA
1 AGAGCCCTTAATCAGGAAGCTCACAA
6424254 AGA
1 AGA
6424257 ACCATATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (26 bp):
AGAGCCCTTAATCAGGAAGCTCACAA
Found at i:6424947 original size:20 final size:20
Alignment explanation
Indices: 6424909--6424948 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
6424899 CCATGTATTT
* *
6424909 CATAAAATTTAGAATTTTTC
1 CATAAAATTTACAACTTTTC
*
6424929 CATAAATTTTACAACTTTTC
1 CATAAAATTTACAACTTTTC
6424949 AATTTAGTCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.45
Consensus pattern (20 bp):
CATAAAATTTACAACTTTTC
Found at i:6426067 original size:25 final size:25
Alignment explanation
Indices: 6426020--6426067 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
6426010 ATTTTTATTT
* **
6426020 AAATAATTCTTTAAATTTGTATAAA
1 AAATAATTATTTAAATTAATATAAA
*
6426045 AAATAATTATTTACATTAATATA
1 AAATAATTATTTAAATTAATATA
6426068 TAAATTTCTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (25 bp):
AAATAATTATTTAAATTAATATAAA
Found at i:6448574 original size:36 final size:36
Alignment explanation
Indices: 6448526--6448619 Score: 109
Period size: 37 Copynumber: 2.6 Consensus size: 36
6448516 GGGTCTCCAA
* *
6448526 AATCACATTTCAATTCAATTTCACTTTTTCACTTTC
1 AATCACAATTCAATTCAATTTCACTTTTCCACTTTC
* *
6448562 AATCACAATTCAATTCAAAATTCACTTTTCCATTTTC
1 AATCACAATTCAATTC-AATTTCACTTTTCCACTTTC
*
6448599 AAGTCA-ATATTCATTTCAATT
1 AA-TCACA-ATTCAATTCAATT
6448620 CCACACATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
36 15 0.31
37 23 0.47
38 11 0.22
ACGTcount: A:0.33, C:0.22, G:0.01, T:0.44
Consensus pattern (36 bp):
AATCACAATTCAATTCAATTTCACTTTTCCACTTTC
Found at i:6448620 original size:36 final size:35
Alignment explanation
Indices: 6448526--6448620 Score: 102
Period size: 36 Copynumber: 2.6 Consensus size: 35
6448516 GGGTCTCCAA
* *
6448526 AATCACATTTCAATTCAATTTCACTTTTTCACTTTC
1 AATCACAATTCAATTCAA-TTCACTTTTCCACTTTC
*
6448562 AATCACAATTCAATTCAAAATTCACTTTTCCATTTTC
1 AATCACAATTCAATTC--AATTCACTTTTCCACTTTC
*
6448599 AAGTCA-ATATTCATTTCAATTC
1 AA-TCACA-ATTCAATTCAATTC
6448621 CACACATATA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
36 20 0.39
37 18 0.35
38 13 0.25
ACGTcount: A:0.33, C:0.23, G:0.01, T:0.43
Consensus pattern (35 bp):
AATCACAATTCAATTCAATTCACTTTTCCACTTTC
Found at i:6448931 original size:17 final size:18
Alignment explanation
Indices: 6448899--6448932 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
6448889 ATTTTCTTTT
6448899 CAATTTATACCCTAATTC
1 CAATTTATACCCTAATTC
*
6448917 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
6448933 AACTCATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (18 bp):
CAATTTATACCCTAATTC
Found at i:6449325 original size:9 final size:8
Alignment explanation
Indices: 6449308--6449358 Score: 57
Period size: 9 Copynumber: 5.9 Consensus size: 8
6449298 AGTTTTTCCT
6449308 TTTCTTTC
1 TTTCTTTC
6449316 TTTCTGTTC
1 TTTCT-TTC
6449325 TTTCTTTCC
1 TTTCTTT-C
6449334 TTTCTTTTC
1 TTTC-TTTC
*
6449343 TCTCTTTCC
1 TTTCTTT-C
6449352 TTTCTTT
1 TTTCTTT
6449359 TCTCCCTGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
8 10 0.27
9 24 0.65
10 3 0.08
ACGTcount: A:0.00, C:0.27, G:0.02, T:0.71
Consensus pattern (8 bp):
TTTCTTTC
Found at i:6449327 original size:13 final size:12
Alignment explanation
Indices: 6449308--6449358 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 12
6449298 AGTTTTTCCT
6449308 TTTCTTTCTTTC
1 TTTCTTTCTTTC
6449320 TGTTCTTTCTTTCC
1 T-TTCTTTCTTT-C
*
6449334 TTTCTTTTCTCTC
1 TTTC-TTTCTTTC
6449347 TTTCCTTTCTTT
1 TTT-CTTTCTTT
6449359 TCTCCCTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 1 0.03
13 23 0.70
14 9 0.27
ACGTcount: A:0.00, C:0.27, G:0.02, T:0.71
Consensus pattern (12 bp):
TTTCTTTCTTTC
Found at i:6449336 original size:18 final size:18
Alignment explanation
Indices: 6449308--6449361 Score: 83
Period size: 18 Copynumber: 3.1 Consensus size: 18
6449298 AGTTTTTCCT
*
6449308 TTTCTTT-CTTTCTGTTC
1 TTTCTTTCCTTTCTTTTC
6449325 TTTCTTTCCTTTCTTTTC
1 TTTCTTTCCTTTCTTTTC
*
6449343 TCTCTTTCCTTTCTTTTC
1 TTTCTTTCCTTTCTTTTC
6449361 T
1 T
6449362 CCCTGTTTCG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
17 7 0.21
18 27 0.79
ACGTcount: A:0.00, C:0.28, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTCTTTCCTTTCTTTTC
Found at i:6449705 original size:31 final size:27
Alignment explanation
Indices: 6449670--6449742 Score: 74
Period size: 31 Copynumber: 2.5 Consensus size: 27
6449660 TACAATTTTC
6449670 ATAATTGAATTTATTAATTAATATAATATTT
1 ATAATT-AATTTATTAA-TAATAT-A-ATTT
* *
6449701 ATAATATAATTAATTTAATAATATACTTT
1 ATAAT-TAATTTA-TTAATAATATAATTT
6449730 ATAATTAATTTAT
1 ATAATTAATTTAT
6449743 ATATTTATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
27 1 0.03
28 6 0.16
29 8 0.22
30 1 0.03
31 16 0.43
32 5 0.14
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (27 bp):
ATAATTAATTTATTAATAATATAATTT
Found at i:6449707 original size:14 final size:17
Alignment explanation
Indices: 6449670--6449725 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
6449660 TACAATTTTC
*
6449670 ATAATTGAATTTATTAAT
1 ATAATT-AATTTAATAAT
*
6449688 -TAATATAATATTTATAAT
