Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001018.1 Hibiscus syriacus cultivar Beakdansim tig00002030_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: 69943
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:7347 original size:14 final size:16
Alignment explanation
Indices: 7328--7365 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
7318 TTAGATTCTA
7328 TAAATATATTT-AT-T
1 TAAATATATTTAATAT
7342 TAAATAATATTTAATAT
1 TAAAT-ATATTTAATAT
7359 TAAATAT
1 TAAATAT
7366 TTTTCCTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.24
15 6 0.29
16 4 0.19
17 6 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAATATATTTAATAT
Found at i:13646 original size:24 final size:24
Alignment explanation
Indices: 13617--13720 Score: 109
Period size: 24 Copynumber: 4.3 Consensus size: 24
13607 GAGATATTGA
*
13617 AAATCAAAACATAATTCAGATCAG
1 AAATCAAAACAGAATTCAGATCAG
* * * *
13641 ATATCATAACAGAATTCAGATAAA
1 AAATCAAAACAGAATTCAGATCAG
* * * *
13665 AAACCAGAACAGAACTCAGATTAG
1 AAATCAAAACAGAATTCAGATCAG
* *
13689 AAATCAGAACAGAATTCAAATCAG
1 AAATCAAAACAGAATTCAGATCAG
13713 AAATCAAA
1 AAATCAAA
13721 TAAAACATTC
Statistics
Matches: 64, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 64 1.00
ACGTcount: A:0.55, C:0.16, G:0.11, T:0.18
Consensus pattern (24 bp):
AAATCAAAACAGAATTCAGATCAG
Found at i:13684 original size:12 final size:12
Alignment explanation
Indices: 13617--13718 Score: 55
Period size: 12 Copynumber: 8.5 Consensus size: 12
13607 GAGATATTGA
* *
13617 AAATCAAAACAT
1 AAATCAGAACAG
* *
13629 AATTCAGATCAG
1 AAATCAGAACAG
* *
13641 ATATCATAACAG
1 AAATCAGAACAG
* *
13653 AATTCAGATA-AA
1 AAATCAGA-ACAG
*
13665 AAACCAGAACAG
1 AAATCAGAACAG
* **
13677 AACTCAGATTAG
1 AAATCAGAACAG
13689 AAATCAGAACAG
1 AAATCAGAACAG
*
13701 AATTCA-AATCAG
1 AAATCAGAA-CAG
13713 AAATCA
1 AAATCA
13719 AATAAAACAT
Statistics
Matches: 63, Mismatches: 24, Indels: 6
0.68 0.26 0.06
Matches are distributed among these distances:
11 3 0.05
12 59 0.94
13 1 0.02
ACGTcount: A:0.54, C:0.17, G:0.11, T:0.19
Consensus pattern (12 bp):
AAATCAGAACAG
Found at i:14631 original size:31 final size:31
Alignment explanation
Indices: 14593--14664 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
14583 CAACATCCAT
* *
14593 ATTTACTTGGATTCCTTAATTAATCTAAAAC
1 ATTTACTTAGATTCCTTAATTAATCCAAAAC
14624 ATTTACTTAGATTCCTTAATTAATCCAAAAC
1 ATTTACTTAGATTCCTTAATTAATCCAAAAC
14655 ATTTACTTAG
1 ATTTACTTAG
14665 TCTAGTCCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.42
Consensus pattern (31 bp):
ATTTACTTAGATTCCTTAATTAATCCAAAAC
Found at i:21149 original size:20 final size:20
Alignment explanation
Indices: 21124--21161 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21114 TTTTGGTGCA
*
21124 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
*
21144 GAGGGAACCGATTCCCCC
1 GAGGGAACCGATACCCCC
21162 TTTGAAGGGG
