Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 110 of 203
Found at i:34899973 original size:28 final size:30
Alignment explanation
Indices: 34899922--34899983 Score: 92
Period size: 28 Copynumber: 2.1 Consensus size: 30
34899912 AAAATTAGAA
34899922 AAAAAATATAAAAATCATAAAAAAAATTAT
1 AAAAAATATAAAAATCATAAAAAAAATTAT
* *
34899952 AAAACATATAGAAAT-AT-AAAAAAATTAT
1 AAAAAATATAAAAATCATAAAAAAAATTAT
34899980 AAAA
1 AAAA
34899984 TTTTATAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 15 0.50
29 2 0.07
30 13 0.43
ACGTcount: A:0.73, C:0.03, G:0.02, T:0.23
Consensus pattern (30 bp):
AAAAAATATAAAAATCATAAAAAAAATTAT
Found at i:34900266 original size:36 final size:36
Alignment explanation
Indices: 34900199--34900268 Score: 115
Period size: 36 Copynumber: 1.9 Consensus size: 36
34900189 GGTCATTAAT
*
34900199 TTTTTTATGATTTTTATAAAAATTTTCAATTTTTTA
1 TTTTTTATGATTTTTATAAAAATTGTCAATTTTTTA
34900235 TTTTTTATGATTTTTATAAAAAATTGT-AATTTTT
1 TTTTTTATGATTTTTAT-AAAAATTGTCAATTTTT
34900269 AATAAATTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 24 0.75
37 8 0.25
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.63
Consensus pattern (36 bp):
TTTTTTATGATTTTTATAAAAATTGTCAATTTTTTA
Found at i:34900268 original size:19 final size:18
Alignment explanation
Indices: 34900244--34900287 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
34900234 ATTTTTTATG
34900244 ATTTTTATAAAAAATTGTA
1 ATTTTT-TAAAAAATTGTA
*
34900263 A-TTTTTAATAAATTGTA
1 ATTTTTTAAAAAATTGTA
34900280 ATTTTTTA
1 ATTTTTTA
34900288 TATTTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 12 0.52
18 10 0.43
19 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
ATTTTTTAAAAAATTGTA
Found at i:34900322 original size:46 final size:46
Alignment explanation
Indices: 34900234--34900346 Score: 115
Period size: 46 Copynumber: 2.4 Consensus size: 46
34900224 TCAATTTTTT
*
34900234 ATTTTTTATGATTTTTATAAAAAATTGTAATTTTTAATAAATTG-TA
1 ATTTTTTAT-ATTTTTATAAAAAATTATAATTTTTAATAAATTGATA
* * * *
34900280 ATTTTTTATATTTTTATTAAAATTTAATAATTTTT-CTAAAATTGATT
1 ATTTTTTATATTTTTATAAAAAATT-ATAATTTTTAAT-AAATTGATA
34900327 ATTATTTTAT-TATTTTATAA
1 ATT-TTTTATAT-TTTTATAA
34900347 TTTTTTTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
45 15 0.27
46 23 0.41
47 5 0.09
48 13 0.23
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (46 bp):
ATTTTTTATATTTTTATAAAAAATTATAATTTTTAATAAATTGATA
Found at i:34900701 original size:22 final size:22
Alignment explanation
Indices: 34900673--34900718 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
34900663 TGGGCCTCAC
34900673 TTAATTCCCCTTTAATCCTTTG
1 TTAATTCCCCTTTAATCCTTTG
34900695 TTAATTCCCCTTTAATCCTTTG
1 TTAATTCCCCTTTAATCCTTTG
34900717 TT
1 TT
34900719 TGGTTCAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.26, G:0.04, T:0.52
Consensus pattern (22 bp):
TTAATTCCCCTTTAATCCTTTG
Found at i:34904273 original size:22 final size:20
Alignment explanation
Indices: 34904223--34904275 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
34904213 TAATAATTAT
*
34904223 TTTAA-ATTATATTTTATAG
1 TTTAATATTATATTTTATAA
34904242 TATTATATATTATGATTTTAGTAA
1 T-TTA-ATATTAT-ATTTTA-TAA
34904266 TTTAATATTA
1 TTTAATATTA
34904276 AGAATATCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 1 0.04
20 3 0.11
21 1 0.04
22 11 0.39
23 9 0.32
24 3 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (20 bp):
TTTAATATTATATTTTATAA
Found at i:34905204 original size:82 final size:83
Alignment explanation
Indices: 34905089--34905251 Score: 202
Period size: 83 Copynumber: 2.0 Consensus size: 83
34905079 CACTTTCGCC
* * *
34905089 ACCAAGAAATCGGTTTGGTTTAATTTAAGTAAGT-TCATTGTTTTTGTATCATGTCTAAGAGATA
1 ACCAAGAAATCGGTTCGGTTCAATTCAAGTAAGTATCATTGTTTTTGTATCATGTCTAAGAGATA
*
34905153 GTTTAATAATGCTTTTCA
66 GTTTAACAATGCTTTTCA
* * * ** * * *
34905171 ACCAAGAGATCGGTTCGGTTCAATTCGATTAAGTATGTTTTTTTTTGTATCATGTCTAAGAGTTG
1 ACCAAGAAATCGGTTCGGTTCAATTCAAGTAAGTATCATTGTTTTTGTATCATGTCTAAGAGATA
*
34905236 GTTTAGCAATGCTTTT
66 GTTTAACAATGCTTTT
34905252 TAAAAGTGTT
Statistics
Matches: 67, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
82 28 0.42
83 39 0.58
ACGTcount: A:0.27, C:0.11, G:0.19, T:0.43
Consensus pattern (83 bp):
ACCAAGAAATCGGTTCGGTTCAATTCAAGTAAGTATCATTGTTTTTGTATCATGTCTAAGAGATA
GTTTAACAATGCTTTTCA
Found at i:34907009 original size:13 final size:13
Alignment explanation
Indices: 34906991--34907031 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
34906981 CAAAACTAAT
*
34906991 AGAAAAGGAAGAA
1 AGAAAAGAAAGAA
34907004 AGAAAAGAAAGAA
1 AGAAAAGAAAGAA
**
34907017 AGACGAGAAAGAA
1 AGAAAAGAAAGAA
34907030 AG
1 AG
34907032 GGGCGCACGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.68, C:0.02, G:0.29, T:0.00
Consensus pattern (13 bp):
AGAAAAGAAAGAA
Found at i:34908153 original size:18 final size:18
Alignment explanation
Indices: 34908130--34908222 Score: 80
Period size: 18 Copynumber: 4.7 Consensus size: 18
34908120 GAAATGACCA
34908130 AGATGAGAAATGAATATG
1 AGATGAGAAATGAATATG
34908148 AGATGAGAAATATTGAAT-TGG
1 AGATGAG-AA-A-TGAATAT-G
34908169 CAAAGATGAGAAATGAATATG
1 ---AGATGAGAAATGAATATG
*
34908190 AGATGAGAAATGTGATATG
1 AGATGAGAAATG-AATATG
*
34908209 AAATGATGAAATGA
1 AGATGA-GAAATGA
34908223 GATGTGAAAC
Statistics
Matches: 62, Mismatches: 3, Indels: 19
0.74 0.04 0.23
Matches are distributed among these distances:
18 19 0.31
19 12 0.19
20 8 0.13
21 12 0.19
22 2 0.03
23 2 0.03
24 7 0.11
ACGTcount: A:0.48, C:0.01, G:0.27, T:0.24
Consensus pattern (18 bp):
AGATGAGAAATGAATATG
Found at i:34908175 original size:42 final size:42
Alignment explanation
Indices: 34908115--34908200 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
34908105 TATGTGATTG
*
34908115 ATATTGAAATGACCAAGATGAGAAATGAATATGAGATGAGAA
1 ATATTGAAATGACAAAGATGAGAAATGAATATGAGATGAGAA
* *
34908157 ATATTGAATTGGCAAAGATGAGAAATGAATATGAGATGAGAA
1 ATATTGAAATGACAAAGATGAGAAATGAATATGAGATGAGAA
34908199 AT
1 AT
34908201 GTGATATGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.49, C:0.03, G:0.24, T:0.23
Consensus pattern (42 bp):
ATATTGAAATGACAAAGATGAGAAATGAATATGAGATGAGAA
Found at i:34911482 original size:19 final size:19
Alignment explanation
Indices: 34911460--34911500 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
34911450 CATTATCAAA
34911460 GATTAAATAACTCAATAAT
1 GATTAAATAACTCAATAAT
*
34911479 GATTCAATAACTCAATAAT
1 GATTAAATAACTCAATAAT
34911498 GAT
1 GAT
34911501 ACATTGGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (19 bp):
GATTAAATAACTCAATAAT
Found at i:34912123 original size:37 final size:38
Alignment explanation
Indices: 34912082--34912157 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
34912072 ATCTATTTTC
34912082 ATTTTCTTTCTTCTATC-TTTTTCCCTGGTCTGCTGGT
1 ATTTTCTTTCTTCTATCTTTTTTCCCTGGTCTGCTGGT
*
34912119 ATTTTTTTTCTTCTATCTTTTTTCCCTGGTCTGCTGGT
1 ATTTTCTTTCTTCTATCTTTTTTCCCTGGTCTGCTGGT
34912157 A
1 A
34912158 AAGAAGATGG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 16 0.43
38 21 0.57
ACGTcount: A:0.07, C:0.22, G:0.13, T:0.58
Consensus pattern (38 bp):
ATTTTCTTTCTTCTATCTTTTTTCCCTGGTCTGCTGGT
Found at i:34916217 original size:40 final size:41
Alignment explanation
Indices: 34916135--34916345 Score: 257
Period size: 41 Copynumber: 5.2 Consensus size: 41
34916125 CTTTCGGGGT
* *
34916135 TTTAGCGGCGTTTTTTAGAAAGCGCCGCTAATGTTCTGGGA
1 TTTAGCGGCGTTTTTTAGGAAGCGCCGCTAATGCTCTGGGA
34916176 TTTAGCGGCGTTTTTTAGGAAGCGCCGCTAATGCTCT-GGA
1 TTTAGCGGCGTTTTTTAGGAAGCGCCGCTAATGCTCTGGGA
*** *
34916216 TTTAGCGATATTTTTTAGGAAGCGCTGCTAATGCTCTGGGA
1 TTTAGCGGCGTTTTTTAGGAAGCGCCGCTAATGCTCTGGGA
* * * * *
34916257 TTTAGCGGCGTCTTTTAGGAAGCGCCGCTATTGCTCAGTGC
1 TTTAGCGGCGTTTTTTAGGAAGCGCCGCTAATGCTCTGGGA
* * * *
34916298 TTTAGCGGCG-TTTTTAGAAAGCACCACTAATACT-TAGGGA
1 TTTAGCGGCGTTTTTTAGGAAGCGCCGCTAATGCTCT-GGGA
34916338 TTTAGCGG
1 TTTAGCGG
34916346 TACTAATGCT
Statistics
Matches: 144, Mismatches: 24, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
40 64 0.44
41 80 0.56
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.33
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTTAGGAAGCGCCGCTAATGCTCTGGGA
Found at i:34916312 original size:81 final size:80
Alignment explanation
Indices: 34916135--34916345 Score: 262
Period size: 81 Copynumber: 2.6 Consensus size: 80
34916125 CTTTCGGGGT
* *
34916135 TTTAGCGGCGTTTTTTAGAAAGCGCCGCTAATGTTCTGGGATTTAGCGGCGTTTTTTAGGAAGCG
1 TTTAGCGGCG-TTTTTAGAAAGCGCCGCTAATGCTCTGGGATTTAGCGGCGTCTTTTAGGAAGCG
*
34916200 CCGCTAATGCTCTGGA
65 CCGCTAATGCTCAGGA
*** * *
34916216 TTTAGCGATATTTTTTAGGAAGCGCTGCTAATGCTCTGGGATTTAGCGGCGTCTTTTAGGAAGCG
1 TTTAGCG-GCGTTTTTAGAAAGCGCCGCTAATGCTCTGGGATTTAGCGGCGTCTTTTAGGAAGCG
* *
34916281 CCGCTATTGCTCAGTGC
65 CCGCTAATGCTCAG-GA
* * *
34916298 TTTAGCGGCGTTTTTAGAAAGCACCACTAATACT-TAGGGATTTAGCGG
1 TTTAGCGGCGTTTTTAGAAAGCGCCGCTAATGCTCT-GGGATTTAGCGG
34916346 TACTAATGCT
Statistics
Matches: 109, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
80 1 0.01
81 100 0.92
82 8 0.07
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.33
Consensus pattern (80 bp):
TTTAGCGGCGTTTTTAGAAAGCGCCGCTAATGCTCTGGGATTTAGCGGCGTCTTTTAGGAAGCGC
CGCTAATGCTCAGGA
Found at i:34916415 original size:40 final size:40
Alignment explanation
Indices: 34916362--34916437 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
34916352 TGCTCGGGGC
**
34916362 TTTAGCGGCGTTTT-TGAAGTAGCGCCGCTAATGCTCTATT
1 TTTAGCGGCGTTTTCT-AAAAAGCGCCGCTAATGCTCTATT
*
34916402 TTTAGCGGCGTTTTCTAAAAAGCGTCGCTAATGCTC
1 TTTAGCGGCGTTTTCTAAAAAGCGCCGCTAATGCTC
34916438 AGGGATTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
40 31 0.97
41 1 0.03
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.36
Consensus pattern (40 bp):
TTTAGCGGCGTTTTCTAAAAAGCGCCGCTAATGCTCTATT
Found at i:34916433 original size:105 final size:105
Alignment explanation
Indices: 34916243--34916446 Score: 252
Period size: 105 Copynumber: 1.9 Consensus size: 105
34916233 GGAAGCGCTG
* * *
34916243 CTAATGCTCTGGGATTTAGCGGCGTCTTTTAGGAAGCGCCGCTATTGCTCAGTGCTTTAGCGGCG
1 CTAATGCTCGGGGATTTAGCGGCGTCTTTTAAGAAGCGCCGCTAATGCTCAGTGCTTTAGCGGCG
* *
