Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000643.1 Hibiscus syriacus cultivar Beakdansim tig00001244_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: 57618
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:807 original size:105 final size:104
Alignment explanation
Indices: 615--1288 Score: 950
Period size: 105 Copynumber: 6.6 Consensus size: 104
605 TTTGTCGGAT
* * *
615 GAGTTCTTCTCATTATGAACTCTT-T-GAAATGTCGATTCACCTCCTTCTG-GG-GAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
*
676 GGAACAT-GCTTCTCATTACGAACCTTCTCCTTTAAGAC
66 GGAACATCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
*
714 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCGTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
779 GGAACATACTCTTCTCATTACGAACCTTCTCCTTTAAGAC
66 GGAACAT-CTCTTCTCATTACGAACCTTCTCCTTTAAGAC
*
819 GAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
* *
884 GGAACAT-GC-TCTCATTACGTACCTTTCTCCTTT-AGAC
66 GGAACATCTCTTCTCATTACGAACC-TTCTCCTTTAAGAC
*
921 GAGTTCTTCTCATTATGAACTCTTCTGG-AATATTGGTT-ACC-CCTTCTGCGGTGGATTTG-AA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
* *
982 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACA-TCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
* *
1022 GAGTTCTTCTC---ATGAACTCTTCTGGAAATGTTGGGTCA-CTCCTTCTGTGGTGGA-TTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
** * *
1082 GGAACAAGTCTTCTCATTATGAACCTTCTCCTTTAGGAC
66 GGAACATCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
* *
1121 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
* * * *
1186 GGAACAGGCTCTTCTCATTACAAACCTTCACCTTTAGGAC
66 GGAACA-TCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
* * * *
1226 GAGTTCTTCTCATTATGAACTGTTCTGGAAATATTGGGTCACCTCCTTCTGTGGTGGATTTGA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGA
1289 TTGTTGTTGA
Statistics
Matches: 528, Mismatches: 26, Indels: 36
0.89 0.04 0.06
Matches are distributed among these distances:
98 22 0.04
99 95 0.18
100 36 0.07
101 58 0.11
102 74 0.14
103 42 0.08
104 12 0.02
105 189 0.36
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (104 bp):
GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
GGAACATCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
Found at i:1165 original size:302 final size:306
Alignment explanation
Indices: 615--1288 Score: 972
Period size: 302 Copynumber: 2.2 Consensus size: 306
605 TTTGTCGGAT
* * * * *
615 GAGTTCTTCTCATTATGAACTCTT-TGAAATGTCGATTCACCTCCTTCTGGG-GAATTTGAAAGG
1 GAGTTCTTCTCATTATGAACTCTTCTGGAATATTGGTT-ACCTCCTTCTGGGTGGATTTG-AAGG
*
678 AACATGCTTCTCATTACGAACCTTCTCCTTTAAGACGAGTTCTTCTCATTATGAACTCTTCTGGA
64 AACAGGCTTCTCATTACGAACCTTCTCCTTTAAGACGAGTTCTTCTC--TATGAACTCTTCTGGA
* *
743 AATGTTGGTTCACCTCGTTCTGCGGTGGATTTGAAAGGAACATACTCTTCTCATTACGAACCTTC
127 AATGTTGGGTCACCTCCTTCTGCGGTGGATTTGAAAGGAACATACTCTTCTCATTACGAACCTTC
*
808 TCCTTTAAGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGGTTCACCTCCTTCTGCGG
192 TCCTTTAAGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGGGTCACCTCCTTCTGCGG
* ** *
873 TGGATTTGAAAGGAACATG-C-TCTCATTACGTACCTTTCTCCTTTA-GAC
257 TGGATTTGAAAGGAACAGGCCTTCTCATTACAAACC-TTCACCTTTAGGAC
921 GAGTTCTTCTCATTATGAACTCTTCTGGAATATTGGTTACC-CCTTCTGCGGTGGATTTGAAGGA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAATATTGGTTACCTCCTTCTG-GGTGGATTTGAAGGA
*
985 ACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTC-ATGAACTCTTCTGGAA
65 ACAGG--CTTCTCATTACGAACCTTCTCCTTTAAGACGAGTTCTTCTCTATGAACTCTTCTGGAA
* * *
1049 ATGTTGGGTCA-CTCCTTCTGTGGTGGA-TTGAAAGGAACA-AGTCTTCTCATTATGAACCTTCT
128 ATGTTGGGTCACCTCCTTCTGCGGTGGATTTGAAAGGAACATACTCTTCTCATTACGAACCTTCT
* * *
1111 CCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGT
193 CCTTTAAGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGGGTCACCTCCTTCTGCGGT
1176 GGATTTGAAAGGAACAGGCTCTTCTCATTACAAACCTTCACCTTTAGGAC
258 GGATTTGAAAGGAACAGGC-CTTCTCATTACAAACCTTCACCTTTAGGAC
* *
1226 GAGTTCTTCTCATTATGAACTGTTCTGGAAATATTGGGTCACCTCCTTCTGTGGTGGATTTGA
1 GAGTTCTTCTCATTATGAACTCTTCTGG-AATATT-GGTTACCTCCTTCTG-GGTGGATTTGA
1289 TTGTTGTTGA
Statistics
Matches: 333, Mismatches: 23, Indels: 22
0.88 0.06 0.06
Matches are distributed among these distances:
302 99 0.30
303 12 0.04
304 24 0.07
305 75 0.23
306 44 0.13
307 21 0.06
308 58 0.17
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (306 bp):
GAGTTCTTCTCATTATGAACTCTTCTGGAATATTGGTTACCTCCTTCTGGGTGGATTTGAAGGAA
CAGGCTTCTCATTACGAACCTTCTCCTTTAAGACGAGTTCTTCTCTATGAACTCTTCTGGAAATG
TTGGGTCACCTCCTTCTGCGGTGGATTTGAAAGGAACATACTCTTCTCATTACGAACCTTCTCCT
TTAAGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGGGTCACCTCCTTCTGCGGTGGA
TTTGAAAGGAACAGGCCTTCTCATTACAAACCTTCACCTTTAGGAC
Found at i:2201 original size:7 final size:7
Alignment explanation
Indices: 2189--2302 Score: 58
Period size: 7 Copynumber: 15.7 Consensus size: 7
2179 CGAACCCTCC
2189 TTTTTCT
1 TTTTTCT
2196 TTTTTC-
1 TTTTTCT
*
2202 -TTTTCA
1 TTTTTCT
2208 TTTTTCAT
1 TTTTTC-T
2216 TTTTTCATTT
1 TTTTTC---T
*
2226 TTTTTCA
1 TTTTTCT
2233 TTTTTCAT
1 TTTTTC-T
2241 TTTATT-T
1 TTT-TTCT
2248 TTTTT-T
1 TTTTTCT
*
2254 TTTTTAT
1 TTTTTCT
2261 TTTTTC-
1 TTTTTCT
*
2267 TTTTTCAC
1 TTTTTC-T
2275 TTTTTCAT
1 TTTTTC-T
2283 TTTTTCAT
1 TTTTTC-T
**
2291 TCATTCT
1 TTTTTCT
2298 TTTTT
1 TTTTT
2303 TTCAAGCATA
Statistics
Matches: 87, Mismatches: 10, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
5 5 0.06
6 14 0.16
7 31 0.36
8 28 0.32
9 2 0.02
10 7 0.08
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTTCT
Found at i:2219 original size:8 final size:8
Alignment explanation
Indices: 2202--2291 Score: 81
Period size: 8 Copynumber: 12.0 Consensus size: 8
2192 TTCTTTTTTC
2202 TTTTCA-T
1 TTTTCATT
2209 TTTTCATT
1 TTTTCATT
2217 TTTTCATTTT
1 TTTTCA--TT
2227 TTTTCA-T
1 TTTTCATT
2234 TTTTCATT
1 TTTTCATT
2242 TTATT--TT
1 TT-TTCATT
2249 TTTT--TT
1 TTTTCATT
2255 TTTT-ATT
1 TTTTCATT
2262 TTTTC--T
1 TTTTCATT
