Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 87 of 125
Found at i:26736926 original size:59 final size:59
Alignment explanation
Indices: 26736815--26736970 Score: 183
Period size: 59 Copynumber: 2.6 Consensus size: 59
26736805 AAATGGTGAT
* * *
26736815 TTTTG-GAAGTTAAAGGGC-AAAAGTGTAATTTTT-TAAAGTTTAAGGGCAAAAATGTAA
1 TTTTGAGAAGTTTAAGGGCTTAAA-TGTAATTTTTGAAAAGTTTAAGGGCAAAAATGTAA
**
26736872 TTTTGAGAAGTTTAAGGGCTTAAATGTAATTTTTGAAAAGTTTAAGGGTTAAAATGTAA
1 TTTTGAGAAGTTTAAGGGCTTAAATGTAATTTTTGAAAAGTTTAAGGGCAAAAATGTAA
* * * *
26736931 TTTTTAGAAATTTTAGGGGTTAAAATGTAATTTTTAGAAA
1 TTTTGAGAAGTTTAAGGGCTT-AAATGTAATTTTT-GAAA
26736971 GCTTAGGGGT
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
57 5 0.06
58 22 0.26
59 41 0.48
60 13 0.15
61 4 0.05
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.38
Consensus pattern (59 bp):
TTTTGAGAAGTTTAAGGGCTTAAATGTAATTTTTGAAAAGTTTAAGGGCAAAAATGTAA
Found at i:26736977 original size:30 final size:30
Alignment explanation
Indices: 26736833--26737008 Score: 171
Period size: 30 Copynumber: 5.9 Consensus size: 30
26736823 GTTAAAGGGC
* * **
26736833 AAAAGTGTAATTTTT-TAAAGTTTAAGGGCA
1 AAAA-TGTAATTTTTAGAAAGTTTAGGGGTT
* *
26736863 AAAATGTAATTTTGAG-AAGTTTAAGGGCTT
1 AAAATGTAATTTTTAGAAAGTTT-AGGGGTT
*
26736893 -AAATGTAATTTTT-GAAAAGTTTAAGGGTT
1 AAAATGTAATTTTTAG-AAAGTTTAGGGGTT
*
26736922 AAAATGTAATTTTTAGAAATTTTAGGGGTT
1 AAAATGTAATTTTTAGAAAGTTTAGGGGTT
* *
26736952 AAAATGTAATTTTTAGAAAGCTTAGGGGTC
1 AAAATGTAATTTTTAGAAAGTTTAGGGGTT
* * * *
26736982 AAAACGTGATTTCTAGATAGTTTAGGG
1 AAAATGTAATTTTTAGAAAGTTTAGGG
26737009 ACCTTCTAGG
Statistics
Matches: 121, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
28 1 0.01
29 32 0.26
30 87 0.72
31 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.38
Consensus pattern (30 bp):
AAAATGTAATTTTTAGAAAGTTTAGGGGTT
Found at i:26738799 original size:11 final size:11
Alignment explanation
Indices: 26738777--26738899 Score: 65
Period size: 11 Copynumber: 11.0 Consensus size: 11
26738767 ATTTGGACTT
26738777 TTAAAGTTTAAA
1 TTAAA-TTTAAA
*
26738789 TTTAATTTAAA
1 TTAAATTTAAA
*
26738800 ATAAATTTAAA
1 TTAAATTTAAA
*
26738811 TTAAA-ATAAA
1 TTAAATTTAAA
* *
26738821 TTCAAACTCAAA
1 TT-AAATTTAAA
** *
26738833 ACAAGTTTAAA
1 TTAAATTTAAA
*
26738844 TTTAAA-GTAAA
1 -TTAAATTTAAA
26738855 TTCAAATTTAAA
1 TT-AAATTTAAA
* *
26738867 GTAAATTCAAA
1 TTAAATTTAAA
26738878 CTTAAA--TAAA
1 -TTAAATTTAAA
26738888 TTAAAATTTAAA
1 TT-AAATTTAAA
26738900 ATTGGGTCCA
Statistics
Matches: 81, Mismatches: 21, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
9 2 0.02
10 14 0.17
11 43 0.53
12 22 0.27
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:26738810 original size:6 final size:6
Alignment explanation
Indices: 26738776--26738899 Score: 50
Period size: 6 Copynumber: 22.0 Consensus size: 6
26738766 TATTTGGACT
* *
26738776 TTTAAA GTTTAAA TTT-AA TTTAAA -ATAAA TTTAAA -TTAAA -ATAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * ** * * *
26738821 TTCAAA CTCAAA -ACAAG TTTAAA TTTAAA -GTAAA TTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
26738867 -GTAAA TTCAAA CTTAAA --TAAA TTAAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
26738900 ATTGGGTCCA
Statistics
Matches: 87, Mismatches: 22, Indels: 17
0.69 0.17 0.13
Matches are distributed among these distances:
4 4 0.05
5 29 0.33
6 48 0.55
7 6 0.07
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (6 bp):
TTTAAA
Found at i:26738863 original size:17 final size:17
Alignment explanation
Indices: 26738792--26738901 Score: 116
Period size: 17 Copynumber: 6.6 Consensus size: 17
26738782 GTTTAAATTT
*
26738792 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTCA
26738809 AA-TTAAAATAAATTCA
1 AATTTAAAATAAATTCA
* * * * *
26738825 AACTCAAAACAAGTTTA
1 AATTTAAAATAAATTCA
*
26738842 AATTTAAAGTAAATTCA
1 AATTTAAAATAAATTCA
*
26738859 AATTTAAAGTAAATTCA
1 AATTTAAAATAAATTCA
* *
26738876 AACTT-AAATAAATTAA
1 AATTTAAAATAAATTCA
26738892 AATTTAAAAT
1 AATTTAAAAT
26738902 TGGGTCCATT
Statistics
Matches: 76, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
16 28 0.37
17 48 0.63
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (17 bp):
AATTTAAAATAAATTCA
Found at i:26738895 original size:50 final size:50
Alignment explanation
Indices: 26738792--26738901 Score: 143
Period size: 50 Copynumber: 2.2 Consensus size: 50
26738782 GTTTAAATTT
* *
26738792 AATTTAAAATAAATTTAAATTAAAATAAATTCAAACTCAAAACAAGTTTA
1 AATTTAAAATAAATTCAAATTAAAATAAATTCAAACTCAAAACAAGTTAA
* * *
26738842 AATTTAAAGTAAATTCAAATTTAAAGTAAATTCAAACTTAAATA-AA-TTAA
1 AATTTAAAATAAATTCAAA-TTAAAATAAATTCAAACTCAAA-ACAAGTTAA
26738892 AATTTAAAAT
1 AATTTAAAAT
26738902 TGGGTCCATT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
50 29 0.56
51 22 0.42
52 1 0.02
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (50 bp):
AATTTAAAATAAATTCAAATTAAAATAAATTCAAACTCAAAACAAGTTAA
Found at i:26740289 original size:16 final size:16
Alignment explanation
Indices: 26740250--26740280 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
26740240 CGTTTGGTTC
*
26740250 GCTGTAATGGAATAGA
1 GCTGTAATAGAATAGA
26740266 GCTGTAATAGAATAG
1 GCTGTAATAGAATAG
26740281 GGTTGTAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.06, G:0.29, T:0.26
Consensus pattern (16 bp):
GCTGTAATAGAATAGA
Found at i:26740521 original size:58 final size:58
Alignment explanation
Indices: 26740443--26740609 Score: 207
Period size: 58 Copynumber: 2.9 Consensus size: 58
26740433 GATTATTGTT
26740443 ATTAAATTTTAATA-AGATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTA
1 ATTAAATTTTAATATA-ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTA
* * * *
26740501 ATTATATTTTAATATAATTATTATTAAATAAAATTTAAT-AAAATAATATATAATTTG
1 ATTAAATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTA
* *
26740558 A-TAACATTTTTAATATAATTATTATTAAAATATGAA-TTAGTAAAAATCATAA
1 ATTAA-A-TTTTAATATAATTATTATT-AAATAT-AATTTAATAAAAATAATAA
26740610 TATATAATAT
Statistics
Matches: 94, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
56 2 0.02
57 18 0.19
58 54 0.57
59 10 0.11
60 10 0.11
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (58 bp):
ATTAAATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTA
Found at i:26745008 original size:137 final size:137
Alignment explanation
Indices: 26744832--26745115 Score: 412
Period size: 137 Copynumber: 2.1 Consensus size: 137
26744822 TAGAGAACAT
* * *
26744832 AGATAAAATTAATATATGAATTTGATTTATACAAAATATTAATTGTATATA-TTTACTAAATTTA
1 AGATATAATTAATATATAAATTTGATTTATACAAAATATTAATTATATATATTTTACTAAATTTA
* * * * *
26744896 TTAATATAAATATTTGTATTAATTAATTTCGGTTAAAATATAAAAGACATGAAAATTAATATTTT
66 TT-ATATAAATAATTATATTAATTAATTTCGATCAAAATATAAAAGACATGAAAATTAATATTCT
*
26744961 TTTG-GAA
130 TTTGAAAA
*
26744968 AGAATATAATTAATATATAAATTTG-TTTCATACAAAATATTAATTATATATATTTTACTGAATT
1 AG-ATATAATTAATATATAAATTTGATTT-ATACAAAATATTAATTATATATATTTTACTAAATT
**
26745032 TATTATATAAATAATTATATTAATTAATTTCGATCAAAATATAAAAGTTATGAAAATTAATATTC
64 TATTATATAAATAATTATATTAATTAATTTCGATCAAAATATAAAAGACATGAAAATTAATATTC
26745097 TTTTGAAAA
129 TTTTGAAAA
26745106 AGATATAATT
1 AGATATAATT
26745116 CATTTTTCTA
Statistics
Matches: 132, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
136 5 0.04
137 109 0.83
138 18 0.14
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (137 bp):
AGATATAATTAATATATAAATTTGATTTATACAAAATATTAATTATATATATTTTACTAAATTTA
TTATATAAATAATTATATTAATTAATTTCGATCAAAATATAAAAGACATGAAAATTAATATTCTT
TTGAAAA
Found at i:26745225 original size:75 final size:75
Alignment explanation
Indices: 26745091--26745238 Score: 217
Period size: 75 Copynumber: 2.0 Consensus size: 75
26745081 ATGAAAATTA
* *
26745091 ATATTCTTTTGAAAAAGATATAATTCATTTTTCTAACTTTCTACTCACCTTCTCTATTAATAAG-
1 ATATTCTTTTGAAAAAGATATAATTCATTTTTCTAACTTTCCACTCACCTTCTCAATTAATAAGT
26745155 GAAATAATCCT
66 G-AATAATCCT
* * ** *
26745166 ATATTCTTTTGAAAAATATATAATTCATTTTTCTAACTTTCCATTTGCCTTTTCAATTAATAAGT
1 ATATTCTTTTGAAAAAGATATAATTCATTTTTCTAACTTTCCACTCACCTTCTCAATTAATAAGT
26745231 GAATAATC
66 GAATAATC
26745239 TTGATTTTCT
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
75 64 0.98
76 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.05, T:0.45
Consensus pattern (75 bp):
ATATTCTTTTGAAAAAGATATAATTCATTTTTCTAACTTTCCACTCACCTTCTCAATTAATAAGT
GAATAATCCT
Found at i:26747499 original size:31 final size:31
Alignment explanation
Indices: 26747437--26747551 Score: 117
Period size: 31 Copynumber: 3.7 Consensus size: 31
26747427 TAAAATGAGG
* * *
26747437 TTTTAGGTTCATTAAAACTTTGAAAAAAAAAA
1 TTTTAGGTCCCTTAAAA-GTTGAAAAAAAAAA
* *
26747469 TTTTAGGTCTCTTAAAAGTTGATAAAAAAAA
1 TTTTAGGTCCCTTAAAAGTTGAAAAAAAAAA
* *
26747500 TTATAGG-CCCTTAAAAGTTAAAAATAAAAAA
1 TTTTAGGTCCCTTAAAAGTTGAAAA-AAAAAA
* *
26747531 TTTGA-GACCCTTAAAAGTTGA
