Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004496.1 Hibiscus syriacus cultivar Beakdansim tig00009914_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: 116290
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:7361 original size:20 final size:20
Alignment explanation
Indices: 7338--7376 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
7328 ATATTTTATA
*
7338 AATTAATTAAAATAAATATG
1 AATTAACTAAAATAAATATG
* *
7358 AATTACCTATAATAAATAT
1 AATTAACTAAAATAAATAT
7377 ATCAGGATTT
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:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (20 bp):
AATTAACTAAAATAAATATG
Found at i:9076 original size:85 final size:85
Alignment explanation
Indices: 8910--9192 Score: 426
Period size: 85 Copynumber: 3.3 Consensus size: 85
8900 GACATGAATT
* * *
8910 TTTATGACGCGCATGTATGACTTACATTGCGTGTCATTG-AAGCCCCGTCATAAATTAAGATGAC
1 TTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAAACCCCGTCATAAATTAAGATGAC
*
8974 ACACATTTGTTCGTCATAAA
66 ACACATTTGTACGTCATAAA
8994 TTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAAACCCCGTCATAAATTAAGATGAC
1 TTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAAACCCCGTCATAAATTAAGATGAC
*
9059 ACACATTTGTGCGTCATAAA
66 ACACATTTGTACGTCATAAA
** * *
9079 TTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAA-TATGCTTGA
1 TTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAAACCCCGTCATAAATTAAG-ATGA
* *
9143 CATACATTTGTATGTCATAAA
65 CACACATTTGTACGTCATAAA
* *
9164 TATATGGCACGCATGTATGACTTACATTG
1 TTTATGACACGCATGTATGACTTACATTG
9193 TTTTCATTGA
Statistics
Matches: 184, Mismatches: 13, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
84 40 0.22
85 144 0.78
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.32
Consensus pattern (85 bp):
TTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAAACCCCGTCATAAATTAAGATGAC
ACACATTTGTACGTCATAAA
Found at i:9267 original size:2 final size:2
Alignment explanation
Indices: 9260--9304 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
9250 TCGTAAATTT
9260 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
9302 TA T
1 TA T
9305 GTAGATTGAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13905 original size:21 final size:22
Alignment explanation
Indices: 13881--13921 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
13871 GCGATTTTAG
13881 GGGAAGAGGAGGA-GGAGATGT
1 GGGAAGAGGAGGAGGGAGATGT
* *
13902 GGGACGAGGCGGAGGGAGAT
1 GGGAAGAGGAGGAGGGAGAT
13922 ACGGTGGCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.29, C:0.05, G:0.59, T:0.07
Consensus pattern (22 bp):
GGGAAGAGGAGGAGGGAGATGT
Found at i:15719 original size:3 final size:3
Alignment explanation
Indices: 15698--15756 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
15688 CGGGTCTTTT
* *
15698 TTA TT- TTA TT- TTAA TTA TTA TTA TTA TAA TTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
15742 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
15757 ATACATATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 4 0.08
3 43 0.88
4 2 0.04
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:18084 original size:24 final size:24
Alignment explanation
Indices: 18056--18105 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
18046 AATTAATTTC
18056 AAAATCACTAAT-TTTTTCAAAATA
1 AAAATCA-TAATCTTTTTCAAAATA
*
18080 AAAATCATAATCGTTTTTTAAAATA
1 AAAATCATAATC-TTTTTCAAAATA
18105 A
1 A
18106 TACTTAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 7 0.30
25 12 0.52
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.38
Consensus pattern (24 bp):
AAAATCATAATCTTTTTCAAAATA
Found at i:33883 original size:61 final size:61
Alignment explanation
Indices: 33808--33956 Score: 253
