Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000115.1 Hibiscus syriacus cultivar Beakdansim tig00000210_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: 67425
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:4961 original size:24 final size:24
Alignment explanation
Indices: 4913--4978 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 24
4903 AAATACGATA
*
4913 TAATGAATAGTATA-TT--TCATC
1 TAATGAATTGTATATTTAATCATC
4934 TAATGAATTGTATATTTAATCATC
1 TAATGAATTGTATATTTAATCATC
* *
4958 TAATG-ATTATATGTTTAATCA
1 TAATGAATTGTATATTTAATCA
4979 AATGAATTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
21 13 0.33
22 2 0.05
23 14 0.36
24 10 0.26
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (24 bp):
TAATGAATTGTATATTTAATCATC
Found at i:4978 original size:23 final size:24
Alignment explanation
Indices: 4929--4989 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 24
4919 ATAGTATATT
*
4929 TCATCTAATGAATTGTATATTTAA
1 TCATCTAATGAATTATATATTTAA
*
4953 TCATCTAATG-ATTATATGTTTAA
1 TCATCTAATGAATTATATATTTAA
4976 TCA---AATGAATTATA
1 TCATCTAATGAATTATA
4990 AAAAATGACA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 4 0.12
21 6 0.18
23 14 0.41
24 10 0.29
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (24 bp):
TCATCTAATGAATTATATATTTAA
Found at i:4987 original size:21 final size:22
Alignment explanation
Indices: 4912--4989 Score: 74
Period size: 21 Copynumber: 3.6 Consensus size: 22
4902 CAAATACGAT
*
4912 ATAATGAA-TAGTATATTTCATC
1 ATAATGAATTA-TATATTTAATC
*
4934 -TAATGAATTGTATATTTAATC
1 ATAATGAATTATATATTTAATC
*
4955 ATCTAATG-ATTATATGTTTAATC
1 A--TAATGAATTATATATTTAATC
4978 A-AATGAATTATA
1 ATAATGAATTATA
4990 AAAAATGACA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
20 4 0.09
21 23 0.49
22 1 0.02
23 14 0.30
24 5 0.11
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (22 bp):
ATAATGAATTATATATTTAATC
Found at i:6719 original size:2 final size:2
Alignment explanation
Indices: 6712--6739 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6702 TTGTTTTGTT
6712 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
6740 ACAATACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13355 original size:22 final size:22
Alignment explanation
Indices: 13330--13395 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
13320 AAACAACGAC
13330 CAAAAGACAGAAGAAAACATGT
1 CAAAAGACAGAAGAAAACATGT
* * *
13352 CAAATGGCAGAAGAAAATATGT
1 CAAAAGACAGAAGAAAACATGT
*
13374 CAAAAGATAGAAGAAAACATGT
1 CAAAAGACAGAAGAAAACATGT
13396 TATACATACA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.56, C:0.11, G:0.20, T:0.14
Consensus pattern (22 bp):
CAAAAGACAGAAGAAAACATGT
Found at i:14689 original size:132 final size:132
Alignment explanation
Indices: 14435--14790 Score: 455
Period size: 132 Copynumber: 2.7 Consensus size: 132
14425 TAATGTTAAG
* * * *
14435 AGAGAAAACGATAATATCTAATTATTTCCAATCAAGAATAAATAATCC-CTCATACCTTAAAACA
1 AGAGAAAACAATAATATCTAATTATTTCCAATCGAGAATAAATGA-CCTCTCATACCTTAAAGCA
* * ** * * *
14499 ATCGTTTATTACTCCAATCGAAATGAAGAGATATCACTATTTTTGTCTTATAATTCAATATTGAT
65 ATCATTTATTACTACAATCGAAATGAAGAGATATCACTATTTTCATCTTAAAAATCAATATTAAT
14564 TCA
130 TCA
* * *
14567 AGTGAAAACTATAATATCTAATGATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAA
1 AGAGAAAACAATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAA
* * *
14632 TCATTTATTGCTATAATCGAATTGAAGAGATATCACTA-TTTCATCTTAAAAAATCAATATTAAT
66 TCATTTATTACTACAATCGAAATGAAGAGATATCACTATTTTCATCTT-AAAAATCAATATTAAT
*
14696 TCG
130 TCA
* * * *
14699 AGAGAAAACAATAATATCGAATTATTTCCAATTGAGAATAAATGATCTCTCATGCCTTAAAGCAA
1 AGAGAAAACAATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAA
* *
14764 TCATTTATTACTCCAACCGAAAATGAA
66 TCATTTATTACTACAATCG-AAATGAA
14791 AAAAATATTA
Statistics
Matches: 192, Mismatches: 29, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
131 9 0.05
132 177 0.92
133 6 0.03
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.32
Consensus pattern (132 bp):
AGAGAAAACAATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAA
TCATTTATTACTACAATCGAAATGAAGAGATATCACTATTTTCATCTTAAAAATCAATATTAATT
CA
Found at i:16903 original size:3 final size:3
Alignment explanation
