Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000510.1 Hibiscus syriacus cultivar Beakdansim tig00000969_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: 80062
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:73 original size:6 final size:6
Alignment explanation
Indices: 62--88 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
52 GACACGTATT
62 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
89 GACCCGACCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:596 original size:6 final size:6
Alignment explanation
Indices: 579--617 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
569 GCTCGTCTCG
579 GGTCGT -GTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
618 ACGTGTCTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.00, C:0.18, G:0.49, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:740 original size:20 final size:20
Alignment explanation
Indices: 715--1021 Score: 288
Period size: 20 Copynumber: 14.8 Consensus size: 20
705 CTCATTTTCT
*
715 GAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
** * *
735 GAATCGTATTGCGATTTTTTTTCT
1 GAATCGCGTTGCGA---TTCTT-G
759 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
780 -AATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
800 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
819 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
839 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
860 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
879 GAAGATCGCGTTGCGATTCTTG
1 G-A-ATCGCGTTGCGATTCTTG
*
901 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
*
921 GAATCGCGTTGCGATTTTTG
1 GAATCGCGTTGCGATTCTTG
*
941 GAAGATCGCGTTGCGATTTTTG
1 G-A-ATCGCGTTGCGATTCTTG
*
963 GAAGATCGCGTTGCGATT-TTAT
1 G-A-ATCGCGTTGCGATTCTT-G
*
985 GAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
1005 GAAGATCGCGTTGCGAT
1 G-A-ATCGCGTTGCGAT
1022 CTTCTTTTCA
Statistics
Matches: 255, Mismatches: 12, Indels: 38
0.84 0.04 0.12
Matches are distributed among these distances:
18 10 0.04
19 2 0.01
20 137 0.54
21 11 0.04
22 73 0.29
23 10 0.04
24 12 0.05
ACGTcount: A:0.17, C:0.18, G:0.26, T:0.38
Consensus pattern (20 bp):
GAATCGCGTTGCGATTCTTG
Found at i:808 original size:40 final size:40
Alignment explanation
Indices: 753--1064 Score: 262
Period size: 40 Copynumber: 7.6 Consensus size: 40
743 TTGCGATTTT
*
753 TTTTCTGAATCGCGTTGCGATTTTCTTAATCGCGTTGCGA
1 TTTTCTAAATCGCGTTGCGATTTTCTTAATCGCGTTGCGA
*
793 TTTTCTTAATCGCGTTGCGA--TTCTTGGAATCGCGTTGCGA
1 TTTTCTAAATCGCGTTGCGATTTTCTT--AATCGCGTTGCGA
**
833 TTCTT-GGAATCGCGTTGCGATTTTCTTAATCGCGTTGCGA
1 TT-TTCTAAATCGCGTTGCGATTTTCTTAATCGCGTTGCGA
**
873 TTCTTGGAAGATCGCGTTGCGA--TTCTTGGAATCGCGTTGCGA
1 TT-TTCTAA-ATCGCGTTGCGATTTTCTT--AATCGCGTTGCGA
* *
915 TTTTCTGAATCGCGTTGCGATTTT-TGGAAGATCGCGTTGCGA
1 TTTTCTAAATCGCGTTGCGATTTTCT--TA-ATCGCGTTGCGA
* * *
957 TTTT-TGGAAGATCGCGTTGCGATTTTATGAATCGCATTGCGA
1 TTTTCT--AA-ATCGCGTTGCGATTTTCTTAATCGCGTTGCGA
** * * * *
999 TTCTTGGAAGATCGCGTTGCGATCTTCTT-TTCAACGTTGCGC
1 TT-TTCTAA-ATCGCGTTGCGATTTTCTTAATC-GCGTTGCGA
*
1041 TTTTCTAAATCGCGTTGCGGTTTT
1 TTTTCTAAATCGCGTTGCGATTTT
1065 GTTGATCATT
Statistics
Matches: 228, Mismatches: 23, Indels: 42
0.78 0.08 0.14
Matches are distributed among these distances:
38 5 0.02
40 96 0.42
41 16 0.07
42 90 0.39
43 4 0.02
44 16 0.07
45 1 0.00
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.39
Consensus pattern (40 bp):
TTTTCTAAATCGCGTTGCGATTTTCTTAATCGCGTTGCGA
Found at i:888 original size:42 final size:41
Alignment explanation
Indices: 760--1027 Score: 284
Period size: 42 Copynumber: 6.5 Consensus size: 41
