Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004217.1 Hibiscus syriacus cultivar Beakdansim tig00009237_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: 66184
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1027 original size:5 final size:5
Alignment explanation
Indices: 962--1007 Score: 56
Period size: 5 Copynumber: 9.0 Consensus size: 5
952 TAAGCATACG
* * *
962 ATAAA ATGAAA ATAAA ATAAA ATAAA ATAAA CTTAA ATGAA ATAAA
1 ATAAA AT-AAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
1008 TTGAGTTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
5 30 0.86
6 5 0.14
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.22
Consensus pattern (5 bp):
ATAAA
Found at i:5550 original size:41 final size:41
Alignment explanation
Indices: 5444--5550 Score: 126
Period size: 41 Copynumber: 2.6 Consensus size: 41
5434 GCCCAGTGGT
* * * ** *
5444 CTTATAGATGGCCTGGAGGACTTAACATCCTGCTCAGAAGA
1 CTTATAGATGGCCCGAAGGACTTAGCATCAGGCTCAGAAAA
*
5485 CTTATAGATGGCCC-ATAGGACTTAGCATTAGGCTCAGAAAA
1 CTTATAGATGGCCCGA-AGGACTTAGCATCAGGCTCAGAAAA
*
5526 CTTTTAGATGGCCCGAAGGACTTAG
1 CTTATAGATGGCCCGAAGGACTTAG
5551 TAATTGAGAA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
41 55 0.98
42 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTAGCATCAGGCTCAGAAAA
Found at i:20105 original size:6 final size:6
Alignment explanation
Indices: 20094--20177 Score: 168
Period size: 6 Copynumber: 14.0 Consensus size: 6
20084 TATGGTAATG
20094 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA
1 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA
20142 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA
1 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA
20178 CATATTGATC
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 78 1.00
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (6 bp):
TGTGTA
Found at i:35473 original size:45 final size:46
Alignment explanation
Indices: 35378--35485 Score: 150
Period size: 45 Copynumber: 2.4 Consensus size: 46
35368 TGCACATACT
* *
35378 ATGCATCGATGCACTCAGAGTTTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACTCTGAGTTTTATGAAAACATCGAATGCATTTC
35424 ATGCATCGATGCACTCTG-GCTATTT-TG-AAACATCGAATGCATTTC
1 ATGCATCGATGCACTCTGAG-T-TTTATGAAAACATCGAATGCATTTC
*
35469 ATGCATCGGTGCACTCT
1 ATGCATCGATGCACTCT
35486 TAGTGCACCG
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
45 34 0.60
46 20 0.35
47 3 0.05
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (46 bp):
ATGCATCGATGCACTCTGAGTTTTATGAAAACATCGAATGCATTTC
Found at i:36913 original size:3 final size:3
Alignment explanation
Indices: 36905--36960 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
36895 GATTGATGTA
36905 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
36953 ATT ATT AT
1 ATT ATT AT
36961 GTTGAATTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:43750 original size:14 final size:14
Alignment explanation
Indices: 43731--43761 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
43721 TTTCAAAACT
43731 CGTCACGCAGCCAC
1 CGTCACGCAGCCAC
43745 CGTCACGCAGCCAC
1 CGTCACGCAGCCAC
43759 CGT
1 CGT
43762 TCCAAATAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.48, G:0.23, T:0.10
Consensus pattern (14 bp):
CGTCACGCAGCCAC
Found at i:47967 original size:14 final size:14
Alignment explanation
Indices: 47948--47975 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
47938 ATTTTATAAT
47948 TTTTTAAAAAATTA
1 TTTTTAAAAAATTA
47962 TTTTTAAAAAATTA
1 TTTTTAAAAAATTA
47976 AAAATATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTTTAAAAAATTA
Found at i:52645 original size:20 final size:21
Alignment explanation
Indices: 52604--52656 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
52594 ATATTATGTG
*
52604 TAAACTATATAGTTTATTTATA
1 TAAACTATATAGTGTA-TTATA
52626 TAAACTATATAGTGTA-TATA
1 TAAACTATATAGTGTATTATA
* *
52646 TTAACTCTATA
1 TAAACTATATA
52657 TATAAACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 13 0.46
22 15 0.54
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.45
Consensus pattern (21 bp):
TAAACTATATAGTGTATTATA
Found at i:52658 original size:22 final size:22
Alignment explanation
Indices: 52604--52646 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
52594 ATATTATGTG
* *
52604 TAAACTATATAGTTTATTTATA
1 TAAACTATATAGTGTATATATA
52626 TAAACTATATAGTGTATATAT
1 TAAACTATATAGTGTATATAT
52647 TAACTCTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (22 bp):
TAAACTATATAGTGTATATATA
Found at i:52682 original size:13 final size:13
Alignment explanation
Indices: 52664--52739 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 13
52654 ATATATAAAC
52664 TATATAGTTTATA
1 TATATAGTTTATA
* *
52677 TTTATATTATTATA
1 TATATAGT-TTATA
* *
52691 TACTATATATATTATG
1 TA-TATA-GT-TTATA
52707 TATATAGTTTATA
1 TATATAGTTTATA
*
52720 TATATAGTTAATA
1 TATATAGTTTATA
52733 TACTATA
1 TA-TATA
52740 TATATATGTA
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
13 24 0.47
14 11 0.22
15 8 0.16
16 8 0.16
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:52691 original size:14 final size:16
Alignment explanation
