Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003610.1 Hibiscus syriacus cultivar Beakdansim tig00007637_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: 115561
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2239 original size:16 final size:16
Alignment explanation
Indices: 2215--2254 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
2205 TTTCAAGGGC
*
2215 ATGACACTGATAACAA
1 ATGATACTGATAACAA
2231 ATGATACTGATAACAA
1 ATGATACTGATAACAA
2247 ATGATACT
1 ATGATACT
2255 TTATTAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.25
Consensus pattern (16 bp):
ATGATACTGATAACAA
Found at i:15174 original size:64 final size:64
Alignment explanation
Indices: 15059--15181 Score: 153
Period size: 64 Copynumber: 1.9 Consensus size: 64
15049 TTAATGAAAG
* * * *
15059 TATGCATCGGTGCATAAAATGTATTCGATGTTTTATTATTAATGGGATGCATCGATGCATGCCT
1 TATGCATCGATGCATAAAATGCATTCGATGTTTTATTATTAAAGAGATGCATCGATGCATGCCT
*
15123 TATGCATCGATGCACT-AATTGCATTCGATGTTTTTATT-TTAAA-AGAGTGCATCGATGCA
1 TATGCATCGATGCA-TAAAATGCATTCGATG-TTTTATTATTAAAGAGA-TGCATCGATGCA
15182 CTACCTGTGC
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
63 2 0.04
64 41 0.80
65 8 0.16
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (64 bp):
TATGCATCGATGCATAAAATGCATTCGATGTTTTATTATTAAAGAGATGCATCGATGCATGCCT
Found at i:19911 original size:27 final size:25
Alignment explanation
Indices: 19881--19969 Score: 94
Period size: 25 Copynumber: 3.4 Consensus size: 25
19871 TTAACTTCAT
19881 AATATTTTATATATATTAACTTTTAAA
1 AATA-TTT-TATATATTAACTTTTAAA
19908 AATATTTT-TATATTAACTTATTAAA
1 AATATTTTATATATTAACTT-TTAAA
19933 TAA-ATTTTAT-TATTAACTTAATTTAAA
1 -AATATTTTATATATTAAC-T--TTTAAA
19960 AATATTTTAT
1 AATATTTTAT
19970 CTTGATTTTA
Statistics
Matches: 55, Mismatches: 0, Indels: 14
0.80 0.00 0.20
Matches are distributed among these distances:
24 11 0.20
25 18 0.33
26 9 0.16
27 16 0.29
28 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (25 bp):
AATATTTTATATATTAACTTTTAAA
Found at i:19923 original size:24 final size:24
Alignment explanation
Indices: 19892--19967 Score: 84
Period size: 24 Copynumber: 3.0 Consensus size: 24
19882 ATATTTTATA
19892 TATATTAACTTTTAAAAATATTTT
1 TATATTAACTTTTAAAAATATTTT
19916 TATATTAACTTATTAAATAA-A-TTT
1 TATATTAACTT-TTAAA-AATATTTT
19940 TATTATTAACTTAATTTAAAAATATTTT
1 TA-TATTAAC-T--TTTAAAAATATTTT
19968 ATCTTGATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
24 16 0.36
25 13 0.30
26 5 0.11
27 6 0.14
28 4 0.09
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (24 bp):
TATATTAACTTTTAAAAATATTTT
Found at i:21072 original size:79 final size:80
Alignment explanation
Indices: 20969--21134 Score: 217
Period size: 79 Copynumber: 2.1 Consensus size: 80
20959 CCGTACAATC
* ** * *
20969 CATGAATCCATGCAATGAAGTGTGAACACATGAGCCACAGTAATGGTTGGAATTAAGGCATTAGT
1 CATGAATCCATGCAATAAAGTGTGAACACATGAGCCACAGTAATGGCAGGAATTAAAGCATTAAT
*
21034 CTAGACTGTATAATG
66 CTAGACTGTATAATA
* * * *
21049 CATGAA-CCATGCAGTAAAGTGTGAATACATGAGCCACATTAATGGCAGGAGTTAAAGCATTAAT
1 CATGAATCCATGCAATAAAGTGTGAACACATGAGCCACAGTAATGGCAGGAATTAAAGCATTAAT
**
21113 CTAGGTTGTATAATA
66 CTAGACTGTATAATA
21128 CATGAAT
1 CATGAAT
21135 TTAGCTGTAT
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
79 67 0.92
80 6 0.08
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (80 bp):
CATGAATCCATGCAATAAAGTGTGAACACATGAGCCACAGTAATGGCAGGAATTAAAGCATTAAT
CTAGACTGTATAATA
Found at i:36393 original size:298 final size:298
Alignment explanation
Indices: 35816--36395 Score: 1090
Period size: 298 Copynumber: 1.9 Consensus size: 298
35806 TATGGTATTC
*
35816 AAGAAATCAAGTACACACTCAAGCTTTGTGGAGAGCGGGTTGAGTATATTGGATACTTCAAACAA
1 AAGAAATCAAGTACACACTCAAGCTTTGTGGAGAGCGGGTTGAGTATACTGGATACTTCAAACAA
*
35881 AGAATCATATGTTATTTTATCAGTCTTTGTAAAACGAAAATAATAGAACAGAAAATTTTCAGTAT
66 AGAATCATATGTTATTTTATCAGTCTTTCTAAAACGAAAATAATAGAACAGAAAATTTTCAGTAT
35946 ACAGAAAGAAACTCTAGCCCAAAGTTCGAATTCAAAGGCTTTATTCCTCTTTCTAAGACCTCGAA
131 ACAGAAAGAAACTCTAGCCCAAAGTTCGAATTCAAAGGCTTTATTCCTCTTTCTAAGACCTCGAA
36011 GCTAAGTACGTTTGATTCCCTTTGACACTTGGAGCTCAAGTGTTTATTCTACTAAAAAAACTCCT
196 GCTAAGTACGTTTGATTCCCTTTGACACTTGGAGCTCAAGTGTTTATTCTACTAAAAAAACTCCT
36076 CTGAACAGCAGCACCCCCCCCCCCAAAAAAAAAAAACT
261 CTGAACAGCAGCACCCCCCCCCCCAAAAAAAAAAAACT
*
36114 AAGAAATCAAGTACGCACTCAAGCTTTGTGGAGAGCGGGTTGAGTATACTGGATACTTCAAACAA
1 AAGAAATCAAGTACACACTCAAGCTTTGTGGAGAGCGGGTTGAGTATACTGGATACTTCAAACAA
*
36179 AGAATCATATGTTATTTTATCAGTCTTTCTAAAACGAAAATAATAGAACATAAAATTTTCAGTAT
66 AGAATCATATGTTATTTTATCAGTCTTTCTAAAACGAAAATAATAGAACAGAAAATTTTCAGTAT
*
36244 ACAGAAAGAAACTCTGGCCCAAAGTTCGAATTCAAAGGCTTTATTCCTCTTTCTAAGACCTCGAA
131 ACAGAAAGAAACTCTAGCCCAAAGTTCGAATTCAAAGGCTTTATTCCTCTTTCTAAGACCTCGAA
*
36309 GCTAAGTACGTTTGATTCCC-TTGACACTTGGAGCTCAAGTGTTTATTCTACTAAAAAACCTCCT
196 GCTAAGTACGTTTGATTCCCTTTGACACTTGGAGCTCAAGTGTTTATTCTACTAAAAAAACTCCT
*
36373 CTGAACAGCAGCTCCCCCCCCCC
261 CTGAACAGCAGCACCCCCCCCCC
36396 AAATACTAAG
Statistics
Matches: 275, Mismatches: 7, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
297 65 0.24
298 210 0.76
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.28
Consensus pattern (298 bp):
AAGAAATCAAGTACACACTCAAGCTTTGTGGAGAGCGGGTTGAGTATACTGGATACTTCAAACAA
AGAATCATATGTTATTTTATCAGTCTTTCTAAAACGAAAATAATAGAACAGAAAATTTTCAGTAT
ACAGAAAGAAACTCTAGCCCAAAGTTCGAATTCAAAGGCTTTATTCCTCTTTCTAAGACCTCGAA
GCTAAGTACGTTTGATTCCCTTTGACACTTGGAGCTCAAGTGTTTATTCTACTAAAAAAACTCCT
CTGAACAGCAGCACCCCCCCCCCCAAAAAAAAAAAACT
Found at i:37279 original size:7 final size:7
Alignment explanation
Indices: 37267--37321 Score: 110
Period size: 7 Copynumber: 7.9 Consensus size: 7
