Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013425.1 Kokia drynarioides strain JFW-HI SEQ_128451, 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: 75275
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 128 characters in sequence are not A, C, G, or T
Found at i:629 original size:24 final size:26
Alignment explanation
Indices: 602--649 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
592 AGAGAAATGT
602 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
626 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
650 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:747 original size:23 final size:23
Alignment explanation
Indices: 712--830 Score: 159
Period size: 23 Copynumber: 5.2 Consensus size: 23
702 ACACTAGCGC
*
712 GCTCTTTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
735 GATCTCTGTTTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
758 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
781 GCTCTTTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
804 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
827 GCTC
1 GCTC
831 AGTACTTTGT
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
22 1 0.01
23 83 0.98
24 1 0.01
ACGTcount: A:0.13, C:0.20, G:0.24, T:0.44
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:828 original size:46 final size:46
Alignment explanation
Indices: 712--830 Score: 175
Period size: 46 Copynumber: 2.6 Consensus size: 46
702 ACACTAGCGC
* * *
712 GCTCTTTGATTAGCACTGTGTGTGATCTCTGTTTAGCACTTCGTGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTCGTGT
* *
758 GCTCTCTGATTAGCACTGTGTGTGCTCTTTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTCGTGT
* *
804 GCTCTCTGATTAGTACTTTGTGTGCTC
1 GCTCTCTGATTAGCACTGTGTGTGCTC
831 AGTACTTTGT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 66 1.00
ACGTcount: A:0.13, C:0.20, G:0.24, T:0.44
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTCGTGT
Found at i:836 original size:16 final size:16
Alignment explanation
Indices: 815--846 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
805 CTCTCTGATT
815 AGTACTTTGTGTGCTC
1 AGTACTTTGTGTGCTC
831 AGTACTTTGTGTGCTC
1 AGTACTTTGTGTGCTC
847 TCTGTTTAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.19, G:0.25, T:0.44
Consensus pattern (16 bp):
AGTACTTTGTGTGCTC
Found at i:838 original size:39 final size:39
Alignment explanation
Indices: 795--869 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
785 TTTGATTAGC
*
795 ACTTTGTGTGCTCTCTGATTAGTACTTTGTGTGCTCAGT
1 ACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
* **
834 ACTTTGTGTGCTCTCTGTTTAGCGTTTTGTGTGCTC
1 ACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTC
870 TCTGTTGCCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.09, C:0.19, G:0.24, T:0.48
Consensus pattern (39 bp):
ACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:2319 original size:23 final size:23
Alignment explanation
Indices: 2291--2398 Score: 103
Period size: 23 Copynumber: 4.7 Consensus size: 23
2281 TTGGGGAAAT
2291 AGTAAGCACACACAGTGCAAAAA
1 AGTAAGCACACACAGTGCAAAAA
**
2314 AGTAAGCACACACAGTGCAAATC
1 AGTAAGCACACACAGTGCAAAAA
* * * **
2337 AGTAA-CACATATAGCGCGAATGA
1 AGTAAGCACACACAGTGC-AAAAA
** *
2360 A-TAAGCACACACAGTGCTGAAC
1 AGTAAGCACACACAGTGCAAAAA
2382 AGTAAGCACACACAGTG
1 AGTAAGCACACACAGTG
2399 ATGAACAGTA
Statistics
Matches: 66, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
22 13 0.20
23 53 0.80
ACGTcount: A:0.44, C:0.23, G:0.19, T:0.13
Consensus pattern (23 bp):
AGTAAGCACACACAGTGCAAAAA
Found at i:2403 original size:23 final size:23
Alignment explanation
Indices: 2361--2411 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
2351 CGCGAATGAA
*
2361 TAAGCACACACAGTGCTGAACAG
1 TAAGCACACACAGTGATGAACAG
2384 TAAGCACACACAGTGATGAACAG
1 TAAGCACACACAGTGATGAACAG
2407 TAAGC
1 TAAGC
2412 GCGCTAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.14
Consensus pattern (23 bp):
TAAGCACACACAGTGATGAACAG
Found at i:4152 original size:31 final size:31
Alignment explanation
Indices: 4117--4189 Score: 137
Period size: 31 Copynumber: 2.4 Consensus size: 31
4107 CTTCACCATC
4117 GTCGTTGTTCTCCTCAAACATACCTATCCCA
1 GTCGTTGTTCTCCTCAAACATACCTATCCCA
4148 GTCGTTGTTCTCCTCAAACATACCTATCCCA
1 GTCGTTGTTCTCCTCAAACATACCTATCCCA
*
4179 GTCGTTATTCT
1 GTCGTTGTTCT
4190 AATCAGTATC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.21, C:0.33, G:0.11, T:0.36
Consensus pattern (31 bp):
GTCGTTGTTCTCCTCAAACATACCTATCCCA
Found at i:6919 original size:59 final size:57
Alignment explanation
Indices: 6795--6995 Score: 210
Period size: 57 Copynumber: 3.5 Consensus size: 57
6785 GGAGGTCCCT
* * *
6795 AAACTATCCAAAAATT-ATATTTCGACCCCAAACTTCCAAAAAATTCAATTTTTA-CCCC
1 AAACT-TCCAAAAATTCA-ATTTTGACCCAAAACTTCC-AAAAATTCCATTTTTACCCCC
*
6853 AAACTTCCAAAAATTCAATTTTTGACCCAAAAACTTTCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCAA-TTTTGACCC-AAAACTTCCAAAAATTCCATTTTTACCCCC
* * * * *
6912 GAACTTCCAAAAATTCCATTTTGACCCCAAACTTCCAAAAATTACATTTTTGCCCCC
1 AAACTTCCAAAAATTCAATTTTGACCCAAAACTTCCAAAAATTCCATTTTTACCCCC
* * *
6969 AGA-TGTCCAAAAACTCCATTTTCGACC
1 AAACT-TCCAAAAATTCAATTTT-GACC
6996 TCGAAACTCT
Statistics
Matches: 124, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
56 1 0.01
57 54 0.44
58 42 0.34
59 27 0.22
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.30
Consensus pattern (57 bp):
AAACTTCCAAAAATTCAATTTTGACCCAAAACTTCCAAAAATTCCATTTTTACCCCC
Found at i:6962 original size:29 final size:29
Alignment explanation
Indices: 6795--6995 Score: 207
Period size: 29 Copynumber: 6.9 Consensus size: 29
6785 GGAGGTCCCT
*
6795 AAACTATCCAAAAATT--ATATTTCGACCCC
1 AAACT-TCCAAAAATTCCAT-TTTTGACCCC
*
6824 AAACTTCCAAAAAATTCAATTTTT-ACCCC
1 AAACTTCC-AAAAATTCCATTTTTGACCCC
* *
6853 AAACTTCCAAAAATTCAATTTTTGACCCAA
1 AAACTTCCAAAAATTCCATTTTTGACCC-C
*
6883 AAACTTTCAAAAATTCCATTTTT-ACCCCC
1 AAACTTCCAAAAATTCCATTTTTGA-CCCC
*
6912 GAACTTCCAAAAATTCCA-TTTTGACCCC
1 AAACTTCCAAAAATTCCATTTTTGACCCC
* *
6940 AAACTTCCAAAAATTACATTTTTGCCCCC
1 AAACTTCCAAAAATTCCATTTTTGACCCC
* * *
6969 AGA-TGTCCAAAAACTCCATTTTCGACC
1 AAACT-TCCAAAAATTCCATTTTTGACC
6996 TCGAAACTCT
Statistics
Matches: 148, Mismatches: 15, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
28 43 0.29
29 76 0.51
30 27 0.18
31 2 0.01
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.30
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTGACCCC
Found at i:7009 original size:116 final size:116
Alignment explanation
Indices: 6796--7084 Score: 277
Period size: 116 Copynumber: 2.5 Consensus size: 116
6786 GAGGTCCCTA
** * *
6796 AACTATCCAAAAATTATATTTCGACCCCAAACTTCCAAAAAATT-CAATTTTT-ACCCCAAACTT
1 AACTATCCAAAAATTCCATTTTGACCCCAAACTTCC-AAAAATTAC-ATTTTTGCCCCCAAACTT
* * * *
6859 CCAAAAATTCAATTTTTGACCCAAAAACTTTCAAAAATTCCATTTTTACCCCCG
64 CCAAAAACTCAATTTTCGACCCAAAAACTCTC-AAAATTCCACTTTTACCCCCG
*
6913 AACT-TCCAAAAATTCCATTTTGACCCCAAACTTCCAAAAATTACATTTTTGCCCCCAGA-TGTC
1 AACTATCCAAAAATTCCATTTTGACCCCAAACTTCCAAAAATTACATTTTTGCCCCCAAACT-TC
* * * **
6976 CAAAAACTCCATTTTCGACCTC-GAAACTCTCAAAATTCCCCTTTTACCTTCG
65 CAAAAACTCAATTTTCGACC-CAAAAACTCTCAAAATTCCACTTTTACCCCCG
* * * * ** *
