Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002674.1 Hibiscus syriacus cultivar Beakdansim tig00005491_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: 94620
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:90 original size:27 final size:27
Alignment explanation
Indices: 33--96 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
23 TTCAAAAAAA
* *
33 TATTTTAAAATTCTAAATAAATCAAAT
1 TATTTAAAAATTATAAATAAATCAAAT
60 TATTTAAATAATTATAAAT-AAT-AAAT
1 TATTTAAA-AATTATAAATAAATCAAAT
*
86 GTATTAAAAAA
1 -TATTTAAAAA
97 ATAAAATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
26 6 0.19
27 17 0.53
28 9 0.28
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (27 bp):
TATTTAAAAATTATAAATAAATCAAAT
Found at i:1028 original size:59 final size:59
Alignment explanation
Indices: 900--1035 Score: 150
Period size: 59 Copynumber: 2.3 Consensus size: 59
890 ATATTCAGGT
* * * * *
900 AATCATTTTGTAACTTTTAATAGTTGAGTGACTCAACGAAACCACTCCTATAGTCAGAG
1 AATCATTTTGTAACTTTTAATAGTCGAGTGACTCAACAAAACAAATCCTATAATCAGAG
* * *
959 AATCATTTTGTAACTTTTAATAGTCGA-TGGGCTCAACAAAACAATATCCTATAATTAGGG
1 AATCATTTTGTAACTTTTAATAGTCGAGT-GACTCAACAAAACAA-ATCCTATAATCAGAG
*
1019 GATCATTTGTGT-ACTTT
1 AATCATTT-TGTAACTTT
1036 ATCCCGATTC
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
58 1 0.02
59 38 0.58
60 23 0.35
61 3 0.05
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (59 bp):
AATCATTTTGTAACTTTTAATAGTCGAGTGACTCAACAAAACAAATCCTATAATCAGAG
Found at i:11812 original size:19 final size:19
Alignment explanation
Indices: 11778--11825 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
11768 TAGAATTTTT
*
11778 AAATATA-TTTTGTATTGA
1 AAATATATTTTTATATTGA
11796 AAATATATTTTTATATTGA
1 AAATATATTTTTATATTGA
*
11815 AATTATATTTT
1 AAATATATTTT
11826 CATTCCCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 7 0.26
19 20 0.74
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (19 bp):
AAATATATTTTTATATTGA
Found at i:12869 original size:10 final size:10
Alignment explanation
Indices: 12851--12880 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
12841 GTGTCTATTG
*
12851 TTATATTTTT
1 TTATTTTTTT
12861 TTATTTTTTT
1 TTATTTTTTT
12871 TTATTTTTTT
1 TTATTTTTTT
12881 AATAATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (10 bp):
TTATTTTTTT
Found at i:12895 original size:20 final size:20
Alignment explanation
Indices: 12872--12925 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
12862 TATTTTTTTT
* *
12872 TATTTTTTTAATAATAAAAA
1 TATTATTTTAAAAATAAAAA
12892 TATTATTTTAAAAATAAAAA
1 TATTATTTTAAAAATAAAAA
12912 TATTATTTTAAAAA
1 TATTATTTTAAAAA
12926 ACTTAATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TATTATTTTAAAAATAAAAA
Found at i:16246 original size:22 final size:22
Alignment explanation
Indices: 16220--16271 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
16210 CCCTAAAGAA
16220 GGGAATCGGTTCACATTAAAGG
1 GGGAATCGGTTCACATTAAAGG
* * *
16242 GGGAATCGGTTCCCCTTCAAGG
1 GGGAATCGGTTCACATTAAAGG
*
16264 GGGTATCG
1 GGGAATCG
16272 ATTCCCTCTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.23
Consensus pattern (22 bp):
GGGAATCGGTTCACATTAAAGG
Found at i:16278 original size:21 final size:21
Alignment explanation
Indices: 16197--16278 Score: 67
Period size: 22 Copynumber: 3.8 Consensus size: 21
16187 CAGAACTCAT
*
16197 GGGGGTATCGATTCCC-TAAA
1 GGGGGAATCGATTCCCTTAAA
* * *
16217 GAAGGGAATCGGTTCACATTAAA
1 G-GGGGAATCGATTC-CCTTAAA
* *
16240 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGATT-CCCTTAAA
*
16262 GGGGGTATCGATTCCCT
1 GGGGGAATCGATTCCCT
16279 CTGCCCTATA
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
20 1 0.02
21 14 0.29
22 28 0.57
23 6 0.12
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.24
Consensus pattern (21 bp):
GGGGGAATCGATTCCCTTAAA
Found at i:23564 original size:103 final size:99
Alignment explanation
Indices: 23385--23573 Score: 220
Period size: 103 Copynumber: 1.8 Consensus size: 99
23375 TAACCGGTGT
* * *
23385 AACCGATTTTTAATCCGGTAAAAAATCCGGTCATCCAATTTTTTAAACCCCAGACCGGATTTTTT
1 AACCGATTTTTAATCCGGTAAAAAATCCGGTCATCCAATTTTTT--A-CCCAAACCGGATTTCTA
*
23450 TCCGGATAAAAAATTGGTTTTTTATCTGGTTTTTTTCA
63 TCCGGA-AAAAAACTGGTTTTTTATCTGGTTTTTTTCA
* *
23488 AACCGGTTTTTAATCCGGTAAAAAATCCGGTCGTCCAATTTTTT-CCCAAACCGG-TTATACTAT
1 AACCGATTTTTAATCCGGTAAAAAATCCGGTCATCCAATTTTTTACCCAAACCGGATT-T-CTAT
*
23551 CTGGTTTAAAAAAACTGGTTTTT
64 CCGG---AAAAAAACTGGTTTTT
23574 CCTAAATCCG
Statistics
Matches: 74, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
