Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005953.1 Hibiscus syriacus cultivar Beakdansim tig00013984_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: 126650
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:4395 original size:3 final size:3
Alignment explanation
Indices: 4387--4418 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
4377 TCTTGAATTC
4387 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
4419 CGATATGGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:6289 original size:25 final size:24
Alignment explanation
Indices: 6261--6307 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
6251 TAATAAAATT
6261 AAACAA-AGATAAATAAATAAATAGA
1 AAACAACA-ATAAATAAA-AAATAGA
*
6286 AAACAACAATGAATAAAAAATA
1 AAACAACAATAAATAAAAAATA
6308 CATGAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 5 0.25
25 14 0.70
26 1 0.05
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.15
Consensus pattern (24 bp):
AAACAACAATAAATAAAAAATAGA
Found at i:6294 original size:28 final size:27
Alignment explanation
Indices: 6262--6315 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
6252 AATAAAATTA
6262 AACAAAG-ATAAATAAATAAATAGAAAAC
1 AACAAAGAATAAA-AAATAAAT-GAAAAC
* *
6290 AACAATGAATAAAAAATACATGAAAA
1 AACAAAGAATAAAAAATAAATGAAAA
6316 AAAATGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 5 0.22
28 13 0.57
29 5 0.22
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.15
Consensus pattern (27 bp):
AACAAAGAATAAAAAATAAATGAAAAC
Found at i:6321 original size:25 final size:29
Alignment explanation
Indices: 6269--6325 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 29
6259 TTAAACAAAG
6269 ATAAATAAATAAATAGAAAACAACAATGA
1 ATAAATAAATAAATAGAAAACAACAATGA
*
6298 ATAAA-AAATACAT-GAAAA-AA-AATGA
1 ATAAATAAATAAATAGAAAACAACAATGA
6323 ATA
1 ATA
6326 TTCATATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 8 0.30
26 2 0.07
27 5 0.19
28 7 0.26
29 5 0.19
ACGTcount: A:0.70, C:0.05, G:0.07, T:0.18
Consensus pattern (29 bp):
ATAAATAAATAAATAGAAAACAACAATGA
Found at i:10415 original size:25 final size:24
Alignment explanation
Indices: 10342--10431 Score: 78
Period size: 24 Copynumber: 3.8 Consensus size: 24
10332 AGCTCGTATA
* *
10342 AATTTGCACCAAAGTGCCACGTAG
1 AATTTGCACCGAAGTGCCGCGTAG
* * *
10366 AATTTATC-CCGAA-TGATCGCTTAG
1 AATTT-GCACCGAAGTG-CCGCGTAG
10390 AAATTTGCACCGAAGTGCCGCGTAG
1 -AATTTGCACCGAAGTGCCGCGTAG
*
10415 AA-TTGCACCGTAGTGCC
1 AATTTGCACCGAAGTGCC
10432 ATATAATATT
Statistics
Matches: 52, Mismatches: 9, Indels: 11
0.72 0.12 0.15
Matches are distributed among these distances:
23 16 0.31
24 17 0.33
25 17 0.33
26 2 0.04
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (24 bp):
AATTTGCACCGAAGTGCCGCGTAG
Found at i:10705 original size:30 final size:31
Alignment explanation
Indices: 10666--10736 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
10656 TCACATAGTA
* *
10666 TATCTCATAGACATATTA-TTTCCATACCTT
1 TATCACATAGACATATCATTTTCCATACCTT
10696 TATCACATAGACATATCATTTTCCATACCTT
1 TATCACATAGACATATCATTTTCCATACCTT
10727 TATCACATAG
1 TATCACATAG
10737 CTCATATAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 16 0.42
31 22 0.58
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.39
Consensus pattern (31 bp):
TATCACATAGACATATCATTTTCCATACCTT
Found at i:12212 original size:39 final size:38
Alignment explanation
Indices: 12150--12385 Score: 186
Period size: 37 Copynumber: 6.3 Consensus size: 38
12140 TTACATATAT
*
12150 GTTTTCATAACTATAT-TATATATGTTTTCAAAAAATA
1 GTTTTCAAAACTATATATATATATGTTTTCAAAAAATA
* * * *
12187 ATTTTCAAAATTATATATATTATATGTTTT-TAAAAATGT
1 GTTTTCAAAACTATATATA-TATATGTTTTCAAAAAAT-A
*
12226 GTTTTCAAAACTATATA-ATATATGTTTTC-AAAAATGT
1 GTTTTCAAAACTATATATATATATGTTTTCAAAAAAT-A
* **
12263 GTTTTCAAAACCATAT-TATATA--TTTTCAAAAACCA
1 GTTTTCAAAACTATATATATATATGTTTTCAAAAAATA
* * * *
12298 ATTTTAAAAACTATATAT-TATATGCTTT-AAAAAA-C
1 GTTTTCAAAACTATATATATATATGTTTTCAAAAAATA
** * *
12333 GTTTTCTAAAAAGATATATATTATATATTTTCAAAACATA
1 GTTTTC-AAAACTATATATA-TATATGTTTTCAAAAAATA
* *
12373 TTTTTAAAAACTA
1 GTTTTCAAAACTA
12386 CAACATATTA
Statistics
Matches: 156, Mismatches: 29, Indels: 26
0.74 0.14 0.12
Matches are distributed among these distances:
35 26 0.17
36 20 0.13
