Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003601.1 Hibiscus syriacus cultivar Beakdansim tig00007616_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: 69800
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:914 original size:31 final size:30
Alignment explanation
Indices: 813--914 Score: 152
Period size: 30 Copynumber: 3.4 Consensus size: 30
803 ATTTAATACA
* * *
813 TAAACTATCAGTTTTTGTCTGTTTTAGTACC
1 TAAACTATCA-ATTTTGTATGTCTTAGTACC
844 TAAACTATCAATTTTGTATGTCTTAGTACC
1 TAAACTATCAATTTTGTATGTCTTAGTACC
874 T-AACTATCAATTTTGGTATGTCTTAGTACC
1 TAAACTATCAATTTT-GTATGTCTTAGTACC
904 TAAACTATCAA
1 TAAACTATCAA
915 ATTTCCCCAA
Statistics
Matches: 66, Mismatches: 3, Indels: 4
0.90 0.04 0.05
Matches are distributed among these distances:
29 13 0.20
30 34 0.52
31 19 0.29
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.43
Consensus pattern (30 bp):
TAAACTATCAATTTTGTATGTCTTAGTACC
Found at i:8784 original size:4 final size:4
Alignment explanation
Indices: 8775--8799 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
8765 ATTCGTAAAA
8775 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
8800 CATTAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:14842 original size:17 final size:16
Alignment explanation
Indices: 14806--14838 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
14796 TTATTAATAG
14806 TAAATATATAAAAAAT
1 TAAATATATAAAAAAT
14822 TAAA-ATATAAGAAAAT
1 TAAATATATAA-AAAAT
14838 T
1 T
14839 TAAAGATTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
TAAATATATAAAAAAT
Found at i:18665 original size:16 final size:17
Alignment explanation
Indices: 18636--18672 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
18626 ACCGCTTATT
18636 TAAGGTTAAAAAAATAA
1 TAAGGTTAAAAAAATAA
18653 TAAGGTT-AAAAAATAA
1 TAAGGTTAAAAAAATAA
18669 TAAG
1 TAAG
18673 AAATTGACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.62, C:0.00, G:0.14, T:0.24
Consensus pattern (17 bp):
TAAGGTTAAAAAAATAA
Found at i:20411 original size:17 final size:17
Alignment explanation
Indices: 20381--20424 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
20371 TATTTTATAG
* * *
20381 TTTATATTATAAATTAT
1 TTTATATAAGAAATAAT
20398 TTTATATAAGAAATAAT
1 TTTATATAAGAAATAAT
*
20415 TATATATAAG
1 TTTATATAAG
20425 TTAGGTAAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (17 bp):
TTTATATAAGAAATAAT
Found at i:21045 original size:21 final size:20
Alignment explanation
Indices: 21000--21037 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
20990 ATAAAATGGT
*
21000 ATAAAAAACACATGATTTAC
1 ATAAAAAACACATCATTTAC
21020 ATAAAAAA-ACATCATTTA
1 ATAAAAAACACATCATTTA
21038 ATCATAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.26
Consensus pattern (20 bp):
ATAAAAAACACATCATTTAC
Found at i:21633 original size:25 final size:25
Alignment explanation
Indices: 21599--21659 Score: 113
Period size: 25 Copynumber: 2.4 Consensus size: 25
21589 ACTACGCCAA
21599 GCATACGAAGGCCGACCACCTAGGG
1 GCATACGAAGGCCGACCACCTAGGG
21624 GCATACGAAGGCCGACCACCTAGGG
1 GCATACGAAGGCCGACCACCTAGGG
*
21649 GCACACGAAGG
1 GCATACGAAGG
21660 AAATCAGTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.30, C:0.31, G:0.33, T:0.07
Consensus pattern (25 bp):
GCATACGAAGGCCGACCACCTAGGG
Found at i:23852 original size:3 final size:3
Alignment explanation
Indices: 23844--23890 Score: 78
Period size: 3 Copynumber: 15.7 Consensus size: 3
23834 TCTAATTGTA
23844 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT
23889 AT
1 AT
23891 GCTTATTTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:23888 original size:21 final size:21
Alignment explanation
Indices: 23844--23906 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
23834 TCTAATTGTA
23844 ATTATTATTA-TTATTATTATT
1 ATTATTATTATTTATTATTA-T
23865 ATTATTATTATTTATTATTAT
1 ATTATTATTATTTATTATTAT
** *
23886 ATTATGCTTATTTATTGTTAT
1 ATTATTATTATTTATTATTAT
23907 TAATATATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 29 0.76
22 9 0.24
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (21 bp):
ATTATTATTATTTATTATTAT
Found at i:27628 original size:30 final size:32
Alignment explanation
Indices: 27594--27654 Score: 108
Period size: 30 Copynumber: 2.0 Consensus size: 32
