Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 132 of 168
Found at i:38525090 original size:9 final size:9
Alignment explanation
Indices: 38525064--38525107 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
38525054 ATTTTACTTT
38525064 AAAATTTT-
1 AAAATTTTA
*
38525072 AAAATATTA
1 AAAATTTTA
38525081 AAAATTTTAA
1 AAAATTTT-A
*
38525091 AAAATTTAA
1 AAAATTTTA
38525100 AAAATTTT
1 AAAATTTT
38525108 TCCATTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
8 7 0.23
9 15 0.50
10 8 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
AAAATTTTA
Found at i:38528698 original size:49 final size:49
Alignment explanation
Indices: 38528645--38528801 Score: 296
Period size: 49 Copynumber: 3.2 Consensus size: 49
38528635 GACATGAATG
* *
38528645 ATATTTTTAAATGAATTGGTTGAATCTAGAGCATGTTTTGATTGTGTTC
1 ATATTTTTAAATGAACTGGTTGAATTTAGAGCATGTTTTGATTGTGTTC
38528694 ATATTTTTAAATGAACTGGTTGAATTTAGAGCATGTTTTGATTGTGTTC
1 ATATTTTTAAATGAACTGGTTGAATTTAGAGCATGTTTTGATTGTGTTC
38528743 ATATTTTTAAATGAACTGGTTGAATTTAGAGCATGTTTTGATTGTGTTC
1 ATATTTTTAAATGAACTGGTTGAATTTAGAGCATGTTTTGATTGTGTTC
38528792 ATATTTTTAA
1 ATATTTTTAA
38528802 TGTTATTGTT
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 106 1.00
ACGTcount: A:0.27, C:0.06, G:0.19, T:0.48
Consensus pattern (49 bp):
ATATTTTTAAATGAACTGGTTGAATTTAGAGCATGTTTTGATTGTGTTC
Found at i:38533159 original size:35 final size:33
Alignment explanation
Indices: 38533103--38533177 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 33
38533093 TATTTTTAAA
*
38533103 AAAATTTAAAATATATTTATATTATTT-TTTAATT
1 AAAATTTAAAATATATATATATT-TTTATTT-ATT
*
38533137 CAAAATTTAATAATTTA-ATATATTTTTATTTATT
1 -AAAATTTAA-AATATATATATATTTTTATTTATT
38533171 AAAATTT
1 AAAATTT
38533178 TATATGTAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
33 7 0.19
34 6 0.17
35 18 0.50
36 5 0.14
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (33 bp):
AAAATTTAAAATATATATATATTTTTATTTATT
Found at i:38534871 original size:58 final size:58
Alignment explanation
Indices: 38534803--38534912 Score: 168
Period size: 58 Copynumber: 1.9 Consensus size: 58
38534793 CCGATGGTAG
38534803 TGATTTGACACGATTTTTATCACGT-AAGTCCAAGCTGAGTAGACTTGGTTGAAAGCTA
1 TGATTTGACACGATTTTTATCACGTAAAGTCCAA-CTGAGTAGACTTGGTTGAAAGCTA
* * * *
38534861 TGATTTGACACGATTTTTATTATGTAAATTCCAATTGAGTAGACTTGGTTGA
1 TGATTTGACACGATTTTTATCACGTAAAGTCCAACTGAGTAGACTTGGTTGA
38534913 TGTGATTTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
58 40 0.85
59 7 0.15
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (58 bp):
TGATTTGACACGATTTTTATCACGTAAAGTCCAACTGAGTAGACTTGGTTGAAAGCTA
Found at i:38535098 original size:49 final size:48
Alignment explanation
Indices: 38535035--38535161 Score: 157
Period size: 48 Copynumber: 2.6 Consensus size: 48
38535025 CAATACCTTC
* * * ** *
38535035 TTACTTTCCGTAAGCCTCCATCCATGCGTTTTGGAGTAGGGCCACTTTA
1 TTACTTTCCATAAGCCTCC-TCCATGCATCTCAGAATAGGGCCACTTTA
*
38535084 TTACTTTCTATAAGCCT-CTCCCATGCATCTCAGAATAGGGCCACTTTA
1 TTACTTTCCATAAGCCTCCT-CCATGCATCTCAGAATAGGGCCACTTTA
38535132 TTACTTTCCATAAGCCTCCCTCCATGCATC
1 TTACTTTCCATAAGCCT-CCTCCATGCATC
38535162 GAGGAATAGG
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
47 1 0.01
48 40 0.60
49 24 0.36
50 2 0.03
ACGTcount: A:0.21, C:0.31, G:0.14, T:0.34
Consensus pattern (48 bp):
TTACTTTCCATAAGCCTCCTCCATGCATCTCAGAATAGGGCCACTTTA
Found at i:38535285 original size:49 final size:48
Alignment explanation
Indices: 38535178--38535396 Score: 154
Period size: 49 Copynumber: 4.5 Consensus size: 48
38535168 TAGGGTTATC
* * * * * * * **
38535178 TTATTACCTTCCGTAAGTCTCCCCTTATACGTTTGGGAGTAAGGTCAAG
1 TTATTACTTTTCGTAAGCCTCCCC-CATACGTCTGGGAGCAAGCTCACT
* *
38535227 TTATCACTTTTCATAAGCCTCCCCCTATACGTCTGGGAGCAAGCTCACT
1 TTATTACTTTTCGTAAGCCTCCCCC-ATACGTCTGGGAGCAAGCTCACT
* * * * ** * * *
38535276 TTATTACTTTTTGTAAGCTTCACCCCATGCGTCTAGGAATAGGGTTA-T
1 TTATTACTTTTCGTAAGCCTC-CCCCATACGTCTGGGAGCAAGCTCACT
** *
38535324 ATTATTACTTTTCGTAAGCCTTCCCCCATGTGTTTGGGAGCAGAGC-CACT
1 -TTATTACTTTTCGTAAGCC-TCCCCCATACGTCTGGGAGCA-AGCTCACT
*
38535374 TTATTACCTTTCGTAAGCCTCCC
1 TTATTACTTTTCGTAAGCCTCCC
38535397 TCATGTGATT
Statistics
Matches: 131, Mismatches: 33, Indels: 13
0.74 0.19 0.07
Matches are distributed among these distances:
48 5 0.04
49 118 0.90
50 8 0.06
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.35
Consensus pattern (48 bp):
TTATTACTTTTCGTAAGCCTCCCCCATACGTCTGGGAGCAAGCTCACT
Found at i:38535392 original size:147 final size:147
Alignment explanation
Indices: 38535125--38535396 Score: 316
Period size: 147 Copynumber: 1.9 Consensus size: 147
38535115 AGAATAGGGC
*
38535125 CACTTTATTACTTTCCATAAGCCTCCCTCCATGCATCGAGGAATAGGGTTATCTTATTACCTTCC
1 CACTTTATTACTTTCCATAAGCCTCCCTCCATGCATCGAGGAATAGGGTTATATTATTACCTTCC
* * * * *
38535190 GTAAGTCTCCCCTTATACGTTTGGGAGTAAGGTCAAGTTATCACTTTTCATAAGCCTCCCCCTAT
66 GTAAGCCTCCCCTCATACGTTTGGGAGCAAGGCCAAGTTATCACCTTTCATAAGCCTCCCCCTAT
38535255 ACGTCTGGGAGCAAGCT
131 ACGTCTGGGAGCAAGCT
*** * * * * *
38535272 CACTTTATTACTTTTTGTAAGCTTCACC-CCATGCGTCTAGGAATAGGGTTATATTATTACTTTT
1 CACTTTATTACTTTCCATAAGCCTC-CCTCCATGCATCGAGGAATAGGGTTATATTATTACCTTC
** ** * *
38535336 CGTAAGCCTTCCCC-CATGTGTTTGGGAGC-AGAGCCACTTTATTACCTTTCGTAAGCCTCCC
65 CGTAAGCC-TCCCCTCATACGTTTGGGAGCAAG-GCCAAGTTATCACCTTTCATAAGCCTCCC
38535397 TCATGTGATT
Statistics
Matches: 102, Mismatches: 20, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
146 2 0.02
147 93 0.91
148 7 0.07
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (147 bp):
CACTTTATTACTTTCCATAAGCCTCCCTCCATGCATCGAGGAATAGGGTTATATTATTACCTTCC
GTAAGCCTCCCCTCATACGTTTGGGAGCAAGGCCAAGTTATCACCTTTCATAAGCCTCCCCCTAT
ACGTCTGGGAGCAAGCT
Found at i:38535428 original size:48 final size:48
Alignment explanation
Indices: 38535327--38535450 Score: 135
Period size: 48 Copynumber: 2.6 Consensus size: 48
38535317 GGGTTATATT
* * * *
38535327 ATTACTTTTCGTAAGCCTTCCCCCATGTGTTTGGGAGCAGAGCCACTTT
1 ATTACCTTTCGTAAGCC-TCCCTCATGTGATTGGGAGCAGAGCCACTTA
* **
38535376 ATTACCTTTCGTAAGCCTCCCTCATGTGATTGGGAGCAGGGTTACTTA
1 ATTACCTTTCGTAAGCCTCCCTCATGTGATTGGGAGCAGAGCCACTTA
*
38535424 ATTA-CTTGCCGTAAGCCTCTCCT-ATGT
1 ATTACCTT-TCGTAAGCCTC-CCTCATGT
38535451 ATCTGGAAGC
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
47 3 0.05
48 43 0.66
49 19 0.29
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.35
Consensus pattern (48 bp):
ATTACCTTTCGTAAGCCTCCCTCATGTGATTGGGAGCAGAGCCACTTA
Found at i:38537344 original size:42 final size:42
Alignment explanation
Indices: 38537285--38537395 Score: 161
Period size: 42 Copynumber: 2.6 Consensus size: 42
38537275 GTTTACTTTA
* * *
38537285 TGTTCAGCTCTTTTGAGCTTCTGTTTAACCCTTATGGGTTTT
1 TGTTCAGCTCTATTGAGCTTCTGTTCAACCCTTATGGGTTTC
38537327 TGTTCAGCTCTATTGAGCTTCTGTTCAACCCTTATGGGTTTC
1 TGTTCAGCTCTATTGAGCTTCTGTTCAACCCTTATGGGTTTC
* *
38537369 TATTTAGCTCTCA-TGAGCTTCTGTTCA
1 TGTTCAGCTCT-ATTGAGCTTCTGTTCA
38537396 GCCTTTAGGC
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
42 62 0.98
43 1 0.02
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (42 bp):
TGTTCAGCTCTATTGAGCTTCTGTTCAACCCTTATGGGTTTC
Found at i:38537353 original size:21 final size:20
Alignment explanation
Indices: 38537285--38537410 Score: 67
Period size: 21 Copynumber: 6.1 Consensus size: 20
38537275 GTTTACTTTA
38537285 TGTTCAGCTCTTTTGAGCTTC
1 TGTTCAGCTC-TTTGAGCTTC
* * * * * *
38537306 TGTTTAACCCTTATGGGTTTT
1 TGTTCAGCTCTT-TGAGCTTC
38537327 TGTTCAGCTCTATTGAGCTTC
1 TGTTCAGCTCT-TTGAGCTTC
* * * *
38537348 TGTTCAACCCTTATGGGTTTC
1 TGTTCAGCTCTT-TGAGCTTC
* * *
38537369 TATTTAGCTCTCATGAGCTTC
1 TGTTCAGCTCT-TTGAGCTTC
38537390 TGTTCAGC-CTTT-AGGCTTC
1 TGTTCAGCTCTTTGA-GCTTC
38537409 TG
1 TG
38537411 AAAATGATGT
Statistics
Matches: 74, Mismatches: 26, Indels: 12
0.66 0.23 0.11
Matches are distributed among these distances:
18 1 0.01
19 8 0.11
20 5 0.07
21 59 0.80
22 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.45
Consensus pattern (20 bp):
TGTTCAGCTCTTTGAGCTTC
Found at i:38540225 original size:21 final size:21
Alignment explanation
Indices: 38540199--38540352 Score: 107
Period size: 21 Copynumber: 7.3 Consensus size: 21
38540189 CATGTTTACT
*
38540199 TTCTGTTTAGCTCTTTTGAGC
1 TTCTGTTTAGCTCTTATGAGC
* * *
38540220 TTCTGTTTAAC-CTTTATGGGT
1 TTCTGTTTAGCTC-TTATGAGC
38540241 TTAC-GTTTAGCTC-TATCGAGC
1 TT-CTGTTTAGCTCTTAT-GAGC
* * * *
38540262 TTCTGTTTAACCCTTATGGGT
1 TTCTGTTTAGCTCTTATGAGC
* **
38540283 TTCTGTTCAGCTCTTACAAGC
1 TTCTGTTTAGCTCTTATGAGC
* * * * *
38540304 TTCTGTTCAACCCTTATGGGT
1 TTCTGTTTAGCTCTTATGAGC
*
38540325 TTCTGTTTAGCTCTCATGAGC
1 TTCTGTTTAGCTCTTATGAGC
38540346 TTCTGTT
1 TTCTGTT
38540353 CAGCCTTCGG
Statistics
Matches: 97, Mismatches: 30, Indels: 12
0.70 0.22 0.09
Matches are distributed among these distances:
20 5 0.05
21 87 0.90
22 5 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (21 bp):
TTCTGTTTAGCTCTTATGAGC
Found at i:38540353 original size:42 final size:42
Alignment explanation
Indices: 38540198--38540354 Score: 210
Period size: 42 Copynumber: 3.7 Consensus size: 42
38540188 TCATGTTTAC
* * *
38540198 TTTCTGTTTAGCTCTTTTGAGCTTCTGTTTAACCTTTATGGG
1 TTTCTGTTTAGCTCTTATGAGCTTCTGTTCAACCCTTATGGG
*
38540240 TTTAC-GTTTAGCTC-TATCGAGCTTCTGTTTAACCCTTATGGG
1 TTT-CTGTTTAGCTCTTAT-GAGCTTCTGTTCAACCCTTATGGG
* **
38540282 TTTCTGTTCAGCTCTTACAAGCTTCTGTTCAACCCTTATGGG
1 TTTCTGTTTAGCTCTTATGAGCTTCTGTTCAACCCTTATGGG
*
38540324 TTTCTGTTTAGCTCTCATGAGCTTCTGTTCA
1 TTTCTGTTTAGCTCTTATGAGCTTCTGTTCA
38540355 GCCTTCGGGC
Statistics
Matches: 101, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
41 3 0.03
42 95 0.94
43 3 0.03
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.46
Consensus pattern (42 bp):
TTTCTGTTTAGCTCTTATGAGCTTCTGTTCAACCCTTATGGG
Found at i:38542814 original size:3 final size:3
Alignment explanation
