Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168137.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_38, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 382840
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.40
Warning! 2000 characters in sequence are not A, C, G, or T
File 4 of 8
Found at i:126053 original size:20 final size:20
Alignment explanation
Indices: 126030--126082 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 20
126020 TATTAGTAGT
*
126030 AATTATTAATATTTATGATA
1 AATTATTAATATTTATAATA
126050 AATTA--AA-ATTTATAATA
1 AATTATTAATATTTATAATA
*
126067 AATAATTAATATTTAT
1 AATTATTAATATTTAT
126083 TATTAATAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 13 0.46
18 2 0.07
19 2 0.07
20 11 0.39
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
AATTATTAATATTTATAATA
Found at i:126090 original size:20 final size:20
Alignment explanation
Indices: 126029--126098 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
126019 ATATTAGTAG
* *
126029 TAATTATTAATATTTATGA-
1 TAATAATTAATATTTATAAT
*
126048 T-A-AATTAAAATTTATAAT
1 TAATAATTAATATTTATAAT
* *
126066 AAATAATTAATATTTATTAT
1 TAATAATTAATATTTATAAT
*
126086 TAATAAGTAATAT
1 TAATAATTAATAT
126099 CAATAAATTA
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
17 12 0.30
18 1 0.03
19 2 0.05
20 25 0.62
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
TAATAATTAATATTTATAAT
Found at i:126225 original size:20 final size:19
Alignment explanation
Indices: 126202--126256 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 19
126192 TATTATTATT
*
126202 ATAATTATTATAATATTTGG
1 ATAATTATTATAATAATT-G
126222 ATAATTTATTCAT-ATAATTG
1 ATAA-TTATT-ATAATAATTG
126242 ATAATTATTA-AATAA
1 ATAATTATTATAATAA
126257 CTAATATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 5 0.16
19 5 0.16
20 9 0.29
21 10 0.32
22 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (19 bp):
ATAATTATTATAATAATTG
Found at i:126359 original size:17 final size:18
Alignment explanation
Indices: 126318--126362 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
126308 AAATTAAAAG
126318 TACTTAAT-TT-ATAATT
1 TACTTAATATTAATAATT
*
126334 TAATTAATATTAATAA-T
1 TACTTAATATTAATAATT
126351 TACTTAATATTA
1 TACTTAATATTA
126363 TTAACATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 7 0.28
17 14 0.56
18 4 0.16
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (18 bp):
TACTTAATATTAATAATT
Found at i:126378 original size:21 final size:21
Alignment explanation
Indices: 126354--126406 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
126344 TAATAATTAC
126354 TTAATATTATTAACATAATGA
1 TTAATATTATTAACATAATGA
** *
126375 TTAATATTATTAGGATAATTA
1 TTAATATTATTAACATAATGA
126396 TATAATATTAT
1 T-TAATATTAT
126407 ATAATATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 19 0.68
22 9 0.32
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (21 bp):
TTAATATTATTAACATAATGA
Found at i:126407 original size:10 final size:10
Alignment explanation
Indices: 126392--126449 Score: 68
Period size: 10 Copynumber: 6.0 Consensus size: 10
126382 TATTAGGATA
126392 ATTATATAAT
1 ATTATATAAT
126402 ATTATATAAT
1 ATTATATAAT
*
126412 ATTAAAT-AT
1 ATTATATAAT
126421 -TTATCATAAT
1 ATTAT-ATAAT
*
126431 ATAATA-AAT
1 ATTATATAAT
126440 ATTATATAAT
1 ATTATATAAT
126450 TATATTATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
8 3 0.08
9 12 0.30
10 22 0.55
11 3 0.08
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (10 bp):
ATTATATAAT
Found at i:126421 original size:17 final size:18
Alignment explanation
Indices: 126389--126453 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 18
126379 TATTATTAGG
126389 ATAAT-TATATAATATTAT
1 ATAATATATA-AATATTAT
126407 ATAATAT-TAAATATTTAT
1 ATAATATATAAATA-TTAT
126425 CATAATATAATAAATATTAT
1 -ATAATAT-ATAAATATTAT
126445 ATAAT-TATA
1 ATAATATATA
126454 TTATTAATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
17 7 0.17
18 12 0.29
19 13 0.31
20 4 0.10
21 6 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
ATAATATATAAATATTAT
Found at i:126429 original size:29 final size:29
Alignment explanation
Indices: 126338--126452 Score: 94
Period size: 28 Copynumber: 3.9 Consensus size: 29
126328 ATAATTTAAT
* *
126338 TAATATTA-ATAATTACTTAATATTATTAACA
1 TAATATTATATAA-TA-TTAA-ATAATTATCA
* *
126369 TAATGATTA-ATATTATTAGGATAATTAT-A
1 TAAT-ATTATATAATATTA-AATAATTATCA
*
126398 TAATATTATATAATATTAAATATTTATCA
1 TAATATTATATAATATTAAATAATTATCA
* *
126427 TAATATAATA-AATATTATATAATTAT
1 TAATATTATATAATATTAAATAATTAT
126453 ATTATTAATT
Statistics
Matches: 70, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
28 25 0.36
29 23 0.33
30 9 0.13
31 6 0.09
32 7 0.10
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (29 bp):
TAATATTATATAATATTAAATAATTATCA
Found at i:126468 original size:17 final size:18
Alignment explanation
Indices: 126446--126491 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
126436 AAATATTATA
*
126446 TAATTATATTATTAAT-T
1 TAATTATATTAATAATAT
126463 TAATTATA-TAATAATAT
1 TAATTATATTAATAATAT
*
126480 TAATTTTATTAA
1 TAATTATATTAA
126492 ACAATTGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 6 0.24
17 16 0.64
18 3 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TAATTATATTAATAATAT
Found at i:126490 original size:22 final size:25
Alignment explanation
Indices: 126439--126490 Score: 74
Period size: 22 Copynumber: 2.2 Consensus size: 25
126429 ATATAATAAA
126439 TATTATATAATTATATTATTAATTT
1 TATTATATAATTATATTATTAATTT
*
126464 AATTATATAA-TA-A-TATTAATTT
1 TATTATATAATTATATTATTAATTT
126486 TATTA
1 TATTA
126491 AACAATTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 13 0.52
23 1 0.04
24 2 0.08
25 9 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATTATATAATTATATTATTAATTT
Found at i:126927 original size:8 final size:8
Alignment explanation
Indices: 126901--126944 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
126891 TATTTATTAA
126901 AATTTATT
1 AATTTATT
*
126909 AATTT-TA
1 AATTTATT
126916 AATTTATT
1 AATTTATT
*
126924 AATTAATT
1 AATTTATT
126932 AATTTAATT
1 AATTT-ATT
126941 AATT
1 AATT
126945 ATATACAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
7 6 0.20
8 17 0.57
9 7 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
AATTTATT
Found at i:127265 original size:22 final size:20
Alignment explanation
Indices: 127240--127297 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
127230 AATTATCGGT
127240 AATAATAATATATCAATATTAC
1 AATAATAATATAT-AATA-TAC
* *
127262 AATAATTATA-ATAATATAT
1 AATAATAATATATAATATAC
*
127281 AATAATAATATTTAATA
1 AATAATAATATATAATA
127298 ATATTAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 11 0.35
20 9 0.29
21 2 0.06
22 9 0.29
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (20 bp):
AATAATAATATATAATATAC
Found at i:127284 original size:19 final size:18
Alignment explanation
Indices: 127241--127305 Score: 68
Period size: 16 Copynumber: 3.8 Consensus size: 18
127231 ATTATCGGTA
127241 ATAATAATATATCAATATT
1 ATAATAATATAT-AATATT
* *
127260 ACAATAAT-TATAATAAT
1 ATAATAATATATAATATT
127277 AT-ATAATA-ATAATATT
1 ATAATAATATATAATATT
127293 -TAATAATAT-TAAT
1 ATAATAATATATAAT
127306 TTAATTTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
15 1 0.03
16 22 0.56
17 6 0.15
18 3 0.08
19 7 0.18
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAATAATATATAATATT
Found at i:128241 original size:178 final size:176
Alignment explanation
Indices: 127893--128460 Score: 610
Period size: 178 Copynumber: 3.2 Consensus size: 176
127883 TTAATAAGAC
* * *
127893 AATTAATAAGTAAAAGATTTAAAAAATAAATCTA-TTTATCGAACAAATTCAAATCGTTATGACT
1 AATTAATAAGTAAAA-ATTT-AAAAATAAAT-AAGTTTATCGAACAAGTTCAAATAGTTATGACT
* * *
127957 ATCTGAATAATTATTTATTTCAAATTC-TTATGACTTTTTTGTTTTGTCATAAAACAATTGTTTC
63 ATCTTAATAATTATCTATTTCAAA-TCATTATAAC--TTTTGTTTTGTCATAAAACAATTGTTTC
* * * * * *
128021 CATCCA-TACGAGCTTA-TTCAGATTAAAATAATATTGATTTATTAATATTTCAAC
125 AATTCATTA--AGCTTATTTCA-AATAAAATAATA-TAATTTATTAATATTCCAAA
* * *
128075 AATTAATAAGTAAAAGATTTAAAAA-AAATAAGTTTACCAAACAAGTTCAAATAGTCATGACTAT
1 AATTAATAAGTAAAA-ATTTAAAAATAAATAAGTTTATCGAACAAGTTCAAATAGTTATGACTAT
* * * * * * *
128139 TTTAATAATTATCTACTTCAAATCATTGTAACATTTGTTTTGTAATAAAATAATTATTTCAATTC
65 CTTAATAATTATCTATTTCAAATCATTATAACTTTTGTTTTGTCATAAAACAATTGTTTCAATTC
* *
128204 ATGTTAGCTTATTTGAAATAAAATAATACTAATTTATTAATATTCCAAA
130 AT-TAAGCTTATTTCAAATAAAATAATA-TAATTTATTAATATTCCAAA
* * * * *
128253 AATTAAAAAG--AGAATTAAAAAAATAAATATGTTTATCGAACAAGTTCAAATAGTTATGATTAT
1 AATTAATAAGTAAAAATT-TAAAAATAAATAAGTTTATCGAACAAGTTCAAATAGTTATGACTAT
* * * * *
128316 CTTAATAATTATCTATTTCAAAACATTACAACCTTTTGTTTTATCATAAAACAATTGGTTCTATT
65 CTTAATAATTATCTATTTCAAATCATTATAA-CTTTTGTTTTGTCATAAAACAATTGTTTCAATT
*
128381 CATTCAAGCTTATTTCAAATAAAATAATATAAATTTATTAATGTTCCAAA
129 CATT-AAGCTTATTTCAAATAAAATAATAT-AATTTATTAATATTCCAAA
128431 AATTAATAAGTAAAAATTTTAAAAATAAAT
1 AATTAATAAGTAAAAA-TTTAAAAATAAAT
128461 TTATTTAAAA
Statistics
Matches: 322, Mismatches: 51, Indels: 28
0.80 0.13 0.07
Matches are distributed among these distances:
175 3 0.01
176 7 0.02
177 62 0.19
178 149 0.46
179 6 0.02
180 68 0.21
181 7 0.02
182 20 0.06
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (176 bp):
AATTAATAAGTAAAAATTTAAAAATAAATAAGTTTATCGAACAAGTTCAAATAGTTATGACTATC
TTAATAATTATCTATTTCAAATCATTATAACTTTTGTTTTGTCATAAAACAATTGTTTCAATTCA
TTAAGCTTATTTCAAATAAAATAATATAATTTATTAATATTCCAAA
Found at i:128770 original size:19 final size:20
Alignment explanation
Indices: 128725--128812 Score: 74
Period size: 20 Copynumber: 4.5 Consensus size: 20
128715 GCTCACTTTG
*
128725 TATT-TTTATT-TTGTATCT
1 TATTATTTATTGTTGTATAT
128743 TATTTATTTATTGTTGT-TAT
1 TA-TTATTTATTGTTGTATAT
* *
128763 TATTATTTATTGATATATAT
1 TATTATTTATTGTTGTATAT
* * ** *
128783 TTTTATCTATTAATATATAT
1 TATTATTTATTGTTGTATAT
128803 TATTATTTAT
1 TATTATTTAT
128813 CTATTAATGT
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
18 2 0.03
19 14 0.24
20 38 0.66
21 4 0.07
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (20 bp):
TATTATTTATTGTTGTATAT
Found at i:128783 original size:20 final size:20
Alignment explanation
Indices: 128746--128812 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
128736 TGTATCTTAT
* *
