Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010790.1 Kokia drynarioides strain JFW-HI SEQ_125757, whole genome shotgun sequence
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: 192150
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 87 characters in sequence are not A, C, G, or T
Found at i:925 original size:21 final size:21
Alignment explanation
Indices: 899--941 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
889 TAGGGTCCAT
*
899 TTGCCCCGGAGGAGTAGAGTA
1 TTGCCCCGGAGGAATAGAGTA
*
920 TTGCCCGGGAGGAATAGAGTA
1 TTGCCCCGGAGGAATAGAGTA
941 T
1 T
942 CACGATGGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.16, G:0.37, T:0.21
Consensus pattern (21 bp):
TTGCCCCGGAGGAATAGAGTA
Found at i:1066 original size:45 final size:45
Alignment explanation
Indices: 947--1072 Score: 173
Period size: 45 Copynumber: 2.8 Consensus size: 45
937 AGTATCACGA
* * **
947 TGGCTCGTCAAACTCA-GCATGATATCCTTCCCTTGAGTATTGCGG
1 TGGCTCATCAAACTGAGGC-TGATATCCTTGGCTTGAGTATTGCGG
*
992 TGGCTCATCAAATTGAGGCTGATATCCTTGGCTTGAGTATTGCGG
1 TGGCTCATCAAACTGAGGCTGATATCCTTGGCTTGAGTATTGCGG
* *
1037 TGGTTCATCAAACTGAGGCTGATGTCCTTGGCTTGA
1 TGGCTCATCAAACTGAGGCTGATATCCTTGGCTTGA
1073 TGAGCTATGC
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
45 70 0.97
46 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (45 bp):
TGGCTCATCAAACTGAGGCTGATATCCTTGGCTTGAGTATTGCGG
Found at i:3949 original size:2 final size:2
Alignment explanation
Indices: 3942--3992 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
3932 TCTAAATTAC
3942 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3984 AT AT GT AT A
1 AT AT AT AT A
3993 AAATAATATA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5203 original size:20 final size:22
Alignment explanation
Indices: 5156--5203 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
5146 AATATATTTT
5156 TTAAATTTTTATTGTATGTAAA
1 TTAAATTTTTATTGTATGTAAA
* *
5178 -TGAATTTTT-TTGTTTG-AAA
1 TTAAATTTTTATTGTATGTAAA
5197 TTAAATT
1 TTAAATT
5204 ACATTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 3 0.14
20 11 0.50
21 8 0.36
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (22 bp):
TTAAATTTTTATTGTATGTAAA
Found at i:22259 original size:22 final size:21
Alignment explanation
Indices: 22242--22282 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
22232 TTTAAAATCC
22242 TAAAAATT-TAAATATAAAAAT
1 TAAAAATTATAAATAT-AAAAT
*
22263 TAAAAATTATTAATATAAAA
1 TAAAAATTATAAATATAAAA
22283 ATTTTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
TAAAAATTATAAATATAAAAT
Found at i:22261 original size:14 final size:14
Alignment explanation
Indices: 22259--22315 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
22249 TTAAATATAA
22259 AAAT-TAAAAATTAT
1 AAATATAAAAATT-T
*
22273 TAATATAAAAATTT
1 AAATATAAAAATTT
* *
22287 TAATATGAAGAATTT
1 AAATAT-AAAAATTT
22302 AAAATATAAAAATT
1 -AAATATAAAAATT
22316 ATTTTTAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 10 0.28
15 21 0.58
16 5 0.14
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (14 bp):
AAATATAAAAATTT
Found at i:22283 original size:22 final size:21
Alignment explanation
Indices: 22242--22285 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
22232 TTTAAAATCC
22242 TAAAAATTTAAATATAAAAAT
1 TAAAAATTTAAATATAAAAAT
*
22263 TAAAAATTATTAATATAAAAAT
1 TAAAAATT-TAAATATAAAAAT
22285 T
1 T
22286 TTAATATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAAAATTTAAATATAAAAAT
Found at i:32934 original size:6 final size:6
Alignment explanation
Indices: 32923--32960 Score: 67
Period size: 6 Copynumber: 6.2 Consensus size: 6
32913 TAGTACTTGC
32923 TTTGTG TTTGTG TTTGTG TTTGTG TTTGTG TGTTGTG T
1 TTTGTG TTTGTG TTTGTG TTTGTG TTTGTG T-TTGTG T
32961 ATAATTATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.00, C:0.00, G:0.34, T:0.66
Consensus pattern (6 bp):
TTTGTG
Found at i:40006 original size:19 final size:19
Alignment explanation
Indices: 39982--40021 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
39972 AGAGTACTGC
39982 ACATGTATTCCATGAATTT
1 ACATGTATTCCATGAATTT
40001 ACATGTATTCCATGAATTT
1 ACATGTATTCCATGAATTT
40020 AC
1 AC
40022 TTTGATGTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (19 bp):
ACATGTATTCCATGAATTT
Found at i:40948 original size:12 final size:12
Alignment explanation
Indices: 40931--40956 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40921 TAAAATAATG
40931 TTATATTAATAA
1 TTATATTAATAA
40943 TTATATTAATAA
1 TTATATTAATAA
40955 TT
1 TT
40957 TATAAGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TTATATTAATAA
Found at i:40997 original size:30 final size:29
Alignment explanation
Indices: 40957--41026 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 29
40947 ATTAATAATT
* *
40957 TATAAGAATTAAATCAAATTAAAATTTCATG
1 TATAA-AATTAAATAAAATTAAAA-TTCATA
*
40988 TATAAAATTATATAAAATTAAAATTCATA
1 TATAAAATTAAATAAAATTAAAATTCATA
*
41017 TATATAATTA
1 TATAAAATTA
41027 TACATTAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 14 0.40
30 16 0.46
31 5 0.14
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (29 bp):
TATAAAATTAAATAAAATTAAAATTCATA
Found at i:41025 original size:29 final size:30
Alignment explanation
Indices: 40957--41028 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
40947 ATTAATAATT
* * *
40957 TATAAGAATTAAATCAAATTAAAATTTCATG
1 TATAA-AATTATATAAAATTAAAATTTCATA
40988 TATAAAATTATATAAAATTAAAA-TTCATA
1 TATAAAATTATATAAAATTAAAATTTCATA
*
41017 TATATAATTATA
1 TATAAAATTATA
41029 CATTAAACCA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 16 0.43
30 16 0.43
31 5 0.14
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (30 bp):
TATAAAATTATATAAAATTAAAATTTCATA
Found at i:46688 original size:2 final size:2