27584 ATTTTACATG
27594 TACTAACTTATTT-TTCTC-TTTGTTTGTGTA
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
27624 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
27655 CATTTTGTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 13 0.45
31 5 0.17
32 11 0.38
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.61
Consensus pattern (32 bp):
TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
Found at i:30745 original size:11 final size:11
Alignment explanation
Indices: 30726--30844 Score: 80
Period size: 11 Copynumber: 10.2 Consensus size: 11
30716 AGATCCAATC
30726 AAAAA-CAAAG
1 AAAAATCAAAG
30736 AAAAATCAAAGAG
1 AAAAATC-AA-AG
*
30749 AAAAGAGCAAAG
1 AAAA-ATCAAAG
** *
30761 AAAAAAAAAAC
1 AAAAATCAAAG
* *
30772 AAAGAGCAGAGAG
1 AAAAATCA-A-AG
30785 AAAAAAATCAAAG
1 -AA-AAATCAAAG
30798 CAAAAA-CAAAG
1 -AAAAATCAAAG
30809 AAAAATCAAAG
1 AAAAATCAAAG
30820 CAAAAATCAAAG
1 -AAAAATCAAAG
*
30832 AAAAAGCAAAG
1 AAAAATCAAAG
30843 AA
1 AA
30845 CAAAAAGAGG
Statistics
Matches: 87, Mismatches: 12, Indels: 19
0.74 0.10 0.16
Matches are distributed among these distances:
10 10 0.11
11 32 0.37
12 23 0.26
13 13 0.15
14 5 0.06
15 4 0.05
ACGTcount: A:0.72, C:0.10, G:0.14, T:0.03
Consensus pattern (11 bp):
AAAAATCAAAG
Found at i:30752 original size:22 final size:22
Alignment explanation
Indices: 30726--30844 Score: 89
Period size: 23 Copynumber: 5.1 Consensus size: 22
30716 AGATCCAATC
30726 AAAAA-CAAAGAAAAATCAAAGAG
1 AAAAAGCAAAGAAAAATC-AA-AG
** *
30749 AAAAGAGCAAAGAAAAAAAAAAC
1 AAAA-AGCAAAGAAAAATCAAAG
*
30772 AAAGAGCAGAGAGAAAAAAATCAAAG
1 AAAAAGCA-A-AG--AAAAATCAAAG
30798 CAAAAA-CAAAGAAAAATCAAAG
1 -AAAAAGCAAAGAAAAATCAAAG
* *
30820 CAAAAATCAAAGAAAAAGCAAAG
1 -AAAAAGCAAAGAAAAATCAAAG
30843 AA
1 AA
30845 CAAAAAGAGG
Statistics
Matches: 79, Mismatches: 9, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
22 23 0.29
23 24 0.30
24 7 0.09
25 11 0.14
26 10 0.13
27 4 0.05
ACGTcount: A:0.72, C:0.10, G:0.14, T:0.03
Consensus pattern (22 bp):
AAAAAGCAAAGAAAAATCAAAG
Found at i:32040 original size:4 final size:4
Alignment explanation
Indices: 32031--32204 Score: 334
Period size: 4 Copynumber: 44.0 Consensus size: 4
32021 AAAAGTATAC
32031 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
32079 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
32127 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
32175 ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
32205 GATACATAAA
Statistics
Matches: 168, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.01
4 166 0.99
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:32874 original size:35 final size:36
Alignment explanation
Indices: 32847--32965 Score: 120
Period size: 36 Copynumber: 3.4 Consensus size: 36
32837 ACAAAGTTGA
*
32847 TCTCACTTGAGATC-GTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAGA-CAATTTCTCTAAAAACAAACTTTG
* *
32882 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
* * * * *
32918 TCTCATTTGAGACTATATCT-T-AAAGCAAATTTTG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
*
32952 TCTCGCTTGAGACA
1 TCTCACTTGAGACA
32966 TCATTTTCTC
Statistics
Matches: 71, Mismatches: 11, Indels: 5
0.82 0.13 0.06
Matches are distributed among these distances:
34 24 0.34
35 18 0.25
36 29 0.41
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (36 bp):
TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
Found at i:32918 original size:36 final size:36
Alignment explanation
Indices: 32862--32965 Score: 133
Period size: 36 Copynumber: 3.0 Consensus size: 36
32852 CTTGAGATCG
*
32862 TTTCTC-AAAAACAAACTTTGTCTCGCTTGAGACAA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
** *
32897 TTTCTCTAAAAACAAATTTTGTCTCATTTGAGACTA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
* *
32933 TATCT-T-AAAGCAAATTTTGTCTCGCTTGAGACA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACA
32966 TCATTTTCTC
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
34 23 0.39
35 7 0.12
36 29 0.49
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (36 bp):
TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
Found at i:33253 original size:29 final size:28
Alignment explanation