Indices: 38542806--38542848 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
38542796 AAGAGTATAA
38542806 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
38542849 AAAATGTCAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:38543233 original size:18 final size:17
Alignment explanation
Indices: 38543206--38543239 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
38543196 ACTTTAAAAT
*
38543206 TATAATTATTATATTTAC
1 TATAAATATT-TATTTAC
38543224 TATAAATATTTATTTA
1 TATAAATATTTATTTA
38543240 ATAATATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TATAAATATTTATTTAC
Found at i:38550233 original size:29 final size:30
Alignment explanation
Indices: 38550174--38550233 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
38550164 CATTATTTTT
** *
38550174 AAAAAATTATTTTATTCTCTCGATTATTTA
1 AAAAAATTAAATTATTCTCTCGATTAATTA
38550204 AAAAAATTAAATTATTC-CTC-ATTTAATTA
1 AAAAAATTAAATTATTCTCTCGA-TTAATTA
38550233 A
1 A
38550234 TATATATTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 1 0.04
29 10 0.38
30 15 0.58
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (30 bp):
AAAAAATTAAATTATTCTCTCGATTAATTA
Found at i:38552336 original size:26 final size:24
Alignment explanation
Indices: 38552280--38552328 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
38552270 ATGATTTTTG
*
38552280 AAGATAATTTATTCAAAATACTTC
1 AAGATAATTTATTCAAAAGACTTC
38552304 AAGATAATTTATTCGAAAAAGACTT
1 AAGATAATTTATTC--AAAAGACTT
38552329 GTAGATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.64
26 8 0.36
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.35
Consensus pattern (24 bp):
AAGATAATTTATTCAAAAGACTTC
Found at i:38553183 original size:11 final size:10
Alignment explanation
Indices: 38553167--38553209 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
38553157 CGTATTTACA
38553167 TTTTATGTTAT
1 TTTTA-GTTAT
* *
38553178 TTTTATTTGT
1 TTTTAGTTAT
38553188 TTTTAGTTAAT
1 TTTTAGTT-AT
38553199 TTTTAGTTAT
1 TTTTAGTTAT
38553209 T
1 T
38553210 CTGAGTAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 13 0.48
11 14 0.52
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (10 bp):
TTTTAGTTAT
Found at i:38555526 original size:21 final size:21
Alignment explanation
Indices: 38555483--38555566 Score: 91
Period size: 21 Copynumber: 4.1 Consensus size: 21
38555473 AATACACCAG
38555483 CAGAAGCTCG-AA-AGTTGAA
1 CAGAAGCTCGTAAGAGTTGAA
* *
38555502 CAGAAGCTCGTAAGAGCTAAA
1 CAGAAGCTCGTAAGAGTTGAA
* *
38555523 CAGAAACTCATAAGAGTTGAA
1 CAGAAGCTCGTAAGAGTTGAA
* * *
38555544 CAGAAACTCATAAAAGTTGAA
1 CAGAAGCTCGTAAGAGTTGAA
38555565 CA
1 CA
38555567 AAAAGTAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
19 10 0.18
20 2 0.04
21 44 0.79
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (21 bp):
CAGAAGCTCGTAAGAGTTGAA
Found at i:38556436 original size:17 final size:17
Alignment explanation
Indices: 38556399--38556437 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
38556389 TTATTTATTC
*
38556399 TATTGTTGGAATTGAAT
1 TATTGTTGGAATTGAAA
38556416 TATTGTTGGAATT-ATAA
1 TATTGTTGGAATTGA-AA
38556433 TATTG
1 TATTG
38556438 AGTTGGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.49
Consensus pattern (17 bp):
TATTGTTGGAATTGAAA
Found at i:38556603 original size:21 final size:21
Alignment explanation
Indices: 38556576--38556685 Score: 116
Period size: 21 Copynumber: 5.3 Consensus size: 21
38556566 GTGTTTTACT
*
38556576 TTCTGTTCAGCTCTTCTGAGC
1 TTCTGTTCAGCTCTTATGAGC
* * *
38556597 TTTTGTTCAACTCTTATGAGT
1 TTCTGTTCAGCTCTTATGAGC
* *
38556618 TTCTGTTTAGCTATTATGAGC
1 TTCTGTTCAGCTCTTATGAGC
*
38556639 TTCTGTTCAACT-TT-TGAGC
1 TTCTGTTCAGCTCTTATGAGC
* * *
38556658 TTCTATTTAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTATGAGC
38556679 TTCTGTT
1 TTCTGTT
38556686 GGTGTATTCA
Statistics
Matches: 71, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
19 14 0.20
20 4 0.06
21 53 0.75
ACGTcount: A:0.15, C:0.20, G:0.16, T:0.48
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTATGAGC
Found at i:38556623 original size:42 final size:40
Alignment explanation
Indices: 38556575--38556685 Score: 134
Period size: 42 Copynumber: 2.7 Consensus size: 40
38556565 TGTGTTTTAC
* *
38556575 TTTCTGTTCAGCTCTTCTGAGCTTTTGTTCAACTCTTATGAG
1 TTTCTGTTTAGCTCTTCTGAGCTTCTGTTCAACT-TT-TGAG
* *
38556617 TTTCTGTTTAGCTATTATGAGCTTCTGTTCAACTTTTGAG
1 TTTCTGTTTAGCTCTTCTGAGCTTCTGTTCAACTTTTGAG
* *
38556657 CTTCTATTTAGCTCTTAC-GAGCTTCTGTT
1 TTTCTGTTTAGCTCTT-CTGAGCTTCTGTT
38556686 GGTGTATTCA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
40 28 0.47
41 2 0.03
42 30 0.50
ACGTcount: A:0.15, C:0.20, G:0.16, T:0.49
Consensus pattern (40 bp):
TTTCTGTTTAGCTCTTCTGAGCTTCTGTTCAACTTTTGAG
Found at i:38556679 original size:40 final size:42
Alignment explanation
Indices: 38556584--38556685 Score: 129
Period size: 40 Copynumber: 2.5 Consensus size: 42
38556574 CTTTCTGTTC
* * *
38556584 AGCTCTT-CTGAGCTTTTGTTCAACTCTTATGAGTTTCTGTTT
1 AGCTCTTAC-GAGCTTCTGTTCAACTCTTATGAGCTTCTATTT
* *
38556626 AGCTATTATGAGCTTCTGTTCAACT-TT-TGAGCTTCTATTT
1 AGCTCTTACGAGCTTCTGTTCAACTCTTATGAGCTTCTATTT
38556666 AGCTCTTACGAGCTTCTGTT
1 AGCTCTTACGAGCTTCTGTT
38556686 GGTGTATTCA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
40 29 0.56
41 2 0.04
42 21 0.40
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.47
Consensus pattern (42 bp):
AGCTCTTACGAGCTTCTGTTCAACTCTTATGAGCTTCTATTT
Found at i:38559789 original size:68 final size:68
Alignment explanation
Indices: 38559680--38559819 Score: 262
Period size: 68 Copynumber: 2.1 Consensus size: 68
38559670 ATGTGATGGG
*
38559680 CACAGGCCCTAGACTGTATCTAACTAAATTATGTTGATTATCTGTATGCATGTTTTCTGTAGGGA
1 CACAGGCCCTAAACTGTATCTAACTAAATTATGTTGATTATCTGTATGCATGTTTTCTGTAGGGA
38559745 TTA
66 TTA
*
38559748 CACAGGCCCTAAACTGTATCTAACTAAATTATGTTGATTATCTGTATGCATGTTTTCTGTGGGGA
1 CACAGGCCCTAAACTGTATCTAACTAAATTATGTTGATTATCTGTATGCATGTTTTCTGTAGGGA
38559813 TTA
66 TTA
38559816 CACA
1 CACA
38559820 CTGAGTTTGC
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (68 bp):
CACAGGCCCTAAACTGTATCTAACTAAATTATGTTGATTATCTGTATGCATGTTTTCTGTAGGGA
TTA
Found at i:38563638 original size:8 final size:8
Alignment explanation
Indices: 38563618--38563656 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
38563608 TTTTCGTCTC
*
38563618 TTTCTCTG
1 TTTCTTTG
38563626 TTTCTTT-
1 TTTCTTTG
38563633 TCTTCTTTG
1 T-TTCTTTG
38563642 TTTCTTTG
1 TTTCTTTG
38563650 TTTCTTT
1 TTTCTTT
38563657 TACTTTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
7 1 0.04
8 26 0.93
9 1 0.04
ACGTcount: A:0.00, C:0.18, G:0.08, T:0.74
Consensus pattern (8 bp):
TTTCTTTG
Found at i:38563846 original size:5 final size:5
Alignment explanation
Indices: 38563838--38563898 Score: 65
Period size: 5 Copynumber: 12.4 Consensus size: 5
38563828 GATATGAAAC
* *
38563838 AATAT AATAT AATAT AATAT AATAT ATTATAT TATAT TATAT AATA- AA-AT
1 AATAT AATAT AATAT AATAT AATAT A--ATAT AATAT AATAT AATAT AATAT
38563888 AATAT -ATAT AA
1 AATAT AATAT AA
38563899 AACATAAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
3 1 0.02
4 8 0.16
5 36 0.73
7 4 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
AATAT
Found at i:38571268 original size:8 final size:8
Alignment explanation
Indices: 38571248--38571286 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
38571238 TTTTCGTCTC
*
38571248 TTTCTCTG
1 TTTCTTTG
38571256 TTTCTTT-
1 TTTCTTTG
38571263 TCTTCTTTG
1 T-TTCTTTG
38571272 TTTCTTTG
1 TTTCTTTG
38571280 TTTCTTT
1 TTTCTTT
38571287 TACTTTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
7 1 0.04
8 26 0.93
9 1 0.04
ACGTcount: A:0.00, C:0.18, G:0.08, T:0.74
Consensus pattern (8 bp):
TTTCTTTG
Found at i:38571460 original size:5 final size:5
Alignment explanation
Indices: 38571452--38571521 Score: 90
Period size: 5 Copynumber: 14.2 Consensus size: 5
38571442 TATTTAATTT
* *
38571452 ATATA ATATA AAACA ATATA ATATA ATATA ATATA ATATA ATATA ATAT-
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
*
38571501 ATAATA AAATA ATAT- ATATA A
1 AT-ATA ATATA ATATA ATATA A
38571522 AACATAAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
4 6 0.11
5 49 0.88
6 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (5 bp):
ATATA
Found at i:38578632 original size:46 final size:46
Alignment explanation
Indices: 38578562--38578655 Score: 134
Period size: 46 Copynumber: 2.0 Consensus size: 46
38578552 GTGATATGAA
* * * *
38578562 CAAAATATGTTTAACTTGATATATTAGAAAGTGTAAGAATAGTGGG
1 CAAAATATGTTTAACTCGAGATATTACAAAATGTAAGAATAGTGGG
* *
38578608 CAAAATATGTTTAACTCGAGATATTACAAAATGTAAGATTAGTTGG
1 CAAAATATGTTTAACTCGAGATATTACAAAATGTAAGAATAGTGGG
38578654 CA
1 CA
38578656 CACTATTGCT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.32
Consensus pattern (46 bp):
CAAAATATGTTTAACTCGAGATATTACAAAATGTAAGAATAGTGGG
Found at i:38587460 original size:3 final size:3
Alignment explanation
Indices: 38587452--38587481 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
38587442 TATAATGTTA
38587452 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
38587482 CAAACCAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:38588176 original size:32 final size:32
Alignment explanation
Indices: 38588110--38588209 Score: 166
Period size: 32 Copynumber: 3.2 Consensus size: 32
38588100 TTCTTTTTTA
* *
38588110 TTTTTTAACTTTAAAATACTTTTAAAATACTT
1 TTTTTTAATTTTAAAATATTTTTAAAATACTT
*
38588142 TTTTTT-ATTTTAAAATTTTTTTAAAATACTT
1 TTTTTTAATTTTAAAATATTTTTAAAATACTT
38588173 TTTTTTAATTTTAAAATATTTTTAAAATACTT
1 TTTTTTAATTTTAAAATATTTTTAAAATACTT
38588205 TTTTT
1 TTTTT
38588210 ATTTTTTATT
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
31 28 0.44
32 35 0.56
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (32 bp):
TTTTTTAATTTTAAAATATTTTTAAAATACTT
Found at i:38588193 original size:10 final size:11
Alignment explanation
Indices: 38588119--38588206 Score: 65