Indices: 16895--17059 Score: 152
Period size: 3 Copynumber: 53.3 Consensus size: 3
16885 TTTGATCTGT
16895 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * *
16943 ATA ATA ATA ATA ATA CATA TTGGC AT- ATT TTA TTT ATA ATA ATA GTA
1 ATA ATA ATA ATA ATA -ATA AT--A ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
16990 ATA ATTA CTA ATA ATA ATA ATA CTA CTTA ATA ATA TTA ATA ATA ATA
1 ATA A-TA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA
* *
17037 ATA CTTA GTA ATA ATA ATA ATA A
1 ATA -ATA ATA ATA ATA ATA ATA A
17060 CGATCTCCAG
Statistics
Matches: 135, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
2 2 0.01
3 123 0.91
4 9 0.07
5 1 0.01
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:17003 original size:19 final size:19
Alignment explanation
Indices: 16979--17051 Score: 69
Period size: 19 Copynumber: 3.8 Consensus size: 19
16969 ATTTTATTTA
16979 TAATAATAGTAATAATTAC
1 TAATAATAGTAATAATTAC
* *
16998 TAATAATAATAAT-ACTAC
1 TAATAATAGTAATAATTAC
* *
17016 TTAATAATATTAATAA-TAA
1 -TAATAATAGTAATAATTAC
*
17035 TAATACTTAGTAATAAT
1 TAATA-ATAGTAATAAT
17052 AATAATAACG
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
18 9 0.20
19 34 0.77
20 1 0.02
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.38
Consensus pattern (19 bp):
TAATAATAGTAATAATTAC
Found at i:17481 original size:134 final size:134
Alignment explanation
Indices: 17234--17809 Score: 724
Period size: 134 Copynumber: 4.3 Consensus size: 134
17224 TCGAGAAACA
* * * * * * *
17234 TTGACTCATTCCACTATCCTTTAGAGAAGATTGAATCGAGGTAAAATTGTTCCACTCTTACTCAG
1 TTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGTTACTCAG
* * * * *
17299 GGAATATCAAATCTTGAAAGAGATGGATTTGTTCAACTTCTTTTTGAGGAAAAATCATATA-CGG
66 GGAAGATCAAATCTTGAAAGAGATGGATTTGTTCCACTTCTTCTTGAGGAAAAATCAGATATGGG
17363 GATCG
131 GAT-G
* * * *
17368 TTGATTTATTCCACTATTCTTCAGGGAATATTGAATCAAGGTAGATTTGTTCTACTGTTACTCAG
1 TTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGTTACTCAG
* * * * *
17433 GGAAGATCAAATCTTGAAAGAGA-GTGATATGTTTCGCTTCTTCTTGAGGGAAAATAAGATATGG
66 GGAAGATCAAATCTTGAAAGAGATG-GATTTGTTCCACTTCTTCTTGAGGAAAAATCAGATATGG
17497 GGATG
130 GGATG
* *
17502 TTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGATTTGTTCCACTGTTACTCAG
1 TTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGTTACTCAG
* * * * *
17567 GGAATATCAAATCTTGAAAGAGATTGATTTGTTCCGCTTTTTCTTGAGGAAAAACCAGATATGGG
66 GGAAGATCAAATCTTGAAAGAGATGGATTTGTTCCACTTCTTCTTGAGGAAAAATCAGATATGGG
*
17632 GACG
131 GATG
* * * * * *
17636 TTGATTCATTCTACTATTTTTCAGTGAAGATTGAATCGAGGTAGACTTGTTACATTGTTACTCAG
1 TTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGTTACTCAG
* * * * * *
17701 GGAAGATCAAATCTTGAAAGATATGGATCTGTTCCACTTCTTCTTGAGGGAAAATCATACATGAG
66 GGAAGATCAAATCTTGAAAGAGATGGATTTGTTCCACTTCTTCTTGAGGAAAAATCAGATATGGG
17766 GATG
131 GATG
* * *
17770 TTGATTCATTCAATTGTTCTTCAGGGAAGATTGAATCGAG
1 TTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAG
17810 TTCGATTCGC
Statistics
Matches: 378, Mismatches: 61, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
133 1 0.00
134 372 0.98
135 5 0.01
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.34
Consensus pattern (134 bp):
TTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGTTACTCAG
GGAAGATCAAATCTTGAAAGAGATGGATTTGTTCCACTTCTTCTTGAGGAAAAATCAGATATGGG
GATG
Found at i:19065 original size:10 final size:9
Alignment explanation
Indices: 19052--19143 Score: 62
Period size: 10 Copynumber: 9.6 Consensus size: 9
19042 TTTGTTCTCA
19052 TTTTTTTC-
1 TTTTTTTCT
*
19060 TCTTTTTCT
1 TTTTTTTCT
*
19069 TTCATTTTCT
1 TT-TTTTTCT
19079 TGTTTTTTCAT
1 T-TTTTTTC-T
19090 TTTTTTT-T
1 TTTTTTTCT
**
19098 CATTTTTCAT
1 TTTTTTTC-T
19108 TTTTCTTTCT
1 TTTT-TTTCT
19118 TTCTTTTATCTT
1 TT-TTTT-TC-T
19130 TTTTTTTCT
1 TTTTTTTCT
19139 TTTTT
1 TTTTT
19144 CAGTTTTCAT
Statistics
Matches: 66, Mismatches: 8, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
8 13 0.20
9 7 0.11
10 28 0.42
11 15 0.23
12 3 0.05
ACGTcount: A:0.05, C:0.14, G:0.01, T:0.79
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:19073 original size:21 final size:20
Alignment explanation
Indices: 19052--19143 Score: 60