Indices: 33213--33284 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 28
33203 CAATTTTGTG
*
33213 AAAAAATCTTTGAGTTTGTTCCTCTTGAA
1 AAAAAATATTTGAGTTTGTTCCTCTTG-A
* *
33242 AAAAAATATTTGAGTTTGTTTCTTTTGA
1 AAAAAATATTTGAGTTTGTTCCTCTTGA
33270 AAAAAATATTTGAGT
1 AAAAAATATTTGAGT
33285 CTATTTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 16 0.40
29 24 0.60
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (28 bp):
AAAAAATATTTGAGTTTGTTCCTCTTGA
Found at i:33272 original size:28 final size:28
Alignment explanation
Indices: 33213--33299 Score: 111
Period size: 28 Copynumber: 3.1 Consensus size: 28
33203 CAATTTTGTG
* * *
33213 AAAAAATCTTTGAGTTTGTTCCTCTTGAA
1 AAAAAATATTTGAGTTTGTTTCTTTTG-A
33242 AAAAAATATTTGAGTTTGTTTCTTTTGA
1 AAAAAATATTTGAGTTTGTTTCTTTTGA
* * *
33270 AAAAAATATTTGAGTCTATTTATTTTGA
1 AAAAAATATTTGAGTTTGTTTCTTTTGA
33298 AA
1 AA
33300 CAAGGTTTTG
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 28 0.54
29 24 0.46
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.45
Consensus pattern (28 bp):
AAAAAATATTTGAGTTTGTTTCTTTTGA
Found at i:33373 original size:52 final size:53
Alignment explanation
Indices: 33295--33398 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 53
33285 CTATTTATTT
*
33295 TGAAACAAGGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAATCTTTGAGTC
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
*
33347 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAATCTTTGAGT
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGT
33399 TTGTTCCTCT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 35 0.71
53 14 0.29
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (53 bp):
TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
Found at i:33460 original size:28 final size:28
Alignment explanation
Indices: 33384--33534 Score: 189
Period size: 29 Copynumber: 5.2 Consensus size: 28
33374 CAATTTTGTG
* *
33384 AAAAAATCTTTGAGTTTGTTCCTCTTGAA
1 AAAAAATCTTTGAGTTTGTTTCTTTTG-A
*
33413 AAAAAATATTTGAGTTTG-TTCATTTTGA
1 AAAAAATCTTTGAGTTTGTTTC-TTTTGA
33441 ATAAAAATCTTTGAG-TTGTTTCTTTTGA
1 A-AAAAATCTTTGAGTTTGTTTCTTTTGA
*
33469 AAAAAATCTTTGAGATTGTTTCTTTTGAA
1 AAAAAATCTTTGAGTTTGTTTCTTTTG-A
*
33498 ACAAAAATCTTTGAGTTTGTTTCTTTGGA
1 A-AAAAATCTTTGAGTTTGTTTCTTTTGA
33527 AACAAAAT
1 AA-AAAAT
33535 TTTTTTTCTC
Statistics
Matches: 109, Mismatches: 6, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
27 13 0.12
28 27 0.25
29 45 0.41
30 24 0.22
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.44
Consensus pattern (28 bp):
AAAAAATCTTTGAGTTTGTTTCTTTTGA
Found at i:33504 original size:57 final size:57
Alignment explanation
Indices: 33385--33534 Score: 196
Period size: 57 Copynumber: 2.6 Consensus size: 57
33375 AATTTTGTGA
* * * *
33385 AAAAATCTTTGAGTTTGTTCCTCTTGAAAAAAAATATTTGAGTTTGTTCATTTTGAAT
1 AAAAATCTTTGAGTTTGTTTCTTTTG-AAAAAAATATTTGAGATTGTTCATTTTGAAC
*
33443 AAAAATCTTTGAG-TTGTTTCTTTTGAAAAAAATCTTTGAGATTGTTTC-TTTTGAAAC
1 AAAAATCTTTGAGTTTGTTTCTTTTGAAAAAAATATTTGAGATTG-TTCATTTTG-AAC
*
33500 AAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAAT
1 AAAAATCTTTGAGTTTGTTTCTTTTGAAA-AAAAT
33535 TTTTTTTCTC
Statistics
Matches: 82, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
56 22 0.27
57 28 0.34
58 27 0.33
59 5 0.06
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (57 bp):
AAAAATCTTTGAGTTTGTTTCTTTTGAAAAAAATATTTGAGATTGTTCATTTTGAAC
Found at i:33568 original size:69 final size:67
Alignment explanation
Indices: 33487--33654 Score: 261
Period size: 69 Copynumber: 2.5 Consensus size: 67
33477 TTTGAGATTG
* *
33487 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTTTTTCTCTCTTAAG
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAA--TTTTATCTCTCTTAAG
33552 ATAA
64 ATAA
33556 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTATCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTATCTCTCTTAAGAT
33621 AA
66 AA
* *
33623 TTTCTTTTG---GAAAAATCTTTGAATCTGTTTCT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCT
33655 CTTAAAATGA
Statistics
Matches: 95, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
64 21 0.22
67 28 0.29
69 46 0.48
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.47
