Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 92 of 290
Found at i:28283874 original size:37 final size:37
Alignment explanation
Indices: 28283822--28283896 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 37
28283812 GCTCTAAAGG
* *
28283822 CCCGATGACTACGTGTGG-GACTTTTGTCCGGGTAAGA
1 CCCGATAACTACGTGTGGAGA-TTATGTCCGGGTAAGA
*
28283859 CCCGATAACTTCGTGTGGAGATTATGTCCGGGTAAGA
1 CCCGATAACTACGTGTGGAGATTATGTCCGGGTAAGA
28283896 C
1 C
28283897 TTCGTAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 32 0.94
38 2 0.06
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.27
Consensus pattern (37 bp):
CCCGATAACTACGTGTGGAGATTATGTCCGGGTAAGA
Found at i:28291905 original size:21 final size:22
Alignment explanation
Indices: 28291876--28291924 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
28291866 GCCTAAATTT
*
28291876 TTTTCGCTATTATTTCG-TGTTA
1 TTTT-GCTACTATTTCGATGTTA
*
28291898 TTTTGCTACTATTTTGATGTTA
1 TTTTGCTACTATTTCGATGTTA
28291920 TTTTG
1 TTTTG
28291925 TTGTCATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.14, C:0.10, G:0.14, T:0.61
Consensus pattern (22 bp):
TTTTGCTACTATTTCGATGTTA
Found at i:28294330 original size:6 final size:6
Alignment explanation
Indices: 28294300--28294329 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
28294290 TTTAAAGCTA
*
28294300 AAGCAG AAGCAG AAGCAG AAGCAG CAGCAG
1 AAGCAG AAGCAG AAGCAG AAGCAG AAGCAG
28294330 CCTAGCTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.47, C:0.20, G:0.33, T:0.00
Consensus pattern (6 bp):
AAGCAG
Found at i:28294517 original size:3 final size:3
Alignment explanation
Indices: 28294511--28294556 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
28294501 GTACTACTCT
28294511 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
28294557 AGTCTGGTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28297747 original size:6 final size:6
Alignment explanation
Indices: 28297736--28297761 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
28297726 TCAAGAAATA
28297736 ATTTTC ATTTTC ATTTTC ATTTTC AT
1 ATTTTC ATTTTC ATTTTC ATTTTC AT
28297762 AGAAAATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.65
Consensus pattern (6 bp):
ATTTTC
Found at i:28301625 original size:13 final size:13
Alignment explanation
Indices: 28301609--28301633 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28301599 TGGATAAATA
28301609 ATTAGAAATATTT
1 ATTAGAAATATTT
28301622 ATTAGAAATATT
1 ATTAGAAATATT
28301634 ATAATATTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
ATTAGAAATATTT
Found at i:28308677 original size:67 final size:67
Alignment explanation
Indices: 28308544--28308700 Score: 178
Period size: 67 Copynumber: 2.3 Consensus size: 67
28308534 GACCTAGCCA
* * *
28308544 ATTTATCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGGATCACACATGCGACCTAACT
1 ATTTATCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTTGGGATCACACATGCAACCTAACT
28308609 AC
66 AC
* * *
28308611 ATTTATCCCGTAGCTCTCTTGTCTACATGG-GATACATC-C-T-GTATCACACATGTAACCTAGC
1 ATTTATCTCGTAGCTCTCTTGTCTACATGGTG-TACATCACTTGGGATCACACATGCAACCTA--
28308672 TACTAC
63 -ACTAC
*
28308678 ATAGTATCTCGTAGCTCTCTTGT
1 AT-TTATCTCGTAGCTCTCTTGT
28308701 ACACATGATG
Statistics
Matches: 77, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
64 16 0.21
65 1 0.01
66 2 0.03
67 40 0.52
68 18 0.23
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.35
Consensus pattern (67 bp):
ATTTATCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTTGGGATCACACATGCAACCTAACT
AC
Found at i:28311165 original size:40 final size:40
Alignment explanation
Indices: 28311121--28311308 Score: 292
Period size: 40 Copynumber: 4.7 Consensus size: 40
28311111 GCTACTTGCT
28311121 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
28311161 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
28311201 CAAATGCCTTCGAGACTTAGCCC-GTATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGT-TATAGTAACTCGCA
* * * *
28311241 CAAATGCCTTCGGG-CTTAGCCCAG-AATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
28311280 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
28311309 CATCCGAATA
Statistics
Matches: 136, Mismatches: 7, Indels: 10
0.89 0.05 0.07
Matches are distributed among these distances:
38 1 0.01
39 34 0.25
40 100 0.74
41 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:28313837 original size:25 final size:25
Alignment explanation
Indices: 28313799--28313882 Score: 75
Period size: 25 Copynumber: 3.4 Consensus size: 25
28313789 TTCATATTCG
28313799 GGAATGCTCATTCGAGCACATA-AACA
1 GGAA-GCTCATTCGAGC-CATATAACA
* *
28313825 GGAAGCTCTTTCGAGCCATATAACG
1 GGAAGCTCATTCGAGCCATATAACA
** *
28313850 GGAAGCTCCA-GGGAGCCAT-TAACG
1 GGAAGCT-CATTCGAGCCATATAACA
28313874 GGAAGCTCA
1 GGAAGCTCA
28313883 CACAAGCATA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
23 2 0.04
24 16 0.31
25 28 0.55
26 5 0.10
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (25 bp):
GGAAGCTCATTCGAGCCATATAACA
Found at i:28313965 original size:26 final size:25
Alignment explanation
Indices: 28313934--28313985 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
28313924 GAAGCTCCGG
28313934 AGAGCCATTAATC-GGAAAGCTCACAA
1 AGAGCC-TTAATCAGGAAA-CTCACAA
*
28313960 AGAGCCTTTATCAGGAAACTCACAA
1 AGAGCCTTAATCAGGAAACTCACAA
28313985 A
1 A
28313986 ATGCCATGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.17
Consensus pattern (25 bp):
AGAGCCTTAATCAGGAAACTCACAA
Found at i:28315055 original size:20 final size:20
Alignment explanation
Indices: 28315030--28315070 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
28315020 ATACCGTCGT
28315030 AACATAGACACATAAAATAC
1 AACATAGACACATAAAATAC
*
28315050 AACATAGACACATGAAATAC
1 AACATAGACACATAAAATAC
28315070 A
1 A
28315071 TTGTGAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.59, C:0.20, G:0.07, T:0.15
Consensus pattern (20 bp):
AACATAGACACATAAAATAC
Found at i:28325069 original size:49 final size:49
Alignment explanation
Indices: 28324953--28325321 Score: 178
Period size: 47 Copynumber: 7.8 Consensus size: 49
28324943 AAACATGGGT
*
28324953 TAAGTTGCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCTTCA
1 TAAG-TGCTGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCTTCA
* * * * *
28325003 TCGAG-GCCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCGTGT-A
1 T-AAGTGCTGATGCCATGTCCCAGACATGGTCTTACACTAGCTATC-T-TCA
*
28325053 TAAGTGCTGATG-CATGTCCCAGACAT-GTCTAACACTAGC-A----C-
1 TAAGTGCTGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCTTCA
* * * ** * * *
28325094 GAAGCTTAGCCGATG-CATGTCCTAGACA-CATCTTACACTGGCTACCATCA
1 TAAG--T-GCTGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCTTCA
* * * * * *
28325144 TTGAG-GCCGATG-TATGTCCCAGACAT-GTCATACATTGGC-ACTCATTTC-
1 -TAAGTGCTGATGCCATGTCCCAGACATGGTCTTACACTAGCTA-TC--TTCA
* *
28325192 T-A-TGCTAATGCCATGTCCCAGACATGGTCTTACACTAGCTAT-TGTAA
1 TAAGTGCTGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCT-TCA
* ** *
28325239 T-A-TAGCTGATG-CATGTCCTAGACAT-GTCTTACACTAGCCCTCGTC-
1 TAAGT-GCTGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCTTCA
*
28325284 TCAA-TGCCGATGCCATGTCCCAGACATGGTCTTACACT
1 T-AAGTGCTGATGCCATGTCCCAGACATGGTCTTACACT
28325322 GGCTCTCACA
Statistics
Matches: 245, Mismatches: 42, Indels: 66
0.69 0.12 0.19
Matches are distributed among these distances:
41 3 0.01
43 1 0.00
44 28 0.11
45 3 0.01
46 29 0.12
47 74 0.30
48 39 0.16
49 53 0.22
50 10 0.04
51 5 0.02
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (49 bp):
TAAGTGCTGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCTTCA
Found at i:28328220 original size:13 final size:13
Alignment explanation
Indices: 28328202--28328227 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28328192 TCGGCAGGGA
28328202 CACGCCCGTGTGC
1 CACGCCCGTGTGC
28328215 CACGCCCGTGTGC
1 CACGCCCGTGTGC
28328228 GATTACTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.46, G:0.31, T:0.15
Consensus pattern (13 bp):
CACGCCCGTGTGC
Found at i:28350022 original size:38 final size:38
Alignment explanation
Indices: 28349974--28350052 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
28349964 AAAAAGTAGT
28349974 TTTAATAAAAATTAAAAACATAAAATAATAAATAAATG
1 TTTAATAAAAATTAAAAACATAAAATAATAAATAAATG
28350012 TTTAATAAAAATTAAAAACATAAAATAATAAATAAATG
1 TTTAATAAAAATTAAAAACATAAAATAATAAATAAATG
28350050 TTT
1 TTT
28350053 TTAAACATCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (38 bp):
TTTAATAAAAATTAAAAACATAAAATAATAAATAAATG
Found at i:28365101 original size:24 final size:24
Alignment explanation
Indices: 28365016--28365103 Score: 81
Period size: 25 Copynumber: 3.6 Consensus size: 24
28365006 ATTTGAGAAT
* * *
28365016 GCTCATTTGAGCACATAAACAGGAA
1 GCTCATATGAGC-CATTAACGGGAA
*
28365041 GCTC-TTTCGAGCCATTTAACGGGAA
1 GCTCATAT-GAGCCA-TTAACGGGAA
*
28365066 GCTCCAGA-GAGCCATTAACGGGAA
1 GCT-CATATGAGCCATTAACGGGAA
28365090 GCTCATATGAGCCA
1 GCTCATATGAGCCA
28365104 ATATAGAGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
23 3 0.06
24 24 0.45
25 25 0.47
26 1 0.02
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.20
Consensus pattern (24 bp):
GCTCATATGAGCCATTAACGGGAA
Found at i:28365211 original size:26 final size:26
Alignment explanation
Indices: 28365154--28365208 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
28365144 GAAGAGACAT
* * * *
28365154 TAATCGGGAAGCTCACAAGGAGTCTT
1 TAATCGGGAAACTCACAAAGAGCCTG
28365180 TAATCGGGAAACTCACAAAGAGCCATG
1 TAATCGGGAAACTCACAAAGAGCC-TG
28365207 TA
1 TA
28365209 TCGAGACGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 21 0.88
27 3 0.12
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (26 bp):
TAATCGGGAAACTCACAAAGAGCCTG
Found at i:28367020 original size:49 final size:49
Alignment explanation
Indices: 28366853--28367161 Score: 171
Period size: 49 Copynumber: 6.3 Consensus size: 49
28366843 CATGGTTAAT
* * * * * *
28366853 AACTAACATGCCCTACT-GATGGCAACACC-CATATCGCTAGTCTGGTTAAC
1 AACTAACATGCCCTACTAG-TGGC-CCACCTTAT-TCGCCAATCTGATTAGC
* * * *
28366903 AACTAACATGCCCTACCAGAGACCCAGCACTTA--CACCAATCT-AGTTAGC
1 AACTAACATGCCCTACTAGTGGCCCA-C-CTTATTCGCCAATCTGA-TTAGC
* * * ** **
28366952 AATTAACATGACCAACTAGTGGCCCACCTTATTTACGGATCTGATTAGC
1 AACTAACATGCCCTACTAGTGGCCCACCTTATTCGCCAATCTGATTAGC
* * * * * *
28367001 AACTAACATGCCCTGCTAGTGGTCTATCATCTTCGCCAATCT-AGTTAGC
1 AACTAACATGCCCTACTAGTGGCCCACCTTATTCGCCAATCTGA-TTAGC
* * * *
28367050 AACTAACATGCCCTACCAGTGGCCCACCTTATTCGCCTATCTGGTTAGA
1 AACTAACATGCCCTACTAGTGGCCCACCTTATTCGCCAATCTGATTAGC
* * * * * * ** * * *
