Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002868.1 Hibiscus syriacus cultivar Beakdansim tig00005915_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: 114281
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8 original size:3 final size:3
Alignment explanation
Indices: 1--34 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
*
1 ATT ATT ATT ATT ATT ATT ATT ATT AGT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
35 AGTGTATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1520 original size:2 final size:2
Alignment explanation
Indices: 1506--1559 Score: 78
Period size: 2 Copynumber: 28.0 Consensus size: 2
1496 TGTGTTAATC
1506 TA TA TA T- TA -A TA TA TA TA TA TA CTA TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
1546 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
1560 ATTAATTTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.06
2 43 0.90
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13401 original size:16 final size:16
Alignment explanation
Indices: 13380--13431 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
13370 TGCTTGAAGA
13380 AAAAAAAGGAACAAAT-
1 AAAAAAAGGAA-AAATG
*
13396 AAAAAAATGAAAAATG
1 AAAAAAAGGAAAAATG
*
13412 AAAAAAA--AGAAATG
1 AAAAAAAGGAAAAATG
13426 AAAAAA
1 AAAAAA
13432 TAAAAAGAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 12 0.36
15 4 0.12
16 17 0.52
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.08
Consensus pattern (16 bp):
AAAAAAAGGAAAAATG
Found at i:13424 original size:29 final size:27
Alignment explanation
Indices: 13392--13445 Score: 72
Period size: 29 Copynumber: 1.9 Consensus size: 27
13382 AAAAAGGAAC
13392 AAATAAAAAAATGAAAAATGAAAAAAAAG
1 AAATAAAAAAAT-AAAAA-GAAAAAAAAG
* *
13421 AAATGAAAAAATAAAAAGAGAAAAA
1 AAATAAAAAAATAAAAAGAAAAAAA
13446 GGAGGGTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 7 0.30
28 5 0.22
29 11 0.48
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (27 bp):
AAATAAAAAAATAAAAAGAAAAAAAAG
Found at i:13445 original size:14 final size:14
Alignment explanation
Indices: 13392--13437 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
13382 AAAAAGGAAC
*
13392 AAATAAAAAAATGAA
1 AAATGAAAAAAT-AA
13407 AAATGAAAAAA-AA
1 AAATGAAAAAATAA
13420 GAAATGAAAAAATAA
1 -AAATGAAAAAATAA
13435 AAA
1 AAA
13438 GAGAAAAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 2 0.07
14 14 0.50
15 12 0.43
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (14 bp):
AAATGAAAAAATAA
Found at i:14884 original size:105 final size:105
Alignment explanation
Indices: 14664--14918 Score: 305
Period size: 105 Copynumber: 2.4 Consensus size: 105
14654 CTCGCTTGAG
*
14664 GGATCGACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAA
1 GGATCAACATTTCC--TGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAA
* * * * **
14729 TGAGAAGAACTTGTTCCTTTCAAATTCACCACAGATGGAGGT
64 TGAGAAAAACATGTTCCTTTCAAATCCACCACAAAAAGAGGT
* * * * *
14771 GAACCAACATTTCCTGAAGAGTTCATAATGACAAGAACTCGTCCTAAAGGAGAAAGTTCATAATG
1 GGATCAACATTTCCTGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAATG
* * * **
14836 AGAAAAACATGTT-CTTTCTAAGTCCATCGCAAAAAGATTT
66 AGAAAAACATGTTCCTTTC-AAATCCACCACAAAAAGAGGT
**
14876 GGATCAACATTTCCAAAAGAGTTCATAATGAGAAGAACTCATC
1 GGATCAACATTTCCTGAAGAGTTCATAATGAGAAGAACTCATC
14919 CACGAGAAAA
Statistics
Matches: 124, Mismatches: 23, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
104 5 0.04
105 108 0.87
107 11 0.09
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (105 bp):
GGATCAACATTTCCTGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAATG
AGAAAAACATGTTCCTTTCAAATCCACCACAAAAAGAGGT
Found at i:15100 original size:3 final size:3
Alignment explanation
Indices: 15085--15127 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
15075 AGTTAAAAAA
* *
15085 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
15128 AGTGTATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 1 0.03
3 34 0.97
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:17044 original size:14 final size:14
Alignment explanation
Indices: 17025--17051 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17015 TAAAATGTTT
17025 GTTATTTTATTTTA
