Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008787.1 Hibiscus syriacus cultivar Beakdansim tig00111927_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: 126699
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3591 original size:2 final size:2
Alignment explanation
Indices: 3586--3619 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3576 GTTTTGAATC
3586 TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3620 TAAGCTTTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:4477 original size:27 final size:28
Alignment explanation
Indices: 4436--4498 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
4426 TTTATTTTTA
4436 TTTTATTTTTGGTTGTTTTCTTAA-TAT
1 TTTTATTTTTGGTTGTTTTCTTAATTAT
*
4463 TTTTATTATTT-GTTGTTTTTTTAATTAT
1 TTTTATT-TTTGGTTGTTTTCTTAATTAT
*
4491 TTTAATTT
1 TTTTATTT
4499 AGTTCATCGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 20 0.62
28 12 0.38
ACGTcount: A:0.17, C:0.02, G:0.08, T:0.73
Consensus pattern (28 bp):
TTTTATTTTTGGTTGTTTTCTTAATTAT
Found at i:7783 original size:5 final size:5
Alignment explanation
Indices: 7773--7857 Score: 56
Period size: 5 Copynumber: 17.6 Consensus size: 5
7763 GATAACATAG
* *
7773 AGAAA AGAAA AGAAA A-AAG A-AAA AGAAA A-AAA A-AAGA AAAAA AGAAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAA-A AGAAA AGAAA
* * *
7820 A-AAC AGAAA TAAAGAA ATAAA A-AAA AGAAA AGAAA AGA
1 AGAAA AGAAA -AGA-AA AGAAA AGAAA AGAAA AGAAA AGA
7858 GAGACGAATA
Statistics
Matches: 66, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
4 19 0.29
5 39 0.59
6 6 0.09
7 2 0.03
ACGTcount: A:0.82, C:0.01, G:0.14, T:0.02
Consensus pattern (5 bp):
AGAAA
Found at i:7795 original size:17 final size:17
Alignment explanation
Indices: 7773--7855 Score: 84
Period size: 17 Copynumber: 4.9 Consensus size: 17
7763 GATAACATAG
7773 AGAAAAGAAAAGAAAAA
1 AGAAAAGAAAAGAAAAA
7790 AGAAAAAGAAAA-AAAAA
1 AG-AAAAGAAAAGAAAAA
7807 AG-AAA-AAAAGAAAAA
1 AGAAAAGAAAAGAAAAA
* *
7822 ACAGAAA-TAAAGAAATAA
1 AGA-AAAGAAAAGAAA-AA
*
7840 AAAAAAGAAAAGAAAA
1 AGAAAAGAAAAGAAAA
7856 GAGAGACGAA
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
14 4 0.07
15 9 0.16
17 23 0.41
18 20 0.36
ACGTcount: A:0.83, C:0.01, G:0.13, T:0.02
Consensus pattern (17 bp):
AGAAAAGAAAAGAAAAA
Found at i:7803 original size:8 final size:8
Alignment explanation
Indices: 7780--7855 Score: 82
Period size: 9 Copynumber: 9.1 Consensus size: 8
7770 TAGAGAAAAG
7780 AAAAG-AA
1 AAAAGAAA
7787 AAAAGAAA
1 AAAAGAAA
*
7795 AAGAAAAAA
1 AA-AAGAAA
7804 AAAAGAAA
1 AAAAGAAA
7812 AAAAGAAA
1 AAAAGAAA
7820 AAACAGAAA
1 AAA-AGAAA
*
7829 TAAAGAAA
1 AAAAGAAA
*
7837 TAAAAAAAA
1 -AAAAGAAA
7846 GAAAAGAAA
1 -AAAAGAAA
7855 A
1 A
7856 GAGAGACGAA
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
7 5 0.09
8 26 0.45
9 27 0.47
ACGTcount: A:0.84, C:0.01, G:0.12, T:0.03
Consensus pattern (8 bp):
AAAAGAAA
Found at i:9948 original size:90 final size:90
Alignment explanation
Indices: 9807--10092 Score: 455
Period size: 90 Copynumber: 3.2 Consensus size: 90
9797 TCAAAAGATT
* ** *
9807 TTTTATGAAACTAAGTCTTCGAAGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCT
1 TTTTA-GAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCT
*
9872 TCAGTGCAGAATGTTTTCAAATGAGA
65 TCAGTGCAGGATGTTTTCAAATGAGA
* *
9898 TTTTAGAAACTAAGCCTTCGGGGGTTTATTGATTTGTAAGTCCTTCGGGCCATCCATAATACCTT
1 TTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTT
* *
9963 CAGTGCTGGATGTTTTCAAATGACA
66 CAGTGCAGGATGTTTTCAAATGAGA
* *
9988 TTTTAGAAACTGAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGTCCATCCATAAGACCTT
1 TTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTT
*
10053 CAGTGCAGGATGTTTTCAAATGAGT
66 CAGTGCAGGATGTTTTCAAATGAGA
10078 TTTTAGAAACTAAGC
1 TTTTAGAAACTAAGC
10093 ATGATTTTCA
Statistics
