Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012859.1 Kokia drynarioides strain JFW-HI SEQ_127873, whole genome shotgun sequence
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: 286603
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 130 characters in sequence are not A, C, G, or T
Found at i:602 original size:2 final size:2
Alignment explanation
Indices: 595--630 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
585 AACTCAGACA
595 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
631 GGCCACTACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:23698 original size:29 final size:28
Alignment explanation
Indices: 23666--23728 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
23656 AAAATGAGAC
* *
23666 TTTTTGGATACTTGGGGGCAAAATGGTA
1 TTTTTGGATACTCGAGGGCAAAATGGTA
* *
23694 ATTTTGGATTCTCGAGGGCAAAATGGTA
1 TTTTTGGATACTCGAGGGCAAAATGGTA
23722 TTTTTGG
1 TTTTTGG
23729 GAAATTTTGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.24, C:0.08, G:0.30, T:0.38
Consensus pattern (28 bp):
TTTTTGGATACTCGAGGGCAAAATGGTA
Found at i:23891 original size:59 final size:60
Alignment explanation
Indices: 23828--23960 Score: 173
Period size: 58 Copynumber: 2.3 Consensus size: 60
23818 ATTCGAAGGC
** * * *
23828 AAAATGGTAATTTTTGAAAGTTTTGGGGTTAAAAATGGAAGTTTTGGAGGTTCG-GGGTA
1 AAAATGGTAATTTTTGAAAGTTTTAAGGTCAAAAATGGAAGTTTTGGAAGCTCGAGGGTA
* * *
23887 AAAATGG-AATTTTTGGAAGTTTTAAGGTCGAAAATGGAATTTTTGGAAGCTCGAGGGTA
1 AAAATGGTAATTTTTGAAAGTTTTAAGGTCAAAAATGGAAGTTTTGGAAGCTCGAGGGTA
23946 AAAAT-GTAATTTTTG
1 AAAATGGTAATTTTTG
23961 GATAGTTTAG
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
58 39 0.61
59 25 0.39
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (60 bp):
AAAATGGTAATTTTTGAAAGTTTTAAGGTCAAAAATGGAAGTTTTGGAAGCTCGAGGGTA
Found at i:23950 original size:29 final size:29
Alignment explanation
Indices: 23828--23967 Score: 131
Period size: 30 Copynumber: 4.7 Consensus size: 29
23818 ATTCGAAGGC
* *
23828 AAAATGGTAATTTTTGAAAGTTTTG-GGGTTA
1 AAAATGG-AATTTTTGGAAG-TTCGAGGG-TA
* *
23859 AAAATGGAAGTTTTGGAGGTTCG-GGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
** * *
23887 AAAATGGAATTTTTGGAAGTTTTAAGGTCG
1 AAAATGGAATTTTTGGAAGTTCGAGGGT-A
*
23917 AAAATGGAATTTTTGGAAGCTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
*
23946 AAAATGTAATTTTTGGATAGTT
1 AAAATGGAATTTTTGGA-AGTT
23968 TAGGGACCTT
Statistics
Matches: 89, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
28 21 0.24
29 25 0.28
30 36 0.40
31 7 0.08
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.36
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTA
Found at i:25083 original size:3 final size:3
Alignment explanation
Indices: 25030--25070 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
25020 TATTAAAAAC
25030 ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
25071 AAAACAATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:25778 original size:6 final size:6
Alignment explanation
Indices: 25767--25861 Score: 67
Period size: 6 Copynumber: 16.7 Consensus size: 6
25757 TTTTTGCATT
* * *
25767 AATTTA AATTTA AATTT- AACTCA AATTTA TAA--TA AATTTA AATTTT
1 AATTTA AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AATTTA
* * * * *
25813 AA-GTA AATTTA AACTTA AA-ATA AATTTA ATTTTA AA-ATA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
25858 AATT
1 AATT
25862 CTGTTGGGCC
Statistics
Matches: 67, Mismatches: 15, Indels: 14
0.70 0.16 0.15
Matches are distributed among these distances:
4 2 0.03
5 16 0.24
6 47 0.70
7 2 0.03
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:25809 original size:17 final size:17
Alignment explanation
Indices: 25767--25861 Score: 109
Period size: 17 Copynumber: 5.6 Consensus size: 17
25757 TTTTTGCATT
* *
25767 AATTTAAATTTAAATTT
1 AATTTAAATTTAAAATA
* * *
25784 AACTCAAATTTATAATA
1 AATTTAAATTTAAAATA
* *
25801 AATTTAAATTTTAAGTA
1 AATTTAAATTTAAAATA
*
25818 AATTTAAACTTAAAATA
1 AATTTAAATTTAAAATA
*
25835 AATTTAATTTTAAAATA
1 AATTTAAATTTAAAATA
25852 AATTTAAATT
1 AATTTAAATT
25862 CTGTTGGGCC
Statistics
Matches: 62, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 62 1.00
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:26633 original size:323 final size:323
Alignment explanation
Indices: 26045--26690 Score: 1211
Period size: 323 Copynumber: 2.0 Consensus size: 323
26035 TTCACCTTTC
26045 CACTTCTTTGAGGTGGTGGTTCCATCTTACCCCTAGGCAATTTTAAAAAGACAAAATTTGCTACT
1 CACTTCTTTGAGGTGGTGGTTCCATCTTACCCCTAGGCAATTTTAAAAAGACAAAATTTGCTACT
* * *
26110 ATAATTTCACTTCATTCTCTTGAATTTTCAAAGAGATTGGGATTCGTCATCGTAGCCTTTTGGGT
66 ATAATTTCACTCCATTCTATTGAATTTTCAAAGAGATTGGGATTCGTCATCATAGCCTTTTGGGT
26175 CTGGTTTCATTGACTTGGCCTTCTTCTCAGTATCTCATTGGGAAGATGACCGCATCACTTGTTTT
131 CTGGTTTCATTGACTTGGCCTTCTTCTCAGTATCTCATTGGGAAGATGACCGCATCACTTGTTTT
* *
26240 GATCCACTTCTCTATGTTTCATCAAGAAGACGAATTTGGTTCACTTCTCCGTATCTCATCAAGAA
196 GATCCACTACTCTATGTTTCATCAAGAAGACAAATTTGGTTCACTTCTCCGTATCTCATCAAGAA
* *
26305 GCTAACCACTTTATTGCTTTAACTTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAGGA
261 GCTAACCACTTTATTGCTTCAACTTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAGGA
*
26368 CACTTCTTTGATGTGGTGGTTCCATCTTACCCCTAGGCAATTTTAAAAAGACAAAATTTGCTACT
1 CACTTCTTTGAGGTGGTGGTTCCATCTTACCCCTAGGCAATTTTAAAAAGACAAAATTTGCTACT
*
26433 GTAATTTCACTCCATTCTATTGAATTTTCAAAGAGATTGGGATTCGTCATCATAGCCTTTTGGGT
66 ATAATTTCACTCCATTCTATTGAATTTTCAAAGAGATTGGGATTCGTCATCATAGCCTTTTGGGT
26498 CTGGTTTCATTGACTTGGCCTTCTTCTCAGTATCTCATTGGGAAGATGACCGCATCACTTGTTTT
131 CTGGTTTCATTGACTTGGCCTTCTTCTCAGTATCTCATTGGGAAGATGACCGCATCACTTGTTTT
26563 GATCCACTACTCTATGTTTCATCAAGAAGACAAATTTGGTTCACTTCTCCGTATCTCATCAAGAA
196 GATCCACTACTCTATGTTTCATCAAGAAGACAAATTTGGTTCACTTCTCCGTATCTCATCAAGAA
26628 GCTAACCACTTTATTGCTTCAACTTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAGGA
261 GCTAACCACTTTATTGCTTCAACTTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAGGA
26691 TTTGCTCTCA
Statistics
Matches: 314, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
323 314 1.00
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (323 bp):
CACTTCTTTGAGGTGGTGGTTCCATCTTACCCCTAGGCAATTTTAAAAAGACAAAATTTGCTACT
ATAATTTCACTCCATTCTATTGAATTTTCAAAGAGATTGGGATTCGTCATCATAGCCTTTTGGGT
CTGGTTTCATTGACTTGGCCTTCTTCTCAGTATCTCATTGGGAAGATGACCGCATCACTTGTTTT
GATCCACTACTCTATGTTTCATCAAGAAGACAAATTTGGTTCACTTCTCCGTATCTCATCAAGAA
GCTAACCACTTTATTGCTTCAACTTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAGGA
Found at i:26813 original size:120 final size:119
Alignment explanation
Indices: 26596--26868 Score: 345
Period size: 120 Copynumber: 2.3 Consensus size: 119
26586 AAGAAGACAA
* * *
26596 ATTTGGTTCACTTCTCCGTATCTCATCAAGAAGCTAACCACTTTATTGCTTCAACTTGCTTCTCA
1 ATTTGG-TCACTTCTCAGTATCTCATCAGGAAGCTAACCACTTTATTGCTTCAACTTGCCTCTCA
* * * *
26661 GTATCTCATCAGGAAGCTGAGGTTCGAGGATTTGCTCTCATCGAGCGTGGGTTTG
65 GTATCTCATCAAGAAGCTGAGGTTCGAAGATTTGCTCACATCGAGCGTGGGGTTG
*
26716 ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTG-TTCCAA-TCTGCCTCT
1 ATTTGGT-CACTTCTCAGTATCTCATCAGGAAGCTAACCACTTTATTGCTT-CAACT-TGCCTCT
* * *
26779 CAGTGTCTTATTAAGAAGCT-AGGTTTCGAAGATTTGCTCACATCGAGCGTGGGGTTG
63 CAGTATCTCATCAAGAAGCTGAGG-TTCGAAGATTTGCTCACATCGAGCGTGGGGTTG
* * *
26836 GTTTGGTCATCTTCTCAGTATTTTATCAGGAAG
1 ATTTGGTCA-CTTCTCAGTATCTCATCAGGAAG
26869 ATGACCGCGT
Statistics
Matches: 134, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
119 9 0.07
120 125 0.93
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.36
Consensus pattern (119 bp):
ATTTGGTCACTTCTCAGTATCTCATCAGGAAGCTAACCACTTTATTGCTTCAACTTGCCTCTCAG
