Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 131 of 316
Found at i:41753110 original size:153 final size:151
Alignment explanation
Indices: 41752938--41753657 Score: 1049
Period size: 151 Copynumber: 4.8 Consensus size: 151
41752928 TCATTTTTTT
41752938 ATATAAAAAACACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAAATAAAA
1 ATATAAAAAA-ACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAAATAAAA
*
41753003 TACGAAAATAGTATATTTTAAAAAATAAAATCCAAAAATATTAAAAATACAAACAAAAGGCCAAA
65 TACGAAAATAGTATATTTTAAAAAATAAAATCCAAAAATTTTAAAAATACAAACAAAAGGCCAAA
*
41753068 ATCAGGGTTATTTATTAAATTA
130 ATCAGGGTTATTTACTAAATTA
41753090 ATATAAAAAAATACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAAATAAA
1 ATAT-AAAAAA-ACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAAATAAA
* * *
41753155 ATACTAAAATAGTATATTTTAAAAAATAAAATCCGAAAATTTTAAAAATACAAAGAAAAGGGCCA
64 ATACGAAAATAGTATATTTTAAAAAATAAAATCCAAAAATTTTAAAAATACAAACAAAA-GGCCA
41753220 AAATCA-GGTTATTTACTAAATTA
128 AAATCAGGGTTATTTACTAAATTA
* *
41753243 ATATAAAAAAACTAAAATAATACATTTGAAAGATTATGTACTGAAATAATAT-AAAAAATAAAAT
1 ATATAAAAAAACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAAATAAAAT
* * ***
41753307 AAGAAAATAGTATATTTTTAAAAATAAAATTTTAAAATTTTAAAAATACAAACAAAAGGCCAAAA
66 ACGAAAATAGTATATTTTAAAAAATAAAATCCAAAAATTTTAAAAATACAAACAAAAGGCCAAAA
*
41753372 TCAGGGTTATTTTCTAAATTA
131 TCAGGGTTATTTACTAAATTA
* *
41753393 ATATAAAAAACACTAAAATAATACATTTGAAACATGATGTACTAAAATAATAT-AAAAAATAATA
1 ATATAAAAAA-ACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAAATAAAA
* * **** * ** *
41753457 TACAAAAATAATATATGTTT-AAAAATAAAATCTGGGAATTTTAAAAATGCAAACAAATTGACAA
65 TACGAAAATAGTATAT-TTTAAAAAATAAAATCCAAAAATTTTAAAAATACAAACAAAAGGCCAA
* *
41753521 ATTTAGGGTTATTTACTAAATTA
129 AATCAGGGTTATTTACTAAATTA
* *
41753544 ATAT-AAAAAACTAAAATAATACATTTGAAACATTATGTATTAAAAT-A-ATAATAAAATAAAAT
1 ATATAAAAAAACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAAATAAAAT
* * *
41753606 ATGAAAATAGTATATTTTAAAAAATAAGATCCAAAAATTTTAAAAATGCAAA
66 ACGAAAATAGTATATTTTAAAAAATAAAATCCAAAAATTTTAAAAATACAAA
41753658 AATTTTTTAT
Statistics
Matches: 515, Mismatches: 46, Indels: 18
0.89 0.08 0.03
Matches are distributed among these distances:
147 5 0.01
148 51 0.10
149 46 0.09
150 93 0.18
151 162 0.31
152 13 0.03
153 134 0.26
154 11 0.02
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (151 bp):
ATATAAAAAAACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAAATAAAAT
ACGAAAATAGTATATTTTAAAAAATAAAATCCAAAAATTTTAAAAATACAAACAAAAGGCCAAAA
TCAGGGTTATTTACTAAATTA
Found at i:41753335 original size:22 final size:22
Alignment explanation
Indices: 41753310--41753354 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
41753300 ATAAAATAAG
* *
41753310 AAAATAGTATATTTTTAAAAAT
1 AAAATAGTAAAATTTTAAAAAT
**
41753332 AAAATTTTAAAATTTTAAAAAT
1 AAAATAGTAAAATTTTAAAAAT
41753354 A
1 A
41753355 CAAACAAAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AAAATAGTAAAATTTTAAAAAT
Found at i:41753453 original size:12 final size:13
Alignment explanation
Indices: 41753436--41753471 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
41753426 ATGATGTACT
41753436 AAAATAATATA-A
1 AAAATAATATACA
41753448 AAAATAATATACA
1 AAAATAATATACA
41753461 AAAATAATATA
1 AAAATAATATA
41753472 TGTTTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (13 bp):
AAAATAATATACA
Found at i:41753970 original size:27 final size:27
Alignment explanation
Indices: 41753935--41753995 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
41753925 AACAGGTGTC
*
41753935 GCCTATGCCAGAGGCACAACTGGTGCCT
1 GCCTCTGCCAGAGGCACAACTGGTG-CT
*
41753963 -CCTCTGCCAGAGGCACAATTGGTGCT
1 GCCTCTGCCAGAGGCACAACTGGTGCT
41753989 GCCTCTG
1 GCCTCTG
41753996 GGACCCACAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 2 0.07
27 28 0.93
ACGTcount: A:0.18, C:0.33, G:0.28, T:0.21
Consensus pattern (27 bp):
GCCTCTGCCAGAGGCACAACTGGTGCT
Found at i:41754043 original size:19 final size:19
Alignment explanation
Indices: 41754021--41754058 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
41754011 CCTTTTTTTG
*
41754021 TTTTTTTTTTATTTTTAAC
1 TTTTTTTTTCATTTTTAAC
*
41754040 TTTTTTTTTCCTTTTTAAC
1 TTTTTTTTTCATTTTTAAC
41754059 AAAAAATGGC
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:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTTTTTTCATTTTTAAC
Found at i:41755183 original size:12 final size:12
Alignment explanation
Indices: 41755163--41755193 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
41755153 ATTAAATAAT
41755163 TTATAAAAAAAA
1 TTATAAAAAAAA
*
41755175 TTGTAAAAAAAA
1 TTATAAAAAAAA
41755187 TTATAAA
1 TTATAAA
41755194 TTTTATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (12 bp):
TTATAAAAAAAA
Found at i:41757228 original size:33 final size:33
Alignment explanation
Indices: 41757173--41757325 Score: 132
Period size: 33 Copynumber: 4.7 Consensus size: 33
41757163 TTTCCAATAG
* * *
41757173 ACATAACCTTTTTC-AGTCGTACACTCGAGGTGT
1 ACAT-ACCCTTTTCAAGTCGTACACTCAAAGTGT
* *
41757206 ACATTCCCTTTTCAAGTGGTACACTCAAAGTGT
1 ACATACCCTTTTCAAGTCGTACACTCAAAGTGT
** *
41757239 ACATAGTCTTTTCAAGTTGTACACGT-AAAGTGT
1 ACATACCCTTTTCAAGTCGTACAC-TCAAAGTGT
* * * *
41757272 ACATAGCCTTTTCAAATTGTACACACAAAGTGT
1 ACATACCCTTTTCAAGTCGTACACTCAAAGTGT
* * *
41757305 ATATAACCATTTCAAGT-GTAC
1 ACATACCCTTTTCAAGTCGTAC
41757326 CATTTAGGTA
Statistics
Matches: 101, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
32 11 0.11
33 89 0.88
34 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (33 bp):
ACATACCCTTTTCAAGTCGTACACTCAAAGTGT
Found at i:41757318 original size:66 final size:65
Alignment explanation
Indices: 41757202--41757325 Score: 158
Period size: 66 Copynumber: 1.9 Consensus size: 65
41757192 TACACTCGAG
* * * ** *
41757202 GTGTACATTCCCTTTTCAAGTGGTACACTCAAAGTGTACATAGTCTTTTCAAGTTGTACACGTAA
1 GTGTACATACCCTTTTCAAATGGTACACACAAAGTGTACATAACCATTTCAAG-TGTACACGTAA
41757267 A
65 A
* * *
41757268 GTGTACATAGCCTTTTCAAATTGTACACACAAAGTGTATATAACCATTTCAAGTGTAC
1 GTGTACATACCCTTTTCAAATGGTACACACAAAGTGTACATAACCATTTCAAGTGTAC
41757326 CATTTAGGTA
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
65 5 0.10
66 44 0.90
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.34
Consensus pattern (65 bp):
GTGTACATACCCTTTTCAAATGGTACACACAAAGTGTACATAACCATTTCAAGTGTACACGTAAA
Found at i:41763370 original size:19 final size:20
Alignment explanation
Indices: 41763332--41763371 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
41763322 TTGTGAAATT
*
41763332 AAATTAAAATTTAATGTATA
1 AAATTAAAATTTAATATATA
41763352 AAATTAAAATTT-ATATATA
1 AAATTAAAATTTAATATATA
41763371 A
1 A
41763372 TATTGAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (20 bp):
AAATTAAAATTTAATATATA
Found at i:41763776 original size:8 final size:8
Alignment explanation
Indices: 41763763--41763789 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
41763753 GACAGGAAAG
41763763 AAAAGAAT
1 AAAAGAAT
41763771 AAAAGAAT
1 AAAAGAAT
41763779 AAAAGAAT
1 AAAAGAAT
41763787 AAA
1 AAA
41763790 TAAATATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (8 bp):
AAAAGAAT
Found at i:41765498 original size:25 final size:23
Alignment explanation
Indices: 41765452--41765496 Score: 81
Period size: 24 Copynumber: 1.9 Consensus size: 23
41765442 TAGCAATTAA
41765452 TTATTTTTTAAAATTTAAAAATT
1 TTATTTTTTAAAATTTAAAAATT
41765475 TTATATTTTTAAAATTTAAAAA
1 TTAT-TTTTTAAAATTTAAAAA
41765497 ATAATTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTATTTTTTAAAATTTAAAAATT
Found at i:41765658 original size:29 final size:29
Alignment explanation
Indices: 41765626--41765681 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
41765616 AGGCGAAAAA
* *
41765626 TTAAATTA-ATGGCTAAAATAATTTTTTTT
1 TTAAATTAGAGGGCT-AAATAAGTTTTTTT
41765655 TTAAATTAGAGGGCTAAATAAGTTTTT
1 TTAAATTAGAGGGCTAAATAAGTTTTT
41765682 ATGCATATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (29 bp):
TTAAATTAGAGGGCTAAATAAGTTTTTTT
Found at i:41770689 original size:27 final size:27
Alignment explanation
Indices: 41770657--41770710 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
41770647 TTTTCTTTTA
*
41770657 TTTGCTTCTGGCAGGTTCCTTTAGTTT
1 TTTGCTTCTGGCAGGTTCATTTAGTTT
* *
41770684 TTTGCTTCTGGTAGGTTTATTTAGTTT
1 TTTGCTTCTGGCAGGTTCATTTAGTTT
41770711 ATAACTAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.09, C:0.13, G:0.22, T:0.56
Consensus pattern (27 bp):
TTTGCTTCTGGCAGGTTCATTTAGTTT
Found at i:41780235 original size:21 final size:21
Alignment explanation
Indices: 41780210--41780249 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41780200 AGGTGAATAG
* *
41780210 TAGCCCTTATGCTGTGCATAA
1 TAGCCCCTATGCTATGCATAA
41780231 TAGCCCCTATGCTATGCAT
1 TAGCCCCTATGCTATGCAT
41780250 CTTGGCGAAA
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:0.23, C:0.28, G:0.17, T:0.33
Consensus pattern (21 bp):
TAGCCCCTATGCTATGCATAA
Found at i:41786496 original size:16 final size:16
Alignment explanation
Indices: 41786415--41786507 Score: 52
Period size: 16 Copynumber: 5.6 Consensus size: 16
41786405 CCCTTCTATG
41786415 TTATTTATTTAATTATTTA
1 TTATTTA-TT-ATTA-TTA
*
41786434 TTTATTTTTTATATATTA
1 -TTATTTATTAT-TATTA
*
41786452 TTATTAATATATTATT-
1 TTATTTAT-TATTATTA
*
41786468 TTCTTTCCA-TATTA-T-
1 TTATTT--ATTATTATTA
41786483 TTA-TTATTATTATTA
1 TTATTTATTATTATTA
41786498 TTATTTATTA
1 TTATTTATTA
41786508 GCAGTTATTT
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
12 1 0.02
13 5 0.08
14 3 0.05
15 6 0.10
16 15 0.25
17 10 0.17
18 9 0.15
19 4 0.07
20 6 0.10
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTTATTATTATTA
Found at i:41788669 original size:20 final size:18
Alignment explanation
Indices: 41788612--41788671 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 18
41788602 TTTTATATAT
41788612 TAAATTATTATATT--AA
1 TAAATTATTATATTAAAA
* *
41788628 TAAAATATTATATTAAAT
1 TAAATTATTATATTAAAA
41788646 TAAATTATTATATTATAAAA
1 TAAATTATTATA-T-TAAAA
41788666 TAAATT
1 TAAATT
41788672 GAGTTGTAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
16 13 0.36
18 12 0.33
19 1 0.03
20 10 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAATTATTATATTAAAA
Found at i:41790464 original size:34 final size:35
Alignment explanation
Indices: 41790426--41790491 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
41790416 CTATTAAAAT
*
41790426 TTTAACTTTAAAA-CTAAATATAA-AAATTAATGAA
1 TTTAAATTTAAAATCTAAA-ATAATAAATTAATGAA
*
41790460 TTTAAATTTAAAATTTAAAATAATAAATTAAT
1 TTTAAATTTAAAATCTAAAATAATAAATTAAT
41790492 AACGCAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (35 bp):
TTTAAATTTAAAATCTAAAATAATAAATTAATGAA
Found at i:41796151 original size:7 final size:7
Alignment explanation
Indices: 41796120--41796174 Score: 56
Period size: 7 Copynumber: 7.4 Consensus size: 7
41796110 ATATTAAATA
41796120 TTTAAGTT
1 TTTAA-TT
*
41796128 TTTTATCT
1 TTTAAT-T
*
41796136 TTTATTT
1 TTTAATT
41796143 TTTAATT
1 TTTAATT
41796150 TTTAATT
1 TTTAATT
41796157 TTTAAATT
1 TTT-AATT
*
41796165 TTAAATT
1 TTTAATT
41796172 TTT
1 TTT
41796175 TTTGAATATT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
7 24 0.62
8 15 0.38
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (7 bp):
TTTAATT
Found at i:41796157 original size:15 final size:15
Alignment explanation
Indices: 41796120--41796175 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
41796110 ATATTAAATA
41796120 TTTAAGTTTTTT-ATCT
1 TTTAA-TTTTTTAAT-T
41796136 TTT-ATTTTTTAATT
1 TTTAATTTTTTAATT
*
41796150 TTTAATTTTTAAATT
1 TTTAATTTTTTAATT
*
41796165 TTAAATTTTTT
1 TTTAATTTTTT
41796176 TTGAATATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 10 0.29
15 22 0.63
16 3 0.09
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTAATTTTTTAATT
Found at i:41796582 original size:15 final size:15
Alignment explanation
Indices: 41796562--41796595 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
41796552 CAATATATAA
41796562 ATATCAAATGATGTT
1 ATATCAAATGATGTT
41796577 ATATCAAATGATGTT
1 ATATCAAATGATGTT
41796592 ATAT
1 ATAT
41796596 TAATAATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (15 bp):
ATATCAAATGATGTT
Found at i:41796976 original size:21 final size:21
Alignment explanation
Indices: 41796959--41797022 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
41796949 AAACCTAACA
* *
41796959 CTTAACCCTTAACCCCTAAAC
1 CTTAAACCTCAACCCCTAAAC
*
41796980 CTTAAACCTCAACCCTTAAAC
1 CTTAAACCTCAACCCCTAAAC
* *
41797001 CATAAACCAT-AATCCCTAAAC
1 CTTAAACC-TCAACCCCTAAAC
41797022 C
1 C
41797023 CATAATCCAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
21 35 0.97
22 1 0.03
ACGTcount: A:0.39, C:0.39, G:0.00, T:0.22
Consensus pattern (21 bp):
CTTAAACCTCAACCCCTAAAC
Found at i:41797025 original size:15 final size:14
Alignment explanation
Indices: 41797000--41797035 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
41796990 AACCCTTAAA
41797000 CCATAAACCATAAT
1 CCATAAACCATAAT
*
41797014 CCCTAAACCCATAAT
1 CCATAAA-CCATAAT
41797029 CCATAAA
1 CCATAAA
41797036 TCTTAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.19
Consensus pattern (14 bp):
CCATAAACCATAAT
Found at i:41797042 original size:22 final size:21
Alignment explanation
Indices: 41796975--41797042 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
41796965 CCTTAACCCC
* ** *
41796975 TAAACCTTAAACCTCAACCCT
1 TAAACCATAAACCATAATCCT
*
41796996 TAAACCATAAACCATAATCCC
1 TAAACCATAAACCATAATCCT
*
41797017 TAAACCCATAATCCATAAAT-CT
1 TAAA-CCATAAACCAT-AATCCT
41797039 TAAA
1 TAAA
41797043 ATAGTAACTC
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
21 20 0.53
22 15 0.39
23 3 0.08
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAACCATAAACCATAATCCT
Found at i:41797095 original size:14 final size:14
Alignment explanation
Indices: 41797061--41797105 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
41797051 TCATACACTT
*
41797061 TAAACCCTCAACTA
1 TAAACCCTAAACTA
* *
41797075 TATACCCTAAACCA
1 TAAACCCTAAACTA
41797089 TAAACCCTAAACTA
1 TAAACCCTAAACTA
41797103 TAA
1 TAA
41797106 TGATAATTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCCTAAACTA
Found at i:41797223 original size:7 final size:7
Alignment explanation
Indices: 41797200--41797305 Score: 72
Period size: 7 Copynumber: 14.9 Consensus size: 7
41797190 CTAATTAATT
41797200 TAAACCC
1 TAAACCC
41797207 TAAACTCC
1 TAAAC-CC
*
41797215 TAATCCC
1 TAAACCC
41797222 TAAACCC
1 TAAACCC
*
41797229 TAAACCA
1 TAAACCC
*
41797236 TAAATCC
1 TAAACCC
* *
41797243 TAAAACA
1 TAAACCC
*
41797250 TAAACCT
1 TAAACCC
* *
41797257 TGAACCA
1 TAAACCC
41797264 TAAACCAC
1 TAAACC-C
41797272 T-AACCAC
1 TAAACC-C
41797279 T-AACCC
1 TAAACCC
*
41797285 TTAACCC
1 TAAACCC
*
41797292 TTAACACC
1 TAAAC-CC
41797300 TAAACC
1 TAAACC
41797306 TTAGACCCCA
Statistics
Matches: 81, Mismatches: 14, Indels: 8
0.79 0.14 0.08
Matches are distributed among these distances:
6 2 0.02
7 66 0.81
8 13 0.16
ACGTcount: A:0.43, C:0.36, G:0.01, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:41797248 original size:22 final size:22
Alignment explanation
Indices: 41797200--41797246 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
41797190 CTAATTAATT
*
41797200 TAAACCCTAAACTCCTAATCCC
1 TAAACCCTAAACTCATAATCCC
41797222 TAAACCCTAAAC-CATAAAT-CC
1 TAAACCCTAAACTCAT-AATCCC
41797243 TAAA
1 TAAA
41797247 ACATAAACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (22 bp):
TAAACCCTAAACTCATAATCCC
Found at i:41797738 original size:76 final size:76
Alignment explanation
Indices: 41797565--41797748 Score: 208
Period size: 76 Copynumber: 2.4 Consensus size: 76
41797555 GTATTTTATT
* * * * * * * * **
41797565 TTTTGTGGCATTTTTCAAAAAGCACCACTAAAGCCACTAAAAGCTTAAGACAAAATGATGGTGTT
1 TTTTGCGGCGTTTTTCAAAAAACGCCGCTAAAGCCACTAAAAGCTCAAGACAAAACGACGACGTT
41797630 TCTCAAAATTC
66 TCTCAAAATTC
* * * *
41797641 TTTTGTGGTGTTTTTCAAAAAATGCCGCTAAAGCCACTAAAAGCTCAATACAAAACGACGACGTT
1 TTTTGCGGCGTTTTTCAAAAAACGCCGCTAAAGCCACTAAAAGCTCAAGACAAAACGACGACGTT
41797706 T-TGCAAAATTC
66 TCT-CAAAATTC
**
41797717 TTTTGCGGCGTTTTTTTAAAAACGCCGCTAAA
1 TTTTGCGGCGTTTTTCAAAAAACGCCGCTAAA
41797749 TGTGTACATA
Statistics
Matches: 90, Mismatches: 17, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
75 1 0.01
76 89 0.99
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (76 bp):
TTTTGCGGCGTTTTTCAAAAAACGCCGCTAAAGCCACTAAAAGCTCAAGACAAAACGACGACGTT
TCTCAAAATTC
Found at i:41797955 original size:40 final size:39
Alignment explanation
Indices: 41797888--41797980 Score: 100
Period size: 40 Copynumber: 2.4 Consensus size: 39
41797878 AGATCGAGTA
*
41797888 TTAGCAGCGTTTTTTAAAAGGTACCGCTAATACTTGATCT
1 TTAGCAGCGTTTTTTAAAAGG-ACCGCTAATACTCGATCT
* * *
41797928 TTAGCTGCGTTTTTTGAAAAGCG-CCGCTAATGCTCGTTCT
1 TTAGCAGCGTTTTTT-AAAAG-GACCGCTAATACTCGATCT
*
41797968 TTAGCGGC-TTTTT
1 TTAGCAGCGTTTTT
41797981 CATTCAAACG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
39 5 0.11
40 35 0.76
41 5 0.11
42 1 0.02
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.40
Consensus pattern (39 bp):
TTAGCAGCGTTTTTTAAAAGGACCGCTAATACTCGATCT
Found at i:41804189 original size:40 final size:40
Alignment explanation
Indices: 41804115--41804336 Score: 367
Period size: 40 Copynumber: 5.6 Consensus size: 40
41804105 AACCCAAGTA
* *
41804115 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* * *
41804154 CCTTCGGGTCTTAGCCTGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
41804194 CCTTCGGGACTTGGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
41804234 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
41804274 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
41804314 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
41804337 CATTCGAATA
Statistics
Matches: 171, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
39 12 0.07
40 158 0.92
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:41819924 original size:40 final size:40
Alignment explanation
Indices: 41819850--41820071 Score: 358
Period size: 40 Copynumber: 5.6 Consensus size: 40
41819840 AACCCAAGTA
* * *
41819850 CCTTCGGGATTTAG-CTGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* *
41819889 CCTTCGGGTCTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
41819929 CCTTCGGGACTTGGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
41819969 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
41820009 CCTTCGAGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
41820049 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
41820072 CATTCGAATA
Statistics
Matches: 170, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 12 0.07
40 157 0.92
41 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:41824270 original size:32 final size:33
Alignment explanation
Indices: 41824229--41824292 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
41824219 TCCTATTATA
*
41824229 CCTCATTTTCTT-TTTATTTTCTTTT-TTATTTC
1 CCTCATTTTCTTCTAT-TTTTCTTTTCTTATTTC
41824261 CCTCATTTTCTTCTATTTTTCTTTTCTTATTT
1 CCTCATTTTCTTCTATTTTTCTTTTCTTATTT
41824293 TTCTGTTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 21 0.72
33 8 0.28
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.70
Consensus pattern (33 bp):
