Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006363.1 Hibiscus syriacus cultivar Beakdansim tig00015265_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: 60141
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:283 original size:21 final size:22
Alignment explanation
Indices: 246--288 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
236 GACCGGATGG
246 GGAGGGTTGAGAGGTTTTTTTT
1 GGAGGGTTGAGAGGTTTTTTTT
*
268 GGAGGTTTGAGA-GTTTTTTTT
1 GGAGGGTTGAGAGGTTTTTTTT
289 AAGAAATGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.14, C:0.00, G:0.37, T:0.49
Consensus pattern (22 bp):
GGAGGGTTGAGAGGTTTTTTTT
Found at i:618 original size:22 final size:23
Alignment explanation
Indices: 593--640 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
583 TTCGAATTTC
593 TTTAATTTT-TTATTCACT-TTAT
1 TTTAATTTTGTT-TTCACTATTAT
*
615 TTT-ATTTTGTTTTCATTATTAT
1 TTTAATTTTGTTTTCACTATTAT
637 TTTA
1 TTTA
641 TTAGCTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.71
Consensus pattern (23 bp):
TTTAATTTTGTTTTCACTATTAT
Found at i:1057 original size:2 final size:2
Alignment explanation
Indices: 1050--1083 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1040 TATTTCCATA
1050 AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1084 CTCGAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4003 original size:55 final size:55
Alignment explanation
Indices: 3930--4233 Score: 430
Period size: 55 Copynumber: 5.5 Consensus size: 55
3920 AAGTAGTGCC
* * *
3930 TTCCGTGG-GTTGCACACATAGTGCATGTACAGTTATTCATCAACTCATGATGAA
1 TTCCGTGGATTTGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAA
* * * *
3984 TTCTGTAGAATTGCACACATAGTGCCTGTACGGATATTCATCAACTCATGATGAA
1 TTCCGTGGATTTGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAA
*
4039 TTCCGTGGATTTACACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAA
1 TTCCGTGGATTTGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAA
* * * *
4094 TTCCATGGATTTACACACATAGTGTCTGTATGGTTATTCATCAACTCATGATGAA
1 TTCCGTGGATTTGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAA
* * *
4149 TTCCGTGGATTTGCACATATAATGCATGTACGGTTATTCATCAACTCATGATGAA
1 TTCCGTGGATTTGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAA
* ** *
4204 TTTCGTAAATTTGCATACATAGTGCCTGTA
1 TTCCGTGGATTTGCACACATAGTGCCTGTA
4234 GTACACTTAG
Statistics
Matches: 221, Mismatches: 28, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
54 6 0.03
55 215 0.97
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (55 bp):
TTCCGTGGATTTGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAA
Found at i:4595 original size:19 final size:19
Alignment explanation
Indices: 4571--4607 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4561 TCGATACCCC
* *
4571 TACTATGGTATCGATACTA
1 TACTATAGTACCGATACTA
4590 TACTATAGTACCGATACT
1 TACTATAGTACCGATACT
4608 CCATTTCATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (19 bp):
TACTATAGTACCGATACTA
Found at i:5019 original size:22 final size:22
Alignment explanation
Indices: 4991--5038 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
4981 ATCTCTCATT
4991 TACCTCTTTGACAAGTCAAATC
1 TACCTCTTTGACAAGTCAAATC
5013 TACCTCTTTGACAAGTCAAATC
1 TACCTCTTTGACAAGTCAAATC
5035 TACC
1 TACC
5039 AGTAAACATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.31
Consensus pattern (22 bp):
TACCTCTTTGACAAGTCAAATC
Found at i:10910 original size:55 final size:55
Alignment explanation
Indices: 10804--11126 Score: 416
Period size: 55 Copynumber: 5.9 Consensus size: 55
10794 CTATAATGTA
* * * * * * *
10804 ATTCATCAATTTATGATGAATTTCGTGG-GTTGCACACATAGTGCTTTTATGGTT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTACGGTT
* * * *
10858 ATTCATCAACTCATGATGAATTCCGTAGAATTGCACACATAGTGCTTGTATGGTT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTACGGTT
* * * * * * **
10913 ATTCATCAACTCATGATGAATTCTGTGGAATTGCATACATAGTTCCTGCACAATT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTACGGTT
*
10968 ATTCATCAACTCATGATGAATTTCGTGGATTTGCACACATAGTGCATGTACGGTT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTACGGTT
* * *
11023 ATTCATCAACACATGATGAATT-TGTGGATTTGCATACATAGTGCATGTACGGTT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTACGGTT
*
11077 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTTCATGTA
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTA
11127 GTACACTAAG
Statistics
Matches: 236, Mismatches: 31, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
54 75 0.32
55 161 0.68
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.36
Consensus pattern (55 bp):
ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTACGGTT
Found at i:10933 original size:109 final size:110
Alignment explanation
Indices: 10804--11126 Score: 436
Period size: 109 Copynumber: 3.0 Consensus size: 110
10794 CTATAATGTA
* * * * * * *
10804 ATTCATCAATTTATGATGAATTTCGTGG-GTTGCACACATAGTGCTTTTATGGTTATTCATCAAC
1 ATTCATCAACTCATGATGAATTTCGTGGAATTGCATACATAGTGCATGTACGGTTATTCATCAAC
* * * *
10868 TCATGATGAATTCCGTAGAATTGCACACATAGTGCTTGTATGGTT
66 TCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTACGGTT
* * * **
10913 ATTCATCAACTCATGATGAA-TTCTGTGGAATTGCATACATAGTTCCTGCACAATTATTCATCAA
1 ATTCATCAACTCATGATGAATTTC-GTGGAATTGCATACATAGTGCATGTACGGTTATTCATCAA
*
10977 CTCATGATGAATTTCGTGGATTTGCACACATAGTGCATGTACGGTT
65 CTCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTACGGTT
* *
11023 ATTCATCAACACATGATGAATTT-GTGGATTTGCATACATAGTGCATGTACGGTTATTCATCAAC
1 ATTCATCAACTCATGATGAATTTCGTGGAATTGCATACATAGTGCATGTACGGTTATTCATCAAC
*
11087 TCATGATGAATTCCGTGGATTTGCACACATAGTTCATGTA
66 TCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTA
11127 GTACACTAAG
Statistics
Matches: 186, Mismatches: 25, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
108 3 0.02
109 95 0.51
110 86 0.46
111 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.36
Consensus pattern (110 bp):
ATTCATCAACTCATGATGAATTTCGTGGAATTGCATACATAGTGCATGTACGGTTATTCATCAAC
TCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTACGGTT
Found at i:11064 original size:164 final size:164
Alignment explanation
Indices: 10804--11121 Score: 476
Period size: 164 Copynumber: 1.9 Consensus size: 164
10794 CTATAATGTA
* * * * * *
10804 ATTCATCAATTTATGATGAATTTCGTGGGTTGCACACATAGTGCTTTTATGGTTATTCATCAACT
1 ATTCATCAACTCATGATGAATTTCGTGGGTTGCACACATAGTGCATGTACGGTTATTCATCAACA
* *
10869 CATGATGAATTCCGTAGAATTGCACACATAGTGCTTGTATGGTTATTCATCAACTCATGATGAAT
66 CATGATGAATTCCGTAGAATTGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAAT
* *
10934 TCTGTGGAATTGCATACATAGTTCCTGCACAATT
131 TCCGTGGAATTGCACACATAGTTCCTGCACAATT
*
10968 ATTCATCAACTCATGATGAATTTCGTGGATTTGCACACATAGTGCATGTACGGTTATTCATCAAC
1 ATTCATCAACTCATGATGAATTTCGTGG-GTTGCACACATAGTGCATGTACGGTTATTCATCAAC
* * * *
11033 ACATGATGAATT-TGTGGATTTGCATACATAGTGCATGTACGGTTATTCATCAACTCATGATGAA
65 ACATGATGAATTCCGTAGAATTGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAA
*
11097 TTCCGTGGATTTGCACACATAGTTC
130 TTCCGTGGAATTGCACACATAGTTC
11122 ATGTAGTACA
Statistics
Matches: 137, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
164 94 0.69
165 43 0.31
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (164 bp):
ATTCATCAACTCATGATGAATTTCGTGGGTTGCACACATAGTGCATGTACGGTTATTCATCAACA
CATGATGAATTCCGTAGAATTGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAAT
TCCGTGGAATTGCACACATAGTTCCTGCACAATT
Found at i:15068 original size:2 final size:2
Alignment explanation
Indices: 15063--15121 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
15053 ACTATATAAC
15063 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
*
15105 AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT A
15122 CTTTAAGAGA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:20857 original size:20 final size:21
Alignment explanation
Indices: 20813--20867 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
20803 AACTAAATAT
*
20813 AATAAACAATAAT-TAACCTA
1 AATAAATAATAATATAACCTA
* *
20833 TATAATTAATAATATAA-CTA
1 AATAAATAATAATATAACCTA
20853 AATAAATAACTAATA
1 AATAAATAA-TAATA
20868 ATATACATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 20 0.71
21 8 0.29
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (21 bp):
AATAAATAATAATATAACCTA
Found at i:20861 original size:12 final size:13
Alignment explanation
Indices: 20840--20872 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
20830 CTATATAATT
20840 AATAATATAACTA
1 AATAATATAACTA
20853 AATAA-ATAACT-
1 AATAATATAACTA
20864 AATAATATA
1 AATAATATA
20873 CATATATAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.26
12 9 0.47
13 5 0.26
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (13 bp):
AATAATATAACTA
Found at i:21427 original size:135 final size:134
Alignment explanation
Indices: 21110--21442 Score: 366
Period size: 134 Copynumber: 2.5 Consensus size: 134
21100 GATTCACTTT
* ** ** * *
21110 GCTGCTCTTCAGGGAAGGTTGAATCAGAA-TCAATTTACTTCGTTGCTCTTTAGGAAGACTAAAT
1 GCTGCTCTTCAAGGAAGACTGAATCA-AACTTGATTTGCTTCGTTGCTCTTTAGGAAGACCAAAT
* * * * *
21174 CTGAAAGAAGAAGAATCTGCTCCACTACTCTTTAAAGGAGATCAAACTCGAGAAAATTTTGATCC
65 ATGAAAGAAGAAGAATATGCTCCACTACTCTTTAAAGGAGATCAAACTCAAGAAAACTTGGATCC
*
21239 ACTTC
