Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002578.1 Hibiscus syriacus cultivar Beakdansim tig00005223_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: 53604
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:657 original size:21 final size:20
Alignment explanation
Indices: 624--1102 Score: 331
Period size: 21 Copynumber: 23.2 Consensus size: 20
614 TTGTTGCGAT
*
624 TTGGACTATCGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
*
643 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
666 TTCGACTATCGCAA-CGAAC
1 TTGGACTATCGCAAGCGAAC
*
685 TTGGAATAAATCGCAATGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
708 TTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAA-GCGAAC
*
729 TTGGACTATCGCAA-CAAAC
1 TTGGACTATCGCAAGCGAAC
*
748 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
771 TTCGACTATCGCAATGCGAAC
1 TTGGACTATCGCAA-GCGAAC
792 TTGGACTATCGCAA-CG-A-
1 TTGGACTATCGCAAGCGAAC
*
809 TTGGAATAATCGCAACGCGAAC
1 TTGGACT-ATCGCAA-GCGAAC
*
831 TTCGACTATCGCAA-CGAAC
1 TTGGACTATCGCAAGCGAAC
*
850 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
873 TTCGACTATCGCAA-CGAAC
1 TTGGACTATCGCAAGCGAAC
* *
892 TTGAAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
915 TTCGACTATCGCAA-CGAAC
1 TTGGACTATCGCAAGCGAAC
*
934 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
* **
957 TTCGACTATCTTAACGCGAAC
1 TTGGACTATCGCAA-GCGAAC
* *
978 TTGGACTATCGTAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
* *
997 TTGAAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
1020 TTCGACTATCGCAA-CGAAC
1 TTGGACTATCGCAAGCGAAC
* *
1039 TTGGACTATTGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
* *
1058 TTGGAATAAATCGCAACGCGAGC
1 TTGGACT--ATCGCAA-GCGAAC
*
1081 -TGGACTA-CGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
1098 TTGGA
1 TTGGA
1103 AAATCACATG
Statistics
Matches: 366, Mismatches: 56, Indels: 77
0.73 0.11 0.15
Matches are distributed among these distances:
17 9 0.02
18 12 0.03
19 98 0.27
20 3 0.01
21 166 0.45
22 10 0.03
23 68 0.19
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (20 bp):
TTGGACTATCGCAAGCGAAC
Found at i:689 original size:42 final size:42
Alignment explanation
Indices: 627--1103 Score: 472
Period size: 42 Copynumber: 11.5 Consensus size: 42
617 TTGCGATTTG
*
627 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
669 GACTATCGCAACGAACTTGGAATAAATCGCAATGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * *
711 GACTATCGCAACGCGAACTTGGACT--ATCGCAA--CAAACTTG
1 GACTATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTC
* * * * *
751 GAATAAATCGCAACGCGAACTTCGACT--ATCGCAATGCGAACTTG
1 GACT--ATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTC
795 GACTATCGCAACG-A-TTGGAAT-AATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
834 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
876 GACTATCGCAACGAACTTGAAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
918 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
** * * *
960 GACTATCTTAACGCGAACTTGGACT--ATCGTAA--CGAA-TTT
1 GACTATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTC
* * * *
999 GAAATAAATCGCAACGCGAACTTCGACT--ATCGCAA--CGAACTTG
1 G-ACT--ATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTC
* * * *
1042 GACTATTGCAACGAATTTGGAATAAATCGCAACGCGAGC-TG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
1083 GACTA-CGCAACGAATTTGGAA
1 GACTATCGCAACGAACTTGGAA
1104 AATCACATGC
Statistics
Matches: 382, Mismatches: 33, Indels: 42
0.84 0.07 0.09
Matches are distributed among these distances:
38 14 0.04
39 32 0.08
40 46 0.12
41 14 0.04
42 241 0.63
43 3 0.01
44 32 0.08
