Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008451.1 Hibiscus syriacus cultivar Beakdansim tig00111258_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: 76373
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:6223 original size:19 final size:18
Alignment explanation
Indices: 6199--6291 Score: 105
Period size: 19 Copynumber: 4.9 Consensus size: 18
6189 GGCTGCTGGA
6199 AACCGGTTTGACCGGTTT
1 AACCGGTTTGACCGGTTT
6217 CAACCGGTTCTGACCGGTTT
1 -AACCGGTT-TGACCGGTTT
*
6237 GACCGGTTCTGACCGGTTT
1 AACCGGTT-TGACCGGTTT
* * *
6256 GACCGGTTTCAACCGGTTCG
1 AACCGGTTT-GACCGGTT-T
6276 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
6292 CTGACCCGAC
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
18 1 0.02
19 47 0.71
20 18 0.27
ACGTcount: A:0.15, C:0.27, G:0.29, T:0.29
Consensus pattern (18 bp):
AACCGGTTTGACCGGTTT
Found at i:6242 original size:29 final size:28
Alignment explanation
Indices: 6200--6297 Score: 128
Period size: 29 Copynumber: 3.4 Consensus size: 28
6190 GCTGCTGGAA
6200 ACCGGTTTGACCGGTTTC-AACCGGTTCTG
1 ACCGGTTTGACCGG-TTCGAACCGGTT-TG
6229 ACCGGTTTGACCGGTTCTG-ACCGGTTTG
1 ACCGGTTTGACCGGTTC-GAACCGGTTTG
*
6257 ACCGGTTTCAACCGGTTCGAACCGGTTTG
1 ACCGGTTT-GACCGGTTCGAACCGGTTTG
*
6286 ACCGGTCTGACC
1 ACCGGTTTGACC
6298 CGACCCGACC
Statistics
Matches: 62, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
28 17 0.27
29 45 0.73
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.29
Consensus pattern (28 bp):
ACCGGTTTGACCGGTTCGAACCGGTTTG
Found at i:6271 original size:48 final size:47
Alignment explanation
Indices: 6200--6297 Score: 171
Period size: 48 Copynumber: 2.1 Consensus size: 47
6190 GCTGCTGGAA
6200 ACCGGTTTGACCGGTTTCAACCGGTTCTG-ACCGGTTTGACCGGTTCTG
1 ACCGGTTTGACCGGTTTCAACCGGTTC-GAACCGGTTTGACCGG-TCTG
6248 ACCGGTTTGACCGGTTTCAACCGGTTCGAACCGGTTTGACCGGTCTG
1 ACCGGTTTGACCGGTTTCAACCGGTTCGAACCGGTTTGACCGGTCTG
6295 ACC
1 ACC
6298 CGACCCGACC
Statistics
Matches: 49, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
47 8 0.16
48 41 0.84
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.29
Consensus pattern (47 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCGAACCGGTTTGACCGGTCTG
Found at i:6308 original size:48 final size:48
Alignment explanation
Indices: 6208--6308 Score: 134
Period size: 48 Copynumber: 2.1 Consensus size: 48
6198 AAACCGGTTT
****
6208 GACCGGTTTCAACCGGTTCTGACCGGTTTGACCGGTTCTGACCGGTTT
1 GACCGGTTTCAACCGGTTCTGACCGGTTTGACCGGTTCTGACCGACCC
6256 GACCGGTTTCAACCGGTTC-GAACCGGTTTGACCGG-TCTGACCCGACCC
1 GACCGGTTTCAACCGGTTCTG-ACCGGTTTGACCGGTTCTGA-CCGACCC
6304 GACCG
1 GACCG
6309 TTGACCCGAC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
47 6 0.13
48 41 0.87
ACGTcount: A:0.15, C:0.32, G:0.29, T:0.25
Consensus pattern (48 bp):
GACCGGTTTCAACCGGTTCTGACCGGTTTGACCGGTTCTGACCGACCC
Found at i:6315 original size:17 final size:17
Alignment explanation
Indices: 6293--6331 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
6283 TTGACCGGTC
6293 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
6310 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
6327 TGACC
1 TGACC
6332 GTTGACCGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:13701 original size:37 final size:36
Alignment explanation
Indices: 13660--13732 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 36
13650 TCATGCGTTG