28367099 AACTAACATGCCTTACAAATGGTCTATCACATCCGCCAAGCTGGTTAGC
1 AACTAACATGCCCTACTAGTGGCCCACCTTATTCGCCAATCTGATTAGC
28367148 AACTAACATGCCCT
1 AACTAACATGCCCT
28367162 GCCAGTGATC
Statistics
Matches: 194, Mismatches: 55, Indels: 21
0.72 0.20 0.08
Matches are distributed among these distances:
47 4 0.02
48 2 0.01
49 165 0.85
50 20 0.10
51 2 0.01
52 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (49 bp):
AACTAACATGCCCTACTAGTGGCCCACCTTATTCGCCAATCTGATTAGC
Found at i:28367071 original size:98 final size:98
Alignment explanation
Indices: 28366938--28367168 Score: 284
Period size: 98 Copynumber: 2.4 Consensus size: 98
28366928 AGCACTTACA
* * * * * * *
28366938 CCAATCTAGTTAGCAATTAACATGACCAACTAGTGGCCCACCTTATTTACGGATCTGATTAGCAA
1 CCAATCTAGTTAGCAACTAACATGCCCTACCAGTGGCCCACCTTATTCACCGATCTGATTAGAAA
* * * *
28367003 CTAACATGCCCTGCTAGTGGTCTATCATC-TTCG
66 CTAACATGCCCTACAAATGGTCTATCA-CATCCG
* * *
28367036 CCAATCTAGTTAGCAACTAACATGCCCTACCAGTGGCCCACCTTATTCGCCTATCTGGTTAGAAA
1 CCAATCTAGTTAGCAACTAACATGCCCTACCAGTGGCCCACCTTATTCACCGATCTGATTAGAAA
*
28367101 CTAACATGCCTTACAAATGGTCTATCACATCCG
66 CTAACATGCCCTACAAATGGTCTATCACATCCG
* * *
28367134 CCAAGCTGGTTAGCAACTAACATGCCCTGCCAGTG
1 CCAATCTAGTTAGCAACTAACATGCCCTACCAGTG
28367169 ATCCATCTTA
Statistics
Matches: 114, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
97 1 0.01
98 113 0.99
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (98 bp):
CCAATCTAGTTAGCAACTAACATGCCCTACCAGTGGCCCACCTTATTCACCGATCTGATTAGAAA
CTAACATGCCCTACAAATGGTCTATCACATCCG
Found at i:28371434 original size:76 final size:76
Alignment explanation
Indices: 28371242--28371466 Score: 243
Period size: 76 Copynumber: 3.0 Consensus size: 76
28371232 AAAGGAGTGA
* * * * * **
28371242 TTGATATCGTCCGTTTATCCGACTAGTGCCGGGCGCGAATCTTCGTCAGTATATCCAACTAAAGC
1 TTGATATCGTCAGTTTATTCGACTAGTGCTGGGCGCAAATCTTCGTTAGTATATCCAACTAGTGC
*
28371307 TAGGTACATAT
66 TAGGCACATAT
* ** * * * * * *
28371318 ATGATATCGTTGGTTTATTCGACTAGCGTTGGGCGTAAATCTTTGTTGGTATATCCAACTAGTGT
1 TTGATATCGTCAGTTTATTCGACTAGTGCTGGGCGCAAATCTTCGTTAGTATATCCAACTAGTGC
*
28371383 TGGGCACATAT
66 TAGGCACATAT
* ** * *
28371394 TTGATATCGTCAGTTTATTCGACTAGTGCTAGGAACAAATCTTCGTTTGTATATCCAATTAGTGC
1 TTGATATCGTCAGTTTATTCGACTAGTGCTGGGCGCAAATCTTCGTTAGTATATCCAACTAGTGC
28371459 TAGGCACA
66 TAGGCACA
28371467 AATCATTGTC
Statistics
Matches: 118, Mismatches: 31, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
76 118 1.00
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.35
Consensus pattern (76 bp):
TTGATATCGTCAGTTTATTCGACTAGTGCTGGGCGCAAATCTTCGTTAGTATATCCAACTAGTGC
TAGGCACATAT
Found at i:28371485 original size:36 final size:36
Alignment explanation
Indices: 28371415--28371502 Score: 97
Period size: 36 Copynumber: 2.4 Consensus size: 36
28371405 AGTTTATTCG
* **
28371415 ACTAGTGCTAGGAACAAATCTTCGTTTGTATATCCA
1 ACTAGTGCTAGGCACAAATCTTCGTCGGTATATCCA
* * *
28371451 ATTAGTGCTAGGCACAAATCATT-GTCGGTTTATCCG
1 ACTAGTGCTAGGCACAAATC-TTCGTCGGTATATCCA
*
28371487 GCTAGTGCTAGGCACA
1 ACTAGTGCTAGGCACA
28371503 CATTTGATAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
36 41 0.95
37 2 0.05
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (36 bp):
ACTAGTGCTAGGCACAAATCTTCGTCGGTATATCCA
Found at i:28380572 original size:21 final size:21
Alignment explanation
Indices: 28380548--28380611 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
28380538 AATGTGTAAG
28380548 TATGTCTTCAAATTTAAGCTA
1 TATGTCTTCAAATTTAAGCTA
*
28380569 TATG---T-GAATGTGTAAG-T-
1 TATGTCTTCAAAT-T-TAAGCTA
28380586 TATGTCTTCAAATTTAAGCTA
1 TATGTCTTCAAATTTAAGCTA
28380607 TATGT
1 TATGT
28380612 GAATGTGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 16
0.65 0.04 0.31
Matches are distributed among these distances:
17 7 0.21
18 3 0.09
19 8 0.24
20 3 0.09
21 12 0.36
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (21 bp):
TATGTCTTCAAATTTAAGCTA
Found at i:28380596 original size:38 final size:38
Alignment explanation
Indices: 28380538--28380645 Score: 209
Period size: 38 Copynumber: 2.9 Consensus size: 38
28380528 TAAGAATGAA
28380538 AATGTGTAAG-TATGTCTTCAAATTTAAGCTATATGTG
1 AATGTGTAAGTTATGTCTTCAAATTTAAGCTATATGTG
28380575 AATGTGTAAGTTATGTCTTCAAATTTAAGCTATATGTG
1 AATGTGTAAGTTATGTCTTCAAATTTAAGCTATATGTG
28380613 AATGTGTAAGTTATGTCTTCAAATTTAAGCTAT
1 AATGTGTAAGTTATGTCTTCAAATTTAAGCTAT
28380646 GCCTATGAAT
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
37 10 0.14
38 60 0.86
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (38 bp):
AATGTGTAAGTTATGTCTTCAAATTTAAGCTATATGTG
Found at i:28380603 original size:19 final size:19
Alignment explanation
Indices: 28380581--28380646 Score: 55
Period size: 19 Copynumber: 3.5 Consensus size: 19
28380571 TGTGAATGTG
*
28380581 TAAGTTATGTCTTCAAATT
1 TAAGCTATGTCTTCAAATT
* * *
28380600 TAAGCTATAT-GT-GAATGT
1 TAAGCTATGTCTTCAAAT-T
*
28380618 GTAAGTTATGTCTTCAAATT
1 -TAAGCTATGTCTTCAAATT
28380638 TAAGCTATG
1 TAAGCTATG
28380647 CCTATGAATA
Statistics
Matches: 34, Mismatches: 9, Indels: 8
0.67 0.18 0.16
Matches are distributed among these distances:
17 3 0.09
18 2 0.06
19 24 0.71
20 2 0.06
21 3 0.09
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (19 bp):
TAAGCTATGTCTTCAAATT
Found at i:28392761 original size:16 final size:16
Alignment explanation
Indices: 28392742--28392772 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28392732 CTTCTTCACT
28392742 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
28392758 TACTTACTTACTTAA
1 TACTCACTTACTTAA
28392773 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:28392778 original size:20 final size:20
Alignment explanation
Indices: 28392739--28392778 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
28392729 AAACTTCTTC
* *
28392739 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
28392759 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
28392779 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:28393152 original size:55 final size:53
Alignment explanation
Indices: 28392974--28393218 Score: 189
Period size: 55 Copynumber: 4.6 Consensus size: 53
28392964 ATTACCATTT
* * * *
28392974 CCATGACTTGTCATGGTCTTACAT-GG-T-A-T-CCTTTTGAAACTTATCATTG
1 CCATGTCTTGACATGGTCTTACATGGGATCATTGCCTTATG-AACTTATCAATG
* * * * * *
28393023 ACATGTCTCGACATGGTTTTACATGGTATCATTGCCTTATGAGCTTACCAATG
1 CCATGTCTTGACATGGTCTTACATGGGATCATTGCCTTATGAACTTATCAATG
* *
28393076 CCATGCCTTGGCATGGTCTTACATGGGA-CATTTGCCTTATAGTAACTTATCAATG
1 CCATGTCTTGACATGGTCTTACATGGGATCA-TTGCCTTAT-G-AACTTATCAATG
* * * * *
28393131 CCATGTCTTGACATAGTCTTACATGGTATCCTTGCCTTA-GAAACCTTACCAATTA
1 CCATGTCTTGACATGGTCTTACATGGGATCATTGCCTTATG-AA-CTTATCAA-TG
* * * *
28393186 CCATGCCTTGGCATGTTCTTACATGGTATCATT
1 CCATGTCTTGACATGGTCTTACATGGGATCATT
28393219 AAACCCTAAT
Statistics
Matches: 154, Mismatches: 31, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
49 19 0.12
50 1 0.01
51 1 0.01
52 3 0.02
53 44 0.29
54 14 0.09
55 71 0.46
56 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (53 bp):
CCATGTCTTGACATGGTCTTACATGGGATCATTGCCTTATGAACTTATCAATG
Found at i:28393153 original size:108 final size:109
Alignment explanation
Indices: 28393011--28393211 Score: 289
Period size: 108 Copynumber: 1.8 Consensus size: 109
28393001 ATCCTTTTGA
* * * *
28393011 AACTTATCATTGACATGTCTCGACATGGTTTTACATGGTATCATTGCCTTATG-AGCTTACCAA-
1 AACTTATCAATGACATGTCTCGACATAGTCTTACATGGTATCATTGCCTTA-GAACCTTACCAAT
*
28393074 TGCCATGCCTTGGCATGGTCTTACATGGGACATTTGCCTTATAGT
65 TACCATGCCTTGGCATGGTCTTACATGGGACATTTGCCTTATAGT
* * *
28393119 AACTTATCAATGCCATGTCTTGACATAGTCTTACATGGTATCCTTGCCTTAGAAACCTTACCAAT
1 AACTTATCAATGACATGTCTCGACATAGTCTTACATGGTATCATTGCCTTAG-AACCTTACCAAT
*
28393184 TACCATGCCTTGGCATGTTCTTACATGG
65 TACCATGCCTTGGCATGGTCTTACATGG
28393212 TATCATTAAA
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
107 1 0.01
108 45 0.56
109 9 0.11
110 26 0.32
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.35
Consensus pattern (109 bp):
AACTTATCAATGACATGTCTCGACATAGTCTTACATGGTATCATTGCCTTAGAACCTTACCAATT
ACCATGCCTTGGCATGGTCTTACATGGGACATTTGCCTTATAGT
Found at i:28396081 original size:50 final size:50
Alignment explanation
Indices: 28396019--28396140 Score: 235
Period size: 50 Copynumber: 2.4 Consensus size: 50
28396009 GCCAATGCCA
28396019 TGTCCCAGACATGGTCTTACACAAGCTCTAGCATATCTATTCTGATGTCG
1 TGTCCCAGACATGGTCTTACACAAGCTCTAGCATATCTATTCTGATGTCG
*
28396069 TGTCCCAAACATGGTCTTACACAAGCTCTAGCATATCTATTCTGATGTCG
1 TGTCCCAGACATGGTCTTACACAAGCTCTAGCATATCTATTCTGATGTCG
28396119 TGTCCCAGACATGGTCTTACAC
1 TGTCCCAGACATGGTCTTACAC
28396141 TGACACATCT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 70 1.00
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (50 bp):
TGTCCCAGACATGGTCTTACACAAGCTCTAGCATATCTATTCTGATGTCG
Found at i:28396188 original size:44 final size:45
Alignment explanation
Indices: 28396119--28396325 Score: 161
Period size: 46 Copynumber: 4.5 Consensus size: 45
28396109 TCTGATGTCG
* *
28396119 TGTCCCAGACATGGTCTTACACTGAC-ACATCTTGTA-GCCGATGTA
1 TGTCCCAGACAT-GTCTTACACTGACTACATCTCG-AGGCCGATGCA
*
28396164 TGTCCCAGACATGTCTTACACTGACTTACGTCTCGAGGCCGATGCA
1 TGTCCCAGACATGTCTTACACTGAC-TACATCTCGAGGCCGATGCA
* * * * * *
28396210 TGTCTCAGACATGTCTTACACTAGCACT-CGTCTCAATGTCGATGCTG
1 TGTCCCAGACATGTCTTACACT-G-ACTACATCTCGAGGCCGATGC-A
* * * * * * *
28396257 TGTCCTAGACATGGTCTTATACTGGCTCTCATAAT-GTGGCCGATACA
1 TGTCCCAGACAT-GTCTTACACTGACT-ACAT-CTCGAGGCCGATGCA
28396304 TGTCCCAGACATGTCTTACACT
1 TGTCCCAGACATGTCTTACACT
28396326 AGTTCACAAT
Statistics
Matches: 130, Mismatches: 22, Indels: 19
0.76 0.13 0.11
Matches are distributed among these distances:
44 13 0.10
45 13 0.10
46 60 0.46
47 24 0.18
48 19 0.15
49 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.30
Consensus pattern (45 bp):
TGTCCCAGACATGTCTTACACTGACTACATCTCGAGGCCGATGCA
Found at i:28399320 original size:25 final size:25
Alignment explanation
Indices: 28399292--28399343 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
28399282 TGGGCTATGA
*
28399292 ATTTTACTATTATAAATGATGCTAC
1 ATTTCACTATTATAAATGATGCTAC
28399317 ATTTCACTATTATAAATGATGCTAC
1 ATTTCACTATTATAAATGATGCTAC
28399342 AT
1 AT
28399344 ACTGCATAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (25 bp):
ATTTCACTATTATAAATGATGCTAC
Found at i:28417156 original size:22 final size:22
Alignment explanation
Indices: 28417109--28417163 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 22
28417099 TTTATTATTT
* * *
28417109 TTATATG-ATTTTTTTTATAATT
1 TTATATGTA-TTTTTATAAAATC
28417131 TTATATGTATTTTTATAAAATC
