Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold132
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: 2458301
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 25 characters in sequence are not A, C, G, or T
File 14 of 15
Found at i:2256989 original size:27 final size:26
Alignment explanation
Indices: 2256959--2257017 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
2256949 ATTGAAAATA
*
2256959 TTATATATTCATATAATTTTGATTTAT
1 TTATATATTAATATAATTTTGATTT-T
** *
2256986 TTATATATTAATATCGTTTTTATTTT
1 TTATATATTAATATAATTTTGATTTT
2257012 TTATAT
1 TTATAT
2257018 TGTATTATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (26 bp):
TTATATATTAATATAATTTTGATTTT
Found at i:2259349 original size:10 final size:9
Alignment explanation
Indices: 2259332--2259410 Score: 65
Period size: 9 Copynumber: 9.0 Consensus size: 9
2259322 AAATAAATAA
2259332 TTTATATAT
1 TTTATATAT
2259341 TTTATTATAT
1 TTTA-TATAT
* *
2259351 TATAAATAT
1 TTTATATAT
* *
2259360 TTAAAATAT
1 TTTATATAT
2259369 TTTATAT-T
1 TTTATATAT
*
2259377 TATATATAT
1 TTTATATAT
2259386 TTTA-ATAT
1 TTTATATAT
* *
2259394 ATTA-ATAA
1 TTTATATAT
2259402 TTTATATAT
1 TTTATATAT
2259411 AAAATTTAAA
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
8 20 0.36
9 27 0.49
10 8 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TTTATATAT
Found at i:2259355 original size:28 final size:27
Alignment explanation
Indices: 2259324--2259396 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
2259314 TTAAATATAA
2259324 ATAAATAATTT-ATATATTTTATTATATT
1 ATAAATAATTTAATATATTTTA-TAT-TT
*
2259352 ATAAAT-ATTTAAAATATTTTATATTT
1 ATAAATAATTTAATATATTTTATATTT
* *
2259378 ATATATATTTTAATATATT
1 ATAAATAATTTAATATATT
2259397 AATAATTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
26 7 0.18
27 17 0.44
28 15 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
ATAAATAATTTAATATATTTTATATTT
Found at i:2259377 original size:16 final size:16
Alignment explanation
Indices: 2259356--2259415 Score: 52
Period size: 16 Copynumber: 3.7 Consensus size: 16
2259346 TATATTATAA
2259356 ATATTTAAAATATTTT
1 ATATTTAAAATATTTT
*
2259372 ATATTTATATATATTTT
1 ATATTTA-AAATATTTT
*
2259389 AATATATT--AATAATTT
1 -ATAT-TTAAAATATTTT
*
2259405 ATATATAAAAT
1 ATATTTAAAAT
2259416 TTAAAATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
14 1 0.03
15 4 0.11
16 16 0.46
17 8 0.23
18 4 0.11
19 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATTTAAAATATTTT
Found at i:2259419 original size:29 final size:30
Alignment explanation
Indices: 2259345--2259436 Score: 102
Period size: 27 Copynumber: 3.1 Consensus size: 30
2259335 ATATATTTTA
*
2259345 TTATATTATAAATATTTAAAATATT-TTATAT
1 TTATA-TATAAA-ATTTAAAATATTAATATAT
* *
2259376 TTATATAT--ATTTTAATATATTAATA-AT
1 TTATATATAAAATTTAAAATATTAATATAT
*
2259403 TTATATATAAAATTTAAAATATTAATATAA
1 TTATATATAAAATTTAAAATATTAATATAT
2259433 TTAT
1 TTAT
2259437 TTTTATTTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
27 20 0.39
28 3 0.06
29 15 0.29
30 8 0.16
31 5 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
TTATATATAAAATTTAAAATATTAATATAT
Found at i:2259465 original size:18 final size:17
Alignment explanation
Indices: 2259365--2259470 Score: 64
Period size: 18 Copynumber: 6.5 Consensus size: 17
2259355 AATATTTAAA
*
2259365 ATATTTTATATTTATAT
1 ATATTTTATATATATAT
2259382 ATATTTTA-ATATAT-T
1 ATATTTTATATATATAT
*
2259397 AATAATTTATATATA-A-
1 -ATATTTTATATATATAT
* *
2259413 A-ATTTAAAATAT-TA-
1 ATATTTTATATATATAT
* * * *
2259427 ATATAATTATTTTTATTT
1 ATAT-TTTATATATATAT
2259445 ATATTATTATATATATAT
1 ATATT-TTATATATATAT
2259463 ATATTTTA
1 ATATTTTA
2259471 ATTTTTTTCT
Statistics
Matches: 65, Mismatches: 15, Indels: 18
0.66 0.15 0.18
Matches are distributed among these distances:
14 10 0.15
15 4 0.06
16 16 0.25
17 17 0.26
18 18 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATATTTTATATATATAT
Found at i:2261182 original size:4 final size:4
Alignment explanation
Indices: 2261175--2261212 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
2261165 TATATATATA
*
2261175 TATG TATG TATG TATG TATC TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
2261213 CATTAATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.26, C:0.03, G:0.21, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:2262939 original size:2 final size:2
Alignment explanation
Indices: 2262932--2262969 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2262922 GGAACTGGAA
2262932 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2262970 GTGTGTGTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2262974 original size:2 final size:2
Alignment explanation
Indices: 2262969--2263011 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2262959 TATATATATA
2262969 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2263011 T
1 T
2263012 TAAATGTAAG
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:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:2265148 original size:21 final size:21
Alignment explanation
Indices: 2265123--2265163 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2265113 TTTTAACATG
2265123 ATATA-AAATA-ATAATATAT
1 ATATATAAATATATAATATAT
*
2265142 ATATATAAATATATATTATAT
1 ATATATAAATATATAATATAT
2265163 A
1 A
2265164 ATTGAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 5 0.26
21 9 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATATATAAATATATAATATAT
Found at i:2265154 original size:14 final size:15
Alignment explanation
Indices: 2265135--2265164 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2265125 ATAAAATAAT
2265135 AATATATA-TATATA
1 AATATATATTATATA
2265149 AATATATATTATATA
1 AATATATATTATATA
2265164 A
1 A
2265165 TTGAAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATATATATTATATA
Found at i:2267266 original size:2 final size:2
Alignment explanation
Indices: 2267261--2267293 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2267251 ATTTTTTTTC
2267261 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2267294 TACTATGATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2268083 original size:2 final size:2
Alignment explanation
Indices: 2268071--2268106 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2268061 AATTAAATCT
* *
2268071 TA TA AA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2268107 AGTAACAATT
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:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2268843 original size:24 final size:23
Alignment explanation
Indices: 2268800--2268845 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
2268790 TTTTATAAAG
*
2268800 TTTAAAAATTTAAAAGTTAAAAT
1 TTTAAAAATTTAAAAATTAAAAT
*
2268823 TTTAATAATTATAAAAATTAAAA
1 TTTAAAAATT-TAAAAATTAAAA
2268846 AATATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
TTTAAAAATTTAAAAATTAAAAT
Found at i:2268873 original size:20 final size:20
Alignment explanation
Indices: 2268850--2268892 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
2268840 TTAAAAAATA
*
2268850 TATATATAAAAGTAATTTTT
1 TATAAATAAAAGTAATTTTT
** *
2268870 TATAAATTTAATTAATTTTT
1 TATAAATAAAAGTAATTTTT
2268890 TAT
1 TAT
2268893 TTTTATATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TATAAATAAAAGTAATTTTT
Found at i:2280135 original size:2 final size:2
Alignment explanation
Indices: 2280128--2280177 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
2280118 TCAATAGAAA
2280128 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2280170 GT AT AT AT
1 AT AT AT AT
2280178 CACCTTCATT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2280785 original size:14 final size:15
Alignment explanation
Indices: 2280766--2280798 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
2280756 ATTATTAAAA
2280766 AATATTTAAATAT-T
1 AATATTTAAATATAT
2280780 AATATTTAAATATAT
1 AATATTTAAATATAT
2280795 AATA
1 AATA
2280799 AAAATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATATTTAAATATAT
Found at i:2281173 original size:43 final size:45
Alignment explanation
Indices: 2281069--2281173 Score: 112
Period size: 44 Copynumber: 2.4 Consensus size: 45
2281059 ATAATATTAA
*
2281069 AAAATAT-AAAATTTTTATATTAATATTTATAATTAAATTTAAAT
1 AAAATATAAAAATTATTATATTAATATTTATAATTAAATTTAAAT
*** *
2281113 AAAA-ATAATTTTTTATTATA-TAATAATTTA-AATTAAA-TTAATT
1 AAAATATAA-AAATTATTATATTAAT-ATTTATAATTAAATTTAAAT
2281156 AAAATATAAAAATTATTA
1 AAAATATAAAAATTATTA
2281174 CTTAAATATG