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:723 original size:63 final size:63
Alignment explanation
Indices: 652--1094 Score: 563
Period size: 63 Copynumber: 7.1 Consensus size: 63
642 TTTGGAATAA
* *
652 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAATGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
*
715 ATCGCAACGCGAACTTGGACTATCGCAACAAACTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
*
778 ATCGCAATGCGAACTTGGACTATCGCAACG-A-TTGGAAT-AATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
* * *
838 ATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTCGACT--ATCGCAA--CGAACTT-GA
1 ATCGCAACGCGAACTTGGACT--ATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTCG-
*
896 AAT
61 ACT
*
899 AAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
** * * *
964 ATCTTAACGCGAACTTGGACTATCGTAACGAATTTGAAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
* * * *
1027 ATCGCAA--CGAACTTGGACTATTGCAACGAATTTGGAATAAATCGCAACGCGAGC-TGGACT
1 ATCGCAACGCGAACTTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
1087 A-CGCAACG
1 ATCGCAACG
1095 AATTTGGAAA
Statistics
Matches: 335, Mismatches: 27, Indels: 38
0.84 0.07 0.09
Matches are distributed among these distances:
58 11 0.03
59 5 0.01
60 43 0.13
61 69 0.21
62 3 0.01
63 179 0.53
64 5 0.01
65 19 0.06
66 1 0.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.21
Consensus pattern (63 bp):
ATCGCAACGCGAACTTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
Found at i:1065 original size:249 final size:247
Alignment explanation
Indices: 627--1103 Score: 778
Period size: 249 Copynumber: 1.9 Consensus size: 247
617 TTGCGATTTG
* *
627 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAAT
1 GACTATCGCAACGAACTTGAAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAAT
* *
692 AAATCGCAATGCGAACTTCGACTATCGCAACGCGAACTTGGACTATCGCAACAAACTTGGAATAA
66 AAATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTGGACTATCGCAACAAACTTGAAATAA
757 ATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAACGATTGGAAT-AATCG
131 ATCGCAACGCGAACTTCGACTATCGCAA-GCGAACTTGGACTATCGCAACGATTGGAATAAATCG
821 CAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
195 CAACGCGAAC-TCGACTA-CGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
876 GACTATCGCAACGAACTTGAAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAAT
1 GACTATCGCAACGAACTTGAAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAAT
** * * *
941 AAATCGCAACGCGAACTTCGACTATCTTAACGCGAACTTGGACTATCGTAACGAATTTGAAATAA
66 AAATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTGGACTATCGCAACAAACTTGAAATAA
*
1006 ATCGCAACGCGAACTTCGACTATCGCAA-CGAACTTGGACTATTGCAACGAATTTGGAATAAATC
131 ATCGCAACGCGAACTTCGACTATCGCAAGCGAACTTGGACTATCGCAACG-A-TTGGAATAAATC
* * *
1070 GCAACGCGAGCTGGACTACGCAACGAATTTGGAA
194 GCAACGCGAACTCGACTACGCAACGAACTTGGAA
1104 AATCACATGC
Statistics
Matches: 212, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
247 20 0.09
248 16 0.08
249 162 0.76
250 14 0.07
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (247 bp):
GACTATCGCAACGAACTTGAAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAAT
AAATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTGGACTATCGCAACAAACTTGAAATAA
ATCGCAACGCGAACTTCGACTATCGCAAGCGAACTTGGACTATCGCAACGATTGGAATAAATCGC
AACGCGAACTCGACTACGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:3220 original size:15 final size:15
Alignment explanation
Indices: 3200--3234 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
3190 ACGATGCGAT
*
3200 GATGAAGAAGAGGAG
1 GATGAAGAAGACGAG
3215 GATGAAGAAGACGAG
1 GATGAAGAAGACGAG
3230 GATGA
1 GATGA
3235 GGTTCCTCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.46, C:0.03, G:0.43, T:0.09
