Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008499.1 Hibiscus syriacus cultivar Beakdansim tig00111344_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: 291584
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:154330 original size:59 final size:59
Alignment explanation
Indices: 154251--154380 Score: 176
Period size: 59 Copynumber: 2.2 Consensus size: 59
154241 TTAAAATCAC
*
154251 ATCTTAACATTGAAAAATATATTTTATTGT-TATCTTAAC-TAAAATATATATTTTAATCTT
1 ATCTTAAC-TTGAAAAATATATTTTATT-TCTACCTTAACTTAAAA-ATATATTTTAATCTT
* *
154311 ATCTTAACTT-ATAAAATATATTTTATTTCTACCTTAACTTAAAAATATATTTTATTTTT
1 ATCTTAACTTGA-AAAATATATTTTATTTCTACCTTAACTTAAAAATATATTTTAATCTT
154370 ATCTTAACTTG
1 ATCTTAACTTG
154381 TTACGTATAT
Statistics
Matches: 63, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
58 2 0.03
59 48 0.76
60 13 0.21
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (59 bp):
ATCTTAACTTGAAAAATATATTTTATTTCTACCTTAACTTAAAAATATATTTTAATCTT
Found at i:154406 original size:59 final size:58
Alignment explanation
Indices: 154251--154422 Score: 165
Period size: 59 Copynumber: 2.9 Consensus size: 58
154241 TTAAAATCAC
*
154251 ATCTTAACATTGA-AAAATATATTTTATTGTTATCTTAACTAAAATATATATTTTAATCTT
1 ATCTTAAC-TT-ATAAAATATATTTTATT-TTAACTTAACTAAAATATATATTTTAATCTT
* * *
154311 ATCTTAACTTATAAAATATATTTTATTTCTACCTTAACTTAAAA-ATATATTTTATTTTT
1 ATCTTAACTTATAAAATATATTTTATTT-TAACTTAAC-TAAAATATATATTTTAATCTT
* * ** * *
154370 ATCTTAACTTGTTACGTATATTATATTCTTAACTT-A--AAATTATATATTTTAAT
1 ATCTTAACTTATAAAATATATTTTATT-TTAACTTAACTAAAATATATATTTTAAT
154423 TTAATTTAAA
Statistics
Matches: 96, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
55 3 0.03
56 11 0.11
58 3 0.03
59 65 0.68
60 14 0.15
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (58 bp):
ATCTTAACTTATAAAATATATTTTATTTTAACTTAACTAAAATATATATTTTAATCTT
Found at i:154444 original size:24 final size:25
Alignment explanation
Indices: 154398--154444 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
154388 TATTATATTC
*
154398 TTAACTTAAAATTATATATTTTAAT
1 TTAACTTAAAAATATATATTTTAAT
*
154423 TTAATTTAAAAAT-TATATTTTA
1 TTAACTTAAAAATATATATTTTA
154445 TTCTTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
TTAACTTAAAAATATATATTTTAAT
Found at i:154453 original size:24 final size:25
Alignment explanation
Indices: 154386--154453 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 25
154376 ACTTGTTACG
* * *
154386 TATATTATATTCTTAACTTAAAATTA
1 TATATTTTATTCTT-ATTTAAAAATA
*
154412 TATATTTTAATT-TAATTTAAAAAT-
1 TATATTTT-ATTCTTATTTAAAAATA
154436 TATATTTTATTCTTATTT
1 TATATTTTATTCTTATTT
154454 TAATTTAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
23 3 0.09
24 13 0.37
25 8 0.23
26 8 0.23
27 3 0.09
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (25 bp):
TATATTTTATTCTTATTTAAAAATA
Found at i:171906 original size:34 final size:34
Alignment explanation
Indices: 171863--171932 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
171853 AAGTTATATA
171863 CTACATATAGTCCATTTCAAGGCAAATAATTAGC