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:0.26, C:0.34, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:23349 original size:17 final size:17
Alignment explanation
Indices: 23327--23461 Score: 112
Period size: 17 Copynumber: 8.0 Consensus size: 17
23317 CTACTGTATC
23327 ATTTCTTTTATTATATT
1 ATTTCTTTTATTATATT
* * *
23344 ATTTC-TCTATTGTATC
1 ATTTCTTTTATTATATT
*
23360 ATTTCTTTTATTATACT
1 ATTTCTTTTATTATATT
* * * *
23377 ATTTCTCTTACTGTATC
1 ATTTCTTTTATTATATT
23394 ATTTCTTTTATTATATT
1 ATTTCTTTTATTATATT
* *
23411 ATTTCTCTTATTATACT
1 ATTTCTTTTATTATATT
* * *
23428 GTATCTTTTACTAT-TCT
1 ATTTCTTTTATTATAT-T
* *
23445 ATATCTTTTATTGTATT
1 ATTTCTTTTATTATATT
23462 GCCTCTTTTC
Statistics
Matches: 89, Mismatches: 26, Indels: 6
0.74 0.21 0.05
Matches are distributed among these distances:
16 13 0.15
17 75 0.84
18 1 0.01
ACGTcount: A:0.21, C:0.13, G:0.03, T:0.62
Consensus pattern (17 bp):
ATTTCTTTTATTATATT
Found at i:23420 original size:34 final size:33
Alignment explanation
Indices: 23299--23418 Score: 195
Period size: 33 Copynumber: 3.6 Consensus size: 33
23289 TGTACTGTTA
*
23299 TTTTATTATACTGTTTCTCTACTGTATCATTTC
1 TTTTATTATACTATTTCTCTACTGTATCATTTC
* *
23332 TTTTATTATATTATTTCTCTATTGTATCATTTC
1 TTTTATTATACTATTTCTCTACTGTATCATTTC
23365 TTTTATTATACTATTTCTCTTACTGTATCATTTC
1 TTTTATTATACTATTTCTC-TACTGTATCATTTC
*
23399 TTTTATTATATTATTTCTCT
1 TTTTATTATACTATTTCTCT
23419 TATTATACTG
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
33 49 0.61
34 31 0.39
ACGTcount: A:0.20, C:0.15, G:0.03, T:0.62
Consensus pattern (33 bp):
TTTTATTATACTATTTCTCTACTGTATCATTTC
Found at i:23439 original size:51 final size:51
Alignment explanation
Indices: 23351--23461 Score: 134
Period size: 51 Copynumber: 2.2 Consensus size: 51
23341 ATTATTTCTC
* * * * *
23351 TATTGTATCATTTCTTTTATTATACTATTTCTCTTACTGTATC-ATTTCTTT
1 TATTGTATTATTTCTCTTATTATACTATATCTCTTACTAT-TCTATATCTTT
* * *
23402 TATTATATTATTTCTCTTATTATACTGTATCTTTTACTATTCTATATCTTT
1 TATTGTATTATTTCTCTTATTATACTATATCTCTTACTATTCTATATCTTT
23453 TATTGTATT
1 TATTGTATT
23462 GCCTCTTTTC
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
50 2 0.04
51 48 0.96
ACGTcount: A:0.22, C:0.14, G:0.04, T:0.61
Consensus pattern (51 bp):
TATTGTATTATTTCTCTTATTATACTATATCTCTTACTATTCTATATCTTT
Found at i:23456 original size:34 final size:34
Alignment explanation
Indices: 23397--23488 Score: 94
Period size: 34 Copynumber: 2.7 Consensus size: 34
23387 CTGTATCATT
* * * * *
23397 TCTTTTATTATATTATTTCTCTTATTATACTGTA
1 TCTTTTACTATACTATATCTTTTATTATACTGCA
* * * *
23431 TCTTTTACTATTCTATATCTTTTATTGTATTGCC
1 TCTTTTACTATACTATATCTTTTATTATACTGCA
*
23465 TCTTTTCCTATACTATATCTTTTA
1 TCTTTTACTATACTATATCTTTTA
23489 CTTTTGTTTT
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.21, C:0.16, G:0.03, T:0.60
Consensus pattern (34 bp):
TCTTTTACTATACTATATCTTTTATTATACTGCA
Found at i:25381 original size:11 final size:11
