Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007031.1 Hibiscus syriacus cultivar Beakdansim tig00018199_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: 103797
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:163 original size:26 final size:26
Alignment explanation
Indices: 142--203 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 26
132 ATAGTAAATT
142 ATATTA-ATTATTTATTAAAGTAATA
1 ATATTATATTATTTATTAAAGTAATA
* * *
167 ATGTTATATTATTTATTAGAAATATTA
1 ATATTATATTATTTATTA-AAGTAATA
*
194 ATAATATATT
1 ATATTATATT
204 TTAAATAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 5 0.17
26 11 0.37
27 14 0.47
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (26 bp):
ATATTATATTATTTATTAAAGTAATA
Found at i:268 original size:24 final size:24
Alignment explanation
Indices: 222--268 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
212 TTTAATAATT
*
222 AATATTTGATTAAAATGATATTAA
1 AATATTTGATTAAAATGAAATTAA
* * *
246 AATATTTTATTAATATTAAATTA
1 AATATTTGATTAAAATGAAATTA
269 TAAAATAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (24 bp):
AATATTTGATTAAAATGAAATTAA
Found at i:8070 original size:112 final size:110
Alignment explanation
Indices: 7871--8092 Score: 277
Period size: 112 Copynumber: 2.0 Consensus size: 110
7861 CGATTCTCCT
* * * *
7871 ATGTAAGATTAGTTTTCGCAAACAATACTTTCGCATAACCTCTTTGTAGTAGAACCCTGAAAGAA
1 ATGTAAGATTAGTTTTCACAAACAATACTTTCACAGAACCTCTTTATAGTAGAACCCTGAAAGAA
* * *
7936 CATCTCTAGAGGTAGGACCTCAAACTCCTGACACT-CTTTGAGGAG
66 CAACTCTAGAAGTAGGACCTCAAACGCCTGACACTGC-TTGAGGAG
* * **
7981 ATGTAAGATTAGTTTTCACTTAACAATACTTTTACAGAATTTCTTTATAGTAGAAACCCTGAAAG
1 ATGTAAGATTAGTTTTCAC-AAACAATACTTTCACAGAACCTCTTTATAGTAG-AACCCTGAAAG
* *
8046 AACAACT-TTGAAAGTAGGATCTCAAACGCCTGACACTGCTTGAGGAG
64 AACAACTCTAG-AAGTAGGACCTCAAACGCCTGACACTGCTTGAGGAG
8093 TGGTGATTTC
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
110 18 0.19
111 28 0.29
112 48 0.51
113 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (110 bp):
ATGTAAGATTAGTTTTCACAAACAATACTTTCACAGAACCTCTTTATAGTAGAACCCTGAAAGAA
CAACTCTAGAAGTAGGACCTCAAACGCCTGACACTGCTTGAGGAG
Found at i:10171 original size:106 final size:106
Alignment explanation
Indices: 9986--10194 Score: 355
Period size: 106 Copynumber: 2.0 Consensus size: 106
9976 GTTGAAAACC
*
9986 TTTGGAATCCTTGTAGGCCATGTTTTACAAGCTTCTCTTCCATCTTTGAATAGAGATGGAGAATA
1 TTTGGAATCCTTGTAGGCCATGTTTTACAAGCTTCTCTTCCATCATTGAATAGAGATGGAGAATA
*
10051 AAAGAAGTTCAAATTTATTTTAACTTTTGGGTTTTTTTTTT
66 AAAGAAGTTCAAATTTATTTTAACTTTTGGGATTTTTTTTT
* * * *
10092 TTTGGAATCTTTGTAGGCCATGTTTTAGAAGCTTCTCTTTCATCATTGAATATAGATGGAGAATA
1 TTTGGAATCCTTGTAGGCCATGTTTTACAAGCTTCTCTTCCATCATTGAATAGAGATGGAGAATA
*
10157 AAAGAAGTTCAAATTTATTTTAGCTTTTGGGATTTTTT
66 AAAGAAGTTCAAATTTATTTTAACTTTTGGGATTTTTT
10195 CCCAATAGGC
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 96 1.00
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.44
Consensus pattern (106 bp):
TTTGGAATCCTTGTAGGCCATGTTTTACAAGCTTCTCTTCCATCATTGAATAGAGATGGAGAATA
AAAGAAGTTCAAATTTATTTTAACTTTTGGGATTTTTTTTT
Found at i:14668 original size:43 final size:43
Alignment explanation
Indices: 14579--14669 Score: 98
Period size: 43 Copynumber: 2.2 Consensus size: 43
14569 TAAGATCTCA
* * * * *
14579 CATA-TTTATAATCATTTTTATATTTTAAATACTTAAAATAAT
1 CATATTTTATAATAATTTTTACATTTTAAACAATCAAAATAAT
*
14621 -ATATTTTATAATAATTTATTACATTTTGAACAATCAAAA-AAT
1 CATATTTTATAATAATTT-TTACATTTTAAACAATCAAAATAAT
14663 CATATTT
1 CATATTT
14670 GGAAAATCTT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