750 TTTTTTTCTG
***
760 AATCGCGTTGCGATTTTCTTAATCGCGTTGCGATT-TTCTT
1 AATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGA
800 AATCGCGTTGCGA--TTCTTGGAATCGCGTTGCGATTCTTGG-
1 AATCGCGTTGCGATTTTCTT--AATCGCGTTGCGATTCTTGGA
840 AATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGA
1 AATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGA
*
881 AGATCGCGTTGCGA--TTCTTGGAATCGCGTTGCGATT-TTCTG-
1 A-ATCGCGTTGCGATTTTCTT--AATCGCGTTGCGATTCTT-GGA
* *
922 AATCGCGTTGCGATTTT-TGGAAGATCGCGTTGCGATTTTTGGA
1 AATCGCGTTGCGATTTTCT--TA-ATCGCGTTGCGATTCTTGGA
* * *
965 AGATCGCGTTGCGATTTTATGAATCGCATTGCGATTCTTGGA
1 A-ATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGA
*
1007 AGATCGCGTTGCGATCTTCTT
1 A-ATCGCGTTGCGATTTTCTT
1028 TTCAACGTTG
Statistics
Matches: 198, Mismatches: 11, Indels: 36
0.81 0.04 0.15
Matches are distributed among these distances:
38 5 0.03
40 78 0.39
41 8 0.04
42 86 0.43
43 4 0.02
44 16 0.08
45 1 0.01
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (41 bp):
AATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGA
Found at i:1039 original size:42 final size:40
Alignment explanation
Indices: 825--1064 Score: 142
Period size: 42 Copynumber: 5.8 Consensus size: 40
815 CTTGGAATCG
*
825 CGTTGCGATTCTTGG-A-ATCGCGTTGCGATTTTCTTAATC-G
1 CGTTGCGATTCTTGGAAGATCGCGTTGCGA-TTT-TT-ATCAA
* *
865 CGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTTGGAATC-G
1 CGTTGCGATTCTTGGAAGATCGCGTTGCGATT-TT--TATCAA
* *
907 CGTTGCGATT-TTCTG-A-ATCGCGTTGCGATTTTTGGAAGATC-G
1 CGTTGCGATTCTT-GGAAGATCGCGTTGCGATTTTT-----ATCAA
* *
949 CGTTGCGATTTTTGGAAGATCGCGTTGCGA-TTTTATGAA
1 CGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTTATCAA
*
988 TCGCATTGCGATTCTTGGAAGATCGCGTTGCGATCTTCTTTTCAA
1 -CG--TTGCGATTCTTGGAAGATCGCGTTGCGAT-TT-TTATCAA
* ** *
1033 CGTTGCGCTT-TTCTAA-ATCGCGTTGCGGTTTT
1 CGTTGCGATTCTTGGAAGATCGCGTTGCGATTTT
1065 GTTGATCATT
Statistics
Matches: 166, Mismatches: 13, Indels: 44
0.74 0.06 0.20
Matches are distributed among these distances:
38 3 0.02
39 4 0.02
40 43 0.26
41 11 0.07
42 77 0.46
43 7 0.04
44 16 0.10
45 5 0.03
ACGTcount: A:0.16, C:0.19, G:0.27, T:0.38
Consensus pattern (40 bp):
CGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTTATCAA
Found at i:5253 original size:45 final size:45
Alignment explanation
Indices: 5220--5313 Score: 125
Period size: 45 Copynumber: 2.1 Consensus size: 45
5210 TTCAAGGAAG
5220 ACAACACTGAAATATTGACTCCTCTACACGAGAAAGTCAAGAATA
1 ACAACACTGAAATATTGACTCCTCTACACGAGAAAGTCAAGAATA
* * * * * * *
5265 ATAATACTGAGATATTGACTTCTCTTCACGAGGAAGTCGAGAATA
1 ACAACACTGAAATATTGACTCCTCTACACGAGAAAGTCAAGAATA
5310 ACAA
1 ACAA
5314 AGATTGACTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.23
Consensus pattern (45 bp):
ACAACACTGAAATATTGACTCCTCTACACGAGAAAGTCAAGAATA
Found at i:5320 original size:38 final size:37
Alignment explanation
Indices: 5278--6006 Score: 538
Period size: 38 Copynumber: 19.7 Consensus size: 37
5268 ATACTGAGAT
5278 ATTGACTTCTCTTCACGAGGAAGTCGAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTC-AGAATAACAAAG
*
5316 ATTGACTTCTTTTCACGAGGAAGTCGAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTC-AGAATAACAAAG
** *
5354 ATTGAC-TCATCTT-TGGAGGGAGTCAGGAATAACAAAG
1 ATTGACTTC-TCTTCACGAGGAAGTCA-GAATAACAAAG
* * *
5391 ATTGACTTCTCTTCACGAGGAAGTTAAGAATAAAAAAT
1 ATTGACTTCTCTTCACGAGGAAG-TCAGAATAACAAAG
5429 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTC-AGAATAACAAAG
* *
5467 ATTGAC-TCATCTTCGCGAGGGAGTCAGGAATAACAAAG
1 ATTGACTTC-TCTTCACGAGGAAGTCA-GAATAACAAAG
* * *
5505 ATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCA-GAATAACAAAG