Matches: 178, Mismatches: 17, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
90 173 0.97
91 5 0.03
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.36
Consensus pattern (90 bp):
TTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTT
CAGTGCAGGATGTTTTCAAATGAGA
Found at i:10179 original size:37 final size:36
Alignment explanation
Indices: 10138--10209 Score: 99
Period size: 37 Copynumber: 2.0 Consensus size: 36
10128 AAAAAATGAA
*
10138 TTTTGTCTCACTTGAGATAATTTTTACTCAAAACAAG
1 TTTTGTCTCACTTGAGACAATTTTT-CTCAAAACAAG
** *
10175 TTTTGTCTCTTTTGAGACAGTTTTTCTCAAAACAA
1 TTTTGTCTCACTTGAGACAATTTTTCTCAAAACAA
10210 AAGTTTGAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 10 0.32
37 21 0.68
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.43
Consensus pattern (36 bp):
TTTTGTCTCACTTGAGACAATTTTTCTCAAAACAAG
Found at i:10310 original size:67 final size:67
Alignment explanation
Indices: 10168--10402 Score: 246
Period size: 67 Copynumber: 3.6 Consensus size: 67
10158 TTTTTACTCA
* * * * * * * * *
10168 AAACAAGTTTTGTCTCTTTTGAGACAGTTTTTC-TCAAA-ACAAAA-GTTTGAGACAGTTTCCTT
1 AAACAAATTTTGTCTCTCTTGAGATAGCTTCTCTTGAAACACAAAATCTTTGCGATAGTTTCCTT
10230 TG
66 TG
* *
10232 AAACAAATTTTGTGTCTCTTGAGATAGTTTCTCTTGAAACACAAAATCTTTGCGATAGTTTCCTT
1 AAACAAATTTTGTCTCTCTTGAGATAGCTTCTCTTGAAACACAAAATCTTTGCGATAGTTTCCTT
10297 TG
66 TG
**** * *
10299 AAATTTTTTTTGTCTCTCTTGAGATAGCTTCTCTTGAAACACAAAATCTTTGTGATAGTTTCCCT
1 AAACAAATTTTGTCTCTCTTGAGATAGCTTCTCTTGAAACACAAAATCTTTGCGATAGTTTCCTT
10364 TG
66 TG
* * *
10366 AAACATGA-TTTGTCTCTCCTGAGACAG-TTCTCTTGAA
1 AAACA-AATTTTGTCTCTCTTGAGATAGCTTCTCTTGAA
10403 GCACCAACCT
Statistics
Matches: 144, Mismatches: 23, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
64 28 0.19
65 4 0.03
66 16 0.11
67 96 0.67
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.40
Consensus pattern (67 bp):
AAACAAATTTTGTCTCTCTTGAGATAGCTTCTCTTGAAACACAAAATCTTTGCGATAGTTTCCTT
TG
Found at i:11339 original size:129 final size:131
Alignment explanation
Indices: 10787--11468 Score: 758
Period size: 129 Copynumber: 5.2 Consensus size: 131
10777 AAGAGATTGT
* * * * * *
10787 TCAACTGTTTGCTCGATTCTATCACATAATGAGGTAGATCAACACCAACATTTTGTTTGATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCAACATTTCGTTCGATTCCA
* * * * *
10852 TCACAGAATGAGGTGGATTGACA-TT-TGTTCGCTCAAATCTATCGCAGAAGGAGTTGGATCAGT
66 TCACAGAAGGAGGTGGATCGACATTTATGTTCGCTCAAATCCATCGCAGAAGAAGTTGGATCAGC
10915 G
131 G
* * * * *
10916 TCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCA-CAGATATCTCGTTTGATACC
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCA-ACATTTCGTTCGATTCC
* *
10980 ATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGAAGTTGGATT
65 ATCACAGAAGGAGGTGGATCGACA--TTTATGTTCGCTCAAATCCATCGCAGAAGAAGTTGGATC
11045 AGCG
128 AGCG
* * **
11049 ACAACTTTTTGCTC-ATTTCTATCACAGAAGGA-GTAGACCAGCACCAACATTTCACTCGATTCC
1 TCAACTTTTTGCTCGA-TTCTATCACAGAAGGAGGTAGATCAGCACCAACATTTCGTTCGATTCC
* * *
11112 ATCACAGAAGGACGTGGATCGACATTTTTATTTTTGCTCAAATCCATCGCAGAAGAAGTTGGATC
65 ATCACAGAAGGAGGTGGATCGACA--TTTATGTTCGCTCAAATCCATCGCAGAAGAAGTTGGATC
11177 AGCG
128 AGCG
* * **
11181 TCAACTTTTTGCTC-ATTTCTATCATAGAAGGAGGTAGATCAGCACCAACATTTCGTTCAATTTT
1 TCAACTTTTTGCTCGA-TTCTATCACAGAAGGAGGTAGATCAGCACCAACATTTCGTTCGATTCC
* ** *
11245 ATCACAGAAAGAGGTGGATCGACA-TT-TGTTCGCTCAAATCCATTACAAAAGGAA-TTGGATCA
65 ATCACAGAAGGAGGTGGATCGACATTTATGTTCGCTCAAATCCATCGCAGAA-GAAGTTGGATCA
11307 GCG
129 GCG
* * * * * *
11310 TCAACTTTTAT-CTCGATTCTATCACAGAAGGAGGTAGATCAACATCGATATATCATTCGATTTC
1 TCAACTTTT-TGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCAACATTTCGTTCGA-TTC
* * * *
11374 CATC-CTAGAAGGAGGTGGATCAACATTTTTATTTTCGCTCAAATCCATCGTAGAAGGAGTTGGA
64 CATCAC-AGAAGGAGGTGGATCGACA--TTTATGTTCGCTCAAATCCATCGCAGAAGAAGTTGGA
11438 TCAGCG
126 TCAGCG
* *
