Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007918.1 Hibiscus syriacus cultivar Beakdansim tig00110321_pilon, 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: 2302251
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 9
Found at i:10191 original size:2 final size:2
Alignment explanation
Indices: 10184--10218 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
10174 GTTCAAACAT
10184 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 T
10219 GTATGTATGT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:26882 original size:35 final size:34
Alignment explanation
Indices: 26797--26883 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
26787 ATTTGATATT
*
26797 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
26831 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
26869 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
26884 ACTAAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:26974 original size:47 final size:47
Alignment explanation
Indices: 26896--27002 Score: 139
Period size: 47 Copynumber: 2.3 Consensus size: 47
26886 TAAAATATAT
*
26896 TAAAAAAATCTAACAAATTTAACAAAATAAAGTAAATATTAAATGAGAAA
1 TAAAAAAATCTAACAAATTAAACAAAATAAAGTAAATA-TAAAT-A-AAA
*
26946 TAAAAAAAT-T-AC-AATTAAACAAAATAAAGTAAATATAAATATAA
1 TAAAAAAATCTAACAAATTAAACAAAATAAAGTAAATATAAATAAAA
26990 TAAAAAAAATCTA
1 T-AAAAAAATCTA
27003 TCGATGCCTA
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
44 3 0.06
45 9 0.17
46 6 0.12
47 22 0.42
48 2 0.04
49 1 0.02
50 9 0.17
ACGTcount: A:0.66, C:0.06, G:0.04, T:0.24
Consensus pattern (47 bp):
TAAAAAAATCTAACAAATTAAACAAAATAAAGTAAATATAAATAAAA
Found at i:29123 original size:111 final size:111
Alignment explanation
Indices: 28986--29199 Score: 383
Period size: 111 Copynumber: 1.9 Consensus size: 111
28976 ATTACAAAAA
* *
28986 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
29051 AATTAAAACGTTAAAATGTTATCGTATCAACAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTCGAGATAT
*
29097 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTACTAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
29162 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGT
66 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGT
29200 AGCGATATAT
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 98 1.00
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTCGAGATAT
Found at i:29345 original size:12 final size:10
Alignment explanation
Indices: 29331--29371 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
29321 ACCTTAAAAA
*
29331 GAGAGTATTT
1 GAGAGAATTT
29341 GAGAGAAATTT
1 GAGAG-AATTT
29352 -AGAGAATTT
1 GAGAGAATTT
29361 GAGAGAATTT
1 GAGAGAATTT
29371 G
1 G
29372 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:29543 original size:50 final size:49
Alignment explanation
Indices: 29489--29609 Score: 134
Period size: 50 Copynumber: 2.4 Consensus size: 49
29479 AGATATCCAG
* *
29489 GTATAACGCGGATCAGGGGGCACGCTATACCCACGTGGTGCCAGATCACC
1 GTATAACGCGG-TCAGGGGGCACGCTATACCCACGTGGCGCCAAATCACC
* * * * *
29539 GTATATCGCGGGGCAGGGCGCGCGCTATACCCACGTGGCGCCAAATCAGC
1 GTATAACGC-GGTCAGGGGGCACGCTATACCCACGTGGCGCCAAATCACC
* *
29589 ATATAGCGCGGTGCAGGGGGC
1 GTATAACGCGGT-CAGGGGGC
29610 GCGTTTTCCT
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
49 2 0.03
50 54 0.93
51 2 0.03
ACGTcount: A:0.21, C:0.29, G:0.35, T:0.15
Consensus pattern (49 bp):
GTATAACGCGGTCAGGGGGCACGCTATACCCACGTGGCGCCAAATCACC
Found at i:29612 original size:50 final size:50
Alignment explanation
Indices: 29502--29612 Score: 150
Period size: 50 Copynumber: 2.2 Consensus size: 50
29492 TAACGCGGAT
* * * * *
29502 CAGGGGGCACGCTATACCCACGTGGTGCCAGATCACCGTATATCGCGGGG
1 CAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACCATATAGCGCGGGG
* * *
29552 CAGGGCGCGCGCTATACCCACGTGGCGCCAAATCAGCATATAGCGCGGTG
1 CAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACCATATAGCGCGGGG
29602 CAGGGGGCGCG
1 CAGGGGGCGCG
29613 TTTTCCTGCT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.20, C:0.31, G:0.36, T:0.14
Consensus pattern (50 bp):
CAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACCATATAGCGCGGGG
Found at i:31313 original size:19 final size:19
Alignment explanation
Indices: 31277--31316 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
31267 ATCATACGTG
31277 TTTTACTATTAAGAATAATT
1 TTTTACTATT-AGAATAATT
31297 TTTTACTATT-GACATAATT
1 TTTTACTATTAGA-ATAATT
31316 T
1 T
31317 ATGTATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.11
19 7 0.37
20 10 0.53
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (19 bp):
TTTTACTATTAGAATAATT
Found at i:40412 original size:21 final size:21
Alignment explanation
Indices: 40383--40422 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
40373 TCTATTGAAA
* *
40383 CTCCACCTGTTTTGGAGTATG
1 CTCCACCTGCTGTGGAGTATG
*
40404 CTCCGCCTGCTGTGGAGTA
1 CTCCACCTGCTGTGGAGTA
40423 CTACTTGTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.12, C:0.28, G:0.28, T:0.33
Consensus pattern (21 bp):
CTCCACCTGCTGTGGAGTATG
Found at i:43941 original size:14 final size:14
Alignment explanation
Indices: 43922--43951 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
43912 TTTAGATTTT
*
43922 TTAAAATTACATTA
1 TTAAAAATACATTA
43936 TTAAAAATACATTA
1 TTAAAAATACATTA
43950 TT
1 TT
43952 GATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:44045 original size:7 final size:7
Alignment explanation
Indices: 44033--44065 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
44023 GTGTGATAGA
44033 GTTTATG
1 GTTTATG
44040 GTTTATG
1 GTTTATG
44047 GTTTATG
1 GTTTATG
44054 GTTTATG
1 GTTTATG
44061 GTTTA
1 GTTTA
44066 GGTAGGGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.58
Consensus pattern (7 bp):
GTTTATG
Found at i:44078 original size:7 final size:7
Alignment explanation
Indices: 44033--44125 Score: 50
Period size: 7 Copynumber: 13.7 Consensus size: 7
44023 GTGTGATAGA
*
44033 GTTTATG
1 GTTTAGG
*
44040 GTTTATG
1 GTTTAGG
*
44047 GTTTATG
1 GTTTAGG
*
44054 GTTTATG
1 GTTTAGG
44061 GTTTA-G
1 GTTTAGG
44067 G--TAGG
1 GTTTAGG
44072 GTTTAGG
1 GTTTAGG
* *
44079 GTTTTGA
1 GTTTAGG
* *
44086 ATTTAGT
1 GTTTAGG
*
44093 GTTTACG
1 GTTTAGG
44100 GTTTA-G
1 GTTTAGG
44106 GTGTTAGG
1 GT-TTAGG
* *
44114 ATTTAAG
1 GTTTAGG
44121 GTTTA
1 GTTTA
44126 ATTTATACAC
Statistics
Matches: 70, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
4 2 0.03
5 2 0.03
6 5 0.07
7 59 0.84
8 2 0.03
ACGTcount: A:0.18, C:0.01, G:0.31, T:0.49
Consensus pattern (7 bp):
GTTTAGG
Found at i:44548 original size:17 final size:18
Alignment explanation
Indices: 44509--44551 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
44499 AATGCCAAAT
44509 AATTAAAATTACAAGACAC
1 AATTAAAA-TACAAGACAC
44528 AATTAAAA-ACAA-ACAC
1 AATTAAAATACAAGACAC
44544 AAATTAAA
1 -AATTAAA
44552 GGAACACTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.17
17 11 0.48
19 8 0.35
ACGTcount: A:0.65, C:0.14, G:0.02, T:0.19
Consensus pattern (18 bp):
AATTAAAATACAAGACAC
Found at i:45628 original size:11 final size:11
Alignment explanation
Indices: 45612--45666 Score: 68
Period size: 11 Copynumber: 5.5 Consensus size: 11
45602 GCATGAATGG
45612 CATGATCGAGT
1 CATGATCGAGT
45623 CATGAT-G-G-
1 CATGATCGAGT
45631 CATGATCGAGT
1 CATGATCGAGT
45642 CATGAT-G-G-
1 CATGATCGAGT
45650 CATGATCGAGT
1 CATGATCGAGT
45661 CATGAT
1 CATGAT
45667 GACATTTTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
8 12 0.32
9 4 0.11
10 4 0.11
11 18 0.47
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.27
Consensus pattern (11 bp):
CATGATCGAGT
Found at i:45632 original size:19 final size:19
Alignment explanation
Indices: 45603--45667 Score: 121
Period size: 19 Copynumber: 3.4 Consensus size: 19
45593 TCTTGAATTG
45603 CATGAATGGCATGATCGAGT
1 CATG-ATGGCATGATCGAGT
45623 CATGATGGCATGATCGAGT
1 CATGATGGCATGATCGAGT
45642 CATGATGGCATGATCGAGT
1 CATGATGGCATGATCGAGT
45661 CATGATG
1 CATGATG
45668 ACATTTTACT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
19 41 0.91
20 4 0.09
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (19 bp):
CATGATGGCATGATCGAGT
Found at i:50519 original size:27 final size:28
Alignment explanation
Indices: 50488--50542 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
50478 GTAAAGTAAA
50488 TTATTT-ATTTATTGTTTGT-TATGTTTT
1 TTATTTGATTTATT-TTTGTGTATGTTTT
* *
50515 TTATTTGTTTTATTTTTGTGTGTGTTTT
1 TTATTTGATTTATTTTTGTGTATGTTTT
50543 CCAATAGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.11, C:0.00, G:0.15, T:0.75
Consensus pattern (28 bp):
TTATTTGATTTATTTTTGTGTATGTTTT
Found at i:51197 original size:17 final size:17
Alignment explanation
Indices: 51170--51211 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
51160 AAGTTTGTCG
* *
51170 TTTTAATTAAAATTAATA
1 TTTT-ATTAAAATGAAAA
51188 TTTTATTAAAATGAAAA
1 TTTTATTAAAATGAAAA
51205 TTTTATT
1 TTTTATT
51212 TTTGGGTGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
TTTTATTAAAATGAAAA
Found at i:57926 original size:142 final size:143
Alignment explanation
Indices: 57667--57942 Score: 317
Period size: 142 Copynumber: 1.9 Consensus size: 143
57657 TGGTTCAAGT
* * * * * *
57667 TAATATAAGCATAAAAATGGTAATTGGAAGAATTTTAGTGAAATAATTTGAAAACGTTAAAGTAA
1 TAATACAAGCATAAAAATGGTAATTGGAAGAATTCTAGTGAAATAATTTAAAAACATAAAACTAA
* *
57732 TTAAATAATTGAAAATGATTAAATTCTAAATTTAAATCATAAGATTAGGTGATACTGAT-TTTTT
66 TTAAATAATTGAAAATAATTAAATTCTAAATTTAAATCATAAGATTAGGTGATACTGATATTATT
57796 TTATAAAAAAATC
131 TTATAAAAAAATC
* * * * *
57809 TAATACAAGCATCAAAAA-GGTAATTTGAATAATTCTAGTGAATTTA-TTAAAAATATAAAACTA
1 TAATACAAGCAT-AAAAATGGTAATTGGAAGAATTCTAGTGAAATAATTTAAAAACATAAAACTA
* * * * * * *
57872 ATTAATTAATTG-AGATAATTGAACTTCTAAATTTTAAGTCATAGGATTATGTGATATTGATATT