41 3 0.08
42 15 0.38
43 22 0.55
ACGTcount: A:0.44, C:0.08, G:0.01, T:0.47
Consensus pattern (43 bp):
CATATTTTATAATAATTTTTACATTTTAAACAATCAAAATAAT
Found at i:14909 original size:2 final size:2
Alignment explanation
Indices: 14904--14945 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
14894 TTAAAAAGTA
14904 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
14946 GTTATCCTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15452 original size:2 final size:2
Alignment explanation
Indices: 15445--15481 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
15435 CTAATTAAGC
15445 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15482 AAAGGGTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18878 original size:59 final size:59
Alignment explanation
Indices: 18810--18932 Score: 228
Period size: 59 Copynumber: 2.1 Consensus size: 59
18800 AGTCGAAGGA
18810 GCTGGAGTATGAAATTAATGATACTTTGAATAAAGTAATGTGAGCATATATTCCATGGT
1 GCTGGAGTATGAAATTAATGATACTTTGAATAAAGTAATGTGAGCATATATTCCATGGT
* *
18869 GCTGGAGTATGAAATTAATGATACTTTGAATAAAGTAGTGTGAGCATATATTCCATGTT
1 GCTGGAGTATGAAATTAATGATACTTTGAATAAAGTAATGTGAGCATATATTCCATGGT
18928 GCTGG
1 GCTGG
18933 TGGCCACTCT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.34
Consensus pattern (59 bp):
GCTGGAGTATGAAATTAATGATACTTTGAATAAAGTAATGTGAGCATATATTCCATGGT
Found at i:25530 original size:6 final size:6
Alignment explanation
Indices: 25519--25553 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
25509 GCAAAGATGA
* *
25519 TATATC TATATC TATATC TATATA TATATA TATAT
1 TATATC TATATC TATATC TATATC TATATC TATAT
25554 ACATGCTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (6 bp):
TATATC
Found at i:28146 original size:17 final size:17
Alignment explanation
Indices: 28126--28161 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
28116 CTAAATGTCG
*
28126 AAAATTATAAAATATAA
1 AAAAATATAAAATATAA
28143 AAAAATATAAAATATAA
1 AAAAATATAAAATATAA
28160 AA
1 AA
28162 TTATTTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
AAAAATATAAAATATAA
Found at i:28299 original size:18 final size:18
Alignment explanation
Indices: 28259--28299 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
28249 ATTTGAGTAA
28259 CAAAAAATCTACTTTAAT
1 CAAAAAATCTACTTTAAT
*
28277 AAAAAAAT-TACTTTCAAT
1 CAAAAAATCTACTTT-AAT
28295 CAAAA
1 CAAAA
28300 GTTAACATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (18 bp):
CAAAAAATCTACTTTAAT
Found at i:31073 original size:19 final size:20
Alignment explanation
Indices: 31035--31070 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31025 TTTACGTTAC
31035 GGTTTAAGATTTAGATTTAG
1 GGTTTAAGATTTAGATTTAG
31055 GGTTTAA-ATTTA-ATTT
1 GGTTTAAGATTTAGATTT
31071 TAGAGATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.25
19 5 0.31
20 7 0.44
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (20 bp):
GGTTTAAGATTTAGATTTAG
Found at i:32349 original size:26 final size:26
Alignment explanation
Indices: 32318--32371 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
32308 TAAAATAACT
32318 CAAATCCATTATAAACGTAGAGATTA
1 CAAATCCATTATAAACGTAGAGATTA
32344 CAAATCCATTATAAACGTAGAGATTA
1 CAAATCCATTATAAACGTAGAGATTA
32370 CA
1 CA
32372 GATAATACGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (26 bp):
CAAATCCATTATAAACGTAGAGATTA
Found at i:35380 original size:19 final size:19
Alignment explanation
Indices: 35373--35420 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
35363 CTGGAAGCTG
35373 TTGAGGCGGCTGGAAACCA
1 TTGAGGCGGCTGGAAACCA
