Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1925
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: 106356
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:1787 original size:21 final size:21
Alignment explanation
Indices: 1763--1809 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1753 TTTGATGCTG
1763 ATTTTG-A-TGAAAAACAAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
1783 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
1804 ATTTTG
1 ATTTTG
1810 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.45, C:0.04, G:0.17, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:4038 original size:15 final size:15
Alignment explanation
Indices: 4018--4048 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4008 ATTTCGTTTG
*
4018 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
4033 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
4048 G
1 G
4049 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:5876 original size:21 final size:21
Alignment explanation
Indices: 5847--5891 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
5837 AAGTTTTCAT
*
5847 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
5867 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
5889 TTT
1 TTT
5892 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:8116 original size:13 final size:13
Alignment explanation
Indices: 8098--8123 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8088 CAATTTTTTG
8098 TGTATCGATACAT
1 TGTATCGATACAT
8111 TGTATCGATACAT
1 TGTATCGATACAT
8124 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:8679 original size:21 final size:21
Alignment explanation
Indices: 8646--8686 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
8636 CTAAGTATAA
8646 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
8667 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
8687 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:8751 original size:20 final size:21
Alignment explanation
Indices: 8720--8778 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
8710 GTCAAAACCC
* *
8720 TGAAAAGTATCGATACACATT
1 TGAATAGTATCGATACACAAT
8741 TGAAT-GTATCGATACA-AAT
1 TGAATAGTATCGATACACAAT
*
8760 TGCATAGTATCGATACACA
1 TGAATAGTATCGATACACA
8779 CAAATATGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 6 0.18
20 22 0.67
21 5 0.15
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (21 bp):
TGAATAGTATCGATACACAAT
Found at i:8849 original size:53 final size:53
Alignment explanation
Indices: 8766--8902 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
8756 AAATTGCATA
8766 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
8820 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
8873 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
8903 TTGGAAGTAG
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
53 67 0.83
54 14 0.17
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
Found at i:8945 original size:10 final size:10
Alignment explanation
Indices: 8926--8986 Score: 54
Period size: 10 Copynumber: 6.0 Consensus size: 10
8916 AATCTCATTT
8926 TCACTGTTCA
1 TCACTGTTCA
*
8936 TCACTATTCA
1 TCACTGTTCA
8946 TCACTGTTCA
1 TCACTGTTCA
* *
8956 TGTA-TCGATACA
1 T-CACT-G-TTCA
8968 TCACTGTTCA
1 TCACTGTTCA
8978 -CACTGTTCA
1 TCACTGTTCA
8987 CGTATCACTA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
9 9 0.22
10 23 0.56
11 4 0.10
12 5 0.12
ACGTcount: A:0.25, C:0.28, G:0.10, T:0.38
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:9072 original size:13 final size:13
Alignment explanation
Indices: 9054--9079 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9044 ACATATTTCT
9054 GTGTATCGATACA
1 GTGTATCGATACA
9067 GTGTATCGATACA
1 GTGTATCGATACA
9080 TCATAAATAG
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:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GTGTATCGATACA
Found at i:14189 original size:17 final size:17
Alignment explanation
Indices: 14159--14196 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
14149 TTGTCAGGAT
*
14159 ATAA-TTATTAAAAATA
1 ATAATTTATTAAAAAAA
*
14175 ATAATTTATTGAAAAAA
1 ATAATTTATTAAAAAAA
14192 ATAAT
1 ATAAT
14197 AAACTTATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (17 bp):
ATAATTTATTAAAAAAA
Found at i:15310 original size:2 final size:2
Alignment explanation
Indices: 15303--15357 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
15293 AATTGCAAAA
*
15303 AG AG AG AG AG AG AG AG AG AG AG AG AG AC AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
15345 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
15358 AAACCAAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.02, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17446 original size:75 final size:75
Alignment explanation
Indices: 17089--17446 Score: 432
Period size: 76 Copynumber: 4.7 Consensus size: 75
17079 AATTGTCTTC
* * *
17089 AGAAGTAAAAATGAGGTT-GAAGTATCTCCTCAAAAATAATGGGGTTGGAGTACCCCCAATAAAA
1 AGAAGTAAAAATGAGGTTAG-AGTATCCCCTCGAAAATAATGGGGTTGGAGTA-TCCCAATAAAA
17153 ATCAACATTTTT
64 ATCAACATTTTT
* * *
17165 AGAAGTAAAAATGAGGTTAGAGTATCCCCTCAAAAATAATGGGGTTAGAGTATTCCTAATAAAAA
1 AGAAGTAAAAATGAGGTTAGAGTATCCCCTCGAAAATAATGGGGTTGGAGTA-TCCCAATAAAAA
**
17230 TTGACATTTTT
65 TCAACATTTTT
* * *
17241 AGAAGTAAAAAT-AGAGTTGGAGTATCCCCTCGGAAATAATGGGGTGGGAGTATCCTCAATAAAA
1 AGAAGTAAAAATGAG-GTTAGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCC-CAATAAAA
17305 ATCAACATTTTT
64 ATCAACATTTTT
* * * * *
17317 AGAAGTAAAAATGGGGTTAGAGTATCCCCTTGAAAATAATTGGGATGGAGTATCCCGATAAAAAT
1 AGAAGTAAAAATGAGGTTAGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCAATAAAAAT
* * *
17382 CGATATTCTT
66 CAACATTTTT
* * * * * *
17392 AGAAGTAAAAACGCGGTTGGAATATCCCCTCGAAAATAATGGTGTTGGAATATCC
1 AGAAGTAAAAATGAGGTTAGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCC
17447 ATGATAAATA
Statistics
Matches: 243, Mismatches: 35, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
75 67 0.28
76 174 0.72
77 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (75 bp):
AGAAGTAAAAATGAGGTTAGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCAATAAAAAT
CAACATTTTT
Found at i:19903 original size:22 final size:20
Alignment explanation
Indices: 19851--19904 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
19841 AAAAACCTAG
19851 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATGCAA
* *
19871 AATATATCGATACAATTGTAA
1 AATGTATCGATACAA-TGCAA
19892 ACATGTATCGATA
1 A-ATGTATCGATA
19905 TATTTTCTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 14 0.48
21 5 0.17
22 10 0.34
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACAATGCAA
Found at i:20676 original size:61 final size:61
Alignment explanation
Indices: 20573--21326 Score: 665
Period size: 61 Copynumber: 12.5 Consensus size: 61
20563 AAAATAAGAG
* *
20573 AGGCGTTCTGCTCTTTGAGGACTAGAAGG-GTCCACCAGCTTGTGTGGGCTTTAAAAAGAAA
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTG-CCACCAGCTTGTGTGGGCTTTAAAAAGAAA
* * * ** * * *
20634 ATGCATCATGCTCTTTGAGGACTAAAAGGTGCCATTAGCTTGTGTGGCCTTTTAAAGGAAA
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAA
* ** * * * *
20695 A--TGTTTTACTCTTTGAGGA-TAGAAGGTGCCACC-GACTTGTGTGAGCTTTAAAAGGAAA
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAG-CTTGTGTGGGCTTTAAAAAGAAA
* * * * * * *
20753 AGGCATCCTGCTCTTTGAGGACTAAAAGGTGCCACTAGTTTGTTTAAGCCTTT--AAAGGAA
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAGCTTGTGT-GGGCTTTAAAAAGAAA
* * *
20813 A-GCGTCCTGCTCTTTAAGGACTAAAAGGTGCCACC-GACTTGTATGGGCTTTAAAAAGAGA
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAG-CTTGTGTGGGCTTTAAAAAGAAA
* * * * * *
20873 AGGTGTCCTGCTCTTTGAGGATTGAAAGGTGCCACTAGCTTGTGTGGGCTTT-TAAAGGAA
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAA
* * * * * * * * * * *
20933 A-GTGTCTTACTCTTTAAAGAC-AAGAAGGTACCATC-GACTTGTGTAGGATTTAAAAGGAGA
1 AGGCGTCCTGCTCTTTGAGGACTAA-AAGGTGCCACCAG-CTTGTGTGGGCTTTAAAAAGAAA
* * *
20993 AGGCGTCCTGCTCTTTGAGGACTTAAAGGTGCCACCAACTTGTGTGGGCTTT-GAAAGAAGA
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAA-A
* * * *
21054 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCTACCAACTAGTGTGGGCTTTGAAAAGAAA