34916308 TTTTTAGAAAGCACCACTAATACTTAGGGATTTAGCGGTA
66 TTTTTAAAAAGCACCACTAATACTCAGGGATTTAGCGGTA
* * *
34916348 CTAATGCTCGGGGCTTTAGCGGCGT-TTTTGAAGTAGCGCCGCTAATGCTCTA-T-TTTTAGCGG
1 CTAATGCTCGGGGATTTAGCGGCGTCTTTT-AAGAAGCGCCGCTAATGCTC-AGTGCTTTAGCGG
** * *
34916410 CGTTTTCTAAAAAGCGTCGCTAATGCTCAGGGATTTA
64 CGTTTT-TAAAAAGCACCACTAATACTCAGGGATTTA
34916447 AAATAATTTA
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
104 18 0.21
105 65 0.77
106 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.32
Consensus pattern (105 bp):
CTAATGCTCGGGGATTTAGCGGCGTCTTTTAAGAAGCGCCGCTAATGCTCAGTGCTTTAGCGGCG
TTTTTAAAAAGCACCACTAATACTCAGGGATTTAGCGGTA
Found at i:34921407 original size:15 final size:15
Alignment explanation
Indices: 34921387--34921417 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
34921377 GAGTTGAAAG
34921387 TGAAGAAGAAGATGA
1 TGAAGAAGAAGATGA
*
34921402 TGAAGATGAAGATGA
1 TGAAGAAGAAGATGA
34921417 T
1 T
34921418 CCATATCCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.32, T:0.19
Consensus pattern (15 bp):
TGAAGAAGAAGATGA
Found at i:34921733 original size:43 final size:43
Alignment explanation
Indices: 34921685--34921929 Score: 266
Period size: 43 Copynumber: 5.7 Consensus size: 43
34921675 ATCAAAGTGT
* * * *
34921685 CGCTAAAGGTCTTGAGCTATAGCGGCATTTGCGGAAAAAGCGC
1 CGCTAAAGGTCTTGAGCTTTAGCGGCGTTTGTGGGAAAAGCGC
* * *
34921728 CGCTAAAGGTC-TGGGTCTTTAGCGGCGTTTGTGGGAACAGCGT
1 CGCTAAAGGTCTTGAG-CTTTAGCGGCGTTTGTGGGAAAAGCGC
* * * *
34921771 CGCTAAAGGTCTGGATCTTTAGCAGCGTTTGTGGGAAAAGCAC
1 CGCTAAAGGTCTTGAGCTTTAGCGGCGTTTGTGGGAAAAGCGC
* ** * *
34921814 CGCTAAAGGTCCTGTTCTTTAGCAGCGTTTGTGGGAAAATCGC
1 CGCTAAAGGTCTTGAGCTTTAGCGGCGTTTGTGGGAAAAGCGC
*
34921857 CGCTAAAGGTCTTG-GTCTTTAGCGGCGTTT-TGGGAAAAGCGT
1 CGCTAAAGGTCTTGAG-CTTTAGCGGCGTTTGTGGGAAAAGCGC
*
34921899 CGCTAAAGGTCTTG-GTCTTTAGC-ACGTTTGT
1 CGCTAAAGGTCTTGAG-CTTTAGCGGCGTTTGT
34921930 TTCTAAAAAT
Statistics
Matches: 173, Mismatches: 25, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
41 5 0.03
42 37 0.21
43 130 0.75
44 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (43 bp):
CGCTAAAGGTCTTGAGCTTTAGCGGCGTTTGTGGGAAAAGCGC
Found at i:34921811 original size:86 final size:84
Alignment explanation
Indices: 34921660--34921929 Score: 301
Period size: 86 Copynumber: 3.2 Consensus size: 84
34921650 TAATAGTACT
**** * * * * * * *
34921660 TTTAGCGCGTTTGTAATCAAAGTGTCGCTAAAGGTCTTGAGCTATAGCGGCATTTGCGGAAAAAG
1 TTTAGCGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCTGGATCTTTAGCGGCGTTTGTGGGAAAAG
34921725 CGCCGCTAAAGGTCTGGGTC
66 CGCCGCTAAAGGTCT-GGTC
* *
34921745 TTTAGCGGCGTTTGTGGGAACAGCGTCGCTAAAGGTCTGGATCTTTAGCAGCGTTTGTGGGAAAA
1 TTTAGC-GCGTTTGTGGGAAAAGCGTCGCTAAAGGTCTGGATCTTTAGCGGCGTTTGTGGGAAAA
* *
34921810 GCACCGCTAAAGGTCCTGTTC
65 GCGCCGCTAAAGGT-CTGGTC
* *
34921831 TTTAGCAGCGTTTGTGGGAAAATCGCCGCTAAAGGTCTTGG-TCTTTAGCGGCGTTT-TGGGAAA
1 TTTAGC-GCGTTTGTGGGAAAAGCGTCGCTAAAGGTC-TGGATCTTTAGCGGCGTTTGTGGGAAA
*
34921894 AGCGTCGCTAAAGGTCTTGGTC
64 AGCGCCGCTAAAGGTC-TGGTC
*
34921916 TTTAGCACGTTTGT
1 TTTAGCGCGTTTGT
34921930 TTCTAAAAAT
Statistics
Matches: 157, Mismatches: 24, Indels: 9
0.83 0.13 0.05
Matches are distributed among these distances:
84 8 0.05
85 36 0.23
86 108 0.69
87 5 0.03
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (84 bp):
TTTAGCGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCTGGATCTTTAGCGGCGTTTGTGGGAAAAG
CGCCGCTAAAGGTCTGGTC
Found at i:34926950 original size:7 final size:7
Alignment explanation
Indices: 34926938--34926980 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
34926928 TCTCTCTTTA
34926938 TTTTCTT
1 TTTTCTT
34926945 TTTTCTT
1 TTTTCTT
34926952 TTTTC-T
1 TTTTCTT
*
34926958 ATTTCTT
1 TTTTCTT
34926965 TCTTTCTT
1 T-TTTCTT
*
34926973 CTTTCTT
1 TTTTCTT
34926980 T
1 T
34926981 ATAATTTCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
6 5 0.17
7 19 0.63
8 6 0.20
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTCTT
Found at i:34926960 original size:21 final size:21
Alignment explanation
Indices: 34926926--34926978 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
34926916 TTACATTATT
*
34926926 TTTCTCTCTTTAT-TTTCTTT-
1 TTTCT-TCTTTCTATTTCTTTC
*
34926946 TTTCTTTTTTCTATTTCTTTC
1 TTTCTTCTTTCTATTTCTTTC
34926967 TTTCTTCTTTCT
1 TTTCTTCTTTCT
34926979 TTATAATTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 5 0.18
20 12 0.43
21 11 0.39
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTCTTCTTTCTATTTCTTTC
Found at i:34931836 original size:24 final size:24
Alignment explanation
Indices: 34931809--34931860 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
34931799 TTAGTAAGTC
* *
34931809 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
34931833 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
34931857 AAAT
1 AAAT
34931861 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:34938490 original size:17 final size:17
Alignment explanation
Indices: 34938468--34938501 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
34938458 TTATGCGTAA
34938468 ACTTTTACGAAAGTTTT
1 ACTTTTACGAAAGTTTT
34938485 ACTTTTACGAAAGTTTT
1 ACTTTTACGAAAGTTTT
34938502 TCAAACTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (17 bp):
ACTTTTACGAAAGTTTT
Found at i:34940211 original size:24 final size:24
Alignment explanation
Indices: 34940184--34940229 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
34940174 AACCTAATTC
34940184 TAATCAAA-GTCAAATATATTATGT
1 TAAT-AAATGTCAAATATATTATGT
*
34940208 TAATAAATGTTAAATATATTAT
1 TAATAAATGTCAAATATATTAT
34940230 ACTCATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (24 bp):
TAATAAATGTCAAATATATTATGT
Found at i:34940245 original size:24 final size:24
Alignment explanation
Indices: 34940195--34940246 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
34940185 AATCAAAGTC
** **
34940195 AAATATATTATGTTAATAAATGTT
1 AAATATATTATACTAATAAATACT
*
34940219 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
34940243 AAAT
1 AAAT
34940247 CTTCTAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:34944637 original size:24 final size:24
Alignment explanation
Indices: 34944610--34944661 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
34944600 AATCAAAGTC
*
34944610 AAATATATTATGT-TAATAAATGCT
1 AAATATATTAT-TCTAATAAATACT
*
34944634 AAATATATTATTCTCATAAATACT
1 AAATATATTATTCTAATAAATACT
34944658 AAAT
1 AAAT
34944662 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (24 bp):
AAATATATTATTCTAATAAATACT
Found at i:34945717 original size:20 final size:21
Alignment explanation
Indices: 34945684--34945725 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
34945674 CTTTTTTCTC
34945684 GTGTGATGCACAAGTGTAATGT
1 GTGTGATG-ACAAGTGTAATGT
34945706 GTGTGATG-CAAGTGTAATGT
1 GTGTGATGACAAGTGTAATGT
34945726 ATGTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 12 0.60
22 8 0.40
ACGTcount: A:0.26, C:0.07, G:0.33, T:0.33
Consensus pattern (21 bp):
GTGTGATGACAAGTGTAATGT
Found at i:34948148 original size:107 final size:108
Alignment explanation
Indices: 34948005--34948418 Score: 681
Period size: 108 Copynumber: 3.9 Consensus size: 108
34947995 AAATAATAAG
* *
34948005 TAAGGCAATGTTTTGCGTTT-GGAAATTCAAGAAAACGTATCCTAATGTGTTGGGTTTCGA-TTT
1 TAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTACCCTAATGTGTTGGGTTTCGATTTT
34948068 TTCGTTCGACCAAATAGCCAAATATCCTTATAAAATTTCAAAA
66 TTCGTTCGACCAAATAGCCAAATATCCTTATAAAATTTCAAAA
*
34948111 TAAGGCAATGTTTTGTGTTTGGGAAATTCGAGAAAACGTACCCTAATGTGTTGGGTTTCGATTTT
1 TAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTACCCTAATGTGTTGGGTTTCGATTTT
*
34948176 TTCATTCGACCAAATAGCCAAATATCCTTATAAAATTTCAAAA
66 TTCGTTCGACCAAATAGCCAAATATCCTTATAAAATTTCAAAA
** * *
34948219 TAAGGCAATGTTTTGTATTTGGAAAATTCGAGAAAACGTACCCTAATGTGTTGGGTTTCAATTTT
1 TAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTACCCTAATGTGTTGGGTTTCGATTTT
*
34948284 TTCGTTCGACCAAATAGCCAAAAATCCTTATAAAATTTCAAAA
66 TTCGTTCGACCAAATAGCCAAATATCCTTATAAAATTTCAAAA
* * *
34948327 TAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAATGTGCTGAGTTTCGA-TTT
1 TAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTACCCTAATGTGTTGGGTTTCGATTTT
* *
34948391 CTCGTTGGACCAAATAGCCAAATATCCT
66 TTCGTTCGACCAAATAGCCAAATATCCT
34948419 CTTGAATCTT
Statistics
Matches: 287, Mismatches: 19, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
106 19 0.07
107 66 0.23
108 202 0.70
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (108 bp):
TAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTACCCTAATGTGTTGGGTTTCGATTTT
TTCGTTCGACCAAATAGCCAAATATCCTTATAAAATTTCAAAA
Found at i:34953128 original size:9 final size:9
Alignment explanation
Indices: 34953090--34953253 Score: 59
Period size: 9 Copynumber: 17.7 Consensus size: 9
34953080 ACATGTGAAA
34953090 AAAAATTAT
1 AAAAATTAT
*
34953099 AAAAA-AAT
1 AAAAATTAT
*
34953107 AAAAAATCAAT
1 -AAAAAT-TAT
*
34953118 AAAAGTTAT
1 AAAAATTAT
34953127 AAAAATTAT
1 AAAAATTAT
* *
34953136 TAAACTTCAAT
1 AAAAATT--AT
*
34953147 AAAAAATAT
1 AAAAATTAT
34953156 AAAAATATATTT
1 AAAAAT-TA--T
**
34953168 AAATGTTACT
1 AAAAATTA-T
*
34953178 AAAAATTAG
1 AAAAATTAT
*
34953187 AAATA-TAT
1 AAAAATTAT
*
34953195 -ATAATGTA-
1 AAAAAT-TAT
*
34953203 AAAAAATAT
1 AAAAATTAT
*
34953212 AAAAATTGT
1 AAAAATTAT
*
34953221 AAAATTTTAT
1 AAAA-ATTAT
*
34953231 AAAAATCAT
1 AAAAATTAT
*
34953240 AAAAAAT-T
1 AAAAATTAT
34953248 AAAAAT
1 AAAAAT
34953254 GCATCAAAAA
Statistics
Matches: 111, Mismatches: 31, Indels: 27
0.66 0.18 0.16
Matches are distributed among these distances:
7 2 0.02
8 12 0.11
9 60 0.54
10 21 0.19
11 11 0.10
12 5 0.05
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:34953262 original size:18 final size:17
Alignment explanation
Indices: 34953230--34953263 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
34953220 TAAAATTTTA
34953230 TAAAAATCATAAAAAAT
1 TAAAAATCATAAAAAAT
*
34953247 TAAAAATGCATCAAAAA
1 TAAAAAT-CATAAAAAA
34953264 GACCATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.68, C:0.09, G:0.03, T:0.21
Consensus pattern (17 bp):
TAAAAATCATAAAAAAT
Found at i:34956840 original size:7 final size:7