CCTCATTTTCTTCTATTTTTCTTTTCTTATTTC
Found at i:41824293 original size:14 final size:15
Alignment explanation
Indices: 41824274--41824302 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41824264 CATTTTCTTC
41824274 TATTTTTCT-TTTCT
1 TATTTTTCTGTTTCT
41824288 TATTTTTCTGTTTCT
1 TATTTTTCTGTTTCT
41824303 GACCTTTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.07, C:0.14, G:0.03, T:0.76
Consensus pattern (15 bp):
TATTTTTCTGTTTCT
Found at i:41825357 original size:6 final size:6
Alignment explanation
Indices: 41825346--41825392 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
41825336 AAGCAGGACT
* *
41825346 AGAAAA AGAAAA AAAAAGA AAATAAA AGAAAA AGAAAA AGAAAA AGA
1 AGAAAA AGAAAA AGAAA-A AGA-AAA AGAAAA AGAAAA AGAAAA AGA
41825393 GGTACAAGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
6 28 0.76
7 7 0.19
8 2 0.05
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (6 bp):
AGAAAA
Found at i:41825363 original size:10 final size:10
Alignment explanation
Indices: 41825348--41825390 Score: 59
Period size: 10 Copynumber: 4.1 Consensus size: 10
41825338 GCAGGACTAG
41825348 AAAAAGAAAA
1 AAAAAGAAAA
41825358 AAAAAGAAAA
1 AAAAAGAAAA
*
41825368 TAAAAGAAAAA
1 AAAAAG-AAAA
41825379 GAAAAAGAAAA
1 -AAAAAGAAAA
41825390 A
1 A
41825391 GAGGTACAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 16 0.55
11 8 0.28
12 5 0.17
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:41825891 original size:13 final size:14
Alignment explanation
Indices: 41825854--41825884 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
41825844 TAGTAAGAAG
*
41825854 ATTAAATTATATAA
1 ATTAAAGTATATAA
41825868 ATTAAAGTATATAA
1 ATTAAAGTATATAA
41825882 ATT
1 ATT
41825885 GAGTATAGTA
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:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (14 bp):
ATTAAAGTATATAA
Found at i:41832792 original size:24 final size:24
Alignment explanation
Indices: 41832747--41832792 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
41832737 AAATATCATA
***
41832747 TTAATTTTAATTGATTTGATTAAT
1 TTAATTTTAATTGATCAAATTAAT
*
41832771 TTAATTTTACTTGATCAAATTA
1 TTAATTTTAATTGATCAAATTA
41832793 TTTTTTCCAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (24 bp):
TTAATTTTAATTGATCAAATTAAT
Found at i:41833951 original size:16 final size:16
Alignment explanation
Indices: 41833930--41833960 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
41833920 CTATGCATGC
41833930 AAAATAAAAAAGACAA
1 AAAATAAAAAAGACAA
41833946 AAAATAAAAAAGACA
1 AAAATAAAAAAGACA
41833961 TAATAGTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.81, C:0.06, G:0.06, T:0.06
Consensus pattern (16 bp):
AAAATAAAAAAGACAA
Found at i:41837682 original size:45 final size:45
Alignment explanation
Indices: 41837631--41837745 Score: 144
Period size: 46 Copynumber: 2.5 Consensus size: 45
41837621 GTGCCAATGC
*
41837631 CATGTCCCAGACATGGTCTTACACTAAC-ACATCGCGTAGTC-GATG
1 CATGTCCCAGACAT-GTCTTACACTAACTACATCGCG-AGGCTGATG
** **
41837676 CATGTCCCAGACATGTCTTACACTGGCTTACATCTTGAGGCTGATG
1 CATGTCCCAGACATGTCTTACACTAAC-TACATCGCGAGGCTGATG
41837722 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
41837746 GGCACACAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
44 11 0.18
45 17 0.27
46 34 0.55
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (45 bp):
CATGTCCCAGACATGTCTTACACTAACTACATCGCGAGGCTGATG
Found at i:41839779 original size:230 final size:231
Alignment explanation
Indices: 41839131--41839821 Score: 1321
Period size: 231 Copynumber: 3.0 Consensus size: 231
41839121 AAAATCGGCT
*
41839131 TGTTACACGGCCGAGGACACGCCTTTGTGCCATGGCCGTGGGAAAACTGGAGGGGTTACTGACTT
1 TGTTACACGGCCGAGGACATGCCTTTGTGCCATGGCCGTGGGAAAACTGGAGGGGTTACTGACTT
41839196 GGGTCACACGGTCGGCCACACGTCCATGTGCTAGCCCGTGTGTCACACACGGCCAGTAAACACAC
66 GGGTCACACGGTCGGCCACACGTCCATGTGCTAGCCCGTGTGTCACACACGGCCAGTAAACACAC
*
41839261 CCGTGTGTCTAGACCCTGTCAAACTTGTAGGGTATACTACATTAAGTCGAAAGGGTATCTTAGGG
131 CCGTGTGTCTAGACCCTGTCAAACTTGTAGGGTATACTACATTAAGTCGAAAGGGTACCTTAGGG
*
41839326 GACACACGGCCTTACAATATGACCGTGTGTCACACC
196 GACACACGGCCTTACAATATGACCGTGTGTCATACC
41839362 TGTTACACGGCCGAGGACATGCCTTTGTGCCATGGCCGTGGGAAAACTGGAGGGGTTACTGACTT
1 TGTTACACGGCCGAGGACATGCCTTTGTGCCATGGCCGTGGGAAAACTGGAGGGGTTACTGACTT
*
41839427 GGGTCACACGGTCGGCCACACGTCCATGTGCTAGCCCGTGGGTCACACACGGCCAGTAAACACAC
66 GGGTCACACGGTCGGCCACACGTCCATGTGCTAGCCCGTGTGTCACACACGGCCAGTAAACACAC
41839492 CCGTGTGTCTAGACCCTGTCAAACTTGTAGGGTATACTACATTAAGTCGAAAGGGTACCTTAGGG
131 CCGTGTGTCTAGACCCTGTCAAACTTGTAGGGTATACTACATTAAGTCGAAAGGGTACCTTAGGG
41839557 GACACACGGCCTTACAATATGACCGTGTGTCATACC
196 GACACACGGCCTTACAATATGACCGTGTGTCATACC
41839593 TGTTACACGGCCGAGGACATGCCTTTGTGCCATGGCCGTGGGAAAACTGGAGGGGTTACTGACTT
1 TGTTACACGGCCGAGGACATGCCTTTGTGCCATGGCCGTGGGAAAACTGGAGGGGTTACTGACTT
*
41839658 -GGTTACACGGTCGGCCACACGTCCATGTGCTAGCCCGTGTGTCACACACGGCCAGTAAACACAC
66 GGGTCACACGGTCGGCCACACGTCCATGTGCTAGCCCGTGTGTCACACACGGCCAGTAAACACAC
41839722 CCGTGTGTCTAGACCCTGTCAAACTTGTAGGGTATACTACATTAAGTCGAAAGGGTACCTTAGGG
131 CCGTGTGTCTAGACCCTGTCAAACTTGTAGGGTATACTACATTAAGTCGAAAGGGTACCTTAGGG
*
41839787 GACACACGACCTTACAATATGACCGTGTGTCATAC
196 GACACACGGCCTTACAATATGACCGTGTGTCATAC
41839822 ACGGTTCAGA
Statistics
Matches: 453, Mismatches: 7, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
230 161 0.36
231 292 0.64
ACGTcount: A:0.24, C:0.26, G:0.27, T:0.22
Consensus pattern (231 bp):
TGTTACACGGCCGAGGACATGCCTTTGTGCCATGGCCGTGGGAAAACTGGAGGGGTTACTGACTT
GGGTCACACGGTCGGCCACACGTCCATGTGCTAGCCCGTGTGTCACACACGGCCAGTAAACACAC
CCGTGTGTCTAGACCCTGTCAAACTTGTAGGGTATACTACATTAAGTCGAAAGGGTACCTTAGGG
GACACACGGCCTTACAATATGACCGTGTGTCATACC
Found at i:41840905 original size:42 final size:40
Alignment explanation
Indices: 41840843--41840952 Score: 116
Period size: 40 Copynumber: 2.7 Consensus size: 40
41840833 TTCATAGATG
*
41840843 AAGCTATCTC-AGTCTCGCACATTAAGTGCCATATAAATAGCCA
1 AAGCTATCTCGA-T-TCGCACACTAAGTG-C-TATAAATAGCCA
* * *
41840886 AAGCTAT-TCCGATTCGCACACTAAGTGCTTTATATAGCCG
1 AAGCTATCT-CGATTCGCACACTAAGTGCTATAAATAGCCA
*
41840926 AAGCTATCTCGATACGCACACTAAGTG
1 AAGCTATCTCGATTCGCACACTAAGTG
41840953 GCAAACATAA
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
40 33 0.56
41 2 0.03
42 14 0.24
43 9 0.15
44 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.26
Consensus pattern (40 bp):
AAGCTATCTCGATTCGCACACTAAGTGCTATAAATAGCCA
Found at i:41843675 original size:54 final size:54
Alignment explanation
Indices: 41843593--41843695 Score: 206
Period size: 54 Copynumber: 1.9 Consensus size: 54
41843583 TGTTTCATAA
41843593 GATTATTAAGCTAGCTCGAGTTGGAGATCGTCGGAGATCCTATCACATTTATAG
1 GATTATTAAGCTAGCTCGAGTTGGAGATCGTCGGAGATCCTATCACATTTATAG
41843647 GATTATTAAGCTAGCTCGAGTTGGAGATCGTCGGAGATCCTATCACATT
1 GATTATTAAGCTAGCTCGAGTTGGAGATCGTCGGAGATCCTATCACATT
41843696 ATCCAGCTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.31
Consensus pattern (54 bp):
GATTATTAAGCTAGCTCGAGTTGGAGATCGTCGGAGATCCTATCACATTTATAG
Found at i:41844247 original size:15 final size:13
Alignment explanation
Indices: 41844214--41844246 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
41844204 GACACACGGG
41844214 CGTGTGTCTAGGC
1 CGTGTGTCTAGGC
41844227 CGTGTGTCTAGGC
1 CGTGTGTCTAGGC
41844240 CGTGTGT
1 CGTGTGT
41844247 GACACACGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.06, C:0.21, G:0.39, T:0.33
Consensus pattern (13 bp):
CGTGTGTCTAGGC
Found at i:41846694 original size:12 final size:12
Alignment explanation
Indices: 41846677--41846706 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
41846667 AGTAACATGC
41846677 CCGTGTGCCAGG
1 CCGTGTGCCAGG
*
41846689 CCGTGTGCTAGG
1 CCGTGTGCCAGG
41846701 CCGTGT
1 CCGTGT
41846707 AATTGCCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.30, G:0.40, T:0.23
Consensus pattern (12 bp):
CCGTGTGCCAGG
Found at i:41848641 original size:18 final size:20
Alignment explanation
Indices: 41848605--41848651 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
41848595 AGTTGTAAGT
41848605 ATATATATGTGAATAATTTG
1 ATATATATGTGAATAATTTG
* *
41848625 ATAT-TATGTGATTATTTTG
1 ATATATATGTGAATAATTTG
41848644 ATGATATA
1 AT-ATATA
41848652 ACATGTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 15 0.65
20 6 0.26
21 2 0.09
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (20 bp):
ATATATATGTGAATAATTTG
Found at i:41849079 original size:50 final size:50
Alignment explanation
Indices: 41849000--41849243 Score: 283
Period size: 50 Copynumber: 4.9 Consensus size: 50
41848990 TTCGTTGTGA
*
41849000 GTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAG
1 GTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGATAG
* ** * * *
41849050 GTCGCATGTGTAGTACTAAGTGCAGGCTACTATACGTACCCG-TTAACTTCG
1 GTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGA--TAG
* * * * ** * * *
41849101 ATCACGTGTGTAGTACTAAGTGCAGGGTACTACGTGTATTAGATGGTTAA
1 GTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGATAG
*
41849151 GTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACTAGATTGATAG
1 GTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGATAG
* * *
41849201 GTCACATTTGTAGTACTAAGTGAAGGCTACTATGCGTACCAGA
1 GTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGA
41849244 GAGCTTCGGT
Statistics
Matches: 157, Mismatches: 34, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
49 3 0.02
50 119 0.76
51 34 0.22
52 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (50 bp):
GTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGATAG
Found at i:41849181 original size:101 final size:101
Alignment explanation