130 ACTCC
* * * *
21244 GCTGCTCTTCAGGGAAGATTGAATCAAACTTGATTTGCTTCATTGCTCTTTAGGAATACCAAATA
1 GCTGCTCTTCAAGGAAGACTGAATCAAACTTGATTTGCTTCGTTGCTCTTTAGGAAGACCAAATA
* * ** *
21309 TGCAAGAAGAAGAATATGCTCCAGTACTCTTTAGGGGA-AGTCAGACTCAAGAAAAACTTGGATC
66 TGAAAGAAGAAGAATATGCTCCACTACTCTTTAAAGGAGA-TCAAACTCAAG-AAAACTTGGATC
21373 CACTCC
129 CACTCC
** * * *
21379 TTTTCTCTT-ATAGGAAGACTGAATCAAACTTGATTTGCTTCGTTGCTCTTCAGGAAGACTAAAT
1 GCTGCTCTTCA-AGGAAGACTGAATCAAACTTGATTTGCTTCGTTGCTCTTTAGGAAGACCAAAT
21443 CGGACTTGAT
Statistics
Matches: 168, Mismatches: 27, Indels: 7
0.83 0.13 0.03
Matches are distributed among these distances:
133 3 0.02
134 97 0.58
135 68 0.40
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (134 bp):
GCTGCTCTTCAAGGAAGACTGAATCAAACTTGATTTGCTTCGTTGCTCTTTAGGAAGACCAAATA
TGAAAGAAGAAGAATATGCTCCACTACTCTTTAAAGGAGATCAAACTCAAGAAAACTTGGATCCA
CTCC
Found at i:21436 original size:40 final size:40
Alignment explanation
Indices: 21390--21483 Score: 143
Period size: 40 Copynumber: 2.4 Consensus size: 40
21380 TTTCTCTTAT
* *
21390 AGGAAGACTGAATCAAACTTGATTTGCTTCGTTGCTCTTC
1 AGGAAGACTAAATCAAACTTGATTTGCTTCATTGCTCTTC
**
21430 AGGAAGACTAAATCGGACTTGATTTGCTTCATTGCTCTTC
1 AGGAAGACTAAATCAAACTTGATTTGCTTCATTGCTCTTC
*
21470 AGGAAGACCAAATC
1 AGGAAGACTAAATC
21484 TAAAAGAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (40 bp):
AGGAAGACTAAATCAAACTTGATTTGCTTCATTGCTCTTC
Found at i:21679 original size:134 final size:135
Alignment explanation
Indices: 21416--22222 Score: 1041
Period size: 135 Copynumber: 6.0 Consensus size: 135
21406 ACTTGATTTG
* * * * *
21416 CTTCGTTGCTCTTCA-GGAAGACTAAATCGGACT-TGATTTGCTTCATTGCTCTTCAGGAAGACC
1 CTTCGCTGCTCTTCAGGGAAGATTGAATC-GAATGTGATTTGCTTCACTGCTCTTCAGGAAGACC
* * * * *
21479 AAATCTAAAAGAA-AAAAATCTACTCCTCTACTCTTTAGAGGAGGTCAGACTCGAG-AAAATTTT
65 AAATCTGAAAGAAGAAGAATCTGCTCCGCTACTCTTTAGGGGAGGTCAGACTCGAGAAAAATTTT
21542 GATTCA
130 GATTCA
* * * *
21548 CTTCGCTGCTCTTTAGGTAAGATTGAATCGAATGTGATTTGCTTCAATGCACTTCAGGAAGACCA
1 CTTCGCTGCTCTTCAGGGAAGATTGAATCGAATGTGATTTGCTTCACTGCTCTTCAGGAAGACCA
* *
21613 AATCTGAAAGAAGAAGAATCTGCTTCGCTACTCTTTAGGGGAGGTAAGACTCGAG-AAAATTTTG
66 AATCTGAAAGAAGAAGAATCTGCTCCGCTACTCTTTAGGGGAGGTCAGACTCGAGAAAAATTTTG
21677 ATTCA
131 ATTCA
*
21682 CTTCGCTGCTCTTCAGGGAAGATTGAATCGAATGTGATTTGCTTCACTGCTCTTTAGGAAGACCA
1 CTTCGCTGCTCTTCAGGGAAGATTGAATCGAATGTGATTTGCTTCACTGCTCTTCAGGAAGACCA
* * * * * *
21747 AATCTGAAAGAATAAGAATATGCCCCGCTAATCTTTAGGGGAGGTCAAACTCGAGAAAAAATTTG
66 AATCTGAAAGAAGAAGAATCTGCTCCGCTACTCTTTAGGGGAGGTCAGACTCGAGAAAAATTTTG
21812 ATTCA
131 ATTCA
* * *
21817 CTTTGCAGCTCTTCAGGGAAGATTGAATCGAATGTGATTTGCTTCACTTCTCTTCAGGAAGACCA
1 CTTCGCTGCTCTTCAGGGAAGATTGAATCGAATGTGATTTGCTTCACTGCTCTTCAGGAAGACCA
* * ** *
21882 AATCTTAAAGAAGAAGAATCTGCTCTGCTACTCTTTATAGGAGGTCAGACTCGAGAAAAACTTTG
66 AATCTGAAAGAAGAAGAATCTGCTCCGCTACTCTTTAGGGGAGGTCAGACTCGAGAAAAATTTTG
21947 ATTCA
131 ATTCA
** * * *
21952 CTTTACTGCTCTTCAGGGAATATTAAATCGAATGTGATTTGCTTCACTGCTCTTCAGGAATACCA
1 CTTCGCTGCTCTTCAGGGAAGATTGAATCGAATGTGATTTGCTTCACTGCTCTTCAGGAAGACCA
* * * * *
22017 AATCTGAAAGAAGAATAATCTGCTCCGCTATTCTTTAGGGTAGGTCAGACTTGAGAAAAACTTTG
66 AATCTGAAAGAAGAAGAATCTGCTCCGCTACTCTTTAGGGGAGGTCAGACTCGAGAAAAATTTTG
22082 ATTCA
131 ATTCA
* * * * * * **
22087 CTCCGATGCTCTTTAGGGAAGATTGAATCGAATGTGATTTGATTTACTACAATTCAGGAAGACCA
1 CTTCGCTGCTCTTCAGGGAAGATTGAATCGAATGTGATTTGCTTCACTGCTCTTCAGGAAGACCA
* * * ** * * * *
22152 AATCTGAAAGAAAAAGAATATGATGTGCTACTCTTTATGGTAGGCCAGACTTGAG-AAAATTTTG
66 AATCTGAAAGAAGAAGAATCTGCTCCGCTACTCTTTAGGGGAGGTCAGACTCGAGAAAAATTTTG
22216 ATTCA
131 ATTCA
22221 CT
1 CT
22223 CCACCACTCT
Statistics
Matches: 592, Mismatches: 79, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
132 16 0.03
133 50 0.08
134 173 0.29
135 353 0.60
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (135 bp):
CTTCGCTGCTCTTCAGGGAAGATTGAATCGAATGTGATTTGCTTCACTGCTCTTCAGGAAGACCA
AATCTGAAAGAAGAAGAATCTGCTCCGCTACTCTTTAGGGGAGGTCAGACTCGAGAAAAATTTTG
ATTCA
Found at i:23348 original size:45 final size:45
Alignment explanation
Indices: 22937--23368 Score: 466
Period size: 45 Copynumber: 9.7 Consensus size: 45
22927 AGTTAAGTTG
* ** * * *
22937 AGAATGACATCACTAAAAGGCTGACTCATCTCCCCGAGAAAGTCA
1 AGAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
* * * * *
22982 AGAATAACACCGCTAAAAGACTGACTCCTCTTCACGAGAAAGTTA
1 AGAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
* * * * *
23027 GGAATAACATCACTAAAAGGTTGACTTCTCTTCACGAGAAAGTCA
1 AGAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
* * *
23072 AGAAGGACAACACTAAAAGAATT-ACTTCTCTT-AGTGAGAAAGTCA
