Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002794.1 Hibiscus syriacus cultivar Beakdansim tig00005755_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: 55613
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1200 original size:6 final size:6
Alignment explanation
Indices: 1191--1217 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1181 AACCCGTCTT
1191 CGTCCC CGTCCC CGTCCC CGTCCC CGT
1 CGTCCC CGTCCC CGTCCC CGTCCC CGT
1218 TTAAAAAATT
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:0.00, C:0.63, G:0.19, T:0.19
Consensus pattern (6 bp):
CGTCCC
Found at i:2484 original size:27 final size:28
Alignment explanation
Indices: 2425--2504 Score: 81
Period size: 27 Copynumber: 2.8 Consensus size: 28
2415 TTTAACAATA
2425 TTAAAATAAGAATAAAATTTATTTTTAAC
1 TTAAAATAAGAATAAAA-TTATTTTTAAC
* * *
2454 TTAAAATAGGATTAAAA-TATTTTTAAG
1 TTAAAATAAGAATAAAATTATTTTTAAC
* * *
2481 TTAAATTAAAAATATAATATATTT
1 TTAAAATAAGAATAAAAT-TATTT
2505 AATAATTTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
27 21 0.51
29 20 0.49
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.42
Consensus pattern (28 bp):
TTAAAATAAGAATAAAATTATTTTTAAC
Found at i:7305 original size:6 final size:6
Alignment explanation
Indices: 7294--7320 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
7284 GCTTTTCGAA
7294 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
7321 CGAGACGGAC
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:7773 original size:5 final size:5
Alignment explanation
Indices: 7759--7789 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
7749 CTGCCGCCGC
7759 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CG
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
7790 GGTCGGGTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.00, C:0.42, G:0.23, T:0.35
Consensus pattern (5 bp):
CGTCT
Found at i:7811 original size:6 final size:6
Alignment explanation
Indices: 7790--7825 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
7780 TCTCGTCTCG
7790 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GG
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GG
7826 AATAAATCGC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.33
6 20 0.67
ACGTcount: A:0.00, C:0.17, G:0.56, T:0.28
Consensus pattern (6 bp):
GGTCGT
Found at i:7885 original size:19 final size:19
Alignment explanation
Indices: 7861--7925 Score: 60
Period size: 21 Copynumber: 3.2 Consensus size: 19
7851 AATCGCAACG
7861 CGAACTTCAACTATCGCAA
1 CGAACTTCAACTATCGCAA
*
7880 CGAACTTGGAA-TAAATCGCAA
1 CGAACTT-CAACT--ATCGCAA
*
7901 CGCGAACTTCGACTATCGCAA
1 --CGAACTTCAACTATCGCAA
7922 CGAA
1 CGAA
7926 TTTGGAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
19 12 0.32
20 2 0.05
21 14 0.38
22 1 0.03
23 8 0.22
ACGTcount: A:0.37, C:0.28, G:0.17, T:0.18
Consensus pattern (19 bp):
CGAACTTCAACTATCGCAA
Found at i:7890 original size:42 final size:42
Alignment explanation
Indices: 7831--8297 Score: 798
Period size: 42 Copynumber: 11.2 Consensus size: 42
7821 CGTGGAATAA
*
7831 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCAACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
*
7873 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
7915 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
* * * *
7957 ATCGCAACCAATTTGGAATAAATCGCAAC-C-AATTTGGAAT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
7997 AAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
*
8041 ATCGCAACGAATTT-GAA-AAATCGCAACGCGAACTTGGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
*
8081 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
8123 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
* *
8165 ATCGCAACGAAGTTGGAATAAATCACAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
8207 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
8249 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
8291 ATCGCAA
1 ATCGCAA
8298 TGCGAACTTG
Statistics
Matches: 402, Mismatches: 17, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
40 43 0.11
41 7 0.02
42 344 0.86
43 1 0.00
44 7 0.02
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (42 bp):
ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
Found at i:8005 original size:105 final size:102
Alignment explanation
Indices: 7823--8806 Score: 662
Period size: 105 Copynumber: 9.4 Consensus size: 102
7813 GTCGTGGTCG
* * * ** *
7823 TGGAATAAATCGCAA-CGAATTTGGAATAAATCGCAACGCGAACTTCAACTATCGCAACGAACTT
1 TGGAATAAATCGCAAGCGAACTTCGACT--ATCGCAAC-C-AACTTGGACTATCGCAACGAATTT
*
