Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006462.1 Hibiscus syriacus cultivar Beakdansim tig00015661_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: 85683
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2227 original size:20 final size:20
Alignment explanation
Indices: 2202--2244 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2192 TCTAAGAGCC
* *
2202 CATTTAGGATCATTTAGATG
1 CATTTAGGAGCATATAGATG
*
2222 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
2242 CAT
1 CAT
2245 GAGGTGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:9913 original size:13 final size:13
Alignment explanation
Indices: 9892--9926 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
9882 CCCACTTACT
9892 TTTCACTTTTCAC
1 TTTCACTTTTCAC
* *
9905 TTTCTCTTTTTAC
1 TTTCACTTTTCAC
9918 TTTCACTTT
1 TTTCACTTT
9927 CTAGTTTCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTCACTTTTCAC
Found at i:12493 original size:20 final size:20
Alignment explanation
Indices: 12468--12510 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
12458 TCTAAGAGCC
* *
12468 CATTTAGGATCATTTAGATG
1 CATTTAGGAGCATATAGATG
*
12488 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
12508 CAT
1 CAT
12511 GAGGTGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:12779 original size:27 final size:27
Alignment explanation
Indices: 12741--12819 Score: 149
Period size: 27 Copynumber: 2.9 Consensus size: 27
12731 TGTTTTCACG
*
12741 GGATCTCTGATCATAACCGAGAAATTC
1 GGATCTCTGATCATGACCGAGAAATTC
12768 GGATCTCTGATCATGACCGAGAAATTC
1 GGATCTCTGATCATGACCGAGAAATTC
12795 GGATCTCTGATCATGACCGAGAAAT
1 GGATCTCTGATCATGACCGAGAAAT
12820 CTGCCTGGAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (27 bp):
GGATCTCTGATCATGACCGAGAAATTC
Found at i:15237 original size:19 final size:19
Alignment explanation
Indices: 15191--15247 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 19
15181 CTAGCCCACG
*
15191 AGTATCGATACTTATGTAAA
1 AGTATCGATACTT-TATAAA
* *
15211 AGTTTCGATACTTTATATA
1 AGTATCGATACTTTATAAA
15230 AGTATCGATACTTT-TAAA
1 AGTATCGATACTTTATAAA
15248 CATTATGTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 3 0.09
19 17 0.53
20 12 0.38
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (19 bp):
AGTATCGATACTTTATAAA
Found at i:20110 original size:141 final size:141
Alignment explanation
Indices: 19922--20178 Score: 406
Period size: 141 Copynumber: 1.8 Consensus size: 141
19912 AACCAGAAAA
* * *
19922 TGGAGGCTCTAATAGTAATCCTAATTTATTTTAACCAATTATTGAGTCGAATAATCGAGATGGTC
1 TGGAAGCTCTAATAGTAATCCTAATTTATTTTAACAAATTATTGAGTCGAATAATCGAAATGGTC
* *
19987 CCTCGGGCATGTTAATGCGAAAGACAAATCAAATTACTCGCTAAATTAAAGTATTAAAATGAAAT
66 CCTCAGGCATGTTAATGCGAAAGACAAATCAAATTACTCCCTAAATTAAAGTATTAAAATGAAAT
20052 TAAACCTAAAG
131 TAAACCTAAAG
* *
20063 TGGAAGCTCTAATATTAATCCTAATTTATTTTAACAAATTATTGAGTCGAATAATTGAAATGGTC
1 TGGAAGCTCTAATAGTAATCCTAATTTATTTTAACAAATTATTGAGTCGAATAATCGAAATGGTC
* * * **
20128 CCTTAGGCATGTTAATGCGAGAGCCAGTTCAAATTACTCCCTAAATTAAAG
66 CCTCAGGCATGTTAATGCGAAAGACAAATCAAATTACTCCCTAAATTAAAG
20179 GACTAAAGTG
Statistics
Matches: 104, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
141 104 1.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (141 bp):
TGGAAGCTCTAATAGTAATCCTAATTTATTTTAACAAATTATTGAGTCGAATAATCGAAATGGTC