11444 TCATCTTCTTGCTCGATTC-ATCACA
1 TCAACTTTTTGCTCGATTCTATCACA
11469 TATGGAGTTG
Statistics
Matches: 471, Mismatches: 63, Indels: 34
0.83 0.11 0.06
Matches are distributed among these distances:
128 2 0.00
129 153 0.32
130 29 0.06
132 120 0.25
133 122 0.26
134 45 0.10
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (131 bp):
TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCAACATTTCGTTCGATTCCA
TCACAGAAGGAGGTGGATCGACATTTATGTTCGCTCAAATCCATCGCAGAAGAAGTTGGATCAGC
G
Found at i:12080 original size:2 final size:2
Alignment explanation
Indices: 12068--12154 Score: 167
Period size: 2 Copynumber: 44.0 Consensus size: 2
12058 TCGGTTTCGA
12068 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12109 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12151 AT AT
1 AT AT
12155 TGAGCTTTGC
Statistics
Matches: 84, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 83 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13010 original size:27 final size:28
Alignment explanation
Indices: 12960--13031 Score: 87
Period size: 27 Copynumber: 2.6 Consensus size: 28
12950 TTATTGTGTA
12960 CTTATATTA-TTTTATTTTTGGTTGTTTT
1 CTTA-ATTATTTTTATTTTTGGTTGTTTT
12988 CTTAA-TATTTTTATTATTT-GTTGTTTT
1 CTTAATTATTTTTATT-TTTGGTTGTTTT
* *
13015 TTTAATTATTTTAATTT
1 CTTAATTATTTTTATTT
13032 AGTTCATCGC
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
26 2 0.05
27 21 0.54
28 16 0.41
ACGTcount: A:0.19, C:0.03, G:0.07, T:0.71
Consensus pattern (28 bp):
CTTAATTATTTTTATTTTTGGTTGTTTT
Found at i:14530 original size:11 final size:11
Alignment explanation
Indices: 14514--14544 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
14504 TCATTGACTA
14514 GGGATGGGCAT
1 GGGATGGGCAT
14525 GGGATGGGCAT
1 GGGATGGGCAT
*
14536 GGGTTGGGC
1 GGGATGGGC
14545 CGGATTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.13, C:0.10, G:0.58, T:0.19
Consensus pattern (11 bp):
GGGATGGGCAT
Found at i:31243 original size:32 final size:33
Alignment explanation
Indices: 31171--31243 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 33
31161 GCTAATCCAG
31171 ATCGAGTA-CTGCATTCTTATTGATTAATTCAT
1 ATCGAGTATCTGCATTCTTATTGATTAATTCAT
* * *
31203 ATCAAGTATC-GCATTCTTTTTTATTAATT-AT
1 ATCGAGTATCTGCATTCTTATTGATTAATTCAT
31234 CATCGAGTAT
1 -ATCGAGTAT
31244 TGTAGAAACT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
31 2 0.06
32 32 0.91
33 1 0.03
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.45
Consensus pattern (33 bp):
ATCGAGTATCTGCATTCTTATTGATTAATTCAT
Found at i:32169 original size:17 final size:18
Alignment explanation
Indices: 32133--32173 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
32123 ATATTATGTA
*
32133 TTTAATTTATTTAAGCAT
1 TTTACTTTATTTAAGCAT
*
32151 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGCAT
32168 TTTACT
1 TTTACT
32174 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAGCAT
Found at i:34445 original size:26 final size:24
Alignment explanation
Indices: 34374--34445 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
34364 TTATATTTGT
34374 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
*
34399 ATTT--TTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
34421 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
34446 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 7 0.19
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:35758 original size:23 final size:23
Alignment explanation
Indices: 35728--35771 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
35718 CAATACCTAT
35728 ATTGGACAAAGGGTGGTTGCCAC
1 ATTGGACAAAGGGTGGTTGCCAC
35751 ATTGGACAAAGGGTGGTTGCC
1 ATTGGACAAAGGGTGGTTGCC
35772 CAAGAATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.25, C:0.16, G:0.36, T:0.23
Consensus pattern (23 bp):
ATTGGACAAAGGGTGGTTGCCAC