1 TTTTAGGTCCCTTAAAAGTTGA
26747552 TAAATTTTTT
Statistics
Matches: 69, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
30 15 0.22
31 40 0.58
32 14 0.20
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (31 bp):
TTTTAGGTCCCTTAAAAGTTGAAAAAAAAAA
Found at i:26750192 original size:21 final size:21
Alignment explanation
Indices: 26750167--26750221 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 21
26750157 GCCTGGAGCA
26750167 AATTTGACTTGTTTTAAAA-G
1 AATTTGACTTGTTTTAAAATG
26750187 CAATTTGA-TT-TTTTAAAATG
1 -AATTTGACTTGTTTTAAAATG
*
26750207 ATTTTGACTTTGTTT
1 AATTTGAC-TTGTTT
26750222 AAATCATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 14 0.48
20 3 0.10
21 9 0.31
22 3 0.10
ACGTcount: A:0.29, C:0.05, G:0.13, T:0.53
Consensus pattern (21 bp):
AATTTGACTTGTTTTAAAATG
Found at i:26758461 original size:102 final size:101
Alignment explanation
Indices: 26758341--26758533 Score: 237
Period size: 100 Copynumber: 1.9 Consensus size: 101
26758331 TGGTTTGTGA
* * * * * *
26758341 AAAATAAAATGTCATTTTGGTATTGCTTTTTATGATGTGTATCAAT-ATTTAATAAAATATCAAT
1 AAAATAAAATGCCATTTTGGTATCGC-TTTTA-AAAGAGTATCAATAATTT-AGAAAATATCAAT
* * *
26758405 ACTTGGC-AAAATGGTATCGGTATTTTTTACCATTTTTG
63 ACTTGGCGAAAAAGGTATCGATACTTTTTACCATTTTTG
* * *
26758443 AAAATAGAATGCCATTTTGGTATCGCTTTTAAAAGAGTATCGATAATTTAGAAAATATCTATACT
1 AAAATAAAATGCCATTTTGGTATCGCTTTTAAAAGAGTATCAATAATTTAGAAAATATCAATACT
26758508 TGGCGAAAAAGGTATCGATACTTTTT
66 TGGCGAAAAAGGTATCGATACTTTTT
26758534 GGTGTGGAGC
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
100 27 0.35
101 27 0.35
102 23 0.30
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (101 bp):
AAAATAAAATGCCATTTTGGTATCGCTTTTAAAAGAGTATCAATAATTTAGAAAATATCAATACT
TGGCGAAAAAGGTATCGATACTTTTTACCATTTTTG
Found at i:26759800 original size:21 final size:21
Alignment explanation
Indices: 26759776--26759828 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
26759766 CCTGCAACTT
26759776 CTACCGATACAAGCTTACCTA
1 CTACCGATACAAGCTTACCTA
26759797 CTACCGATACAAGCTTACCTA
1 CTACCGATACAAGCTTACCTA
*
26759818 TTACCGATACA
1 CTACCGATACA
26759829 TTAGTACTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.34, C:0.32, G:0.09, T:0.25
Consensus pattern (21 bp):
CTACCGATACAAGCTTACCTA
Found at i:26764724 original size:52 final size:51
Alignment explanation
Indices: 26764660--26764835 Score: 237
Period size: 52 Copynumber: 3.4 Consensus size: 51
26764650 ATGATTACGA
* * *
26764660 GTCATCGTGAGTATATGAATCCTTTACGAATTAAACGGTTCGATGACTAAGT
1 GTCATCGTGAGTATATGAATCCTTTACGGATTAAA-GGTCCGATGACTATGT
* * *
26764712 GTTATCGTGAGTATATGGATCCTTTACGGATTAAGAGGTCCGATGACTCTGT
1 GTCATCGTGAGTATATGAATCCTTTACGGATTAA-AGGTCCGATGACTATGT
* *
26764764 GTCATCGTGAGTATATGAAT-CTCTTGCGGATTATAAGGTCCGGTGACTATGT
1 GTCATCGTGAGTATATGAATCCT-TTACGGATTA-AAGGTCCGATGACTATGT
26764816 GTCATCGTGAGTATATGAAT
1 GTCATCGTGAGTATATGAAT
26764836 GAAGTGAAAT
Statistics
Matches: 110, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
51 2 0.02
52 106 0.96
53 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (51 bp):
GTCATCGTGAGTATATGAATCCTTTACGGATTAAAGGTCCGATGACTATGT
Found at i:26772157 original size:21 final size:21
Alignment explanation
Indices: 26772131--26772180 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
26772121 ATTTTAGTAC
* *
26772131 CGGTAGAAG-CATGACTTGTAT
1 CGGTAGAAGTC-TCACTTATAT
*
26772152 CGGTAGATGTCTCACTTATAT
1 CGGTAGAAGTCTCACTTATAT
26772173 CGGTAGAA
1 CGGTAGAA
26772181 CTATCATAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (21 bp):
CGGTAGAAGTCTCACTTATAT
Found at i:26775441 original size:22 final size:23
Alignment explanation
Indices: 26775416--26775463 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 23
26775406 AATATGAAGA
26775416 AAAAAAT-TAATAATCTAT-CCT
1 AAAAAATATAATAATCTATCCCT
* * *
26775437 TAAAACTATCATAATCTATCCCT
1 AAAAAATATAATAATCTATCCCT
26775460 AAAA
1 AAAA
26775464 CTACTACACA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 5 0.24
22 10 0.48
23 6 0.29
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAAAATATAATAATCTATCCCT
Found at i:26775464 original size:22 final size:22
Alignment explanation
Indices: 26775425--26775466 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
26775415 AAAAAAATTA
*
26775425 ATAATCTATCCTTAAAACTATC
1 ATAATCTATCCCTAAAACTATC
26775447 ATAATCTATCCCTAAAACTA
1 ATAATCTATCCCTAAAACTA
26775467 CTACACATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.24, G:0.00, T:0.33
Consensus pattern (22 bp):
ATAATCTATCCCTAAAACTATC
Found at i:26777183 original size:10 final size:10
Alignment explanation
Indices: 26777170--26777212 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
26777160 AAATTGTAAA
26777170 AAAAAATTAT
1 AAAAAATTAT
26777180 AAAAAATTAT
1 AAAAAATTAT
***
26777190 AAACTTTTAT
1 AAAAAATTAT
26777200 AAAAAATTAT
1 AAAAAATTAT
26777210 AAA
1 AAA
26777213 TATATAAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:26777190 original size:31 final size:30
Alignment explanation
Indices: 26777155--26777212 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
26777145 TAGATTTTTT
26777155 TTATAAAATTGTAAAAAAAAATTATAAAAAA
1 TTATAAAATT-TAAAAAAAAATTATAAAAAA
* * *
26777186 TTATAAACTTTTATAAAAAATTATAAA
1 TTATAAAATTTAAAAAAAAATTATAAA
26777213 TATATAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 15 0.62
31 9 0.38
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (30 bp):
TTATAAAATTTAAAAAAAAATTATAAAAAA
Found at i:26777218 original size:18 final size:17
Alignment explanation
Indices: 26777173--26777223 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 17
26777163 TTGTAAAAAA
26777173 AAATTATAAAAAATTAT
1 AAATTATAAAAAATTAT
26777190 AAACTTTTATAAAAAATTAT
1 AAA---TTATAAAAAATTAT
26777210 AAATATATAAAAAA
1 AAAT-TATAAAAAA
26777224 GTCCTTTAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.13
18 9 0.30
20 17 0.57
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATTATAAAAAATTAT
Found at i:26777504 original size:8 final size:9
Alignment explanation
Indices: 26777474--26777524 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
26777464 TTTTTCTATA
*
26777474 TTTTATAAT
1 TTTTATGAT
*
26777483 TTTTATAATT
1 TTTTATGA-T
26777493 TTTTATGAT
1 TTTTATGAT
26777502 TTTTATGAT
1 TTTTATGAT
* *
26777511 TTTTTTAAT
1 TTTTATGAT
26777520 TTTTA
1 TTTTA
26777525 ATAAAATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
9 29 0.78
10 8 0.22
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (9 bp):
TTTTATGAT
Found at i:26777534 original size:28 final size:28
Alignment explanation
Indices: 26777475--26777576 Score: 78
Period size: 28 Copynumber: 3.5 Consensus size: 28
26777465 TTTTCTATAT
* * **
26777475 TTTATAATTTTTATAATTTTTTATGATT
1 TTTATAATTTTTATAATTTTTAATAAAA
* *
26777503 TTTATGATTTTTTTAATTTTTAATAAAA
1 TTTATAATTTTTATAATTTTTAATAAAA
* * *
26777531 TTTAAACATTTGTTATAGTTTTTTTATTAAAA
1 TTTATA-ATTT-TTATA--ATTTTTAATAAAA
26777563 TTTAATAATTTTTA
1 TTT-ATAATTTTTA
26777577 CTTTATTATT
Statistics
Matches: 57, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
28 26 0.46
29 4 0.07
30 4 0.07
31 3 0.05
32 18 0.32
33 2 0.04
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (28 bp):
TTTATAATTTTTATAATTTTTAATAAAA
Found at i:26777832 original size:88 final size:88
Alignment explanation
Indices: 26777670--26777919 Score: 265
Period size: 88 Copynumber: 2.8 Consensus size: 88
26777660 TTAGAGATGA
* *
26777670 TTCAAGTATCCAATTGAGTGCAAAAAAATAAGGGGTTTAATTGCTTTTTTTTAAAAAGTTTGAGG
1 TTCAAGTATCCAATTGAGTGCAAAAAAATAAGGGGCTTAATTGATTTTTTTTAAAAAGTTTGAGG
* *
26777735 GCTTTTTTGATGTATTTTGAAAG
66 GCTTGTTTGATGCATTTTGAAAG
* * * *
26777758 TTCAAGTA-CCTAATTGAGTGC-AAAAAATGTA-GTGCTTAATTTATTTTTTTTGAAAAAGTTTT
1 TTCAAGTATCC-AATTGAGTGCAAAAAAAT-AAGGGGCTTAATTGATTTTTTTT-AAAAAGTTTG
*
26777820 AGGG-TCTGTTTGATGCATTTTGATAG
63 AGGGCT-TGTTTGATGCATTTTGAAAG
* * * * *
26777846 TTCAAGTATCCAACTAAGTGTAAAAAAATATAGGGGCTTATTTGCTTTTTTTTTTTGAAAAAGTT
1 TTCAAGTATCCAATTGAGTGCAAAAAAATA-AGGGGCTTAATTG---ATTTTTTTT-AAAAAGTT
26777911 TGAGGGCTT
61 TGAGGGCTT
26777920 TTTACCCCTT
Statistics
Matches: 132, Mismatches: 18, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
87 26 0.20
88 64 0.48
89 10 0.08
90 8 0.06
93 23 0.17
94 1 0.01
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.42
Consensus pattern (88 bp):
TTCAAGTATCCAATTGAGTGCAAAAAAATAAGGGGCTTAATTGATTTTTTTTAAAAAGTTTGAGG
GCTTGTTTGATGCATTTTGAAAG
Found at i:26788254 original size:30 final size:31
Alignment explanation
Indices: 26788218--26788281 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
26788208 TACATTTCAA
26788218 TCCCTCAAC-TTTGAAAATATAACAAAACAG
1 TCCCTCAACTTTTGAAAATATAACAAAACAG
* * *
26788248 TCCCTCAACTTTTGAAAATGTGACAAAATAG
1 TCCCTCAACTTTTGAAAATATAACAAAACAG
26788279 TCC
1 TCC
26788282 TTTTCCATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.41, C:0.23, G:0.09, T:0.27
