Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003290.1 Hibiscus syriacus cultivar Beakdansim tig00006920_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: 73423
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:2338 original size:18 final size:17
Alignment explanation
Indices: 2297--2357 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 17
2287 GTGGCAATAA
*
2297 TTTTATACATTTTCACAT
1 TTTTAT-CATTTTTACAT
2315 TCTTTATCATTCTTTACAT
1 T-TTTATCATT-TTTACAT
*
2334 TTTTATTATTTTTTACAT
1 TTTTATCA-TTTTTACAT
2352 TTTTAT
1 TTTTAT
2358 TCTTTCAATC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
18 24 0.63
19 14 0.37
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTATCATTTTTACAT
Found at i:2358 original size:18 final size:18
Alignment explanation
Indices: 2306--2358 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
2296 ATTTTATACA
* *
2306 TTTTCACATTCTTTATCAT
1 TTTTTACATT-TTTATTAT
*
2325 TCTTTACATTTTTATTAT
1 TTTTTACATTTTTATTAT
2343 TTTTTACATTTTTATT
1 TTTTTACATTTTTATT
2359 CTTTCAATCA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 22 0.73
19 8 0.27
ACGTcount: A:0.21, C:0.13, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTTACATTTTTATTAT
Found at i:4013 original size:11 final size:11
Alignment explanation
Indices: 3999--4036 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
3989 AAAGGAGAGA
3999 AAAAGAATAAT
1 AAAAGAATAAT
4010 AAAAGAATAAT
1 AAAAGAATAAT
*
4021 AAAA-AA-AAG
1 AAAAGAATAAT
4030 AAAAGAA
1 AAAAGAA
4037 AATGTTAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
9 6 0.24
10 4 0.16
11 15 0.60
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.11
Consensus pattern (11 bp):
AAAAGAATAAT
Found at i:8525 original size:13 final size:13
Alignment explanation
Indices: 8507--8539 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
8497 ATGGTTCAAC
8507 AGAAAAGAAAAAA-
1 AGAAAA-AAAAAAG
8520 AGAAAAAAAAAAG
1 AGAAAAAAAAAAG
8533 AGAAAAA
1 AGAAAAA
8540 GTGAAGGGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAAAAG
Found at i:10898 original size:44 final size:44
Alignment explanation
Indices: 10842--10943 Score: 127
Period size: 44 Copynumber: 2.3 Consensus size: 44
10832 TTTTATAGAT
*
10842 TGGATTCTATCACATAAGAAGGTGAATCAACATTCCCTTT-TTGC
1 TGGATTCTATCACATAAGAAGGTGAATCAACA-TCACTTTGTTGC
* * *
10886 TGGATT-TCATCACATAAGGAGTTGGATCAACATCACTTTGTTGC
1 TGGATTCT-ATCACATAAGAAGGTGAATCAACATCACTTTGTTGC
*
10930 TCGATTCTATCACA
1 TGGATTCTATCACA
10944 GAATGAGGTA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
43 7 0.14
44 42 0.84
45 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (44 bp):
TGGATTCTATCACATAAGAAGGTGAATCAACATCACTTTGTTGC
Found at i:11101 original size:131 final size:131
Alignment explanation
Indices: 10893--11268 Score: 440
Period size: 131 Copynumber: 2.9 Consensus size: 131
10883 TGCTGGATTT
* * * * *
10893 CATCACATAAGGAGTTGGATCA-ACATCACTTTGTTGCTCGATTCTATCACAGAATGAGGTATAT
1 CATCAGATAAGGAGTTGGATCAGA-ATCCCTTT-TTGCTTGATTATATCACAGAATGAGGTAAAT
* * *
10957 CAGCAACGACATTTTGTTTGATTTCATCAAAGAATGA-GTGGATCAACATTGCCATTTCCCTCAA
64 CAGCATCGACATTTTGTTTGATTCCATCACAGAATGAGGTGGATCAACATTGCCATTTCCCTCAA
11021 ATC
129 ATC
* * *
11024 TATCAGATAAGGAGTTGGATTAGAATCGCCTTTTTGCTTGATTTTATCACAGAATGAGGTAAATC
1 CATCAGATAAGGAGTTGGATCAGAATC-CCTTTTTGCTTGATTATATCACAGAATGAGGTAAATC
* * * **
11089 AGCATCGACATTTTGTTTAATTCCATCACAGAAAGAGGTGGATCAACATTGTCATTTTGCTCAAA
65 AGCATCGACATTTTGTTTGATTCCATCACAGAATGAGGTGGATCAACATTGCCATTTCCCTCAAA
11154 TC
130 TC
* ** * **
11156 CATC-GCATAAAGAGTTGGATCAGCGTCACC-TTTTGCTTGATTATATCACAGAATTATATAAAT
1 CATCAG-ATAAGGAGTTGGATCAGAATC-CCTTTTTGCTTGATTATATCACAGAATGAGGTAAAT
* * *
11219 -A-CATTGACATTATGTTCGATTCCATCACAGAATGAGGTGGATCAACATTG
64 CAGCATCGACATTTTGTTTGATTCCATCACAGAATGAGGTGGATCAACATTG
11269 TCAGTTTTTT
Statistics
Matches: 211, Mismatches: 30, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
129 44 0.21
130 1 0.00
131 112 0.53
132 54 0.26
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (131 bp):
CATCAGATAAGGAGTTGGATCAGAATCCCTTTTTGCTTGATTATATCACAGAATGAGGTAAATCA
GCATCGACATTTTGTTTGATTCCATCACAGAATGAGGTGGATCAACATTGCCATTTCCCTCAAAT
C
Found at i:11145 original size:44 final size:44
Alignment explanation
Indices: 11069--11177 Score: 110
Period size: 44 Copynumber: 2.5 Consensus size: 44
11059 GCTTGATTTT
* ** * * * *
11069 ATCACAGAATGAGGTAAATCAGCATCGACATTTTGTTTAATTCC
1 ATCACAGAAAGAGGTGGATCAACATCGACATTTTGCTCAAATCC
* *
11113 ATCACAGAAAGAGGTGGATCAACATTGTCATTTTGCTCAAATCC
1 ATCACAGAAAGAGGTGGATCAACATCGACATTTTGCTCAAATCC
* * *
11157 ATCGCATAAAGAGTTGGATCA
1 ATCACAGAAAGAGGTGGATCA
11178 GCGTCACCTT
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (44 bp):
ATCACAGAAAGAGGTGGATCAACATCGACATTTTGCTCAAATCC
Found at i:11513 original size:8 final size:8
Alignment explanation
Indices: 11502--11607 Score: 61
Period size: 8 Copynumber: 12.5 Consensus size: 8
11492 AAAAAAGGAT
11502 AAAAAAAG
1 AAAAAAAG
11510 -AAAAAAG
1 AAAAAAAG
**
11517 AAAACGAG
1 AAAAAAAG
*
11525 AAAAATAAA
1 AAAAA-AAG
11534 AATAAAAAG
1 AA-AAAAAG
** *
11543 GGAAGAAG
1 AAAAAAAG
11551 AAAAAAAG
1 AAAAAAAG
11559 AAAAAAAAG
1 -AAAAAAAG
11568 ATGAAAAAATG
1 A--AAAAAA-G
*
11579 AAAATGAAG
1 AAAA-AAAG
* *
11588 AAAGAGAG
1 AAAAAAAG
11596 AAAAAAAG
1 AAAAAAAG
11604 AAAA
1 AAAA
11608 TAATAAATGA
Statistics
Matches: 72, Mismatches: 18, Indels: 16
0.68 0.17 0.15
Matches are distributed among these distances:
7 7 0.10
8 32 0.44
9 20 0.28
10 11 0.15
11 2 0.03
ACGTcount: A:0.76, C:0.01, G:0.18, T:0.05
Consensus pattern (8 bp):
AAAAAAAG
Found at i:11541 original size:45 final size:46
Alignment explanation
Indices: 11492--11607 Score: 105
Period size: 45 Copynumber: 2.5 Consensus size: 46
11482 TTAGTTGATA
*
11492 AAAAAAGGATAAAAAAAGAAAAAAGAAAACGA-G-AAAAATAAAAAT-
1 AAAAAAGGA-AAAAAAAGAAAAAA-AAAAAGATGAAAAAATAAAAATG
* *
11537 AAAAAGGGAAGAAGAAAA-AAAGAAAAAAAAGATGAAAAAATGAAAATG
1 AAAAAAGGAA-AA-AAAAGAAA-AAAAAAAAGATGAAAAAATAAAAATG
*
11585 AAGAAAGAGAGAAAAAAAGAAAA
1 AAAAAAG-GA-AAAAAAAGAAAA
11608 TAATAAATGA
Statistics
Matches: 57, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
44 1 0.02
45 19 0.33
46 8 0.14
47 11 0.19
48 10 0.18
49 7 0.12
50 1 0.02
ACGTcount: A:0.76, C:0.01, G:0.18, T:0.05
Consensus pattern (46 bp):
AAAAAAGGAAAAAAAAGAAAAAAAAAAAGATGAAAAAATAAAAATG
Found at i:11568 original size:20 final size:21
Alignment explanation
Indices: 11510--11607 Score: 67
Period size: 20 Copynumber: 4.5 Consensus size: 21
11500 ATAAAAAAAG
*
11510 AAAAAAGAAAACGAGAAA-AATA