7028 AA-TGTCTAAAAATTCCATTTTAACCTCGAATTTTCCCAAAATTACCA-TTTTGCCCCC
1 AACTATCCAAAAATTCCATTTTGACC-CCAAACTTCCAAAAATTA-CATTTTTGCCCCC
7085 CGGGTATCCG
Statistics
Matches: 145, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
114 1 0.01
115 52 0.36
116 85 0.59
117 7 0.05
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.31
Consensus pattern (116 bp):
AACTATCCAAAAATTCCATTTTGACCCCAAACTTCCAAAAATTACATTTTTGCCCCCAAACTTCC
AAAAACTCAATTTTCGACCCAAAAACTCTCAAAATTCCACTTTTACCCCCG
Found at i:7048 original size:28 final size:28
Alignment explanation
Indices: 6891--7058 Score: 81
Period size: 29 Copynumber: 5.9 Consensus size: 28
6881 AAAAACTTTC
* * *
6891 AAAAATTCCATTTTTACCCCCGAACT-TCC
1 AAAAATTCCA-TTTTAACCTCGAA-TGTCT
* * * *
6920 AAAAATTCCATTTTGACCCCAAACT-TCC
1 AAAAATTCCATTTTAACCTCGAA-TGTCT
* ** * * *
6948 AAAAATTACATTTTTGCCCCCAGATGTCC
1 AAAAATTCCATTTTAACCTCGA-ATGTCT
* * **
6977 AAAAACTCCATTTTCGACCTCGAAACTCT
1 AAAAATTCCATTTT-AACCTCGAATGTCT
* *
7006 CAAAATTCCCCTTTT-ACCTTCGAATGTCT
1 AAAAATT-CCATTTTAACC-TCGAATGTCT
7035 AAAAATTCCATTTTAACCTCGAAT
1 AAAAATTCCATTTTAACCTCGAAT
7059 TTTCCCAAAA
Statistics
Matches: 110, Mismatches: 23, Indels: 13
0.75 0.16 0.09
Matches are distributed among these distances:
28 49 0.45
29 51 0.46
30 10 0.09
ACGTcount: A:0.33, C:0.30, G:0.06, T:0.32
Consensus pattern (28 bp):
AAAAATTCCATTTTAACCTCGAATGTCT
Found at i:11626 original size:96 final size:96
Alignment explanation
Indices: 11442--11633 Score: 239
Period size: 96 Copynumber: 2.0 Consensus size: 96
11432 TTTTTGGGAA
** * *
11442 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACTTAGTAAGTTAAGGCGCAATATTTTA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTGA
*
11507 AAATCGAAGATAAGGAAACATTGCCTCGATT
66 AAATCGAAGATAAAGAAACATTGCCTCGATT
* *
11538 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCATG-AAT-TTT
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGC--GCAATATTT
* *
11601 CGAAACTCGAA-ATAAA-AGAATATTGCCTCGATT
64 -GAAAATCGAAGATAAAGA-AACATTGCCTCGATT
11634 TTAAAGTTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
95 1 0.01
96 70 0.84
97 11 0.13
98 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTGA
AAATCGAAGATAAAGAAACATTGCCTCGATT
Found at i:11924 original size:29 final size:28
Alignment explanation
Indices: 11887--12054 Score: 81
Period size: 29 Copynumber: 5.9 Consensus size: 28
11877 TTTTGGGAAA
11887 ATTCGAGGTTAAAATGGAATTTTTAGAC
1 ATTCGAGGTTAAAATGGAATTTTTAGAC
* * *
11915 ATTCGAAGG-TAAAAGGGGAATTTTGAGAG
1 ATTCG-AGGTTAAAA-TGGAATTTTTAGAC
* * * *
11944 TTTCGAGGTCGAAAATGGAGTTTTTGGAC
1 ATTCGAGGT-TAAAATGGAATTTTTAGAC
* * ** * *
11973 ATCTGGGGGCAAAAATGTAATTTTTGGA-
1 AT-TCGAGGTTAAAATGGAATTTTTAGAC
* * * *
12001 AGTTTGGGGTCAAAATGGAATTTTTGGA-
1 A-TTCGAGGTTAAAATGGAATTTTTAGAC
* *
12029 AGTTCGGGGGTAAAAATGGAATTTTT
1 A-TTC-GAGGTTAAAATGGAATTTTT
12055 GAAAGTTTTT
Statistics
Matches: 110, Mismatches: 23, Indels: 13
0.75 0.16 0.09
Matches are distributed among these distances:
28 39 0.35
29 63 0.57
30 8 0.07
ACGTcount: A:0.32, C:0.06, G:0.30, T:0.33
Consensus pattern (28 bp):
ATTCGAGGTTAAAATGGAATTTTTAGAC
Found at i:12026 original size:87 final size:86
Alignment explanation
Indices: 11955--12120 Score: 210
Period size: 87 Copynumber: 1.9 Consensus size: 86
11945 TTCGAGGTCG
* * *
11955 AAAATGGAGTTTTTGGACA-TCTGGGGGCAAAAA-TGTAATTTTTGGAAGTTTGGGGTCAAAATG
1 AAAATGGAATTTTT-GAAAGTCTGGGGGCAAAAATTG-AATTTTTGGAAGTTTGGGGTAAAAATG
*
12018 GAATTTTTGGAAGTTCGGGGGTA
64 GAATTTTTGGAAGTTCGGAGGTA
* * * *
12041 AAAATGGAATTTTTGAAAGTTTTTGGGTCAAAAATTGAATTTTTGGAAGTTTGGGGTAAAAATTG
1 AAAATGGAATTTTTGAAAG-TCTGGGGGCAAAAATTGAATTTTTGGAAGTTTGGGGTAAAAATGG
12106 AATTTTTTGGAAGTT
65 AA-TTTTTGGAAGTT
12121 TGGGGTCGAA
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
85 3 0.04
86 13 0.19
87 39 0.57
88 14 0.20
ACGTcount: A:0.31, C:0.04, G:0.28, T:0.37
Consensus pattern (86 bp):
AAAATGGAATTTTTGAAAGTCTGGGGGCAAAAATTGAATTTTTGGAAGTTTGGGGTAAAAATGGA
ATTTTTGGAAGTTCGGAGGTA
Found at i:12055 original size:29 final size:28
Alignment explanation
Indices: 11955--12149 Score: 176
Period size: 29 Copynumber: 6.8 Consensus size: 28
11945 TTCGAGGTCG
* *
11955 AAAATGGAGTTTTTGGACA-TCTGGGGGCA
1 AAAATGGAATTTTTGGA-AGT-TGGGGGTA
* * *
11984 AAAATGTAATTTTTGGAAGTTTGGGGTC
1 AAAATGGAATTTTTGGAAGTTGGGGGTA
12012 AAAATGGAATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTT-GGGGGTA
* **
12041 AAAATGGAATTTTTGAAAGTTTTTGGGTCA
1 AAAATGGAATTTTTGGAAG-TTGGGGGT-A
* *
12071 AAAATTGAATTTTTGGAAGTTTGGGGTA
1 AAAATGGAATTTTTGGAAGTTGGGGGTA
* * *
12099 AAAATTGAATTTTTTGGAAGTTTGGGGTC
1 AAAATGGAA-TTTTTGGAAGTTGGGGGTA
* **
12128 GAAATATAATTTTTGGATAGTT
1 AAAATGGAATTTTTGGA-AGTT
12150 TAGGGACCTC
Statistics
Matches: 142, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
28 44 0.31
29 78 0.55
30 20 0.14
ACGTcount: A:0.31, C:0.04, G:0.28, T:0.37
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTGGGGGTA
Found at i:12075 original size:116 final size:115
Alignment explanation
Indices: 11861--12149 Score: 275
Period size: 116 Copynumber: 2.5 Consensus size: 115
11851 CGGATACCCG
* * * * * *
11861 GGGGGC-AAAATGGTAATTTTGGGAAAATTCGAGGTTAAAATGGAATTTTTAGACA-TTCGAAGG
1 GGGGGCAAAAAT-GTAATTTTTGG-AAGTTTGGGGTCAAAATGGAATTTTTGGACAGTTCGAAGG
* * * *
11924 TAAAAGGGGAATTTTGAGAGTTTCGAGGTCGAAAATGGAGTTTTTGGACA-TCT
64 TAAAAAGGGAATTTTGAAAGTTTCGAGGTCAAAAATGGAATTTTTGGA-AGT-T
**
11977 GGGGGCAAAAATGTAATTTTTGGAAGTTTGGGGTCAAAATGGAATTTTTGGA-AGTTCGGGGGTA
1 GGGGGCAAAAATGTAATTTTTGGAAGTTTGGGGTCAAAATGGAATTTTTGGACAGTTCGAAGGTA
* * *
12041 AAAATGGAATTTTTGAAAGTTTTTG-GGTCAAAAATTGAATTTTTGGAAGTT
66 AAAAGGGAA-TTTTGAAAG-TTTCGAGGTCAAAAATGGAATTTTTGGAAGTT
* * * ** *
12092 TGGGGTAAAAAT-TGAATTTTTTGGAAGTTTGGGGTCGAAATATAATTTTTGGATAGTT
1 GGGGGCAAAAATGT-AA-TTTTTGGAAGTTTGGGGTCAAAATGGAATTTTTGGACAGTT
12150 TAGGGACCTC
Statistics
Matches: 145, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
114 2 0.01
115 53 0.37
116 77 0.53
117 13 0.09
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.35
Consensus pattern (115 bp):
GGGGGCAAAAATGTAATTTTTGGAAGTTTGGGGTCAAAATGGAATTTTTGGACAGTTCGAAGGTA
AAAAGGGAATTTTGAAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTT
Found at i:12091 original size:59 final size:57
Alignment explanation
Indices: 11950--12149 Score: 217
Period size: 57 Copynumber: 3.4 Consensus size: 57
11940 AGAGTTTCGA
* * *
11950 GGTCGAAAATGGAGTTTTTGGACA-TCTGGGGGCAAAAATGTAATTTTTGGAAG-TTTGG
1 GGTC-AAAATGGAATTTTTGGA-AGT-TGGGGGTAAAAATGGAATTTTTGGAAGTTTTGG
* *
12008 GGTCAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGAAAGTTTTTG
1 GGTCAAAATGGAATTTTTGGAAGTT-GGGGGTAAAAATGGAATTTTTGGAAGTTTTGG
* * *
12066 GGTCAAAAATTGAATTTTTGGAAGTTTGGGGTAAAAATTGAATTTTTTGGAAG-TTTGG
1 GGTC-AAAATGGAATTTTTGGAAGTTGGGGGTAAAAATGGAA-TTTTTGGAAGTTTTGG
* **
12124 GGTCGAAATATAATTTTTGGATAGTT
1 GGTCAAAATGGAATTTTTGGA-AGTT
12150 TAGGGACCTC
Statistics
Matches: 123, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
56 2 0.02
57 54 0.44
58 38 0.31
59 29 0.24
ACGTcount: A:0.30, C:0.04, G:0.29, T:0.37
Consensus pattern (57 bp):
GGTCAAAATGGAATTTTTGGAAGTTGGGGGTAAAAATGGAATTTTTGGAAGTTTTGG
Found at i:12102 original size:28 final size:28
