Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold144
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: 3311329
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
File 19 of 21
Found at i:2876768 original size:20 final size:20
Alignment explanation
Indices: 2876743--2876793 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
2876733 CGATACATTA
2876743 TATCGATACATCATAAAATG
1 TATCGATACATCATAAAATG
2876763 TATCGATACATCATAAAATG
1 TATCGATACATCATAAAATG
2876783 TATCGATACAT
1 TATCGATACAT
2876794 TAGCTTGTAA
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:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (20 bp):
TATCGATACATCATAAAATG
Found at i:2882988 original size:13 final size:13
Alignment explanation
Indices: 2882969--2883007 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2882959 ACAGCATTCT
2882969 CTGTATCGATACA
1 CTGTATCGATACA
*
2882982 TTGTATCGATACA
1 CTGTATCGATACA
2882995 CTGTATCGATACA
1 CTGTATCGATACA
2883008 AGGGGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (13 bp):
CTGTATCGATACA
Found at i:2883473 original size:20 final size:21
Alignment explanation
Indices: 2883441--2883492 Score: 79
Period size: 20 Copynumber: 2.4 Consensus size: 21
2883431 CCCCTAGGCA
2883441 GCACCCACCAGGTCGCAACC-G
1 GCACCC-CCAGGTCGCAACCGG
2883462 GCACCCCCAGGTCGCAACCGG
1 GCACCCCCAGGTCGCAACCGG
2883483 GCAGCCCCCA
1 GCA-CCCCCA
2883493 CACTAGCAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 13 0.45
21 10 0.34
22 6 0.21
ACGTcount: A:0.21, C:0.50, G:0.25, T:0.04
Consensus pattern (21 bp):
GCACCCCCAGGTCGCAACCGG
Found at i:2885572 original size:13 final size:13
Alignment explanation
Indices: 2885554--2885579 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2885544 ACACATAGTA
2885554 TGTATCGATACAT
1 TGTATCGATACAT
2885567 TGTATCGATACAT
1 TGTATCGATACAT
2885580 CATAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2885575 original size:32 final size:33
Alignment explanation
Indices: 2885534--2885601 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
2885524 GTAGCCAAAC
**
2885534 TTGTATCGATACA-CATAGTATGTATCGATACA
1 TTGTATCGATACATCATAAAATGTATCGATACA
* *
2885566 TTGTATCGATACATCATAAAATGTCTTGATACA
1 TTGTATCGATACATCATAAAATGTATCGATACA
2885599 TTG
1 TTG
2885602 GCTTGTAACG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 13 0.42
33 18 0.58
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (33 bp):
TTGTATCGATACATCATAAAATGTATCGATACA
Found at i:2887277 original size:18 final size:18
Alignment explanation
Indices: 2887254--2887289 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2887244 GGTGATTGGG
*
2887254 ATAAATCATATTATAATA
1 ATAAATCATACTATAATA
2887272 ATAAATCATACTATAATA
1 ATAAATCATACTATAATA
2887290 TATCAAAATG
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:0.08, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAAATCATACTATAATA
Found at i:2891654 original size:72 final size:72
Alignment explanation
Indices: 2891333--2892370 Score: 704
Period size: 72 Copynumber: 14.3 Consensus size: 72
2891323 TCATGATTTC
* * * * * *
2891333 TACAAACAGAAATAAATTATAACTTAAAAATTTTAAACTCATATAATCATACCAAAAAAACAAAT
1 TACAAATAAAAATAAATTATACCTTAAAAA-TTTAAACTCATATAATAATA-CTAAAAAATAAAT
2891398 TTAAACTTT
64 TTAAACTTT
* * * ** * *
2891407 CA-AAAAAAAAATAAAAATAAAATACCTTAAAAAAATTTAAACTTGTATAATCAA-ACCAGAAAA
1 TACAAATAAAAAT--AAAT--TATACCTT--AAAAATTTAAACTCATATAAT-AATACTAAAAAA
* * *
2891470 CAAATTTAAAGTTC
59 TAAATTTAAACTTT
* * * ** * ** *
2891484 TATAAAT-AAAAT-CA-TATA--TTAAAAATTTAAATTTGTATAATTATACCCAAAAACAAATTT
1 TACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCATATAATAATACTAAAAAATAAATTT
* *
2891544 ATACTCT
66 AAACTTT
* * * * * *
2891551 TACGAATAGAAATAAATTATAGCTTAAAAATTTTAAACTCGTATAATAATACGAACAAATAAATT
1 TACAAATAAAAATAAATTATACCTTAAAAA-TTTAAACTCATATAATAATACTAAAAAATAAATT
*
2891616 TAAACTTC
65 TAAACTTT
* * * * * * * * * *
2891624 TACAAATAAAGATAAATAATATCTTTAAATTTTAAAATCATAAAATCATACCCAAAAAACCAAAT
1 TACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCATATAATAATA-CTAAAAAA-TAAAT
* *
2891689 TTGAACTTC
64 TTAAACTTT
* * * *
2891698 TACAAATAAAGATAAATAATACCTTGAAAATTTAAACTCGTATAAT--TA--AATAAAA-AAATT
1 TACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCATATAATAATACTAA-AAAATAAATT
2891758 TAAACTTT
65 TAAACTTT
* * * * *
2891766 TTCACATAAAAATAAATTATACTTTCAAATATTTAAA-T-ATGTATAATCATACCT-AAAAATAA
1 TACAAATAAAAATAAATTATACCTT-AAAAATTTAAACTCA--TATAATAATA-CTAAAAAATAA
*
2891828 ATTTTAACTTT
62 ATTTAAACTTT
* *
2891839 TACAAATAAAAATAAATTATATCC-CAAAAATTTGAACTCATATAATTAA-ACTAAAAAATAAAT
1 TACAAATAAAAATAAATTATA-CCTTAAAAATTTAAACTCATATAA-TAATACTAAAAAATAAAT
*
2891902 TTAAACTTC
64 TTAAACTTT
* * * * * * * *
2891911 CATAATTAAAAATAAATTATAACTTAAAAATTTAAATTGATATAATCAA-ACCAAAAAACAAATT
1 TACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCATATAAT-AATACTAAAAAATAAATT
*
2891975 TAAATTTT
65 TAAACTTT
* * * *
2891983 TACAAATTAAAATAAATTATACCTTCAAAAATTTAAGCTCGTATAATCAAT--TTAAAAATAAAT
1 TACAAATAAAAATAAATTATACCTT-AAAAATTTAAACTCATATAAT-AATACTAAAAAATAAAT
*
2892046 TTAAATTTT
64 TTAAACTTT
* * * * *
2892055 TACAAATAAAAATAAATTATACCCTAATAATTTAAATTCATATAATCAA-ATTAAAAAATAAAAT
1 TACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCATATAAT-AATACTAAAAAATAAATT
2892119 TAAACTTT
65 TAAACTTT
** * * * * * *
2892127 TA-AAATAAAAATAAATTATATTTTAAAAATCTAAATTCATATAATCATATCAAAAAAAATTAAC
1 TACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCATATAATAATA-C-TAAAAAATAAAT
*
2892191 TTAAACTTC
64 TTAAACTTT
** * * * * *
2892200 TGTAAATAAAAATAAATTATATCCTAAAAAATTTTAAAATCTTATAATTATACCAAAAAAAATAA
1 TACAAATAAAAATAAATTATA-CCTTAAAAA-TTTAAACTCATATAATAATA-C-TAAAAAATAA
**
2892265 ATTTAAACTCC
62 ATTTAAACTTT
* ** * *
2892276 TATAAATAAAAATAAAAAATACCTTAAAAATTCAAACTCATATAATTAA-A--GAAAAATAAATT
1 TACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCATATAA-TAATACTAAAAAATAAATT
*
2892338 TAAATTTT
65 TAAACTTT
*
2892346 TACAAATAAAAATAAATAATACCTT
1 TACAAATAAAAATAAATTATACCTT
2892371 TAATTAAACT
Statistics
Matches: 770, Mismatches: 149, Indels: 94
0.76 0.15 0.09
Matches are distributed among these distances:
66 1 0.00
67 42 0.05
68 36 0.05
69 20 0.03
70 48 0.06
71 68 0.09
72 198 0.26
73 142 0.18
74 87 0.11
75 20 0.03
76 54 0.07
77 30 0.04
78 18 0.02
79 6 0.01
ACGTcount: A:0.55, C:0.11, G:0.02, T:0.32
Consensus pattern (72 bp):
TACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCATATAATAATACTAAAAAATAAATTT
AAACTTT
Found at i:2891812 original size:215 final size:214
Alignment explanation
Indices: 2891437--2892366 Score: 613
Period size: 215 Copynumber: 4.3 Consensus size: 214
2891427 AATACCTTAA
* ** * * * * * *
2891437 AAAAATTTAAACTTGTATAATCAAACCAGAAAACAAATTTAAAGTTCTATAAAT-AAAAT-CAT-
1 AAAAATTTAAAATCATAAAATCAAACCAAAAAACAAATTTAAACTTCCACAAATAAAAATAAATA
* * * * * * * * *
2891499 AT-A-TTAAAAATTTAAATTTG-TATAATTATACCCAAAAACAAATTTATACTCTTACGAATAGA
66 ATAACTTAAAAATTTAAA-TCGATATAATCA-AACAAAAAACAAATTTAAATTTTTACAAATAAA
** * *
2891561 AATAAATTATAGCTTAAAAAT-TTTAAACTCGTATAATAATACGAACAAATAAATTTAAACTTCT
129 AATAAATTATA-CTTTCAAATATTTAAA-TCGTATAATAATACTAA-AAATAAATTTAAACTTTT
* **
2891625 ACAAATAAAGATAAATAATATCTT
191 ACAAATAAAAATAAATAATATCCC
* * * * * *
2891649 TAAATTTTAAAATCATAAAATCATACCCAAAAAACCAAATTTGAACTTCTACAAATAAAGATAAA
1 AAAAATTTAAAATCATAAAATCA-AACCAAAAAA-CAAATTTAAACTTCCACAAATAAAAATAAA
* * * * *
2891714 TAATACCTTGAAAATTTAAACTCG-TATAAT-TAA-ATAAAA-AAATTTAAACTTTTT-CACATA
64 TAATAACTTAAAAATTTAAA-TCGATATAATCAAACAAAAAACAAATTTAAA-TTTTTACAAATA
* * *
2891774 AAAATAAATTATACTTTCAAATATTTAAATATGTATAATCATACCTAAAAATAAATTTTAACTTT
127 AAAATAAATTATACTTTCAAATATTTAAAT-CGTATAATAATA-CTAAAAATAAATTTAAACTTT
*
2891839 TACAAATAAAAATAAATTATATCCC
190 TACAAATAAAAATAAATAATATCCC
* * * * * * * * *
2891864 AAAAATTTGAACTCATATAATTAAACTAAAAAATAAATTTAAACTTCCATAATTAAAAATAAATT
1 AAAAATTTAAAATCATAAAATCAAACCAAAAAACAAATTTAAACTTCCACAAATAAAAATAAATA
* *
2891929 ATAACTTAAAAATTTAAATTGATATAATCAAACCAAAAAACAAATTTAAATTTTTACAAATTAAA
66 ATAACTTAAAAATTTAAATCGATATAATCAAA-CAAAAAACAAATTTAAATTTTTACAAATAAAA
* * * * *
2891994 ATAAATTATACCTTCAAAAATTTAAGCTCGTATAATCAAT-TTAAAAATAAATTTAAATTTTTAC
130 ATAAATTATACTTTCAAATATTTAA-ATCGTATAAT-AATACTAAAAATAAATTTAAACTTTTAC
*
2892058 AAATAAAAATAAATTATA-CCC
193 AAATAAAAATAAATAATATCCC
* * * ** * * **
2892079 TAATAATTTAAATTCATATAATCAAATTAAAAAATAAAATTAAACTTTTA-AAATAAAAATAAAT
1 -AAAAATTTAAAATCATAAAATCAAACCAAAAAACAAATTTAAACTTCCACAAATAAAAATAAAT
* ** * * * * * * **
2892143 TATATTTTAAAAATCTAAATTC-ATATAATCATATCAAAAAAAATTAACTTAAACTTCTGTAAAT
65 AATAACTTAAAAATTTAAA-TCGATATAATCA-AACAAAAAACA--AATTTAAATTTTTACAAAT
* * * * * *
2892207 AAAAATAAATTATA-TCCTAAAAAATTTTAAAATCTTATAATTATACCAAAAAAAATAAATTTAA
126 AAAAATAAATTATACT-TTCAAATA-TTT-AAATCGTATAATAATA-C--TAAAAATAAATTTAA
** * * *
2892271 ACTCCTATAAATAAAAATAAAAAATA-CCTT
185 ACTTTTACAAATAAAAATAAATAATATCC-C
* * * * * * * **
2892301 AAAAATTCAAACTCATATAATTAAA--GAAAAATAAATTTAAATTTTTACAAATAAAAATAAATA
1 AAAAATTTAAAATCATAAAATCAAACCAAAAAACAAATTTAAACTTCCACAAATAAAAATAAATA
2892364 ATA
66 ATA
2892367 CCTTTAATTA
Statistics
Matches: 573, Mismatches: 112, Indels: 58
0.77 0.15 0.08
Matches are distributed among these distances:
212 19 0.03
213 55 0.10
214 36 0.06
215 146 0.25
216 104 0.18
217 84 0.15
218 14 0.02
219 41 0.07
220 17 0.03
221 57 0.10
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.33
Consensus pattern (214 bp):
AAAAATTTAAAATCATAAAATCAAACCAAAAAACAAATTTAAACTTCCACAAATAAAAATAAATA
ATAACTTAAAAATTTAAATCGATATAATCAAACAAAAAACAAATTTAAATTTTTACAAATAAAAA
