Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004571.1 Hibiscus syriacus cultivar Beakdansim tig00010157_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: 157003
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6614 original size:39 final size:39
Alignment explanation
Indices: 6559--6635 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
6549 AATACAAATC
* * *
6559 AAATGCTCTATGCCACTGCTGCCATGTCCTTGAGCCAGA
1 AAATGCCCTATACCACTGCTGACATGTCCTTGAGCCAGA
6598 AAATGCCCTATACCACTGCTGACATGTCCTTGAGCCAG
1 AAATGCCCTATACCACTGCTGACATGTCCTTGAGCCAG
6636 TCATCCAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (39 bp):
AAATGCCCTATACCACTGCTGACATGTCCTTGAGCCAGA
Found at i:27898 original size:34 final size:36
Alignment explanation
Indices: 27855--27923 Score: 115
Period size: 34 Copynumber: 2.0 Consensus size: 36
27845 TTTCAATGTT
27855 ACAAAATGGTCATTAATT-A-CTTGTTGATATAATC
1 ACAAAATGGTCATTAATTAAGCTTGTTGATATAATC
*
27889 ACAAAATGGTCATTAATTAAGTTTGTTGATATAAT
1 ACAAAATGGTCATTAATTAAGCTTGTTGATATAAT
27924 TACATATGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 18 0.56
35 1 0.03
36 13 0.41
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (36 bp):
ACAAAATGGTCATTAATTAAGCTTGTTGATATAATC
Found at i:32256 original size:17 final size:17
Alignment explanation
Indices: 32199--32249 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 17
32189 CGATCATTTC
*
32199 AACCACTATCTGTCATT
1 AACCACTATATGTCATT
*
32216 AACCACTATTTGTCATT
1 AACCACTATATGTCATT
32233 AACCACTATATGTCATT
1 AACCACTATATGTCATT
32250 GAACACTCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.37
Consensus pattern (17 bp):
AACCACTATATGTCATT
Found at i:34268 original size:2 final size:2
Alignment explanation
Indices: 34261--34290 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
34251 GTATTTTACT
34261 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34291 CCTCGTAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34953 original size:21 final size:21
Alignment explanation
Indices: 34929--34973 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
34919 AGGTTTTGAA
34929 AAAACTGA-AAGTTTA-AGTACT
1 AAAACTGATAA-TTTATA-TACT
34950 AAAACTGATAATTTATATACT
1 AAAACTGATAATTTATATACT
34971 AAA
1 AAA
34974 TACATAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (21 bp):
AAAACTGATAATTTATATACT
Found at i:39725 original size:35 final size:35
Alignment explanation
Indices: 39679--39748 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
39669 AATGTGATAA
39679 GTTAGTTCAAATAATAGACACTACTAACTAATCTC
1 GTTAGTTCAAATAATAGACACTACTAACTAATCTC
*
39714 GTTAGTTCAAATAATAGACACTAGTAACTAATCTC
1 GTTAGTTCAAATAATAGACACTACTAACTAATCTC
39749 ATTTCCCAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (35 bp):
GTTAGTTCAAATAATAGACACTACTAACTAATCTC
Found at i:40292 original size:16 final size:16
Alignment explanation
Indices: 40271--40301 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40261 ACTTTCTTAA
*
40271 ATTTTGATCGGATCAT
1 ATTTTGATCGAATCAT
40287 ATTTTGATCGAATCA
1 ATTTTGATCGAATCA
40302 AATTGACCGG
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:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (16 bp):
ATTTTGATCGAATCAT
Found at i:41387 original size:25 final size:24
Alignment explanation
Indices: 41354--41400 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
41344 CAATTTTTAA
41354 AAATAACTTTTAAAAGTGTTATAG
1 AAATAACTTTTAAAAGTGTTATAG
41378 AAATGAACTTTTAAAAGTGTTAT
1 AAAT-AACTTTTAAAAGTGTTAT
41401 TTGAAAGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.38
Consensus pattern (24 bp):
AAATAACTTTTAAAAGTGTTATAG
Found at i:42220 original size:18 final size:19
Alignment explanation
Indices: 42194--42239 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
42184 CGCTAAATTT
*
42194 AAAAT-AAAACGTAT-AAC
1 AAAATAAAAACCTATAAAC
42211 AAAATAAAAACCTATAAAC
1 AAAATAAAAACCTATAAAC
*
42230 AAAACAAAAA
1 AAAATAAAAA
42240 ATAAGATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 5 0.20
18 8 0.32
19 12 0.48
ACGTcount: A:0.72, C:0.13, G:0.02, T:0.13
Consensus pattern (19 bp):
AAAATAAAAACCTATAAAC
Found at i:42577 original size:13 final size:13
Alignment explanation
Indices: 42559--42588 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
42549 AATCACGGGC
42559 TTAAATTTTCGAG
1 TTAAATTTTCGAG
42572 TTAAATTTTCGAG
1 TTAAATTTTCGAG
42585 TTAA
1 TTAA
42589 CATTAAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (13 bp):
TTAAATTTTCGAG
Found at i:47595 original size:13 final size:14
Alignment explanation
Indices: 47579--47609 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
47569 CCCTAAATAA
47579 TAAA-TATAAACCC
1 TAAATTATAAACCC
47592 TAAATTATAAACCC
1 TAAATTATAAACCC
47606 TAAA
1 TAAA
47610 CCCCCAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.55, C:0.19, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAATTATAAACCC
Found at i:54169 original size:6 final size:6
Alignment explanation
Indices: 54158--54308 Score: 302
Period size: 6 Copynumber: 25.2 Consensus size: 6
54148 AGTTTCTTTA
54158 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
54206 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
54254 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
54302 TATATG T
1 TATATG T
54309 CAGACTAGAA
Statistics
Matches: 145, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 145 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:59509 original size:2 final size:2
Alignment explanation
Indices: 59497--59528 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
59487 TAATACAAAA
*
59497 AT AT GT 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
59529 TGTGACAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60560 original size:18 final size:18
Alignment explanation
Indices: 60537--60577 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
60527 CGCCTCTGAA
60537 ATTTTAAAATTACTATAT
1 ATTTTAAAATTACTATAT
* **
60555 ATTTTAAATTTTTTATAT
1 ATTTTAAAATTACTATAT
60573 ATTTT
1 ATTTT
60578 TATTAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTAAAATTACTATAT
Found at i:61271 original size:60 final size:60
Alignment explanation
Indices: 61189--61331 Score: 146
Period size: 60 Copynumber: 2.4 Consensus size: 60
61179 GAGGGTAAAA
* ** *
61189 TACACAAATGGTACATC-GACTATAGCGTATTATTTTATTTAGT-CATTCGACTATTAAAAGT
1 TACA-AAATGGT-CATCTAACTATAGAATATTATTTTATTGAGTCCATT-GACTATTAAAAGT
* * * * * *
61250 TACATAATGGTCCTCTAACTATGGAATGTTGTTTTATTGAGTCCGTTGACTATTAAAAGT
1 TACAAAATGGTCATCTAACTATAGAATATTATTTTATTGAGTCCATTGACTATTAAAAGT
*
61310 TACAAAATGGTCATCTGACTAT
1 TACAAAATGGTCATCTAACTAT
61332 TCATTATATT
Statistics
Matches: 67, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
59 3 0.04
60 57 0.85
61 7 0.10
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (60 bp):
TACAAAATGGTCATCTAACTATAGAATATTATTTTATTGAGTCCATTGACTATTAAAAGT
Found at i:66131 original size:21 final size:21
Alignment explanation
Indices: 66105--66144 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
66095 TTTTTAAGTA
*
66105 TTTTATCGATTTTGTTATTTT
1 TTTTATCGATTTTATTATTTT
66126 TTTTATCGATTTTATTATT
1 TTTTATCGATTTTATTATT
66145 ATTGGACACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.05, G:0.07, T:0.70
Consensus pattern (21 bp):
TTTTATCGATTTTATTATTTT
Found at i:66191 original size:21 final size:21
Alignment explanation
Indices: 66166--66208 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
66156 TATCCAAAAT
*
66166 ATTAAAAATATTAATATTTTA
1 ATTAAAAATAATAATATTTTA
66187 ATTAAAAATAATAATATTTTA
1 ATTAAAAATAATAATATTTTA
66208 A
1 A
66209 ATATATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTAAAAATAATAATATTTTA
Found at i:67791 original size:9 final size:9
Alignment explanation
Indices: 67779--67804 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
67769 TTTTTAGGTT
67779 TTAATATTA
1 TTAATATTA
67788 TTAATATTA
1 TTAATATTA
67797 TTAATATT
1 TTAATATT
67805 TTTGGTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TTAATATTA
Found at i:68843 original size:34 final size:36
Alignment explanation
Indices: 68797--68870 Score: 116
Period size: 35 Copynumber: 2.1 Consensus size: 36
68787 ATTAAATTAA
68797 ACGGGATAAGG-AAAAATCGTTTATGTTAAAAGGGG
1 ACGGGATAAGGAAAAAATCGTTTATGTTAAAAGGGG
* *
68832 ACGGGAT-AGGAAAAAATTGTTTATGTTAAACGGGG
1 ACGGGATAAGGAAAAAATCGTTTATGTTAAAAGGGG
68867 ACGG
1 ACGG
68871 ATTTAGTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 3 0.08
35 33 0.92
ACGTcount: A:0.38, C:0.07, G:0.32, T:0.23
Consensus pattern (36 bp):
ACGGGATAAGGAAAAAATCGTTTATGTTAAAAGGGG
Found at i:69002 original size:13 final size:13
Alignment explanation
Indices: 68925--69005 Score: 51
Period size: 13 Copynumber: 6.2 Consensus size: 13
68915 AATATTAAAA
68925 ATAAT-TATATAT
1 ATAATATATATAT
68937 ATATATATATATAT
1 ATA-ATATATATAT
* *
68951 ATAAGATTAATAAAT
1 ATAATA-T-ATATAT
* *
68966 TTAA-AT-TAAATT
1 ATAATATATATA-T
*
68978 AAAATATATATAT
1 ATAATATATATAT
*
68991 ATAATATTTATAT
1 ATAATATATATAT
69004 AT
1 AT
69006 TTAATTTAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
11 4 0.07
12 6 0.11
13 21 0.39
14 15 0.28
15 8 0.15
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (13 bp):
ATAATATATATAT
Found at i:69008 original size:40 final size:40
Alignment explanation
Indices: 68941--69016 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
68931 ATATATATAT
68941 ATATATATATATAAGATTAATAAATTTAAATTAAATTAAA
1 ATATATATATATAAGATTAATAAATTTAAATTAAATTAAA
* * * *
68981 ATATATATATATAATATTTATATATTTAATTTAAAT
1 ATATATATATATAAGATTAATAAATTTAAATTAAAT
69017 ATATATACCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (40 bp):
