Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 169 of 193
Found at i:52624988 original size:46 final size:46
Alignment explanation
Indices: 52624931--52625057 Score: 184
Period size: 46 Copynumber: 2.7 Consensus size: 46
52624921 TGCTGGGCAA
*
52624931 CAGAGAGCACACACAGTGCTAAACAGAGAGTACACAAAGTATTAAT
1 CAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTATTAAT
* * *
52624977 C-GAAGAGCACACAAAGTGCTAATCAGAGAGCACACAAAGTGTTAAT
1 CAG-AGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTATTAAT
52625023 CAGAGAGCACACACAGTGCTAATAACAGAGAGCAC
1 CAGAGAGCACACACAGTGCT-A-AACAGAGAGCAC
52625058 GAGACGTGCT
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
45 1 0.01
46 57 0.80
47 2 0.03
48 11 0.15
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.13
Consensus pattern (46 bp):
CAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTATTAAT
Found at i:52634235 original size:60 final size:60
Alignment explanation
Indices: 52634120--52634236 Score: 139
Period size: 60 Copynumber: 1.9 Consensus size: 60
52634110 CCTTGACATT
* * * * *
52634120 TTACATATTATGTCAATTTGGTCTTAATTTTAAAAATTCAACAAGTTTAGCTTACAATGC
1 TTACACATTATGTCAATTCGATCTTAATTTTAAAAATTCAACAAATTTAGATTACAATGC
* *
52634180 TTACACATTATGTCAATTCGATCTTGATTTTAGAAATTCATA-AAATTATA-ATTACAA
1 TTACACATTATGTCAATTCGATCTTAATTTTAAAAATTCA-ACAAATT-TAGATTACAA
52634237 AAAAAAAAGA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
60 45 0.94
61 3 0.06
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.41
Consensus pattern (60 bp):
TTACACATTATGTCAATTCGATCTTAATTTTAAAAATTCAACAAATTTAGATTACAATGC
Found at i:52635994 original size:24 final size:24
Alignment explanation
Indices: 52635967--52636040 Score: 121
Period size: 24 Copynumber: 3.1 Consensus size: 24
52635957 TAATTCTCAG
* *
52635967 GCAAATGTTGCAGCCAGTAGGCCA
1 GCAAGTGTTGCAGCCAATAGGCCA
*
52635991 GCAAGTGTCGCAGCCAATAGGCCA
1 GCAAGTGTTGCAGCCAATAGGCCA
52636015 GCAAGTGTTGCAGCCAATAGGCCA
1 GCAAGTGTTGCAGCCAATAGGCCA
52636039 GC
1 GC
52636041 GCCAGCAAGC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.28, C:0.27, G:0.30, T:0.15
Consensus pattern (24 bp):
GCAAGTGTTGCAGCCAATAGGCCA
Found at i:52636316 original size:19 final size:19
Alignment explanation
Indices: 52636278--52636318 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
52636268 CTTTCAATTT
* *
52636278 ATAGTTGTCTTTTTCAATA
1 ATAGTTGTCCTTTCCAATA
*
52636297 ATAGTTGTCCTTTCCGATA
1 ATAGTTGTCCTTTCCAATA
52636316 ATA
1 ATA
52636319 TTATATTTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (19 bp):
ATAGTTGTCCTTTCCAATA
Found at i:52642609 original size:241 final size:239
Alignment explanation
Indices: 52642177--52642770 Score: 679
Period size: 241 Copynumber: 2.5 Consensus size: 239
52642167 CATTGGAAAG
* * * * *
52642177 TTGATCTTTAATTGAGAGTCAAATTAATGTCGACTTTATTGAATTA-GAAATTTAATTTTCCTTT
1 TTGATCATTAATTGAGAGTCAAATTAATATCGACTTT-TTGAATTATG-AGTCTAAATTTCCTTT
* * * * *
52642241 TATTTGCATGCAATGATGAAAAAAAATGAAAATTAAACTCATAATCCAGTAAAGTTGGCATCATA
64 CATTTGCATGCAATGATG--AAGAAATGAAAATT-AACTCATAATCCAGCAAAATTGACATCATA
* * * * *
52642306 AGGCTACGAGCATTGGAAAGCATGTTATATTTGTTAAAAATAGATAAATGGGTACTAATTAATAG
126 AAGCTACGAGCATTGAAAAGCATGTTATATTTGTTAAAAATAAATAAAAGGGTACTAATTAATAA
* * * *
52642371 ATTGATCATGATCAGTTTAAATCAATCTAGTTTGTTTATCTAATAAATA
191 ATCGATCATGACCAGTTTAAATCAATCTAATTTATTTATCTAATAAATA
* * *
52642420 TTGATCATTAATTGAGAGCCAAATTAATATCGACTTTGCTGAATTATGAGTCTAACTTTCCTTTC
1 TTGATCATTAATTGAGAGTCAAATTAATATCGACTTT-TTGAATTATGAGTCTAAATTTCCTTTC
* *
52642485 ATTTGCATGCAATGATGAAGAAATGAAAATTAGACTCATAATCCAGCAAAATTGATATTATAAAG
65 ATTTGCATGCAATGATGAAGAAATGAAAATTA-ACTCATAATCCAGCAAAATTGACATCATAAAG
* * *
52642550 CTACGAGCATTGAAAAGCATTTTATATTTGTTAAAACTAAATAAAAGGGTATTAATTAATAAATC
129 CTACGAGCATTGAAAAGCATGTTATATTTGTTAAAAATAAATAAAAGGGTACTAATTAATAAATC
* * * *
52642615 GATCATGACCGGTTTCAATCGATCTAATTTATTTATCTAATAAATG
194 GATCATGACCAGTTTAAATCAATCTAATTTATTTATCTAATAAATA
** * * * * * * *
52642661 CCGATCCA-TAATTTAAAGTCAAATTAATATTGAGTTCTTTAAATTATAAGTCTAAATTTCTTTT
1 TTGAT-CATTAATTGAGAGTCAAATTAATATCGACTT-TTTGAATTATGAGTCTAAATTTCCTTT
* * * * *
52642725 CATGTGCATGCAATAATTAAGAAATAAAAATTAAGCTAATAATCCA
64 CATTTGCATGCAATGATGAAGAAATGAAAATTAA-CTCATAATCCA
52642771 ACATTATTGC
Statistics
Matches: 298, Mismatches: 48, Indels: 12
0.83 0.13 0.03
Matches are distributed among these distances:
240 2 0.01
241 221 0.74
242 3 0.01
243 71 0.24
244 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (239 bp):
TTGATCATTAATTGAGAGTCAAATTAATATCGACTTTTTGAATTATGAGTCTAAATTTCCTTTCA
TTTGCATGCAATGATGAAGAAATGAAAATTAACTCATAATCCAGCAAAATTGACATCATAAAGCT
ACGAGCATTGAAAAGCATGTTATATTTGTTAAAAATAAATAAAAGGGTACTAATTAATAAATCGA
TCATGACCAGTTTAAATCAATCTAATTTATTTATCTAATAAATA
Found at i:52643328 original size:22 final size:22
Alignment explanation
Indices: 52643277--52643331 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
52643267 AAAATGATTT
*
52643277 TTCCTTATAAAAACCCAAAATT
1 TTCCTTATAAAAACCCAAAATA
* *
52643299 TTCC-TATAAAAA-TCAAAGTAA
1 TTCCTTATAAAAACCCAAAAT-A
52643320 TTCCTTATAAAA
1 TTCCTTATAAAA
52643332 CACTACAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 5 0.18
21 12 0.43
22 11 0.39
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (22 bp):
TTCCTTATAAAAACCCAAAATA
Found at i:52650565 original size:2 final size:2
Alignment explanation
Indices: 52650558--52650585 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
52650548 AATCAAATAC
52650558 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52650586 GTTTAATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52651228 original size:180 final size:180
Alignment explanation
Indices: 52650799--52651234 Score: 554
Period size: 180 Copynumber: 2.4 Consensus size: 180
52650789 CAAATTGATC
* * * * *
52650799 ATTGCTTGTAAATGAAA-GAAAAGTTAGACTAATAATTCAGCAAAGTCGATATTAATTTGGCTCT
1 ATTGCATGCAAATGAAAGGAAAA-CTAGACTCATAATTCAGCAAAGTCGATATTAATTT-G-ACT
* *** * *
52650863 CTCAATTAGAGATGTTGATTGATCATTTGCAAGTACAAGTTGCTATCCATTGCTAATAGTCTTAT
63 CTCAATAAG-GATGCAAATTGATCATTGGCAAGTACAAGTTGCTATCCATTGCTAATAGCCTTAT
* * *
52650928 AATGTTGACTTTGCTGGATTATGAGCCTAGTTTTTATCTCTTCATCAACTAATG
127 AATATTGACTTTGCTAGATTATGAACCTAGTTTTTATCTCTTCATCAACTAATG
* * * * * * * *
52650982 ATTACATGCCAATGAAAGAAAAACTAGACTCATAATTCAACAAAGTTGACAATAAATTGACTCTC
1 ATTGCATGCAAATGAAAGGAAAACTAGACTCATAATTCAGCAAAGTCGATATTAATTTGACTCTC
*
52651047 AACTAAGGAT-CAAATTGATCATTGGCAAGTACAAGTTGCTATCCATTGCTAATAGCCTTGTAAT
66 AA-TAAGGATGCAAATTGATCATTGGCAAGTACAAGTTGCTATCCATTGCTAATAGCCTTATAAT
*
52651111 ATTGACTTTGCTAGATTATGAACCTAGTTTTTATCTTTTCATCAACTAATG
130 ATTGACTTTGCTAGATTATGAACCTAGTTTTTATCTCTTCATCAACTAATG
* *
52651162 ATTGCATGCAAATGAAAGGAAAACTAGACTCATAATTCAGTAAAATCGATATTAATTT-AGCTCT
1 ATTGCATGCAAATGAAAGGAAAACTAGACTCATAATTCAGCAAAGTCGATATTAATTTGA-CTCT
52651226 CAATTAAGG
65 CAA-TAAGG
52651235 GTTAACATTT
Statistics
Matches: 215, Mismatches: 35, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
179 1 0.00
180 155 0.72
181 10 0.05
182 4 0.02
183 41 0.19
184 4 0.02
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (180 bp):
ATTGCATGCAAATGAAAGGAAAACTAGACTCATAATTCAGCAAAGTCGATATTAATTTGACTCTC
AATAAGGATGCAAATTGATCATTGGCAAGTACAAGTTGCTATCCATTGCTAATAGCCTTATAATA
TTGACTTTGCTAGATTATGAACCTAGTTTTTATCTCTTCATCAACTAATG
Found at i:52651732 original size:2 final size:2
Alignment explanation
Indices: 52651727--52651754 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
52651717 TTATCTTTTC
52651727 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52651755 TTAAGAGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52654701 original size:21 final size:21
Alignment explanation
Indices: 52654640--52654702 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
52654630 AAGCAGCATT
* *
52654640 AATGTTTTGATAATAATAACA
1 AATGTTTTAATAATAATAATA
*
52654661 AACGTTTTAATAATAATAATA
1 AATGTTTTAATAATAATAATA
*
52654682 AATGTTTTTATAATAATAATA
1 AATGTTTTAATAATAATAATA
52654703 TTAACTATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.41
Consensus pattern (21 bp):
AATGTTTTAATAATAATAATA
Found at i:52654854 original size:28 final size:28
Alignment explanation
Indices: 52654819--52654872 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
52654809 CCCAAATTTT
*
52654819 TTCAAAATTACCATTTTGCCCTCGAGAG
1 TTCAAAATTACCATTTTGCCCCCGAGAG
52654847 TTCAAAATTACCATTTTGCCCCCGAG
1 TTCAAAATTACCATTTTGCCCCCGAG
52654873 TATCCAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (28 bp):
TTCAAAATTACCATTTTGCCCCCGAGAG
Found at i:52654880 original size:28 final size:28
Alignment explanation
Indices: 52654821--52654881 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
52654811 CAAATTTTTT
* *
52654821 CAAAATTACCATTTTGCCCTCGAGAGTT
1 CAAAATTACCATTTTGCCCCCGAGAGTC
52654849 CAAAATTACCATTTTGCCCCCGAGTA-TC
1 CAAAATTACCATTTTGCCCCCGAG-AGTC
52654877 CAAAA
1 CAAAA
52654882 GTTTCGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.33, C:0.28, G:0.11, T:0.28
Consensus pattern (28 bp):
CAAAATTACCATTTTGCCCCCGAGAGTC
Found at i:52660513 original size:18 final size:18
Alignment explanation
Indices: 52660487--52660521 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52660477 AATCATGTTG
* *
52660487 ACTTTAATAATTCGATTA
1 ACTTGAATAACTCGATTA
52660505 ACTTGAATAACTCGATT
1 ACTTGAATAACTCGATT
52660522 CGTTTAACTA
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:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (18 bp):
ACTTGAATAACTCGATTA
Found at i:52665095 original size:23 final size:23
Alignment explanation
Indices: 52665069--52665116 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
52665059 AAACTTTTGA
52665069 TTTAATACTT-TAAAAATTACAAT
1 TTTAATA-TTATAAAAATTACAAT
* *
52665092 TTTACTATTATAAAAATTATAAT
1 TTTAATATTATAAAAATTACAAT
52665115 TT
1 TT
52665117 AATTTCGATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (23 bp):
TTTAATATTATAAAAATTACAAT
Found at i:52666987 original size:230 final size:226
Alignment explanation
Indices: 52666574--52666990 Score: 599
Period size: 230 Copynumber: 1.8 Consensus size: 226
52666564 TTCATAACCC
52666574 AACAAAAGTGATCAACTTCACTCTCACCTCATATTCCCAATATTTATATACAGATACAAGAAGGT
1 AACAAAAGTGATCAACTTCACTCTCACCTCATATTCCCAATATTTATAT--A-ATACAAGAAGGT