1 AAAAAAGAAAA--AGAAAGAAGA
* * *
11532 AAAATA-AAAAGGGAAGAAGA
1 AAAAAAGAAAAAGAAAGAAGA
*
11552 AAAAAAGAAAAA-AAAGATGA
1 AAAAAAGAAAAAGAAAGAAGA
*
11572 AAAAATGAAAATGAAGAAAGAGAGA
1 AAAAAAG-AAA--AAGAAAGA-AGA
11597 AAAAAAGAAAA
1 AAAAAAGAAAA
11608 TAATAAATGA
Statistics
Matches: 58, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
19 3 0.05
20 20 0.34
21 11 0.19
22 6 0.10
23 2 0.03
24 8 0.14
25 8 0.14
ACGTcount: A:0.76, C:0.01, G:0.18, T:0.05
Consensus pattern (21 bp):
AAAAAAGAAAAAGAAAGAAGA
Found at i:11582 original size:25 final size:25
Alignment explanation
Indices: 11553--11608 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
11543 GGAAGAAGAA
* *
11553 AAAAAGAAAAAAAAGATGAAAAAATG
1 AAAATGAAAAAAAAGA-GAAAAAAAG
* *
11579 AAAATGAAGAAAGAGAGAAAAAAAG
1 AAAATGAAAAAAAAGAGAAAAAAAG
11604 AAAAT
1 AAAAT
11609 AATAAATGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 13 0.50
26 13 0.50
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (25 bp):
AAAATGAAAAAAAAGAGAAAAAAAG
Found at i:11582 original size:26 final size:25
Alignment explanation
Indices: 11553--11607 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
11543 GGAAGAAGAA
*
11553 AAAAAGAAAAAAAAGATGAAAAAATG
1 AAAAAGAAAAAAAAGA-GAAAAAAAG
* * *
11579 AAAATGAAGAAAGAGAGAAAAAAAG
1 AAAAAGAAAAAAAAGAGAAAAAAAG
11604 AAAA
1 AAAA
11608 TAATAAATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.05
Consensus pattern (25 bp):
AAAAAGAAAAAAAAGAGAAAAAAAG
Found at i:14173 original size:136 final size:137
Alignment explanation
Indices: 13921--14223 Score: 333
Period size: 136 Copynumber: 2.2 Consensus size: 137
13911 TAGTCCTTTT
*
13921 AATTTAGGGAAATTTTTAATTTGGTCCTCGTTTTTGCTCAGGGTTCCATTTTAATTATTCAAATC
1 AATTTAGGG-AATTTTTAATTTGGTCCTCGTCTTTGCTCAGGGTTCCATTTTAATTATTCAAATC
* ** *** *
13986 AAATAATTGGTTAAAATTAACTAGGTTAACAATTAGAGTCTCTATTTTAGGCTTAACTTCACACT
65 -AATAATTGATTAAAATTAACTAGGTTAACAATTAGAACCTCTACCATAGGCTTAACTTCACAAT
14051 TAATCCTTA
129 TAATCCTTA
* * ** ** *
14060 AATTTAAGGGAATTTTTAATTTGGTCTTC-TCTTTGCTC-GAGTTTGTATTTTAATTATTTGAGT
1 AATTT-AGGGAATTTTTAATTTGGTCCTCGTCTTTGCTCAG-GGTTCCATTTTAATTATTCAAAT
** * * *
14123 C-ATAATTGATTAAAATTAGTTAGGTTAATAATTAGAACCTCTACCATAGGCTTAATTTCATAAT
64 CAATAATTGATTAAAATTAACTAGGTTAACAATTAGAACCTCTACCATAGGCTTAACTTCACAAT
* *
14187 TAGTCCTTG
129 TAATCCTTA
*
14196 AATTTAGGAGAATTTTTTATTTGGTCCT
1 AATTTAGG-GAATTTTTAATTTGGTCCT
14224 TGCTTACGCT
Statistics
Matches: 137, Mismatches: 24, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
135 3 0.02
136 80 0.58
137 1 0.01
138 26 0.19
139 23 0.17
140 4 0.03
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (137 bp):
AATTTAGGGAATTTTTAATTTGGTCCTCGTCTTTGCTCAGGGTTCCATTTTAATTATTCAAATCA
ATAATTGATTAAAATTAACTAGGTTAACAATTAGAACCTCTACCATAGGCTTAACTTCACAATTA
ATCCTTA
Found at i:17341 original size:2 final size:2
Alignment explanation
Indices: 17336--17411 Score: 61
Period size: 2 Copynumber: 39.5 Consensus size: 2
17326 TGATATATGC
* * * *
17336 AT AT AT AT AT AT AT AT AC AT AC AT AC AT AT AC AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
17377 AT AA AT CA- AT AT AT AT A- AT AT AT TT AT A- AT AT AT A
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17412 ACACACGCAG
Statistics
Matches: 57, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
1 4 0.07
2 52 0.91
3 1 0.02
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:18630 original size:54 final size:54
Alignment explanation
Indices: 18558--18663 Score: 158
Period size: 54 Copynumber: 2.0 Consensus size: 54
18548 GTTTTGAAAG
* * * * *
18558 TCTGGGAAGACTTTGAGGACATGAAACATCATCAGGTCTCCATGCTCTACAAAT
1 TCTGGGAAGACCTCGAGGACACGAAACATCATCAGGTCTCCAAGCTCGACAAAT
*
18612 TCTGGGAAGACCTCGAGGACGCGAAACATCATCAGGTCTCCAAGCTCGACAA
1 TCTGGGAAGACCTCGAGGACACGAAACATCATCAGGTCTCCAAGCTCGACAA
18664 TTTGTCAGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (54 bp):
TCTGGGAAGACCTCGAGGACACGAAACATCATCAGGTCTCCAAGCTCGACAAAT
Found at i:20535 original size:31 final size:31
Alignment explanation
Indices: 20500--20589 Score: 108
Period size: 32 Copynumber: 2.9 Consensus size: 31
20490 ATTTTTTATT
*
20500 AATTTTTTAAATAATTATAAAATAATCATTA
1 AATTTTTTAAATTATTATAAAATAATCATTA
* * *
20531 AATTTTATCAAATTATTATAAAAAAATCTTTA
1 AATTTT-TTAAATTATTATAAAATAATCATTA
* * *
20563 AATTTATTAAGTTGTTATAAAATAATC
1 AATTTTTTAAATTATTATAAAATAATC
20590 CTTAGACTTA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
31 23 0.47
32 26 0.53
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (31 bp):
AATTTTTTAAATTATTATAAAATAATCATTA
Found at i:20564 original size:32 final size:32
Alignment explanation
Indices: 20500--20589 Score: 112
Period size: 31 Copynumber: 2.9 Consensus size: 32
20490 ATTTTTTATT
*
20500 AATTTT-TTAAATAATTATAAAATAATCATTA
1 AATTTTATTAAATTATTATAAAATAATCATTA
* * *
20531 AATTTTATCAAATTATTATAAAAAAATCTTTA
1 AATTTTATTAAATTATTATAAAATAATCATTA
* *
20563 AA-TTTATTAAGTTGTTATAAAATAATC
1 AATTTTATTAAATTATTATAAAATAATC
20590 CTTAGACTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
31 27 0.54
32 23 0.46
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (32 bp):
AATTTTATTAAATTATTATAAAATAATCATTA
Found at i:20601 original size:31 final size:31
Alignment explanation
Indices: 20500--20613 Score: 111
Period size: 31 Copynumber: 3.6 Consensus size: 31
20490 ATTTTTTATT
* *
20500 AATTTTTTAAATAATTATAAAATAATCATTA
1 AATTTATTAAATTATTATAAAATAATCATTA
* * *
20531 AATTTTATCAAATTATTATAAAAAAATCTTTA
1 AA-TTTATTAAATTATTATAAAATAATCATTA
* * *
20563 AATTTATTAAGTTGTTATAAAATAATCCTTA
1 AATTTATTAAATTATTATAAAATAATCATTA
* *
20594 GACTTATTAAAAGTTATTAT
1 AATTTATT-AAA-TTATTAT
20614 TTTATAGCAT
Statistics
Matches: 66, Mismatches: 14, Indels: 4
0.79 0.17 0.05
Matches are distributed among these distances:
31 32 0.48
32 28 0.42
33 6 0.09
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (31 bp):
AATTTATTAAATTATTATAAAATAATCATTA
Found at i:21838 original size:65 final size:63
Alignment explanation
Indices: 21768--21897 Score: 206
Period size: 65 Copynumber: 2.0 Consensus size: 63
21758 GTAAAACGTA
* *
21768 AAGCAAATATGAAAAATAGAGTAAATTGTATTTATTTCAAAAGTTAAAGAAAAAAAAATTAAAAC
1 AAGCAAATATGAAAAATAAAGTAAATTGCATTTATTTCAAAAGTT-AA-AAAAAAAAATTAAAAC
* *
21833 AAGCAAATCTGAAAAATAAAGTAAATTGCATTTATTTCAAAAGTTAAAAGAAAAAATTAAAAC
1 AAGCAAATATGAAAAATAAAGTAAATTGCATTTATTTCAAAAGTTAAAAAAAAAAATTAAAAC
21896 AA
1 AA
21898 TATATATAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
63 17 0.28
64 2 0.03
65 42 0.69
ACGTcount: A:0.58, C:0.06, G:0.10, T:0.25