1 AGAATGACAACACTAAAAG-ATTGACTCCTCTTCA-CGAGAAAGTCA
** *
23117 AGAATGACAACACTAAAAGATTGACTTATCTTCATGAGAAAGT-A
1 AGAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
* ** * *
23161 AAAATGACAACACT-AAAGATTGACTTATTTTCACGA-AAATGTAA
1 AGAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAAA-GTCA
* *
23205 AGAATGACAACACT-AAATATTGATTCCTCTTCACGAGAAAGTCA
1 AGAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
* *
23249 AGAATGACAACACT-AAAGATTGATTCCTCTTCATGAGAAAGTCA
1 AGAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
*
23293 ATAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
1 AGAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
* *
23338 A-AAGTTACAACACTGAAAGATTGACTCCTCT
1 AGAA-TGACAACACTAAAAGATTGACTCCTCT
23369 ATCAATCTGT
Statistics
Matches: 338, Mismatches: 40, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
42 3 0.01
43 22 0.07
44 109 0.32
45 201 0.59
46 3 0.01
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (45 bp):
AGAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
Found at i:36289 original size:13 final size:13
Alignment explanation
Indices: 36271--36295 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36261 TCCCTTATTG
36271 CTTTGGGCTTATC
1 CTTTGGGCTTATC
36284 CTTTGGGCTTAT
1 CTTTGGGCTTAT
36296 GATTGGGCTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.20, G:0.24, T:0.48
Consensus pattern (13 bp):
CTTTGGGCTTATC
Found at i:36414 original size:25 final size:24
Alignment explanation
Indices: 36386--36434 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
36376 ATTAACCTAT
* *
36386 ATAATTAATAATATAACATTTATAA
1 ATAACTAATAATAT-ACATATATAA
36411 ATAACTAATAATATACATATATAA
1 ATAACTAATAATATACATATATAA
36435 CCCAAACGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (24 bp):
ATAACTAATAATATACATATATAA
Found at i:42679 original size:28 final size:30
Alignment explanation
Indices: 42636--42697 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
42626 ATTTATTTAG
*
42636 TATTATTTATGTCAATATTATTATT-AAAA
1 TATTATTTATGTCAATATTATAATTAAAAA
* *
42665 TATTATTTTTG-CAATTTTATAATTAAAAA
1 TATTATTTATGTCAATATTATAATTAAAAA
42694 TATT
1 TATT
42698 TAGATTAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 11 0.38
29 18 0.62
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (30 bp):
TATTATTTATGTCAATATTATAATTAAAAA
Found at i:43066 original size:11 final size:11
Alignment explanation
Indices: 43050--43074 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
43040 ATTAATATTT
43050 TTATTAAAATA
1 TTATTAAAATA
43061 TTATTAAAATA
1 TTATTAAAATA
43072 TTA
1 TTA
43075 ACATTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TTATTAAAATA
Found at i:49320 original size:2 final size:2
Alignment explanation
Indices: 49313--49349 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
49303 CATTTTTGTC
49313 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49350 TTTGTAAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:49402 original size:38 final size:37
Alignment explanation
Indices: 49335--49471 Score: 147
Period size: 38 Copynumber: 3.6 Consensus size: 37
49325 TATATATATA
* **
49335 TATATATATATATATTTTGTAAATGATTTTTGAAAATAC
1 TATATA-ATATATAGTTT-TAAAACATTTTTGAAAATAC
49374 GTATATAATATATAGTTTTAAAACA-TTTTGAAAAATA-
1 -TATATAATATATAGTTTTAAAACATTTTTG-AAAATAC
49411 TATATAATATATAGGTTTTAAAATCATTTTTG-AAA-AC
1 TATATAATATATA-GTTTTAAAA-CATTTTTGAAAATAC
49448 TTATATAATATATAGTTTTTAAAA
1 -TATATAATATATAG-TTTTAAAA
49472 AAATATTTTT
Statistics
Matches: 87, Mismatches: 3, Indels: 16
0.82 0.03 0.15
Matches are distributed among these distances:
36 14 0.16
37 18 0.21
38 34 0.39
39 15 0.17
40 6 0.07
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (37 bp):
TATATAATATATAGTTTTAAAACATTTTTGAAAATAC
Found at i:49643 original size:24 final size:23
Alignment explanation
Indices: 49573--49644 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 23
49563 ATATAATATA
* *
49573 TATTTATTTTTATTATTTGTTTTA
1 TATTTA-TTTTATTTTTTGTTTTT
**
49597 T-TTTATTTTACTTTTTTCATTTT
1 TATTTATTTTA-TTTTTTGTTTTT
49620 TATTTATTTTATTCTTTTGTTTTT
1 TATTTATTTTATT-TTTTGTTTTT
49644 T
1 T
49645 CTCATGTCCA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
22 5 0.13
23 15 0.38
24 19 0.49
ACGTcount: A:0.15, C:0.04, G:0.03, T:0.78
Consensus pattern (23 bp):
TATTTATTTTATTTTTTGTTTTT
Found at i:51008 original size:15 final size:15
Alignment explanation
Indices: 50988--51018 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
50978 ACTAACCTTC
*
50988 TTATTATTTTTTATT
1 TTATTATTTTCTATT
51003 TTATTATTTTCTATT
1 TTATTATTTTCTATT
51018 T