Alignment explanation
Indices: 11978--12150 Score: 188
Period size: 29 Copynumber: 6.0 Consensus size: 28
11968 TGGACATCTG
*
11978 GGGGCAAAAA-TGTAATTTTTGGAAGTTT
1 GGGGTAAAAATTG-AATTTTTGGAAGTTT
* * *
12006 GGGGTCAAAATGGAATTTTTGGAAGTTCG
1 GGGGTAAAAATTGAATTTTTGGAAGTT-T
* *
12035 GGGGTAAAAATGGAATTTTTGAAAGTTTT
1 GGGGTAAAAATTGAATTTTTGGAAG-TTT
*
12064 TGGGTCAAAAATTGAATTTTTGGAAGTTT
1 GGGGT-AAAAATTGAATTTTTGGAAGTTT
12093 GGGGTAAAAATTGAATTTTTTGGAAGTTT
1 GGGGTAAAAATTGAA-TTTTTGGAAGTTT
**
12122 GGGGTCGAAATAT-AATTTTTGGATAGTTT
1 GGGGTAAAAAT-TGAATTTTTGGA-AGTTT
12151 AGGGACCTCC
Statistics
Matches: 125, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
28 40 0.32
29 64 0.51
30 21 0.17
ACGTcount: A:0.31, C:0.03, G:0.28, T:0.38
Consensus pattern (28 bp):
GGGGTAAAAATTGAATTTTTGGAAGTTT
Found at i:12139 original size:87 final size:87
Alignment explanation
Indices: 11982--12142 Score: 227
Period size: 87 Copynumber: 1.9 Consensus size: 87
11972 CATCTGGGGG
* *
11982 CAAAAATGTAATTTTTGGAAGTTTGGGGTCAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATG
1 CAAAAATGTAATTTTTGGAAGTTTGGGGTAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATA
12047 GAATTTTTGAAAGTTTTTGGGT
66 GAATTTTTGAAAGTTTTTGGGT
* * **
12069 CAAAAAT-TGAATTTTTGGAAGTTTGGGGTAAAAATTGAATTTTTTGGAAGTT-TGGGGTCGAAA
1 CAAAAATGT-AATTTTTGGAAGTTTGGGGTAAAAATGGAA-TTTTTGGAAGTTCGGGGGTAAAAA
*
12132 TATAATTTTTG
64 TAGAATTTTTG
12143 GATAGTTTAG
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
86 1 0.02
87 52 0.80
88 12 0.18
ACGTcount: A:0.32, C:0.03, G:0.27, T:0.39
Consensus pattern (87 bp):
CAAAAATGTAATTTTTGGAAGTTTGGGGTAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATA
GAATTTTTGAAAGTTTTTGGGT
Found at i:14799 original size:31 final size:31
Alignment explanation
Indices: 14756--14828 Score: 137
Period size: 31 Copynumber: 2.4 Consensus size: 31
14746 GATACTGATT
*
14756 AGAATAACGACTGGGATAGGTATGTTTGAGG
1 AGAACAACGACTGGGATAGGTATGTTTGAGG
14787 AGAACAACGACTGGGATAGGTATGTTTGAGG
1 AGAACAACGACTGGGATAGGTATGTTTGAGG
14818 AGAACAACGAC
1 AGAACAACGAC
14829 GATGGTGAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.36, C:0.11, G:0.33, T:0.21
Consensus pattern (31 bp):
AGAACAACGACTGGGATAGGTATGTTTGAGG
Found at i:16564 original size:23 final size:23
Alignment explanation
Indices: 16534--16654 Score: 113
Period size: 23 Copynumber: 5.3 Consensus size: 23
16524 ATATTAGCGC
*
16534 GCTTACTGTTCATCACTGTGTGT
1 GCTTACTGTTCAGCACTGTGTGT
16557 GCTTACTGTTCAGCACTGTGTGT
1 GCTTACTGTTCAGCACTGTGTGT
* * * * *
16580 GCTTATTCATTC-GCGCTATATGT
1 GCTTACT-GTTCAGCACTGTGTGT
*
16603 G-TTACTGATT-TGCACTGTGTGT
1 GCTTACTG-TTCAGCACTGTGTGT
* **
16625 GCTTACTTTTTTGCACTGTGTGT
1 GCTTACTGTTCAGCACTGTGTGT
16648 GCTTACT
1 GCTTACT
16655 ATTTCCCCAA
Statistics
Matches: 81, Mismatches: 12, Indels: 10
0.79 0.12 0.10
Matches are distributed among these distances:
22 17 0.21
23 61 0.75
24 3 0.04
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (23 bp):
GCTTACTGTTCAGCACTGTGTGT
Found at i:17843 original size:23 final size:23
Alignment explanation
Indices: 17815--17922 Score: 103
Period size: 23 Copynumber: 4.7 Consensus size: 23
17805 TTGGGGAAAT
17815 AGTAAGCACACACAGTGCAAAAA
1 AGTAAGCACACACAGTGCAAAAA
**
17838 AGTAAGCACACACAGTGCAAATC
1 AGTAAGCACACACAGTGCAAAAA
* * * **
17861 AGTAA-CACATATAGCGCGAATGA
1 AGTAAGCACACACAGTGC-AAAAA
** *
17884 A-TAAGCACACACAGTGCTGAAC
1 AGTAAGCACACACAGTGCAAAAA
17906 AGTAAGCACACACAGTG
1 AGTAAGCACACACAGTG
17923 ATGAACAGTA
Statistics
Matches: 66, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
22 13 0.20
23 53 0.80
ACGTcount: A:0.44, C:0.23, G:0.19, T:0.13
Consensus pattern (23 bp):
AGTAAGCACACACAGTGCAAAAA
Found at i:17927 original size:23 final size:23
Alignment explanation
Indices: 17885--17935 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
17875 CGCGAATGAA
*
17885 TAAGCACACACAGTGCTGAACAG
1 TAAGCACACACAGTGATGAACAG
17908 TAAGCACACACAGTGATGAACAG
1 TAAGCACACACAGTGATGAACAG
17931 TAAGC
1 TAAGC
17936 GCGCTAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.14
Consensus pattern (23 bp):
TAAGCACACACAGTGATGAACAG
Found at i:19676 original size:31 final size:31
Alignment explanation
Indices: 19641--19713 Score: 137
Period size: 31 Copynumber: 2.4 Consensus size: 31
19631 CTTCACCATC
19641 GTCGTTGTTCTCCTCAAACATACCTATCCCA
1 GTCGTTGTTCTCCTCAAACATACCTATCCCA
19672 GTCGTTGTTCTCCTCAAACATACCTATCCCA
1 GTCGTTGTTCTCCTCAAACATACCTATCCCA
*
19703 GTCGTTATTCT
1 GTCGTTGTTCT
19714 AATCAGTATC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.21, C:0.33, G:0.11, T:0.36
Consensus pattern (31 bp):
GTCGTTGTTCTCCTCAAACATACCTATCCCA
Found at i:22443 original size:59 final size:57
Alignment explanation
Indices: 22319--22519 Score: 210
Period size: 57 Copynumber: 3.5 Consensus size: 57
22309 GGAGGTCCCT
* * *
22319 AAACTATCCAAAAATT-ATATTTCGACCCCAAACTTCCAAAAAATTCAATTTTTA-CCCC
1 AAACT-TCCAAAAATTCA-ATTTTGACCCAAAACTTCC-AAAAATTCCATTTTTACCCCC
*
22377 AAACTTCCAAAAATTCAATTTTTGACCCAAAAACTTTCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCAA-TTTTGACCC-AAAACTTCCAAAAATTCCATTTTTACCCCC
* * * * *
22436 GAACTTCCAAAAATTCCATTTTGACCCCAAACTTCCAAAAATTACATTTTTGCCCCC
1 AAACTTCCAAAAATTCAATTTTGACCCAAAACTTCCAAAAATTCCATTTTTACCCCC
* * *
22493 AGA-TGTCCAAAAACTCCATTTTCGACC
1 AAACT-TCCAAAAATTCAATTTT-GACC
22520 TCGAAACTCT
Statistics
Matches: 124, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
56 1 0.01
57 54 0.44
58 42 0.34
59 27 0.22
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.30
Consensus pattern (57 bp):
AAACTTCCAAAAATTCAATTTTGACCCAAAACTTCCAAAAATTCCATTTTTACCCCC
Found at i:22486 original size:29 final size:29
Alignment explanation
Indices: 22319--22519 Score: 207
Period size: 29 Copynumber: 6.9 Consensus size: 29
22309 GGAGGTCCCT
*
22319 AAACTATCCAAAAATT--ATATTTCGACCCC
1 AAACT-TCCAAAAATTCCAT-TTTTGACCCC
*
22348 AAACTTCCAAAAAATTCAATTTTT-ACCCC
1 AAACTTCC-AAAAATTCCATTTTTGACCCC
* *
22377 AAACTTCCAAAAATTCAATTTTTGACCCAA
1 AAACTTCCAAAAATTCCATTTTTGACCC-C
*
22407 AAACTTTCAAAAATTCCATTTTT-ACCCCC
1 AAACTTCCAAAAATTCCATTTTTGA-CCCC
*
22436 GAACTTCCAAAAATTCCA-TTTTGACCCC
1 AAACTTCCAAAAATTCCATTTTTGACCCC
* *
22464 AAACTTCCAAAAATTACATTTTTGCCCCC
1 AAACTTCCAAAAATTCCATTTTTGACCCC
* * *
22493 AGA-TGTCCAAAAACTCCATTTTCGACC
1 AAACT-TCCAAAAATTCCATTTTTGACC
22520 TCGAAACTCT
Statistics
Matches: 148, Mismatches: 15, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
28 43 0.29
29 76 0.51
30 27 0.18
31 2 0.01
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.30
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTGACCCC
Found at i:22533 original size:116 final size:116
Alignment explanation
Indices: 22320--22608 Score: 277
Period size: 116 Copynumber: 2.5 Consensus size: 116
22310 GAGGTCCCTA
** * *
22320 AACTATCCAAAAATTATATTTCGACCCCAAACTTCCAAAAAATT-CAATTTTT-ACCCCAAACTT
1 AACTATCCAAAAATTCCATTTTGACCCCAAACTTCC-AAAAATTAC-ATTTTTGCCCCCAAACTT
* * * *
22383 CCAAAAATTCAATTTTTGACCCAAAAACTTTCAAAAATTCCATTTTTACCCCCG
64 CCAAAAACTCAATTTTCGACCCAAAAACTCTC-AAAATTCCACTTTTACCCCCG
*
22437 AACT-TCCAAAAATTCCATTTTGACCCCAAACTTCCAAAAATTACATTTTTGCCCCCAGA-TGTC
