Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009164.1 Hibiscus syriacus cultivar Beakdansim tig00112699_pilon, 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: 622707
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:1961 original size:152 final size:153
Alignment explanation
Indices: 1615--1923 Score: 480
Period size: 152 Copynumber: 2.0 Consensus size: 153
1605 AATTTACAGG
* * * * *
1615 AGCATGATATAGTGTGCGTGTCCCCTGGTTAGCTTTTGTGGATGTGTTGTACAAATTCGGGGATT
1 AGCATGACATAGTG-GCGTGGCACCT-GTTAGCTTCTGTGGATGTGTTGTACAAATGCGGGGATT
1680 CCGATTGGGTAACCCTATTAGGGTTATGGGGGGGAGTAGGTTATGCGCCACTGATGGTACTGAGG
64 CCGATTGGGTAACCCTATTAGGGTTATGGGGGGGAGTAGGTTATGCGCCACTGATGGTACTGAGG
1745 CAATTTGGGGCACGCCAATTCATCC
129 CAATTTGGGGCACGCCAATTCATCC
* * * *
1770 AGCATGATATAGTGGCGTGTCCCCTGTTAGCTTTTGTGGATGTGTTGTAC-AATGCGGGGATTCC
1 AGCATGACATAGTGGCGTGGCACCTGTTAGCTTCTGTGGATGTGTTGTACAAATGCGGGGATTCC
*
1834 GATTGGGTAACCCTATTAGGGTTATGGGGTGGAGTAGGTTATGCGCC-CTGATGGTACTGAGGCA
66 GATTGGGTAACCCTATTAGGGTTATGGGGGGGAGTAGGTTATGCGCCACTGATGGTACTGAGGCA
1898 ATTTGGGGCACG-CAATTCATCTC
131 ATTTGGGGCACGCCAATTCATC-C
1921 AGC
1 AGC
1924 TACATCGGTC
Statistics
Matches: 151, Mismatches: 2, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
150 9 0.06
151 33 0.22
152 59 0.39
153 25 0.17
154 11 0.07
155 14 0.09
ACGTcount: A:0.20, C:0.17, G:0.32, T:0.30
Consensus pattern (153 bp):
AGCATGACATAGTGGCGTGGCACCTGTTAGCTTCTGTGGATGTGTTGTACAAATGCGGGGATTCC
GATTGGGTAACCCTATTAGGGTTATGGGGGGGAGTAGGTTATGCGCCACTGATGGTACTGAGGCA
ATTTGGGGCACGCCAATTCATCC
Found at i:10608 original size:20 final size:20
Alignment explanation
Indices: 10555--10621 Score: 70
Period size: 19 Copynumber: 3.4 Consensus size: 20
10545 AAAGAAGAAG
*
10555 AAAAATGAGTGAAAAAATATA
1 AAAAATGAATGAAAAAA-ATA
10576 ATAAAA--AAT-AAAAAAATA
1 A-AAAATGAATGAAAAAAATA
10594 AAAAATGAATG-AAAAAATGA
1 AAAAATGAATGAAAAAAAT-A
10614 AAAAATGA
1 AAAAATGA
10622 GGGTTCAAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
17 4 0.10
18 4 0.10
19 16 0.40
20 11 0.28
21 1 0.03
22 4 0.10
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.16
Consensus pattern (20 bp):
AAAAATGAATGAAAAAAATA
Found at i:11698 original size:55 final size:55
Alignment explanation
Indices: 11614--11882 Score: 373
Period size: 55 Copynumber: 4.9 Consensus size: 55
11604 AGATTTCCCA
*
11614 ACGATTATTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
11669 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
*
11724 ACGATTGTTGAAGATTGTTCAAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * * *
11779 ACGATTGTTGAAGATTGTTCGAGTTTCATACTCCCT-AGAGAAAGAGGGAGCAAAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGA-AGAAATAGGGAGCAGAC
* * ** * * * *
11834 TCGTTTGAAGAAGA-TATTCGAGT-TCTATTCTCCCTGAAGAAAGAGGGAG
1 ACGATTGTTGAAGATTGTTCGAGTCTC-ATACTCTCTGAAGAAATAGGGAG
11883 TGAACCCGTT
Statistics
Matches: 198, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
53 2 0.01
54 29 0.15
55 167 0.84
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (55 bp):
ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
Found at i:11847 original size:110 final size:109
Alignment explanation
Indices: 11623--11977 Score: 375
Period size: 110 Copynumber: 3.3 Consensus size: 109
11613 AACGATTATT
11623 GAAGATTGTTCGAG-TCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGT
1 GAAGA-TGTTCGAGTTCT-ATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGT
* * * * * **
11687 TCGAGTCTCATACTCTCT-GAAGAAATAGGGAGCAGACACGATTGTT
64 TCGAGTTTCATACTCCCTAG-AGAAAGAGGGAGCAAACACGTTTGAA
*
11733 GAAGATTGTTCAAG-TCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGT
1 GAAGA-TGTTCGAGTTCT-ATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGT
*
11797 TCGAGTTTCATACTCCCTAGAGAAAGAGGGAGCAAACTCGTTTGAA
64 TCGAGTTTCATACTCCCTAGAGAAAGAGGGAGCAAACACGTTTGAA
* * * * * * * *
11843 GAAGATATTCGAGTTCTATTCTCCCTGAAGAAAGAGGGAG-TGAACCCG--T-TTAAAGA-CGTT
1 GAAGATGTTCGAGTTCTATACTCTCTGAAGAAATAGGGAGCAG-ACACGATTGTTGAAGATTGTT
* * * * * * **
11903 CGAGTTCCACACTCCCTAGATAAAGAGGGAACGAACCCGTAAGAA
65 CGAGTTTCATACTCCCTAGAGAAAGAGGGAGCAAACACGTTTGAA
11948 GAAGATGTTCGAGTTCTATACTCTCTGAAG
1 GAAGATGTTCGAGTTCTATACTCTCTGAAG
11978 GACTGGGGAA
Statistics
Matches: 213, Mismatches: 29, Indels: 11
0.84 0.11 0.04
Matches are distributed among these distances:
105 67 0.31
106 6 0.03
107 1 0.00
108 1 0.00
109 30 0.14
110 107 0.50
111 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (109 bp):
GAAGATGTTCGAGTTCTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTC
GAGTTTCATACTCCCTAGAGAAAGAGGGAGCAAACACGTTTGAA
Found at i:11875 original size:54 final size:54
Alignment explanation
Indices: 11623--11977 Score: 233
Period size: 55 Copynumber: 6.6 Consensus size: 54
11613 AACGATTATT
* * * * * **
11623 GAAGATTGTTCGAG-TCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
1 GAAGA-TGTTCGAGTTCT-ATACTCCCTGAAGAAAGAGGGAGCAAACCCGTTTGAA
* * * * * **
11678 GAAGATTGTTCGAG-TCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
1 GAAGA-TGTTCGAGTTCT-ATACTCCCTGAAGAAAGAGGGAGCAAACCCGTTTGAA
* * * * * * **
11733 GAAGATTGTTCAAG-TCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
1 GAAGA-TGTTCGAGTTCT-ATACTCCCTGAAGAAAGAGGGAGCAAACCCGTTTGAA
*
11788 GAAGATTGTTCGAGTT-TCATACTCCCT-AGAGAAAGAGGGAGCAAACTCGTTTGAA
1 GAAGA-TGTTCGAGTTCT-ATACTCCCTGA-AGAAAGAGGGAGCAAACCCGTTTGAA
* * **
11843 GAAGATATTCGAGTTCTATTCTCCCTGAAGAAAGAGGGAGTGAACCCGTTT--A
1 GAAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCAAACCCGTTTGAA
* * * * * * **
11895 -AAGACGTTCGAGTTCCACACTCCCT-AGATAAAGAGGGAACGAACCCGTAAGAA
1 GAAGATGTTCGAGTTCTATACTCCCTGA-AGAAAGAGGGAGCAAACCCGTTTGAA
*
11948 GAAGATGTTCGAGTTCTATACTCTCTGAAG
1 GAAGATGTTCGAGTTCTATACTCCCTGAAG
11978 GACTGGGGAA
Statistics
Matches: 262, Mismatches: 29, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
50 1 0.00
51 38 0.15
52 1 0.00
53 1 0.00
54 60 0.23
55 160 0.61
56 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (54 bp):
GAAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCAAACCCGTTTGAA
Found at i:11928 original size:51 final size:53
Alignment explanation
Indices: 11795--11970 Score: 169
Period size: 54 Copynumber: 3.3 Consensus size: 53
11785 GTTGAAGATT
* * * *
11795 GTTCGAGTTTCATACTCCCTAGAGAAAGAGGGAGCAAACTCGTTTGAAGAAGAT
1 GTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT-AAGAAGAC
* * * *
11849 ATTCGAGTTCTATTCTCCCT-GAAGAAAGAGGGAGTGAACCCGTTT-A-AAGAC
1 GTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTTAAGAAGAC
* * * ** *
11900 GTTCGAGTTCCACACTCCCTAGATAAAGAGGGAACGAACCCGTAAGAAGAAGAT
1 GTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT-TTAAGAAGAC
*
11954 GTTCGAGTTCTATACTC
1 GTTCGAGTTCCATACTC
11971 TCTGAAGGAC
Statistics
Matches: 97, Mismatches: 20, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
51 38 0.39
52 2 0.02
53 2 0.02
54 55 0.57
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (53 bp):
GTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTAAGAAGAC
Found at i:12383 original size:2 final size:2
Alignment explanation
Indices: 12376--12404 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12366 TGTAGTCATG
12376 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
12405 GTGTGTGTGT
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:22825 original size:23 final size:23
Alignment explanation
Indices: 22795--22846 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
22785 ATTTACGTTA
* *
22795 ATTTTTTT-AATTTAATAAATTAT
1 ATTTTTTTAAATTTAA-AAAATAC
22818 ATTTTTTTAAATTTAAAAAATAC
1 ATTTTTTTAAATTTAAAAAATAC
22841 ATTTTT
1 ATTTTT
22847 AATAAACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTTTTTTAAATTTAAAAAATAC
Found at i:22852 original size:24 final size:24
Alignment explanation
Indices: 22795--22852 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 24
22785 ATTTACGTTA
* * *
22795 ATTTTT-TTAATTTAATAAATTAT
1 ATTTTTATAAATTTAATAAAATAC
*
22818 ATTTTTTTAAATTTAA-AAAATAC
1 ATTTTTATAAATTTAATAAAATAC
22841 ATTTTTAATAAA
