Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 83 of 318
Found at i:28237963 original size:6 final size:6
Alignment explanation
Indices: 28237949--28237982 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
28237939 ACACTATAGG
* *
28237949 GTAACA GTAATA GTAATA GTAATA GTAACA GTAA
1 GTAATA GTAATA GTAATA GTAATA GTAATA GTAA
28237983 CAATCATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.26
Consensus pattern (6 bp):
GTAATA
Found at i:28237969 original size:12 final size:12
Alignment explanation
Indices: 28237949--28237982 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
28237939 ACACTATAGG
28237949 GTAACAGTAATA
1 GTAACAGTAATA
*
28237961 GTAATAGTAATA
1 GTAACAGTAATA
28237973 GTAACAGTAA
1 GTAACAGTAA
28237983 CAATCATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.26
Consensus pattern (12 bp):
GTAACAGTAATA
Found at i:28238864 original size:20 final size:18
Alignment explanation
Indices: 28238826--28238869 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 18
28238816 AAAACCTAAT
28238826 TTTCCC-TTTTCTTTTTC
1 TTTCCCTTTTTCTTTTTC
28238843 TTTCCCTTTTTCATTCTTTC
1 TTTCCCTTTTTC-TT-TTTC
28238863 TTTCCCT
1 TTTCCCT
28238870 GCTAATCGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.25
18 5 0.21
19 2 0.08
20 11 0.46
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTCCCTTTTTCTTTTTC
Found at i:28246434 original size:4 final size:4
Alignment explanation
Indices: 28246425--28246452 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
28246415 AGCCATTTAG
28246425 CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA
28246453 GAAACAGCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:28251114 original size:25 final size:26
Alignment explanation
Indices: 28251079--28251145 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 26
28251069 TTTATATTAA
28251079 AATAAATTTAAAAATATAATATATT-G
1 AATAAA-TTAAAAATATAATATATTCG
* *
28251105 AA-AACATT-AAAATA-AATATTTTCT
1 AATAA-ATTAAAAATATAATATATTCG
28251129 AATAAATTAAAAATATA
1 AATAAATTAAAAATATA
28251146 TTAAAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
23 7 0.21
24 11 0.32
25 12 0.35
26 4 0.12
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (26 bp):
AATAAATTAAAAATATAATATATTCG
Found at i:28251283 original size:22 final size:22
Alignment explanation
Indices: 28251235--28251285 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
28251225 ATAACAAAAT
*
28251235 AATAACAACAAAATAGTAATAA
1 AATAACAACAAAATAGTAACAA
* * * *
28251257 TATAATAACAAAATGGTAGCAA
1 AATAACAACAAAATAGTAACAA
28251279 AATAACA
1 AATAACA
28251286 TCAGTAGTGA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.63, C:0.10, G:0.08, T:0.20
Consensus pattern (22 bp):
AATAACAACAAAATAGTAACAA
Found at i:28251510 original size:3 final size:3
Alignment explanation
Indices: 28251502--28251531 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
28251492 AGTTAAACTT
28251502 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28251532 AGGATAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28252183 original size:37 final size:37
Alignment explanation
Indices: 28252128--28252201 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
28252118 ATAAAAGGAA
28252128 AACACATCCAGATTGATATAAGAGGATACAAACATAT
1 AACACATCCAGATTGATATAAGAGGATACAAACATAT
*
28252165 AACATATCCAGATTGATATAAGAGGATACAAACATAT
1 AACACATCCAGATTGATATAAGAGGATACAAACATAT
28252202 GCAGATTCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.23
Consensus pattern (37 bp):
AACACATCCAGATTGATATAAGAGGATACAAACATAT
Found at i:28256086 original size:21 final size:20
Alignment explanation
Indices: 28256044--28256087 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
28256034 AAACTTATTT
*
28256044 TTACATACCAAATATTAAAA
1 TTACATACCAAAAATTAAAA
* *
28256064 TTACATCCCAAAAAATTATAA
1 TTACATACC-AAAAATTAAAA
28256085 TTA
1 TTA
28256088 TTAAAAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (20 bp):
TTACATACCAAAAATTAAAA
Found at i:28257383 original size:38 final size:39
Alignment explanation
Indices: 28257318--28257417 Score: 157
Period size: 38 Copynumber: 2.5 Consensus size: 39
28257308 CTTAATACTC
*
28257318 TTATTTTCATTTTTTTCTTTTATATTATTTATCTCCCTCT
1 TTATTTTC-TTTTTTTCTTTTACATTATTTATCTCCCTCT
28257358 TTA-TTTCTTTTTTTCTTTTACATTATTTATCTCCCTCT
1 TTATTTTCTTTTTTTCTTTTACATTATTTATCTCCCTCT
28257396 TTATTTTTCTATTTTTTCTTTT
1 TTA-TTTTCT-TTTTTTCTTTT
28257418 TTCTTCCTTT
Statistics
Matches: 56, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
38 33 0.59
39 4 0.07
40 8 0.14
41 11 0.20
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (39 bp):
TTATTTTCTTTTTTTCTTTTACATTATTTATCTCCCTCT
Found at i:28258642 original size:20 final size:21
Alignment explanation
Indices: 28258603--28258642 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28258593 AAGAGAATGT
*
28258603 ATTTTTGTAATGCAATAATTG
1 ATTTTTGTAATGCAACAATTG
*
28258624 ATTTTTGTATTGC-ACAATT
1 ATTTTTGTAATGCAACAATT
28258643 AGGCATTGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.50
Consensus pattern (21 bp):
ATTTTTGTAATGCAACAATTG
Found at i:28258843 original size:5 final size:5
Alignment explanation
Indices: 28258833--28258860 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
28258823 ACGAACCTCC
28258833 CCCTT CCCTT CCCTT CCCTT CCCTT CCC
1 CCCTT CCCTT CCCTT CCCTT CCCTT CCC
28258861 ACCAATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (5 bp):
CCCTT
Found at i:28268629 original size:20 final size:20
Alignment explanation
Indices: 28268604--28268644 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
28268594 AAGAAGAAAG
*
28268604 TAAGAGAAATGCTACAACTC
1 TAAGAGAAATGCTAAAACTC
28268624 TAAGAGAAATGCTAAAACTC
1 TAAGAGAAATGCTAAAACTC
28268644 T
1 T
28268645 CCACCATGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.46, C:0.17, G:0.15, T:0.22
Consensus pattern (20 bp):
TAAGAGAAATGCTAAAACTC
Found at i:28271908 original size:16 final size:17
Alignment explanation
Indices: 28271875--28271909 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
28271865 TCATGTATTT
*
28271875 TTTTATTTTTTTATAAA
1 TTTTAGTTTTTTATAAA
28271892 TTTTAGTTTTTTA-AAA
1 TTTTAGTTTTTTATAAA
28271908 TT
1 TT
28271910 AGGACTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTTAGTTTTTTATAAA
Found at i:28277569 original size:17 final size:17
Alignment explanation
Indices: 28277535--28277569 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
28277525 AACTTGAGCC
* *
28277535 TTTATTTATTTATTCAT
1 TTTATTTATGTATCCAT
28277552 TTTATTTATGTATCCAT
1 TTTATTTATGTATCCAT
28277569 T
1 T
28277570 ATCGGAATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.09, G:0.03, T:0.66
Consensus pattern (17 bp):
TTTATTTATGTATCCAT
Found at i:28279750 original size:15 final size:15
Alignment explanation
Indices: 28279718--28279751 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
28279708 TTTATTTTTG
* *
28279718 TTATTTTTGCTTGTA
1 TTATTTTTGCTCGCA
28279733 TTATTTTTGCTCGCA
1 TTATTTTTGCTCGCA
28279748 TTAT
1 TTAT
28279752 CGTAATTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.12, T:0.62
Consensus pattern (15 bp):
TTATTTTTGCTCGCA
Found at i:28280865 original size:16 final size:17
Alignment explanation
Indices: 28280834--28280866 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28280824 TTCATAAGTA
28280834 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
28280851 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
28280867 ACTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:28281418 original size:46 final size:46
Alignment explanation
Indices: 28281147--28281420 Score: 379
Period size: 46 Copynumber: 6.0 Consensus size: 46
28281137 TTATCTTTGA
* * * * * * *
28281147 CATGATGCCATAGTGTCTTTCAACTACGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATAT
* * ** ***
28281193 CATGCTGCCATGGTATCTTTCAACCATTGTCTTATTCATTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
28281239 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
28281285 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
28281331 CATGTTGTCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
28281377 CACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
28281421 TTCAAAGAGC
Statistics
Matches: 207, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 4 0.02
46 203 0.98
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.40
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
Found at i:28288111 original size:9 final size:9
Alignment explanation
Indices: 28288094--28288130 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