7887 GGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATT
62 GGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATT
* * *
7928 TGGAATAAATCGCAACGCGAACTTCGACTATCGCAACCAATTTGGAATAAATCGCAACCAATTTG
1 TGGAATAAATCGCAA-GCGAACTTCGACTATCGCAACCAACTTGGACT--ATCGCAACGAATTTG
* * *
7993 GAATAAATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACT
63 GAATAAATCGCAACGCGAACTTGGACT--ATCGCAA--CGAATT
* * * **
8035 TCGACT--ATCGCAA-CGAA-TTTGAAAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTG
1 TGGAATAAATCGCAAGCGAACTTCG-ACTATCGCAAC-C-AACTTGGACTATCGCAACGAATTTG
8096 GAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATT
63 GAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATT
* * * * *
8136 TGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAAGTTGGAATAAATCACAACGCGAACT
1 TGGAATAAATCGCAA-GCGAACTTCGACTATCGCAACCAACTTGGACT--ATCGCAA--CGAATT
* * * * *
8201 TCGACT--ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACT
61 TGGAATAAATCGCAACGCGAACTTGGACT--ATCGCAA--CGAATT
* * * * * * *
8243 TCGACT--ATCGCAA-CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGAAC
1 TGGAATAAATCGCAAGCGAACTTCGACT--ATCGCAAC-C-AACTTGGACTATCGCAA--CGAAT
* * * * *
8305 TTGGACT--ATCGCAA--CGAATTTGGAATAAATCACAACGCGAACT
60 TTGGAATAAATCGCAACGCGAACTTGGACT--ATCGCAA--CGAATT
* * * * * *
8348 TCGACT--ATCGCAA-CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTT
1 TGGAATAAATCGCAAGCGAACTTCGACT--ATCGCAAC-C-AACTTGGACTATCGCAACGAATTT
*
8410 GG-A-AAATCGCAACGCGAACTTGGACTACCGCAA-GAATT
62 GGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATT
* * * * *
8448 TGG-A-AAATCGCAATGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACT
1 TGGAATAAATCGCAA-GCGAACTTCGACTATCGCAACCAACTTGGACT--ATCGCAA--CGAATT
* * * *
8511 TCGACT--ATCGCAACGCGAACTTCGACTATCGCAATGCGAACT
61 TGGAATAAATCGCAACGCGAACTTGGACTATCGCAA--CGAATT
* * * * *
8553 TGGACT--ATCGCAA-CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTT
1 TGGAATAAATCGCAAGCGAACTTCGACT--ATCGCAAC-C-AACTTGGACTATCGCAACGAATTT
* *
8615 TGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATT
62 GGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATT
*
8656 TGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAACGAATTTG
1 TGGAATAAATCGCAA-GCGAACTTCGACTATCGCAA--CCAACTTGGACTATCGCAACGAATTTG
* *
8721 GAATAAATCACAACGCGAACTTCGACTATCGCAACGAATT
63 GAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATT
* * *
8761 TGGAATAAATCGCAACGCGAACTTCGACTATCACAACGAATTTGGA
1 TGGAATAAATCGCAA-GCGAACTTCGACTATCGCAACCAACTTGGA
8807 AAAATCGCAA
Statistics
Matches: 724, Mismatches: 94, Indels: 124
0.77 0.10 0.13
Matches are distributed among these distances:
98 7 0.01
100 28 0.04
101 9 0.01
102 46 0.06
103 154 0.21
104 2 0.00
105 415 0.57
106 3 0.00
107 60 0.08
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (102 bp):
TGGAATAAATCGCAAGCGAACTTCGACTATCGCAACCAACTTGGACTATCGCAACGAATTTGGAA
TAAATCGCAACGCGAACTTGGACTATCGCAACGAATT
Found at i:8316 original size:42 final size:40
Alignment explanation
Indices: 7831--8837 Score: 702
Period size: 42 Copynumber: 24.2 Consensus size: 40
7821 CGTGGAATAA
* **
7831 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCAACT
1 ATCGCAACGAACTTGGAAT--ATCGCAACGCGAACTTGGACT
*
7873 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAACTTGGAAT--ATCGCAACGCGAACTTGGACT
* *
7915 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAACTTGGAAT--ATCGCAACGCGAACTTGGACT
* * * *
7957 ATCGCAACCAATTTGGAATAAATCGCAAC-C-AATTTGGAAT
1 ATCGCAACGAACTTGGAAT--ATCGCAACGCGAACTTGGACT
* *
7997 AAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGAACTTGGAAT--ATCGCAACGCGAACTTGGACT
* * *
8041 ATCGCAACGAATTTGAAAAATCGCAACGCGAACTTGGACT
1 ATCGCAACGAACTTGGAATATCGCAACGCGAACTTGGACT
*
8081 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACT
1 ATCGCAACGAACTTGGAAT--ATCGCAACGCGAACTTGGACT
* *
8123 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAACTTGGAAT--ATCGCAACGCGAACTTGGACT
* * *
8165 ATCGCAACGAAGTTGGAATAAATCACAACGCGAACTTCGACT
1 ATCGCAACGAACTTGGAAT--ATCGCAACGCGAACTTGGACT
* *
8207 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAACTTGGAAT--ATCGCAACGCGAACTTGGACT
* *
8249 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAACTTGGAAT--ATCGCAACGCGAACTTGGACT
* * *
8291 ATCGCAATGCGAACTTGGACTATCGCAA--CGAATTTGGAAT
1 ATCGCAA--CGAACTTGGAATATCGCAACGCGAACTTGGACT
* * * * *
8331 AAATCACAACGCGAACTTCGACTATCGCAA--CGAATTTGGAAT
1 --ATCGCAA--CGAACTTGGAATATCGCAACGCGAACTTGGACT
* * * **
8373 AAATCGCAACGCGAACTTCGACTATCGCAA--CGAATTTGGAAA
1 --ATCGCAA--CGAACTTGGAATATCGCAACGCGAACTTGGACT
* * * **
8415 ATCGCAACGCGAACTTGGACTACCGCAA---GAATTTGGAAA