98 2 0.03
99 10 0.14
100 5 0.07
102 14 0.19
103 43 0.58
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (99 bp):
AACCGATTTTTAATCCGGTAAAAAATCCGGTCATCCAATTTTTTACCCAAACCGGATTTCTATCC
GGAAAAAAACTGGTTTTTTATCTGGTTTTTTTCA
Found at i:24056 original size:71 final size:71
Alignment explanation
Indices: 23981--24124 Score: 193
Period size: 71 Copynumber: 2.0 Consensus size: 71
23971 TTTTTAAGTT
*
23981 AAACAAATAATAATTTATCA-AATAAAAT-AGATAGTAGCAACTAGCAAATCAAGCACCATATAA
1 AAACAAATAA-AATCT-TCATAATAAAATAAGATAGTAGCAACTAGCAAATCAAGCACCATATAA
24044 TATTAAAG
64 TATTAAAG
** * * * *
24052 AAACATGTAAACTCTTCATGATCACATAAGATAGTAGCAACTAGCAAATCAAGCACCATATAATA
1 AAACAAATAAAATCTTCATAATAAAATAAGATAGTAGCAACTAGCAAATCAAGCACCATATAATA
24117 TTAAAG
66 TTAAAG
24123 AA
1 AA
24125 GGCGATGATA
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
69 3 0.05
70 8 0.12
71 53 0.83
ACGTcount: A:0.51, C:0.15, G:0.10, T:0.24
Consensus pattern (71 bp):
AAACAAATAAAATCTTCATAATAAAATAAGATAGTAGCAACTAGCAAATCAAGCACCATATAATA
TTAAAG
Found at i:28723 original size:45 final size:45
Alignment explanation
Indices: 28671--28797 Score: 236
Period size: 45 Copynumber: 2.8 Consensus size: 45
28661 TGAATAAATA
* *
28671 TATGCGAACTAGAAATCATGCAGTTAGGTTTATTTTTTGAGCATG
1 TATGCGAACTAGAAATCATGCGGCTAGGTTTATTTTTTGAGCATG
28716 TATGCGAACTAGAAATCATGCGGCTAGGTTTATTTTTTGAGCATG
1 TATGCGAACTAGAAATCATGCGGCTAGGTTTATTTTTTGAGCATG
28761 TATGCGAACTAGAAATCATGCGGCTAGGTTTATTTTT
1 TATGCGAACTAGAAATCATGCGGCTAGGTTTATTTTT
28798 CTCGAACAAG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 80 1.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.37
Consensus pattern (45 bp):
TATGCGAACTAGAAATCATGCGGCTAGGTTTATTTTTTGAGCATG
Found at i:29206 original size:55 final size:55
Alignment explanation
Indices: 29142--29277 Score: 236
Period size: 55 Copynumber: 2.5 Consensus size: 55
29132 AGCCGTTCAG
*
29142 ATGATTCATGAAGAAGAACATCCGATGAATGAAAAAATTTGAACCTGACTGAAGA
1 ATGATTCATGAAGAAGGACATCCGATGAATGAAAAAATTTGAACCTGACTGAAGA
*
29197 ATGATTCATGAAGAAGGACATCCGATGAATGAAGAAATTTGAACCTGACTGAAGA
1 ATGATTCATGAAGAAGGACATCCGATGAATGAAAAAATTTGAACCTGACTGAAGA
* *
29252 ACGATTCATGAAGAAGGACAACCGAT
1 ATGATTCATGAAGAAGGACATCCGAT
29278 TTCATCAAAT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 77 1.00
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.21
Consensus pattern (55 bp):
ATGATTCATGAAGAAGGACATCCGATGAATGAAAAAATTTGAACCTGACTGAAGA
Found at i:29934 original size:72 final size:72
Alignment explanation
Indices: 29809--29959 Score: 239
Period size: 72 Copynumber: 2.1 Consensus size: 72
29799 CCGTATTACA
* * *
29809 CAAGAAAATATGAAGACTTCGGGTGAGAATCTGAATGTTAGTGGTGCAACCAATGTGATGATAGC
1 CAAGAACAGATGAAGACTTCGGGTGAGAATCTGAATGTTAGTGGTACAACCAATGTGATGATAGC
29874 AAATGAT
66 AAATGAT
* * *
29881 CAAGAACAGATGATGACTTCTGGTGAGAATCTGAATGTTAGTGGTACAGCCAATGTGATGATAGC
1 CAAGAACAGATGAAGACTTCGGGTGAGAATCTGAATGTTAGTGGTACAACCAATGTGATGATAGC
*
29946 AACTGAT
66 AAATGAT
29953 CAAGAAC
1 CAAGAAC
29960 CTGTTAGGGG
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.25
Consensus pattern (72 bp):
CAAGAACAGATGAAGACTTCGGGTGAGAATCTGAATGTTAGTGGTACAACCAATGTGATGATAGC
AAATGAT
Found at i:33447 original size:125 final size:125
Alignment explanation
Indices: 33210--33449 Score: 322
Period size: 125 Copynumber: 1.9 Consensus size: 125
33200 ATTGGAGCAT
** * ** * *
33210 GATTAAACCCACATCATGTTGAGATGACAAGATTTGGACCAAGGAGTCATGAAGAATGAGCCTTA
1 GATTAAACCCACATCATGTTGAGATGACAAGATTCAGACCAAGAAGGAATGAAGAATAAGCATTA
* *
33275 CAAATTGAGGTGATGGGGCATTTTGAAGGCCTATACCAGTATGAGATAATGTCGGGGCAC
66 CAAATTGAGGTGATGGGGCATTTTGAAGGCCTATACCAGAATAAGATAATGTCGGGGCAC
*
33335 GATTAAACCCACATCATGTTGAGATGATAAGATTCAGACCAAGAAGGAATTGAA-AATAAGCATT
1 GATTAAACCCACATCATGTTGAGATGACAAGATTCAGACCAAGAAGGAA-TGAAGAATAAGCATT
* * * *
33399 ATAATTTGAGGTGTTGGGGCATTTTGAAGGCTCT-TACCTGAATAAGATAAT
65 ACAAATTGAGGTGATGGGGCATTTTGAAGGC-CTATACCAGAATAAGATAAT
33450 ATTGCGGCAT
Statistics
Matches: 99, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
125 93 0.94
126 6 0.06
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (125 bp):
GATTAAACCCACATCATGTTGAGATGACAAGATTCAGACCAAGAAGGAATGAAGAATAAGCATTA
CAAATTGAGGTGATGGGGCATTTTGAAGGCCTATACCAGAATAAGATAATGTCGGGGCAC
Found at i:34701 original size:37 final size:37
Alignment explanation
Indices: 34651--34763 Score: 165
Period size: 37 Copynumber: 3.1 Consensus size: 37
34641 AAATTCAAGT
*
34651 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTGAGC
1 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGC
* *
34688 CTTCACCAAAGAGTAGTGAAGCAAA-CTATCTTAAGC
1 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGC
* * *
34724 CTTCACCGAAGAGTAGTGAAGCATATCCTTTTTAAGC
1 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGC
34761 CTT
1 CTT
34764 ATCGGAAGAG
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 31 0.46
37 36 0.54
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.27
Consensus pattern (37 bp):
CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGC
Found at i:35220 original size:54 final size:54
Alignment explanation
Indices: 35151--35420 Score: 434
Period size: 54 Copynumber: 5.0 Consensus size: 54
35141 GTAGTAAAGC
35151 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGTGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGTGAACCCGTA
* *
35205 AGAAAAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGA-TCGAACCTGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGT-GAACCCGTA
35259 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGTGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGTGAACCCGTA
* * *
35313 AGAAGAAGATGTTCGAGTTCCATACTCCTTAGAGAAAGAGGGAGCGAACCTGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGTGAACCCGTA
* * * *
35367 AGAAGAAGATGTTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGT
1 AGAAGAAGATGTTCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGTGAACCCGT
35421 TTAATGAAGA
Statistics
Matches: 201, Mismatches: 12, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
53 1 0.00
54 178 0.89
55 22 0.11
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.20
Consensus pattern (54 bp):
AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGTGAACCCGTA
Found at i:35243 original size:30 final size:30
Alignment explanation
Indices: 35156--35243 Score: 82
Period size: 30 Copynumber: 3.1 Consensus size: 30
35146 AAAGCAGAAG
35156 AAGATGTTCGAGTTCCATACTCCCTAGAGA
1 AAGATGTTCGAGTTCCATACTCCCTAGAGA
* * * *
35186 AAGA-G--GGAG-T-GA-AC-CCGTAAGAAA
1 AAGATGTTCGAGTTCCATACTCCCT-AGAGA
35210 AAGATGTTCGAGTTCCATACTCCCTAGAGA
1 AAGATGTTCGAGTTCCATACTCCCTAGAGA
35240 AAGA
1 AAGA
35244 GGGATCGAAC
Statistics
Matches: 42, Mismatches: 8, Indels: 16
0.64 0.12 0.24
Matches are distributed among these distances:
23 3 0.07
24 10 0.24
25 2 0.05
26 1 0.02
27 6 0.14
28 1 0.02
29 2 0.05
30 14 0.33
31 3 0.07
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.20
Consensus pattern (30 bp):
AAGATGTTCGAGTTCCATACTCCCTAGAGA
Found at i:35430 original size:55 final size:55
Alignment explanation
Indices: 35151--35599 Score: 401
Period size: 54 Copynumber: 8.3 Consensus size: 55
35141 GTAGTAAAGC
* *
35151 AGAAGAAGATGTTCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGTGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTA
* * * *
35205 AGAAAAAGATGTTCGAGTTCCATACTCCCT-AGAGAAAGAGGGATCGAACCTGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTA
* *
35259 AGAAGAAGATGTTCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGTGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTA
* * *
35313 AGAAGAAGATGTTCGAGTTCCATACT-CCTTAGAGAAAGAGGGAGCGAACCTGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTA
* * *
35367 AGAAGAAGATGTTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTT
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTGAAAGAAAGAGGGAGCGAACCCG-TA
* * * * * * *
35423 A-ATGAAGATTGTTCGAG-TCTTATACTCTCTG-AAGAGATAGGGAGC-AGACACGATT
1 AGAAGAAGA-TGTTCGAGTTC-CATACTCCCTGAAAGAAAGAGGGAGCGA-ACCCG-TA
** * * *
35478 ATTA-AAGATTGTTCGAG-TCTCATACTCTCTG-AAGAAATAGGGAGC-AGACCCGATT
1 AGAAGAAGA-TGTTCGAGTTC-CATACTCCCTGAAAGAAAGAGGGAGCGA-ACCCG-TA
* * *
35533 A-CAGAAGATTATTCGAGTT-C-TACTCCCTG-AAGCAAGAGGGAGCGAACCCGCT-
1 AGAAGAAGA-TGTTCGAGTTCCATACTCCCTGAAAGAAAGAGGGAGCGAACCCG-TA
*
35585 AGTAGAAGAATGTTC
1 AGAAGAAG-ATGTTC
35600 AAAGAAGAGG
Statistics
Matches: 348, Mismatches: 35, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
52 1 0.00
53 38 0.11
54 178 0.51
55 111 0.32
56 20 0.06
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.22
Consensus pattern (55 bp):
AGAAGAAGATGTTCGAGTTCCATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTA
Found at i:36283 original size:18 final size:18
Alignment explanation
Indices: 36260--36301 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
36250 CATAAAGGAG
36260 TTAGTTTAAACGCTTACC
1 TTAGTTTAAACGCTTACC
36278 TTAGTTTAAACGCTTACC
1 TTAGTTTAAACGCTTACC
36296 TTAGTT
1 TTAGTT