* *
5543 ATTGACTTCTCTTCGCGAGGGAGTCATGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCA-GAATAACAAAG
*
5581 ATTGACTTCTCTTCACGAGGAAGTCATGAATAACAGAG
1 ATTGACTTCTCTTCACGAGGAAGTCA-GAATAACAAAG
* * *
5619 ATTGACTTC-C-T--CG-TG-A--CA-AA-GACTAA-
1 ATTGACTTCTCTTCACGAGGAAGTCAGAATAACAAAG
* ** * *** * * * * **
5645 CTTCTCTTCACGAGGA--AGTCAAG-AATAATACAGATTG
1 ATTGACTTCTC-TTCACGAG-GAAGTCAGAATA-ACAAAG
* * * *** * ** ** * *
5682 AATCA-TTTTCGCGAGGGAGTCAGGAATAACAA-AGATTA-
1 ATTGACTTCTCTTCA-CGAGGAAGTCAGAATAACA-A--AG
* *
5720 ACT--C--CTCTTCACGAGTG-AGTCAGGAGTAACAAAG
1 ATTGACTTCTCTTCACGAG-GAAGTCA-GAATAACAAAG
5754 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTC-AGAATAACAAAG
5792 ATTGACTTCTCTTCACGAGGAAGTCGAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTC-AGAATAACAAAG
* * * *
5830 ATTGACTCCTTTTTACGAGGGAGTCAGGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCA-GAATAACAAAG
*
5868 ATTAACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTC-AGAATAACAAAG
* *
5906 ACTGACTTCTC-TCACGAGGAAGTCATGAATAACAAAT
1 ATTGACTTCTCTTCACGAGGAAGTCA-GAATAACAAAG
* * *
5943 ATTGACTTCTCTTCATGAGTAAGTTAAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAG-TCAGAATAACAAAG
5981 ATTGACTTCTCTTCACGAGGAAGTCA
1 ATTGACTTCTCTTCACGAGGAAGTCA
6007 AGTTGAAGTT
Statistics
Matches: 561, Mismatches: 85, Indels: 91
0.76 0.12 0.12
Matches are distributed among these distances:
26 6 0.01
27 4 0.01
28 2 0.00
30 2 0.00
32 2 0.00
33 3 0.01
34 12 0.02
35 9 0.02
36 10 0.02
37 78 0.14
38 426 0.76
39 7 0.01
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (37 bp):
ATTGACTTCTCTTCACGAGGAAGTCAGAATAACAAAG
Found at i:5703 original size:97 final size:96
Alignment explanation
Indices: 5537--5726 Score: 229
Period size: 97 Copynumber: 2.0 Consensus size: 96
5527 GTCAGGAATA
* * * * * *
5537 ACAAAGATTGACTTCTCTTCGCGAGGGAGTCATGAATAACAAAGATTGACTTCTCTTCACGAGGA
1 ACAAAGACTAACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACATCTCTTCACGAGGA
* * *
5602 AGTCATGAATAACAGAGATTGACTTCCTCGTG
66 AGTCAGGAATAACAAAGATTAAC-TCCTCGTG
* * * *
5634 ACAAAGACTAACTTCTCTTCACGAGGAAGTCAAGAATAATACAGATTGA-ATCATTTTCGCGAGG
1 ACAAAGACTAACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACATC-TCTTCACGAGG
*
5698 GAGTCAGGAATAACAAAGATTAACTCCTC
65 AAGTCAGGAATAACAAAGATTAACTCCTC
5727 TTCACGAGTG
Statistics
Matches: 78, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
96 7 0.09
97 71 0.91
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.25
Consensus pattern (96 bp):
ACAAAGACTAACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACATCTCTTCACGAGGA
AGTCAGGAATAACAAAGATTAACTCCTCGTG
Found at i:5741 original size:135 final size:135
Alignment explanation
Indices: 5499--5762 Score: 352
Period size: 135 Copynumber: 2.0 Consensus size: 135
5489 GTCAGGAATA
* * * * * *
5499 ACAAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCGCGAGGG
1 ACAAAGACTAACTCCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACATCTCTTCGCGAGGG
* * * * *
5564 AGTCATGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCATGAATAACAGAGATTGACTTCC
66 AGTCAGGAATAACAAAGATTAACTCCTCTTCACGAGGAAGTCAGGAATAACAAAGATTGACTTCC
5629 TCGTG
131 TCGTG
* * * *
5634 ACAAAGACTAACTTCTCTTCACGAGGAAGTCAAGAATAATACAGATTGA-ATCATTTTCGCGAGG
1 ACAAAGACTAACTCCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACATC-TCTTCGCGAGG
*
5698 GAGTCAGGAATAACAAAGATTAACTCCTCTTCACGAGTG-AGTCAGGAGTAACAAAGATTGACTT
65 GAGTCAGGAATAACAAAGATTAACTCCTCTTCACGAG-GAAGTCAGGAATAACAAAGATTGACTT
5762 C
129 C
5763 TCTTCACGAG
Statistics
Matches: 111, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