65 ATTAAATAATTGAAAATAATT-AAATTCTAAA-TTTAAATCATAAGATTAGGTGATACTGATATT
57936 ATTTTAT
128 ATTTTAT
57943 TTTCGTCAAA
Statistics
Matches: 110, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
140 6 0.05
141 32 0.29
142 59 0.54
143 13 0.12
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (143 bp):
TAATACAAGCATAAAAATGGTAATTGGAAGAATTCTAGTGAAATAATTTAAAAACATAAAACTAA
TTAAATAATTGAAAATAATTAAATTCTAAATTTAAATCATAAGATTAGGTGATACTGATATTATT
TTATAAAAAAATC
Found at i:65759 original size:65 final size:66
Alignment explanation
Indices: 65629--65761 Score: 250
Period size: 66 Copynumber: 2.0 Consensus size: 66
65619 TTGAAAAATT
*
65629 TTGTTACACGTTGTCGTAATTTTGATTTTTTTTAAAATAAAAAAATATTATATTAAAAAATCATA
1 TTGTTACACGTTATCGTAATTTTGATTTTTTTTAAAATAAAAAAATATTATATTAAAAAATCATA
65694 A
66 A
65695 TTGTTACACGTTATCGTAATTTTGATTTTTTTTAAAAT-AAAAAATATTATATTAAAAAATCATA
1 TTGTTACACGTTATCGTAATTTTGATTTTTTTTAAAATAAAAAAATATTATATTAAAAAATCATA
65759 A
66 A
65760 TT
1 TT
65762 TCTCTTAAAT
Statistics
Matches: 66, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
65 29 0.44
66 37 0.56
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (66 bp):
TTGTTACACGTTATCGTAATTTTGATTTTTTTTAAAATAAAAAAATATTATATTAAAAAATCATA
A
Found at i:93980 original size:13 final size:13
Alignment explanation
Indices: 93962--93986 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
93952 AACAATAACA
93962 AATCAATTTAATT
1 AATCAATTTAATT
93975 AATCAATTTAAT
1 AATCAATTTAAT
93987 GGAATATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
AATCAATTTAATT
Found at i:94514 original size:26 final size:26
Alignment explanation
Indices: 94479--94538 Score: 120
Period size: 26 Copynumber: 2.3 Consensus size: 26
94469 AACTACTATT
94479 AAAATTAATATATCATTAATTAAACA
1 AAAATTAATATATCATTAATTAAACA
94505 AAAATTAATATATCATTAATTAAACA
1 AAAATTAATATATCATTAATTAAACA
94531 AAAATTAA
1 AAAATTAA
94539 AATAAATAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (26 bp):
AAAATTAATATATCATTAATTAAACA
Found at i:96856 original size:60 final size:59
Alignment explanation
Indices: 96705--96869 Score: 190
Period size: 60 Copynumber: 2.7 Consensus size: 59
96695 GAATTTGGAG
** * * * *
96705 ATGAAATTGTAATATTTAAAAGTTT-GAGGACCAATTTAGAATGAAGGTTATAGGTTGAGG
1 ATGAAATTG-AATATTTAAAAGTTTAGA-GATTAATTTAGAATGAAGATCATAGATTGAGA
*
96765 ATGAAATTGGAATATTTAAAAGTTTAAAGATTAATTTAGAAT-AAGAATCATAGATTGAGA
1 ATGAAATT-GAATATTTAAAAGTTTAGAGATTAATTTAGAATGAAG-ATCATAGATTGAGA
* *
96825 ATGAAATTAGAATATTCAAAAGTTTAGAGATTAATTTAAAATGAA
1 ATGAAATT-GAATATTTAAAAGTTTAGAGATTAATTTAGAATGAA
96870 AAATATAATT
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
59 3 0.03
60 83 0.92
61 4 0.04
ACGTcount: A:0.45, C:0.02, G:0.19, T:0.33
Consensus pattern (59 bp):
ATGAAATTGAATATTTAAAAGTTTAGAGATTAATTTAGAATGAAGATCATAGATTGAGA
Found at i:104287 original size:14 final size:14
Alignment explanation
Indices: 104268--104298 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
104258 CATTTATTAT
104268 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
*
104282 GTTCGTTTGTGTTC
1 GTTCGTTTATGTTC
104296 GTT
1 GTT
104299 TACATTCGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.03, C:0.13, G:0.26, T:0.58
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:109253 original size:20 final size:21
Alignment explanation
Indices: 109216--109255 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
109206 CAAATTATAT
*
109216 TTTTAATTAAATATTTAAATC
1 TTTTAATTAAATACTTAAATC
*
109237 TTTT-ATTAGATACTTAAAT
1 TTTTAATTAAATACTTAAAT
109256 TATATCTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (21 bp):
TTTTAATTAAATACTTAAATC
Found at i:112605 original size:31 final size:30
Alignment explanation
Indices: 112554--112612 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
112544 AAATTTAATC
112554 TATTTTAATTAATTATATAAATATATATTAA
1 TATTTTAATTAA-TATATAAATATATATTAA
*
112585 TATTTTATATTAA-ATCATAAATTTATAT
1 TATTTTA-ATTAATAT-ATAAATATATAT
112613 ATATATAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 2 0.08
31 18 0.72
32 5 0.20
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (30 bp):
TATTTTAATTAATATATAAATATATATTAA
Found at i:117956 original size:21 final size:21
Alignment explanation
Indices: 117932--117974 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
117922 TGAGCCGAAG
117932 TAGACAACATGCAGCCCAAAA
1 TAGACAACATGCAGCCCAAAA
117953 TAGACAACATGCAGCCCAAAA
1 TAGACAACATGCAGCCCAAAA
117974 T
1 T
117975 TCATGTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.28, G:0.14, T:0.12
Consensus pattern (21 bp):
TAGACAACATGCAGCCCAAAA
Found at i:119364 original size:44 final size:44
Alignment explanation
Indices: 119301--119387 Score: 174
Period size: 44 Copynumber: 2.0 Consensus size: 44
119291 TGGTCGCAGT
119301 CAATGGCAGCACGAACTGTATTTTGAGGGGTCATGAACTGGTTC
1 CAATGGCAGCACGAACTGTATTTTGAGGGGTCATGAACTGGTTC
119345 CAATGGCAGCACGAACTGTATTTTGAGGGGTCATGAACTGGTT
1 CAATGGCAGCACGAACTGTATTTTGAGGGGTCATGAACTGGTT
119388 AATTAGGCTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (44 bp):
CAATGGCAGCACGAACTGTATTTTGAGGGGTCATGAACTGGTTC
Found at i:141999 original size:14 final size:16
Alignment explanation
Indices: 141977--142014 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
141967 GTAAATTATT
141977 AATATTATATCTTA-A
1 AATATTATATCTTAGA
*
141992 AA-ATTATATTTTAGA
1 AATATTATATCTTAGA
142007 AATATTAT
1 AATATTAT
142015 CGATAGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 10 0.50
15 5 0.25
16 5 0.25
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (16 bp):
AATATTATATCTTAGA
Found at i:145436 original size:23 final size:23
Alignment explanation
Indices: 145410--145476 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
145400 TTATTATATA
*
145410 GCACTACGGTGCTATTCTACGCG
1 GCACTACGGTGCAATTCTACGCG
* *
145433 GCACTCCGGTGCAATTCTACGTG
1 GCACTACGGTGCAATTCTACGCG
* *
145456 GCACTTCGGTGCAATTATACG
1 GCACTACGGTGCAATTCTACG
145477 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.19, C:0.28, G:0.25, T:0.27
Consensus pattern (23 bp):
GCACTACGGTGCAATTCTACGCG
Found at i:150951 original size:35 final size:34
Alignment explanation
Indices: 150906--151004 Score: 108
Period size: 35 Copynumber: 2.9 Consensus size: 34
150896 TTGAGAATGG
* * **
150906 ATTTTGAATTTGGGGTTGGGCATGTAATTGAAGT
1 ATTTTGAATTTGGGGTTGAGAATGTAATTGAAAC
* *
150940 ATTTTAGAATTTGAGGTTTAGAATGTAATTGAAAC
1 ATTTT-GAATTTGGGGTTGAGAATGTAATTGAAAC
* *
150975 ATTTTGGATTTTGGGGTTTAGAATGTAATT
1 ATTTT-GAATTTGGGGTTGAGAATGTAATT
151005 AATGACTGTG
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
34 5 0.09
35 50 0.91
ACGTcount: A:0.28, C:0.02, G:0.26, T:0.43
Consensus pattern (34 bp):
ATTTTGAATTTGGGGTTGAGAATGTAATTGAAAC
Found at i:154772 original size:17 final size:17
Alignment explanation
Indices: 154743--154798 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
154733 GATTGTACAA
154743 ATTTAA-AATATAAAATT
1 ATTTAATAA-ATAAAATT
*
154760 ATTTAATAAATAAATATC
1 ATTTAATAAATAAA-ATT
*
154778 ATATTAATAAA-AATATT
1 AT-TTAATAAATAAAATT
154795 ATTT
1 ATTT
154799 CAATTCATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 2 0.06
17 15 0.45
18 8 0.24
19 8 0.24
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTTAATAAATAAAATT
Found at i:155255 original size:15 final size:14
Alignment explanation
Indices: 155198--155264 Score: 53
Period size: 15 Copynumber: 4.4 Consensus size: 14
155188 ATTAAATTAC
155198 ATTTAAATTTTTAACTA
1 ATTTAAA-TTTT-A-TA
*
155215 ATTTATAATTATATA
1 ATTTA-AATTTTATA
* *
155230 TTTTATATTTTATA
1 ATTTAAATTTTATA
155244 ATTTAAATTTTTATA
1 ATTTAAA-TTTTATA
*
155259 AATTAA
1 ATTTAA
155265 TTTAATGATA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
14 12 0.29
15 18 0.44
16 1 0.02
17 8 0.20
18 2 0.05
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTAAATTTTATA
Found at i:176300 original size:21 final size:21
Alignment explanation
Indices: 176245--176312 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 21
176235 GAATCAATAA
176245 CCCCAT-GAGGGAACCGATTCC
1 CCCCATAG-GGGAACCGATTCC
**
176266 CCCTTTGAAGGGGAACCGATTCC
1 CCCCAT--AGGGGAACCGATTCC
* *
176289 CCCCATAGGGGAATCGATACC
1 CCCCATAGGGGAACCGATTCC
176310 CCC
1 CCC
176313 ATGGGGTTCT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 20 0.53
23 17 0.45
24 1 0.03
ACGTcount: A:0.24, C:0.37, G:0.24, T:0.16
Consensus pattern (21 bp):
CCCCATAGGGGAACCGATTCC
Found at i:178650 original size:13 final size:14
Alignment explanation
Indices: 178632--178661 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
178622 TAAGGGGGAG
178632 TAATTTCAAAA-CT
1 TAATTTCAAAATCT
178645 TAATTTCAAAATCT
1 TAATTTCAAAATCT
178659 TAA
1 TAA
178662 AATTACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (14 bp):
TAATTTCAAAATCT
Found at i:182835 original size:22 final size:22
Alignment explanation
Indices: 182807--182856 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
182797 TAAAACATTA
*
182807 AATTATAAAGTAATAAATGTAT
1 AATTATAAAGTAATAAACGTAT
*
182829 ACTTATAAAGTAATAAACGTAT
1 AATTATAAAGTAATAAACGTAT
182851 AATTAT
1 AATTAT
182857 TTAAATCTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.36
Consensus pattern (22 bp):
AATTATAAAGTAATAAACGTAT
Found at i:190813 original size:13 final size:13
Alignment explanation
Indices: 190781--190805 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
190771 CTCAAATGAA
190781 CTAATTTCTAATC
1 CTAATTTCTAATC
190794 CTAATTTCTAAT
1 CTAATTTCTAAT
190806 ATCTATTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (13 bp):
CTAATTTCTAATC
Found at i:195086 original size:25 final size:25
Alignment explanation
Indices: 195052--195100 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
195042 GGCTGGAACA
195052 TTTAGGGTTTGAAACCCTAATCTGT