1 TTATATGTATTTTTATAAAATC
28417153 -T-TATGTATTTT
1 TTATATGTATTTT
28417164 AATTAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 10 0.34
21 1 0.03
22 17 0.59
23 1 0.03
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (22 bp):
TTATATGTATTTTTATAAAATC
Found at i:28417565 original size:29 final size:29
Alignment explanation
Indices: 28417523--28417581 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
28417513 ATTATAAAAG
28417523 TATAAAAAATTGGTAAAACACAACTACCT
1 TATAAAAAATTGGTAAAACACAACTACCT
28417552 TATAAAAAATTGGTAAAACACAACTACCT
1 TATAAAAAATTGGTAAAACACAACTACCT
28417581 T
1 T
28417582 GAAGTTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.51, C:0.17, G:0.07, T:0.25
Consensus pattern (29 bp):
TATAAAAAATTGGTAAAACACAACTACCT
Found at i:28423875 original size:35 final size:35
Alignment explanation
Indices: 28423836--28423947 Score: 88
Period size: 35 Copynumber: 3.1 Consensus size: 35
28423826 TTTAGATGAA
28423836 AGATTTGGGACCAGCAAAGAAGATACTTGGTATGG
1 AGATTTGGGACCAGCAAAGAAGATACTTGGTATGG
* * * * *
28423871 AGATTCTCAGAGA-TAGAAAAGCAAG-TAAATT-GT-TGAA
1 AGATT-T--GGGACCAGCAAAG-AAGAT-ACTTGGTATG-G
*
28423908 AGATTTAGGACCAGCAAAGAAGATACTTGGTATGG
1 AGATTTGGGACCAGCAAAGAAGATACTTGGTATGG
28423943 AGATT
1 AGATT
28423948 CTTAGAGATA
Statistics
Matches: 56, Mismatches: 11, Indels: 20
0.64 0.13 0.23
Matches are distributed among these distances:
34 8 0.14
35 19 0.34
36 6 0.11
37 14 0.25
38 9 0.16
ACGTcount: A:0.39, C:0.10, G:0.27, T:0.24
Consensus pattern (35 bp):
AGATTTGGGACCAGCAAAGAAGATACTTGGTATGG
Found at i:28423910 original size:72 final size:72
Alignment explanation
Indices: 28423832--28423975 Score: 270
Period size: 72 Copynumber: 2.0 Consensus size: 72
28423822 GAATTTTAGA
*
28423832 TGAAAGATTTGGGACCAGCAAAGAAGATACTTGGTATGGAGATTCTCAGAGATAGAAAAGCAAGT
1 TGAAAGATTTAGGACCAGCAAAGAAGATACTTGGTATGGAGATTCTCAGAGATAGAAAAGCAAGT
28423897 AAATTGT
66 AAATTGT
*
28423904 TGAAAGATTTAGGACCAGCAAAGAAGATACTTGGTATGGAGATTCTTAGAGATAGAAAAGCAAGT
1 TGAAAGATTTAGGACCAGCAAAGAAGATACTTGGTATGGAGATTCTCAGAGATAGAAAAGCAAGT
28423969 AAATTGT
66 AAATTGT
28423976 ACCTAAGTCA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.41, C:0.09, G:0.26, T:0.24
Consensus pattern (72 bp):
TGAAAGATTTAGGACCAGCAAAGAAGATACTTGGTATGGAGATTCTCAGAGATAGAAAAGCAAGT
AAATTGT
Found at i:28425965 original size:15 final size:17
Alignment explanation
Indices: 28425931--28425969 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
28425921 TCTAATAAAA
28425931 TAAA-TAAATAATTAAT
1 TAAATTAAATAATTAAT
28425947 TAAATTAAA-AATT-AT
1 TAAATTAAATAATTAAT
28425962 TAAATTAA
1 TAAATTAA
28425970 TAGAATGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.45
16 8 0.36
17 4 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATTAAATAATTAAT
Found at i:28426179 original size:21 final size:22
Alignment explanation
Indices: 28426149--28426205 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
28426139 TAATTACTTA
*
28426149 TTTAGCTTTTTTTAAAAATTAAT
1 TTTAG-TTTTTTTAAAAATTAAC
* *
28426172 TTTA-TTTTTTTTAGAATTAAC
1 TTTAGTTTTTTTAAAAATTAAC
*
28426193 TTTAGATTTTTTA
1 TTTAGTTTTTTTA
28426206 GTAAAAGGGA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 18 0.64
22 6 0.21
23 4 0.14
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.61
Consensus pattern (22 bp):
TTTAGTTTTTTTAAAAATTAAC
Found at i:28428346 original size:12 final size:12
Alignment explanation
Indices: 28428329--28428354 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28428319 AAACAGTATG
28428329 AAAAAATAGAAA
1 AAAAAATAGAAA
28428341 AAAAAATAGAAA
1 AAAAAATAGAAA
28428353 AA
1 AA
28428355 TAATGTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (12 bp):
AAAAAATAGAAA
Found at i:28429338 original size:69 final size:70
Alignment explanation
Indices: 28429208--28429338 Score: 151
Period size: 69 Copynumber: 1.9 Consensus size: 70
28429198 GTTTTATTAG
* ** *
28429208 TTTTTTTACAATTTAGGCCCCTAAATTCTATTTAAATTTTGATTCAATCCTTTTTATATTTATTC
1 TTTTATTACAATTTAGGCCCCTAAATTCTATTTAAATTTCAATTCAATCCTTTTTACATTTATTC
28429273 ATTTA
66 ATTTA
* * * *
28429278 TTTTATTATAATTTAGG-CTCTAAATT-TCATTTTAATTTCAATTTAATCCTTTATT-CATTTA
1 TTTTATTACAATTTAGGCCCCTAAATTCT-ATTTAAATTTCAATTCAATCCTTT-TTACATTTA
28429339 ATTTCAACCT
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
68 1 0.02
69 33 0.65
70 17 0.33
ACGTcount: A:0.28, C:0.13, G:0.04, T:0.55
Consensus pattern (70 bp):
TTTTATTACAATTTAGGCCCCTAAATTCTATTTAAATTTCAATTCAATCCTTTTTACATTTATTC
ATTTA
Found at i:28429394 original size:4 final size:4
Alignment explanation
Indices: 28429385--28429432 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
28429375 TCTGTTCTGT
* ** * *
28429385 TTTA TTTA TTTA TTTA TTTA TGTA TTCG TTCA TTTA TTTA TTTC TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
28429433 ATGTTTTTGT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.69
Consensus pattern (4 bp):
TTTA
Found at i:28433261 original size:19 final size:20
Alignment explanation
Indices: 28433218--28433263 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
28433208 TTGCATTCAT
28433218 TTTTCATTCATCAGCATTACA
1 TTTTCA-TCATCAGCATTACA
28433239 -TTTCATCAT-ATGCATTA-A
1 TTTTCATCATCA-GCATTACA
28433257 TTTTCAT
1 TTTTCAT
28433264 AAAAAGGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 2 0.09
19 16 0.70
20 5 0.22
ACGTcount: A:0.28, C:0.20, G:0.04, T:0.48
Consensus pattern (20 bp):
TTTTCATCATCAGCATTACA
Found at i:28436103 original size:21 final size:22
Alignment explanation
Indices: 28436070--28436110 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
28436060 TTCATTTATG
*
28436070 TTTCATTGGCACATA-ATCATA
1 TTTCATTGCCACATACATCATA
*
28436091 TTTCATTTCCACATACATCA
1 TTTCATTGCCACATACATCA
28436111 CAATACATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (22 bp):
TTTCATTGCCACATACATCATA
Found at i:28436512 original size:28 final size:28
Alignment explanation
Indices: 28436481--28436559 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
28436471 GAATTATTCG
*
28436481 ATATTTCGCACACTAAGTGTCATTCTCA
1 ATATTTCGCACACTAAGTGCCATTCTCA
* * *
28436509 ATATCTCACACGCTAAGTGCCATTCTCA
1 ATATTTCGCACACTAAGTGCCATTCTCA
* * * *
28436537 AAATTTCGTACACTGAGAGCCAT
1 ATATTTCGCACACTAAGTGCCAT
28436560 ATTTGATTGG
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (28 bp):
ATATTTCGCACACTAAGTGCCATTCTCA
Found at i:28442484 original size:7 final size:7
Alignment explanation
Indices: 28442474--28442502 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
28442464 TATAAAACCT
28442474 ACCCTAA
1 ACCCTAA
28442481 ACCCTAA
1 ACCCTAA
28442488 ACCCTAA
1 ACCCTAA
28442495 ACCCTAA
1 ACCCTAA
28442502 A
1 A
28442503 TGTTTGGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.41, G:0.00, T:0.14
Consensus pattern (7 bp):
ACCCTAA
Found at i:28443754 original size:40 final size:35
Alignment explanation
Indices: 28443667--28443963 Score: 281
Period size: 35 Copynumber: 8.5 Consensus size: 35
28443657 GGCAAAGTGC
28443667 GAAACGTAGGTATGGTATCATCCATACCGAGTTGT
1 GAAACGTAGGTATGGTATCATCCATACCGAGTTGT
* * * **
28443702 GAAATGTAGGTATGGTATTAACCATATTGAGTTGT
1 GAAACGTAGGTATGGTATCATCCATACCGAGTTGT
28443737 GAAACGTAGGTATGGTATCATCCATACCGAGTTGT
1 GAAACGTAGGTATGGTATCATCCATACCGAGTTGT
* * * ** *
28443772 GAAACGTAGGTATGGTATTAACCATACTGAACTAT
1 GAAACGTAGGTATGGTATCATCCATACCGAGTTGT
* * * * *
28443807 GAAACGTAGGTATGGTGTCGTCCATACTGAGCTAT
1 GAAACGTAGGTATGGTATCATCCATACCGAGTTGT
* * * * * *
28443842 GATACGTAGGTATGGCATCGTCCATTCTGAGTTAT
1 GAAACGTAGGTATGGTATCATCCATACCGAGTTGT
** * * ** **
28443877 GAAATATAGCTATGGTCTTTTCCATACCGAG-CAT
1 GAAACGTAGGTATGGTATCATCCATACCGAGTTGT
* * **
28443911 GAAAAGTAGGTATGGTGTTTTCCATACCGAGTTGT
1 GAAACGTAGGTATGGTATCATCCATACCGAGTTGT
28443946 GAAACGTAGGTATGGTAT
1 GAAACGTAGGTATGGTAT
28443964 TTCAATGAGG
Statistics
Matches: 216, Mismatches: 45, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
34 29 0.13
35 187 0.87
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.31
Consensus pattern (35 bp):
GAAACGTAGGTATGGTATCATCCATACCGAGTTGT
Found at i:28443781 original size:70 final size:70
Alignment explanation
Indices: 28443667--28443963 Score: 317
Period size: 70 Copynumber: 4.3 Consensus size: 70
28443657 GGCAAAGTGC
* * *
28443667 GAAACGTAGGTATGGTATCATCCATACCGAGTTGTGAAATGTAGGTATGGTATTAACCATATTGA
1 GAAACGTAGGTATGGTATCATCCATACCGAGTTATGAAACGTAGGTATGGTATTAACCATACTGA
*
28443732 GTTGT
66 GTTAT
*
28443737 GAAACGTAGGTATGGTATCATCCATACCGAGTTGTGAAACGTAGGTATGGTATTAACCATACTGA
1 GAAACGTAGGTATGGTATCATCCATACCGAGTTATGAAACGTAGGTATGGTATTAACCATACTGA
**
28443802 ACTAT
66 GTTAT
* * * * * * *** *
28443807 GAAACGTAGGTATGGTGTCGTCCATACTGAGCTATGATACGTAGGTATGGCATCGTCCATTCTGA
1 GAAACGTAGGTATGGTATCATCCATACCGAGTTATGAAACGTAGGTATGGTATTAACCATACTGA
28443872 GTTAT
66 GTTAT
** * * ** * * * ** *
28443877 GAAATATAGCTATGGTCTTTTCCATACCGAG-CATGAAAAGTAGGTATGGTGTTTTCCATACCGA
1 GAAACGTAGGTATGGTATCATCCATACCGAGTTATGAAACGTAGGTATGGTATTAACCATACTGA
*
28443941 GTTGT
66 GTTAT
28443946 GAAACGTAGGTATGGTAT
1 GAAACGTAGGTATGGTAT
28443964 TTCAATGAGG
Statistics
Matches: 188, Mismatches: 39, Indels: 1
0.82 0.17 0.00
Matches are distributed among these distances:
69 42 0.22
70 146 0.78
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.31
Consensus pattern (70 bp):
GAAACGTAGGTATGGTATCATCCATACCGAGTTATGAAACGTAGGTATGGTATTAACCATACTGA
GTTAT
Found at i:28443849 original size:105 final size:105
Alignment explanation
Indices: 28443667--28443963 Score: 335
Period size: 105 Copynumber: 2.8 Consensus size: 105
28443657 GGCAAAGTGC
* * * * * * *
28443667 GAAACGTAGGTATGGTATCATCCATACCGAGTTGTGAAATGTAGGTATGGTATTAACCATATTGA
1 GAAACGTAGGTATGGTATTATCCATACCGAGCTATGAAAAGTAGGTATGGTGTTATCCATACTGA
*
28443732 GTTGTGAAACGTAGGTATGGTATCATCCATACCGAGTTGT
66 GTTGTGAAACGTAGGTATGGTATCATCCATACCGAGTTAT
* * * * **
28443772 GAAACGTAGGTATGGTATTAACCATACTGAACTATGAAACGTAGGTATGGTGTCGTCCATACTGA
1 GAAACGTAGGTATGGTATTATCCATACCGAGCTATGAAAAGTAGGTATGGTGTTATCCATACTGA
* * * * * * *
28443837 GCTATGATACGTAGGTATGGCATCGTCCATTCTGAGTTAT
66 GTTGTGAAACGTAGGTATGGTATCATCCATACCGAGTTAT
** * * * * *
28443877 GAAATATAGCTATGGTCTTTTCCATACCGAGC-ATGAAAAGTAGGTATGGTGTTTTCCATACCGA
1 GAAACGTAGGTATGGTATTATCCATACCGAGCTATGAAAAGTAGGTATGGTGTTATCCATACTGA
28443941 GTTGTGAAACGTAGGTATGGTAT
66 GTTGTGAAACGTAGGTATGGTAT
28443964 TTCAATGAGG
Statistics
Matches: 156, Mismatches: 36, Indels: 1
0.81 0.19 0.01
Matches are distributed among these distances:
104 47 0.30
105 109 0.70
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.31
Consensus pattern (105 bp):
