Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000237.1 Hibiscus syriacus cultivar Beakdansim tig00000411_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: 120346
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:850 original size:24 final size:24
Alignment explanation
Indices: 822--901 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
812 CACTTAACAA
822 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCATCCCTTTGAATG
* *
846 TGCATCGATTCAT-CATATTG-A--
1 TGCATCGATGCATCCCT-TTGAATG
*
867 TGCACCGATGCA-CGCC-TTGAATG
1 TGCATCGATGCATC-CCTTTGAATG
890 TGCATCGATGCA
1 TGCATCGATGCA
902 CGGGGTCATG
Statistics
Matches: 44, Mismatches: 6, Indels: 13
0.70 0.10 0.21
Matches are distributed among these distances:
20 3 0.07
21 11 0.25
22 1 0.02
23 14 0.32
24 15 0.34
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (24 bp):
TGCATCGATGCATCCCTTTGAATG
Found at i:3613 original size:65 final size:64
Alignment explanation
Indices: 3483--3624 Score: 173
Period size: 65 Copynumber: 2.2 Consensus size: 64
3473 ATTAAAATTG
3483 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGATTTTATGAA
1 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGATTTTATG-A
* * * * * *
3548 AACATCGAATGCATTTGATGCATCGATGTACCA-GCCATGCATCGATGCACTCTA-GCTATTT-T
1 AACATCGAATGCATTTCATGCATCGATGCA-CATACCATGCACCGATGCACT-GAGGAT-TTTAT
3610 GA
63 GA
3612 AACATCGAATGCA
1 AACATCGAATGCA
3625 CTCTTAGTGC
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
64 14 0.21
65 48 0.71
66 6 0.09
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGATTTTATGA
Found at i:10580 original size:5 final size:5
Alignment explanation
Indices: 10570--10603 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
10560 AGGGGAGAGA
10570 GAAGG GAAGG GAAGG GAAGG GAAGG GAAGG GAAG
1 GAAGG GAAGG GAAGG GAAGG GAAGG GAAGG GAAG
10604 AAGGTAGCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (5 bp):
GAAGG
Found at i:11250 original size:23 final size:23
Alignment explanation
Indices: 11220--11266 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
11210 AATAGCAGTT
11220 TGGAGAATGTTGAACCAGCCAAG
1 TGGAGAATGTTGAACCAGCCAAG
* *
11243 TGGAGAATGTTGAACGAGTCAAG
1 TGGAGAATGTTGAACCAGCCAAG
11266 T
1 T
11267 TCTAAAGCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.34, C:0.13, G:0.32, T:0.21
Consensus pattern (23 bp):
TGGAGAATGTTGAACCAGCCAAG
Found at i:12932 original size:13 final size:13
Alignment explanation
Indices: 12906--12940 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
12896 CAATCCTGGC
12906 GACATACG-GGGT
1 GACATACGAGGGT
12918 GACATACGAGGGT
1 GACATACGAGGGT
12931 GACATACGAG
1 GACATACGAG
12941 CCATATACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.31, C:0.17, G:0.37, T:0.14
Consensus pattern (13 bp):
GACATACGAGGGT
Found at i:12950 original size:11 final size:11
Alignment explanation
Indices: 12934--12967 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
12924 CGAGGGTGAC
12934 ATACGAGCCAT
1 ATACGAGCCAT
12945 ATACGAGCCAT
1 ATACGAGCCAT
*
12956 ATACGAGTCAT
1 ATACGAGCCAT
12967 A
1 A
12968 CGAGCCAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.21
Consensus pattern (11 bp):
ATACGAGCCAT
Found at i:12998 original size:22 final size:22
Alignment explanation
Indices: 12967--13046 Score: 79
Period size: 22 Copynumber: 3.4 Consensus size: 22
12957 TACGAGTCAT
*
12967 ACGAGCCAATGGGGAGGATGCA
1 ACGAGCCAATGGGGAGCATGCA
*
12989 ACGAGGCAATGGGGAGCATGCAGGAA
1 ACGAGCCAATGGGGAGCATGC----A
*
13015 TAGAGAGCCAATGGGGAGCATGCA
1 -A-CGAGCCAATGGGGAGCATGCA
13039 ACGAGCCA
1 ACGAGCCA
13047 TATACGAGCC
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
22 25 0.53
23 1 0.02
24 1 0.02
26 1 0.02
27 1 0.02
28 18 0.38
ACGTcount: A:0.34, C:0.19, G:0.39, T:0.09
Consensus pattern (22 bp):
ACGAGCCAATGGGGAGCATGCA
Found at i:13027 original size:28 final size:28
Alignment explanation
Indices: 12995--13160 Score: 188
Period size: 28 Copynumber: 5.6 Consensus size: 28
12985 TGCAACGAGG
12995 CAATGGGGAGCATGCAGGAATAGAGAGC
1 CAATGGGGAGCATGCAGGAATAGAGAGC
* *
13023 CAATGGGGAGCATGCAACGAGCCATATACGAGC
1 CAATGGGGAGCATGC-A-G-G-AATAGA-GAGC
* *
13056 CCACGGGGAGCATGCAGGAATAGAGAGC
1 CAATGGGGAGCATGCAGGAATAGAGAGC
* *
13084 CAATGGGGAGCATGCAACGAGCCATATACGAGC
1 CAATGGGGAGCATGC-A-G-G-AATAGA-GAGC
13117 CAATGGGGAGCATGCAGGAATAGAGAGC
1 CAATGGGGAGCATGCAGGAATAGAGAGC
13145 CAATGGGGAGCATGCA
1 CAATGGGGAGCATGCA
13161 ACGAGCCATA
Statistics
Matches: 116, Mismatches: 12, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
28 52 0.45
29 10 0.09
30 4 0.03
31 4 0.03
32 10 0.09
33 36 0.31
ACGTcount: A:0.34, C:0.20, G:0.36, T:0.11
Consensus pattern (28 bp):
CAATGGGGAGCATGCAGGAATAGAGAGC
Found at i:13028 original size:50 final size:51
Alignment explanation
Indices: 12969--13194 Score: 213
Period size: 61 Copynumber: 4.1 Consensus size: 51
12959 CGAGTCATAC
* *
12969 GAGCCAATGGGGAGGATGCAACGAGGCA-ATGGGGAGCATGCAGGAATAGA
1 GAGCCAATGGGGAGCATGCAACGAGCCATATGGGGAGCATGCAGGAATAGA
13019 GAGCCAATGGGGAGCATGCAACGAGCCATATACGAGCCCACGGGGAGCATGCAGGAATAGA
1 GAGCCAATGGGGAGCATGCAACGAGCCATAT----------GGGGAGCATGCAGGAATAGA
13080 GAGCCAATGGGGAGCATGCAACGAGCCATATACGAGCCAATGGGGAGCATGCAGGAATAGA
1 GAGCCAATGGGGAGCATGCAACGAGCC--AT--------ATGGGGAGCATGCAGGAATAGA
**
13141 GAGCCAATGGGGAGCATGCAACGAGCCATAT-ACGAGCCATGCAGGAATAGA
1 GAGCCAATGGGGAGCATGCAACGAGCCATATGGGGAG-CATGCAGGAATAGA
13192 GAG
1 GAG
13195 GTCGCCATGC
Statistics
Matches: 150, Mismatches: 4, Indels: 43
0.76 0.02 0.22
Matches are distributed among these distances:
50 29 0.19
51 21 0.14
59 2 0.01
61 94 0.63
63 2 0.01
71 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.36, T:0.11
Consensus pattern (51 bp):
GAGCCAATGGGGAGCATGCAACGAGCCATATGGGGAGCATGCAGGAATAGA
Found at i:13084 original size:61 final size:61
Alignment explanation
Indices: 12989--13179 Score: 346
Period size: 61 Copynumber: 3.1 Consensus size: 61
12979 GGAGGATGCA
* *
12989 ACGAGGCAATGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
1 ACGAGCCAACGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
*
13050 ACGAGCCCACGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
1 ACGAGCCAACGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
*
13111 ACGAGCCAATGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
1 ACGAGCCAACGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
13172 ACGAGCCA
1 ACGAGCCA
13180 TGCAGGAATA
Statistics
Matches: 125, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 125 1.00
ACGTcount: A:0.34, C:0.21, G:0.35, T:0.10
Consensus pattern (61 bp):
ACGAGCCAACGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
Found at i:13243 original size:29 final size:29
Alignment explanation
Indices: 13193--13301 Score: 184
Period size: 29 Copynumber: 3.8 Consensus size: 29
13183 AGGAATAGAG
* *
13193 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGT
13222 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
13251 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
13280 AGGTCGCCATGTAGTCCCGGCG
1 AGGTCGCCATGTAGTCCCGGCG
13302 CCATTCCATC
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
29 75 0.97
30 2 0.03
ACGTcount: A:0.15, C:0.31, G:0.32, T:0.22
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:13419 original size:36 final size:37
Alignment explanation
Indices: 13351--13424 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
13341 CATAGATTCC
13351 TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
1 TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
13388 TTCACGTGCTCCCCGCTGCA-TGCCTACACCTCCCAA
1 TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
13424 T
1 T
13425 GCATGCATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 17 0.46
37 20 0.54
ACGTcount: A:0.16, C:0.46, G:0.14, T:0.24
Consensus pattern (37 bp):
TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
Found at i:13452 original size:18 final size:18
Alignment explanation
Indices: 13429--13463 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
13419 CCCAATGCAT