Alignment explanation
Indices: 25362--25402 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
25352 CCAAAGTATC
*
25362 GAAATTTTAGG
1 GAAAGTTTAGG
25373 GAAAGTTTA--
1 GAAAGTTTAGG
*
25382 GAAACTTTAGG
1 GAAAGTTTAGG
25393 GAAAGTTTAG
1 GAAAGTTTAG
25403 AAACTTTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
9 8 0.32
11 17 0.68
ACGTcount: A:0.39, C:0.02, G:0.27, T:0.32
Consensus pattern (11 bp):
GAAAGTTTAGG
Found at i:25385 original size:20 final size:20
Alignment explanation
Indices: 25362--25410 Score: 80
Period size: 20 Copynumber: 2.4 Consensus size: 20
25352 CCAAAGTATC
25362 GAAATTTTAGGGAAAGTTTA
1 GAAATTTTAGGGAAAGTTTA
*
25382 GAAACTTTAGGGAAAGTTTA
1 GAAATTTTAGGGAAAGTTTA
25402 GAAACTTTT
1 GAAA-TTTT
25411 GATATAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (20 bp):
GAAATTTTAGGGAAAGTTTA
Found at i:25419 original size:20 final size:20
Alignment explanation
Indices: 25373--25449 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 20
25363 AAATTTTAGG
* *
25373 GAAAGTTTAGAAACTTTAGG
1 GAAAGTTTAGAAACTTTTGA
25393 GAAAGTTTAGAAACTTTTGA
1 GAAAGTTTAGAAACTTTTGA
* * * *
25413 TATAGTTTCGAAACTCTTGA
1 GAAAGTTTAGAAACTTTTGA
* *
25433 -AAAGTATCGAAACTTTT
1 GAAAGTTTAGAAACTTTT
25450 TGGATTATTG
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
19 14 0.29
20 34 0.71
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (20 bp):
GAAAGTTTAGAAACTTTTGA
Found at i:25515 original size:21 final size:21
Alignment explanation
Indices: 25466--25534 Score: 88
Period size: 21 Copynumber: 3.3 Consensus size: 21
25456 ATTGTCTTGG
* *
25466 AAAGTTTCGAAA-TTCTTAT-
1 AAAGCTTCGAAACTTCTTGTC
*
25485 ATAAGTTTCGAAACTTCTTGTC
1 A-AAGCTTCGAAACTTCTTGTC
25507 AAAGCTTCGAAACTTCTTGTC
1 AAAGCTTCGAAACTTCTTGTC
25528 AAAGCTT
1 AAAGCTT
25535 GTTTAAAAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.02
20 11 0.24
21 32 0.71
22 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (21 bp):
AAAGCTTCGAAACTTCTTGTC
Found at i:28329 original size:21 final size:20
Alignment explanation
Indices: 28265--28335 Score: 108
Period size: 20 Copynumber: 3.5 Consensus size: 20
28255 TTTACTACTG
28265 TCTTG-AAAAGTTTCGAAAT
1 TCTTGTAAAAGTTTCGAAAT
28284 TCTTGTAAAAGTTTCGAAAT
1 TCTTGTAAAAGTTTCGAAAT
*
28304 TCTTGTAAAAGTTTCAAAACT
1 TCTTGTAAAAGTTTCGAAA-T
28325 TCTTGTCAAAA
1 TCTTGT-AAAA
28336 CTTGTTTAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
19 5 0.10
20 32 0.67
21 7 0.15
22 4 0.08
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.38
Consensus pattern (20 bp):
TCTTGTAAAAGTTTCGAAAT
Found at i:29003 original size:31 final size:31
Alignment explanation
Indices: 28965--29025 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
28955 TTAGATCTCA
*
28965 ACCATCACACAAAAGAACACATGATGAGTAT
1 ACCATCACACAAAAGAACAAATGATGAGTAT
28996 ACCATCACACAAAAGAACAAATGATGAGTA
1 ACCATCACACAAAAGAACAAATGATGAGTA
