Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000695.1 Hibiscus syriacus cultivar Beakdansim tig00001355_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: 80144
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:779 original size:24 final size:25
Alignment explanation
Indices: 752--814 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
742 CAATTTACAT
* *
752 GGCACTACGGTTGC-ATTTCTACGC
1 GGCACTTCGGTTGCAAATTCTACGC
*
776 GGCACTTCGG-TGCAAATTCTACGT
1 GGCACTTCGGTTGCAAATTCTACGC
800 GGCACTTCGG-TGCAA
1 GGCACTTCGGTTGCAA
815 TGATACGAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
23 3 0.09
24 32 0.91
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (25 bp):
GGCACTTCGGTTGCAAATTCTACGC
Found at i:5303 original size:23 final size:22
Alignment explanation
Indices: 5259--5304 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
5249 AAATCATAAG
*
5259 TTATATGATATGAGGTAAGTTA
1 TTATATGACATGAGGTAAGTTA
* *
5281 TTATATGTACATGATGTATGTTA
1 TTATATG-ACATGAGGTAAGTTA
5304 T
1 T
5305 GATGATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.46
Consensus pattern (22 bp):
TTATATGACATGAGGTAAGTTA
Found at i:5631 original size:20 final size:20
Alignment explanation
Indices: 5606--5643 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5596 GTCTACGCGG
*
5606 TCCTTTGGGACATATATGTA
1 TCCTTTGGAACATATATGTA
*
5626 TCCTTTGGAACATTTATG
1 TCCTTTGGAACATATATG
5644 AGGTCCTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (20 bp):
TCCTTTGGAACATATATGTA
Found at i:5783 original size:24 final size:24
Alignment explanation
Indices: 5729--5791 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
5719 ACAATTTACA
* * *
5729 TGGCACTACGGTGC-ATTTCTACG
1 TGGCACTTCGGTGCAAATTCAACG
*
5752 CGGCACTTCGGTGCAAATTCAACG
1 TGGCACTTCGGTGCAAATTCAACG
5776 TGGCACTTCGGTGCAA
1 TGGCACTTCGGTGCAA
5792 TGATACGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 12 0.35
24 22 0.65
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (24 bp):
TGGCACTTCGGTGCAAATTCAACG
Found at i:10467 original size:23 final size:22
Alignment explanation
Indices: 10423--10468 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
10413 AAATCATAAG
*
10423 TTATATTATATGAGGTAAGTTA
1 TTATATTACATGAGGTAAGTTA
* *
10445 TTATATGTACATGATGTATGTTA
1 TTATAT-TACATGAGGTAAGTTA
10468 T
1 T
10469 GAGACATGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.48
Consensus pattern (22 bp):
TTATATTACATGAGGTAAGTTA
Found at i:10944 original size:24 final size:24
Alignment explanation
Indices: 10917--10963 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
10907 TACGGTTCAT
10917 TTCTACGCGACACTTCGGTGCAAA
1 TTCTACGCGACACTTCGGTGCAAA
* * *
10941 TTCTACGTGGCACTTTGGTGCAA
1 TTCTACGCGACACTTCGGTGCAA
10964 TTATAGGAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (24 bp):
TTCTACGCGACACTTCGGTGCAAA
Found at i:12849 original size:14 final size:14
Alignment explanation
Indices: 12805--12852 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
12795 TATTATTATT
12805 ATTATTATTAAAT-
1 ATTATTATTAAATA
*
12818 ATTATTATT-AGTA
1 ATTATTATTAAATA
12831 TATTATTATTAAATA
1 -ATTATTATTAAATA
12846 ATTATTA
1 ATTATTA
12853 CAAGCCCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 2 0.07
13 9 0.30
14 16 0.53
15 3 0.10
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (14 bp):
ATTATTATTAAATA
Found at i:12852 original size:3 final size:3
Alignment explanation
Indices: 12794--12841 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
12784 TCATTTAAAT
* *
12794 TTA TTA TTA TTA TTA TTA TTAA ATA TTA TTA TTA GTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
12839 TTA
1 TTA
12842 AATAATTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
2 2 0.05
3 36 0.90
4 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:15146 original size:19 final size:19
Alignment explanation
Indices: 15106--15149 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
15096 TCTTTTCAAA
*
15106 ATTTTTATATATACTTATT
1 ATTTTCATATATACTTATT
*
15125 ATTTTCATA-ATATTTATAT
1 ATTTTCATATATACTTAT-T
15144 ATTTTC
1 ATTTTC
15150 TTATTAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTCATATATACTTATT
Found at i:15146 original size:22 final size:22
Alignment explanation
Indices: 15121--15194 Score: 52
Period size: 22 Copynumber: 3.4 Consensus size: 22
15111 TATATATACT
15121 TATTATTTTCATAATATTTATA