Consensus pattern (15 bp):
GATGAAGAAGACGAG
Found at i:3224 original size:18 final size:18
Alignment explanation
Indices: 3197--3231 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3187 ATGACGATGC
*
3197 GATGATGAAGAAGAGGAG
1 GATGAAGAAGAAGAGGAG
*
3215 GATGAAGAAGACGAGGA
1 GATGAAGAAGAAGAGGA
3232 TGAGGTTCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.03, G:0.43, T:0.09
Consensus pattern (18 bp):
GATGAAGAAGAAGAGGAG
Found at i:10524 original size:23 final size:23
Alignment explanation
Indices: 10479--10526 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
10469 TCGTATATTA
* *
10479 TTATATATTACTTTATTATATAT
1 TTATATAATACTATATTATATAT
10502 TTATATAATACTATATGTAATATAT
1 TTATATAATACTATAT-T-ATATAT
10527 ATTGTGTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 14 0.67
24 1 0.05
25 6 0.29
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (23 bp):
TTATATAATACTATATTATATAT
Found at i:17825 original size:38 final size:37
Alignment explanation
Indices: 17783--17899 Score: 96
Period size: 38 Copynumber: 3.1 Consensus size: 37
17773 AAGATTTGTC
*
17783 TCACTTGAGACAATTTTTACTCAAAAAAGACATTTATT
1 TCACTTGAGACAGTTTTTACT-AAAAAAGACATTTATT
** ** * *
17821 TCACTCAAGATTGTTTTT-CTTAAAACAAG--ATTTGTC
1 TCACTTGAGACAGTTTTTAC-TAAAA-AAGACATTTATT
**
17857 TCACTTGAGACAGTTTTTACTTGAAAAGACATTTCATT
1 TCACTTGAGACAGTTTTTACTAAAAAAGACATTT-ATT
17895 TCACT
1 TCACT
17900 CAAGATTGTT
Statistics
Matches: 58, Mismatches: 15, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
35 3 0.05
36 22 0.38
37 10 0.17
38 23 0.40
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.39
Consensus pattern (37 bp):
TCACTTGAGACAGTTTTTACTAAAAAAGACATTTATT
Found at i:17873 original size:36 final size:37
Alignment explanation
Indices: 17759--17883 Score: 130
Period size: 36 Copynumber: 3.4 Consensus size: 37
17749 AAGATTTATT
17759 GTTTTT-CTTAAAACAAGATTTGTCTCACTTGAGACA
1 GTTTTTACTTAAAACAAGATTTGTCTCACTTGAGACA
* * * * ** **
17795 ATTTTTACTCAAAA-AAGACATTTATTTCACTCAAGATT
1 GTTTTTACTTAAAACAAG--ATTTGTCTCACTTGAGACA
17833 GTTTTT-CTTAAAACAAGATTTGTCTCACTTGAGACA
1 GTTTTTACTTAAAACAAGATTTGTCTCACTTGAGACA
17869 GTTTTTACTTGAAAA
1 GTTTTTACTT-AAAA
17884 GACATTTCAT
Statistics
Matches: 67, Mismatches: 16, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
36 27 0.40
37 15 0.22
38 25 0.37
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (37 bp):
GTTTTTACTTAAAACAAGATTTGTCTCACTTGAGACA
Found at i:17877 original size:74 final size:74
Alignment explanation
Indices: 17756--17912 Score: 271
Period size: 74 Copynumber: 2.1 Consensus size: 74
17746 CAGAAGATTT
17756 ATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACAATTTTTACTCAAAAAAGACATTT-AT
1 ATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACAATTTTTACT-AAAAAAGACATTTCAT
17820 TTCACTCAAG
65 TTCACTCAAG
* **
17830 ATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACAGTTTTTACTTGAAAAGACATTTCATT
1 ATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACAATTTTTACTAAAAAAGACATTTCATT
17895 TCACTCAAG
66 TCACTCAAG
17904 ATTGTTTTT
1 ATTGTTTTT
17913 AAAGAAGATT
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
73 11 0.14
74 68 0.86
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (74 bp):
ATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACAATTTTTACTAAAAAAGACATTTCATT
TCACTCAAG
Found at i:17911 original size:38 final size:36
Alignment explanation
Indices: 17807--17913 Score: 108
Period size: 36 Copynumber: 2.9 Consensus size: 36
17797 TTTTACTCAA
17807 AAAAGACATTTATTTCACTCAAGATTGTTTTT-CTT
1 AAAAGACATTTATTTCACTCAAGATTGTTTTTACTT
* * * * ** **
17842 AAAACAAGATTTGTCTCACTTGAGACAGTTTTTACTT