37 54 0.35
38 17 0.11
39 35 0.22
40 4 0.03
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (38 bp):
GTTTTCAAAACTATATATATATATGTTTTCAAAAAATA
Found at i:13781 original size:31 final size:31
Alignment explanation
Indices: 13720--13783 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 31
13710 CCGAGACCCG
*
13720 ACCCGACCCAACCCGAATATATGAATTAAAA
1 ACCCGACCCAACCCGAATAAATGAATTAAAA
*
13751 ACCCGACCCAACCCGACATGAAAT-AATAAAAA
1 ACCCGACCCAACCCGA-AT-AAATGAATTAAAA
13783 A
1 A
13784 ATATTTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 16 0.55
32 10 0.34
33 3 0.10
ACGTcount: A:0.48, C:0.30, G:0.09, T:0.12
Consensus pattern (31 bp):
ACCCGACCCAACCCGAATAAATGAATTAAAA
Found at i:14013 original size:39 final size:36
Alignment explanation
Indices: 13939--14030 Score: 96
Period size: 36 Copynumber: 2.5 Consensus size: 36
13929 GATATAAAAC
* * * *
13939 TTAAAAAAAACCAGACCCGAACCCTACCTCGAATTTTTT
1 TTAAAAAAAACCCGACCCGAACCCGACC-CCAA--ATTT
13978 TTAAAAAAAACCCGACCCG-ACCCGACCCCAAAATTT
1 TTAAAAAAAACCCGACCCGAACCCGACCCC-AAATTT
*
14014 TTAAAAAAAGCCCGACC
1 TTAAAAAAAACCCGACC
14031 TGAATATCAC
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
36 19 0.40
37 1 0.02
38 9 0.19
39 18 0.38
ACGTcount: A:0.41, C:0.32, G:0.09, T:0.18
Consensus pattern (36 bp):
TTAAAAAAAACCCGACCCGAACCCGACCCCAAATTT
Found at i:14069 original size:33 final size:33
Alignment explanation
Indices: 14013--14094 Score: 100
Period size: 33 Copynumber: 2.6 Consensus size: 33
14003 CCCCAAAATT
* *
14013 TTTAAAAAA-A-G-CCCGACCTGAATATCACAC
1 TTTAAAAAACATGACCCGACCCGAATATCAAAC
14043 TTTAAAAAACATGACCCGACCCGAATATCAAAC
1 TTTAAAAAACATGACCCGACCCGAATATCAAAC
*
14076 TTAAAAAAATC-TGACCCGA
1 TTTAAAAAA-CATGACCCGA
14095 TCTCGAATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
30 9 0.20
31 1 0.02
32 1 0.02
33 33 0.73
34 1 0.02
ACGTcount: A:0.45, C:0.26, G:0.10, T:0.20
Consensus pattern (33 bp):
TTTAAAAAACATGACCCGACCCGAATATCAAAC
Found at i:21765 original size:18 final size:18
Alignment explanation
Indices: 21742--21784 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
21732 TGTCCTCTTC
*
21742 ACTTCCTTCTAAAGTTGG
1 ACTTCCTTCTAAAATTGG
21760 ACTTCCTTCTAAAATTGG
1 ACTTCCTTCTAAAATTGG
21778 ACTTCCT
1 ACTTCCT
21785 CGGACAGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.40
Consensus pattern (18 bp):
ACTTCCTTCTAAAATTGG
Found at i:25628 original size:41 final size:40
Alignment explanation
Indices: 25450--25746 Score: 142
Period size: 41 Copynumber: 7.2 Consensus size: 40
25440 TAACATTAAC
* *
25450 GGCGTTTCTCAACAAACGCCGCTAAAA-CTCATACTTTAGT
1 GGCGTTTTTCAACAAACACCGCTAAAACCT-ATACTTTAGT
* * * * *
25490 GGCGTTTGTT-TACAAACGCCACCATATAATC-ATTA-TTTAGT
1 GGCGTTT-TTCAACAAACACC-GC-TAAAACCTA-TACTTTAGT
* * *** *
25531 GGCGTTTTTAAACAAACGCCGC-AATAGGGTATA-TATATCGT
1 GGCGTTTTTCAACAAACACCGCTAA-AACCTATACT-T-TAGT
* **
25572 GGCATTTTT-AGACAAACACCATTAAAACCTAGTACTTTAGT
1 GGCGTTTTTCA-ACAAACACCGCTAAAACCTA-TACTTTAGT
* * *
25613 GGCGTTTTTCAACAAAAAGCCGCTAAAACGTAATACTTTAAT
1 GGCGTTTTTCAACAAACA-CCGCTAAAACCT-ATACTTTAGT
* * * *
25655 GTCGTTTTAAGCAAAAAACACTGCTAAATA-CTCATACTTTAGT
1 GGCGTTTT--TCAACAAACACCGCTAAA-ACCT-ATACTTTAGT
* * * *
25698 GGTGTTTTCCAACAAACGCCGCTAAAACGTATTACTTTAGT
1 GGCGTTTTTCAACAAACACCGCTAAAACCTA-TACTTTAGT
25739 GGCGTTTT
1 GGCGTTTT
25747 AATTAAAACG
Statistics
Matches: 194, Mismatches: 41, Indels: 43
0.70 0.15 0.15
Matches are distributed among these distances:
38 1 0.01
39 4 0.02
40 24 0.12
41 95 0.49
42 36 0.19
43 26 0.13
44 8 0.04
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (40 bp):
GGCGTTTTTCAACAAACACCGCTAAAACCTATACTTTAGT
Found at i:25661 original size:42 final size:42
Alignment explanation
Indices: 25594--25788 Score: 152
Period size: 41 Copynumber: 4.7 Consensus size: 42
25584 CAAACACCAT
* *
25594 TAAAACCTAGTACTTTAGTGGCGTTTTTCAACAAAAAGCCGC
1 TAAAACGTAATACTTTAGTGGCGTTTTTCAACAAAAAGCCGC
* * *
25636 TAAAACGTAATACTTTAATGTCG-TTTT-AAGCAAAAAACACTGC
1 TAAAACGTAATACTTTAGTGGCGTTTTTCAA-CAAAAAGC-C-GC
* * * *
25679 TAAATAC-TCATACTTTAGTGGTGTTTTCCAAC-AAACGCCGC
1 TAAA-ACGTAATACTTTAGTGGCGTTTTTCAACAAAAAGCCGC
* * * *
25720 TAAAACGTATTACTTTAGTGGCG-TTTT-AATTAAAACGCCTC
1 TAAAACGTAATACTTTAGTGGCGTTTTTCAA-CAAAAAGCCGC
* *
25761 TAAAGAC-TCATACTTTAGTGGCATTTTT