Alignment explanation
Indices: 46681--46708 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
46671 AATTAAAATA
46681 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46709 TTAAAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48437 original size:21 final size:21
Alignment explanation
Indices: 48413--48468 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
48403 AGACATATAC
48413 AAATGATA-TTAATGTATAATG
1 AAATGATATTTAAT-TATAATG
**
48434 AAATTTTATTTAATTATAATG
1 AAATGATATTTAATTATAATG
**
48455 AAATTTTATTTAAT
1 AAATGATATTTAAT
48469 CCAACCTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 27 0.84
22 5 0.16
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (21 bp):
AAATGATATTTAATTATAATG
Found at i:53657 original size:16 final size:17
Alignment explanation
Indices: 53624--53661 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
53614 CAAATAATTT
53624 AAAAATTAAAAATATTC
1 AAAAATTAAAAATATTC
* *
53641 AAAATTTAAAAA-CTTC
1 AAAAATTAAAAATATTC
53657 AAAAA
1 AAAAA
53662 GTTCAAAAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAAATTAAAAATATTC
Found at i:55034 original size:90 final size:90
Alignment explanation
Indices: 54920--55100 Score: 317
Period size: 90 Copynumber: 2.0 Consensus size: 90
54910 CATGTGATAT
* *
54920 GTTAAAGATAGATAGGTTACATGCGTAATAACATGTTACTCCCCAAGAGTTGCAAGCGTCTTAGC
1 GTTAAAGATAGATAGGCTACATGCGTAATAACATGTTACTCCCCAAGAGTTGCAAACGTCTTAGC
54985 AAAGGGCTCGTCAAACTATGGGTGA
66 AAAGGGCTCGTCAAACTATGGGTGA
* * *
55010 GTTAAGGATAGATAGGCTACATGCGTAGTGACATGTTACTCCCCAAGAGTTGCAAACGTCTTAGC
1 GTTAAAGATAGATAGGCTACATGCGTAATAACATGTTACTCCCCAAGAGTTGCAAACGTCTTAGC
55075 AAAGGGCTCGTCAAACTATGGGTGA
66 AAAGGGCTCGTCAAACTATGGGTGA
55100 G
1 G
55101 ACATTGGGGA
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 86 1.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (90 bp):
GTTAAAGATAGATAGGCTACATGCGTAATAACATGTTACTCCCCAAGAGTTGCAAACGTCTTAGC
AAAGGGCTCGTCAAACTATGGGTGA
Found at i:72756 original size:18 final size:19
Alignment explanation
Indices: 72720--72756 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
72710 TTCCATTTTT
*
72720 ATCTGTTAACATTTGTTTG
1 ATCTGTTAACATCTGTTTG
72739 ATCTGTTAACA-CTGTTTG
1 ATCTGTTAACATCTGTTTG
72757 GGATTTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.49
Consensus pattern (19 bp):
ATCTGTTAACATCTGTTTG
Found at i:72763 original size:29 final size:29
Alignment explanation
Indices: 72730--72791 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
72720 ATCTGTTAAC
*
72730 ATTTGTTTGATCTGTTAACACTGTTTGGG
1 ATTTGTTTGATCTATTAACACTGTTTGGG
72759 ATTTGTTTGATCTATTAACACTGTTTGGG
1 ATTTGTTTGATCTATTAACACTGTTTGGG
72788 ATTT
1 ATTT
72792 AAGGTTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.19, C:0.10, G:0.21, T:0.50
Consensus pattern (29 bp):
ATTTGTTTGATCTATTAACACTGTTTGGG
Found at i:75896 original size:12 final size:12
Alignment explanation
Indices: 75869--75903 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
75859 ATTGTTGTTC
*
75869 TGAACTATTT-T
1 TGAACTTTTTGT
75880 TGAACTTTTTGT
1 TGAACTTTTTGT
75892 TGAACTTTTTGT
1 TGAACTTTTTGT
75904 AAAGTTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.20, C:0.09, G:0.14, T:0.57
Consensus pattern (12 bp):
TGAACTTTTTGT
Found at i:76216 original size:13 final size:13
Alignment explanation
Indices: 76198--76222 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
76188 CTTTTTGTAA
76198 AGTTTCCTATCAT
1 AGTTTCCTATCAT
76211 AGTTTCCTATCA
1 AGTTTCCTATCA
76223 AATTTGGCAA
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:0.24, C:0.24, G:0.08, T:0.44
Consensus pattern (13 bp):
AGTTTCCTATCAT
Found at i:76544 original size:16 final size:16
Alignment explanation
Indices: 76523--76556 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
76513 ATCAAACCAG
*
76523 CAGCCATGAGAAGTAA
1 CAGCCATGAGAAGCAA
76539 CAGCCATGAGAAGCAA
1 CAGCCATGAGAAGCAA
76555 CA
1 CA
76557 ACCAACAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.24, G:0.24, T:0.09
Consensus pattern (16 bp):
CAGCCATGAGAAGCAA
Found at i:84561 original size:13 final size:13
Alignment explanation
Indices: 84545--84570 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
84535 GTTTCTAACC
84545 CTTTTCTTTTTTT
1 CTTTTCTTTTTTT
84558 CTTTTCTTTTTTT
1 CTTTTCTTTTTTT
84571 TTCCTAAGAT
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:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
CTTTTCTTTTTTT
Found at i:91341 original size:23 final size:22
Alignment explanation
Indices: 91302--91350 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
91292 TAATATTTTT
*
91302 ATATAAAATCAATAAAATCTTAC
1 ATATAAAATCAATAAAAT-TTAA
*
91325 ATATAAAA-CATTGAAAATTTAA
1 ATATAAAATCAAT-AAAATTTAA
91347 ATAT
1 ATAT
91351 TCAATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.33
Consensus pattern (22 bp):
ATATAAAATCAATAAAATTTAA
Found at i:91640 original size:3 final size:3
Alignment explanation
Indices: 91632--91657 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
91622 AAAGCTACTC
91632 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
91658 CTTAAAGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:101817 original size:25 final size:24
Alignment explanation
Indices: 101782--101884 Score: 105
Period size: 25 Copynumber: 4.5 Consensus size: 24
101772 CGAAGTATTT
101782 AACAGTAAGCACACA-AGTGCTGGGG
1 AACAG-AAGCACACACAGTGCT-GGG
101807 AAACAGAAGCACACACAG-G-T---
1 -AACAGAAGCACACACAGTGCTGGG
101827 AACAGAAGCACACACAGTGCTGGG
1 AACAGAAGCACACACAGTGCTGGG
*
101851 TAACAGAAGCACACACAATGCT--G
1 -AACAGAAGCACACACAGTGCTGGG
101874 AACAGAAGCAC
1 AACAGAAGCAC
101885 GCTAGCGTTC
Statistics
Matches: 69, Mismatches: 1, Indels: 18
0.78 0.01 0.20
