Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001668.1 Hibiscus syriacus cultivar Beakdansim tig00003340_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: 67474
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:770 original size:12 final size:11
Alignment explanation
Indices: 737--789 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
727 AAATTAAAAC
737 AGAATTCAGAAT
1 AGAA-TCAGAAT
*
749 AGGTATCAGAAT
1 A-GAATCAGAAT
761 AGAATCCAGAAT
1 AGAAT-CAGAAT
*
773 AGAAATCAGAAC
1 AG-AATCAGAAT
785 AGAAT
1 AGAAT
790 TCAGGTAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
11 6 0.17
12 24 0.69
13 5 0.14
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (11 bp):
AGAATCAGAAT
Found at i:770 original size:24 final size:24
Alignment explanation
Indices: 725--789 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
715 CGGAGATATC
* * *
725 AGAAATTAAAACAGAATTCAGAAT
1 AGAAATCAGAACAGAATCCAGAAT
** *
749 AGGTATCAGAATAGAATCCAGAAT
1 AGAAATCAGAACAGAATCCAGAAT
773 AGAAATCAGAACAGAAT
1 AGAAATCAGAACAGAAT
790 TCAGGTAATA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.18
Consensus pattern (24 bp):
AGAAATCAGAACAGAATCCAGAAT
Found at i:790 original size:48 final size:48
Alignment explanation
Indices: 722--840 Score: 127
Period size: 48 Copynumber: 2.5 Consensus size: 48
712 AAACGGAGAT
* * *
722 ATCAGAAATTAAAACAGAATTCA-G-AATAGGTATCAGAATAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGGTAATA--TATCAGAACAGAATCCAG
*
770 AAT-AGAAATCAGAACAGAATTCAGGTAATATATCAGAACAGAATTCAG
1 -ATCAGAAATCAGAACAGAATTCAGGTAATATATCAGAACAGAATCCAG
* * *
818 GTCATATATCAGAACAGAATTCA
1 ATCAGAAATCAGAACAGAATTCA
841 AGTCGAAAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
47 1 0.02
48 52 0.87
49 3 0.05
50 4 0.07
ACGTcount: A:0.49, C:0.13, G:0.16, T:0.22
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGGTAATATATCAGAACAGAATCCAG
Found at i:793 original size:12 final size:12
Alignment explanation
Indices: 734--840 Score: 51
Period size: 12 Copynumber: 8.9 Consensus size: 12
724 CAGAAATTAA
734 AACAGAATTCAG
1 AACAGAATTCAG
* *
746 AATAG-GTATCAG
1 AACAGAAT-TCAG
* *
758 AATAGAATCCAG
1 AACAGAATTCAG
* *
770 AATAGAAATCAG
1 AACAGAATTCAG
782 AACAGAATTCAGG
1 AACAGAATTCA-G
* *
795 TA-A-TATATCAG
1 AACAGAAT-TCAG
806 AACAGAATTCAG
1 AACAGAATTCAG
** *
818 GTCA-TATATCAG
1 AACAGAAT-TCAG
830 AACAGAATTCA
1 AACAGAATTCA
841 AGTCGAAAAT
Statistics
Matches: 69, Mismatches: 18, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
11 7 0.10
12 55 0.80
13 7 0.10
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.21
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:804 original size:24 final size:24
Alignment explanation
Indices: 777--840 Score: 119
Period size: 24 Copynumber: 2.7 Consensus size: 24
767 CAGAATAGAA
777 ATCAGAACAGAATTCAGGTAATAT
1 ATCAGAACAGAATTCAGGTAATAT
*
801 ATCAGAACAGAATTCAGGTCATAT
1 ATCAGAACAGAATTCAGGTAATAT
825 ATCAGAACAGAATTCA
1 ATCAGAACAGAATTCA
841 AGTCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGGTAATAT
Found at i:852 original size:24 final size:23
Alignment explanation
Indices: 775--854 Score: 99
Period size: 24 Copynumber: 3.3 Consensus size: 23
765 TCCAGAATAG
775 AAATCAGAACAGAATTCAGGT-A
1 AAATCAGAACAGAATTCAGGTCA
797 ATATATCAGAACAGAATTCAGGTCA
1 A-A-ATCAGAACAGAATTCAGGTCA
* *
822 TATATCAGAACAGAATTCAAGTCGA
1 -AAATCAGAACAGAATTCAGGTC-A
847 AAATCAGA
1 AAATCAGA
855 TAAAATATTT
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
22 1 0.02
23 1 0.02
24 45 0.90
25 2 0.04
26 1 0.02
ACGTcount: A:0.47, C:0.15, G:0.16, T:0.21
Consensus pattern (23 bp):
AAATCAGAACAGAATTCAGGTCA
Found at i:3333 original size:12 final size:12
Alignment explanation
