Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002845.1 Hibiscus syriacus cultivar Beakdansim tig00005857_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: 71601
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:7845 original size:19 final size:20
Alignment explanation
Indices: 7821--7860 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
7811 GAGAAGTGTA
*
7821 AAATGTTTTA-AAGGGGGAG
1 AAATGTTATAGAAGGGGGAG
7840 AAATGTTATAGTAAGGGGGAG
1 AAATGTTATAG-AAGGGGGAG
7861 TAATTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.25
Consensus pattern (20 bp):
AAATGTTATAGAAGGGGGAG
Found at i:8252 original size:45 final size:46
Alignment explanation
Indices: 8201--8304 Score: 133
Period size: 45 Copynumber: 2.3 Consensus size: 46
8191 GCATGCACCG
*
8201 ATGCATCGATGCACCATT-GAATAAATT-GAACATCGAATGCATTTC
1 ATGCATCGATGCACC-TTGGAATAAATTAAAACATCGAATGCATTTC
** **
8246 ATGCATCGATGCA-CTTGGGTTTTATTAAAACATCGAATGCATTTC
1 ATGCATCGATGCACCTTGGAATAAATTAAAACATCGAATGCATTTC
8291 ATGCATCGATGCAC
1 ATGCATCGATGCAC
8305 AAGCAATGCA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
43 2 0.04
44 6 0.12
45 43 0.84
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (46 bp):
ATGCATCGATGCACCTTGGAATAAATTAAAACATCGAATGCATTTC
Found at i:11874 original size:32 final size:32
Alignment explanation
Indices: 11833--11939 Score: 130
Period size: 31 Copynumber: 3.4 Consensus size: 32
11823 AGTCGAGGGT
11833 TTACCTATGTTCTATGGAACATATGGACAGAA
1 TTACCTATGTTCTATGGAACATATGGACAGAA
* * *
11865 TTACCTATG-TCTTTCGGGACATATGGACAGTA
1 TTACCTATGTTCTAT-GGAACATATGGACAGAA
* *
11897 -TACCTATGTTCTAAGGAACATATGGACA-AT
1 TTACCTATGTTCTATGGAACATATGGACAGAA
*
11927 TTACCTAGGTTCT
1 TTACCTATGTTCT
11940 TTATGACCTA
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
31 36 0.57
32 27 0.43
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (32 bp):
TTACCTATGTTCTATGGAACATATGGACAGAA
Found at i:12720 original size:21 final size:23
Alignment explanation
Indices: 12683--12729 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
12673 TGAAAGTTAC
*
12683 TGTAGCAAGGGTATCGGTA-CAT
1 TGTAGCAAGGATATCGGTACCAT
12705 TGTAGC-AGGATATCGGTACCAT
1 TGTAGCAAGGATATCGGTACCAT
12727 TGT
1 TGT
12730 TCAATTCTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.30
Consensus pattern (23 bp):
TGTAGCAAGGATATCGGTACCAT
Found at i:12832 original size:19 final size:19
Alignment explanation
Indices: 12808--12869 Score: 97
Period size: 19 Copynumber: 3.3 Consensus size: 19
12798 TACGATATTG
*
12808 TTCATACAGTATAATACTA
1 TTCATACAGTATAGTACTA
12827 TTCATACAGTATAGTACTA
1 TTCATACAGTATAGTACTA
* *
12846 TTCATACCGTATAGTATTA
1 TTCATACAGTATAGTACTA
12865 TTCAT
1 TTCAT
12870 CGAAAACATA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.40
Consensus pattern (19 bp):
TTCATACAGTATAGTACTA
Found at i:16438 original size:16 final size:16
Alignment explanation
Indices: 16393--16439 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
16383 ATAAATTTTT
*
16393 ATAAGTTTAAGGA-TA
1 ATAAGTTTAATGACTA
*
16408 ATTA-TTTAATCGACTA
1 ATAAGTTTAAT-GACTA
16424 ATAAGTTTAATGACTA
1 ATAAGTTTAATGACTA
16440 TTTTTCATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
14 5 0.19
15 5 0.19
16 10 0.38
17 6 0.23
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.38
Consensus pattern (16 bp):
ATAAGTTTAATGACTA
Found at i:18165 original size:20 final size:20
Alignment explanation
Indices: 18108--18166 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
18098 GATTTTTCAG
18108 TTATTAAAGTT-TT-TAAAA-
1 TTATTAAA-TTATTATAAAAT
* * * *
18126 TTATAAAATAATCATTAAAT
1 TTATTAAATTATTATAAAAT
18146 TTATTAAATTATTATAAAAT
1 TTATTAAATTATTATAAAAT
18166 T
1 T
18167 CTCATTATAT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
17 1 0.03
18 8 0.27
19 4 0.13
20 17 0.57
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (20 bp):
TTATTAAATTATTATAAAAT
Found at i:18597 original size:17 final size:18
Alignment explanation
Indices: 18575--18611 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
18565 CTAAAGTTTA
18575 TAATTAAAATTTTAT-TT
1 TAATTAAAATTTTATCTT
*
18592 TAATTAAACTTTTATCTT
1 TAATTAAAATTTTATCTT
18610 TA
1 TA
18612 TATTTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (18 bp):
TAATTAAAATTTTATCTT
Found at i:23603 original size:72 final size:73
Alignment explanation
Indices: 23485--23632 Score: 280
Period size: 72 Copynumber: 2.0 Consensus size: 73
23475 ATCCAATTTG
23485 TATCTTGGTTCCAACTTTAAACATGCTCGATTAGATACAATATAAAATTAATAGGCTAAATTAGA
1 TATCTTGGTTCCAACTTTAAACATGCTCGATTAGATACAATATAAAATTAATAGGCTAAATTAGA
23550 CTTAAAAA
66 CTTAAAAA
*
23558 TATCTTGGTT-CAACTTTAAACATGCTCGATTCGATACAATATAAAATTAATAGGCTAAATTAGA
1 TATCTTGGTTCCAACTTTAAACATGCTCGATTAGATACAATATAAAATTAATAGGCTAAATTAGA
23622 CTTAAAAA
66 CTTAAAAA
23630 TAT
1 TAT
23633 ATAAAATCCA
Statistics