TATCTCATCAAGAAGCTGAGGTTCGAAGATTTGCTCACATCGAGCGTGGGGTTG
Found at i:27075 original size:204 final size:204
Alignment explanation
Indices: 26716--27288 Score: 770
Period size: 204 Copynumber: 2.8 Consensus size: 204
26706 CGTGGGTTTG
* * *
26716 ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTG-TTCCAATCTGCCTCTC
1 ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAA-CATTTTATTGCTT-CGACCTGCTTCTC
* * * * *
26780 AGTGTCTTATTAAGAAGCTAGGTTTCGAAGATTTGCTCACATCGAGCGTGGGGTTGGTTTGGTCA
64 AGTGTCTCATCAAGAAG-TTGGGTTCGAAGATTTGCTCACATCGAGCGTGGGGTTGGTTTGGTCT
* * * ** * *
26845 TCTTCTCAGTATTTTATCAGGAAGATGACCGCGTCGTTTGTTTCAATTTGTTTCTCTGTATCTCA
128 TCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATTCGTTTCCCTGTATCTCA
26910 TCAGGAAGACGA
193 TCAGGAAGACGA
* * * * **
26922 ATTTGGTCAAATTCTTAGTATCTTATCAGGAAGCTAACATTTTATTGCTTCGACCTATTTCTCAG
1 ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACATTTTATTGCTTCGACCTGCTTCTCAG
*
26987 TGTCTCATCATGAAGTTGGGTTCGAAGATTTGCTCACATCGAGCGTGGGGTTGGTTTGGTCTTCT
66 TGTCTCATCAAGAAGTTGGGTTCGAAGATTTGCTCACATCGAGCGTGGGGTTGGTTTGGTCTTCT
* * *
27052 TCTCAGTATCTCATGAAGAAGATGGCCGCATCACTTGTTTCAATTCGTTTCCCTGTATCTCATCA
131 TCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATTCGTTTCCCTGTATCTCATCA
27117 GGAAGACGA
196 GGAAGACGA
* ** * *
27126 ATTTGGTCCACTTCTCAGTACCTCATCAATAAGCTAACCTTTTATTGCTTCGACCTGCTTCTTAG
1 ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACATTTTATTGCTTCGACCTGCTTCTCAG
* * * * *
27191 TGTCTCATCAGGAAGGTTGGGTTCGAAGATTTGCTCAAATCGAGCGTGGGTTTGATTTAGTCTTC
66 TGTCTCATCAAGAA-GTTGGGTTCGAAGATTTGCTCACATCGAGCGTGGGGTTGGTTTGGTCTTC
* *
27256 TTCTCAGTATCTCGTTAGGAAGATGACCGCATC
130 TTCTCAGTATCTCATCAGGAAGATGACCGCATC
27289 GCTGTTTGTG
Statistics
Matches: 320, Mismatches: 45, Indels: 5
0.86 0.12 0.01
Matches are distributed among these distances:
204 178 0.56
205 107 0.33
206 35 0.11
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (204 bp):
ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACATTTTATTGCTTCGACCTGCTTCTCAG
TGTCTCATCAAGAAGTTGGGTTCGAAGATTTGCTCACATCGAGCGTGGGGTTGGTTTGGTCTTCT
TCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATTCGTTTCCCTGTATCTCATCA
GGAAGACGA
Found at i:29354 original size:120 final size:119
Alignment explanation
Indices: 29137--29409 Score: 345
Period size: 120 Copynumber: 2.3 Consensus size: 119
29127 NNNNNNNNNA
* * *
29137 ATTTGGTTCACTTCTCCGTATCTCATCAAGAAGCTAACCACTTTATTGCTTCAACTTGCTTCTCA
1 ATTTGG-TCACTTCTCAGTATCTCATCAGGAAGCTAACCACTTTATTGCTTCAACTTGCCTCTCA
* * * *
29202 GTATCTCATCAGGAAGCTGAGGTTCGAGGATTTGCTCTCATCGAGCGTGGGTTTG
65 GTATCTCATCAAGAAGCTGAGGTTCGAAGATTTGCTCACATCGAGCGTGGGGTTG
*
29257 ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTG-TTCCAA-TCTGCCTCT
1 ATTTGGT-CACTTCTCAGTATCTCATCAGGAAGCTAACCACTTTATTGCTT-CAACT-TGCCTCT
* * *
29320 CAGTGTCTTATTAAGAAGCT-AGGTTTCGAAGATTTGCTCACATCGAGCGTGGGGTTG
63 CAGTATCTCATCAAGAAGCTGAGG-TTCGAAGATTTGCTCACATCGAGCGTGGGGTTG
* * *
29377 GTTTGGTCATCTTCTCAGTATTTTATCAGGAAG
1 ATTTGGTCA-CTTCTCAGTATCTCATCAGGAAG
29410 ATGACCGCGT
Statistics
Matches: 134, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
119 9 0.07
120 125 0.93
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.36
Consensus pattern (119 bp):
ATTTGGTCACTTCTCAGTATCTCATCAGGAAGCTAACCACTTTATTGCTTCAACTTGCCTCTCAG
TATCTCATCAAGAAGCTGAGGTTCGAAGATTTGCTCACATCGAGCGTGGGGTTG
Found at i:29616 original size:204 final size:204
Alignment explanation
Indices: 29257--29829 Score: 770
Period size: 204 Copynumber: 2.8 Consensus size: 204
29247 CGTGGGTTTG
* * *
29257 ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTG-TTCCAATCTGCCTCTC
1 ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAA-CATTTTATTGCTT-CGACCTGCTTCTC
* * * * *
29321 AGTGTCTTATTAAGAAGCTAGGTTTCGAAGATTTGCTCACATCGAGCGTGGGGTTGGTTTGGTCA
64 AGTGTCTCATCAAGAAG-TTGGGTTCGAAGATTTGCTCACATCGAGCGTGGGGTTGGTTTGGTCT
* * * ** * *
29386 TCTTCTCAGTATTTTATCAGGAAGATGACCGCGTCGTTTGTTTCAATTTGTTTCTCTGTATCTCA
128 TCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATTCGTTTCCCTGTATCTCA
29451 TCAGGAAGACGA
193 TCAGGAAGACGA
* * * * **
29463 ATTTGGTCAAATTCTTAGTATCTTATCAGGAAGCTAACATTTTATTGCTTCGACCTATTTCTCAG
1 ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACATTTTATTGCTTCGACCTGCTTCTCAG
*
29528 TGTCTCATCATGAAGTTGGGTTCGAAGATTTGCTCACATCGAGCGTGGGGTTGGTTTGGTCTTCT
66 TGTCTCATCAAGAAGTTGGGTTCGAAGATTTGCTCACATCGAGCGTGGGGTTGGTTTGGTCTTCT
* * *
29593 TCTCAGTATCTCATGAAGAAGATGGCCGCATCACTTGTTTCAATTCGTTTCCCTGTATCTCATCA
131 TCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATTCGTTTCCCTGTATCTCATCA
29658 GGAAGACGA
196 GGAAGACGA
* ** * *
29667 ATTTGGTCCACTTCTCAGTACCTCATCAATAAGCTAACCTTTTATTGCTTCGACCTGCTTCTTAG
1 ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACATTTTATTGCTTCGACCTGCTTCTCAG
* * * * *
29732 TGTCTCATCAGGAAGGTTGGGTTCGAAGATTTGCTCAAATCGAGCGTGGGTTTGATTTAGTCTTC
66 TGTCTCATCAAGAA-GTTGGGTTCGAAGATTTGCTCACATCGAGCGTGGGGTTGGTTTGGTCTTC
* *
29797 TTCTCAGTATCTCGTTAGGAAGATGACCGCATC
130 TTCTCAGTATCTCATCAGGAAGATGACCGCATC
29830 GCTGTTTGTG
Statistics
Matches: 320, Mismatches: 45, Indels: 5
0.86 0.12 0.01
Matches are distributed among these distances:
204 178 0.56
205 107 0.33
206 35 0.11
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (204 bp):
ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACATTTTATTGCTTCGACCTGCTTCTCAG
TGTCTCATCAAGAAGTTGGGTTCGAAGATTTGCTCACATCGAGCGTGGGGTTGGTTTGGTCTTCT
TCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATTCGTTTCCCTGTATCTCATCA
GGAAGACGA
Found at i:41185 original size:96 final size:96
Alignment explanation
Indices: 41008--41188 Score: 242
Period size: 96 Copynumber: 1.9 Consensus size: 96
40998 AGGATGCTTG
* * * * *
41008 ATTATCTCGATTTGAGGAAAAGTTGCACCTAGTAAGTTAAGGCGCAAATTTTCATAATCGAAGAT
1 ATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGACGCAAATTTTCATAATCCAAGAT
*
41073 AAGGACACATTGCCTCGATTAAGGGTATTCA
66 AAGGACACATTACCTCGATTAAGGGTATTCA
*
41104 ATTATTTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGACGCAAATTTTCGA-AACTCCAA-
1 ATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGACGCAAATTTTC-ATAA-TCCAAG
*
41167 ATAAGAGA-ATATTACCTCGATT
64 ATAAG-GACACATTACCTCGATT
41189 TTAAAGTTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
96 67 0.91
97 7 0.09
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (96 bp):
ATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGACGCAAATTTTCATAATCCAAGAT
AAGGACACATTACCTCGATTAAGGGTATTCA
Found at i:41648 original size:59 final size:57
Alignment explanation
Indices: 41573--41771 Score: 222
Period size: 59 Copynumber: 3.4 Consensus size: 57
41563 GCAAAATTGT
* * * **
41573 AATTTTTGAAAGTTTCGAGGTTAAAAATGGAAAATTTT-GAGGTTCGGGGGTAAAAATGG
1 AATTTTTGGAAG-TTCGAGGGT-AAAATGG-AAATTTTGGAAGTTTTGGGGTAAAAATGG
* * *
41632 AATTTTTGGAAGTTTCGAGGGTAAAATTGAATTTTTGGAAGTTTTAGGGTCAAAAATGG
1 AATTTTTGGAAG-TTCGAGGGTAAAATGGAAATTTTGGAAGTTTTGGGGT-AAAAATGG
* * *
41691 AATTTTTGGAAGTTCGGGGGTAAAATTG-AATTTTGGAAGTTTTGGGGTCAAAATGG
1 AATTTTTGGAAGTTCGAGGGTAAAATGGAAATTTTGGAAGTTTTGGGGTAAAAATGG
* *
41747 GATTTTTGGAAGCTCGAGGGTAAAA
1 AATTTTTGGAAGTTCGAGGGTAAAA
41772 ATGTAATTTT
Statistics
Matches: 123, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
56 29 0.24
57 24 0.20
58 30 0.24
59 40 0.33
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (57 bp):
AATTTTTGGAAGTTCGAGGGTAAAATGGAAATTTTGGAAGTTTTGGGGTAAAAATGG
Found at i:41657 original size:29 final size:30
Alignment explanation
Indices: 41556--41781 Score: 218
Period size: 29 Copynumber: 7.8 Consensus size: 30