1 AACTATCCAAAAATTCCATTTTGACCCCAAACTTCCAAAAATTACATTTTTGCCCCCAAACT-TC
* * * **
22500 CAAAAACTCCATTTTCGACCTC-GAAACTCTCAAAATTCCCCTTTTACCTTCG
65 CAAAAACTCAATTTTCGACC-CAAAAACTCTCAAAATTCCACTTTTACCCCCG
* * * * ** *
22552 AA-TGTCTAAAAATTCCATTTTAACCTCGAATTTTCCCAAAATTACCA-TTTTGCCCCC
1 AACTATCCAAAAATTCCATTTTGACC-CCAAACTTCCAAAAATTA-CATTTTTGCCCCC
22609 CGGGTATCCG
Statistics
Matches: 145, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
114 1 0.01
115 52 0.36
116 85 0.59
117 7 0.05
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.31
Consensus pattern (116 bp):
AACTATCCAAAAATTCCATTTTGACCCCAAACTTCCAAAAATTACATTTTTGCCCCCAAACTTCC
AAAAACTCAATTTTCGACCCAAAAACTCTCAAAATTCCACTTTTACCCCCG
Found at i:22572 original size:28 final size:28
Alignment explanation
Indices: 22415--22582 Score: 81
Period size: 29 Copynumber: 5.9 Consensus size: 28
22405 AAAAACTTTC
* * *
22415 AAAAATTCCATTTTTACCCCCGAACT-TCC
1 AAAAATTCCA-TTTTAACCTCGAA-TGTCT
* * * *
22444 AAAAATTCCATTTTGACCCCAAACT-TCC
1 AAAAATTCCATTTTAACCTCGAA-TGTCT
* ** * * *
22472 AAAAATTACATTTTTGCCCCCAGATGTCC
1 AAAAATTCCATTTTAACCTCGA-ATGTCT
* * **
22501 AAAAACTCCATTTTCGACCTCGAAACTCT
1 AAAAATTCCATTTT-AACCTCGAATGTCT
* *
22530 CAAAATTCCCCTTTT-ACCTTCGAATGTCT
1 AAAAATT-CCATTTTAACC-TCGAATGTCT
22559 AAAAATTCCATTTTAACCTCGAAT
1 AAAAATTCCATTTTAACCTCGAAT
22583 TTTCCCAAAA
Statistics
Matches: 110, Mismatches: 23, Indels: 13
0.75 0.16 0.09
Matches are distributed among these distances:
28 49 0.45
29 51 0.46
30 10 0.09
ACGTcount: A:0.33, C:0.30, G:0.06, T:0.32
Consensus pattern (28 bp):
AAAAATTCCATTTTAACCTCGAATGTCT
Found at i:25735 original size:18 final size:18
Alignment explanation
Indices: 25714--25757 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
25704 AACTACAAAC
*
25714 TTTTAAATAT-TTTTATTT
1 TTTTAAATATAATTTA-TT
*
25732 TTTTAAAAATAATTTATT
1 TTTTAAATATAATTTATT
25750 TTTTAAAT
1 TTTTAAAT
25758 TAAATGAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTAAATATAATTTATT
Found at i:26341 original size:9 final size:10
Alignment explanation
Indices: 26325--26349 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
26315 AGGTAGATAC
26325 ATTTTTTTTA
1 ATTTTTTTTA
26335 ATTTTTTTTA
1 ATTTTTTTTA
26345 ATTTT
1 ATTTT
26350 AAAAAATGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
ATTTTTTTTA
Found at i:27136 original size:21 final size:21
Alignment explanation
Indices: 27096--27159 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
27086 ATTTAACAAC
27096 TTTTTTTAATTTGATATTTAATTT
1 TTTTTTTAATTT--T-TTTAATTT
27120 TTTTTTTAATTTTTTTAATTT
1 TTTTTTTAATTTTTTTAATTT
** *
27141 AATATTTAACTTTTTTTAA
1 TTTTTTTAA-TTTTTTTAA
27160 ATTTAATTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 14 0.39
22 10 0.28
24 12 0.33
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (21 bp):
TTTTTTTAATTTTTTTAATTT
Found at i:27157 original size:22 final size:22
Alignment explanation
Indices: 27124--27166 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
27114 TAATTTTTTT
27124 TTTAATTTTTTT-AATTTAATA
1 TTTAATTTTTTTAAATTTAATA
27145 TTTAACTTTTTTTAAATTTAAT
1 TTTAA-TTTTTTTAAATTTAAT
27167 TTAGCATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.25
22 7 0.35
23 8 0.40
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTAATTTTTTTAAATTTAATA
Found at i:27164 original size:28 final size:28
Alignment explanation
Indices: 27133--27187 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
27123 TTTTAATTTT
* * *
27133 TTTAATTTAATATTTAACTTTTTTTAAA
1 TTTAATTTAACATTTAAATTTATTTAAA
*
27161 TTTAATTTAGCATTTAAATTTATTTAA
1 TTTAATTTAACATTTAAATTTATTTAA
27188 TATTATAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (28 bp):
TTTAATTTAACATTTAAATTTATTTAAA
Found at i:27308 original size:26 final size:24
Alignment explanation
Indices: 27266--27319 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 24
27256 CAATATTAAA
27266 AAAATTATATTAAAAA-TAGATATT
1 AAAATTATATTAAAAATTA-ATATT
*
27290 AAAATTATTCTTAATAAATTAATATT
1 AAAATTA-TATTAA-AAATTAATATT
27316 AAAA
1 AAAA
27320 AAATAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 7 0.27
25 5 0.19
26 12 0.46
27 2 0.08
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (24 bp):
AAAATTATATTAAAAATTAATATT
Found at i:27317 original size:14 final size:13
Alignment explanation
Indices: 27265--27320 Score: 55
Period size: 12 Copynumber: 4.4 Consensus size: 13
27255 TCAATATTAA
27265 AAAAATT-ATATT
1 AAAAATTAATATT
27277 AAAAA-TAGATATT
1 AAAAATTA-ATATT
* *
27290 -AAAATTATTCTT
1 AAAAATTAATATT
27302 AATAAATTAATATT
1 AA-AAATTAATATT
27316 AAAAA
1 AAAAA
27321 AATAAATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
11 1 0.03
12 12 0.34
13 11 0.31
14 11 0.31
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (13 bp):
AAAAATTAATATT
Found at i:27323 original size:15 final size:14
Alignment explanation
Indices: 27257--27333 Score: 56
Period size: 14 Copynumber: 5.6 Consensus size: 14
27247 AAATATTATC
27257 AATATTAAAAAAATT
1 AATATT-AAAAAATT
27272 -ATATT-AAAAA-T
1 AATATTAAAAAATT
27283 AGATATT--AAAATT
1 A-ATATTAAAAAATT
* * *
27296 ATTCTTAATAAATT
1 AATATTAAAAAATT
*
27310 AATATTAAAAAAATA
1 AATATT-AAAAAATT
27325 AATATTAAA
1 AATATTAAA
27334 TTTTAAATAC
Statistics
Matches: 49, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
11 1 0.02
12 12 0.24
13 7 0.14
14 17 0.35
15 12 0.24
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (14 bp):
AATATTAAAAAATT
Found at i:27353 original size:12 final size:12
Alignment explanation
Indices: 27336--27364 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
27326 ATATTAAATT
27336 TTAAATACCAAC
1 TTAAATACCAAC
27348 TTAAATACCAAC
1 TTAAATACCAAC
27360 TTAAA
1 TTAAA
27365 AAAAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (12 bp):
TTAAATACCAAC
Found at i:28001 original size:3 final size:3
Alignment explanation
Indices: 27993--28020 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
27983 CAACATGCAT
27993 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
28021 AGAAACCACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:42808 original size:20 final size:21
Alignment explanation
Indices: 42769--42809 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
42759 TCAAATTTAG
*
42769 AATTTTAATATTAGTTATTTT
1 AATTTTAATATTAATTATTTT
*
42790 AATTTTGAT-TTAATTATTTT
1 AATTTTAATATTAATTATTTT
42810 CATTAATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (21 bp):
AATTTTAATATTAATTATTTT
Found at i:45403 original size:20 final size:18
Alignment explanation
Indices: 45378--45477 Score: 71
Period size: 20 Copynumber: 5.3 Consensus size: 18
45368 AAAAAATCAT
*
45378 TAAAAATATCTATAAAATTG
1 TAAAAATAT-T-TAAAATTA
45398 TAAAAATATTTAAAATTA
1 TAAAAATATTTAAAATTA
* *
45416 TAAAAA-AATT-AAATAA
1 TAAAAATATTTAAAATTA
* *
45432 CTAAAAAAATTAAAAAATGTA
1 -TAAAAATATT-TAAAAT-TA
45453 -AACAAATATTTAAAAATTA
1 TAA-AAATATTT-AAAATTA
45472 TAAAAA
1 TAAAAA
45478 AAATCCAAGA
Statistics
Matches: 64, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
16 5 0.08
17 9 0.14
18 15 0.23
19 8 0.12
20 26 0.41
21 1 0.02
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (18 bp):
TAAAAATATTTAAAATTA
Found at i:45413 original size:18 final size:20
Alignment explanation