Matches: 74, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
72 64 0.86
73 10 0.14
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.34
Consensus pattern (73 bp):
TATCTTGGTTCCAACTTTAAACATGCTCGATTAGATACAATATAAAATTAATAGGCTAAATTAGA
CTTAAAAA
Found at i:25405 original size:81 final size:82
Alignment explanation
Indices: 25257--25712 Score: 265
Period size: 80 Copynumber: 5.6 Consensus size: 82
25247 CGTTTTCTGA
* * * * * * * * *
25257 ATAATCGCCAGTAAAAACTCGTAC-TTAGTGGCATTTTTGTACAAACGCC-CTAAATACTCGTAC
1 ATAAACGCCACTAAATACTAGTACTTTAGTGGCA-TTTTATAAAAACACCGCTAAAGACTCATAC
25320 TTTAGTGGCATTTTAAGC
65 TTTAGTGGCATTTTAAGC
* * *
25338 ATAAGCGCCACTAAATACTA-TACTTTAGTGGCGTTTGTATAAAAACATCGC-AATA-ACTCATA
1 ATAAACGCCACTAAATACTAGTACTTTAGTGGCATTT-TATAAAAACACCGCTAA-AGACTCATA
* * *
25400 TTTTAGTGGCGCTTTT-A-T
64 CTTTAGTGGC-ATTTTAAGC
* * * *
25418 ATAAATGCCTCTAAATACTAGTACTTTAGTGGCATTTTATACAAACACCGCTAAAGACTCGTACT
1 ATAAACGCCACTAAATACTAGTACTTTAGTGGCATTTTATAAAAACACCGCTAAAGACTCATACT
* *
25483 TCAGTGGCGTTTTAAGC
66 TTAGTGGCATTTTAAGC
* *** * ** * *
25500 ATAAATGTTGCTAAATACTCGTACTTTAGTGGCATTTTA-AGCACAAACGTCGCTAAATACTCGT
1 ATAAACGCCACTAAATACTAGTACTTTAGTGGCATTTTATA--A-AAACACCGCTAAAGACTCAT
*
25564 ACTTTAGTGGCGTTTTAAGC
63 ACTTTAGTGGCATTTTAAGC
* * * ** * * * ** *
25584 ----ACACAACTAAATACTCGTACTTTAGAAGCGTTTTAAGAACAAACGCCGCTAATTACTCGTA
1 ATAAACGCCACTAAATACTAGTACTTTAGTGGCATTTT-ATAA-AAACACCGCTAAAGACTCATA
* * * * *
25645 TTTTAGTGTCGTTTTTA-T
64 CTTTAGTGGCATTTTAAGC
* ** *
25663 ATAAACGCCGCTAAATACTA-TACTTTAGTGGTGTTTTTATACAAACACCG
1 ATAAACGCCACTAAATACTAGTACTTTAGTGG-CATTTTATAAAAACACCG
25713 TGAAATACTC
Statistics
Matches: 297, Mismatches: 58, Indels: 40
0.75 0.15 0.10
Matches are distributed among these distances:
80 101 0.34
81 91 0.31
82 53 0.18
83 16 0.05
84 36 0.12
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.34
Consensus pattern (82 bp):
ATAAACGCCACTAAATACTAGTACTTTAGTGGCATTTTATAAAAACACCGCTAAAGACTCATACT
TTAGTGGCATTTTAAGC
Found at i:25496 original size:80 final size:80
Alignment explanation
Indices: 25257--25727 Score: 357
Period size: 81 Copynumber: 5.8 Consensus size: 80
25247 CGTTTTCTGA
* * * * * *
25257 ATAATCGCCAGTAAAAACTCGTAC-TTAGTGGCATTTTTGTACAAACGCC-CTAAATACTCGTAC
1 ATAAACGCCACTAAATACTAGTACTTTAGTGGCA-TTTTATACAAACACCGCTAAATACTCGTAC
*
25320 TTTAGTGGCATTTTAAGC
65 TTTAGTGGCGTTTT-A-C
* * * * *
25338 ATAAGCGCCACTAAATACTA-TACTTTAGTGGCGTTTGTATAAAAACATCGC--AATAACTCATA
1 ATAAACGCCACTAAATACTAGTACTTTAGTGGCATTT-TATACAAACACCGCTAAAT-ACTCGTA
* *
25400 TTTTAGTGGCGCTTTTAT
64 CTTTAGTGGCG-TTTTAC
* * *
25418 ATAAATGCCTCTAAATACTAGTACTTTAGTGGCATTTTATACAAACACCGCTAAAGACTCGTACT
1 ATAAACGCCACTAAATACTAGTACTTTAGTGGCATTTTATACAAACACCGCTAAATACTCGTACT
*
25483 TCAGTGGCGTTTTAAGC
66 TTAGTGGCGTTTT-A-C
* *** * * **
25500 ATAAATGTTGCTAAATACTCGTACTTTAGTGGCATTTTAAGCACAAACGTCGCTAAATACTCGTA
1 ATAAACGCCACTAAATACTAGTACTTTAGTGGCATTTT-A-TACAAACACCGCTAAATACTCGTA
25565 CTTTAGTGGCGTTTTA-
64 CTTTAGTGGCGTTTTAC
** * * * ** * * * *
25581 A-GCACACAACTAAATACTCGTACTTTAGAAGCGTTTTAAGAACAAACGCCGCTAATTACTCGTA
1 ATAAACGCCACTAAATACTAGTACTTTAGTGGCATTTT-A-TACAAACACCGCTAAATACTCGTA
* * *
25645 TTTTAGTGTCGTTTTTAT
64 CTTTAGTGGCG-TTTTAC
* **
25663 ATAAACGCCGCTAAATACTA-TACTTTAGTGGTGTTTTTATACAAACACCG-TGAAATACTCGTA
1 ATAAACGCCACTAAATACTAGTACTTTAGTGG-CATTTTATACAAACACCGCT-AAATACTCGTA
25726 CT
64 CT
25728 GGCCTTTATA
Statistics
Matches: 311, Mismatches: 62, Indels: 34
0.76 0.15 0.08
Matches are distributed among these distances:
80 102 0.33
81 105 0.34
82 52 0.17
83 18 0.06
84 34 0.11
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (80 bp):
ATAAACGCCACTAAATACTAGTACTTTAGTGGCATTTTATACAAACACCGCTAAATACTCGTACT
TTAGTGGCGTTTTAC
Found at i:25531 original size:42 final size:42
Alignment explanation
Indices: 25268--25699 Score: 312
Period size: 42 Copynumber: 10.6 Consensus size: 42
25258 TAATCGCCAG
* * * * *
25268 TAAAAACTCGTAC-TTAGTGGCATTTT-TGTACAAACGCC-C
1 TAAATACTCGTACTTTAGTGGCGTTTTAAGCATAAACGCCGC
* * *
25307 TAAATACTCGTACTTTAGTGGCATTTTAAGCATAAGCGCCAC
1 TAAATACTCGTACTTTAGTGGCGTTTTAAGCATAAACGCCGC
* **
25349 TAAATACT-ATACTTTAGTGGCGTTTGTATA--A-AAACATCGC
1 TAAATACTCGTACTTTAGTGGCGTTT-TA-AGCATAAACGCCGC
* * * * *
25389 --AATAACTCATATTTTAGTGGCGCTTTT-A-TATAAATGCCTC
1 TAAAT-ACTCGTACTTTAGTGGCG-TTTTAAGCATAAACGCCGC
* * *
25429 TAAATACTAGTACTTTAGTGGCATTTTATA-C--AAACACCGC
1 TAAATACTCGTACTTTAGTGGCGTTTTA-AGCATAAACGCCGC
* * * **
25469 TAAAGACTCGTACTTCAGTGGCGTTTTAAGCATAAATGTTGC
1 TAAATACTCGTACTTTAGTGGCGTTTTAAGCATAAACGCCGC
* * *
25511 TAAATACTCGTACTTTAGTGGCATTTTAAGCACAAACGTCGC
1 TAAATACTCGTACTTTAGTGGCGTTTTAAGCATAAACGCCGC
*
25553 TAAATACTCGTACTTTAGTGGCGTTTTAAGCACACAA-----C
1 TAAATACTCGTACTTTAGTGGCGTTTTAAGCATA-AACGCCGC
** * *
25591 TAAATACTCGTACTTTAGAAGCGTTTTAAGAACAAACGCCGC
1 TAAATACTCGTACTTTAGTGGCGTTTTAAGCATAAACGCCGC
