Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold74
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: 4633657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 2 of 24
Found at i:200173 original size:2 final size:2
Alignment explanation
Indices: 200166--200198 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
200156 AGCAGCTTAC
200166 AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
200199 CCATGTGCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:201828 original size:2 final size:2
Alignment explanation
Indices: 201821--201847 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
201811 ATAAACATAA
201821 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
201848 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:205069 original size:2 final size:2
Alignment explanation
Indices: 205064--205089 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
205054 TGTGTGTGTG
205064 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
205090 GAGAGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:205094 original size:2 final size:2
Alignment explanation
Indices: 205089--205117 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
205079 ATATATATAT
205089 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 A
205118 AGCGGTAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:205251 original size:5 final size:5
Alignment explanation
Indices: 205236--205297 Score: 56
Period size: 5 Copynumber: 11.6 Consensus size: 5
205226 CGAAAAAATT
205236 ATTTAA ATTTA ATTTA A-TTA ATTTA ATTTAAA ATTTA A-TTA ATTTAAA
1 ATTT-A ATTTA ATTTA ATTTA ATTTA ATTT--A ATTTA ATTTA ATTT--A
205284 ATATTA ATTTA ATT
1 AT-TTA ATTTA ATT
205298 GATTAATTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 15
0.77 0.00 0.23
Matches are distributed among these distances:
4 8 0.16
5 24 0.49
6 7 0.14
7 8 0.16
8 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (5 bp):
ATTTA
Found at i:205256 original size:9 final size:9
Alignment explanation
Indices: 205244--205282 Score: 51
Period size: 9 Copynumber: 4.0 Consensus size: 9
205234 TTATTTAAAT
205244 TTAATTTAA
1 TTAATTTAA
205253 TTAATTTAA
1 TTAATTTAA
205262 TTTAAAATTTAA
1 -TT--AATTTAA
205274 TTAATTTAA
1 TTAATTTAA
205283 AATATTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 16 0.59
10 2 0.07
11 2 0.07
12 7 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
TTAATTTAA
Found at i:205338 original size:22 final size:20
Alignment explanation
Indices: 205307--205365 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
205297 TGATTAATTT
*
205307 TTAATTATTAAAATATAAAA
1 TTAATAATTAAAATATAAAA
*
205327 TTAAATAAATTAAAATAATTAAA
1 TT-AAT-AATTAAAAT-ATAAAA
*
205350 TTAATATTTAAAATAT
1 TTAATAATTAAAATAT
205366 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 4 0.12
21 11 0.33
22 11 0.33
23 7 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAATAATTAAAATATAAAA
Found at i:205348 original size:18 final size:18
Alignment explanation
Indices: 205325--205386 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 18
205315 TAAAATATAA
205325 AATTAAATAAATTAAAAT
1 AATTAAATAAATTAAAAT
205343 AATTAAATTAATATTTAAAAT
1 AATTAAA-TAA-A-TTAAAAT
* ** *
205364 ATTTTTA-AAATTAAAAA
1 AATTAAATAAATTAAAAT
205381 AATTAA
1 AATTAA
205387 TCAAAATTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 7
0.71 0.15 0.15
Matches are distributed among these distances:
17 9 0.26
18 8 0.24
19 5 0.15
20 1 0.03
21 11 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AATTAAATAAATTAAAAT
Found at i:205351 original size:14 final size:15
Alignment explanation
Indices: 205317--205386 Score: 52
Period size: 14 Copynumber: 4.5 Consensus size: 15
205307 TTAATTATTA
205317 AAATATAAAATTAAAT
1 AAAT-TAAAATTAAAT
*
205333 AAATTAAAA-TAATT
1 AAATTAAAATTAAAT
*
205347 AAATTAATATTTAAAAT
1 AAATTAA-AATT-AAAT
** *
205364 ATTTTTAAAATTAAAA
1 A-AATTAAAATTAAAT
205380 AAATTAA
1 AAATTAA
205387 TCAAAATTTT
Statistics
Matches: 41, Mismatches: 9, Indels: 9
0.69 0.15 0.15
Matches are distributed among these distances:
14 11 0.27
15 10 0.24
16 9 0.22
17 7 0.17
18 4 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATTAAAATTAAAT
Found at i:211055 original size:2 final size:2
Alignment explanation
Indices: 211048--211077 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
211038 ATTTGTTAAC
211048 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
211078 CTTACCCATA
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:215647 original size:2 final size:2
Alignment explanation
Indices: 215640--215665 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
215630 AAAACAGCAC
215640 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
215666 CGCTGGGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:221995 original size:10 final size:10
Alignment explanation
Indices: 221959--222008 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
221949 AAGTTAGGTA
221959 AAAAAGAAAG
1 AAAAAGAAAG
*
221969 AAAGAAG-ATG
1 AAA-AAGAAAG
221979 AAGAAAGAAAG
1 AA-AAAGAAAG
*
221990 AAAAAGAAAA
1 AAAAAGAAAG
222000 AAAAAGAAA
1 AAAAAGAAA
222009 AAATATGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
10 26 0.76
11 8 0.24
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:222010 original size:17 final size:18
Alignment explanation
Indices: 221958--222012 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 18
221948 AAAGTTAGGT
221958 AAAAAAGAAAGAAAGAAGATG
1 AAAAAA-AAAGAAA-AA-ATG
*
221979 AAGAAAGAAAG-AAAAA-G
1 AA-AAAAAAAGAAAAAATG
221996 AAAAAAAAAGAAAAAAT
1 AAAAAAAAAGAAAAAAT
222013 ATGAAATGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
16 7 0.24
17 8 0.28
18 1 0.03
19 2 0.07
20 2 0.07
21 6 0.21
22 3 0.10
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (18 bp):
AAAAAAAAAGAAAAAATG
Found at i:229895 original size:2 final size:2
Alignment explanation
Indices: 229888--229916 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
229878 CCTACTTATC
229888 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
229917 ATTAGTTTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:231853 original size:298 final size:298
Alignment explanation
Indices: 231312--231906 Score: 1109
Period size: 298 Copynumber: 2.0 Consensus size: 298
231302 CACATCAAGA
*
231312 GTTGTTCCAAGGTTTACAAGACCGATAACTGATATGATAGATGGCTTATGGTAGGGTTCGTTTCT
1 GTTGTTCCAAGGTTTACAAGACCAATAACTGATATGATAGATGGCTTATGGTAGGGTTCGTTTCT
*
231377 TTTTTTCAGTTTGTGTTGATTCGAAGTAGTGCAAATTTTCTTTGGGCTGAGATTTAGCTATTGAT
66 TTTTTTCAGTTTGTGTTGATTCGAAGTAGTGCAAATTTTCTTTGGGCTGAGATTCAGCTATTGAT
231442 TTATTTAAACACCAGTAGCCTTTTTATCGAAGTAACTATGCTCTGTTTATCTAATGTGCTAGGGT
131 TTATTTAAACACCAGTAGCCTTTTTATCGAAGTAACTATGCTCTGTTTATCTAATGTGCTAGGGT
*
231507 TTCTTGTGATCGGGCGCTCATGCAACAACCTGCCTTACGGCCCAGCATTATAATCTATTGGGCTG
196 TTCTTGTGATCGGGCACTCATGCAACAACCTGCCTTACGGCCCAGCATTATAATCTATTGGGCTG
231572 TACTGCATACACTGTTGGCAGCTTTTGTATTTTGACGT
261 TACTGCATACACTGTTGGCAGCTTTTGTATTTTGACGT
231610 GTTGTTCCAAGGTTTACAAGACCAATAACTGATATGATAGATGGCTTATGGTAGGGTTCGTTTCT
1 GTTGTTCCAAGGTTTACAAGACCAATAACTGATATGATAGATGGCTTATGGTAGGGTTCGTTTCT
*
231675 TTTTTTCAGTTTGTGTTGATTTGAAGTAGTGCAAATTTTCTTTGGGCTGAGATTCAGCTATTGAT
66 TTTTTTCAGTTTGTGTTGATTCGAAGTAGTGCAAATTTTCTTTGGGCTGAGATTCAGCTATTGAT
* * *
231740 TTATTTACACACCAGTAGGCTTTTTATTGAAGTAACTATGCTCTGTTTATCTAATGTGCTAGGGT
131 TTATTTAAACACCAGTAGCCTTTTTATCGAAGTAACTATGCTCTGTTTATCTAATGTGCTAGGGT
*
231805 TTCTTGTGATCGGGCACTCATGCAACAACCTGCCTTACGGCTCAGCATTATAATCTATTGGGCTG
196 TTCTTGTGATCGGGCACTCATGCAACAACCTGCCTTACGGCCCAGCATTATAATCTATTGGGCTG
*
231870 TACTGCATACACTGTTGGCAGCTTTTGTGTTTTGACG
261 TACTGCATACACTGTTGGCAGCTTTTGTATTTTGACG
231907 AGCCAATCTG
Statistics
Matches: 288, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
298 288 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (298 bp):
GTTGTTCCAAGGTTTACAAGACCAATAACTGATATGATAGATGGCTTATGGTAGGGTTCGTTTCT
TTTTTTCAGTTTGTGTTGATTCGAAGTAGTGCAAATTTTCTTTGGGCTGAGATTCAGCTATTGAT
TTATTTAAACACCAGTAGCCTTTTTATCGAAGTAACTATGCTCTGTTTATCTAATGTGCTAGGGT
TTCTTGTGATCGGGCACTCATGCAACAACCTGCCTTACGGCCCAGCATTATAATCTATTGGGCTG
TACTGCATACACTGTTGGCAGCTTTTGTATTTTGACGT
