Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006183.1 Hibiscus syriacus cultivar Beakdansim tig00014709_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: 57104
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:3020 original size:15 final size:15
Alignment explanation
Indices: 2981--3063 Score: 60
Period size: 15 Copynumber: 5.3 Consensus size: 15
2971 CTTGGGTAGT
2981 TTCTTCTCGGCTCTAGGC
1 TTCTTCTCGG--CT-GGC
*
2999 TTTTTCTCGGCTGGC
1 TTCTTCTCGGCTGGC
* ***
3014 TTCTTCTCAGCTTTT
1 TTCTTCTCGGCTGGC
*
3029 TTC-TCTTCTGCTGGC
1 TTCTTC-TCGGCTGGC
*
3044 TTCTTCTCGGCAGGC
1 TTCTTCTCGGCTGGC
3059 TTCTT
1 TTCTT
3064 TTCAGCTTTT
Statistics
Matches: 51, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
14 2 0.04
15 36 0.71
16 4 0.08
18 9 0.18
ACGTcount: A:0.04, C:0.30, G:0.19, T:0.47
Consensus pattern (15 bp):
TTCTTCTCGGCTGGC
Found at i:3724 original size:32 final size:32
Alignment explanation
Indices: 3683--3749 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
3673 GGTATTACCC
* *
3683 GACATGTTTTCAACCTGACCTGTTTTCAACTT
1 GACATGTTTTCAACCTGACATGTTTTCAACAT
* *
3715 GACATGTTTTTAACCTGACATGTTTTTAACAT
1 GACATGTTTTCAACCTGACATGTTTTCAACAT
3747 GAC
1 GAC
3750 CTGTAAATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.40
Consensus pattern (32 bp):
GACATGTTTTCAACCTGACATGTTTTCAACAT
Found at i:3749 original size:16 final size:16
Alignment explanation
Indices: 3683--3740 Score: 89
Period size: 16 Copynumber: 3.6 Consensus size: 16
3673 GGTATTACCC
3683 GACATGTTTTCAACCT
1 GACATGTTTTCAACCT
* *
3699 GACCTGTTTTCAACTT
1 GACATGTTTTCAACCT
*
3715 GACATGTTTTTAACCT
1 GACATGTTTTCAACCT
3731 GACATGTTTT
1 GACATGTTTT
3741 TAACATGACC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.22, C:0.21, G:0.14, T:0.43
Consensus pattern (16 bp):
GACATGTTTTCAACCT
Found at i:3934 original size:30 final size:28
Alignment explanation
Indices: 3887--3954 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 28
3877 TTAAATGTTA
*
3887 TAATAAAATATTTATTATGAT-AATTATAT
1 TAATAAAATACTTATTAT-ATAAATTAT-T
3916 TAATAAATATACTTATTATATAAAATTATT
1 TAATAAA-ATACTTATTATAT-AAATTATT
3946 TAATAAAAT
1 TAATAAAAT
3955 TAATAAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
29 11 0.31
30 18 0.51
31 6 0.17
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (28 bp):
TAATAAAATACTTATTATATAAATTATT
Found at i:4043 original size:23 final size:23
Alignment explanation
Indices: 4009--4079 Score: 119
Period size: 21 Copynumber: 3.1 Consensus size: 23
3999 ATGCAAAGGA
4009 AAATTAATATAGTTTAATTTATAT
1 AAATT-ATATAGTTTAATTTATAT
4033 AAATTATATAGTTTAA-TTATAT
1 AAATTATATAGTTTAATTTATAT
4055 -AATTATATAGTTTAATTTATAT
1 AAATTATATAGTTTAATTTATAT
4077 AAA
1 AAA
4080 GAATAATAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.33
22 12 0.27
23 13 0.29
24 5 0.11
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
AAATTATATAGTTTAATTTATAT
Found at i:5152 original size:2 final size:2
Alignment explanation
Indices: 5145--5175 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5135 TATGTTTAAT
5145 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 T
5176 TATTCAAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5298 original size:19 final size:19
Alignment explanation
Indices: 5276--5320 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
5266 TTGAGAATAT
5276 AGGGAAACT-GATAATTTAG
1 AGGGAAACTGGA-AATTTAG
*
5295 AGGGAAATTGGGAAATTTAG
1 AGGGAAACT-GGAAATTTAG
5315 AGGGAA
1 AGGGAA
5321 TAGAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 8 0.35
20 13 0.57
21 2 0.09
ACGTcount: A:0.42, C:0.02, G:0.33, T:0.22
Consensus pattern (19 bp):
AGGGAAACTGGAAATTTAG
Found at i:5560 original size:7 final size:7
Alignment explanation
Indices: 5550--5628 Score: 70
Period size: 7 Copynumber: 11.4 Consensus size: 7
5540 ATAGTTTATA
*
5550 TAAACCT
1 TAAACCC
5557 TAAACCC
1 TAAACCC
*
5564 TAAACCT
1 TAAACCC
5571 TAAACCC
1 TAAACCC
*
5578 TAAATCC
1 TAAACCC
**
5585 TAAACTT
1 TAAACCC
***
5592 TAAAAAA
1 TAAACCC
*
5599 TAAACCA
1 TAAACCC
5606 TAAACCC
1 TAAACCC
5613 TAAA-CC
1 TAAACCC
5619 TAAACCC
1 TAAACCC
5626 TAA
1 TAA
5629 TGTATGTATA
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
6 6 0.10
7 52 0.90