Alignment explanation
Indices: 34956820--34956874 Score: 67
Period size: 7 Copynumber: 7.7 Consensus size: 7
34956810 TATTTAAAAA
34956820 TATTATT
1 TATTATT
34956827 T-TTATT
1 TATTATT
34956833 TATTATT
1 TATTATT
34956840 TATTATT
1 TATTATT
*
34956847 TAATATT
1 TATTATT
*
34956854 TAATATT
1 TATTATT
34956861 TATATATTT
1 TAT-TA-TT
34956870 TATTA
1 TATTA
34956875 CAATTATACA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
6 6 0.14
7 28 0.65
8 4 0.09
9 5 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (7 bp):
TATTATT
Found at i:34956855 original size:21 final size:20
Alignment explanation
Indices: 34956799--34956873 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
34956789 AACATTGTCC
34956799 ATTTATT-TTTATATTTAA-
1 ATTTATTATTTATATTTAAT
** * *
34956817 AAATATTATTTTTATTTATT
1 ATTTATTATTTATATTTAAT
34956837 ATTTATTATTTAATATTTAAT
1 ATTTATTATTT-ATATTTAAT
34956858 ATTTATATATTT-TATT
1 ATTTAT-TATTTATATT
34956874 ACAATTATAC
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
18 5 0.11
19 9 0.20
20 13 0.29
21 13 0.29
22 5 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTTATTATTTATATTTAAT
Found at i:34959769 original size:41 final size:42
Alignment explanation
Indices: 34959674--34959814 Score: 196
Period size: 41 Copynumber: 3.4 Consensus size: 42
34959664 AGCGTTTACA
* *
34959674 AAAATAAACGCCGCTGAAGGTCATGTTCTTTAGCGGCGCTTAG
1 AAAA-AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
34959717 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGC-CTTAG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
* * **
34959758 AAAAAAACGCCGTTAAAGATCATGTTTTTTAGCGGCGCCCAG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
*
34959800 -AAAAAACGCCACTAA
1 AAAAAAACGCCGCTAA
34959815 TGTTGGGATT
Statistics
Matches: 89, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
41 52 0.58
42 33 0.37
43 4 0.04
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.23
Consensus pattern (42 bp):
AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
Found at i:34960191 original size:21 final size:21
Alignment explanation
Indices: 34960165--34960204 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
34960155 CGTTGCTTCT
*
34960165 CTCGCTGTAGCCTCTGCATCC
1 CTCGCTGCAGCCTCTGCATCC
*
34960186 CTCGCTGCCGCCTCTGCAT
1 CTCGCTGCAGCCTCTGCAT
34960205 TAAGTTGTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.45, G:0.20, T:0.28
Consensus pattern (21 bp):
CTCGCTGCAGCCTCTGCATCC
Found at i:34966305 original size:9 final size:9
Alignment explanation
Indices: 34966291--34966529 Score: 103
Period size: 9 Copynumber: 27.4 Consensus size: 9
34966281 AGTATATATG
34966291 AGTTATGTA
1 AGTTATGTA
34966300 AGTTATGATA
1 AGTTATG-TA
* * *
34966310 TGATATAT-
1 AGTTATGTA
*
34966318 ATTTATGT-
1 AGTTATGTA
*
34966326 A-TTACGTA
1 AGTTATGTA
*
34966334 AATTATGTA
1 AGTTATGTA
*
34966343 AATTATGTA
1 AGTTATGTA
34966352 AGTTATGTA
1 AGTTATGTA
* *
34966361 AGTAATAT-
1 AGTTATGTA
34966369 A-TTATGTA
1 AGTTATGTA
*
34966377 AGTTGTGTATA
1 AGTTATG--TA
*
34966388 ATGTAAT-TA
1 A-GTTATGTA
34966397 AGTTATGTA
1 AGTTATGTA
*
34966406 AG-T-TGCA
1 AGTTATGTA
34966413 AGTTATGT-
1 AGTTATGTA
34966421 A-TTATGTA
1 AGTTATGTA
*
34966429 AGTTATTTA
1 AGTTATGTA
*
34966438 AGTTATATA
1 AGTTATGTA
*
34966447 AGTTGTGT-
1 AGTTATGTA
*
34966455 A-TTATGTG
1 AGTTATGTA
*
34966463 AGTTATGCA
1 AGTTATGTA
*
34966472 ATTTATGTA
1 AGTTATGTA
* * *
34966481 GGCTATAT-
1 AGTTATGTA
34966489 A-TTATGTA
1 AGTTATGTA
34966497 AGTTAT-TA
1 AGTTATGTA
*
34966505 TGTTATTATGTA
1 AG---TTATGTA
*
34966517 AGTTATGCA
1 AGTTATGTA
34966526 AGTT
1 AGTT
34966530 TAATTATATA
Statistics
Matches: 170, Mismatches: 39, Indels: 42
0.68 0.16 0.17
Matches are distributed among these distances:
7 29 0.17
8 22 0.13
9 100 0.59
10 6 0.04
11 7 0.04
12 6 0.04
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.46
Consensus pattern (9 bp):
AGTTATGTA
Found at i:34966372 original size:25 final size:25
Alignment explanation
Indices: 34966344--34966408 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
34966334 AATTATGTAA
34966344 ATTATGTAAGTTATGTAAGTAATAT
1 ATTATGTAAGTTATGTAAGTAATAT
* *
34966369 ATTATGTAAGTTGTGT-A-TAATGT
1 ATTATGTAAGTTATGTAAGTAATAT
34966392 A--AT-TAAGTTATGTAAGT
1 ATTATGTAAGTTATGTAAGT
34966409 TGCAAGTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
20 9 0.26
21 3 0.09
22 1 0.03
23 6 0.17
24 1 0.03
25 15 0.43
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (25 bp):
ATTATGTAAGTTATGTAAGTAATAT
Found at i:34966460 original size:41 final size:42
Alignment explanation
Indices: 34966325--34966461 Score: 125
Period size: 41 Copynumber: 3.2 Consensus size: 42
34966315 TATATTTATG
* * **
34966325 TATTACGTAAATTATGTAAATTATGTAAGTTATGTAAGTAATA
1 TATTATGT-AATTATGTAAATTATTTAAGTTATGTAAGTTGTA
* * *
34966368 TATTATGTAAGTTGTGTATAATGTAATTAAGTTATGTAAGTTGCA
1 TATTATGTAA-TTATGTA-AAT-TATTTAAGTTATGTAAGTTGTA
* * *
34966413 -AGTTATGT-ATTATGTAAGTTATTTAAGTTATATAAGTTGTG
1 TA-TTATGTAATTATGTAAATTATTTAAGTTATGTAAGTTGTA
34966454 TATTATGT
1 TATTATGT
34966462 GAGTTATGCA
Statistics
Matches: 76, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
41 24 0.32
42 5 0.07
43 19 0.25
44 5 0.07
45 23 0.30
ACGTcount: A:0.35, C:0.01, G:0.18, T:0.46
Consensus pattern (42 bp):
TATTATGTAATTATGTAAATTATTTAAGTTATGTAAGTTGTA
Found at i:34966625 original size:16 final size:15
Alignment explanation
Indices: 34966603--34966646 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
34966593 TTTTACTTAC
34966603 TTATATAATTAAG-T
1 TTATATAATTAAGTT
34966617 TTATAT-A-TAAGTT
1 TTATATAATTAAGTT
34966630 TCTATATAATTAAGTT
1 T-TATATAATTAAGTT
34966646 T
1 T
34966647 ATTTTACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.15
13 3 0.12
14 11 0.42
15 1 0.04
16 7 0.27
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (15 bp):
TTATATAATTAAGTT
Found at i:34966636 original size:28 final size:27
Alignment explanation
Indices: 34966548--34966687 Score: 142
Period size: 27 Copynumber: 5.1 Consensus size: 27
34966538 TATAAGTTTC
*
34966548 TATATAATTAAGTTTATTTTACTTACT
1 TATATAATTAAGTTTATTTAACTTACT
* * *
34966575 TCATTATATAGTCA-TTTATTTTACTTACT
1 T-A-TATA-ATTAAGTTTATTTAACTTACT
* *
34966604 TATATAATTAAGTTTATATATAAGTTTC-
1 TATATAATTAAGTTTAT-T-TAACTTACT
*
34966632 TATATAATTAAGTTTATTTTACTTACT
1 TATATAATTAAGTTTATTTAACTTACT
34966659 TATATAATTAAGTTTAATTT-ACTTACT
1 TATATAATTAAGTTT-ATTTAACTTACT
34966686 TA
1 TA
34966688 ATTATATAGT
Statistics
Matches: 95, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
26 8 0.08
27 35 0.37
28 24 0.25
29 25 0.26
30 3 0.03
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.54
Consensus pattern (27 bp):
TATATAATTAAGTTTATTTAACTTACT
Found at i:34966705 original size:84 final size:84
Alignment explanation
Indices: 34966533--34966687 Score: 244
Period size: 84 Copynumber: 1.9 Consensus size: 84
34966523 GCAAGTTTAA
* *
34966533 TTATATATAAGTTTCTATATAATTAAGTTTATTTTACTTACTTCATTATATAGTCATTTATTTTA
1 TTATATATAAGTTTCTATATAATTAAGTTTATTTTACTTACTTCATTATATAGTAATTTAATTTA
*
34966598 CTTACTTATATAATTAAGT
66 CTTACTTATATAAGTAAGT
*
34966617 TTATATATAAGTTTCTATATAATTAAGTTTATTTTACTTACTT-A-TATA-ATTAAGTTTAATTT
1 TTATATATAAGTTTCTATATAATTAAGTTTATTTTACTTACTTCATTATATAGTAA-TTTAATTT
34966679 ACTTACTTA
65 ACTTACTTA
34966688 ATTATATAGT
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
81 3 0.04
82 20 0.30
83 1 0.01
84 43 0.64
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.54
Consensus pattern (84 bp):
TTATATATAAGTTTCTATATAATTAAGTTTATTTTACTTACTTCATTATATAGTAATTTAATTTA
CTTACTTATATAAGTAAGT
Found at i:34969173 original size:21 final size:22
Alignment explanation
Indices: 34969149--34969202 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
34969139 AAACTTAAAT
*
34969149 TAAACCCTAAACCC-TAAATTA
1 TAAACCCTAAACCCGTAAACTA
*
34969170 TAAA--CTATAACCCGTAAACTG
1 TAAACCCTA-AACCCGTAAACTA
34969191 TAAACCCTAAAC
1 TAAACCCTAAAC
34969203 TATAAACAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
19 3 0.11
20 5 0.19
21 13 0.48
22 3 0.11
23 3 0.11
ACGTcount: A:0.46, C:0.28, G:0.04, T:0.22
Consensus pattern (22 bp):
TAAACCCTAAACCCGTAAACTA
Found at i:34969187 original size:14 final size:14
Alignment explanation
Indices: 34969170--34969222 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
34969160 CCCTAAATTA
34969170 TAAACTATAACCCG
1 TAAACTATAACCCG
*
34969184 TAAACTGTAAACCC-
1 TAAACTAT-AACCCG
* *
34969198 TAAACTATAAACAG
1 TAAACTATAACCCG
34969212 TAAACCTATAA
1 TAAA-CTATAA
34969223 ACCGCAAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
13 3 0.09
14 18 0.56
15 11 0.34
ACGTcount: A:0.49, C:0.23, G:0.06, T:0.23
Consensus pattern (14 bp):
TAAACTATAACCCG
Found at i:34969246 original size:22 final size:22
Alignment explanation
Indices: 34969221--34969265 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
34969211 GTAAACCTAT
34969221 AAACCGCAAACA-CCAACCACCA
1 AAACCGCAAA-ATCCAACCACCA
* *
34969243 AAACCTCAAAATCCAACCCCCA
1 AAACCGCAAAATCCAACCACCA
34969265 A
1 A
34969266 TATACCATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.49, C:0.44, G:0.02, T:0.04
Consensus pattern (22 bp):
AAACCGCAAAATCCAACCACCA
Found at i:34969381 original size:15 final size:15
Alignment explanation
Indices: 34969341--34969382 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
34969331 ATTGTAAATT
*
34969341 GTAAACCCTAAA-CC
1 GTAAACCATAAACCC
34969355 GTAAA-CATTAAACCC
1 GTAAACCA-TAAACCC
34969370 GTAAACCATAAAC
1 GTAAACCATAAAC
34969383 ACCAACCAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 1 0.04
14 9 0.38
15 12 0.50
16 2 0.08
ACGTcount: A:0.48, C:0.29, G:0.07, T:0.17
Consensus pattern (15 bp):
GTAAACCATAAACCC
Found at i:34969381 original size:22 final size:21
Alignment explanation
Indices: 34969342--34969383 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
34969332 TTGTAAATTG
*
34969342 TAAACCCTAAACCGTAAACAT
1 TAAACCCTAAACCATAAACAT
34969363 TAAACCCGTAAACCATAAACA
1 TAAACCC-TAAACCATAAACA
34969384 CCAACCAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.50, C:0.29, G:0.05, T:0.17
Consensus pattern (21 bp):
TAAACCCTAAACCATAAACAT