Found at i:234061 original size:17 final size:17
Alignment explanation
Indices: 234039--234074 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
234029 AAATTCCCCG
234039 AAGAAACAAAA-AAAATA
1 AAGAAA-AAAATAAAATA
234056 AAGAAAAAAATAAAATA
1 AAGAAAAAAATAAAATA
234073 AA
1 AA
234075 AGCCGAAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.83, C:0.03, G:0.06, T:0.08
Consensus pattern (17 bp):
AAGAAAAAAATAAAATA
Found at i:235847 original size:11 final size:11
Alignment explanation
Indices: 235805--235853 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
235795 AATAATATTA
*
235805 AAATTTAATTT
1 AAATTTAATAT
235816 AAATTTAATA-
1 AAATTTAATAT
*
235826 ATA-TT-ATAT
1 AAATTTAATAT
235835 AAATTTAATAT
1 AAATTTAATAT
*
235846 AAAATTAA
1 AAATTTAA
235854 AATTAATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
8 3 0.10
9 4 0.13
10 4 0.13
11 20 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
AAATTTAATAT
Found at i:238203 original size:2 final size:2
Alignment explanation
Indices: 238196--238223 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
238186 TCAAATTTTG
238196 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
238224 CACACACACA
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):
TA
Found at i:238260 original size:4 final size:4
Alignment explanation
Indices: 238253--238282 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
238243 ATGCATACAC
*
238253 ATGT ATGT ATGT ATGT ACGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
238283 CTGTACCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.27, C:0.03, G:0.23, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:247627 original size:2 final size:2
Alignment explanation
Indices: 247620--247661 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
247610 TGCTGTATAC
247620 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
247662 ATATATGAAG
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:248046 original size:17 final size:17
Alignment explanation
Indices: 248024--248059 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
248014 TAATAACTAG
248024 TGTCACAACAGGCAATT
1 TGTCACAACAGGCAATT
248041 TGTCACAACAGGCAATT
1 TGTCACAACAGGCAATT
248058 TG
1 TG
248060 GCCAATCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.25
Consensus pattern (17 bp):
TGTCACAACAGGCAATT
Found at i:248670 original size:24 final size:24
Alignment explanation
Indices: 248620--248671 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
248610 TATTAATATG
* *
248620 TAAAATTTTTATTGTTTAAATTTA
1 TAAAATTATTATTGTATAAATTTA
*
248644 TAAAATTATTATT-TATAATTTTAA
1 TAAAATTATTATTGTATAAATTT-A
248668 TAAA
1 TAAA
248672 TAAAAAGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
TAAAATTATTATTGTATAAATTTA
Found at i:250688 original size:2 final size:2
Alignment explanation
Indices: 250683--250724 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
250673 TGTGTGTGTG
250683 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
250725 CCCCCATTTT
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:252006 original size:2 final size:2
Alignment explanation
Indices: 251993--252047 Score: 60
Period size: 2 Copynumber: 28.5 Consensus size: 2
251983 AAACAAGTGA
* * *
251993 AT AT AA AT AT AT AT AT AT AT AT AT AA AT -T AT CT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
252033 AT AT AT AA AT AT AT A
1 AT AT AT AT AT AT AT A
252048 GAAAAGGATT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:252736 original size:39 final size:39
Alignment explanation
Indices: 252682--252761 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
252672 TTTAAGTTAG
*
252682 TACATAGGTCGATGATTGTATTTGTAATGATTTGATGAT
1 TACATAGGTCGATGATTGCATTTGTAATGATTTGATGAT
252721 TACATAGGTCGATGATTGCATTTGTAATGATTTGATGAT
1 TACATAGGTCGATGATTGCATTTGTAATGATTTGATGAT
252760 TA
1 TA
252762 ACGCGGATGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.42
Consensus pattern (39 bp):
TACATAGGTCGATGATTGCATTTGTAATGATTTGATGAT
Found at i:256291 original size:2 final size:2
Alignment explanation
Indices: 256286--256327 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
256276 AAATGAGTGT
256286 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
256328 GTGCATGTAG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:262593 original size:19 final size:18
Alignment explanation
Indices: 262562--262610 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
262552 ATGAATCTAA
* *
262562 AAATAAAATAAAATAAAG
1 AAATAAAAGAAAAGAAAG
262580 AAATAAAAAGAAAAGAAAG
1 AAAT-AAAAGAAAAGAAAG
* *
262599 AGAGAAAAGAAA
1 AAATAAAAGAAA
262611 CAGTGAGTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (18 bp):
AAATAAAAGAAAAGAAAG
Found at i:262772 original size:6 final size:6
Alignment explanation
Indices: 262743--262784 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
262733 CCACTTAAAA
* *
262743 TTCTTC TTCTTC TTCTTT TTCTTT TTCTTT TT-TTT TT-TTT TT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TT
262785 GTAAAGTTAC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
5 10 0.29
6 25 0.71
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTCTTT
Found at i:262893 original size:15 final size:14
Alignment explanation
Indices: 262873--262924 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
262863 TTTTTAAAAT
*
262873 TTAATAAAAATTATA
1 TTAA-AAAAATAATA
*
262888 TTAATATAAAA-AATT
1 TTAA-A-AAAATAATA
262903 TTAAAAAAATAATA
1 TTAAAAAAATAATA
262917 TTAAAAAA
1 TTAAAAAA
262925 TTTTTAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 4 0.12
14 12 0.38
15 12 0.38
16 4 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TTAAAAAAATAATA
Found at i:263496 original size:2 final size:2
Alignment explanation
Indices: 263489--263542 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
263479 ATGAATTAAG
* * * *
263489 AT AT AT AT AT AT AT AT AG AT AT AT GT AT AT AT AT CT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
263531 AT AT AT AT AT AT
1 AT AT AT AT AT AT
263543 TCTTAACCTT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (2 bp):
AT
Found at i:263512 original size:16 final size:16
Alignment explanation
Indices: 263489--263542 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
263479 ATGAATTAAG
*
263489 ATATATATATATATAT
1 ATATATATGTATATAT
*
263505 AGATATATGTATATAT
1 ATATATATGTATATAT
*
263521 ATCTATATGTATATAT
1 ATATATATGTATATAT
263537 ATATAT
1 ATATAT
263543 TCTTAACCTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (16 bp):
ATATATATGTATATAT
Found at i:271637 original size:24 final size:22
Alignment explanation
Indices: 271600--271644 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
271590 CTGGAATTAT
271600 TTTATTTTTAATTTTAAGTAAGTA
1 TTTATTTTTAA-TTTAA-TAAGTA
271624 TTTATATTTT-ATTTAATAAGT
1 TTTAT-TTTTAATTTAATAAGT
271645 TTCATTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 5 0.25
23 5 0.25
24 6 0.30
25 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (22 bp):
TTTATTTTTAATTTAATAAGTA
Found at i:271731 original size:30 final size:30
Alignment explanation
Indices: 271693--271778 Score: 136
Period size: 30 Copynumber: 2.9 Consensus size: 30
271683 TTATTATATG
271693 AATTTATTTAAATATAAATTAAAGATTAAA
1 AATTTATTTAAATATAAATTAAAGATTAAA
* * *
271723 ATTTTATTTGAATATAAATTAAAAATTAAA
1 AATTTATTTAAATATAAATTAAAGATTAAA
*
271753 AATTTATTAAAATATAAATTAAAGAT
1 AATTTATTTAAATATAAATTAAAGAT
271779 AACGTTTTAT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (30 bp):
AATTTATTTAAATATAAATTAAAGATTAAA
Found at i:273236 original size:2 final size:2
Alignment explanation
Indices: 273229--273262 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
273219 CTTTGACGTG
273229 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
273263 CTATTTAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:273457 original size:2 final size:2
Alignment explanation
Indices: 273450--273482 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
273440 TAATTGATTT
273450 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
273483 CAGTGTTCAA
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:288810 original size:15 final size:16