35392 TTGAGGCGGCTGGAAACCA
1 TTGAGGCGGCTGGAAACCA
35411 TTGAGGCGGC
1 TTGAGGCGGC
35421 GGCATGTGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.23, C:0.21, G:0.40, T:0.17
Consensus pattern (19 bp):
TTGAGGCGGCTGGAAACCA
Found at i:35550 original size:3 final size:3
Alignment explanation
Indices: 35542--35613 Score: 72
Period size: 3 Copynumber: 24.0 Consensus size: 3
35532 TTAATGTATT
* * * * *
35542 TAA TAA TAA TAA TTA TAA TAA TAA TAT TAT TTA TAA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
35590 TAT TTA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
35614 ATAAATTAAT
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (3 bp):
TAA
Found at i:35551 original size:15 final size:14
Alignment explanation
Indices: 35533--35596 Score: 53
Period size: 15 Copynumber: 4.5 Consensus size: 14
35523 TTATAATATT
35533 TAATGTATTTAATAA
1 TAAT-TATTTAATAA
*
35548 TAATAATTATAATAA
1 TAATTATT-TAATAA
35563 TAATATTATTT-ATAA
1 T-A-ATTATTTAATAA
35578 TAATTA--TAATAA
1 TAATTATTTAATAA
*
35590 TATTTAT
1 TAATTAT
35597 AATTATAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
11 1 0.02
12 9 0.22
13 4 0.10
14 4 0.10
15 16 0.39
16 2 0.05
17 5 0.12
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
TAATTATTTAATAA
Found at i:35554 original size:18 final size:16
Alignment explanation
Indices: 35518--35581 Score: 69
Period size: 15 Copynumber: 3.9 Consensus size: 16
35508 AATTTTTATT
*
35518 ATTATTTATAATATTTA
1 ATTATTTATAATA-ATA
35535 ATGTATTTAATAATAATA
1 AT-TATTT-ATAATAATA
*
35553 ATTA-TAATAATAAT-
1 ATTATTTATAATAATA
35567 ATTATTTATAATAAT
1 ATTATTTATAATAAT
35582 TATAATAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
14 4 0.10
15 17 0.41
16 1 0.02
17 4 0.10
18 9 0.22
19 6 0.15
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
ATTATTTATAATAATA
Found at i:35580 original size:21 final size:21
Alignment explanation
Indices: 35542--35612 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
35532 TTAATGTATT
*
35542 TAATAATAATAATTATAATAA
1 TAATAATAATATTTATAATAA
35563 TAAT-AT--TATTTATAATAA
1 TAATAATAATATTTATAATAA
* *
35581 TTATAATAATATTTATAATTA
1 TAATAATAATATTTATAATAA
35602 TAATAATAATA
1 TAATAATAATA
35613 AATAAATTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
18 14 0.33
19 2 0.05
20 2 0.05
21 25 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TAATAATAATATTTATAATAA
Found at i:46362 original size:3 final size:3
Alignment explanation
Indices: 46356--46388 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
46346 ATTTCTTTCT
*
46356 TTC TTC TTC TTC TAC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
46389 AACAACAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:49476 original size:67 final size:67
Alignment explanation
Indices: 49368--49503 Score: 272
Period size: 67 Copynumber: 2.0 Consensus size: 67
49358 ACACATTTTA
49368 TATATGTTATTTGCATATTCTCTCAATTTAATCATACTTTTAATAAATTAAAATAGATTTAATCC
1 TATATGTTATTTGCATATTCTCTCAATTTAATCATACTTTTAATAAATTAAAATAGATTTAATCC
49433 TC
66 TC
49435 TATATGTTATTTGCATATTCTCTCAATTTAATCATACTTTTAATAAATTAAAATAGATTTAATCC
1 TATATGTTATTTGCATATTCTCTCAATTTAATCATACTTTTAATAAATTAAAATAGATTTAATCC
49500 TC
66 TC
49502 TA
1 TA
49504 ATTGAATGAT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 69 1.00
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.46
Consensus pattern (67 bp):
TATATGTTATTTGCATATTCTCTCAATTTAATCATACTTTTAATAAATTAAAATAGATTTAATCC
TC
Found at i:49731 original size:27 final size:28
Alignment explanation
Indices: 49695--49769 Score: 72