1 TAAA-ACGTAATACTTTAGTGGCGTTTTT
25789 TTGAATAAAC
Statistics
Matches: 121, Mismatches: 21, Indels: 22
0.74 0.13 0.13
Matches are distributed among these distances:
39 2 0.02
40 7 0.06
41 55 0.45
42 27 0.22
43 22 0.18
44 6 0.05
45 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (42 bp):
TAAAACGTAATACTTTAGTGGCGTTTTTCAACAAAAAGCCGC
Found at i:25745 original size:84 final size:83
Alignment explanation
Indices: 25604--25787 Score: 235
Period size: 84 Copynumber: 2.2 Consensus size: 83
25594 TAAAACCTAG
* *
25604 TACTTTAGTGGCGTTTTTCAACAAAAAGCCGCTAAAACGTAATACTTTAATGTCGTTTTAAGCAA
1 TACTTTAGTGGCGTTTTCCAACAAAAAGCCGCTAAAACGTAATACTTTAATGGCGTTTTAAGCAA
*
25669 AAAACACTGCTAAATACTCA
66 AAAAC-CT-CTAAAGACTCA
* * * * **
25689 TACTTTAGTGGTGTTTTCCAAC-AAACGCCGCTAAAACGTATTACTTTAGTGGCGTTTTAATTAA
1 TACTTTAGTGGCGTTTTCCAACAAAAAGCCGCTAAAACGTAATACTTTAATGGCGTTTTAAGCAA
**
25753 AACGCCTCTAAAGACTCA
66 AAAACCTCTAAAGACTCA
*
25771 TACTTTAGTGGCATTTT
1 TACTTTAGTGGCGTTTT
25788 TTTGAATAAA
Statistics
Matches: 86, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
82 25 0.29
83 2 0.02
84 39 0.45
85 20 0.23
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.34
Consensus pattern (83 bp):
TACTTTAGTGGCGTTTTCCAACAAAAAGCCGCTAAAACGTAATACTTTAATGGCGTTTTAAGCAA
AAAACCTCTAAAGACTCA
Found at i:30264 original size:42 final size:41
Alignment explanation
Indices: 30216--30414 Score: 177
Period size: 42 Copynumber: 4.8 Consensus size: 41
30206 CGTTTGTATC
* * *
30216 CAAAAACGCTGCTATATATCTGACCTTTTGCAGCCTTTCTT
1 CAAAAACGCCGCTATAGATCTGACCTTTTGCAGCGTTTCTT
* * *
30257 CTAAAAACGCCGCTATAGATATGACCTTTTGCAACATTTCTTT
1 C-AAAAACGCCGCTATAGATCTGACCTTTTGCAGCGTTTC-TT
* * * * * * *
30300 TAAAAATGCCGCGATAGATTTCGATCTTTTGCGGCGTTTGTT
1 CAAAAACGCCGCTATAGATCT-GACCTTTTGCAGCGTTTCTT
* * *
30342 ACAAAAATGCCGCTATAGATCTGAGCTTTTGC-GACGTTTGTT
1 -CAAAAACGCCGCTATAGATCTGACCTTTTGCAG-CGTTTCTT
*
30384 CAAAAACACCGCTAT-GTATCTGACCTTTTGC
1 CAAAAACGCCGCTATAG-ATCTGACCTTTTGC
30415 GGTGTTTATT
Statistics
Matches: 131, Mismatches: 21, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
40 1 0.01
41 28 0.21
42 69 0.53
43 33 0.25
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.35
Consensus pattern (41 bp):
CAAAAACGCCGCTATAGATCTGACCTTTTGCAGCGTTTCTT
Found at i:37946 original size:2 final size:2
Alignment explanation
Indices: 37898--37928 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
37888 GCATGCATTC
37898 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 A
37929 GTCATCCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58903 original size:34 final size:34
Alignment explanation
Indices: 58856--58923 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
58846 ATTAACTTTG
*
58856 CCATTGCTGATCTCTCCAAAGCGCCGGCGTTTTT
1 CCATTGCTAATCTCTCCAAAGCGCCGGCGTTTTT
58890 CCATTGCTAATCTCTCCAAAGCGCCGGCGTTTTT
1 CCATTGCTAATCTCTCCAAAGCGCCGGCGTTTTT
58924 ACCAAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.16, C:0.32, G:0.19, T:0.32
Consensus pattern (34 bp):
CCATTGCTAATCTCTCCAAAGCGCCGGCGTTTTT
Found at i:62925 original size:27 final size:27
Alignment explanation
Indices: 62887--62971 Score: 134
Period size: 27 Copynumber: 3.1 Consensus size: 27
62877 ATAATAAAAT
* *
62887 AATATATCATCGATGAATTTTTATTTA
1 AATATATTATCGATGAATTTTTATATA
* *
62914 AATATATTATCGATGAGTTTTTATCTA
1 AATATATTATCGATGAATTTTTATATA
62941 AATATATTATCGATGAATTTTTATATA
1 AATATATTATCGATGAATTTTTATATA
62968 AATA
1 AATA
62972 ATTTTTATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (27 bp):
AATATATTATCGATGAATTTTTATATA
Found at i:63199 original size:20 final size:20
Alignment explanation
Indices: 63142--63192 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
63132 ATCATATTAT
63142 CTGATAATCTTTTATTCCTA
1 CTGATAATCTTTTATTCCTA
63162 CTGATAATCTTTTATTCCTA
1 CTGATAATCTTTTATTCCTA
63182 CTGATAATCTT
1 CTGATAATCTT
63193 ACATTCCGTG
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:0.25, C:0.20, G:0.06, T:0.49
Consensus pattern (20 bp):
CTGATAATCTTTTATTCCTA
Found at i:63313 original size:2 final size:2
Alignment explanation
Indices: 63308--63369 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
63298 TTATAAAAAA
63308 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