1 TTTAGGGTTTGAAACCCTAATCTGT
195077 TTTAGGGTTTGAAACCCTAATCTG
1 TTTAGGGTTTGAAACCCTAATCTG
195101 ATGGGTTGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.39
Consensus pattern (25 bp):
TTTAGGGTTTGAAACCCTAATCTGT
Found at i:195253 original size:17 final size:16
Alignment explanation
Indices: 195216--195257 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
195206 TAATAAACAT
*
195216 AATAATAAAAAATAAT
1 AATAATAAAAAATAAC
195232 AATAATAATAAAATAAC
1 AATAATAA-AAAATAAC
*
195249 GATAA-AAAA
1 AATAATAAAA
195258 CCCGGACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 2 0.09
16 10 0.43
17 11 0.48
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (16 bp):
AATAATAAAAAATAAC
Found at i:195495 original size:40 final size:41
Alignment explanation
Indices: 195446--195646 Score: 174
Period size: 40 Copynumber: 4.8 Consensus size: 41
195436 CGTCTAAAAG
195446 TGACACGGCTCCTACGTGATGAGGAGATCTGG-TCTGGGGA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGGATCTGGGGA
* * * *
195486 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGG--ATCT---GGGGA
* * * * * ** *
195532 TAACATGGTTCCTACGTGACGAGGACG-GCTGGTTATCTATGGT
1 TGACACGGCTCCTACGTGATGAGGA-GATCTGG--ATCTGGGGA
195575 TGACACGGCTCCTACGTGATGAGGAGATCTGG-TCTGGGGA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGGATCTGGGGA
* * *
195615 TGACACGGCTCATACGTGATGAAGAGTTCTGG
1 TGACACGGCTCCTACGTGATGAGGAGATCTGG
195647 CCATCTAAAG
Statistics
Matches: 125, Mismatches: 28, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
40 63 0.50
42 1 0.01
43 29 0.23
46 31 0.25
47 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (41 bp):
TGACACGGCTCCTACGTGATGAGGAGATCTGGATCTGGGGA
Found at i:195645 original size:129 final size:129
Alignment explanation
Indices: 195446--195698 Score: 488
Period size: 129 Copynumber: 2.0 Consensus size: 129
195436 CGTCTAAAAG
195446 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGA
*
195511 GTTCTGGCCATCTAAAGGTGATAACATGGTTCCTACGTGACGAGGACGGCTGGTTATCTATGGT
66 GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGACGAGGACGGCTGGTTATCTATGGT
195575 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGA
*
195640 GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGACGAGGATGGCTGGTTATCT
66 GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGACGAGGACGGCTGGTTATCT
195699 CTAGGATAAT
Statistics
Matches: 122, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 122 1.00
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (129 bp):
TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGA
GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGACGAGGACGGCTGGTTATCTATGGT
Found at i:196081 original size:35 final size:36
Alignment explanation
Indices: 196034--196116 Score: 100
Period size: 35 Copynumber: 2.3 Consensus size: 36
196024 ACAAAATTCA
**
196034 TTTCAAGAGAAAC-GATCTCAAAGAT-GTTTATTTTG
1 TTTCAAGAGAAACAGAT-TCAAAGATGGTAAATTTTG
*
196069 TTTCAAGGGAAACAGATTCAAAGATGGTAAATTTTG
1 TTTCAAGAGAAACAGATTCAAAGATGGTAAATTTTG
196105 TTTCCAA-AGAAA
1 TTT-CAAGAGAAA
196117 TAAACTCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
35 20 0.49
36 18 0.44
37 3 0.07
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.33
Consensus pattern (36 bp):
TTTCAAGAGAAACAGATTCAAAGATGGTAAATTTTG
Found at i:196516 original size:40 final size:40
Alignment explanation
Indices: 196472--196551 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
196462 GTTTTAATAG
*
196472 AAACGATATCAAATGTGGGTATTTTCAAAAGAAGTTGTCT
1 AAACGATATCAAAGGTGGGTATTTTCAAAAGAAGTTGTCT
*
196512 AAACGATCTCAAAGGTGGGTATTTTCAAAAGAAGTTGTCT
1 AAACGATATCAAAGGTGGGTATTTTCAAAAGAAGTTGTCT
196552 CGAGAGACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.31
Consensus pattern (40 bp):
AAACGATATCAAAGGTGGGTATTTTCAAAAGAAGTTGTCT
Found at i:196666 original size:30 final size:30
Alignment explanation
Indices: 196632--197096 Score: 176
Period size: 30 Copynumber: 15.1 Consensus size: 30
196622 AGAGACAAAA
196632 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
* ** * * *
196662 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTCCAAAGAAACAAAC-TCA-A-AG----AT
196699 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
* * * * *
196729 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGACAAAA
1 TTTTGTTTCCAAAGAAACAAAC-TCA-A-AG----AT
196766 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
* ** * * *
196796 TTTTGTTTCAAAAGAAATTATCTTAAAAGAGACAAAA
1 TTTTGTTTCCAAAGAAACAAAC-T-CAA-AG----AT
196833 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
* *
196863 TTTTGTTTCAAAAGAAACAATCTCAAAGAT
1 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
** * * * * **
196893 TTTT-TCACAAAATTGTCTCAAGAGAGACAAA-A-
1 TTTTGTTTCCAAA--G---AAACAAACTCAAAGAT
* * *
196925 CTTTGTTT-CAAAGTAAATAGACTCAAAGA-
1 TTTTGTTTCCAAAG-AAACAAACTCAAAGAT
*
196954 -TTT-TTT-CAAACGAAAC-AACTCACAGAT
1 TTTTGTTTCCAAA-GAAACAAACTCAAAGAT
* * *
196981 TTTT-ATTCCAAAGGAACAAACTCCAAGAT
1 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
* * *
197010 TTTT-ATTCAAAAGGAACAAACTCAAAGA-
1 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
*
197038 -TTT-TTT-CAAGAGGAACAAACTCAAAGA-
1 TTTTGTTTCCAA-AGAAACAAACTCAAAGAT
*
197065 -TTT-TTT-CAAGAGGAACAAACTCAAAGAT
1 TTTTGTTTCCAA-AGAAACAAACTCAAAGAT
197093 TTTT
1 TTTT
197097 TCCTCAAAAG
Statistics
Matches: 336, Mismatches: 63, Indels: 73
0.71 0.13 0.15
Matches are distributed among these distances:
26 10 0.03
27 59 0.18
28 23 0.07
29 49 0.15
30 91 0.27
31 6 0.02
32 10 0.03
33 8 0.02
34 13 0.04
35 4 0.01
36 5 0.01
37 58 0.17
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.30
Consensus pattern (30 bp):
TTTTGTTTCCAAAGAAACAAACTCAAAGAT
Found at i:196702 original size:67 final size:67
Alignment explanation
Indices: 196553--196879 Score: 577
Period size: 67 Copynumber: 4.9 Consensus size: 67
196543 AAGTTGTCTC
* *
196553 GAGAGACAAAATTTTGTTT-CAAAGGAAACAAACTCAGAGATTTTT-TTCTCAAAAGAAATTGTC
1 GAGAGACAAAATTTTGTTTCCAAA-GAAACAAACTCAAAGATTTTTGTT-TCAAAAGAAATTATC
196616 TTTAA
64 -TTAA
196621 GAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTT
1 GAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTT
196686 AA
66 AA
*
196688 GAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTT
1 GAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTT
196753 AA
66 AA
196755 GAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTT
1 GAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTT
196820 AA
66 AA
*
196822 AAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAA
1 GAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAA
196880 CAATCTCAAA
Statistics
Matches: 252, Mismatches: 5, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
67 193 0.77
68 53 0.21
69 6 0.02
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.31
Consensus pattern (67 bp):
GAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTT
AA
Found at i:196713 original size:37 final size:36
Alignment explanation
Indices: 196662--196850 Score: 150
Period size: 37 Copynumber: 5.5 Consensus size: 36
196652 ACTCAAAGAT
*
196662 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAACTATCTTAA-AGAGACAAAA
* * * * *
196699 TTTTGTTTCCAAAGAAACAAAC-TCAA-AG----AT
1 TTTTGTTTCAAAAGAAACTATCTTAAAGAGACAAAA
196729 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAACTATCTTAA-AGAGACAAAA
* * * * *
196766 TTTTGTTTCCAAAGAAACAAAC-TCAA-AG----AT
1 TTTTGTTTCAAAAGAAACTATCTTAAAGAGACAAAA
*
196796 TTTTGTTTCAAAAGAAATTATCTTAAAAGAGACAAAA
1 TTTTGTTTCAAAAGAAACTATCTT-AAAGAGACAAAA
*
196833 TTTTGTTTCCAAAGAAAC
1 TTTTGTTTCAAAAGAAAC
196851 AAACTCAAAG
Statistics
Matches: 114, Mismatches: 24, Indels: 28
0.69 0.14 0.17
Matches are distributed among these distances:
30 39 0.34
31 3 0.03
32 3 0.03
33 4 0.04
34 4 0.04
35 2 0.02
36 4 0.04
37 55 0.48
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (36 bp):
TTTTGTTTCAAAAGAAACTATCTTAAAGAGACAAAA
Found at i:196953 original size:92 final size:92
Alignment explanation
Indices: 196761--196984 Score: 253
Period size: 92 Copynumber: 2.4 Consensus size: 92
196751 TTAAGAGAGA
* *
196761 CAAA-ATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAAAG
1 CAAAGATTTTGTTTCAAAAGAAAC-AACTCAAAGA--TTT-TTTCAAAAGAAATTATCTCAAAAG
*
196825 AGACAAAATTTTGTTTCCAAAGAAACAAACT
62 AGACAAAACTTTGTTTCCAAAGAAACAAACT
* * *
196856 CAAAGATTTTTGTTTCAAAAGAAACAATCTCAAAGATTTTTTC-ACA-AAATTGTCTCAAGAGAG
1 CAAAGA-TTTTGTTTCAAAAGAAACAA-CTCAAAGATTTTTTCAAAAGAAATTATCTCAAAAGAG
* *
196919 ACAAAACTTTGTTT-CAAAGTAAATAGACT
64 ACAAAACTTTGTTTCCAAAG-AAACAAACT
* *
196948 CAAAGA-TTT-TTTCAAACGAAACAACTCACAGATTTTT
1 CAAAGATTTTGTTTCAAAAGAAACAACTCAAAGATTTTT
196985 ATTCCAAAGG
Statistics
Matches: 115, Mismatches: 10, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
88 12 0.10
89 14 0.12
90 3 0.03
91 5 0.04
92 40 0.35
93 2 0.02
94 4 0.03
95 7 0.06
96 3 0.03
97 25 0.22
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (92 bp):
CAAAGATTTTGTTTCAAAAGAAACAACTCAAAGATTTTTTCAAAAGAAATTATCTCAAAAGAGAC
AAAACTTTGTTTCCAAAGAAACAAACT
Found at i:196960 original size:27 final size:26
Alignment explanation
Indices: 196945--197098 Score: 193
Period size: 27 Copynumber: 5.6 Consensus size: 26
196935 AAGTAAATAG
*
196945 ACTCAAAGATTTTTTCAAACGAA-ACA
1 ACTCAAAGATTTTTTCAAAGGAACA-A
*
196971 ACTCACAGATTTTTATTCCAAAGGAACAA
1 ACTCAAAGA-TTTT-TT-CAAAGGAACAA
*
197000 ACTCCAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGA-TTTT-TTC-AAAGGAACAA
197029 ACTCAAAGATTTTTTCAAGAGGAACAA
1 ACTCAAAGATTTTTTCAA-AGGAACAA
197056 ACTCAAAGATTTTTTCAAGAGGAACAA
1 ACTCAAAGATTTTTTCAA-AGGAACAA
197083 ACTCAAAGATTTTTTC
1 ACTCAAAGATTTTTTC
197099 CTCAAAAGAA
Statistics
Matches: 117, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