1 CTACATATAGTCCATTTCAAGGCAAATAATTAGC
171897 CTACATATAGTCCATTTCAAGGCAAATAATTAGC
1 CTACATATAGTCCATTTCAAGGCAAATAATTAGC
171931 CT
1 CT
171933 CGTGCCAGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.30
Consensus pattern (34 bp):
CTACATATAGTCCATTTCAAGGCAAATAATTAGC
Found at i:172979 original size:35 final size:37
Alignment explanation
Indices: 172908--172980 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
172898 GTTAAAAAAT
* *
172908 ATTTATATATTTTCTTTAAGAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAGAAATTAAAAATCATAAA
172945 ATTTATATATTTT-TTTACA-AAATTAAAAAT-ATAAA
1 ATTTATATATTTTCTTTA-AGAAATTAAAAATCATAAA
172980 A
1 A
172981 AGTTAATGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 6 0.18
36 13 0.39
37 14 0.42
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAGAAATTAAAAATCATAAA
Found at i:179818 original size:30 final size:30
Alignment explanation
Indices: 179784--179877 Score: 188
Period size: 30 Copynumber: 3.1 Consensus size: 30
179774 GTATGCATAT
179784 AAAACATGACATAAACACGAGTCTCGTTAA
1 AAAACATGACATAAACACGAGTCTCGTTAA
179814 AAAACATGACATAAACACGAGTCTCGTTAA
1 AAAACATGACATAAACACGAGTCTCGTTAA
179844 AAAACATGACATAAACACGAGTCTCGTTAA
1 AAAACATGACATAAACACGAGTCTCGTTAA
179874 AAAA
1 AAAA
179878 TTTCTCTAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.49, C:0.19, G:0.13, T:0.19
Consensus pattern (30 bp):
AAAACATGACATAAACACGAGTCTCGTTAA
Found at i:180153 original size:21 final size:21
Alignment explanation
Indices: 180127--180167 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
180117 TCATCCGATC
*
180127 TGTAAAAGAAAGCCTAGATAG
1 TGTAAAAAAAAGCCTAGATAG
180148 TGTAAAAAAAAGCCTAGATA
1 TGTAAAAAAAAGCCTAGATA
180168 CACAAACTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.10, G:0.20, T:0.20
Consensus pattern (21 bp):
TGTAAAAAAAAGCCTAGATAG
Found at i:181957 original size:31 final size:31
Alignment explanation
Indices: 181871--181987 Score: 103
Period size: 31 Copynumber: 3.8 Consensus size: 31
181861 ACTTAATGCA
* * *
181871 TTTAGTACATAAACTATCAATTTCGATTCGT
1 TTTAGTACCTAAATTATCAATTTTGATTCGT
* * * * *
181902 TATAGTAACAAAATTATCAGTTTTGGTAT-GT
1 TTTAGTACCTAAATTATCAATTTTGAT-TCGT
* *
181933 TTTAGTACCTAAATTATCAATTTTGATCCAT
1 TTTAGTACCTAAATTATCAATTTTGATTCGT
*
181964 TTTAGTACTTAAACTT-TCAATTTT
1 TTTAGTACCTAAA-TTATCAATTTT
181988 TAAAAAATTT
Statistics
Matches: 67, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
31 64 0.96
32 3 0.04
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.45
Consensus pattern (31 bp):
TTTAGTACCTAAATTATCAATTTTGATTCGT
Found at i:186332 original size:30 final size:30
Alignment explanation
Indices: 186298--186360 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
186288 GACTACATCA
* * * *
186298 ACACCACCTCTTTGTACACTAACAACCTTT
1 ACACCACATCTTTATACACCAACAACCATT
* *
186328 ACACCTCATCTTTATGCACCAACAACCATT
1 ACACCACATCTTTATACACCAACAACCATT
186358 ACA
1 ACA
186361 ACCCCTGTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.37, G:0.03, T:0.27
Consensus pattern (30 bp):
ACACCACATCTTTATACACCAACAACCATT