*
52666639 GTTGCAAATGCTGAAACTTTAAATTGATTCATATTTAAGGTGATTGTTTAAACGAAAATATCTCT
63 GTTGCAAATGCTGAAACTTTAAATTGATTCATATTTAAGGTGATTGCTTAAACGAAAATATCTCT
*
52666704 TATATGTGCACTTTAATTGGCTTAGAAACTAGTTTCTCTCTTGCTCCATTATTCATATTTTTCCT
128 TATATATGCACTTTAATTGGCTTAGAAACTAGTTTCTCTCTTGCTCCATTATTCATATTTTTCCT
52666769 TGTCAAAATACATGTTCAAGAGAGTAAGGGGCCT
193 TGTCAAAATACATGTTCAAGAGAGTAAGGGGCCT
* * * * *
52666803 AACAAAAGTGATCGATTTGACTCTCATCTCATATTCCCAATATTT-T-T-ATACGAGAAGGTGTT
1 AACAAAAGTGATCAACTTCACTCTCACCTCATATTCCCAATATTTATATAATACAAGAAGGTGTT
* *
52666865 GCAGATGTTGAAACTTT-AATCTGATTCATATTTAAGGTGATTGCTTAAACGAACCGAGCTAATA
66 GCAAATGCTGAAACTTTAAAT-TGATTCATATTTAAGGTGATTGCTTAAACG-A---A---AATA
* * *
52666929 TCTCTTATATATGCACTTTAATTGGCTTAGAATCTAGTTTCTTTCTTGCTCTATTATTCATA
123 TCTCTTATATATGCACTTTAATTGGCTTAGAAACTAGTTTCTCTCTTGCTCCATTATTCATA
52666991 AACAGTAACC
Statistics
Matches: 168, Mismatches: 12, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
222 3 0.02
223 58 0.35
224 1 0.01
227 2 0.01
228 1 0.01
229 41 0.24
230 62 0.37
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.37
Consensus pattern (226 bp):
AACAAAAGTGATCAACTTCACTCTCACCTCATATTCCCAATATTTATATAATACAAGAAGGTGTT
GCAAATGCTGAAACTTTAAATTGATTCATATTTAAGGTGATTGCTTAAACGAAAATATCTCTTAT
ATATGCACTTTAATTGGCTTAGAAACTAGTTTCTCTCTTGCTCCATTATTCATATTTTTCCTTGT
CAAAATACATGTTCAAGAGAGTAAGGGGCCT
Found at i:52668652 original size:17 final size:18
Alignment explanation
Indices: 52668623--52668664 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
52668613 TCATTTATTG
52668623 TTTG-ATAAATTTAAAAT
1 TTTGTATAAATTTAAAAT
* *
52668640 TTT-TATAATTTTATAAT
1 TTTGTATAAATTTAAAAT
52668657 TTTGTATA
1 TTTGTATA
52668665 TGAAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
TTTGTATAAATTTAAAAT
Found at i:52672863 original size:37 final size:38
Alignment explanation
Indices: 52672769--52672865 Score: 99
Period size: 40 Copynumber: 2.5 Consensus size: 38
52672759 CACATCAGAA
*
52672769 TGGCACCCAGTGCCTCATCGGATAGTTCGAAGCAATAAAG
1 TGGCACCCAGTGCCTCATCGGATAGTCCGAAG--ATAAAG
* * * *
52672809 TGACACCCACTGTCTCATCGGCTTAG-CCGAAG-TAAAG
1 TGGCACCCAGTGCCTCATCGG-ATAGTCCGAAGATAAAG
*
52672846 TGGCACCCAGTACCTCATCG
1 TGGCACCCAGTGCCTCATCG
52672866 AATCTATCCG
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
37 21 0.45
40 23 0.49
41 3 0.06
ACGTcount: A:0.27, C:0.30, G:0.23, T:0.21
Consensus pattern (38 bp):
TGGCACCCAGTGCCTCATCGGATAGTCCGAAGATAAAG
Found at i:52673724 original size:17 final size:17
Alignment explanation
Indices: 52673698--52673732 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
52673688 CGTGAGCTTC
*
52673698 TGTTTTTTTTCTTCTTT
1 TGTTTCTTTTCTTCTTT
*
52673715 TGTTTCTTTTTTTCTTT
1 TGTTTCTTTTCTTCTTT
52673732 T
1 T
52673733 CTTTAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (17 bp):
TGTTTCTTTTCTTCTTT
Found at i:52674852 original size:13 final size:13
Alignment explanation
Indices: 52674834--52674862 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
52674824 TTTCTTTTCC
52674834 TTTCATTTTTCTT
1 TTTCATTTTTCTT
52674847 TTTCATTTTTCTT
1 TTTCATTTTTCTT
52674860 TTT
1 TTT
52674863 TCCTACCAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTCATTTTTCTT
Found at i:52686753 original size:17 final size:17
Alignment explanation
Indices: 52686731--52686788 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 17
52686721 CGACTCGATT
*
52686731 TATTTTTAATTTTATAA
1 TATTTTTAATATTATAA
*
52686748 TA-TTTT-ATATTATAT
1 TATTTTTAATATTATAA
*
52686763 TATTTTTATATATCAT-A
1 TATTTTTA-ATATTATAA
*
52686780 TAATTTTAA
1 TATTTTTAA
52686789 AATACATTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
15 9 0.27
16 9 0.27
17 9 0.27
18 6 0.18
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTTTTAATATTATAA
Found at i:52686780 original size:18 final size:16
Alignment explanation
Indices: 52686732--52686786 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
52686722 GACTCGATTT
*
52686732 ATTTTTA-ATTTTATA
1 ATTTTTATATTATATA
*
52686747 ATATTTTATATTATATT
1 AT-TTTTATATTATATA
52686764 ATTTTTATATATCATATA
1 ATTTTTATAT-T-ATATA
52686782 ATTTT
1 ATTTT
52686787 AAAATACATT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 2 0.06
16 13 0.39
17 9 0.27
18 9 0.27
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTTTATATTATATA
Found at i:52686893 original size:70 final size:67
Alignment explanation
Indices: 52686815--52686951 Score: 175
Period size: 72 Copynumber: 2.0 Consensus size: 67
52686805 AATTTATATT
* * *
52686815 AAATATATAATATTACTTTAATATAAAAATTAAAATAATATTAATGATTATAGAAAAATTTTAAT
1 AAATATATAAAATTA-TTAAATATAAAAA-TAAAATAATATAAAT-ATTATA-AAAAATTTTAA-
52686880 AAATAAA
61 AAATAAA
* * *
52686887 AAATATATAAAATTATTAAATATTAAAATAATATAATATAAATATTTTAAAAAATTTTAAAAATA
1 AAATATATAAAATTATTAAATATAAAAATAAAATAATATAAATATTATAAAAAATTTTAAAAATA
52686952 TATGAACAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
67 5 0.08
68 11 0.19
69 5 0.08
70 13 0.22
71 11 0.19
72 14 0.24
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (67 bp):
AAATATATAAAATTATTAAATATAAAAATAAAATAATATAAATATTATAAAAAATTTTAAAAATA
AA
Found at i:52689571 original size:10 final size:9
Alignment explanation
Indices: 52689546--52689570 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
52689536 TGAAAATAAG
52689546 AAAAAAATT
1 AAAAAAATT
52689555 AAAAAAATT
1 AAAAAAATT
52689564 AAAAAAA
1 AAAAAAA
52689571 AATGAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (9 bp):
AAAAAAATT
Found at i:52689581 original size:20 final size:20
Alignment explanation
Indices: 52689537--52689586 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
52689527 TTCTCGGACT
*
52689537 GAAAATAAGAAAAAAATTAA
1 GAAAATAAGAAAAAAATGAA
*
52689557 AAAAATTAA-AAAAAAATGAA
1 GAAAA-TAAGAAAAAAATGAA
52689577 GAAAA-AAGAA
1 GAAAATAAGAA
52689587 GAAATCCTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 2 0.08
19 2 0.08
20 18 0.72
21 3 0.12
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (20 bp):
GAAAATAAGAAAAAAATGAA
Found at i:52689708 original size:6 final size:6
Alignment explanation
Indices: 52689697--52689740 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
52689687 TGAGAGTAAG
* * *
52689697 AAGCAA AAGCAA ACGCAA ACGCAA ACGCAA AAGCAA AAGCAA AA
1 AAGCAA AAGCAA AAGCAA AAGCAA AAGCAA AAGCAA AAGCAA AA
52689741 CCCTAAAACC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.61, C:0.23, G:0.16, T:0.00
Consensus pattern (6 bp):
AAGCAA
Found at i:52691626 original size:29 final size:29
Alignment explanation
Indices: 52691573--52691630 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
52691563 ATTTGGTTCA
*
52691573 GGACTAAAATTCCATACTTCTAAAAGTAT
1 GGACTAAAATTCCATACTTCAAAAAGTAT
52691602 GGACTAAAATTAACCA-A-TTCAAAAAGTAT
1 GGACTAAAATT--CCATACTTCAAAAAGTAT
52691631 AAAGACTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 22 0.85
30 1 0.04
31 3 0.12
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.28
Consensus pattern (29 bp):
GGACTAAAATTCCATACTTCAAAAAGTAT
Found at i:52693263 original size:22 final size:24
Alignment explanation
Indices: 52693238--52693283 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
52693228 GGTAAGTCAA
52693238 TATTTGTATAC-T-AAAATTTTAT
1 TATTTGTATACTTAAAAATTTTAT
* *
52693260 TATTTTTATTCTTAAAAATTTTAT
1 TATTTGTATACTTAAAAATTTTAT
52693284 ACACGATATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 9 0.45
23 1 0.05
24 10 0.50
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (24 bp):
TATTTGTATACTTAAAAATTTTAT
Found at i:52696315 original size:111 final size:111
Alignment explanation
Indices: 52696192--52696412 Score: 442
Period size: 111 Copynumber: 2.0 Consensus size: 111
52696182 CATCATTGAC
52696192 ATCAATTTTGCATAGATTTTGAATGTTGTTTGAGTATTTATGGTATATACATGTATATATTATTT
1 ATCAATTTTGCATAGATTTTGAATGTTGTTTGAGTATTTATGGTATATACATGTATATATTATTT
52696257 TTTTATGACACTTACATGTTTTAATTATTTTATATATTTGTATAAA
66 TTTTATGACACTTACATGTTTTAATTATTTTATATATTTGTATAAA
52696303 ATCAATTTTGCATAGATTTTGAATGTTGTTTGAGTATTTATGGTATATACATGTATATATTATTT
1 ATCAATTTTGCATAGATTTTGAATGTTGTTTGAGTATTTATGGTATATACATGTATATATTATTT
52696368 TTTTATGACACTTACATGTTTTAATTATTTTATATATTTGTATAA
66 TTTTATGACACTTACATGTTTTAATTATTTTATATATTTGTATAA
52696413 CATATTGAAT
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 110 1.00
ACGTcount: A:0.30, C:0.05, G:0.12, T:0.52
Consensus pattern (111 bp):
ATCAATTTTGCATAGATTTTGAATGTTGTTTGAGTATTTATGGTATATACATGTATATATTATTT
TTTTATGACACTTACATGTTTTAATTATTTTATATATTTGTATAAA
Found at i:52699646 original size:24 final size:24
Alignment explanation
Indices: 52699616--52699663 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
52699606 TATATTAAAT
*
52699616 ATTAATAATAAATGTAAAATTTAA
1 ATTAATAATAAATATAAAATTTAA
52699640 ATTAATAATAAATATAAAATTTAA
1 ATTAATAATAAATATAAAATTTAA
52699664 TATATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
ATTAATAATAAATATAAAATTTAA
Found at i:52706785 original size:19 final size:18
Alignment explanation
Indices: 52706745--52706785 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
52706735 AGTTACTCAA
52706745 CAAAAAATAGTTTTTTTT
1 CAAAAAATAGTTTTTTTT
52706763 -AAAAAATA-TTATTTTGTT
1 CAAAAAATAGTT-TTTT-TT
52706781 CAAAA
1 CAAAA
52706786 TTTTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 2 0.10
17 12 0.60
18 2 0.10
19 4 0.20
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (18 bp):
CAAAAAATAGTTTTTTTT
Found at i:52722516 original size:28 final size:29
Alignment explanation
Indices: 52722450--52722517 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 29
52722440 TTTTATCCTC
*
52722450 AACCCCAAA-TCTTAAACTCTAAATCTAA
1 AACCCCAAACTCTTAAACTCTAAATATAA
* * *
52722478 AATCTCGAACT-TTAAACT-TATAATATAA
1 AACCCCAAACTCTTAAACTCTA-AATATAA
52722506 AACCCCAAACTC
1 AACCCCAAACTC
52722518 GTAATCCCAA
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
27 2 0.07
28 27 0.90
29 1 0.03
ACGTcount: A:0.46, C:0.26, G:0.01, T:0.26
Consensus pattern (29 bp):
AACCCCAAACTCTTAAACTCTAAATATAA
Found at i:52726061 original size:82 final size:80
Alignment explanation
Indices: 52725924--52726082 Score: 246
Period size: 82 Copynumber: 2.0 Consensus size: 80
52725914 CGATAGTGAA
* *