1 ATAAT-TAAT-TTAATAAT
6449706 ATAATTAATTTAATAAT
1 ATAATTAATTTAATAAT
6449723 ATA
1 ATA
6449726 CTTTATAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
17 17 0.53
18 11 0.34
19 4 0.12
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
ATAATTAATTTAATAAT
Found at i:6449743 original size:11 final size:11
Alignment explanation
Indices: 6449705--6449743 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
6449695 ATATTTATAA
6449705 TATAATTAATT
1 TATAATTAATT
*
6449716 TAATAATATACTT
1 T-ATAAT-TAATT
6449729 TATAATTAATT
1 TATAATTAATT
6449740 TATA
1 TATA
6449744 TATTTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 10 0.42
13 5 0.21
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (11 bp):
TATAATTAATT
Found at i:6450684 original size:11 final size:10
Alignment explanation
Indices: 6450671--6450779 Score: 73
Period size: 10 Copynumber: 10.9 Consensus size: 10
6450661 AAAAAAGTAT
6450671 TTTTAAAATA
1 TTTTAAAATA
6450681 TTTTTAAAATA
1 -TTTTAAAATA
6450692 TTTT-AAA-A
1 TTTTAAAATA
* *
6450700 TTTAAAAAAA
1 TTTTAAAATA
**
6450710 TTAAAAAATA
1 TTTTAAAATA
6450720 TTTTTAAAATA
1 -TTTTAAAATA
6450731 TTTT-AAA-A
1 TTTTAAAATA
**
6450739 TTAAAAAATA
1 TTTTAAAATA
* **
6450749 ATAAAAAAGTA
1 TTTTAAAA-TA
6450760 TTTTAAAAATA
1 TTTT-AAAATA
6450771 TTTTAAAAT
1 TTTTAAAAT
6450780 TAAAAAAATT
Statistics
Matches: 80, Mismatches: 11, Indels: 15
0.75 0.10 0.14
Matches are distributed among these distances:
8 7 0.09
9 12 0.15
10 30 0.38
11 27 0.34
12 4 0.05
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (10 bp):
TTTTAAAATA
Found at i:6450725 original size:29 final size:28
Alignment explanation
Indices: 6450686--6450748 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 28
6450676 AAATATTTTT
6450686 AAAATATTTTAAAAT-TTAAAAAAATTAA
1 AAAATATTTTAAAATATT-AAAAAATTAA
**
6450714 AAAATATTTTTAAAATATTTTAAAATTAA
1 AAAATA-TTTTAAAATATTAAAAAATTAA
6450743 AAAATA
1 AAAATA
6450749 ATAAAAAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 6 0.19
29 23 0.74
30 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
AAAATATTTTAAAATATTAAAAAATTAA
Found at i:6450761 original size:29 final size:29
Alignment explanation
Indices: 6450706--6450767 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
6450696 AAAATTTAAA
* **
6450706 AAAATTAAAAAATATTTTTAAAATATTTT
1 AAAATTAAAAAATATATAAAAAATATTTT
6450735 AAAATTAAAAAATA-ATAAAAAAGTATTTT
1 AAAATTAAAAAATATATAAAAAA-TATTTT
6450764 AAAA
1 AAAA
6450768 ATATTTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 5 0.17
29 24 0.83
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (29 bp):
AAAATTAAAAAATATATAAAAAATATTTT
Found at i:6450769 original size:40 final size:38
Alignment explanation
Indices: 6450675--6450797 Score: 201
Period size: 39 Copynumber: 3.2 Consensus size: 38
6450665 AAGTATTTTT
6450675 AAAATATTTTTAAAATATTTTAAAATTTAAAAAAATTAA
1 AAAATATTTTTAAAATATTTTAAAA-TTAAAAAAATTAA
*
6450714 AAAATATTTTTAAAATATTTTAAAATTAAAAAATAATAA
1 AAAATATTTTTAAAATATTTTAAAATTAAAAAA-ATTAA
*
6450753 AAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTAA
1 AAAA-TATTTTTAAAATATTTTAAAATTAAAAAAATTAA
6450792 AAAATA
1 AAAATA
6450798 AATATATTTA
Statistics
Matches: 79, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
38 10 0.13
39 41 0.52
40 28 0.35
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (38 bp):
AAAATATTTTTAAAATATTTTAAAATTAAAAAAATTAA
Found at i:6455257 original size:11 final size:11
Alignment explanation
Indices: 6455241--6455266 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6455231 AGAAAATTAA
6455241 TTTTTTCATAT
1 TTTTTTCATAT
6455252 TTTTTTCATAT
1 TTTTTTCATAT
6455263 TTTT
1 TTTT
6455267 CCCTAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTTCATAT
Found at i:6456146 original size:11 final size:11
Alignment explanation
Indices: 6456130--6456186 Score: 68
Period size: 11 Copynumber: 5.4 Consensus size: 11
6456120 ATTTTTTTAA
6456130 TTTTAAAATAT
1 TTTTAAAATAT
6456141 TTTTAAAATACT
1 TTTTAAAATA-T
6456153 TTTT-AAA-A-
1 TTTTAAAATAT
6456161 TTTT-AAATAT
1 TTTTAAAATAT
6456171 TTTTAAAATACT
1 TTTTAAAATA-T
6456183 TTTT
1 TTTT
6456187 TTAATTTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
8 7 0.17
9 1 0.02
10 5 0.12
11 18 0.44
12 10 0.24
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:6456163 original size:31 final size:32
Alignment explanation
Indices: 6456128--6456201 Score: 116
Period size: 30 Copynumber: 2.4 Consensus size: 32
6456118 TTATTTTTTT
6456128 AATTTTAAAATATTTTTAAAATAC-TTTTTAA
1 AATTTTAAAATATTTTTAAAATACTTTTTTAA
*
6456159 AATTTT-AAATATTTTTAAAATACTTTTTTTA
1 AATTTTAAAATATTTTTAAAATACTTTTTTAA
*
6456190 ATTTTTAAAATA
1 AATTTTAAAATA
6456202 AATTTTTGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
30 17 0.44
31 17 0.44
32 5 0.13
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (32 bp):
AATTTTAAAATATTTTTAAAATACTTTTTTAA
Found at i:6456175 original size:18 final size:20
Alignment explanation
Indices: 6456141--6456179 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
6456131 TTTAAAATAT
6456141 TTTTAAAATACTTTTTAAAA
1 TTTTAAAATACTTTTTAAAA
6456161 TTTT-AAATA-TTTTTAAAA
1 TTTTAAAATACTTTTTAAAA