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
43 17 0.35
44 20 0.41
45 12 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (45 bp):
AAAATATAAAAATTATTATATTAATATTTATAATTAAATTTAAAT
Found at i:2281826 original size:2 final size:2
Alignment explanation
Indices: 2281819--2281846 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2281809 TAAGCAAATA
2281819 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2281847 GACATTTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2282908 original size:19 final size:19
Alignment explanation
Indices: 2282884--2282941 Score: 89
Period size: 19 Copynumber: 3.0 Consensus size: 19
2282874 ATCAAACACA
2282884 AATAAATTTAAAATAAATT
1 AATAAATTTAAAATAAATT
*
2282903 AATAAATATAAAATAAATT
1 AATAAATTTAAAATAAATT
*
2282922 AATAAATATAAAAATAAATT
1 AATAAAT-TTAAAATAAATT
2282942 TATTTTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
19 25 0.71
20 10 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AATAAATTTAAAATAAATT
Found at i:2283175 original size:2 final size:2
Alignment explanation
Indices: 2283168--2283202 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2283158 AAACCCACCC
2283168 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2283203 ATTTTTCCCA
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:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:2283731 original size:15 final size:15
Alignment explanation
Indices: 2283706--2283744 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
2283696 CTGGGATTTC
* *
2283706 TTTTCTCTTCTTGGT
1 TTTTCTTTTCTGGGT
*
2283721 TTTTGTTTTCTGGGT
1 TTTTCTTTTCTGGGT
2283736 TTTTCTTTT
1 TTTTCTTTT
2283745 TCCCATGATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.00, C:0.13, G:0.15, T:0.72
Consensus pattern (15 bp):
TTTTCTTTTCTGGGT
Found at i:2288324 original size:2 final size:2
Alignment explanation
Indices: 2288317--2288341 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2288307 GCATGCCATT
2288317 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
2288342 GGATGTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2289356 original size:2 final size:2
Alignment explanation
Indices: 2289349--2289380 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2289339 AAATTCAACC
*
2289349 TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2289381 CTTACATATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2290930 original size:13 final size:12
Alignment explanation
Indices: 2290912--2291010 Score: 58
Period size: 12 Copynumber: 8.1 Consensus size: 12
2290902 ATATTTGAGA
2290912 ATAAATATCATAT
1 ATAAATAT-ATAT
2290925 ATAAATATATAT
1 ATAAATATATAT
*
2290937 -TGAATATATGTAT
1 AT-AA-ATATATAT
* * *
2290950 ATTTAAT-TCTTT
1 A-TAAATATATAT
* * *
2290962 TTAAGTTTATAT
1 ATAAATATATAT
*
2290974 ATATATATATAT
1 ATAAATATATAT
*
2290986 ATATATATATAT
1 ATAAATATATAT
*
2290998 ATATATATATAT
1 ATAAATATATAT
2291010 A
1 A
2291011 CACACACGAA
Statistics
Matches: 68, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
11 4 0.06
12 45 0.66
13 17 0.25
14 1 0.01
15 1 0.01
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.49
Consensus pattern (12 bp):
ATAAATATATAT
Found at i:2290976 original size:2 final size:2
Alignment explanation
Indices: 2290969--2291010 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2290959 TTTTTAAGTT
2290969 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2291011 CACACACGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2292847 original size:66 final size:66
Alignment explanation
Indices: 2292769--2292900 Score: 183
Period size: 66 Copynumber: 2.0 Consensus size: 66
2292759 TGCCACGGCG
** ** * *
2292769 GCAGGAGCTTCAGGCTGTGGTGGATCAGCACCATCATCGTCATCCTCCGGGCCACTTGCGGTGGC
1 GCAGGAGCTTCAGGCAATGGTAAATCAGAACCATCATCATCATCCTCCGGGCCACTTGCGGTGGC
2292834 A
66 A
* * *
2292835 GCAGGGGCTTCAGGCAATGGTAAATCAGAACCATCATCATCATCCTCTGGGCCACTTGGGGTGGC
1 GCAGGAGCTTCAGGCAATGGTAAATCAGAACCATCATCATCATCCTCCGGGCCACTTGCGGTGGC
2292900 A
66 A
2292901 CTGGCAGCAG
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.20, C:0.28, G:0.30, T:0.21
Consensus pattern (66 bp):
GCAGGAGCTTCAGGCAATGGTAAATCAGAACCATCATCATCATCCTCCGGGCCACTTGCGGTGGC
A
Found at i:2295649 original size:15 final size:13
Alignment explanation
Indices: 2295623--2295661 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
2295613 ATCAAATATG
2295623 AATAATTATATTTA
1 AATAA-TATATTTA
2295637 ATATTAATATATTTA
1 A-A-TAATATATTTA
2295652 AATAATATAT
1 AATAATATAT
2295662 ATATATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 8 0.35
14 2 0.09
15 10 0.43
16 3 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
AATAATATATTTA
Found at i:2301395 original size:3 final size:3
Alignment explanation
Indices: 2301387--2301426 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2301377 TTTATACTTC
2301387 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2301427 GTATAAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2301766 original size:29 final size:29
Alignment explanation
Indices: 2301733--2301801 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
2301723 TTTAATTACA
*
2301733 AAATTAAATAATAATATTGAGATATTAAAT
1 AAATTAAATAATAA-ATTGAAATATTAAAT
* * *
2301763 -AATTAATTAATAAATTTAAATTTTAAAT
1 AAATTAAATAATAAATTGAAATATTAAAT
*
2301791 AAATTAGATAA
1 AAATTAAATAA
2301802 ATTCAACCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
28 12 0.38
29 20 0.62
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (29 bp):
AAATTAAATAATAAATTGAAATATTAAAT
Found at i:2302135 original size:24 final size:25
Alignment explanation
Indices: 2302090--2302136 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
2302080 TAAGCTTTTT
* * *
2302090 TTTTTTTTTTTTTTTCCTATTTCCC
1 TTTTGTTTTCTTTTTCCGATTTCCC
2302115 TTTTGTTTTCTTTTT-CGATTTC
1 TTTTGTTTTCTTTTTCCGATTTC
2302137 TTCAGTGGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 6 0.32
25 13 0.68
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.74
Consensus pattern (25 bp):
TTTTGTTTTCTTTTTCCGATTTCCC
Found at i:2304861 original size:16 final size:17
Alignment explanation
Indices: 2304842--2304898 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 17
2304832 TTCGGATTTA
2304842 AAATGAATT-AAACTTG
1 AAATGAATTCAAACTTG
*
2304858 AAATG-ATTCAAATTTG
1 AAATGAATTCAAACTTG
2304874 AAATG-ATTCAAA-TATG
1 AAATGAATTCAAACT-TG
*
2304890 AAATAAATT
1 AAATGAATT
2304899 TGAATTTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
15 4 0.11
16 29 0.81
17 3 0.08
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.33
Consensus pattern (17 bp):
AAATGAATTCAAACTTG
Found at i:2304892 original size:32 final size:31
Alignment explanation
Indices: 2304826--2304920 Score: 84
Period size: 32 Copynumber: 2.9 Consensus size: 31
2304816 TTTAAATTCA
* *
2304826 AAATGATTCGGATTTAAAATGAATTAAACT-TG
1 AAATGATTCGAATTTGAAATG-ATTAAA-TATG
*
2304858 AAATGATTCAAATTTGAAATGATTCAAATATG
1 AAATGATTCGAATTTGAAATGATT-AAATATG
* * *
2304890 AAATAAATTTGAATTTGAAATTATTTAAATA
1 AAAT-GATTCGAATTTGAAATGA-TTAAATA
2304921 ATTAACTCAA
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
31 4 0.08
32 27 0.52
33 19 0.37
34 2 0.04
ACGTcount: A:0.47, C:0.04, G:0.12, T:0.37
Consensus pattern (31 bp):
AAATGATTCGAATTTGAAATGATTAAATATG
Found at i:2304984 original size:15 final size:15
Alignment explanation
Indices: 2304964--2304995 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2304954 GAGTTTGATA
*
2304964 AACTTAATTGATTTG
1 AACTTAATTGATATG
2304979 AACTTAATTGATATG
1 AACTTAATTGATATG
2304994 AA
1 AA
2304996 TTCGGCTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (15 bp):
AACTTAATTGATATG
Found at i:2305891 original size:2 final size:2
Alignment explanation
Indices: 2305884--2305911 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2305874 AAAATAATAC
2305884 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2305912 GTCTGTACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2308518 original size:28 final size:28
Alignment explanation
Indices: 2308486--2308555 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
2308476 TAGTGAAAAA
* *
2308486 AGTATTTTAATTTTATACTATTAAATTC
1 AGTATTTTAATCTCATACTATTAAATTC
2308514 AGTATTTTAATCTCATACTATTAAATTC
1 AGTATTTTAATCTCATACTATTAAATTC
2308542 AGTATTTTAATCTC
1 AGTATTTTAATCTC
2308556 TATGTTTTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.34, C:0.11, G:0.04, T:0.50
Consensus pattern (28 bp):
