Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016406.1 Corchorus capsularis cultivar CVL-1 contig16427, 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: 70478
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:97 original size:32 final size:32
Alignment explanation
Indices: 60--154 Score: 80
Period size: 32 Copynumber: 3.2 Consensus size: 32
50 TTTACACCAA
60 ATTAATTGGGACTTGTACAATAGACCAGAAGG
1 ATTAATTGGGACTTGTACAATAGACCAGAAGG
** * * *
92 ATTAA-T-ACAATAT-TGC-ATACACC--AA--
1 ATTAATTGGGACT-TGTACAATAGACCAGAAGG
117 ATTAATTGGGACTTGTACAATAGACCAGAAGG
1 ATTAATTGGGACTTGTACAATAGACCAGAAGG
149 ATTAAT
1 ATTAAT
155 ACAATATTGC
Statistics
Matches: 44, Mismatches: 10, Indels: 18
0.61 0.14 0.25
Matches are distributed among these distances:
25 5 0.11
26 2 0.05
27 6 0.14
28 6 0.14
29 6 0.14
30 6 0.14
31 2 0.05
32 11 0.25
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (32 bp):
ATTAATTGGGACTTGTACAATAGACCAGAAGG
Found at i:140 original size:57 final size:57
Alignment explanation
Indices: 52--166 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
42 AACGCGACTT
52 TACACCAAATTAATTGGGACTTGTACAATAGACCAGAAGGATTAATACAATATTGCA
1 TACACCAAATTAATTGGGACTTGTACAATAGACCAGAAGGATTAATACAATATTGCA
109 TACACCAAATTAATTGGGACTTGTACAATAGACCAGAAGGATTAATACAATATTGCA
1 TACACCAAATTAATTGGGACTTGTACAATAGACCAGAAGGATTAATACAATATTGCA
166 T
1 T
167 CTAATAACTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.27
Consensus pattern (57 bp):
TACACCAAATTAATTGGGACTTGTACAATAGACCAGAAGGATTAATACAATATTGCA
Found at i:1266 original size:15 final size:15
Alignment explanation
Indices: 1248--1287 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
1238 TATTTGCACC
*
1248 ATATATAATATTTAT
1 ATATATAATATTAAT
1263 ATATATAATATTAAT
1 ATATATAATATTAAT
1278 A-ATATAATAT
1 ATATATAATAT
1288 ATATTAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 9 0.38
15 15 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATAATATTAAT
Found at i:3476 original size:24 final size:24
Alignment explanation
Indices: 3449--3494 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3439 TATAAATAAA
*
3449 TTATTATACATTAAAACTAAAAAC
1 TTATTATAAATTAAAACTAAAAAC
* *
3473 TTATTGTAAATTAAAATTAAAA
1 TTATTATAAATTAAAACTAAAA
3495 TTATTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (24 bp):
TTATTATAAATTAAAACTAAAAAC
Found at i:5409 original size:49 final size:47
Alignment explanation
Indices: 5057--5439 Score: 264
Period size: 48 Copynumber: 7.8 Consensus size: 47
5047 AAAGTGAACT
* * * ** *
5057 TGCCTTTCGTCCGGAAAGGGCATTTTAAGAAAACGCGAGTAAAACT-AA
1 TGCCTTCCGTCCGGGAAGGGCATTTT-GGAAAAAACAAGTAAAA-TAAA
* * ** * * *
5105 CGCCTTCCATCCGGGAAGGGTGTTTTAGGAAAAAAGCAAGTGGAAATTAG
1 TGCCTTCCGTCCGGGAAGGGCATTTT-GGAAAAAA-CAAGT-AAAATAAA
* * * *** *
5155 TTCCTTCCATCCGGGAAGGGCACTTTGGGAAAAAGTGAGTAAAAATAAC
1 TGCCTTCCGTCCGGGAAGGGCA-TTTTGGAAAAAACAAGT-AAAATAAA
* * * * *
5204 CGTCTTCCGTCCGGGAAGGGTATTTTTGAAAAAAAAATAGCAAGTAAAATAAG
1 TGCCTTCCGTCCGGGAAGGGCA-TTTTG---GAAAAA-A-CAAGTAAAATAAA
* * * * *
5257 TGCCTCCCGTCCGGGAAGGGCATTTTGGGAAAAACAAGTAAGGATTAG
1 TGCCTTCCGTCCGGGAAGGGCATTTTGGAAAAAACAAGTAA-AATAAA
* * *
5305 TGCCTTCCATCCGGGAAGGGCGTTTTGGGAAAAACAAGTAAAATCAAA
1 TGCCTTCCGTCCGGGAAGGGCATTTTGGAAAAAACAAGTAAAAT-AAA
* *
5353 TACCTTCCGTCCGGGAAGGGCATTTTGGAAAATAACAGGTAAAATCAAA
1 TGCCTTCCGTCCGGGAAGGGCATTTTGGAAAA-AACAAGTAAAAT-AAA
* *
5402 TGCCTTCCGTCCGGGAAGGGTATTTTGGGAAAAGACAA
1 TGCCTTCCGTCCGGGAAGGGCATTTT-GGAAAAAACAA
5440 AATTTGAGAG
Statistics
Matches: 263, Mismatches: 59, Indels: 25
0.76 0.17 0.07
Matches are distributed among these distances:
47 9 0.03
48 98 0.37
49 80 0.30
50 35 0.13
51 3 0.01
52 10 0.04
53 25 0.10