128746 TTATTTATTGTTGT-TATTA
1 TTATTTATTGATATATATTA
*
128765 TTATTTATTGATATATATTT
1 TTATTTATTGATATATATTA
* *
128785 TTATCTATTAATATATATTA
1 TTATTTATTGATATATATTA
128805 TTATTTAT
1 TTATTTAT
128813 CTATTAATGT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 12 0.30
20 28 0.70
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.64
Consensus pattern (20 bp):
TTATTTATTGATATATATTA
Found at i:128833 original size:48 final size:48
Alignment explanation
Indices: 128775--128866 Score: 143
Period size: 48 Copynumber: 1.9 Consensus size: 48
128765 TTATTTATTG
*
128775 ATATATATTTTTATCTATTAA-TATATAT-TATTATTTATCTATTAATGT
1 ATATAAATTTTTAT-TATTAACTAT-TATCTATTATTTATCTATTAATGT
128823 ATATAAATTTTTATTATTAACTATTATCTATTATTTATCTATTA
1 ATATAAATTTTTATTATTAACTATTATCTATTATTTATCTATTA
128867 GTATTTATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
47 9 0.22
48 32 0.78
ACGTcount: A:0.36, C:0.05, G:0.01, T:0.58
Consensus pattern (48 bp):
ATATAAATTTTTATTATTAACTATTATCTATTATTTATCTATTAATGT
Found at i:128836 original size:28 final size:24
Alignment explanation
Indices: 128775--128910 Score: 110
Period size: 24 Copynumber: 5.9 Consensus size: 24
128765 TTATTTATTG
128775 ATATA-TATT-TTTATCTATTAAT
1 ATATATTATTATTTATCTATTAAT
128797 ATATATTATTATTTATCTATTAAT
1 ATATATTATTATTTATCTATTAAT
* *
128821 GTATATAAATT-TTTAT-TATTAACT
1 ATATAT-TATTATTTATCTATTAA-T
*
128845 AT-TATCTATTATTTATCTATTAGT
1 ATATAT-TATTATTTATCTATTAAT
* * *
128869 ATTTA-TA-TATATATGTA-T-AT
1 ATATATTATTATTTATCTATTAAT
*
128889 ATATATTTGTTATTTATCTATT
1 ATATA-TTATTATTTATCTATT
128911 GTTTTTTTCT
Statistics
Matches: 90, Mismatches: 13, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
20 5 0.06
21 1 0.01
22 14 0.16
23 26 0.29
24 34 0.38
25 10 0.11
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.58
Consensus pattern (24 bp):
ATATATTATTATTTATCTATTAAT
Found at i:128871 original size:14 final size:14
Alignment explanation
Indices: 128854--128910 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 14
128844 TATTATCTAT
*
128854 TATTTATCTATTAG
1 TATTTATATATTAG
128868 TATTTATATATATATG
1 TATTTATATAT-TA-G
* *
128884 TATATATATATTTG
1 TATTTATATATTAG
*
128898 TTATTTATCTATT
1 -TATTTATATATT
128911 GTTTTTTTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
14 11 0.31
15 13 0.37
16 11 0.31
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.60
Consensus pattern (14 bp):
TATTTATATATTAG
Found at i:128902 original size:62 final size:61
Alignment explanation
Indices: 128785--128902 Score: 148
Period size: 62 Copynumber: 1.9 Consensus size: 61
128775 ATATATATTT
* * *
128785 TTATCTATTAATATATATTATTATTTATCTATTAATGTATATAAATTTTTATTATTAACTA
1 TTATCTATTAATATATATTAGTATTTATATATTAATGTATATAAATATTTATTATTAACTA
* * * *
128846 TTATCTATTATTTATCTATTAGTATTTATATA-TATATGTATATATATATTTGTTATT
1 TTATCTATTA-ATATATATTAGTATTTATATATTA-ATGTATATAAATATTTATTATT
128903 TATCTATTGT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
61 12 0.25
62 36 0.75
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.58
Consensus pattern (61 bp):
TTATCTATTAATATATATTAGTATTTATATATTAATGTATATAAATATTTATTATTAACTA
Found at i:129692 original size:22 final size:22
Alignment explanation
Indices: 129651--129700 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
129641 TAATTAATTA
* *
129651 ATTATTATTATTTCTTTTTATT
1 ATTATTATTATTACTATTTATT
*
129673 ATTATTATTATTAGTATTTATT
1 ATTATTATTATTACTATTTATT
129695 A-TATTA
1 ATTATTA
129701 GAATTATTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (22 bp):
ATTATTATTATTACTATTTATT
Found at i:129731 original size:11 final size:11
Alignment explanation
Indices: 129715--129748 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
129705 TATTTGGTAT
129715 TCTTTATTTTA
1 TCTTTATTTTA
129726 TCTTTATTTTTA
1 TCTTTA-TTTTA
129738 T-TTTATTTTA
1 TCTTTATTTTA
129748 T
1 T
129749 TTTTTTAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.27
11 10 0.45
12 6 0.27
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (11 bp):
TCTTTATTTTA
Found at i:129741 original size:5 final size:5
Alignment explanation
Indices: 129717--129751 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
129707 TTTGGTATTC
129717 TTTAT TTTAT CTTTATT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT -TTTA-T TTTAT TTTAT TTTAT TTT
129752 TTTAATGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 19 0.68
6 8 0.29
7 1 0.04
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:129753 original size:17 final size:18
Alignment explanation
Indices: 129712--129753 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
129702 AATTATTTGG
*
129712 TATTCTTTATTTTATCTT
1 TATTTTTTATTTTATCTT
129730 TA-TTTTTATTTTAT-TT
1 TATTTTTTATTTTATCTT
129746 TATTTTTT
1 TATTTTTT
129754 TAATGATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 4 0.18
17 16 0.73
18 2 0.09
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.79
Consensus pattern (18 bp):
TATTTTTTATTTTATCTT
Found at i:130005 original size:15 final size:14
Alignment explanation
Indices: 129969--130007 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
129959 TCAATTTTCC
129969 TTGAAAATAAAATTT
1 TTGAAAA-AAAATTT
* *
129984 TTTAAAAAATATTT
1 TTGAAAAAAAATTT
129998 TTGAAAAAAA
1 TTGAAAAAAA
130008 GTTGAAAGTA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (14 bp):
TTGAAAAAAAATTT
Found at i:130008 original size:59 final size:59
Alignment explanation
Indices: 129888--130211 Score: 326
Period size: 59 Copynumber: 5.6 Consensus size: 59
129878 AATTTTAGGG
* *
129888 AAAAGTTGAAAGTATCAATTTTCCTTGAAAAT--AATTTTCTAAAAAATATTTTTGAAG
1 AAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATTTTTTAAAAAATATTTTTGAAA
* *
129945 AAAAGGTAAAAGTATCAATTTTCCTTGAAAATAAAATTTTTTAAAAAATATTTTTGAAA
1 AAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATTTTTTAAAAAATATTTTTGAAA
* * * * **
130004 AAAAGTTGAAAGTATCAATTTTCTTTAAAAATAAATTTTTTTTAAAAATATTTTTGAGG
1 AAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATTTTTTAAAAAATATTTTTGAAA
* * * * * * **
130063 AAAAGTTGAAAGTATCAATTTTTCTCG-AAATTAAA-GTTTCAGAAAAACA-TTTTGGGA
1 AAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATTTTTTA-AAAAATATTTTTGAAA
* * *
130120 AAAAGTTGAAAGTA-CTAATTTTCCTT-AAAA-AAAATTTTCTAAAAAAAAAATATTTT-AAGG
1 AAAAGTTGAAAGTATC-AATTTTCCTTGAAAATAAAATTTT-T-TAAAAAATAT-TTTTGAA-A
*
130180 AAAAGTTGAAAGTTTCAATTTTCCTT-AAAATA
1 AAAAGTTGAAAGTATCAATTTTCCTTGAAAATA
130212 GAAACTCTCA
Statistics
Matches: 220, Mismatches: 34, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
56 4 0.02
57 66 0.30
58 19 0.09
59 98 0.45
60 31 0.14
61 2 0.01
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.37
Consensus pattern (59 bp):
AAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATTTTTTAAAAAATATTTTTGAAA
Found at i:130058 original size:16 final size:17
Alignment explanation
Indices: 130020--130053 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
130010 TGAAAGTATC
130020 AATTTTCTTTAAAAATA
1 AATTTTCTTTAAAAATA
*
130037 AATTTTTTTTAAAAATA
1 AATTTTCTTTAAAAATA
130054 TTTTTGAGGA
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:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTTTCTTTAAAAATA
Found at i:130128 original size:116 final size:116
Alignment explanation
Indices: 129875--130204 Score: 368
Period size: 116 Copynumber: 2.8 Consensus size: 116
129865 AATAAATAAT
* *
129875 AAAAATTTTAGGG-AAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AA-TTTTCTAAAAAATAT
1 AAAAATTTT-GGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTTATAAAAAATAT
* * * * * *
129937 TTTTGAAGAAAAGGTAAAAGTATCAATTTTCCTTGAAAATAAAATTTTTTAA
65 TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAATAAAATGTTTCAA
** * * *
129989 AAAATATTTTTGAAAAAAAGTTGAAAGTATCAATTTTCTTTAAAAATAAATTTTTTTTAAAAATA
1 AAAA-A-TTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTTATAAAAAATA
* *
130054 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCG-AAATTAAA-GTTTCAGA
64 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAATAAAATGTTTCA-A
* *
130106 AAAACATTTTGGGAAAAAGTTGAAAGTA-CTAATTTTCCTTAAAAA-AAATTTTCTAAAAAAAAA
1 AAAA-ATTTTGGGAAAAAGTTGAAAGTATC-AATTTTCCTTAAAAATAAATTTT-TATAAAAAAT
* *
130169 ATATTTTAAGGAAAAGTTGAAAGTTTCAATTTTCCT
63 AT-TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
130205 TAAAATAGAA
Statistics
Matches: 182, Mismatches: 25, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
114 4 0.02
115 10 0.05
116 80 0.44
117 45 0.25
118 43 0.24
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.37
Consensus pattern (116 bp):
AAAAATTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTTATAAAAAATATT
TTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAATAAAATGTTTCAA
Found at i:130166 original size:15 final size:16
Alignment explanation
Indices: 130136--130168 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
130126 TGAAAGTACT
*
130136 AATTTTCCTTAAAAAA
1 AATTTTCCTAAAAAAA
130152 AATTTT-CTAAAAAAA
1 AATTTTCCTAAAAAAA
130167 AA
1 AA
130169 ATATTTTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (16 bp):
AATTTTCCTAAAAAAA
Found at i:130237 original size:116 final size:111
Alignment explanation
Indices: 129880--130258 Score: 343
Period size: 116 Copynumber: 3.3 Consensus size: 111
129870 ATAATAAAAA
* * *
129880 TTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAATTTTCTAAAAAATATTTTTGAA-
1 TTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAAAAATTTTCTAAAAAATATTTTT-AAG
* * * *
129944 GAAAAGGTAAAAGTATCAATTTTCCTTGAAAATAAAATTTTTTAAAAAATA-
65 GAAAAGTTGAAAGTATCAATTTTCCTT-AAAATAAAA--CTTT--CAAATAC
* * * * * *
129995 TTTTTGAAAAAAAGTTGAAAGTATCAATTTTCTTTAAAAATAAATTTTTTTTAAAAATATTTTTG
1 TTTTAG-GAAAAAGTTGAAAGTATCAATTTTCCTTAAAAA-AAA-TTTTCTAAAAAATATTTTTA
* ** * * *
130060 AGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTCAGAAAAAC
63 AGGAAAAGTTGAAAGTATCAATTTTCCTTAAAATAAAACTTTC--AAATAC
* *
130111 ATTTTGGGAAAAAGTTGAAAGTA-CTAATTTTCCTTAAAAAAAATTTTCTAAAAAAAAAATATTT
1 -TTTTAGGAAAAAGTTGAAAGTATC-AATTTTCCTTAAAAAAAATTTTCT--AAAAAATAT-TTT
* * *
130175 TAAGGAAAAGTTGAAAGTTTCAATTTTCCTTAAAATAGAAACTCTCAAATGC
61 TAAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAATA-AAACTTTCAAATAC
130227 TTTTAAGG-AAAAGTTGAAAAGTATCAATTTTC
1 TTTT-AGGAAAAAGTTG-AAAGTATCAATTTTC