AGTATTTTAATCTCATACTATTAAATTC
Found at i:2308523 original size:14 final size:14
Alignment explanation
Indices: 2308506--2308551 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
2308496 TTTTATACTA
2308506 TTAAATTCAGTATT
1 TTAAATTCAGTATT
*
2308520 TT-AATCTCA-TACTA
1 TTAAAT-TCAGTA-TT
2308534 TTAAATTCAGTATT
1 TTAAATTCAGTATT
2308548 TTAA
1 TTAA
2308552 TCTCTATGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
13 5 0.19
14 16 0.62
15 5 0.19
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.48
Consensus pattern (14 bp):
TTAAATTCAGTATT
Found at i:2310727 original size:14 final size:14
Alignment explanation
Indices: 2310705--2310749 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
2310695 TTTGAGAATG
*
2310705 TTAAAAATTAAACT
1 TTAAAAATTAAAAT
*
2310719 TTAATAATTAAAAT
1 TTAAAAATTAAAAT
*
2310733 TAAAAAATTAAATAT
1 TTAAAAATTAAA-AT
2310748 TT
1 TT
2310750 TATTAACGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 22 0.88
15 3 0.12
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
TTAAAAATTAAAAT
Found at i:2312460 original size:25 final size:25
Alignment explanation
Indices: 2312389--2312484 Score: 88
Period size: 25 Copynumber: 3.6 Consensus size: 25
2312379 AAAAGTTTAA
*
2312389 AATTAAATTTAAATATAAATTTTTTT
1 AATT-AATTTAAATATAAATTTATTT
*
2312415 AATTCAAATTAAAT-TAAATTTATTT
1 AATT-AATTTAAATATAAATTTATTT
*
2312440 AATT-TTTTAAATATAATATTTATTT
1 AATTAATTTAAATATAA-ATTTATTT
2312465 AAATTTAATTATAAAATATA
1 -AA-TTAATT-T-AAATATA
2312485 TAAAATATTA
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
23 6 0.11
24 3 0.05
25 22 0.39
26 14 0.25
27 2 0.04
28 2 0.04
29 1 0.02
30 7 0.12
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (25 bp):
AATTAATTTAAATATAAATTTATTT
Found at i:2313788 original size:2 final size:2
Alignment explanation
Indices: 2313783--2313815 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2313773 ATATATATAT
2313783 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2313816 TGTGGATACG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2314766 original size:20 final size:21
Alignment explanation
Indices: 2314743--2314787 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
2314733 TAATATTTTT
2314743 TATTTAA-ATTTAATTATAAA
1 TATTTAATATTTAATTATAAA
**
2314763 TA-TTAATATTTTTTTATAAA
1 TATTTAATATTTAATTATAAA
2314783 -ATTTA
1 TATTTA
2314788 TAATACTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTTAATATTTAATTATAAA
Found at i:2315060 original size:13 final size:13
Alignment explanation
Indices: 2315033--2315074 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
2315023 ACACTTCAAC
2315033 TTTTTAAATATTAA
1 TTTTTAAATA-TAA
2315047 TTTTTAAATATAA
1 TTTTTAAATATAA
*
2315060 TTATATAAA-ATAA
1 TT-TTTAAATATAA
2315073 TT
1 TT
2315075 AAATTAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTTTAAATATAA
Found at i:2315808 original size:22 final size:22
Alignment explanation
Indices: 2315781--2315824 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2315771 TAAAAGTAAT
2315781 TATATTTTTA-TATTAATATTTA
1 TATATTTTTATTATTAA-ATTTA
2315803 TATATTTTTATTATTAAATTTA
1 TATATTTTTATTATTAAATTTA
2315825 AATTAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TATATTTTTATTATTAAATTTA
Found at i:2315857 original size:29 final size:30
Alignment explanation
Indices: 2315802--2315861 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
2315792 ATTAATATTT
*
2315802 ATATATTTTTATTATTAAATTTAAATTAAA
1 ATATATTTTTATTATTAAATATAAATTAAA
*
2315832 ATAT-TTTTTATTATTAAATAATAATTTAAA
1 ATATATTTTTATTATTAAAT-ATAAATTAAA
2315862 TTAAATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
ATATATTTTTATTATTAAATATAAATTAAA
Found at i:2315862 original size:29 final size:28
Alignment explanation
Indices: 2315794--2315862 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 28
2315784 ATTTTTATAT
*
2315794 TAAT-ATTTATATATTTTTATTATTAAA
1 TAATAATTTAAATATTTTTATTATTAAA
* *
2315821 T-TTAAATTAAAATATTTTTTATTATTAAA
1 TAAT-AATTTAAATA-TTTTTATTATTAAA
2315850 TAATAATTTAAAT
1 TAATAATTTAAAT
2315863 TAAATTAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
26 1 0.03
27 1 0.03
28 7 0.21
29 23 0.70
30 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
TAATAATTTAAATATTTTTATTATTAAA
Found at i:2315867 original size:5 final size:5
Alignment explanation
Indices: 2315857--2315915 Score: 52
Period size: 5 Copynumber: 12.2 Consensus size: 5
2315847 AAATAATAAT
** *
2315857 TTAAA TTAAA TTAAA TT-AA TTTTA TATAAA TTAAA TT-TA TTAAA TTAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA T-TAAA TTAAA TTAAA TTAAA TTAAA
*
2315906 TCAAA -TAAA T
1 TTAAA TTAAA T
2315916 AGATTTAAAG
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
4 10 0.23
5 30 0.70
6 3 0.07
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (5 bp):
TTAAA
Found at i:2315876 original size:20 final size:20
Alignment explanation
Indices: 2315853--2315911 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
2315843 TATTAAATAA
2315853 TAATTTAAATTAAATTAAAT
1 TAATTTAAATTAAATTAAAT
*
2315873 TAATTT-TATATAAATTAAAT
1 TAATTTAAAT-TAAATTAAAT
* *
2315893 TTA-TTAAATTAAATCAAAT
1 TAATTTAAATTAAATTAAAT
2315912 AAATAGATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
19 13 0.39
20 20 0.61
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
TAATTTAAATTAAATTAAAT
Found at i:2315886 original size:15 final size:14
Alignment explanation
Indices: 2315866--2315906 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 14
2315856 TTTAAATTAA
*
2315866 ATTAAATTAATTTT
1 ATTAAATTAAATTT
2315880 ATATAAATTAAATTT
1 AT-TAAATTAAATTT
2315895 ATTAAATTAAAT
1 ATTAAATTAAAT
2315907 CAAATAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTAAATTAAATTT
Found at i:2316598 original size:22 final size:22
Alignment explanation
Indices: 2316556--2316601 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2316546 TAAATAAAAA
*
2316556 TATTAATAAATTTATATATATT
1 TATTAATAAATTTATAAATATT
*
2316578 TATTAAT-ATTTTATAAAATATT
1 TATTAATAAATTTAT-AAATATT
2316600 TA
1 TA
2316602 AAAATAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TATTAATAAATTTATAAATATT
Found at i:2317279 original size:23 final size:22
Alignment explanation
Indices: 2317253--2317295 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
2317243 AAATAATATT
2317253 AAATATTTATATACATAAATTAG
1 AAATATTTATA-ACATAAATTAG
* *
2317276 AAATGTTTATAACTTAAATT
1 AAATATTTATAACATAAATT
2317296 TTTATTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.42
Consensus pattern (22 bp):
AAATATTTATAACATAAATTAG
Found at i:2317716 original size:32 final size:32
Alignment explanation
Indices: 2317674--2317734 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
2317664 TTATTTCATT
*
2317674 TAATACATTTAGTT-TATTAAATTTTTAAAAAG
1 TAATACATTTAATTATA-TAAATTTTTAAAAAG
* *
2317706 TAATTCATTTAATTATATATATTTTTAAA
1 TAATACATTTAATTATATAAATTTTTAAA
2317735 TATTATCTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 23 0.92
33 2 0.08
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (32 bp):
TAATACATTTAATTATATAAATTTTTAAAAAG
Found at i:2318268 original size:18 final size:18
Alignment explanation
Indices: 2318245--2318281 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2318235 CTAAAAGAAA
* *
2318245 TTTTATATTATTTCATTT
1 TTTTATATAATTTAATTT
2318263 TTTTATATAATTTAATTT
1 TTTTATATAATTTAATTT
2318281 T
1 T
2318282 ATGCATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTATATAATTTAATTT
Found at i:2318763 original size:50 final size:50
Alignment explanation
Indices: 2318704--2318962 Score: 356
Period size: 50 Copynumber: 5.2 Consensus size: 50
2318694 TATACTTAGA
* *
2318704 GTCAACAATTATGACCACCTCCCTCTATTGTCAAAGGTTGGTAAAAAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAAAATC
*
2318754 GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAAAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAAAATC
* *
2318804 GTCAACAATTATGGCTACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAAAATC
* * * * * *
2318854 GTCAACAATAATAGCCACATCTCTCTATTATCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAAAATC
* * * * ** *
2318904 GTCAACAATAATGGTCACCTCTCTTTATTGTCAAAGGTTGGTGAAGGATA
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAAAATC
2318954 GTCAACAAT
1 GTCAACAAT
2318963 GGCAACAACT
Statistics
Matches: 190, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 190 1.00
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAAAATC
Found at i:2321237 original size:15 final size:15
Alignment explanation
Indices: 2321217--2321252 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
2321207 GCATAGCTCT
*
2321217 AGTTCTTTGGAGTAG
1 AGTTCTTTCGAGTAG
2321232 AGTTCTTTCGAGTAG
1 AGTTCTTTCGAGTAG
2321247 AGTTCT
1 AGTTCT
2321253 ATTCATCCGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.19, C:0.11, G:0.28, T:0.42
Consensus pattern (15 bp):
AGTTCTTTCGAGTAG
Found at i:2323432 original size:50 final size:50
Alignment explanation
Indices: 2323373--2323617 Score: 357
Period size: 50 Copynumber: 4.9 Consensus size: 50
2323363 TATACTTATA
* *
2323373 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTAAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
2323423 GTCAACAATTATGGTCACCTCTTTCTATTGTTAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
2323473 GTCAACAATTATGGCCTCCT-TCTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTC-TCTATTGTCAAAGGTTGGTGAAGAATC
*
2323523 GTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * * * * *
2323573 GTCAACAATAATGGTCACATCTCTTTATTGTTAAAGGTTGATGAA
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAA
2323618 AGATAGTCAA
Statistics
Matches: 177, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
49 1 0.01
50 174 0.98
51 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:2326794 original size:24 final size:24
Alignment explanation
Indices: 2326767--2326856 Score: 74
Period size: 25 Copynumber: 3.6 Consensus size: 24
2326757 ATTTTATTTA
*
2326767 AATTATTATTAAATTAATAAAAAT
1 AATTTTTATTAAATTAATAAAAAT
* * *
2326791 AATTTTTATTTAAATTTATATAAGT
1 AATTTTTA-TTAAATTAATAAAAAT
* *
2326816 AA-ATTTATAAATATTAATATAAAAAT
1 AATTTTTATTAA-ATT-A-ATAAAAAT
*
2326842 AATTTTTAATAAATT
1 AATTTTTATTAAATT
2326857 TTAAATAATA
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
23 3 0.06
24 14 0.29
25 15 0.31
26 11 0.22
27 6 0.12
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (24 bp):
AATTTTTATTAAATTAATAAAAAT
Found at i:2326877 original size:28 final size:27
Alignment explanation
Indices: 2326815--2326878 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 27
2326805 TTTATATAAG
2326815 TAAATTT-ATAAATATTAATATAAAAA
1 TAAATTTAATAAATATTAATATAAAAA
* *
2326841 TAATTTTTAATAAATTTTAA-ATAATAAAA
1 TAA-ATTTAATAAATATTAATAT-A-AAAA
2326870 TAAATTTAA
1 TAAATTTAA
2326879 ATCCACCTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 3 0.10
27 5 0.16
28 16 0.52
29 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
TAAATTTAATAAATATTAATATAAAAA
Found at i:2327239 original size:17 final size:17
Alignment explanation
Indices: 2327217--2327250 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2327207 TAAATATAGG
*
2327217 TTAAAACATTAAATTTT
1 TTAAAAAATTAAATTTT
2327234 TTAAAAAATTAAATTTT
1 TTAAAAAATTAAATTTT
2327251 ATTTGTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAAAAATTAAATTTT
Found at i:2327666 original size:29 final size:29
Alignment explanation
Indices: 2327633--2327698 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
2327623 AGTCTTTAAA
*
2327633 TTATTTTTTTAAAATAAATT-TTTATACTT
1 TTATTTATTT-AAATAAATTATTTATACTT
* *
2327662 TTATTATATTTAAATAATTTATTTATATTT
1 TTATT-TATTTAAATAAATTATTTATACTT
2327692 TTATTTA
1 TTATTTA
2327699 GATAAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (29 bp):
TTATTTATTTAAATAAATTATTTATACTT
Found at i:2327704 original size:29 final size:30
Alignment explanation
Indices: 2327644--2327714 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 30
2327634 TATTTTTTTA
* **
2327644 AAATAAATT-TTTATACTTTTATTATATTT
1 AAATAATTTATTTATACTTTTATTATAGAT
*
2327673 AAATAATTTATTTATATTTTTATT-TAGAT
1 AAATAATTTATTTATACTTTTATTATAGAT
*
2327702 AAAT-TTTTATTTA
1 AAATAATTTATTTA
2327715 AAATAAAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 8 0.22
29 15 0.42
30 13 0.36
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (30 bp):
AAATAATTTATTTATACTTTTATTATAGAT
Found at i:2327720 original size:17 final size:16
Alignment explanation
Indices: 2327688--2327721 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2327678 ATTTATTTAT
*
2327688 ATTTTTATTTAGATAA
1 ATTTTTATTTAAATAA
2327704 ATTTTTATTTAAAATAA
1 ATTTTTATTT-AAATAA
2327721 A
1 A
2327722 ATATGAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
ATTTTTATTTAAATAA
Found at i:2327916 original size:21 final size:21
Alignment explanation
Indices: 2327876--2327931 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
2327866 CATTATTATT
* *
2327876 TTAATAAAAAATTATTTAAAT-
1 TTAATATAAAA-TATATAAATA
*
2327897 TTAATTTTAAAATATATAAATA
1 TTAA-TATAAAATATATAAATA
2327919 TTAATATAAAATA
1 TTAATATAAAATA
2327932 ATATTTTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 20 0.69
22 9 0.31
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TTAATATAAAATATATAAATA
Found at i:2328614 original size:6 final size:6
Alignment explanation
Indices: 2328603--2328640 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
2328593 GATTATCACC
* *
2328603 ATATAT ATATAT ATATGT ATATGT ATATGT ATATGT AT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT AT
2328641 GTAAATATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (6 bp):
ATATGT
Found at i:2329203 original size:2 final size:2
Alignment explanation
Indices: 2329196--2329235 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2329186 AAGTTAGTGT
2329196 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2329236 GAGAGAGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2329240 original size:2 final size:2
Alignment explanation
Indices: 2329235--2329273 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2329225 ATATATATAT
2329235 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2329274 TGTGGATACG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2330236 original size:19 final size:19
Alignment explanation
Indices: 2330172--2330258 Score: 63
Period size: 19 Copynumber: 4.6 Consensus size: 19
2330162 CCTTAATGAT
* *
2330172 TATTTTAAATAATAATAAA
1 TATTTTAAATATTAATATA
** *
2330191 TATTTTTTAT-TTAA-ATT
1 TATTTTAAATATTAATATA
*
2330208 TACTTATAAATATTAATATA
1 TA-TTTTAAATATTAATATA
*
2330228 TATTTTAAA-ATTTATAATA
1 TATTTTAAATATTAAT-ATA
2330247 TTATTTTAAATA
1 -TATTTTAAATA
2330259 ATAAAAATAA
Statistics
Matches: 51, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
17 3 0.06
18 13 0.25
19 21 0.41
20 13 0.25
21 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTTTAAATATTAATATA
Found at i:2330238 original size:20 final size:20
Alignment explanation
Indices: 2330215--2330256 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2330205 ATTTACTTAT
2330215 AAATAT-TAATATATATTTTA
1 AAATATATAATAT-TATTTTA
*
2330235 AAATTTATAATATTATTTTA
1 AAATATATAATATTATTTTA
2330255 AA
1 AA
2330257 TAATAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AAATATATAATATTATTTTA
Found at i:2330493 original size:31 final size:31
Alignment explanation
Indices: 2330428--2330488 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
2330418 CTTAAATCGA
2330428 TTAAAAATTTAAATTATTATTTATAAATTAAT
1 TTAAAAA-TTAAATTATTATTTATAAATTAAT
* *
2330460 TTAAAAA-TAAATTA-TATTTTTATATTAAT
1 TTAAAAATTAAATTATTATTTATAAATTAAT
2330489 ATTTATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 13 0.48
30 7 0.26
32 7 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
TTAAAAATTAAATTATTATTTATAAATTAAT
Found at i:2330499 original size:22 final size:22
Alignment explanation
Indices: 2330472--2330515 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2330462 AAAAATAAAT
2330472 TATATTTTTA-TATTAATATTTA
1 TATATTTTTATTATTAA-ATTTA
2330494 TATATTTTTATTATTAAATTTA
1 TATATTTTTATTATTAAATTTA
2330516 AATTAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TATATTTTTATTATTAAATTTA
Found at i:2330588 original size:39 final size:38
Alignment explanation
Indices: 2330502--2330601 Score: 100
Period size: 39 Copynumber: 2.6 Consensus size: 38
2330492 TATATATTTT
*
2330502 TATTATTAAATTTAAATTAAA-AATGTTTTATTATTAAA
1 TATTATTAAA-TTAAATTAAATAATGTTTTATAATTAAA
*
2330540 TAATAATTAAATTAAATTAAATTAAT-TTTATATAAATTAAA
1 T-ATTATTAAATTAAATTAAA-TAATGTTT-TAT-AATTAAA
*
2330581 T-TTATTAAATCAAA-TAAATAA
1 TATTATTAAATTAAATTAAATAA
2330602 GTAGATTTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
37 3 0.06
38 15 0.28
39 22 0.42
40 6 0.11
41 7 0.13
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (38 bp):
TATTATTAAATTAAATTAAATAATGTTTTATAATTAAA
Found at i:2332875 original size:6 final size:6