1 T
51019 CTTTTTTTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (15 bp):
TTATTATTTTCTATT
Found at i:51222 original size:40 final size:40
Alignment explanation
Indices: 51175--51255 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
51165 AGTGGTAATT
*
51175 TCAATCAATCGAAGGTGAGTAATTCGAATCGAGTTTTTAA
1 TCAATCAATCGAAGGTAAGTAATTCGAATCGAGTTTTTAA
51215 TCAATCAATCGAAGGTAAGTAATTCGAATCGAGTTTTTAA
1 TCAATCAATCGAAGGTAAGTAATTCGAATCGAGTTTTTAA
51255 T
1 T
51256 TTTAATTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (40 bp):
TCAATCAATCGAAGGTAAGTAATTCGAATCGAGTTTTTAA
Found at i:55229 original size:84 final size:83
Alignment explanation
Indices: 54658--56007 Score: 1670
Period size: 84 Copynumber: 16.4 Consensus size: 83
54648 CTATCGACAT
* * *
54658 CATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTC
*
54723 AAAGGCACATCATTTGCAG
65 AAAGGCACATCATTTGCAA
*
54742 CATAGTTCAAGGCAAGAAGGGTTATCTG-C--CAAAGACCTTCGAGTTCGATTACACTCAGCTCA
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCA
54804 AAGGCACATCATTTGCAA
66 AAGGCACATCATTTGCAA
* * *
54822 -ATAGCTCAAGGCAAGAATGGTTATTTGCCAACAAAAGACCTTTGAGTTCGATTACACTCAGCTC
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTC
* * *
54886 GAAGGCACATCATTTGTAG
65 AAAGGCACATCATTTGCAA
*
54905 CATAGCTCAAGGCAAGAAGGGTTACCTG-C--CAAAGACCTTCGAGTTCGATTACACTCAGCTCA
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCA
* *
54967 AAGGCATATCATTTACAA
66 AAGGCACATCATTTGCAA
* * * * * *
54985 CATAACTCAATGCTAGAA-GGTTATCTGTCAACAAAGACCTTCGAGTTTGATTATACTCAGCTCA
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCA
55049 AAGGCACATCATTTGCAGA
66 AAGGCACATCATTTGCA-A
* *
55068 -ATAACTCAAGGCGAGAAGGGTTATCTGCCAACAAA-ACCTTCGAGTTCGATTACACTCAGCTCA
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCA
55131 AAGGCACATCATTTGCAA
66 AAGGCACATCATTTGCAA
* * * * * * *
55149 CATATCTCAAGACAAGAAGGGCTATTTGTCAACAAAAGTCCTTCGAGTTCGATAACACTCAGCTC
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTC
* *
55214 AAAGCCACATCATTTGCAG
65 AAAGGCACATCATTTGCAA
* * * *
55233 TATAGCTCAAGGCTAGAAGGGCTA-CATG-C--CAAAGACCTTCGAGTTCGATTACGCTCAGCTC
1 CATAGCTCAAGGCAAGAAGGGTTATC-TGCCAACAAAGACCTTCGAGTTCGATTACACTCAGCTC
* *
55294 AAAGGCACGTCATTTACAA
65 AAAGGCACATCATTTGCAA
* * * *
55313 CATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTATACTCAGCTCA
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCA
* *
55378 AAGGCACATCATTTGTAG
66 AAGGCACATCATTTGCAA
* * * *
55396 CAT-GCTCAAGGCAAGAA-GGTCTA-C--CTACCAAAGACCATCGAGTTCAATTACACTCAGCTC
1 CATAGCTCAAGGCAAGAAGGGT-TATCTGCCAACAAAGACCTTCGAGTTCGATTACACTCAGCTC
* *
55456 AAAGACACATCATTTACAA
65 AAAGGCACATCATTTGCAA
* * * * *
55475 CATAACTCAATGCTAGAAGGGTTATCTGTCAACAAAGACCTTTGAGTTCGATTACACTCAGCTCA
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCA
55540 AAGGCACATCATTTGCAA
66 AAGGCACATCATTTGCAA
* * * *
55558 CATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGATTACAGTTAGCTC
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTC
* *
55623 AAAGGCATATCATTTGCAG
65 AAAGGCACATCATTTGCAA
*
55642 CATAGCTCAAGGCAAGAAGGGCTATCTG-C--CAAAGACCTTCGAGTTCGATTACACTCAGCTCA
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCA
55704 AAGGCACATCATTTGCAA
66 AAGGCACATCATTTGCAA
*
55722 CATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTC
* *
55787 AAATGTACATCATTTGCAA
65 AAAGGCACATCATTTGCAA
** * *
55806 CATAGCTCAAGGCAAGAACTGTTATTTGCCAACAAAAGACCTTCGAGTTCGATTACACTAAGCTC
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTC
55871 AAAGGCACATCATTTGCAA
65 AAAGGCACATCATTTGCAA
* * * * * * * *
55890 CATAGCTCAAGGTAAAAAGGGCTATCTG-C--CAAATACCTTCGAGTTTGATTACATTCAACTTA
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCA
* * * *
55952 GAGGCAAATCAAATTTACAG
66 AAGGCACATC--ATTTGCAA
* * * *
55972 TATAGCTCAAGGCAAGAAGGGCTATTTGTCAACAAA
1 CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAA
56008 ATTATCGAGT
Statistics
Matches: 1100, Mismatches: 132, Indels: 67
0.85 0.10 0.05
Matches are distributed among these distances:
79 80 0.07
80 295 0.27
81 17 0.02
82 175 0.16
83 195 0.18
84 334 0.30
85 4 0.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (83 bp):
CATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCA
AAGGCACATCATTTGCAA
Found at i:55273 original size:164 final size:163
Alignment explanation
Indices: 54658--56008 Score: 1723
Period size: 164 Copynumber: 8.2 Consensus size: 163
54648 CTATCGACAT
*
54658 CATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
1 CATAACTCAAGGCAAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
* *