Matches are distributed among these distances:
19 17 0.25
20 1 0.01
21 1 0.01
22 11 0.16
23 1 0.01
24 1 0.01
25 30 0.43
26 7 0.10
ACGTcount: A:0.43, C:0.24, G:0.24, T:0.09
Consensus pattern (24 bp):
AACAGAAGCACACACAGTGCTGGG
Found at i:101840 original size:44 final size:45
Alignment explanation
Indices: 101781--101867 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 45
101771 CCGAAGTATT
101781 TAACAGTAAGCACACA-AGTGCTGGGGAAACAGAAGCACACACAGG
1 TAACAGTAAGCACACACAGTGCT-GGGAAACAGAAGCACACACAGG
*
101826 TAACAG-AAGCACACACAGTGCTGGGTAACAGAAGCACACACA
1 TAACAGTAAGCACACACAGTGCTGGGAAACAGAAGCACACACA
101868 ATGCTGAACA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
44 28 0.70
45 12 0.30
ACGTcount: A:0.43, C:0.24, G:0.24, T:0.09
Consensus pattern (45 bp):
TAACAGTAAGCACACACAGTGCTGGGAAACAGAAGCACACACAGG
Found at i:103328 original size:13 final size:13
Alignment explanation
Indices: 103310--103337 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
103300 CTTTTATAGC
103310 CTTTTCATCATTT
1 CTTTTCATCATTT
103323 CTTTTCATCATTT
1 CTTTTCATCATTT
103336 CT
1 CT
103338 CTAGATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.25, G:0.00, T:0.61
Consensus pattern (13 bp):
CTTTTCATCATTT
Found at i:104650 original size:5 final size:5
Alignment explanation
Indices: 104642--104669 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
104632 TTAAAAAATA
104642 TATAT TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TAT
104670 TGTAATATTT
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:105682 original size:2 final size:2
Alignment explanation
Indices: 105675--105711 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
105665 GTTAAAATGG
105675 TA TA TA TA 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 TA TA TA TA T
105712 TTACATTCCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:119437 original size:23 final size:23
Alignment explanation
Indices: 119364--119585 Score: 180
Period size: 23 Copynumber: 9.6 Consensus size: 23
119354 TATACGGAAC
* *
119364 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
119386 -AACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
119407 GGGCAACAGAGAGCACACACAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* **
119433 AAACAGAGAGTACACAAAGTATT
1 AAACAGAGAGCACACAAAGTGCT
* *
119456 AATCGGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
119479 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * * *
119502 AATAACAAAGAGTACACAAAATACT
1 -A-AACAGAGAGCACACAAAGTGCT
**
119527 AATTAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
119550 AATCAGAGAGCACACGAAGTGGT
1 AAACAGAGAGCACACAAAGTGCT
*
119573 AATCAGAGAGCAC
1 AAACAGAGAGCAC
119586 GAGACGTGCT
Statistics
Matches: 160, Mismatches: 32, Indels: 15
0.77 0.15 0.07
Matches are distributed among these distances:
21 17 0.11
23 106 0.66
24 2 0.01
25 29 0.18
26 6 0.04
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.14
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:119516 original size:71 final size:69
Alignment explanation
Indices: 119364--119564 Score: 248
Period size: 71 Copynumber: 2.9 Consensus size: 69
119354 TATACGGAAC
* * *
119364 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACA-TAAGTGCTGGGCAA-CAGAGAGCACAC
1 AAACAAAGAGTACACAAAATACTAATCAGAGAGCACACAAAGTGCT----AATCAGAGAGCACAC
119425 ACAGTGCT
62 ACAGTGCT
* * * *
119433 AAACAGAGAGTACACAAAGTATTAATCGGAGAGCACACAAAGTGCTAATCAGAGAGCACACACAG
1 AAACAAAGAGTACACAAAATACTAATCAGAGAGCACACAAAGTGCTAATCAGAGAGCACACACAG
119498 TGCT
66 TGCT
*
119502 AATAACAAAGAGTACACAAAATACTAATTAGAGAGCACACAAAGTGCTAATCAGAGAGCACAC
1 -A-AACAAAGAGTACACAAAATACTAATCAGAGAGCACACAAAGTGCTAATCAGAGAGCACAC
119565 GAAGTGGTAA
Statistics
Matches: 118, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
68 2 0.02
69 33 0.28
70 11 0.09
71 65 0.55
72 7 0.06
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.13
Consensus pattern (69 bp):
AAACAAAGAGTACACAAAATACTAATCAGAGAGCACACAAAGTGCTAATCAGAGAGCACACACAG
TGCT
Found at i:119583 original size:46 final size:46
Alignment explanation
Indices: 119367--119585 Score: 203
Period size: 46 Copynumber: 4.7 Consensus size: 46
119357 ACGGAACAAA
* * *
119367 CAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACA-TAAGTGCTGGGCAA-
1 CAGAGAGCACACAAAGTGCTAATCAGAGAGCACACAAAGTGCT----AAT
* * * **
119413 CAGAGAGCACACACAGTGCTAAACAGAGAGTACACAAAGTATTAAT
1 CAGAGAGCACACAAAGTGCTAATCAGAGAGCACACAAAGTGCTAAT
* *
119459 CGGAGAGCACACAAAGTGCTAATCAGAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAATCAGAGAGCACACAAAGTGCTAAT
* * * * *
119505 AACAAAGAGTACACAAAATACTAATTAGAGAGCACACAAAGTGCTAAT
1 --CAGAGAGCACACAAAGTGCTAATCAGAGAGCACACAAAGTGCTAAT
* *
119553 CAGAGAGCACACGAAGTGGTAATCAGAGAGCAC
1 CAGAGAGCACACAAAGTGCTAATCAGAGAGCAC
119586 GAGACGTGCT
Statistics
Matches: 139, Mismatches: 28, Indels: 12
0.78 0.16 0.07
Matches are distributed among these distances:
45 2 0.01
46 74 0.53
47 9 0.06
48 49 0.35
49 5 0.04
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.14
Consensus pattern (46 bp):
CAGAGAGCACACAAAGTGCTAATCAGAGAGCACACAAAGTGCTAAT
Found at i:119586 original size:21 final size:22
Alignment explanation
Indices: 119413--119605 Score: 115
Period size: 23 Copynumber: 8.3 Consensus size: 22
119403 TGCTGGGCAA
*
119413 CAGAGAGCACAC-ACAGTGCTAAA
1 CAGAGAG-ACACGA-AGTGCTAAT
* **
119436 CAGAGAGTACACAAAGTATTAAT
1 CAGAGAG-ACACGAAGTGCTAAT
* *
119459 CGGAGAGCACACAAAGTGCTAAT
1 CAGAGAG-ACACGAAGTGCTAAT
119482 CAGAGAGCACAC-ACAGTGCTAAT
1 CAGAGAG-ACACGA-AGTGCTAAT
* * * *
119505 AACAAAGAGTACACAAAATACTAAT
1 --CAGAGAG-ACACGAAGTGCTAAT
* *
119530 TAGAGAGCACACAAAGTGCTAAT
1 CAGAGAG-ACACGAAGTGCTAAT
*
119553 CAGAGAGCACACGAAGTGGTAAT
1 CAGAGAG-ACACGAAGTGCTAAT