Found at i:34970015 original size:72 final size:71
Alignment explanation
Indices: 34969909--34970410 Score: 459
Period size: 72 Copynumber: 6.9 Consensus size: 71
34969899 TTTTCAAGAA
* * * * *
34969909 AAACGCCGCTAATACCACTGCATCTCAAATCAAAATGATGCGTTTTAATTATTTTTTGCGGCGTT
1 AAACGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGATT-TTTTTTGCGGCGCT
34969974 TTTACAG
65 TTTACAG
* * * * * *
34969981 AAACACCGCTAATGCCACTAAATCTGAAACCAAAACGATGCGTTTTGGTTTTTTTTGGTGGCGCT
1 AAACGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGATTTTTTTT-GCGGCGCT
34970046 TTTACAG
65 TTTACAG
* * * *
34970053 AAGCGCCGCTAATGCCACTACATCTCATATCAAAACGATGCGTTTTGGTTTGTTTTTTGTGGCGC
1 AAACGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTT-GATT-TTTTTTGCGGCGC
*
34970118 TTATACAG
64 TTTTACAG
* * * * ** *
34970126 AAGCGCCACTAATGCCACTACATCTCAAATCAAAACGATGTGTTTTGGTTATTCCTTGCTGCGCT
1 AAACGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGATT-TTTTTTGCGGCGCT
**
34970191 TTTATGG
65 TTTACAG
* * * * * *
34970198 AAGCGCCGCTAATGCAACTACATCCCAAAT-AAAAGCGATGTGTTTTGATTATTATTTGCGGTGC
1 AAACGCCGCTAATGCCACTACATCTCAAATCAAAA-CGATGCGTTTTGATT-TTTTTTGCGGCGC
***
34970262 TTTTGTGG
64 TTTTACAG
* * * *
34970270 AATCGCCGCTAATGCCACAACATCTCAAATCAAAACGAAGCGTTTGGGTTATTTTTTGTTGCGGC
1 AAACGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTT---TGATTTTTT-TTGCGGC
* *
34970335 GTTTTTACGG
62 GCTTTTACAG
* * * * * * *
34970345 AATA-GTCACTAATCCCACTACAACTCAAATCAAAACGATGTGTTTGGATTTTTTTTGCGGTGCT
1 AA-ACGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGATTTTTTTTGCGGCGCT
34970409 TT
65 TT
34970411 ATCGAAAATG
Statistics
Matches: 356, Mismatches: 64, Indels: 21
0.81 0.15 0.05
Matches are distributed among these distances:
71 20 0.06
72 210 0.59
73 64 0.18
74 9 0.03
75 53 0.15
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (71 bp):
AAACGCCGCTAATGCCACTACATCTCAAATCAAAACGATGCGTTTTGATTTTTTTTGCGGCGCTT
TTACAG
Found at i:34970562 original size:40 final size:40
Alignment explanation
Indices: 34970506--34970600 Score: 104
Period size: 40 Copynumber: 2.4 Consensus size: 40
34970496 GCTAAATTCA
* *
34970506 TATTATTAGCGGCGTTTACT-TAGAAT-CGCCGTTAATGCTC
1 TATTTTTAGCGGCGTTTACTCT-G-ATGCGCCGTTAATACTC
* *
34970546 TATTTTTAGTGGCGTTTTCTCTGATGCGCCGTTAATACTC
1 TATTTTTAGCGGCGTTTACTCTGATGCGCCGTTAATACTC
* *
34970586 GATTTTTACCGGCGT
1 TATTTTTAGCGGCGT
34970601 CTGTTATCCA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
39 2 0.04
40 43 0.93
41 1 0.02
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (40 bp):
TATTTTTAGCGGCGTTTACTCTGATGCGCCGTTAATACTC
Found at i:34972247 original size:48 final size:49
Alignment explanation
Indices: 34972155--34972248 Score: 127
Period size: 48 Copynumber: 1.9 Consensus size: 49
34972145 GGGAATTCTA
* *
34972155 TTGAATCCTTTATCATTGCGAGATTAAGCTAACTTAGGTGTTTTTACTG
1 TTGAATCCGTTATCATTGCGAGATTAAGCTAACTTAGGTATTTTTACTG
* * * *
34972204 TTGAGTCCGTTATCATTGTGAG-TTAGGCTGACTTAGGTATTTTTA
1 TTGAATCCGTTATCATTGCGAGATTAAGCTAACTTAGGTATTTTTA
34972249 AGCAAAGAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
48 20 0.51
49 19 0.49
ACGTcount: A:0.22, C:0.13, G:0.21, T:0.44
Consensus pattern (49 bp):
TTGAATCCGTTATCATTGCGAGATTAAGCTAACTTAGGTATTTTTACTG
Found at i:34976185 original size:40 final size:40
Alignment explanation
Indices: 34976113--34976232 Score: 116
Period size: 40 Copynumber: 3.0 Consensus size: 40
34976103 TACGTGTATA
* * * *
34976113 TATATATATTCATATATTTTAA-TTCATGTACATATATATG
1 TATATATATACATATTTTTTAACTT-GTATACATATATATG
* * * *
34976153 TATATATATACTTATTTTTTAACTTGTATACATGTCTATA
1 TATATATATACATATTTTTTAACTTGTATACATATATATG
* * * *
34976193 TATTTATGTACATATTTTTTAACTTTTATAAATATATATG
1 TATATATATACATATTTTTTAACTTGTATACATATATATG
34976233 CATACTTGAA
Statistics
Matches: 63, Mismatches: 16, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
40 61 0.97
41 2 0.03
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (40 bp):
TATATATATACATATTTTTTAACTTGTATACATATATATG
Found at i:34976268 original size:24 final size:24
Alignment explanation
Indices: 34976204--34976275 Score: 72
Period size: 28 Copynumber: 2.8 Consensus size: 24
34976194 ATTTATGTAC
* * *
34976204 ATATTTTTTAACTTTTATAAATAT
1 ATATCTTTTAATTTTTATATATAT
*
34976228 ATATGCATACTTGAATTTTTATATATAT
1 ATAT-C-T--TTTAATTTTTATATATAT
34976256 ATATCTTTTAATTTTTATAT
1 ATATCTTTTAATTTTTATAT
34976276 GTGTGTACAT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
24 17 0.44
26 2 0.05
27 1 0.03
28 19 0.49
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.57
Consensus pattern (24 bp):
ATATCTTTTAATTTTTATATATAT
Found at i:34976408 original size:12 final size:13
Alignment explanation
Indices: 34976391--34976419 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
34976381 GTTTTAATAT
34976391 TATTTG-TTTGTA
1 TATTTGTTTTGTA
34976403 TATTTGTTTTGTA
1 TATTTGTTTTGTA
34976416 TATT
1 TATT
34976420 ATGGGTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (13 bp):
TATTTGTTTTGTA
Found at i:34978456 original size:153 final size:153
Alignment explanation
Indices: 34978178--34978563 Score: 736
Period size: 153 Copynumber: 2.5 Consensus size: 153
34978168 ATAGCATATA
34978178 TATATTCATCATTCTCAAAATAACAACCTTTAATGAACATTATCATAAGAATTAAGCAATAGACC
1 TATATTCATCATTCTCAAAATAACAACCTTTAATGAACATTATCATAAGAATTAAGCAATAGACC
*
34978243 AAACCAACCATCACCTATATAAGCATATAAGCAATCAGAACATTAGCATATAAGCAATCAACTAA
66 AAACCAACCATCACCTATATAAGCATATAAGCAATCAGAACATTAGCATATAAGCAATCAAATAA
34978308 TTAAATGTAGTAAAAATATAACC
131 TTAAATGTAGTAAAAATATAACC
* *
34978331 TATATTCATCATTCTCAAAATAACAACCTTTAATGAACATTATCATAAGAGTTAAGCGATAGACC
1 TATATTCATCATTCTCAAAATAACAACCTTTAATGAACATTATCATAAGAATTAAGCAATAGACC
*
34978396 AGACCAACCATCACCTATATAAGCATATAAGCAATCAGAACATTAGCATATAAGCAATCAAATAA
66 AAACCAACCATCACCTATATAAGCATATAAGCAATCAGAACATTAGCATATAAGCAATCAAATAA
34978461 TTAAATGTAGTAAAAATATAACC
131 TTAAATGTAGTAAAAATATAACC
34978484 TATATTCATCATTCTCAAAATAACAACCTTTAATGAACATTATCATAAGAATTAAGCAATAGACC
1 TATATTCATCATTCTCAAAATAACAACCTTTAATGAACATTATCATAAGAATTAAGCAATAGACC
34978549 AAACCAACCATCACC
66 AAACCAACCATCACC
34978564 AAAACATGCA
Statistics
Matches: 226, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
153 226 1.00
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.26
Consensus pattern (153 bp):
TATATTCATCATTCTCAAAATAACAACCTTTAATGAACATTATCATAAGAATTAAGCAATAGACC
AAACCAACCATCACCTATATAAGCATATAAGCAATCAGAACATTAGCATATAAGCAATCAAATAA
TTAAATGTAGTAAAAATATAACC
Found at i:34978463 original size:23 final size:23
Alignment explanation
Indices: 34978417--34978463 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
34978407 CACCTATATA
*
34978417 AGCATATAAGCAATCAGAACATT
1 AGCATATAAGCAATCAGAAAATT
34978440 AGCATATAAGCAATCA-AATAATT
1 AGCATATAAGCAATCAGAA-AATT
34978463 A
1 A
34978464 AATGTAGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.51, C:0.15, G:0.11, T:0.23
Consensus pattern (23 bp):
AGCATATAAGCAATCAGAAAATT
Found at i:34978602 original size:102 final size:102
Alignment explanation
Indices: 34978484--34978692 Score: 391
Period size: 102 Copynumber: 2.0 Consensus size: 102
34978474 AAATATAACC
* *
34978484 TATATTCATCATTCTCAAAATAACAACCTTTAATGAACATTATCATAAGAATTAAGCAATAGACC
1 TATATTCATCACTCTCAAAACAACAACCTTTAATGAACATTATCATAAGAATTAAGCAATAGACC
*
34978549 AAACCAACCATCACCAAAACATGCAACATAGCATATA
66 AAACCAACCATCACCAAAACATGAAACATAGCATATA
34978586 TATATTCATCACTCTCAAAACAACAACCTTTAATGAACATTATCATAAGAATTAAGCAATAGACC
1 TATATTCATCACTCTCAAAACAACAACCTTTAATGAACATTATCATAAGAATTAAGCAATAGACC
34978651 AAACCAACCATCACCAAAACATGAAACATAGCATATA
66 AAACCAACCATCACCAAAACATGAAACATAGCATATA
34978688 TATAT
1 TATAT
34978693 ACTTTCACAA
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 104 1.00
ACGTcount: A:0.47, C:0.22, G:0.06, T:0.24
Consensus pattern (102 bp):
TATATTCATCACTCTCAAAACAACAACCTTTAATGAACATTATCATAAGAATTAAGCAATAGACC
AAACCAACCATCACCAAAACATGAAACATAGCATATA
Found at i:34980790 original size:3 final size:3
Alignment explanation
Indices: 34980772--34980859 Score: 77
Period size: 3 Copynumber: 28.7 Consensus size: 3
34980762 AAAAGGTATT
* * ** * *
34980772 TAA TAA TAT TAG TAA TAA TAA TGC TAA TAA TAA TAA TAA TTA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* **
34980820 TAG TGT TAA TAA TAA TATA TAA TAA TAA TAA TAAA TAA TA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA T-AA TAA TA
34980860 GCACACATTA
Statistics
Matches: 69, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
3 63 0.91
4 6 0.09
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:34981378 original size:2 final size:2
Alignment explanation
Indices: 34981373--34981409 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
34981363 AAAAAAAAAC
34981373 AG AG AG AG 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 AG AG AG AG A
34981410 TGCTCTCTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:34981655 original size:16 final size:17
Alignment explanation
Indices: 34981629--34981660 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
34981619 CAAGTAAGGC
34981629 TTTTCCTTTTCTTTTTG
1 TTTTCCTTTTCTTTTTG
34981646 TTTT-CTTTTCTTTTT
1 TTTTCCTTTTCTTTTT
34981661 AGTATGAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (17 bp):
TTTTCCTTTTCTTTTTG
Found at i:34997431 original size:3 final size:3
Alignment explanation
Indices: 34997423--34997459 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
34997413 CCGTATGAAC
34997423 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
34997460 GCTCCTGCGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:34999099 original size:21 final size:21
Alignment explanation
Indices: 34999073--34999117 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
34999063 ACAAGGAAAC
*
34999073 AAAACAACAAGGAAAGAAATA
1 AAAACAACAAGGAAAGAAAGA
* *
34999094 AAAACAGCAAGGATAGAAAGA
1 AAAACAACAAGGAAAGAAAGA
34999115 AAA
1 AAA
34999118 TCAAAGATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.69, C:0.09, G:0.18, T:0.04
Consensus pattern (21 bp):
AAAACAACAAGGAAAGAAAGA
Found at i:34999341 original size:23 final size:23
Alignment explanation
Indices: 34999297--34999342 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