Period size: 61 Copynumber: 2.4 Consensus size: 61
33798 ACTATCGCAA
33808 TGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGT
1 TGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGT
* *
33869 TGCGATAGTCCAAGTTCGTTACGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAATTCGT
1 TGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGT
*
33930 TGCGATAGTCGAAGTTCGCGTTGCGAT
1 TGCGATAGTCCAAGTT--CGTTGCGAT
33957 TTATTCCAAG
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
61 74 0.90
63 8 0.10
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (61 bp):
TGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGT
Found at i:33923 original size:42 final size:42
Alignment explanation
Indices: 33877--33992 Score: 205
Period size: 42 Copynumber: 2.8 Consensus size: 42
33867 GTTGCGATAG
* *
33877 TCCAAGTTCGTTACGATAGTCGAAGTTCGCGTTGTGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
*
33919 TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
33961 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
33993 ATTACCACGA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (42 bp):
TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
Found at i:33928 original size:23 final size:23
Alignment explanation
Indices: 33838--33977 Score: 101
Period size: 21 Copynumber: 6.7 Consensus size: 23
33828 GCGATAGTCG
33838 AAGTTCGCGTTGCGATTTATTCC
1 AAGTTCGCGTTGCGATTTATTCC
* *
33861 AAATT--CGTTGCGA--TAGTCC
1 AAGTTCGCGTTGCGATTTATTCC
* * *
33880 AAGTT--CGTTACGA--TAGTCG
1 AAGTTCGCGTTGCGATTTATTCC
*
33899 AAGTTCGCGTTGTGATTTATTCC
1 AAGTTCGCGTTGCGATTTATTCC
* * *
33922 AAATT--CGTTGCGA--TAGTCG
1 AAGTTCGCGTTGCGATTTATTCC
33941 AAGTTCGCGTTGCGATTTATTCC
1 AAGTTCGCGTTGCGATTTATTCC
33964 AAGTT--CGTTGCGAT
1 AAGTTCGCGTTGCGAT
33978 AGTCGAAGTT
Statistics
Matches: 93, Mismatches: 16, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
19 34 0.37
21 38 0.41
23 21 0.23
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (23 bp):
AAGTTCGCGTTGCGATTTATTCC
Found at i:34387 original size:11 final size:11
Alignment explanation
Indices: 34371--34398 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
34361 CAATAATCGC
34371 GATTGATTGTA
1 GATTGATTGTA
34382 GATTGATTGTA
1 GATTGATTGTA
34393 GATTGA
1 GATTGA
34399 CTTTTAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (11 bp):
GATTGATTGTA
Found at i:43761 original size:3 final size:3
Alignment explanation
Indices: 43753--43786 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
43743 GCATTATAAA
43753 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
43787 TTAAGTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:46705 original size:2 final size:2
Alignment explanation
Indices: 46700--46726 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
46690 CTTTTATTTC
46700 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
46727 CATGTTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47970 original size:10 final size:10
Alignment explanation
Indices: 47934--47962 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
47924 TCCTTTACCA
47934 TTTATTTATT
1 TTTATTTATT
47944 TTTATTTATT
1 TTTATTTATT
47954 TTTATTTAT
1 TTTATTTAT
47963 CTCTATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTATTTATT
Found at i:58433 original size:105 final size:105
Alignment explanation
Indices: 58251--59342 Score: 1864
Period size: 105 Copynumber: 10.4 Consensus size: 105
58241 TAGGTTTTAC
*
58251 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
*
58316 GACGAAGGGACCGCTGGTTGTCAACAAACATCTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
**
58356 TCAGAGCCAATTTCAACTTTGCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
*