* * * *
13660 TTATCCTGAGACTTCAAATTGTTCGAACTATATCCTT
1 TTATCCTGACAATGCAAATTGTTCGAACCATA-CCTT
*
13697 TTATCCTGACAATGCAAATTGTTTGAACCATACCTT
1 TTATCCTGACAATGCAAATTGTTCGAACCATACCTT
13733 GCTACCCTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
36 4 0.13
37 27 0.87
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (36 bp):
TTATCCTGACAATGCAAATTGTTCGAACCATACCTT
Found at i:15291 original size:19 final size:19
Alignment explanation
Indices: 15264--15311 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
15254 ACGATGCTTG
*
15264 GGTCATCACAAGGTACAAT
1 GGTCCTCACAAGGTACAAT
15283 GGTCCTCACAAGGTACAAT
1 GGTCCTCACAAGGTACAAT
*
15302 AGTCCTCACA
1 GGTCCTCACA
15312 TATGTTTACG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (19 bp):
GGTCCTCACAAGGTACAAT
Found at i:17443 original size:23 final size:23
Alignment explanation
Indices: 17417--17467 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
17407 TCAAAATTCA
17417 TTAATTACTTTTAATCAAAACAT
1 TTAATTACTTTTAATCAAAACAT
17440 TTAATTACTTTTAATCAAAACAT
1 TTAATTACTTTTAATCAAAACAT
17463 TTAAT
1 TTAAT
17468 AAAATTCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (23 bp):
TTAATTACTTTTAATCAAAACAT
Found at i:18764 original size:27 final size:28
Alignment explanation
Indices: 18718--18777 Score: 104
Period size: 27 Copynumber: 2.2 Consensus size: 28
18708 ATATTATTTG
18718 AAAATTATTCGAACCCTAATATATGAAT
1 AAAATTATTCGAACCCTAATATATGAAT
*
18746 AAAATT-TTTGAACCCTAATATATGAAT
1 AAAATTATTCGAACCCTAATATATGAAT
18773 AAAAT
1 AAAAT
18778 AAATTATTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 25 0.81
28 6 0.19
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (28 bp):
AAAATTATTCGAACCCTAATATATGAAT
Found at i:20699 original size:357 final size:358
Alignment explanation
Indices: 20044--20763 Score: 1327
Period size: 357 Copynumber: 2.0 Consensus size: 358
20034 TATTGATATA
*
20044 TATATTATTAATAAAAACATTGATGTGTATTATATAATAATACAATGTGACATGAACGTTAATTA
1 TATATTACTAATAAAAACATTGATGTGTATTATATAATAATACAATGTGACATGAACGTTAATTA
20109 TATTTATTTTAACACACATTGAAGTCATCATTTATAATAAAATTAAAATATTGTTTACTTTTATT
66 TATTTATTTTAACACACATTGAAGTCATCATTTATAATAAAATTAAAATATTGTTTACTTTTATT
20174 TTTTTTATCGATTTGTTTACAATTAATTCTACATTTGAAGGTTAATGATATTTTATTTAAACCTG
131 TTTTTTATCGATTTGTTTACAATTAATTCTACATTTGAAGGTTAATGATATTTTATTTAAACCTG
*
20239 ATATTAATTATCATGCATATCATTATATTATTATATAATATACATTATTATTTACATGAAAATTA
196 ATATTAATTATCATGCATATCATTATATTATTATATAATATACACTATTATTTACATGAAAATTA
* *
20304 ACAATTTCTATAACACTTCTATTAATATAAAATATGATTAATAGATACTAATAGTTTAGAGATGA
261 ACAATTTCTATAACACTTCTATCAATATAAAATATGATTAACAGATACTAATAGTTTAGAGATGA
20369 AATTAAAATATTT-AAAAAATTAAAGATTAATT
326 AATTAAAATATTTAAAAAAATTAAAGATTAATT
20401 TATATTACTAATAAAAACATTGATGTGTATTATATAATAATACAATGTGACATGAACGTTAATTA
1 TATATTACTAATAAAAACATTGATGTGTATTATATAATAATACAATGTGACATGAACGTTAATTA
*
20466 TCTTT-TTTTAACACACATTGAAGTCATCATTTATAATAAAATTAAAATATTGTTTACTTTTACT
66 TATTTATTTTAACACACATTGAAGTCATCATTTATAATAAAATTAAAATATTGTTTACTTTTA-T
20530 TTTTTTTATCGATTTGTTTACAATTAATTCTACATTTGAAGGTTAATGATATTTTATTTAAACCT
130 TTTTTTTATCGATTTGTTTACAATTAATTCTACATTTGAAGGTTAATGATATTTTATTTAAACCT
*
20595 GATATTAATTATCATGCATATCATTATATTATTATATAATATACACTATTATTTACATGAAAGTT
195 GATATTAATTATCATGCATATCATTATATTATTATATAATATACACTATTATTTACATGAAAATT
* * **
20660 AACAATTTCTATAACACTTCTCTCAATATAGAATATGATTAACATTTACTAATAGTTTAGAGATG