TAAATTATACTTTCAAATATTTAAATCGTATAATAATACTAAAAATAAATTTAAACTTTTACAAA
TAAAAATAAATAATATCCC
Found at i:2891948 original size:20 final size:20
Alignment explanation
Indices: 2891898--2891948 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 20
2891888 ACTAAAAAAT
2891898 AAATTTAAACTTCCATAATTAA
1 AAATTTAAA-TT-CATAATTAA
2891920 AAA--TAAATT-ATAACTTAA
1 AAATTTAAATTCATAA-TTAA
2891938 AAATTTAAATT
1 AAATTTAAATT
2891949 GATATAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
17 4 0.15
18 7 0.27
19 2 0.08
20 10 0.38
22 3 0.12
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATTTAAATTCATAATTAA
Found at i:2892039 original size:145 final size:144
Alignment explanation
Indices: 2891342--2892362 Score: 804
Period size: 144 Copynumber: 7.1 Consensus size: 144
2891332 CTACAAACAG
* *
2891342 AAATAAATTATAACTTAAAAATTTTAAACTCATATAATCATACCAAAAAAACAAATTTAAACTTT
1 AAATAAATTATAACTTAAAAA-TTTAAATTCATATAATCAAACC-AAAAAACAAATTTAAACTTT
* * * * * * * *
2891407 CA-AAAAAAAAATAAAAATAAAATACCTTAAAAAAATTTAAACTTGTATAATCAAACCAGAAAAC
64 TACAAATAAAAAT--AAAT--TATACCTT--AAAAATTTAAACTCGTATAATCAATCTAAAAAAT
*
2891471 AAATTTAAAGTTCTATAAAT-A
123 AAATTTAAACTTCTATAAATAA
* ** * * * * *
2891492 AAAT-CA-TAT-A-TTAAAAATTTAAATTTGTATAATTATACCCAAAAACAAATTTATACTCTTA
1 AAATAAATTATAACTTAAAAATTTAAATTCATATAATCAAACCAAAAAACAAATTTAAACTTTTA
* * * * *
2891553 CGAATAGAAATAAATTATAGCTTAAAAATTTTAAACTCGTATAAT-AATACGAACAAATAAATTT
66 CAAATAAAAATAAATTATACCTTAAAAA-TTTAAACTCGTATAATCAAT-CTAAAAAATAAATTT
*
2891617 AAACTTCTACAAATAA
129 AAACTTCTATAAATAA
* * * * * * * * * *
2891633 AGATAAATAATATCTTTAAATTTTAAAATCATAAAATCATACCCAAAAAACCAAATTTGAACTTC
1 AAATAAATTATAACTTAAAAATTTAAATTCATATAATCA-AACCAAAAAA-CAAATTTAAACTTT
* * * * *
2891698 TACAAATAAAGATAAATAATACCTTGAAAATTTAAACTCGTATAATTAA---ATAAAA-AAATTT
64 TACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCAATCTAAAAAATAAATTT
* *
2891759 AAACTT-TTTCACATAA
129 AAACTTCTAT-AAATAA
* * * * * *
2891775 AAATAAATTAT-ACTTTCAAATATTTAAATAT-GTATAATCATACCTAAAAATAAATTTTAACTT
1 AAATAAATTATAAC-TT-AAAAATTTAAAT-TCATATAATCAAACCAAAAAACAAATTTAAACTT
* * * * *
2891838 TTACAAATAAAAATAAATTATATCC-CAAAAATTTGAACTCATATAATTAAACTAAAAAATAAAT
63 TTACAAATAAAAATAAATTATA-CCTTAAAAATTTAAACTCGTATAATCAATCTAAAAAATAAAT
* *
2891902 TTAAACTTCCATAATTAA
127 TTAAACTTCTATAAATAA
* *
2891920 AAATAAATTATAACTTAAAAATTTAAATTGATATAATCAAACCAAAAAACAAATTTAAATTTTTA
1 AAATAAATTATAACTTAAAAATTTAAATTCATATAATCAAACCAAAAAACAAATTTAAACTTTTA
* * *
2891985 CAAATTAAAATAAATTATACCTTCAAAAATTTAAGCTCGTATAATCAAT-TTAAAAATAAATTTA
66 CAAATAAAAATAAATTATACCTT-AAAAATTTAAACTCGTATAATCAATCTAAAAAATAAATTTA
* * *
2892049 AATTTTTACAAATAA
130 AACTTCTATAAATAA
* * * ** * *
2892064 AAATAAATTATACCCTAATAATTTAAATTCATATAATCAAATTAAAAAATAAAATTAAACTTTTA
1 AAATAAATTATAACTTAAAAATTTAAATTCATATAATCAAACCAAAAAACAAATTTAAACTTTTA
** * * * * * *
2892129 -AAATAAAAATAAATTATATTTTAAAAATCTAAATTCATATAATCATATCAAAAAAAATTAACTT
66 CAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCA-ATC-TAAAAAATAAATTT
*
2892193 AAACTTCTGTAAATAA
129 AAACTTCTATAAATAA
* * * * * * *
2892209 AAATAAATTATATCCTAAAAAATTTTAAAATCTTATAATTATACCAAAAAAAATAAATTTAAACT
1 AAATAAATTATA-ACTTAAAAA-TTTAAATTCATATAATCAAACC--AAAAAACAAATTTAAACT
** * ** * * *
2892274 CCTATAAATAAAAATAAAAAATACCTTAAAAATTCAAACTCATATAATTAA---AGAAAAATAAA
62 TTTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCAATCTA-AAAAATAAA
* * *
2892336 TTTAAATTTTTACAAATAA
126 TTTAAACTTCTATAAATAA
2892355 AAATAAAT
1 AAATAAAT
2892363 AATACCTTTA
Statistics
Matches: 690, Mismatches: 147, Indels: 72
0.76 0.16 0.08
Matches are distributed among these distances:
139 7 0.01
140 38 0.06
141 63 0.09
142 57 0.08
143 49 0.07
144 162 0.23
145 127 0.18
146 69 0.10
147 53 0.08
148 3 0.00
149 21 0.03
150 41 0.06
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (144 bp):
AAATAAATTATAACTTAAAAATTTAAATTCATATAATCAAACCAAAAAACAAATTTAAACTTTTA
CAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCAATCTAAAAAATAAATTTAA
ACTTCTATAAATAA
Found at i:2892070 original size:20 final size:20
Alignment explanation
Indices: 2892033--2892072 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2892023 GTATAATCAA
**
2892033 TTTAAAAATAAATTTAAATT
1 TTTAAAAATAAAAATAAATT
*
2892053 TTTACAAATAAAAATAAATT
1 TTTAAAAATAAAAATAAATT
2892073 ATACCCTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (20 bp):
TTTAAAAATAAAAATAAATT
Found at i:2892156 original size:24 final size:25
Alignment explanation
Indices: 2892108--2892154 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
2892098 AATCAAATTA
2892108 AAAAATAAAATTAAACTTTTAAAAT
1 AAAAATAAAATTAAACTTTTAAAAT
*
2892133 AAAAAT-AAATTATA-TTTTAAAA
1 AAAAATAAAATTAAACTTTTAAAA
2892155 ATCTAAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
24 7 0.33
25 6 0.29
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (25 bp):
AAAAATAAAATTAAACTTTTAAAAT
Found at i:2892342 original size:76 final size:76
Alignment explanation
Indices: 2892107--2892366 Score: 205
Period size: 76 Copynumber: 3.5 Consensus size: 76
2892097 TAATCAAATT
* ** ** * * * *
2892107 AAAAAATAAAATTAAACTTTTA-AAATAAAAATAAATTATAT-TTTAAAAATCT-AAATTCATAT
1 AAAAAATAAATTTAAACTCCTATAAATAAAAATAAAAAATATCCTAAAAAATTTCAAAATCATAT
* *
2892169 AATCATATCAA
66 AATTATAACAA
* * * * ** * *
2892180 AAAAAATTAACTTAAACTTCTGTAAATAAAAATAAATTATATCCTAAAAAATTTTAAAATCTTAT
1 AAAAAATAAATTTAAACTCCTATAAATAAAAATAAAAAATATCCTAAAAAATTTCAAAATCATAT
*
2892245 AATTATACCAA
66 AATTATAACAA
* *
2892256 AAAAAATAAATTTAAACTCCTATAAATAAAAATAAAAAATA-CCTTAAAAA-TTCAAACTCATAT
1 AAAAAATAAATTTAAACTCCTATAAATAAAAATAAAAAATATCCTAAAAAATTTCAAAATCATAT
2892319 AA-T-T-A-AA
66 AATTATAACAA
* * ** * *
2892326 GAAAAATAAATTTAAATTTTTACAAATAAAAATAAATAATA
1 AAAAAATAAATTTAAACTCCTATAAATAAAAATAAAAAATA
2892367 CCTTTAATTA
Statistics
Matches: 156, Mismatches: 28, Indels: 9
0.81 0.15 0.05
Matches are distributed among these distances:
70 37 0.24
72 1 0.01
73 19 0.12
74 31 0.20
75 16 0.10
76 52 0.33
ACGTcount: A:0.59, C:0.08, G:0.01, T:0.32
Consensus pattern (76 bp):
AAAAAATAAATTTAAACTCCTATAAATAAAAATAAAAAATATCCTAAAAAATTTCAAAATCATAT
AATTATAACAA
Found at i:2892429 original size:40 final size:39
Alignment explanation
Indices: 2892344--2892429 Score: 91
Period size: 40 Copynumber: 2.2 Consensus size: 39
2892334 AATTTAAATT
* * * *
2892344 TTTACAAATAAAAATAAATAATACCTTTAATTAAACTAA
1 TTTAAAAATAAAAATAAATAATACCTTAAAATAAAATAA
* * *
2892383 TCTTAAAAATAAAAATAACTCATATCTTAAAATAAAATAAA
1 T-TTAAAAATAAAAATAAATAATACCTTAAAATAAAAT-AA
2892424 TTTAAA
1 TTTAAA
2892430 CTTTTATACA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
39 1 0.03
40 34 0.89
41 3 0.08
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (39 bp):
TTTAAAAATAAAAATAAATAATACCTTAAAATAAAATAA
Found at i:2894966 original size:22 final size:21
Alignment explanation
Indices: 2894935--2894996 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
2894925 TTTTTTACAC
*
2894935 ATGTTGTGTTTGTGTTTTTTT
1 ATGTTATGTTTGTGTTTTTTT
2894956 -TGTATCATGTTT-TAGTTATTTTT
1 ATGT-T-ATGTTTGT-GTT-TTTTT
*
2894979 ATGTTATGTGTGTGTTTT
1 ATGTTATGTTTGTGTTTT
2894997 ATAATTATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
20 3 0.09
21 4 0.12
22 16 0.48
23 7 0.21
24 3 0.09
ACGTcount: A:0.11, C:0.02, G:0.21, T:0.66
Consensus pattern (21 bp):
ATGTTATGTTTGTGTTTTTTT
Found at i:2895934 original size:24 final size:22
Alignment explanation
Indices: 2895907--2895963 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 22
2895897 GAAAGAAAAG
* *
2895907 AAAGAGAAAGAAAAGAGGGAAGGA
1 AAAGAGAAAAAAAAGAAGGAA--A
*
2895931 AAAGGGAAAAAAAAGAAGGAAA
1 AAAGAGAAAAAAAAGAAGGAAA
2895953 AAAGAGAAAAA
1 AAAGAGAAAAA
2895964 GCGAAAAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 11 0.38
24 18 0.62
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (22 bp):
AAAGAGAAAAAAAAGAAGGAAA
Found at i:2895955 original size:13 final size:13
Alignment explanation
Indices: 2895891--2895952 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 13
2895881 GATTGTGGTG
*
2895891 AAGAAAGAAAGAA
1 AAGAAGGAAAGAA
2895904 AAGAAAGAGAAAGAA
1 AAG-AAG-GAAAGAA
* *
2895919 AAGAGGGAAGGAA
1 AAGAAGGAAAGAA
*
2895932 AAG--GGAAAAAA
1 AAGAAGGAAAGAA
2895943 AAGAAGGAAA
1 AAGAAGGAAA
2895953 AAAGAGAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
11 9 0.22
13 17 0.43
14 4 0.10
15 10 0.25
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
AAGAAGGAAAGAA
Found at i:2895962 original size:20 final size:20
Alignment explanation
Indices: 2895894--2895963 Score: 52
Period size: 20 Copynumber: 3.5 Consensus size: 20
2895884 TGTGGTGAAG
* * *
2895894 AAAGAAAGAAAAGAAAG-AG
1 AAAGAAAAAAAAGAAGGAAA
* **
2895913 AAAGAAAAGAGGGAAGGAAA
1 AAAGAAAAAAAAGAAGGAAA
**
2895933 AGGGAAAAAAAAGAAGGAAA
1 AAAGAAAAAAAAGAAGGAAA
*
2895953 AAAGAGAAAAA
1 AAAGAAAAAAA
2895964 GCGAAAAATC
Statistics
Matches: 36, Mismatches: 14, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
19 12 0.33
20 24 0.67
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAAAAGAAGGAAA
Found at i:2900669 original size:20 final size:18
Alignment explanation
Indices: 2900638--2900674 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
2900628 AATTTGAAAG
2900638 AAAAAAAGAGATAAATAA
1 AAAAAAAGAGATAAATAA
2900656 AAAAAAAGAAAGATAAATA
1 AAAAAAAG--AGATAAATA
2900675 TGGCTAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
20 9 0.53
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (18 bp):
AAAAAAAGAGATAAATAA
Found at i:2901294 original size:19 final size:20
Alignment explanation