1 ATTTTT-ATAAA
22853 CTTATCACCT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 17 0.59
24 12 0.41
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
ATTTTTATAAATTTAATAAAATAC
Found at i:23166 original size:20 final size:20
Alignment explanation
Indices: 23141--23233 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
23131 TTTTCCCAAT
23141 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
23161 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
23181 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
23202 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
23223 TCGCAATGCGA
1 TCGCAATGCGA
23234 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:23183 original size:41 final size:41
Alignment explanation
Indices: 23138--23233 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
23128 CGATTTTCCC
23138 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
23179 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
23220 AAATCGCAATGCGA
1 AATTCGCAATGCGA
23234 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:23187 original size:21 final size:20
Alignment explanation
Indices: 23141--23233 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
23131 TTTTCCCAAT
*
23141 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
23161 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
23181 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
23202 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
23223 TCGCAATGCGA
1 TCGCAATGCGA
23234 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:23247 original size:20 final size:20
Alignment explanation
Indices: 23222--23315 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
23212 AATTGGGAAA
*
23222 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
23242 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
23263 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
23283 TTCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
*
23303 TTCGCAACGCGAT
1 ATCGCAACGCGAT
23316 TTACTTAGCG
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 44 0.76
21 14 0.24
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:23296 original size:41 final size:41
Alignment explanation
Indices: 23219--23296 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
23209 GCGAATTGGG
* * **
23219 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
* *
23260 AAAATCGCAACGAGATACTTACTTTCGCAACACGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATA
23297 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
Found at i:23887 original size:19 final size:19
Alignment explanation
Indices: 23863--23907 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
23853 GCAACGAGAT
*
23863 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
23882 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
23901 AATCGCA
1 AATCGCA
23908 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:23925 original size:19 final size:19
Alignment explanation
Indices: 23903--24087 Score: 174
Period size: 19 Copynumber: 10.1 Consensus size: 19
23893 GAAACCAAAA
*
23903 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
23922 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
23941 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
23960 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
23980 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
23996 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
24013 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
24027 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
24046 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
24066 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
24086 TC
1 TC
24088 AACCAAAAGA
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 20 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 60 0.43
20 49 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:23980 original size:39 final size:38
Alignment explanation
Indices: 23903--23992 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
23893 GAAACCAAAA
* *
23903 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
23941 TCGCGTTGCGATTTTAATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGC-GTTGCGATTTTCATT
23980 TCGCGTTGCGATT
1 TCGCGTTGCGATT
23993 GTCTGGTCGC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 21 0.43
39 28 0.57
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
Found at i:24012 original size:33 final size:33
Alignment explanation
Indices: 23975--24062 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
23965 GTTGCGATTT
* *
23975 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
24008 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
24041 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
24063 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:24064 original size:20 final size:20
Alignment explanation
Indices: 24030--24087 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
24020 GCGATTCTCT
**
24030 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
24050 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
24070 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
24088 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:26141 original size:42 final size:42
Alignment explanation
Indices: 26082--26202 Score: 111
Period size: 42 Copynumber: 2.9 Consensus size: 42
26072 CCGACTCGCC
* * *
26082 TATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCA
1 TATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCA
* * *
26124 TATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGG-CCA
1 TATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCA
* ** * *
26165 CTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 -TATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
26203 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
41 3 0.05
42 57 0.89
43 4 0.06
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.23
Consensus pattern (42 bp):
TATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCA
Found at i:26201 original size:21 final size:20
Alignment explanation
Indices: 26142--26202 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
26132 CTCGAGAGTC
26142 CCCTCCCACCGTTCAAGAGG
1 CCCTCCCACCGTTCAAGAGG
** * *
26162 CCACTGTCATCGTTGAAGAGG
1 CC-CTCCCACCGTTCAAGAGG
*
26183 TCCCTCCCACCATTCAAGAG
1 -CCCTCCCACCGTTCAAGAG
26203 CCCGATTCAC
Statistics
Matches: 30, Mismatches: 9, Indels: 3
0.71 0.21 0.07
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.23, C:0.38, G:0.20, T:0.20
Consensus pattern (20 bp):
CCCTCCCACCGTTCAAGAGG
Found at i:27577 original size:14 final size:14
Alignment explanation
Indices: 27558--27593 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
27548 ATTGTTTAAT
27558 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
27572 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
27586 TGATTTGT
1 TGATTTGT
27594 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:27794 original size:19 final size:19
Alignment explanation
Indices: 27772--27889 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
27762 CGAAATTAAA
27772 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
27791 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
27806 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
27824 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
27839 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
27857 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
27876 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
27890 GGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:27818 original size:33 final size:33
Alignment explanation
Indices: 27776--27869 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
27766 ATTAAATTCG
27776 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
27809 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