1 TATTATTTTCATAATATTTATA
15143 TATT-TTCTT-ATTAATATTTCAT-
1 TATTATT-TTCA-TAATATTT-ATA
*
15165 T-TTATTTGCA-AATATTT-TA
1 TATTATTTTCATAATATTTATA
15184 TTATTTATTTT
1 -TA-TTATTTT
15195 TCTGTTAGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 18
0.67 0.03 0.30
Matches are distributed among these distances:
18 1 0.02
20 8 0.20
21 6 0.15
22 24 0.59
23 2 0.05
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64
Consensus pattern (22 bp):
TATTATTTTCATAATATTTATA
Found at i:15153 original size:30 final size:30
Alignment explanation
Indices: 15098--15164 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
15088 ACATTCTTTC
*
15098 TTTTCA-AAATTTTTATATATACTTATT-A
1 TTTTCATAAATTTATATATATACTTATTAA
* *
15126 TTTTCATAATATTTATATATTTTCTTATTAA
1 TTTTCATAA-ATTTATATATATACTTATTAA
15157 TATTTCAT
1 T-TTTCAT
15165 TTTATTTGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 6 0.19
29 2 0.06
30 16 0.50
31 2 0.06
32 6 0.19
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (30 bp):
TTTTCATAAATTTATATATATACTTATTAA
Found at i:19809 original size:18 final size:17
Alignment explanation
Indices: 19786--19819 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
19776 TCATCCAGCA
19786 AAGAAAGAAGAAAAAAAG
1 AAGAAA-AAGAAAAAAAG
19804 AAGAAAAAGAAAAAAA
1 AAGAAAAAGAAAAAAA
19820 TTGAATCAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAGAAAAAGAAAAAAAG
Found at i:22367 original size:92 final size:92
Alignment explanation
Indices: 22101--22370 Score: 427
Period size: 92 Copynumber: 2.9 Consensus size: 92
22091 TAAGGAGACC
* * *
22101 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTTGGTATGAACCACAGAACCAG
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACTACAGAACCAA
* *
22166 TTATTGAATTTGGAAGAGGAATGTGCT
66 TCATTGAATTTGGAAGATGAATGTGCT
*
22193 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAA-TCACAGAACTA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACT-ACAGAACCA
22257 ATCATTGAATTTGGAAGATGAATGTGCT
65 ATCATTGAATTTGGAAGATGAATGTGCT
* *
22285 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTTGGTAAGAACTACAGAACCAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACTACAGAACCAA
*
22350 TCATTGGAA-TTGAAAGATGAA
66 TCATT-GAATTTGGAAGATGAA
22371 CTGCATGATC
Statistics
Matches: 165, Mismatches: 10, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
92 161 0.98
93 4 0.02
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (92 bp):
CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACTACAGAACCAA
TCATTGAATTTGGAAGATGAATGTGCT
Found at i:24927 original size:22 final size:22
Alignment explanation
Indices: 24894--24948 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
24884 ATCTACACTC
*
24894 TTCAAAAATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
24916 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
24938 TTCAAAGATGA
1 TTCAAAGATGA
24949 AAGCTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:25819 original size:76 final size:76
Alignment explanation
Indices: 25625--27177 Score: 2900
Period size: 76 Copynumber: 20.5 Consensus size: 76
25615 CTATTTCCCA
*
25625 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
*
25690 AAACCTTCGGGT
65 AAGCCTTCGGGT
*
25702 CATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
25767 AGCCTTCGGGT
66 AGCCTTCGGGT
25778 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
25843 AGTCTTCGGGT
66 AGCCTTCGGGT
25854 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
25919 AGCCTTCGGGT
66 AGCCTTCGGGT
25930 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
25995 AGCCTTCTGGT
66 AGCCTTCGGGT
26006 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
26071 AGCCTTCGGGT
66 AGCCTTCGGGT
26082 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
*
26147 AAACCTTCGGGT
65 AAGCCTTCGGGT
*
26159 CATCTGTAAGTCCTCCAGTGCATGATGTTTCC-AAAAGCCTTC-GGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
26222 AGCCTTCGGGT
66 AGCCTTCGGGT
*
26233 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGAAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
26297 AACCTTCGGGT
66 AGCCTTCGGGT
*
26308 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTATCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
26373 AGCCTTCGGGT
66 AGCCTTCGGGT
26384 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
26449 AGCCTTCGGGT
66 AGCCTTCGGGT