Indices: 2901266--2901304 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2901256 TTTTAGACAC
*
2901266 GATTT-TTTTAATTTGAATT
1 GATTTGTTTAAATTTGAATT
2901285 GATTTGTTTAAATTTGAATT
1 GATTTGTTTAAATTTGAATT
2901305 ACTATTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (20 bp):
GATTTGTTTAAATTTGAATT
Found at i:2901619 original size:43 final size:43
Alignment explanation
Indices: 2901566--2901648 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
2901556 AAAAAGTAAT
*
2901566 AAATAAAATTAATATATTATATTAAATTCAATGAATGAGAATC
1 AAATAAAATTAATATATTATATTAAATACAATGAATGAGAATC
*
2901609 AAATAAAATTAATATATTATATTAAATACGATGAATGAGA
1 AAATAAAATTAATATATTATATTAAATACAATGAATGAGA
2901649 TAAAATTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.34
Consensus pattern (43 bp):
AAATAAAATTAATATATTATATTAAATACAATGAATGAGAATC
Found at i:2901931 original size:117 final size:119
Alignment explanation
Indices: 2901742--2901978 Score: 304
Period size: 117 Copynumber: 2.0 Consensus size: 119
2901732 TTATATTTTG
* * *
2901742 AGTAATTTAACTTTCAAATTCTATTAAAAAGAGTTAAAATAAAATTTAGAAAAAGAATTAATGAA
1 AGTAATTTAACTTTCAAACTCTATTAAAAAGAGTTAAAATAAAATTTAGAAAAAGAATGAATAAA
* * * *
2901807 ATTAATATGTTATATTAAATTCAATAAATGAGACTGAGATGAAATTAAGATATT
66 ATTAATATATTATATTAAATTCAATAAATGAGAATAAGATAAAATTAAGATATT
**
2901861 AGTAATTTAACCATTT-AAACTCTATT-AAAA-AGTTAAAA-GGAATTTA-AAAAAGTAATGAAT
1 AGTAATTTAA-C-TTTCAAACTCTATTAAAAAGAGTTAAAATAAAATTTAGAAAAAG-AATGAAT
* * *
2901921 AAAATTAATATATTATATTAAATTTAATAATTGAGAATAAGATAAAATTAATATATT
63 AAAATTAATATATTATATTAAATTCAATAAATGAGAATAAGATAAAATTAAGATATT
2901978 A
1 A
2901979 TATTGAATAT
Statistics
Matches: 103, Mismatches: 12, Indels: 8
0.84 0.10 0.07
Matches are distributed among these distances:
116 6 0.06
117 62 0.60
118 8 0.08
119 14 0.14
120 10 0.10
121 3 0.03
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (119 bp):
AGTAATTTAACTTTCAAACTCTATTAAAAAGAGTTAAAATAAAATTTAGAAAAAGAATGAATAAA
ATTAATATATTATATTAAATTCAATAAATGAGAATAAGATAAAATTAAGATATT
Found at i:2901968 original size:43 final size:46
Alignment explanation
Indices: 2901918--2902040 Score: 139
Period size: 43 Copynumber: 2.7 Consensus size: 46
2901908 AAAAGTAATG
2901918 AATAAAATTAATATATTATATTAAATTTAAT-AATTGA-G-AA-TA-
1 AATAAAATTAATATATTATATTAAATTTAATGAA-TGAGGAAATTAT
* *
2901960 AGATAAAATTAATATATTATATTGAATATAATGAATGAGGTAAAATTTAT
1 A-ATAAAATTAATATATTATATTAAATTTAATGAATGAGG--AAA-TTAT
2902010 AAGTAAAATTAATATATTATATTAAATTTAA
1 AA-TAAAATTAATATATTATATTAAATTTAA
2902041 ATTCAATGAA
Statistics
Matches: 67, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
42 1 0.01
43 31 0.46
44 3 0.04
47 2 0.03
49 3 0.04
50 27 0.40
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (46 bp):
AATAAAATTAATATATTATATTAAATTTAATGAATGAGGAAATTAT
Found at i:2902414 original size:36 final size:37
Alignment explanation
Indices: 2902372--2902441 Score: 115
Period size: 36 Copynumber: 1.9 Consensus size: 37
2902362 AGTTAACATT
*
2902372 TATGTCAAAAATTATATTTTATATATAT-TATATAGA
1 TATGTCAAAAATTATATTATATATATATATATATAGA
*
2902408 TATGTCAAAAATTGTATTATATATATATATATAT
1 TATGTCAAAAATTATATTATATATATATATATAT
2902442 TATATAGAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 26 0.84
37 5 0.16
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (37 bp):
TATGTCAAAAATTATATTATATATATATATATATAGA
Found at i:2907246 original size:33 final size:33
Alignment explanation
Indices: 2907206--2907274 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
2907196 CCGTTACAAG
*
2907206 CAATGTATCGATACAAT-TCATCATGTATTGATA
1 CAATGTATCGATACAATGTC-TCATGTATCGATA
* *
2907239 CAATGTATCGATACGATGTCTTATGTATCGATA
1 CAATGTATCGATACAATGTCTCATGTATCGATA
2907272 CAA
1 CAA
2907275 ACAGTGGTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 30 0.94
34 2 0.06
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACAATGTCTCATGTATCGATA
Found at i:2907328 original size:20 final size:19
Alignment explanation
Indices: 2907302--2907353 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
2907292 ACTGCCAGTT
2907302 TCATGTATCGATACAATTG-
1 TCATGTATCGATACAA-TGA
* *
2907321 TCCATGTATAGATATAATGA
1 T-CATGTATCGATACAATGA
2907341 TCATGTATCGATA
1 TCATGTATCGATA
2907354 TAATATATCG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (19 bp):
TCATGTATCGATACAATGA
Found at i:2910454 original size:34 final size:35
Alignment explanation
Indices: 2910388--2910455 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
2910378 CAAGTAATTG
* *
2910388 AGAGGTGCTATTTTAGCCTTTCTAAAAGATAGGGA
1 AGAGGTGCTATCTTAGCCTTTCGAAAAGATAGGGA
*
2910423 AGAGGTTCTATCTTAGCCTTT-GAAAAGATAGGG
1 AGAGGTGCTATCTTAGCCTTTCGAAAAGATAGGG
2910456 TTGTAAGGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 11 0.37
35 19 0.63
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (35 bp):
AGAGGTGCTATCTTAGCCTTTCGAAAAGATAGGGA
Found at i:2911579 original size:3 final size:3
Alignment explanation
Indices: 2911571--2911599 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2911561 AAGTGAAGAG
2911571 GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
2911600 ACAAGAGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:2917301 original size:51 final size:51
Alignment explanation
Indices: 2917242--2917376 Score: 182
Period size: 51 Copynumber: 2.7 Consensus size: 51
2917232 ATTTACTGTT
* *
2917242 TGTATCGATGTATTCTTCATTGTATCAATACATTCTGGGTTTTAACCCAGA
1 TGTATCGATATATTCTTCATTGTATCAATACATTCTGGGTTTTAACCCAAA
* * *
2917293 TGTATCGATATATTTTTTATTGTATCAATACATTTTGGGTTTTAACCCAAA
1 TGTATCGATATATTCTTCATTGTATCAATACATTCTGGGTTTTAACCCAAA
* * * *
2917344 TGTATCGATACATTC-TCAATGTTTCGATACATT
1 TGTATCGATATATTCTTCATTGTATCAATACATT
2917377 TAGGCATTTT
Statistics
Matches: 73, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
50 14 0.19
51 59 0.81
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (51 bp):
TGTATCGATATATTCTTCATTGTATCAATACATTCTGGGTTTTAACCCAAA
Found at i:2920000 original size:78 final size:79
Alignment explanation
Indices: 2919757--2920066 Score: 340
Period size: 79 Copynumber: 3.9 Consensus size: 79
2919747 CTACCATCGG
* * *
2919757 GGATACTCCAA-CCCTGGTTTTATTTTTAAAATATCGATTTTTCACAATCGCAGATACTCCAACC
1 GGATACTCCAATCCC-GGTTTTATTTCTAAAACATCGATTTTTCACAATCGAAGATACTCCAACC
* * *
2919821 CTATTATTTTCGAGA
65 CCATTATTTTTGAGT
* * * * * ** *
2919836 GAATACTCCAACCCCGATTTTATTTCTAAAATATCGATTTTTCACCATCGGGGATACTCCAACCT
1 GGATACTCCAATCCCGGTTTTATTTCTAAAACATCGATTTTTCACAATCGAAGATACTCCAACCC
* * *
2919901 CGTTATTTATGAAAT
66 CATTATTTTTG-AGT
* * * * *
2919916 -GATACTCTAATCCCGGTTTTGTTTCTAAAACATCAATTTTTCATAATCG-GGATACTCCAACCC
1 GGATACTCCAATCCCGGTTTTATTTCTAAAACATCGATTTTTCACAATCGAAGATACTCCAACCC
*
2919979 CGTTATTTTTGAGT
66 CATTATTTTTGAGT
* *
2919993 GGATACTCCAATCCCAGTTTTATTTCTAAAACA-CTGATTTTTCACTATCGAAGATACTCCAACC
1 GGATACTCCAATCCCGGTTTTATTTCTAAAACATC-GATTTTTCACAATCGAAGATACTCCAACC
2920057 CCATTATTTT
65 CCATTATTTT
2920067 CAAGATGATG
Statistics
Matches: 193, Mismatches: 33, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
77 3 0.02
78 64 0.33
79 122 0.63
80 4 0.02
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.37
Consensus pattern (79 bp):
GGATACTCCAATCCCGGTTTTATTTCTAAAACATCGATTTTTCACAATCGAAGATACTCCAACCC
CATTATTTTTGAGT
Found at i:2920016 original size:157 final size:158
Alignment explanation
Indices: 2919758--2920083 Score: 392
Period size: 157 Copynumber: 2.1 Consensus size: 158
2919748 TACCATCGGG
* * * *
2919758 GATACTCCAACCCTGGTTTTATTTTTAAAATATCGATTTTTCACAATCGCAGATACTCCAACCCT
1 GATACTCCAACCCTGGTTTTATTTCTAAAACATCAATTTTTCACAATCGCAGATACTCCAACCCC
* * *
2919823 ATTATTTTCGAGAGAATACTCCAACCCCGATTTTATTTCTAAAATA-TCGATTTTTCACCATCGG
66 ATTATTTTCGAGAGAATACTCCAACCCAGATTTTATTTCTAAAACACT-GATTTTTCACCATCGA
* * *
2919887 GGATACTCCAACCTCGTTATTTATGAAAT
130 AGATACTCCAACCCCATTATTTATGAAAT
* * * *
2919916 GATACTCTAATCCC-GGTTTTGTTTCTAAAACATCAATTTTTCATAATCG-GGATACTCCAACCC
1 GATACTCCAA-CCCTGGTTTTATTTCTAAAACATCAATTTTTCACAATCGCAGATACTCCAACCC
* * * * *
2919979 CGTTATTTTTGAGTGGATACTCCAATCCCAG-TTTTATTTCTAAAACACTGATTTTTCACTATCG
65 CATTATTTTCGAGAGAATACTCCAA-CCCAGATTTTATTTCTAAAACACTGATTTTTCACCATCG
*
2920043 AAGATACTCCAACCCCATTATTT-TCAAGAT
129 AAGATACTCCAACCCCATTATTTATGAA-AT
*
2920073 GATGCTCCAAC
1 GATACTCCAAC
2920084 TCGTTTTTAT
Statistics
Matches: 142, Mismatches: 22, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
156 4 0.03
157 91 0.64
158 44 0.31
159 3 0.02
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (158 bp):
GATACTCCAACCCTGGTTTTATTTCTAAAACATCAATTTTTCACAATCGCAGATACTCCAACCCC
ATTATTTTCGAGAGAATACTCCAACCCAGATTTTATTTCTAAAACACTGATTTTTCACCATCGAA
GATACTCCAACCCCATTATTTATGAAAT
Found at i:2925384 original size:20 final size:19
Alignment explanation
Indices: 2925315--2925387 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 19
2925305 CTGCCAGTTT
***
2925315 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TAAA
2925335 CATGTATCGATACAATAAA
1 CATGTATCGATACAATAAA
* *
2925354 CATGAATCGATACAATGCATA
1 CATGTATCGATACAAT--AAA
2925375 -ATGTATCGATACA
1 CATGTATCGATACA
2925388 TCTGGCGTGT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 16 0.36
20 27 0.60
21 2 0.04
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATAAA
Found at i:2925979 original size:22 final size:20
Alignment explanation
Indices: 2925938--2925982 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
2925928 AGGCTCTCGT
*
2925938 TAAAAAAAAATTCCCTTTGA
1 TAAAAAAAAATTCCCCTTGA
*
2925958 TAAAAAAAATTCTCCCCCTTGA
1 TAAAAAAAAAT-T-CCCCTTGA
2925980 TAA
1 TAA
2925983 TCGGTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.48