1 ATCGCAA--CGAACTTGGAATATCGCAACGCGAACTTGGACT
* * *
8454 ATCGCAATGCGAACTTGGACTATCGCAA--CGAATTTGGAAT
1 ATCGCAA--CGAACTTGGAATATCGCAACGCGAACTTGGACT
* * *
8494 AAATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTCGACT
1 --ATCGCAA--CGAACTTGGAATATCGCAACGCGAACTTGGACT
* * *
8538 ATCGCAATGCGAACTTGGACTATCGCAA--CGAATTTGGAAT
1 ATCGCAA--CGAACTTGGAATATCGCAACGCGAACTTGGACT
* * * * *
8578 AAATCGCAACGCGAACTTCGACTATCGCAA--CGAATTTTGAAT
1 --ATCGCAA--CGAACTTGGAATATCGCAACGCGAACTTGGACT
* * * *
8620 AAATCGCAACGCGAACTTCGACTATCGCAA--CGAATTTGGAAT
1 --ATCGCAA--CGAACTTGGAATATCGCAACGCGAACTTGGACT
* * *
8662 AAATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACT
1 --ATCGCAA--CGAACTTGGAATATCGCAACGCGAACTTGGACT
* * *
8706 ATCGCAACGAATTTGGAATAAATCACAACGCGAACTTCGACT
1 ATCGCAACGAACTTGGAAT--ATCGCAACGCGAACTTGGACT
* *
8748 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAACTTGGAAT--ATCGCAACGCGAACTTGGACT
* * *
8790 ATCACAACGAATTTGGAAAAATCGCAACGCGAACTTGGACT
1 ATCGCAACGAACTTGG-AATATCGCAACGCGAACTTGGACT
8831 ATCGCAA
1 ATCGCAA
8838 TACGAATATG
Statistics
Matches: 880, Mismatches: 63, Indels: 45
0.89 0.06 0.05
Matches are distributed among these distances:
39 37 0.04
40 107 0.12
41 27 0.03
42 670 0.76
43 3 0.00
44 36 0.04
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (40 bp):
ATCGCAACGAACTTGGAATATCGCAACGCGAACTTGGACT
Found at i:8316 original size:84 final size:81
Alignment explanation
Indices: 7831--8837 Score: 782
Period size: 84 Copynumber: 12.1 Consensus size: 81
7821 CGTGGAATAA
*
7831 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCAACTATCGCAACGAACTTGGAATAAAT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAAT--AT
* *
7896 CGCAACGCGAACTTCGACT
64 CGCAAC-CGAACTTGGAAT
* *
7915 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACCAATTTGGAATAAAT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAAT--AT
*
7980 CGCAACC-AATTTGGAAT
64 CGCAACCGAACTTGGAAT
* * *
7997 AAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGAAAAAT
1 --ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAT
*
8062 CGCAACGCGAACTTGGACT
64 CGCAAC-CGAACTTGGAAT
* *
8081 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAAT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAAT--AT
* *
8146 CGCAACGCGAACTTCGACT
64 CGCAAC-CGAACTTGGAAT
* * *
8165 ATCGCAACGAAGTTGGAATAAATCACAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAAT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAAT--AT
* *
8230 CGCAACGCGAACTTCGACT
64 CGCAAC-CGAACTTGGAAT
*
8249 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTAT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA--CGAACTTGGAATAT
*
8314 CGCAA-CGAATTTGGAAT
64 CGCAACCGAACTTGGAAT
* * * * * * * *
8331 AAATCACAACGCGAACTTCGACT--ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTC
1 --ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTCGACT--ATCGCAA--CGAACTTG
* * *
8392 GACTATCGCAA-CGAATTTGGAAA
58 GAATATCGCAACCGAACTTGGAAT
* * * * * ** *
8415 ATCGCAACGCGAACTTGGACT--ACCGCAA---GAATTTGGAAAATCGCAATGCGAACTTGGACT
1 ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA--CGAACTTGGAAT
*
8475 ATCGCAA-CGAATTTGGAAT
62 ATCGCAACCGAACTTGGAAT
* * *
8494 AAATCGCAACGCGAACTTCGACT--ATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGA
1 --ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA--CGAACTTGGA
* *
8557 CTATCGCAA-CGAATTTGGAAT
60 ATATCGCAACCGAACTTGGAAT
* * * * * * *
8578 AAATCGCAACGCGAACTTCGACT--ATCGCAA--CGAATTTTGAATAAATCGCAACGCGAACTTC
1 --ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTCGACT--ATCGCAA--CGAACTTG
* *
8639 GACTATCGCAA-CGAATTTGGAAT
58 GAATATCGCAACCGAACTTGGAAT
* * * * * *
8662 AAATCGCAACGCGAACTTCGACT--ATCGCAATGCGAACTTGGACTATCGCAACGAATTTGGAAT
1 --ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAAT
* * *
8725 AAATCACAACGCGAACTTCGACT
62 --ATCGCAAC-CGAACTTGGAAT
* * *
8748 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCACAACGAATTTGGAAAAATC
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGG-AATATC
*
8813 GCAACGCGAACTTGGACT
65 GCAAC-CGAACTTGGAAT
8831 ATCGCAA
1 ATCGCAA
8838 TACGAATATG
Statistics
Matches: 821, Mismatches: 72, Indels: 61
0.86 0.08 0.06
Matches are distributed among these distances:
79 37 0.05
81 36 0.04
82 143 0.17
83 28 0.03
84 538 0.66
85 2 0.00
86 37 0.05
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (81 bp):
ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATATCG
CAACCGAACTTGGAAT
Found at i:8853 original size:41 final size:41
Alignment explanation
Indices: 8685--8862 Score: 234
Period size: 42 Copynumber: 4.3 Consensus size: 41
