Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 59 of 250
Found at i:18373117 original size:10 final size:10
Alignment explanation
Indices: 18373090--18373123 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
18373080 TAAATGAGCT
18373090 AAAATTTCTAG
1 AAAA-TTCTAG
18373101 AAAAATTCTAG
1 -AAAATTCTAG
18373112 AAAATTCTAG
1 AAAATTCTAG
18373122 AA
1 AA
18373124 TGCTTCCTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
11 6 0.27
12 4 0.18
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.29
Consensus pattern (10 bp):
AAAATTCTAG
Found at i:18379959 original size:21 final size:21
Alignment explanation
Indices: 18379930--18379969 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
18379920 GCTGGAACCT
18379930 TCCTTGAAGCTT-CTTGAACG
1 TCCTTGAAGCTTCCTTGAACG
18379950 TCCTTGGAAGCTTCCTTGAA
1 TCCTT-GAAGCTTCCTTGAA
18379970 GTTTCCAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 7 0.39
22 6 0.33
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (21 bp):
TCCTTGAAGCTTCCTTGAACG
Found at i:18379975 original size:11 final size:11
Alignment explanation
Indices: 18379928--18379975 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
18379918 GGGCTGGAAC
18379928 CTTCCTTGAAG
1 CTTCCTTGAAG
18379939 CTT-CTTGAA-
1 CTTCCTTGAAG
*
18379948 CGTCCTTGGAAG
1 CTTCCTT-GAAG
18379960 CTTCCTTGAAG
1 CTTCCTTGAAG
*
18379971 TTTCC
1 CTTCC
18379976 AAGCATGAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
9 2 0.06
10 9 0.29
11 14 0.45
12 6 0.19
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.38
Consensus pattern (11 bp):
CTTCCTTGAAG
Found at i:18380789 original size:32 final size:32
Alignment explanation
Indices: 18380744--18380808 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
18380734 CAAATTAATT
*
18380744 AGCAGCAGCTAATAAATTTGTCCTAAAACTAG
1 AGCAGCAGCTAATAAATTAGTCCTAAAACTAG
* *
18380776 AGCAGCAGTTAATAAATTAGTCCTAAGACTAG
1 AGCAGCAGCTAATAAATTAGTCCTAAAACTAG
18380808 A
1 A
18380809 CACTTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (32 bp):
AGCAGCAGCTAATAAATTAGTCCTAAAACTAG
Found at i:18380828 original size:29 final size:33
Alignment explanation
Indices: 18380744--18380828 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 33
18380734 CAAATTAATT
*
18380744 AGCAGCAGCTAATAAATT-TGTCCTAAAACTAG
1 AGCAGCAGTTAATAAATTATGTCCTAAAACTAG
*
18380776 AGCAGCAGTTAATAAATTA-GTCCTAAGACTAG
1 AGCAGCAGTTAATAAATTATGTCCTAAAACTAG
*
18380808 A-CA-C-TTTAA-AAATTATGTCCT
1 AGCAGCAGTTAATAAATTATGTCCT
18380829 CAACTAAAGA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
28 6 0.12
29 9 0.19
30 1 0.02
31 2 0.04
32 30 0.62
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (33 bp):
AGCAGCAGTTAATAAATTATGTCCTAAAACTAG
Found at i:18380834 original size:28 final size:29
Alignment explanation
Indices: 18380757--18380848 Score: 73
Period size: 32 Copynumber: 3.1 Consensus size: 29
18380747 AGCAGCTAAT
* *
18380757 AAATTTGTCCTAAAACT-AGAGCAGCAGTTAA
1 AAATTAGTCCTAAGACTAAGA-CA-CA-TTAA
*
18380788 TAAATTAGTCCTAAGACT-AGACACTTTAA
1 -AAATTAGTCCTAAGACTAAGACACATTAA
*
18380817 AAATTATGTCCTCA-ACTAAAGACACATTAA
1 AAATTA-GTCCTAAGACT-AAGACACATTAA
18380847 AA
1 AA
18380849 CTTTAATTAG
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
28 9 0.17
29 10 0.19
30 13 0.25
31 2 0.04
32 18 0.35
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.27
Consensus pattern (29 bp):
AAATTAGTCCTAAGACTAAGACACATTAA
Found at i:18383096 original size:30 final size:30
Alignment explanation
Indices: 18383011--18383098 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 30
18383001 TAAATTAAAA
* * *
18383011 TGAGTTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * *
18383041 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
18383071 TGAGCTAAGGTTTAGCTCGTGAGCTGAA
1 TGAGCTAAGATTTAGCTCGTGAGCTGAA
18383099 TAAGAGCTAG
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:18395736 original size:63 final size:64
Alignment explanation
Indices: 18395656--18395839 Score: 192
Period size: 67 Copynumber: 2.8 Consensus size: 64
18395646 CATGTAGTTC
* * * * *
18395656 GCTCTCTTGTAC-ACATGGTGAACACTTAGTACCACCCATGTGACCTAGCCA-ATTTATCTCGTA
1 GCTCTCTTGT-CTACATGGTGTACACATAGTACCACCCATGCGACCTAGCCACATATATCCCGTA
* * * * * *
18395719 GCTCTCTTGTCTACATGGTGTCCTTCACCTGGAACCACGCATGCGACCTAGCTACATATATCCCG
1 GCTCTCTTGTCTACATGGTG---TACACATAGTACCACCCATGCGACCTAGCCACATATATCCCG
18395784 TA
63 TA
* * *
18395786 GCTCTCCTGTCTACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACAT
1 GCTCTCTTGTCTACATGGTGTACACATAGTACCACCCATGCGACCTAGCCACAT
18395840 CATAATGTCT
Statistics
Matches: 99, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
62 1 0.01
63 18 0.18
64 28 0.28
66 23 0.23
67 29 0.29
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.29
Consensus pattern (64 bp):
GCTCTCTTGTCTACATGGTGTACACATAGTACCACCCATGCGACCTAGCCACATATATCCCGTA
Found at i:18396605 original size:30 final size:30
Alignment explanation
Indices: 18396571--18396631 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
18396561 TCCTTAACTC
18396571 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
18396601 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
18396631 A
1 A
18396632 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:18397860 original size:30 final size:30
Alignment explanation
Indices: 18397833--18397920 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 30
18397823 CTTGCTCATA
18397833 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
1 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
* * * * * *
18397863 TTCAGCTTAGGAGTTTAATCTCAGCTCAAC
1 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
* * *
18397893 TTTAGCTCACAAGCTAAAGCTTAGCTCA
1 TTCAGCTCACGAGCTAAACCTTAGCTCA
18397921 TTTTAGTTTA
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (30 bp):
TTCAGCTCACGAGCTAAACCTTAGCTCAAC
Found at i:18398808 original size:22 final size:20
Alignment explanation
Indices: 18398776--18398824 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
18398766 GCCAAATTTA
18398776 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
18398799 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
18398819 TGAACA
1 TGAACA
18398825 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:18403473 original size:46 final size:45
Alignment explanation
Indices: 18403423--18403595 Score: 163
Period size: 46 Copynumber: 3.8 Consensus size: 45
18403413 GTTGAGCATT
* *
18403423 CGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTA-GGATGCAAACGTC
* * * * *
18403469 CGAACTCGTTGAGTTGAGTCTGAGTTC-GTGA-GATGTAACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGATGCAA--A--CGTC
* **
18403516 CGAACTTGTTGAGTTGAGTCCGAGTTCACTTAGGGATGGGAACG-C
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTA-GGATGCAAACGTC
*
18403561 CTAAGCTCGTTGAGTTGAGTCCGAGTTCACTTAGG
1 CGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTAGG
18403596 GGCGGGTTAC
Statistics
Matches: 103, Mismatches: 16, Indels: 17
0.76 0.12 0.12
Matches are distributed among these distances:
43 6 0.06
45 9 0.09
46 53 0.51
47 27 0.26
48 3 0.03
50 5 0.05
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.29
Consensus pattern (45 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGATGCAAACGTC
Found at i:18408269 original size:20 final size:21
Alignment explanation
Indices: 18408241--18408279 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
18408231 CAAAATGAGC
*
18408241 AAACAAGCT-TATTGAGCTGG
1 AAACAAGCTAAATTGAGCTGG
*
18408261 AAACGAGCTAAATTGAGCT
1 AAACAAGCTAAATTGAGCT
18408280 CAACGAGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (21 bp):
AAACAAGCTAAATTGAGCTGG
Found at i:18410811 original size:20 final size:20
Alignment explanation
Indices: 18410765--18410811 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
18410755 AGCTCGTTTC
*
18410765 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
18410785 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
18410805 CAGCTCA
1 CAGCTCA
18410812 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:18412375 original size:26 final size:26
Alignment explanation
Indices: 18412320--18412378 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
18412310 GAGGAAATTC
** *
18412320 AAAAAAAAATCAAAAAAAATTGATTG