26460 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
*
26525 AAACCTTCGGGT
65 AAGCCTTCGGGT
*
26537 CATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
26602 AGCCTTCGGGT
66 AGCCTTCGGGT
*
26613 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGAAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
26678 AACCTTCGGGT
66 AGCCTTCGGGT
26689 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
26754 AGCCTTCGGGT
66 AGCCTTCGGGT
26765 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
26830 AGCCTTCGGGT
66 AGCCTTCGGGT
26841 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
26906 AGCCTTCGGGT
66 AGCCTTCGGGT
26917 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
26982 AGCCTTCGGGT
66 AGCCTTCGGGT
26993 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
27057 AGCCTTCGGGT
66 AGCCTTCGGGT
27068 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
27132 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
27143 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
27178 CATTTCCATC
Statistics
Matches: 1442, Mismatches: 28, Indels: 14
0.97 0.02 0.01
Matches are distributed among these distances:
74 51 0.04
75 218 0.15
76 995 0.69
77 178 0.12
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:27340 original size:27 final size:26
Alignment explanation
Indices: 27302--27378 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 26
27292 TCATTTAAAT
27302 TTATTATTATTATTAAA-T-TTATTA
1 TTATTATTATTATTAAATTATTATTA
27326 TTATTATTATTATTAAA-TATTATTA
1 TTATTATTATTATTAAATTATTATTA
*
27351 TTAGTATATTATTATTAAATAATTATTA
1 TTA-T-TATTATTATTAAATTATTATTA
27379 CAAGCCCAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
24 18 0.38
25 9 0.19
26 1 0.02
27 13 0.27
28 7 0.15
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (26 bp):
TTATTATTATTATTAAATTATTATTA
Found at i:27378 original size:3 final size:3
Alignment explanation
Indices: 27302--27367 Score: 73
Period size: 3 Copynumber: 22.0 Consensus size: 3
27292 TCATTTAAAT
* *
27302 TTA TTA TTA TTA TTA -AA TTTA TTA TTA TTA TTA TTA TTAA ATA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT-A TTA TTA
*
27348 TTA TTA GTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
27368 AATAATTATT
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
2 3 0.06
3 48 0.89
4 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:33259 original size:80 final size:81
Alignment explanation
Indices: 33127--33366 Score: 322
Period size: 81 Copynumber: 3.0 Consensus size: 81
33117 TAAAATTTCT
* * ** * * * * *
33127 TTATTCTCTTACTCAACAGTTTTTAA-CGTTCGTCTAACTGGCATAATTGACACCTTTCTACCA-
1 TTATTCTTTTACTCAACGGTACTTAATCATTCATCTAACTGGCATAAATGACACATTTCTATCAT
*
33190 ATGCACAGTTAGGCCA
66 ATGCACAGCTAGGCCA
*
33206 TTATTCTTTTACTCAACGGTACTTAATCATTCATCTAACTGGCATAAATGACACATTTCTTTCAT
1 TTATTCTTTTACTCAACGGTACTTAATCATTCATCTAACTGGCATAAATGACACATTTCTATCAT
* *
33271 ATGTACAGCTAGACCA
66 ATGCACAGCTAGGCCA
* * *
33287 TTATTCCTTTACTCAAGGGTACTTAATCATTCATCTAACTGGCATAAATGACACATTTCTGTCAT
1 TTATTCTTTTACTCAACGGTACTTAATCATTCATCTAACTGGCATAAATGACACATTTCTATCAT
33352 ATGCACAGCTAGGCC
66 ATGCACAGCTAGGCC
33367 TCAAAGACAC
Statistics
Matches: 141, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
79 22 0.16
80 31 0.22
81 88 0.62
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (81 bp):
TTATTCTTTTACTCAACGGTACTTAATCATTCATCTAACTGGCATAAATGACACATTTCTATCAT
ATGCACAGCTAGGCCA
Found at i:33407 original size:68 final size:68
Alignment explanation
Indices: 33307--33844 Score: 731
Period size: 68 Copynumber: 7.9 Consensus size: 68
33297 ACTCAAGGGT
* * * * *
33307 ACTTAATCATTCATCTAACTGGCATAAATGACACATTTCTGTCATATGCACAGCTAGGCCTCAAA
1 ACTTAGTCTTTCATCTAACTGACATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAAA
33372 GAC
66 GAC
* * *
33375 ACTTAGTCTTTCATCTAACTGACATAATTGACACCTTTTTTTCATATGCACAGTTAGGCCTCAAA
1 ACTTAGTCTTTCATCTAACTGACATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAAA
33440 GAC
66 GAC
* * * *
33443 ACTTAGTCTTTCATCTAATTGGA-ATAAATGACACATTTCTTTCATATACACAGTTAGGCCTCAA
1 ACTTAGTCTTTCATCTAACT-GACATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAA
*
33507 AGAA
65 AGAC
* * * * *
33511 ACTTAGTCTTTCATCTAACTGGCATAAATGATATCTTTCTGTCATATACACAGCTAGGCCTCAAA
1 ACTTAGTCTTTCATCTAACTGACATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAAA
33576 GAC
66 GAC
* ** *
33579 ACTTACTCTTTCATCTAACTTCCATAAATGACACCTTTCTGTCATATGCACAGCTAGGCCTCAAA