41546 GTTTTGGATA
* * * *
41556 TTCGAGGGCAAAATTGTAATTTTTGAAAGT
1 TTCGAGGGTAAAAATGGAATTTTTGGAAGT
* * *
41586 TTCGAGGTTAAAAATGGAAAATTTT-G-AGG
1 TTCGAGGGTAAAAATGG-AATTTTTGGAAGT
*
41615 TTCGGGGGTAAAAATGGAATTTTTGGAAGT
1 TTCGAGGGTAAAAATGGAATTTTTGGAAGT
*
41645 TTCGAGGGT-AAAATTGAATTTTTGGAAGT
1 TTCGAGGGTAAAAATGGAATTTTTGGAAGT
*
41674 TT-TAGGGTCAAAAATGGAATTTTTGGAAG-
1 TTCGAGGGT-AAAAATGGAATTTTTGGAAGT
* *
41703 TTCGGGGGT-AAAATTGAA-TTTTGGAAGT
1 TTCGAGGGTAAAAATGGAATTTTTGGAAGT
* * *
41731 TTTG-GGGTCAAAATGGGATTTTTGGAAG-
1 TTCGAGGGTAAAAATGGAATTTTTGGAAGT
* *
41759 CTCGAGGGTAAAAATGTAATTTT
1 TTCGAGGGTAAAAATGGAATTTT
41782 CGAACAGTTT
Statistics
Matches: 160, Mismatches: 26, Indels: 21
0.77 0.13 0.10
Matches are distributed among these distances:
27 13 0.08
28 31 0.19
29 65 0.41
30 45 0.28
31 6 0.04
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (30 bp):
TTCGAGGGTAAAAATGGAATTTTTGGAAGT
Found at i:41743 original size:57 final size:57
Alignment explanation
Indices: 41619--41781 Score: 240
Period size: 56 Copynumber: 2.8 Consensus size: 57
41609 TTGAGGTTCG
41619 GGGGT-AAAAATGGAATTTTTGGAAGTTTCGAGGGTAAAATTGAATTTTTGGAAGTTTT
1 GGGGTCAAAAATGGAATTTTTGGAAG-TTCGAGGGTAAAATTGAA-TTTTGGAAGTTTT
* *
41677 AGGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAATTGAATTTTGGAAGTTTT
1 GGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAATTGAATTTTGGAAGTTTT
* * *
41734 GGGGTC-AAAATGGGATTTTTGGAAGCTCGAGGGTAAAAATGTAATTTT
1 GGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAATTG-AATTTT
41782 CGAACAGTTT
Statistics
Matches: 96, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
56 31 0.32
57 24 0.25
58 21 0.22
59 20 0.21
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (57 bp):
GGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAATTGAATTTTGGAAGTTTT
Found at i:43546 original size:6 final size:6
Alignment explanation
Indices: 43535--43611 Score: 65
Period size: 6 Copynumber: 13.5 Consensus size: 6
43525 TTTGGCATTT
* *
43535 ATTTAA ATTTAA ATTT-A ATTCAA ATTTATA A--TAA ATTTAA ATTTTA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA
* * *
43581 A-GTAA ATTTAA ACTTAA A-ATAA ATTTAA ATT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATT
43612 CTATTGGGCC
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
4 2 0.04
5 13 0.23
6 39 0.70
7 2 0.04
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:43571 original size:17 final size:17
Alignment explanation
Indices: 43535--43611 Score: 86
Period size: 17 Copynumber: 4.5 Consensus size: 17
43525 TTTGGCATTT
*
43535 ATTTAAATTTA-AATTTA
1 ATTTAAATTTATAA-TAA
*
43552 ATTCAAATTTATAATAA
1 ATTTAAATTTATAATAA
43569 ATTTAAATTT-TAAGTAA
1 ATTTAAATTTATAA-TAA
* *
43586 ATTTAAACTTAAAATAA
1 ATTTAAATTTATAATAA
43603 ATTTAAATT
1 ATTTAAATT
43612 CTATTGGGCC
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
16 3 0.06
17 44 0.86
18 4 0.08
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (17 bp):
ATTTAAATTTATAATAA
Found at i:43573 original size:34 final size:34
Alignment explanation
Indices: 43535--43611 Score: 100
Period size: 34 Copynumber: 2.3 Consensus size: 34
43525 TTTGGCATTT
* * * *
43535 ATTTAAATTTAAATTTAATTCAAATTTATAATAA
1 ATTTAAATTTAAAGTAAATTCAAACTTAAAATAA
* *
43569 ATTTAAATTTTAAGTAAATTTAAACTTAAAATAA
1 ATTTAAATTTAAAGTAAATTCAAACTTAAAATAA
43603 ATTTAAATT
1 ATTTAAATT
43612 CTATTGGGCC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (34 bp):
ATTTAAATTTAAAGTAAATTCAAACTTAAAATAA
Found at i:44151 original size:14 final size:14
Alignment explanation
Indices: 44132--44158 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44122 TTTTAGTCAC
44132 TTATGTTTGAAATG
1 TTATGTTTGAAATG
44146 TTATGTTTGAAAT
1 TTATGTTTGAAAT
44159 CTCAATTGGA
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:0.30, C:0.00, G:0.19, T:0.52
Consensus pattern (14 bp):
TTATGTTTGAAATG
Found at i:48115 original size:13 final size:13
Alignment explanation
Indices: 48097--48130 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
48087 GAGTTTTTTT
48097 CAAAAAAATACGA
1 CAAAAAAATACGA
48110 C--AAAAATACGA
1 CAAAAAAATACGA
48121 CAAAAAAATA
1 CAAAAAAATA
48131 TCTGACACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 11 0.58
13 8 0.42
ACGTcount: A:0.71, C:0.15, G:0.06, T:0.09
Consensus pattern (13 bp):
CAAAAAAATACGA
Found at i:51933 original size:17 final size:17
Alignment explanation
Indices: 51911--51947 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
51901 AACTTGTTGG
51911 CACGTCAAACATCATGC
1 CACGTCAAACATCATGC
*
51928 CACGTCAAACATCTTGC
1 CACGTCAAACATCATGC
51945 CAC
1 CAC
51948 AAACTCAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.38, G:0.11, T:0.19
Consensus pattern (17 bp):
CACGTCAAACATCATGC
Found at i:69059 original size:29 final size:30
Alignment explanation
Indices: 69005--69061 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
68995 AAATTGAATT
69005 AAATCAAAATTTTATGTATAAAATTACACA
1 AAATCAAAATTTTATGTATAAAATTACACA
* * *
69035 AAATTAAAA-TTTATGTATGACATTACA
1 AAATCAAAATTTTATGTATAAAATTACA
69062 TATTGAATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.35
Consensus pattern (30 bp):
AAATCAAAATTTTATGTATAAAATTACACA
Found at i:69574 original size:20 final size:22
Alignment explanation
Indices: 69549--69600 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 22
69539 ATTAATTATT
69549 TATAAAATTTA-ATT-TAAATA
1 TATAAAATTTATATTATAAATA
69569 TAT-AAA-TTATATTATAAATA
1 TATAAAATTTATATTATAAATA
69589 T-TAAAATGTTAT
1 TATAAAAT-TTAT
69601 CAATGCAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
18 3 0.11
19 7 0.26
20 13 0.48
22 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
TATAAAATTTATATTATAAATA
Found at i:71032 original size:51 final size:51
Alignment explanation
Indices: 70956--71057 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 51
70946 TCATGTTACA
* *
70956 AATTTCATGTGCGTGATGTTTTTAGTGTTGCTTTTATTGACGGCAAAAACT
1 AATTTCATGTGCGCGATGTTTTTAGTGTTGCTTTTATTGACGACAAAAACT
*
71007 AATTTCATGTGCGCGATGTTTTTAGTGTTGCTTTTATTGACGATAAAAACT
1 AATTTCATGTGCGCGATGTTTTTAGTGTTGCTTTTATTGACGACAAAAACT
71058 TTTTTTTTCC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.43
Consensus pattern (51 bp):
AATTTCATGTGCGCGATGTTTTTAGTGTTGCTTTTATTGACGACAAAAACT
Found at i:82507 original size:35 final size:34
Alignment explanation
Indices: 82468--82574 Score: 85
Period size: 35 Copynumber: 3.1 Consensus size: 34
82458 TATGGCTTAA
82468 ATTTTTTTTACCAATTTTTAAGGGTCCCAATTTTT
1 ATTTTTTTTACCAATTTTTAAGGG-CCCAATTTTT
** * * *
82503 ATTTTTATTT-TTAGTTTTTAAGGGCTCAA-ATTT
1 ATTTTT-TTTACCAATTTTTAAGGGCCCAATTTTT
* * * *
82536 ATTGTTTTTACCAACTTTTAAGAGACCTAATTTTT
1 ATTTTTTTTACCAATTTTTAAG-GGCCCAATTTTT
82571 -TTTT
1 ATTTT
82575 CCAACTTTTA
Statistics
Matches: 53, Mismatches: 15, Indels: 9
0.69 0.19 0.12
Matches are distributed among these distances:
32 3 0.06
33 16 0.30
34 11 0.21
35 20 0.38
36 3 0.06
ACGTcount: A:0.24, C:0.11, G:0.09, T:0.55
Consensus pattern (34 bp):
ATTTTTTTTACCAATTTTTAAGGGCCCAATTTTT
Found at i:85324 original size:17 final size:16
Alignment explanation
Indices: 85302--85336 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
85292 ATTTAATTAA
*
85302 AATTAATTAATTATTTT
1 AATTAA-TAATTAATTT
85319 AATTAATAATTAATTT
1 AATTAATAATTAATTT
85335 AA
1 AA
85337 AGGAACATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AATTAATAATTAATTT
Found at i:92675 original size:37 final size:38
Alignment explanation
Indices: 92625--92696 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 38
92615 ATAAAGTGAC
** *
92625 ACCCAGTGTCTCATCG-GCCTAGCCGAAGTAAAATGGT