58421 GACGAAGGGACCGCTGGTTGTCAACAAACATCTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
* * *
58461 TCAGAGCCAATTTCAACTTCGCAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCAT
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
58526 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
*
58566 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
*
58631 GACGAAGGGACCGCTGGTTGTCAACAAACATCTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
*
58671 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAT
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
58736 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
*
58776 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
* *
58841 GACGAAGGGACCACTGGTTGTC-ACTTAACATTTCTCCAA-T
66 GACGAAGGGACCGCTGGTTGTCAAC-AAACATTTCT-CAATT
* *
58881 TCAGAGCCAATCTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAT
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
58946 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
58986 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
* *
59051 GACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
*
59091 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGAACTCCAGACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
* *
59156 GACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
*
59196 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
* * *
59261 GACGAAGGGACCGCTGGTTGTCAACAAGCAATTTCCCAGTT
66 GACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATT
* * * * * *
59302 CCAGAACCAGTTTCAACGTCACAGCGGAGGATATTGGACTC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
59343 GGAACAATAC
Statistics
Matches: 940, Mismatches: 42, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
104 5 0.01
105 887 0.94
106 48 0.05
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
Found at i:61076 original size:2 final size:2
Alignment explanation
Indices: 61071--61117 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
61061 CTTTTATTTC
61071 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
61113 AT AT A
1 AT AT A
61118 CATGTTTTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:64678 original size:232 final size:232
Alignment explanation
Indices: 64383--64846 Score: 910
Period size: 232 Copynumber: 2.0 Consensus size: 232
64373 GCGCCTTGTT
*
64383 AAATGTGTAAAAAAACTAAGTGTTAATTTTGTAAATATTTTTAAATTAGTGCCTAATATGTAATT
1 AAATGTGTAAAAAAACTAAGTGTTAATTTTGTAAATATTTTTAAACTAGTGCCTAATATGTAATT
64448 AATTTCTTTTAGGGTAATATTTGTATAAAAACGCTAACTTTATCTATTTATTTTTTTTGATATTA
66 AATTTCTTTTAGGGTAATATTTGTATAAAAACGCTAACTTTATCTATTTATTTTTTTTGATATTA
64513 TTTTTAACAACAATTACTAATATTTATTGACTTTTAAATTTAATTGTTTAAAAATATTAAAATAA
131 TTTTTAACAACAATTACTAATATTTATTGACTTTTAAATTTAATTGTTTAAAAATATTAAAATAA
64578 ACTTTTAATTACAATGAATATATCAAATGAATTATTG
196 ACTTTTAATTACAATGAATATATCAAATGAATTATTG
64615 AAATGTGTAAAAAAACTAAGTGTTAATTTTGTAAATATTTTTAAACTAGTGCCTAATATGTAATT
1 AAATGTGTAAAAAAACTAAGTGTTAATTTTGTAAATATTTTTAAACTAGTGCCTAATATGTAATT
*
64680 AATTTCTTTTAGGGTAATATTTGTATAAAAATGCTAACTTTATCTATTTATTTTTTTTGATATTA
66 AATTTCTTTTAGGGTAATATTTGTATAAAAACGCTAACTTTATCTATTTATTTTTTTTGATATTA
64745 TTTTTAACAACAATTACTAATATTTATTGACTTTTAAATTTAATTGTTTAAAAATATTAAAATAA
131 TTTTTAACAACAATTACTAATATTTATTGACTTTTAAATTTAATTGTTTAAAAATATTAAAATAA
64810 ACTTTTAATTACAATGAATATATCAAATGAATTATTG
196 ACTTTTAATTACAATGAATATATCAAATGAATTATTG
64847 TTTACTTTTT
Statistics
Matches: 230, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
232 230 1.00
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (232 bp):
AAATGTGTAAAAAAACTAAGTGTTAATTTTGTAAATATTTTTAAACTAGTGCCTAATATGTAATT
AATTTCTTTTAGGGTAATATTTGTATAAAAACGCTAACTTTATCTATTTATTTTTTTTGATATTA