52725924 AACTTTTAAAATGAGAATCAAAATGATTTTAATCATTATATCAAAATAAATTATTCTATAAGCCT
1 AACTTTTAAAATGAGAATCAAAATGATTTTAACCATTAGATCAAAATAAATTATTCTA-AA-CCT
52725989 TAGATTTTGTATTTGAG
64 TAGATTTTGTATTTGAG
* * * *
52726006 AACTTTTAAAGTGAGAATCAAAATTATTTTAGCCATTAGATCAAAATAAATTATTCTAAATCTTA
1 AACTTTTAAAATGAGAATCAAAATGATTTTAACCATTAGATCAAAATAAATTATTCTAAACCTTA
52726071 GATTTTGTATTT
66 GATTTTGTATTT
52726083 ATCATACTTT
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
80 16 0.23
81 2 0.03
82 53 0.75
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (80 bp):
AACTTTTAAAATGAGAATCAAAATGATTTTAACCATTAGATCAAAATAAATTATTCTAAACCTTA
GATTTTGTATTTGAG
Found at i:52734104 original size:18 final size:17
Alignment explanation
Indices: 52734078--52734139 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
52734068 TTAGATTAGT
*
52734078 TTTAGATTTATTTCTAAA
1 TTTAAATTTATTT-TAAA
*
52734096 TTTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
*
52734113 TTTGAAA-TAATTTTAAA
1 TTT-AAATTTATTTTAAA
* *
52734130 CTTAACTTTA
1 TTTAAATTTA
52734140 AAATAAAATT
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
16 2 0.06
17 19 0.54
18 14 0.40
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:52734114 original size:17 final size:18
Alignment explanation
Indices: 52734078--52734120 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
52734068 TTAGATTAGT
*
52734078 TTTAGATTTATTTCTAAA
1 TTTAAATTTATTTCTAAA
*
52734096 TTTAAATTTGTTT-TAAA
1 TTTAAATTTATTTCTAAA
52734113 TTTGAAAT
1 TTT-AAAT
52734121 AATTTTAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (18 bp):
TTTAAATTTATTTCTAAA
Found at i:52745607 original size:17 final size:17
Alignment explanation
Indices: 52745585--52745618 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
52745575 AGGGGTACTT
52745585 ACAGTATGGGATAAAGA
1 ACAGTATGGGATAAAGA
52745602 ACAGTATGGGATAAAGA
1 ACAGTATGGGATAAAGA
52745619 GTATTTTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.29, T:0.18
Consensus pattern (17 bp):
ACAGTATGGGATAAAGA
Found at i:52746482 original size:19 final size:21
Alignment explanation
Indices: 52746438--52746487 Score: 68
Period size: 19 Copynumber: 2.4 Consensus size: 21
52746428 TTACAACAAT
*
52746438 AAATAATTTAAAAATTATGTAA
1 AAAT-ATTTAAAAAATATGTAA
52746460 AAATATTTAAAAAATA-G-AA
1 AAATATTTAAAAAATATGTAA
52746479 AAATATTTA
1 AAATATTTA
52746488 TGTAATTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 11 0.41
20 1 0.04
21 11 0.41
22 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (21 bp):
AAATATTTAAAAAATATGTAA
Found at i:52747387 original size:13 final size:13
Alignment explanation
Indices: 52747369--52747394 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52747359 AAGGGGCCAA
52747369 TATGTTAGCATCC
1 TATGTTAGCATCC
52747382 TATGTTAGCATCC
1 TATGTTAGCATCC
52747395 CCAAATAGGA
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:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (13 bp):
TATGTTAGCATCC
Found at i:52748489 original size:19 final size:19
Alignment explanation
Indices: 52748440--52748490 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
52748430 GAGGGATTAG
* *
52748440 ATATTTATAATATTAATTT
1 ATATTTATATTATTAATAT
*
52748459 ATATTT-TGTTATTCAATAT
1 ATATTTATATTATT-AATAT
52748478 ATATTTAT-TTATT
1 ATATTTATATTATT
52748491 TTCACTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 5 0.19
19 21 0.78
20 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (19 bp):
ATATTTATATTATTAATAT
Found at i:52755250 original size:345 final size:351
Alignment explanation
Indices: 52754825--52755521 Score: 1056
Period size: 345 Copynumber: 2.0 Consensus size: 351
52754815 TGCGACACGT
*
52754825 AAAAACATTAAAAGGTACATAAAAAATATATGTTAAAAATGAAAAAATTAAAATATTATTCTTTA
1 AAAAACATTAAAAGGTACATAAAAAATATATGTTAAAAATGAAAAAACTAAAATATTATTCTTTA
* *
52754890 AAATAATTTTATACAATAATTGTGGTTATTTATATAGATATTTTAGAGTTTCTAAAAATTAAAAA
66 AAATAATTTTATACAATAATTGTGGCTATTTATATAGATATTTTAGAATTTCTAAAAATTAAAAA
*
52754955 TTTATATATCTAGTTAATTTAAAT-AAATTAATATATATTTTAAGATAATTTTTAAATTTAAT-A
131 TTTATATATCTAGTTAATTTAAATCAAA-TAATACATATTTTAAGATAATTTTT-AATTTAATAA
52755018 A-AA-TAATTAAA-T-TTAAA-T-TT-AAAATTTT-AAAATAGAATGATAACAAATTTATATATT
194 ATAATTAATTAAATTATTAAATTATTAAAAATTTTAAAAATAGAATGATAACAAATTTATATATT
52755075 AAGATAAATAATATTTATCTTACTA-ATAATTAAACGATATTATGTTTATGATAATTTTATATTT
259 AA-ATAAATAATATTTATCTTAC-AGATAATTAAACGATATTATGTTTATGATAATTTTATATTT
*
52755139 TATATTTCTATTTAAATTAAGACGGCATGC
322 TATATTTCTATTCAAATTAAGACGGCATGC
* *
52755169 AAAAACATTGAAAGGTACATAGAAAAATATATGTTAAAAATGAAGAAACTAAAATATTATTCTTT
1 AAAAACATTAAAAGGTACATA-AAAAATATATGTTAAAAATGAAAAAACTAAAATATTATTCTTT
* * *
52755234 AAAATAATTTTATACAATAATTGTGGCTATTTATATAGATTTTTTAGAATTTTTAAAAGTTAAAA
65 AAAATAATTTTATACAATAATTGTGGCTATTTATATAGATATTTTAGAATTTCTAAAAATTAAAA
* *
52755299 ATTTATATATTTAGTTAATTTAAATCAAATAATACATATTTTATGATAATTTTTAATTTAATAAA
130 ATTTATATATCTAGTTAATTTAAATCAAATAATACATATTTTAAGATAATTTTTAATTTAAT-AA
*
52755364 ATAATTAATTAAATTTAAAAAATTAAATTAAATTAAAAATTTTAAAAATATAATGATAACAAATT
194 ATAATTAATTAAA-TT-----ATTAAATT--ATTAAAAATTTTAAAAATAGAATGATAACAAATT
* *
52755429 TATATATTAAATAAATAATATTTATCTTACAGATAATTAAATGATTTTATGTTTATGATAATTTT
251 TATATATTAAATAAATAATATTTATCTTACAGATAATTAAACGATATTATGTTTATGATAATTTT
52755494 ATATTTTATATTTCTATTCAAATTAAGA
316 ATATTTTATATTTCTATTCAAATTAAGA
52755522 TTCCAACAGT
Statistics
Matches: 317, Mismatches: 15, Indels: 25
0.89 0.04 0.07
Matches are distributed among these distances:
344 28 0.09
345 148 0.47
346 5 0.02
347 2 0.01
348 8 0.03
350 1 0.00
356 5 0.02
357 1 0.00
360 3 0.01
361 86 0.27
362 30 0.09
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (351 bp):
AAAAACATTAAAAGGTACATAAAAAATATATGTTAAAAATGAAAAAACTAAAATATTATTCTTTA
AAATAATTTTATACAATAATTGTGGCTATTTATATAGATATTTTAGAATTTCTAAAAATTAAAAA
TTTATATATCTAGTTAATTTAAATCAAATAATACATATTTTAAGATAATTTTTAATTTAATAAAT
AATTAATTAAATTATTAAATTATTAAAAATTTTAAAAATAGAATGATAACAAATTTATATATTAA
ATAAATAATATTTATCTTACAGATAATTAAACGATATTATGTTTATGATAATTTTATATTTTATA
TTTCTATTCAAATTAAGACGGCATGC
Found at i:52755392 original size:19 final size:17
Alignment explanation
Indices: 52755351--52755402 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 17
52755341 ATGATAATTT
*
52755351 TTAATTTAA-TAAAATAA
1 TTAATTAAATTAAAA-AA
52755368 TTAATTAAATTTAAAAAA
1 TTAATTAAA-TTAAAAAA
52755386 TTAAATTAAATTAAAAA
1 TT-AATTAAATTAAAAA
52755403 TTTTAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
17 8 0.26
18 11 0.35
19 12 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAATTAAATTAAAAAA
Found at i:52755409 original size:19 final size:19
Alignment explanation
Indices: 52755360--52755402 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
52755350 TTTAATTTAA
52755360 TAAAATAATT-AATTAAATT
1 TAAAA-AATTAAATTAAATT
52755379 TAAAAAATTAAATTAAA-T
1 TAAAAAATTAAATTAAATT
52755397 TAAAAA
1 TAAAAA
52755403 TTTTAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAAATTAAATTAAATT
Found at i:52767157 original size:20 final size:20
Alignment explanation
Indices: 52767128--52767171 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
52767118 AACTCTCGAT
52767128 TTTAGATTTAGGATATTGAG
1 TTTAGATTTAGGATATTGAG
* * * *
52767148 TTTAGGTTTATGATCTTGGG
1 TTTAGATTTAGGATATTGAG
52767168 TTTA
1 TTTA
52767172 AAGTTTAAGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.23, C:0.02, G:0.25, T:0.50
Consensus pattern (20 bp):
TTTAGATTTAGGATATTGAG
Found at i:52767569 original size:17 final size:17
Alignment explanation
Indices: 52767537--52767568 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
52767527 AATAAAAACT
52767537 ATATTTTAATATTTTTA
1 ATATTTTAATATTTTTA
52767554 ATATTTTAAT-TTTTT
1 ATATTTTAATATTTTT
52767569 TTAAAAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATATTTTAATATTTTTA
Found at i:52772950 original size:25 final size:24
Alignment explanation
Indices: 52772893--52772950 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
52772883 TTAAAAATAT
*
52772893 TTAAAATTTATTTTTTTATATATTA
1 TTAAAA-TTATTTTTCTATATATTA
* *
52772918 TAATAAATTATTTTTCTATATTCTTA
1 TTA-AAATTATTTTTCTATA-TATTA
52772944 TTAAAAT
1 TTAAAAT
52772951 ATCATAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
25 18 0.67
26 9 0.33
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (24 bp):
TTAAAATTATTTTTCTATATATTA
Found at i:52773099 original size:14 final size:13
Alignment explanation
Indices: 52773084--52773118 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
52773074 TAAATTAAAT
*
52773084 TTTTTAAAAATTA
1 TTTTTAAAAATCA
*
52773097 TTTTTCAAAATCA
1 TTTTTAAAAATCA
52773110 TTTTTAAAA
1 TTTTTAAAA
52773119 GCACTCTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (13 bp):
TTTTTAAAAATCA
Found at i:52783786 original size:58 final size:57
Alignment explanation
Indices: 52783724--52783882 Score: 164
Period size: 58 Copynumber: 2.7 Consensus size: 57
52783714 TGAAATGGTA
* * * *
52783724 ATTTTTGATTTTCGAGGGTAAAA-ATGTAATTTTTGGTGAAA-CTGAGGTTGAAAATGAG
1 ATTTTGGAATTTCG-GGGTAAAATA-GTAATTTTTGGTGAAATC-AAGGTTAAAAATGAG
* * *
52783782 ATTTTAGGAAATTCGGGGGTAAAATGGTAA-TTTTGGTGAAATCAAGGTTAAAAATGGG
1 ATTTT-GGAATTTC-GGGGTAAAATAGTAATTTTTGGTGAAATCAAGGTTAAAAATGAG
52783840 ATTTTGGAAAGTTT-GGGGTAAAATAGTAATTTTTGGTGAAATC
1 ATTTTGG-AA-TTTCGGGGTAAAATAGTAATTTTTGGTGAAATC
52783883 GGGAAAATTC
Statistics
Matches: 85, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
57 16 0.19
58 48 0.56
59 20 0.24
60 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (57 bp):
ATTTTGGAATTTCGGGGTAAAATAGTAATTTTTGGTGAAATCAAGGTTAAAAATGAG
Found at i:52783932 original size:30 final size:30
Alignment explanation
Indices: 52783894--52784050 Score: 107
Period size: 30 Copynumber: 5.3 Consensus size: 30
52783884 GGAAAATTCG
*
52783894 AGGG-TAAAATGGTAATTTTTGGTGAAATC
1 AGGGTTAAAATGGTAATTTTTGGTGAAATT
*
52783923 AGGGTTAAAAATAGT-A-TTTT-G-GAAAGTTT
1 AGGGTT-AAAATGGTAATTTTTGGTGAAA--TT
* * * *
52783952 GGGGGTAAAATGGTAATTTTTGGTAAAATC
1 AGGGTTAAAATGGTAATTTTTGGTGAAATT
*
52783982 AGGGTTAAAAATGG-GA-TTTT-GT-AAAGTTT
1 AGGGTT-AAAATGGTAATTTTTGGTGAAA--TT
* *
52784011 GGGGGTAAAATGGTAATTTTTGGTGAAATT
1 AGGGTTAAAATGGTAATTTTTGGTGAAATT
*
52784041 GGGGTTAAAA
1 AGGGTTAAAA
52784051 ATGAGATTTT
Statistics