13429 GCATGTGAACCATTTGAG
1 GCATGTGAACCATTTGAG
13447 GCATGTGAACCATTTGA
1 GCATGTGAACCATTTGA
13464 TTATTGGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (18 bp):
GCATGTGAACCATTTGAG
Found at i:13588 original size:22 final size:23
Alignment explanation
Indices: 13553--13597 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
13543 AAAAGAAAGA
13553 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
13576 AAGAAA-GGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
13598 CCGAGAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.49, C:0.04, G:0.38, T:0.09
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGATTGCAG
Found at i:13636 original size:21 final size:21
Alignment explanation
Indices: 13600--13658 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
13590 GATTGCAGCC
13600 GAGAAA-GAAAGAAAGAAAGG
1 GAGAAAGGAAAGAAAGAAAGG
*
13620 GAGAAAGGAAAGGAAGAAAGG
1 GAGAAAGGAAAGAAAGAAAGG
*
13641 GAGAAAGGAAAGTAAGAA
1 GAGAAAGGAAAGAAAGAA
13659 GAAGAAAGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 6 0.17
21 30 0.83
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.02
Consensus pattern (21 bp):
GAGAAAGGAAAGAAAGAAAGG
Found at i:13836 original size:41 final size:42
Alignment explanation
Indices: 13791--13930 Score: 119
Period size: 41 Copynumber: 3.3 Consensus size: 42
13781 TATATGATTG
* *
13791 TTAGTTTAAGTT-ATAGTATACATAAATTAAAAATTATTTAA
1 TTAGTTTATGTTAATAGTATATATAAATTAAAAATTATTTAA
* * * * *
13832 TTAGTATATGTTTGATAGT-TATAT-AGTTAAAAAATAATTAA
1 TTAGTTTATG-TTAATAGTATATATAAATTAAAAATTATTTAA
13873 TTAGTTGTATTGTTAATAGTTAGTTATATAAA--AAAAATTATTTAA
1 TTAGTT-TA-TGTTAATAG-TA--TATATAAATTAAAAATTATTTAA
*
13918 TTAGTTTGTGTTA
1 TTAGTTTATGTTA
13931 GTTAAATAGT
Statistics
Matches: 78, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
41 27 0.35
42 14 0.18
43 13 0.17
44 1 0.01
45 17 0.22
46 5 0.06
47 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.11, T:0.46
Consensus pattern (42 bp):
TTAGTTTATGTTAATAGTATATATAAATTAAAAATTATTTAA
Found at i:13950 original size:49 final size:44
Alignment explanation
Indices: 13860--13950 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 44
13850 TTATATAGTT
13860 AAAAAATAATTAATTAGTTGTATTGTTAATAGTTAGTTATATAA
1 AAAAAATAATTAATTAGTTGTATTGTTAATAGTTAGTTATATAA
* *
13904 AAAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAA-TAATTAATTAG-TTGTATT-GTT-AATAGTT-AGTTATAT
13951 TTGTTTGTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
44 6 0.15
45 10 0.25
46 6 0.15
47 3 0.08
48 7 0.17
49 8 0.20
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (44 bp):
AAAAAATAATTAATTAGTTGTATTGTTAATAGTTAGTTATATAA
Found at i:16342 original size:14 final size:13
Alignment explanation
Indices: 16323--16365 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
16313 AAATCATTAC
16323 TAGTATCAAATAAT
1 TAGTAT-AAATAAT
*
16337 TAGTATTAAATCAT
1 TAGTA-TAAATAAT
*
16351 TATTATAAATAAT
1 TAGTATAAATAAT
16364 TA
1 TA
16366 CTAAATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 9 0.36
14 15 0.60
15 1 0.04
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.42
Consensus pattern (13 bp):
TAGTATAAATAAT
Found at i:16355 original size:17 final size:17
Alignment explanation
Indices: 16305--16355 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
16295 ACAATGATTT
16305 TTAGTATCAAATCATTA
1 TTAGTATCAAATCATTA
*
16322 CTAGTATCAAAT-A--A
1 TTAGTATCAAATCATTA
*
16336 TTAGTATTAAATCATTA
1 TTAGTATCAAATCATTA
16353 TTA
1 TTA
16356 TAAATAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 11 0.39
15 1 0.04
16 1 0.04
17 15 0.54
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (17 bp):
TTAGTATCAAATCATTA
Found at i:16407 original size:26 final size:25
Alignment explanation
Indices: 16343--16649 Score: 198
Period size: 26 Copynumber: 12.4 Consensus size: 25
16333 TAATTAGTAT
*
16343 TAAATCATTATTATAA--ATAATTA
1 TAAATCATTATTATAATGATTATTA
* ** *
16366 CTAAAT-AATAACATAATAATTATTA
1 -TAAATCATTATTATAATGATTATTA
16391 TAAAATCATTATTATAATGATTATTA
1 T-AAATCATTATTATAATGATTATTA
* * * *
16417 TCAAATCATTACTA-AATCATCAAATCA
1 T-AAATCATTATTATAATGAT--TATTA
*
16444 TTAAAT-A-T-TTA-AATCATTA-T-
1 -TAAATCATTATTATAATGATTATTA
*
16464 TAAATCATTTTTATAATGATTATTA
1 TAAATCATTATTATAATGATTATTA
*
16489 CTAAATCATTACTATAATGATTATTA
1 -TAAATCATTATTATAATGATTATTA
* * * *
16515 TCAAATCATTACTA-AATCATCAAATCA
1 T-AAATCATTATTATAATGAT--TATTA
*
16542 TTAAAT-A-T-TTA-AATCATTA-T-
1 -TAAATCATTATTATAATGATTATTA
*
16562 TAAATCATTTTTATAATGATTATTA
1 TAAATCATTATTATAATGATTATTA
16587 CTAAATCATTATTATAATGATTATTA
1 -TAAATCATTATTATAATGATTATTA
*
16613 TCAAATCATTACTATAATGATTATTA
1 T-AAATCATTATTATAATGATTATTA
16639 TCAAATCATTA
1 T-AAATCATTA
16650 CTAAATCATC
Statistics
Matches: 229, Mismatches: 28, Indels: 50
0.75 0.09 0.16
Matches are distributed among these distances:
19 10 0.04
20 2 0.01
21 2 0.01
22 8 0.03
23 21 0.09
24 24 0.10
25 24 0.10
26 122 0.53
27 14 0.06
28 2 0.01
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.43
Consensus pattern (25 bp):
TAAATCATTATTATAATGATTATTA
Found at i:16415 original size:12 final size:12
Alignment explanation
Indices: 16340--16417 Score: 54
Period size: 11 Copynumber: 6.5 Consensus size: 12
16330 AAATAATTAG
*
16340 TATTA-AATCAT
1 TATTATAATAAT
16351 TATTATAAATAAT
1 TATTAT-AATAAT
*
16364 TACTA-AATAA-
1 TATTATAATAAT
**
16374 TAACATAATAAT
1 TATTATAATAAT
*
16386 TATTATAAAATCAT
1 TATTAT--AATAAT
*
16400 TATTATAATGAT
1 TATTATAATAAT
16412 TATTAT
1 TATTAT
16418 CAAATCATTA
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
10 3 0.06
11 15 0.28
12 15 0.28
13 9 0.17
14 11 0.21
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (12 bp):
TATTATAATAAT
Found at i:16547 original size:98 final size:98
Alignment explanation
Indices: 16378--16626 Score: 464
Period size: 98 Copynumber: 2.5 Consensus size: 98
16368 AAATAATAAC
*
16378 ATAATAATTATTA-TAAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAAT
1 ATAATGATTATTACT-AAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAAT
16442 CATTAAATATTTAAATCATTATTAAATCATTTTT
65 CATTAAATATTTAAATCATTATTAAATCATTTTT
*
16476 ATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATC
1 ATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAATC
16541 ATTAAATATTTAAATCATTATTAAATCATTTTT
66 ATTAAATATTTAAATCATTATTAAATCATTTTT
16574 ATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTA
1 ATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTA
16627 TAATGATTAT
Statistics
Matches: 147, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
98 146 0.99
99 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (98 bp):
ATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAATC
ATTAAATATTTAAATCATTATTAAATCATTTTT
Found at i:16593 original size:124 final size:124
Alignment explanation
Indices: 16459--16707 Score: 464
Period size: 124 Copynumber: 2.0 Consensus size: 124
16449 TATTTAAATC
* *
16459 ATTATTAAATCATTTTTATAATGATTATTA-CTAAATCATTACTATAATGATTATTATCAAATCA
1 ATTACTAAATCATTATTATAATGATTATTATC-AAATCATTACTATAATGATTATTATCAAATCA
16523 TTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATT
65 TTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATT
16583 ATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
1 ATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
16648 TACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATT
66 TACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATT
16707 A
1 A
16708 ATAAATACAT
Statistics
Matches: 122, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
124 121 0.99
125 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.44
Consensus pattern (124 bp):
ATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
TACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATT
Found at i:19341 original size:28 final size:30
Alignment explanation
Indices: 19301--19363 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
19291 ATTTTTTATA
*
19301 TAATATAATATATAACTTAAACTAATAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