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (7 bp):
TAAACCC
Found at i:5874 original size:70 final size:71
Alignment explanation
Indices: 5795--5942 Score: 237
Period size: 70 Copynumber: 2.1 Consensus size: 71
5785 TAATGCATAC
*
5795 ATATATATACTATATTAATATAAATTATAACTTATAAACTATATA-TTTTATATAGTTTATACAT
1 ATATATATACTATATTAATATAAATAATAACTTATAAACTATATACTTTT-TATAGTTTATACAT
5859 ATATA-T
65 ATATAGT
**
5865 ATATATATACTATATTAATATAAATAATATTTTATAAACTATATACTTTTTATAGTTTATACATA
1 ATATATATACTATATTAATATAAATAATAACTTATAAACTATATACTTTTTATAGTTTATACATA
5930 TATAGT
66 TATAGT
*
5936 TTATATA
1 ATATATA
5943 CATAGTTTGT
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
70 61 0.85
71 11 0.15
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (71 bp):
ATATATATACTATATTAATATAAATAATAACTTATAAACTATATACTTTTTATAGTTTATACATA
TATAGT
Found at i:6049 original size:13 final size:13
Alignment explanation
Indices: 6033--6110 Score: 75
Period size: 13 Copynumber: 5.6 Consensus size: 13
6023 AGTTTATAAT
*
6033 TTTATATACATAG
1 TTTATATATATAG
6046 TTTATATATATAG
1 TTTATATATATAG
* * *
6059 TTCACATAAATATAA
1 TT--TATATATATAG
6074 TTTATATATATAG
1 TTTATATATATAG
6087 TTTATAATATATATAG
1 -TT-T-ATATATATAG
6103 TTTATATA
1 TTTATATA
6111 AATTTTGTTG
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
13 27 0.51
14 3 0.06
15 13 0.25
16 10 0.19
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (13 bp):
TTTATATATATAG
Found at i:6099 original size:18 final size:18
Alignment explanation
Indices: 5978--6101 Score: 81
Period size: 18 Copynumber: 6.4 Consensus size: 18
5968 AAACATAATT
* *
5978 TATATGTATAGCTTATAA
1 TATATATATAGTTTATAA
5996 TA-ATTATATAGTTTATAA
1 TATA-TATATAGTTTATAA
*
6014 TATAAATATAGTTTATAA
1 TATATATATAGTTTATAA
*
6032 TTTTATATACATAGTTTATATA
1 ---TATATATATAGTTTATA-A
* **
6054 TATAGTTCACATA-AATATAA
1 TATA--T-ATATAGTTTATAA
6074 TTTATATATATAGTTTATAA
1 --TATATATATAGTTTATAA
6094 TATATATA
1 TATATATA
6102 GTTTATATAA
Statistics
Matches: 84, Mismatches: 10, Indels: 24
0.71 0.08 0.20
Matches are distributed among these distances:
17 1 0.01
18 37 0.44
19 9 0.11
20 7 0.08
21 20 0.24
22 10 0.12
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.48
Consensus pattern (18 bp):
TATATATATAGTTTATAA
Found at i:6938 original size:388 final size:386
Alignment explanation
Indices: 6145--6886 Score: 1041
Period size: 388 Copynumber: 1.9 Consensus size: 386
6135 CGAATATGGG
* *
6145 CAAGAGGAGGGTGAATTGGCAATTAAAATTTCGGTGGAAGCTTTTGCAGAAAATTGAAAATATTT
1 CAAGAGG-GCGTGAATTGGCAATTAAAATTTCGGTGGAAGCTTTTGCAGAAAATTGAAAAGATTT
6210 GCACAACGATTTAGAGTGGTTCGACTTTCTCAACCAAAGACTACGTCCACTACCTTAGCTATCCA
65 GCACAACGATTTAGAGTGGTTCGACTTTCTCAACCAAAGACTACGTCCACTACCTTAGCTATCCA
6275 CACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTCTTTTGAGGACAAAGAGTAACCTTACAA
130 CACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTCTTTTGAGGACAAAGAGTAACCTTACAA
* *
6340 ATCCCTCAATAATTATACCACAAATTCTTGAGAACATTCTCTCCCAAAGAGAACAATACAAATTT
195 ATCCCTCAAGAATTATACCACAAATTCTTGAGAACACTCTCTCCCAAAGAGAACAATACAAATTT
** * *
6405 TGCAAACTTACAAGAAAATCCTCATAAGGCAAGATATTTGCACAATTCTAGAACAAAGAAAGAAC
260 CACAAACTTACAAGAAAATCCTCACAAGGCAAGATATTTGCACAATTCTAAAACAAAGAAAGAAC
* * ** *
6470 ACTCAAGAATAATACAATTGAGTACAATAAGTGTTTGTTGAGTTAATCGATCGATGGAATCGA
325 ACTCAAGAATAATACAATTGAGCACAATAAGTGTTTCTTGAGAAAATCGATC-ATGGAAACGA
* *
6533 CCAAGAGGGGGTGAATTGGCAATTAAAATTTTGGTGGAAGCTTTTGCAGAAAATTGAAAAGATTT
1 -CAAGAGGGCGTGAATTGGCAATTAAAATTTCGGTGGAAGCTTTTGCAGAAAATTGAAAAGATTT
* * * *
6598 GCACAGCGATTTATAGTGGTTCGACTTTCTCAATCAAAGTCTACGTCCACTACCTTAGCTATCCA
65 GCACAACGATTTAGAGTGGTTCGACTTTCTCAACCAAAGACTACGTCCACTACCTTAGCTATCCA
* *
6663 TACTAAGGATTTTCCAACAAATTCACTAATTTGTTCTTTCTTTTGAGGCCAAAGAGTTAACCTTA
130 CACTAAGGATTTTCC-ACAAATTCACTAATTTG-TCTTTCTTTTGAGGACAAAGAG-TAACCTTA
* * * * **
6728 CAACA-CCGTCAAGAATTATACC-CCAATTCTTGAGCACACTCTTTTTCAAAGAGAA-ATATACA
192 CAA-ATCCCTCAAGAATTATACCACAAATTCTTGAGAACACTCTCTCCCAAAGAGAACA-ATACA
* * *
6790 AA-TTCACAAACTTGCAAGGAAAA-CCTCACAAGG-TAGATTGTTTGCACAATTCTAAAAC-AAG
255 AATTTCACAAACTTACAA-GAAAATCCTCACAAGGCAAGA-TATTTGCACAATTCTAAAACAAAG
6851 ATAAGAACACTCAA-AGATAAATACAATTGAGCACAA
318 A-AAGAACACTCAAGA-AT-AATACAATTGAGCACAA