Indices: 3292--3333 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
3282 TGTGGTTAAC
3292 GTCGGTCAACAG
1 GTCGGTCAACAG
*
3304 GTCGGGAT-AACGG
1 GTC-GG-TCAACAG
3317 GTCGGTCAACAG
1 GTCGGTCAACAG
3329 GTCGG
1 GTCGG
3334 GTCGGGTCGG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 1 0.04
12 14 0.56
13 9 0.36
14 1 0.04
ACGTcount: A:0.21, C:0.21, G:0.40, T:0.17
Consensus pattern (12 bp):
GTCGGTCAACAG
Found at i:3336 original size:13 final size:13
Alignment explanation
Indices: 3295--3336 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
3285 GGTTAACGTC
3295 GGTCAACAGGTCG
1 GGTCAACAGGTCG
*
3308 GGAT-AACGGGTC-
1 GG-TCAACAGGTCG
3320 GGTCAACAGGTCG
1 GGTCAACAGGTCG
3333 GGTC
1 GGTC
3337 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
11 1 0.04
12 9 0.38
13 13 0.54
14 1 0.04
ACGTcount: A:0.21, C:0.21, G:0.40, T:0.17
Consensus pattern (13 bp):
GGTCAACAGGTCG
Found at i:5468 original size:12 final size:11
Alignment explanation
Indices: 5434--5486 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
5424 AAATCAAAAT
5434 AGAATTCAGAAC
1 AGAA-TCAGAAC
* *
5446 AAGTATCAGAAT
1 -AGAATCAGAAC
5458 AGAATCTAGAAC
1 AGAATC-AGAAC
5470 AGAAATCAGAAC
1 AG-AATCAGAAC
5482 AGAAT
1 AGAAT
5487 TAAGGTCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
11 8 0.24
12 19 0.56
13 7 0.21
ACGTcount: A:0.53, C:0.13, G:0.17, T:0.17
Consensus pattern (11 bp):
AGAATCAGAAC
Found at i:5477 original size:24 final size:24
Alignment explanation
Indices: 5421--5487 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
5411 ATGGAGATAT
*
5421 CAGAAATCAAAATAGAATTCAGAA
1 CAGAAATCAGAATAGAATTCAGAA
*
5445 CA-AGTATCAGAATAGAA-TCTAGAA
1 CAGA-AATCAGAATAGAATTC-AGAA
*
5469 CAGAAATCAGAACAGAATT
1 CAGAAATCAGAATAGAATT
5488 AAGGTCATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
23 3 0.09
24 30 0.86
25 2 0.06
ACGTcount: A:0.54, C:0.13, G:0.15, T:0.18
Consensus pattern (24 bp):
CAGAAATCAGAATAGAATTCAGAA
Found at i:5525 original size:24 final size:24
Alignment explanation
Indices: 5472--5527 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
5462 TCTAGAACAG
5472 AAATCAGAACAGAATTAAGGTCAT
1 AAATCAGAACAGAATTAAGGTCAT
* *
5496 ATATCATAACAGAATTCAA-GTCGA-
1 AAATCAGAACAGAATT-AAGGTC-AT
5520 AAATCAGA
1 AAATCAGA
5528 TAAAATATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.21
Consensus pattern (24 bp):
AAATCAGAACAGAATTAAGGTCAT
Found at i:15683 original size:20 final size:20
Alignment explanation
Indices: 15658--15696 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
15648 CAGTGGCGAC
15658 GTCGGGAGTCCTGTACTAGT
1 GTCGGGAGTCCTGTACTAGT
*
15678 GTCGGGAGTCTTGTACTAG
1 GTCGGGAGTCCTGTACTAG
15697 CGGCGACGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.18, G:0.36, T:0.31
Consensus pattern (20 bp):
GTCGGGAGTCCTGTACTAGT
Found at i:16238 original size:134 final size:134
Alignment explanation
Indices: 16045--16348 Score: 405
Period size: 134 Copynumber: 2.3 Consensus size: 134
16035 TCGAGAAATA
* * * * * * * *
16045 TTGATCCATACCACTGTTCTTCAGGGAATATTGAATCGAGGCATACTTGTTCCACTGTTACTCAG
1 TTGATTCATTCCACTATTCTTCAGGGAAAATTGAATCAAGGCAAACTTGTTCCACTGTTACTAAA
* * * *
16110 GGAATATCAAATCTTGAAAGAGA-GAGATTTGGTCCGCTTCTTCTTGAGGGAAAATCAGATCTGG
66 GGAATATCAAATCTTCAAAGAAATG-GATATGGTCCGCTTCTTCTTGAGGGAAAATCAGATATGG
16174 GGATT
130 GGATT
* * * *
16179 TTTATTTATTCCACTATTACTT-AGGGAAAATTGAATCAAGTCAAACTTGTTTCACTGTTACTAA
1 TTGATTCATTCCACTATT-CTTCAGGGAAAATTGAATCAAGGCAAACTTGTTCCACTGTTACTAA
* *
16243 AGGAATATCAAATCTTCAAAGAAATGGATATGTTTCGCTTCTTCTTGAGGGAAAATCAGATATGG
65 AGGAATATCAAATCTTCAAAGAAATGGATATGGTCCGCTTCTTCTTGAGGGAAAATCAGATATGG
16308 GGATT
130 GGATT
*
16313 TTGATTCATTCCACTATTCTTCAGGGAAGATTGAAT