119576 CAGAGAG-CACGAGACGTGCTAAAT
1 CAGAGAGACACGA-A-GTGCT-AAT
119600 -AGAGAG
1 CAGAGAG
119606 CGCGCTAGTG
Statistics
Matches: 140, Mismatches: 22, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
21 5 0.04
22 2 0.01
23 111 0.79
24 4 0.03
25 17 0.12
26 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (22 bp):
CAGAGAGACACGAAGTGCTAAT
Found at i:121747 original size:23 final size:23
Alignment explanation
Indices: 121713--121839 Score: 166
Period size: 23 Copynumber: 5.4 Consensus size: 23
121703 TGCTGGGTAA
*
121713 CAGAGAGCACACATAGTGCTAAAT
1 CAGAGAGCACACAAAGTGCT-AAT
* * *
121737 -AGAGAGTACACAAAGTACTAGT
1 CAGAGAGCACACAAAGTGCTAAT
*
121759 CAGAGAGCACACAAAGTGCTAGT
1 CAGAGAGCACACAAAGTGCTAAT
121782 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
121805 CAGAGAGCACACATAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
121828 AACAGAGAGCAC
1 --CAGAGAGCAC
121840 GAGACGTGCT
Statistics
Matches: 92, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
22 2 0.02
23 80 0.87
25 10 0.11
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.14
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Found at i:121860 original size:48 final size:46
Alignment explanation
Indices: 121711--121860 Score: 133
Period size: 46 Copynumber: 3.2 Consensus size: 46
121701 AGTGCTGGGT
* * * *
121711 AACAGAGAGCACACATAGTGCTAAAT-AGAGAGTACACAAAGTACTA
1 AACAAAGAGCACACAAAGTGCT-AATCAGAGAGCACACAAAGTGCTA
** * *
121757 GTCAGAGAGCACACAAAGTGCTAGTCAGAGAGCACACAAAGTGCTA
1 AACAAAGAGCACACAAAGTGCTAATCAGAGAGCACACAAAGTGCTA
* * * * *
121803 ATCAGAGAGCACACATAGTGCTAATAACAGAGAGCACGA-GACGTGCTA
1 AACAAAGAGCACACAAAGTGCTAAT--CAGAGAGCAC-ACAAAGTGCTA
121851 AACAAAGAGC
1 AACAAAGAGC
121861 GCGCTAGTGT
Statistics
Matches: 87, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
45 2 0.02
46 59 0.68
48 25 0.29
49 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.13
Consensus pattern (46 bp):
AACAAAGAGCACACAAAGTGCTAATCAGAGAGCACACAAAGTGCTA
Found at i:127818 original size:23 final size:23
Alignment explanation
Indices: 127784--127910 Score: 166
Period size: 23 Copynumber: 5.4 Consensus size: 23
127774 TGCTGGGTAA
*
127784 CAGAGAGCACACATAGTGCTAAAT
1 CAGAGAGCACACAAAGTGCT-AAT
* * *
127808 -AGAGAGTACACAAAGTACTAGT
1 CAGAGAGCACACAAAGTGCTAAT
*
127830 CAGAGAGCACACAAAGTGCTAGT
1 CAGAGAGCACACAAAGTGCTAAT
127853 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
127876 CAGAGAGCACACATAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
127899 AACAGAGAGCAC
1 --CAGAGAGCAC
127911 GAGACGTGCT
Statistics
Matches: 92, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
22 2 0.02
23 80 0.87
25 10 0.11
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.14
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Found at i:127931 original size:48 final size:46
Alignment explanation
Indices: 127782--127931 Score: 133
Period size: 46 Copynumber: 3.2 Consensus size: 46
127772 AGTGCTGGGT
* * * *
127782 AACAGAGAGCACACATAGTGCTAAAT-AGAGAGTACACAAAGTACTA
1 AACAAAGAGCACACAAAGTGCT-AATCAGAGAGCACACAAAGTGCTA
** * *
127828 GTCAGAGAGCACACAAAGTGCTAGTCAGAGAGCACACAAAGTGCTA
1 AACAAAGAGCACACAAAGTGCTAATCAGAGAGCACACAAAGTGCTA
* * * * *
127874 ATCAGAGAGCACACATAGTGCTAATAACAGAGAGCACGA-GACGTGCTA
1 AACAAAGAGCACACAAAGTGCTAAT--CAGAGAGCAC-ACAAAGTGCTA
127922 AACAAAGAGC
1 AACAAAGAGC
127932 GCGCTAGTGT
Statistics
Matches: 87, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
45 2 0.02
46 59 0.68
48 25 0.29
49 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.13
Consensus pattern (46 bp):
AACAAAGAGCACACAAAGTGCTAATCAGAGAGCACACAAAGTGCTA
Found at i:132972 original size:57 final size:58
Alignment explanation
Indices: 132804--133326 Score: 265
Period size: 60 Copynumber: 8.7 Consensus size: 58
132794 AAAAATCAAA
* * *
132804 TTTTTGGATGTTGGTCATGCAATGGCCGACATCCCTTTTTGTTAGATGAAAAATTCAATT
1 TTTTTGG-TGTTGGTCATGCAATGGCCGACACCCCTTTTTGTCAGATAAAAAATT-AATT
* * * * *
132864 TTTTTGGTGTTGATCATGCCATGGCCGACACCCCTATTT-ACTGATAAAAAAATT-ATT
1 TTTTTGGTGTTGGTCATGCAATGGCCGACACCCCTTTTTGTCAGAT-AAAAAATTAATT
* * * *
132921 ATTTTTTG-GTTGGTCATGTAATGGCTGACACCCCCTTTTTGTCAGATAAAAAATCCAATT
1 -TTTTTGGTGTTGGTCATGCAATGGCCGACA-CCCCTTTTTGTCAGATAAAAAAT-TAATT
* * * * * * *
132981 CTTTTAGTGTTGGCCATGTC-ATGGTCGACACACCTATTTATCAGATAAAAAAATTTAAATTT
1 TTTTTGGTGTTGGTCATG-CAATGGCCGACACCCCTTTTTGTCAGAT-AAAAAA-TT-AA-TT
** * * * * * * * *
133043 TTTTTAATGTTAG-CTAAGCCATGACCGACACCCCCTTTTTTATCTGAATAAAAAATCAAAT
1 TTTTTGGTGTTGGTC-ATGCAATGGCCGACA-CCCC-TTTTTGTCAG-ATAAAAAATTAATT
* * * * * * * *
133104 TTTTGGGTGTTGGCCGTGCCATGGCCGACATCCCTATTTATTAGATAAAAAATTTCAATT
1 TTTTTGGTGTTGGTCATGCAATGGCCGACACCCCTTTTTGTCAGATAAAAAA-TT-AATT
* * * * *
133164 CTTTTT-GTGTTGGTCATCCCATGGCTGACACCCCCTTTTTGAT-ATGAATAAAAAATCAAAT
1 -TTTTTGGTGTTGGTCATGCAATGGCCGACA-CCCCTTTTTG-TCA-G-ATAAAAAATTAATT
* * * * *
133225 TTTTTAGTGTTGGTCATGTC-ATGGTCGATA-CCTTTATTTATCAGATTAAAAAAATTCAATT
1 TTTTTGGTGTTGGTCATG-CAATGGCCGACACCCCTT-TTTGTCAGA-T-AAAAAATT-AATT
* *
133286 ATTTTTTGTGTTGGCCATGTC-ATGGCCGACATCCCCTTTTT
1 -TTTTTGGTGTTGGTCATG-CAATGGCCGACA-CCCCTTTTT
133327 TATCTGAATA
Statistics
Matches: 354, Mismatches: 74, Indels: 67
0.72 0.15 0.14
Matches are distributed among these distances:
57 21 0.06
58 33 0.09
59 72 0.20
60 75 0.21
61 63 0.18
62 55 0.16
63 15 0.04
64 18 0.05
65 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.38
Consensus pattern (58 bp):
TTTTTGGTGTTGGTCATGCAATGGCCGACACCCCTTTTTGTCAGATAAAAAATTAATT
Found at i:133011 original size:60 final size:58
Alignment explanation
Indices: 132749--133435 Score: 358
Period size: 59 Copynumber: 11.5 Consensus size: 58
132739 AAAAAAAAAA
** * * * * *
132749 TTAGTGTTGGCCAT-TGCATGATCGACATCCCTTTTAATCATATAAAAAAATCAAATTT