Consensus pattern (31 bp):
TCCCTCAACTTTTGAAAATATAACAAAACAG
Found at i:26789463 original size:21 final size:22
Alignment explanation
Indices: 26789392--26789466 Score: 73
Period size: 21 Copynumber: 3.5 Consensus size: 22
26789382 ACAACAACCA
** * *
26789392 AAATAGCAGGAAAAATAACAGC
1 AAATAGCAACAAAAACAATAGC
* * *
26789414 AAATAACAACAAACACAATA-A
1 AAATAGCAACAAAAACAATAGC
26789435 AAATAGCAACAAAAACAATAGC
1 AAATAGCAACAAAAACAATAGC
26789457 AAA-AGCAACA
1 AAATAGCAACA
26789467 CCAAAAAAGT
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
21 25 0.60
22 17 0.40
ACGTcount: A:0.65, C:0.17, G:0.09, T:0.08
Consensus pattern (22 bp):
AAATAGCAACAAAAACAATAGC
Found at i:26789504 original size:24 final size:24
Alignment explanation
Indices: 26789477--26789529 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
26789467 CCAAAAAAGT
26789477 AAAAAC-CAGCACCA-AAACAACAA
1 AAAAACACA-CACCAGAAACAACAA
*
26789500 CAAAAACACACACCAGAAACAGCAA
1 -AAAAACACACACCAGAAACAACAA
26789525 AAAAA
1 AAAAA
26789530 TAGCAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 16 0.62
25 10 0.38
ACGTcount: A:0.66, C:0.28, G:0.06, T:0.00
Consensus pattern (24 bp):
AAAAACACACACCAGAAACAACAA
Found at i:26792765 original size:19 final size:20
Alignment explanation
Indices: 26792726--26792771 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
26792716 ATAGCAAATG
*
26792726 TCACAATATCTCATGCTTTT
1 TCACAATATCACATGCTTTT
26792746 TCACAATATCACAT-CTTTT
1 TCACAATATCACATGCTTTT
26792765 TCACAAT
1 TCACAAT
26792772 TACACAAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.30, C:0.26, G:0.02, T:0.41
Consensus pattern (20 bp):
TCACAATATCACATGCTTTT
Found at i:26794247 original size:21 final size:21
Alignment explanation
Indices: 26794174--26794250 Score: 61
Period size: 21 Copynumber: 3.7 Consensus size: 21
26794164 TAGTAGCAAA
26794174 CTTTTACCGATACTTGAAATG
1 CTTTTACCGATACTTGAAATG
* * *
26794195 GTTTTACTGATAC---AAGTG
1 CTTTTACCGATACTTGAAATG
* *
26794213 TACTTTCTATCGATACTTGACATG
1 --CTTT-TACCGATACTTGAAATG
26794237 CTTTTACCGATACT
1 CTTTTACCGATACT
26794251 AAAAACTCTA
Statistics
Matches: 41, Mismatches: 9, Indels: 12
0.66 0.15 0.19
Matches are distributed among these distances:
18 4 0.10
20 3 0.07
21 27 0.66
22 4 0.10
24 3 0.07
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.40
Consensus pattern (21 bp):
CTTTTACCGATACTTGAAATG
Found at i:26798660 original size:20 final size:20
Alignment explanation
Indices: 26798635--26798685 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
26798625 TTATTTTTAA
26798635 AAATTTTGAAATGAGTAGAT
1 AAATTTTGAAATGAGTAGAT
26798655 AAATTTTGAAATGAGTAGAT
1 AAATTTTGAAATGAGTAGAT
26798675 AAATTTTGAAA
1 AAATTTTGAAA
26798686 GTTTTAACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (20 bp):
AAATTTTGAAATGAGTAGAT
Found at i:26806142 original size:28 final size:30
Alignment explanation
Indices: 26806085--26806145 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
26806075 TAATAAAAAT
* * *
26806085 TAAAAAAATTTATATTTTTTCATAATTTTC
1 TAAAAAAATATATATATTTTAATAATTTTC
26806115 TAAAAAAATATA-ATATTTTAATAA-TTTC
1 TAAAAAAATATATATATTTTAATAATTTTC
26806143 TAA
1 TAA
26806146 TAATTTTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 7 0.25
29 10 0.36
30 11 0.39
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (30 bp):
TAAAAAAATATATATATTTTAATAATTTTC
Found at i:26806468 original size:20 final size:18
Alignment explanation
Indices: 26806443--26806502 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 18
26806433 TTTTTACAAC
26806443 TTTTTATACTTTTAATTAGT
1 TTTTTAT-CTTTTAATTA-T
* *
26806463 TTTTTATTTTTTTATT-T
1 TTTTTATCTTTTAATTAT
26806480 TTTTTATCATTTTAATTAT
1 TTTTTATC-TTTTAATTAT
26806499 TTTT
1 TTTT
26806503 ATATAATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
17 8 0.24
18 7 0.21
19 12 0.35
20 7 0.21
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.75
Consensus pattern (18 bp):
TTTTTATCTTTTAATTAT
Found at i:26806511 original size:20 final size:19
Alignment explanation
Indices: 26806443--26806512 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
26806433 TTTTTACAAC
*
26806443 TTTTTATACTTTTAATTAGT
1 TTTTTATAATTTTAATTA-T
* *
26806463 TTTTTAT-TTTTTTATT-T
1 TTTTTATAATTTTAATTAT
*
26806480 TTTTTATCATTTTAATTAT
1 TTTTTATAATTTTAATTAT
26806499 TTTTATATAATTTT
1 TTTT-TATAATTTT
26806513 CTATCATTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
17 8 0.19
18 7 0.17
19 12 0.29
20 15 0.36
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.73
Consensus pattern (19 bp):
TTTTTATAATTTTAATTAT
Found at i:26807864 original size:67 final size:68
Alignment explanation
Indices: 26807775--26807924 Score: 239
Period size: 67 Copynumber: 2.2 Consensus size: 68
26807765 TATATTCATA
* *
26807775 AAATAAAAAAACAAAATTAATATTATTTTACATTTATTTATTTATATTCAT-GAAATAATAAATA
1 AAATAAAAAAACAAAATTAATATTATTTTACATTTATTTATATATATTCATAAAAATAATAAATA
26807839 AAT
66 AAT
* * *
26807842 AAATAATAAAATAAAATTAATATTATTTTATATTTATTTATATATATTCATAAAAATAATAAATA
1 AAATAAAAAAACAAAATTAATATTATTTTACATTTATTTATATATATTCATAAAAATAATAAATA
26807907 AAT
66 AAT
26807910 AAATAAAAATAACAA
1 AAATAAAAA-AACAA
26807925 GAAAAATAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
67 47 0.64
68 23 0.31
69 4 0.05
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (68 bp):
AAATAAAAAAACAAAATTAATATTATTTTACATTTATTTATATATATTCATAAAAATAATAAATA
AAT
Found at i:26811468 original size:32 final size:32
Alignment explanation
Indices: 26811432--26811519 Score: 167
Period size: 32 Copynumber: 2.8 Consensus size: 32
26811422 TTACATTGTC
26811432 AATAATTTCAATATCCAACAAGCTTAAAACAT
1 AATAATTTCAATATCCAACAAGCTTAAAACAT
26811464 AATAATTTCAATATCCAACAAGCTTAAAACAT
1 AATAATTTCAATATCCAACAAGCTTAAAACAT
*
26811496 AATAATTTCATTATCCAACAAGCT
1 AATAATTTCAATATCCAACAAGCT
26811520 AATTTCAATA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.48, C:0.19, G:0.03, T:0.30
Consensus pattern (32 bp):
AATAATTTCAATATCCAACAAGCTTAAAACAT
Found at i:26812001 original size:27 final size:27
Alignment explanation
Indices: 26811934--26812002 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 27
26811924 CTAGGGTTCG
** *
26811934 CCAATTGAGCTGCAAATTGGGGGCTCA
1 CCAATTGAGCTGTGAGTTGGGGGCTCA
*
26811961 CCAATTGAGCTGTGAGTTGGGGGCTCG
1 CCAATTGAGCTGTGAGTTGGGGGCTCA
* *
26811988 CCAGTTGAGTTGTGA
1 CCAATTGAGCTGTGA
26812003 ACTGGGGTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.20, C:0.19, G:0.35, T:0.26
Consensus pattern (27 bp):
CCAATTGAGCTGTGAGTTGGGGGCTCA
Found at i:26816192 original size:31 final size:31
Alignment explanation
Indices: 26816149--26816216 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
26816139 ATTTCAATAT
26816149 TTTAAATATTAAATAATTA-AATAA-TTTTTAA
1 TTTAAATATTAAAT-A-TAGAATAATTTTTTAA
* *
26816180 TTTAAATTTTAAATATAGTATAATTTTTTAA
1 TTTAAATATTAAATATAGAATAATTTTTTAA
26816211 TTTAAA
1 TTTAAA
26816217 AAATAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 2 0.06
30 5 0.15
31 26 0.79
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (31 bp):
TTTAAATATTAAATATAGAATAATTTTTTAA
Found at i:26817500 original size:12 final size:12
Alignment explanation
Indices: 26817468--26817501 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
26817458 AGTTTAAAAG
* *
26817468 CTCGTTTACTGG
1 CTCGTTTATTGA
26817480 CTCGTTTATTGA
1 CTCGTTTATTGA
26817492 CTCGTTTATT
1 CTCGTTTATT
26817502 TATTTATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.12, C:0.21, G:0.18, T:0.50
Consensus pattern (12 bp):
CTCGTTTATTGA
Found at i:26817622 original size:24 final size:23
Alignment explanation
Indices: 26817595--26817654 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 23
26817585 TCATTAACAT
*
26817595 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATATTCAATTA-A
* **
26817619 TGTTCATGAACATATTCGTTTAA
1 TGTTCGTGAACATATTCAATTAA
26817642 TGTTCGTGAACAT
1 TGTTCGTGAACAT
26817655 TAAACAAACG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
23 13 0.42
24 18 0.58
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (23 bp):
TGTTCGTGAACATATTCAATTAA
Found at i:26822570 original size:9 final size:9
Alignment explanation
Indices: 26822525--26822583 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 9
26822515 AATGTTATTA
26822525 AAAATTATAT
1 AAAATT-TAT
26822535 AAAATATTAT
1 AAAAT-TTAT
***
26822545 AAAAAGCAT
1 AAAATTTAT
26822554 AAAA-TTAT
1 AAAATTTAT
26822562 AAAATTTAT
1 AAAATTTAT
26822571 GAAAA-TTAT
1 -AAAATTTAT
26822580 AAAA
1 AAAA
26822584 CTATTTTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
8 10 0.24
9 14 0.34
10 16 0.39
11 1 0.02
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (9 bp):
AAAATTTAT
Found at i:26832285 original size:86 final size:86
Alignment explanation
Indices: 26832140--26832390 Score: 493