GAAACGTAGGTATGGTATTATCCATACCGAGCTATGAAAAGTAGGTATGGTGTTATCCATACTGA
GTTGTGAAACGTAGGTATGGTATCATCCATACCGAGTTAT
Found at i:28455872 original size:14 final size:14
Alignment explanation
Indices: 28455853--28455883 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28455843 AACATTTTAA
*
28455853 TGGAATGTAATTTT
1 TGGAATGTAATTGT
28455867 TGGAATGTAATTGT
1 TGGAATGTAATTGT
28455881 TGG
1 TGG
28455884 GTGAAAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.45
Consensus pattern (14 bp):
TGGAATGTAATTGT
Found at i:28457893 original size:11 final size:11
Alignment explanation
Indices: 28457877--28457901 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28457867 GTATAAATGT
28457877 AATATCCCTAA
1 AATATCCCTAA
28457888 AATATCCCTAA
1 AATATCCCTAA
28457899 AAT
1 AAT
28457902 TGATATCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (11 bp):
AATATCCCTAA
Found at i:28462222 original size:16 final size:14
Alignment explanation
Indices: 28462202--28462231 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28462192 TTTAAAACAG
28462202 AAAGAA-AGAAAAA
1 AAAGAAGAGAAAAA
28462215 AAAGAAGAGAAAAA
1 AAAGAAGAGAAAAA
28462229 AAA
1 AAA
28462232 CTTACCGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAGAAGAGAAAAA
Found at i:28468836 original size:14 final size:13
Alignment explanation
Indices: 28468818--28468861 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 13
28468808 TTAAAAAATC
28468818 AAAATAAAAAAAG
1 AAAATAAAAAAAG
28468831 AGAAATAAAAAGAA-
1 A-AAATAAAAA-AAG
28468845 AAAATCAAAAAAAG
1 AAAAT-AAAAAAAG
28468859 AAA
1 AAA
28468862 GAAAGAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 7 0.26
14 18 0.67
15 2 0.07
ACGTcount: A:0.82, C:0.02, G:0.09, T:0.07
Consensus pattern (13 bp):
AAAATAAAAAAAG
Found at i:28468874 original size:24 final size:24
Alignment explanation
Indices: 28468839--28468884 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
28468829 AGAGAAATAA
28468839 AAAGAAAAAATCAAAAAAAGAAAG
1 AAAGAAAAAATCAAAAAAAGAAAG
* *
28468863 AAAGAAAGAATCAATAAAAGAA
1 AAAGAAAAAATCAAAAAAAGAA
28468885 GTTGAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.07
Consensus pattern (24 bp):
AAAGAAAAAATCAAAAAAAGAAAG
Found at i:28470135 original size:67 final size:64
Alignment explanation
Indices: 28469975--28470159 Score: 244
Period size: 64 Copynumber: 2.8 Consensus size: 64
28469965 TCATTCATAA
* *
28469975 CACATCTAGTTAGGAGCATTTGATTCATTGCGATCATAGCATCCTAATTAATTGACATCAACAT
1 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATCAACAT
* * * *
28470039 CACATCTAGTTAGGAGCATTTGATTCATTTTGATCGTAGCATCCTAATTATTTGACATCGCTCAT
1 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACAT--C-AAC
28470104 AT
63 AT
* * * * *
28470106 CTCATTTAGTTAGAAGCATTGGATTCATTTCAATCATAGCATCCTAATTATTTG
1 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTG
28470160 GCACAAACAT
Statistics
Matches: 105, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
64 54 0.51
66 1 0.01
67 50 0.48
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (64 bp):
CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATCAACAT
Found at i:28470845 original size:176 final size:176
Alignment explanation
Indices: 28470523--28470906 Score: 481
Period size: 176 Copynumber: 2.2 Consensus size: 176
28470513 AGGCAAATCC
* * * *
28470523 TATCTCTATGTATCGGCAATGAAGCAGATTTAAGCCTCAAGCCTTATCTCTCTGATGTAACAATA
1 TATCTCCATGTATCGGCAATGAAGCAGATTTAAGCCACAAGCCTTATCTCTCTGAGGTAACAAGA
28470588 GAGCAAGTTGAAGATTGAGTCTTATCTTTCTAAGGTAGCAAGAAAGCAGACTGAAGATTGAAGAT
66 GAGCAAGTTGAAGATTGAGTCTTATCTTTCTAAGGTAGCAAGAAAGCAGACTGAAGATTGAAGAT
28470653 CTTATCTCCCTAAGCAGTAGCGGAGCAGATCAAAGATGGCGAGTCT
131 CTTATCTCCCTAAGCAGTAGCGGAGCAGATCAAAGATGGCGAGTCT
* * * * *
28470699 TATCTCCATGTATCGGTAATGGAGTAGATTTTAGCCACTAGCCTTATCTCTCTGAGGTAACAAGA
1 TATCTCCATGTATCGGCAATGAAGCAGATTTAAGCCACAAGCCTTATCTCTCTGAGGTAACAAGA
* ** * *
28470764 GAGCAGGTTGGCGATTGTAGTCTTATC-TTCT-TGAGTAAGCAAGGAAGCAGACTGAAGATTGAA
66 GAGCAAGTTGAAGATTG-AGTCTTATCTTTCTAAG-GT-AGCAAGAAAGCAGACTGAAGATTGAA
* * * ** * * *
28470827 GATC-TATTTCCTTAAGCAGTTGTAGAGC--ATCAAGGATGGCAAATCT
128 GATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCAAAGATGGCGAGTCT
* * *
28470873 TATTTCTATGTATTGGCAATGAAGCAGATTTAAG
1 TATCTCCATGTATCGGCAATGAAGCAGATTTAAG
28470907 TCCCCAAGAT
Statistics
Matches: 176, Mismatches: 29, Indels: 8
0.83 0.14 0.04
Matches are distributed among these distances:
174 42 0.24
175 1 0.01
176 95 0.54
177 38 0.22
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (176 bp):
TATCTCCATGTATCGGCAATGAAGCAGATTTAAGCCACAAGCCTTATCTCTCTGAGGTAACAAGA
GAGCAAGTTGAAGATTGAGTCTTATCTTTCTAAGGTAGCAAGAAAGCAGACTGAAGATTGAAGAT
CTTATCTCCCTAAGCAGTAGCGGAGCAGATCAAAGATGGCGAGTCT
Found at i:28471021 original size:264 final size:266
Alignment explanation
Indices: 28470686--28471181 Score: 646
Period size: 264 Copynumber: 1.9 Consensus size: 266
28470676 AGCAGATCAA
* *
28470686 AGATGGCGAGTCTTATCTCCATGTATCGGTAATGGAGTAGATTTTAGCCACTAGCCTTATCTCTC
1 AGATGGCGAATCTTATCTCCATGTATCGGCAATGGAGTAGATTTTAGCCACTAGCCTTATCTCTC
* * *** **
28470751 TGAGGTAACAAGAGAGCAGGTTGGCGATTGTAGTCTTATCTT-CTTGAGTAAGCAAGGAAGCAGA
66 TGAGGTAACAAGAAAGCAGGCTAAAGATTG-AGTCTTATCTTCCTAAAGTAA-CAAGGAAGCAGA
*
28470815 CTGAAGATTGAAGAT-CTATTTCCTTA-AGCAGTTGTA-GAGC-ATCAAGGATGGCAAATCTTAT
129 CTGAAGATTGAAGATACTATTTCCCTAGAGCAGTTG-AGGAGCAATCAAGGATGGCAAATCTTAT
* * * * *
28470876 TTCTATGTATTGGCAATGAAGCAGATTTAAGTCCCCAAGATTTATTTCCCTAAAGTTGCAGCAGA
193 CTCCATGTATTAGCAATGAAGCAAATTTAAGTCACCAAGATTTATTTCCCTAAAGTTGCAGCAGA
28470941 GTAATTTAC
258 GTAATTTAC
*
28470950 AGATGGTGAATCTTATCTCCATGTATCGGCAATGGAGTAGA-TTTAGACCA-TCAGCCTTATCTC
1 AGATGGCGAATCTTATCTCCATGTATCGGCAATGGAGTAGATTTTAG-CCACT-AGCCTTATCTC
* * * * *
28471013 TCTGAGGTAGCAAGAAAGCAGGCTAAAGTTTGGGTCTTATCTTCCTAAAGTGACAATGAAGCAGA
64 TCTGAGGTAACAAGAAAGCAGGCTAAAGATTGAGTCTTATCTTCCTAAAGTAACAAGGAAGCAGA
* ** * *
28471078 CTGAAGATTGAAGATATTATTTCCCTAGAGCAGTTGAGGAGCAGATTGATGATGGCGAATCTTAT
129 CTGAAGATTGAAGATACTATTTCCCTAGAGCAGTTGAGGAGCA-ATCAAGGATGGCAAATCTTAT
*
28471143 CTCCATGTATTAGCAATGGAGCAAATTTAAGTCACCAAG
193 CTCCATGTATTAGCAATGAAGCAAATTTAAGTCACCAAG
28471182 CCTATTTCCT
Statistics
Matches: 197, Mismatches: 27, Indels: 13
0.83 0.11 0.05
Matches are distributed among these distances:
263 42 0.21
264 93 0.47
265 12 0.06
267 50 0.25
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (266 bp):
AGATGGCGAATCTTATCTCCATGTATCGGCAATGGAGTAGATTTTAGCCACTAGCCTTATCTCTC
TGAGGTAACAAGAAAGCAGGCTAAAGATTGAGTCTTATCTTCCTAAAGTAACAAGGAAGCAGACT
GAAGATTGAAGATACTATTTCCCTAGAGCAGTTGAGGAGCAATCAAGGATGGCAAATCTTATCTC
CATGTATTAGCAATGAAGCAAATTTAAGTCACCAAGATTTATTTCCCTAAAGTTGCAGCAGAGTA
ATTTAC
Found at i:28471637 original size:4 final size:4
Alignment explanation
Indices: 28471628--28471652 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
28471618 ATGAAATTTG
28471628 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
28471653 TTTTCAGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:28475999 original size:26 final size:26
Alignment explanation
Indices: 28475970--28476077 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
28475960 TGGTACAAAT
*
28475970 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
28475996 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28476022 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
28476048 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28476074 TGAT
1 TGAT
28476078 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:28478039 original size:15 final size:15
Alignment explanation
Indices: 28478019--28478047 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28478009 AATTTGTGAA
28478019 AAAATAAAATAAAAG
1 AAAATAAAATAAAAG
28478034 AAAATAAAATAAAA
1 AAAATAAAATAAAA
28478048 AATATAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (15 bp):
AAAATAAAATAAAAG
Found at i:28479201 original size:29 final size:29
Alignment explanation
Indices: 28479169--28479245 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 29
28479159 TAAATTTTAT
28479169 TAAAAATTAGAAAAAAATTATAAAA-ACCA
1 TAAAAATTAGAAAAAAATTATAAAATA-CA
*
28479198 TAAAAATT-GTAAAAAAATTATAAAATATA
1 TAAAAATTAG-AAAAAAATTATAAAATACA
*
28479227 TAGAAAAATAGAAAAAAAT
1 TA-AAAATTAGAAAAAAAT
28479246 GAAATTTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
28 1 0.02
29 26 0.62
30 14 0.33
31 1 0.02
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (29 bp):
TAAAAATTAGAAAAAAATTATAAAATACA
Found at i:28479820 original size:88 final size:88
Alignment explanation
Indices: 28479666--28479935 Score: 393
Period size: 88 Copynumber: 3.1 Consensus size: 88
28479656 TCAAAGGATT
* * *
28479666 TTTTTGATGCATTTTGATAGTTCAAGTACCCAATTGAGTG-AAAAAAAAGTAGGGGCTTAATAGC
1 TTTTTGATACATTTTGAAAGTTCAAGTA-CCAATTGAGTGCAAAAAAAAGTAGGGGCTTAATTGC
*
28479730 TTTTTTTGAAAAAGTTTGAGGGTC
65 TTTTTTTGAAAAAGTTTGAGGGCC
*
28479754 TTTTTGATACATTTTGAAAGTTCAAGTACCAAATTGAGTGCAAAAAAAAG-GGGGGCTTAATTGC
1 TTTTTGATACATTTTGAAAGTTCAAGTACC-AATTGAGTGCAAAAAAAAGTAGGGGCTTAATTGC
* *
28479818 TTTTTTTTAAAAAGTTTGAGAGCC
65 TTTTTTTGAAAAAGTTTGAGGGCC
* *
28479842 TTTTTGATACATTTTGAAAGTTCAAGTATCCAATTGAGTGCATAAAAAGAGTAGGGACTTAATTG
1 TTTTTGATACATTTTGAAAGTTCAAGTA-CCAATTGAGTGCA-AAAAAAAGTAGGGGCTTAATTG
*
28479907 CTTGTTTTGAAAAAGTTTGA-GGCC
64 CTTTTTTTGAAAAAGTTTGAGGGCC
28479931 TTTTT
1 TTTTT
28479936 TACTTTAAAA
Statistics
Matches: 164, Mismatches: 13, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
87 2 0.01
88 107 0.65
89 26 0.16
90 29 0.18
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.37
Consensus pattern (88 bp):
TTTTTGATACATTTTGAAAGTTCAAGTACCAATTGAGTGCAAAAAAAAGTAGGGGCTTAATTGCT
TTTTTTGAAAAAGTTTGAGGGCC
Found at i:28482703 original size:17 final size:16
Alignment explanation
Indices: 28482681--28482712 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
28482671 AATCAATTGA
28482681 ATAAATTATTAAAAATT
1 ATAAATT-TTAAAAATT
28482698 ATAAATTTTAAAAAT
1 ATAAATTTTAAAAAT
28482713 ATCATAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATAAATTTTAAAAATT
Found at i:28492849 original size:49 final size:49
Alignment explanation
Indices: 28492777--28492874 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
28492767 ATAAAACATA
28492777 AGTCTTTAATAGTAATGCTTAAAAGGAAAGATAAATGTTTTATCGAGCT
1 AGTCTTTAATAGTAATGCTTAAAAGGAAAGATAAATGTTTTATCGAGCT
28492826 AGTCTTTAATAGTAATGCTTAAAAGGAAAGATAAATGTTTTATCGAGCT
1 AGTCTTTAATAGTAATGCTTAAAAGGAAAGATAAATGTTTTATCGAGCT
28492875 CCCGTGACAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (49 bp):