TTTTTAACAACAATTACTAATATTTATTGACTTTTAAATTTAATTGTTTAAAAATATTAAAATAA
ACTTTTAATTACAATGAATATATCAAATGAATTATTG
Found at i:64873 original size:11 final size:10
Alignment explanation
Indices: 64859--64916 Score: 71
Period size: 10 Copynumber: 5.6 Consensus size: 10
64849 TACTTTTTTA
*
64859 AAAAATAAAT
1 AAAAATGAAT
64869 AAAAATGCAAT
1 AAAAATG-AAT
64880 AAAAATGAATT
1 AAAAATGAA-T
64891 AAAAATGAAT
1 AAAAATGAAT
* *
64901 AAAATTCAAT
1 AAAAATGAAT
64911 AAAAAT
1 AAAAAT
64917 ATAATGTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
10 22 0.52
11 20 0.48
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.22
Consensus pattern (10 bp):
AAAAATGAAT
Found at i:64884 original size:21 final size:20
Alignment explanation
Indices: 64859--64916 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
64849 TACTTTTTTA
64859 AAAAATAAATAAAAATGCAAT
1 AAAAATAAATAAAAATG-AAT
*
64880 AAAAATGAATTAAAAATGAAT
1 AAAAAT-AAATAAAAATGAAT
* *
64901 AAAATTCAATAAAAAT
1 AAAAATAAATAAAAAT
64917 ATAATGTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 8 0.25
21 14 0.44
22 10 0.31
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.22
Consensus pattern (20 bp):
AAAAATAAATAAAAATGAAT
Found at i:66477 original size:19 final size:19
Alignment explanation
Indices: 66453--66523 Score: 117
Period size: 19 Copynumber: 3.7 Consensus size: 19
66443 TTTAAGCAGG
*
66453 TGCATCGATGCACTCCTCA
1 TGCATCGATGCACTCTTCA
66472 TGCATC-ACTGCACTCTTCA
1 TGCATCGA-TGCACTCTTCA
66491 TGCATCGATGCACTCTTCA
1 TGCATCGATGCACTCTTCA
66510 TGCATCGATGCACT
1 TGCATCGATGCACT
66524 AATTGCAATC
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
18 1 0.02
19 47 0.96
20 1 0.02
ACGTcount: A:0.21, C:0.34, G:0.15, T:0.30
Consensus pattern (19 bp):
TGCATCGATGCACTCTTCA
Found at i:74742 original size:21 final size:21
Alignment explanation
Indices: 74717--74804 Score: 167
Period size: 21 Copynumber: 4.2 Consensus size: 21
74707 GTATATGATT
74717 CTTAAGGAATGATATGTGGTC
1 CTTAAGGAATGATATGTGGTC
74738 CTTAAGGAATGATATGTGGTC
1 CTTAAGGAATGATATGTGGTC
*
74759 CTTAAGGAATGATATGTAGTC
1 CTTAAGGAATGATATGTGGTC
74780 CTTAAGGAATGATATGTGGTC
1 CTTAAGGAATGATATGTGGTC
74801 CTTA
1 CTTA
74805 TGGACATTAT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 65 1.00
ACGTcount: A:0.30, C:0.10, G:0.26, T:0.34
Consensus pattern (21 bp):
CTTAAGGAATGATATGTGGTC
Found at i:74863 original size:22 final size:22
Alignment explanation
Indices: 74821--74863 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
74811 TTATTATATG
**
74821 GCACTACGGTGCAATTCTACGT
1 GCACTACGGTGCAATGATACGT
*
74843 GCACTTCGGTGCAATGATACG
1 GCACTACGGTGCAATGATACG
74864 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (22 bp):
GCACTACGGTGCAATGATACGT
Found at i:80673 original size:30 final size:30
Alignment explanation
Indices: 80637--80799 Score: 308
Period size: 30 Copynumber: 5.4 Consensus size: 30
80627 TCCGAAGGAC
80637 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
80667 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
80697 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
80727 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
80757 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
80787 CTGTCCATAGGTC
1 CTATCCAGAGGTC
80800 CCGAAGAACC
Statistics
Matches: 131, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 131 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:80816 original size:30 final size:30
Alignment explanation
Indices: 80773--80866 Score: 89
Period size: 31 Copynumber: 3.1 Consensus size: 30
80763 AGAGGTCATA
* * *
80773 AAGATCCTCGGTAACTGTCCATAGGTCCCG
1 AAGAACCTAGGTAACTGTCCATATGTCCCG
* * *
80803 AAGAACCTAGGTAAACTATCCATATGTTCCT