260 AACAATTTCTATAACACTTCTATCAATATAAAATATGATTAACAGATACTAATAGTTTAGAGATG
20725 AAATTAAAATATTTAAAAAAATTAAAGATTAATT
325 AAATTAAAATATTTAAAAAAATTAAAGATTAATT
20759 TATAT
1 TATAT
20764 CGAGAATTAT
Statistics
Matches: 351, Mismatches: 10, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
356 57 0.16
357 270 0.77
358 24 0.07
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.43
Consensus pattern (358 bp):
TATATTACTAATAAAAACATTGATGTGTATTATATAATAATACAATGTGACATGAACGTTAATTA
TATTTATTTTAACACACATTGAAGTCATCATTTATAATAAAATTAAAATATTGTTTACTTTTATT
TTTTTTATCGATTTGTTTACAATTAATTCTACATTTGAAGGTTAATGATATTTTATTTAAACCTG
ATATTAATTATCATGCATATCATTATATTATTATATAATATACACTATTATTTACATGAAAATTA
ACAATTTCTATAACACTTCTATCAATATAAAATATGATTAACAGATACTAATAGTTTAGAGATGA
AATTAAAATATTTAAAAAAATTAAAGATTAATT
Found at i:21873 original size:3 final size:3
Alignment explanation
Indices: 21865--21923 Score: 82
Period size: 3 Copynumber: 19.7 Consensus size: 3
21855 TGTCGACTTA
* * * *
21865 CCT CCT CCT CCT CCT CCC CCT CCT CCG CCC CCT CCT CCT CCT CCT CGT
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
21913 CCT CCT CCT CC
1 CCT CCT CCT CC
21924 CCGTCCTATA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.00, C:0.69, G:0.03, T:0.27
Consensus pattern (3 bp):
CCT
Found at i:24425 original size:17 final size:15
Alignment explanation
Indices: 24383--24433 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 15
24373 CGTTCAAAAG
24383 ATAAAATTAATAT-A
1 ATAAAATTAATATGA
* *
24397 ATTAAATGAATATGGGA
1 ATAAAATTAATAT--GA
24414 ATAAAATTAATATG-
1 ATAAAATTAATATGA
24428 ATAAAA
1 ATAAAA
24434 ATATAGATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 17 0.57
15 1 0.03
17 12 0.40
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.31
Consensus pattern (15 bp):
ATAAAATTAATATGA
Found at i:24443 original size:26 final size:29
Alignment explanation
Indices: 24381--24445 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 29
24371 ATCGTTCAAA
24381 AGATAAAATTAATATAATTAAATGAATATG
1 AGATAAAATTAATATAATTAAA-GAATATG
* *
24411 GGAATAAAATTAATATGA-TAAA-AATAT-
1 AG-ATAAAATTAATATAATTAAAGAATATG
24438 AGATAAAA
1 AGATAAAA
24446 CTTCTAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 6 0.19
27 1 0.03
28 5 0.16
30 5 0.16
31 14 0.45
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (29 bp):
AGATAAAATTAATATAATTAAAGAATATG
Found at i:25245 original size:43 final size:43
Alignment explanation
Indices: 25186--25395 Score: 201
Period size: 43 Copynumber: 4.9 Consensus size: 43
25176 TTGAGAATAA
* * * *
25186 AAACGCTGCAATAGGTCAAGATATATCGCGACGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCAAGATATATAGCGGCGTTTTTGGAAC
* * *
25229 AAACGCCGCAAAAGGTCGATATATATAGCGGCATTTTTGGAAC
1 AAACGCCGCAAAAGGTCAAGATATATAGCGGCGTTTTTGGAAC
* * * * * * *
25272 AAATGCCGAAAAAGATCGATATCTATAACGGCGTTTTTGGGAA-
1 AAACGCCGCAAAAGGTCAAGATATATAGCGGCGTTTTT-GGAAC
* * *
25315 AAACGCCACAAAAGAT-AAGATCTATAGCGGCGTTTTTTGGAAAC
1 AAACGCCGCAAAAGGTCAAGATATATAGCGGCG-TTTTTGG-AAC
* *
25359 AAACGCTGCAAAAGGTC-AGATTTATAGCGGCGTTTTT
1 AAACGCCGCAAAAGGTCAAGATATATAGCGGCGTTTTT
25396 TTATACAAAC
Statistics
Matches: 139, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
42 15 0.11
43 93 0.67
44 31 0.22
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCAAGATATATAGCGGCGTTTTTGGAAC
Found at i:25411 original size:43 final size:44