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAA
* * ** ** * *
21115 AGGCGTCTTGCTCTTAGAGGACTAAAAGGTGCCACCAAATTGTGTAAGCTTTAAAAGGGAA
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAA
* * ** * * * * *
21176 AGACGTCCTGCTCTTTAAGGACTAAAACCTGCCACCAACTTGTATGGGCTTTGAAAGGAGA
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAA
* * * * *
21237 AGGCGTCCTACTCTTTGAGGACTGAAAA-ATGCCACCAACTTGTGTGAGCTTTGAAAAGAAA
1 AGGCGTCCTGCTCTTTGAGGACT-AAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAA
*
21298 AGGCATCCTGCTCTTTGAGGACTAAAAGG
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGG
21327 ATAAAAGGTT
Statistics
Matches: 551, Mismatches: 120, Indels: 44
0.77 0.17 0.06
Matches are distributed among these distances:
57 1 0.00
58 40 0.07
59 84 0.15
60 44 0.08
61 364 0.66
62 18 0.03
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (61 bp):
AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAA
Found at i:22324 original size:20 final size:20
Alignment explanation
Indices: 22310--22347 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
22300 TTTTTCTTTC
22310 TTTTT-TTGGTTTTTTTTAT
1 TTTTTGTTGGTTTTTTTTAT
22329 TTTTTGTTGGTTTTTTTTA
1 TTTTTGTTGGTTTTTTTTA
22348 AGAAAAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.05, C:0.00, G:0.13, T:0.82
Consensus pattern (20 bp):
TTTTTGTTGGTTTTTTTTAT
Found at i:31090 original size:52 final size:52
Alignment explanation
Indices: 31030--31365 Score: 199
Period size: 51 Copynumber: 6.4 Consensus size: 52
31020 AAATAACGAG
*
31030 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGT
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
* ** * * * * *
31082 GTTGGAGTATCCTCGATTAAAGGAAAATTGGT-GTTTTGAAAATAAAACCGGG
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
* *** *
31134 GTTGGAGTATCCCCGATTATGAAAAATCAATA-TTTTGGAAATAAAGTCAGG-
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATC-GGA
* **** * * *
31185 GTTGGAGTATCCCC--TCG-GAAATAACGGGGTTGG-AGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTGTGAAA-AA-----TTGGTA-T-TTTTGGA-AATAAAATCGGA
* * *
31240 GTTGGAGTGTCCCCAATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGA
* * * *
31294 GTTGGAGTATCCCCGATTAT-AGAAAATTAGT-GTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTATTTTTGGAAATAAAATCGGA
*
31345 GTTGGAATATCCCCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
31366 GAGAATTGAG
Statistics
Matches: 213, Mismatches: 47, Indels: 48
0.69 0.15 0.16
Matches are distributed among these distances:
48 4 0.02
49 3 0.01
51 71 0.33
52 54 0.25
53 28 0.13
54 25 0.12
55 14 0.07
56 4 0.02
57 4 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
Found at i:31187 original size:51 final size:50
Alignment explanation
Indices: 31029--31198 Score: 196
Period size: 52 Copynumber: 3.3 Consensus size: 50
31019 GAAATAACGA
*
31029 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGGAAATAAAATCG
* * * * * *
31080 GTGTTGGAGTATCCTCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGG
1 G-GTTGGAGTATCCCCGATT-ATGAAAAATTGGTATTTTGGAAATAAAATC-G
*** *
31133 GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCAG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGGAAATAAAATC-G
31184 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
31199 TCGGAAATAA
Statistics
Matches: 98, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
51 38 0.39
52 48 0.49
53 12 0.12
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGGAAATAAAATCG
Found at i:31244 original size:27 final size:28
Alignment explanation
Indices: 31183--31253 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 28
31173 AATAAAGTCA
**
31183 GGGTTGGAGTATCCCCTCGGAAATAACG
1 GGGTTGGAGTATCCCCGAGGAAATAACG
* *
31211 GGGTTGGAGTATCCCCGATG-ATTAACG
1 GGGTTGGAGTATCCCCGAGGAAATAACG
*
31238 GGGTTGGAGTGTCCCC
1 GGGTTGGAGTATCCCC
31254 AATTGTGAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
27 21 0.55
28 17 0.45
ACGTcount: A:0.20, C:0.21, G:0.35, T:0.24
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCGAGGAAATAACG
Found at i:31321 original size:211 final size:211
Alignment explanation
Indices: 30972--31362 Score: 597
Period size: 211 Copynumber: 1.9 Consensus size: 211
30962 GATAATAACG
* * * *
30972 GGGTTGGAGTGTTCCCTTGGAAGTAACAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAG
1 GGGTTGGAGTATCCCCTCGGAAATAACAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAG
* * *
31037 TATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGTGTTGGAGTATCCTCGATTAA
66 TATCCCCAATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAA
* * *
31102 AGGAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATCAATAT
131 AGGAAAATTAGTGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTATGAAAAATCAATAT
31167 TTTGGAAATAAAGTCA
196 TTTGGAAATAAAGTCA
* * *
31183 GGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAG
1 GGGTTGGAGTATCCCCTCGGAAATAACAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAG
* *
31247 TGTCCCCAATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATT
66 TATCCCCAATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATT
* *
31312 ATA-GAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATT
129 AAAGGAAAATTAGTGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATT
31363 GTGGAGAATT
Statistics
Matches: 161, Mismatches: 17, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
210 28 0.17
211 95 0.59
212 38 0.24
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (211 bp):
GGGTTGGAGTATCCCCTCGGAAATAACAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAG
TATCCCCAATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAA
AGGAAAATTAGTGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTATGAAAAATCAATAT
TTTGGAAATAAAGTCA
Found at i:32163 original size:11 final size:11
Alignment explanation
Indices: 32147--32173 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
32137 AGGGGAGGTA
32147 ACATGGGCATC
1 ACATGGGCATC
32158 ACATGGGCATC
1 ACATGGGCATC
32169 ACATG
1 ACATG
32174 TTCATTTCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.19
Consensus pattern (11 bp):
ACATGGGCATC
Found at i:33742 original size:13 final size:13
Alignment explanation
Indices: 33724--33749 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33714 ACAAAGATCC
33724 ATGTATCGATACA
1 ATGTATCGATACA
33737 ATGTATCGATACA
1 ATGTATCGATACA
33750 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:33744 original size:33 final size:33
Alignment explanation
Indices: 33707--33769 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
33697 TTTCCAAATA
***
33707 TATCGATACAAAGATCCATGTATCGATACAATG
1 TATCGATACAAAGAAAAATGTATCGATACAATG
*
33740 TATCGATACACAGAAAAATGTATCGATACA
1 TATCGATACAAAGAAAAATGTATCGATACA
33770 TTTCCTTGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.25
Consensus pattern (33 bp):
TATCGATACAAAGAAAAATGTATCGATACAATG
Found at i:33813 original size:19 final size:18
Alignment explanation
Indices: 33789--33853 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
33779 TAGTAGCTAA
33789 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
33808 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
33823 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
33840 TTATGTATCGATAC
1 TTATGTATCGATAC
33854 TTTCATTCTC
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 2 0.05
18 1 0.03
19 25 0.62
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.37
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:33829 original size:13 final size:13
Alignment explanation
Indices: 33811--33835 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33801 ACAATACTTA
33811 TGTATCGATACAT
1 TGTATCGATACAT
33824 TGTATCGATACA
1 TGTATCGATACA
33836 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:33833 original size:32 final size:32
Alignment explanation
Indices: 33792--33853 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
33782 TAGCTAATTA
*
33792 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
33824 TGTATCGATACAAAACTTATGTATCGATAC
1 TGTATCGATACAAAACTTATGTATCGATAC
33854 TTTCATTCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:34589 original size:55 final size:54