28288084 TGAGTTTTCG
28288094 AATTCGAAT
1 AATTCGAAT
*
28288103 AACTCGAAT
1 AATTCGAAT
28288112 AATTCGAAT
1 AATTCGAAT
28288121 AATTCGAAT
1 AATTCGAAT
28288130 A
1 A
28288131 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:28299652 original size:3 final size:3
Alignment explanation
Indices: 28299644--28299677 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
28299634 TTTGTTTATG
28299644 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
28299678 AACCTAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28302743 original size:27 final size:28
Alignment explanation
Indices: 28302712--28302778 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 28
28302702 TCAAATTCCA
*
28302712 TATGTATAATTACACA-AAATCAAAATT
1 TATGTATAATTACACATAAAACAAAATT
*
28302739 TATGTATCAAATTGCACATTAAAACAAAATT
1 TATGTAT--AATTACACA-TAAAACAAAATT
28302770 TATGTATAA
1 TATGTATAA
28302779 ATTTGATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 7 0.21
29 10 0.29
31 17 0.50
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.34
Consensus pattern (28 bp):
TATGTATAATTACACATAAAACAAAATT
Found at i:28309642 original size:30 final size:29
Alignment explanation
Indices: 28309585--28309642 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
28309575 CCTTTTTACT
* *
28309585 TTTCCCTCAAAACTTTTACTCCTTCCCAC
1 TTTCCCCCAAAACTTTTACTCCCTCCCAC
*
28309614 TTTCCCCCCAAACTTTTACTCCCCTCCCA
1 TTTCCCCCAAAACTTTTACT-CCCTCCCA
28309643 TCCCAACCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.19, C:0.47, G:0.00, T:0.34
Consensus pattern (29 bp):
TTTCCCCCAAAACTTTTACTCCCTCCCAC
Found at i:28310015 original size:17 final size:17
Alignment explanation
Indices: 28309995--28310041 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
28309985 CACATTTTAT
*
28309995 ATTATTTATATTATTGA
1 ATTATTTATATTATCGA
28310012 ATTATTTAGTCA-TATCGA
1 ATTATTTA-T-ATTATCGA
28310030 A-TATTTATATTA
1 ATTATTTATATTA
28310042 AAATTGAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
15 1 0.04
16 3 0.12
17 14 0.54
18 7 0.27
19 1 0.04
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.53
Consensus pattern (17 bp):
ATTATTTATATTATCGA
Found at i:28312004 original size:49 final size:49
Alignment explanation
Indices: 28311918--28312013 Score: 120
Period size: 49 Copynumber: 2.0 Consensus size: 49
28311908 GTCGCATTGC
* * * * *
28311918 AACTTGGGTTCCCAAATGACAGTGGTTATACGGTCACGAGTTGAAGTAT
1 AACTAGGGCTCCCAAATGACAGTAGTTATACGATCACGAGTTCAAGTAT
* * *
28311967 AACTAGGGCTCCCAATTGACGGTAGTTATGCGATCACGAGTTCAAGT
1 AACTAGGGCTCCCAAATGACAGTAGTTATACGATCACGAGTTCAAGT
28312014 TTTATGCCAC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
49 39 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (49 bp):
AACTAGGGCTCCCAAATGACAGTAGTTATACGATCACGAGTTCAAGTAT
Found at i:28314046 original size:21 final size:21
Alignment explanation
Indices: 28314020--28314063 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
28314010 AATGAAAGTT
28314020 AAACAATATTTATATTGTATG
1 AAACAATATTTATATTGTATG
28314041 AAACAATATTTATATTGTATG
1 AAACAATATTTATATTGTATG
28314062 AA
1 AA
28314064 CTTGCTTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (21 bp):
AAACAATATTTATATTGTATG
Found at i:28314883 original size:15 final size:15
Alignment explanation
Indices: 28314863--28314892 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28314853 CCGTGTACCA
*
28314863 TGATCAACTTTCTAT
1 TGATCAACTTCCTAT
28314878 TGATCAACTTCCTAT
1 TGATCAACTTCCTAT
28314893 CAAATAACCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.23, G:0.07, T:0.43
Consensus pattern (15 bp):
TGATCAACTTCCTAT
Found at i:28327046 original size:158 final size:158
Alignment explanation
Indices: 28326758--28327083 Score: 510
Period size: 158 Copynumber: 2.1 Consensus size: 158
28326748 TTAGAATATA
* * * *
28326758 ATTCATTTTTATTAAGTAAAGCTAAAAATCAATATAAGATAATTTTGATGTAATTCCATAAGAGC
1 ATTCATATTTATAAAGTAAAACTAAAAATCAACATAAGATAATTTTGATGTAATTCCATAAGAGC
* * * * * * *
28326823 CTTGATATAATCCAATGCCTTTAAATATGGAGAGTGATCTTACTTGATCTTCAAGTAACCATTTT
66 CTCGATATAATCCAATACCTTTAAACATGAAAAATGATCTTACTTGATCATCAAGTAACCATTTT
28326888 TCAAGTTTTCAACCTTAACTCAATTGGT
131 TCAAGTTTTCAACCTTAACTCAATTGGT
28326916 ATTCATATTTATAAAGTAAAACTAAAAATCAACATAAGATAATTTTGATGTAATTCCATAAGAGC
1 ATTCATATTTATAAAGTAAAACTAAAAATCAACATAAGATAATTTTGATGTAATTCCATAAGAGC
* *
28326981 CTCGATATAATCCAATACCTTTGAACATGAAAAATGA-CTCTACTTGTTCATCAAGTAACCATTT
66 CTCGATATAATCCAATACCTTTAAACATGAAAAATGATCT-TACTTGATCATCAAGTAACCATTT
28327045 TTCAAGTTTTCAACCTTAACTCAATTGGT
130 TTCAAGTTTTCAACCTTAACTCAATTGGT
*
28327074 CTTCATATTT
1 ATTCATATTT
28327084 TGAGTTTTAA
Statistics
Matches: 153, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
157 2 0.01
158 151 0.99
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (158 bp):
ATTCATATTTATAAAGTAAAACTAAAAATCAACATAAGATAATTTTGATGTAATTCCATAAGAGC
CTCGATATAATCCAATACCTTTAAACATGAAAAATGATCTTACTTGATCATCAAGTAACCATTTT
TCAAGTTTTCAACCTTAACTCAATTGGT
Found at i:28328859 original size:9 final size:9
Alignment explanation
Indices: 28328845--28328871 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
28328835 CTGAAATTTG
28328845 TCACGGGCC
1 TCACGGGCC
28328854 TCACGGGCC
1 TCACGGGCC
28328863 TCACGGGCC
1 TCACGGGCC
28328872 CCATCCCCCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.44, G:0.33, T:0.11
Consensus pattern (9 bp):
TCACGGGCC
Found at i:28329771 original size:22 final size:23
Alignment explanation
Indices: 28329739--28329795 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
28329729 AGATGGGGGG
*
28329739 ATCGATGGTATTTTGAGGA-AGA
1 ATCGATTGTATTTTGAGGAGAGA
*
28329761 ATCGATTGTATTTTGGGGAGAGA
1 ATCGATTGTATTTTGAGGAGAGA
**
28329784 AGAGATTGTATT
1 ATCGATTGTATT
28329796 AGAAGGGGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 17 0.57
23 13 0.43
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.35
Consensus pattern (23 bp):
ATCGATTGTATTTTGAGGAGAGA
Found at i:28329790 original size:23 final size:22
Alignment explanation
Indices: 28329746--28329795 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
28329736 GGGATCGATG
**
28329746 GTATTTTGAGGAAGAATCGATT
1 GTATTTTGAGGAAGAAGAGATT
*
28329768 GTATTTTGGGGAGAGAAGAGATT
1 GTATTTTGAGGA-AGAAGAGATT
28329791 GTATT
1 GTATT
28329796 AGAAGGGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.30, C:0.02, G:0.32, T:0.36
Consensus pattern (22 bp):
GTATTTTGAGGAAGAAGAGATT
Found at i:28340389 original size:40 final size:40
Alignment explanation
Indices: 28340270--28340391 Score: 176
Period size: 41 Copynumber: 3.0 Consensus size: 40
28340260 GATTTCAGCA
*
28340270 TGGCATCCCTGTGTTATAGGAACAAGTTGAAGATAGCAGATT
1 TGGCAT-CCTGTGTTATAGGAACAAGTTGAAGACAGCAGA-T
28340312 TGGCATCCTGTGTTATAGGAACAAGTTGAAGACAGCAGAT
1 TGGCATCCTGTGTTATAGGAACAAGTTGAAGACAGCAGAT
*
28340352 TGGCATCCTGTGTTTATAGGAAC-AGATCGAAGA-AGCAGAT
1 TGGCATCCTGTG-TTATAGGAACAAG-TTGAAGACAGCAGAT
28340392 CGAAGAACTC
Statistics
Matches: 76, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
40 22 0.29
41 48 0.63
42 6 0.08
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (40 bp):
TGGCATCCTGTGTTATAGGAACAAGTTGAAGACAGCAGAT
Found at i:28340392 original size:13 final size:13
Alignment explanation
Indices: 28340374--28340398 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28340364 TTTATAGGAA
28340374 CAGATCGAAGAAG
1 CAGATCGAAGAAG
28340387 CAGATCGAAGAA
1 CAGATCGAAGAA
28340399 CTCAAAACTC
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:0.16, G:0.28, T:0.08
Consensus pattern (13 bp):
CAGATCGAAGAAG
Found at i:28340896 original size:23 final size:22
Alignment explanation
Indices: 28340853--28340901 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
28340843 GGATCGATGG
**
28340853 TATTTTGAGGAAGAATCGATTA
1 TATTTTGAGGAAGAAGAGATTA
* *
28340875 TATTTTGGGGAGAGAAGAGATTG
1 TATTTTGAGGA-AGAAGAGATTA
28340898 TATT
1 TATT
28340902 AGAGGGGGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.33, C:0.02, G:0.29, T:0.37
Consensus pattern (22 bp):
TATTTTGAGGAAGAAGAGATTA
Found at i:28341625 original size:39 final size:39
Alignment explanation
Indices: 28341510--28341626 Score: 189
Period size: 39 Copynumber: 3.0 Consensus size: 39
28341500 ATAAAGTATG
*
28341510 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGGAATA
1 GTTTTAATTAATAAT-AAAACAAAATAGTATGGGGGAGTA
*
28341550 GTTTTAATTAATAATAAAACAAAATAGTGTGGGGGAGTA
1 GTTTTAATTAATAATAAAACAAAATAGTATGGGGGAGTA
* *
28341589 GTTTTAATTAATAATAAAACAAAGTAGCATGGGGGAGT
1 GTTTTAATTAATAATAAAACAAAATAGTATGGGGGAGT
28341627 GGAATCAACT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