Indices: 45378--45421 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
45368 AAAAAATCAT
*
45378 TAAAAATATCTATAAAATTG
1 TAAAAATATCTATAAAATTA
45398 TAAAAATAT-T-TAAAATTA
1 TAAAAATATCTATAAAATTA
45416 TAAAAA
1 TAAAAA
45422 AATTAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.57
19 1 0.04
20 9 0.39
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (20 bp):
TAAAAATATCTATAAAATTA
Found at i:45454 original size:18 final size:18
Alignment explanation
Indices: 45391--45478 Score: 63
Period size: 18 Copynumber: 4.8 Consensus size: 18
45381 AAATATCTAT
* * *
45391 AAAATTGTAAAAATATTT
1 AAAAATGTAAAAAAATTA
* *
45409 AAAATTATAAAAAAATTA
1 AAAAATGTAAAAAAATTA
* *
45427 AATAA-CTAAAAAAATTA
1 AAAAATGTAAAAAAATTA
*
45444 AAAAATGTAAACAAATATTT
1 AAAAATGTAAA-AAA-ATTA
45464 AAAAAT-TATAAAAAA
1 AAAAATGTA-AAAAAA
45479 AATCCAAGAT
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
17 15 0.26
18 23 0.40
19 8 0.14
20 11 0.19
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (18 bp):
AAAAATGTAAAAAAATTA
Found at i:46136 original size:28 final size:28
Alignment explanation
Indices: 46102--46177 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 28
46092 GGCCCAACAG
46102 AATTTAAATTTATTTTAAAATTAAGTTT-
1 AATTTAAATTTA-TTTAAAATTAAGTTTA
* ** *
46130 ATTTTAAATTTAATTTATTA-TAATTTTA
1 AATTTAAATTT-ATTTAAAATTAAGTTTA
46158 AATTTAAATTTATTTAAAAT
1 AATTTAAATTTATTTAAAAT
46178 AATGTCCAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
27 12 0.32
28 25 0.66
29 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (28 bp):
AATTTAAATTTATTTAAAATTAAGTTTA
Found at i:46172 original size:17 final size:17
Alignment explanation
Indices: 46102--46163 Score: 81
Period size: 17 Copynumber: 3.7 Consensus size: 17
46092 GGCCCAACAG
46102 AATTTAAATTTATTTTA
1 AATTTAAATTTATTTTA
* *
46119 AAATTAAGTTTATTTTA
1 AATTTAAATTTATTTTA
*
46136 AATTT-AATTTATTATA
1 AATTTAAATTTATTTTA
*
46152 ATTTTAAATTTA
1 AATTTAAATTTA
46164 AATTTATTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
16 13 0.34
17 25 0.66
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:46177 original size:17 final size:17
Alignment explanation
Indices: 46102--46177 Score: 64
Period size: 17 Copynumber: 4.2 Consensus size: 17
46092 GGCCCAACAG
46102 AATTTAAATTTATTTTAA
1 AATTTAAATTTA-TTTAA
* *
46120 AA-TTAAGTTTATTTTA
1 AATTTAAATTTATTTAA
*
46136 AATTTAATTTATTATAATTTTA
1 AATTTAA---ATT-T-ATTTAA
46158 AATTTAAATTTATTTAA
1 AATTTAAATTTATTTAA
46175 AAT
1 AAT
46178 AATGTCCAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
16 6 0.12
17 20 0.42
18 3 0.06
19 3 0.06
20 2 0.04
21 1 0.02
22 13 0.27
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (17 bp):
AATTTAAATTTATTTAA
Found at i:46783 original size:12 final size:12
Alignment explanation
Indices: 46766--46864 Score: 64
Period size: 12 Copynumber: 8.5 Consensus size: 12
46756 TCAAAATGTC
46766 ATTAATAATATT
1 ATTAATAATATT
46778 ATTAAT--TATT
1 ATTAATAATATT
46788 ATGGTAATAATA--
1 AT--TAATAATATT
*
46800 A-TAATAATAAT
1 ATTAATAATATT
* *
46811 ATTACTAATATC
1 ATTAATAATATT
46823 ATTAATAATATT
1 ATTAATAATATT
* * * *
46835 AATGACAATAAT
1 ATTAATAATATT
*
46847 AATAATAATATT
1 ATTAATAATATT
*
46859 AATAAT
1 ATTAAT
46865 GACATTAATT
Statistics
Matches: 68, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
9 8 0.12
10 6 0.09
11 1 0.01
12 51 0.75
14 2 0.03
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (12 bp):
ATTAATAATATT
Found at i:46798 original size:3 final size:3
Alignment explanation
Indices: 46792--46864 Score: 67
Period size: 3 Copynumber: 24.3 Consensus size: 3
46782 ATTATTATGG
* * * *
46792 TAA TAA TAA TAA TAA TAA TAT TAC TAA T-A TCAT TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
* * *
46837 TGA CAA TAA TAA TAA TAA TAT TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
46865 GACATTAATT
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
2 2 0.04
3 52 0.95
4 1 0.02
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:47856 original size:29 final size:29
Alignment explanation
Indices: 47813--48039 Score: 264
Period size: 29 Copynumber: 7.8 Consensus size: 29
47803 GGAGGTCCCG
47813 AAACTTCCAAAAATTCCATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCT
* *
47842 GAACTTTCAAAAATTCCA-TTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCT
* *
47870 AAACTTCCAAAAAATTCCATTTTAACCCCA
1 AAACTTCC-AAAAATTCCATTTTTACCCCT
* *
47900 AAACTTTCAAAAATTCCATTTTTA-CACT
1 AAACTTCCAAAAATTCCATTTTTACCCCT
* *
47928 CAAACTTCCAAAAATTCCATTTTTGACCTCG
1 -AAACTTCCAAAAATTCCATTTTT-ACCCCT
*
47959 AAACTTCCAAAAATTCCA-TTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCT
* *
47987 GAACTTCCAAAAATTCTATTTTTGA-CCCT
1 AAACTTCCAAAAATTCCATTTTT-ACCCCT
*
48016 AAAACTTCTAAAAATTACCATTTT
1 -AAACTTCCAAAAATT-CCATTTT
48040 GCCCCCGAAT
Statistics
Matches: 168, Mismatches: 21, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
28 38 0.23
29 74 0.44
30 48 0.29
31 8 0.05
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCT
Found at i:47905 original size:58 final size:58
Alignment explanation
Indices: 47813--48126 Score: 291
Period size: 58 Copynumber: 5.4 Consensus size: 58
47803 GGAGGTCCCG
**
47813 AAACTTCCAAAAATTCCATTTTT-ACCCCTGAACTTTCAAAAATTCCATTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTTCAAAAATTCCATTTTACCCCT
* *
47870 AAACTTCCAAAAAATTCCA-TTTTAACCCCAAAACTTTCAAAAATTCCATTTTTA-CACT
1 AAACTTCC-AAAAATTCCATTTTTGACCCCAAAACTTTCAAAAATTCCA-TTTTACCCCT
* * * *
47928 CAAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTACCCCC
1 -AAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTTCAAAAATTCCATTTTACCCCT
* * * * *
47987 GAACTTCCAAAAATTCTATTTTTGACCCTAAAAC-TTCTAAAAATTACCATTTTGCCCCC
1 AAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTTC-AAAAATT-CCATTTTACCCCT
* * * * * * * * *
48046 GAA-TATCCAAAAACTCCATTTTCGGCCTCGAAACTCTC-AAAATTACCCTTTTACCCCC
1 AAACT-TCCAAAAATTCCATTTTTGACCCCAAAACTTTCAAAAATT-CCATTTTACCCCT
* *
48104 GAA-TGTCAAAAAATTCCATTTTT
1 AAACT-TCCAAAAATTCCATTTTT
48127 TTAACTTCAA
Statistics
Matches: 217, Mismatches: 30, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
57 14 0.06
58 124 0.57
59 77 0.35
60 2 0.01
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTTCAAAAATTCCATTTTACCCCT
Found at i:48020 original size:117 final size:117
Alignment explanation
Indices: 47813--48126 Score: 349
Period size: 117 Copynumber: 2.7 Consensus size: 117
47803 GGAGGTCCCG
* * **
47813 AAACTTCCAAAAATTCCATTTTT-ACCCCTG-AACTTTCAAAAATTCCATTTTACCCCTAAACTT
1 AAACTTCCAAAAATTCCATTTTTGACCTC-GAAACTTCCAAAAATTCCATTTTACCCCCGAACTT
*
47876 CCAAAAAATTCCA-TTTTAACCCCAAAACTT-TCAAAAATT-CCATTTTTACACTC
65 CC-AAAAATTCCATTTTTAACCCCAAAACTTCT-AAAAATTACCA-TTTTACACCC
47929 AAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTACCCCCGAACTTC
1 AAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTACCCCCGAACTTC
* * * * *
47994 CAAAAATTCTATTTTTGACCCTAAAACTTCTAAAAATTACCATTTTGCCCCC
66 CAAAAATTCCATTTTTAACCCCAAAACTTCTAAAAATTACCATTTTACACCC
* * * * *
48046 GAA-TATCCAAAAACTCCATTTTCGGCCTCGAAAC-TCTC-AAAATTACCCTTTTACCCCCGAA-
1 AAACT-TCCAAAAATTCCATTTTTGACCTCGAAACTTC-CAAAAATT-CCATTTTACCCCCGAAC
*
48107 TGTCAAAAAATTCCATTTTT