Period size: 25 Copynumber: 2.9 Consensus size: 28
49685 ATCTTAAAAA
* *
49695 ATATTTT-TATATTAACTT-A-TTAAAT
1 ATATTTTATTTATTAACTTAATTTAAAC
*
49720 GTATTTTA-TTATTAACTTAATTTAAAC
1 ATATTTTATTTATTAACTTAATTTAAAC
*
49747 ATATTTTATTT-TT-ATTTAATTTA
1 ATATTTTATTTATTAACTTAATTTA
49770 TATATATATA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
25 15 0.37
26 10 0.24
27 14 0.34
28 2 0.05
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (28 bp):
ATATTTTATTTATTAACTTAATTTAAAC
Found at i:49776 original size:26 final size:27
Alignment explanation
Indices: 49699--49769 Score: 78
Period size: 27 Copynumber: 2.8 Consensus size: 27
49689 TAAAAAATAT
**
49699 TTTTA-TATTAACTT-A-TTAAATGTA
1 TTTTATTATTAACTTAATTTAAACATA
49723 TTTTATTATTAACTTAATTTAAACATA
1 TTTTATTATTAACTTAATTTAAACATA
* *
49750 TTTTATT-TTTATTTAATTTA
1 TTTTATTATTAACTTAATTTA
49770 TATATATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.12
25 9 0.22
26 12 0.30
27 14 0.35
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.59
Consensus pattern (27 bp):
TTTTATTATTAACTTAATTTAAACATA
Found at i:49946 original size:32 final size:32
Alignment explanation
Indices: 49858--49977 Score: 110
Period size: 31 Copynumber: 3.9 Consensus size: 32
49848 ATATATTTAG
* *
49858 TAAATTAAG-ATAAAATATATACTTTAAAAAGT
1 TAAACTAAGAATAAAATATATA-TTTTAAAAGT
* *
49890 TAAACAAATAATAAAATATA-ATTTTAAAAGTT
1 TAAACTAAGAATAAAATATATATTTTAAAAG-T
* *
49922 TAGA-TAAGAATAAAATATATATTTTAAAA-A
1 TAAACTAAGAATAAAATATATATTTTAAAAGT
*
49952 TAAAATAA-AATAAAATAT-T-TTTTAAA
1 TAAACTAAGAATAAAATATATATTTTAAA
49978 TTAAGTTAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 12
0.78 0.09 0.12
Matches are distributed among these distances:
28 7 0.09
29 1 0.01
30 13 0.17
31 24 0.32
32 20 0.27
33 10 0.13
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (32 bp):
TAAACTAAGAATAAAATATATATTTTAAAAGT
Found at i:50007 original size:25 final size:28
Alignment explanation
Indices: 49896--50024 Score: 88
Period size: 31 Copynumber: 4.5 Consensus size: 28
49886 AAGTTAAACA
* * *
49896 AATAATAAAATATAATTTTAAAAGTTTAGAT
1 AATAATAAAATAT--TTTTTAAA-TTAAGTT
* * **
49927 AAGAATAAAATATATATTTTAAAAATAAAAT
1 AATAATAAAATAT-T-TTTT-AAATTAAGTT
49958 AA-AATAAAATATTTTTTAAATTAAGTT
1 AATAATAAAATATTTTTTAAATTAAGTT
*
49985 AATAATAAATTA-TTTTT-AA-TAAGTT
1 AATAATAAAATATTTTTTAAATTAAGTT
50010 AAT-ATAAAAATATTT
1 AATAAT-AAAATATTT
50025 CCTAAAGTTA
Statistics
Matches: 83, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
24 2 0.02
25 14 0.17
26 4 0.05
27 14 0.17
28 12 0.14
29 1 0.01
30 12 0.14
31 21 0.25
32 3 0.04
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (28 bp):
AATAATAAAATATTTTTTAAATTAAGTT
Found at i:50044 original size:25 final size:26
Alignment explanation
Indices: 49961--50048 Score: 85
Period size: 25 Copynumber: 3.4 Consensus size: 26
49951 ATAAAATAAA
*
49961 ATAAAATATTTTTTAAATTAAGTTAATA-
1 ATAAAATA-TTTCT-AA-TAAGTTAATAT
* *
49989 ATAAATTATTTTTAATAAGTTAATAT
1 ATAAAATATTTCTAATAAGTTAATAT
50015 A-AAAATATTTCCT-A-AAGTTAATAT
1 ATAAAATATTT-CTAATAAGTTAATAT
50039 ATAAAATATT
1 ATAAAATATT
50049 ATAAATTTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
24 11 0.20
25 27 0.50
26 4 0.07
27 5 0.09
28 7 0.13
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.44
Consensus pattern (26 bp):
ATAAAATATTTCTAATAAGTTAATAT
Found at i:50058 original size:23 final size:23
Alignment explanation
Indices: 50008--50090 Score: 59
Period size: 23 Copynumber: 3.7 Consensus size: 23
49998 TTTTAATAAG
* *
50008 TTAATATA-AAAATATTTCCTAAAG
1 TTAATATATAAAATA-TT-ATAAAT