26 10 0.09
27 58 0.50
28 7 0.06
29 41 0.35
30 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.29
Consensus pattern (26 bp):
ACTCAAAGATTTTTTCAAAGGAACAA
Found at i:197435 original size:36 final size:34
Alignment explanation
Indices: 197351--197443 Score: 105
Period size: 36 Copynumber: 2.7 Consensus size: 34
197341 GAGAAAATGA
*
197351 TGTCTCAAGCGAGACAAAATTTGCTTTAAGATAC
1 TGTCTCAAGCGAGACAAAATTTGCTTTAAGAAAC
* ** * *
197385 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTG-CTTTA-AGAAAC
*
197421 TGTCTCAAGCGAGACAAAGTTTG
1 TGTCTCAAGCGAGACAAAATTTG
197444 AGAAAACGAT
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
34 20 0.43
35 4 0.09
36 23 0.49
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (34 bp):
TGTCTCAAGCGAGACAAAATTTGCTTTAAGAAAC
Found at i:197710 original size:21 final size:21
Alignment explanation
Indices: 197649--197710 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 21
197639 TTGTGGAAAA
*
197649 TGTCTCAAGCGAGACATAATT
1 TGTCTCAAGCGAGACAAAATT
* * * *
197670 TGTTTTAA---AGA-GAAAGT
1 TGTCTCAAGCGAGACAAAATT
197687 TGTCTCAAGCGAGACAAAATT
1 TGTCTCAAGCGAGACAAAATT
197708 TGT
1 TGT
197711 TTTTAAGAAA
Statistics
Matches: 28, Mismatches: 9, Indels: 8
0.62 0.20 0.18
Matches are distributed among these distances:
17 9 0.32
18 3 0.11
20 3 0.11
21 13 0.46
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (21 bp):
TGTCTCAAGCGAGACAAAATT
Found at i:197727 original size:36 final size:35
Alignment explanation
Indices: 197644--197751 Score: 117
Period size: 38 Copynumber: 2.9 Consensus size: 35
197634 AAAGTTTGTG
* *
197644 GAAAATGTCTCAAGCGAGACATAATTTGTTTTAAA
1 GAAAATGTCTCAAGCGAGACAAAATTTGTTTTTAA
197679 GAGAAAGTTGTCTCAAGCGAGACAAAATTTGTTTTTAA
1 GA-AAA--TGTCTCAAGCGAGACAAAATTTGTTTTTAA
* * * *
197717 GAAAACTGTCTCTAGTGAGACGACACTTTGTTTTT
1 GAAAA-TGTCTCAAGCGAGAC-AAAATTTGTTTTT
197752 TTAATAAGAT
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
35 2 0.03
36 16 0.26
37 14 0.23
38 30 0.48
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.33
Consensus pattern (35 bp):
GAAAATGTCTCAAGCGAGACAAAATTTGTTTTTAA
Found at i:199301 original size:11 final size:11
Alignment explanation
Indices: 199287--199344 Score: 82
Period size: 11 Copynumber: 5.2 Consensus size: 11
199277 CCTCTTTTTG
*
199287 TTCTTTGCTTT
1 TTCTTTGATTT
199298 TTCTTTGATTT
1 TTCTTTGATTT
199309 TTGCTTTGATTT
1 TT-CTTTGATTT
199321 TTCTTTG-TTT
1 TTCTTTGATTT
199331 TTGCTTTGATTT
1 TT-CTTTGATTT
199343 TT
1 TT
199345 TTCTCTCTGC
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
10 5 0.12
11 22 0.51
12 16 0.37
ACGTcount: A:0.05, C:0.10, G:0.12, T:0.72
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:199331 original size:22 final size:23
Alignment explanation
Indices: 199280--199404 Score: 98
Period size: 23 Copynumber: 5.3 Consensus size: 23
199270 TCTTTGTCCT
*
199280 CTTTTTGTTCTTTGCTTTTTCTTTG
1 CTTTTTG--CTTTGATTTTTCTTTG
*
199305 ATTTTTGCTTTGATTTTTCTTTG
1 CTTTTTGCTTTGATTTTTCTTTG
199328 -TTTTTGCTTTGATTTTTTTCTCTCTG
1 CTTTTTGCTTTGA--TTTTTCT-T-TG
*
199354 CTCTTTG-TTT--TTTTTCTTTG
1 CTTTTTGCTTTGATTTTTCTTTG
* *
199374 CTCTTTTCTCTTTTATTTTTCTTTG
1 CT-TTTT-GCTTTGATTTTTCTTTG
199399 -TTTTTG
1 CTTTTTG
199405 ATTGGATCTT
Statistics
Matches: 84, Mismatches: 6, Indels: 23
0.74 0.05 0.20
Matches are distributed among these distances:
20 4 0.05
21 4 0.05
22 19 0.23
23 22 0.26
24 8 0.10
25 17 0.20
26 5 0.06
27 5 0.06
ACGTcount: A:0.03, C:0.14, G:0.10, T:0.72
Consensus pattern (23 bp):
CTTTTTGCTTTGATTTTTCTTTG
Found at i:199364 original size:20 final size:20
Alignment explanation
Indices: 199341--199379 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
199331 TTGCTTTGAT
199341 TTTTTTCTCTCTGCTCTTTG
1 TTTTTTCTCTCTGCTCTTTG
* *
199361 TTTTTTTTCTTTGCTCTTT
1 TTTTTTCTCTCTGCTCTTT
199380 TCTCTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.00, C:0.21, G:0.08, T:0.72
Consensus pattern (20 bp):
TTTTTTCTCTCTGCTCTTTG
Found at i:199387 original size:20 final size:22
Alignment explanation
Indices: 199334--199387 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 22
199324 TTTGTTTTTG
199334 CTTTGATT-TTTTTCTCTCTGCT
1 CTTTG-TTCTTTTTCTCTCTGCT
*
199356 CTTTGTT-TTTTT-TCTTTGCT
1 CTTTGTTCTTTTTCTCTCTGCT
199376 CTTT-TCTCTTTT
1 CTTTGT-TCTTTT
199388 ATTTTTCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 1 0.03
20 12 0.41
21 11 0.38
22 5 0.17
ACGTcount: A:0.02, C:0.20, G:0.07, T:0.70
Consensus pattern (22 bp):
CTTTGTTCTTTTTCTCTCTGCT
Found at i:202524 original size:31 final size:32
Alignment explanation
Indices: 202468--202529 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
202458 TGACAAAATG
202468 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
202500 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
202530 CATGCAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:206182 original size:25 final size:25
Alignment explanation
Indices: 206148--206196 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
206138 GGCTGGAACA
206148 TTTAGGGTTTGAAACCCTAATCTGT
1 TTTAGGGTTTGAAACCCTAATCTGT
206173 TTTAGGGTTTGAAACCCTAATCTG
1 TTTAGGGTTTGAAACCCTAATCTG
206197 ATGGGTTGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.39
Consensus pattern (25 bp):
TTTAGGGTTTGAAACCCTAATCTGT
Found at i:206318 original size:3 final size:3
Alignment explanation
Indices: 206310--206349 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
206300 ATTAATAAAC
206310 ATA ATA ATA A-A A-A ATA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
206350 CGATAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 6 0.17
3 29 0.83
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:206501 original size:22 final size:23
Alignment explanation
Indices: 206457--206513 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
206447 ATTAAATTAC
*
206457 ATTTAGATTTTTAACTAATTTATA
1 ATTTA-ATGTTTAACTAATTTATA
*
206481 A-TTATATGTTTAA-TATTTTATA
1 ATTTA-ATGTTTAACTAATTTATA
206503 ATTTAATGTTT
1 ATTTAATGTTT
206514 TATAAATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 15 0.52
23 13 0.45
24 1 0.03
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (23 bp):
ATTTAATGTTTAACTAATTTATA
Found at i:206509 original size:15 final size:15
Alignment explanation
Indices: 206489--206524 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
206479 TAATTATATG
206489 TTTAATATTTTATAA
1 TTTAATATTTTATAA
*
206504 TTTAATGTTTTATAA
1 TTTAATATTTTATAA
*
206519 ATTAAT
1 TTTAAT
206525 TTAATGGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
TTTAATATTTTATAA
Found at i:206679 original size:20 final size:21
Alignment explanation
Indices: 206646--206685 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
206636 ACCCTTAAAA
* *
206646 TTTTATAAATATATATATTTT
1 TTTTATAAAAATATAAATTTT
206667 TTTTA-AAAAATATAAATTT
1 TTTTATAAAAATATAAATTT
206686 ATTCTCCAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTATAAAAATATAAATTTT
Found at i:207483 original size:37 final size:33
Alignment explanation
Indices: 207436--207512 Score: 100
Period size: 33 Copynumber: 2.2 Consensus size: 33
207426 TCTTCATAAT
*
207436 ATTTTCGGTTGCAATCAAATATGTTAAAAAAATTAAC
1 ATTTTAGGTTGCAA--AAATAT-TT-AAAAAATTAAC
*
207473 ATTTTAGGTTGTAAAAATATTTAAAAAATTAAC
1 ATTTTAGGTTGCAAAAATATTTAAAAAATTAAC
207506 ATTTTAG
1 ATTTTAG
207513 ATTACGCTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
33 18 0.47
34 2 0.05
35 6 0.16
37 12 0.32
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.39
Consensus pattern (33 bp):
ATTTTAGGTTGCAAAAATATTTAAAAAATTAAC
Found at i:210455 original size:19 final size:21
Alignment explanation
Indices: 210410--210463 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
210400 TATAATATTT
* *
210410 ATATTTATATGTTATTTTTAA
1 ATATATATATATTATTTTTAA
210431 ATATATATATATTATTTTTAA
1 ATATATATATATTATTTTTAA
210452 ATATATATATAT
1 ATATATATATAT
210464 AATATAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
ATATATATATATTATTTTTAA
Found at i:210474 original size:21 final size:21
Alignment explanation
Indices: 210429--210474 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
210419 TGTTATTTTT
* * **
210429 AAATATATATATATTATTTTT
1 AAATATATATATATAATATAA
210450 AAATATATATATATAATATAA
1 AAATATATATATATAATATAA
210471 AAAT
1 AAAT
210475 TTCATGTACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATATATATATATAATATAA
Found at i:220898 original size:24 final size:24
Alignment explanation
Indices: 220856--220916 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
220846 TTTTTCAATT
*
220856 AAATAAT-TGTTTTTATTGAATAA
1 AAATAATATTTTTTTATTGAATAA
*
220879 AAATAATATTTTTTTTTTGAATAA
1 AAATAATATTTTTTTATTGAATAA
220903 AAATAATATTTTTT
1 AAATAATATTTTTT
220917 ATTATTTCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
23 7 0.20
24 28 0.80
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (24 bp):
AAATAATATTTTTTTATTGAATAA
Found at i:229913 original size:21 final size:21
Alignment explanation
Indices: 229889--229954 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
229879 AATATAAATA
229889 TATTAAACTTATATCATCGTT
1 TATTAAACTTATATCATCGTT
* *
229910 TATTTAA-TTA-AGT-AT-GAATA
1 TATTAAACTTATA-TCATCG--TT
229930 TATTAAACTTATATCATCGTT
1 TATTAAACTTATATCATCGTT
229951 TATT
1 TATT
229955 TAATTAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
18 1 0.03
19 3 0.09
20 11 0.32
21 15 0.44
22 3 0.09
23 1 0.03
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (21 bp):
TATTAAACTTATATCATCGTT
Found at i:229916 original size:22 final size:22
Alignment explanation
Indices: 229891--229957 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
229881 TATAAATATA
229891 TTAAACTTATATCATCGTTTAT
1 TTAAACTTATATCATCGTTTAT
**
229913 TT-AA-TTA-AGT-AT-GAATAT