Alignment explanation
Indices: 288774--288813 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
288764 TTTAATATTT
*
288774 ATAAAATTTTTAATTAA
1 ATAAAA-TTATAATTAA
288791 ATAAAATTATAATT-A
1 ATAAAATTATAATTAA
288806 ATAAAATT
1 ATAAAATT
288814 TATTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 7 0.32
17 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAATTATAATTAA
Found at i:288816 original size:16 final size:17
Alignment explanation
Indices: 288774--288816 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
288764 TTTAATATTT
*
288774 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
288791 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
288806 ATAAAATTTAT
1 ATAAAATTTAT
288817 TTAAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 11 0.46
17 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:288945 original size:29 final size:30
Alignment explanation
Indices: 288878--288945 Score: 68
Period size: 31 Copynumber: 2.2 Consensus size: 30
288868 AAATATTATG
* *
288878 ATAAATTATGTAAAATAAGTCATAAATTAAT
1 ATAAA-TATGAAAAATAAGTCATAAATTAAC
*
288909 ATGTAATATGAAAAATAA-T-ATAAATATAAC
1 AT-AAATATGAAAAATAAGTCATAAAT-TAAC
288939 ATAAATA
1 ATAAATA
288946 CATAAATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
29 10 0.32
30 6 0.19
31 13 0.42
32 2 0.06
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (30 bp):
ATAAATATGAAAAATAAGTCATAAATTAAC
Found at i:289159 original size:21 final size:19
Alignment explanation
Indices: 289126--289169 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
289116 TATACATAAA
* *
289126 ATAAAAAAATTATTAATAT
1 ATAAAAAAATTATAAAAAT
289145 ATAAAAAAATTTTATAAAAAT
1 ATAAAAAAA--TTATAAAAAT
289166 ATAA
1 ATAA
289170 TATTTTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.43
21 12 0.57
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
ATAAAAAAATTATAAAAAT
Found at i:289197 original size:35 final size:37
Alignment explanation
Indices: 289107--289203 Score: 94
Period size: 35 Copynumber: 2.7 Consensus size: 37
289097 ATATACGTAC
*
289107 ATATAAAAATATACAT-AAAATAAAAAAATTATTAAT
1 ATATAAAAAAATACATAAAAATAAAAAAATTATTAAT
** * *
289143 ATATAAAAAAATTTTATAAAAAT-ATAATATT-TTAA-
1 ATATAAAAAAA-TACATAAAAATAAAAAAATTATTAAT
*
289178 ATATAAAAAAATAACATAAATATAAA
1 ATATAAAAAAAT-ACATAAAAATAAA
289204 GACGTAAATT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
34 1 0.02
35 18 0.38
36 15 0.31
37 9 0.19
38 5 0.10
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (37 bp):
ATATAAAAAAATACATAAAAATAAAAAAATTATTAAT
Found at i:289374 original size:15 final size:15
Alignment explanation
Indices: 289354--289390 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
289344 ATAGGTATAA
289354 AAAATTTTAATAAAT
1 AAAATTTTAATAAAT
* *
289369 AAAATTATAATTAAT
1 AAAATTTTAATAAAT
289384 AAAATTT
1 AAAATTT
289391 ATTTAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAATTTTAATAAAT
Found at i:289724 original size:57 final size:59
Alignment explanation
Indices: 289656--289771 Score: 155
Period size: 57 Copynumber: 2.0 Consensus size: 59
289646 AAATAATTTT
* *
289656 TTTAAATTAAATCATTATAACAAATTATG-AAAA-AAATCACAAATTGAGATATGATAC
1 TTTAAATTAAATCATTATAACAAATTATGTAAAATAAATCACAAATGGAGATACGATAC
* * * **
289713 TTTAAATTAAATTATTATGATAAATTATGTAAAATATGTCACAAATGGAGATACGATAC
1 TTTAAATTAAATCATTATAACAAATTATGTAAAATAAATCACAAATGGAGATACGATAC
289772 GAACATAACA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
57 26 0.52
58 4 0.08
59 20 0.40
ACGTcount: A:0.49, C:0.08, G:0.09, T:0.34
Consensus pattern (59 bp):
TTTAAATTAAATCATTATAACAAATTATGTAAAATAAATCACAAATGGAGATACGATAC
Found at i:290440 original size:23 final size:23
Alignment explanation
Indices: 290383--290442 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
290373 ATATGGACAT
* *
290383 ATAAAAAAAT-ATATATAATAAA
1 ATAAAAATATAATATATAAAAAA
* *
290405 AT-AAATTATTAATATGTAAAAAA
1 ATAAAAATA-TAATATATAAAAAA
290428 ATAAAAATATAATAT
1 ATAAAAATATAATAT
290443 TTTATATAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
21 4 0.13
22 3 0.10
23 18 0.60
24 5 0.17
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (23 bp):
ATAAAAATATAATATATAAAAAA
Found at i:290443 original size:29 final size:28
Alignment explanation
Indices: 290402--290456 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
290392 TATATATAAT
*
290402 AAAATAAATTATTAATATGTAAAAAAATA
1 AAAATAAATTATT-ATATATAAAAAAATA
*
290431 AAAATATAA-TATTTTATATAAAAAAA
1 AAAATA-AATTATTATATATAAAAAAA
290457 CATAAAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 11 0.48
29 10 0.43
30 2 0.09
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (28 bp):
AAAATAAATTATTATATATAAAAAAATA
Found at i:290726 original size:18 final size:19
Alignment explanation
Indices: 290703--290741 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
290693 TTAGGTCAAT
290703 AAATAATATT-TTTAATTA
1 AAATAATATTATTTAATTA
*
290721 AAATAATATTATTTATTTA
1 AAATAATATTATTTAATTA
290740 AA
1 AA
290742 TTTAATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATAATATTATTTAATTA
Found at i:290805 original size:20 final size:20
Alignment explanation
Indices: 290740--290806 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
290730 TATTTATTTA
*
290740 AATTTAATTATAAAAAT-AT
1 AATTTAATAATAAAAATAAT
290759 AAATATTAATAA-AAAAATAAT
1 -AAT-TTAATAATAAAAATAAT
** *
290780 TTTTTAATAATATAAATAAT
1 AATTTAATAATAAAAATAAT
290800 AATTTAA
1 AATTTAA
290807 ATTTAAATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 7 0.18
20 23 0.61
21 8 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AATTTAATAATAAAAATAAT
Found at i:297984 original size:1 final size:1
Alignment explanation
Indices: 297978--298005 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
297968 AATCAACGAC
297978 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
298006 GCCAGACAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:299293 original size:11 final size:11
Alignment explanation
Indices: 299277--299306 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
299267 CGAAACATGT
*
299277 TTTAAAATCAC
1 TTTAAAATCAA
299288 TTTAAAATCAA
1 TTTAAAATCAA
299299 TTTAAAAT
1 TTTAAAAT
299307 ACTCAATCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (11 bp):
TTTAAAATCAA
Found at i:302069 original size:2 final size:2
Alignment explanation
Indices: 302064--302108 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
302054 TGTGTGTGTG
302064 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
302106 TA T
1 TA T
302109 GGACAAGAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:306925 original size:2 final size:2
Alignment explanation
Indices: 306920--306962 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
306910 CCAAAAAACA
306920 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
306962 A
1 A
306963 CAGAGAAGGG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:308215 original size:2 final size:2
Alignment explanation
Indices: 308205--308237 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
308195 TTTGCGTGTG
*
308205 TA TA CA 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
308238 TTTCAGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:319602 original size:2 final size:2
Alignment explanation
Indices: 319592--319624 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
319582 AAAAAAAAAA
*
319592 AC AC GC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
319625 TATTTGAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.48, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:323227 original size:26 final size:25
Alignment explanation
Indices: 323198--323266 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 25
323188 CTGTAATTTT
323198 ATTTAAAATATTTAATATTTATATAA
1 ATTTAAAATATTTAATATTTATAT-A
* *
323224 ATTTAATATA-TTAATCATTTATATT
1 ATTTAAAATATTTAAT-ATTTATATA
* *
323249 ATTTAAATTATTAAATAT
1 ATTTAAAATATTTAATAT
323267 ATATTTATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
25 15 0.42
26 21 0.58
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTTAAAATATTTAATATTTATATA
Found at i:323252 original size:25 final size:23
Alignment explanation