50032 TTAATATATAAAATATTATAAAT
1 TTAATATATAAAATATTATAAAT
* *
50055 TTAA-GT-T-AAATATTA-ATAT
1 TTAATATATAAAATATTATAAAT
*
50074 ACTAATATATAAAATAT
1 -TTAATATATAAAATAT
50091 ATGCATCATG
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
19 3 0.06
20 11 0.23
21 2 0.04
22 2 0.04
23 14 0.29
24 10 0.21
25 6 0.12
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (23 bp):
TTAATATATAAAATATTATAAAT
Found at i:51028 original size:27 final size:28
Alignment explanation
Indices: 50989--51087 Score: 119
Period size: 27 Copynumber: 3.5 Consensus size: 28
50979 AAAAATTAAG
*
50989 ATAATAATAAAATATATTTTTATTGAAA
1 ATAAGAATAAAATATATTTTTATTGAAA
* * * *
51017 ATAAGAAT-AAATATAGTTTAAGTGAAG
1 ATAAGAATAAAATATATTTTTATTGAAA
*
51044 ATAAGAATAAAATATATTTTTATATTAAA
1 ATAAGAATAAAATATATTTTTAT-TGAAA
*
51073 ATAAAAATAAAATAT
1 ATAAGAATAAAATAT
51088 TTAAATATAT
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
27 23 0.40
28 18 0.31
29 17 0.29
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (28 bp):
ATAAGAATAAAATATATTTTTATTGAAA
Found at i:51053 original size:55 final size:54
Alignment explanation
Indices: 50986--51091 Score: 160
Period size: 55 Copynumber: 1.9 Consensus size: 54
50976 TTTAAAAATT
* *
50986 AAGATAATAATAAAATATATTTTTAT-TGAAAATAAGAATAAATATAGTTTAAGTG
1 AAGATAAGAATAAAATATATTTTTATATGAAAATAAAAATAAA-ATA-TTTAAGTG
*
51041 AAGATAAGAATAAAATATATTTTTATATTAAAATAAAAATAAAATATTTAA
1 AAGATAAGAATAAAATATATTTTTATATGAAAATAAAAATAAAATATTTAA
51092 ATATATTTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
54 5 0.11
55 28 0.60
56 14 0.30
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.36
Consensus pattern (54 bp):
AAGATAAGAATAAAATATATTTTTATATGAAAATAAAAATAAAATATTTAAGTG
Found at i:51095 original size:27 final size:27
Alignment explanation
Indices: 50971--51091 Score: 86
Period size: 28 Copynumber: 4.4 Consensus size: 27
50961 ATATATATAT
* * *
50971 ATATATTTAAAAATTAAGATAATAATAAA
1 ATATATTT-AATATTAAAATAAGAAT-AA
*
51000 ATATATTT-TTATTGAAAATAAGAATAA
1 ATATATTTAATATT-AAAATAAGAATAA
* * *
51027 ATATAGTTTAA-GTGAAGATAAGAATAAA
1 ATATA-TTTAATATTAAAATAAGAAT-AA
* *
51055 ATATATTTTTATATTAAAATAAAAATAA
1 ATATA-TTTAATATTAAAATAAGAATAA
51083 A-ATATTTAA
1 ATATATTTAA
51092 ATATATTTTA
Statistics
Matches: 72, Mismatches: 15, Indels: 13
0.72 0.15 0.13
Matches are distributed among these distances:
26 4 0.06
27 23 0.32
28 27 0.38
29 18 0.25
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (27 bp):
ATATATTTAATATTAAAATAAGAATAA
Found at i:51855 original size:20 final size:20
Alignment explanation
Indices: 51818--51859 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
51808 ATTTAAATTT
*
51818 ATTATAAAATAAAGGATCAA
1 ATTATAAAATAAAAGATCAA
51838 ATTA-AAAATAGAAAGATCAA
1 ATTATAAAATA-AAAGATCAA
51858 AT
1 AT
51860 GTCAAATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.24
Consensus pattern (20 bp):
ATTATAAAATAAAAGATCAA
Found at i:61754 original size:22 final size:22
Alignment explanation
Indices: 61727--61790 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
61717 ATGTTACAGG
61727 TTTAATGCAAGAGTTACAAAGC
1 TTTAATGCAAGAGTTACAAAGC
* *
61749 TTTAATGCAAGAGTTACATAGT
1 TTTAATGCAAGAGTTACAAAGC
* *
61771 TTTATTGCATGAGTTACAAA
1 TTTAATGCAAGAGTTACAAA
61791 CTGCTTGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (22 bp):
TTTAATGCAAGAGTTACAAAGC
Found at i:80196 original size:20 final size:20
Alignment explanation
Indices: 80160--80212 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
80150 TAATACAAAA
* *
