Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007063.1 Hibiscus syriacus cultivar Beakdansim tig00018345_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: 123613
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:1539 original size:2 final size:2
Alignment explanation
Indices: 1526--1557 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1516 AATGATTTAC
*
1526 AT AT AC 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
1558 GATAAGAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4002 original size:28 final size:29
Alignment explanation
Indices: 3961--4034 Score: 105
Period size: 28 Copynumber: 2.6 Consensus size: 29
3951 GGTACTTAGA
* *
3961 AAAAAATATTTTAGGTACTTATTTTGACC
1 AAAAAATACTTTAGGTACTTATTGTGACC
*
3990 AAAAAATA-TTTAGGTACTTATTGTGATC
1 AAAAAATACTTTAGGTACTTATTGTGACC
*
4018 AAAAAATACTTTTGGTA
1 AAAAAATACTTTAGGTA
4035 TTTAAATGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 26 0.63
29 15 0.37
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (29 bp):
AAAAAATACTTTAGGTACTTATTGTGACC
Found at i:9351 original size:60 final size:58
Alignment explanation
Indices: 9254--9384 Score: 167
Period size: 60 Copynumber: 2.2 Consensus size: 58
9244 GCATCATATG
* * *
9254 TCCTCAAACTATGAATCATTCTAAATTGGTCTCTAAACTTTTGAATATACCAATTTCA
1 TCCTCAAACTATGAATCATTATAAATTAGTCTCTAAACTTTTGAACATACCAATTTCA
*
9312 TCCTCAAACTAT-AATTTTCATTATAAATTAGTC-CTTAAACTTTTGAACATTCCAATTTCA
1 TCCTCAAACTATGAA---TCATTATAAATTAGTCTC-TAAACTTTTGAACATACCAATTTCA
*
9372 TTCTCAAACTATG
1 TCCTCAAACTATG
9385 GCCCTCATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
57 2 0.03
58 12 0.19
59 1 0.02
60 48 0.76
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.40
Consensus pattern (58 bp):
TCCTCAAACTATGAATCATTATAAATTAGTCTCTAAACTTTTGAACATACCAATTTCA
Found at i:9412 original size:60 final size:60
Alignment explanation
Indices: 9254--9415 Score: 141
Period size: 60 Copynumber: 2.7 Consensus size: 60
9244 GCATCATATG
* * * * *
9254 TCCTCAAACTATGAA---TCATTCTAAATTGGTCTCTAAACTTTTGAATATACCAATTTCA
1 TCCTCAAACTAT-AACCCTCATTATAAATTAGTCCCCAAACTTTTGAACATACCAATTTCA
*** ** *
9312 TCCTCAAACTATAATTTTCATTATAAATTAGTCCTTAAACTTTTGAACATTCCAATTTCA
1 TCCTCAAACTATAACCCTCATTATAAATTAGTCCCCAAACTTTTGAACATACCAATTTCA
* ** * * *
9372 TTCTCAAACTATGGCCCTCATTTTGAATTTGTCCCCAAACTTTT
1 TCCTCAAACTATAACCCTCATTATAAATTAGTCCCCAAACTTTT
9416 AAATCTTTCA
Statistics
Matches: 84, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
57 2 0.02
58 12 0.14
60 70 0.83
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.40
Consensus pattern (60 bp):
TCCTCAAACTATAACCCTCATTATAAATTAGTCCCCAAACTTTTGAACATACCAATTTCA
Found at i:9668 original size:59 final size:60
Alignment explanation
Indices: 9605--9729 Score: 148
Period size: 60 Copynumber: 2.1 Consensus size: 60
9595 TATTAGGAGT
* * * *
9605 AATTTAGAATGAATGAT-ATAGTTT-GGGGTGAAAATAAAATATTCAAAAGTTT-GAGGATA
1 AATTTAGAATG-ATAATCATAGTTTAAGGATGAAAATAAAATATTCAAAAATTTAGA-GATA
* * *
9664 AATTTAGAATGATAATCATAGTTTAAGGATGAAATTAAAATATTTAAAAATTTAGAGATC
1 AATTTAGAATGATAATCATAGTTTAAGGATGAAAATAAAATATTCAAAAATTTAGAGATA
9724 AATTTA
1 AATTTA
9730 AAAAAAAGAA
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
58 4 0.07
59 18 0.32
60 32 0.57
61 2 0.04
ACGTcount: A:0.46, C:0.02, G:0.17, T:0.34