37257 TTTAAGCTTC
37267 GCGTTTT
1 GCGTTTT
37274 GCGTTTT
1 GCGTTTT
37281 GCGTTTT
1 GCGTTTT
37288 GCGTTTT
1 GCGTTTT
37295 GCGTTTT
1 GCGTTTT
37302 GCGTTTT
1 GCGTTTT
37309 GCGTTTT
1 GCGTTTT
37316 GCGTTT
1 GCGTTT
37322 GGTGCTTATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 48 1.00
ACGTcount: A:0.00, C:0.15, G:0.29, T:0.56
Consensus pattern (7 bp):
GCGTTTT
Found at i:38346 original size:47 final size:48
Alignment explanation
Indices: 38266--38358 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 48
38256 AGAATTTCAC
* *
38266 ATATACCTCTAGAAAAATATAATAATTCGAACATTATCACCTTTTAAT
1 ATATACCTCTAGAAAAACATAAAAATTCGAACATTATCACCTTTTAAT
* *
38314 ATATACCTCTA-ATAAACATAAAAATTCGAACATTGTCACCTTTTA
1 ATATACCTCTAGAAAAACATAAAAATTCGAACATTATCACCTTTTA
38359 TCATAAAACT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 30 0.73
48 11 0.27
ACGTcount: A:0.43, C:0.18, G:0.04, T:0.34
Consensus pattern (48 bp):
ATATACCTCTAGAAAAACATAAAAATTCGAACATTATCACCTTTTAAT
Found at i:56448 original size:22 final size:21
Alignment explanation
Indices: 56422--56471 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
56412 AAAAGTTTGG
56422 TTAATTTAAAGATTTAATTGAT
1 TTAATTTAAAGATTTAA-TGAT
* * *
56444 TTAATATTGATGCTTTAATGAT
1 TTAAT-TTAAAGATTTAATGAT
56466 TTAATT
1 TTAATT
56472 ATAATATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 14 0.58
23 9 0.38
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (21 bp):
TTAATTTAAAGATTTAATGAT
Found at i:62742 original size:63 final size:64
Alignment explanation
Indices: 62671--62820 Score: 266
Period size: 63 Copynumber: 2.3 Consensus size: 64
62661 GTAAAGCGTC
*
62671 AAATAATAACAAAATCAGTAGAAAAAGTAATGTTTTAGATAATTTTTTATTGAAAATATT-AAA
1 AAATAATAACAAAATCAGTAGAAAAAATAATGTTTTAGATAATTTTTTATTGAAAATATTAAAA
62734 AAATAATAACAAAATCAGTAGAAAAAATAATGTTTTAGATAATTTTTTATTGAAAATATTAAAAA
1 AAATAATAACAAAATCAGTAGAAAAAATAATGTTTTAGATAATTTTTTATTGAAAATATT-AAAA
*
62799 AAATAATAACAAAACCAGTAGA
1 AAATAATAACAAAATCAGTAGA
62821 GCGTTTTTTT
Statistics
Matches: 83, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
63 59 0.71
65 24 0.29
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.31
Consensus pattern (64 bp):
AAATAATAACAAAATCAGTAGAAAAAATAATGTTTTAGATAATTTTTTATTGAAAATATTAAAA
Found at i:70512 original size:14 final size:14
Alignment explanation
Indices: 70493--70541 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
70483 TAATATGAGA
70493 ACATGACATGAGCT
1 ACATGACATGAGCT
* **
70507 ACATGATCACGAGAG
1 ACATGA-CATGAGCT
*
70522 AAATGACATGAGCT
1 ACATGACATGAGCT
70536 ACATGA
1 ACATGA
70542 TCACAAGAGA
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
14 16 0.62
15 10 0.38
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.18
Consensus pattern (14 bp):
ACATGACATGAGCT
Found at i:70528 original size:29 final size:29
Alignment explanation
Indices: 70489--70598 Score: 177
Period size: 29 Copynumber: 3.8 Consensus size: 29
70479 TATGTAATAT
*
70489 GAGAACATGACATGAGCTACATGATCACGA
1 GAGAA-ATGACATGAGCTACATGATCACAA
70519 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
**
70548 GAGAAATGACATGAATTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
70577 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
70599 ACATATGAAA
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
28 7 0.09
29 64 0.84
30 5 0.07
ACGTcount: A:0.45, C:0.15, G:0.22, T:0.18
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:74160 original size:36 final size:36
Alignment explanation
Indices: 74120--74191 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
74110 TATTTCCAAC
74120 AAACATCTACCAAACTTTGAAAAATATTTTTCAAAG
1 AAACATCTACCAAACTTTGAAAAATATTTTTCAAAG
*
74156 AAACATTTACCAAACTTTGAAAAATATTTTTCAAAG
1 AAACATCTACCAAACTTTGAAAAATATTTTTCAAAG
74192 TTGGTTGCCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (36 bp):
AAACATCTACCAAACTTTGAAAAATATTTTTCAAAG
Found at i:76609 original size:37 final size:37
Alignment explanation
Indices: 76556--76652 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 37
76546 CCTTTTCGTC
76556 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
76593 TTGCTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* *
76630 CTACTATGATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
76653 GATAAGATCC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:77490 original size:2 final size:2
Alignment explanation
Indices: 77485--77511 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
77475 TTTACTCATT
77485 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
77512 TTTTATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:77522 original size:8 final size:8
Alignment explanation
Indices: 77511--77599 Score: 63
Period size: 8 Copynumber: 10.4 Consensus size: 8
77501 TATATATATA
77511 TTTTTATT
1 TTTTTATT
77519 TTTTTATT
1 TTTTTATT
77527 TTTTTATT
1 TTTTTATT
*
77535 TATTTATTTT
1 T-TTT-TATT
77545 TCCTTTTATT
1 T--TTTTATT
77555 TTTTTACTT
1 TTTTTA-TT
77564 ATTTTTA-T
1 -TTTTTATT
* *
77572 TCTTCATT
1 TTTTTATT
77580 TTTTTCATT
1 TTTTT-ATT
* *
77589 TATTCATT
1 TTTTTATT
77597 TTT
1 TTT
77600 CCCTCTAACA
Statistics
Matches: 64, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
7 4 0.06
8 32 0.50
9 11 0.17
10 14 0.22
11 3 0.05
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTATT
Found at i:77530 original size:16 final size:16
Alignment explanation
Indices: 77511--77599 Score: 63
Period size: 17 Copynumber: 5.2 Consensus size: 16
77501 TATATATATA
77511 TTTTTATTTTTTTATT
1 TTTTTATTTTTTTATT
*
77527 TTTTTATTTATTTATTTT
1 TTTTTATTT-TTT-TATT
77545 TCCTTTTATTTTTTTACTT
1 T--TTTTATTTTTTTA-TT
* *