63 T-TCCAAAAATTCCATTTTT
48127 TTAACTTCAA
Statistics
Matches: 172, Mismatches: 17, Indels: 17
0.83 0.08 0.08
Matches are distributed among these distances:
116 43 0.25
117 125 0.73
118 4 0.02
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (117 bp):
AAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTACCCCCGAACTTC
CAAAAATTCCATTTTTAACCCCAAAACTTCTAAAAATTACCATTTTACACCC
Found at i:48126 original size:29 final size:29
Alignment explanation
Indices: 47809--48126 Score: 249
Period size: 29 Copynumber: 10.9 Consensus size: 29
47799 GCCAGGAGGT
47809 CCCGAAACTTCCAAAAATTCCATTTTTACC
1 CCCG-AACTTCCAAAAATTCCATTTTTACC
* *
47839 CCTGAACTTTCAAAAATTCCA-TTTTACC
1 CCCGAACTTCCAAAAATTCCATTTTTACC
** *
47867 CCTAAACTTCCAAAAAATTCCATTTTAACC
1 CCCGAACTTCC-AAAAATTCCATTTTTACC
** * *
47897 CCAAAACTTTCAAAAATTCCATTTTTACA
1 CCCGAACTTCCAAAAATTCCATTTTTACC
* *
47926 CTCAAACTTCCAAAAATTCCATTTTTGA-C
1 CCCGAACTTCCAAAAATTCCATTTTT-ACC
*
47955 CTCGAAACTTCCAAAAATTCCA-TTTTACC
1 CCCG-AACTTCCAAAAATTCCATTTTTACC
*
47984 CCCGAACTTCCAAAAATTCTATTTTTGACC
1 CCCGAACTTCCAAAAATTCCATTTTT-ACC
*** * *
48014 CTAAAACTTCTAAAAATTACCA-TTTTGCC
1 CCCGAACTTCCAAAAATT-CCATTTTTACC
* ***
48043 CCCGAA-TATCCAAAAACTCCATTTTCGGC
1 CCCGAACT-TCCAAAAATTCCATTTTTACC
* *
48072 CTCGAAAC-TCTC-AAAATTACC-CTTTTACC
1 CCCG-AACTTC-CAAAAATT-CCATTTTTACC
*
48101 CCCGAA-TGTCAAAAAATTCCATTTTT
1 CCCGAACT-TCCAAAAATTCCATTTTT
48127 TTAACTTCAA
Statistics
Matches: 232, Mismatches: 38, Indels: 37
0.76 0.12 0.12
Matches are distributed among these distances:
28 41 0.18
29 127 0.55
30 62 0.27
31 2 0.01
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (29 bp):
CCCGAACTTCCAAAAATTCCATTTTTACC
Found at i:50011 original size:14 final size:13
Alignment explanation
Indices: 49966--50013 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
49956 ATTGATATTA
49966 TAATAAATATGAATT
1 TAATAAA-A-GAATT
* *
49981 TAACAAATGAATT
1 TAATAAAAGAATT
49994 TAATAAAAGAATTT
1 TAATAAAAGAA-TT
50008 TAATAA
1 TAATAA
50014 TATTAATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
13 14 0.50
14 8 0.29
15 6 0.21
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.35
Consensus pattern (13 bp):
TAATAAAAGAATT
Found at i:54072 original size:23 final size:24
Alignment explanation
Indices: 54026--54072 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
54016 ATAATAACGA
**
54026 AACAACACCAAAACAGTGGTAACAT
1 AACAACA-CAAAACAGTGAAAACAT
54051 AACAACA-AAAACAGTGAAAACA
1 AACAACACAAAACAGTGAAAACA
54073 ACAGCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 13 0.65
25 7 0.35
ACGTcount: A:0.60, C:0.21, G:0.11, T:0.09
Consensus pattern (24 bp):
AACAACACAAAACAGTGAAAACAT
Found at i:55810 original size:58 final size:59
Alignment explanation
Indices: 55700--55927 Score: 189
Period size: 59 Copynumber: 3.9 Consensus size: 59
55690 GGTTTCTCGA
* * * * * *
55700 GGGTGAAATGGTAATTTTGGGAAAGTTCG-GGGTTAAAAAT-GAATTTTTTGGACATTCAT
1 GGGTAAAAGGGTAATTTT-TGAAAGTTTGAGGGTCAAAAATGGAA-TTTTTGGACATTCAG
* * * *
55759 GGGTAAAAGGGTAA-TTTTGAGAGTTTCGA-GGTCGAAAATGGAGTTTTTGGACATTCGG
1 GGGTAAAAGGGTAATTTTTGAAAGTTT-GAGGGTCAAAAATGGAATTTTTGGACATTCAG
* * * * **
55817 GGGCAAAATGGTAATTTTTGAAAGTTTTAGGGTCAAAAATGGAAATTTTGGAGGTTCAG
1 GGGTAAAAGGGTAATTTTTGAAAGTTTGAGGGTCAAAAATGGAATTTTTGGACATTCAG
* * * *
55876 GGGTAAAAATGG-AATTTTTGGAAGTTTTG-GGGTAAAAAATGTAATTTTTGGA
1 GGGT-AAAAGGGTAATTTTTGAAAG-TTTGAGGGTCAAAAATGGAATTTTTGGA
55928 AGTTTCGAGG
Statistics
Matches: 136, Mismatches: 26, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
57 6 0.04
58 38 0.28
59 82 0.60
60 10 0.07
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (59 bp):
GGGTAAAAGGGTAATTTTTGAAAGTTTGAGGGTCAAAAATGGAATTTTTGGACATTCAG
Found at i:55835 original size:29 final size:29
Alignment explanation
Indices: 55705--55836 Score: 74
Period size: 29 Copynumber: 4.5 Consensus size: 29
55695 CTCGAGGGTG
* * **
55705 AAATGGTAATTTTGGGAAAGTTCGGGGTTAA
1 AAATGGTAATTTTTGGACA-TTCGGGG-GCA
** *
55736 AAAT-G-AATTTTTTGGACATTCATGGGTA
1 AAATGGTAA-TTTTTGGACATTCGGGGGCA
* ** * *
55764 AAAGGGTAA-TTTTGAGAGTTTCGAGGTCGA
1 AAATGGTAATTTTTG-GACATTCGGGGGC-A
*
55794 AAATGG-AGTTTTTGGACATTCGGGGGCA
1 AAATGGTAATTTTTGGACATTCGGGGGCA
55822 AAATGGTAATTTTTG
1 AAATGGTAATTTTTG
55837 AAAGTTTTAG
Statistics
Matches: 74, Mismatches: 20, Indels: 16
0.67 0.18 0.15
Matches are distributed among these distances:
28 16 0.22
29 32 0.43
30 22 0.30
31 4 0.05
ACGTcount: A:0.30, C:0.06, G:0.30, T:0.34
Consensus pattern (29 bp):
AAATGGTAATTTTTGGACATTCGGGGGCA
Found at i:55887 original size:29 final size:30
Alignment explanation
Indices: 55705--55995 Score: 191
Period size: 30 Copynumber: 9.8 Consensus size: 30
55695 CTCGAGGGTG
* *
55705 AAATGGTAATTTTGGGAAAGTTC-GGGGTTAA
1 AAATGG-AATTTTTGG-AAGTTCAGGGGTCAA
*
55736 AAAT-GAATTTTTTGGACA-TTCATGGGT--A
1 AAATGGAA-TTTTTGGA-AGTTCAGGGGTCAA
* * *
55764 AAAGGGTAA-TTTT-GAGAGTTTC-GAGGTCGA
1 AAATGG-AATTTTTGGA-AG-TTCAGGGGTCAA
* *
55794 AAATGGAGTTTTTGGACA-TTC-GGGGGC-A
1 AAATGGAATTTTTGGA-AGTTCAGGGGTCAA
* *
55822 AAATGGTAATTTTTGAAAGTTTTA-GGGTCAA
1 AAATGG-AATTTTTGGAAG-TTCAGGGGTCAA
* *
55853 AAATGGAAATTTTGGAGGTTCAGGGGT-AA
1 AAATGGAATTTTTGGAAGTTCAGGGGTCAA
** *
55882 AAATGGAATTTTTGGAAGTTTTGGGGTAAA
1 AAATGGAATTTTTGGAAGTTCAGGGGTCAA
* *
55912 AAATGTAATTTTTGGAAGTTTC-GAGGTCAA
1 AAATGGAATTTTTGGAAG-TTCAGGGGTCAA
55942 AAATGGAATTTTTGGAAGTTCAGGGGT--A
1 AAATGGAATTTTTGGAAGTTCAGGGGTCAA
* *
55970 AAATGTAATTTTTGGACAGTTTAGGG
1 AAATGGAATTTTTGGA-AGTTCAGGG
55996 ACCTTCAAGG
Statistics
Matches: 208, Mismatches: 31, Indels: 44
0.73 0.11 0.16
Matches are distributed among these distances:
27 3 0.01
28 35 0.17
29 65 0.31
30 89 0.43
31 16 0.08
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (30 bp):
AAATGGAATTTTTGGAAGTTCAGGGGTCAA
Found at i:55956 original size:89 final size:90
Alignment explanation
Indices: 55821--55991 Score: 258
Period size: 89 Copynumber: 1.9 Consensus size: 90
55811 ATTCGGGGGC
* *
55821 AAAATGGTAATTTTTGAAAGTTTTAGGGTCAAAAATGGAAATTTTGGAGGTTCAGGGGTAAAAAT
1 AAAATGGTAATTTTTGAAAGTTTGAGGGTCAAAAATGGAAATTTTGGAAGTTCAGGGGT-AAAAT
55886 GGAATTTTTGGA-AGTTTTGGGGTAA
65 GGAATTTTTGGACAGTTTTGGGGTAA
* *
55911 AAAAT-GTAATTTTTGGAAGTTTCGA-GGTCAAAAATGGAATTTTTGGAAGTTCAGGGGTAAAAT
1 AAAATGGTAATTTTTGAAAGTTT-GAGGGTCAAAAATGGAAATTTTGGAAGTTCAGGGGTAAAAT
*
55974 GTAATTTTTGGACAGTTT
65 GGAATTTTTGGACAGTTT
55992 AGGGACCTTC
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
88 16 0.22
89 52 0.70
90 6 0.08
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.36
Consensus pattern (90 bp):
AAAATGGTAATTTTTGAAAGTTTGAGGGTCAAAAATGGAAATTTTGGAAGTTCAGGGGTAAAATG
GAATTTTTGGACAGTTTTGGGGTAA
Found at i:55960 original size:60 final size:59
Alignment explanation
Indices: 55821--55991 Score: 204
Period size: 59 Copynumber: 2.9 Consensus size: 59
55811 ATTCGGGGGC
* * * * * *
55821 AAAATGGTAATTTTTGAAAGTTTTAGGGTCAAAAATGGAAATTTTGG-AGGTTCAGGGGTA
1 AAAATGG-AATTTTTGGAAGTTTTGGGGT-AAAAATGTAATTTTTGGAAGTTTCAGAGGTA
55881 AAAATGGAATTTTTGGAAGTTTTGGGGTAAAAAATGTAATTTTTGGAAGTTTC-GAGGTCA
1 AAAATGGAATTTTTGGAAGTTTTGGGGT-AAAAATGTAATTTTTGGAAGTTTCAGAGGT-A
**
55941 AAAATGGAATTTTTGGAAGTTCAGGGGT-AAAATGTAATTTTTGGACAGTTT