* * * * *
25633 TAATTACTCGTATTTTAGTGTCGTTTTTA-TATAAACGCCGC
1 TAAATACTCGTACTTTAGTGGCGTTTTAAGCATAAACGCCGC
* *
25674 TAAATACT-ATACTTTAGTGGTGTTTT
1 TAAATACTCGTACTTTAGTGGCGTTTT
25700 TATACAAACA
Statistics
Matches: 315, Mismatches: 55, Indels: 45
0.76 0.13 0.11
Matches are distributed among these distances:
37 2 0.01
38 36 0.11
39 17 0.05
40 86 0.27
41 58 0.18
42 113 0.36
43 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (42 bp):
TAAATACTCGTACTTTAGTGGCGTTTTAAGCATAAACGCCGC
Found at i:27061 original size:13 final size:13
Alignment explanation
Indices: 27043--27067 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27033 ATACCCTTAT
27043 TTGTTATGATAAA
1 TTGTTATGATAAA
27056 TTGTTATGATAA
1 TTGTTATGATAA
27068 GGGTTCAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
TTGTTATGATAAA
Found at i:29002 original size:44 final size:44
Alignment explanation
Indices: 28954--29054 Score: 166
Period size: 44 Copynumber: 2.3 Consensus size: 44
28944 TTTTACATTC
* *
28954 ACAAACGCCACTATATGACATAACATTTAGCGGCATTTTTAGGA
1 ACAAACGCCACTATATGACAGAACATTTAGCGGCACTTTTAGGA
* *
28998 ACAAACGCCACTATATGTCAGAATATTTAGCGGCACTTTTAGGA
1 ACAAACGCCACTATATGACAGAACATTTAGCGGCACTTTTAGGA
29042 ACAAACGCCACTA
1 ACAAACGCCACTA
29055 AATATCGTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.25
Consensus pattern (44 bp):
ACAAACGCCACTATATGACAGAACATTTAGCGGCACTTTTAGGA
Found at i:32742 original size:16 final size:16
Alignment explanation
Indices: 32723--32756 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
32713 CAATATACGA
32723 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
32739 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
32755 AT
1 AT
32757 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:32825 original size:16 final size:18
Alignment explanation
Indices: 32793--32826 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
32783 CATATATTAA
32793 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
32811 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
32827 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:33534 original size:128 final size:129
Alignment explanation
Indices: 33296--33541 Score: 404
Period size: 128 Copynumber: 1.9 Consensus size: 129
33286 AATTTTCTTC
* *
33296 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACA-GTCAGAT
** *
33361 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
65 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
33426 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACA-TCAGATC
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACAGTCAGATC
33490 CTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
33542 TATATAAATA
Statistics
Matches: 108, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
128 56 0.52
130 52 0.48
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (129 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACAGTCAGATC
CTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:33988 original size:35 final size:35
Alignment explanation
Indices: 33938--34013 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
33928 AATTGAATTG
* *
33938 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
33973 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
34008 AATTGA
1 AATTGA
34014 GGAATGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:35658 original size:31 final size:31
Alignment explanation
Indices: 35622--35680 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
35612 AACTTAAAAG
* * *
35622 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTAAAATTTAAATAATTTT
35653 AGTTTTACAATACTAAAATTTAAATAAT
1 AGTTTTACAATACTAAAATTTAAATAAT
35681 CCATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTAAAATTTAAATAATTTT
Found at i:35731 original size:22 final size:22
Alignment explanation
Indices: 35705--35747 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
35695 TAATAAATTA
35705 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
35727 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
35748 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:35756 original size:22 final size:22
Alignment explanation
Indices: 35707--35755 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
35697 ATAAATTATT
**
35707 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
35729 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
35752 TAAA
1 TAAA
35756 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:35760 original size:54 final size:54
Alignment explanation
Indices: 35695--36256 Score: 540
Period size: 54 Copynumber: 10.4 Consensus size: 54
35685 ACAACTATAA
35695 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
35749 TAATAAATTATTTAAAATAAATCAATACATTCTAATAAATTATTTAAAATAAATCAATCCGTA-
1 TAATAAATTATTTAAAATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAATCCATAC
** * ** * ** ** *
35812 TTTTAAAATAAAT-CAATCCATACTAATAAAT-TATTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
* *
35867 -AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATACATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *
35915 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCAATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
35969 TAATAAATTATTTAAAATAAATCAATCCACA-TTT----T-AATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*** *
36017 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATATTAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTA-AA-A-TAAATCAATCCATAC
*
36075 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
36129 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
36183 TAATAAATTATTTAAAAT--A--AAT---TATTTTAAAATAAATCAATCCATATTTTA
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA----C
36234 TAATAAATTATTTTAAAATAAAT
1 TAATAAATTA-TTTAAAATAAAT
36257 TATTTTATAA
Statistics
Matches: 428, Mismatches: 40, Indels: 79
0.78 0.07 0.14
Matches are distributed among these distances:
47 23 0.05
48 70 0.16
49 5 0.01
50 10 0.02
51 11 0.03
52 10 0.02
53 4 0.01
54 198 0.46
55 5 0.01
56 2 0.00
57 3 0.01
58 46 0.11
60 2 0.00
62 6 0.01
63 10 0.02
64 23 0.05
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:35765 original size:32 final size:32
Alignment explanation
Indices: 35727--35997 Score: 211
Period size: 32 Copynumber: 9.6 Consensus size: 32
35717 CAATCCATAT
35727 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
35759 TTTAAAATAAATCAATACATTCTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
35791 TTTAAAATAAATCAAT-C---C--GT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
35813 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
35845 TTTAAAATAAATCAATCTATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
35875 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
35893 TTTAAAATAAATCAATACATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
35925 TTTAAAATAAATC-A---AT-CT-AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
35947 TTTAAAATAAATCAATCAATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
35979 TTTAAAATAAATCAATCCA
1 TTTAAAATAAATCAATCCA
35998 CATTTTAATC
Statistics
Matches: 194, Mismatches: 9, Indels: 72
0.71 0.03 0.26
Matches are distributed among these distances:
20 1 0.01
22 42 0.22
23 5 0.03
24 4 0.02
25 1 0.01
26 20 0.10
27 4 0.02
28 7 0.04
30 3 0.02
31 6 0.03
32 101 0.52
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:35793 original size:86 final size:84
Alignment explanation
Indices: 35695--35940 Score: 378
Period size: 86 Copynumber: 3.0 Consensus size: 84
35685 ACAACTATAA
35695 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
35760 TTAAAATAAATCAATACATTC
66 TTAAAATAAATCAATA-A-TC
*
35781 TAATAAATTATTTAAAATAAATCAATCCGTATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
35846 TTAAAATAAATC---AATC
66 TTAAAATAAATCAATAATC
* * *
35862 T-ATACAACTA--CAATAATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAATT
1 TAATA-AATTATTTAA-AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATT
35924 ATTTAAAATAAATCAAT
64 ATTTAAAATAAATCAAT
35941 CTATATTTTA
Statistics
Matches: 150, Mismatches: 5, Indels: 13
0.89 0.03 0.08
Matches are distributed among these distances:
79 2 0.01
80 63 0.42
81 7 0.05
82 1 0.01
83 1 0.01
86 76 0.51
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (84 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
TTAAAATAAATCAATAATC
Found at i:35842 original size:22 final size:22
Alignment explanation
Indices: 35793--35841 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
35783 ATAAATTATT
* **
35793 TAAAATAAATCAATCCGTATTT
1 TAAAATAAATCAATCCATATAA
35815 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
35838 TAAA
1 TAAA
35842 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:35922 original size:22 final size:22
Alignment explanation
Indices: 35850--35922 Score: 53
Period size: 22 Copynumber: 3.3 Consensus size: 22
35840 AATTATTTAA
* *
35850 AATAAATCAATCTATACA-ACT
1 AATAAATAAATCAATACATACT
*
35871 ACA-ATAATAAATCAATCCATA-T
1 A-ATA-AATAAATCAATACATACT
**
35893 TTTAAAATAAATCAATACATACT
1 AAT-AAATAAATCAATACATACT
35916 AATAAAT
1 AATAAAT
35923 TATTTAAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 11
0.67 0.14 0.19
Matches are distributed among these distances:
21 2 0.05
22 32 0.84
23 4 0.11
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (22 bp):
AATAAATAAATCAATACATACT
Found at i:35976 original size:22 final size:22
Alignment explanation
Indices: 35927--35975 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
35917 ATAAATTATT
* **
35927 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCAATATAA
35949 TAAAATAAATCAATCAATACTAA
1 TAAAATAAATCAATCAATA-TAA
35972 TAAA
1 TAAA
35976 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCAATATAA
Found at i:36031 original size:134 final size:134
Alignment explanation
Indices: 35695--36048 Score: 464
Period size: 134 Copynumber: 2.6 Consensus size: 134
35685 ACAACTATAA
*
35695 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCACA-TTT----T-AATCAATCCATACTAATAAATTAT
* *
35760 TTAAAATAAATCAATACATTCTAATAAATTATTTAAAATAAATCAATCCGTATTTTAAAATAAAT
60 TTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAAT
*
35825 CAATCCATAC
125 CAATCAATAC
* * ** ** **
35835 TAATAAATTATTTAAAATAAATCAATCTATACAACTACAAT-AATAAAT-C-AATCCA-TATTTT
1 TAATAAATTATTTAAAATAAATCAATC--CAC-ATTTTAATCAATCCATACTAATAAATTA-TTT
*
35896 AAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCA
62 AAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCA
35961 ATCAATAC
127 ATCAATAC
35969 TAATAAATTATTTAAAATAAATCAATCCACATTTTAATCAATCCATACTAATAAATTATTTAAAA
1 TAATAAATTATTTAAAATAAATCAATCCACATTTTAATCAATCCATACTAATAAATTATTTAAAA
*
36034 TAAATCAATCCATAC
66 TAAATCAATACATAC
36049 AACTACAATA
Statistics
Matches: 184, Mismatches: 22, Indels: 22
0.81 0.10 0.10
Matches are distributed among these distances:
131 5 0.03
132 7 0.04
133 3 0.02
134 128 0.70
135 3 0.02
136 5 0.03
137 3 0.02
140 27 0.15
142 2 0.01
143 1 0.01
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (134 bp):
TAATAAATTATTTAAAATAAATCAATCCACATTTTAATCAATCCATACTAATAAATTATTTAAAA
TAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCA
ATAC
Found at i:36042 original size:32 final size:32
Alignment explanation
Indices: 36004--36204 Score: 161
Period size: 32 Copynumber: 7.1 Consensus size: 32
35994 TCCACATTTT
36004 AATCAATCCATACTAATAAATTATTTAAAATA
1 AATCAATCCATACTAATAAATTATTTAAAATA
36036 AATCAATCCATAC-AACTACAA-TA--T----TA
1 AATCAATCCATACTAA-TA-AATTATTTAAAATA
*
36062 AATCAATCTATACTAATAAATTATTTAAAATA
1 AATCAATCCATACTAATAAATTATTTAAAATA
36094 AATCAAT-C---C--AT--A-T-TTTAAAATA
1 AATCAATCCATACTAATAAATTATTTAAAATA
*
36116 AATCAATTCATACTAATAAATTATTTAAAATA
1 AATCAATCCATACTAATAAATTATTTAAAATA
36148 AATCAAT-C---C--AT--A-T-TTTAAAATA
1 AATCAATCCATACTAATAAATTATTTAAAATA
*
36170 AATCAATTCATACTAATAAATTATTTAAAATA
1 AATCAATCCATACTAATAAATTATTTAAAATA
36202 AAT
1 AAT
36205 TATTTTAAAA
Statistics
Matches: 137, Mismatches: 2, Indels: 60
0.69 0.01 0.30
Matches are distributed among these distances:
22 32 0.23
23 4 0.03
24 2 0.01
25 2 0.01
26 24 0.18
27 2 0.01
28 7 0.05
30 3 0.02
31 5 0.04
32 54 0.39
33 2 0.01
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (32 bp):
AATCAATCCATACTAATAAATTATTTAAAATA
Found at i:36097 original size:160 final size:163
Alignment explanation
Indices: 35900--36204 Score: 503
Period size: 160 Copynumber: 1.9 Consensus size: 163
35890 TATTTTAAAA
*
35900 TAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAA-TC
1 TAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTC
35964 AATACTAATAAATTATTTAAAATAAATCAATCCACA-TTT-T-AATCAATCCATACTAATAAATT
66 -ATACTAATAAATTATTTAAAATAAATCAATCCACATTTTATAAATCAATCCATACTAATAAATT
36026 ATTTAAAATAAATCAATCCATACAACTACAATAT
130 ATTTAAAATAAATCAATCCATACAACTACAATAT
36060 TAAATCAAT-CTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATT
1 TAAATCAATAC-ATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATT
* *
36124 CATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAA
65 CATACTAATAAATTATTTAAAATAAATCAATCCACATTTT---ATAAATCAATCCATACTAATAA
36189 ATTATTTAAAATAAAT
127 ATTATTTAAAATAAAT
36205 TATTTTAAAA
Statistics
Matches: 134, Mismatches: 3, Indels: 10
0.91 0.02 0.07
Matches are distributed among these distances:
159 1 0.01
160 93 0.69
161 5 0.04
165 1 0.01
166 34 0.25
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (163 bp):
TAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTC
ATACTAATAAATTATTTAAAATAAATCAATCCACATTTTATAAATCAATCCATACTAATAAATTA
TTTAAAATAAATCAATCCATACAACTACAATAT
Found at i:36111 original size:22 final size:22
Alignment explanation
Indices: 36085--36127 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
36075 TAATAAATTA
36085 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
36107 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
36128 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:36128 original size:80 final size:77
Alignment explanation
Indices: 35705--36136 Score: 296
Period size: 80 Copynumber: 5.4 Consensus size: 77
35695 TAATAAATTA
***
35705 TTTAAAATAAATCAATCCATATTTTAAA-A-TAAATCAATCCATACTAATAAATTATTTAAAATA
1 TTTAAAATAAATCAATCCATACAATAAATATTAAATCAAT-CATACTAATAAATTATTTAAAATA
35768 AATCAATACATTCTAATAAATT
65 AATC---A-A-TCT-AT--A-T
* ***
35790 ATTTAAAATAAATCAATCCGTATTTTAAA-A-TAAATCAATCCATACTAATAAATTATTTAAAAT
1 -TTTAAAATAAATCAATCCATACAATAAATATTAAATCAAT-CATACTAATAAATTATTTAAAAT