Consensus pattern (60 bp):
AATTTAGAATGATAATCATAGTTTAAGGATGAAAATAAAATATTCAAAAATTTAGAGATA
Found at i:14013 original size:30 final size:31
Alignment explanation
Indices: 13949--14018 Score: 133
Period size: 31 Copynumber: 2.3 Consensus size: 31
13939 GTAACTTTTA
13949 ATAGTCGAGAGATTTAATAAAGCAGTACCCT
1 ATAGTCGAGAGATTTAATAAAGCAGTACCCT
13980 ATAGTCGAGAGATTTAATAAAGCAGTA-CCT
1 ATAGTCGAGAGATTTAATAAAGCAGTACCCT
14010 ATAGTCGAG
1 ATAGTCGAG
14019 GGACCATTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
30 12 0.31
31 27 0.69
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (31 bp):
ATAGTCGAGAGATTTAATAAAGCAGTACCCT
Found at i:14131 original size:2 final size:2
Alignment explanation
Indices: 14124--14194 Score: 135
Period size: 2 Copynumber: 36.0 Consensus size: 2
14114 AAATGCTTTC
14124 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14165 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
14195 TCCTAGAACT
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 67 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21759 original size:2 final size:2
Alignment explanation
Indices: 21752--21782 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
21742 AAGGGATAAT
21752 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21783 GAACCAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24531 original size:38 final size:38
Alignment explanation
Indices: 24484--24561 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
24474 ATACCTAAAG
24484 TTTAATTTTTGTTTCA-TTTTAGTACCC-GCCTTTAAAAT
1 TTTAATTTTTGTTTCATTTTTAGTACCCTG--TTTAAAAT
*
24522 TTTAGTTTTTGTTTCATTTTTAGTACCCTGTTTAAAAT
1 TTTAATTTTTGTTTCATTTTTAGTACCCTGTTTAAAAT
24560 TT
1 TT
24562 AACGTTAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
38 25 0.68
39 11 0.30
40 1 0.03
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56
Consensus pattern (38 bp):
TTTAATTTTTGTTTCATTTTTAGTACCCTGTTTAAAAT
Found at i:35972 original size:21 final size:21
Alignment explanation
Indices: 35941--35996 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
35931 TACGGTGCTA
* *
35941 ACATAACAGTCCATTGTACTG
1 ACATGACAGTCCACTGTACTG
** *
35962 ATGTGACAGTCCACTGTGCTG
1 ACATGACAGTCCACTGTACTG
35983 ACATGACAGTCCAC
1 ACATGACAGTCCAC
35997 AATGGTTGAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.25
Consensus pattern (21 bp):
ACATGACAGTCCACTGTACTG
Found at i:36521 original size:41 final size:41
Alignment explanation
Indices: 36465--36580 Score: 114
Period size: 39 Copynumber: 2.9 Consensus size: 41
36455 CGTTTTTTGA
* *
36465 ATAAACGCCGGTAAATACTTGTACTTTAGTGGTGTTTT-TAT
1 ATAAAAGCCGCTAAATA-TTGTACTTTAGTGGTGTTTTGTAT
* * * *
36506 ATAAAAGCCGCTAAATATTATACTTTCGTGGCGTTTTGTGT
1 ATAAAAGCCGCTAAATATTGTACTTTAGTGGTGTTTTGTAT
* *
36547 A-AACAA--CTCTAAATATTGTACTTTAGCGGTGTTT
1 ATAA-AAGCCGCTAAATATTGTACTTTAGTGGTGTTT
36581 GTGTGGCGTT
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
39 23 0.37
40 19 0.31
41 20 0.32
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (41 bp):
ATAAAAGCCGCTAAATATTGTACTTTAGTGGTGTTTTGTAT
Found at i:36542 original size:40 final size:41
Alignment explanation
Indices: 36447--36542 Score: 106
Period size: 40 Copynumber: 2.3 Consensus size: 41
36437 TAGCGGTATT
* * * *
36447 TTTAGAGGCGTTTTT-TGAATAAACGCCGGTAAATACTTGTAC