130259 TTTGTACAAA
Statistics
Matches: 213, Mismatches: 35, Indels: 31
0.76 0.13 0.11
Matches are distributed among these distances:
114 5 0.02
115 28 0.13
116 84 0.39
117 50 0.23
118 46 0.22
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (111 bp):
TTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAAAAATTTTCTAAAAAATATTTTTAAGG
AAAAGTTGAAAGTATCAATTTTCCTTAAAATAAAACTTTCAAATAC
Found at i:133485 original size:15 final size:15
Alignment explanation
Indices: 133465--133495 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
133455 TTTGTATACA
*
133465 TGCATTTTCATTCAT
1 TGCATTCTCATTCAT
133480 TGCATTCTCATTCAT
1 TGCATTCTCATTCAT
133495 T
1 T
133496 ACACTTAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.23, G:0.06, T:0.52
Consensus pattern (15 bp):
TGCATTCTCATTCAT
Found at i:140761 original size:21 final size:23
Alignment explanation
Indices: 140732--140787 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 23
140722 TACTATGCTT
* *
140732 AAAAGGAAAAAAAGA-TAAA-AA
1 AAAATGAAAAAAAGAGAAAAGAA
140753 AAAATGAAAAAAAGAGAAAAGTAA
1 AAAATGAAAAAAAGAGAAAAG-AA
140777 AAAATGAAAAA
1 AAAATGAAAAA
140788 GGAAGACTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 14 0.47
22 3 0.10
24 13 0.43
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (23 bp):
AAAATGAAAAAAAGAGAAAAGAA
Found at i:141830 original size:42 final size:41
Alignment explanation
Indices: 141783--141906 Score: 128
Period size: 42 Copynumber: 3.0 Consensus size: 41
141773 CATTTACATT
141783 CAAAGTTGTGATGCCTCT-ATTTAGAGGAGCCATTTATTTTTC
1 CAAAGTTGTGA-GCCTCTGA-TTAGAGGAGCCATTTATTTTTC
* * * *
141825 CAAAGTCAT-TGAGCCTTTGAATAGAGGAGCAATTTA-CTTTC
1 CAAAGT--TGTGAGCCTCTGATTAGAGGAGCCATTTATTTTTC
*
141866 CAAAAGTCGTTGAGCCTCTGATTAGAGGAGCCATTTATTTT
1 C-AAAGTTG-TGAGCCTCTGATTAGAGGAGCCATTTATTTT
141907 CGAGGTCATG
Statistics
Matches: 66, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
41 5 0.08
42 54 0.82
43 6 0.09
44 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.35
Consensus pattern (41 bp):
CAAAGTTGTGAGCCTCTGATTAGAGGAGCCATTTATTTTTC
Found at i:142222 original size:21 final size:21
Alignment explanation
Indices: 142192--142246 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
142182 TTTTGTATCT
*
142192 TATTTATTATTTATTGATATA
1 TATTTATTATTTATTAATATA
* *
142213 TATTTTTTATCTATTAATATA
1 TATTTATTATTTATTAATATA
142234 TA-TTATTATTTAT
1 TATTTATTATTTAT
142247 CTATTAATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 9 0.31
21 20 0.69
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (21 bp):
TATTTATTATTTATTAATATA
Found at i:142270 original size:28 final size:24
Alignment explanation
Indices: 142191--142343 Score: 110
Period size: 24 Copynumber: 6.6 Consensus size: 24
142181 ATTTTGTATC
*
142191 TTATTTAT-TATTTAT-TGATATATA
1 TTATTTATCTATTAATAT-ATAT-TA
*
142215 TTTTTTATCTATTAATATATATTA
1 TTATTTATCTATTAATATATATTA
* *
142239 TTATTTATCTATTAATGTATATAAA
1 TTATTTATCTATTAATATATAT-TA
142264 TT-TTTAT-TATTAACTAT-TATCTA
1 TTATTTATCTATTAA-TATATAT-TA
* *
142287 TTATTTATCGATTAGTATATA-TA
1 TTATTTATCTATTAATATATATTA
* * *
142310 -TATGTATATA-T-ATTTAT-TTA
1 TTATTTATCTATTAATATATATTA
142330 TTATTTATCTATTA
1 TTATTTATCTATTA
142344 TTATTTTTTC
Statistics
Matches: 101, Mismatches: 17, Indels: 23
0.72 0.12 0.16
Matches are distributed among these distances:
20 6 0.06
21 9 0.09
22 8 0.08
23 14 0.14
24 44 0.44
25 19 0.19
26 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (24 bp):
TTATTTATCTATTAATATATATTA
Found at i:142346 original size:14 final size:14
Alignment explanation
Indices: 142285--142349 Score: 51
Period size: 14 Copynumber: 4.6 Consensus size: 14
142275 AACTATTATC
*
142285 TATTATTTATCGAT
1 TATTATTTATCTAT
* * *
142299 TAGTATATATATAT
1 TATTATTTATCTAT
* *
142313 GTA-TATATATTTATT
1 -TATTATTTATCTA-T
142328 TATTATTTATCTAT
1 TATTATTTATCTAT
142342 TATTATTT
1 TATTATTT
142350 TTTCTTTTCT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
14 30 0.73
15 11 0.27
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (14 bp):
TATTATTTATCTAT
Found at i:143104 original size:12 final size:13
Alignment explanation
Indices: 143064--143105 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
143054 TATATATTTA
143064 ATTATTTAATTATT
1 ATTATTT-ATTATT
*
143078 CTTA-TTATTATT
1 ATTATTTATTATT
143090 ATTATTTATTA-T
1 ATTATTTATTATT
143102 ATTA
1 ATTA
143106 GAATTATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 14 0.56
13 8 0.32
14 3 0.12
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTATTTATTATT
Found at i:143162 original size:6 final size:5
Alignment explanation
Indices: 143123--143161 Score: 60
Period size: 5 Copynumber: 7.4 Consensus size: 5
143113 TTGGTATTCC
143123 TTATT TTATCT TTATTT TTATT TTATT TTATT TTATT TT
1 TTATT TTAT-T TTA-TT TTATT TTATT TTATT TTATT TT
143162 TTAATGATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 23 0.72
6 8 0.25
7 1 0.03
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:143217 original size:16 final size:16
Alignment explanation
Indices: 143198--143228 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
143188 CAAAAACAAA
143198 AAAAAAAATATTTTTG
1 AAAAAAAATATTTTTG
*
143214 AAAAAAAATGTTTTT
1 AAAAAAAATATTTTT
143229 AAGGAAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (16 bp):
AAAAAAAATATTTTTG
Found at i:143291 original size:57 final size:59
Alignment explanation
Indices: 143216--143452 Score: 222
Period size: 57 Copynumber: 4.1 Consensus size: 59
143206 TATTTTTGAA
*
143216 AAAAAATGTTTTTAAGGAAAAATTGAAAGTATCAATTTTTC-TTGAAAAT-AATTTTCT
1 AAAAAATATTTTTAAGGAAAAATTGAAAGTATCAATTTTTCTTTGAAAATAAATTTTCT
* ** * *
143273 AAAAAATATTTTTGAGGAAAAGGTAAAAGTATCAA-TTTTCTTTTAAAATAAATTTT-T
1 AAAAAATATTTTTAAGGAAAAATTGAAAGTATCAATTTTTCTTTGAAAATAAATTTTCT
* * * * *
143330 AAAAAAAATTTTTTTAAGGAAAAGTTGAAAGTATCAATTTTTC-TCGAAATTAAAGTTTC-
1 --AAAAAATATTTTTAAGGAAAAATTGAAAGTATCAATTTTTCTTTGAAAATAAATTTTCT
* * * * * *
143389 AGAAAAACA-TTTT-GGGAAAAAATTGGAAGTACCAATTTTCCTTT-AAAAAAAATTTTCT
1 A-AAAAATATTTTTAAGG-AAAAATTGAAAGTATCAATTTTTCTTTGAAAATAAATTTTCT
143447 AAAAAA
1 AAAAAA
143453 AAAAAACGTT
Statistics
Matches: 145, Mismatches: 25, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
56 7 0.05
57 78 0.54
58 13 0.09
59 42 0.29
60 5 0.03
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (59 bp):
AAAAAATATTTTTAAGGAAAAATTGAAAGTATCAATTTTTCTTTGAAAATAAATTTTCT
Found at i:143343 original size:14 final size:13
Alignment explanation
Indices: 143313--143342 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
143303 ATCAATTTTC
*
143313 TTTTAAAATAAAT
1 TTTTAAAAAAAAT
143326 TTTTAAAAAAAAT
1 TTTTAAAAAAAAT
143339 TTTT
1 TTTT
143343 TTAAGGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTTAAAAAAAAT
Found at i:143347 original size:116 final size:117
Alignment explanation
Indices: 143199--143495 Score: 332
Period size: 116 Copynumber: 2.5 Consensus size: 117
143189 AAAAACAAAA
* * *
143199 AAAAAAATATTTTTGAAAAAAAATGTTTTTAAGGAAAAATTGAAAGTATCAATTTTTCTTGAAAA
1 AAAAAAA-ATTTTTAAAAAAAAATCTTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAA
* * * * *
143264 T-AATTTTCTA-AAAAATATTTTTGAGG-AAAAGGTAAAAGTATCAATTTTCTTTT
65 TAAAGTTTC-AGAAAAACA-TTTTG-GGAAAAAAGTAAAAGTACCAATTTTCCTTT
* * * *
143317 AAAATAAATTTTT-AAAAAAAATTTTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATT
1 AAAAAAAATTTTTAAAAAAAAATCTTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAAT
* **
143381 AAAGTTTCAGAAAAACATTTTGGGAAAAAATTGGAAGTACCAATTTTCCTTT
66 AAAGTTTCAGAAAAACATTTTGGGAAAAAAGTAAAAGTACCAATTTTCCTTT
* * * *
143433 AAAAAAAATTTTCTAAAAAAAAAAAACGTTTTAAGGAAAAGTTGAAAGTATCAGTTTTCCTTG
1 AAAAAAAATTTT-T--AAAAAAAAATCTTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTG
143496 TACAAAAGCA
Statistics
Matches: 152, Mismatches: 20, Indels: 12
0.83 0.11 0.07
Matches are distributed among these distances:
115 2 0.01
116 85 0.56
117 19 0.12
118 6 0.04
120 40 0.26
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.36
Consensus pattern (117 bp):
AAAAAAAATTTTTAAAAAAAAATCTTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAAT
AAAGTTTCAGAAAAACATTTTGGGAAAAAAGTAAAAGTACCAATTTTCCTTT
Found at i:144095 original size:21 final size:21
Alignment explanation
Indices: 144071--144123 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
144061 TTTTGTAATA
*
144071 ATTAATATTATCAATTTAGTT
1 ATTAATAATATCAATTTAGTT
* * *
144092 ATTATTAATATTAATTTATTT
1 ATTAATAATATCAATTTAGTT
144113 ATTAATTAATA
1 ATTAA-TAATA
144124 AAAATGATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTAATAATATCAATTTAGTT
Found at i:144263 original size:7 final size:7
Alignment explanation
Indices: 144251--144315 Score: 51
Period size: 7 Copynumber: 8.9 Consensus size: 7
144241 ATTAATTTAT
144251 TTAATAA
1 TTAATAA
144258 TTAATAA
1 TTAATAA
*
144265 CTAAT-A
1 TTAATAA
144271 TATAATAA
1 T-TAATAA
*
144279 TAAATATA
1 TTAATA-A
*
144287 TAATAAAAA
1 T--TAATAA
*
144296 TTAATAG
1 TTAATAA
144303 TTAATAA
1 TTAATAA
144310 TTAATA
1 TTAATA
144316 TATATGGGAG
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
6 1 0.02
7 35 0.78
8 4 0.09
9 2 0.04
10 3 0.07
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (7 bp):
TTAATAA
Found at i:144394 original size:23 final size:24
Alignment explanation
Indices: 144357--144411 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 24
144347 TAATAAAATT
144357 ATTAATTATTATATT-TTA-AATA
1 ATTAATTATTATATTATTATAATA
144379 ATATAATTAATT-TATTAATTATAATA
1 AT-TAATT-ATTATATT-ATTATAATA
144405 ATTAATT
1 ATTAATT
144412 TAACCTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
22 2 0.07
23 9 0.32
24 3 0.11
25 8 0.29
26 6 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
ATTAATTATTATATTATTATAATA
Found at i:144705 original size:15 final size:16
Alignment explanation
Indices: 144685--144719 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
144675 TATATTATCT
144685 ATATTATAA-TAAATA
1 ATATTATAACTAAATA
*
144700 ATATTATAACTAATTA
1 ATATTATAACTAAATA
144716 ATAT
1 ATAT
144720 ATAGATTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAACTAAATA
Found at i:145244 original size:22 final size:22
Alignment explanation
Indices: 145180--145238 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
145170 ATTCATAAGT
* *