ATATATATATATAAGATTAATAAATTTAAATTAAATTAAA
Found at i:70330 original size:2 final size:2
Alignment explanation
Indices: 70323--70350 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
70313 GTATACATAC
70323 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
70351 GGTTGTCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70333 original size:16 final size:16
Alignment explanation
Indices: 70299--70349 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
70289 TTGCACATAC
* *
70299 ATACATACATGTATGT
1 ATACATACATATATAT
70315 ATACATACATATATAT
1 ATACATACATATATAT
* *
70331 ATATATATATATATAT
1 ATACATACATATATAT
70347 ATA
1 ATA
70350 TGGTTGTCTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (16 bp):
ATACATACATATATAT
Found at i:71606 original size:36 final size:38
Alignment explanation
Indices: 71566--71648 Score: 104
Period size: 36 Copynumber: 2.3 Consensus size: 38
71556 ATTATTATAT
71566 ATATATATATAATAT-TAATAAATT-TA-ATTTAAATTA
1 ATATATATATAATATATAAT-AATTATATATTTAAATTA
* *
71602 ATATATATAT-ATATATAATATTTATATATTTAATTTA
1 ATATATATATAATATATAATAATTATATATTTAAATTA
71639 A-ATATATATA
1 ATATATATATA
71649 CTTAGCCCGA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
35 7 0.17
36 24 0.59
37 10 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (38 bp):
ATATATATATAATATATAATAATTATATATTTAAATTA
Found at i:71607 original size:42 final size:42
Alignment explanation
Indices: 71555--71648 Score: 147
Period size: 42 Copynumber: 2.3 Consensus size: 42
71545 TATTAAAAAT
*
71555 AATTATTATATATATATATATAATATTAATAAATTTAATTTA
1 AATTAATATATATATATATATAATATTAATAAATTTAATTTA
* *
71597 AATTAATATATATATATATATAATATTTATATATTTAATTTA
1 AATTAATATATATATATATATAATATTAATAAATTTAATTTA
71639 AA-T-ATATATA
1 AATTAATATATA
71649 CTTAGCCCGA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
40 7 0.14
41 1 0.02
42 41 0.84
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (42 bp):
AATTAATATATATATATATATAATATTAATAAATTTAATTTA
Found at i:77520 original size:36 final size:36
Alignment explanation
Indices: 77469--77551 Score: 139
Period size: 36 Copynumber: 2.3 Consensus size: 36
77459 ACCGAATTAA
* *
77469 ACGGGGACGGAGAAAAATCGTTTATGCTAAACGGGG
1 ACGGGGACGGGGAAAAACCGTTTATGCTAAACGGGG
*
77505 ACGGGGACGGGGAAAAACCGTTTATGTTAAACGGGG
1 ACGGGGACGGGGAAAAACCGTTTATGCTAAACGGGG
77541 ACGGGGACGGG
1 ACGGGGACGGG
77552 TTTAGTAATC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.30, C:0.14, G:0.41, T:0.14
Consensus pattern (36 bp):
ACGGGGACGGGGAAAAACCGTTTATGCTAAACGGGG
Found at i:77617 original size:2 final size:2
Alignment explanation
Indices: 77610--77651 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
77600 TAAAAAGAAT
77610 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
77651 T
1 T
77652 TAATAAATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:77655 original size:6 final size:7
Alignment explanation
Indices: 77610--77656 Score: 51
Period size: 8 Copynumber: 6.3 Consensus size: 7
77600 TAAAAAGAAT
77610 TATATATA
1 TATATA-A
77618 TATATATA
1 TATATA-A
77626 TATATATA
1 TATATA-A
77634 TATATATA
1 TATATA-A
77642 TATATAA
1 TATATAA
77649 TAT-TAA
1 TATATAA
77655 TA
1 TA
77657 AATTTAATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 5 0.13
7 4 0.10
8 30 0.77
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (7 bp):
TATATAA
Found at i:79712 original size:22 final size:22
Alignment explanation
Indices: 79673--79731 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
79663 TCCAACTGTT
* * *
79673 TGTAACTCATGTAATAAATCTC
1 TGTAACTCTTGCAATAAAGCTC
* *
79695 TGTAACTCTTGCATTAAAGCTT
1 TGTAACTCTTGCAATAAAGCTC
79717 TGTAACTCTCTGCAA
1 TGTAACTCT-TGCAA
79732 ATTTAAAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 26 0.87
23 4 0.13
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (22 bp):
TGTAACTCTTGCAATAAAGCTC
Found at i:80919 original size:2 final size:2
Alignment explanation
Indices: 80912--80954 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
80902 CTATAATGTT
80912 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
80954 T
1 T
80955 TGGACTTGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:83058 original size:2 final size:2
Alignment explanation
Indices: 83045--83083 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
83035 TCTTCGTAAT
*
83045 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
83084 TCAAAATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:86977 original size:12 final size:12
Alignment explanation
Indices: 86957--87003 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
86947 TGTTGGTCAT
86957 CATGAACATCAC
1 CATGAACATCAC
*
86969 CATGCACATCAC
1 CATGAACATCAC
*
86981 CTTGAACATCAC
1 CATGAACATCAC
* *
86993 CGTGCACATCA
1 CATGAACATCA
87004 TCCTGAATAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.34, C:0.36, G:0.11, T:0.19