1 AAAAAAAAATCAAAAAAAATAAAGTG
18412346 AAAAAAAAATCAAAAAAAA-AAAGTG
1 AAAAAAAAATCAAAAAAAATAAAGTG
18412371 AAAAAAAA
1 AAAAAAAA
18412379 TCGAGCAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 11 0.37
26 19 0.63
ACGTcount: A:0.78, C:0.03, G:0.07, T:0.12
Consensus pattern (26 bp):
AAAAAAAAATCAAAAAAAATAAAGTG
Found at i:18412388 original size:27 final size:26
Alignment explanation
Indices: 18412356--18412420 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 26
18412346 AAAAAAAAAT
18412356 CAAAAAAAAAAAGTGAAAAAAAATCGAG
1 CAAAAAAAAAAA--GAAAAAAAATCGAG
18412384 CAAAAAAAAGAAAGAAAAAAAAGT-GAG
1 CAAAAAAAA-AAAGAAAAAAAA-TCGAG
18412411 CAAAAAAAAA
1 CAAAAAAAAA
18412421 TCAAGTTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
26 1 0.03
27 21 0.60
28 10 0.29
29 3 0.09
ACGTcount: A:0.75, C:0.06, G:0.14, T:0.05
Consensus pattern (26 bp):
CAAAAAAAAAAAGAAAAAAAATCGAG
Found at i:18412389 original size:15 final size:14
Alignment explanation
Indices: 18412346--18412436 Score: 55
Period size: 13 Copynumber: 6.5 Consensus size: 14
18412336 AAATTGATTG
*
18412346 AAAAAAA-AATCAA
1 AAAAAAATAAGCAA
**
18412359 AAAAAAA-AAGTGA
1 AAAAAAATAAGCAA
*
18412372 AAAAAAATCGAGCAA
1 AAAAAAAT-AAGCAA
18412387 AAAAAAGA-AAG-AA
1 AAAAAA-ATAAGCAA
* *
18412400 AAAAAAGTGAGCAA
1 AAAAAAATAAGCAA
*
18412414 AAAAAAATCAAGTTAA
1 AAAAAAAT-AAG-CAA
18412430 AAAAAAA
1 AAAAAAA
18412437 GTGAAAAGTA
Statistics
Matches: 59, Mismatches: 12, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
13 27 0.46
14 11 0.19
15 11 0.19
16 10 0.17
ACGTcount: A:0.76, C:0.05, G:0.11, T:0.08
Consensus pattern (14 bp):
AAAAAAATAAGCAA
Found at i:18421188 original size:48 final size:47
Alignment explanation
Indices: 18421109--18421214 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
18421099 GAGTGTCATG
*
18421109 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
18421157 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
18421205 GAAAAAGAAA
1 GAAAAAGAAA
18421215 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:18422919 original size:20 final size:20
Alignment explanation
Indices: 18422873--18422919 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
18422863 AGCTCGTTTC
*
18422873 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
18422893 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
18422913 CAGCTCA
1 CAGCTCA
18422920 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:18428688 original size:55 final size:52
Alignment explanation
Indices: 18428600--18428855 Score: 222
Period size: 55 Copynumber: 4.9 Consensus size: 52
18428590 CATTAGGGTT
*
18428600 TAAGGATACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAA
1 TAAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAA-GTTTCTAA
* * * * *
18428653 GGTAAGGAAATCATGTAAGACCATGTCAAGACATGGC-ATTGATAAGTTACT-A
1 --TAAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAA
* * *
18428705 TAAGGCAAAGGTCCCATGTAAGACCATGCCAAGGCATGGC-ATTGGTGAG-TTCATAA
1 TAAGG---A--TACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTC-TAA
* * *
18428761 GGCAAGGATACCATGTAAGACCATGTCAAGACATGG-AAATGGTAAGTTTC-AA
1 --TAAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAA
* * *
18428813 -AAGGATACCACGTAAGACCATGACAAGTCATGGCAA-TGGTAAG
1 TAAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAG
18428856 GTACCAACGT
Statistics
Matches: 166, Mismatches: 23, Indels: 30
0.76 0.11 0.14
Matches are distributed among these distances:
49 37 0.22
50 7 0.04
52 3 0.02
53 38 0.23
54 12 0.07
55 64 0.39
56 1 0.01
58 4 0.02
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (52 bp):
TAAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAA
Found at i:18428807 original size:108 final size:110
Alignment explanation
Indices: 18428608--18428808 Score: 309
Period size: 108 Copynumber: 1.8 Consensus size: 110
18428598 TTTAAGGATA
* *
18428608 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGTAAGGAAATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
* *
18428673 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CCATGTCAAGACATGGAAATGATAAGTTACTATAAGGCAAAGGTC
* *
18428718 CCATGTAAGACCATGCCAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAG
*
18428780 ACCATGTCAAGACATGGAAATGGTAAGTT
65 ACCATGTCAAGACATGGAAATGATAAGTT
18428809 TCAAAAGGAT
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
107 3 0.04
108 46 0.55
109 7 0.08
110 27 0.33
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
CCATGTCAAGACATGGAAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:18429068 original size:16 final size:16
Alignment explanation
Indices: 18429047--18429077 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18429037 ATAAATTTGG
18429047 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
18429063 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
18429078 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:18434285 original size:4 final size:4
Alignment explanation
Indices: 18434276--18434311 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
18434266 AAGTTTTATT
18434276 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
18434312 CTTAGTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:18439501 original size:4 final size:4
Alignment explanation
Indices: 18439492--18439519 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
18439482 TTATTTTATT
18439492 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
18439520 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:18443556 original size:21 final size:21
Alignment explanation
Indices: 18443529--18443589 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
18443519 TATAGTGAGT
18443529 ATATCATAGCATATCATGTGC
1 ATATCATAGCATATCATGTGC
* *
18443550 ATCTCATAACATATCATGTGC
1 ATATCATAGCATATCATGTGC
*
18443571 ATATTAT-GTCATATCATGT
1 ATATCATAG-CATATCATGT
18443590 ATAACAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (21 bp):
ATATCATAGCATATCATGTGC
Found at i:18443583 original size:10 final size:11
Alignment explanation
Indices: 18443537--18443589 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 11
18443527 GTATATCATA
18443537 GCATATCATGT
1 GCATATCATGT
* *
18443548 GCATCTCAT-A
1 GCATATCATGT
*
18443558 ACATATCATGT
1 GCATATCATGT
*
18443569 GCATATTATGT
1 GCATATCATGT
18443580 -CATATCATGT
1 GCATATCATGT
18443590 ATAACAATAT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
10 16 0.48
11 17 0.52
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (11 bp):
GCATATCATGT
Found at i:18443673 original size:25 final size:26
Alignment explanation
Indices: 18443626--18443675 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
18443616 ATAATTAAAC
* *
18443626 CCTAGGGTGTATAATGGTCATTTTTA
1 CCTAGGGTGTAAAATAGTCATTTTTA
18443652 CCTAGGG-GTAAAATAGTCATTTTT
1 CCTAGGGTGTAAAATAGTCATTTTT
18443676 CATATTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (26 bp):
CCTAGGGTGTAAAATAGTCATTTTTA
Found at i:18445299 original size:11 final size:11
Alignment explanation
Indices: 18445283--18445312 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
18445273 CTTGGACCCA
18445283 TGAGCTGGTAG
1 TGAGCTGGTAG
18445294 TGAGCTGGTAG
1 TGAGCTGGTAG
18445305 TGAGCTGG
1 TGAGCTGG
18445313 ACCCGAGCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.17, C:0.10, G:0.47, T:0.27
Consensus pattern (11 bp):
TGAGCTGGTAG
Found at i:18455881 original size:23 final size:22
Alignment explanation
Indices: 18455829--18455881 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
18455819 TCCACGTCTT
*
18455829 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
18455851 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
18455874 TTTCTTTT
1 TTTCTTTT
18455882 TCACTCAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:18459698 original size:27 final size:27
Alignment explanation
Indices: 18459668--18459899 Score: 237
Period size: 27 Copynumber: 8.7 Consensus size: 27
18459658 TAGTAAAGAG
*
18459668 AAATTATCGAAACACCCTCGATTTGTA
1 AAATTATCGAAATACCCTCGATTTGTA
*
18459695 AAATTAAT-GAAATACCCTCGATGTGTA
1 AAATT-ATCGAAATACCCTCGATTTGTA
* * * *
18459722 AAATTACCAAAATACCCTCAATTTGTG
1 AAATTATCGAAATACCCTCGATTTGTA
*
18459749 AAATTATCGAAACGA-CCTCGATTTGTA
1 AAATTATCGAAA-TACCCTCGATTTGTA
*