*
2268 TTTTCACT
1 TTTTCATT
2276 TTTTCATT
1 TTTTCATT
2284 TTTTCATT
1 TTTTCATT
2292 CATTCTTTTT
Statistics
Matches: 73, Mismatches: 1, Indels: 17
0.80 0.01 0.19
Matches are distributed among these distances:
6 14 0.19
7 23 0.32
8 26 0.36
9 2 0.03
10 8 0.11
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTCATT
Found at i:2237 original size:37 final size:37
Alignment explanation
Indices: 2189--2306 Score: 120
Period size: 37 Copynumber: 3.2 Consensus size: 37
2179 CGAACCCTCC
*
2189 TTTTTCTTTTTTC-TTTTCATTTTTCATTTTTTCATTT
1 TTTTTCATTTTTCATTTTCATTTTTCATTTTTTC-TTT
*
2226 TTTTTCATTTTTCATTTT-ATTTTT--TTTTTTTTTAT
1 TTTTTCATTTTTCATTTTCATTTTTCATTTTTTCTT-T
**
2261 TTTTTC-TTTTTCACTTTTTCATTTTTTCATTCATTCTTT
1 TTTTTCATTTTTCA--TTTTCA-TTTTTCATTTTTTCTTT
2300 TTTTTCA
1 TTTTTCA
2307 AGCATAGTAC
Statistics
Matches: 67, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
34 9 0.13
35 13 0.19
36 4 0.06
37 19 0.28
38 9 0.13
39 7 0.10
40 6 0.09
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (37 bp):
TTTTTCATTTTTCATTTTCATTTTTCATTTTTTCTTT
Found at i:5816 original size:14 final size:14
Alignment explanation
Indices: 5797--5823 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5787 AAATGAATGT
5797 AAAGAATGAAGAAC
1 AAAGAATGAAGAAC
5811 AAAGAATGAAGAA
1 AAAGAATGAAGAA
5824 TGAAATGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.04, G:0.22, T:0.07
Consensus pattern (14 bp):
AAAGAATGAAGAAC
Found at i:15448 original size:15 final size:16
Alignment explanation
Indices: 15430--15463 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
15420 TTTGAATTTT
*
15430 TGAGATTTGA-GGTTA
1 TGAGATTTAAGGGTTA
15445 TGAGATTTAAGGGTTA
1 TGAGATTTAAGGGTTA
15461 TGA
1 TGA
15464 AAAATGGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.38
Consensus pattern (16 bp):
TGAGATTTAAGGGTTA
Found at i:18427 original size:17 final size:17
Alignment explanation
Indices: 18389--18429 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
18379 AGACACAATT
18389 AAAATT-TTAAAATAAA
1 AAAATTATTAAAATAAA
*
18405 ATAAATTATTAATATAAA
1 A-AAATTATTAAAATAAA
18423 AAAATTA
1 AAAATTA
18430 AATTTTAAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 11 0.50
18 10 0.45
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATTAAAATAAA
Found at i:18437 original size:21 final size:23
Alignment explanation
Indices: 18396--18437 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
18386 ATTAAAATTT
18396 TAAAATAAAATAAATTATTAATA
1 TAAAATAAAATAAATTATTAATA
*
18419 TAAAA-AAATTAAATT-TTAA
1 TAAAATAAAATAAATTATTAA
18438 GCGAACACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 9 0.50
23 5 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
TAAAATAAAATAAATTATTAATA
Found at i:19371 original size:60 final size:60
Alignment explanation
Indices: 19253--19421 Score: 177
Period size: 60 Copynumber: 2.8 Consensus size: 60
19243 ATACATATAA
* * ** *
19253 TTTGGGT-TGAAATTGAAATGTTGAAAAAGTTTGGGGGACCAATTTAGAATGAAGGTCATAG