1 TTAGTGTTGGCCATGT-CATGGCCGACACCCCTTTTTATCAGATAAAAAATTCAATTTT
* * * * * *
132807 TTGGATGTTGGTCATG-CAATGGCCGACATCCCTTTTTGTTAGATGAAAAATTCAATTTTT
1 TTAG-TGTTGGCCATGTC-ATGGCCGACACCCCTTTTTATCAGATAAAAAATTCAA-TTTT
* ** * * *
132867 TTGGTGTTGATCATGCCATGGCCGACACCCCTATTTA-CTGATAAAAAAATT-ATTATTTT
1 TTAGTGTTGGCCATGTCATGGCCGACACCCCTTTTTATCAGAT-AAAAAATTCA--ATTTT
* * * * *
132926 TT-G-GTTGGTCATGTAATGGCTGACACCCCCTTTTTGTCAGATAAAAAATCCAATTCTT
1 TTAGTGTTGGCCATGTCATGGCCGACA-CCCCTTTTTATCAGATAAAAAATTCAATT-TT
* * * *
132984 TTAGTGTTGGCCATGTCATGGTCGACACACCTATTTATCAGATAAAAAAATTTAAATTTTTT
1 TTAGTGTTGGCCATGTCATGGCCGACACCCCTTTTTATCAGAT-AAAAAA-TTCAA--TTTT
* * * * * * *
133046 TTAATGTTAGCTAAGCCATGACCGACACCCCCTTTTTTATCTGAATAAAAAA-TCAAATTTT
1 TTAGTGTTGGCCATGTCATGGCCGACA-CCCC-TTTTTATCAG-ATAAAAAATTC-AATTTT
** * * * * *
133107 TGGGTGTTGGCCGTGCCATGGCCGACATCCCTATTTATTAGATAAAAAATTTCAATTCTT
1 TTAGTGTTGGCCATGTCATGGCCGACACCCCTTTTTATCAGATAAAAAA-TTCAATT-TT
* * ** *
133167 TTTGTGTTGGTCATCCCATGGCTGACACCCCCTTTTTGAT-ATGAATAAAAAA-TCAAATTTT
1 TTAGTGTTGGCCATGTCATGGCCGACA-CCCCTTTTT-ATCA-G-ATAAAAAATTC-AATTTT
* * * *
133228 TTAGTGTTGGTCATGTCATGGTCGATA-CCTTTATTTATCAGATTAAAAAAATTCAATTATTT
1 TTAGTGTTGGCCATGTCATGGCCGACACCCCTT-TTTATCAGA-T-AAAAAATTCAA-T-TTT
* *
133290 TTTGTGTTGGCCATGTCATGGCCGACATCCCCTTTTTTATCTGAATAAAAAA-TCAAATTTT
1 TTAGTGTTGGCCATGTCATGGCCGACA-CCCC-TTTTTATCAG-ATAAAAAATTC-AATTTT
* * * * * ** * *
133351 TGAGTATTGACAATGCCATGATCGATA-CCCTTATTTATCTA-A-AAAAAATTAAATTTT
1 TTAGTGTTGGCCATGTCATGGCCGACACCCCTT-TTTATC-AGATAAAAAATTCAATTTT
** ** *
133408 TGGGTGTTAACCATGTAATGGCCGACAC
1 TTAGTGTTGGCCATGTCATGGCCGACAC
133436 TAACTTTCCC
Statistics
Matches: 484, Mismatches: 99, Indels: 92
0.72 0.15 0.14
Matches are distributed among these distances:
57 51 0.11
58 41 0.08
59 125 0.26
60 73 0.15
61 83 0.17
62 59 0.12
63 23 0.05
64 24 0.05
65 5 0.01
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (58 bp):
TTAGTGTTGGCCATGTCATGGCCGACACCCCTTTTTATCAGATAAAAAATTCAATTTT
Found at i:133226 original size:121 final size:120
Alignment explanation
Indices: 132749--133408 Score: 553
Period size: 123 Copynumber: 5.5 Consensus size: 120
132739 AAAAAAAAAA
** * * *
132749 TTAGTGTTGGCCATTG-CATGATCGACATCCCT-TTTAATCATATAAAAAAA-TCAA-ATTTTTG
1 TTAGTGTTGGCCA-TGCCATGGCCGACA-CCCTATTT-ATCAGATAAAAAAATTCAATTTTTTTT
* * * * *
132810 GATGTTGGTCATGCAATGGCCGACA-TCCCTTTTTGTTA-G-ATGAAAAATTCAATTTTT
63 G-TGTTGGTCATGCCATGGCCGACACCCCCTTTTTGATATGAAT-AAAAAATCAAATTTT
* ** *
132867 TTGGTGTTGATCATGCCATGGCCGACACCCCTATTTA-CTGATAAAAAAATT--ATTATTTTTTG
1 TTAGTGTTGGCCATGCCATGGCCGACA-CCCTATTTATCAGATAAAAAAATTCAATT-TTTTTTG
** * *
132929 -GTTGGTCATGTAATGGCTGACACCCCCTTTTTG-TCA-G-ATAAAAAATCCAATTCTT
64 TGTTGGTCATGCCATGGCCGACACCCCCTTTTTGAT-ATGAATAAAAAATCAAATT-TT
* * *
132984 TTAGTGTTGGCCATGTCATGGTCGACACACCTATTTATCAGATAAAAAAATTTAAATTTTTTTTA
1 TTAGTGTTGGCCATGCCATGGCCGACAC-CCTATTTATCAGATAAAAAAA-TTCAATTTTTTTT-
* * * * * *
133049 ATGTTAG-CTAAGCCATGACCGACACCCCCTTTTTTATCTGAATAAAAAATCAAATTTT
63 GTGTTGGTC-ATGCCATGGCCGACACCCCCTTTTTGATATGAATAAAAAATCAAATTTT
** * * * *
133107 TGGGTGTTGGCCGTGCCATGGCCGACATCCCTATTTATTAGATAAAAAATTTCAATTCTTTTTGT
1 TTAGTGTTGGCCATGCCATGGCCGACA-CCCTATTTATCAGATAAAAAAATTCAATTTTTTTTGT
* *
133172 GTTGGTCATCCCATGGCTGACACCCCCTTTTTGATATGAATAAAAAATCAAATTTT
65 GTTGGTCATGCCATGGCCGACACCCCCTTTTTGATATGAATAAAAAATCAAATTTT
* * * * *
133228 TTAGTGTTGGTCATGTCATGGTCGATACCTTTATTTATCAGATTAAAAAAATTCAATTATTTTTT
1 TTAGTGTTGGCCATGCCATGGCCGACACC-CTATTTATCAGA-TAAAAAAATTCAATT-TTTTTT
* * * * *
133293 GTGTTGGCCATGTCATGGCCGACATCCCCTTTTTTATCTGAATAAAAAATCAAATTTT
63 GTGTTGGTCATGCCATGGCCGACACCCCCTTTTTGATATGAATAAAAAATCAAATTTT
* * * * ** * * *
133351 TGAGTATTGACAATGCCATGATCGATACCCTTATTTATC-TA-AAAAAAATTAAATTTTT
1 TTAGTGTTGGCCATGCCATGGCCGACACCC-TATTTATCAGATAAAAAAATTCAATTTTT
133409 GGGTGTTAAC
Statistics
Matches: 440, Mismatches: 77, Indels: 49
0.78 0.14 0.09
Matches are distributed among these distances:
116 33 0.08
117 57 0.13
118 42 0.10
119 8 0.02
120 21 0.05
121 82 0.19
122 51 0.12
123 131 0.30
124 15 0.03
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (120 bp):
TTAGTGTTGGCCATGCCATGGCCGACACCCTATTTATCAGATAAAAAAATTCAATTTTTTTTGTG
TTGGTCATGCCATGGCCGACACCCCCTTTTTGATATGAATAAAAAATCAAATTTT
Found at i:133270 original size:244 final size:240
Alignment explanation
Indices: 132852--133401 Score: 657
Period size: 244 Copynumber: 2.3 Consensus size: 240
132842 TTGTTAGATG
* * * *
132852 AAAAATTCAATTTTTTTGGTGTTGATCATGCCATGGCCGACACCCCTATTTACTGATAAAAAAAT
1 AAAAAATCAAATTTTTGGGTGTTGACCATGCCATGGCCGACACCCCTATTTACTGATAAAAAAAT
** *
132917 TATTATTTTTTGGTTGGTCATGTAATGGCTGACACCCCCTTTTTGTCAGATAAAAAATCCAATTC
66 TATTATTTTTTGGTTGGTCATCCAATGGCTGACACCCCCTTTTTGTCAGATAAAAAATCAAATTC
132982 TTTTAGTGTTGGCCATGTCATGGTCGACACACCTATTTATCAGA-TAAAAAAATTTAAATT-TTT
131 TTTTAGTGTTGGCCATGTCATGGTCGACACACCTATTTATCAGATTAAAAAAA-TTAAATTATTT
*
133045 TTTAATGTTAGCTAAGCCATGACCGACACCCCCTTTTTTATCTGAAT
195 TTT-ATGTTAGCCAAGCCATGACCGACACCCCCTTTTTTATCTGAAT
* * * * *
133092 AAAAAATCAAATTTTTGGGTGTTGGCCGTGCCATGGCCGACATCCCTATTTATTAGATAAAAAAT
1 AAAAAATCAAATTTTTGGGTGTTGACCATGCCATGGCCGACACCCCTATTTACT-GATAAAAAAA
* *
133157 TTCAATT-CTTTTTGTGTTGGTCATCCCATGGCTGACACCCCCTTTTTGAT-ATGAATAAAAAAT
65 TT--ATTATTTTTTG-GTTGGTCATCCAATGGCTGACACCCCCTTTTTG-TCA-G-ATAAAAAAT
* * * *
133220 CAAATT-TTTTAGTGTTGGTCATGTCATGGTCGATAC-CTTTATTTATCAGATTAAAAAAATTCA
124 CAAATTCTTTTAGTGTTGGCCATGTCATGGTCGACACAC-CTATTTATCAGATTAAAAAAATTAA
* * * * * *
133283 ATTATTTTTTGTGTTGGCCATGTCATGGCCGACATCCCCTTTTTTATCTGAAT
188 ATTATTTTTTATGTTAGCCAAGCCATGACCGACACCCCCTTTTTTATCTGAAT
* * * ** * *
133336 AAAAAATCAAATTTTTGAGTATTGACAATGCCATGATCGATACCCTTATTTATCT-A-AAAAAAA