*
35853 AAATCAATCTATACAAC
64 AAATCAATCTAT---AT
** ***
35870 TACAATAATAAATCAATCCATATTTTAAA-A-TAAATCAATACATACTAATAAATTATTTAAAAT
1 TTTAA-AATAAATCAATCCATACAATAAATATTAAATCAAT-CATACTAATAAATTATTTAAAAT
35933 AAATCAATCTATAT
64 AAATCAATCTATAT
* ** * *
35947 TTTAAAATAAATCAATCAATACTAATAAATTATTTAAAAT-AA--AT-C-AATCCA-CATTT-TA
1 TTTAAAATAAATCAATCCATAC-AATAAA-TA-TT-AAATCAATCATACTAATAAATTATTTAAA
* *
36005 ATCAATCCATACTAATAAATT
62 ATAAATCAAT-CT-AT--A-T
36026 ATTTAAAATAAATCAATCCATACAACTACAATATTAAATCAATCTATACTAATAAATTATTTAAA
1 -TTTAAAATAAATCAATCCATACAA-TA-AATATTAAATCAATC-ATACTAATAAATTATTTAAA
*
36091 ATAAATCAATCCATAT
62 ATAAATCAATCTATAT
*
36107 TTTAAAATAAATCAATTCATACTAATAAAT
1 TTTAAAATAAATCAATCCATAC-AATAAAT
36137 TATTTAAAAT
Statistics
Matches: 292, Mismatches: 29, Indels: 57
0.77 0.08 0.15
Matches are distributed among these distances:
74 9 0.03
75 6 0.02
76 21 0.07
77 9 0.03
78 7 0.02
79 14 0.05
80 117 0.40
81 13 0.04
82 8 0.03
83 2 0.01
84 6 0.02
85 5 0.02
86 75 0.26
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (77 bp):
TTTAAAATAAATCAATCCATACAATAAATATTAAATCAATCATACTAATAAATTATTTAAAATAA
ATCAATCTATAT
Found at i:36136 original size:22 final size:22
Alignment explanation
Indices: 36087--36135 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
36077 ATAAATTATT
**
36087 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
36109 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
36132 TAAA
1 TAAA
36136 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:36165 original size:22 final size:22
Alignment explanation
Indices: 36139--36241 Score: 89
Period size: 22 Copynumber: 4.5 Consensus size: 22
36129 TAATAAATTA
36139 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
36161 TTTAAAATAAATCAATTCATACT
1 TTTAAAATAAATCAATCCATA-T
** * ** * **
36184 AATAAATTATTTAAAATAAATTAT
1 TTTAAAATAAAT-CAATCCA-TAT
36208 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
36230 TTTATAATAAAT
1 TTTAAAATAAAT
36242 TATTTTAAAA
Statistics
Matches: 60, Mismatches: 18, Indels: 6
0.71 0.21 0.07
Matches are distributed among these distances:
22 34 0.57
23 12 0.20
24 12 0.20
25 2 0.03
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:36213 original size:15 final size:15
Alignment explanation
Indices: 36184--36286 Score: 118
Period size: 15 Copynumber: 6.5 Consensus size: 15
36174 AATTCATACT
36184 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
36198 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
36213 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
36235 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
36250 AATAAATTATTTTAT
1 AATAAATTATTTTAA
36265 AATAAATTATTTTAA
1 AATAAATTATTTTAA
36280 AATAAAT
1 AATAAAT
36287 AACCTTATTA
Statistics
Matches: 77, Mismatches: 4, Indels: 15
0.80 0.04 0.16
Matches are distributed among these distances:
14 9 0.12
15 50 0.65
17 1 0.01
18 3 0.04
19 3 0.04
20 1 0.01
22 10 0.13
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:36219 original size:69 final size:67
Alignment explanation
Indices: 36130--36286 Score: 228
Period size: 69 Copynumber: 2.3 Consensus size: 67
36120 AATTCATACT
*
36130 AATAAATTA-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTA-
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAAAT-AATT-ATA-AAATAAATTAT
36193 TTTAA
63 TTTAA
* * *
36198 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTTTAAAATAAATTATTTT
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAAATAATTATAAAATAAATTATTTT
*
36263 AT
66 AA
36265 AATAAATTATTTTAAAATAAAT
1 AATAAATTATTTTAAAATAAAT
36287 AACCTTATTA
Statistics
Matches: 82, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
66 9 0.11
67 28 0.34
68 12 0.15
69 33 0.40
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (67 bp):
AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAAATAATTATAAAATAAATTATTTT
AA
Found at i:36251 original size:160 final size:152
Alignment explanation
Indices: 35890--36256 Score: 431
Period size: 160 Copynumber: 2.3 Consensus size: 152
35880 AATCAATCCA
* *
35890 TATTTTAAAATAAATCAATACATA---CTAATAAATTATTTAAAATAAATCAATCTATATTTTAA
1 TATTTTAAAATAAATCAAT-CATATTTATAATAAATTATTTAAAATAAATCAATCCATATTTTAA
35952 AATAAATCAATCAATACTAATAAATTATTTAAAATAAATCAATCCACATTTTAATCAATCCATAC
65 AATAAATCAATCAATACTAATAAATTATTTAAAATAAATCAATCCACATTTTAATCAATCCATAC
36017 TAATAAATTATTTAAAATAAATC
130 TAATAAATTATTTAAAATAAATC
* ** * *
36040 AATCCATACAACTACAATATTAAATCA-ATCTATACTAATAAATTATTTAAAATAAATCAATCCA
1 TAT-TTTA-AA--ATAA-A-TCAATCATAT-T-TA-TAATAAATTATTTAAAATAAATCAATCCA
*
36104 TATTTTAAAATAAATCAATTC-ATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAA
57 TATTTTAAAATAAATCAA-TCAATACTAATAAATTATTTAAAATAAATCAATCCACA-TTT----
*
36168 TAAATCAATTCATACTAATAAATTATTTAAAATAAAT-
116 T-AATCAATCCATACTAATAAATTATTTAAAATAAATC