27842 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
27870 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:30173 original size:12 final size:12
Alignment explanation
Indices: 30156--30180 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30146 TTCTTCGGGA
30156 CTTTTTCTTCTT
1 CTTTTTCTTCTT
30168 CTTTTTCTTCTT
1 CTTTTTCTTCTT
30180 C
1 C
30181 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:30422 original size:24 final size:24
Alignment explanation
Indices: 30371--30422 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
30361 ATTCGTGTAT
** *
30371 TGACCAATATCAAAGTCCGGGTAT
1 TGACCAATATCAAAGTCCGAATAC
* *
30395 TGACCAATATCAAATTTCGAATAC
1 TGACCAATATCAAAGTCCGAATAC
30419 TGAC
1 TGAC
30423 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (24 bp):
TGACCAATATCAAAGTCCGAATAC
Found at i:31520 original size:19 final size:19
Alignment explanation
Indices: 31496--31543 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
31486 ATCGCAACGA
31496 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
31515 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
31534 GAAAATCGCA
1 GAAAATCGCA
31544 TTGTGATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.48, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:31690 original size:14 final size:14
Alignment explanation
Indices: 31671--31707 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
31661 CATCAATTAA
31671 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
31685 ACAAATCATCTTTT
1 ACAAATCAACATTT
31699 ACAAATCAA
1 ACAAATCAA
31708 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:32520 original size:22 final size:22
Alignment explanation
Indices: 32479--32545 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
32469 CTCGTATAAA
32479 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
32502 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
32524 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
32546 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:34233 original size:21 final size:21
Alignment explanation
Indices: 34209--34249 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
34199 ATTTGTTCGT
* *
34209 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
34230 TTGAATGGGTACCGATTCCC
1 TTGAAGGGGTACCGATTCCC
34250 TTGCCAGAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:37334 original size:24 final size:24
Alignment explanation
Indices: 37307--37374 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 24
37297 GTCACCAGCT
*
37307 CGTATAAATGCACCGAAGTGCCCC
1 CGTAGAAATGCACCGAAGTGCCCC
*
37331 CGTAGAATTGCACCGAAGTG---C
1 CGTAGAAATGCACCGAAGTGCCCC
* *
37352 CGTAGAATTGCACCGTAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
37375 GTAGAATGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
21 20 0.53
24 18 0.47
ACGTcount: A:0.26, C:0.29, G:0.25, T:0.19
Consensus pattern (24 bp):
CGTAGAAATGCACCGAAGTGCCCC
Found at i:37356 original size:21 final size:22
Alignment explanation
Indices: 37315--37381 Score: 100
Period size: 21 Copynumber: 3.0 Consensus size: 22
37305 CTCGTATAAA
37315 TGCACCGAAGTGCCCCCGTAGAAT
1 TGCACCGAAGTG--CCCGTAGAAT
37339 TGCACCGAAGTG-CCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
37360 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
37382 GATGTCCATA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
21 20 0.49
22 9 0.22
24 12 0.29
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:39043 original size:21 final size:21
Alignment explanation
Indices: 39019--39063 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
39009 ATTTGTTCGT
* *
39019 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
39040 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
39061 TTG
1 TTG
39064 CCCAGAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:42140 original size:23 final size:22
Alignment explanation
Indices: 42114--42180 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
42104 GCTCGTATAA
42114 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
42137 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
42159 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
42181 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:43846 original size:21 final size:21
Alignment explanation
Indices: 43822--43862 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
43812 TCTTGTTCGT
* *
43822 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
43843 TTGAATGGGTACCGATTCCC
1 TTGAAGGGGTACCGATTCCC
43863 TTTGCCAGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:44818 original size:20 final size:20
Alignment explanation
Indices: 44793--44843 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
44783 ATTCATTTGA
*
44793 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGCGAAAATGG
44813 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
44833 TTATCACAACG
1 CTATCGCAACG
44844 AGAATATCGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.20
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:44935 original size:18 final size:18
Alignment explanation
Indices: 44868--44949 Score: 102
Period size: 17 Copynumber: 4.8 Consensus size: 18
44858 CGAAATGAAA
*
44868 TCGCATTGCGATTT--TC
1 TCGCATTGCGATTTCATT
44884 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
44901 TCGCATTGCGA-TTCATT
1 TCGCATTGCGATTTCATT
*
44918 TCGCATTGTGATTTCATT
1 TCGCATTGCGATTTCATT
44936 TCGCATTGCGATTT
1 TCGCATTGCGATTT
44950 TCGTTGCGAT
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
14 6 0.11
15 3 0.05
16 3 0.05
17 20 0.35
18 19 0.33
19 6 0.11
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:46971 original size:39 final size:38
Alignment explanation
Indices: 46928--47001 Score: 112
Period size: 39 Copynumber: 1.9 Consensus size: 38
46918 GAAACTTAAA
**
46928 ATCGCAACGCGAAATGACTATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAATGAAAATCGCAACGC-GAAATGGCT
*
46967 ATCGCAATGCGAAATGAAAATCGCAACGCGAAATG
1 ATCGCAACGCGAAATGAAAATCGCAACGCGAAATG
47002 AAATCGCAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 6 0.19
39 26 0.81
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (38 bp):
ATCGCAACGCGAAATGAAAATCGCAACGCGAAATGGCT
Found at i:47018 original size:18 final size:19
Alignment explanation
Indices: 46909--47012 Score: 111
Period size: 19 Copynumber: 5.4 Consensus size: 19
46899 TAGTTTACTT
* *
46909 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
46929 TCGCAACGCGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
46948 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
46968 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
46987 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
47005 TCGCAACG
1 TCGCAACG
47013 ACAAATCACA
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
18 11 0.15
19 33 0.45
20 29 0.40
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:47078 original size:14 final size:14
Alignment explanation
Indices: 47059--47115 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
47049 TTTCATTTCG
47059 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
47073 CGTTGCGATTTCAT-T
1 CGTTGCGATTT--TGT
47088 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
47104 CGTTGCGATTTT
1 CGTTGCGATTTT
47116 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 23 0.61
15 2 0.05
16 2 0.05
17 11 0.29
ACGTcount: A:0.09, C:0.18, G:0.26, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:47093 original size:31 final size:33
Alignment explanation
Indices: 47042--47131 Score: 157
Period size: 31 Copynumber: 2.8 Consensus size: 33
47032 ACAAATCGCA
47042 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
47075 TTGCGA-TTTCA-TTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
47106 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
47132 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
31 26 0.48
32 10 0.19
33 18 0.33
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:47150 original size:20 final size:19
Alignment explanation