29026 GTTGATGCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.51, C:0.21, G:0.13, T:0.15
Consensus pattern (31 bp):
ACCATCACACAAAAGAACAAATGATGAGTAT
Found at i:30738 original size:3 final size:3
Alignment explanation
Indices: 30730--30773 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
30720 TGTGAGACCA
30730 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
30774 AACCCAATTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:33176 original size:2 final size:2
Alignment explanation
Indices: 33169--33194 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
33159 GCTTGTTGCC
33169 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
33195 GGGTTAGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37460 original size:22 final size:22
Alignment explanation
Indices: 37427--37468 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
37417 ACTGAAAGGG
37427 AGTATCAGTACCATAATATAGA
1 AGTATCAGTACCATAATATAGA
37449 AGTATC-GATACCATAATATA
1 AGTATCAG-TACCATAATATA
37469 TAAAATGAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (22 bp):
AGTATCAGTACCATAATATAGA
Found at i:37663 original size:49 final size:50
Alignment explanation
Indices: 37608--37709 Score: 134
Period size: 49 Copynumber: 2.1 Consensus size: 50
37598 TCTAAAATGA
* ** * *
37608 ACTAATGATAGTTAAATGCATAATTGTGCA-TTTCGGCATTAAAGGTGCC
1 ACTAATGAAAGTTAAATGCATAACAGTGCATTTTCGGCATAAAAGGTACC
**
37657 ACTAATGAAAGTTAGGTGCATAACAGTGCATTTTCGGCATAAAAGGTACC
1 ACTAATGAAAGTTAAATGCATAACAGTGCATTTTCGGCATAAAAGGTACC
37707 ACT
1 ACT
37710 CATGGTATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
49 25 0.56
50 20 0.44
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (50 bp):
ACTAATGAAAGTTAAATGCATAACAGTGCATTTTCGGCATAAAAGGTACC
Found at i:43191 original size:16 final size:17
Alignment explanation
Indices: 43170--43201 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
43160 ATTGTATTGA
43170 AAGGATTTAA-AATTTG
1 AAGGATTTAAGAATTTG
43186 AAGGATTTAAGAATTT
1 AAGGATTTAAGAATTT
43202 TTTTAAGACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.38
Consensus pattern (17 bp):
AAGGATTTAAGAATTTG
Found at i:44810 original size:579 final size:578
Alignment explanation
Indices: 43698--44855 Score: 2111
Period size: 579 Copynumber: 2.0 Consensus size: 578
43688 GAGATCAGAT
43698 GGAGAATGCTTCTTCCCAAACCCTACCCCTCCAAAATCCAATCGAAAACACCCAAAATCATCTAA
1 GGAGAATGCTTCTTCCCAAACCCTACCCCTCCAAAATCCAATCGAAAACACCCAAAATCATCTAA
* * *
43763 GGAGGACCAATTGGCTCTCTTCAAAGGGGTCAGTACTCTTTCTCGTCTTTTTAATTTGATGGTAT
66 GGAGGACCAATTGGCTCGCTTCAAAGGGGTCAATACTCTTTCTCGTCTTTTTAATTTGATGATAT
*
43828 TTCAACGAAATACTGGAAATTCTTTGGTGTCCTGACTTTGCTTGGAGAAAACCGCAACATTGTGG
131 TTCAACGAAATACTGGAAATTATTTGGTGTCCTGACTTTGCTTGGAGAAAACCGCAACATTGTGG
* *
43893 AGATAAACAAAAAAATATGAGTTGTTTCCCTTTCTTTAATCCTCATTCTAAAGATTCAAGGATCG
196 AGATAAACAAAAAAAGATGAGTTGTTTCCCTTGCTTTAATCCTCATTCTAAAGATTCAAGGATCG
* *
