Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003826.1 Hibiscus syriacus cultivar Beakdansim tig00008204_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: 93003
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:911 original size:20 final size:20
Alignment explanation
Indices: 882--919 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
872 CGGTAATTAG
882 CGTTGCGAATTTGAAAATCA
1 CGTTGCGAATTTGAAAATCA
* *
902 CGTTGTGAATTTGGAAAT
1 CGTTGCGAATTTGAAAAT
920 GTGTTGCGAA
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:0.32, C:0.11, G:0.24, T:0.34
Consensus pattern (20 bp):
CGTTGCGAATTTGAAAATCA
Found at i:10245 original size:21 final size:22
Alignment explanation
Indices: 10215--10255 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
10205 ACAAGCATCG
*
10215 TAATTGTCAA-ATAAATAAACA
1 TAATTCTCAATATAAATAAACA
*
10236 TAATTCTCAATTTAAATAAA
1 TAATTCTCAATATAAATAAA
10256 TAAAATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (22 bp):
TAATTCTCAATATAAATAAACA
Found at i:12130 original size:18 final size:18
Alignment explanation
Indices: 12107--12145 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
12097 TAATTTGTTT
*
12107 GATTTAATTACTCTTTTG
1 GATTTAATTACTCTTTAG
12125 GATTTAATTACTCTTTAG
1 GATTTAATTACTCTTTAG
12143 GAT
1 GAT
12146 CTTTTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.51
Consensus pattern (18 bp):
GATTTAATTACTCTTTAG
Found at i:13358 original size:19 final size:19
Alignment explanation
Indices: 13334--13379 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
13324 TAAAAACACA
13334 TTAAATA-GTAGAATACTAT
1 TTAAATATGTAGAATA-TAT
* *
13353 TTAAATATGTATAATATTT
1 TTAAATATGTAGAATATAT
13372 TTAAATAT
1 TTAAATAT
13380 TAAACTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (19 bp):
TTAAATATGTAGAATATAT
Found at i:16013 original size:16 final size:16
Alignment explanation
Indices: 15992--16025 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
15982 TTTTCACCTC
*
15992 TTGTATTATAATCACT
1 TTGTATTACAATCACT
16008 TTGTATTACAATCACT
1 TTGTATTACAATCACT
16024 TT
1 TT
16026 TTTCACCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.15, G:0.06, T:0.50
Consensus pattern (16 bp):
TTGTATTACAATCACT
Found at i:19565 original size:11 final size:11
Alignment explanation
Indices: 19549--19585 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
19539 TTATTTAAAA
19549 TATTAATTTTT
1 TATTAATTTTT
19560 TATTAATTTTT
1 TATTAATTTTT
19571 T-TATAA-TTTT
1 TAT-TAATTTTT
19581 TATTA
1 TATTA
19586 GAAGTATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TATTAATTTTT
Found at i:19572 original size:12 final size:12
Alignment explanation
Indices: 19549--19581 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
19539 TTATTTAAAA
19549 TATTAA-TTTTT
1 TATTAATTTTTT
19560 TATTAATTTTTT
1 TATTAATTTTTT
19572 TA-TAATTTTT
1 TATTAATTTTT
19582 ATTAGAAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TATTAATTTTTT
Found at i:22730 original size:22 final size:22
Alignment explanation
Indices: 22710--22756 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
22700 AAAATATATT
22710 TATTAATATTTCTAATAATATAA
1 TATT-ATATTTCTAATAATATAA
* *
22733 TATTATATTTTTAATATTATAA
1 TATTATATTTCTAATAATATAA
22755 TA
1 TA
22757 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTATATTTCTAATAATATAA
Found at i:22770 original size:32 final size:32