CCTCAGGCATGTTAATGCGAAAGACAAATCAAATTACTCCCTAAATTAAAGTATTAAAATGAAAT
TAAACCTAAAG
Found at i:25377 original size:23 final size:24
Alignment explanation
Indices: 25306--25377 Score: 101
Period size: 23 Copynumber: 3.0 Consensus size: 24
25296 TGCCACATAG
* *
25306 ATTTATCCTGAAGGACCGCGTAGA
1 ATTTGTCCCGAAGGACCGCGTAGA
* *
25330 ATTTGTCTCGAAGGACCACGTAGA
1 ATTTGTCCCGAAGGACCGCGTAGA
25354 A-TTGTCCCGAAGGACCGCGTAGA
1 ATTTGTCCCGAAGGACCGCGTAGA
25377 A
1 A
25378 CCCTCGACTC
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 21 0.50
24 21 0.50
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.22
Consensus pattern (24 bp):
ATTTGTCCCGAAGGACCGCGTAGA
Found at i:25542 original size:30 final size:30
Alignment explanation
Indices: 25508--25564 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
25498 ACTCATAGTT
*
25508 CATATTCATATAAAACATTTTCACGTAGAA
1 CATATTCACATAAAACATTTTCACGTAGAA
*
25538 CATATTCACATATAACATTTTCACGTA
1 CATATTCACATAAAACATTTTCACGTA
25565 TAACCAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.35
Consensus pattern (30 bp):
CATATTCACATAAAACATTTTCACGTAGAA
Found at i:25566 original size:15 final size:15
Alignment explanation
Indices: 25521--25568 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
25511 ATTCATATAA
*
25521 AACATTTTCACGTAG
1 AACATTTTCACGTAT
* *
25536 AACATATTCACATAT
1 AACATTTTCACGTAT
25551 AACATTTTCACGTAT
1 AACATTTTCACGTAT
25566 AAC
1 AAC
25569 CAATTGACAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.33
Consensus pattern (15 bp):
AACATTTTCACGTAT
Found at i:25579 original size:30 final size:30
Alignment explanation
Indices: 25508--25585 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
25498 ACTCATAGTT
* *
25508 CATATTCATATAAAACATTTTCACGTAGAA
1 CATATTCACATAGAACATTTTCACGTAGAA
* *
25538 CATATTCACATATAACATTTTCACGTATAA
1 CATATTCACATAGAACATTTTCACGTAGAA
*
25568 CCA-ATTGACATAGAACAT
1 -CATATTCACATAGAACAT
25586 ATTTAAATCC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
30 40 0.95
31 2 0.05
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (30 bp):
CATATTCACATAGAACATTTTCACGTAGAA
Found at i:26269 original size:19 final size:20
Alignment explanation
Indices: 26220--26270 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
26210 TTTTCAATTG
*
26220 CAGTATCGATACCATACTAT
1 CAGTATCGATACCACACTAT
* * *
26240 TAGTATTGATACCCCAC-AT
1 CAGTATCGATACCACACTAT
26259 CAGTATCGATAC
1 CAGTATCGATAC
26271 TACTTCAATC
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.29
Consensus pattern (20 bp):
CAGTATCGATACCACACTAT
Found at i:26286 original size:21 final size:20
Alignment explanation
Indices: 26257--26297 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
26247 GATACCCCAC
*
26257 ATCAGTATCGATACTACTTCA
1 ATCAATATCGATACTA-TTCA
26278 ATCAATATCGATACTATTCA
1 ATCAATATCGATACTATTCA
26298 TCTGATTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.34
Consensus pattern (20 bp):
ATCAATATCGATACTATTCA
Found at i:31380 original size:23 final size:23
Alignment explanation
Indices: 31350--31399 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
31340 CTATTCTTCT
31350 AAGTCTTTTCTTGTAAAAGATGG
1 AAGTCTTTTCTTGTAAAAGATGG
*
31373 AAGTCTTTTCTTTTAAAAGATGG
1 AAGTCTTTTCTTGTAAAAGATGG
31396 AAGT
1 AAGT