Indices: 41849001--41849183 Score: 294
Period size: 101 Copynumber: 1.8 Consensus size: 101
41848991 TCGTTGTGAG
* * *
41849001 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCATGTGTAGTAC
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGATAAGTCACATGTGTAGTAC
41849066 TAAGTGCAGGCTACTATACGTACCCGTTAACTTCGA
66 TAAGTGCAGGCTACTATACGTACCCGTTAACTTCGA
* * ** *
41849102 TCACGTGTGTAGTACTAAGTGCAGGGTACTACGTGTATTAGATGGTTAAGTCACATGTGTAGTAC
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGATAAGTCACATGTGTAGTAC
41849167 TAAGTGCAGGCTACTAT
66 TAAGTGCAGGCTACTAT
41849184 GTGTACTAGA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
101 74 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (101 bp):
TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGATAAGTCACATGTGTAGTAC
TAAGTGCAGGCTACTATACGTACCCGTTAACTTCGA
Found at i:41854607 original size:39 final size:39
Alignment explanation
Indices: 41854553--41854824 Score: 463
Period size: 39 Copynumber: 7.0 Consensus size: 39
41854543 AAGACACTGA
41854553 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
41854592 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
41854631 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGTTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
41854670 AAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* * *
41854709 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTTGTGCTAG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
41854748 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
41854787 AAATGTATCCGGGTTAAAGTCCCGCAGGCTTTGTGCTG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
41854825 ATAATATAAT
Statistics
Matches: 221, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 221 1.00
ACGTcount: A:0.21, C:0.25, G:0.30, T:0.24
Consensus pattern (39 bp):
AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
Found at i:41860014 original size:40 final size:39
Alignment explanation
Indices: 41859960--41860093 Score: 115
Period size: 39 Copynumber: 3.4 Consensus size: 39
41859950 TGAATTCAAT
* * *
41859960 CACCAACACAAAGCCTACGGGACGTTAACCCCGGATATAG
1 CACCAGCACGAAGCCTAC-GGACCTTAACCCCGGATATAG
* * **
41860000 CACCAGTACGAAGCCTGCGGACCTTAAGTCCGGATATAG
1 CACCAGCACGAAGCCTACGGACCTTAACCCCGGATATAG
* * * ** * *
41860039 TACCAGCACGAAGCCTGCGGATCTTAAGTCCGGATACAA
1 CACCAGCACGAAGCCTACGGACCTTAACCCCGGATATAG
**
41860078 TTCCAGCACGAAGCCT
1 CACCAGCACGAAGCCT
41860094 GCGGGTCTTT
Statistics
Matches: 81, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
39 67 0.83
40 14 0.17
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16
Consensus pattern (39 bp):
CACCAGCACGAAGCCTACGGACCTTAACCCCGGATATAG
Found at i:41860117 original size:40 final size:40
Alignment explanation
Indices: 41860002--41860274 Score: 286
Period size: 40 Copynumber: 6.9 Consensus size: 40
41859992 GGATATAGCA
* * * * * * *
41860002 CCAGTACGAAGCCTGC-GGACCTTAAGTCCGGATATAGTA
1 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACAATT
* *
41860041 CCAGCACGAAGCCTGCGGATC-TTAAGTCCGGATACAATT
1 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACAATT
41860080 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACAATT
1 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACAATT
* *
41860120 CCAGCA-TATAGCCTGCTGGTCTTTAAGCCCGGATACAATT
1 CCAGCACGA-AGCCTGCGGGTCTTTAAGCCCGGATACAATT
* * * * *
41860160 CCAGCACGAAACCTGCGGATCTTTAAGCCTGAATATAATT
1 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACAATT
* * *
41860200 CCAGCA-TATAGCCTGCGGGTCTTTAAGCCCGAATATAATT
1 CCAGCACGA-AGCCTGCGGGTCTTTAAGCCCGGATACAATT
* * *
41860240 CCAGCA-TATAGCCTGTGGGTCTTTAGGCCCGGATA
1 CCAGCACGA-AGCCTGCGGGTCTTTAAGCCCGGATA
41860275 TACATCAAAT
Statistics
Matches: 205, Mismatches: 24, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
39 52 0.25
40 152 0.74
41 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACAATT
Found at i:41860167 original size:80 final size:79
Alignment explanation
Indices: 41860002--41860276 Score: 315
Period size: 80 Copynumber: 3.5 Consensus size: 79
41859992 GGATATAGCA
* * * * * * *
41860002 CCAGTACGAAGCCTGC-GGACCTTAAGTCCGGATATAGTACCAGCACGA-AGCCTGCGGATC-TT
1 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATATAATTCCAGCA-TATAGCCTGCGG-TCTTT
*
41860064 AAGTCCGGATACAATT
64 AAGCCCGGATACAATT
*
41860080 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCATATAGCCTGCTGGTCTTTA
1 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATATAATTCCAGCATATAGCCTGC-GGTCTTTA
41860145 AGCCCGGATACAATT
65 AGCCCGGATACAATT
* * * *
41860160 CCAGCACGAAACCTGCGGATCTTTAAGCCTGAATATAATTCCAGCATATAGCCTGCGGGTCTTTA
1 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATATAATTCCAGCATATAGCCTGC-GGTCTTTA
* *
41860225 AGCCCGAATATAATT
65 AGCCCGGATACAATT
* * *
41860240 CCAGCA-TATAGCCTGTGGGTCTTTAGGCCCGGATATA
1 CCAGCACGA-AGCCTGCGGGTCTTTAAGCCCGGATATA
41860277 CATCAAATAT
Statistics
Matches: 168, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
78 16 0.10
79 33 0.20
80 119 0.71
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.24
Consensus pattern (79 bp):
CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATATAATTCCAGCATATAGCCTGCGGTCTTTAA
GCCCGGATACAATT
Found at i:41860227 original size:120 final size:119
Alignment explanation
Indices: 41860023--41860274 Score: 348
Period size: 120 Copynumber: 2.1 Consensus size: 119
41860013 CCTGCGGACC
* * * * *
41860023 TTAAGTCCGGATATAGTACCAGCACGAAGCCTGCGGATCTTAAGTCCGGATACAATTCCAGCACG
1 TTAAGCCCGGATACAATACCAGCACGAAACCTGCGGATCTTAAGTCCGAATACAATTCCAGCACG
*
41860088 AAGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCATATAGCCTGCT-GGTCT
66 AAGCCTGCGGGTCTTTAAGCCCGAATACAATTCCAGCATATAGCCTG-TGGGTCT
* *
41860142 TTAAGCCCGGATACAATTCCAGCACGAAACCTGCGGATCTTTAAG-CCTGAATATAATTCCAGCA
1 TTAAGCCCGGATACAATACCAGCACGAAACCTGCGGATC-TTAAGTCC-GAATACAATTCCAGCA
* *
41860206 -TATAGCCTGCGGGTCTTTAAGCCCGAATATAATTCCAGCATATAGCCTGTGGGTCT
64 CGA-AGCCTGCGGGTCTTTAAGCCCGAATACAATTCCAGCATATAGCCTGTGGGTCT
*
41860262 TTAGGCCCGGATA
1 TTAAGCCCGGATA
41860275 TACATCAAAT
Statistics
Matches: 118, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
119 38 0.32
120 80 0.68
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (119 bp):
TTAAGCCCGGATACAATACCAGCACGAAACCTGCGGATCTTAAGTCCGAATACAATTCCAGCACG
AAGCCTGCGGGTCTTTAAGCCCGAATACAATTCCAGCATATAGCCTGTGGGTCT
Found at i:41886922 original size:25 final size:25
Alignment explanation
Indices: 41886894--41886961 Score: 100
Period size: 25 Copynumber: 2.7 Consensus size: 25
41886884 GTACATGTAC
*
41886894 GCTCACATGAGCTGTGAATCAAAAT
1 GCTCACACGAGCTGTGAATCAAAAT
* *
41886919 GCTCACACAAGCTGTGAATCAGAAT
1 GCTCACACGAGCTGTGAATCAAAAT
*
41886944 GCTCACACGAGTTGTGAA
1 GCTCACACGAGCTGTGAA
41886962 AATGGGCCTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (25 bp):
GCTCACACGAGCTGTGAATCAAAAT
Found at i:41887703 original size:21 final size:20
Alignment explanation
Indices: 41887678--41887721 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
41887668 TACTTTTAAA
*
41887678 TATCAATCAACATTCTAAATT
1 TATCAATCAACA-TCTAAAAT
* *
41887699 TATCAGTTAACATCTAAAAT
1 TATCAATCAACATCTAAAAT
41887719 TAT
1 TAT
41887722 AAGTTTCATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.43, C:0.16, G:0.02, T:0.39
Consensus pattern (20 bp):
TATCAATCAACATCTAAAAT
Found at i:41887716 original size:20 final size:21
Alignment explanation
Indices: 41887686--41887726 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
41887676 AATATCAATC
* *
41887686 AACATTCTAAATTTATCAGTT
1 AACATTCTAAAATTATAAGTT
41887707 AACA-TCTAAAATTATAAGTT
1 AACATTCTAAAATTATAAGTT
41887727 TCATCAATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (21 bp):
AACATTCTAAAATTATAAGTT
Found at i:41889013 original size:30 final size:30
Alignment explanation
Indices: 41888977--41889039 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
41888967 ACTTAACAAG
*
41888977 CAAATGT-TTCTAAAATAATAACAAAATTAA
1 CAAATGTCTT-TAAAATAATAAAAAAATTAA
41889007 CAAATGTCTTTAAAATAATAAAAAAATTAA
1 CAAATGTCTTTAAAATAATAAAAAAATTAA
41889037 CAA
1 CAA
41889040 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 29 0.94
31 2 0.06
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.29
Consensus pattern (30 bp):
CAAATGTCTTTAAAATAATAAAAAAATTAA
Found at i:41889094 original size:22 final size:22
Alignment explanation
Indices: 41889068--41889116 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
41889058 ATATCCAAAC
41889068 AATAACAACAAAATAGTAGCAA
1 AATAACAACAAAATAGTAGCAA
* * **
41889090 CATAATAGTAAAATAGTAGCAA
1 AATAACAACAAAATAGTAGCAA
41889112 AATAA
1 AATAA
41889117 AGAGAAAGTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.61, C:0.10, G:0.10, T:0.18
Consensus pattern (22 bp):
AATAACAACAAAATAGTAGCAA
Found at i:41889115 original size:11 final size:11
Alignment explanation
Indices: 41889076--41889115 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
41889066 ACAATAACAA
41889076 CAAAATAGTAG
1 CAAAATAGTAG
* *
41889087 CAACATAATAG
1 CAAAATAGTAG
*
41889098 TAAAATAGTAG
1 CAAAATAGTAG
41889109 CAAAATA
1 CAAAATA
41889116 AAGAGAAAGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:41902356 original size:51 final size:49
Alignment explanation
Indices: 41902228--41902366 Score: 188
Period size: 51 Copynumber: 2.8 Consensus size: 49
41902218 TATTGTGAGG
* * * * * *
41902228 TCACGTGTATAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATTGG
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCAAAAATTGA
* *
41902277 TCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCAAAAACTGTGA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCAAAAA-T-TGA