6456179 T
1 T
6456180 ACTTTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
19 5 0.26
20 4 0.21
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTAAAATACTTTTTAAAA
Found at i:6456207 original size:21 final size:21
Alignment explanation
Indices: 6456169--6456208 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6456159 AATTTTAAAT
**
6456169 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
6456190 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
6456209 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:6456215 original size:22 final size:20
Alignment explanation
Indices: 6456168--6456222 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
6456158 AAATTTTAAA
* *
6456168 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAATAATTTTTG
6456188 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAAT-AATTTTT-G
6456211 TATTTATTAAAA
1 TATTT-TTAAAA
6456223 AATGGGTCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 1 0.03
21 11 0.38
22 10 0.34
23 7 0.24
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTTTTAAAATAATTTTTG
Found at i:6463474 original size:93 final size:92
Alignment explanation
Indices: 6463311--6463487 Score: 221
Period size: 93 Copynumber: 1.9 Consensus size: 92
6463301 CTCAGTTGAT
* * * * * **
6463311 GTTTAAAGGTTAGTTGCATTAAGTTCGCAACCTCCAGATTATTCGAGTTAACTTAGTTAAGCTTG
1 GTTTAAAGGTTAGTTGCATTAAGCTCGCAACCTCCAAATTATTCAAGTTAACTGAATTAAGCTCA
*
6463376 TAACTCTAAAACAACTCGCAAACTTAC
66 CAACTCTAAAACAACTCGCAAACTTAC
* *
6463403 GTTTCAAAGGTTAGTTG-AGTTAAGCTCGCAGCCTCCAAATTATTCAAGTTAGCTGAATTAAGCT
1 GTTT-AAAGGTTAGTTGCA-TTAAGCTCGCAACCTCCAAATTATTCAAGTTAACTGAATTAAGCT
* *
6463467 CACAACTCTGAAACAGCTCGC
64 CACAACTCTAAAACAACTCGC
6463488 GAACCTATGT
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
92 5 0.07
93 66 0.93
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31
Consensus pattern (92 bp):
GTTTAAAGGTTAGTTGCATTAAGCTCGCAACCTCCAAATTATTCAAGTTAACTGAATTAAGCTCA
CAACTCTAAAACAACTCGCAAACTTAC
Found at i:6463996 original size:104 final size:104
Alignment explanation
Indices: 6463876--6464072 Score: 231
Period size: 104 Copynumber: 1.9 Consensus size: 104
6463866 GTAACTTCAA
* * * *
6463876 AACAGCTCACAGACCTATGTTC-CTAGCTCAT-TCTACTAAGGTTAGCTAAATTAATATCGCAAT
1 AACAGCTCACAGACCTACGTTCAC-AGCTAATAT-TACTAAGGCTAGCTAAATTAAGATCGCAA-
*
6463939 C-TCCGATTATTTAAGTTCACTGATTTAAGATTGCAACTCTT
63 CATCCAATTATTTAAGTTCACTGATTTAAGATTGCAACTCTT
* * * *
6463980 AACAGCTCACTA-ACCTACGTTCACAGCTAATATTACTAAGGCTCGTTGATTTAAGATCGCAACA
1 AACAGCTCAC-AGACCTACGTTCACAGCTAATATTACTAAGGCTAGCTAAATTAAGATCGCAACA
* *
6464044 TCCAATTATTTGAGTTCGCTGATTTAAGA
65 TCCAATTATTTAAGTTCACTGATTTAAGA
6464073 ACGCAACTGC
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
103 1 0.01
104 74 0.95
105 3 0.04
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (104 bp):
AACAGCTCACAGACCTACGTTCACAGCTAATATTACTAAGGCTAGCTAAATTAAGATCGCAACAT
CCAATTATTTAAGTTCACTGATTTAAGATTGCAACTCTT
Found at i:6464245 original size:104 final size:104
Alignment explanation
Indices: 6463940--6464250 Score: 327
Period size: 104 Copynumber: 3.0 Consensus size: 104
6463930 TATCGCAATC
* * * * * *
6463940 TCCGATTATTTAAGTTCA-CTGATTTAAGATTGCAACTCTTAACAGCTCACTAACCTACGTTCAC
1 TCCGATTATTTGAGTT-AGCTGATTTAAGATTGCAACTCCTAACAACTCGCTGACATACGTTCAC
* * * *
6464004 AGCTAATATTACTAAGGCTCGTTGATTTAAGATCGCAACA
65 AGCTGATATTACTAAGGCTCGCTGATTTAAGATTGCAGCA
* * ** * * ** *
6464044 TCCAATTATTTGAGTTCGCTGATTTAAGAACGCAACTGCTAACAACTCGGTGATTTATGTTCACA
1 TCCGATTATTTGAGTTAGCTGATTTAAGATTGCAACTCCTAACAACTCGCTGACATACGTTCACA
* ** **
6464109 ACTGATGCTACTAAGGCTCGCTGATTTAAGATTGCAGTT
66 GCTGATATTACTAAGGCTCGCTGATTTAAGATTGCAGCA
* * * *
6464148 TCCGATTATTTGAGTTAGTTGATTTAAGATTGCAATTCCTAACAACTTGCTGACATACGTTCAGA
1 TCCGATTATTTGAGTTAGCTGATTTAAGATTGCAACTCCTAACAACTCGCTGACATACGTTCACA
* * *
6464213 GTTGATATTACTAAAGCTCGCTGATTTGAGATTGCAGC
66 GCTGATATTACTAAGGCTCGCTGATTTAAGATTGCAGC
6464251 CTTCGAATGG
Statistics
Matches: 163, Mismatches: 43, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
104 163 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.34
Consensus pattern (104 bp):
TCCGATTATTTGAGTTAGCTGATTTAAGATTGCAACTCCTAACAACTCGCTGACATACGTTCACA
GCTGATATTACTAAGGCTCGCTGATTTAAGATTGCAGCA
Found at i:6467808 original size:12 final size:12
Alignment explanation
Indices: 6467791--6467824 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
6467781 AAATTAATCC
6467791 TTTCTCAATTAT
1 TTTCTCAATTAT
6467803 TTTCTCAATTAT
1 TTTCTCAATTAT
6467815 TTTCTCAATT
1 TTTCTCAATT
6467825 TCCTCTCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.24, C:0.18, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTCTCAATTAT
Found at i:6467833 original size:11 final size:11
Alignment explanation
Indices: 6467817--6467925 Score: 75
Period size: 11 Copynumber: 10.3 Consensus size: 11
6467807 TCAATTATTT
6467817 TCTCAATTTCC
1 TCTCAATTTCC
6467828 TCTCAATTTCC
1 TCTCAATTTCC
* * *
6467839 TTTCAAATTGC
1 TCTCAATTTCC
6467850 TCTCAATTTCC
1 TCTCAATTTCC
*
6467861 TTTCAAATTT-C
1 TCTC-AATTTCC
*
6467872 TCTCAA-ATCC
1 TCTCAATTTCC
* **
6467882 -AT--ATTTAA
1 TCTCAATTTCC
*