54 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.22
Consensus pattern (47 bp):
TGCCTTCCGTCCGGGAAGGGCATTTTGGAAAAAACAAGTAAAATAAA
Found at i:8645 original size:20 final size:20
Alignment explanation
Indices: 8616--8664 Score: 80
Period size: 20 Copynumber: 2.4 Consensus size: 20
8606 CAAAGCTACT
*
8616 ACCCAGAAGCCCAAGTTTAA
1 ACCCAAAAGCCCAAGTTTAA
8636 ACCCAAAAGCCCAAGTTTAA
1 ACCCAAAAGCCCAAGTTTAA
8656 AGCCCAAAA
1 A-CCCAAAA
8665 TGATGGCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 20 0.74
21 7 0.26
ACGTcount: A:0.45, C:0.31, G:0.12, T:0.12
Consensus pattern (20 bp):
ACCCAAAAGCCCAAGTTTAA
Found at i:11998 original size:16 final size:16
Alignment explanation
Indices: 11977--12009 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
11967 CAGTGTAATT
11977 AAGAGGTAATTAAGAA
1 AAGAGGTAATTAAGAA
11993 AAGAGGTAATTAAGAA
1 AAGAGGTAATTAAGAA
12009 A
1 A
12010 GTCAAGTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.24, T:0.18
Consensus pattern (16 bp):
AAGAGGTAATTAAGAA
Found at i:12103 original size:70 final size:70
Alignment explanation
Indices: 12024--12476 Score: 726
Period size: 70 Copynumber: 6.5 Consensus size: 70
12014 AGTACAGTTA
12024 AAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTTGGTAATTAAGA
1 AAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTTGGTAATTAAGA
12089 AAAGC
66 AAAGC
* *
12094 AAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACATAGTTAAGGTCTTAATTTGGTAATTAAGA
1 AAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTTGGTAATTAAGA
*
12159 AAAGT
66 AAAGC
12164 AAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTTGGTAATTAAGA
1 AAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTTGGTAATTAAGA
*
12229 AAAGT
66 AAAGC
* * *
12234 AAAGTCTTAATTTAGGGTAATTAAGAAAAGTAAGCAAAGTCCAGGTCTTAATTTGGTAATTAAGA
1 AAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTTGGTAATTAAGA
*
12299 AAAAC
66 AAAGC
* * *
12304 AAAGTCTTAATTCATGGTAATTAAGAAAAGTAAACACAGTCAAGGTCTTAATTTGGTAATTAAGA
1 AAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTTGGTAATTAAGA
12369 AAAGC
66 AAAGC
* * * * * * * *
12374 AAATTCTTAATTCGGGGAAATTAGGAAAAGTAACCACAGTCAAAGTCTTAATTGGGTAATTAAGA
1 AAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTTGGTAATTAAGA
12439 AAAGC
66 AAAGC
*
12444 AAAGTCTTAATTCAGGGTAATTAAGAAGAGTAA
1 AAAGTCTTAATTCAGGGTAATTAAGAAAAGTAA
12477 ACACAGTTAG
Statistics
Matches: 354, Mismatches: 29, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 354 1.00
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.29
Consensus pattern (70 bp):
AAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTTGGTAATTAAGA
AAAGC
Found at i:12116 original size:31 final size:31
Alignment explanation
Indices: 12078--12193 Score: 110
Period size: 31 Copynumber: 3.5 Consensus size: 31
12068 GTCTTAATTT
12078 GGTAATTAAGAAAAGCAAAGTCTTAATTCAG
1 GGTAATTAAGAAAAGCAAAGTCTTAATTCAG
*
12109 GGTAATTAAGAAAAGTAAACATAGTTAAGGTCTTAATT--T
1 GGTAATTAAGAAAAG----C--A---AA-GTCTTAATTCAG
*
12148 GGTAATTAAGAAAAGTAAAGTCTTAATTCAG
1 GGTAATTAAGAAAAGCAAAGTCTTAATTCAG
12179 GGTAATTAAGAAAAG
1 GGTAATTAAGAAAAG
12194 TAAGCATAGT
Statistics
Matches: 70, Mismatches: 3, Indels: 24
0.72 0.03 0.25
Matches are distributed among these distances:
29 9 0.13
30 2 0.03
31 30 0.43
33 1 0.01
35 1 0.01
37 1 0.01
39 15 0.21
40 2 0.03
41 9 0.13
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.28
Consensus pattern (31 bp):
GGTAATTAAGAAAAGCAAAGTCTTAATTCAG
Found at i:12256 original size:31 final size:30
Alignment explanation
Indices: 12208--12477 Score: 109
Period size: 31 Copynumber: 8.0 Consensus size: 30
12198 CATAGTCAAG
12208 GTCTTAATTT-GGTAATTAAGAAAAGTAAA