Alignment explanation
Indices: 25292--25416 Score: 130
Period size: 44 Copynumber: 2.9 Consensus size: 44
25282 AAAGATCGAT
* * * ** *
25292 ATCTATAACGGCG-TTTTTGGGAA-AAACGCCACAAAAGATAAG
1 ATCTATAGCGGCGTTTTTTGGAAACAAACACTGCAAAAGGTAAG
* *
25334 ATCTATAGCGGCGTTTTTTGGAAACAAACGCTGCAAAAGGTCAG
1 ATCTATAGCGGCGTTTTTTGGAAACAAACACTGCAAAAGGTAAG
* * *
25378 ATTTATAGCGGCGTTTTTT-TATACAAACACTGCAAAAGG
1 ATCTATAGCGGCGTTTTTTGGAAACAAACACTGCAAAAGG
25417 GCTCATGATA
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
42 12 0.17
43 26 0.37
44 33 0.46
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (44 bp):
ATCTATAGCGGCGTTTTTTGGAAACAAACACTGCAAAAGGTAAG
Found at i:25482 original size:3 final size:3
Alignment explanation
Indices: 25474--25518 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
25464 ACTAATATGA
25474 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
25519 CTCTAAGGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:28025 original size:41 final size:41
Alignment explanation
Indices: 27968--28162 Score: 205
Period size: 41 Copynumber: 4.7 Consensus size: 41
27958 TGTATGAGTT
* * * * *
27968 TATAGCGGCGTTTGTATATAAATGCCACTAAAGTATAAGTG
1 TATAGCGACGTTTGTATAAAAACGCCACTAAAGTACAAGTC
* *
28009 TATAGCGACGTTTGTATAAAAAAGTCACTAAAGTACAAGTC
1 TATAGCGACGTTTGTATAAAAACGCCACTAAAGTACAAGTC
*
28050 TATAGCGGA-GTTTGTATAAAAACGCCACTAAAGTACGAGTC
1 TATAGC-GACGTTTGTATAAAAACGCCACTAAAGTACAAGTC
* * * * *
28091 TTTAGCGGCGTTTGTATATAAACGCCACTAAAGTACTACTC
1 TATAGCGACGTTTGTATAAAAACGCCACTAAAGTACAAGTC
* * *
28132 TATTGCGGCGTTT-TTTGAAAAAACGCCACTA
1 TATAGCGACGTTTGTAT--AAAAACGCCACTA
28163 TGGATGAACC
Statistics
Matches: 132, Mismatches: 18, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
40 3 0.02
41 115 0.87
42 14 0.11
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (41 bp):
TATAGCGACGTTTGTATAAAAACGCCACTAAAGTACAAGTC
Found at i:28105 original size:82 final size:82
Alignment explanation
Indices: 27968--28162 Score: 230
Period size: 82 Copynumber: 2.4 Consensus size: 82
27958 TGTATGAGTT
* * * *
27968 TATAGCGGCGTTTGTATATAAATGCCACTAAAGTATAAGTGTATAGCGACGTTTGTATAAAAAAG
1 TATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATAGCGACGTTTGTATAAAAAAG
* *
28033 TCACTAAAGTACAAGTC
66 CCACTAAAGTACAACTC
* * * * * *
28050 TATAGCGGAGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATATAAACG
1 TATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATAGCGACGTTTGTATAAAAAAG
*
28115 CCACTAAAGTACTACTC
66 CCACTAAAGTACAACTC
* *
28132 TATTGCGGCGTTT-TTTGAAAAAACGCCACTA
1 TATAGCGGCGTTTGTAT--AAAAACGCCACTA
28163 TGGATGAACC
Statistics
Matches: 95, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 2 0.02
82 80 0.84
83 13 0.14
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (82 bp):
TATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATAGCGACGTTTGTATAAAAAAG
CCACTAAAGTACAACTC
Found at i:33601 original size:148 final size:148
Alignment explanation
Indices: 33317--33664 Score: 432
Period size: 148 Copynumber: 2.3 Consensus size: 148
33307 TTGACCTTTT
* * * * * * *
33317 ACTGAAAAGTTGTTGGCATTTT-TTGCCATCTTGCATTATTAATGACCCATTTTGAAGAGTATTA
1 ACTGAAAAGTTGCTGACATTTTCTAG-CATCATGCATTATTAATGGCCCGTTCTGAAGAGTATTA
* * * * * * *
33381 ATGGTCATTTTTTTACATTTTCGGGCTTGGTGCATTATTAGAGATGATATTTCATTGAAAAGTTG
65 ATGCTCA-GTTTTGACATTTTCGGGCATAGTGCATTATTAGAGATGATATTTCACTGAAAAGTTA