Consensus pattern (63 bp):
AAGCAAATATGAAAAATAAAGTAAATTGCATTTATTTCAAAAGTTAAAAAAAAAAATTAAAAC
Found at i:21910 original size:9 final size:9
Alignment explanation
Indices: 21896--22063 Score: 78
Period size: 9 Copynumber: 17.4 Consensus size: 9
21886 AAATTAAAAC
21896 AATATATAT
1 AATATATAT
21905 AATATATAT
1 AATATATAT
21914 -ATATATAT
1 AATATATAT
21922 -ATATATAT
1 AATATATAT
21930 -ATATATAT
1 AATATATAT
*
21938 AATTTATATTT
1 AA--TATATAT
21949 ACATATTTATAT
1 A-ATA--TATAT
*
21961 AATGTATAT
1 AATATATAT
*
21970 AA-ACTATGT
1 AATA-TATAT
*
21979 AGTGTATATAT
1 A--ATATATAT
21990 GAACTATATAT
1 -AA-TATATAT
22001 AA-ACTATAT
1 AATA-TATAT
22010 AATATACTAT
1 AATATA-TAT
22020 ATATAAAGTATAT
1 A-AT--A-TATAT
*
22033 AATTTATAT
1 AATATATAT
* *
22042 ACTTTATAT
1 AATATATAT
22051 AAT-TATATT
1 AATATATA-T
22060 AATA
1 AATA
22064 AACTATATAG
Statistics
Matches: 127, Mismatches: 11, Indels: 41
0.71 0.06 0.23
Matches are distributed among these distances:
8 29 0.23
9 50 0.39
10 9 0.07
11 22 0.17
12 10 0.08
13 5 0.04
14 2 0.02
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (9 bp):
AATATATAT
Found at i:21945 original size:27 final size:27
Alignment explanation
Indices: 21898--22058 Score: 94
Period size: 27 Copynumber: 5.6 Consensus size: 27
21888 ATTAAAACAA
21898 TATATATAATATATATATATATATATA
1 TATATATAATATATATATATATATATA
* * *
21925 TATATATATATATAATTTATATTTACATA
1 TATATATA-ATAT-ATATATATATATATA
* * * * *
21954 TTTATATAATGTATATAAACTATGTAGTG
1 TATATATAATATATATATA-TATATA-TA
21983 TATATATGAACTATATATAAACTATATAATATA
1 TATATAT-AA-TATATAT--A-TATAT-ATATA
*
22016 CTATATATAA-AGTATATA-ATTTATATA
1 -TATATATAATA-TATATATATATATATA
*
22043 CTTTATATAAT-TATAT
1 -TATATATAATATATAT
22059 TAATAAACTA
Statistics
Matches: 103, Mismatches: 18, Indels: 27
0.70 0.12 0.18
Matches are distributed among these distances:
26 5 0.05
27 27 0.26
28 13 0.13
29 26 0.25
30 3 0.03
31 7 0.07
32 5 0.05
33 7 0.07
34 10 0.10
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (27 bp):
TATATATAATATATATATATATATATA
Found at i:21999 original size:11 final size:11
Alignment explanation
Indices: 21983--22033 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
21973 CTATGTAGTG
*
21983 TATATATGAAC
1 TATATATAAAC
21994 TATATATAAAC
1 TATATATAAAC
*
22005 TATATAATATAC
1 TATAT-ATAAAC
*
22017 TATATATAAAG
1 TATATATAAAC
22028 TATATA
1 TATATA
22034 ATTTATATAC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
11 25 0.71
12 10 0.29
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (11 bp):
TATATATAAAC
Found at i:22051 original size:2 final size:2
Alignment explanation
Indices: 21897--22042 Score: 88
Period size: 2 Copynumber: 72.5 Consensus size: 2
21887 AATTAAAACA
21897 AT AT AT AT A- 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
* * * * * * *
21938 A- AT TT AT AT TT AC AT AT TT AT AT A- AT GT AT AT AA ACT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* *
21979 AGT GT AT AT AT GA- ACT AT AT AT AA ACT AT AT A- AT AT ACT AT AT
1 A-T AT AT AT AT -AT A-T AT AT AT AT A-T AT AT AT AT AT A-T AT AT
* *
22022 AT AA AGT AT AT A- AT TT AT AT A
1 AT AT A-T AT AT AT AT AT AT AT A
22043 CTTTATATAA
Statistics
Matches: 109, Mismatches: 22, Indels: 26
0.69 0.14 0.17
Matches are distributed among these distances:
1 6 0.06
2 95 0.87
3 8 0.07
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:22062 original size:27 final size:27
Alignment explanation
Indices: 21992--22052 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 27
21982 GTATATATGA
*
21992 ACTATATATAAACTATAT-A---ATAT
1 ACTATATATAAAGTATATAATTTATAT
22015 ACTATATATAAAGTATATAATTTATAT
1 ACTATATATAAAGTATATAATTTATAT
*
22042 ACTTTATATAA
1 ACTATATATAA
22053 TTATATTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 17 0.53
24 1 0.03
27 14 0.44
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.43
Consensus pattern (27 bp):
ACTATATATAAAGTATATAATTTATAT
Found at i:22107 original size:33 final size:33
Alignment explanation
Indices: 22067--22472 Score: 468
Period size: 33 Copynumber: 13.1 Consensus size: 33
22057 ATTAATAAAC
*
22067 TATATAGTTCATTAGTATATATAAACTCTATAT
1 TATATAGTTCATTAGTATATATAAACTATATAT
* *
22100 TTTATAGTTCATTAGTATATATAAATTATATAT
1 TATATAGTTCATTAGTATATATAAACTATATAT
*
22133 TATATAGTTCATTAGTATATATAAACTATATAG
1 TATATAGTTCATTAGTATATATAAACTATATAT
* *
22166 TATATAGTTCATTAG----TGT--A-TA-GT-T
1 TATATAGTTCATTAGTATATATAAACTATATAT
* *
22190 CATATAGTTCATTAGTTTATATAAAC--TA---
1 TATATAGTTCATTAGTATATATAAACTATATAT
*
22218 --TATAGTTCATTAGTATATATAAACTATATAG
1 TATATAGTTCATTAGTATATATAAACTATATAT
*
22249 TATATAGTTCATTAGTATATATAAACTATATAG
1 TATATAGTTCATTAGTATATATAAACTATATAT
* *
22282 TATATTA-TTCATTGGTATATATAAATTATATAT
1 TATA-TAGTTCATTAGTATATATAAACTATATAT
*
22315 TATATAGTTCATTAGCATATATAAACTATATAT
1 TATATAGTTCATTAGTATATATAAACTATATAT
* *
22348 TATATAATTCATTAG----TAT--A-TA-GT-T
1 TATATAGTTCATTAGTATATATAAACTATATAT
* *
22372 CATATAGTTCATTAGTATATATAAACTAAATAT
1 TATATAGTTCATTAGTATATATAAACTATATAT
22405 TATATAGTTCATTAGTATATATAAACTATATAT
1 TATATAGTTCATTAGTATATATAAACTATATAT
22438 TATATAGTTCATTAGTATATATAAACTATATAT
1 TATATAGTTCATTAGTATATATAAACTATATAT
22471 TA
1 TA
22473 ATTTATTAAT
Statistics
Matches: 321, Mismatches: 26, Indels: 52
0.80 0.07 0.13
Matches are distributed among these distances:
24 28 0.09
25 2 0.01
26 27 0.08
27 2 0.01
28 7 0.02
29 5 0.02
30 2 0.01
31 2 0.01
32 3 0.01
33 241 0.75
34 2 0.01
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (33 bp):
TATATAGTTCATTAGTATATATAAACTATATAT
Found at i:22194 original size:24 final size:25
Alignment explanation
Indices: 22166--22249 Score: 100
Period size: 26 Copynumber: 3.3 Consensus size: 25
22156 AACTATATAG
* *
22166 TATATAGTTCATTAGTGTATAGT-TC
1 TATATAGTTCATTAGTATATA-TAAC
*
22191 -ATATAGTTCATTAGTTTATATAAAC
1 TATATAGTTCATTAGTATATAT-AAC
22216 TATATAGTTCATTAGTATATATAAAC
1 TATATAGTTCATTAGTATATAT-AAC
22242 TATATAGT
1 TATATAGT
22250 ATATAGTTCA
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
23 1 0.02
24 19 0.36
25 1 0.02
26 32 0.60
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.45
Consensus pattern (25 bp):
TATATAGTTCATTAGTATATATAAC
Found at i:22197 original size:57 final size:57
Alignment explanation
Indices: 22126--22425 Score: 308
Period size: 57 Copynumber: 5.1 Consensus size: 57
22116 ATATATAAAT
22126 TATATA-TT-ATATAGTTCATTAGTATATATAAACTATATAGTATATAGTTCATTAG
1 TATATAGTTCATATAGTTCATTAGTATATATAAACTATATAGTATATAGTTCATTAG
* * *