Indices: 47116--47169 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
47106 TTGCGATTTT
*
47116 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
47135 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
47155 CATTTCGTGTTGCGA
1 CATTTCGCGTTGCGA
47170 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:47168 original size:19 final size:19
Alignment explanation
Indices: 47104--47169 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
47094 GCGATTTTGT
**
47104 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
47123 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
47143 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
47162 TGTTGCGA
1 CGTTGCGA
47170 AAGTAAACTA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 22 0.56
20 17 0.44
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:47657 original size:18 final size:18
Alignment explanation
Indices: 47631--47675 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
47621 GTCGATCAGA
*
47631 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
47649 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
47667 TGATGGCTC
1 TGATGGCTC
47676 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:49192 original size:21 final size:21
Alignment explanation
Indices: 49168--49210 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
49158 GATTTAGATA
49168 GACGGATTTCGCCGGAGATGG
1 GACGGATTTCGCCGGAGATGG
*
49189 GACGGATTTCGTCGGAGATGG
1 GACGGATTTCGCCGGAGATGG
49210 G
1 G
49211 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.16, G:0.44, T:0.21
Consensus pattern (21 bp):
GACGGATTTCGCCGGAGATGG
Found at i:49421 original size:20 final size:20
Alignment explanation
Indices: 49396--49489 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
49386 GATTATGTAT
49396 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
49416 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
49436 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
49457 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
49477 TATCGCATTGCGA
1 TATCGCGTTGCGA
49490 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:49490 original size:20 final size:20
Alignment explanation
Indices: 49376--49490 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
49366 CGCTTTGAAA
*
49376 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
49397 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
49417 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
49437 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
49458 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
49478 ATCGCATTGCGAT
1 ATCGCATTGCGAT
49491 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:49508 original size:21 final size:21
Alignment explanation
Indices: 49479--49554 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
49469 ATAGTCAGTA
49479 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
49500 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
*
49520 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
*
49541 TCGCGTTGCGATTT
1 TCGCATTGCGATTT
49555 ACTTATTCGC
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 16 0.36
21 28 0.64
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:49509 original size:41 final size:41
Alignment explanation
Indices: 49418--49552 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
49408 AAAGTCAGTA
* * * ** *
49418 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
49458 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
49500 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
49541 TCGCGTTGCGAT
1 TCGCGTTGCGAT
49553 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:49523 original size:20 final size:20
Alignment explanation
Indices: 49498--49564 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
49488 GATTTTCCCA
49498 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
* * **
49518 ATTCGCATTGCGAATTTCCCA
1 ATTCGCGTTGCG-ATTTACTT
49539 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
49559 ATTCGC
1 ATTCGC
49565 ATTACGAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACTT
Found at i:49553 original size:41 final size:41
Alignment explanation
Indices: 49479--49574 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
49469 ATAGTCAGTA
*
49479 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
49520 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
*
49561 TCGCATTACGAATT
1 TCGCATTGCGAATT
49575 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:50682 original size:33 final size:32
Alignment explanation
Indices: 50642--50714 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 32
50632 CAGAGCCTTC
* *
50642 CTTCGCCGCTGAAA-CCGGCCAGAAAATCGATTT
1 CTTCGCCGC-CAAAGCCGCCCAGAAAATCG-TTT
*
50675 GTTCGCCGCCAAAGCCGCCCAGAAAATCGTTT
1 CTTCGCCGCCAAAGCCGCCCAGAAAATCGTTT
50707 CTTCGCCG
1 CTTCGCCG
50715 ACTTCGTCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 13 0.37
33 22 0.63
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (32 bp):
CTTCGCCGCCAAAGCCGCCCAGAAAATCGTTT
Found at i:51666 original size:19 final size:20
Alignment explanation
Indices: 51639--51681 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
51629 AATTTTAAAA
51639 AATTAAAATAATTTATTTAT
1 AATTAAAATAATTTATTTAT
* *
51659 AATT-AAATATTTTTTTTAT
1 AATTAAAATAATTTATTTAT
51678 AATT
1 AATT
51682 TTATTAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
AATTAAAATAATTTATTTAT
Found at i:51666 original size:25 final size:25
Alignment explanation
Indices: 51594--51666 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 25
51584 TAAATACAAT
*
51594 AAATAATATTATTTATCATAAAATTTA
1 AAATAAT-TTATTTATAATAAAA-TTA
* * *
51621 ATATTATTAATTT-TAA-AAAATTA
1 AAATAATTTATTTATAATAAAATTA
*
51644 AAATAATTTATTTATAATTAAAT
1 AAATAATTTATTTATAATAAAAT
51667 ATTTTTTTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
23 13 0.36
24 7 0.19
25 6 0.17
26 5 0.14
27 5 0.14
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (25 bp):
AAATAATTTATTTATAATAAAATTA
Found at i:51922 original size:22 final size:23
Alignment explanation
Indices: 51897--51956 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
51887 TTTCTATGAA
51897 ATTAATAAATAATATAAATT-TT
1 ATTAATAAATAATATAAATTATT
* * *
51919 ATTAATAATTATTATATATTATT
1 ATTAATAAATAATATAAATTATT
*
51942 A-AAATAAA-AATATAA
1 ATTAATAAATAATATAA
51957 TAACCTATAT
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
21 5 0.17
22 22 0.73
23 3 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTAATAAATAATATAAATTATT
Found at i:52031 original size:17 final size:17
Alignment explanation
Indices: 51992--52041 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
51982 GATTATTTTA
*
51992 TTAAATATT-ATATTAT
1 TTAAATATTAATAATAT
*
52008 TAGAAATATTAATAATAT
1 T-TAAATATTAATAATAT
52026 TTAAATATTTAATAAT
1 TTAAATA-TTAATAAT
52042 TAATATTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 1 0.04
17 12 0.43
18 15 0.54
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
TTAAATATTAATAATAT
Found at i:52987 original size:6 final size:6
Alignment explanation
Indices: 52976--53002 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
52966 CTATAAAAAA
52976 TAATTT TAATTT TAATTT TAATTT TAA
1 TAATTT TAATTT TAATTT TAATTT TAA
53003 ATATTGTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
TAATTT
Found at i:56535 original size:66 final size:66
Alignment explanation
Indices: 56429--56556 Score: 229
Period size: 66 Copynumber: 1.9 Consensus size: 66
56419 TTCTATCTAA
* *
56429 ACATCTGTATTCCTACCACAAACAGATCTTATGTTTCTCTGTGATAGAAGTTCAGCCTTTCTCTT
1 ACATCTGTATTCCTACAACAAACAGATCTTATGTTTCTCTGTGATAGAAGTTCAACCTTTCTCTT
56494 G
66 G
*
56495 ACATCTGTATTTCTACAACAAACAGATCTTATGTTTCTCTGTGATAGAAGTTCAACCTTTCT
1 ACATCTGTATTCCTACAACAAACAGATCTTATGTTTCTCTGTGATAGAAGTTCAACCTTTCT
56557 ACTCTTGTTC
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (66 bp):
ACATCTGTATTCCTACAACAAACAGATCTTATGTTTCTCTGTGATAGAAGTTCAACCTTTCTCTT
G