19331 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
19359 TAATA
1 TAATA
19364 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:19370 original size:28 final size:28
Alignment explanation
Indices: 19305--19370 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
19295 TTTATATAAT
*
19305 ATAATATATAACTTAAACTAATAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
19333 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
19361 ATAATTTATA
1 ATAATATATA
19371 CTAACAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:19373 original size:21 final size:21
Alignment explanation
Indices: 19340--19388 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
19330 CTAATATAAT
19340 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
19361 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
19382 ATTAACT
1 A-TAACT
19389 AGATTTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:19933 original size:25 final size:25
Alignment explanation
Indices: 19879--19936 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
19869 GTTCCCACGT
* *
19879 CCCATGCACAGCATGCATCTGCATG
1 CCCATGCACAGCATGCATCTCCATC
* *
19904 ACCATGCACAGCATGCATC-CCCTCC
1 CCCATGCACAGCATGCATCTCCAT-C
19929 CCCATGCA
1 CCCATGCA
19937 TTCCCACGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 2 0.07
25 25 0.93
ACGTcount: A:0.24, C:0.43, G:0.16, T:0.17
Consensus pattern (25 bp):
CCCATGCACAGCATGCATCTCCATC
Found at i:20026 original size:29 final size:29
Alignment explanation
Indices: 19994--20073 Score: 151
Period size: 29 Copynumber: 2.8 Consensus size: 29
19984 TATACCTTGG
*
19994 AGGTCGCCCGGATTGCATGGCGACCTCCA
1 AGGTCGCCTGGATTGCATGGCGACCTCCA
20023 AGGTCGCCTGGATTGCATGGCGACCTCCA
1 AGGTCGCCTGGATTGCATGGCGACCTCCA
20052 AGGTCGCCTGGATTGCATGGCG
1 AGGTCGCCTGGATTGCATGGCG
20074 TCCTATGGCG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.16, C:0.30, G:0.34, T:0.20
Consensus pattern (29 bp):
AGGTCGCCTGGATTGCATGGCGACCTCCA
Found at i:23931 original size:113 final size:113
Alignment explanation
Indices: 23788--24776 Score: 1561
Period size: 113 Copynumber: 8.8 Consensus size: 113
23778 TTAAAGTAGA
* *
23788 AAGGCCAGTGAGATTATTAATAGGGATGCCAAACAACAAAAATAATTTTTTGGGTCAACAGGGAC
1 AAGGCCAGTGATATTATTAATAGGGATGCCATACAACAAAAATAATTTTTTGGGTCAACAGGGAC
* *
23853 AAACCCAAAACCACAAAAATAATATGTGTACAGAATAGGAACAACAGG
66 AAACCCAAAACCACAAAAATAATCTGTGTACAGAGTAGGAACAACAGG
*
23901 AAGGCCAGTGATATTATTAATAGGGATGCCATACAACAAAAATAATTTTTTGGGTAAACAGGGAC
1 AAGGCCAGTGATATTATTAATAGGGATGCCATACAACAAAAATAATTTTTTGGGTCAACAGGGAC
* * *
23966 AAACCCAAAACCATAAAAATAATATGTGTACAAAGTAGGAACAACAGG
66 AAACCCAAAACCACAAAAATAATCTGTGTACAGAGTAGGAACAACAGG
* * * *
24014 AAGGCAAGTGATATTATTAATAGGGATGCCACAGAAAAAAAATAATTTTTTGGGTCAACAGGGAC
1 AAGGCCAGTGATATTATTAATAGGGATGCCATACAACAAAAATAATTTTTTGGGTCAACAGGGAC
* * *
24079 AAACCCAAAATCAAAAAAATAATCTGTGTACATAGTAGGAACAACAGG
66 AAACCCAAAACCACAAAAATAATCTGTGTACAGAGTAGGAACAACAGG
* *
24127 AAGGCCAGTGATATAATTAATAGGGATGCCATACAACAAAAATAATTTTTTGGGTCAACATGGAC
1 AAGGCCAGTGATATTATTAATAGGGATGCCATACAACAAAAATAATTTTTTGGGTCAACAGGGAC
*
24192 AAACCCAAAACCACAAAAATAATCTGTGAACAGAGTAGGAACAACAGG
66 AAACCCAAAACCACAAAAATAATCTGTGTACAGAGTAGGAACAACAGG
* * *
24240 AAGGCCATTGATATTATTAATAGGGATGTCATACAATAAAAATAATTTTTTGGGTCAACAGGGAC
1 AAGGCCAGTGATATTATTAATAGGGATGCCATACAACAAAAATAATTTTTTGGGTCAACAGGGAC
* *
24305 AAACCCAAAACCACAAAAATAATCTGTGTACATAGTATGAACAACAGG
66 AAACCCAAAACCACAAAAATAATCTGTGTACAGAGTAGGAACAACAGG
* * * * *
24353 AAGGCCATTGATATTATTAATAGGGATGCCATATAACAAAAATATTTTTTTGGGTCAATAAGGAC
1 AAGGCCAGTGATATTATTAATAGGGATGCCATACAACAAAAATAATTTTTTGGGTCAACAGGGAC
*
24418 AAACCCAAAACCACAAAAATAATCTGTGTACATAGTAGGAACAACAGG
66 AAACCCAAAACCACAAAAATAATCTGTGTACAGAGTAGGAACAACAGG
* * *
24466 AAGGCCAGTGAGATTATTAATAGGGATGCCAAACAACAAAAATAATTTTTTGGATCAACAGGGAC
1 AAGGCCAGTGATATTATTAATAGGGATGCCATACAACAAAAATAATTTTTTGGGTCAACAGGGAC
*
24531 AAACCCAAAACCACAAAAATAATATGTGTACAGAGTAGGAACAACAGG
66 AAACCCAAAACCACAAAAATAATCTGTGTACAGAGTAGGAACAACAGG
* * *
24579 AAGGCCAGTGATAATATTAATAGGGATGCCATACAATAAAAATAATTTTTTGGGTTAACAGGGAC
1 AAGGCCAGTGATATTATTAATAGGGATGCCATACAACAAAAATAATTTTTTGGGTCAACAGGGAC
* * *
24644 AAACCCAAAACCACAAAAAATAAT-T-TGTAGAGAGTAGAAACAATAGG
66 AAACCCAAAACCAC-AAAAATAATCTGTGTACAGAGTAGGAACAACAGG
* *
24691 AAGG-CAATGATATTATTAATAGGGATGCCCATACAACAAAAATAGTTTTTTTGGGTCAACAGGG
1 AAGGCCAGTGATATTATTAATAGGGATG-CCATACAACAAAAATA-ATTTTTTGGGTCAACAGGG
24755 ACAAACCCAAAACCACAAAAAT
64 ACAAACCCAAAACCACAAAAAT
24777 GGGATGGCAA
Statistics
Matches: 809, Mismatches: 64, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
111 21 0.03
112 44 0.05
113 735 0.91
114 9 0.01
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.21
Consensus pattern (113 bp):
AAGGCCAGTGATATTATTAATAGGGATGCCATACAACAAAAATAATTTTTTGGGTCAACAGGGAC
AAACCCAAAACCACAAAAATAATCTGTGTACAGAGTAGGAACAACAGG
Found at i:29112 original size:36 final size:36
Alignment explanation
Indices: 29054--29193 Score: 167
Period size: 36 Copynumber: 3.9 Consensus size: 36
29044 TGAATAAGAA
* *
29054 GAACGAAAGGAAGCGTCAGCACTTTCGATTCAAAAT
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAAT
* *
29090 GAACGGAAGTAAGCATCGGCACTTTCGATTCAAGAA-
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAA-AAT
* ** * *
29126 GAACGAAAGAAAATATCGGCAGTTTCGATTC-AAGT
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAAT
*
29161 GAACGAAAGGAAGCATCCGCACTTTCGATTCAA
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAA
29194 TTGTTCATCT
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
34 1 0.01
35 27 0.31
36 56 0.65
37 2 0.02
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.20
Consensus pattern (36 bp):
GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAAT
Found at i:29190 original size:71 final size:72
Alignment explanation
Indices: 29049--29193 Score: 193
Period size: 71 Copynumber: 2.0 Consensus size: 72
29039 GAAGGTGAAT
* * * * * *
29049 AAGAAGAACGAAAGGAAGCGTCAGCACTTTCGATTCAAAATGAACGGAAGTAAGCATCGGCACTT
1 AAGAAGAACGAAAGAAAACATCAGCACTTTCGATTCAAAATGAACGAAAGGAAGCATCCGCACTT
29114 TCGATTC
66 TCGATTC
* * * *
29121 AAGAAGAACGAAAGAAAATATCGGCAGTTTCGATTC-AAGTGAACGAAAGGAAGCATCCGCACTT
1 AAGAAGAACGAAAGAAAACATCAGCACTTTCGATTCAAAATGAACGAAAGGAAGCATCCGCACTT
29185 TCGATTC
66 TCGATTC
29192 AA
1 AA
29194 TTGTTCATCT
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
71 33 0.52
72 30 0.48
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (72 bp):
AAGAAGAACGAAAGAAAACATCAGCACTTTCGATTCAAAATGAACGAAAGGAAGCATCCGCACTT
TCGATTC
Found at i:30950 original size:14 final size:14
Alignment explanation
Indices: 30931--30958 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
30921 TTTGTATTTT
30931 GTTTTTACAGAAAA
1 GTTTTTACAGAAAA
30945 GTTTTTACAGAAAA
1 GTTTTTACAGAAAA
30959 TTTAACATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (14 bp):
GTTTTTACAGAAAA
Found at i:34794 original size:168 final size:166
Alignment explanation
Indices: 34395--34998 Score: 635
Period size: 168 Copynumber: 3.6 Consensus size: 166
34385 ATTGATCGAC
* * * * *
34395 TTACATGTGTTTCACTATATATGATTAAATAAGGTAATATTTATTCTATTTATGAATCTTTAGAA
1 TTACACGTGCTTCATTATATATGATTAAATAAGATAATATTTATTCTATTTATGAATCTTTAGGA
* **
34460 GTATCTTGTAACGAGATTATTGACTCAT--ATGTTCCATTATATAATTAAACTAATT-TTTCGTT
66 GTATCTTGTAACGAGTTTATCAACTCATACATGTTCCATTATATAATTAAA-T--TTATTT--TT
* * * *
34522 TCTTGTACATATGAATGTCATAAGCTGTAATGAGTTTATCAA
126 T-TTGTATATATGAATATCATAAGATGTAATGAGTTTATCAT
* * *
34564 TAACATGTGCTAT-ATTATATATGACTAAATAAGATAA-AGTTTATTCTATTTATGAATCTTTAG
1 TTACACGTGCT-TCATTATATATGATTAAATAAGATAATA-TTTATTCTATTTATGAATCTTTAG
* * * *
34627 GAGTATCTTGTAACAAGTTTATCGACTTATACATATTCCATTATATAATTAAATTTATTTTTTAT
64 GAGTATCTTGTAACGAGTTTATCAACTCATACATGTTCCATTATATAATTAAATTTATTTTTT-T
*
34692 TGTATATATGAATATCATAAGTTGTAATGAGTTTATCGAT
128 TGTATATATGAATATCATAAGATGTAATGAGTTTATC-AT
* * * * *
34732 TTCCACGTGCTTCATTATATATGATTGAATAAGATAACATTTATTCTGTTTATGTATCTTTAGGA
1 TTACACGTGCTTCATTATATATGATTAAATAAGATAATATTTATTCTATTTATGAATCTTTAGGA