1 ACCCAGTACCTCATCGAACCTAGCCGAAGTAAAATGGT
* *
92662 ACCCAGTACCTCATCGAATCTATCCGAAGTAAAAT
1 ACCCAGTACCTCATCGAACCTAGCCGAAGTAAAAT
92697 AATGACACCC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 14 0.48
38 15 0.52
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (38 bp):
ACCCAGTACCTCATCGAACCTAGCCGAAGTAAAATGGT
Found at i:96936 original size:15 final size:16
Alignment explanation
Indices: 96909--96938 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
96899 GAATTAAAAA
96909 TAAAAGTAAATAGAAT
1 TAAAAGTAAATAGAAT
96925 TAAAAG-AAATAGAA
1 TAAAAGTAAATAGAA
96939 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (16 bp):
TAAAAGTAAATAGAAT
Found at i:96941 original size:22 final size:22
Alignment explanation
Indices: 96881--96943 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
96871 CGATCTAAGG
* *
96881 AAAAATAAAAAAAAAACAGAATT
1 AAAAAT-AAAAGAAAATAGAATT
*
96904 AAAAATAAAAGTAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
96926 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
96944 GGAAGTCGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
22 27 0.79
23 7 0.21
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.16
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:100989 original size:15 final size:14
Alignment explanation
Indices: 100965--100997 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
100955 TGTTAAAAAC
100965 TAAT-TTTTAAAGTT
1 TAATATTTTAAA-TT
100979 TAATATTTTAAATT
1 TAATATTTTAAATT
100993 TAATA
1 TAATA
100998 AAATACAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (14 bp):
TAATATTTTAAATT
Found at i:110160 original size:134 final size:134
Alignment explanation
Indices: 109920--110187 Score: 527
Period size: 134 Copynumber: 2.0 Consensus size: 134
109910 GTTTATAAAG
109920 GGATAAAAATCTTTTTGTTATAATTACTCTGATAATCTTTTGCACACAACTCTTTTGTGCTCCTG
1 GGATAAAAATCTTTTTGTTATAATTACTCTGATAATCTTTTGCACACAACTCTTTTGTGCTCCTG
109985 CTGCTGCTTTACTGATGTGTGCTGGATCTCTTGATCCTTTACTGTGAATATTGATTTATTAGGAG
66 CTGCTGCTTTACTGATGTGTGCTGGATCTCTTGATCCTTTACTGTGAATATTGATTTATTAGGAG
110050 CCCT
131 CCCT
110054 GGATAAAAATCTTTTTGTTATAATTACTCTGATAATCTTTTGCACACAACTCTTTTGTGCTCCTG
1 GGATAAAAATCTTTTTGTTATAATTACTCTGATAATCTTTTGCACACAACTCTTTTGTGCTCCTG
*
110119 CTGCTGCTTTACTTATGTGTGCTGGATCTCTTGATCCTTTACTGTGAATATTGATTTATTAGGAG
66 CTGCTGCTTTACTGATGTGTGCTGGATCTCTTGATCCTTTACTGTGAATATTGATTTATTAGGAG
110184 CCCT
131 CCCT
110188 CTTTCCTGTT
Statistics
Matches: 133, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
134 133 1.00
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.43
Consensus pattern (134 bp):
GGATAAAAATCTTTTTGTTATAATTACTCTGATAATCTTTTGCACACAACTCTTTTGTGCTCCTG
CTGCTGCTTTACTGATGTGTGCTGGATCTCTTGATCCTTTACTGTGAATATTGATTTATTAGGAG
CCCT
Found at i:111135 original size:2 final size:2
Alignment explanation
Indices: 111128--111152 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
111118 ATGCTGATTA
111128 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
111153 CACATGCAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:133199 original size:6 final size:6
Alignment explanation
Indices: 133185--133218 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
133175 AGACACAATC
* *
133185 TGAATT TGAACT TGAATT TGAATT TGACTT TGAA
1 TGAATT TGAATT TGAATT TGAATT TGAATT TGAA
133219 ATAACAAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (6 bp):
TGAATT
Found at i:141357 original size:63 final size:62
Alignment explanation
Indices: 141240--141366 Score: 200
Period size: 63 Copynumber: 2.0 Consensus size: 62
141230 AATAGGATTG
* * * *
141240 TTATTGAATATAATTTAATAAAAAAGATAGTAAATAATTTAATCATATTTTTAATATAATTA
1 TTATTAAATATAATTTAATAAAAAAAATAATAAATAATTTAATAATATTTTTAATATAATTA
*
141302 TTATTAAATATAATTTAATAAAAAATAATAATATATAATTTAATAATATTTTTAATATAATTA
1 TTATTAAATATAATTTAATAAAAAA-AATAATAAATAATTTAATAATATTTTTAATATAATTA
141365 TT
1 TT
141367 TTTATACTAA
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
62 24 0.41
63 35 0.59
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (62 bp):
TTATTAAATATAATTTAATAAAAAAAATAATAAATAATTTAATAATATTTTTAATATAATTA
Found at i:142392 original size:8 final size:8
Alignment explanation
Indices: 142381--142410 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
142371 ATTTAAACAT
142381 TTTTATAA
1 TTTTATAA
142389 TTTTATAA
1 TTTTATAA
142397 TTTTATAA
1 TTTTATAA
142405 TTTTAT
1 TTTTAT
142411 GAGTGCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTTATAA
Found at i:142892 original size:13 final size:12
Alignment explanation
Indices: 142874--142903 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
142864 AAAATATTCA
142874 AAAAAATGAAAAT
1 AAAAAATG-AAAT
142887 AAAAAATGAAAT
1 AAAAAATGAAAT
142899 AAAAA
1 AAAAA
142904 TTATTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (12 bp):
AAAAAATGAAAT
Found at i:145926 original size:105 final size:106
Alignment explanation
Indices: 145644--145926 Score: 316
Period size: 106 Copynumber: 2.7 Consensus size: 106
145634 TAGAGTTGAT
* *
145644 GAAATTCTAAATAAACCAAACAGAACCCATCACTCATTTACAACTTTTTAGTCTTGCTTTCAGAA
1 GAAATTCTAAATAAACCAAACA-AACCCATCACTTATTTACAAC-TTTTAGTCTTCCTTTCAGAA
* * * * * * *
145709 TGTATCAAGCCATGGAGTCTGCAATTGCAATGGCAGACTTGAT
64 TGTATCAAGCCATAGAATCAGCAAATGCAATAGCAGACTTCAC
* * * * * *
145752 GAAATTTTAAATAAACCAAACAAAACCAATCACTTATTTACGACATTTAGTCTTCCATTCAGTAT
1 GAAATTCTAAATAAACCAAAC-AAACCCATCACTTATTTACAACTTTTAGTCTTCCTTTCAGAAT
** * *
145817 GTATCAA-CCATAGAATCAGCAAATGCAATATTATAGTTCAC
65 GTATCAAGCCATAGAATCAGCAAATGCAATAGCAGACTTCAC
* * * * *
145858 GAAATTCTAAAAAAACCAAACAAACCCATCACTTATTCACAAGTTTTAGTCTTTCTTTCAGAACG
1 GAAATTCTAAATAAACCAAACAAACCCATCACTTATTTACAACTTTTAGTCTTCCTTTCAGAATG
145923 TATC
66 TATC
145927 GGCCATGTAG
Statistics
Matches: 144, Mismatches: 30, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
105 39 0.27
106 42 0.29
107 24 0.17
108 38 0.26
109 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (106 bp):
GAAATTCTAAATAAACCAAACAAACCCATCACTTATTTACAACTTTTAGTCTTCCTTTCAGAATG
TATCAAGCCATAGAATCAGCAAATGCAATAGCAGACTTCAC
Found at i:146900 original size:17 final size:16
Alignment explanation
Indices: 146880--146913 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
146870 ATTTTTTTTA
146880 TTTATAGGCTATAATTT
1 TTTATAGG-TATAATTT
*
146897 TTTATAGGTATTATTT
1 TTTATAGGTATAATTT
146913 T
1 T
146914 GGTAAGGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.26, C:0.03, G:0.12, T:0.59
Consensus pattern (16 bp):
TTTATAGGTATAATTT
Found at i:146949 original size:21 final size:23
Alignment explanation
Indices: 146925--146970 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
146915 GTAAGGTATG
146925 TTTCTATTTTATT-T-TTTTTTA
1 TTTCTATTTTATTATATTTTTTA
*
146946 TTTCTATTTTTTTATATTTTTTA
1 TTTCTATTTTATTATATTTTTTA
146969 TT
1 TT
146971 AGATTCAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.55
22 1 0.05
23 9 0.41
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTCTATTTTATTATATTTTTTA
Found at i:146955 original size:16 final size:15
Alignment explanation
Indices: 146929--146965 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
146919 GGTATGTTTC
*
146929 TATTTTATTTTTTTT
1 TATTTTATTTTTTTA
146944 TATTTCTATTTTTTTA
1 TATTT-TATTTTTTTA
146960 TATTTT
1 TATTTT
146966 TTATTAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (15 bp):
TATTTTATTTTTTTA
Found at i:150185 original size:28 final size:28
Alignment explanation
Indices: 150143--150196 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
150133 CTTATTTTAA
**
150143 TACCTAAACTTCTTTTTATTACAAGTGG