AGTCTTTAATAGTAATGCTTAAAAGGAAAGATAAATGTTTTATCGAGCT
Found at i:28495171 original size:17 final size:17
Alignment explanation
Indices: 28495136--28495168 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28495126 ACAAGATAAG
*
28495136 TATTAAATTAAATTAAA
1 TATTAAAATAAATTAAA
28495153 TATTAAAAT-AATTAAA
1 TATTAAAATAAATTAAA
28495169 ATAATATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TATTAAAATAAATTAAA
Found at i:28495530 original size:19 final size:19
Alignment explanation
Indices: 28495490--28495532 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
28495480 TTCTCAAGCT
* *
28495490 CAATTTTCAATCTTAGGTC
1 CAATTTTCAATCTCAGGCC
*
28495509 CAATTTTCAATCTCGGGCC
1 CAATTTTCAATCTCAGGCC
28495528 CAATT
1 CAATT
28495533 ATTGTAACAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.37
Consensus pattern (19 bp):
CAATTTTCAATCTCAGGCC
Found at i:28498750 original size:27 final size:27
Alignment explanation
Indices: 28498702--28498754 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
28498692 GCGAGGCTGC
*
28498702 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGATA
*
28498729 CAGATATTGTGGC-AGAGCCACCAGAT
1 CAGATATTGTGACGA-AGCCACCAGAT
28498755 GTGGCAGAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.21
Consensus pattern (27 bp):
CAGATATTGTGACGAAGCCACCAGATA
Found at i:28498757 original size:18 final size:18
Alignment explanation
Indices: 28498736--28498790 Score: 110
Period size: 18 Copynumber: 3.1 Consensus size: 18
28498726 ATACAGATAT
28498736 TGTGGCAGAGCCACCAGA
1 TGTGGCAGAGCCACCAGA
28498754 TGTGGCAGAGCCACCAGA
1 TGTGGCAGAGCCACCAGA
28498772 TGTGGCAGAGCCACCAGA
1 TGTGGCAGAGCCACCAGA
28498790 T
1 T
28498791 CAGATAATTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.27, C:0.27, G:0.33, T:0.13
Consensus pattern (18 bp):
TGTGGCAGAGCCACCAGA
Found at i:28498802 original size:27 final size:27
Alignment explanation
Indices: 28498772--28498869 Score: 146
Period size: 27 Copynumber: 3.6 Consensus size: 27
28498762 AGCCACCAGA
28498772 TGTGGCAGAGCCACCAGATCAGATAAT
1 TGTGGCAGAGCCACCAGATCAGATAAT
*
28498799 TGTGGCATAGCCACCAGGA-CAGAT-AT
1 TGTGGCAGAGCCACCA-GATCAGATAAT
28498825 ATGTGGCAGAGCCACCAGATCAGATAAT
1 -TGTGGCAGAGCCACCAGATCAGATAAT
*
28498853 TGTGGCATAGCCACCAG
1 TGTGGCAGAGCCACCAG
28498870 GACGCTTCCT
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
26 4 0.06
27 56 0.88
28 4 0.06
ACGTcount: A:0.32, C:0.23, G:0.27, T:0.18
Consensus pattern (27 bp):
TGTGGCAGAGCCACCAGATCAGATAAT
Found at i:28500498 original size:26 final size:26
Alignment explanation
Indices: 28500467--28500574 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
28500457 TGAAATGCCC
*
28500467 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
28500493 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
28500519 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
28500545 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
28500571 ATCA
1 ATCA
28500575 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:28504636 original size:27 final size:27
Alignment explanation
Indices: 28504553--28504638 Score: 103
Period size: 26 Copynumber: 3.3 Consensus size: 27
28504543 CAGATGTGCA
28504553 AGCCACCA-ATCAGA-AATT-TGGCAT
1 AGCCACCAGATCAGATAATTGTGGCAT
*
28504577 AGCCACCAGGA-CAGAT-ATATG-GGCAG
1 AGCCACCA-GATCAGATAAT-TGTGGCAT
28504603 AGCCACCAGATCAGATAATTGTGGCAT
1 AGCCACCAGATCAGATAATTGTGGCAT
28504630 AGCCACCAG
1 AGCCACCAG
28504639 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
24 8 0.15
25 8 0.15
26 21 0.40
27 15 0.29
ACGTcount: A:0.35, C:0.26, G:0.23, T:0.16
Consensus pattern (27 bp):
AGCCACCAGATCAGATAATTGTGGCAT
Found at i:28506294 original size:27 final size:26
Alignment explanation
Indices: 28506218--28506325 Score: 173
Period size: 26 Copynumber: 4.2 Consensus size: 26
28506208 TGAAATGCCC
*
28506218 ATCAT-GAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
28506243 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
28506269 ATCATGGAAATATTTACCTAATCCATT
1 ATCATGG-AACATTTACCTAACCCATT
28506296 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
28506322 ATCA
1 ATCA
28506326 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
25 5 0.07
26 47 0.62
27 24 0.32
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:28510321 original size:18 final size:18
Alignment explanation
Indices: 28510300--28510352 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
28510290 ATACAGATAT
28510300 TGTGGCAGAGCCACCAGA
1 TGTGGCAGAGCCACCAGA
*
28510318 TGTGGTAGAGCCACCAGA
1 TGTGGCAGAGCCACCAGA
28510336 TGTGGCAGAGCCACCAG
1 TGTGGCAGAGCCACCAG
28510353 GACAGATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.26, C:0.26, G:0.34, T:0.13
Consensus pattern (18 bp):
TGTGGCAGAGCCACCAGA
Found at i:28510365 original size:27 final size:27
Alignment explanation
Indices: 28510335--28510430 Score: 151
Period size: 27 Copynumber: 3.6 Consensus size: 27
28510325 GAGCCACCAG
28510335 ATGTGGCAGAGCCACCAGGACAGATAT
1 ATGTGGCAGAGCCACCAGGACAGATAT
28510362 ATGTGGCAGAGCCACCAGGACAGATAT
1 ATGTGGCAGAGCCACCAGGACAGATAT
28510389 ATGTGGCAGAGCCACCA-GATCAGATA-
1 ATGTGGCAGAGCCACCAGGA-CAGATAT
*
28510415 ATTGTGGCATAGCCAC
1 A-TGTGGCAGAGCCAC
28510431 GAAGACGCTT
Statistics
Matches: 66, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
26 3 0.05
27 63 0.95
ACGTcount: A:0.32, C:0.23, G:0.28, T:0.17
Consensus pattern (27 bp):
ATGTGGCAGAGCCACCAGGACAGATAT
Found at i:28512061 original size:26 final size:26
Alignment explanation
Indices: 28512030--28512137 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
28512020 TGAAATGCCC
*
28512030 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
28512056 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
28512082 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
28512108 ATCATGGAACATTTACATAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
28512134 ATCA
1 ATCA
28512138 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:28517475 original size:19 final size:19
Alignment explanation
Indices: 28517451--28517488 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
28517441 TCTTTAATTG
*
28517451 AGAGAAAAGATGAGTAAAA
1 AGAGAAAAGAAGAGTAAAA
*
28517470 AGAGAAGAGAAGAGTAAAA
1 AGAGAAAAGAAGAGTAAAA
28517489 GAAGATAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.29, T:0.08
Consensus pattern (19 bp):
AGAGAAAAGAAGAGTAAAA
Found at i:28520053 original size:42 final size:43
Alignment explanation
Indices: 28519939--28520192 Score: 186
Period size: 42 Copynumber: 6.0 Consensus size: 43
28519929 ATATGTTGTA
* * * * * *
28519939 CAATGCCATTTCCCGGATATGGTCTTACATGTAATCTTAT-AT
1 CAATGCCATGTCCCAGACATGGTCTTACACGAAATCTCATAAT
28519981 CGAA-GCCAATAG-CCCAG-CTATGGTCTTACACGAAATCTCATAAT
1 C-AATGCC-AT-GTCCCAGAC-ATGGTCTTACACGAAATCTCATAAT
* * * * *
28520025 -GATGCCATGTCCTAGACATGGTCTTACACGTAATATCAT-AC
1 CAATGCCATGTCCCAGACATGGTCTTACACGAAATCTCATAAT
* * *
28520066 CGATGCTAATAG-CCCAG-CTATGGTCTTACACGAAATCTCGT-AT
1 CAATGC-CAT-GTCCCAGAC-ATGGTCTTACACGAAATCTCATAAT
* * *
28520109 CAATGCCATGTCCCAGACACGGTCTTACATGAAATATCAT-AT
1 CAATGCCATGTCCCAGACATGGTCTTACACGAAATCTCATAAT
* * * *
28520151 CAAAGACATGTCCCAGACATGGTCTTACATGAAGTCTCATAA
1 CAATGCCATGTCCCAGACATGGTCTTACACGAAATCTCATAA
28520193 CGGTGCCGAT
Statistics
Matches: 169, Mismatches: 28, Indels: 29
0.75 0.12 0.13
Matches are distributed among these distances:
41 3 0.02
42 99 0.59
43 64 0.38
44 3 0.02
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (43 bp):
CAATGCCATGTCCCAGACATGGTCTTACACGAAATCTCATAAT
Found at i:28520084 original size:85 final size:85
Alignment explanation
Indices: 28519939--28520191 Score: 280
Period size: 85 Copynumber: 3.0 Consensus size: 85
28519929 ATATGTTGTA
* * * * * *
28519939 CAATGCCATTTCCCGGATATGGTCTTACATGTAATCTTATATCGAAGCCAATAGCCCAGCTATGG
1 CAATGCCATGTCCCAGACATGGTCTTACATGTAATATCATACCGAAGCCAATAGCCCAGCTATGG
28520004 TCTTACACGAAATCTCATAAT
66 TCTTACACGAAATCTCAT-AT
* * * * *
28520025 -GATGCCATGTCCTAGACATGGTCTTACACGTAATATCATACCGATGCTAATAGCCCAGCTATGG
1 CAATGCCATGTCCCAGACATGGTCTTACATGTAATATCATACCGAAGCCAATAGCCCAGCTATGG
*
28520089 TCTTACACGAAATCTCGTAT
66 TCTTACACGAAATCTCATAT
* * * * *
28520109 CAATGCCATGTCCCAGACACGGTCTTACATGAAATATCATATCAAAGAC-AT-GTCCCAGAC-AT
1 CAATGCCATGTCCCAGACATGGTCTTACATGTAATATCATACCGAAGCCAATAG-CCCAG-CTAT
* *
28520171 GGTCTTACATGAAGTCTCATA
64 GGTCTTACACGAAATCTCATA
28520192 ACGGTGCCGA
Statistics
Matches: 139, Mismatches: 25, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
83 1 0.01
84 29 0.21
85 109 0.78
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (85 bp):
CAATGCCATGTCCCAGACATGGTCTTACATGTAATATCATACCGAAGCCAATAGCCCAGCTATGG
TCTTACACGAAATCTCATAT
Found at i:28520661 original size:115 final size:115
Alignment explanation
Indices: 28520459--28520690 Score: 464
Period size: 115 Copynumber: 2.0 Consensus size: 115
28520449 ATAAATACAT
28520459 ATACATATACATTTCATGAAATATTTAAGCATTAAACATATAATAATAACATGTTGCATTATACT
1 ATACATATACATTTCATGAAATATTTAAGCATTAAACATATAATAATAACATGTTGCATTATACT
28520524 CATACAAACTTACCTCAACACCAAAATGGCAAAAAGGGACCTAACCGTCA
66 CATACAAACTTACCTCAACACCAAAATGGCAAAAAGGGACCTAACCGTCA
28520574 ATACATATACATTTCATGAAATATTTAAGCATTAAACATATAATAATAACATGTTGCATTATACT
1 ATACATATACATTTCATGAAATATTTAAGCATTAAACATATAATAATAACATGTTGCATTATACT
28520639 CATACAAACTTACCTCAACACCAAAATGGCAAAAAGGGACCTAACCGTCA
66 CATACAAACTTACCTCAACACCAAAATGGCAAAAAGGGACCTAACCGTCA
28520689 AT
1 AT
28520691 TTCTCGTTTT
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
115 117 1.00
ACGTcount: A:0.44, C:0.20, G:0.09, T:0.27
Consensus pattern (115 bp):
ATACATATACATTTCATGAAATATTTAAGCATTAAACATATAATAATAACATGTTGCATTATACT
CATACAAACTTACCTCAACACCAAAATGGCAAAAAGGGACCTAACCGTCA
Found at i:28521570 original size:13 final size:13
Alignment explanation
Indices: 28521554--28521590 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
28521544 CAAACAAAAT
*
28521554 TTTCATGAAATCA
1 TTTCATAAAATCA
28521567 TTTCATAAAATCA
1 TTTCATAAAATCA
28521580 TTTCATAAAAT
1 TTTCATAAAAT
28521591 TATAGACCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.41
Consensus pattern (13 bp):
TTTCATAAAATCA
Found at i:28522498 original size:16 final size:17
Alignment explanation
Indices: 28522479--28522511 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28522469 AATATTTTCA
28522479 TTATTA-CTTATTAATT
1 TTATTATCTTATTAATT
*
28522495 TTATTATCTTGTTAATT
1 TTATTATCTTATTAATT
28522512 AATCATTCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (17 bp):
TTATTATCTTATTAATT
Found at i:28522626 original size:24 final size:24