1 GTCTTAATTTGGGTAATTAAGAAAAGTAAA
12237 GTCTTAATTTAGGGTAATTAAGAAAAGTAAGCAAAGTCCA
1 GTCTTAATTT-GGGTAATTAAGAAAAGT-----AA----A
**
12277 GGTCTTAATTT-GGTAATTAAGAAAAACAAA
1 -GTCTTAATTTGGGTAATTAAGAAAAGTAAA
12307 GTCTTAATTCAT-GGTAATTAAGAAAAGTAAACACAGTCAA
1 GTCTTAATT--TGGGTAATTAAGAAAAGT------A---AA
*
12347 GGTCTTAATTT-GGTAATTAAGAAAAGCAAA
1 -GTCTTAATTTGGGTAATTAAGAAAAGTAAA
* * *
12377 TTCTTAATTCGGGGAAATTAGGAAAAGTAACCACAGTCAAA
1 GTCTTAATT-TGGGTAATT-----AAG-AA--A-AGT-AAA
*
12418 GTCTTAA-TTGGGTAATTAAGAAAAGCAAA
1 GTCTTAATTTGGGTAATTAAGAAAAGTAAA
* *
12447 GTCTTAATTCAGGGTAATTAAGAAGAGTAAA
1 GTCTTAATT-TGGGTAATTAAGAAAAGTAAA
12478 CACAGTTAGG
Statistics
Matches: 187, Mismatches: 16, Indels: 74
0.68 0.06 0.27
Matches are distributed among these distances:
29 37 0.20
30 6 0.03
31 56 0.30
33 3 0.02
34 5 0.03
36 5 0.03
37 3 0.02
39 38 0.20
40 6 0.03
41 28 0.15
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.29
Consensus pattern (30 bp):
GTCTTAATTTGGGTAATTAAGAAAAGTAAA
Found at i:12539 original size:40 final size:40
Alignment explanation
Indices: 12490--12637 Score: 235
Period size: 40 Copynumber: 3.7 Consensus size: 40
12480 CAGTTAGGGG
* *
12490 CTTAATTCATAGAAATTAAGTAAAAACAGCAGTTAAAGAA
1 CTTAATTCATGGAAATTAAGTAAAAACAACAGTTAAAGAA
* *
12530 CTTAATTCATGGAAATTAAGTAAGAACAACAGTTAAAGGA
1 CTTAATTCATGGAAATTAAGTAAAAACAACAGTTAAAGAA
*
12570 CTTAATTCATGGAAATTAAGTGAAAACAACAGTTAAA-AGA
1 CTTAATTCATGGAAATTAAGTAAAAACAACAGTTAAAGA-A
12610 CTTAATTCATGGAAATTAAGTAAAAACA
1 CTTAATTCATGGAAATTAAGTAAAAACA
12638 GACAAGCACA
Statistics
Matches: 99, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
40 99 1.00
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.26
Consensus pattern (40 bp):
CTTAATTCATGGAAATTAAGTAAAAACAACAGTTAAAGAA
Found at i:12698 original size:41 final size:41
Alignment explanation
Indices: 12641--13083 Score: 685
Period size: 41 Copynumber: 10.8 Consensus size: 41
12631 AAAAACAGAC
*
12641 AAGCACAGACTTAATTTCAATGAAGGAAATTAGGTAAAGTA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
* * *
12682 AAGCATAAACATAATTTCAAGGAAGGAAATTAGGTAAAGTAA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGT-A
12724 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
*
12765 AAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAA-TA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
*
12805 CAAGCACAGACTTATTTTCAAGGAAGGAAATTAGGTAAAGTA
1 -AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
12847 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAG-A
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
* * *
12887 CAAGCACAGACTTAATTTTAAGGAAGGAAATTAGGTCAAGTG
1 -AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
* *
12929 AAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTGAAGTA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
* *
12970 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTGAGGTA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
*
13011 AAGCACATACTTAATTTCAAGGAAGGAAATTAGGTAAAG-A
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
* *
13051 CAGACACAGACTTAATTTCAGGGAAGGAAATTA
1 AAG-CACAGACTTAATTTCAAGGAAGGAAATTA
13084 AGTAGAGTTA
Statistics
Matches: 370, Mismatches: 26, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
40 6 0.02
41 324 0.88
42 40 0.11
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.22
Consensus pattern (41 bp):
AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
Found at i:13138 original size:32 final size:34
Alignment explanation
Indices: 13079--13378 Score: 327
Period size: 32 Copynumber: 8.8 Consensus size: 34
13069 CAGGGAAGGA
* **
13079 AATTAAGTAGAGTTAATAAAGGGCTTAATTCAGGGT
1 AATTAAGT-GAG-CAATAAAGAACTTAATTCAGGGT