1 ACTTAGTCTTTCATCTAACTGACATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAAA
33644 GAC
66 GAC
* *
33647 ACTTAGTCTTTCATCTAACTGACATAATTGACACCTTTCTATCATATGCACAGTTAGGCCTCAAA
1 ACTTAGTCTTTCATCTAACTGACATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAAA
33712 GAC
66 GAC
* * * **
33715 ACTTGGTCTTTCATCTAACTGGCATAAATGACACCTTTCTTTCATATGTGCAGTTAGGCCTCAAA
1 ACTTAGTCTTTCATCTAACTGACATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAAA
33780 G-C
66 GAC
* * * *
33782 AAATTAGCCTTTCATCTAACTGGA-ATAAATGACACATTTATGTCATATGCACAGTTAGGCCTC
1 -ACTTAGTCTTTCATCTAACT-GACATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTC
33845 TTGATCTTTT
Statistics
Matches: 417, Mismatches: 49, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
67 2 0.00
68 412 0.99
69 3 0.01
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (68 bp):
ACTTAGTCTTTCATCTAACTGACATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAAA
GAC
Found at i:34345 original size:59 final size:57
Alignment explanation
Indices: 34209--34383 Score: 235
Period size: 59 Copynumber: 3.0 Consensus size: 57
34199 ACCCATATAT
* * *
34209 TTCCCATATGGAAATTCATACTCTTAGTATGAATTTCTTATCCTTTAGCACAC-AAGG
1 TTCCCATATAGAAATTCATACACTTAGTATGAATTTCTTATCATTTAGCACACGAA-G
* *
34266 TGCCCAATATAGAAATTCATACAATTAGTATGAATTTCTTATCATGTTAGCACACGAAG
1 TTCCC-ATATAGAAATTCATACACTTAGTATGAATTTCTTATCAT-TTAGCACACGAAG
* * *
34325 TTCCCTATATTGAAATTCATACACTTAGTATGAATTTCTTAACATTTTGCACACGAAG
1 TTCCC-ATATAGAAATTCATACACTTAGTATGAATTTCTTATCATTTAGCACACGAAG
34383 T
1 T
34384 GTCATTTGGT
Statistics
Matches: 104, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
57 4 0.04
58 48 0.46
59 50 0.48
60 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (57 bp):
TTCCCATATAGAAATTCATACACTTAGTATGAATTTCTTATCATTTAGCACACGAAG
Found at i:34733 original size:20 final size:22
Alignment explanation
Indices: 34710--34757 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
34700 TTCATAGTAT
34710 CGATACTACTAT-C-ATGGTAC
1 CGATACTACTATACTATGGTAC
*
34730 CGATACTTCTATACTATGGTAC
1 CGATACTACTATACTATGGTAC
34752 CGATAC
1 CGATAC
34758 CCCATTCCGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 11 0.44
21 1 0.04
22 13 0.52
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (22 bp):
CGATACTACTATACTATGGTAC
Found at i:34824 original size:20 final size:19
Alignment explanation
Indices: 34798--34850 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 19
34788 TCGATGTTTC
34798 ATGGTATCGATACCCTCACC-
1 ATGGTATCGATACCC-C-CCT
*
34818 GTGGTATCGATACCCCCCT
1 ATGGTATCGATACCCCCCT
34837 ATGGTATCGATACC
1 ATGGTATCGATACC
34851 AAAATTAGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 2 0.07
19 14 0.47
20 14 0.47
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (19 bp):
ATGGTATCGATACCCCCCT
Found at i:34843 original size:19 final size:20
Alignment explanation
Indices: 34797--34850 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
34787 TTCGATGTTT
34797 CATGGTATCGATACCCTCAC
1 CATGGTATCGATACCCTCAC
*
34817 CGTGGTATCGATACCC-C-C
1 CATGGTATCGATACCCTCAC
34835 CTATGGTATCGATACC
1 C-ATGGTATCGATACC
34851 AAAATTAGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 2 0.06
19 14 0.45
20 15 0.48
ACGTcount: A:0.22, C:0.33, G:0.19, T:0.26
Consensus pattern (20 bp):
CATGGTATCGATACCCTCAC
Found at i:34843 original size:73 final size:73
Alignment explanation
Indices: 34766--34903 Score: 195
Period size: 73 Copynumber: 1.9 Consensus size: 73
34756 ACCCCATTCC
* * * * *
34766 GGTATCGATACCAAAATTAAGTTCGATGTTTCATGGTATCGATACCCTCACCGTGGTATCGATAC
1 GGTATCGATACCAAAATTAAGTTCGATGCTGCATAGTATCGATACCCTCACCATGGTATCAATAC
34831 CCCCCTAT
66 CCCCCTAT
* * * *
34839 GGTATCGATACCAAAATTAGGTTCGATGCTGCTTAGTATCGATACCTTTACCATGGTATCAATAC
1 GGTATCGATACCAAAATTAAGTTCGATGCTGCATAGTATCGATACCCTCACCATGGTATCAATAC
34904 TACCTCATAG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
73 56 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (73 bp):
GGTATCGATACCAAAATTAAGTTCGATGCTGCATAGTATCGATACCCTCACCATGGTATCAATAC
CCCCCTAT
Found at i:46046 original size:15 final size:15
Alignment explanation
Indices: 46026--46064 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
46016 GAAATATATT
46026 TTTCAAGGTAAATAA
1 TTTCAAGGTAAATAA
46041 TTTCAAGGTAAATAA
1 TTTCAAGGTAAATAA
46056 TTTCAAGGT
1 TTTCAAGGT