36302 GTCTCGTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.43
Consensus pattern (18 bp):
TTAGTTTAAACGCTTACC
Found at i:36901 original size:3 final size:3
Alignment explanation
Indices: 36893--36937 Score: 81
Period size: 3 Copynumber: 14.7 Consensus size: 3
36883 AGTCCTTAGG
36893 TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
36938 TTGTCATGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:37828 original size:17 final size:17
Alignment explanation
Indices: 37802--37848 Score: 85
Period size: 17 Copynumber: 2.8 Consensus size: 17
37792 CAATTTGTTG
*
37802 TTTTAATTAAAATTAAT
1 TTTTATTTAAAATTAAT
37819 TTTTATTTAAAATTAAT
1 TTTTATTTAAAATTAAT
37836 TTTTATTTAAAAT
1 TTTTATTTAAAAT
37849 GACAAAGCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTATTTAAAATTAAT
Found at i:44734 original size:19 final size:20
Alignment explanation
Indices: 44700--44739 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
44690 AATAAATATG
* *
44700 TATGTTTTTTTTATAT-TTT
1 TATGTTTTTATGATATGTTT
44719 TATGTTTTTATGATATGTTT
1 TATGTTTTTATGATATGTTT
44739 T
1 T
44740 TTTTCTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.72
Consensus pattern (20 bp):
TATGTTTTTATGATATGTTT
Found at i:44736 original size:32 final size:33
Alignment explanation
Indices: 44696--44781 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 33
44686 TTTTAATAAA
44696 TATGTATGTTTTTTTTAT-ATTTT-TATGTTTT
1 TATGTATGTTTTTTTTATGATTTTATATGTTTT
*
44727 TATGATATGTTTTTTTTCTGATTTTAGTATGTTTTT
1 TATG-TATGTTTTTTTTATGATTTTA-TATG-TTTT
*
44763 TACTGTTTGATTTTTTTTA
1 TA-TGTATG-TTTTTTTTA
44782 AGTATTGATT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
31 4 0.09
32 13 0.29
33 5 0.11
35 4 0.09
36 9 0.20
37 10 0.22
ACGTcount: A:0.16, C:0.02, G:0.12, T:0.70
Consensus pattern (33 bp):
TATGTATGTTTTTTTTATGATTTTATATGTTTT
Found at i:44751 original size:24 final size:22
Alignment explanation
Indices: 44715--44763 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
44705 TTTTTTTATA
*
44715 TTTTTATGTTTTTATGATATGTTT
1 TTTTTATGATTTTA-G-TATGTTT
*
44739 TTTTTCTGATTTTAGTATGTTT
1 TTTTTATGATTTTAGTATGTTT
44761 TTT
1 TTT
44764 ACTGTTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 10 0.43
23 1 0.04
24 12 0.52
ACGTcount: A:0.14, C:0.02, G:0.12, T:0.71
Consensus pattern (22 bp):
TTTTTATGATTTTAGTATGTTT
Found at i:49280 original size:2 final size:2
Alignment explanation
Indices: 49269--49330 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
49259 GCATGATTCA
49269 AT AT -T 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
49310 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
49331 ATTTGGAGGT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 58 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56742 original size:29 final size:30
Alignment explanation
Indices: 56710--56848 Score: 131
Period size: 29 Copynumber: 4.5 Consensus size: 30
56700 AAAAGATAAG
*
56710 ATAATAATAAAATATA-GTTTTAATTTAAA
1 ATAAGAATAAAATATATGTTTTAATTTAAA
*
56739 ATAAGAATAAAATATAT-TTTTAA-GTAAA
1 ATAAGAATAAAATATATGTTTTAATTTAAA
56767 GATAAGAATAAAATATTTTATGTTTTTTAATTTAAA
1 -ATAAGAATAAAATA---TATG--TTTTAATTTAAA
* * *
56803 ATAAGAGTAAAATATATATTTTTATATTAAA
1 ATAAGAATAAAATATATGTTTTAAT-TTAAA
* *
56834 TTAATAATAAAATAT
1 ATAAGAATAAAATAT
56849 TTAAATATAT
Statistics
Matches: 91, Mismatches: 9, Indels: 18
0.77 0.08 0.15
Matches are distributed among these distances:
28 4 0.04
29 35 0.38
30 6 0.07
31 17 0.19
32 6 0.07
35 19 0.21
36 4 0.04
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (30 bp):
ATAAGAATAAAATATATGTTTTAATTTAAA
Found at i:56780 original size:58 final size:62
Alignment explanation
Indices: 56685--56824 Score: 164
Period size: 64 Copynumber: 2.2 Consensus size: 62
56675 TCTTTACTTA
*
56685 AAAATATATATTTTAA--AAAGATAAG-ATAATAATAAAATATAG-TTTTAATTTAAAATAAGAA
1 AAAATATATATTTTAAGTAAAGATAAGAATAA-AAT--ATTAT-GTTTTTAATTTAAAATAAGAA
56746 T
62 T
*
56747 AAAATATAT-TTTTAAGTAAAGATAAGAATAAAATATTTTATGTTTTTTAATTTAAAATAAGAGT
1 AAAATATATATTTTAAGTAAAGATAAGAATAAAATA--TTATG-TTTTTAATTTAAAATAAGAAT
56811 AAAATATATATTTT
1 AAAATATATATTTT
56825 TATATTAAAT
Statistics
Matches: 68, Mismatches: 2, Indels: 13
0.82 0.02 0.16
Matches are distributed among these distances:
61 7 0.10
62 10 0.15
63 15 0.22
64 32 0.47
65 4 0.06
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (62 bp):
AAAATATATATTTTAAGTAAAGATAAGAATAAAATATTATGTTTTTAATTTAAAATAAGAAT
Found at i:56805 original size:64 final size:66