1 GTTATTTTATTTTA
17039 GTTATTTTATTTT
1 GTTATTTTATTTT
17052 CTATTTTTAC
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:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (14 bp):
GTTATTTTATTTTA
Found at i:17456 original size:15 final size:16
Alignment explanation
Indices: 17426--17462 Score: 58
Period size: 15 Copynumber: 2.3 Consensus size: 16
17416 GCAGACCAGC
17426 TTTTGTCTTAAAAATTA
1 TTTT-TCTTAAAAATTA
17443 TTTTTCTT-AAAATTA
1 TTTTTCTTAAAAATTA
17458 TTTTT
1 TTTTT
17463 AAAAAGATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 12 0.60
16 4 0.20
17 4 0.20
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (16 bp):
TTTTTCTTAAAAATTA
Found at i:21191 original size:14 final size:15
Alignment explanation
Indices: 21165--21199 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
21155 ATTTGATTGG
21165 ATAAAAAATTATTAA
1 ATAAAAAATTATTAA
21180 ATAAAAAA-TATTAA
1 ATAAAAAATTATTAA
21194 A-AAAAA
1 ATAAAAA
21200 TCAAATCACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.25
14 7 0.35
15 8 0.40
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
ATAAAAAATTATTAA
Found at i:28289 original size:24 final size:24
Alignment explanation
Indices: 28271--28359 Score: 160
Period size: 24 Copynumber: 3.7 Consensus size: 24
28261 TTTCTATTAT
*
28271 AATACCTGACCTGGATTCTGATCG
1 AATACTTGACCTGGATTCTGATCG
*
28295 GATACTTGACCTGGATTCTGATCG
1 AATACTTGACCTGGATTCTGATCG
28319 AATACTTGACCTGGATTCTGATCG
1 AATACTTGACCTGGATTCTGATCG
28343 AATACTTGACCTGGATT
1 AATACTTGACCTGGATT
28360 ATGTTTTGAT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (24 bp):
AATACTTGACCTGGATTCTGATCG
Found at i:37865 original size:14 final size:14
Alignment explanation
Indices: 37846--37874 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
37836 TTAAGAAGCT
37846 AGCTTATTAAGTGG
1 AGCTTATTAAGTGG
37860 AGCTTATTAAGTGG
1 AGCTTATTAAGTGG
37874 A
1 A
37875 ATGATGGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.07, G:0.28, T:0.34
Consensus pattern (14 bp):
AGCTTATTAAGTGG
Found at i:40609 original size:63 final size:66
Alignment explanation
Indices: 40499--40690 Score: 187
Period size: 63 Copynumber: 2.9 Consensus size: 66
40489 ATAATTATTC
* * *
40499 TTTGAATATGTCAAAAATAAAAGATATTTATTACCTATTTAACTTTGAATATTAAAGATAA-TTA
1 TTTGAATATTTC-AAATTAAAAGATA--TATTATCTATTTAACTTTGAATATTAAAGATAACTT-
40563 TATCCT
62 TAT-CT
* * * * *
40569 TTTGAATATTT-TAATTTAAA-ATA-A-TATCTATTTAAGTTTGAATAGTAAAAGGTAACTTTAT
1 TTTGAATATTTCAAATTAAAAGATATATTATCTATTTAACTTTGAATA-TTAAAGATAACTTTAT
40630 CT
65 CT
* *
40632 TTTGAATATTTCAAATTAAAAGATATTATTATCTGTTTAATTTTGAATATTAAAAGATA
1 TTTGAATATTTCAAATTAAAAGATA-TATTATCTATTTAACTTTGAATATT-AAAGATA
40691 TATAGTTGAA
Statistics
Matches: 100, Mismatches: 14, Indels: 18
0.76 0.11 0.14
Matches are distributed among these distances:
63 31 0.31
64 19 0.19
65 5 0.05
67 5 0.05
68 30 0.30
70 10 0.10
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (66 bp):
TTTGAATATTTCAAATTAAAAGATATATTATCTATTTAACTTTGAATATTAAAGATAACTTTATC
T
Found at i:40664 original size:34 final size:34
Alignment explanation
Indices: 40626--40691 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 34
40616 AAAGGTAACT
40626 TTATCT-TTTGAATATTTCAA-ATTAAAAGATATTA
1 TTATCTGTTT-AAT-TTTCAATATTAAAAGATATTA
*
40660 TTATCTGTTTAATTTTGAATATTAAAAGATAT
1 TTATCTGTTTAATTTTCAATATTAAAAGATAT
40692 ATAGTTGAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 5 0.17
34 21 0.72
35 3 0.10
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (34 bp):
TTATCTGTTTAATTTTCAATATTAAAAGATATTA
Found at i:46338 original size:59 final size:60
Alignment explanation
Indices: 46242--46401 Score: 151
Period size: 59 Copynumber: 2.7 Consensus size: 60
46232 GAATTGAGGG
* * ** ** * ** * *
46242 ATGAAATTGGAATTTTTGAAAGTTTTGAGACCAATTTAAAAAGAGGGCCATATTTTAGAA
1 ATGAAATTAGAATATTCAAAAGTTTAAAGACTAATTTAAAAAGAGAACCACAGTTTAGAA
* * * * * *
46302 ATTAAATTA-AATGTTCAAAAGTTTAAGGACTGATTTAAAATGAGAATCACAGTTTAGAA
1 ATGAAATTAGAATATTCAAAAGTTTAAAGACTAATTTAAAAAGAGAACCACAGTTTAGAA
*
46361 ATGAAATTAGAATATTCAAAAGTTTAAAGATTAATTTAAAA
1 ATGAAATTAGAATATTCAAAAGTTTAAAGACTAATTTAAAA
46402 TAAGATTAAA
Statistics