Matches: 98, Mismatches: 15, Indels: 29
0.69 0.11 0.20
Matches are distributed among these distances:
27 7 0.07
28 17 0.17
29 24 0.24
30 27 0.28
31 17 0.17
32 6 0.06
ACGTcount: A:0.34, C:0.01, G:0.29, T:0.35
Consensus pattern (30 bp):
AGGGTTAAAATGGTAATTTTTGGTGAAATT
Found at i:52783942 original size:98 final size:98
Alignment explanation
Indices: 52783790--52783981 Score: 314
Period size: 98 Copynumber: 2.0 Consensus size: 98
52783780 AGATTTTAGG
* *
52783790 AAATTCGGGGGTAAAATGGTAATTTTGGTGAAATCAAGGTTAAAAATGGGATTTTGGAAAGTTT-
1 AAATTCGAGGGTAAAATGGTAATTTTGGTGAAATCAAGGTTAAAAATAGGATTTTGGAAAGTTTG
*
52783854 GGGGTAAAATAGTAATTTTTGGTGAAATCGGGA
66 GGGGTAAAATAGTAATTTTTGGTAAAATCGGGA
* *
52783887 AAATTCGAGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATAGTATTTTGGAAAGTTT
1 AAATTCGAGGGTAAAATGGTAA-TTTTGGTGAAATCAAGGTTAAAAATAGGATTTTGGAAAGTTT
*
52783952 GGGGGTAAAATGGTAATTTTTGGTAAAATC
65 GGGGGTAAAATAGTAATTTTTGGTAAAATC
52783982 AGGGTTAAAA
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
97 21 0.24
98 39 0.45
99 27 0.31
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.33
Consensus pattern (98 bp):
AAATTCGAGGGTAAAATGGTAATTTTGGTGAAATCAAGGTTAAAAATAGGATTTTGGAAAGTTTG
GGGGTAAAATAGTAATTTTTGGTAAAATCGGGA
Found at i:52783960 original size:29 final size:29
Alignment explanation
Indices: 52783928--52784089 Score: 104
Period size: 29 Copynumber: 5.5 Consensus size: 29
52783918 AAATCAGGGT
*
52783928 TAAAAATAGTATTTTGGAAAGTTTGGGGG
1 TAAAAATGGTATTTTGGAAAGTTTGGGGG
* ** *
52783957 T-AAAATGGTAATTTTTGGTAAA-ATCAGGGT
1 TAAAAATGGT-A-TTTTGG-AAAGTTTGGGGG
* *
52783987 TAAAAATGGGATTTTGTAAAGTTTGGGGG
1 TAAAAATGGTATTTTGGAAAGTTTGGGGG
*
52784016 T-AAAATGGTAATTTTTGGTGAAA--TTGGGGT
1 TAAAAATGGT-A-TTTT-G-GAAAGTTTGGGGG
* *
52784046 TAAAAATGAG-ATTTTGAAAAGTTTGAGGG
1 TAAAAATG-GTATTTTGGAAAGTTTGGGGG
52784075 T-AAAATGGTAATTTT
1 TAAAAATGGT-ATTTT
52784090 TGGACAGTCT
Statistics
Matches: 101, Mismatches: 17, Indels: 30
0.68 0.11 0.20
Matches are distributed among these distances:
27 4 0.04
28 24 0.24
29 28 0.28
30 24 0.24
31 17 0.17
32 4 0.04
ACGTcount: A:0.35, C:0.01, G:0.28, T:0.36
Consensus pattern (29 bp):
TAAAAATGGTATTTTGGAAAGTTTGGGGG
Found at i:52783962 original size:59 final size:58
Alignment explanation
Indices: 52783895--52784092 Score: 306
Period size: 59 Copynumber: 3.4 Consensus size: 58
52783885 GAAAATTCGA
*
52783895 GGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATAGTATTTTGGAAAGTTTGG
1 GGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATAG-ATTTTGAAAAGTTTGG
* * *
52783954 GGGTAAAATGGTAATTTTTGGTAAAATCAGGGTTAAAAATGGGATTTTGTAAAGTTTGG
1 GGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAAT-AGATTTTGAAAAGTTTGG
** *
52784013 GGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGAGATTTTGAAAAGTTTGA
1 GGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAAT-AGATTTTGAAAAGTTTGG
52784072 GGGTAAAATGGTAATTTTTGG
1 GGGTAAAATGGTAATTTTTGG
52784093 ACAGTCTAGG
Statistics
Matches: 129, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
59 128 0.99
60 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.29, T:0.36
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATAGATTTTGAAAAGTTTGG
Found at i:52784893 original size:17 final size:15
Alignment explanation
Indices: 52784854--52784897 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
52784844 ATTTAATCTT
52784854 AAATTTAAATTTATA
1 AAATTTAAATTTATA
52784869 ATAGATTTAAATTGTATA
1 A-A-ATTTAAATT-TATA
52784887 CAAATTTAAAT
1 -AAATTTAAAT
52784898 CCAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.04
16 1 0.04
17 17 0.68
18 5 0.20
19 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (15 bp):
AAATTTAAATTTATA
Found at i:52785604 original size:200 final size:200
Alignment explanation
Indices: 52785244--52786006 Score: 1208
Period size: 200 Copynumber: 3.8 Consensus size: 200
52785234 TTCATTGATC
* * * * * *
52785244 TGGTCTTCTTTTCTGTGTCTCATCAGGAAGATGACCGCAAT-TC-TATTTTAATTCGCTTCTCTG
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGC-CTCGCTTATTTTGATTCGCTTCTCTG
* * * * * *
52785307 GATCTCCTCAGGAAGACAAATTTGGTCCATTTCTCTGTGTTTCATAAGGAAGCTAACCTTTTTAT
65 GATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCTTTTTAT
* *
52785372 TGCTTC-ATCCTGCTTCTCAGTGTCTCATCAGGAAGCCGGGTTCGAAGATTTACTCGCATTGAGC
130 TGCTTCGA-CCTGCTTCTCAATGTCTCATCAGGAAGCCGGGTTCGAAGATTTGCTCGCATTGAGC
52785436 GTTGAGT
194 GTTGAGT
52785443 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTATTTTGATTCGCTTCTCTGG
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTATTTTGATTCGCTTCTCTGG
* *
52785508 ATCTCCTTAGGAGGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCTTTTTATT
66 ATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCTTTTTATT
*
52785573 GCTTCGACCTGCTTCTCAATGTCTTATCAGGAAGCCGGGTTCGAAGATTTGCTCGCATTGAGCGT
131 GCTTCGACCTGCTTCTCAATGTCTCATCAGGAAGCCGGGTTCGAAGATTTGCTCGCATTGAGCGT
52785638 TGAGT
196 TGAGT
* * * *
52785643 TGGTATTCTTCTCTATATCTCATCAAGAAGATGACTGCCTCGCTTGTTTTGATTCGCTTCTCTGG
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTATTTTGATTCGCTTCTCTGG
* *
52785708 ATCTCCTCAAGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAAGAAGCTAACCTTTTTATT
66 ATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCTTTTTATT
* *
52785773 GCTTCGACCTGCTTCTCAATATCTCATCAGGAAGCCGGGTTTGAAGATTTGCTCGCATTGAGCGT
131 GCTTCGACCTGCTTCTCAATGTCTCATCAGGAAGCCGGGTTCGAAGATTTGCTCGCATTGAGCGT
52785838 TGAGT
196 TGAGT
* *
52785843 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTGATTCGCTTCTCTAG
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTATTTTGATTCGCTTCTCTGG
* *
52785908 ATCTCTTCAGGAAAACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCTTTTTATT
66 ATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCTTTTTATT
* *
52785973 GCTTCGACCTGCTTCTCAGTGTCTCATCAAGAAG
131 GCTTCGACCTGCTTCTCAATGTCTCATCAGGAAG
52786007 ATGACCGCCT
Statistics
Matches: 522, Mismatches: 39, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
198 1 0.00
199 36 0.07
200 484 0.93
201 1 0.00
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (200 bp):
TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTATTTTGATTCGCTTCTCTGG
ATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCTTTTTATT
GCTTCGACCTGCTTCTCAATGTCTCATCAGGAAGCCGGGTTCGAAGATTTGCTCGCATTGAGCGT
TGAGT
Found at i:52798227 original size:28 final size:27
Alignment explanation
Indices: 52798160--52798328 Score: 114
Period size: 29 Copynumber: 5.9 Consensus size: 27
52798150 TTGACTTTCA
* *
52798160 GGGGTAAAAATGTAATTTTTGGTGAAA-TC
1 GGGGTTAAAATGGAA-TTTT-G-GAAATTC
*
52798189 GGGGTTGAAAATGGGATTTTAGGAAATTC
1 GGGGTT-AAAATGGAATTTT-GGAAATTC
*
52798218 GGGGGTAAAATGGTAATTTTGGTAAAATT-
1 GGGGTTAAAATGG-AATTTTGG--AAATTC
* *
52798247 AGGGTTAAAATGGAATTTTGGAAAGTTT
1 GGGGTTAAAATGGAATTTTGGAAA-TTC
52798275 GAGGG-TAAAATGGTAATTTTTGGTGAAA-TC
1 G-GGGTTAAAATGG-AA-TTTT-G-GAAATTC
52798305 GGGGTTAAAAT-GAGATTTTGGAAA
1 GGGGTTAAAATGGA-ATTTTGGAAA
52798329 GTTTAAGGGT
Statistics
Matches: 116, Mismatches: 10, Indels: 31
0.74 0.06 0.20
Matches are distributed among these distances:
26 7 0.06
27 3 0.03
28 34 0.29
29 43 0.37
30 24 0.21
31 1 0.01
32 4 0.03
ACGTcount: A:0.34, C:0.02, G:0.31, T:0.33
Consensus pattern (27 bp):
GGGGTTAAAATGGAATTTTGGAAATTC
Found at i:52798240 original size:58 final size:58
Alignment explanation
Indices: 52798161--52798355 Score: 270
Period size: 58 Copynumber: 3.4 Consensus size: 58
52798151 TGACTTTCAG
* *
52798161 GGGTAAAAAT-GTAATTTTTGGTGAAATCGGGGTTGAAAATGGGATTTTAGGAAA-TTCGG
1 GGGT-AAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATGGGATTTT-GGAAAGTTTGA
* ** *
52798220 GGGTAAAATGGTAA-TTTTGGTAAAATTAGGGTTAAAATGGAATTTTGGAAAGTTTGA
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGGATTTTGGAAAGTTTGA
* *
52798277 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGAGATTTTGGAAAGTTTAA
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGGATTTTGGAAAGTTTGA
52798335 GGGTAAAATGGTAATTTTTGG
1 GGGTAAAATGGTAATTTTTGG
52798356 ATAGTCCAAG
Statistics
Matches: 121, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
56 5 0.04
57 29 0.24
58 79 0.65
59 8 0.07
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.34
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGGATTTTGGAAAGTTTGA
Found at i:52798351 original size:29 final size:27
Alignment explanation
Indices: 52798220--52798352 Score: 112
Period size: 28 Copynumber: 4.7 Consensus size: 27
52798210 GGAAATTCGG
*
52798220 GGGTAAAATGGTAATTTTGGTAAAATTA
1 GGGTAAAATGGTAATTTTGG-AAATTTA
52798248 GGGTTAAAATGG-AATTTTGGAAAGTTTGA
1 GGG-TAAAATGGTAATTTTGGAAA-TTT-A
**
52798277 GGGTAAAATGGTAATTTTTGGTGAAA-TCG
1 GGGTAAAATGGTAA-TTTT-G-GAAATTTA
52798306 GGGTTAAAAT-G-AGATTTTGGAAAGTTTAA
1 GGG-TAAAATGGTA-ATTTTGGAAA-TTT-A
52798335 GGGTAAAATGGTAATTTT
1 GGGTAAAATGGTAATTTT
52798353 TGGATAGTCC
Statistics
Matches: 86, Mismatches: 5, Indels: 27
0.73 0.04 0.23
Matches are distributed among these distances:
26 4 0.05
27 4 0.05
28 33 0.38
29 28 0.33
30 12 0.14
31 1 0.01
32 4 0.05
ACGTcount: A:0.35, C:0.01, G:0.29, T:0.35
Consensus pattern (27 bp):
GGGTAAAATGGTAATTTTGGAAATTTA
Found at i:52799155 original size:17 final size:15
Alignment explanation
Indices: 52799116--52799159 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
52799106 ATTTAATCTT
52799116 AAATTTAAATTTATA
1 AAATTTAAATTTATA
52799131 ATAGATTTAAATTGTATA
1 A-A-ATTTAAATT-TATA
52799149 CAAATTTAAAT
1 -AAATTTAAAT
52799160 CCAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.04
16 1 0.04
17 17 0.68
18 5 0.20
19 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (15 bp):
AAATTTAAATTTATA
Found at i:52802822 original size:18 final size:17
Alignment explanation
Indices: 52802791--52802825 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
52802781 GTTAAAATGA
52802791 AGTTTTATCATTTTAAT
1 AGTTTTATCATTTTAAT
*
52802808 AGTTTATATCTTTTTAAT
1 AGTTT-TATCATTTTAAT
52802826 TTTTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.60
Consensus pattern (17 bp):
AGTTTTATCATTTTAAT
Found at i:52804036 original size:15 final size:15
Alignment explanation
Indices: 52804016--52804044 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
52804006 ATATTTTTTC