Alignment explanation
Indices: 22704--22784 Score: 94
Period size: 32 Copynumber: 2.5 Consensus size: 32
22694 ATATTTAAAA
* *
22704 TATATTTATTAATATTTCTAATAATATAATAT
1 TATATTTATTAATATTTATAATAAAATAATAT
22736 TATATTT-TTAATA-TTATAATAAAATAATCAAT
1 TATATTTATTAATATTTATAATAAAATAAT--AT
*
22768 TATATTATAATAATATT
1 TATATT-TATTAATATT
22785 AGATATTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 13 0.32
31 6 0.15
32 15 0.37
33 1 0.02
34 5 0.12
35 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAAAATAATAT
Found at i:22962 original size:23 final size:23
Alignment explanation
Indices: 22936--22980 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
22926 AATAATATTT
22936 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
22959 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
22981 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:23349 original size:29 final size:29
Alignment explanation
Indices: 23302--23358 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
23292 TTTGGAAATG
*
23302 TAATTCATTTTCTAGAATTCAAATTCCAA
1 TAATTCATTTTCTACAATTCAAATTCCAA
*
23331 TAATTCATTTT-TCACAATTCAATTTCCA
1 TAATTCATTTTCT-ACAATTCAAATTCCA
23359 GAAAACCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 24 0.96
ACGTcount: A:0.35, C:0.19, G:0.02, T:0.44
Consensus pattern (29 bp):
TAATTCATTTTCTACAATTCAAATTCCAA
Found at i:28397 original size:13 final size:14
Alignment explanation
Indices: 28379--28408 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28369 GACTACAATT
28379 TAATTA-TTTAAAA
1 TAATTATTTTAAAA
28392 TAATTATTTTAAAA
1 TAATTATTTTAAAA
28406 TAA
1 TAA
28409 AAAGATGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAATTATTTTAAAA
Found at i:30442 original size:2 final size:2
Alignment explanation
Indices: 30435--30463 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30425 TGTTCATTCC
30435 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 T
30464 CAATTTCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30769 original size:16 final size:16
Alignment explanation
Indices: 30744--30818 Score: 123
Period size: 16 Copynumber: 4.7 Consensus size: 16
30734 GTTTTTCCGG
* *
30744 GTACCTGGTTACTCGA
1 GTACCCGGTTACCCGA
30760 GTACCCGGTTACCCGA
1 GTACCCGGTTACCCGA
*
30776 GTACCCGGTTACTCGA
1 GTACCCGGTTACCCGA
30792 GTACCCGGTTACCCGA
1 GTACCCGGTTACCCGA
30808 GTACCCGGTTA
1 GTACCCGGTTA
30819 GTTTTTATTT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 55 1.00
ACGTcount: A:0.19, C:0.32, G:0.25, T:0.24
Consensus pattern (16 bp):
GTACCCGGTTACCCGA
Found at i:30774 original size:8 final size:8
Alignment explanation
Indices: 30761--30818 Score: 59
Period size: 8 Copynumber: 7.2 Consensus size: 8
30751 GTTACTCGAG
30761 TACCCGGT
1 TACCCGGT
30769 TACCCGAG-
1 TACCCG-GT
30777 TACCCGGT
1 TACCCGGT
*
30785 TACTCGAG-
1 TACCCG-GT
30793 TACCCGGT
1 TACCCGGT
30801 TACCCGAG-
1 TACCCG-GT
30809 TACCCGGT
1 TACCCGGT
30817 TA
1 TA
30819 GTTTTTATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
7 3 0.07
8 36 0.86
9 3 0.07
ACGTcount: A:0.19, C:0.34, G:0.24, T:0.22
Consensus pattern (8 bp):
TACCCGGT
Found at i:30786 original size:32 final size:32
Alignment explanation
Indices: 30744--30818 Score: 141
Period size: 32 Copynumber: 2.3 Consensus size: 32
30734 GTTTTTCCGG
*
30744 GTACCTGGTTACTCGAGTACCCGGTTACCCGA
1 GTACCCGGTTACTCGAGTACCCGGTTACCCGA