63350 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
63370 GGAATTGGAC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:64840 original size:77 final size:77
Alignment explanation
Indices: 64741--64888 Score: 278
Period size: 77 Copynumber: 1.9 Consensus size: 77
64731 AACGTTTTAA
*
64741 ACTAAAATGCCCTTAATTTTTTTTTCCAAAAATATCCTTATTTTGTCATTGAATAATAAAAATTC
1 ACTAAAATGCCCTTAATTTTTTTTTCCAAAAATATACTTATTTTGTCATTGAATAATAAAAATTC
64806 TATGAAGGTTGG
66 TATGAAGGTTGG
*
64818 ACTAAAATGCCCTTAATTTTTTTTTTCAAAAATATACTTATTTTGTCATTGAATAATAAAAATTC
1 ACTAAAATGCCCTTAATTTTTTTTTCCAAAAATATACTTATTTTGTCATTGAATAATAAAAATTC
64883 TATGAA
66 TATGAA
64889 TGTTAAATTA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 69 1.00
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (77 bp):
ACTAAAATGCCCTTAATTTTTTTTTCCAAAAATATACTTATTTTGTCATTGAATAATAAAAATTC
TATGAAGGTTGG
Found at i:70693 original size:21 final size:21
Alignment explanation
Indices: 70669--70731 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
70659 ATTTGATAAT
70669 TTTTACATAATAATTAAAATA
1 TTTTACATAATAATTAAAATA
*
70690 TTTTACATAATATATTACTAAT-
1 TTTTACATAATA-ATTA-AAATA
* *
70712 TTATA-ATAATAATAAAAATA
1 TTTTACATAATAATTAAAATA
70732 AAATATTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
19 3 0.09
20 3 0.09
21 18 0.51
22 8 0.23
23 3 0.09
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTTACATAATAATTAAAATA
Found at i:72246 original size:2 final size:2
Alignment explanation
Indices: 72236--72273 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
72226 TTTATGTGTG
72236 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
72274 TTAGTTACTC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:74885 original size:23 final size:23
Alignment explanation
Indices: 74835--74885 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
74825 TATTCATGAC
* * * *
74835 TAAACTGGGATTATTTTTTAATA
1 TAAATTGGGATTACTTTTAAAAA
*
74858 GAAATTGGGATTACTTTTAAAAA
1 TAAATTGGGATTACTTTTAAAAA
74881 TAAAT
1 TAAAT
74886 GATTGTGAAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.04, G:0.14, T:0.41
Consensus pattern (23 bp):
TAAATTGGGATTACTTTTAAAAA
Found at i:79412 original size:23 final size:26
Alignment explanation
Indices: 79363--79411 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
79353 TGGGTTGTAA
*
79363 TTAATTAAATATTATTTTGATTAAAAT
1 TTAATTAAATATTA-TTTAATTAAAAT
79390 TTAATT-AATATTA-TTAATTAAA
1 TTAATTAAATATTATTTAATTAAA
79412 TAAATATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 8 0.38
26 7 0.33
27 6 0.29
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (26 bp):
TTAATTAAATATTATTTAATTAAAAT
Found at i:88771 original size:24 final size:25
Alignment explanation
Indices: 88743--88790 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
88733 TGAAGTTTGT
88743 GAATGATTT-TATTTGTTTCTATAA
1 GAATGATTTCTATTTGTTTCTATAA
* * *
88767 GAATGTTTTCTGTTTGTTTTTATA
1 GAATGATTTCTATTTGTTTCTATA
88791 CCATGTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.23, C:0.04, G:0.15, T:0.58
Consensus pattern (25 bp):
GAATGATTTCTATTTGTTTCTATAA
Found at i:89665 original size:17 final size:17
Alignment explanation
Indices: 89643--89675 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
89633 AAATGATAAT
89643 TTTTATAACGTTACACG
1 TTTTATAACGTTACACG
89660 TTTTATAACGTTACAC
1 TTTTATAACGTTACAC
89676 ATCAAGGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.42
Consensus pattern (17 bp):
TTTTATAACGTTACACG
Found at i:89860 original size:24 final size:23
Alignment explanation
Indices: 89836--89885 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 23
89826 AAACAATTAT
89836 TTTTATTTTTTTAAAT-ATTAATA
1 TTTTA-TTTTTTAAATAATTAATA
89859 --TTATTTTTTAAATAATTAATA
1 TTTTATTTTTTAAATAATTAATA
89880 TCTTTA
1 T-TTTA
89886 AAGAAATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
20 10 0.43
21 10 0.43
24 3 0.13
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTATTTTTTAAATAATTAATA
Found at i:89867 original size:20 final size:21
Alignment explanation
Indices: 89842--89880 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
89832 TTATTTTTAT
89842 TTTTTTAAAT-ATTAATATTA
1 TTTTTTAAATAATTAATATTA
89862 TTTTTTAAATAATTAATAT
1 TTTTTTAAATAATTAATAT