Found at i:38680 original size:22 final size:22
Alignment explanation
Indices: 38648--38690 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
38638 CATTTAATCC
38648 TCAATGCTTATATATTCTATCT
1 TCAATGCTTATATATTCTATCT
*
38670 TCAATGTTTATATATTCTATC
1 TCAATGCTTATATATTCTATC
38691 AATTTAATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.28, C:0.16, G:0.05, T:0.51
Consensus pattern (22 bp):
TCAATGCTTATATATTCTATCT
Found at i:39127 original size:24 final size:24
Alignment explanation
Indices: 39090--39145 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
39080 AACTATATTT
*
39090 ATTTTTATAAATAATCGTTAAATTA
1 ATTTTTATAAATAAT-ATTAAATTA
* *
39115 ATTTTT-TATATAATATTAAATTT
1 ATTTTTATAAATAATATTAAATTA
*
39138 ATTATTAT
1 ATTTTTAT
39146 TTTAAATCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 12 0.46
24 8 0.31
25 6 0.23
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
ATTTTTATAAATAATATTAAATTA
Found at i:53705 original size:36 final size:37
Alignment explanation
Indices: 53649--53723 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 37
53639 TCTTACATTA
* * * * *
53649 TTTATACATATATTTTTTAAATATTTAAATATAATAT
1 TTTAAACATATATTTATTAAACAATTAAAGATAATAT
*
53686 TTTAAACATATA-TTATTAAACAATTGAAGATAATAT
1 TTTAAACATATATTTATTAAACAATTAAAGATAATAT
53722 TT
1 TT
53724 ATACACGCGC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
36 21 0.66
37 11 0.34
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (37 bp):
TTTAAACATATATTTATTAAACAATTAAAGATAATAT
Found at i:54127 original size:3 final size:3
Alignment explanation
Indices: 54119--54206 Score: 158
Period size: 3 Copynumber: 29.3 Consensus size: 3
54109 TACCCATATC
*
54119 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
54167 ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
54207 AATATATTAA
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:54249 original size:21 final size:21
Alignment explanation
Indices: 54205--54249 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
54195 TTATTATTAT
* *
54205 TAAATATATTAAATACATATA
1 TAAATATATTAAAAAAATATA
54226 TAAATATTATTAAAAAAATA-A
1 TAAATA-TATTAAAAAAATATA
54247 TAA
1 TAA
54250 TTACAGGCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAATATATTAAAAAAATATA
Found at i:54790 original size:15 final size:15
Alignment explanation
Indices: 54762--54803 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
54752 ACCACTCAGC
54762 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
*
54777 AAAGGAAAGAAAAAG
1 AAAGAAAAGAAAAAG
*
54792 GAAGAAAAGAAA
1 AAAGAAAAGAAA
54804 CTTACCGAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 2 0.09
15 21 0.91
ACGTcount: A:0.74, C:0.02, G:0.24, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:55659 original size:13 final size:13
Alignment explanation
Indices: 55643--55689 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
55633 ATATAATAAA
55643 TAAATATTTATTT
1 TAAATATTTATTT
*
55656 TAAATAAATTATTT
1 TAAAT-ATTTATTT
55670 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
55683 TCAATAT
1 TAAATAT
55690 CAAAGAACAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:63795 original size:20 final size:21
Alignment explanation
Indices: 63770--63811 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
63760 AAGATATCTT
63770 TGCCTGGTCTT-ATCA-AGATA
1 TGCCTGGT-TTAATCACAGATA
63790 TGCCTGGTTTAATCACAGATA
1 TGCCTGGTTTAATCACAGATA
63811 T
1 T
63812 AGTGATACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 2 0.10
20 12 0.60
21 6 0.30
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (21 bp):
TGCCTGGTTTAATCACAGATA
Found at i:66882 original size:11 final size:11
Alignment explanation
Indices: 66857--66900 Score: 63
Period size: 11 Copynumber: 4.0 Consensus size: 11
66847 ATTATGCTTG
*
66857 AAGAAAAAAGTA
1 AAGAAAAAA-AA