22181 TGTATAGTTCATATAGTTCATTAGTTTATATAAACTATATAGT-TCATTAGTAT-ATATAAAC
1 TATATAGTTCATATAGTTCATTAGTATATATAAACTATATAGTAT-A-TAGT-TCAT-T--AG
*
22242 TATATAG-T-ATATAGTTCATTAGTATATATAAACTATATAGTATATTA-TTCATTGGTATA
1 TATATAGTTCATATAGTTCATTAGTATATATAAACTATATAGTATA-TAGTTCA-T--TA-G
* * * * *
22301 TATAAATTATATATTATATAGTTCATTAGCATATATAAACTATATATTATATAATTCATTAG
1 TAT--A-TA-GT-TCATATAGTTCATTAGTATATATAAACTATATAGTATATAGTTCATTAG
* *
22363 TATATAGTTCATATAGTTCATTAGTATATATAAACTAAATATTATATAGTTCATTAG
1 TATATAGTTCATATAGTTCATTAGTATATATAAACTATATAGTATATAGTTCATTAG
22420 TATATA
1 TATATA
22426 TAAACTATAT
Statistics
Matches: 208, Mismatches: 16, Indels: 40
0.79 0.06 0.15
Matches are distributed among these distances:
55 5 0.02
56 3 0.01
57 85 0.41
58 10 0.05
59 44 0.21
60 4 0.02
61 8 0.04
62 5 0.02
63 2 0.01
65 4 0.02
66 38 0.18
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.45
Consensus pattern (57 bp):
TATATAGTTCATATAGTTCATTAGTATATATAAACTATATAGTATATAGTTCATTAG
Found at i:22211 original size:90 final size:90
Alignment explanation
Indices: 22102--22458 Score: 478
Period size: 90 Copynumber: 3.9 Consensus size: 90
22092 CTCTATATTT
22102 TATAGTTCATTAGTATATATAAATTATATATTATATAGTTCATTAGTATATATAAACTATATAGT
1 TATAGTTCATTAGTATATATAAATTATATATTATATAGTTCATTAGTATATATAAACTATATAGT
*
22167 ATATAGTTCATTAGTGTATAGTTCA
66 ATATAGTTCATTAGTATATAGTTCA
*
22192 TATAGTTCATTAGT-T-TAT--A-TA-A-ACTATATAGTTCATTAGTATATATAAACTATATAGT
1 TATAGTTCATTAGTATATATAAATTATATATTATATAGTTCATTAGTATATATAAACTATATAGT
*
22250 ATATAGTTCATTAGTATATA-TAAACTA
66 ATATAGTTCATTAGTATATAGT--TC-A
* *
22277 TATAGTATATTATTCATTGGTATATATAAATTATATATTATATAGTTCATTAGCATATATAAACT
1 TATAG-------TTCATTAGTATATATAAATTATATATTATATAGTTCATTAGTATATATAAACT
* *
22342 ATATATTATATAATTCATTAGTATATAGTTCA
59 ATATAGTATATAGTTCATTAGTATATAGTTCA
* * *
22374 TATAGTTCATTAGTATATATAAACTAAATATTATATAGTTCATTAGTATATATAAACTATATATT
1 TATAGTTCATTAGTATATATAAATTATATATTATATAGTTCATTAGTATATATAAACTATATAGT
22439 ATATAGTTCATTAGTATATA
66 ATATAGTTCATTAGTATATA
22459 TAAACTATAT
Statistics
Matches: 235, Mismatches: 14, Indels: 36
0.82 0.05 0.13
Matches are distributed among these distances:
82 1 0.00
83 54 0.23
84 2 0.01
85 8 0.03
86 1 0.00
88 3 0.01
89 1 0.00
90 89 0.38
92 8 0.03
93 1 0.00
94 3 0.01
96 1 0.00
97 8 0.03
98 2 0.01
99 52 0.22
100 1 0.00
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (90 bp):
TATAGTTCATTAGTATATATAAATTATATATTATATAGTTCATTAGTATATATAAACTATATAGT
ATATAGTTCATTAGTATATAGTTCA
Found at i:22266 original size:182 final size:188
Alignment explanation
Indices: 22067--22472 Score: 655
Period size: 182 Copynumber: 2.2 Consensus size: 188
22057 ATTAATAAAC
* *
22067 TATATAGTTCATTAGTATATATAAACTCTATATTTTA-TAGTTCATTAGTATATATAAATTATAT
1 TATATAGTTCATTAGTATATATAAACTATATATTATATTA-TTCATTAGTATATATAAATTATAT
* * *
22131 ATTATATAGTTCATTAGTATATATAAACTATATAGTATATAGTTCATTAGTGTATAGTTCATATA
65 ATTATATAGTTCATTAGCATATATAAACTATATAGTATATAATTCATTAGTATATAGTTCATATA
22196 GTTCATTAGT-T-TAT-A-T-AA-ACTATATAGTTCATTAGTATATATAAACTATATAG
130 GTTCATTAGTATATATAACTAAATACTATATAGTTCATTAGTATATATAAACTATATAG
* *
22249 TATATAGTTCATTAGTATATATAAACTATATAGTATATTATTCATTGGTATATATAAATTATATA
1 TATATAGTTCATTAGTATATATAAACTATATATTATATTATTCATTAGTATATATAAATTATATA
*
22314 TTATATAGTTCATTAGCATATATAAACTATATATTATATAATTCATTAGTATATAGTTCATATAG
66 TTATATAGTTCATTAGCATATATAAACTATATAGTATATAATTCATTAGTATATAGTTCATATAG
* *
22379 TTCATTAGTATATATAAACTAAATATTATATAGTTCATTAGTATATATAAACTATATAT
131 TTCATTAGTATATAT-AACTAAATACTATATAGTTCATTAGTATATATAAACTATATAG
22438 TATATAGTTCATTAGTATATATAAACTATATATTA
1 TATATAGTTCATTAGTATATATAAACTATATATTA
22473 ATTTATTAAT
Statistics
Matches: 205, Mismatches: 11, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
182 128 0.62
183 3 0.01
184 3 0.01
186 1 0.00
187 1 0.00
188 2 0.01
189 67 0.33
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (188 bp):
TATATAGTTCATTAGTATATATAAACTATATATTATATTATTCATTAGTATATATAAATTATATA
TTATATAGTTCATTAGCATATATAAACTATATAGTATATAATTCATTAGTATATAGTTCATATAG
TTCATTAGTATATATAACTAAATACTATATAGTTCATTAGTATATATAAACTATATAG
Found at i:22392 original size:15 final size:16
Alignment explanation
Indices: 22117--22379 Score: 89
Period size: 15 Copynumber: 16.1 Consensus size: 16
22107 TTCATTAGTA
*
22117 TATATAAATT-ATATAT
1 TATAT-AATTCATATAG
*
22133 TATATAGTTCAT-TAG
1 TATATAATTCATATAG
**
22148 TATATATAAACTATATAG
1 TATATA-ATTC-ATATAG
*
22166 TATATAGTTCAT-TAG
1 TATATAATTCATATAG
* *
22181 TGTATAGTTCATATAG
1 TATATAATTCATATAG
* * *
22197 T-TCATTAGTTTATATAAAC
1 TAT-A-TAATTCATAT--AG
*
22216 TATATAGTTCAT-TAG
1 TATATAATTCATATAG
**
22231 TATATATAAACTATATAG
1 TATATA-ATTC-ATATAG
*
22249 TATATAGTTCAT-TAG
1 TATATAATTCATATAG
**
22264 TATATATAAACTATATAG
1 TATATA-ATTC-ATATAG
* *
22282 TATATTATTCAT-TGG
1 TATATAATTCATATAG
*
22297 TATATATAAATT-ATATAT
1 --TATAT-AATTCATATAG
*
22315 TATATAGTTCAT-TAG
1 TATATAATTCATATAG
* *
22330 CATATATAA-ACTATATAT
1 --TATATAATTC-ATATAG
22348 TATATAATTCAT-TAG
1 TATATAATTCATATAG
*
22363 TATATAGTTCATATAG
1 TATATAATTCATATAG
22379 T
1 T
22380 TCATTAGTAT
Statistics
Matches: 183, Mismatches: 37, Indels: 54
0.67 0.14 0.20
Matches are distributed among these distances:
15 62 0.34
16 42 0.23
17 36 0.20
18 39 0.21
19 3 0.02
20 1 0.01
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.45
Consensus pattern (16 bp):
TATATAATTCATATAG
Found at i:22426 original size:123 final size:121
Alignment explanation
Indices: 22242--22472 Score: 383
Period size: 123 Copynumber: 1.9 Consensus size: 121
22232 ATATATAAAC
* *
22242 TATATAGTATATAGTTCATTAGTATATATAAACTATATAGTATATTATTCATTGGTATATATAAA
1 TATATAGTATATAGTTCATTAGTATATATAAACTAAATAGTATATTATTCATTAGTATATATAAA
*
22307 TTATATATTATATAGTTCATTAGCATATATAAACTATATATTATATAATTCATTAG
66 CTATATATTATATAGTTCATTAGCATATATAAACTATATATTATATAATTCATTAG
*
22363 TATATAGTTCATATAGTTCATTAGTATATATAAACTAAATATTATA-TAGTTCATTAGTATATAT
1 TATATAG-T-ATATAGTTCATTAGTATATATAAACTAAATAGTATATTA-TTCATTAGTATATAT
*
22427 AAACTATATATTATATAGTTCATTAGTATATATAAACTATATATTA
63 AAACTATATATTATATAGTTCATTAGCATATATAAACTATATATTA
22473 ATTTATTAAT
Statistics
Matches: 102, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
121 7 0.07
122 3 0.03
123 92 0.90
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (121 bp):
TATATAGTATATAGTTCATTAGTATATATAAACTAAATAGTATATTATTCATTAGTATATATAAA
CTATATATTATATAGTTCATTAGCATATATAAACTATATATTATATAATTCATTAG
Found at i:22434 original size:26 final size:27
Alignment explanation
Indices: 22373--22495 Score: 90
Period size: 33 Copynumber: 4.2 Consensus size: 27