52804016 ATTCTCTTTGCTTCG
1 ATTCTCTTTGCTTCG
52804031 ATTCTCTTTGCTTC
1 ATTCTCTTTGCTTC
52804045 TATAAGTCCT
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:0.07, C:0.28, G:0.10, T:0.55
Consensus pattern (15 bp):
ATTCTCTTTGCTTCG
Found at i:52806143 original size:19 final size:21
Alignment explanation
Indices: 52806121--52806170 Score: 68
Period size: 19 Copynumber: 2.4 Consensus size: 21
52806111 TAAAATTACA
*
52806121 TAAATATTTTT-C-TATTTTT
1 TAAATATTTTTACATAATTTT
52806140 TAAATATTTTTACATAATTTT
1 TAAATATTTTTACATAATTTT
52806161 TAAATTATTT
1 TAAA-TATTT
52806171 ATTGTTGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 11 0.41
20 1 0.04
21 10 0.37
22 5 0.19
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (21 bp):
TAAATATTTTTACATAATTTT
Found at i:52806454 original size:322 final size:326
Alignment explanation
Indices: 52805859--52806514 Score: 1115
Period size: 322 Copynumber: 2.0 Consensus size: 326
52805849 GAGGCCAAAT
*
52805859 ATATCAAAATCACCCACTTCTGTCTGAAAGCTTTTCAAATTATTCATTTTTTTTTTATAAATATA
1 ATATCAAAATCACCCACTTCTGTCTGAAAGCTTTTCAAATTATTCATTTTTTTTTGATAAATATA
52805924 CATGTAGTCAATCAAGCATTTCATGCAACCCCATTAAAAGTGTTTAAAAATAAGTACAAATAGTT
66 CATGTAGTCAATCAAGCATTTCATGCAACCCCATTAAAAGTGTTTAAAAATAAGTACAAATAGTT
52805989 GATGATACATTGGTTTAATGGTATGATGGAAACTTTAGCAACTTTTATTTCTACATTTAAAAATA
131 GATGATACATTGGTTTAATGGTATGATGGAAACTTTAGCAACTTTTATTTCTACATTTAAAAATA
* * * * *
52806054 TTATTTTTAAACATGATAACTCTCATGATAATCCATGTTTACTCCATTCTATTTTTTTAAAATTA
196 TTATTTTTAAACATGACAACTCGCATGATAATCCATGTGTACTCCATTCTATTCTTATAAAATTA
*
52806119 CATAAATATTTTTCT-A-T-TTTTTAAATATTTTTACATAATTTTTAAATTATTTATTGTTGTAA
261 CATAAACATTTTTCTAATTATTTTTAAATATTTTTACATAATTTTTAAATTATTTATTGTTGTAA
52806181 C
326 C
52806182 ATATCAAAATCACCCACTTCTGTCTGAAAGCTTTTCAAATTATTCA-TTTTTTTTGATAAATATA
1 ATATCAAAATCACCCACTTCTGTCTGAAAGCTTTTCAAATTATTCATTTTTTTTTGATAAATATA
52806246 CATGTAGTCAATCAAGCATTTCATGCAACCCCATTAAAAGTGTTTAAAAATAAGTACAAATAGTT
66 CATGTAGTCAATCAAGCATTTCATGCAACCCCATTAAAAGTGTTTAAAAATAAGTACAAATAGTT
52806311 GATGATACATTGGTTTAATGGTATGATGGAAACTTTAGCAACTTTTATTTCTACATTTAAAAATA
131 GATGATACATTGGTTTAATGGTATGATGGAAACTTTAGCAACTTTTATTTCTACATTTAAAAATA
* * *
52806376 TTATTTTTAAACATGGCAACTCGCATGGTAATCCATGTGTACTTCATGT-TATTCTTATAAAATT
196 TTATTTTTAAACATGACAACTCGCATGATAATCCATGTGTACTCCAT-TCTATTCTTATAAAATT
* *
52806440 ATATAAACATTTTTCTGAATTTTTATTTTTTAATATTTTTACATAATTTTTAAATTATTTATTGT
260 ACATAAACATTTTTCT-AA---TTATTTTTAAATATTTTTACATAATTTTTAAATTATTTATTGT
*
52806505 TGTGAC
321 TGTAAC
52806511 ATAT
1 ATAT
52806515 ACGATAAATA
Statistics
Matches: 312, Mismatches: 13, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
322 215 0.69
323 47 0.15
324 1 0.00
328 1 0.00
329 48 0.15
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (326 bp):
ATATCAAAATCACCCACTTCTGTCTGAAAGCTTTTCAAATTATTCATTTTTTTTTGATAAATATA
CATGTAGTCAATCAAGCATTTCATGCAACCCCATTAAAAGTGTTTAAAAATAAGTACAAATAGTT
GATGATACATTGGTTTAATGGTATGATGGAAACTTTAGCAACTTTTATTTCTACATTTAAAAATA
TTATTTTTAAACATGACAACTCGCATGATAATCCATGTGTACTCCATTCTATTCTTATAAAATTA
CATAAACATTTTTCTAATTATTTTTAAATATTTTTACATAATTTTTAAATTATTTATTGTTGTAA
C
Found at i:52811518 original size:45 final size:45
Alignment explanation
Indices: 52811461--52811635 Score: 157
Period size: 45 Copynumber: 4.0 Consensus size: 45
52811451 ACCGCTGCCG
*
52811461 CTGCCATTGCCACCTCCACTTTCAGTTCCAGAAGCACCCCAACCA
1 CTGCCACTGCCACCTCCACTTTCAGTTCCAGAAGCACCCCAACCA
* * * * * * **
52811506 CTGCCACCGCCACC-CCAAC---CACTGCC---ACCGCCACTGCCA
1 CTGCCACTGCCACCTCC-ACTTTCAGTTCCAGAAGCACCCCAACCA
* * ** *
52811545 TTGCCATTGCCATTTCCACTTTCAGTTCCAGAAGCACCCCAACCG
1 CTGCCACTGCCACCTCCACTTTCAGTTCCAGAAGCACCCCAACCA
*
52811590 CTGCCACTGCCACCTCCATTTTCAGTTCCAGAAGCACCCCAACCA
1 CTGCCACTGCCACCTCCACTTTCAGTTCCAGAAGCACCCCAACCA
52811635 C
1 C
52811636 CAGGGAAAGC
Statistics
Matches: 94, Mismatches: 28, Indels: 16
0.68 0.20 0.12
Matches are distributed among these distances:
39 19 0.20
40 2 0.02
42 10 0.11
44 2 0.02
45 61 0.65
ACGTcount: A:0.23, C:0.46, G:0.12, T:0.19
Consensus pattern (45 bp):
CTGCCACTGCCACCTCCACTTTCAGTTCCAGAAGCACCCCAACCA
Found at i:52811519 original size:21 final size:21
Alignment explanation
Indices: 52811495--52811539 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
52811485 GTTCCAGAAG
52811495 CACCCCAACCACTGCCACCGC
1 CACCCCAACCACTGCCACCGC
52811516 CACCCCAACCACTGCCACCGC
1 CACCCCAACCACTGCCACCGC
52811537 CAC
1 CAC
52811540 TGCCATTGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.24, C:0.62, G:0.09, T:0.04
Consensus pattern (21 bp):
CACCCCAACCACTGCCACCGC
Found at i:52834748 original size:38 final size:38
Alignment explanation
Indices: 52834695--52834777 Score: 121
Period size: 38 Copynumber: 2.2 Consensus size: 38
52834685 ATATTTTAAC
52834695 TTTTAAAATGATAAGATTTTAATTTAATCTTTTAAAAA
1 TTTTAAAATGATAAGATTTTAATTTAATCTTTTAAAAA
* * * *
52834733 TTTTAGAATGGTAAGATTTTAATTTGATTTTTTAAAAA
1 TTTTAAAATGATAAGATTTTAATTTAATCTTTTAAAAA
*
52834771 TTATAAA
1 TTTTAAA
52834778 GATATTACTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.42, C:0.01, G:0.08, T:0.48
Consensus pattern (38 bp):
TTTTAAAATGATAAGATTTTAATTTAATCTTTTAAAAA
Found at i:52840666 original size:12 final size:12
Alignment explanation
Indices: 52840625--52840666 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
52840615 ATAAAGGAAG
52840625 AAGAAAGAAAATTA
1 AAGAAA-AAAA-TA
52840639 AA-AAAAAAATA
1 AAGAAAAAAATA
52840650 GAAGAAAAAAATA
1 -AAGAAAAAAATA
52840663 AAGA
1 AAGA
52840667 GAGATGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.08
12 10 0.38
13 12 0.46
14 2 0.08
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.10
Consensus pattern (12 bp):
AAGAAAAAAATA
Found at i:52841287 original size:19 final size:21
Alignment explanation
Indices: 52841243--52841288 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
52841233 ATAGAGTGAC
52841243 TAAAAAATAAAATTAAACTAA
1 TAAAAAATAAAATTAAACTAA
* *
52841264 -CAAAAAT-AAATT-AATTAA
1 TAAAAAATAAAATTAAACTAA
52841282 TAAAAAA
1 TAAAAAA
52841289 ACTTCAACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
18 5 0.24
19 10 0.48
20 6 0.29
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAAAAATAAAATTAAACTAA
Found at i:52841864 original size:22 final size:20
Alignment explanation
Indices: 52841822--52841864 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
52841812 GAAATAACAA
*
52841822 TTAAAATTAAATTTTTAAAT
1 TTAAAATTAAATTATTAAAT
52841842 TTAAAATATAAATTGATTAAAT
1 TTAAAAT-TAAATT-ATTAAAT
52841864 T
1 T
52841865 CTTGAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 6 0.30
22 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
TTAAAATTAAATTATTAAAT
Found at i:52846199 original size:22 final size:22
Alignment explanation
Indices: 52846171--52846216 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
52846161 TATCTAGTTA
52846171 CATTAGATTAATCCATATCTAC
1 CATTAGATTAATCCATATCTAC
52846193 CATTAGATTAATCCATATCTAC
1 CATTAGATTAATCCATATCTAC
52846215 CA
1 CA
52846217 ATTTCAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (22 bp):
CATTAGATTAATCCATATCTAC
Found at i:52847109 original size:11 final size:11
Alignment explanation
Indices: 52847085--52847164 Score: 52
Period size: 11 Copynumber: 6.9 Consensus size: 11
52847075 ATTATTTCGC
* *
52847085 TATTATATTGT
1 TATTATTTTAT
52847096 TATTATTTTAT
1 TATTATTTTAT
*
52847107 TATTATTATTTAGA
1 TATTA-T-TTTA-T
* *
52847121 TATTATATAAT
1 TATTATTTTAT
*
52847132 TTTTATTTTAT
1 TATTATTTTAT
* *
52847143 TGTTAATTTTAC
1 TATT-ATTTTAT
52847155 TATTATTTTA
1 TATTATTTTA
52847165 GAGACATTTA
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
11 31 0.58
12 12 0.23
13 5 0.09
14 5 0.09
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:52847116 original size:36 final size:36
Alignment explanation
Indices: 52847074--52847143 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
52847064 GCTGCTTTGA
* * **
52847074 TATTATTTCGCTATTATATTGTTATTATTTTATTAT
1 TATTATTTAGATATTATATAATTATTATTTTATTAT
*
52847110 TATTATTTAGATATTATATAATTTTTATTTTATT
1 TATTATTTAGATATTATATAATTATTATTTTATT
52847144 GTTAATTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.64
Consensus pattern (36 bp):
TATTATTTAGATATTATATAATTATTATTTTATTAT
Found at i:52850121 original size:29 final size:28
Alignment explanation
Indices: 52850038--52850127 Score: 83
Period size: 30 Copynumber: 3.1 Consensus size: 28
52850028 ATCTATTTAG
*
52850038 TTTTTCAAAATTTTAAAATTAAAAAA-A
1 TTTTTTAAAATTTTAAAATTAAAAAATA
* * *
52850065 TATTTTTAAAAATTGAAAATCATTAAAAATA
1 T-TTTTTAAAATTTTAAAAT--TAAAAAATA
*
52850096 TTTTTTAATATTTTTAAAATTAAAAAAATA
1 TTTTTTAA-AATTTTAAAATT-AAAAAATA
52850126 TT
1 TT
52850128 GACATGTCAT
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
27 1 0.02
28 15 0.31
29 1 0.02
30 22 0.45
31 10 0.20
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (28 bp):
TTTTTTAAAATTTTAAAATTAAAAAATA
Found at i:52850850 original size:61 final size:58
Alignment explanation
Indices: 52850776--52851035 Score: 253
Period size: 61 Copynumber: 4.4 Consensus size: 58
52850766 GACACCATCT
* *
52850776 TTTTGTATCTGATAGAAAAGAA-TCAAAGTTTTTGGTGTTAGCCATTGCATGGTCGATACACC
1 TTTT-TATCTGATA-AAAA-AATTCAAATTTTTTGGTGTTGGCCATTGCATGG-CGA-ACACC
* * * *
52850838 TTTTTATCTGATAAAAAAATTTAAATTTTTTCTGTATTGGCCA-TGCATTGGC---CTCC
1 TTTTTATCTGATAAAAAAATTCAAATTTTTT-GGTGTTGGCCATTGCA-TGGCGAACACC
* * * *
52850894 TTTTTATCTGATAAAAAAAATCAAATATTTTGGTGTTGGCCATTGTATGACCGACATCACC
1 TTTTTATCTGATAAAAAAATTCAAATTTTTTGGTGTTGGCCATTGCATG-GCGA-A-CACC
*
52850955 TTTTTATCTGATAAAAAAATTCAAATTTTTTGGTGTTGGCCATTGCATGACCG-ACACTC
1 TTTTTATCTGATAAAAAAATTCAAATTTTTTGGTGTTGGCCATTGCATG-GCGAACAC-C
*
52851014 TTTTTTAACTGATAAAAAAATT
1 -TTTTTATCTGATAAAAAAATT
52851036 TATTTTTTTG
Statistics
Matches: 168, Mismatches: 18, Indels: 26
0.79 0.08 0.12
Matches are distributed among these distances:
55 11 0.07
56 35 0.21
58 3 0.02
59 4 0.02
60 38 0.23
61 73 0.43
62 4 0.02
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (58 bp):
TTTTTATCTGATAAAAAAATTCAAATTTTTTGGTGTTGGCCATTGCATGGCGAACACC
Found at i:52850936 original size:116 final size:119
Alignment explanation
Indices: 52850776--52851002 Score: 320
Period size: 117 Copynumber: 1.9 Consensus size: 119