1 TACCTAAACGACTTTTTATTACAAGTGG
* *
150171 TACCTAAACGACTTTTTTTTCCAAGT
1 TACCTAAACGACTTTTTATTACAAGT
150197 TGGTTCCTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.43
Consensus pattern (28 bp):
TACCTAAACGACTTTTTATTACAAGTGG
Found at i:150930 original size:2 final size:2
Alignment explanation
Indices: 150925--150963 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
150915 ATATATATAT
150925 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
150964 TTTTGTTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:151444 original size:31 final size:31
Alignment explanation
Indices: 151403--151498 Score: 131
Period size: 31 Copynumber: 3.1 Consensus size: 31
151393 TAATAAAATG
*
151403 ACAACTTATCTAATTGGAGTGACTAAAATTA
1 ACAACTTATCTAATAGGAGTGACTAAAATTA
* *
151434 ACAATTTATCTAATGGGAGTGACTAAAATTA
1 ACAACTTATCTAATAGGAGTGACTAAAATTA
* * *
151465 ACACCTTATCTAATAAGAGTGATTAAAA-TA
1 ACAACTTATCTAATAGGAGTGACTAAAATTA
151495 ACAA
1 ACAA
151499 ATTTTTAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 5 0.09
31 52 0.91
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (31 bp):
ACAACTTATCTAATAGGAGTGACTAAAATTA
Found at i:154319 original size:29 final size:27
Alignment explanation
Indices: 154287--154379 Score: 80
Period size: 29 Copynumber: 3.3 Consensus size: 27
154277 AAATTTCATT
154287 TTTTACCCCGAACTTCCCAAAAGTTACCA
1 TTTTACCCCGAACTT-CCAAAA-TTACCA
* *
154316 TTTTACCCCCGAA-TATCCAAAATTATCG
1 TTTTA-CCCCGAACT-TCCAAAATTACCA
* * *
154344 TTTTACCCCTTAACCTCTAAAAATTACCA
1 TTTTACCCC-GAACTTC-CAAAATTACCA
154373 TTTTACC
1 TTTTACC
154380 TCGAGTATCC
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
27 4 0.08
28 13 0.25
29 27 0.52
30 8 0.15
ACGTcount: A:0.31, C:0.31, G:0.04, T:0.33
Consensus pattern (27 bp):
TTTTACCCCGAACTTCCAAAATTACCA
Found at i:161456 original size:30 final size:30
Alignment explanation
Indices: 161422--161487 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
161412 TTAAAGAAAC
*
161422 AATTAAACCCTCG-TAAAATC-ATTAAAAATA
1 AATTAAACCCT-GATAAAA-CAATAAAAAATA
* *
161452 AATTACACCCTGATAAAACAATAAAAAATC
1 AATTAAACCCTGATAAAACAATAAAAAATA
161482 AATTAA
1 AATTAA
161488 CCTATCATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
29 2 0.07
30 28 0.93
ACGTcount: A:0.56, C:0.17, G:0.03, T:0.24
Consensus pattern (30 bp):
AATTAAACCCTGATAAAACAATAAAAAATA
Found at i:164911 original size:17 final size:19
Alignment explanation
Indices: 164875--164921 Score: 71
Period size: 17 Copynumber: 2.6 Consensus size: 19
164865 GTTTAAATTG
*
164875 ATTTAAATTTATCTTTTAA
1 ATTTAAATTTAGCTTTTAA
164894 ATTTAAATTT-GC-TTTAA
1 ATTTAAATTTAGCTTTTAA
164911 ATTTAAATTTA
1 ATTTAAATTTA
164922 ATTAAAAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 15 0.58
18 1 0.04
19 10 0.38
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.55
Consensus pattern (19 bp):
ATTTAAATTTAGCTTTTAA
Found at i:164933 original size:17 final size:17
Alignment explanation
Indices: 164913--164965 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
164903 TGCTTTAAAT
*
164913 TTAAATTTAATTAAAAG
1 TTAAATTCAATTAAAAG
* * *
164930 TTAAATTGATTTAAAAC
1 TTAAATTCAATTAAAAG
164947 TTAATATTCAATTAAAAG
1 TTAA-ATTCAATTAAAAG
164965 T
1 T
164966 CCAAAACAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
17 18 0.62
18 11 0.38
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.42
Consensus pattern (17 bp):
TTAAATTCAATTAAAAG
Found at i:166857 original size:29 final size:29
Alignment explanation
Indices: 166777--167152 Score: 214
Period size: 29 Copynumber: 12.8 Consensus size: 29
166767 TATAGGTCCT
* ** *
166777 TAAACTTCTCCAAAATTATATTTTGACCCC
1 TAAACTT-TCAAAAATTCCATTTTTACCCC
** * *
166807 TGAAACTTTTGAAGATTACATTTTTACCCC
1 T-AAACTTTCAAAAATTCCATTTTTACCCC
* *
166837 TAAACTTTCAAAACTTCCATTTTTAACCTC
1 TAAACTTTCAAAAATTCCATTTTT-ACCCC
* ** *
166867 GAAACTTTCAAAAATTATAATTTTACCCC
1 TAAACTTTCAAAAATTCCATTTTTACCCC
* * *
166896 TAAACTTCCAAAAATTCTATTTTTGACCTC
1 TAAACTTTCAAAAATTCCATTTTT-ACCCC
* * **
166926 AAAACTTCCAAAAATTAGATTTTTA-CCC
1 TAAACTTTCAAAAATTCCATTTTTACCCC
* * *
166954 TCGAACTTCCAAAAATTCCATTTTTGACCTC
1 T-AAACTTTCAAAAATTCCATTTTT-ACCCC
*
166985 GAAACTTTCAAAAATTACCA-TTTTA-CCC
1 TAAACTTTCAAAAATT-CCATTTTTACCCC
* *
167013 TCAAACTTTC-AAAATTCCATTTTTGCCCT
1 T-AAACTTTCAAAAATTCCATTTTTACCCC
* * * *
167042 TGAAAGTTTTAAAAATTACCA-TTTTACTCT
1 T-AAACTTTCAAAAATT-CCATTTTTACCCC
** * *
167072 TGGA-TATCCAAAAACTCC-TTTTTGACCCC
1 TAAACT-TTCAAAAATTCCATTTTT-ACCCC
*
167101 GAAACTTTCAAAAATTACCA-TTTTACCCC
1 TAAACTTTCAAAAATT-CCATTTTTACCCC
* *
167130 -GAA-TGTCTAAAAATTCCATTTTT
1 TAAACTTTC-AAAAATTCCATTTTT
167153 GATCCCAATT
Statistics
Matches: 269, Mismatches: 57, Indels: 42
0.73 0.15 0.11
Matches are distributed among these distances:
27 9 0.03
28 34 0.13
29 106 0.39
30 106 0.39
31 14 0.05
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (29 bp):
TAAACTTTCAAAAATTCCATTTTTACCCC
Found at i:166871 original size:59 final size:59
Alignment explanation
Indices: 166797--167154 Score: 331
Period size: 59 Copynumber: 6.1 Consensus size: 59
166787 CAAAATTATA
* ** * * *
166797 TTTTGACCCCTGAAACTTTTGAAGATTACATTTTTACCC-CTAAACTTTCAAAACTTCCAT
1 TTTTGACCTC-GAAACTTTCAAAAATTACATTTTTACCCTC-AAACTTCCAAAAATTCCAT
* * * *
166857 TTTTAACCTCGAAACTTTCAAAAATTATAATTTTACCC-CTAAACTTCCAAAAATTCTAT
1 TTTTGACCTCGAAACTTTCAAAAATTACATTTTTACCCTC-AAACTTCCAAAAATTCCAT
* * * *
166916 TTTTGACCTCAAAACTTCCAAAAATTAGATTTTTACCCTCGAACTTCCAAAAATTCCAT
1 TTTTGACCTCGAAACTTTCAAAAATTACATTTTTACCCTCAAACTTCCAAAAATTCCAT
*
166975 TTTTGACCTCGAAACTTTCAAAAATTACCA-TTTTACCCTCAAACTTTC-AAAATTCCAT
1 TTTTGACCTCGAAACTTTCAAAAATTA-CATTTTTACCCTCAAACTTCCAAAAATTCCAT
* * * * * *** *
167033 TTTTGCCCTTGAAAGTTTTAAAAATTACCA-TTTTACTCTTGGA-TATCCAAAAACTCC-T
1 TTTTGACCTCGAAACTTTCAAAAATTA-CATTTTTACCCTCAAACT-TCCAAAAATTCCAT
* * *
167091 TTTTGACCCCGAAACTTTCAAAAATTACCA-TTTTACCC-CGAA-TGTCTAAAAATTCCAT
1 TTTTGACCTCGAAACTTTCAAAAATTA-CATTTTTACCCTCAAACT-TCCAAAAATTCCAT
167149 TTTTGA
1 TTTTGA
167155 TCCCAATTTT
Statistics
Matches: 250, Mismatches: 43, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
57 14 0.06
58 87 0.35
59 139 0.56
60 10 0.04
ACGTcount: A:0.34, C:0.24, G:0.06, T:0.37
Consensus pattern (59 bp):
TTTTGACCTCGAAACTTTCAAAAATTACATTTTTACCCTCAAACTTCCAAAAATTCCAT
Found at i:167172 original size:58 final size:57
Alignment explanation
Indices: 166846--167240 Score: 302
Period size: 58 Copynumber: 6.8 Consensus size: 57
166836 CTAAACTTTC
* * ** * *
166846 AAAACTTCCATTTTTAACCTCGAAACTTTCAAAAATTATAATTTTACCC-CTAAACTTCC
1 AAAAATTCCATTTTTGACC-CGAAACTTTCAAAAATTACCATTTTACCCTC-GAA-TTCT
* * * * *
166905 AAAAATTCTATTTTTGACCTCAAAACTTCCAAAAATTA-GATTTTTACCCTCGAACTTCC
1 AAAAATTCCATTTTTGACC-CGAAACTTTCAAAAATTACCA-TTTTACCCTCGAA-TTCT
*
166964 AAAAATTCCATTTTTGACCTCGAAACTTTCAAAAATTACCATTTTACCCTCAAACTT-T
1 AAAAATTCCATTTTTGACC-CGAAACTTTCAAAAATTACCATTTTACCCTCGAA-TTCT
* * * * * * *
167022 CAAAATTCCATTTTTG-CCCTTGAAAGTTTTAAAAATTACCATTTTACTCTTGGATATCC
1 AAAAATTCCATTTTTGACCC--GAAACTTTCAAAAATTACCATTTTACCCTCGAAT-TCT
*
167081 AAAAACTCC-TTTTTGACCCCGAAACTTTCAAAAATTACCATTTTACCC-CGAATGTCT
1 AAAAATTCCATTTTTGA-CCCGAAACTTTCAAAAATTACCATTTTACCCTCGAAT-TCT
** *** *
167138 AAAAATTCCATTTTTGATCCC-AATTTTTCTAAAAATTATTGTTTTACCCTCGGATATCT
1 AAAAATTCCATTTTTGA-CCCGAAACTTTC-AAAAATTACCATTTTACCCTCGAAT-TCT
* * * * *
167197 -AAAATTTCATTTTTAACCCTAAAATTTCCCAAAATTACCATTTT
1 AAAAATTCCATTTTTGACCCGAAACTTT-CAAAAATTACCATTTT
167241 GCCCCAAGAG
Statistics
Matches: 275, Mismatches: 47, Indels: 29
0.78 0.13 0.08
Matches are distributed among these distances:
56 1 0.00
57 25 0.09