Consensus pattern (12 bp):
CATGAACATCAC
Found at i:87010 original size:24 final size:24
Alignment explanation
Indices: 86953--87010 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
86943 ATCTTGTTGG
*
86953 TCATCATGAACATCACCATGCACA
1 TCATCCTGAACATCACCATGCACA
*
86977 TCA-CCTTGAACATCACCGTGCACA
1 TCATCC-TGAACATCACCATGCACA
87001 TCATCCTGAA
1 TCATCCTGAA
87011 TAGGATATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 1 0.03
24 27 0.90
25 2 0.07
ACGTcount: A:0.33, C:0.34, G:0.10, T:0.22
Consensus pattern (24 bp):
TCATCCTGAACATCACCATGCACA
Found at i:103081 original size:19 final size:18
Alignment explanation
Indices: 103058--103095 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
103048 CTAAGCTGAC
103058 CTTTTTGAAGGAAGATGA
1 CTTTTTGAAGGAAGATGA
*
103076 CTTTTTGAAGGAAGAGGA
1 CTTTTTGAAGGAAGATGA
103094 CT
1 CT
103096 GTATATCAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.08, G:0.29, T:0.32
Consensus pattern (18 bp):
CTTTTTGAAGGAAGATGA
Found at i:105587 original size:27 final size:28
Alignment explanation
Indices: 105551--105615 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
105541 AACTTTATTT
105551 TGTGATATTCGGGTAGGG-TTTTTTAAG
1 TGTGATATTCGGGTAGGGTTTTTTTAAG
*
105578 TGTGATATTCGGGTCGGGTTTTTTTAAG
1 TGTGATATTCGGGTAGGGTTTTTTTAAG
105606 TGTGATATTC
1 TGTGATATTC
105616 AGGTCAGGTC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 17 0.47
28 19 0.53
ACGTcount: A:0.17, C:0.06, G:0.31, T:0.46
Consensus pattern (28 bp):
TGTGATATTCGGGTAGGGTTTTTTTAAG
Found at i:106534 original size:104 final size:104
Alignment explanation
Indices: 106354--106567 Score: 428
Period size: 104 Copynumber: 2.1 Consensus size: 104
106344 TTTTCCTTTT
106354 TCCGACGTCCGATGACCCGTTCTTTGCCATGATTATTTGGTTCAGTCGAGTAAACTTTGCTGTAG
1 TCCGACGTCCGATGACCCGTTCTTTGCCATGATTATTTGGTTCAGTCGAGTAAACTTTGCTGTAG
106419 CTTTGGCTTCTTCATTATTACCAATATTCATCCGTATAA
66 CTTTGGCTTCTTCATTATTACCAATATTCATCCGTATAA
106458 TCCGACGTCCGATGACCCGTTCTTTGCCATGATTATTTGGTTCAGTCGAGTAAACTTTGCTGTAG
1 TCCGACGTCCGATGACCCGTTCTTTGCCATGATTATTTGGTTCAGTCGAGTAAACTTTGCTGTAG
106523 CTTTGGCTTCTTCATTATTACCAATATTCATCCGTATAA
66 CTTTGGCTTCTTCATTATTACCAATATTCATCCGTATAA
106562 TCCGAC
1 TCCGAC
106568 CTTGATGTTT
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 110 1.00
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (104 bp):
TCCGACGTCCGATGACCCGTTCTTTGCCATGATTATTTGGTTCAGTCGAGTAAACTTTGCTGTAG
CTTTGGCTTCTTCATTATTACCAATATTCATCCGTATAA
Found at i:106841 original size:17 final size:17
Alignment explanation
Indices: 106801--106833 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
106791 TATGGTCGGG
106801 CATCGGGGACAATGGGC
1 CATCGGGGACAATGGGC
106818 CATCGGGGACAATGGG
1 CATCGGGGACAATGGG
106834 GGTTCGGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.42, T:0.12
Consensus pattern (17 bp):
CATCGGGGACAATGGGC
Found at i:115321 original size:17 final size:16
Alignment explanation
Indices: 115277--115323 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
115267 GGTTAACCGT
115277 TAATAAATTATATTTC
1 TAATAAATTATATTTC
** *
115293 TAATTTATTATATTTT
1 TAATAAATTATATTTC
115309 TACATAAATTATATT
1 TA-ATAAATTATATT
115324 ATAAGTTTCT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (16 bp):
TAATAAATTATATTTC
Found at i:115709 original size:21 final size:21
Alignment explanation
Indices: 115683--115818 Score: 141
Period size: 21 Copynumber: 6.6 Consensus size: 21
115673 GCGTTGCATT
*
115683 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
115704 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
115725 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
* ** **
115745 TCGCGTTGCGAT-TTTCCAGT
1 TCGCGTTGCGATAGTTGAAAA
115765 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
**
115786 TCGCGTTGTAATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
115807 TCGCGTTGCGAT
1 TCGCGTTGCGAT
115819 TTTCCAGTTC
Statistics
Matches: 98, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
20 34 0.35
21 64 0.65
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:115750 original size:20 final size:20
Alignment explanation
Indices: 115725--115970 Score: 120
Period size: 20 Copynumber: 12.4 Consensus size: 20
115715 TAGTTGAAAA
*
115725 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
115745 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* ** **
115765 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCAGT
** * ** **
115786 TCGCGTTGTAATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCAGT
115807 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* *
115827 TCGCGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAGT
*
115849 T-GCCGTTGCGATTTTCCAAAT
1 TCG-CGTTGCGATTTTCC-AGT
* *
115870 T--CGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAGT
*
115890 T-GTCGTTGCGATTTTCCAAAT
1 TCG-CGTTGCGATTTTCC-AGT
**
115911 T--CGTTGCGA------AAA
1 TCGCGTTGCGATTTTCCAGT
*
115923 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
115943 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
115963 TCGCGTTG
1 TCGCGTTG
115971 GTAATGCTCA
Statistics
Matches: 178, Mismatches: 30, Indels: 36
0.73 0.12 0.15
Matches are distributed among these distances:
12 3 0.02
14 8 0.04
19 17 0.10
20 83 0.47
21 42 0.24
22 25 0.14
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.37
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAGT
Found at i:115756 original size:41 final size:41
Alignment explanation
Indices: 115704--115954 Score: 161
Period size: 41 Copynumber: 6.3 Consensus size: 41
115694 TAATTGAAAA
*
115704 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAAT
* ** ** * ** *
115745 TCGCGTTGCGAT-TTTCCAGTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT-TTTCCAAT
** *
115786 TCGCGTTGTAATAGTTGAAAATCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAAT
* * *
115827 TCGCGTTGCGATAGTCT-ACAGTTGCCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCC-AAT
* * *
115870 T--CGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCC-AAT
*
115911 T--CGTTGC-------GAAAATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAAT
115943 TCGCGTTGCGAT
1 TCGCGTTGCGAT
115955 TTTCCAGTTC
Statistics
Matches: 166, Mismatches: 33, Indels: 26
0.74 0.15 0.12
Matches are distributed among these distances:
32 3 0.02
33 14 0.08
34 10 0.06
40 15 0.09
41 91 0.55
42 30 0.18
43 3 0.02
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.36
Consensus pattern (41 bp):
TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAAT
Found at i:115772 original size:82 final size:82
Alignment explanation
Indices: 115682--115838 Score: 278
Period size: 82 Copynumber: 1.9 Consensus size: 82
115672 CGCGTTGCAT
* *
115682 TTCGCGTTGCGATAATTGAAAATCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTC
1 TTCGCGTTGCGATAATTGAAAATCGCGTTGCAATAGTTGAAAATCGCGTTGCGATTTTCCAGTTC
115747 GCGTTGCGATTTTCCAG
66 GCGTTGCGATTTTCCAG
* *
115764 TTCGCGTTGCGATAGTTGAAAATCGCGTTGTAATAGTTGAAAATCGCGTTGCGATTTTCCAGTTC
1 TTCGCGTTGCGATAATTGAAAATCGCGTTGCAATAGTTGAAAATCGCGTTGCGATTTTCCAGTTC
115829 GCGTTGCGAT
66 GCGTTGCGAT
115839 AGTCTACAGT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 71 1.00
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.35
Consensus pattern (82 bp):
TTCGCGTTGCGATAATTGAAAATCGCGTTGCAATAGTTGAAAATCGCGTTGCGATTTTCCAGTTC
GCGTTGCGATTTTCCAG
Found at i:115855 original size:22 final size:21
Alignment explanation
Indices: 115823--115901 Score: 81
Period size: 22 Copynumber: 3.7 Consensus size: 21
115813 TGCGATTTTC
115823 CAGTTCGCGTTGCGATAGTCTA
1 CAGTT-GCGTTGCGATAGTCTA
** *
115845 CAGTTGCCGTTGCGATTTTCCA
1 CAGTTG-CGTTGCGATAGTCTA
*
115867 -AATT-CGTTGCGATAGTCTA
1 CAGTTGCGTTGCGATAGTCTA
115886 CAGTTGTCGTTGCGAT
1 CAGTTG-CGTTGCGAT
115902 TTTCCAAATT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
19 12 0.27
20 3 0.07
21 4 0.09
22 26 0.58
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (21 bp):
CAGTTGCGTTGCGATAGTCTA
Found at i:115876 original size:19 final size:19
Alignment explanation
Indices: 115852--115919 Score: 73
Period size: 19 Copynumber: 3.4 Consensus size: 19
115842 CTACAGTTGC
115852 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
* * **
115871 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGAT--TTTCCAAAT-T
115893 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
115912 CGTTGCGA
1 CGTTGCGA
115920 AAATCGCGTT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
19 18 0.47
20 5 0.13
21 5 0.13
22 10 0.26
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (19 bp):
CGTTGCGATTTTCCAAATT
Found at i:115882 original size:82 final size:82
Alignment explanation
Indices: 115682--115882 Score: 255
Period size: 82 Copynumber: 2.5 Consensus size: 82
115672 CGCGTTGCAT
* * *
115682 TTCGCGTTGCGATAATTGAAAATCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTC
1 TTCGCGTTGCGATAGTTCAAAATCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAGTTC
* *
115747 GCGTTGCGATTTTCCAG
66 GCGTTGCGATTCTACAG
* **
115764 TTCGCGTTGCGATAGTTGAAAATCGCGTTGTAATAGTTGAAAATCGCGTTGCGATTTTCCAGTTC
1 TTCGCGTTGCGATAGTTCAAAATCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAGTTC
115829 GCGTTGCGATAGTCTACAG
66 GCGTTGCGAT--TCTACAG
* * *
115848 TT-GCCGTTGCGAT-TTTCCAAAT-TCGTTGCGATAGT
1 TTCG-CGTTGCGATAGTTCAAAATCGCGTTGCGATAGT
115883 CTACAGTTGT
Statistics
Matches: 104, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
82 81 0.78
83 7 0.07
84 16 0.15
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (82 bp):
TTCGCGTTGCGATAGTTCAAAATCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAGTTC
GCGTTGCGATTCTACAG