* * *
34797 TTATCTTGTAACGAGTTTATTAACTCATACATGTTCCATTATATAAATTAATTAATTTATCTTTT
66 GTATCTTGTAACGAGTTTATCAACTCATACATGTTCCATTATAT-AATT-A--AATTTATTTTTT
* * *
34862 TTGTATATATGAATACCGTAAGATGTAATGAATTTATCAAT
127 TTGTATATATGAATATCATAAGATGTAATGAGTTTATC-AT
* * * * * * * * *
34903 TTACACATACTTTATTATACATGATTGAATAAGGTAATA-TTATTTTATTTATGACTCTCTAGGA
1 TTACACGTGCTTCATTATATATGATTAAATAAGATAATATTTATTCTATTTATGAATCTTTAGGA
* * * *
34967 ATATTTTGTAACTAGCTTATCAACTCATACAT
66 GTATCTTGTAACGAGTTTATCAACTCATACAT
34999 TTTTTTTTGC
Statistics
Matches: 371, Mismatches: 52, Indels: 23
0.83 0.12 0.05
Matches are distributed among these distances:
167 39 0.11
168 96 0.26
169 87 0.23
170 50 0.13
171 88 0.24
172 11 0.03
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (166 bp):
TTACACGTGCTTCATTATATATGATTAAATAAGATAATATTTATTCTATTTATGAATCTTTAGGA
GTATCTTGTAACGAGTTTATCAACTCATACATGTTCCATTATATAATTAAATTTATTTTTTTTGT
ATATATGAATATCATAAGATGTAATGAGTTTATCAT
Found at i:42781 original size:2 final size:2
Alignment explanation
Indices: 42774--42837 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
42764 TTTCCATGTA
42774 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
42816 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
42838 TTTCGTACGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50846 original size:23 final size:23
Alignment explanation
Indices: 50800--50865 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 23
50790 ATGAAGAATA
*
50800 AAATAAGTAAAAAAT-AA-A-AGG
1 AAATAA-TAAAAAATAAATATATG
50821 AAA-AATAAATAAATAAATATATG
1 AAATAATAAA-AAATAAATATATG
* *
50844 AAATATTAAAAAATATATATAT
1 AAATAATAAAAAATAAATATAT
50866 ATAAATGAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
19 4 0.11
20 6 0.16
21 5 0.14
22 1 0.03
23 16 0.43
24 5 0.14
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (23 bp):
AAATAATAAAAAATAAATATATG
Found at i:50987 original size:29 final size:30
Alignment explanation
Indices: 50920--50987 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
50910 AGTAATATGA
*
50920 AAATAT-AATATAATATAAATAAAAAAACC
1 AAATATAAAAATAATATAAATAAAAAAACC
* * * *
50949 AAAAACAAAAATAA-ATAAATATATAAACC
1 AAATATAAAAATAATATAAATAAAAAAACC
50978 AAATATAAAA
1 AAATATAAAA
50988 GTATACATAT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
29 25 0.81
30 6 0.19
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (30 bp):
AAATATAAAAATAATATAAATAAAAAAACC
Found at i:51148 original size:19 final size:18
Alignment explanation
Indices: 51117--51175 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
51107 CGCTTATAAG
*
51117 TAAA-ATATTTAAAAAAA
1 TAAATATATATAAAAAAA
*
51134 GTATATATATATAAAAATAA
1 -TAAATATATATAAAAA-AA
*
51154 TAAATATAGTATTAAAAAA
1 TAAATATA-TATAAAAAAA
51173 TAA
1 TAA
51176 CCAAATGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
18 3 0.09
19 22 0.65
20 9 0.26
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.32
Consensus pattern (18 bp):
TAAATATATATAAAAAAA
Found at i:51174 original size:22 final size:21
Alignment explanation
Indices: 51136--51238 Score: 77
Period size: 22 Copynumber: 4.7 Consensus size: 21
51126 TAAAAAAAGT
51136 ATATA-TATATAAAAATAATAA
1 ATATAGTATA-AAAAATAATAA
*
51157 ATATAGTATTAAAAAATAACCAA
1 ATATAGTA-TAAAAAATAA-TAA
*
51180 ATGA-A-TATAAATAAATAAAAA
1 AT-ATAGTATAAA-AAATAATAA
* *
51201 ATATATGTATATATAATAATAA
1 ATATA-GTATAAAAAATAATAA
*
51223 TATATAGTGTAAAAAA
1 -ATATAGTATAAAAAA
51239 AATCAATTGA
Statistics
Matches: 65, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
20 1 0.02
21 14 0.22
22 32 0.49
23 17 0.26
24 1 0.02
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (21 bp):
ATATAGTATAAAAAATAATAA
Found at i:51279 original size:67 final size:67
Alignment explanation
Indices: 51126--51308 Score: 160
Period size: 67 Copynumber: 2.7 Consensus size: 67
51116 GTAAAATATT
* * *
51126 TAAAAAA-AGTATATATATATAAAAATAATAAATATAGTATTAAAAAATAACCAAATGAATATAA
1 TAAAAAATAGTATATATATATAATAATAAT--ATATAGT-GTAAAAAATAACCAAATGAAAATAA
51190 ATAAA
63 ATAAA
* * * **
51195 TAAAAAATA-TATGTATATATAATAATAATATATAGTGTAAAAAA-AATCAATTGAAAATCATTT
1 TAAAAAATAGTATATATATATAATAATAATATATAGTGTAAAAAATAACCAAATGAAAAT-AAAT
51258 AAA
65 AAA
* * * * *
51261 -AAAACATACGTATATATATTTATATAATGATA-ATAATGTAAATAATAA
1 TAAAAAATA-GTATATATATATA-ATAATAATATATAGTGTAAAAAATAA
51309 TTAAATAAAA
Statistics
Matches: 94, Mismatches: 14, Indels: 13
0.78 0.12 0.11
Matches are distributed among these distances:
65 18 0.19
66 12 0.13
67 28 0.30
68 10 0.11
69 25 0.27
70 1 0.01
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (67 bp):
TAAAAAATAGTATATATATATAATAATAATATATAGTGTAAAAAATAACCAAATGAAAATAAATA
AA
Found at i:51742 original size:37 final size:37
Alignment explanation
Indices: 51701--51805 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
51691 GTGCTTGTGG
* * *
51701 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * *
51738 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
51775 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
51806 GACGAAAAGG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:52861 original size:106 final size:106
Alignment explanation
Indices: 52536--54016 Score: 2127
Period size: 106 Copynumber: 14.0 Consensus size: 106
52526 GCATTGTTCT
* * * ** *
52536 GAGTCCTATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * * * * *
52600 ACCAGCTGTCCCTTCATTGTGAAGTTGAACTTGTGTTGCCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
52642 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * * * *
52701 TCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGCCTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * * *
52743 G-GTTCAAGATCCTTTGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
52807 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTGGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
52848 GATTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
52913 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
52954 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
53019 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
53060 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
53125 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
53166 GAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
53231 CCAGCGGTCCCTTCATCGTGAAGTTGCACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * * ** *
53272 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGATATGAAATTAAGAATTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
53337 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
53378 GAGTCCAAAATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
53443 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
53484 TAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
53549 TCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
53590 GAGTCCAATATCCTTCGTTATGAAGTTTAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
53655 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
53696 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
53761 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
53802 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGATCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
53867 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
53908 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCCGAAACTGGAAACTT-ATTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
53972 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
54013 GAGT
1 GAGT
54017 GGCATGATAT
Statistics
Matches: 1245, Mismatches: 120, Indels: 21
0.90 0.09 0.02
Matches are distributed among these distances:
100 77 0.06
101 5 0.00
102 4 0.00
104 3 0.00
105 53 0.04
106 1102 0.89
107 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:54865 original size:22 final size:22
Alignment explanation
Indices: 54839--54908 Score: 104
Period size: 22 Copynumber: 3.2 Consensus size: 22
54829 TTATGTTTGG
*
54839 TCAAAGGTTTGGCATTTGATGA
1 TCAAAGGTTTGGCATTTGATGC