Alignment explanation
Indices: 2332864--2332892 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2332854 AAAATCATAA
2332864 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
2332893 ACTTGATTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:2336354 original size:28 final size:30
Alignment explanation
Indices: 2336298--2336355 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
2336288 ATAATATTAT
*
2336298 AATTATTTATATATTGATTAAATTCAATTAAA
1 AATTATTTATATATTGAATAAA-T-AATTAAA
2336330 AATTATTTATATATT-AATAAA-AATTA
1 AATTATTTATATATTGAATAAATAATTA
2336356 TATAACTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 5 0.20
31 5 0.20
32 15 0.60
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (30 bp):
AATTATTTATATATTGAATAAATAATTAAA
Found at i:2336627 original size:2 final size:2
Alignment explanation
Indices: 2336620--2336649 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2336610 AACTATATGA
2336620 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2336650 CATTCAATCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2338472 original size:2 final size:2
Alignment explanation
Indices: 2338465--2338511 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2338455 AAGATGTAAA
2338465 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2338507 TC TC T
1 TC TC T
2338512 TGTTTCTTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2340079 original size:19 final size:20
Alignment explanation
Indices: 2340049--2340088 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
2340039 TTTAGGGATA
2340049 CATATCTTCATATTCATGTT
1 CATATCTTCATATTCATGTT
*
2340069 CATAT-TTCATATTTATGTT
1 CATATCTTCATATTCATGTT
2340088 C
1 C
2340089 GAGTGTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.25, C:0.17, G:0.05, T:0.53
Consensus pattern (20 bp):
CATATCTTCATATTCATGTT
Found at i:2341368 original size:18 final size:20
Alignment explanation
Indices: 2341342--2341379 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
2341332 ATAAGGTCAC
*
2341342 AATTTTTCTT-GC-AAAATT
1 AATTGTTCTTAGCTAAAATT
2341360 AATTGTTCTTAGCTAAAATT
1 AATTGTTCTTAGCTAAAATT
2341380 CAAGTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 2 0.12
20 6 0.35
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (20 bp):
AATTGTTCTTAGCTAAAATT
Found at i:2342152 original size:3 final size:3
Alignment explanation
Indices: 2342146--2342179 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2342136 TTAATATCAA
2342146 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2342180 GTGATCAGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2342441 original size:71 final size:70
Alignment explanation
Indices: 2342349--2342501 Score: 270
Period size: 71 Copynumber: 2.1 Consensus size: 70
2342339 GTCCCCCCCC
*
2342349 AAAAAAAAAACAAACAAATGATGAAAAGTATTTTTCTATGATTCTAAACAAATATTTTTCTTTTT
1 AAAAAAAAAACAAACAAATGATGAAAAGTATTTTTCTATGATTCTAAACAAATATTTTTCTTGTT
2342414 CAAAA
66 CAAAA
2342419 AAAAAAACAAACAAACAAATGATGAAAAGTATTTTTCTATGATTCTAAACAAATATTTTTCTTGT
1 AAAAAAA-AAACAAACAAATGATGAAAAGTATTTTTCTATGATTCTAAACAAATATTTTTCTTGT
2342484 TCAACAA
65 TCAA-AA
2342491 AAAAAATAAAA
1 AAAAAA-AAAA
2342502 AGATGCCTTT
Statistics
Matches: 79, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
70 7 0.09
71 60 0.76
72 11 0.14
73 1 0.01
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.31
Consensus pattern (70 bp):
AAAAAAAAAACAAACAAATGATGAAAAGTATTTTTCTATGATTCTAAACAAATATTTTTCTTGTT
CAAAA
Found at i:2342974 original size:16 final size:16
Alignment explanation
Indices: 2342920--2342974 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
2342910 ATTTAAAAAT
2342920 ATTTTATATT-TATATA
1 ATTTTATATTATATA-A
* *
2342936 ATTTT-TAATACATTAA
1 ATTTTATATTATA-TAA
2342952 ATATTTATATTATATAA
1 AT-TTTATATTATATAA
2342969 ATTTTA
1 ATTTTA
2342975 AAATATGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
15 3 0.10
16 13 0.42
17 10 0.32
18 5 0.16
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTTATATTATATAA
Found at i:2343816 original size:6 final size:6
Alignment explanation
Indices: 2343805--2343838 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
2343795 ATTAGAAATT
*
2343805 ATAATC ATAATC ATAATC ATAATC A-AATC TTAAT
1 ATAATC ATAATC ATAATC ATAATC ATAATC ATAAT
2343839 TTTATATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (6 bp):
ATAATC
Found at i:2343862 original size:10 final size:9
Alignment explanation
Indices: 2343851--2343901 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
2343841 TATATTATAT
2343851 TAAATTAAA
1 TAAATTAAA
*
2343860 TTAAAATAAA
1 -TAAATTAAA
*
2343870 TAAAATAAA
1 TAAATTAAA
2343879 TAAA-TAAA
1 TAAATTAAA
2343887 TAAATCTAATA
1 TAAAT-TAA-A
2343898 TAAA
1 TAAA
2343902 ATTGGAATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
8 8 0.22
9 13 0.35
10 11 0.30
11 5 0.14
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (9 bp):
TAAATTAAA
Found at i:2343875 original size:9 final size:9
Alignment explanation
Indices: 2343851--2343890 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
2343841 TATATTATAT
*
2343851 TAAATTAAA
1 TAAAATAAA
2343860 TTAAAATAAA
1 -TAAAATAAA
2343870 TAAAATAAA
1 TAAAATAAA
2343879 T-AAATAAA
1 TAAAATAAA
2343887 TAAA
1 TAAA
2343891 TCTAATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 8 0.29
9 12 0.43
10 8 0.29
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (9 bp):
TAAAATAAA
Found at i:2350461 original size:13 final size:13
Alignment explanation
Indices: 2350443--2350470 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2350433 ATCTTTTATT
2350443 TTAAATATAAATA
1 TTAAATATAAATA
2350456 TTAAATATAAATA
1 TTAAATATAAATA
2350469 TT
1 TT
2350471 TTTAAAAAAT
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TTAAATATAAATA
Found at i:2350733 original size:29 final size:29
Alignment explanation
Indices: 2350691--2350753 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
2350681 TTTTAAAAAA
*
2350691 TAATATTTAAAAATACAAAATTTTAATTT
1 TAATATTTAAAAATACAAAATTTAAATTT
2350720 TAAT-TTTAATAAATACAAAATTTAAATTT
1 TAATATTTAA-AAATACAAAATTTAAATTT
2350749 TAATA
1 TAATA
2350754 ACCTTTTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
28 5 0.16
29 26 0.84
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (29 bp):
TAATATTTAAAAATACAAAATTTAAATTT
Found at i:2352290 original size:2 final size:2
Alignment explanation
Indices: 2352283--2352310 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2352273 TTGTTCCTTA
2352283 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2352311 GACTCTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2355221 original size:15 final size:16
Alignment explanation
Indices: 2355191--2355230 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
2355181 AAATCTCTCA
2355191 AAATATATAATAAATT
1 AAATATATAATAAATT
*
2355207 AAATATAT-TTAAATT
1 AAATATATAATAAATT
2355222 AAATATATA
1 AAATATATA
2355231 TTTATATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATATATAATAAATT
Found at i:2355533 original size:52 final size:53
Alignment explanation
Indices: 2355459--2355582 Score: 123
Period size: 52 Copynumber: 2.4 Consensus size: 53
2355449 TCAAATTCTA
* *
2355459 ATAAATATTTAATATAAA-TATATGTAATT-TTTAAAATTT-TTAATATATTAAA-
1 ATAAATATTT-TTAAAAATTATATGTAATTATTTAAAATTTATT-A-ATATTAAAT
* * **
2355511 A-AATTATATTTTAAAAATTATATTTAATTATTTATTATTTATTAATATTAAAT
1 ATAAATAT-TTTTAAAAATTATATGTAATTATTTAAAATTTATTAATATTAAAT
2355564 ATAAATATTTTTAAAAATT
1 ATAAATATTTTTAAAAATT
2355583 CAGATAAAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
51 10 0.17
52 21 0.36
53 21 0.36
54 7 0.12
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (53 bp):
ATAAATATTTTTAAAAATTATATGTAATTATTTAAAATTTATTAATATTAAAT
Found at i:2355536 original size:13 final size:13
Alignment explanation
Indices: 2355502--2355537 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
2355492 AAATTTTTAA
*
2355502 TATATTAAAAAAT
1 TATATTTAAAAAT
2355515 TATATTTTAAAAAT
1 TATA-TTTAAAAAT
2355529 TATATTTAA
1 TATATTTAA
2355538 TTATTTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TATATTTAAAAAT
Found at i:2356165 original size:2 final size:2
Alignment explanation
Indices: 2356158--2356189 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2356148 CATAAATAAT
2356158 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2356190 AAGAGAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2356540 original size:15 final size:15