Found at i:197751 original size:32 final size:32
Alignment explanation
Indices: 197715--197796 Score: 103
Period size: 32 Copynumber: 2.6 Consensus size: 32
197705 AACTACTATA
* *
197715 CATTATCTAAATGCGATATTGAC-ACTCATGTG
1 CATTATCTAAATGCAACATTGACTA-TCATGTG
**
197747 CATTATCTAAATGCAACATTGACTATGTTGTG
1 CATTATCTAAATGCAACATTGACTATCATGTG
*
197779 CATTATCTAAATACAACA
1 CATTATCTAAATGCAACA
197797 CTACTAGTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
32 43 0.98
33 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.34
Consensus pattern (32 bp):
CATTATCTAAATGCAACATTGACTATCATGTG
Found at i:198502 original size:20 final size:21
Alignment explanation
Indices: 198479--198525 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
198469 TCCTCTACTG
*
198479 TGGATACCAG-TCCTCTGGTA
1 TGGATACCAGTTCATCTGGTA
* *
198499 TGGATACTAGTTTATCTGGTA
1 TGGATACCAGTTCATCTGGTA
198520 TGGATA
1 TGGATA
198526 TTCATGGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (21 bp):
TGGATACCAGTTCATCTGGTA
Found at i:202715 original size:18 final size:18
Alignment explanation
Indices: 202673--202717 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
202663 CCTTTGGTAT
*
202673 GAATACCCAAATTCGGTAC
1 GAATA-CCAAATTCGATAC
202692 -AGATACCAAATTCGATAC
1 GA-ATACCAAATTCGATAC
202710 GAATACCA
1 GAATACCA
202718 GTTCATCAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.42, C:0.24, G:0.13, T:0.20
Consensus pattern (18 bp):
GAATACCAAATTCGATAC
Found at i:204322 original size:12 final size:13
Alignment explanation
Indices: 204300--204328 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
204290 CATAAAATAC
204300 TTTATATTTTAAT
1 TTTATATTTTAAT
204313 TTTA-ATTTTAAT
1 TTTATATTTTAAT
204325 TTTA
1 TTTA
204329 GTAACTACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTATATTTTAAT
Found at i:209147 original size:14 final size:14
Alignment explanation
Indices: 209128--209175 Score: 78
Period size: 14 Copynumber: 3.4 Consensus size: 14
209118 GACTGAGAAA
209128 AACCTTTAGCAACC
1 AACCTTTAGCAACC
209142 AACCTTTAGCAACC
1 AACCTTTAGCAACC
*
209156 AGCCTTTAGCAACC
1 AACCTTTAGCAACC
*
209170 AGCCTT
1 AACCTT
209176 GCCTTGTATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.31, C:0.35, G:0.10, T:0.23
Consensus pattern (14 bp):
AACCTTTAGCAACC
Found at i:212008 original size:2 final size:2
Alignment explanation
Indices: 212001--212038 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
211991 CAATTTCAAA
212001 AT AT AT 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 AT AT AT
212039 TACAAAAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:212336 original size:33 final size:34
Alignment explanation
Indices: 212290--212361 Score: 128
Period size: 33 Copynumber: 2.1 Consensus size: 34
212280 AATAACTTGG
212290 ATAAACAATTTCTTAAATTTCAACTAGAAGAAAC
1 ATAAACAATTTCTTAAATTTCAACTAGAAGAAAC
*
212324 ATAAAGAA-TTCTTAAATTTCAACTAGAAGAAAC
1 ATAAACAATTTCTTAAATTTCAACTAGAAGAAAC
212357 ATAAA
1 ATAAA
212362 TTCTTTAAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 30 0.81
34 7 0.19