Found at i:116146 original size:6 final size:6
Alignment explanation
Indices: 116107--116149 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
116097 TCTCATCTCG
*
116107 GGTCG- GGTCG- GGTCGG GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
116150 AATACTTGTC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
5 10 0.28
6 26 0.72
ACGTcount: A:0.00, C:0.16, G:0.56, T:0.28
Consensus pattern (6 bp):
GGTCGT
Found at i:116275 original size:22 final size:22
Alignment explanation
Indices: 116247--116339 Score: 95
Period size: 22 Copynumber: 4.4 Consensus size: 22
116237 AATTTGGAAA
116247 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* *
116269 TTCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
116291 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
*
116310 ATCGCAACGAC-ATTGTAGACT
1 ATCGCAACGACAACTGTAGACT
116331 ATCGCAACG
1 ATCGCAACG
116340 CGAAATGCAA
Statistics
Matches: 56, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
19 13 0.23
20 3 0.05
21 13 0.23
22 27 0.48
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:117797 original size:21 final size:19
Alignment explanation
Indices: 117751--117800 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
117741 TTTTTTTTTA
*
117751 ACTATCGCAACGAATTTGG
1 ACTATCGCAACGAACTTGG
**
117770 AAAATCGCAACGGCAACTTGG
1 ACTATCGCAAC-G-AACTTGG
117791 ACTATCGCAA
1 ACTATCGCAA
117801 TGCAAAATGG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 9 0.38
20 1 0.04
21 14 0.58
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (19 bp):
ACTATCGCAACGAACTTGG
Found at i:117811 original size:20 final size:20
Alignment explanation
Indices: 117754--117890 Score: 105
Period size: 20 Copynumber: 6.8 Consensus size: 20
117744 TTTTTTAACT
**
117754 ATCGCAACG-AATTTGGAAA
1 ATCGCAACGCAAAATGGAAA
** **
117773 ATCGCAACGGCAACTTGGACT
1 ATCGCAAC-GCAAAATGGAAA
*
117794 ATCGCAATGCAAAATGGAAA
1 ATCGCAACGCAAAATGGAAA
117814 ATCGCAACGCAAAATGGAAA
1 ATCGCAACGCAAAATGGAAA
* ** ** *
117834 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCAAAATGGAA-A
* *
117855 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCAAAATGGAAA
*
117875 ATCGCAACGCGAAATG
1 ATCGCAACGCAAAATG
117891 CAACGCGAAT
Statistics
Matches: 95, Mismatches: 20, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
19 8 0.08
20 58 0.61
21 29 0.31
ACGTcount: A:0.41, C:0.22, G:0.20, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCAAAATGGAAA
Found at i:122909 original size:5 final size:5
Alignment explanation
Indices: 122899--122927 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
122889 AGAGAATGGA
122899 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
122928 AGCTGAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:131067 original size:14 final size:14
Alignment explanation
Indices: 131044--131085 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
131034 CTTGCTGTTG
131044 CTAT-GTCAATACC
1 CTATAGTCAATACC
131057 CTATAGTCAATACC
1 CTATAGTCAATACC
131071 CTATAGTCAATACC
1 CTATAGTCAATACC
131085 C
1 C
131086 ACCCATTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 4 0.14
14 24 0.86
ACGTcount: A:0.33, C:0.31, G:0.07, T:0.29
Consensus pattern (14 bp):
CTATAGTCAATACC
Found at i:132143 original size:35 final size:35
Alignment explanation
Indices: 132097--132172 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
132087 AAAACAGTCC
* *
132097 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
132132 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
132167 TCAATT
1 TCAATT
132173 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:132652 original size:23 final size:23
Alignment explanation
Indices: 132622--132681 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
132612 ATTTAATTAG
*
132622 GATC-TGACATGTGTTAGCACAT
1 GATCATGACACGTGTTAGCACAT
132644 GATCATGACACGTGTTAGCACAT
1 GATCATGACACGTGTTAGCACAT
132667 GATCATGACACGTGT
1 GATCATGACACGTGT
132682 CATTGGTGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 4 0.11
23 32 0.89
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (23 bp):
GATCATGACACGTGTTAGCACAT
Found at i:133198 original size:28 final size:27
Alignment explanation
Indices: 133167--133229 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
133157 AGTTGATACA
*
133167 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
133195 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
133223 ATATTTT
1 ATATTTT
133230 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:133330 original size:16 final size:18
Alignment explanation
Indices: 133309--133342 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
133299 ATTTCTTATT
133309 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
133325 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