13115 AATTAAGT-AG-AATAAAGAACTTAATTCAGGGT
1 AATTAAGTGAGCAATAAAGAACTTAATTCAGGGT
*
13147 AATTAAGTGGAGTCAATAAA-AGGCTTAATTCAGGGT
1 AATTAAGT-GAG-CAATAAAGA-ACTTAATTCAGGGT
*
13183 AATTAAGT-AG-AATAAAGAATTTAATTCAGGGT
1 AATTAAGTGAGCAATAAAGAACTTAATTCAGGGT
13215 AATTAAGTGGAGTCAATAAA-AGACTTAATTCAGGGT
1 AATTAAGT-GAG-CAATAAAGA-ACTTAATTCAGGGT
13251 AATTAAGT-AG-AATAAAGAACTTAATTCAGGGT
1 AATTAAGTGAGCAATAAAGAACTTAATTCAGGGT
* *
13283 AATTAAGTGGAGTCAATAAA-AGGCTTAA-TCGGGGT
1 AATTAAGT-GAG-CAATAAAGA-ACTTAATTCAGGGT
*
13318 AATTAAGT-AG-AATAAAGAACTTAATTCCGGGT
1 AATTAAGTGAGCAATAAAGAACTTAATTCAGGGT
13350 AATTAAGTGGAGTCAATAAAGAACTTAAT
1 AATTAAGT-GAG-CAATAAAGAACTTAAT
13379 CAAAAAAAGA
Statistics
Matches: 231, Mismatches: 10, Indels: 46
0.80 0.03 0.16
Matches are distributed among these distances:
31 11 0.05
32 97 0.42
33 4 0.02
34 14 0.06
35 17 0.07
36 88 0.38
ACGTcount: A:0.43, C:0.07, G:0.22, T:0.28
Consensus pattern (34 bp):
AATTAAGTGAGCAATAAAGAACTTAATTCAGGGT
Found at i:13154 original size:68 final size:68
Alignment explanation
Indices: 13079--13369 Score: 512
Period size: 68 Copynumber: 4.3 Consensus size: 68
13069 CAGGGAAGGA
* * *
13079 AATTAAGTAGAGTTAATAAAGGGCTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATTCAG
1 AATTAAGTGGAGTCAATAAAAGGCTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATTCAG
13144 GGT
66 GGT
*
13147 AATTAAGTGGAGTCAATAAAAGGCTTAATTCAGGGTAATTAAGTAGAATAAAGAATTTAATTCAG
1 AATTAAGTGGAGTCAATAAAAGGCTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATTCAG
13212 GGT
66 GGT
*
13215 AATTAAGTGGAGTCAATAAAAGACTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATTCAG
1 AATTAAGTGGAGTCAATAAAAGGCTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATTCAG
13280 GGT
66 GGT
* *
13283 AATTAAGTGGAGTCAATAAAAGGCTTAA-TCGGGGTAATTAAGTAGAATAAAGAACTTAATTCCG
1 AATTAAGTGGAGTCAATAAAAGGCTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATTCAG
13347 GGT
66 GGT
13350 AATTAAGTGGAGTCAATAAA
1 AATTAAGTGGAGTCAATAAA
13370 GAACTTAATC
Statistics
Matches: 214, Mismatches: 9, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
67 57 0.27
68 157 0.73
ACGTcount: A:0.43, C:0.07, G:0.22, T:0.28
Consensus pattern (68 bp):
AATTAAGTGGAGTCAATAAAAGGCTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATTCAG
GGT
Found at i:14044 original size:30 final size:31
Alignment explanation
Indices: 14002--14063 Score: 117
Period size: 30 Copynumber: 2.0 Consensus size: 31
13992 AAGACATCAA
14002 TGGATGGGAGGAATCGCACCAAAGATGCCAT
1 TGGATGGGAGGAATCGCACCAAAGATGCCAT
14033 TGGAT-GGAGGAATCGCACCAAAGATGCCAT
1 TGGATGGGAGGAATCGCACCAAAGATGCCAT
14063 T
1 T
14064 TTATCCTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 26 0.84
31 5 0.16
ACGTcount: A:0.32, C:0.19, G:0.31, T:0.18
Consensus pattern (31 bp):
TGGATGGGAGGAATCGCACCAAAGATGCCAT
Found at i:18462 original size:10 final size:10
Alignment explanation
Indices: 18449--18474 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
18439 TTAGGAGATT
18449 TTATGTTTGA
1 TTATGTTTGA
18459 TTATGTTTGA
1 TTATGTTTGA
18469 TTATGT
1 TTATGT
18475 CTTATAATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.62
Consensus pattern (10 bp):
TTATGTTTGA
Found at i:21511 original size:14 final size:14
Alignment explanation
Indices: 21492--21525 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
21482 ACAATTTTAG
21492 AACATTTAT-TATAT
1 AACATTTATGT-TAT
21506 AACATTTATGTTAT
1 AACATTTATGTTAT
21520 AACATT
1 AACATT
21526 GAATTTATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 18 0.95
15 1 0.05
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (14 bp):
AACATTTATGTTAT
Found at i:22934 original size:27 final size:29