22363 TATATAGTTC
22373 ATATAGTTCATTAGTATATATAAACTAAATATT
1 ATATAGTTCATTAGTATATATAAAC-----A-T
22406 ATATAGTTCATTAGTATATATAAACTATATATT
1 ATATAGTTCATTAGTATATATAAAC-----A-T
22439 ATATAGTTCATTAGTATATATAAAC-T
1 ATATAGTTCATTAGTATATATAAACAT
* *
22465 ATATA-TTAATTTATTA-ATATAAACAT
1 ATATAGTTCA-TTAGTATATATAAACAT
22491 ATATA
1 ATATA
22496 TTAATTGAAA
Statistics
Matches: 85, Mismatches: 3, Indels: 11
0.86 0.03 0.11
Matches are distributed among these distances:
25 11 0.13
26 17 0.20
33 57 0.67
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.44
Consensus pattern (27 bp):
ATATAGTTCATTAGTATATATAAACAT
Found at i:22493 original size:66 final size:68
Alignment explanation
Indices: 22363--22493 Score: 171
Period size: 66 Copynumber: 2.0 Consensus size: 68
22353 AATTCATTAG
* * *
22363 TATATAGTTCATATAGTTCATTAGTATATATAAACTAAATATTATATAGTTCATTAGTATATATA
1 TATATAGTTCATATAGTTCATTAGTATATATAAACTAAATATTATATAGTTAATTAGAACATATA
22428 AAC
66 AAC
* *
22431 TATATA-TT-ATATAGTTCATTAGTATATATAAACTATATATTAATTTA-TTAATATA-AACATA
1 TATATAGTTCATATAGTTCATTAGTATATATAAACTAAATATT-ATATAGTTAAT-TAGAACATA
22492 TA
64 TA
22494 TATTAATTGA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
66 42 0.75
67 8 0.14
68 6 0.11
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.44
Consensus pattern (68 bp):
TATATAGTTCATATAGTTCATTAGTATATATAAACTAAATATTATATAGTTAATTAGAACATATA
AAC
Found at i:22513 original size:26 final size:26
Alignment explanation
Indices: 22456--22522 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
22446 TCATTAGTAT
* **
22456 ATATAAAC-TATATATTAATTTATTA
1 ATATAAACATATATATTAATTAAAGA
22481 ATATAAACATATATATTAATTGAAAGA
1 ATATAAACATATATATTAATT-AAAGA
*
22508 AT-TAAAAAGTATATA
1 ATATAAACA-TATATA
22523 AGGATCAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
25 8 0.23
26 17 0.49
27 10 0.29
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.39
Consensus pattern (26 bp):
ATATAAACATATATATTAATTAAAGA
Found at i:23289 original size:52 final size:51
Alignment explanation
Indices: 23232--23568 Score: 413
Period size: 52 Copynumber: 6.5 Consensus size: 51
23222 CCCACAAATG
* * * *
23232 TTCATCTTCTCTAACCCAAACCCTAACCGAGTCTCTTCACTTTCTATCTCTA
1 TTCATCTTCTCTAACCCAAACCCAAATCGAGCCTCTTTA-TTTCTATCTCTA
* * * * *
23284 TTCATCTTCTCTAATCCCAAACCCAAACCTAACCTCTTCATTTTTATCTCTA
1 TTCATCTTCTCTAA-CCCAAACCCAAATCGAGCCTCTTTATTTCTATCTCTA
* * * *
23336 TTTATCTTCTCTAACCCTAAACCTAAATCAAGTCTCTTTATCTTCTATCTCTA
1 TTCATCTTCTCTAACCC-AAACCCAAATCGAGCCTCTTTAT-TTCTATCTCTA
*
23389 TTCATCTTCTCTAACCCCAAACCCAAATTGAGCCTCTTTATTTCTATCTCTA
1 TTCATCTTCTCTAA-CCCAAACCCAAATCGAGCCTCTTTATTTCTATCTCTA
* *
23441 TTTATCTTCTCTAACCCTAAACCCAAATCAAGCCTCTTTATTTCTATCTCTA
1 TTCATCTTCTCTAACCC-AAACCCAAATCGAGCCTCTTTATTTCTATCTCTA
* * * *
23493 TTTATCTTCTCTAACCCTAAACCCAAATCGAGCCTCTTTATATTTTGTCTATA
1 TTCATCTTCTCTAACCC-AAACCCAAATCGAGCCTCTTTAT-TTCTATCTCTA
*
23546 TTCATCTTCTCTAACCCTAACCC
1 TTCATCTTCTCTAACCCAAACCC
23569 TTATTTTTCA
Statistics
Matches: 252, Mismatches: 27, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
51 6 0.02
52 156 0.62
53 87 0.35
54 3 0.01
ACGTcount: A:0.26, C:0.32, G:0.03, T:0.39
Consensus pattern (51 bp):
TTCATCTTCTCTAACCCAAACCCAAATCGAGCCTCTTTATTTCTATCTCTA
Found at i:23383 original size:105 final size:103
Alignment explanation
Indices: 23235--23565 Score: 427
Period size: 105 Copynumber: 3.2 Consensus size: 103
23225 ACAAATGTTC
* * *
23235 ATCTTCTCTAACCC-AAACCCT-AACCGAGTCTCTTCA-CTTTCTATCTCTATTCATCTTCTCTA
1 ATCTTCTCTAACCCTAAA-CCTAAATCAAGTCTCTTTATC-TTCTATCTCTATTCATCTTCTCTA
* *
23297 ATCCCAAACCCAAACCTAACCTCTTCATTTTTATCTCTATTT
64 A-CCCAAACCCAAA-CTAGCCTCTTTATTTTTATCTCTATTT
23339 ATCTTCTCTAACCCTAAACCTAAATCAAGTCTCTTTATCTTCTATCTCTATTCATCTTCTCTAAC
1 ATCTTCTCTAACCCTAAACCTAAATCAAGTCTCTTTATCTTCTATCTCTATTCATCTTCTCTAA-
* *
23404 CCCAAACCCAAATTGAGCCTCTTTATTTCTATCTCTATTT
65 CCCAAACCCAAACT-AGCCTCTTTATTTTTATCTCTATTT
* * *
23444 ATCTTCTCTAACCCTAAACCCAAATCAAGCCTCTTTAT-TTCTATCTCTATTTATCTTCTCTAAC
1 ATCTTCTCTAACCCTAAACCTAAATCAAGTCTCTTTATCTTCTATCTCTATTCATCTTCTCTAAC
* * * *
23508 CCTAAACCCAAATCGAGCCTCTTTATATTTTGTCTATATTC
66 CC-AAACCCAAA-CTAGCCTCTTTAT-TTTTATCTCTATTT
23549 ATCTTCTCTAACCCTAA
1 ATCTTCTCTAACCCTAA
23566 CCCTTATTTT
Statistics
Matches: 203, Mismatches: 17, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
103 3 0.01
104 62 0.31
105 137 0.67
106 1 0.00
ACGTcount: A:0.26, C:0.32, G:0.03, T:0.40
Consensus pattern (103 bp):
ATCTTCTCTAACCCTAAACCTAAATCAAGTCTCTTTATCTTCTATCTCTATTCATCTTCTCTAAC
CCAAACCCAAACTAGCCTCTTTATTTTTATCTCTATTT
Found at i:23463 original size:157 final size:158
Alignment explanation
Indices: 23232--23562 Score: 472
Period size: 157 Copynumber: 2.1 Consensus size: 158
23222 CCCACAAATG
* *
23232 TTCATCTTCTCTAA-CCCAAACCCTAACCGAGTCTCTTCACTTTCTATCTCTATTCATCTTCTCT
1 TTCATCTTCTCTAACCCCAAACCCAAACCGAGCCTCTTCACTTTCTATCTCTATTCATCTTCTCT
* *
23296 AATCCCAAACCCAAACCTAA-CCTCTTCATTTTTATCTCTATTTATCTTCTCTAACCCTAAACCT
66 AATCCCAAACCCAAACC-AAGCCTCTTCATTTCTATCTCTATTTATCTTCTCTAACCCTAAACCC
* * *
23360 AAATCAAGTCTCTTTATCTTCTATCTCTA
130 AAATCAAGCCTCTTTATATTCTATCTATA
** * *
23389 TTCATCTTCTCTAACCCCAAACCCAAATTGAGCCTCTTTA-TTTCTATCTCTATTTATCTTCTCT
1 TTCATCTTCTCTAACCCCAAACCCAAACCGAGCCTCTTCACTTTCTATCTCTATTCATCTTCTCT
* *
23453 AA-CCCTAAACCCAAATCAAGCCTCTTTATTTCTATCTCTATTTATCTTCTCTAACCCTAAACCC
66 AATCCC-AAACCCAAACCAAGCCTCTTCATTTCTATCTCTATTTATCTTCTCTAACCCTAAACCC
* * *
23517 AAATCGAGCCTCTTTATATTTTGTCTATA
130 AAATCAAGCCTCTTTATATTCTATCTATA
23546 TTCATCTTCTCTAACCC
1 TTCATCTTCTCTAACCC
23563 TAACCCTTAT
Statistics
Matches: 155, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
156 5 0.03
157 130 0.84
158 20 0.13
ACGTcount: A:0.25, C:0.32, G:0.03, T:0.40
Consensus pattern (158 bp):
TTCATCTTCTCTAACCCCAAACCCAAACCGAGCCTCTTCACTTTCTATCTCTATTCATCTTCTCT
AATCCCAAACCCAAACCAAGCCTCTTCATTTCTATCTCTATTTATCTTCTCTAACCCTAAACCCA
AATCAAGCCTCTTTATATTCTATCTATA
Found at i:27312 original size:16 final size:16
Alignment explanation
Indices: 27291--27341 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
27281 TCATTTACAT
*
27291 GTCAGGTTGAAAACAG
1 GTCAGGTTGAAAACAA
* *
27307 GTCAGGTTCATAACAA
1 GTCAGGTTGAAAACAA
*
27323 GTAAGGTTGAAAACAA
1 GTCAGGTTGAAAACAA
27339 GTC
1 GTC
27342 GAGTAATATC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.22
Consensus pattern (16 bp):
GTCAGGTTGAAAACAA
Found at i:28013 original size:18 final size:18
Alignment explanation
Indices: 27987--28027 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