31400 TCTATATACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (23 bp):
AAGTCTTTTCTTGTAAAAGATGG
Found at i:33233 original size:76 final size:76
Alignment explanation
Indices: 33079--33275 Score: 274
Period size: 75 Copynumber: 2.6 Consensus size: 76
33069 GTTGTACAAG
* * * * *
33079 GGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCAAGCATACTGGAATTCTCGGAGC
1 GGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGC
**
33143 AAAACTGTTTA
66 AAAACCATTTA
* *
33154 GGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGC
1 GGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG-
33218 CAAAACCATTTA
65 CAAAACCATTTA
*
33230 GGGGGG-ATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCA
1 GGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCA
33276 ATCTATAATT
Statistics
Matches: 109, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
75 69 0.63
76 40 0.37
ACGTcount: A:0.19, C:0.24, G:0.33, T:0.23
Consensus pattern (76 bp):
GGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGC
AAAACCATTTA
Found at i:36733 original size:20 final size:20
Alignment explanation
Indices: 36683--36735 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
36673 CTGATTGGAG
*
36683 AAAAATAAATCTATTAAATT
1 AAAAATAAATTTATTAAATT
36703 AAAAATAAATTTATTAAATT
1 AAAAATAAATTTATTAAATT
36723 AAAAATAAATTTA
1 AAAAATAAATTTA
36736 GTCCTCCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAATAAATTTATTAAATT
Found at i:38845 original size:76 final size:74
Alignment explanation
Indices: 38755--38901 Score: 215
Period size: 76 Copynumber: 2.0 Consensus size: 74
38745 TAAACTCAAA
*
38755 TTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTA
1 TTTAGGATAATATTTT-AACATTATATCTTTATCTTTGTATTTTAATTTAAATA-G-TTTTAGTA
38819 TTTTAATTAAAT
63 TTTTAATTAAAT
* * * *
38831 TTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAATTTAAATAGTTTTAGTATTT
1 TTTAGGATAATATTTTAACATTATATCTTTATCTTTGTATTTTAATTTAAATAGTTTTAGTATTT
38896 TAATTA
66 TAATTA
38902 GGATTTAGAA
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
74 17 0.26
75 8 0.12
76 40 0.62
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.59
Consensus pattern (74 bp):
TTTAGGATAATATTTTAACATTATATCTTTATCTTTGTATTTTAATTTAAATAGTTTTAGTATTT
TAATTAAAT
Found at i:38908 original size:29 final size:29
Alignment explanation
Indices: 38875--38984 Score: 78
Period size: 30 Copynumber: 3.6 Consensus size: 29
38865 TTGTATTTTA
38875 ATTTAAATAGTTTTAGTATTTTAATTAGG
1 ATTTAAATAGTTTTAGTATTTTAATTAGG
* * * ***
38904 ATTTAGAATATTATATTATTTTTTTAGGTATTTTA
1 ATTTA-AATAGT-T-TTAGTATTTTA---ATTAGG
*
38939 ATTTAAATAGTTTTAAGTGTTTTAATTAGG
1 ATTTAAATAGTTTT-AGTATTTTAATTAGG
38969 ATTTAAGAT-GTTTTAG
1 ATTTAA-ATAGTTTTAG
38985 CTTGTTTTTA
Statistics
Matches: 61, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
29 7 0.11
30 19 0.31
31 3 0.05
32 11 0.18
33 8 0.13
34 5 0.08
35 8 0.13
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.54
Consensus pattern (29 bp):
ATTTAAATAGTTTTAGTATTTTAATTAGG
Found at i:39592 original size:21 final size:20
Alignment explanation
Indices: 39566--39610 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
39556 TTTTAATTTG
*
39566 TTTATTTAATTATTTTTTTCT
1 TTTATTTAATTATTATTTT-T
*
39587 TTTATTTAATTCTTATTTTT
1 TTTATTTAATTATTATTTTT