8675 AACTTCGACT
* *
8685 ATCGCAATGCGAACTTGGACTATCGCAACGAATTTGGAATAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGG-ATAA
*
8727 ATCACAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGG-ATAA
* *
8769 ATCGCAACGCGAACTTCGACTATCACAACGAATTTGGAAAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGATAA
* *
8810 ATCGCAACGCGAACTTGGACTATCGCAATACGAATAT-G-TAA
1 ATCGCAACGCGAACTTCGACTATCGC-A-ACGAATTTGGATAA
*
8851 ATCGCAATGCGA
1 ATCGCAACGCGA
8863 TAGTCGAAGT
Statistics
Matches: 123, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
41 40 0.33
42 76 0.62
43 7 0.06
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGATAA
Found at i:10862 original size:27 final size:26
Alignment explanation
Indices: 10831--10911 Score: 72
Period size: 27 Copynumber: 2.9 Consensus size: 26
10821 AGATAATAAC
10831 AAAAAACATTTTTAAGTTAATAAAAG
1 AAAAAACATTTTTAAGTTAATAAAAG
* * * * *
10857 ATAAAATATATTTTTTGGAGTTAAGATAAT
1 A-AAAA-ACA-TTTTT-AAGTTAATAAAAG
10887 AAAAAACTATTTTTAAGTTAATAAA
1 AAAAAAC-ATTTTTAAGTTAATAAA
10912 GTAATAAAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 9
0.69 0.15 0.15
Matches are distributed among these distances:
26 1 0.02
27 12 0.29
28 8 0.20
29 10 0.24
30 10 0.24
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.37
Consensus pattern (26 bp):
AAAAAACATTTTTAAGTTAATAAAAG
Found at i:10920 original size:28 final size:27
Alignment explanation
Indices: 10832--11048 Score: 104
Period size: 28 Copynumber: 7.5 Consensus size: 27
10822 GATAATAACA
*
10832 AAAAACATTTTTAAGTTAATAAA-AGAT
1 AAAAATATTTTTAAGTTAATAAATA-AT
* *
10859 AAAATATATTTTTTGGAGTTAAGATAATAA-
1 AAAA-ATA-TTTTT-AAGTTAATA-AATAAT
*
10889 AAAACTATTTTTAAGTTAATAAAGTAAT
1 AAAAATATTTTTAAGTTAATAAA-TAAT
* *
10917 AAAATATATTATTTGAATTTAAGATAATAA-
1 AAAA-ATATT-TTT-AAGTTAATA-AATAAT
* *
10947 CAAAATATTTTTTAAGTTAATAAAAGAAT
1 AAAAATA-TTTTTAAGTTAAT-AAATAAT
*
10976 AAAATATATTATTT--GAT-ATAAGATAAT
1 AAAA-ATATT-TTTAAGTTAATAA-ATAAT
*
11003 AACATAATACATTTTTAAGTTAATAAAAAATT
1 AA-A-AAT--ATTTTTAAGTTAATAAATAA-T
* *
11035 AAATATAATTTTAA
1 AAAAATATTTTTAA
11049 AAGTAAAATA
Statistics
Matches: 145, Mismatches: 20, Indels: 49
0.68 0.09 0.23
Matches are distributed among these distances:
26 4 0.03
27 22 0.15
28 33 0.23
29 27 0.19
30 30 0.21
31 19 0.13
32 10 0.07
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (27 bp):
AAAAATATTTTTAAGTTAATAAATAAT
Found at i:10947 original size:117 final size:118
Alignment explanation
Indices: 10809--11029 Score: 344
Period size: 117 Copynumber: 1.9 Consensus size: 118
10799 CTTTAAAATG
*
10809 TATTTGAATTTAAGATAATAACAAAAAACATTTTTAAGTTAATAAAAG-ATAAAATATATTTTTT
1 TATTTGAATTTAAGATAATAACAAAAAA-ATTTTTAAGTTAATAAAAGAATAAAATATATTATTT
10873 GGAGT-TAAGATAATAA-A-AA-ACTATTTTTAAGTTAATAAAGTAATAAAATATAT
65 -GA-TATAAGATAATAACATAATAC-ATTTTTAAGTTAATAAAGTAATAAAATATAT
* *
10926 TATTTGAATTTAAGATAATAACAAAATATTTTTTAAGTTAATAAAAGAATAAAATATATTATTTG
1 TATTTGAATTTAAGATAATAACAAAAAAATTTTTAAGTTAATAAAAGAATAAAATATATTATTTG
10991 ATATAAGATAATAACATAATACATTTTTAAGTTAATAAA
66 ATATAAGATAATAACATAATACATTTTTAAGTTAATAAA
11030 AAATTAAATA
Statistics
Matches: 96, Mismatches: 3, Indels: 9
0.89 0.03 0.08
Matches are distributed among these distances:
115 1 0.01
116 31 0.32
117 43 0.45
118 19 0.20
119 2 0.02
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (118 bp):
TATTTGAATTTAAGATAATAACAAAAAAATTTTTAAGTTAATAAAAGAATAAAATATATTATTTG
ATATAAGATAATAACATAATACATTTTTAAGTTAATAAAGTAATAAAATATAT
Found at i:10984 original size:59 final size:60
Alignment explanation
Indices: 10809--11041 Score: 320
Period size: 59 Copynumber: 4.0 Consensus size: 60
10799 CTTTAAAATG
*
10809 TATTTGAATTTAAGATAATAACAAAAAACATTTTTAAGTTAATAAAAG-ATAAAATATAT
1 TATTTGAATTTAAGATAATAACAAAATACATTTTTAAGTTAATAAAAGAATAAAATATAT
* * *
10868 TTTTTGGAGTTAAGATAAT-A-AAAA-ACTATTTTTAAGTTAAT-AAAGTAATAAAATATAT
1 TATTTGAATTTAAGATAATAACAAAATAC-ATTTTTAAGTTAATAAAAG-AATAAAATATAT
*
10926 TATTTGAATTTAAGATAATAACAAAATA-TTTTTTAAGTTAATAAAAGAATAAAATATAT
1 TATTTGAATTTAAGATAATAACAAAATACATTTTTAAGTTAATAAAAGAATAAAATATAT
* * *
10985 TATTTG-ATATAAGATAATAACATAATACATTTTTAAGTTAATAAAA-AATTAAATATA
1 TATTTGAATTTAAGATAATAACAAAATACATTTTTAAGTTAATAAAAGAATAAAATATA
11042 ATTTTAAAAG
Statistics
Matches: 155, Mismatches: 11, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
56 6 0.04
57 18 0.12
58 57 0.37
59 65 0.42
60 8 0.05
61 1 0.01
ACGTcount: A:0.52, C:0.03, G:0.07, T:0.38
Consensus pattern (60 bp):
TATTTGAATTTAAGATAATAACAAAATACATTTTTAAGTTAATAAAAGAATAAAATATAT
Found at i:14799 original size:4 final size:4