134 2 0.02
135 108 0.97
136 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (135 bp):
ACAAAGACTAACTCCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACATCTCTTCGCGAGGG
AGTCAGGAATAACAAAGATTAACTCCTCTTCACGAGGAAGTCAGGAATAACAAAGATTGACTTCC
TCGTG
Found at i:5752 original size:173 final size:173
Alignment explanation
Indices: 5476--5989 Score: 521
Period size: 173 Copynumber: 2.9 Consensus size: 173
5466 GATTGACTCA
* * * * *
5476 TCTTCGCGAGGGAGTCAGGAATAACAAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAA
1 TCTTCACGAGGAAGTCAAGAATAACAAAGATTGAATCATCTTCGCGAGGGAGTCAGGAATAACAA
* * * *
5541 AGATTGACTTCTCTTCGCGAGGGAGTCATGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTC
66 AGATTAACTCCTCTTCACGAGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTC
* *
5606 ATGAATAACAGAGATTGACTTCCTCGTGACAAAGACTAACTTC
131 AAGAATAACAAAGATTGACTTCCTCGTGACAAAGACTAACTTC
* * *
5649 TCTTCACGAGGAAGTCAAGAATAATACAGATTGAATCATTTTCGCGAGGGAGTCAGGAATAACAA
1 TCTTCACGAGGAAGTCAAGAATAACAAAGATTGAATCATCTTCGCGAGGGAGTCAGGAATAACAA
* *
5714 AGATTAACTCCTCTTCACGAGTGAGTCAGGAGTAACAAAGATTGACTTCTCTTCACGAGGAAGTC
66 AGATTAACTCCTCTTCACGAGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTC
* * *
5779 AAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCGAGAATAACAAAGATTGACTCC
131 AAGAATAACAAAGATTGACTTC-C-T--C------GT---G----ACAAAGACTAACTTC
* * * * * * *
5839 TTTTTACGAGGGAGTCAGGAATAACAAAGATT-AACTTC-TCTTCACGAGGAAGTCAAGAATAAC
1 TCTTCACGAGGAAGTCAAGAATAACAAAGATTGAA--TCATCTTCGCGAGGGAGTCAGGAATAAC
* * * * * * * *
5902 AAAGACTGACTTCTC-TCACGAGGAAGTCATGAATAACAAATATTGACTTCTCTTCATGAGTAAG
64 AAAGATTAACTCCTCTTCACGAGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCACGAGGAAG
*
5966 TTAAGAATAACAAAGATTGACTTC
129 TCAAGAATAACAAAGATTGACTTC
5990 TCTTCACGAG
Statistics
Matches: 282, Mismatches: 40, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
173 136 0.48
174 1 0.00
175 1 0.00
177 1 0.00
183 2 0.01
186 1 0.00
189 67 0.24
190 71 0.25
191 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (173 bp):
TCTTCACGAGGAAGTCAAGAATAACAAAGATTGAATCATCTTCGCGAGGGAGTCAGGAATAACAA
AGATTAACTCCTCTTCACGAGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTC
AAGAATAACAAAGATTGACTTCCTCGTGACAAAGACTAACTTC
Found at i:15850 original size:22 final size:24
Alignment explanation
Indices: 15820--15863 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
15810 GATGAAGTTG
*
15820 AAAAGATATAT-TAA-AATAAAAT
1 AAAAAATATATATAATAATAAAAT
15842 AAAAAATATATATAATAATAAA
1 AAAAAATATATATAATAATAAA
15864 TATTAATAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 3 0.16
24 6 0.32
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (24 bp):
AAAAAATATATATAATAATAAAAT
Found at i:15864 original size:16 final size:16
Alignment explanation
Indices: 15839--15881 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
15829 ATTAAAATAA
*
15839 AATAAAAAATA-TATAT
1 AATAATAAATATTA-AT
15855 AATAATAAATATTAAT
1 AATAATAAATATTAAT
*
15871 AGTAATAAATA
1 AATAATAAATA
15882 GAAAAGAGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 22 0.92
17 2 0.08
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
AATAATAAATATTAAT
Found at i:16684 original size:68 final size:68
Alignment explanation
Indices: 16558--16686 Score: 174
Period size: 68 Copynumber: 1.9 Consensus size: 68
16548 TAAAACATCT
* *
16558 TAAATCCTAATTAAAACACTTAAAACTATTTAAATTAAAATACCTAAAAAAATAATAATATAATA
1 TAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCAAAAAAAATAATAATATAATA
16623 TTC
66 TTC
* *
16626 TAAATCTTAATTAAAATAC-TAAAACCTATTTAAACTAAAATA-CAAAGATAAAAT-ATAATAT