Indices: 323196--323271 Score: 73
Period size: 25 Copynumber: 3.1 Consensus size: 23
323186 TGCTGTAATT
323196 TTATTTAAAATATTTAATATTTATA
1 TTATTT-AAATA-TTAATATTTATA
*
323221 TAAATTTAATATATTAATCATTTATA
1 T-TATTTAA-ATATTAAT-ATTTATA
*
323247 TTATTTAAATTATTAA-ATATATA
1 TTATTTAAA-TATTAATATTTATA
323270 TT
1 TT
323272 TATATTATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
23 8 0.18
24 1 0.02
25 20 0.45
26 15 0.34
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (23 bp):
TTATTTAAATATTAATATTTATA
Found at i:323274 original size:29 final size:29
Alignment explanation
Indices: 323205--323299 Score: 88
Period size: 29 Copynumber: 3.1 Consensus size: 29
323195 TTTATTTAAA
323205 ATATTTAATATT-TATATAAA-TTTAATATATT
1 ATATTT-ATATTATAT-TAAATTTTAA-ATA-T
323236 AATCATTTATATTAT-TTAAATTATTAAATAT
1 -AT-ATTTATATTATATTAAATT-TTAAATAT
* *
323267 ATATTTATATTATATTATATTTTAATTAT
1 ATATTTATATTATATTAAATTTTAAATAT
323296 ATAT
1 ATAT
323300 GTTTTTATTA
Statistics
Matches: 56, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
29 22 0.39
30 8 0.14
31 5 0.09
32 12 0.21
33 9 0.16
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (29 bp):
ATATTTATATTATATTAAATTTTAAATAT
Found at i:323286 original size:20 final size:18
Alignment explanation
Indices: 323240--323287 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 18
323230 TATATTAATC
323240 ATTTATATTATTTAAATT
1 ATTTATATTATTTAAATT
* *
323258 ATTAAATATATATTTATATT
1 ATT-TATAT-TATTTAAATT
323278 ATATTATATT
1 AT-TTATATT
323288 TTAATTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
18 3 0.12
19 5 0.21
20 15 0.62
21 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTATATTATTTAAATT
Found at i:323472 original size:14 final size:14
Alignment explanation
Indices: 323453--323479 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
323443 TTATTTTGAG
323453 CATAATAATAATAA
1 CATAATAATAATAA
323467 CATAATAATAATA
1 CATAATAATAATA
323480 TTACTATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (14 bp):
CATAATAATAATAA
Found at i:323683 original size:16 final size:17
Alignment explanation
Indices: 323662--323705 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
323652 TAATTTTTTA
*
323662 ATTTTTAATTTTAAA-T
1 ATTTTTAATTTAAAATT
*
323678 ATTTTTAACTATAAAATT
1 ATTTTTAA-TTTAAAATT
323696 ATTTTTAATT
1 ATTTTTAATT
323706 ATTATCAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 8 0.35
17 6 0.26
18 9 0.39
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTTAATTTAAAATT
Found at i:324202 original size:29 final size:29
Alignment explanation
Indices: 324121--324208 Score: 83
Period size: 29 Copynumber: 3.0 Consensus size: 29
324111 TTAAAGATAT
* *
324121 ATATATTTTTGATTAAATTTTTAAAAAAATTA
1 ATATATTTTT-A-TAAATATTT-AAAAAATAA
*
324153 A-ATA-TTTT-TAAATATTAAAAAAATAA
1 ATATATTTTTATAAATATTTAAAAAATAA
* *
324179 ATATATTTTTATAAAAATTTAAAAGATAA
1 ATATATTTTTATAAATATTTAAAAAATAA
324208 A
1 A
324209 CCTTTTTTAC
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
26 9 0.19
27 10 0.21
28 4 0.09
29 16 0.34
30 4 0.09
31 3 0.06
32 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (29 bp):
ATATATTTTTATAAATATTTAAAAAATAA
Found at i:324229 original size:3 final size:3
Alignment explanation
Indices: 324221--324250 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
324211 TTTTTTACTC
324221 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
324251 GGCAATGGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:324599 original size:3 final size:3
Alignment explanation
Indices: 324586--324620 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
324576 AAATTTAAAA
324586 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
324621 CTTCTCCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:326763 original size:2 final size:2
Alignment explanation
Indices: 326756--326804 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
326746 CTTCGCATGT
326756 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
326798 TC TC TC T
1 TC TC TC T
326805 ATGTTTCTCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:332281 original size:47 final size:47
Alignment explanation
Indices: 332230--332326 Score: 176
Period size: 47 Copynumber: 2.1 Consensus size: 47
332220 TAATAATAAC
*
332230 TAAGTTATTTAAATGATATAATAAATATTCAAAATTAGAAAACAATA
1 TAAGTTATTTAAATGATATAATAAATATTCAAAATTAAAAAACAATA
*
332277 TAAGTTATTTAAATGATATAATAACTATTCAAAATTAAAAAACAATA
1 TAAGTTATTTAAATGATATAATAAATATTCAAAATTAAAAAACAATA
332324 TAA
1 TAA
332327 ATATCAAATC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (47 bp):
TAAGTTATTTAAATGATATAATAAATATTCAAAATTAAAAAACAATA
Found at i:335658 original size:2 final size:2
Alignment explanation
Indices: 335651--335681 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
335641 TTTCTCCTAT
335651 GA GA GA 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 GA GA GA G
335682 GCGATAAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:340187 original size:6 final size:6
Alignment explanation
Indices: 340178--340235 Score: 52
Period size: 6 Copynumber: 9.8 Consensus size: 6
340168 TTTAATTTTA
*
340178 TATATT TATATT TATATT T-T-TT ATATATT TAATAAT TA-ATAT TATA-T
1 TATATT TATATT TATATT TATATT -TATATT T-ATATT TATAT-T TATATT
340225 TATATT TATAT
1 TATATT TATAT
340236 ATGACAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
4 2 0.05
5 8 0.19
6 25 0.58
7 8 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
TATATT
Found at i:340203 original size:23 final size:22
Alignment explanation
Indices: 340172--340235 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
340162 AATAAATTTA
340172 ATTTTATATATTTATATTTATAT
1 ATTTTATATATTTATATTTA-AT
* *
340195 TTTTTATATATTTAATAATTAAT
1 ATTTTATATATTT-ATATTTAAT
*
340218 ATTATATTATATTTATAT
1 ATTTTA-TATATTTATAT
340236 ATGACAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
23 21 0.62
24 13 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTTTATATATTTATATTTAAT
Found at i:340451 original size:30 final size:28
Alignment explanation
Indices: 340385--340466 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
340375 TAATTTATTT
* *
340385 AAATAA-TTTTTATTTTCTATTATACTC
1 AAATAATTTTTTATTTTTTATTTTACTC
*
340412 AAATTATTTTTTATTTTTTATTTTACAGTC
1 AAATAATTTTTTATTTTTTATTTTAC--TC
*
340442 AAATAATTTTTGAATTTTTTATTTT
1 AAATAATTTTT-TATTTTTTATTTT
340467 TGTCCAAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
27 5 0.11
28 17 0.37
30 12 0.26
31 12 0.26
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.61
Consensus pattern (28 bp):
AAATAATTTTTTATTTTTTATTTTACTC
Found at i:340475 original size:30 final size:29
Alignment explanation
Indices: 340385--340479 Score: 88
Period size: 30 Copynumber: 3.3 Consensus size: 29
340375 TAATTTATTT
* * *
340385 AAATAATTTTT-ATTTTCTATTAT-ACTC
1 AAATAATTTTTAATTTTTTATTTTAAGTC
* *
340412 AAATTATTTTTTATTTTTTATTTTACAGTC
1 AAATAATTTTTAATTTTTTATTTTA-AGTC
*
340442 AAATAATTTTTGAATTTTTTATTTT-TGTCC
1 AAATAATTTTT-AATTTTTTATTTTAAGT-C
340472 AAATAATT
1 AAATAATT
340480 ATATTTTTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
27 10 0.18
28 10 0.18
29 2 0.04
30 22 0.39
31 12 0.21
ACGTcount: A:0.32, C:0.07, G:0.03, T:0.58
Consensus pattern (29 bp):
AAATAATTTTTAATTTTTTATTTTAAGTC
Found at i:345464 original size:740 final size:739
Alignment explanation
Indices: 342849--345809 Score: 5575
Period size: 740 Copynumber: 4.0 Consensus size: 739
342839 AAATAATTAA
342849 TAAAATTATTAATTATTATATTTAATATAATAATATTTATTATAAACGATATATGGGTTTTTTAT
1 TAAAATTATTAATTATTATATTTAATATAATAATATTTATTATAAACGATATATGGGTTTTTTAT
342914 CATTTACAATTATAAAATTATATTAAATGGTAATAATTTATAATTTTATTTTGTAATAAAATTCA
66 CATTTACAATTATAAAATTATATTAAATGGTAATAATTTATAATTTTA-TTTGTAATAAAATTCA
342979 AATTTTATTATTATTTTTAAAAAAATTGTGTACAATTAATTAATGTGCTCCTTTTATTAAATACA
130 AATTTTATTATTATTTTTAAAAAAATTGTGTACAATTAATTAATGTGCTCCTTTTATTAAATACA
343044 AGAAAAATTATACATTAATTTTTTTTAATAAACATCATTTTAATTGATATCATTAAACATTAAAT
195 AGAAAAATTATACATTAATTTTTTTTAATAAACATCATTTTAATTGATATCATTAAACATTAAAT
343109 AATATTTTCCATTAATATTGAATTATATATATCTGCTGCCAATGACACATGACTGATTCAGAATT
260 AATATTTTCCATTAATATTGAATTATATATATCTGCTGCCAATGACACATGACTGATTCAGAATT