54723 AAAGGCACATCATTTGCAGCATAGTTCAAGGCAAGAAGGGTTATCTGCCAAAGACCTTCGAGTTC
66 AAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTA-CTGCCAAAGACCTTCGAGTTC
*
54788 GATTACACTCAGCTCAAAGGCACATCATTTGCAA
130 GATTACACTCAGCTCAAAGGCACATCATTTACAA
* * * * *
54822 -ATAGCTCAAGGCAAGAATGGTTATTTGCCAACAAAAGACCTTTGAGTTCGATTACACTCAGCTC
1 CATAACTCAAGGCAAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
* * *
54886 GAAGGCACATCATTTGTAGCATAGCTCAAGGCAAGAAGGGTTACCTGCCAAAGACCTTCGAGTTC
66 AAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTA-CTGCCAAAGACCTTCGAGTTC
*
54951 GATTACACTCAGCTCAAAGGCATATCATTTACAA
130 GATTACACTCAGCTCAAAGGCACATCATTTACAA
* * * *
54985 CATAACTCAATGCTAGAA-GGTTATCTGTCAAC-AAAGACCTTCGAGTTTGATTATACTCAGCTC
1 CATAACTCAAGGCAAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
* * * * *
55048 AAAGGCACATCATTTGCAGAATAACTCAAGGCGAGAAGGGTTATCTGCCAACAAAACCTTCGAGT
66 AAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTA-CTGCC-A-AAGACCTTCGAGT
*
55113 TCGATTACACTCAGCTCAAAGGCACATCATTTGCAA
128 TCGATTACACTCAGCTCAAAGGCACATCATTTACAA
* * * * * *
55149 CATATCTCAAGACAAGAAGGGCTATTTGTCAACAAAAGTCCTTCGAGTTCGATAACACTCAGCTC
1 CATAACTCAAGGCAAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
* * *
55214 AAAGCCACATCATTTGCAGTATAGCTCAAGGCTAGAAGGGCTACATGCCAAAGACCTTCGAGTTC
66 AAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTAC-TGCCAAAGACCTTCGAGTTC
* *
55279 GATTACGCTCAGCTCAAAGGCACGTCATTTACAA
130 GATTACACTCAGCTCAAAGGCACATCATTTACAA
* *
55313 CATAACTCAAGGCTAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTATACTCAGCTC
1 CATAACTCAAGGCAAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
* * * *
55377 AAAGGCACATCATTTGTAGCAT-GCTCAAGGCAAGAAGGTCTACCTACCAAAGACCATCGAGTTC
66 AAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTA-CTGCCAAAGACCTTCGAGTTC
* *
55441 AATTACACTCAGCTCAAAGACACATCATTTACAA
130 GATTACACTCAGCTCAAAGGCACATCATTTACAA
* * *
55475 CATAACTCAATGCTAGAAGGGTTATCTGTCAAC-AAAGACCTTTGAGTTCGATTACACTCAGCTC
1 CATAACTCAAGGCAAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
* *
55539 AAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGA
66 AAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTA-CTG-C--C-AAAGACCTTCGA
* * * * *
55604 GTTCGATTACAGTTAGCTCAAAGGCATATCATTTGCAG
126 GTTCGATTACACTCAGCTCAAAGGCACATCATTTACAA
* *
55642 CATAGCTCAAGGCAAGAAGGGCTATCTG-C--C-AAAGACCTTCGAGTTCGATTACACTCAGCTC
1 CATAACTCAAGGCAAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
* * *
55703 AAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGACCTTCGA
66 AAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTA-CTG-C--C-AAAGACCTTCGA
* * *
55768 GTTCGATTACACTCAGCTCAAATGTACATCATTTGCAA
126 GTTCGATTACACTCAGCTCAAAGGCACATCATTTACAA
* ** * * *
55806 CATAGCTCAAGGCAAGAACTGTTATTTGCCAACAAAAGACCTTCGAGTTCGATTACACTAAGCTC
1 CATAACTCAAGGCAAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
* * * * *
55871 AAAGGCACATCATTTGCAACATAGCTCAAGGTAAAAAGGGCTATCTGCCAAATACCTTCGAGTTT
66 AAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTA-CTGCCAAAGACCTTCGAGTTC
* * * * * *
55936 GATTACATTCAACTTAGAGGCAAATCAAATTTACAG
130 GATTACACTCAGCTCAAAGGCACATC--ATTTACAA
* * * *
55972 TATAGCTCAAGGCAAGAAGGGCTATTTGTCAACAAAA
1 CATAACTCAAGGCAAGAAGGGTTATCTGTCAACAAAA
56009 TTATCGAGTT
Statistics
Matches: 1048, Mismatches: 121, Indels: 34
0.87 0.10 0.03
Matches are distributed among these distances:
162 218 0.21
163 232 0.22
164 332 0.32
165 16 0.02
166 109 0.10
167 68 0.06
168 73 0.07
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (163 bp):
CATAACTCAAGGCAAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
AAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTACTGCCAAAGACCTTCGAGTTCG
ATTACACTCAGCTCAAAGGCACATCATTTACAA
Found at i:55594 original size:491 final size:493
Alignment explanation
Indices: 54658--55934 Score: 1901
Period size: 491 Copynumber: 2.6 Consensus size: 493
54648 CTATCGACAT
* *
54658 CATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
1 CATAACTCAAGGCAAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
*
54723 AAAGGCACATCATTTGCAGCATAGTTCAAGGCAAGAAGGGTTATCTGCCAAAGACCTTCGAGTTC
66 AAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTA-CTGCCAAAGACCTTCGAGTTC
*
54788 GATTACACTCAGCTCAAAGGCACATCATTTGCAA-ATAGCTCAAGGCAAGAATGGTTATTTGCCA
130 GATTACACTCAGCTCAAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAACGGTTATTTGCCA
* *
54852 ACAAAAGACCTTTGAGTTCGATTACACTCAGCTCGAAGGCACATCATTTGTAGCATAGCTCAAGG
195 ACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGTAGCATAGCTCAAGG
* * *
54917 CAAGAAGGGT-TACCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCATTT
260 CAAGAA-GGTCTACCTGCCAAAGACCTTCGAGTTCAATTACACTCAGCTCAAAGACACATCATTT
* *
54981 ACAACATAACTCAATGCTAGAAGGTTATCTGTCAACAAAGACCTTCGAGTTTGATTATACTCAGC
324 ACAACATAACTCAATGCTAGAAGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGC
* *
55046 TCAAAGGCACATCATTTGCAGAATAACTCAAGGCGAGAAGGGTTATCTGCCAAC-AAA-ACCTTC
389 TCAAAGGCACATCATTTGCAGAATAACTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTC
55109 GAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAA
454 GAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAA
* * * * *
55149 CATATCTCAAGACAAGAAGGGCTATTTGTCAACAAAAGTCCTTCGAGTTCGATAACACTCAGCTC
1 CATAACTCAAGGCAAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
* * * *
55214 AAAGCCACATCATTTGCAGTATAGCTCAAGGCTAGAAGGGCTACATGCCAAAGACCTTCGAGTTC
66 AAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTAC-TGCCAAAGACCTTCGAGTTC
* * * * * * * *
55279 GATTACGCTCAGCTCAAAGGCACGTCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCA
130 GATTACACTCAGCTCAAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAACGGTTATTTGCCA
*
55344 AC-AAAGACCTTCGAGTTCGATTATACTCAGCTCAAAGGCACATCATTTGTAGCAT-GCTCAAGG
195 ACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGTAGCATAGCTCAAGG
* *
55407 CAAGAAGGTCTACCTACCAAAGACCATCGAGTTCAATTACACTCAGCTCAAAGACACATCATTTA
260 CAAGAAGGTCTACCTGCCAAAGACCTTCGAGTTCAATTACACTCAGCTCAAAGACACATCATTTA
*
55472 CAACATAACTCAATGCTAGAAGGGTTATCTGTCAACAAAGACCTTTGAGTTCGATTACACTCAGC
325 CAACATAACTCAATGCTAGAA-GGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGC
* *
55537 TCAAAGGCACATCATTTGCA-ACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTT
389 TCAAAGGCACATCATTTGCAGA-ATAACTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTT
* * * *
55601 CGAGTTCGATTACAGTTAGCTCAAAGGCATATCATTTGCAG
453 CGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAA
*
55642 CATAGCTCAAGGCAAGAAGGGCTATCTG-C--C-AAAGACCTTCGAGTTCGATTACACTCAGCTC
1 CATAACTCAAGGCAAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
* *
55703 AAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGACCTTCGA
66 AAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTA-CTG-C--C-AAAGACCTTCGA
* * *
55768 GTTCGATTACACTCAGCTCAAATGTACATCATTTGCAACATAGCTCAAGGCAAGAACTGTTATTT
126 GTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAACGGTTATTT
* * *
55833 GCCAACAAAAGACCTTCGAGTTCGATTACACTAAGCTCAAAGGCACATCATTTGCAACATAGCTC
191 GCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGTAGCATAGCTC
* * * * *
55898 AAGGTAAAAAGGGCTATCTGCCAAATACCTTCGAGTT
256 AAGGCAAGAAGGTCTACCTGCCAAAGACCTTCGAGTT
55935 TGATTACATT
Statistics
Matches: 700, Mismatches: 72, Indels: 24
0.88 0.09 0.03
Matches are distributed among these distances:
489 72 0.10
490 89 0.13
491 285 0.41
492 32 0.05
493 139 0.20
494 49 0.07
495 34 0.05
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (493 bp):
CATAACTCAAGGCAAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
AAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTACTGCCAAAGACCTTCGAGTTCG
ATTACACTCAGCTCAAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAACGGTTATTTGCCAA
CAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGTAGCATAGCTCAAGGC
AAGAAGGTCTACCTGCCAAAGACCTTCGAGTTCAATTACACTCAGCTCAAAGACACATCATTTAC
AACATAACTCAATGCTAGAAGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTC
AAAGGCACATCATTTGCAGAATAACTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGA
GTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAA
Found at i:56621 original size:39 final size:38
Alignment explanation
Indices: 56565--56848 Score: 233
Period size: 37 Copynumber: 7.6 Consensus size: 38
56555 TATATATATA
** *
56565 TATATATATATTATAGTTTGCAAATGATTTTTGAAAATAC
1 TATATA-ATA-TATAGTTTTAAAATCATTTTTGAAAATAC
*
56605 GTATATAATATATAGTTTTTAAAA-CATTTTGGAAAATA-
1 -TATATAATATATAG-TTTTAAAATCATTTTTGAAAATAC
56643 TATATAATATATAGGTTTTAAAATCATTTTTG-AAA-AC
1 TATATAATATATA-GTTTTAAAATCATTTTTGAAAATAC
* **
56680 TTATATAATATATAGTTTTAAAAACATTTTAAAAACATA-
1 -TATATAATATATAGTTTTAAAATCATTTTTGAAA-ATAC
*
56719 TATATATATATAATAGTTTTTAAAATCA-TTTTGAAACT--
1 TATATA-ATAT-ATAG-TTTTAAAATCATTTTTGAAAATAC
*
56757 TATATAAT-TATA-TTTTAAAAAACA-TTTT-AAAA-AC
1 TATATAATATATAGTTTT-AAAATCATTTTTGAAAATAC
* *
56791 ATATATAATATATAGTTTTTAAATCA-TTTTGAAAACA-
1 -TATATAATATATAGTTTTAAAATCATTTTTGAAAATAC
56828 TATAT-ATATAGT-GTTTTAAAA
1 TATATAATATA-TAGTTTTAAAA
56849 AAATATTTTT
Statistics
Matches: 206, Mismatches: 17, Indels: 46
0.77 0.06 0.17
Matches are distributed among these distances:
33 7 0.03
34 10 0.05
35 24 0.12
36 21 0.10
37 49 0.24
38 36 0.17
39 23 0.11