39 57 0.79
40 15 0.21
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.30
Consensus pattern (39 bp):
GTTTTAATTAATAATAAAACAAAATAGTATGGGGGAGTA
Found at i:28346384 original size:42 final size:42
Alignment explanation
Indices: 28346337--28346418 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
28346327 TAGTCTCTCC
28346337 CTGTTTTGTTTTAGGA-GGAGAGAATCTCCATTGTATAATCCG
1 CTGTTTTGTTTTAGGATGG-GAGAATCTCCATTGTATAATCCG
28346379 CTGTTTTGTTTTAGGATGGGAGAATCTCCATTGTATAATC
1 CTGTTTTGTTTTAGGATGGGAGAATCTCCATTGTATAATC
28346419 GAGCAGAGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
42 37 0.95
43 2 0.05
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.40
Consensus pattern (42 bp):
CTGTTTTGTTTTAGGATGGGAGAATCTCCATTGTATAATCCG
Found at i:28347087 original size:6 final size:6
Alignment explanation
Indices: 28347076--28347106 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
28347066 GTCTTCTGTC
28347076 TTGTAG TTGTAG TTGTAG TTGTAG TTGTAG T
1 TTGTAG TTGTAG TTGTAG TTGTAG TTGTAG T
28347107 CGTACACCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (6 bp):
TTGTAG
Found at i:28358417 original size:26 final size:26
Alignment explanation
Indices: 28358381--28358433 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
28358371 GGGAGAACCT
28358381 ATGAAAATTGGGTGAAATTTCATGAG
1 ATGAAAATTGGGTGAAATTTCATGAG
28358407 ATGAAAATTGGGTGAAATTTCATGAG
1 ATGAAAATTGGGTGAAATTTCATGAG
28358433 A
1 A
28358434 AATATATCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.04, G:0.26, T:0.30
Consensus pattern (26 bp):
ATGAAAATTGGGTGAAATTTCATGAG
Found at i:28361028 original size:3 final size:3
Alignment explanation
Indices: 28361020--28361061 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
28361010 TATTCCAATT
28361020 TTA TTA TTA TTA TTA TTA TTA TTTA TT- TTA TT- TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT
28361062 TCTTTTTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 6 0.17
3 26 0.74
4 3 0.09
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (3 bp):
TTA
Found at i:28361031 original size:6 final size:6
Alignment explanation
Indices: 28361020--28361061 Score: 54
Period size: 5 Copynumber: 7.3 Consensus size: 6
28361010 TATTCCAATT
28361020 TTATTA TTATTA TTATTA TTATTTA TT-TTA TT-TTA TT-TTA TT
1 TTATTA TTATTA TTATTA TTA-TTA TTATTA TTATTA TTATTA TT
28361062 TCTTTTTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 15 0.43
6 15 0.43
7 5 0.14
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (6 bp):
TTATTA
Found at i:28361067 original size:9 final size:9
Alignment explanation
Indices: 28361017--28361067 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
28361007 AAGTATTCCA
28361017 ATTTTA-TT
1 ATTTTATTT
28361025 ATTATTA-TT
1 ATT-TTATTT
28361034 ATTATTATTT
1 ATT-TTATTT
28361044 ATTTTATTTT
1 ATTTTA-TTT
28361054 ATTTTATTT
1 ATTTTATTT
*
28361063 CTTTT
1 ATTTT
28361068 TTATAAATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
8 3 0.08
9 22 0.56
10 14 0.36
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (9 bp):
ATTTTATTT
Found at i:28361804 original size:6 final size:6
Alignment explanation
Indices: 28361793--28361817 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
28361783 TCGAAGCCGG
28361793 AACAGT AACAGT AACAGT AACAGT A
1 AACAGT AACAGT AACAGT AACAGT A
28361818 CGGTACACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
AACAGT
Found at i:28361863 original size:6 final size:6
Alignment explanation
Indices: 28361852--28361882 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
28361842 ACAAATCCGA
*
28361852 AACAGT AACAGT AACAGT AACGGT AACAGT A
1 AACAGT AACAGT AACAGT AACAGT AACAGT A
28361883 TTCGACACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.16, G:0.19, T:0.16
Consensus pattern (6 bp):
AACAGT
Found at i:28361922 original size:12 final size:12
Alignment explanation
Indices: 28361905--28361929 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28361895 AGTGTCGAAT
28361905 CGGTAACAGTAA
1 CGGTAACAGTAA
28361917 CGGTAACAGTAA
1 CGGTAACAGTAA
28361929 C
1 C
28361930 AATAGTCGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTAACAGTAA
Found at i:28363208 original size:32 final size:32
Alignment explanation
Indices: 28363170--28363237 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
28363160 AATTAAACTT
28363170 TTACCCTTATTCAATTTAATCCTTTTTACTAA
1 TTACCCTTATTCAATTTAATCCTTTTTACTAA
28363202 TTACCCTTATTCAATTTAATCCTTTTTACTAA
1 TTACCCTTATTCAATTTAATCCTTTTTACTAA
28363234 TTAC
1 TTAC
28363238 TCTAAATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.28, C:0.22, G:0.00, T:0.50
Consensus pattern (32 bp):
TTACCCTTATTCAATTTAATCCTTTTTACTAA
Found at i:28363801 original size:43 final size:43
Alignment explanation
Indices: 28363748--28363902 Score: 292
Period size: 43 Copynumber: 3.6 Consensus size: 43
28363738 CCGGCATTAC
*
28363748 GCCTGTTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
28363791 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACTAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
28363834 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
28363877 GCCTGCTAGGCACGAAGGCCCGAATA
1 GCCTGCTAGGCACGAAGGCCCGAATA
28363903 TAATACCAGC
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 109 1.00
ACGTcount: A:0.30, C:0.34, G:0.26, T:0.11
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
Found at i:28363880 original size:86 final size:85
Alignment explanation
Indices: 28363735--28363923 Score: 308
Period size: 86 Copynumber: 2.2 Consensus size: 85
28363725 ACATATCATT
* * *
28363735 TCACCGGCATTACGCCTGTTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAGCCTGCTAG
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAGCCTGCTAG
28363800 GCACGAAGGCCCGAATACACA
66 GCACGAAGGCCCGAATACA-A
28363821 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAGCCTGCTAG
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAGCCTGCTAG
*
28363886 GCACGAAGGCCCGAATATAA
66 GCACGAAGGCCCGAATACAA
* *
28363906 T-ACCAGCACTAGGCCTGC
1 TCACCGGCACTAAGCCTGC
28363924 GGGATTTATC
Statistics
Matches: 97, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
84 15 0.15
85 2 0.02
86 80 0.82
ACGTcount: A:0.29, C:0.34, G:0.24, T:0.13
Consensus pattern (85 bp):
TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAGCCTGCTAG
GCACGAAGGCCCGAATACAA
Found at i:28363943 original size:38 final size:38
Alignment explanation
Indices: 28363895--28363978 Score: 132
Period size: 38 Copynumber: 2.2 Consensus size: 38
28363885 GGCACGAAGG
* * *
28363895 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAT
1 CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
28363933 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAA
28363971 CCCGAATA
1 CCCGAATA
28363979 CACATCAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (38 bp):
CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:28373099 original size:96 final size:96
Alignment explanation
Indices: 28372932--28373165 Score: 319
Period size: 96 Copynumber: 2.4 Consensus size: 96
28372922 TAGGGTAAAT
* * * *
28372932 TGCCGATACCAGGTCCCAGACATGGTCTTACACTGGCTCACATGTTGAGGCCGATGCCATGTCCC
1 TGCCGATGCCATGTCCCAGACATAGTCTTACACTGGCTCTCATGTTGAGGCCGATGCCATGTCCC
* **
28372997 AAACATGGTCTTACATTAGCT-CTAGTC-TCAA
66 AAACATGGTCTTACACTAG-TAC-ACACATCAA
* *
28373028 TGCCGATGCCATGTCCCAGGCATAGTCTTACACTGGCTCTCATGTTGTGGCCGATGCCATGTCCC
1 TGCCGATGCCATGTCCCAGACATAGTCTTACACTGGCTCTCATGTTGAGGCCGATGCCATGTCCC
*
28373093 AGACATGGTCTTACACTAGTACACACATCAA
66 AAACATGGTCTTACACTAGTACACACATCAA
* * *
28373124 TGCCAATGCCATGTCCCAGACATTGTCTTACATTGGCTCTCA
1 TGCCGATGCCATGTCCCAGACATAGTCTTACACTGGCTCTCA
28373166 CAACATCATC
Statistics
Matches: 122, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
95 3 0.02
96 119 0.98
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (96 bp):
TGCCGATGCCATGTCCCAGACATAGTCTTACACTGGCTCTCATGTTGAGGCCGATGCCATGTCCC
AAACATGGTCTTACACTAGTACACACATCAA
Found at i:28373261 original size:144 final size:143
Alignment explanation
Indices: 28372944--28373266 Score: 373
Period size: 144 Copynumber: 2.2 Consensus size: 143
28372934 CCGATACCAG
* * ** *
28372944 GTCCCAGACATGGTCTTACACTGGCTCACATGTTGAGGCCGATGCCATGTCCCAAACATGGTCTT
1 GTCCCAGACATGGTCTTACACTGGCACACATATCAAGGCCAATGCCATGTCCCAAACATGGTCTT
** ** * * *
28373009 ACATTAGCTCTAGTCTCAATGCCGATGCCATGTCCCAGGCATAGTCTTACACTGGCTCTCATGTT
66 ACATTAGCTCTAAACTCAAT-CCGATGCCATGTCCCAAACATAGTCTTACACTAGCTCTCATATC
*
28373074 GTGGCCGATGCCAT
130 GTGGCCGACGCCAT
* * * * * *