77564 ATTTTTA-TTCTTCATT
1 -TTTTTATTTTTTTATT
* *
77580 TTTTTCATTTATTCATT
1 TTTTT-ATTTTTTTATT
77597 TTT
1 TTT
77600 CCCTCTAACA
Statistics
Matches: 60, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
15 5 0.08
16 12 0.20
17 19 0.32
18 10 0.17
19 5 0.08
20 9 0.15
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTATTTTTTTATT
Found at i:77538 original size:12 final size:12
Alignment explanation
Indices: 77513--77592 Score: 74
Period size: 12 Copynumber: 6.5 Consensus size: 12
77503 TATATATATT
77513 TTTATTTTTTTA
1 TTTATTTTTTTA
77525 TTT-TTTTATTTA
1 TTTATTTT-TTTA
*
77537 TTTATTTTTCCT-
1 TTTATTTTT-TTA
77549 TTTATTTTTTTA
1 TTTATTTTTTTA
* *
77561 CTTATTTTTATTC
1 TTTATTTTT-TTA
*
77574 TTCATTTTTTTCA
1 TTTATTTTTTT-A
77587 TTTATT
1 TTTATT
77593 CATTTTTCCC
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
11 5 0.09
12 30 0.56
13 19 0.35
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTATTTTTTTA
Found at i:80686 original size:15 final size:15
Alignment explanation
Indices: 80666--80696 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
80656 GAACATTTCA
80666 TGCATTCTTGCATTT
1 TGCATTCTTGCATTT
*
80681 TGCATTTTTGCATTT
1 TGCATTCTTGCATTT
80696 T
1 T
80697 TTGCATCTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.16, G:0.13, T:0.58
Consensus pattern (15 bp):
TGCATTCTTGCATTT
Found at i:81879 original size:17 final size:15
Alignment explanation
Indices: 81847--81916 Score: 76
Period size: 14 Copynumber: 4.7 Consensus size: 15
81837 AGATCCAATC
81847 AAGAACAAAAAAGAA
1 AAGAACAAAAAAGAA
81862 AAGAAGCAAAAGAAGAA
1 AAGAA-CAAAA-AAGAA
*
81879 AA-AA-AAGAAAAAAA
1 AAGAACAA-AAAAGAA
81893 AAGAA-AAAAAAG-A
1 AAGAACAAAAAAGAA
81906 AAGAACAAAAA
1 AAGAACAAAAA
81917 TCAAAAAGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
13 6 0.12
14 17 0.35
15 11 0.23
16 7 0.15
17 7 0.15
ACGTcount: A:0.81, C:0.04, G:0.14, T:0.00
Consensus pattern (15 bp):
AAGAACAAAAAAGAA
Found at i:81904 original size:31 final size:33
Alignment explanation
Indices: 81854--81928 Score: 91
Period size: 31 Copynumber: 2.3 Consensus size: 33
81844 ATCAAGAACA
**
81854 AAAAAGAAAAGAAGCAAAAG-AAGAAAAAAAAG
1 AAAAAGAAAAGAAAAAAAAGAAAGAAAAAAAAG
**
81886 AAAAA-AAAAGAAAAAAAAGAAAGAACAAAAATC
1 AAAAAGAAAAGAAAAAAAAGAAAGAA-AAAAAAG
81919 AAAAAGAAAA
1 AAAAAGAAAA
81929 AGGGACAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
31 12 0.33
32 10 0.28
33 10 0.28
34 4 0.11
ACGTcount: A:0.81, C:0.04, G:0.13, T:0.01
Consensus pattern (33 bp):
AAAAAGAAAAGAAAAAAAAGAAAGAAAAAAAAG
Found at i:82608 original size:22 final size:22
Alignment explanation
Indices: 82534--82608 Score: 132
Period size: 22 Copynumber: 3.4 Consensus size: 22
82524 GCTACCCCAT
*
82534 CAAACCGTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
82556 CAAACCTATGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
82578 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
82600 CAAACCTTT
1 CAAACCTTT
82609 AACCAAACAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.37, C:0.28, G:0.13, T:0.21
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:83552 original size:106 final size:106
Alignment explanation
Indices: 83356--84616 Score: 1849
Period size: 106 Copynumber: 12.0 Consensus size: 106
83346 GCCACTCAAT
* * * * * *
83356 ACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAATTTTCCAATTTCG
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCA
83420 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
66 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
* * * *
83461 ACAATGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAATAAACAATTTCCCAATTTCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCA
*
83526 GATCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
66 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
* * *
83567 ACAACACAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAATAAACAACTTCCCAATTTCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCA
83632 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
66 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
* * *
83673 ACAACGCAAGTTCAACTTCACAACGAAGGGACCACTGGTTGTCAACAAACAACTTCTCAATTTCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCA
* * *
83738 TAGCCAATTTTAACTTCACAACGAAGGATATTGGACTCCAG
66 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
* * *
83779 ACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAACAAACAACTGCTCAATTTCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCA
**
83844 GAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAG
66 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
* *
83885 ACAACGCAAGTTCAACTTCACGAAGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCA
*
83950 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAG
66 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
** *
83991 ACAACGCAAGTTCAACTTCACGACGAAAAGACCGCTGGTTGTCAATAAACAACTTCCCAA-TTCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCA
84055 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
66 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
* * * *
84096 ACAACGCAAGTTCAACTTTACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTAA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCA
*
84161 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAG
66 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
* * *
84202 ACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCA
* *
84267 GAGCCAATTTCAACTTCACAGCGTAGGATATTGGACTCAAG
66 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
* * *
84308 ACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTTA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCA
* * *
84373 GAGCCAATTTCAACTTCTCAGCGAAGGATCTTGAAC-CCAAG
66 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC-AG
* * * * * *
84414 GCAACACAAGCTCAACTTCACGACGAAGGGACGGCTGATTGTCAAC-AA-AA-TT-TC-A-TTCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCA
* * *
84473 GAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAG
66 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
* * * * * ** *
84514 ACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCGGTTCCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCA
*
84579 GAGCCAATTTCAACTTCAC-GACGGAGGATATTGGACTC
66 GAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
84617 AGAACAATGC
Statistics
Matches: 1052, Mismatches: 93, Indels: 21
0.90 0.08 0.02
Matches are distributed among these distances:
100 78 0.07
101 4 0.00
102 3 0.00
103 4 0.00
104 3 0.00
105 141 0.13
106 819 0.78
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCA
GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
Found at i:84168 original size:423 final size:422
Alignment explanation
Indices: 83356--84616 Score: 1958
Period size: 423 Copynumber: 3.0 Consensus size: 422
83346 GCCACTCAAT
* ** * * *
83356 ACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAATTTTCCAATTTCG
1 ACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAACAAACAATTCT-CAATTTCA
*
83420 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGAC
65 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
* *
83485 GAAGGGACCGTTGGTTGTCAATAAACAATTTCCCAATTTCAGATCCAATTTCAACTTCACAGCGA
130 GAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGA
* *
83550 AGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAATAA
195 AGGATATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAA
83615 ACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGC
260 ACAACTTCCCAA-TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGC
* *
83680 AAGTTCAACTTCACAACGAAGGGACCACTGGTTGTCAACAAACAACTTCTCAATTTCATAGCCAA
324 AAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAA
*
83745 TTTTAACTTCACAACGAAGGATATTGGACTCCAG
389 TTTCAACTTCACAACGAAGGATATTGGACTCCAG
*
83779 ACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAACAAACAACTGCTCAATTTCA
1 ACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAACAAACAA-TTCTCAATTTCA
** *
83844 GAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAA
65 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
*
83909 GAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGA
130 GAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGA
* **
83974 AGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAAAGACCGCTGGTTGTCAATAA
195 AGGATATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAA
84039 ACAACTTCCCAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
260 ACAACTTCCCAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
* *
84104 AGTTCAACTTTACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTAAGAGCCAAT
325 AGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
84169 TTCAACTTCACAACGAAGGATATTGGACTCCAG
390 TTCAACTTCACAACGAAGGATATTGGACTCCAG
* *
84202 ACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCA
1 ACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAACAAACAA-TTCTCAATTTCA
* * *
84267 GAGCCAATTTCAACTTCACAGCGTAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCATGAC
65 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
* * *
84332 GAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTTAGAGCCAATTTCAACTTCTCAGCGA
130 GAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGA
* * * * * * * *
84397 AGGATCTTGAACCCAAGGCAACACAAGCTCAACTTCACGACGAAGGGACGGCTGATTGTCAA-CA
195 AGGATATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAA
* * * * *
84461 A-AA-TT-TC-ATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACA
260 ACAACTTCCCAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
* * * * ** *
84522 AGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCGGTTCCAGAGCCAAT
325 AGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
* *
84587 TTCAACTTCACGACGGAGGATATTGGACTC
390 TTCAACTTCACAACGAAGGATATTGGACTC
84617 AGAACAATGC
Statistics
Matches: 771, Mismatches: 65, Indels: 9
0.91 0.08 0.01
Matches are distributed among these distances:
418 134 0.17
419 1 0.00
420 2 0.00
421 2 0.00
422 2 0.00
423 421 0.55
424 207 0.27
425 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (422 bp):
ACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAACAAACAATTCTCAATTTCAG
AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
AAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAA
GGATATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAA
CAACTTCCCAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
GTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATT
TCAACTTCACAACGAAGGATATTGGACTCCAG
Found at i:85400 original size:37 final size:37
Alignment explanation
Indices: 85347--85451 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
85337 CCTTTTCGTC
85347 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
85384 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
85421 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
85452 CCACAAGCAC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:86316 original size:16 final size:16
Alignment explanation
Indices: 86295--86335 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
86285 ATATATTTTA
*
86295 TTTATTTATTTTTCCT
1 TTTATTTATTTTTACT
86311 TTTATTT-TTTTTACT
1 TTTATTTATTTTTACT
86326 TATT-TTTATT
1 T-TTATTTATT