89881 CTTTAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTTTAAATAATTAATATTA
Found at i:95265 original size:71 final size:71
Alignment explanation
Indices: 95141--95274 Score: 214
Period size: 71 Copynumber: 1.9 Consensus size: 71
95131 GGTAATTCCG
*
95141 AAATTCTAAGAATGATATCCATCACCATCCTTAAGCACTGTGAGAGAGTTTGCTAGCATGGGGCA
1 AAATTCTAAGAATGATATCCATCACCATCCTTAAGCACTGTGAGAGAGCTTGCTAGCATGGGGCA
95206 ATGCCA
66 ATGCCA
* * * * *
95212 AAATTCTATGAGTGATATCCATCACCATCCTTAAGCAGTGTGAGGGTGCTTGCTAGCATGGGG
1 AAATTCTAAGAATGATATCCATCACCATCCTTAAGCACTGTGAGAGAGCTTGCTAGCATGGGG
95275 TTGTGCAGAG
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 57 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (71 bp):
AAATTCTAAGAATGATATCCATCACCATCCTTAAGCACTGTGAGAGAGCTTGCTAGCATGGGGCA
ATGCCA
Found at i:104474 original size:81 final size:82
Alignment explanation
Indices: 104331--104541 Score: 352
Period size: 81 Copynumber: 2.6 Consensus size: 82
104321 CCAGAACCGC
* * *
104331 GTCCATAGGGCTTACCTTAAGCACACGGCAAAAAGGAAGCCAACCTAAGGATAGGCTTTGGGGCC
1 GTCCATAGGGCTTACCCTAAGCACACAGC--AAAGGGAGCCAACCTAAGGATAGGCTTTGGGGCC
*
104396 TGTATCCTTAAGTCCGTAA
64 TGTACCCTTAAGTCCGTAA
*
104415 GTCCATAGGGCTTACCCTAAGCACACAGC-AAGGGAGCCAACTTAAGGATAGGCTTTGGGGCCTG
1 GTCCATAGGGCTTACCCTAAGCACACAGCAAAGGGAGCCAACCTAAGGATAGGCTTTGGGGCCTG
104479 TACCCTTAAGTCCGTAA
66 TACCCTTAAGTCCGTAA
104496 GTCCATAGGGCTTACCCTAAGCACACAGCAAAGGGAGCCAACCTAA
1 GTCCATAGGGCTTACCCTAAGCACACAGCAAAGGGAGCCAACCTAA
104542 TGGAGCATGT
Statistics
Matches: 120, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
81 78 0.65
82 15 0.12
84 27 0.22
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.19
Consensus pattern (82 bp):
GTCCATAGGGCTTACCCTAAGCACACAGCAAAGGGAGCCAACCTAAGGATAGGCTTTGGGGCCTG
TACCCTTAAGTCCGTAA
Found at i:108512 original size:21 final size:20
Alignment explanation
Indices: 108470--108507 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
108460 TTGAAAAAAT
108470 ATTTCCATTTCCAATTTTAAC
1 ATTTCCATTTCC-ATTTTAAC
108491 ATTTCCATTTCC-TTTTA
1 ATTTCCATTTCCATTTTA
108508 CAACAATAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
21 12 0.71
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTCCATTTCCATTTTAAC
Found at i:110286 original size:16 final size:18
Alignment explanation
Indices: 110258--110294 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
110248 AGATTAGAGA
110258 TTTAATTATAATAAT-AT
1 TTTAATTATAATAATAAT
110275 TTTAATTA-AATAATAAT
1 TTTAATTATAATAATAAT
110292 TTT
1 TTT
110295 TAACAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTAATTATAATAATAAT
Found at i:110305 original size:16 final size:19
Alignment explanation
Indices: 110265--110306 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
110255 AGATTTAATT
*
110265 ATAATAATATTTTAATTAA
1 ATAATAATATTTTAATCAA
110284 ATAATAAT-TTTTAA-CAA
1 ATAATAATATTTTAATCAA
110301 A-AATAA
1 ATAATAA
110307 CTCGATTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 5 0.23
17 3 0.14
18 6 0.27
19 8 0.36
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAATAATATTTTAATCAA
Found at i:113576 original size:214 final size:215
Alignment explanation
Indices: 113279--113741 Score: 610
Period size: 214 Copynumber: 2.2 Consensus size: 215
113269 GACTAATGAC
*
113279 AAATCACAAATCAAAGTTCAACAATATAAAAAAACTATTCAAAAGCGTAAATCACAAATCCAAAT
1 AAATCACAAATCAAAGTCCAACAATAT-AAAAAACTATTCAAAAGCGTAAATCACAAATCCAAAT
* * * * * * *
113344 ATAATATGAGGCTCCAAAGAAGGGAGGATCATATACGGAAAATGTAAAAAACCTAATTAAAAAAA
65 ACAATATAAGGCTCCAAAGAAGGAAGAACCATACAAGGAAAATGTAAAAAACCTAATTAAAAAAA
*
113409 CCTTGAACAAAATATAGATATGAACACATCTAATTTTATCATAAAATGAACCACAAAAAGAGATT
130 -CTTGAACAAAATATAGATATGAACACATCTAATTGTATCATAAAATGAACCACAAAAAGAGATT
*
113474 AAACTA-CTAAAGACCATCGAG
194 AAACTACCGAAAGACCATCGAG
* * ***
113495 AAATCATAAATCAAAGTCCAACAATAT-AAAAACTATTCACAAA-TGTAAATCATGTATCCAAAT
1 AAATCACAAATCAAAGTCCAACAATATAAAAAACTATTCA-AAAGCGTAAATCACAAATCCAAAT
* * * *
113558 CCAATCTAAGGGTCCAAAGAAGGAAGAACCATACAAGGAAAATGTTAAAAACCTAATTAAAAAAA
65 ACAATATAAGGCTCCAAAGAAGGAAGAACCATACAAGGAAAATGTAAAAAACCTAATTAAAAAAA
* * ** *
113623 CTTGAACAAAATATAGATATGAATATATCTAATTGTATTGTAAAATGAATCACAAAAAGAGATTA
130 CTTGAACAAAATATAGATATGAACACATCTAATTGTATCATAAAATGAACCACAAAAAGAGATTA
* * *
113688 AGCTACCGAAAGATCATCGAT