41902328 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACC
41902367 AGATAGCTTC
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
49 38 0.49
50 1 0.01
51 39 0.50
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (49 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCAAAAATTGA
Found at i:41908404 original size:30 final size:26
Alignment explanation
Indices: 41908336--41908390 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
41908326 TAATCTCATG
*
41908336 ACCATAATTCCTTCCATCACAAACTT
1 ACCATAATTCATTCCATCACAAACTT
41908362 ACCATAATTCATTCCATCACAAACTT
1 ACCATAATTCATTCCATCACAAACTT
41908388 ACC
1 ACC
41908391 TTGAAATCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.36, C:0.35, G:0.00, T:0.29
Consensus pattern (26 bp):
ACCATAATTCATTCCATCACAAACTT
Found at i:41910599 original size:18 final size:17
Alignment explanation
Indices: 41910563--41910601 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
41910553 ATCAAAGGAT
41910563 ATAAACTTACTATTAAC
1 ATAAACTTACTATTAAC
41910580 ATAAACTTA-TATGCTAAC
1 ATAAACTTACTAT--TAAC
41910598 ATAA
1 ATAA
41910602 TCCCATCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 3 0.15
17 9 0.45
18 8 0.40
ACGTcount: A:0.49, C:0.15, G:0.03, T:0.33
Consensus pattern (17 bp):
ATAAACTTACTATTAAC
Found at i:41912956 original size:50 final size:50
Alignment explanation
Indices: 41912902--41913002 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
41912892 ACGGGAATTT
*
41912902 TTTAAATTTTTAGCTAAATGTTAAATATGTCTGTAGGTAAAAGTAGAGCA
1 TTTAAATTTTTAGCTAAATATTAAATATGTCTGTAGGTAAAAGTAGAGCA
41912952 TTTAAATTTTTAGCTAAATATTAAATATGTCTGTAGGTAAAAGTAGAGCA
1 TTTAAATTTTTAGCTAAATATTAAATATGTCTGTAGGTAAAAGTAGAGCA
41913002 T
1 T
41913003 CAGGTATCGT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.39
Consensus pattern (50 bp):
TTTAAATTTTTAGCTAAATATTAAATATGTCTGTAGGTAAAAGTAGAGCA
Found at i:41915631 original size:23 final size:23
Alignment explanation
Indices: 41915601--41915650 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
41915591 AATTGTTGTA
*
41915601 TTTATTTCATTAAGATTTTTGGT
1 TTTATTTCAGTAAGATTTTTGGT
*
41915624 TTTATTTCAGTAAGATTTTTTGT
1 TTTATTTCAGTAAGATTTTTGGT
41915647 TTTA
1 TTTA
41915651 ATACGTCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.22, C:0.04, G:0.12, T:0.62
Consensus pattern (23 bp):
TTTATTTCAGTAAGATTTTTGGT
Found at i:41926767 original size:17 final size:19
Alignment explanation
Indices: 41926731--41926767 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
41926721 TAAAGAGCAA
*
41926731 AAATGTTGTTCTATTAGCT
1 AAATGTTGTTCTAATAGCT
41926750 AAATG-TGTTC-AATAGCT
1 AAATGTTGTTCTAATAGCT
41926767 A
1 A
41926768 TAGAACCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 7 0.41
18 5 0.29
19 5 0.29
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (19 bp):
AAATGTTGTTCTAATAGCT
Found at i:41933679 original size:40 final size:40
Alignment explanation
Indices: 41933624--41933766 Score: 236
Period size: 40 Copynumber: 3.6 Consensus size: 40
41933614 GATGATAACG
41933624 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
41933664 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
* *
41933704 GGGCTAAGTCCCGAAGGCATTTGTGCGAACT-ACT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-TAGTGACTAAT-TCC
41933744 GGGCTAAGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
41933767 AGCGAGTAGC
Statistics
Matches: 99, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
39 2 0.02
40 95 0.96
41 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
Found at i:41936562 original size:8 final size:8
Alignment explanation
Indices: 41936541--41936573 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
41936531 AAAAATTTTG
41936541 AAAGAATAA
1 AAAGAAT-A
41936550 AAAGAATA
1 AAAGAATA
41936558 AAAGAATA
1 AAAGAATA
41936566 AAAGAATA
1 AAAGAATA
41936574 GGAAAACTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAGAATA
Found at i:41937610 original size:21 final size:21
Alignment explanation
Indices: 41937586--41937655 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
41937576 ACTATGTGAG
41937586 CTGAACTCATTGAGTTGTGGT
1 CTGAACTCATTGAGTTGTGGT
** *
41937607 CTGAGTTCA-TGATATATGTGGCAT
1 CTGAACTCATTGA-GT-TGTGG--T
*
41937631 CTGAACTCATTGAGTTATGGT
1 CTGAACTCATTGAGTTGTGGT
41937652 CTGA
1 CTGA
41937656 GTTCATGATG
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
20 3 0.08
21 13 0.35
22 5 0.14
23 4 0.11
24 9 0.24
25 3 0.08
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.37
Consensus pattern (21 bp):
CTGAACTCATTGAGTTGTGGT
Found at i:41937640 original size:45 final size:45
Alignment explanation
Indices: 41937586--41937671 Score: 154
Period size: 45 Copynumber: 1.9 Consensus size: 45
41937576 ACTATGTGAG
*
41937586 CTGAACTCATTGAGTTGTGGTCTGAGTTCATGATATATGTGGCAT
1 CTGAACTCATTGAGTTATGGTCTGAGTTCATGATATATGTGGCAT
*
41937631 CTGAACTCATTGAGTTATGGTCTGAGTTCATGATGTATGTG
1 CTGAACTCATTGAGTTATGGTCTGAGTTCATGATATATGTG
41937672 ACACAAGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.22, C:0.13, G:0.27, T:0.38
Consensus pattern (45 bp):
CTGAACTCATTGAGTTATGGTCTGAGTTCATGATATATGTGGCAT
Found at i:41949265 original size:82 final size:83
Alignment explanation
Indices: 41949079--41949265 Score: 218
Period size: 83 Copynumber: 2.3 Consensus size: 83
41949069 TAGTAACATG
** * *
41949079 GGCATGTGGTTAGGTCGTGTGTCACCTGTACCTTAATATTGAGAAACAGAATGCTCATAATTGGT
1 GGCATGTGGTTAGACCGTGTGTCACCTGCACCTTAATATTGAGAAACAGAATGCTCAGAATTGGT
* **
41949144 CACACGGGCAGAGACATG
66 CACACGAGCAGAGACACA
* * * *
41949162 GGCATGTGGTTAGGCCATGTGTCTCCTGCACCTTAATTTTGAGAAACA-AATGCTCAGAATTGGG
1 GGCATGTGGTTAGACCGTGTGTCACCTGCACCTTAATATTGAGAAACAGAATGCTCAGAATT-GG
*
41949226 T-ACACGAGTAGAGACACA
65 TCACACGAGCAGAGACACA
*
41949244 GGCATGT-GTCTCGACCGTGTGT
1 GGCATGTGGT-TAGACCGTGTGT
41949266 GCTACATAGC
Statistics
Matches: 89, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
81 2 0.02
82 41 0.46
83 46 0.52
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (83 bp):
GGCATGTGGTTAGACCGTGTGTCACCTGCACCTTAATATTGAGAAACAGAATGCTCAGAATTGGT
CACACGAGCAGAGACACA
Found at i:41957818 original size:49 final size:49
Alignment explanation
Indices: 41957762--41957986 Score: 306
Period size: 49 Copynumber: 4.5 Consensus size: 49
41957752 CTAGTACGCA
*
41957762 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGATACACG
* * ** **
41957811 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTAATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACC-AATTATCCGATACACG
* * * * * *
41957861 TAGTAGCCTGCACTTAGTACTACACATGTGATCGAAGTTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-TTATCCGATACACG
41957912 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGATACACG
41957961 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
41957987 CGTGACCTCA
Statistics
Matches: 151, Mismatches: 22, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
49 67 0.44
50 46 0.30
51 38 0.25
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGATACACG
Found at i:41971211 original size:17 final size:17
Alignment explanation
Indices: 41971189--41971222 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41971179 ATCCACTAAT
*
41971189 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
41971206 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
41971223 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:41975849 original size:17 final size:17
Alignment explanation
Indices: 41975827--41975860 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41975817 ATCCACTAAT
*
41975827 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
41975844 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
41975861 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:41979539 original size:7 final size:7
Alignment explanation
Indices: 41979527--41979551 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41979517 TTAGCTTCCA
41979527 TTTTCTT
1 TTTTCTT
41979534 TTTTCTT
1 TTTTCTT
41979541 TTTTCTT
1 TTTTCTT
41979548 TTTT
1 TTTT
41979552 ATTACTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTCTT
Found at i:41979953 original size:17 final size:18
Alignment explanation
Indices: 41979931--41979971 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
41979921 AAAAAACCTA
41979931 TAAAAATTATTAAA-AAT
1 TAAAAATTATTAAATAAT
*
41979948 TAAAAATTATTAAATTAT
1 TAAAAATTATTAAATAAT
41979966 TAAAAA
1 TAAAAA
41979972 AGTATAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAAAATTATTAAATAAT
Found at i:41980267 original size:18 final size:19
Alignment explanation
Indices: 41980245--41980287 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
41980235 TATGAACGTG
* *
41980245 TATAAATTTTTTATTTAAA
1 TATAAATGTATTATTTAAA
41980264 -ATAAA-GTATTATTTAAA
1 TATAAATGTATTATTTAAA
41980281 TATAAAT
1 TATAAAT
41980288 AAATTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
TATAAATGTATTATTTAAA
Found at i:41991410 original size:35 final size:36
Alignment explanation
Indices: 41991370--41991445 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 36
41991360 CACTAGTCAG
**
41991370 ACAGATTTACA-A-TAGGGCCTGCGCCCATGTCAGAT
1 ACAGA-TTACAGATTAGGGCCTGAACCCATGTCAGAT
* *
41991405 ACAGA-TACAGATTCGGGCCTGAACCCATTTCAGAT
1 ACAGATTACAGATTAGGGCCTGAACCCATGTCAGAT
41991440 ACAGAT
1 ACAGAT
41991446 ATAGTTACAG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
33 4 0.12
34 1 0.03
35 29 0.85
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (36 bp):
ACAGATTACAGATTAGGGCCTGAACCCATGTCAGAT
Found at i:41993109 original size:21 final size:21