18459776 AAATTA-CTGAAACACCCTCGATTTGTA
1 AAATTATC-GAAATACCCTCGATTTGTA
* * *
18459803 AAATTA-CTAAAATACACTTGA-TT-TA
1 AAATTATC-GAAATACCCTCGATTTGTA
*
18459828 AAATTATTGAAATACCCTCGATTTGTA
1 AAATTATCGAAATACCCTCGATTTGTA
*
18459855 AAATTA-CTGAAACACCC-CTGATTTGTA
1 AAATTATC-GAAATACCCTC-GATTTGTA
18459882 AAATTATCGAAATACCCT
1 AAATTATCGAAATACCCT
18459900 TGTAGTGTAA
Statistics
Matches: 169, Mismatches: 24, Indels: 23
0.78 0.11 0.11
Matches are distributed among these distances:
25 18 0.11
26 8 0.05
27 139 0.82
28 4 0.02
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (27 bp):
AAATTATCGAAATACCCTCGATTTGTA
Found at i:18459747 original size:54 final size:54
Alignment explanation
Indices: 18459668--18459952 Score: 242
Period size: 54 Copynumber: 5.3 Consensus size: 54
18459658 TAGTAAAGAG
* * *
18459668 AAATTATCGAAACACCCTCGATTTGTAAAATTAATGAAATACCCTCGATGTGTA
1 AAATTACCGAAATACCCTCGATTTGTAAAATTAATGAAATACCCTCGATTTGTA
* * * *
18459722 AAATTACCAAAATACCCTCAATTTGTGAAATT-ATCGAAACGA-CCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTAAAATTAAT-GAAA-TACCCTCGATTTGTA
* * * * * *
18459776 AAATTACTGAAACACCCTCGATTTGTAAAATTACTAAAATACACTTGA-TT-TA
1 AAATTACCGAAATACCCTCGATTTGTAAAATTAATGAAATACCCTCGATTTGTA
** * *
18459828 AAATTATTGAAATACCCTCGATTTGTAAAATTACTGAAACACCC-CTGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTAAAATTAATGAAATACCCTC-GATTTGTA
* * * * * * *
18459882 AAATTATCGAAATACCCTTG-TAGTGTAAAATTACTTAAATACCCTTG-TAGTGTA
1 AAATTACCGAAATACCCTCGAT-TTGTAAAATTAATGAAATACCCTCGAT-TTGTA
* *
18459936 AAATGACCGACATACCC
1 AAATTACCGAAATACCC
18459953 CTGTAGGGTA
Statistics
Matches: 188, Mismatches: 33, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
52 43 0.23
53 9 0.05
54 134 0.71
55 2 0.01
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (54 bp):
AAATTACCGAAATACCCTCGATTTGTAAAATTAATGAAATACCCTCGATTTGTA
Found at i:18459803 original size:81 final size:79
Alignment explanation
Indices: 18459667--18459899 Score: 308
Period size: 81 Copynumber: 2.9 Consensus size: 79
18459657 ATAGTAAAGA
* * *
18459667 GAAATTATCGAAACACCCTCGATTTGTAAAATTAATGAAATACCCTCGATGTGTAAAATTACCAA
1 GAAATTATCGAAACACCCTCGATTTGTAAAATTACTGAAACACCCTCGATTTGTAAAATTACCAA
18459732 AATACCCTCAATTTGT
66 AATACCCTCAA-TT-T
*
18459748 GAAATTATCGAAACGA-CCTCGATTTGTAAAATTACTGAAACACCCTCGATTTGTAAAATTACTA
1 GAAATTATCGAAAC-ACCCTCGATTTGTAAAATTACTGAAACACCCTCGATTTGTAAAATTACCA
* **
18459812 AAATACACTTGATTT
65 AAATACCCTCAATTT
* * * * *
18459827 AAAATTATTGAAATACCCTCGATTTGTAAAATTACTGAAACACCC-CTGATTTGTAAAATTATCG
1 GAAATTATCGAAACACCCTCGATTTGTAAAATTACTGAAACACCCTC-GATTTGTAAAATTACCA
18459891 AAATACCCT
65 AAATACCCT
18459900 TGTAGTGTAA
Statistics
Matches: 135, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
78 2 0.01
79 63 0.47
80 2 0.01
81 67 0.50
82 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (79 bp):
GAAATTATCGAAACACCCTCGATTTGTAAAATTACTGAAACACCCTCGATTTGTAAAATTACCAA
AATACCCTCAATTT
Found at i:18459908 original size:27 final size:26
Alignment explanation
Indices: 18459772--18459966 Score: 112
Period size: 27 Copynumber: 7.3 Consensus size: 26
18459762 GACCTCGATT
* * *
18459772 TGTAAAATTACTGAAACACCCTCG-ATT
1 TGTAAAATTAC-GAAATACCCTTGTA-G
* *
18459799 TGTAAAATTACTAAAATACACTTG-A-
1 TGTAAAATTAC-GAAATACCCTTGTAG
* * * *
18459824 TTTAAAATTATTGAAATACCCTCG-ATT
1 TGTAAAATTA-CGAAATACCCTTGTA-G
* * *
18459851 TGTAAAATTACTGAAACACCCCTG-ATT
1 TGTAAAATTAC-GAAATACCCTTGTA-G
18459878 TGTAAAATTATCGAAATACCCTTGTAG
1 TGTAAAATTA-CGAAATACCCTTGTAG
*
18459905 TGTAAAATTACTTAAATACCCTTGTAG
1 TGTAAAATTAC-GAAATACCCTTGTAG
* * *
18459932 TGTAAAATGACCGACATACCCCTGTAG
1 TGTAAAATTA-CGAAATACCCTTGTAG
*
18459959 GGTAAAAT
1 TGTAAAAT
18459967 AACTGTTTTG
Statistics
Matches: 137, Mismatches: 23, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
25 19 0.14
26 1 0.01
27 114 0.83
28 3 0.02
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (26 bp):
TGTAAAATTACGAAATACCCTTGTAG
Found at i:18459953 original size:81 final size:79
Alignment explanation
Indices: 18459668--18459955 Score: 201
Period size: 81 Copynumber: 3.6 Consensus size: 79
18459658 TAGTAAAGAG
* * * * ** * * *
18459668 AAATTATCGAAACACCCTCGATTTGTAAAATTAATGAAATA-CCCTCGATGTGTAAAATTACCAA
1 AAATTATTGAAATACCCTCGATGTGTAAAATGACCGAAACACCCCT-GATTTGTAAAATTACTAA
* ** *
18459732 AATACCCTCAATTTGTG
65 AATACACTTGA--TGTA
* * * * *
18459749 AAATTATCGAAACGA-CCTCGATTTGTAAAATTACTGAAACA-CCCTCGATTTGTAAAATTACTA
1 AAATTATTGAAA-TACCCTCGATGTGTAAAATGACCGAAACACCCCT-GATTTGTAAAATTACTA
*
18459812 AAATACACTTGATTTA
64 AAATACACTTGATGTA
* * * *
18459828 AAATTATTGAAATACCCTCGATTTGTAAAATTACTGAAACACCCCTGATTTGTAAAATTA-TCGA
1 AAATTATTGAAATACCCTCGATGTGTAAAATGACCGAAACACCCCTGATTTGTAAAATTACT-AA
*
18459892 AATACCCTTGTAGTGTA
65 AATACACTTG-A-TGTA
* * *
18459909 AAATTACTT-AAATACCCTTG-TAGTGTAAAATGACCGACATACCCCTG
1 AAATTA-TTGAAATACCCTCGAT-GTGTAAAATGACCGAAACACCCCTG
18459956 TAGGGTAAAA
Statistics
Matches: 178, Mismatches: 21, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.01
79 63 0.35
80 6 0.03
81 104 0.58
82 3 0.02
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (79 bp):
AAATTATTGAAATACCCTCGATGTGTAAAATGACCGAAACACCCCTGATTTGTAAAATTACTAAA
ATACACTTGATGTA
Found at i:18459958 original size:54 final size:54
Alignment explanation
Indices: 18459851--18459971 Score: 136
Period size: 54 Copynumber: 2.2 Consensus size: 54
18459841 ACCCTCGATT
* * * *
18459851 TGTAAAATTACTGAAACACCCCTGATTTGTAAAATTATCGAAATACCCTTGTAG
1 TGTAAAATTACTGAAACACCCCTGATGTGTAAAATGACCGAAATACCCCTGTAG
* * * *
18459905 TGTAAAATTACTTAAATACCCTTG-TAGTGTAAAATGACCGACATACCCCTGTAG
1 TGTAAAATTACTGAAACACCCCTGAT-GTGTAAAATGACCGAAATACCCCTGTAG
* *
18459959 GGTAAAATAACTG
1 TGTAAAATTACTG
18459972 TTTTGCCCTT
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
53 1 0.02
54 54 0.98
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (54 bp):
TGTAAAATTACTGAAACACCCCTGATGTGTAAAATGACCGAAATACCCCTGTAG
Found at i:18461460 original size:30 final size:29
Alignment explanation
Indices: 18461417--18461480 Score: 119
Period size: 30 Copynumber: 2.2 Consensus size: 29
18461407 CAAGTAGCCG
18461417 AAGCTAGTTAAATCGCACACTTAGTGCCA
1 AAGCTAGTTAAATCGCACACTTAGTGCCA
18461446 AAGCTAGTTTAAATCGCACACTTAGTGCCA
1 AAGCTAG-TTAAATCGCACACTTAGTGCCA
18461476 AAGCT
1 AAGCT
18461481 TCTGATTCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 7 0.21
30 27 0.79
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.25
Consensus pattern (29 bp):
AAGCTAGTTAAATCGCACACTTAGTGCCA
Found at i:18476845 original size:46 final size:46
Alignment explanation
Indices: 18476792--18476967 Score: 149
Period size: 46 Copynumber: 3.8 Consensus size: 46
18476782 TATTTGGGCA
18476792 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * **** * * * *
18476838 TCCGAACTCGTTGAGTTGAGTCTGAGTTTGAGAGCTGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAG-TTCACTTATGGATGCGA-GCG
* * * * *
18476885 TCCGAGCTCATTGAGTTGAGTCTGAGTTCACTTATGGATGTGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * *
18476931 -CTCGAGCTCGTTGAGTTGAGTTCGAGTTTACTTATGG
1 TC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
18476968 GCGGGTTACA
Statistics
Matches: 99, Mismatches: 27, Indels: 8
0.74 0.20 0.06
Matches are distributed among these distances:
45 1 0.01
46 65 0.66
47 33 0.33
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.32
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:18476947 original size:93 final size:93
Alignment explanation
Indices: 18476788--18476959 Score: 258
Period size: 93 Copynumber: 1.8 Consensus size: 93
18476778 GGGATATTTG
* *
18476788 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
18476853 TTGAG-TCTGAGTTTGAGAGCTGTAACTA
66 TTGAGTTC-GAGTTTGAGAGCTGTAACTA
* * * *
18476881 GGCATCCGAGCTCATTGAGTTGAGTCTGAGTTCACTTATGGATGTGAACG-CTCGAGCTCGTTGA
1 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTC-CGAACTCGTTGA
18476945 GTTGAGTTCGAGTTT
65 GTTGAGTTCGAGTTT
18476960 ACTTATGGGC
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
92 1 0.01
93 68 0.96
94 2 0.03
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.31
Consensus pattern (93 bp):
GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
TTGAGTTCGAGTTTGAGAGCTGTAACTA
Found at i:18477669 original size:4 final size:4
Alignment explanation