133343 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:134553 original size:60 final size:59
Alignment explanation
Indices: 134485--134714 Score: 232
Period size: 60 Copynumber: 3.8 Consensus size: 59
134475 AGCTATGGCC
*
134485 CTCATTTTAAATTGGTCCTTCAACTTTCAAACATTTTAATTTCTTCCCTAAATTACGATT
1 CTCATTTTAAATTGGTCCTT-AACTTTCAAACATTTTAATTTCATCCCTAAATTACGATT
* *
134545 CTCATTTTAAATTGCTCCTTAAGCTTT-AAACATTTTAATCTCATCCCTAAATTACGATT
1 CTCATTTTAAATTGGTCCTTAA-CTTTCAAACATTTTAATTTCATCCCTAAATTACGATT
* * * * * ** * *
134604 ATCATTCTAAATTAGTCCTTAAACTTTCAAACATTTCAATTTCATTCAAAAACTGA-TATT
1 CTCATTTTAAATTGGTCCTT-AACTTTCAAACATTTTAATTTCATCCCTAAA-TTACGATT
* * * * *
134664 CTCATTCTAAATTAGTCCTTAAACTTTTGAATC-TTCTAATTTCATCCCTAA
1 CTCATTTTAAATTGGTCCTT-AAC-TTTCAAACATTTTAATTTCATCCCTAA
134715 TTTCATCCAA
Statistics
Matches: 143, Mismatches: 22, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
59 52 0.36
60 83 0.58
61 8 0.06
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.43
Consensus pattern (59 bp):
CTCATTTTAAATTGGTCCTTAACTTTCAAACATTTTAATTTCATCCCTAAATTACGATT
Found at i:136843 original size:30 final size:30
Alignment explanation
Indices: 136807--136870 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
136797 CGTTCTTGCC
*
136807 ATGGATTCAATCTCTGGGTTTAGAAATTTA
1 ATGGATTCAATCTCTGGGTTTAGAAATTCA
*
136837 ATGGATTTAATCTCTGGGTTTAGAAATTCA
1 ATGGATTCAATCTCTGGGTTTAGAAATTCA
136867 ATGG
1 ATGG
136871 GTTTTGAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (30 bp):
ATGGATTCAATCTCTGGGTTTAGAAATTCA
Found at i:138421 original size:20 final size:20
Alignment explanation
Indices: 138393--138433 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
138383 TATAGGTTCC
*
138393 GAAGCGTTGTTTGCAGATTT
1 GAAGAGTTGTTTGCAGATTT
138413 GAAGAGTTGTTTGCAGATTT
1 GAAGAGTTGTTTGCAGATTT
138433 G
1 G
138434 GGTCATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.22, C:0.07, G:0.32, T:0.39
Consensus pattern (20 bp):
GAAGAGTTGTTTGCAGATTT
Found at i:139931 original size:40 final size:40
Alignment explanation
Indices: 139887--139967 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
139877 ACTCTCATTT
* * * * *
139887 TAAATTGGTCTTTAAACTTTTTAAAATTCCAATTTCATCC
1 TAAATTAGTCCTTAAACTATTGAAAATTCCAATTCCATCC
* *
139927 TAAATTAGTCCTTAAACTATTGAACATTCTAATTCCATCC
1 TAAATTAGTCCTTAAACTATTGAAAATTCCAATTCCATCC
139967 T
1 T
139968 TAAACTATGA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.42
Consensus pattern (40 bp):
TAAATTAGTCCTTAAACTATTGAAAATTCCAATTCCATCC
Found at i:140193 original size:60 final size:59
Alignment explanation
Indices: 140126--140262 Score: 143
Period size: 60 Copynumber: 2.3 Consensus size: 59
140116 ACTATTTTAT
* *** *
140126 TAGTTT-GGGATAAAACTAAAATGTTCAAAAAGTTTGGGGACCAATTTAGAATGA-AGATCA
1 TAGTTTAGGGATAAAA-TAAAATATTC-AAAAGTTTCAAGACAAATTTAGAATGATAG-TCA
* * *
140186 TAGTTTGGGGATGAAAATGAAATATTCAAAAGTTTCAAGATAAATTTAGAATGATAGTCA
1 TAGTTTAGGGAT-AAAATAAAATATTCAAAAGTTTCAAGACAAATTTAGAATGATAGTCA
*
140246 TATTTTAGGGATAAAAT
1 TAGTTTAGGGATAAAAT
140263 TGGTATATTT
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
59 5 0.08
60 41 0.63
61 15 0.23
62 4 0.06
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.31
Consensus pattern (59 bp):
TAGTTTAGGGATAAAATAAAATATTCAAAAGTTTCAAGACAAATTTAGAATGATAGTCA
Found at i:140271 original size:60 final size:60
Alignment explanation
Indices: 140163--140307 Score: 145
Period size: 60 Copynumber: 2.4 Consensus size: 60
140153 AAAAGTTTGG
* *
140163 GGACCAATTTAGAATGAAGATCATAGTTTGGGGATGAAAATGAAATATTCAAAAGTTTCAA
1 GGACTAATTTAGAATGAAGATCATAGTTTAGGGATGAAAATGAAATATTCAAAAG-TTCAA
* ** * *
140224 -GA-TAAATTTAGAATGATAG-TCATATTTTAGGGAT-AAAATTGGTATATTTACAAGTTCAA
1 GGACT-AATTTAGAATGA-AGATCATAGTTTAGGGATGAAAA-TGAAATATTCAAAAGTTCAA
* *
140283 GGACTAATTTAGAATAAATATCATA
1 GGACTAATTTAGAATGAAGATCATA
140308 ATTGAAGGAC
Statistics
Matches: 69, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
59 10 0.14
60 56 0.81
61 3 0.04
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.32
Consensus pattern (60 bp):
GGACTAATTTAGAATGAAGATCATAGTTTAGGGATGAAAATGAAATATTCAAAAGTTCAA
Found at i:141148 original size:21 final size:21
Alignment explanation
Indices: 141123--141162 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
141113 TAAACAATAG
*
141123 CTAAAACATTATTATTTTTAC
1 CTAAAACATTAATATTTTTAC
141144 CTAAAACATTAATATTTTT
1 CTAAAACATTAATATTTTT
141163 TAATATTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.47
Consensus pattern (21 bp):
CTAAAACATTAATATTTTTAC
Found at i:141422 original size:2 final size:2
Alignment explanation
Indices: 141415--141507 Score: 186
Period size: 2 Copynumber: 46.5 Consensus size: 2
141405 CTCTCCGTTC
141415 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
141457 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