1 TTTAGTGGCGTTTTTAT--ATAAAAGCCGCTAAATACTTATAC
*
36489 TTTAGTGGTGTTTTTATATAAAAGCCGCTAAATA-TTATAC
1 TTTAGTGGCGTTTTTATATAAAAGCCGCTAAATACTTATAC
*
36529 TTTCGTGGCGTTTT
1 TTTAGTGGCGTTTT
36543 GTGTAAACAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
40 17 0.37
41 15 0.33
42 13 0.28
43 1 0.02
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42
Consensus pattern (41 bp):
TTTAGTGGCGTTTTTATATAAAAGCCGCTAAATACTTATAC
Found at i:36668 original size:41 final size:41
Alignment explanation
Indices: 36618--36776 Score: 141
Period size: 41 Copynumber: 3.9 Consensus size: 41
36608 TAAATACTCT
* * *
36618 TATTTTAGTGGCGTTTTTATATAAACG-CCGTCAAAGAGTTG
1 TATTTTAGTGGCGTTTTTATACAAACGTCCGT-AAAGAATCG
*
36659 TATTTTAGTGGCGTTTTTATACAAACGTCGGTAAAGAATCG
1 TATTTTAGTGGCGTTTTTATACAAACGTCCGTAAAGAATCG
* * * *
36700 TACTTTAGTAGC-TTTTTATACAAACATCAC-TGAAA-AATCA
1 TATTTTAGTGGCGTTTTTATACAAACGTC-CGT-AAAGAATCG
**
36740 TGA-TTTAGTGGTATTTTTATACAAACG-CCGCTAAAGA
1 T-ATTTTAGTGGCGTTTTTATACAAACGTCCG-TAAAGA
36777 GTGGTGTTTT
Statistics
Matches: 98, Mismatches: 12, Indels: 16
0.78 0.10 0.13
Matches are distributed among these distances:
39 1 0.01
40 32 0.33
41 62 0.63
42 3 0.03
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (41 bp):
TATTTTAGTGGCGTTTTTATACAAACGTCCGTAAAGAATCG
Found at i:38583 original size:29 final size:29
Alignment explanation
Indices: 38540--38622 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
38530 CTCACCTAAC
38540 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
38570 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
38599 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
38623 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:43350 original size:29 final size:29
Alignment explanation
Indices: 43307--43389 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
43297 CTCACCTAAC
43307 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
43337 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
43366 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
43390 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:46319 original size:21 final size:21
Alignment explanation
Indices: 46295--46364 Score: 104
Period size: 21 Copynumber: 3.3 Consensus size: 21
46285 TAAACTTTGA
*
46295 TTTATTATTATGGATTTCAAG
1 TTTATTGTTATGGATTTCAAG
*
46316 TTTACTGTTATGGATTTCAAG
1 TTTATTGTTATGGATTTCAAG
* *
46337 TTTGTTGTTATGGATGTCAAG
1 TTTATTGTTATGGATTTCAAG
46358 TTTATTG
1 TTTATTG
46365 GATAATGCTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.23, C:0.06, G:0.20, T:0.51
Consensus pattern (21 bp):
TTTATTGTTATGGATTTCAAG
Found at i:46754 original size:42 final size:43
Alignment explanation
Indices: 46676--46767 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 43
46666 TAAATAGTGG
* * * *
46676 CGTTTGTATAAAAAATGCCGCTAAATATCATTACCTTTAGCGA
1 CGTTTGTATAAAAAACGCCGCTAAAAAACATAACCTTTAGCGA
* * *
46719 CGTTTGTA-AAAAAACGTCGTTAAAAAACATAACCTTTAGCGG
1 CGTTTGTATAAAAAACGCCGCTAAAAAACATAACCTTTAGCGA
46761 CGTTTGT
1 CGTTTGT
46768 CTATCTTTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 34 0.81
43 8 0.19
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (43 bp):
CGTTTGTATAAAAAACGCCGCTAAAAAACATAACCTTTAGCGA
Found at i:51937 original size:27 final size:27