Consensus pattern (67 bp):
TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTATCTCTCTTAAGAT
AA
Found at i:33940 original size:27 final size:27
Alignment explanation
Indices: 33910--34010 Score: 69
Period size: 27 Copynumber: 3.4 Consensus size: 27
33900 TTAAAGACAA
*
33910 TTTCTTTTGAAAAAATCTTTGAGTTGG
1 TTTCCTTTGAAAAAATCTTTGAGTTGG
**
33937 TTTCCTTTGAAACAAAAT-TTTGTCTCTCGAG
1 TTTCCTTTG-AA-AAAATCTTTGAGT-T-G-G
* *
33968 ACAACTTCTTTTGAAAAAATCTTTGAGTTGG
1 ----TTTCCTTTGAAAAAATCTTTGAGTTGG
33999 TTTCCTTTGAAA
1 TTTCCTTTGAAA
34011 CAAAATTTTG
Statistics
Matches: 55, Mismatches: 9, Indels: 20
0.65 0.11 0.24
Matches are distributed among these distances:
27 18 0.33
28 7 0.13
29 6 0.11
30 1 0.02
31 2 0.04
32 1 0.02
33 6 0.11
34 7 0.13
35 7 0.13
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.44
Consensus pattern (27 bp):
TTTCCTTTGAAAAAATCTTTGAGTTGG
Found at i:33997 original size:62 final size:62
Alignment explanation
Indices: 33873--34046 Score: 294
Period size: 62 Copynumber: 2.8 Consensus size: 62
33863 CTTTGTGTCT
* * ** *
33873 GTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAATCTTTGAGTTG
1 GTTTCCTTTGAAACAAAATTTTGTCTC-TCGAGACAACTTCTTTTGAAAAAATCTTTGAGTTG
33936 GTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAAAAATCTTTGAGTTG
1 GTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAAAAATCTTTGAGTTG
33998 GTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAAA
1 GTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAAA
34047 TACCCACCTT
Statistics
Matches: 106, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
62 81 0.76
63 25 0.24
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (62 bp):
GTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAAAAATCTTTGAGTTG
Found at i:34683 original size:28 final size:28
Alignment explanation
Indices: 34612--34693 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
34602 TAAAAATATC
* * *
34612 ATCTTTGAGTTTATTTTTCTTGAAACAA
1 ATCTTTGAATTTGTTTCTCTTGAAACAA
** *
34640 ATCTTTGGGTTTGTTTCTTTTGAAACAA
1 ATCTTTGAATTTGTTTCTCTTGAAACAA
34668 ATCTTT-AATTTGGTTTCTCTTGAAAC
1 ATCTTTGAATTT-GTTTCTCTTGAAAC
34694 CATAACTCCT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
27 3 0.07
28 43 0.93
ACGTcount: A:0.24, C:0.12, G:0.13, T:0.50
Consensus pattern (28 bp):
ATCTTTGAATTTGTTTCTCTTGAAACAA
Found at i:34774 original size:40 final size:40
Alignment explanation
Indices: 34719--34900 Score: 143
Period size: 40 Copynumber: 4.3 Consensus size: 40
34709 TGGCCAGCCG
*
34719 TCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATC
1 TCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGATC
* * **
34759 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCA-ATC
1 TCCTCATCACGTAGGAACCGTGTCATCCCCAG---ACCAGATC
* * *
34801 GTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 -TCCTCATCACGTAGGAACCGTGTCATC-CC--CAGA---CCAGATC
* * *
34848 TCTTCATCACGTATGAGCCGTGTCATTCCCC-GACCAGATC
1 TCCTCATCACGTAGGAACCGTGTCA-TCCCCAGACCAGATC
*
34888 TCTTCATCACGTA
1 TCCTCATCACGTA
34901 TGAGCTGTAG
Statistics
Matches: 114, Mismatches: 16, Indels: 24
0.74 0.10 0.16
Matches are distributed among these distances:
40 46 0.40
42 3 0.03
43 31 0.27
44 1 0.01
46 29 0.25
47 4 0.04
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (40 bp):
TCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGATC
Found at i:34936 original size:129 final size:133
Alignment explanation
Indices: 34702--35049 Score: 413
Period size: 129 Copynumber: 2.6 Consensus size: 133
34692 ACCATAACTC
** * * *
34702 CTAAAGATGGCCAGCCGTCCTCATCATGTAGGAACCGTGTCA-TCCCCAGACCAGATCTCCTCAT
1 CTAAAGATGGCCAAACATCCTCATCACGTAGGAACCGTGTCATTCCCC-GACCAGATCTCTTCAT
* * *
34766 CACGTAGGAGCCGTGTCAACCATAGATAACCAATCGTCCTCATCACGTAGGAACCGTGTTATCA-
65 CACGTATGAGCCGTGTCAACCATAGATAACCAATCGTCCTCATCACGTAGGAACCGAGCTATCAC
34830 C-CT
130 CACT
* * * *
34833 -T-TAGATGGCCAGAAC-TCTTCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCAT
1 CTAAAGATGGCCA-AACATCCTCATCACGTAGGAACCGTGTCATTCCCCGACCAGATCTCTTCAT
* * * *
34895 CACGTATGAGCTGTAGTC-ACCCTAGATAACCAGTCGTCCTCATCACGTAGGAGCCGAGCTATCA
65 CACGTATGAGCCGT-GTCAACCATAGATAACCAATCGTCCTCATCACGTAGGAACCGAGCTATCA
34959 CCACT
129 CCACT
* * * * *