58 131 0.48
59 113 0.41
60 5 0.02
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (57 bp):
AAAAATTCCATTTTTGACCCGAAACTTTCAAAAATTACCATTTTACCCTCGAATTCT
Found at i:167391 original size:7 final size:7
Alignment explanation
Indices: 167361--167390 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
167351 TATTATGCAC
167361 TTGTATT
1 TTGTATT
167368 TTGTATT
1 TTGTATT
167375 TTGTATT
1 TTGTATT
*
167382 TTTTATT
1 TTGTATT
167389 TT
1 TT
167391 TGCATATCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (7 bp):
TTGTATT
Found at i:178802 original size:18 final size:20
Alignment explanation
Indices: 178781--178818 Score: 53
Period size: 18 Copynumber: 1.9 Consensus size: 20
178771 AACTTGAACG
178781 TTAATT-ATTGA-TTGATTC
1 TTAATTCATTGACTTGATTC
178799 TTAATTCGATTGACTTGATT
1 TTAATTC-ATTGACTTGATT
178819 GGCATGAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
20 5 0.29
21 6 0.35
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (20 bp):
TTAATTCATTGACTTGATTC
Found at i:182908 original size:80 final size:80
Alignment explanation
Indices: 182769--182929 Score: 250
Period size: 80 Copynumber: 2.0 Consensus size: 80
182759 TTGATGCTGC
* * * * *
182769 TGTTAATGATGGTTTGTGGGAGCCTCTCATGCTATCTCGATGAGGGCCTGGTCTCTCCCACCTAT
1 TGTTAATGATGGTTCGTGGGAGCCTCTCATGCTATCTCGACGACGGCCTAGTCTATCCCACCTAT
182834 TCTTTACGGATGATT
66 TCTTTACGGATGATT
* *
182849 TGTTGATGATGGTTCGTGGGATCCTCTCATGCTATCTCGACGACGGCCTAGTCTATCCCACCTAT
1 TGTTAATGATGGTTCGTGGGAGCCTCTCATGCTATCTCGACGACGGCCTAGTCTATCCCACCTAT
*
182914 TCTTTGCGGATGATT
66 TCTTTACGGATGATT
182929 T
1 T
182930 ATTGCTTTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 73 1.00
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (80 bp):
TGTTAATGATGGTTCGTGGGAGCCTCTCATGCTATCTCGACGACGGCCTAGTCTATCCCACCTAT
TCTTTACGGATGATT
Found at i:190000 original size:18 final size:19
Alignment explanation
Indices: 189959--190005 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
189949 AATTTTATAC
*
189959 TATTTTAATAAATTTGGAA
1 TATTTTAATAAATTTGCAA
*
189978 T-TTTTAATTAA-TTGCAA
1 TATTTTAATAAATTTGCAA
*
189995 TATTTTTATAA
1 TATTTTAATAA
190006 GTTTCTATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 6 0.26
18 16 0.70
19 1 0.04
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.53
Consensus pattern (19 bp):
TATTTTAATAAATTTGCAA
Found at i:201323 original size:16 final size:16
Alignment explanation
Indices: 201302--201355 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
201292 TTTGATTCGC
* *
201302 TGTAATAAAATAGAGT
1 TGTAATAAAATAAAAT
** *
201318 TGTAATGTAATAAAAC
1 TGTAATAAAATAAAAT
201334 TGTAATAAAATAAAAT
1 TGTAATAAAATAAAAT
201350 TGTAAT
1 TGTAAT
201356 TAGTATTTCA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.52, C:0.02, G:0.13, T:0.33
Consensus pattern (16 bp):
TGTAATAAAATAAAAT
Found at i:201599 original size:56 final size:56
Alignment explanation
Indices: 201531--201680 Score: 171
Period size: 56 Copynumber: 2.6 Consensus size: 56
201521 TTGTTAAATT
* * * *
201531 TTAATAAAATTATTATTAAATATAATTTAATAAAAAATAAATATTTTAATCATATT-
1 TTAATATAATTATTATTAAATATAATTTAATAAAAAATAAATA-ATTAATAACATTC
* * *
201587 TTAACT-TGATTATTATTAAATACAATTTAATAAAATAGTAAATAATTAATAACATTC
1 TTAA-TATAATTATTATTAAATATAATTTAATAAAA-AATAAATAATTAATAACATTC
201644 TTAATATAATTATTATTAAAATATGAA-TTAATAAAAA
1 TTAATATAATTATTATT-AAATAT-AATTTAATAAAAA
201681 TCATAATATA
Statistics
Matches: 79, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
56 40 0.51
57 23 0.29
58 14 0.18
59 2 0.03
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (56 bp):
TTAATATAATTATTATTAAATATAATTTAATAAAAAATAAATAATTAATAACATTC
Found at i:221459 original size:23 final size:25
Alignment explanation
Indices: 221406--221460 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
221396 TAAAATAATG
*
221406 TTAAGATAACTATATAAAAAACTTCA
1 TTAA-ATAAATATATAAAAAACTTCA
*
221432 ATAAATAAATATATAAAAAA-TT-A
1 TTAAATAAATATATAAAAAACTTCA
221455 TTAAAT
1 TTAAAT
221461 TTTAAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 6 0.23
24 2 0.08
25 15 0.58
26 3 0.12
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (25 bp):
TTAAATAAATATATAAAAAACTTCA
Found at i:221491 original size:28 final size:27
Alignment explanation
Indices: 221460--221512 Score: 88
Period size: 27 Copynumber: 1.9 Consensus size: 27
221450 AATTATTAAA
*
221460 TTTTAAAATAATATAATATTAATATATT
1 TTTTAAAATAA-ATAATAATAATATATT
221488 TTTTAAAATAAATAATAATAATATA
1 TTTTAAAATAAATAATAATAATATA
221513 GACAGGTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TTTTAAAATAAATAATAATAATATATT
Found at i:225693 original size:12 final size:12
Alignment explanation
Indices: 225676--225700 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
225666 GCCACCATCT
225676 TGGCCTCCTACA
1 TGGCCTCCTACA
225688 TGGCCTCCTACA
1 TGGCCTCCTACA
225700 T
1 T
225701 CCACACCTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.40, G:0.16, T:0.28
Consensus pattern (12 bp):
TGGCCTCCTACA
Found at i:227119 original size:26 final size:28
Alignment explanation
Indices: 227079--227130 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
227069 ATGTCAAGTT
*
227079 TATTATATTTATTAATTAACTTAATTCA
1 TATTATATTTATTAAATAACTTAATTCA
*
227107 TATTAT-TTT-TTAAATAATTTAATT
1 TATTATATTTATTAAATAACTTAATT
227131 GGTTATGTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 13 0.59
27 3 0.14
28 6 0.27
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (28 bp):
TATTATATTTATTAAATAACTTAATTCA
Found at i:229448 original size:11 final size:11
Alignment explanation
Indices: 229432--229456 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
229422 CAGGTCCCTG
229432 TTATTTTAAAT
1 TTATTTTAAAT
229443 TTATTTTAAAT
1 TTATTTTAAAT
229454 TTA
1 TTA
229457 CCCAGAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTATTTTAAAT
Found at i:229762 original size:30 final size:30
Alignment explanation
Indices: 229728--230083 Score: 253
Period size: 30 Copynumber: 12.1 Consensus size: 30
229718 ATTTTCTTTG
* *
229728 AAAATAACATTTTGACCCTCAAACTTTTCC
1 AAAATTACATTTTAACCCTCAAACTTTTCC
* *
229758 AAAATTACATTTTGACCCAT-AAACTTTTTC
1 AAAATTACATTTTAACCC-TCAAACTTTTCC
* *
229788 AAAATCACATTTTAACCCTCAAACTTCTCC
1 AAAATTACATTTTAACCCTCAAACTTTTCC
* * *
229818 AAAATTATATTTTGA-CCTCTAAACTTTTCT
1 AAAATTACATTTTAACCCTC-AAACTTTTCC
*
229848 AAAA-TAGCATTTTAATCCT-AAACTTTTCC
1 AAAATTA-CATTTTAACCCTCAAACTTTTCC
* * *
229877 AAAATTACATTTTAACTCTCGAACTTCTCC
1 AAAATTACATTTTAACCCTCAAACTTTTCC
*
229907 AAAATTACATTTTAACCCTTAAA-TTTCTCC
1 AAAATTACATTTTAACCCTCAAACTTT-TCC
* *
229937 AAAATCT-TATTTTAACCCT-AAACTTCTCC
1 AAAAT-TACATTTTAACCCTCAAACTTTTCC
* ** * *
229966 AAAATTATGATTTTGCCCCT-AAA--TATCAA
1 AAAATTA-CATTTTAACCCTCAAACTTTTC-C
* ** *
229995 AAAATTATCATTTT-GCCCTTGAAC--ATCC
1 AAAATTA-CATTTTAACCCTCAAACTTTTCC
*
230023 AAAATTACTATTTT-ACCCTTAAA-TTTT-C
1 AAAATTAC-ATTTTAACCCTCAAACTTTTCC
*
230051 AAAATCACATTTTCAA-CCTCAAA-TTTTCC
1 AAAATTACATTTT-AACCCTCAAACTTTTCC
230080 AAAA
1 AAAA
230084 GTTCGATTTT
Statistics
Matches: 267, Mismatches: 38, Indels: 43
0.77 0.11 0.12
Matches are distributed among these distances:
27 6 0.02
28 45 0.17
29 68 0.25
30 143 0.54
31 5 0.02
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (30 bp):
AAAATTACATTTTAACCCTCAAACTTTTCC
Found at i:229906 original size:89 final size:87
Alignment explanation
Indices: 229728--229972 Score: 296
Period size: 89 Copynumber: 2.7 Consensus size: 87
229718 ATTTTCTTTG
* * *
229728 AAAATAACATTTTGACCCTCAAACTTTTCCAAAATTACATTTTGACCCATAAACTTTTTCAAAAT
1 AAAATTACATTTTGACCCT-AAACTTTTCCAAAA-TACATTTTAACCC-TAAACTTTTCCAAAAT