145180 ATAAATATTTATTATTACATTATA
1 ATAAATA--TATTATAATATTATA
145204 ATAAATATATTATAATATTATA
1 ATAAATATATTATAATATTATA
145226 ATAAA-ATAGTTAT
1 ATAAATATA-TTAT
145239 TTTATTTGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 3 0.09
22 22 0.69
24 7 0.22
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (22 bp):
ATAAATATATTATAATATTATA
Found at i:145424 original size:12 final size:11
Alignment explanation
Indices: 145406--145452 Score: 53
Period size: 11 Copynumber: 4.2 Consensus size: 11
145396 ATAAATAATA
145406 ATATATATTAT
1 ATATATATTAT
145417 ATATTATATTAT
1 ATA-TATATTAT
145429 CA-ATATATT-T
1 -ATATATATTAT
145439 ATATATAATTAT
1 ATATAT-ATTAT
145451 AT
1 AT
145453 GTTATTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
9 1 0.03
10 5 0.16
11 12 0.39
12 12 0.39
13 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (11 bp):
ATATATATTAT
Found at i:145425 original size:16 final size:16
Alignment explanation
Indices: 145406--145457 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
145396 ATAAATAATA
145406 ATATATATTATATATT
1 ATATATATTATATATT
*
145422 ATAT-TATCAATATATTT
1 ATATATAT-TATATA-TT
*
145439 ATATATAATTATATGTT
1 ATATAT-ATTATATATT
145456 AT
1 AT
145458 TTTTAAATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
15 3 0.10
16 9 0.31
17 10 0.34
18 5 0.17
19 2 0.07
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (16 bp):
ATATATATTATATATT
Found at i:145764 original size:181 final size:177
Alignment explanation
Indices: 145473--146683 Score: 887
Period size: 181 Copynumber: 6.8 Consensus size: 177
145463 AATCTCTTAG
* * *
145473 TTTATT-ATTTTT-AGAATATTATTATATTAGTATTATTTTATTTCAAATAAACTTGTGTGAATA
1 TTTATTAATTTTTGA-AATATTAATAAATTAGTATTATTTTATTTCAAATAAACTTGTATGAATA
* * * *
145536 GAAATAATTGTTTTATGAGATAACAAAAGGTT-ATAACAATTTGAAATATATAATTGTTCAAATA
65 GAAATAATTGTTTTATGACAAAACAAAA-GTTCATAACGATTTGAAATAGATAATTGTTCAAATA
* *
145600 GTCATAACTATTTGAACTAGTTTAG-TAAATAGTTTAACTTTTTAAA-TAG
129 GTCATAACTATTTAAACTAGTTTAGATAAATAGTTT-A-TTTTTAAACTAA
* * **
145649 TTTATTAATTTTTGAAATATTAGTAAATTAGTATTATTTTATTCCAAATAGGCTTGTAT-AATGA
1 TTTATTAATTTTTGAAATATTAATAAATTAGTATTATTTTATTTCAAATAAACTTGTATGAAT--
* * * *
145713 AAAACAATCAATTGTTTTATGACAAAACAAAAGTTCATAACGATATGAAATAGATAGTTATTCAA
64 -AGA-AAT-AATTGTTTTATGACAAAACAAAAGTTCATAACGATTTGAAATAGATAATTGTTCAA
* * * *
145778 ATGGCCATAATTATTTAAA-TAATTT-GATAAACT-GATTTATTTTTTAAAACTCCAA
126 ATAGTCATAACTATTTAAACTAGTTTAGATAAA-TAG-TTTA-TTTTT-AAACT--AA
* * * * ** * *
145833 CTTCTTAATTTTTGAAATATTAATAAAGTAATATTATTTTATTTTGAA-AAACTTTTATGTACT-
1 TTTATTAATTTTTGAAATATTAATAAATTAGTATTATTTTATTTCAAATAAACTTGTATG-AATA
* * * * * *
145896 GAAACATTTGTTTTATGATAAAATAAAAGGTT-ATAATGATTTTAAATAGATAATTGTTCAAATA
65 GAAATAATTGTTTTATGACAAAACAAAA-GTTCATAACGATTTGAAATAGATAATTGTTCAAATA
* * * *
145960 GTCATAACTATTTAAACT--TATTCGATAAATAGATT-TTTTTAAAAT-T
129 GTCATAACTATTTAAACTAGT-TTAGATAAATAGTTTATTTTTAAACTAA
* * * * * *
146006 TCTTATTAATTTTCT-AAATTTTAATAAATTAGTATTACTATATTTCGAATAAGCATGTATGAAC
1 T-TTATTAATTTT-TGAAATATTAATAAATTAGTATTATTTTATTTCAAATAAACTTGTATGAA-
* * * * * * * ** * * *
146070 TA-AAATGATTATTTTTTGATC-GAATAAAAGATCAGAATAATTTGGAATAAATAATTGTTCTAA
63 TAGAAATAATTGTTTTATGA-CAAAACAAAAGTTCATAACGATTTGAAATAGATAATTGTTCAAA
** * * * * * * *
146133 TAGTTTTAACTATTTAAACT-GCCTCA-AAAAACACATTTA-TTTTAAAAT-C
127 TAGTCATAACTATTTAAACTAG-TTTAGATAAATA-GTTTATTTTTAAACTAA
* * * ** **
146182 CTTATTAATTTTTGAAATAGTAATAAATTGGTATTATTTTATTTTGAATAATTTTGTATGAATAG
1 TTTATTAATTTTTGAAATATTAATAAATTAGTATTATTTTATTTCAAATAAACTTGTATGAATAG
* * * * * * ** *
146247 AAACAATTATTTTATAATAAAACAAAA-TGTCATAACGATTCGAAATAAATAACAGTTCAAATGG
66 AAATAATTGTTTTATGACAAAACAAAAGT-TCATAACGATTTGAAATAGATAATTGTTCAAATAG
* * *
146311 ACATGACTATTTAAACTTA-TTT-GGTAAATAGATTTATTTTTTAAATCTCTAA
130 TCATAACTATTTAAAC-TAGTTTAGATAAATAG-TTTA-TTTTTAAA---CTAA
* * * * *
146363 CTTATTAATTTTT-AGAATAATAATAAATTAGTATTACTTTATTCCAAATAAACTTGTGTGAATA
1 TTTATTAATTTTTGA-AATATTAATAAATTAGTATTATTTTATTTCAAATAAACTTGTATGAATA
* * * * *
146427 GAAACAATTATTTTATGACAAAACAAAAGATCATAAAGATTTGAAATATATAATTGTTCAAATAG
65 GAAATAATTGTTTTATGACAAAACAAAAGTTCATAACGATTTGAAATAGATAATTGTTCAAATAG
* * * * ** * * *
146492 TAATAACTATTTGAACTTGCTCGGTTAACA-AATTTATTATTTAAATCTTTTA
130 TCATAACTATTTAAACTAGTTTAGATAA-ATAGTTTATT-TTTAAA-C--TAA
* * * *
146544 CTTATTAATTTTAGAAATATTAATAAATTAATATTATTTTATTTCAAATAAGCTTGTATGAATAG
1 TTTATTAATTTTTGAAATATTAATAAATTAGTATTATTTTATTTCAAATAAACTTGTATGAATAG
* *
146609 AAATAATTGGTTTATGACAAAAC-AAATTATCATAACGATTTGAAATAGATAATTGTTCAAATAG
66 AAATAATTGTTTTATGACAAAACAAAAGT-TCATAACGATTTGAAATAGATAATTGTTCAAATAG
146673 TCATAACTATT
130 TCATAACTATT
146684 GAATGTGTTC
Statistics
Matches: 811, Mismatches: 167, Indels: 109
0.75 0.15 0.10
Matches are distributed among these distances:
174 44 0.05
175 192 0.24
176 26 0.03
177 56 0.07
178 2 0.00
179 70 0.09
180 43 0.05
181 320 0.39
182 7 0.01
183 8 0.01
184 41 0.05
185 2 0.00
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (177 bp):
TTTATTAATTTTTGAAATATTAATAAATTAGTATTATTTTATTTCAAATAAACTTGTATGAATAG
AAATAATTGTTTTATGACAAAACAAAAGTTCATAACGATTTGAAATAGATAATTGTTCAAATAGT
CATAACTATTTAAACTAGTTTAGATAAATAGTTTATTTTTAAACTAA
Found at i:146457 original size:356 final size:352
Alignment explanation
Indices: 145474--146683 Score: 968
Period size: 356 Copynumber: 3.4 Consensus size: 352
145464 ATCTCTTAGT
* * * ** *
145474 TTATT-ATTTTT-AGAATATTATTATATTAGTATTATTTTATTTCAAATAAAC-TTGTGTGAATA
1 TTATTAATTTTTGA-AATATTAATAAATTAATATTATTTTATTTTGAAT-AACTTTGTATGAATA
* * * * * * *
145536 GAAATAATTGTTTTATGAGATAACAAAAGGTTATAACAATTTGAAATATATAATTGTTCAAATAG
64 GAAACAATTGTTTTATGATAAAACAAAATGTCATAACGATTTGAAATAGATAATTGTTCAAATAG
* * * * *
145601 TCATAACTATTTGAAC-TAGTT-TAGTAAATAG-TTTAACTTTTTAAATAGT-TTATTAATTTT-
129 ACATAACTATTTAAACTTA-TTCGA-TAAATAGATTT---TTTTAAAAT-TTCTTATTAATTTTC
* * * * ** * *
145661 TGAAATATTAGTAAATTAGTATTATTTTATTCCAAATAGGCTTGTATAATGAA-AAACAATCAAT
188 T-AAATAATAATAAATTAGTATTACTATATTCCAAATAAACATG--T-ATGAACTAA-AA-CAAT
* * * * * * * * * ** *
145725 TGTTTTATGA-CAAAACAAAAGTTCATAACGATATGAAATAGATAGTTATTCAAATGGCCATAAT
247 TATTTTATGATC-AAACAAAAGATCAGAAAGATTTGAAATAAATAATTGTTCAAATAGTAATAAC
*** ** * ** * *
145789 TATTTAAA-TAATTTGATAAACTGATTTATTTTTTAAAACTCCAAC
311 TATTTAAACTTGCTCAAAAAACAAATTTA-TTATTAAAA-T-C-TC
* * * *
145834 TTCTTAATTTTTGAAATATTAATAAAGTAATATTATTTTATTTTGAAAAACTTT-TATGTACT-G
1 TTATTAATTTTTGAAATATTAATAAATTAATATTATTTTATTTTGAATAACTTTGTATG-AATAG
* * * * * * *
145897 AAACATTTGTTTTATGATAAAATAAAAGGTTATAATGATTTTAAATAGATAATTGTTCAAATAGT
65 AAACAATTGTTTTATGATAAAACAAAATGTCATAACGATTTGAAATAGATAATTGTTCAAATAGA
**
145962 CATAACTATTTAAACTTATTCGATAAATAGATTTTTTTAAAATTTCTTATTAATTTTCTAAATTT
130 CATAACTATTTAAACTTATTCGATAAATAGATTTTTTTAAAATTTCTTATTAATTTTCTAAATAA
* * * ** * *
146027 TAATAAATTAGTATTACTATATTTCGAATAAGCATGTATGAACTAAAATGATTATTTTTTGATCG
195 TAATAAATTAGTATTACTATATTCCAAATAAACATGTATGAACTAAAACAATTATTTTATGATCA
* * * **
146092 AATAAAAGATCAGAATA-ATTTGGAATAAATAATTGTTCTAATAGTTTTAACTATTTAAAC-TGC
260 AACAAAAGATCAGAA-AGATTTGAAATAAATAATTGTTCAAATAGTAATAACTATTTAAACTTG-
*
146155 CTCAAAAAACACATTTATT-TTAAAATC-C
323 CTCAAAAAACAAATTTATTATTAAAATCTC
* ** *
146183 TTATTAATTTTTGAAATAGTAATAAATTGGTATTATTTTATTTTGAATAATTTTGTATGAATAGA
1 TTATTAATTTTTGAAATATTAATAAATTAATATTATTTTATTTTGAATAACTTTGTATGAATAGA
* * * * ** *
146248 AACAATTATTTTATAATAAAACAAAATGTCATAACGATTCGAAATAAATAACAGTTCAAATGGAC
66 AACAATTGTTTTATGATAAAACAAAATGTCATAACGATTTGAAATAGATAATTGTTCAAATAGAC
* * * *
146313 ATGACTATTTAAACTTATTTGGTAAATAGATTTATTTTTTAAATCTCTAACTTATTAATTTT-TA
131 ATAACTATTTAAACTTATTCGATAAATAGA-TT-TTTTTAAAAT-T-T--CTTATTAATTTTCTA
* * *
146377 GAATAATAATAAATTAGTATTACTTTATTCCAAATAAACTTGTGTGAA-TAGAAACAATTATTTT
190 -AATAATAATAAATTAGTATTACTATATTCCAAATAAACATGTATGAACTA-AAACAATTATTTT
* * *
146441 ATGA-CAAAACAAAAGATCATAAAGATTTGAAATATATAATTGTTCAAATAGTAATAACTATTTG
253 ATGATC-AAACAAAAGATCAGAAAGATTTGAAATAAATAATTGTTCAAATAGTAATAACTATTTA
**** *
146505 AACTTGCTCGGTTAACAAATTTATTATTTAAATCTTTTAC
317 AACTTGCTCAAAAAACAAATTTATTATTAAAATC---T-C
* **
146545 TTATTAATTTTAGAAATATTAATAAATTAATATTATTTTATTTCAAATAAGC-TTGTATGAATAG
1 TTATTAATTTTTGAAATATTAATAAATTAATATTATTTTATTTTGAATAA-CTTTGTATGAATAG
* * * * * *
146609 AAATAATTGGTTTATGACAAAACAAATTATCATAACGATTTGAAATAGATAATTGTTCAAATAGT
65 AAACAATTGTTTTATGATAAAACAAAATGTCATAACGATTTGAAATAGATAATTGTTCAAATAGA
146674 CATAACTATT
130 CATAACTATT
146684 GAATGTGTTC
Statistics
Matches: 683, Mismatches: 133, Indels: 66
0.77 0.15 0.07
Matches are distributed among these distances:
349 50 0.07
350 84 0.12
351 3 0.00
352 10 0.01
353 7 0.01
354 56 0.08
355 25 0.04
356 132 0.19
357 10 0.01
358 53 0.08
359 1 0.00
360 90 0.13
361 43 0.06
362 119 0.17
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (352 bp):
TTATTAATTTTTGAAATATTAATAAATTAATATTATTTTATTTTGAATAACTTTGTATGAATAGA
AACAATTGTTTTATGATAAAACAAAATGTCATAACGATTTGAAATAGATAATTGTTCAAATAGAC
ATAACTATTTAAACTTATTCGATAAATAGATTTTTTTAAAATTTCTTATTAATTTTCTAAATAAT
AATAAATTAGTATTACTATATTCCAAATAAACATGTATGAACTAAAACAATTATTTTATGATCAA
ACAAAAGATCAGAAAGATTTGAAATAAATAATTGTTCAAATAGTAATAACTATTTAAACTTGCTC
AAAAAACAAATTTATTATTAAAATCTC
Found at i:146995 original size:16 final size:15
Alignment explanation
Indices: 146956--147004 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
146946 AATCAAATAT
*
146956 TATTAATTAATATAA
1 TATTAAATAATATAA
*
146971 CATTAAAATAATATTAA
1 TATT-AAATAATA-TAA
*
146988 TATTAAATATTATAA
1 TATTAAATAATATAA
147003 TA
1 TA
147005 GTATTAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 8 0.29
16 14 0.50
17 6 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
TATTAAATAATATAA
Found at i:147004 original size:24 final size:24
Alignment explanation
Indices: 146932--147012 Score: 66
Period size: 24 Copynumber: 3.5 Consensus size: 24
146922 TATAATTACT
*
146932 TAATAATAATTAATAATCAAATATTA
1 TAATAAT-ATTAAT-ATTAAATATTA
*
146958 T--T-A-ATTAATA-T-AACATTA
1 TAATAATATTAATATTAAATATTA
*
146976 AAATAATATTAATATTAAATATTA
1 TAATAATATTAATATTAAATATTA
*
147000 TAATAGTATTAAT
1 TAATAATATTAAT
147013 TTATTACTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 14
0.68 0.10 0.22
Matches are distributed among these distances:
18 6 0.14
20 2 0.05
21 7 0.16
22 7 0.16
23 2 0.05
24 18 0.42