28373088 GTCCCAGACATGGTCTTACACTAGTACACACATCAATGCCAATGCCATGTCCCAGACATTGTCTT
1 GTCCCAGACATGGTCTTACACTGGCACACATATCAAGGCCAATGCCATGTCCCAAACATGGTCTT
* * *
28373153 ACATTGGCTCTCACAACATC-AT-CGATGCTATGTTCCAAACAT-GATCTTACACTAGCTCTCAT
66 ACATTAGCTCT-A-AAC-TCAATCCGATGCCATGTCCCAAACATAG-TCTTACACTAGCTCTCAT
28373215 ATCGTGGCCGACGCCAT
127 ATCGTGGCCGACGCCAT
*
28373232 GTCCCAGACATGGTCTTATACTGGCACACATATCA
1 GTCCCAGACATGGTCTTACACTGGCACACATATCA
28373267 CCCAAATATC
Statistics
Matches: 149, Mismatches: 26, Indels: 8
0.81 0.14 0.04
Matches are distributed among these distances:
143 1 0.01
144 142 0.95
145 1 0.01
146 3 0.02
147 2 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (143 bp):
GTCCCAGACATGGTCTTACACTGGCACACATATCAAGGCCAATGCCATGTCCCAAACATGGTCTT
ACATTAGCTCTAAACTCAATCCGATGCCATGTCCCAAACATAGTCTTACACTAGCTCTCATATCG
TGGCCGACGCCAT
Found at i:28373264 original size:48 final size:48
Alignment explanation
Indices: 28372933--28373266 Score: 264
Period size: 48 Copynumber: 7.0 Consensus size: 48
28372923 AGGGTAAATT
* * * *
28372933 GCCGATACCAGGTCCCAGACATGGTCTTACACTGGCTCACATGTTGA-G
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACAT-ATCATG
* * * * *
28372981 GCCGATGCCATGTCCCAAACATGGTCTTACATTAGCTCTA-GTCTCAAT-
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-ACATATC-ATG
* * * * **
28373029 GCCGATGCCATGTCCCAGGCATAGTCTTACACTGGCTCTCATGTTGTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCATG
* *
28373077 GCCGATGCCATGTCCCAGACATGGTCTTACACTAG-TACACACATCAAT-
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCT-CACATATC-ATG
* * * * * * *
28373125 GCCAATGCCATGTCCCAGACATTGTCTTACATTGGCTCTCACAACATC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCATG
** * * * * * * *
28373173 ATCGATGCTATGTTCCAAACATGATCTTACACTAGCTCTCATATCGTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCATG
* * *
28373221 GCCGACGCCATGTCCCAGACATGGTCTTATACTGGCACACATATCA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCA
28373267 CCCAAATATC
Statistics
Matches: 219, Mismatches: 58, Indels: 18
0.74 0.20 0.06
Matches are distributed among these distances:
47 5 0.02
48 211 0.96
49 3 0.01
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.27
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCATG
Found at i:28379064 original size:24 final size:23
Alignment explanation
Indices: 28379003--28379070 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 23
28378993 AATCTTTCTT
*
28379003 TCTTTCTTCCTCTGTTTCTGTTTC
1 TCTTTCTT-CTCTGTTTCTGTTAC
28379027 TCTTTC-TCATTCTGTTTCTGTTAC
1 TCTTTCTTC--TCTGTTTCTGTTAC
28379051 TCTTATCTTCTCTGCTTTCT
1 TCTT-TCTTCTCTG-TTTCT
28379071 ATCTATAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
22 1 0.03
23 1 0.03
24 27 0.71
25 7 0.18
26 2 0.05
ACGTcount: A:0.04, C:0.28, G:0.07, T:0.60
Consensus pattern (23 bp):
TCTTTCTTCTCTGTTTCTGTTAC
Found at i:28379627 original size:22 final size:22
Alignment explanation
Indices: 28379582--28379627 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
28379572 ATTAGCAAAT
* *
28379582 ATATTTTTTAAAAATTATAGAA
1 ATATTATTTAAAAATTATAAAA
28379604 ATATTATTTAATAAATT-TAAAA
1 ATATTATTTAA-AAATTATAAAA
28379626 AT
1 AT
28379628 TAACATGTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
ATATTATTTAAAAATTATAAAA
Found at i:28384873 original size:46 final size:46
Alignment explanation
Indices: 28384730--28384873 Score: 123
Period size: 46 Copynumber: 3.1 Consensus size: 46
28384720 CCCGCCCATA
* * *
28384730 AGTGAACTCGGACTCAACTCAGCGAGCTCGGATGCCTAGTTACATCTC
1 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTA--AACATCCC
* * * * *** *
28384778 A-CGAACTCGGACTCAACTCAACGAGTTC-GA-ACATTCGCATCCATA
1 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAAACATCC--C
*
28384823 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAAATATCCC
1 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAAACATCCC
28384869 AGTGA
1 AGTGA
28384874 CATGTCACTT
Statistics
Matches: 72, Mismatches: 19, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
43 4 0.06
45 3 0.04
46 32 0.44
47 26 0.36
48 7 0.10
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAAACATCCC
Found at i:28401780 original size:9 final size:9
Alignment explanation
Indices: 28401766--28401790 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
28401756 CTTGGGTCAG
28401766 AACCTCTTC
1 AACCTCTTC
28401775 AACCTCTTC
1 AACCTCTTC
28401784 AACCTCT
1 AACCTCT
28401791 AATTCCTCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.44, G:0.00, T:0.32
Consensus pattern (9 bp):
AACCTCTTC
Found at i:28401878 original size:21 final size:21
Alignment explanation
Indices: 28401852--28401892 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28401842 ATCTGCTCAA
* *
28401852 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
28401873 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
28401893 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:28415242 original size:21 final size:21
Alignment explanation
Indices: 28415208--28415248 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28415198 AGACGAGCAA
* * *
28415208 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTAGAGTG
28415229 TACTCCAAAACAGGTAGAGT
1 TACTCCAAAACAGGTAGAGT
28415249 TTGAGCAGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTAGAGTG
Found at i:28420811 original size:29 final size:28
Alignment explanation
Indices: 28420757--28420827 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 28
28420747 AAAATATGCT
28420757 TTTTATACTCTTTATCTATCTGAATTTTAG
1 TTTTATACT-TTTATCTATCTGAA-TTTAG
* *
28420787 TTTTATACTTTTAT-TTTCTATAATTTAG
1 TTTTATACTTTTATCTATCT-GAATTTAG
*
28420815 TTCTTCTACTTTT
1 TT-TTATACTTTT
28420828 TGAATTAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 11 0.31
29 16 0.44
30 9 0.25
ACGTcount: A:0.21, C:0.13, G:0.04, T:0.62
Consensus pattern (28 bp):
TTTTATACTTTTATCTATCTGAATTTAG
Found at i:28421977 original size:21 final size:23
Alignment explanation
Indices: 28421930--28421983 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
28421920 CATTCAAGAT
**
28421930 AAAATAATATATAAAACTCTTTA
1 AAAATAATATATAAAACTAATTA
*
28421953 AAAATAATATAT-AAAC-AATTC
1 AAAATAATATATAAAACTAATTA
28421974 AAAAT-ATATA
1 AAAATAATATA
28421984 ATGTGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 7 0.25
22 4 0.14
23 12 0.43
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATAATATATAAAACTAATTA
Found at i:28422208 original size:12 final size:14
Alignment explanation
Indices: 28422197--28422311 Score: 51
Period size: 15 Copynumber: 7.9 Consensus size: 14
28422187 TAGAAATAAA
28422197 AAATATAATAAATAG
1 AAATATAAT-AATAG
28422212 AAATATAATAATAG
1 AAATATAATAATAG
28422226 TAGACATAT-A-AATAG
1 -A-A-ATATAATAATAG
*
28422241 ATAA-ATAAAAATTAG
1 A-AATATAATAA-TAG
28422256 ATAA-ATAATAATAG
1 A-AATATAATAATAG
* * * *
28422270 TATTAGAATAACA-
1 AAATATAATAATAG
*
28422283 AAATAAATATAAATAG
1 AAATATA-AT-AATAG
*
28422299 AAACATAATAATA
1 AAATATAATAATA
28422312 ATAGCAATAA
Statistics
Matches: 78, Mismatches: 12, Indels: 21
0.70 0.11 0.19
Matches are distributed among these distances:
12 2 0.03
13 7 0.09
14 25 0.32
15 33 0.42
16 7 0.09
17 4 0.05
ACGTcount: A:0.63, C:0.03, G:0.07, T:0.27
Consensus pattern (14 bp):
AAATATAATAATAG
Found at i:28422217 original size:15 final size:17
Alignment explanation
Indices: 28422197--28422236 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
28422187 TAGAAATAAA
28422197 AAATATAATAA-A-TAG
1 AAATATAATAATAGTAG
28422212 AAATATAATAATAGTAG
1 AAATATAATAATAGTAG
*
28422229 ACATATAA
1 AAATATAA
28422237 ATAGATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.50
16 1 0.05
17 10 0.45
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (17 bp):
AAATATAATAATAGTAG
Found at i:28423209 original size:25 final size:26
Alignment explanation
Indices: 28423180--28423228 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
28423170 AATTAAAAGT
* *
28423180 AAGAGAACTAA-ATTTTAAATATAAA
1 AAGAGAACAAAGATTTAAAATATAAA
*
28423205 AAGAGTACAAAGATTTAAAATATA
1 AAGAGAACAAAGATTTAAAATATA
28423229 TTTTAAGCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 9 0.45
26 11 0.55
ACGTcount: A:0.59, C:0.04, G:0.10, T:0.27
Consensus pattern (26 bp):
AAGAGAACAAAGATTTAAAATATAAA
Found at i:28426609 original size:27 final size:27
Alignment explanation
Indices: 28426551--28426610 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
28426541 TCTAGTAGGG
* *
28426551 GCGACTGGTTGAGCCTATCTGATAGGC
1 GCGACTAGTTGAGCCTATCTGATAGAC
* *
28426578 ACGACTAGTTGAGCCTGT-TAGATAGAC
1 GCGACTAGTTGAGCCTATCT-GATAGAC
28426605 GCGACT
1 GCGACT