Period size: 86 Copynumber: 2.9 Consensus size: 86
26832130 CTATTGATAC
26832140 GGTATTGACTACATTATTTGTGACATTTTAAACTATTGTCTAATAAAAATTTGGATCTCTATTTA
1 GGTATTGACTACATTATTTGTGACATTTTAAACTATTGTCTAATAAAAATTTGGATCTCTATTTA
26832205 CTTGTAACTTAATAAAAATTT
66 CTTGTAACTTAATAAAAATTT
26832226 GGTATTGACTACATTATTTGTGACATTTTAAACTATTGTCTAATAAAAATTTGGATCTCTATTTA
1 GGTATTGACTACATTATTTGTGACATTTTAAACTATTGTCTAATAAAAATTTGGATCTCTATTTA
26832291 CTTGTAACTTAATAAAAATTT
66 CTTGTAACTTAATAAAAATTT
26832312 GGTATTGACTACATTATTTGTGACATTTTAAACTATTGTCTAATAAAAATTTGGATCTCTATTTA
1 GGTATTGACTACATTATTTGTGACATTTTAAACTATTGTCTAATAAAAATTTGGATCTCTATTTA
*
26832377 CTTGTAATTTAATA
66 CTTGTAACTTAATA
26832391 TATACATTCT
Statistics
Matches: 164, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 164 1.00
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.45
Consensus pattern (86 bp):
GGTATTGACTACATTATTTGTGACATTTTAAACTATTGTCTAATAAAAATTTGGATCTCTATTTA
CTTGTAACTTAATAAAAATTT
Found at i:26839070 original size:16 final size:15
Alignment explanation
Indices: 26839040--26839068 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
26839030 AGACTATATA
26839040 AAAAAATTTATAAAT
1 AAAAAATTTATAAAT
26839055 AAAAAATTTATAAA
1 AAAAAATTTATAAA
26839069 ATTATTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAAAATTTATAAAT
Found at i:26844958 original size:18 final size:18
Alignment explanation
Indices: 26844927--26844961 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
26844917 TTATTTAAAT
**
26844927 ATGTTTTGTTTAAATATG
1 ATGTTTTGCATAAATATG
26844945 ATGTTTTGCATAAATAT
1 ATGTTTTGCATAAATAT
26844962 AAATATTTGT
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:0.31, C:0.03, G:0.14, T:0.51
Consensus pattern (18 bp):
ATGTTTTGCATAAATATG
Found at i:26846560 original size:43 final size:43
Alignment explanation
Indices: 26846512--26846597 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
26846502 CTGCACATTT
26846512 AGAATCACATTTAGAATTAACTTTGATAGTTGAAAAATTTTTA
1 AGAATCACATTTAGAATTAACTTTGATAGTTGAAAAATTTTTA
* *
26846555 AGAATCATATTTAGAATTAACTTTGATAGTTGGAAAATTTTTA
1 AGAATCACATTTAGAATTAACTTTGATAGTTGAAAAATTTTTA
26846598 TTGATTACTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.41, C:0.06, G:0.13, T:0.41
Consensus pattern (43 bp):
AGAATCACATTTAGAATTAACTTTGATAGTTGAAAAATTTTTA
Found at i:26846866 original size:15 final size:15
Alignment explanation
Indices: 26846846--26846878 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
26846836 TTCCTTTCGA
*
26846846 TGACCTATGTTATGT
1 TGACCTATATTATGT
26846861 TGACCTATATTATGT
1 TGACCTATATTATGT
26846876 TGA
1 TGA
26846879 AGGGATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.45
Consensus pattern (15 bp):
TGACCTATATTATGT
Found at i:26847889 original size:20 final size:20
Alignment explanation
Indices: 26847866--26847904 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
26847856 TGGCAATTTT
26847866 TGTTCAATTTCTTTAATTAC
1 TGTTCAATTTCTTTAATTAC
***
26847886 TGTTTTGTTTCTTTAATTA
1 TGTTCAATTTCTTTAATTA
26847905 TCTTTAAATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.10, G:0.08, T:0.62
Consensus pattern (20 bp):
TGTTCAATTTCTTTAATTAC
Found at i:26851678 original size:11 final size:11
Alignment explanation
Indices: 26851649--26851688 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
26851639 TGAGCTTCTG
*
26851649 TTCTTCCTTCTT
1 TTCTTTCTT-TT
*
26851661 TTGTTTCTTTT
1 TTCTTTCTTTT
26851672 TTCTTTCTTTT
1 TTCTTTCTTTT
26851683 TTCTTT
1 TTCTTT
26851689 TATTTCTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
11 18 0.72
12 7 0.28
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.78
Consensus pattern (11 bp):
TTCTTTCTTTT
Found at i:26851679 original size:27 final size:28
Alignment explanation
Indices: 26851644--26851696 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
26851634 TCGTTTGAGC
*
26851644 TTCTGTTCTTCCTTCTTTTGTTTCTTTT
1 TTCTGTTCTTCCTTCTTTTATTTCTTTT
**
26851672 TTCT-TTCTTTTTTCTTTTATTTCTT
1 TTCTGTTCTTCCTTCTTTTATTTCTT
26851697 ATATATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.02, C:0.19, G:0.04, T:0.75
Consensus pattern (28 bp):
TTCTGTTCTTCCTTCTTTTATTTCTTTT
Found at i:26854059 original size:34 final size:34
Alignment explanation
Indices: 26854016--26854085 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
26854006 AGAATATGAA
*
26854016 AGGTTAAGGAAAAT-GAAGGGTTAAAGGTCAAGGG
1 AGGTTAAGGAAAATAGAA-GGTTAAAAGTCAAGGG
**
26854050 AGGTTAAGGAAGGTAGAAGGTTAAAAGTCAAGGG
1 AGGTTAAGGAAAATAGAAGGTTAAAAGTCAAGGG
26854084 AG
1 AG
26854086 ATGAAAGGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
34 29 0.91
35 3 0.09
ACGTcount: A:0.41, C:0.03, G:0.39, T:0.17
Consensus pattern (34 bp):
AGGTTAAGGAAAATAGAAGGTTAAAAGTCAAGGG
Found at i:26858917 original size:31 final size:31
Alignment explanation
Indices: 26858882--26858943 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
26858872 GTGCTGATAA
26858882 CGTGTTATAAAATAATAACAATGATGTAAAG
1 CGTGTTATAAAATAATAACAATGATGTAAAG
26858913 CGTGTTATAAAATAATAACAATGATGTAAAG
1 CGTGTTATAAAATAATAACAATGATGTAAAG
26858944 AACATAAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.48, C:0.06, G:0.16, T:0.29
Consensus pattern (31 bp):
CGTGTTATAAAATAATAACAATGATGTAAAG
Found at i:26860979 original size:13 final size:13
Alignment explanation
Indices: 26860961--26860988 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
26860951 TGTATCTAAA
26860961 ATTTATTTTTTTT
1 ATTTATTTTTTTT
26860974 ATTTATTTTTTTT
1 ATTTATTTTTTTT
26860987 AT
1 AT
26860989 ATGAGTATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (13 bp):
ATTTATTTTTTTT
Found at i:26863658 original size:2 final size:2
Alignment explanation
Indices: 26863653--26863685 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
26863643 ATATATATAT
*
26863653 AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
26863686 TTAAACTCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:26870141 original size:70 final size:68
Alignment explanation
Indices: 26870053--26870191 Score: 190
Period size: 70 Copynumber: 2.0 Consensus size: 68
26870043 AAACAAAACG
* * *
26870053 CATAGATATATTACAGAGAACTGCAAAGCAATACAACTTGAAAAA-ATTGCAAGCCATATTAATA
1 CATAGATATATTAAAGAGAACTGAAAAGAAATACAACTTGAAAAAGA-TGCAAGCCATATTAATA
26870117 TTCA
65 TTCA
* * *
26870121 CATAGATATATATGAAAGAGAACTGAAAAGAAATATAACTTGAAAAAGATGCGAGCCATATTGAT
1 CATAGATATAT-T-AAAGAGAACTGAAAAGAAATACAACTTGAAAAAGATGCAAGCCATATTAAT
26870186 ATTCA
64 ATTCA
26870191 C
1 C
26870192 CATTTAGTCC
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
68 11 0.18
69 1 0.02
70 49 0.79
71 1 0.02
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.24
Consensus pattern (68 bp):
CATAGATATATTAAAGAGAACTGAAAAGAAATACAACTTGAAAAAGATGCAAGCCATATTAATAT
TCA
Found at i:26873924 original size:45 final size:45
Alignment explanation
Indices: 26873858--26873970 Score: 158
Period size: 45 Copynumber: 2.5 Consensus size: 45
26873848 GTCTACCATA
*
26873858 TCTATGAATCTGCATGTATGAGTCC-CC-TATACTCATGAATCTTCT
1 TCTATGAATTTGCATGTATGAGTCCACCATAT-CT-ATGAATCTTCT
*
26873903 TTTATGAATTTGCATGTATGAGTCCACCATATCTATGAATCTTCT
1 TCTATGAATTTGCATGTATGAGTCCACCATATCTATGAATCTTCT
* *
26873948 TCTATGAGTTCGCATGTATGAGT
1 TCTATGAATTTGCATGTATGAGT
26873971 TCGCATATAA
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
45 54 0.89
46 4 0.07
47 3 0.05
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (45 bp):
TCTATGAATTTGCATGTATGAGTCCACCATATCTATGAATCTTCT
Found at i:26873967 original size:14 final size:14
Alignment explanation
Indices: 26873950--26873976 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
26873940 AATCTTCTTC
26873950 TATGAGTTCGCATG
1 TATGAGTTCGCATG
26873964 TATGAGTTCGCAT
1 TATGAGTTCGCAT
26873977 ATAAGAATCC
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:0.22, C:0.15, G:0.26, T:0.37
Consensus pattern (14 bp):
TATGAGTTCGCATG
Found at i:26874861 original size:24 final size:24
Alignment explanation
Indices: 26874791--26874861 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 24
26874781 TGGAATGAGC
26874791 TTATACGGTGTGTTTTGATGTTAG
1 TTATACGGTGTGTTTTGATGTTAG
* * *
26874815 TTATACAGTTTG-TTT--TG--AC
1 TTATACGGTGTGTTTTGATGTTAG
*
26874834 TTATACGGTGCGTTTTGATGTTAG
1 TTATACGGTGTGTTTTGATGTTAG
26874858 TTAT
1 TTAT
26874862 GCAATGCGTT
Statistics
Matches: 35, Mismatches: 7, Indels: 10
0.67 0.13 0.19
Matches are distributed among these distances:
19 10 0.29
20 3 0.09
21 2 0.06
22 2 0.06
23 3 0.09
24 15 0.43
ACGTcount: A:0.18, C:0.07, G:0.24, T:0.51
Consensus pattern (24 bp):
TTATACGGTGTGTTTTGATGTTAG
Found at i:26874873 original size:43 final size:43
Alignment explanation
Indices: 26874790--26874874 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
26874780 TTGGAATGAG
* * **
26874790 CTTATACGGTGTGTTTTGATGTTAGTTATACAGTTTGTTTTGA