54861 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
* **
54883 TCATAGGTTTACCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
54905 TCAA
1 TCAA
54909 CGGTATGATG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:55577 original size:47 final size:47
Alignment explanation
Indices: 55521--55622 Score: 116
Period size: 47 Copynumber: 2.2 Consensus size: 47
55511 TTTTTGTCCC
* *
55521 TTTTTCTTTTTGATTT-TTGTTCTTTCTTTTTTTCCTTTTGTTTCTCT
1 TTTTTCTTTTTGATTTCTTGTTCTTTCTTCTTTTCCTTCT-TTTCTCT
** * * * *
55568 TTTTTCTTTTTTTTTTCTTTTTTTTTCTTCTTTTGCTTCTTTTCTTT
1 TTTTTCTTTTTGATTTCTTGTTCTTTCTTCTTTTCCTTCTTTTCTCT
55615 TTTTTCTT
1 TTTTTCTT
55623 GATTGGATCT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
47 28 0.61
48 18 0.39
ACGTcount: A:0.01, C:0.15, G:0.04, T:0.80
Consensus pattern (47 bp):
TTTTTCTTTTTGATTTCTTGTTCTTTCTTCTTTTCCTTCTTTTCTCT
Found at i:55593 original size:42 final size:40
Alignment explanation
Indices: 55534--55619 Score: 102
Period size: 42 Copynumber: 2.1 Consensus size: 40
55524 TTCTTTTTGA
* *
55534 TTTTTGTTCTTTCTTTTT-TTCCTTTTGTTTCTCTTTTTTCTT
1 TTTTTGTTCTTTCTTTTTCTT-CTTTTGCTTCT-TTTCTT-TT
* *
55576 TTTTTTTTCTTTTTTTTTCTTCTTTTGCTTCTTTTCTTTT
1 TTTTTGTTCTTTCTTTTTCTTCTTTTGCTTCTTTTCTTTT
55616 TTTT
1 TTTT
55620 CTTGATTGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
40 6 0.15
41 5 0.13
42 26 0.67
43 2 0.05
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.81
Consensus pattern (40 bp):
TTTTTGTTCTTTCTTTTTCTTCTTTTGCTTCTTTTCTTTT
Found at i:55596 original size:28 final size:28
Alignment explanation
Indices: 55521--55619 Score: 85
Period size: 27 Copynumber: 3.5 Consensus size: 28
55511 TTTTTGTCCC
** *
55521 TTTTTCTTTTTGATT-TTTGTTCTTTCTT
1 TTTTTCTTTTTTTTTCTTTTTTCTTT-TT
*
55549 TTTTTCCTTTTGTTTCTCTTTTTTCTTTTT
1 TTTTT-CTTTT-TTTTTCTTTTTTCTTTTT
* **
55579 TTTTTCTTTTTTTTTCTTCTTT-TGCTT
1 TTTTTCTTTTTTTTTCTTTTTTCTTTTT
*
55606 CTTTTCTTTTTTTT
1 TTTTTCTTTTTTTT
55620 CTTGATTGGA
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
27 16 0.27
28 15 0.25
29 10 0.17
30 9 0.15
31 9 0.15
ACGTcount: A:0.01, C:0.14, G:0.04, T:0.81
Consensus pattern (28 bp):
TTTTTCTTTTTTTTTCTTTTTTCTTTTT
Found at i:55622 original size:9 final size:9
Alignment explanation
Indices: 55521--55622 Score: 75
Period size: 9 Copynumber: 10.9 Consensus size: 9
55511 TTTTTGTCCC
55521 TTTTTCTTT
1 TTTTTCTTT
55530 TTGATTT-TTGT
1 TT--TTTCTT-T
*
55541 TCTTTCTTT
1 TTTTTCTTT
*
55550 TTTTCCTTT
1 TTTTTCTTT
55559 TGTTTCTCTTT
1 T-TTT-TCTTT
55570 TTTCTT-TTT
1 TTT-TTCTTT
55579 TTTTTCTTTT
1 TTTTTC-TTT
*
55589 TTTTTCTTC
1 TTTTTCTTT
*
55598 TTTTGC-TT
1 TTTTTCTTT
*
55606 CTTTTCTTT
1 TTTTTCTTT
55615 TTTTTCTT
1 TTTTTCTT
55623 GATTGGATCT
Statistics
Matches: 73, Mismatches: 10, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
8 7 0.10
9 36 0.49
10 19 0.26
11 11 0.15
ACGTcount: A:0.01, C:0.15, G:0.04, T:0.80
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:60257 original size:29 final size:30
Alignment explanation
Indices: 60190--60257 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
60180 AGTAATATGA
*
60190 AAATAT-AATATAATATAAATAAAAAAACC
1 AAATATAAAAATAATATAAATAAAAAAACC
* * * *
60219 AAAAACAAAAATAA-ATAAATATATAAACC
1 AAATATAAAAATAATATAAATAAAAAAACC
60248 AAATATAAAA
1 AAATATAAAA
60258 GTATACATAT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
29 25 0.81
30 6 0.19
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (30 bp):
AAATATAAAAATAATATAAATAAAAAAACC
Found at i:60449 original size:19 final size:19
Alignment explanation
Indices: 60418--60455 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
60408 GTGTATATAT
*
60418 ATATATATATAAATAATAA
1 ATATATATATAAAAAATAA
60437 ATATAGTAT-TAAAAAATAA
1 ATATA-TATATAAAAAATAA
60456 CCAAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
ATATATATATAAAAAATAA
Found at i:61033 original size:37 final size:37
Alignment explanation
Indices: 60984--61088 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
60974 GTGCTTGTGG
* * *
60984 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
61021 ATCTTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
61058 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
61089 GACGAAAAGG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:62780 original size:10 final size:9
Alignment explanation
Indices: 62734--62856 Score: 84
Period size: 10 Copynumber: 12.8 Consensus size: 9
62724 GGCTGCTGGA
62734 AACCGGTTT
1 AACCGGTTT
62743 AACCGGTTTT
1 AACCGG-TTT
*
62753 CAACCAGTTCT
1 -AACCGGTT-T
*
62764 GACCGGTTT
1 AACCGGTTT
*
62773 CAACCGGTTCG
1 -AACCGGTT-T
62784 AACCGGTTT
1 AACCGGTTT
* *
62793 GACCGGTCTG
1 AACCGGT-TT
62803 AACCGGTTT
1 AACCGGTTT
* *
62812 GACCGGTCTG
1 AACCGGT-TT
62822 AACCGGTTT
1 AACCGGTTT
* *
62831 GACCGGTCTG
1 AACCGGT-TT
62841 AACCGGTTT
1 AACCGGTTT
*
62850 GACCGGT
1 AACCGGT
62857 CTGACCCGAC
Statistics
Matches: 87, Mismatches: 19, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
9 34 0.39
10 47 0.54
11 6 0.07
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.28
Consensus pattern (9 bp):
AACCGGTTT
Found at i:62799 original size:19 final size:19
Alignment explanation
Indices: 62761--62860 Score: 159
Period size: 19 Copynumber: 5.3 Consensus size: 19
62751 TTCAACCAGT
*
62761 TCTG-ACCGGTTTCAACCGG
1 TCTGAACCGGTTT-GACCGG
62780 T-TCGAACCGGTTTGACCGG
1 TCT-GAACCGGTTTGACCGG
62799 TCTGAACCGGTTTGACCGG
1 TCTGAACCGGTTTGACCGG
62818 TCTGAACCGGTTTGACCGG
1 TCTGAACCGGTTTGACCGG
62837 TCTGAACCGGTTTGACCGG
1 TCTGAACCGGTTTGACCGG
62856 TCTGA
1 TCTGA
62861 CCCGACCCGA
Statistics
Matches: 77, Mismatches: 1, Indels: 6
0.92 0.01 0.07
Matches are distributed among these distances:
18 1 0.01
19 67 0.87
20 9 0.12
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.27
Consensus pattern (19 bp):
TCTGAACCGGTTTGACCGG
Found at i:62861 original size:9 final size:9
Alignment explanation
Indices: 62785--62862 Score: 93
Period size: 9 Copynumber: 8.3 Consensus size: 9
62775 ACCGGTTCGA
*
62785 ACCGGTTTG
1 ACCGGTCTG
62794 ACCGGTCTG
1 ACCGGTCTG
*
62803 AACCGGTTTG
1 -ACCGGTCTG
62813 ACCGGTCTG
1 ACCGGTCTG
*
62822 AACCGGTTTG
1 -ACCGGTCTG
62832 ACCGGTCTG
1 ACCGGTCTG
*
62841 AACCGGTTTG
1 -ACCGGTCTG
62851 ACCGGTCTG
1 ACCGGTCTG
62860 ACC
1 ACC
62863 CGACCCGACC
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
9 35 0.59
10 24 0.41
ACGTcount: A:0.15, C:0.28, G:0.31, T:0.26
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:62869 original size:5 final size:5
Alignment explanation
Indices: 62859--62911 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
62849 TGACCGGTCT
* *
62859 GACCC GACCC GACCATT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
62908 GACC
1 GACC
62912 GTTGACCGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.21, C:0.51, G:0.21, T:0.08
Consensus pattern (5 bp):
GACCC
Found at i:62880 original size:17 final size:17
Alignment explanation
Indices: 62858--62918 Score: 68
Period size: 17 Copynumber: 3.3 Consensus size: 17
62848 TTGACCGGTC
62858 TGACCCGACCCGACCAT
1 TGACCCGACCCGACCAT
62875 TGACCCGACCCGACCCGACCGT
1 TGACCCGACCCGA-CC-A---T
*
62897 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCAT
62914 TGACC
1 TGACC
62919 GTTGACCATT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
17 19 0.50
18 2 0.05
19 1 0.03
21 2 0.05
22 14 0.37
ACGTcount: A:0.20, C:0.48, G:0.21, T:0.11
Consensus pattern (17 bp):
TGACCCGACCCGACCAT
Found at i:62884 original size:22 final size:22
Alignment explanation
Indices: 62859--62911 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
62849 TGACCGGTCT
62859 GACCCGACCCGACCATTGACCC
1 GACCCGACCCGACCATTGACCC
*
62881 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCATTGACCC
62903 GACCCGACC
1 GACCCGACC
62912 GTTGACCGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.21, C:0.51, G:0.21, T:0.08
Consensus pattern (22 bp):
GACCCGACCCGACCATTGACCC
Found at i:62918 original size:7 final size:7
Alignment explanation
Indices: 62908--62938 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