43958 ACATTGACAATGAAAGTCAAACCACTTCTCGCCATTCTGCTGATTCCTCAGGTTTCCTTTTCATT
261 ACATTGACAATGAAAGTCAAACCACTTATCGCCATTCCGCTGATTCCTCAGGTTTCCTTTTCATT
*
44023 TCCCTTTTTCTCATTACTTTTCCATACAATCTTGCTTATCTATAAAATCTTTCTTCATTTTTGTA
326 TCCCTTTTTCTCATTACCTTTCCATACAATCTTGCTTATCTATAAAATCTTTCTTCATTTTTGTA
* * *
44088 ACCAGTTTCCTACGCTACGAGAAGAAAGGCAATTCTAGATGGTAATACTAAGTATTCTAACACCA
391 ACCAGTTTCCTACGCTACGAGAAGAAAGGCAACTCTAGAAGGTAATACTAAGTATTCTAACAACA
44153 AATTTCTCGGGAAACTTTCTTCTTTCCCAGTGGTTTTGATTATTAGTTTGTTCGAAATTTTGGTA
456 AATTTCTCGGGAAACTTTCTTCTTTCCCAGTGGTTTTGATTATTAGTTTGTTCGAAATTTTGGTA
44218 ACAGAGCATAAGAAAGGAAATGATCAGGGACATGGCTCCAAAGACAATAGGGCGCGTA
521 ACAGAGCATAAGAAAGGAAATGATCAGGGACATGGCTCCAAAGACAATAGGGCGCGTA
*
44276 GGAGAATGCTTCTTCCCCAAACCCTACCCCTCCAAAATCCAATCGAAAACACCCAAAATCATTTA
1 GGAGAATGCTTCTT-CCCAAACCCTACCCCTCCAAAATCCAATCGAAAACACCCAAAATCATCTA
44341 AGGAGGACCAATTGGCTCGCTTCAAAGGGGTCAATACTCTTTCTCGTCTTTTTAATTTGATGATA
65 AGGAGGACCAATTGGCTCGCTTCAAAGGGGTCAATACTCTTTCTCGTCTTTTTAATTTGATGATA
*
44406 TTTCAACGAAATACTGGAAATTATTTGGTGTCCTGACTTTGCTTGGAGAAAACTGCAACATTGTG
130 TTTCAACGAAATACTGGAAATTATTTGGTGTCCTGACTTTGCTTGGAGAAAACCGCAACATTGTG
44471 GAGATAAACAAAAAGAAGATGAGTTGTTTCCCTTGCTTTAATCCTCATTCTAAAGATTCAAGGAT
195 GAGATAAACAAAAA-AAGATGAGTTGTTTCCCTTGCTTTAATCCTCATTCTAAAGATTCAAGGAT
* *
44536 CGACATTGACAATGGAAGTCGAACCACTTATCGCCATTCCGCTGATTCCTCAGGTTTCCTTTTCA
259 CGACATTGACAATGAAAGTCAAACCACTTATCGCCATTCCGCTGATTCCTCAGGTTTCCTTTTCA
*
44601 TTTCCCTTTTTCTCATTACCTTTCCGTACAATCTTGCTTATCTATAAAATCTTTCTTCATTTTTG
324 TTTCCCTTTTTCTCATTACCTTTCCATACAATCTTGCTTATCTATAAAATCTTTCTTCATTTTTG
*
44666 TAACCAGTTTCCTACGCTACGAGAAGAAAGGCAACTCTAGAAGGTAATGCTAAGTATTCTAACAA
389 TAACCAGTTTCCTACGCTACGAGAAGAAAGGCAACTCTAGAAGGTAATACTAAGTATTCTAACAA
44731 CAAATTTCTCGGGAAACTTTCTTCTTT-CCAGTGGTTTTGATTATTAGTTTGTTCGAAATTTTGG
454 CAAATTTCTCGGGAAACTTTCTTCTTTCCCAGTGGTTTTGATTATTAGTTTGTTCGAAATTTTGG
**
44795 TAACAGAGCATAAGAAAGGAAATGATCAGGGACATGGCTCCAAAGGTAATAGGGCGCGTA
519 TAACAGAGCATAAGAAAGGAAATGATCAGGGACATGGCTCCAAAGACAATAGGGCGCGTA
44855 G
1 G
44856 TTTCACATTC
Statistics
Matches: 558, Mismatches: 20, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
578 14 0.03
579 284 0.51
580 260 0.47
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (578 bp):
GGAGAATGCTTCTTCCCAAACCCTACCCCTCCAAAATCCAATCGAAAACACCCAAAATCATCTAA
GGAGGACCAATTGGCTCGCTTCAAAGGGGTCAATACTCTTTCTCGTCTTTTTAATTTGATGATAT
TTCAACGAAATACTGGAAATTATTTGGTGTCCTGACTTTGCTTGGAGAAAACCGCAACATTGTGG
AGATAAACAAAAAAAGATGAGTTGTTTCCCTTGCTTTAATCCTCATTCTAAAGATTCAAGGATCG
ACATTGACAATGAAAGTCAAACCACTTATCGCCATTCCGCTGATTCCTCAGGTTTCCTTTTCATT
TCCCTTTTTCTCATTACCTTTCCATACAATCTTGCTTATCTATAAAATCTTTCTTCATTTTTGTA
ACCAGTTTCCTACGCTACGAGAAGAAAGGCAACTCTAGAAGGTAATACTAAGTATTCTAACAACA
AATTTCTCGGGAAACTTTCTTCTTTCCCAGTGGTTTTGATTATTAGTTTGTTCGAAATTTTGGTA
ACAGAGCATAAGAAAGGAAATGATCAGGGACATGGCTCCAAAGACAATAGGGCGCGTA