39607 TTTA
1 TTTA
39611 ACCACAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTATTTAATTATTATTTTT
Found at i:47069 original size:76 final size:75
Alignment explanation
Indices: 46978--47142 Score: 233
Period size: 76 Copynumber: 2.2 Consensus size: 75
46968 TTAAACTCAA
* * *
46978 ATTTAGGATAATATTTTAAACATTATAT-TTTATCTTTTTATTTTAGTTTAAATATGTTTTTAGT
1 ATTTAGGATATTATTTT-AACATTATATCTTTATCTTTGTATTTTAGTTTAAATA-GGTTTTAGT
47042 ATTTTAATTAAG
64 ATTTTAATTAAG
* * * *
47054 TTTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
1 ATTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
47119 TTTAATTAAG
66 TTTAATTAAG
*
47129 ATTTAGAATATTAT
1 ATTTAGGATATTAT
47143 ATTATTTTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
75 39 0.49
76 40 0.51
ACGTcount: A:0.31, C:0.02, G:0.09, T:0.58
Consensus pattern (75 bp):
ATTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
TTTAATTAAG
Found at i:47829 original size:21 final size:21
Alignment explanation
Indices: 47790--47829 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
47780 CTTTAATTTG
*
47790 TTTATTTAATAATTTTTTTCT
1 TTTATTTAATAATTATTTTCT
**
47811 TTTATTTAATTCTTATTTT
1 TTTATTTAATAATTATTTT
47830 TTTAACCATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTATTTAATAATTATTTTCT
Found at i:47898 original size:16 final size:16
Alignment explanation
Indices: 47862--47911 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
47852 ATCTCTCTTT
*
47862 TATATTTATTACTAT-
1 TATATTTATTATTATA
47877 TAATATTTATTATTATA
1 T-ATATTTATTATTATA
47894 TATATTT-TT-TTA-A
1 TATATTTATTATTATA
47907 TATAT
1 TATAT
47912 CTTTTCAACT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 6 0.19
14 3 0.09
15 3 0.09
16 19 0.59
17 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (16 bp):
TATATTTATTATTATA
Found at i:48344 original size:4 final size:4
Alignment explanation
Indices: 48327--48369 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
48317 ATTATTCAGT
* * *
48327 ATAC ATAT ATAC ATAC ATAC ATAC ATAT GTAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
48370 TACATGTATG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.49, C:0.19, G:0.02, T:0.30
Consensus pattern (4 bp):
ATAC
Found at i:48376 original size:20 final size:20
Alignment explanation
Indices: 48336--48377 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
48326 TATACATATA
*
48336 TACATACATACATACATATG
1 TACATACATACATACACATG
*
48356 TACATACATACATATACATG
1 TACATACATACATACACATG
48376 TA
1 TA
48378 TGAATATATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (20 bp):
TACATACATACATACACATG
Found at i:49063 original size:31 final size:31
Alignment explanation
Indices: 49025--49085 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
49015 AGTTATGATC
*
49025 ACTTTCGTTTTTAGTTAATTAAGATTTGGTT
1 ACTTTCGTTTTTAGTTAATTAAGATGTGGTT
*
49056 ACTTTCGTTTTTATTTAATTAAGATGTGGT
1 ACTTTCGTTTTTAGTTAATTAAGATGTGGT
49086 CATCCCGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.23, C:0.07, G:0.16, T:0.54
Consensus pattern (31 bp):
ACTTTCGTTTTTAGTTAATTAAGATGTGGTT
Found at i:49912 original size:16 final size:16
Alignment explanation
Indices: 49883--49924 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
49873 TGTATATCAC
49883 ATATGAAG-AAAAAAA
1 ATATGAAGAAAAAAAA