66869 AAGAAAAAAAA
1 AAGAAAAAAAA
66880 AAG-AAAAAAA
1 AAGAAAAAAAA
66890 AAGAAAAAAAA
1 AAGAAAAAAAA
66901 GAAAAAGGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 10 0.33
11 11 0.37
12 9 0.30
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.02
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:66886 original size:10 final size:10
Alignment explanation
Indices: 66857--66906 Score: 66
Period size: 10 Copynumber: 4.8 Consensus size: 10
66847 ATTATGCTTG
66857 AAGAAAAAAGTA
1 AAGAAAAAA--A
66869 AAGAAAAAAAA
1 AAG-AAAAAAA
66880 AAGAAAAAAA
1 AAGAAAAAAA
66890 AAG-AAAAAA
1 AAGAAAAAAA
66899 AAGAAAAA
1 AAGAAAAA
66907 GGGGGGTCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.25
10 14 0.39
11 4 0.11
12 3 0.08
13 6 0.17
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:66888 original size:9 final size:9
Alignment explanation
Indices: 66874--66906 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
66864 AAGTAAAGAA
66874 AAAAAAAAG
1 AAAAAAAAG
66883 AAAAAAAAAG
1 -AAAAAAAAG
66893 AAAAAAAAG
1 AAAAAAAAG
66902 AAAAA
1 AAAAA
66907 GGGGGGTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:67245 original size:16 final size:16
Alignment explanation
Indices: 67219--67263 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
67209 TTTGAATACA
*
67219 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
67236 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
67251 ATTCAATTTATTT
1 ATTCAATTTATTT
67264 TTGAAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:68521 original size:83 final size:83
Alignment explanation
Indices: 68061--68518 Score: 828
Period size: 83 Copynumber: 5.5 Consensus size: 83
68051 CAAAATACTC
68061 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
* **
68126 TAGAAGATGAATTTGTTA
66 TGGAAGATGAATTTGCCA
68144 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
68209 TGGAAGATGAATTTGCCA
66 TGGAAGATGAATTTGCCA
*
68227 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCACTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
*
68292 TAGAAGATGAATTTGCCA
66 TGGAAGATGAATTTGCCA
68310 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
68375 TGGAAGATGAATTTGCCA
66 TGGAAGATGAATTTGCCA
* *
68393 ATAGCATCTTCTGGATGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAACCAATCATTGAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAATCAATCATTGAAT
68457 TTGGAAGATGAATTTGCCA
65 TTGGAAGATGAATTTGCCA
*
68476 ATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
68519 TGGTAGGAAC
Statistics
Matches: 363, Mismatches: 11, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
82 2 0.01
83 357 0.98
84 4 0.01
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.37
Consensus pattern (83 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
TGGAAGATGAATTTGCCA
Found at i:69451 original size:113 final size:113
Alignment explanation
Indices: 69243--69801 Score: 976
Period size: 113 Copynumber: 5.0 Consensus size: 113
69233 CAAAGATTCA
* * * *
69243 AATCTATCAATTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
69308 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
69356 AATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
69421 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
*
69469 AATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTTATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
69534 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* *
69582 AATTCATCATTTGATGGATCATCTTTTCCAGAGAAATTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
69647 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * * *
69695 AATTCATCACTTGATGGATTATCTTTTCCGGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * * *
69759 AGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTT
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