141499 AT AT AT AT A
1 AT AT AT AT A
141508 CATGTCAATT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 91 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:144592 original size:17 final size:17
Alignment explanation
Indices: 144539--144592 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 17
144529 ACTTAAATAC
*
144539 TTAAAAATTTTGTTTTAT
1 TTAAAAATTTT-TTTTCT
*
144557 TTAATAATTTTTTTATCT
1 TTAAAAATTTTTTT-TCT
*
144575 TTAAAAAGTTTTTTTCT
1 TTAAAAATTTTTTTTCT
144592 T
1 T
144593 AATCATATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 7 0.23
18 24 0.77
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.63
Consensus pattern (17 bp):
TTAAAAATTTTTTTTCT
Found at i:145575 original size:18 final size:18
Alignment explanation
Indices: 145549--145629 Score: 71
Period size: 17 Copynumber: 4.7 Consensus size: 18
145539 TCTACGTTTA
* *
145549 ATAATTGTAAAACATCTT
1 ATAACTGTAAAACATCTG
145567 ATAACTGT-AAACATCTG
1 ATAACTGTAAAACATCTG
* *
145584 ATAAAT-AAAAATCATCTG
1 ATAACTGTAAAA-CATCTG
* *
145602 ATAACTGT-AAATATTTG
1 ATAACTGTAAAACATCTG
145619 ATAACT-TAAAA
1 ATAACTGTAAAA
145630 TCATATGAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
16 1 0.02
17 29 0.57
18 21 0.41
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.33
Consensus pattern (18 bp):
ATAACTGTAAAACATCTG
Found at i:145580 original size:17 final size:17
Alignment explanation
Indices: 145558--145628 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
145548 AATAATTGTA
*
145558 AAACATCTTATAACTGT
1 AAACATCTGATAACTGT
* **
145575 AAACATCTGATAAATAA
1 AAACATCTGATAACTGT
145592 AAATCATCTGATAACTGT
1 AAA-CATCTGATAACTGT
* *
145610 AAATATTTGATAACT-T
1 AAACATCTGATAACTGT
145626 AAA
1 AAA
145629 ATCATATGAA
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
16 4 0.09
17 26 0.59
18 14 0.32
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.32
Consensus pattern (17 bp):
AAACATCTGATAACTGT
Found at i:145600 original size:35 final size:35
Alignment explanation
Indices: 145557--145647 Score: 103
Period size: 35 Copynumber: 2.6 Consensus size: 35
145547 TAATAATTGT
*
145557 AAAA-CATCTTATAACTGTAAACATCTGATAAATA
1 AAAATCATCTGATAACTGTAAACATCTGATAAATA
* * * *
145591 AAAATCATCTGATAACTGTAAATATTTGATAACTT
1 AAAATCATCTGATAACTGTAAACATCTGATAAATA
* * *
145626 AAAATCATATGAAAATTGTAAA
1 AAAATCATCTGATAACTGTAAA
145648 TATTTAGAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
34 4 0.08
35 44 0.92
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (35 bp):
AAAATCATCTGATAACTGTAAACATCTGATAAATA
Found at i:145648 original size:35 final size:35
Alignment explanation
Indices: 145569--145652 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 35
145559 AACATCTTAT
* * * *
145569 AACTGTAAACATCTGATAAATAAAAATCATCTGAT
1 AACTGTAAATATTTGATAAATAAAAATCATATGAA
* *
145604 AACTGTAAATATTTGATAACTTAAAATCATATGAA
1 AACTGTAAATATTTGATAAATAAAAATCATATGAA
*
145639 AATTGTAAATATTT
1 AACTGTAAATATTT
145653 AGAATTCATC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.35
Consensus pattern (35 bp):
AACTGTAAATATTTGATAAATAAAAATCATATGAA
Found at i:154009 original size:14 final size:15
Alignment explanation
Indices: 153984--154012 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
153974 ATCAGGATCT
153984 ACAAACAAAACAACA
1 ACAAACAAAACAACA
153999 ACAAA-AAAACAACA
1 ACAAACAAAACAACA
154013 GCATGCATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (15 bp):
ACAAACAAAACAACA
Found at i:154567 original size:2 final size:2
Alignment explanation
Indices: 154560--154585 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
154550 TATATTTCTA
154560 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
154586 CCATACCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:154883 original size:15 final size:15
Alignment explanation
Indices: 154863--154891 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
154853 CCGGTCCGAA
154863 CATGTACATCTCTAC
1 CATGTACATCTCTAC
154878 CATGTACATCTCTA
1 CATGTACATCTCTA
154892 TTTAAAAGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.31, G:0.07, T:0.34
Consensus pattern (15 bp):
CATGTACATCTCTAC
Found at i:155776 original size:37 final size:37
Alignment explanation
Indices: 155673--155783 Score: 102
Period size: 38 Copynumber: 3.0 Consensus size: 37
155663 AAGTTTAAAT
*
155673 AAATTTAGAATGTTAAT-GTGAAATAATTTAAGAAATTA
1 AAATTTAGAATGCT-ATGGTGAAATAATTTAAG-AATTA
** *
155711 AAATTTAGAATGCTATGGTGGTACAATTTAAGAATTA
1 AAATTTAGAATGCTATGGTGAAATAATTTAAGAATTA
* * *
155748 GGAATTTTGAATG-TA-GAGTGAAATAATTTGAGAATT
1 -AAATTTAGAATGCTATG-GTGAAATAATTTAAGAATT
155784 CTAAATAAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
36 1 0.02
37 24 0.40
38 35 0.58
ACGTcount: A:0.43, C:0.02, G:0.19, T:0.36
Consensus pattern (37 bp):
AAATTTAGAATGCTATGGTGAAATAATTTAAGAATTA
Done.