46065 TAGTATCTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (15 bp):
TTTCAAGGTAAATAA
Found at i:46349 original size:36 final size:35
Alignment explanation
Indices: 46224--46352 Score: 120
Period size: 36 Copynumber: 3.6 Consensus size: 35
46214 AAGAAATCCA
* *
46224 AAGTGAAATG-AATTTTTTTTAAAGAAAAACAA-TGT
1 AAGTGAAACGAAATTTGTTTT-AAGAAAAACAACT-T
*
46259 CAAGTGAAACGAAATTTGTTTTAAGAAAAATAATCTT
1 -AAGTGAAACGAAATTTGTTTTAAGAAAAACAA-CTT
* *
46296 AAG-AAAGACAAAATTTGTTTTAAGAAAAACAACATT
1 AAGTGAA-ACGAAATTTGTTTTAAGAAAAACAAC-TT
* *
46332 AAGTGAGACGAATTTTGTTTT
1 AAGTGAAACGAAATTTGTTTT
46353 TAGTGAAAAC
Statistics
Matches: 77, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
35 3 0.04
36 62 0.81
37 11 0.14
38 1 0.01
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.33
Consensus pattern (35 bp):
AAGTGAAACGAAATTTGTTTTAAGAAAAACAACTT
Found at i:46930 original size:258 final size:256
Alignment explanation
Indices: 46370--46946 Score: 687
Period size: 258 Copynumber: 2.2 Consensus size: 256
46360 AACATAAAAC
* * *
46370 GAGAAACTTTGAAAATCGCTTTCTCATTTTTTTTCTCTCAAATATCATATGAATACATCTTGCCA
1 GAGAAACTTTGAAAATCGCTTTCTCA----TTTT-T-TCAAATATCATATAAAAACATCTTACCA
** *** * * *
46435 GGAGGTCTTATAAATGACTCGGAGGACTTATCATCTTGCTTGGAAGACTTACATATGACCTGGGG
60 GGAGGTCTTATAAATGACTCGGAGGACTTATCATCTCACTCAAAAGACTTACAGATGACCTAGAG
* * * *
46500 GATTTAATCAACAGGATCAAAAGACTTATTGATAGCCCAAATGACTTAAGTTTTGGAAAGAATCT
125 GATATAAACAACAGGATCAAAAGACTTACTGATAGCCCAAATGACTTAAATTTTGGAAAGAATCT
* * *
46565 ACTAGGTAAGAAACTTTGAAAATTGCTTTCTTACTTTTAAAAAAATCATTTTCATAAAAGATTAA
190 ACTAGGTAAGAAACTTTAAAAATTGATTTCTTACTTTTAAAAAAATCATTTTCAGAAAAGATTAA
46630 AT
255 AT
* *
46632 GAGAAACTTTGAAAATCGCTTTCTCATTTTTTCACAAATATTATATAAAAACATCTTACCCGGAG
1 GAGAAACTTTGAAAATCGCTTTCTCATTTTTT--CAAATATCATATAAAAACATCTTACCAGGAG
* * * *
46697 TTCTTATAGATGGC-CTGGAGGACTTATCATCTCACTCAAAAGACTTATAGATGACCTAGAGGAT
64 GTCTTATAAATGACTC-GGAGGACTTATCATCTCACTCAAAAGACTTACAGATGACCTAGAGGAT
** * * *
46761 ATAAACATTAGGCTCAAAAGACTTACTGATAGCCCGAAA-GACTTACTAATTTTGGAAATACTCT
128 ATAAACAACAGGATCAAAAGACTTACTGATAGCCC-AAATGACTTA--AATTTTGGAAAGAATCT
* * *
46825 ACT-GGATAAGAAACTTTAAAAATTGATTTCTTACTTTTCAAAAAATTTC-TTTTTAGAAAATAT
190 ACTAGG-TAAGAAACTTTAAAAATTGATTTCTTACTTTT-AAAAAA-ATCATTTTCAGAAAAGAT
46888 TAAAT
252 TAAAT
*
46893 GAGAAACTTTGAAAATCACTTTCTCA-TTTTTCAAATATCATATAAAAACATCTT
1 GAGAAACTTTGAAAATCGCTTTCTCATTTTTTCAAATATCATATAAAAACATCTT
46947 GGTGGTCGAG
Statistics
Matches: 272, Mismatches: 34, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
256 1 0.00
257 2 0.01
258 137 0.50
259 5 0.02
260 52 0.19
261 47 0.17
262 28 0.10
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (256 bp):
GAGAAACTTTGAAAATCGCTTTCTCATTTTTTCAAATATCATATAAAAACATCTTACCAGGAGGT
CTTATAAATGACTCGGAGGACTTATCATCTCACTCAAAAGACTTACAGATGACCTAGAGGATATA
AACAACAGGATCAAAAGACTTACTGATAGCCCAAATGACTTAAATTTTGGAAAGAATCTACTAGG
TAAGAAACTTTAAAAATTGATTTCTTACTTTTAAAAAAATCATTTTCAGAAAAGATTAAAT
Found at i:54557 original size:20 final size:20
Alignment explanation
Indices: 54532--54571 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
54522 AATTTAATCG
* *
54532 AATATATAATTTTAAAATTC
1 AATATAAAATCTTAAAATTC
54552 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
54572 GTTAACACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:54796 original size:35 final size:35
Alignment explanation
Indices: 54752--54826 Score: 150
Period size: 35 Copynumber: 2.1 Consensus size: 35
54742 TTTTTTTAAA
54752 TAAAAAAGAAGACTCTAAAAAGTTTAAAACAAGTT
1 TAAAAAAGAAGACTCTAAAAAGTTTAAAACAAGTT
54787 TAAAAAAGAAGACTCTAAAAAGTTTAAAACAAGTT
1 TAAAAAAGAAGACTCTAAAAAGTTTAAAACAAGTT
54822 TAAAA
1 TAAAA
54827 CCCTCGGAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.59, C:0.08, G:0.11, T:0.23
Consensus pattern (35 bp):
TAAAAAAGAAGACTCTAAAAAGTTTAAAACAAGTT
Found at i:58626 original size:19 final size:20
Alignment explanation
Indices: 58597--58634 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
58587 TTGAAAAATA
58597 GCTTGGTGCATCGATGCATG
1 GCTTGGTGCATCGATGCATG
58617 GCTT-GTGCATCGATGCAT
1 GCTTGGTGCATCGATGCAT
58635 CAAATGCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.16, C:0.21, G:0.32, T:0.32
Consensus pattern (20 bp):
GCTTGGTGCATCGATGCATG
Found at i:58746 original size:64 final size:64
Alignment explanation
Indices: 58554--58715 Score: 186