21 1 0.05
22 10 0.48
ACGTcount: A:0.47, C:0.20, G:0.04, T:0.29
Consensus pattern (20 bp):
TAAAAAAAAATTCCCCTTGA
Found at i:2926465 original size:12 final size:12
Alignment explanation
Indices: 2926448--2926476 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2926438 CTTTAGGTGG
2926448 AGGAGGAGGAGA
1 AGGAGGAGGAGA
2926460 AGGAGGAGGAGA
1 AGGAGGAGGAGA
2926472 AGGAG
1 AGGAG
2926477 CATCTTCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (12 bp):
AGGAGGAGGAGA
Found at i:2928394 original size:52 final size:52
Alignment explanation
Indices: 2928316--2928416 Score: 193
Period size: 52 Copynumber: 1.9 Consensus size: 52
2928306 TGAAATCAAA
2928316 GTGGATTCATAAGACCAAGTTCTCTCCTTATGGTGCAAAATCTACTTTTGTC
1 GTGGATTCATAAGACCAAGTTCTCTCCTTATGGTGCAAAATCTACTTTTGTC
*
2928368 GTGGATTCATAAGACTAAGTTCTCTCCTTATGGTGCAAAATCTACTTTT
1 GTGGATTCATAAGACCAAGTTCTCTCCTTATGGTGCAAAATCTACTTTT
2928417 TTCAAGTGGT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.38
Consensus pattern (52 bp):
GTGGATTCATAAGACCAAGTTCTCTCCTTATGGTGCAAAATCTACTTTTGTC
Found at i:2934253 original size:19 final size:20
Alignment explanation
Indices: 2934209--2934261 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
2934199 CTGCCAGTTT
* *
2934209 CATGTATCGATACAATTATC
1 CATGTATCGATACAATGATA
2934229 CATGTATCGATACAATGA-A
1 CATGTATCGATACAATGATA
2934248 CATGTATCGATACA
1 CATGTATCGATACA
2934262 TTGTATCAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATGATA
Found at i:2937396 original size:13 final size:13
Alignment explanation
Indices: 2937361--2937399 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
2937351 TCCTGTATTT
*
2937361 TCTTTCTTTTTAC
1 TCTTTCTTTTTTC
*
2937374 TCTATCTTTTTTC
1 TCTTTCTTTTTTC
*
2937387 TCTTTTTTTTTTC
1 TCTTTCTTTTTTC
2937400 AAGCTACCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (13 bp):
TCTTTCTTTTTTC
Found at i:2937859 original size:20 final size:19
Alignment explanation
Indices: 2937836--2937909 Score: 87
Period size: 19 Copynumber: 3.7 Consensus size: 19
2937826 CACACCCAGA
*
2937836 TGTATCGATACATGCTGCTT
1 TGTATCGATACATG-TGCAT
*
2937856 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTGCAT
2937875 TGTATCGATACATG-GCCAAAT
1 TGTATCGATACATGTG-C--AT
2937896 TGTATCGATACATG
1 TGTATCGATACATG
2937910 AAACTGGCAG
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.38
20 14 0.29
21 16 0.33
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATGTGCAT
Found at i:2939188 original size:28 final size:26
Alignment explanation
Indices: 2939153--2939316 Score: 120
Period size: 28 Copynumber: 6.0 Consensus size: 26
2939143 CACGTGAATA
2939153 TTTAATTAGAAATTTTATGTGTGAAAAG
1 TTTAATTAGAAATTTTAT-TGT-AAAAG
* * **
2939181 TTCAATTAAAAATGTGCA-TGTAACAAG
1 TTTAATTAGAAAT-TTTATTGTAA-AAG
*
2939208 TTTAATT-GATAATTTTATT-TATAGAG
1 TTTAATTAGA-AATTTTATTGTA-AAAG
*
2939234 TTTGATTAGAAATTTTATCTGTTAAAAG
1 TTTAATTAGAAATTTTAT-TG-TAAAAG
* *
2939262 TTTAATTAAAAATTTTATGTGTAAAAA
1 TTTAATTAGAAATTTTAT-TGTAAAAG
2939289 TTATAATT-GAAATTTTTATATGTAAAAG
1 TT-TAATTAGAAA-TTTTAT-TGTAAAAG
2939317 CCTAATTAAA
Statistics
Matches: 107, Mismatches: 18, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
26 23 0.21
27 30 0.28
28 50 0.47
29 4 0.04
ACGTcount: A:0.41, C:0.02, G:0.13, T:0.44
Consensus pattern (26 bp):
TTTAATTAGAAATTTTATTGTAAAAG
Found at i:2939621 original size:2 final size:2
Alignment explanation
Indices: 2939616--2939651 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2939606 ACACACACAC
* *
2939616 AT AT AT AT AA AT AT AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2939652 TTGGGTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2940947 original size:25 final size:25
Alignment explanation
Indices: 2940911--2940962 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
2940901 CCTCTTACCT
* *
2940911 AATAAAAAAGACTTATAATGAGATA
1 AATAAAAAAGACCTATAATAAGATA
*
2940936 AATAAAAGAGACCTATAATAAGATA
1 AATAAAAAAGACCTATAATAAGATA
2940961 AA
1 AA
2940963 AGTTTAGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.21
Consensus pattern (25 bp):
AATAAAAAAGACCTATAATAAGATA
Found at i:2941283 original size:18 final size:17
Alignment explanation
Indices: 2941260--2941296 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
2941250 TTATCTTTAA
2941260 ATATTTAAAATTTATAAT
1 ATATTTAAAATTTA-AAT
*
2941278 ATATTTAAGATTTAAAT
1 ATATTTAAAATTTAAAT
2941295 AT
1 AT
2941297 CAAATTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
ATATTTAAAATTTAAAT
Found at i:2942075 original size:16 final size:16
Alignment explanation
Indices: 2942031--2942078 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
2942021 ACCGACCCTT
*
2942031 CTGAACCCAAAAT-AA
1 CTGAACCCAAAATGAC
* *
2942046 CTCGAATCCTAAATGAC
1 CT-GAACCCAAAATGAC
2942063 CTGAACCCAAAATGAC
1 CTGAACCCAAAATGAC
2942079 TCAAATTCGA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 2 0.08
16 21 0.81
17 3 0.12
ACGTcount: A:0.44, C:0.29, G:0.10, T:0.17
Consensus pattern (16 bp):
CTGAACCCAAAATGAC
Found at i:2942092 original size:32 final size:32
Alignment explanation
Indices: 2942031--2942093 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
2942021 ACCGACCCTT
* *
2942031 CTGAACCCAAAATAACTCGAATCCTAAATGAC
1 CTGAACCCAAAATAACTCAAATCCGAAATGAC
* *
2942063 CTGAACCCAAAATGACTCAAATTCGAAATGA
1 CTGAACCCAAAATAACTCAAATCCGAAATGA
2942094 TCCAAACCGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.44, C:0.25, G:0.11, T:0.19
Consensus pattern (32 bp):
CTGAACCCAAAATAACTCAAATCCGAAATGAC
Found at i:2943136 original size:13 final size:13
Alignment explanation
Indices: 2943101--2943153 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 13
2943091 ATGCTTATAC
*
2943101 ATAAATTTTTTTAT
1 ATAAA-TTTTTAAT
2943115 ATAAATTTTTAAT
1 ATAAATTTTTAAT
2943128 -TAAACTTTTTACAT
1 ATAAA-TTTTTA-AT
2943142 ATAGAATTTTTA
1 ATA-AATTTTTA
2943154 TCAAACTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
12 4 0.12
13 13 0.38
14 7 0.21
15 8 0.24
16 2 0.06
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (13 bp):
ATAAATTTTTAAT
Found at i:2943395 original size:20 final size:20
Alignment explanation
Indices: 2943365--2943403 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
2943355 TATGAATTTT
2943365 TAAATTAAAA-TTTTAAATA
1 TAAATTAAAATTTTTAAATA
2943384 TAAATATAAAATTTTTAAAT
1 TAAAT-TAAAATTTTTAAAT
2943404 TTGTAAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 5 0.28
21 8 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAAATTAAAATTTTTAAATA
Found at i:2945557 original size:2 final size:2
Alignment explanation
Indices: 2945545--2945573 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2945535 AGTACCTTGT
2945545 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2945574 AATGATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2949155 original size:49 final size:49
Alignment explanation
Indices: 2949083--2949180 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
2949073 GAGCCCATTT
*
2949083 TGAGAGGTGACTTCTTGTTCGTGGCTCTTCCCTTCCACTTGGGAAGTAG
1 TGAGAGGTGAATTCTTGTTCGTGGCTCTTCCCTTCCACTTGGGAAGTAG
2949132 TGAGAGGTGAATTCTTGTTCGTGGCTCTTCCCTTCCACTTGGGAAGTAG
1 TGAGAGGTGAATTCTTGTTCGTGGCTCTTCCCTTCCACTTGGGAAGTAG
2949181 CGGCTCCCTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.15, C:0.21, G:0.29, T:0.35
Consensus pattern (49 bp):
TGAGAGGTGAATTCTTGTTCGTGGCTCTTCCCTTCCACTTGGGAAGTAG
Found at i:2950642 original size:37 final size:37
Alignment explanation
Indices: 2950601--2950685 Score: 109
Period size: 37 Copynumber: 2.3 Consensus size: 37
2950591 GATTTATTAG
* *
2950601 TTGTTCATA-TTAATAGTAGTTGTTATTAGTGGTCAGT
1 TTGTT-ATATTTAACAGGAGTTGTTATTAGTGGTCAGT
* *
2950638 TTGTTTTATTTAGCAGGAGTTGTTATTAGTGGTCAGT
1 TTGTTATATTTAACAGGAGTTGTTATTAGTGGTCAGT
*
2950675 TTGTTTTATTT
1 TTGTTATATTT
2950686 TACTAAGTCT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 2 0.05
37 41 0.95
ACGTcount: A:0.20, C:0.05, G:0.22, T:0.53
Consensus pattern (37 bp):
TTGTTATATTTAACAGGAGTTGTTATTAGTGGTCAGT
Found at i:2954516 original size:20 final size:20
Alignment explanation
Indices: 2954486--2954539 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
2954476 TGCACATAAA
*
2954486 AAATGTATCGATACAAGCC-
1 AAATATATCGATACAAGCCT
**
2954505 ATAATATATCGATACATTCCT
1 A-AATATATCGATACAAGCCT
2954526 AAATATATCGATAC
1 AAATATATCGATAC
2954540 CTTAAGTTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.30
Consensus pattern (20 bp):
AAATATATCGATACAAGCCT
Found at i:2960390 original size:41 final size:41
Alignment explanation
Indices: 2960333--2960413 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
2960323 TATATGAGAA
* *
2960333 AGAAATGCTGGTTATTTTATCTGTTGTTAAAAAAGGAGTTC
1 AGAAATGCTGGCTATTTTATCTGCTGTTAAAAAAGGAGTTC
*
2960374 AGAAATGTTGGCTATTTTATCTGCTGTTAAAAAAGGAGTT
1 AGAAATGCTGGCTATTTTATCTGCTGTTAAAAAAGGAGTT
2960414 ATTATTGGGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.32, C:0.07, G:0.22, T:0.38
Consensus pattern (41 bp):
AGAAATGCTGGCTATTTTATCTGCTGTTAAAAAAGGAGTTC
Found at i:2962818 original size:11 final size:11
Alignment explanation
Indices: 2962799--2962855 Score: 55
Period size: 11 Copynumber: 5.0 Consensus size: 11
2962789 TAAATTATTT
2962799 ATATAATATAA
1 ATATAATATAA
*
2962810 ATATCATATAA
1 ATATAATATAA
2962821 A-A-AATATTAAA
1 ATATAATA-T-AA
2962832 ATATAATATAAA
1 ATATAATAT-AA
2962844 ATATAAATATAA
1 ATAT-AATATAA
2962856 TCTTATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
9 3 0.08
10 2 0.05
11 14 0.36
12 11 0.28
13 9 0.23