86336 CTTCATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTATTTATTTTTACT
Found at i:86343 original size:26 final size:25
Alignment explanation
Indices: 86288--86347 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
86278 TATATATATA
* * *
86288 TATTTTATTTATTTATTTTTCCTTT
1 TATTTTTTTTACTTATTTTTCATTT
86313 TATTTTTTTTACTTATTTTT-ATTCT
1 TATTTTTTTTACTTATTTTTCATT-T
86338 TCATTTTTTT
1 T-ATTTTTTT
86348 CATTTATTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 2 0.07
25 20 0.67
26 8 0.27
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (25 bp):
TATTTTTTTTACTTATTTTTCATTT
Found at i:86354 original size:26 final size:24
Alignment explanation
Indices: 86288--86355 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 24
86278 TATATATATA
*
86288 TATTTTATTTATTTATTTTTCCTTT
1 TATTTT-TTTATTTATTTTTCATTT
*
86313 TATTTTTTTTACTTATTTTT-ATTCT
1 TA-TTTTTTTATTTATTTTTCATT-T
86338 TCATTTTTTTCATTTATT
1 T-ATTTTTTT-ATTTATT
86356 CATTTTTTCC
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
24 2 0.06
25 23 0.64
26 11 0.31
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.75
Consensus pattern (24 bp):
TATTTTTTTATTTATTTTTCATTT
Found at i:88346 original size:17 final size:17
Alignment explanation
Indices: 88324--88392 Score: 65
Period size: 16 Copynumber: 4.2 Consensus size: 17
88314 TTTTTATAGA
88324 TTTTAAGTTTCTTA-ATT
1 TTTTAA-TTTCTTAGATT
88341 TTTTAATTTCTTAGA-T
1 TTTTAATTTCTTAGATT
****
88357 TTTT-ATTT-TTATCCA
1 TTTTAATTTCTTAGATT
88372 TTTTAATTTCTTAGATT
1 TTTTAATTTCTTAGATT
88389 TTTT
1 TTTT
88393 TAATCTCATA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
14 3 0.07
15 8 0.20
16 16 0.39
17 14 0.34
ACGTcount: A:0.22, C:0.07, G:0.04, T:0.67
Consensus pattern (17 bp):
TTTTAATTTCTTAGATT
Found at i:88350 original size:16 final size:18
Alignment explanation
Indices: 88324--88360 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
88314 TTTTTATAGA
88324 TTTTAAGTTTCTTA-ATT
1 TTTTAAGTTTCTTAGATT
88341 TTTTAA-TTTCTTAGATT
1 TTTTAAGTTTCTTAGATT
88358 TTT
1 TTT
88361 ATTTTTATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTTAAGTTTCTTAGATT
Found at i:96695 original size:18 final size:18
Alignment explanation
Indices: 96669--96709 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
96659 GATTGTATGC
* *
96669 AAAAAAGAGGAAGGAACT
1 AAAAGAGAGGAAGAAACT
*
96687 AAAAGAGAGGCAGAAACT
1 AAAAGAGAGGAAGAAACT
96705 AAAAG
1 AAAAG
96710 TGACTATCTC
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:0.61, C:0.07, G:0.27, T:0.05
Consensus pattern (18 bp):
AAAAGAGAGGAAGAAACT
Found at i:97761 original size:14 final size:14
Alignment explanation
Indices: 97742--97770 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
97732 AGGCTTTGCC
97742 TCTTAGTCTTCTTT
1 TCTTAGTCTTCTTT
97756 TCTTAGTCTTCTTT
1 TCTTAGTCTTCTTT
97770 T
1 T
97771 TCTAATTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.21, G:0.07, T:0.66
Consensus pattern (14 bp):
TCTTAGTCTTCTTT
Found at i:104845 original size:20 final size:19
Alignment explanation
Indices: 104799--104846 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
104789 ATGACCAACA
* * *
104799 AAATAGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCC
104818 AAATCGCAACGCGATCTCC
1 AAATCGCAACGCGATCTCC
104837 AATATCGCAA
1 AA-ATCGCAA
104847 ATCAATTTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.21
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCC
Found at i:104874 original size:20 final size:20
Alignment explanation
Indices: 104820--104874 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
104810 CGATCTCTAA
*
104820 ATCGCAACGCGATCTCCAAT
1 ATCGCAACGCGATTTCCAAT
** *
104840 ATCGCAAATCAATTTCCAGAT
1 ATCGCAACGCGATTTCCA-AT
104861 -TCGCAACGCGATTT
1 ATCGCAACGCGATTT
104875 TGACTATCGC
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 25 0.93
21 2 0.07
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTTCCAAT
Found at i:104944 original size:20 final size:20
Alignment explanation
Indices: 104919--104957 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
104909 CGATTTTAGA
*
104919 AAATCGCAATGCGAATATGT
1 AAATCGCAACGCGAATATGT
*
104939 AAATCGCAACGCGATTATG
1 AAATCGCAACGCGAATATG
104958 ACTATCGCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (20 bp):
AAATCGCAACGCGAATATGT
Found at i:104964 original size:20 final size:20
Alignment explanation
Indices: 104941--105051 Score: 134
Period size: 20 Copynumber: 5.5 Consensus size: 20
104931 GAATATGTAA
*
104941 ATCGCAACGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
*
104961 ATCGCAACACGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* **
104981 ATCGCAACACGATAAT-ACAT
1 ATCGCAACGCGATTCTGAC-T
*
105001 AATCGCAACGCAATTCTGACT
1 -ATCGCAACGCGATTCTGACT
105022 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
105042 GTCGCAACGC
1 ATCGCAACGC
105052 TGAATTTCAA
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.03
20 61 0.78
21 13 0.17
22 2 0.03
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:105920 original size:24 final size:24
Alignment explanation
Indices: 105863--105922 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
105853 TAGTCAGTAT
105863 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
* * *
105887 CCGGACTTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
*
105911 TCGAATTTTGAT
1 TCGAAATTTGAT
105923 GATGTTTCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (24 bp):
TCGAAATTTGATCTTGGTCAATAC
Found at i:105949 original size:30 final size:30
Alignment explanation
Indices: 105915--105975 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
105905 CAATACTCGA
105915 ATTTTGATGATGTTTCATAAGAAGAAACAG