1 CTTATACGGTGCGTTTTGATGTTAGTTATACAATGCGTTTTGA
*
26874833 CTTATACGGTGCGTTTTGATGTTAGTTATGCAATGCGTTTTG
1 CTTATACGGTGCGTTTTGATGTTAGTTATACAATGCGTTTTG
26874875 TTGCTTAGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.18, C:0.09, G:0.25, T:0.48
Consensus pattern (43 bp):
CTTATACGGTGCGTTTTGATGTTAGTTATACAATGCGTTTTGA
Found at i:26890954 original size:16 final size:17
Alignment explanation
Indices: 26890929--26890962 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
26890919 ATTTGTTGTG
26890929 TTTTCAACAAATTTTTT
1 TTTTCAACAAATTTTTT
26890946 TTTTC-ACAAATTTTTT
1 TTTTCAACAAATTTTTT
26890962 T
1 T
26890963 ACTTTTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.26, C:0.12, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTCAACAAATTTTTT
Found at i:26897130 original size:4 final size:4
Alignment explanation
Indices: 26897123--26897194 Score: 90
Period size: 4 Copynumber: 18.0 Consensus size: 4
26897113 ACATACATGA
* *
26897123 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG CATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * *
26897171 CATG CATG TATT TATG CATG TATG
1 TATG TATG TATG TATG TATG TATG
26897195 AATGAATGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 62 1.00
ACGTcount: A:0.25, C:0.07, G:0.24, T:0.44
Consensus pattern (4 bp):
TATG
Found at i:26897811 original size:219 final size:220
Alignment explanation
Indices: 26897432--26897876 Score: 847
Period size: 219 Copynumber: 2.0 Consensus size: 220
26897422 ATGTATCAGA
26897432 TAACTTTCTTATTTACCTAGTGGCGTCAGTTCCTCCATGTGACTCTGATGCTCAGTCTCTATATT
1 TAACTTTCTTATTTACCTAGTGGCGTCAGTTCCTCCATGTGACTCTGATGCTCAGTCTCTATATT
*
26897497 CACCTGGTCTTCGCTTCCGCTACTTTTGACATCATCATCAACTGTAAGCACAAGGTTGAGATGTA
66 CACCTGGTCTTCGCTTCCGCTACTTTTGACATCATCATCAACTGTAAGCAAAAGGTTGAGATGTA
26897562 GTGAAATGTGCATTAGATACAAAACTTTAGTGGTATGCAGTAGTAACCCTGCGATGAATTTTAAA
131 GTGAAATGTGCATTAGATACAAAACTTTAGTGGTATGCAGTAGTAACCCTGCGATGAATTTTAAA
26897627 AGAT-AAAGACAGCTCCTACATTGT
196 AGATAAAAGACAGCTCCTACATTGT
*
26897651 TAACTTTCTTATTTACCTAGTGGCGTCAGTTTCTCCATGTGACTCTGATGCTCAGTCTCTATATT
1 TAACTTTCTTATTTACCTAGTGGCGTCAGTTCCTCCATGTGACTCTGATGCTCAGTCTCTATATT
*
26897716 CACCTGGTCTTCGCTTCCGCTACTTTTGACATCATCATCAACTGTAAGCAAAAGGTTGGGATGTA
66 CACCTGGTCTTCGCTTCCGCTACTTTTGACATCATCATCAACTGTAAGCAAAAGGTTGAGATGTA
26897781 GTGAAATGTGCATTAGATACAAAACTTTAGTGGTATGCAGTAGTAACCCTGCGATGAATTTTAAA
131 GTGAAATGTGCATTAGATACAAAACTTTAGTGGTATGCAGTAGTAACCCTGCGATGAATTTTAAA
*
26897846 GGATAAAAGACAGCTCCTACATTGT
196 AGATAAAAGACAGCTCCTACATTGT
26897871 TAACTT
1 TAACTT
26897877 ACCAGACAGA
Statistics
Matches: 221, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
219 195 0.88
220 26 0.12
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Consensus pattern (220 bp):
TAACTTTCTTATTTACCTAGTGGCGTCAGTTCCTCCATGTGACTCTGATGCTCAGTCTCTATATT
CACCTGGTCTTCGCTTCCGCTACTTTTGACATCATCATCAACTGTAAGCAAAAGGTTGAGATGTA
GTGAAATGTGCATTAGATACAAAACTTTAGTGGTATGCAGTAGTAACCCTGCGATGAATTTTAAA
AGATAAAAGACAGCTCCTACATTGT
Found at i:26899339 original size:14 final size:14
Alignment explanation
Indices: 26899320--26899349 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
26899310 AAGTAGATTG
26899320 ACAGTTTGAACCTT
1 ACAGTTTGAACCTT
26899334 ACAGTTTGAACCTT
1 ACAGTTTGAACCTT
26899348 AC
1 AC
26899350 TTGTATAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.33
Consensus pattern (14 bp):
ACAGTTTGAACCTT
Found at i:26901018 original size:34 final size:34
Alignment explanation
Indices: 26900959--26901023 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
26900949 ACAAGTGAAG
*
26900959 GTAATAAGATTGCGGGAATGCAAGATTATGTTTC
1 GTAATAAGATTGCGGCAATGCAAGATTATGTTTC
* * *
26900993 GTAATAGGATTTCGGCAATGTAAGATTATGT
1 GTAATAAGATTGCGGCAATGCAAGATTATGT
26901024 GTTTACAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.34
Consensus pattern (34 bp):
GTAATAAGATTGCGGCAATGCAAGATTATGTTTC
Found at i:26908767 original size:21 final size:21
Alignment explanation
Indices: 26908743--26908796 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
26908733 GAAATTTAAA
*
26908743 ACAAACACAATGATGAGAGTT
1 ACAAACACAATGAGGAGAGTT
*
26908764 ACAAA-ACTTATGAGGAGAGTT
1 ACAAACAC-AATGAGGAGAGTT
*
26908785 ACAAACATAATG
1 ACAAACACAATG
26908797 TTTTGTAGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 2 0.07
21 24 0.89
22 1 0.04
ACGTcount: A:0.48, C:0.13, G:0.19, T:0.20
Consensus pattern (21 bp):
ACAAACACAATGAGGAGAGTT
Found at i:26910139 original size:29 final size:29
Alignment explanation
Indices: 26910070--26910142 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 29
26910060 TACGTTAACA
* *
26910070 AGACACCTCCACATTTTCAAGTAGTTCTT
1 AGACACCCCCACATTTCCAAGTAGTTCTT
* *
26910099 AGACACCCCCCATATTTCCAAGTGGTTC-T
1 AGACA-CCCCCACATTTCCAAGTAGTTCTT
26910128 AGGACACCCCCACAT
1 A-GACACCCCCACAT
26910143 GTTCTGTGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 15 0.41
30 22 0.59
ACGTcount: A:0.27, C:0.34, G:0.12, T:0.26
Consensus pattern (29 bp):
AGACACCCCCACATTTCCAAGTAGTTCTT
Found at i:26912072 original size:19 final size:20
Alignment explanation
Indices: 26912024--26912073 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
26912014 AGGTAATATA
*
26912024 TAAAAATATA-AATATAATT
1 TAAAAATAAATAATATAATT
* *
26912043 T-AAATTTAATAATA-AATT
1 TAAAAATAAATAATATAATT
26912061 TAAAAATAAATAA
1 TAAAAATAAATAA
26912074 CAAGTATACT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAAAATAAATAATATAATT
Found at i:26912436 original size:21 final size:21
Alignment explanation
Indices: 26912412--26912465 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
26912402 GAAATTTAAA
*
26912412 ACAAACATAATGATGAGAGTT
1 ACAAACATAATGAGGAGAGTT
* *
26912433 ACAAA-ACTTATGAGGTGAGTT
1 ACAAACA-TAATGAGGAGAGTT
26912454 ACAAACATAATG
1 ACAAACATAATG
26912466 TTTTGTAGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.46, C:0.11, G:0.19, T:0.24
Consensus pattern (21 bp):
ACAAACATAATGAGGAGAGTT
Found at i:26915099 original size:16 final size:16
Alignment explanation
Indices: 26915078--26915108 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
26915068 TAATTTAAAT
*
26915078 TAATTAATTAATTTTC
1 TAATTAAATAATTTTC
26915094 TAATTAAATAATTTT
1 TAATTAAATAATTTT
26915109 ATTAATTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TAATTAAATAATTTTC
Found at i:26917944 original size:20 final size:21
Alignment explanation
Indices: 26917919--26917959 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
26917909 AAAATAATTT
*
26917919 AATAATTTTAT-ATTTTAAAA
1 AATAATTTAATAATTTTAAAA
26917939 AATAATTTAATAATTTTAAAA
1 AATAATTTAATAATTTTAAAA
26917960 TTATTTGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AATAATTTAATAATTTTAAAA
Found at i:26923076 original size:20 final size:20
Alignment explanation
Indices: 26923040--26923090 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
26923030 ATTAGCATGA
26923040 TTTATATTAAATGTAAATAG-G
1 TTTA-ATTAAATGTAAA-AGTG
26923061 TTTAATTAAGAT-TAAAAGTG
1 TTTAATTAA-ATGTAAAAGTG
*
26923081 ATTAATTAAA
1 TTTAATTAAA
26923091 GCTTAATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 3 0.11
20 18 0.67
21 6 0.22
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (20 bp):
TTTAATTAAATGTAAAAGTG
Found at i:26924967 original size:21 final size:20
Alignment explanation
Indices: 26924943--26924992 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
26924933 GACTCGTTTG
26924943 GATAGAAGAGTCACTTGTATC
1 GATAGAAGA-TCACTTGTATC
* *
26924964 GATAGAACTATCATTTGTATC
1 GATAGAA-GATCACTTGTATC
*
26924985 GGTAGAAG
1 GATAGAAG
26924993 TCTGCACTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (20 bp):
GATAGAAGATCACTTGTATC
Found at i:26930158 original size:91 final size:90
Alignment explanation
Indices: 26930058--26930275 Score: 261
Period size: 91 Copynumber: 2.5 Consensus size: 90
26930048 AAAAAATAAT
* * *
26930058 AATTAAGCCCCTGTTTTTTTTTTTCACT-AACTTGGGTACTTCAACTTTCAAAATGCATTAAAAA
1 AATTAAGCCCCTGATTTTTTTTTGCACTCAA-TTGGGTACTT-AACTTTCAAAATGCATCAAAAA
*
26930122 -GACCTTCAAACTTTTTTCAAAAAAAG-C
64 GGACC-ACAAAC-TTTTTCAAAAAAAGTC
* *
26930149 AATTAAGCCCCTGCTTTTATTTTGCACTCAATTGGGTACTTAACTTTCAAAATGCATCAAAAAGG
1 AATTAAGCCCCTGATTTTTTTTTGCACTCAATTGGGTACTTAACTTTCAAAATGCATCAAAAAGG
* *
26930214 ATCACAAACTTTTTCAAAAAATGTC
66 ACCACAAACTTTTTCAAAAAAAGTC
* *
26930239 -ATTAAGCCCCT-A-ATTTTTTT-CACTCAATTGGATACTT
1 AATTAAGCCCCTGATTTTTTTTTGCACTCAATTGGGTACTT
26930276 GAATCACTCC
Statistics
Matches: 113, Mismatches: 11, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
86 16 0.14
87 6 0.05
89 24 0.21
90 27 0.24
91 38 0.34
92 2 0.02
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (90 bp):
AATTAAGCCCCTGATTTTTTTTTGCACTCAATTGGGTACTTAACTTTCAAAATGCATCAAAAAGG
ACCACAAACTTTTTCAAAAAAAGTC
Found at i:26930223 original size:90 final size:89