Alignment explanation
Indices: 22881--22954 Score: 98
Period size: 27 Copynumber: 2.6 Consensus size: 29
22871 CTCCTATGTA
*
22881 TAAAATTTAAAATAATAATTTTACCTATTT
1 TAAAATGTAAAATAA-AATTTTACCTATTT
*
22911 TGAAA-GTAAAATAAAA-TTTACCTATTT
1 TAAAATGTAAAATAAAATTTTACCTATTT
*
22938 TAAAATTTAAAATAAAA
1 TAAAATGTAAAATAAAA
22955 AATTGAGGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
27 15 0.38
28 12 0.31
29 8 0.21
30 4 0.10
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (29 bp):
TAAAATGTAAAATAAAATTTTACCTATTT
Found at i:23731 original size:77 final size:77
Alignment explanation
Indices: 23600--23754 Score: 292
Period size: 77 Copynumber: 2.0 Consensus size: 77
23590 CCAAACTCAG
*
23600 ATGCATGAATCAAATTCAGATTAGTCAGAGCAAATCTCTAAATATTGGGTAGAAAACATTATTAT
1 ATGCATGAATCAAATTCAGATTAGTCAGAGCAAATCTCTAAATATTGGGAAGAAAACATTATTAT
23665 TATTATAATAAA
66 TATTATAATAAA
*
23677 ATGCATGAATCAAATTTAGATTAGTCAGAGCAAATCTCTAAATATTGGGAAGAAAACATTATTAT
1 ATGCATGAATCAAATTCAGATTAGTCAGAGCAAATCTCTAAATATTGGGAAGAAAACATTATTAT
23742 TATTATAATAAA
66 TATTATAATAAA
23754 A
1 A
23755 AAAACAACTC
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (77 bp):
ATGCATGAATCAAATTCAGATTAGTCAGAGCAAATCTCTAAATATTGGGAAGAAAACATTATTAT
TATTATAATAAA
Found at i:27144 original size:42 final size:42
Alignment explanation
Indices: 27097--27188 Score: 157
Period size: 42 Copynumber: 2.2 Consensus size: 42
27087 GTGTTGTTAC
27097 TTAATTATCGTTGATTAGTATTTGTTTCAATTTATAATTTGA
1 TTAATTATCGTTGATTAGTATTTGTTTCAATTTATAATTTGA
* *
27139 TTAATTATCGTTGATTAGTCTTTGTTTCAATTTGTAATTTGA
1 TTAATTATCGTTGATTAGTATTTGTTTCAATTTATAATTTGA
*
27181 TTAGTTAT
1 TTAATTAT
27189 ATTGATATTG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.26, C:0.05, G:0.13, T:0.55
Consensus pattern (42 bp):
TTAATTATCGTTGATTAGTATTTGTTTCAATTTATAATTTGA
Found at i:36396 original size:16 final size:17
Alignment explanation
Indices: 36365--36397 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
36355 TTAATTCGTT
*
36365 TTATTTATATTTATAAA
1 TTATTTATAATTATAAA
36382 TTATTTA-AATTATAAA
1 TTATTTATAATTATAAA
36398 AATTTTGTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATTTATAATTATAAA
Found at i:36627 original size:16 final size:18
Alignment explanation
Indices: 36603--36643 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
36593 AAAGTTTAAC
*
36603 TTGAGAAGC-AAAA-GTT
1 TTGAAAAGCGAAAATGTT
*
36619 TTGAAAAGCGAAAATTTT
1 TTGAAAAGCGAAAATGTT
36637 TTGAAAA
1 TTGAAAA
36644 ATTTTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 8 0.38
17 4 0.19
18 9 0.43
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.29
Consensus pattern (18 bp):
TTGAAAAGCGAAAATGTT
Found at i:40434 original size:2 final size:2
Alignment explanation
Indices: 40427--40452 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40417 AGATAATGCA
40427 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
40453 CCTATAGACA
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:40602 original size:24 final size:27
Alignment explanation
Indices: 40561--40615 Score: 71
Period size: 25 Copynumber: 2.1 Consensus size: 27
40551 TTAAGTGAAC
40561 AATAAAAATAAATAAACAAGA-AAA-A
1 AATAAAAATAAATAAACAAGATAAATA
* *
40586 AATAAAATTAAGT-AACAAGATAAATA
1 AATAAAAATAAATAAACAAGATAAATA
40612 AATA
1 AATA
40616 CTCCAATCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 7 0.27
25 14 0.54
26 5 0.19
ACGTcount: A:0.73, C:0.04, G:0.05, T:0.18
Consensus pattern (27 bp):
AATAAAAATAAATAAACAAGATAAATA
Found at i:43606 original size:9 final size:8
Alignment explanation
Indices: 43587--43662 Score: 62
Period size: 8 Copynumber: 9.0 Consensus size: 8
43577 GATTTTTCAG
43587 AAAATAAA