1 ATTTTGATGATGTTTCATAAGAAGAAACAG
105945 ATTTTGATGATGTTTCATAAGAAGAAACAG
1 ATTTTGATGATGTTTCATAAGAAGAAACAG
105975 A
1 A
105976 CCATGCGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.33
Consensus pattern (30 bp):
ATTTTGATGATGTTTCATAAGAAGAAACAG
Found at i:106168 original size:14 final size:14
Alignment explanation
Indices: 106149--106175 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
106139 GAAAAAGAAA
106149 TCCCCGAAGAAAAG
1 TCCCCGAAGAAAAG
106163 TCCCCGAAGAAAA
1 TCCCCGAAGAAAA
106176 TTCCACGGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.30, G:0.19, T:0.07
Consensus pattern (14 bp):
TCCCCGAAGAAAAG
Found at i:108530 original size:140 final size:140
Alignment explanation
Indices: 108278--108700 Score: 774
Period size: 140 Copynumber: 3.0 Consensus size: 140
108268 GCAAACGTTG
108278 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
* *
108343 TTGAACATTGCTATGATATGTTCAGTTGTTATCATTTATTACACATTCATTTGAATATCACAACG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
*
108408 TGAATTTGAC
131 CGAATTTGAC
*
108418 TATTATGTGTATTTTATTTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
* *
108483 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCACTTGAATATCGCAACG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
108548 CGAATTTGAC
131 CGAATTTGAC
*
108558 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGCCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
108623 TTAAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
108688 CGAATTTGAC
131 CGAATTTGAC
108698 TAT
1 TAT
108701 CGCAACGCGA
Statistics
Matches: 272, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 272 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:108696 original size:20 final size:20
Alignment explanation
Indices: 108671--108910 Score: 245
Period size: 20 Copynumber: 12.7 Consensus size: 20
108661 TTACACATTC
*
108671 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
108691 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
108711 ATATGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
*
108730 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
108745 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
108765 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
108785 ATTTGATTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
108805 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
** *
108825 ATTTGACTATCTTAACGAGA
1 ATTTGACTATCGCAACGCGA
*
108845 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
108865 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
108879 ATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
108899 A-TTGACTTTCGC
1 ATTTGACTATCGC
108911 GTTGCGATTT
Statistics
Matches: 188, Mismatches: 20, Indels: 25
0.81 0.09 0.11
Matches are distributed among these distances:
14 20 0.11
15 3 0.02
16 1 0.01
18 1 0.01
19 12 0.06
20 151 0.80
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:108761 original size:54 final size:57
Alignment explanation
Indices: 108679--108835 Score: 212
Period size: 54 Copynumber: 2.8 Consensus size: 57
108669 TCATTTGAAT
*
108679 ATCGCAACGCGAATTTGACTATCGCAACGCGAATATGACTATCGCAACG-CAA-A-A
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGTCAATATA
* *
108733 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGTGAATTTGATT
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGTCAA--T-ATA
* * *
108793 ATCGCAACGTGAATTTGATTATCGCAACGGGAATTTGACTATC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATC
108836 TTAACGAGAA
Statistics
Matches: 91, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
54 48 0.53
55 2 0.02
59 1 0.01
60 40 0.44
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.25
Consensus pattern (57 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGTCAATATA
Found at i:108929 original size:20 final size:21
Alignment explanation
Indices: 108900--108957 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
108890 GCAACGCGAA
108900 TTGA-CTTTCGCGTTGCGATT
1 TTGAGCTTTCGCGTTGCGATT
* *
108920 TTG-GCTTTCGCATTGTGATT
1 TTGAGCTTTCGCGTTGCGATT
*
108940 TTGAG-TTTAGCGTTGCGA
1 TTGAGCTTTCGCGTTGCGA
108958 AAGTGTACCT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.12, C:0.16, G:0.28, T:0.45
Consensus pattern (21 bp):
TTGAGCTTTCGCGTTGCGATT
Found at i:109098 original size:27 final size:27
Alignment explanation
Indices: 109066--109227 Score: 108
Period size: 27 Copynumber: 5.3 Consensus size: 27
109056 AATTATTTAC
109066 ATTAAACAAATCAACTTTTACAAATCA
1 ATTAAACAAATCAACTTTTACAAATCA
* * *
109093 ATTAAACAAACACAAATAAGAATTATTTACACATCA
1 ATT-----AA-ACAAAT--CAACT-TTTACAAATCA
109129 ATTAAACAAATCAACTTTTACAAATCA
1 ATTAAACAAATCAACTTTTACAAATCA
* * *
109156 ATTAAACAAGCACAAATAAGAATTATTTACACATCA
1 ATT----AA--ACAAAT--CAACT-TTTACAAATCA
109192 ATTAAACAAATCAACTTTTACAAATCA
1 ATTAAACAAATCAACTTTTACAAATCA
109219 ATTAAACAA
1 ATTAAACAA
109228 GCAAAACATA
Statistics
Matches: 105, Mismatches: 12, Indels: 36
0.69 0.08 0.24
Matches are distributed among these distances:
27 35 0.33
28 6 0.06
30 12 0.11
31 4 0.04
32 4 0.04
33 12 0.11
35 6 0.06
36 26 0.25
ACGTcount: A:0.54, C:0.17, G:0.02, T:0.27
Consensus pattern (27 bp):
ATTAAACAAATCAACTTTTACAAATCA
Found at i:109122 original size:36 final size:36
Alignment explanation
Indices: 109082--109201 Score: 132
Period size: 36 Copynumber: 3.6 Consensus size: 36
109072 CAAATCAACT
109082 TTTACAAATCAATTAAACAAACACAAATAAGAATTA
1 TTTACAAATCAATTAAACAAACACAAATAAGAATTA
* * *
109118 TTTACACATCAATT-----AA-ACAAAT--CAACT-
1 TTTACAAATCAATTAAACAAACACAAATAAGAATTA
*
109145 TTTACAAATCAATTAAACAAGCACAAATAAGAATTA