Period size: 11 Copynumber: 8.3 Consensus size: 11
38588109 ATTTTTTAAC
38588119 TTTAAAATACT
1 TTTAAAATACT
38588130 TTTAAAATACT
1 TTTAAAATACT
***
38588141 TTT-TTTTA-T
1 TTTAAAATACT
**
38588150 TTTAAAATTTT
1 TTTAAAATACT
38588161 TTTAAAATACT
1 TTTAAAATACT
*** *
38588172 TTT-TTTTAAT
1 TTTAAAATACT
*
38588182 TTTAAAATATT
1 TTTAAAATACT
38588193 TTTAAAATACT
1 TTTAAAATACT
38588204 TTT
1 TTT
38588207 TTTATTTTTT
Statistics
Matches: 56, Mismatches: 18, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
9 4 0.07
10 9 0.16
11 43 0.77
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTAAAATACT
Found at i:38588217 original size:32 final size:31
Alignment explanation
Indices: 38588110--38588214 Score: 158
Period size: 31 Copynumber: 3.4 Consensus size: 31
38588100 TTCTTTTTTA
* * *
38588110 TTTTTTAACTTTAAAATACTTTTAAAATACT
1 TTTTTTTATTTTAAAATATTTTTAAAATACT
*
38588141 TTTTTTTATTTTAAAATTTTTTTAAAATACT
1 TTTTTTTATTTTAAAATATTTTTAAAATACT
38588172 TTTTTTTAATTTTAAAATATTTTTAAAATAC-
1 TTTTTTT-ATTTTAAAATATTTTTAAAATACT
38588203 TTTTTTTATTTT
1 TTTTTTTATTTT
38588215 TTATTTTAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
30 5 0.07
31 41 0.60
32 22 0.32
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (31 bp):
TTTTTTTATTTTAAAATATTTTTAAAATACT
Found at i:38594438 original size:37 final size:36
Alignment explanation
Indices: 38594392--38594463 Score: 99
Period size: 37 Copynumber: 2.0 Consensus size: 36
38594382 GTTCGGAGTC
* * *
38594392 TGTCATTTTTTGCCTGGGACAATTTCTTTCTGGCTG
1 TGTCATTTTTTGCCTGAGACAATGTCTCTCTGGCTG
*
38594428 TGTCATTTTTTTTCCTGAGACAATGTCTCTCTGGCT
1 TGTCA-TTTTTTGCCTGAGACAATGTCTCTCTGGCT
38594464 CAGTGCAGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 5 0.16
37 26 0.84
ACGTcount: A:0.12, C:0.21, G:0.19, T:0.47
Consensus pattern (36 bp):
TGTCATTTTTTGCCTGAGACAATGTCTCTCTGGCTG
Found at i:38598629 original size:20 final size:21
Alignment explanation
Indices: 38598603--38598647 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
38598593 CCAAATTAAA
38598603 AAAAAAAGATAGTTGAGTGA-C
1 AAAAAAA-ATAGTTGAGTGATC
*
38598624 AAAAAAAATAGTTGGGTGATC
1 AAAAAAAATAGTTGAGTGATC
38598645 AAA
1 AAA
38598648 TTAAATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.53, C:0.04, G:0.22, T:0.20
Consensus pattern (21 bp):
AAAAAAAATAGTTGAGTGATC
Found at i:38600434 original size:6 final size:6
Alignment explanation
Indices: 38600401--38600432 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
38600391 CTACGATGAC
*
38600401 GACGAT GACGAT GACGAT GACGAT GATGAT GA
1 GACGAT GACGAT GACGAT GACGAT GACGAT GA
38600433 TGTTGAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.19
Consensus pattern (6 bp):
GACGAT
Found at i:38603308 original size:34 final size:34
Alignment explanation
Indices: 38603270--38603338 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
38603260 TTATCCTAAT
*
38603270 TTCCAAGAGTAAGTGTTTTTATTCAACCCTAAGA
1 TTCCAAGAGTAAGTGTTTTTACTCAACCCTAAGA
*
38603304 TTCCAAGAGTAAGTGTTTTTACTCAACCCTGAGA
1 TTCCAAGAGTAAGTGTTTTTACTCAACCCTAAGA
38603338 T
1 T
38603339 ACTTTGCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (34 bp):
TTCCAAGAGTAAGTGTTTTTACTCAACCCTAAGA
Found at i:38603398 original size:21 final size:19
Alignment explanation
Indices: 38603355--38603408 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
38603345 CAAATAAAGC
38603355 TTATATGTGATGTGATATG
1 TTATATGTGATGTGATATG
38603374 -TATATGATG-TGTTGATATG
1 TTATATG-TGATG-TGATATG
*
38603393 ATTATATGTTATGTGA
1 -TTATATGTGATGTGA
38603409 GAATGTCAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
18 8 0.28
19 9 0.31
20 4 0.14
21 8 0.28
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (19 bp):
TTATATGTGATGTGATATG
Found at i:38604435 original size:10 final size:10
Alignment explanation
Indices: 38604422--38604446 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
38604412 TGTTAATGTA
38604422 TGATTTAGTG
1 TGATTTAGTG
38604432 TGATTTAGTG
1 TGATTTAGTG
38604442 TGATT
1 TGATT
38604447 GAGCATGATT
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:0.28, T:0.52
Consensus pattern (10 bp):
TGATTTAGTG
Found at i:38609872 original size:20 final size:21
Alignment explanation
Indices: 38609815--38609872 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
38609805 AAACAACAAT
38609815 AAAATAGCACCAAAAACAACTCC
1 AAAATAGCA-CAAAAACAAC-CC
* * *
38609838 AAAACATCACCAAAACAA-CC
1 AAAATAGCACAAAAACAACCC
38609858 AAAATAGCACAAAAA
1 AAAATAGCACAAAAA
38609873 ATAACCTGCA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 14 0.48
22 8 0.28
23 7 0.24
ACGTcount: A:0.62, C:0.28, G:0.03, T:0.07
Consensus pattern (21 bp):
AAAATAGCACAAAAACAACCC
Found at i:38614246 original size:3 final size:3
Alignment explanation
Indices: 38614238--38614306 Score: 129
Period size: 3 Copynumber: 23.0 Consensus size: 3
38614228 ATAAATTTCA
*
38614238 TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
38614286 TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT
38614307 AATTGCTTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:38614939 original size:18 final size:18
Alignment explanation
Indices: 38614908--38614945 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
38614898 TATATGTCCA
38614908 TAATTTTCTTTTAATGTTT
1 TAATTTTCTTTTAAT-TTT
38614927 TAATTTT-TTTTAATTTT
1 TAATTTTCTTTTAATTTT
38614944 TA
1 TA
38614946 CTTGTTATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.26
18 7 0.37
19 7 0.37
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (18 bp):
TAATTTTCTTTTAATTTT
Found at i:38615258 original size:109 final size:109
Alignment explanation
Indices: 38615062--38615595 Score: 815
Period size: 109 Copynumber: 4.9 Consensus size: 109
38615052 AAGGAAAATT
*
38615062 TTTCTAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
*
38615127 CGATTTTTCTCGTTCAACCAAATAGCTAAGTATCCTTTTAAAAA
66 CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAA
* * ** *
38615171 TTTCAAAATAAGGCAATGTTTGGCGTTTGGGAATTCGAGGTAACGTGCCCTAATGTGTTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
* *
38615236 CGATTTTTCTCGTTCAACCAAATAGCTAAGTATCCTTTTGAAAA
66 CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAA
* * *
38615280 TTTCAAAAATAAGGTAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCACTAATGTGCTGGGTT
1 TTTC-AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTT
* *
38615345 TTGATTTCT-TCGTTCAACCAAATAGCTAAATATCCTTTTAAAAA
65 TCGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAA
* *
38615389 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTAGAGAAAACGTGCCCTAATATGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
* *
38615454 CGATTTTTCTCGTTCAACCAAATAGCCAAATATCCTTTCAAAAA
66 CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAA
* * * *
38615498 TTTCAAAATAAGGAAATGTTTCGCGTTTGGAAATTCGAG-GAACGTGCCTTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
* *
38615562 CGA--TTTCTCGTTTAACCAAATAGCCAAATATCCT
66 CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCT
38615596 CTTGAATTTT
Statistics
Matches: 388, Mismatches: 35, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
106 30 0.08
108 87 0.22
109 212 0.55
110 59 0.15
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (109 bp):
TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAA
Found at i:38616007 original size:24 final size:24
Alignment explanation
Indices: 38615978--38616041 Score: 101
Period size: 24 Copynumber: 2.7 Consensus size: 24
38615968 CACGTTCAAC
*
38615978 AACATAGGTTCGTATACTTCATAT
1 AACATAGGTTCGCATACTTCATAT
*
38616002 AGCATAGGTTCGCATACTTCATAT
1 AACATAGGTTCGCATACTTCATAT
*
38616026 AACATAGGTTTGCATA
1 AACATAGGTTCGCATA
38616042 ACAACATAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (24 bp):
AACATAGGTTCGCATACTTCATAT
Found at i:38618358 original size:10 final size:9
Alignment explanation
Indices: 38618339--38618428 Score: 56
Period size: 10 Copynumber: 9.0 Consensus size: 9
38618329 AGAATTTACA
38618339 TTTTATAAAT
1 TTTTA-AAAT
38618349 TTTTACAAAT
1 TTTTA-AAAT
*
38618359 TTTT-AATT
1 TTTTAAAAT
38618367 TTTTAACAATT
1 TTTTAA-AA-T
38618378 TTTTAAAACT
1 TTTTAAAA-T
*
38618388 TTTTAAATAAA
1 TTTT-AA-AAT
*
38618399 ATTTAAAAT
1 TTTTAAAAT
38618408 TTATTAACTAAT
1 TT-TTAA--AAT
38618420 TTTTAAAAT
1 TTTTAAAAT
38618429 GCTTTTTCAT
Statistics
Matches: 64, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
8 7 0.11
9 7 0.11
10 27 0.42
11 16 0.25
12 7 0.11
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (9 bp):
TTTTAAAAT
Found at i:38618371 original size:18 final size:19
Alignment explanation
Indices: 38618338--38618426 Score: 72
Period size: 20 Copynumber: 4.5 Consensus size: 19
38618328 CAGAATTTAC
38618338 ATTTTATAAATTTTT-ACAA
1 ATTTT-TAAATTTTTAACAA
*
38618357 ATTTTTAATTTTTTAACAA
1 ATTTTTAAATTTTTAACAA
* *
38618376 TTTTTTAAAACTTTTTAAATAA
1 ATTTTT-AAA-TTTTT-AACAA
* * *
38618398 AATTTAAAATTTATTAACTA
1 ATTTTTAAATTT-TTAACAA
38618418 ATTTTTAAA
1 ATTTTTAAA
38618427 ATGCTTTTTC
Statistics
Matches: 54, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
18 8 0.15
19 14 0.26
20 15 0.28
21 10 0.19
22 7 0.13
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTTTAAATTTTTAACAA
Found at i:38618593 original size:39 final size:39
Alignment explanation
Indices: 38618539--38618614 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
38618529 ATCAACTTGA
* * *
38618539 TCAATGTGCTATGTCATTGATGAACCTGCCATGTCATGG
1 TCAATGTGCTATGTCATCGATCAACCTACCATGTCATGG
*
38618578 TCAATGTG-TCATGTCATCGGTCAACCTACCATGTCAT
1 TCAATGTGCT-ATGTCATCGATCAACCTACCATGTCAT
38618615 CAATCACATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.03
39 31 0.97
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (39 bp):
TCAATGTGCTATGTCATCGATCAACCTACCATGTCATGG
Found at i:38622210 original size:6 final size:6
Alignment explanation