1 TTAAACTTATA-TCATCGTTTAT
229931 ATTAAACTTATATCATCGTTTAT
1 -TTAAACTTATATCATCGTTTAT
229954 TTAA
1 TTAA
229958 TTAATTATGG
Statistics
Matches: 34, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
18 4 0.12
19 5 0.15
20 6 0.18
21 6 0.18
22 9 0.26
23 4 0.12
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.48
Consensus pattern (22 bp):
TTAAACTTATATCATCGTTTAT
Found at i:229942 original size:41 final size:41
Alignment explanation
Indices: 229885--229971 Score: 156
Period size: 41 Copynumber: 2.1 Consensus size: 41
229875 ATAAAATATA
229885 AATATATTAAACTTATATCATCGTTTATTTAATTAAGTATG
1 AATATATTAAACTTATATCATCGTTTATTTAATTAAGTATG
*
229926 AATATATTAAACTTATATCATCGTTTATTTAATTAATTATG
1 AATATATTAAACTTATATCATCGTTTATTTAATTAAGTATG
*
229967 GATAT
1 AATAT
229972 TATATGAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (41 bp):
AATATATTAAACTTATATCATCGTTTATTTAATTAAGTATG
Found at i:230887 original size:16 final size:16
Alignment explanation
Indices: 230855--230908 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
230845 TGTTGAGTGA
* *
230855 TTGAAAATGAAACAAT
1 TTGAAAATTAAATAAT
230871 TTGAAAATTAAATAA-
1 TTGAAAATTAAATAAT
* *
230886 TTAAAAATTAAATTAT
1 TTGAAAATTAAATAAT
*
230902 TTCAAAA
1 TTGAAAA
230909 AGATTTAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
15 13 0.41
16 19 0.59
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (16 bp):
TTGAAAATTAAATAAT
Found at i:235356 original size:29 final size:29
Alignment explanation
Indices: 235301--235378 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
235291 TTAGTATTCG
235301 GGTCGGATTTTTTTTTAAAAAAATTCGGGATCA
1 GGTCGGA--TTTTTTT--AAAAATTCGGGATCA
* * *
235334 GGTCGGATTTTTTTAAAATTTCGGGTTCG
1 GGTCGGATTTTTTTAAAAATTCGGGATCA
*
235363 GGTCGGGTTTTTTTAA
1 GGTCGGATTTTTTTAA
235379 GTTTGATATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 27 0.66
31 7 0.17
33 7 0.17
ACGTcount: A:0.22, C:0.09, G:0.26, T:0.44
Consensus pattern (29 bp):
GGTCGGATTTTTTTAAAAATTCGGGATCA
Found at i:237291 original size:22 final size:23
Alignment explanation
Indices: 237259--237305 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
237249 AAAATTTATT
237259 TATTAATATTTATAATAATATAA
1 TATTAATATTTATAATAATATAA
* *
237282 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTATAATAATATAA
237304 TA
1 TA
237306 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTATAATAATATAA
Found at i:237304 original size:30 final size:33
Alignment explanation
Indices: 237251--237332 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 33
237241 AAATATTTAA
*
237251 AATT-TATTTATTAATATTTATAATAATATAAT
1 AATTATATTTATTAATATTTATAATAAAATAAT
237283 -ATTATATTT-TTAATA-TTATAATAAAATAAT
1 AATTATATTTATTAATATTTATAATAAAATAAT
*
237313 CAATTATATTATAATAATAT
1 -AATTATATT-TATTAATAT
237333 AAGATATTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
30 14 0.33
31 9 0.21
32 13 0.31
33 1 0.02
34 5 0.12
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (33 bp):
AATTATATTTATTAATATTTATAATAAAATAAT
Found at i:241423 original size:40 final size:40
Alignment explanation
Indices: 241352--241436 Score: 145
Period size: 40 Copynumber: 2.1 Consensus size: 40
241342 TGTTATTATC
241352 TATGTTGTGCTGTTTTTGCCAATAGCAACATGCCACGTATT
1 TATGTTGTGCTGTTTTTGCCAATAGCAACATGCCACGTA-T
*
241393 TATGTTGTGCTG-TTTTGCCAATAGCGACATGCCACGTAT
1 TATGTTGTGCTGTTTTTGCCAATAGCAACATGCCACGTAT
241432 TATGT
1 TATGT
241437 AAATTTTCTG
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
39 6 0.14
40 25 0.58
41 12 0.28
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (40 bp):
TATGTTGTGCTGTTTTTGCCAATAGCAACATGCCACGTAT
Found at i:262164 original size:18 final size:18
Alignment explanation
Indices: 262123--262157 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
262113 ACAAAGGTCC
*
262123 TCTCTCCCTCCCTCTCTG
1 TCTCTCCCTCCCTCGCTG
*
262141 TCTCTCTCTCCCTCGCT
1 TCTCTCCCTCCCTCGCT
262158 CGCTCTCACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.00, C:0.54, G:0.06, T:0.40
Consensus pattern (18 bp):
TCTCTCCCTCCCTCGCTG
Found at i:266330 original size:61 final size:61
Alignment explanation
Indices: 266235--266358 Score: 212
Period size: 61 Copynumber: 2.0 Consensus size: 61
266225 CTTGTTTTTC
266235 TGATACGAGTAGTAATCAACAAACAATGCACCGTGATTGTGCTTATAATAATGAAATATGT
1 TGATACGAGTAGTAATCAACAAACAATGCACCGTGATTGTGCTTATAATAATGAAATATGT
* * * *
266296 TGATACGAGTAGTAATTAACAAACAATGCACCGTGATTTTGCTTATATTTATGAAATATGT
1 TGATACGAGTAGTAATCAACAAACAATGCACCGTGATTGTGCTTATAATAATGAAATATGT
266357 TG
1 TG
266359 GTACTTTGTT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (61 bp):
TGATACGAGTAGTAATCAACAAACAATGCACCGTGATTGTGCTTATAATAATGAAATATGT
Found at i:270236 original size:42 final size:42
Alignment explanation
Indices: 270186--270333 Score: 142
Period size: 43 Copynumber: 3.5 Consensus size: 42
270176 ATTAAGGGTT
*
270186 TCAATTATAAAAGTAAAAAATGAGATTGAAAAAATTAGGGCC
1 TCAATTATAAAAGTAAAAAATGAGATTGAAAAAATTAGGACC
* * * * *
270228 TCAATTATAAATGTAAAAAGTGATATTGAAAAAAATTTGGACT
1 TCAATTATAAAAGTAAAAAATGAGATTG-AAAAAATTAGGACC
*
270271 TCTATTAT-AAAGATAAAAAAATGAGATT-ACAAAAATTAGAGATCC
1 TCAATTATAAAAG-T-AAAAAATGAGATTGA-AAAAATTAG-GA-CC
270316 -CAATTATAAAGAG-AAAAA
1 TCAATTATAAA-AGTAAAAA
270334 TAAAATTTTA
Statistics
Matches: 85, Mismatches: 13, Indels: 15
0.75 0.12 0.13
Matches are distributed among these distances:
42 29 0.34
43 32 0.38
44 19 0.22
45 3 0.04
46 2 0.02
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (42 bp):
TCAATTATAAAAGTAAAAAATGAGATTGAAAAAATTAGGACC
Found at i:270278 original size:43 final size:41
Alignment explanation
Indices: 270186--270334 Score: 142
Period size: 42 Copynumber: 3.5 Consensus size: 41
270176 ATTAAGGGTT
*
270186 TCAATTATAAAAGTAAAAAATGAGATTGAAAAAATTAGGGCC
1 TCAATTAT-AAAGTAAAAAATGAGATTGAAAAAATTAGGACC
* * * *
270228 TCAATTATAAATGTAAAAAGTGATATTGAAAAAAATTTGGACT
1 TCAATTATAAA-GTAAAAAATGAGATTG-AAAAAATTAGGACC
*
270271 TCTATTATAAAGATAAAAAAATGAGATT-ACAAAAATTAGAGATCC
1 TCAATTATAAAG-T-AAAAAATGAGATTGA-AAAAATTAG-GA-CC
270316 -CAATTATAAAG-AGAAAAAT
1 TCAATTATAAAGTA-AAAAAT
270335 AAAATTTTAA
Statistics
Matches: 88, Mismatches: 11, Indels: 16
0.77 0.10 0.14
Matches are distributed among these distances:
41 4 0.05
42 30 0.34
43 30 0.34
44 23 0.26
45 1 0.01
ACGTcount: A:0.53, C:0.07, G:0.13, T:0.27
Consensus pattern (41 bp):
TCAATTATAAAGTAAAAAATGAGATTGAAAAAATTAGGACC
Found at i:270626 original size:20 final size:20
Alignment explanation
Indices: 270579--270641 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
270569 CTAATTTTAC
*
270579 ATTCATTTAAATTTT-ATAAT
1 ATTCTTTTAAATTTTAAT-AT
* *
270599 TTTTTTTTAAATTTTAATAT
1 ATTCTTTTAAATTTTAATAT
*
270619 ATTCTTTTGATAAATTTAATAT
1 ATTCTTTT-A-AATTTTAATAT
270641 A
1 A
270642 AATTCTTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 20 0.59
21 3 0.09
22 11 0.32
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.59
Consensus pattern (20 bp):
ATTCTTTTAAATTTTAATAT
Found at i:272152 original size:32 final size:32
Alignment explanation
Indices: 272108--272169 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
272098 ATATTTTAAT
* *
272108 AAATTTAAATATCGTTTTCTAATAATTTGATA
1 AAATTTAAATATCATTTTATAATAATTTGATA
*
272140 AAATTTAGATATCATTTTATAATAATTTGA
1 AAATTTAAATATCATTTTATAATAATTTGA
272170 AAGAGTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (32 bp):
AAATTTAAATATCATTTTATAATAATTTGATA
Found at i:272478 original size:198 final size:195
Alignment explanation
Indices: 272143--272539 Score: 742
Period size: 198 Copynumber: 2.0 Consensus size: 195
272133 TTTGATAAAA
272143 TTTAGATATCATTTTATAATAATTTGAAAGAGTTAAATTTTTATATAATTTTTAAAACTTTAATA
1 TTTAGATATCATTTTATAATAATTTGAAAGAGTTAAATTTTTATATAATTTTTAAAACTTTAATA
272208 ATTAAAAATATCATTTTTAACATGATTTAATGATTATTTATACATTTTATCTTTACATTTATGCG
66 ATTAAAAATATCATTTTTAACATGATTTAATGATTATTTATACATTTTATCTTTACATTTATGCG
272273 CGGATCT-AGTTGCTTGAAGAGTTAAATTCGCTTTTTTCCGTTTTAGGTAATAAATATATGCAGG
131 CGGATCTAAGTTGCTTGAAGAGTTAAATTCGC-TTTTTCCGTTTTAGGTAATAAATATATGCAGG
272337 T
195 T
272338 TTTAGATATCATTTTATAATAATTTGAAAGAGTTAAATATTTTTTATATAATTTTTAAAACTTTA
1 TTTAGATATCATTTTATAATAATTTGAAAGAGTT-AA-A-TTTTTATATAATTTTTAAAACTTTA
272403 ATAATTAAAAATATCATTTTTAACATGATTTAATGATTATTTATACATTTTATCTTTACATTTAT
63 ATAATTAAAAATATCATTTTTAACATGATTTAATGATTATTTATACATTTTATCTTTACATTTAT
*
272468 GCGCGGATCTAAGTTGCTTGAAGAGTTAAATTCGCTTTTTCCGTTTTAGGTAATAAGTATATGCA
128 GCGCGGATCTAAGTTGCTTGAAGAGTTAAATTCGCTTTTTCCGTTTTAGGTAATAAATATATGCA
272533 GGT
193 GGT
272536 TTTA
1 TTTA
272540 CTGGAACAAA
Statistics
Matches: 197, Mismatches: 1, Indels: 5
0.97 0.00 0.02
Matches are distributed among these distances:
195 34 0.17
196 2 0.01
197 1 0.01
198 136 0.69
199 24 0.12
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.46
Consensus pattern (195 bp):
TTTAGATATCATTTTATAATAATTTGAAAGAGTTAAATTTTTATATAATTTTTAAAACTTTAATA
ATTAAAAATATCATTTTTAACATGATTTAATGATTATTTATACATTTTATCTTTACATTTATGCG
CGGATCTAAGTTGCTTGAAGAGTTAAATTCGCTTTTTCCGTTTTAGGTAATAAATATATGCAGGT
Found at i:275705 original size:2 final size:2
Alignment explanation
Indices: 275698--275724 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
275688 TTCAGACGTG
275698 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 T
275725 TGAATAATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:278339 original size:20 final size:20
Alignment explanation
Indices: 278292--278619 Score: 312
Period size: 20 Copynumber: 16.2 Consensus size: 20
278282 AATGACCAAC
**
278292 AAAATCGCAACGCGA-TATC
1 AAAATCGCAACGCGATTAAG
* *
278311 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* * *
278331 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
* ***