1 TTTGGGTATGAAATTAAAATGTT-AAAAAGTTT-AGGGATAAATTTAAAATGAAGGTCATAG
*
19314 TTTGGGTATGAAATTAAAATGTTAAAAAGTTTAAGGATAAATTTAAAATGATA-GTCATAG
1 TTTGGGTATGAAATTAAAATGTTAAAAAGTTTAGGGATAAATTTAAAATGA-AGGTCATAG
* *
19374 TTTAGGG-ATGAAATTGAAATAT-TTATAAA-TTTAGGGATTAATTTAAAA
1 TTT-GGGTATGAAATT-AAA-ATGTTAAAAAGTTTAGGGATAAATTTAAAA
19422 AGTGGATTTA
Statistics
Matches: 94, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
60 49 0.52
61 29 0.31
62 16 0.17
ACGTcount: A:0.41, C:0.02, G:0.22, T:0.35
Consensus pattern (60 bp):
TTTGGGTATGAAATTAAAATGTTAAAAAGTTTAGGGATAAATTTAAAATGAAGGTCATAG
Found at i:27255 original size:32 final size:32
Alignment explanation
Indices: 27214--27300 Score: 124
Period size: 31 Copynumber: 2.8 Consensus size: 32
27204 AATAATCCCC
27214 TAATAATAAATATTAGAAAAAAATTAAACCCA
1 TAATAATAAATATTAGAAAAAAATTAAACCCA
**
27246 TAATAATAAATATT-GAAAAAAATTAAACCTT
1 TAATAATAAATATTAGAAAAAAATTAAACCCA
* *
27277 TAATAATAAGTATTA-AAAATAATT
1 TAATAATAAATATTAGAAAAAAATT
27301 GGGCCCTATA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
31 36 0.72
32 14 0.28
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (32 bp):
TAATAATAAATATTAGAAAAAAATTAAACCCA
Found at i:30516 original size:119 final size:119
Alignment explanation
Indices: 30305--30544 Score: 444
Period size: 119 Copynumber: 2.0 Consensus size: 119
30295 GCCAGTTTCC
30305 CCACGCAATTGAGAGTCAGTGACATCAACGCCACCAAGGAAGTTTCCAACCGAAGGACTTTGGTC
1 CCACGCAATTGAGAGTCAGTGACATCAACGCCACCAAGGAAGTTTCCAACCGAAGGACTTTGGTC
30370 AATATCCCTGTAAGAAATAAATGTTCCAGGTCTCTGTCTGCTGAAAATTCTGAA
66 AATATCCCTGTAAGAAATAAATGTTCCAGGTCTCTGTCTGCTGAAAATTCTGAA
* *
30424 CCACGCAATTGAGAGTCAGTGACATCAACGCGACCAAGGAAGTTTCCAACGGAAGGACTTTGGTC
1 CCACGCAATTGAGAGTCAGTGACATCAACGCCACCAAGGAAGTTTCCAACCGAAGGACTTTGGTC
* *
30489 AATATCCCTGTAAGAAATTAATGTTCCAGGTCTCTGTCTGCTGAAAGTTCTGAA
66 AATATCCCTGTAAGAAATAAATGTTCCAGGTCTCTGTCTGCTGAAAATTCTGAA
30543 CC
1 CC
30545 TCAATTGTTC
Statistics
Matches: 117, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
119 117 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (119 bp):
CCACGCAATTGAGAGTCAGTGACATCAACGCCACCAAGGAAGTTTCCAACCGAAGGACTTTGGTC
AATATCCCTGTAAGAAATAAATGTTCCAGGTCTCTGTCTGCTGAAAATTCTGAA
Found at i:36418 original size:38 final size:38
Alignment explanation
Indices: 36376--36454 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
36366 TGTAAATACA
*
36376 TGATTATGTGATAATATGAGAATATA-ATATAAGTTATG
1 TGATTATGTGATAATATGAGAATA-AGATATAAGTCATG
* **
36414 TGATTATGTGATTATATGATCATAAGATATAAGTCATG
1 TGATTATGTGATAATATGAGAATAAGATATAAGTCATG
36452 TGA
1 TGA
36455 CAAGATATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
37 1 0.03
38 35 0.97
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (38 bp):
TGATTATGTGATAATATGAGAATAAGATATAAGTCATG
Found at i:36839 original size:21 final size:21
Alignment explanation
Indices: 36814--36868 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