52850766 GACACCATCT
* ** *
52850776 TTTTGTATCTGATAGAAAAGAATCAAAGTTTTTGGTGTTAGCCATTGCATGGTCGATA-CACCTT
1 TTTTGTATCTGATAGAAAAAAATCAAAGTTTTTGGTGTTAGCCATTGCATGACCGACATCACCTT
* *
52850840 TTTATCTGATAAAAAAATTTAAATTTTTTCTGTATTGGCCA-TGCATTGGCCTCC
66 TTTATCTGATAAAAAAATTCAAATTTTTT-GGTATTGGCCATTGCATTGGCCTCC
* *
52850894 TTTT-TATCTGATA-AAAAAAATCAAA-TATTTTGGTGTTGGCCATTGTATGACCGACATCACCT
1 TTTTGTATCTGATAGAAAAAAATCAAAGT-TTTTGGTGTTAGCCATTGCATGACCGACATCACCT
*
52850956 TTTTATCTGATAAAAAAATTCAAATTTTTTGGTGTTGGCCATTGCAT
65 TTTTATCTGATAAAAAAATTCAAATTTTTTGGTATTGGCCATTGCAT
52851003 GACCGACACT
Statistics
Matches: 97, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
115 1 0.01
116 44 0.45
117 48 0.49
118 4 0.04
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.40
Consensus pattern (119 bp):
TTTTGTATCTGATAGAAAAAAATCAAAGTTTTTGGTGTTAGCCATTGCATGACCGACATCACCTT
TTTATCTGATAAAAAAATTCAAATTTTTTGGTATTGGCCATTGCATTGGCCTCC
Found at i:52851041 original size:117 final size:116
Alignment explanation
Indices: 52850742--52851034 Score: 292
Period size: 117 Copynumber: 2.4 Consensus size: 116
52850732 AAAAACAAAA
* *
52850742 TTTGATGTTGGTCATTGCATGACTGACACCATCTTTTTGTATCTGATAGAAAAGAATCAA-AGTT
1 TTTGGTGTTGGCCATTGCATGAC-GACA-C-TCTTTTT-TATCTGATA-AAAA-AAT-AATA--T
** * *
52850806 TTTGGTGTTAGCCATTGCATGGTCGATACACCTTTTTATCTGATAAAAAAATTTAAATTT
57 TTTGGTGTTAGCCATTGCATGACCGACACACCTTTTTATCTGATAAAAAAATTCAAATTT
* * *
52850866 TTTCTGTATTGGCCA-TGCATTG--G-C-CTCCTTTTTATCTGATAAAAAAAATCAAATATTTTG
1 TTT-GGTGTTGGCCATTGCA-TGACGACACTCTTTTTTATCTGAT-AAAAAAAT--AATATTTTG
* *
52850926 GTGTTGGCCATTGTATGACCGACATCACCTTTTTATCTGATAAAAAAATTCAAATTT
61 GTGTTAGCCATTGCATGACCGACA-CACCTTTTTATCTGATAAAAAAATTCAAATTT
*
52850983 TTTGGTGTTGGCCATTGCATGACCGACACTCTTTTTTAACTGATAAAAAAAT
1 TTTGGTGTTGGCCATTGCATGA-CGACACTCTTTTTTATCTGATAAAAAAAT
52851035 TTATTTTTTT
Statistics
Matches: 141, Mismatches: 16, Indels: 28
0.76 0.09 0.15
Matches are distributed among these distances:
116 38 0.27
117 52 0.37
118 8 0.06
119 2 0.01
120 9 0.06
121 15 0.11
122 1 0.01
124 7 0.05
125 9 0.06
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (116 bp):
TTTGGTGTTGGCCATTGCATGACGACACTCTTTTTTATCTGATAAAAAAATAATATTTTGGTGTT
AGCCATTGCATGACCGACACACCTTTTTATCTGATAAAAAAATTCAAATTT
Found at i:52853148 original size:18 final size:18
Alignment explanation
Indices: 52853125--52853174 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
52853115 GAGAAACATG
52853125 GAAGGAGAAA-CCATGGGA
1 GAAGGAGAAATCC-TGGGA
*
52853143 GAAGGAGAAATGCTGGGA
1 GAAGGAGAAATCCTGGGA
*
52853161 GGAGGAGAAATCCT
1 GAAGGAGAAATCCT
52853175 AGAACGAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 27 0.96
19 1 0.04
ACGTcount: A:0.40, C:0.10, G:0.40, T:0.10
Consensus pattern (18 bp):
GAAGGAGAAATCCTGGGA
Found at i:52859048 original size:32 final size:32
Alignment explanation
Indices: 52859002--52859070 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
52858992 TTGCTAGAAA
52859002 TCAAACACTCGATTTTCCTACCGGTACTCAAT
1 TCAAACACTCGATTTTCCTACCGGTACTCAAT
* * * *
52859034 TCAAACGCTTGATTTTCCTACTGGTACTCGAT
1 TCAAACACTCGATTTTCCTACCGGTACTCAAT
52859066 TCAAA
1 TCAAA
52859071 ACTAAGAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.33
Consensus pattern (32 bp):
TCAAACACTCGATTTTCCTACCGGTACTCAAT
Found at i:52860121 original size:17 final size:17
Alignment explanation
Indices: 52860093--52860136 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
52860083 AACACAACAT
*
52860093 AAATTGAAAATTATTTAA
1 AAATT-AAAATTAATTAA
52860111 CAAA-TAAAATTAATTAA
1 -AAATTAAAATTAATTAA
52860128 AAATTAAAA
1 AAATTAAAA
52860137 AGAAAATAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 3 0.13
17 16 0.70
18 1 0.04
19 3 0.13
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (17 bp):
AAATTAAAATTAATTAA
Found at i:52864013 original size:4 final size:4
Alignment explanation
Indices: 52864004--52864038 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
52863994 TCTAGTTCAT
*
52864004 ATAC ATAC ATAC ATAC ATAC ATAC GTAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
52864039 TATGGAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.49, C:0.23, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:52869675 original size:22 final size:22
Alignment explanation
Indices: 52869630--52869676 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
52869620 TTTTTAAAAA
*
52869630 TTTAAAAAATATAAAAAATGTT
1 TTTAAAAAATATAAAAAATATT
* * *
52869652 TTTAAAAATTATCAAAATTATT
1 TTTAAAAAATATAAAAAATATT
52869674 TTT
1 TTT
52869677 TTATATTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
TTTAAAAAATATAAAAAATATT
Found at i:52883187 original size:2 final size:2
Alignment explanation
Indices: 52883180--52883208 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
52883170 AAATACTTAG
52883180 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52883209 TTCATTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52885560 original size:17 final size:17
Alignment explanation
Indices: 52885538--52885571 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
52885528 ATTGTATAAC
52885538 TTTTGTT-TTATTATTAA
1 TTTTGTTATTATT-TTAA
52885555 TTTTGTTATTATTTTAA
1 TTTTGTTATTATTTTAA
52885572 AGATATTTGC
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:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTTGTTATTATTTTAA
Found at i:52887206 original size:28 final size:24
Alignment explanation
Indices: 52887167--52887225 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 24
52887157 TGAAAAATAG
*
52887167 TAAAAAAATAATTAACTATATCATTATT
1 TAAAATAATAA-TAACT-TAT--TTATT
*
52887195 TATAATAATAATAACTTATTTATT
1 TAAAATAATAATAACTTATTTATT
52887219 TAAAATA
1 TAAAATA
52887226 TTCAAGTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 11 0.39
26 3 0.11
27 5 0.18
28 9 0.32
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (24 bp):
TAAAATAATAATAACTTATTTATT
Found at i:52895290 original size:23 final size:23
Alignment explanation
Indices: 52895257--52895377 Score: 154
Period size: 23 Copynumber: 5.3 Consensus size: 23
52895247 ACTAGCGCGT
* *
52895257 TCTCTGTTTAGCAC-GTCTCGTGC
1 TCTCTGATTAGCACTGTGT-GTGC
52895280 TCTCTGATTAGCACTGTGTGTGC
1 TCTCTGATTAGCACTGTGTGTGC
52895303 TCTCTGATTAGCACTGTGTGTGC
1 TCTCTGATTAGCACTGTGTGTGC
* * * *
52895326 TCTCTAATTAGTACTTTGTGTAC
1 TCTCTGATTAGCACTGTGTGTGC
* *
52895349 TCTCTGTTTAGTACTGTGTGTGC
1 TCTCTGATTAGCACTGTGTGTGC
52895372 TCTCTG
1 TCTCTG
52895378 TTGCCCAGCA
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
23 84 0.97
24 3 0.03
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (23 bp):
TCTCTGATTAGCACTGTGTGTGC
Found at i:52895368 original size:69 final size:66
Alignment explanation
Indices: 52895279--52895426 Score: 190
Period size: 69 Copynumber: 2.2 Consensus size: 66
52895269 ACGTCTCGTG
* *
52895279 CTCTCTGATTAGCACTGTGTGTGCTCTCTGATT-AGCACTGTGTGTGCTCTCTAATTAGTACTTT
1 CTCTCTGTTTAGCACTGTGTGTGCTCTCTG-TTCAGCACT-TATGTGCTCTCT-ATTAGTACTTT
52895343 GTGTA
63 G-GTA
* *
52895348 CTCTCTGTTTAGTACTGTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTGTTAGTACTTT
1 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGTT---CAGCACTTATGTGCTCTCTATTAGTACTTT
52895413 GGTA
63 GGTA
52895417 CTCTCTGTTT
1 CTCTCTGTTT
52895427 GTTCTGCATA
Statistics
Matches: 71, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
68 2 0.03
69 41 0.58
70 11 0.15
71 11 0.15
72 6 0.08
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (66 bp):
CTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTCAGCACTTATGTGCTCTCTATTAGTACTTTGGT
A
Found at i:52895378 original size:23 final size:23
Alignment explanation
Indices: 52895257--52895426 Score: 150
Period size: 23 Copynumber: 7.4 Consensus size: 23
52895247 ACTAGCGCGT
*
52895257 TCTCTGTTTAGCAC-GTCTCGTGC
1 TCTCTGTTTAGCACTGTGT-GTGC
*
52895280 TCTCTGATTAGCACTGTGTGTGC
1 TCTCTGTTTAGCACTGTGTGTGC
*
52895303 TCTCTGATTAGCACTGTGTGTGC
1 TCTCTGTTTAGCACTGTGTGTGC
** * * *
52895326 TCTCTAATTAGTACTTTGTGTAC
1 TCTCTGTTTAGCACTGTGTGTGC
*
52895349 TCTCTGTTTAGTACTGTGTGTGC
1 TCTCTGTTTAGCACTGTGTGTGC
* *
52895372 TCTCTGTTGCCCAGCACT-TATGTGC
1 TCTCTGTT---TAGCACTGTGTGTGC
* * *
52895397 TCTCTG-TTAGTACTTTG-GTAC
1 TCTCTGTTTAGCACTGTGTGTGC
52895418 TCTCTGTTT
1 TCTCTGTTT
52895427 GTTCTGCATA
Statistics
Matches: 124, Mismatches: 17, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
21 14 0.11
22 3 0.02
23 86 0.69
24 4 0.03
25 12 0.10
26 5 0.04
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (23 bp):
TCTCTGTTTAGCACTGTGTGTGC
Found at i:52898789 original size:41 final size:39
Alignment explanation
Indices: 52898728--52898823 Score: 99
Period size: 41 Copynumber: 2.4 Consensus size: 39
52898718 TTTTTGATAA
* *
52898728 TTTTTCAT-ATATTTTTAATTTGCTTTATAATTTT-TATG
1 TTTTT-ATAATATTTTTAATTTGATTAATAATTTTCTATG
*
52898766 CTTTTTATAATATTTTATAAATTTTATTAATAATTTTCTATG
1 -TTTTTATAATATTTT-T-AATTTGATTAATAATTTTCTATG
52898808 TTTTTA-AATATGTTTT
1 TTTTTATAATAT-TTTT
52898824 CATAATTTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
38 2 0.04
39 12 0.24
40 7 0.14
41 24 0.49
42 4 0.08
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (39 bp):
TTTTTATAATATTTTTAATTTGATTAATAATTTTCTATG
Found at i:52898811 original size:21 final size:20
Alignment explanation
Indices: 52898754--52898817 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 20
52898744 AATTTGCTTT
52898754 ATAATTTTTATGCTTTTTATA
1 ATAATTTTTATG-TTTTTATA
**
52898775 AT-A-TTTTATAAATTTTATTA
1 ATAATTTTTAT-GTTTTTA-TA
52898795 ATAATTTTCTATGTTTTTA-A
1 ATAATTTT-TATGTTTTTATA
52898815 ATA
1 ATA
52898818 TGTTTTCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 11
0.69 0.08 0.22
Matches are distributed among these distances:
19 11 0.32
20 9 0.26
21 3 0.09
22 8 0.24
23 3 0.09
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (20 bp):
ATAATTTTTATGTTTTTATA
Found at i:52898897 original size:23 final size:24
Alignment explanation
Indices: 52898871--52898916 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
52898861 ATATTTGTTA
52898871 TTTTAATAATTATTAAT-ATTTTCT
1 TTTTAA-AATTATTAATAATTTTCT
*
52898895 TTTTAAAATTTTTAATAATTTT
1 TTTTAAAATTATTAATAATTTT