Alignment explanation
Indices: 41993067--41993109 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
41993057 TTAATTTTAG
***
41993067 TCTTAGTTTTTCTAGGTTTTC
1 TCTTAGTTTTTCTAGAACTTC
*
41993088 TCTTAGTTTTTCTATAACTTC
1 TCTTAGTTTTTCTAGAACTTC
41993109 T
1 T
41993110 TCTACGGTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.14, C:0.16, G:0.09, T:0.60
Consensus pattern (21 bp):
TCTTAGTTTTTCTAGAACTTC
Found at i:41994486 original size:24 final size:23
Alignment explanation
Indices: 41994450--41994535 Score: 84
Period size: 23 Copynumber: 3.7 Consensus size: 23
41994440 CCGATATATT
*
41994450 AGCTCATAAGAGCTTACTATTTTC
1 AGCTCATTAGAGCTTAC-ATTTTC
* **
41994474 AGCTCATTGGAGCTTACCGTTTC
1 AGCTCATTAGAGCTTACATTTTC
*
41994497 AGCTCAATAGAGCTTACCATTTT-
1 AGCTCATTAGAGCTTA-CATTTTC
* *
41994520 TGCTCAATAGAGCTTA
1 AGCTCATTAGAGCTTA
41994536 TTGTTCATCA
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
23 33 0.63
24 19 0.37
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (23 bp):
AGCTCATTAGAGCTTACATTTTC
Found at i:41994500 original size:23 final size:23
Alignment explanation
Indices: 41994470--41994535 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
41994460 AGCTTACTAT
* *
41994470 TTTCAGCTCATTGGAGCTTACCG
1 TTTCAGCTCAATAGAGCTTACCG
*
41994493 TTTCAGCTCAATAGAGCTTACCA
1 TTTCAGCTCAATAGAGCTTACCG
**
41994516 TTTTTGCTCAATAGAGCTTA
1 TTTCAGCTCAATAGAGCTTA
41994536 TTGTTCATCA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (23 bp):
TTTCAGCTCAATAGAGCTTACCG
Found at i:41996372 original size:13 final size:13
Alignment explanation
Indices: 41996354--41996380 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41996344 TTTTGCAAAA
41996354 GTTGTAAAAATGT
1 GTTGTAAAAATGT
41996367 GTTGTAAAAATGT
1 GTTGTAAAAATGT
41996380 G
1 G
41996381 AAAATAATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (13 bp):
GTTGTAAAAATGT
Found at i:41998692 original size:46 final size:46
Alignment explanation
Indices: 41998625--41998802 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
41998615 TGTAACCCGC
*
41998625 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGTTCGCAT
* * * *
41998671 CCATAAGTAAACTCGGACTCAACTCAACGAGCTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATG-TTCGCAT
* *** * * **
41998717 ACATCTCTCGAACTCGGACTCAACTCAATGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGATGTTCGCAT
41998764 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATG
41998803 CTCAACCATC
Statistics
Matches: 104, Mismatches: 25, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
46 71 0.68
47 33 0.32
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGTTCGCAT
Found at i:41998761 original size:93 final size:93
Alignment explanation
Indices: 41998633--41998803 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
41998623 GCCCATAAGT
***
41998633 GAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCATCCATAAGTAAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTAAACTCGGACTCAACTCAA
41998698 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* * *
41998726 GAACTCGGACTCAACTCAATGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTAAACTCGGACTCAACTCAA
41998791 CGAGCTCGGATGC
66 CGAGCTCGGATGC
41998804 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTAAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:42001971 original size:19 final size:19
Alignment explanation
Indices: 42001947--42002006 Score: 120
Period size: 19 Copynumber: 3.2 Consensus size: 19
42001937 TTAGAATACT
42001947 CTAGTGTTTTATTGTAACA
1 CTAGTGTTTTATTGTAACA
42001966 CTAGTGTTTTATTGTAACA
1 CTAGTGTTTTATTGTAACA
42001985 CTAGTGTTTTATTGTAACA
1 CTAGTGTTTTATTGTAACA
42002004 CTA
1 CTA
42002007 AAAATATTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.47
Consensus pattern (19 bp):
CTAGTGTTTTATTGTAACA
Found at i:42006512 original size:2 final size:2
Alignment explanation
Indices: 42006505--42006539 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
42006495 ATATCACATT
42006505 CA CA CA CA CA CA CA CA CA C- CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
42006540 TATATATACA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:42006529 original size:17 final size:17
Alignment explanation
Indices: 42006507--42006539 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
42006497 ATCACATTCA
42006507 CACACACACACACACAC
1 CACACACACACACACAC
42006524 CACACACACACACACA
1 CACACACACACACACA
42006540 TATATATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (17 bp):
CACACACACACACACAC
Found at i:42006862 original size:26 final size:25
Alignment explanation
Indices: 42006827--42006899 Score: 69
Period size: 26 Copynumber: 2.9 Consensus size: 25
42006817 AATTCCTCCT
*
42006827 TTTTTTTTTCTCTTTCTCTTTTTCC
1 TTTTTCTTTCTCTTTCTCTTTTTCC
* *
42006852 TTCTTTCTTTC-CCTTCTCTGTTTTCG
1 TT-TTTCTTTCTCTTTCTCT-TTTTCC
* *
42006878 TTTTTCATTCTGTTTCT-TTTTT
1 TTTTTCTTTCTCTTTCTCTTTTT
42006900 ATTTCTTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
24 4 0.10
25 17 0.44
26 18 0.46
ACGTcount: A:0.01, C:0.23, G:0.04, T:0.71
Consensus pattern (25 bp):
TTTTTCTTTCTCTTTCTCTTTTTCC
Found at i:42010344 original size:22 final size:22
Alignment explanation
Indices: 42010316--42010360 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
42010306 GTATGCATTG
42010316 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
42010338 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
42010360 T
1 T
42010361 CTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:42014117 original size:22 final size:22
Alignment explanation
Indices: 42014089--42014133 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
42014079 AGGGGGAGTG
42014089 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
42014111 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
42014133 T
1 T
42014134 CTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:42049780 original size:46 final size:46
Alignment explanation
Indices: 42049727--42049902 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
42049717 TGGTTGAGCA
42049727 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
42049773 TCTGAACTCGTTGAGTTGAGTCCGAGTT---TGA-GAGATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCGAA-T--G
* *
42049818 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
42049866 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42049903 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 9, Indels: 22
0.78 0.06 0.16
Matches are distributed among these distances:
42 3 0.03
43 7 0.06
45 1 0.01
46 63 0.57
47 26 0.24
48 1 0.01
50 6 0.05
51 3 0.03
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:42049883 original size:93 final size:93
Alignment explanation
Indices: 42049724--42049893 Score: 295
Period size: 93 Copynumber: 1.8 Consensus size: 93
42049714 GGATGGTTGA
* * *
42049724 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCTGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
42049789 TGAGTCCGAGTTTGAGAGATGTAACTAG
66 TGAGTCCGAGTTTGAGAGATGTAACTAG
* *
42049817 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
42049882 TGAGTCCGAGTT
66 TGAGTCCGAGTT
42049894 CACTTATGGG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTTGAGAGATGTAACTAG
Found at i:42051438 original size:26 final size:26
Alignment explanation
Indices: 42051407--42051466 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
42051397 GCCTTTTGAA
* *
42051407 TCATTCGATATTTCGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
* *
42051433 TTATTCTCAATATCTCGCACAGTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
42051461 TCATTC
1 TCATTC
42051467 TCAATATTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
26 4 0.15
27 2 0.07
28 21 0.78
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:42051488 original size:28 final size:28
Alignment explanation
Indices: 42051414--42051477 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
42051404 GAATCATTCG
*
42051414 ATATTTCGCACACTAAGTGTTATTCTCA
1 ATATTTCGCACACTAAGTGTCATTCTCA
* *
42051442 ATATCTCGCACAGTAAGTGTCATTCTCA
1 ATATTTCGCACACTAAGTGTCATTCTCA
42051470 ATATTTCG
1 ATATTTCG
42051478 TACATTGAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (28 bp):
ATATTTCGCACACTAAGTGTCATTCTCA
Found at i:42053753 original size:79 final size:79
Alignment explanation
Indices: 42053622--42053782 Score: 286
Period size: 79 Copynumber: 2.0 Consensus size: 79
42053612 AACTCAAATA
*
42053622 ATTGATTTAGAACTTTGAATCAAAATGCTTGAAGAAATTCGGATGACTTTTTGCCCAACTTTGAA
1 ATTGATTTAGAACTTTGAATCAAAATGCTTGAAGAAATTCGGATGACTTTTTGCCCAACTTTAAA
* *
42053687 AATTATTTTGATAG
66 AATTATTTCGAGAG
*
42053701 ATTGATTTAGAAGTTTGAATCAAAATGCTTGAAGAAATTCGGATGACTTTTTGCCCAACTTTAAA
1 ATTGATTTAGAACTTTGAATCAAAATGCTTGAAGAAATTCGGATGACTTTTTGCCCAACTTTAAA
42053766 AATTATTTCGAGAG
66 AATTATTTCGAGAG
42053780 ATT
1 ATT
42053783 TTAAAGGGAA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (79 bp):
ATTGATTTAGAACTTTGAATCAAAATGCTTGAAGAAATTCGGATGACTTTTTGCCCAACTTTAAA
AATTATTTCGAGAG
Found at i:42054125 original size:20 final size:21
Alignment explanation
Indices: 42054102--42054140 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
42054092 TAAATTTTAA
*
42054102 TTTAACCGAAAA-TATTTATT
1 TTTAACCAAAAATTATTTATT
*
42054122 TTTACCCAAAAATTATTTA
1 TTTAACCAAAAATTATTTA
42054141 AAATCATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.41, C:0.13, G:0.03, T:0.44
Consensus pattern (21 bp):
TTTAACCAAAAATTATTTATT
Found at i:42060270 original size:131 final size:131
Alignment explanation