Alignment explanation
Indices: 51906--51963 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
51896 TTTGTTTTCG
* *
51906 TCGCTAAAACATATTTTCTTTTATCTT
1 TCGCTAAAACATATTTTCTTTAATATT
*
51933 TCGCTATAACATATTTTCTTTAATATT
1 TCGCTAAAACATATTTTCTTTAATATT
51960 TCGC
1 TCGC
51964 CGCTATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.26, C:0.19, G:0.05, T:0.50
Consensus pattern (27 bp):
TCGCTAAAACATATTTTCTTTAATATT
Found at i:51970 original size:30 final size:29
Alignment explanation
Indices: 51901--51970 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 29
51891 ATATCTTTGT
* * *
51901 TTTCGTCGCTAAAACATATTTTCTTTTATC
1 TTTCG-CGCTATAACATATTTTCTTTAATA
51931 TTT--CGCTATAACATATTTTCTTTAATA
1 TTTCGCGCTATAACATATTTTCTTTAATA
51958 TTTCGCCGCTATA
1 TTTCG-CGCTATA
51971 TATTTCTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 24 0.71
30 10 0.29
ACGTcount: A:0.24, C:0.20, G:0.07, T:0.49
Consensus pattern (29 bp):
TTTCGCGCTATAACATATTTTCTTTAATA
Found at i:51979 original size:46 final size:47
Alignment explanation
Indices: 51929--52031 Score: 131
Period size: 46 Copynumber: 2.2 Consensus size: 47
51919 TTTTCTTTTA
* *
51929 TCTTTCG-CTATAACA-TATTTTCTTTAATATTTCGCCGCTATATA-TT
1 TCTTTCGTCTATAAAAGTATTTTCTTT-AT-TTTCACCGCTATATACTT
*
51975 TCTTTCGTCTCTAAAAGTATTTTCTTTATTTTCACCGCTATATATCTT
1 TCTTTCGTCTATAAAAGTATTTTCTTTATTTTCACCGCTATATA-CTT
52023 TCTTTCGTC
1 TCTTTCGTC
52032 GCTCCATTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
46 21 0.42
47 8 0.16
48 21 0.42
ACGTcount: A:0.20, C:0.21, G:0.07, T:0.51
Consensus pattern (47 bp):
TCTTTCGTCTATAAAAGTATTTTCTTTATTTTCACCGCTATATACTT
Found at i:52197 original size:47 final size:46
Alignment explanation
Indices: 51944--52201 Score: 161
Period size: 48 Copynumber: 5.4 Consensus size: 46
51934 CGCTATAACA
* ** * * *
51944 TATTTTCTTTAATATTTCGCCGCTATATATTTCTTTCGTCTCTAAAAG
1 TATTTTCTTTTAT-TTTCATCGCTATATCTTTCTTTCGTCCCT-AAAC
* *
51992 TATTTTC-TTTATTTTCACCGCTATATATCTTTCTTTCGTCGCT---C
1 TATTTTCTTTTATTTTCATCGC--TATATCTTTCTTTCGTCCCTAAAC
* * * **
52036 CATTTTC-CTTATTTTCA-CTGCTATATCTTTGTTTTCGTTGCTAGAAC
1 TATTTTCTTTTATTTTCATC-GCTATATCTTT-CTTTCGTCCCTA-AAC
* * *
52083 ATATTTTCTTTTATCTTTCGTCTTTCGCCGCTATATCTTTCTTTCGTCGCTAAAT
1 -TATTTTCTTTTA--TTT--TC-AT---CGCTATATCTTTCTTTCGTCCCTAAAC
52138 TATTTTCTTTTATCTTTCATCGCTATATCTTTCTTTCGTCCCTATAAC
1 TATTTTCTTTTAT-TTTCATCGCTATATCTTTCTTTCGTCCCTA-AAC
52186 TATTTTC-TTTATTTTC
1 TATTTTCTTTTATTTTC
52202 GCCGCTCTAA
Statistics
Matches: 171, Mismatches: 18, Indels: 44
0.73 0.08 0.19
Matches are distributed among these distances:
42 9 0.05
43 10 0.06
44 17 0.10
46 12 0.07
47 33 0.19
48 40 0.23
49 3 0.02
50 1 0.01
51 5 0.03
52 1 0.01
53 4 0.02
54 12 0.07
55 2 0.01
56 10 0.06
57 11 0.06
58 1 0.01
ACGTcount: A:0.17, C:0.22, G:0.07, T:0.54
Consensus pattern (46 bp):
TATTTTCTTTTATTTTCATCGCTATATCTTTCTTTCGTCCCTAAAC
Found at i:52202 original size:27 final size:27
Alignment explanation
Indices: 52171--52237 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
52161 TATATCTTTC
52171 TTTCGTCC-CTATAACTATTTTCTTTAT
1 TTTCG-CCGCTATAACTATTTTCTTTAT
*
52198 TTTCGCCGCTCTAACTATTTTCTTTAT
1 TTTCGCCGCTATAACTATTTTCTTTAT
* *
52225 TTCCGCTGCTATA
1 TTTCGCCGCTATA
52238 TCTTTGTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 2 0.06