1 AAAA-GACATTTATTTCACTCAAGATTGTTTTTACTT
17879 GAAAAGACATTTCATTTCACTCAAGATTGTTTTTA
1 -AAAAGACATTT-ATTTCACTCAAGATTGTTTTTA
17914 AAGAAGATTT
Statistics
Matches: 52, Mismatches: 16, Indels: 5
0.71 0.22 0.07
Matches are distributed among these distances:
35 4 0.08
36 20 0.38
37 8 0.15
38 20 0.38
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (36 bp):
AAAAGACATTTATTTCACTCAAGATTGTTTTTACTT
Found at i:17967 original size:21 final size:21
Alignment explanation
Indices: 17938--18007 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
17928 TCGCTTGAGA
*
17938 TAGTTTCCCTTGAAACAAATT
1 TAGTCTCCCTTGAAACAAATT
*
17959 TAGTCTCCCTTGAGAC-----
1 TAGTCTCCCTTGAAACAAATT
*
17975 -AGTTTCCCTTGAAACAAATT
1 TAGTCTCCCTTGAAACAAATT
*
17995 TTGTCTCCCTTGA
1 TAGTCTCCCTTGA
18008 GACAGTCTCC
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
15 13 0.35
21 24 0.65
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (21 bp):
TAGTCTCCCTTGAAACAAATT
Found at i:17979 original size:36 final size:36
Alignment explanation
Indices: 17922--18022 Score: 159
Period size: 36 Copynumber: 2.8 Consensus size: 36
17912 TAAAGAAGAT
* *
17922 TTTA-TCTCGCTTGAGATAGTTTCCCTTGAAACAAA
1 TTTAGTCTCCCTTGAGACAGTTTCCCTTGAAACAAA
17957 TTTAGTCTCCCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTAGTCTCCCTTGAGACAGTTTCCCTTGAAACAAA
* *
17993 TTTTGTCTCCCTTGAGACAGTCTCCCTTGA
1 TTTAGTCTCCCTTGAGACAGTTTCCCTTGA
18023 GATAGTTTCC
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
35 4 0.07
36 57 0.93
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.37
Consensus pattern (36 bp):
TTTAGTCTCCCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:17984 original size:15 final size:15
Alignment explanation
Indices: 17964--18034 Score: 52
Period size: 15 Copynumber: 4.3 Consensus size: 15
17954 AAATTTAGTC
17964 TCCCTTGAGACAGTT
1 TCCCTTGAGACAGTT
* *
17979 TCCCTTGAAACAAATTTT
1 TCCCTTGAGAC--A-GTT
*
17997 GTCTCCCTTGAGACAGTC
1 -T--CCCTTGAGACAGTT
*
18015 TCCCTTGAGATAGTT
1 TCCCTTGAGACAGTT
18030 TCCCT
1 TCCCT
18035 CGAAATAGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
15 27 0.63
17 2 0.05
18 3 0.07
19 2 0.05
21 9 0.21
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.35
Consensus pattern (15 bp):
TCCCTTGAGACAGTT
Found at i:18072 original size:39 final size:39
Alignment explanation
Indices: 18013--18091 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
18003 CTTGAGACAG
* *
18013 TCTCCCTTGAGATAGTTTCCCTCGAAATAGAAGATTTTA
1 TCTCCCTTGAGATAGTTTCCCTCAAAACAGAAGATTTTA
*
18052 TCTCGCTTGAGATAGTTTCCCTCAAAACAGAAGATTTTA
1 TCTCCCTTGAGATAGTTTCCCTCAAAACAGAAGATTTTA
18091 T
1 T
18092 AAGAAACTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.35
Consensus pattern (39 bp):
TCTCCCTTGAGATAGTTTCCCTCAAAACAGAAGATTTTA
Found at i:18378 original size:42 final size:40
Alignment explanation
Indices: 18312--18425 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 40
18302 AAGGGTTTCT
* *
18312 TGATGAGTAAGTCATTCCGGCCATC-AGTAAGTCTTTCGAGCA
1 TGATG-GTAAGTCCTT-CGGCCATCTA-TAAGTCTTTCGAGAA
*
18354 TGATGCGTAAGTCCTTCGGACCATCTATAATTCTTTCGAGAA
1 TGATG-GTAAGTCCTTCGG-CCATCTATAAGTCTTTCGAGAA
* * *
18396 AGATGATAAGTCCTTCGAGCCATCCATAAG
1 TGATGGTAAGTCCTTCG-GCCATCTATAAG
18426 ACCTTCGGGC
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
41 23 0.38
42 37 0.61
43 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (40 bp):
TGATGGTAAGTCCTTCGGCCATCTATAAGTCTTTCGAGAA
Found at i:18683 original size:36 final size:36
Alignment explanation
Indices: 18616--18724 Score: 119
Period size: 36 Copynumber: 3.0 Consensus size: 36
18606 AAAAAACATG
* * * * *
18616 AATTTTGTCTCGCTTGAGACAATTTTTACTTGAAACC
1 AATTTTATCTCGCTTGAAAC-AGTTTCACTTGAAACA