80160 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
*
80180 TCGTAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
80200 TCGCAACGCGATT
1 TCGCAACGCGATT
80213 TACATAGCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:80845 original size:14 final size:14
Alignment explanation
Indices: 80826--80882 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
80816 TTTCATTTCG
80826 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
80840 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
80857 CGCATTGCGATTCCCT
1 CG--TTGCGATTCTCT
80873 CGTTGCGATT
1 CGTTGCGATT
80883 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 7 0.20
19 6 0.17
ACGTcount: A:0.11, C:0.26, G:0.21, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:80856 original size:33 final size:33
Alignment explanation
Indices: 80809--80967 Score: 230
Period size: 33 Copynumber: 4.8 Consensus size: 33
80799 CAAAATCGCA
* *
80809 TTGCAATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
80842 TTGCGATTTTCATTTCGCATTGCGATTCCCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* **
80875 TTGCGATTTTCATTTCGCATTGCGAAAT-TAGCG
1 TTGCGATTTTCATTTCGCATTGCG-ATTCTCTCG
*
80908 TTGCGATTTTTCATTTCGTATTGCGATTCTCTCG
1 TTGCGA-TTTTCATTTCGCATTGCGATTCTCTCG
80942 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
80968 AGTAATTTCC
Statistics
Matches: 111, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
33 83 0.75
34 28 0.25
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:80947 original size:67 final size:67
Alignment explanation
Indices: 80809--80966 Score: 230
Period size: 67 Copynumber: 2.4 Consensus size: 67
80799 CAAAATCGCA
* * * **
80809 TTGCAATTTTCATTTCGCGTTGCG-ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 TTGCGATTTTCATTTCGCATTGCGAAATCTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCT
80873 CG
66 CG
* *
80875 TTGCGATTTTCATTTCGCATTGCGAAAT-TAGCGTTGCGATTTTTCATTTCGTATTGCGATTCTC
1 TTGCGATTTTCATTTCGCATTGCGAAATCTAGCGTTGCGA-TTTTCATTTCGCATTGCGATTCCC
80939 TCG
65 TCG
80942 TTGCGATTTTCATTTCGCATTGCGA
1 TTGCGATTTTCATTTCGCATTGCGA
80967 TAGTAATTTC
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
66 31 0.37
67 52 0.63
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (67 bp):
TTGCGATTTTCATTTCGCATTGCGAAATCTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCT
CG
Found at i:83274 original size:12 final size:12
Alignment explanation
Indices: 83257--83281 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
83247 TCTTCGGGGA
83257 CTTTTTCTTCTT
1 CTTTTTCTTCTT
83269 CTTTTTCTTCTT
1 CTTTTTCTTCTT
83281 C
1 C
83282 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:83490 original size:24 final size:24
Alignment explanation
Indices: 83456--83509 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
83446 CTGAAACATC
*
83456 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
83480 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
83504 ATCAAA
1 ATCAAA
83510 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:84279 original size:20 final size:20
Alignment explanation
Indices: 84254--84304 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
84244 TGTATTATCT
84254 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
84274 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
84294 CGTTGCGAAAG
1 CGTTGCGAAAG
84305 GCAATCATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.20, G:0.31, T:0.20
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:84555 original size:19 final size:20
Alignment explanation
Indices: 84517--84566 Score: 93