Indices: 38622199--38622223 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
38622189 CGCCACAGGT
38622199 AGACTG AGACTG AGACTG AGACTG A
1 AGACTG AGACTG AGACTG AGACTG A
38622224 TGACAGCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (6 bp):
AGACTG
Found at i:38628312 original size:26 final size:25
Alignment explanation
Indices: 38628291--38628358 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 25
38628281 CTTAATATTT
*
38628291 AAGTAAATATATATAATATAATAATA
1 AAGTAAATATA-ATAAAATAATAATA
38628317 AAGTAAATATAATAAAATAAATAAGTA
1 AAGTAAATATAATAAAAT-AATAA-TA
38628344 AA-TGAAATA-AATAAA
1 AAGT-AAATATAATAAA
38628359 GAAAATAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
25 6 0.16
26 23 0.61
27 9 0.24
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (25 bp):
AAGTAAATATAATAAAATAATAATA
Found at i:38628329 original size:22 final size:22
Alignment explanation
Indices: 38628290--38628358 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 22
38628280 ACTTAATATT
*
38628290 TAAGTAAATATATATAATATAATAA
1 TAAGTAAATATA-ATAAAAT-A-AA
38628315 TAAAGTAAATATAATAAAATAAA
1 T-AAGTAAATATAATAAAATAAA
38628338 TAAGTAAATGA-AAT-AAATAAA
1 TAAGTAAAT-ATAATAAAATAAA
38628359 GAAAATAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
21 7 0.17
22 11 0.27
23 4 0.10
24 1 0.02
25 7 0.17
26 11 0.27
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (22 bp):
TAAGTAAATATAATAAAATAAA
Found at i:38628351 original size:5 final size:4
Alignment explanation
Indices: 38628294--38628358 Score: 51
Period size: 4 Copynumber: 15.0 Consensus size: 4
38628284 AATATTTAAG
* *
38628294 TAAA TATA TATAA TATAA T-AA TAAA GTAAA TATAA TAAAA TAAA TAAG
1 TAAA TAAA TA-AA TA-AA TAAA TAAA -TAAA TA-AA T-AAA TAAA TAAA
38628342 TAAA TGAAA TAAA TAAA
1 TAAA T-AAA TAAA TAAA
38628359 GAAAATAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
3 3 0.06
4 26 0.51
5 21 0.41
6 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (4 bp):
TAAA
Found at i:38628371 original size:12 final size:13
Alignment explanation
Indices: 38628313--38628373 Score: 56
Period size: 13 Copynumber: 4.7 Consensus size: 13
38628303 ATAATATAAT
*
38628313 AATAAAGTAAATA
1 AATAAAGAAAATA
38628326 TAATAAA-ATAAATA
1 -AATAAAGA-AAATA
*
38628340 AGTAAATG-AAATA
1 AATAAA-GAAAATA
38628353 AATAAAGAAAATA
1 AATAAAGAAAATA
38628366 AA-AAAGAA
1 AATAAAGAA
38628374 TAGAAAGAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
12 7 0.17
13 22 0.55
14 11 0.28
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (13 bp):
AATAAAGAAAATA
Found at i:38629405 original size:37 final size:38
Alignment explanation
Indices: 38629341--38629417 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 38
38629331 GTCAATTTAC
* * *
38629341 TACTTCGGATTAGTTCGATGAGGCACTGTGTGCCAATT
1 TACTTCGGATTAGTCCGATGAGACACTGGGTGCCAATT
* *
38629379 TACTTCGGTTTAG-CCGATGAGACACTGGGTGTCAATT
1 TACTTCGGATTAGTCCGATGAGACACTGGGTGCCAATT
38629416 TA
1 TA
38629418 TTATTTCAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
37 22 0.65
38 12 0.35
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (38 bp):
TACTTCGGATTAGTCCGATGAGACACTGGGTGCCAATT
Found at i:38631506 original size:27 final size:26
Alignment explanation
Indices: 38631464--38631525 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
38631454 TTTAAAATAC
* * *
38631464 TTTTAAAATAATTTTTTTATTTTATAT
1 TTTTAAAATAAATTTTTAATGTT-TAT
38631491 TTTTAAAATAAATTTTTAATGTTTAT
1 TTTTAAAATAAATTTTTAATGTTTAT
*
38631517 TTTAAAAAT
1 TTTTAAAAT
38631526 GGGCCGGGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 11 0.35
27 20 0.65
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (26 bp):
TTTTAAAATAAATTTTTAATGTTTAT
Found at i:38632755 original size:2 final size:2
Alignment explanation
Indices: 38632722--38632746 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38632712 AGTTAAGGCC
38632722 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
38632747 CAAATATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38633442 original size:24 final size:24
Alignment explanation
Indices: 38633410--38633574 Score: 122
Period size: 24 Copynumber: 6.8 Consensus size: 24
38633400 AGCCATGTAA
38633410 CGGGAAGCTCATAAGAGCCATAAT
1 CGGGAAGCTCATAAGAGCCATAAT
**
38633434 CGGGAAGCTCATGCGAGCCA-ACAT
1 CGGGAAGCTCATAAGAGCCATA-AT
38633458 CGGGAAGCTC-TAGAGAGCCATTAAT
1 CGGGAAGCTCATA-AGAGCCA-TAAT
*** * *
38633483 CGGGAAGCTCCGGAGAACCAATTAT
1 CGGGAAGCTCATAAGAGCC-ATAAT
* * * *
38633508 CGAGAAGCTCATACGAGCCGTAAA
1 CGGGAAGCTCATAAGAGCCATAAT
*
38633532 CGAGAAGCTCA-AGAGAGCCATTAAT
1 CGGGAAGCTCATA-AGAGCCA-TAAT
*
38633557 C-GGAATGCTCATGAGAGC
1 CGGGAA-GCTCATAAGAGC
38633575 TAAATAACGG
Statistics
Matches: 109, Mismatches: 22, Indels: 19
0.73 0.15 0.13
Matches are distributed among these distances:
23 3 0.03
24 57 0.52
25 47 0.43
26 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.27, T:0.16
Consensus pattern (24 bp):
CGGGAAGCTCATAAGAGCCATAAT
Found at i:38633453 original size:49 final size:49
Alignment explanation
Indices: 38633381--38633492 Score: 138
Period size: 49 Copynumber: 2.3 Consensus size: 49
38633371 TAAGTGCACG
* * **
38633381 TAATCGGGAAGCTCTTTCAAGCCATGTAACGGGAAGCTCATA-AGAGCCA-
1 TAATCGGGAAGCTCATGCAAGCCA-ACAACGGGAAGCTC-TAGAGAGCCAT
* *
38633430 TAATCGGGAAGCTCATGCGAGCCAACATCGGGAAGCTCTAGAGAGCCAT
1 TAATCGGGAAGCTCATGCAAGCCAACAACGGGAAGCTCTAGAGAGCCAT
38633479 TAATCGGGAAGCTC
1 TAATCGGGAAGCTC
38633493 CGGAGAACCA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
47 2 0.04
48 18 0.33
49 35 0.64
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.19
Consensus pattern (49 bp):
TAATCGGGAAGCTCATGCAAGCCAACAACGGGAAGCTCTAGAGAGCCAT
Found at i:38633498 original size:25 final size:25
Alignment explanation
Indices: 38633381--38633574 Score: 147
Period size: 25 Copynumber: 7.9 Consensus size: 25
38633371 TAAGTGCACG
* *
38633381 TAATCGGGAAGCTCTTTCA-AGCCAT
1 TAATCGGGAAGCTC-ATGAGAGCCAT
*
38633406 GTAA-CGGGAAGCTCATAAGAGCCA-
1 -TAATCGGGAAGCTCATGAGAGCCAT
*
38633430 TAATCGGGAAGCTCATGCGAGCCA-
1 TAATCGGGAAGCTCATGAGAGCCAT
38633454 -ACATCGGGAAGCTC-TAGAGAGCCAT
1 TA-ATCGGGAAGCTCAT-GAGAGCCAT
** *
38633479 TAATCGGGAAGCTCCGGAGAACCAAT
1 TAATCGGGAAGCTCATGAGAGCC-AT
* *
38633505 T-ATCGAGAAGCTCAT-ACGAGCC-G
1 TAATCGGGAAGCTCATGA-GAGCCAT
* * *
38633528 TAAACGAGAAGCTCAAGAGAGCCAT
1 TAATCGGGAAGCTCATGAGAGCCAT
38633553 TAATC-GGAATGCTCATGAGAGC
1 TAATCGGGAA-GCTCATGAGAGC
38633575 TAAATAACGG
Statistics
Matches: 137, Mismatches: 18, Indels: 27
0.75 0.10 0.15
Matches are distributed among these distances:
23 6 0.04
24 60 0.44
25 64 0.47
26 7 0.05
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.18
Consensus pattern (25 bp):
TAATCGGGAAGCTCATGAGAGCCAT
Found at i:38635529 original size:19 final size:18
Alignment explanation
Indices: 38635501--38635537 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
38635491 TTATTTGATC
38635501 TTTAAACCAACTCATATAA
1 TTTAAACCAACTCA-ATAA
*
38635520 TTTAATCCAACTCAATAA
1 TTTAAACCAACTCAATAA
38635538 ACAATTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (18 bp):
TTTAAACCAACTCAATAA
Found at i:38635589 original size:23 final size:23
Alignment explanation
Indices: 38635547--38635590 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
38635537 AACAATTTTC
*
38635547 TATTTATTAAAATATTATTTATT
1 TATTTATTAAAATATAATTTATT
38635570 TATTTATTTAAAATA-AATTTA
1 TATTTA-TTAAAATATAATTTA
38635591 ATTAATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TATTTATTAAAATATAATTTATT
Found at i:38636389 original size:14 final size:14
Alignment explanation
Indices: 38636370--38636407 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
38636360 TATAAATTTT
38636370 TTTATTAATTTATA
1 TTTATTAATTTATA
*
38636384 TTTATTAA-ATATA
1 TTTATTAATTTATA
*
38636397 TTTTTTAATTT
1 TTTATTAATTT
38636408 TTCTAATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTATTAATTTATA
Found at i:38638483 original size:12 final size:12
Alignment explanation
Indices: 38638466--38638492 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
38638456 AGGCGTTGCT
38638466 GAAGATGAAGAG
1 GAAGATGAAGAG
38638478 GAAGATGAAGAG
1 GAAGATGAAGAG
38638490 GAA
1 GAA
38638493 AAGATGGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.41, T:0.07
Consensus pattern (12 bp):
GAAGATGAAGAG
Found at i:38639082 original size:2 final size:2
Alignment explanation
Indices: 38639070--38639099 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
38639060 TTCATAAAGA
38639070 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38639100 AAAGTCTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:38640696 original size:8 final size:8
Alignment explanation
Indices: 38640683--38640725 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
38640673 TCTTGGTATT
38640683 TATATCTA
1 TATATCTA
38640691 TATATCTA
1 TATATCTA
38640699 TATATCTA
1 TATATCTA
*
38640707 TATATATA
1 TATATCTA
* *
38640715 TCTGTCTA
1 TATATCTA
38640723 TAT
1 TAT
38640726 TAGTTCTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.51
Consensus pattern (8 bp):
TATATCTA
Found at i:38650560 original size:11 final size:11
Alignment explanation
Indices: 38650546--38650589 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
38650536 AGATAAATAT
38650546 TATTTTATTAA
1 TATTTTATTAA
*
38650557 TATTTTAATGAGA
1 TATTTT-ATTA-A
*
38650570 TATTTTATTAT
1 TATTTTATTAA
38650581 TATTTTATT
1 TATTTTATT
38650590 TAGTATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
11 15 0.54
12 6 0.21
13 7 0.25
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:38659859 original size:22 final size:22
Alignment explanation
Indices: 38659834--38659876 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
38659824 ATCATGGCTA
38659834 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTC
38659856 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