*
229793 CACATTTTAACCCTCAAACTTCTCC
63 TACATTTTAACCCTCAAACTTCTCC
* * *
229818 AAAATTATATTTTGACCTCTAAACTTTTCTAAAATAGCATTTTAATCCTAAACTTTTCCAAAATT
1 AAAATTACATTTTGACC-CTAAACTTTTCCAAAATA-CATTTTAACCCTAAACTTTTCCAAAATT
* *
229883 ACATTTTAACTCTCGAACTTCTCC
64 ACATTTTAACCCTCAAACTTCTCC
* *
229907 AAAATTACATTTTAACCCTTAAA-TTTCTCCAAAAT-CTTATTTTAACCCTAAACTTCTCCAAAA
1 AAAATTACATTTTGACCC-TAAACTTT-TCCAAAATAC--ATTTTAACCCTAAACTTTTCCAAAA
229970 TTA
62 TTA
229973 TGATTTTGCC
Statistics
Matches: 135, Mismatches: 14, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
87 1 0.01
88 4 0.03
89 91 0.67
90 37 0.27
91 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.38
Consensus pattern (87 bp):
AAAATTACATTTTGACCCTAAACTTTTCCAAAATACATTTTAACCCTAAACTTTTCCAAAATTAC
ATTTTAACCCTCAAACTTCTCC
Found at i:230008 original size:59 final size:61
Alignment explanation
Indices: 229758--230008 Score: 136
Period size: 59 Copynumber: 4.2 Consensus size: 61
229748 AAACTTTTCC
* * * * **
229758 AAAATTA-CATTTTGACCCAT-AAACTTTTTCAAAATCACATTTTAA-CCCTCAAACT-TCTCC
1 AAAATTATCATTTTAACCC-TCAAACTTCTCCAAAATTACATTTTAACCCCT-AAA-TATCTAA
* * * * * **
229818 AAAATTAT-ATTTTGA-CCTCTAAACTTTTCTAAAA-TAGCATTTTAA-TCCTAAACT-TTTCC
1 AAAATTATCATTTTAACCCTC-AAACTTCTCCAAAATTA-CATTTTAACCCCTAAA-TATCTAA
* * * * **
229877 AAAATTA-CATTTTAACTCTCGAACTTCTCCAAAATTACATTTTAACCCTTAAATTTCTCC
1 AAAATTATCATTTTAACCCTCAAACTTCTCCAAAATTACATTTTAACCCCTAAATATCTAA
* *
229937 AAAATCT-T-ATTTTAACCCT-AAACTTCTCCAAAATTATGATTTT-GCCCCTAAATATC-AA
1 AAAAT-TATCATTTTAACCCTCAAACTTCTCCAAAATTA-CATTTTAACCCCTAAATATCTAA
229995 AAAATTATCATTTT
1 AAAATTATCATTTT
230009 GCCCTTGAAC
Statistics
Matches: 156, Mismatches: 21, Indels: 29
0.76 0.10 0.14
Matches are distributed among these distances:
57 1 0.01
58 7 0.04
59 76 0.49
60 71 0.46
61 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.02, T:0.39
Consensus pattern (61 bp):
AAAATTATCATTTTAACCCTCAAACTTCTCCAAAATTACATTTTAACCCCTAAATATCTAA
Found at i:230027 original size:28 final size:28
Alignment explanation
Indices: 229963--230045 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 28
229953 CCTAAACTTC
* * *
229963 TCCAAAATTATGATTTTGCCCCTAAATA
1 TCCAAAATTATCATTTTGCCCTTAAACA
* *
229991 TCAAAAAATTATCATTTTGCCCTTGAACA
1 TC-CAAAATTATCATTTTGCCCTTAAACA
*
230020 TCCAAAATTA-CTATTTTACCCTTAAA
1 TCCAAAATTATC-ATTTTGCCCTTAAA
230046 TTTTCAAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
27 1 0.02
28 21 0.47
29 23 0.51
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.36
Consensus pattern (28 bp):
TCCAAAATTATCATTTTGCCCTTAAACA
Found at i:235566 original size:2 final size:2
Alignment explanation
Indices: 235559--235583 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
235549 GAAGATTAAT
235559 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 T
235584 GTGTGTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:235588 original size:2 final size:2
Alignment explanation
Indices: 235583--235628 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
235573 TATATATATA
* *
235583 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG TA TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
235625 TG TG
1 TG TG
235629 AATGATTATG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.04, C:0.00, G:0.46, T:0.50
Consensus pattern (2 bp):
TG
Found at i:235638 original size:18 final size:18
Alignment explanation
Indices: 235581--235632 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
235571 TATATATATA
**
235581 TATGTGTGTGTGTGTGTG
1 TATGTGTGTGTGAATGTG
* *
235599 TGTGTGTGTGTGTATGTG
1 TATGTGTGTGTGAATGTG
235617 TATGTGTGTGTGAATG
1 TATGTGTGTGTGAATG
235633 ATTATGAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.10, C:0.00, G:0.42, T:0.48
Consensus pattern (18 bp):
TATGTGTGTGTGAATGTG
Found at i:241371 original size:17 final size:16
Alignment explanation
Indices: 241351--241397 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 16
241341 TAAATATTTG
241351 ATATATAAAAATTATAT
1 ATATATAAAAATTA-AT
241368 ATATATAGAAAA--AAT
1 ATATATA-AAAATTAAT
241383 ATATA-AAAAATTAAT
1 ATATATAAAAATTAAT
241398 TGATGTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
13 4 0.15
14 1 0.04
15 10 0.37
16 1 0.04
17 7 0.26
18 4 0.15
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
ATATATAAAAATTAAT
Found at i:241379 original size:19 final size:19
Alignment explanation
Indices: 241351--241387 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
241341 TAAATATTTG
* *
241351 ATATATAAAAATTATATAT
1 ATATAGAAAAAATATATAT
241370 ATATAGAAAAAATATATA
1 ATATAGAAAAAATATATA
241388 AAAAATTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (19 bp):
ATATAGAAAAAATATATAT
Found at i:241417 original size:2 final size:2
Alignment explanation
Indices: 241410--241437 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
241400 ATGTTTTTGA
241410 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
241438 TATTTTGTCT
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:244160 original size:211 final size:211
Alignment explanation
Indices: 243796--244218 Score: 747
Period size: 211 Copynumber: 2.0 Consensus size: 211
243786 TTGTTTAATC
* *
243796 ACGTACACTAATTATTGTTTGATGAGTAATGACTTGGTTGTTGCCATCAAATAAAGAGAAAAGAT
1 ACGTACACTAATTATTGTTTGAGGAGTAATGACTAGGTTGTTGCCATCAAATAAAGAGAAAAGAT
* *
243861 TGTATGAAATAGTGATATTATCTCTTTTCAATAATTTTATGTCATATCAACAATTTCATCTTAAA
66 TGTATGAAATAGGGATATTATCTCTTTTCAATAATTTTATGTCACATCAACAATTTCATCTTAAA
243926 TTTCAAGATTTTAATTTTAATTTGATTTTTTAAAATATTGAAATTAAGAATGAAAAACTGTTGGA
131 TTTCAAGATTTTAATTTTAATTTGATTTTTTAAAATATTGAAATTAAGAATGAAAAACTGTTGGA
* *
243991 AAGAAAGACGCAAATA
196 AAAAAAGACACAAATA
244007 ACGTACACTAATTATTGTTTGAGGAGTAATGACTAGGTTGTTGCCATCAAATAAAGAGAAAAGAT
1 ACGTACACTAATTATTGTTTGAGGAGTAATGACTAGGTTGTTGCCATCAAATAAAGAGAAAAGAT
* *
244072 TGTATGAAATAGGGATATTATCTCTTTTCAATAGTTTTATGTCACGTCAACAATTTCATCTTAAA
66 TGTATGAAATAGGGATATTATCTCTTTTCAATAATTTTATGTCACATCAACAATTTCATCTTAAA
* *
244137 TTTCAATATTTTAATTTTAATTTGATTTTTTAAAATGTTGAAATTAAGAATGAAAAACTGTTGGA
131 TTTCAAGATTTTAATTTTAATTTGATTTTTTAAAATATTGAAATTAAGAATGAAAAACTGTTGGA
*
244202 AAAAAATACACAAATA
196 AAAAAAGACACAAATA
244218 A
1 A
244219 AGTGGTATCA
Statistics
Matches: 201, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
211 201 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.37
Consensus pattern (211 bp):
ACGTACACTAATTATTGTTTGAGGAGTAATGACTAGGTTGTTGCCATCAAATAAAGAGAAAAGAT
TGTATGAAATAGGGATATTATCTCTTTTCAATAATTTTATGTCACATCAACAATTTCATCTTAAA
TTTCAAGATTTTAATTTTAATTTGATTTTTTAAAATATTGAAATTAAGAATGAAAAACTGTTGGA
AAAAAAGACACAAATA
Found at i:248040 original size:23 final size:22
Alignment explanation
Indices: 247992--248041 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
247982 TTTTATGTGT
247992 AAAATTTTTTTAAAAAAGTTTA
1 AAAATTTTTTTAAAAAAGTTTA
* *
248014 AAAATATTTTCTTATAAAA-TTTC
1 AAAAT-TTTT-TTAAAAAAGTTTA
248037 AAAAT
1 AAAAT
248042 GATAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.21
23 12 0.50
24 7 0.29
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (22 bp):
AAAATTTTTTTAAAAAAGTTTA
Found at i:248068 original size:18 final size:18
Alignment explanation
Indices: 248025--248068 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
248015 AAATATTTTC
*
248025 TTATAAAATTTCAAAATG
1 TTATAAAATTTCAAAACG
* * *
248043 ATAAAAAATTTTAAAACG
1 TTATAAAATTTCAAAACG
248061 TTATAAAA
1 TTATAAAA
248069 ATTAAAAATA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.34
Consensus pattern (18 bp):
TTATAAAATTTCAAAACG
Found at i:263286 original size:25 final size:25