34964 CCTAAATATGGCCAACCATCCTCAACACGTAGGAACCGTGTCATTCCTCGACCAGAACTCTTCAT
1 -CTAAAGATGGCCAAACATCCTCATCACGTAGGAACCGTGTCATTCCCCGACCAGATCTCTTCAT
*
35029 CACGTATGAGCAGTGTCAACC
65 CACGTATGAGCCGTGTCAACC
35050 CTCGACCCGA
Statistics
Matches: 182, Mismatches: 25, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
129 98 0.54
130 11 0.06
131 2 0.01
133 6 0.03
134 65 0.36
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.23
Consensus pattern (133 bp):
CTAAAGATGGCCAAACATCCTCATCACGTAGGAACCGTGTCATTCCCCGACCAGATCTCTTCATC
ACGTATGAGCCGTGTCAACCATAGATAACCAATCGTCCTCATCACGTAGGAACCGAGCTATCACC
ACT
Found at i:35045 original size:40 final size:40
Alignment explanation
Indices: 35009--35085 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
34999 CCGTGTCATT
35009 CCTCGACCAGAACTCTTCATCACGTATGAGCAGTGTCAAC
1 CCTCGACCAGAACTCTTCATCACGTATGAGCAGTGTCAAC
*
35049 CCTCGACCCGAACTCTTCATCACGTATGAGCAGTGTC
1 CCTCGACCAGAACTCTTCATCACGTATGAGCAGTGTC
35086 GTCCCCAACA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.23
Consensus pattern (40 bp):
CCTCGACCAGAACTCTTCATCACGTATGAGCAGTGTCAAC
Found at i:35259 original size:3 final size:3
Alignment explanation
Indices: 35251--35300 Score: 84
Period size: 3 Copynumber: 16.7 Consensus size: 3
35241 TCTAATTGTA
35251 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
35296 ATT AT
1 ATT AT
35301 GCTTATTTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 40 0.89
4 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:35277 original size:21 final size:22
Alignment explanation
Indices: 35252--35326 Score: 93
Period size: 21 Copynumber: 3.5 Consensus size: 22
35242 CTAATTGTAA
35252 TTATTATTATTA-TTATTATTA
1 TTATTATTATTATTTATTATTA
35273 TTATTATTATTATTTATTATTA
1 TTATTATTATTATTTATTATTA
** *
35295 -TATTATGCTTATTTATTGTTA
1 TTATTATTATTATTTATTATTA
*
35316 TTAATA-TATTA
1 TTATTATTATTA
35327 CAAATTTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
21 33 0.72
22 13 0.28
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (22 bp):
TTATTATTATTATTTATTATTA
Found at i:40352 original size:16 final size:16
Alignment explanation
Indices: 40327--40366 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
40317 TTTCATATAT
40327 ATACATACATAAACAC
1 ATACATACATAAACAC
* *
40343 ATATATACATAAATAC
1 ATACATACATAAACAC
40359 ATACATAC
1 ATACATAC
40367 CTGTATGTCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.55, C:0.20, G:0.00, T:0.25
Consensus pattern (16 bp):
ATACATACATAAACAC
Found at i:44058 original size:20 final size:20
Alignment explanation
Indices: 44033--44070 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
44023 TCCATCCATG
*
44033 CATACATACATACATAAACA
1 CATACACACATACATAAACA
44053 CATACACACATACATAAA
1 CATACACACATACATAAA
44071 AATGATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.18
Consensus pattern (20 bp):
CATACACACATACATAAACA
Found at i:44329 original size:4 final size:4
Alignment explanation
Indices: 44320--44346 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
44310 AACATTTCAT
44320 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
44347 TAATAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:44802 original size:30 final size:30
Alignment explanation
Indices: 44761--44818 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
44751 TAATTTAATA
44761 ATTAAAATGTTACGAAATAGTCA-TAAATTT
1 ATTAAAATGTTAC-AAATAGTCATTAAATTT
* *
44791 ATTAGAATGTTACAAATATTCATTAAAT
1 ATTAAAATGTTACAAATAGTCATTAAAT
44819 CCATCTGACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.38
Consensus pattern (30 bp):
ATTAAAATGTTACAAATAGTCATTAAATTT
Found at i:44923 original size:31 final size:31
Alignment explanation
Indices: 44851--44921 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
44841 CAACGACGCG
* * *
44851 TGATCATTATGTAATAGTTTAATAAATATAG
1 TGATTATTTTGTAATAGTTTAATAAATATAA
* * *
44882 TGATTATTTTGTAATGGTTTGATAACTATAA
1 TGATTATTTTGTAATAGTTTAATAAATATAA
44913 TGA-TATTTT
1 TGATTATTTT
44922 TGATTTTCGA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 6 0.18
31 28 0.82
ACGTcount: A:0.35, C:0.03, G:0.14, T:0.48
Consensus pattern (31 bp):
TGATTATTTTGTAATAGTTTAATAAATATAA
Found at i:46569 original size:18 final size:18
Alignment explanation