195 AACTACCGAAAGACCATCGAG
*
113709 AAATCACAAATCAAAGTCCAGC-ATCATAAAAAA
1 AAATCACAAATCAAAGTCCAACAAT-ATAAAAAA
113742 ATATAACCCC
Statistics
Matches: 214, Mismatches: 29, Indels: 9
0.85 0.12 0.04
Matches are distributed among these distances:
213 65 0.30
214 116 0.54
215 8 0.04
216 25 0.12
ACGTcount: A:0.52, C:0.16, G:0.11, T:0.22
Consensus pattern (215 bp):
AAATCACAAATCAAAGTCCAACAATATAAAAAACTATTCAAAAGCGTAAATCACAAATCCAAATA
CAATATAAGGCTCCAAAGAAGGAAGAACCATACAAGGAAAATGTAAAAAACCTAATTAAAAAAAC
TTGAACAAAATATAGATATGAACACATCTAATTGTATCATAAAATGAACCACAAAAAGAGATTAA
ACTACCGAAAGACCATCGAG
Found at i:114443 original size:29 final size:29
Alignment explanation
Indices: 114347--114498 Score: 144
Period size: 29 Copynumber: 5.2 Consensus size: 29
114337 TAGAGGATCT
* * * *
114347 CATGCAAAATCATGACGGGGATATAATCC
1 CATGCAGAATCAGGATGAGGATATAATCC
* * * *
114376 CATACAGAATTAGAATGGGGGATATAATCC
1 CATGCAGAATCAGGAT-GAGGATATAATCC
* *
114406 TATGCAGAATCATGATGAGGATATAATCC
1 CATGCAGAATCAGGATGAGGATATAATCC
* * * * *
114435 CATGTAGAATAAGGACGTGGATATAATTC
1 CATGCAGAATCAGGATGAGGATATAATCC
114464 CATGCAGAATCAGGATGAGGATCA-AATCC
1 CATGCAGAATCAGGATGAGGAT-ATAATCC
114493 CATGCA
1 CATGCA
114499 AAAACATGAA
Statistics
Matches: 97, Mismatches: 24, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
29 72 0.74
30 25 0.26
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.23
Consensus pattern (29 bp):
CATGCAGAATCAGGATGAGGATATAATCC
Found at i:114444 original size:59 final size:58
Alignment explanation
Indices: 114347--114498 Score: 173
Period size: 58 Copynumber: 2.6 Consensus size: 58
114337 TAGAGGATCT
* * * * * *
114347 CATGCAAAATCATGACGGGGATATAATCCCATACAGAATTAGAATGGGGGATATAA-TC
1 CATGCAGAATCATGATGAGGATATAATCCCATGCAGAATAAGAA-CGGGGATATAATTC
* * *
114405 CTATGCAGAATCATGATGAGGATATAATCCCATGTAGAATAAGGACGTGGATATAATTC
1 C-ATGCAGAATCATGATGAGGATATAATCCCATGCAGAATAAGAACGGGGATATAATTC
*
114464 CATGCAGAATCAGGATGAGGATCA-AATCCCATGCA
1 CATGCAGAATCATGATGAGGAT-ATAATCCCATGCA
114499 AAAACATGAA
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
58 40 0.50
59 40 0.50
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.23
Consensus pattern (58 bp):
CATGCAGAATCATGATGAGGATATAATCCCATGCAGAATAAGAACGGGGATATAATTC
Found at i:121327 original size:40 final size:41
Alignment explanation
Indices: 121251--121744 Score: 338
Period size: 41 Copynumber: 11.8 Consensus size: 41
121241 TTTTTAGAAT
*
121251 AAACGCCGCTAAATACTCA-TACTTTAGTGGCATTTTTATAC
1 AAACGCCGCTAAAGACT-AGTACTTTAGTGGCATTTTTATAC
* * * ** *
121292 AAATGCCGCTAAATACT-GTACTTTAATGGTGTTTTTAGAAC
1 AAACGCCGCTAAAGACTAGTACTTTAGTGGCATTTTTA-TAC
* * *
121333 AAACGCCGCTATAGATTAGTACTTTAGTGG-ATTTTTTTAAAC
1 AAACGCCGCTAAAGACTAGTACTTTAGTGGCA--TTTTTATAC
* * *
121375 AAACGACGCTATAGACTAGTACTTTCGTGGCATTTTTAT-C
1 AAACGCCGCTAAAGACTAGTACTTTAGTGGCATTTTTATAC
* *
121415 AAACGCCGCTAAAGACT-GTACTTTAGTGGCATTTGTATAA
1 AAACGCCGCTAAAGACTAGTACTTTAGTGGCATTTTTATAC
* * * * *
121455 AAACGCCGCTAAAGACT-GTACTATAGACTAGTACTTTAGTGGCGTTTGTAT
1 AAACGCCGCTAAAGACTAGTACTTTAG--T-G-GC---A-T---TTTTATAC
** *** * * * * *
121506 AAA-AACGCCGCTAGA-GACTGTACTTTTGTGGCGTTTGTATAA
1 AAACGCCG-CTAAAGACTA--GTACTTTAGTGGCATTTTTATAC
* *
121548 AAACGCCGTTAAAGACTCGTACTTTAGTGGCATTTTTATAC
1 AAACGCCGCTAAAGACTAGTACTTTAGTGGCATTTTTATAC
* * * *
121589 AAACGTCGCTAAAGACTCGTACTTTTGTGGCTTTTTTATAC
1 AAACGCCGCTAAAGACTAGTACTTTAGTGGCATTTTTATAC
* * *
121630 AAACGCCGCTAAAGACTCGTACTTTTGTGGCACTTTTTAGAAC
1 AAACGCCGCTAAAGACTAGTACTTTAGTGGCA-TTTTTA-TAC
* * * *
121673 AAATGCCGCTAAAGACTCGTACTTTAATGGCGTTTTTATAC
1 AAACGCCGCTAAAGACTAGTACTTTAGTGGCATTTTTATAC
* * *
121714 AAACGCCACTAAAAACTCGTACTTTAGTGGC
1 AAACGCCGCTAAAGACTAGTACTTTAGTGGC
121745 GTTTATAAAA
Statistics
Matches: 359, Mismatches: 68, Indels: 52
0.75 0.14 0.11
Matches are distributed among these distances:
39 19 0.05
40 57 0.16
41 152 0.42
42 64 0.18
43 40 0.11
44 1 0.00
45 1 0.00
47 1 0.00
48 1 0.00
49 1 0.00
50 3 0.01
51 12 0.03
53 7 0.02
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (41 bp):
AAACGCCGCTAAAGACTAGTACTTTAGTGGCATTTTTATAC
Found at i:121356 original size:82 final size:82
Alignment explanation
Indices: 121237--121748 Score: 442
Period size: 82 Copynumber: 6.1 Consensus size: 82