Indices: 18477650--18477686 Score: 56
Period size: 4 Copynumber: 9.0 Consensus size: 4
18477640 GTTGTAAAGT
*
18477650 TTTA TTTT TATTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA
18477687 CTTAGTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 27 0.90
5 3 0.10
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:18484391 original size:20 final size:20
Alignment explanation
Indices: 18484368--18484414 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
18484358 GGGTTAAGAT
*
18484368 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
18484388 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
18484408 TGAGCTG
1 TGAGCTG
18484415 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:18486140 original size:48 final size:48
Alignment explanation
Indices: 18486085--18486190 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
18486075 TTGTCTTTTC
*
18486085 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
18486133 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
18486181 TTTCTTTTTC
1 TTTCTTTTTC
18486191 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:18487285 original size:11 final size:11
Alignment explanation
Indices: 18487271--18487295 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18487261 TTTTTTTCCT
18487271 TTTTTTTTGAA
1 TTTTTTTTGAA
18487282 TTTTTTTTGAA
1 TTTTTTTTGAA
18487293 TTT
1 TTT
18487296 CTTCTCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:18488831 original size:20 final size:20
Alignment explanation
Indices: 18488808--18488854 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
18488798 GGGTTAAGAT
*
18488808 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
18488828 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
18488848 TGAGCTG
1 TGAGCTG
18488855 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:18490635 original size:15 final size:15
Alignment explanation
Indices: 18490596--18490666 Score: 81
Period size: 15 Copynumber: 4.7 Consensus size: 15
18490586 GTATCTTGGG
*
18490596 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
18490611 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
18490626 TTTCTTTATTCCGGG
1 TTTCTTTATTCTGGA
*
18490641 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
18490656 TTTCTTTATTC
1 TTTCTTTATTC
18490667 GGTTTTTCTT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
14 2 0.04
15 41 0.91
16 2 0.04
ACGTcount: A:0.11, C:0.20, G:0.13, T:0.56
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:18490665 original size:30 final size:31
Alignment explanation
Indices: 18490587--18490666 Score: 94
Period size: 30 Copynumber: 2.6 Consensus size: 31
18490577 CATAGTATCG
* *
18490587 TATCTTGGGTTTCTTTA-TCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCCTGGATCTCTC
* *
18490617 TAT-TCTGGATTTCTTTATTCC-GGGTTTCTC
1 TATCT-TGGATTTCTTTATTCCTGGATCTCTC
18490647 TATCTTGGATTTCTTTATTC
1 TATCTTGGATTTCTTTATTC
18490667 GGTTTTTCTT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
29 1 0.02
30 38 0.88
31 4 0.09
ACGTcount: A:0.11, C:0.19, G:0.15, T:0.55
Consensus pattern (31 bp):
TATCTTGGATTTCTTTATTCCTGGATCTCTC
Found at i:18495042 original size:20 final size:20
Alignment explanation
Indices: 18495019--18495065 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
18495009 GGGTTAAGAT
*
18495019 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
18495039 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
18495059 TGAGCTG
1 TGAGCTG
18495066 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:18496795 original size:47 final size:45
Alignment explanation
Indices: 18496719--18496820 Score: 120
Period size: 47 Copynumber: 2.2 Consensus size: 45
18496709 TTGTCTTTTC
*
18496719 TTTCTTTTTCAATTTTCTCTTTTTCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTTCTCTTTTTCTCACATCCTTT-TTC-AT-TCAA
*
18496766 TTTCTTTTTCGATTCTT-TCTCTTTT-TCACATCCTTTTTCATTCAA
1 TTTCTTTTTCAATT-TTCTCT-TTTTCTCACATCCTTTTTCATTCAA
18496811 TTTCTTTTTC
1 TTTCTTTTTC
18496821 CATGACACTC
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
45 14 0.28
46 2 0.04
47 24 0.48
48 10 0.20
ACGTcount: A:0.14, C:0.24, G:0.02, T:0.61
Consensus pattern (45 bp):
TTTCTTTTTCAATTTTCTCTTTTTCTCACATCCTTTTTCATTCAA
Found at i:18501365 original size:23 final size:22
Alignment explanation
Indices: 18501339--18501390 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
18501329 GGAAAATTGA
*
18501339 AAAAGAAGTT-GAAGAAAGAAGAG
1 AAAAGAAGTTAGAA-AAAGAA-AC
18501362 AAAATG-AGTTAGAAAAAGAAAC
1 AAAA-GAAGTTAGAAAAAGAAAC
18501384 AAAAGAA
1 AAAAGAA
18501391 AAAGACGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 1 0.04
22 6 0.24
23 14 0.56
24 4 0.16
ACGTcount: A:0.65, C:0.02, G:0.23, T:0.10
Consensus pattern (22 bp):
AAAAGAAGTTAGAAAAAGAAAC
Found at i:18502764 original size:12 final size:13
Alignment explanation
Indices: 18502742--18502770 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
18502732 AAGTTTTATT
18502742 TTTATTTTATTTA
1 TTTATTTTATTTA
18502755 TTTA-TTTATTTA
1 TTTATTTTATTTA
18502767 TTTA
1 TTTA
18502771 CTTAGTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:18504644 original size:29 final size:29
Alignment explanation
Indices: 18504611--18504670 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
18504601 ATAACCAAAC
*
18504611 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
* *
18504640 CTACATAAACTTCATATCCATAAACCTAT
1 CTACAAAAACTTCATATCCATAAACCCAT
18504669 CT
1 CT
18504671 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:18504663 original size:15 final size:15
Alignment explanation
Indices: 18504617--18504664 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
18504607 AAACCTACAA
*
18504617 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
18504632 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
18504646 AAACTTCATATCCAT
1 AAACTTCATATCCAT
18504661 AAAC
1 AAAC
18504665 CTATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:18508292 original size:10 final size:10
Alignment explanation
Indices: 18508276--18508333 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
18508266 CAACTCCGAC
18508276 CAGCTCAATT
1 CAGCTCAATT
* *
18508286 GAGCTCATTT
1 CAGCTCAATT
18508296 CAGCTCAA-T
1 CAGCTCAATT
18508305 CGAGCTCAATT
1 C-AGCTCAATT
*
18508316 TAGCTACAATT
1 CAGCT-CAATT
18508327 CAGCTCA
1 CAGCTCA
18508334 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:18508299 original size:20 final size:20
Alignment explanation
Indices: 18508276--18508336 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
18508266 CAACTCCGAC
18508276 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
18508296 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
18508317 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
18508337 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:18509712 original size:10 final size:11
Alignment explanation
Indices: 18509690--18509725 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
18509680 AAAAGAGAAG
18509690 AAATTCAAAAA
1 AAATTCAAAAA
18509701 AAATTCAAAAA
1 AAATTCAAAAA
18509712 AAA-TCGAAAAA
1 AAATTC-AAAAA
18509723 AAA
1 AAA
18509726 GAAGTGACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 2 0.08
11 22 0.92
ACGTcount: A:0.75, C:0.08, G:0.03, T:0.14
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:18510795 original size:30 final size:30
Alignment explanation
Indices: 18510752--18510896 Score: 88
Period size: 30 Copynumber: 4.9 Consensus size: 30
18510742 CATTGAGCGA
* *
18510752 GAAAAGGAGAAAGAGATTGAAAAAGAAATT
1 GAAAAAGAAAAAGAGATTGAAAAAGAAATT
* * * ** **
18510782 GCAAAAGAAAAAGA-AATCAAAATAGTGAGA
1 GAAAAAGAAAAAGAGATTGAAAA-AGAAATT
*
18510812 GAAAAAGAAAATGA-A--G-AAAAGAAAATT
1 GAAAAAGAAAAAGAGATTGAAAAAG-AAATT
**
18510839 GAAAAAGAAATTGAGATTGAGAAAA-AAATT
1 GAAAAAGAAAAAGAGATTGA-AAAAGAAATT
*
18510869 GAAAAAGAAAAAGATG-TTGAAGAAGAAA
1 GAAAAAGAAAAAGA-GATTGAAAAAGAAA
18510897 CGAGAGAAAA
Statistics
Matches: 86, Mismatches: 20, Indels: 18
0.69 0.16 0.15
Matches are distributed among these distances:
26 2 0.02
27 17 0.20
28 1 0.01
29 9 0.10
30 52 0.60
31 1 0.01
32 4 0.05
ACGTcount: A:0.63, C:0.01, G:0.22, T:0.13
Consensus pattern (30 bp):
GAAAAAGAAAAAGAGATTGAAAAAGAAATT