34999287 TACTTGTATT
*
34999297 TCTATTTTATTTTTTCCGTTATA
1 TCTATTTTATTTTTTCAGTTATA
*
34999320 TCTA-TTTATTTTTATCATTTATA
1 TCTATTTTATTTTT-TCAGTTATA
34999343 AATAATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.22, C:0.11, G:0.02, T:0.65
Consensus pattern (23 bp):
TCTATTTTATTTTTTCAGTTATA
Found at i:35002778 original size:23 final size:22
Alignment explanation
Indices: 35002735--35002780 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
35002725 TGTTTGTTTA
35002735 TATAAAAATGATATATATTATT
1 TATAAAAATGATATATATTATT
*
35002757 TATAAATAAT-ATAATATTTTATT
1 TATAAA-AATGAT-ATATATTATT
35002780 T
1 T
35002781 TGAGACCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
TATAAAAATGATATATATTATT
Found at i:35022177 original size:17 final size:17
Alignment explanation
Indices: 35022151--35022186 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
35022141 TAATATCCAT
*
35022151 AATTTGAATTAAATTTA
1 AATTTAAATTAAATTTA
*
35022168 AATTTAAATTAAGTTTA
1 AATTTAAATTAAATTTA
35022185 AA
1 AA
35022187 ATATTTAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
AATTTAAATTAAATTTA
Found at i:35024107 original size:103 final size:103
Alignment explanation
Indices: 35023923--35024132 Score: 316
Period size: 103 Copynumber: 2.0 Consensus size: 103
35023913 TACCACTATT
* * *
35023923 AACTTGTTTACTCATAACAAGCTGTTCACTTAAGTCATGGTCACTAAATTAATTATATCTTAAGC
1 AACTTGTTTACTCATAACAAGCTGTTCACTTAACTCATAGTCACTAAATTAATTATATCTTAAGA
*
35023988 TACAGAAATCTAAATTGAGATC-CATTAATTTTATATGA
66 TACAGAAATCTAAATTGAGATCTCA-AAATTTTATATGA
*
35024026 AACTTGTTTACTCATAACAAGCTGTTCACTTGACTCATAGTCACTAAATTAATTATATCTTAAGA
1 AACTTGTTTACTCATAACAAGCTGTTCACTTAACTCATAGTCACTAAATTAATTATATCTTAAGA
* * *
35024091 TACAGAACT-TCGAATTGAGATCTGAAAATTTTATATGA
66 TACAGAAATCT-AAATTGAGATCTCAAAATTTTATATGA
35024129 AACT
1 AACT
35024133 AGACTTACAT
Statistics
Matches: 97, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
102 1 0.01
103 95 0.98
104 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (103 bp):
AACTTGTTTACTCATAACAAGCTGTTCACTTAACTCATAGTCACTAAATTAATTATATCTTAAGA
TACAGAAATCTAAATTGAGATCTCAAAATTTTATATGA
Found at i:35027032 original size:21 final size:21
Alignment explanation
Indices: 35027008--35027051 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
35026998 TAGCTTAGTG
35027008 TTTGTATTCATTCTTTATCCT
1 TTTGTATTCATTCTTTATCCT
35027029 TTTGTATTCATTCTTTATCCT
1 TTTGTATTCATTCTTTATCCT
35027050 TT
1 TT
35027052 CATTTCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.18, G:0.05, T:0.64
Consensus pattern (21 bp):
TTTGTATTCATTCTTTATCCT
Found at i:35028344 original size:50 final size:50
Alignment explanation
Indices: 35028268--35028599 Score: 268
Period size: 50 Copynumber: 6.6 Consensus size: 50
35028258 TTTTCTGTAC
* * * * *
35028268 TGCCAATGTCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATCGA
* ** * * *
35028318 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTTTCATCTC-A
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATCGA
* * * * *
35028367 GTGCCAAAGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATCGA
* * *
35028418 TGCCAACGTCATGTCCCAGACATGGTCTTACA-GGGGGCCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAG-CTCTCAT-A--TC---GA
* *
35028474 TGCCAATGCCATGTCCCAGACATGGTCTTACACT--G-GCTCACATACCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACA-TGGGAGCTCTCATATCGA
* * * *
35028522 TGTCGATGCCATGTCCCAAACATGGTCTTACACT---AGCTCACATATCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACA-TGGGAGCTCTCATATCGA
*
35028570 T-CTCGATGCCATGTCCCAGACATGGTCTTA
1 TGC-CAATGCCATGTCCCAGACATGGTCTTA
35028600 TATGAGATCG
Statistics
Matches: 234, Mismatches: 35, Indels: 28
0.79 0.12 0.09
Matches are distributed among these distances:
48 72 0.31
49 3 0.01
50 116 0.50
51 1 0.00
53 3 0.01
54 6 0.03
55 1 0.00
56 32 0.14
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATCGA
Found at i:35028397 original size:100 final size:105
Alignment explanation
Indices: 35028281--35028553 Score: 312
Period size: 100 Copynumber: 2.7 Consensus size: 105
35028271 CAATGTCATA
* * *
35028281 TCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTCT
1 TCCCAGACATGGTCTTACATGGGAGCTCTCATATCGGTGCCAATGCCATGTCCCAGACATGGTCT
*
35028346 TAC-GGGGGACCT-T-TCATCTC-A-G-TGCCAAAGCCATG
66 TACAGGGGG-CCTCTATAATCTCAATGATGCCAAAGCCATG
* * * * *
35028381 TCCTAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGTCATGTCCCAGACATGGTCT
1 TCCCAGACATGGTCTTACATGGGAGCTCTCATATCGGTGCCAATGCCATGTCCCAGACATGGTCT
*
35028446 TACAGGGGGCCTCTCATAATCTCAATGATGCCAATGCCATG
66 TACAGGGGGCCTCT-ATAATCTCAATGATGCCAAAGCCATG
* * * * * *
35028487 TCCCAGACATGGTCTTACACT--G-GCTCACATACCGATGTCGATGCCATGTCCCAAACATGGTC
1 TCCCAGACATGGTCTTACA-TGGGAGCTCTCATATCGGTGCCAATGCCATGTCCCAGACATGGTC
35028549 TTACA
65 TTACA
35028554 CTAGCTCACA
Statistics
Matches: 144, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
100 63 0.44
101 6 0.04
103 6 0.04
104 36 0.25
105 2 0.01
106 30 0.21
107 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (105 bp):
TCCCAGACATGGTCTTACATGGGAGCTCTCATATCGGTGCCAATGCCATGTCCCAGACATGGTCT
TACAGGGGGCCTCTATAATCTCAATGATGCCAAAGCCATG
Found at i:35028550 original size:48 final size:48
Alignment explanation
Indices: 35028479--35028599 Score: 206
Period size: 48 Copynumber: 2.5 Consensus size: 48
35028469 AATGATGCCA
* *
35028479 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATACCGATGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATACCGATCTCG
* *
35028527 ATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCGATCTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATACCGATCTCG
35028575 ATGCCATGTCCCAGACATGGTCTTA
1 ATGCCATGTCCCAGACATGGTCTTA
35028600 TATGAGATCG
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 68 1.00
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATACCGATCTCG
Found at i:35032692 original size:29 final size:29
Alignment explanation
Indices: 35032635--35032693 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
35032625 CAATGTTTAC
* *
35032635 TTTTCAAAATGAATCATTTACGTACATAA
1 TTTTCAAAATGAATCATTTACATAAATAA
* * *
35032664 TTTTCAAAGTGGATCATTTTCATAAATAA
1 TTTTCAAAATGAATCATTTACATAAATAA
35032693 T
1 T
35032694 CAAAATTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (29 bp):
TTTTCAAAATGAATCATTTACATAAATAA
Found at i:35033592 original size:29 final size:29
Alignment explanation
Indices: 35033526--35033591 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
35033516 GTAATTTACC
**
35033526 AATATATATACATTTATTATCTGTTTTAA
1 AATATATATACATTTATTATCTGTGATAA
*
35033555 AAAATATATACATTTATTAT-TG-GATAA
1 AATATATATACATTTATTATCTGTGATAA
*
35033582 AATTTATATA
1 AATATATATA
35033592 TTTAATTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 11 0.34
28 2 0.06
29 19 0.59
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (29 bp):
AATATATATACATTTATTATCTGTGATAA
Found at i:35036754 original size:52 final size:52
Alignment explanation
Indices: 35036650--35036754 Score: 115
Period size: 52 Copynumber: 2.0 Consensus size: 52
35036640 CTGACTTGCT
* * * * *
35036650 AACATGCATTAAGTCTATCCGAATTATAACATATTTAATAAGTATGACTCAA
1 AACATGCATTAAGTCTATCCGAATTAGAACATACTTAATAAGCATAAATCAA
* *
35036702 AACATGCATTGA-TGCTATCCTAATTAGAACATACTTAAT-AGACATAAATCAA
1 AACATGCATTAAGT-CTATCCGAATTAGAACATACTTAATAAG-CATAAATCAA
35036754 A
1 A
35036755 GTAAAATACC
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
51 3 0.07
52 41 0.93
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.30
Consensus pattern (52 bp):
AACATGCATTAAGTCTATCCGAATTAGAACATACTTAATAAGCATAAATCAA
Found at i:35050303 original size:5 final size:5
Alignment explanation
Indices: 35050293--35050318 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
35050283 AGTATACAGA
35050293 GGAGT GGAGT GGAGT GGAGT GGAGT G
1 GGAGT GGAGT GGAGT GGAGT GGAGT G
35050319 AATGACCGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.62, T:0.19
Consensus pattern (5 bp):
GGAGT
Found at i:35051293 original size:22 final size:23
Alignment explanation
Indices: 35051262--35051310 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
35051252 CTTTATGAAA
35051262 TTTTCAAAAAATTTAACTAATT-
1 TTTTCAAAAAATTTAACTAATTC
* *
35051284 TTTTCTAAAATTTTAACTAATTC
1 TTTTCAAAAAATTTAACTAATTC
35051307 TTTT
1 TTTT
35051311 TATATTTGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTTCAAAAAATTTAACTAATTC
Found at i:35051432 original size:21 final size:22
Alignment explanation
Indices: 35051408--35051453 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
35051398 AATATTTTTC
*
35051408 TAAGATATAT-GTT-TTATTAAA
1 TAAGATAT-TGGTTATTATAAAA
35051429 TAAGATATTGGTTATTATAAAA
1 TAAGATATTGGTTATTATAAAA
35051451 TAA
1 TAA
35051454 TTTTTTATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 11 0.50
22 10 0.45
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (22 bp):
TAAGATATTGGTTATTATAAAA
Found at i:35051951 original size:22 final size:23
Alignment explanation
Indices: 35051925--35052135 Score: 147
Period size: 22 Copynumber: 9.0 Consensus size: 23
35051915 ATTTTCACAC
*
35051925 CAAAATTTGGACAGCATATATA-
1 CAAAATTTGGACAGCATATACAT
*
35051947 CAAAATTTGGACTGCATTTATACAT
1 CAAAATTTGGACAGCA--TATACAT
35051972 CAAAATTT-GACAGCATATACAT
1 CAAAATTTGGACAGCATATACAT
*
35051994 -ATATAA-TTGGACTGCATTTATACAT
1 CA-A-AATTTGGACAGCA--TATACAT
35052019 CAAAATTT-GACAGCATATACAT
1 CAAAATTTGGACAGCATATACAT
* *
35052041 -ATATAA-TTGGACTGCATTTTGTACAT
1 CA-A-AATTTGGACAGCA---TATACAT
35052067 CAAAATTT-GACAGCATATACAT
1 CAAAATTTGGACAGCATATACAT
* *
35052089 -ATATAA-TTGGACTGCATTTGTACAT
1 CA-A-AATTTGGACAGCA--TATACAT
35052114 CAAAATTT-GACAGCATATACAT
1 CAAAATTTGGACAGCATATACAT
35052136 TCATTTACTC
Statistics
Matches: 151, Mismatches: 13, Indels: 50
0.71 0.06 0.23
Matches are distributed among these distances:
21 3 0.02
22 50 0.33
23 24 0.16
24 27 0.18
25 35 0.23
26 11 0.07
27 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (23 bp):
CAAAATTTGGACAGCATATACAT
Found at i:35052089 original size:95 final size:95
Alignment explanation
Indices: 35051925--35052135 Score: 347
Period size: 95 Copynumber: 2.2 Consensus size: 95