1 TTGATTCATTCCACTATTCTTCAGGGAAAATTGAAT
16349 AAAATTTGAT
Statistics
Matches: 146, Mismatches: 21, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
133 3 0.02
134 139 0.95
135 4 0.03
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (134 bp):
TTGATTCATTCCACTATTCTTCAGGGAAAATTGAATCAAGGCAAACTTGTTCCACTGTTACTAAA
GGAATATCAAATCTTCAAAGAAATGGATATGGTCCGCTTCTTCTTGAGGGAAAATCAGATATGGG
GATT
Found at i:17596 original size:11 final size:11
Alignment explanation
Indices: 17582--17700 Score: 74
Period size: 12 Copynumber: 10.8 Consensus size: 11
17572 TTATTTTCCT
17582 TTTCTTTTTTC
1 TTTCTTTTTTC
17593 TTTC--TTTTC
1 TTTCTTTTTTC
*
17602 TTTTTTTTTTC
1 TTTCTTTTTTC
17613 ATTT-TTTTTTC
1 -TTTCTTTTTTC
*
17624 ATTT-TCTTTATC
1 -TTTCT-TTTTTC
17636 -TTCATTTTTTC
1 TTTC-TTTTTTC
17647 ATTT-TCTTTTT-
1 -TTTCT-TTTTTC
*
17658 TTTCTTTTTCC
1 TTTCTTTTTTC
17669 TTTTCTTTTTTC
1 -TTTCTTTTTTC
*
17681 TTTCATTTTCTC
1 TTTC-TTTTTTC
17693 TTT-TTTTT
1 TTTCTTTTT
17701 CTTCTGGTGA
Statistics
Matches: 88, Mismatches: 7, Indels: 27
0.72 0.06 0.22
Matches are distributed among these distances:
9 8 0.09
10 13 0.15
11 32 0.36
12 33 0.38
13 2 0.02
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:17623 original size:38 final size:37
Alignment explanation
Indices: 17581--17703 Score: 114
Period size: 38 Copynumber: 3.4 Consensus size: 37
17571 TTTATTTTCC
17581 TTTTCTTTTTTCTTTCTTTTCTTTTTTTTTTCATTTTT
1 TTTTC-TTTTTCTTTCTTTTCTTTTTTTTTTCATTTTT
* * *
17619 TTTTCATTTTCTTTATCTTCATTTTTTCATTTTC--TTTT
1 TTTTCTTTTTCTTTCTTTTC-TTTTTT--TTTTCATTTTT
*
17657 TTTTCTTTTTC---CTTTTCTTTTTTCTTTCATTTTCT
1 TTTTCTTTTTCTTTCTTTTCTTTTTTTTTTCATTTT-T
*
17692 CTTT-TTTTTCTT
1 TTTTCTTTTTCTT
17704 CTGGTGAAGT
Statistics
Matches: 69, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
32 4 0.06
34 15 0.22
35 8 0.12
37 12 0.17
38 25 0.36
40 5 0.07
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (37 bp):
TTTTCTTTTTCTTTCTTTTCTTTTTTTTTTCATTTTT
Found at i:17701 original size:21 final size:21
Alignment explanation
Indices: 17636--17703 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 21
17626 TTTCTTTATC
* *
17636 TTCATTTTTTCATTTTCTTTTTT
1 TTCATTTTCTC-TTTT-TTTTCT
* *
17659 TTCTTTTTCCTTTTCTTTTTTCT
1 TTCATTTT-CTCTT-TTTTTTCT
17682 TTCATTTTCTCTTTTTTTTCT
1 TTCATTTTCTCTTTTTTTTCT
17703 T
1 T
17704 CTGGTGAAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 9 0.24
22 4 0.11
23 21 0.57
24 3 0.08
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (21 bp):
TTCATTTTCTCTTTTTTTTCT
Found at i:18354 original size:23 final size:23
Alignment explanation
Indices: 18317--18380 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
18307 GTCAAGGGTT
* *
18317 CTATGTGGGCATTCGGGATAAAA
1 CTATGTGGTCCTTCGGGATAAAA
* * *
18340 TTATGTGGTCCTTCGAGATAAAC
1 CTATGTGGTCCTTCGGGATAAAA
*
18363 CTATGTGGTCCTTTGGGA
1 CTATGTGGTCCTTCGGGA
18381 CAATTATGTG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGATAAAA
Found at i:21577 original size:20 final size:20
Alignment explanation
Indices: 21554--21596 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
21544 AAAGTCTCCA
21554 GGTAATTTGTAAAACCTTCG
1 GGTAATTTGTAAAACCTTCG
* *
21574 GGTAATTTGTAAATCCTTTG
1 GGTAATTTGTAAAACCTTCG
21594 GGT
1 GGT
21597 CACCTGTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.40
Consensus pattern (20 bp):
GGTAATTTGTAAAACCTTCG
Found at i:21978 original size:187 final size:188
Alignment explanation
Indices: 21643--22258 Score: 855
Period size: 188 Copynumber: 3.3 Consensus size: 188
21633 AGGGCTCGAT
* * * * * *
21643 GAAAGAGTAGTGG-ATTAAATCAACTTCAAATATGATCTTCACAGAAGATTAGTGAAACAAACTC
1 GAAAGAGTAGTGGAATCAAATCAACTTCGAATCTGATCTTCACAGAAGAGTAGTAAAACAAATTC
*