Found at i:18510857 original size:18 final size:18
Alignment explanation
Indices: 18510836--18510870 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
18510826 AGAAAAGAAA
18510836 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
18510854 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
18510871 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:18512961 original size:20 final size:20
Alignment explanation
Indices: 18512933--18512993 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
18512923 CAACTCCGAC
*
18512933 CAGCCCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
18512953 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
18512974 -AGCTACAATTTAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
18512994 ATTTTATTGG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 22 0.63
21 13 0.37
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:18512984 original size:11 final size:10
Alignment explanation
Indices: 18512938--18512994 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
18512928 CCGACCAGCC
*
18512938 CAATTGAGCT
1 CAATTTAGCT
18512948 C-ATTTCAGCT
1 CAATTT-AGCT
**
18512958 CAATCGAGCT
1 CAATTTAGCT
18512968 CAATTTAGCT
1 CAATTTAGCT
18512978 ACAATTTAGCT
1 -CAATTTAGCT
18512989 C-ATTTA
1 CAATTTA
18512995 TTTTATTGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
9 8 0.21
10 19 0.49
11 12 0.31
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (10 bp):
CAATTTAGCT
Found at i:18516266 original size:6 final size:6
Alignment explanation
Indices: 18516255--18516295 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
18516245 AATTTTTTTC
* * *
18516255 TCAATA TCAATA TCAATA TCAATC TCAATC TCAATC TCAAT
1 TCAATA TCAATA TCAATA TCAATA TCAATA TCAATA TCAAT
18516296 TTTTTTTTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.34
Consensus pattern (6 bp):
TCAATA
Found at i:18516270 original size:12 final size:12
Alignment explanation
Indices: 18516253--18516295 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
18516243 TCAATTTTTT
18516253 TCTCAATATCAA
1 TCTCAATATCAA
*
18516265 TATCAATATCAA
1 TCTCAATATCAA
*
18516277 TCTCAATCTCAA
1 TCTCAATATCAA
18516289 TCTCAAT
1 TCTCAAT
18516296 TTTTTTTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.35
Consensus pattern (12 bp):
TCTCAATATCAA
Found at i:18516313 original size:26 final size:27
Alignment explanation
Indices: 18516283--18516348 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 27
18516273 TCAATCTCAA
18516283 TCTCAATCTCAATTTT-TTTTTCTT-TT-
1 TCTCAATCTC-ATTTTCTTTTT-TTCTTC
*
18516309 TCTCACTCTCATTTTCTTTTTTTCTTC
1 TCTCAATCTCATTTTCTTTTTTTCTTC
*
18516336 TCTCAATTTCATT
1 TCTCAATCTCATT
18516349 CAAGATTCGT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 7 0.21
26 16 0.47
27 11 0.32
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.62
Consensus pattern (27 bp):
TCTCAATCTCATTTTCTTTTTTTCTTC
Found at i:18516345 original size:21 final size:20
Alignment explanation
Indices: 18516301--18516345 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
18516291 TCAATTTTTT
*
18516301 TTTCTTTTTCTCACTCTCAT
1 TTTCTTTTTCTCACTCTCAA
* *
18516321 TTTCTTTTTTTCTTCTCTCAA
1 TTTCTTTTTCTC-ACTCTCAA
18516342 TTTC
1 TTTC
18516346 ATTCAAGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.09, C:0.27, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCTTTTTCTCACTCTCAA
Found at i:18517186 original size:30 final size:31
Alignment explanation
Indices: 18517152--18517230 Score: 88
Period size: 32 Copynumber: 2.5 Consensus size: 31
18517142 TCAATCACTC
** *
18517152 TTTCTTTTTTTTTTTCAATTTTG-ATTTTTT
1 TTTCTTTTTTTTTTTCAATTCCGAAATTTTT
*
18517182 TTTCTTCTTTTTTTTTTTAATTCCGAAATTTTT
1 TTTC-T-TTTTTTTTTTCAATTCCGAAATTTTT
*
18517215 TTTCTTCTTTTTTTTC
1 TTTCTTTTTTTTTTTC
18517231 TTCAATACTA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
30 4 0.10
31 10 0.25
32 16 0.40
33 10 0.25
ACGTcount: A:0.10, C:0.11, G:0.03, T:0.76
Consensus pattern (31 bp):
TTTCTTTTTTTTTTTCAATTCCGAAATTTTT
Found at i:18517195 original size:33 final size:34
Alignment explanation
Indices: 18517153--18517236 Score: 118
Period size: 33 Copynumber: 2.5 Consensus size: 34
18517143 CAATCACTCT
** *
18517153 TTCTTTTTTTTTTTCAATTTTG-ATTTTTTTTTC
1 TTCTTTTTTTTTTTCAATTCCGAAATTTTTTTTC
18517186 TTCTTTTTTTTTTT-AATTCCGAAATTTTTTTTC
1 TTCTTTTTTTTTTTCAATTCCGAAATTTTTTTTC
*
18517219 TTCTTTTTTTTCTTCAAT
1 TTCTTTTTTTTTTTCAAT
18517237 ACTAAATACA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
32 5 0.11
33 37 0.82
34 3 0.07
ACGTcount: A:0.12, C:0.12, G:0.02, T:0.74
Consensus pattern (34 bp):
TTCTTTTTTTTTTTCAATTCCGAAATTTTTTTTC
Found at i:18517292 original size:13 final size:13
Alignment explanation
Indices: 18517274--18517318 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
18517264 GAATACAAAC
18517274 TTTTTTTTT-GAA
1 TTTTTTTTTCGAA
*
18517286 TTTTTTTTTCAAA
1 TTTTTTTTTCGAA
18517299 TTTTTTTTTCGAA
1 TTTTTTTTTCGAA
18517312 TTTTTTT
1 TTTTTTT
18517319 ATATTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 9 0.30
13 21 0.70
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:18517298 original size:26 final size:26
Alignment explanation
Indices: 18517269--18517318 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
18517259 AAATTGAATA
18517269 CAAACTTTTTTTTT-GAATTTTTTTTT
1 CAAA-TTTTTTTTTCGAATTTTTTTTT
18517295 CAAATTTTTTTTTCGAATTTTTTT
1 CAAATTTTTTTTTCGAATTTTTTT
18517319 ATATTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.20, C:0.08, G:0.04, T:0.68
Consensus pattern (26 bp):
CAAATTTTTTTTTCGAATTTTTTTTT
Found at i:18523862 original size:15 final size:15
Alignment explanation
Indices: 18523842--18523888 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 15
18523832 TCAAAGATGG
18523842 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
18523857 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
18523871 GTTTATGGATAT-AA
1 GTTTATGGATATGAA
18523885 GTTT
1 GTTT
18523889 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:18523876 original size:14 final size:14
Alignment explanation
Indices: 18523836--18523879 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
18523826 AAGGATTCAA
18523836 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
18523850 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
18523865 AGATGGGTTTATGG
1 AGATGGGTTTATGG
18523879 A
1 A
18523880 TATAAGTTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:18523904 original size:28 final size:29
Alignment explanation
Indices: 18523836--18523894 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
18523826 AAGGATTCAA
18523836 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATGAAGTTTATGT
*
18523865 AGATGGGTTTATGGATAT-AAGTTTTTGT
1 AGATGGGTTTATGGATATGAAGTTTATGT
18523893 AG
1 AG
18523895 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 11 0.38
29 18 0.62
ACGTcount: A:0.27, C:0.00, G:0.31, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATGAAGTTTATGT
Found at i:18524520 original size:20 final size:20
Alignment explanation
Indices: 18524474--18524520 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
18524464 AGCTCGTTTC
*
18524474 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
18524494 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
18524514 CAGCTCA
1 CAGCTCA
18524521 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:18526040 original size:29 final size:28
Alignment explanation
Indices: 18525981--18526040 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
18525971 ATTGTAATTG
* **
18525981 AAAAAAAAATCAAAAAAAAATTGATTGAA
1 AAAAAAAAATCAAAAAAAAAGTGA-AAAA
*
18526010 AAAAAAAATTCAAAAAAAAAGTGAAAAA
1 AAAAAAAAATCAAAAAAAAAGTGAAAAA
18526038 AAA
1 AAA
18526041 TCGAGCAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.77, C:0.03, G:0.07, T:0.13
Consensus pattern (28 bp):
AAAAAAAAATCAAAAAAAAAGTGAAAAA
Found at i:18526050 original size:25 final size:25
Alignment explanation
Indices: 18526020--18526081 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 25
18526010 AAAAAAAATT
*
18526020 CAAAAAAAAAGTGAAAAAAAA-TCGAG
1 CAAAAAAAAA-AGAAAAAAAAGT-GAG
18526046 CAAAAAAAAAAGAAAAAAAAGGTGAG
1 CAAAAAAAAAAGAAAAAAAA-GTGAG
18526072 CAAAAAAAAA
1 CAAAAAAAAA