Period size: 21 Copynumber: 4.3 Consensus size: 20
19042 TTTGTTCTCA
*
19052 TTTTTTTCTCTTTTTCTTTC
1 TTTTTTTATCTTTTTCTTTC
* * *
19072 ATTTTCTTGT-TTTTTCATTTTT
1 -TTTTTTTATCTTTTTC--TTTC
*
19094 TTTTCATTTTTCATTTTTCTTTC
1 TTTT--TTTATC-TTTTTCTTTC
*
19117 TTTCTTTTATCTTTTTTTTTC
1 TTT-TTTTATCTTTTTCTTTC
19138 TTTTTT
1 TTTTTT
19144 CAGTTTTCAT
Statistics
Matches: 56, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
20 9 0.16
21 23 0.41
22 8 0.14
23 9 0.16
24 1 0.02
25 6 0.11
ACGTcount: A:0.05, C:0.14, G:0.01, T:0.79
Consensus pattern (20 bp):
TTTTTTTATCTTTTTCTTTC
Found at i:19076 original size:18 final size:17
Alignment explanation
Indices: 19055--19144 Score: 66
Period size: 17 Copynumber: 5.4 Consensus size: 17
19045 GTTCTCATTT
19055 TTTTCTCTTTTTCTTTCA
1 TTTT-TCTTTTTCTTTCA
19073 -TTTTCTTGTTT-TTTCA
1 TTTTTCTT-TTTCTTTCA
*
19089 TTTTT-TTTTCATTTTTCA
1 TTTTTCTTTT--TCTTTCA
19107 TTTTTC--TTTCTTTC-
1 TTTTTCTTTTTCTTTCA
* *
19121 TTTTATCTTTTTTTTTCT
1 TTTT-TCTTTTTCTTTCA
19139 TTTTTC
1 TTTTTC
19145 AGTTTTCATT
Statistics
Matches: 60, Mismatches: 2, Indels: 21
0.72 0.02 0.25
Matches are distributed among these distances:
14 4 0.07
15 9 0.15
16 11 0.18
17 22 0.37
18 14 0.23
ACGTcount: A:0.06, C:0.16, G:0.01, T:0.78
Consensus pattern (17 bp):
TTTTTCTTTTTCTTTCA
Found at i:19103 original size:7 final size:7
Alignment explanation
Indices: 19082--19166 Score: 60
Period size: 7 Copynumber: 13.0 Consensus size: 7
19072 ATTTTCTTGT
19082 TTTTTCA
1 TTTTTCA
19089 -TTTT--
1 TTTTTCA
19093 TTTTTCA
1 TTTTTCA
19100 TTTTTCA
1 TTTTTCA
*
19107 TTTTTCT
1 TTTTTCA
19114 TTCTTTC-
1 TT-TTTCA
19121 -TTTT-A
1 TTTTTCA
19126 TCTTTT--
1 T-TTTTCA
*
19132 TTTTTCT
1 TTTTTCA
19139 TTTTTCA
1 TTTTTCA
*
19146 GTTTTCA
1 TTTTTCA
19153 TTTTTCA
1 TTTTTCA
*
19160 TTCTTCA
1 TTTTTCA
19167 GCCGAAGTAC
Statistics
Matches: 64, Mismatches: 5, Indels: 18
0.74 0.06 0.21
Matches are distributed among these distances:
5 11 0.17
6 6 0.09
7 43 0.67
8 4 0.06
ACGTcount: A:0.09, C:0.15, G:0.01, T:0.74
Consensus pattern (7 bp):
TTTTTCA
Found at i:19111 original size:27 final size:27
Alignment explanation
Indices: 19049--19119 Score: 76
Period size: 27 Copynumber: 2.6 Consensus size: 27
19039 TTATTTGTTC
19049 TCATTTTTTTCTCTTTTTCTTTCATTT
1 TCATTTTTTTCTCTTTTTCTTTCATTT
*
19076 TC-TTGTTTTT-TCATTTTTTTTTCATTTT
1 TCATT-TTTTTCTC-TTTTTCTTTCA-TTT
19104 TCATTTTTCTT-TCTTT
1 TCATTTTT-TTCTCTTT
19120 CTTTTATCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
26 4 0.11
27 17 0.45
28 11 0.29
29 6 0.16
ACGTcount: A:0.07, C:0.15, G:0.01, T:0.76
Consensus pattern (27 bp):
TCATTTTTTTCTCTTTTTCTTTCATTT
Found at i:19117 original size:39 final size:39
Alignment explanation
Indices: 19049--19151 Score: 108
Period size: 39 Copynumber: 2.7 Consensus size: 39
19039 TTATTTGTTC
* *
19049 TCATTTTTTTCTCTTTTTC-TTTCAT-TTTCTTGT-TTTT-
1 TCATTTTTTTTTCTTTTTCATTT-TTCTTTCTT-TCTTTTA
19086 TCATTTTTTTTTCATTTTTCATTTTTCTTTCTTTCTTTTA
1 TCATTTTTTTTTC-TTTTTCATTTTTCTTTCTTTCTTTTA
*
19126 TC-TTTTTTTTTCTTTTTTCAGTTTTC
1 TCATTTTTTTTTC-TTTTTCATTTTTC
19152 ATTTTTCATT
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
37 12 0.21
38 8 0.14
39 35 0.61
40 2 0.04
ACGTcount: A:0.07, C:0.16, G:0.02, T:0.76
Consensus pattern (39 bp):
TCATTTTTTTTTCTTTTTCATTTTTCTTTCTTTCTTTTA
Found at i:19121 original size:53 final size:51
Alignment explanation
Indices: 19054--19161 Score: 121
Period size: 53 Copynumber: 2.0 Consensus size: 51
19044 TGTTCTCATT
*
19054 TTTTTCTCTTTTTCTTTCATTTTCTTGTTTTTTCATTTTT-TTTTCATTTTTCA
1 TTTTTCTCTTTTTC-TT--TTATCTTGTTTTTTCATTTTTATTTTCATTTTTCA
* *
19107 TTTTTCT-TTCTTTCTTTTATCTTTTTTTTTCTTTTTTCAGTTTTCATTTTTCA
1 TTTTTCTCTT-TTTCTTTTATCTTGTTTTTTCATTTTT-A-TTTTCATTTTTCA
19160 TT
1 TT
19162 CTTCAGCCGA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
50 18 0.38
52 4 0.08
53 26 0.54
ACGTcount: A:0.07, C:0.15, G:0.02, T:0.76
Consensus pattern (51 bp):
TTTTTCTCTTTTTCTTTTATCTTGTTTTTTCATTTTTATTTTCATTTTTCA
Found at i:19142 original size:11 final size:11
Alignment explanation
Indices: 19081--19143 Score: 54
Period size: 11 Copynumber: 5.2 Consensus size: 11
19071 CATTTTCTTG
*
19081 TTTTTTCATTT
1 TTTTTTCTTTT
19092 TTTTTTCATTTT
1 TTTTTTC-TTTT