121227 CATTTCTAGC
* * * *
121237 GGCGTTTTTAGAATAAACGCCGCTAAATACTCATACTTTAGTGGCATTTTTATACAAATGCCGCT
1 GGCGTTTTTAGAACAAACGCCGCTAAAGACT-GTACTTTAGTGGCATTTTTATACAAACGCCGCT
* *
121302 AAATACT-GTACTTTAAT
65 AAAGACTCGTACTTTAGT
* * * * *
121319 GGTGTTTTTAGAACAAACGCCGCTATAGATTAGTACTTTAGTGG-ATTTTTTTAAACAAACGACG
1 GGCGTTTTTAGAACAAACGCCGCTAAAGACT-GTACTTTAGTGGCA--TTTTTATACAAACGCCG
* * *
121383 CTATAGACTAGTACTTTCGT
63 CTAAAGACTCGTACTTTAGT
* * * *
121403 GGCATTTTT--ATCAAACGCCGCTAAAGACTGTACTTTAGTGGCATTTGTATAAAAACGCCGCTA
1 GGCGTTTTTAGAACAAACGCCGCTAAAGACTGTACTTTAGTGGCATTTTTATACAAACGCCGCTA
*
121466 AAGACT-GTACTATAGACT
66 AAGACTCGTACTTTAG--T
* * * * * * * * *
121484 AGTACTTTAGTGGCGTTTGTATAAAAACGCCGCTAGAGACTGTACTTTTGTGGCGTTTGTATAAA
1 -G-GCGTT--T----TTAG-A-ACAAACGCCGCTAAAGACTGTACTTTAGTGGCATTTTTATACA
*
121549 AACGCCGTTAAAGACTCGTACTTTAGT
56 AACGCCGCTAAAGACTCGTACTTTAGT
* * * * *
121576 GGCATTTTTA-TACAAACGTCGCTAAAGACTCGTACTTTTGTGGCTTTTTTATACAAACGCCGCT
1 GGCGTTTTTAGAACAAACGCCGCTAAAGACT-GTACTTTAGTGGCATTTTTATACAAACGCCGCT
*
121640 AAAGACTCGTACTTTTGT
65 AAAGACTCGTACTTTAGT
* * * * *
121658 GGCACTTTTTAGAACAAATGCCGCTAAAGACTCGTACTTTAATGGCGTTTTTATACAAACGCCAC
1 GGC-GTTTTTAGAACAAACGCCGCTAAAGACT-GTACTTTAGTGGCATTTTTATACAAACGCCGC
*
121723 TAAAAACTCGTACTTTAGT
64 TAAAGACTCGTACTTTAGT
121742 GGCGTTT
1 GGCGTTT
121749 ATAAAAACAA
Statistics
Matches: 350, Mismatches: 58, Indels: 43
0.78 0.13 0.10
Matches are distributed among these distances:
79 7 0.02
80 21 0.06
81 30 0.09
82 105 0.30
83 33 0.09
84 83 0.24
85 1 0.00
88 1 0.00
89 2 0.01
90 3 0.01
91 1 0.00
92 2 0.01
93 53 0.15
94 8 0.02
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (82 bp):
GGCGTTTTTAGAACAAACGCCGCTAAAGACTGTACTTTAGTGGCATTTTTATACAAACGCCGCTA
AAGACTCGTACTTTAGT
Found at i:121543 original size:93 final size:93
Alignment explanation
Indices: 121383--121652 Score: 289
Period size: 93 Copynumber: 3.0 Consensus size: 93
121373 ACAAACGACG
* * *
121383 CTATAGACTAGTACTTTCGTGGCATTTTTATCAAACGCCGCTAAAGACTGTACTTTAGTGGCATT
1 CTATAGACTAGTACTTTAGTGGCATTTGTATAAAACGCCGCTAAAGACTGTACTTTAGTGGCATT
121448 TGTATAAAAACGCCGCTAAAGACT-GTA
66 TGTATAAAAACGCCGCTAAAGACTCGTA
* * * *
121475 CTATAGACTAGTACTTTAGTGGCGTTTGTATAAAAACGCCGCTAGAGACTGTACTTTTGTGGCGT
1 CTATAGACTAGTACTTTAGTGGCATTTGTAT-AAAACGCCGCTAAAGACTGTACTTTAGTGGCAT
121540 TTGTATAAAAACG-C-C----G--T--TA
65 TTGTATAAAAACGCCGCTAAAGACTCGTA
* * * * *
121559 --A-AGACTCGTACTTTAGTGGCATTTTTATACAAACGTCGCTAAAGACTCGTACTTTTGTGGCT
1 CTATAGACTAGTACTTTAGTGGCATTTGTATA-AAACGCCGCTAAAGACT-GTACTTTAGTGGCA
* *
121621 TTTTTATACAAACGCCGCTAAAGACTCGTA
64 TTTGTATAAAAACGCCGCTAAAGACTCGTA
121651 CT
1 CT
121653 TTTGTGGCAC
Statistics
Matches: 148, Mismatches: 15, Indels: 28
0.77 0.08 0.15
Matches are distributed among these distances:
80 1 0.01
81 39 0.26
82 26 0.18
83 1 0.01
84 3 0.02
85 1 0.01
87 1 0.01
88 1 0.01
90 1 0.01
91 1 0.01
92 31 0.21
93 42 0.28
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (93 bp):
CTATAGACTAGTACTTTAGTGGCATTTGTATAAAACGCCGCTAAAGACTGTACTTTAGTGGCATT
TGTATAAAAACGCCGCTAAAGACTCGTA
Found at i:121581 original size:134 final size:135
Alignment explanation
Indices: 121341--121611 Score: 361
Period size: 134 Copynumber: 2.0 Consensus size: 135
121331 ACAAACGCCG
* * * *
121341 CTATAGATTAGTACTTTAGTGGATTTTTTTAAACAAACGACGCTATAGACTAGTACTTTCGTGGC
1 CTATAGACTAGTACTTTAGTGGATTTGTATAAACAAACGACGCTAGAGACTAGTACTTTCGTGGC
* *
121406 ATTTTTATCAAACGCCGCTAAAGACTGTACTTTAGTGGCATTTGTATAAAAACGCCGCTAAAGAC
66 ATTTGTATAAAACGCCGCTAAAGACTGTACTTTAGTGGCATTTGTATAAAAACGCCGCTAAAGAC
121471 T-GTA
131 TCGTA
* * *
121475 CTATAGACTAGTACTTTAGTGGCGTTTGTAT-AA-AAACGCCGCTAGAGACT-GTACTTTTGTGG
1 CTATAGACTAGTACTTTAGTGG-ATTTGTATAAACAAACGACGCTAGAGACTAGTACTTTCGTGG
* * * * *
121537 CGTTTGTATAAAAACGCCGTTAAAGACTCGTACTTTAGTGGCATTTTTATACAAACGTCGCTAAA
65 CATTTGTAT-AAAACGCCGCTAAAGACT-GTACTTTAGTGGCATTTGTATAAAAACGCCGCTAAA
121602 GACTCGTA
128 GACTCGTA
121610 CT
1 CT
121612 TTTGTGGCTT
Statistics
Matches: 119, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
132 18 0.15
133 31 0.26
134 60 0.50
135 10 0.08
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (135 bp):
CTATAGACTAGTACTTTAGTGGATTTGTATAAACAAACGACGCTAGAGACTAGTACTTTCGTGGC
ATTTGTATAAAACGCCGCTAAAGACTGTACTTTAGTGGCATTTGTATAAAAACGCCGCTAAAGAC