Indices: 52653--52774 Score: 59
Period size: 16 Copynumber: 8.0 Consensus size: 16
52643 ATATTAACTC
*
52653 TATA-TATAAACTATA
1 TATATTATATACTATA
*
52668 TAGT-TTATAT-TTATA
1 TA-TATTATATACTATA
52683 T-TATTATATACTATA
1 TATATTATATACTATA
*
52698 TATATTATGTA-TATA
1 TATATTATATACTATA
*
52713 -GT-TTATATA-TATA
1 TATATTATATACTATA
*
52726 GT-TAATATACTA-TATA
1 -TATATTATA-TACTATA
*
52742 TATATGTATAAACTATA
1 TATAT-TATATACTATA
*
52759 TACTAGTATA-ACTATA
1 TA-TATTATATACTATA
52775 GAGTTTATAT
Statistics
Matches: 84, Mismatches: 10, Indels: 25
0.71 0.08 0.21
Matches are distributed among these distances:
13 11 0.13
14 8 0.10
15 21 0.25
16 28 0.33
17 14 0.17
18 2 0.02
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (16 bp):
TATATTATATACTATA
Found at i:52701 original size:11 final size:11
Alignment explanation
Indices: 52652--52745 Score: 51
Period size: 11 Copynumber: 9.0 Consensus size: 11
52642 TATATTAACT
*
52652 CTATATATAAA
1 CTATATATATA
52663 CTATATAGT-T-
1 CTATATA-TATA
*
52673 -TATATTTATA
1 CTATATATATA
*
52683 TTAT-TATATA
1 CTATATATATA
52693 CTATATATAT-
1 CTATATATATA
*
52703 -TATGTATATA
1 CTATATATATA
* *
52713 GTTTATATATA
1 CTATATATATA
52724 -TAGT-TAATATA
1 CTA-TAT-ATATA
52735 CTATATATATA
1 CTATATATATA
52746 TGTATAAACT
Statistics
Matches: 64, Mismatches: 8, Indels: 22
0.68 0.09 0.23
Matches are distributed among these distances:
8 1 0.02
9 14 0.22
10 10 0.16
11 35 0.55
12 4 0.06
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.50
Consensus pattern (11 bp):
CTATATATATA
Found at i:52742 original size:9 final size:8
Alignment explanation
Indices: 52653--52751 Score: 55
Period size: 9 Copynumber: 12.2 Consensus size: 8
52643 ATATTAACTC
52653 TATATATA
1 TATATATA
*
52661 AACTATATA
1 TA-TATATA
* *
52670 GTTTATATT
1 -TATATATA
52679 TATAT-TA
1 TATATATA
52686 T-TATATA
1 TATATATA
52693 CTATATATA
1 -TATATATA
*
52702 T-TATGTA
1 TATATATA
*
52709 TATAGTTTA
1 TATA-TATA
52718 TATATATA
1 TATATATA
52726 GT-TA-ATA
1 -TATATATA
52733 TACTATATA
1 TA-TATATA
*
52742 TATATGTA
1 TATATATA
52750 TA
1 TA
52752 AACTATATAC
Statistics
Matches: 70, Mismatches: 10, Indels: 22
0.69 0.10 0.22
Matches are distributed among these distances:
6 4 0.06
7 13 0.19
8 23 0.33
9 30 0.43
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (8 bp):
TATATATA
Found at i:52746 original size:13 final size:14
Alignment explanation
Indices: 52653--52768 Score: 55
Period size: 13 Copynumber: 8.3 Consensus size: 14
52643 ATATTAACTC
*
52653 TATA-TATAAACTA
1 TATAGTATATACTA
* *
52666 TATAGTTTATATTTA
1 TATAGTATATA-CTA
*
52681 TATTATTATATACTA
1 TA-TAGTATATACTA
*
52696 TATA-TAT-TATGTA
1 TATAGTATATA-CTA
*
52709 TATAGTTTATA-TA
1 TATAGTATATACTA
52722 TATAGTTAATATACTA
1 TATAG-T-ATATACTA
*
52738 TATA-TATAT-GTA
1 TATAGTATATACTA
* *
52750 TAAACTATATACTA
1 TATAGTATATACTA
52764 GTATA
1 -TATA
52769 ACTATAGAGT
Statistics
Matches: 78, Mismatches: 13, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
12 7 0.09
13 29 0.37
14 12 0.15
15 17 0.22
16 13 0.17
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.48
Consensus pattern (14 bp):
TATAGTATATACTA
Found at i:52760 original size:2 final size:2
Alignment explanation
Indices: 52653--52751 Score: 55
Period size: 2 Copynumber: 49.0 Consensus size: 2
52643 ATATTAACTC
* * *
52653 TA TA TA TA AA CTA TA TA GTT TA TA TT TA TA T- TA T- TA TA TA CTA
1 TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA
* *
52696 TA TA TA T- TA TG TA TA TA GTT TA TA TA TA TA GT- TA -A TA TA CTA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA -TA
*
52738 TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA
52752 AACTATATAC
Statistics
Matches: 74, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
1 5 0.07
2 61 0.82
3 8 0.11
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:52809 original size:36 final size:33
Alignment explanation
Indices: 52768--52834 Score: 89
Period size: 36 Copynumber: 1.9 Consensus size: 33
52758 ATACTAGTAT
52768 AACTATAGAGTTTATATAAGTATTGAATCATATATA
1 AACTATAGAGTTTAT-TAA-TA-TGAATCATATATA
* *
52804 AACTATATAGTTTATTAATATGAATTATATA
1 AACTATAGAGTTTATTAATATGAATCATATA
52835 GTTTATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 10 0.34
34 2 0.07
35 3 0.10
36 14 0.48
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (33 bp):
AACTATAGAGTTTATTAATATGAATCATATATA
Found at i:52824 original size:22 final size:21
Alignment explanation
Indices: 52798--52854 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
52788 TATTGAATCA
*
52798 TATATAAACTATATAGTTTAT
1 TATATAAATTATATAGTTTAT
*
52819 TAATATGAATTATATAGTTTAT
1 T-ATATAAATTATATAGTTTAT
52841 T-TATAAATTATATA
1 TATATAAATTATATA
52855 TGAATTATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.38
21 1 0.03
22 19 0.59
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (21 bp):
TATATAAATTATATAGTTTAT
Found at i:52851 original size:11 final size:11
Alignment explanation
Indices: 52837--52936 Score: 59
Period size: 11 Copynumber: 9.6 Consensus size: 11
52827 ATTATATAGT
*
52837 TTATTTATAAA
1 TTATATATAAA
*
52848 TTATATATGAA
1 TTATATATAAA
*
52859 TTATATTTAAA
1 TTATATATAAA