Matches: 78, Mismatches: 21, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
59 44 0.56
60 34 0.44
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.33
Consensus pattern (60 bp):
ATGAAATTAGAATATTCAAAAGTTTAAAGACTAATTTAAAAAGAGAACCACAGTTTAGAA
Found at i:46417 original size:59 final size:59
Alignment explanation
Indices: 46295--46418 Score: 151
Period size: 60 Copynumber: 2.1 Consensus size: 59
46285 AGGGCCATAT
* * * * * * *
46295 TTTAGAAATTAAATTAAATGTTCAAAAGTTTAAGGACTGATTTAAAATGAGAATCACAG
1 TTTAGAAATGAAATTAAATATTCAAAAGTTTAAAGACTAATTTAAAATAAGAATCAAAA
* *
46354 TTTAGAAATGAAATTAGAATATTCAAAAGTTTAAAGATTAATTTAAAATAAG-ATTAAAA
1 TTTAGAAATGAAATTA-AATATTCAAAAGTTTAAAGACTAATTTAAAATAAGAATCAAAA
46413 TTTAGA
1 TTTAGA
46419 GACATATGAT
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 25 0.45
60 30 0.55
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.34
Consensus pattern (59 bp):
TTTAGAAATGAAATTAAATATTCAAAAGTTTAAAGACTAATTTAAAATAAGAATCAAAA
Found at i:49201 original size:20 final size:19
Alignment explanation
Indices: 49166--49231 Score: 89
Period size: 20 Copynumber: 3.5 Consensus size: 19
49156 CGAAACTTAA
49166 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
49185 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* *
49205 ATCGCAATGCGAAATGA-A
1 ATCGCAACGCGAAATGACT
49223 ATCGCAACG
1 ATCGCAACG
49232 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
18 8 0.20
19 16 0.39
20 17 0.41
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:49240 original size:14 final size:14
Alignment explanation
Indices: 49221--49277 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
49211 ATGCGAAATG
49221 AAATCGCAACGACA
1 AAATCGCAACGACA
*
49235 AAATCGCAACGCGAAA
1 AAATCGCAA--CGACA
49251 TGAAATCGCAACGACA
1 --AAATCGCAACGACA
49267 AAATCGCAACG
1 AAATCGCAACG
49278 CGAAACACAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.47, C:0.26, G:0.18, T:0.09
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:49249 original size:32 final size:32
Alignment explanation
Indices: 49205--49282 Score: 147
Period size: 32 Copynumber: 2.4 Consensus size: 32
49195 GGAAATGGCT
*
49205 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
49237 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
49269 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
49283 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:49311 original size:19 final size:17
Alignment explanation
Indices: 49289--49384 Score: 78
Period size: 19 Copynumber: 5.6 Consensus size: 17
49279 GAAACACAAA
49289 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
49308 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
49324 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
49340 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
49356 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
49373 TCGCATTGCGAT
1 TCGC-TTGCGAT
49385 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
14 15 0.24
15 3 0.05
16 12 0.19
17 4 0.06
18 13 0.21
19 16 0.25
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:49330 original size:14 final size:14
Alignment explanation
Indices: 49311--49368 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
49301 TTTCATTTCG
49311 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
49325 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
49341 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
49357 CGTTGCGATTTT
1 CGTTGCGATTTT
49369 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:49375 original size:33 final size:33
Alignment explanation
Indices: 49294--49384 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
49284 ACAAATCGCA
49294 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
49327 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
49359 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
49385 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:49403 original size:20 final size:20
Alignment explanation
Indices: 49369--49443 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
49359 TTGCGATTTT
*
49369 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
49388 CATTTCCGCGTTGCGATGGC
1 CATTTCCGCGTTGCGATAGC
*