18526082 TTAAGTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
25 9 0.27
26 23 0.70
27 1 0.03
ACGTcount: A:0.74, C:0.06, G:0.15, T:0.05
Consensus pattern (25 bp):
CAAAAAAAAAAGAAAAAAAAGTGAG
Found at i:18527153 original size:18 final size:18
Alignment explanation
Indices: 18527127--18527227 Score: 76
Period size: 18 Copynumber: 5.4 Consensus size: 18
18527117 AAATTGAAAG
*
18527127 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
18527145 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
*
18527163 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAAACGA
** * *
18527181 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
18527199 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
18527220 AAAAGAAA
1 AAAAGAAA
18527228 GAAAAGACAA
Statistics
Matches: 63, Mismatches: 17, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
18 47 0.75
19 2 0.03
20 8 0.13
21 6 0.10
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:18527155 original size:6 final size:6
Alignment explanation
Indices: 18527123--18527227 Score: 68
Period size: 6 Copynumber: 17.2 Consensus size: 6
18527113 ATTGAAATTG
* * ** *
18527123 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
18527170 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
18527221 AAAGAA A
1 AAAGAA A
18527228 GAAAAGACAA
Statistics
Matches: 72, Mismatches: 24, Indels: 7
0.70 0.23 0.07
Matches are distributed among these distances:
5 3 0.04
6 58 0.81
7 7 0.10
8 4 0.06
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:18528943 original size:20 final size:20
Alignment explanation
Indices: 18528897--18528943 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
18528887 AGCTCGTTTC
*
18528897 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
18528917 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
18528937 CAGCTCA
1 CAGCTCA
18528944 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:18531520 original size:21 final size:20
Alignment explanation
Indices: 18531496--18531541 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
18531486 TATACAAGTT
18531496 AAAAAAATCAAAAAAATTCAA
1 AAAAAAATCAAAAAAA-TCAA
* *
18531517 AAAAAAATTAAAAAAATCGA
1 AAAAAAATCAAAAAAATCAA
18531537 AAAAA
1 AAAAA
18531542 GTGATTTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.78, C:0.07, G:0.02, T:0.13
Consensus pattern (20 bp):
AAAAAAATCAAAAAAATCAA
Found at i:18537051 original size:11 final size:12
Alignment explanation
Indices: 18537035--18537067 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
18537025 AGGAAATTTG
18537035 AAAAAAAATTCA
1 AAAAAAAATTCA
18537047 AAAAAAAATTCA
1 AAAAAAAATTCA
18537059 AAAAAAAAT
1 AAAAAAAAT
18537068 CGAAGTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:18540157 original size:17 final size:17
Alignment explanation
Indices: 18540127--18540161 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
18540117 TGCTGGAATA
*
18540127 AATTAATTATTTTAGTT
1 AATTAATTAATTTAGTT
*
18540144 AATTAGTTAATTTAGTT
1 AATTAATTAATTTAGTT
18540161 A
1 A
18540162 CAGCTCTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (17 bp):
AATTAATTAATTTAGTT
Found at i:18543143 original size:17 final size:17
Alignment explanation
Indices: 18543118--18543171 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
18543108 TCTCTTTTCA
*
18543118 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* *
18543135 TTCTTTTTTTTTCATTT
1 TTCTTTTTTTTTGAATT
* *
18543152 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
18543169 TTC
1 TTC
18543172 ACTCTTTTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.07, C:0.13, G:0.04, T:0.76
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:18546205 original size:23 final size:22
Alignment explanation
Indices: 18546154--18546205 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
18546144 CCTCGTCTTT
*
18546154 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
18546176 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
18546199 TTCTTTT
1 TTCTTTT
18546206 TCAATTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:18546214 original size:12 final size:12
Alignment explanation
Indices: 18546163--18546218 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
18546153 TTTCTTTTGT
18546163 TTCTTTTTCTAAC
1 TTCTTTTTC-AAC
* *
18546176 -TCATTTTC-TC
1 TTCTTTTTCAAC
18546186 TTCTTTCTTCAAC
1 TTCTTT-TTCAAC
*
18546199 TTCTTTTTCAAT
1 TTCTTTTTCAAC
18546211 TTCTTTTT
1 TTCTTTTT
18546219 GTTTCACATT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 1 0.03
11 4 0.11
12 23 0.66
13 7 0.20
ACGTcount: A:0.12, C:0.23, G:0.00, T:0.64
Consensus pattern (12 bp):
TTCTTTTTCAAC
Found at i:18547952 original size:34 final size:34
Alignment explanation
Indices: 18547914--18547978 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
18547904 AAATTGAGAA
18547914 TAGAAATAAGTGTTAATAAGGAATCTTGAAACCC
1 TAGAAATAAGTGTTAATAAGGAATCTTGAAACCC
18547948 TAGAAATAAGTGTTAATAAGGAATCTTGAAA
1 TAGAAATAAGTGTTAATAAGGAATCTTGAAA
18547979 TAAAATCCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.28
Consensus pattern (34 bp):
TAGAAATAAGTGTTAATAAGGAATCTTGAAACCC
Found at i:18548046 original size:35 final size:35
Alignment explanation
Indices: 18547899--18548069 Score: 157
Period size: 35 Copynumber: 5.0 Consensus size: 35
18547889 AATCAGCAAA
18547899 GAATCAAATTGAGAATAGAAATAAGTGTTAATAAG
1 GAATCAAATTGAGAATAGAAATAAGTGTTAATAAG
18547934 GAATC---TTGA-AACCCTAGAAATAAGTGTTAATAAG
1 GAATCAAATTGAGAA---TAGAAATAAGTGTTAATAAG
* * ** *
18547968 GAATC---TTGA-AATA-AAATCCCCAA--ATCAGCAAA
1 GAATCAAATTGAGAATAGAAAT----AAGTGTTAATAAG
18548000 GAATCAAATTGAGAATAGAAATAAGTGTTAATAAG
1 GAATCAAATTGAGAATAGAAATAAGTGTTAATAAG
18548035 GAATCAAATTGAGAATAGAAATAAGTGTTAATAAG
1 GAATCAAATTGAGAATAGAAATAAGTGTTAATAAG
18548070 TGTTAATAAG
Statistics
Matches: 112, Mismatches: 10, Indels: 28
0.75 0.07 0.19
Matches are distributed among these distances:
30 4 0.04
31 4 0.04
32 13 0.12
33 2 0.02
34 33 0.29
35 48 0.43
36 4 0.04
37 4 0.04
ACGTcount: A:0.50, C:0.08, G:0.18, T:0.25
Consensus pattern (35 bp):
GAATCAAATTGAGAATAGAAATAAGTGTTAATAAG
Found at i:18548069 original size:10 final size:10
Alignment explanation
Indices: 18548054--18548079 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
18548044 TGAGAATAGA
18548054 AATAAGTGTT
1 AATAAGTGTT
18548064 AATAAGTGTT
1 AATAAGTGTT
18548074 AATAAG
1 AATAAG
18548080 GAGTGTTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.19, T:0.35
Consensus pattern (10 bp):
AATAAGTGTT
Found at i:18553740 original size:21 final size:21
Alignment explanation
Indices: 18553714--18553776 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
18553704 TTGGTATTTG
18553714 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
18553735 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
18553756 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
18553777 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:18556400 original size:33 final size:33
Alignment explanation
Indices: 18556363--18556428 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
18556353 AGTTTAACTT
*
18556363 ACAATTGTTTCATATTTCCCCTGTGCTGTTGTC
1 ACAATTGTTTCATATTCCCCCTGTGCTGTTGTC
*
18556396 ACAATTGTTTCATATTCCCCCTGTGTTGTTGTC
1 ACAATTGTTTCATATTCCCCCTGTGCTGTTGTC
18556429 TATCAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.15, C:0.24, G:0.15, T:0.45
Consensus pattern (33 bp):
ACAATTGTTTCATATTCCCCCTGTGCTGTTGTC
Found at i:18572104 original size:30 final size:30
Alignment explanation
Indices: 18572070--18572166 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
18572060 TAAACTAAAA
18572070 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
18572100 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
18572130 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
18572159 ATGAGCTA
1 -TGAGCTA
18572167 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:18572437 original size:10 final size:9
Alignment explanation
Indices: 18572391--18572450 Score: 50
Period size: 9 Copynumber: 6.2 Consensus size: 9
18572381 AATTAAATTA
18572391 AATGAGCTG
1 AATGAGCTG
*
18572400 AGTGAGCT-
1 AATGAGCTG
*
18572408 AATAACGAGCTT
1 AAT---GAGCTG
18572420 AATGAGCTG
1 AATGAGCTG
18572429 AATTGAGCTCG
1 AA-TGAGCT-G
18572440 AATGAGCTG
1 AATGAGCTG