1 AAAATAAA
43595 AAAATGAAA
1 AAAAT-AAA
* *
43604 AAATTTAA
1 AAAATAAA
* *
43612 AAATTAGA
1 AAAATAAA
43620 AAAATAAA
1 AAAATAAA
43628 AAAATTAATA
1 AAAA-TAA-A
43638 AATAATAAA
1 AA-AATAAA
*
43647 TAAATAAA
1 AAAATAAA
*
43655 CAAATAAA
1 AAAATAAA
43663 TTTTGCCTTC
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
8 36 0.64
9 12 0.21
10 6 0.11
11 2 0.04
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.21
Consensus pattern (8 bp):
AAAATAAA
Found at i:43622 original size:17 final size:17
Alignment explanation
Indices: 43587--43634 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
43577 GATTTTTCAG
*
43587 AAAATAAAAAAATGA-A
1 AAAATAAAAAAATTAGA
**
43603 AAAATTTAAAAATTAGA
1 AAAATAAAAAAATTAGA
43620 AAAATAAAAAAATTA
1 AAAATAAAAAAATTA
43635 ATAAATAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (17 bp):
AAAATAAAAAAATTAGA
Found at i:43646 original size:19 final size:19
Alignment explanation
Indices: 43610--43661 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
43600 GAAAAAATTT
*
43610 AAAAATT-AGAAA-AATAA
1 AAAAATTAACAAATAATAA
*
43627 AAAAATTAATAAATAATAA
1 AAAAATTAACAAATAATAA
* *
43646 ATAAATAAACAAATAA
1 AAAAATTAACAAATAA
43662 ATTTTGCCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 7 0.24
18 4 0.14
19 18 0.62
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (19 bp):
AAAAATTAACAAATAATAA
Found at i:43648 original size:4 final size:4
Alignment explanation
Indices: 43621--43663 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
43611 AAAATTAGAA
* * *
43621 AAAT AAAA AAAT TAAT AAAT -AAT AAAT AAAT AAAC AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
43664 TTTGCCTTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
3 3 0.09
4 29 0.91
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:45241 original size:26 final size:26
Alignment explanation
Indices: 45181--45241 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
45171 TACAGCCACT
*
45181 GGTAAGTTCATCTCAAGTTTTTCCTGC
1 GGTAA-TTCATCTCAAGTTTTTCCTAC
* *
45208 GATGAATTCATCTCCAGTTTTTCCTAC
1 GGT-AATTCATCTCAAGTTTTTCCTAC
45235 GGTAATT
1 GGTAATT
45242 GATTTTCCTG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 4 0.14
27 23 0.79
28 2 0.07
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.41
Consensus pattern (26 bp):
GGTAATTCATCTCAAGTTTTTCCTAC
Found at i:45975 original size:113 final size:112
Alignment explanation
Indices: 45805--46157 Score: 480
Period size: 113 Copynumber: 3.1 Consensus size: 112
45795 AAAATTGAAT
* * * *
45805 ATAGCGGCGTC-TGGGCAAAAGACGCCGCTAAAT-GTGGCGTCTGAAGTACAAAACGCCGCATTA
1 ATAGCGGCGTCTTGGACTAAA-ATGCCGTTAAATGGTGGCGTCTGAAGTACAAAACGCCGCATTA
45868 TTTAATTTTTTTGGAGAAATGTAAATTGAGTAAAAATGAAGCCTAAAAA
65 TTT-ATTTTTTTGGAGAAATGTAAATTGAGTAAAAATGAAGCCTAAAAA
45917 ATAGCGGCGTCTTGGACTAAAATGCCGTTAAATGGTGGCGTCTGAAGTACAAAACGCCGCATTAT
1 ATAGCGGCGTCTTGGACTAAAATGCCGTTAAATGGTGGCGTCTGAAGTACAAAACGCCGCATTAT
* *
45982 TTGATTTTTTCGGAGAAATGTAAATTGAGTAACAATGAAGCCTAAAAA
66 TT-ATTTTTTTGGAGAAATGTAAATTGAGTAAAAATGAAGCCTAAAAA
* * * * *
46030 ATAGCGGCGTCTTGGACTAAAATGTCGTTAAATGGTGGCGTCTGAGGTTCGAAACGCCACCA-TA
1 ATAGCGGCGTCTTGGACTAAAATGCCGTTAAATGGTGGCGTCTGAAGTACAAAACGCC-GCATTA
* ** *
46094 TTTATTTTTTTCGGAGAAATG-CAATAAAACCTAAAAATGAAGCCTAAAAA
65 TTTATTTTTTT-GGAGAAATGTAAAT-TGA-GTAAAAATGAAGCCTAAAAA
46144 ATAGCGGCGTCTTG
1 ATAGCGGCGTCTTG
46158 ACCCTAAACA
Statistics
Matches: 217, Mismatches: 18, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
112 31 0.14
113 152 0.70
114 34 0.16
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.27
Consensus pattern (112 bp):
ATAGCGGCGTCTTGGACTAAAATGCCGTTAAATGGTGGCGTCTGAAGTACAAAACGCCGCATTAT