343174 TAATTATATATATTTGATTTGTTTTGAATGTTGAAACTGCATATTCTTAAATCAACATTTCTCTT
325 TAATTATATATATTTGATTTGTTTTGAATGTTGAAACTGCATATTCTTAAATCAACATTTCTCTT
343239 ATAGTTAAGAGTAGTTGCTAATAATAAAATAAAGCTCGAAGATGTTATACCTTCAAAGACATGAA
390 ATAGTTAAGAGTAGTTGCTAATAATAAAATAAAGCTCGAAGATGTTATACCTTCAAAGACATGAA
343304 AAACGTGCATGGATTTCTTTTTATTTTTTATTTCATAAGATTATATATGAATAAAAAGTAAATTA
455 AAACGTGCATGGATTTCTTTTTATTTTTTATTTCATAAGATTATATATGAATAAAAAGTAAATTA
343369 CAATAAAATCAATTCTTATATATTAAGTCTTAATGTGCATAATATAATGATTAATATATCCACAC
520 CAATAAAATCAATTCTTATATATTAAGTCTTAATGTGCATAATATAATGATTAATATATCCACAC
343434 GTAAAAAATTCGATAAAAAAATAAAATTATATAATATTTAAAAATTTCAAGATGTATTGAAACAG
585 GTAAAAAATTCGATAAAAAAATAAAATTATATAATATTTAAAAATTTCAAGATGTATTGAAACAG
343499 ATGTAATTAGATATTATTTTATTTTTATTAAGTATTTAAATTTTATTATTTAAATAAAATGAGAA
650 ATGTAATTAGATATTATTTTATTTTTATTAAGTATTTAAATTTTATTATTTAAATAAAATGAGAA
343564 GTATTTGAATGACATAATTTTTACT
715 GTATTTGAATGACATAATTTTTACT
343589 TAAAATTATTAATTATTATATTTAATATAATAATATTTATTATAAACGATATATGGG-TTTTTAT
1 TAAAATTATTAATTATTATATTTAATATAATAATATTTATTATAAACGATATATGGGTTTTTTAT
343653 CATTTACAATTATAAAATTATATTAAATGGTAATAATTTATAATTTTATTTGTAATAAAATTCAA
66 CATTTACAATTATAAAATTATATTAAATGGTAATAATTTATAATTTTATTTGTAATAAAATTCAA
343718 ATTTTATTATTATTTTTTAAAAAAATTGTGTACAATTAATTAATGTGCTCCTTTTATTAAATACA
131 ATTTTATTATTA-TTTTTAAAAAAATTGTGTACAATTAATTAATGTGCTCCTTTTATTAAATACA
343783 AGAAAAATTATACATTAATTTTTTTTAATAAACATCATTTTAATTGATATCATTAAACATTAAAT
195 AGAAAAATTATACATTAATTTTTTTTAATAAACATCATTTTAATTGATATCATTAAACATTAAAT
343848 AATATTTTCCATTAATATTGAATTATATATATCTGCTGCCAATGACACATGACTGATTCAGAATT
260 AATATTTTCCATTAATATTGAATTATATATATCTGCTGCCAATGACACATGACTGATTCAGAATT
343913 TAATTATATATATTTGATTTGTTTTGAATGTTGAAACTGCATATTCTTAAATCAACATTTCTCTT
325 TAATTATATATATTTGATTTGTTTTGAATGTTGAAACTGCATATTCTTAAATCAACATTTCTCTT
343978 ATAGTTAAGAGTAGTTGCTAATAATAAAATAAAGCTCGAAGATGTTATACCTTCAAAGACATGAA
390 ATAGTTAAGAGTAGTTGCTAATAATAAAATAAAGCTCGAAGATGTTATACCTTCAAAGACATGAA
344043 AAACGTGCATGGATTTCTTTTTA-TTTTTATTTCATAAGATTATATATGAATAAAAAGTAAATTA
455 AAACGTGCATGGATTTCTTTTTATTTTTTATTTCATAAGATTATATATGAATAAAAAGTAAATTA
344107 CAATAAAATCAATTCTTATATATTAAGTCTTAATGTGCATAATATAATGATTAATATATCCACAC
520 CAATAAAATCAATTCTTATATATTAAGTCTTAATGTGCATAATATAATGATTAATATATCCACAC
*
344172 GTAAAAAATTCGATAAAAAAATAAAATTATATAATATTT-AAAATTTCAAGATGTATTGGAACAG
585 GTAAAAAATTCGATAAAAAAATAAAATTATATAATATTTAAAAATTTCAAGATGTATTGAAACAG
344236 ATGTAATTAGATATTATTTTATTTTTATTAAGTATTTAAATTTTATTATTTAAATAAAATGAGAA
650 ATGTAATTAGATATTATTTTATTTTTATTAAGTATTTAAATTTTATTATTTAAATAAAATGAGAA
344301 GTATTTGAATGACATAATTTTTACT
715 GTATTTGAATGACATAATTTTTACT
344326 TAAAATTATT-ATTATTATATTTAATATAAT-ATATTTATTATAAACGATATATGGGTTTTTTAA
1 TAAAATTATTAATTATTATATTTAATATAATAATATTTATTATAAACGATATATGGGTTTTTT-A
* * * * * * *
344389 TCATTTACACTTCTCAAACTTATATTAAATGGGTCAT-CTTTATAA-TTTCTTGGTAATAAAATT
65 TCATTTACAATTAT-AAAATTATATTAAAT-GGTAATAATTTATAATTTTATTTGTAATAAAATT
*
344452 C-AA-TTTATTATTATTTTTACAACAAAATTGTGT-CAAATTACTTAATGTGCTCCTTTTATTAA
128 CAAATTTTATTATTATTTTTA-AA-AAAATTGTGTAC-AATTAATTAATGTGCTCCTTTTATTAA
*
344514 ATACAAGAAAAAATTATACATTAATTTTTTTTAAT-AACCTCATTTTAATTGATATCATTAAACA
190 ATACAAG-AAAAATTATACATTAATTTTTTTTAATAAACATCATTTTAATTGATATCATTAAACA
344578 TTAAATAATATTTTCCATTAATATTGAATTATATATATCTGCTGCCAATGACACATGACTGATTC
254 TTAAATAATATTTTCCATTAATATTGAATTATATATATCTGCTGCCAATGACACATGACTGATTC
344643 AGAATTTAATTATATATATTTGATTTGTTTTGAATGTTGAAACTGCATATTCTTAAATCAACATT
319 AGAATTTAATTATATATATTTGATTTGTTTTGAATGTTGAAACTGCATATTCTTAAATCAACATT
344708 TCTCTTATAGTTAAGAGTAGTTGCTAATAATAAAATAAAGCTCGAAGATGTTATACCTTCAAAGA
384 TCTCTTATAGTTAAGAGTAGTTGCTAATAATAAAATAAAGCTCGAAGATGTTATACCTTCAAAGA
344773 CATGAAAAACGTGCATGGATTTCTTTTTATTTTTTATTTCATAAGATTATATATGAATAAAAAGT
449 CATGAAAAACGTGCATGGATTTCTTTTTATTTTTTATTTCATAAGATTATATATGAATAAAAAGT
344838 AAATTACAATAAAATCAATTCTTATATATTAAGTCTTAATGTGCATAATATAATGATTAATATAT
514 AAATTACAATAAAATCAATTCTTATATATTAAGTCTTAATGTGCATAATATAATGATTAATATAT
344903 CCACACGTAAAAAATTCGATAAAAAAATAAAATTATATAATATTTAAAAATTTCAAGATGTATTG
579 CCACACGTAAAAAATTCGATAAAAAAATAAAATTATATAATATTTAAAAATTTCAAGATGTATTG
*
344968 GAACAGATGTAATTAGATATTATTTTATTTTTATTAAGTATTTAAATTTTATTATTTAAATAAAA
644 AAACAGATGTAATTAGATATTATTTTATTTTTATTAAGTATTTAAATTTTATTATTTAAATAAAA
345033 TGAGAAGTATTTGAATGACATAATTTTTACT
709 TGAGAAGTATTTGAATGACATAATTTTTACT
345064 TAAAATTATTAATTATTATATTTAATATAATAATATTTATTATAAACGATATATGGGTTTTTTAT
1 TAAAATTATTAATTATTATATTTAATATAATAATATTTATTATAAACGATATATGGGTTTTTTAT
345129 CATTTACAATTATAAAATTATATTAAATGGTAATAATTTATAATTTTATTTGTAATAAAATTCAA
66 CATTTACAATTATAAAATTATATTAAATGGTAATAATTTATAATTTTATTTGTAATAAAATTCAA
345194 ATTTTATTATTATTTTTTAAAAAAATTGTGTACAATTAATTAATGTGCTCCTTTTATTAAATACA
131 ATTTTATTATTA-TTTTTAAAAAAATTGTGTACAATTAATTAATGTGCTCCTTTTATTAAATACA
345259 AGAAAAATTATACATTAATTTTTTTTAATAAACATCATTTTAATTGATATCATTAAACATTAAAT
195 AGAAAAATTATACATTAATTTTTTTTAATAAACATCATTTTAATTGATATCATTAAACATTAAAT
345324 AATATTTTCCATTAATATTGAATTATATATATCTGCTGCCAATGACACATGACTGATTCAGAATT
260 AATATTTTCCATTAATATTGAATTATATATATCTGCTGCCAATGACACATGACTGATTCAGAATT
345389 TAATTATATATATTTGATTTGTTTTGAATGTTGAAACTGCATATTCTTAAATCAACATTTCTCTT
325 TAATTATATATATTTGATTTGTTTTGAATGTTGAAACTGCATATTCTTAAATCAACATTTCTCTT
345454 ATAGTTAAGAGTAGTTGCTAATAATAAAATAAAGCTCGAAGATGTTATACCTTCAAAGACATGAA
390 ATAGTTAAGAGTAGTTGCTAATAATAAAATAAAGCTCGAAGATGTTATACCTTCAAAGACATGAA
345519 AAACGTGCATGGATTTCTTTTTATTTTTTATTTCATAAGATTATATATGAATAAAAAGTAAATTA
455 AAACGTGCATGGATTTCTTTTTATTTTTTATTTCATAAGATTATATATGAATAAAAAGTAAATTA
345584 CAATAAAATCAATTCTTATATATTAAGTCTTAATGTGCATAATATAATGATTAATATATCCACAC
520 CAATAAAATCAATTCTTATATATTAAGTCTTAATGTGCATAATATAATGATTAATATATCCACAC
** * * * * * * *
345649 ACAAAAAATTTGATAAAAAAATAAAGTTACATAATATTTAAAGATTTTAAAACGTATTGAAACAG
585 GTAAAAAATTCGATAAAAAAATAAAATTATATAATATTTAAAAATTTCAAGATGTATTGAAACAG
345714 ATGTAATTAGATATTATTTTATTTTTATTAAGTATTTAAATTTTATTATTTAAATAAAATGAGAA
650 ATGTAATTAGATATTATTTTATTTTTATTAAGTATTTAAATTTTATTATTTAAATAAAATGAGAA
345779 GTATTTGAATGACATAATTTTTACT
715 GTATTTGAATGACATAATTTTTACT
345804 TAAAAT
1 TAAAAT
345810 GATTTATTTA
Statistics
Matches: 2172, Mismatches: 29, Indels: 40
0.97 0.01 0.02
Matches are distributed among these distances:
734 6 0.00
735 38 0.02
736 322 0.15
737 331 0.15
738 341 0.16
739 472 0.22
740 643 0.30
741 13 0.01
742 6 0.00
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (739 bp):
TAAAATTATTAATTATTATATTTAATATAATAATATTTATTATAAACGATATATGGGTTTTTTAT
CATTTACAATTATAAAATTATATTAAATGGTAATAATTTATAATTTTATTTGTAATAAAATTCAA
ATTTTATTATTATTTTTAAAAAAATTGTGTACAATTAATTAATGTGCTCCTTTTATTAAATACAA
GAAAAATTATACATTAATTTTTTTTAATAAACATCATTTTAATTGATATCATTAAACATTAAATA
ATATTTTCCATTAATATTGAATTATATATATCTGCTGCCAATGACACATGACTGATTCAGAATTT
AATTATATATATTTGATTTGTTTTGAATGTTGAAACTGCATATTCTTAAATCAACATTTCTCTTA
TAGTTAAGAGTAGTTGCTAATAATAAAATAAAGCTCGAAGATGTTATACCTTCAAAGACATGAAA
AACGTGCATGGATTTCTTTTTATTTTTTATTTCATAAGATTATATATGAATAAAAAGTAAATTAC
AATAAAATCAATTCTTATATATTAAGTCTTAATGTGCATAATATAATGATTAATATATCCACACG
TAAAAAATTCGATAAAAAAATAAAATTATATAATATTTAAAAATTTCAAGATGTATTGAAACAGA
TGTAATTAGATATTATTTTATTTTTATTAAGTATTTAAATTTTATTATTTAAATAAAATGAGAAG
TATTTGAATGACATAATTTTTACT
Found at i:345847 original size:3 final size:3
Alignment explanation
Indices: 345839--345867 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
345829 ATGAGTTCTT
345839 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
345868 TTGAATTTCA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:346932 original size:21 final size:21
Alignment explanation
Indices: 346877--346937 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
346867 TTTTAAATTA
*
346877 ATTTAATTTTAAATATAATTTT
1 ATTTAAATTT-AATATAATTTT
* ** *
346899 AATTAAAAATAATATATTTTT
1 ATTTAAATTTAATATAATTTT
346920 ATTTAAATTTAATTATAA
1 ATTTAAATTTAA-TATAA
346938 AATATATAAA
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
21 19 0.66
22 10 0.34
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTTAAATTTAATATAATTTT
Found at i:346954 original size:33 final size:31
Alignment explanation
Indices: 346889--346959 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 31