Alignment explanation
Indices: 34505--35171 Score: 845
Period size: 55 Copynumber: 12.0 Consensus size: 54
34495 ATAAAGTGTA
* * * *
34505 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
34560 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
34615 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
34670 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
34725 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
34780 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* * *
34835 TCCTGCTCTTTGAAGACTGGAAAATGCCACCAACTTATGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
34890 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
34945 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
* * **
35004 TCCCGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAG---GTG
** * * **
35061 GGCTCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAGGCA
1 TCCT-GCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTT---GAAAGGTG
* * * *
35119 TCCCGCTCTTTGAGGACTAGAAAATGCCACCAACTCGTGTGGGCTTTAAAAGG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGG
35172 AAAAGGCATC
Statistics
Matches: 549, Mismatches: 38, Indels: 50
0.86 0.06 0.08
Matches are distributed among these distances:
54 47 0.09
55 345 0.63
56 18 0.03
57 16 0.03
58 68 0.12
59 50 0.09
61 5 0.01
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (54 bp):
TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:34690 original size:26 final size:26
Alignment explanation
Indices: 34661--34805 Score: 75
Period size: 26 Copynumber: 5.3 Consensus size: 26
34651 GTGTGGGCTT
34661 TGAAAGGTGTCCTGCTCTTTGGGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** *
34687 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
* *
34714 TTTAAGAGGTGTCCTGCTCTTTGAGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGGGGAC
* ** *
34742 TGGAAA-ATG-CCACCAACTTGTGTGGG-C
1 T-GAAAGGTGTCCTGC-TCTT-TG-GGGAC
34769 TTTGAAAGGTGTCCTGCTCTTTGGGGAC
1 --TGAAAGGTGTCCTGCTCTTTGGGGAC
34797 TGAAAGGTG
1 TGAAAGGTG
34806 CCACCAACTT
Statistics
Matches: 85, Mismatches: 18, Indels: 32
0.63 0.13 0.24
Matches are distributed among these distances:
25 6 0.07
26 26 0.31
27 13 0.15
28 20 0.24
29 14 0.16
30 6 0.07
ACGTcount: A:0.20, C:0.19, G:0.32, T:0.29
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:36214 original size:13 final size:12
Alignment explanation
Indices: 36189--36232 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 12
36179 TTTTTCTTTG
36189 TTTTGTTTCTTTT
1 TTTTGTTT-TTTT
*
36202 GTTTGTTTTTTT
1 TTTTGTTTTTTT
36214 TTCTTGCTTTTTTT
1 TT-TTG-TTTTTTT
36228 TTTTG
1 TTTTG
36233 AAGAGAAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 5 0.19
13 13 0.48
14 9 0.33
ACGTcount: A:0.00, C:0.07, G:0.11, T:0.82
Consensus pattern (12 bp):
TTTTGTTTTTTT
Found at i:50409 original size:13 final size:13
Alignment explanation
Indices: 50391--50416 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
50381 ACAAAGATCC
50391 ATGTATCGATACA
1 ATGTATCGATACA
50404 ATGTATCGATACA
1 ATGTATCGATACA
50417 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:50412 original size:33 final size:33
Alignment explanation
Indices: 50370--50436 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
50360 AAAATTTCCA
***
50370 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
50403 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
50436 A
1 A
50437 TTTCCTTGGC
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:50480 original size:19 final size:18
Alignment explanation
Indices: 50456--50527 Score: 84
Period size: 19 Copynumber: 4.2 Consensus size: 18
50446 CAGTAGCTAA
50456 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
50475 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
50490 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
50507 TTATGTATCGATACAAA-
1 TTATGTATCGATACAAAC
50524 TTAT
1 TTAT
50528 TGAATGTCAA
Statistics
Matches: 47, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.23
14 1 0.02
16 2 0.04
17 4 0.09
18 4 0.09
19 25 0.53
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:50496 original size:13 final size:13
Alignment explanation
Indices: 50478--50502 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
50468 ACAATACTTA
50478 TGTATCGATACAT
1 TGTATCGATACAT
50491 TGTATCGATACA
1 TGTATCGATACA
50503 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:50500 original size:32 final size:32
Alignment explanation
Indices: 50459--50521 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
50449 TAGCTAATTA
*
50459 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
50491 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
50522 AATTATTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:51049 original size:33 final size:33
Alignment explanation
Indices: 51012--51093 Score: 128
Period size: 33 Copynumber: 2.5 Consensus size: 33
51002 TAGCCCTTAA
*
51012 AGAGAAAGAAGAGATAGGAGGGATGATAGAAGG
1 AGAGATAGAAGAGATAGGAGGGATGATAGAAGG
* *
51045 AGAGATAGTAGAGATAGGAGGGATGATAGGAGG
1 AGAGATAGAAGAGATAGGAGGGATGATAGAAGG
*
51078 AGAGATAGGAGAGATA
1 AGAGATAGAAGAGATA
51094 ATAGAGAGAG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.45, C:0.00, G:0.43, T:0.12
Consensus pattern (33 bp):
AGAGATAGAAGAGATAGGAGGGATGATAGAAGG
Found at i:51051 original size:12 final size:12
Alignment explanation
Indices: 51021--51088 Score: 65
Period size: 12 Copynumber: 5.9 Consensus size: 12
51011 AAGAGAAAGA
51021 AGAGATAGGAGG
1 AGAGATAGGAGG
*
51033 -GATGATAGAAGG
1 AGA-GATAGGAGG
*
51045 AGAGAT---AGT
1 AGAGATAGGAGG
51054 AGAGATAGGAGG
1 AGAGATAGGAGG
51066 -GATGATAGGAGG
1 AGA-GATAGGAGG
51078 AGAGATAGGAG
1 AGAGATAGGAG
51089 AGATAATAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
9 8 0.17
11 4 0.09
12 30 0.65
13 4 0.09
ACGTcount: A:0.41, C:0.00, G:0.46, T:0.13
Consensus pattern (12 bp):
AGAGATAGGAGG
Found at i:51089 original size:42 final size:42
Alignment explanation
Indices: 51042--51122 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
51032 GGATGATAGA
* * * *
51042 AGGAGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGAT
1 AGGAGAGATAATAGAGAGAGGAAGGATGACAGGAGGAGAGAT
51084 AGGAGAGATAATAGAGAGAGGAAGGATGACAGGAGGAGA
1 AGGAGAGATAATAGAGAGAGGAAGGATGACAGGAGGAGA
51123 AGAGAAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.43, C:0.01, G:0.44, T:0.11
Consensus pattern (42 bp):
AGGAGAGATAATAGAGAGAGGAAGGATGACAGGAGGAGAGAT
Found at i:51097 original size:12 final size:12
Alignment explanation
Indices: 51024--51102 Score: 53
Period size: 12 Copynumber: 6.9 Consensus size: 12
51014 AGAAAGAAGA
*
51024 GATAGGAGGGAT
1 GATAGGAGAGAT
*
51036 GATAGAAGGAGA-
1 GATAGGA-GAGAT
*
51048 GATA-G-TAGA-
1 GATAGGAGAGAT
*
51057 GATAGGAGGGAT
1 GATAGGAGAGAT
51069 GATAGGAGGAGA-
1 GATAGGA-GAGAT
51081 GATAGGAGAGAT
1 GATAGGAGAGAT
*
51093 AATA-GAGAGA
1 GATAGGAGAGA
51103 GGAAGGATGA
Statistics
Matches: 53, Mismatches: 8, Indels: 13
0.72 0.11 0.18
Matches are distributed among these distances:
9 7 0.13
10 1 0.02
11 12 0.23
12 27 0.51
13 6 0.11
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.14
Consensus pattern (12 bp):
GATAGGAGAGAT
Found at i:51135 original size:42 final size:42
Alignment explanation
Indices: 51047--51135 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 42
51037 ATAGAAGGAG
* * * * * * *
51047 AGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGATAGGAG
1 AGATAATAGAGAGAGGAAGGATGACAGGAGGAGAGAGAGAAA
51089 AGATAATAGAGAGAGGAAGGATGACAGGAGGAGA-AGAGAAAA
1 AGATAATAGAGAGAGGAAGGATGACAGGAGGAGAGAGAG-AAA
51131 AGATA
1 AGATA
51136 GAAGAGTGAG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 3 0.08
42 36 0.92
ACGTcount: A:0.47, C:0.01, G:0.40, T:0.11
Consensus pattern (42 bp):
AGATAATAGAGAGAGGAAGGATGACAGGAGGAGAGAGAGAAA
Found at i:54748 original size:10 final size:10
Alignment explanation
Indices: 54735--54815 Score: 74
Period size: 10 Copynumber: 7.9 Consensus size: 10
54725 TTCACTGTTT
54735 ATCACTATTC
1 ATCACTATTC
54745 ATCACTATTC
1 ATCACTATTC
54755 ATCACTATTC
1 ATCACTATTC
* * *
54765 ATGTATCGATAC
1 AT-CA-CTATTC
*
54777 ATCACTGTTC