278351 AAGATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
* * *
278372 AAGAATCGCAATGCGATTCAT
1 AA-AATCGCAACGCGATTAAG
* ***
278393 AAAATCGTAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
278414 AAGAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
278435 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
278455 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
278475 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
278495 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
278517 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
*
278535 AAAATCGCAACACGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
278557 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
278575 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
* *
278597 --AATCGCAATGCGATTCAG
1 AAAATCGCAACGCGATTAAG
278615 AAAAT
1 AAAAT
278620 GAGTAAATTC
Statistics
Matches: 257, Mismatches: 33, Indels: 37
0.79 0.10 0.11
Matches are distributed among these distances:
18 8 0.03
19 16 0.06
20 186 0.72
21 13 0.05
22 34 0.13
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:278726 original size:6 final size:6
Alignment explanation
Indices: 278715--278756 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
278705 GACACGTATT
278715 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
278757 CGAGACGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 15 0.42
6 21 0.58
ACGTcount: A:0.29, C:0.55, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:278747 original size:5 final size:5
Alignment explanation
Indices: 278719--278759 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
278709 CGTATTACCA
278719 CGACC ACGACC ACGACC ACGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC -CGACC -CGACC CGACC CGACC CGACC CGA
278760 GACGAGACGG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.51
6 17 0.49
ACGTcount: A:0.27, C:0.54, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:282369 original size:28 final size:28
Alignment explanation
Indices: 282338--282396 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
282328 TTGATCCTTG
282338 AATTACATTATATATTTTCTTCAAATGA
1 AATTACATTATATATTTTCTTCAAATGA
282366 AATTACATTATATATTTTCTTCAAATGA
1 AATTACATTATATATTTTCTTCAAATGA
282394 AAT
1 AAT
282397 ATCACATTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (28 bp):
AATTACATTATATATTTTCTTCAAATGA
Found at i:284453 original size:21 final size:20
Alignment explanation
Indices: 284428--284467 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
284418 AACCTAAGTT
*
284428 TCAAACTTCAAACAATACAAG
1 TCAAACTT-AAACAAAACAAG
*
284449 TCAAAGTTAAACAAAACAA
1 TCAAACTTAAACAAAACAA
284468 AGAATTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.57, C:0.20, G:0.05, T:0.17
Consensus pattern (20 bp):
TCAAACTTAAACAAAACAAG
Found at i:284601 original size:42 final size:42
Alignment explanation
Indices: 284542--284627 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
284532 TAAATTACTC
*
284542 TACGAAATGTCTTTTCTTTTTGTTTATTATAAGGCAAATATT
1 TACGAAATGTCTTTTCTTTTTGTTCATTATAAGGCAAATATT
* *
284584 TACGAAATGTCTTTTCTTTTTGTTCATTATCAGGTAAATATT
1 TACGAAATGTCTTTTCTTTTTGTTCATTATAAGGCAAATATT
284626 TA
1 TA
284628 ATGTAAAATG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (42 bp):
TACGAAATGTCTTTTCTTTTTGTTCATTATAAGGCAAATATT
Found at i:291584 original size:23 final size:22
Alignment explanation
Indices: 291549--291594 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
291539 TTATTGAATT
* *
291549 TATATTTTGTATACTGATGATA
1 TATAATTTGTATACTGATAATA
*
291571 TATAATTTGATATATTGATAATA
1 TATAATTTG-TATACTGATAATA
291594 T
1 T
291595 TTATTTCTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.50
Consensus pattern (22 bp):
TATAATTTGTATACTGATAATA
Found at i:291648 original size:5 final size:5
Alignment explanation
Indices: 291628--291660 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
291618 CTAGATGAAA
*
291628 AAATT -AATT AAGTT AAATT AAATT AAATT AAAT
1 AAATT AAATT AAATT AAATT AAATT AAATT AAAT
291661 GGACTATTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (5 bp):
AAATT
Found at i:299544 original size:29 final size:29
Alignment explanation
Indices: 299511--299568 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
299501 AGAAAAAAGT
299511 TGCTCTTCACCTGAGCCCTCACCTACCAA
1 TGCTCTTCACCTGAGCCCTCACCTACCAA
299540 TGCTCTTCACCTGAGCCCTCACCTACCAA
1 TGCTCTTCACCTGAGCCCTCACCTACCAA
299569 AGCTTGCTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.21, C:0.45, G:0.10, T:0.24
Consensus pattern (29 bp):
TGCTCTTCACCTGAGCCCTCACCTACCAA
Found at i:303169 original size:12 final size:12
Alignment explanation
Indices: 303152--303177 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
303142 TACTTTTCAA
303152 TTTTTATTAAAT
1 TTTTTATTAAAT
303164 TTTTTATTAAAT
1 TTTTTATTAAAT
303176 TT
1 TT
303178 GAATTACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTTATTAAAT
Found at i:306615 original size:8 final size:8
Alignment explanation
Indices: 306602--306626 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
306592 ATGCATGCAC
306602 ACATATAT
1 ACATATAT
306610 ACATATAT
1 ACATATAT
306618 ACATATAT
1 ACATATAT
306626 A
1 A
306627 TGCACGTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (8 bp):
ACATATAT
Found at i:307565 original size:19 final size:18
Alignment explanation
Indices: 307538--307573 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
307528 TGTGAAATAA
307538 TTAGAACACAATGTTACAC
1 TTAGAACACAAT-TTACAC
*
307557 TTAGCACACAATTTACA
1 TTAGAACACAATTTACA
307574 GAAGCTAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (18 bp):
TTAGAACACAATTTACAC
Found at i:308934 original size:26 final size:26
Alignment explanation
Indices: 308904--308956 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
308894 AATTGCCAAC
308904 GCAATAACATAGGAATTGGAATATGA
1 GCAATAACATAGGAATTGGAATATGA
308930 GCAATAACATAGGAATTGGAATATGA
1 GCAATAACATAGGAATTGGAATATGA
308956 G
1 G
308957 AAGATGATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.45, C:0.08, G:0.25, T:0.23
Consensus pattern (26 bp):
GCAATAACATAGGAATTGGAATATGA
Found at i:312821 original size:2 final size:2
Alignment explanation
Indices: 312809--312859 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
312799 TAAATACATT
312809 TA TA T- TA TA TA TA TA TA TA T- 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
312849 TA TA TA TA TA T
1 TA TA TA TA TA T
312860 TAAATATTCA
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:313939 original size:36 final size:37
Alignment explanation
Indices: 313895--313964 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
313885 TCCCATTATC
313895 ATTTTTC-AACAAACATCTACCAAACTTTGAAAAATT
1 ATTTTTCAAACAAACATCTACCAAACTTTGAAAAATT
* *
313931 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAA
1 ATTTTTCAAACAAACATCTACCAAACTTTGAAAA
313965 CCATTTTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 7 0.23
37 24 0.77
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (37 bp):
ATTTTTCAAACAAACATCTACCAAACTTTGAAAAATT
Found at i:313971 original size:36 final size:37
Alignment explanation
Indices: 313894--313990 Score: 110
Period size: 36 Copynumber: 2.7 Consensus size: 37
313884 ATCCCATTAT
* * *
313894 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAT
1 CATTTTTCAAAAAAACATTTACCAAACTTTGAAAAAC
* *
313930 TATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
1 CATTTTTCAAAAAAACATTTACCAAACTTTGAAAAAC
*
313966 CA-TTTTCAAAAAAAATATTTACCAA
1 CATTTTTC-AAAAAAACATTTACCAA
313991 CTTGAACTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
35 5 0.10
36 27 0.52
37 20 0.38
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (37 bp):
CATTTTTCAAAAAAACATTTACCAAACTTTGAAAAAC
Found at i:315074 original size:6 final size:6
Alignment explanation
Indices: 315057--316422 Score: 1825
Period size: 6 Copynumber: 233.3 Consensus size: 6
315047 ATTTAATTAT
*
315057 TGTATA TATATA TGTATA TGTATA TGTA-A -GATATA TGTATA --TATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TG-TATA TGTATA TGTATA
* *
315102 TGTATA TGTATA TTGTATA TGTATA TGTATA TG--TA TGCATA TGCATA
1 TGTATA TGTATA -TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
* * * * * *
315149 TGTATA TGCATA TGCATA TGCATA TGCATA TGCATA TGCATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
315197 TGT-TA --TATA TGTATA TGTATA TGTGTATA TGGTATA TGTATA -GTATA
1 TGTATA TGTATA TGTATA TGTATA --TGTATA T-GTATA TGTATA TGTATA
315244 T-TATA TGTATA TGTATA TGTATA TGTATA TG--TA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
315289 TGT-TA -GTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
315335 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
*
315383 TGTATA TGTATA -G-GTA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
315429 TGTA-A TGTATA TGTATA TGTAT- TGTATA TGTATATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TG--TATA TGTATA TGTATA
315477 TGTATA TGTATA TG-ATA TGTATA TGTATA TGTATA -GTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
315523 TGTATA TGTATA TGTATA TG--TA T-TATA TGTATA TG--TA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
315566 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
*
315614 TGTATA GTTATATA TGTATA -GTATA TGTATATA TGTATA TGTATGTA
1 TGTATA --TGTATA TGTATA TGTATA TG--TATA TGTATA TGTA--TA
* *
315661 TATATA TGTATA TGTATA TG-ATA TGTATA TG--TA TGTATA TGTATG
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
** *
315706 T-TACGTA TGTATA TACGTATA TGTATA CATATA CGTATA TGTATACA
1 TGTA--TA TGTATA T--GTATA TGTATA TGTATA TGTATA TGTAT--A
*
315753 TGTATA TGTATA TGTATA TGTACA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
* *
315801 TGTATA TGTATACA TGTATA TATGTA TGTATA TGT-TA TGTATA TGTATGTA