346879 TTAATTTTAA
* * *
346889 ATATAATTTTAATTAAAAATAATATATTTTT
1 ATATAAATTTAATTAAAAATAATAAATATTT
*
346920 ATTTAAATTTAATTATAAAATATATAAATATTT
1 ATATAAATTTAATTA-AAAATA-ATAAATATTT
346953 ATATAAA
1 ATATAAA
346960 AATAATTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
31 13 0.39
32 6 0.18
33 14 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
ATATAAATTTAATTAAAAATAATAAATATTT
Found at i:346966 original size:33 final size:31
Alignment explanation
Indices: 346898--346966 Score: 75
Period size: 33 Copynumber: 2.2 Consensus size: 31
346888 AATATAATTT
* * * **
346898 TAATTAAAAATAATATATTTTTATTTAAATT
1 TAATTAAAAATAATAAATATTTATATAAAAA
346929 TAATTATAAAATATATAAATATTTATATAAAAA
1 TAATTA-AAAATA-ATAAATATTTATATAAAAA
346962 TAATT
1 TAATT
346967 TTTAATATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 6 0.19
32 6 0.19
33 19 0.61
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
TAATTAAAAATAATAAATATTTATATAAAAA
Found at i:346997 original size:25 final size:26
Alignment explanation
Indices: 346937--346997 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 26
346927 TTTAATTATA
*
346937 AAATATATAA-ATATTTATATAAAAAT
1 AAATA-ATAATATATTTAAATAAAAAT
* **
346963 AATTTTTAATAT-TTTAAATAAAAAT
1 AAATAATAATATATTTAAATAAAAAT
346988 AAATAATAAT
1 AAATAATAAT
346998 TTAAATTATC
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
AAATAATAATATATTTAAATAAAAAT
Found at i:347000 original size:22 final size:22
Alignment explanation
Indices: 346925--347003 Score: 61
Period size: 22 Copynumber: 3.4 Consensus size: 22
346915 TTTTTATTTA
* *
346925 AATTTAATTATAAAATATATAA-
1 AATTTAAATA-AAAATAAATAAT
* *
346947 ATATTTATATAAAAATAATTTTTAAT
1 A-ATTTAAATAAAAATAA---ATAAT
*
346973 ATTTTAAATAAAAATAAATAAT
1 AATTTAAATAAAAATAAATAAT
346995 AATTTAAAT
1 AATTTAAAT
347004 TATCAAATTA
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
22 19 0.43
23 7 0.16
25 17 0.39
26 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTTAAATAAAAATAAATAAT
Found at i:349166 original size:12 final size:12
Alignment explanation
Indices: 349149--349200 Score: 67
Period size: 12 Copynumber: 4.7 Consensus size: 12
349139 AAAATTTAAT
349149 TTTTATATTATA
1 TTTTATATTATA
349161 TTTTATATTATA
1 TTTTATATTATA
*
349173 TTATA-ATTA-A
1 TTTTATATTATA
349183 TTTT-TATTATA
1 TTTTATATTATA
349194 -TTTATAT
1 TTTTATAT
349201 GGTAGAGTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
10 11 0.31
11 8 0.23
12 16 0.46
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTTATATTATA
Found at i:353896 original size:2 final size:2
Alignment explanation
Indices: 353889--353916 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
353879 AAATTTCTAC
353889 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
353917 TATATATCAT
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:358000 original size:16 final size:16
Alignment explanation
Indices: 357967--358000 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
357957 AATATTTTAG
*
357967 TAAACATAAAATGTAA
1 TAAACATAAAATGAAA
*
357983 TAAACATAACATGAAA
1 TAAACATAAAATGAAA
357999 TA
1 TA
358001 TTTAAACATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.09, G:0.06, T:0.24
Consensus pattern (16 bp):
TAAACATAAAATGAAA
Found at i:360297 original size:16 final size:17
Alignment explanation
Indices: 360276--360310 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
360266 ATATTTTGTT
360276 TAAATTTA-AAATAAAA
1 TAAATTTAGAAATAAAA
360292 TAAATTTATGAAATAAAA
1 TAAATTTA-GAAATAAAA
360310 T
1 T
360311 GAAAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
TAAATTTAGAAATAAAA
Found at i:360373 original size:2 final size:2
Alignment explanation
Indices: 360366--360399 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
360356 TTATCTTGTA
360366 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
360400 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:366623 original size:9 final size:9
Alignment explanation
Indices: 366593--366617 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
366583 TCTCTTTTTT
366593 TTTTTTTAA
1 TTTTTTTAA
366602 TTTTTTTAA
1 TTTTTTTAA
366611 TTTTTTT
1 TTTTTTT
366618 CTTTTTGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:366629 original size:26 final size:24
Alignment explanation
Indices: 366587--366648 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
366577 CTTTTCTCTC
* *
366587 TTTTTTTTTTTTTAATTTTTTTAA
1 TTTTTTTTTTTTGAATTTATTTAA
366611 TTTTTTTCTTTTTGGAATTTATTT-A
1 TTTTTTT-TTTTT-GAATTTATTTAA
* *
366636 TTTATTTATTTTG
1 TTTTTTTTTTTTG
366649 TTGTTATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
23 1 0.03
24 11 0.34
25 12 0.38
26 8 0.25
ACGTcount: A:0.16, C:0.02, G:0.05, T:0.77
Consensus pattern (24 bp):
TTTTTTTTTTTTGAATTTATTTAA
Found at i:378192 original size:5 final size:5
Alignment explanation
Indices: 378182--378206 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
378172 TGAACCTGCT
378182 TTGGA TTGGA TTGGA TTGGA TTGGA
1 TTGGA TTGGA TTGGA TTGGA TTGGA
378207 GCACAAAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (5 bp):
TTGGA
Found at i:379220 original size:2 final size:2
Alignment explanation
Indices: 379213--379247 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
379203 TATTTTAAAA
379213 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
379248 AATACCTAAT
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:395965 original size:12 final size:12
Alignment explanation
Indices: 395948--395972 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
395938 GGCAACACAT
395948 ACGTATAGCCAA
1 ACGTATAGCCAA
395960 ACGTATAGCCAA
1 ACGTATAGCCAA
395972 A
1 A
395973 TATACAGCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.24, G:0.16, T:0.16
Consensus pattern (12 bp):
ACGTATAGCCAA
Found at i:397059 original size:2 final size:2
Alignment explanation
Indices: 397052--397082 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
397042 AAAAAGTAAA
397052 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
397083 GCAATAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:397759 original size:2 final size:2
Alignment explanation
Indices: 397752--397778 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
397742 CAAAGGGGGA
397752 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 A
397779 ACGAGTCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:398678 original size:24 final size:24
Alignment explanation
Indices: 398651--398706 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
398641 TTTAAACACA
398651 AAATA-AATATAATAAAATATATTT
1 AAATATAAT-TAATAAAATATATTT
**
398675 AAATATAATTAATATGATATATTT
1 AAATATAATTAATAAAATATATTT
398699 AATATATA
1 AA-ATATA
398707 TTATATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 20 0.71
25 8 0.29
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
AAATATAATTAATAAAATATATTT
Found at i:398700 original size:14 final size:13
Alignment explanation
Indices: 398667--398707 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 13
398657 ATATAATAAA
398667 ATATATTTAA-AT
1 ATATATTTAATAT
398679 ATA-A-TTAATAT
1 ATATATTTAATAT
398690 GATATATTTAATAT
1 -ATATATTTAATAT
398704 ATAT
1 ATAT
398708 TATATTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
10 4 0.16
11 3 0.12
12 6 0.24
13 5 0.20
14 7 0.28
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (13 bp):
ATATATTTAATAT
Found at i:398707 original size:11 final size:12
Alignment explanation
Indices: 398667--398723 Score: 57
Period size: 11 Copynumber: 4.9 Consensus size: 12
398657 ATATAATAAA
*
398667 ATATATTTAAAT
1 ATATATTTATAT
*
398679 ATA-ATTAATAT
1 ATATATTTATAT
398690 GATATATTTA-AT
1 -ATATATTTATAT
398702 ATATA-TTATAT
1 ATATATTTATAT
*
398713 TTATATTTATA
1 ATATATTTATA
398724 AATAACATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 3 0.08
11 17 0.46
12 13 0.35
13 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (12 bp):
ATATATTTATAT
Found at i:398709 original size:24 final size:22
Alignment explanation
Indices: 398654--398721 Score: 70
Period size: 23 Copynumber: 3.1 Consensus size: 22
398644 AAACACAAAA
*
398654 TAAATATAA-TA-AAATATATT
1 TAAATATAATTATATATATATT