Alignment explanation
Indices: 2356517--2356563 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
2356507 TTTAAAAAAT
*
2356517 TAATATTAAATTTAA
1 TAATATTAAATATAA
*
2356532 TAATTTTAAATATAA
1 TAATATTAAATATAA
* *
2356547 TTATAATAAATATAA
1 TAATATTAAATATAA
2356562 TA
1 TA
2356564 CGAATAAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATATTAAATATAA
Found at i:2356563 original size:30 final size:29
Alignment explanation
Indices: 2356506--2356563 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
2356496 AATCTTAATT
* *
2356506 TTTTAAAAAATTAATATTAAATTTAATAA
1 TTTTAAAAAATTAATAATAAATATAATAA
2356535 TTTTAAATATAATT-ATAATAAATATAATA
1 TTTTAAA-A-AATTAATAATAAATATAATA
2356564 CGAATAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.28
30 14 0.56
31 4 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
TTTTAAAAAATTAATAATAAATATAATAA
Found at i:2356586 original size:11 final size:11
Alignment explanation
Indices: 2356549--2356596 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 11
2356539 AAATATAATT
2356549 ATAATAAATATA
1 ATAA-AAATATA
*
2356561 ATACGAATAAAATA
1 ATA--AA-AATATA
2356575 ATAAAAATATA
1 ATAAAAATATA
2356586 ATAAAAATATA
1 ATAAAAATATA
2356597 TTTTTTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 16 0.52
12 5 0.16
13 1 0.03
14 9 0.29
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (11 bp):
ATAAAAATATA
Found at i:2363928 original size:14 final size:14
Alignment explanation
Indices: 2363909--2363937 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2363899 ATTGTTTTCT
2363909 AACATGAATTATCA
1 AACATGAATTATCA
2363923 AACATGAATTATCA
1 AACATGAATTATCA
2363937 A
1 A
2363938 GACTCACCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.28
Consensus pattern (14 bp):
AACATGAATTATCA
Found at i:2368277 original size:16 final size:16
Alignment explanation
Indices: 2368256--2368288 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2368246 GAAATGGGAA
*
2368256 TTTTTTTTT-TTTGTG
1 TTTTTTTTTGTTTTTG
2368271 TTTTTTTTTGTTTTTG
1 TTTTTTTTTGTTTTTG
2368287 TT
1 TT
2368289 CGGATGATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (16 bp):
TTTTTTTTTGTTTTTG
Found at i:2368563 original size:11 final size:11
Alignment explanation
Indices: 2368549--2368573 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2368539 TAACTAAAAA
2368549 ATAAATATAAT
1 ATAAATATAAT
2368560 ATAAATATAAT
1 ATAAATATAAT
2368571 ATA
1 ATA
2368574 TTTAAACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAAATATAAT
Found at i:2368658 original size:17 final size:17
Alignment explanation
Indices: 2368604--2368658 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
2368594 TAATATAACA
* *
2368604 TATTTAAAATATAT-AT
1 TATTTTAAATATTTAAT
*
2368620 TATATT-AATATTTAAAT
1 TATTTTAAATATTT-AAT
2368637 T-TTTTAAATATTTAAT
1 TATTTTAAATATTTAAT
2368653 TATTTT
1 TATTTT
2368659 TATTTTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
15 6 0.19
16 11 0.35
17 14 0.45
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTTTAAATATTTAAT
Found at i:2369184 original size:2 final size:2
Alignment explanation
Indices: 2369179--2369211 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2369169 TATATAAAAC
2369179 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 A
2369212 GTCGTTCTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2369371 original size:17 final size:17
Alignment explanation
Indices: 2369341--2369385 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
2369331 ATTTGAACTG
2369341 AATTTAAA--TAATTTA
1 AATTTAAATTTAATTTA
2369356 AATTTAAATTTAATTTA
1 AATTTAAATTTAATTTA
* *
2369373 ATTTTAATTTTAA
1 AATTTAAATTTAA
2369386 AATTCAAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 8 0.31
17 18 0.69
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTTAAATTTAATTTA
Found at i:2369513 original size:12 final size:12
Alignment explanation
Indices: 2369469--2369531 Score: 58
Period size: 11 Copynumber: 5.2 Consensus size: 12
2369459 GAATTTTATT
2369469 TTTATATTT-AA
1 TTTATATTTAAA
*
2369480 TTTAAATTTAATTA
1 TTTATATTTAA--A
2369494 TTTATATTTAAA
1 TTTATATTTAAA
* *
2369506 TTTCTATTTAAG
1 TTTATATTTAAA
*
2369518 TTTA-AATTAAA
1 TTTATATTTAAA
2369529 TTT
1 TTT
2369532 TTTTAATATT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
11 16 0.38
12 15 0.36
14 11 0.26
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (12 bp):
TTTATATTTAAA
Found at i:2369515 original size:18 final size:18
Alignment explanation
Indices: 2369469--2369525 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
2369459 GAATTTTATT
2369469 TTTA-TATTTAATTTAAA
1 TTTACTATTTAATTTAAA
*
2369486 TTTAATTATTTATATTTAAA
1 TTT-ACTATTTA-ATTTAAA
2369506 TTT-CTATTTAAGTTTAAA
1 TTTACTATTTAA-TTTAAA
2369524 TT
1 TT
2369526 AAATTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
17 4 0.11
18 15 0.43
19 6 0.17
20 10 0.29
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTACTATTTAATTTAAA
Found at i:2372287 original size:11 final size:10
Alignment explanation
Indices: 2372256--2372289 Score: 52
Period size: 9 Copynumber: 3.4 Consensus size: 10
2372246 CACGAGTTTC
2372256 AGAAAAAAAA
1 AGAAAAAAAA
2372266 A-AAAAAAAA
1 AGAAAAAAAA
2372275 AGAAAAGAAAA
1 AGAAAA-AAAA
2372286 AGAA
1 AGAA
2372290 GGCCAATAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.41
10 5 0.23
11 8 0.36
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:2375137 original size:10 final size:10
Alignment explanation
Indices: 2375122--2375162 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
2375112 ACGACATCAT
2375122 TTTTTAAAAA
1 TTTTTAAAAA
2375132 TTTTT--AAA
1 TTTTTAAAAA
*
2375140 TTTATAAAAA
1 TTTTTAAAAA
*
2375150 TTTTGAAAAA
1 TTTTTAAAAA
2375160 TTT
1 TTT
2375163 AAATATATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
8 7 0.27
10 19 0.73
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (10 bp):
TTTTTAAAAA
Found at i:2377482 original size:17 final size:17
Alignment explanation
Indices: 2377462--2377516 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
2377452 AATATTAAAT
2377462 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
*
2377479 ATTTTA-ATTCAT-TAA
1 ATTTTATATTTATATAA
* *
2377494 TAATTCATA-TTATATAA
1 -ATTTTATATTTATATAA
2377511 ATTTTA
1 ATTTTA
2377517 AAATATTTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 7
0.69 0.14 0.17
Matches are distributed among these distances:
15 3 0.10
16 16 0.55
17 10 0.34
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:2379265 original size:287 final size:289
Alignment explanation
Indices: 2378094--2379984 Score: 1576
Period size: 289 Copynumber: 6.6 Consensus size: 289
2378084 GTTTAACCTG
* * * ** * * * * *
2378094 TTTTCTTTGTAATTGGAGCAATTTAAACTGGTTTGGCTATTGTATTTATTTTGACAGATTCGTGA
1 TTTTCTTTGTAATTGGAACGACTCGAACTGGTTTGGCCATTATATTTATTTTAACAGATTCGGGG
* * ** ** * * *
2378159 AGAAATTTACTATCATTGGTTTAGTGATGGAGAACCAATGACGGAAACTGTTGTCAC--AGATTA
66 AGGAATTTGCTATCATTGGTTTAGTGACAGAGAACCTGTGACGGAAAGTGCTGTCACAAAGTTTA
* * * *
2378222 AAAT--A---AACTTAAATTTTTTCTCTCCCACATTTTAACCCTAAACCCATTATTGTTTCTC-T
131 AAATAAACTTAACTTAAATCTTTTCTCTCCCACGTTTTAACCCTAAACCCATTCTTGTTTGTCTT
* * * *
2378281 -TCCAGC-GATGCAAACTC-GAGCATCACCTGATCCATCCACCAGAAATCTTGCAACTACAAAGG
196 CTCCAGCAG-CGCAAACTCAG-GCATCACCTGATCCACCCACCACAAATCTTGCAACTACAAAAG
* * **
2378343 ACGGATTTGT-CTGAC-GATACAGTTTGACCTGT
259 ACGAATTTGTCCCG-CTG-TACAGTTTGACC-CA
* * * * * * *
2378375 TTTTTTTTATAATTGG-A--A-T-G-AC----TTAGCCATTGTATTTATTATGACAGATTCGGAG
1 TTTTCTTTGTAATTGGAACGACTCGAACTGGTTTGGCCATTATATTTATTTTAACAGATTCGGGG
* ** *
2378430 AGGAATTTGCTATCATTGGTTTAGTGACAAAGAACCTGTGACAAAAAGTGCTGTCACAAAATTTT
66 AGGAATTTGCTATCATTGGTTTAGTGACAGAGAACCTGTGACGGAAAGTGCTGTCAC-AAA---G
* * * * *
2378495 TTTAAAA-AAA---AACTTAAATTTTTTTTCTCTCACATTTTAACCCTAAACCCATTCTTGTTTA
127 TTTAAAATAAACTTAACTTAAATCTTTTCTCTCCCACGTTTTAACCCTAAACCCATTCTTGTTTG
* * * * * * *
2378556 TCTTCTCTAGCGGTGCAAACTCAAGCATTACCTGATCCTA-CGACCACAAATCTTGCAACGACAA
192 TCTTCTCCAGCAGCGCAAACTCAGGCATCACCTGATCC-ACCCACCACAAATCTTGCAACTACAA
** *
2378620 GGGAC-AGATTTGTCCCGC-G-ACACGTTTTGA-CCT
256 AAGACGA-ATTTGTCCCGCTGTACA-G-TTTGACCCA
* * * *** * *
2378653 TTTTTTTATGTAATT-GAAGTGACTCGAACTAGTTTGATTATTGTATTTATTTTGACAGATTCGG
1 TTTTCTT-TGTAATTGGAA-CGACTCGAACTGGTTTGGCCATTATATTTATTTTAACAGATTCGG
* * * * *
2378717 AGAGGAATTTGCTATCATTGGTTTAGTGATAGAGAACTTGTGACGAAAAGTGCTGTCACAAAATT
64 GGAGGAATTTGCTATCATTGGTTTAGTGACAGAGAACCTGTGACGGAAAGTGCTGTCACAAAGTT