30776 GTACCCGGTTACTCGAGTACCCGGTTACCCGA
1 GTACCCGGTTACTCGAGTACCCGGTTACCCGA
30808 GTACCCGGTTA
1 GTACCCGGTTA
30819 GTTTTTATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.19, C:0.32, G:0.25, T:0.24
Consensus pattern (32 bp):
GTACCCGGTTACTCGAGTACCCGGTTACCCGA
Found at i:31151 original size:22 final size:22
Alignment explanation
Indices: 31126--31326 Score: 154
Period size: 22 Copynumber: 9.1 Consensus size: 22
31116 GCACACACAG
*
31126 ACACACACACACGCACGCACGC
1 ACACACACACGCGCACGCACGC
* * *
31148 ACACGCACGCACGCGCGCGCACAC
1 ACA--CACACACGCGCACGCACGC
* * * * *
31172 ACGCACGCGCGCACACACACGC
1 ACACACACACGCGCACGCACGC
*
31194 ACGCACACACGCGCACGCACGC
1 ACACACACACGCGCACGCACGC
* * *
31216 GCACACGCACACGCACGCACGC
1 ACACACACACGCGCACGCACGC
* * *
31238 GCACACGCACGCGCACGCGCGC
1 ACACACACACGCGCACGCACGC
*
31260 ACACACATACGCG--CGCACGC
1 ACACACACACGCGCACGCACGC
* * *
31280 ACACGCACACGCACACGTACGC
1 ACACACACACGCGCACGCACGC
* * * *
31302 GCACGCGCACGCGCACGCACAC
1 ACACACACACGCGCACGCACGC
31324 ACA
1 ACA
31327 TTTTCAATCA
Statistics
Matches: 141, Mismatches: 34, Indels: 8
0.77 0.19 0.04
Matches are distributed among these distances:
20 16 0.11
22 108 0.77
24 17 0.12
ACGTcount: A:0.28, C:0.49, G:0.22, T:0.01
Consensus pattern (22 bp):
ACACACACACGCGCACGCACGC
Found at i:31185 original size:40 final size:40
Alignment explanation
Indices: 31127--31323 Score: 172
Period size: 40 Copynumber: 5.0 Consensus size: 40
31117 CACACACAGA
* * * *
31127 CACACACACACGCACGCACGCACACGCACGCACGCGCGCG
1 CACACACGCACGCGCGCACGCACACGCACGCACGCACACG
*
31167 CACACACGCACGCGCGCACACACACGCACGCA--CACACG
1 CACACACGCACGCGCGCACGCACACGCACGCACGCACACG
* * * *
31205 --CGCACGCACGCGCACACGCACACGCACGCACGCGCACA
1 CACACACGCACGCGCGCACGCACACGCACGCACGCACACG
* * * *
31243 CGCACGCGCACGCGCGCACACACATACGCGCGCACGCACACG
1 CACACACGCACGCGCGCACGCAC--ACGCACGCACGCACACG
* * *
31285 CACACGCACACGTACGCGCACGCGCACG--CGCACGCACAC
1 CACACACGCACG--CGCGCACGCACACGCACGCACGCACAC
31324 ACATTTTCAA
Statistics
Matches: 128, Mismatches: 21, Indels: 16
0.78 0.13 0.10
Matches are distributed among these distances:
36 27 0.21
38 8 0.06
40 57 0.45
42 27 0.21
44 9 0.07
ACGTcount: A:0.27, C:0.49, G:0.23, T:0.01
Consensus pattern (40 bp):
CACACACGCACGCGCGCACGCACACGCACGCACGCACACG
Found at i:31280 original size:28 final size:28
Alignment explanation
Indices: 31243--31327 Score: 80
Period size: 30 Copynumber: 2.9 Consensus size: 28
31233 CACGCGCACA
*
31243 CGCACGCGCACGCGCGCACACACATACG
1 CGCACACGCACGCGCGCACACACATACG
* * * *
31271 CGCGCACGCACACGCACACGCACACGTACG
1 CGCACACGCACGCGCGCA--CACACATACG
*
31301 CGCACGCGCACGCGCACGCACACACAT
1 CGCACACGCACGCG--CGCACACACAT
31328 TTTCAATCAA
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
28 14 0.33
30 26 0.60
32 3 0.07
ACGTcount: A:0.26, C:0.47, G:0.24, T:0.04
Consensus pattern (28 bp):
CGCACACGCACGCGCGCACACACATACG
Found at i:31296 original size:18 final size:18
Alignment explanation
Indices: 31127--31317 Score: 156
Period size: 18 Copynumber: 10.5 Consensus size: 18
31117 CACACACAGA
*
31127 CACACACACACGCACGCACG
1 CACACGCACACGCACG--CG
31147 CACACG--CACGCACGCG
1 CACACGCACACGCACGCG
* * *
31163 CGCGCACACACGCACGCG
1 CACACGCACACGCACGCG
* * *
31181 CGCACACACACGCACGCA
1 CACACGCACACGCACGCG
*
31199 CACACGCGCACGCACGCG
1 CACACGCACACGCACGCG
31217 CACACGCACACGCA--CG
1 CACACGCACACGCACGCG