* *
33446 TTGAAGATGATTAATGGGGC
129 CTAAAGATGATTAATGGGGC
* *
33466 ACTGAAAAGGTGCTGACATTTTCTAGCATCATGCATTATTAATGGTCCGTTCTGAAGAGTATTAA
1 ACTGAAAAGTTGCTGACATTTTCTAGCATCATGCATTATTAATGGCCCGTTCTGAAGAGTATTAA
*
33531 TGACTC-GTTTTGACATTTTCGGGCATAGTGTATTATTAGAGATGATATTTCACTGAAAAGTTAC
66 TG-CTCAGTTTTGACATTTTCGGGCATAGTGCATTATTAGAGATGATATTTCACTGAAAAGTTAC
*
33595 TAAAGATGATTGATGGGGC
130 TAAAGATGATTAATGGGGC
* * *
33614 ACTGAAAAGTTACTGGA-ATTTTCTGGCATCCTGCATTATTAATGGCCCGTT
1 ACTGAAAAGTTGCT-GACATTTTCTAGCATCATGCATTATTAATGGCCCGTT
33665 TTGACATTTT
Statistics
Matches: 171, Mismatches: 25, Indels: 7
0.84 0.12 0.03
Matches are distributed among these distances:
148 110 0.64
149 57 0.33
150 4 0.02
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.38
Consensus pattern (148 bp):
ACTGAAAAGTTGCTGACATTTTCTAGCATCATGCATTATTAATGGCCCGTTCTGAAGAGTATTAA
TGCTCAGTTTTGACATTTTCGGGCATAGTGCATTATTAGAGATGATATTTCACTGAAAAGTTACT
AAAGATGATTAATGGGGC
Found at i:33760 original size:125 final size:125
Alignment explanation
Indices: 33525--33786 Score: 357
Period size: 125 Copynumber: 2.1 Consensus size: 125
33515 TTCTGAAGAG
* * *
33525 TATTAATGACTCGTTTTGACATTTTCGGGCATAGTGTATTATTAGAGATGATATTTCACTGAAAA
1 TATTAATGGCCCGTTTTGACATTTTCGGGCATAGTGCATTATTAGAGATGATATTTCACTGAAAA
* * * *
33590 GTTACTAAAGATGATTGATGGGGCACTGAAAAGTTACTGGAATTTTCTGGCATCCTGCAT
66 GTTACTAAAGATGATTGATGGGGCACCGAAAAGTTACTAGAATTTTATGGCATCCTACAT
*
33650 TATTAATGGCCCGTTTTGACATTTTCGGGCATTGTGCATTATTAGAGATGATATTTCACTGAAAC
1 TATTAATGGCCCGTTTTGACATTTTCGGGCATAGTGCATTATTAGAGATGATATTTCACTGAAA-
** * * ** *
33715 A-TTTTTGAAGATGATTGATGGGGCACCGAAAA-TCTGCTATCATTTTATGGTATCCTACAT
65 AGTTACTAAAGATGATTGATGGGGCACCGAAAAGT-TACTAGAATTTTATGGCATCCTACAT
33775 TATTAATGGCCC
1 TATTAATGGCCC
33787 ATTCTGAAGA
Statistics
Matches: 120, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
124 1 0.01
125 118 0.98
126 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.37
Consensus pattern (125 bp):
TATTAATGGCCCGTTTTGACATTTTCGGGCATAGTGCATTATTAGAGATGATATTTCACTGAAAA
GTTACTAAAGATGATTGATGGGGCACCGAAAAGTTACTAGAATTTTATGGCATCCTACAT
Found at i:33890 original size:14 final size:14
Alignment explanation
Indices: 33871--33897 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
33861 TATCTTCAGC
33871 AAAAAACCTTTCTA
1 AAAAAACCTTTCTA
33885 AAAAAACCTTTCT
1 AAAAAACCTTTCT
33898 GAAGCTATGG
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:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAAAACCTTTCTA
Found at i:37883 original size:26 final size:26
Alignment explanation
Indices: 37853--37915 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
37843 ATTTAATTTT
*
37853 TTATATTTAAATTTA-TAAAATAATT
1 TTATATTTAAATTTATTAAAATAATG
* *
37878 TATATATTTTAA-TTATTCAAATAATG
1 T-TATATTTAAATTTATTAAAATAATG
37904 TTAT-TTTAAATT
1 TTATATTTAAATT
37916 AACTAGAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
24 5 0.16
25 8 0.26
26 18 0.58
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (26 bp):
TTATATTTAAATTTATTAAAATAATG
Found at i:38514 original size:34 final size:34
Alignment explanation
Indices: 38476--38541 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
38466 CTACATCACA
* *
38476 TATTCTAACACCATTAAATATTGCAACAAAATGC
1 TATTCTAACACAAGTAAATATTGCAACAAAATGC
38510 TATTCTAACACAAGTAAATATTGCAACAAAAT
1 TATTCTAACACAAGTAAATATTGCAACAAAAT