19104 TCATTTTTCTTTCT
1 T--TTTTTCTTT-T
*
19118 TTCTTTTATCTTT
1 TT-TTTTCT-TTT
19131 TTTTTTCTTTT
1 TTTTTTCTTTT
19142 TT
1 TT
19144 CAGTTTTCAT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
11 12 0.28
12 10 0.23
13 11 0.26
14 10 0.23
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:20922 original size:23 final size:23
Alignment explanation
Indices: 20896--20959 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
20886 CAACTCATAT
20896 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCTAAGTGCCACGTAG
* *
20919 AATTGCACC-AGAATGCCGCGTAG
1 AATTGCACCTA-AGTGCCACGTAG
20942 AATTGCACCGT-AGTGCCA
1 AATTGCACC-TAAGTGCCA
20960 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
22 1 0.03
23 33 0.97
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (23 bp):
AATTGCACCTAAGTGCCACGTAG
Found at i:21100 original size:103 final size:103
Alignment explanation
Indices: 20975--21295 Score: 615
Period size: 103 Copynumber: 3.1 Consensus size: 103
20965 TAATGTCCAT
20975 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
21040 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
21078 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
21143 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
21181 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
21246 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
21284 AAGGACCACATA
1 AAGGACCACATA
21296 GACCCTCTAC
Statistics
Matches: 212, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 212 1.00
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:21814 original size:19 final size:20
Alignment explanation
Indices: 21777--21814 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21767 TTTTTTATTA
*
21777 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
21797 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
21815 TCTAGCGTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:21866 original size:21 final size:21
Alignment explanation
Indices: 21842--21884 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
21832 TCATATTCGT
*
21842 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
21863 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
21884 T
1 T
21885 AGCCCAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:27945 original size:23 final size:22
Alignment explanation
Indices: 27919--27982 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
27909 CAGCTCATAT
27919 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* *
27942 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
27965 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
27983 TATAATAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:28129 original size:103 final size:103
Alignment explanation
Indices: 27998--28318 Score: 545
Period size: 103 Copynumber: 3.1 Consensus size: 103
27988 TAATGTCCAT
27998 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
* *
28063 AACTTCACACATATTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
28101 AAGGACCACATATCATTCCTTACA-AATCATATACATATACCAAGGATCAAGTAGGTGTCTCACC
1 AAGGACCACATATCATTCCTTA-AGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACC
* *
28165 AGACCTCACACATGTTCCAAAGAATACATATATGTCTCG
65 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
28204 AAGAACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
28269 GACTTCACACATGTTCTAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
28307 AAAGACCACATA
1 AAGGACCACATA
28319 GACCCTCTAC
Statistics
Matches: 202, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
102 1 0.00
103 200 0.99
104 1 0.00
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:28890 original size:21 final size:21
Alignment explanation
Indices: 28866--28905 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28856 TCATATTCGT
*
28866 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
28887 TTGAATGGGTATCGATTCC
1 TTGAAGGGGTATCGATTCC
28906 TCTAGCCCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.20, G:0.30, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:31796 original size:127 final size:127
Alignment explanation
Indices: 31553--31790 Score: 279
Period size: 127 Copynumber: 1.9 Consensus size: 127