27977 TTATAAATTT
*
27987 ATATATAAATATTAAAAA
1 ATATTTAAATATTAAAAA
* *
28005 ATATTTAAATTTTAAAAG
1 ATATTTAAATATTAAAAA
28023 ATATT
1 ATATT
28028 CTAAGATGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
ATATTTAAATATTAAAAA
Found at i:28787 original size:58 final size:58
Alignment explanation
Indices: 28679--28803 Score: 137
Period size: 58 Copynumber: 2.1 Consensus size: 58
28669 TCGGGTGATT
* * * * *
28679 ATTTTATAATTTTTAATAGTCAAGAGACTCAATAAAATAACTCTTTATAGTTGGGGATC
1 ATTTTATAAGTTTTAATAGTCAAGAGACTCAACAAAACAACTATTTATAG-TCGGGATC
* * *
28738 ATTTTGTAAGTTTTAATATTTAAG-GACTCAACAAAACAA-TATTATATAGTCGGGATC
1 ATTTTATAAGTTTTAATAGTCAAGAGACTCAACAAAACAACTATT-TATAGTCGGGATC
28795 ATTTGTATA
1 ATTT-TATA
28804 TTTTATCCTA
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
57 14 0.25
58 21 0.38
59 20 0.36
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.39
Consensus pattern (58 bp):
ATTTTATAAGTTTTAATAGTCAAGAGACTCAACAAAACAACTATTTATAGTCGGGATC
Found at i:29528 original size:15 final size:15
Alignment explanation
Indices: 29510--29548 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
29500 AATCTAAACC
29510 TGAAAAGATTCGAAT
1 TGAAAAGATTCGAAT
29525 TGAAAAGATTCGAAT
1 TGAAAAGATTCGAAT
29540 TGAAAAGAT
1 TGAAAAGAT
29549 CTTAAACCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.49, C:0.05, G:0.21, T:0.26
Consensus pattern (15 bp):
TGAAAAGATTCGAAT
Found at i:31311 original size:15 final size:14
Alignment explanation
Indices: 31286--31315 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
31276 ATGCGAGCTT
31286 TTTAACCCGCACCG
1 TTTAACCCGCACCG
31300 TTTAAGCCCGCACCG
1 TTTAA-CCCGCACCG
31315 T
1 T
31316 CAAAACCCGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.20, C:0.40, G:0.17, T:0.23
Consensus pattern (14 bp):
TTTAACCCGCACCG
Found at i:33054 original size:16 final size:16
Alignment explanation
Indices: 33033--33083 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
33023 TCATTTACAT
*
33033 GTCAGGTTGAAAACAG
1 GTCAGGTTGAAAACAA
* *
33049 GTCAGGTTCATAACAA
1 GTCAGGTTGAAAACAA
*
33065 GTAAGGTTGAAAACAA
1 GTCAGGTTGAAAACAA
33081 GTC
1 GTC
33084 GAGTAATACC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.22
Consensus pattern (16 bp):
GTCAGGTTGAAAACAA
Found at i:33754 original size:18 final size:18
Alignment explanation
Indices: 33728--33768 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
33718 TTATAAATTT
*
33728 ATATATAAATATTAAAAA
1 ATATTTAAATATTAAAAA
* *
33746 ATATTTAAATTTTAAAAG
1 ATATTTAAATATTAAAAA
33764 ATATT
1 ATATT
33769 CTAAGATGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
ATATTTAAATATTAAAAA
Found at i:34530 original size:58 final size:58
Alignment explanation
Indices: 34422--34546 Score: 137
Period size: 58 Copynumber: 2.1 Consensus size: 58
34412 TCGGGTGATT
* * * * *
34422 ATTTTATAATTTTTAATAGTCAAGAGACTCAATAAAATAACTCTTTATAGTTGGGGATC
1 ATTTTATAAGTTTTAATAGTCAAGAGACTCAACAAAACAACTATTTATAG-TCGGGATC
* * *
34481 ATTTTGTAAGTTTTAATATTTAAG-GACTCAACAAAACAA-TATTATATAGTCGGGATC
1 ATTTTATAAGTTTTAATAGTCAAGAGACTCAACAAAACAACTATT-TATAGTCGGGATC
34538 ATTTGTATA
1 ATTT-TATA
34547 TTTTATCCTA
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
57 14 0.25
58 21 0.38
59 20 0.36
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.39
Consensus pattern (58 bp):
ATTTTATAAGTTTTAATAGTCAAGAGACTCAACAAAACAACTATTTATAGTCGGGATC
Found at i:34705 original size:27 final size:29
Alignment explanation
Indices: 34665--34721 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
34655 TCAAACACGC
* *
34665 ATTTTTAACTAAATATAAC-TTCA-AAAT
1 ATTTTTAACGAAATAAAACATTCACAAAT
*
34692 ATTTTTATCGAAATAAAACATTCACAAAT
1 ATTTTTAACGAAATAAAACATTCACAAAT
34721 A
1 A
34722 ATTATCGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 16 0.64
28 4 0.16
29 5 0.20
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (29 bp):
ATTTTTAACGAAATAAAACATTCACAAAT
Found at i:35269 original size:15 final size:15
Alignment explanation
Indices: 35251--35289 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
35241 AATCTAAACC
35251 TGAAAAGATTCGAAT
1 TGAAAAGATTCGAAT
35266 TGAAAAGATTCGAAT
1 TGAAAAGATTCGAAT
35281 TGAAAAGAT
1 TGAAAAGAT
35290 CTTAAACCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.49, C:0.05, G:0.21, T:0.26
Consensus pattern (15 bp):
TGAAAAGATTCGAAT
Found at i:37062 original size:15 final size:14
Alignment explanation
Indices: 37037--37066 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
37027 ATGCGAGCTT
37037 TTTAACCCGCACCG
1 TTTAACCCGCACCG
37051 TTTAAGCCCGCACCG
1 TTTAA-CCCGCACCG
37066 T
1 T
37067 CAAAACCCGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.20, C:0.40, G:0.17, T:0.23
Consensus pattern (14 bp):
TTTAACCCGCACCG
Found at i:38805 original size:16 final size:16
Alignment explanation
Indices: 38784--38834 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
38774 TCATTTACAT
*
38784 GTCAGGTTGAAAACAG
1 GTCAGGTTGAAAACAA
* *
38800 GTCAGGTTCATAACAA
1 GTCAGGTTGAAAACAA
*
38816 GTAAGGTTGAAAACAA
1 GTCAGGTTGAAAACAA
38832 GTC
1 GTC
38835 GAGTAATACC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.22
Consensus pattern (16 bp):
GTCAGGTTGAAAACAA
Found at i:39505 original size:17 final size:18
Alignment explanation
Indices: 39479--39527 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
39469 TAAATTTATA
39479 TAAATATTAAAAAATATT-
1 TAAAT-TTAAAAAATATTC
*
39497 TAAATTTAAAAGATATTC
1 TAAATTTAAAAAATATTC
*
39515 TAAGATGTAAAAA
1 TAA-ATTTAAAAA
39528 CAATGAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 11 0.42
18 8 0.31
19 7 0.27
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (18 bp):
TAAATTTAAAAAATATTC
Found at i:40271 original size:58 final size:58
Alignment explanation
Indices: 40163--40287 Score: 137
Period size: 58 Copynumber: 2.1 Consensus size: 58
40153 TCGGGTGATT
* * * * *
40163 ATTTTATAATTTTTAATAGTCAAGAGACTCAATAAAATAACTCTTTATAGTTGGGGATC
1 ATTTTATAAGTTTTAATAGTCAAGAGACTCAACAAAACAACTATTTATAG-TCGGGATC
* * *
40222 ATTTTGTAAGTTTTAATATTTAAG-GACTCAACAAAACAA-TATTATATAGTCGGGATC
1 ATTTTATAAGTTTTAATAGTCAAGAGACTCAACAAAACAACTATT-TATAGTCGGGATC
40279 ATTTGTATA
1 ATTT-TATA
40288 TTTTATCCTA
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
57 14 0.25
58 21 0.38
59 20 0.36
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.39
Consensus pattern (58 bp):
ATTTTATAAGTTTTAATAGTCAAGAGACTCAACAAAACAACTATTTATAGTCGGGATC
Found at i:41010 original size:15 final size:15
Alignment explanation