* *
52870 -TATATACAAC
1 TTATATATAAA
* *
52880 TTATATTTATA
1 TTATATATAAA
**
52891 -TAT-TATGTA
1 TTATATATAAA
*
52900 TAAT-TATAAA
1 TTATATATAAA
52910 TTATATAT--A
1 TTATATATAAA
*
52919 TTATGTATAAA
1 TTATATATAAA
52930 TTATATA
1 TTATATA
52937 GTTTATATAG
Statistics
Matches: 65, Mismatches: 19, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
9 12 0.18
10 19 0.29
11 34 0.52
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (11 bp):
TTATATATAAA
Found at i:52855 original size:22 final size:21
Alignment explanation
Indices: 52807--52942 Score: 67
Period size: 20 Copynumber: 6.6 Consensus size: 21
52797 ATATATAAAC
*
52807 TATATAGTTTATTAATATGAAT-
1 TATATAGTTTATT--TATAAATA
52829 TATATAGTTTATTTATAAAT-
1 TATATAGTTTATTTATAAATA
*
52849 TATATATGAATTATATT-TAAATA
1 TATATA-G-TTTAT-TTATAAATA
* *
52872 TATACAACTTATATTTAT--ATA
1 TATA-TAGTT-TATTTATAAATA
* *
52893 T-TAT-GTATAATTATAAAT-
1 TATATAGTTTATTTATAAATA
*
52911 TATATA-TATTATGTATAAAT-
1 TATATAGT-TTATTTATAAATA
52931 TATATAGTTTAT
1 TATATAGTTTAT
52943 ATAGTTTAAA
Statistics
Matches: 89, Mismatches: 12, Indels: 28
0.69 0.09 0.22
Matches are distributed among these distances:
17 6 0.07
18 2 0.02
19 6 0.07
20 33 0.37
21 6 0.07
22 25 0.28
23 10 0.11
24 1 0.01
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (21 bp):
TATATAGTTTATTTATAAATA
Found at i:52875 original size:21 final size:22
Alignment explanation
Indices: 52844--52897 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
52834 AGTTTATTTA
52844 TAAATTATATATGAA-TTATATT
1 TAAA-TATATATGAACTTATATT
*
52866 TAAATATATA-CAACTTATATT
1 TAAATATATATGAACTTATATT
*
52887 TATATAT-TATG
1 TAAATATATATG
52898 TATAATTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 4 0.15
21 19 0.70
22 4 0.15
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (22 bp):
TAAATATATATGAACTTATATT
Found at i:52901 original size:17 final size:17
Alignment explanation
Indices: 52881--52936 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
52871 ATATACAACT
* *
52881 TATATTTATATATTATG
1 TATATTTATAAATTATA
*
52898 TATAATTATAAATTATA
1 TATATTTATAAATTATA
52915 TATATTATGTATAAATTATA
1 TATA-T-T-TATAAATTATA
52935 TA
1 TA
52937 GTTTATATAG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
17 18 0.56
19 1 0.03
20 13 0.41
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (17 bp):
TATATTTATAAATTATA
Found at i:52984 original size:14 final size:15
Alignment explanation
Indices: 52965--52993 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
52955 TAAAGTACAT
52965 AAGTATATA-ATATA
1 AAGTATATATATATA
52979 AAGTATATATATATA
1 AAGTATATATATATA
52994 TATACTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (15 bp):
AAGTATATATATATA
Found at i:52993 original size:22 final size:24
Alignment explanation
Indices: 52913--52995 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 24
52903 TTATAAATTA
*
52913 TATATATTATGTATA-AATTATATAG
1 TATATA-TA-GTATATAATTATAAAG
* *
52938 TTTATATAGT-T-TAAATATAAAG
1 TATATATAGTATATAATTATAAAG
*
52960 TACATA-AGTATATAA-TATAAAG
1 TATATATAGTATATAATTATAAAG
52982 TATATATA-TATATA
1 TATATATAGTATATA
52996 TACTTTATAG
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
21 3 0.06
22 32 0.67
23 6 0.12
24 2 0.04
25 5 0.10
ACGTcount: A:0.48, C:0.01, G:0.07, T:0.43
Consensus pattern (24 bp):
TATATATAGTATATAATTATAAAG
Found at i:53004 original size:7 final size:7
Alignment explanation
Indices: 52994--53054 Score: 56
Period size: 7 Copynumber: 8.6 Consensus size: 7
52984 TATATATATA
52994 TATACTT
1 TATACTT
*
53001 TATAGTT
1 TATACTT
53008 TATA-TAT
1 TATACT-T
53015 T-TACTT
1 TATACTT
53021 ATATACTT
1 -TATACTT
53029 TATA-TT
1 TATACTT
53035 TAATACTT
1 T-ATACTT
53043 ATATACTT
1 -TATACTT
53051 TATA
1 TATA
53055 TTATTATAGA
Statistics
Matches: 46, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
6 7 0.15
7 25 0.54
8 13 0.28
9 1 0.02
ACGTcount: A:0.34, C:0.08, G:0.02, T:0.56
Consensus pattern (7 bp):
TATACTT
Found at i:53004 original size:26 final size:27
Alignment explanation
Indices: 52975--53032 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
52965 AAGTATATAA
52975 TATAAAGTATATATATA-TATATACTT
1 TATAAAGTATATATATACTATATACTT
*** *
53001 TATAGTTTATATATTTACTTATATACTT
1 TATAAAGTATATATATAC-TATATACTT
53029 TATA
1 TATA
53033 TTTAATACTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 13 0.50
28 13 0.50
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (27 bp):
TATAAAGTATATATATACTATATACTT
Found at i:53011 original size:22 final size:23
Alignment explanation
Indices: 52986--53771 Score: 168
Period size: 22 Copynumber: 34.5 Consensus size: 23
52976 ATAAAGTATA
*
52986 TATATATATATACTT-TATAGTT
1 TATATATATATACTTATATACTT
53008 TATATAT-T-TACTTATATACTT
1 TATATATATATACTTATATACTT
*
53029 TATATTTA-ATACTTATATACTT
1 TATATATATATACTTATATACTT
* * * *
53051 TATATTATTATAGACGTGTGTAT-GTA
1 TATA-TA-TATATAC-T-TATATACTT
53077 TATATATATATACGTATATATACTT
1 TATATATATATAC-T-TATATACTT
* * *
53102 TATATTTA-ACACTTATATATTT
1 TATATATATATACTTATATACTT
53124 TATAT-TATATACTTATATACTT
1 TATATATATATACTTATATACTT
* *
53146 TATAT-TATATGCCTATATACTT
1 TATATATATATACTTATATACTT