27 33 0.94
ACGTcount: A:0.16, C:0.25, G:0.07, T:0.51
Consensus pattern (27 bp):
TTTCGCCGCTATAACTATTTTCTTTAT
Found at i:52393 original size:48 final size:47
Alignment explanation
Indices: 52210--52492 Score: 238
Period size: 46 Copynumber: 6.0 Consensus size: 47
52200 TCGCCGCTCT
** ** * *
52210 AACTATTTTC-TTTATTTCCGCTGCTATATCTTTGTTTTTGTCGCTAA
1 AACTATTTTCTTTTATTTTTGCCACTATATCTTT-CTTTCGTCGCTAA
52257 AAC-ATTCCTTCTTTTATTTTTCGCCACTATATCTTTCTTTCGTCGCTAA
1 AACTATT--TTCTTTTATTTTT-GCCACTATATCTTTCTTTCGTCGCTAA
* * *
52306 AACTA-TTTCCTTTATTTTCGCCTCTATATCTTTCTTTCGTCGCTAA
1 AACTATTTTCTTTTATTTTTGCCACTATATCTTTCTTTCGTCGCTAA
* * * *
52352 AATTATTTTCTTTTAATTTTTGACACTATATGTTTCCTTCGTCGCTAA
1 AACTATTTTCTTTT-ATTTTTGCCACTATATCTTTCTTTCGTCGCTAA
* * * * *
52400 AACTA-TTT-TTTTATTTTCGCCGCTATAGCTTTCTCTCCGTCACTAA
1 AACTATTTTCTTTTATTTTTGCCACTATATCTTTCT-TTCGTCGCTAA
** ** * *
52446 ATGTATTTTCTTTT-TTTTCACC-GTATATCTTTTCCTTCGTCGCTAA
1 AACTATTTTCTTTTATTTTTGCCACTATATC-TTTCTTTCGTCGCTAA
52492 A
1 A
52493 GGTCATTTTA
Statistics
Matches: 192, Mismatches: 33, Indels: 23
0.77 0.13 0.09
Matches are distributed among these distances:
45 16 0.08
46 64 0.33
47 38 0.20
48 39 0.20
49 22 0.11
50 13 0.07
ACGTcount: A:0.19, C:0.23, G:0.08, T:0.51
Consensus pattern (47 bp):
AACTATTTTCTTTTATTTTTGCCACTATATCTTTCTTTCGTCGCTAA
Found at i:52398 original size:94 final size:92
Alignment explanation
Indices: 52210--52492 Score: 299
Period size: 94 Copynumber: 3.0 Consensus size: 92
52200 TCGCCGCTCT
* * * *
52210 AACTATTTTCTTTATTTCCG-CTGCTATATCTTTGTTTTTGTCGCTAAAA-CATTCCTTCTTTTA
1 AACTA-TTTCTTTATTTTCGCCT-CTATATCTTT-CTTTCGTCGCTAAAATTATT--TTCTTTTA
* *
52273 TTTTTCGCCACTATATCTTTCTTTCGTCGCTAA
61 TTTTT-GACACTATATCTTTCCTTCGTCGCTAA
52306 AACTATTTCCTTTATTTTCGCCTCTATATCTTTCTTTCGTCGCTAAAATTATTTTCTTTTAATTT
1 AACTATTT-CTTTATTTTCGCCTCTATATCTTTCTTTCGTCGCTAAAATTATTTTCTTTT-ATTT
*
52371 TTGACACTATATGTTTCCTTCGTCGCTAA
64 TTGACACTATATCTTTCCTTCGTCGCTAA
* * * * *
52400 AACTATTTTTTTATTTTCGCCGCTATAGCTTTCTCTCCGTCACT-AAATGTATTTTC-TTT-TTT
1 AACTATTTCTTTATTTTCGCCTCTATATCTTTCT-TTCGTCGCTAAAAT-TATTTTCTTTTATTT
*
52462 TTCAC-CGTATATCTTTTCCTTCGTCGCTAA
64 TTGACAC-TATATC-TTTCCTTCGTCGCTAA
52492 A
1 A
52493 GGTCATTTTA
Statistics
Matches: 165, Mismatches: 14, Indels: 20
0.83 0.07 0.10
Matches are distributed among these distances:
90 1 0.01
91 12 0.07
92 17 0.10
93 30 0.18
94 53 0.32
95 22 0.13
96 28 0.17
97 2 0.01
ACGTcount: A:0.19, C:0.23, G:0.08, T:0.51
Consensus pattern (92 bp):
AACTATTTCTTTATTTTCGCCTCTATATCTTTCTTTCGTCGCTAAAATTATTTTCTTTTATTTTT
GACACTATATCTTTCCTTCGTCGCTAA
Found at i:61754 original size:60 final size:60
Alignment explanation
Indices: 61690--61814 Score: 135
Period size: 60 Copynumber: 2.1 Consensus size: 60
61680 GTTTTGTAAT
* * * *
61690 ATATTGAATAATCAAATGATTAATTTATAATTTTTAAT-AGTTAAAAAATTTAATAAAATA
1 ATATTGAATAATCAAAAGATCAATTTATAACTTTTAATGA-TCAAAAAATTTAATAAAATA
** * * * * *
61750 ATATTTTATAATTAAAAGATCATTTTGTAACTTTTAATGATCGATAAATTTAATAAAATA
1 ATATTGAATAATCAAAAGATCAATTTATAACTTTTAATGATCAAAAAATTTAATAAAATA
61810 ATATT
1 ATATT
61815 CTATAATTGA
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
60 52 0.98
61 1 0.02
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (60 bp):