1 AAAAAATCAAATTTTTGGGTGTTGACCATGCCATGGCCGACACCCCTATTTA-CTGATAAAAAAA
133399 TTA
65 TTA
133402 AATTTTTGGG
Statistics
Matches: 262, Mismatches: 37, Indels: 22
0.82 0.12 0.07
Matches are distributed among these distances:
240 47 0.18
241 11 0.04
242 14 0.05
243 36 0.14
244 125 0.48
245 29 0.11
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (240 bp):
AAAAAATCAAATTTTTGGGTGTTGACCATGCCATGGCCGACACCCCTATTTACTGATAAAAAAAT
TATTATTTTTTGGTTGGTCATCCAATGGCTGACACCCCCTTTTTGTCAGATAAAAAATCAAATTC
TTTTAGTGTTGGCCATGTCATGGTCGACACACCTATTTATCAGATTAAAAAAATTAAATTATTTT
TTATGTTAGCCAAGCCATGACCGACACCCCCTTTTTTATCTGAAT
Found at i:137250 original size:12 final size:12
Alignment explanation
Indices: 137233--137280 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
137223 TATTTGTGTG
137233 AAAATTAATTTA
1 AAAATTAATTTA
137245 AAAATTAATTTA
1 AAAATTAATTTA
*
137257 AGTTGAAATTAATTTG
1 A----AAATTAATTTA
137273 AAAATTAA
1 AAAATTAA
137281 GATACATGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 20 0.65
16 11 0.35
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (12 bp):
AAAATTAATTTA
Found at i:137630 original size:84 final size:85
Alignment explanation
Indices: 137395--138029 Score: 996
Period size: 84 Copynumber: 7.5 Consensus size: 85
137385 AATTTAACAT
* *
137395 TATTTAAATAAAAAAGATTATTATTATATTTCAATTTTTATCAAATAATTTGTTGATTTGACAAT
1 TATTTAAAT-AAAAA-ATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAAT
* *
137460 ACATTATTTA-TCAAATTTTAA
64 ACATTATTTATTAAAATTTGAA
* * *
137481 TATTTAAATAAAAAATTTATTATTATATTATATTTTTTATCAAATAATATGTTGATTTGACAATA
1 TATTTAAATAAAAAA-TTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATA
* *
137546 TATTATTTACT-AAATTTGAA
65 CATTATTTATTAAAATTTGAA
* *
137566 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATTTGTTGATTTGACAATAT
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
* *
137631 ATTATTTA-TCAAATTTTAA
66 ATTATTTATTAAAATTTGAA
*
137650 TATGTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
137715 ATTATTTATTAAAATTT-AA
66 ATTATTTATTAAAATTTGAA
* * *
137734 TATGTAAATAAAAAATTATTATTATATTATAATTTTTATTAAATAATGTGTTGATTTGACAATAC
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
137799 ATTATTTATTAAAATTT-AA
66 ATTATTTATTAAAATTTGAA
* *
137818 TATGTAAATAAAAAATTATTATTATATTATAATTTTTATCAAATAATGTGTTGATTTGACAATAC
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
137883 ATTATTTATT-AAATTTGAA
66 ATTATTTATTAAAATTTGAA
*
137902 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGGCAATAC
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
*
137967 ATTATTTACT-AAATTTGAA
66 ATTATTTATTAAAATTTGAA
*
137986 TATTTAAATAAAAAATTATTATTATATTATAATTTTTATCAAAT
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAAT
138030 TTTAAATTTA
Statistics
Matches: 522, Mismatches: 22, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
83 7 0.01
84 417 0.80
85 88 0.17
86 10 0.02
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.47
Consensus pattern (85 bp):
TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
ATTATTTATTAAAATTTGAA
Found at i:139260 original size:19 final size:19
Alignment explanation
Indices: 139221--139265 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
139211 TTTTTATAAT
*
139221 ATTTTTTTCTATTTTCGAA
1 ATTTTTTTATATTTTCGAA
139240 ATGTTTTTTATATTTTC-AA
1 AT-TTTTTTATATTTTCGAA
139259 ATTTTTT
1 ATTTTTT
139266 AAAAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 5 0.21
19 6 0.25
20 13 0.54
ACGTcount: A:0.22, C:0.07, G:0.04, T:0.67
Consensus pattern (19 bp):
ATTTTTTTATATTTTCGAA
Found at i:139353 original size:22 final size:22
Alignment explanation
Indices: 139293--139353 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
139283 TATTTTTTAC
*
139293 AAATATTTTTTTTTACATTTTCG
1 AAATA-TTATTTTTACATTTTCG
* ****
139316 AAATATAAAAAATACATTTTCG
1 AAATATTATTTTTACATTTTCG
139338 AAATATTATTTTTACA
1 AAATATTATTTTTACA
139354 AAAAGAAATC
Statistics
Matches: 27, Mismatches: 11, Indels: 1
0.69 0.28 0.03
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.48
Consensus pattern (22 bp):
AAATATTATTTTTACATTTTCG
Found at i:140461 original size:30 final size:30
Alignment explanation
Indices: 140427--140518 Score: 130
Period size: 30 Copynumber: 3.1 Consensus size: 30
140417 TCTGTTTACT
* * * *
140427 TTTTAAATTTAATTTGTAATTTCGTTTTTA
1 TTTTAAATTTAATTTCTAATTTCCTGTATA
140457 TTTTAAATTTAATTTCTAATTTCCTGTATA
1 TTTTAAATTTAATTTCTAATTTCCTGTATA
* *
140487 TTTTAATTTTAATTTCTAATTTCCTGTGTA
1 TTTTAAATTTAATTTCTAATTTCCTGTATA
140517 TT
1 TT
140519 CTAATTATTA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.61
Consensus pattern (30 bp):
TTTTAAATTTAATTTCTAATTTCCTGTATA
Found at i:141435 original size:60 final size:60
Alignment explanation
Indices: 141342--141918 Score: 454
Period size: 60 Copynumber: 9.5 Consensus size: 60
141332 GGGAAAGTTA
* * *
141342 GTGTCGGCTATTGCATGGCCAACACCCAAAAATTTGATTTTTTTTATCAGATAAATAGGG
1 GTGTCGGCCATGGCATGGCCAACACCAAAAAATTTGATTTTTTTTATCAGATAAATAGGG
* * * * *
141402 GTGTCGGTCATGGCATGGCCAACATCTAAAAATTTGATTTTTTAT-TCAGATAAAAAAGGGG
1 GTGTCGGCCATGGCATGGCCAACACCAAAAAATTTGATTTTTTTTATCAGAT-AAATA-GGG
* * * * * * * *
141463 GTGTCGACTATGGCATGACCAACACAAAAAAAAATTGAAATTATTTTATCTGATAAATAGGG
1 GTGTCGGCCATGGCATGGCCAACAC-CAAAAAATTTG-ATTTTTTTTATCAGATAAATAGGG
* * * * * *
141525 GTGTCGACAATGGCATGGTCAACACCCAAAAATTTGATTTTTTATT-T-AGATAAAAAAAGG
1 GTGTCGGCCATGGCATGGCCAACACCAAAAAATTTGATTTTTT-TTATCAGAT-AAATAGGG
* * * ** *
141585 ATGTCGACCATGACATGGCCAACACCAAAAAATAATTGAAATTTTTTATCTGATAAATAGGG
1 GTGTCGGCCATGGCATGGCCAACACCAAAAAAT--TTGATTTTTTTTATCAGATAAATAGGG
* *
141647 GTGTCGGCCATGGCATGGCCAACATCC-AAAAATTTGATTTTTTAT-TCAGATGAAAAAGGGG
1 GTGTCGGCCATGGCATGGCCAACA-CCAAAAAATTTGATTTTTTTTATCAGAT-AAATA-GGG