1 TGTATA TGTAT--A TGTATA TGTATA TGTATA TGTATA TGTATA TGTA--TA
*
315852 T-TGTA TGTA-A TGTATA TGTATA TGGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA T-GTATA TGTATA TGTATA TGTATA
315899 TGTATA TGTATA TG--TA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
315945 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATGTA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTA--TA
315995 TGTATA TGTATA TGTATA TGTATA TG--TA TGTATA TGTATA TGGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA T-GTATA
*
316042 TGT-TA TGTATA TGTATA TATATA TGTA-A TGTATA TGTAT- TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
316087 TGTATA TG--TA TGTA-A TGTATA TGTATA TGTATA TG-ATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
316131 TGTATA TGTATA TGTATA --TATA TGTATA T-T-TA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
316175 TGTATA -G--TA TGTATA TGTAT- TGTATA TG--TA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
316217 TGTATA TGTATA TGTA-A TGTATA TGTATA TGTATA -GTAGATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGT--ATA TGTATA
316265 TGTATA --T-TA TGTA-A TGTATA TGTATA TGGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA T-GTATA TGTATA TGTATA
316310 TG--TA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TG-ATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
316355 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
316403 TGTATA TGTATA TGTATA TG
1 TGTATA TGTATA TGTATA TG
316423 ACCAGTCCCA
Statistics
Matches: 1239, Mismatches: 27, Indels: 188
0.85 0.02 0.13
Matches are distributed among these distances:
3 5 0.00
4 59 0.05
5 120 0.10
6 959 0.77
7 37 0.03
8 59 0.05
ACGTcount: A:0.33, C:0.01, G:0.17, T:0.48
Consensus pattern (6 bp):
TGTATA
Found at i:315207 original size:9 final size:8
Alignment explanation
Indices: 315188--316409 Score: 267
Period size: 8 Copynumber: 150.2 Consensus size: 8
315178 ATGCATATGC
315188 ATATGTAT
1 ATATGTAT
*
315196 ATGT-TAT
1 ATATGTAT
315203 ATATG--T
1 ATATGTAT
315209 ATATG--T
1 ATATGTAT
*
315215 ATATGTGT
1 ATATGTAT
*
315223 ATATG-GT
1 ATATGTAT
315230 ATATGTAT
1 ATATGTAT
*
315238 AGTATAT-T
1 A-TATGTAT
315246 ATATGTAT
1 ATATGTAT
* *
315254 ATGTATATGT
1 A--TATGTAT
315264 ATATGTAT
1 ATATGTAT
* * *
315272 ATGTATGT
1 ATATGTAT
315280 ATATGTAT
1 ATATGTAT
*
315288 ATGT-TAGT
1 ATATGTA-T
315296 ATATGTAT
1 ATATGTAT
* *
315304 ATGTATATGT
1 A--TATGTAT
315314 ATATGTAT
1 ATATGTAT
* *
315322 ATGTATAT
1 ATATGTAT
* * *
315330 GTATATGT
1 ATATGTAT
315338 ATATGTAT
1 ATATGTAT
* *
315346 ATGTATAT
1 ATATGTAT
* * *
315354 GTATATGT
1 ATATGTAT
315362 ATATGTAT
1 ATATGTAT
* *
315370 ATGTATAT
1 ATATGTAT
* * *
315378 GTATATGT
1 ATATGTAT
315386 ATATGTAT
1 ATATGTAT
315394 AGGTATGTAT
1 A--TATGTAT
* *
315404 ATGTATATGT
1 A--TATGTAT
315414 ATATGTAT
1 ATATGTAT
* *
315422 ATGTATAT
1 ATATGTAT
*
315430 GTAATGTAT
1 AT-ATGTAT
* *
315439 ATGTATAT
1 ATATGTAT
* *
315447 GTAT-TGT
1 ATATGTAT
315454 ATATGTAT
1 ATATGTAT
315462 ATATGTAT
1 ATATGTAT
* *
315470 ATGTATATGT
1 A--TATGTAT
315480 ATATGTAT
1 ATATGTAT
* *
315488 ATGATATGT
1 AT-ATGTAT
315497 ATATGTAT
1 ATATGTAT
* *
315505 ATGTATAGT
1 ATATGTA-T
315514 ATATGTAT
1 ATATGTAT
* *
315522 ATGTATAT
1 ATATGTAT
* * *
315530 GTATATGT
1 ATATGTAT
315538 ATATGTATT
1 ATATGTA-T
315547 ATATGTAT
1 ATATGTAT
* * *
315555 ATGTATGT
1 ATATGTAT
315563 ATATGTAT
1 ATATGTAT
* *
315571 ATGTATAT
1 ATATGTAT
* * *
315579 GTATATGT
1 ATATGTAT
315587 ATATGTAT
1 ATATGTAT
* *
315595 ATGTATAT
1 ATATGTAT
* * *
315603 GTATATGT
1 ATATGTAT
315611 ATATGTAT
1 ATATGTAT
*
315619 A-GT-TAT
1 ATATGTAT
315625 ATATGTATAGT
1 ATATG--TA-T
315636 ATATGTAT
1 ATATGTAT
315644 ATATGTAT
1 ATATGTAT
315652 ATGTATGTAT
1 A--TATGTAT
* *
315662 ATATATGT
1 ATATGTAT
315670 ATATGTAT
1 ATATGTAT
* *
315678 ATGATATGT
1 AT-ATGTAT
315687 ATATGTAT
1 ATATGTAT
*
315695 GTA--TAT
1 ATATGTAT
*
315701 GTATGT-T
1 ATATGTAT
315708 ACGTATGTAT
1 A--TATGTAT
*
315718 ATACG--T
1 ATATGTAT
315724 ATATGTAT
1 ATATGTAT
* *
315732 ACATATACGT
1 ATATGTA--T
315742 ATATGTAT
1 ATATGTAT
*
315750 ACATG--T
1 ATATGTAT
315756 ATATGTAT
1 ATATGTAT
* *
315764 ATGTATAT
1 ATATGTAT
* ** *
315772 GTACATGT
1 ATATGTAT
315780 ATATGTAT
1 ATATGTAT
* *
315788 ATGTATAT
1 ATATGTAT
* * *
315796 GTATATGT
1 ATATGTAT
315804 ATATGTAT
1 ATATGTAT
*
315812 ACATGTAT
1 ATATGTAT
315820 ATATGTATGT
1 ATATGTA--T
315830 ATATGTTATGT
1 ATATG-TA--T
315841 ATATGTAT
1 ATATGTAT
*
315849 GTATTGTAT
1 ATA-TGTAT
*
315858 GTAATG--T
1 AT-ATGTAT
315865 ATATGTAT
1 ATATGTAT
*
315873 AT-GGTAT
1 ATATGTAT
* *
315880 ATGTATAT
1 ATATGTAT
* * *
315888 GTATATGT
1 ATATGTAT
315896 ATATGTAT
1 ATATGTAT
* *
315904 ATGTATAT
1 ATATGTAT
*
315912 GTATGTAT
1 ATATGTAT
* *
315920 ATGTATAT
1 ATATGTAT
* * *
315928 GTATATGT
1 ATATGTAT
315936 ATATGTAT
1 ATATGTAT
* *
315944 ATGTATAT
1 ATATGTAT
* * *
315952 GTATATGT
1 ATATGTAT
315960 ATATGTAT
1 ATATGTAT
* *
315968 ATGTATAT
1 ATATGTAT
* * *
315976 GTATATGT
1 ATATGTAT
315984 ATATGTAT
1 ATATGTAT
*
315992 GTATGTAT
1 ATATGTAT
* *
316000 ATGTATATGT
1 A--TATGTAT
316010 ATATGTAT
1 ATATGTAT
* * *
316018 ATGTATGT
1 ATATGTAT
316026 ATATGTAT
1 ATATGTAT
*
316034 AT-GGTAT
1 ATATGTAT
*
316041 ATGT-TATGT
1 ATATGTA--T
316050 ATATGTAT
1 ATATGTAT
*
316058 ATATATAT
1 ATATGTAT
*
316066 GTAATGTAT
1 AT-ATGTAT
*
316075 ATGTAT-TGT
1 A--TATGTAT
316084 ATATGTAT
1 ATATGTAT
316092 ATGTATGTAAT
1 A--TATGT-AT
* * *
316103 GTATATGT
1 ATATGTAT
316111 ATATGTAT
1 ATATGTAT
* *
316119 ATGATATGT
1 AT-ATGTAT
316128 ATATG--T
1 ATATGTAT
316134 ATATGTAT
1 ATATGTAT
* *
316142 ATGTATAT
1 ATATGTAT
316150 ATATGTAT
1 ATATGTAT
316158 AT-T-TAT
1 ATATGTAT
* * *
316164 GTATATGT
1 ATATGTAT
316172 ATATGTAT
1 ATATGTAT
316180 AGTATGTAT
1 A-TATGTAT
*
316189 ATGTAT-TGT
1 A--TATGTAT
316198 ATATGTAT
1 ATATGTAT
* * *
316206 GTATATGT
1 ATATGTAT
316214 ATATGTAT
1 ATATGTAT
* *
316222 ATGTATAT
1 ATATGTAT
*
316230 GTAATGTAT
1 AT-ATGTAT
* *
316239 ATGTATAT
1 ATATGTAT
* *
316247 GTATAGTAG
1 ATAT-GTAT
316256 ATATG--T
1 ATATGTAT
316262 ATATGTAT
1 ATATGTAT
316270 ATTATGTAAT
1 A-TATGT-AT
* * *
316280 GTATATGT
1 ATATGTAT
*
316288 ATATG-GT
1 ATATGTAT
316295 ATATGTAT
1 ATATGTAT
* *
316303 ATGTATAT
1 ATATGTAT
*
316311 GTATGTAT
1 ATATGTAT
* *
316319 ATGTATAT
1 ATATGTAT
* * *
316327 GTATATGT
1 ATATGTAT
316335 ATATGTAT
1 ATATGTAT
* *
316343 ATGTATAT
1 ATATGTAT
316351 GATATGTAT
1 -ATATGTAT
* *
316360 ATGTATAT
1 ATATGTAT
* * *
316368 GTATATGT
1 ATATGTAT
316376 ATATGTAT
1 ATATGTAT
* *
316384 ATGTATAT
1 ATATGTAT
* * *
316392 GTATATGT
1 ATATGTAT
316400 ATATGTAT
1 ATATGTAT
316408 AT
1 AT
316410 GTATATGTAT
Statistics
Matches: 850, Mismatches: 287, Indels: 154
0.66 0.22 0.12
Matches are distributed among these distances:
6 50 0.06
7 58 0.07
8 531 0.62
9 111 0.13
10 81 0.10
11 19 0.02
ACGTcount: A:0.33, C:0.01, G:0.17, T:0.49
Consensus pattern (8 bp):
ATATGTAT
Found at i:322440 original size:15 final size:15
Alignment explanation
Indices: 322420--322451 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
322410 AGAGTGAACC
322420 TCCCAAAGAGGTTGA
1 TCCCAAAGAGGTTGA
322435 TCCCAAAGAGGTTGA
1 TCCCAAAGAGGTTGA
322450 TC
1 TC
322452 TTTATGATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (15 bp):
TCCCAAAGAGGTTGA
Found at i:337216 original size:38 final size:39
Alignment explanation
Indices: 337167--337290 Score: 139
Period size: 38 Copynumber: 3.2 Consensus size: 39
337157 AAACTTAAGG
*
337167 AAAAATGAATTATGTTCTAATGTGAAAGGGAAAGTAAAC
1 AAAAAGGAATTATGTTCTAATGTGAAAGGGAAAGTAAAC
* **
337206 AAAAA-GAATTATGTTCTAATGTG--AGGGAAAAAACTTAAGG
1 AAAAAGGAATTATGTTCTAATGTGAAAGGG---AAA-GTAAAC
337246 AAAAAGGAACTT-TGTTCTAATGTGAAAGGGAAAGTAAAC
1 AAAAAGGAA-TTATGTTCTAATGTGAAAGGGAAAGTAAAC
337285 AAAAAG
1 AAAAAG
337291 AAGACTTTAG
Statistics
Matches: 71, Mismatches: 6, Indels: 16
0.76 0.06 0.17
Matches are distributed among these distances:
36 4 0.06
38 18 0.25
39 17 0.24
40 11 0.15
41 15 0.21
42 2 0.03
43 4 0.06
ACGTcount: A:0.49, C:0.06, G:0.22, T:0.23
Consensus pattern (39 bp):
AAAAAGGAATTATGTTCTAATGTGAAAGGGAAAGTAAAC
Found at i:337267 original size:41 final size:38
Alignment explanation
Indices: 337153--337270 Score: 125
Period size: 41 Copynumber: 3.0 Consensus size: 38
337143 ATTTATAGGG
337153 GGGAAAACTTAAGGAAAAATGAATTATGTTCTAATGTGAAA
1 GGGAAAACTTAAGGAAAAA-GAATTATGTTCTAATGTG--A
* **
337194 GGG-AAA-GTAAACAAAAAGAATTATGTTCTAATGTGA
1 GGGAAAACTTAAGGAAAAAGAATTATGTTCTAATGTGA
337230 GGGAAAAAACTTAAGGAAAAAGGAACTT-TGTTCTAATGTGA
1 GGG--AAAACTTAAGGAAAAA-GAA-TTATGTTCTAATGTGA
337271 AAGGGAAAGT
Statistics
Matches: 65, Mismatches: 6, Indels: 12
0.78 0.07 0.14
Matches are distributed among these distances:
36 4 0.06
38 18 0.28
39 11 0.17
40 11 0.17
41 19 0.29
42 2 0.03
ACGTcount: A:0.46, C:0.06, G:0.23, T:0.25
Consensus pattern (38 bp):
GGGAAAACTTAAGGAAAAAGAATTATGTTCTAATGTGA
Found at i:338269 original size:32 final size:32
Alignment explanation
Indices: 338230--338297 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 32
338220 GTAAGATTAC
338230 AATGTTTGGTTTGA-GAAATATAAGATTATTTA
1 AATGTTTGGTTTGATG-AATATAAGATTATTTA
*
338262 AATGTTTGGTTTGATGAATATAAGATTATTTG
1 AATGTTTGGTTTGATGAATATAAGATTATTTA
338294 AATG
1 AATG
338298 CATATTTTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 33 0.97
33 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (32 bp):
AATGTTTGGTTTGATGAATATAAGATTATTTA
Found at i:338953 original size:12 final size:12
Alignment explanation
Indices: 338936--338961 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
338926 TCCGCGAACC
338936 AAACACACCCTT
1 AAACACACCCTT
338948 AAACACACCCTT
1 AAACACACCCTT
338960 AA
1 AA
338962 GAAATAAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.38, G:0.00, T:0.15