38659877 GAACAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTC
Found at i:38660770 original size:7 final size:7
Alignment explanation
Indices: 38660758--38660789 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
38660748 GCCTTTGTTC
38660758 TTCAATT
1 TTCAATT
38660765 TTCAATT
1 TTCAATT
38660772 TTCAATT
1 TTCAATT
38660779 TTCAATT
1 TTCAATT
38660786 TTCA
1 TTCA
38660790 TATACTATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.16, G:0.00, T:0.56
Consensus pattern (7 bp):
TTCAATT
Found at i:38669454 original size:17 final size:17
Alignment explanation
Indices: 38669432--38669469 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
38669422 TCACACACCC
38669432 AACAATAGATCAGAAAG
1 AACAATAGATCAGAAAG
38669449 AACAATAGATCAGAAAG
1 AACAATAGATCAGAAAG
38669466 AACA
1 AACA
38669470 GGAGAAAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.61, C:0.13, G:0.16, T:0.11
Consensus pattern (17 bp):
AACAATAGATCAGAAAG
Found at i:38673627 original size:18 final size:18
Alignment explanation
Indices: 38673604--38673641 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
38673594 AATGAATAAA
38673604 TATCCATAAAGAGAACTG
1 TATCCATAAAGAGAACTG
38673622 TATCCATAAAGAGAACTG
1 TATCCATAAAGAGAACTG
38673640 TA
1 TA
38673642 ATTTTAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.24
Consensus pattern (18 bp):
TATCCATAAAGAGAACTG
Found at i:38677171 original size:22 final size:22
Alignment explanation
Indices: 38677146--38677187 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
38677136 ATCTATATCT
*
38677146 TTTTAATTTTTA-ATTTTAAATA
1 TTTT-ATTTTTAGATATTAAATA
38677168 TTTTATTTTTAGATATTAAA
1 TTTTATTTTTAGATATTAAA
38677188 GACACCTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTTATTTTTAGATATTAAATA
Found at i:38679994 original size:32 final size:33
Alignment explanation
Indices: 38679936--38679997 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
38679926 ACTGTAATTG
* *
38679936 TAAAAAGTTATAATTTTTTTAAACAATTTTGAT
1 TAAAAAGTTATAATATTTTAAAACAATTTTGAT
*
38679969 TAAAAA-TTTTAATATTTTAAAACAATTTT
1 TAAAAAGTTATAATATTTTAAAACAATTTT
38679998 ACAACTGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 20 0.77
33 6 0.23
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (33 bp):
TAAAAAGTTATAATATTTTAAAACAATTTTGAT
Found at i:38689279 original size:42 final size:42
Alignment explanation
Indices: 38689210--38689360 Score: 140
Period size: 42 Copynumber: 3.6 Consensus size: 42
38689200 AGGCTATACA
* * * * *
38689210 GAAGCACATAAGTGCTAAGCGGAAACCCATAAGGGTTGAATG
1 GAAGCTCATAAGAGCTAAACGAAAACCCATAAGGGTTAAATG
* * * **
38689252 GAAGCTCATAGGAGCTGAACGAAAACCCAGAAGGGTTAAACA
1 GAAGCTCATAAGAGCTAAACGAAAACCCATAAGGGTTAAATG
* * *
38689294 GAAGCTTAAAAGAGCTAAACGAAAACCCATTAGGGTTAAATG
1 GAAGCTCATAAGAGCTAAACGAAAACCCATAAGGGTTAAATG
* * * *
38689336 AAAACTCATATGAGTTAAACAGAAA
1 GAAGCTCATAAGAGCTAAAC-GAAA
38689361 CTCGAAAGAG
Statistics
Matches: 84, Mismatches: 24, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
42 80 0.95
43 4 0.05
ACGTcount: A:0.44, C:0.16, G:0.23, T:0.17
Consensus pattern (42 bp):
GAAGCTCATAAGAGCTAAACGAAAACCCATAAGGGTTAAATG
Found at i:38694812 original size:20 final size:17
Alignment explanation
Indices: 38694787--38694832 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 17
38694777 ATCAATTATT
38694787 TTTTAAAAATTTTAATATA
1 TTTTAAAAATTTT-ATA-A
*
38694806 GTTTTAATAATTTTATAA
1 -TTTTAAAAATTTTATAA
38694824 TTTTAAAAA
1 TTTTAAAAA
38694833 ATTAATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 8 0.33
18 1 0.04
19 3 0.12
20 12 0.50
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
TTTTAAAAATTTTATAA
Found at i:38700487 original size:992 final size:984
Alignment explanation
Indices: 38697777--38700492 Score: 3497
Period size: 992 Copynumber: 2.8 Consensus size: 984
38697767 GACTAGAATC
38697777 AAACTACGTATTGAAAACCCACAAATGATATTTATGCATGGTGGGAGTCGACTTGATATCACAAA
1 AAACTACGTATTGAAAACCCACAAATGATATTTATGCATGGTGGGAGTCGACTTGATATCACAAA
* * *
38697842 GTTTTTACTTTGCCA--T--CAA-ACCAC--TGACAAAAGAATTTTAACATTAAACTAAACATCG
66 GTTTCTACTTTGCCATCTAACAAGACCACATTGACAAAAGAATTTTAATATTAAAAT-AA-A-C-
* * * * *
38697900 ATCAAAGGTTAAGCGACTTAGACTTGAGCAATAAATTCTTTCATTATCTAAATTTTTTTCAATAC
127 ATCAAAGGTTAAGCGACTTAGACATAAGCAAGAAATTCTTTAATTATCTAAATTTATTTCAATAC
* * *
38697965 AATTGTTGAATAATTCTATTAGTAAAATATAATTTAAATATTATACATTATATTTTGAAAGTTCT
192 AATCGTTGAATAATTCTACTAGTAAAATATAATTTAAATATTATATATTATATTTTGAAAGTTCT
* * * * **
38698030 AAAACAATATTTGTAAGCAAATTGAGTAATGCCAACTATTTTCGACACTGATGATTAACAATAAA
257 AAAACGATACTTGCAAGCAAATTGAGTAGTGCCAACTATTTTCGACACTGATGAAGAACAATAAA
* * * * *
38698095 GAACACAAC---ATGTTTGCGTAGTTTAGTTTCCATACATTAGCAAGGCCGTAGCTGTGAGATAA
322 GAACACAACAATATGTTTGCGTAGTTTAGTTTCCATACATCAACGAGGCCTTAGCAGTGAGATAA
* * * * * *
38698157 TCTATTATCTTAGTATTTTG-TACAACAAATAGTTACAAACACAAGCTTTCACAAAGATAGGATC
387 TCCATCATCTTAGCACTTTGTTACAACAAGTAGTTACAAACACAA-CTTTCACAAAAATAGGATC
* * * * * *
38698221 ACACTTTTGTACTTAAGATCTAGACAAGTTCCATTTAAATTTCCTCCCCGCATATATAGGAT-AA
451 TCACTTTTGTACCTAAGATCTAGACAAGTTCC-TCTAAATTTCCTCCCTGAAAATATAGGATAAA
* * * *
38698285 AACC---CAACACAATTGATTTTATACTCAGTGCAATCTAACTAAACATTCCTCACTAAACAGAA
515 AACCAAGTAACACACTTGATTTTACACTCAGTG-AATCTAAATAAACATTCCTCACTAAACAGAA
*
38698347 ATAAGTGCTCTCAAATTAG---------TA-T-AGTCTTCTCAATTTATAATGAAATTAGAC--T
579 ATAAGTGCTCTCAAATTAGTACATAACCTATTAAGTCTTCTCAATTTATAATGAAATAAGACTGT
* * *
38698399 ----TGCTAGATCAGTGACAATCAATCTTCCAACTAAAACAATAAGATAATCAGCTCTAAGAATA
644 AACATGCTAGATCAATGACAATCAATCTTCCAACTAAAACAACAAGATAATCAGCTCTAACAATA
* *
38698460 ATGGATTCGGATTCTTTTTAGTTTAAAATTTTTATTTACTTTTACTTACAAAAACCCTTTAAAAA
709 ATGGATTCGGATTCTTTTTAATTTTAAATTTTTATTTAC---T--TT---AAAA--CTTTAAAAA
* *
38698525 GATAATTTTAATATTTTTTGAAGATACAATTATAATTAATATACCTATATAACAATAATCACAAT
764 GATAATTTTAATAATTTTTGAAGATACAATTATAATTAATATACCTATATAACAATAATAACAAT
* *
38698590 TAGTTAGTGCAATACATAAATAAAATCACAAGTACAATCGATACATCCATACAACTACGACTAGA
829 TAATTAGTGCAATACATAAACAAAATCACAAGTACAATCGATACATCCATACAACTACGACTAGA
*
38698655 ATCAACCAAAGCAATTTAATGCACAAAGAGACATATTAATAATCAAAATATATATAGATATGGAA
894 ATCAACCAAAGCAATTTAATGCACAAAGAGACATATTAATAATCAAAATATATACAGATATGGAA
*
38698720 TGCACGTATTTTGATTTAAATAAAAA
959 GGCACGTATTTTGATTTAAATAAAAA
* * * * *
38698746 AAACTATGTATTAAAAACCTACAAATGATATTTATGCATGGTTGGAGTCGACTTGGA-ATAACAA
1 AAACTACGTATTGAAAACCCACAAATGATATTTATGCATGGTGGGAGTCGACTT-GATATCACAA
*
38698810 AGTTTCTACTTTGCCATCAAACCAAGACCACATTGACAAAAGAATTTTAATATTAAAA-AAACAT
65 AGTTTCTACTTTGCCATCTAA-CAAGACCACATTGACAAAAGAATTTTAATATTAAAATAAACAT
* * * * *
38698874 CAAAAGTTAAGTGACTTAGAAATAAGCAAGAAATTATTTTATTATCTAAATTTGA-TTCAATACA
129 CAAAGGTTAAGCGACTTAGACATAAGCAAGAAATTCTTTAATTATCTAAATTT-ATTTCAATACA
* * *
38698938 ATCATTGAATAATTCTACTACTAAAATATAATTTAAATTTTATATATTATATTTTGAAAGTTCTA
193 ATCGTTGAATAATTCTACTAGTAAAATATAATTTAAATATTATATATTATATTTTGAAAGTTCTA
* * * * * *
38699003 GAACGATACTTGCAAGCAAATTAAATAGTGCCAACTATTTTCGGCACTCATGAAGAACAATAAAT
258 AAACGATACTTGCAAGCAAATTGAGTAGTGCCAACTATTTTCGACACTGATGAAGAACAATAAAG
* * * *
38699068 AACACAACAATATGTTTGTGCATTTTAGTTTGCATACATCAACGAGGCCTTAGCAGTGAGATAAT
323 AACACAACAATATGTTTGCGTAGTTTAGTTTCCATACATCAACGAGGCCTTAGCAGTGAGATAAT
* *
38699133 TCATCATCTTAGCACTTTG-TACAATAAGTAGTTACAAACACAAACTTTCACAAAAATAGGATCT
388 CCATCATCTTAGCACTTTGTTACAACAAGTAGTTACAAACAC-AACTTTCACAAAAATAGGATCT
* * * * *
38699197 CACTTTTGTACCTAAGAT-TAAGACAAGTCCCCTCTAAATTTCATCACTAAAAATATAAGATAAA
452 CACTTTTGTACCTAAGATCT-AGACAAGT-TCCTCTAAATTTCCTCCCTGAAAATATAGGATAAA
* * * *
38699261 AACCAAGTAACACACTAGATTTTACACTAAGTGCAGA-CTAAATAAACATTCCTTAATAAACAGA
515 AACCAAGTAACACACTTGATTTTACACTCAGTG-A-ATCTAAATAAACATTCCTCACTAAACAGA
* * * * *
38699325 AATAAGTGTTCTCAAATCAGTACATAACCTATACAAATCTTCTCAATTTATAATGAAACAAGACT
578 AATAAGTGCTCTCAAATTAGTACATAACCTAT-TAAGTCTTCTCAATTTATAATGAAATAAGACT
* * **
38699390 CGCTAACATACTAGATCAATGACAATTAATCTTCCAACTAAAACAACAAGATAATCAGCTAAAAC
642 -G-TAACATGCTAGATCAATGACAATCAATCTTCCAACTAAAACAACAAGATAATCAGCTCTAAC
* * * *
38699455 AATAATGGATTTGGATTCTTTTTAATTTTAAATCTTTATTTACTTT-AAA--TTATGAAA-ATCA
705 AATAATGGATTCGGATTCTTTTTAATTTTAAATTTTTATTTACTTTAAAACTTTA-AAAAGATAA
* * *
38699516 TTTTAATAATTTTTGAAGTTACAATTATAATTAATATATCTATGTAACAATAATAACAATTAATT
769 TTTTAATAATTTTTGAAGATACAATTATAATTAATATACCTATATAACAATAATAACAATTAATT
* * ** * * * *
38699581 AGTGCAATACATAAACAAAATCACGATTACAATCGATATGTCCGTACAATTATGACTAGAATTAA
834 AGTGCAATACATAAACAAAATCACAAGTACAATCGATACATCCATACAACTACGACTAGAATCAA
* * * **
38699646 CCAATGGAATTTAATGCACAAACG-GACAT-TT-ATAATCGACGTATATACAGATATGGAAGGCA
899 CCAAAGCAATTTAATGCACAAA-GAGACATATTAATAATCAAAATATATACAGATATGGAAGGCA
*
38699708 CGTGTTTTGATTTAAATAAATAAAAA
963 CGTATTTTGA-TT---TAAATAAAAA
* * *
38699734 AAACTACGTATTGAAAACCCACAAATGATATTTATGCATGGTGGGAGTCAACCTGTTATCACAAA
1 AAACTACGTATTGAAAACCCACAAATGATATTTATGCATGGTGGGAGTCGACTTGATATCACAAA
*
38699799 GTTTCTATTTTGCCATCTAACGAAGACCACATTGACAAAAGAATTTTAATATTAAAATAAACATC
66 GTTTCTACTTTGCCATCTAAC-AAGACCACATTGACAAAAGAATTTTAATATTAAAATAAACATC
* *
38699864 AAAGGTTAAGCCACTTAGACATAAGCAAGAAATTCTTTAATTATCTAAATTTATTTCACTACAAT
130 AAAGGTTAAGCGACTTAGACATAAGCAAGAAATTCTTTAATTATCTAAATTTATTTCAATACAAT
* * *
38699929 CGTTGAATAATTCTACTAGTAAAATTTAATTTAAATATTATATATTATATTTTAAAAATTCTAAA
195 CGTTGAATAATTCTACTAGTAAAATATAATTTAAATATTATATATTATATTTTGAAAGTTCTAAA
* *
38699994 ACGATACTTGCAAGCAAATTGAGTAGTGTCAACTATTTTCGACAATGATGAAGAACAATAAAGAA
260 ACGATACTTGCAAGCAAATTGAGTAGTGCCAACTATTTTCGACACTGATGAAGAACAATAAAGAA
38700059 CACAACAATATGTTTGCGTAGTTTAGTTTCCATACATCAACGAGGCCTTAGCAGTGAGATAATCC
325 CACAACAATATGTTTGCGTAGTTTAGTTTCCATACATCAACGAGGCCTTAGCAGTGAGATAATCC
*
38700124 ATCATCTTAGCACTTTGTATAACAACAAGTAGTTACAAACACTAACTCTCACAAAAATAGGATCT
390 ATCATCTTAGCACTTTGT-T-ACAACAAGTAGTTACAAACAC-AACTTTCACAAAAATAGGATCT
* *
38700189 CACTTTTATACCTGAGATCTAGACAAGTTCTCTCTAAATTTCCTCCCTGAAAATATAGGATAAAA