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.28
Consensus pattern (34 bp):
ATAAACAATTTCTTAAATTTCAACTAGAAGAAAC
Found at i:222051 original size:60 final size:60
Alignment explanation
Indices: 221958--222101 Score: 191
Period size: 60 Copynumber: 2.4 Consensus size: 60
221948 GTATTTCCTC
* * * *
221958 AAACTATGAATCTTATT-TCATATTAGTCCTTAAACTTTTAAACATTTCAATTTCATCCAA
1 AAACTATGAATCTCATTCT-AAATTAATCCTTAAACTTTTAAACATTCCAATTTCATCCAA
* **
222018 AAACTATGAATCTCATTCTAAATTAATCCTTAAACTTTTGAACATTCCAATTTCATCCCC
1 AAACTATGAATCTCATTCTAAATTAATCCTTAAACTTTTAAACATTCCAATTTCATCCAA
* *
222078 AAACCATGAATATCATTCTAAATT
1 AAACTATGAATCTCATTCTAAATT
222102 TGCACCTAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
60 73 0.99
61 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (60 bp):
AAACTATGAATCTCATTCTAAATTAATCCTTAAACTTTTAAACATTCCAATTTCATCCAA
Found at i:222075 original size:29 final size:29
Alignment explanation
Indices: 221984--222075 Score: 78
Period size: 29 Copynumber: 3.1 Consensus size: 29
221974 TTCATATTAG
* *
221984 TCCTTAAACTTTTAAACATTTCAATTTCA
1 TCCTTAAACTTTTGAACATTCCAATTTCA
** * * * *
222013 TCCAAAAAC-TATGAATCTCATTCTAAATTAA
1 TCCTTAAACTTTTGAA---CATTCCAATTTCA
222044 TCCTTAAACTTTTGAACATTCCAATTTCA
1 TCCTTAAACTTTTGAACATTCCAATTTCA
222073 TCC
1 TCC
222076 CCAAACCATG
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
28 4 0.09
29 20 0.44
31 16 0.36
32 5 0.11
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.39
Consensus pattern (29 bp):
TCCTTAAACTTTTGAACATTCCAATTTCA
Found at i:222112 original size:60 final size:59
Alignment explanation
Indices: 221979--222139 Score: 164
Period size: 60 Copynumber: 2.7 Consensus size: 59
221969 CTTATTTCAT
* * ** * *
221979 ATTAGTCCTTAAACTTTTAAACATTTCAATTTCATCCAAAAACTATGAATCTCATTCTAA
1 ATTA-TCCCTAAACTTTTAAACATTCCAATTTCATCCCCAAACCATGAATATCATTCTAA
* *
222039 ATTAATCCTTAAACTTTTGAACATTCCAATTTCATCCCCAAACCATGAATATCATTCTAA
1 ATT-ATCCCTAAACTTTTAAACATTCCAATTTCATCCCCAAACCATGAATATCATTCTAA
* * *
222099 ATT-TGCACCTAAACTTTTTCATCA-TCCAATTTTATCCCCAA
1 ATTAT-C-CCTAAAC-TTTTAAACATTCCAATTTCATCCCCAA
222140 GTTCATCCAA
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
58 1 0.01
59 1 0.01
60 77 0.89
61 8 0.09
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.37
Consensus pattern (59 bp):
ATTATCCCTAAACTTTTAAACATTCCAATTTCATCCCCAAACCATGAATATCATTCTAA
Found at i:222435 original size:59 final size:60
Alignment explanation
Indices: 222264--222428 Score: 210
Period size: 59 Copynumber: 2.8 Consensus size: 60
222254 TATATACATC
* * ** *
222264 TAATTTA-GGATTAAATTGAAATGTTCAAAAAGTTTGGGGACCAATTTAGAATGAAGATCA
1 TAATTTAGGGATAAAATTGAAATGTT-TAAAAGTTTAAGGACCAATTTAGAATGAAAATCA
* * * *
222324 TAATTTGGGGATAAAAATGAAATG-TTAAAAGTTTAAGGACTAAATTAGAATGAAAATCA
1 TAATTTAGGGATAAAATTGAAATGTTTAAAAGTTTAAGGACCAATTTAGAATGAAAATCA
*
222383 TAGTTTAGGGATAAAATTGAAATGTTTAAAAG-TTAAGGACCAATTT
1 TAATTTAGGGATAAAATTGAAATGTTTAAAAGTTTAAGGACCAATTT
222429 GAAATGAGGG
Statistics
Matches: 89, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