62898 GACCCGACCC
62908 GACCGTT
1 GACCGTT
62915 GACCGTT
1 GACCGTT
*
62922 GACCATT
1 GACCGTT
62929 GACCGTT
1 GACCGTT
62936 GAC
1 GAC
62939 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:63860 original size:18 final size:18
Alignment explanation
Indices: 63837--63872 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
63827 CCTATCCTTA
63837 AGTCGGCTTTCTTTTTGC
1 AGTCGGCTTTCTTTTTGC
63855 AGTCGGCTTTCTTTTTGC
1 AGTCGGCTTTCTTTTTGC
63873 TATGTGCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.06, C:0.22, G:0.22, T:0.50
Consensus pattern (18 bp):
AGTCGGCTTTCTTTTTGC
Found at i:70134 original size:19 final size:19
Alignment explanation
Indices: 70060--70151 Score: 89
Period size: 19 Copynumber: 4.7 Consensus size: 19
70050 GGCTGCTGGA
*
70060 AACCGGTTTAACCGGTTTTC-
1 AACCGGTTTGACCGG--TTCG
*
70080 AACCGGTTTGATCGGTTCTG
1 AACCGGTTTGACCGGTTC-G
* *
70100 -ATCGGTTTCAACCGGTTCG
1 AACCGGTTT-GACCGGTTCG
*
70119 AACCGGTTTGACCGGTCCG
1 AACCGGTTTGACCGGTTCG
70138 AACCGGTTTGACCG
1 AACCGGTTTGACCG
70152 TTCTGACCTG
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
18 3 0.05
19 30 0.50
20 27 0.45
ACGTcount: A:0.17, C:0.26, G:0.27, T:0.29
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:70134 original size:29 final size:29
Alignment explanation
Indices: 70060--70134 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
70050 GGCTGCTGGA
* *
70060 AACCGGTTTAACCGGTTTTCAACCGGTTTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCG
* *
70090 -ATCGGTTCTGATCGGTTTCAACCGGTTCG
1 AACCGGTT-TGACCGGTTTCAACCGGTTCG
70119 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
70135 CCGAACCGGT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
29 26 0.70
30 11 0.30
ACGTcount: A:0.17, C:0.24, G:0.27, T:0.32
Consensus pattern (29 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCG
Found at i:70145 original size:39 final size:39
Alignment explanation
Indices: 70060--70151 Score: 100
Period size: 39 Copynumber: 2.4 Consensus size: 39
70050 GGCTGCTGGA
* *
70060 AACCGGTTTAACCGGTTTTCAACCGGTTTGATCGGTTCTG
1 AACCGGTTTAACCGG-TTTCAACCGGTTTGACCGGTTCCG
*
70100 -ATCGGTTTCAACCGG-TTCGAACCGGTTTGACCGG-TCCG
1 AACCGGTTT-AACCGGTTTC-AACCGGTTTGACCGGTTCCG
*
70138 AACCGGTTTGACCG
1 AACCGGTTTAACCG
70152 TTCTGACCTG
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
38 10 0.23
39 28 0.64
40 6 0.14
ACGTcount: A:0.17, C:0.26, G:0.27, T:0.29
Consensus pattern (39 bp):
AACCGGTTTAACCGGTTTCAACCGGTTTGACCGGTTCCG
Found at i:70181 original size:22 final size:22
Alignment explanation
Indices: 70156--70198 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
70146 TGACCGTTCT
* * *
70156 GACCTGACCCGATCGTTGACCC
1 GACCCGACCCGACCATTGACCC
70178 GACCCGACCCGACCATTGACC
1 GACCCGACCCGACCATTGACC
70199 GTTGACTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.44, G:0.21, T:0.14
Consensus pattern (22 bp):
GACCCGACCCGACCATTGACCC
Found at i:72920 original size:24 final size:25
Alignment explanation
Indices: 72888--72934 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
72878 TCTTCCAAAT
72888 GATGTAT-AAAACATCTATGTACAA
1 GATGTATAAAAACATCTATGTACAA
72912 GATGTATAAAAACATCTATGTAC
1 GATGTATAAAAACATCTATGTAC
72935 CATATCATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.30
Consensus pattern (25 bp):
GATGTATAAAAACATCTATGTACAA
Found at i:80361 original size:43 final size:43
Alignment explanation
Indices: 80313--80801 Score: 692
Period size: 43 Copynumber: 11.3 Consensus size: 43
80303 AATGGATTAA
* * *
80313 TTACAGTTTCCCCATGTTCATTTGTTGTGTGAAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCC
* * *
80356 TTACAGTTTCCCCAAGTTCGTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCC
* *
80399 TTACAATTTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTT-CCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCC
* * *
80443 TTACAGTTTCCCCAAGTTCCTTTGTTGTATGCAAGGATAAGCC
1 TTACAGTTTCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCC
* * **
80486 TTACAGTTTCCCCATGTTTCTTTACTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCC
* * *
80529 TTACAGTTTCCCCAAGTTCCTTTGCTGTGTACAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCC
*
80572 TTACAGTTTCCCCATGTTCCTTTGTTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCC
* * *
80615 TTACAGCTTCCTCAGGTTCCTTTGTTGTGCT-CAAGGATAAGCC
1 TTACAGTTTCCCCAGGTTCCTTTGTTGTG-TGCAAGGGTAAGCC
*
80658 TTACAGTTTTCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCC
* *
80701 TTATAGTTTCCCCTAGGTTCCTTTGATGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCC-AGGTTCCTTTGTTGTGTGCAAGGGTAAGCC
* * *
80745 TTACAGTTTCCTCAGGTTCCTTTGTTGTGTGAAAGGGTAGGCC
1 TTACAGTTTCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCC
80788 TTACAGTTTCCCCA
1 TTACAGTTTCCCCA
80802 AGCTCTTTTT
Statistics
Matches: 400, Mismatches: 42, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
42 1 0.00
43 318 0.80
44 81 0.20
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (43 bp):
TTACAGTTTCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCC
Found at i:80746 original size:173 final size:172
Alignment explanation
Indices: 80313--80803 Score: 750
Period size: 173 Copynumber: 2.8 Consensus size: 172
80303 AATGGATTAA
* * *
80313 TTACAGTTTCCCCATGTTCATTTGTTGTGTGAAAGGGTAAGCCTTACAGTTTCCCCAAGTTCGTT
1 TTACAGTTTCCCCATGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGTTCCTT
* *
80378 TGCTGTGTGCAAGGGTAAGCCTTACAATTTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
66 TGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCC
80443 TTACAGTTTCCCCAAGTTCCTTTGTTGTATGCAAGGATAAGCC
130 TTACAGTTTCCCCAAGTTCCTTTGTTGTATGCAAGGATAAGCC
* **
80486 TTACAGTTTCCCCATGTTTCTTTACTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGTTCCTT
1 TTACAGTTTCCCCATGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGTTCCTT
* *
80551 TGCTGTGTACAAGGGTAAGCCTTACAGTTTCCCCATGTTCCTTTGTTGTGTGCAAGGGTAAGCCT
66 TGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCT
* * * *
80616 TACAGCTTCCTCAGGTTCCTTTGTTGTGCT-CAAGGATAAGCC
131 TACAGTTTCCCCAAGTTCCTTTGTTGT-ATGCAAGGATAAGCC
* * * *
80658 TTACAGTTTTCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTATAGTTTCCCCTAGGTTCCT
1 TTACAGTTTCCCCATGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC-AAGTTCCT
* * * *
80723 TTGATGTGTGCAAGGGTAAGCCTTACAGTTTCCTCAGGTTCCTTTGTTGTGTGAAAGGGTAGGCC
65 TTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCC
80788 TTACAGTTTCCCCAAG
130 TTACAGTTTCCCCAAG
80804 CTCTTTTTCT
Statistics
Matches: 286, Mismatches: 30, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
172 119 0.42
173 167 0.58
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (172 bp):
TTACAGTTTCCCCATGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGTTCCTT
TGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCT
TACAGTTTCCCCAAGTTCCTTTGTTGTATGCAAGGATAAGCC
Found at i:80864 original size:130 final size:129
Alignment explanation
Indices: 80313--80840 Score: 716
Period size: 130 Copynumber: 4.1 Consensus size: 129
80303 AATGGATTAA
* * * *
80313 TTACAGTTTCCCCATGTTCATTTGTTGTGTGAAAGGGTAAGCCTTACAGTTTCCCCAAGTTCGTT
1 TTACAGTTTCCCCATGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTT
* * *
80378 TGCTGTGTGCAAGGGTAAGCCTTACAATTTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
66 TGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CCCCAAGTTCCTTTGCTGTGTACAAGGGTAAGCC
* * * * *
80443 TTACAGTTTCCCCAAGTTCCTTTGTTGTATGCAAGGATAAGCCTTACAGTTTCCCCATGTTTCTT
1 TTACAGTTTCCCCATGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTT
*
80508 TACTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGTTCCTTTGCTGTGTACAAGGGTAAGCC
66 TGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGTTCCTTTGCTGTGTACAAGGGTAAGCC
* *
80572 TTACAGTTTCCCCATGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGCTTCCTCAGGTTCCTT
1 TTACAGTTTCCCCATGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTT
* * * * * *
80637 TGTTGTGCT-CAAGGATAAGCCTTACAGTTTTCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCC
66 TGCTGTG-TGCAAGGGTAAGCCTTACAGTTTCCCCAAGTTCCTTTGCTGTGTACAAGGGTAAGCC
* * * *
80701 TTATAGTTTCCCCTAGGTTCCTTTGATGTGTGCAAGGGTAAGCCTTACAGTTTCCTCAGGTTCCT
1 TTACAGTTTCCCC-ATGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCT
* * * * * * *
80766 TTGTTGTGTGAAAGGGTAGGCCTTACAGTTTCCCCAAGCTCTTTTTCTATGTACAAGGGTAAGAC
65 TTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGTTCCTTTGCTGTGTACAAGGGTAAG-C
80831 C
129 C
*
80832 TTACCGTTT
1 TTACAGTTT
80841 TTACATGCTC
Statistics
Matches: 351, Mismatches: 43, Indels: 7
0.88 0.11 0.02
Matches are distributed among these distances:
129 158 0.45
130 184 0.52
131 9 0.03
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (129 bp):
TTACAGTTTCCCCATGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTT
TGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGTTCCTTTGCTGTGTACAAGGGTAAGCC
Found at i:91221 original size:23 final size:23
Alignment explanation
Indices: 91190--91234 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
91180 AAGGATTAAC
*
91190 TGATTTTATGGTAAGAAATTTGA
1 TGATGTTATGGTAAGAAATTTGA
*
91213 TGATGTTATTGTAAGAAATTTG
1 TGATGTTATGGTAAGAAATTTG
91235 TTGCATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (23 bp):
TGATGTTATGGTAAGAAATTTGA
Found at i:92765 original size:37 final size:36
Alignment explanation
Indices: 92690--92765 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
92680 TTTTTATATT
*
92690 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
92726 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
92763 TTT
1 TTT
92766 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:96968 original size:18 final size:18
Alignment explanation
Indices: 96941--97001 Score: 51
Period size: 18 Copynumber: 3.6 Consensus size: 18
96931 ACTTAGATTT
*
96941 ATTTTTATTTTTACATTC
1 ATTTTCATTTTTACATTC
96959 ATTTTCATTTCTGT-C-TTC
1 ATTTTCATTT-T-TACATTC
*
96977 ATATTCA---TTACATTC
1 ATTTTCATTTTTACATTC
96992 ATTTTCATTT
1 ATTTTCATTT
97002 CCATCTTCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 14
0.66 0.06 0.28
Matches are distributed among these distances:
13 1 0.03
14 2 0.06
15 9 0.27
18 18 0.55
19 2 0.06
20 1 0.03
ACGTcount: A:0.21, C:0.16, G:0.02, T:0.61
Consensus pattern (18 bp):
ATTTTCATTTTTACATTC
Found at i:97152 original size:49 final size:49
Alignment explanation
Indices: 97091--97186 Score: 174
Period size: 49 Copynumber: 2.0 Consensus size: 49
97081 AAATGCATTT
*
97091 TATGAGAGATGATTATGAATTTTCACAAGTCAAATTTCTTTTTGAAATG
1 TATGAGAGATGATTATGAATTTTCACAAGTCAAATTTCTTTTCGAAATG
*
97140 TATGAGATATGATTATGAATTTTCACAAGTCAAATTTCTTTTCGAAA
1 TATGAGAGATGATTATGAATTTTCACAAGTCAAATTTCTTTTCGAAA
97187 GCTCTGAACG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (49 bp):
TATGAGAGATGATTATGAATTTTCACAAGTCAAATTTCTTTTCGAAATG
Found at i:98239 original size:51 final size:51
Alignment explanation
Indices: 98133--98241 Score: 141
Period size: 51 Copynumber: 2.2 Consensus size: 51
98123 CCGGAAAATT
* *
98133 CGGGTA-CCGATTGTCGGGACACAAACCGACAAATCAACTACCCGAATATC
1 CGGGTACCCGATTGTCGGGACACAAACCGACAAATCAACTACCCAAAGATC
* ***
98183 CGGGTACCCGGTTGTCGGGACACGGGCCGACAAATCAACTACCCAAAGA-C
1 CGGGTACCCGATTGTCGGGACACAAACCGACAAATCAACTACCCAAAGATC
98233 CTGGGTACC
1 C-GGGTACC
98242 TGGATTTGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
50 8 0.16
51 43 0.84
ACGTcount: A:0.29, C:0.31, G:0.25, T:0.15
Consensus pattern (51 bp):
CGGGTACCCGATTGTCGGGACACAAACCGACAAATCAACTACCCAAAGATC
Found at i:98788 original size:98 final size:95
Alignment explanation
Indices: 98696--98870 Score: 226
Period size: 98 Copynumber: 1.8 Consensus size: 95
98686 TTAACTTATG
* *
98696 AAATATATTTTATTATTATCTTAACTAAAATTTTATATTTTAATCATATCTTAA-TTTCAAAAAC
1 AAATATATTTTATTATTACCTTAACTAAAA-TATATATTTTAATCATATCTTAACTTT-AAAAA-
*
98760 TTTTTTTGTTATTTTAAACTCATCTTAACTTTAA
63 TTTTATT-TTATTTTAAACTCATCTTAACTTTAA
* * * * * *
98794 AAATATTTTTTATTCTTACCTTAACTTAAATATATATTTTATTCTTATCTTAACTTTTAAAATTT
1 AAATATATTTTATTATTACCTTAACTAAAATATATATTTTAATCATATCTTAACTTTAAAAATTT
98859 TATTTTATTTTA
66 TATTTTATTTTA
98871 TTTTTATCTT
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
95 8 0.12
96 6 0.09
97 24 0.36
98 29 0.43
ACGTcount: A:0.35, C:0.10, G:0.01, T:0.55
Consensus pattern (95 bp):
AAATATATTTTATTATTACCTTAACTAAAATATATATTTTAATCATATCTTAACTTTAAAAATTT
TATTTTATTTTAAACTCATCTTAACTTTAA
Found at i:98977 original size:35 final size:30
Alignment explanation
Indices: 98781--99018 Score: 168
Period size: 30 Copynumber: 7.8 Consensus size: 30
98771 TTTTAAACTC
*
98781 ATCTTAACTTTAAAA-ATATTTTTTATTCTT
1 ATCTTAAC-TTAAAATATATATTTTATTCTT
*
98811 ACCTTAACTT-AAATATATATTTTATTCTT
1 ATCTTAACTTAAAATATATATTTTATTCTT
* *
98840 ATCTTAACTTTTAAAATTTTATTTTATTTTATTTTT
1 ATCTTAAC--TTAAAA---TA-TATATTTTATTCTT
** * * *
98876 ATCTTAACTTATTACATTTATTATATTCTT
1 ATCTTAACTTAAAATATATATTTTATTCTT
** * *
98906 AAATTAAATTATTAAATATATA--CTATTCTT
1 ATCTTAACTTA--AAATATATATTTTATTCTT
* *
98936 ACCTTAAATTATTAAATAT-T-TTTTATTCTT
1 ATCTTAACTTA--AAATATATATTTTATTCTT
98966 AT-TGTAACTTAAAATATATATTTTATTCTT
1 ATCT-TAACTTAAAATATATATTTTATTCTT
*
98996 ATCTTAACTTAAAAAAT-TATTTT
1 ATCTTAACTTAAAATATATATTTT
99019 TACTTTTATT
Statistics
Matches: 168, Mismatches: 24, Indels: 33
0.75 0.11 0.15
Matches are distributed among these distances:
28 9 0.05
29 32 0.19
30 89 0.53
31 4 0.02
32 8 0.05
34 4 0.02
35 2 0.01
36 20 0.12
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.55
Consensus pattern (30 bp):
ATCTTAACTTAAAATATATATTTTATTCTT
Found at i:100880 original size:21 final size:21
Alignment explanation
Indices: 100856--100926 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
100846 GAAAAACAGA
100856 AAATAAAATTAATAAAATAAT
1 AAATAAAATTAATAAAATAAT
* *
100877 AAATAGTAA-TAATAATATAAT
1 AAATA-AAATTAATAAAATAAT
*
100898 GAAATAATATT-ATAAATATAAT
1 -AAATAAAATTAATAAA-ATAAT
*
100920 ATATAAA
1 AAATAAA
100927 TAATATATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
21 26 0.67
22 13 0.33
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (21 bp):
AAATAAAATTAATAAAATAAT
Found at i:100890 original size:16 final size:16
Alignment explanation
Indices: 100871--100928 Score: 52
Period size: 16 Copynumber: 3.7 Consensus size: 16
100861 AAATTAATAA
100871 AATAATAAATAGTAAT
1 AATAATAAATAGTAAT
*
100887 AATAATATAAT-GAAAT
1 AATAATA-AATAGTAAT
100903 AATATTATAAATA-TAAT
1 AATA--ATAAATAGTAAT
100920 -AT-ATAAATA
1 AATAATAAATA
100929 ATATATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
13 7 0.19
16 17 0.47
17 9 0.25
18 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (16 bp):
AATAATAAATAGTAAT
Found at i:100903 original size:13 final size:12
Alignment explanation
Indices: 100866--101106 Score: 95
Period size: 12 Copynumber: 19.1 Consensus size: 12
100856 AAATAAAATT
*
100866 AATAAAATAATA
1 AATAATATAATA
*
100878 AAT-A-GTAAT-
1 AATAATATAATA
100887 AATAATATAATGA
1 AATAATATAAT-A
*
100900 AATAATATTATA
1 AATAATATAATA
100912 AAT-ATAATATATA
1 AATAAT-ATA-ATA
100925 AATAATATATATA
1 AATAATATA-ATA
100938 TATATAA-ACTAATA
1 -A-ATAATA-TAATA
*
100952 TATAATATATACTA
1 AATAATATA-A-TA
100966 AATATATATATATA
1 AATA-ATATA-ATA
* *
100980 TATAATATTATA
1 AATAATATAATA
*
100992 TATAATAATAAT-
1 AATAAT-ATAATA
101004 AATAATATTATATA
1 AATAATA-TA-ATA
* *
101018 TAATTATATACTA
1 -AATAATATAATA
* *
101031 TATCATATAATA
1 AATAATATAATA
* *
101043 TACAATAT-ATA
1 AATAATATAATA
*
101054 ATATACTATACTATA
1 A-ATAATATA--ATA
101069 ATATATATATATATA
1 A-ATA-ATATA-ATA
*
101084 TATAATATAAT-
1 AATAATATAATA
101095 -ATAATATAATA
1 AATAATATAATA
101106 A
1 A
101107 TGTACCATAA
Statistics
Matches: 181, Mismatches: 22, Indels: 52
0.71 0.09 0.20
Matches are distributed among these distances:
9 3 0.02
10 15 0.08
11 11 0.06
12 53 0.29
13 42 0.23
14 22 0.12
15 31 0.17
16 4 0.02
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (12 bp):
AATAATATAATA
Found at i:100934 original size:2 final size:2
Alignment explanation
Indices: 100904--101102 Score: 145
Period size: 2 Copynumber: 107.5 Consensus size: 2
100894 TAATGAAATA
* *