1 TTTACAAATCAATTAAACAAACACAAATAAGAATTA
*
109181 TTTACACATCAATTAAACAAA
1 TTTACAAATCAATTAAACAAA
109202 TCAACTTTTA
Statistics
Matches: 66, Mismatches: 9, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
27 13 0.20
28 3 0.05
30 6 0.09
31 2 0.03
32 1 0.02
33 6 0.09
35 3 0.05
36 32 0.48
ACGTcount: A:0.54, C:0.17, G:0.03, T:0.27
Consensus pattern (36 bp):
TTTACAAATCAATTAAACAAACACAAATAAGAATTA
Found at i:109148 original size:63 final size:63
Alignment explanation
Indices: 109009--109299 Score: 333
Period size: 63 Copynumber: 4.5 Consensus size: 63
108999 GATTGAAATC
* *
109009 AACAAATCAACTTTTACATTTCAATCAATTAAATAAGCACAAATAAGAATTATTT----A-C-AT
1 AACAAATCAACTTTTACA----AATCAATTAAACAAACACAAATAAGAATTATTTACACATCAAT
109068 TA
62 TA
109070 AACAAATCAACTTTTACAAATCAATTAAACAAACACAAATAAGAATTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAACACAAATAAGAATTATTTACACATCAATTA
*
109133 AACAAATCAACTTTTACAAATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAACACAAATAAGAATTATTTACACATCAATTA
* * * * *
109196 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAACATACTAATAATTCTTATTTTCCTCAT
1 AACAAATCAACTTTTACAAATCAATTAAAC-A--AACACA-AATAAGAA---TTA-TTTACACAT
109261 CAATTA
58 CAATTA
**
109267 AACAAATCAGACTTTTATGAATCAATTAAACAA
1 AACAAATCA-ACTTTTACAAATCAATTAAACAA
109300 TCAAAAAAGT
Statistics
Matches: 204, Mismatches: 11, Indels: 22
0.86 0.05 0.09
Matches are distributed among these distances:
57 31 0.15
61 19 0.09
62 1 0.00
63 96 0.47
64 1 0.00
66 4 0.02
67 6 0.03
69 1 0.00
70 3 0.01
71 23 0.11
72 19 0.09
ACGTcount: A:0.51, C:0.17, G:0.03, T:0.30
Consensus pattern (63 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAACACAAATAAGAATTATTTACACATCAATTA
Found at i:110673 original size:42 final size:42
Alignment explanation
Indices: 110606--110726 Score: 136
Period size: 42 Copynumber: 2.9 Consensus size: 42
110596 ATGAATCGGG
* * *
110606 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAAAGGC
1 CTCTTGAACGGTGGGAGAGACCTCTTGAACGATGACAAAGGC
** * **
110648 CTCTTGAACGGTGGGATGAGA-CTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGGTGGGA-GAGACCTCTTGAACGATGACAAAGGC
* *
110690 CTCTTGAACGATAGGAGAGACCTCTTGAACGATGACA
1 CTCTTGAACGGTGGGAGAGACCTCTTGAACGATGACA
110727 GGTGAGTCGG
Statistics
Matches: 64, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
41 4 0.06
42 57 0.89
43 3 0.05
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGAGACCTCTTGAACGATGACAAAGGC
Found at i:111248 original size:19 final size:20
Alignment explanation
Indices: 111213--111255 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
111203 AATAGTTTCT
111213 GAAACTTAAAGTCGCAACAC
1 GAAACTTAAAGTCGCAACAC
*
111233 GAAACTTAAA-TCGCAACGC
1 GAAACTTAAAGTCGCAACAC
111252 GAAA
1 GAAA
111256 ATGACTATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.47, C:0.23, G:0.16, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAGTCGCAACAC
Found at i:111267 original size:20 final size:20
Alignment explanation
Indices: 111242--111290 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
111232 CGAAACTTAA
111242 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
111262 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
111282 ATCGCAACG
1 ATCGCAACG
111291 GGATAATCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:111317 original size:19 final size:19
Alignment explanation
Indices: 111295--111348 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
111285 GCAACGGGAT
* *
111295 AATCGCAATGCAAAATAAA
1 AATCGCAACGCAAAACAAA
* *
111314 AATCGCAACGCGAAACCAA
1 AATCGCAACGCAAAACAAA
*
111333 AATCGCAACGCGAAAC
1 AATCGCAACGCAAAAC
111349 TAAATTCGCG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.50, C:0.26, G:0.15, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCAAAACAAA
Found at i:111357 original size:19 final size:19
Alignment explanation
Indices: 111312--111348 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
111302 ATGCAAAATA
111312 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
111331 AAAATCGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
111349 TAAATTCGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.30, G:0.16, T:0.05
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACC
Found at i:111418 original size:33 final size:34
Alignment explanation
Indices: 111352--111432 Score: 112
Period size: 33 Copynumber: 2.4 Consensus size: 34
111342 GCGAAACTAA
*
111352 ATTCGCGTTGCGATTTTCATTTTTGCATTGCGATT
1 ATTC-CGTTGCGATTTTCATTTTCGCATTGCGATT
*
111387 -TTCACGTTGCGATTTTTA-TTTCGCATTGCGATT
1 ATTC-CGTTGCGATTTTCATTTTCGCATTGCGATT
111420 ATTCCGTTGCGAT
1 ATTCCGTTGCGAT
111433 AGTCAAATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
33 23 0.55
34 19 0.45
ACGTcount: A:0.15, C:0.19, G:0.20, T:0.47
Consensus pattern (34 bp):
ATTCCGTTGCGATTTTCATTTTCGCATTGCGATT
Found at i:111449 original size:20 final size:21
Alignment explanation
Indices: 111424--111492 Score: 81
Period size: 20 Copynumber: 3.4 Consensus size: 21
111414 GCGATTATTC
111424 CGTTGCGATAGTCAAATTT-G
1 CGTTGCGATAGTCAAATTTCG
*
111444 CGTTGCGATAGTC-ATTTTCG
1 CGTTGCGATAGTCAAATTTCG
* *
111464 CGTTGTGATAGTC-ATTTTCG
1 CGTTGCGATAGTCAAATTTCG
*
111484 CGTTACGAT
1 CGTTGCGAT
111493 TTAAGTTTCG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.09
20 40 0.91
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (21 bp):
CGTTGCGATAGTCAAATTTCG
Found at i:111511 original size:19 final size:20
Alignment explanation
Indices: 111479--111521 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
111469 TGATAGTCAT
111479 TTTCGCGTTACGA-TTTAAG
1 TTTCGCGTTACGATTTTAAG
* *