6467890 TCTCAATTTGC
1 TCTCAATTTCC
* *
6467901 TTTCAATTTGC
1 TCTCAATTTCC
6467912 TCTCAATTTCC
1 TCTCAATTTCC
6467923 TCT
1 TCT
6467926 TAAATCCTTA
Statistics
Matches: 73, Mismatches: 19, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
7 1 0.01
8 1 0.01
9 3 0.04
10 3 0.04
11 60 0.82
12 5 0.07
ACGTcount: A:0.23, C:0.28, G:0.03, T:0.47
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:6467852 original size:22 final size:22
Alignment explanation
Indices: 6467827--6467923 Score: 94
Period size: 22 Copynumber: 4.6 Consensus size: 22
6467817 TCTCAATTTC
6467827 CTCTCAATTTCCTTTCAAATTG
1 CTCTCAATTTCCTTTCAAATTG
*
6467849 CTCTCAATTTCCTTTCAAATTT
1 CTCTCAATTTCCTTTCAAATTG
* * * *
6467871 CTCTCAA-ATCC-AT--ATTTA
1 CTCTCAATTTCCTTTCAAATTG
* * *
6467889 ATCTCAATTTGCTTTCAATTTG
1 CTCTCAATTTCCTTTCAAATTG
6467911 CTCTCAATTTCCT
1 CTCTCAATTTCCT
6467924 CTTAAATCCT
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
18 9 0.15
19 2 0.03
20 2 0.03
21 3 0.05
22 43 0.73
ACGTcount: A:0.24, C:0.27, G:0.03, T:0.46
Consensus pattern (22 bp):
CTCTCAATTTCCTTTCAAATTG
Found at i:6467907 original size:51 final size:51
Alignment explanation
Indices: 6467841--6467938 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 51
6467831 CAATTTCCTT
*
6467841 TCAAATTGCTCTCAATTTCCTTTCAAATTT-CTCTCAAATCCATATTTAATC
1 TCAAATTGCTCTCAATTTCCTCTC-AATTTCCTCTCAAATCCATATTTAATC
* * * * *
6467892 TCAATTTGCTTTCAATTTGCTCTCAATTTCCTCTTAAATCCTTATTT
1 TCAAATTGCTCTCAATTTCCTCTCAATTTCCTCTCAAATCCATATTT
6467939 TTAATTATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
50 5 0.12
51 35 0.88
ACGTcount: A:0.26, C:0.24, G:0.03, T:0.47
Consensus pattern (51 bp):
TCAAATTGCTCTCAATTTCCTCTCAATTTCCTCTCAAATCCATATTTAATC
Found at i:6472714 original size:125 final size:125
Alignment explanation
Indices: 6472492--6472902 Score: 662
Period size: 125 Copynumber: 3.3 Consensus size: 125
6472482 CCCAAACATG
* * * *
6472492 CTACTGTAGCAAAAGTGCGTCCACGTGGGAGCGATTTAAAAAATTCTTCTAATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATTCTGC
* *
6472557 TTGAAGCATTTTTTATACTATTTGCTTAGAAACGTCAACTCGAAATTACTTTTTCAGGAC
66 TTGAAGCATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
* *
6472617 CTACTGTAGCAAAAGCGTGTCCACGTGGGAGCGGTTTCAAAAATTCTTCTGATAAAGCATTCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATTCTGC
* * *
6472682 TTGAAGCGTTTTTTATATTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
66 TTGAAGCATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
*
6472742 CTACTGTAGCAAAAGCGCGTCCATGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCA-TCTTG
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATTC-TG
*
6472806 CTTGAAGCATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTTAGGAC
65 CTTGAAGCATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
* * *
6472867 CTACTGTATCAAAAACGTGTCCACGTGGGAGCGATT
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATT
6472903 CCCTCAATAA
Statistics
Matches: 263, Mismatches: 22, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
124 2 0.01
125 261 0.99
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATTCTGC
TTGAAGCATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
Found at i:6477989 original size:16 final size:16
Alignment explanation
Indices: 6477968--6478003 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
6477958 TTTGGTTCGC
6477968 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
6477984 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
6478000 TGTA
1 TGTA
6478004 ATAGCTAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:6478068 original size:44 final size:45
Alignment explanation
Indices: 6477984--6478074 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
6477974 GGATTAGAGG
* * *
6477984 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
6478029 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
6478073 TG
1 TG
6478075 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:6478260 original size:18 final size:19
Alignment explanation
Indices: 6478239--6478275 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
6478229 TTATTATTAA
6478239 ATAT-ATTT-TAATTAAAAT
1 ATATAATTTATAA-TAAAAT
6478257 ATATAATTTATAATAAAAT
1 ATATAATTTATAATAAAAT
6478276 TCTTAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.24
19 10 0.59
20 3 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATAATTTATAATAAAAT
Found at i:6478334 original size:61 final size:58
Alignment explanation
Indices: 6478269--6478456 Score: 138
Period size: 61 Copynumber: 3.1 Consensus size: 58
6478259 ATAATTTATA
6478269 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 ATAAAATTCTTAATAAT-AATATTCTTATATGAATTT-CT-AAATCATAATATATGATACT
* ** * * *
6478330 ATAAAATATAATTTGAAATAATTAATATT-AAATAT--ATTT-T-AATTAAAATATATGAT-TT
1 ATAAAAT-T--CTT--AATAA-TAATATTCTTATATGAATTTCTAAATCATAATATATGATACT
*
6478388 AATAAAATTCTTAATGTAA-AATATTCTTATATGAATTTTCTAAAATCATAATATATAATACT
1 -ATAAAATTCTTAA--TAATAATATTCTTATATGAA-TTTCT-AAATCATAATATATGATACT
6478450 ATAAAAT
1 ATAAAAT
6478457 ATAATTTAAC
Statistics
Matches: 97, Mismatches: 13, Indels: 34
0.67 0.09 0.24
Matches are distributed among these distances:
54 8 0.08
55 4 0.04
56 5 0.05
57 1 0.01
58 5 0.05
59 22 0.23
61 28 0.29
62 2 0.02
63 4 0.04
64 2 0.02
65 4 0.04
66 11 0.11
67 1 0.01
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (58 bp):
ATAAAATTCTTAATAATAATATTCTTATATGAATTTCTAAATCATAATATATGATACT
Found at i:6478383 original size:59 final size:58
Alignment explanation
Indices: 6478317--6478502 Score: 148
Period size: 59 Copynumber: 3.1 Consensus size: 58
6478307 CTCAAATCAT
* *
6478317 AATATATGATACTATAAAATATAATTTGAAATAATTAATATTAAATATATTTTAATTAA
1 AATATATGATACTATAAAATATAATTT-AAATAATTATTATTAAATATATTTTAATAAA
* * * * * *
6478376 AATATATGAT-TTAATAAAATTCTTAATGTAAA-ATATTCTTATATGAAT-T-TTCTAA-AATCA
1 AATATATGATACT-ATAAAA-T-ATAATTTAAATA-ATTATTAT-TAAATATATTTTAATAA--A
* **
6478436 TAATATATAATACTATAAAATATAATTTAACATAATTATTATTAAATATAAGTTAATAAA
1 -AATATATGATACTATAAAATATAATTTAA-ATAATTATTATTAAATATATTTTAATAAA
6478496 AATATAT
1 AATATAT
6478503 AATTTATCAT
Statistics
Matches: 96, Mismatches: 17, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
58 2 0.02
59 40 0.42
60 23 0.24
61 28 0.29
62 3 0.03
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (58 bp):
AATATATGATACTATAAAATATAATTTAAATAATTATTATTAAATATATTTTAATAAA
Found at i:6478440 original size:120 final size:119
Alignment explanation
Indices: 6478219--6478508 Score: 440
Period size: 120 Copynumber: 2.4 Consensus size: 119
6478209 TTGATCATAT
6478219 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTATAATAAAATTCTTAATA
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAA-TT-TAATAAAATTCTTAATA
* *
6478284 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
64 A-CAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* *
6478341 TTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATGT
1 TTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAA--T
*
6478405 AA-AATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
63 AACAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
** *
6478461 TTTAACATAATTATTATTAAATATAAGTTAATAAAAATATATAATTTA
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTA
6478509 TCATCATACT
Statistics
Matches: 154, Mismatches: 10, Indels: 10
0.89 0.06 0.06
Matches are distributed among these distances:
119 2 0.01
120 106 0.69
121 2 0.01
122 42 0.27
123 2 0.01
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.43
Consensus pattern (119 bp):
TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAC
AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:6484973 original size:38 final size:38
Alignment explanation
Indices: 6484922--6484998 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
6484912 AAGAATGGTA
6484922 AATTTGTATGTCATTATAGTGGTGTTATAGGACACACT
1 AATTTGTATGTCATTATAGTGGTGTTATAGGACACACT
6484960 AATTTGTATGTCATTATAGTGGTGTTATAGGACACACT
1 AATTTGTATGTCATTATAGTGGTGTTATAGGACACACT
6484998 A
1 A
6484999 GACCTATATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (38 bp):
AATTTGTATGTCATTATAGTGGTGTTATAGGACACACT
Found at i:6485622 original size:21 final size:23
Alignment explanation
Indices: 6485586--6485629 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
6485576 ATTATACCTC
*
6485586 ATTTTTCTATTTCTTTTATTTTT
1 ATTTTTCTATTTCTTTCATTTTT
6485609 ATTTTT-TA-TTCTTTCATTTTT
1 ATTTTTCTATTTCTTTCATTTTT
6485630 GTTTCTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
22 2 0.10
23 6 0.30
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (23 bp):
ATTTTTCTATTTCTTTCATTTTT
Found at i:6485623 original size:25 final size:24
Alignment explanation
Indices: 6485595--6485654 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
6485585 CATTTTTCTA
*
6485595 TTTCTTTTATTTTTATTTTTTATTC
1 TTTCTTTT-TGTTTATTTTTTATTC
*
6485620 TTTCATTTTTGTTTCTTTTTTATTC
1 TTTC-TTTTTGTTTATTTTTTATTC
*
6485645 TTTTTTTTTG
1 TTTCTTTTTG
6485655 GGTATTCTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 21 0.68
26 4 0.13
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.80
Consensus pattern (24 bp):
TTTCTTTTTGTTTATTTTTTATTC
Found at i:6488375 original size:93 final size:91
Alignment explanation
Indices: 6488210--6488398 Score: 245
Period size: 93 Copynumber: 2.1 Consensus size: 91
6488200 TGAAATTGAG
** * *
6488210 TTTCATATGATAATGGCTTCTTGCTTTCTTCCCCATGTTTATTTTCTTCTTATTTATACTGATGT
1 TTTCATATGATAATGGCTTCTTGCTTTCTTCCCCATCATTATTTGCTTCTTATCTATACTGATGT
* * *
6488275 TTGATAGTTAATTTTTTTTTTGTAGATAT
66 TTAATAG-T--TGTTTCTTTTGTAGATAT
* ** *
6488304 TTTCATATGATAATGGC-TCTTGCTTTCTTCCCCCTCATTATTTGCTTCTTATCTATTTTGATTT
1 TTTCATATGATAATGGCTTCTTGCTTTCTTCCCCATCATTATTTGCTTCTTATCTATACTGATGT
6488368 TTAATAGTTGTTTCTTTTGTAGATAT
66 TTAATAGTTGTTTCTTTTGTAGATAT
6488394 TTTCA
1 TTTCA
6488399 CTTTAATCTA
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
90 21 0.25
92 1 0.01
93 45 0.54
94 17 0.20
ACGTcount: A:0.19, C:0.15, G:0.11, T:0.56
Consensus pattern (91 bp):
TTTCATATGATAATGGCTTCTTGCTTTCTTCCCCATCATTATTTGCTTCTTATCTATACTGATGT
TTAATAGTTGTTTCTTTTGTAGATAT
Found at i:6488522 original size:33 final size:33
Alignment explanation
Indices: 6488485--6488588 Score: 127
Period size: 33 Copynumber: 3.4 Consensus size: 33
6488475 CATTTTGTGT