52898917 ATAATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTTAAAATTATTAATAATTTTCT
Found at i:52898953 original size:9 final size:9
Alignment explanation
Indices: 52898718--52898954 Score: 66
Period size: 9 Copynumber: 25.7 Consensus size: 9
52898708 AAAAATGATT
52898718 TTTTTGATAA
1 TTTTT-ATAA
52898728 TTTTTCATATA
1 TTTTT-ATA-A
*
52898739 TTTTTA-AT
1 TTTTTATAA
52898747 TTGCTTTATAA
1 TT--TTTATAA
**
52898758 TTTTTATGC
1 TTTTTATAA
52898767 TTTTTATAA
1 TTTTTATAA
52898776 TATTTTATAAA
1 T-TTTTAT-AA
52898787 TTTTATTAATAA
1 -TTT-TT-ATAA
*
52898799 TTTTCTAT-G
1 TTTT-TATAA
*
52898808 TTTTTAAATA
1 TTTTTATA-A
52898818 TGTTTTCATAA
1 T-TTTT-ATAA
*
52898829 -TTTTACAA
1 TTTTTATAA
52898837 TTTTTAT-A
1 TTTTTATAA
*
52898845 TTTTTTTAA
1 TTTTTATAA
*
52898854 TTTATATATA
1 TTTTTATA-A
*
52898864 TTTGT-T-A
1 TTTTTATAA
*
52898871 TTTTAATAA
1 TTTTTATAA
*
52898880 -TTAT-TAA
1 TTTTTATAA
* *
52898887 TATTT-T-C
1 TTTTTATAA
*
52898894 TTTTTAAAA
1 TTTTTATAA
52898903 TTTTTAATAA
1 TTTTT-ATAA
52898913 -TTTTATAA
1 TTTTTATAA
52898921 TATTTT-TAA
1 T-TTTTATAA
* ***
52898930 ATGGAATATA
1 TTTTTATA-A
52898940 TTTTTATAA
1 TTTTTATAA
52898949 TTTTTA
1 TTTTTA
52898955 ATATAAAATA
Statistics
Matches: 164, Mismatches: 36, Indels: 55
0.64 0.14 0.22
Matches are distributed among these distances:
7 11 0.07
8 25 0.15
9 57 0.35
10 40 0.24
11 22 0.13
12 7 0.04
13 2 0.01
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:52903265 original size:17 final size:17
Alignment explanation
Indices: 52903243--52903277 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
52903233 CGAATAATAT
52903243 AATAAATATATT-TAAAA
1 AATAAATAT-TTATAAAA
52903260 AATAAATATTTATAAAA
1 AATAAATATTTATAAAA
52903277 A
1 A
52903278 TTTAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AATAAATATTTATAAAA
Found at i:52903456 original size:62 final size:62
Alignment explanation
Indices: 52903275--52903457 Score: 187
Period size: 62 Copynumber: 2.9 Consensus size: 62
52903265 ATATTTATAA
* *
52903275 AAATTTAATTTAATAGTTATCTCA-AT-AATATTTTATTAATTTAATATTAAAATAATTATTTAA
1 AAATTTAATTTAATATTTATAT-AGATAAATATTTTATTAATTTAATATT---A-AA--ATTTAA
52903338 TATT
59 TATT
* *
52903342 AAATCTAATTTAATGTTTATTTTATAGATAAATATTTTATTAATTT-A-A-TAAAATTTAATATT
1 AAATTTAATTTAATATTTA---TATAGATAAATATTTTATTAATTTAATATTAAAATTTAATATT
* *
52903404 AAATTTAATTTAATATTTATATTGATAAATATTATATTAATTTAATATTAAAAT
1 AAATTTAATTTAATATTTATATAGATAAATATTTTATTAATTTAATATTAAAAT
52903458 GATTAAATTT
Statistics
Matches: 100, Mismatches: 8, Indels: 21
0.78 0.06 0.16
Matches are distributed among these distances:
59 22 0.22
60 1 0.01
61 1 0.01
62 33 0.33
64 2 0.02
65 1 0.01
67 16 0.16
68 1 0.01
69 2 0.02
70 5 0.05
71 16 0.16
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (62 bp):
AAATTTAATTTAATATTTATATAGATAAATATTTTATTAATTTAATATTAAAATTTAATATT
Found at i:52905183 original size:39 final size:39
Alignment explanation
Indices: 52905129--52905323 Score: 191
Period size: 39 Copynumber: 5.0 Consensus size: 39
52905119 GACCTAACTG
*
52905129 ACCTAGAATAATCATCCCTTTTCAGATCATCTTTCTCCC
1 ACCTAGAATATTCATCCCTTTTCAGATCATCTTTCTCCC
* *
52905168 ACCTAGAATATTCATCCCTCTTCTGATCATCTTT-TCCCC
1 ACCTAGAATATTCATCCCTTTTCAGATCATCTTTCT-CCC
* * * ** *
52905207 ATCTAGAGTATTCAT-CCTTATTCCAG-TCACCCATCCCCC
1 ACCTAGAATATTCATCCCTT-TT-CAGATCATCTTTCTCCC
* * *
52905246 ACCTAGAATATTCAT-CCTTATTCCGCTCATCTTTCCCCC
1 ACCTAGAATATTCATCCCTT-TTCAGATCATCTTTCTCCC
* * *
52905285 ACCTAGAATATTCATCCCTATTCCGATCATCATTCTCCC
1 ACCTAGAATATTCATCCCTTTTCAGATCATCTTTCTCCC
52905324 CATAAGCTTT
Statistics
Matches: 129, Mismatches: 21, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
38 6 0.05
39 118 0.91
40 5 0.04
ACGTcount: A:0.23, C:0.36, G:0.06, T:0.35
Consensus pattern (39 bp):
ACCTAGAATATTCATCCCTTTTCAGATCATCTTTCTCCC
Found at i:52905260 original size:78 final size:78
Alignment explanation
Indices: 52905129--52905308 Score: 218
Period size: 78 Copynumber: 2.3 Consensus size: 78
52905119 GACCTAACTG
* * * ** * * *
52905129 ACCTAGAATAATCATCCCT-TTTCAGATCATCTTTCTCCCACCTAGAATATTCATCCCTCTTCTG
1 ACCTAGAATATTCATCCCTATTCCAG-TCACCCATCCCCCACCTAGAATATTCATCCCTATTCCG
*
52905193 ATCATCTTTTCCCC
65 ATCATCTTTCCCCC
* * * * *
52905207 ATCTAGAGTATTCATCCTTATTCCAGTCACCCATCCCCCACCTAGAATATTCATCCTTATTCCGC
1 ACCTAGAATATTCATCCCTATTCCAGTCACCCATCCCCCACCTAGAATATTCATCCCTATTCCGA
52905272 TCATCTTTCCCCC
66 TCATCTTTCCCCC
52905285 ACCTAGAATATTCATCCCTATTCC
1 ACCTAGAATATTCATCCCTATTCC
52905309 GATCATCATT
Statistics
Matches: 84, Mismatches: 17, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
78 79 0.94
79 5 0.06
ACGTcount: A:0.23, C:0.36, G:0.06, T:0.35
Consensus pattern (78 bp):
ACCTAGAATATTCATCCCTATTCCAGTCACCCATCCCCCACCTAGAATATTCATCCCTATTCCGA
TCATCTTTCCCCC
Found at i:52906203 original size:189 final size:188
Alignment explanation
Indices: 52905996--52906552 Score: 812
Period size: 189 Copynumber: 2.9 Consensus size: 188
52905986 CTATCCCTGC
* * * *
52905996 CTCTCCTCTGGCTCCCAGTCAACTCGATCTTCCCTTTCTGAACTTCACCTCTCTTCTTTTTCCTC
1 CTCTCCTCTGGCTCCCAGTCGACTCAATCTTCCCTTTTTGAACTTCACCTCTCTTCTTTTGCCTC
* * * * **
52906061 TCAACATCAGAATCAGAGTCATCTTCACTGGAGTCATTCCTACAACGACCTTTCTTAACCATTTC
66 CCACCATCAGAATCAGAGTCATCCTCACTGGAGTCATGCCTATGACGACCTTTCTTAACCATTTC
*
52906126 CTTCTTACGACCTCTTGCTCTGTCAGTATCAGAATCAGATTCACTACCCATGTCCCTCT
131 CTT-TTACGACCTCTTGCTCTGTCAGCATCAGAATCAGATTCACTACCCATGTCCCTCT
52906185 CTCTCCTCTGGCTCCCAGTCGACTCAATCTGT-CCTTTTTGAACTTCACCTCTCTTCTTTTGCCT
1 CTCTCCTCTGGCTCCCAGTCGACTCAATCT-TCCCTTTTTGAACTTCACCTCTCTTCTTTTGCCT
** **
52906249 CCCACCATCAGAATCA-AGGTTGTCCTCACTGGAGTTGTGCCTATGACGACCTTTCTTAACCATT
65 CCCACCATCAGAATCAGA-GTCATCCTCACTGGAGTCATGCCTATGACGACCTTTCTTAACCATT
*
52906313 TCCTTTCTATGACCTCTTGCTCTGTCAGCATCAGAATCAGATTCACTACCCATGTCCCTCT
129 TCCTTT-TACGACCTCTTGCTCTGTCAGCATCAGAATCAGATTCACTACCCATGTCCCTCT
* * * **
52906374 CTCTCCTCTGGCTCCTAGTTGACTCAATATTCTGTTTTTGAACTTCACCTCTCTTCTTTTGCCTC
1 CTCTCCTCTGGCTCCCAGTCGACTCAATCTTCCCTTTTTGAACTTCACCTCTCTTCTTTTGCCTC
* * * *
52906439 CCACCATCAGAATCAGAGTCACCCTCGCTGGAGTCATGCCTTTGATGACCTTTCTTAACCATTTC
66 CCACCATCAGAATCAGAGTCATCCTCACTGGAGTCATGCCTATGACGACCTTTCTTAACCATTTC
* *
52906504 CTTTTTACGACCTCTCGCTCTGTCAGCACCAGAATCAGATTCACTACCC
131 C-TTTTACGACCTCTTGCTCTGTCAGCATCAGAATCAGATTCACTACCC
52906553 TCAAACTTCT
Statistics
Matches: 330, Mismatches: 32, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
188 3 0.01
189 322 0.98
190 5 0.02
ACGTcount: A:0.19, C:0.34, G:0.12, T:0.35
Consensus pattern (188 bp):
CTCTCCTCTGGCTCCCAGTCGACTCAATCTTCCCTTTTTGAACTTCACCTCTCTTCTTTTGCCTC
CCACCATCAGAATCAGAGTCATCCTCACTGGAGTCATGCCTATGACGACCTTTCTTAACCATTTC
CTTTTACGACCTCTTGCTCTGTCAGCATCAGAATCAGATTCACTACCCATGTCCCTCT
Found at i:52915249 original size:18 final size:19
Alignment explanation
Indices: 52915218--52915258 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
52915208 TATTTATGAA
52915218 ATTTTTATA-ATTTTAATTT
1 ATTTTTATATATTTTAA-TT
*
52915237 ATTTTT-TATTTTTTAATT
1 ATTTTTATATATTTTAATT
52915255 ATTT
1 ATTT
52915259 GTTGACGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
ATTTTTATATATTTTAATT
Found at i:52923181 original size:24 final size:24
Alignment explanation
Indices: 52923153--52923215 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
52923143 AGAAATAATT
*
52923153 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTAGTTG
*
52923177 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAGTTAAACTCTGTTTAGTTG
* *
52923201 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
52923216 TATTACTCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.24, C:0.14, G:0.13, T:0.49
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTAGTTG
Found at i:52924616 original size:24 final size:24
Alignment explanation
Indices: 52924588--52924650 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
52924578 AGAAATAATC
52924588 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
*
52924612 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
* *
52924636 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
52924651 TATTACTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.24, C:0.14, G:0.11, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTATTTG
Found at i:52928112 original size:22 final size:21
Alignment explanation
Indices: 52928064--52928114 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
52928054 TTCAAGTTTT
52928064 TTTATTTTTAATCAATAAATA
1 TTTATTTTTAATCAATAAATA
*
52928085 TATTATTTTTAATTAA-AAACTCA
1 T-TTATTTTTAATCAATAAA-T-A
52928108 TTTATTT
1 TTTATTT
52928115 ATAAAATCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 4 0.15
22 20 0.77
23 2 0.08
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTATTTTTAATCAATAAATA
Found at i:52929182 original size:13 final size:13
Alignment explanation
Indices: 52929164--52929221 Score: 50
Period size: 13 Copynumber: 4.6 Consensus size: 13
52929154 CATGATTTAA
52929164 AATATTATAAATT
1 AATATTATAAATT
*
52929177 AATATTA-GAATAT
1 AATATTATAAAT-T
*
52929190 AATAATATAAATT
1 AATATTATAAATT
*
52929203 ATTATT-T-AATT
1 AATATTATAAATT
*
52929214 AGTATTAT
1 AATATTAT
52929222 TTTATTATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
11 9 0.25
12 5 0.14
13 19 0.53
14 3 0.08
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (13 bp):
AATATTATAAATT
Found at i:52929763 original size:18 final size:16
Alignment explanation
Indices: 52929734--52929768 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
52929724 TAAATGAGTT
52929734 AATTAGGTTAAATTGG
1 AATTAGGTTAAATTGG
52929750 AATTAAGGTATAAATTGG
1 AATT-AGGT-TAAATTGG
52929768 A
1 A
52929769 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 4 0.24
18 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.34
Consensus pattern (16 bp):
AATTAGGTTAAATTGG
Found at i:52932456 original size:23 final size:22
Alignment explanation
Indices: 52932415--52932460 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
52932405 ACCTATCCAA
* * *
52932415 TATATCTTATTAATGAACAGTAC
1 TATATCATATAAATAAACA-TAC
52932438 TATATCATATAAATAAACATAC
1 TATATCATATAAATAAACATAC
52932460 T
1 T
52932461 TCATTATCTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (22 bp):
TATATCATATAAATAAACATAC
Found at i:52938902 original size:17 final size:17