Period size: 64 Copynumber: 2.5 Consensus size: 64
58544 CGGTGCACTA
* * * * *
58554 AGAGTGCATCGATGCATGAAGTTCATTCGATG-TTTGA-AAAATAGCTTG-GTGCATCGATGCAT
1 AGAGTGCATCGGTGCATGAAATGCATTCGATGTTTTCATAAAAT---TCGAGTGCATCGATGCAT
58616 GG
63 GG
*** * *
58618 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATTCGAGTGCATCGATGCATGG
1 AGAGTGCATCGGTGCATGAAATGCATTCGATGTTTTCATAAAATTCGAGTGCATCGATGCATGG
58682 AGAGTGCATCGGTGCATGAAATGCATTCGATGTT
1 AGAGTGCATCGGTGCATGAAATGCATTCGATGTT
58716 CAATTTATTC
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
63 2 0.02
64 71 0.87
65 4 0.05
66 5 0.06
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (64 bp):
AGAGTGCATCGGTGCATGAAATGCATTCGATGTTTTCATAAAATTCGAGTGCATCGATGCATGG
Found at i:64255 original size:74 final size:74
Alignment explanation
Indices: 64122--64306 Score: 225
Period size: 74 Copynumber: 2.5 Consensus size: 74
64112 GTTAAATGAC
* * *
64122 TAGGGGTATCGGTACCTCTA-G-GGGGTATCGGTACCCTTAGGACATTCTATTTTTCTCGGAGAC
1 TAGGGGTATCGGTACC-CTATGAGGGGTATCGGTACCCTTAGGACAATATATTTTCCTCGGAGAC
64185 AAAACTT-GCA
65 AAAA-TTGGCA
* * * *
64195 TAGGGATATCGGTACCCTATGAGGGGTATCAGTACCCATTAGG-CAATATGTTTTCCTCGGAGCC
1 TAGGGGTATCGGTACCCTATGAGGGGTATCGGTACCC-TTAGGACAATATATTTTCCTCGGAGAC
*
64259 AAGATTGGCA
65 AAAATTGGCA
64269 TAGGGGTATCGGTACACCCTATGAGGGGTATCGGTACC
1 TAGGGGTATCGGT--ACCCTATGAGGGGTATCGGTACC
64307 TCCTTATTTA
Statistics
Matches: 96, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
72 3 0.03
73 18 0.19
74 48 0.50
75 5 0.05
76 22 0.23
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (74 bp):
TAGGGGTATCGGTACCCTATGAGGGGTATCGGTACCCTTAGGACAATATATTTTCCTCGGAGACA
AAATTGGCA
Found at i:65194 original size:51 final size:51
Alignment explanation
Indices: 65139--65242 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
65129 AACAAATTAA
65139 CAAACAAAATATTTATATTAATTAAGTTGAAATTGACGGGGTTTTTTCACT
1 CAAACAAAATATTTATATTAATTAAGTTGAAATTGACGGGGTTTTTTCACT
*
65190 CAAACAAAATATTTATATTAATTAAGTTGAAATTGATGGGGTTTTTTCACT
1 CAAACAAAATATTTATATTAATTAAGTTGAAATTGACGGGGTTTTTTCACT
65241 CA
1 CA
65243 TGCGTTTTAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (51 bp):
CAAACAAAATATTTATATTAATTAAGTTGAAATTGACGGGGTTTTTTCACT
Found at i:65657 original size:14 final size:14
Alignment explanation
Indices: 65632--65673 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
65622 TTATCAAGTG
*
65632 AAAAATACAATAACT
1 AAAAATA-AATAAAT
65647 AAAAATAAATAAAT
1 AAAAATAAATAAAT
65661 -AAAATATAATAAA
1 AAAAATA-AATAAA
65674 AAAGAAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 6 0.24
14 12 0.48
15 7 0.28
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAAATAAATAAAT
Found at i:67191 original size:14 final size:14
Alignment explanation
Indices: 67156--67194 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
67146 TAAAATAATT
* *
67156 ATATTTTTTGAAAA
1 ATATTTTATGGAAA
67170 ATATTTTATGGAAA
1 ATATTTTATGGAAA
*
67184 TTATTTTATGG
1 ATATTTTATGG
67195 TGTTTATAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (14 bp):
ATATTTTATGGAAA
Found at i:67296 original size:23 final size:23
Alignment explanation
Indices: 67257--67331 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 23
67247 AAATATAAAA
*
67257 TATAATAAA-TAATATTATTTAT
1 TATAAAAAATTAATATTATTTAT
67279 TATAAAAAATTAATATTA-TTAT
1 TATAAAAAATTAATATTATTTAT
*
67301 TTTAAAAATATTTGAATAATTTATTTAT
1 TATAAAAA-A-TT-AAT-A-TTATTTAT
67329 TAT
1 TAT
67332 TATTGAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
22 19 0.44
23 9 0.21
24 2 0.05
25 3 0.07
26 1 0.02
27 3 0.07
28 6 0.14
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (23 bp):
TATAAAAAATTAATATTATTTAT
Found at i:67570 original size:22 final size:24
Alignment explanation
Indices: 67521--67570 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
67511 TAATAAATAA
*
67521 AAATATTCACTTTAATAATTCAAT
1 AAATATTCACTTTAAAAATTCAAT
*
67545 -AATATT-ATTTTAAAAATT-AAT
1 AAATATTCACTTTAAAAATTCAAT
67566 AAATA
1 AAATA
67571 ATATAACTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 3 0.13
22 14 0.61
23 6 0.26
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATATTCACTTTAAAAATTCAAT
Found at i:67657 original size:23 final size:25
Alignment explanation
Indices: 67627--67685 Score: 77
Period size: 23 Copynumber: 2.4 Consensus size: 25
67617 AATAGTATCA
67627 TATATTATTATAAT-ATAAT-TGAG
1 TATATTATTATAATAATAATATGAG