Indices: 40992--41030 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
40982 AATCTAAACC
40992 TGAAAAGATTCGAAT
1 TGAAAAGATTCGAAT
41007 TGAAAAGATTCGAAT
1 TGAAAAGATTCGAAT
41022 TGAAAAGAT
1 TGAAAAGAT
41031 CTTAAACCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.49, C:0.05, G:0.21, T:0.26
Consensus pattern (15 bp):
TGAAAAGATTCGAAT
Found at i:47261 original size:22 final size:22
Alignment explanation
Indices: 47236--47302 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 22
47226 CCACAGCTCG
*
47236 TAATTTG-CACCGAAGTACCACA
1 TAATTTGTC-CCGAAGGACCACA
*
47258 TAA-TTGTCCCAAAGGACCACA
1 TAATTTGTCCCGAAGGACCACA
47279 TAATTTGTCCCGAAGGACCACA
1 TAATTTGTCCCGAAGGACCACA
47301 TA
1 TA
47303 GAACCCTCGA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
21 17 0.43
22 23 0.57
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.22
Consensus pattern (22 bp):
TAATTTGTCCCGAAGGACCACA
Found at i:51018 original size:3 final size:3
Alignment explanation
Indices: 51010--51126 Score: 121
Period size: 3 Copynumber: 38.7 Consensus size: 3
51000 TTTATTAAAT
*
51010 ATA ATA AT- ATA TATA TTA ATA ATA ATA ATAA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA
* * * * * *
51056 ATA ATT ATT ATT ATA ATA ATA ATA ATA CTA ATA CTA ATA ATA ATA CTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
51104 ATAA ATA AT- TTA ATA ATA ATA AT
1 AT-A ATA ATA ATA ATA ATA ATA AT
51127 TTTAAATGAA
Statistics
Matches: 97, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
2 3 0.03
3 85 0.88
4 9 0.09
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:51026 original size:21 final size:23
Alignment explanation
Indices: 50994--51126 Score: 119
Period size: 21 Copynumber: 6.2 Consensus size: 23
50984 TCCAGTTTTG
*
50994 TAAT-TATTTATTA-AAT-ATAA
1 TAATATATATATTATAATAATAA
51014 TAATATATATATTAATAATAATAA
1 TAATATATATATT-ATAATAATAA
51038 TAA-ATA-ATA--ATAATAATAA
1 TAATATATATATTATAATAATAA
51057 TAAT-TAT-TATTATAATAATAA
1 TAATATATATATTATAATAATAA
* *
51078 TAATACTA-ATACTAATAATAATAC
1 TAATA-TATATA-TTATAATAATAA
*
51102 TAATAAATA-ATT-TAATAATAA
1 TAATATATATATTATAATAATAA
51123 TAAT
1 TAAT
51127 TTTAAATGAA
Statistics
Matches: 94, Mismatches: 6, Indels: 25
0.75 0.05 0.20
Matches are distributed among these distances:
19 17 0.18
20 4 0.04
21 33 0.35
22 5 0.05
23 12 0.13
24 23 0.24
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
TAATATATATATTATAATAATAA
Found at i:51726 original size:151 final size:152
Alignment explanation
Indices: 51259--52189 Score: 1676
Period size: 151 Copynumber: 6.2 Consensus size: 152
51249 GAAACGTTGA
*
51259 AAACATCATGCACCGAAGGACTTACAGATGA-CCGAAGGCTTTG-AAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
51322 A-GCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTG--AACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
51384 AAAGCTCCCGAAGGCTTTTTGG
131 AAAGCTCCCGAAGGCTTTTTGG
*
51406 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAATCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
51470 AGGCTTTTTGG-AACATCATGC-CTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
51533 AAAGCTCCCGAAGGCTTTTTGG
131 AAAGCTCCCGAAGGCTTTTTGG
51555 AAACATCATGCACTGAAAGGACTTACAGATGACCCGAAGGCTTTGAAAA-ATCAAAAAGCT-CCG
1 AAACATCATGCACTG-AAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG
51618 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCA
65 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCA
51683 AAAAGCTCCCGAAGGCTTTTTTGG
130 AAAAGCTCCCGAAGGC-TTTTTGG
51707 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
51771 AGACTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
51836 AAAGCTCCCGAAGGCTTTTTGG
131 AAAGCTCCCGAAGGCTTTTTGG
51858 AAA-ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
51922 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATC-A
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
51986 AAAGCTCCCGAAGGCTTTTTTGG
131 AAAGCTCCCGAAGGC-TTTTTGG
52009 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG-AAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
52073 AGGCTTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA-CCGAAGGCTTTGAAAACATCA
66 AGGC-TTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCA
52137 AAAAGCTCCCGAAGGCTTTTTGG
130 AAAAGCTCCCGAAGGCTTTTTGG
52160 AAACATCATGCACTGAAGGACTTACAGATG
1 AAACATCATGCACTGAAGGACTTACAGATG
52190 TGAGAAATAG
Statistics
Matches: 759, Mismatches: 8, Indels: 30
0.95 0.01 0.04
Matches are distributed among these distances:
147 61 0.08
148 34 0.04
149 79 0.10
150 113 0.15
151 270 0.36
152 202 0.27
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (152 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
AAAGCTCCCGAAGGCTTTTTGG
Found at i:51772 original size:76 final size:76
Alignment explanation
Indices: 51259--52189 Score: 1676
Period size: 75 Copynumber: 12.4 Consensus size: 76
51249 GAAACGTTGA
*
51259 AAACATCATGCACCGAAGGACTTACAGATGA-CCGAAGGCTTTG-AAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
51322 A-GCTTTTTGG
66 AGGCTTTTTGG
*
51332 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTG--AACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
51395 AGGCTTTTTGG
66 AGGCTTTTTGG
*
51406 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAATCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
51470 AGGCTTTTTGG
66 AGGCTTTTTGG
51481 -AACATCATGC-CTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
51544 AGGCTTTTTGG
66 AGGCTTTTTGG
51555 AAACATCATGCACTGAAAGGACTTACAGATGACCCGAAGGCTTTGAAAA-ATCAAAAAGCT-CCG
1 AAACATCATGCACTG-AAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG
51618 AAGGCTTTTTGG
65 AAGGCTTTTTGG
51630 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
51695 AGGCTTTTTTGG
66 AGGC-TTTTTGG
51707 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
51771 AGACTTTTTGG
66 AGGCTTTTTGG
51782 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
51847 AGGCTTTTTGG
66 AGGCTTTTTGG
51858 AAA-ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
51922 AGGCTTTTTGG
66 AGGCTTTTTGG
*
51933 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATC-AAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
51997 AGGCTTTTTTGG
66 AGGC-TTTTTGG
52009 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG-AAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
52073 AGGCTTTTTTGG
66 AGGC-TTTTTGG
52085 AAACATCATGCACTGAAGGACTTACAGATGA-CCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
52149 AGGCTTTTTGG
66 AGGCTTTTTGG
52160 AAACATCATGCACTGAAGGACTTACAGATG