26 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (24 bp):
TAATAATATTAATATTAAATATTA
Found at i:147192 original size:22 final size:25
Alignment explanation
Indices: 147142--147192 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
147132 ATAATTTATA
*
147142 ATTATTAGTTATTATCTAATAAATT
1 ATTATTAGTTATTATCTAATAAATG
147167 ATTATTAGTTATT-T-TAAT-AATG
1 ATTATTAGTTATTATCTAATAAATG
147189 ATTA
1 ATTA
147193 ATAAAATTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 7 0.28
23 4 0.16
24 1 0.04
25 13 0.52
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (25 bp):
ATTATTAGTTATTATCTAATAAATG
Found at i:147192 original size:25 final size:24
Alignment explanation
Indices: 147127--147192 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 24
147117 AAGACTATAG
*
147127 TTTTAATAATTTATAATTATTAGTTA
1 TTTTAATAA--TATTATTATTAGTTA
147153 TTATCTAATAA-ATTATTATTAGTTA
1 TT-T-TAATAATATTATTATTAGTTA
147178 TTTTAATAATGATTA
1 TTTTAATAAT-ATTA
147193 ATAAAATTGG
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
23 6 0.17
24 1 0.03
25 19 0.54
26 2 0.06
27 1 0.03
28 6 0.17
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (24 bp):
TTTTAATAATATTATTATTAGTTA
Found at i:147727 original size:28 final size:29
Alignment explanation
Indices: 147696--147753 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
147686 ATATCGATAA
147696 TTAAATA-ATAAAAATTAAATATT-TTAAT
1 TTAAATATATAAAAATTAAA-ATTGTTAAT
* *
147724 TTAAATATTTAAAATTTAAAATTGTTAAT
1 TTAAATATATAAAAATTAAAATTGTTAAT
147753 T
1 T
147754 ATTAACAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 10 0.38
29 16 0.62
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
TTAAATATATAAAAATTAAAATTGTTAAT
Found at i:147734 original size:13 final size:14
Alignment explanation
Indices: 147710--147753 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
147700 ATAATAAAAA
147710 TTAAATATTTTAAT
1 TTAAATATTTTAAT
*
147724 TTAAATATTTAAAAT
1 TTAAATATTT-TAAT
147739 TTAAA-ATTGTTAAT
1 TTAAATATT-TTAAT
147753 T
1 T
147754 ATTAACAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 17 0.65
15 9 0.35
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (14 bp):
TTAAATATTTTAAT
Found at i:148233 original size:15 final size:17
Alignment explanation
Indices: 148213--148244 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
148203 GCTTAAAGAA
148213 ATTTGA-TA-TAATAAT
1 ATTTGATTATTAATAAT
148228 ATTTGATTATTAATAAT
1 ATTTGATTATTAATAAT
148245 TTATTAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (17 bp):
ATTTGATTATTAATAAT
Found at i:148246 original size:15 final size:15
Alignment explanation
Indices: 148212--148254 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
148202 TGCTTAAAGA
148212 AATTTGATATAATAAT
1 AATTTGAT-TAATAAT
*
148228 -ATTTGATTATTAAT
1 AATTTGATTAATAAT
148242 AATTT-ATTAATAA
1 AATTTGATTAATAA
148255 ATATAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (15 bp):
AATTTGATTAATAAT
Found at i:152059 original size:180 final size:177
Alignment explanation
Indices: 151626--152113 Score: 464
Period size: 180 Copynumber: 2.7 Consensus size: 177
151616 AATAAAGGTT
* * * ** *
151626 ATAACGATTTAAAATAGATAAATGTTCAAATAGTAATAACTATTTGC-ACTTGTTTGGTAAATAT
1 ATAACGATTTGAAATAGAT-AATATTCATATAGTCTTAACTATTT-CAAC-TGTTTGGT-AATAA
* * * * *
151690 ATTTATTTTTTTAAATCTCATTTTTATTAATTTTTTG-AATGTAACTAAATTAGTATTAATTTAT
62 ATTTA-TTTTTTAAATCTC-TTGTTATTAA-TTTTTGAAATATAATTAAATTAGTATTATTTTAA
* * * * * *
151754 TCTAAACAACCTTTTATGAACTAAAACAATTGTTTTATAACCAAATAAAATATT
124 TCTAAACAACCTTGTACGAACTAAAACAATTGTTTTACAACAAAAGAAAATATC
* * * * *
151808 AGAACGATTTGAAATAGATAATTATTC-TAATAGTCTTAACCATTTGAACTGATTCGGTAAAAAA
1 ATAACGATTTGAAATAGATAA-TATTCAT-ATAGTCTTAACTATTTCAACTG-TTTGGTAATAAA
* *
151872 TTTTATTTTTTAAATCTCTTAGTTATTAATTTTTGAAATATTATTGAATTAGTATTATTTTAATC
63 -TTTATTTTTTAAATCTCTT-GTTATTAATTTTTGAAATATAATTAAATTAGTATTATTTTAATC
* * * *
151937 TAAATAAGCTTGTACGAAC-AAAATAATTGTTTTACAACAAAAGAAAATGTC
126 TAAACAACCTTGTACGAACTAAAACAATTGTTTTACAACAAAAGAAAATATC
* * *
151988 ATAACGATTTGAAATAGATAATCATTCATATAGTCTTAACTATTTCAACTAGTTTAGCAATTAGA
1 ATAACGATTTGAAATAGATAAT-ATTCATATAGTCTTAACTATTTCAACT-GTTTGGTAA-TAAA
* * * * *
152053 TTTATTTTTTAATTTTCTTGGTTATTAA-GTTTCAGAATATAATTAAATTAGTTTTATTTTA
63 TTTATTTTTTAAATCTCTT-GTTATTAATTTTTGA-AATATAATTAAATTAGTATTATTTTA
152114 TTTCAAATAA
Statistics
Matches: 250, Mismatches: 44, Indels: 26
0.78 0.14 0.08
Matches are distributed among these distances:
179 5 0.02
180 130 0.52
181 70 0.28
182 45 0.18
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.44
Consensus pattern (177 bp):
ATAACGATTTGAAATAGATAATATTCATATAGTCTTAACTATTTCAACTGTTTGGTAATAAATTT
ATTTTTTAAATCTCTTGTTATTAATTTTTGAAATATAATTAAATTAGTATTATTTTAATCTAAAC
AACCTTGTACGAACTAAAACAATTGTTTTACAACAAAAGAAAATATC
Found at i:152403 original size:23 final size:22
Alignment explanation
Indices: 152377--152455 Score: 72
Period size: 23 Copynumber: 3.5 Consensus size: 22
152367 ATTTATATCA
152377 ATTAATTCAATAAATATATATTT
1 ATTAATT-AATAAATATATATTT
*
152400 ATTAATATTAATAAATTAAATATTT
1 ATT-A-ATTAATAAA-TATATATTT
* *
152425 AATAATTAATAATTAGTATATTT
1 ATTAATTAATAAATA-TATATTT
152448 A--AATTAAT
1 ATTAATTAAT
152456 TTATATTAGT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
21 7 0.15
22 2 0.04
23 18 0.38
24 8 0.17
25 13 0.27
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (22 bp):
ATTAATTAATAAATATATATTT
Found at i:152425 original size:25 final size:23
Alignment explanation
Indices: 152377--152436 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 23
152367 ATTTATATCA
*
152377 ATTAATTCAATAAATATATATTT
1 ATTAATTCAATAAATAAATATTT
*
152400 ATTAATATTAATAAATTAAATATTT
1 ATTAAT-TCAATAAA-TAAATATTT
*
152425 AATAATT-AATAA
1 ATTAATTCAATAA
152437 TTAGTATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 11 0.34
24 8 0.25
25 13 0.41
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
ATTAATTCAATAAATAAATATTT
Found at i:152637 original size:23 final size:23
Alignment explanation
Indices: 152600--152646 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
152590 AATTATTAAA
*
152600 TTAATTAAATAATAATTAAATAT
1 TTAATTAAATAATAAATAAATAT
* * *
152623 TTAATTAATTTATAAATAATTAT
1 TTAATTAAATAATAAATAAATAT
152646 T
1 T
152647 AAAATTACGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTAATTAAATAATAAATAAATAT
Found at i:153154 original size:13 final size:13
Alignment explanation
Indices: 153132--153164 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
153122 TATTTATAAA
153132 TTAA-TATAATAT
1 TTAATTATAATAT
153144 TTAATTATAATAT
1 TTAATTATAATAT
153157 TTAATTAT
1 TTAATTAT
153165 TAAATAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTAATTATAATAT
Found at i:153325 original size:14 final size:14
Alignment explanation
Indices: 153306--153334 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
153296 ATTGTTTTTT
153306 ATATAAATAATATA
1 ATATAAATAATATA
153320 ATATAAATAATATA
1 ATATAAATAATATA
153334 A
1 A
153335 AAATTAATAA
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATATAAATAATATA
Found at i:153362 original size:15 final size:15
Alignment explanation
Indices: 153344--153385 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
153334 AAAATTAATA
*
153344 ATAAATTATTATTAT
1 ATAAATTAGTATTAT
153359 ATAAATTAGTATTAT
1 ATAAATTAGTATTAT
* *
153374 TTATATTAGTAT
1 ATAAATTAGTAT
153386 AAATATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (15 bp):
ATAAATTAGTATTAT
Found at i:153493 original size:24 final size:20
Alignment explanation
Indices: 153452--153492 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
153442 AACAAATATA
153452 TTATAATAATTTTGATTAAT
1 TTATAATAATTTTGATTAAT
153472 TTATGAATAATTTTG-TTAAT
1 TTAT-AATAATTTTGATTAAT
153492 T
1 T
153493 ATTATCTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (20 bp):
TTATAATAATTTTGATTAAT
Found at i:153797 original size:9 final size:9
Alignment explanation
Indices: 153778--153816 Score: 51
Period size: 9 Copynumber: 4.0 Consensus size: 9
153768 AAATAATAAT
153778 TTATAAATTA
1 TTAT-AATTA
153788 TTATAATTA
1 TTATAATTA
153797 TTATAATATA
1 TTATAAT-TA
153807 TTATTAATTA
1 TTA-TAATTA
153817 AATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 12 0.44
10 11 0.41
11 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
TTATAATTA
Found at i:153812 original size:16 final size:16
Alignment explanation
Indices: 153796--153833 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 16
153786 TATTATAATT
153796 ATTATAATATATTATTA
1 ATTA-AATATATTATTA
153813 ATTAAATATA-TA-TA
1 ATTAAATATATTATTA
153827 ATTAAAT
1 ATTAAAT
153834 TAATATGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 2 0.10
16 6 0.29
17 4 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTAAATATATTATTA
Found at i:153839 original size:18 final size:18
Alignment explanation
Indices: 153758--153836 Score: 62
Period size: 17 Copynumber: 4.5 Consensus size: 18
153748 ATATATTCAT
*
153758 ATTAATT-AATAAATAATA
1 ATTAATTAAATATAT-ATA
*
153776 ATTTA-TAAAT-TATTATA
1 ATTAATTAAATATA-TATA
153793 ATT-ATTATAATATAT-T-
1 ATTAATTA-AATATATATA
153809 ATTAATTAAATATATATA
1 ATTAATTAAATATATATA
153827 ATTAAATTAA
1 ATT-AATTAA
153837 TATGTGAATA
Statistics
Matches: 50, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
16 11 0.22
17 16 0.32
18 15 0.30
19 8 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTAATTAAATATATATA
Found at i:154614 original size:181 final size:179
Alignment explanation
Indices: 154108--154621 Score: 549
Period size: 177 Copynumber: 2.9 Consensus size: 179
154098 ATTTGAGATT
* *
154108 GATAATTATTCAAATAGTCATAATTATTTGAAATGGTTTGGTAAACAGATTTATTGTTTAAATCT
1 GATAATTATTCAAATAGTCATAATTATTTG-AATTGTTTGGTAAACAGATTTATTTTTTAAATCT
* * * * *
154173 GTTACCTATT-ATTTTTGAAATATTAATCAATTAGTATTATTTTATTTTGAATAAACTTGTATG-
65 -TTTCTTATTAATTTTTGAAATATTAATAAATTAGTATTATTTTATTCTGAATAAGCTTGTATGA
* * * * *
154236 ATAAAAAACAATTGTATTATGACAAAATAAAATGTCATAATGATTTGAAATA
129 AT-TAAAACAATTATTTTATGACAAAATAAAATGTCATAATCATTTAAAATA
* * * *
154288 GATAATTATTCAAATGGCCATAATTATTTTAATTGATTTGGTAAACAGATTTACTTTTTAAA---
1 GATAATTATTCAAATAGTCATAATTATTTGAATTG-TTTGGTAAACAGATTTATTTTTTAAATCT
* ** * * *
154350 TTTATTATTAATTTAGGAAATATTAATAAATTAGTATTATTTTATTC-CATCTAAGCTTGTATTA