40 20 0.10
41 16 0.08
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (38 bp):
TATATAATATATAGTTTTAAAATCATTTTTGAAAATAC
Found at i:56661 original size:38 final size:36
Alignment explanation
Indices: 56593--56837 Score: 266
Period size: 38 Copynumber: 6.6 Consensus size: 36
56583 TGCAAATGAT
56593 TTTTGAAAATACGTATATAATATATAGTTTTTAAAACA
1 TTTTGAAAATA--TATATAATATATAGTTTTTAAAACA
*
56631 TTTTGGAAAATATATATAATATATAGGTTTTAAAATCA
1 TTTT-GAAAATATATATAATATATAGTTTTTAAAA-CA
*
56669 TTTTTGAAAACT-TATATAATATATAGTTTTAAAAACA
1 -TTTTGAAAA-TATATATAATATATAGTTTTTAAAACA
*
56706 TTTTAAAAACATATATATATATATAATAGTTTTTAAAATCA
1 TTTT-GAAA-ATATATATA-ATAT-ATAGTTTTTAAAA-CA
* *
56747 TTTTGAAACT-TATATAAT-TATA-TTTTAAAAAACA
1 TTTTGAAAATATATATAATATATAGTTTT-TAAAACA
* * *
56781 TTTTAAAAACATATATAATATATAGTTTTTAAATCA
1 TTTTGAAAATATATATAATATATAGTTTTTAAAACA
*
56817 TTTTGAAAACATATAT-ATATA
1 TTTTGAAAATATATATAATATA
56838 GTGTTTTAAA
Statistics
Matches: 179, Mismatches: 14, Indels: 31
0.80 0.06 0.14
Matches are distributed among these distances:
34 13 0.07
35 20 0.11
36 29 0.16
37 34 0.19
38 45 0.25
39 17 0.09
40 15 0.08
41 6 0.03
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (36 bp):
TTTTGAAAATATATATAATATATAGTTTTTAAAACA
Found at i:56696 original size:75 final size:73
Alignment explanation
Indices: 56562--56849 Score: 329
Period size: 75 Copynumber: 3.9 Consensus size: 73
56552 ATATATATAT
** * * *
56562 ATATATATATATATTATAGTTTGCAAATGATTTTTGAAAATACGTATATAATATATAGTTTTTAA
1 ATATATATATATA-TATAGTTTTAAAATCA-TTTTG-AAA-ACTTATATAATATATAGTTTTAAA
*
56627 AACATTTTGGAAA
62 AACATTTT-AAAA
56640 ATATATATA-ATATATAGGTTTTAAAATCATTTTTGAAAACTTATATAATATATAGTTTTAAAAA
1 ATATATATATATATATA-GTTTTAAAATCA-TTTTGAAAACTTATATAATATATAGTTTTAAAAA
56704 CATTTTAAAAA
64 CATTTT-AAAA
56715 CATATATATATATATAATAGTTTTTAAAATCATTTTG-AAACTTATATAAT-TATA-TTTTAAAA
1 -ATATATATATATAT-ATAG-TTTTAAAATCATTTTGAAAACTTATATAATATATAGTTTT-AAA
56777 AACATTTTAAAA
62 AACATTTTAAAA
* * *
56789 ACATATATA-ATATATAGTTTTTAAATCATTTTGAAAACATATAT-ATATAGT-GTTTTAAAAA
1 ATATATATATATATATAGTTTTAAAATCATTTTGAAAACTTATATAATATA-TAGTTTTAAAAA
56850 AATATTTTTT
Statistics
Matches: 190, Mismatches: 10, Indels: 27
0.84 0.04 0.12
Matches are distributed among these distances:
70 17 0.09
71 20 0.11
72 9 0.05
73 8 0.04
74 8 0.04
75 48 0.25
76 29 0.15
77 28 0.15
78 23 0.12
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (73 bp):
ATATATATATATATATAGTTTTAAAATCATTTTGAAAACTTATATAATATATAGTTTTAAAAACA
TTTTAAAA
Found at i:56800 original size:111 final size:113
Alignment explanation
Indices: 56606--56837 Score: 323
Period size: 111 Copynumber: 2.1 Consensus size: 113
56596 TGAAAATACG
*
56606 TATATA-ATATATAGTTTTTAAAACATTTTGGAAAATATATATAATATATAGGTTTTAAAATCAT
1 TATATATATATATAGTTTTTAAAACATTTTGGAAAATATATATAATATATA-GTTTTAAAAACAT
* *
56670 TTTTGAAAACTTATATAATATATAGTTTTAAAAACATTTTAAAAACATA
65 TTTTAAAAACATATATAATATATAGTTTTAAAAACATTTTAAAAACATA
*
56719 TATATATATATAATAGTTTTTAAAATCATTTT-GAAACT-TATATAAT-TATA-TTTTAAAAAAC
1 TATATATATAT-ATAGTTTTTAAAA-CATTTTGGAAAATATATATAATATATAGTTTT-AAAAAC
* * *
56780 A-TTTTAAAAACATATATAATATATAGTTTTTAAATCATTTTGAAAACATA
63 ATTTTTAAAAACATATATAATATATAGTTTTAAAAACATTTTAAAAACATA
56830 TATATATA
1 TATATATA
56838 GTGTTTTAAA
Statistics
Matches: 108, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
111 56 0.52
112 6 0.06
113 10 0.09
114 12 0.11
115 18 0.17
116 6 0.06
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (113 bp):
TATATATATATATAGTTTTTAAAACATTTTGGAAAATATATATAATATATAGTTTTAAAAACATT
TTTAAAAACATATATAATATATAGTTTTAAAAACATTTTAAAAACATA
Found at i:56998 original size:25 final size:25
Alignment explanation
Indices: 56949--56997 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
56939 ATATAATATA
56949 TATTTATTTTTATTTTTTTCGTTTT
1 TATTTATTTTTATTTTTTTCGTTTT
*
56974 TATTTA-TTTTATTTATTT-GTTTT
1 TATTTATTTTTATTTTTTTCGTTTT
56997 T
1 T
56998 TCTCAAGTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.26
24 11 0.48
25 6 0.26
ACGTcount: A:0.14, C:0.02, G:0.04, T:0.80
Consensus pattern (25 bp):
TATTTATTTTTATTTTTTTCGTTTT
Found at i:58320 original size:27 final size:27
Alignment explanation
Indices: 58290--58341 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
58280 TTTTATATTA
*
58290 TTTA-ATCCTTTTTTAATTTCTTTTTGT
1 TTTAGATCCTTTTTT-ATTTATTTTTGT
*
58317 TTTAGTTCCTTTTTTATTTATTTTT
1 TTTAGATCCTTTTTTATTTATTTTT
58342 TCTTTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 13 0.59
28 9 0.41
ACGTcount: A:0.13, C:0.10, G:0.04, T:0.73
Consensus pattern (27 bp):
TTTAGATCCTTTTTTATTTATTTTTGT
Done.