* *
18653 AGTTTTATCTCTCTTGAAACAGTTTCACTTGAAACA
1 AATTTTATCTCGCTTGAAACAGTTTCACTTGAAACA
* * *
18689 AATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACA
1 AATTTTATCTCGCTTGAAACAGTTTCACTTGAAACA
18725 CAAAATCTTT
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
36 44 0.73
37 16 0.27
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (36 bp):
AATTTTATCTCGCTTGAAACAGTTTCACTTGAAACA
Found at i:19244 original size:91 final size:91
Alignment explanation
Indices: 19106--19955 Score: 1293
Period size: 91 Copynumber: 9.4 Consensus size: 91
19096 AGATAATCGA
19106 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
19171 ATGAGAAGAACTTGTTCAACCTTGGT
66 ATGAGAAGAACTTGTTCAACCTTGGT
* * * * *
19197 TTATCATTTGCAGTGGAGAGTTCATAATGAGAATAACTCATCTAACGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
*
19262 ATGAGAAGAACTTGTTCAACCTTGGC
66 ATGAGAAGAACTTGTTCAACCTTGGT
* *
19288 TCAGCATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAAAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
*
19353 ATGAGAAGAA-------AACCTTGGC
66 ATGAGAAGAACTTGTTCAACCTTGGT
* * * *
19372 TCATCATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCAAAGATGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
*
19437 ATGAGAAGAACTTGTTCAACTTTGGT
66 ATGAGAAGAACTTGTTCAACCTTGGT
* * *
19463 TCATCATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAATAAGTTTATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
**
19528 ATGAGAAGAACTTGTTCAACCTTGCA
66 ATGAGAAGAACTTGTTCAACCTTGGT
*
19554 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAAAT-AGTCCAACGAGGGAGAAGAAGTTCAT
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCA-TCCAACGAGGGAGAAGAAGTTCAT
* *
19618 AATGAGAAGAACTTATTCAACATTGGT
65 AATGAGAAGAACTTGTTCAACCTTGGT
* * *
19645 TCATCATTTCCAGTGGAGAGTTCATAATGAGAAGAACTTATCTAACGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
**
19710 ATGAGAAGAACTTGTTCAACCTTGCA
66 ATGAGAAGAACTTGTTCAACCTTGGT
* *
19736 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCGTCCAACGAGGGAGAATAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
**
19801 ATGAGAAGAACTTGTTCAACCTCAGT
66 ATGAGAAGAACTTGTTCAACCTTGGT
* * *
19827 TTAAGATTTCCAGTGGAGAGTTCATAATGAGAAAAACTCATCCAACGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
**
19892 ATGAGAAGAACTTGTTCAACCTTGCA
66 ATGAGAAGAACTTGTTCAACCTTGGT
* *
19918 TCAACATTTCCAGCGAAGAGTTCATAATGAGAAGAACT
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACT
19956 TGTTCAACCT
Statistics
Matches: 685, Mismatches: 65, Indels: 18
0.89 0.08 0.02
Matches are distributed among these distances:
84 79 0.12
90 1 0.00
91 604 0.88
92 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (91 bp):
TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTGGT
Found at i:19453 original size:20 final size:19
Alignment explanation
Indices: 19391--19454 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
19381 CTAGTGGAGA
19391 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* * *
19410 CATCCAAAGATGGAGAAGAA--
1 -GTTCATA-AT-GAGAAGAACT
19430 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
19450 GTTCA
1 GTTCA
19455 ACTTTGGTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 8 0.24
18 2 0.06
19 4 0.12
20 9 0.27
21 2 0.06
22 8 0.24
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.23
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:19682 original size:143 final size:143
Alignment explanation
Indices: 19520--20098 Score: 478
Period size: 143 Copynumber: 4.1 Consensus size: 143
19510 AGGGAGAATA
* *
19520 AGTTTATAATGAGAAGAACTTGTTCAACCTTGCATCAACATTTCCAGTGGAGAGTTCATAATGAG
1 AGTTCATAATGAGAAGAACTTGTTCAACCTTGCATCAAGATTTCCAGTGGAGAGTTCATAATGAG