TTATTTTTTTGGAGAAATGTAAATTGAGTAAAAATGAAGCCTAAAAA
Found at i:46192 original size:114 final size:110
Alignment explanation
Indices: 45805--46295 Score: 408
Period size: 113 Copynumber: 4.4 Consensus size: 110
45795 AAAATTGAAT
* * * * *
45805 ATAGCGGCGTC-TGGGCAAAAGACGCCGCTAAAT-GTGGCGTCTGAA-GTACAAAACGCCGCATT
1 ATAGCGGCGTCTTGGACTAAA-A-GCCGCTAAATGGTGGCGTC-CAAGGTTCAAAACGCCCCA-T
* * ** *
45867 ATTTAATTTTTTTGGAGAAATGTAAATTGA-GTAAAAATGAAGCCTAAAAA
62 ATTT-ATTTTTTCGGAGAAATGCAAA-AAACCTAAAAATGAAGCCTAAAAA
* * * *
45917 ATAGCGGCGTCTTGGACTAAAATGCCGTTAAATGGTGGCGTCTGAA-GTACAAAACGCCGCATTA
1 ATAGCGGCGTCTTGGACTAAAA-GCCGCTAAATGGTGGCGTC-CAAGGTTCAAAACGCCCCA-TA
* ** * *
45981 TTTGATTTTTTCGGAGAAATGTAAATTGA-GTAACAATGAAGCCTAAAAA
63 TTT-ATTTTTTCGGAGAAATGCAAA-AAACCTAAAAATGAAGCCTAAAAA
* * ** *
46030 ATAGCGGCGTCTTGGACTAAAATGTCGTTAAATGGTGGCGTCTGAGGTTCGAAACGCCACCATAT
1 ATAGCGGCGTCTTGGACTAAAA-GCCGCTAAATGGTGGCGTCCAAGGTTCAAAACGCC-CCATAT
46095 TTATTTTTTTCGGAGAAATGCAATAAAACCTAAAAATGAAGCCTAAAAA
64 TTA-TTTTTTCGGAGAAATGCAA-AAAACCTAAAAATGAAGCCTAAAAA
* *
46144 ATAGCGGCGTCTT-GACCCTAAACA-CCGCTAAATGGTGGTGTCCAAGGTTCAAAACACCGCCAT
1 ATAGCGGCGTCTTGGA--CTAAA-AGCCGCTAAATGGTGGCGTCCAAGGTTCAAAACGCC-CCAT
* * * *
46207 ATTTAATTTTTTCGAAGAACTACAAAAAACCTAAAAGTGAAGCCT-AAAA
62 ATTT-ATTTTTTCGGAGAAATGCAAAAAACCTAAAAATGAAGCCTAAAAA
* * * *
46256 ATAGCGACGTCTT-GACCCTAAACGCCACTAAATAGTGGCG
1 ATAGCGGCGTCTTGGA--CTAAAAGCCGCTAAATGGTGGCG
46296 CCTTGCCGTG
Statistics
Matches: 332, Mismatches: 35, Indels: 24
0.85 0.09 0.06
Matches are distributed among these distances:
112 61 0.18
113 179 0.54
114 85 0.26
115 6 0.02
116 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.25
Consensus pattern (110 bp):
ATAGCGGCGTCTTGGACTAAAAGCCGCTAAATGGTGGCGTCCAAGGTTCAAAACGCCCCATATTT
ATTTTTTCGGAGAAATGCAAAAAACCTAAAAATGAAGCCTAAAAA
Found at i:49238 original size:114 final size:112
Alignment explanation
Indices: 49088--49333 Score: 359
Period size: 114 Copynumber: 2.2 Consensus size: 112
49078 TACTTCCATA
* ** *
49088 AAACGCCGCTAAATGGTGGTGTCTGAGGTTCAAAACGCCGCCATATTTAATTCTTTCGGAGAAAT
1 AAACGCCGCTAAATGGTGGCGTCAAAGGTTCAAAACGCCGCCATATTTAATTCTTTCGAAGAAAT
*
49153 GCAATAAAACCTAAAAATT-AAGCCTAAAAAATAGCGGCATCTTGACCCT
66 GCAA-AAAACCT-AAAATTGAAGCCT-AAAAATAGCAGCATCTTGACCCT
* * *
49202 AAACGCCGCTAAATGGTGGCGTCAAAGGTTCAAAACGCCGCCGTATTTAATTTTTTCGAAGAACT
1 AAACGCCGCTAAATGGTGGCGTCAAAGGTTCAAAACGCCGCCATATTTAATTCTTTCGAAGAAAT
*
49267 GCAAAAAACCTAAAATTGAAGCCTAAAAATAGCAGCGTCTTGACCCT
66 GCAAAAAACCTAAAATTGAAGCCTAAAAATAGCAGCATCTTGACCCT
* *
49314 AAACACCGCTAAATAGTGGC
1 AAACGCCGCTAAATGGTGGC
49334 ACCTTGCCGT
Statistics
Matches: 120, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
112 45 0.38
113 13 0.11
114 62 0.52
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (112 bp):
AAACGCCGCTAAATGGTGGCGTCAAAGGTTCAAAACGCCGCCATATTTAATTCTTTCGAAGAAAT
GCAAAAAACCTAAAATTGAAGCCTAAAAATAGCAGCATCTTGACCCT
Found at i:52279 original size:21 final size:21
Alignment explanation
Indices: 52253--52292 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
52243 AAAATCTGGA
*
52253 TTGCTAAACACCGCCCCCCAT
1 TTGCTAAACAACGCCCCCCAT
*
52274 TTGCTAAATAACGCCCCCC
1 TTGCTAAACAACGCCCCCC
52293 TTTATACACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.45, G:0.10, T:0.20
Consensus pattern (21 bp):
TTGCTAAACAACGCCCCCCAT
Found at i:52499 original size:22 final size:23
Alignment explanation
Indices: 52460--52513 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
52450 AAATTAATTT
*
52460 TTAATTAATTAGTATTTAATTAC
1 TTAATTTATTAGTATTTAATTAC
* *
52483 TTAGTTTATTAGT-TTTAATTAG
1 TTAATTTATTAGTATTTAATTAC
52505 TTAATTTAT
1 TTAATTTAT
52514 GATTAACTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.57