65 TTTCTTATTAATTTTTGAAATATTAATAAATTAGTATTATTTTATTCTGA-ATAAGCTTGTATGA
* * *
154414 ACTAAAACAATTATTTTATGAC-AAATTAAATGGTTATAA-CATTTTAAAATA
129 ATTAAAACAATTATTTTATGACAAAATAAAAT-GTCATAATCA-TTTAAAATA
* * * * * *
154465 GATAATTGTTCAAATAATAATAAGTATTTGAACTTGTTCGGCAAACAGATTTATTTTTTAAATCT
1 GATAATTATTCAAATAGTCATAATTATTTGAA-TTGTTTGGTAAACAGATTTATTTTTTAAATCT
* * *
154530 CTTTCTTATTAATTTTTCAAATGTTAATAAATTAGTATTAATTTATTCTGAATAAGCTTGTATGA
65 -TTTCTTATTAATTTTTGAAATATTAATAAATTAGTATTATTTTATTCTGAATAAGCTTGTATGA
* * *
154595 ATTGAAATAATTTTTTTATGACTAAAA
129 ATTAAAACAATTATTTTATGAC-AAAA
154622 AATGGTCAAA
Statistics
Matches: 272, Mismatches: 48, Indels: 25
0.79 0.14 0.07
Matches are distributed among these distances:
176 16 0.06
177 122 0.45
178 4 0.01
179 4 0.01
180 51 0.19
181 71 0.26
182 1 0.00
183 3 0.01
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (179 bp):
GATAATTATTCAAATAGTCATAATTATTTGAATTGTTTGGTAAACAGATTTATTTTTTAAATCTT
TTCTTATTAATTTTTGAAATATTAATAAATTAGTATTATTTTATTCTGAATAAGCTTGTATGAAT
TAAAACAATTATTTTATGACAAAATAAAATGTCATAATCATTTAAAATA
Found at i:155236 original size:17 final size:16
Alignment explanation
Indices: 155213--155256 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
155203 TTAAATTGTT
155213 AATATTAATAATAG-AA
1 AATATTAATAAT-GTAA
155229 ATATATTAAT-ATGTAA
1 A-ATATTAATAATGTAA
155245 AATATTAATAAT
1 AATATTAATAAT
155257 TAAGATTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 9 0.36
16 8 0.32
17 8 0.32
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (16 bp):
AATATTAATAATGTAA
Found at i:155254 original size:23 final size:22
Alignment explanation
Indices: 155211--155259 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
155201 TTTTAAATTG
155211 TTAATATTAATAATAGAAATATA
1 TTAATATTAATAATAGAAATA-A
**
155234 TTAATATGTAA-AATATTAATAA
1 TTAATAT-TAATAATAGAAATAA
155256 TTAA
1 TTAA
155260 GATTGTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 5 0.22
23 15 0.65
24 3 0.13
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (22 bp):
TTAATATTAATAATAGAAATAA
Found at i:155509 original size:26 final size:24
Alignment explanation
Indices: 155480--155547 Score: 64
Period size: 26 Copynumber: 2.7 Consensus size: 24
155470 ACTAAATAAA
155480 TATTTTATTAATTATTCAAACAGAAT
1 TATTTTATTAATTATTCAAA-A-AAT
* * *
155506 TATTTTATCAATAATCCAAAAAAT
1 TATTTTATTAATTATTCAAAAAAT
*
155530 TAATCATTATTAATTATT
1 T-AT-TTTATTAATTATT
155548 AATAATGTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
24 4 0.12
25 3 0.09
26 26 0.79
ACGTcount: A:0.44, C:0.09, G:0.01, T:0.46
Consensus pattern (24 bp):
TATTTTATTAATTATTCAAAAAAT
Found at i:155716 original size:12 final size:12
Alignment explanation
Indices: 155661--155721 Score: 52
Period size: 12 Copynumber: 4.9 Consensus size: 12
155651 TAATAAGGTA
155661 AATATTTATAATT
1 AATATTT-TAATT
*
155674 AATATTTAAATT
1 AATATTTTAATT
* *
155686 ATAAATATTAA-T
1 A-ATATTTTAATT
*
155698 AATTATTTTAATG
1 AA-TATTTTAATT
155711 AATATTTTAAT
1 AATATTTTAAT
155722 AATCAATTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
11 1 0.03
12 22 0.58
13 15 0.39
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (12 bp):
AATATTTTAATT
Found at i:155742 original size:39 final size:36
Alignment explanation
Indices: 155686--155777 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 36
155676 TATTTAAATT
* *
155686 ATAA-ATATTAATAATTATTTTAATGAATATT-TTAATA
1 ATAATATATT-ATTATTATTTTAAT-AA-ATTAATAATA
*
155723 ATCAATTTATTAGTTATTATTTTAATAAATTAATAATA
1 AT-AATATATTA-TTATTATTTTAATAAATTAATAATA
155761 ATAATATATTATTATTA
1 ATAATATATTATTATTA
155778 CTAGTAACAT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
36 6 0.13
37 13 0.28
38 12 0.26
39 16 0.34
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (36 bp):
ATAATATATTATTATTATTTTAATAAATTAATAATA
Found at i:155952 original size:22 final size:22
Alignment explanation
Indices: 155919--155961 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
155909 CTTTTAGCTA
*
155919 TATTCAAATAATACTATAATAT
1 TATTCAAATAATACAATAATAT
155941 TATT-AAATTAATACAATAATA
1 TATTCAAA-TAATACAATAATA
155962 ATTTTTTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (22 bp):
TATTCAAATAATACAATAATAT
Found at i:157062 original size:41 final size:41
Alignment explanation
Indices: 157005--157089 Score: 143
Period size: 41 Copynumber: 2.1 Consensus size: 41
156995 CCTTGATAGT
*
157005 GGATGCTCAAAACACATGACCAGGGATAAAAATCTTTTCAA
1 GGATGCTCAAAACACATGACCAGGGACAAAAATCTTTTCAA
* *
157046 GGATGCTCAAAACACATGACCGGGGACAAAACTCTTTTCAA
1 GGATGCTCAAAACACATGACCAGGGACAAAAATCTTTTCAA
157087 GGA
1 GGA
157090 CTTGAAAGCT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (41 bp):
GGATGCTCAAAACACATGACCAGGGACAAAAATCTTTTCAA
Found at i:163771 original size:50 final size:54
Alignment explanation
Indices: 163717--163829 Score: 121
Period size: 52 Copynumber: 2.1 Consensus size: 54
163707 CGTTATATTT
* *
163717 TTATAAATTAAAT-TAGAATAA-A-GAATTTATTATTATTT-TATATT-T-TATAA
1 TTAT-AATTAAATATAAAATAATATGAATTTATTA-TATTTATAAATTATATATAA
* *
163767 TTATAATTTAATATAAAATAATATTAATTTATTATATTTATAAATTATATATAA
1 TTATAATTAAATATAAAATAATATGAATTTATTATATTTATAAATTATATATAA
163821 TTATTAATT
1 TTA-TAATT
163830 TATAATCTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
49 7 0.13
50 11 0.21
51 6 0.12
52 14 0.27
53 1 0.02
54 8 0.15
55 5 0.10
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (54 bp):
TTATAATTAAATATAAAATAATATGAATTTATTATATTTATAAATTATATATAA
Found at i:163808 original size:27 final size:26
Alignment explanation
Indices: 163778--163834 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
163768 TATAATTTAA
163778 TATAAAATAATAT-TAATTTATTATATT
1 TATAAAATAATATATAA-TTATTA-ATT
*
163805 TAT-AAATTATATATAATTATTAATT
1 TATAAAATAATATATAATTATTAATT
163830 TATAA
1 TATAA
163835 TCTTATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 6 0.22
26 15 0.56
27 6 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TATAAAATAATATATAATTATTAATT
Found at i:163841 original size:33 final size:33
Alignment explanation
Indices: 163783--163861 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 33
163773 TTTAATATAA
163783 AATAA-TATTAATTTATTATATTTATAAATTAT
1 AATAATTATTAATTTATTATATTTATAAATTAT
*
163815 ATATAATTATTAATTTA-TA-ATCTTATAATTTAT
1 A-ATAATTATTAATTTATTATAT-TTATAAATTAT
*
163848 AATATATTAATAAT
1 AATA-ATTATTAAT
163862 AATGTGATGT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
32 6 0.15
33 25 0.61
34 10 0.24
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (33 bp):
AATAATTATTAATTTATTATATTTATAAATTAT
Found at i:164084 original size:18 final size:18
Alignment explanation
Indices: 164061--164104 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
164051 AATTTATTTT
*
164061 TATTAATTATTAAGTTAA
1 TATTAATTATTAAATTAA
164079 TATTAAATT-TTAAATTAA
1 TATT-AATTATTAAATTAA
164097 T-TTAATTA
1 TATTAATTA
164105 ATTCAAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 4 0.17
17 2 0.09
18 13 0.57
19 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TATTAATTATTAAATTAA
Found at i:164838 original size:25 final size:24
Alignment explanation
Indices: 164784--164838 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
164774 ATTTCATAAT
*
164784 TAATAATTTAATTTAATTTTTAAA
1 TAATAATTTAATATAATTTTTAAA
*
164808 TGAATAATTTAA-ATAATATTTCTATA
1 T-AATAATTTAATATAAT-TTT-TAAA
164834 TAATA
1 TAATA
164839 TTAGTATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 5 0.19
25 17 0.65
26 4 0.15
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
TAATAATTTAATATAATTTTTAAA
Found at i:166093 original size:23 final size:24
Alignment explanation
Indices: 166049--166093 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
166039 TATATTTTAA
*
166049 TTTAAATATTTAAAATTTAAAATT
1 TTTAAATATTTAAAATTCAAAATT
* *
166073 TTTAATTA-TTAACATTCAAAA
1 TTTAAATATTTAAAATTCAAAA
166094 ATTTAATAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (24 bp):
TTTAAATATTTAAAATTCAAAATT
Found at i:166342 original size:181 final size:177
Alignment explanation
Indices: 166078--166460 Score: 459
Period size: 181 Copynumber: 2.1 Consensus size: 177
166068 AAATTTTTAA
* * * *
166078 TTATTAACA-TTCAAAAATTTAATAAGCAAAAGATATGAAAAAATAAATTTGTTTACCGATCAAG
1 TTATTAATATTTCAAAAA-TTAATAAGCAAAAGATATAAAAAAATAAATTTGTTTACCGAACAAA
* * * *
166142 TTCAAATAGTTATGACTATTTGAGCAATTATTTATTTAAAATCATTATGACCTTTTGTTTTAACC
65 TTCAAATAGCTACGACTATTTGAACAATTATCTATTTAAAATCATTATGACCTTTTGTTTT-ACC
166207 A-AAAACAATTGTTTTAGTTCATAAAAGCTTATCCAAAATAAAATAATACTAAT
129 ATAAAACAATTGTTTTAGTTCATAAAAGCTTATCCAAAAT---A-AA-ACTAAT
* * * *
166260 TTGTTAATATTTCAAAAATTAATAAGCAAGAG-TTTAAAAAAACT-AATTTGTTTACTGAACAAA
1 TTATTAATATTTCAAAAATTAATAAGCAAAAGATATAAAAAAA-TAAATTTGTTTACCGAACAAA
* * * * * * **
166323 TTTAAATAGCTACGACTATTTTAATAATTGTCTATTTAAAATCGTTATGACTTTTTGTTTTGTCA
65 TTCAAATAGCTACGACTATTTGAACAATTATCTATTTAAAATCATTATGACCTTTTGTTTTACCA
* *
166388 TAAAACAATTGTTTTAGTTCATACAAGCTTATTCAAAATAAAACTAAT
130 TAAAACAATTGTTTTAGTTCATAAAAGCTTATCCAAAATAAAACTAAT
*
166436 TTATTAATATTCCAAAAATTAATAA
1 TTATTAATATTTCAAAAATTAATAA
166461 CTAATTGATT
Statistics
Matches: 174, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
176 29 0.17
177 2 0.01
178 1 0.01
180 2 0.01
181 111 0.64
182 21 0.12
183 8 0.05
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (177 bp):
TTATTAATATTTCAAAAATTAATAAGCAAAAGATATAAAAAAATAAATTTGTTTACCGAACAAAT
TCAAATAGCTACGACTATTTGAACAATTATCTATTTAAAATCATTATGACCTTTTGTTTTACCAT
AAAACAATTGTTTTAGTTCATAAAAGCTTATCCAAAATAAAACTAAT
Found at i:166552 original size:15 final size:17
Alignment explanation
Indices: 166532--166563 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
166522 GTTTAAAGAA
166532 ATTTGA-TA-TAATAAT
1 ATTTGATTATTAATAAT
166547 ATTTGATTATTAATAAT
1 ATTTGATTATTAATAAT
166564 TTACTAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (17 bp):
ATTTGATTATTAATAAT
Found at i:166592 original size:26 final size:27
Alignment explanation
Indices: 166563--166614 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
166553 TTATTAATAA
*
166563 TTTACTAATAAATATAATA-TTATATT
1 TTTACTAAGAAATATAATAGTTATATT
*
166589 TTTACTTAGAAATATAATAGTTATAT
1 TTTACTAAGAAATATAATAGTTATAT
166615 AAATTATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (27 bp):
TTTACTAAGAAATATAATAGTTATATT