28426611 GGTAGAGTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.25
Consensus pattern (27 bp):
GCGACTAGTTGAGCCTATCTGATAGAC
Found at i:28426845 original size:104 final size:104
Alignment explanation
Indices: 28426658--28426920 Score: 392
Period size: 104 Copynumber: 2.5 Consensus size: 104
28426648 CTATATATAT
*
28426658 ATAACCTAAACACTAACAATTTATATAACCTAATCATAAATTACTAACAAAATAACTATAAAATT
1 ATAA-CTAAACACTAACAATTTATATAACCTAACCATAAATTACTAACAAAATAACTATAAAATT
*
28426723 ATTTTTTTTTAAAATACATTACTAAAAAATCACAAAA-CAC
65 ATTTTTTTTAAAAATACATTACTAAAAAATCACAAAATC-C
28426763 ATAACTAAACACTAACAATTTATATAACCTAACCATAAATTACTAACAAAATAACTATAAAATTA
1 ATAACTAAACACTAACAATTTATATAACCTAACCATAAATTACTAACAAAATAACTATAAAATTA
28426828 -TTTTTTTAAAAATTACATTACTAAAAAATCACAAAATCC
66 TTTTTTTTAAAAA-TACATTACTAAAAAATCACAAAATCC
* * *
28426867 -TATACTAAACACTAACAA-TT-TGTAATCTAATCTCATAAATTATTAACAAAATAA
1 ATA-ACTAAACACTAACAATTTATATAACCTAA-C-CATAAATTACTAACAAAATAA
28426921 ATAACTATAA
Statistics
Matches: 148, Mismatches: 5, Indels: 11
0.90 0.03 0.07
Matches are distributed among these distances:
102 8 0.05
103 16 0.11
104 119 0.80
105 5 0.03
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (104 bp):
ATAACTAAACACTAACAATTTATATAACCTAACCATAAATTACTAACAAAATAACTATAAAATTA
TTTTTTTTAAAAATACATTACTAAAAAATCACAAAATCC
Found at i:28428120 original size:33 final size:33
Alignment explanation
Indices: 28428078--28428146 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
28428068 AATTCAATAT
28428078 AAAACAGAGATTTATCGCGCTTTAATGAAAATC
1 AAAACAGAGATTTATCGCGCTTTAATGAAAATC
* *
28428111 AAAACAGAGATTTATGGCGTTTTAATGAAAATC
1 AAAACAGAGATTTATCGCGCTTTAATGAAAATC
28428144 AAA
1 AAA
28428147 CAAAAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.28
Consensus pattern (33 bp):
AAAACAGAGATTTATCGCGCTTTAATGAAAATC
Found at i:28430096 original size:15 final size:15
Alignment explanation
Indices: 28430076--28430108 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
28430066 AGGTGAGCTA
28430076 AGAAAGACAGAGAAG
1 AGAAAGACAGAGAAG
28430091 AGAAAGACAGAGAAG
1 AGAAAGACAGAGAAG
28430106 AGA
1 AGA
28430109 TTGTTGTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.61, C:0.06, G:0.33, T:0.00
Consensus pattern (15 bp):
AGAAAGACAGAGAAG
Found at i:28435771 original size:48 final size:49
Alignment explanation
Indices: 28435658--28435852 Score: 186
Period size: 48 Copynumber: 4.0 Consensus size: 49
28435648 CTGATGGCCG
* * * * *
28435658 GCACCAGAGATGTAAAAAAAAAATTTGGATGCTAG-CAAGTAGATAGCCA
1 GCACTAGAGATGTAAAAAAAAAATTTGGGTGCTGGCCAA-TAGATGGCTA
* *
28435707 GCAAC-AGATAT-TAAAAATAAAAA-TTGGGTGCTTGCCAATAGATGGCTA
1 GC-ACTAGAGATGTAAAAA-AAAAATTTGGGTGCTGGCCAATAGATGGCTA
* * * * *
28435755 GCACTAGAGATG-AAAAAAAAATTTTGGGTGCTGGCCAGTATATGAC-C
1 GCACTAGAGATGTAAAAAAAAAATTTGGGTGCTGGCCAATAGATGGCTA
28435802 GACACTAGAGATGTAAAAAAAAAAATTTTGGGTGCTGGCCAATAGATGGCT
1 G-CACTAGAGATGT-AAAAAAAAAA-TTTGGGTGCTGGCCAATAGATGGCT
28435853 GGCATTAGGT
Statistics
Matches: 119, Mismatches: 16, Indels: 19
0.77 0.10 0.12
Matches are distributed among these distances:
47 7 0.06
48 65 0.55
49 15 0.13
50 11 0.09
51 21 0.18
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.23
Consensus pattern (49 bp):
GCACTAGAGATGTAAAAAAAAAATTTGGGTGCTGGCCAATAGATGGCTA
Found at i:28436384 original size:16 final size:16
Alignment explanation
Indices: 28436375--28436426 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
28436365 TAAATAAATT
28436375 TAAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
* * *
28436391 TGAATTGAAATGTAAA
1 TAAATTTAAATTTAAA
*
28436407 TGAAATTTGAAATTCAAA
1 T-AAATTT-AAATTTAAA
28436425 TA
1 TA
28436427 GAAGTGAAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
16 14 0.52
17 5 0.19
18 8 0.30
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.37
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:28436396 original size:22 final size:22
Alignment explanation
Indices: 28436365--28436407 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
28436355 GACAAATAAA
* *
28436365 TAAATAAATTTAAATTTAAATT
1 TAAATAAATTGAAATGTAAATT
*
28436387 TAAATGAATTGAAATGTAAAT
1 TAAATAAATTGAAATGTAAAT
28436408 GAAATTTGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (22 bp):
TAAATAAATTGAAATGTAAATT
Found at i:28437614 original size:5 final size:5
Alignment explanation
Indices: 28437604--28437635 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
28437594 CATACTGTGA
28437604 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
28437636 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:28437629 original size:9 final size:9
Alignment explanation
Indices: 28437605--28437635 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
28437595 ATACTGTGAA
28437605 AAATAAAAT
1 AAATAAAAT
28437614 AAAATAAAAT
1 -AAATAAAAT
28437624 AAATAAAAT
1 AAATAAAAT
28437633 AAA
1 AAA
28437636 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:28442065 original size:5 final size:5
Alignment explanation
Indices: 28442055--28442086 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
28442045 CAATTTGTGA
28442055 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
28442087 GAACACATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:28442080 original size:9 final size:9
Alignment explanation
Indices: 28442056--28442086 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
28442046 AATTTGTGAA
28442056 AAATAAAAT
1 AAATAAAAT
28442065 AAAATAAAAT
1 -AAATAAAAT
28442075 AAATAAAAT
1 AAATAAAAT
28442084 AAA
1 AAA
28442087 GAACACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:28443702 original size:89 final size:88
Alignment explanation
Indices: 28443602--28443922 Score: 267
Period size: 90 Copynumber: 3.6 Consensus size: 88
28443592 AGTACACGAC
* **
28443602 AAATTAAATTTACAGATACAATAAAATACAAACATTCTAAAATATTAATACAAAAAAAATATAAA
1 AAATTAAATTTACAGATACAAAAAAATACAAACATTCTAAAA-ATTAATAC-ACGAAAATATAAA
*
28443667 ATTCAAACAAAA-ATAA-ATCTCACT
64 ATTCAAACAAAATATAATA-CGCACT
* * * * * * * *
28443691 AAATTATATTTAAACACT-CAACAAACTACAAACATATGGGT-AAAATTAATACACGAAAATTTT
1 AAATTAAATTTACAGA-TACAAAAAAATACAAACAT-T--CTAAAAATTAATACACGAAAATATA
* * *
28443754 AAATTCAAACTACATATAATACGGACT
62 AAATTCAAACAAAATATAATACGCACT
*
28443781 AAATTAAATTAACAGATACAAAAAAATACAAACATTCTAAGAAATTAATACACGAAAATATAAAA
1 AAATTAAATTTACAGATACAAAAAAATACAAACATTCTAA-AAATTAATACACGAAAATATAAAA
* * * * * *
28443846 ATGAAACTTTAAATCCT-AGAC-AACT
65 TTCAAAC--AAAAT-ATAATACGCACT
* * *
28443871 ACATTAAATTTACAGATATAAAAAAATACAAACATTCTAAAGAAATAATACA
1 AAATTAAATTTACAGATACAAAAAAATACAAACATTCTAAA-AATTAATACA
28443923 ATTATTTTGA
Statistics
Matches: 186, Mismatches: 33, Indels: 25
0.76 0.14 0.10
Matches are distributed among these distances:
87 1 0.01
88 1 0.01
89 77 0.41
90 94 0.51
91 11 0.06
92 2 0.01
ACGTcount: A:0.57, C:0.13, G:0.04, T:0.26
Consensus pattern (88 bp):
AAATTAAATTTACAGATACAAAAAAATACAAACATTCTAAAAATTAATACACGAAAATATAAAAT
TCAAACAAAATATAATACGCACT
Found at i:28444434 original size:27 final size:27
Alignment explanation
Indices: 28444403--28444463 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
28444393 TACACTACGG
28444403 AAAACTCCCATCTACAATCAACTACAA
1 AAAACTCCCATCTACAATCAACTACAA
* *
28444430 AAAACTTCCATCTACAATCTACTACAA
1 AAAACTCCCATCTACAATCAACTACAA
28444457 AAAACTC
1 AAAACTC
28444464 ATTTGATGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (27 bp):
AAAACTCCCATCTACAATCAACTACAA
Found at i:28444664 original size:53 final size:51
Alignment explanation
Indices: 28444594--28444814 Score: 217
Period size: 51 Copynumber: 4.4 Consensus size: 51
28444584 AAATAATTTT
* *
28444594 TTTTTTACATCTTTGGTGCCGGCCATCTATTGGCTAGCACCCAAAAAAAATA
1 TTTTTTACATCTCTGGTGCCGGCCATCTACTGGCTAGCACCC-AAAAAAATA
* * *
28444646 TGTTTTTACATCTCTGGTGCTGGCCATCTACTGGCCAACACCC----AAA-A
1 T-TTTTTACATCTCTGGTGCCGGCCATCTACTGGCTAGCACCCAAAAAAATA
* * * * *
28444693 --TTTT-CATCTCTGGTGCCGACTATCTACTGGCAAGTACTCAAAAAAGAT-
1 TTTTTTACATCTCTGGTGCCGGCCATCTACTGGCTAGCACCCAAAAAA-ATA
* * *
28444741 TTTTTTTCATCTCTGGTGCCGGCCATCTACTGGTTAGCACCCAAAAAAATTT
1 TTTTTTACATCTCTGGTGCCGGCCATCTACTGGCTAGCACCCAAAAAAA-TA
*
28444793 TTTTTTACATCTCTGATGCCGG
1 TTTTTTACATCTCTGGTGCCGG
28444815 TCATTATATG
Statistics
Matches: 137, Mismatches: 20, Indels: 24
0.76 0.11 0.13
Matches are distributed among these distances:
43 28 0.20
44 4 0.03
47 3 0.02
48 4 0.03
50 5 0.04
51 36 0.26
52 21 0.15
53 36 0.26
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (51 bp):
TTTTTTACATCTCTGGTGCCGGCCATCTACTGGCTAGCACCCAAAAAAATA
Found at i:28444786 original size:94 final size:97