Consensus pattern (12 bp):
AAACACACCCTT
Found at i:351903 original size:119 final size:119
Alignment explanation
Indices: 351692--351910 Score: 386
Period size: 119 Copynumber: 1.8 Consensus size: 119
351682 TCGCTCAAGA
* * * *
351692 AAACAAAAGAAGAAATACACTCAGCTAGATGTAAAACCGTTGAATCTGAATATATGAAGAAAAGA
1 AAACAAAAGAAAAAATAAACTCAGCTAGATGTAAAAACGCTGAATCTGAATATATGAAGAAAAGA
351757 AAAATTAAGAAAGAGAGGTTTTATATGTAAAGAAGAGCATAGAAATGAAAGAGG
66 AAAATTAAGAAAGAGAGGTTTTATATGTAAAGAAGAGCATAGAAATGAAAGAGG
351811 AAACAAAAGAAAAAATAAACTCAGCTAGATGTAAAAACGCTGAATCTGAATATATGAA-AAAAGA
1 AAACAAAAGAAAAAATAAACTCAGCTAGATGTAAAAACGCTGAATCTGAATATATGAAGAAAAGA
351875 AAAATTAAGAAAGAGAGGGTTTTATATGTAAAGAAG
66 AAAATTAAGAAAGAGA-GGTTTTATATGTAAAGAAG
351911 TTAAGAAGAG
Statistics
Matches: 95, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
118 22 0.23
119 73 0.77
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (119 bp):
AAACAAAAGAAAAAATAAACTCAGCTAGATGTAAAAACGCTGAATCTGAATATATGAAGAAAAGA
AAAATTAAGAAAGAGAGGTTTTATATGTAAAGAAGAGCATAGAAATGAAAGAGG
Found at i:357430 original size:2 final size:2
Alignment explanation
Indices: 357423--357472 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
357413 ATGGTGTTTG
357423 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
357465 AT AT AT AT
1 AT AT AT AT
357473 GTTCAAGAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:360156 original size:19 final size:19
Alignment explanation
Indices: 360132--360168 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
360122 CCCCATATCT
360132 ACCTAATATTTTTCAATCC
1 ACCTAATATTTTTCAATCC
360151 ACCTAATATTTTTCAATC
1 ACCTAATATTTTTCAATC
360169 TACCACCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.43
Consensus pattern (19 bp):
ACCTAATATTTTTCAATCC
Found at i:362239 original size:22 final size:23
Alignment explanation
Indices: 362193--362241 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
362183 ATTCTGAAAT
**
362193 ATTTAGTTTATAAAATATATTAA
1 ATTTAGTTTATAAAATATACCAA
*
362216 ATTTTGTTTAT-AAATATACCAA
1 ATTTAGTTTATAAAATATACCAA
362238 ATTT
1 ATTT
362242 GGCAGTCTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (23 bp):
ATTTAGTTTATAAAATATACCAA
Found at i:375021 original size:24 final size:24
Alignment explanation
Indices: 374994--375077 Score: 96
Period size: 24 Copynumber: 3.5 Consensus size: 24
374984 AATACAAATG
* *
374994 AATGAACATAAAAGAACGGATGTA
1 AATGAACATAAAAGAACGAACGTA
* *
375018 AATGAACACAAACGAACGAACGTA
1 AATGAACATAAAAGAACGAACGTA
** * *
375042 AACAAACATAAATGAACGAACATA
1 AATGAACATAAAAGAACGAACGTA
375066 AATGAACATAAA
1 AATGAACATAAA
375078 CCACAACAAC
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.58, C:0.14, G:0.14, T:0.13
Consensus pattern (24 bp):
AATGAACATAAAAGAACGAACGTA
Found at i:375063 original size:14 final size:14
Alignment explanation
Indices: 375046--375072 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
375036 AACGTAAACA
375046 AACATAAATGAACG
1 AACATAAATGAACG
375060 AACATAAATGAAC
1 AACATAAATGAAC
375073 ATAAACCACA
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:0.59, C:0.15, G:0.11, T:0.15
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:381445 original size:12 final size:12
Alignment explanation
Indices: 381412--381482 Score: 79
Period size: 12 Copynumber: 5.9 Consensus size: 12
381402 GCATGCCCAG
381412 CAGCAGCAACAA
1 CAGCAGCAACAA
* * *
381424 CAACAACAACAC
1 CAGCAGCAACAA
*
381436 CAGCAGCAACAC
1 CAGCAGCAACAA
* *
381448 CAGCAGCAGCAG
1 CAGCAGCAACAA
381460 CAGCAGCAACAA
1 CAGCAGCAACAA
*
381472 CAGCAACAACA
1 CAGCAGCAACA
381483 GCAACAGCAG
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 49 1.00
ACGTcount: A:0.48, C:0.37, G:0.15, T:0.00
Consensus pattern (12 bp):
CAGCAGCAACAA
Found at i:381451 original size:9 final size:9
Alignment explanation
Indices: 381421--381493 Score: 65
Period size: 9 Copynumber: 8.1 Consensus size: 9
381411 GCAGCAGCAA
*
381421 CAACAACAA
1 CAACAACAG
*
381430 CAACACCAG
1 CAACAACAG
* *
381439 CAGCAACAC
1 CAACAACAG
* *
381448 CAGCAGCAG
1 CAACAACAG
* *
381457 CAGCAGCAG
1 CAACAACAG
381466 CAACAACAG
1 CAACAACAG
381475 CAACAACAG
1 CAACAACAG
*
381484 CAACAGCAG
1 CAACAACAG
381493 C
1 C
381494 CGCCACCGCA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 54 1.00
ACGTcount: A:0.47, C:0.37, G:0.16, T:0.00
Consensus pattern (9 bp):
CAACAACAG
Found at i:381508 original size:3 final size:3
Alignment explanation
Indices: 381436--381493 Score: 53
Period size: 3 Copynumber: 19.3 Consensus size: 3
381426 ACAACAACAC
* * * * * *
381436 CAG CAG CAA CAC CAG CAG CAG CAG CAG CAG CAA CAA CAG CAA CAA CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
*
381484 CAA CAG CAG C
1 CAG CAG CAG C
381494 CGCCACCGCA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.43, C:0.36, G:0.21, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:381521 original size:18 final size:18
Alignment explanation
Indices: 381500--381534 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
381490 CAGCCGCCAC
* *
381500 CGCAGCAGCCTCAGCAGG
1 CGCAGCAACCCCAGCAGG
381518 CGCAGCAACCCCAGCAG
1 CGCAGCAACCCCAGCAG
381535 CGAAGGGATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.43, G:0.29, T:0.03
Consensus pattern (18 bp):
CGCAGCAACCCCAGCAGG
Found at i:382871 original size:24 final size:24
Alignment explanation
Indices: 382844--382894 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
382834 AATGAAGGTA
382844 TTAATGTCCCTATGAAGTGTGCTT
1 TTAATGTCCCTATGAAGTGTGCTT
382868 TTAATGTCCCTATGAAGTGTGCTT
1 TTAATGTCCCTATGAAGTGTGCTT
382892 TTA
1 TTA
382895 CCTTGATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.43
Consensus pattern (24 bp):
TTAATGTCCCTATGAAGTGTGCTT
Found at i:386307 original size:87 final size:87
Alignment explanation
Indices: 386161--386336 Score: 289
Period size: 87 Copynumber: 2.0 Consensus size: 87
386151 TTGGCCGTAT
* ***
386161 CACCGGTGACGAGGCTGGTTTCGTCCGCAAGTCATGACAAGTTTGTTAAACTCTGGAAGTGATAC
1 CACCGGTGACGAGGCTGATTTCAAACGCAAGTCATGACAAGTTTGTTAAACTCTGGAAGTGATAC
*
386226 AATTGCTAGCCAGATTTCCCAA
66 AATTGCTAGCCAGATTTACCAA
* *
386248 CACCGGTTACGAGGCTGATTTCAAACGCAAGTCATGATAAGTTTGTTAAACTCTGGAAGTGATAC
1 CACCGGTGACGAGGCTGATTTCAAACGCAAGTCATGACAAGTTTGTTAAACTCTGGAAGTGATAC
386313 AATTGCTAGCCAGATTTACCAA
66 AATTGCTAGCCAGATTTACCAA
386335 CA
1 CA
386337 TGTTCGGTAA
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 82 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (87 bp):
CACCGGTGACGAGGCTGATTTCAAACGCAAGTCATGACAAGTTTGTTAAACTCTGGAAGTGATAC
AATTGCTAGCCAGATTTACCAA
Found at i:387126 original size:22 final size:22
Alignment explanation
Indices: 387089--387130 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
387079 ATTTGTACCA
387089 TATAGATTACGAATACAAAAAT
1 TATAGATTACGAATACAAAAAT
387111 TATAGTATTACG-ATACAAAA
1 TATAG-ATTACGAATACAAAA
387131 CAACATAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.29
Consensus pattern (22 bp):
TATAGATTACGAATACAAAAAT
Found at i:387138 original size:23 final size:22
Alignment explanation
Indices: 387090--387141 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
387080 TTTGTACCAT
**
387090 ATAGATTACGAATACAAAAATT
1 ATAGATTACGAATACAAAAAAC
387112 ATAGTATTACG-ATACAAAACAAC
1 ATAG-ATTACGAATACAAAA-AAC
387135 ATAGATT
1 ATAGATT
387142 TCGAGATGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 15 0.58
23 11 0.42
ACGTcount: A:0.52, C:0.12, G:0.10, T:0.27
Consensus pattern (22 bp):
ATAGATTACGAATACAAAAAAC
Found at i:402492 original size:23 final size:23
Alignment explanation
Indices: 402466--402535 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
402456 AACAATAAAA
402466 AGGTACCCTAGTTTTTATAAGAG
1 AGGTACCCTAGTTTTTATAAGAG
* * *
402489 AGGTACTCTA-----CACT-AGAA
1 AGGTACCCTAGTTTTTA-TAAGAG
402507 AGGTACCCTAGTTTTTATAAGAG
1 AGGTACCCTAGTTTTTATAAGAG
402530 AGGTAC
1 AGGTAC
402536 TCTACACTAG
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
18 13 0.38
19 1 0.03
22 1 0.03
23 19 0.56
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (23 bp):
AGGTACCCTAGTTTTTATAAGAG
Found at i:402521 original size:41 final size:41
Alignment explanation
Indices: 402464--402623 Score: 261
Period size: 41 Copynumber: 3.9 Consensus size: 41
402454 AAAACAATAA
402464 AAAGGTACCCTAGTTTTTATAAGAGAGGTACTCTACACTAG
1 AAAGGTACCCTAGTTTTTATAAGAGAGGTACTCTACACTAG
402505 AAAGGTACCCTAGTTTTTATAAGAGAGGTACTCTACACTAG
1 AAAGGTACCCTAGTTTTTATAAGAGAGGTACTCTACACTAG
* *
402546 AAAGGTACCCTAGTTTTTATAAGAGAGTTACCTCTACACTAA
1 AAAGGTACCCTAGTTTTTATAAGAGAGGTA-CTCTACACTAG
* *
402588 AAAGGTTCCCTAGTTTTTATAAGATA--TACTCTACAC
1 AAAGGTACCCTAGTTTTTATAAGAGAGGTACTCTACAC
402624 ATGTCCAAAA
Statistics
Matches: 114, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
39 8 0.07
40 2 0.02
41 70 0.61
42 34 0.30
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (41 bp):
AAAGGTACCCTAGTTTTTATAAGAGAGGTACTCTACACTAG
Found at i:402605 original size:83 final size:80
Alignment explanation
Indices: 402464--402623 Score: 257
Period size: 83 Copynumber: 2.0 Consensus size: 80
402454 AAAACAATAA
*
402464 AAAGGTACCCTAGTTTTTATAAGAGAGGTACTCTACACTAGAAAGGTACCCTAGTTTTTATAAGA
1 AAAGGTACCCTAGTTTTTATAAGAGAGGTACTCTACACTAAAAAGGTACCCTAGTTTTTATAAGA
402529 GAGGTACTCTACACTAG
66 GA--TACTCTACACTAG
* *
402546 AAAGGTACCCTAGTTTTTATAAGAGAGTTACCTCTACACTAAAAAGGTTCCCTAGTTTTTATAAG
1 AAAGGTACCCTAGTTTTTATAAGAGAGGTA-CTCTACACTAAAAAGGTACCCTAGTTTTTATAAG
*
402611 ATATACTCTACAC
65 AGATACTCTACAC
402624 ATGTCCAAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
81 10 0.14
82 29 0.40
83 34 0.47
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (80 bp):
AAAGGTACCCTAGTTTTTATAAGAGAGGTACTCTACACTAAAAAGGTACCCTAGTTTTTATAAGA
GATACTCTACACTAG
Done.