* *
53168 TAGTCT-T-TATA-AT-TATACTT
1 TA-TATATATATACTTATATACTT
* *
53188 TATATATATAATA-TATTTACACTT
1 TATATATAT-ATACT-TATATACTT
*
53212 TAT-TAT-TATTA-TTAT-TATTAT
1 TATATATATA-TACTTATATACT-T
* *
53233 TAT-TATATATAGTT-TATA-GT
1 TATATATATATACTTATATACTT
53253 T-TATATATATACTT-T-TACTT
1 TATATATATATACTTATATACTT
* * **
53273 TATAT-TTTATA-TTTTATACACA
1 TATATATATATACTTATATAC-TT
* * * *
53295 CACACATATATTACATATATAC-T
1 TATATATATA-TACTTATATACTT
* * *
53318 TATACTTTATAT-GTATATATACAT
1 TATA-TATATATACT-TATATACTT
* *
53342 TATAAACGTATATA-TTTTAGT-CTT
1 TATATA--TATATACTTATA-TACTT
53366 TATA-AT-TATACTT-TATA---
1 TATATATATATACTTATATACTT
53383 TATATA-ATATAC-T-TATACTT
1 TATATATATATACTTATATACTT
*
53403 TATATGTACATATACTT-TATA-TT
1 TATA--TATATATACTTATATACTT
* * *
53426 TA-ATACTTATATAGTTTTATTAGTAT
1 TATATA--TATATACTTATA-TACT-T
*
53452 ATATGTATATATACTTTATACTAAAACTT
1 -TATATATATATAC-TTATA-T---ACTT
*
53481 TATATATTTATTTATACTT-TATAGTT
1 TATATA--TA--TATACTTATATACTT
* *
53507 TATATATATATACTTATAAAC-C
1 TATATATATATACTTATATACTT
* * *
53529 TATAAACTTTATA-TTATTATA-TG
1 TATATA-TATATACTTA-TATACTT
* *
53552 TATATATTTTATAC-TA-A-A-AT
1 TATATA-TATATACTTATATACTT
*
53572 TATATATATATA--TATATA-TA
1 TATATATATATACTTATATACTT
*
53592 TATATATATATAC-T-TGTACTT
1 TATATATATATACTTATATACTT
53613 TATATGTATATATACTTTATATAC-T
1 TATA--TATATATAC-TTATATACTT
* *
53638 TATATATGTTGTA-TTATATAC-T
1 TATATAT-ATATACTTATATACTT
*
53660 TATATACTTTAGT-CTTTATAATTATACTT
1 TATATA-TATA-TAC--T-T-A-TATACTT
53689 TATATATATATA--TACTTATACTT
1 TATATATATATACTTA--TATACTT
*
53712 TATATTATCATATATGTATATATACTT
1 TATA-TAT-ATATA-CT-TATATACTT
* *
53739 TATAT-TA-AAACTATATATA-TA
1 TATATATATATACT-TATATACTT
53760 TATATATATATA
1 TATATATATATA
53772 TATAAGTATA
Statistics
Matches: 581, Mismatches: 85, Indels: 195
0.67 0.10 0.23
Matches are distributed among these distances:
17 9 0.02
18 8 0.01
19 14 0.02
20 73 0.13
21 52 0.09
22 142 0.24
23 90 0.15
24 62 0.11
25 40 0.07
26 28 0.05
27 24 0.04
28 15 0.03
29 11 0.02
30 6 0.01
31 2 0.00
32 5 0.01
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.52
Consensus pattern (23 bp):
TATATATATATACTTATATACTT
Found at i:53013 original size:9 final size:8
Alignment explanation
Indices: 52984--53150 Score: 53
Period size: 8 Copynumber: 20.6 Consensus size: 8
52974 ATATAAAGTA
*
52984 TATATATA
1 TATATATT
52992 TATATACTT
1 TATATA-TT
*
53001 TATA-GTT
1 TATATATT
53008 TATATATT
1 TATATATT
53016 TACTTATATACT
1 TA--TATAT--T
53028 T-TATATT
1 TATATATT
*
53035 TA-ATACT
1 TATATATT
53042 TATATACTT
1 TATATA-TT
53051 TATAT-TAT
1 TATATAT-T
* **
53059 TATAGACG
1 TATATATT
* * *
53067 TGTGTATG
1 TATATATT
*
53075 TATATATA
1 TATATATT
*
53083 TATATACGTA
1 TATATA--TT
*
53093 TATATACT
1 TATATATT
53101 T-TATATT
1 TATATATT
* *
53108 TA-ACACT
1 TATATATT
53115 TATATATT
1 TATATATT
53123 T-TATA-T
1 TATATATT
*
53129 TATATACT
1 TATATATT
53137 TATATACTT
1 TATATA-TT
53146 TATAT
1 TATAT
53151 TATATGCCTA
Statistics
Matches: 118, Mismatches: 23, Indels: 35
0.67 0.13 0.20
Matches are distributed among these distances:
6 2 0.02
7 34 0.29
8 45 0.38
9 22 0.19
10 13 0.11
12 2 0.02
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.53
Consensus pattern (8 bp):
TATATATT
Found at i:53109 original size:6 final size:7
Alignment explanation
Indices: 53095--53191 Score: 51
Period size: 7 Copynumber: 13.6 Consensus size: 7
53085 TATACGTATA
53095 TATACTT
1 TATACTT
53102 TATA-TT
1 TATACTT
*
53108 TAACACTT
1 T-ATACTT
*
53116 ATATATTT
1 -TATACTT
53124 TATA-TT
1 TATACTT
53130 ATATACTT
1 -TATACTT
53138 ATATACTT
1 -TATACTT
53146 TATA-TT
1 TATACTT
* *
53152 ATATGCCTA
1 -TAT-ACTT
53161 TATACTT
1 TATACTT
53168 TAGT-CTT
1 TA-TACTT
*
53175 TATA-AT
1 TATACTT
53181 TATACTT
1 TATACTT
53188 TATA
1 TATA
53192 TATATAATAT
Statistics
Matches: 70, Mismatches: 9, Indels: 22
0.69 0.09 0.22
Matches are distributed among these distances:
6 13 0.19
7 35 0.50
8 20 0.29
9 2 0.03
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.54
Consensus pattern (7 bp):
TATACTT
Found at i:53120 original size:95 final size:91
Alignment explanation
Indices: 52984--53153 Score: 245
Period size: 95 Copynumber: 1.8 Consensus size: 91
52974 ATATAAAGTA
* *
52984 TATATATATATATACTTTATAGTTTATATATTTACTTATATACTTTATATT-TAATACTTATATA
1 TATATATATATATACTTTATACTTTATATATTCACTTATATACTTTATATTAT-ATACTTATATA
53048 CTTTATATTATTATAGACGTGTGTATG
65 CTTTATATTATTATAGACGTGTGTATG
*
53075 TATATATATATATACGTATATATACTTTATAT-TTAACACTTATATATTTTATATTATATACTTA
1 TATATATATATATAC-T-T-TATACTTTATATATT--CACTTATATACTTTATATTATATACTTA
53139 TATACTTTATATTAT
61 TATACTTTATATTAT
53154 ATGCCTATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
91 15 0.21
92 1 0.01
93 3 0.04
94 11 0.16
95 39 0.56
96 1 0.01
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.53
Consensus pattern (91 bp):
TATATATATATATACTTTATACTTTATATATTCACTTATATACTTTATATTATATACTTATATAC
TTTATATTATTATAGACGTGTGTATG
Found at i:53129 original size:7 final size:7
Alignment explanation
Indices: 53114--53242 Score: 51
Period size: 7 Copynumber: 18.1 Consensus size: 7
53104 TATTTAACAC
53114 TTATATA
1 TTATATA
*
53121 TTTTATA