6488485 CTTATTTAGGATATTATGATGACATTTGATGGG
1 CTTATTTAGGATATTATGATGACATTTGATGGG
* *
6488518 CTTATTTAGG--A-TAT-CT---ATTTG-T-GT
1 CTTATTTAGGATATTATGATGACATTTGATGGG
6488542 CTTATTTAGGATATTATGATGACATTTGATGGG
1 CTTATTTAGGATATTATGATGACATTTGATGGG
6488575 CTTATTTAGGATAT
1 CTTATTTAGGATAT
6488589 CTATTGTTGG
Statistics
Matches: 58, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
24 11 0.19
25 1 0.02
26 6 0.10
27 3 0.05
28 1 0.02
29 1 0.02
30 3 0.05
31 6 0.10
32 1 0.02
33 25 0.43
ACGTcount: A:0.26, C:0.07, G:0.21, T:0.46
Consensus pattern (33 bp):
CTTATTTAGGATATTATGATGACATTTGATGGG
Found at i:6488566 original size:57 final size:57
Alignment explanation
Indices: 6488478--6488593 Score: 232
Period size: 57 Copynumber: 2.0 Consensus size: 57
6488468 TCATCTTCAT
6488478 TTTGTGTCTTATTTAGGATATTATGATGACATTTGATGGGCTTATTTAGGATATCTA
1 TTTGTGTCTTATTTAGGATATTATGATGACATTTGATGGGCTTATTTAGGATATCTA
6488535 TTTGTGTCTTATTTAGGATATTATGATGACATTTGATGGGCTTATTTAGGATATCTA
1 TTTGTGTCTTATTTAGGATATTATGATGACATTTGATGGGCTTATTTAGGATATCTA
6488592 TT
1 TT
6488594 GTTGGATTCA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.24, C:0.07, G:0.21, T:0.48
Consensus pattern (57 bp):
TTTGTGTCTTATTTAGGATATTATGATGACATTTGATGGGCTTATTTAGGATATCTA
Found at i:6513288 original size:18 final size:19
Alignment explanation
Indices: 6513256--6513293 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
6513246 TTCTATTTAA
6513256 TATTTTTAATATTTT-TTT
1 TATTTTTAATATTTTATTT
* *
6513274 TATTTTTATTTTTTTATTT
1 TATTTTTAATATTTTATTT
6513293 T
1 T
6513294 TTAGAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (19 bp):
TATTTTTAATATTTTATTT
Found at i:6513296 original size:15 final size:14
Alignment explanation
Indices: 6513268--6513294 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6513258 TTTTTAATAT
6513268 TTTTTTTATTTTTA
1 TTTTTTTATTTTTA
6513282 TTTTTTTATTTTT
1 TTTTTTTATTTTT
6513295 TAGAATTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (14 bp):
TTTTTTTATTTTTA
Found at i:6514104 original size:22 final size:22
Alignment explanation
Indices: 6514063--6514105 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
6514053 AAGAAAATTT
* * *
6514063 AAAATTTATTTTTTATATTATG
1 AAAATTAATTTTTCAAATTATG
6514085 AAAATTAATTTTTCAAATTAT
1 AAAATTAATTTTTCAAATTAT
6514106 AATCTTGTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
AAAATTAATTTTTCAAATTATG
Found at i:6514680 original size:18 final size:16
Alignment explanation
Indices: 6514648--6514682 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
6514638 CAAGAGAGGG
6514648 AGAAAAGAAGAAAGAA
1 AGAAAAGAAGAAAGAA
6514664 AGAAAAGAGACGAAAGAA
1 AGAAAAGA-A-GAAAGAA
6514682 A
1 A
6514683 ATGTATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 1 0.06
18 8 0.47
ACGTcount: A:0.71, C:0.03, G:0.26, T:0.00
Consensus pattern (16 bp):
AGAAAAGAAGAAAGAA
Found at i:6518069 original size:62 final size:62
Alignment explanation
Indices: 6517832--6518059 Score: 386
Period size: 62 Copynumber: 3.7 Consensus size: 62
6517822 CAATGTACCT
6517832 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATTTATA-TAGCAA
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATTTATATTA-CAA
* * * *
6517894 AATTTATATTACAAAGTTTGTTCTAATTTTTAATGTTGTGATGTATTTAATTTATATAAAAA
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATTTATATTACAA
6517956 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATTTATATTACAA
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATTTATATTACAA
* *
6518018 AATTTATATTATAAAGTTTGTTCCAAGTTTTAATGTTGTAAT
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAAT
6518060 TAATCTAATT
Statistics
Matches: 155, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
62 154 0.99
63 1 0.01
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.50
Consensus pattern (62 bp):
AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATTTATATTACAA
Found at i:6518415 original size:33 final size:33
Alignment explanation
Indices: 6518332--6518418 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 33
6518322 TTGAACTGGA
* * *
6518332 AGGAGTGCTGTACTACGATGGATACGACCCGGG
1 AGGAGTGCTGTACTGCGGTGGATACGACCCAGG
** * *
6518365 AGGAGTGGAGTAATGCGGTGGATAC-AGGCCAGG
1 AGGAGTGCTGTACTGCGGTGGATACGA-CCCAGG
6518398 AGGAGTGCTGTACTGCGGTGG
1 AGGAGTGCTGTACTGCGGTGG
6518419 TACTGGACTA
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
32 1 0.02
33 42 0.98
ACGTcount: A:0.23, C:0.16, G:0.43, T:0.18
Consensus pattern (33 bp):
AGGAGTGCTGTACTGCGGTGGATACGACCCAGG
Found at i:6521118 original size:26 final size:25
Alignment explanation
Indices: 6521089--6521137 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
6521079 TTCTATTTAT
6521089 TTTTTTACCTTCTTTTTCTCCTTCTC
1 TTTTTTACCTTCTTTTTC-CCTTCTC
* *
6521115 TTTTTTTCTTTCTTTTTCCCTTC
1 TTTTTTACCTTCTTTTTCCCTTC
6521138 CCTTCCCTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTTTACCTTCTTTTTCCCTTCTC
Found at i:6522538 original size:56 final size:56
Alignment explanation
Indices: 6522452--6522576 Score: 223
Period size: 56 Copynumber: 2.2 Consensus size: 56
6522442 TCTGCACAAA
*
6522452 ACCCTCATTTGGCACACCTCTTTTGTTGTAGGATAGTTTCAAAAAATATGGTTCCT