* *
19585 AAGAAAT-AGTCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTATTCAACATTGGTTCAT
66 AAGAAATCA-TCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTGGTTCAA
19649 CATTTCCAGTGGAG
130 CATTTCCAGTGGAG
* *** * * * * *
19663 AGTTCATAATGAGAAGAACTT-ATCTAACGAGGGA-GAAGAAGTTCATAATGAGAAGAACTTGTT
1 AGTTCATAATGAGAAGAACTTGTTC-AACCTTGCATCAAG-ATTTC-CAGTG-G-AG-A---GTT
* * * ** * * * *
19726 CA-ACCT-TGCATCAA-CATTTC--C-AGTG-G-AG-AGTTCATAATGAGAAGAACTCGTCCAAC
57 CATA-ATGAGAAGAAATCA-TCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
* *
19782 GA--GG---GAGA-----A-T--A-
120 -ATTGGTTCAACATTTCCAGTGGAG
*
19793 AGTTCATAATGAGAAGAACTTGTTCAACC-T-CAGTTTAAGATTTCCAGTGGAGAGTTCATAATG
1 AGTTCATAATGAGAAGAACTTGTTCAACCTTGCA--TCAAGATTTCCAGTGGAGAGTTCATAATG
* **
19856 AGAA-AAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGCATC
64 AGAAGAAA-TCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTGGTTC
* *
19920 AACATTTCCAGCGAAG
128 AACATTTCCAGTGGAG
**
19936 AGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTCAAGATTTCCAGTGGAGAGTTCATAATGAG
1 AGTTCATAATGAGAAGAACTTGTTCAACCTTGCATCAAGATTTCCAGTGGAGAGTTCATAATGAG
* * *
20001 AAGAACTCATCCAACGAGAGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTGATTCAAC
66 AAGAAATCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTGGTTCAAC
* *
20066 AATACCAGTGGAG
131 ATTTCCAGTGGAG
20079 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
20099 CATCCAACGA
Statistics
Matches: 335, Mismatches: 58, Indels: 86
0.70 0.12 0.18
Matches are distributed among these distances:
123 8 0.02
124 5 0.01
125 2 0.01
126 2 0.01
127 5 0.01
128 3 0.01
129 5 0.01
130 54 0.16
131 7 0.02
133 1 0.00
134 3 0.01
139 2 0.01
142 7 0.02
143 199 0.59
144 9 0.03
145 2 0.01
146 5 0.01
147 2 0.01
149 8 0.02
150 6 0.02
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.25
Consensus pattern (143 bp):
AGTTCATAATGAGAAGAACTTGTTCAACCTTGCATCAAGATTTCCAGTGGAGAGTTCATAATGAG
AAGAAATCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTGGTTCAAC
ATTTCCAGTGGAG
Found at i:19958 original size:52 final size:52
Alignment explanation
Indices: 19879--20007 Score: 204
Period size: 52 Copynumber: 2.5 Consensus size: 52
19869 CAACGAGGGA
19879 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGCATCAACATTTCCAGC
1 GAAG-AGTTCATAATGAGAAGAACTTGTTCAACCTTGCATCAACATTTCCAGC
** * *
19932 GAAGAGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTCAAGATTTCCAGT
1 GAAGAGTTCATAATGAGAAGAACTTGTTCAACCTTGCATCAACATTTCCAGC
*
19984 GGAGAGTTCATAATGAGAAGAACT
1 GAAGAGTTCATAATGAGAAGAACT
20008 CATCCAACGA
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
52 67 0.94
53 4 0.06
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (52 bp):
GAAGAGTTCATAATGAGAAGAACTTGTTCAACCTTGCATCAACATTTCCAGC
Found at i:19983 original size:234 final size:235
Alignment explanation
Indices: 19697--20145 Score: 731
Period size: 234 Copynumber: 1.9 Consensus size: 235
19687 TAACGAGGGA
19697 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGCATCAACATTTCCAGTGGAGAGTTCATA
1 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGCATCAACATTTCCAGTGGAGAGTTCATA
* * * *
19762 ATGAGAAGAACTCGTCCAACGAGGGAGAATAAGTTCATAATGAGAAGAACTTGTTCAACCTCAG-
66 ATGAGAAGAACTCATCCAACGAGAGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACAT-AGA
* * * * **
19826 TTTAAGATTTCCAGTGGAGAGTTCATAATGAGAAAAACTCATCCAACGAGGGAGAAGAAGTTCAT
130 TTCAACAATACCAGTGGAGAGTTCATAATGAGAAAAACTCATCCAACGAAAGAGAAGAAGTTCAT
19891 AATGAGAAGAACTTGTTCAACCTTGCATCAACATTTCCAGC
195 AATGAGAAGAACTTGTTCAACCTTGCATCAACATTTCCAGC
** *
19932 GAAG-AGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTCAAGATTTCCAGTGGAGAGTTCATA