6887 ATTGTGTTCT
Statistics
Matches: 319, Mismatches: 24, Indels: 19
0.88 0.07 0.05
Matches are distributed among these distances:
388 138 0.43
389 78 0.24
390 76 0.24
391 26 0.08
392 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (386 bp):
CAAGAGGGCGTGAATTGGCAATTAAAATTTCGGTGGAAGCTTTTGCAGAAAATTGAAAAGATTTG
CACAACGATTTAGAGTGGTTCGACTTTCTCAACCAAAGACTACGTCCACTACCTTAGCTATCCAC
ACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTCTTTTGAGGACAAAGAGTAACCTTACAAA
TCCCTCAAGAATTATACCACAAATTCTTGAGAACACTCTCTCCCAAAGAGAACAATACAAATTTC
ACAAACTTACAAGAAAATCCTCACAAGGCAAGATATTTGCACAATTCTAAAACAAAGAAAGAACA
CTCAAGAATAATACAATTGAGCACAATAAGTGTTTCTTGAGAAAATCGATCATGGAAACGA
Found at i:7151 original size:21 final size:21
Alignment explanation
Indices: 7125--7180 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
7115 GGGAGCGTCA
*
7125 GTGCATCGATGCATACCCATG
1 GTGCATCGATGCATACCAATG
7146 GTGCATCGATGCATACCAATG
1 GTGCATCGATGCATACCAATG
*
7167 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
7181 CAGTGTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (21 bp):
GTGCATCGATGCATACCAATG
Found at i:7365 original size:45 final size:45
Alignment explanation
Indices: 7280--7367 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
7270 CAAAATAGCA
* *
7280 GAGTGCATCGATGCATGGCTTGTGCATCGATACATCAAATGCACT
1 GAGTGCATCAATGCATGGCTTGTGCATCGATACATAAAATGCACT
7325 GAGTGCATCAATGCATGG-TATGTGCATCGATGA-ATAAAATGCA
1 GAGTGCATCAATGCATGGCT-TGTGCATCGAT-ACATAAAATGCA
7368 TTCGATGTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 1 0.03
45 37 0.95
46 1 0.03
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (45 bp):
GAGTGCATCAATGCATGGCTTGTGCATCGATACATAAAATGCACT
Found at i:12791 original size:45 final size:45
Alignment explanation
Indices: 12742--12829 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
12732 AAAATAGCCA
*
12742 GAGTGCATCGATGCATGGCT-TGTGCATCGATGCATCAAATGCACT
1 GAGTGCATCGATGCATGG-TATGTGCATCGATGCATAAAATGCACT
12787 GAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGCA
1 GAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGCA
12830 TTCGATGTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 1 0.02
45 40 0.98
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.26
Consensus pattern (45 bp):
GAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGCACT
Found at i:13446 original size:111 final size:111
Alignment explanation
Indices: 13252--13474 Score: 446
Period size: 111 Copynumber: 2.0 Consensus size: 111
13242 TTGATCAATG
13252 GCTTCTAAGCTTGCTTAAATACTCCTTCAATTGATTCTGAACGTTGAGGATGATTAGTGGAGTCA
1 GCTTCTAAGCTTGCTTAAATACTCCTTCAATTGATTCTGAACGTTGAGGATGATTAGTGGAGTCA
13317 ATAGAGCCGCTTAAGTGTGAAAACAATTAATAAAACAGGTGGGAGC
66 ATAGAGCCGCTTAAGTGTGAAAACAATTAATAAAACAGGTGGGAGC
13363 GCTTCTAAGCTTGCTTAAATACTCCTTCAATTGATTCTGAACGTTGAGGATGATTAGTGGAGTCA
1 GCTTCTAAGCTTGCTTAAATACTCCTTCAATTGATTCTGAACGTTGAGGATGATTAGTGGAGTCA
13428 ATAGAGCCGCTTAAGTGTGAAAACAATTAATAAAACAGGTGGGAGC
66 ATAGAGCCGCTTAAGTGTGAAAACAATTAATAAAACAGGTGGGAGC
13474 G
1 G
13475 TATGGTGCAT
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 112 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (111 bp):
GCTTCTAAGCTTGCTTAAATACTCCTTCAATTGATTCTGAACGTTGAGGATGATTAGTGGAGTCA
ATAGAGCCGCTTAAGTGTGAAAACAATTAATAAAACAGGTGGGAGC
Found at i:13709 original size:65 final size:64
Alignment explanation
Indices: 13572--13709 Score: 181
Period size: 64 Copynumber: 2.1 Consensus size: 64
13562 GTACATTGAG
* *
13572 TGTGCATCGATGCATAAAATACATTTGGTATTTCAAGCAAGCATGAGTGCATCGATGCATGGTC
1 TGTGCATCGATGCATAAAATACATTTGATATTTCAAGCAAGCATGAGTGCATCGATGCATGGTA
* * * *
13636 TGTACATCGATGCATAAAAT-CAATTTGATGTTTTAATCATA-CATGGAGTGCATCGATGCATGG
1 TGTGCATCGATGCATAAAATAC-ATTTGATATTTCAAGCA-AGCAT-GAGTGCATCGATGCATGG
13699 TA
63 TA
13701 TGTGCATCG
1 TGTGCATCG
13710 GTACACAAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
63 1 0.02
64 35 0.55
65 28 0.44
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (64 bp):
TGTGCATCGATGCATAAAATACATTTGATATTTCAAGCAAGCATGAGTGCATCGATGCATGGTA
Found at i:16635 original size:151 final size:152
Alignment explanation
Indices: 16461--16763 Score: 547
Period size: 151 Copynumber: 2.0 Consensus size: 152