21707 CTTCTGTTCAAGTCATTCAAATTAAGCCTTCACAGAAGAGTAGTGAAGCAGGAGCAAGATCAAAA
66 CTTCTGTTCAAGTCATTCAAATTAAGCCTTCACATAAGAGTAGTGAAGCAGGAGCAAGATCAAAA
* * *
21772 TTCGCTCTCCACAGAAGAGTAGTGGAACGGATTTTTCAGCAAAGTATGAAGT-TCCAT
131 TTCGCTCTCCACGGAAGAGTAGTGGAACGGATTTTTCAGCAAAGTATGAAATCTCCAC
* * *
21829 GAAAGAGTAGTGGAATCAAATCAACTTCGAATCGGATCTTCACATAAGAGTAGTAAAACATATTC
1 GAAAGAGTAGTGGAATCAAATCAACTTCGAATCTGATCTTCACAGAAGAGTAGTAAAACAAATTC
*
21894 CTTCTGTTCAAGTCATTCAAATTAAGCCTTCACATAAGAGTAGTGAAGCATGAGCAAGATCAAAA
66 CTTCTGTTCAAGTCATTCAAATTAAGCCTTCACATAAGAGTAGTGAAGCAGGAGCAAGATCAAAA
** *
21959 TTTTCTCTCCACGGAAGAGTAGTGGAACGGATTTTTCAGCAAAATATGAAATCTCCAC
131 TTCGCTCTCCACGGAAGAGTAGTGGAACGGATTTTTCAGCAAAGTATGAAATCTCCAC
* * * *
22017 GAAA-ATGTAGTGGAATCAAATCAACTTTGAATTTGATCTTCA-AGGAAGAGTAGTTAAACAGAT
1 GAAAGA-GTAGTGGAATCAAATCAACTTCGAATCTGATCTTCACA-GAAGAGTAGTAAAACAAAT
* * * * * *
22080 TCTTTTTGTTCAAGTCATTCAAATCAAGCATTCA-TTAAAGAGTAGTGAAGCAGGAACAAGATCA
64 TCCTTCTGTTCAAGTCATTCAAATTAAGCCTTCACAT-AAGAGTAGTGAAGCAGGAGCAAGATCA
* * * *
22144 AAGTTCGCTCTCCACGTAAAAGTAGTGGAACGGATTTTTCAGCAAAGTATGAATTCTCCAC
128 AAATTCGCTCTCCACGGAAGAGTAGTGGAACGGATTTTTCAGCAAAGTATGAAATCTCCAC
* * * *
22205 GAAAGAGTAGTGGAATCAAATCAACTTCGAATCTAATTTTCACAAAAAAGTAGT
1 GAAAGAGTAGTGGAATCAAATCAACTTCGAATCTGATCTTCACAGAAGAGTAGT
22259 GAAGTTGAAT
Statistics
Matches: 380, Mismatches: 43, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
186 13 0.03
187 155 0.41
188 210 0.55
189 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.27
Consensus pattern (188 bp):
GAAAGAGTAGTGGAATCAAATCAACTTCGAATCTGATCTTCACAGAAGAGTAGTAAAACAAATTC
CTTCTGTTCAAGTCATTCAAATTAAGCCTTCACATAAGAGTAGTGAAGCAGGAGCAAGATCAAAA
TTCGCTCTCCACGGAAGAGTAGTGGAACGGATTTTTCAGCAAAGTATGAAATCTCCAC
Found at i:26971 original size:18 final size:18
Alignment explanation
Indices: 26948--26984 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
26938 TGTCATACCC
*
26948 TATGTTGCCTTAACACCA
1 TATGTTACCTTAACACCA
26966 TATGTTACCTTAACACCA
1 TATGTTACCTTAACACCA
26984 T
1 T
26985 TAGTGGATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.27, G:0.08, T:0.35
Consensus pattern (18 bp):
TATGTTACCTTAACACCA
Found at i:29664 original size:3 final size:3
Alignment explanation
Indices: 29656--29757 Score: 163
Period size: 3 Copynumber: 34.7 Consensus size: 3
29646 TTAATATATT
29656 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
29702 TAA TAA TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
29750 TAA TAA TA
1 TAA TAA TA
29758 TGGATAAAAA
Statistics
Matches: 91, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
2 4 0.04
3 87 0.96
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:30086 original size:119 final size:119
Alignment explanation
Indices: 29911--30561 Score: 1131
Period size: 119 Copynumber: 5.5 Consensus size: 119
29901 TTCTCCAGAT
** * *
29911 GAGTTCTTCTCATTATGAACT-TT-CTGCTGGGGATGATGTTCCATCAA-ATGATGAATTCAAGC
1 GAGTTCTTCTCATTATGAACTCTTCCT-CTGGAAATGATGATCCATCAATTTGATGAATTCAAGC
*
29973 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
65 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
*
30028 GAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCA
1 GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCA
30093 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
66 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
30147 GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCA
1 GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCA
*
30212 AAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT---
66 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
* *
30263 GAGTTCTTCTCATTATGAACT-TT-CTCTGGAAAAGAATGATCCATCAA-GTGATGAATTCAAGC