1 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGCATCAACATTTCCAGTGGAGAGTTCATA
*
19996 ATGAGAAGAACTCATCCAACGAGAGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTGAT
66 ATGAGAAGAACTCATCCAACGAGAGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATAGAT
* *
20061 TCAACAATACCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAAAGAGAATAAGTTCATA
131 TCAACAATACCAGTGGAGAGTTCATAATGAGAAAAACTCATCCAACGAAAGAGAAGAAGTTCATA
20126 ATGAGAAGAACTTGTTCAAC
196 ATGAGAAGAACTTGTTCAAC
20146 TTATATCACA
Statistics
Matches: 197, Mismatches: 16, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
233 1 0.01
234 192 0.97
235 4 0.02
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (235 bp):
GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGCATCAACATTTCCAGTGGAGAGTTCATA
ATGAGAAGAACTCATCCAACGAGAGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATAGAT
TCAACAATACCAGTGGAGAGTTCATAATGAGAAAAACTCATCCAACGAAAGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTGCATCAACATTTCCAGC
Found at i:20034 original size:273 final size:258
Alignment explanation
Indices: 19211--20046 Score: 710
Period size: 273 Copynumber: 3.1 Consensus size: 258
19201 CATTTGCAGT
* * *
19211 GGAGAGTTCATAATGAGAATAACTCATCTAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTG
1 GGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAATAAGTTCATAATGAGAAGAACTTG
** * * *
19276 TTCAACCTTGGCTCAGCATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAG
66 TTCAACCTCAGTTAAG-ATTTCCAGTGGAGAGTTCATAATGAGAAAAACTCATCCAACGAGGGAG
* *
19341 AAAAAGTTCATAATGAGAAGAA------AACCTTGGCTCATCATTTCTAGTGGAGAGTTCATAAT
130 AAGAAGTTCATAATGAGAAGAACTTTTCAACCTT-GCTCATCATTTCCAGTGGAGAGTTCATAAT
* * *
19400 GAGAAGAACTCATCCAAAGATGG-AGA---A--GA-AGTTCATAATGAGAAGAACTTGTTCAACT
194 GAGAAGAACT-TTTC-AACATGGAAGATTCATGGAGAGTTCATAATGAGAAGAAC----TC-A--
* *
19458 TTGGTTCATCATTTCCAGT
250 -----TC--CA---ACAGA
*
19477 GGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAATAAGTTTATAATGAGAAGAACTTG
1 GGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAATAAGTTCATAATGAGAAGAACTTG
* *
19542 TTCAACCTTGCA-TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAAA-T-AGTCCAACGAGG
66 TTCAACC-T-CAGTTAAGATTTCCAGTGGAGAGTTCATAATGAGAA-AAACTCA-TCCAACGAGG
* *
19604 GAGAAGAAGTTCATAATGAGAAGAACTTATTCAACATTGGTTCATCATTTCCAGTGGAGAGTTCA
127 GAGAAGAAGTTCATAATGAGAAGAACTT-TTCAACCTT-GCTCATCATTTCCAGTGGAGAGTTCA
* *
19669 TAATGAGAAGAACTTATCTAACGA-GGGAGA---A--GA-AGTTCATAATGAGAAGAACTTGTTC
190 TAATGAGAAGAACTTTTC-AAC-ATGGAAGATTCATGGAGAGTTCATAATGAGAAGAAC----TC
*
19727 AACCTTGCATCAACATTTCCAGT
249 -A---T-C--C-A-A----CAGA
*
19750 GGAGAGTTCATAATGAGAAGAACTCGTCCAACGAGGGAGAATAAGTTCATAATGAGAAGAACTTG
1 GGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAATAAGTTCATAATGAGAAGAACTTG
19815 TTCAACCTCAGTTTAAGATTTCCAGTGGAGAGTTCATAATGAGAAAAACTCATCCAACGAGGGAG
66 TTCAACCTCAG-TTAAGATTTCCAGTGGAGAGTTCATAATGAGAAAAACTCATCCAACGAGGGAG
* * *
19880 AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGCATCAACATTTCCAGCGAAGAGTTCATAA
130 AAGAAGTTCATAATGAGAAGAACTT-TTCAACCTTGC-TCATCATTTCCAGTGGAGAGTTCATAA
*
19945 TGAGAAGAACTTGTTCAACCTTGGTTCAAGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCA
193 TGAGAAGAACTT-TTCAA-CATGG---AAGA-TT-CA-TGGAGAGTTCATAATGAGAAGAACTCA
20010 TCCAACGAGA
250 TCCAAC-AGA
20020 GAGAAGAAGTTCATAATGAGAAGAACT
1 G-G-AG-AGTTCATAATGAGAAGAACT
20047 TGTTCAACAT
Statistics
Matches: 489, Mismatches: 38, Indels: 79
0.81 0.06 0.13
Matches are distributed among these distances:
265 1 0.00
266 131 0.27
267 4 0.01
269 3 0.01
270 7 0.01
271 4 0.01
272 12 0.02
273 289 0.59
274 7 0.01
275 1 0.00
277 4 0.01
278 1 0.00
281 1 0.00