31543 TTTAAATTAT
* * *
31553 TTTAATTATGTTTTAAATATTAAGAAAGGACAGTCTTAAAACAACTGGATGTCCATTTTATGATA
1 TTTAATTATGTTTTAAATATTAAGAAAGAACAGTCTTAAAACAACTAGAAGTCCATTTTATGATA
*
31618 TTTTAAATAATAAAATATATTACTTTTATAAATTATATCTATTTTAAATAAATGCTTTAATA
66 TTTTAAATAATAAAATATATTACTTTTATAAATTATATATATTTTAAATAAATGCTTTAATA
* * * * * * *
31680 TTTATTTAT-TTTTTAATATTAAGAAAAGAACTGTCTTAAAGCACCTAGAAG-CCCTTTTCTGAT
1 TTTAATTATGTTTTAAATATTAAG-AAAGAACAGTCTTAAAACAACTAGAAGTCCATTTTATGAT
*
31743 ATTTCTAAATAAGT-AAATATCTTA-TTTATATTTAAATTA-ATATATTTT
65 ATTT-TAAATAA-TAAAATATATTACTTT-TA--TAAATTATATATATTTT
31791 CATAAAATTA
Statistics
Matches: 93, Mismatches: 12, Indels: 11
0.80 0.10 0.09
Matches are distributed among these distances:
126 30 0.32
127 47 0.51
128 9 0.10
129 7 0.08
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (127 bp):
TTTAATTATGTTTTAAATATTAAGAAAGAACAGTCTTAAAACAACTAGAAGTCCATTTTATGATA
TTTTAAATAATAAAATATATTACTTTTATAAATTATATATATTTTAAATAAATGCTTTAATA
Found at i:32325 original size:26 final size:27
Alignment explanation
Indices: 32273--32330 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
32263 TAATTCTTTC
*
32273 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATAC-TATTA
* *
32301 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCAAAATATTTATATATACTATTA
32327 TTTT
1 TTTT
32331 ATTAATTCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
28 18 0.67
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATACTATTA
Found at i:33631 original size:30 final size:30
Alignment explanation
Indices: 33597--33660 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
33587 AGAGAATGTC
* *
33597 ATGGAAGAAGCTGCAGTCCAGATAAGCAAT
1 ATGGAAGAAGCTGCAATCCAGACAAGCAAT
* *
33627 ATGGAAGAAGCTGTAATCTAGACAAGCAAT
1 ATGGAAGAAGCTGCAATCCAGACAAGCAAT
33657 ATGG
1 ATGG
33661 CCCATAAGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.41, C:0.14, G:0.27, T:0.19
Consensus pattern (30 bp):
ATGGAAGAAGCTGCAATCCAGACAAGCAAT
Found at i:34502 original size:2 final size:2
Alignment explanation
Indices: 34495--34550 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
34485 ATCCTTTCAA
34495 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
34537 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
34551 CCCTTGTTAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34841 original size:8 final size:8
Alignment explanation
Indices: 34828--34899 Score: 80
Period size: 8 Copynumber: 9.5 Consensus size: 8
34818 TTATACTCAT
34828 AAAAAGGA
1 AAAAAGGA
34836 AAAAAGG-
1 AAAAAGGA
34843 AAAAAGG-
1 AAAAAGGA
*
34850 AAAAAGAA
1 AAAAAGGA
34858 AAAAAGG-
1 AAAAAGGA
34865 AAAAAGGA
1 AAAAAGGA
*
34873 GAAAA-GA
1 AAAAAGGA
*
34880 AAAAAAGA
1 AAAAAGGA
*
34888 AAAAAAGA
1 AAAAAGGA
34896 AAAA
1 AAAA
34900 TTGAATCAAG
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
7 26 0.46
8 31 0.54
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (8 bp):
AAAAAGGA
Found at i:34846 original size:7 final size:7
Alignment explanation
Indices: 34828--34891 Score: 74
Period size: 7 Copynumber: 8.7 Consensus size: 7
34818 TTATACTCAT
34828 AAAAAGG
1 AAAAAGG
34835 AAAAAAGG
1 -AAAAAGG
34843 AAAAAGG
1 AAAAAGG
*
34850 AAAAAGAA
1 AAAAAG-G
34858 AAAAAGG
1 AAAAAGG
34865 AAAAAGG
1 AAAAAGG
*
34872 AGAAAAGA
1 A-AAAAGG
*
34880 AAAAAAG
1 AAAAAGG
34887 AAAAA
1 AAAAA
34892 AAGAAAAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
7 30 0.61
8 19 0.39
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (7 bp):
AAAAAGG
Found at i:34848 original size:15 final size:15
Alignment explanation
Indices: 34828--34899 Score: 83
Period size: 15 Copynumber: 4.8 Consensus size: 15
34818 TTATACTCAT
34828 AAAAAGGAAAAAAGG-
1 AAAAAGG-AAAAAGGA
*
34843 AAAAAGGAAAAAGAA
1 AAAAAGGAAAAAGGA
34858 AAAAAGGAAAAAGGA
1 AAAAAGGAAAAAGGA
* * *
34873 GAAAAGAAAAAAAGA
1 AAAAAGGAAAAAGGA
*
34888 AAAAAAGAAAAA
1 AAAAAGGAAAAA
34900 TTGAATCAAG
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
14 6 0.12
15 42 0.88
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAAAGGAAAAAGGA
Found at i:34892 original size:7 final size:7
Alignment explanation
Indices: 34828--34899 Score: 63
Period size: 7 Copynumber: 9.7 Consensus size: 7