Found at i:59612 original size:17 final size:17
Alignment explanation
Indices: 59586--59621 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
59576 ATAAAACTTC
59586 GAGTTAGAGGCTTTTTT
1 GAGTTAGAGGCTTTTTT
*
59603 GAGTTGGAGGCTTTTTT
1 GAGTTAGAGGCTTTTTT
59620 GA
1 GA
59622 AGTGTAGTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.06, G:0.33, T:0.44
Consensus pattern (17 bp):
GAGTTAGAGGCTTTTTT
Found at i:61244 original size:17 final size:17
Alignment explanation
Indices: 61219--61254 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
61209 GATTCGTGTG
*
61219 TTTAGTAAAATTTAAAT
1 TTTAGTAAAATATAAAT
*
61236 TTTATTAAAATATAAAT
1 TTTAGTAAAATATAAAT
61253 TT
1 TT
61255 GATAAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TTTAGTAAAATATAAAT
Found at i:61589 original size:3 final size:3
Alignment explanation
Indices: 61581--61649 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
61571 TAGACCACTA
61581 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
61629 AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT
61650 GGGGGTTTTA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:65645 original size:28 final size:27
Alignment explanation
Indices: 65614--65673 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 27
65604 ATGTAATGCT
*
65614 TAGTATGATACAT-ATTTTTATTTTATAA
1 TAGTAT-ATAAATAATTTTTATTTTAT-A
*
65642 TAGTGTATAAATAGATTTTTATTTTATA
1 TAGTATATAAATA-ATTTTTATTTTATA
65670 TAGT
1 TAGT
65674 TTTCAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 5 0.18
28 10 0.36
29 13 0.46
ACGTcount: A:0.35, C:0.02, G:0.10, T:0.53
Consensus pattern (27 bp):
TAGTATATAAATAATTTTTATTTTATA
Found at i:65844 original size:18 final size:19
Alignment explanation
Indices: 65802--65846 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
65792 AATAATAATT
*
65802 ATAAATTTAAATTTATCAA
1 ATAAAATTAAATTTATCAA
*
65821 AT--AATTACATTT-TCAA
1 ATAAAATTAAATTTATCAA
65837 ATAAAATTAA
1 ATAAAATTAA
65847 TAAATTTTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 5
0.72 0.10 0.17
Matches are distributed among these distances:
16 6 0.29
17 8 0.38
18 5 0.24
19 2 0.10
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAAAATTAAATTTATCAA
Found at i:66384 original size:6 final size:6
Alignment explanation
Indices: 66373--66416 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
66363 TCAAAGAGAG
66373 GGGTTA GGGTTA GGGTTA GGGTTA GGGTTA GGGTTA GGGTTA GG
1 GGGTTA GGGTTA GGGTTA GGGTTA GGGTTA GGGTTA GGGTTA GG
66417 AAATTAGGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (6 bp):
GGGTTA
Found at i:72783 original size:30 final size:31
Alignment explanation
Indices: 72739--72838 Score: 89
Period size: 30 Copynumber: 3.3 Consensus size: 31
72729 TTAGTTTAAT
**
72739 CTCTAAATGGTAGATTGAATATTAATTTGAC
1 CTCTAAATTTTAGATTGAATATTAATTTGAC
*
72770 C-CTAAATTTTAGA-TGAA-ATTCATTTTGAC
1 CTCTAAATTTTAGATTGAATATT-AATTTGAC
* * * ** *
72799 CTTTAAACTTTAAATAAAATATCAATTTGAC
1 CTCTAAATTTTAGATTGAATATTAATTTGAC
72830 CTCTAAATT
1 CTCTAAATT
72839 CGATCAAAGT
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
28 3 0.06
29 12 0.23
30 19 0.36
31 17 0.32
32 2 0.04
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (31 bp):
CTCTAAATTTTAGATTGAATATTAATTTGAC
Found at i:72831 original size:31 final size:31
Alignment explanation
Indices: 72756--72836 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 31
72746 TGGTAGATTG
* * * *
72756 AATATTAATTTGACC-CTAAATTTTAGATGA
1 AATATCAATTTGACCTCTAAACTTTAAATAA
* *
72786 AAT-TCATTTTGACCTTTAAACTTTAAATAA
1 AATATCAATTTGACCTCTAAACTTTAAATAA
72816 AATATCAATTTGACCTCTAAA
1 AATATCAATTTGACCTCTAAA
72837 TTCGATCAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 9 0.22
30 17 0.41
31 15 0.37
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.40
Consensus pattern (31 bp):
AATATCAATTTGACCTCTAAACTTTAAATAA
Found at i:74764 original size:28 final size:29
Alignment explanation
Indices: 74709--74765 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
74699 ACGTGGCGTG
* *
74709 TGAGCTGTTAGGAAGTTAGATGTTGTTAGC
1 TGAGCAGTTAGG-AGTTAGATGTAGTTAGC
*
74739 TGAGCAGTTAGG-GTTAGTTGTAGTTAG
1 TGAGCAGTTAGGAGTTAGATGTAGTTAG
74766 TTGGGTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 13 0.54
30 11 0.46
ACGTcount: A:0.23, C:0.05, G:0.35, T:0.37
Consensus pattern (29 bp):
TGAGCAGTTAGGAGTTAGATGTAGTTAGC
Found at i:77937 original size:19 final size:20
Alignment explanation
Indices: 77913--77955 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
77903 GGGAACACCC
*
77913 TTATAA-CCTTCCCATACAT
1 TTATAAGCCTTACCATACAT
*
77932 TTATAAGCCTTACCATGCAT
1 TTATAAGCCTTACCATACAT
77952 TTAT
1 TTAT
77956 GTAGCTTGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.30, C:0.26, G:0.05, T:0.40
Consensus pattern (20 bp):
TTATAAGCCTTACCATACAT
Found at i:79203 original size:63 final size:64
Alignment explanation
Indices: 79068--79207 Score: 156
Period size: 63 Copynumber: 2.2 Consensus size: 64
79058 TTGTTCAAGG
* * *** *
79068 TGTATCGATGCACATGAAGTGCATCGATGCACTCTTTTTAAATACAAACATCGAATTCCATCGA
1 TGTATCGATGCATAAGAAGTGCATCGATGCACTCCCCTTAAATACAAACATCGAATACCATCGA
* * * ** **
79132 TGCATCGATGCATAAGGAGTGCATCGATGCAC-CCCCTTAAATATAAACATCGAATAGGATTTA
1 TGTATCGATGCATAAGAAGTGCATCGATGCACTCCCCTTAAATACAAACATCGAATACCATCGA
79195 TGTATCGATGCAT
1 TGTATCGATGCAT
79208 GGTGTGGTGC
Statistics
Matches: 62, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
63 34 0.55
64 28 0.45
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.29
Consensus pattern (64 bp):
TGTATCGATGCATAAGAAGTGCATCGATGCACTCCCCTTAAATACAAACATCGAATACCATCGA
Found at i:79520 original size:25 final size:25
Alignment explanation
Indices: 79470--79526 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
79460 TCTAGATTTT
* *
79470 ATATTTTGATACATGATCGCATTTC
1 ATATTATGATACATGATCGCAATTC
*
79495 ATATTATGATACATGATATG-AATTC
1 ATATTATGATACATGAT-CGCAATTC
79520 ATATTAT
1 ATATTAT
79527 ATGCATTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 27 0.96
26 1 0.04
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.44
Consensus pattern (25 bp):
ATATTATGATACATGATCGCAATTC
Found at i:79607 original size:31 final size:30
Alignment explanation
Indices: 79569--79628 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
79559 TTATATAAGC
79569 TATGTGATAAAG-TGATGGAACATGATATGTT
1 TATGTGATAAAGAT-ATGGAA-ATGATATGTT
*
79600 TATGTGATAAAGATATGGAAATTATATGT
1 TATGTGATAAAGATATGGAAATGATATGT
79629 CTATACAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.30
31 18 0.67
32 1 0.04
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (30 bp):
TATGTGATAAAGATATGGAAATGATATGTT
Found at i:79877 original size:23 final size:23
Alignment explanation
Indices: 79860--79909 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
79850 TGGCACTATG
*
79860 GTGCAATTCTATGCGGCACTTCA
1 GTGCAATTCTACGCGGCACTTCA
* *
79883 GTGCAATTCTACGTGGCACTTCG
1 GTGCAATTCTACGCGGCACTTCA
79906 GTGC
1 GTGC
79910 GTTTATACGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (23 bp):
GTGCAATTCTACGCGGCACTTCA
Found at i:79918 original size:23 final size:23
Alignment explanation
Indices: 79860--79918 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 23
79850 TGGCACTATG
* * *
79860 GTGCAATTCTATGCGGCACTTCA
1 GTGCAATTATACGTGGCACTTCA
* *
79883 GTGCAATTCTACGTGGCACTTCG
1 GTGCAATTATACGTGGCACTTCA
**
79906 GTGCGTTTATACG
1 GTGCAATTATACG
79919 AGATGTGGTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (23 bp):
GTGCAATTATACGTGGCACTTCA
Found at i:86436 original size:25 final size:25
Alignment explanation
Indices: 86383--86439 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
86373 TCTAGATTCA
* *
86383 ATATTTTGATACATGATCGCATTTC
1 ATATTATGATACATGATCGAATTTC
*
86408 ATATTATGATACATGATATGAATTT-
1 ATATTATGATACATGAT-CGAATTTC
86433 ATATTAT
1 ATATTAT
86440 ATGCATTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 23 0.82
26 5 0.18
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.46
Consensus pattern (25 bp):
ATATTATGATACATGATCGAATTTC