Indices: 42060036--42060303 Score: 518
Period size: 131 Copynumber: 2.0 Consensus size: 131
42060026 TTTCCTTGCA
*
42060036 GTTTGGATGTTTGATAAACAAAATAATAATGGAAGGACGACACTTGAAGTTTTGATGGGTGGCAA
1 GTTTGGATGTTTGATAAACAAAATAATAATGGAAGGACGACACTTGAAGTTTTGATAGGTGGCAA
42060101 CCATAATTAGAAGGGTCACTATAAGAATACCCATAACAGTAATTGTATTGATCATGTGGTGTGTT
66 CCATAATTAGAAGGGTCACTATAAGAATACCCATAACAGTAATTGTATTGATCATGTGGTGTGTT
42060166 G
131 G
*
42060167 GTTTGGATGTTTGATAAACAAAATAATAATGGAAGGACGACACTTGAAGTTTTGATAGGTGGTAA
1 GTTTGGATGTTTGATAAACAAAATAATAATGGAAGGACGACACTTGAAGTTTTGATAGGTGGCAA
42060232 CCATAATTAGAAGGGTCACTATAAGAATACCCATAACAGTAATTGTATTGATCATGTGGTGTGTT
66 CCATAATTAGAAGGGTCACTATAAGAATACCCATAACAGTAATTGTATTGATCATGTGGTGTGTT
42060297 G
131 G
42060298 GTTTGG
1 GTTTGG
42060304 TACCATTGAC
Statistics
Matches: 135, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
131 135 1.00
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.31
Consensus pattern (131 bp):
GTTTGGATGTTTGATAAACAAAATAATAATGGAAGGACGACACTTGAAGTTTTGATAGGTGGCAA
CCATAATTAGAAGGGTCACTATAAGAATACCCATAACAGTAATTGTATTGATCATGTGGTGTGTT
G
Found at i:42074810 original size:20 final size:20
Alignment explanation
Indices: 42074782--42074826 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
42074772 TTTTTAAACA
*
42074782 TATTTATTTAATATAATATC-
1 TATTAATTTAAT-TAATATCT
*
42074802 TATTAATTTCATTAATATCT
1 TATTAATTTAATTAATATCT
42074822 TATTA
1 TATTA
42074827 TCTTTAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTAATTTAATTAATATCT
Found at i:42081597 original size:19 final size:19
Alignment explanation
Indices: 42081575--42081613 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
42081565 CAAAATGGTT
42081575 CAACAATAAGAAAATAATA
1 CAACAATAAGAAAATAATA
42081594 CAACAATAAGAAAATAATA
1 CAACAATAAGAAAATAATA
42081613 C
1 C
42081614 CTGGCTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.67, C:0.13, G:0.05, T:0.15
Consensus pattern (19 bp):
CAACAATAAGAAAATAATA
Found at i:42086206 original size:21 final size:21
Alignment explanation
Indices: 42086182--42086222 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
42086172 TCAACTATGA
*
42086182 TTAAATTTAATCAATTTAATG
1 TTAAATTTAATAAATTTAATG
*
42086203 TTAAATTTATTAAATTTAAT
1 TTAAATTTAATAAATTTAAT
42086223 AATAAATCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
TTAAATTTAATAAATTTAATG
Found at i:42086228 original size:21 final size:21
Alignment explanation
Indices: 42086183--42086238 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
42086173 CAACTATGAT
* * **
42086183 TAAATTTAATCAATTTAATGT
1 TAAATTTATTAAATTTAATAA
42086204 TAAATTTATTAAATTTAATAA
1 TAAATTTATTAAATTTAATAA
*
42086225 TAAATCTCATTAAA
1 TAAAT-TTATTAAA
42086239 ATATAGAATG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 22 0.76
22 7 0.24
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (21 bp):
TAAATTTATTAAATTTAATAA
Found at i:42086314 original size:20 final size:18
Alignment explanation
Indices: 42086267--42086373 Score: 60
Period size: 19 Copynumber: 5.8 Consensus size: 18
42086257 GTAAATAAAC
42086267 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
42086284 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
** *
42086304 ATTAAATTAATAAAATACT
1 ATTAAATTAAT-ATTTAAT
*
42086323 ATTAAGA-TAAGTATTAAAT
1 ATTAA-ATTAA-TATTTAAT
* *
42086342 -TTAATTTAATATTAAACT
1 ATTAAATTAATATTTAA-T
*
42086360 ATTAAAATAATATT
1 ATTAAATTAATATT
42086374 ATTTTTGAAT
Statistics
Matches: 69, Mismatches: 11, Indels: 18
0.70 0.11 0.18
Matches are distributed among these distances:
17 15 0.22
18 9 0.13
19 27 0.39
20 18 0.26
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:42096743 original size:40 final size:40
Alignment explanation
Indices: 42096665--42096888 Score: 292
Period size: 40 Copynumber: 5.5 Consensus size: 40
42096655 ACCCAAGTAT
* *
42096665 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* **
42096704 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
42096744 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
42096784 CTTCGGGACTTAGCCTGGGTATAG-CAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATGC
* * *
42096827 CTTCGGGACATAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
42096867 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
42096889 TATTCGAATA
Statistics
Matches: 162, Mismatches: 16, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
39 12 0.07
40 115 0.71
41 1 0.01
43 34 0.21
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:42096851 original size:83 final size:80
Alignment explanation
Indices: 42096665--42096888 Score: 292
Period size: 83 Copynumber: 2.8 Consensus size: 80
42096655 ACCCAAGTAT
* * *
42096665 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAG
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
**
42096728 TCACTAGCATGAATGC
65 TCACTAGCACAAATGC
* *
42096744 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCTGGGTATAG-
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
42096808 CAACTACTCGCACAAATGC
66 C-ACTA---GCACAAATGC
* * *
42096827 CTTCGGGACATAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
42096889 TATTCGAATA
Statistics
Matches: 127, Mismatches: 12, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
79 13 0.10
80 48 0.38
81 1 0.01
83 65 0.51
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:42101334 original size:38 final size:38
Alignment explanation
Indices: 42101283--42101439 Score: 161
Period size: 38 Copynumber: 3.9 Consensus size: 38
42101273 GGAATGAAAA
42101283 AACGTGGTGCTAAGTGGATATACCACGGTTATACTTGT
1 AACGTGGTGCTAAGTGGATATACCACGGTTATACTTGT
* *
42101321 AACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATT
1 AACGTGGTGCTAAGTGGATATACCACGGTT--ATA-CTTG------T
* * *
42101368 AACGTGGTGTTAAGTGGATATACCACGGTTAAACATGT
1 AACGTGGTGCTAAGTGGATATACCACGGTTATACTTGT
* * *
42101406 AACGTGCTGCTAAGTGGATATGCCACAGTTATAC
1 AACGTGGTGCTAAGTGGATATACCACGGTTATAC
42101440 ATGTTAATTT
Statistics
Matches: 98, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
38 59 0.60
40 3 0.03
41 3 0.03
44 2 0.02
45 2 0.02
47 29 0.30
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.31
Consensus pattern (38 bp):
AACGTGGTGCTAAGTGGATATACCACGGTTATACTTGT
Found at i:42109881 original size:40 final size:39
Alignment explanation
Indices: 42109827--42109912 Score: 102
Period size: 40 Copynumber: 2.2 Consensus size: 39
42109817 TAATGACTTA
* **
42109827 TCGGCGAAAATGGCACT-GAGTGTGCGGTTCGAAATAGCT
1 TCGGCTAAAATGGCACTAGA-TGTGCAATTCGAAATAGCT
* *
42109866 TCGGCTAAAAGTGGCACTAGATGTGCAATTTGAGATAGCT
1 TCGGCTAAAA-TGGCACTAGATGTGCAATTCGAAATAGCT
42109906 TCGGCTA
1 TCGGCTA
42109913 TATATATATA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
39 9 0.22
40 29 0.73
41 2 0.05
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (39 bp):
TCGGCTAAAATGGCACTAGATGTGCAATTCGAAATAGCT
Found at i:42114049 original size:43 final size:43
Alignment explanation
Indices: 42113988--42114176 Score: 267
Period size: 43 Copynumber: 4.4 Consensus size: 43
42113978 ACATATCATT
* * *
42113988 TCACCGGCATTACGCCTGCTAGGTACGAAGGCCCGAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
*
42114031 TCACCAGCA-TGAAGCCTGCTAGGCACGAAGGCCCGAATACACA
1 TCACCGGCACT-AAGCCTGCTAGGCACGAAGGCCCGAATACACA
*
42114074 TCACCGGCACTAAGCCTACTAGGCACGAAGGCCCGAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
* *
42114117 TCACCGGCACTAAGCCTGTTAGGCACGAAGGCCCGAATATA-A
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
* *
42114159 T-ACCAGCACTAGGCCTGC
1 TCACCGGCACTAAGCCTGC
42114177 GAGATTTATC
Statistics
Matches: 133, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
41 14 0.11
42 3 0.02
43 115 0.86
44 1 0.01
ACGTcount: A:0.30, C:0.33, G:0.23, T:0.14
Consensus pattern (43 bp):
TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
Found at i:42114201 original size:38 final size:38
Alignment explanation
Indices: 42114148--42114231 Score: 114
Period size: 38 Copynumber: 2.2 Consensus size: 38
42114138 GGCACGAAGG
* *
42114148 CCCGAATATAATACCAGCACTAGGCCTGCGAGATTTAT
1 CCCGAATATAATACCAGCACGAAGCCTGCGAGATTTAT
* * *
42114186 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGAATATAATACCAGCACGAAGCCTGCGAGATTTAT
*
42114224 CCTGAATA
1 CCCGAATA
42114232 CACATCAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.21
Consensus pattern (38 bp):
CCCGAATATAATACCAGCACGAAGCCTGCGAGATTTAT
Found at i:42117256 original size:29 final size:30
Alignment explanation
Indices: 42117224--42117299 Score: 104
Period size: 29 Copynumber: 2.6 Consensus size: 30
42117214 TCTTATTGAA
* * *
42117224 ATGGCCCATCT-GGCCCAGTTCATATTCTT
1 ATGGCCCATCTAGGCCCAATTCACATTCAT
42117253 ATGGCCCA-CTAGGCCCAATTCACATTCAT
1 ATGGCCCATCTAGGCCCAATTCACATTCAT
42117282 ATGGCCCAT-TAGGCCCAA
1 ATGGCCCATCTAGGCCCAA
42117300 ATCAACCCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 2 0.05
29 40 0.95
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.26
Consensus pattern (30 bp):
ATGGCCCATCTAGGCCCAATTCACATTCAT
Found at i:42119965 original size:47 final size:48
Alignment explanation
Indices: 42119903--42120028 Score: 154
Period size: 47 Copynumber: 2.7 Consensus size: 48
42119893 ATCTCATAGT
*
42119903 CGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTC-TCA-CT-GC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCACTC-TCATAATCTGGC
* *
42119949 CGATGCCATGTCCCAGACATGGTCTTACACT-G-GCTCTCATAATGTGGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCACTCTCATAATCTGGC
*
42119997 CTATGCATGTCCCAGACATGTCTTACACTAGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGC
42120029 TCACACAAGT