69802 GCATAATTCT
Statistics
Matches: 430, Mismatches: 16, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
112 69 0.16
113 361 0.84
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (113 bp):
AATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
Found at i:69908 original size:95 final size:93
Alignment explanation
Indices: 69782--69969 Score: 216
Period size: 95 Copynumber: 2.0 Consensus size: 93
69772 TCATAATAAG
* * * * * * * * * *
69782 AAGAACTTGTTCAACTTTTTGCATAATTCTATCACAGAAGGAGATAGATTAGCATCAGTCTTTCT
1 AAGAACTTATTCAACCTTTTGAATAACTCTATCACAGAAAGAAAGAGATCAGCATCA-TC--CCC
69847 AG-AGAAAGTTCATAATGAGAAGAACTCATC
63 AGCAGAAAGTTCATAATGAGAAGAACTCATC
* * * *
69877 AAGAGCTTATTCAACCTTTTGAATGACTCTATCACAGAAAGAAAGAGGTCAGTATCATCCCCAGC
1 AAGAACTTATTCAACCTTTTGAATAACTCTATCACAGAAAGAAAGAGATCAGCATCATCCCCAGC
69942 AGAAAGTTCATAATGAGAAGAACTCATC
66 AGAAAGTTCATAATGAGAAGAACTCATC
69970 TGAAGAAAGA
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
92 3 0.04
93 28 0.36
94 2 0.03
95 45 0.58
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (93 bp):
AAGAACTTATTCAACCTTTTGAATAACTCTATCACAGAAAGAAAGAGATCAGCATCATCCCCAGC
AGAAAGTTCATAATGAGAAGAACTCATC
Found at i:70133 original size:3 final size:3
Alignment explanation
Indices: 70125--70254 Score: 233
Period size: 3 Copynumber: 43.3 Consensus size: 3
70115 TACCCATATC
*
70125 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
70173 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
* *
70221 ATT ATT ATT ATC ATC ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
70255 AATATATTAA
Statistics
Matches: 123, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 123 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:71722 original size:13 final size:13
Alignment explanation
Indices: 71706--71752 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
71696 ATATAATAAA
71706 TAAATATTTATTT
1 TAAATATTTATTT
*
71719 TAAATAAATTATTT
1 TAAAT-ATTTATTT
71733 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
71746 TCAATAT
1 TAAATAT
71753 CAAAGAACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:73901 original size:7 final size:7
Alignment explanation
Indices: 73889--73926 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
73879 ATTACAAAAA
73889 AAATCCC
1 AAATCCC
73896 AAATCCC
1 AAATCCC
73903 AAATCCC
1 AAATCCC
73910 AAATCCC
1 AAATCCC
73917 AAATCCC
1 AAATCCC
73924 AAA
1 AAA
73927 ATCCTTACCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.47, C:0.39, G:0.00, T:0.13
Consensus pattern (7 bp):
AAATCCC
Found at i:75390 original size:2 final size:2
Alignment explanation
Indices: 75385--75444 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
75375 TACATGTGTG
75385 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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 TA
75427 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
75445 CACACTTAAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:78286 original size:23 final size:23
Alignment explanation
Indices: 78249--78312 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
78239 CAGCTCGTAT
78249 AAATGCACCGAAGTGCCACATAG
1 AAATGCACCGAAGTGCCACATAG
* * * *
78272 AATTGCACCGTAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACATAG
*
78295 AAATGCGCCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
78313 TATAAGGTTG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.31, C:0.27, G:0.27, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACATAG
Found at i:78813 original size:2 final size:2
Alignment explanation
Indices: 78808--78837 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
78798 TACCTTATTC
78808 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