100904 AT AT -T AT AA AT AT A- AT AT AT AA AT A- 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
* *
100943 AA ACT A- AT AT AT A- AT AT AT ACT AA AT AT AT AT AT AT AT AT A-
1 AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
100984 AT AT -T AT AT AT A- AT A- AT A- AT A- AT A- AT AT -T 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
*
101019 A- AT -T AT AT ACT AT AT CAT AT A- AT AT AC A- AT AT AT A- AT AT
1 AT AT AT AT AT A-T AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
101058 ACT AT ACT AT A- AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT A-
1 A-T AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
101098 AT AT A
1 AT AT A
101103 ATAATGTACC
Statistics
Matches: 160, Mismatches: 9, Indels: 56
0.71 0.04 0.25
Matches are distributed among these distances:
1 22 0.14
2 127 0.79
3 11 0.07
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:101103 original size:34 final size:34
Alignment explanation
Indices: 100878--101105 Score: 188
Period size: 36 Copynumber: 6.6 Consensus size: 34
100868 TAAAATAATA
*
100878 AATAGTAATAATAATATAATGAAATA-ATAT-TATA-
1 AATA-TAAT-ATAATATAAT-ATATATATATATATAT
* *
100912 AATATAATATATAAATAATATATATATATATAAACT
1 AATATAATATA-ATATAATATATATATATATATA-T
100948 AATAT-ATAATATATACTAA-ATATATATATATATAT
1 AATATAAT-ATA-ATA-TAATATATATATATATATAT
100983 AATATTATATATAATAATAATA-ATA-ATATTATATAT
1 AATA-TA-ATATAAT-ATAATATATATATA-TATATAT
* *
101019 AAT-T-ATATACTAT-ATCATATAATATACAATATAT
1 AATATAATATAATATAAT-ATAT-ATATA-TATATAT
* *
101053 AATATACTATACTATAATATATATATATATATAT
1 AATATAATATAATATAATATATATATATATATAT
101087 AATATAATATAATATAATA
1 AATATAATATAATATAATA
101106 ATGTACCATA
Statistics
Matches: 162, Mismatches: 12, Indels: 40
0.76 0.06 0.19
Matches are distributed among these distances:
30 2 0.01
31 3 0.02
32 15 0.09
33 15 0.09
34 43 0.27
35 16 0.10
36 56 0.35
37 10 0.06
38 2 0.01
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (34 bp):
AATATAATATAATATAATATATATATATATATAT
Found at i:101317 original size:29 final size:29
Alignment explanation
Indices: 101270--101326 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
101260 TGATTCGTGT
* * * *
101270 TGTATATATTATTATTAAATTATTTAAAA
1 TGTATATACTATGAATAAATTAGTTAAAA
101299 TGTATATACTATGAATAAATTAGTTAAA
1 TGTATATACTATGAATAAATTAGTTAAA
101327 TTTTAATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (29 bp):
TGTATATACTATGAATAAATTAGTTAAAA
Found at i:106136 original size:8 final size:8
Alignment explanation
Indices: 106124--106212 Score: 63
Period size: 8 Copynumber: 11.1 Consensus size: 8
106114 TAATTCTTCG
106124 ACTCTTAA
1 ACTCTTAA
*
106132 TCTCTTAA
1 ACTCTTAA
106140 ACTCTTAA
1 ACTCTTAA
** *
106148 GTTCTCAA
1 ACTCTTAA
*
106156 ACTCTCAA
1 ACTCTTAA
*
106164 ACTCTGAA
1 ACTCTTAA
* *
106172 ACTATCAA
1 ACTCTTAA
*
106180 ACTCTCAA
1 ACTCTTAA
*
106188 ACT-TTCGA
1 ACTCTT-AA
106196 ACTCTTAA
1 ACTCTTAA
*
106204 ATTCTTAA
1 ACTCTTAA
106212 A
1 A
106213 ATGACTCATA
Statistics
Matches: 64, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
7 1 0.02
8 61 0.95
9 2 0.03
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (8 bp):
ACTCTTAA
Found at i:107514 original size:43 final size:43
Alignment explanation
Indices: 107403--107795 Score: 442
Period size: 43 Copynumber: 9.2 Consensus size: 43
107393 TGAGAACAAA
* * *
107403 AAACACCGCAATAGGTCATATCTATTA-CGGCGTTTTT-GA-AC
1 AAACGCCGCAAAAGGTCAGATCTA-TAGCGGCGTTTTTGGATAC
* *
107444 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGA-AT
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGATAC
* * * * *
107487 AAACGCCGCACAAA-GTTATGATATATAGCGGCGTTTCTAGA-AA
1 AAACGCCGCA-AAAGGTCA-GATCTATAGCGGCGTTTTTGGATAC
*
107530 AAACGCCGCAAAATGTCAGATCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
* * * *
107573 AAACGCCGCAAAAGATAAGACCTATA-CTGGCGTTTTTAGA-AC
1 AAACGCCGCAAAAGGTCAGATCTATAGC-GGCGTTTTTGGATAC
* * * *
107615 AAACGCCGTAAAAGGTCATACCTATAGCGGCGTTTTTGGACAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
* * * *
107658 AAACACCGCAAAAGGTCAGATATATAGCGGCATTTTTTGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
*
107701 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGACAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
* * *
107744 AAACGTCGCAAAAGGTCGGATATATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
107787 AAACGCCGC
1 AAACGCCGC
107796 TAATTACCAT
Statistics
Matches: 300, Mismatches: 42, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
41 17 0.06
42 76 0.25
43 204 0.68
44 3 0.01
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
Found at i:110464 original size:43 final size:40
Alignment explanation
Indices: 110368--110750 Score: 267
Period size: 40 Copynumber: 9.4 Consensus size: 40
110358 TTTGCGGTAC
* * ** *
110368 AAACGCCACTAAAGTACGAGTCTTTTGCGGTGTTTTTAT-A
1 AAACGCCACTAAAGTACGAGT-TATAGCGACGTTTGTATAA
* * *
110408 AAACACCACTAAAGTACAAGTCTATAGCGACGTTTGTAAACAA
1 AAACGCCACTAAAGTACGAGT-TATAGCGACGTTTGT--ATAA
* *
110451 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTAAACAA
1 AAACGCCACTAAAGTACGAGT-TATAGCGACGTTTGT--ATAA
* *
110494 AAACGCCACTAAAGTAAGAGTTATAGC-AGCGTTTTTATAA
1 AAACGCCACTAAAGTACGAGTTATAGCGA-CGTTTGTATAA
* * *
110534 AAACACCAGTAAAGTATGAGTTATAGC-AGCGCTTT-TATAA
1 AAACGCCACTAAAGTACGAGTTATAGCGA-CG-TTTGTATAA
* *
110574 AAACGCCACTAAAGTACGAGTTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTTATAGCGACGTTTGTATAA
* * * * * * *
110614 AAACGCCCCTAAAGAACGATTCTATACCGGCATTTGTGTAA
1 AAACGCCACTAAAGTACGAGT-TATAGCGACGTTTGTATAA
** * * *
110655 AAACGCCACTACAA-TATTAATCTTTAGC-AGCGTTTGTATAC
1 AAACGCCACTA-AAGTACGAGT-TATAGCGA-CGTTTGTATAA
* * * * *
110696 AAACGCCACTAAAGTAAGA-TCTTTTGCGGCGTTTGTATAC
1 AAACGCCACTAAAGTACGAGT-TATAGCGACGTTTGTATAA
*
110736 AAACGCCTCTAAAGT
1 AAACGCCACTAAAGT
110751 TAGGTTTTTT
Statistics
Matches: 285, Mismatches: 46, Indels: 24
0.80 0.13 0.07
Matches are distributed among these distances:
39 3 0.01
40 148 0.52
41 58 0.20
42 15 0.05
43 61 0.21
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (40 bp):
AAACGCCACTAAAGTACGAGTTATAGCGACGTTTGTATAA
Found at i:110700 original size:122 final size:121
Alignment explanation
Indices: 110449--110750 Score: 335
Period size: 122 Copynumber: 2.5 Consensus size: 121
110439 GTTTGTAAAC
* *
110449 AAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTAAACAAAAACGCCACTAAAGTAAGAG
1 AAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGT--ATAAAAACGCCACTAAAGTAAGAG
* * * * *
110514 TTATAGCAGCGTTTTTATAAAAACACCAGTAAAGTATGAGTTATAGCAGCGCTTTTAT
64 TTATACCAGCATTTGTATAAAAACACCACTAAAGTATGAATTATAGCAGCGCTTTTAT
* *
110572 AAAAACGCCACTAAAGTACGAGT-TTTAGCGGCGTTTGTATAAAAACGCCCCTAAAG-AACGATT
1 AAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTAA-GAGT
* * * * *
110635 CTATACCGGCATTTGTGTAAAAACGCCACTACAA-TATTAATCTTTAGCAGCG-TTTGTAT
65 -TATACCAGCATTTGTATAAAAACACCACTA-AAGTATGAAT-TATAGCAGCGCTTT-TAT
* * * * *
110694 ACAAACGCCACTAAAGTAAGA-TCTTTTGCGGCGTTTGTATACAAACGCCTCTAAAGT
1 AAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAGT
110751 TAGGTTTTTT
Statistics
Matches: 153, Mismatches: 19, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
119 2 0.01
120 19 0.12
121 32 0.21
122 77 0.50
123 23 0.15
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (121 bp):
AAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTAAGAGTT
ATACCAGCATTTGTATAAAAACACCACTAAAGTATGAATTATAGCAGCGCTTTTAT
Found at i:112325 original size:31 final size:32
Alignment explanation
Indices: 112289--112377 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 32
112279 AAGGGGGCAC
* *
112289 CTTGGGGCCA-GAAAGCTTACCCAAGAAAGTT
1 CTTGGGGCCACGAAAGCCTACCCAAGAAAGAT
* *
112320 CTTGGGGCCACGGAGGCCTACCCAAGAAAGAT
1 CTTGGGGCCACGAAAGCCTACCCAAGAAAGAT
* *
112352 CTTGGGGGC-CGTATAGCCTACCCAAG
1 CTTGGGGCCACG-AAAGCCTACCCAAG
112378 GGTCACCTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
31 12 0.25
32 36 0.75
ACGTcount: A:0.27, C:0.27, G:0.29, T:0.17
Consensus pattern (32 bp):
CTTGGGGCCACGAAAGCCTACCCAAGAAAGAT
Done.