35051915 ATTTTCACAC
35051925 CAAAATTTGGACAGCATAT--ATACAAAATTTGGACTGCATTTATACATCAAAATTTGACAGCAT
1 CAAAATTT-GACAGCATATACATACAAAATTTGGACTGCATTTATACATCAAAATTTGACAGCAT
35051988 ATACATATATAATTGGACTGCATTTATACAT
65 ATACATATATAATTGGACTGCATTTATACAT
* * *
35052019 CAAAATTTGACAGCATATACATATATAA-TTGGACTGCATTTTGTACATCAAAATTTGACAGCAT
1 CAAAATTTGACAGCATATACATACAAAATTTGGACTGCA-TTTATACATCAAAATTTGACAGCAT
*
35052083 ATACATATATAATTGGACTGCATTTGTACAT
65 ATACATATATAATTGGACTGCATTTATACAT
35052114 CAAAATTTGACAGCATATACAT
1 CAAAATTTGACAGCATATACAT
35052136 TCATTTACTC
Statistics
Matches: 110, Mismatches: 4, Indels: 5
0.92 0.03 0.04
Matches are distributed among these distances:
93 10 0.09
94 18 0.16
95 82 0.75
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (95 bp):
CAAAATTTGACAGCATATACATACAAAATTTGGACTGCATTTATACATCAAAATTTGACAGCATA
TACATATATAATTGGACTGCATTTATACAT
Found at i:35052133 original size:47 final size:47
Alignment explanation
Indices: 35051925--35052135 Score: 345
Period size: 47 Copynumber: 4.5 Consensus size: 47
35051915 ATTTTCACAC
* *
35051925 CAAAATTTGGACAGCATAT--ATACAAAATTTGGACTGCATTTATACAT
1 CAAAATTT-GACAGCATATACATATATAA-TTGGACTGCATTTATACAT
35051972 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAT
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAT
*
35052019 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTTGTACAT
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCA-TTTATACAT
*
35052067 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTGTACAT
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAT
35052114 CAAAATTTGACAGCATATACAT
1 CAAAATTTGACAGCATATACAT
35052136 TCATTTACTC
Statistics
Matches: 158, Mismatches: 3, Indels: 6
0.95 0.02 0.04
Matches are distributed among these distances:
46 10 0.06
47 96 0.61
48 52 0.33
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (47 bp):
CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAT
Found at i:35052421 original size:15 final size:15
Alignment explanation
Indices: 35052387--35052418 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
35052377 TATATACATT
35052387 ACCATATAAATACTA
1 ACCATATAAATACTA
35052402 ACCATA-AAATACTA
1 ACCATATAAATACTA
35052416 ACC
1 ACC
35052419 CATGATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.22
Consensus pattern (15 bp):
ACCATATAAATACTA
Found at i:35053151 original size:43 final size:43
Alignment explanation
Indices: 35053063--35053186 Score: 137
Period size: 43 Copynumber: 2.9 Consensus size: 43
35053053 AGCTAGTGCA
* *** * *
35053063 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATA-CCG
1 ATGCCGACGTCCCAGACGTGGTCTTACACAAAAACACA-AGTCG
35053106 ATGCC-ACTGTCCCAGACAG-GGTCTTACACAAAAACACAAGTCG
1 ATGCCGAC-GTCCCAGAC-GTGGTCTTACACAAAAACACAAGTCG
*
35053149 ATGCCGACGTCCCAGACGTGGTCTTACACGAAAACACA
1 ATGCCGACGTCCCAGACGTGGTCTTACACAAAAACACA
35053187 TATCGGAGTC
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
42 4 0.06
43 63 0.90
44 3 0.04
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (43 bp):
ATGCCGACGTCCCAGACGTGGTCTTACACAAAAACACAAGTCG
Found at i:35055201 original size:15 final size:16
Alignment explanation
Indices: 35055175--35055204 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
35055165 GATTCAGTTG
35055175 ATTTTGAATTGGATCC
1 ATTTTGAATTGGATCC
35055191 ATTTT-AATTGGATC
1 ATTTTGAATTGGATC
35055205 AACATAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.47
Consensus pattern (16 bp):
ATTTTGAATTGGATCC
Found at i:35056908 original size:12 final size:13
Alignment explanation
Indices: 35056891--35056922 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
35056881 TTCTCTCTTA
35056891 AAATTTTTTA-CT
1 AAATTTTTTATCT
35056903 AAATTTTTTATCT
1 AAATTTTTTATCT
35056916 AAATTTT
1 AAATTTT
35056923 ATTTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.59
Consensus pattern (13 bp):
AAATTTTTTATCT
Found at i:35056928 original size:18 final size:18
Alignment explanation
Indices: 35056905--35056940 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
35056895 TTTTTACTAA
35056905 ATTTTTTATCTAA-ATTTT
1 ATTTTTTAT-TAATATTTT
35056923 ATTTTTTATTAATATTTT
1 ATTTTTTATTAATATTTT
35056941 CAAGAATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTTTTATTAATATTTT
Found at i:35063399 original size:21 final size:21
Alignment explanation
Indices: 35063348--35063401 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
35063338 TAATTATTTA
35063348 AAATTTAA-AATTACAATATT
1 AAATTTAATAATTACAATATT
*
35063368 AAATATAAATAATTA-AATATGT
1 AAAT-TTAATAATTACAATAT-T
*
35063390 ACATTTAATAAT
1 AAATTTAATAAT
35063402 GTCGAACATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 4 0.14
21 15 0.54
22 9 0.32
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (21 bp):
AAATTTAATAATTACAATATT
Found at i:35077789 original size:22 final size:22
Alignment explanation
Indices: 35077764--35077839 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 22
35077754 TTGCACTACA
* * *
35077764 GTGCCTTCTAATTTGCACTTTG
1 GTGCCTACTAATTCGCACTTCG
*
35077786 GTGCCTACTGATTCGCACTTCG
1 GTGCCTACTAATTCGCACTTCG
** *
35077808 GTGCCTACT-GCTCGGCACTTCA
1 GTGCCTACTAATTC-GCACTTCG
35077830 GTGCCTACTA
1 GTGCCTACTA
35077840 TTAAAGCATT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
21 2 0.04
22 43 0.96
ACGTcount: A:0.14, C:0.30, G:0.21, T:0.34
Consensus pattern (22 bp):
GTGCCTACTAATTCGCACTTCG
Found at i:35084637 original size:39 final size:40
Alignment explanation
Indices: 35084594--35084698 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 40
35084584 TTCCATTATG
35084594 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
* *** *
35084633 CTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTATT-C----CATTCAACCAAACACAAGATTTA
35084678 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
35084699 ACACCTCTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
39 15 0.28
40 5 0.09
44 17 0.31
45 17 0.31
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:35084692 original size:45 final size:44
Alignment explanation
Indices: 35084592--35084701 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
35084582 TTTTCCATTA
35084592 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
35084631 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
35084676 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
35084702 CCTCTATTCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 25 0.43
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:35084701 original size:16 final size:16
Alignment explanation
Indices: 35084680--35084749 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
35084670 TTGATTTGCT
*
35084680 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
*
35084696 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
35084712 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
35084728 AATACACCTCTAATCC
1 ATTACACCTCTAATCC
*
35084744 AATACA
1 ATTACA
35084750 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:35087137 original size:610 final size:610
Alignment explanation
Indices: 35085971--35087189 Score: 2384
Period size: 610 Copynumber: 2.0 Consensus size: 610
35085961 AATGAACTCC
*
35085971 AGATTCCAGCATCTGGTTCATCAGGCATTTCATTTACATGTCGACCTCACCCTATGTTTATGCAT
1 AGATTCCAGCATCTGGTTCATCAGGCATTTCATTTACATGTCGACCACACCCTATGTTTATGCAT
35086036 TTTTATTTGTTTTAGGGTAGCATAGATAGTCAATCTTGGTTTCAGTTGAATATTTTAACTTCAAA
66 TTTTATTTGTTTTAGGGTAGCATAGATAGTCAATCTTGGTTTCAGTTGAATATTTTAACTTCAAA
35086101 AAACAGATTTAATGTTGGAATTATTAAATGATTAAATTCAACAAACAAGTATCCTCTTTATTGAT
131 AAACAGATTTAATGTTGGAATTATTAAATGATTAAATTCAACAAACAAGTATCCTCTTTATTGAT
35086166 TTTTGCTGTCTCTCAACACTTAATCGATTTCCCTTTTATCATTACAGGTTCTTTCTTCCAACACT
196 TTTTGCTGTCTCTCAACACTTAATCGATTTCCCTTTTATCATTACAGGTTCTTTCTTCCAACACT
35086231 TCTTCATCGCAGTCGTCCCCGATTTGCTCATTACAGGTTAGTTTTCCATTGGTATTTATGGTTTT
261 TCTTCATCGCAGTCGTCCCCGATTTGCTCATTACAGGTTAGTTTTCCATTGGTATTTATGGTTTT
35086296 GTTTGTATGTTTGTATTGCTCATTACAGCCTTTGTATTGCTCATTACTTGTTTCTCGATGGCACA
326 GTTTGTATGTTTGTATTGCTCATTACAGCCTTTGTATTGCTCATTACTTGTTTCTCGATGGCACA
35086361 GTATTTGATATTTAGCTTTGTAAACTTGTAGTCATTAAGGAGGAGTAAAATAACATTTGAATGTT
391 GTATTTGATATTTAGCTTTGTAAACTTGTAGTCATTAAGGAGGAGTAAAATAACATTTGAATGTT
*
35086426 CATTGTCACGTGAAAATTCATTTCTTATGTATTTATATGTACCGTTTCTGTTTGAAGTTTTCCCT
456 CATTGTCACGTGAAAATTCATTTCTTATGTATTTATATGTACCGTTTCTGTTTGAAGCTTTCCCT
35086491 GCACCGGGTAGATAAATGAGTCACTTTTAAATGCTTTATGCTATTGTTCATGATTTCTATGCTAT
521 GCACCGGGTAGATAAATGAGTCACTTTTAAATGCTTTATGCTATTGTTCATGATTTCTATGCTAT
35086556 ACAACTAAATGATGTTTATTTTTAT
586 ACAACTAAATGATGTTTATTTTTAT
* **
35086581 AGATTCTAGCATCTGGTTCATCAGGCATTTCATTTACATGTCGACCACACCCTATGTTTATTTAT
1 AGATTCCAGCATCTGGTTCATCAGGCATTTCATTTACATGTCGACCACACCCTATGTTTATGCAT
35086646 TTTTATTTGTTTTAGGGTAGCATAGATAGTCAATCTTGGTTTCAGTTGAATATTTTAACTTCAAA
66 TTTTATTTGTTTTAGGGTAGCATAGATAGTCAATCTTGGTTTCAGTTGAATATTTTAACTTCAAA
35086711 AAACAGATTTAATGTTGGAATTATTAAATGATTAAATTCAACAAACAAGTATCCTCTTTATTGAT
131 AAACAGATTTAATGTTGGAATTATTAAATGATTAAATTCAACAAACAAGTATCCTCTTTATTGAT
35086776 TTTTGCTGTCTCTCAACACTTAATCGATTTCCCTTTTATCATTACAGGTTCTTTCTTCCAACACT
196 TTTTGCTGTCTCTCAACACTTAATCGATTTCCCTTTTATCATTACAGGTTCTTTCTTCCAACACT
35086841 TCTTCATCGCAGTCGTCCCCGATTTGCTCATTACAGGTTAGTTTTCCATTGGTATTTATGGTTTT
261 TCTTCATCGCAGTCGTCCCCGATTTGCTCATTACAGGTTAGTTTTCCATTGGTATTTATGGTTTT
35086906 GTTTGTATGTTTGTATTGCTCATTACAGCCTTTGTATTGCTCATTACTTGTTTCTCGATGGCACA
326 GTTTGTATGTTTGTATTGCTCATTACAGCCTTTGTATTGCTCATTACTTGTTTCTCGATGGCACA
35086971 GTATTTGATATTTAGCTTTGTAAACTTGTAGTCATTAAGGAGGAGTAAAATAACATTTGAATGTT
391 GTATTTGATATTTAGCTTTGTAAACTTGTAGTCATTAAGGAGGAGTAAAATAACATTTGAATGTT
*
35087036 CATTGTCACGTGAAAATTCATTTCTTATGTATTTATATGTACTGTTTCTGTTTGAAGCTTTCCCT
456 CATTGTCACGTGAAAATTCATTTCTTATGTATTTATATGTACCGTTTCTGTTTGAAGCTTTCCCT
35087101 GCACCGGGTAGATAAATGAGTCACTTTTAAATGCTTTATGCTATTGTTCATGATTTCTATGCTAT
521 GCACCGGGTAGATAAATGAGTCACTTTTAAATGCTTTATGCTATTGTTCATGATTTCTATGCTAT
35087166 ACAACTAAATGATGTTTATTTTTA
586 ACAACTAAATGATGTTTATTTTTA
35087190 CTGATATTCT
Statistics
Matches: 603, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