1 TTATATA
53128 TTATATA
1 TTATATA
53135 CTTATATA
1 -TTATATA
53143 CTT-TATA
1 -TTATATA
*
53150 TTATATGC
1 TTATAT-A
*
53158 CTATATA
1 TTATATA
*
53165 CTT-TAGTC
1 -TTATA-TA
53173 TT-TATAA
1 TTATAT-A
53180 TTATACT-
1 TTATA-TA
53187 TTATATA
1 TTATATA
53194 TATAATATA
1 T-T-ATATA
*
53203 TT-TACA
1 TTATATA
53209 CTT-TATTA
1 -TTATA-TA
53217 TTAT-TA
1 TTATATA
53223 TTAT-TA
1 TTATATA
53229 TTAT-TA
1 TTATATA
53235 TTATATA
1 TTATATA
53242 T
1 T
53243 AGTTTATAGT
Statistics
Matches: 97, Mismatches: 10, Indels: 30
0.71 0.07 0.22
Matches are distributed among these distances:
6 25 0.26
7 42 0.43
8 23 0.24
9 7 0.07
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.57
Consensus pattern (7 bp):
TTATATA
Found at i:53219 original size:3 final size:3
Alignment explanation
Indices: 53211--53238 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
53201 TATTTACACT
53211 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
53239 ATATAGTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:53486 original size:26 final size:26
Alignment explanation
Indices: 53457--53517 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
53447 AGTATATATG
53457 TATATATACTTTATAC-TAAAACTTTA
1 TATATATA-TTTATACTTAAAACTTTA
* * * *
53483 TATATTTATTTATACTTTATAGTTTA
1 TATATATATTTATACTTAAAACTTTA
53509 TATATATAT
1 TATATATAT
53518 ACTTATAAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 7 0.24
26 22 0.76
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.54
Consensus pattern (26 bp):
TATATATATTTATACTTAAAACTTTA
Found at i:53517 original size:32 final size:33
Alignment explanation
Indices: 53422--53523 Score: 84
Period size: 32 Copynumber: 3.1 Consensus size: 33
53412 ATATACTTTA
* *
53422 TATTTAATACTTATATAGTTT-TATTAGTATATATG
1 TATTT-ATACTT-TATAGTTTATACTA-TATATATT
* * * * *
53457 TATATATACTTTATA-CTAAAACTTTATATATT
1 TATTTATACTTTATAGTTTATACTATATATATT
*
53489 TATTTATACTTTATAGTTTATA-TATATATACT
1 TATTTATACTTTATAGTTTATACTATATATATT
53521 TAT
1 TAT
53524 AAACCTATAA
Statistics
Matches: 52, Mismatches: 13, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
32 33 0.63
33 9 0.17
34 6 0.12
35 4 0.08
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.54
Consensus pattern (33 bp):
TATTTATACTTTATAGTTTATACTATATATATT
Found at i:53577 original size:2 final size:2
Alignment explanation
Indices: 53572--53893 Score: 106
Period size: 2 Copynumber: 159.0 Consensus size: 2
53562 ATACTAAAAT
* *
53572 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CT- TG TA CTT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA
* * * *
53615 TA TG TA TA TA TA CTT TA TA TA CT- TA TA TA TG T- TG TA T- TA TA
1 TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * * *
53656 TA CT- TA TA TA CTT TA GTC TT TA TA -A T- TA TA CTT TA TA TA TA
1 TA -TA TA TA TA -TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * *
53697 TA TA TA CT- TA TA CTT TA TA T- TA TCA TA TA TG TA TA TA TA CTT
1 TA TA TA -TA TA TA -TA TA TA TA TA T-A TA TA TA TA TA TA TA -TA
*
53739 TA TA T- TA -A AA CTA TA TA TA TA TA TA TA TA TA TA TA TA -A GTA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * *
53780 TA TGA TA TA AA GTA TA TA -A TA TA TA TA AA GT- TT TA GTA TA AA
1 TA T-A TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
* *
53822 GTA TA TA TA T- TT TA TA -A TT TA TA TA TA TA TA CTA -A TA -A TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* *
53862 TA CT- TA TA GTT TA TA GTT TA TA TA TA TA TA TA
1 TA -TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA
53894 CACACTTTAT
Statistics
Matches: 241, Mismatches: 37, Indels: 84
0.67 0.10 0.23
Matches are distributed among these distances:
1 19 0.08
2 196 0.81
3 26 0.11
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53873 original size:61 final size:63
Alignment explanation
Indices: 53750--53893 Score: 147
Period size: 62 Copynumber: 2.3 Consensus size: 63
53740 ATATTAAAAC
* *
53750 TATA-TATATATATATATATATATATAAGTATATGATATAAAGTATATAATATATATAAAGTT
1 TATAGTATAAATATATATATATATATAAGTATATGATATAAACTATATAATATATATAAAGTT
* * * *
53812 T-TAGTATAAAGTATATATAT-TTTATAATTTATAT-ATATATACTA-ATAATATACT-TATAGT
1 TATAGTATAAA-TATATATATATATATAA-GTATATGATATAAACTATATAATATA-TATAAAGT
53872 T
63 T
* *
53873 TATAGTTTATATATATATATA
1 TATAGTATAAATATATATATA
53894 CACACTTTAT
Statistics
Matches: 68, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
61 26 0.38
62 28 0.41
63 14 0.21
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.47
Consensus pattern (63 bp):
TATAGTATAAATATATATATATATATAAGTATATGATATAAACTATATAATATATATAAAGTT
Found at i:53978 original size:58 final size:57
Alignment explanation
Indices: 53859--53965 Score: 146
Period size: 56 Copynumber: 1.9 Consensus size: 57
53849 TATACTAATA
**
53859 ATATACTTATAGTTTATAGTTTATATATATATATACACACTTTATACTTTAAAGTAT
1 ATATACTTATAGTTTATAGAATATATATATATATACACACTTTATACTTTAAAGTAT
* * *
53916 ATATACCTTATAGTTTATA-AATATAT-TATATATATATACTTTATAGTTTA
1 ATATA-CTTATAGTTTATAGAATATATATATATATACACACTTTATACTTTA
53966 CACTTTATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
56 21 0.48
57 10 0.23
58 13 0.30