34818 TTATACTCAT
*
34828 AAAAAGG
1 AAAAAAG
34835 AAAAAAG
1 AAAAAAG
*
34842 GAAAAAG
1 AAAAAAG
*
34849 GAAAAAG
1 AAAAAAG
34856 AAAAAAAGG
1 -AAAAAA-G
*
34865 AAAAAGG
1 AAAAAAG
*
34872 AGAAAAG
1 AAAAAAG
34879 AAAAAAAG
1 -AAAAAAG
34887 AAAAAAAG
1 -AAAAAAG
34895 AAAAA
1 AAAAA
34900 TTGAATCAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
7 30 0.55
8 24 0.44
9 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:37786 original size:32 final size:32
Alignment explanation
Indices: 37667--37790 Score: 139
Period size: 31 Copynumber: 3.9 Consensus size: 32
37657 ATCCTCAGCA
* * * *
37667 ACTGTCCATAGGTTCTGAAGAACCTAGGTAA-
1 ACTGTCCATATGTTCCGTAGAACATAGGTAAT
*
37698 ACTGTCCATATGTTCCTTAGAACATAGGT-AT
1 ACTGTCCATATGTTCCGTAGAACATAGGTAAT
*
37729 ACTGTCCATATG-TCTCG-AAAGACATAGGTAAT
1 ACTGTCCATATGTTC-CGTAGA-ACATAGGTAAT
*
37761 TCTGTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATATGTTCCGTAGAACATAGGTA
37791 TACCCTCAAC
Statistics
Matches: 78, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
30 5 0.06
31 45 0.58
32 24 0.31
33 4 0.05
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (32 bp):
ACTGTCCATATGTTCCGTAGAACATAGGTAAT
Found at i:41919 original size:30 final size:30
Alignment explanation
Indices: 41883--41954 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
41873 CCCGAAGGAC
* *
41883 CTATCCAGAGGTCACAAGGAACCTCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTCGGCAA
* *
41913 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCACAAAGAACCTCGGCAA
* *
41943 CTGTCCATAGGT
1 CTATCCAGAGGT
41955 TCCGAAGAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCTCGGCAA
Found at i:41979 original size:31 final size:31
Alignment explanation
Indices: 41941--42064 Score: 144
Period size: 31 Copynumber: 4.0 Consensus size: 31
41931 GATCCTCGGC
* *
41941 AACTGTCCATAGGTTCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
**
41972 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
*
42003 TACTGTCCATATG-TCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTTC-CGAAGA-ACATAGGTA
* *
42034 ATTCTGTCCATATGTTCCGTAGAACATAGGT
1 A-ACTGTCCATATGTTCCGAAGAACATAGGT
42065 TTACCCTCAA
Statistics
Matches: 78, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
30 3 0.04
31 50 0.64
32 22 0.28
33 3 0.04
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGAAGAACATAGGTA
Found at i:44752 original size:75 final size:75
Alignment explanation
Indices: 44633--44806 Score: 305
Period size: 75 Copynumber: 2.3 Consensus size: 75
44623 AACAACAATC
44633 AGCAAATACTGGGGCATGCTGAAAGCTCATTTCAATCAGAATCAAGAATGTTGGCACATTTTGAA
1 AGCAAATACTGGGGCATGCTGAAAGCTCATTTCAATCAGAATCAAGAATGTTGGCACATTTTGAA
44698 CGTTTGTATT
66 CGTTTGTATT
*
44708 AGCAAATACTGGGGCATGCTGAAAGC-CTATTTCAATCAGAATCAAGAATGTTGGTACATTTTGA
1 AGCAAATACTGGGGCATGCTGAAAGCTC-ATTTCAATCAGAATCAAGAATGTTGGCACATTTTGA
44772 ACGTTTGTATT
65 ACGTTTGTATT
* *
44783 AGCCAATGCTGGGGCATGCTGAAA
1 AGCAAATACTGGGGCATGCTGAAA
44807 CCCATATCAT
Statistics
Matches: 95, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
74 1 0.01
75 94 0.99
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (75 bp):
AGCAAATACTGGGGCATGCTGAAAGCTCATTTCAATCAGAATCAAGAATGTTGGCACATTTTGAA
CGTTTGTATT
Found at i:46046 original size:22 final size:22
Alignment explanation
Indices: 46021--46078 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
46011 TACATCTACA
*
46021 CTCTTCAAATATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
46043 CTCTCCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
46065 CTTTTCAAAGATGA
1 CTCTTCAAAGATGA
46079 AAGTTTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:46858 original size:73 final size:73
Alignment explanation
Indices: 46739--46911 Score: 285
Period size: 73 Copynumber: 2.4 Consensus size: 73
46729 CTATTTCCCA
* *
46739 CATCTGTAAGACCTACAGTGTATGATGCTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGT
1 CATCTGTAAGACCTACAGTGCATGATGCTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
*
46804 CTCAGGTT
66 CTCAGGGT
46812 CATCTGTAAGACCTACAGTGCATGATG-TATTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAG
1 CATCTGTAAGACCTACAGTGCATGATGCT-TTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAG
46876 CCTCAGGGT
65 CCTCAGGGT
* *
46885 CATCTGTAAGCCCTACAGTGCAAGATG
1 CATCTGTAAGACCTACAGTGCATGATG
46912 ATAAGACCTT
Statistics
Matches: 94, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
72 1 0.01
73 93 0.99
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (73 bp):
CATCTGTAAGACCTACAGTGCATGATGCTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
CTCAGGGT
Found at i:47170 original size:112 final size:114
Alignment explanation
Indices: 46967--47400 Score: 360
Period size: 123 Copynumber: 3.6 Consensus size: 114
46957 CAATATTTCC
*
46967 AGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGGAA-AAGTTCATAATGAGAAGAACT
1 AGAA-AGTTCATAATGAGAAGAACTTATCTGAAGAGGAA-GAAGAAGTTCATAATGAGAAGAACT
* * * * * * *
47031 TGTTCAACCTTTTTCTCAAAT-TCATCAC-CCGATGGAT-CAGCGTTGCCAT
64 TGTTCAACCTTTTGCT-GACTCTCATCACACAGATAGATACAACGTTGCCAG
* * *
47080 AGAAAGTTCATAATGAGAAGAATTTATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAGCTTG
1 AGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* * * *
47145 TTCAATCTTTTGCATGACTCT-ATCACATAAGGAGATAGATCAACACCAACTTTTCCAG
66 TTCAACCTTTTGC-TGACTCTCATCAC---A-CAGATAGAT----A-CAACGTTGCCAG
* *
47203 AGAAAGTTCATAATGAGAAGAACTTATTTGAAGAGGAAGAGGAAGTTCATAATGAGAAGAACTTG
1 AGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* * * * *
47268 TTCAACCTTTTGCTTGACTC-CATTTCCAAAAAGAGATAGAACAGCAGAGCTATTTCCAG
66 TTCAACCTTTTGC-TGACTCTCA--T-C--ACACAGATAG-ATA-CA-A-C-GTTGCCAG
* * *
47327 -GTGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATGAGAAGAACTT
1 AG-AAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTT
*
47391 GTCCAACCTT
65 GTTCAACCTT
47401 GCATTGATTC
Statistics
Matches: 264, Mismatches: 32, Indels: 39
0.79 0.10 0.12
Matches are distributed among these distances:
111 3 0.01
112 71 0.27
113 6 0.02
117 6 0.02
121 3 0.01
122 1 0.00
123 89 0.34
124 80 0.30
125 3 0.01
126 1 0.00
128 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (114 bp):
AGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
TTCAACCTTTTGCTGACTCTCATCACACAGATAGATACAACGTTGCCAG
Found at i:47365 original size:124 final size:123
Alignment explanation
Indices: 47080--47400 Score: 423
Period size: 124 Copynumber: 2.6 Consensus size: 123
47070 GCGTTGCCAT
* * *
47080 AGAAAGTTCATAATGAGAAGAATTTATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAGCTTG
1 AGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* * * *
47145 TTCAATCTTTTGCATGACTCTATCACATAAGGAGATAGATCAACACCAACTTTTCCAG
66 TTCAACCTTTTGCATGACTCTATCACAAAAAGAGATAGAACAACACCAACTTTTCCAG
* *
47203 AGAAAGTTCATAATGAGAAGAACTTATTTGAAGAGGAAGAGGAAGTTCATAATGAGAAGAACTTG
1 AGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* * * * *
47268 TTCAACCTTTTGCTTGACTCCATTTC-CAAAAAGAGATAGAACAGCA-GAGCTATTTCCAG
66 TTCAACCTTTTGCATGACT-C-TATCACAAAAAGAGATAGAACAACACCAACT-TTTCCAG
* * *
47327 -GTGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATGAGAAGAACTT
1 AG-AAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTT
*
47391 GTCCAACCTT
65 GTTCAACCTT
47401 GCATTGATTC
Statistics
Matches: 174, Mismatches: 20, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
123 81 0.47
124 90 0.52
125 3 0.02
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (123 bp):
AGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
TTCAACCTTTTGCATGACTCTATCACAAAAAGAGATAGAACAACACCAACTTTTCCAG
Found at i:47650 original size:138 final size:139
Alignment explanation
Indices: 47319--47674 Score: 439
Period size: 139 Copynumber: 2.6 Consensus size: 139
47309 CAGCAGAGCT
47319 ATTTCCAG-GTGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATGAG
1 ATTTCCAGAG-GAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATGAG
* * * * * * * * *
47383 AAGAACTTGTCCAACCTTGCATTGATTCATCTCCTATGGAATTGAATGAAAGAATAACCTCATTT
65 AAGAATTTGTTCAACATTACATTAATTCATCACATATGGAATTGAATCAAAAAATAACCTCATTT
* *
47448 GAGGATCAAT
130 GAAGATCAAC
* * * * *
47458 ATTTTCAGAGGAAATTAATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATAAGA
1 ATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATGAGA
* * * * *
47523 AAAATTTGTTCAACATTACCTTAATTCATCACATATGGAGTTGAATCAAAAAAT-CCCTCTTTTG
66 AGAATTTGTTCAACATTACATTAATTCATCACATATGGAATTGAATCAAAAAATAACCTCATTTG