ATATTGAATAATCAAAAGATCAATTTATAACTTTTAATGATCAAAAAATTTAATAAAATA
Found at i:63880 original size:29 final size:29
Alignment explanation
Indices: 63838--63901 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
63828 CGAAGTGGTC
*
63838 GAAAACTTTTAAATAAGATTTTCGAATCA
1 GAAAACTTATAAATAAGATTTTCGAATCA
63867 GAAAACTTATAAATAAGATTTTCGAATCA
1 GAAAACTTATAAATAAGATTTTCGAATCA
63896 GAAAAC
1 GAAAAC
63902 GAACGTGTCC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.30
Consensus pattern (29 bp):
GAAAACTTATAAATAAGATTTTCGAATCA
Found at i:70971 original size:30 final size:32
Alignment explanation
Indices: 70936--71019 Score: 84
Period size: 30 Copynumber: 2.7 Consensus size: 32
70926 AAAAAATTAG
*
70936 GTTTAATTAAAATT-TTTGAAAATTTGAGA-GA
1 GTTTAATTAAAATTATTT-AAAATTAGAGAGGA
* * *
70967 -TTTAATGAGAATTATTTCAAATTAGAGAGGA
1 GTTTAATTAAAATTATTTAAAATTAGAGAGGA
* *
70998 GTTTAATTAAAAATATTCAAAA
1 GTTTAATTAAAATTATTTAAAA
71020 AAATTAAAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
30 20 0.49
31 5 0.12
32 16 0.39
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.38
Consensus pattern (32 bp):
GTTTAATTAAAATTATTTAAAATTAGAGAGGA
Found at i:84829 original size:20 final size:21
Alignment explanation
Indices: 84782--84829 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
84772 AATTATGTAA
84782 AATTATTA-CAAAATGATATT
1 AATTATTATCAAAATGATATT
* *
84802 AAAT-TTATCAAAATGTTA-T
1 AATTATTATCAAAATGATATT
84821 AATTATTAT
1 AATTATTAT
84830 AACATCATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (21 bp):
AATTATTATCAAAATGATATT
Found at i:88766 original size:25 final size:25
Alignment explanation
Indices: 88732--88781 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
88722 ATTGATGATC
88732 TAATTGTGCATC-TCTTAAAAGTTTA
1 TAATTGTGCATCTTC-TAAAAGTTTA
*
88757 TAATTTTGCATCTTCTAAAAGTTTA
1 TAATTGTGCATCTTCTAAAAGTTTA
88782 CAACTACTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 21 0.91
26 2 0.09
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (25 bp):
TAATTGTGCATCTTCTAAAAGTTTA
Found at i:92337 original size:16 final size:16
Alignment explanation
Indices: 92313--92353 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
92303 GATTTAAACT
*
92313 TAAAATAATT-TCATA
1 TAAAATAATTAGCATA
92328 TAAAAGTAATTAGCATA
1 TAAAA-TAATTAGCATA
92345 TAAAATAAT
1 TAAAATAAT
92354 CTAAATCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 5 0.22
16 9 0.39
17 9 0.39
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (16 bp):
TAAAATAATTAGCATA
Found at i:93500 original size:30 final size:30
Alignment explanation
Indices: 93466--93525 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
93456 AAACCATTTT
93466 GTAACTTTAATAGTC-AGAGGACTTAATAAA
1 GTAACTTTAATAGTCTAGA-GACTTAATAAA
93496 GTAACTTTAATAGTCTAGAGACTTAATAAA
1 GTAACTTTAATAGTCTAGAGACTTAATAAA
93526 TCAATTTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 26 0.90
31 3 0.10
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (30 bp):
GTAACTTTAATAGTCTAGAGACTTAATAAA
Found at i:93785 original size:3 final size:3
Alignment explanation
Indices: 93777--93801 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
93767 TTGACCTAAC
93777 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
93802 TATAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:95712 original size:31 final size:31