16451 CACTCATATA
* *
16461 TAAAAAATTATATTATTAATATATGCATATCAATTCTCAAAAATATTTTTGAATTTGTCACTACA
1 TAAAAAAATATATTATTAATATATGCATATCAATTCTCAAAAATATTTTTGAATATGTCACTACA
*
16526 AATATAATCCTTCAAATTAACATGTAAAAACAAATATGTATTAAAATCCATAGCCTATATATA-G
66 AATATAATCCTTCAAATTAACATGTAAAAACAAATATGTACTAAAATCCATAGCCTATATATAGG
16590 GGTTTTCAAAATAAGG-TACCCG
131 GGTTTTCAAAAT-AGGATACCCG
*
16612 TAAAAAAATATATTATTAATATATGTATATCAATTCTCAAAAATATTTTTGAATATGTCACTACA
1 TAAAAAAATATATTATTAATATATGCATATCAATTCTCAAAAATATTTTTGAATATGTCACTACA
16677 AATATAATCCTTCAAATTAACATGTAAAAACAAATATGTACTAAAATCCATAGCCTATATATAGG
66 AATATAATCCTTCAAATTAACATGTAAAAACAAATATGTACTAAAATCCATAGCCTATATATAGG
16742 GGTTTTCAAAATAGGATACCCG
131 GGTTTTCAAAATAGGATACCCG
16764 AGATTTCTAG
Statistics
Matches: 146, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
151 127 0.87
152 19 0.13
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.34
Consensus pattern (152 bp):
TAAAAAAATATATTATTAATATATGCATATCAATTCTCAAAAATATTTTTGAATATGTCACTACA
AATATAATCCTTCAAATTAACATGTAAAAACAAATATGTACTAAAATCCATAGCCTATATATAGG
GGTTTTCAAAATAGGATACCCG
Found at i:16969 original size:17 final size:18
Alignment explanation
Indices: 16937--16975 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
16927 TAATATATAT
16937 ATATAAATATAATTTAAA
1 ATATAAATATAATTTAAA
*
16955 ATATAATTA-AATTTAAA
1 ATATAAATATAATTTAAA
16972 ATAT
1 ATAT
16976 TTTGAAGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATAAATATAATTTAAA
Found at i:17035 original size:39 final size:39
Alignment explanation
Indices: 16991--17177 Score: 295
Period size: 39 Copynumber: 4.8 Consensus size: 39
16981 AGTTAATAGA
* *
16991 AATAATTTAGATTGTTAGGGTGAAATAATTTAAGAAATT
1 AATAATTTAGAATGTTATGGTGAAATAATTTAAGAAATT
*
17030 AATAATTTAGAATGTTATGGTGAAATAATTTAAGAAAAT
1 AATAATTTAGAATGTTATGGTGAAATAATTTAAGAAATT
* *
17069 AAGAATTAAGAATGTTATGGTGAAATAATTTAAGAAATT
1 AATAATTTAGAATGTTATGGTGAAATAATTTAAGAAATT
17108 AATAATTTAGAATGTTATGGTGAAATAATTTAAGATAA-T
1 AATAATTTAGAATGTTATGGTGAAATAATTTAAGA-AATT
* *
17147 AAGAATTAAGAATGTTATGGTGAAATAATTT
1 AATAATTTAGAATGTTATGGTGAAATAATTT
17178 GACAATTAGG
Statistics
Matches: 137, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
39 135 0.99
40 2 0.01
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.36
Consensus pattern (39 bp):
AATAATTTAGAATGTTATGGTGAAATAATTTAAGAAATT
Found at i:17092 original size:78 final size:78
Alignment explanation
Indices: 16994--17177 Score: 332
Period size: 78 Copynumber: 2.4 Consensus size: 78
16984 TAATAGAAAT
* * *
16994 AATTTAGATTGTTAGGGTGAAATAATTTAAGAAATTAATAATTTAGAATGTTATGGTGAAATAAT
1 AATTAAGAATGTTATGGTGAAATAATTTAAGAAATTAATAATTTAGAATGTTATGGTGAAATAAT
17059 TTAAGAAAATAAG
66 TTAAGAAAATAAG
17072 AATTAAGAATGTTATGGTGAAATAATTTAAGAAATTAATAATTTAGAATGTTATGGTGAAATAAT
1 AATTAAGAATGTTATGGTGAAATAATTTAAGAAATTAATAATTTAGAATGTTATGGTGAAATAAT
*
17137 TTAAGATAATAAG
66 TTAAGAAAATAAG
17150 AATTAAGAATGTTATGGTGAAATAATTT
1 AATTAAGAATGTTATGGTGAAATAATTT
17178 GACAATTAGG
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 102 1.00
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.36
Consensus pattern (78 bp):
AATTAAGAATGTTATGGTGAAATAATTTAAGAAATTAATAATTTAGAATGTTATGGTGAAATAAT
TTAAGAAAATAAG
Found at i:22924 original size:2 final size:2
Alignment explanation
Indices: 22881--22908 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22871 ACAACAAATA
22881 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
22909 TGTAATTTAA
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):
AT
Found at i:23044 original size:29 final size:29
Alignment explanation
Indices: 22980--23051 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 29
22970 TAAAATTATC
22980 TTTTATTTTTGTTATAAATTATTAAATACA
1 TTTTATTTTT-TTATAAATTATTAAATACA
* * *
23010 TTTTATTTTTTTCTTAACTTATTAAATATA
1 TTTTATTTTTTT-ATAAATTATTAAATACA
23040 -TTTATTTTTTTA
1 TTTTATTTTTTTA
23052 ATGTAAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 13 0.35
30 24 0.65
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (29 bp):
TTTTATTTTTTTATAAATTATTAAATACA
Found at i:23497 original size:180 final size:182
Alignment explanation
Indices: 23162--23507 Score: 633
Period size: 180 Copynumber: 1.9 Consensus size: 182