36205 TATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTTTAAAATAAAT
1 TATTTTAAAATAAATCAAT-CATA-TTTATAATAAATTA-TTTAAAATAAAT
36257 TATTTTATAA
Statistics
Matches: 180, Mismatches: 14, Indels: 36
0.78 0.06 0.16
Matches are distributed among these distances:
150 2 0.01
151 2 0.01
152 2 0.01
154 4 0.02
155 3 0.02
156 4 0.02
159 14 0.08
160 97 0.54
161 10 0.06
162 1 0.01
163 2 0.01
164 2 0.01
165 3 0.02
166 34 0.19
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (152 bp):
TATTTTAAAATAAATCAATCATATTTATAATAAATTATTTAAAATAAATCAATCCATATTTTAAA
ATAAATCAATCAATACTAATAAATTATTTAAAATAAATCAATCCACATTTTAATCAATCCATACT
AATAAATTATTTAAAATAAATC
Found at i:38858 original size:17 final size:17
Alignment explanation
Indices: 38836--38868 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
38826 ATTTTAGGAG
38836 ATAAAAACAT-ATTTTTA
1 ATAAAAA-ATAATTTTTA
38853 ATAAAAAATAATTTTT
1 ATAAAAAATAATTTTT
38869 TTTTGTCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAAAAATAATTTTTA
Found at i:38974 original size:33 final size:33
Alignment explanation
Indices: 38932--38997 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
38922 TAGATCTATC
38932 TTCGCTTATAAAACACAAAAAGTGGTGCATAAG
1 TTCGCTTATAAAACACAAAAAGTGGTGCATAAG
38965 TTCGCTTATAAAACACAAAAAGTGGTGCATAAG
1 TTCGCTTATAAAACACAAAAAGTGGTGCATAAG
38998 AAAGGACCGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.24
Consensus pattern (33 bp):
TTCGCTTATAAAACACAAAAAGTGGTGCATAAG
Found at i:44876 original size:38 final size:38
Alignment explanation
Indices: 44830--44906 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 38
44820 TCAGGTAGGG
44830 TTTTTTAAGTGTAATATTCGGGTC-GAGTCGGGTCGGGT
1 TTTTTTAAGTGTAATATTCGGGTCAG-GTCGGGTCGGGT
* *
44868 TTTTTTAAGTTTGATATTCGGGTCAGGTCGGGTCGGGT
1 TTTTTTAAGTGTAATATTCGGGTCAGGTCGGGTCGGGT
44906 T
1 T
44907 CGGGTTTAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 35 0.97
39 1 0.03
ACGTcount: A:0.14, C:0.10, G:0.34, T:0.42
Consensus pattern (38 bp):
TTTTTTAAGTGTAATATTCGGGTCAGGTCGGGTCGGGT
Found at i:46164 original size:30 final size:27
Alignment explanation
Indices: 46109--46164 Score: 67
Period size: 30 Copynumber: 2.0 Consensus size: 27
46099 TATGATCTTG
*
46109 AATAACTAATTTTTTATACTGTAAGAA
1 AATAACTAATTTTTTATAATGTAAGAA
*
46136 AATAACTTAATTTTTATTATAATTTAAGA
1 AATAAC-TAA-TTTT-TTATAATGTAAGA
46165 TATTTCATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 6 0.25
28 3 0.12
29 4 0.17
30 11 0.46
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (27 bp):
AATAACTAATTTTTTATAATGTAAGAA
Found at i:54125 original size:2 final size:2
Alignment explanation
Indices: 54118--54161 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
54108 GTCAAGTATC
54118 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
54160 AT
1 AT
54162 CGAAGATTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54278 original size:2 final size:2
Alignment explanation
Indices: 54271--54304 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
54261 GTTGTAAGTG
54271 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54305 CGCAAATAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55916 original size:18 final size:18
Alignment explanation
Indices: 55889--55981 Score: 105
Period size: 18 Copynumber: 4.9 Consensus size: 18
55879 ACTGAATATT
55889 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
55907 TGTCCTGAAGGACCACTGGT
1 TGTCCCGAAGGACCACT--A
* *
55927 TGTTCCGAAGAACCACTA
1 TGTCCCGAAGGACCACTA
*
55945 TGTCCCGAAGGACCACTGTT
1 TGTCCCGAAGGACCAC--TA
55965 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
55982 GATAATCCCT
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
18 31 0.50
20 31 0.50
ACGTcount: A:0.25, C:0.30, G:0.24, T:0.22
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:55935 original size:38 final size:38
Alignment explanation
Indices: 55888--55981 Score: 152
Period size: 38 Copynumber: 2.5 Consensus size: 38
55878 CACTGAATAT
*
55888 TTGTCCCGAAGGACCACTATGTCCTGAAGGACCACTGG
1 TTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGG
* * *
55926 TTGTTCCGAAGAACCACTATGTCCCGAAGGACCACTGT
1 TTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGG
55964 TTGTCCCGAAGGACCACT
1 TTGTCCCGAAGGACCACT
55982 GATAATCCCT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.24, C:0.30, G:0.23, T:0.22
Consensus pattern (38 bp):
TTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGG
Found at i:55990 original size:20 final size:19
Alignment explanation
Indices: 55889--55984 Score: 115
Period size: 20 Copynumber: 5.1 Consensus size: 19
55879 ACTGAATATT
55889 TGTCCCGAAGGACCACT-A
1 TGTCCCGAAGGACCACTGA
* *
55907 TGTCCTGAAGGACCACTGGT
1 TGTCCCGAAGGACCACT-GA
* *
55927 TGTTCCGAAGAACCACT-A
1 TGTCCCGAAGGACCACTGA
*
55945 TGTCCCGAAGGACCACTGTT
1 TGTCCCGAAGGACCACTG-A