1 GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATG-ATGATCCATCAATTTGATGAATTCAAGC
30325 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
65 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
30380 GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCA
1 GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCA
30445 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
66 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
*
30499 GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAGTTTGATGAATTCAAG
1 GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAG
30562 TCTTTGCTAA
Statistics
Matches: 511, Mismatches: 13, Indels: 18
0.94 0.02 0.03
Matches are distributed among these distances:
114 75 0.15
115 14 0.03
116 21 0.04
117 42 0.08
118 34 0.07
119 325 0.64
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (119 bp):
GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCA
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
Found at i:30356 original size:233 final size:233
Alignment explanation
Indices: 29911--30561 Score: 1078
Period size: 233 Copynumber: 2.8 Consensus size: 233
29901 TTCTCCAGAT
** * *
29911 GAGTTCTTCTCATTATGAACT-TT-CTGCTGGGGATGATGTTCCATCAA-ATGATGAATTCAAGC
1 GAGTTCTTCTCATTATGAACTCTTCCT-CTGGAAATGATGATCCATCAATTTGATGAATTCAAGC
*
29973 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCT
65 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCT
*
30038 CATTATGAACTCTTTCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAA
128 CATTATGAA--CTTTCTCTGGAAATGATGATCCATCAA-GTGATGAATTCAAGCAAAAGGTTGAA
30103 CAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
190 CAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
30147 GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCA
1 GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCA
*
30212 AAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT-GAGTTCTTCTCAT
66 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCAT
*
30276 TATGAACTTTCTCTGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAGT
131 TATGAACTTTCTCTGGAAATG-ATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAGT
30341 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
195 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
30380 GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCA
1 GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCA
30445 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTC
66 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTC
30510 ATTATGAACTCTTCCTCTGGAAATGATGATCCATC-AGTTTGATGAATTCAAG
129 ATTATGAACT-TT-CTCTGGAAATGATGATCCATCAAG--TGATGAATTCAAG
30562 TCTTTGCTAA
Statistics
Matches: 394, Mismatches: 10, Indels: 20
0.93 0.02 0.05
Matches are distributed among these distances:
233 198 0.50
234 12 0.03
235 19 0.05
236 44 0.11
237 32 0.08
238 89 0.23
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (233 bp):
GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCA
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAATGATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAGTT
CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
Found at i:30553 original size:352 final size:350
Alignment explanation
Indices: 29893--30561 Score: 1223
Period size: 352 Copynumber: 1.9 Consensus size: 350
29883 ATTGAATAAA
** * *
29893 TTCTTCTTTTCTCCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGTTCCATCAA
1 TTCTTCTTTTCTCCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGAAAAGATGATCCATCAA
29958 ATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
66 ATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
*