* * * *
2378782 TAAAATAAATTTTACTTAAATCTTTTCTCTCCCACATTTTAACTCTAAACCCATTCTTGTTTGTC
129 TAAAATAAACTTAACTTAAATCTTTTCTCTCCCACGTTTTAACCCTAAACCCATTCTTGTTTGTC
* * * * * * * *
2378847 TTCTCTAGCAGCACACACTCAGGCATCACCTAATCCACTCACCATAAATCTTGCAAGTGCAAAAG
194 TTCTCCAGCAGCGCAAACTCAGGCATCACCTGATCCACCCACCACAAATCTTGCAACTACAAAAG
* * *
2378912 ACGAATTTGCCCCG-TGATATAGTTGGACCCA
259 ACGAATTTGTCCCGCTG-TACAGTTTGACCCA
*
2378943 TTTTCTTTGTAATTGGAACGACTCGAACTGGTTTGGCCATTATATTTATTTTAACAAATTCGGGG
1 TTTTCTTTGTAATTGGAACGACTCGAACTGGTTTGGCCATTATATTTATTTTAACAGATTCGGGG
* ** * * * *
2379008 AAGAATTTATTATCATTAGTTTAGTGCCAGAGAACCTGTGACGAAAAATGCTGTC-CAAAGTTTA
66 AGGAATTTGCTATCATTGGTTTAGTGACAGAGAACCTGTGACGGAAAGTGCTGTCACAAAGTTTA
* **
2379072 AAATAAACTTAACTTAAATCTTTTCTCTCCAACGTTTTAACCCTAAGTCCATTCTTGTTTGTCTT
131 AAATAAACTTAACTTAAATCTTTTCTCTCCCACGTTTTAACCCTAAACCCATTCTTGTTTGTCTT
* * * ** * * * * *
2379137 TTCCAGCGGTGCAAACTTGGGTATCAACTTATTCACCCACCAC-AATCTTGCAACTACAAAAGAT
196 CTCCAGCAGCGCAAACTCAGGCATCACCTGATCCACCCACCACAAATCTTGCAACTACAAAAGAC
* * * *
2379201 GGATTTATCCCGCAGTACGGTTTGACCCA
261 GAATTTGTCCCGCTGTACAGTTTGACCCA
* * *
2379230 TTTTCTTTATAATTGGAACGA-TCCAAACTGGTTTGGCCATTATATTTATTCTAACAGATTCGAG
1 TTTTCTTTGTAATTGGAACGACT-CGAACTGGTTTGGCCATTATATTTATTTTAACAGATTCG-G
* * * * * * **
2379294 GG-GGAATTTGCTGTCATTGGTTTGGTAAC-GTAGAACCTGTGATGGAAAATGCTATCGTAAAGT
64 GGAGGAATTTGCTATCATTGGTTTAGTGACAG-AGAACCTGTGACGGAAAGTGCTGTCACAAAGT
* *
2379357 TTAAAAT--A---AACTTAAATCTTTTCTCTCCCATGTTTTAA-CTTAAACCCATTCTTGTTTGT
128 TTAAAATAAACTTAACTTAAATCTTTTCTCTCCCACGTTTTAACCCTAAACCCATTCTTGTTTGT
*
2379416 CTTCTCCAGCAGCGCAAACT-TGAGCATCACCTGATCCACCCACCACAAATCTTGCAACTACAAA
193 CTTCTCCAGCAGCGCAAACTCAG-GCATCACCTGATCCACCCACCACAAATCTTGCAACTACAAA
* ** * * *
2379480 GGACGAATTTGTCTTGCGGTATAGTTTGACTCA
257 AGACGAATTTGTCCCGCTGTACAGTTTGACCCA
* * * * * * * *
2379513 TTTTCTTTGTAATTGGAGCAACTCGAACTGATTTGGCCCTTGTATTTATTCTAACAAATTTGGGG
1 TTTTCTTTGTAATTGGAACGACTCGAACTGGTTTGGCCATTATATTTATTTTAACAGATTCGGGG
* * * * * *
2379578 AGGAATTTCCTATCATTGGTTTAGTGATAGAGAACTTATGATGGAAAGTACTGTCACAAAGTTTA
66 AGGAATTTGCTATCATTGGTTTAGTGACAGAGAACCTGTGACGGAAAGTGCTGTCACAAAGTTTA
** * * * * * *
2379643 AAATAAACTTAACCGAATTTTTTTTTTCTCCCATGTTTTAACCTTAAACCCATTCTTATTTGTCT
131 AAATAAACTTAACTTAA-ATCTTTTCTCTCCCACGTTTTAACCCTAAACCCATTCTTGTTTGTCT
* * * * ** *
2379708 TCTCTAGCGGTGTAAACTCAGGCATCACCTGATCCACCCATTACAAATCTTGCAACTACAAAGGA
195 TCTCCAGCAGCGCAAACTCAGGCATCACCTGATCCACCCACCACAAATCTTGCAACTACAAAAGA
* * * * ***
2379773 GGGATTTGTCTCGCTGTACAATTTGATCTTT
260 CGAATTTGTCCCGCTGTACAGTTTGA-CCCA
* * * * * * *
2379804 TTTTTTTTGTAATTGGAGTAAG-C-CTAACTAGTTTGGCCATTATATTTATTTTGACAGATTTGA
1 TTTTCTTTGTAATTGGA--ACGACTCGAACTGGTTTGGCCATTATATTTATTTTAACAGATTCGG
* * * * * *
2379867 GGAGGAATTTGCTATCATTAGTTTACTGACGGAGCATCTGTGACGGAAAGTGCTGTCATAAAGTT
64 GGAGGAATTTGCTATCATTGGTTTAGTGACAGAGAACCTGTGACGGAAAGTGCTGTCACAAAGTT
* * **
2379932 TAAAATAAACTTCACTTAAATATTTTCT-TTTCACGTTTTAACCCTAAACCCAT
129 TAAAATAAACTTAACTTAAATCTTTTCTCTCCCACGTTTTAACCCTAAACCCAT
2379985 CAGCGCAAAC
Statistics
Matches: 1310, Mismatches: 239, Indels: 114
0.79 0.14 0.07
Matches are distributed among these distances:
271 73 0.06
274 1 0.00
275 2 0.00
277 7 0.01
278 63 0.05
279 10 0.01
280 65 0.05
281 19 0.01
282 58 0.04
283 174 0.13
284 3 0.00
285 10 0.01
286 6 0.00
287 135 0.10
288 120 0.09
289 325 0.25
290 117 0.09
291 121 0.09
292 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (289 bp):
TTTTCTTTGTAATTGGAACGACTCGAACTGGTTTGGCCATTATATTTATTTTAACAGATTCGGGG
AGGAATTTGCTATCATTGGTTTAGTGACAGAGAACCTGTGACGGAAAGTGCTGTCACAAAGTTTA
AAATAAACTTAACTTAAATCTTTTCTCTCCCACGTTTTAACCCTAAACCCATTCTTGTTTGTCTT
CTCCAGCAGCGCAAACTCAGGCATCACCTGATCCACCCACCACAAATCTTGCAACTACAAAAGAC
GAATTTGTCCCGCTGTACAGTTTGACCCA
Found at i:2379517 original size:570 final size:567
Alignment explanation
Indices: 2378077--2379943 Score: 1783
Period size: 570 Copynumber: 3.3 Consensus size: 567
2378067 GCGGAAGGCT
* * * * ** * * *
2378077 CAGTACGGTTTAACCTGTTTTCTTTGTAATTGGAGCAATTTAAACTGGTTTGGCTATTGTATTTA
1 CAGTACGGTTTGACC-CTTTTCTTTATAATTGGAACAATCCAAACTAGTTTGGCCATTATATTTA
* * * * * * ** *
2378142 TTTTGACAGATTCGTGAAGAAATTTACTATCATTGGTTTAGTGATGGAGAACCAATGACGGAAAC
65 TTTTGACAGATTCGAGGAGGAATTTGCTATCATTGGTTTAGTAACGGAGAACCTGTGACGGAAAA
* * * * *
2378207 TGTTGTC--ACAGATTAAAATAAACTTAAATTTTTTCTCTCCCACATTTTAACCCTAAACCCATT
130 TGCTGTCATAAAGTTTAAAATAAACTTAAATCTTTTCTCTCCCACATTTTAA-CTTAAACCCATT
* * * * * *
2378270 ATTGTTTCTC-T-TCCAGC-GATGCAAACTCGAGCATCACCTGATCCATCCACCAGAAATCTTGC
194 CTTGTTTGTCTTCTCCAGCAG-CGCAAACTTGAGCATCACCTGATCCACCCACCACAAATCTTGC
* * ** * *
2378332 AACTACAAAGGACGGATTTGTCTGACGATACAGTTTGACCTGTTTTTTTTTATAATTGG-A-A-T
258 AACTACAAAGGACGAATTTGTCTG-CGATATAGTTTGA-CTCATTTTCTTTGTAATTGGAACACT
* * * * *
2378394 -G-AC---TTAGCCATTGTATTTATTATGACAGATTCGGAGAGGAATTTGCTATCATTGGTTTAG
321 CGAACTGTTTGGCCATTGTATTTATTATAACAAATTCGGGGAGGAATTTACTATCATTGGTTTAG
* *
2378454 TGACAAAGAACCTGTGAC-AAAAAGTGCTGTCACAAAATTTTTTTAAAA-AAA---AACTTAAAT
386 TGACAGAGAACCTGTGACGAAAAA-TGCTGTCAC-AAA---GTTTAAAATAAACTTAACTTAAAT
* *
2378514 TTTTTTTCTCTCACATTTTAACCCTAAACCCATTCTTGTTTATCTTCTCTAGCGGTGCAAACTCA
446 TTTTTTTCTC-CACGTTTTAACCCTAAACCCATTCTTGTTTGTCTTCTCTAGCGGTGCAAACTCA
* * * * * *
2378579 AGCATTACCTGATCCTA-CGACCACAAATCTTGCAACGACAAGGGACAGATTTGTCCCG
510 GGCATCACCTGATCC-ACCCACCACAAATCTTGCAACTACAAAGGACGGATTTGTCCCG
* * * ** * *** *
2378637 C-GACACGTTTTGA-CCTTTTTTTTATGTAATT-GAAGTGA-CTCGAACTAGTTTGATTATTGTA
1 CAG-TACGGTTTGACCCTTTTCTTTA--TAATTGGAA-CAATC-CAAACTAGTTTGGCCATTATA
* ** *
2378698 TTTATTTTGACAGATTCG-GAGAGGAATTTGCTATCATTGGTTTAGTGATAGAGAACTTGTGAC-
61 TTTATTTTGACAGATTCGAG-GAGGAATTTGCTATCATTGGTTTAGTAACGGAGAACCTGTGACG
* *
2378761 GAAAAGTGCTGTCACAAAATTTAAAATAAATTTTACTTAAATCTTTTCTCTCCCACATTTTAACT
125 GAAAA-TGCTGTCATAAAGTTTAAAAT-AA----ACTTAAATCTTTTCTCTCCCACATTTTAACT
* * * * * *
2378826 CTAAACCCATTCTTGTTTGTCTTCTCTAGCAGCACACAC-TCAGGCATCACCTAATCCACTCACC
184 -TAAACCCATTCTTGTTTGTCTTCTCCAGCAGCGCAAACTTGA-GCATCACCTGATCCACCCACC
* * * * * * * * *
2378890 ATAAATCTTGCAAGTGCAAAAGACGAATTTGCCCCGTGATATAGTTGGACCCATTTTCTTTGTAA
247 ACAAATCTTGCAACTACAAAGGACGAATTTG-TCTGCGATATAGTTTGACTCATTTTCTTTGTAA
* * * *
2378955 TTGGAACGACTCGAACTGGTTTGGCCATTATATTTATTTTAACAAATTCGGGGAAGAATTTATTA
311 TTGGAAC-ACTCGAACT-GTTTGGCCATTGTATTTATTATAACAAATTCGGGGAGGAATTTACTA
* *
2379020 TCATTAGTTTAGTGCCAGAGAACCTGTGACGAAAAATGCTGTC-CAAAGTTTAAAATAAACTTAA
374 TCATTGGTTTAGTGACAGAGAACCTGTGACGAAAAATGCTGTCACAAAGTTTAAAATAAACTTAA
* * ** * *
2379084 CTTAAATCTTTTCTCTCCAACGTTTTAACCCTAAGTCCATTCTTGTTTGTCTTTTCCAGCGGTGC
439 CTTAAATTTTTTTTCTCC-ACGTTTTAACCCTAAACCCATTCTTGTTTGTCTTCTCTAGCGGTGC
** * * * * * * *
2379149 AAACTTGGGTATCAACTTATTCACCCACCAC-AATCTTGCAACTACAAAAGATGGATTTATCCCG
503 AAACTCAGGCATCACCTGATCCACCCACCACAAATCTTGCAACTACAAAGGACGGATTTGTCCCG
* *
2379213 CAGTACGGTTTGACCCATTTTCTTTATAATTGGAACGATCCAAACTGGTTTGGCCATTATATTTA
1 CAGTACGGTTTGACCC-TTTTCTTTATAATTGGAACAATCCAAACTAGTTTGGCCATTATATTTA
* * * * * * *
2379278 TTCTAACAGATTCGAGGGGGAATTTGCTGTCATTGGTTTGGTAACGTAGAACCTGTGATGGAAAA
65 TTTTGACAGATTCGAGGAGGAATTTGCTATCATTGGTTTAGTAACGGAGAACCTGTGACGGAAAA
* * **
2379343 TGCTATCGTAAAGTTTAAAATAAACTTAAATCTTTTCTCTCCCATGTTTTAACTTAAACCCATTC
130 TGCTGTCATAAAGTTTAAAATAAACTTAAATCTTTTCTCTCCCACATTTTAACTTAAACCCATTC
2379408 TTGTTTGTCTTCTCCAGCAGCGCAAACTTGAGCATCACCTGATCCACCCACCACAAATCTTGCAA
195 TTGTTTGTCTTCTCCAGCAGCGCAAACTTGAGCATCACCTGATCCACCCACCACAAATCTTGCAA
* *
2379473 CTACAAAGGACGAATTTGTCTTGCGGTATAGTTTGACTCATTTTCTTTGTAATTGGAGCAACTCG
260 CTACAAAGGACGAATTTGTC-TGCGATATAGTTTGACTCATTTTCTTTGTAATTGGAAC-ACTCG
* * * *
2379538 AACTGATTTGGCCCTTGTATTTATTCTAACAAATTTGGGGAGGAATTTCCTATCATTGGTTTAGT
323 AACTG-TTTGGCCATTGTATTTATTATAACAAATTCGGGGAGGAATTTACTATCATTGGTTTAGT
* * * * * * * ** *
2379603 GATAGAGAACTTATGATGGAAAGTACTGTCACAAAGTTTAAAATAAACTTAACCGAATTTTTTTT
387 GACAGAGAACCTGTGACGAAAAATGCTGTCACAAAGTTTAAAATAAACTTAACTTAA-ATTTTTT
* * * *
2379668 TTCTCCCATGTTTTAACCTTAAACCCATTCTTATTTGTCTTCTCTAGCGGTGTAAACTCAGGCAT
451 TTCT-CCACGTTTTAACCCTAAACCCATTCTTGTTTGTCTTCTCTAGCGGTGCAAACTCAGGCAT
** * *
2379733 CACCTGATCCACCCATTACAAATCTTGCAACTACAAAGGAGGGATTTGTCTCG
515 CACCTGATCCACCCACCACAAATCTTGCAACTACAAAGGACGGATTTGTCCCG
* ** ** * * ** * *
2379786 CTGTACAATTTGATCTTTTTTTTTTTGTAATTGGAGTAAGCCTAACTAGTTTGGCCATTATATTT
1 CAGTACGGTTTGA-C-CCTTTTCTTTATAATTGGAACAATCCAAACTAGTTTGGCCATTATATTT
* * * * * *