* * *
67650 TATATTATTGTAATAATATTATGAT
1 TATATTATTATAATAATAATATGAG
67675 TATATTATTAT
1 TATATTATTAT
67686 TAAAAAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 13 0.43
24 4 0.13
25 13 0.43
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.53
Consensus pattern (25 bp):
TATATTATTATAATAATAATATGAG
Found at i:71858 original size:15 final size:16
Alignment explanation
Indices: 71816--71862 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
71806 GCCAATTTGG
71816 ACCATTTGCACCGAAA
1 ACCATTTGCACCGAAA
*** *
71832 TTGATTTCCACC-AAA
1 ACCATTTGCACCGAAA
71847 ACCATTTGCACCGAAA
1 ACCATTTGCACCGAAA
71863 GTGGCCAAGT
Statistics
Matches: 22, Mismatches: 8, Indels: 2
0.69 0.25 0.06
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.36, C:0.30, G:0.11, T:0.23
Consensus pattern (16 bp):
ACCATTTGCACCGAAA
Found at i:73951 original size:25 final size:26
Alignment explanation
Indices: 73897--73951 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 26
73887 ATAAGAGATA
* * * *
73897 AAATAAAATATAATAATAATAATAGT
1 AAATAAAAAAGAATAATAAAAAAAGT
73923 -AATAAAAAAGAAT-ATAAAAAAAGT
1 AAATAAAAAAGAATAATAAAAAAAGT
73947 AAATA
1 AAATA
73952 TATATACCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (26 bp):
AAATAAAAAAGAATAATAAAAAAAGT
Found at i:74025 original size:11 final size:11
Alignment explanation
Indices: 74009--74051 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
73999 ATGAAATGTA
*
74009 AAAATAATATT
1 AAAATAATAAT
*
74020 AAAATAATAGT
1 AAAATAATAAT
74031 --AATAATAAT
1 AAAATAATAAT
74040 AAAATAATAAT
1 AAAATAATAAT
74051 A
1 A
74052 TAAAAAGGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 8 0.29
11 20 0.71
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:74028 original size:3 final size:3
Alignment explanation
Indices: 74011--74051 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
74001 GAAATGTAAA
* *
74011 AAT AAT ATT AA- AAT AAT AGT AAT AAT AAT AA- AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
74052 TAAAAAGGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:74036 original size:20 final size:20
Alignment explanation
Indices: 74011--74048 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
74001 GAAATGTAAA
*
74011 AATAATATTAAAATAATAGT
1 AATAATAATAAAATAATAGT
74031 AATAATAATAAAATAATA
1 AATAATAATAAAATAATA
74049 ATATAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (20 bp):
AATAATAATAAAATAATAGT
Found at i:74048 original size:23 final size:23
Alignment explanation
Indices: 73991--74057 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
73981 ATATATATAT
*
73991 ATAATAAAATGA-AAT-GTAAAA
1 ATAATAAAATAATAATAGTAAAA
* *
74012 ATAATATTAA-AATAATAGTAATA
1 ATAATA-AAATAATAATAGTAAAA
74035 ATAATAAAATAATAATA-TAAAA
1 ATAATAAAATAATAATAGTAAAA
74057 A
1 A
74058 GGTATGTACA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
21 7 0.19
22 12 0.32
23 18 0.49
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.28
Consensus pattern (23 bp):
ATAATAAAATAATAATAGTAAAA
Found at i:74126 original size:2 final size:2
Alignment explanation
Indices: 74119--74143 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
74109 AATAAGAATA
74119 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 A
74144 CGAATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:74276 original size:17 final size:17
Alignment explanation
Indices: 74254--74291 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
74244 ATATGTATAT
74254 ATATAATAATAAAATAC
1 ATATAATAATAAAATAC
*
74271 ATATAATAATAAAATAT
1 ATATAATAATAAAATAC
74288 ATAT
1 ATAT
74292 TTAAAATACG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
ATATAATAATAAAATAC
Found at i:76074 original size:105 final size:105
Alignment explanation
Indices: 75660--76601 Score: 1312
Period size: 105 Copynumber: 9.0 Consensus size: 105
75650 GTATTGTTCC
* * * * * * * * *
75660 GAGTCCAA-ATCCTCCACTGTGAAGTTGAATTTGGTTTTGGAACTGGGAAATTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAA
* * * * *
75724 TCAGCCG-CCCTTCG-CTGTGAAGTT-AAGCTTGTGCTGTCTC
65 CCAGCGGTCCCTTCGTC-GTGAAGTTGAA-CTTGCGTTGTCTG
* *** * * **
75764 GAGTCTAATATCCTTTATTATGAAGTTGAAATTGACTCTG-AA-T--GAAACT-TTGTTGACAAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAC
*
75824 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCCG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