1 ATCACTATTC
*
54787 ATCACTGTTAC
1 ATCACTATT-C
*
54798 ATCACTGTTC
1 ATCACTATTC
54808 A-CACTATT
1 ATCACTATT
54816 TAATAAAAGC
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
9 6 0.10
10 36 0.60
11 12 0.20
12 6 0.10
ACGTcount: A:0.28, C:0.27, G:0.06, T:0.38
Consensus pattern (10 bp):
ATCACTATTC
Found at i:54802 original size:11 final size:11
Alignment explanation
Indices: 54774--54806 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
54764 CATGTATCGA
54774 TACATCACTGT
1 TACATCACTGT
54785 T-CATCACTGT
1 TACATCACTGT
54795 TACATCACTGT
1 TACATCACTGT
54806 T
1 T
54807 CACACTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.24, C:0.27, G:0.09, T:0.39
Consensus pattern (11 bp):
TACATCACTGT
Found at i:59376 original size:21 final size:19
Alignment explanation
Indices: 59342--59381 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
59332 CTAACAAAAA
*
59342 AATGGGTATTTTTAGGAAG
1 AATGGGTATTTTTAAGAAG
59361 AATGGGTAGTTTTTTAAGAAG
1 AATGGGTA--TTTTTAAGAAG
59382 TAAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
21 10 0.56
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.38
Consensus pattern (19 bp):
AATGGGTATTTTTAAGAAG
Found at i:60437 original size:2 final size:2
Alignment explanation
Indices: 60430--60458 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
60420 TATTATTATC
60430 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60459 CAAAAAAGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60745 original size:2 final size:2
Alignment explanation
Indices: 60740--60786 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
60730 ATATATATAT
*
60740 AG AG AG AG AG AG AG AG AG AG AT AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
60782 AG AG A
1 AG AG A
60787 CAATAGTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.47, T:0.02
Consensus pattern (2 bp):
AG
Found at i:61064 original size:23 final size:23
Alignment explanation
Indices: 61030--61076 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
61020 ATGCATAGAC
*
61030 AATTTAGGCTTATTTATAAAATT
1 AATTTAGACTTATTTATAAAATT
*
61053 AATTTAGACTTATTTATGAAATT
1 AATTTAGACTTATTTATAAAATT
61076 A
1 A
61077 TTATTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (23 bp):
AATTTAGACTTATTTATAAAATT
Found at i:61560 original size:23 final size:22
Alignment explanation
Indices: 61527--61582 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
61517 TATGTTTGAC
61527 ATAAGAAAAATAACATGAACATA
1 ATAA-AAAAATAACATGAACATA
* *
61550 ATACAAAAAATAACTTGAACATG
1 ATA-AAAAAATAACATGAACATA
61573 ATAAAAAAAT
1 ATAAAAAAAT
61583 TATATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 7 0.23
23 22 0.73
24 1 0.03
ACGTcount: A:0.64, C:0.09, G:0.07, T:0.20
Consensus pattern (22 bp):
ATAAAAAAATAACATGAACATA
Found at i:61628 original size:23 final size:25
Alignment explanation
Indices: 61596--61644 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 25
61586 ATAAAAAAAA
61596 TTCATATCATAT-TT-ATATTATTT
1 TTCATATCATATATTCATATTATTT
*
61619 TTCATTTCATATATTCATATTATTT
1 TTCATATCATATATTCATATTATTT
61644 T
1 T
61645 AATAATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.48
24 2 0.09
25 10 0.43
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (25 bp):
TTCATATCATATATTCATATTATTT
Found at i:64483 original size:12 final size:14
Alignment explanation
Indices: 64453--64490 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
64443 CGTGAGTAAA
*
64453 AATAAAAATATTTT
1 AATAAAATTATTTT
64467 AAT-AAATTATTTT
1 AATAAAATTATTTT
64480 -ATAAAATTATT
1 AATAAAATTATT
64491 ATTGAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 2 0.09
13 17 0.77
14 3 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATAAAATTATTTT
Found at i:65028 original size:15 final size:15
Alignment explanation
Indices: 65002--65044 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
64992 AGACTTAAAT
65002 AAATTAATAAAAATTA
1 AAATTAA-AAAAATTA
65018 AAATTAAAAAAATTA
1 AAATTAAAAAAATTA
* *
65033 TATTTAAAAAAA
1 AAATTAAAAAAA
65045 ATTACCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 18 0.72
16 7 0.28
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATTAAAAAAATTA
Found at i:65045 original size:16 final size:16
Alignment explanation
Indices: 65002--65048 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
64992 AGACTTAAAT
*
65002 AAATTAATAAAAATTA
1 AAATTAAAAAAAATTA
65018 AAATT-AAAAAAATTA
1 AAATTAAAAAAAATTA
* *
65033 TATTTAAAAAAAATTA
1 AAATTAAAAAAAATTA
65049 CCAAAAGAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 12 0.44
16 15 0.56
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTAAAAAAAATTA
Found at i:68419 original size:21 final size:21
Alignment explanation
Indices: 68390--68432 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
68380 GCTATTGCCA
*
68390 ACAAAATGTATCGATACATTC
1 ACAAAATGTATCAATACATTC
* *
68411 ACAAGATGTATTAATACATTC
1 ACAAAATGTATCAATACATTC
68432 A
1 A
68433 ATCCTTAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.30
Consensus pattern (21 bp):
ACAAAATGTATCAATACATTC
Found at i:75722 original size:51 final size:50
Alignment explanation
Indices: 75667--75778 Score: 118
Period size: 50 Copynumber: 2.2 Consensus size: 50
75657 CAACGGGGCC
* *
75667 GGAGTATCCCCAATTATGGAAAATGGGTGTTCCAG-AAATAAAATCGGGGTT
1 GGAGTATCCCCAATTAT-AAAAATGGGTATT-CAGAAAATAAAATCGGGGTT
*** * ** *
75718 GGAGTATCCTTGATTATAAAAATTGGTATTTTGAAAATGAAATCGGGGTT
1 GGAGTATCCCCAATTATAAAAATGGGTATTCAGAAAATAAAATCGGGGTT
75768 GGAGTATCCCC
1 GGAGTATCCCC
75779 TCGAAAATAA
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
49 1 0.02
50 34 0.69
51 14 0.29
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (50 bp):
GGAGTATCCCCAATTATAAAAATGGGTATTCAGAAAATAAAATCGGGGTT
Found at i:75846 original size:79 final size:79
Alignment explanation
Indices: 75761--75935 Score: 228
Period size: 79 Copynumber: 2.2 Consensus size: 79
75751 AAAATGAAAT
75761 CGGGGTTGGAGTATCCCC-TCGAAAATAACAAGGTTGGAGTATCCCCGATTGTGAAAAATCGATG
1 CGGGGTTGGAGTATCCCCTTCGAAAA-AACAAGGTTGGAGTATCCCCGATTGTGAAAAATCGATG
75825 ATTTAGAAAT-AAGAC
65 ATTTAGAAATAAAG-C
* * ** * * * *
75840 CGGGGTTGAAGTATCCCCTTGGAAAAAATGAGGTTGGAGTATCCCCTATTGTGAAAAATTGGTGT
1 CGGGGTTGGAGTATCCCCTTCGAAAAAACAAGGTTGGAGTATCCCCGATTGTGAAAAATCGATGA
*
75905 TTTGGAAATAAAGC
66 TTTAGAAATAAAGC
*
75919 CGGAGTTGGAGTATCCC
1 CGGGGTTGGAGTATCCC
75936 TGATTGTGAA
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
79 74 0.89
80 9 0.11
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.26
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTTCGAAAAAACAAGGTTGGAGTATCCCCGATTGTGAAAAATCGATGA
TTTAGAAATAAAGC
Found at i:75931 original size:51 final size:52
Alignment explanation
Indices: 75872--75988 Score: 175
Period size: 51 Copynumber: 2.3 Consensus size: 52
75862 AAAAAATGAG
* * *
75872 GTTGGAGTATCCCCT-ATTGTGAAAAATTGGTGTTTTGGAAATAAAGCCGGA
1 GTTGGAGTATCCCCTGATTGTGAAAAATTGGTATTTTAGAAATAAAACCGGA
* *
75923 GTTGGAGTAT-CCCTGATTGTGAAAAATTGGTATTTTAGAAATAAAATCGGG
1 GTTGGAGTATCCCCTGATTGTGAAAAATTGGTATTTTAGAAATAAAACCGGA
75974 GTTGGAGTATCCCCT
1 GTTGGAGTATCCCCT
75989 CGAAAATAAC
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
50 4 0.07
51 51 0.86
52 4 0.07
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.32
Consensus pattern (52 bp):
GTTGGAGTATCCCCTGATTGTGAAAAATTGGTATTTTAGAAATAAAACCGGA
Found at i:75948 original size:130 final size:127
Alignment explanation
Indices: 75793--76040 Score: 322
Period size: 130 Copynumber: 1.9 Consensus size: 127
75783 AAATAACAAG
*
75793 GTTGGAGTATCCCCGATTGTGAAAAATCGATGA-TTTAGAAATAAGACCGGGGTTGAAGTATCCC
1 GTTGGAGTATCCCCGATTGTGAAAAATCGAT-ATTTTAGAAATAAAACCGGGGTTGAAGTATCCC
* * * *
75857 CTTGGAAAA-AATGAGGTTGGAGTATCCCCT-ATTGTGAAAAATTGGTGTTTTGGAAATAAAGCC
65 C-TCGAAAATAACGAGGTTAGAGTAT-CCCTGA---TGAAAAATTGATGTTTTGGAAATAAAGCC
75920 GGA
125 GGA
* * * * *
75923 GTTGGAGTATCCCTGATTGTGAAAAATTGGTATTTTAGAAATAAAATCGGGGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTGTGAAAAATCGATATTTTAGAAATAAAACCGGGGTTGAAGTATCCCC
*
75988 TCGAAAATAACGGGGTTAGAGTATCCCTGATGAAAAATTGATGTTTTGGAAAT
66 TCGAAAATAACGAGGTTAGAGTATCCCTGATGAAAAATTGATGTTTTGGAAAT
76041 GAAATCGGGA