111498 TTTCGTGTTGCGATTTTAAG
1 TTTCGCGTTACGATTTTAAG
111518 TTTC
1 TTTC
111522 AGAAACTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.16, C:0.14, G:0.21, T:0.49
Consensus pattern (20 bp):
TTTCGCGTTACGATTTTAAG
Found at i:113428 original size:20 final size:20
Alignment explanation
Indices: 113405--113521 Score: 104
Period size: 20 Copynumber: 6.2 Consensus size: 20
113395 GAAACTTAAA
113405 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* **
113425 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
*
113445 ATCGC-A-ACG-AGAT-A--
1 ATCGCAACACGAAAATGACT
**
113459 ATCGCAACACG-AAATGAAA
1 ATCGCAACACGAAAATGACT
113478 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* **
113498 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
113518 ATCG
1 ATCG
113522 TTGCGATTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
14 5 0.06
15 1 0.01
16 7 0.09
17 3 0.04
18 2 0.03
19 12 0.15
20 49 0.62
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.18
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:113497 original size:53 final size:54
Alignment explanation
Indices: 113404--113506 Score: 154
Period size: 53 Copynumber: 1.9 Consensus size: 54
113394 TGAAACTTAA
** * **
113404 AATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGAGAT
1 AATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGAGAT
113458 AATCGCAACACG-AAATGAAAATCGCAACACGAAAATGACTATCGCAACG
1 AATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACG
113507 CGAATTTGAC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
53 32 0.73
54 12 0.27
ACGTcount: A:0.43, C:0.24, G:0.17, T:0.16
Consensus pattern (54 bp):
AATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGAGAT
Found at i:113926 original size:22 final size:22
Alignment explanation
Indices: 113896--113953 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
113886 GATGGAGATA
113896 GACGGATTTCG-CGGGAGATGGG
1 GACGGATTTCGTC-GGAGATGGG
*
113918 GATGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
*
113940 GACGGATGTCGTCG
1 GACGGATTTCGTCG
113954 TAGAGAGTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
22 31 0.97
23 1 0.03
ACGTcount: A:0.17, C:0.14, G:0.47, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:114186 original size:41 final size:39
Alignment explanation
Indices: 114131--114243 Score: 145
Period size: 40 Copynumber: 2.8 Consensus size: 39
114121 CGATAGTCAG
* **
114131 ATCGCATTGTGATAGTCAAAATCGCGTTGCGATTATGTATT
1 ATCGCATTGCGATAGTCAAAATCGCGTTGCGATT-TACA-T
* * *
114172 ATCGCGTTGCGATAGTCAGAATCGCATTGCGATTTACAT
1 ATCGCATTGCGATAGTCAAAATCGCGTTGCGATTTACAT
114211 ATTCGCATTGCGATAGTCAAAATCGCGTTGCGA
1 A-TCGCATTGCGATAGTCAAAATCGCGTTGCGA
114244 ATTTGGAAAC
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
39 2 0.03
40 30 0.48
41 30 0.48
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.32
Consensus pattern (39 bp):
ATCGCATTGCGATAGTCAAAATCGCGTTGCGATTTACAT
Found at i:114201 original size:20 final size:20
Alignment explanation
Indices: 114120--114243 Score: 101
Period size: 20 Copynumber: 6.2 Consensus size: 20
114110 TTATCGCAAC
*
114120 GCGATAGTC-AGATCGCATT
1 GCGATAGTCAAAATCGCATT
* *
114139 GTGATAGTCAAAATCGCGTT
1 GCGATAGTCAAAATCGCATT
** *
114159 GCGATTATGT-ATTATCGCGTT
1 GCGA-TA-GTCAAAATCGCATT
*
114180 GCGATAGTCAGAATCGCATT
1 GCGATAGTCAAAATCGCATT
* * *
114200 GCGAT-TTACATATTCGCATT
1 GCGATAGT-CAAAATCGCATT
*
114220 GCGATAGTCAAAATCGCGTT
1 GCGATAGTCAAAATCGCATT
114240 GCGA
1 GCGA
114244 ATTTGGAAAC
Statistics
Matches: 83, Mismatches: 16, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
19 11 0.13
20 54 0.65
21 16 0.19
22 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
GCGATAGTCAAAATCGCATT
Found at i:114235 original size:40 final size:41
Alignment explanation
Indices: 114131--114243 Score: 149
Period size: 41 Copynumber: 2.8 Consensus size: 41
114121 CGATAGTCAG
* **
114131 ATCGCATTGTGATAGTCAAAATCGCGTTGCGATTATGTATT
1 ATCGCATTGCGATAGTCAAAATCGCGTTGCGATTACATATT
* * *
114172 ATCGCGTTGCGATAGTCAGAATCGCATTGCGATTTACATA-T
1 ATCGCATTGCGATAGTCAAAATCGCGTTGCGA-TTACATATT
114213 -TCGCATTGCGATAGTCAAAATCGCGTTGCGA
1 ATCGCATTGCGATAGTCAAAATCGCGTTGCGA
114244 ATTTGGAAAC
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
40 28 0.45
41 29 0.47
42 5 0.08
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.32
Consensus pattern (41 bp):
ATCGCATTGCGATAGTCAAAATCGCGTTGCGATTACATATT
Found at i:114281 original size:20 final size:19
Alignment explanation
Indices: 114258--114303 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
114248 GGAAACTGAT
* *
114258 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
114278 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
114297 TTGCGAT
1 TTGCGAT
114304 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:114293 original size:19 final size:19
Alignment explanation
Indices: 114269--114305 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
114259 TGCGATACTG
*
114269 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
114288 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
114306 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:114609 original size:18 final size:20
Alignment explanation
Indices: 114568--114610 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
114558 TTTGGTTCAC
*
114568 GGAATGTAAGATTAACAGTG
1 GGAATGTAAGATTAACACTG
114588 GGAATGTAAGATT-AC-CTG
1 GGAATGTAAGATTAACACTG
114606 GGAAT
1 GGAAT
114611 AGGATTATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.32
19 2 0.09
20 13 0.59
ACGTcount: A:0.37, C:0.07, G:0.30, T:0.26
Consensus pattern (20 bp):
GGAATGTAAGATTAACACTG
Done.