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (11 bp):
ATATAATATAA
Found at i:2962901 original size:17 final size:17
Alignment explanation
Indices: 2962881--2962937 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
2962871 TTTATAATAT
2962881 AAATTATTAAAAAATTA
1 AAATTATTAAAAAATTA
* *
2962898 AAATTTATTTAAATATATA
1 AAA-TTATTAAAAAAT-TA
*
2962917 AAATT-TTAAATAAAATA
1 AAATTATTAAA-AAATTA
2962934 AAAT
1 AAAT
2962938 CACAAAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
17 13 0.41
18 14 0.44
19 5 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATTATTAAAAAATTA
Found at i:2963635 original size:10 final size:10
Alignment explanation
Indices: 2963620--2963648 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
2963610 CCTGTCAAAG
2963620 GTAAATATAA
1 GTAAATATAA
2963630 GTAAATATAA
1 GTAAATATAA
2963640 GTAAATATA
1 GTAAATATA
2963649 TATATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.31
Consensus pattern (10 bp):
GTAAATATAA
Found at i:2968115 original size:2 final size:2
Alignment explanation
Indices: 2968110--2968152 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2968100 GTGTGTATGT
2968110 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2968152 G
1 G
2968153 TGAACAATGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2971969 original size:14 final size:13
Alignment explanation
Indices: 2971950--2972007 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 13
2971940 CATGTAAAAT
2971950 TAAATTTAATATTA
1 TAAATTTAATA-TA
*
2971964 TAAATTAAATAATA
1 TAAATTTAAT-ATA
*
2971978 TTAATTTAATCA-A
1 TAAATTTAAT-ATA
*
2971991 TAAATTTAAAATA
1 TAAATTTAATATA
2972004 TAAA
1 TAAA
2972008 ATAATAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
12 1 0.03
13 14 0.39
14 20 0.56
15 1 0.03
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (13 bp):
TAAATTTAATATA
Found at i:2972218 original size:18 final size:19
Alignment explanation
Indices: 2972195--2972256 Score: 76
Period size: 18 Copynumber: 3.4 Consensus size: 19
2972185 AAAAATTTTT
2972195 AATTAAATTAATATT-ATA
1 AATTAAATTAATATTAATA
*
2972213 AATTAATTTAATATTAATTA
1 AATTAAATTAATATTAA-TA
*
2972233 AATTAAA--AATATTAAAA
1 AATTAAATTAATATTAATA
2972250 AATTAAA
1 AATTAAA
2972257 AAAATAATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
17 8 0.21
18 22 0.56
19 1 0.03
20 8 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AATTAAATTAATATTAATA
Found at i:2972259 original size:18 final size:18
Alignment explanation
Indices: 2972222--2972258 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
2972212 AAATTAATTT
*
2972222 AATATTAATTAAATTAAA
1 AATATTAATAAAATTAAA
2972240 AATATTAA-AAAATTAAA
1 AATATTAATAAAATTAAA
2972257 AA
1 AA
2972259 AATAATATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AATATTAATAAAATTAAA
Found at i:2972392 original size:20 final size:20
Alignment explanation
Indices: 2972354--2972392 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2972344 AAAAACTACT
* *
2972354 TAATTTTTTACTTTTAAAAC
1 TAATTATTTACTTTAAAAAC
2972374 TAATTATTTACTTTAAAAA
1 TAATTATTTACTTTAAAAA
2972393 TTGTTATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (20 bp):
TAATTATTTACTTTAAAAAC
Found at i:2972426 original size:11 final size:11
Alignment explanation
Indices: 2972396--2972432 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
2972386 TTAAAAATTG
2972396 TTATTAATTTT
1 TTATTAATTTT
*
2972407 TTATATAATTAT
1 TTAT-TAATTTT
2972419 TTATTAATTTT
1 TTATTAATTTT
2972430 TTA
1 TTA
2972433 AAATATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATTAATTTT
Found at i:2973013 original size:18 final size:18
Alignment explanation
Indices: 2972979--2973013 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2972969 AGAAAGTGAA
*
2972979 AGGAAAAGAAAGAAAAAT
1 AGGAAAAGAAAAAAAAAT
*
2972997 AGGAAGAGAAAAAAAAA
1 AGGAAAAGAAAAAAAAA
2973014 GAAAAATTTA
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:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (18 bp):
AGGAAAAGAAAAAAAAAT
Found at i:2973185 original size:19 final size:17
Alignment explanation
Indices: 2973139--2973187 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
2973129 ATTTATGTTG
2973139 TTATTATTTTTTATTATA
1 TTATTATTTTTT-TTATA
*
2973157 TT-TTAATTTTTTTATA
1 TTATTATTTTTTTTATA
2973173 TTACATTATTTTTTT
1 TT--ATTATTTTTTT
2973188 ATGTGTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 7 0.27
17 8 0.31
18 2 0.08
19 9 0.35
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (17 bp):
TTATTATTTTTTTTATA
Found at i:2978464 original size:18 final size:17
Alignment explanation
Indices: 2978441--2978477 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
2978431 TTCCCTATTT
*
2978441 ATATATATATAATATTAA
1 ATATATAAATAA-ATTAA
2978459 ATATATAAATAAATTAA
1 ATATATAAATAAATTAA
2978476 AT
1 AT
2978478 TAAACTACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATATAAATAAATTAA
Found at i:2985683 original size:17 final size:16
Alignment explanation
Indices: 2985656--2985687 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2985646 TCGATGAGAA
2985656 ATTTAAAATATAATAT
1 ATTTAAAATATAATAT
2985672 ATTTATAAATATAATA
1 ATTTA-AAATATAATA
2985688 AATATTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTTAAAATATAATAT
Found at i:2985691 original size:21 final size:22
Alignment explanation
Indices: 2985662--2985742 Score: 71
Period size: 22 Copynumber: 3.6 Consensus size: 22
2985652 AGAAATTTAA
2985662 AATATAATA-TATTTATAAATAT
1 AATA-AATATTATTTATAAATAT
*
2985684 AATAAATATTATTATAATTAATTAT
1 AATAAATATTATT-T-A-TAAATAT
2985709 AATAAAATATTAATTT-TAAAT-T
1 AAT-AAATATT-ATTTATAAATAT
2985731 AATAAA-ATTATT
1 AATAAATATTATT
2985743 AAATAATAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
19 3 0.06
20 3 0.06
21 7 0.14
22 12 0.24
23 5 0.10
24 1 0.02
25 9 0.18
26 8 0.16
27 3 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AATAAATATTATTTATAAATAT
Found at i:2985727 original size:23 final size:23
Alignment explanation
Indices: 2985672--2985744 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 23
2985662 AATATAATAT
2985672 ATTTATAAATATAATAAATATTATT-
1 ATTT-TAAAT-TAATAAA-ATTATTA
* *
2985697 ATAATTAATTATAATAAAA-TATTA
1 AT-TTTAAAT-TAATAAAATTATTA
2985721 ATTTTAAATTAATAAAATTATTA
1 ATTTTAAATTAATAAAATTATTA
2985744 A
1 A
2985745 ATAATAATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
22 8 0.20
23 15 0.37
24 3 0.07
25 14 0.34
26 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
ATTTTAAATTAATAAAATTATTA
Found at i:2985753 original size:23 final size:23
Alignment explanation
Indices: 2985683--2985754 Score: 60
Period size: 23 Copynumber: 3.1 Consensus size: 23
2985673 TTTATAAATA
*
2985683 TAATAAATATTATTATAATTAATTA-
1 TAATAAA-ATTATTA-AA-TAATAAT
**
2985708 TAATAAAA-TATT-AATTTTAAAT
1 TAATAAAATTATTAAATAAT-AAT
2985730 TAATAAAATTATTAAATAATAAT
1 TAATAAAATTATTAAATAATAAT
2985753 TA
1 TA
2985755 TAACGTCACT
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
20 2 0.05
21 3 0.08
22 8 0.21
23 13 0.34
24 5 0.13
25 7 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TAATAAAATTATTAAATAATAAT
Found at i:2986907 original size:20 final size:21
Alignment explanation
Indices: 2986869--2986918 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
2986859 TTTTTAAGAG
* * *
2986869 TTATTTTTTTAATTATTTAAT
1 TTATTATTTAAATTATTTAAC
*
2986890 TTA-TATTTAAATTTTTTAAC
1 TTATTATTTAAATTATTTAAC
2986910 TTATTATTT
1 TTATTATTT
2986919 TATTCACCCG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (21 bp):
TTATTATTTAAATTATTTAAC
Found at i:2987154 original size:26 final size:25
Alignment explanation
Indices: 2987111--2987162 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 25
2987101 TAATTGGATA
2987111 AAAAATTTAAAAAAAAATTAT-TTT
1 AAAAATTTAAAAAAAAATTATATTT
*
2987135 AAAAATTTAAACAATCAAATTATATTT
1 AAAAATTTAAA-AA-AAAATTATATTT
2987162 A
1 A
2987163 TTTATATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 11 0.46
25 2 0.08
26 7 0.29
27 4 0.17
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (25 bp):
AAAAATTTAAAAAAAAATTATATTT
Found at i:2989564 original size:27 final size:29
Alignment explanation
Indices: 2989533--2989587 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
2989523 AAAAAAGTTT
*
2989533 TGGATCTG-TTTT-GAATTTTGTTTTCCA
1 TGGATATGCTTTTCGAATTTTGTTTTCCA
* *
2989560 TGGATATGCTTTTCTATTTTTGTTTTCC
1 TGGATATGCTTTTCGAATTTTGTTTTCC
2989588 CTTTTTTCTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 7 0.30
28 4 0.17
29 12 0.52
ACGTcount: A:0.13, C:0.13, G:0.16, T:0.58
Consensus pattern (29 bp):
TGGATATGCTTTTCGAATTTTGTTTTCCA
Found at i:2991471 original size:17 final size:16
Alignment explanation
Indices: 2991405--2991471 Score: 52
Period size: 17 Copynumber: 4.2 Consensus size: 16
2991395 ACCCGAAATT
*
2991405 AATTTAAATTTTATAAA
1 AATTTAAAATTTAT-AA
2991422 AATTTAAAA-TTATTAA
1 AATTTAAAATTTA-TAA
**
2991438 AA--T-AAATAAATAA
1 AATTTAAAATTTATAA
2991451 AATTTAAAATTTATCAA
1 AATTTAAAATTTAT-AA
2991468 AATT
1 AATT
2991472 AAGTTAAATC
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
13 8 0.21
14 2 0.05
15 1 0.03
16 13 0.33
17 15 0.38
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTTAAAATTTATAA
Found at i:2991607 original size:20 final size:20
Alignment explanation
Indices: 2991579--2991620 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2991569 ATAATTATGT
* * *
2991579 ATTATGTGACAAATTTTAAA
1 ATTAAGTGAAAAATGTTAAA
2991599 ATTAAGTGAAAAATGTTAAA
1 ATTAAGTGAAAAATGTTAAA
2991619 AT
1 AT
2991621 AATTTTATTT