Statistics
Matches: 104, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
127 22 0.21
129 11 0.11
130 71 0.68
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (127 bp):
GTTGGAGTATCCCCGATTGTGAAAAATCGATATTTTAGAAATAAAACCGGGGTTGAAGTATCCCC
TCGAAAATAACGAGGTTAGAGTATCCCTGATGAAAAATTGATGTTTTGGAAATAAAGCCGGA
Found at i:78382 original size:20 final size:20
Alignment explanation
Indices: 78357--78450 Score: 95
Period size: 20 Copynumber: 4.7 Consensus size: 20
78347 AAAATGCCTG
78357 AATGTATCGATACATTGTAA
1 AATGTATCGATACATTGTAA
*
78377 AATGTATCGATACA--ATAA
1 AATGTATCGATACATTGTAA
* *
78395 GCAATGTATCGATACAATGCAA
1 --AATGTATCGATACATTGTAA
*
78417 AATGTATCGATACATT-TCTA
1 AATGTATCGATACATTGT-AA
*
78437 GATGTATCGATACA
1 AATGTATCGATACA
78451 AAGATCGATG
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
18 3 0.05
20 57 0.92
22 2 0.03
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACATTGTAA
Found at i:78450 original size:60 final size:60
Alignment explanation
Indices: 78357--78503 Score: 161
Period size: 60 Copynumber: 2.6 Consensus size: 60
78347 AAAATGCCTG
78357 AATGTATCGATACATTGTAAAATGTATCGATACAATA-AGCAATGTATCGATACAATGCAA
1 AATGTATCGATACATTGTAAAATGTATCGATACAA-AGAGCAATGTATCGATACAATGCAA
* * * *
78417 AATGTATCGATACATT-TCTAGATGTATCGATACAAAGATCGATGTATCGAT---AT----
1 AATGTATCGATACATTGT-AAAATGTATCGATACAAAGAGCAATGTATCGATACAATGCAA
78470 AATGTATCGATACATTG-AATAATGTATCGATACA
1 AATGTATCGATACATTGTAA-AATGTATCGATACA
78504 TTTCCTTGGC
Statistics
Matches: 77, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
52 1 0.01
53 29 0.38
57 2 0.03
59 2 0.03
60 43 0.56
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (60 bp):
AATGTATCGATACATTGTAAAATGTATCGATACAAAGAGCAATGTATCGATACAATGCAA
Found at i:78493 original size:20 final size:20
Alignment explanation
Indices: 78468--78505 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
78458 ATGTATCGAT
78468 ATAATGTATCGATACATTGA
1 ATAATGTATCGATACATTGA
78488 ATAATGTATCGATACATT
1 ATAATGTATCGATACATT
78506 TCCTTGGCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (20 bp):
ATAATGTATCGATACATTGA
Found at i:84380 original size:19 final size:19
Alignment explanation
Indices: 84335--84405 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 19
84325 ACTGCCAGTT
84335 TCATGTATCGATACAATTG-
1 TCATGTATCGATACAA-TGA
84354 TGCATGTATCGATACAATGA
1 T-CATGTATCGATACAATGA
*
84374 TCATGTATCGATACAAAGCA
1 TCATGTATCGATACAATG-A
*
84394 TAATGTATCGAT
1 TCATGTATCGAT
84406 TCATTGGGTA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
19 19 0.40
20 28 0.60
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Consensus pattern (19 bp):
TCATGTATCGATACAATGA
Found at i:90477 original size:154 final size:152
Alignment explanation
Indices: 90067--90509 Score: 454
Period size: 155 Copynumber: 2.9 Consensus size: 152
90057 GAAAACATCA
* **
90067 TAAAAAGGCGAACCTATCCTAAATGTAAACACTTGGCATAAAAGTGACTGGGTGACTACCTA--A
1 TAAAAAGGCAAACCTATCCTAAATGT-AAC-CTTGGCATAAAAGTGACTTAGTGACTACCTAGGA
* ** * * * *
90130 ---GCTTTTAGGAAAAATTACCAAAATACCCTAGAGGTATACCTTTGACGTGAAAGTATCCCGAT
64 CTCGGTTTTAAAAAAAATTACCAAAATACCCT-TAGGTATACCTTCGACATGAAAGTATCCAGAT
* *
90192 AACTCTAAAGGAGTCAAAATGATTG
128 AACTCTAAAGGAGACAAAAGGATTG
* * * * * * **
90217 TAAAAAGGCAAACCTATCCTAAATGCAGGCCCATAGCATAAAATTGACCTAGTGACTATGTAGGA
1 TAAAAAGGCAAACCTATCCTAAATGTA--ACCTTGGCATAAAAGTGACTTAGTGACTACCTAGGA
* *
90282 CTCGGTTTTAAAAAAAATTACCAAAATACTCCTAAGGTATACCTTCGACATGAACGTATCCA-AG
64 CTCGGTTTTAAAAAAAATTACCAAAATAC-CCTTAGGTATACCTTCGACATGAAAGTATCCAGA-
*
90346 TAAC-CTTAAGG-GACATGAAAGGATTG
127 TAACTCTAAAGGAGACA--AAAGGATTG
**
90372 TAAAAAGGCAAACCTATCCTAAATGTAACCTTTGGCATAAAAGCAACTTAGTGACTACCTAGGAC
1 TAAAAAGGCAAACCTATCCTAAATGTAACC-TTGGCATAAAAGTGACTTAGTGACTACCTAGGAC
* **
90437 TCGGTTTTAAAAAAAATTACTAAAATACCCTTAGGATATACCTTCGATGTGAAAGTATCCCA-AT
65 TCGGTTTTAAAAAAAATTACCAAAATACCCTTAGG-TATACCTTCGACATGAAAGTAT-CCAGAT
*
90501 AACTTTAAA
128 AACTCTAAA
90510 AAAAACGAAA
Statistics
Matches: 239, Mismatches: 39, Indels: 25
0.79 0.13 0.08
Matches are distributed among these distances:
149 1 0.00
150 47 0.20
151 1 0.00
152 1 0.00
153 11 0.05
154 83 0.35
155 92 0.38
156 3 0.01
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (152 bp):
TAAAAAGGCAAACCTATCCTAAATGTAACCTTGGCATAAAAGTGACTTAGTGACTACCTAGGACT
CGGTTTTAAAAAAAATTACCAAAATACCCTTAGGTATACCTTCGACATGAAAGTATCCAGATAAC
TCTAAAGGAGACAAAAGGATTG
Found at i:90738 original size:29 final size:28
Alignment explanation
Indices: 90602--90744 Score: 117
Period size: 29 Copynumber: 5.0 Consensus size: 28
90592 CTACTAAGTT
* * ** *
90602 CCTAGACTTTCCAAAATTACACATTGAT
1 CCTAAACTTTTCAAAATTACATGTTGAC
* * *
90630 CCTGAACTTTTTAAAATTATACT-TTGATC
1 CCTAAACTTTTCAAAATTACA-TGTTGA-C
* * *
90659 CCTAAACTTTTTAAAATTACACGTTAAC
1 CCTAAACTTTTCAAAATTACATGTTGAC
* * *
90687 CCCAATCTTTTCAAAATTTCATGTTGAC
1 CCTAAACTTTTCAAAATTACATGTTGAC
*
90715 TCCTAAAATTTTCAAAATTACATGTTGAC
1 -CCTAAACTTTTCAAAATTACATGTTGAC
90744 C
1 C
90745 TCAAAATGGC
Statistics
Matches: 90, Mismatches: 21, Indels: 8
0.76 0.18 0.07
Matches are distributed among these distances:
28 44 0.49
29 46 0.51
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.38
Consensus pattern (28 bp):
CCTAAACTTTTCAAAATTACATGTTGAC
Found at i:91715 original size:11 final size:10
Alignment explanation
Indices: 91661--91716 Score: 51
Period size: 11 Copynumber: 5.3 Consensus size: 10
91651 GCCAGCTTTC
91661 TTTTT-TTTT
1 TTTTTATTTT
*
91670 TTTTAATTTT
1 TTTTTATTTT
*
91680 TATCTTGATTTT
1 T-T-TTTATTTT
91692 TCTTTTATTTT
1 T-TTTTATTTT
91703 TTTTTCATTTT
1 TTTTT-ATTTT
91714 TTT
1 TTT
91717 CATTATTATC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
9 4 0.10
10 9 0.23
11 17 0.44
12 9 0.23
ACGTcount: A:0.11, C:0.05, G:0.02, T:0.82
Consensus pattern (10 bp):
TTTTTATTTT
Found at i:91934 original size:6 final size:6
Alignment explanation
Indices: 91882--91945 Score: 53
Period size: 6 Copynumber: 10.7 Consensus size: 6
91872 ACTAGTTAAC
* * *
91882 AAATATA AAA-TA AAA-TA AAATAA AAATTTCA AAATTA AGA-GA AAATTA
1 AAAT-TA AAATTA AAATTA AAATTA AAA-TT-A AAATTA AAATTA AAATTA
91930 AAATTA AAATTA AAAT
1 AAATTA AAATTA AAAT
91946 ATTTATCATA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
5 13 0.28
6 24 0.51
7 6 0.13
8 4 0.09
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.27
Consensus pattern (6 bp):
AAATTA
Found at i:92353 original size:154 final size:153
Alignment explanation
Indices: 92061--92398 Score: 357
Period size: 153 Copynumber: 2.2 Consensus size: 153
92051 TGATATATAC
* * * *
92061 AAAC-AAAAAATTC-AAAACTCATATAATAAATTGAATTTTATAAAACTAATTTACTATGAATTT
1 AAACAAAAAAATTCTAAAACTCATAAAATAAATTGAATTTTATAAAACTAATTTAATATGAACTA
** * * *
92124 AATGAAAATATTTGATGAATTTTAAAAATTTTGAACTGAGAAAAATCTAACTGAAAAATTTTACG
66 AAAAAAAATATTTGATGAATTTTAAAAATTATAAACTGAGAAAAATCTAACTGAAAAATTTTACA
* *
92189 GAGTAGAAAAC-TCTGTATTTTAG
131 GAGTAAAAAACTTC-GTATCTTAG
* * *
92212 AAATAAAAAAATTCTAAAACTTATAAAATAAATTGAATTTT-TCAAAATTAATTTAATATGAACT
1 AAACAAAAAAATTCTAAAACTCATAAAATAAATTGAATTTTAT-AAAACTAATTTAATATGAACT
* * * *** **
92276 AAAAAAATAATATTTGAAT-AATTTTGAAAATTATAAACTTAGGAAAATCTTTGTAGTGAAA-TT
65 AAAAAAA-AATATTTG-ATGAATTTTAAAAATTATAAACTGAGAAAAATCTAACT-GAAAAATTT
*
92339 TACAGAGTAAAAAACTTCGTATCTTGG
127 TACAGAGTAAAAAACTTCGTATCTTAG
* *
92366 TAACAAAAAAA-TCTAAAGCTCATAAAATAAATT
1 AAACAAAAAAATTCTAAAACTCATAAAATAAATT
92399 AAAACTTTTA
Statistics
Matches: 153, Mismatches: 27, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
151 3 0.02
152 10 0.07
153 66 0.43
154 66 0.43
155 8 0.05
ACGTcount: A:0.50, C:0.08, G:0.09, T:0.34
Consensus pattern (153 bp):
AAACAAAAAAATTCTAAAACTCATAAAATAAATTGAATTTTATAAAACTAATTTAATATGAACTA
AAAAAAAATATTTGATGAATTTTAAAAATTATAAACTGAGAAAAATCTAACTGAAAAATTTTACA
GAGTAAAAAACTTCGTATCTTAG
Found at i:93356 original size:66 final size:66
Alignment explanation
Indices: 93249--93776 Score: 431
Period size: 66 Copynumber: 8.0 Consensus size: 66
93239 AAGTGAGACA
* * ** * * *
93249 TAAGTC-AGAAAGAAGTTAACTAGGGCAAAACCGTAACGTCAACTAAAAGGTGACAAGGG-AAAA
1 TAAGTCGA-AAAGAGGTTGACTAGGGTGAAACCATCACGTCAACTAAAAGGTGACTAGGGCAAAA
93312 GCC
65 -CC