Alignment explanation
Indices: 56727--56850 Score: 182
Period size: 66 Copynumber: 1.9 Consensus size: 66
56717 TAAAATATAG
56727 TTTTAATTTAAAATAAGAAT-AAA-ATATATTTTTA-AGTAAAGATAAGAATAAAATATTTTATG
1 TTTTAATTTAAAATAAGAATAAAATATATATTTTTATAGTAAA-ATAAGAATAAAATATTTTATG
56789 TT
65 TT
* * * *
56791 TTTTAATTTAAAATAAGAGTAAAATATATATTTTTATATTAAATTAATAATAAAATATTT
1 TTTTAATTTAAAATAAGAATAAAATATATATTTTTATAGTAAAATAAGAATAAAATATTT
56851 AAATATATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
64 19 0.36
65 3 0.06
66 26 0.49
67 5 0.09
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (66 bp):
TTTTAATTTAAAATAAGAATAAAATATATATTTTTATAGTAAAATAAGAATAAAATATTTTATGT
T
Found at i:56983 original size:36 final size:37
Alignment explanation
Indices: 56924--57005 Score: 116
Period size: 36 Copynumber: 2.2 Consensus size: 37
56914 ATTTTTACAT
56924 TAAAATAAAAAACATATTTAATAAATTAAGAA-AAAAA
1 TAAAATAAAAAACATATTTAATAAATTAA-AACAAAAA
56961 TAAAA-AATAAAA-ATATTTAATAAATTAAAACAAAAA
1 TAAAATAA-AAAACATATTTAATAAATTAAAACAAAAA
56997 TAAATATAA
1 TAAA-ATAA
57006 TTTTAAAATG
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
35 2 0.05
36 27 0.66
37 10 0.24
38 2 0.05
ACGTcount: A:0.71, C:0.02, G:0.01, T:0.26
Consensus pattern (37 bp):
TAAAATAAAAAACATATTTAATAAATTAAAACAAAAA
Found at i:58497 original size:23 final size:23
Alignment explanation
Indices: 58471--58518 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
58461 ATAAAGTACA
*
58471 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
58494 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
58517 AT
1 AT
58519 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:58921 original size:21 final size:20
Alignment explanation
Indices: 58891--58944 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
58881 GATAGACACT
*
58891 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
58912 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
58935 TTACATTATA
1 TTACATTATA
58945 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:58932 original size:23 final size:23
Alignment explanation
Indices: 58906--58968 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
58896 ATATAACCAT
58906 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
58929 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
58952 TACCTATTACATCATAT
1 TACCTATTACATTATAT
58969 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:59323 original size:430 final size:427
Alignment explanation
Indices: 58630--59473 Score: 1645
Period size: 430 Copynumber: 2.0 Consensus size: 427
58620 GGATCGATAC
58630 TTTAACAGTGTTTCATGTTTTCCACCTACAATATGATTTAATAATTTCATTTGCACAAAAAATTA
1 TTTAACAGTGTTTCATGTTTTCCACCTACAATATGATTTAATAATTTCATTTGCACAAAAAATTA
58695 TTTGATTGTTTTGATATTTTAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACCGTA
66 TTTGATTGTTTTGATATTTTAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACCGTA
58760 ACGTAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGA
131 ACGTAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGA
58825 TAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACAC
196 TAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACAC
58890 TTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTAC
261 TTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTAC
58955 CTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATA
326 CTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATA
59020 CTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
391 CTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
59057 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
1 TTTAACAGTGTTTCATGTTTTCCACCTACAATA-TGATTTAATAATTTCATTTGCACAAAAAATT
59122 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACC
65 ATTTGATTGTTTTGATA-TTT-TAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACC
59187 GTAACGTAAGAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
128 GTAACGTAA-AAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
59252 AAGATAACCTTAAATTAATGTTTTCCACAGTG-AAAAAGTATGGACACTTTTATAAAAAGGATAG
192 AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAG
59316 ACACTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGG
257 ACACTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGG
59381 CTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATC
322 CTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATC
59446 GATACTTTTTTTAAAACTTATGTAATTT
387 GATACTTTTTTTAAAACTTATGTAATTT
59474 TTTTTAAAAT
Statistics