Indices: 46546--46627 Score: 118
Period size: 16 Copynumber: 4.8 Consensus size: 18
46536 TGTTTCTGAG
46546 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
* *
46564 GGAATTGAAATTTGTGAA
1 GGAATTGGAATCTGTGAA
46582 GGAATTGGAATC--TGAA
1 GGAATTGGAATCTGTGAA
46598 GGAATTGGAATC--TGAA
1 GGAATTGGAATCTGTGAA
46614 GGAATTGGAATCTG
1 GGAATTGGAATCTG
46628 AATTTGAAAC
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
16 32 0.55
18 26 0.45
ACGTcount: A:0.35, C:0.05, G:0.32, T:0.28
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:47699 original size:30 final size:30
Alignment explanation
Indices: 47657--48139 Score: 414
Period size: 30 Copynumber: 15.9 Consensus size: 30
47647 CCATTATTTT
* *
47657 CTCCGTACAAGTATGAGTCACCACCTCCAC
1 CTCCATACAAGTATAAGTCACCACCTCCAC
* * * *
47687 CTCCATATAAGTACAAGTCACC-CTCACCTC
1 CTCCATACAAGTATAAGTCACCAC-CTCCAC
* * *
47717 CTCCGTACAAGTATGAGTCACCACCTCCAA
1 CTCCATACAAGTATAAGTCACCACCTCCAC
* * * *
47747 CTCCATACAAGTACAAGTCACCATCACCTC
1 CTCCATACAAGTATAAGTCACCACCTCCAC
* * * *
47777 CTCCGTACAAGAATGAGTCATCACCTCCAC
1 CTCCATACAAGTATAAGTCACCACCTCCAC
* * ** *
47807 CTCCATACAAGTACATGTCACCACCAACTC
1 CTCCATACAAGTATAAGTCACCACCTCCAC
* * *
47837 CTCCGTACAAGTACAAGTCACC-CCTCCTC
1 CTCCATACAAGTATAAGTCACCACCTCCAC
* * *
47866 CTCCGTACAAGTACAAGTCACC-CCTACCTC
1 CTCCATACAAGTATAAGTCACCACCT-CCAC
* *
47896 CTCCGTACAAGTATGAGTCACCACCTCCAC
1 CTCCATACAAGTATAAGTCACCACCTCCAC
* * * * *
47926 CTCTATATAAATACAAGTCACCACCACCAC
1 CTCCATACAAGTATAAGTCACCACCTCCAC
* * * * *
47956 CTCCGTACAAGTATGAGTCTCCGCCTCCAG
1 CTCCATACAAGTATAAGTCACCACCTCCAC
* * *
47986 CTCCATACAAGTACAAGTCACCACCACCCC
1 CTCCATACAAGTATAAGTCACCACCTCCAC
* *
48016 CTCCTTACAAGTATGAGTCACCACCTCCAC
1 CTCCATACAAGTATAAGTCACCACCTCCAC
* *
48046 CTCCATACAAGTATAAATCACCACCACCAC
1 CTCCATACAAGTATAAGTCACCACCTCCAC
* *
48076 CTCCTTACAAGTATGAGTTTCCACCTCCACCTCCAC
1 CTCCATACAAGTATAAG--T-CA---CCACCTCCAC
* *
48112 CTCCATACAAGTACAAGTCCCCACCTCC
1 CTCCATACAAGTATAAGTCACCACCTCC
48140 CCATATGCTT
Statistics
Matches: 357, Mismatches: 86, Indels: 20
0.77 0.19 0.04
Matches are distributed among these distances:
29 31 0.09
30 294 0.82
31 4 0.01
32 1 0.00
33 3 0.01
34 1 0.00
36 23 0.06
ACGTcount: A:0.29, C:0.41, G:0.10, T:0.20
Consensus pattern (30 bp):
CTCCATACAAGTATAAGTCACCACCTCCAC
Found at i:47728 original size:60 final size:60
Alignment explanation
Indices: 47657--48136 Score: 642
Period size: 60 Copynumber: 7.9 Consensus size: 60
47647 CCATTATTTT
*
47657 CTCCGTACAAGTATGAGTCACCACCTCCACCTCCATATAAGTACAAGTCACC-CTCACCTC
1 CTCCGTACAAGTATGAGTCACCACCTCCACCTCCATACAAGTACAAGTCACCAC-CACCTC
* *
47717 CTCCGTACAAGTATGAGTCACCACCTCCAACTCCATACAAGTACAAGTCACCATCACCTC
1 CTCCGTACAAGTATGAGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCTC
* * * *
47777 CTCCGTACAAGAATGAGTCATCACCTCCACCTCCATACAAGTACATGTCACCACCAACTC
1 CTCCGTACAAGTATGAGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCTC
** * *
47837 CTCCGTACAAGTACAAGTCACC-CCTCCTCCTCCGTACAAGTACAAGTCACC-CCTACCTC
1 CTCCGTACAAGTATGAGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACC-ACCTC
* * * *
47896 CTCCGTACAAGTATGAGTCACCACCTCCACCTCTATATAAATACAAGTCACCACCACCAC
1 CTCCGTACAAGTATGAGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCTC
* * * *
47956 CTCCGTACAAGTATGAGTCTCCGCCTCCAGCTCCATACAAGTACAAGTCACCACCACCCC
1 CTCCGTACAAGTATGAGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCTC
* * * *
48016 CTCCTTACAAGTATGAGTCACCACCTCCACCTCCATACAAGTATAAATCACCACCACCAC
1 CTCCGTACAAGTATGAGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCTC
* *
48076 CTCCTTACAAGTATGAGTTTCCACCTCCACCTCCACCTCCATACAAGTACAAGTCCCCACC
1 CTCCGTACAAGTATGAG--T-CA---CCACCTCCACCTCCATACAAGTACAAGTCACCACC
48137 TCCCCATATG
Statistics
Matches: 368, Mismatches: 42, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
58 2 0.01
59 50 0.14
60 279 0.76
61 2 0.01
62 1 0.00
63 2 0.01
66 32 0.09
ACGTcount: A:0.30, C:0.40, G:0.10, T:0.20
Consensus pattern (60 bp):
CTCCGTACAAGTATGAGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCTC
Found at i:47863 original size:23 final size:25
Alignment explanation
Indices: 47834--47888 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 25
47824 TCACCACCAA