78838 CCGCAAATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:83270 original size:23 final size:23
Alignment explanation
Indices: 83244--83312 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
83234 CACCACAGCT
*
83244 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
83267 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
83290 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
83313 TATAAGGTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:87094 original size:36 final size:36
Alignment explanation
Indices: 87053--87125 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
87043 CGGAAGGTGA
87053 CATGCTTTCCCATAGACTAACTTAAAGAGGGACATT
1 CATGCTTTCCCATAGACTAACTTAAAGAGGGACATT
87089 CATGCTTTCCCATAGACTAACTTAAAGAGGGACATT
1 CATGCTTTCCCATAGACTAACTTAAAGAGGGACATT
87125 C
1 C
87126 CAAGGGGTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.27
Consensus pattern (36 bp):
CATGCTTTCCCATAGACTAACTTAAAGAGGGACATT
Found at i:95419 original size:3 final size:3
Alignment explanation
Indices: 95411--95435 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
95401 TGGAATTTTG
95411 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
95436 CTACTCTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:96062 original size:19 final size:20
Alignment explanation
Indices: 96038--96077 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
96028 TGCAATATGA
96038 GTATCGATACC-TAGGTAGG
1 GTATCGATACCATAGGTAGG
*
96057 GTATCGATACCATAGTTAGG
1 GTATCGATACCATAGGTAGG
96077 G
1 G
96078 AAGTATCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.28
Consensus pattern (20 bp):
GTATCGATACCATAGGTAGG
Found at i:96939 original size:32 final size:32
Alignment explanation
Indices: 96898--96988 Score: 128
Period size: 32 Copynumber: 2.8 Consensus size: 32
96888 GAGTCGAGGG
96898 TTACCTATGTCCTTCGGGATATATGGACATGA
1 TTACCTATGTCCTTCGGGATATATGGACATGA
* * * * *
96930 TTACCTATGTTCTTCGGTACATATAGACATGT
1 TTACCTATGTCCTTCGGGATATATGGACATGA
*
96962 TTACCTATGCCCTTCGGGATATATGGA
1 TTACCTATGTCCTTCGGGATATATGGA
96989 TAGGTCATTC
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (32 bp):
TTACCTATGTCCTTCGGGATATATGGACATGA
Found at i:97541 original size:14 final size:16
Alignment explanation
Indices: 97512--97543 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
97502 AAGGAAGAAA
97512 AAGACAAAAGATATTG
1 AAGACAAAAGATATTG
97528 AAGA-AAAAGA-ATTG
1 AAGACAAAAGATATTG
97542 AA
1 AA
97544 ATGACTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 6 0.38
16 4 0.25
ACGTcount: A:0.62, C:0.03, G:0.19, T:0.16
Consensus pattern (16 bp):
AAGACAAAAGATATTG
Found at i:99876 original size:64 final size:63
Alignment explanation
Indices: 99786--99947 Score: 175
Period size: 63 Copynumber: 2.6 Consensus size: 63
99776 ATCCCTTAAC
* * * *
99786 GGGTTCATCGATGCACTA-TCTATGCATCGGTACA-TAAATCCCATTCGATGTTTTTATTTTAAG
1 GGGTGCATCGATGCACTACT-TGTGCATCGATACACT-AATCCCATTCGAT-TTTTTATTTTAAA
99849 G
63 G
* * **
99850 GGGTGCATCAATGCACTACTTGTGCATCGATACACTGATGGCATTCGATTTTTTATTTTAAAG
1 GGGTGCATCGATGCACTACTTGTGCATCGATACACTAATCCCATTCGATTTTTTATTTTAAAG
* * * *
99913 GAGTGCATCGATACACTTCATGTGCATCGATACAC
1 GGGTGCATCGATGCACTACTTGTGCATCGATACAC
99948 CTTGAACAAT
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
63 43 0.52
64 38 0.46
65 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.35
Consensus pattern (63 bp):
GGGTGCATCGATGCACTACTTGTGCATCGATACACTAATCCCATTCGATTTTTTATTTTAAAG
Found at i:99937 original size:63 final size:64
Alignment explanation
Indices: 99827--99947 Score: 181
Period size: 63 Copynumber: 1.9 Consensus size: 64
99817 ACATAAATCC
* * * *
99827 CATTCGATGTTTTTATTTTAAGGGGGTGCATCAATGCACTACTTGTGCATCGATACACTGATGG
1 CATTCGATGTTTTTATTTTAAAGGAGTGCATCAATACACTACATGTGCATCGATACACTGATGG
* *
99891 CATTCGAT-TTTTTATTTTAAAGGAGTGCATCGATACACTTCATGTGCATCGATACAC