59 61 0.69
60 14 0.16
61 14 0.16
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.32
Consensus pattern (60 bp):
TAATTTAGGGATAAAATTGAAATGTTTAAAAGTTTAAGGACCAATTTAGAATGAAAATCA
Found at i:222514 original size:15 final size:17
Alignment explanation
Indices: 222483--222517 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
222473 AATATTTATA
222483 TAATTATAATAATATTT
1 TAATTATAATAATATTT
222500 TAATTA-AAT-ATATTT
1 TAATTATAATAATATTT
222515 TAA
1 TAA
222518 AATCATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 3 0.17
17 6 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TAATTATAATAATATTT
Found at i:222767 original size:6 final size:6
Alignment explanation
Indices: 222756--222784 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
222746 CTCCATTCAA
222756 ATAATT ATAATT ATAATT ATAATT ATAAT
1 ATAATT ATAATT ATAATT ATAATT ATAAT
222785 CAATTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATAATT
Found at i:232881 original size:21 final size:21
Alignment explanation
Indices: 232838--232881 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
232828 AGATAAACTA
* *
232838 TGGCTTTGCAAAAGTGTTGCT
1 TGGCTTTGAAAAAGTGTTCCT
232859 TGGCTTTGAAACAAGT-TTCCT
1 TGGCTTTGAAA-AAGTGTTCCT
232880 TG
1 TG
232882 ATTTTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (21 bp):
TGGCTTTGAAAAAGTGTTCCT
Found at i:252584 original size:29 final size:28
Alignment explanation
Indices: 252537--252604 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
252527 ATTTTATGCA
* * *
252537 TATTTAAATTTCTGCCCTTTACTTTTTATT
1 TATTT-AATTTCAGCCCTTTA-ATTTCATT
*
252567 TATTTAATTTCAGTCCTTTAATTTCATT
1 TATTTAATTTCAGCCCTTTAATTTCATT
*
252595 AATTTAATTT
1 TATTTAATTT
252605 TCTATCTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 15 0.45
29 13 0.39
30 5 0.15
ACGTcount: A:0.25, C:0.13, G:0.03, T:0.59
Consensus pattern (28 bp):
TATTTAATTTCAGCCCTTTAATTTCATT
Found at i:252710 original size:2 final size:2
Alignment explanation
Indices: 252703--252742 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
252693 AGTCCCAAGA
252703 AT AT AT AT 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 AT AT AT AT
252743 GCATGTTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:274419 original size:23 final size:22
Alignment explanation
Indices: 274393--274460 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
274383 AAAATTAAAT
274393 TTAATAACTTATTATAAAAATTA
1 TTAAT-ACTTATTATAAAAATTA
* *
274416 TTAAATA-TCTAATATAAATATTA
1 TT-AATACT-TATTATAAAAATTA
274439 TTAAT-CTTATTATAAAATATTA
1 TTAATACTTATTATAAAA-ATTA
274461 ACTATATAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
21 8 0.22
22 9 0.24
23 17 0.46
24 3 0.08
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (22 bp):
TTAATACTTATTATAAAAATTA
Found at i:274476 original size:42 final size:41
Alignment explanation
Indices: 274385--274477 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 41
274375 AAACTTTTAA
*
274385 AATTAAATTTAATAACTTATTATAAAAATTATTAAATATCT
1 AATTAAATTTAATAACTTATTATAAAAATTATTAAATATAT