1 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCAAA-A-AAAATAATAATAT
16687 TTAAAATATT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
67 8 0.15
68 41 0.76
69 5 0.09
ACGTcount: A:0.57, C:0.11, G:0.01, T:0.32
Consensus pattern (68 bp):
TAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCAAAAAAAATAATAATATAATA
TTC
Found at i:17600 original size:36 final size:37
Alignment explanation
Indices: 17559--17639 Score: 94
Period size: 36 Copynumber: 2.2 Consensus size: 37
17549 CGAATTAAAT
* * *
17559 GGGGACATG-GAAAAATTATTTATGCTAAACGGGGAC
1 GGGGACATGAGAAAAATCATTTATACTAAACGGGAAC
* * *
17595 GGGGAC-GGAGAAAAATCGTTTATATTAAACGGGAAC
1 GGGGACATGAGAAAAATCATTTATACTAAACGGGAAC
17631 GGGGACATG
1 GGGGACATG
17640 TTTAGTAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
35 1 0.03
36 34 0.94
37 1 0.03
ACGTcount: A:0.36, C:0.11, G:0.33, T:0.20
Consensus pattern (37 bp):
GGGGACATGAGAAAAATCATTTATACTAAACGGGAAC
Found at i:17757 original size:2 final size:2
Alignment explanation
Indices: 17750--17777 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17740 ATTTAAATTA
17750 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
17778 GTATCCAGCC
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:22228 original size:14 final size:14
Alignment explanation
Indices: 22209--22246 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
22199 TGAGGTATTT
22209 TGTTTAGGGTTTAG
1 TGTTTAGGGTTTAG
*
22223 TGTTTAGAGTTTAG
1 TGTTTAGGGTTTAG
22237 -GATTTAGGGT
1 TG-TTTAGGGT
22247 GTGTTCCAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 1 0.05
14 20 0.95
ACGTcount: A:0.18, C:0.00, G:0.34, T:0.47
Consensus pattern (14 bp):
TGTTTAGGGTTTAG
Found at i:22830 original size:2 final size:2
Alignment explanation
Indices: 22825--22858 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
22815 TATATATATA
*
22825 TG TG TG TG TG TG TG TG TA TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
22859 ATTTTTCGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (2 bp):
TG
Found at i:26722 original size:77 final size:77
Alignment explanation
Indices: 26641--26796 Score: 276
Period size: 77 Copynumber: 2.0 Consensus size: 77
26631 TCTATCACGA
*
26641 ATCAAGTGATCTTTATAATAAAATAATAATTATTATTTTTTGAGGACTTAAGTTCGAGCACAATA
1 ATCAAGTGATCTTTATAATAAAAGAATAATTATTATTTTTTGAGGACTTAAGTTCGAGCACAATA
*
26706 GATGACAGTGGT
66 GATGACAGGGGT
**
26718 ATCAAGTGATCTTTATAATAAAAGAATTGTTATTATTTTTTGAGGACTTAAGTTCGAGCACAATA
1 ATCAAGTGATCTTTATAATAAAAGAATAATTATTATTTTTTGAGGACTTAAGTTCGAGCACAATA
26783 GATGACAGGGGT
66 GATGACAGGGGT
26795 AT
1 AT
26797 GAGCGTTCAA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
77 75 1.00
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.36
Consensus pattern (77 bp):
ATCAAGTGATCTTTATAATAAAAGAATAATTATTATTTTTTGAGGACTTAAGTTCGAGCACAATA
GATGACAGGGGT
Found at i:27916 original size:18 final size:18
Alignment explanation
Indices: 27895--27933 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
27885 TTTTTAATAA
27895 AAAATACATAAAAAAATT
1 AAAATACATAAAAAAATT
* * *
27913 AAAATATATAATAAATTT
1 AAAATACATAAAAAAATT
27931 AAA
1 AAA
27934 TTTTTTGTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAATACATAAAAAAATT
Found at i:28063 original size:3 final size:3
Alignment explanation
Indices: 28057--28081 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
28047 ATATTATAAA
28057 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
28082 TAATTAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:38109 original size:7 final size:7
Alignment explanation
Indices: 38087--38148 Score: 60