2379851 ATTTTGACAGATTTGAGGAGGAATTTGCTATCATTAGTTTACTGACGGAGCATCTGTGACGGAAA
64 ATTTTGACAGATTCGAGGAGGAATTTGCTATCATTGGTTTAGTAACGGAGAACCTGTGACGGAAA
*
2379916 GTGCTGTCATAAAGTTTAAAATAAACTT
129 ATGCTGTCATAAAGTTTAAAATAAACTT
2379944 CACTTAAATA
Statistics
Matches: 1048, Mismatches: 206, Indels: 92
0.78 0.15 0.07
Matches are distributed among these distances:
558 7 0.01
559 9 0.01
560 90 0.09
562 9 0.01
563 2 0.00
566 1 0.00
567 46 0.04
568 17 0.02
569 66 0.06
570 198 0.19
571 56 0.05
572 70 0.07
573 49 0.05
574 122 0.12
575 2 0.00
576 130 0.12
577 91 0.09
578 78 0.07
579 5 0.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (567 bp):
CAGTACGGTTTGACCCTTTTCTTTATAATTGGAACAATCCAAACTAGTTTGGCCATTATATTTAT
TTTGACAGATTCGAGGAGGAATTTGCTATCATTGGTTTAGTAACGGAGAACCTGTGACGGAAAAT
GCTGTCATAAAGTTTAAAATAAACTTAAATCTTTTCTCTCCCACATTTTAACTTAAACCCATTCT
TGTTTGTCTTCTCCAGCAGCGCAAACTTGAGCATCACCTGATCCACCCACCACAAATCTTGCAAC
TACAAAGGACGAATTTGTCTGCGATATAGTTTGACTCATTTTCTTTGTAATTGGAACACTCGAAC
TGTTTGGCCATTGTATTTATTATAACAAATTCGGGGAGGAATTTACTATCATTGGTTTAGTGACA
GAGAACCTGTGACGAAAAATGCTGTCACAAAGTTTAAAATAAACTTAACTTAAATTTTTTTTCTC
CACGTTTTAACCCTAAACCCATTCTTGTTTGTCTTCTCTAGCGGTGCAAACTCAGGCATCACCTG
ATCCACCCACCACAAATCTTGCAACTACAAAGGACGGATTTGTCCCG
Found at i:2382917 original size:18 final size:18
Alignment explanation
Indices: 2382896--2382953 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
2382886 TTATATCTTA
2382896 TTATATTTTAATTATTTT
1 TTATATTTTAATTATTTT
* *
2382914 TTATATTATATTTATTTT
1 TTATATTTTAATTATTTT
* *
2382932 TAATATTATTAAATATTTT
1 TTATATT-TTAATTATTTT
2382951 TTA
1 TTA
2382954 ATGTTTTGCA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 22 0.69
19 10 0.31
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATATTTTAATTATTTT
Found at i:2383078 original size:18 final size:19
Alignment explanation
Indices: 2383047--2383083 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2383037 GAAAGGAAGA
2383047 AGAAAATAATAAATTATAT
1 AGAAAATAATAAATTATAT
*
2383066 AGAAATTAA-AAATTATAT
1 AGAAAATAATAAATTATAT
2383084 TATTTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (19 bp):
AGAAAATAATAAATTATAT
Found at i:2383754 original size:2 final size:2
Alignment explanation
Indices: 2383747--2383779 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2383737 AAATTGCAGA
2383747 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 A
2383780 CACCAGAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2384538 original size:26 final size:28
Alignment explanation
Indices: 2384477--2384539 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
2384467 TCATTTATTG
2384477 TTTAA-AAAATATTATTTTTTAATTAAA
1 TTTAATAAAATATTATTTTTTAATTAAA
*
2384504 TTTAAATAAAATATT-TTTTATTATTTAAA
1 TTT-AATAAAATATTATTTT-TTAATTAAA
2384533 TTATAAT
1 TT-TAAT
2384540 TTAAATTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
27 3 0.10
28 6 0.19
29 21 0.68
30 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
TTTAATAAAATATTATTTTTTAATTAAA
Found at i:2385157 original size:33 final size:35
Alignment explanation
Indices: 2385119--2385203 Score: 101
Period size: 33 Copynumber: 2.6 Consensus size: 35
2385109 AAAATTATTT
2385119 TTTTATTATTTAAATAATATTAAAATA-TTTA-AA
1 TTTTATTATTTAAATAATATTAAAATATTTTATAA
* *
2385152 TTTTATT-TTTAAATTAATATTTATATATTTTATAA
1 TTTTATTATTTAAA-TAATATTAAAATATTTTATAA
2385187 --TTA-TATTTAAATAATAT
1 TTTTATTATTTAAATAATAT
2385204 ATATTTTATT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
32 13 0.28
33 27 0.59
34 4 0.09
35 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (35 bp):
TTTTATTATTTAAATAATATTAAAATATTTTATAA
Found at i:2385180 original size:22 final size:21
Alignment explanation
Indices: 2385151--2385195 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
2385141 AAATATTTAA
2385151 ATTT-TAT-TTTTA-AATTAAT
1 ATTTATATATTTTATAATT-AT
2385170 ATTTATATATTTTATAATTAT
1 ATTTATATATTTTATAATTAT
2385191 ATTTA
1 ATTTA
2385196 AATAATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.17
20 3 0.13
21 12 0.52
22 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTATATATTTTATAATTAT
Found at i:2385192 original size:15 final size:15
Alignment explanation
Indices: 2385172--2385217 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 15
2385162 AAATTAATAT
2385172 TTATATATTTTATAA
1 TTATATATTTTATAA
**
2385187 TTATAT-TTAAATAA
1 TTATATATTTTATAA
*
2385201 -TATATATTTTATTA
1 TTATATATTTTATAA
2385215 TTA
1 TTA
2385218 AATAGTAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
13 5 0.21
14 11 0.46
15 8 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATATATTTTATAA
Found at i:2385193 original size:13 final size:13
Alignment explanation
Indices: 2385175--2385217 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2385165 TTAATATTTA
2385175 TATATTTTATAAT
1 TATATTTTATAAT
*
2385188 TATATTTAAATAAT
1 TATATTT-TATAAT
*
2385202 ATATATTTTATTAT
1 -TATATTTTATAAT
2385216 TA
1 TA
2385218 AATAGTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
13 9 0.36
14 9 0.36
15 7 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TATATTTTATAAT
Found at i:2385206 original size:21 final size:22
Alignment explanation
Indices: 2385125--2385206 Score: 55
Period size: 21 Copynumber: 3.8 Consensus size: 22
2385115 ATTTTTTTAT
2385125 TATTTAAATAATAT-TAA--AA
1 TATTTAAATAATATATAATTAA
* * *
2385144 TATTTAAATTTTATTTTTAAATTAA
1 TATTTAAA--TAATATAT-AATTAA
* * *
2385169 TATTTATATATTTTATAATT-A
1 TATTTAAATAATATATAATTAA
2385190 TATTTAAATAATATATA
1 TATTTAAATAATATATA
2385207 TTTTATTATT
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
19 8 0.17
21 19 0.40
22 5 0.10
23 7 0.15
25 9 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TATTTAAATAATATATAATTAA
Found at i:2389110 original size:48 final size:48
Alignment explanation
Indices: 2389039--2389135 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 48
2389029 ACGATTATGG
*
2389039 AAAGACAGAATTCAGTCCCATTAAGAAACCATCTGTTATACATTACAC
1 AAAGACAGAATTCAGTCCCATTAACAAACCATCTGTTATACATTACAC
* * *
2389087 AAAGACGGAATTCGGTCCCATTAACAAACCATCTGTTATATATTACAC
1 AAAGACAGAATTCAGTCCCATTAACAAACCATCTGTTATACATTACAC
2389135 A
1 A
2389136 TTTTAATAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (48 bp):
AAAGACAGAATTCAGTCCCATTAACAAACCATCTGTTATACATTACAC
Found at i:2397666 original size:18 final size:18
Alignment explanation
Indices: 2397624--2397658 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2397614 TTCAAAGTGC
2397624 TAAAA-TTTTATTTTTTA
1 TAAAATTTTTATTTTTTA
2397641 TAAAATTTTTATTTTTTA
1 TAAAATTTTTATTTTTTA
2397659 ATTAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TAAAATTTTTATTTTTTA
Found at i:2397681 original size:18 final size:18
Alignment explanation
Indices: 2397660--2397694 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2397650 TATTTTTTAA
2397660 TTAAT-TTATAAATAATAT
1 TTAATATTATAAA-AATAT
2397678 TTAATATTATAAAAATA
1 TTAATATTATAAAAATA
2397695 AAATATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAATATTATAAAAATAT
Found at i:2401182 original size:18 final size:19
Alignment explanation
Indices: 2401145--2401182 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2401135 TCTCTGAGGG
* *
2401145 TAAACATTATCAGAAGACA
1 TAAAAATTATAAGAAGACA
2401164 TAAAAATTATAAG-AGACA
1 TAAAAATTATAAGAAGACA
2401182 T
1 T
2401183 TTATTAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.55, C:0.11, G:0.11, T:0.24
Consensus pattern (19 bp):
TAAAAATTATAAGAAGACA
Found at i:2401452 original size:27 final size:27
Alignment explanation
Indices: 2401413--2401472 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
2401403 ATCCCCCTTA
2401413 TTAACATCGTCACTTGCATCATCACCAT
1 TTAA-ATCGTCACTTGCATCATCACCAT
2401441 TTAAATCGTCACTTGCATCATCACCAT
1 TTAAATCGTCACTTGCATCATCACCAT
2401468 TTAAA
1 TTAAA
2401473 GTTGCTTCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 28 0.88
28 4 0.12
ACGTcount: A:0.32, C:0.28, G:0.07, T:0.33
Consensus pattern (27 bp):
TTAAATCGTCACTTGCATCATCACCAT
Found at i:2403805 original size:27 final size:27
Alignment explanation
Indices: 2403764--2403817 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
2403754 CTGCACGACT
*
2403764 ACTAACATTCAAACTCGCTGCAACACC
1 ACTAACATTCAAACTCCCTGCAACACC
** *
2403791 ACTAACATTTGAACTCCCTGCAGCACC
1 ACTAACATTCAAACTCCCTGCAACACC
2403818 GCTAGTGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.33, C:0.37, G:0.09, T:0.20
Consensus pattern (27 bp):
ACTAACATTCAAACTCCCTGCAACACC
Done.