398674 TAAATATAATTAATATGATATATT
1 TAAATATAATT-ATAT-ATATATT
*
398698 T-AATATATATTATATTTATATT
1 TAAATATA-ATTATATATATATT
398720 TA
1 TA
398722 TAAATAACAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
20 9 0.22
21 1 0.03
22 8 0.20
23 11 0.28
24 11 0.28
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (22 bp):
TAAATATAATTATATATATATT
Found at i:407890 original size:10 final size:11
Alignment explanation
Indices: 407852--407890 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
407842 GATATAAAAA
*
407852 ATAACATAAAT
1 ATAAAATAAAT
407863 ATAAAATAAAT
1 ATAAAATAAAT
*
407874 ATAAAATATAT
1 ATAAAATAAAT
407885 -TAAAAT
1 ATAAAAT
407891 TTATATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 6 0.23
11 20 0.77
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (11 bp):
ATAAAATAAAT
Found at i:422671 original size:2 final size:2
Alignment explanation
Indices: 422666--422692 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
422656 AAAAAAGAGC
422666 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 C
422693 AGAGAGAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:424865 original size:16 final size:17
Alignment explanation
Indices: 424846--424879 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
424836 AAAATGTTAG
*
424846 AAAAGTAAAAAAT-AAA
1 AAAAATAAAAAATGAAA
424862 AAAAATAAAAAATGAAA
1 AAAAATAAAAAATGAAA
424879 A
1 A
424880 TATAGTAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (17 bp):
AAAAATAAAAAATGAAA
Found at i:426644 original size:80 final size:80
Alignment explanation
Indices: 426552--426715 Score: 310
Period size: 80 Copynumber: 2.0 Consensus size: 80
426542 AAATAAAACA
*
426552 AACAAAAAATAAAAAAATAAAACCAAAATTCATTTTTAGCATTTAAGTTTCACATTGTGCTTTCT
1 AACAAAAAATAAAAAAATAAAACCAAAATTCATTTTTAGCATTTAAGTTTCACATTATGCTTTCT
426617 GATGTTCAAAGCTCT
66 GATGTTCAAAGCTCT
*
426632 AACAAAATATAAAAAAATAAAACCAAAATTCATTTTTAGCATTTAAGTTTCACATTATGCTTTCT
1 AACAAAAAATAAAAAAATAAAACCAAAATTCATTTTTAGCATTTAAGTTTCACATTATGCTTTCT
426697 GATGTTCAAAGCTCT
66 GATGTTCAAAGCTCT
426712 AACA
1 AACA
426716 TCCCATGTGA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
80 82 1.00
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.34
Consensus pattern (80 bp):
AACAAAAAATAAAAAAATAAAACCAAAATTCATTTTTAGCATTTAAGTTTCACATTATGCTTTCT
GATGTTCAAAGCTCT
Found at i:429933 original size:30 final size:30
Alignment explanation
Indices: 429892--429960 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
429882 CATATACAGG
*
429892 AGCTGGCGGTGGAGGTGAA-TGGTAATGAAC
1 AGCTGGTGGTGGAGGTGAAGT-GTAATGAAC
*
429922 TGCTGGTGGTGGAGGTGAAGTGTAATGAAC
1 AGCTGGTGGTGGAGGTGAAGTGTAATGAAC
*
429952 AGGTGGTGG
1 AGCTGGTGG
429961 CGGCGGTGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 33 0.97
31 1 0.03
ACGTcount: A:0.23, C:0.07, G:0.46, T:0.23
Consensus pattern (30 bp):
AGCTGGTGGTGGAGGTGAAGTGTAATGAAC
Found at i:430002 original size:30 final size:30
Alignment explanation
Indices: 429926--430003 Score: 81
Period size: 30 Copynumber: 2.7 Consensus size: 30
429916 ATGAACTGCT
*
429926 GGTGGTGGAGGTGAA-GTG--TAATGAACA
1 GGTGGTGGAGGTGAAGGTGATTAATAAACA
* * ** *
429953 GGTGGTGGCGGCGGTGGTGATTTATAAACA
1 GGTGGTGGAGGTGAAGGTGATTAATAAACA
429983 GGTGGTGGAGGTGAAGGTGAT
1 GGTGGTGGAGGTGAAGGTGAT
430004 GGGGGTGGTT
Statistics
Matches: 38, Mismatches: 10, Indels: 3
0.75 0.20 0.06
Matches are distributed among these distances:
27 11 0.29
28 3 0.08
30 24 0.63
ACGTcount: A:0.23, C:0.05, G:0.47, T:0.24
Consensus pattern (30 bp):
GGTGGTGGAGGTGAAGGTGATTAATAAACA
Found at i:430224 original size:21 final size:22
Alignment explanation
Indices: 430173--430230 Score: 57
Period size: 24 Copynumber: 2.6 Consensus size: 22
430163 GGAGGGGGTG
*
430173 AATGAGGAGGTGGCGGTGGAGA
1 AATGTGGAGGTGGCGGTGGAGA
430195 ATATAGTGGAGGTGGCGGT-GA-A
1 A-AT-GTGGAGGTGGCGGTGGAGA
*
430217 TAATGTGGTGGTGG
1 -AATGTGGAGGTGG
430231 TGGGGAGCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
21 9 0.29
22 4 0.13
23 5 0.16
24 13 0.42
ACGTcount: A:0.24, C:0.03, G:0.50, T:0.22
Consensus pattern (22 bp):
AATGTGGAGGTGGCGGTGGAGA
Found at i:430367 original size:12 final size:12
Alignment explanation
Indices: 430352--430423 Score: 51
Period size: 12 Copynumber: 5.8 Consensus size: 12
430342 AGTTGGTGAA
430352 GGTGGTGGAGGT
1 GGTGGTGGAGGT
430364 GGTGATAGTGG-GGAT
1 GGTG---GTGGAGG-T
430379 GG-GGATGGAGGT
1 GGTGG-TGGAGGT
*
430391 GGAGGTGGAGGT
1 GGTGGTGGAGGT
* *
430403 GGAGGTGGAGGC
1 GGTGGTGGAGGT
430415 GGTGG-GGAG
1 GGTGGTGGAG
430424 TAAACTGGTG
Statistics
Matches: 51, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
11 5 0.10
12 32 0.63
13 4 0.08
14 3 0.06
15 7 0.14
ACGTcount: A:0.15, C:0.01, G:0.65, T:0.18
Consensus pattern (12 bp):
GGTGGTGGAGGT
Found at i:430393 original size:6 final size:6
Alignment explanation
Indices: 430384--430413 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
430374 GGGATGGGGA
430384 TGGAGG TGGAGG TGGAGG TGGAGG TGGAGG
1 TGGAGG TGGAGG TGGAGG TGGAGG TGGAGG
430414 CGGTGGGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.67, T:0.17
Consensus pattern (6 bp):
TGGAGG
Found at i:430487 original size:9 final size:9
Alignment explanation
Indices: 430333--430479 Score: 70
Period size: 9 Copynumber: 16.0 Consensus size: 9
430323 CACAGTATGT
*
430333 AGGTGTTGG
1 AGGTGGTGG
* *
430342 AGTTGGTGA
1 AGGTGGTGG
430351 AGGTGGTGG
1 AGGTGGTGG
430360 AGGTGGT-G
1 AGGTGGTGG
*
430368 ATAGTGG-GG
1 A-GGTGGTGG
430377 ATGG-GGATGG
1 A-GGTGG-TGG
*
430387 AGGTGGAGG
1 AGGTGGTGG
* *
430396 TGGAGGTGG
1 AGGTGGTGG
*
430405 AGGTGGAGG
1 AGGTGGTGG
*
430414 CGGTGG-GG
1 AGGTGGTGG
*
430422 AGTAAACTGGTGG
1 AG----GTGGTGG
430435 AGGTGGTGG
1 AGGTGGTGG
* *
430444 CGGTGGTGA
1 AGGTGGTGG
430453 AGGTGGTGG
1 AGGTGGTGG
430462 AGGTGAG-GG
1 AGGTG-GTGG
*
430471 CGGTGGTGG
1 AGGTGGTGG
430480 GGGAGGTGAG
Statistics
Matches: 103, Mismatches: 23, Indels: 24
0.69 0.15 0.16
Matches are distributed among these distances:
8 8 0.08
9 82 0.80
10 6 0.06
12 3 0.03
13 4 0.04
ACGTcount: A:0.16, C:0.03, G:0.61, T:0.21
Consensus pattern (9 bp):
AGGTGGTGG
Found at i:430581 original size:48 final size:48
Alignment explanation
Indices: 430529--430636 Score: 146
Period size: 48 Copynumber: 2.2 Consensus size: 48
430519 GGGAGTGGGA
*
430529 GGTGGAGGTGG-AGAGTAAACAGGTGGTGGGGGCGGAGGTGAATAAACT
1 GGTGGAGGAGGTAGAG-AAACAGGTGGTGGGGGCGGAGGTGAATAAACT
* * ***
430577 GGTGGAGGAGGTGGAGGAGGGGGTGGTGGGGGCGGAGGTGAATAAACT
1 GGTGGAGGAGGTAGAGAAACAGGTGGTGGGGGCGGAGGTGAATAAACT
430625 GGTGGAGGAGGT
1 GGTGGAGGAGGT
430637 GGAGGAGGGG
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
48 50 0.94
49 3 0.06
ACGTcount: A:0.23, C:0.05, G:0.56, T:0.16
Consensus pattern (48 bp):
GGTGGAGGAGGTAGAGAAACAGGTGGTGGGGGCGGAGGTGAATAAACT
Found at i:430637 original size:48 final size:48
Alignment explanation
Indices: 430550--430653 Score: 208
Period size: 48 Copynumber: 2.2 Consensus size: 48
430540 AGAGTAAACA
430550 GGTGGTGGGGGCGGAGGTGAATAAACTGGTGGAGGAGGTGGAGGAGGG
1 GGTGGTGGGGGCGGAGGTGAATAAACTGGTGGAGGAGGTGGAGGAGGG
430598 GGTGGTGGGGGCGGAGGTGAATAAACTGGTGGAGGAGGTGGAGGAGGG
1 GGTGGTGGGGGCGGAGGTGAATAAACTGGTGGAGGAGGTGGAGGAGGG
430646 GGTGGTGG
1 GGTGGTGG
430654 AGAGTATAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 56 1.00
ACGTcount: A:0.19, C:0.04, G:0.62, T:0.15
Consensus pattern (48 bp):
GGTGGTGGGGGCGGAGGTGAATAAACTGGTGGAGGAGGTGGAGGAGGG
Found at i:430640 original size:27 final size:27
Alignment explanation
Indices: 430526--430641 Score: 73
Period size: 27 Copynumber: 4.4 Consensus size: 27
430516 AGGGGGAGTG
* *
430526 GGAGGTGGAGGTGGAGAGTAAACAGGTGGT
1 GGAGGTGGAGGT-GA-A-TAAACTGGTGGA
* *
430556 GGGGGCGGAGGTGAATAAACTGGTGGA
1 GGAGGTGGAGGTGAATAAACTGGTGGA
*** *
430583 GGAGGTGGA-G-G----AGGGGGTGGT
1 GGAGGTGGAGGTGAATAAACTGGTGGA
* *
430604 GGGGGCGGAGGTGAATAAACTGGTGGA
1 GGAGGTGGAGGTGAATAAACTGGTGGA
430631 GGAGGTGGAGG
1 GGAGGTGGAGG
430642 AGGGGGTGGT
Statistics
Matches: 62, Mismatches: 18, Indels: 15
0.65 0.19 0.16
Matches are distributed among these distances:
21 13 0.21
22 1 0.02
23 1 0.02
25 1 0.02
26 1 0.02
27 32 0.52
28 1 0.02
29 2 0.03
30 10 0.16
ACGTcount: A:0.23, C:0.04, G:0.58, T:0.15