Statistics
Matches: 69, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
45 2 0.03
46 20 0.29
47 31 0.45
48 16 0.23
ACGTcount: A:0.22, C:0.32, G:0.19, T:0.27
Consensus pattern (48 bp):
CGATGCATGTCCCAGACATGTCTTACACTAGCACTCTCATAATCTGGC
Found at i:42121149 original size:18 final size:18
Alignment explanation
Indices: 42121123--42121157 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42121113 ATATATGTCT
*
42121123 TTCATAACAAAGCACAAA
1 TTCACAACAAAGCACAAA
*
42121141 TTCACAACAAATCACAA
1 TTCACAACAAAGCACAA
42121158 GACTTATTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
TTCACAACAAAGCACAAA
Found at i:42131534 original size:25 final size:25
Alignment explanation
Indices: 42131500--42131594 Score: 93
Period size: 25 Copynumber: 3.8 Consensus size: 25
42131490 ACTTGTACAT
*
42131500 GTATGCTCATACGAGCTGTGAATCG
1 GTATGCTCATACGAGCTGTAAATCG
* ** * *
42131525 GTATGCTCATTCGAGCTACAGATCA
1 GTATGCTCATACGAGCTGTAAATCG
*
42131550 GTATGCTC-TCATGAGCTGTAAATCG
1 GTATGCTCAT-ACGAGCTGTAAATCG
* *
42131575 GTATGCTCACATGAGCTGTA
1 GTATGCTCATACGAGCTGTA
42131595 GGTCAGGATG
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
24 1 0.02
25 54 0.98
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.29
Consensus pattern (25 bp):
GTATGCTCATACGAGCTGTAAATCG
Found at i:42141498 original size:13 final size:13
Alignment explanation
Indices: 42141480--42141505 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42141470 GGGATTTGCT
42141480 TTAACTAAACTAA
1 TTAACTAAACTAA
42141493 TTAACTAAACTAA
1 TTAACTAAACTAA
42141506 GAATGCATAG
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:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAACTAAACTAA
Found at i:42141945 original size:14 final size:14
Alignment explanation
Indices: 42141926--42141952 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42141916 TATTAAAGCA
42141926 ATAATTAAGAACAC
1 ATAATTAAGAACAC
42141940 ATAATTAAGAACA
1 ATAATTAAGAACA
42141953 AATCAAGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.11, G:0.07, T:0.22
Consensus pattern (14 bp):
ATAATTAAGAACAC
Found at i:42161535 original size:49 final size:49
Alignment explanation
Indices: 42161463--42161737 Score: 361
Period size: 49 Copynumber: 5.5 Consensus size: 49
42161453 TGAGTTCACG
*
42161463 TGTGTAATACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
* * * * * * *
42161512 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-T-TGGTCGCA
42161563 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
* * * * * * *
42161612 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-T-TGGTCGCA
* *
42161663 TGTGTAGTACTAAGTGCAGGCTACTACGTATACCGGATTATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
42161712 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
42161738 TGCGTACCAG
Statistics
Matches: 191, Mismatches: 31, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
49 107 0.56
50 4 0.02
51 80 0.42
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
Found at i:42161631 original size:100 final size:100
Alignment explanation
Indices: 42161458--42161745 Score: 540
Period size: 100 Copynumber: 2.9 Consensus size: 100
42161448 TATTGTGAGT
*
42161458 TCACGTGTGTAATACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACT
42161523 AAGTGCAGGCTACTATGCGTACCCGAAAACTGTGA
66 AAGTGCAGGCTACTATGCGTACCCGAAAACTGTGA
42161558 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACT
*
42161623 AAGTGCAGGCTACTATGCGTACCTGAAAACTGTGA
66 AAGTGCAGGCTACTATGCGTACCCGAAAACTGTGA
* *
42161658 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTATACCGGATTATTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACT
42161723 AAGTGCAGGCTACTATGCGTACC
66 AAGTGCAGGCTACTATGCGTACC
42161746 AGATAGCTTC
Statistics
Matches: 184, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 184 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (100 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACT
AAGTGCAGGCTACTATGCGTACCCGAAAACTGTGA
Found at i:42164780 original size:34 final size:35
Alignment explanation
Indices: 42164707--42164793 Score: 90
Period size: 34 Copynumber: 2.5 Consensus size: 35
42164697 AGGTAAGTAT
42164707 ATGT-AAGCTTATATTGAACTTGATTATTCGATCAC
1 ATGTGAAG-TTATATTGAACTTGATTATTCGATCAC
* ***
42164742 ATGTGAA-TTATATTGAACTT-ATATATTCGGTTTT
1 ATGTGAAGTTATATTGAACTTGAT-TATTCGATCAC
*
42164776 ATGTGAAGTTATTTTGAA
1 ATGTGAAGTTATATTGAA
42164794 TATGCATATT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
33 2 0.05
34 27 0.61
35 13 0.30
36 2 0.05
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (35 bp):
ATGTGAAGTTATATTGAACTTGATTATTCGATCAC
Found at i:42167221 original size:28 final size:28
Alignment explanation
Indices: 42167202--42167293 Score: 121
Period size: 28 Copynumber: 3.2 Consensus size: 28
42167192 ATAATGTCAT
*
42167202 TTGGGCCGGATGGGCCATATAAATGAGA
1 TTGGGCCGGATGGGCCATATAAATGTGA
* * *
42167230 TTGGGCCTGATGGGCCATATGAACGTGAA
1 TTGGGCCGGATGGGCCATATAAATGTG-A
* *
42167259 TTGGGCTGGATGGGCCATATAAATGGGA
1 TTGGGCCGGATGGGCCATATAAATGTGA
42167287 TTGGGCC
1 TTGGGCC
42167294 TAGTGAGCCA
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
28 30 0.57
29 23 0.43
ACGTcount: A:0.24, C:0.15, G:0.37, T:0.24
Consensus pattern (28 bp):
TTGGGCCGGATGGGCCATATAAATGTGA
Found at i:42169619 original size:20 final size:21
Alignment explanation
Indices: 42169594--42169633 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
42169584 AAAGAGAAAG
*
42169594 TGAAAGTA-CTTCACATTGTT
1 TGAAAGCAGCTTCACATTGTT
*
42169614 TGAAAGCAGCTTCAGATTGT
1 TGAAAGCAGCTTCACATTGT
42169634 CAAAAATCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (21 bp):
TGAAAGCAGCTTCACATTGTT
Found at i:42175503 original size:34 final size:34
Alignment explanation
Indices: 42175443--42175544 Score: 91
Period size: 34 Copynumber: 3.0 Consensus size: 34
42175433 CAATGTTGAA
* * *
42175443 CAGTCTGGGCCTAAGACCATATCAGTCGCAATAT
1 CAGTGTGGGCCTTAGACCATATCAGTCACAATAT
* *
42175477 CAGTGTGGGCCTTAGTCCA-ATACAGTCACAGTAT
1 CAGTGTGGGCCTTAGACCATAT-CAGTCACAATAT
* * * * *
42175511 CAATGTGGACCTTAGCCCATTTCAGT-ACAGTAT
1 CAGTGTGGGCCTTAGACCATATCAGTCACAATAT
42175544 C
1 C
42175545 CAAAATGTAT
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
33 10 0.18
34 46 0.81
35 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.26
Consensus pattern (34 bp):
CAGTGTGGGCCTTAGACCATATCAGTCACAATAT
Found at i:42185653 original size:42 final size:41
Alignment explanation
Indices: 42185593--42185917 Score: 220
Period size: 48 Copynumber: 7.3 Consensus size: 41
42185583 ATAGTCCAAC
*
42185593 TATGGTCTTACACAAAATCTCACATCGATGCCATGTCCTAGA
1 TATGGTCTTACAC-AAATCTCACATCGATGCCATATCCTAGA
* * * * **
42185635 CATGGTCTTATACGAAATCACATATCGATGCCGCATCCTAGA
1 TATGGTCTTACAC-AAATCTCACATCGATGCCATATCCTAGA
* ** * *
42185677 CACAGTCTTACACGAAATCTCATATCGAAGCCATAT-CTCAGA
1 TATGGTCTTACAC-AAATCTCACATCGATGCCATATCCT-AGA
* *
42185719 TATGGTCTTACACGCAATCTCATGTCGATGCTGATGTCATATCCTAGA
1 TATGGTCTTACAC-AAATCTCA---C-AT-C-GATGCCATATCCTAGA
*
42185767 TATGGTCTTACACAAGATCTCATATCGATGCTGATGCCATACCCTAGA
1 TATGGTCTTACACAA-ATCTC--A-C-AT-C-GATGCCATATCCTAGA
*
42185815 TATGGTCTTACACAAGATCTCATATCGATGCTGATGCCATATCCCAGA
1 TATGGTCTTACACAA-ATCTC--A-C-AT-C-GATGCCATATCCTAGA
* * * *
42185863 TATGGTCTTACACAGGATCTCATATCGATGCCATGTCCCAGA
1 TATGGTCTTACACA-AATCTCACATCGATGCCATATCCTAGA
*
42185905 CATGGTCTTACAC
1 TATGGTCTTACAC
42185918 GTATCACAAT
Statistics
Matches: 240, Mismatches: 31, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
41 2 0.01
42 111 0.46
43 1 0.00
44 2 0.01
46 3 0.01
47 2 0.01
48 116 0.48
49 2 0.01
50 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (41 bp):
TATGGTCTTACACAAATCTCACATCGATGCCATATCCTAGA
Found at i:42185779 original size:48 final size:48
Alignment explanation
Indices: 42185706--42185893 Score: 290
Period size: 48 Copynumber: 3.9 Consensus size: 48
42185696 TCATATCGAA
* *
42185706 GCCATAT-CTCAGATATGGTCTTACACGCA-ATCTCATGTCGATGCTGAT
1 GCCATATCCT-AGATATGGTCTTACAC-AAGATCTCATATCGATGCTGAT
*
42185754 GTCATATCCTAGATATGGTCTTACACAAGATCTCATATCGATGCTGAT
1 GCCATATCCTAGATATGGTCTTACACAAGATCTCATATCGATGCTGAT
*
42185802 GCCATACCCTAGATATGGTCTTACACAAGATCTCATATCGATGCTGAT
1 GCCATATCCTAGATATGGTCTTACACAAGATCTCATATCGATGCTGAT
* *
42185850 GCCATATCCCAGATATGGTCTTACACAGGATCTCATATCGATGC
1 GCCATATCCTAGATATGGTCTTACACAAGATCTCATATCGATGC
42185894 CATGTCCCAG
Statistics
Matches: 130, Mismatches: 8, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
47 1 0.01
48 127 0.98
49 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (48 bp):
GCCATATCCTAGATATGGTCTTACACAAGATCTCATATCGATGCTGAT
Found at i:42185970 original size:37 final size:37
Alignment explanation
Indices: 42185847--42186029 Score: 205
Period size: 37 Copynumber: 4.8 Consensus size: 37
42185837 TATCGATGCT
* *
42185847 GATGCCATATCCCAGATATGGTCTTACACAGGATC-TCATATC
1 GATGCCATAGCCCAGCTATGGTCTTACAC--G-TCATC--A-C
42185889 GATGCCAT-GTCCCAGAC-ATGGTCTTACACGT-ATCAC
1 GATGCCATAG-CCCAG-CTATGGTCTTACACGTCATCAC
* *
42185925 AATGCCATAGCCCAGCTATGGTCTTACATGTCATCAC
1 GATGCCATAGCCCAGCTATGGTCTTACACGTCATCAC
*
42185962 GATGCCATAGCCCAGCTATGGTCTTACACG-CTATTAC
1 GATGCCATAGCCCAGCTATGGTCTTACACGTC-ATCAC
42185999 GATGCCATAGCCCAGCTATGGTCTTACACGT
1 GATGCCATAGCCCAGCTATGGTCTTACACGT
42186030 ACCACATGTA
Statistics
Matches: 126, Mismatches: 7, Indels: 20
0.82 0.05 0.13
Matches are distributed among these distances:
35 1 0.01
36 27 0.21
37 69 0.55
39 3 0.02
40 1 0.01
42 25 0.20
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.27
Consensus pattern (37 bp):
GATGCCATAGCCCAGCTATGGTCTTACACGTCATCAC
Done.