Matches: 413, Mismatches: 0, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
427 33 0.08
428 48 0.12
429 3 0.01
430 242 0.59
431 87 0.21
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (427 bp):
TTTAACAGTGTTTCATGTTTTCCACCTACAATATGATTTAATAATTTCATTTGCACAAAAAATTA
TTTGATTGTTTTGATATTTTAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACCGTA
ACGTAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGA
TAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACAC
TTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTAC
CTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATA
CTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
Found at i:59351 original size:21 final size:20
Alignment explanation
Indices: 59321--59374 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
59311 GATAGACACT
*
59321 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
59342 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
59365 TTACATTATA
1 TTACATTATA
59375 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:59362 original size:23 final size:23
Alignment explanation
Indices: 59336--59398 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
59326 ATATAACCAT
59336 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
59359 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
59382 TACCTATTACATCATAT
1 TACCTATTACATTATAT
59399 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:60348 original size:198 final size:198
Alignment explanation
Indices: 59479--61204 Score: 3237
Period size: 198 Copynumber: 8.7 Consensus size: 198
59469 AATTTTTTTT
59479 AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGG
1 AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGG
*
59544 ATCGACACTTTATTGATTCACCTTGTAAAAATTCATTCTGGAAAAAAAATATCGACACAAAATAT
66 ATCGACACTTTATTGATTCACCTTGTAAAAATTCATTCTGGAAAAAAAATATCGACACAAACTAT
*
59609 ATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGAT
131 ATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGAT
59674 TAA
196 TAA
59677 AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGG
1 AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGG
*
59742 ATCGACACTTTATTGATTCACCTTGT-AAAATTCATTCTGGAAAAAAAATATCGACACAAAATAT
66 ATCGACACTTTATTGATTCACCTTGTAAAAATTCATTCTGGAAAAAAAATATCGACACAAACTAT
*
59806 ATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGAT
131 ATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGAT
59871 TAA
196 TAA
59874 AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGG
1 AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGG
*
59939 ATCGACACTTTATTGATTAACCTTGTAAAAATTCATTCTGGAAAAAAAATATCGACACAAACTAT
66 ATCGACACTTTATTGATTCACCTTGTAAAAATTCATTCTGGAAAAAAAATATCGACACAAACTAT
60004 ATTAGTGTCGACACATT-TTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGAT
131 ATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGAT
*
60068 T-G
196 TAA
60070 AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGG
1 AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGG
60135 ATCGACACTTTATTGATTCACCTTGTAAAAATTCATTCTGGAAAAAAAATATCGACACAAACTAT
66 ATCGACACTTTATTGATTCACCTTGTAAAAATTCATTCTGGAAAAAAAATATCGACACAAACTAT
60200 ATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGAT
131 ATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGAT
60265 TAA
196 TAA
60268 AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGG
1 AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGG
60333 ATCGACACTTTATTGATTCACCTTGTAAAAATTCATTCTGGAAAAAAAATATCGACACAAACTAT
66 ATCGACACTTTATTGATTCACCTTGTAAAAATTCATTCTGGAAAAAAAATATCGACACAAACTAT
60398 ATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGAT
131 ATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGAT
60463 TAA
196 TAA
60466 AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGG
1 AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGG
60531 ATCGACACTTTATTGATTCACCTTGTAAAAATTCATTCTGG-AAAAAAATATCGACACAAACTAT
66 ATCGACACTTTATTGATTCACCTTGTAAAAATTCATTCTGGAAAAAAAATATCGACACAAACTAT
60595 ATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGAT
131 ATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGAT
60660 TAA
196 TAA
60663 AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTTATATATG
1 AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACAC-TTTTTATATATG
60728 GATCGACACTTTATTGATTCACCTTGTAAAAATTCATTCTGGAAAAAAAATATCGACACAAACTA
65 GATCGACACTTTATTGATTCACCTTGTAAAAATTCATTCTGGAAAAAAAATATCGACACAAACTA