1 CATTCGATGTTTTTATTTTAAAGGAGTGCATCAATACACTACATGTGCATCGATACAC
99948 CTTGAACAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
63 43 0.84
64 8 0.16
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (64 bp):
CATTCGATGTTTTTATTTTAAAGGAGTGCATCAATACACTACATGTGCATCGATACACTGATGG
Found at i:101506 original size:19 final size:19
Alignment explanation
Indices: 101482--101529 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
101472 ATGTATAGTT
* *
101482 GAGTTTAATAGCATGAAGG
1 GAGTTTAATAGCATAAAGA
101501 GAGTTTAATAGCATAAAGA
1 GAGTTTAATAGCATAAAGA
*
101520 GAGTTAAATA
1 GAGTTTAATA
101530 AAAGGAGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.44, C:0.04, G:0.25, T:0.27
Consensus pattern (19 bp):
GAGTTTAATAGCATAAAGA
Found at i:103778 original size:28 final size:28
Alignment explanation
Indices: 103727--103800 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
103717 ATTAAGTGAC
* *
103727 ATGAGTTATATGATCATATAAGAATATGCT
1 ATGAGATATATGAT-A-ATAAGAATATGAT
* * *
103757 GTGAGATATATGATAATGAGAATATTAT
1 ATGAGATATATGATAATAAGAATATGAT
*
103785 ATGACATATATGATAA
1 ATGAGATATATGATAA
103801 GAAGCCATAA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
28 24 0.65
29 1 0.03
30 12 0.32
ACGTcount: A:0.43, C:0.04, G:0.18, T:0.35
Consensus pattern (28 bp):
ATGAGATATATGATAATAAGAATATGAT
Found at i:103781 original size:14 final size:15
Alignment explanation
Indices: 103758--103800 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
103748 GAATATGCTG
103758 TGAGATATATGATAA
1 TGAGATATATGATAA
*
103773 TGAGA-ATATTAT-A
1 TGAGATATATGATAA
*
103786 TGACATATATGATAA
1 TGAGATATATGATAA
103801 GAAGCCATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 5 0.22
14 12 0.52
15 6 0.26
ACGTcount: A:0.47, C:0.02, G:0.16, T:0.35
Consensus pattern (15 bp):
TGAGATATATGATAA
Found at i:103958 original size:22 final size:22
Alignment explanation
Indices: 103930--104002 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
103920 AGTCAAGGGT
103930 TTCATAGGTCCTTCGGGACATA
1 TTCATAGGTCCTTCGGGACATA
*
103952 TTCATAGGTTCTTCGGGACATA
1 TTCATAGGTCCTTCGGGACATA
* *
103974 TTTATAGGTCCTTCAGGACATA
1 TTCATAGGTCCTTCGGGACATA
103996 TTTCATA
1 -TTCATA
104003 TGCCACTTAG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 40 0.89
23 5 0.11
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (22 bp):
TTCATAGGTCCTTCGGGACATA
Found at i:110119 original size:21 final size:21
Alignment explanation
Indices: 110072--110122 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
110062 CCTTAAGGAG
* *
110072 TGGTCATTCGGGACATATATG
1 TGGTCTTTCGGGACATATATA
110093 TGGTCTTTCGGGACATATATA
1 TGGTCTTTCGGGACATATATA
110114 TGGTCTTTC
1 TGGTCTTTC
110123 ATGACAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (21 bp):
TGGTCTTTCGGGACATATATA
Found at i:110128 original size:21 final size:21
Alignment explanation
Indices: 110072--110128 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
110062 CCTTAAGGAG
* * *
110072 TGGTCATTCGGGACATATATG
1 TGGTCTTTCAGGACATATATA
*
110093 TGGTCTTTCGGGACATATATA
1 TGGTCTTTCAGGACATATATA
*
110114 TGGTCTTTCATGACA
1 TGGTCTTTCAGGACA
110129 AATTCTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.37
Consensus pattern (21 bp):
TGGTCTTTCAGGACATATATA
Found at i:120458 original size:19 final size:20
Alignment explanation
Indices: 120413--120471 Score: 75
Period size: 19 Copynumber: 2.9 Consensus size: 20
120403 TTCCCCTGTG
120413 GGGGGAATCGGTTCCCTTCAAA
1 GGGGGAATCGGTTCCC-TC-AA
120435 GGGGGAATCGGTTCCCTC-A
1 GGGGGAATCGGTTCCCTCAA
* *
120454 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
120472 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
19 17 0.49
21 2 0.06
22 16 0.46
ACGTcount: A:0.17, C:0.25, G:0.36, T:0.22
Consensus pattern (20 bp):
GGGGGAATCGGTTCCCTCAA
Done.