18572449 AA
1 AA
18572451 CCAAAAATGT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
8 2 0.05
9 17 0.40
10 12 0.29
11 8 0.19
12 3 0.07
ACGTcount: A:0.35, C:0.13, G:0.28, T:0.23
Consensus pattern (9 bp):
AATGAGCTG
Found at i:18574680 original size:17 final size:17
Alignment explanation
Indices: 18574660--18574770 Score: 50
Period size: 18 Copynumber: 6.4 Consensus size: 17
18574650 TTTTTTTTCC
18574660 TCTTTTTCTTTTCAATT
1 TCTTTTTCTTTTCAATT
* **
18574677 TCTTTCTTCATTTCTTTT
1 TCTTT-TTCTTTTCAATT
* ** *
18574695 TCTCTCACTTTTTCGA-T
1 TCTTTTTC-TTTTCAATT
18574712 TC-TTTTCTTTTGCAA-T
1 TCTTTTTCTTTT-CAATT
*
18574728 TCTTTTTCTTTTTC-GTT
1 TCTTTTTC-TTTTCAATT
*
18574745 TCTTTTTGTTTTTTTCAATT
1 TC--TTT-TTCTTTTCAATT
18574765 TCTTTT
1 TCTTTT
18574771 CAATCTCTTT
Statistics
Matches: 68, Mismatches: 16, Indels: 20
0.65 0.15 0.19
Matches are distributed among these distances:
15 4 0.06
16 7 0.10
17 19 0.28
18 24 0.35
19 8 0.12
20 6 0.09
ACGTcount: A:0.08, C:0.19, G:0.04, T:0.69
Consensus pattern (17 bp):
TCTTTTTCTTTTCAATT
Found at i:18574750 original size:16 final size:16
Alignment explanation
Indices: 18574702--18574750 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
18574692 TTTTCTCTCA
18574702 CTTTTTCGATTCTTTT
1 CTTTTTCGATTCTTTT
* *
18574718 CTTTTGCAATTCTTTTT
1 CTTTTTCGATTC-TTTT
*
18574735 CTTTTTCGTTTCTTTT
1 CTTTTTCGATTCTTTT
18574751 TGTTTTTTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 14 0.52
17 13 0.48
ACGTcount: A:0.06, C:0.18, G:0.06, T:0.69
Consensus pattern (16 bp):
CTTTTTCGATTCTTTT
Found at i:18575857 original size:40 final size:39
Alignment explanation
Indices: 18575771--18575884 Score: 108
Period size: 38 Copynumber: 2.9 Consensus size: 39
18575761 GACTTTTCAC
* *
18575771 TTTTTTTTTAAACTTGATTTTTTTGCTCACTTTTTTTTCT
1 TTTTTTTTTAAACTCGATTTTTTT-CTAACTTTTTTTTCT
***
18575811 TCTTTTTTTT-AACTCGATTTTTTT-TAACTTTTTTTGAA
1 T-TTTTTTTTAAACTCGATTTTTTTCTAACTTTTTTTTCT
* * * *
18575849 TTTTTTTTTCAA-TCAATTTTTTTCGAATTTTTTTTT
1 TTTTTTTTTAAACTCGATTTTTTTCTAACTTTTTTTT
18575885 TGATTTTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
37 18 0.29
38 22 0.35
40 14 0.23
41 8 0.13
ACGTcount: A:0.16, C:0.11, G:0.04, T:0.69
Consensus pattern (39 bp):
TTTTTTTTTAAACTCGATTTTTTTCTAACTTTTTTTTCT
Found at i:18578733 original size:11 final size:11
Alignment explanation
Indices: 18578719--18578773 Score: 58
Period size: 11 Copynumber: 4.7 Consensus size: 11
18578709 ATTTGAATTG
18578719 AAAAAAAATCAA
1 AAAAAAAAT-AA
*
18578731 AAAAAAAGTAA
1 AAAAAAAATAA
18578742 AAAAAAAATGAGA
1 AAAAAAAAT-A-A
18578755 AAAAAAAA-AGA
1 AAAAAAAATA-A
18578766 AAAAAAAA
1 AAAAAAAA
18578774 GTGAGCAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
11 21 0.54
12 9 0.23
13 9 0.23
ACGTcount: A:0.85, C:0.02, G:0.07, T:0.05
Consensus pattern (11 bp):
AAAAAAAATAA
Found at i:18578736 original size:12 final size:12
Alignment explanation
Indices: 18578719--18578788 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
18578709 ATTTGAATTG
*
18578719 AAAAAAAATCAA
1 AAAAAAAATGAA
*
18578731 AAAAAAAGT-AA
1 AAAAAAAATGAA
18578742 AAAAAAAATGAGA
1 AAAAAAAATGA-A
*
18578755 AAAAAAAAAGAA
1 AAAAAAAATGAA
* *
18578767 AAAAAAAGTGAGC
1 AAAAAAAATGA-A
18578780 AAAAAAAAT
1 AAAAAAAAT
18578789 CAAGTTAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
11 10 0.21
12 19 0.40
13 19 0.40
ACGTcount: A:0.80, C:0.03, G:0.10, T:0.07
Consensus pattern (12 bp):
AAAAAAAATGAA
Found at i:18578783 original size:26 final size:26
Alignment explanation
Indices: 18578729--18578804 Score: 100
Period size: 26 Copynumber: 2.8 Consensus size: 26
18578719 AAAAAAAATC
18578729 AAAAAAAAAGTAAAAAAAAAATGAGA
1 AAAAAAAAAGTAAAAAAAAAATGAGA
*
18578755 AAAAAAAAAG-AAAAAAAAAGTGAGCA
1 AAAAAAAAAGTAAAAAAAAAATGAG-A
18578781 AAAAAAATCAAGTTAAAAAAAAAA
1 AAAAAAA--AAG-TAAAAAAAAAA
18578805 GTGAAAGTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
25 13 0.30
26 18 0.42
28 3 0.07
30 9 0.21
ACGTcount: A:0.79, C:0.03, G:0.11, T:0.08
Consensus pattern (26 bp):
AAAAAAAAAGTAAAAAAAAAATGAGA
Found at i:18579812 original size:11 final size:12
Alignment explanation
Indices: 18579798--18579828 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
18579788 AAAGAAATTG
18579798 AAAGAAAAC-AA
1 AAAGAAAACGAA
18579809 AAAGAAAACGAA
1 AAAGAAAACGAA
18579821 AAAGAAAA
1 AAAGAAAA
18579829 AGTAAATTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (12 bp):
AAAGAAAACGAA
Found at i:18585426 original size:23 final size:23
Alignment explanation
Indices: 18585374--18585426 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
18585364 TTTTTCTCCC
18585374 TTTTTTTTATTCTTGTTTTCTGA
1 TTTTTTTTATTCTTGTTTTCTGA
* * *
18585397 TTATTTTTATTTTTTTTTTC-GA
1 TTTTTTTTATTCTTGTTTTCTGA
*
18585419 ATTTTTTT
1 TTTTTTTT
18585427 CTTATTAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.11, C:0.06, G:0.06, T:0.77
Consensus pattern (23 bp):
TTTTTTTTATTCTTGTTTTCTGA
Found at i:18589588 original size:33 final size:33
Alignment explanation
Indices: 18589550--18589612 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
18589540 GATTACTCAC
18589550 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
18589583 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
18589613 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:18589639 original size:21 final size:21
Alignment explanation
Indices: 18589610--18589665 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
18589600 CAAGCTCTCT
*
18589610 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
18589631 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
18589652 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
18589666 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:18589658 original size:14 final size:14
Alignment explanation
Indices: 18589609--18589665 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
18589599 TCAAGCTCTC
18589609 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
18589622 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
18589636 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
18589650 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
18589664 TT
1 TT
18589666 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:18589725 original size:18 final size:18
Alignment explanation
Indices: 18589627--18589730 Score: 84
Period size: 18 Copynumber: 5.6 Consensus size: 18
18589617 TCTTTTTTCG
18589627 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
* *
18589646 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
* **
18589666 CTCTCACTTTTTCGA-TTT
1 CTTTTTCTTTTTC-ATTTT
* *
18589684 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCATTTT
*
18589702 CTTTTTCTTTTTCGTTTT
1 CTTTTTCTTTTTCATTTT
*
18589720 CTTTTTGTTTT
1 CTTTTTCTTTT
18589731 CTTTCAATTT
Statistics
Matches: 66, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
17 1 0.02
18 46 0.70
19 3 0.05
20 8 0.12
21 8 0.12
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.71
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:18589747 original size:6 final size:6
Alignment explanation
Indices: 18589627--18589734 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
18589617 TCTTTTTTCG
* * * **
18589627 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
18589678 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
18589726 -GTTTT CTTT
1 CTTTTT CTTT
18589735 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 25, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
5 4 0.05
6 58 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:18590873 original size:10 final size:12
Alignment explanation
Indices: 18590810--18590877 Score: 54
Period size: 11 Copynumber: 5.7 Consensus size: 12
18590800 TTTTAACTCG
18590810 ATTTTTTTTC-A
1 ATTTTTTTTCGA
*
18590821 CTTTTTTTT-GA
1 ATTTTTTTTCGA
*
18590832 ATTTTTTTTCAATCA
1 ATTTTTTTTC---GA
18590847 ATTTTTTTTTCGA
1 A-TTTTTTTTCGA
18590860 ATTTTTTTT-G-
1 ATTTTTTTTCGA
18590870 ATTTTTTT
1 ATTTTTTT
18590878 GTTACTCCAA
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
10 8 0.17
11 18 0.38
12 8 0.17
13 2 0.04
15 2 0.04
16 9 0.19
ACGTcount: A:0.16, C:0.07, G:0.04, T:0.72
Consensus pattern (12 bp):
ATTTTTTTTCGA
Found at i:18593784 original size:29 final size:28