Alignment explanation
Indices: 28522596--28522646 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
28522586 TGTTAAAACG
28522596 TTTGGTTCTTTTCAAAACTCAAGT
1 TTTGGTTCTTTTCAAAACTCAAGT
*
28522620 TTTGGTTCTTTTGAAAACTCAAGT
1 TTTGGTTCTTTTCAAAACTCAAGT
28522644 TTT
1 TTT
28522647 CCTAAAGCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (24 bp):
TTTGGTTCTTTTCAAAACTCAAGT
Found at i:28523865 original size:29 final size:29
Alignment explanation
Indices: 28523787--28523866 Score: 101
Period size: 28 Copynumber: 2.8 Consensus size: 29
28523777 AACAGAAATG
* * *
28523787 TCCAACCAAAACACACCAGTATTATATAA
1 TCCATCCAAAACACACCAGAATAATATAA
*
28523816 TCC-TCTC-AAACACACTAGAATAATATAA
1 TCCATC-CAAAACACACCAGAATAATATAA
28523844 TCCATCCAAAACACACCAGAATA
1 TCCATCCAAAACACACCAGAATA
28523867 GCACAGAATG
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
28 23 0.53
29 20 0.47
ACGTcount: A:0.47, C:0.29, G:0.04, T:0.20
Consensus pattern (29 bp):
TCCATCCAAAACACACCAGAATAATATAA
Found at i:28524044 original size:17 final size:17
Alignment explanation
Indices: 28524004--28524045 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
28523994 CTTTTTTTTT
*
28524004 ATTTCAATTTAATTTTC
1 ATTTCAATTTAATTTCC
*
28524021 ATATCAATTTCAA-TTCC
1 ATTTCAATTT-AATTTCC
28524038 ATTTCAAT
1 ATTTCAAT
28524046 ATACAATCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 19 0.90
18 2 0.10
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTCAATTTAATTTCC
Found at i:28525325 original size:17 final size:17
Alignment explanation
Indices: 28525305--28525338 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
28525295 ATACACTAAT
28525305 ATAAT-ATCAATTAAATA
1 ATAATAATCAA-TAAATA
28525322 ATAATAATCAATAAATA
1 ATAATAATCAATAAATA
28525339 TCTTTTACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAATAATCAATAAATA
Found at i:28525522 original size:29 final size:29
Alignment explanation
Indices: 28525464--28525523 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
28525454 TTTAAGTTAT
* *
28525464 AAATTAATAATACTATAAATTAACATAAA
1 AAATTAATAATACTATAAATTAAAACAAA
28525493 AAATATAAT-ATA-TATATAATTAAAACAAA
1 AAAT-TAATAATACTATA-AATTAAAACAAA
28525522 AA
1 AA
28525524 TCATAGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 4 0.15
29 19 0.70
30 4 0.15
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (29 bp):
AAATTAATAATACTATAAATTAAAACAAA
Found at i:28531618 original size:28 final size:28
Alignment explanation
Indices: 28531586--28531669 Score: 123
Period size: 28 Copynumber: 3.0 Consensus size: 28
28531576 AACAAACCAG
* *
28531586 TATAATCCTCCAAAACACACCAGTATTA
1 TATAATCCTCCAAAACACACCAGAATAA
*
28531614 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
*
28531642 TATAATCCATCCAAAACACACCATAATA
1 TATAATCC-TCCAAAACACACCAGAATA
28531670 GCACAGAATG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 33 0.66
29 17 0.34
ACGTcount: A:0.46, C:0.30, G:0.02, T:0.21
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:28531641 original size:23 final size:23
Alignment explanation
Indices: 28531572--28531642 Score: 70
Period size: 28 Copynumber: 2.9 Consensus size: 23
28531562 AAATGTCCAA
* *
28531572 CCAAAACAAACCAGTATAATCCT
1 CCAAAACACACCAGAATAATCCT
28531595 CCAAAACACACCAGTATTATATAATCCT
1 CCAAAACACACCAG----A-ATAATCCT
*
28531623 CCCAAACACACCAGAATAAT
1 CCAAAACACACCAGAATAAT
28531643 ATAATCCATC
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
23 18 0.45
24 1 0.03
28 21 0.52
ACGTcount: A:0.46, C:0.31, G:0.04, T:0.18
Consensus pattern (23 bp):
CCAAAACACACCAGAATAATCCT
Found at i:28532791 original size:8 final size:8
Alignment explanation
Indices: 28532757--28532816 Score: 59
Period size: 8 Copynumber: 7.5 Consensus size: 8
28532747 TAGTGATGTG
*
28532757 AATAATAA
1 AATATTAA
*
28532765 AGTATATAA
1 AATAT-TAA
28532774 AATA-TAA
1 AATATTAA
28532781 AATATTAA
1 AATATTAA
*
28532789 AATATCAA
1 AATATTAA
*
28532797 AATATCAA
1 AATATTAA
*
28532805 AATATTAG
1 AATATTAA
28532813 AATA
1 AATA
28532817 ATAATAATTA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
7 7 0.16
8 31 0.70
9 6 0.14
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (8 bp):
AATATTAA
Found at i:28532816 original size:24 final size:22
Alignment explanation
Indices: 28532768--28532816 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 22
28532758 ATAATAAAGT
28532768 ATATAAAATATAAAATATTAAA
1 ATATAAAATATAAAATATTAAA
*
28532790 ATATCAAAATATCAAAATATTAGA
1 ATAT-AAAATAT-AAAATATTAAA
28532814 ATA
1 ATA
28532817 ATAATAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 4 0.17
23 7 0.29
24 13 0.54
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (22 bp):
ATATAAAATATAAAATATTAAA
Found at i:28532984 original size:20 final size:20
Alignment explanation
Indices: 28532927--28532986 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 20
28532917 AATACTACAT
28532927 AAATATGTACAT-ATATAAA
1 AAATATGTACATAATATAAA
** *
28532946 AAATAAATACGTGATAATATTAA
1 AAATATGTAC---ATAATATAAA
28532969 AAATATGTACATAATATA
1 AAATATGTACATAATATA
28532987 GTATAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
19 8 0.26
20 7 0.23
22 2 0.06
23 14 0.45
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
AAATATGTACATAATATAAA
Found at i:28533025 original size:22 final size:22
Alignment explanation
Indices: 28532927--28533034 Score: 71
Period size: 25 Copynumber: 4.9 Consensus size: 22
28532917 AATACTACAT
*
28532927 AAATATGTACAT-ATATAA--A
1 AAATATATACATAATATAATTA
* * *
28532946 AAATAAATACGTGATA-ATATTAA
1 AAATATATACATAATATA-ATT-A
* *
28532969 AAATATGTACATAATATAGTATAAA
1 AAATATATACATAATATA--AT-TA
*
28532994 AAATACATACATAATATAATTA
1 AAATATATACATAATATAATTA
*
28533016 AAATATATACATAAGATAA
1 AAATATATACATAATATAA
28533035 CATGTAGAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 13
0.72 0.14 0.14
Matches are distributed among these distances:
19 10 0.15
20 4 0.06
22 18 0.26
23 15 0.22
24 1 0.01
25 20 0.29
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (22 bp):
AAATATATACATAATATAATTA
Found at i:28533093 original size:25 final size:25
Alignment explanation
Indices: 28533057--28533192 Score: 86
Period size: 25 Copynumber: 5.6 Consensus size: 25
28533047 ATATATATAT
*
28533057 ATATATAAATAATATAGTATTAAAG
1 ATATATACATAATATAGTATTAAAG
* * *
28533082 ATATATACATAAAATAGTATAATATAT
1 ATATATACATAATATAGTAT--TAAAG
* * *
28533109 ATATATACGTAATATAGAATT-TAG
1 ATATATACATAATATAGTATTAAAG
* *
28533133 A-ATATACCTAATATA-T-TAAAAG
1 ATATATACATAATATAGTATTAAAG
* * *
28533155 AATATATATAAAATATAATATT-AAG
1 -ATATATACATAATATAGTATTAAAG
*
28533180 AAATATA-ATAATA
1 ATATATACATAATA
28533193 ACAAAAAAAG
Statistics
Matches: 86, Mismatches: 18, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
21 1 0.01
22 2 0.02
23 19 0.22
24 20 0.23
25 23 0.27
26 1 0.01
27 20 0.23
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (25 bp):
ATATATACATAATATAGTATTAAAG
Found at i:28533484 original size:16 final size:16
Alignment explanation
Indices: 28533446--28533484 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
28533436 TCTCCAAAAA
*
28533446 AAAAACTAGCCTCTCC
1 AAAAACTAGCCTCTAC
*
28533462 AAAAACTAGCCTTTAC
1 AAAAACTAGCCTCTAC
*
28533478 AATAACT
1 AAAAACT
28533485 CTTCTCCTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.28, G:0.05, T:0.23
Consensus pattern (16 bp):
AAAAACTAGCCTCTAC
Found at i:28533699 original size:30 final size:30
Alignment explanation
Indices: 28533663--28533731 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
28533653 TAGGTACAAG
28533663 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
*
28533693 TGGTGGTGGAGCAATTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
28533723 TGGTGGTGG
1 TGGTGGTGG
28533732 CAAAGGCTAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.14, C:0.06, G:0.51, T:0.29
Consensus pattern (30 bp):
TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
Found at i:28534525 original size:88 final size:86
Alignment explanation
Indices: 28534385--28534682 Score: 298
Period size: 87 Copynumber: 3.4 Consensus size: 86
28534375 GTGATCCTGA
* * * *
28534385 GCTCAACTCATTTCTCGCAATATGAATTGACTCTTTAAAACTAGACA-T-TAAAAACATAAATTG
1 GCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTAAAAC-A-AAATTGTAAAAACATAAATTG
* *
28534448 AAAATAGCTCAGCACGTGAGCCAAG
63 AAAATACCTCAG-ACGTGACCCAAG
* **
28534473 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAACAAAATTTGT-AAAACAGATTTTGAA
1 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAACAAAA-TTGTAAAAACATAAATTGAA
* *
28534537 AATACCTCGGTATGTGACCCAAG
65 AATACCTCAG-ACGTGACCCAAG
* * * * * * *
28534560 GCTCAACTCATTTCTCGTAATATGAGTTGATTCTTGAAAAGTATAAATTGAAAAAACATTAATTA
1 GCTCAACTCACTTCTCGCAATATGAGTTGATT-TTTAAAA-CA-AAATTGTAAAAACATAAATTG
* *
28534625 AAAATACCTCAG-CGTGCCCCGAG
63 AAAATACCTCAGACGTGACCCAAG
*
28534648 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTT
28534683 TTGAAAAACA
Statistics
Matches: 173, Mismatches: 30, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
85 2 0.01
86 1 0.01
87 72 0.42
88 72 0.42
89 4 0.02
90 22 0.13
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (86 bp):
GCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAACAAAATTGTAAAAACATAAATTGAAA
ATACCTCAGACGTGACCCAAG
Found at i:28534560 original size:87 final size:85
Alignment explanation
Indices: 28534385--28534706 Score: 288
Period size: 88 Copynumber: 3.6 Consensus size: 85
28534375 GTGATCCTGA
* * * * * * **
28534385 GCTCAACTCATTTCTCGCAATATGAATTGACTCTTTAAAACTAGACATTAAAAACATAAATTGAA
1 GCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTAAAAC-AGAAATTGAAAACACATTTTGAA
* *
28534450 AATAGCTCAGCACGTGAGCCAAG
64 AATACCTCAG-ACGTGACCCAAG
*
28534473 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAACA-AAATTTGTAAAACAGATTTTGAA
1 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAACAGAAA-TTG-AAAACACATTTTGAA
* *
28534537 AATACCTCGGTATGTGACCCAAG
64 AATACCTCAG-ACGTGACCCAAG
* * * * * * *
28534560 GCTCAACTCATTTCTCGTAATATGAGTTGATTCTTGAAAAGTATAAATTGAAAAAACATTAATTA
1 GCTCAACTCACTTCTCGCAATATGAGTTGATT-TTTAAAA-CAGAAATTGAAAACACATT--TTG
* *
28534625 AAAATACCTCAG-CGTGCCCCGAG
62 AAAATACCTCAGACGTGACCCAAG
* *
28534648 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACATAAATTGAAAACAC
1 GCTCAACTCACTTCTCGCAATATGAGTTGA--TTTTT--AAAACAGAAATTGAAAACAC
28534707 CTCAGCGTGT
Statistics
Matches: 193, Mismatches: 30, Indels: 20
0.79 0.12 0.08
Matches are distributed among these distances:
85 2 0.01
86 3 0.02
87 69 0.36
88 77 0.40
89 6 0.03
90 32 0.17
91 4 0.02