452 CACTTTTGTACCTAAGATCTAGACAAGTTC-CTCTAAATTTCCTCCCTGAAAATATAGGATAAAA
* * * *
38700254 ACCAAGTAACACACTTGATTCTACACTCAGTGAACTCTAAATAAACTTTCCTCGCTAAGCAGAAA
516 ACCAAGTAACACACTTGATTTTACACTCAGTGAA-TCTAAATAAACATTCCTCACTAAACAGAAA
* *
38700319 TAAATGCTCTCAAATTAGTACATAACCTATGTAAGTATTCTCAATTTATAATGAAATAAGACTTG
580 TAAGTGCTCTCAAATTAGTACATAACCTAT-TAAGTCTTCTCAATTTATAATGAAATAAGAC-TG
* *
38700384 TTAACATGCTAAATTAATGACAATCAATCTTCCAACTAAAACAACAAGATAATCAGCTCTAACAA
643 -TAACATGCTAGATCAATGACAATCAATCTTCCAACTAAAACAACAAGATAATCAGCTCTAACAA
38700449 TAATGGATTCGGATTCTTTTTAATTTTAAATTTTTATTTACTTT
707 TAATGGATTCGGATTCTTTTTAATTTTAAATTTTTATTTACTTT
38700493 TAATCTGAAC
Statistics
Matches: 1503, Mismatches: 185, Indels: 95
0.84 0.10 0.05
Matches are distributed among these distances:
969 71 0.05
970 2 0.00
972 176 0.12
973 1 0.00
974 5 0.00
975 150 0.10
976 10 0.01
977 23 0.02
979 65 0.04
980 1 0.00
984 35 0.02
985 4 0.00
986 146 0.10
987 6 0.00
988 121 0.08
989 256 0.17
990 4 0.00
991 29 0.02
992 303 0.20
993 2 0.00
994 2 0.00
995 1 0.00
996 1 0.00
999 89 0.06
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (984 bp):
AAACTACGTATTGAAAACCCACAAATGATATTTATGCATGGTGGGAGTCGACTTGATATCACAAA
GTTTCTACTTTGCCATCTAACAAGACCACATTGACAAAAGAATTTTAATATTAAAATAAACATCA
AAGGTTAAGCGACTTAGACATAAGCAAGAAATTCTTTAATTATCTAAATTTATTTCAATACAATC
GTTGAATAATTCTACTAGTAAAATATAATTTAAATATTATATATTATATTTTGAAAGTTCTAAAA
CGATACTTGCAAGCAAATTGAGTAGTGCCAACTATTTTCGACACTGATGAAGAACAATAAAGAAC
ACAACAATATGTTTGCGTAGTTTAGTTTCCATACATCAACGAGGCCTTAGCAGTGAGATAATCCA
TCATCTTAGCACTTTGTTACAACAAGTAGTTACAAACACAACTTTCACAAAAATAGGATCTCACT
TTTGTACCTAAGATCTAGACAAGTTCCTCTAAATTTCCTCCCTGAAAATATAGGATAAAAACCAA
GTAACACACTTGATTTTACACTCAGTGAATCTAAATAAACATTCCTCACTAAACAGAAATAAGTG
CTCTCAAATTAGTACATAACCTATTAAGTCTTCTCAATTTATAATGAAATAAGACTGTAACATGC
TAGATCAATGACAATCAATCTTCCAACTAAAACAACAAGATAATCAGCTCTAACAATAATGGATT
CGGATTCTTTTTAATTTTAAATTTTTATTTACTTTAAAACTTTAAAAAGATAATTTTAATAATTT
TTGAAGATACAATTATAATTAATATACCTATATAACAATAATAACAATTAATTAGTGCAATACAT
AAACAAAATCACAAGTACAATCGATACATCCATACAACTACGACTAGAATCAACCAAAGCAATTT
AATGCACAAAGAGACATATTAATAATCAAAATATATACAGATATGGAAGGCACGTATTTTGATTT
AAATAAAAA
Found at i:38714888 original size:2 final size:2
Alignment explanation
Indices: 38714881--38714908 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38714871 CATTGGTTTC
38714881 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38714909 TAAAAAAGCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38720359 original size:139 final size:139
Alignment explanation
Indices: 38720109--38720389 Score: 544
Period size: 139 Copynumber: 2.0 Consensus size: 139
38720099 TCCGTTTAAC
* *
38720109 TAAAGCCCATGATTATTAGAGACAGAAGTATGGTAAATTTTGATGCTTCATGTCGTACAAAAGAC
1 TAAAGACCATGATTATTAGAGACAGAAGTATGGTAAATTTGGATGCTTCATGTCGTACAAAAGAC
38720174 GAGTAAGAAAGATAGCCCATTATAATAATGTCTGATATGATAGCATATGTTCTTTGTAAACCTAA
66 GAGTAAGAAAGATAGCCCATTATAATAATGTCTGATATGATAGCATATGTTCTTTGTAAACCTAA
38720239 GCTTCAAAG
131 GCTTCAAAG
38720248 TAAAGACCATGATTATTAGAGACAGAAGTATGGTAAATTTGGATGCTTCATGTCGTACAAAAGAC
1 TAAAGACCATGATTATTAGAGACAGAAGTATGGTAAATTTGGATGCTTCATGTCGTACAAAAGAC
38720313 GAGTAAGAAAGATAGCCCATTATAATAATGTCTGATATGATAGCATATGTTCTTTGTAAACCTAA
66 GAGTAAGAAAGATAGCCCATTATAATAATGTCTGATATGATAGCATATGTTCTTTGTAAACCTAA
38720378 GCTTCAAAG
131 GCTTCAAAG
38720387 TAA
1 TAA
38720390 TTTATAAGAA
Statistics
Matches: 140, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 140 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (139 bp):
TAAAGACCATGATTATTAGAGACAGAAGTATGGTAAATTTGGATGCTTCATGTCGTACAAAAGAC
GAGTAAGAAAGATAGCCCATTATAATAATGTCTGATATGATAGCATATGTTCTTTGTAAACCTAA
GCTTCAAAG
Found at i:38723822 original size:136 final size:136
Alignment explanation
Indices: 38723641--38723911 Score: 526
Period size: 136 Copynumber: 2.0 Consensus size: 136
38723631 ATTTTTTGGG
38723641 CGTTTGTGAAATCAAACCTAGCTCGCTTCATTACAATCGCGGAATAATTATAAATTACAG-AAAA
1 CGTTTGTGAAATCAAACCTAGCTCGCTTCATTACAATCGCGGAATAATTATAAATTACAGAAAAA
38723705 AAAATCAATAGAAAGTCGGGATGAAAGATTTTTTTCGCTTAAAATCATGTCGAGGCAGAGAATCA
66 AAAATCAATAGAAAGTCGGGATGAAAGA-TTTTTTCGCTTAAAATCATGTCGAGGCAGAGAATCA
38723770 AAAAACT
130 AAAAACT
38723777 CGTTTGTGAAATCAAACCTAGCTCGCTTCATTACAATCGCGGAATAATTATAAATTACAGAAAAA
1 CGTTTGTGAAATCAAACCTAGCTCGCTTCATTACAATCGCGGAATAATTATAAATTACAGAAAAA
38723842 AAAATCAATAGAAAGTCGGGATGAAAGATTTTTTCGCTTAAAATCATGTCGAGGCAGAGAATCAA
66 AAAATCAATAGAAAGTCGGGATGAAAGATTTTTTCGCTTAAAATCATGTCGAGGCAGAGAATCAA
38723907 AAAAC
131 AAAAC
38723912 CCCACACAAA
Statistics
Matches: 134, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
136 102 0.76
137 32 0.24
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (136 bp):
CGTTTGTGAAATCAAACCTAGCTCGCTTCATTACAATCGCGGAATAATTATAAATTACAGAAAAA
AAAATCAATAGAAAGTCGGGATGAAAGATTTTTTCGCTTAAAATCATGTCGAGGCAGAGAATCAA
AAAACT
Found at i:38740369 original size:21 final size:21
Alignment explanation
Indices: 38740340--38740379 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
38740330 ACATATACAA
38740340 AAACAACTT-AAAAACACTAGT
1 AAACAACTTGAAAAA-ACTAGT
*
38740361 AAACCACTTGAAAAAACTA
1 AAACAACTTGAAAAAACTA
38740380 AAACACCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.57, C:0.20, G:0.05, T:0.17
Consensus pattern (21 bp):
AAACAACTTGAAAAAACTAGT
Found at i:38741226 original size:11 final size:11
Alignment explanation
Indices: 38741204--38741254 Score: 77
Period size: 11 Copynumber: 4.6 Consensus size: 11
38741194 AACAAATCCT
38741204 CTCTCAAATTTC
1 CTCTC-AATTTC
*
38741216 CTCTTAATTTC
1 CTCTCAATTTC
38741227 CTCTCAATTTC
1 CTCTCAATTTC
38741238 CTCTCAATTT-
1 CTCTCAATTTC
38741248 CTCTCAA
1 CTCTCAA
38741255 ATTTATATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
10 7 0.19
11 26 0.70
12 4 0.11
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.45
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:38741257 original size:22 final size:22
Alignment explanation
Indices: 38741203--38741258 Score: 87
Period size: 22 Copynumber: 2.5 Consensus size: 22
38741193 AAACAAATCC
*
38741203 TCTCTCAAATTTCCTCTTAATT
1 TCTCTCAAATTTCCTCTCAATT
38741225 TCCTCTC-AATTTCCTCTCAATT
1 T-CTCTCAAATTTCCTCTCAATT
38741247 TCTCTCAAATTT
1 TCTCTCAAATTT
38741259 ATATTTAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 5 0.16
22 21 0.68
23 5 0.16
ACGTcount: A:0.21, C:0.30, G:0.00, T:0.48
Consensus pattern (22 bp):
TCTCTCAAATTTCCTCTCAATT
Found at i:38742062 original size:7 final size:8
Alignment explanation
Indices: 38742046--38742071 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
38742036 TTGAAAGATG
38742046 AAGTGAAA
1 AAGTGAAA
38742054 AAGTGAAA
1 AAGTGAAA
38742062 AAGTGAAA
1 AAGTGAAA
38742070 AA
1 AA
38742072 AAAATCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.23, T:0.12
Consensus pattern (8 bp):
AAGTGAAA
Found at i:38742700 original size:18 final size:18
Alignment explanation
Indices: 38742677--38742719 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
38742667 TTTTTATTTT
38742677 TTTTAAAATATTTTTTAA
1 TTTTAAAATATTTTTTAA
** * *
38742695 TTTTAATTTTTTTTTTAC
1 TTTTAAAATATTTTTTAA
38742713 TTTTAAA
1 TTTTAAA
38742720 GGGTAATGAC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTAAAATATTTTTTAA
Found at i:38746125 original size:18 final size:18
Alignment explanation
Indices: 38746089--38746124 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
38746079 ATTAAAGGAG
*
38746089 GGAAGAAGAAAGGTAAAA
1 GGAAGAAGAAAGATAAAA
38746107 GGAAGAAGAAAAGATAAA
1 GGAAGAAG-AAAGATAAA
38746125 GTACTGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.64, C:0.00, G:0.31, T:0.06
Consensus pattern (18 bp):
GGAAGAAGAAAGATAAAA
Found at i:38751271 original size:23 final size:22
Alignment explanation
Indices: 38751228--38751271 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
38751218 TTCTAAGTCG
38751228 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
38751251 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
38751272 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:38751388 original size:45 final size:45
Alignment explanation
Indices: 38751324--38751409 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
38751314 CTCGATGGAT
*
38751324 TCAGCACATAGCAACCACCTTATTAATCAATGATGTCCGGTAGAA
1 TCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGGTAGAA
* *
38751369 TCAGCACATAGCAACCACCTTACTAATTAATGATGTTCGGT
1 TCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGGT
38751410 TCACATAGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (45 bp):
TCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGGTAGAA
Found at i:38751473 original size:51 final size:50
Alignment explanation
Indices: 38751406--38751601 Score: 205
Period size: 51 Copynumber: 3.9 Consensus size: 50
38751396 TAATGATGTT
* * **
38751406 CGGTTCACATAGTAGCCTGCACATAGTACTACACATATGACCATTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATC
* * * * * *
38751457 CGATACATGTAGTAGCCTACACATAGTACTACACACGTGATCGAAACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATC
* * * * ** *
38751508 TGGTACGCATAGTAGCCTGCACATAGTACTACACATGCAACC-TATCATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATACCA-TC
38751558 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
38751602 CATTTTCACT
Statistics
Matches: 113, Mismatches: 29, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
49 2 0.02
50 39 0.35
51 70 0.62
52 2 0.02
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATACCATC
Found at i:38751595 original size:101 final size:101
Alignment explanation
Indices: 38751413--38751597 Score: 282
Period size: 101 Copynumber: 1.8 Consensus size: 101
38751403 GTTCGGTTCA
** *
38751413 CATAGTAGCCTGCACATAGTACTACACATATGACCATTACCATCCGATACATGTAGTAGCCTACA
1 CATAGTAGCCTGCACATAGTACTACACATACAACCA-TACCATCCGATACACGTAGTAGCCTACA
38751478 CATAGTACTACACACGTGATCGAAACTATCTGGTACG