1 ACCCTCATTTGGCACACCTCTTTTGTTGTAGGACAGTTTCAAAAAATATGGTTCCT
6522508 ACCCTCATTTGGCACACCTCTTTTGTTGTAGGACAGTTTCAAAAAATATGGTTCCT
1 ACCCTCATTTGGCACACCTCTTTTGTTGTAGGACAGTTTCAAAAAATATGGTTCCT
* *
6522564 ATCCTCCTTTGGC
1 ACCCTCATTTGGC
6522577 CCGCGACATT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 66 1.00
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (56 bp):
ACCCTCATTTGGCACACCTCTTTTGTTGTAGGACAGTTTCAAAAAATATGGTTCCT
Found at i:6526430 original size:23 final size:23
Alignment explanation
Indices: 6526404--6526459 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
6526394 CACTTATGGG
6526404 CCTAAAATTGGGCTTACGTGGCC
1 CCTAAAATTGGGCTTACGTGGCC
6526427 CCTAAAATTGGGCTTACGTGGCC
1 CCTAAAATTGGGCTTACGTGGCC
6526450 CCTAACAATT
1 CCTAA-AATT
6526460 CAGGGTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 28 0.88
24 4 0.12
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (23 bp):
CCTAAAATTGGGCTTACGTGGCC
Found at i:6527113 original size:20 final size:20
Alignment explanation
Indices: 6527088--6527129 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
6527078 TCATGTTTGG
6527088 TTGGAGGGAATAGGAATGCA
1 TTGGAGGGAATAGGAATGCA
6527108 TTGGAGGGAATAGGAATGCA
1 TTGGAGGGAATAGGAATGCA
6527128 TT
1 TT
6527130 TCCCCCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.05, G:0.38, T:0.24
Consensus pattern (20 bp):
TTGGAGGGAATAGGAATGCA
Found at i:6530360 original size:13 final size:13
Alignment explanation
Indices: 6530342--6530366 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6530332 AATTGCTTAT
6530342 CAAATGCATATAC
1 CAAATGCATATAC
6530355 CAAATGCATATA
1 CAAATGCATATA
6530367 TATTTAATAT
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:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (13 bp):
CAAATGCATATAC
Found at i:6530615 original size:41 final size:41
Alignment explanation
Indices: 6530554--6530656 Score: 118
Period size: 41 Copynumber: 2.5 Consensus size: 41
6530544 ATTCGGTACG
* * *
6530554 CCGGCTTTTAGCCTGCTAGACTTATAGTCCGAA-ATATATCA
1 CCGGCATTAAGCCTGCTAGACGTATAGTCCGAATA-ATATCA
* * *
6530595 CCGGCATTAAGCCTGTTAGACGTATAGTCTGAATAATTTCA
1 CCGGCATTAAGCCTGCTAGACGTATAGTCCGAATAATATCA
* *
6530636 CCGGCATAAAGCCTACTAGAC
1 CCGGCATTAAGCCTGCTAGAC
6530657 ATAAAGTCTG
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 51 0.98
42 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (41 bp):
CCGGCATTAAGCCTGCTAGACGTATAGTCCGAATAATATCA
Found at i:6530665 original size:41 final size:41
Alignment explanation
Indices: 6530592--6530687 Score: 120
Period size: 41 Copynumber: 2.3 Consensus size: 41
6530582 CCGAAATATA
* ** * *
6530592 TCACCGGCATTAAGCCTGTTAGACGTATAGTCTGAATAATT
1 TCACCGGCATAAAGCCTACTAGACATAAAGTCTGAATAATT
*
6530633 TCACCGGCATAAAGCCTACTAGACATAAAGTCTGAATTATT
1 TCACCGGCATAAAGCCTACTAGACATAAAGTCTGAATAATT
*
6530674 TCACTGGCAATAAA
1 TCACCGGC-ATAAA
6530688 TCAGATTAGT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 42 0.89
42 5 0.11
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (41 bp):
TCACCGGCATAAAGCCTACTAGACATAAAGTCTGAATAATT
Found at i:6533234 original size:16 final size:16
Alignment explanation
Indices: 6533213--6533268 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
6533203 CAAGAATATT
6533213 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
* *
6533229 ATTACAGCTCAATTCA
1 ATTACAGCTCTATTCC
*
6533245 ATTACATCTCTATTCC
1 ATTACAGCTCTATTCC
6533261 ATTACAGC
1 ATTACAGC
6533269 GAACCAAACG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.30, C:0.29, G:0.05, T:0.36
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:6533928 original size:20 final size:20
Alignment explanation
Indices: 6533842--6533928 Score: 84
Period size: 20 Copynumber: 4.3 Consensus size: 20
6533832 GCATTATAGA
6533842 TGCATAACAGAGGCACCAAAG
1 TGCA-AACAGAGGCACCAAAG
* * * *
6533863 TGCAGATAGAGGCACTAATG
1 TGCAAACAGAGGCACCAAAG
* * *
6533883 TGCGATCAGAGGCACCGAAG
1 TGCAAACAGAGGCACCAAAG
* *
6533903 TACAAACAAAGGCACCAAAG
1 TGCAAACAGAGGCACCAAAG
6533923 TGCAAA
1 TGCAAA
6533929 TCCCGACAAG
Statistics
Matches: 49, Mismatches: 17, Indels: 1
0.73 0.25 0.01
Matches are distributed among these distances:
20 45 0.92
21 4 0.08
ACGTcount: A:0.41, C:0.22, G:0.25, T:0.11
Consensus pattern (20 bp):
TGCAAACAGAGGCACCAAAG
Found at i:6538548 original size:24 final size:24
Alignment explanation
Indices: 6538512--6538670 Score: 127
Period size: 24 Copynumber: 7.0 Consensus size: 24
6538502 CAAGCTGTAT
6538512 CGTTGTGGTCAAGCCACTCAATAA
1 CGTTGTGGTCAAGCCACTCAATAA
*
6538536 CGTTGTGGCCAAGCCACTCAAT-A
1 CGTTGTGGTCAAGCCACTCAATAA
* * *
6538559 --TCGTAGTCAA---ACT--ATAT
1 CGTTGTGGTCAAGCCACTCAATAA
6538576 CGTTGTGGTCAAGCCACTCAATAA
1 CGTTGTGGTCAAGCCACTCAATAA
* * *
6538600 TGTTGTGGACAAGCCACTCAATAG
1 CGTTGTGGTCAAGCCACTCAATAA
* * * * * *
6538624 TGCTATGGCCAAACCACTCAGTAA
1 CGTTGTGGTCAAGCCACTCAATAA
* *
6538648 CATTATGGTCAAGCCACTCAATA
1 CGTTGTGGTCAAGCCACTCAATA
6538671 TTGCAATAAA
Statistics
Matches: 104, Mismatches: 23, Indels: 16
0.73 0.16 0.11
Matches are distributed among these distances:
16 2 0.02
18 3 0.03
19 8 0.08
21 7 0.07
22 3 0.03
23 1 0.01
24 80 0.77