610 603 1.00
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.43
Consensus pattern (610 bp):
AGATTCCAGCATCTGGTTCATCAGGCATTTCATTTACATGTCGACCACACCCTATGTTTATGCAT
TTTTATTTGTTTTAGGGTAGCATAGATAGTCAATCTTGGTTTCAGTTGAATATTTTAACTTCAAA
AAACAGATTTAATGTTGGAATTATTAAATGATTAAATTCAACAAACAAGTATCCTCTTTATTGAT
TTTTGCTGTCTCTCAACACTTAATCGATTTCCCTTTTATCATTACAGGTTCTTTCTTCCAACACT
TCTTCATCGCAGTCGTCCCCGATTTGCTCATTACAGGTTAGTTTTCCATTGGTATTTATGGTTTT
GTTTGTATGTTTGTATTGCTCATTACAGCCTTTGTATTGCTCATTACTTGTTTCTCGATGGCACA
GTATTTGATATTTAGCTTTGTAAACTTGTAGTCATTAAGGAGGAGTAAAATAACATTTGAATGTT
CATTGTCACGTGAAAATTCATTTCTTATGTATTTATATGTACCGTTTCTGTTTGAAGCTTTCCCT
GCACCGGGTAGATAAATGAGTCACTTTTAAATGCTTTATGCTATTGTTCATGATTTCTATGCTAT
ACAACTAAATGATGTTTATTTTTAT
Found at i:35088833 original size:52 final size:51
Alignment explanation
Indices: 35088772--35088877 Score: 144
Period size: 50 Copynumber: 2.1 Consensus size: 51
35088762 ATAATATGTA
* *
35088772 ATTGCAACTAACGATATAATTTTA-AATTTATTATTGAGCTTTTGATTCATGAT
1 ATTGCAACTAACGATATAATTTTATAA---ATTATTCACCTTTTGATTCATGAT
*
35088825 ATTG-AACTAACGATATAATTTTATAAATTGTTCACCTTTTGATTCATGAT
1 ATTGCAACTAACGATATAATTTTATAAATTATTCACCTTTTGATTCATGAT
35088875 ATT
1 ATT
35088878 AAAAGAAGTA
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
50 24 0.49
52 19 0.39
53 6 0.12
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.45
Consensus pattern (51 bp):
ATTGCAACTAACGATATAATTTTATAAATTATTCACCTTTTGATTCATGAT
Found at i:35090273 original size:91 final size:91
Alignment explanation
Indices: 35090126--35090333 Score: 335
Period size: 91 Copynumber: 2.3 Consensus size: 91
35090116 TTGATTTTAG
* *
35090126 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
35090191 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
*
35090218 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
35090283 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
35090309 CAAATTCATATAAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
35090334 GTTATAATTA
Statistics
Matches: 108, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 92 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:35090302 original size:26 final size:28
Alignment explanation
Indices: 35090248--35090308 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
35090238 TATTATCAAG
* *
35090248 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
35090276 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
35090302 AATTATA
1 AATTATA
35090309 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:35090308 original size:44 final size:43
Alignment explanation
Indices: 35090166--35090308 Score: 121
Period size: 44 Copynumber: 3.2 Consensus size: 43
35090156 GAATTTTATG
* *
35090166 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATAATAATTATTTT
* ** * *
35090210 AAATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAGAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAAT-AATAATTATT-TT
35090257 AAATTATATATTATTATTAAATTATATGTAATAATAATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATAATAATTATTTT
35090301 AAATTATA
1 AAATTATA
35090309 CAAATTCATA
Statistics
Matches: 76, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 21 0.28
45 12 0.16
46 11 0.14
47 13 0.17
48 3 0.04
49 6 0.08
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.48
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATAATAATTATTTT
Found at i:35090427 original size:59 final size:58
Alignment explanation
Indices: 35090337--35090548 Score: 172
Period size: 54 Copynumber: 3.6 Consensus size: 58
35090327 TTTATTAGTT
* *
35090337 ATAATTATTTTAAATT-TTATTA-A--ATCATATATTTTAATTAAAATATATTTAATA
1 ATAATTATGTTAAATTATTTTTATAGTATCATATATTTTAATTAAAATATATTTAATA
* * **
35090391 ATAATTATGTTAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAAT
1 ATAATTATGTTAAATTAT-TTTTATAGTATCATATATT-TTAATT-A--AAA-T-ATAT-TTAAT
35090456 A
58 A
* * * * *
35090457 TTAATTAT-TAAGAATT-TTATTA-A--ATTATATATTTTAATTATAATATATTTAATA
1 ATAATTATGTTA-AATTATTTTTATAGTATCATATATTTTAATTAAAATATATTTAATA
35090511 ATAATTATGTTAAATTATATTTTATAGTATCATATATT
1 ATAATTATGTTAAATTAT-TTTTATAGTATCATATATT
35090549 ATGATTTGAG
Statistics
Matches: 120, Mismatches: 19, Indels: 33
0.70 0.11 0.19
Matches are distributed among these distances:
54 30 0.25
55 8 0.07
56 9 0.08
57 4 0.03
59 20 0.17
60 8 0.07
61 10 0.08
63 4 0.03
64 5 0.04
65 7 0.06
66 15 0.12
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (58 bp):
ATAATTATGTTAAATTATTTTTATAGTATCATATATTTTAATTAAAATATATTTAATA
Found at i:35090462 original size:66 final size:65
Alignment explanation
Indices: 35090387--35090576 Score: 197
Period size: 66 Copynumber: 3.1 Consensus size: 65
35090377 AAATATATTT
35090387 AATAATAATTATGTTAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATAATAATTATGTTAAATTAT-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
35090452 G
65 G
* * * * * * *
35090453 AATATTAATTAT-TAAGAATT-TTATTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT-T
1 AATAATAATTATGTTA-AATTATTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
*
35090506 T
65 G
35090507 AATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATAATAATTATGTTAAATTAT-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
35090572 G
65 G
35090573 AATA
1 AATA
35090577 TTGATTATTA
Statistics
Matches: 94, Mismatches: 16, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
54 15 0.16
55 7 0.07
56 5 0.05
57 3 0.03
58 1 0.01
59 10 0.11
60 8 0.09
61 10 0.11
62 1 0.01
63 3 0.03
64 5 0.05
65 7 0.07
66 19 0.20
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (65 bp):
AATAATAATTATGTTAAATTATTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:35090473 original size:120 final size:120
Alignment explanation
Indices: 35090349--35090646 Score: 542
Period size: 120 Copynumber: 2.5 Consensus size: 120
35090339 AATTATTTTA
* * *
35090349 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
35090414 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
35090469 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
*
35090534 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
35090589 AATTTTATTAAATTATATATTTAAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
35090647 ATGATTAAAT
Statistics
Matches: 172, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
120 166 0.97
121 6 0.03
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:35090504 original size:16 final size:16
Alignment explanation
Indices: 35090483--35090529 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
35090473 TTATTAAATT
35090483 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
35090499 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
35090514 AT-TATGTTAAATTATA
1 ATATAT-TTTAATTATA
35090530 TTTTATAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.42
16 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:35090607 original size:61 final size:61
Alignment explanation
Indices: 35090422--35090609 Score: 192
Period size: 61 Copynumber: 3.1 Consensus size: 61
35090412 TTATAGTATC
*
35090422 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
* * * * * * * *
35090483 ATATATTTTAATTAT-AATATATTTA-ATAATAAT-TATG-TTAAATT-A-TATTTTA-TAGTAT
1 ATATATTATGATT-TGAGTAAATTCATATAAGAATAT-TGATT--ATTAAGAATTTTATTA-AAT
*
35090541 C
61 T
35090542 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
35090603 ATATATT
1 ATATATT
35090610 TAAATTATAA
Statistics
Matches: 96, Mismatches: 19, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
58 3 0.03
59 32 0.33
60 19 0.20
61 39 0.41
62 3 0.03
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
Found at i:35090622 original size:16 final size:16
Alignment explanation
Indices: 35090603--35090647 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
35090593 TTATTAAATT
*
35090603 ATATATTTAAATTATA
1 ATATATTTAAATAATA
35090619 ATATATTT-AATAATA
1 ATATATTTAAATAATA
*
35090634 ATTATGTTTAAATA
1 A-TATATTTAAATA
35090648 TGATTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.28
16 14 0.56
17 4 0.16
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
ATATATTTAAATAATA
Found at i:35090883 original size:16 final size:16
Alignment explanation
Indices: 35090858--35090890 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
35090848 TTGATTTGCT
35090858 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
35090874 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
35090890 A
1 A
35090891 ATATAGCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.36, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:35092493 original size:16 final size:16
Alignment explanation
Indices: 35092472--35092523 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
35092462 TTTGGTTCGC
35092472 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
35092488 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
35092504 TGTATTAGAATAGAGG
1 TGTATTGGATTAGAGG
35092520 TGTA
1 TGTA
35092524 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:35092775 original size:16 final size:16
Alignment explanation
Indices: 35092738--35092779 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
35092728 TTAATCATAT
*
35092738 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
35092754 TT-AAATATATTATAA
1 TTAAAATATATTATAA
35092769 TTAAAATATAT
1 TTAAAATATAT
35092780 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:35092786 original size:14 final size:15
Alignment explanation
Indices: 35092747--35092788 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
35092737 TTTAAACATA
*
35092747 ATTATTATTAAATAT
1 ATTATAATTAAATAT
35092762 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
35092776 A-TATAATTTAATA
1 ATTATAATTAAATA
35092789 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:35092880 original size:120 final size:121
Alignment explanation
Indices: 35092736--35093004 Score: 456
Period size: 120 Copynumber: 2.2 Consensus size: 121
35092726 ATTTAATCAT
35092736 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
35092801 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAA-GATA