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:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (20 bp):
ATTAAGTGAAAAATGTTAAA
Found at i:2991884 original size:20 final size:20
Alignment explanation
Indices: 2991861--2991901 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
2991851 AAGTATATAT
2991861 ATTTTAAT-ATATTATTTTAA
1 ATTTTAATGATATT-TTTTAA
*
2991881 A-TTTATTGATATTTTTTAA
1 ATTTTAATGATATTTTTTAA
2991900 AT
1 AT
2991902 ATATATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 4
0.78 0.04 0.17
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
ATTTTAATGATATTTTTTAA
Found at i:2991909 original size:17 final size:17
Alignment explanation
Indices: 2991867--2991911 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
2991857 ATATATTTTA
*
2991867 ATATATTATTTTAAATTT
1 ATATATT-TTTTAAATAT
2991885 ATTGATATTTTTTAAATAT
1 A-T-ATATTTTTTAAATAT
2991904 ATATATTT
1 ATATATTT
2991912 ATAGCTTACT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 6 0.25
18 2 0.08
19 11 0.46
20 5 0.21
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
ATATATTTTTTAAATAT
Found at i:2992677 original size:16 final size:16
Alignment explanation
Indices: 2992656--2992696 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
2992646 TATTTATTTA
2992656 TATTTATAAATAAATT
1 TATTTATAAATAAATT
*
2992672 TATTTATAAAATAACTT
1 TATTTAT-AAATAAATT
2992689 T-TTTATAA
1 TATTTATAA
2992697 TTTTATATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 2 0.09
16 12 0.52
17 9 0.39
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
TATTTATAAATAAATT
Found at i:2994170 original size:21 final size:20
Alignment explanation
Indices: 2994124--2994170 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
2994114 AATTATTTAT
*
2994124 ATATTAATAATTTAAAATAA
1 ATATTAATAATTAAAAATAA
2994144 ATTATTAAT-ATATAAAAATATA
1 A-TATTAATAAT-TAAAAATA-A
2994166 ATATT
1 ATATT
2994171 TTAAATACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 3 0.13
21 18 0.78
22 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATTAATAATTAAAAATAA
Found at i:2994174 original size:23 final size:22
Alignment explanation
Indices: 2994140--2994192 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
2994130 ATAATTTAAA
*
2994140 ATAAATTATTAATATATAAAAAT
1 ATAAATTATTAA-ATACAAAAAT
2994163 ATAATATT-TTAAATACAAAAAATT
1 ATAA-ATTATTAAATAC-AAAAA-T
2994187 ATAAAT
1 ATAAAT
2994193 ATAAACAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 3 0.12
23 15 0.58
24 8 0.31
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
ATAAATTATTAAATACAAAAAT
Found at i:2994227 original size:14 final size:13
Alignment explanation
Indices: 2994208--2994253 Score: 65
Period size: 14 Copynumber: 3.4 Consensus size: 13
2994198 CAGATAAAAA
*
2994208 TTTTTTTCTTTTC
1 TTTTTTTTTTTTC
2994221 TTTTTTTTTTCTTC
1 TTTTTTTTTT-TTC
2994235 TTTTTTTTTCTTTC
1 TTTTTTTTT-TTTC
2994249 TTTTT
1 TTTTT
2994254 ACTTTCTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 9 0.30
14 20 0.67
15 1 0.03
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTTTTTTTTC
Found at i:2994230 original size:11 final size:11
Alignment explanation
Indices: 2994209--2994264 Score: 58
Period size: 11 Copynumber: 4.7 Consensus size: 11
2994199 AGATAAAAAT
2994209 TTTTTTCTTTTC
1 TTTTTT-TTTTC
2994221 TTTTTTTTTTC
1 TTTTTTTTTTC
2994232 TTCTTTTTTTTTC
1 -T-TTTTTTTTTC
* *
2994245 TTTCTTTTTAC
1 TTTTTTTTTTC
2994256 TTTCTTTTT
1 TTT-TTTTT
2994265 GTGCAAGACG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
11 16 0.42
12 12 0.32
13 10 0.26
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:2994243 original size:24 final size:26
Alignment explanation
Indices: 2994210--2994264 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 26
2994200 GATAAAAATT
* *
2994210 TTTTTCTTTTCTTTTTTTTTTC-TTC
1 TTTTTCTTTTCTTTCTTTTTACTTTC
2994235 TTTTT-TTTTCTTTCTTTTTACTTTC
1 TTTTTCTTTTCTTTCTTTTTACTTTC
2994260 TTTTT
1 TTTTT
2994265 GTGCAAGACG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 14 0.52
25 13 0.48
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.84
Consensus pattern (26 bp):
TTTTTCTTTTCTTTCTTTTTACTTTC
Found at i:2995077 original size:32 final size:34
Alignment explanation
Indices: 2995041--2995108 Score: 106
Period size: 31 Copynumber: 2.1 Consensus size: 34
2995031 TGAATATAAA
2995041 AATATGTTAAAATTTATATAAA-ATA-AAT-TATT
1 AATATGTT-AAATTTATATAAATATATAATATATT
2995073 AATATGTTAAATTTATATAAATATATAATATATT
1 AATATGTTAAATTTATATAAATATATAATATATT
2995107 AA
1 AA
2995109 ATATAATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
31 13 0.39
32 11 0.33
33 3 0.09
34 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (34 bp):
AATATGTTAAATTTATATAAATATATAATATATT
Found at i:2998722 original size:104 final size:104
Alignment explanation
Indices: 2998542--2998749 Score: 335
Period size: 104 Copynumber: 2.0 Consensus size: 104
2998532 CCATTTTTCA
*
2998542 GAAATCCAAACCAAATACAACATCAGGCAACAAATTCATATGCTCCAACACAATGAAGAAAAGAA
1 GAAATCCAAACCAAATACAACATCAGGCAACAAATTCAAATGCTCCAACACAATGAAGAAAAGAA
* *
2998607 AATTAAAGATAGTGAAGATAATGAATCACATATAGTACG
66 AATTAAAGATAGTGAAGATAATGAATCAAAAATAGTACG
* * * *
2998646 GAAATCCAAAGCAAATACAACATCTGGTAACAAATTCAAATGCTCCAACACAATGAAGAAAAGAC
1 GAAATCCAAACCAAATACAACATCAGGCAACAAATTCAAATGCTCCAACACAATGAAGAAAAGAA
* *
2998711 AATTCAAGATAGTGAGGATAATGAATCAAAAATAGTACG
66 AATTAAAGATAGTGAAGATAATGAATCAAAAATAGTACG
2998750 AGGAAATCAG
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
104 95 1.00
ACGTcount: A:0.50, C:0.17, G:0.14, T:0.18
Consensus pattern (104 bp):
GAAATCCAAACCAAATACAACATCAGGCAACAAATTCAAATGCTCCAACACAATGAAGAAAAGAA
AATTAAAGATAGTGAAGATAATGAATCAAAAATAGTACG
Found at i:3001432 original size:29 final size:27
Alignment explanation
Indices: 3001369--3001457 Score: 76
Period size: 29 Copynumber: 3.1 Consensus size: 27
3001359 TCAAGACTTA
*
3001369 TATAA-ATATAAATTATTTTAAATATGAT-
1 TATAATATATAAATTA---TAAATATAATG
3001397 TATAATATAATAAAATATATAAATATAATG
1 TATAATAT-AT-AAAT-TATAAATATAATG
3001427 TA-AATATATAAATTATAAATTATAAATG
1 TATAATATATAAATTATAAA-TAT-AATG
3001455 TAT
1 TAT
3001458 CGAGAGGATT
Statistics
Matches: 52, Mismatches: 1, Indels: 15
0.76 0.01 0.22
Matches are distributed among these distances:
26 6 0.12
27 7 0.13
28 13 0.25
29 16 0.31
30 4 0.08
31 4 0.08
32 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (27 bp):
TATAATATATAAATTATAAATATAATG
Found at i:3001433 original size:19 final size:18
Alignment explanation
Indices: 3001400--3001444 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
3001390 ATATGATTAT
3001400 AATATAATAAAATATATA
1 AATATAATAAAATATATA
*
3001418 AATATAATGTAAATATATA
1 AATATAAT-AAAATATATA
3001437 AATTATAA
1 AA-TATAA
3001445 ATTATAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 8 0.33
19 11 0.46
20 5 0.21
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
AATATAATAAAATATATA
Found at i:3002196 original size:15 final size:17
Alignment explanation
Indices: 3002172--3002204 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3002162 TTGATTGAAA
3002172 ATTTTATGAT-ATTTTT
1 ATTTTATGATGATTTTT
3002188 ATTTT-TGATGATTTTT
1 ATTTTATGATGATTTTT
3002204 A
1 A
3002205 GTTCACACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (17 bp):
ATTTTATGATGATTTTT
Found at i:3002905 original size:13 final size:13
Alignment explanation
Indices: 3002887--3002955 Score: 50
Period size: 13 Copynumber: 4.9 Consensus size: 13
3002877 ACATGATAAT
*
3002887 TTATATTTTTATA
1 TTATATTTATATA
3002900 TTATATTTATATA
1 TTATATTTATATA
3002913 TTTTATCATATTATA-A
1 --TTAT-AT-TTATATA
* *
3002929 TTATATTAAAATATT
1 TTATATT--TATATA
3002944 TTATATTTATAT
1 TTATATTTATAT
3002956 TAATTTTAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
12 1 0.02
13 18 0.40
14 7 0.16
15 11 0.24
16 3 0.07
17 5 0.11
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (13 bp):
TTATATTTATATA
Found at i:3002914 original size:21 final size:23
Alignment explanation
Indices: 3002882--3002934 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
3002872 AGTAAACATG
3002882 ATAATT-TATATTTT-T-ATATT
1 ATAATTATATATTTTATCATATT
*
3002902 ATATTTATATATTTTATCATATT
1 ATAATTATATATTTTATCATATT
3002925 ATAATTATAT
1 ATAATTATAT
3002935 TAAAATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 5 0.18
21 8 0.29
22 1 0.04
23 14 0.50
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
ATAATTATATATTTTATCATATT
Found at i:3002942 original size:29 final size:27
Alignment explanation
Indices: 3002886--3002954 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 27
3002876 AACATGATAA
* * *
3002886 TTTATATTTTTATATTATATTTATATAT
1 TTTATATTTATA-ATTATATTAAAATAT
3002914 TTTATCATATTATAATTATATTAAAATAT
1 TTTAT-AT-TTATAATTATATTAAAATAT
3002943 TTTATATTTATA
1 TTTATATTTATA
3002955 TTAATTTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 5 0.14
28 7 0.19
29 20 0.56
30 4 0.11
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (27 bp):
TTTATATTTATAATTATATTAAAATAT
Found at i:3005160 original size:7 final size:7
Alignment explanation
Indices: 3005150--3005216 Score: 55
Period size: 7 Copynumber: 9.6 Consensus size: 7
3005140 TCCCCCCAAA
3005150 AAAAAAG
1 AAAAAAG
3005157 AAAAAAG
1 AAAAAAG
3005164 AAAAAAG
1 AAAAAAG
* *
3005171 AAATAAT
1 AAAAAAG
*
3005178 AAAAATG
1 AAAAAAG
3005185 AATAAAAG
1 AA-AAAAG
* **
3005193 GAAAACT
1 AAAAAAG
*
3005200 AGAAAAG
1 AAAAAAG
3005207 AAAAAA-
1 AAAAAAG
3005213 AAAA
1 AAAA
3005217 TGGCAGCTAT
Statistics
Matches: 45, Mismatches: 14, Indels: 3
0.73 0.23 0.05
Matches are distributed among these distances:
6 4 0.09
7 36 0.80
8 5 0.11
ACGTcount: A:0.79, C:0.01, G:0.12, T:0.07
Consensus pattern (7 bp):
AAAAAAG
Found at i:3007136 original size:158 final size:157
Alignment explanation
Indices: 3006830--3007133 Score: 477
Period size: 158 Copynumber: 1.9 Consensus size: 157
3006820 TAGAGATAAG
*
3006830 ATAGTTGACTTGGGCACTTAAATTAGGATTTTCTAGTATCCTTTCCTATCTAGGATACTATATTT
1 ATAGTTGACTTGGGCACTTAAATTAGGATTTTCTAGTATCATTTCCTATCTAGGATACTATATTT
3006895 GAAAGTTCAGACTACCATATAAACAGACTTAAAAACAACTTGTAAAAAATACATAAAAATAAGAA
66 GAAAGTTCAGACTACCATATAAACAGACTTAAAAACAACTTGTAAAAAATACATAAAAATAAGAA
3006960 ATTTATTGATTTAGTTTCACTTTTCAAC
131 ATTTATT-ATTTAGTTTCACTTTTCAAC
* * * * *
3006988 ATAGTTGACTTGGGTACTTAAATTAGGATTTTCTAGTTTCATTTTCTGTCTAGGATGCTATATTT
1 ATAGTTGACTTGGGCACTTAAATTAGGATTTTCTAGTATCATTTCCTATCTAGGATACTATATTT
** **
3007053 G-AAGATTCAGACCTACCATATAAACAGACTTGGAAACTGCTTGTAAAAAATACATAAAAATAAG
66 GAAAG-TTCAGA-CTACCATATAAACAGACTTAAAAACAACTTGTAAAAAATACATAAAAATAAG
3007117 AAATTTATT-TTTAGTTT
129 AAATTTATTATTTAGTTT
3007134 TCAACATGGT
Statistics
Matches: 134, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
157 11 0.08
158 66 0.49
159 57 0.43
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (157 bp):
ATAGTTGACTTGGGCACTTAAATTAGGATTTTCTAGTATCATTTCCTATCTAGGATACTATATTT
GAAAGTTCAGACTACCATATAAACAGACTTAAAAACAACTTGTAAAAAATACATAAAAATAAGAA
ATTTATTATTTAGTTTCACTTTTCAAC
Found at i:3019381 original size:21 final size:20
Alignment explanation
Indices: 3019355--3019402 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 20
3019345 TAATAATAAA
3019355 AAATATGATAAAAAATAATAT
1 AAATATGAT-AAAAATAATAT
*
3019376 AAATATGATATAAATATATAT
1 AAATATGATAAAAATA-ATAT
3019397 AAATAT
1 AAATAT
3019403 TAAAATTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (20 bp):
AAATATGATAAAAATAATAT
Found at i:3019386 original size:11 final size:11
Alignment explanation
Indices: 3019355--3019402 Score: 64
Period size: 10 Copynumber: 4.5 Consensus size: 11
3019345 TAATAATAAA
3019355 AAATATGATA-
1 AAATATGATAT
* *
3019365 AAAAATAATAT
1 AAATATGATAT
3019376 AAATATGATAT
1 AAATATGATAT
3019387 AAATAT-ATAT
1 AAATATGATAT
3019397 AAATAT
1 AAATAT
3019403 TAAAATTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
10 18 0.55
11 15 0.45
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (11 bp):
AAATATGATAT
Found at i:3019429 original size:24 final size:23
Alignment explanation
Indices: 3019388--3019466 Score: 79
Period size: 24 Copynumber: 3.3 Consensus size: 23
3019378 ATATGATATA
*
3019388 AATATATATAAATATTAAAATTT
1 AATATAAATAAATATTAAAATTT
*
3019411 -ATATAAAATAAATTATTAATATGTT
1 AATAT-AAATAAA-TATTAAAAT-TT
* *
3019436 AATATATATAAATATTAAATTTT
1 AATATAAATAAATATTAAAATTT
3019459 AATTATAA
1 AA-TATAA
3019467 TTATAATGTA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
22 4 0.09
23 10 0.22
24 19 0.42
25 8 0.18
26 4 0.09
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (23 bp):
AATATAAATAAATATTAAAATTT
Found at i:3019860 original size:19 final size:20
Alignment explanation
Indices: 3019818--3019868 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
3019808 AAATTATAAT
*
3019818 AAAAATATAAAAATAAATTT
1 AAAAATATAAAAATAAATTC
**
3019838 AAAAAT-TAAAAATTTATTC
1 AAAAATATAAAAATAAATTC
3019857 AAAAAATATAAA
1 -AAAAATATAAA
3019869 TTCTAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 10 0.38
20 12 0.46
21 4 0.15
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAAATATAAAAATAAATTC
Found at i:3019974 original size:32 final size:32
Alignment explanation
Indices: 3019923--3019983 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
3019913 TATTAAATAT
** * * *
3019923 TAATTTTAATTTAATTTAAATTTAAAACAATC
1 TAATTTTAAAATAAATTAAACTCAAAACAATC
3019955 TAATTTTAAAATAAATTAAACTCAAAACA
1 TAATTTTAAAATAAATTAAACTCAAAACA
3019984 TTCAAAATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.39
Consensus pattern (32 bp):
TAATTTTAAAATAAATTAAACTCAAAACAATC
Found at i:3020420 original size:16 final size:16
Alignment explanation
Indices: 3020390--3020431 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3020380 TAATTTAATT
*
3020390 ATTATAAATATAAAATA
1 ATTATAAA-ATAAAAAA
3020407 ATTATAAAATAAAAAA
1 ATTATAAAATAAAAAA
*
3020423 ATCATAAAA
1 ATTATAAAA
3020432 AATTTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
ATTATAAAATAAAAAA
Found at i:3020689 original size:7 final size:7
Alignment explanation
Indices: 3020671--3020704 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
3020661 TAAATAATTT
3020671 TTTTTAA
1 TTTTTAA
3020678 TTTTTTAA
1 -TTTTTAA
*
3020686 TTTTTAG
1 TTTTTAA
3020693 TTTTTAA
1 TTTTTAA
3020700 TTTTT
1 TTTTT
3020705 TTAGCGATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (7 bp):
TTTTTAA
Found at i:3020886 original size:16 final size:17
Alignment explanation
Indices: 3020865--3020905 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
3020855 GTTGGCAACT
3020865 AAAAAAA-CTAAAA-AAA
1 AAAAAAAGC-AAAACAAA
3020881 AAAAAAAGCAAAACTAAA
1 AAAAAAAGCAAAAC-AAA
3020899 AAAAAAA
1 AAAAAAA
3020906 AAACTTATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 11 0.50
17 1 0.05
18 10 0.45
ACGTcount: A:0.85, C:0.07, G:0.02, T:0.05
Consensus pattern (17 bp):
AAAAAAAGCAAAACAAA
Found at i:3022299 original size:19 final size:18
Alignment explanation
Indices: 3022224--3022309 Score: 88
Period size: 18 Copynumber: 4.8 Consensus size: 18
3022214 CTTTTTTTAT
*
3022224 AAAAAAATAAAAAAAATT-
1 AAAAAAA-ATAAAAAATTC
* *
3022242 AAAAATAATAATAAAAATC
1 AAAAAAAATAA-AAAATTC
*
3022261 --AAGAAATAAAAAATTC
1 AAAAAAAATAAAAAATTC
3022277 AAAAAAAATAAAAAATTC
1 AAAAAAAATAAAAAATTC
3022295 AAAAAAAAATAAAAA
1 -AAAAAAAATAAAAA
3022310 TGGCCAATTT
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
16 6 0.11
17 10 0.18
18 26 0.46
19 14 0.25
ACGTcount: A:0.79, C:0.03, G:0.01, T:0.16
Consensus pattern (18 bp):
AAAAAAAATAAAAAATTC
Found at i:3030283 original size:27 final size:26
Alignment explanation
Indices: 3030234--3030284 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
3030224 ATTTTTGATT
*
3030234 GAAAAATGGGGTTGGAGTATCCCCTC
1 GAAAAATGGGGTTGGAATATCCCCTC
*
3030260 GAAAGAATGGGGTTGGAATGTCCCC
1 GAAA-AATGGGGTTGGAATATCCCC
3030285 AGTGATGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.27, C:0.18, G:0.33, T:0.22
Consensus pattern (26 bp):
GAAAAATGGGGTTGGAATATCCCCTC
Found at i:3032625 original size:51 final size:51
Alignment explanation
Indices: 3032537--3032681 Score: 188
Period size: 50 Copynumber: 2.9 Consensus size: 51
3032527 TTTTAACTAG
* *
3032537 ATGTATTGATATATTGAAAAA-ATAAT-GATACATCTGGGTAAAAAGACAAA
1 ATGTATCGATACATTGAAAAATAT-ATCGATACATCTGGGTAAAAAGACAAA
* * * *
3032587 ATGTATCGATACATTGAAGAATGTATCGATACATCTGGGT-AAAAGATAGA
1 ATGTATCGATACATTGAAAAATATATCGATACATCTGGGTAAAAAGACAAA
* *
3032637 ATGTATCGATTCATTGAAAAATATATCGATACATCTTGGTAAAAA
1 ATGTATCGATACATTGAAAAATATATCGATACATCTGGGTAAAAA
3032682 TGTGACTTTT
Statistics
Matches: 82, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
50 64 0.78
51 18 0.22
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.30
Consensus pattern (51 bp):
ATGTATCGATACATTGAAAAATATATCGATACATCTGGGTAAAAAGACAAA
Found at i:3035576 original size:26 final size:26
Alignment explanation
Indices: 3035547--3035671 Score: 168
Period size: 26 Copynumber: 4.8 Consensus size: 26
3035537 TATATTTTTG
3035547 TTTTTAGAATTTTTTATTTTTTAAAA
1 TTTTTAGAATTTTTTATTTTTTAAAA
3035573 TTTTTTAGAATTTATTTA-TTTTT--AA
1 -TTTTTAGAATTT-TTTATTTTTTAAAA
*
3035598 TTTTTAGAATTTTTAATTTTTTAAAA
1 TTTTTAGAATTTTTTATTTTTTAAAA
3035624 TTTTTAGAATTTTTTATTTTTTAAAA
1 TTTTTAGAATTTTTTATTTTTTAAAA
* *
3035650 TTTTTTGAAGTTTTCT-TTTTTT
1 TTTTTAGAA-TTTTTTATTTTTT
3035672 CTTTTTAATT
Statistics
Matches: 89, Mismatches: 4, Indels: 11
0.86 0.04 0.11
Matches are distributed among these distances:
23 3 0.03
24 17 0.19
25 2 0.02
26 41 0.46
27 22 0.25
28 4 0.04
ACGTcount: A:0.27, C:0.01, G:0.05, T:0.67
Consensus pattern (26 bp):
TTTTTAGAATTTTTTATTTTTTAAAA
Found at i:3035611 original size:50 final size:50
Alignment explanation
Indices: 3035533--3035644 Score: 167
Period size: 50 Copynumber: 2.3 Consensus size: 50
3035523 AATTTTCTAT
* *
3035533 TTTATATATTTTTGTTTTTAGAATTTTTT-ATTTTTTAAAATTTTTTAGAA
1 TTTATTTATTTTTATTTTTAGAATTTTTTAATTTTTTAAAA-TTTTTAGAA
3035583 TTTATTTATTTTTAATTTTTAGAA-TTTTTAATTTTTTAAAATTTTTAGAA
1 TTTATTTATTTTT-ATTTTTAGAATTTTTTAATTTTTTAAAATTTTTAGAA
3035633 TTT-TTTATTTTT
1 TTTATTTATTTTT
3035645 TAAAATTTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
49 9 0.16
50 29 0.50
51 20 0.34
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (50 bp):
TTTATTTATTTTTATTTTTAGAATTTTTTAATTTTTTAAAATTTTTAGAA
Found at i:3035629 original size:17 final size:17
Alignment explanation
Indices: 3035547--3035639 Score: 77
Period size: 17 Copynumber: 5.4 Consensus size: 17
3035537 TATATTTTTG
* *
3035547 TTTTTAGAATTTTTTAT
1 TTTTTAAAATTTTTAAT
3035564 TTTTTAAAATTTTTTAGAAT
1 TTTTTAAAA-TTTTT--AAT
3035584 TTATTT---ATTTTTAA-
1 TT-TTTAAAATTTTTAAT
*
3035598 TTTTTAGAATTTTTAAT
1 TTTTTAAAATTTTTAAT
3035615 TTTTTAAAATTTTTAGAAT
1 TTTTTAAAATTTTT--AAT
3035634 TTTTTA
1 TTTTTA
3035640 TTTTTTAAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 18
0.75 0.04 0.21
Matches are distributed among these distances:
13 3 0.05
14 2 0.03
15 2 0.03
16 8 0.13
17 26 0.41
18 6 0.10
19 9 0.14
20 4 0.06
21 3 0.05
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (17 bp):
TTTTTAAAATTTTTAAT
Found at i:3035653 original size:9 final size:9
Alignment explanation
Indices: 3035596--3035654 Score: 59