30023 ATGACGAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGATGATCCATCAATTTGATGAATTC
131 ATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAATTTGATGAATTC
30088 AAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTC
196 AAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTC
30153 TTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGGT
261 TTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGGT
30218 TGAACAAGTTCTTCTCATTATGAAT
326 TGAACAAGTTCTTCTCATTATGAAT
*
30243 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT-CTGGAAAAGAATGATCCAT
1 TTCTTCTT--TTCTCCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGAAAAG-ATGATCCAT
* *
30307 CAAGTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTT
63 CAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTT
30372 CAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAATTTGATGAA
128 CAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAATTTGATGAA
30437 TTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAG
193 TTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAG
*
30502 TTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAGTTTGATGAATTCAAG
258 TTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAG
30562 TCTTTGCTAA
Statistics
Matches: 307, Mismatches: 9, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
350 8 0.03
351 6 0.02
352 293 0.95
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (350 bp):
TTCTTCTTTTCTCCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGAAAAGATGATCCATCAA
ATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
ATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAATTTGATGAATTC
AAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTC
TTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGGT
TGAACAAGTTCTTCTCATTATGAAT
Found at i:31271 original size:52 final size:52
Alignment explanation
Indices: 31192--31500 Score: 559
Period size: 52 Copynumber: 5.9 Consensus size: 52
31182 TACTTGATTT
*
31192 TGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
1 TGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
*
31244 TGTCCAACCAGATCAGATAACTTAAAGAACACTTCCAGAAGATGCTATGTTC
1 TGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
31296 TGAT-CAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
1 TG-TCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
*
31348 TGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGTTC
1 TGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
31400 TGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
1 TGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
31452 TGAT-CAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1 TG-TCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
31501 AGCACATTCA
Statistics
Matches: 249, Mismatches: 5, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
51 1 0.00
52 246 0.99
53 2 0.01
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.24
Consensus pattern (52 bp):
TGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC
Found at i:32386 original size:19 final size:19
Alignment explanation
Indices: 32364--32400 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
32354 AATAGAAAAG
*
32364 AATAAATTGAATTTCCAAA
1 AATAAATTGAATCTCCAAA
32383 AATAAATTGAATCTCCAA
1 AATAAATTGAATCTCCAA
32401 TAAGTTGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (19 bp):
AATAAATTGAATCTCCAAA
Found at i:32749 original size:15 final size:14
Alignment explanation
Indices: 32729--32760 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
32719 CTTGACCCCC
*
32729 TTTTTTCGTTTTTT
1 TTTTTTTGTTTTTT
32743 TTTTTTTGTTTTTT
1 TTTTTTTGTTTTTT
32757 TTTT
1 TTTT