Alignment explanation
Indices: 14790--14817 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
14780 GATAAAAACG
14790 AAGA AAGA AAGA AAGA AAGA AAGA AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA
14818 GGGATAAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:15845 original size:28 final size:26
Alignment explanation
Indices: 15807--15868 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 26
15797 TTTGTATTTC
*
15807 TTATA-ATTTTTATCATGTATGTATAT-
1 TTATATATTTTT-T-ATGTAAGTATATA
15833 TTATATATGTTTTTATGTAAGTATATA
1 TTATATAT-TTTTTATGTAAGTATATA
15860 TTCATATAT
1 TT-ATATAT
15869 CATATTATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
26 16 0.52
27 5 0.16
28 10 0.32
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.56
Consensus pattern (26 bp):
TTATATATTTTTTATGTAAGTATATA
Found at i:15877 original size:20 final size:19
Alignment explanation
Indices: 15854--15894 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
15844 TTTATGTAAG
15854 TATATAT-TCATATATCATAT
1 TATATATGT-ATATATC-TAT
15874 TATATATGTATATATCTAT
1 TATATATGTATATATCTAT
15893 TA
1 TA
15895 AATGTTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 14 0.70
21 1 0.05
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.51
Consensus pattern (19 bp):
TATATATGTATATATCTAT
Found at i:19554 original size:11 final size:11
Alignment explanation
Indices: 19538--19562 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19528 AAAAGCAAAT
19538 AAAGAAAAAGA
1 AAAGAAAAAGA
19549 AAAGAAAAAGA
1 AAAGAAAAAGA
19560 AAA
1 AAA
19563 ACGTATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAGA
Found at i:20668 original size:32 final size:32
Alignment explanation
Indices: 20632--20726 Score: 145
Period size: 32 Copynumber: 3.0 Consensus size: 32
20622 GAGAAATAAT
* * *
20632 GAATGATGGGGCATATTTGGAGATTTAACATC
1 GAATGTTGGGGCATCTTTGGAGATTCAACATC
20664 GAATGTTGGGGCATCTTTGGAGATTCAACATC
1 GAATGTTGGGGCATCTTTGGAGATTCAACATC
* *
20696 AAATGTTGGGGAATCTTTGGAGATTCAACAT
1 GAATGTTGGGGCATCTTTGGAGATTCAACAT
20727 TCTGAAGTGA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 58 1.00
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (32 bp):
GAATGTTGGGGCATCTTTGGAGATTCAACATC
Found at i:20930 original size:36 final size:35
Alignment explanation
Indices: 20829--20960 Score: 138
Period size: 36 Copynumber: 3.7 Consensus size: 35
20819 ACAAAAGGTC
20829 GTCTCACTTGAGACAAGTTTTCTTAAAAACAAAATTTA
1 GTCTCACTTGAGACAA-TTTTCTT-AAAAC-AAATTTA
** * * * *
20867 GTCTTGCTTGAGATAGTTTTCTGAAAACAAATTTT
1 GTCTCACTTGAGACAATTTTCTTAAAACAAATTTA
* *
20902 GTCTCACTTGAGACAATTTCTCTTAAAACCAATTTC
1 GTCTCACTTGAGACAATTT-TCTTAAAACAAATTTA
* *
20938 GTCTCGCTTGAGACATTTTTCTT
1 GTCTCACTTGAGACAATTTTCTT
20961 TTGAGATACA
Statistics
Matches: 78, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
35 25 0.32
36 35 0.45
37 6 0.08
38 12 0.15
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (35 bp):
GTCTCACTTGAGACAATTTTCTTAAAACAAATTTA
Found at i:21022 original size:36 final size:36
Alignment explanation
Indices: 20975--21072 Score: 101
Period size: 36 Copynumber: 2.7 Consensus size: 36
20965 GATACAAATT
* *
20975 TTGAGTTTGTTTCACTTGAAACAAA-GTTGATCTCAC
1 TTGAGATTGTTTCACTTAAAACAAACGTTG-TCTCAC
** *
21011 TTGAGATTGTTTTTCTTAAAACAAACTTTGTCTCAC
1 TTGAGATTGTTTCACTTAAAACAAACGTTGTCTCAC
* *
21047 TTGAGATAGTCTTC-CTTAAGACAAAC
1 TTGAGATTGT-TTCACTTAAAACAAAC
21073 TTTGAAATTA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
36 47 0.90
37 5 0.10
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (36 bp):
TTGAGATTGTTTCACTTAAAACAAACGTTGTCTCAC
Found at i:21073 original size:36 final size:36
Alignment explanation
Indices: 21005--21076 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
20995 ACAAAGTTGA
* * *
21005 TCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTG
1 TCTCACTTGAGATAGTCTTCCTTAAAACAAACTTTG
*
21041 TCTCACTTGAGATAGTCTTCCTTAAGACAAACTTTG
1 TCTCACTTGAGATAGTCTTCCTTAAAACAAACTTTG
21077 AAATTATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.40
Consensus pattern (36 bp):
TCTCACTTGAGATAGTCTTCCTTAAAACAAACTTTG
Found at i:21316 original size:104 final size:104
Alignment explanation
Indices: 21125--21317 Score: 278
Period size: 104 Copynumber: 1.9 Consensus size: 104
21115 GATGGTTTCC
* *
21125 CTTGAAACAAAACAAACATCTTAGAGATCATTTCACTTAAAATGAATTTTATCTCTCTTGAGACA
1 CTTGAAACAAAAAAAACATCTTAGAGATCATTTCACTTAAAACGAATTTTATCTCTCTTGAGACA
**
21190 ATTTCTCTTAAAACACCCATCTTTTTTTAGTATGTTTAT
66 ATTTCTCTTAAAACACAAATCTTTTTTTAGTATGTTTAT
* ** ** * *
21229 CTTGAAACAAAAAAAACATCTTTGAGATTGTTTTTCTTGAAACGAATTTTGTCTCTCTTGAGACA