Found at i:48091 original size:85 final size:85
Alignment explanation
Indices: 47991--48156 Score: 287
Period size: 85 Copynumber: 2.0 Consensus size: 85
47981 ATACAATCAC
* *
47991 GACACACGAATGTGTGTCATTTTCATTTATGACGGGGGCTTCAATGACACGCAATGTAAGTCATA
1 GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGTAAGTCATA
48056 AATGCGTGTCATAAATTTAT
66 AATGCGTGTCATAAATTTAT
* * *
48076 GACACACAAATGTGTGTCATCTTCATTTATGATGGGGGCTTCAATGACGCGCAATGTAAGTCGTA
1 GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGTAAGTCATA
48141 AATGCGTGTCATAAAT
66 AATGCGTGTCATAAAT
48157 GCACGTCATA
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 76 1.00
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (85 bp):
GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGTAAGTCATA
AATGCGTGTCATAAATTTAT
Found at i:55803 original size:23 final size:23
Alignment explanation
Indices: 55777--55920 Score: 225
Period size: 23 Copynumber: 6.3 Consensus size: 23
55767 AAGTGCCATG
*
55777 TAGATTTGTCCCGAAGGACCACA
1 TAGAATTGTCCCGAAGGACCACA
55800 TAGAATTGTCCCGAAGGACCACA
1 TAGAATTGTCCCGAAGGACCACA
55823 TAGAATTGTCCCGAAGGACCACA
1 TAGAATTGTCCCGAAGGACCACA
* *
55846 TAGAATTGTCCCGAATGACCACG
1 TAGAATTGTCCCGAAGGACCACA
* *
55869 TAGAATTATCCTGAAGGACCACA
1 TAGAATTGTCCCGAAGGACCACA
* *
55892 TAGAATTGTCCCGAAGGACCGCG
1 TAGAATTGTCCCGAAGGACCACA
55915 TAGAAT
1 TAGAAT
55921 CCCTCGACTC
Statistics
Matches: 110, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 110 1.00
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.20
Consensus pattern (23 bp):
TAGAATTGTCCCGAAGGACCACA
Found at i:59901 original size:14 final size:14
Alignment explanation
Indices: 59882--59911 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
59872 ACTATTCATG
*
59882 TGAATAGTGAATTT
1 TGAATAGTGAAATT
59896 TGAATAGTGAAATT
1 TGAATAGTGAAATT
59910 TG
1 TG
59912 GTCGGCGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (14 bp):
TGAATAGTGAAATT
Found at i:60755 original size:45 final size:45
Alignment explanation
Indices: 60700--60805 Score: 212
Period size: 45 Copynumber: 2.4 Consensus size: 45
60690 TGCACCAGCC
60700 ATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTT
60745 ATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTT
60790 ATGCATCGATGCACTC
1 ATGCATCGATGCACTC
60806 TTAGTGCACC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 61 1.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (45 bp):
ATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTT
Found at i:60758 original size:64 final size:66
Alignment explanation
Indices: 60599--60758 Score: 222
Period size: 65 Copynumber: 2.5 Consensus size: 66
60589 GAAAAAATCG
* *
60599 AACATCGAATGCATTTCATGCACCGATGCA-CATACTATGCATCGATGCACTCAGAGTTTTATGA
1 AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATGCACTCAGAGTTTTATGA
60663 A
66 A
* *
60664 AACATCGAATGCATTTGATGCATCGATGCACCA-GCCATGCATCGATGCACTCAG-GCTATTT-T