65 CATAGTACTACACACGTGATCGAAACTATCTGGTACG
* * * *
38751515 CATAGTAGCCTGCACATAGTACTACACATGCAACC-TATCATTCCGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATACAACCATACCA-TCCGATACACGTAGTAGCCTACA
38751579 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
38751598 CCATCATTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
100 4 0.05
101 39 0.52
102 32 0.43
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATACAACCATACCATCCGATACACGTAGTAGCCTACAC
ATAGTACTACACACGTGATCGAAACTATCTGGTACG
Found at i:38758022 original size:9 final size:9
Alignment explanation
Indices: 38758010--38758035 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
38758000 GTTGTTGTTG
38758010 TTATTATTC
1 TTATTATTC
38758019 TTATTATTC
1 TTATTATTC
38758028 TTATTATT
1 TTATTATT
38758036 ATACGACTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (9 bp):
TTATTATTC
Found at i:38763008 original size:14 final size:14
Alignment explanation
Indices: 38762956--38763008 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
38762946 ACTAAAAATT
38762956 TATTTTAAAAATAAA
1 TATTTTAAAAA-AAA
* *
38762971 AATTTTAAAAAAAG
1 TATTTTAAAAAAAA
38762985 TATTTT---AAAAA
1 TATTTTAAAAAAAA
38762996 TATTTTAAAAAAA
1 TATTTTAAAAAAA
38763009 TAAAAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
11 10 0.32
14 11 0.35
15 10 0.32
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (14 bp):
TATTTTAAAAAAAA
Found at i:38764507 original size:21 final size:21
Alignment explanation
Indices: 38764483--38764522 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
38764473 TACTGGGAAA
38764483 TGACCAAAATAAAAATAATTG
1 TGACCAAAATAAAAATAATTG
*
38764504 TGACCAAAATAGAAATAAT
1 TGACCAAAATAAAAATAAT
38764523 AAAAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.23
Consensus pattern (21 bp):
TGACCAAAATAAAAATAATTG
Found at i:38768331 original size:2 final size:2
Alignment explanation
Indices: 38768324--38768350 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38768314 GAAATAAGAC
38768324 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
38768351 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38768355 original size:2 final size:2
Alignment explanation
Indices: 38768350--38768379 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
38768340 ATATATATAT
38768350 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
38768380 GAGGGACGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38771786 original size:20 final size:21
Alignment explanation
Indices: 38771746--38771789 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
38771736 CTTCAAGCAC
38771746 TTATAATTAAATATAATATAA
1 TTATAATTAAATATAATATAA
* *
38771767 TTATATTTAAATA-CATATAA
1 TTATAATTAAATATAATATAA
38771787 TTA
1 TTA
38771790 AAATCTTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TTATAATTAAATATAATATAA
Found at i:38773466 original size:6 final size:6
Alignment explanation
Indices: 38773455--38773485 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
38773445 TTCCACTATC
38773455 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT T
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT T
38773486 GGTAATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTAAT
Found at i:38780123 original size:36 final size:36
Alignment explanation
Indices: 38780076--38780152 Score: 154
Period size: 36 Copynumber: 2.1 Consensus size: 36
38780066 AATATGTAAA
38780076 AATTTTATTAATTCAAATAGTTGGAAACATTACAAG
1 AATTTTATTAATTCAAATAGTTGGAAACATTACAAG
38780112 AATTTTATTAATTCAAATAGTTGGAAACATTACAAG
1 AATTTTATTAATTCAAATAGTTGGAAACATTACAAG
38780148 AATTT
1 AATTT
38780153 GCAACGAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (36 bp):
AATTTTATTAATTCAAATAGTTGGAAACATTACAAG
Found at i:38792510 original size:2 final size:2
Alignment explanation
Indices: 38792505--38792533 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
38792495 ATATATAAAT
38792505 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
38792534 AGTTTTTTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38797410 original size:19 final size:21
Alignment explanation
Indices: 38797386--38797432 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
38797376 ATAATTTGTT
* *
38797386 TTTCAAT-CATA-AAATTTGG
1 TTTCAATCCATAGAAAGTTGA
38797405 TTTCAATCCATAGAAAGTTGA
1 TTTCAATCCATAGAAAGTTGA
38797426 TTTCAAT
1 TTTCAAT
38797433 AAATTTTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.29
20 4 0.17
21 13 0.54
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (21 bp):
TTTCAATCCATAGAAAGTTGA
Found at i:38800910 original size:23 final size:24
Alignment explanation
Indices: 38800881--38800925 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
38800871 AAACTGAACA
38800881 AAAATAAAATAAAAAT-AGAAAAC
1 AAAATAAAATAAAAATGAGAAAAC
* *
38800904 AAAATAAACTGAAAATGAGAAA
1 AAAATAAAATAAAAATGAGAAA
38800926 TAAACATGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.73, C:0.04, G:0.09, T:0.13
Consensus pattern (24 bp):
AAAATAAAATAAAAATGAGAAAAC
Found at i:38802149 original size:14 final size:14
Alignment explanation
Indices: 38802130--38802156 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38802120 AAGCACATAG
38802130 AGTGTACAAAACTA
1 AGTGTACAAAACTA
38802144 AGTGTACAAAACT
1 AGTGTACAAAACT
38802157 GTAATCCGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (14 bp):
AGTGTACAAAACTA
Found at i:38802257 original size:25 final size:24
Alignment explanation
Indices: 38802229--38802290 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
38802219 CATATAACAA
* * *
38802229 GAAGCTCATGTGAGTCGTATATCGG
1 GAAGCTCATGAGAATCATA-ATCGG
*
38802254 GAAGCTCATAAGAATCATAATCGG
1 GAAGCTCATGAGAATCATAATCGG
38802278 GAAGCTCATGAGA
1 GAAGCTCATGAGA
38802291 GAACCTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 17 0.53
25 15 0.47
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (24 bp):
GAAGCTCATGAGAATCATAATCGG
Found at i:38807525 original size:81 final size:81
Alignment explanation
Indices: 38807350--38807529 Score: 229
Period size: 81 Copynumber: 2.2 Consensus size: 81
38807340 AAAGGTTGTT
** * *
38807350 AAATGACTGAAATACCCTCGAAGGGTAAAATTACTGAAATCCCCCTGAAGGGTAAAATTACCGAA
1 AAATGACCAAAATACCCTCGAAGGGTAAAATTACTGAAATACCCCTGAAAGGTAAAATTACCGAA
38807415 ATACCTTCAAAGAGTA
66 ATACCTTCAAAGAGTA
* * * * *
38807431 AAATTACCGAAATACCTTCGATGGGTAAAATTACTGAAATACCCCT-ATAAGGTAAAATTACTGA
1 AAATGACCAAAATACCCTCGAAGGGTAAAATTACTGAAATACCCCTGA-AAGGTAAAATTACCGA
*
38807495 AATACCTT-AATAGGGTA
65 AATACCTTCAA-AGAGTA
*
38807512 GAATGACCAAAATACCCT
1 AAATGACCAAAATACCCT
38807530 TATTAGTGTA
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
80 3 0.04
81 82 0.96
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (81 bp):
AAATGACCAAAATACCCTCGAAGGGTAAAATTACTGAAATACCCCTGAAAGGTAAAATTACCGAA
ATACCTTCAAAGAGTA
Found at i:38807583 original size:27 final size:26
Alignment explanation
Indices: 38807350--38807665 Score: 179
Period size: 27 Copynumber: 11.7 Consensus size: 26
38807340 AAAGGTTGTT
*
38807350 AAATGACTGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTC-AAGGGTA
* * * *
38807377 AAATTACTGAAATCCCCCTGAAGGGTA
1 AAATGACCGAAAT-ACCCTCAAGGGTA
* * *
38807404 AAATTACCGAAATACCTTCAAAGAGTA
1 AAATGACCGAAATACCCTC-AAGGGTA
* * *
38807431 AAATTACCGAAATACCTTCGATGGGTA
1 AAATGACCGAAATACCCTC-AAGGGTA
* * *
38807458 AAATTACTGAAATACCC-CTATAAGGTA
1 AAATGACCGAAATACCCTC-A-AGGGTA
* * * *
38807485 AAATTACTGAAATACCTTAATAGGGTA
1 AAATGACCGAAATACCCTCA-AGGGTA
* * * *
38807512 GAATGACCAAAATACCCTTATTAGTGTA
1 AAATGACCGAAATACCCTCA--AGGGTA
* *
38807540 AAATAACCAAAATACCCTCACAGGGTA
1 AAATGACCGAAATACCCTCA-AGGGTA
*
38807567 AAATGACCGAAATACCCCCACAGGGTA
1 AAATGACCGAAATACCCTCA-AGGGTA
* * * *
38807594 AAA-GAACCGTAATACCCCCATAAGGTT
1 AAATG-ACCGAAATACCCTCA-AGGGTA
** *
38807621 AAATGGTCGAAATACTCCTGTAA-GGTA
1 AAATGACCGAAATAC-CCT-CAAGGGTA
*
38807648 AAATGACCGTAATACCCT
1 AAATGACCGAAATACCCT
38807666 TGGAGGGTAA
Statistics
Matches: 233, Mismatches: 47, Indels: 19
0.78 0.16 0.06
Matches are distributed among these distances:
26 9 0.04
27 192 0.82
28 31 0.13
29 1 0.00
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (26 bp):
AAATGACCGAAATACCCTCAAGGGTA
Found at i:38807728 original size:24 final size:24
Alignment explanation
Indices: 38807697--38807793 Score: 126
Period size: 24 Copynumber: 4.0 Consensus size: 24
38807687 TCCCCTCGAG
* *
38807697 TGTAAATGATTGATTTGTCCGTGA
1 TGTAAATGACTGATTTGTCTGTGA
38807721 TGTAAATGACTGATTTGTCTGTGA
1 TGTAAATGACTGATTTGTCTGTGA
*
38807745 TTTAAATGACTGATTTGTCTGTGAA
1 TGTAAATGACTGATTTGTCTGTG-A
*
38807770 TGGT--ATGACTGATTTGTCTATGA
1 T-GTAAATGACTGATTTGTCTGTGA
38807793 T
1 T
38807794 TTGTATGATT
Statistics
Matches: 66, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
23 2 0.03
24 61 0.92
25 2 0.03
26 1 0.02
ACGTcount: A:0.25, C:0.08, G:0.24, T:0.43
Consensus pattern (24 bp):
TGTAAATGACTGATTTGTCTGTGA
Found at i:38807799 original size:24 final size:24
Alignment explanation
Indices: 38807702--38807807 Score: 113
Period size: 24 Copynumber: 4.4 Consensus size: 24
38807692 TCGAGTGTAA
* * * **
38807702 ATGATTGATTTGTCCGTGATGTAA
1 ATGACTGATTTGTCTGTGATTTGT
**
38807726 ATGACTGATTTGTCTGTGATTTAA
1 ATGACTGATTTGTCTGTGATTTGT
* *
38807750 ATGACTGATTTGTCTGTGAATGGT
1 ATGACTGATTTGTCTGTGATTTGT
*
38807774 ATGACTGATTTGTCTATGATTTGT
1 ATGACTGATTTGTCTGTGATTTGT
*
38807798 ATGATTGATT
1 ATGACTGATT
38807808 CTGAGTATGG
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 71 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.45
Consensus pattern (24 bp):
ATGACTGATTTGTCTGTGATTTGT
Found at i:38807807 original size:48 final size:47
Alignment explanation
Indices: 38807699--38807807 Score: 139
Period size: 48 Copynumber: 2.3 Consensus size: 47
38807689 CCCTCGAGTG
*
38807699 TAAATGATTGATTTGTCCGTGATGTAAATGACTGATTTGTCTGTGATT