1 CTTGAAACAAAAAAAACATCTTAGAGATCATTTCACTTAAAACGAATTTTATCTCTCTTGAGACA
*
21294 TTTTCTCTTAAAACACAAATCTTT
66 ATTTCTCTTAAAACACAAATCTTT
21318 AGTTTGTTTC
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
104 77 1.00
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (104 bp):
CTTGAAACAAAAAAAACATCTTAGAGATCATTTCACTTAAAACGAATTTTATCTCTCTTGAGACA
ATTTCTCTTAAAACACAAATCTTTTTTTAGTATGTTTAT
Found at i:21415 original size:40 final size:40
Alignment explanation
Indices: 21360--21544 Score: 115
Period size: 40 Copynumber: 4.3 Consensus size: 40
21350 TGGTATGTTG
**
21360 TCCTCATCGTGTAGGAACCGTGTCATCCACCGACCATACC
1 TCCTCATCACGTAGGAACCGTGTCATCCACCGACCATACC
* * * *
21400 TCCTCATCACGTAGGAGCCGTATCA-CCCCCTAGATAACCAGT-CG
1 TCCTCATCACGTAGGAACCGTGTCATCCACC--G---ACCA-TACC
* ** *
21444 TCCTCATCACGTAGGAATCGTGTTATCATCCATAAAGATGGCC-TGCC
1 TCCTCATCACGTAGGAACCGTG---TCATCC--ACCGA---CCATACC
*
21491 ATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAAACC
1 -TCCTCATCACGTAGGAACCGTGTCATCCACCGACCATACC
21532 TCCTCATCACGTA
1 TCCTCATCACGTA
21545 AGAGACGTGT
Statistics
Matches: 109, Mismatches: 18, Indels: 36
0.67 0.11 0.22
Matches are distributed among these distances:
39 4 0.04
40 36 0.33
41 3 0.03
43 3 0.03
44 24 0.22
45 8 0.07
46 1 0.01
47 4 0.04
48 26 0.24
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (40 bp):
TCCTCATCACGTAGGAACCGTGTCATCCACCGACCATACC
Found at i:21675 original size:134 final size:131
Alignment explanation
Indices: 21359--21692 Score: 384
Period size: 134 Copynumber: 2.5 Consensus size: 131
21349 ATGGTATGTT
* * * *
21359 GTCCTCATCGTGTAGGAACCGTGTCATCCACCGACCATACCTCCTCATCACGTAGGAGCCGTATC
1 GTCCTCATCGCGTAGGAACCGTGTCATCCACCGACCAAACCTCCTCATCACGTAGGAGACGTGTC
* * * * * *
21424 ACCCCCTAGATAACCAGTCGTCCTCATCACGTAGGAATCGTGTTATCATCCATAAAGATGGCCTG
66 A-CCCATAGATAACCAGCCATCCTCATCACGTAGGAATCATGTTATCATCCATAAAGATAGCCAG
21489 CC
130 CC
* * *
21491 ATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAAACCTCCTCATCACGTAAGAGACGTGTC
1 GTCCTCATCGCGTAGGAACCGTGTCATCCACCGACCAAACCTCCTCATCACGTAGGAGACGTGTC
* * *
21556 ACTCATAGATAACCAGCCATTCTCATCGCGTAGGAA-CTATGTTATCACCCTTCC-TAAAGATAG
66 ACCCATAGATAACCAGCCATCCTCATCACGTAGGAATC-ATGTTATCA----TCCATAAAGATAG
21619 CCAGCC
126 CCAGCC
* ** * * * * *
21625 GTCCTTATCGCGTAGGAAATGTGTTATCCACCAACCAGATCTCCTCATCACGTAGGAGTCGTGTC
1 GTCCTCATCGCGTAGGAACCGTGTCATCCACCGACCAAACCTCCTCATCACGTAGGAGACGTGTC
21690 ACC
66 ACC
21693 TTTAGATGAC
Statistics
Matches: 169, Mismatches: 28, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
130 1 0.01
131 37 0.22
132 59 0.35
134 69 0.41
135 3 0.02
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (131 bp):
GTCCTCATCGCGTAGGAACCGTGTCATCCACCGACCAAACCTCCTCATCACGTAGGAGACGTGTC
ACCCATAGATAACCAGCCATCCTCATCACGTAGGAATCATGTTATCATCCATAAAGATAGCCAGC
C
Found at i:24272 original size:20 final size:22
Alignment explanation
Indices: 24247--24294 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
24237 TTTTTTAAAA
*
24247 TAAAAATCATAATT-ATT-TTT
1 TAAAAATAATAATTAATTGTTT
*
24267 TAAAAATAATATTTAATTGTTT
1 TAAAAATAATAATTAATTGTTT
24289 TAAAAA
1 TAAAAA
24295 AATGGTTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 12 0.50
21 3 0.12
22 9 0.38
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (22 bp):
TAAAAATAATAATTAATTGTTT
Found at i:24607 original size:33 final size:33
Alignment explanation
Indices: 24565--24633 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
24555 GACACATTAC
*
24565 ATGATTAAGTGCTTTAGTCTTTCTGATATTCTT
1 ATGATTAAGTGCTTAAGTCTTTCTGATATTCTT
24598 ATGATTAAGTGCTTAAGTCTTTCTGATATTCTT
1 ATGATTAAGTGCTTAAGTCTTTCTGATATTCTT
24631 ATG
1 ATG
24634 TCTTTGAGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.23, C:0.12, G:0.16, T:0.49
Consensus pattern (33 bp):
ATGATTAAGTGCTTAAGTCTTTCTGATATTCTT
Found at i:28093 original size:39 final size:36
Alignment explanation
Indices: 27984--28189 Score: 212
Period size: 39 Copynumber: 5.6 Consensus size: 36
27974 TTTGAAAATA
*
27984 TTTTTGAAAACATATAATATATAG-TTTAAAAACGG
1 TTTTTGAAAACATATAATATATAGTTTTTAAAACGG
* *
28019 -TTTTGAAAATATATAACATATAGTTTTT---ACGG
1 TTTTTGAAAACATATAATATATAGTTTTTAAAACGG
28051 TTTTTGAAAACATATAATATATAGTTTTTTAAAAAACGG
1 TTTTTGAAAACATATAATATATAG-TTTTT--AAAACGG
* *
28090 TTTTTGAAAACGAATATAATATA-A-TTTTGAAAAC-A
1 TTTTTGAAAAC--ATATAATATATAGTTTTTAAAACGG
28125 TATTTTGAAAACATATATATATATATAGTTTTTAAAACGG
1 T-TTTTGAAAAC--ATATA-ATATATAGTTTTTAAAACGG
28165 TTTTTGAAAACATGTATAATATATA
1 TTTTTGAAAACA--TATAATATATA
28190 TAACTTTTGG
Statistics
Matches: 143, Mismatches: 11, Indels: 31
0.77 0.06 0.17