*
31233 CACGCGCACACGCACGCG
1 CACACGCACACGCACGCG
* *
31251 CACGCGCGCACACACATACGCG
1 CA--CACGCACACGC--ACGCG
* *
31273 CGCACGCACACGCACACG
1 CACACGCACACGCACGCG
* *
31291 CACACGTACGCGCACGCG
1 CACACGCACACGCACGCG
*
31309 CACGCGCAC
1 CACACGCAC
31318 GCACACACAT
Statistics
Matches: 140, Mismatches: 23, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
16 20 0.14
18 90 0.64
20 24 0.17
22 6 0.04
ACGTcount: A:0.27, C:0.49, G:0.23, T:0.01
Consensus pattern (18 bp):
CACACGCACACGCACGCG
Found at i:43838 original size:36 final size:36
Alignment explanation
Indices: 43797--43878 Score: 137
Period size: 36 Copynumber: 2.3 Consensus size: 36
43787 TCAAAATGCA
*
43797 AAGAAAAGAAAACAGAAGGTTCAACAAATATATTAC
1 AAGAAAAGAAAACAGAAGGTTCAACAAATAAATTAC
* *
43833 AAGAAAAGAAAGCAGAAGTTTCAACAAATAAATTAC
1 AAGAAAAGAAAACAGAAGGTTCAACAAATAAATTAC
43869 AAGAAAAGAA
1 AAGAAAAGAA
43879 GAAACTAACT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (36 bp):
AAGAAAAGAAAACAGAAGGTTCAACAAATAAATTAC
Found at i:47772 original size:34 final size:34
Alignment explanation
Indices: 47729--47812 Score: 118
Period size: 34 Copynumber: 2.5 Consensus size: 34
47719 CCCCGCCCCG
47729 ATTATATATATATATAATATT-T-TTTTTTATATTA
1 ATTATATATATA-AT-ATATTATATTTTTTATATTA
*
47763 ATTATATATATAATATTTTATATTTTTTATATTA
1 ATTATATATATAATATATTATATTTTTTATATTA
*
47797 ATTATATATAAAATAT
1 ATTATATATATAATAT
47813 TTTCGAGTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
32 4 0.09
33 3 0.07
34 39 0.85
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (34 bp):
ATTATATATATAATATATTATATTTTTTATATTA
Found at i:47813 original size:34 final size:34
Alignment explanation
Indices: 47751--47815 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
47741 TATAATATTT
*
47751 TTTTTTATATTAATTATATATATAATATTTTATA
1 TTTTTTATATTAATTATATATAAAATATTTTATA
47785 TTTTTTATATTAATTATATATAAAATATTTT
1 TTTTTTATATTAATTATATATAAAATATTTT
47816 CGAGTTCGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (34 bp):
TTTTTTATATTAATTATATATAAAATATTTTATA
Found at i:59683 original size:19 final size:20
Alignment explanation
Indices: 59651--59688 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
59641 CTCTCTCATC
59651 TCTTCTTCCTTCTT-TCTTA
1 TCTTCTTCCTTCTTCTCTTA
59670 TCTTCTTCAC-TCTTCTCTT
1 TCTTCTTC-CTTCTTCTCTT
59689 CTTCCAAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.61
Consensus pattern (20 bp):
TCTTCTTCCTTCTTCTCTTA
Found at i:60712 original size:22 final size:21
Alignment explanation
Indices: 60658--60721 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
60648 AGTCGAGGGT
*
60658 TTCATAGGTCCTTTGGGACAA
1 TTCATAGGTCCTTCGGGACAA
*
60679 CTCATAGGTCCTTCGGGACATA
1 TTCATAGGTCCTTCGGGACA-A
*
60701 TTCACAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
60722 ATTTCATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 19 0.50
22 19 0.50
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.28
Consensus pattern (21 bp):
TTCATAGGTCCTTCGGGACAA
Found at i:61603 original size:3 final size:3
Alignment explanation
Indices: 61595--61627 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
61585 AATCTCCTAT
61595 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
61628 GGTGACGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:61698 original size:16 final size:18
Alignment explanation
Indices: 61660--61707 Score: 73