47834 CTCCTCCGTACAAGTACAAGTCACCCCTC
1 CTCCTCCGTACAAGTACAAGTCA---C-C
47863 CTCCTCCGTACAAGTACAAGTCACC
1 CTCCTCCGTACAAGTACAAGTCACC
47888 C
1 C
47889 CTACCTCCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 2 0.08
26 1 0.04
29 23 0.88
ACGTcount: A:0.25, C:0.44, G:0.11, T:0.20
Consensus pattern (25 bp):
CTCCTCCGTACAAGTACAAGTCACC
Found at i:48069 original size:239 final size:239
Alignment explanation
Indices: 47657--48088 Score: 695
Period size: 239 Copynumber: 1.8 Consensus size: 239
47647 CCATTATTTT
* *
47657 CTCCGTACAAGTATGAGTCACCACCTCCACCTCCATATAAGTACAAGTCACCCTCACCTCCTCCG
1 CTCCGTACAAGTATGAGTCACCACCTCCACCTCCATATAAATACAAGTCACCCTCACCACCTCCG
* *
47722 TACAAGTATGAGTCACCACCTCCAACTCCATACAAGTACAAGTCACCATCACCTCCTCCGTACAA
66 TACAAGTATGAGTCACCACCTCCAACTCCATACAAGTACAAGTCACCACCACCCCCTCCGTACAA
* ** *
47787 GAATGAGTCATCACCTCCACCTCCATACAAGTACATGTCACCACCAACTCCTCCGTACAAGTACA
131 GAATGAGTCACCACCTCCACCTCCATACAAGTACAAATCACCACCAACACCTCCGTACAAGTACA
47852 AGTCACCCCTCCTCCTCCGTACAAGTACAAGTCACCCCTACCTC
196 AGTCACCCCTCCTCCTCCGTACAAGTACAAGTCACCCCTACCTC
*
47896 CTCCGTACAAGTATGAGTCACCACCTCCACCTCTATATAAATACAAGTCACCAC-CACCACCTCC
1 CTCCGTACAAGTATGAGTCACCACCTCCACCTCCATATAAATACAAGTCACC-CTCACCACCTCC
* * * *
47960 GTACAAGTATGAGTCTCCGCCTCCAGCTCCATACAAGTACAAGTCACCACCACCCCCTCCTTACA
65 GTACAAGTATGAGTCACCACCTCCAACTCCATACAAGTACAAGTCACCACCACCCCCTCCGTACA
* * * *
48025 AGTATGAGTCACCACCTCCACCTCCATACAAGTATAAATCACCACCACCACCTCCTTACAAGTA
130 AGAATGAGTCACCACCTCCACCTCCATACAAGTACAAATCACCACCAACACCTCCGTACAAGTA
48089 TGAGTTTCCA
Statistics
Matches: 175, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
239 174 0.99
240 1 0.01
ACGTcount: A:0.30, C:0.40, G:0.10, T:0.20
Consensus pattern (239 bp):
CTCCGTACAAGTATGAGTCACCACCTCCACCTCCATATAAATACAAGTCACCCTCACCACCTCCG
TACAAGTATGAGTCACCACCTCCAACTCCATACAAGTACAAGTCACCACCACCCCCTCCGTACAA
GAATGAGTCACCACCTCCACCTCCATACAAGTACAAATCACCACCAACACCTCCGTACAAGTACA
AGTCACCCCTCCTCCTCCGTACAAGTACAAGTCACCCCTACCTC
Found at i:48783 original size:2 final size:2
Alignment explanation
Indices: 48776--48811 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
48766 ACTCAATTTA
48776 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
48812 GAATTGTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50313 original size:30 final size:30
Alignment explanation
Indices: 50279--51407 Score: 705
Period size: 30 Copynumber: 37.6 Consensus size: 30
50269 CCTTTATACG
*
50279 AGTCACCACCACCACCAT-CATACAAATACA
1 AGTCACCACCACCACC-TCCATACAAGTACA
* * * * *
50309 AGTCACCATCACCTCTTCCGTACAAATACA
1 AGTCACCACCACCACCTCCATACAAGTACA
* * * * * *
50339 AGTCTCCTCCTCCTCCTCCATAAAAATACA
1 AGTCACCACCACCACCTCCATACAAGTACA
*
50369 AGTCACCACCACCACCTCCGTACAAGTACA
1 AGTCACCACCACCACCTCCATACAAGTACA
* * **
50399 AGTCACCACCTCTACCTCCATACAAGTATG
1 AGTCACCACCACCACCTCCATACAAGTACA
* * *
50429 AGTCCCCACCTCCACCTCCATGCAAGTACA
1 AGTCACCACCACCACCTCCATACAAGTACA
* * * *
50459 AGTCATCTCCACCACCTCCGTACAAGTATA
1 AGTCACCACCACCACCTCCATACAAGTACA
* *
50489 AGTCCCCACCTCCACCTCCATACAAGT-C-
1 AGTCACCACCACCACCTCCATACAAGTACA
* *
50517 A-CCACCACCACCACCT---TACAAGTACG
1 AGTCACCACCACCACCTCCATACAAGTACA
* * * *
50543 AGTCGCCACCTCCACATTCATACAAGTACA
1 AGTCACCACCACCACCTCCATACAAGTACA
* * * *
50573 AATCAACACCACCACCTCCTTACAAGTATA
1 AGTCACCACCACCACCTCCATACAAGTACA
* *
50603 AGTCTCCACCTCCACCTCCATACAAGTACA
1 AGTCACCACCACCACCTCCATACAAGTACA
** * *
50633 AGTCAAAACCACCACCTCCTTACAAGTATGA
1 AGTCACCACCACCACCTCCATACAAGTA-CA
* * *
50664 A-TCCCCACCTCCATCTCCATACAAGTACA
1 AGTCACCACCACCACCTCCATACAAGTACA
* * ** **
50693 AATCACCACCACCACATCTTTACAAGTATG
1 AGTCACCACCACCACCTCCATACAAGTACA
*
50723 AGTTC-CCACCTCCACCTCCATACAAGTACA
1 AG-TCACCACCACCACCTCCATACAAGTACA
* * * * **
50753 AATCAACACCACCACCTCCTTATAAGTATG
1 AGTCACCACCACCACCTCCATACAAGTACA
* * *
50783 AGTCCCCA-CATTCACCTCCAAACAAGTACA
1 AGTCACCACCA-CCACCTCCATACAAGTACA
* * **
50813 AGTCACC-CCACCACTTCCGTACAAGTATG
1 AGTCACCACCACCACCTCCATACAAGTACA
* * * *
50842 AGTCCCCACCTCTACCTCCATTCAAGTACA
1 AGTCACCACCACCACCTCCATACAAGTACA
* * ***
50872 AGTCACCACCATCACCACCACCACCTCCTTCCTTACAA
1 AGTCACCA-C--CACCACCTCCA--TAC--AAGTAC-A
* * * **
50910 GTATGAGTCACCACCACCTCCTTCTTACAAGTATG
1 -----AGTCACCACCACCACCTCCATACAAGTACA