60793 TATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGA
130 TATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGA
*
60858 TTGA
195 TTAA
60862 AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTTATATATG
1 AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACAC-TTTTTATATATG
* * * *** *
60927 GATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAAAAAATATCGACACAAACT
65 GATCGACACTTTATTGATTCACCTTG-TAAAAATTCATTCTGGAAAAAAAATATCGACACAAACT
60992 ATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTAG
129 ATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTAG
61057 ATT-A
194 ATTAA
61061 AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTTATATATG
1 AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACAC-TTTTTATATATG
*
61126 GATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAAAAAATATCGACACAAACTA
65 GATCGACACTTTATTGATTCACCTTGTAAAAATTCATTCTGGAAAAAAAATATCGACACAAACTA
*
61191 TATTAGTATCGACA
130 TATTAGTGTCGACA
61205 TGACCCTTAA
Statistics
Matches: 1501, Mismatches: 21, Indels: 12
0.98 0.01 0.01
Matches are distributed among these distances:
196 146 0.10
197 434 0.29
198 551 0.37
199 268 0.18
200 102 0.07
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (198 bp):
AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGG
ATCGACACTTTATTGATTCACCTTGTAAAAATTCATTCTGGAAAAAAAATATCGACACAAACTAT
ATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGAT
TAA
Found at i:61311 original size:37 final size:38
Alignment explanation
Indices: 61270--61349 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
61260 TCTCATTCAT
*
61270 AATTAT-ATTCACATAAAAAAATATAAATCGTATACAA
1 AATTATAAATCACATAAAAAAATATAAATCGTATACAA
** * * *
61307 AATTATAAATCGTATACAAAATTATAAATCTTATACAA
1 AATTATAAATCACATAAAAAAATATAAATCGTATACAA
61345 AATTA
1 AATTA
61350 ACTCGACATT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 6 0.17
38 30 0.83
ACGTcount: A:0.55, C:0.10, G:0.03, T:0.33
Consensus pattern (38 bp):
AATTATAAATCACATAAAAAAATATAAATCGTATACAA
Found at i:61313 original size:19 final size:19
Alignment explanation
Indices: 61286--61349 Score: 110
Period size: 19 Copynumber: 3.4 Consensus size: 19
61276 ATTCACATAA
*
61286 AAAAATATAAATCGTATAC
1 AAAATTATAAATCGTATAC
61305 AAAATTATAAATCGTATAC
1 AAAATTATAAATCGTATAC
*
61324 AAAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
61343 AAAATTA
1 AAAATTA
61350 ACTCGACATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.31
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:63181 original size:33 final size:33
Alignment explanation
Indices: 63144--63209 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
63134 CATCTTAATA
*
63144 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
63177 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
63210 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:65363 original size:24 final size:24
Alignment explanation
Indices: 65326--65378 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
65316 CCGTTCTATC
65326 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
65350 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
65374 TATTT
1 TATTT
65379 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:65734 original size:20 final size:20
Alignment explanation
Indices: 65686--65735 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
65676 TCGACACTTT
65686 TAATTTTACCGGTTTTATCA
1 TAATTTTACCGGTTTTATCA
*
65706 T-TTTGTTACCGGTTTTATCA
1 TAATT-TTACCGGTTTTATCA
65726 TAATTTTACC
1 TAATTTTACC
65736 TGGTATATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.22, C:0.16, G:0.10, T:0.52
Consensus pattern (20 bp):
TAATTTTACCGGTTTTATCA
Found at i:66219 original size:229 final size:228
Alignment explanation
Indices: 65801--66250 Score: 785
Period size: 229 Copynumber: 2.0 Consensus size: 228
65791 TTAAAACTGC
*
65801 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTTATGTTTTCCACCTACAATA
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
**
65866 TTAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTAT
66 TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
* *
65931 TTAGAATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAA
131 TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATAA
*
65996 GTATGGACACTTTTATAAAAATGATATATACTT
196 GTATGGACACTTTTATAAAAAGGATATATACTT
*
66029 TTTTGAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAAT
1 TTTT-AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAAT
*