1 AAGAACCTAGGT-AACTGTCCATATGTCCCG
* * *
80834 TAGAACATAGGTATACTGTCCATATGTCTCG
1 AAGAACCTAGGTA-ACTGTCCATATGTCCCG
80865 AA
1 AA
80867 AGACATAAGT
Statistics
Matches: 49, Mismatches: 13, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
30 11 0.22
31 38 0.78
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (30 bp):
AAGAACCTAGGTAACTGTCCATATGTCCCG
Found at i:80816 original size:90 final size:91
Alignment explanation
Indices: 80637--80824 Score: 306
Period size: 90 Copynumber: 2.1 Consensus size: 91
80627 TCCGAAGGAC
80637 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
* * *
80702 CAGAGGTCATAAAGATCCTCGGT-AA
66 CAGAGGTCACAAAGAACCTAGGTAAA
*
80727 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTGTC
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
* * *
80792 CATAGGTCCCGAAGAACCTAGGTAAA
66 CAGAGGTCACAAAGAACCTAGGTAAA
80818 CTATCCA
1 CTATCCA
80825 TATGTTCCTT
Statistics
Matches: 90, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
90 81 0.90
91 9 0.10
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (91 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
CAGAGGTCACAAAGAACCTAGGTAAA
Found at i:81060 original size:4 final size:4
Alignment explanation
Indices: 81051--81075 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
81041 ATATAACCAT
81051 TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA T
81076 GTCATCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:82008 original size:21 final size:21
Alignment explanation
Indices: 81984--82026 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
81974 TCATATTCGT
* *
81984 TTGAGGGGGAATCGATTCCCC
1 TTGAAGGGGAACCGATTCCCC
* *
82005 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGAACCGATTCCCC
82026 T
1 T
82027 AGCCCATAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGAACCGATTCCCC
Found at i:82825 original size:21 final size:21
Alignment explanation
Indices: 82801--82907 Score: 196
Period size: 21 Copynumber: 5.1 Consensus size: 21
82791 ATATGATTCC
*
82801 TAAGGAATGATTTGTGGTCCT
1 TAAGGAATGATATGTGGTCCT
82822 TAAGGAATGATATGTGGTCCT
1 TAAGGAATGATATGTGGTCCT
82843 TAAGGAATGATATGTGGTCCT
1 TAAGGAATGATATGTGGTCCT
*
82864 TAAGGAATGATATGTAGTCCT
1 TAAGGAATGATATGTGGTCCT
82885 TAAGGAATGATATGTGGTCCT
1 TAAGGAATGATATGTGGTCCT
82906 TA
1 TA
82908 TGAATATTAT
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 83 1.00
ACGTcount: A:0.29, C:0.09, G:0.27, T:0.35
Consensus pattern (21 bp):
TAAGGAATGATATGTGGTCCT
Found at i:92570 original size:18 final size:18
Alignment explanation
Indices: 92547--92615 Score: 111
Period size: 18 Copynumber: 3.8 Consensus size: 18
92537 ACTGAATATT
92547 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* * *
92565 TGTCCCGAAGGACTAGTG
1 TGTCCCGAAGGACCACTA
92583 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
92601 TGTCCCGAAGGACCA
1 TGTCCCGAAGGACCA
92616 TTGATAATCC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.26, C:0.30, G:0.26, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:93278 original size:19 final size:19
Alignment explanation
Indices: 93254--93400 Score: 258
Period size: 19 Copynumber: 7.7 Consensus size: 19
93244 TTTAAGCAGG
93254 TGCATCGATGCACTCCTCA
1 TGCATCGATGCACTCCTCA
93273 TGCATCGATGCACTCCTCA
1 TGCATCGATGCACTCCTCA
93292 TGCATCGATGCACTCCTCA
1 TGCATCGATGCACTCCTCA
93311 TGCATCGATGCACTCCTCA
1 TGCATCGATGCACTCCTCA
93330 TGCATCGATGCACTCCTCA
1 TGCATCGATGCACTCCTCA
*
93349 TGCATCGATGCACTCTTCA
1 TGCATCGATGCACTCCTCA
* *
93368 TGTATCGATGCACTCTTCA
1 TGCATCGATGCACTCCTCA
*
93387 TGCATCAATGCACT
1 TGCATCGATGCACT
93401 AATTGCAATC
Statistics
Matches: 124, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 124 1.00