38542 ACAATCTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.47, C:0.18, G:0.06, T:0.29
Consensus pattern (34 bp):
TATTCTAACACAAGTAAATATTGCAACAAAATGC
Found at i:39384 original size:71 final size:74
Alignment explanation
Indices: 39198--39387 Score: 244
Period size: 76 Copynumber: 2.6 Consensus size: 74
39188 TTTTATCTTT
* * * * * *
39198 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGTATATTATTTTTATATTTTAT
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTAGTTTTAAATATTA-
39263 CTTTGTTTTAG
65 -TTTGTTTTAG
*
39274 GTATTTTAATTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATT-GTTTTAAATATTA-
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTAGTTTTAAATATTAT
39337 TT-TTTTAG
66 TTGTTTTAG
* *
39345 GTATTTTAGTTTAAATA-TTTTTAAGTGTTTTAATTAGGATTTA
1 GTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAGGATTTA
39388 AGATGTTTTA
Statistics
Matches: 103, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
70 4 0.04
71 41 0.40
72 2 0.02
75 10 0.10
76 46 0.45
ACGTcount: A:0.29, C:0.01, G:0.13, T:0.57
Consensus pattern (74 bp):
GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTAGTTTTAAATATTAT
TTGTTTTAG
Found at i:40018 original size:18 final size:19
Alignment explanation
Indices: 39979--40022 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
39969 CTTTAATTTG
* *
39979 TTTATTTAATTATTTTTCT
1 TTTATTTAATTACTTGTCT
39998 TTTATTTAATT-CTTGTCT
1 TTTATTTAATTACTTGTCT
40016 TTTATTT
1 TTTATTT
40023 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTATTTAATTACTTGTCT
Found at i:43023 original size:14 final size:15
Alignment explanation
Indices: 42998--43044 Score: 62
Period size: 14 Copynumber: 3.2 Consensus size: 15
42988 ACCCATTTGG
42998 TTTCATTTTCATTTTA
1 TTTCA-TTTCATTTTA
*
43014 TTT-ATTTCATTTCA
1 TTTCATTTCATTTTA
43028 TTTCATTT-ATTTTA
1 TTTCATTTCATTTTA
43042 TTT
1 TTT
43045 TAACATATGC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 20 0.71
15 5 0.18
16 3 0.11
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTCATTTCATTTTA
Found at i:43025 original size:5 final size:5
Alignment explanation
Indices: 42998--43044 Score: 53
Period size: 5 Copynumber: 9.6 Consensus size: 5
42988 ACCCATTTGG
* *
42998 TTTCA TTTTCA TTTTA TTT-A TTTCA TTTCA TTTCA TTT-A TTTTA TTT
1 TTTCA -TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTT
43045 TAACATATGC
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
4 8 0.21
5 25 0.66
6 5 0.13
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (5 bp):
TTTCA
Found at i:43028 original size:19 final size:19
Alignment explanation
Indices: 42998--43044 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
42988 ACCCATTTGG
*
42998 TTTCATTTTCATTTTATTTA
1 TTTCA-TTTCATTTCATTTA
43018 TTTCATTTCATTTCATTTA
1 TTTCATTTCATTTCATTTA
*
43037 TTTTATTT
1 TTTCATTT
43045 TAACATATGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTCATTTCATTTCATTTA
Found at i:45537 original size:18 final size:19
Alignment explanation
Indices: 45498--45541 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
45488 CTTTAATTTG
* *
45498 TTTATTTAATTATTTTTCT
1 TTTATTTAATTACTTATCT
45517 TTTATTTAATT-CTTATCT
1 TTTATTTAATTACTTATCT
45535 TTTATTT
1 TTTATTT
45542 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTATTTAATTACTTATCT
Found at i:45603 original size:8 final size:8
Alignment explanation