Alignment explanation
Indices: 28444596--28444773 Score: 245
Period size: 96 Copynumber: 1.9 Consensus size: 97
28444586 ATAATTTTTT
* * * *
28444596 TTTTACATCTTTGGTGCCGGCCATCTATTGGCTAGCACCCAAAAAAAATATGTTTTTACATCTCT
1 TTTTACATCTCTGGTGCCGACCATCTACTGGCAAGCACCCAAAAAAAATATGTTTTTACATCTCT
*
28444661 GGTGCTGGCCATCTACTGGCCAACACCCAAAA
66 GGTGCCGGCCATCTACTGGCCAACACCCAAAA
* * * * *
28444693 TTTT-CATCTCTGGTGCCGACTATCTACTGGCAAGTACTCAAAAAAGAT-T-TTTTTTCATCTCT
1 TTTTACATCTCTGGTGCCGACCATCTACTGGCAAGCACCCAAAAAAAATATGTTTTTACATCTCT
28444755 GGTGCCGGCCATCTACTGG
66 GGTGCCGGCCATCTACTGG
28444774 TTAGCACCCA
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
94 30 0.42
95 1 0.01
96 36 0.51
97 4 0.06
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (97 bp):
TTTTACATCTCTGGTGCCGACCATCTACTGGCAAGCACCCAAAAAAAATATGTTTTTACATCTCT
GGTGCCGGCCATCTACTGGCCAACACCCAAAA
Found at i:28444827 original size:52 final size:51
Alignment explanation
Indices: 28444693--28444833 Score: 133
Period size: 51 Copynumber: 2.7 Consensus size: 51
28444683 ACACCCAAAA
* * * * ** * *
28444693 TTTTCATCTCTGGTGCCGACTATCTACTGGCAAGTACTCAAAAAAGATTTT
1 TTTTCATCTCTGATGCCGGCCATCTAATGGTTAGCACCCAAAAAAGATTTT
* *
28444744 TTTTCATCTCTGGTGCCGGCCATCTACTGGTTAGCACCCAAAAAA-ATTTTT
1 TTTTCATCTCTGATGCCGGCCATCTAATGGTTAGCACCCAAAAAAGA-TTTT
* *
28444795 TTTTACATCTCTGATGCCGGTCAT-TATATGGTTTGCACC
1 TTTT-CATCTCTGATGCCGGCCATCTA-ATGGTTAGCACC
28444834 TAATTTTTTT
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
50 1 0.01
51 49 0.64
52 27 0.35
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.37
Consensus pattern (51 bp):
TTTTCATCTCTGATGCCGGCCATCTAATGGTTAGCACCCAAAAAAGATTTT
Found at i:28446004 original size:48 final size:47
Alignment explanation
Indices: 28445947--28446081 Score: 137
Period size: 48 Copynumber: 2.8 Consensus size: 47
28445937 CTAAAAAAAA
*
28445947 TTTTACATCTCTGGTGCCGCTCATCTATTGGCCAGCACCCCAAATTTT
1 TTTTTCATCTCTGGTGCCGC-CATCTATTGGCCAGCACCCCAAATTTT
* * * * *
28445995 TTTTTCATCTCTGGTGTCGACCATCTACTGGCTAACA-TCCAAATTTT
1 TTTTTCATCTCTGGTGCCG-CCATCTATTGGCCAGCACCCCAAATTTT
* * * *
28446042 TGTTTTCATATTTGGTGTCGGCCATCTATTAGCCAGCACC
1 T-TTTTCATCTCTGGTG-CCGCCATCTATTGGCCAGCACC
28446082 TAAAAAAAAA
Statistics
Matches: 68, Mismatches: 15, Indels: 7
0.76 0.17 0.08
Matches are distributed among these distances:
47 10 0.15
48 56 0.82
49 2 0.03
ACGTcount: A:0.19, C:0.27, G:0.16, T:0.38
Consensus pattern (47 bp):
TTTTTCATCTCTGGTGCCGCCATCTATTGGCCAGCACCCCAAATTTT
Found at i:28447975 original size:34 final size:32
Alignment explanation
Indices: 28447885--28447990 Score: 88
Period size: 34 Copynumber: 3.2 Consensus size: 32
28447875 GGGTTTTCTT
* * *
28447885 AAAA-TAATTGAATTATGTTTTAGGGGTTTTAA
1 AAAATTAATTAAATTATGATTTA-GAGTTTTAA
* * *
28447917 ATAAATAAATTAAATTAGGGTTTAGAGTTGTTAA
1 A-AAATTAATTAAATTATGATTTAGAGTT-TTAA
**
28447951 GAAAATTAATTAAATTATGATTTAGTTTTTTAA
1 -AAAATTAATTAAATTATGATTTAGAGTTTTAA
28447984 AATAATT
1 AA-AATT
28447991 TTGTGTTTAG
Statistics
Matches: 59, Mismatches: 10, Indels: 9
0.76 0.13 0.12
Matches are distributed among these distances:
32 3 0.05
33 15 0.25
34 40 0.68
35 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.43
Consensus pattern (32 bp):
AAAATTAATTAAATTATGATTTAGAGTTTTAA
Found at i:28448386 original size:127 final size:126
Alignment explanation
Indices: 28448060--28448551 Score: 566
Period size: 126 Copynumber: 3.9 Consensus size: 126
28448050 GATAGTTCTT
** * *
28448060 TAAAAAATAATTTTGAGAAGACCTTTCTAAA-AATATAATGTCAAAAACGCTTCAAGCAGGATGC
1 TAAAAAATAATTTTGAGAAGACGATTCTAAACAA-ATAGTGTCAAAAACGCTTTAAGCAGGATGC
* * * * *
28448124 ACTGTCAGCAAAATT-ACTGAAAAAAGCTCCCATGTGGACGCTTTTTTTCTACGGTA-ATTCC
65 ACTATCAGCAAAATTGA-TGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTTTCC
* * * * * *
28448185 TAAAAAAATAATCTTGAGAAGACTATTTTGAACAAATAGTGTAAAAAACGCTTTAAGTAGGATGC
1 T-AAAAAATAATTTTGAGAAGACGATTCTAAACAAATAGTGTCAAAAACGCTTTAAGCAGGATGC
* * **
28448250 ACTGTCAGCAAAATT-ACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTGCAGTAGTTTTT
65 ACTATCAGCAAAATTGA-TGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTTTCC
* * * * *
28448312 TAAAAAAATAATTTTGAGAAGATGGTTCTAAATAAATGGTGTCAAAAATG-TTTCAAGCAGGATG
1 T-AAAAAATAATTTTGAGAAGACGATTCTAAACAAATAGTGTCAAAAACGCTTT-AAGCAGGATG
* *
28448376 CACTATCAGCAAAATTGATAAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAATAG-TTCC
64 CACTATCAGCAAAATTGATGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTTTCC
* * * *
28448438 TGAAAAATAATTTTGAGAAGACGATTTTGAACAAATGGTGT-AAAAACGCTTTAAGCAGGATGCA
1 TAAAAAATAATTTTGAGAAGACGATTCTAAACAAATAGTGTCAAAAACGCTTTAAGCAGGATGCA
* * * **
28448502 CTATAAACAAAATTGATGAAAAAAGCTCCCAGGTGGATACTCTTTTTCTA
66 CTATCAGCAAAATTGATGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTA
28448552 TAGTGTTCCT
Statistics
Matches: 315, Mismatches: 46, Indels: 13
0.84 0.12 0.03
Matches are distributed among these distances:
124 62 0.20
125 38 0.12
126 109 0.35
127 105 0.33
128 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (126 bp):
TAAAAAATAATTTTGAGAAGACGATTCTAAACAAATAGTGTCAAAAACGCTTTAAGCAGGATGCA
CTATCAGCAAAATTGATGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTTTCC
Found at i:28450959 original size:21 final size:20
Alignment explanation
Indices: 28450910--28450956 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
28450900 GCTTCTGACA
* * *
28450910 GGGGTTGTGGTTGCTCTGGT
1 GGGGTTGTGGTTCCTCCGGC
28450930 GAGGGTTGTGGTTCCTCCGGC
1 G-GGGTTGTGGTTCCTCCGGC
28450951 GGGGTT
1 GGGGTT
28450957 TGTAGTTGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.02, C:0.15, G:0.49, T:0.34
Consensus pattern (20 bp):
GGGGTTGTGGTTCCTCCGGC
Found at i:28451230 original size:18 final size:18
Alignment explanation
Indices: 28451204--28451246 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
28451194 GACTGGGAAA
* *
28451204 AGGAAACATATAAGGATT
1 AGGATACATATAAGGACT
*
28451222 AGGATACATATAAGGGCT
1 AGGATACATATAAGGACT
28451240 AGGATAC
1 AGGATAC
28451247 GCACCTAGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.26, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAGGACT
Found at i:28451586 original size:13 final size:14
Alignment explanation
Indices: 28451568--28451596 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28451558 TACCGACTAA
28451568 TTCGT-AGTCGATT
1 TTCGTAAGTCGATT
28451581 TTCGTAAGTCGATT
1 TTCGTAAGTCGATT
28451595 TT
1 TT
28451597 GTACTCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (14 bp):
TTCGTAAGTCGATT
Found at i:28452729 original size:24 final size:22
Alignment explanation
Indices: 28452685--28452725 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
28452675 AAAGACAAAT
28452685 GTATAGTAAATAAAATATACAA
1 GTATAGTAAATAAAATATACAA
28452707 GTATA-TAAATAAAA-ATACA
1 GTATAGTAAATAAAATATACA
28452726 TACATTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.27
Consensus pattern (22 bp):
GTATAGTAAATAAAATATACAA
Found at i:28452799 original size:22 final size:22
Alignment explanation
Indices: 28452753--28452799 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
28452743 TATTAGATAT
**
28452753 TAAATAGATATTTATTATTTTA
1 TAAATAGATATTTATTATTAAA
28452775 TAAA-AGATATTTATTAATTAAA
1 TAAATAGATATTTATT-ATTAAA
28452797 TAA
1 TAA
28452800 TTATATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
TAAATAGATATTTATTATTAAA
Found at i:28455415 original size:46 final size:45
Alignment explanation
Indices: 28455363--28455532 Score: 198
Period size: 46 Copynumber: 3.7 Consensus size: 45
28455353 GATCTTTGAA
* *
28455363 ATGAAATGTGTAAGACAATCATTGAAAGATACCATGGCAACCTGAT
1 ATGAAATGTGTAAGACCAT-ATTGAAAGATACCATGGCAACCTGAC
* *
28455409 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGTGTAAGACCAT-ATTGAAAGATACCATGGCAACCTGAC
** * *
28455455 ATGAAATGAATAAGACCATAGTTGAAAGATACCATGACAACATGAC
1 ATGAAATGTGTAAGACCATA-TTGAAAGATACCATGGCAACCTGAC
* *
28455501 A-GAAAACGAGTAAGACCATAGTTGAAAGATAC
1 ATG-AAATGTGTAAGACCATA-TTGAAAGATAC
28455533 TATGACATCA
Statistics
Matches: 110, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
45 1 0.01
46 109 0.99
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.21
Consensus pattern (45 bp):
ATGAAATGTGTAAGACCATATTGAAAGATACCATGGCAACCTGAC
Found at i:28456842 original size:25 final size:24
Alignment explanation
Indices: 28456793--28456844 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
28456783 CTGTTATAAA
* *
28456793 AAAATTATAAAATAAAAATTAATT
1 AAAATTACAAAATAAAAAATAATT
28456817 AAAATTACATAAATAAAAAA-ATATT
1 AAAATTACA-AAATAAAAAATA-ATT
28456842 AAA
1 AAA