* *
274426 AATATAAATATTATTAATCTTATTAT-AAAA-TATTAACTATAT
1 AAT-TAAAT-TTAATAA-CTTATTATAAAAATTATTAAATATAT
274468 AGATTAAATT
1 A-ATTAAATT
274478 ATAAATTATG
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
41 4 0.09
42 21 0.47
43 12 0.27
44 8 0.18
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (41 bp):
AATTAAATTTAATAACTTATTATAAAAATTATTAAATATAT
Found at i:276845 original size:22 final size:22
Alignment explanation
Indices: 276820--276908 Score: 108
Period size: 22 Copynumber: 4.0 Consensus size: 22
276810 TAACTTTCTG
276820 TCTTTGAAAAAAGAATCTATCA
1 TCTTTGAAAAAAGAATCTATCA
*
276842 TCTTTGAAAAGAGAATCTATCA
1 TCTTTGAAAAAAGAATCTATCA
* * *
276864 TCATTGAAAAGATAATCTATCA
1 TCTTTGAAAAAAGAATCTATCA
* *
276886 T-TCTTGTAGAAAGAATCTATCA
1 TCT-TTGAAAAAAGAATCTATCA
276908 T
1 T
276909 TCTTGCAGAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (22 bp):
TCTTTGAAAAAAGAATCTATCA
Found at i:276909 original size:22 final size:21
Alignment explanation
Indices: 276829--276920 Score: 82
Period size: 22 Copynumber: 4.2 Consensus size: 21
276819 GTCTTTGAAA
*
276829 AAAGAATCTATCATCTT-TGAA
1 AAAGAATCTATCATCTTGT-AG
276850 AAGAGAATCTATCATCATTG-A-
1 AA-AGAATCTATCATC-TTGTAG
276871 AAAGATAATCTATCATTCTTGTAG
1 AAAG--AATCTATCA-TCTTGTAG
*
276895 AAAGAATCTATCATTCTTGCAG
1 AAAGAATCTATCA-TCTTGTAG
276917 AAAG
1 AAAG
276921 TATATATATA
Statistics
Matches: 62, Mismatches: 1, Indels: 15
0.79 0.01 0.19
Matches are distributed among these distances:
20 2 0.03
21 4 0.06
22 47 0.76
23 5 0.08
24 4 0.06
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (21 bp):
AAAGAATCTATCATCTTGTAG
Found at i:283529 original size:23 final size:22
Alignment explanation
Indices: 283473--283533 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
283463 ATTTAATAAA
283473 CTTATTATAAAAT-TTATTAAT
1 CTTATTATAAAATATTATTAAT
* *
283494 ATCTAATAT-AAATATTATTTAAT
1 CT-TATTATAAAATATTA-TTAAT
283517 CTTATTATAAAATATTA
1 CTTATTATAAAATATTA
283534 ACTATATAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
21 5 0.16
22 13 0.41
23 14 0.44
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (22 bp):
CTTATTATAAAATATTATTAAT
Found at i:284017 original size:28 final size:28
Alignment explanation
Indices: 283978--284043 Score: 132
Period size: 28 Copynumber: 2.4 Consensus size: 28
283968 CTTCTTCTTC
283978 TCTCTCTAAATGAGAGAATCCTCTCGAT
1 TCTCTCTAAATGAGAGAATCCTCTCGAT
284006 TCTCTCTAAATGAGAGAATCCTCTCGAT
1 TCTCTCTAAATGAGAGAATCCTCTCGAT
284034 TCTCTCTAAA
1 TCTCTCTAAA
284044 AACCCTCGCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (28 bp):
TCTCTCTAAATGAGAGAATCCTCTCGAT
Found at i:284137 original size:20 final size:20
Alignment explanation
Indices: 284112--284153 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
284102 GGCACCACCT
284112 ACGGTGGCCAGAAAACACAA
1 ACGGTGGCCAGAAAACACAA
284132 ACGGTGGCCAGAAAACACAA
1 ACGGTGGCCAGAAAACACAA
284152 AC
1 AC
284154 TCTACTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.45, C:0.26, G:0.24, T:0.05
Consensus pattern (20 bp):
ACGGTGGCCAGAAAACACAA
Done.