47587 AAGATCAAC
131 AAGATCAAC
* * * * *
47596 ATTTCCAGAAGG-AGTTCATAATGAGAATAACTCATCTGAAAAAGAAGAATAAGTTCATAATGAT
1 ATTTCCAG-AGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATGAG
47660 AAGAATTTGTTCAAC
65 AAGAATTTGTTCAAC
47675 TTTTTTCTAG
Statistics
Matches: 184, Mismatches: 31, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
138 80 0.43
139 103 0.56
140 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (139 bp):
ATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATGAGA
AGAATTTGTTCAACATTACATTAATTCATCACATATGGAATTGAATCAAAAAATAACCTCATTTG
AAGATCAAC
Found at i:49041 original size:2 final size:2
Alignment explanation
Indices: 49034--49106 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
49024 ATTTAATTAT
49034 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
49076 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49107 TTGATTTTAG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:58224 original size:19 final size:21
Alignment explanation
Indices: 58189--58234 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
58179 GAAAAAGAGA
58189 AAACAAAGAAAATAAAA-CC-
1 AAACAAAGAAAATAAAATCCT
*
58208 AAACAAA-AAACTCAAAATCCT
1 AAACAAAGAAAAT-AAAATCCT
58229 AAACAA
1 AAACAA
58235 TTATCTACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 4 0.17
19 11 0.48
20 2 0.09
21 6 0.26
ACGTcount: A:0.70, C:0.20, G:0.02, T:0.09
Consensus pattern (21 bp):
AAACAAAGAAAATAAAATCCT
Found at i:59166 original size:129 final size:131
Alignment explanation
Indices: 58932--59298 Score: 483
Period size: 129 Copynumber: 2.8 Consensus size: 131
58922 ATAATTTTAA
* * * * *
58932 GAGAGAAAATGATAATATCTAATTATTTTCGATTGAGAATAAATGACCTCTCATACCTTAAAACA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCA
* * *
58997 ATCATTTATTACTCCAATCCAAATGAAGAGATATCACTATTCCATCTTAAAATTC-A-ATCGATT
66 ATCATTTATTACTCCAATCAAAATGAAGAGATATCACTATTCCATCTTAAAAATCAATATCAATT
59060 C
131 C
* * * *
59061 GAGTGAAAACGATAATATCTAATGATTTCCAATCGAGAATAATTGACATCTCATACCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCA
* * *
59126 CTCATTTATTACTCCAATCAAAATTAAGAGATATCACTATTCCATCTTAAAAATCAATATTAATT
66 ATCATTTATTACTCCAATCAAAATGAAGAGATATCACTATTCCATCTTAAAAATCAATATCAATT
59191 C
131 C
* * *
59192 GAGAGAAAAC-AGTAATAT-TGAATTATTTCTAATCGAGAATAAATGACCTTTCATGCCTTAAAG
1 GAGAGAAAACGA-TAATATCT-AATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAG
* * *
59255 CAATCATTTATTACT-CAAACTAAAATGAAAAGATATTACTATTC
64 CAATCATTTATTACTCCAATC-AAAATGAAGAGATATCACTATTC
59299 TCAATATCGA
Statistics
Matches: 206, Mismatches: 27, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
129 107 0.52
130 7 0.03
131 92 0.45
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (131 bp):
GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCA
ATCATTTATTACTCCAATCAAAATGAAGAGATATCACTATTCCATCTTAAAAATCAATATCAATT
C
Found at i:60306 original size:20 final size:20
Alignment explanation
Indices: 60270--60333 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
60260 AATGTTTTTT
* * *
60270 AGTATCGGTACTGTTCATAT
1 AGTATCGATACTATTCATAC
*
60290 AGTATCGATAATATTCATAC
1 AGTATCGATACTATTCATAC
* *
60310 AGTGTTGATACTATTCATAC
1 AGTATCGATACTATTCATAC
60330 AGTA
1 AGTA
60334 CAATACAATT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38
Consensus pattern (20 bp):
AGTATCGATACTATTCATAC
Found at i:62581 original size:18 final size:18
Alignment explanation
Indices: 62558--62620 Score: 108
Period size: 18 Copynumber: 3.5 Consensus size: 18
62548 GAAAATCAAG
62558 AGTGCATCGATGCATGGT
1 AGTGCATCGATGCATGGT
62576 AGTGCATCGATGCATGGT
1 AGTGCATCGATGCATGGT
*
62594 TGTGCATCGATGCATGGT
1 AGTGCATCGATGCATGGT
*
62612 TGTGCATCG
1 AGTGCATCG
62621 GTACAAAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.30
Consensus pattern (18 bp):
AGTGCATCGATGCATGGT
Found at i:64943 original size:23 final size:23
Alignment explanation
Indices: 64917--64965 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
64907 ATAAGGAACC
*
64917 AAAATAAA-CTTAAATATACCATT
1 AAAATAAAGCTTAAACAT-CCATT
*
64940 AAAATAAAGTTTAAACATCCATT
1 AAAATAAAGCTTAAACATCCATT
64963 AAA
1 AAA
64966 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATAAAGCTTAAACATCCATT
Done.