55965 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACTGA
55984 T
1 T
55985 AATCCCTCGA
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
18 31 0.48
19 1 0.02
20 32 0.50
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (19 bp):
TGTCCCGAAGGACCACTGA
Found at i:56934 original size:26 final size:24
Alignment explanation
Indices: 56898--56959 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
56888 CATGTTAACA
*
56898 CATATAATCATGCAAACATACAATT
1 CATATATTCATGCAAACATACAA-T
* *
56923 CATGTCATTCAT--AAACATATAAT
1 CATAT-ATTCATGCAAACATACAAT
56946 CATATATTCATGCA
1 CATATATTCATGCA
56960 TTCTAATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
22 6 0.20
23 5 0.17
24 10 0.33
25 4 0.13
26 5 0.17
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.32
Consensus pattern (24 bp):
CATATATTCATGCAAACATACAAT
Found at i:57265 original size:20 final size:22
Alignment explanation
Indices: 57240--57297 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
57230 TTCCCCTTGA
57240 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
57260 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
57283 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
57298 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:58565 original size:20 final size:20
Alignment explanation
Indices: 58536--58573 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
58526 TTTCAAAGGA
58536 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
58556 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
58574 GAATAAATTG
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:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:58653 original size:65 final size:63
Alignment explanation
Indices: 58584--58736 Score: 180
Period size: 56 Copynumber: 2.5 Consensus size: 63
58574 GAATAAATTG
*
58584 AACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAAAG-T-TTTATG
1 AACATCGAATGCATTTTATGCATCGATGCACAGA-CATGCATCGATGCACTC-AAGCTATTT-TG
58647 AA
63 -A
* *
58649 AACATTGAATGCATTTGATG---C-A--CA-AGACATGCATCGATGCACTCAAGCTATTTTGA
1 AACATCGAATGCATTTTATGCATCGATGCACAGACATGCATCGATGCACTCAAGCTATTTTGA
58705 AACATCGAATGCATTTTATGCATCGATGCACA
1 AACATCGAATGCATTTTATGCATCGATGCACA
58737 CTTAGTTCAC
Statistics
Matches: 74, Mismatches: 5, Indels: 20
0.75 0.05 0.20
Matches are distributed among these distances:
56 22 0.30
57 20 0.27
58 5 0.07
59 3 0.04
60 1 0.01
61 1 0.01
62 3 0.04
63 1 0.01
65 18 0.24
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (63 bp):
AACATCGAATGCATTTTATGCATCGATGCACAGACATGCATCGATGCACTCAAGCTATTTTGA
Found at i:58661 original size:56 final size:55
Alignment explanation
Indices: 58601--58718 Score: 143
Period size: 57 Copynumber: 2.1 Consensus size: 55
58591 AATGCATTTT
* *
58601 ATGCATCGATGCACATA-CCATGCATCGATGCACTCAAAG-T-TTTATGAAAACATTGA
1 ATGCATCGATGCACA-AGACATGCATCGATGCACTC-AAGCTATTT-TG-AAACATCGA
*
58657 ATGCATTTGATGCACAAGACATGCATCGATGCACTCAAGCTATTTTGAAACATCGA
1 ATGCA-TCGATGCACAAGACATGCATCGATGCACTCAAGCTATTTTGAAACATCGA
58713 ATGCAT
1 ATGCAT
58719 TTTATGCATC
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
55 1 0.02
56 22 0.40
57 29 0.53
58 3 0.05
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (55 bp):
ATGCATCGATGCACAAGACATGCATCGATGCACTCAAGCTATTTTGAAACATCGA
Found at i:64204 original size:44 final size:44
Alignment explanation
Indices: 64119--64215 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 44
64109 TTGTACTTAA
* *
64119 TGCATCGATACACTGAATAGTGCATCGATGCATCCCTTTGAATG
1 TGCATCGATACACTGAAGAGTGCACCGATGCATCCCTTTGAATG
64163 TGCATCGATACATCATGAAGA-TGCACCGATGCA-CGCC-TTGAATG
1 TGCATCGATACA-C-TGAAGAGTGCACCGATGCATC-CCTTTGAATG
64207 TGCATCGAT
1 TGCATCGAT
64216 GCACAAGGCC
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
44 29 0.60
45 14 0.29
46 5 0.10
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.27
Consensus pattern (44 bp):
TGCATCGATACACTGAAGAGTGCACCGATGCATCCCTTTGAATG
Found at i:66864 original size:20 final size:20
Alignment explanation
Indices: 66835--66872 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
66825 TTTCAAAGGA
66835 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
66855 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
66873 GAATAAATTG
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:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:67766 original size:42 final size:42
Alignment explanation
Indices: 67718--67802 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
67708 CTCTTGGTCG
67718 ATTCCATCGATCGATTAACTCAACATGTTTGATAAAATAACT
1 ATTCCATCGATCGATTAACTCAACATGTTTGATAAAATAACT
67760 ATTCCATCGATCGATTAACTCAACATGTTTGATAAAATAACT
1 ATTCCATCGATCGATTAACTCAACATGTTTGATAAAATAACT
67802 A
1 A
67803 ACCGAATTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (42 bp):
ATTCCATCGATCGATTAACTCAACATGTTTGATAAAATAACT
Done.