Indices: 45590--45624 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
45580 CCTATTACTA
45590 TTTATTAT
1 TTTATTAT
45598 TTTATTAT
1 TTTATTAT
*
45606 TTTCTT-T
1 TTTATTAT
45613 TTTATTAT
1 TTTATTAT
45621 TTTA
1 TTTA
45625 ATATACTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 6 0.25
8 18 0.75
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTATTAT
Found at i:46317 original size:19 final size:20
Alignment explanation
Indices: 46293--46347 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
46283 TCTCTAGCTC
46293 AAATGATCGATCCTTAGA-A
1 AAATGATCGATCCTTAGACA
* *
46312 AAATGATCGATCTCTTTGACC
1 AAATGATCGATC-CTTAGACA
*
46333 AAAGGATCGATCCTT
1 AAATGATCGATCCTT
46348 TGGACAACAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.39
20 8 0.26
21 11 0.35
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (20 bp):
AAATGATCGATCCTTAGACA
Found at i:46770 original size:36 final size:36
Alignment explanation
Indices: 46727--46802 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
46717 TTTTTAGAGT
*
46727 TTTTCTTGTTTACAATACTTTTCCTTTGTAAAGGGG
1 TTTTCTTGTTTACAATACTTTTCCTTTGTAAAGGGA
46763 TTTTCTTGTTTACAATACTTTTCCTTTGTAAAGGGA
1 TTTTCTTGTTTACAATACTTTTCCTTTGTAAAGGGA
46799 TTTT
1 TTTT
46803 GGTTCTAGCT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.20, C:0.13, G:0.14, T:0.53
Consensus pattern (36 bp):
TTTTCTTGTTTACAATACTTTTCCTTTGTAAAGGGA
Found at i:46784 original size:18 final size:18
Alignment explanation
Indices: 46727--46785 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
46717 TTTTTAGAGT
46727 TTTTCTTGTTTACAATAC
1 TTTTCTTGTTTACAATAC
* ***
46745 TTTTCCTT-TGTA-AAGGGG
1 TTTT-CTTGTTTACAA-TAC
46763 TTTTCTTGTTTACAATAC
1 TTTTCTTGTTTACAATAC
46781 TTTTC
1 TTTTC
46786 CTTTGTAAAG
Statistics
Matches: 29, Mismatches: 8, Indels: 8
0.64 0.18 0.18
Matches are distributed among these distances:
17 5 0.17
18 19 0.66
19 5 0.17
ACGTcount: A:0.19, C:0.15, G:0.12, T:0.54
Consensus pattern (18 bp):
TTTTCTTGTTTACAATAC
Found at i:48237 original size:21 final size:21
Alignment explanation
Indices: 48208--48266 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
48198 CAAGCTTCTC
* *
48208 TGACTCAAAGGATCGATCCCTT
1 TGAC-CAAATGATCGATCCCCT
*
48230 TGACCAAATGATCAATCCCCT
1 TGACCAAATGATCGATCCCCT
*
48251 TGA-AAAATGATCGATC
1 TGACCAAATGATCGATC
48267 TCTTGGACAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 11 0.34
21 17 0.53
22 4 0.12
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.25
Consensus pattern (21 bp):
TGACCAAATGATCGATCCCCT
Found at i:48383 original size:20 final size:21
Alignment explanation
Indices: 48360--48400 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
48350 CAGTCGAAAT
48360 ATTT-GAAAAATGATCGATCC
1 ATTTGGAAAAATGATCGATCC
*
48380 ATTTGGTAAAATGATCGATCC
1 ATTTGGAAAAATGATCGATCC
48401 CTTGTGCCTT
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:0.15, G:0.17, T:0.32
Consensus pattern (21 bp):
ATTTGGAAAAATGATCGATCC
Found at i:49424 original size:53 final size:53
Alignment explanation
Indices: 49344--49478 Score: 173
Period size: 53 Copynumber: 2.5 Consensus size: 53
49334 TATATACTAG
* * * * ** *
49344 TGTAAGTTTGTACATATCTCAATATCTTAGAAATTGACATGTACTTACA-CTGT
1 TGTAAGTATGTATATCTCTCAATATCTTAGAAATTAACACATACTTACATC-GA
*
49397 TGTAAGTATGTATATCTCTCAATATCTTAGCAATTAACACATACTTACATCGA
1 TGTAAGTATGTATATCTCTCAATATCTTAGAAATTAACACATACTTACATCGA