Found at i:86520 original size:31 final size:29
Alignment explanation
Indices: 86482--86540 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 29
86472 TTTTATAAGC
*
86482 TATGTGATAAAGTGATGGAACATGATATGTT
1 TATGTGATAAAAT-ATGGAA-ATGATATGTT
*
86513 TATGTGATAAAATATGGAAATTATATGT
1 TATGTGATAAAATATGGAAATGATATGT
86541 CTATACAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
30 6 0.23
31 12 0.46
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.37
Consensus pattern (29 bp):
TATGTGATAAAATATGGAAATGATATGTT
Found at i:86829 original size:23 final size:23
Alignment explanation
Indices: 86761--86820 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
86751 CAATCTTATA
*
86761 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
86784 TGGCACTTCTGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
86807 TGGCACTTCGGTGC
1 TGGCACTTCGGTGC
86821 GTTTATACGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:89227 original size:30 final size:30
Alignment explanation
Indices: 89193--89279 Score: 133
Period size: 30 Copynumber: 3.0 Consensus size: 30
89183 CGTGGTGTAT
89193 GAGCTGTTAGGAGATTAGATGTTGTTAGCC
1 GAGCTGTTAGGAGATTAGATGTTGTTAGCC
89223 GAGCTGTTAGGAGATTAGATGTTGTTAGCC
1 GAGCTGTTAGGAGATTAGATGTTGTTAGCC
* * *
89253 GAGCAGTTAGG-G-TTAGCTGTAGTTAGC
1 GAGCTGTTAGGAGATTAGATGTTGTTAGC
89280 TAGTCGTTAG
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
28 13 0.24
29 1 0.02
30 40 0.74
ACGTcount: A:0.23, C:0.10, G:0.34, T:0.32
Consensus pattern (30 bp):
GAGCTGTTAGGAGATTAGATGTTGTTAGCC
Found at i:99652 original size:17 final size:17
Alignment explanation
Indices: 99617--99651 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
99607 CGGGTTAAGG
99617 TTAGAGATTTAGGATTT
1 TTAGAGATTTAGGATTT
*
99634 TTAGGGATTT-GGATTT
1 TTAGAGATTTAGGATTT
99650 TT
1 TT
99652 TTGTAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (17 bp):
TTAGAGATTTAGGATTT
Found at i:101132 original size:30 final size:30
Alignment explanation
Indices: 101098--101154 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
101088 GGAGAGAGAA
*
101098 AGGGAAAGGGAGAGGGAGGAGAAGGGGACG
1 AGGGAAAGGAAGAGGGAGGAGAAGGGGACG
* * *
101128 AGGGATAGGAAGAGGTAGGAGACGGGG
1 AGGGAAAGGAAGAGGGAGGAGAAGGGG
101155 TTAGGGGCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.58, T:0.04
Consensus pattern (30 bp):
AGGGAAAGGAAGAGGGAGGAGAAGGGGACG
Found at i:101182 original size:14 final size:15
Alignment explanation
Indices: 101163--101219 Score: 75
Period size: 16 Copynumber: 3.9 Consensus size: 15
101153 GGTTAGGGGC
101163 ATTTTTTAAAATAT-
1 ATTTTTTAAAATATA
101177 A-TTTTT-AAATATA
1 ATTTTTTAAAATATA
*
101190 ATTTTTTTAAATATA
1 ATTTTTTAAAATATA
101205 ATTTTTTTAAAATAT
1 A-TTTTTTAAAATAT
101220 CAAATATGAC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
12 6 0.16
13 6 0.16
14 6 0.16
15 8 0.21
16 12 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTTTTTAAAATATA
Found at i:101210 original size:16 final size:15
Alignment explanation
Indices: 101164--101215 Score: 81
Period size: 15 Copynumber: 3.6 Consensus size: 15
101154 GTTAGGGGCA
101164 TTTTTTAAA-AT-AT
1 TTTTTTAAATATAAT
*
101177 ATTTTTAAATATAAT
1 TTTTTTAAATATAAT
101192 TTTTTTAAATATAAT
1 TTTTTTAAATATAAT
101207 TTTTTTAAA
1 TTTTTTAAA
101216 ATATCAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.23
14 2 0.06
15 25 0.71
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTTTAAATATAAT
Found at i:101901 original size:20 final size:19
Alignment explanation
Indices: 101858--101901 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
101848 TATTATATAT
*
101858 TAAAAATTTTATATAAACA
1 TAAAAATTTTAAATAAACA
*
101877 TAAAATATATTAAATAAA-A
1 TAAAA-ATTTTAAATAAACA
101896 TAAAAA
1 TAAAAA
101902 AATAAGAACG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 1 0.05
19 11 0.50
20 10 0.45
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAATTTTAAATAAACA
Found at i:102747 original size:22 final size:22
Alignment explanation
Indices: 102722--102788 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
102712 CGGCGACATC
*
102722 CCCCATCTCCGACGAAATCCGT
1 CCCCATTTCCGACGAAATCCGT
102744 CCCCATTTCCGACGAAATCCGT
1 CCCCATTTCCGACGAAATCCGT
*
102766 CCTCATTTCCGACGAAATCCGT
1 CCCCATTTCCGACGAAATCCGT
102788 C
1 C
102789 TATCTCCATC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.22, C:0.42, G:0.13, T:0.22
Consensus pattern (22 bp):
CCCCATTTCCGACGAAATCCGT
Found at i:103109 original size:20 final size:20
Alignment explanation
Indices: 103068--103109 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
103058 GAAACTAAAA
* * *
103068 TCGCGTTGCGATTTTCATTT
1 TCGCGTTGCGAATTTAAGTT
103088 TCGCGTTGCGAATTTAAGTT
1 TCGCGTTGCGAATTTAAGTT
103108 TC
1 TC
103110 AGAAACTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGAATTTAAGTT
Found at i:104784 original size:21 final size:21
Alignment explanation
Indices: 104760--104809 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
104750 GTTAGGGGAA
*
104760 TTACGTGATGAGGTCGGTGCT
1 TTACGTGATGAGGTCGGTACT
*
104781 TTACGTTATGAGGTCGGTACT
1 TTACGTGATGAGGTCGGTACT
104802 TTACGTGA
1 TTACGTGA
104810 AGATAATGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.18, C:0.14, G:0.32, T:0.36
Consensus pattern (21 bp):
TTACGTGATGAGGTCGGTACT
Found at i:105250 original size:21 final size:20
Alignment explanation
Indices: 105215--105311 Score: 63
Period size: 21 Copynumber: 4.7 Consensus size: 20
105205 CCTATCATCA
**
105215 TTCAAGAGGGGCCTCCTATCG
1 TTCAAGAGGCCCCT-CTATCG
105236 TTCAAGAGGCCCCTCTCATC-
1 TTCAAGAGGCCCCTCT-ATCG
* * * * *
105256 ATCGAAGAAGCCCATCCCACCG
1 TTC-AAGAGGCCCCT-CTATCG
105278 TTCAAGAGGCACCCGTC-ATCG
1 TTCAAGAGGC-CCC-TCTATCG
105299 TTCAAGAGGCCCC
1 TTCAAGAGGCCCC
105312 GCCCGCCGTT
Statistics
Matches: 59, Mismatches: 11, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
20 7 0.12
21 45 0.76
22 6 0.10
23 1 0.02
ACGTcount: A:0.24, C:0.36, G:0.22, T:0.19
Consensus pattern (20 bp):
TTCAAGAGGCCCCTCTATCG
Found at i:105321 original size:21 final size:21
Alignment explanation
Indices: 105272--105327 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
105262 GAAGCCCATC
105272 CCACCGTTCAAGAGGCACCCG
1 CCACCGTTCAAGAGGCACCCG
* *
105293 TCATCGTTCAAGAGGC-CCCG
1 CCACCGTTCAAGAGGCACCCG
*
105313 CCCGCCGTTCAAGAG
1 -CCACCGTTCAAGAG
105328 CCAGATGCAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.21, C:0.39, G:0.25, T:0.14
Consensus pattern (21 bp):
CCACCGTTCAAGAGGCACCCG
Found at i:107202 original size:39 final size:39
Alignment explanation
Indices: 107148--107312 Score: 303
Period size: 39 Copynumber: 4.2 Consensus size: 39
107138 TCAAGTTGTA
* *
107148 GATTTTGATTTCCTTTTGTTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
107187 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
107226 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
*
107265 GATTTTGATTTCCTTTTGCTTAGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
107304 GATTTTGAT
1 GATTTTGAT
107313 GAGCATCGGA
Statistics
Matches: 123, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 123 1.00
ACGTcount: A:0.17, C:0.16, G:0.20, T:0.47
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
Found at i:107644 original size:18 final size:18
Alignment explanation
Indices: 107621--107657 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
107611 CGAAATTTAT
107621 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
107639 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
107657 A
1 A
107658 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:108078 original size:25 final size:25
Alignment explanation
Indices: 108044--108093 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
108034 ATTATTTTTC
*
108044 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
108069 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
108094 TAATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:108293 original size:20 final size:19
Alignment explanation