49898 ATATGAAGAAAAAAAA
1 ATATGAAGAAAAAAAA
49914 ATATGAAGAAA
1 ATATGAAGAAA
49925 TACACATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (16 bp):
ATATGAAGAAAAAAAA
Found at i:50966 original size:19 final size:19
Alignment explanation
Indices: 50942--50978 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
50932 ATGACCAACA
*
50942 AAATCGCAATGCGATCTCT
1 AAATCGCAAAGCGATCTCT
50961 AAATCGCAAAGCGATCTC
1 AAATCGCAAAGCGATCTC
50979 CAGTATCGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAAAGCGATCTCT
Found at i:51530 original size:19 final size:19
Alignment explanation
Indices: 51452--51537 Score: 64
Period size: 19 Copynumber: 4.2 Consensus size: 19
51442 TGTTTTGGAT
* * *
51452 TTTTCACTATCGCATCACT
1 TTTTAACTATCGCAACACA
*
51471 TTTTCACTATCGCAACAACA
1 TTTTAACTATCGCAAC-ACA
* *
51491 CGTTTTTCAAACTCTCACAACACA
1 ---TTTT--AACTATCGCAACACA
51515 TTTTAACTATCGCAACACA
1 TTTTAACTATCGCAACACA
51534 TTTT
1 TTTT
51538 TTAAAATCGT
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
19 32 0.59
20 2 0.04
21 4 0.07
23 4 0.07
24 3 0.06
25 9 0.17
ACGTcount: A:0.30, C:0.29, G:0.05, T:0.36
Consensus pattern (19 bp):
TTTTAACTATCGCAACACA
Found at i:57401 original size:31 final size:31
Alignment explanation
Indices: 57358--57427 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
57348 TTTTAAAACG
* *
57358 TACAATACAGTCCCCCAATATTTAGTCCGTT
1 TACAATATAGTCCCCCAACATTTAGTCCGTT
* *
57389 TGCAATATAGTCCCTCAACATTTAGTCCGTT
1 TACAATATAGTCCCCCAACATTTAGTCCGTT
57420 TACAATAT
1 TACAATAT
57428 GATCCCCGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.30, C:0.26, G:0.10, T:0.34
Consensus pattern (31 bp):
TACAATATAGTCCCCCAACATTTAGTCCGTT
Found at i:59458 original size:31 final size:31
Alignment explanation
Indices: 59423--59487 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
59413 CGGTTACGTC
*
59423 GGGGACCATATTGCAAACGGACTAAATATTG
1 GGGGACCATATTGCAAACAGACTAAATATTG
** * *
59454 GGGGACTGTATTGCAAACATACTAAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATATTG
59485 GGG
1 GGG
59488 ACTGTATTGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.29, T:0.25
Consensus pattern (31 bp):
GGGGACCATATTGCAAACAGACTAAATATTG
Found at i:59490 original size:30 final size:31
Alignment explanation
Indices: 59431--59497 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
59421 TCGGGGACCA
*
59431 TATTGCAAACGGACTAAATATTGGGGGACTG
1 TATTGCAAACAGACTAAATATTGGGGGACTG
* *
59462 TATTGCAAACATACTAAATGTT-GGGGACTG
1 TATTGCAAACAGACTAAATATTGGGGGACTG
59492 TATTGC
1 TATTGC
59498 TAGTTTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 14 0.42
31 19 0.58
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.30
Consensus pattern (31 bp):
TATTGCAAACAGACTAAATATTGGGGGACTG
Found at i:60233 original size:32 final size:32
Alignment explanation
Indices: 60192--60300 Score: 139
Period size: 32 Copynumber: 3.4 Consensus size: 32
60182 TTCGGTTTGG
* *
60192 ATCGGTTGATTTTTGGATCGGGTCAATACCGA
1 ATCGGTTGATTTTTGGGTCGGGTCAATATCGA
*
60224 ATCGGTTGATTTTTGGGTCGGGTTAATATCGA
1 ATCGGTTGATTTTTGGGTCGGGTCAATATCGA
* * * *
60256 ATAGCTTAGA-TTTTGGGTCGAGTCAATATCGG
1 ATCGGTT-GATTTTTGGGTCGGGTCAATATCGA
60288 ATCGGTTGATTTT
1 ATCGGTTGATTTT
60301 CGGTTTAGCT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