Alignment explanation
Indices: 26930058--26930275 Score: 259
Period size: 90 Copynumber: 2.4 Consensus size: 89
26930048 AAAAAATAAT
* *
26930058 AATTAAGCCCCTGTTTTTTTTTTTCACT-AACTTGGGTACTTCAACTTTCAAAATGCATTAAAAA
1 AATTAAGCCCCTG--ATTTTTTTTCACTCAA-TTGGGTACTTCAACTTTCAAAATGCATCAAAAA
*
26930122 GACCTTCAAACTTTTTTCAAAAAAAG-C
63 GACCTACAAAC-TTTTTCAAAAAAAGTC
*
26930149 AATTAAGCCCCTGCTTTTATTTTGCACTCAATTGGGTACTT-AACTTTCAAAATGCATCAAAAAG
1 AATTAAGCCCCTGATTTT-TTTT-CACTCAATTGGGTACTTCAACTTTCAAAATGCATCAAAAA-
* *
26930213 GATC-ACAAACTTTTTCAAAAAATGTC
63 GACCTACAAACTTTTTCAAAAAAAGTC
* *
26930239 -ATTAAGCCCCT-AATTTTTTTCACTCAATTGGATACTT
1 AATTAAGCCCCTGATTTTTTTTCACTCAATTGGGTACTT
26930276 GAATCACTCC
Statistics
Matches: 114, Mismatches: 8, Indels: 15
0.83 0.06 0.11
Matches are distributed among these distances:
86 16 0.14
87 4 0.04
88 3 0.03
89 28 0.25
90 31 0.27
91 30 0.26
92 2 0.02
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (89 bp):
AATTAAGCCCCTGATTTTTTTTCACTCAATTGGGTACTTCAACTTTCAAAATGCATCAAAAAGAC
CTACAAACTTTTTCAAAAAAAGTC
Found at i:26930384 original size:19 final size:19
Alignment explanation
Indices: 26930352--26930398 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
26930342 AAATGATAAA
*
26930352 AATAAAAA-AATAAAACTT
1 AATAAAAATATTAAAACTT
* **
26930370 ATTAAAAATATTAAATTTT
1 AATAAAAATATTAAAACTT
26930389 AATAAAAATA
1 AATAAAAATA
26930399 GAAAACATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
AATAAAAATATTAAAACTT
Found at i:26930403 original size:27 final size:28
Alignment explanation
Indices: 26930373--26930437 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
26930363 AAAACTTATT
26930373 AAAAATATTAAATTTTAAT-AAAAA-TAG
1 AAAAATATTAAATTTT-ATCAAAAATTAG
26930400 AAAACAT-TTAAATTTTATCAAAAATTAG
1 AAAA-ATATTAAATTTTATCAAAAATTAG
*
26930428 AAAAAAATTA
1 AAAAATATTA
26930438 TAAAAATCGT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
26 2 0.06
27 19 0.58
28 12 0.36
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (28 bp):
AAAAATATTAAATTTTATCAAAAATTAG
Found at i:26930489 original size:31 final size:31
Alignment explanation
Indices: 26930451--26930547 Score: 94
Period size: 31 Copynumber: 3.1 Consensus size: 31
26930441 AAATCGTAAG
26930451 AAAAATTATAAAATATATAGAAATATAGAAA
1 AAAAATTATAAAATATATAGAAATATAGAAA
* *
26930482 AAAAATTATAAAATTTTATA-AAGT-T-GTAAA
1 AAAAATTATAAAA-TATATAGAAATATAG-AAA
* *
26930512 AAAAATTATAAAAAATGTAAAGAAATATA-AAA
1 AAAAATTAT--AAAATATATAGAAATATAGAAA
26930544 AAAA
1 AAAA
26930548 TATCGTACTA
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
29 1 0.02
30 13 0.24
31 20 0.37
32 19 0.35
33 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (31 bp):
AAAAATTATAAAATATATAGAAATATAGAAA
Found at i:26930530 original size:21 final size:21
Alignment explanation
Indices: 26930414--26930545 Score: 62
Period size: 21 Copynumber: 6.5 Consensus size: 21
26930404 CATTTAAATT
*
26930414 TTATCAAAAAT-TAGAAAAAAA
1 TTATAAAAAATGTA-AAAAAAA
*
26930435 TTAT-AAAAATCGTAAGAAAAA
1 TTATAAAAAAT-GTAAAAAAAA
* * * *
26930456 TTATAAAATATAT-AGAAATA
1 TTATAAAAAATGTAAAAAAAA
* * * **
26930476 TAGAAAAAAAAT-TATAAAATT
1 T-TATAAAAAATGTAAAAAAAA
**
26930497 TTAT-AAAGTTGTAAAAAAAA
1 TTATAAAAAATGTAAAAAAAA
*
26930517 TTATAAAAAATGT-AAAGAAA
1 TTATAAAAAATGTAAAAAAAA
26930537 -TATAAAAAA
1 TTATAAAAAA
26930546 AATATCGTAC
Statistics
Matches: 84, Mismatches: 20, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
19 13 0.15
20 31 0.37
21 33 0.39
22 7 0.08
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (21 bp):
TTATAAAAAATGTAAAAAAAA
Found at i:26930605 original size:17 final size:18
Alignment explanation
Indices: 26930565--26930605 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
26930555 CTAAAAGAAG
*
26930565 CATTTTATATTTTTTATT
1 CATTTTTTATTTTTTATT
*
26930583 GA-TTTTTATTTTTTA-T
1 CATTTTTTATTTTTTATT
26930599 CATTTTT
1 CATTTTT
26930606 CGCATGCATG
Statistics
Matches: 19, Mismatches: 3, Indels: 3
0.76 0.12 0.12
Matches are distributed among these distances:
16 2 0.11
17 16 0.84
18 1 0.05
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (18 bp):
CATTTTTTATTTTTTATT
Found at i:26930774 original size:20 final size:19
Alignment explanation
Indices: 26930749--26930815 Score: 62
Period size: 21 Copynumber: 3.3 Consensus size: 19
26930739 TCTTATAAAA
26930749 TTTTACAATTTTTGATATTT
1 TTTTACAATTTTT-ATATTT
* *
26930769 TTTTACCATCTTTATAATTTT
1 TTTTACAATTTTTAT-A-TTT
*
26930790 TTTTTCTAATTTTTAATATTT
1 TTTTAC-AATTTTT-ATATTT
26930811 TTTTA
1 TTTTA
26930816 TTTTTATTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
19 2 0.05
20 12 0.32
21 15 0.41
22 6 0.16
23 2 0.05
ACGTcount: A:0.24, C:0.07, G:0.01, T:0.67
Consensus pattern (19 bp):
TTTTACAATTTTTATATTT
Found at i:26931412 original size:19 final size:19
Alignment explanation
Indices: 26931390--26931427 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
26931380 CACTGTCACC
*
26931390 CACCGTAATCAAATTTGTT
1 CACCATAATCAAATTTGTT
26931409 CACCATAATCAAATTTGTT
1 CACCATAATCAAATTTGTT
26931428 ATTGACTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.37
Consensus pattern (19 bp):
CACCATAATCAAATTTGTT
Found at i:26932213 original size:21 final size:21
Alignment explanation
Indices: 26932173--26932213 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
26932163 GGAGGAAAGT
*
26932173 GGGAAAGAGTAAAAGTTTTGA
1 GGGAAAGAGTAAAAATTTTGA
26932194 GGGAAA-AGTAAAAATGTTTG
1 GGGAAAGAGTAAAAAT-TTTG
26932214 GAGATTTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.44, C:0.00, G:0.32, T:0.24
Consensus pattern (21 bp):
GGGAAAGAGTAAAAATTTTGA
Found at i:26936378 original size:29 final size:30
Alignment explanation
Indices: 26936321--26936379 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
26936311 ATGTTGAGGG
* *
26936321 CTAAATTGATTAAATTTTTTAGAATTTGAA
1 CTAAAATGATTAAATTTTGTAGAATTTGAA
26936351 CTAAAATGA-TAAATTTTGTA-AATATTGAA
1 CTAAAATGATTAAATTTTGTAGAAT-TTGAA
26936380 GATCAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 3 0.12
29 15 0.58
30 8 0.31
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.42
Consensus pattern (30 bp):
CTAAAATGATTAAATTTTGTAGAATTTGAA
Found at i:26943777 original size:21 final size:22
Alignment explanation
Indices: 26943753--26943796 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
26943743 ATTTAAAGTC
* *
26943753 ATTTCAATATTTTTAT-CTTAA
1 ATTTCAACATTTTCATCCTTAA
26943774 ATTTCAACATTTTCATCCTTAA
1 ATTTCAACATTTTCATCCTTAA
26943796 A
1 A
26943797 AAATCAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTTCAACATTTTCATCCTTAA
Found at i:26956562 original size:14 final size:14
Alignment explanation
Indices: 26956543--26956584 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
26956533 AAAATTAAAT
*
26956543 TTTTTACATTTTTA
1 TTTTTAAATTTTTA
*
26956557 TTTTTAAATTTTAA
1 TTTTTAAATTTTTA
*
26956571 TTATTAAATTTTTA
1 TTTTTAAATTTTTA
26956585 AATTTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTTAAATTTTTA
Found at i:26956586 original size:8 final size:8
Alignment explanation
Indices: 26956537--26956589 Score: 51
Period size: 8 Copynumber: 7.0 Consensus size: 8
26956527 TATAAAAAAA
26956537 TTAAATTTT
1 TTAAA-TTT
*
26956546 TTACATTT
1 TTAAATTT
26956554 TT--ATTT
1 TTAAATTT
26956560 TTAAA-TT
1 TTAAATTT
*
26956567 TT-AATTA
1 TTAAATTT
26956574 TTAAATTT
1 TTAAATTT
26956582 TTAAATTT
1 TTAAATTT
26956590 AAAAATTTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
6 8 0.22
7 7 0.19
8 18 0.49
9 4 0.11
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (8 bp):
TTAAATTT
Found at i:26956591 original size:14 final size:14
Alignment explanation
Indices: 26956544--26956592 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
26956534 AAATTAAATT
* *
26956544 TTTTACATTTTTAT
1 TTTTAAATTTTTAA
26956558 TTTTAAA-TTTTAA
1 TTTTAAATTTTTAA
26956571 TTATTAAATTTTTAA
1 TT-TTAAATTTTTAA
*
26956586 ATTTAAA
1 TTTTAAA
26956593 AATTTAGATC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 7 0.23
14 16 0.53
15 7 0.23
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTTAAATTTTTAA
Found at i:26962640 original size:16 final size:17
Alignment explanation
Indices: 26962609--26962640 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
26962599 TAAATTTTAA
26962609 TAATTTTTTTACAAATT
1 TAATTTTTTTACAAATT
26962626 TAATTTTTTTA-AAAT
1 TAATTTTTTTACAAAT
26962641 GGATAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (17 bp):
TAATTTTTTTACAAATT
Found at i:26964275 original size:30 final size:29
Alignment explanation
Indices: 26964215--26964287 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 29
26964205 ACTTATGAAA
*
26964215 AATTTTCAAA-ATCCGAAAATCTCATGAT
1 AATTTTCAAACATCCGAAAATCTAATGAT
*
26964243 AATTTTCAAACATCCTAAGAATCTTAAT-AT
1 AATTTTCAAACATCCGAA-AATC-TAATGAT
* *
26964273 AATTTTTAGACATCC
1 AATTTTCAAACATCC