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (24 bp):
CGTTGTGGTCAAGCCACTCAATAA
Found at i:6538577 original size:64 final size:64
Alignment explanation
Indices: 6538471--6538622 Score: 214
Period size: 64 Copynumber: 2.4 Consensus size: 64
6538461 ATAACACACC
* * * * * *
6538471 ACGTTCTGGCTAAACCACTTAATATCACAGTCAAGCTGTATCGTTGTGGTCAAGCCACTCAATA
1 ACGTTGTGGCCAAGCCACTCAATATCACAGTCAAACTATATCGTTGTGGTCAAGCCACTCAATA
**
6538535 ACGTTGTGGCCAAGCCACTCAATATCGTAGTCAAACTATATCGTTGTGGTCAAGCCACTCAATA
1 ACGTTGTGGCCAAGCCACTCAATATCACAGTCAAACTATATCGTTGTGGTCAAGCCACTCAATA
* *
6538599 ATGTTGTGGACAAGCCACTCAATA
1 ACGTTGTGGCCAAGCCACTCAATA
6538623 GTGCTATGGC
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 78 1.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.27
Consensus pattern (64 bp):
ACGTTGTGGCCAAGCCACTCAATATCACAGTCAAACTATATCGTTGTGGTCAAGCCACTCAATA
Found at i:6548388 original size:7 final size:7
Alignment explanation
Indices: 6548376--6548407 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
6548366 TGATGTGTGT
6548376 AATTGAA
1 AATTGAA
6548383 AATTGAA
1 AATTGAA
6548390 AATTGAA
1 AATTGAA
6548397 AATTGAA
1 AATTGAA
6548404 AATT
1 AATT
6548408 ATGAATTGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.31
Consensus pattern (7 bp):
AATTGAA
Found at i:6548559 original size:19 final size:19
Alignment explanation
Indices: 6548515--6548560 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
6548505 GAAATGTTTG
6548515 ATGATATAATGTGATATAAT
1 ATGATAT-ATGTGATATAAT
*
6548535 AT-ATATATTTGATTATAA-
1 ATGATATATGTGA-TATAAT
6548553 ATGATATA
1 ATGATATA
6548561 AAGTTATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 7 0.30
19 14 0.61
20 2 0.09
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (19 bp):
ATGATATATGTGATATAAT
Found at i:6548656 original size:36 final size:36
Alignment explanation
Indices: 6548616--6548685 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
6548606 TGAACGCGGA
6548616 ATGGATTAGCTCTTTTGAGCATCCGGTGTGTTTCGG
1 ATGGATTAGCTCTTTTGAGCATCCGGTGTGTTTCGG
*
6548652 ATGGATTAGCTCTTTTGAGCATCTGGTGTGTTTC
1 ATGGATTAGCTCTTTTGAGCATCCGGTGTGTTTC
6548686 AATTGGAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.14, C:0.16, G:0.29, T:0.41
Consensus pattern (36 bp):
ATGGATTAGCTCTTTTGAGCATCCGGTGTGTTTCGG
Found at i:6550491 original size:17 final size:17
Alignment explanation
Indices: 6550461--6550494 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6550451 ATTACAAAAT
**
6550461 CAAATCTTCTAAGATTA
1 CAAATCTTAGAAGATTA
6550478 CAAATCTTAGAAGATTA
1 CAAATCTTAGAAGATTA
6550495 GTTTCCCTAT
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:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (17 bp):
CAAATCTTAGAAGATTA
Found at i:6555273 original size:28 final size:28
Alignment explanation
Indices: 6555234--6555289 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
6555224 CACATTACAG
6555234 AAAAAACACCAGGACACTTGATGAAGCA
1 AAAAAACACCAGGACACTTGATGAAGCA
6555262 AAAAAACACCAGGACACTTGATGAAGCA
1 AAAAAACACCAGGACACTTGATGAAGCA
6555290 TCTTAAATCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.50, C:0.21, G:0.18, T:0.11
Consensus pattern (28 bp):
AAAAAACACCAGGACACTTGATGAAGCA
Found at i:6558756 original size:3 final size:3
Alignment explanation
Indices: 6558750--6558806 Score: 71
Period size: 3 Copynumber: 19.3 Consensus size: 3
6558740 TCATGGTTGT
* * * *
6558750 TGG TGG TGG TGG AGG TGG AGG TGG TGG TGG T-G TCG TGG TTG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
6558797 TGG TGG TGG T
1 TGG TGG TGG T
6558807 TGAGGTTGCT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.04, C:0.02, G:0.61, T:0.33
Consensus pattern (3 bp):
TGG
Found at i:6560137 original size:31 final size:31
Alignment explanation
Indices: 6560087--6560146 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
6560077 TTAAATTGAA
*
6560087 TTCTTAAAACCCAAAAATCTCAAGATAAAGT
1 TTCTGAAAACCCAAAAATCTCAAGATAAAGT
* * *
6560118 TTCTGAAAACTCAAGAATCTCGAGATAAA
1 TTCTGAAAACCCAAAAATCTCAAGATAAA
6560147 ATTTACATCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.47, C:0.18, G:0.10, T:0.25
Consensus pattern (31 bp):
TTCTGAAAACCCAAAAATCTCAAGATAAAGT
Found at i:6568592 original size:22 final size:23
Alignment explanation
Indices: 6568554--6568608 Score: 94
Period size: 22 Copynumber: 2.4 Consensus size: 23
6568544 GTGTACATAA
6568554 TAGAATTAAATTGATTATAAATAT
1 TAGAA-TAAATTGATTATAAATAT
6568578 TAGAATAAA-TGATTATAAATAT
1 TAGAATAAATTGATTATAAATAT
6568600 TAGAATAAA
1 TAGAATAAA
6568609 ACTTTGGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 22 0.71
23 4 0.13
24 5 0.16
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (23 bp):
TAGAATAAATTGATTATAAATAT
Found at i:6569750 original size:9 final size:9
Alignment explanation
Indices: 6569734--6569767 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
6569724 GGTATTTTTC
6569734 GGTAATTCG
1 GGTAATTCG
*
6569743 GTTAATTCG
1 GGTAATTCG
6569752 GGTAATTCG
1 GGTAATTCG
6569761 GGTAATT
1 GGTAATT
6569768 TTTAACCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.24, C:0.09, G:0.29, T:0.38
Consensus pattern (9 bp):
GGTAATTCG
Done.