23152 TTATTTGAAA
23162 AAAATACCTTAACTTAAAATAAATTTAAATATTTTATTATTAATTTAATATAAAAATAAATATTT
1 AAAATACCTTAACTTAAAATAAATTTAAATATTTTATTATTAATTTAATATAAAAATAAATATTT
*
23227 TATTATTATCTTAACTTTTAAAATTTATTTTTTTTAAATATATTAACTTAAATTATATTTTATTT
66 TATTATTATCTTAACTTTTAAAATTTATTTTTTTAAAATATATTAACTTAAATTATATTTTATTT
* *
23292 TTAAATTAAAATAAATTTTGAAGTTAAGATATTTTATTATTAATTTAATATT
131 TAAAATTAAAATAAATTTTGAAGTTAAGACATTTTATTATTAATTTAATATT
*
23344 AAAATACCTTAACTTAAAATATATTTAAATATTTTATTATTAA-TTAATATAAAAATAAATATTT
1 AAAATACCTTAACTTAAAATAAATTTAAATATTTTATTATTAATTTAATATAAAAATAAATATTT
23408 TATTATTATCTTAACTTTTAAAATTTA-TTTTTTAAAATATATTAACTTAAATTATATTTTATTT
66 TATTATTATCTTAACTTTTAAAATTTATTTTTTTAAAATATATTAACTTAAATTATATTTTATTT
*
23472 TAAAATTAAAATACATTTTGAAGTTAAGACATTTTA
131 TAAAATTAAAATAAATTTTGAAGTTAAGACATTTTA
23508 ATATATTTTT
Statistics
Matches: 159, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
180 69 0.43
181 48 0.30
182 42 0.26
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.50
Consensus pattern (182 bp):
AAAATACCTTAACTTAAAATAAATTTAAATATTTTATTATTAATTTAATATAAAAATAAATATTT
TATTATTATCTTAACTTTTAAAATTTATTTTTTTAAAATATATTAACTTAAATTATATTTTATTT
TAAAATTAAAATAAATTTTGAAGTTAAGACATTTTATTATTAATTTAATATT
Found at i:23593 original size:29 final size:28
Alignment explanation
Indices: 23526--23599 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 28
23516 TTAAAATTTT
* *
23526 AGATAATG-ATAAAATATATTTTAATTTA
1 AGAT-ATGAATAAAATATATTTTAAGTGA
* **
23554 AAATAAAAATAAAATATATTTTTAAGTGA
1 AGATATGAATAAAATATA-TTTTAAGTGA
23583 AGATATGAATAAAATAT
1 AGATATGAATAAAATAT
23600 TTAAATGTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
27 1 0.03
28 13 0.36
29 22 0.61
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.36
Consensus pattern (28 bp):
AGATATGAATAAAATATATTTTAAGTGA
Found at i:23722 original size:29 final size:30
Alignment explanation
Indices: 23677--23751 Score: 118
Period size: 29 Copynumber: 2.6 Consensus size: 30
23667 TTTTTTTACA
*
23677 TTAAAATAAAAAT-AAATATATTTAATAAG
1 TTAAAACAAAAATAAAATATATTTAATAAG
*
23706 TTAAGA-AAAAATAAAATATATTTAATAAG
1 TTAAAACAAAAATAAAATATATTTAATAAG
23735 TTAAAACAAAAATAAAA
1 TTAAAACAAAAATAAAA
23752 GATAATTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
28 6 0.14
29 26 0.62
30 10 0.24
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.29
Consensus pattern (30 bp):
TTAAAACAAAAATAAAATATATTTAATAAG
Found at i:24026 original size:17 final size:17
Alignment explanation
Indices: 24000--24033 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
23990 GGTGGAAAAT
* *
24000 AAATATATTAAATTAAA
1 AAATAAATTAAAATAAA
24017 AAATAAATTAAAATAAA
1 AAATAAATTAAAATAAA
24034 TTTAGTCATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATAAATTAAAATAAA
Found at i:24277 original size:39 final size:39
Alignment explanation
Indices: 24234--24319 Score: 163
Period size: 39 Copynumber: 2.2 Consensus size: 39
24224 CGGTGACTTG
*
24234 ATTGAAACATTTAAATAGTTGAGTGGTCTGATTGATTCA
1 ATTGAAACATTTAAATAGTTGAGTGGTCTAATTGATTCA
24273 ATTGAAACATTTAAATAGTTGAGTGGTCTAATTGATTCA
1 ATTGAAACATTTAAATAGTTGAGTGGTCTAATTGATTCA
24312 ATTGAAAC
1 ATTGAAAC
24320 TTCGATGGTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.37
Consensus pattern (39 bp):
ATTGAAACATTTAAATAGTTGAGTGGTCTAATTGATTCA
Found at i:25634 original size:18 final size:17
Alignment explanation
Indices: 25601--25634 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
25591 GAATAATTAA
25601 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
25618 ATAAAATCATTAAAATA
1 ATAAAAT-ATCAAAATA
25635 ATACAGACTG
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:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:29394 original size:18 final size:17
Alignment explanation
Indices: 29367--29400 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
29357 AGAATAGAAA
*
29367 TCAAATAATTTGAATAAC
1 TCAAAAAATTT-AATAAC
29385 TCAAAAAATTTAATAA
1 TCAAAAAATTTAATAA
29401 TTAGTTGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.32
Consensus pattern (17 bp):
TCAAAAAATTTAATAAC
Found at i:30142 original size:11 final size:10
Alignment explanation
Indices: 30125--30161 Score: 56