** * * * * * * *
93315 TAAGTTTAAAAGTGGTTGACCAGGGCGAAACCATCATGTCAACTAAAA-ATCAACTAAAAGG--A
1 TAAGTCGAAAAGAGGTTGACTAGGGTGAAACCATCACGTCAACTAAAAGGT-GACT--AGGGCAA
93377 AACC
63 AACC
* * * * *
93381 TAAGTAGAAAAGAGGTTGACTAGGGTGAAACCATAATGTCAACTAAAAGGTGATTAGGACAAAAC
1 TAAGTCGAAAAGAGGTTGACTAGGGTGAAACCATCACGTCAACTAAAAGGTGACTAGGGCAAAAC
93446 C
66 C
* * * * * *
93447 TAGGTCGAGAAGAGGTTAATTAGGGTGAAACCATC-CTGTTAACTAAAAGGTGACTAGGGCACAA
1 TAAGTCGAAAAGAGGTTGACTAGGGTGAAACCATCAC-GTCAACTAAAAGGTGACTAGGGCAAAA
*
93511 CA
65 CC
* ** ** * * **
93513 TAAGTTGAATGGAGGTTGACTAGGGAAAAACCATCACATCAACTAAAAAGTGACTAGGGTGAAAC
1 TAAGTCGAAAAGAGGTTGACTAGGGTGAAACCATCACGTCAACTAAAAGGTGACTAGGGCAAAAC
93578 C
66 C
* * * ** * * * * * *
93579 TAAGTTGAAAAGAGATTAAAAAAGGTGGAACCATCACGTCAAGTAATAGGTGACTAGGGCAATAT
1 TAAGTCGAAAAGAGGTTGACTAGGGTGAAACCATCACGTCAACTAAAAGGTGACTAGGGCAAAAC
93644 C
66 C
* * *
93645 TAAGTCGAAAGGAGGTTGACTAGGGTGAAACCATCACATCAAGTAAAAGGTGACTAGGGCAAAAC
1 TAAGTCGAAAAGAGGTTGACTAGGGTGAAACCATCACGTCAACTAAAAGGTGACTAGGGCAAAAC
93710 C
66 C
* * ** * *
93711 TAAGTCGAAAGGATGTTGACTAGGGCAAAACCATCACGTCAACT-AAAGGTTGACCAGGGCAGAA
1 TAAGTCGAAAAGAGGTTGACTAGGGTGAAACCATCACGTCAACTAAAAGG-TGACTAGGGCAAAA
93775 CC
65 CC
93777 ATCACATCAA
Statistics
Matches: 363, Mismatches: 89, Indels: 20
0.77 0.19 0.04
Matches are distributed among these distances:
64 2 0.01
65 6 0.02
66 346 0.95
67 6 0.02
68 3 0.01
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.19
Consensus pattern (66 bp):
TAAGTCGAAAAGAGGTTGACTAGGGTGAAACCATCACGTCAACTAAAAGGTGACTAGGGCAAAAC
C
Found at i:93671 original size:198 final size:198
Alignment explanation
Indices: 93249--93757 Score: 490
Period size: 198 Copynumber: 2.6 Consensus size: 198
93239 AAGTGAGACA
* ** * * * *
93249 TAAGTC-AGAAAGAAGTTAACTAGGGCAAAACCGTAACGTCAACTAAAAGGTGACAAGGG-AAAA
1 TAAGTCGAG-AAGAGGTTAACTAGGGTGAAACCATCACATCAACTAAAAGGTGACTAGGGCAAAA
* ** * * * ** ** * **
93312 GCCTAAGTTTAAAAGTGGTTGACCAGGGCGAAACCATCATGTCAACTAAAAA-TCAACTAAAAG-
65 -CATAAGTCGAAAGGAGGTTGACTAGGGAAAAACCATCACATCAACTAAAAAGT-GACT-AGGGT
* * ** * * *
93375 GAAACCTAAGTAGAAAAGAGGTTGACTAGGGTGAAACCATAATGTCAACTAAAAGGTGATTAGGA
127 GAAACCTAAGTAGAAAAGAGATTAAAAAAGGTGAAACCATAACGTCAACTAAAAGGTGACTAGGA
93440 CAAAACC
192 CAAAACC
* * * * *
93447 TAGGTCGAGAAGAGGTTAATTAGGGTGAAACCATC-CTGTTAACTAAAAGGTGACTAGGGCACAA
1 TAAGTCGAGAAGAGGTTAACTAGGGTGAAACCATCAC-ATCAACTAAAAGGTGACTAGGGCAAAA
* *
93511 CATAAGTTGAATGGAGGTTGACTAGGGAAAAACCATCACATCAACTAAAAAGTGACTAGGGTGAA
65 CATAAGTCGAAAGGAGGTTGACTAGGGAAAAACCATCACATCAACTAAAAAGTGACTAGGGTGAA
* * * * * *
93576 ACCTAAGTTGAAAAGAGATTAAAAAAGGTGGAACCATCACGTCAAGTAATAGGTGACTAGGGCAA
130 ACCTAAGTAGAAAAGAGATTAAAAAAGGTGAAACCATAACGTCAACTAAAAGGTGACTAGGACAA
* *
93641 TATC
195 AACC
* *
93645 TAAGTCGA-AAGGAGGTTGACTAGGGTGAAACCATCACATCAAGTAAAAGGTGACTAGGGCAAAA
1 TAAGTCGAGAA-GAGGTTAACTAGGGTGAAACCATCACATCAACTAAAAGGTGACTAGGGCAAAA
* * * *
93709 CCTAAGTCGAAAGGATGTTGACTAGGGCAAAACCATCACGTCAACTAAA
65 CATAAGTCGAAAGGAGGTTGACTAGGGAAAAACCATCACATCAACTAAA
93758 GGTTGACCAG
Statistics
Matches: 253, Mismatches: 51, Indels: 14
0.80 0.16 0.04
Matches are distributed among these distances:
197 5 0.02
198 241 0.95
199 7 0.03
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.19
Consensus pattern (198 bp):
TAAGTCGAGAAGAGGTTAACTAGGGTGAAACCATCACATCAACTAAAAGGTGACTAGGGCAAAAC
ATAAGTCGAAAGGAGGTTGACTAGGGAAAAACCATCACATCAACTAAAAAGTGACTAGGGTGAAA
CCTAAGTAGAAAAGAGATTAAAAAAGGTGAAACCATAACGTCAACTAAAAGGTGACTAGGACAAA
ACC
Found at i:93710 original size:34 final size:34
Alignment explanation
Indices: 93661--93810 Score: 123
Period size: 34 Copynumber: 4.5 Consensus size: 34
93651 GAAAGGAGGT
** *
93661 TGACTAGGGTGAAACCATCACATCAAGTAAAAGG
1 TGACTAGGGCAAAACCATCACATCAACTAAAAGG
* * *
93695 TGACTAGGGCAAAACC-T-A-AGTCGAA--AGGATGT
1 TGACTAGGGCAAAACCATCACA-TC-AACTA-AAAGG
*
93727 TGACTAGGGCAAAACCATCACGTCAACT-AAAGG
1 TGACTAGGGCAAAACCATCACATCAACTAAAAGG
* * *
93760 TTGACCAGGGCAGAACCATCACATCAACTAATAGG
1 -TGACTAGGGCAAAACCATCACATCAACTAAAAGG
*
93795 CGACTAGGGCAAAACC
1 TGACTAGGGCAAAACC
93811 TAAGTTGAAA
Statistics
Matches: 90, Mismatches: 16, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
31 2 0.02
32 21 0.23
33 8 0.09
34 55 0.61
35 4 0.04
ACGTcount: A:0.39, C:0.22, G:0.23, T:0.16
Consensus pattern (34 bp):
TGACTAGGGCAAAACCATCACATCAACTAAAAGG
Found at i:93802 original size:166 final size:166
Alignment explanation
Indices: 93606--93922 Score: 465
Period size: 166 Copynumber: 1.9 Consensus size: 166
93596 AAAAAAGGTG
* * * * * * * *
93606 GAACCATCACGTCAAGTAATAGGTGACTAGGGCAATATCTAAGTCGAAAGGAGGTTGACTAGGGT
1 GAACCATCACATCAACTAATAGGCGACTAGGGCAAAACCTAAGTCGAAAAGAGGTTGACTAAGAT
* * *
93671 GAAACCATCACATCAAGTAAAAGGTGACTAGGGCAAAACCTAAGTCGAAAGGATG-TTGACTAGG
66 GAAACCATCACATCAACTAAAAGGTGACTAAGGCAAAACCTAAGTCGAAA-GACGATTGACTAGG
93735 GCAAAACCATCACGTCAACTAAAGGTTGACCAGGGCA
130 GCAAAACCATCACGTCAACTAAAGGTTGACCAGGGCA
* *
93772 GAACCATCACATCAACTAATAGGCGACTAGGGCAAAACCTAAGTTGAAAAGAGGTTGATTAAGAT
1 GAACCATCACATCAACTAATAGGCGACTAGGGCAAAACCTAAGTCGAAAAGAGGTTGACTAAGAT
* *
93837 GAAACCATCCCATCAACTAATAGGTGACTAAGGCAAAACCTAAGTCGAAAGACGATTGACTAGGG
66 GAAACCATCACATCAACTAAAAGGTGACTAAGGCAAAACCTAAGTCGAAAGACGATTGACTAGGG
**
93902 CGGAACCATCACGTCAACTAA
131 CAAAACCATCACGTCAACTAA
93923 TAAGTGACTA
Statistics
Matches: 133, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
165 3 0.02
166 130 0.98
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (166 bp):
GAACCATCACATCAACTAATAGGCGACTAGGGCAAAACCTAAGTCGAAAAGAGGTTGACTAAGAT
GAAACCATCACATCAACTAAAAGGTGACTAAGGCAAAACCTAAGTCGAAAGACGATTGACTAGGG
CAAAACCATCACGTCAACTAAAGGTTGACCAGGGCA
Found at i:93842 original size:100 final size:101
Alignment explanation
Indices: 93673--93861 Score: 254
Period size: 100 Copynumber: 1.9 Consensus size: 101
93663 ACTAGGGTGA
* * * * * *
93673 AACCATCACATCAAGTAAAAGGTGACTAGGGCAAAACCTAAGTCGAAAGGATGTTGACTAGGGCA
1 AACCATCACATCAACTAAAAGGCGACTAGGGCAAAACCTAAGTCGAAAAGAGGTTGACTAAGACA
*
93738 AAACCATCACGTCAACTAA-AGGTTGACCAGGGCAG
66 AAACCATCACATCAACTAATAGGTTGACCAGGGCAG
* * * **
93773 AACCATCACATCAACTAATAGGCGACTAGGGCAAAACCTAAGTTGAAAAGAGGTTGATTAAGATG
1 AACCATCACATCAACTAAAAGGCGACTAGGGCAAAACCTAAGTCGAAAAGAGGTTGACTAAGACA
*
93838 AAACCATCCCATCAACTAATAGGT
66 AAACCATCACATCAACTAATAGGT
93862 GACTAAGGCA
Statistics
Matches: 75, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
100 71 0.95
101 4 0.05
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.18
Consensus pattern (101 bp):
AACCATCACATCAACTAAAAGGCGACTAGGGCAAAACCTAAGTCGAAAAGAGGTTGACTAAGACA
AAACCATCACATCAACTAATAGGTTGACCAGGGCAG
Found at i:93851 original size:66 final size:66
Alignment explanation
Indices: 93773--94335 Score: 496
Period size: 66 Copynumber: 8.5 Consensus size: 66
93763 ACCAGGGCAG
* * * **
93773 AACCATCACATCAACTAATAGGCGACTAGGGCAAAACCTAAGTTGAAAAGAGGTTGATTAAGATG
1 AACCATCACGTCAACTAATAGGTGACTAGGGCAAAACCTAAGTCGAAAAGAGGTTGACCAAGATG
93838 A
66 A
* * * * * * **
93839 AACCATCCCATCAACTAATAGGTGACTAAGGCAAAACCTAAGTCG-AAAGACGATTGACTAGGGC
1 AACCATCACGTCAACTAATAGGTGACTAGGGCAAAACCTAAGTCGAAAAGA-GGTTGACCAAGAT
*
93903 GG
65 GA
* *** * * * ** *
93905 AACCATCACGTCAACTAATAAGTGACTACAACGGAAACATAAGTTGAAAAGAGACTGACC-AGGT
1 AACCATCACGTCAACTAATAGGTGACTAGGGC-AAAACCTAAGTCGAAAAGAGGTTGACCAAGAT
93969 -A
65 GA
* **** * *
93970 GAACCATCACGTCAACTAATAAGTGACTAGATTGAAACCTAAGTCGAAAGGAGGTTGA-CTAGAG
1 -AACCATCACGTCAACTAATAGGTGACTAGGGCAAAACCTAAGTCGAAAAGAGGTTGACCAAGA-
*
94034 TGG
64 TGA
** * * *
94037 AACCATCATATCAACTAATAGGTGACTCAGGTG--AAACCTAACTCAAAAAAAGGTTGACCAAGA
1 AACCATCACGTCAACTAATAGGTGACT-AGG-GCAAAACCTAAGTCGAAAAGAGGTTGACCAAGA
94100 TGA
64 TGA
** * * * * *
94103 AACCATCACGTCAACTAATAGGTGACTAGGGTGAAACCCAAGTCGAAACGAGGTTGACCAGGGTA
1 AACCATCACGTCAACTAATAGGTGACTAGGGCAAAACCTAAGTCGAAAAGAGGTTGACCAAGATG
94168 A
66 A
* ** * *
94169 AACCATCACGTCAACTAATAGGGGACTA-AACGAAACCTAAGTCG-AAAGAAGGTTGACCAAGGT
1 AACCATCACGTCAACTAATAGGTGACTAGGGCAAAACCTAAGTCGAAAAG-AGGTTGACCAAGAT
*
94232 AA
65 GA
* * *
94234 AACCATCACGTCAACTAATATGTGACTAGGGCAAAACCTAAGTCGAAAGGAGGTTGA-CTAGAGT
1 AACCATCACGTCAACTAATAGGTGACTAGGGCAAAACCTAAGTCGAAAAGAGGTTGACCAAGA-T
94298 GA
65 GA
* *