1 AAAATGGAATTTTTGGAAGTTTTGGGGTAAAAATGTAATTTTTGGA-AGTTT
55992 AGGGACCTTC
Statistics
Matches: 99, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
58 17 0.17
59 43 0.43
60 39 0.39
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.36
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGTTTTGGGGTAAAAATGTAATTTTTGGAAGTTTCAGAGGTA
Found at i:57801 original size:16 final size:16
Alignment explanation
Indices: 57780--57832 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
57770 GTTTTTGGAC
* *
57780 TTTTAATTTAATTAAG
1 TTTTAATTAAATTAAA
* *
57796 TTTTAAATCAATTTAAA
1 TTTT-AATTAAATTAAA
57813 TTTTAATTAAATTTAAA
1 TTTTAATTAAA-TTAAA
57830 TTT
1 TTT
57833 AAAGCAAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (16 bp):
TTTTAATTAAATTAAA
Found at i:57816 original size:17 final size:17
Alignment explanation
Indices: 57791--57860 Score: 79
Period size: 17 Copynumber: 4.1 Consensus size: 17
57781 TTTAATTTAA
* *
57791 TTAAGTTTTAAATCAAT
1 TTAAATTTTAAATAAAT
*
57808 TTAAATTTTAATTAAAT
1 TTAAATTTTAAATAAAT
*
57825 TTAAA-TTTAAAGCAAAT
1 TTAAATTTTAAA-TAAAT
*
57842 TTAAATTTAAAATAAAT
1 TTAAATTTTAAATAAAT
57859 TT
1 TT
57861 GAATCAATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
16 5 0.11
17 34 0.77
18 5 0.11
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (17 bp):
TTAAATTTTAAATAAAT
Found at i:57820 original size:6 final size:6
Alignment explanation
Indices: 57805--57852 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
57795 GTTTTAAATC
* **
57805 AATTTA AATTTT AA-TTA AATTTA AATTTA AA-GCA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
57851 AA
1 AA
57853 ATAAATTTGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
5 7 0.21
6 27 0.79
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:59940 original size:29 final size:28
Alignment explanation
Indices: 59886--59949 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
59876 TTTTATTGGG
**
59886 TTTAAATTGATTCAAATTTATTTTTAAA
1 TTTAAATTGATTCAAATTTAAATTTAAA
* *
59914 TTTAAATCTGCTTTAAATTTAAATTT-AA
1 TTTAAAT-TGATTCAAATTTAAATTTAAA
*
59942 TTAAAATT
1 TTTAAATT
59950 TAAATGGATT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 1 0.03
28 15 0.50
29 14 0.47
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.52
Consensus pattern (28 bp):
TTTAAATTGATTCAAATTTAAATTTAAA
Found at i:61044 original size:30 final size:30
Alignment explanation
Indices: 61010--61106 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
61000 GGAAACAGTG
* *
61010 GCGCGTGCACCGGAGGATTGTGGGACGGCA
1 GCGCGTGCACCGGAGGACTATGGGACGGCA
* * **
61040 GCGCGTGCACCGAAGGACTATGGGACTGTG
1 GCGCGTGCACCGGAGGACTATGGGACGGCA
* * * *
61070 GCACGTGCACCAGAGGACTACGGGACGACA
1 GCGCGTGCACCGGAGGACTATGGGACGGCA
61100 GCGCGTG
1 GCGCGTG
61107 GTACGCGTGG
Statistics
Matches: 52, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.21, C:0.26, G:0.41, T:0.12
Consensus pattern (30 bp):
GCGCGTGCACCGGAGGACTATGGGACGGCA
Found at i:61791 original size:29 final size:29
Alignment explanation
Indices: 61758--62280 Score: 449
Period size: 29 Copynumber: 17.8 Consensus size: 29
61748 GTCAAGAAAC
*
61758 TCCATTTTTACCCCTGAACTTCAAAAAAT
1 TCCATTTTTACCCCTGAACTTCCAAAAAT
* **
61787 TCCATTTTGACCCCAAAACTTCCAAAAAT
1 TCCATTTTTACCCCTGAACTTCCAAAAAT
* * *
61816 TCCAATTTTACCCCTAAACTTCAAAAAAT
1 TCCATTTTTACCCCTGAACTTCCAAAAAT
* *
61845 TTCATTTTTA-ACCTCGAAACTTCCAAAAAT
1 TCCATTTTTACCCCT-G-AACTTCCAAAAAT
61875 TCCATTTTTACCCCTGAACTTCCAAAAA-
1 TCCATTTTTACCCCTGAACTTCCAAAAAT
* **
61903 TCTCATTTTTGACCTCAAAACTTCCAAAAAT
1 TC-CATTTTT-ACCCCTGAACTTCCAAAAAT
61934 TCCATTTTTA-CCCTCGAACTTCC-AAAAT
1 TCCATTTTTACCCCT-GAACTTCCAAAAAT
* **
61962 CCCATTTTTGACCCCAAAACTTCCAAAAAT
1 TCCATTTTT-ACCCCTGAACTTCCAAAAAT
* *
61992 TCCATTTTTA-CCCTCGAACTTCAAAAAAA
1 TCCATTTTTACCCCT-GAACTTCCAAAAAT
* *
62021 TCCATTTTTGACCTC-GAAACTCCCAAAAAT
1 TCCATTTTT-ACCCCTG-AACTTCCAAAAAT
*
62051 TTCATTTTTA-CCCTGAACTTCCAAAAAT
1 TCCATTTTTACCCCTGAACTTCCAAAAAT
* ** * *
62079 CCCATTCATAACTCTGAAACTTCCAAAAAT
1 TCCATTTTTACCCCTG-AACTTCCAAAAAT
**
62109 TCCATTTTTACCCCCAAAC-TCCTAAAAAT
1 TCCATTTTTACCCCTGAACTTCC-AAAAAT
* * * *
62138 TACATTTTTAACCTTAAAACTTCCAAAAAT
1 TCCATTTTTACCCCT-GAACTTCCAAAAAT
* *
62168 TCCATTTTTA-CCCTCAAACTTCTAAAAA-
1 TCCATTTTTACCCCT-GAACTTCCAAAAAT
*
62196 TCTCATTTTTAACCCC-GAAACTCCCAAAAAAAT
1 TC-CATTTTT-ACCCCTG-AACTTCC--AAAAAT
** *
62229 TCCATTTTTAACCCCAAAACTCCCAAAAAT
1 TCCATTTTT-ACCCCTGAACTTCCAAAAAT
62259 TCCATTTTTA-CCCTCGAACTTC
1 TCCATTTTTACCCCT-GAACTTC
62281 TAAAGTCTAA
Statistics
Matches: 402, Mismatches: 63, Indels: 58
0.77 0.12 0.11
Matches are distributed among these distances:
28 51 0.13
29 169 0.42
30 142 0.35
31 13 0.03
32 25 0.06
33 2 0.00
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.32
Consensus pattern (29 bp):
TCCATTTTTACCCCTGAACTTCCAAAAAT
Found at i:61869 original size:59 final size:59
Alignment explanation
Indices: 61758--62280 Score: 553
Period size: 59 Copynumber: 8.9 Consensus size: 59
61748 GTCAAGAAAC
* * *
61758 TCCATTTTTACCCCTGAACTTCAAAAAATTCCA-TTTTGACCCCAAAACTTCCAAAAAT
1 TCCATTTTTACCCCTGAACTTCAAAAAATTCCATTTTTAACCTCGAAACTTCCAAAAAT
* * *
61816 TCCAATTTTACCCCTAAACTTCAAAAAATTTCATTTTTAACCTCGAAACTTCCAAAAAT
1 TCCATTTTTACCCCTGAACTTCAAAAAATTCCATTTTTAACCTCGAAACTTCCAAAAAT
* * *
61875 TCCATTTTTACCCCTGAACTTCCAAAAA-TCTCATTTTTGACCTCAAAACTTCCAAAAAT
1 TCCATTTTTACCCCTGAACTTCAAAAAATTC-CATTTTTAACCTCGAAACTTCCAAAAAT
* * * * *
61934 TCCATTTTTA-CCCTCGAACTTC-CAAAATCCCATTTTTGACCCCAAAACTTCCAAAAAT
1 TCCATTTTTACCCCT-GAACTTCAAAAAATTCCATTTTTAACCTCGAAACTTCCAAAAAT
* * *
61992 TCCATTTTTA-CCCTCGAACTTCAAAAAAATCCATTTTTGACCTCGAAACTCCCAAAAAT
1 TCCATTTTTACCCCT-GAACTTCAAAAAATTCCATTTTTAACCTCGAAACTTCCAAAAAT
* * * **
62051 TTCATTTTTA-CCCTGAACTTCCAAAAATCCCATTCATAA-CTCTGAAACTTCCAAAAAT
1 TCCATTTTTACCCCTGAACTTCAAAAAATTCCATTTTTAACCTC-GAAACTTCCAAAAAT
** * * * **
62109 TCCATTTTTACCCCCAAACTCCTAAAAATTACATTTTTAACCTTAAAACTTCCAAAAAT
1 TCCATTTTTACCCCTGAACTTCAAAAAATTCCATTTTTAACCTCGAAACTTCCAAAAAT
* * * *
62168 TCCATTTTTA-CCCTCAAACTTCTAAAAA-TCTCATTTTTAACCCCGAAACTCCCAAAAAAAT
1 TCCATTTTTACCCCT-GAACTTCAAAAAATTC-CATTTTTAACCTCGAAACTTCC--AAAAAT
** * * *
62229 TCCATTTTTAACCCCAAAACTCCCAAAAATTCCATTTTTACCCTCG-AACTTC
1 TCCATTTTT-ACCCCTGAACTTCAAAAAATTCCATTTTTAACCTCGAAACTTC
62281 TAAAGTCTAA
Statistics
Matches: 397, Mismatches: 53, Indels: 27
0.83 0.11 0.06
Matches are distributed among these distances:
57 3 0.01
58 134 0.34
59 209 0.53
60 2 0.01
61 20 0.05
62 24 0.06
63 5 0.01
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.32
Consensus pattern (59 bp):
TCCATTTTTACCCCTGAACTTCAAAAAATTCCATTTTTAACCTCGAAACTTCCAAAAAT
Found at i:61968 original size:117 final size:118
Alignment explanation
Indices: 61758--62267 Score: 620
Period size: 117 Copynumber: 4.3 Consensus size: 118
61748 GTCAAGAAAC
* * *
61758 TCCATTTTTACCCCTGAACTTCAAAAAATTCCA-TTTTGACCCCAAAACTTCCAAAAATTCCAAT
1 TCCATTTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTCCATT
** *
61822 TTTACCC-CTAAACTTCAAAAAATTTCATTTTTAACCTCGAAACTTCCAAAAAT
66 TTTACCCTC-AAACTTCAAAAAATCCCATTTTTAACCCCGAAACTTCCAAAAAT
61875 TCCATTTTTACCCCTGAACTTCCAAAAA-TCTCATTTTTGACCTCAAAACTTCCAAAAATTCCAT