Period size: 11 Copynumber: 3.5 Consensus size: 10
30115 TAGATTTATT
30125 AAAAAAAATA
1 AAAAAAAATA
30135 AGAAAAAAATA
1 A-AAAAAAATA
30146 AAAAAATAATA
1 AAAAAA-AATA
30157 AAAAA
1 AAAAA
30162 TACTAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 6 0.24
11 19 0.76
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (10 bp):
AAAAAAAATA
Found at i:43803 original size:14 final size:15
Alignment explanation
Indices: 43784--43823 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
43774 AATGGGAAGT
43784 AATCCCTGC-TAATA
1 AATCCCTGCATAATA
43798 AATCCCTGCATAAT-
1 AATCCCTGCATAATA
*
43812 AATCTCTGCATA
1 AATCCCTGCATA
43824 TAGACAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 20 0.83
15 4 0.17
ACGTcount: A:0.35, C:0.28, G:0.07, T:0.30
Consensus pattern (15 bp):
AATCCCTGCATAATA
Found at i:51736 original size:29 final size:29
Alignment explanation
Indices: 51703--51778 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
51693 GCCCAACACA
*
51703 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCCCTCCGCGCGACCTTG
*
51732 TAGGTCGCCATGCCATCCGCGCGACCTTG
1 TAGGTCGCCATGCCCTCCGCGCGACCTTG
*
51761 TAGGTCGCCATGCACTCC
1 TAGGTCGCCATGCCCTCC
51779 CAGCGTCCTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.13, C:0.38, G:0.28, T:0.21
Consensus pattern (29 bp):
TAGGTCGCCATGCCCTCCGCGCGACCTTG
Found at i:51788 original size:29 final size:27
Alignment explanation
Indices: 51703--51788 Score: 100
Period size: 29 Copynumber: 3.0 Consensus size: 27
51693 GCCCAACACA
*
51703 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATG-CCTCC-CGCGACCTTG
51732 TAGGTCGCCATGCCATCCGCGCGACCTTG
1 TAGGTCGCCATGCC-TCC-CGCGACCTTG
*
51761 TAGGTCGCCATGCACTCCCAGCGTCCTT
1 TAGGTCGCCATGC-CTCCC-GCGACCTT
51789 AGACTGCTCC
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
28 3 0.06
29 48 0.92
30 1 0.02
ACGTcount: A:0.13, C:0.38, G:0.27, T:0.22
Consensus pattern (27 bp):
TAGGTCGCCATGCCTCCCGCGACCTTG
Found at i:52265 original size:10 final size:10
Alignment explanation
Indices: 52249--52283 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
52239 ATTTGGCGAG
52249 AGAAAGGAAA
1 AGAAAGGAAA
*
52259 GGAAAGGAAA
1 AGAAAGGAAA
52269 AGAAAGGAAA
1 AGAAAGGAAA
52279 A-AAAG
1 AGAAAG
52284 AAGAATAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 4 0.17
10 19 0.83
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (10 bp):
AGAAAGGAAA
Found at i:52435 original size:21 final size:21
Alignment explanation
Indices: 52410--52453 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
52400 AATTTAGTTA
52410 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
52431 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
52452 AT
1 AT
52454 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:52463 original size:28 final size:28
Alignment explanation
Indices: 52430--52483 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
52420 TAGTATAAAT
52430 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAGTTTGTTAGTTTAAGTTATATTA
52458 TATTAGTTTGTTAGTTTAAGTTATAT
1 TATTAGTTTGTTAGTTTAAGTTATAT
52484 ATTAGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (28 bp):
TATTAGTTTGTTAGTTTAAGTTATATTA
Found at i:53226 original size:2 final size:2
Alignment explanation
Indices: 53221--53251 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
53211 AATCTAAATT
53221 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 T
53252 TTATTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53256 original size:4 final size:4
Alignment explanation
Indices: 53249--53275 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
53239 TATATATATA
53249 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
53276 AGAGAAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:56107 original size:27 final size:25
Alignment explanation
Indices: 56076--56125 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 25
56066 AAATTATAAT
56076 AATTATTAGTAATGATTATAATAATGA
1 AATTATTAGTAAT-ATT-TAATAATGA
*
56103 AATTATTATTAATATTTAATAAT
1 AATTATTAGTAATATTTAATAAT
56126 TTGATAGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.32
26 3 0.14
27 12 0.55
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (25 bp):
AATTATTAGTAATATTTAATAATGA