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (57 bp):
ATATACTTATAGTTTATAGAATATATATATATATACACACTTTATACTTTAAAGTAT
Found at i:54055 original size:44 final size:43
Alignment explanation
Indices: 53971--54056 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 43
53961 GTTTACACTT
*
53971 TATATATATACTTATACTTATACTTTTTTATATGTGTATATATA
1 TATATATATACTTATACTTATAC-TTTTTATATGTATATATATA
54015 TATATATATACTTATACGTATATAC-TTTTATAT-TA-ATATATA
1 TATATATATACTTATAC-T-TATACTTTTTATATGTATATATATA
54057 CATCATATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
42 7 0.18
43 1 0.03
44 25 0.64
45 1 0.03
46 5 0.13
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.52
Consensus pattern (43 bp):
TATATATATACTTATACTTATACTTTTTATATGTATATATATA
Found at i:54100 original size:12 final size:12
Alignment explanation
Indices: 54083--54129 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
54073 CATTAATTAC
54083 ACACACATACAT
1 ACACACATACAT
*
54095 ACACAC--ACAC
1 ACACACATACAT
54105 ACACACATACAT
1 ACACACATACAT
* *
54117 ATATACATACAT
1 ACACACATACAT
54129 A
1 A
54130 TATATATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 9 0.31
12 20 0.69
ACGTcount: A:0.51, C:0.32, G:0.00, T:0.17
Consensus pattern (12 bp):
ACACACATACAT
Found at i:54130 original size:12 final size:12
Alignment explanation
Indices: 54109--54133 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54099 ACACACACAC
54109 ACATACATATAT
1 ACATACATATAT
54121 ACATACATATAT
1 ACATACATATAT
54133 A
1 A
54134 TATAAAGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
ACATACATATAT
Found at i:54706 original size:2 final size:2
Alignment explanation
Indices: 54695--54737 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
54685 CATATTTTAC
54695 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54735 AT A
1 AT A
54738 ATTGTGTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:55213 original size:27 final size:27
Alignment explanation
Indices: 55177--55232 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
55167 TATATAAACT
*
55177 ATAAAATATAA-GTATATATATACATAC
1 ATAAAATATAATGTACAT-TATACATAC
* *
55204 ATAAAGTATAATGTACATTATATATAC
1 ATAAAATATAATGTACATTATACATAC
55231 AT
1 AT
55233 GCATCATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (27 bp):
ATAAAATATAATGTACATTATACATAC
Found at i:55291 original size:576 final size:578
Alignment explanation
Indices: 54180--55776 Score: 2371
Period size: 584 Copynumber: 2.8 Consensus size: 578
54170 TATTTTTTTA
* * * *
54180 CCAACCTTTGAAATTAATGCAATTCAGTCCATTTTATAATTTTTCCTCACATTTTACAACTTTTT
1 CCAACTTTTGAAATTAATGTAATTCAGT-CATTTTACAA-TTTTCCTCACATTTTACAATTTTTT
* *
54245 TGATTTGATCCTTTTATGTTGTTTATTGTATTT--A----ATTTGTAATTTCATATTTTTTTCAA
64 TGATTTGATCC-TTTATGTTGTTTATTGTATTTAAATTTTATTTTTAATTTCATA-TTTGTTCAA
* * * *
54304 TTTAGTCCTTCAAATTATATTTGTATATGAAATTAACCCATACTTATTTATATTTTTGTAATTTA
127 TTTAGTCCTTCAAATTATATTTTTATCTAAAATTGACCCATACTTATTTATATTTTTGTAATTTA
*
54369 CTTAAAACAAACCCTATAAAATGTAAATCACATAATAAATTTATTTTCAGATTATGTTCACCAAC
192 CTTAAAACAAACCCTATAAAATGTAAATCACATAATAAATTTATTTTCAAATTATGTTCACCAAC
* * *
54434 GTTTTAAATGTATGCAAATTAGTCCA-TTTTTATATTAATATCAGCTTCTCATTTTATAATTAAT
257 TTTTTAAATGTATGCAATTTAGTCCATTTTTTATATTAATATCAGCTTCACATTTTATAATTAAT
*
54498 TCAATTTCATCCCTCATCAATGTGTGTTGCTTAATTTATTCAATTTTTTTTATTTCCAATTTCAT
322 TCAATTTCATCCCTCATCAATGTGTGTTGTTTAATTTATTCAA--TTTTTTATTTCCAATTTCAT
* *
54563 GTTTGTTCAATTTGGTACTTTATATACATATATAAAGTATAAAGA-ATAAGTATATATATATATA
385 GTTTGTTCAATTTGGTACTTTATATACATATATAAACTATAAA-ATATAAGTATATATATACATA
* * *
54627 TATAAAGTATAATGTACATTATATATACGTGCATCATATTATCATAACATTCATTATACATATTT
449 CATAAAGTATAATGTACATTATATATACATGCATCATATTATCATAACATTCATTATACATATTA
*
54692 TACATATTATATATATATATATATAT-ATA-TAT-ATATATATATTATAATTGTGT-TAATT-TT
514 TACATATTATATATACATATATATATAATATTATAATATATATATTATAATTGT-TCTAATTCTT
54752 CC
578 -C
54754 CCAACTTTTGAAATTAATGTAATTCAGT-ATTTTACAATTTTCCTCACATTTTACAATTTTTTTG
1 CCAACTTTTGAAATTAATGTAATTCAGTCATTTTACAATTTTCCTCACATTTTACAATTTTTTTG
* **
54818 ACTTGATTATTGTATGTTGTTTATTGTATTTAAATTTTATTTTTTAATTTCATATTTGTTCAATT
66 ATTTGATCCTT-TATGTTGTTTATTGTATTTAAATTTTA-TTTTTAATTTCATATTTGTTCAATT
*
54883 TAGTCCTTCAAATTATATTTTTATCTTAAATTGACCCATACTTATTTATATTTTTGTAATTTACT
129 TAGTCCTTCAAATTATATTTTTATCTAAAATTGACCCATACTTATTTATATTTTTGTAATTTACT
** *
54948 TAAAACAAACCCTATAAAATGTAAATCACATAATACTTTTATTTTCAAATTATGTTCATCAACTT
194 TAAAACAAACCCTATAAAATGTAAATCACATAATAAATTTATTTTCAAATTATGTTCACCAACTT
* * * *
55013 TTTAAATGTATGCAATTTTGTCCATTTTTTATATTAATATCAGCTTGAAATTTTATAATTAATTT
259 TTTAAATGTATGCAATTTAGTCCATTTTTTATATTAATATCAGCTTCACATTTTATAATTAATTC
* * * * *
55078 AGTTTCATCCCTTATCAATTTGTGTTGTTTAATTTATTCAATGTTGTATTTCCAATTTCATGTTT
324 AATTTCATCCCTCATCAATGTGTGTTGTTTAATTTATTCAATTTTTTATTTCCAATTTCATGTTT
* *
55143 GTTCAATTTGGTACATTATTTACATATATAAACTATAAAATATAAGTATATATATACATACATAA
389 GTTCAATTTGGTACTTTATATACATATATAAACTATAAAATATAAGTATATATATACATACATAA
**
55208 AGTATAATGTACATTATATATACATGCATCATATTATCATAACATTCATTATACATATTATATGT
454 AGTATAATGTACATTATATATACATGCATCATATTATCATAACATTCATTATACATATTATACAT
*
55273 ATTATATATACATATATATATAAAATATTTGTAATATATATATTATAATTGTTCTAATTCTTC