36804 TAAGGAGTCA
* **
36814 TCATTCGGGATATCTATGTGG
1 TCATTCGGGACATAAATGTGG
36835 TCATTCGGGACATAAATGTGG
1 TCATTCGGGACATAAATGTGG
36856 TCATTCGGGACAT
1 TCATTCGGGACAT
36869 TTTTACACGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (21 bp):
TCATTCGGGACATAAATGTGG
Found at i:40227 original size:21 final size:21
Alignment explanation
Indices: 40201--40252 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
40191 TCTTTAAGGA
* *
40201 GTGGTCCTTTGGGACATCTAT
1 GTGGTCCTTCGGGACATATAT
40222 GTGGTCCTTCGGGACATATAT
1 GTGGTCCTTCGGGACATATAT
40243 GTGGTCCTTC
1 GTGGTCCTTC
40253 AAAACATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.13, C:0.21, G:0.29, T:0.37
Consensus pattern (21 bp):
GTGGTCCTTCGGGACATATAT
Found at i:40259 original size:21 final size:21
Alignment explanation
Indices: 40214--40259 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
40204 GTCCTTTGGG
* ***
40214 ACATCTATGTGGTCCTTCGGG
1 ACATATATGTGGTCCTTCAAA
40235 ACATATATGTGGTCCTTCAAA
1 ACATATATGTGGTCCTTCAAA
40256 ACAT
1 ACAT
40260 TTCTACGCGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (21 bp):
ACATATATGTGGTCCTTCAAA
Found at i:41272 original size:45 final size:45
Alignment explanation
Indices: 41223--41355 Score: 239
Period size: 45 Copynumber: 3.0 Consensus size: 45
41213 AAAATAGCCA
41223 GAGTGCATCGATGCATGGTTTGTGCATCGATGCATCAAATGCACT
1 GAGTGCATCGATGCATGGTTTGTGCATCGATGCATCAAATGCACT
41268 GAGTGCATCGATGCATGGTTTGTGCATCGATGCATCAAATGCACT
1 GAGTGCATCGATGCATGGTTTGTGCATCGATGCATCAAATGCACT
* * *
41313 GAGTGCATCGATGCATGGTATGTTCATCGATGCATAAAATGCA
1 GAGTGCATCGATGCATGGTTTGTGCATCGATGCATCAAATGCA
41356 TTCGATGTTC
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 85 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (45 bp):
GAGTGCATCGATGCATGGTTTGTGCATCGATGCATCAAATGCACT
Found at i:41275 original size:26 final size:26
Alignment explanation
Indices: 41244--41328 Score: 94
Period size: 26 Copynumber: 3.5 Consensus size: 26
41234 TGCATGGTTT
41244 GTGCATCGATGCATCAAATGCACTGA
1 GTGCATCGATGCATCAAATGCACTGA
* **
41270 GTGCATCGATG---C--ATG--GTTT
1 GTGCATCGATGCATCAAATGCACTGA
41289 GTGCATCGATGCATCAAATGCACTGA
1 GTGCATCGATGCATCAAATGCACTGA
41315 GTGCATCGATGCAT
1 GTGCATCGATGCAT
41329 GGTATGTTCA
Statistics
Matches: 46, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
19 12 0.26
21 3 0.07
22 1 0.02
23 1 0.02
24 3 0.07
26 26 0.57
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (26 bp):
GTGCATCGATGCATCAAATGCACTGA
Found at i:42084 original size:14 final size:15
Alignment explanation
Indices: 42065--42093 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
42055 TCAAACATTT
42065 AACAATCCA-AAACA
1 AACAATCCAGAAACA
42079 AACAATCCAGAAACA
1 AACAATCCAGAAACA
42094 TCAAAACAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.28, G:0.03, T:0.07
Consensus pattern (15 bp):
AACAATCCAGAAACA
Found at i:43663 original size:21 final size:22
Alignment explanation