1 TAAATGATTGATTTGTCCGTGATGT-AATGACTGATTTGTCTATGATT
* *
38807747 TAAATGACTGATTTGTCTGTGAATGGT-ATGACTGATTTGTCTATGATT
1 TAAATGATTGATTTGTCCGTG-AT-GTAATGACTGATTTGTCTATGATT
**
38807795 TGTATGATTGATT
1 TAAATGATTGATT
38807808 CTGAGTATGG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
48 49 0.92
49 2 0.04
50 2 0.04
ACGTcount: A:0.25, C:0.07, G:0.23, T:0.45
Consensus pattern (47 bp):
TAAATGATTGATTTGTCCGTGATGTAATGACTGATTTGTCTATGATT
Found at i:38808040 original size:32 final size:32
Alignment explanation
Indices: 38807950--38808047 Score: 108
Period size: 32 Copynumber: 3.1 Consensus size: 32
38807940 TTTGCTACGA
*
38807950 TGCTACTGATGGCTTTGTGTCGATCATATTA-
1 TGCTACTGATGGCTTTGTGCCGATCATATTAC
* * * * * *
38807981 TCGTTATTGATGGCTGTGTACTGATCATATCAC
1 T-GCTACTGATGGCTTTGTGCCGATCATATTAC
*
38808014 TGCTACTGATGGCTTTGTGCCAATCATATTAC
1 TGCTACTGATGGCTTTGTGCCGATCATATTAC
38808046 TG
1 TG
38808048 TATTTATGGC
Statistics
Matches: 51, Mismatches: 14, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
31 1 0.02
32 49 0.96
33 1 0.02
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.40
Consensus pattern (32 bp):
TGCTACTGATGGCTTTGTGCCGATCATATTAC
Found at i:38815420 original size:17 final size:17
Alignment explanation
Indices: 38815379--38815431 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
38815369 ATAGAAAGTC
* *
38815379 AAAGATATGGGTATTAG
1 AAAGATATGGGTATCAA
* *
38815396 AAATATATAGGTATCAA
1 AAAGATATGGGTATCAA
38815413 AAAGATATGGGTATCAA
1 AAAGATATGGGTATCAA
38815430 AA
1 AA
38815432 TCTGAGATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.49, C:0.04, G:0.21, T:0.26
Consensus pattern (17 bp):
AAAGATATGGGTATCAA
Found at i:38818131 original size:15 final size:15
Alignment explanation
Indices: 38818093--38818121 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
38818083 GAAATTTGAG
38818093 AACAAAT-AATAAAT
1 AACAAATAAATAAAT
38818107 AACAAATAAATAAAT
1 AACAAATAAATAAAT
38818122 GAAAATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (15 bp):
AACAAATAAATAAAT
Found at i:38825907 original size:2 final size:2
Alignment explanation
Indices: 38825902--38825936 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
38825892 TCTCTGATTT
38825902 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38825937 TGAGTGTGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38827296 original size:2 final size:2
Alignment explanation
Indices: 38827289--38827317 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
38827279 TATTTTTGTT
38827289 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38827318 GAAATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38828357 original size:76 final size:76
Alignment explanation
Indices: 38828231--38828381 Score: 257
Period size: 76 Copynumber: 2.0 Consensus size: 76
38828221 AATAGTGACA
*
38828231 TGCGTGAAGATGGTTCTCGGATGCATACAAAACTGTGGCAGAACAAGATGGATGCCTTATGTAGG
1 TGCGTGAAGATGGTTCTCGGATGCATACAAAACCGTGGCAGAACAAGATGGATGCCTTATGTAGG
38828296 GATGTTCAGGT
66 GATGTTCAGGT
* ** *
38828307 TGCGTGAAGATGGTTCTCGGATGCATGCAAAACCGTGGCAGAATGAGATGGATGCCTTGTGTAGG
1 TGCGTGAAGATGGTTCTCGGATGCATACAAAACCGTGGCAGAACAAGATGGATGCCTTATGTAGG
38828372 GATGTTCAGG
66 GATGTTCAGG
38828382 CTTTGCATCG
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
76 70 1.00
ACGTcount: A:0.26, C:0.15, G:0.34, T:0.26
Consensus pattern (76 bp):
TGCGTGAAGATGGTTCTCGGATGCATACAAAACCGTGGCAGAACAAGATGGATGCCTTATGTAGG
GATGTTCAGGT
Found at i:38830030 original size:31 final size:31
Alignment explanation
Indices: 38829952--38830137 Score: 238
Period size: 31 Copynumber: 6.1 Consensus size: 31
38829942 TGAATTTAAA
*
38829952 TGTATATGTTATATACATT-TCCGAATTTGATT
1 TGTATATG-GATATACATTGT-CGAATTTGATT
38829984 TGTATA--GATATACATTGTCGAATTTGATT
1 TGTATATGGATATACATTGTCGAATTTGATT
* *
38830013 TGTATATGGTTATACATTGTCGAATTTTATT
1 TGTATATGGATATACATTGTCGAATTTGATT
*
38830044 TGTATATGGATACT-CATTGCCGAATTTGATT
1 TGTATATGGATA-TACATTGTCGAATTTGATT
* *
38830075 TGTATATAGATATACATTGTCGAATTTGATA
1 TGTATATGGATATACATTGTCGAATTTGATT
* *
38830106 CGTATATGGATATATATTGTCGAA-TTGATT
1 TGTATATGGATATACATTGTCGAATTTGATT
38830136 TG
1 TG
38830138 AGCATTGGAT
Statistics
Matches: 135, Mismatches: 14, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
29 26 0.19
30 8 0.06
31 94 0.70
32 7 0.05
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46
Consensus pattern (31 bp):
TGTATATGGATATACATTGTCGAATTTGATT
Found at i:38837403 original size:31 final size:31
Alignment explanation
Indices: 38837368--38837513 Score: 181
Period size: 31 Copynumber: 4.7 Consensus size: 31
38837358 GTATATGTTT
*
38837368 TATACATTGCTGAATTTGATTTGTATATAGA
1 TATACATTGCTGAATTTGATTTGTATATGGA
*
38837399 TATACATTG-TCGAATTTGATTTGTATATGGT
1 TATACATTGCT-GAATTTGATTTGTATATGGA
*
38837430 TATACATTG-TCGAATTTGATTTGTATATTGA
1 TATACATTGCT-GAATTTGATTTGTATATGGA
* * *
38837461 TATTCATTGCCGAATTTGATTTATATATGGA
1 TATACATTGCTGAATTTGATTTGTATATGGA
* *
38837492 TATATATTGCCGAA-TTGATTTG
1 TATACATTGCTGAATTTGATTTG
38837514 AGCATTGGAT
Statistics
Matches: 102, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
30 8 0.08
31 94 0.92
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.47
Consensus pattern (31 bp):
TATACATTGCTGAATTTGATTTGTATATGGA
Found at i:38837445 original size:62 final size:61
Alignment explanation
Indices: 38837357--38837513 Score: 208
Period size: 62 Copynumber: 2.5 Consensus size: 61
38837347 TGAATTTAAA
* *
38837357 TGTATATGTTTTATACATTGCTGAATTTGATTTGTATATAGATATACATTGTCGAATTTGATT
1 TGTATATG-GTTATACATTGC-GAATTTGATTTGTATATAGATATACATTGCCGAATTTGATT
* *
38837420 TGTATATGGTTATACATTGTCGAATTTGATTTGTATATTGATATTCATTGCCGAATTTGATT
1 TGTATATGGTTATACATTG-CGAATTTGATTTGTATATAGATATACATTGCCGAATTTGATT
* * *
38837482 TATATATGGATATATATTGCCGAA-TTGATTTG
1 TGTATATGGTTATACATTG-CGAATTTGATTTG
38837514 AGCATTGGAT
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
61 8 0.09
62 68 0.80
63 9 0.11
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.48
Consensus pattern (61 bp):
TGTATATGGTTATACATTGCGAATTTGATTTGTATATAGATATACATTGCCGAATTTGATT
Found at i:38840280 original size:121 final size:121
Alignment explanation
Indices: 38840066--38840307 Score: 484
Period size: 121 Copynumber: 2.0 Consensus size: 121
38840056 TATGACTCTC
38840066 CCTTTTAATCAAATAGGGGACAAATTATTAGGATAGTTACCATCTGTTAAGATAGTTACCACCAT
1 CCTTTTAATCAAATAGGGGACAAATTATTAGGATAGTTACCATCTGTTAAGATAGTTACCACCAT
38840131 TGGCCCAAAATCTATTTGGGTTTGGGCCGGCAACCCACAAGAATACGTGTTAAATT
66 TGGCCCAAAATCTATTTGGGTTTGGGCCGGCAACCCACAAGAATACGTGTTAAATT
38840187 CCTTTTAATCAAATAGGGGACAAATTATTAGGATAGTTACCATCTGTTAAGATAGTTACCACCAT
1 CCTTTTAATCAAATAGGGGACAAATTATTAGGATAGTTACCATCTGTTAAGATAGTTACCACCAT
38840252 TGGCCCAAAATCTATTTGGGTTTGGGCCGGCAACCCACAAGAATACGTGTTAAATT
66 TGGCCCAAAATCTATTTGGGTTTGGGCCGGCAACCCACAAGAATACGTGTTAAATT
38840308 TAGAGTAGAG
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
121 121 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (121 bp):
CCTTTTAATCAAATAGGGGACAAATTATTAGGATAGTTACCATCTGTTAAGATAGTTACCACCAT
TGGCCCAAAATCTATTTGGGTTTGGGCCGGCAACCCACAAGAATACGTGTTAAATT
Found at i:38840432 original size:3 final size:3
Alignment explanation
Indices: 38840426--38840515 Score: 108
Period size: 3 Copynumber: 30.0 Consensus size: 3
38840416 AACAACAACA
* ** ** *
38840426 ATT ATT ATT ATT ATT ATA ACA ACA ATT GTT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
38840474 ATT ATT ATT TTT ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
38840516 CGGCAAAGTC
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:38840446 original size:27 final size:27
Alignment explanation
Indices: 38840416--38840469 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
38840406 ATACCTCAAC
38840416 AACAACAACAATTATTATTATTATTAT
1 AACAACAACAATTATTATTATTATTAT
***
38840443 AACAACAATTGTTATTATTATTATTAT
1 AACAACAACAATTATTATTATTATTAT
38840470 TATTATTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (27 bp):
AACAACAACAATTATTATTATTATTAT
Found at i:38840451 original size:24 final size:24
Alignment explanation
Indices: 38840419--38840466 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
38840409 CCTCAACAAC
38840419 AACAACAATTATTATTATTATTAT
1 AACAACAATTATTATTATTATTAT
*
38840443 AACAACAATTGTTATTATTATTAT
1 AACAACAATTATTATTATTATTAT
38840467 TATTATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (24 bp):
AACAACAATTATTATTATTATTAT
Found at i:38840926 original size:25 final size:26
Alignment explanation
Indices: 38840892--38840945 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
38840882 TGGAAACTTC
* *
38840892 TTTACTTTTTTTAA-TTATTTTTAAT
1 TTTACATTTTCTAATTTATTTTTAAT
*
38840917 TTTACATTTTCTAATTTCTTTTTAAT
1 TTTACATTTTCTAATTTATTTTTAAT
38840943 TTT
1 TTT
38840946 CAACAGCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.70
Consensus pattern (26 bp):
TTTACATTTTCTAATTTATTTTTAAT
Found at i:38847701 original size:17 final size:18
Alignment explanation
Indices: 38847665--38847701 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
38847655 TTCCTGGACT
*
38847665 TTTATCCAACACTTATAA
1 TTTATCCAACACTAATAA
38847683 TTTATCCAAC-CTAATAA
1 TTTATCCAACACTAATAA
38847700 TT
1 TT
38847702 ATTTTCTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (18 bp):
TTTATCCAACACTAATAA
Found at i:38853219 original size:34 final size:34
Alignment explanation
Indices: 38853149--38853220 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
38853139 AAATAAAAAC
* ***
38853149 AAATTAAACCCAATATCCAAATATAATTTTGGAA
1 AAATTAAACCCAATATCAAAATATAATTTAACAA
*
38853183 AAATTAAAACCCAAT-TCAAAATTTAATTTAACAA
1 AAATT-AAACCCAATATCAAAATATAATTTAACAA
38853217 AAAT
1 AAAT
38853221 AATATTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
34 23 0.72
35 9 0.28
ACGTcount: A:0.54, C:0.14, G:0.03, T:0.29
Consensus pattern (34 bp):
AAATTAAACCCAATATCAAAATATAATTTAACAA
Done.