519 ATTATATATACATATATATAT--AATA-TTATAATATATATATTATAATTGTTCTAATTCTTC
* * * *
55336 CCAACTTCTGAAATTAATGTAATTTAGTCCATTTTACAAATTTTCTTCACATTTTATAATTTTTT
1 CCAACTTTTGAAATTAATGTAATTCAGT-CATTTTAC-AATTTTCCTCACATTTTACAATTTTTT
* *
55401 TGATTTGATCCTTTATGGTGTTTATTGTATTTAAATTTTAAATTTTAATTTCATATTTGTTCAAT
64 TGATTTGATCCTTTATGTTGTTTATTGTATTTAAATTTT-ATTTTTAATTTCATATTTGTTCAAT
**
55466 TTAGTCCTTCAAATTATATTTTTATCTAAAATTGACCCATACTTATTTATATTTTT-TAATTTGT
128 TTAGTCCTTCAAATTATATTTTTATCTAAAATTGACCCATACTTATTTATATTTTTGTAATTTAC
* *
55530 TTAAAACAAACCCTATAAAATGTAAATCACATAATAAATTTCTTTTCAAATTATGTTAACCAACT
193 TTAAAACAAACCCTATAAAATGTAAATCACATAATAAATTTATTTTCAAATTATGTTCACCAACT
* * *
55595 TTTTAAATGTATGCAATTTAGTCTATTTTTTTATATTAATACCAACTTCACATTTTATAATTAAT
258 TTTTAAATGTATGCAATTTAGTCCA-TTTTTTATATTAATATCAGCTTCACATTTTATAATTAAT
* * *
55660 TCAATTTCATCCATCATCAATGTGTGTT-TCTTAATTTATTCAATTTTTTATTTCCAATTTAATA
322 TCAATTTCATCCCTCATCAATGTGTGTTGT-TTAATTTATTCAATTTTTTATTTCCAATTTCATG
* *
55724 TTTGTTCAATTTGGTACTTTATATACATATATAAACTATAGAGTATAAGTATA
386 TTTGTTCAATTTGGTACTTTATATACATATATAAACTATAAAATATAAGTATA
55777 AACGTATATG
Statistics
Matches: 922, Mismatches: 77, Indels: 38
0.89 0.07 0.04
Matches are distributed among these distances:
570 2 0.00
571 51 0.06
572 8 0.01
573 1 0.00
574 26 0.03
575 1 0.00
576 161 0.17
577 154 0.17
578 86 0.09
579 3 0.00
581 3 0.00
582 51 0.06
583 92 0.10
584 247 0.27
585 36 0.04
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.48
Consensus pattern (578 bp):
CCAACTTTTGAAATTAATGTAATTCAGTCATTTTACAATTTTCCTCACATTTTACAATTTTTTTG
ATTTGATCCTTTATGTTGTTTATTGTATTTAAATTTTATTTTTAATTTCATATTTGTTCAATTTA
GTCCTTCAAATTATATTTTTATCTAAAATTGACCCATACTTATTTATATTTTTGTAATTTACTTA
AAACAAACCCTATAAAATGTAAATCACATAATAAATTTATTTTCAAATTATGTTCACCAACTTTT
TAAATGTATGCAATTTAGTCCATTTTTTATATTAATATCAGCTTCACATTTTATAATTAATTCAA
TTTCATCCCTCATCAATGTGTGTTGTTTAATTTATTCAATTTTTTATTTCCAATTTCATGTTTGT
TCAATTTGGTACTTTATATACATATATAAACTATAAAATATAAGTATATATATACATACATAAAG
TATAATGTACATTATATATACATGCATCATATTATCATAACATTCATTATACATATTATACATAT
TATATATACATATATATATAATATTATAATATATATATTATAATTGTTCTAATTCTTC
Found at i:55324 original size:20 final size:20
Alignment explanation
Indices: 55286--55324 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
55276 ATATATACAT
*
55286 ATATATATAAAATATTTGTA
1 ATATATATAAAATAATTGTA
**
55306 ATATATATATTATAATTGT
1 ATATATATAAAATAATTGT
55325 TCTAATTCTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
ATATATATAAAATAATTGTA
Found at i:55960 original size:37 final size:36
Alignment explanation
Indices: 55836--56269 Score: 317
Period size: 37 Copynumber: 11.9 Consensus size: 36
55826 CGATTTTTAG
* * * * *
55836 TATATATTATATAT-AGTTTGAAATCATTTTGGAAA
1 TATATATAATATATGATTTTTAAAACATTTTGAAAA
* *
55871 T-TATATAATATATGGTTTTTCAAAATATTTTTGAAAA
1 TATATATAATATATGATTTTT-AAAACA-TTTTGAAAA
*
55908 CTTATATATAATATATGATTTTTAAAATATTTTGAAAAA
1 --TATATATAATATATGATTTTTAAAACATTTTG-AAAA
*
55947 TATATATAATATAT-AGTTTTTAAAACGTTTTGAAAA
1 TATATATAATATATGA-TTTTTAAAACATTTTGAAAA
* * *
55983 TATATATTATATA-G-TTCTTGAAAA-ATATTTTAAAA
1 TATATATAATATATGATT-TTTAAAACAT-TTTGAAAA
* *
56018 TATATATATTATATGGTTTTTTTCAATAACATTTTGAAAAAA
1 TATATATAATATAT-G-ATTTTT-AA-AACATTTTG--AAAA
* *
56060 TGTATATAATATAT-AGTTTTAAAA-ATTTTGAAAAA
1 TATATATAATATATGATTTTTAAAACATTTTG-AAAA
*
56095 TATATATAATATATGGTTTTTGAAAAACATTTTGAAAA
1 TATATATAATATATGATTTTT--AAAACATTTTGAAAA
*
56133 TATA-AT-ATATA-G-TTTTTAAAATTATTTTG-AAA
1 TATATATAATATATGATTTTTAAAA-CATTTTGAAAA
* *
56165 -GTATATAATATATCATTTTTAAAACATTTTTGAAAA
1 TATATATAATATATGATTTTTAAAACA-TTTTGAAAA
* *
56201 TATATATATTATAT-AGTTTTAAAAAACATTTTGGGAAAA
1 TATATATAATATATGA-TTTT-TAAAACATTTT--GAAAA
* *
56240 TATATAT--TATATAATTTTTGAAAATATTTT
1 TATATATAATATATGATTTTT-AAAACATTTT
56270 TATATATTAT
Statistics
Matches: 327, Mismatches: 34, Indels: 74
0.75 0.08 0.17
Matches are distributed among these distances:
31 2 0.01
32 9 0.03
33 11 0.03
34 20 0.06
35 61 0.19
36 40 0.12
37 78 0.24
38 28 0.09
39 37 0.11
40 23 0.07
41 2 0.01
42 16 0.05
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.46
Consensus pattern (36 bp):
TATATATAATATATGATTTTTAAAACATTTTGAAAA
Found at i:56094 original size:148 final size:145
Alignment explanation
Indices: 55839--56269 Score: 458
Period size: 148 Copynumber: 3.0 Consensus size: 145
55829 TTTTTAGTAT
* * *
55839 ATATTATATATAG-TTTG--AAATCATTTTGGAAAT-TATATAATATATGGTTTTTCAAAATATT
1 ATATAATATATAGTTTTGAAAAAT-ATTTTGAAAATATATAT-ATATATGGTTTTTCAAAACATT
** * *
55900 TTTGAAAACTTATATATAATATATGATTTTTAAAATATTTTGAAAAATATATATAATATATAGTT
64 TTTGAAAAAATATATATAATATAT-AGTTTTAAAACATTTTGAAAAATATATATAATATATAGTT
*
55965 TTT-AAAACGTTTTGAAA
128 TTTAAAAACATTTTGAAA
55982 ATATATATTATATAGTTCTTGAAAAATATTTT-AAAATATATATATTATATGGTTTTTTTCAATA
1 ATATA-A-TATATAGTT-TTGAAAAATATTTTGAAAATATATATA-TATATGG--TTTTTCAA-A
*
56046 ACA-TTTTGAAAAAATGTATATAATATATAGTTTTAAAA-ATTTTGAAAAATATATATAATATAT
59 ACATTTTTGAAAAAATATATATAATATATAGTTTTAAAACATTTTGAAAAATATATATAATATAT
*
56109 GGTTTTTGAAAAACATTTTGAAA
124 AGTTTTT-AAAAACATTTTGAAA
* * * **
56132 ATATAATATATAGTTTTTAAAATTATTTTGAAAGTATATA-ATATATCATTTTT-AAAACATTTT