* * * ** * * ** *
141708 GTGTCGAG-CATGACATGACCAATATAAACAAAAATTAAAATTTTTTATCTGATAAATAGGG
1 GTGTCG-GCCATGGCATGGCCAACACCAA-AAAATTTGATTTTTTTTATCAGATAAATAGGG
* * * * * * *
141769 GTGTTGGCCATGGCATGGTCAATACCAAAAAATTTGA-ATTTTTTATCTGACAAAAAGGG
1 GTGTCGGCCATGGCATGGCCAACACCAAAAAATTTGATTTTTTTTATCAGATAAATAGGG
* * * *
141828 AGTGTCGGTCATTGCATGACCAACA-CAAAAAATTTTGA-TTTTTTTATCCG-TAAATAGGG
1 -GTGTCGGCCATGGCATGGCCAACACCAAAAAA-TTTGATTTTTTTTATCAGATAAATAGGG
* * * *
141887 GTGTTGGCCATGGTATGACCAACACAAAAAAA
1 GTGTCGGCCATGGCATGGCCAACACCAAAAAA
141919 AATTGAATTT
Statistics
Matches: 409, Mismatches: 86, Indels: 45
0.76 0.16 0.08
Matches are distributed among these distances:
58 20 0.05
59 54 0.13
60 137 0.33
61 81 0.20
62 92 0.22
63 20 0.05
64 5 0.01
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (60 bp):
GTGTCGGCCATGGCATGGCCAACACCAAAAAATTTGATTTTTTTTATCAGATAAATAGGG
Found at i:141524 original size:123 final size:122
Alignment explanation
Indices: 141381--141911 Score: 630
Period size: 122 Copynumber: 4.4 Consensus size: 122
141371 AAATTTGATT
* * * *
141381 TTTTTTATCAGATAAATAGGGGTGTCGGTCATGGCATGGCCAACATCTAAAAATTTGATTTTTTA
1 TTTTTTATCTGATAAATAGGGGTGTCGGCCATGGCATGGCCAACACCCAAAAATTTGATTTTTTA
*
141446 TTCAGATAAAAAAGGGGGTGTCGACTATGGCATGACCAACACAAAAAAAAATTGAAA
66 TTCAGATAAAAAAGGGGGTGTCGACTATGACATGACCAACACAAAAAAAAATTGAAA
* * *
141503 TTATTTTATCTGATAAATAGGGGTGTCGACAATGGCATGGTCAACACCCAAAAATTTGATTTTTT
1 TT-TTTTATCTGATAAATAGGGGTGTCGGCCATGGCATGGCCAACACCCAAAAATTTGATTTTTT
* * * * * *
141568 ATTTAGATAAAAAA-AGGATGTCGACCATGACATGGCCAACACCAAAAAATAATTGAAA
65 ATTCAGATAAAAAAGGGGGTGTCGACTATGACATGACCAACA-CAAAAAAAAATTGAAA
*
141626 TTTTTTATCTGATAAATAGGGGTGTCGGCCATGGCATGGCCAACATCCAAAAATTTGATTTTTTA
1 TTTTTTATCTGATAAATAGGGGTGTCGGCCATGGCATGGCCAACACCCAAAAATTTGATTTTTTA
* * * * *
141691 TTCAGATGAAAAAGGGGGTGTCGAGC-ATGACATGACCAATATAAACAAAAATTAAAA
66 TTCAGATAAAAAAGGGGGTGTCGA-CTATGACATGACCAACACAAAAAAAAATTGAAA
* * * *
141748 TTTTTTATCTGATAAATAGGGGTGTTGGCCATGGCATGGTCAATACCAAAAAATTTGAATTTTTT
1 TTTTTTATCTGATAAATAGGGGTGTCGGCCATGGCATGGCCAACACCCAAAAATTTG-ATTTTTT
* * * * ** *
141813 A-TCTGA-CAAAAAGGGAGTGTCG-GTCATTG-CATGACCAACAC-AAAAAATTTTG-AT
65 ATTCAGATAAAAAAGGGGGTGTCGACT-A-TGACATGACCAACACAAAAAAAAATTGAAA
* * * *
141867 TTTTTTATCCG-TAAATAGGGGTGTTGGCCATGGTATGACCAACAC
1 TTTTTTATCTGATAAATAGGGGTGTCGGCCATGGCATGGCCAACAC
141912 AAAAAAAAAT
Statistics
Matches: 352, Mismatches: 49, Indels: 20
0.84 0.12 0.05
Matches are distributed among these distances:
118 30 0.09
119 11 0.03
120 7 0.02
121 25 0.07
122 164 0.47
123 114 0.32
124 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (122 bp):
TTTTTTATCTGATAAATAGGGGTGTCGGCCATGGCATGGCCAACACCCAAAAATTTGATTTTTTA
TTCAGATAAAAAAGGGGGTGTCGACTATGACATGACCAACACAAAAAAAAATTGAAA
Found at i:147233 original size:36 final size:37
Alignment explanation
Indices: 147193--147262 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
147183 ATTTATTTTT
* *
147193 TGTTAATTTT-AAAAAAT-TATTTTTAAACTTTTAAAA
1 TGTT-ATTTTAAAAAAATATATATTTAAAATTTTAAAA
147229 TGTTATTTTAAAAAAATATATATTTAAAATTTTA
1 TGTTATTTTAAAAAAATATATATTTAAAATTTTA
147263 CTGATGTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
35 5 0.17
36 11 0.37
37 14 0.47
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (37 bp):
TGTTATTTTAAAAAAATATATATTTAAAATTTTAAAA
Found at i:147608 original size:88 final size:88
Alignment explanation
Indices: 147506--147679 Score: 276
Period size: 88 Copynumber: 2.0 Consensus size: 88
147496 GAAAATGTTG
* * * * * *
147506 TTTATTCTAAAAAATCTGGGTTCGAGCACTTGTGAGTACAAAATGTGTCTGTGTTGTCAAAGAAT
1 TTTATCCTAAAAAATCTGGATTCGAGCACCTGTGAGTACAAAATGTGTATGTGTTATCAAAAAAT
147571 TAAGAAAATATGAATAGAGTCAA
66 TAAGAAAATATGAATAGAGTCAA
* *
147594 TTTATCCTAAAAAATTTGGATTCGAGCACCTGTGTGTACAAAATGTGTATGTGTTATCAAAAAAT
1 TTTATCCTAAAAAATCTGGATTCGAGCACCTGTGAGTACAAAATGTGTATGTGTTATCAAAAAAT
147659 TAAGAAAATATGAATAGAGTC
66 TAAGAAAATATGAATAGAGTC
147680 GGTAGGAATA
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 78 1.00
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (88 bp):
TTTATCCTAAAAAATCTGGATTCGAGCACCTGTGAGTACAAAATGTGTATGTGTTATCAAAAAAT
TAAGAAAATATGAATAGAGTCAA
Found at i:155992 original size:2 final size:2
Alignment explanation
Indices: 155985--156011 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
155975 AAATAATAGT
155985 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 T
156012 TGCCATTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:156534 original size:21 final size:19
Alignment explanation
Indices: 156505--156545 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
156495 TTGTGGGAAT
*
156505 ATTTTATTATTATTTTTTAA
1 ATTTTATTAAT-TTTTTTAA
156525 ATTTATATTAATTTTTTTAA
1 ATTT-TATTAATTTTTTTAA
156545 A
1 A
156546 AAAATATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTTTATTAATTTTTTTAA
Found at i:156812 original size:18 final size:18
Alignment explanation
Indices: 156772--156823 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
156762 TTTTTAGTTA
*
156772 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAATTTATT
*
156790 AAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
156808 TAATTAA--AAATTTATT
1 TAATTAATTAAATTTATT
156824 CTCATCCCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 9 0.30
17 7 0.23
18 14 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:160704 original size:23 final size:23
Alignment explanation
Indices: 160674--160721 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
160664 AAGGCCATCG
160674 ATACAAAAAAGTTTCATCAAACC
1 ATACAAAAAAGTTTCATCAAACC
160697 ATACAAAAAAGTTTCATCAAACC
1 ATACAAAAAAGTTTCATCAAACC
160720 AT
1 AT
160722 GATCACTGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.52, C:0.21, G:0.04, T:0.23