32761 CTTCAAGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.00, C:0.03, G:0.06, T:0.91
Consensus pattern (14 bp):
TTTTTTTGTTTTTT
Found at i:43334 original size:13 final size:15
Alignment explanation
Indices: 43312--43347 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
43302 TTTGACAGAA
43312 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
43324 AAATAAAATACTTGC
1 AAATAAAATACTTGC
43339 AAATAAAAT
1 AAATAAAAT
43348 GAAACATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.19
13 6 0.29
14 2 0.10
15 9 0.43
ACGTcount: A:0.61, C:0.08, G:0.06, T:0.25
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:43367 original size:18 final size:18
Alignment explanation
Indices: 43346--43380 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
43336 TGCAAATAAA
43346 ATGAAACAT-ATAAATATT
1 ATGAAA-ATAATAAATATT
43364 ATGAAAATAATAAATAT
1 ATGAAAATAATAAATAT
43381 ATATAAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.31
Consensus pattern (18 bp):
ATGAAAATAATAAATATT
Found at i:45526 original size:3 final size:3
Alignment explanation
Indices: 45518--45612 Score: 133
Period size: 3 Copynumber: 32.7 Consensus size: 3
45508 ATTTAATATT
*
45518 TAA TAA TAA -AA TAA TAA TAA TAA TAA -AA -AA TAA AAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
45563 TAA TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
45611 TA
1 TA
45613 TGGATAAAAA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
2 6 0.07
3 76 0.93
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:47157 original size:13 final size:13
Alignment explanation
Indices: 47128--47174 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
47118 TCGAATACCT
47128 AAAAATACATTTT-
1 AAAAATA-ATTTTA
47141 -AAAATAATTTTAA
1 AAAAATAATTTT-A
47154 AAAAATAATTTTA
1 AAAAATAATTTTA
*
47167 AAAGATAA
1 AAAAATAA
47175 AAAATGATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 5 0.17
12 6 0.20
13 8 0.27
14 11 0.37
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (13 bp):
AAAAATAATTTTA
Found at i:47160 original size:14 final size:14
Alignment explanation
Indices: 47141--47169 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
47131 AATACATTTT
47141 AAAATAATTTTAAA
1 AAAATAATTTTAAA
47155 AAAATAATTTTAAA
1 AAAATAATTTTAAA
47169 A
1 A
47170 GATAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AAAATAATTTTAAA
Found at i:49175 original size:9 final size:9
Alignment explanation
Indices: 49141--49173 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
49131 ATTTGGCCTG
49141 TATAAAGTAA
1 TATAAA-TAA
49151 TATAAATAA
1 TATAAATAA
49160 TATAAAT-A
1 TATAAATAA
49168 TATAAA
1 TATAAA
49174 ATTATTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 7 0.30
9 10 0.43
10 6 0.26
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (9 bp):
TATAAATAA
Found at i:52162 original size:18 final size:18
Alignment explanation
Indices: 52139--52177 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
52129 GTCCAACTCA
52139 AACGACCGTTAATTTTGT
1 AACGACCGTTAATTTTGT
52157 AACGACCGTTAATTTTGT
1 AACGACCGTTAATTTTGT
52175 AAC
1 AAC
52178 AAAAAATGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (18 bp):
AACGACCGTTAATTTTGT
Found at i:52281 original size:60 final size:60
Alignment explanation
Indices: 52217--52344 Score: 161
Period size: 60 Copynumber: 2.1 Consensus size: 60
52207 CAAGTGAATG
* *
52217 TTTTGTAACTTTTAATAGTCAATG-GACTCAATAAAGTAACATCCTATAGT-TGGAGGACTA
1 TTTTGTAACTTTTAATAGTC-AGGAGACTCAATAAAGTAACATCCTATAGTCGGGA-GACTA
* * **
52277 TTTTGTAACTTTTAATAGTCGGGAGACTCGATAAAGTAGTATCCTATAGTCGGGAGACTA
1 TTTTGTAACTTTTAATAGTCAGGAGACTCAATAAAGTAACATCCTATAGTCGGGAGACTA
52337 TTTGTGTA
1 TTT-TGTA
52345 TTTTACCCTT