66 ATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATG-TA
35092857 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
35092921 ATTAATATTCTTATATGAATTTATTAAAATCATAATATATGATACTATAAAATGTA
66 ATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATGTA
* *
35092977 ATTTGAA-ATAATTAATATTAAATA-ATTA
1 ATTTAAACATAATTATTATTAAATATATTA
35093005 ATGTTGACAA
Statistics
Matches: 142, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
119 4 0.03
120 131 0.92
121 7 0.05
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.43
Consensus pattern (121 bp):
ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATGTA
Found at i:35092897 original size:16 final size:16
Alignment explanation
Indices: 35092854--35092899 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
35092844 ACTATAAAAG
*
35092854 ATAATTTAACATA-ATT
1 ATAA-TTAAAATATATT
*
35092870 ATTATT-AAATATATT
1 ATAATTAAAATATATT
35092885 ATAATTAAAATATAT
1 ATAATTAAAATATAT
35092900 AATTTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 4 0.16
15 10 0.40
16 11 0.44
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAATTAAAATATATT
Found at i:35092906 original size:14 final size:15
Alignment explanation
Indices: 35092854--35092908 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
35092844 ACTATAAAAG
35092854 ATAATTTAACATA-ATT
1 ATAA-TTAA-ATATATT
*
35092870 ATTATTAAATATATT
1 ATAATTAAATATATT
35092885 ATAATTAAA-ATA-T
1 ATAATTAAATATATT
*
35092898 ATAATTTAATA
1 ATAATTAAATA
35092909 AAATTCTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.26
14 7 0.21
15 15 0.44
16 3 0.09
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATTAAATATATT
Found at i:35092971 original size:61 final size:61
Alignment explanation
Indices: 35092786--35092973 Score: 181
Period size: 61 Copynumber: 3.1 Consensus size: 61
35092776 ATATAATTTA
* * *
35092786 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 ATAAAATTCTTAATAATTAATATTCTTATATGAATTTATTAAAATCATAATATATGATACT
** * * * * * * * *
35092847 ATAAAA--GATAAT--TTAACATAATTATTAT-TAAATATATTATAATTAAAATATATAAT-TT
1 ATAAAATTCTTAATAATT-A-AT-ATTCTTATATGAATTTATTAAAATCATAATATATGATACT
35092905 AATAAAATTCTTAATAATTAATATTCTTATATGAATTTATTAAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAATTAATATTCTTATATGAATTTATTAAAATCATAATATATGATACT
35092967 ATAAAAT
1 ATAAAAT
35092974 GTAATTTGAA
Statistics
Matches: 94, Mismatches: 23, Indels: 20
0.69 0.17 0.15
Matches are distributed among these distances:
57 1 0.01
58 2 0.02
59 32 0.34
60 14 0.15
61 41 0.44
62 2 0.02
63 2 0.02
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (61 bp):
ATAAAATTCTTAATAATTAATATTCTTATATGAATTTATTAAAATCATAATATATGATACT
Found at i:35097178 original size:10 final size:10
Alignment explanation
Indices: 35097159--35097189 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
35097149 AATAAAAGCT
*
35097159 ATAAATATTA
1 ATAAAAATTA
35097169 ATAAAAATTA
1 ATAAAAATTA
35097179 ATAAAAATTA
1 ATAAAAATTA
35097189 A
1 A
35097190 AAATTAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
ATAAAAATTA
Found at i:35097192 original size:17 final size:18
Alignment explanation
Indices: 35097169--35097210 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
35097159 ATAAATATTA
35097169 ATAAAAATTA-ATAAAAAT
1 ATAAAAATTAGA-AAAAAT
35097187 -TAAAAATTAGAAAAAAT
1 ATAAAAATTAGAAAAAAT
35097204 ATAAAAA
1 ATAAAAA
35097211 ATGTAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (18 bp):
ATAAAAATTAGAAAAAAT
Found at i:35097607 original size:19 final size:19
Alignment explanation
Indices: 35097557--35097598 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
35097547 TTCAAGTTTT
*
35097557 TTTAA-AATTTTTATTAAAA
1 TTTAATAATTTTT-CTAAAA
35097576 TTTAATAATTTTTCTAAAA
1 TTTAATAATTTTTCTAAAA
35097595 TTTA
1 TTTA
35097599 TTATTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTAATAATTTTTCTAAAA
Found at i:35097614 original size:18 final size:19
Alignment explanation
Indices: 35097557--35097615 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 19
35097547 TTCAAGTTTT
35097557 TTTAA-AATTTTTATTAAAA
1 TTTAATAATTTTT-TTAAAA
*
35097576 TTTAATAATTTTTCTAAAA
1 TTTAATAATTTTTTTAAAA
* *
35097595 TTT-ATTATTTTTTTATAA
1 TTTAATAATTTTTTTAAAA
35097613 TTT
1 TTT
35097616 TTTCTATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.43
19 13 0.37
20 7 0.20
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTAATAATTTTTTTAAAA
Found at i:35116802 original size:18 final size:18
Alignment explanation
Indices: 35116781--35116817 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
35116771 GAGTAATAAG
*
35116781 AGCAGTTAGAAGTCAGTT
1 AGCAATTAGAAGTCAGTT
35116799 AGCAATTAGAAGTCAGTT
1 AGCAATTAGAAGTCAGTT
35116817 A
1 A
35116818 ACACAAACTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (18 bp):
AGCAATTAGAAGTCAGTT
Found at i:35124043 original size:10 final size:11
Alignment explanation
Indices: 35124013--35124042 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
35124003 TCAGACTTGT
*
35124013 AAATATTTTTA
1 AAATATTTTAA
35124024 AAATATTTTAA
1 AAATATTTTAA
35124035 AAATATTT
1 AAATATTT
35124043 ACAAAGTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AAATATTTTAA
Found at i:35124312 original size:7 final size:7
Alignment explanation
Indices: 35124300--35124325 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
35124290 ATATATGTAT
35124300 TATATAA
1 TATATAA
35124307 TATATAA
1 TATATAA
35124314 TATATAA
1 TATATAA
35124321 TATAT
1 TATAT
35124326 GATAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
TATATAA
Found at i:35124394 original size:9 final size:9
Alignment explanation
Indices: 35124379--35124439 Score: 61
Period size: 9 Copynumber: 6.3 Consensus size: 9
35124369 ATGCAAATTG
35124379 AAAGAAA-A
1 AAAGAAATA
35124387 AGAAGAAATA
1 A-AAGAAATA
35124397 AAAGAAATAA
1 AAAGAAAT-A
*
35124407 AATAGAAAGAA
1 AA-AGAAA-TA
35124418 AGAAGAAATA
1 A-AAGAAATA
35124428 AAAGAAATA
1 AAAGAAATA
35124437 AAA
1 AAA
35124440 TAGAAAGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
8 1 0.02
9 24 0.53
10 7 0.16
11 12 0.27
12 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (9 bp):
AAAGAAATA
Found at i:35124420 original size:31 final size:31
Alignment explanation
Indices: 35124385--35124455 Score: 142
Period size: 31 Copynumber: 2.3 Consensus size: 31
35124375 ATTGAAAGAA
35124385 AAAGAAGAAATAAAAGAAATAAAATAGAAAG
1 AAAGAAGAAATAAAAGAAATAAAATAGAAAG
35124416 AAAGAAGAAATAAAAGAAATAAAATAGAAAG
1 AAAGAAGAAATAAAAGAAATAAAATAGAAAG
35124447 AAAGAAGAA
1 AAAGAAGAA
35124456 GGGTGACCGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (31 bp):
AAAGAAGAAATAAAAGAAATAAAATAGAAAG
Found at i:35126061 original size:24 final size:24
Alignment explanation
Indices: 35126015--35126062 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
35126005 GGATTGTAAA
*
35126015 TTGAGTTATAAATATAATGTTGGT
1 TTGAGTTATAAATATAATATTGGT
35126039 TTGAGTATATAAATAT-ATATTGGT
1 TTGAGT-TATAAATATAATATTGGT
35126063 GTTTGAAGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (24 bp):
TTGAGTTATAAATATAATATTGGT
Found at i:35132814 original size:43 final size:43
Alignment explanation
Indices: 35132753--35132890 Score: 179
Period size: 43 Copynumber: 3.2 Consensus size: 43
35132743 AGTTTTGTAT
* ** *
35132753 TTCACCAATGGGCGAATTGTATAAAGTTTGCTTGTGTATAGTA
1 TTCACCAATTGGAAAATTGTATAAAGTCTGCTTGTGTATAGTA
35132796 TTCACCAATTGGAAAATTGTATAAAGTCTGCTTGTGTATAGTA
1 TTCACCAATTGGAAAATTGTATAAAGTCTGCTTGTGTATAGTA
** * *
35132839 TTTGCCAA-TAGACAAATTGTATAAAGCCTGCTTGTGTATAGTA
1 TTCACCAATTGGA-AAATTGTATAAAGTCTGCTTGTGTATAGTA
*
35132882 TTCGCCAAT
1 TTCACCAAT
35132891 AGGTGAACTA
Statistics
Matches: 84, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
42 3 0.04
43 81 0.96
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (43 bp):
TTCACCAATTGGAAAATTGTATAAAGTCTGCTTGTGTATAGTA
Found at i:35132891 original size:43 final size:42
Alignment explanation
Indices: 35132767--35132892 Score: 189
Period size: 43 Copynumber: 3.0 Consensus size: 42
35132757 CCAATGGGCG
* * *
35132767 AATTGTATAAAGTTTGCTTGTGTATAGTATTCACCAATTGGAA
1 AATTGTATAAAGTCTGCTTGTGTATAGTATTCGCCAA-TAGAA
*
35132810 AATTGTATAAAGTCTGCTTGTGTATAGTATTTGCCAATAGACA
1 AATTGTATAAAGTCTGCTTGTGTATAGTATTCGCCAATAGA-A
*
35132853 AATTGTATAAAGCCTGCTTGTGTATAGTATTCGCCAATAG
1 AATTGTATAAAGTCTGCTTGTGTATAGTATTCGCCAATAG
35132893 GTGAACTATG
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
42 3 0.04
43 73 0.96
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (42 bp):
AATTGTATAAAGTCTGCTTGTGTATAGTATTCGCCAATAGAA
Found at i:35137116 original size:22 final size:20
Alignment explanation
Indices: 35137086--35137125 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
35137076 TACATAACCA
35137086 AATCAAATATGATAATATATGC
1 AATCAAATA-GA-AATATATGC
*
35137108 AATCTAATAGAAATATAT
1 AATCAAATAGAAATATAT
35137126 ATTCGAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 2 0.12
22 8 0.47
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (20 bp):
AATCAAATAGAAATATATGC
Found at i:35138763 original size:9 final size:9
Alignment explanation
Indices: 35138749--35138804 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
35138739 CAACATGGTT
*
35138749 TTTTATTGA
1 TTTTATTTA
35138758 TTTTATTTTA
1 TTTTA-TTTA
35138768 TTTTATTTA
1 TTTTATTTA
35138777 -TTTATTTTA
1 TTTTA-TTTA
* *
35138786 TCTTATCT-
1 TTTTATTTA
35138794 TTTTATTTA
1 TTTTATTTA
35138803 TT
1 TT
35138805 ACCCTAGCTA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
8 10 0.26
9 17 0.45
10 11 0.29
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.75
Consensus pattern (9 bp):
TTTTATTTA
Found at i:35138777 original size:23 final size:22
Alignment explanation
Indices: 35138748--35138800 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 22
35138738 TCAACATGGT
* *
35138748 TTTTTATTGATTTTATTTTATT
1 TTTTTATTGATTTTATCTTATC
*
35138770 TTATTTATTTATTTTATCTTATC
1 TT-TTTATTGATTTTATCTTATC
35138793 TTTTTATT
1 TTTTTATT
35138801 TATTACCCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 8 0.30
23 19 0.70
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (22 bp):
TTTTTATTGATTTTATCTTATC
Done.