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (85 bp):
GCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAACAGAAATTGAAAACACATTTTGAAAA
TACCTCAGACGTGACCCAAG
Found at i:28534737 original size:77 final size:76
Alignment explanation
Indices: 28534611--28535160 Score: 533
Period size: 77 Copynumber: 7.2 Consensus size: 76
28534601 TATAAATTGA
** * * *
28534611 AAAAACATTAATTAAAAATACCTCAGC--GTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
28534674 TTGATTTTTTTG
66 TTGA-TTTTTTG
*
28534686 AAAAACATAAATTGAAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
28534751 TTGATTTTTTG
66 TTGATTTTTTG
** * * * * *
28534762 ATGAACAGAAATT-AAAACTACCTCAAC-T-TGTCCTGAAGCTCAACTCACCTCTCGCAACATGA
1 AAAAACAGAAATTGAAAAC-ACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA
28534824 GTTGATTTTTTTG
65 GTTGA-TTTTTTG
*
28534837 AAAAACAGAAGTTGAAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
28534902 TTGATTTTTTTG
66 TTGA-TTTTTTG
* *
28534914 ACAAACAGAAATTGAAAACACCTCAGCATGT-----GAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
28534974 TTGA-TTTTTG
66 TTGATTTTTTG
* * * * ** *
28534984 AAAAACATAAATTGAGCAGAAAATGAAAATACCTCAACG-G-GTCTTGAGGCCCAACTCACCTCT
1 ------A-AAA---A-CAGAAATTGAAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCT
28535047 CGCAATATGAGTTGATTTTTTG
55 CGCAATATGAGTTGATTTTTTG
** * * * ** *
28535069 ---ATGATAAATTGAAAATACCTCA--ATGTGACTTGAGGCTCAACTCACCTCTCGCAATATGAT
1 AAAAACAGAAATTGAAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
28535129 TTGATTTTTTG
66 TTGATTTTTTG
28535140 AATTAAAACAGAAATTGAAAA
1 -A--AAAACAGAAATTGAAAA
28535161 TAGAAATGGA
Statistics
Matches: 403, Mismatches: 40, Indels: 62
0.80 0.08 0.12
Matches are distributed among these distances:
70 7 0.02
71 59 0.15
72 33 0.08
74 35 0.09
75 55 0.14
76 31 0.08
77 124 0.31
80 2 0.00
81 19 0.05
84 32 0.08
85 6 0.01
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (76 bp):
AAAAACAGAAATTGAAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTTTTTG
Found at i:28534833 original size:151 final size:150
Alignment explanation
Indices: 28534645--28535160 Score: 606
Period size: 151 Copynumber: 3.4 Consensus size: 150
28534635 AGCGTGCCCC
*
28534645 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACATAAATTGAAAACACCTC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAACAGAAATTGAAAACACCTC
28534710 AGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGATGAACAGAAATT
65 AGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGATGAACAGAAATT
28534775 -AAAACTACCTCAACTTGTCCT
130 GAAAACTACCTCAACTTG-CCT
* * *
28534796 GAAGCTCAACTCACCTCTCGCAACATGAGTTGATTTTTTTGAAAAACAGAAGTTGAAAACACCTC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAACAGAAATTGAAAACACCTC
**
28534861 AGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACAGAAAT
65 AGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGATGAACAGAAAT
* *
28534926 TGAAAAC-ACCTCAGCATG--T
129 TGAAAACTACCTCAACTTGCCT
*
28534945 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACATAAATTGAGCAGAAAATG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG------A-AAA---A-CAGAAATTG
* * * ** *
28535009 AAAATACCTCAACG-G-GTCTTGAGGCCCAACTCACCTCTCGCAATATGAGTTGATTTTTTGATG
55 AAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGATG
* *
28535072 ---ATAAATTGAAAA-TACCTCAA-TGTGACTT
120 AACAGAAATTGAAAACTACCTCAACT-TG-CCT
*
28535100 GAGGCTCAACTCACCTCTCGCAATATGATTTGATTTTTTGAATTAAAACAGAAATTGAAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG-A--AAAACAGAAATTGAAAA
28535161 TAGAAATGGA
Statistics
Matches: 319, Mismatches: 26, Indels: 43
0.82 0.07 0.11
Matches are distributed among these distances:
147 6 0.02
148 12 0.04
149 33 0.10
151 107 0.34
152 50 0.16
153 6 0.02
154 3 0.01
155 41 0.13
156 40 0.13
157 2 0.01
158 19 0.06
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (150 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAACACCTCA
GCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGATGAACAGAAATTG
AAAACTACCTCAACTTGCCT
Found at i:28535123 original size:71 final size:71
Alignment explanation
Indices: 28535007--28535140 Score: 223
Period size: 71 Copynumber: 1.9 Consensus size: 71
28534997 GAGCAGAAAA
*
28535007 TGAAAATACCTCAACGGGTCTTGAGGCCCAACTCACCTCTCGCAATATGAGTTGATTTTTTGATG
1 TGAAAATACCTCAACGGGACTTGAGGCCCAACTCACCTCTCGCAATATGAGTTGATTTTTTGATG
28535072 ATAAAT
66 ATAAAT
* * * *
28535078 TGAAAATACCTCAATGTGACTTGAGGCTCAACTCACCTCTCGCAATATGATTTGATTTTTTGA
1 TGAAAATACCTCAACGGGACTTGAGGCCCAACTCACCTCTCGCAATATGAGTTGATTTTTTGA
28535141 ATTAAAACAG
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 58 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (71 bp):
TGAAAATACCTCAACGGGACTTGAGGCCCAACTCACCTCTCGCAATATGAGTTGATTTTTTGATG
ATAAAT
Found at i:28535222 original size:159 final size:155
Alignment explanation
Indices: 28534873--28535226 Score: 405
Period size: 159 Copynumber: 2.3 Consensus size: 155
28534863 CGTGTGACCC
* * ** * *
28534873 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACAGAAATTGAAAACACCTC
1 GAGGCCCAACTCACCTCTCGCAATATGAGCTGA-TTTTTTG---ATGATAAATTGAAAATACCTC
* *
28534938 -A-G-CA-TGTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGA
62 AATGTGACT-TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGA
** * *
28534999 GCAGAAAATGAAAATACCTCAACGGGTCTT
126 AAAGAAAATGAAAACACCTCAACGCGTCTT
*
28535029 GAGGCCCAACTCACCTCTCGCAATATGAGTTGATTTTTTGATGATAAATTGAAAATACCTCAATG
1 GAGGCCCAACTCACCTCTCGCAATATGAGCTGATTTTTTGATGATAAATTGAAAATACCTCAATG
*
28535094 TGACTTGAGGCTCAACTCACCTCTCGCAATATGATTTGATTTTTTGAATTAAAACAGAAATTGAA
66 TGACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG-A--AAAACAGAAATTGAA
*
28535159 AATAGAAATGGAAAACACCTC-A-GCGTCTT
127 AAGA-AAAT-GAAAACACCTCAACGCGTCTT
** *
28535188 GAGGTTCAACTGACCTCTCGCAATATGAGCTGATTTTTT
1 GAGGCCCAACTCACCTCTCGCAATATGAGCTGATTTTTT
28535227 TGAAACACAT
Statistics
Matches: 171, Mismatches: 17, Indels: 17
0.83 0.08 0.08
Matches are distributed among these distances:
152 17 0.10
153 1 0.01
154 1 0.01
155 41 0.24
156 39 0.23
157 1 0.01
159 56 0.33
160 5 0.03
161 10 0.06
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (155 bp):
GAGGCCCAACTCACCTCTCGCAATATGAGCTGATTTTTTGATGATAAATTGAAAATACCTCAATG
TGACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAAGA
AAATGAAAACACCTCAACGCGTCTT
Found at i:28535393 original size:75 final size:75
Alignment explanation
Indices: 28535258--28535561 Score: 366
Period size: 77 Copynumber: 4.0 Consensus size: 75
28535248 AAAAGAAATT
* ** * *
28535258 AAAAACAGAATTTGAAAGGACCTC-GACGTGTGGCCCGAGACTCAACTCACCTCTCCCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAG-CGTGT--CCCGAGGCTCAACTCACCTCTCGCAATATGA
*
28535322 GTTGATTCTTTTG
63 GTTGATTTTTTTG
28535335 AAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
28535400 GATTTTTTTG
66 GATTTTTTTG
* * * *
28535410 ATACAAATAGAATTTGAAAATATCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 A-A-AAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAG
28535475 TTGA--TTTTTG
64 TTGATTTTTTTG
* * * * ** *
28535485 ACAAACAAAAATTGAAATTACCTCAAC--GTCTTGAGGCTCAACTCACTTCTCGCAATATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
28535548 GATTTTTTTTG
66 GA-TTTTTTTG
28535559 AAA
1 AAA
28535562 CATAAATTAA
Statistics
Matches: 201, Mismatches: 20, Indels: 15
0.85 0.08 0.06
Matches are distributed among these distances:
71 36 0.18
73 19 0.09
74 8 0.04
75 49 0.24
76 1 0.00
77 87 0.43
78 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.30
Consensus pattern (75 bp):
AAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
GATTTTTTTG
Found at i:28535460 original size:77 final size:76
Alignment explanation
Indices: 28535298--28535556 Score: 368
Period size: 77 Copynumber: 3.5 Consensus size: 76
28535288 TGGCCCGAGA
* *
28535298 CTCAACTCACCTCTCCCAATATGAGTTGATTCTTTTGAA-AAACAGAAATTGAAAATACCTCAGC
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAACAAACAGAAATTGAAAATACCTCAGC
*
28535362 GTGTCCCGAGG
66 GTGTCCTGAGG
* * *
28535373 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGATACAAATAGAATTTGAAAATATCTCAG
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGA-ACAAACAGAAATTGAAAATACCTCAG
28535438 CGTGTCCTGAGG
65 CGTGTCCTGAGG
* * *
28535450 CTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTG-ACAAACAAAAATTGAAATTACCTCAAC
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAACAAACAGAAATTGAAAATACCTCAGC
*
28535512 --GTCTTGAGG
66 GTGTCCTGAGG
*
28535521 CTCAACTCACTTCTCGCAATATGAGTTGATTTTTTT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
28535557 TGAAACATAA
Statistics
Matches: 166, Mismatches: 14, Indels: 10
0.87 0.07 0.05
Matches are distributed among these distances:
71 36 0.22
73 26 0.16
75 42 0.25
76 1 0.01
77 61 0.37
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (76 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAACAAACAGAAATTGAAAATACCTCAGC
GTGTCCTGAGG
Found at i:28535779 original size:14 final size:13
Alignment explanation
Indices: 28535744--28535788 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
28535734 TTGATTTTTG
*
28535744 AAAAACATAAATT
1 AAAAACAGAAATT
*
28535757 AAAAGCAGAAATT
1 AAAAACAGAAATT
28535770 GAAAAACAGAAATT
1 -AAAAACAGAAATT
28535784 AAAAA
1 AAAAA
28535789 TACCTCGGCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 16 0.57
14 12 0.43
ACGTcount: A:0.69, C:0.07, G:0.09, T:0.16
Consensus pattern (13 bp):
AAAAACAGAAATT
Found at i:28535800 original size:100 final size:101
Alignment explanation
Indices: 28535572--28535860 Score: 415
Period size: 100 Copynumber: 2.9 Consensus size: 101
28535562 CATAAATTAA
* * * *
28535572 AAAAAC-GAAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACTTCTCACAATATGAGT
1 AAAAACAG-AAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
* * * *
28535636 TGA--TTTGAAAAGCAGAATTTGTAAGGCAAAAATTG
65 TGATTTTTGAAAAGCATAAATTGAAAAGCAAAAATTG
28535671 AAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
* *
28535736 GATTTTTGAAAAACATAAATT-AAAAGCAGAAATTG
66 GATTTTTGAAAAGCATAAATTGAAAAGCAAAAATTG
* * * *
28535771 AAAAACAGAAATTAAAAATACCTCGGCGTGCCCCGAGGCTCAGCTCACCTCTCGCAATATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
28535836 GATTTTTGAAAAGCATAAATTGAAA
66 GATTTTTGAAAAGCATAAATTGAAA
28535861 TTACCTCAGC
Statistics
Matches: 171, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
99 61 0.36
100 93 0.54
101 17 0.10
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (101 bp):
AAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
GATTTTTGAAAAGCATAAATTGAAAAGCAAAAATTG
Found at i:28535866 original size:73 final size:74