Indices: 43611--43686 Score: 91
Period size: 23 Copynumber: 3.5 Consensus size: 22
43601 CATGGCCTTG
43611 TGCATCGATGTACATTCAAGGCA
1 TGCATCGATGTACATTCAAGG-A
* *
43634 TGCATCGATGTACCTTCATGG-
1 TGCATCGATGTACATTCAAGGA
* * *
43655 TGTATCGATGCACATTCAATGA
1 TGCATCGATGTACATTCAAGGA
43677 TGCATCGATG
1 TGCATCGATG
43687 CAGTGTTAGG
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
21 16 0.36
22 9 0.20
23 19 0.43
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.30
Consensus pattern (22 bp):
TGCATCGATGTACATTCAAGGA
Found at i:49575 original size:45 final size:45
Alignment explanation
Indices: 49521--49608 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
49511 AAAATAGCCA
* * *
49521 GAGTGCATCGATGCATGGTTTGTGCATCGATGCATCAAATGCACT
1 GAGTACATCGATGCATGGTATGTGCATCGATGCATAAAATGCACT
49566 GAGTACATCGATGCATGGTATGTGCATCGATGCATAAAATGCA
1 GAGTACATCGATGCATGGTATGTGCATCGATGCATAAAATGCA
49609 TTCGATGTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.27
Consensus pattern (45 bp):
GAGTACATCGATGCATGGTATGTGCATCGATGCATAAAATGCACT
Found at i:52753 original size:44 final size:44
Alignment explanation
Indices: 52687--52812 Score: 198
Period size: 44 Copynumber: 2.9 Consensus size: 44
52677 AATCTGTCAG
* * *
52687 GAATTGTAATCCAATTCAATATTTTGTTTGGTTGGCAGGAAATA
1 GAATTGAAATCCAATTCCATATTATGTTTGGTTGGCAGGAAATA
*
52731 GAATTGGAATCCAATTCCATATTATGTTTGGTTGGCAGGAAATA
1 GAATTGAAATCCAATTCCATATTATGTTTGGTTGGCAGGAAATA
* *
52775 GAATTGAAATCTAATTCCATATTATGTTTGGTTCGCAG
1 GAATTGAAATCCAATTCCATATTATGTTTGGTTGGCAG
52813 ACATGTCAGA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 76 1.00
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.37
Consensus pattern (44 bp):
GAATTGAAATCCAATTCCATATTATGTTTGGTTGGCAGGAAATA
Found at i:57468 original size:36 final size:36
Alignment explanation
Indices: 57408--57508 Score: 141
Period size: 36 Copynumber: 2.8 Consensus size: 36
57398 GTGCGATACA
* *
57408 TCCTTCTGTTCG-CCTGAATCGGAAGTGTCAATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCAATGCT
* *
57443 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCAATGCT
* *
57479 TCCTTTCGTTCTACTTGAATCGGAAGTGTC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTC
57509 GACGCTTTCT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
35 11 0.19
36 47 0.81
ACGTcount: A:0.17, C:0.26, G:0.23, T:0.35
Consensus pattern (36 bp):
TCCTTCCGTTCGACTTGAATCGGAAGTGTCAATGCT
Found at i:57521 original size:36 final size:36
Alignment explanation
Indices: 57422--57521 Score: 146
Period size: 36 Copynumber: 2.8 Consensus size: 36
57412 TCTGTTCGCC
* *
57422 TGAATCGGAAGTGTCAATGCTTCCTTCCGTTCGACT
1 TGAATCGGAAGTGTCGATGCTTCCTTTCGTTCGACT
* *
57458 TGAATCGGAAGTGCCGATGCTTCCTTTCGTTCTACT
1 TGAATCGGAAGTGTCGATGCTTCCTTTCGTTCGACT
* *
57494 TGAATCGGAAGTGTCGACGCTTTCTTTC
1 TGAATCGGAAGTGTCGATGCTTCCTTTC
57522 ATTTTTCTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (36 bp):
TGAATCGGAAGTGTCGATGCTTCCTTTCGTTCGACT
Done.