TCGTA
Found at i:121593 original size:41 final size:41
Alignment explanation
Indices: 121479--121748 Score: 344
Period size: 41 Copynumber: 6.6 Consensus size: 41
121469 ACTGTACTAT
* * * *
121479 AGACTAGTACTTTAGTGGCGTTTGTATAAAAACGCCGCTAG
1 AGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAA
* * * *
121520 AGACT-GTACTTTTGTGGCGTTTGTATAAAAACGCCGTTAA
1 AGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAA
* *
121560 AGACTCGTACTTTAGTGGCATTTTTATACAAACGTCGCTAA
1 AGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAA
* *
121601 AGACTCGTACTTTTGTGGCTTTTTTATACAAACGCCGCTAA
1 AGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAA
* * * *
121642 AGACTCGTACTTTTGTGGCACTTTTTAGAACAAATGCCGCTAA
1 AGACTCGTACTTTAGTGGC-GTTTTTA-TACAAACGCCGCTAA
* *
121685 AGACTCGTACTTTAATGGCGTTTTTATACAAACGCCACTAA
1 AGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAA
*
121726 AAACTCGTACTTTAGTGGCGTTT
1 AGACTCGTACTTTAGTGGCGTTT
121749 ATAAAAACAA
Statistics
Matches: 203, Mismatches: 23, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
40 37 0.18
41 124 0.61
42 12 0.06
43 30 0.15
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (41 bp):
AGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAA
Found at i:121726 original size:125 final size:122
Alignment explanation
Indices: 121474--121756 Score: 372
Period size: 125 Copynumber: 2.3 Consensus size: 122
121464 TAAAGACTGT
* * * *
121474 ACTATAGACTAGTACTTTAGTGGCGTTTGTATAAAAACGCCGCTAGAGACTGTACTTTTGTGGCG
1 ACTAAAGACTCGTACTTTAGTGGCGTTTGTATAAAAACGCCGCTAAAGACTGTACTTTTGTGGCC
* * * *
121539 TTTGTATAAAAACGCCGTTAAAGACTCGTACTTTAGTGGCATTTTTATACAAACGTC
66 TTTGTAGAAAAACGCCGCTAAAGACTCGTACTTTAATGGCATTTTTATACAAACGCC
* * * * *
121596 GCTAAAGACTCGTACTTTTGTGGCTTTTTTATACAAACGCCGCTAAAGACTCGTACTTTTGTGGC
1 ACTAAAGACTCGTACTTTAGTGGCGTTTGTATAAAAACGCCGCTAAAGACT-GTACTTTTGTGGC
* * *
121661 ACTTTTTAGAACAAATGCCGCTAAAGACTCGTACTTTAATGGCGTTTTTATACAAACGCC
65 -CTTTGTAGAA-AAACGCCGCTAAAGACTCGTACTTTAATGGCATTTTTATACAAACGCC
*
121721 ACTAAAAACTCGTACTTTAGTGGCG-TT-TATAAAAAC
1 ACTAAAGACTCGTACTTTAGTGGCGTTTGTATAAAAAC
121757 AAATGCGACA
Statistics
Matches: 137, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
122 43 0.31
123 21 0.15
124 9 0.07
125 64 0.47
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33
Consensus pattern (122 bp):
ACTAAAGACTCGTACTTTAGTGGCGTTTGTATAAAAACGCCGCTAAAGACTGTACTTTTGTGGCC
TTTGTAGAAAAACGCCGCTAAAGACTCGTACTTTAATGGCATTTTTATACAAACGCC
Found at i:121732 original size:84 final size:82
Alignment explanation
Indices: 121479--121753 Score: 347
Period size: 84 Copynumber: 3.3 Consensus size: 82
121469 ACTGTACTAT
* * * *
121479 AGACTAGTACTTTAGTGGCGTTTGTATAA-AAACGCCGCTAGAGACT-GTACTTTTGTGGCGTTT
1 AGACTCGTACTTTAGTGGCATTTTTA-AACAAACGCCGCTAAAGACTCGTACTTTTGTGGCGTTT
* * *
121542 GTATAAAAACGCCGTTAA
65 TTATACAAACGCCGCTAA
* * *
121560 AGACTCGTACTTTAGTGGCATTTTTATACAAACGTCGCTAAAGACTCGTACTTTTGTGGCTTTTT
1 AGACTCGTACTTTAGTGGCATTTTTAAACAAACGCCGCTAAAGACTCGTACTTTTGTGGCGTTTT
121625 TATACAAACGCCGCTAA
66 TATACAAACGCCGCTAA
* * **
121642 AGACTCGTACTTTTGTGGCACTTTTTAGAACAAATGCCGCTAAAGACTCGTACTTTAATGGCGTT
1 AGACTCGTACTTTAGTGGCA-TTTTTA-AACAAACGCCGCTAAAGACTCGTACTTTTGTGGCGTT
*
121707 TTTATACAAACGCCACTAA
64 TTTATACAAACGCCGCTAA
* * *
121726 AAACTCGTACTTTAGTGGCGTTTATAAA
1 AGACTCGTACTTTAGTGGCATTTTTAAA
121754 AACAAATGCG
Statistics
Matches: 168, Mismatches: 22, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
80 1 0.01
81 38 0.23
82 52 0.31
83 11 0.07
84 66 0.39
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (82 bp):
AGACTCGTACTTTAGTGGCATTTTTAAACAAACGCCGCTAAAGACTCGTACTTTTGTGGCGTTTT
TATACAAACGCCGCTAA
Found at i:125907 original size:29 final size:29
Alignment explanation
Indices: 125865--125939 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
125855 TCCGTAGAGG
125865 ATCCCATGCAGAATCAGGACGGA-GATATA
1 ATCCCATGCAGAATCAGGA-GGAGGATATA
* * *
125894 ATCCCATGCAGAATAAGGATGAGGATATT
1 ATCCCATGCAGAATCAGGAGGAGGATATA
* *
125923 ATTCTATGCAGAATCAG
1 ATCCCATGCAGAATCAG
125940 AATGGGAATC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.05
29 37 0.95
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (29 bp):
ATCCCATGCAGAATCAGGAGGAGGATATA
Done.