94300 AACCATCATGTCAACTAATAGGAGACTAGGGCAAAA
1 AACCATCACGTCAACTAATAGGTGACTAGGGCAAAA
94336 TCATCACGTC
Statistics
Matches: 407, Mismatches: 74, Indels: 32
0.79 0.14 0.06
Matches are distributed among these distances:
64 5 0.01
65 86 0.21
66 286 0.70
67 25 0.06
68 5 0.01
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.18
Consensus pattern (66 bp):
AACCATCACGTCAACTAATAGGTGACTAGGGCAAAACCTAAGTCGAAAAGAGGTTGACCAAGATG
A
Found at i:93919 original size:132 final size:132
Alignment explanation
Indices: 93757--94335 Score: 573
Period size: 132 Copynumber: 4.4 Consensus size: 132
93747 CGTCAACTAA
* ** * * *
93757 AGGTTGACCAGGGCAGAACCATCACATCAACTAATAGGCGACTAGGGCAAAACCTAAGTTGAAAA
1 AGGTTGACTAGGGTGGAACCATCACGTCAACTAATAGGTGACTAGGGCAAAACCTAAGTCGAAAA
** * *
93822 GAGGTTGATTAAGATGAAACCATCCCATCAACTAATAGGTGACTAAGGCAAAACCTAAGTCGAAA
66 GAGGTTGACCAAGATGAAACCATCACGTCAACTAATAGGTGACTAAGGCAAAACCTAAGTCGAAA
93887 -G
131 GG
* * * *** * * *
93888 ACGATTGACTAGGGCGGAACCATCACGTCAACTAATAAGTGACTACAACGGAAACATAAGTTGAA
1 A-GGTTGACTAGGGTGGAACCATCACGTCAACTAATAGGTGACTAGGGC-AAAACCTAAGTCGAA
** * * *
93953 AAGAGACTGACC-AGGT-AGAACCATCACGTCAACTAATAAGTGACTAGATTG--AAACCTAAGT
64 AAGAGGTTGACCAAGATGA-AACCATCACGTCAACTAATAGGTGACTA-A-GGCAAAACCTAAGT
94014 CGAAAGG
126 CGAAAGG
* ** * *
94021 AGGTTGACTAGAGTGGAACCATCATATCAACTAATAGGTGACTCAGGTG--AAACCTAACTCAAA
1 AGGTTGACTAGGGTGGAACCATCACGTCAACTAATAGGTGACT-AGG-GCAAAACCTAAGTCGAA
* * ** *
94084 AAAAGGTTGACCAAGATGAAACCATCACGTCAACTAATAGGTGACTAGGGTGAAACCCAAGTCGA
64 AAGAGGTTGACCAAGATGAAACCATCACGTCAACTAATAGGTGACTAAGGCAAAACCTAAGTCGA
*
94149 AACG
129 AAGG
* ** * ** *
94153 AGGTTGACCAGGGTAAAACCATCACGTCAACTAATAGGGGACTA-AACGAAACCTAAGTCG-AAA
1 AGGTTGACTAGGGTGGAACCATCACGTCAACTAATAGGTGACTAGGGCAAAACCTAAGTCGAAAA
* * * *
94216 GAAGGTTGACCAAGGTAAAACCATCACGTCAACTAATATGTGACTAGGGCAAAACCTAAGTCGAA
66 G-AGGTTGACCAAGATGAAACCATCACGTCAACTAATAGGTGACTAAGGCAAAACCTAAGTCGAA
94281 AGG
130 AGG
* * * *
94284 AGGTTGACTAGAGTGAAACCATCATGTCAACTAATAGGAGACTAGGGCAAAA
1 AGGTTGACTAGGGTGGAACCATCACGTCAACTAATAGGTGACTAGGGCAAAA
94336 TCATCACGTC
Statistics
Matches: 363, Mismatches: 69, Indels: 31
0.78 0.15 0.07
Matches are distributed among these distances:
130 4 0.01
131 130 0.36
132 202 0.56
133 26 0.07
134 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.18
Consensus pattern (132 bp):
AGGTTGACTAGGGTGGAACCATCACGTCAACTAATAGGTGACTAGGGCAAAACCTAAGTCGAAAA
GAGGTTGACCAAGATGAAACCATCACGTCAACTAATAGGTGACTAAGGCAAAACCTAAGTCGAAA
GG
Found at i:93977 original size:232 final size:232
Alignment explanation
Indices: 93525--93988 Score: 540
Period size: 232 Copynumber: 2.0 Consensus size: 232
93515 AGTTGAATGG
* * **
93525 AGGTTGACTAGGGAAAAACCATCACATCAACTAAAAAGTGACTAGGGTGAAACCTAAGTTGAAAA
1 AGGTTGACCAGGGAAAAACCATCACATCAACTAAAAAGCGACTAGGGCAAAACCTAAGTTGAAAA
* * * * * * *
93590 GAGATTAAAAAAGGTGGAACCATCACGTCAAGTAATAGGTGACTAGGGCAATATCTAAGTCGAAA
66 GAGATTAAAAAAGATGAAACCATCACATCAACTAATAGGTGACTAAGGCAAAACCTAAGTCGAAA
* * * *** *
93655 GGAGGTTGACTAGGGTGAAACCATCACATCAAGTAAAAGGTGACTAGGGCAAAACCTAAGTCGAA
131 GGAGATTGACTAGGGCGAAACCATCACATCAACTAAAAGGTGACTACAACAAAACATAAGTCGAA
* * *
93720 AGGATGTTGACTAGGGCAAAACCATCACGTCAACTAA
196 AAGATGCTGACCAGGGCAAAACCATCACGTCAACTAA
* * * *
93757 AGGTTGACCAGGGCAGAACCATCACATCAACTAATAGGCGACTAGGGCAAAACCTAAGTTGAAAA
1 AGGTTGACCAGGGAAAAACCATCACATCAACTAAAAAGCGACTAGGGCAAAACCTAAGTTGAAAA
* * ** *
93822 GAGGTTGATTAAGATGAAACCATCCCATCAACTAATAGGTGACTAAGGCAAAACCTAAGTCGAAA
66 GAGATTAAAAAAGATGAAACCATCACATCAACTAATAGGTGACTAAGGCAAAACCTAAGTCGAAA
* * * *
93887 -GACGATTGACTAGGGCGGAACCATCACGTCAACTAATAA-GTGACTACAACGGAAACATAAGTT
131 GGA-GATTGACTAGGGCGAAACCATCACATCAACTAA-AAGGTGACTACAAC-AAAACATAAGTC
* *
93950 GAAAAGA-GACTGACCA-GGTAGAACCATCACGTCAACTAA
193 GAAAAGATG-CTGACCAGGGCAAAACCATCACGTCAACTAA
93989 TAAGTGACTA
Statistics
Matches: 192, Mismatches: 36, Indels: 8
0.81 0.15 0.03
Matches are distributed among these distances:
231 2 0.01
232 168 0.88
233 22 0.11
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.18
Consensus pattern (232 bp):
AGGTTGACCAGGGAAAAACCATCACATCAACTAAAAAGCGACTAGGGCAAAACCTAAGTTGAAAA
GAGATTAAAAAAGATGAAACCATCACATCAACTAATAGGTGACTAAGGCAAAACCTAAGTCGAAA
GGAGATTGACTAGGGCGAAACCATCACATCAACTAAAAGGTGACTACAACAAAACATAAGTCGAA
AAGATGCTGACCAGGGCAAAACCATCACGTCAACTAA
Found at i:94043 original size:198 final size:196
Alignment explanation
Indices: 93761--94319 Score: 611
Period size: 198 Copynumber: 2.8 Consensus size: 196
93751 AACTAAAGGT
* * ** * * *
93761 TGACCAGGGCAGAACCATCACATCAACTAATAGGCGACTAGGGCAAAACCTAAGTTGAAAAGAGG
1 TGACCAGGGTAGAACCATCACGTCAACTAATAGGCGACTAGAACGAAACCTAAGTCGAAAGGAGG
* *
93826 TTGATTAAGATGAAACCATCCCATCAACTAATAGGTGACTAAGGCAAAACCTAAGTCGAAAGACG
66 TTGACTAAG-TGAAACCATCACATCAACTAATAGGTGACTAAGGCAAAACCTAAGTCGAAAGA-G
* * * * *
93891 ATTGACTAGGGCGGAACCATCACGTCAACTAATAAGTGACTACAACG-GAAACATAAGTTGAAAA
129 GTTGACTAGGGTGAAACCATCACGTCAACTAATAAGTGACT--AACGTGAAACACAAGTCGAAAA
93955 GAGAC
192 GAGAC
* * **
93960 TGACCA-GGTAGAACCATCACGTCAACTAATAAGTGACTAGATTGAAACCTAAGTCGAAAGGAGG
1 TGACCAGGGTAGAACCATCACGTCAACTAATAGGCGACTAGAACGAAACCTAAGTCGAAAGGAGG
* * * ** * * *
94024 TTGACTAGAGTGGAACCATCATATCAACTAATAGGTGACTCAGGTGAAACCTAACTCAAAAAAAG
66 TTGACTA-AGTGAAACCATCACATCAACTAATAGGTGACTAAGGCAAAACCTAAGTC-GAAAGAG
* * * * ** * *
94089 GTTGACCAAGATGAAACCATCACGTCAACTAATAGGTGACTAGGGTGAAACCCAAGTCGAAACGA
129 GTTGACTAGGGTGAAACCATCACGTCAACTAATAAGTGACTAACGTGAAACACAAGTCGAAAAGA
**
94154 GGT
194 GAC
* * *
94157 TGACCAGGGTAAAACCATCACGTCAACTAATAGGGGACTA-AACGAAACCTAAGTCGAAAGAAGG
1 TGACCAGGGTAGAACCATCACGTCAACTAATAGGCGACTAGAACGAAACCTAAGTCGAAAGGAGG
* * * * *
94221 TTGACCAAGGTAAAACCATCACGTCAACTAATATGTGACTAGGGCAAAACCTAAGTCGAAAGGAG
66 TTGACTAA-GTGAAACCATCACATCAACTAATAGGTGACTAAGGCAAAACCTAAGTCGAAA-GAG
* *
94286 GTTGACTAGAGTGAAACCATCATGTCAACTAATA
129 GTTGACTAGGGTGAAACCATCACGTCAACTAATA
94320 GGAGACTAGG
Statistics
Matches: 295, Mismatches: 59, Indels: 14
0.80 0.16 0.04
Matches are distributed among these distances:
196 6 0.02
197 118 0.40
198 159 0.54
199 12 0.04
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (196 bp):
TGACCAGGGTAGAACCATCACGTCAACTAATAGGCGACTAGAACGAAACCTAAGTCGAAAGGAGG
TTGACTAAGTGAAACCATCACATCAACTAATAGGTGACTAAGGCAAAACCTAAGTCGAAAGAGGT
TGACTAGGGTGAAACCATCACGTCAACTAATAAGTGACTAACGTGAAACACAAGTCGAAAAGAGA
C
Found at i:94327 original size:34 final size:34
Alignment explanation
Indices: 94289--94368 Score: 88
Period size: 34 Copynumber: 2.4 Consensus size: 34
94279 AAAGGAGGTT
** * *
94289 GACTAGAGTGAAACCATCATGTCAACTAATAGGA
1 GACTAGAGCAAAACCATCACGTCAACTAATAAGA
* * *
94323 GACTAGGGCAAAATCATCACGTCAACTAATAAGT
1 GACTAGAGCAAAACCATCACGTCAACTAATAAGA
*
94357 GACTAGGGCAAA
1 GACTAGAGCAAA
94369 GCCAAAGTCG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.19
Consensus pattern (34 bp):
GACTAGAGCAAAACCATCACGTCAACTAATAAGA
Found at i:94406 original size:166 final size:165
Alignment explanation
Indices: 94162--94502 Score: 434
Period size: 166 Copynumber: 2.1 Consensus size: 165
94152 GAGGTTGACC
* * * *
94162 AGGGTAAAACCATCACGTCAACTAATAGGGGACTAAACGAAACCTAAGTCGAAAGAAGGTTGACC
1 AGGGCAAAATCATCACGTCAACTAATAAGGGACTAAACGAAACCAAAGTCGAAAGAAGGTTGACC
* *
94227 AAGGTAAAACCATCACGTCAACTAATATGTGACTAGGGCAAAACCTAAGTCGAAAGGAGGTTGAC
66 AAGGTAAAACCATCACGTCAACTAATAGGCGACTAGGGCAAAACCTAAGTCGAAAGGAGGTTGAC
** *
94292 TAGAGTGAAACCATCATGTCAACTAATAG-GAGACT
131 TAGAGCAAAACCATCACGTCAACTAATAGAG-GACT
* ** *
94327 AGGGCAAAATCATCACGTCAACTAATAAGTGACT-AGGGCAAAGCCAAAGTCGAAAGGAGGTTGA
1 AGGGCAAAATCATCACGTCAACTAATAAGGGACTAAACG-AAA-CCAAAGTCGAAAGAAGGTTGA
** * * ** * *
94391 TTAAGGTAGAACCATCACGTTAACTAATAGGCGACTAGGGTGAAACCTAAGTTGAAAGGAGTTTG
64 CCAAGGTAAAACCATCACGTCAACTAATAGGCGACTAGGGCAAAACCTAAGTCGAAAGGAGGTTG
* *
94456 ACTAGGGCAAAATCATCACGTCAACTAATAGAGGACT
129 ACTAGAGCAAAACCATCACGTCAACTAATAGAGGACT
94493 AGGGCAAAAT
1 AGGGCAAAAT
94503 GTAAGTCAAA
Statistics
Matches: 150, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
164 2 0.01
165 33 0.22
166 114 0.76
167 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (165 bp):
AGGGCAAAATCATCACGTCAACTAATAAGGGACTAAACGAAACCAAAGTCGAAAGAAGGTTGACC