26964288 CATCCCGAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 10 0.26
29 6 0.16
30 19 0.50
31 3 0.08
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (29 bp):
AATTTTCAAACATCCGAAAATCTAATGAT
Found at i:26966356 original size:29 final size:30
Alignment explanation
Indices: 26966295--26966363 Score: 108
Period size: 29 Copynumber: 2.4 Consensus size: 30
26966285 TAGATATATA
26966295 TTATTTCTAAAATTTAAAATAAAAAAAACT
1 TTATTTCTAAAATTTAAAATAAAAAAAACT
26966325 TTATTTCTAAAA-TTAAAATAAAAAATAA-T
1 TTATTTCTAAAATTTAAAATAAAAAA-AACT
26966354 TTATTT-TAAA
1 TTATTTCTAAA
26966364 CCTTTTAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
28 4 0.11
29 20 0.53
30 14 0.37
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (30 bp):
TTATTTCTAAAATTTAAAATAAAAAAAACT
Found at i:26968893 original size:7 final size:7
Alignment explanation
Indices: 26968881--26968933 Score: 81
Period size: 7 Copynumber: 7.7 Consensus size: 7
26968871 TTTCAAAAAA
26968881 GTCAACG
1 GTCAACG
26968888 GTCAACG
1 GTCAACG
26968895 GTCAACG
1 GTCAACG
*
26968902 GTCAA-A
1 GTCAACG
26968908 GTCAACG
1 GTCAACG
*
26968915 GTCAATG
1 GTCAACG
26968922 GTCAACG
1 GTCAACG
26968929 GTCAA
1 GTCAA
26968934 TCACCACCTG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
6 5 0.12
7 36 0.88
ACGTcount: A:0.32, C:0.25, G:0.26, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:26968913 original size:20 final size:20
Alignment explanation
Indices: 26968888--26968926 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
26968878 AAAGTCAACG
26968888 GTCAACGGTCAACGGTCAAA
1 GTCAACGGTCAACGGTCAAA
*
26968908 GTCAACGGTCAATGGTCAA
1 GTCAACGGTCAACGGTCAA
26968927 CGGTCAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (20 bp):
GTCAACGGTCAACGGTCAAA
Found at i:26968914 original size:27 final size:27
Alignment explanation
Indices: 26968878--26968933 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
26968868 GTTTTTCAAA
26968878 AAAGTCAACGGTCAACGGTCAACGGTC
1 AAAGTCAACGGTCAACGGTCAACGGTC
*
26968905 AAAGTCAACGGTCAATGGTCAACGGTC
1 AAAGTCAACGGTCAACGGTCAACGGTC
26968932 AA
1 AA
26968934 TCACCACCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.16
Consensus pattern (27 bp):
AAAGTCAACGGTCAACGGTCAACGGTC
Found at i:26969035 original size:15 final size:15
Alignment explanation
Indices: 26968999--26969044 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
26968989 TGGTTTGGGT
* **
26968999 TGGACTTGGTTCATT
1 TGGATTTGGTTCAAA
26969014 TGG-TTTGGTTCAAA
1 TGGATTTGGTTCAAA
26969028 TGGATTTGGTTCAAA
1 TGGATTTGGTTCAAA
26969043 TG
1 TG
26969045 AATGTGGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.20, C:0.09, G:0.28, T:0.43
Consensus pattern (15 bp):
TGGATTTGGTTCAAA
Found at i:26969052 original size:15 final size:15
Alignment explanation
Indices: 26969019--26969053 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
26969009 TCATTTGGTT
* *
26969019 TGGTTCAAATGGATT
1 TGGTTCAAATGAATG
26969034 TGGTTCAAATGAATG
1 TGGTTCAAATGAATG
26969049 TGGTT
1 TGGTT
26969054 TTGGTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.06, G:0.29, T:0.40
Consensus pattern (15 bp):
TGGTTCAAATGAATG
Found at i:26982704 original size:41 final size:42
Alignment explanation
Indices: 26982603--26982762 Score: 107
Period size: 41 Copynumber: 3.9 Consensus size: 42
26982593 ATTTATGAGA
* * *
26982603 AAAT-GCCACTAAAGGTCAA-AGCATTAG-CA-GTGTTTATTAG
1 AAATCGCCGCTAAAGGT-AAGAGCATTAGTGACGT-TTTAGTAG
* * ** * *
26982643 AAAACGCCACTAAATATAAGAGCATTATTGGC-TTTTAGTAG
1 AAATCGCCGCTAAAGGTAAGAGCATTAGTGACGTTTTAGTAG
* * * * *
26982684 AAATCGCCGCTAAAGGTAAGAACAGTAGTGACGTTTATGGGAA
1 AAATCGCCGCTAAAGGTAAGAGCATTAGTGACGTTT-TAGTAG
*
26982727 AAAT-GCCGCTAAAGGGTAAGAGCATTAGCGACGTTT
1 AAATCGCCGCTAAA-GGTAAGAGCATTAGTGACGTTT
26982763 ATGGGGAAAA
Statistics
Matches: 92, Mismatches: 21, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
40 5 0.05
41 48 0.52
42 13 0.14
43 26 0.28
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (42 bp):
AAATCGCCGCTAAAGGTAAGAGCATTAGTGACGTTTTAGTAG
Found at i:26982760 original size:43 final size:43
Alignment explanation
Indices: 26982684--26982789 Score: 151
Period size: 43 Copynumber: 2.5 Consensus size: 43
26982674 CTTTTAGTAG
*
26982684 AAATCGCCGCTAAA-GGTAAGAACAGTAGTGACGTTTATGGGAA
1 AAAT-GCCGCTAAAGGGTAAGAACAGTAGCGACGTTTATGGGAA
* * *
26982727 AAATGCCGCTAAAGGGTAAGAGCATTAGCGACGTTTATGGGGA
1 AAATGCCGCTAAAGGGTAAGAACAGTAGCGACGTTTATGGGAA
*
26982770 AAATGCCGCTAAAGGTTAAG
1 AAATGCCGCTAAAGGGTAAG
26982790 CAATAGCGGC
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
42 9 0.16
43 48 0.84
ACGTcount: A:0.36, C:0.14, G:0.29, T:0.21
Consensus pattern (43 bp):
AAATGCCGCTAAAGGGTAAGAACAGTAGCGACGTTTATGGGAA
Found at i:26985329 original size:13 final size:13
Alignment explanation
Indices: 26985311--26985335 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26985301 TGTTTTGATG
26985311 AAAATGGTAGTTC
1 AAAATGGTAGTTC
26985324 AAAATGGTAGTT
1 AAAATGGTAGTT
26985336 GACATTGAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.32
Consensus pattern (13 bp):
AAAATGGTAGTTC
Found at i:26986281 original size:69 final size:69
Alignment explanation
Indices: 26986144--26986277 Score: 189
Period size: 69 Copynumber: 1.9 Consensus size: 69
26986134 ACGAGTTATT
* *
26986144 TAAATATTTAATTATTAAAAGCAACCAAATATTTATTTCAAAATATTTAATTATTTAATTATATT
1 TAAATATTTAATTATTAAAAACAACCAAATATTTATTTCAAAATATTTAATTAGTTAATTATATT
26986209 TAAA
66 TAAA
* *
26986213 TAAATATTTAATTATTAAAAACAACCCAAATATTTAAGTATT-TAAATATTTAATTAGTTATTTA
1 TAAATATTTAATTATTAAAAACAA-CCAAATATTT-A-T-TTCAAAATATTTAATTAGTTAATTA
26986277 T
62 T
26986278 TAAACCCTAA
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
69 23 0.40
70 10 0.18
71 1 0.02
72 21 0.37
73 2 0.04
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (69 bp):
TAAATATTTAATTATTAAAAACAACCAAATATTTATTTCAAAATATTTAATTAGTTAATTATATT
TAAA
Found at i:26986356 original size:8 final size:8
Alignment explanation
Indices: 26986343--26986371 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
26986333 TAATTCAAAA
26986343 TATTTAAT
1 TATTTAAT
26986351 TATTTAAT
1 TATTTAAT
26986359 TATTTAAT
1 TATTTAAT
26986367 TATTT
1 TATTT
26986372 GCAACTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TATTTAAT
Found at i:26988485 original size:16 final size:17
Alignment explanation
Indices: 26988466--26988503 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
26988456 TCATTACGTT
26988466 TTTTAATCCT-ATAAGG
1 TTTTAATCCTAATAAGG
26988482 TTTT-ATCCTAATAAGG
1 TTTTAATCCTAATAAGG
26988498 TTTTAA
1 TTTTAA
26988504 CGAGGCACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 5 0.25
16 14 0.70
17 1 0.05
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (17 bp):
TTTTAATCCTAATAAGG
Found at i:26988599 original size:18 final size:18
Alignment explanation
Indices: 26988572--26988607 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
26988562 ATGGATGTCC
26988572 ATCAACATCAAGATAAAG
1 ATCAACATCAAGATAAAG
*
26988590 ATCAAGATCAAGATAAAG
1 ATCAACATCAAGATAAAG
26988608 TTTGGTATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.14, G:0.14, T:0.17
Consensus pattern (18 bp):
ATCAACATCAAGATAAAG
Found at i:26988833 original size:21 final size:21
Alignment explanation
Indices: 26988779--26988838 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
26988769 TGTTTCTTTA
*
26988779 TTTTATAACATTTTTATATTC
1 TTTTATAAAATTTTTATATTC
* * *
26988800 TTTGAT-AATTTTTTCTGATT-
1 TTTTATAAAATTTTTAT-ATTC
26988820 TTTTATAAAATTTTT-TATT
1 TTTTATAAAATTTTTATATT
26988839 TTAATCATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
19 3 0.10
20 13 0.42
21 15 0.48
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.65
Consensus pattern (21 bp):
TTTTATAAAATTTTTATATTC
Found at i:26994523 original size:16 final size:16
Alignment explanation
Indices: 26994485--26994523 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
26994475 TAGAATAAGA
26994485 CTGTAATGAAATAAAG
1 CTGTAATGAAATAAAG
* *
26994501 CTCTAATGAAATAGAG
1 CTGTAATGAAATAAAG
*
26994517 TTGTAAT
1 CTGTAAT
26994524 TAAAAGTAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.31
Consensus pattern (16 bp):
CTGTAATGAAATAAAG
Found at i:26994932 original size:6 final size:7
Alignment explanation
Indices: 26994916--26994940 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
26994906 ACTCTTTCCT
26994916 AAAATTA
1 AAAATTA
26994923 AAAATTA
1 AAAATTA
26994930 AAAATTA
1 AAAATTA
26994937 AAAA
1 AAAA
26994941 CAAGGCTTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATTA
Found at i:26998193 original size:53 final size:51
Alignment explanation
Indices: 26998083--26998234 Score: 189
Period size: 53 Copynumber: 2.9 Consensus size: 51
26998073 AGCCCTCCCA
* *
26998083 AAATCAATTGTTATGGTGGAATACTTATTTTGAATCGATTGTTATATGTTT