Consensus pattern (27 bp):
GGAGGTGGAGGTGAATAAACTGGTGGA
Found at i:433122 original size:21 final size:21
Alignment explanation
Indices: 433079--433122 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
433069 TTTTTAATTA
* * * *
433079 ATAATATATTATATATTATAT
1 ATAATAAATTAAATAATAAAT
433100 ATAATAAATTAAATAATAAAT
1 ATAATAAATTAAATAATAAAT
433121 AT
1 AT
433123 TTAATTTAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATAATAAATTAAATAATAAAT
Found at i:436382 original size:11 final size:12
Alignment explanation
Indices: 436366--436397 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
436356 TAATATATGA
436366 AATAATAATA-T
1 AATAATAATAGT
436377 AATAATAATAGT
1 AATAATAATAGT
436389 AATAA-AATA
1 AATAATAATA
436398 ATACAACAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (12 bp):
AATAATAATAGT
Found at i:436391 original size:17 final size:17
Alignment explanation
Indices: 436366--436400 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
436356 TAATATATGA
*
436366 AATAATAATATAATAAT
1 AATAATAATAAAATAAT
*
436383 AATAGTAATAAAATAAT
1 AATAATAATAAAATAAT
436400 A
1 A
436401 CAACAATCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (17 bp):
AATAATAATAAAATAAT
Found at i:442335 original size:30 final size:30
Alignment explanation
Indices: 442301--442359 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
442291 TCTGCTGCAG
*
442301 ATCCTCTAACTAGTGGTTATCACTGTAACC
1 ATCCTCTAACTAGTAGTTATCACTGTAACC
*
442331 ATCCTGTAACTAGTAGTTATCACTGTAAC
1 ATCCTCTAACTAGTAGTTATCACTGTAAC
442360 TTAGCTTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.34
Consensus pattern (30 bp):
ATCCTCTAACTAGTAGTTATCACTGTAACC
Found at i:445156 original size:2 final size:2
Alignment explanation
Indices: 445101--445137 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
445091 TTCCATGAAG
445101 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
445138 GCTAAATAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:448687 original size:2 final size:2
Alignment explanation
Indices: 448682--448707 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
448672 ATTTTTTAAC
448682 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
448708 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:448712 original size:2 final size:2
Alignment explanation
Indices: 448707--448743 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
448697 TCTCTCTCTC
448707 TA TA 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 TA TA T
448744 CTAAGTATAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:448948 original size:2 final size:2
Alignment explanation
Indices: 448943--448967 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
448933 AATGTATGTG
448943 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
448968 GAAATTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:449735 original size:20 final size:19
Alignment explanation
Indices: 449686--449735 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
449676 CATAAAATCG
449686 TAATTGAAATCAAATTCAT
1 TAATTGAAATCAAATTCAT
*
449705 TAA-TGCAAAATCAAATTTATT
1 TAATTG--AAATCAAATTCA-T
449726 TAATTGAAAT
1 TAATTGAAAT
449736 ATTTAAGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 2 0.08
19 3 0.12
20 15 0.58
21 4 0.15
22 2 0.08
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (19 bp):
TAATTGAAATCAAATTCAT
Found at i:449944 original size:2 final size:2
Alignment explanation
Indices: 449925--449960 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
449915 TGTATATGTC
449925 AT AT AT -T AT A- AT AT -T AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
449961 AATTTTTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.10
2 28 0.90
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:452473 original size:17 final size:18
Alignment explanation
Indices: 452438--452549 Score: 74
Period size: 18 Copynumber: 6.2 Consensus size: 18
452428 GACATATGAA
452438 AAAATAATATAAATATAT
1 AAAATAATATAAATATAT
*
452456 AAAATATTA-AAATTTATAT
1 AAAATAATATAAA--TATAT
**
452475 CAAAATAATA-ATTTATAT
1 -AAAATAATATAAATATAT
*
452493 -AAA-AATA-AAATACTTT
1 AAAATAATATAAATA-TAT
*
452509 AAATATAATTATAAA-ATGTT
1 AAA-ATAA-TATAAATAT-AT
452529 AAAATAATATAAATATAT
1 AAAATAATATAAATATAT
452547 AAA
1 AAA
452550 TTATCAAATT
Statistics
Matches: 75, Mismatches: 8, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
15 7 0.09
16 5 0.07
17 5 0.07
18 24 0.32
19 14 0.19
20 17 0.23
21 3 0.04
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.36
Consensus pattern (18 bp):
AAAATAATATAAATATAT
Found at i:461216 original size:2 final size:2
Alignment explanation
Indices: 461209--461246 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
461199 TTTCATTAAA
461209 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
461247 CAATGAGATT
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:461644 original size:279 final size:288
Alignment explanation
Indices: 461331--461892 Score: 831
Period size: 279 Copynumber: 2.0 Consensus size: 288
461321 CAAAAAAAAA
* * * *
461331 TTTGTATTTTGTTGATAATAGTAGATCAATATATATATATATATATAATATTTATATCTAAGTGA
1 TTTGTATTATGTTGATAATAATAGATCAATATATATATATATATATAATATTTATATCTAAATAA
* ** *
461396 ATATTGAATAGGATTATGTATTAAATATAAATATATTTAATTTTTGT-AAAAAATATTATTTGTA
66 ATATTAAATAAAATTATGTATTAAATATAAATATATTTAATTTTTATAAAAAAATATTATTTGTA
* *
461460 TTTAAAAAAATTATATTTTATATTTATACTCGAA-T-ATGTATAGA-ATA-A-A-ATAT-TAGAT
131 TTTAAAAAAATTATATTTTATATTCATACTC-AATTCATATATAGATATATATATATATATAGAT
* *
461518 ATA-AAT-ATA-TAAAGAATTCAAAACACAAATATATATATATCTATACACGCCCGCGCAGGAGA
195 ATAGAATAATATTAAAAAATTCAAAACAC-AATATATATATATATATACACGCCCGCGCAGGAGA
461580 TGGCCCTCCCTGATCAATAATGCAAAATTT
259 TGGCCCTCCCTGATCAATAATGCAAAATTT
*
461610 TTTGTATTATGTTGATAATAATAGATCAATATATATATATATATATAATATTTATATGTAAATAA
1 TTTGTATTATGTTGATAATAATAGATCAATATATATATATATATATAATATTTATATCTAAATAA
* *
461675 ATATTAAATAAAATTATGTATTAAATATAAATGTATTTAGTTTTTATAAAAAAATATTATTTGTA
66 ATATTAAATAAAATTATGTATTAAATATAAATATATTTAATTTTTATAAAAAAATATTATTTGTA
* * *
461740 TTTAAAAAAATTATATTTTATATTCATATTCAATTCATATATATATATATATATATATATATATA
131 TTTAAAAAAATTATATTTTATATTCATACTCAATTCATATATAGATATATATATATATATAGATA
**
461805 TAGAATAATATTTAAAAAATTCAAAACACAATATATATATATATATACACGCGTGCGCAGGAGAT
196 TAGAATAATA-TTAAAAAATTCAAAACACAATATATATATATATATACACGCCCGCGCAGGAGAT
*
461870 GGCCCTCCCTGATCAATACTGCA
260 GGCCCTCCCTGATCAATAATGCA
461893 TGGACTCCCC
Statistics
Matches: 250, Mismatches: 21, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
279 103 0.41
280 47 0.19
281 7 0.03
282 3 0.01
283 1 0.00
284 1 0.00
285 4 0.02
286 7 0.03
287 3 0.01
288 3 0.01
289 55 0.22
290 16 0.06
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.40
Consensus pattern (288 bp):
TTTGTATTATGTTGATAATAATAGATCAATATATATATATATATATAATATTTATATCTAAATAA
ATATTAAATAAAATTATGTATTAAATATAAATATATTTAATTTTTATAAAAAAATATTATTTGTA
TTTAAAAAAATTATATTTTATATTCATACTCAATTCATATATAGATATATATATATATATAGATA
TAGAATAATATTAAAAAATTCAAAACACAATATATATATATATATACACGCCCGCGCAGGAGATG
GCCCTCCCTGATCAATAATGCAAAATTT
Found at i:461763 original size:22 final size:21
Alignment explanation
Indices: 461721--461763 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
461711 TTAGTTTTTA
*
461721 TAAAAAAATATTATTTGTATT
1 TAAAAAAATATTATTTATATT
461742 TAAAAAAAT-TATATTTTATATT
1 TAAAAAAATAT-TA-TTTATATT
461764 CATATTCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 1 0.05
21 11 0.58
22 7 0.37
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
TAAAAAAATATTATTTATATT
Found at i:461783 original size:2 final size:2
Alignment explanation
Indices: 461776--461806 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
461766 TATTCAATTC
461776 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 A
461807 GAATAATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:480860 original size:16 final size:16
Alignment explanation
Indices: 480839--480869 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
480829 ATTTGAAATG
480839 ACAAATTAAATTTTAA
1 ACAAATTAAATTTTAA
480855 ACAAATTAAATTTTA
1 ACAAATTAAATTTTA
480870 CATTATCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (16 bp):
ACAAATTAAATTTTAA
Done.