*
49450 TGTAAGTATTTATATCTCTCAATATCTTA
1 TGTAAGTATGTATATCTCTCAATATCTTA
49479 ATACCTAAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
53 71 0.99
54 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.40
Consensus pattern (53 bp):
TGTAAGTATGTATATCTCTCAATATCTTAGAAATTAACACATACTTACATCGA
Found at i:50165 original size:28 final size:28
Alignment explanation
Indices: 50133--50189 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
50123 GTCTCTGTTT
* *
50133 ACATTAAATCATCGAACTAGTGCTTGAA
1 ACATTAAATCAGCGAACCAGTGCTTGAA
* * *
50161 ACATTATATCGGCGAGCCAGTGCTTGAA
1 ACATTAAATCAGCGAACCAGTGCTTGAA
50189 A
1 A
50190 ATGATGATTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (28 bp):
ACATTAAATCAGCGAACCAGTGCTTGAA
Found at i:60412 original size:42 final size:43
Alignment explanation
Indices: 60316--60413 Score: 110
Period size: 42 Copynumber: 2.3 Consensus size: 43
60306 CACAACTGTA
* * *
60316 TCAGATGACACCG-TAGCCATTTCAGATGCCACCGTAGTTAGG
1 TCAGATGACACCGCTAGCCATATCAAATGCCACCGTAGATAGG
* * * * *
60358 TTAGACGCCACCGCT-TCCATATCAAATGCCATCGTAGATAGG
1 TCAGATGACACCGCTAGCCATATCAAATGCCACCGTAGATAGG
60400 TCAGATGACACCGC
1 TCAGATGACACCGC
60414 AGCTGGTTCA
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
42 43 0.98
43 1 0.02
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (43 bp):
TCAGATGACACCGCTAGCCATATCAAATGCCACCGTAGATAGG
Found at i:66565 original size:19 final size:18
Alignment explanation
Indices: 66534--66569 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
66524 TTTCACTAAT
*
66534 AGAGGAAATATTACAAAG
1 AGAGGAAAGATTACAAAG
66552 AGAGAGAAAGATTACAAA
1 AGAG-GAAAGATTACAAA
66570 TACCTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.58, C:0.06, G:0.22, T:0.14
Consensus pattern (18 bp):
AGAGGAAAGATTACAAAG
Found at i:70345 original size:24 final size:25
Alignment explanation
Indices: 70303--70357 Score: 103
Period size: 24 Copynumber: 2.2 Consensus size: 25
70293 GAGCCAGATC
70303 TTCATCTTCAAAAGTCACGTCCATA
1 TTCATCTTCAAAAGTCACGTCCATA
70328 TTCATCTTC-AAAGTCACGTCCATA
1 TTCATCTTCAAAAGTCACGTCCATA
70352 TTCATC
1 TTCATC
70358 AGATCAGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 21 0.70
25 9 0.30
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.35
Consensus pattern (25 bp):
TTCATCTTCAAAAGTCACGTCCATA
Found at i:72324 original size:22 final size:24
Alignment explanation
Indices: 72297--72342 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
72287 TAAATCACAT
72297 AATTAAAAGAAAAAT-T-ATTAAA
1 AATTAAAAGAAAAATATAATTAAA
*
72319 AATTAAAATAAAAATATAATTAAA
1 AATTAAAAGAAAAATATAATTAAA
72343 TTTCAAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
23 1 0.05
24 6 0.29
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (24 bp):
AATTAAAAGAAAAATATAATTAAA
Found at i:72426 original size:39 final size:39
Alignment explanation
Indices: 72383--72462 Score: 108
Period size: 39 Copynumber: 2.1 Consensus size: 39
72373 TTTAAAAAAT
* * *
72383 AATTTAGAATGTTCATGTGAA-ATAATTTAAAAAATTAAG
1 AATTTAAAATGTT-ATGTCAATAAAATTTAAAAAATTAAG
*
72422 AATTTAAAATGTTATGTCAATAAAATTTAAGAAATTAAG
1 AATTTAAAATGTTATGTCAATAAAATTTAAAAAATTAAG
72461 AA
1 AA
72463 CTTTGGTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
38 6 0.17
39 30 0.83
ACGTcount: A:0.51, C:0.03, G:0.11, T:0.35
Consensus pattern (39 bp):
AATTTAAAATGTTATGTCAATAAAATTTAAAAAATTAAG
Done.