49408 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
* *
49428 CATTTTCGTGTTGCGA
1 CATTTCCGCGTTGCGA
49444 AAGTAAACTA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
19 5 0.10
20 44 0.90
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:49948 original size:18 final size:18
Alignment explanation
Indices: 49922--49966 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
49912 GTCGATCAGA
*
49922 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
49940 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
49958 TGATGGCTC
1 TGATGGCTC
49967 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:51304 original size:20 final size:20
Alignment explanation
Indices: 51279--51316 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
51269 AATAGTTTCT
51279 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
51299 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
51317 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:51584 original size:22 final size:22
Alignment explanation
Indices: 51557--51600 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
51547 GATGGAGATA
51557 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
51579 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
51601 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:51813 original size:20 final size:20
Alignment explanation
Indices: 51788--51881 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
51778 GATTATGTAT
51788 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
51808 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
51828 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
51849 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
51869 TATCGCATTGCGA
1 TATCGCGTTGCGA
51882 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:51853 original size:41 final size:41
Alignment explanation
Indices: 51808--51885 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
51798 CGAAAGTCAG
* * *
51808 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
51849 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
51886 CCCAATTCAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:51882 original size:20 final size:20
Alignment explanation
Indices: 51768--51882 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
51758 CGCTTTGAAA
*
51768 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
51789 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
51809 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
51829 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
51850 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
51870 ATCGCATTGCGAT
1 ATCGCATTGCGAT
51883 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:51921 original size:19 final size:20
Alignment explanation
Indices: 51897--51981 Score: 111
Period size: 19 Copynumber: 4.3 Consensus size: 20
51887 CCAATTCACG
51897 TTGCGATTTACTTA-TCGCA
1 TTGCGATTTACTTATTCGCA
51916 TTGCGATTTACTTA-TCGCA
1 TTGCGATTTACTTATTCGCA
* ** *
51935 TTGCGATTTTCCCAATTCGCG
1 TTGCGA-TTTACTTATTCGCA
51956 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACTTATTCGCA
51976 TTGCGA
1 TTGCGA
51982 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
19 25 0.45
20 21 0.38
21 10 0.18
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.41
Consensus pattern (20 bp):
TTGCGATTTACTTATTCGCA
Found at i:51942 original size:59 final size:60
Alignment explanation
Indices: 51844--51981 Score: 210
Period size: 59 Copynumber: 2.3 Consensus size: 60
51834 GTTGCGATTT
51844 TTTA-TTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAATTCACGTTGCGA
1 TTTACTTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAATTCACGTTGCGA
* * *
51903 TTTACTTATCGCATTGCGAT--TTACTTATCGCATTGCGATTTTCCCAATTCGCGTTGCGA
1 TTTACTTATCGCATTGCGATAGTCA-GTATCGCATTGCGATTTTCCCAATTCACGTTGCGA
51962 TTTACTTATTCGCATTGCGA
1 TTTACTTA-TCGCATTGCGA
51982 ATTGGGAAAA
Statistics
Matches: 73, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
58 2 0.03
59 45 0.62
60 26 0.36
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.40
Consensus pattern (60 bp):
TTTACTTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAATTCACGTTGCGA
Found at i:65911 original size:2 final size:2
Alignment explanation
Indices: 65904--65963 Score: 70
Period size: 2 Copynumber: 31.0 Consensus size: 2
65894 ATCGGGCCAG
* * *
65904 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AA AT -T AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
65945 AT AA AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
65964 TTTTAATTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
1 2 0.04
2 46 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:77026 original size:22 final size:22
Alignment explanation
Indices: 76995--77036 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
76985 GTTTAAAAAT
76995 ACTAACATTTATATAGCTATCA
1 ACTAACATTTATATAGCTATCA
*
77017 ACTAATATTTATATAGCTAT
1 ACTAACATTTATATAGCTAT
77037 TTAATAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.40
Consensus pattern (22 bp):
ACTAACATTTATATAGCTATCA
Found at i:78007 original size:22 final size:21
Alignment explanation
Indices: 77982--78025 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
77972 TATTTTCATA
*
77982 TAATAACTTTATATCAATGCAT
1 TAAT-ACTTTATAACAATGCAT
* *
78004 TAATAGTTTATAACCATGCAT
1 TAATACTTTATAACAATGCAT
78025 T
1 T
78026 TTAATGAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.41
Consensus pattern (21 bp):
TAATACTTTATAACAATGCAT
Found at i:79830 original size:15 final size:15
Alignment explanation
Indices: 79810--79852 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
79800 AATCTTAATA
*
79810 TATTTAGATAATTAG
1 TATTTAAATAATTAG
** *
79825 TATTTATCTAATTTG
1 TATTTAAATAATTAG
79840 TATTTAAATAATT
1 TATTTAAATAATT
79853 GATAAAAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.53
Consensus pattern (15 bp):
TATTTAAATAATTAG
Found at i:85106 original size:2 final size:2
Alignment explanation
Indices: 85099--85135 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
85089 TATTTGATAT
85099 GA GA GA GA -A GCA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA G-A GA GA GA GA GA GA GA GA GA GA GA GA G
85136 TGGCAAACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:91333 original size:30 final size:29
Alignment explanation
Indices: 91273--91334 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
91263 TTTTAATATT
* *
91273 AAATAATAATAAAAATATCACATCATACAA
1 AAATAATAATAAAAAAATCACAT-AGACAA
91303 AAATAATAATAAAATAAATCAGCAT-GACAA
1 AAATAATAATAAAA-AAATCA-CATAGACAA
91333 AA
1 AA
91335 TATGATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 20 0.71
31 5 0.18
32 3 0.11
ACGTcount: A:0.65, C:0.11, G:0.03, T:0.21
Consensus pattern (29 bp):
AAATAATAATAAAAAAATCACATAGACAA
Found at i:91554 original size:2 final size:2
Alignment explanation
Indices: 91547--91578 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
91537 TAATATTGAA
91547 AT AT AT 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 AT AT AT
91579 TTGAAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:97194 original size:2 final size:2
Alignment explanation
Indices: 97187--97235 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
97177 CATCAAGTTT
97187 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
97229 TA TA TA T
1 TA TA TA T
97236 GAGTTAGGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:100781 original size:23 final size:23
Alignment explanation
Indices: 100755--100805 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
100745 AAATATACAT
100755 TCCAATAATATTTTATTCCTTTA
1 TCCAATAATATTTTATTCCTTTA
100778 TCCAATAATATTTTATTCCTTTA
1 TCCAATAATATTTTATTCCTTTA
*
100801 ACCAA
1 TCCAA
100806 ATACGATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (23 bp):
TCCAATAATATTTTATTCCTTTA
Found at i:100900 original size:20 final size:20
Alignment explanation
Indices: 100875--100932 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
100865 ATCCTATTCC
100875 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
*
100895 CTGGTAATCTTACATTCTCA
1 CTGGTAATCTTACATTCCCA
100915 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
100933 ATAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.24, C:0.28, G:0.10, T:0.38
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:101168 original size:10 final size:10