75864 AAGTCCAATATCCTTCGCTGGGAAGTTGAAATTGGCTCTGAAA-TGGGAAGTTGTTGTTGACAAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAC
*
75928 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
75968 GAGTCTAATATCTTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAC
* * **
76033 CAGCGATCCCTTCGTCGTGAAGTTGAACTTGCATTACCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
76073 GAATCCAATATCCTTCGGTGTGACGTTGAAATCGGCTCTGAAATTGGGAAGTTGTTGTTGACAAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAC
* *
76138 CAGCGGTCCCTTCGTTGTGAAATTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
76178 GAGTCCAATATCCTTCGCAGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAA
* *
76243 CCAGCGGTCCCTTCGTCGAGAAGTTGAACTTGCGTTGTCTT
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
76284 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAC
76349 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
76389 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAGTTGTTGTTGACAAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAC
*
76454 CAGTGGTCCCTTCGTCGTGAAG-TGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
76493 GAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAC
*
76558 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
76598 GAGT
1 GAGT
76602 GATATCCTCC
Statistics
Matches: 752, Mismatches: 75, Indels: 21
0.89 0.09 0.02
Matches are distributed among these distances:
99 14 0.02
100 56 0.07
101 11 0.01
103 5 0.01
104 198 0.26
105 372 0.49
106 96 0.13
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:76336 original size:316 final size:315
Alignment explanation
Indices: 75813--76601 Score: 1296
Period size: 316 Copynumber: 2.5 Consensus size: 315
75803 GAATGAAACT
* * *
75813 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCCGAAGTCCAATATCCT
1 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAATTGAACTTGCGTTGTCTGGAGTCCAATATCCT
* *
75878 TCGCTGGGAAGTTGAAATTGGCTCTGAAA-TGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCA
66 TCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCG
*
75942 TCGTGAAGTTGAACTTGCGTTGTCTGGAGTCTAATATCTTTCGCTGTGAAGTTGAAATTGGCTCT
131 TCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCT
76007 GAAATTGGGAAGTTGTTGTTGACAACCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCATTACCT
196 GAAATTGGGAAGTTGTTGTTGACAACCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCATTACCT
* *
76072 GGAATCCAATATCCTTCGGTGTGACGTTGAAATCGGCTCTGAAATTGGGAAGTTG
261 GGAATCCAATATCCTTCGGTGTGAAGTTGAAATCGGCTCCGAAATTGGGAAGTTG
*
76127 TTGTTGACAACCAGCGGTCCCTTCGTTGTGAAATTGAACTTGCGTTGTCTGGAGTCCAATATCCT
1 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAATTGAACTTGCGTTGTCTGGAGTCCAATATCCT
* * *
76192 TCGCAGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTC
66 TCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAACCAGCGGTCCCTTC
* * *
76257 GTCGAGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTT-GTTGTGAAGTTGAAATTGGCT
130 GTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT-CTTTCGCTGTGAAGTTGAAATTGGCT
* * **
76321 CTGAAATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
194 CTGAAATTGGGAAGTTGTTGTTGACAACCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCATTAC
* * *
76386 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAGTTG
259 CTGGAATCCAATATCCTTCGGTGTGAAGTTGAAATCGGCTCCGAAATTGGGAAGTTG
* * *
76443 TTGTTGACAACCAGTGGTCCCTTCGTCGTG-AAGTGAACTTGCGTTGTCTGGAGTCTAATATCCT
1 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAATTGAACTTGCGTTGTCTGGAGTCCAATATCCT
*
76507 TCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCG
66 TCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCG
*
76572 TCGTGAAGTTGAACTTGCGTTGTTTGGAGT
131 TCGTGAAGTTGAACTTGCGTTGTCTGGAGT
76602 GATATCCTCC
Statistics
Matches: 439, Mismatches: 33, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
314 138 0.31
315 79 0.18
316 218 0.50
317 4 0.01
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.33
Consensus pattern (315 bp):
TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAATTGAACTTGCGTTGTCTGGAGTCCAATATCCT
TCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCG
TCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCT
GAAATTGGGAAGTTGTTGTTGACAACCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCATTACCT
GGAATCCAATATCCTTCGGTGTGAAGTTGAAATCGGCTCCGAAATTGGGAAGTTG
Done.