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
59 1 0.02
60 51 0.86
61 7 0.12
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.36
Consensus pattern (60 bp):
TTTTGTAACTTTTAATAGTCAGGAGACTCAATAAAGTAACATCCTATAGTCGGGAGACTA
Found at i:57622 original size:20 final size:20
Alignment explanation
Indices: 57592--57724 Score: 115
Period size: 20 Copynumber: 6.5 Consensus size: 20
57582 ATGTCCAACT
*
57592 AAGGATTGATCCCTTTTCAA
1 AAGGATCGATCCCTTTTCAA
* ****
57612 AAGGGTCGATCCCTCAGGAGA
1 AAGGATCGATCCCTTTTCA-A
* *
57633 AAGGATCGGTCTCTTTTCAA
1 AAGGATCGATCCCTTTTCAA
**
57653 AAGGATTTATCCCTTTTCAA
1 AAGGATCGATCCCTTTTCAA
* *
57673 AAGGATAGAT-CCTTTTGGAGA
1 AAGGATCGATCCCTTTT-CA-A
*
57694 AATGATCGATCCCTTTTCAA
1 AAGGATCGATCCCTTTTCAA
57714 AAGGATCGATC
1 AAGGATCGATC
57725 GCTTAGAGAA
Statistics
Matches: 85, Mismatches: 24, Indels: 8
0.73 0.21 0.07
Matches are distributed among these distances:
19 6 0.07
20 50 0.59
21 23 0.27
22 6 0.07
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (20 bp):
AAGGATCGATCCCTTTTCAA
Found at i:57693 original size:61 final size:61
Alignment explanation
Indices: 57592--57724 Score: 176
Period size: 61 Copynumber: 2.2 Consensus size: 61
57582 ATGTCCAACT
* * * *
57592 AAGGATTGATCCCTTTTCAAAAGGGTCGATCCCTCAGGAGAAAGGATCGGTCTCTTTTCAA
1 AAGGATTGATCCCTTTTCAAAAGGATAGATCCCTCAGGAGAAAGGATCGATCCCTTTTCAA
* * ** *
57653 AAGGATTTATCCCTTTTCAAAAGGATAGATCCTTTTGGAGAAATGATCGATCCCTTTTCAA
1 AAGGATTGATCCCTTTTCAAAAGGATAGATCCCTCAGGAGAAAGGATCGATCCCTTTTCAA
*
57714 AAGGATCGATC
1 AAGGATTGATC
57725 GCTTAGAGAA
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (61 bp):
AAGGATTGATCCCTTTTCAAAAGGATAGATCCCTCAGGAGAAAGGATCGATCCCTTTTCAA
Found at i:57743 original size:41 final size:41
Alignment explanation
Indices: 57661--57748 Score: 117
Period size: 41 Copynumber: 2.1 Consensus size: 41
57651 AAAAGGATTT
* *
57661 ATCCCTTTTCAAAAGGATAGATCCTTTTGGAGAAATGATCG
1 ATCCCTTTTCAAAAGGATAGATCCTTTAGGAAAAATGATCG
*
57702 ATCCCTTTTCAAAAGGATCGATCGC-TTAGAGAAAAAT-ATCG
1 ATCCCTTTTCAAAAGGATAGATC-CTTTAG-GAAAAATGATCG
57743 ATCCCT
1 ATCCCT
57749 CAAAAGAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
41 35 0.83
42 7 0.17
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (41 bp):
ATCCCTTTTCAAAAGGATAGATCCTTTAGGAAAAATGATCG
Found at i:63105 original size:20 final size:20
Alignment explanation
Indices: 63058--63134 Score: 73
Period size: 21 Copynumber: 3.8 Consensus size: 20
63048 TTGTCTATCT
* *
63058 AAGGATCAATCCCTTGGGAGA
1 AAGGATCGATCCCTT-AGAGA
* ***
63079 AATGATCGATCCCTTTTCGA
1 AAGGATCGATCCCTTAGAGA
*
63099 AAGGATCGGTCCCTTAGAGAA
1 AAGGATCGATCCCTTAGAG-A
63120 AAGGATCGATCCCTT
1 AAGGATCGATCCCTT
63135 CTCTATTTTA
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 16 0.36
21 28 0.64
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (20 bp):
AAGGATCGATCCCTTAGAGA
Found at i:63560 original size:65 final size:65
Alignment explanation
Indices: 63491--63645 Score: 186
Period size: 65 Copynumber: 2.4 Consensus size: 65
63481 CACCCATTTT
* * * *
63491 GAATGCATTTTGTGTACCGATGCA-GAAGCCATGCATCGATGCACTCTTTAATATTTTGAAACAT
1 GAATGCATTTTGTGTACCGATGCACGAA-CCATGCAACGATGCACTCCTGAATATTTTAAAACAT
63555 C
65 C
* * ** *
63556 GAATGCATTTTGTGTACTGATGCACGGACCATGCAACGATGCACTCCTGGCTCTTTTAAAACATC
1 GAATGCATTTTGTGTACCGATGCACGAACCATGCAACGATGCACTCCTGAATATTTTAAAACATC
* * *
63621 GAATGTAATTAGTGTACCGATGCAC
1 GAATGCATTTTGTGTACCGATGCAC
63646 CCCTAGTGTA
Statistics
Matches: 76, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
65 74 0.97
66 2 0.03
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.30
Consensus pattern (65 bp):
GAATGCATTTTGTGTACCGATGCACGAACCATGCAACGATGCACTCCTGAATATTTTAAAACATC
Done.