31 2 0.03
32 61 0.94
33 2 0.03
ACGTcount: A:0.21, C:0.12, G:0.28, T:0.39
Consensus pattern (32 bp):
ATCGGTTGATTTTTGGGTCGGGTCAATATCGA
Found at i:60932 original size:18 final size:18
Alignment explanation
Indices: 60884--60936 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
60874 ACTTTCTATT
60884 ATTTTATTATAAATCTAACA
1 ATTTTATT-TAAAT-TAACA
* * *
60904 TTTTTA-ATAAATTATCA
1 ATTTTATTTAAATTAACA
60921 ATTTTATTTAAATTAA
1 ATTTTATTTAAATTAA
60937 TTTATTGTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
17 9 0.35
18 12 0.46
20 5 0.19
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTTATTTAAATTAACA
Found at i:66017 original size:58 final size:58
Alignment explanation
Indices: 65918--66043 Score: 188
Period size: 58 Copynumber: 2.2 Consensus size: 58
65908 ATATCAAATC
* * *
65918 TAAAATATAATTAA--T-TTATTAGGTCTGTTTTGGTCCAAACCTATAACATTAAAAG
1 TAAAAAATAATTAATTTGTTATTAGGCCTGTTTTGGTCCAAACCTAAAACATTAAAAG
65973 TAAAAAATTAATTAATTTGTTATTAGGCCTG-TTTGGTCCAAACCTAAAACATTAAAAG
1 TAAAAAA-TAATTAATTTGTTATTAGGCCTGTTTTGGTCCAAACCTAAAACATTAAAAG
66031 TAAAAAATAATTA
1 TAAAAAATAATTA
66044 TTTAAAACAT
Statistics
Matches: 64, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
55 6 0.09
56 7 0.11
57 6 0.09
58 34 0.53
59 11 0.17
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (58 bp):
TAAAAAATAATTAATTTGTTATTAGGCCTGTTTTGGTCCAAACCTAAAACATTAAAAG
Found at i:68524 original size:29 final size:29
Alignment explanation
Indices: 68482--68541 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
68472 TTGATAATAA
*
68482 CTCTGAATCATTCAGAATGTACTTCTGTG
1 CTCTCAATCATTCAGAATGTACTTCTGTG
*
68511 CTCTCAATCATTCAGAATGTATTTCTGTG
1 CTCTCAATCATTCAGAATGTACTTCTGTG
68540 CT
1 CT
68542 GAATCATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.40
Consensus pattern (29 bp):
CTCTCAATCATTCAGAATGTACTTCTGTG
Found at i:68568 original size:23 final size:23
Alignment explanation
Indices: 68554--68602 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
68544 ATCATTCATT
68554 ACTATTTTGATGAATCAGTCAAC
1 ACTATTTTGATGAATCAGTCAAC
*
68577 ACTATTTTGATGAATCAGTCAGC
1 ACTATTTTGATGAATCAGTCAAC
68600 ACT
1 ACT
68603 GAATCATTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (23 bp):
ACTATTTTGATGAATCAGTCAAC
Found at i:68664 original size:22 final size:22
Alignment explanation
Indices: 68639--68681 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
68629 GCGCTGAATG
68639 TTGAACGATTCAACATTCAGAA
1 TTGAACGATTCAACATTCAGAA
* *
68661 TTGAATGCTTCAACATTCAGA
1 TTGAACGATTCAACATTCAGA
68682 GCTGAATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (22 bp):
TTGAACGATTCAACATTCAGAA
Found at i:68687 original size:22 final size:22
Alignment explanation
Indices: 68647--68689 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
68637 TGTTGAACGA
*
68647 TTCAACATTCAGAATTGAATGC
1 TTCAACATTCAGAACTGAATGC
*
68669 TTCAACATTCAGAGCTGAATG
1 TTCAACATTCAGAACTGAATG
68690 ATTCGATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (22 bp):
TTCAACATTCAGAACTGAATGC
Found at i:71763 original size:17 final size:17
Alignment explanation
Indices: 71739--71803 Score: 57
Period size: 17 Copynumber: 4.0 Consensus size: 17
71729 AACTTTATGT
71739 ATAATTTAAAAACTTAAA
1 ATAATTTAAAAA-TTAAA
*
71757 A-AATTTAAATATTAAA
1 ATAATTTAAAAATTAAA