Period size: 19 Copynumber: 2.5 Consensus size: 20
84507 ATTCATTTGA
84517 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
84537 CTATCGCAACGCG-AAATGG
1 CTATCGCAACGCGAAAATGG
84556 CTATCGCAACG
1 CTATCGCAACG
84567 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.32, C:0.28, G:0.24, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:84633 original size:19 final size:19
Alignment explanation
Indices: 84611--84656 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
84601 GATTTTCTCG
84611 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
84630 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
84649 TTGCGATT
1 TTGCGATT
84657 CTCTCGTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:84687 original size:20 final size:20
Alignment explanation
Indices: 84662--84700 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
84652 CGATTCTCTC
84662 GTTGCGATAGTCAGTTTTGT
1 GTTGCGATAGTCAGTTTTGT
*
84682 GTTGCGATAGTCTGTTTTG
1 GTTGCGATAGTCAGTTTTG
84701 CCTTCAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.31, T:0.46
Consensus pattern (20 bp):
GTTGCGATAGTCAGTTTTGT
Found at i:86709 original size:19 final size:20
Alignment explanation
Indices: 86655--86721 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
86645 TAGTTTACTT
* *
86655 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
86675 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
86695 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
86714 TCGCAACG
1 TCGCAACG
86722 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:86729 original size:14 final size:14
Alignment explanation
Indices: 86710--86767 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
86700 ATGCGAAATG
86710 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
86724 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
86740 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
86756 AAAATCGCAACG
1 AAAATCGCAACG
86768 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:86752 original size:32 final size:33
Alignment explanation
Indices: 86694--86772 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
86684 GGAAATGGCT
86694 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
86727 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
86759 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
86773 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 29 0.64
33 16 0.36
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:86820 original size:14 final size:14
Alignment explanation
Indices: 86801--86858 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
86791 TTTCATTTCG
86801 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
86815 CGTTGCGATTTTATTT
1 CGTTGCGA-TTT-TGT
86831 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
86847 CGTTGCGATTTT
1 CGTTGCGATTTT
86859 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 8 0.21
17 3 0.08
18 6 0.16
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:86839 original size:32 final size:33
Alignment explanation
Indices: 86784--86874 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
86774 ACAAATCGCA
*
86784 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
86817 TTGCGATTTT-ATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
86849 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
86875 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:86893 original size:20 final size:19
Alignment explanation
Indices: 86859--86913 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