1 AAATCAATTGTTATGTTGAAATACTTATTTTGAATCGATTGTTATATGTTT
* *
26998134 AAATCAATTATTATGTTGAAATA-TTAATTTTTTAATCGATTGTTTATATGTTT
1 AAATCAATTGTTATGTTGAAATACTT-A-TTTTGAATCGATTG-TTATATGTTT
* *
26998187 AAATCAATTGTTATGTTGGAATGATGCTTCTTTTGAATCGATTGTTAT
1 AAATCAATTGTTATGTT-GAA--ATACTTATTTTGAATCGATTGTTAT
26998235 GTAGCACGTC
Statistics
Matches: 86, Mismatches: 8, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
50 2 0.02
51 21 0.24
52 13 0.15
53 26 0.30
54 7 0.08
55 13 0.15
56 2 0.02
57 2 0.02
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.49
Consensus pattern (51 bp):
AAATCAATTGTTATGTTGAAATACTTATTTTGAATCGATTGTTATATGTTT
Found at i:26998200 original size:20 final size:20
Alignment explanation
Indices: 26998115--26998200 Score: 53
Period size: 20 Copynumber: 4.7 Consensus size: 20
26998105 ACTTATTTTG
*
26998115 AATCGATTGTTATATGTTTA
1 AATCAATTGTTATATGTTTA
* *
26998135 AATCAATT-AT-TATGTTGA
1 AATCAATTGTTATATGTTTA
* *
26998153 AAT--A---TTA-ATTTTTT
1 AATCAATTGTTATATGTTTA
*
26998167 AATCGATTGTTTATATGTTTA
1 AATCAATTG-TTATATGTTTA
26998188 AATCAATTGTTAT
1 AATCAATTGTTAT
26998201 GTTGGAATGA
Statistics
Matches: 48, Mismatches: 10, Indels: 16
0.65 0.14 0.22
Matches are distributed among these distances:
14 8 0.17
16 2 0.04
18 10 0.21
19 1 0.02
20 14 0.29
21 13 0.27
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.51
Consensus pattern (20 bp):
AATCAATTGTTATATGTTTA
Found at i:27003545 original size:27 final size:28
Alignment explanation
Indices: 27003491--27003548 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
27003481 CCAAATGTAT
*
27003491 TATGTTATAAAAATAATTATATTAATTA
1 TATGTTATAAAAATAAATATATTAATTA
*
27003519 TATGTTA-AATAATAAATATTATT-ATTA
1 TATGTTATAAAAATAAATA-TATTAATTA
27003546 TAT
1 TAT
27003549 ATATATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 16 0.59
28 11 0.41
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (28 bp):
TATGTTATAAAAATAAATATATTAATTA
Found at i:27003545 original size:31 final size:30
Alignment explanation
Indices: 27003497--27003558 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 30
27003487 GTATTATGTT
*
27003497 ATAAAAATAATTATATTA-ATTATATGTTAA
1 ATAAAAATAATTATATTATA-TATATATTAA
27003527 ATAATAAAT-ATTATTATTATATATATATTAA
1 ATAA-AAATAATTA-TATTATATATATATTAA
27003558 A
1 A
27003559 CCACTAATCC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 8 0.29
31 19 0.68
32 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (30 bp):
ATAAAAATAATTATATTATATATATATTAA
Found at i:27009846 original size:5 final size:6
Alignment explanation
Indices: 27009831--27009860 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
27009821 GAAGCATGGG
*
27009831 TTTTTG TTTTTA TTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
27009861 AATTAATCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:27020639 original size:28 final size:27
Alignment explanation
Indices: 27020546--27020639 Score: 74
Period size: 28 Copynumber: 3.5 Consensus size: 27
27020536 TGGAAAATAT
*
27020546 ATAATCTAATTTTTATTTGAAATATAAA
1 ATAATATAA-TTTTATTTGAAATATAAA
*
27020574 ATAA-ATAATCATTTATTTG---T-TTAA
1 ATAATATAAT--TTTATTTGAAATATAAA
*
27020598 CTAA-ATTAATTTTATTTGAAATATAAA
1 ATAATA-TAATTTTATTTGAAATATAAA
27020625 ATATATATAATTTTA
1 ATA-ATATAATTTTA
27020640 AATACAATTA
Statistics
Matches: 52, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
23 8 0.15
24 7 0.13
25 5 0.10
26 2 0.04
27 8 0.15
28 21 0.40
29 1 0.02
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (27 bp):
ATAATATAATTTTATTTGAAATATAAA
Found at i:27021296 original size:18 final size:18
Alignment explanation
Indices: 27021273--27021311 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
27021263 AAAGTTTATT
27021273 TAATTTACGATATTAAAC
1 TAATTTACGATATTAAAC
27021291 TAATTTACGATATTAAAC
1 TAATTTACGATATTAAAC
27021309 TAA
1 TAA
27021312 GTTATATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.38
Consensus pattern (18 bp):
TAATTTACGATATTAAAC
Found at i:27023218 original size:6 final size:6
Alignment explanation
Indices: 27023207--27023247 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
27023197 TAGAATTAAA
*
27023207 TATGTT TATGTT TATGTT TATGTT CT-TATT TATGTT TATGT
1 TATGTT TATGTT TATGTT TATGTT -TATGTT TATGTT TATGT
27023248 ATGCAAACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 1 0.03
6 29 0.94
7 1 0.03
ACGTcount: A:0.17, C:0.02, G:0.15, T:0.66
Consensus pattern (6 bp):
TATGTT
Found at i:27023376 original size:26 final size:26
Alignment explanation
Indices: 27023321--27023396 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
27023311 GCTAAACCTC
**
27023321 ATTAAATAAATTCAAACATAAAAATT
1 ATTAAATAAATTCAAACATAAAAAGA
** *
27023347 ATTAAATAAATTCAAATTTAAACAGA
1 ATTAAATAAATTCAAACATAAAAAGA
* *
27023373 ATTAATTCCAAATTCAATCATAAA
1 ATTAAAT--AAATTCAAACATAAA
27023397 CTTAATTAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
26 27 0.69
28 12 0.31
ACGTcount: A:0.57, C:0.11, G:0.01, T:0.32
Consensus pattern (26 bp):
ATTAAATAAATTCAAACATAAAAAGA
Found at i:27026171 original size:25 final size:25
Alignment explanation
Indices: 27026123--27026173 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
27026113 AACCTTCTGT
*
27026123 TTCCTTTCTTCTTCAAAACTTTTGC
1 TTCCTTTCTTCTTCAAAACATTTGC
*
27026148 TTCCTTTCCTTCTTTAAAA-ATTTGC
1 TTCCTTT-CTTCTTCAAAACATTTGC
27026173 T
1 T
27026174 GTTAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.18, C:0.25, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCCTTTCTTCTTCAAAACATTTGC
Found at i:27027557 original size:9 final size:8
Alignment explanation
Indices: 27027541--27027567 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
27027531 TTATAAAAAA
27027541 TATTTTTT
1 TATTTTTT
27027549 TATTTTTT
1 TATTTTTT
27027557 TATTTTTT
1 TATTTTTT
27027565 TAT
1 TAT
27027568 AATTTGAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (8 bp):
TATTTTTT
Found at i:27027635 original size:15 final size:14
Alignment explanation
Indices: 27027610--27027661 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
27027600 TTATTTAAGT
27027610 TATTAATTTTTTTTG
1 TATT-ATTTTTTTTG
**
27027625 TATTATATTTTGGTG
1 TATTAT-TTTTTTTG
*
27027640 TATAATTTTTTTTG
1 TATTATTTTTTTTG
27027654 TATTATTT
1 TATTATTT
27027662 AGGTAAAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
14 15 0.50
15 15 0.50
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (14 bp):
TATTATTTTTTTTG
Found at i:27030159 original size:16 final size:15
Alignment explanation
Indices: 27030138--27030197 Score: 57
Period size: 16 Copynumber: 3.9 Consensus size: 15
27030128 CAAAAAAATG
27030138 TATAAAAATATTAAA
1 TATAAAAATATTAAA
* *
27030153 TATTAAAATAATATAA
1 TATAAAAATATTA-AA
* *
27030169 TATAAATATTTTAAAA
1 TATAAAAATATT-AAA
*
27030185 AATAAAAATATTA
1 TATAAAAATATTA
27030198 TGAAAAGATC
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
15 12 0.35
16 21 0.62
17 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TATAAAAATATTAAA
Found at i:27034232 original size:21 final size:21
Alignment explanation
Indices: 27034208--27034248 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
27034198 AACAATTTTT
*
27034208 TCATGGGGGATAATTCACAAA
1 TCATGAGGGATAATTCACAAA
*
27034229 TCATGAGTGATAATTCACAA
1 TCATGAGGGATAATTCACAA
27034249 CCTGTAAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (21 bp):
TCATGAGGGATAATTCACAAA
Found at i:27034404 original size:29 final size:29
Alignment explanation
Indices: 27034366--27034434 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 29
27034356 ATTAAAAATC
* *
27034366 AAAATTATTTAATAATTTTTTATTTCAAA
1 AAAATAATTTAATAATTTTATATTTCAAA
**
27034395 AAAATAATTTTAATAATTTTATATTTTTAA
1 AAAATAA-TTTAATAATTTTATATTTCAAA
27034425 AAAATAATTT
1 AAAATAATTT
27034435 TAAAATCATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 9 0.26
30 26 0.74
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (29 bp):
AAAATAATTTAATAATTTTATATTTCAAA
Found at i:27034409 original size:30 final size:30
Alignment explanation
Indices: 27034373--27034437 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
27034363 ATCAAAATTA
*
27034373 TTTAATAATTTTTTATTTCAAAAAAATAAT
1 TTTAATAATTTTATATTTCAAAAAAATAAT
**
27034403 TTTAATAATTTTATATTTTTAAAAAATAAT
1 TTTAATAATTTTATATTTCAAAAAAATAAT
27034433 TTTAA
1 TTTAA
27034438 AATCATTTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (30 bp):
TTTAATAATTTTATATTTCAAAAAAATAAT
Found at i:27035333 original size:19 final size:19
Alignment explanation
Indices: 27035300--27035339 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
27035290 AAATGAATAT
* * *
27035300 TTTTTTTTTAGATTTTTAA
1 TTTTTTTTAAAATTTTAAA
27035319 TTTTTTTTAAAATTTTAAA
1 TTTTTTTTAAAATTTTAAA
27035338 TT
1 TT
27035340 AATAAAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (19 bp):
TTTTTTTTAAAATTTTAAA
Done.