AAGGTAAAACCATCACGTCAACTAATAGGCGACTAGGGCAAAACCTAAGTCGAAAGGAGGTTGAC
TAGAGCAAAACCATCACGTCAACTAATAGAGGACT
Found at i:94416 original size:100 final size:100
Alignment explanation
Indices: 94232--94430 Score: 294
Period size: 100 Copynumber: 2.0 Consensus size: 100
94222 TGACCAAGGT
* *
94232 AAAACCATCACGTCAACTAATATGTGACTAGGGCAAAACCTAAGTCGAAAGGAGGTTGACTAGAG
1 AAAACCATCACGTCAACTAATAAGTGACTAGGGCAAAACCAAAGTCGAAAGGAGGTTGACTAGAG
*
94297 TGAAACCATCATGTCAACTAATAGGAGACTAGGGC
66 TGAAACCATCACGTCAACTAATAGGAGACTAGGGC
* * *
94332 AAAATCATCACGTCAACTAATAAGTGACTAGGGCAAAGCCAAAGTCGAAAGGAGGTTGATTA-AG
1 AAAACCATCACGTCAACTAATAAGTGACTAGGGCAAAACCAAAGTCGAAAGGAGGTTGACTAGAG
* *
94396 -GTAGAACCATCACGTTAACTAATAGGCGACTAGGG
66 TG-A-AACCATCACGTCAACTAATAGGAGACTAGGG
94431 TGAAACCTAA
Statistics
Matches: 89, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
98 1 0.01
99 3 0.03
100 85 0.96
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (100 bp):
AAAACCATCACGTCAACTAATAAGTGACTAGGGCAAAACCAAAGTCGAAAGGAGGTTGACTAGAG
TGAAACCATCACGTCAACTAATAGGAGACTAGGGC
Found at i:94418 original size:66 final size:64
Alignment explanation
Indices: 94323--94537 Score: 205
Period size: 66 Copynumber: 3.3 Consensus size: 64
94313 ACTAATAGGA
* *
94323 GACTAGGGCAAAATCATCACGTCAACTAATAAGTGACTAGGGCAAAGCCAAAGTCGAAAGGAGGT
1 GACTAAGGCAAAACCATCACGTCAACTAATAAG-GACTAGGGCAAA-CCAAAGTCGAAAGGAGGT
94388 T
64 T
* * * * * * * * *
94389 GATTAAGGTAGAACCATCACGTTAACTAATAGGCGACTAGGGTGAAACCTAAGTTGAAAGGAGTT
1 GACTAAGGCAAAACCATCACGTCAACTAATAAG-GACTAGGG-CAAACCAAAGTCGAAAGGAGGT
94454 T
64 T
* * *** *
94455 GACTAGGGCAAAATCATCACGTCAACTAATAGAGGACTAGGGCAAAATGTAAGTCAAAAGGAGGT
1 GACTAAGGCAAAACCATCACGTCAACTAATA-AGGACTAGGGC-AAACCAAAGTCGAAAGGAGGT
94520 T
64 T
* *
94521 GACCAAGGCGAAACCAT
1 GACTAAGGCAAAACCAT
94538 TACATGACTA
Statistics
Matches: 117, Mismatches: 29, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
66 113 0.97
67 4 0.03
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.19
Consensus pattern (64 bp):
GACTAAGGCAAAACCATCACGTCAACTAATAAGGACTAGGGCAAACCAAAGTCGAAAGGAGGTT
Found at i:94722 original size:185 final size:186
Alignment explanation
Indices: 94379--94722 Score: 399
Period size: 185 Copynumber: 1.9 Consensus size: 186
94369 GCCAAAGTCG
** * * * ** * *
94379 AAAGGAGGTTGATTAAGGTAGAACCATCACGTTAACTAATAGGCGACTAGGGTGAAACCTAAGTT
1 AAAGGAGGTTGACCAAGGTAGAACCATCACATCAACTAAGAGGCGACTAACGCGAAACCTAAGTC
* * * ** *
94444 GAAAGGAGTTTGACTAGGGCAAAATCATCACGTCAACTAATAGAGGACTAGGGCAAAATGTAAGT
66 GAAAGGAGGTTCACTAGGGCAAAACCATCACGTCAACTAATAGAGGACTAGGGCAAAACCTAACT
* * **
94509 CAAAAGGAGGTTGACCAAGGCGAAACCATTACATGACTAAGACGAAGCCTAAGCTA
131 CAAAAGAACGTTGACCAAGGAAAAACCATTACATGACTAAGACGAAGCCTAAGCTA
*
94565 AAAGGAGGTTGACCAAGGT-GAAACCATCACATCAACTAAGAGGTGACTAACGCGAAACC-AAGT
1 AAAGGAGGTTGACCAAGGTAG-AACCATCACATCAACTAAGAGGCGACTAACGCGAAACCTAAGT
* * *
94628 CGAAAGGAGGTTCACTAGGGCGAAACCATCACGTCTAC-AGATAGGGGACTAGGGCAAAACCTAA
65 CGAAAGGAGGTTCACTAGGGCAAAACCATCACGTCAACTA-ATAGAGGACTAGGGCAAAACCT-A
* * *
94692 ACT-AAAATAACGTTGACTAGGGAAAAACCAT
128 ACTCAAAAGAACGTTGACCAAGGAAAAACCAT
94723 CATGTCAACT
Statistics
Matches: 129, Mismatches: 26, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
184 1 0.01
185 77 0.60
186 51 0.40
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (186 bp):
AAAGGAGGTTGACCAAGGTAGAACCATCACATCAACTAAGAGGCGACTAACGCGAAACCTAAGTC
GAAAGGAGGTTCACTAGGGCAAAACCATCACGTCAACTAATAGAGGACTAGGGCAAAACCTAACT
CAAAAGAACGTTGACCAAGGAAAAACCATTACATGACTAAGACGAAGCCTAAGCTA
Found at i:95009 original size:21 final size:21
Alignment explanation
Indices: 94985--95041 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
94975 AAAAAATTTA
94985 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
95006 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
95027 AATGTATCGATACAT
1 AATGTATCGATACAT
95042 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:95121 original size:19 final size:19
Alignment explanation
Indices: 95097--95164 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
95087 AATTCAACAA
95097 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
95116 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
95131 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
95148 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
95165 TTAGCTATTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:95136 original size:13 final size:13
Alignment explanation
Indices: 95118--95142 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
95108 ACATAAGTTT
95118 TGTATCGATACAA
1 TGTATCGATACAA
95131 TGTATCGATACA
1 TGTATCGATACA
95143 TAAGTATTGT
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:95140 original size:32 final size:32
Alignment explanation
Indices: 95099--95161 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
95089 TTCAACAATT
*
95099 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
95131 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
95162 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:95222 original size:13 final size:13
Alignment explanation
Indices: 95204--95229 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
95194 CATTTTTCTG
95204 TGTATCGATACAT
1 TGTATCGATACAT
95217 TGTATCGATACAT
1 TGTATCGATACAT
95230 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:95226 original size:33 final size:33
Alignment explanation
Indices: 95184--95250 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
95174 GCCAAGGAAA
***
95184 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
95217 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
95250 T
1 T
95251 TGGAAATTTT
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:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:97763 original size:28 final size:29
Alignment explanation
Indices: 97694--97766 Score: 91
Period size: 27 Copynumber: 2.6 Consensus size: 29
97684 CTTCACAATC
*
97694 GGGGACACTCCAACCCCGTTAATCATCGA
1 GGGGATACTCCAACCCCGTTAATCATCGA
*
97723 --GGATACTCCAACCCCGTT-AT-TTCTGA
1 GGGGATACTCCAACCCCGTTAATCATC-GA
97749 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
97767 ACTTTATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
25 2 0.05
26 4 0.10
27 17 0.44
28 16 0.41
ACGTcount: A:0.25, C:0.34, G:0.21, T:0.21
Consensus pattern (29 bp):
GGGGATACTCCAACCCCGTTAATCATCGA
Found at i:97811 original size:51 final size:51
Alignment explanation
Indices: 97584--97919 Score: 198
Period size: 51 Copynumber: 6.4 Consensus size: 51
97574 AATTCTCCAC
* * * * * **
97584 AATCGAGGATATTCCAACTCCGATTTTACTTTCAAAACATTAA-TTTTCTAT
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTC-AT
* * * *
97635 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAAACACCAATTTCTTCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTTC---AAAATACCAATTT-TTCAT
* * ** **
97690 AATCGGGGACACTCCAACCCCG--TTAATCATCGAGGATACTCCAACCCCGTTATTTC-T
1 AATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAATA--CCAA-----TT-TTTCAT
* * * *
97747 GA--GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCAT
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCAT
* * * * *
97796 AATCGGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTT
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-AT
** * *
97849 AATCGGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCAT
*
97901 AATCGAGGATACTCCAACC
1 AATCGGGGATACTCCAACC
97920 TCGTTATTTC
Statistics
Matches: 216, Mismatches: 48, Indels: 41
0.71 0.16 0.13
Matches are distributed among these distances:
48 4 0.02
49 4 0.02
51 68 0.31
52 18 0.08
53 41 0.19
54 21 0.10
55 40 0.19
56 7 0.03
57 7 0.03
58 5 0.02
59 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (51 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCAT
Found at i:97938 original size:28 final size:28
Alignment explanation
Indices: 97902--97983 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
97892 ATTTTTCACA
*
97902 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
97930 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
97958 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
97984 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Done.