86849 TTGCGATTTT
*
86859 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
86878 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
86898 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
86914 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:87421 original size:18 final size:18
Alignment explanation
Indices: 87395--87439 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
87385 GTCGATCAAA
*
87395 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
87413 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
87431 TGATGGCTC
1 TGATGGCTC
87440 CCGAATTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:88783 original size:20 final size:20
Alignment explanation
Indices: 88758--88831 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
88748 AATAGTTTCT
*
88758 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACGC
**
88778 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
** **
88798 GAATTTGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
*
88818 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
88832 GTTGCGATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 6 0.13
20 39 0.87
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACGC
Found at i:89337 original size:41 final size:41
Alignment explanation
Indices: 89274--89371 Score: 133
Period size: 41 Copynumber: 2.4 Consensus size: 41
89264 CGCTTTGAAA
* *
89274 ATCGCATTGCGATTATGTATTATCACGTTACGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCACATTACGAAAGTCAGT
* * * * *
89315 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCACATTACGAAAGTCAGT
89356 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
89372 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.39
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCACATTACGAAAGTCAGT
Found at i:90100 original size:30 final size:31
Alignment explanation
Indices: 90041--90130 Score: 112
Period size: 29 Copynumber: 3.0 Consensus size: 31
90031 TAATTTCTTA
* * *
90041 AAATTTAATGATTGTTTTATAATAATTAATT
1 AAATTTAATGATTATTTTATGATATTTAATT
* * *
90072 AATTTTAGTGATTATTTTAT-ATTTTTAA-T
1 AAATTTAATGATTATTTTATGATATTTAATT
90101 AAATTTAATGATTATTTTATGATATTTAAT
1 AAATTTAATGATTATTTTATGATATTTAAT
90131 AGGGTAAATT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 19 0.39
30 13 0.27
31 17 0.35
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (31 bp):
AAATTTAATGATTATTTTATGATATTTAATT
Found at i:90127 original size:21 final size:20
Alignment explanation
Indices: 90043--90131 Score: 58
Period size: 21 Copynumber: 4.4 Consensus size: 20
90033 ATTTCTTAAA
* *
90043 ATTTAATGATTGTTTTATAAT
1 ATTTAAT-ATTATTTTATGAT
* *
90064 AATTAAT-TAATTTTAGTGATT
1 ATTTAATATTATTTTA-TGA-T
* * *
90085 ATTTTATATT-TTTAAT-AA
1 ATTTAATATTATTTTATGAT
90103 ATTTAATGATTATTTTATGAT
1 ATTTAAT-ATTATTTTATGAT
90124 ATTTAATA
1 ATTTAATA
90132 GGGTAAATTA
Statistics
Matches: 50, Mismatches: 12, Indels: 13
0.67 0.16 0.17
Matches are distributed among these distances:
18 6 0.12
19 10 0.20
20 9 0.18
21 24 0.48
22 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (20 bp):
ATTTAATATTATTTTATGAT
Found at i:102884 original size:24 final size:25
Alignment explanation
Indices: 102847--102893 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
102837 CTATTCTTTC
102847 ACTTCAATCAAGC-TCAAATTTTAG
1 ACTTCAATCAAGCTTCAAATTTTAG
** *
102871 ACTTCAATTGAGCTTCTAATTTT
1 ACTTCAATCAAGCTTCAAATTTT
102894 TTTAGTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (25 bp):
ACTTCAATCAAGCTTCAAATTTTAG
Done.