28456845 TAATTTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (24 bp):
AAAATTACAAAATAAAAAATAATT
Found at i:28457047 original size:20 final size:21
Alignment explanation
Indices: 28457022--28457070 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
28457012 TAAAGAGAGC
*
28457022 TTTGAGA-AATTTAGGGATAA
1 TTTGAGAGAATTTAGGGAGAA
**
28457042 TTTGAGAGCTTTTAGGGAGAA
1 TTTGAGAGAATTTAGGGAGAA
28457063 TTTGAGAG
1 TTTGAGAG
28457071 CGTTTTTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.33, C:0.02, G:0.31, T:0.35
Consensus pattern (21 bp):
TTTGAGAGAATTTAGGGAGAA
Found at i:28457057 original size:21 final size:22
Alignment explanation
Indices: 28457031--28457076 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
28457021 CTTTGAGAAA
*
28457031 TTTAGGGATAATTTGAGAGC-T
1 TTTAGGGAGAATTTGAGAGCGT
28457052 TTTAGGGAGAATTTGAGAGCGT
1 TTTAGGGAGAATTTGAGAGCGT
28457074 TTT
1 TTT
28457077 TGAAGAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.26, C:0.04, G:0.30, T:0.39
Consensus pattern (22 bp):
TTTAGGGAGAATTTGAGAGCGT
Found at i:28457083 original size:21 final size:21
Alignment explanation
Indices: 28457031--28457086 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
28457021 CTTTGAGAAA
* *
28457031 TTTAGGGATAATTTGAGAGCT
1 TTTAGGAAGAATTTGAGAGCT
*
28457052 TTTAGGGAGAATTTGAGAGCGT
1 TTTAGGAAGAATTTGAGAGC-T
*
28457074 TTT-TGAAGAATTT
1 TTTAGGAAGAATTT
28457087 TGAAGAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 27 0.87
22 4 0.13
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.39
Consensus pattern (21 bp):
TTTAGGAAGAATTTGAGAGCT
Found at i:28460304 original size:22 final size:22
Alignment explanation
Indices: 28460270--28460312 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
28460260 TATTTAGATA
28460270 ATAATAATAAAA-TAGTAGCAAT
1 ATAATAATAAAATTA-TAGCAAT
* *
28460292 ATAATAGTGAAATTATAGCAA
1 ATAATAATAAAATTATAGCAA
28460313 AATGAAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.56, C:0.05, G:0.12, T:0.28
Consensus pattern (22 bp):
ATAATAATAAAATTATAGCAAT
Found at i:28492903 original size:14 final size:15
Alignment explanation
Indices: 28492871--28492904 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28492861 CAATTATTTT
28492871 TTTAAAATAAAATAA
1 TTTAAAATAAAATAA
*
28492886 TTTATAATAAAA-AA
1 TTTAAAATAAAATAA
28492900 TTTAA
1 TTTAA
28492905 GCTCAGACGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TTTAAAATAAAATAA
Found at i:28507651 original size:23 final size:24
Alignment explanation
Indices: 28507625--28507671 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
28507615 AATTGGACTT
* *
28507625 AATTTTAAGATTT-AATTCTTATA
1 AATTTTAAAATTTCAATTATTATA
28507648 AATTTTAAAATTTCAATTATTATA
1 AATTTTAAAATTTCAATTATTATA
28507672 GTGAGCTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (24 bp):
AATTTTAAAATTTCAATTATTATA
Found at i:28513246 original size:6 final size:6
Alignment explanation
Indices: 28513235--28513275 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
28513225 AAGTAGTAGT
* * *
28513235 CTCAGG CTCAGG CTAAGG CTAAGG CTAAGG CTCAGG CTCAG
1 CTCAGG CTCAGG CTCAGG CTCAGG CTCAGG CTCAGG CTCAG
28513276 ACTCTATAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.24, C:0.27, G:0.32, T:0.17
Consensus pattern (6 bp):
CTCAGG
Found at i:28513259 original size:12 final size:12
Alignment explanation
Indices: 28513238--28513272 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
28513228 TAGTAGTCTC
28513238 AGGCTCAGGCTA
1 AGGCTCAGGCTA
*
28513250 AGGCTAAGGCTA
1 AGGCTCAGGCTA
28513262 AGGCTCAGGCT
1 AGGCTCAGGCT
28513273 CAGACTCTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.26, C:0.23, G:0.34, T:0.17
Consensus pattern (12 bp):
AGGCTCAGGCTA
Found at i:28515976 original size:17 final size:17
Alignment explanation
Indices: 28515944--28515987 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
28515934 ATATATTATA
**
28515944 TTTTAAAATTTTAAAAT
1 TTTTAAAATTAAAAAAT
28515961 TTTTAAAATTAAAAAAT
1 TTTTAAAATTAAAAAAT
**
28515978 AATTAAAATT
1 TTTTAAAATT
28515988 TCAAATGATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTTAAAATTAAAAAAT
Found at i:28516617 original size:15 final size:15
Alignment explanation
Indices: 28516581--28516615 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
28516571 ACTGTCATGT
*
28516581 ATATATATTTTTTAA
1 ATATTTATTTTTTAA
28516596 ATATTTATTTTTT-A
1 ATATTTATTTTTTAA
28516610 ATATTT
1 ATATTT
28516616 TACTATACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
ATATTTATTTTTTAA
Found at i:28525040 original size:49 final size:49
Alignment explanation
Indices: 28524987--28525084 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 49
28524977 CATTAGTTAG
28524987 TCCAAATAATTAGCTGTATTAATAAATTTAATAGTTGATGTGAATTTTT
1 TCCAAATAATTAGCTGTATTAATAAATTTAATAGTTGATGTGAATTTTT
* *
28525036 TCCAAATAATTAGCTGTATTAATAAATTTGATCGTTGATGTGAATTTTT
1 TCCAAATAATTAGCTGTATTAATAAATTTAATAGTTGATGTGAATTTTT
28525085 AAAAAAGACT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.45
Consensus pattern (49 bp):
TCCAAATAATTAGCTGTATTAATAAATTTAATAGTTGATGTGAATTTTT
Found at i:28534777 original size:4 final size:4
Alignment explanation
Indices: 28534768--28534832 Score: 55
Period size: 4 Copynumber: 17.0 Consensus size: 4
28534758 TACAAATTGT
* * * * *
28534768 TTTA TTTA TTTG TTTG TTTG TTTA TTT- TCTA TTTA TTTA -TTA TTTC
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
*
28534814 TTTC TTTA TTT- TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA
28534833 GAAAAAATCA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
3 8 0.15
4 44 0.85
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:28534824 original size:30 final size:31
Alignment explanation
Indices: 28534768--28534832 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
28534758 TACAAATTGT
* * *
28534768 TTTATTTATTTGTTTGTTTGTTTATTTTCTA
1 TTTATTTATTTATTTCTTTCTTTATTTTCTA
*
28534799 TTTATTTA-TTATTTCTTTCTTTATTTTTTA
1 TTTATTTATTTATTTCTTTCTTTATTTTCTA
28534829 TTTA
1 TTTA
28534833 GAAAAAATCA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 22 0.73
31 8 0.27
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.75
Consensus pattern (31 bp):
TTTATTTATTTATTTCTTTCTTTATTTTCTA
Found at i:28537696 original size:48 final size:48
Alignment explanation
Indices: 28537585--28537806 Score: 203
Period size: 43 Copynumber: 4.8 Consensus size: 48
28537575 TGCCAAATAA
* * * * * *
28537585 ATAGCCGAAGCTATATCAATCTCGTACACTAAGTGACAATATGTATAT
1 ATAGCCGAAGCTATCTCAATCTCGCACACTTAGTGCCAATATATGTAT
* * * * *
28537633 AGAGCTGGAGCTATCTCAATCACGCACACTAAGTGCCAATATATGTAT
1 ATAGCCGAAGCTATCTCAATCTCGCACACTTAGTGCCAATATATGTAT
* * *
28537681 ATAGCCGAAGTTATCT-GATCTCACACACTTAGTGCC---A-ATGTAT
1 ATAGCCGAAGCTATCTCAATCTCGCACACTTAGTGCCAATATATGTAT
* **
28537724 TTAGCCGAAGCTATCT-GGTCTCGCACACTTAGTGCCAATATA--T-T
1 ATAGCCGAAGCTATCTCAATCTCGCACACTTAGTGCCAATATATGTAT
* *
28537768 -TAGCCAAAGCTATCTCAGTCTCGCACACTTAGTGCCAAT
1 ATAGCCGAAGCTATCTCAATCTCGCACACTTAGTGCCAAT
28537807 GTACAATATA
Statistics
Matches: 146, Mismatches: 23, Indels: 14
0.80 0.13 0.08
Matches are distributed among these distances:
43 52 0.36
44 24 0.16
45 1 0.01
46 1 0.01
47 17 0.12
48 51 0.35
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (48 bp):
ATAGCCGAAGCTATCTCAATCTCGCACACTTAGTGCCAATATATGTAT
Found at i:28541039 original size:4 final size:4
Alignment explanation
Indices: 28541030--28541076 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
28541020 ATTGTTCTAT
** * *
28541030 TTTA TTTA TTTA TTTA TTTA TTTA TACA TTCA TTCA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
28541077 CTTCACTCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (4 bp):
TTTA
Found at i:28555814 original size:25 final size:24
Alignment explanation
Indices: 28555786--28555858 Score: 78
Period size: 25 Copynumber: 2.9 Consensus size: 24
28555776 TATATTTTAA
28555786 ACTTGTTATATA-TTATTTTAAATT
1 ACTT-TTATATACTTATTTTAAATT
*
28555810 GACTTATATATTACTTATTTTAAAATT
1 -ACTTTTATA-TACTTATTTT-AAATT
28555837 A-TTTTATATACCTTATTTTAAA
1 ACTTTTATATA-CTTATTTTAAA
28555859 CCCCATTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
24 9 0.21
25 20 0.48
26 8 0.19
27 5 0.12
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.55
Consensus pattern (24 bp):
ACTTTTATATACTTATTTTAAATT
Found at i:28555817 original size:20 final size:20
Alignment explanation
Indices: 28555773--28555818 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
28555763 CCTTTACCTA
*
28555773 TTATA-TATTTTAAACTTGT
1 TTATATTATTTTAAACTTGC
28555792 TATATATTATTTTAAA-TTGAC
1 T-TATATTATTTTAAACTTG-C