Found at i:167179 original size:176 final size:173
Alignment explanation
Indices: 166820--167392 Score: 447
Period size: 176 Copynumber: 3.2 Consensus size: 173
166810 ATAATACTAC
** *
166820 TTTATTAATATTTCAAAAATTAATAAACAAGAGATTTAAAAAATAAATCAGTTTACTGAATCAAT
1 TTTATTAATATTTCAAAAA-T--TAAA-AAGAGATTTAAAAAATAAATCA-TTTGTTG-ATCAGT
* * * * * * * ** *
166885 TCAAATAATCATGGCCATTTAAACAACTATCTATTTTAAATCATTATTACCTTTGTTTTATCATA
60 TCAAATAGTTATGACTATTTGAACAATTATCTATTTCAAATTGTTATAACCTTTGTTTTATCATA
* * * * * * *** *
166950 AAACAATTGTTTTTCAACAAATAAGATTTTTTTAAATAAAAGAATACTAA
125 AAATAATTGTTTTTGATCATACAAGATTATTCGGAAT-AAAGAATAATAA
* *
167000 TTTATTAATATTTCAAGAATTAAAAAGAGATTTAAAAAAGAAATCTATTTGTTGATCTAGTTCAA
1 TTTATTAATATTTCAAAAATTAAAAAGAGATTTAAAAAATAAATC-ATTTGTTGATC-AGTTCAA
* * *
167065 ATAGTTATGATTATTTGAACAATTATCTATTTCAAATTGTTATAACCTTTGCTCTATCATAAAAT
64 ATAGTTATGACTATTTGAACAATTATCTATTTCAAATTGTTATAACCTTTGTTTTATCATAAAAT
* *
167130 AATTGTTTTTGTTCATACAAAATTATTCGGAATAAAGTAATAATAA
129 AATTGTTTTTGATCATACAAGATTATTCGGAATAAAG-AATAATAA
* * * * * * ** *
167176 TTTAGTAATATTTTGAAATGAA-TAATTATGAGATTTAAAAAATTAATCCGTTTGTCAAACCAGT
1 TTTATTAATA-TTTCAAA--AATTAA-AAAGAGATTTAAAAAATAAAT-CATTTGT-TGATCAGT
* * * * * *
167240 TCAAATAGTTAAGACTATATGAA-ATTTATTTATTTCAACTTGTTATAACCTTTTGTTTTGTCAT
60 TCAAATAGTTATGACTATTTGAACAATTATCTATTTCAAATTGTTATAACC-TTTGTTTTATCAT
* * * * * * *
167304 AAAATAATT-ATTTAGCTCATAGAAGCTTGTTCGGAAT--AGAATAAATTA
124 AAAATAATTGTTTTTGATCATACAAGATTATTCGGAATAAAGAAT-AATAA
* * *
167352 TTTATTAATATTT-AAAAATTTATAAGAGATTTAGAAAATAA
1 TTTATTAATATTTCAAAAATTAAAAAGAGATTTAAAAAATAA
167393 TTCTACTTAC
Statistics
Matches: 318, Mismatches: 63, Indels: 32
0.77 0.15 0.08
Matches are distributed among these distances:
172 18 0.06
173 2 0.01
174 3 0.01
175 13 0.04
176 136 0.43
177 10 0.03
178 48 0.15
179 67 0.21
180 21 0.07
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (173 bp):
TTTATTAATATTTCAAAAATTAAAAAGAGATTTAAAAAATAAATCATTTGTTGATCAGTTCAAAT
AGTTATGACTATTTGAACAATTATCTATTTCAAATTGTTATAACCTTTGTTTTATCATAAAATAA
TTGTTTTTGATCATACAAGATTATTCGGAATAAAGAATAATAA
Found at i:168102 original size:25 final size:23
Alignment explanation
Indices: 168071--168136 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 23
168061 TATAATAAAA
*
168071 TATAATATAATAATTATTATATTT
1 TATAA-ATAATAATTATTATAATT
*
168095 TATTAATAATAAATTATTTATAATT
1 TATAAATAAT-AATTA-TTATAATT
*
168120 TATAAAATTATAATTAT
1 TAT-AAATAATAATTAT
168137 AATGGTAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
23 5 0.14
24 10 0.29
25 15 0.43
26 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TATAAATAATAATTATTATAATT
Found at i:168704 original size:15 final size:15
Alignment explanation
Indices: 168681--168710 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
168671 TCTATTATAT
168681 CTATATTAACTAATA
1 CTATATTAACTAATA
*
168696 CTATGTTAACTAATA
1 CTATATTAACTAATA
168711 GTATCAATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.13, G:0.03, T:0.40
Consensus pattern (15 bp):
CTATATTAACTAATA
Found at i:169064 original size:16 final size:17
Alignment explanation
Indices: 169043--169075 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
169033 TTGTTATTTA
169043 AAATAG-ATAATTATTC
1 AAATAGTATAATTATTC
169059 AAATAGTTATAATTATT
1 AAATAG-TATAATTATT
169076 TGAACATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (17 bp):
AAATAGTATAATTATTC
Found at i:177741 original size:22 final size:22
Alignment explanation
Indices: 177716--177770 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
177706 TTGAATTGAT
*
177716 CAAAAGTTTTGATTTGACAAAA
1 CAAAAATTTTGATTTGACAAAA
177738 CAAAAATTTTGATTTGACAAAA
1 CAAAAATTTTGATTTGACAAAA
177760 CAAAAATTTTG
1 CAAAAATTTTG
177771 CCTAACTTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.33
Consensus pattern (22 bp):
CAAAAATTTTGATTTGACAAAA
Found at i:178775 original size:18 final size:19
Alignment explanation
Indices: 178754--178789 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
178744 ATTATAAATC
178754 AATTAATTA-TTATTTATT
1 AATTAATTATTTATTTATT
178772 AATTAATTATTTATTTAT
1 AATTAATTATTTATTTAT
178790 ATTTGATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
AATTAATTATTTATTTATT
Found at i:178779 original size:22 final size:22
Alignment explanation
Indices: 178745--178786 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
178735 TTTTAATAAA
178745 TTATAAATCAATTAATTATTAT
1 TTATAAATCAATTAATTATTAT
* * *
178767 TTATTAATTAATTATTTATT
1 TTATAAATCAATTAATTATT
178787 TATATTTGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TTATAAATCAATTAATTATTAT
Found at i:179200 original size:27 final size:27
Alignment explanation
Indices: 179165--179230 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
179155 TTTAAACAAA
*
179165 TTAATATATTAAAA-TAATATATATTAGT
1 TTAA-ATATTAAAATTAATATATAATA-T
* *
179193 TTTAATATTTAAAATTAATATTTAATAT
1 TTAAATA-TTAAAATTAATATATAATAT
179221 TTAAATATTA
1 TTAAATATTA
179231 TATATATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
27 6 0.19
28 16 0.50
29 10 0.31
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
TTAAATATTAAAATTAATATATAATAT
Found at i:179212 original size:13 final size:14
Alignment explanation
Indices: 179162--179230 Score: 54
Period size: 14 Copynumber: 5.0 Consensus size: 14
179152 TAATTTAAAC
179162 AAATTAATATATTA
1 AAATTAATATATTA
*
179176 AAATAATATATATTA
1 AAATTA-ATATATTA
***
179191 GTTTTAATAT-TTA
1 AAATTAATATATTA
179204 AAATTAATAT-TTA
1 AAATTAATATATTA
*
179217 ATATTTAA-ATATTA
1 A-AATTAATATATTA
179231 TATATATTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
13 16 0.37
14 17 0.40
15 10 0.23
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (14 bp):
AAATTAATATATTA
Found at i:179218 original size:20 final size:22
Alignment explanation
Indices: 179193--179235 Score: 72
Period size: 20 Copynumber: 2.0 Consensus size: 22
179183 ATATATTAGT
179193 TTTAATATTTAAA-ATTA-ATA
1 TTTAATATTTAAATATTATATA
179213 TTTAATATTTAAATATTATATA
1 TTTAATATTTAAATATTATATA
179235 T
1 T
179236 ATTATCTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 13 0.62
21 4 0.19
22 4 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTAATATTTAAATATTATATA
Found at i:179354 original size:11 final size:11
Alignment explanation
Indices: 179338--179367 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
179328 TAGGTATCTA
179338 ATATAATTACG
1 ATATAATTACG
*
179349 ATATAATTATG
1 ATATAATTACG
179360 ATATAATT
1 ATATAATT
179368 GTGTAATAGT
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:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (11 bp):
ATATAATTACG
Found at i:179524 original size:23 final size:23
Alignment explanation
Indices: 179487--179533 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
179477 AATTATTAAA
*
179487 TTAATTAAATAATAATTAAATAT
1 TTAATTAAATAATAAATAAATAT
* * *
179510 TTAATTAATTTATAAATAATTAT
1 TTAATTAAATAATAAATAAATAT
179533 T
1 T
179534 AAAATTACTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTAATTAAATAATAAATAAATAT
Found at i:179595 original size:18 final size:17
Alignment explanation
Indices: 179551--179594 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
179541 CTAGTTATAT
*
179551 TTAATTCTATAATATAAA
1 TTAATTTTA-AATATAAA
179569 TTAATTTTAAATATTAAA
1 TTAATTTTAAATA-TAAA
179587 TCTAATTT
1 T-TAATTT
179595 ATTAATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 13 0.57
19 6 0.26
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATTTTAAATATAAA
Found at i:179774 original size:10 final size:10
Alignment explanation
Indices: 179694--179776 Score: 57
Period size: 10 Copynumber: 8.1 Consensus size: 10
179684 CTCATCTTAT
*
179694 AATATTAACA
1 AATATTAATA
179704 AATATTATATA
1 AATATTA-ATA
179715 AAT-TT-ATA
1 AATATTAATA
179723 ATATATTAATTA
1 A-ATATTAA-TA
*
179735 AATTAATGAAATA
1 AA-T-AT-TAATA
179748 AATATTAAT-
1 AATATTAATA
*
179757 TA-ATTAATA
1 AATATTAATA
179766 AATATTAATA
1 AATATTAATA
179776 A
1 A
179777 TCTTATAATA
Statistics
Matches: 58, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
8 10 0.17
9 4 0.07
10 22 0.38
11 9 0.16
12 5 0.09
13 6 0.10
14 2 0.03
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (10 bp):
AATATTAATA
Found at i:179775 original size:24 final size:24
Alignment explanation
Indices: 179720--179769 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
179710 ATATAAATTT
179720 ATAATATATTAATTAAATTAATGAA
1 ATAA-ATATTAATTAAATTAATGAA
179745 ATAAATATTAATT-AATTAAT-AA
1 ATAAATATTAATTAAATTAATGAA
179767 ATA
1 ATA
179770 TTAATAATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 5 0.20
23 7 0.28
24 9 0.36
25 4 0.16
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
ATAAATATTAATTAAATTAATGAA
Found at i:179784 original size:18 final size:17
Alignment explanation
Indices: 179744--179777 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
179734 AAATTAATGA
179744 AATAAATATTAATTAATT
1 AATAAATATTAA-TAATT
179762 AATAAATATTAATAAT
1 AATAAATATTAATAAT
179778 CTTATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATAAATATTAATAATT
Found at i:179885 original size:27 final size:27
Alignment explanation
Indices: 179716--179885 Score: 72
Period size: 27 Copynumber: 6.3 Consensus size: 27
179706 TATTATATAA
179716 ATTT-ATAATA-TATTA-ATTA-AATT
1 ATTTAATAATATTATTATATTATAATT
** *
179739 AATGAAATAAATATTAATTA-ATTAATAAAT
1 -ATTTAAT-AATATT-ATTATATT-ATAATT
* * *
179769 A-TTAATAATCTTATAATA-TATAAAT
1 ATTTAATAATATTATTATATTATAATT
*
179794 AGTTTAAT--TTTTATATATATTAATAATT
1 A-TTTAATAATATTAT-TATATT-ATAATT
* *
179822 ATATTAATTTAAT-TCTATTTTATTATTATT
1 AT-TTAA--TAATAT-TATTATATTATAATT
**
179852 AAGTAATAATATTATTATATTATAATT
1 ATTTAATAATATTATTATATTATAATT
179879 ATTTAAT
1 ATTTAAT
179886 TATTTTATAA
Statistics
Matches: 109, Mismatches: 18, Indels: 35
0.67 0.11 0.22
Matches are distributed among these distances:
24 2 0.02
25 14 0.13
26 11 0.10
27 36 0.33
28 21 0.19
29 5 0.05
30 10 0.09
31 6 0.06
32 4 0.04
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (27 bp):
ATTTAATAATATTATTATATTATAATT
Found at i:179893 original size:27 final size:27
Alignment explanation
Indices: 179802--179893 Score: 76
Period size: 27 Copynumber: 3.2 Consensus size: 27
179792 ATAGTTTAAT
179802 TTTTATATATATTAATAATTATATTAATTTAA