Alignment explanation
Indices: 28535768--28535935 Score: 248
Period size: 73 Copynumber: 2.3 Consensus size: 74
28535758 AAAGCAGAAA
* * * * *
28535768 TTGAAAAACAGAAATTAAAAATACCTCGGCGTGCCCCGAGGCTCAGCTCACCTCTCGCAATATGA
1 TTGAAAAGCATAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGA
28535833 GTTGA-TTT
66 GTTGATTTT
* * **
28535841 TTGAAAAGCATAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAGCATAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGA
28535906 GTTGATTTT
66 GTTGATTTT
28535915 TTGAAAAGCATAAATTGAAAA
1 TTGAAAAGCATAAATTGAAAA
28535936 AATGGAAATT
Statistics
Matches: 84, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
73 61 0.73
74 23 0.27
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (74 bp):
TTGAAAAGCATAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTT
Found at i:28543013 original size:24 final size:24
Alignment explanation
Indices: 28542986--28543041 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
28542976 TAGTGATGTG
28542986 AATAATAAAGTATAT-AAAATA-TAA
1 AATAATAAA--ATATCAAAATATTAA
* *
28543010 AATATTAAAATATCAAAATATTAG
1 AATAATAAAATATCAAAATATTAA
28543034 AATAATAA
1 AATAATAA
28543042 TAATTAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 4 0.15
23 6 0.22
24 17 0.63
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (24 bp):
AATAATAAAATATCAAAATATTAA
Found at i:28543020 original size:8 final size:8
Alignment explanation
Indices: 28542986--28543037 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
28542976 TAGTGATGTG
*
28542986 AATAATAA
1 AATATTAA
*
28542994 AGTATATAA
1 AATAT-TAA
28543003 AATA-TAA
1 AATATTAA
28543010 AATATTAA
1 AATATTAA
*
28543018 AATATCAA
1 AATATTAA
*
28543026 AATATTAG
1 AATATTAA
28543034 AATA
1 AATA
28543038 ATAATAATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
7 7 0.19
8 23 0.64
9 6 0.17
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:28543027 original size:16 final size:15
Alignment explanation
Indices: 28542990--28543037 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
28542980 GATGTGAATA
*
28542990 ATAAAGTATATAAAAT
1 ATAAAATAT-TAAAAT
28543006 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
28543021 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
28543037 A
1 A
28543038 ATAATAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:28543215 original size:24 final size:23
Alignment explanation
Indices: 28543186--28543379 Score: 94
Period size: 23 Copynumber: 8.1 Consensus size: 23
28543176 ACGTGATAAT
*
28543186 ATTAAAAATATGTACATAATATA
1 ATTAAAAATATATACATAATATA
* *
28543209 GTGTAAAAATACATACATAATATA
1 AT-TAAAAATATATACATAATATA
*
28543233 ATT-AAAATATATACATAAGATAA
1 ATTAAAAATATATACATAATAT-A
*
28543256 CATGTAGAAAAATATATATAAATAATATA
1 -AT-T---AAAA-ATATATACATAATATA
* *
28543285 GTATTAAAGATATATACATAAAAT-
1 --ATTAAAAATATATACATAATATA
* * *
28543309 AGTATAATATATATACGTAATATAGA
1 ATTA-AAAATATATACATAATAT--A
* * *
28543335 ATT-TAGA-ATATACCTAATAT-
1 ATTAAAAATATATACATAATATA
*
28543355 ATTAAAAGA-ATATATATAATATA
1 ATTAAAA-ATATATACATAATATA
28543378 AT
1 AT
28543380 ATTAAGAAAT
Statistics
Matches: 130, Mismatches: 24, Indels: 34
0.69 0.13 0.18
Matches are distributed among these distances:
20 3 0.02
21 1 0.01
22 31 0.24
23 32 0.25
24 24 0.18
25 14 0.11
26 5 0.04
29 5 0.04
30 15 0.12
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.34
Consensus pattern (23 bp):
ATTAAAAATATATACATAATATA
Found at i:28543246 original size:22 final size:24
Alignment explanation
Indices: 28543188--28543332 Score: 93
Period size: 24 Copynumber: 5.9 Consensus size: 24
28543178 GTGATAATAT
* *
28543188 TAAAAATATGTACATAATATAGTG
1 TAAAAATATATACATAATATAATG
*
28543212 TAAAAATACATACATAATATAAT-
1 TAAAAATATATACATAATATAATG
*
28543235 T-AAAATATATACATAAGATAACATG
1 TAAAAATATATACATAATAT-A-ATG
*
28543260 TAGAAAAATATATATAAATAATATAGTAT-
1 T---AAAA-ATATATACATAATATA--ATG
* *
28543289 TAAAGATATATACATAAAAT-A-G
1 TAAAAATATATACATAATATAATG
* *
28543311 TATAATATATATACGTAATATA
1 TA-AAAATATATACATAATATA
28543333 GAATTTAGAA
Statistics
Matches: 95, Mismatches: 14, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
22 19 0.20
23 17 0.18
24 22 0.23
25 14 0.15
26 3 0.03
29 5 0.05
30 15 0.16
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (24 bp):
TAAAAATATATACATAATATAATG
Found at i:28543297 original size:25 final size:24
Alignment explanation
Indices: 28543269--28543398 Score: 108
Period size: 23 Copynumber: 5.6 Consensus size: 24
28543259 GTAGAAAAAT
*
28543269 ATATATAAATAATATAGTATTAAAG
1 ATATATACATAATATAGTATT-AAG
* *
28543294 ATATATACATAAAATAGTA-TAAT
1 ATATATACATAATATAGTATTAAG
* * *
28543317 ATATATACGTAATATAGAATTTAG
1 ATATATACATAATATAGTATTAAG
* * *
28543341 A-ATATACCTAATATATTA-AAAG
1 ATATATACATAATATAGTATTAAG
* *
28543363 A-ATATATATAATATAATATTAAG
1 ATATATACATAATATAGTATTAAG
*
28543386 AAATATA-ATAATA
1 ATATATACATAATA
28543399 ACAAAAAAAA
Statistics
Matches: 85, Mismatches: 17, Indels: 8
0.77 0.15 0.07
Matches are distributed among these distances:
22 17 0.20
23 42 0.49
24 9 0.11
25 17 0.20
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.35
Consensus pattern (24 bp):
ATATATACATAATATAGTATTAAG
Found at i:28543719 original size:16 final size:16
Alignment explanation
Indices: 28543681--28543719 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
28543671 ATCTTCAAAA
*
28543681 AAAAACTAGCCTCTCC
1 AAAAACTAGCCTCTAC
*
28543697 AAAAACTAGCCTTTAC
1 AAAAACTAGCCTCTAC
*
28543713 AATAACT
1 AAAAACT
28543720 CTTCTCCTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.28, G:0.05, T:0.23
Consensus pattern (16 bp):
AAAAACTAGCCTCTAC
Found at i:28543987 original size:30 final size:30
Alignment explanation
Indices: 28543897--28543995 Score: 153
Period size: 30 Copynumber: 3.3 Consensus size: 30
28543887 TAGGTACAAG
*
28543897 TGGTGGTGGAGTAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
* * *
28543927 AGGTAGTGAAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
*
28543957 TGGTGGTGGAGCAATTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
28543987 TGGTGGTGG
1 TGGTGGTGG
28543996 CAAAGGCTAG
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.18, C:0.05, G:0.48, T:0.28
Consensus pattern (30 bp):
TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
Found at i:28546296 original size:29 final size:29
Alignment explanation
Indices: 28546217--28546288 Score: 101
Period size: 28 Copynumber: 2.5 Consensus size: 29
28546207 AACAGAAATG
* * *
28546217 TCCAACCAAAACACACCAGTATTATATAA
1 TCCATCCAAAACACACCAGAATAATATAA
*
28546246 TCC-TCCCAAACACACCAGAATAATATAA
1 TCCATCCAAAACACACCAGAATAATATAA
28546274 TCCATCCAAAACACA
1 TCCATCCAAAACACA
28546289 ATAGAATAGC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 24 0.65
29 13 0.35
ACGTcount: A:0.47, C:0.32, G:0.03, T:0.18
Consensus pattern (29 bp):
TCCATCCAAAACACACCAGAATAATATAA
Found at i:28546359 original size:13 final size:13
Alignment explanation
Indices: 28546341--28546366 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28546331 ATAAACATCA
28546341 ACATCTCCAAATC
1 ACATCTCCAAATC
28546354 ACATCTCCAAATC
1 ACATCTCCAAATC
28546367 CCTTCTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.23
Consensus pattern (13 bp):
ACATCTCCAAATC
Found at i:28546472 original size:17 final size:17
Alignment explanation
Indices: 28546450--28546488 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
28546440 TTTTTTTATT
*
28546450 TCAATTTCATTTCCATA
1 TCAATTTCAATTCCATA
*
28546467 TCAATTTCAATTCCATT
1 TCAATTTCAATTCCATA
28546484 TCAAT
1 TCAAT
28546489 ATACAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (17 bp):
TCAATTTCAATTCCATA
Found at i:28546474 original size:23 final size:24
Alignment explanation
Indices: 28546447--28546495 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
28546437 CTTTTTTTTT
* *
28546447 ATTTCAATTTCATTTCCATAT-CA
1 ATTTCAATTCCATTTCAATATACA
28546470 ATTTCAATTCCATTTCAATATACA
1 ATTTCAATTCCATTTCAATATACA
28546494 AT
1 AT
28546496 CAATTCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.45
Consensus pattern (24 bp):
ATTTCAATTCCATTTCAATATACA
Found at i:28547745 original size:17 final size:16
Alignment explanation
Indices: 28547721--28547758 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
28547711 TTTATTCACT
28547721 AATATAAT-ATCAATTA
1 AATATAATAATCAA-TA
28547737 AATAGTAATAATCAATA
1 AATA-TAATAATCAATA
28547754 AATAT
1 AATAT
28547759 CTTTTACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.25
17 10 0.50
18 5 0.25
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (16 bp):
AATATAATAATCAATA
Found at i:28548970 original size:18 final size:18
Alignment explanation
Indices: 28548932--28548966 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
28548922 ATGTTGTCAA
28548932 CCCGTGTGAACCCACACG
1 CCCGTGTGAACCCACACG
*
28548950 CCCGTGTG-GCCCACACG
1 CCCGTGTGAACCCACACG
28548967 GCCCAAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.17, C:0.46, G:0.26, T:0.11
Consensus pattern (18 bp):
CCCGTGTGAACCCACACG
Found at i:28553774 original size:15 final size:16
Alignment explanation
Indices: 28553742--28553776 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
28553732 TAAATATTTT
28553742 TTATAAAGATTATATA
1 TTATAAAGATTATATA
*
28553758 TTATAAAG-TTTTATA
1 TTATAAAGATTATATA
28553773 TTAT
1 TTAT
28553777 TTTTATTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (16 bp):
TTATAAAGATTATATA
Found at i:28554501 original size:19 final size:18
Alignment explanation
Indices: 28554477--28554519 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
28554467 TTAGAAATTA
28554477 TTTTTATCA-TACTAATAAT
1 TTTTTAT-AGTACTAAT-AT
*
28554496 TTTTTATAGTATTAATAT
1 TTTTTATAGTACTAATAT
28554514 TTTTTA
1 TTTTTA
28554520 AAAATATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTTTATAGTACTAATAT
Found at i:28558765 original size:26 final size:26
Alignment explanation
Indices: 28558733--28558840 Score: 162
Period size: 26 Copynumber: 4.2 Consensus size: 26
28558723 TGAAATGCCC
* *
28558733 ATCATGGAACATTTACTTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
*
28558759 ATTATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
28558785 ATCATGAAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
28558811 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
28558837 ATCA
1 ATCA
28558841 ATTTGTATCA
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 72 1.00
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.34
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Done.