1 ATATAATATATAGTTTTGAAAAATATTTTGAAAATATATATATATATGGTTTTTCAAAACATTTT
* * *
56195 TG--AAAATATATATATTATATAGTTTTAAAAAACATTTTGGGAAAATATATAT--TATATAATT
66 TGAAAAAATATATATAATATATAGTTTT--AAAACATTTT-GAAAAATATATATAATATATAGTT
* *
56256 TTTGAAAATATTTT
128 TTTAAAAACATTTT
56270 TATATATTAT
Statistics
Matches: 248, Mismatches: 21, Indels: 39
0.81 0.07 0.13
Matches are distributed among these distances:
141 22 0.09
142 13 0.05
143 25 0.10
144 11 0.04
145 19 0.08
146 6 0.02
147 21 0.08
148 66 0.27
149 14 0.06
150 48 0.19
151 3 0.01
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.46
Consensus pattern (145 bp):
ATATAATATATAGTTTTGAAAAATATTTTGAAAATATATATATATATGGTTTTTCAAAACATTTT
TGAAAAAATATATATAATATATAGTTTTAAAACATTTTGAAAAATATATATAATATATAGTTTTT
AAAAACATTTTGAAA
Found at i:56257 original size:25 final size:23
Alignment explanation
Indices: 56228--56275 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
56218 TTTAAAAAAC
56228 ATTTTGGGAAAATATATATTATATA
1 ATTTT-GGAAAATAT-TATTATATA
* *
56253 ATTTTTGAAAATATTTTTATATA
1 ATTTTGGAAAATATTATTATATA
56276 TTATTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.38
24 8 0.38
25 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (23 bp):
ATTTTGGAAAATATTATTATATA
Found at i:62281 original size:79 final size:80
Alignment explanation
Indices: 62150--62419 Score: 425
Period size: 80 Copynumber: 3.4 Consensus size: 80
62140 ACCTCCAACA
* *
62150 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCGCATCATTTGCAGCATAGCTC-AGGAAA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
62214 GAAGGGCTACCTGCC
66 GAAGGGCTACCTGCC
*
62229 AAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
* *
62294 GAAGGGCTACCAGGC
66 GAAGGGCTACCTGCC
* * * *
62309 AAATACCTTCGAGTTCGATTACACTCAGCTCAAAGGAACATCATTTGTAGTATAGCTCAAGGCAA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
*
62374 GAAGGGTTACCTGCC
66 GAAGGGCTACCTGCC
* *
62389 AAAAATCTTCGAGTTCGATTACACTCAGCTC
1 AAAGACCTTCGAGTTCGATTACACTCAGCTC
62420 TGTTGAAAAC
Statistics
Matches: 175, Mismatches: 15, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
79 56 0.32
80 119 0.68
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (80 bp):
AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
GAAGGGCTACCTGCC
Found at i:62790 original size:65 final size:64
Alignment explanation
Indices: 62668--62877 Score: 223
Period size: 65 Copynumber: 3.2 Consensus size: 64
62658 TTTTCAAAGG
* * * *
62668 GATGCAACGATGCACCA-ATCCATGCATCGATGCACTAATGAATTAATTG--AACATCGAATGCA
1 GATGCATCGATGCA-CATA-CCATGCATCAATGCACTCA-GAATT-TTTGAAAACATCGAATGCA
*
62730 GTT
62 TTT
* * *
62733 CATGCATCGATGCAC-TCTCCATGCATCAATGCACTCAG-GTTTTAATGAAAACATCGAATGCAT
1 GATGCATCGATGCACAT-ACCATGCATCAATGCACTCAGAATTTT--TGAAAACATCGAATGCAT
62796 TT
63 TT
* *
62798 GATGCATCGATGCACATACCATGCATCGATGCACTCAGAATTTTTTAAAACATCGAATGCATTT
1 GATGCATCGATGCACATACCATGCATCAATGCACTCAGAATTTTTGAAAACATCGAATGCATTT
*
62862 GATGCATCGTTGCACA
1 GATGCATCGATGCACA
62878 CTTAGTGCAC
Statistics
Matches: 123, Mismatches: 14, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
61 1 0.01
62 2 0.02
63 3 0.02
64 52 0.42
65 60 0.49
66 5 0.04
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (64 bp):
GATGCATCGATGCACATACCATGCATCAATGCACTCAGAATTTTTGAAAACATCGAATGCATTT
Found at i:62877 original size:64 final size:65
Alignment explanation
Indices: 62687--62877 Score: 228
Period size: 64 Copynumber: 3.0 Consensus size: 65
62677 ATGCACCAAT
* ** * * *
62687 CCATGCATCGATGCACTAATGAATTAATT-GAACATCGAATGCAGTTCATGCATCGATGCAC-TC
1 CCATGCATCGATGCACTCA-GAATTTTTTAAAACATCGAATGCATTTGATGCATCGATGCACATC
*
62750 T
65 A
* * *
62751 CCATGCATCAATGCACTCAG-GTTTTAATGAAAACATCGAATGCATTTGATGCATCGATGCACAT
1 CCATGCATCGATGCACTCAGAATTTT--TTAAAACATCGAATGCATTTGATGCATCGATGCACAT
62815 -A
64 CA
*
62816 CCATGCATCGATGCACTCAGAATTTTTTAAAACATCGAATGCATTTGATGCATCGTTGCACA
1 CCATGCATCGATGCACTCAGAATTTTTTAAAACATCGAATGCATTTGATGCATCGATGCACA
62878 CTTAGTGCAC
Statistics
Matches: 108, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
62 2 0.02
63 1 0.01
64 52 0.48
65 48 0.44
66 5 0.05
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.29
Consensus pattern (65 bp):
CCATGCATCGATGCACTCAGAATTTTTTAAAACATCGAATGCATTTGATGCATCGATGCACATCA
Found at i:62892 original size:64 final size:63
Alignment explanation
Indices: 62717--62896 Score: 202
Period size: 65 Copynumber: 2.8 Consensus size: 63
62707 GAATTAATTG
* * * * * *
62717 AACATCGAATGCAGTTCATGCATCGATGCACTCTCCATGCATCAATGCACTCAGGTTTTAATGAA
1 AACATCGAATGCATTTGATGCATCGATGCACACT-TATGCATCGATGCACTCAGATTTT-ATGAA
* *
62782 AACATCGAATGCATTTGATGCATCGATGCACA-TACCATGCATCGATGCACTCAGAATTTT-TTA
1 AACATCGAATGCATTTGATGCATCGATGCACACT--TATGCATCGATGCACTCAG-ATTTTATGA
62845 A
63 A
* *
62846 AACATCGAATGCATTTGATGCATCGTTGCACACTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTGATGCATCGATGCACACTTA-TGCATCGATGCACT
62897 AAGTGTTCCA
Statistics
Matches: 102, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
63 1 0.01
64 48 0.47
65 49 0.48
66 4 0.04
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACACTTATGCATCGATGCACTCAGATTTTATGAA
Done.