Consensus pattern (23 bp):
ATACAAAAAAGTTTCATCAAACC
Found at i:161539 original size:35 final size:36
Alignment explanation
Indices: 161494--161570 Score: 104
Period size: 35 Copynumber: 2.2 Consensus size: 36
161484 GTTGAGAGAT
*
161494 TGAAATGTTAA-TCCGATGACTGTTTGTTTAGGAAAA
1 TGAAATGTTAACT-CGATGACTGTTTATTTAGGAAAA
* *
161530 TGAAA-GTTAACTCGGTGACTGTTTATTTATGAAAA
1 TGAAATGTTAACTCGATGACTGTTTATTTAGGAAAA
161565 TGAAAT
1 TGAAAT
161571 TTGGGTGACT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 30 0.83
36 6 0.17
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.36
Consensus pattern (36 bp):
TGAAATGTTAACTCGATGACTGTTTATTTAGGAAAA
Found at i:161578 original size:31 final size:33
Alignment explanation
Indices: 161510--161583 Score: 89
Period size: 35 Copynumber: 2.2 Consensus size: 33
161500 GTTAATCCGA
*
161510 TGACTGTTTGTTTAGGAAAATGAAAGTTAACTCGG
1 TGACTGTTTATTTAGGAAAATGAAAGTT-A-TCGG
* *
161545 TGACTGTTTATTTATGAAAATGAAA-TT-TGGG
1 TGACTGTTTATTTAGGAAAATGAAAGTTATCGG
161576 TGACTGTT
1 TGACTGTT
161584 GGTGTAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 11 0.31
34 2 0.06
35 23 0.64
ACGTcount: A:0.30, C:0.07, G:0.24, T:0.39
Consensus pattern (33 bp):
TGACTGTTTATTTAGGAAAATGAAAGTTATCGG
Found at i:168622 original size:35 final size:36
Alignment explanation
Indices: 168583--168673 Score: 105
Period size: 36 Copynumber: 2.6 Consensus size: 36
168573 TTTTTGGTCC
168583 AATTTGGTACTCAAACTTGACA-TTTTTTTTTTTTT
1 AATTTGGTACTCAAACTTGACACTTTTTTTTTTTTT
* ** * *
168618 AATTTAGTACTTGAACTTAATACTTTTTTTTTTTTT
1 AATTTGGTACTCAAACTTGACACTTTTTTTTTTTTT
*
168654 AAGTTGGTAC-CTAAACTTGA
1 AATTTGGTACTC-AAACTTGA
168674 GGTATCTAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
35 17 0.39
36 27 0.61
ACGTcount: A:0.26, C:0.11, G:0.10, T:0.53
Consensus pattern (36 bp):
AATTTGGTACTCAAACTTGACACTTTTTTTTTTTTT
Found at i:168915 original size:26 final size:25
Alignment explanation
Indices: 168850--168915 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 25
168840 ATACTAAATT
168850 AAATCTAA-AAAAAAAAATTAAAACC
1 AAATC-AATAAAAAAAAATTAAAACC
* * *
168875 AAATTAGATCCAAAAAAATTTAAACACC
1 AAATCA-AT-AAAAAAAAATTAAA-ACC
168903 AAATCAATAAAAA
1 AAATCAATAAAAA
168916 CTATCAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
24 1 0.03
25 5 0.16
26 4 0.12
27 14 0.44
28 8 0.25
ACGTcount: A:0.67, C:0.14, G:0.02, T:0.18
Consensus pattern (25 bp):
AAATCAATAAAAAAAAATTAAAACC
Found at i:169499 original size:18 final size:19
Alignment explanation
Indices: 169462--169501 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
169452 CAAATTTTAG
*
169462 TTTTAGTATTTCAATTTAA
1 TTTTAGTATTTCAATATAA
*
169481 TTTTA-TATTTTAATATAA
1 TTTTAGTATTTCAATATAA
169499 TTT
1 TTT
169502 ATTTAGTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTTAGTATTTCAATATAA
Found at i:186580 original size:5 final size:5
Alignment explanation
Indices: 186562--186595 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
186552 GACGCGAAAA
*
186562 GGAA- GGAAG AGAAG GGAAG GGAAG GGAAG GGAAG
1 GGAAG GGAAG GGAAG GGAAG GGAAG GGAAG GGAAG
186596 AAGAGAGTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (5 bp):
GGAAG
Found at i:189999 original size:23 final size:23
Alignment explanation
Indices: 189969--190072 Score: 138
Period size: 23 Copynumber: 4.4 Consensus size: 23
189959 ACACTAGCGC
*
189969 GCCCTCTGTTTAGCACGTTT-CGT
1 GCCCTCTGTTTAGCAC-TTTGTGT
*
189992 GCCCTCTGTTTAGCACTGTGTGT
1 GCCCTCTGTTTAGCACTTTGTGT
190015 GCCCTCTGTTATTAGCACTTTGTGT
1 GCCCTCTG-T-TTAGCACTTTGTGT
*
190040 GCCCTCTGATTAGCACTTTGTGT
1 GCCCTCTGTTTAGCACTTTGTGT
*
190063 GCCCTATGTT
1 GCCCTCTGTT
190073 ACCCAGCACT
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
22 2 0.03
23 48 0.67
24 1 0.01
25 21 0.29
ACGTcount: A:0.11, C:0.27, G:0.22, T:0.40
Consensus pattern (23 bp):
GCCCTCTGTTTAGCACTTTGTGT
Found at i:190042 original size:48 final size:48
Alignment explanation
Indices: 189969--190073 Score: 144
Period size: 48 Copynumber: 2.2 Consensus size: 48
189959 ACACTAGCGC
*
189969 GCCCTCTG-T-TTAGCACGTTTCGTGCCCTCTGTTTAGCACTGTGTGT
1 GCCCTCTGTTATTAGCACGTTTCGTGCCCTCTGATTAGCACTGTGTGT
* *
190015 GCCCTCTGTTATTAGCAC-TTTGTGTGCCCTCTGATTAGCACTTTGTGT
1 GCCCTCTGTTATTAGCACGTTT-CGTGCCCTCTGATTAGCACTGTGTGT
*
190063 GCCCTATGTTA
1 GCCCTCTGTTA
190074 CCCAGCACTT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
46 8 0.15
47 4 0.08
48 40 0.77
ACGTcount: A:0.11, C:0.27, G:0.22, T:0.40
Consensus pattern (48 bp):
GCCCTCTGTTATTAGCACGTTTCGTGCCCTCTGATTAGCACTGTGTGT
Found at i:190089 original size:48 final size:48
Alignment explanation
Indices: 189990--190092 Score: 136
Period size: 48 Copynumber: 2.1 Consensus size: 48
189980 AGCACGTTTC
* * ** *
189990 GTGCCCTCTGTTTAGCACTGTGTGTGCCCTCTGTTATTAGCACTTTGT
1 GTGCCCTCTGATTAGCACTGTGTGTGCCCTATGTTACCAGCACTTTAT
*
190038 GTGCCCTCTGATTAGCACTTTGTGTGCCCTATGTTACCCAGCAC-TTAT
1 GTGCCCTCTGATTAGCACTGTGTGTGCCCTATGTTA-CCAGCACTTTAT
190086 GTGCCCT
1 GTGCCCT
190093 TTGTTAAGTA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
48 43 0.90
49 5 0.10
ACGTcount: A:0.13, C:0.28, G:0.21, T:0.38
Consensus pattern (48 bp):
GTGCCCTCTGATTAGCACTGTGTGTGCCCTATGTTACCAGCACTTTAT
Found at i:190843 original size:27 final size:27
Alignment explanation
Indices: 190780--190851 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 27
190770 TTTAGGTTAT
**
190780 GCCACAAAGGTAGTTCATTCAGAGTTT
1 GCCACAAAGGTAGTTCATTCAGAGTGC
* * *
190807 GCTACGAAGGTAGTTCTTTCAGAGTGC
1 GCCACAAAGGTAGTTCATTCAGAGTGC
*
190834 GCCACAAAGGTTGTTCAT
1 GCCACAAAGGTAGTTCAT
190852 AAATGTCATG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.29
Consensus pattern (27 bp):
GCCACAAAGGTAGTTCATTCAGAGTGC
Done.