282 3 0.01
285 2 0.00
286 19 0.04
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (258 bp):
GGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAATAAGTTCATAATGAGAAGAACTTG
TTCAACCTCAGTTAAGATTTCCAGTGGAGAGTTCATAATGAGAAAAACTCATCCAACGAGGGAGA
AGAAGTTCATAATGAGAAGAACTTTTCAACCTTGCTCATCATTTCCAGTGGAGAGTTCATAATGA
GAAGAACTTTTCAACATGGAAGATTCATGGAGAGTTCATAATGAGAAGAACTCATCCAACAGA
Found at i:20038 original size:91 final size:91
Alignment explanation
Indices: 19932--20145 Score: 358
Period size: 91 Copynumber: 2.4 Consensus size: 91
19922 CATTTCCAGC
* * * * *
19932 GAAG-AGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTCAAGATTTCCAGTGGAGAGTTCATA
1 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTGATTCAACAATACCAGTGGAGAGTTCATA
*
19996 ATGAGAAGAACTCATCCAACGAGAGA
66 ATGAGAAGAACTCATCCAACGAAAGA
20022 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTGATTCAACAATACCAGTGGAGAGTTCATA
1 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTGATTCAACAATACCAGTGGAGAGTTCATA
20087 ATGAGAAGAACTCATCCAACGAAAGA
66 ATGAGAAGAACTCATCCAACGAAAGA
*
20113 GAATAAGTTCATAATGAGAAGAACTTGTTCAAC
1 GAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
20146 TTATATCACA
Statistics
Matches: 116, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
90 4 0.03
91 112 0.97
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (91 bp):
GAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTGATTCAACAATACCAGTGGAGAGTTCATA
ATGAGAAGAACTCATCCAACGAAAGA
Found at i:30032 original size:18 final size:19
Alignment explanation
Indices: 29998--30034 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
29988 TTAATATTAG
29998 ATCCAAGCCCGGTGATGTT
1 ATCCAAGCCCGGTGATGTT
*
30017 ATCCACGCCC-GTGATGTT
1 ATCCAAGCCCGGTGATGTT
30035 TCGATCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.19, C:0.30, G:0.24, T:0.27
Consensus pattern (19 bp):
ATCCAAGCCCGGTGATGTT
Found at i:33942 original size:35 final size:34
Alignment explanation
Indices: 33857--33943 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
33847 AAAATAACTT
* *
33857 TAAATACAACAAACTTACAATAAATATTAAATGG
1 TAAATACAACAAAATTACAATAAATATTAAAAGG
* *
33891 TAAATGATAACCAAATTACAATAACTGATATTAAAAGG
1 TAAAT-ACAACAAAATTACAATAA---ATATTAAAAGG
33929 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
33944 ACTGAAATAC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 3 0.07
38 11 0.25
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAATATTAAAAGG
Found at i:34170 original size:6 final size:6
Alignment explanation
Indices: 34155--34201 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
34145 TTGTGACTCC
* * * *
34155 TCATTG TCATCA TCATCG TCATCG TCATCG TCGTCG TCGTCG TCATC
1 TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG TCATC
34202 CTGAGTAGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.15, C:0.32, G:0.17, T:0.36
Consensus pattern (6 bp):
TCATCG
Found at i:36280 original size:20 final size:20
Alignment explanation
Indices: 36241--36280 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
36231 CAAAAAAAAT
*
36241 TAATTAAATAAAATATTAAA
1 TAATTAAATAAAATACTAAA
*
36261 TAATTAAATAAATTACTAAA
1 TAATTAAATAAAATACTAAA
36281 ATATACTAAA
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:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (20 bp):
TAATTAAATAAAATACTAAA
Found at i:48640 original size:15 final size:16
Alignment explanation
Indices: 48614--48643 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
48604 TTCATGAACA
48614 ATTTATTAATTTTTTT
1 ATTTATTAATTTTTTT
48630 ATTTA-TAATTTTTT
1 ATTTATTAATTTTTT
48644 AGTAGTTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
ATTTATTAATTTTTTT
Done.