Found at i:56215 original size:117 final size:104
Alignment explanation
Indices: 56071--56309 Score: 300
Period size: 117 Copynumber: 2.2 Consensus size: 104
56061 TATTTAAATT
*
56071 ATAATAATTA-TTAGTAATGATTATAATAATGAAATTATTATTAATATTTAATAATTTGATAGTA
1 ATAATAATGATTTAGTAATGATTATAATAATGAAATTATTATTAATATTTAATAATTTGATAGTA
*
56135 ATGATTTAGTAATGATTAGTAATAATGAATTATTATTAATTTAATGATTTG
66 ATGA--TAGTAAT-A--A--AAT--T--ATTATTAAT-ATTTAATGATTTG
* * * *
56186 ATAGTAATGATTTAGTAATTATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGGTAGT
1 ATAATAATGATTTAGTAATGATTA-TAATAATGAAATTATTATTAATATTTAATAATTTGATAGT
56251 AATGATAGTAATAAAATTATTATTAATATTTAATGATTTG
65 AATGATAGTAATAAAATTATTATTAATATTTAATGATTTG
56291 ATAATAATGATTTAGTAAT
1 ATAATAATGATTTAGTAAT
56310 AATGAAATTA
Statistics
Matches: 115, Mismatches: 7, Indels: 14
0.85 0.05 0.10
Matches are distributed among these distances:
105 31 0.27
106 8 0.07
108 1 0.01
110 3 0.03
112 1 0.01
114 1 0.01
115 15 0.13
116 12 0.10
117 43 0.37
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (104 bp):
ATAATAATGATTTAGTAATGATTATAATAATGAAATTATTATTAATATTTAATAATTTGATAGTA
ATGATAGTAATAAAATTATTATTAATATTTAATGATTTG
Found at i:56272 original size:45 final size:46
Alignment explanation
Indices: 56214--56311 Score: 153
Period size: 45 Copynumber: 2.1 Consensus size: 46
56204 TTATTAGTAA
* * *
56214 TAATGAAATTATTATTAATATTTAATGATTTGGTAGTAATGA-TAG
1 TAATAAAATTATTATTAATATTTAATGATTTGATAATAATGATTAG
56259 TAATAAAATTATTATTAATATTTAATGATTTGATAATAATGATTTAG
1 TAATAAAATTATTATTAATATTTAATGATTTGATAATAATGA-TTAG
56306 TAATAA
1 TAATAA
56312 TGAAATTATA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
45 39 0.81
47 9 0.19
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.45
Consensus pattern (46 bp):
TAATAAAATTATTATTAATATTTAATGATTTGATAATAATGATTAG
Found at i:56340 original size:14 final size:14
Alignment explanation
Indices: 56281--56340 Score: 68
Period size: 14 Copynumber: 4.3 Consensus size: 14
56271 TATTAATATT
*
56281 TAATGATTTGATAA
1 TAATGATTTAATAA
*
56295 TAATGATTTAGTAA
1 TAATGATTTAATAA
*
56309 TAATGAAATT-ATAA
1 TAATG-ATTTAATAA
*
56323 TAATGATTTAATAC
1 TAATGATTTAATAA
56337 TAAT
1 TAAT
56341 AGAGTAATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
13 3 0.08
14 32 0.84
15 3 0.08
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.42
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:56520 original size:11 final size:11
Alignment explanation
Indices: 56504--56818 Score: 67
Period size: 11 Copynumber: 28.3 Consensus size: 11
56494 TAACCATAAA
56504 AATGATTTAAT
1 AATGATTTAAT
56515 AATGATTTAAT
1 AATGATTTAAT
* * * * *
56526 ATTTAATGATTT
1 AATGATTTA-AT
* *
56538 GATGATTTAGT
1 AATGATTTAAT
56549 AATGATTT--T
1 AATGATTTAAT
56558 AAT-ATTTAAT
1 AATGATTTAAT
*
56568 GATTTGATGATTTAGT
1 -A----ATGATTTAAT
56584 AATGATTTGATAAT
1 AATGA-TT--TAAT
56598 AATGATTTAAT
1 AATGATTTAAT
*
56609 CATGATTT--T
1 AATGATTTAAT
56618 AA--ATTTAAT
1 AATGATTTAAT
*
56627 GATTGATGATTTAGT
1 -A---ATGATTTAAT
*
56642 AATG-TGATAAT
1 AATGAT-TTAAT
*
56653 AATCA--TAAT
1 AATGATTTAAT
56662 AATGATTTAAT
1 AATGATTTAAT
*
56673 AATCA--TAAT
1 AATGATTTAAT
* * *
56682 ATTAATTTAGT
1 AATGATTTAAT
*
56693 AATCATTATAAT
1 AATGATT-TAAT
56705 AATGATTTAAT
1 AATGATTTAAT
56716 AATGA--TAAT
1 AATGATTTAAT
*
56725 -ATGA-TTAGT
1 AATGATTTAAT
*
56734 -ATGATTGAGATTAT
1 AATGATT----TAAT
56748 AATGATTTGAAACT
1 AATGATTT--AA-T
*
56762 AATGA-TTACT
1 AATGATTTAAT
*
56772 AATGA-TAAAT
1 AATGATTTAAT
*
56782 AATGAAATTATAT
1 AATG-ATTTA-AT
*
56795 AATAATTT-AT
1 AATGATTTAAT
56805 AATGATTTAAT
1 AATGATTTAAT
56816 AAT
1 AAT
56819 TATTACAAAT
Statistics
Matches: 223, Mismatches: 40, Indels: 82
0.65 0.12 0.24
Matches are distributed among these distances:
7 4 0.02
8 8 0.04
9 33 0.15
10 26 0.12
11 82 0.37
12 21 0.09
13 11 0.05
14 17 0.08
15 15 0.07
16 6 0.03
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.44
Consensus pattern (11 bp):
AATGATTTAAT
Found at i:56537 original size:8 final size:8
Alignment explanation
Indices: 56514--56581 Score: 68
Period size: 8 Copynumber: 8.2 Consensus size: 8
56504 AATGATTTAA
56514 TAATGATT
1 TAATGATT
56522 TAAT-ATT
1 TAATGATT
56529 TAATGATT
1 TAATGATT