1 TTTTAT-TATATT-ATAATTAT-TTAA-TT-A
* * * ** *
179834 TTCTATTTTATTATTATTAAGTAATAA
1 TTTTATTATATTATAATTATTTAATTA
*
179861 TATTATTATATTATAATTATTTAATTA
1 TTTTATTATATTATAATTATTTAATTA
179888 TTTTAT
1 TTTTAT
179894 AAATATTAAG
Statistics
Matches: 46, Mismatches: 14, Indels: 5
0.71 0.22 0.08
Matches are distributed among these distances:
27 26 0.57
28 1 0.02
29 3 0.07
30 6 0.13
31 5 0.11
32 5 0.11
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (27 bp):
TTTTATTATATTATAATTATTTAATTA
Found at i:181406 original size:23 final size:24
Alignment explanation
Indices: 181362--181406 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
181352 TATATTTTAA
*
181362 TTTAAATATTTAAAATTTAAAATT
1 TTTAAATATTTAAAATTAAAAATT
* *
181386 TTTAATTA-TTAACATTAAAAA
1 TTTAAATATTTAAAATTAAAAA
181407 AATTAATAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
TTTAAATATTTAAAATTAAAAATT
Found at i:181640 original size:17 final size:18
Alignment explanation
Indices: 181620--181653 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
181610 TATTATTATA
*
181620 ATAATATAG-TAATTAAT
1 ATAAAATAGTTAATTAAT
181637 ATAAAATAGTTAATTAA
1 ATAAAATAGTTAATTAA
181654 CGATATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
ATAAAATAGTTAATTAAT
Found at i:181970 original size:22 final size:22
Alignment explanation
Indices: 181919--181972 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
181909 AAAATTCTTA
*
181919 AAATTAATTAATAATTTATCAAT
1 AAATTAA-TAATAAATTATCAAT
* *
181942 TAGTTAATAATAAATTA-CTAAT
1 AAATTAATAATAAATTATC-AAT
181964 AAATTAATA
1 AAATTAATA
181973 TTTATACTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 1 0.04
22 19 0.76
23 5 0.20
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (22 bp):
AAATTAATAATAAATTATCAAT
Found at i:182034 original size:11 final size:12
Alignment explanation
Indices: 181997--182120 Score: 51
Period size: 12 Copynumber: 10.2 Consensus size: 12
181987 TCTATATATG
*
181997 TTATTAGTAATA
1 TTATTATTAATA
* *
182009 ATAATA-TAATA
1 TTATTATTAATA
182020 TTATTATTAAT-
1 TTATTATTAATA
*
182031 TTATTA-AAATAA
1 TTATTATTAAT-A
* *
182043 TAATTAATAA-A
1 TTATTATTAATA
182054 TTGATTATTAA-A
1 TT-ATTATTAATA
* *
182066 ATATTCATTAAAA
1 TTATT-ATTAATA
*
182079 TAATTATTAATA
1 TTATTATTAATA
*
182091 TTTATAATTTAAATA
1 -TTATTA-TT-AATA
*
182106 TTAATTATAAATA
1 TT-ATTATTAATA
182119 TT
1 TT
182121 TACCTTATTA
Statistics
Matches: 84, Mismatches: 17, Indels: 21
0.69 0.14 0.17
Matches are distributed among these distances:
10 3 0.04
11 20 0.24
12 33 0.39
13 16 0.19
14 5 0.06
15 7 0.08
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.48
Consensus pattern (12 bp):
TTATTATTAATA
Found at i:182087 original size:27 final size:27
Alignment explanation
Indices: 182031--182087 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
182021 TATTATTAAT
*
182031 TTATTAAAATAATAATTAATAAATTGA
1 TTATTAAAATAATAATTAAAAAATTGA
* *
182058 TTATTAAAATATTCATTAAAATAATT-A
1 TTATTAAAATAATAATTAAAA-AATTGA
182085 TTA
1 TTA
182088 ATATTTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (27 bp):
TTATTAAAATAATAATTAAAAAATTGA
Found at i:182200 original size:26 final size:24
Alignment explanation
Indices: 182164--182225 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 24
182154 GTATTAAGTA
182164 AATAATAAATAATAATTATTTATTA-T
1 AATAATAAAT-ATAA-TATTT-TTATT
*
182190 AATAATGAATATAATATTTTTATT
1 AATAATAAATATAATATTTTTATT
182214 AAT-ATAAATATA
1 AATAATAAATATA
182226 CCTTATTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
23 11 0.33
24 9 0.27
25 4 0.12
26 9 0.27
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
AATAATAAATATAATATTTTTATT
Found at i:182299 original size:26 final size:25
Alignment explanation
Indices: 182233--182309 Score: 68
Period size: 26 Copynumber: 3.0 Consensus size: 25
182223 ATACCTTATT
*
182233 AATAATTAATAATGATTAATTTTTTAG
1 AATAATTAATAA--AATAATTTTTTAG
* * *
182260 -ATTATTGATAAAATAATTTTGTTTG
1 AATAATTAATAAAATAATTTT-TTAG
182285 AATAATTAATAAAAT-ATTTATTTAG
1 AATAATTAATAAAATAATTT-TTTAG
182310 TTTATATTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
24 8 0.20
25 10 0.25
26 22 0.55
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (25 bp):
AATAATTAATAAAATAATTTTTTAG
Found at i:182469 original size:27 final size:25
Alignment explanation
Indices: 182429--182542 Score: 81
Period size: 28 Copynumber: 4.3 Consensus size: 25
182419 TATTAAATAT
*
182429 TATATA-TTAT-ATATTAACTTATGTA
1 TATATATTTATAATATTAA-TAAT-TA
182454 TATATATTTATAATA-TAATAATTA
1 TATATATTTATAATATTAATAATTA
*
182478 TATTAATAATTTATAATATTATTAAATTA
1 TA-T-AT-ATTTATAATATTAAT-AATTA
* *
182507 TATAAATATTATTAATATTATTATATTA
1 TATATAT-TTA-TAATATTAATA-ATTA
182535 TATTATAT
1 TA-TATAT
182543 ATTAATTTAG
Statistics
Matches: 74, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
24 4 0.05
25 10 0.14
26 11 0.15
27 18 0.24
28 20 0.27
29 11 0.15
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.53
Consensus pattern (25 bp):
TATATATTTATAATATTAATAATTA
Found at i:182523 original size:9 final size:9
Alignment explanation
Indices: 182477--182629 Score: 89
Period size: 9 Copynumber: 17.6 Consensus size: 9
182467 TATAATAATT
*
182477 ATATTAATA
1 ATATTATTA
182486 AT-TTA-TA
1 ATATTATTA
182493 ATATTATTA
1 ATATTATTA
182502 A-ATTATATAA
1 ATATTAT-T-A
182512 ATATTATTA
1 ATATTATTA
182521 ATATTATT-
1 ATATTATTA
182529 ATATTA-TA
1 ATATTATTA
*
182537 TTATATATTA
1 ATAT-TATTA
182547 AT-TTAGTTA
1 ATATTA-TTA
*
182556 AT-TTATAA
1 ATATTATTA
182564 AT-TATATTAA
1 ATAT-TATT-A
182574 ATATTA-TA
1 ATATTATTA
182582 ATA-TATTTA
1 ATATTA-TTA
182591 ATA-TATTA
1 ATATTATTA
182599 AT-TTCATTA
1 ATATT-ATTA
* *
182608 ATCTTATAA
1 ATATTATTA
*
182617 ATAAT-TTA
1 ATATTATTA
182625 ATATT
1 ATATT
182630 TAAAATTAAT
Statistics
Matches: 118, Mismatches: 9, Indels: 35
0.73 0.06 0.22
Matches are distributed among these distances:
7 7 0.06
8 43 0.36
9 49 0.42
10 13 0.11
11 6 0.05
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (9 bp):
ATATTATTA
Found at i:182539 original size:38 final size:37
Alignment explanation
Indices: 182418--182588 Score: 108
Period size: 38 Copynumber: 4.5 Consensus size: 37
182408 ATTTAATCTA
* *
182418 ATATTAAATATTATATATTATATATTAA-CTTATGTATA-T
1 ATATTAAATA-TATA-AATAT-TATTAATATTAT-TATATT
* * *
182457 ATATTTATAATATAATAATTA-TATTAATAAT-TTATAAT
1 ATA-TTA-AATAT-ATAAATATTATTAATATTATTATATT
182495 ATTATTAAATTATATAAATATTATTAATATTATTATATT
1 A-TATTAAA-TATATAAATATTATTAATATTATTATATT
* *
182534 ATATT--ATATATTAAT-TTAGTTAAT-TTA-TAAATT
1 ATATTAAATATATAAATATTA-TTAATATTATTATATT
182567 ATATTAAATATTATAATATATT
1 ATATTAAATA-TATAA-ATATT
182589 TAATATATTA
Statistics
Matches: 109, Mismatches: 8, Indels: 31
0.74 0.05 0.21
Matches are distributed among these distances:
33 10 0.09
34 6 0.06
35 16 0.15
36 5 0.05
37 14 0.13
38 30 0.28
39 13 0.12
40 8 0.07
41 7 0.06
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (37 bp):
ATATTAAATATATAAATATTATTAATATTATTATATT
Found at i:182540 original size:33 final size:32
Alignment explanation
Indices: 182497--182577 Score: 85
Period size: 33 Copynumber: 2.5 Consensus size: 32
182487 TTTATAATAT
*
182497 TATTAAATTATATA-AATATTA-TTAATATTATTA
1 TATTATATTATATATAAT-TTAGTTAAT-TTA-TA
182530 TATTATATTATATATTAATTTAGTTAATTTATA
1 TATTATATTATATA-TAATTTAGTTAATTTATA
* *
182563 AATTATATTAAATAT
1 TATTATATTATATAT
182578 TATAATATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
32 1 0.02
33 27 0.64
34 6 0.14
35 8 0.19
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (32 bp):
TATTATATTATATATAATTTAGTTAATTTATA
Found at i:182578 original size:33 final size:33
Alignment explanation
Indices: 182477--182579 Score: 95
Period size: 35 Copynumber: 3.0 Consensus size: 33
182467 TATAATAATT
*
182477 ATATTAATAATTTAT-AA-TATTATTAAATTATATAA
1 ATATTATTAATTTATAAATTA-TATTAAA-TAT-T-A
* *
182512 ATATTATTAATATTATTATATTATATTATATATTA
1 ATATTATTAAT-TTA-TAAATTATATTAAATATTA
182547 AT-TTAGTTAATTTATAAATTATATTAAATATTA
1 ATATTA-TTAATTTATAAATTATATTAAATATTA
182580 TAATATATTT
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
33 17 0.29
34 6 0.10
35 18 0.31
36 4 0.07
37 4 0.07
38 7 0.12
39 2 0.03
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (33 bp):
ATATTATTAATTTATAAATTATATTAAATATTA
Found at i:182609 original size:26 final size:24
Alignment explanation
Indices: 182491--182619 Score: 82
Period size: 26 Copynumber: 4.9 Consensus size: 24
182481 TAATAATTTA
182491 TAATATTATTAAATTATATAAATATTAT
1 TAAT-TTATT-AA-TATATAAATA-TAT
*
182519 TAATATTATT-ATATTATATTATATAT
1 TAAT-TTATTAATA-TATA-AATATAT
*
182545 TAATTTAGTTAATTTATAAATTATAT
1 TAATTTA-TTAATATATAAA-TATAT
*
182571 TAAATATTA-TAATATATTTAATATAT
1 T-AAT-TTATTAATATA-TAAATATAT
*
182597 TAATTTCATTAATCTTATAAATA
1 TAATTT-ATTAAT-ATATAAATA
182620 ATTTAATATT
Statistics
Matches: 83, Mismatches: 7, Indels: 24
0.73 0.06 0.21
Matches are distributed among these distances:
24 2 0.02
25 10 0.12
26 45 0.54
27 13 0.16
28 13 0.16
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.52
Consensus pattern (24 bp):
TAATTTATTAATATATAAATATAT
Found at i:182784 original size:13 final size:12
Alignment explanation
Indices: 182766--182808 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
182756 ATTATCTATA
182766 ATATATTACAATT
1 ATATATTA-AATT
182779 ATATATTAAATT
1 ATATATTAAATT
182791 ATATAATT-AA-T
1 ATAT-ATTAAATT
182802 ATATATT
1 ATATATT
182809 CTAAATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 3 0.10
11 5 0.17
12 10 0.34
13 11 0.38
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (12 bp):
ATATATTAAATT
Found at i:184347 original size:18 final size:18
Alignment explanation
Indices: 184324--184411 Score: 55
Period size: 17 Copynumber: 5.1 Consensus size: 18
184314 TCATAATGAT
184324 ATTAATTATATATTATTA
1 ATTAATTATATATTATTA
* *
184342 ATTAA-TATATAATA-GA
1 ATTAATTATATATTATTA
184358 ATTTAATT-TATTATTA-TA
1 A-TTAATTATA-TATTATTA
* *
184376 CTT-ATTA-ATTTTATTA
1 ATTAATTATATATTATTA
*
184392 TATT-TTTATATATTATTA
1 -ATTAATTATATATTATTA
184410 AT
1 AT
184412 AAAAATCATT
Statistics
Matches: 54, Mismatches: 9, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
15 4 0.07
16 8 0.15
17 23 0.43
18 19 0.35
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (18 bp):
ATTAATTATATATTATTA
Done.