Alignment explanation
Indices: 95674--95796 Score: 212
Period size: 31 Copynumber: 4.0 Consensus size: 31
95664 GGGTCGAGGG
95674 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
95705 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
95736 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
95767 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
95797 GTCCTTCGGG
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:100074 original size:31 final size:31
Alignment explanation
Indices: 100036--100158 Score: 212
Period size: 31 Copynumber: 4.0 Consensus size: 31
100026 GGGTCGAGGG
100036 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
100067 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
100098 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
100129 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
100159 GTCCTTCGGG
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:101598 original size:24 final size:24
Alignment explanation
Indices: 101571--101658 Score: 115
Period size: 24 Copynumber: 3.6 Consensus size: 24
101561 AATTTAATGA
*
101571 TTTTTAGGTACCTTTTATTACTTG
1 TTTTTAGTTACCTTTTATTACTTG
* **
101595 TTTTTAGTTACC-TTTATTTCCATAA
1 TTTTTAGTTACCTTTTA-TTAC-TTG
101620 TTTTTAGTTACCTTTTATTACTTG
1 TTTTTAGTTACCTTTTATTACTTG
101644 TTTTTAGTTACCTTT
1 TTTTTAGTTACCTTT
101659 ATTTCCATTA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
23 4 0.07
24 30 0.56
25 16 0.30
26 4 0.07
ACGTcount: A:0.18, C:0.14, G:0.08, T:0.60
Consensus pattern (24 bp):
TTTTTAGTTACCTTTTATTACTTG
Found at i:101623 original size:25 final size:25
Alignment explanation
Indices: 101595--101671 Score: 95
Period size: 24 Copynumber: 3.1 Consensus size: 25
101585 TTATTACTTG
101595 TTTTTAGTTACCTTTATTTCCATAA
1 TTTTTAGTTACCTTTATTTCCATAA
* **
101620 TTTTTAGTTACCTTT-TATTAC-TTG
1 TTTTTAGTTACCTTTAT-TTCCATAA
101644 TTTTTAGTTACCTTTATTTCCATTAA
1 TTTTTAGTTACCTTTATTTCCA-TAA
101670 TT
1 TT
101672 CAATCAACCT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
24 20 0.48
25 19 0.45
26 3 0.07
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60
Consensus pattern (25 bp):
TTTTTAGTTACCTTTATTTCCATAA
Found at i:101632 original size:49 final size:50
Alignment explanation
Indices: 101570--101671 Score: 188
Period size: 49 Copynumber: 2.1 Consensus size: 50
101560 AAATTTAATG
101570 ATTTTTAGGTACCTTTTATTACTTGTTTTTAGTTACCTTTATTTCCA-TA
1 ATTTTTAGGTACCTTTTATTACTTGTTTTTAGTTACCTTTATTTCCATTA
*
101619 ATTTTTAGTTACCTTTTATTACTTGTTTTTAGTTACCTTTATTTCCATTA
1 ATTTTTAGGTACCTTTTATTACTTGTTTTTAGTTACCTTTATTTCCATTA
101669 ATT
1 ATT
101672 CAATCAACCT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 46 0.90
50 5 0.10
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.59
Consensus pattern (50 bp):
ATTTTTAGGTACCTTTTATTACTTGTTTTTAGTTACCTTTATTTCCATTA
Found at i:101682 original size:49 final size:48
Alignment explanation
Indices: 101580--101687 Score: 155
Period size: 49 Copynumber: 2.2 Consensus size: 48
101570 ATTTTTAGGT
* * *
101580 ACCTTTTATTACTTGTTTTTAGTTACCTTTATTTCCATAATTTTTAGTT
1 ACCTTTTATTACTTGTTTTTAGTTACCTTTATTTCCATAA-TTTCAATA
101629 ACCTTTTATTACTTGTTTTTAGTTACCTTTATTTCCATTAA-TTCAATCA
1 ACCTTTTATTACTTGTTTTTAGTTACCTTTATTTCCA-TAATTTCAAT-A
101678 ACCTTTTATT