Alignment explanation
Indices: 52938880--52938919 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
52938870 TAAAATTGCT
*
52938880 ATATAAGTTTTAGG-TGA
1 ATATAAGTATT-GGATGA
52938897 ATATAAGTATTGGATGA
1 ATATAAGTATTGGATGA
52938914 ATATAA
1 ATATAA
52938920 CCCTTGAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 2 0.10
17 19 0.90
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (17 bp):
ATATAAGTATTGGATGA
Found at i:52938945 original size:10 final size:10
Alignment explanation
Indices: 52938930--52938955 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
52938920 CCCTTGAACT
52938930 ATTAAAAAGA
1 ATTAAAAAGA
52938940 ATTAAAAAGA
1 ATTAAAAAGA
52938950 ATTAAA
1 ATTAAA
52938956 TAAGTTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (10 bp):
ATTAAAAAGA
Found at i:52939479 original size:21 final size:21
Alignment explanation
Indices: 52939441--52939480 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
52939431 AAACTTTGAA
*
52939441 CCTAAACACTAAATCTCGAAT
1 CCTAAACACTAAACCTCGAAT
* *
52939462 CCTAAACATTGAACCTCGA
1 CCTAAACACTAAACCTCGA
52939481 CCTCAAATTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.30, G:0.07, T:0.23
Consensus pattern (21 bp):
CCTAAACACTAAACCTCGAAT
Found at i:52948677 original size:17 final size:17
Alignment explanation
Indices: 52948657--52948694 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
52948647 AAAGAATTTT
52948657 AAATAAAA-AACAATAAC
1 AAATAAAATAA-AATAAC
*
52948674 AAATAAAATAAAATAAG
1 AAATAAAATAAAATAAC
52948691 AAAT
1 AAAT
52948695 TAAGCCTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (17 bp):
AAATAAAATAAAATAAC
Found at i:52949080 original size:29 final size:27
Alignment explanation
Indices: 52949014--52949080 Score: 64
Period size: 31 Copynumber: 2.3 Consensus size: 27
52949004 AAGTTTTATG
* *
52949014 TGTATAATTGCATGAAATCAAAGTTTA
1 TGTATAATTGCATGAAATCAAAATTCA
52949041 TGTATCAAATTGCACATTG-AATCAAAATTCA
1 TGTAT--AATTG--CA-TGAAATCAAAATTCA
52949072 TGTATAATT
1 TGTATAATT
52949081 TTGATATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
27 5 0.15
29 9 0.27
31 17 0.52
32 2 0.06
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.37
Consensus pattern (27 bp):
TGTATAATTGCATGAAATCAAAATTCA
Found at i:52956775 original size:17 final size:17
Alignment explanation
Indices: 52956745--52956778 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
52956735 ATTTAAGTTA
**
52956745 TTTAAATTTTTAAAAAT
1 TTTAAATTAGTAAAAAT
52956762 TTTAAATTAGTAAAAAT
1 TTTAAATTAGTAAAAAT
52956779 AAAATTACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TTTAAATTAGTAAAAAT
Found at i:52957092 original size:16 final size:16
Alignment explanation
Indices: 52957061--52957090 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52957051 GAATAAATAT
52957061 TTAATTAATAATTTTA
1 TTAATTAATAATTTTA
52957077 TTAATTAA-AATTTT
1 TTAATTAATAATTTT
52957091 TAAACCCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTAATTAATAATTTTA
Found at i:52957305 original size:111 final size:113
Alignment explanation
Indices: 52957167--52957389 Score: 369
Period size: 111 Copynumber: 2.0 Consensus size: 113
52957157 TCTTCTTCCC
*
52957167 TTTTGATTCCAATATCTTTAGTTACAAATCTGTCTTAAAACTTGAATCTTTAAAACCCATTAACC
1 TTTTGATTCCAATATCTTTAGTTACAAATCTGTCTCAAAACTTGAATCTTTAAAACCCATTAACC
52957232 AAAAGATTCAATATCTTTGGTTCCAATATC-T-TTCCCGTTAAGTTTT
66 AAAAGATTCAATATCTTTGGTTCCAATATCTTCTTCCCGTTAAGTTTT
* * * ** *
52957278 TTTTTATTCTAATATCTTTAGTTACAAATTTGTCTCAAAGTTTGAATCTTTAAAATCCATTAACC
1 TTTTGATTCCAATATCTTTAGTTACAAATCTGTCTCAAAACTTGAATCTTTAAAACCCATTAACC
52957343 AAAAGATTCAATATCTTTGGTTCCAATATCTTCTTCCCGTTAAGTTT
66 AAAAGATTCAATATCTTTGGTTCCAATATCTTCTTCCCGTTAAGTTT
52957390 CTTTAGGTTA
Statistics
Matches: 103, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
111 88 0.85
112 1 0.01
113 14 0.14
ACGTcount: A:0.31, C:0.18, G:0.08, T:0.43
Consensus pattern (113 bp):
TTTTGATTCCAATATCTTTAGTTACAAATCTGTCTCAAAACTTGAATCTTTAAAACCCATTAACC
AAAAGATTCAATATCTTTGGTTCCAATATCTTCTTCCCGTTAAGTTTT
Found at i:52963977 original size:19 final size:19
Alignment explanation
Indices: 52963936--52963976 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
52963926 TAATTAACAA
52963936 TTTTAATAATTTTCATAAT
1 TTTTAATAATTTTCATAAT
* *
52963955 TTTTCATAATTTT-ACAAT
1 TTTTAATAATTTTCATAAT
52963973 TTTT
1 TTTT
52963977 TATCTTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTAATAATTTTCATAAT
Found at i:52963992 original size:2 final size:2
Alignment explanation
Indices: 52963987--52964029 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
52963977 TATCTTTTTG
52963987 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52964029 T
1 T
52964030 TATTTTAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:52964114 original size:19 final size:18
Alignment explanation
Indices: 52964086--52964138 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 18
52964076 TTTTGTTCCA
52964086 TTTATAATATTTTTTAAATT
1 TTTAT-ATATTTTTT-AATT
52964106 TTTATATATTATTATT-ATT
1 TTTATATATT-TT-TTAATT
52964125 TTTATA-ATTTTTTA
1 TTTATATATTTTTTA
52964139 TGACTTATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
16 2 0.07
17 2 0.07
18 3 0.10
19 14 0.47
20 7 0.23
21 2 0.07
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTATATATTTTTTAATT
Found at i:52965905 original size:160 final size:160
Alignment explanation
Indices: 52965714--52966036 Score: 547
Period size: 160 Copynumber: 2.0 Consensus size: 160
52965704 CTTCGAAATT
** * * *
52965714 TAACAAATCCATAGGATTATGTACCAATAAAAGCTTATTTCTGAAATTATTTATTGAAATAGTTC
1 TAACAAATCCATAGGATTATGTAAAAATAAAAGCTTATTACCGAAATTATTTATTGAAATAGATC
*
52965779 AAAAAGAAAAATAATTATTAGAATGGGTCACTTTTGCAAAAATGCGTCTATGTGATGTCGTTTTC
66 AAAAAGAAAAATAATTATTAGAATGGGTCACTTTTACAAAAATGCGTCTATGTGATGTCGTTTTC
*
52965844 AAGGGTTTTTTCATAAAAAGCATTTTAATG
131 AAGGGTTTTTTCATAAAAAGCATTTCAATG
*
52965874 TAACAAATCCATAGGGTTATGTAAAAATAAAAGCTTATTACCGAAATTATTTATTGAAATAGATC
1 TAACAAATCCATAGGATTATGTAAAAATAAAAGCTTATTACCGAAATTATTTATTGAAATAGATC
* * *
52965939 AAAAGGAAAAATAATTATTGGAATGGGTCACTTTTACAAAAATGCGTCTATGTGATGTTGTTTTC
66 AAAAAGAAAAATAATTATTAGAATGGGTCACTTTTACAAAAATGCGTCTATGTGATGTCGTTTTC
52966004 AAGGGTTTTTTCATAAAAAGCATTTCAATG
131 AAGGGTTTTTTCATAAAAAGCATTTCAATG
52966034 TAA
1 TAA
52966037 AAGCTTTTGT
Statistics
Matches: 152, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
160 152 1.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.35
Consensus pattern (160 bp):
TAACAAATCCATAGGATTATGTAAAAATAAAAGCTTATTACCGAAATTATTTATTGAAATAGATC
AAAAAGAAAAATAATTATTAGAATGGGTCACTTTTACAAAAATGCGTCTATGTGATGTCGTTTTC
AAGGGTTTTTTCATAAAAAGCATTTCAATG
Found at i:52966344 original size:21 final size:22
Alignment explanation
Indices: 52966318--52966358 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
52966308 ACAAATATAT
*
52966318 TATATATTAT-TTTTTAAAATA
1 TATATATAATCTTTTTAAAATA
52966339 TATATATAATCTTTTTAAAA
1 TATATATAATCTTTTTAAAA
52966359 AATAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
TATATATAATCTTTTTAAAATA
Found at i:52966362 original size:24 final size:24
Alignment explanation
Indices: 52966310--52966359 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
52966300 AGATAGAAAC
* *
52966310 AAATATATTATATATTATTTTTTA
1 AAATATATTATATAATATTTTTAA
*
52966334 AAATATA-TATATAATCTTTTTAA
1 AAATATATTATATAATATTTTTAA
52966357 AAA
1 AAA
52966360 ATAAATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
AAATATATTATATAATATTTTTAA
Found at i:52973352 original size:27 final size:28
Alignment explanation
Indices: 52973320--52973376 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
52973310 TTTTATATTT
* *
52973320 TTTAAAAGATTAAATTA-AATTTTATCA
1 TTTAAAAGACTAAAATATAATTTTATCA
* *
52973347 TTTAAAGGGCTAAAATATAATTTTATCA
1 TTTAAAAGACTAAAATATAATTTTATCA
52973375 TT
1 TT
52973377 ATTAATTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (28 bp):
TTTAAAAGACTAAAATATAATTTTATCA
Found at i:52982123 original size:29 final size:29
Alignment explanation
Indices: 52982081--52982137 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
52982071 AGAAACTCTT
52982081 AATTATTGCAATTGTTCTTGAGTAGCAAC
1 AATTATTGCAATTGTTCTTGAGTAGCAAC
* * *
52982110 AATTATTTCTATTGTTCTTGATTAGCAA
1 AATTATTGCAATTGTTCTTGAGTAGCAA
52982138 AAAAAGGTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (29 bp):
AATTATTGCAATTGTTCTTGAGTAGCAAC
Found at i:52995868 original size:22 final size:23
Alignment explanation
Indices: 52995842--52995885 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
52995832 TTTCTTTTTG
* *
52995842 AAAAGCA-ATTATTAAAATTAGA
1 AAAAGCATAATATCAAAATTAGA
52995864 AAAAGCATAATATCAAAATTAG
1 AAAAGCATAATATCAAAATTAG
52995886 TCTTTAACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.59, C:0.07, G:0.09, T:0.25
Consensus pattern (23 bp):
AAAAGCATAATATCAAAATTAGA
Found at i:53002156 original size:21 final size:21
Alignment explanation
Indices: 53002113--53002156 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
53002103 TGGTTATTAT
* * *
53002113 ATACCTATAATAACATTTGAG
1 ATACCTATAACAACATCTAAG
*
53002134 ATACTTATAACAACATCTAAG
1 ATACCTATAACAACATCTAAG
53002155 AT
1 AT
53002157 TTATATTATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.32
Consensus pattern (21 bp):
ATACCTATAACAACATCTAAG
Found at i:53003271 original size:22 final size:20
Alignment explanation
Indices: 53003228--53003274 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
53003218 AGAATAGTTG
* *
53003228 TAAAGTTTTGTTTTTCTTTT
1 TAAAATTTTGTTTTTATTTT
53003248 TAAAATTTTGATTATTTATTTT
1 TAAAATTTTG-TT-TTTATTTT
53003270 TAAAA
1 TAAAA
53003275 ATTTACATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 9 0.39
21 2 0.09
22 12 0.52
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (20 bp):
TAAAATTTTGTTTTTATTTT
Found at i:53008853 original size:16 final size:16
Alignment explanation
Indices: 53008821--53008858 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
53008811 GAGACTAAAA
53008821 TTATAATATTATGATAT
1 TTAT-ATATTATGATAT
53008838 TTATATATTGAT-ATAT
1 TTATATATT-ATGATAT
53008854 TTATA
1 TTATA
53008859 AACACATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (16 bp):
TTATATATTATGATAT
Done.