Indices: 108246--108298 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
108236 TTCAGTTTGC
*
108246 GATTTCGCGTTGTGAATTT
1 GATTTCGCGTTGCGAATTT
* *
108265 GACTATCGCATTGCGAATTT
1 GA-TTTCGCGTTGCGAATTT
108285 GTATTTCGCGTTGC
1 G-ATTTCGCGTTGC
108299 TTATTTCGCG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.42
Consensus pattern (19 bp):
GATTTCGCGTTGCGAATTT
Found at i:108346 original size:17 final size:17
Alignment explanation
Indices: 108324--108365 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
108314 CGCAACATAC
108324 AACATCAAGGTATATAA
1 AACATCAAGGTATATAA
*
108341 AACATCAAGGTATATAC
1 AACATCAAGGTATATAA
108358 AACATCAA
1 AACATCAA
108366 ACACATTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.52, C:0.17, G:0.10, T:0.21
Consensus pattern (17 bp):
AACATCAAGGTATATAA
Found at i:110914 original size:24 final size:24
Alignment explanation
Indices: 110880--110933 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
110870 CCATCACATC
*
110880 ATCAAAATCTGAGTATTTACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
* *
110904 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
110928 ATCAAA
1 ATCAAA
110934 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.26
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTGACCAAG
Found at i:111887 original size:20 final size:20
Alignment explanation
Indices: 111864--111909 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
111854 TTCAGTTGCA
*
111864 AATTTGACTTTCGCGTTGAG
1 AATTTGACTATCGCGTTGAG
*
111884 AATTTGACTATCGCGTTGCG
1 AATTTGACTATCGCGTTGAG
111904 AATTTG
1 AATTTG
111910 GAAAATCGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (20 bp):
AATTTGACTATCGCGTTGAG
Found at i:111982 original size:20 final size:20
Alignment explanation
Indices: 111936--111986 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
111926 ATTACATATT
111936 TGCGTTGCGAAATTGGAAAC
1 TGCGTTGCGAAATTGGAAAC
* * *
111956 TGGGTTGTGAAATTGG-AAT
1 TGCGTTGCGAAATTGGAAAC
111975 TCGCGTTGCGAA
1 T-GCGTTGCGAA
111987 TTTGTTGGTC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.25, C:0.12, G:0.33, T:0.29
Consensus pattern (20 bp):
TGCGTTGCGAAATTGGAAAC
Found at i:113469 original size:21 final size:20
Alignment explanation
Indices: 113418--113465 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
113408 TTTATTTATT
113418 AAAAAGTTAAATATATACAG
1 AAAAAGTTAAATATATACAG
113438 AAAAAGTTAAATATATACAG
1 AAAAAGTTAAATATATACAG
113458 AAAAAGTT
1 AAAAAGTT
113466 TAAAAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.60, C:0.04, G:0.10, T:0.25
Consensus pattern (20 bp):
AAAAAGTTAAATATATACAG
Found at i:117609 original size:3 final size:3
Alignment explanation
Indices: 117601--117651 Score: 52
Period size: 3 Copynumber: 16.7 Consensus size: 3
117591 ATTTATTTAT
*
117601 ATA ATA ATA ATA AT- ATA TATA TATA TTA ATA ATA ATA ATA A-A ATTA
1 ATA ATA ATA ATA ATA ATA -ATA -ATA ATA ATA ATA ATA ATA ATA A-TA
117647 ATA AT
1 ATA AT
117652 TTTAATTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 4 0.10
3 29 0.69
4 9 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:117614 original size:22 final size:22
Alignment explanation
Indices: 117589--117637 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
117579 TCCAGTTTTG
* *
117589 TAATTTATTTATATAATAATAA
1 TAATATATATATATAATAATAA
*
117611 TAATATATATATATATTAATAA
1 TAATATATATATATAATAATAA
117633 TAATA
1 TAATA
117638 ATAAAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATATATATATATAATAATAA
Found at i:121423 original size:2 final size:2
Alignment explanation
Indices: 121416--121454 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
121406 ACCACAAAGA
121416 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
121455 AAATTTGATC
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:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:130560 original size:23 final size:23
Alignment explanation
Indices: 130528--130575 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
130518 AATTACGTCA
130528 TTGTGACACGTTTATCTCTGTCT
1 TTGTGACACGTTTATCTCTGTCT
*
130551 TTGTGGCACGTTTATCTCTGTCT
1 TTGTGACACGTTTATCTCTGTCT
130574 TT
1 TT
130576 TGATAGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.10, C:0.21, G:0.19, T:0.50
Consensus pattern (23 bp):
TTGTGACACGTTTATCTCTGTCT
Found at i:141110 original size:25 final size:25
Alignment explanation
Indices: 141082--141156 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
141072 TATAAATTTT
*
141082 TTAATTTTTATTTAAATTAAAAAAC
1 TTAATTTTTATTTAATTTAAAAAAC
* *
141107 TTAAAATTATAATTT-ATTTAAAAAAC
1 TT--AATTTTTATTTAATTTAAAAAAC
*
141133 -TAATTTTTATATAATTATAAAAAA
1 TTAATTTTTATTTAATT-TAAAAAA
141157 ATCAAAATCT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
23 8 0.20
24 3 0.08
25 10 0.25
26 10 0.25
27 9 0.22
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (25 bp):
TTAATTTTTATTTAATTTAAAAAAC
Found at i:147488 original size:2 final size:2
Alignment explanation
Indices: 147481--147571 Score: 173
Period size: 2 Copynumber: 45.5 Consensus size: 2
147471 AAGTTTAAAC
147481 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
147523 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CA CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
147565 CT CT CT C
1 CT CT CT C
147572 CCTCCCTCCA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 87 1.00
ACGTcount: A:0.01, C:0.51, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:150355 original size:19 final size:18
Alignment explanation
Indices: 150314--150358 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
150304 TATCTATATT
150314 TAAAATATATTTAAAAAA
1 TAAAATATATTTAAAAAA
* * *
150332 TAAAATTTATTTTAATAA
1 TAAAATATATTTAAAAAA
150350 TAAAA-ATAT
1 TAAAATATAT
150359 AAAAATATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAAATATATTTAAAAAA
Found at i:150384 original size:23 final size:24
Alignment explanation
Indices: 150355--150399 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
150345 AATAATAAAA
150355 ATATAAA-AATATTTTATTAACTT
1 ATATAAAGAATATTTTATTAACTT
*
150378 ATATAAAGCATATTTTATTAAC
1 ATATAAAGAATATTTTATTAAC
150400 ATTTTTGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (24 bp):
ATATAAAGAATATTTTATTAACTT
Found at i:157031 original size:21 final size:22
Alignment explanation
Indices: 157005--157045 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
156995 AATTGTGGGG
157005 ATGTTTTTAGT-TTTTTATTAA
1 ATGTTTTTAGTATTTTTATTAA
*
157026 ATGTTTTTGGTATTTTTATT
1 ATGTTTTTAGTATTTTTATT
157046 TAGTTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (22 bp):
ATGTTTTTAGTATTTTTATTAA
Found at i:160297 original size:14 final size:13
Alignment explanation
Indices: 160259--160312 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 13
160249 TATTAATATG
*
160259 ATTAAAATAAAATA
1 ATTAAAATATAA-A
**
160273 ATTTAAAATATTGA
1 A-TTAAAATATAAA
160287 ATTAAACATATAAA
1 ATTAAA-ATATAAA
160301 ATTAAAATATAA
1 ATTAAAATATAA
160313 CTAAACATGG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
13 11 0.33
14 14 0.42
15 8 0.24
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (13 bp):
ATTAAAATATAAA
Found at i:161614 original size:3 final size:3
Alignment explanation
Indices: 161606--161656 Score: 61
Period size: 3 Copynumber: 17.0 Consensus size: 3
161596 GACTGAAATG
*
161606 TAA TAA TAA TAA TAA TAAA TAAA TAA -AA AAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
161652 -AA TAA
1 TAA TAA
161657 AAAACCAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
2 4 0.09
3 33 0.75
4 7 0.16
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (3 bp):
TAA
Found at i:161638 original size:25 final size:25
Alignment explanation
Indices: 161610--161660 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 25
161600 GAAATGTAAT
161610 AATAATAATAATAA-ATAAATAAAAA
1 AATAATAATAATAATA-AAATAAAAA
161635 AATAATAATAATAATAAAATAAAAA
1 AATAATAATAATAATAAAATAAAAA
161660 A
1 A
161661 CCAAATAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 24 0.96
26 1 0.04