Alignment explanation
Indices: 101153--101227 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
101143 CATTTAATAA
101153 ATAAACGAAC
1 ATAAACGAAC
101163 ATAAACGAAC
1 ATAAACGAAC
*
101173 ----ACAAAC
1 ATAAACGAAC
101179 ATAAACGAAC
1 ATAAACGAAC
** *
101189 ACGAAC-ATAA
1 ATAAACGA-AC
101199 ATGAACACGAAC
1 AT-AA-ACGAAC
101211 ATAAACGAAC
1 ATAAACGAAC
101221 ATAAACG
1 ATAAACG
101228 TTAGAGACCC
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 5 0.10
9 1 0.02
10 34 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.59, C:0.21, G:0.11, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:101181 original size:16 final size:16
Alignment explanation
Indices: 101160--101226 Score: 98
Period size: 16 Copynumber: 4.2 Consensus size: 16
101150 TAAATAAACG
101160 AACATAAACGAACACA
1 AACATAAACGAACACA
*
101176 AACATAAACGAACACG
1 AACATAAACGAACACA
* *
101192 AACATAAATGAACACG
1 AACATAAACGAACACA
*
101208 AACATAAACGAACATA
1 AACATAAACGAACACA
101224 AAC
1 AAC
101227 GTTAGAGACC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.60, C:0.22, G:0.09, T:0.09
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:101193 original size:32 final size:32
Alignment explanation
Indices: 101157--101221 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
101147 TAATAAATAA
101157 ACGAACATAAACGAACACAAACATAAACGAAC
1 ACGAACATAAACGAACACAAACATAAACGAAC
* *
101189 ACGAACATAAATGAACACGAACATAAACGAAC
1 ACGAACATAAACGAACACAAACATAAACGAAC
101221 A
1 A
101222 TAAACGTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.58, C:0.23, G:0.11, T:0.08
Consensus pattern (32 bp):
ACGAACATAAACGAACACAAACATAAACGAAC
Found at i:102504 original size:33 final size:33
Alignment explanation
Indices: 102450--102539 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
102440 GGGAAAGAGA
* *
102450 TGAAGCTCTGTCGAATTGTTGCAGTTGAAGACT
1 TGAAGCTCCGTCGAATCGTTGCAGTTGAAGACT
*
102483 TGAAGCTCCGTCAAATCGTTGCAGTTGAAGACT
1 TGAAGCTCCGTCGAATCGTTGCAGTTGAAGACT
102516 TGAAGCTCCGTCGAATCGTTGCAG
1 TGAAGCTCCGTCGAATCGTTGCAG
102540 AAATGAAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (33 bp):
TGAAGCTCCGTCGAATCGTTGCAGTTGAAGACT
Found at i:102798 original size:24 final size:24
Alignment explanation
Indices: 102761--102816 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
102751 TATTAGGTTA
* *
102761 AACATAAATGAACGCACATAAACG
1 AACATAACTAAACGCACATAAACG
*
102785 AACATAACTAAACGCATATAAACG
1 AACATAACTAAACGCACATAAACG
102809 AACATAAC
1 AACATAAC
102817 CGAATGTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.55, C:0.21, G:0.09, T:0.14
Consensus pattern (24 bp):
AACATAACTAAACGCACATAAACG
Found at i:103408 original size:3 final size:3
Alignment explanation
Indices: 103400--103431 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
103390 GTATATTTAT
103400 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
103432 TAATTTGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:110645 original size:3 final size:3
Alignment explanation
Indices: 110637--110692 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
110627 GTATATTTAT
110637 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
110685 ATA ATA AT
1 ATA ATA AT
110693 TAATTTGAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:114007 original size:18 final size:18
Alignment explanation
Indices: 113945--114008 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
113935 TTTATTGAAA
*
113945 AACCGATAAACCGAACCG
1 AACCGAAAAACCGAACCG
113963 AACCGAAAAACCCGAACCG
1 AACCGAAAAA-CCGAACCG
*
113982 TTAA---AAAAACTGAACCG
1 --AACCGAAAAACCGAACCG
113999 AACCGAAAAA
1 AACCGAAAAA
114009 ACCGGTTTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
15 2 0.05
17 7 0.18
18 19 0.50
19 8 0.21
21 2 0.05
ACGTcount: A:0.52, C:0.28, G:0.14, T:0.06
Consensus pattern (18 bp):
AACCGAAAAACCGAACCG
Found at i:114253 original size:15 final size:15
Alignment explanation
Indices: 114233--114262 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
114223 TAGGTGGAGC
114233 CTAACTCAAATGAGT
1 CTAACTCAAATGAGT
114248 CTAACTCAAATGAGT
1 CTAACTCAAATGAGT
114263 TCGTAAGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (15 bp):
CTAACTCAAATGAGT
Done.