Alignment explanation
Indices: 263237--263286 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
263227 TCACATAATT
*
263237 ATTAGTAATTTGTTTTATCATTCAA
1 ATTAGTAATTTGTTTTATCACTCAA
263262 ATTAGTAAATTT-TTTTAAT-ACTCAA
1 ATTAGT-AATTTGTTTT-ATCACTCAA
263287 TTATGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.50
Consensus pattern (25 bp):
ATTAGTAATTTGTTTTATCACTCAA
Found at i:265855 original size:90 final size:91
Alignment explanation
Indices: 265647--265911 Score: 327
Period size: 90 Copynumber: 2.9 Consensus size: 91
265637 GATTTGCATG
* * * * * * * * *
265647 TTGCTTAAAATGCTTATTGTTGATCTCTTCCTGAATTTTCTTTCCACCAGTTAGCATTTAAATGC
1 TTGCCTAAAATGCTTGTTGTTGATCTCCTCTTGGATTTTCTTTCCTCTAGTTGGCATATAAATGC
* * * * *
265712 CTTGAATAGATTTTGTGCTACAACTT
66 CTTGCACAGACTCTGTGCTACAACCT
**
265738 TTTTCTAAAATGCTTGTTGTTGATCTCCTCTTGGATTTTCTTTCCTCTAGTTGGCATATAAATGC
1 TTGCCTAAAATGCTTGTTGTTGATCTCCTCTTGGATTTTCTTTCCTCTAGTTGGCATATAAATGC
* *
265803 CTTGCACAGACTCTATGCT-CCACCT
66 CTTGCACAGACTCTGTGCTACAACCT
*
265828 TTGCCTAAAATGCTTGTTGTTGGTCTCCTCCTT-GATTTTCTTTCCTCTAGTTGGCATATAAATG
1 TTGCCTAAAATGCTTGTTGTTGATCTCCT-CTTGGATTTTCTTTCCTCTAGTTGGCATATAAATG
*
265892 CCTTGCAGAGACTCTGTGCT
65 CCTTGCACAGACTCTGTGCT
265912 TTACTTTTGG
Statistics
Matches: 150, Mismatches: 23, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
90 79 0.53
91 71 0.47
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.43
Consensus pattern (91 bp):
TTGCCTAAAATGCTTGTTGTTGATCTCCTCTTGGATTTTCTTTCCTCTAGTTGGCATATAAATGC
CTTGCACAGACTCTGTGCTACAACCT
Found at i:267889 original size:18 final size:17
Alignment explanation
Indices: 267865--267908 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
267855 TATATCATAC
267865 ATACATAA-TATAGTAAT
1 ATACATAACTATA-TAAT
267882 ATATCATAACTTATATAAT
1 ATA-CATAAC-TATATAAT
267901 ATACATAA
1 ATACATAA
267909 ATACATCGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 3 0.12
18 10 0.42
19 7 0.29
20 4 0.17
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.36
Consensus pattern (17 bp):
ATACATAACTATATAAT
Found at i:268305 original size:85 final size:85
Alignment explanation
Indices: 268210--268379 Score: 331
Period size: 85 Copynumber: 2.0 Consensus size: 85
268200 AAAAACCATA
268210 AAAAAAGGTAAACTATAAAAATAGTCACTTTTGTTTACCTTAAATTACATTTTAGTTACATATGT
1 AAAAAAGGTAAACTATAAAAATAGTCACTTTTGTTTACCTTAAATTACATTTTAGTTACATATGT
268275 TTGAAATGTTACGTTTTAGT
66 TTGAAATGTTACGTTTTAGT
*
268295 AAAAAGGGTAAACTATAAAAATAGTCACTTTTGTTTACCTTAAATTACATTTTAGTTACATATGT
1 AAAAAAGGTAAACTATAAAAATAGTCACTTTTGTTTACCTTAAATTACATTTTAGTTACATATGT
268360 TTGAAATGTTACGTTTTAGT
66 TTGAAATGTTACGTTTTAGT
268380 CACTTATGTT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.41
Consensus pattern (85 bp):
AAAAAAGGTAAACTATAAAAATAGTCACTTTTGTTTACCTTAAATTACATTTTAGTTACATATGT
TTGAAATGTTACGTTTTAGT
Found at i:271294 original size:27 final size:28
Alignment explanation
Indices: 271255--271308 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
271245 CATTTGGGTT
*
271255 AATTGAATATTAATTAGATTAAAAAATA
1 AATTGAATATTAACTAGATTAAAAAATA
*
271283 AATT-AATATTAACTCGATTAAAAAAT
1 AATTGAATATTAACTAGATTAAAAAAT
271309 TTATTAAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.35
Consensus pattern (28 bp):
AATTGAATATTAACTAGATTAAAAAATA
Found at i:276915 original size:23 final size:23
Alignment explanation
Indices: 276889--276949 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
276879 AATGTTCACT
*
276889 AACATGTTCATTTAACT-TAATCG
1 AACATGTTCA-TGAACTATAATCG
*
276912 AACATGTTCATGAACTATAATTG
1 AACATGTTCATGAACTATAATCG
* *
276935 AACATATTCACGAAC
1 AACATGTTCATGAAC
276950 AATGTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 5 0.15
23 28 0.85
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (23 bp):
AACATGTTCATGAACTATAATCG
Found at i:277525 original size:14 final size:14
Alignment explanation
Indices: 277501--277534 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
277491 CGAATCGTAC
*
277501 TAAAGTATATATTTA
1 TAAA-TATATATATA
277516 TAAATATATATATA
1 TAAATATATATATA
277530 TAAAT
1 TAAAT
277535 TAAATTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (14 bp):
TAAATATATATATA
Found at i:277558 original size:15 final size:16
Alignment explanation
Indices: 277538--277567 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
277528 TATAAATTAA
277538 ATTA-TTTTTTAAAAT
1 ATTATTTTTTTAAAAT
277553 ATTATTTTTTTAAAA
1 ATTATTTTTTTAAAA
277568 AAATTTGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTATTTTTTTAAAAT
Found at i:278219 original size:9 final size:9
Alignment explanation
Indices: 278205--278272 Score: 60
Period size: 9 Copynumber: 8.1 Consensus size: 9
278195 GCAAATGATT
278205 TTAAAATTA
1 TTAAAATTA
278214 TTAAAATTA
1 TTAAAATTA
*
278223 TT----TTT
1 TTAAAATTA
278228 TTAAAATT-
1 TTAAAATTA
278236 TTAAAA-TA
1 TTAAAATTA
278244 -TAAAATTA
1 TTAAAATTA
278252 TTAAAATTA
1 TTAAAATTA
278261 TTTTAAAATTA
1 --TTAAAATTA
278272 T
1 T
278273 AATAATCATC
Statistics
Matches: 49, Mismatches: 1, Indels: 18
0.72 0.01 0.26
Matches are distributed among these distances:
5 4 0.08
7 6 0.12
8 8 0.16
9 22 0.45
11 9 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
TTAAAATTA
Found at i:278249 original size:15 final size:16
Alignment explanation
Indices: 278229--278258 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
278219 ATTATTTTTT
278229 TAAAATT-TTAAAATA
1 TAAAATTATTAAAATA
278244 TAAAATTATTAAAAT
1 TAAAATTATTAAAAT
278259 TATTTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAAATTATTAAAATA
Found at i:281346 original size:21 final size:21
Alignment explanation
Indices: 281285--281359 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
281275 AGAGTTTTTA
*
281285 GTATCGGTAGAAGC-ATGACTT
1 GTATCGGTAGAA-CTATCACTT
* * *
281306 GTTTCAGTAGAAGTGA-CACTT
1 GTATCGGTAGAACT-ATCACTT
*
281327 GTGTCGGTAGAACTATCACTT
1 GTATCGGTAGAACTATCACTT
*
281348 GTATTGGTAGAA
1 GTATCGGTAGAA
281360 ATCTACATTG
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
20 1 0.02
21 40 0.95
22 1 0.02
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.32
Consensus pattern (21 bp):
GTATCGGTAGAACTATCACTT
Found at i:281785 original size:28 final size:29
Alignment explanation
Indices: 281732--281805 Score: 93
Period size: 28 Copynumber: 2.6 Consensus size: 29
281722 AAAATTATTT
281732 AATAATTTTAATAA--TTTTATATTTAAAA
1 AATAA-TTTAATAATTTTTTATATTTAAAA
281760 AAT-ATTTAA-AATTTTTTATATTTTAAAA
1 AATAATTTAATAATTTTTTATA-TTTAAAA
281788 AATAAATTTAATAATTTT
1 AAT-AATTTAATAATTTT
281806 AAAATTATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
25 2 0.05
26 5 0.12
27 8 0.20
28 13 0.32
30 6 0.15
31 6 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
AATAATTTAATAATTTTTTATATTTAAAA
Found at i:286227 original size:18 final size:18
Alignment explanation
Indices: 286204--286238 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
286194 AATTCATATA
286204 ACTTTCAATTCCAATTTC
1 ACTTTCAATTCCAATTTC
* *
286222 ACTTTCACTTTCAATTT
1 ACTTTCAATTCCAATTT
286239 TGATCACAAA
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:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (18 bp):
ACTTTCAATTCCAATTTC
Found at i:286570 original size:17 final size:18
Alignment explanation
Indices: 286536--286571 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
286526 TGAATTTCTA
286536 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
286554 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
286571 T
1 T
286572 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Done.