Period size: 9 Copynumber: 6.8 Consensus size: 9
3035586 ATTTATTTTT
*
3035596 AATTTTTAG
1 AATTTTTAA
3035605 AATTTTT-A
1 AATTTTTAA
*
3035613 ATTTTTTAA
1 AATTTTTAA
*
3035622 AATTTTTAG
1 AATTTTTAA
*
3035631 AATTTTT-T
1 AATTTTTAA
*
3035639 ATTTTTTAA
1 AATTTTTAA
3035648 AATTTTT
1 AATTTTT
3035655 TGAAGTTTTC
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
8 12 0.30
9 28 0.70
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.64
Consensus pattern (9 bp):
AATTTTTAA
Found at i:3035663 original size:10 final size:10
Alignment explanation
Indices: 3035562--3035655 Score: 54
Period size: 10 Copynumber: 10.7 Consensus size: 10
3035552 AGAATTTTTT
3035562 ATTTTTTAAA
1 ATTTTTTAAA
*
3035572 ATTTTTTAGA
1 ATTTTTTAAA
3035582 ATTTATTT---
1 ATTT-TTTAAA
3035590 A-TTTTT--A
1 ATTTTTTAAA
*
3035597 A-TTTTTAGA
1 ATTTTTTAAA
3035606 A-TTTTT--A
1 ATTTTTTAAA
3035613 ATTTTTTAAA
1 ATTTTTTAAA
*
3035623 A-TTTTTAGA
1 ATTTTTTAAA
3035632 ATTTTTT---
1 ATTTTTTAAA
3035639 ATTTTTTAAA
1 ATTTTTTAAA
3035649 ATTTTTT
1 ATTTTTT
3035656 GAAGTTTTCT
Statistics
Matches: 71, Mismatches: 2, Indels: 22
0.75 0.02 0.23
Matches are distributed among these distances:
6 3 0.04
7 17 0.24
8 6 0.08
9 15 0.21
10 27 0.38
11 3 0.04
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (10 bp):
ATTTTTTAAA
Found at i:3036314 original size:15 final size:15
Alignment explanation
Indices: 3036294--3036344 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
3036284 GTAATTTATA
3036294 TATTTTTATTATATT
1 TATTTTTATTATATT
*
3036309 TATTTTTA-TAT-TA
1 TATTTTTATTATATT
*
3036322 T-TTTTTATTATAAT
1 TATTTTTATTATATT
*
3036336 TATGTTTAT
1 TATTTTTAT
3036345 AATGTTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
12 6 0.21
13 5 0.17
14 4 0.14
15 14 0.48
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TATTTTTATTATATT
Found at i:3036326 original size:27 final size:25
Alignment explanation
Indices: 3036288--3036345 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 25
3036278 AATTTGGTAA
* *
3036288 TTTATATATTTTTATTATATTTATT
1 TTTATATATTTTTATTATAATTATG
3036313 TTTATATTATTTTTTATTATAATTATG
1 TTTATA-TA-TTTTTATTATAATTATG
3036340 TTTATA
1 TTTATA
3036346 ATGTTATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 6 0.21
26 2 0.07
27 21 0.72
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (25 bp):
TTTATATATTTTTATTATAATTATG
Found at i:3036330 original size:10 final size:11
Alignment explanation
Indices: 3036287--3036332 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
3036277 AAATTTGGTA
*
3036287 ATTTATATATT
1 ATTTTTATATT
3036298 -TTTATTATATTT
1 ATTT-TTATA-TT
3036310 ATTTTTATATT
1 ATTTTTATATT
3036321 ATTTTT-TATT
1 ATTTTTATATT
3036331 AT
1 AT
3036333 AATTATGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
10 9 0.29
11 12 0.39
12 7 0.23
13 3 0.10
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTTTTATATT
Found at i:3036355 original size:60 final size:60
Alignment explanation
Indices: 3036285--3036431 Score: 142
Period size: 60 Copynumber: 2.5 Consensus size: 60
3036275 TGAAATTTGG
* ** * *
3036285 TAAT-TTATATATTTTTATTATATTTATTTTTATATTATT-TT-TTATTATAATTATGTTTA
1 TAATGTTATATATTTATATTATATTTATTGATATATTATTATTCATATTA-AATAAT-TTTA
* *
3036344 TAATGTTATATATTTATATCA-AATT-TTGATATATTATTAATTCATATTAAATAATTTTA
1 TAATGTTATATATTTATATTATATTTATTGATATATTATT-ATTCATATTAAATAATTTTA
* *
3036403 TTATGTTCATATATTTGTATTATATTTAT
1 TAATGTT-ATATATTTATATTATATTTAT
3036432 ATTATTTTTT
Statistics
Matches: 70, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
58 11 0.16
59 17 0.24
60 33 0.47
61 8 0.11
62 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (60 bp):
TAATGTTATATATTTATATTATATTTATTGATATATTATTATTCATATTAAATAATTTTA
Found at i:3036357 original size:27 final size:27
Alignment explanation
Indices: 3036288--3036357 Score: 63
Period size: 27 Copynumber: 2.7 Consensus size: 27
3036278 AATTTGGTAA
* * *
3036288 TTTAT-ATATT-TTTATTATATTTATT
1 TTTATAATATTATATATTATAATTATG
* * *
3036313 TTTATATTATTTTTTATTATAATTATG
1 TTTATAATATTATATATTATAATTATG
*
3036340 TTTATAATGTTATATATT
1 TTTATAATATTATATATT
3036358 TATATCAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
25 5 0.14
26 4 0.11
27 27 0.75
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (27 bp):
TTTATAATATTATATATTATAATTATG
Found at i:3037372 original size:38 final size:36
Alignment explanation
Indices: 3037330--3037412 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 36
3037320 CAATATTCTA
*
3037330 ATTCTTAACCGATGGCATGGTTCAGAACAAAAA-TCACT
1 ATTCTTAA--GATGGCATGGGTCAGAACAAAAACT-ACT
* *
3037368 ATTCTTATAGGTGGCATGGGTCGGAACAAAAACTACT
1 ATTCTTA-AGATGGCATGGGTCAGAACAAAAACTACT
3037405 ATTCTTAA
1 ATTCTTAA
3037413 TCGGTGGTAC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
36 1 0.03
37 30 0.75
38 8 0.20
39 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (36 bp):
ATTCTTAAGATGGCATGGGTCAGAACAAAAACTACT
Found at i:3039654 original size:2 final size:2
Alignment explanation
Indices: 3039647--3039681 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3039637 GAGATTTTCA
3039647 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 A
3039682 AACAAGCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3040885 original size:17 final size:19
Alignment explanation
Indices: 3040853--3040894 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
3040843 TTCTCTCTTT
*
3040853 TTTTTTAATTTATTTTTTA
1 TTTTTTAATTTATTTTGTA
3040872 TTTTTT-ATTT-TTTTGTA
1 TTTTTTAATTTATTTTGTA
3040889 TTTTTT
1 TTTTTT
3040895 CAAATAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.55
18 4 0.18
19 6 0.27
ACGTcount: A:0.14, C:0.00, G:0.02, T:0.83
Consensus pattern (19 bp):
TTTTTTAATTTATTTTGTA
Found at i:3041154 original size:16 final size:16
Alignment explanation
Indices: 3041121--3041170 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
3041111 ACAAAAACAA
*
3041121 AAATCACA-TATTTCAC
1 AAATCACATTATCT-AC
3041137 AAATCACATTATCTAC
1 AAATCACATTATCTAC
* *
3041153 AAAACA-ATTATGTAC
1 AAATCACATTATCTAC
3041168 AAA
1 AAA
3041171 GCAAATTTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
15 11 0.37
16 15 0.50
17 4 0.13
ACGTcount: A:0.50, C:0.20, G:0.02, T:0.28
Consensus pattern (16 bp):
AAATCACATTATCTAC
Found at i:3043798 original size:156 final size:156
Alignment explanation
Indices: 3043502--3043816 Score: 474
Period size: 156 Copynumber: 2.0 Consensus size: 156
3043492 TTTAACCTTC
* *
3043502 TTTTAGAATATAGGCACTTTACTTTTAAACAGGTAGTATGCTTTTTTAAGTATATTATCATGTAA
1 TTTTAGAATACAGGCACTTTACTTTTAAACAGGTAGTATGCATTTTTAAGTATATTATCATGTAA
* ** *
3043567 CCATTGAAATACTCTTGAGGATGTAACTTTCATACAACTTCCATTTCGATCCTCTACTTTTGGCA
66 CCATTGAAACACTCTTGAAAATGTAACTTTCATACAACCTCCATTTCGATCCTCTACTTTTGGCA
* *
3043632 ACCTCCCTCTCTTTAACTACTCATGG
131 ACCTCCCTCTCTCTAACTACCCATGG
*
3043658 TTTTGGAATACAGGCACTTTA-TTGTTAAACAGGTAGTATGCATTTTTAAGTATATTATCATGTA
1 TTTTAGAATACAGGCACTTTACTT-TTAAACAGGTAGTATGCATTTTTAAGTATATTATCATGTA
* *
3043722 ACCATTGAAACACTCTTGAAAATGTAACTTTCATACAACCTCCA-TTCTGATCTTTTACTTTTGG
65 ACCATTGAAACACTCTTGAAAATGTAACTTTCATACAACCTCCATTTC-GATCCTCTACTTTTGG
*
3043786 CAACC-CCTCTCTCTCTAGCTACCCATGG
129 CAACCTCC-CTCTCTCTAACTACCCATGG
3043814 TTT
1 TTT
3043817 ATGACATTTT
Statistics
Matches: 144, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
155 7 0.05
156 137 0.95
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (156 bp):
TTTTAGAATACAGGCACTTTACTTTTAAACAGGTAGTATGCATTTTTAAGTATATTATCATGTAA
CCATTGAAACACTCTTGAAAATGTAACTTTCATACAACCTCCATTTCGATCCTCTACTTTTGGCA
ACCTCCCTCTCTCTAACTACCCATGG
Found at i:3044401 original size:15 final size:15
Alignment explanation
Indices: 3044378--3044424 Score: 67
Period size: 16 Copynumber: 3.0 Consensus size: 15
3044368 TGATTATGGT
3044378 AAAGAAAAGAAAAAA
1 AAAGAAAAGAAAAAA
*
3044393 AATGAAAAGGAAAAAA
1 AAAGAAAA-GAAAAAA
3044409 AAAGAAAGAGAAAAAA
1 AAAGAAA-AGAAAAAA
3044425 GAGAAAGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 7 0.25
16 20 0.71
17 1 0.04
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (15 bp):
AAAGAAAAGAAAAAA
Found at i:3044686 original size:32 final size:34
Alignment explanation
Indices: 3044627--3044694 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 34
3044617 ATAATTGTAT
* *
3044627 TTAAAAATTATATATTTATATAAATTTTGATATA
1 TTAAAAATTATATATTTAGATAAATTTTAATATA
* *
3044661 TTAATAATT-TAT-TTTAGATAGATTTTAATATA
1 TTAAAAATTATATATTTAGATAAATTTTAATATA
3044693 TT
1 TT
3044695 CATTTATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 19 0.63
33 3 0.10
34 8 0.27
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (34 bp):
TTAAAAATTATATATTTAGATAAATTTTAATATA
Found at i:3044748 original size:28 final size:32
Alignment explanation
Indices: 3044717--3044779 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 32
3044707 TTATATTCGT
3044717 ATTAATTTTTC-TAATATGTT-ATATT-T-TA
1 ATTAATTTTTCTTAATATGTTGATATTATCTA
*
3044745 ATT-ATTTTTCTTATTATGTTGATATTATCTA
1 ATTAATTTTTCTTAATATGTTGATATTATCTA
3044776 ATTA
1 ATTA
3044780 TATAATTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
27 7 0.24
28 11 0.38
29 5 0.17
30 1 0.03
31 5 0.17
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (32 bp):
ATTAATTTTTCTTAATATGTTGATATTATCTA
Found at i:3047417 original size:3 final size:3
Alignment explanation
Indices: 3047409--3047435 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3047399 GTTTCCTCCA
3047409 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
3047436 TTTTTTGTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Done.