1 ACCTTTTATT
101688 TATGTGCATT
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
48 4 0.07
49 47 0.87
50 3 0.06
ACGTcount: A:0.22, C:0.17, G:0.05, T:0.56
Consensus pattern (48 bp):
ACCTTTTATTACTTGTTTTTAGTTACCTTTATTTCCATAATTTCAATA
Found at i:107804 original size:4 final size:4
Alignment explanation
Indices: 107795--107821 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
107785 ATGCATAACC
107795 TGTA TGTA TGTA TGTA TGTA TGTA TGT
1 TGTA TGTA TGTA TGTA TGTA TGTA TGT
107822 GCCTGCATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:117038 original size:54 final size:54
Alignment explanation
Indices: 116956--117118 Score: 281
Period size: 54 Copynumber: 3.0 Consensus size: 54
116946 CGAGTCTCGA
* * * * *
116956 ATACGAGAATGTGTCCGGCATGTGTATGACGTCTCGAATATGGGAATGTGTCCG
1 ATACGAGTACGTGTCTGACATGTGTATGATGTCTCGAATATGGGAATGTGTCCG
117010 ATACGAGTACGTGTCTGACATGTGTATGATGTCTCGAATATGGGAATGTGTCCG
1 ATACGAGTACGTGTCTGACATGTGTATGATGTCTCGAATATGGGAATGTGTCCG
117064 ATACGAGTACGTGTCTGACATGTGTATGATGTCTCGAATATGGGAATGTGTCCG
1 ATACGAGTACGTGTCTGACATGTGTATGATGTCTCGAATATGGGAATGTGTCCG
117118 A
1 A
117119 ATAGAGAATG
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 104 1.00
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.30
Consensus pattern (54 bp):
ATACGAGTACGTGTCTGACATGTGTATGATGTCTCGAATATGGGAATGTGTCCG
Found at i:117133 original size:18 final size:20
Alignment explanation
Indices: 117035--117139 Score: 66
Period size: 17 Copynumber: 5.7 Consensus size: 20
117025 TGACATGTGT
*
117035 ATGATGTCTCGAATATGGGA
1 ATGATGTCTCGAATATGAGA
* *
117055 ATG-TGTC-CG-ATACGAGT
1 ATGATGTCTCGAATATGAGA
* * * *
117072 ACG-TGTCT-G-ACATGTGT
1 ATGATGTCTCGAATATGAGA
*
117089 ATGATGTCTCGAATATGGGA
1 ATGATGTCTCGAATATGAGA
117109 ATG-TGTC-CGAATA-GAGA
1 ATGATGTCTCGAATATGAGA
*
117126 ATGATGTCTGGAAT
1 ATGATGTCTCGAAT
117140 TTGAACTTGT
Statistics
Matches: 66, Mismatches: 13, Indels: 13
0.72 0.14 0.14
Matches are distributed among these distances:
17 25 0.38
18 17 0.26
19 13 0.20
20 11 0.17
ACGTcount: A:0.28, C:0.12, G:0.30, T:0.30
Consensus pattern (20 bp):
ATGATGTCTCGAATATGAGA
Found at i:120104 original size:21 final size:22
Alignment explanation
Indices: 120078--120120 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
120068 ATTAAATATA
*
120078 AATAAATTAAAA-GAAAAAAAG
1 AATAAAATAAAATGAAAAAAAG
120099 AATAAAATAAAATGAAAAAAAG
1 AATAAAATAAAATGAAAAAAAG
120121 GACATGAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (22 bp):
AATAAAATAAAATGAAAAAAAG
Found at i:120863 original size:58 final size:59
Alignment explanation
Indices: 120719--120864 Score: 201
Period size: 58 Copynumber: 2.5 Consensus size: 59
120709 GCACGTTATG
* * * *
120719 AAGATTTAATGCTTTGGGGTTTGAGC-T-AAAAACTAACATCTCGTGGAGTGCGTTGCG
1 AAGACTTAATGCTTTGGGGTTTGAGCTTAAAAAACTAACATCTCGTGGAGAGCGCTGCA
*
120776 AAGACTTACTGCTTTGGGGTTTGAG-TTAAAAAACTAACATCTCGTGGAGAGCGCTGCA
1 AAGACTTAATGCTTTGGGGTTTGAGCTTAAAAAACTAACATCTCGTGGAGAGCGCTGCA
* *
120834 AAGGCTTAATGCTCT-GGGTTTGAGCTTAAAA
1 AAGACTTAATGCTTTGGGGTTTGAGCTTAAAA
120865 CATCACGTGG
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
57 33 0.42
58 45 0.58
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (59 bp):
AAGACTTAATGCTTTGGGGTTTGAGCTTAAAAAACTAACATCTCGTGGAGAGCGCTGCA
Done.