Matches are distributed among these distances:
32 4 0.03
33 21 0.15
34 26 0.18
35 4 0.03
36 20 0.14
37 6 0.04
38 12 0.08
39 38 0.27
40 2 0.01
41 10 0.07
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (36 bp):
TTTTTGAAAACATATAATATATAGTTTTTAAAACGG
Found at i:28131 original size:13 final size:13
Alignment explanation
Indices: 28113--28140 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
28103 ATATAATATA
28113 ATTTTGAAAACAT
1 ATTTTGAAAACAT
28126 ATTTTGAAAACAT
1 ATTTTGAAAACAT
28139 AT
1 AT
28141 ATATATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (13 bp):
ATTTTGAAAACAT
Found at i:28163 original size:75 final size:78
Alignment explanation
Indices: 28052--28208 Score: 209
Period size: 75 Copynumber: 2.0 Consensus size: 78
28042 TTTTTACGGT
28052 TTTTGAAAACATATAATATATAGTTTTTTAAAAAACGGTTTTTGAAAAC-GAAT-ATA-ATATAA
1 TTTTGAAAACATATAATATATAGTTTTTT-AAAAACGGTTTTTGAAAACAGAATAATATATATAA
28114 -TTTTGAAAACATA
65 CTTTTGAAAACATA
*
28127 TTTTGAAAACATATATATATATA-TAGTTTTT-AAAACGGTTTTTGAAAACATGTATAATATATA
1 TTTTGAAAACATATA-ATATATAGT--TTTTTAAAAACGGTTTTTGAAAACA-GAATAATATATA
*
28190 TAACTTTTGGAAACATA
62 TAACTTTTGAAAACATA
28207 TT
1 TT
28209 ATATAGTTTT
Statistics
Matches: 72, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
75 34 0.47
76 7 0.10
77 8 0.11
78 3 0.04
79 6 0.08
80 14 0.19
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.41
Consensus pattern (78 bp):
TTTTGAAAACATATAATATATAGTTTTTTAAAAACGGTTTTTGAAAACAGAATAATATATATAAC
TTTTGAAAACATA
Found at i:28227 original size:20 final size:21
Alignment explanation
Indices: 28194--28232 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
28184 TATATATAAC
*
28194 TTTTGGAAACATATTATATAG
1 TTTTGGAAACATATAATATAG
*
28215 TTTTTGAAA-ATATAATAT
1 TTTTGGAAACATATAATAT
28233 GTTATATAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (21 bp):
TTTTGGAAACATATAATATAG
Found at i:28279 original size:12 final size:11
Alignment explanation
Indices: 28264--28315 Score: 65
Period size: 12 Copynumber: 4.8 Consensus size: 11
28254 TATATAGTAC
28264 ATATTATATTAT
1 ATATTAT-TTAT
28276 ATATTATTTAT
1 ATATTATTTAT
28287 AGTATTATTTAT
1 A-TATTATTTAT
28299 -TATT-TTTA-
1 ATATTATTTAT
28307 ATATTATTT
1 ATATTATTT
28316 TTCGGTTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
9 8 0.22
10 7 0.19
11 5 0.14
12 17 0.46
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (11 bp):
ATATTATTTAT
Found at i:28314 original size:19 final size:19
Alignment explanation
Indices: 28269--28315 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
28259 AGTACATATT
*
28269 ATATTATATATTATTTATA
1 ATATTATTTATTATTTATA
* *
28288 GTATTATTTATTATTTTTA
1 ATATTATTTATTATTTATA
28307 ATATTATTT
1 ATATTATTT
28316 TTCGGTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
ATATTATTTATTATTTATA
Found at i:31732 original size:20 final size:20
Alignment explanation
Indices: 31707--31758 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
31697 AAATTTTATC
*
31707 GGTTTTGTCATAATGAAATT
1 GGTTTTGTCATAATGAAACT
31727 GGTTTTGTCATAATGAAACT
1 GGTTTTGTCATAATGAAACT
31747 GGTTTTGTCATA
1 GGTTTTGTCATA
31759 TTTATACATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.27, C:0.08, G:0.21, T:0.44
Consensus pattern (20 bp):
GGTTTTGTCATAATGAAACT
Found at i:32408 original size:23 final size:23
Alignment explanation
Indices: 32361--32409 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
32351 CCTATTTTAA
* * *
32361 TATATAAGCGCTACTTATTACGT
1 TATATAAGAGCTACCTAATACGT
*
32384 TATATAAGAGCTACCTAATATGT
1 TATATAAGAGCTACCTAATACGT
32407 TAT
1 TAT
32410 TGTGCTTGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (23 bp):
TATATAAGAGCTACCTAATACGT
Found at i:32466 original size:23 final size:23
Alignment explanation
Indices: 32437--32503 Score: 107
Period size: 23 Copynumber: 2.9 Consensus size: 23
32427 CTAGTAATTA
**
32437 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
*
32460 ACTTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
32483 ACCTATTACATTATATAAGCG
1 ACCTATTACATTATATAAGCG
32504 ATACATAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:32519 original size:23 final size:23
Alignment explanation
Indices: 32446--32510 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
32436 AACCTATTTT
*
32446 ATTATATAAGCGCTACTTATTAC
1 ATTATATAAGCGCTACATATTAC
*
32469 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACATATTAC
*
32492 ATTATATAAGCGATACATA
1 ATTATATAAGCGCTACATA
32511 ATATGTTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.35
Consensus pattern (23 bp):
ATTATATAAGCGCTACATATTAC