66094 ATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTTGATATTTTATAAAATATT
65 ATTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTG-TTTTGATATTTTATAAAATATT
* *
66159 ATTTAGATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTC-ACAGTGAAAT
129 ATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAAT
66223 AAGTATGGACACTTTTATAAAAAGGATA
194 AAGTATGGACACTTTTATAAAAAGGATA
66251 GATAATTTAC
Statistics
Matches: 210, Mismatches: 10, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
228 4 0.02
229 134 0.64
230 72 0.34
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (228 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATAA
GTATGGACACTTTTATAAAAAGGATATATACTT
Found at i:71141 original size:32 final size:31
Alignment explanation
Indices: 71069--71145 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
71059 CTAATGTGAC
* *
71069 TCTTAGGTAGGCTCTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
** * *
71100 TCTCGGGTAGGCCCTGTGGCCCTAAGATATAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-CAT
71132 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
71146 CGAAACTTTC
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 23 0.62
32 14 0.38
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.29
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
Found at i:71732 original size:20 final size:21
Alignment explanation
Indices: 71692--71732 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
71682 TTAAAATATG
*
71692 TTTTATTTTGAATACTGATAAC
1 TTTTATTTTG-ATACTCATAAC
71714 TTTTATTTTG-TACTCATAA
1 TTTTATTTTGATACTCATAA
71733 ATGATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.29, C:0.10, G:0.07, T:0.54
Consensus pattern (21 bp):
TTTTATTTTGATACTCATAAC
Found at i:76314 original size:2 final size:2
Alignment explanation
Indices: 76307--76334 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
76297 TTATAGTAGT
76307 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
76335 ATAACATACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:77284 original size:2 final size:2
Alignment explanation
Indices: 77277--77302 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
77267 AATTTCGAGT
77277 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
77303 AATCTAGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:78890 original size:2 final size:2
Alignment explanation
Indices: 78883--78931 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
78873 TATTATTCAA
78883 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
78925 AT AT AT A
1 AT AT AT A
78932 ATTAAAGAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:82268 original size:40 final size:40
Alignment explanation
Indices: 82213--82291 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
82203 TGAATTACTA
*
82213 AAACCTTTGTCCAAAGCTTGATCTTGACAAGTCTAACTTG
1 AAACCTTTGTCCAAAGCCTGATCTTGACAAGTCTAACTTG
82253 AAACCTTTGTCCAAAGCCTGATCTTGACAAGTCTAACTT
1 AAACCTTTGTCCAAAGCCTGATCTTGACAAGTCTAACTT
82292 ACCGGATCAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (40 bp):
AAACCTTTGTCCAAAGCCTGATCTTGACAAGTCTAACTTG
Found at i:85359 original size:2 final size:2
Alignment explanation
Indices: 85354--85379 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
85344 TTTGTGTGTG
85354 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
85380 CATTCACAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:91448 original size:17 final size:18
Alignment explanation
Indices: 91426--91459 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
91416 ATCCATCGAG
91426 GCTGATC-CTACTCCTCT
1 GCTGATCTCTACTCCTCT
*
91443 GCTGATCTCTCCTCCTC
1 GCTGATCTCTACTCCTC
91460 CTCTCGCCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.09, C:0.44, G:0.12, T:0.35
Consensus pattern (18 bp):
GCTGATCTCTACTCCTCT
Found at i:91823 original size:28 final size:28
Alignment explanation
Indices: 91791--91885 Score: 77
Period size: 28 Copynumber: 3.3 Consensus size: 28
91781 AAAAATTATT
91791 TAAAATATTAATTTTTTAATATTTTCGA
1 TAAAATATTAATTTTTTAATATTTTCGA
* * * * * *
91819 TAAAAAAAT-ACTTATAACATTATTTT-TA
1 TAAAATATTAATTTTTTA-A-TATTTTCGA
*
91847 TCTAAAATATTATTTTTTTAATATTTTCGA
1 --TAAAATATTAATTTTTTAATATTTTCGA
91877 TAAAATATT
1 TAAAATATT
91886 TAATATTAAC
Statistics
Matches: 48, Mismatches: 13, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
27 5 0.10
28 18 0.38
29 12 0.25
30 9 0.19
31 4 0.08
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (28 bp):
TAAAATATTAATTTTTTAATATTTTCGA
Done.