ACGTcount: A:0.22, C:0.34, G:0.16, T:0.29
Consensus pattern (19 bp):
TGCATCGATGCACTCCTCA
Found at i:94647 original size:12 final size:11
Alignment explanation
Indices: 94611--94652 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
94601 AAATAATTCA
94611 TATTTTAAAA-
1 TATTTTAAAAT
94621 TACTTTTAAATAT
1 TA-TTTTAAA-AT
94634 TATTTTACAAAT
1 TATTTTA-AAAT
94646 TATTTTA
1 TATTTTA
94653 TAACTCGACA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 2 0.07
11 7 0.25
12 15 0.54
13 4 0.14
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (11 bp):
TATTTTAAAAT
Found at i:101674 original size:14 final size:14
Alignment explanation
Indices: 101655--101684 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
101645 CAAGCACTGA
101655 TTGCTCATGGCTGT
1 TTGCTCATGGCTGT
101669 TTGCTCATGGCTGT
1 TTGCTCATGGCTGT
101683 TT
1 TT
101685 TGTCAAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.07, C:0.20, G:0.27, T:0.47
Consensus pattern (14 bp):
TTGCTCATGGCTGT
Found at i:106737 original size:206 final size:206
Alignment explanation
Indices: 106383--106795 Score: 808
Period size: 206 Copynumber: 2.0 Consensus size: 206
106373 AACTCGCTTA
* *
106383 TGCCAAATCAGACGTGGGAATTAGCTGAATTACCACCAGACAAGAAAGTACTCCATAACAAGTGG
1 TGCCAAATCAGACGTGGGAATTAGCTGAATTACCACCAGACAAGAAAGCACTACATAACAAGTGG
106448 ATTTACGGGATCAAATAAGAGCGCGATGGGAGCAAACGCTACAAAGCAAGATTGGTTGTCAAAGG
66 ATTTACGGGATCAAATAAGAGCGCGATGGGAGCAAACGCTACAAAGCAAGATTGGTTGTCAAAGG
106513 CTTTTAGCAAAAAGAATTTATTAACTACAATGAAATTTTCTCTCCAGTCGTGAAGCTATCTACAA
131 CTTTTAGCAAAAAGAATTTATTAACTACAATGAAATTTTCTCTCCAGTCGTGAAGCTATCTACAA
106578 TTAGACTGGTG
196 TTAGACTGGTG
106589 TGCCAAATCAGACGTGGGAATTAGCTGAATTACCACCAGACAAGAAAGCACTACATAACAAGTGG
1 TGCCAAATCAGACGTGGGAATTAGCTGAATTACCACCAGACAAGAAAGCACTACATAACAAGTGG
106654 ATTTACGGGATCAAATAAGAGCGCGATGGGAGCAAACGCTACAAAGCAAGATTGGTTGTCAAAGG
66 ATTTACGGGATCAAATAAGAGCGCGATGGGAGCAAACGCTACAAAGCAAGATTGGTTGTCAAAGG
106719 CTTTTAGCAAAAAGAATTTATTAACTACAATGAAATTTTCTCTCCAGTCGTGAAGCTATCTACAA
131 CTTTTAGCAAAAAGAATTTATTAACTACAATGAAATTTTCTCTCCAGTCGTGAAGCTATCTACAA
106784 TTAGACTGGTG
196 TTAGACTGGTG
106795 T
1 T
106796 TGAAAATTGT
Statistics
Matches: 205, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
206 205 1.00
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (206 bp):
TGCCAAATCAGACGTGGGAATTAGCTGAATTACCACCAGACAAGAAAGCACTACATAACAAGTGG
ATTTACGGGATCAAATAAGAGCGCGATGGGAGCAAACGCTACAAAGCAAGATTGGTTGTCAAAGG
CTTTTAGCAAAAAGAATTTATTAACTACAATGAAATTTTCTCTCCAGTCGTGAAGCTATCTACAA
TTAGACTGGTG
Found at i:109465 original size:70 final size:70
Alignment explanation
Indices: 109340--109471 Score: 210
Period size: 70 Copynumber: 1.9 Consensus size: 70
109330 GTGACACAAA
* * *
109340 TAGTTCATTTCAAAATCATTGTAAAAGCAGAAATGGAATCTTATCCTCCCGAATTGATGTAATGG
1 TAGTTCATTTCAAAACCATTGTAAAAGCAGAAATGGAATCTTAACCTCCCAAATTGATGTAATGG
109405 TTTTC
66 TTTTC
** *
109410 TAGTTCATTTCAAAACCATTGTAAAAGTGGAAATGGAATCTTAACCTCTCAAATTGATGTAA
1 TAGTTCATTTCAAAACCATTGTAAAAGCAGAAATGGAATCTTAACCTCCCAAATTGATGTAA
109472 CTGCTTATGG
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
70 56 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (70 bp):
TAGTTCATTTCAAAACCATTGTAAAAGCAGAAATGGAATCTTAACCTCCCAAATTGATGTAATGG
TTTTC
Found at i:110357 original size:24 final size:23
Alignment explanation
Indices: 110330--110379 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
110320 AAAAAAAATC
110330 TTTAATCTATATATGTTT-TTTCAG
1 TTTAATCTATA-ATGTTTATTTC-G
* *
110354 TTTAGTGTATAATGTTTATTTCG
1 TTTAATCTATAATGTTTATTTCG
110377 TTT
1 TTT
110380 TAGTCTGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.22, C:0.06, G:0.12, T:0.60
Consensus pattern (23 bp):
TTTAATCTATAATGTTTATTTCG
Done.