* *
71773 ATAAATT-AAAACT--A
1 ATAATTTAAAAATTAAA
*
71787 ATAATTTAAATATTAAA
1 ATAATTTAAAAATTAAA
71804 GATGTACTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 9
0.69 0.13 0.17
Matches are distributed among these distances:
14 7 0.19
15 4 0.11
16 10 0.28
17 14 0.39
18 1 0.03
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAATTTAAAAATTAAA
Found at i:74881 original size:16 final size:16
Alignment explanation
Indices: 74860--74891 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
74850 GATTTTTAAG
74860 TGTTTTATTTTCTTTA
1 TGTTTTATTTTCTTTA
74876 TGTTTTATTTTCTTTA
1 TGTTTTATTTTCTTTA
74892 CGTTATCTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.75
Consensus pattern (16 bp):
TGTTTTATTTTCTTTA
Found at i:79613 original size:23 final size:24
Alignment explanation
Indices: 79587--79661 Score: 66
Period size: 24 Copynumber: 3.1 Consensus size: 24
79577 AATTAAATAA
*
79587 TTATTTATATATATT-TATAAAGT
1 TTATTTATATATATTCTAAAAAGT
*
79610 TTATATTAAAT-TATTCTAAAAAGT
1 TTAT-TTATATATATTCTAAAAAGT
* *
79634 ATATTTATA-ATATTATGAAAATAGT
1 TTATTTATATATATTCT-AAAA-AGT
79659 TTA
1 TTA
79662 AAATATTGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
23 17 0.41
24 19 0.46
25 5 0.12
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.49
Consensus pattern (24 bp):
TTATTTATATATATTCTAAAAAGT
Found at i:79714 original size:24 final size:23
Alignment explanation
Indices: 79694--79740 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
79684 ATCATATTAT
79694 TTATTTATTTGGAAATAATATTTA
1 TTATTTATTT-GAAATAATATTTA
79718 TTATTTATTTGAAATAATTATTT
1 TTATTTATTTGAAATAA-TATTT
79741 TAAATTATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.57
Consensus pattern (23 bp):
TTATTTATTTGAAATAATATTTA
Found at i:81059 original size:13 final size:13
Alignment explanation
Indices: 81043--81073 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
81033 TTGTGTTTGT
81043 GTTTTTTATGTTC
1 GTTTTTTATGTTC
*
81056 GTTTATTATGTTC
1 GTTTTTTATGTTC
81069 GTTTT
1 GTTTT
81074 GTTCATTATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.06, G:0.16, T:0.68
Consensus pattern (13 bp):
GTTTTTTATGTTC
Found at i:81083 original size:31 final size:32
Alignment explanation
Indices: 81039--81123 Score: 113
Period size: 31 Copynumber: 2.8 Consensus size: 32
81029 GTTTTTGTGT
*
81039 TTGTGTT-TTTTATGTTCGTTTATTATGTTCG
1 TTGTGTTCATTTATGTTCGTTTATTATGTTCG
* *
81070 TTTTGTTCA-TTATGTTCGTTTA-TGTGTTCG
1 TTGTGTTCATTTATGTTCGTTTATTATGTTCG
*
81100 TTGTGTTCATTTACGTTCGTTTAT
1 TTGTGTTCATTTATGTTCGTTTAT
81124 CATTTAAATG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
30 15 0.33
31 31 0.67
ACGTcount: A:0.11, C:0.09, G:0.19, T:0.61
Consensus pattern (32 bp):
TTGTGTTCATTTATGTTCGTTTATTATGTTCG
Found at i:81097 original size:21 final size:20
Alignment explanation
Indices: 81060--81112 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 20
81050 ATGTTCGTTT
81060 ATTATGTTCG-TT-TTGTTC
1 ATTATGTTCGTTTATTGTTC
81078 ATTATGTTCGTTTATGTGTTC
1 ATTATGTTCGTTTAT-TGTTC
* * *
81099 GTTGTGTTCATTTA
1 ATTATGTTCGTTTA
81113 CGTTCGTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 10 0.34
19 2 0.07
20 1 0.03
21 16 0.55
ACGTcount: A:0.13, C:0.09, G:0.19, T:0.58
Consensus pattern (20 bp):
ATTATGTTCGTTTATTGTTC
Done.