** * **
50945 AGTCACCACCTTCACCTCCTTACAAGTATG
1 AGTCACCACCACCACCTCCATACAAGTACA
** * **
50975 AGTCACCACCACCACCTCTGTACAAATATG
1 AGTCACCACCACCACCTCCATACAAGTACA
* * *
51005 AGTCTCCACCTCCACCTCCGTACAAGTACA
1 AGTCACCACCACCACCTCCATACAAGTACA
* * * * * *
51035 ATTTACTC-CCACCTCCTTCGTACAAGTACG
1 AGTCAC-CACCACCACCTCCATACAAGTACA
* *
51065 AGTCTCCACCTCCACCTCCATACAAGTACA
1 AGTCACCACCACCACCTCCATACAAGTACA
* *
51095 AGTCACCACCACCACCTCCTTACAAGTATA
1 AGTCACCACCACCACCTCCATACAAGTACA
* * * * *
51125 AGTCCCCACCTCCACCTCTATATATGTACA
1 AGTCACCACCACCACCTCCATACAAGTACA
* * * **
51155 AATCACCACCACCACCTCCTTATAAGTATG
1 AGTCACCACCACCACCTCCATACAAGTACA
* *
51185 AGTCACCA-CATCCACCTCTATATAAGTACA
1 AGTCACCACCA-CCACCTCCATACAAGTACA
* * * * **
51215 AATCACTACCACCACCTCCTTACAGGTATG
1 AGTCACCACCACCACCTCCATACAAGTACA
51245 AGTCACCACCACCATCCTCCATACAAGTACA
1 AGTCACCACCACCA-CCTCCATACAAGTACA
* * * *
51276 AGTCACC-CCTACCTCATTCATACAAATACA
1 AGTCACCACC-ACCACCTCCATACAAGTACA
* *
51306 AGT------CACCACCTCCACACGAGTACA
1 AGTCACCACCACCACCTCCATACAAGTACA
* * **
51330 AATCACCACCACCACCTCCTTACAAGTATG
1 AGTCACCACCACCACCTCCATACAAGTACA
* * *
51360 AGTCTCCACCTCCACCTCTATACAAGTACA
1 AGTCACCACCACCACCTCCATACAAGTACA
* * *
51390 AGTCTCCCCCACCTCCTC
1 AGTCACCACCACCACCTC
51408 TATATGCTTA
Statistics
Matches: 826, Mismatches: 234, Indels: 78
0.73 0.21 0.07
Matches are distributed among these distances:
24 23 0.03
25 2 0.00
26 1 0.00
27 23 0.03
28 1 0.00
29 29 0.04
30 683 0.83
31 30 0.04
33 8 0.01
35 2 0.00
36 2 0.00
37 3 0.00
38 3 0.00
40 7 0.01
42 1 0.00
43 8 0.01
ACGTcount: A:0.31, C:0.40, G:0.08, T:0.21
Consensus pattern (30 bp):
AGTCACCACCACCACCTCCATACAAGTACA
Found at i:50515 original size:24 final size:24
Alignment explanation
Indices: 50488--50539 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
50478 GTACAAGTAT
* * *
50488 AAGTCCCCACCTCCACCTCCATAC
1 AAGTCACCACCACCACCACCATAC
*
50512 AAGTCACCACCACCACCACCTTAC
1 AAGTCACCACCACCACCACCATAC
50536 AAGT
1 AAGT
50540 ACGAGTCGCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.31, C:0.48, G:0.06, T:0.15
Consensus pattern (24 bp):
AAGTCACCACCACCACCACCATAC
Found at i:62021 original size:17 final size:19
Alignment explanation
Indices: 62001--62035 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
61991 TCCCCAGGAA
62001 TTTAAAA-AAAA-ACTTTG
1 TTTAAAACAAAATACTTTG
62018 TTTAAAACAAAATACTTT
1 TTTAAAACAAAATACTTT
62036 AATTTACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (19 bp):
TTTAAAACAAAATACTTTG
Found at i:62376 original size:22 final size:22
Alignment explanation
Indices: 62336--62377 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
62326 ATATGCATAT
*
62336 ATATATATATATATTTCATGAC
1 ATATATATATATATGTCATGAC
62358 ATATATATA-ATCATGTCATG
1 ATATATATATAT-ATGTCATG
62378 CACACATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (22 bp):
ATATATATATATATGTCATGAC
Found at i:62906 original size:14 final size:15
Alignment explanation
Indices: 62879--62907 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
62869 ATATCATATA
62879 TCTTATGTTTTATGC
1 TCTTATGTTTTATGC
62894 TCTTATG-TTTATGC
1 TCTTATGTTTTATGC
62908 ATATCATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (15 bp):
TCTTATGTTTTATGC
Found at i:63286 original size:19 final size:20
Alignment explanation
Indices: 63249--63287 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
63239 TTTTTCATTT
63249 AGGGGGAATCGATACCCCCC
1 AGGGGGAATCGATACCCCCC
63269 AGGGGGAATCGATACCCCC
1 AGGGGGAATCGATACCCCC
63288 TGGACATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.33, G:0.31, T:0.10
Consensus pattern (20 bp):
AGGGGGAATCGATACCCCCC
Found at i:64341 original size:21 final size:21
Alignment explanation
Indices: 64312--64387 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 21
64302 CGTGGAAGGT
64312 ATCGATTCCC-TCAAGGAGGGA
1 ATCGATTCCCTTCAAGG-GGGA
* *
64333 ATCGGTTCCCATTCAAAGGGGA
1 ATCGATTCCC-TTCAAGGGGGA
* *
64355 ATCGGTTCCCCTTCAAGGGGGT
1 ATCGATT-CCCTTCAAGGGGGA
64377 ATCGATTCCCT
1 ATCGATTCCCT
64388 CTGCACTAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
21 13 0.28
22 26 0.55
23 8 0.17
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.25
Consensus pattern (21 bp):
ATCGATTCCCTTCAAGGGGGA
Done.