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (25 bp):
AATAATAATAATAATAAAATAAAAA
Found at i:162028 original size:117 final size:118
Alignment explanation
Indices: 161819--162147 Score: 531
Period size: 117 Copynumber: 2.8 Consensus size: 118
161809 GGATTAGTTA
*
161819 TTCTCATTATGAACTTTTCCACCGGGGATGACAATTTATCTCCTTTGTGATGTAATCTAGCAAAA
1 TTCTCATTATGAACTTTTCCACTGGGGATGACAATTTATCTCCTTTGTGATGTAATCTAGCAAAA
*
161884 AGTTGAACAAATTCTTATCATTATGAACTTATTC-TTTTTTT-AGATGAGTCC
66 AGTTGAACAAATTCTTCTCATTATGAACTTATTCTTTTTTTTCAGATGAGTCC
* *
161935 TTCTCATTATGAACTTTTCCACTAGGGATGAAAATTTATCTCCTTCTGTGATGTAATCTAGCAAA
1 TTCTCATTATGAACTTTTCCACTGGGGATGACAATTTATCTCCTT-TGTGATGTAATCTAGCAAA
* * *
162000 AAGTTGAACAAAGTATTCTCATTATGAACTTATTCTTTTTTTTTCCAGATGAGTTC
65 AAGTTGAACAAATTCTTCTCATTATGAACTTATTC-TTTTTTTT-CAGATGAGTCC
*
162056 TTCTCATTATGAAC-TTTCCTCTGGGGATGACAATTTATCTCCTTTGTGATGTAATCTAGCAAAA
1 TTCTCATTATGAACTTTTCCACTGGGGATGACAATTTATCTCCTTTGTGATGTAATCTAGCAAAA
162120 AGTTGAACAAATTCTTC-CATTATGAACT
66 AGTTGAACAAATTCTTCTCATTATGAACT
162148 CTTTCTGGAA
Statistics
Matches: 196, Mismatches: 12, Indels: 8
0.91 0.06 0.04
Matches are distributed among these distances:
116 42 0.21
117 51 0.26
118 11 0.06
119 42 0.21
120 27 0.14
121 23 0.12
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (118 bp):
TTCTCATTATGAACTTTTCCACTGGGGATGACAATTTATCTCCTTTGTGATGTAATCTAGCAAAA
AGTTGAACAAATTCTTCTCATTATGAACTTATTCTTTTTTTTCAGATGAGTCC
Found at i:162479 original size:123 final size:122
Alignment explanation
Indices: 162215--162662 Score: 650
Period size: 123 Copynumber: 3.7 Consensus size: 122
162205 GAATTAAGGC
* * *
162215 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCATCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * * **
162280 GAACACTTCTGGAAATGTTTATGCTT-ATCTATCTCCTTCTGTGATAGCTTC-ATGCAA
66 GAACTCTTCTGGAAAAGTGTATG-TTGATCTATCTCCTTCTGTGATAGAGTCTA-GCAA
*
162337 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAAATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
*
162402 GAACTTTATCTGGAAAAGTGTATGTTGATCTATCTCCTTCTGTGATAGAGTCTAGCAA
66 GAACTCT-TCTGGAAAAGTGTATGTTGATCTATCTCCTTCTGTGATAGAGTCTAGCAA
** * * *
162460 AAGGTTGAACATTTTCTTCTCATTATGAACTTTTTCTCCCTCTTCATATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* *
162525 GAACTTTCTCTGGAAAAATGTATGTTGATCTATCTCCTTCTGTGATAGAGTCTAGCAA
66 GAACTCT-TCTGGAAAAGTGTATGTTGATCTATCTCCTTCTGTGATAGAGTCTAGCAA
* * *
162583 AAGGTTGAACAAGTTCTTCTCATTACGAACTTTTTC-TCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTA
162647 TGAACTCTTCTGGAAA
65 TGAACTCTTCTGGAAA
162663 TGTTGATTCA
Statistics
Matches: 298, Mismatches: 24, Indels: 8
0.90 0.07 0.02
Matches are distributed among these distances:
122 78 0.26
123 219 0.73
124 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.41
Consensus pattern (122 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
GAACTCTTCTGGAAAAGTGTATGTTGATCTATCTCCTTCTGTGATAGAGTCTAGCAA
Found at i:163110 original size:22 final size:22
Alignment explanation
Indices: 163052--163114 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
163042 AAATCCAATA
* * * *
163052 AATCTTTCTTCTTTAAAAAGAG
1 AATCTATCATCTTTGAAGAGAG
163074 AATCTATCATCTTTGAAGAGAG
1 AATCTATCATCTTTGAAGAGAG
163096 AATCTATCATCTTTGAAGA
1 AATCTATCATCTTTGAAGA
163115 ATGTAGATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (22 bp):
AATCTATCATCTTTGAAGAGAG
Found at i:164092 original size:18 final size:18
Alignment explanation
Indices: 164055--164092 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
164045 TTATATAAAG
*
164055 AATAAATTGAATTTCTAA
1 AATAAATTGAATTTCAAA
164073 AATAAATTGAATTTCAAA
1 AATAAATTGAATTTCAAA
164091 AA
1 AA
164093 GATAAACTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (18 bp):
AATAAATTGAATTTCAAA
Found at i:175262 original size:30 final size:31
Alignment explanation
Indices: 175204--175276 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
175194 GGACTAAAAT
* **
175204 AAATAAAATTAAAACTATAGTATTAAATATA
1 AAATAAAATTAAAAATATAGTAAAAAATATA
*
175235 AAATGAAATTAAAAAT-TAGTAAAAAATA-A
1 AAATAAAATTAAAAATATAGTAAAAAATATA
* *
175264 TATTAAAATTAAA
1 AAATAAAATTAAA
175277 TACCCTAATT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
29 11 0.31
30 10 0.29
31 14 0.40
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.30
Consensus pattern (31 bp):
AAATAAAATTAAAAATATAGTAAAAAATATA
Found at i:176508 original size:3 final size:3
Alignment explanation
Indices: 176500--176586 Score: 135
Period size: 3 Copynumber: 29.3 Consensus size: 3
176490 GGCCTAAAAT
176500 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
176546 ATAA ATAA ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 AT-A AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
176587 AACCAAATGG
Statistics
Matches: 80, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
2 6 0.08
3 67 0.84
4 7 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:177823 original size:3 final size:3
Alignment explanation
Indices: 177817--177887 Score: 94
Period size: 3 Copynumber: 24.0 Consensus size: 3
177807 GGGTCTTTTT
177817 TTA TTA TTTA TTA -TA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
177861 TTTA TTA -TA TTA TTA TTA TTA ATA TTA
1 -TTA TTA TTA TTA TTA TTA TTA TTA TTA
177888 CATTTACATA
Statistics
Matches: 61, Mismatches: 2, Indels: 10
0.84 0.03 0.14
Matches are distributed among these distances:
2 6 0.10
3 49 0.80
4 6 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:178021 original size:23 final size:22
Alignment explanation
Indices: 177994--178063 Score: 104
Period size: 23 Copynumber: 3.0 Consensus size: 22
177984 AACCCAACCC
177994 AAAGATTAGGGTTTCAAACCCTA
1 AAAGATTAGGGTTTC-AACCCTA
178017 AAAGATTAGGGTTTCAACCCTAA
1 AAAGATTAGGGTTTCAACCCT-A
*
178040 AACAAATTAGGGTTTCAACCCTA
1 AA-AGATTAGGGTTTCAACCCTA
178063 A
1 A
178064 TCCCCTAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
22 6 0.14
23 20 0.45
24 18 0.41
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.26
Consensus pattern (22 bp):
AAAGATTAGGGTTTCAACCCTA
Found at i:178053 original size:24 final size:23
Alignment explanation
Indices: 177998--178063 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 23
177988 CAACCCAAAG
*
177998 ATTAGGGTTTCAAACCCT-AAAAG
1 ATTAGGGTTTC-AACCCTAAAAAA
178021 ATTAGGGTTTCAACCCTAAAACAA
1 ATTAGGGTTTCAACCCTAAAA-AA
178045 ATTAGGGTTTCAACCCTAA
1 ATTAGGGTTTCAACCCTAA
178064 TCCCCTAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
22 6 0.15
23 14 0.35
24 20 0.50
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (23 bp):
ATTAGGGTTTCAACCCTAAAAAA
Found at i:179838 original size:29 final size:28
Alignment explanation
Indices: 179783--179839 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
179773 TATTTGTATT
* *
179783 ATGTAAATAATGTGTTTAATTCCATTTA
1 ATGTAAATAATGTATTTAATTACATTTA
*
179811 ATGTAAATATTGTATTTCAATTACATTTA
1 ATGTAAATAATGTATTT-AATTACATTTA
179840 TTCTCATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 15 0.60
29 10 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.47
Consensus pattern (28 bp):
ATGTAAATAATGTATTTAATTACATTTA
Found at i:194326 original size:13 final size:12
Alignment explanation
Indices: 194307--194340 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 12
194297 TTAATATATC
194307 ATTTAAAATTAT
1 ATTTAAAATTAT
194319 ATTTTAAAAATTAT
1 A-TTT-AAAATTAT
194333 ATTTAAAA
1 ATTTAAAA
194341 AAATAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 5 0.25
13 6 0.30
14 9 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATTTAAAATTAT
Found at i:194341 original size:13 final size:13
Alignment explanation
Indices: 194307--194341 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
194297 TTAATATATC
194307 ATTT-AAAATTAT
1 ATTTAAAAATTAT
194319 ATTTTAAAAATTAT
1 A-TTTAAAAATTAT
194333 ATTTAAAAA
1 ATTTAAAAA
194342 AATAAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 1 0.05
13 11 0.52
14 9 0.43
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTTAAAAATTAT
Done.