1 TCCATTTTTACCCCTGAACTTCCAAAAATTC-CATTTTTGACCTCAAAACTTCCAAAAATTCCAT
* * * *
61939 TTTTACCCTCGAACTTC-CAAAATCCCATTTTTGACCCCAAAACTTCCAAAAAT
65 TTTTACCCTCAAACTTCAAAAAATCCCATTTTTAACCCCGAAACTTCCAAAAAT
* * * * *
61992 TCCATTTTTA-CCCTCGAACTTCAAAAAAATCCATTTTTGACCTCGAAACTCCCAAAAATTTCAT
1 TCCATTTTTACCCCT-GAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTCCAT
* * ** * *
62056 TTTTACCCT-GAACTTCCAAAAATCCCATTCATAACTCTGAAACTTCCAAAAAT
65 TTTTACCCTCAAACTTCAAAAAATCCCATTTTTAACCCCGAAACTTCCAAAAAT
** * * *
62109 TCCATTTTTACCCCCAAAC-TCCTAAAAATTACATTTTTAACCTTAAAACTTCCAAAAATTCCAT
1 TCCATTTTTACCCCTGAACTTCC-AAAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTCCAT
* * *
62173 TTTTACCCTCAAACTTCTAAAAATCTCATTTTTAACCCCGAAACTCCCAAAAAAAT
65 TTTTACCCTCAAACTTCAAAAAATCCCATTTTTAACCCCGAAACTTCC--AAAAAT
** *
62229 TCCATTTTTAACCCCAAAACTCCCAAAAATTCCATTTTT
1 TCCATTTTT-ACCCCTGAACTTCCAAAAATTCCATTTTT
62268 ACCCTCGAAC
Statistics
Matches: 338, Mismatches: 42, Indels: 22
0.84 0.10 0.05
Matches are distributed among these distances:
116 15 0.04
117 205 0.61
118 77 0.23
119 1 0.00
120 15 0.04
121 23 0.07
122 2 0.01
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.33
Consensus pattern (118 bp):
TCCATTTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTCCATT
TTTACCCTCAAACTTCAAAAAATCCCATTTTTAACCCCGAAACTTCCAAAAAT
Found at i:74128 original size:168 final size:169
Alignment explanation
Indices: 73810--74139 Score: 439
Period size: 168 Copynumber: 2.0 Consensus size: 169
73800 GACCATCCAC
* * * *
73810 AAACAACGACGCGGTCATCTTCCTGATGAGATACCGAGAAGAAGACCAAATCAAACCCATGCTCA
1 AAACAACGACGCGGTCATATTCCTGAAGAGATACCGAGAAGAAGACCAAATCAAACACACGCTCA
* * * * * *
73875 AAGCGAGCAAAATCTTCTAACCCCCAGCTTCCTGATGAGATACTAAGAAGCAGGTTGAAGCAATG
66 AAGCGAGCAAAATCTTCGAACCCCCAGCTTCCTGATGAGACACCAAGAAGCAGATCGAAGCAATA
*
73940 AACGGTTAGCTTCTTGATGAGATACAGAGAAGCGAATCG
131 AACGGTTAGCTTCCTGATGAGATACAGAGAAGCGAATCG
* *
73979 AAACAAACGACGCGGTCATATTCCTGAAGAGATATCGAGAAGAAGATCAAATCAAACACACGCTC
1 AAAC-AACGACGCGGTCATATTCCTGAAGAGATACCGAGAAGAAGACCAAATCAAACACACGCTC
* * * * * * * *
74044 GATGTGAG-TAAATCTTCGAA-TCCTAGCTTCTTGATGAGACACCGAGAAGCAGATCGAAGCAAT
65 AAAGCGAGCAAAATCTTCGAACCCCCAGCTTCCTGATGAGACACCAAGAAGCAGATCGAAGCAAT
*
74107 AAACGGTTAGCTTCCTGATGAGATACTGAGAAG
130 AAACGGTTAGCTTCCTGATGAGATACAGAGAAG
74140 TGGACCAAAT
Statistics
Matches: 138, Mismatches: 22, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
168 65 0.47
169 14 0.10
170 59 0.43
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.20
Consensus pattern (169 bp):
AAACAACGACGCGGTCATATTCCTGAAGAGATACCGAGAAGAAGACCAAATCAAACACACGCTCA
AAGCGAGCAAAATCTTCGAACCCCCAGCTTCCTGATGAGACACCAAGAAGCAGATCGAAGCAATA
AACGGTTAGCTTCCTGATGAGATACAGAGAAGCGAATCG
Found at i:74353 original size:206 final size:205
Alignment explanation
Indices: 73949--74639 Score: 1042
Period size: 205 Copynumber: 3.4 Consensus size: 205
73939 GAACGGTTAG
* * * * *
73949 CTTCTTGATGAGATACAGAGAAGCGAATCGAAACAAACGACGCGGTCATATTCCTGAAGAGATAT
1 CTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATAC
* * * *
74014 CGAGAAGAAGATCAAATCAAACACACGCTCGATGTGAGTAAATCTTCGAATCCTAGCTTCTTGAT
66 CGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGTAAATCTTCGAATCCCAGCTTCCTGAT
74079 GAGACACCGAGAAGCAGATCGAAGCAATAAACGGTTAGCTTCCTGATGAGATACTGAGAAGTGGA
131 GAGACACCGAGAAGCAGATCGAAGCAATAAACGGTTAGCTTCCTGATGAGATACTGAGAAGTGGA
74144 CCAAATTCGT
196 CCAAATTCGT
* *
74154 CTTCCTGATGAGATACAAAGAAGCGAATTGAAACAAACGACGCGGTCATCTTTCTGATGAGATAC
1 CTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATAC
* * * * * * *
74219 CGAGAAGAAGACCAAATCAAACCCACGCTCAAAGCGAGCAAAATCTTCAAACCCCATCTTCCTGA
66 CGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAG-TAAATCTTCGAATCCCAGCTTCCTGA
* * * * * *
74284 TGAGATACTGAGAAGCAGGTCGAAGCAATGAACAGTTAGCTTCTTGATGAGATACTGAGAAGTGG
130 TGAGACACCGAGAAGCAGATCGAAGCAATAAACGGTTAGCTTCCTGATGAGATACTGAGAAGTGG
74349 ACCAAATTCGT
195 ACCAAATTCGT
* * *
74360 CTTCCTGATGAGATGCAGAGAAGCAAATTGAAACAAACGACGCGGTCATCTTCCTGATAAGATAC
1 CTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATAC
*
74425 CGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGTAAATCTTCGAATCCCAGCTGCCTGAT
66 CGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGTAAATCTTCGAATCCCAGCTTCCTGAT
*
74490 GAGACACCGAGAAGCAGATCGAAGCAATAAACGGTTAGCTTCCTGATGAGATACTGAAAAGTGGA
131 GAGACACCGAGAAGCAGATCGAAGCAATAAACGGTTAGCTTCCTGATGAGATACTGAGAAGTGGA
74555 CCAAATTCGT
196 CCAAATTCGT
* * * *
74565 CTTCCTAATGAGATACAGAGAAGC-ATATTGAAATAAATGACGCGGTCATCTTCCTAATGAGATA
1 CTTCCTGATGAGATACAGAGAAGCGA-ATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATA
**
74629 TTGAGAAGAAG
65 CCGAGAAGAAG
74640 GTCAAGTCAA
Statistics
Matches: 432, Mismatches: 52, Indels: 4
0.89 0.11 0.01
Matches are distributed among these distances:
204 1 0.00
205 246 0.57
206 185 0.43
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (205 bp):
CTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATAC
CGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGTAAATCTTCGAATCCCAGCTTCCTGAT
GAGACACCGAGAAGCAGATCGAAGCAATAAACGGTTAGCTTCCTGATGAGATACTGAGAAGTGGA
CCAAATTCGT
Found at i:75019 original size:6 final size:6
Alignment explanation
Indices: 75008--75073 Score: 55
Period size: 6 Copynumber: 11.2 Consensus size: 6
74998 TCAAATTTAT
** * **
75008 TTTAAA TTTAAA TTTACCT TTTAAA TTTAAA TAT-GC TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
75056 TTT-AA TTAAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA T
75074 GGAATTAAAA
Statistics
Matches: 45, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
5 6 0.13
6 35 0.78
7 4 0.09
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:75022 original size:17 final size:17
Alignment explanation
Indices: 75000--75073 Score: 85
Period size: 17 Copynumber: 4.2 Consensus size: 17
74990 AAATTGATTC
75000 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
75017 AAATTTACCTTTTAAATTT
1 AAATTTA--TTTTAAATTT
* **
75036 AAATATGCTTTAAATTT
1 AAATTTATTTTAAATTT
* *
75053 AAATTTAATTAAAATTT
1 AAATTTATTTTAAATTT
75070 AAAT
1 AAAT
75074 GGAATTAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
17 33 0.69
19 15 0.31
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.50
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:75031 original size:19 final size:19
Alignment explanation
Indices: 75007--75059 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 19
74997 TTCAAATTTA
75007 TTTTAAATTTAAATTTACC
1 TTTTAAATTTAAATTTACC
* *
75026 TTTTAAATTTAAATAT-GC
1 TTTTAAATTTAAATTTACC
75044 -TTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
75060 ATTAAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 14 0.47
18 1 0.03
19 15 0.50
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.53
Consensus pattern (19 bp):
TTTTAAATTTAAATTTACC
Found at i:75079 original size:17 final size:17
Alignment explanation
Indices: 75047--75088 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
75037 AATATGCTTT
**
75047 AAATTTAAATTTAATTA
1 AAATTTAAATGGAATTA
75064 AAATTTAAATGGAATTA
1 AAATTTAAATGGAATTA
*
75081 AAACTTAA
1 AAATTTAA
75089 TTAAAAGTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (17 bp):
AAATTTAAATGGAATTA
Done.