Period size: 7 Copynumber: 9.1 Consensus size: 7
38077 AAAAAAAAAC
*
38087 AAATAAA
1 AAATGAA
38094 AAGATGAA
1 AA-ATGAA
38102 AAATGAAA
1 AAATG-AA
38110 AAATGAA
1 AAATGAA
38117 AAA-G-A
1 AAATGAA
38122 AAA--AA
1 AAATGAA
38127 AAATGAA
1 AAATGAA
38134 AAATGAA
1 AAATGAA
*
38141 AAAAGAA
1 AAATGAA
38148 A
1 A
38149 TGAAAAAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
5 8 0.17
6 1 0.02
7 26 0.54
8 13 0.27
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (7 bp):
AAATGAA
Found at i:38119 original size:25 final size:24
Alignment explanation
Indices: 38087--38155 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 24
38077 AAAAAAAAAC
38087 AAAT-AAAAAG-ATGAAAAATGAAA
1 AAATGAAAAAGAATGAAAAATG-AA
**
38110 AAATGAAAAAGAAAAAAAAATGAA
1 AAATGAAAAAGAATGAAAAATGAA
38134 AAATGAAAAAAGAAATGAAAAA
1 AAATG-AAAAAG-AATGAAAAA
38156 ATAAAAAGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
23 4 0.11
24 13 0.34
25 14 0.37
26 7 0.18
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (24 bp):
AAATGAAAAAGAATGAAAAATGAA
Found at i:38127 original size:17 final size:18
Alignment explanation
Indices: 38091--38155 Score: 84
Period size: 17 Copynumber: 3.8 Consensus size: 18
38081 AAAAACAAAT
*
38091 AAAAAGATGAAAAATG--
1 AAAAAAATGAAAAATGAA
38107 -AAAAAATGAAAAA-GAA
1 AAAAAAATGAAAAATGAA
38123 AAAAAAATGAAAAATGAA
1 AAAAAAATGAAAAATGAA
38141 AAAAGAAATGAAAAA
1 AAAA-AAATGAAAAA
38156 ATAAAAAGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
14 1 0.02
15 12 0.28
17 13 0.30
18 7 0.16
19 10 0.23
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (18 bp):
AAAAAAATGAAAAATGAA
Found at i:38133 original size:32 final size:32
Alignment explanation
Indices: 38072--38170 Score: 105
Period size: 32 Copynumber: 3.0 Consensus size: 32
38062 GTACTATGCT
*
38072 TGAAGAAAA-AAAAACAAATAAAAAGATGAAAAA
1 TGAA-AAAAGAAAAAGAAA-AAAAAGATGAAAAA
38105 TGAAAAAATGAAAAAGAAAAAAAA-ATGAAAAA
1 TGAAAAAA-GAAAAAGAAAAAAAAGATGAAAAA
*
38137 TGAAAAAAGAAATGAAAAAATAAAAAGA-GAAAAA
1 TGAAAAAAGAAA--AAGAAA-AAAAAGATGAAAAA
38171 GGAGGGTTTG
Statistics
Matches: 58, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
31 4 0.07
32 20 0.34
33 14 0.24
34 19 0.33
35 1 0.02
ACGTcount: A:0.77, C:0.01, G:0.13, T:0.09
Consensus pattern (32 bp):
TGAAAAAAGAAAAAGAAAAAAAAGATGAAAAA
Found at i:39290 original size:136 final size:136
Alignment explanation
Indices: 39044--39353 Score: 503
Period size: 136 Copynumber: 2.3 Consensus size: 136
39034 GGTGAACCAG
* *
39044 CATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATTCGACAGAGGGAGAAGAAGTTCATAATG
1 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
* * * *
39109 ATAAGAGCTTGTTCGACCTATCACTAGATTCACGACATTTTGAATCAGTGACACCTTGCTTGAAG
66 AGAAGAGCTTGTTCGACCTATCACTAGATTCACAACATTTCGAATCAGTGACACCTCGCTTGAAG
*
39174 GATCAG
131 GATCAA
* *
39180 TATTTCTAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
1 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
* *
39245 AGAAGAGCTTGTTCGACCTATCACTCGATTCACAACATTTCGAATCAGTGACACCTCGCTTGAGG
66 AGAAGAGCTTGTTCGACCTATCACTAGATTCACAACATTTCGAATCAGTGACACCTCGCTTGAAG
39310 GATCAA
131 GATCAA
* *
39316 CATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATC
1 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATC
39354 AAATGAAGAA
Statistics
Matches: 159, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
136 159 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (136 bp):
CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
AGAAGAGCTTGTTCGACCTATCACTAGATTCACAACATTTCGAATCAGTGACACCTCGCTTGAAG
GATCAA
Found at i:39382 original size:19 final size:18
Alignment explanation