28555813 TTATAT
1 TTATAT
28555819 ATTACTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 1 0.04
20 12 0.52
21 10 0.43
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (20 bp):
TTATATTATTTTAAACTTGC
Found at i:28555819 original size:22 final size:21
Alignment explanation
Indices: 28555774--28555822 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
28555764 CTTTACCTAT
28555774 TATA-TATTTTAAACTTGTTA
1 TATATTATTTTAAACTTGTTA
28555794 TATATTATTTTAAA-TTGACTTA
1 TATATTATTTTAAACTTG--TTA
28555816 TATATTA
1 TATATTA
28555823 CTTATTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.27
21 9 0.35
22 10 0.38
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (21 bp):
TATATTATTTTAAACTTGTTA
Found at i:28565857 original size:18 final size:18
Alignment explanation
Indices: 28565834--28565873 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
28565824 ATGACTTTTA
*
28565834 AATAATTTTTTATTAAAT
1 AATAATATTTTATTAAAT
*
28565852 AATAATATTTTATTAATT
1 AATAATATTTTATTAAAT
28565870 AATA
1 AATA
28565874 TTATAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATAATATTTTATTAAAT
Found at i:28573658 original size:26 final size:26
Alignment explanation
Indices: 28573629--28573694 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 26
28573619 GATGCAAGCG
*
28573629 ATGAGATAAGTAATAA-A-AATAATAGT
1 ATGA-ATAA-TAATAATATAATAATAAT
28573655 ATGAATAATAATAATATAATAATAAT
1 ATGAATAATAATAATATAATAATAAT
*
28573681 ATTAATAATAATAA
1 ATGAATAATAATAA
28573695 CCAATGCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
24 6 0.17
25 5 0.14
26 25 0.69
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.32
Consensus pattern (26 bp):
ATGAATAATAATAATATAATAATAAT
Found at i:28573664 original size:3 final size:3
Alignment explanation
Indices: 28573634--28573694 Score: 63
Period size: 3 Copynumber: 20.3 Consensus size: 3
28573624 AAGCGATGAG
* *
28573634 ATA AGTA ATA AAA ATA ATA GT- ATGA ATA ATA ATA AT- ATA ATA ATA
1 ATA A-TA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA
*
28573679 ATA TTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
28573695 CCAATGCAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 3 0.06
3 40 0.83
4 5 0.10
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:28574386 original size:55 final size:55
Alignment explanation
Indices: 28574302--28574411 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
28574292 TCGTTTGGAC
*
28574302 GTTCAACATCCAGCCCAAAACGGTGCCGTTTTGCAATGCTATAAAATCAACATTT
1 GTTCAACATCCAGCCCAAAACGGCGCCGTTTTGCAATGCTATAAAATCAACATTT
*
28574357 GTTCAACATCCGGCCCAAAACGGCGCCGTTTTGCAATGCTATAAAATCAACATTT
1 GTTCAACATCCAGCCCAAAACGGCGCCGTTTTGCAATGCTATAAAATCAACATTT
28574412 CTAAAAAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (55 bp):
GTTCAACATCCAGCCCAAAACGGCGCCGTTTTGCAATGCTATAAAATCAACATTT
Found at i:28577008 original size:20 final size:21
Alignment explanation
Indices: 28576976--28577018 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
28576966 TCGCTGCCTA
28576976 ACGGTTGAAAAAACTACATAG
1 ACGGTTGAAAAAACTACATAG
28576997 ACGGTT-AAAAAACTACATAG
1 ACGGTTGAAAAAACTACATAG
28577017 AC
1 AC
28577019 AATTTTACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.19
Consensus pattern (21 bp):
ACGGTTGAAAAAACTACATAG
Found at i:28577185 original size:6 final size:5
Alignment explanation
Indices: 28577171--28577226 Score: 60
Period size: 5 Copynumber: 10.8 Consensus size: 5
28577161 TTAGTTTAGG
* *
28577171 TTTTC TTTTC ATTTTC TTTTC TCTTA TTTTC TTTT- TTTTC TTTTTC TTTTTC
1 TTTTC TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC -TTTTC
28577223 TTTT
1 TTTT
28577227 TGTTGTAGTA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
4 4 0.09
5 24 0.55
6 16 0.36
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:28577227 original size:6 final size:6
Alignment explanation
Indices: 28577171--28577227 Score: 57
Period size: 6 Copynumber: 9.7 Consensus size: 6
28577161 TTAGTTTAGG
* *
28577171 TTTTC- TTTTCA TTTTCT TTTCTCT TATTT-T CTTT-T TTTTCT TTTTCT
1 TTTTCT TTTTCT TTTTCT TTT-TCT T-TTTCT TTTTCT TTTTCT TTTTCT
28577218 TTTTCT TTTT
1 TTTTCT TTTT
28577228 GTTGTAGTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
5 12 0.27
6 26 0.58
7 5 0.11
8 2 0.04
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:28579209 original size:20 final size:20
Alignment explanation
Indices: 28579183--28579228 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
28579173 TGAAAGTTCC
* *
28579183 AAAAATAATAAAAGAAATAA
1 AAAAATAACAAAAAAAATAA
*
28579203 TAAAATAACAAAAAAAATAA
1 AAAAATAACAAAAAAAATAA
28579223 AAAAAT
1 AAAAAT
28579229 GAAATAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.15
Consensus pattern (20 bp):
AAAAATAACAAAAAAAATAA
Found at i:28585192 original size:79 final size:79
Alignment explanation
Indices: 28585100--28585256 Score: 233
Period size: 79 Copynumber: 2.0 Consensus size: 79
28585090 GCAAAATTAA
* * * * * * *
28585100 ATAAATTCGCAATCAATACTAAATTTATTTTTCAAAATCATGAAAAATTCAAGCCTAGTAGTATT
1 ATAAATTCACAATCAACACTAAATATATTCTACAAAATCATGAAAAATTCAAACCTAGTAGTATC
28585165 AGCAATTAACTTTC
66 AGCAATTAACTTTC
* *
28585179 ATAAATTCACAATCAGCACTAAATATATTCTACAAAATCATGAAAAATTCAAATCTAGTAGTATC
1 ATAAATTCACAATCAACACTAAATATATTCTACAAAATCATGAAAAATTCAAACCTAGTAGTATC
28585244 AGCAATTAACTTT
66 AGCAATTAACTTT
28585257 TATCAAATCA
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 69 1.00
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (79 bp):
ATAAATTCACAATCAACACTAAATATATTCTACAAAATCATGAAAAATTCAAACCTAGTAGTATC
AGCAATTAACTTTC
Found at i:28587413 original size:5 final size:5
Alignment explanation
Indices: 28587403--28587431 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
28587393 TTTTTCATAG
28587403 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
28587432 ATTGCAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:28588649 original size:38 final size:37
Alignment explanation
Indices: 28588565--28588659 Score: 97
Period size: 38 Copynumber: 2.5 Consensus size: 37
28588555 TATACGTACT
*
28588565 TATACATACTTAAATATATTTTTCATATTTCATAATTC
1 TATACATACTTAAATATATTTTACATATTT-ATAATTC
* *
28588603 T-TATATACTTACATATATTTATACATATTT-TACA-TC
1 TATACATACTTAAATATATTT-TACATATTTATA-ATTC
*
28588639 ATATACATACTTATATATATT
1 -TATACATACTTAAATATATT
28588660 CTTTATATTC
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
36 4 0.08
37 19 0.40
38 25 0.52
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (37 bp):
TATACATACTTAAATATATTTTACATATTTATAATTC
Found at i:28590117 original size:19 final size:20
Alignment explanation
Indices: 28590075--28590123 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
28590065 TAATTATTTG
* * *
28590075 TAAAATTTAATTTGAATATA
1 TAAAATATATTTTAAATATA
28590095 TAAAATATATTTTAAATAT-
1 TAAAATATATTTTAAATATA
28590114 TAAAATATAT
1 TAAAATATAT
28590124 AATGTTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
TAAAATATATTTTAAATATA
Found at i:28593689 original size:13 final size:13
Alignment explanation
Indices: 28593671--28593696 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28593661 TTAAAAAATA
28593671 TTAAATTTTAACT
1 TTAAATTTTAACT
28593684 TTAAATTTTAACT
1 TTAAATTTTAACT
28593697 AATGTAAAGT
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:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
TTAAATTTTAACT
Found at i:28593959 original size:29 final size:29
Alignment explanation
Indices: 28593927--28593984 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
28593917 GATTTGTTAA
*
28593927 AACGTAGAATTTTAT-TTGTAAAATTTATT
1 AACGAAGAATTTTATATT-TAAAATTTATT
*
28593956 AACGAATAATTTTATATTTAAAATTTATT
1 AACGAAGAATTTTATATTTAAAATTTATT
28593985 TAATTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.48
Consensus pattern (29 bp):
AACGAAGAATTTTATATTTAAAATTTATT
Found at i:28603705 original size:61 final size:61
Alignment explanation
Indices: 28603615--28603744 Score: 253
Period size: 61 Copynumber: 2.1 Consensus size: 61
28603605 TCCCTACTAC
28603615 TTTT-TTCAAGGATCAATATTGATATTGATATTTTTACTTTTATATAATATAGTTTGTACT
1 TTTTATTCAAGGATCAATATTGATATTGATATTTTTACTTTTATATAATATAGTTTGTACT
28603675 TTTTATTCAAGGATCAATATTGATATTGATATTTTTACTTTTATATAATATAGTTTGTACT
1 TTTTATTCAAGGATCAATATTGATATTGATATTTTTACTTTTATATAATATAGTTTGTACT
28603736 TTTTATTCA
1 TTTTATTCA
28603745 TTTCAATTAT
Statistics
Matches: 69, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
60 4 0.06
61 65 0.94
ACGTcount: A:0.30, C:0.07, G:0.09, T:0.54
Consensus pattern (61 bp):
TTTTATTCAAGGATCAATATTGATATTGATATTTTTACTTTTATATAATATAGTTTGTACT
Done.