1 AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATGCACTCAGAG-T-TTTAT
60726 G-A
64 GAA
*
60728 AACATCGAATGCATTTTATGCATCGATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
60759 TCAGGCTATT
Statistics
Matches: 87, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
64 32 0.37
65 50 0.57
66 5 0.06
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.28
Consensus pattern (66 bp):
AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATGCACTCAGAGTTTTATGA
A
Found at i:66691 original size:23 final size:22
Alignment explanation
Indices: 66620--66698 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 22
66610 ACACTTAACA
66620 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCA-CCC-TTGAAT
* * *
66644 GTGCATCGATACA-CCATGAAG
1 GTGCATCGATGCACCCTTGAAT
*
66665 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCAC-CCTTGAAT
66688 GTGCATCGATG
1 GTGCATCGATG
66699 TACAATGCCA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
21 15 0.33
22 2 0.04
23 16 0.36
24 12 0.27
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACCCTTGAAT
Found at i:68570 original size:2 final size:2
Alignment explanation
Indices: 68563--68588 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
68553 TTTGAACTTA
68563 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
68589 TTGGTTTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:68894 original size:45 final size:43
Alignment explanation
Indices: 68830--68919 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 43
68820 AAGGGAGAAG
68830 TTAAAGTAAGGGGGAGTAATTTCAAACTTAATTTTTCAAAATTTA
1 TTAAAGTAAGGGGGAGTAATTTC-AACTTAATTTTTC-AAATTTA
68875 TTAAAGTAAGGGGGAGTAATTTCAACTTAATTTTTCAAATTTA
1 TTAAAGTAAGGGGGAGTAATTTCAACTTAATTTTTCAAATTTA
68918 TT
1 TT
68920 TTCAAAGAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
43 9 0.20
44 13 0.29
45 23 0.51
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.40
Consensus pattern (43 bp):
TTAAAGTAAGGGGGAGTAATTTCAACTTAATTTTTCAAATTTA
Found at i:69396 original size:65 final size:65
Alignment explanation
Indices: 69269--69424 Score: 178
Period size: 65 Copynumber: 2.4 Consensus size: 65
69259 TAAATCGAAT
* * *
69269 ATCGAAAGCATTTCATGCACCGATGCA-CATACTATGCATCGATGCACTCAAAGTTTTATGAAAA
1 ATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATGCACTCAAAGTTTTATG-AAA
69333 C
65 C
* * *
69334 ATCGAATGCATTTGATGCATCGATGCACCA-GCCATGCATCGATGCACTC-ATGCTATTT-TGAA
1 ATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATGCACTCAAAG-T-TTTATGAA
69396 AC
64 AC
* *
69398 ATCG-ATGCATTTTATGCATTGATGCAC
1 ATCGAATGCATTTCATGCATCGATGCAC
69425 TCTTAGTGCA
Statistics
Matches: 80, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
63 21 0.26
64 10 0.12
65 44 0.55
66 5 0.06
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (65 bp):
ATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATGCACTCAAAGTTTTATGAAAC
Done.