*
56537 TGATGATTT
1 TAATGA-TT
56546 AGTAATGATTT
1 --TAATGA-TT
56557 TAAT-ATT
1 TAATGATT
56564 TAATGATT
1 TAATGATT
*
56572 TGATGATT
1 TAATGATT
56580 TA
1 TA
56582 GTAATGATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
7 13 0.25
8 24 0.47
9 6 0.12
11 8 0.16
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.51
Consensus pattern (8 bp):
TAATGATT
Found at i:56553 original size:19 final size:18
Alignment explanation
Indices: 56505--56594 Score: 84
Period size: 19 Copynumber: 5.1 Consensus size: 18
56495 AACCATAAAA
*
56505 ATGATTTAATAATGATTTA
1 ATGATTT-ATAATGATTTG
56524 AT-A-TT-TAATGATTTG
1 ATGATTTATAATGATTTG
56539 ATGATTTAGTAATGATTT-
1 ATGATTTA-TAATGATTTG
*
56557 -TAATATT-TAATGATTTG
1 ATGAT-TTATAATGATTTG
56574 ATGATTTAGTAATGATTTG
1 ATGATTTA-TAATGATTTG
56593 AT
1 AT
56595 AATAATGATT
Statistics
Matches: 59, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
15 11 0.19
16 10 0.17
17 9 0.15
18 6 0.10
19 23 0.39
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (18 bp):
ATGATTTATAATGATTTG
Found at i:56566 original size:35 final size:35
Alignment explanation
Indices: 56505--56591 Score: 158
Period size: 35 Copynumber: 2.5 Consensus size: 35
56495 AACCATAAAA
*
56505 ATGATTTAATAATGA-TTTAATATTTAATGATTTG
1 ATGATTTAGTAATGATTTTAATATTTAATGATTTG
56539 ATGATTTAGTAATGATTTTAATATTTAATGATTTG
1 ATGATTTAGTAATGATTTTAATATTTAATGATTTG
56574 ATGATTTAGTAATGATTT
1 ATGATTTAGTAATGATTT
56592 GATAATAATG
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
34 14 0.27
35 37 0.73
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.51
Consensus pattern (35 bp):
ATGATTTAGTAATGATTTTAATATTTAATGATTTG
Found at i:56569 original size:16 final size:15
Alignment explanation
Indices: 56514--56608 Score: 66
Period size: 19 Copynumber: 5.8 Consensus size: 15
56504 AATGATTTAA
56514 TAATGATTTAATATT
1 TAATGATTTAATATT
*
56529 TAATGATTTGATGATTT
1 TAATGATTTAAT-A-TT
56546 AGTAATGATTTTAATATT
1 --TAATGA-TTTAATATT
*
56564 TAATGATTTGATGATTT
1 TAATGATTTAAT-A-TT
* *
56581 AGTAATGATTTGATA-A
1 --TAATGATTTAATATT
56597 TAATGATTTAAT
1 TAATGATTTAAT
56609 CATGATTTTA
Statistics
Matches: 66, Mismatches: 5, Indels: 19
0.73 0.06 0.21
Matches are distributed among these distances:
14 11 0.17
15 16 0.24
16 8 0.12
17 4 0.06
18 3 0.05
19 19 0.29
20 5 0.08
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (15 bp):
TAATGATTTAATATT
Found at i:56687 original size:23 final size:23
Alignment explanation
Indices: 56649--56726 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 23
56639 AGTAATGTGA
56649 TAATAATCAT-A-A-TAATGATT
1 TAATAATCATAATATTAATGATT
56669 TAATAATCATAATATT-A--ATT
1 TAATAATCATAATATTAATGATT
* * *
56689 TAGTAATCATTATAATAATGATT
1 TAATAATCATAATATTAATGATT
*
56712 TAATAATGATAATAT
1 TAATAATCATAATAT
56727 GATTAGTATG
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
20 26 0.58
21 2 0.04
22 2 0.04
23 15 0.33
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (23 bp):
TAATAATCATAATATTAATGATT
Found at i:56952 original size:18 final size:18
Alignment explanation
Indices: 56893--56956 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 18
56883 ATAGTCAAAT
56893 TTATTAATGATTTA-TAA
1 TTATTAATGATTTAGTAA
*
56910 ATATTTAATGATTT-G--A
1 TTA-TTAATGATTTAGTAA
*
56926 -TACTAATGATTTAGTAA
1 TTATTAATGATTTAGTAA
56943 TTATTAATGATTTA
1 TTATTAATGATTTA
56957 TTATTAATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
14 9 0.24
15 3 0.08
16 1 0.03
17 3 0.08
18 22 0.58
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (18 bp):
TTATTAATGATTTAGTAA
Found at i:56961 original size:14 final size:15
Alignment explanation
Indices: 56893--56975 Score: 64
Period size: 14 Copynumber: 5.3 Consensus size: 15
56883 ATAGTCAAAT
56893 TTATTAATGATTTATAA
1 TTATTAATGA-TT-TAA
* *
56910 ATATTTAATGATTTGA
1 TTA-TTAATGATTTAA
*
56926 -TACTAATGATTTAGTAA
1 TTATTAATGA-TT--TAA
56943 TTATTAATGATTT-A
1 TTATTAATGATTTAA
56957 TTATTAAT-ATTTAA
1 TTATTAATGATTTAA
56971 TTATT
1 TTATT
56976 TGATACTAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
13 4 0.07
14 21 0.38
15 5 0.09
16 2 0.04
17 8 0.15
18 15 0.27
ACGTcount: A:0.39, C:0.01, G:0.07, T:0.53
Consensus pattern (15 bp):
TTATTAATGATTTAA
Done.