Consensus pattern (23 bp):
TTAATTTATTAGTATTTAATTAC
Found at i:52575 original size:10 final size:9
Alignment explanation
Indices: 52549--52583 Score: 54
Period size: 10 Copynumber: 3.9 Consensus size: 9
52539 ATTTTGATTG
52549 TTTATTAG-
1 TTTATTAGT
52557 TTTATTAGT
1 TTTATTAGT
52566 TTTAATTAGT
1 TTT-ATTAGT
52576 TTTATTAG
1 TTTATTAG
52584 GGCGGTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.32
9 8 0.32
10 9 0.36
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (9 bp):
TTTATTAGT
Found at i:57714 original size:32 final size:33
Alignment explanation
Indices: 57673--57738 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
57663 TTGATGACGA
*
57673 GCGGCCTG-CCGTGGCGAAGCCGCCCCAGTGGG
1 GCGGCCTGCCCGTGGCGAAGCCACCCCAGTGGG
*
57705 GCGGCCTGCCCGTGGTGAAGCCACCCCAGTGGG
1 GCGGCCTGCCCGTGGCGAAGCCACCCCAGTGGG
57738 G
1 G
57739 AGGCTCCGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 8 0.26
33 23 0.74
ACGTcount: A:0.11, C:0.36, G:0.42, T:0.11
Consensus pattern (33 bp):
GCGGCCTGCCCGTGGCGAAGCCACCCCAGTGGG
Found at i:57751 original size:33 final size:32
Alignment explanation
Indices: 57675--57751 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 32
57665 GATGACGAGC
* * *
57675 GGCCTGCCGTGGCGAAGCCGCCCCAGTGGGGC
1 GGCCCGCCGTGGCGAAGCCACCCCAGTGGGGA
* *
57707 GGCCTGCCCGTGGTGAAGCCACCCCAGTGGGGA
1 GGCCCG-CCGTGGCGAAGCCACCCCAGTGGGGA
57740 GGCTCCGCCGTG
1 GGC-CCGCCGTG
57752 CCTGAGCCGT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
32 6 0.15
33 31 0.79
34 2 0.05
ACGTcount: A:0.10, C:0.36, G:0.42, T:0.12
Consensus pattern (32 bp):
GGCCCGCCGTGGCGAAGCCACCCCAGTGGGGA
Found at i:64358 original size:18 final size:17
Alignment explanation
Indices: 64335--64431 Score: 113
Period size: 18 Copynumber: 5.4 Consensus size: 17
64325 CCAACCTGTT
64335 AACACAGTCCCACTACCG
1 AACACAGTCCCAC-ACCG
*
64353 AACACAGTCCTAGCACCG
1 AACACAGTCCCA-CACCG
* *
64371 ACCATAGTCCCAGCACCG
1 AACACAGTCCCA-CACCG
*
64389 AACACAATCCCAACACCG
1 AACACAGTCCC-ACACCG
64407 AACACAGTCCCAACACCG
1 AACACAGTCCC-ACACCG
64425 AACACAG
1 AACACAG
64432 ATTCTGTTCC
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
18 67 0.97
19 2 0.03
ACGTcount: A:0.37, C:0.42, G:0.12, T:0.08
Consensus pattern (17 bp):
AACACAGTCCCACACCG
Found at i:68875 original size:32 final size:32
Alignment explanation
Indices: 68839--68900 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
68829 GGAACGGTTT
* *
68839 GCCGTGGTAAAGCCGCCCCAAAGGGGCGGCCC
1 GCCGTGGCAAAGCCGCCCCAAAGGAGCGGCCC
* *
68871 GCCGTGGCAAAGCCTCCCCACAGGAGCGGC
1 GCCGTGGCAAAGCCGCCCCAAAGGAGCGGC
68901 TAGGCCAGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.19, C:0.39, G:0.35, T:0.06
Consensus pattern (32 bp):
GCCGTGGCAAAGCCGCCCCAAAGGAGCGGCCC
Found at i:69062 original size:32 final size:32
Alignment explanation
Indices: 69033--69103 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
69023 GGGCGGCCGC
* * *
69033 GCCACGGTAGGCCGCACCCTGGGGTCGGCCTT
1 GCCACGGCAGGCCGCACCATGGGGTCGGCCAT
69065 GCCACGGCAGGCCGCACCATGGGGTCGGCCAT
1 GCCACGGCAGGCCGCACCATGGGGTCGGCCAT
69097 GCCACGG
1 GCCACGG
69104 AAGGTCGCCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.13, C:0.38, G:0.38, T:0.11
Consensus pattern (32 bp):
GCCACGGCAGGCCGCACCATGGGGTCGGCCAT
Found at i:69179 original size:13 final size:13
Alignment explanation
Indices: 69157--69199 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 13
69147 TTTTTTTTGT
69157 TTTTTCTTAAATTA
1 TTTTT-TTAAATTA
*
69171 TTTTTTTAAGGTTA
1 TTTTTTTAA-ATTA
69185 TTTTTTTAAATTA
1 TTTTTTTAAATTA
69198 TT
1 TT
69200 AGTTTTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (13 bp):
TTTTTTTAAATTA
Done.