Period size: 16 Copynumber: 2.8 Consensus size: 18
61650 TGTTTCTGAG
61660 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
*
61678 GGAATTGGAAT-T-TGTA
1 GGAATTGGAATCTGTGAA
61694 GGAATTGGAATCTG
1 GGAATTGGAATCTG
61708 AATCTAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 14 0.52
17 2 0.07
18 11 0.41
ACGTcount: A:0.31, C:0.04, G:0.33, T:0.31
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:65493 original size:198 final size:198
Alignment explanation
Indices: 65150--65556 Score: 760
Period size: 198 Copynumber: 2.1 Consensus size: 198
65140 GGTGTATATC
* *
65150 ATTGATTATGGCCTTGCTAAAAAGTATAGGGATCTTCAAACTCATAAACACATACCATATAGGTA
1 ATTGCTTATGGCCTTGCCAAAAAGTATAGGGATCTTCAAACTCATAAACACATACCATATAGGTA
** *
65215 TGCATTTACCGTTGTTGGTTATCCATAATAGTCTTACAATGAGTCCTTGTTTCCTGCAATTTCAT
66 TGCATTTACAATTGTTAGTTATCCATAATAGTCTTACAATGAGTCCTTGTTTCCTGCAATTTCAT
*
65280 TTATCTAGTATGTTTATCAGCTGTATGTAACATGTTTTTCTATCTGAAAGGTAGATATATGTAAA
131 TTATCTAGTATGTTTATCAGCTGTATGTAACATGTTTTTCTATCTGAAAGGTAGATACATGTAAA
65345 CTA
196 CTA
65348 ATTGCTTATGGCCTTGCCAAAAAGTATAGGGATCTTCAAACTCATAAACACATACCATATAGGTA
1 ATTGCTTATGGCCTTGCCAAAAAGTATAGGGATCTTCAAACTCATAAACACATACCATATAGGTA
65413 TGCATTTACAATTGTTAGTTATCCATAATAGTCTTACAATGAGTCCTTGTTTCCTGCAATTTCAT
66 TGCATTTACAATTGTTAGTTATCCATAATAGTCTTACAATGAGTCCTTGTTTCCTGCAATTTCAT
65478 TTATCTAGTATGTTTATCAGCTGTATGTAACATGTTTTTCTATCTGAAAGGTAGATACATGTAAA
131 TTATCTAGTATGTTTATCAGCTGTATGTAACATGTTTTTCTATCTGAAAGGTAGATACATGTAAA
65543 CTA
196 CTA
65546 ATTGCTTATGG
1 ATTGCTTATGG
65557 GTGGTGATTC
Statistics
Matches: 203, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
198 203 1.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.38
Consensus pattern (198 bp):
ATTGCTTATGGCCTTGCCAAAAAGTATAGGGATCTTCAAACTCATAAACACATACCATATAGGTA
TGCATTTACAATTGTTAGTTATCCATAATAGTCTTACAATGAGTCCTTGTTTCCTGCAATTTCAT
TTATCTAGTATGTTTATCAGCTGTATGTAACATGTTTTTCTATCTGAAAGGTAGATACATGTAAA
CTA
Found at i:70152 original size:22 final size:22
Alignment explanation
Indices: 70124--70174 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
70114 CCTTCTTTTT
*
70124 TCGTCGGCAGTCACAGCCTCCA
1 TCGTCGGCAGTCACAACCTCCA
*
70146 TCGTCGGCAGTCACAACTTCCA
1 TCGTCGGCAGTCACAACCTCCA
70168 TCGTCGG
1 TCGTCGG
70175 GCGCTAACAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.18, C:0.37, G:0.24, T:0.22
Consensus pattern (22 bp):
TCGTCGGCAGTCACAACCTCCA
Found at i:78011 original size:20 final size:18
Alignment explanation
Indices: 77979--78017 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 18
77969 TTTTAAGAGA
77979 TATAAATAATAATTAAAT
1 TATAAATAATAATTAAAT
77997 TATAAATAAACTAATTAAAT
1 TATAAAT-AA-TAATTAAAT
78017 T
1 T
78018 CTTTAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 2 0.11
20 10 0.53
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
TATAAATAATAATTAAAT
Found at i:80163 original size:25 final size:26
Alignment explanation
Indices: 80135--80191 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
80125 TCATTTTTAT
*
80135 AATTTTAGGGTTTTTA-TAAAAATAA
1 AATTTTAAGGTTTTTATTAAAAATAA
* **
80160 AATTTTAAGTTTTTTATTTTAAATAA
1 AATTTTAAGGTTTTTATTAAAAATAA
80186 AATTTT
1 AATTTT
80192 TAAAATTCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 14 0.52
26 13 0.48
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (26 bp):
AATTTTAAGGTTTTTATTAAAAATAA
Done.