Indices: 39337--39404 Score: 61
Period size: 16 Copynumber: 3.7 Consensus size: 18
39327 AAGAGTTCAT
39337 AATGAGAAGAACTCATCA
1 AATGAGAAGAACTCATCA
*
39355 AAT--GAAGAACTCATCC
1 AATGAGAAGAACTCATCA
*
39371 AATGAGAGAGAA-TAAGTTCA
1 AATGAGA-AGAACTCA--TCA
39391 TAATGAGAAGAACT
1 -AATGAGAAGAACT
39405 TGTCCAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
16 15 0.38
18 7 0.17
19 4 0.10
20 6 0.15
21 8 0.20
ACGTcount: A:0.49, C:0.13, G:0.19, T:0.19
Consensus pattern (18 bp):
AATGAGAAGAACTCATCA
Found at i:45271 original size:2 final size:2
Alignment explanation
Indices: 45266--45319 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
45256 TGTTTTTTAA
45266 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45308 AT AT AT AT AT AT
1 AT AT AT AT AT AT
45320 GGATGGATAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45854 original size:28 final size:28
Alignment explanation
Indices: 45814--45872 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
45804 CGATGGTAGA
45814 ATTCAAACTTAACCTTA-ACATTTCAACC
1 ATTCAAACTTAACCTTAGA-ATTTCAACC
45842 ATTCAAACTTAACCTTAGAATTTCAACC
1 ATTCAAACTTAACCTTAGAATTTCAACC
45870 ATT
1 ATT
45873 TGTGCCAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.39, C:0.25, G:0.02, T:0.34
Consensus pattern (28 bp):
ATTCAAACTTAACCTTAGAATTTCAACC
Found at i:47563 original size:3 final size:3
Alignment explanation
Indices: 47555--47586 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
47545 ATTTTTTCAG
47555 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
47587 AAATTAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:49194 original size:28 final size:29
Alignment explanation
Indices: 49162--49238 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
49152 TATTCGTTTA
* * *
49162 ATTTATTTTCTGTTATTTATATTTTGTTC
1 ATTTATTTTCAGTTATTTATAATTTGTGC
*
49191 -TTTAAATTTCAGTTATTT-TAATTTGTGC
1 ATTT-ATTTTCAGTTATTTATAATTTGTGC
49219 ATTTACTTTTCAG-TATTTAT
1 ATTTA-TTTTCAGTTATTTAT
49239 GTTACATTCC
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
28 17 0.44
29 22 0.56
ACGTcount: A:0.22, C:0.08, G:0.08, T:0.62
Consensus pattern (29 bp):
ATTTATTTTCAGTTATTTATAATTTGTGC
Found at i:51094 original size:16 final size:14
Alignment explanation
Indices: 51065--51093 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
51055 CCAAAAAAAC
51065 TCAAAATTTATATA
1 TCAAAATTTATATA
51079 TCAAAATTTATATA
1 TCAAAATTTATATA
51093 T
1 T
51094 AGATATTGTT
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:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (14 bp):
TCAAAATTTATATA
Found at i:57252 original size:2 final size:2
Alignment explanation
Indices: 57245--57272 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
57235 TGGGTAGTTG
57245 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
57273 TTGTTTCGAC
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:60407 original size:75 final size:75
Alignment explanation
Indices: 60317--60565 Score: 344
Period size: 75 Copynumber: 3.4 Consensus size: 75
60307 AACTTAATCG
** * * *
60317 GTTAAAATAAAATAGGCGCTACCTATTATATTAAACTACCTACTGATTTGTTTGAAGGTTACTAA
1 GTTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAA
60382 TAATGTAAAC
66 TAATGTAAAC
* * * * *
60392 GTTAAAACATAATAGGTGCTA---ATTACGTTAAAATATCTACCGGTTTGTTTAAAGGTTACTAA
1 GTTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAA
60454 TAATGTAAAC
66 TAATGTAAAC
* * *
60464 GGTAAAATAAAATAGGCACTATCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAA
1 GTTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAA
60529 TAATGTAAAC
66 TAATGTAAAC
60539 AG-TAAAATAAAATAGGCGCTACCTATT