1 AAACATCATGCACTGAAGGACTTACAGATG
52190 TGAGAAATAG
Statistics
Matches: 833, Mismatches: 9, Indels: 30
0.96 0.01 0.03
Matches are distributed among these distances:
73 90 0.11
74 128 0.15
75 279 0.33
76 244 0.29
77 92 0.11
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:62616 original size:18 final size:17
Alignment explanation
Indices: 62568--62618 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
62558 AAATACTTGC
*
62568 AAATAAAATAAAACATAT
1 AAAT-AAATAAAAAATAT
*
62586 AAAT-ATTATAAAAATAAT
1 AAATAAATA-AAAAAT-AT
62604 AAATAAATAAAAAAT
1 AAATAAATAAAAAAT
62619 TTGACAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 3 0.11
17 5 0.19
18 16 0.59
19 3 0.11
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATAAATAAAAAATAT
Found at i:64773 original size:3 final size:3
Alignment explanation
Indices: 64767--64900 Score: 178
Period size: 3 Copynumber: 44.0 Consensus size: 3
64757 ATTATTATTA
*
64767 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* * * *
64814 AAT AAT AAT AAT TAT AAT AAT AAT AAT ACT AAT ACT AAT AAT AAT ACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* **
64862 AAT AAT AAT ACT AAT AAT AAT AAT TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
64901 TTTAAATGAA
Statistics
Matches: 113, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
3 107 0.95
4 6 0.05
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:67103 original size:37 final size:36
Alignment explanation
Indices: 67047--67389 Score: 356
Period size: 37 Copynumber: 9.4 Consensus size: 36
67037 TATAACCATG
* *
67047 TAATATATAGTTTTT-AAAATAACTTTGAAAATGTA
1 TAATATATAGTTTTTAAAAATAATTTTGAAAACGTA
* *
67082 TAATATATAGTTTTTAAAAAATATTTTTAAAAACGTA
1 TAATATATAGTTTTT-AAAAATAATTTTGAAAACGTA
* *
67119 TAATATATAGTTTTTAAAAAATATTTTTGAAAACATA
1 TAATATATAGTTTTT-AAAAATAATTTTGAAAACGTA
* *
67156 TAATATATAG-TTTT-AAAATAAATTTGAAAACATA
1 TAATATATAGTTTTTAAAAATAATTTTGAAAACGTA
*
67190 TAATATATAGTTTTTACAAAAATATTTTTGAAAACGTA
1 TAATATATAGTTTTT--AAAAATAATTTTGAAAACGTA
** *
67228 TAATATATAGTTGTTTTTAAATATTTTTGAAAACGTA
1 TAATATATAGTT-TTTAAAAATAATTTTGAAAACGTA
* * *
67265 TAATATATAGTTTTTAAAAATACTTTTGAAAACATG
1 TAATATATAGTTTTTAAAAATAATTTTGAAAACGTA
* * *
67301 TAATATATAGTTTTTAAAAATGACTTTGAAAACATA
1 TAATATATAGTTTTTAAAAATAATTTTGAAAACGTA
* * * **
67337 TACA-ATATAATGGTTTTGAAAA-CATTTAAAAAACGTA
1 TA-ATATAT-A-GTTTTTAAAAATAATTTTGAAAACGTA
67374 T-ATAATATAGTTTTTA
1 TAAT-ATATAGTTTTTA
67390 GTTGTTATTA
Statistics
Matches: 265, Mismatches: 31, Indels: 24
0.83 0.10 0.08
Matches are distributed among these distances:
34 28 0.11
35 25 0.09
36 62 0.23
37 109 0.41
38 38 0.14
39 3 0.01
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (36 bp):
TAATATATAGTTTTTAAAAATAATTTTGAAAACGTA
Found at i:67238 original size:109 final size:109
Alignment explanation
Indices: 67047--67320 Score: 417
Period size: 109 Copynumber: 2.5 Consensus size: 109
67037 TATAACCATG
* **
67047 TAATATATAGTTTTTAAAATAACTTTGAAAATGTATAATATATAGTTTTTAAAAAATATTTTTAA
1 TAATATATAGTTTTTAAAATAAATTTGAAAACATATAATATATAGTTTTTAAAAAATATTTTTAA
67112 AAACGTATAATATATAGTT-TTTAAAAAATATTTTTGAAAACATA
66 AAACGTATAATATATAGTTGTTT-AAAAATATTTTTGAAAACATA
*
67156 TAATATATAG-TTTTAAAATAAATTTGAAAACATATAATATATAGTTTTTACAAAAATATTTTTG
1 TAATATATAGTTTTTAAAATAAATTTGAAAACATATAATATATAGTTTTTA-AAAAATATTTTTA
** *
67220 AAAACGTATAATATATAGTTGTTTTTAAATATTTTTGAAAACGTA
65 AAAACGTATAATATATAGTTGTTTAAAAATATTTTTGAAAACATA
** *
67265 TAATATATAGTTTTTAAAAATACTTTTGAAAACATGTAATATATAGTTTTTAAAAA
1 TAATATATAGTTTTT-AAAATAAATTTGAAAACATATAATATATAGTTTTTAAAAA
67321 TGACTTTGAA
Statistics
Matches: 151, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
108 37 0.25
109 70 0.46
110 11 0.07
111 33 0.22
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.43
Consensus pattern (109 bp):
TAATATATAGTTTTTAAAATAAATTTGAAAACATATAATATATAGTTTTTAAAAAATATTTTTAA
AAACGTATAATATATAGTTGTTTAAAAATATTTTTGAAAACATA
Found at i:67321 original size:109 final size:108
Alignment explanation
Indices: 67047--67389 Score: 412
Period size: 109 Copynumber: 3.1 Consensus size: 108
67037 TATAACCATG
** *
67047 TAATATATAGTTTTTAAAATAACTTTGAAAATGTATAATATATAGTTTTTAAAAAATATTTTTAA
1 TAATATATAGTTTTTAAAAT-ACTTTGAAAACATATAATATATAGTTTTTAAAAAATATTTTTGA
* *
67112 AAACGTATAATATATAGTT-TTTAAAAAATATTTTTGAAAACATA
65 AAACGTATAATATATAGTTGTTT-TAAAATATTTTTGAAAACGTA
*
67156 TAATATATAG-TTTTAAAATAAATTTGAAAACATATAATATATAGTTTTTACAAAAATATTTTTG
1 TAATATATAGTTTTTAAAAT-ACTTTGAAAACATATAATATATAGTTTTTA-AAAAATATTTTTG
*
67220 AAAACGTATAATATATAGTTGTTTTTAAATATTTTTGAAAACGTA
64 AAAACGTATAATATATAGTTGTTTTAAAATATTTTTGAAAACGTA
* *
67265 TAATATATAGTTTTTAAAAATACTTTTGAAAACATGTAATATATAGTTTTT-AAAAATGA-CTTT
1 TAATATATAGTTTTT-AAAATAC-TTTGAAAACATATAATATATAGTTTTTAAAAAAT-ATTTTT
* * * * **
67328 GAAAACATATACA-ATATAATGGTTTTGAAAACA-TTTAAAAAACGTA
63 GAAAACGTATA-ATATATAGTTGTTTT-AAAATATTTTTGAAAACGTA
67374 T-ATAATATAGTTTTTA
1 TAAT-ATATAGTTTTTA
67390 GTTGTTATTA
Statistics
Matches: 208, Mismatches: 17, Indels: 19
0.85 0.07 0.08
Matches are distributed among these distances:
108 40 0.19
109 123 0.59
110 14 0.07
111 31 0.15
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (108 bp):
TAATATATAGTTTTTAAAATACTTTGAAAACATATAATATATAGTTTTTAAAAAATATTTTTGAA
AACGTATAATATATAGTTGTTTTAAAATATTTTTGAAAACGTA
Found at i:67345 original size:36 final size:36
Alignment explanation
Indices: 67047--67338 Score: 367
Period size: 37 Copynumber: 8.1 Consensus size: 36
67037 TATAACCATG
** **
67047 TAATATATAGTTTTT-AAAATAACTTTGAAAATGTA
1 TAATATATAGTTTTTAAAAATATTTTTGAAAACATA
* *
67082 TAATATATAGTTTTTAAAAAATATTTTTAAAAACGTA
1 TAATATATAGTTTTT-AAAAATATTTTTGAAAACATA
67119 TAATATATAGTTTTTAAAAAATATTTTTGAAAACATA
1 TAATATATAGTTTTT-AAAAATATTTTTGAAAACATA
**
67156 TAATATATAG-TTTT-AAAATAAATTTGAAAACATA
1 TAATATATAGTTTTTAAAAATATTTTTGAAAACATA
*
67190 TAATATATAGTTTTTACAAAAATATTTTTGAAAACGTA
1 TAATATATAGTTTTT--AAAAATATTTTTGAAAACATA
** *
67228 TAATATATAGTTGTTTTTAAATATTTTTGAAAACGTA
1 TAATATATAGTT-TTTAAAAATATTTTTGAAAACATA
* *
67265 TAATATATAGTTTTTAAAAATACTTTTGAAAACATG
1 TAATATATAGTTTTTAAAAATATTTTTGAAAACATA
*
67301 TAATATATAGTTTTTAAAAATGA-CTTTGAAAACATA
1 TAATATATAGTTTTTAAAAAT-ATTTTTGAAAACATA
67337 TA
1 TA
67339 CAATATAATG
Statistics
Matches: 229, Mismatches: 20, Indels: 15
0.87 0.08 0.06
Matches are distributed among these distances:
34 28 0.12
35 19 0.08
36 57 0.25
37 93 0.41
38 29 0.13
39 3 0.01
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (36 bp):
TAATATATAGTTTTTAAAAATATTTTTGAAAACATA
Done.