Alignment explanation
Indices: 18593739--18593798 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
18593729 AAAAAAATTC
*
18593739 AAAAAAAAGTAAAAAAA-ATAGAGCAAAA
1 AAAAAAAAGAAAAAAAAGAT-GAGCAAAA
*
18593767 AAAAGAAAAGAAAAAAAAGGTGAGCAAAA
1 AAAA-AAAAGAAAAAAAAGATGAGCAAAA
18593796 AAA
1 AAA
18593799 TCAAGTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 4 0.14
29 23 0.82
30 1 0.04
ACGTcount: A:0.77, C:0.03, G:0.15, T:0.05
Consensus pattern (28 bp):
AAAAAAAAGAAAAAAAAGATGAGCAAAA
Found at i:18594861 original size:6 final size:6
Alignment explanation
Indices: 18594829--18594906 Score: 61
Period size: 6 Copynumber: 13.3 Consensus size: 6
18594819 AAAGAAATTG
* * ** *
18594829 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** *
18594876 AAAG-A AATGAA AAAGTG AGAGAA AAAGAA AA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AA
18594907 TGAAGAAAAG
Statistics
Matches: 53, Mismatches: 18, Indels: 3
0.72 0.24 0.04
Matches are distributed among these distances:
5 7 0.13
6 46 0.87
ACGTcount: A:0.73, C:0.04, G:0.18, T:0.05
Consensus pattern (6 bp):
AAAGAA
Found at i:18594962 original size:33 final size:33
Alignment explanation
Indices: 18594922--18594984 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
18594912 AAAAGAAATT
18594922 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
18594955 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
18594985 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:18596793 original size:20 final size:20
Alignment explanation
Indices: 18596768--18596813 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
18596758 CCCAGCTCGA
*
18596768 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
18596788 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
18596808 TTAGCT
1 TTAGCT
18596814 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:18596804 original size:30 final size:30
Alignment explanation
Indices: 18596761--18596833 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
18596751 AGTTTTTCCC
*
18596761 AGCTCGATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCGTTTGAGCTCA-ATTGAGCTTAATTT
* *
18596790 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
18596820 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
18596834 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 9 0.23
30 30 0.77
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:18602626 original size:16 final size:16
Alignment explanation
Indices: 18602605--18602635 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18602595 CGTAGCTTCG
*
18602605 AAAAAAAAATTTGCAA
1 AAAAAAAAAATTGCAA
18602621 AAAAAAAAAATTGCA
1 AAAAAAAAAATTGCA
18602636 TACGGTCTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.16
Consensus pattern (16 bp):
AAAAAAAAAATTGCAA
Found at i:18604913 original size:24 final size:25
Alignment explanation
Indices: 18604886--18604939 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
18604876 ATGAGTGATA
*
18604886 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
18604910 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
18604934 AAAAAA
1 AAAAAA
18604940 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:18612650 original size:56 final size:55
Alignment explanation
Indices: 18612534--18612651 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
18612524 TGCATGCTTT
* * * *
18612534 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
18612588 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
18612644 CATTAAAT
1 CATTAAAT
18612652 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:18613669 original size:20 final size:20
Alignment explanation
Indices: 18613644--18613698 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
18613634 ACGAGTTAAA
*
18613644 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTTGAATGAGCTAAC
*
18613664 TTGAGCATGAATGAGCTAAC
1 TTGAGCTTGAATGAGCTAAC
*
18613684 TTGAGCTCGAATGAG
1 TTGAGCTTGAATGAG
18613699 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (20 bp):
TTGAGCTTGAATGAGCTAAC
Found at i:18614968 original size:20 final size:20
Alignment explanation
Indices: 18614943--18614997 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
18614933 ACGAGTTAAA
* *
18614943 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
18614963 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
18614983 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
18614998 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:18616656 original size:12 final size:13
Alignment explanation
Indices: 18616630--18616674 Score: 58
Period size: 12 Copynumber: 3.6 Consensus size: 13
18616620 TCAGATTTTG
* *
18616630 TTTTTTTTCCAAA
1 TTTTTTTTTCGAA
18616643 TTTTTTTTT-GAA
1 TTTTTTTTTCGAA
18616655 TTTTTTTTTCG-A
1 TTTTTTTTTCGAA
18616667 TTTTTTTT
1 TTTTTTTT
18616675 GAAACTTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 20 0.69
13 9 0.31
ACGTcount: A:0.13, C:0.07, G:0.04, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:18618470 original size:14 final size:14
Alignment explanation
Indices: 18618450--18618479 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
18618440 CGTAGCTTCG
18618450 AAAAAAAAAATTTGC
1 AAAAAAAAAA-TTGC
18618465 AAAAAAAAAATTGC
1 AAAAAAAAAATTGC
18618479 A
1 A
18618480 TACGGTCTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.17
Consensus pattern (14 bp):
AAAAAAAAAATTGC
Found at i:18620760 original size:24 final size:25
Alignment explanation
Indices: 18620733--18620786 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
18620723 ATGAGTGATA
*
18620733 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
18620757 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
18620781 AAAAAA
1 AAAAAA
18620787 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:18626091 original size:14 final size:14
Alignment explanation
Indices: 18626049--18626093 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
18626039 TTAAAGAAGC
18626049 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
18626063 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
18626076 AACTCATTTAATTA
1 AACTCATTAAATTA
18626090 AACT
1 AACT
18626094 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:18626886 original size:15 final size:15
Alignment explanation
Indices: 18626854--18626900 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
18626844 TCCTATTTTT
18626854 TTTTTCTTGTTCT-TC
1 TTTTTCTT-TTCTCTC
*
18626869 TTTTTCTTTTCTCAC
1 TTTTTCTTTTCTCTC
18626884 -TTTT-TTTTCTCTC
1 TTTTTCTTTTCTCTC
18626897 TTTT
1 TTTT
18626901 GCTATTTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 8 0.29
14 11 0.39
15 9 0.32
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.74
Consensus pattern (15 bp):
TTTTTCTTTTCTCTC
Found at i:18626938 original size:18 final size:18
Alignment explanation
Indices: 18626869--18626939 Score: 65
Period size: 18 Copynumber: 3.7 Consensus size: 18
18626859 CTTGTTCTTC
18626869 TTTTTC-TTTTCTCACTTT
1 TTTTTCTTTTTCTCA-TTT
18626887 TTTTTCTCTCTTT-TGCTATTT
1 TTTTTCT-T-TTTCT-C-ATTT
18626908 TTGTGTTCTTTTTCTCATTT
1 TT-T-TTCTTTTTCTCATTT
18626928 TTTTTCTTTTTC
1 TTTTTCTTTTTC
18626940 ATTTCCTTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
18 15 0.33
19 1 0.02
20 8 0.18
21 13 0.29
22 4 0.09
23 4 0.09
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.73
Consensus pattern (18 bp):
TTTTTCTTTTTCTCATTT
Found at i:18639818 original size:12 final size:13
Alignment explanation
Indices: 18639801--18639832 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
18639791 TTGTAGATTC
18639801 AAAAAAATCGA-A
1 AAAAAAATCGAGA
18639813 AAAAAAATCGAGA
1 AAAAAAATCGAGA
18639826 AAAAAAA
1 AAAAAAA
18639833 AATTTGCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.78, C:0.06, G:0.09, T:0.06
Consensus pattern (13 bp):
AAAAAAATCGAGA
Found at i:18640222 original size:20 final size:20
Alignment explanation
Indices: 18640199--18640244 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
18640189 CCAGCTCGAA
*
18640199 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
18640219 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
18640239 TTAGCT
1 TTAGCT
18640245 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Done.