1 -GTTAAAATAAAATAGGCGCTACCTATT
60566 GTTGAAAACA
Statistics
Matches: 151, Mismatches: 19, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
72 60 0.40
75 90 0.60
76 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.33
Consensus pattern (75 bp):
GTTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAA
TAATGTAAAC
Found at i:66852 original size:20 final size:20
Alignment explanation
Indices: 66826--66875 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
66816 CTGCTAGCAT
66826 CATTAAAATCGTGCAAACAA
1 CATTAAAATCGTGCAAACAA
*
66846 TATTAAAATCGTGCAAACAA
1 CATTAAAATCGTGCAAACAA
*
66866 CATCAAAATC
1 CATTAAAATC
66876 CACTCAATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.50, C:0.20, G:0.08, T:0.22
Consensus pattern (20 bp):
CATTAAAATCGTGCAAACAA
Found at i:70569 original size:151 final size:148
Alignment explanation
Indices: 70183--70639 Score: 607
Period size: 150 Copynumber: 3.0 Consensus size: 148
70173 AGGTTAATAA
* * *
70183 TAATGTAAACGGTAAAATATATACAATTTGATC-GTTTGAAATAATTTTTTAAAATTCGAAAGTA
1 TAATGTAAACGGT--AA-ATATACAACTT-AACAGTTTGAAATATTTTTTTAAAATTCGAAAGTA
* *
70247 TGGATACTTACTCTAAAAGTATGGATACTCTAAAGTTTGATAATAATGTATCCATACTTACTCTA
62 TGGATACTTACTCTAAAAGTATGGATACTCTAAAGTTTAATAATAATGTATCTATACTTA--CTA
*
70312 AAAGTATGGATATTGTTTCGACAG
125 AAAGTATGAATATTGTTTCGACAG
*
70336 TAATGTAAACGGTAAATATACAACTTAATAGTTTGAAATATTTTTTTAAAATTCGAAAGTATGGA
1 TAATGTAAACGGTAAATATACAACTTAACAGTTTGAAATATTTTTTTAAAATTCGAAAGTATGGA
* * * *
70401 TATTTACTCTAAAAGTATGAATACTTTAAAATTTAATAATAATGTATCTATACTTACTAAAAGTA
66 TACTTACTCTAAAAGTATGGATACTCTAAAGTTTAATAATAATGTATCTATACTTACTAAAAGTA
70466 TGAAT-TTGTTTCGACAG
131 TGAATATTGTTTCGACAG
* * * *
70483 TAATTTTAAACGGTAAAATATACAAGTTAACCA-TTTGAAATCTTTTTTTTTTAAATTCGAAAGT
1 TAA-TGTAAACGGT-AAATATACAACTTAA-CAGTTTGAAA--TATTTTTTTAAAATTCGAAAGT
*
70547 ATGGATACTTACTCTAAAAGTATGGATACTCTAAAGGTTAATAATAATGTAT-TCATACTTACTC
61 ATGGATACTTACTCTAAAAGTATGGATACTCTAAAGTTTAATAATAATGTATCT-ATACTTACT-
*
70611 CAAAAGTATGAATAATGTTTCGACAG
124 -AAAAGTATGAATATTGTTTCGACAG
70637 TAA
1 TAA
70640 GTTATGTCCA
Statistics
Matches: 272, Mismatches: 22, Indels: 19
0.87 0.07 0.06
Matches are distributed among these distances:
147 15 0.06
148 22 0.08
149 22 0.08
150 96 0.35
151 78 0.29
153 25 0.09
154 14 0.05
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (148 bp):
TAATGTAAACGGTAAATATACAACTTAACAGTTTGAAATATTTTTTTAAAATTCGAAAGTATGGA
TACTTACTCTAAAAGTATGGATACTCTAAAGTTTAATAATAATGTATCTATACTTACTAAAAGTA
TGAATATTGTTTCGACAG
Found at i:70997 original size:118 final size:115
Alignment explanation
Indices: 70802--71043 Score: 306
Period size: 118 Copynumber: 2.1 Consensus size: 115
70792 TGAAAAATCA
* * * *
70802 AGTAATTAACCTATTTTGTTATCGGCTTTCTAAGGCCCCATCAACTTTAAACATGCGCTATCTAT
1 AGTAATTAACCTATTTTGTTATCGGATTTATAAGGCCCCATCAACTTTAAAAATGCACTATCTAT
* * *
70867 TACATTAAATAAGTATTACTTGTTATGTTATTATGGTTAATAATGTTTCC
66 TACATTAAATAAGCACTACCTGTTATGTTATTATGGTTAATAATGTTTCC
* * *
70917 AGTAATTAACCTATTTTGTTATCGTCGAATTTATAATGCTCCATCAGCTTTAAAAATGCACTA-C
1 AGTAATTAACCTATTTTGTTATCG--G-ATTTATAAGGCCCCATCAACTTTAAAAATGCACTATC
* * * *
70981 TTATTACGTTACATAAGCGCTACCTGTTATGTTATTATGGTTGATAATGTTTCC
63 -TATTACATTAAATAAGCACTACCTGTTATGTTATTATGGTTAATAATGTTTCC
*
71035 AATAATTAA
1 AGTAATTAA
71044 TCGGTTATGT
Statistics
Matches: 108, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
115 24 0.22
117 2 0.02
118 82 0.76
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (115 bp):
AGTAATTAACCTATTTTGTTATCGGATTTATAAGGCCCCATCAACTTTAAAAATGCACTATCTAT
TACATTAAATAAGCACTACCTGTTATGTTATTATGGTTAATAATGTTTCC
Done.