Found at i:32554 original size:110 final size:110
Alignment explanation
Indices: 32361--32597 Score: 393
Period size: 110 Copynumber: 2.2 Consensus size: 110
32351 CCTATTTTAA
* * * *
32361 TATATAAGCGCTACTTATTACGTTATATAAGAGCTACCTAATATGTTATTGTGCTTGATAATATT
1 TATATAAGCGCTACCTATTACATTATATAAGAGATACATAATATGTTATTGTGCTTGATAATATT
*
32426 TCTAGTAATTAACCTATTTTATTATATAAGCGCTACTTATTACAT
66 TCTAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACAT
* *
32471 TATATAAGCGCTACCTATTACATTATATAAGCGATACATAATATGTTATTGTGCTTGATAATGTT
1 TATATAAGCGCTACCTATTACATTATATAAGAGATACATAATATGTTATTGTGCTTGATAATATT
*
32536 TCTAGTAATTAATCTATTTTATTATATAAGCGCTACCTATTACAT
66 TCTAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACAT
*
32581 TATATAAGCGGTACCTA
1 TATATAAGCGCTACCTA
32598 ATATGTTATT
Statistics
Matches: 118, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
110 118 1.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.41
Consensus pattern (110 bp):
TATATAAGCGCTACCTATTACATTATATAAGAGATACATAATATGTTATTGTGCTTGATAATATT
TCTAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACAT
Found at i:32606 original size:23 final size:23
Alignment explanation
Indices: 32556--32600 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
32546 AATCTATTTT
*
32556 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
32579 ATTATATAAGCGGTACCTAATA
1 ATTATATAAGCGCTACCTAATA
32601 TGTTATTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:34812 original size:29 final size:29
Alignment explanation
Indices: 34770--34828 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
34760 GCAACGACTC
* *
34770 AAGGTTTCATTCTCCCTTTAGTGAGCTGA
1 AAGGTTTCAGTCTCCCTTTAATGAGCTGA
*
34799 AAGGTTTCAGTCTCCTTTTAATGAGCTGA
1 AAGGTTTCAGTCTCCCTTTAATGAGCTGA
34828 A
1 A
34829 CTATCAAGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (29 bp):
AAGGTTTCAGTCTCCCTTTAATGAGCTGA
Found at i:39188 original size:31 final size:31
Alignment explanation
Indices: 39150--39305 Score: 269
Period size: 31 Copynumber: 5.0 Consensus size: 31
39140 CCCGAAGGAC
* * *
39150 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
39181 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
39212 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
39243 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
39274 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
39305 C
1 C
39306 CCTCGACATT
Statistics
Matches: 121, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
31 120 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:43580 original size:31 final size:31
Alignment explanation
Indices: 43555--43697 Score: 259
Period size: 31 Copynumber: 4.6 Consensus size: 31
43545 TCCATAGATT
* *
43555 CCGAAGAACCTAGGTAATCAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
43586 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
43617 CCGAAGAACATAGGTAAACAGTCCATAAGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
43648 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
43679 CCGAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
43698 CCTCGACCCT
Statistics
Matches: 108, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 108 1.00
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTC
Found at i:50661 original size:22 final size:22
Alignment explanation
Indices: 50622--50663 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
50612 CAAATTTGTC
* * *
50622 TTTTTAAATATTTTTTTTTAAT
1 TTTTTAAAAATATATTTTTAAT
50644 TTTTTAAAAATATATTTTTA
1 TTTTTAAAAATATATTTTTA
50664 GGTATCCGAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTTAAAAATATATTTTTAAT
Found at i:53671 original size:18 final size:18
Alignment explanation
Indices: 53648--53690 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
53638 GTATACCTCG
*
53648 AGAAGAAGGAC-GAGACAA
1 AGAAGAA-GACGGAGAAAA
53666 AGAAGAAGACGGAGAAAA
1 AGAAGAAGACGGAGAAAA
53684 AGAAGAA
1 AGAAGAA
53691 CGTATGAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.60, C:0.07, G:0.33, T:0.00
Consensus pattern (18 bp):
AGAAGAAGACGGAGAAAA
Found at i:54219 original size:21 final size:20
Alignment explanation
Indices: 54194--54255 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
54184 CCAATACCAA
54194 CAATGATATTGAAAGTAAAAT
1 CAATGATATTGAAA-TAAAAT
*
54215 TAATGA-ATTGCAAATCAAAAT
1 CAATGATATTG-AAAT-AAAAT
*
54236 CAATGATTTTGAAAATAAAA
1 CAATGATATTG-AAATAAAA
54256 ATTCTGATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 5 0.15
21 22 0.65
22 7 0.21
ACGTcount: A:0.53, C:0.06, G:0.11, T:0.29
Consensus pattern (20 bp):
CAATGATATTGAAATAAAAT
Done.