Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003807.1 Hibiscus syriacus cultivar Beakdansim tig00008160_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: 56712
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4103 original size:44 final size:45
Alignment explanation
Indices: 3999--4111 Score: 131
Period size: 44 Copynumber: 2.5 Consensus size: 45
3989 TTGGGTAGAC
** * * *
3999 CTGGGTCACACATTATCAACATCTCCCAAGTATCTCAGGCGAGGT
1 CTGGGTCACACAGCATCGACACCTCCCAAGTACCTCAGGCGAGGT
* * *
4044 CTGGGTTC-CATAGCATCGACACCTCCCAA-TACCTTAGGCTAGGT
1 CTGGG-TCACACAGCATCGACACCTCCCAAGTACCTCAGGCGAGGT
4088 CTGGGTCACACAGCATCGACACCT
1 CTGGGTCACACAGCATCGACACCT
4112 TGCCTAGGTA
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
43 2 0.04
44 32 0.56
45 21 0.37
46 2 0.04
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (45 bp):
CTGGGTCACACAGCATCGACACCTCCCAAGTACCTCAGGCGAGGT
Found at i:8586 original size:64 final size:65
Alignment explanation
Indices: 8475--8681 Score: 221
Period size: 64 Copynumber: 3.2 Consensus size: 65
8465 TGCACTAAGA
*
8475 GTGCATCGATGCATGAAATGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCT-
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAGCCAGAGTGCATCGATGCATAG-TA
8538 G
65 G
* *
8539 GTGCATCGATGCATCAAATGCA-TCGATGTTTTCATAAA-A-CACTGAGTGCATCGATGCATAGT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTCA-AAATAGC-CAGAGTGCATCGATGCATAGT
*
8601 AT
64 AG
* ** * *
8603 GTGCATCGGTGCATGAAATGCATTCGATG--TTCAATTTATTCCATAGTGCATCGATGCATAGAT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATA-GCCAGAGTGCATCGATGCATAG-T
*
8666 TG
64 AG
*
8668 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
8682 CACTTTGAAA
Statistics
Matches: 122, Mismatches: 12, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
62 1 0.01
63 13 0.11
64 83 0.68
65 25 0.20
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAGCCAGAGTGCATCGATGCATAGTAG
Found at i:11367 original size:23 final size:22
Alignment explanation
Indices: 11337--11415 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 22
11327 GCATGGCCTT
11337 GTGCATCGATGTACATTCAAGG
1 GTGCATCGATGTACATTCAAGG
* *
11359 CGTGCATCGATGTACCTTC-ATG
1 -GTGCATCGATGTACATTCAAGG
* *
11381 GTGTATCGATGCACATTCAAAGG
1 GTGCATCGATGTACATTC-AAGG
11404 GATGCATCGATG
1 G-TGCATCGATG
11416 CACTGTTAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
21 15 0.33
22 2 0.04
23 20 0.43
24 9 0.20
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (22 bp):
GTGCATCGATGTACATTCAAGG
Found at i:16718 original size:918 final size:919
Alignment explanation
Indices: 14938--16731 Score: 2759
Period size: 918 Copynumber: 2.0 Consensus size: 919
14928 GTAATGAGTT
* *
14938 CTTTAGGAACCCATATACTTCTAACGATTTTTCCATTAGACGTTCTTTGGAGACCTCTATGATTG
1 CTTTAGGAACCCATATACTTCTAACGATTTTTCCATTAGACGTTCTTCGGAGACCTATATGATTG
* *
15003 TAGTTTCTAAAACTTTTTCTAACAAAGTTGGTCTTTGATTTTTCTCCTTTTTCAAAACATTTTGA
66 TAGTTTCTAAAACTTTTTCTAACAAAGTTGGTCTTTGAATTTTCTCCATTTTCAAAACATTTTGA
* * *
15068 TCCAACTTTATCAAAAGAAGTTTTAAGATCATCAATTTCCTTTTGATGATCATCGTTGACTCTTG
131 TCCAACTTTATCAAAAGAAGCTTTAAGATCATCAATTTCCTTTTGATGATCATCATTGACTCTTA
** *
15133 AAAGTAAATTTTGTAAATAAGAATTTTTCTTTTCAAACTCTTCTAGTTTGATTTGTAAATCTTTG
196 AAAGTAAATTTTACAAATAAGAATTTTTCTTTTCAAACTCTTCTAGTTTGATTTGCAAATCTTTG
* *
15198 ATTTTACTTTCAAGATCATTGTTGGTCTTGGATATGAGATTATTTTCATTCTTCAATTTTGAAAT
261 ATTTTACTTTCAAAATCATTGTTCGTCTTGGATATGAGATTATTTTCATTCTTCAATTTTGAAAT
*
15263 ATCATTTTTGTATTTTAAAAACAATTTCTCATAATCCGAAGCCAACCCATTATATTCCTCTAATA
326 ATCATTTTTATATTTTAAAAACAATTTCTCATAATCCGAAGCCAACCCATTATATTCCTCTAATA
15328 ACTCATCATAAGACAAATCATCTAAATCAAATGAGTTAGAGGTTACCTCAGAATCTTCCCCCAAT
391 ACTCATCATAAGACAAATCATCTAAATCAAATGAGTTAGAGGTTACCTCAGAATCTTCCCCCAAT
15393 ACCATCAAGAACAAGTTTGCTACTTCTTGTTCCTCTTCATATGAACCTTCTTCATCGCTCCATGT
456 ACCATCAAGAACAAGTTTGCTACTTCTTGTTCCTCTTCATATGAACCTTCTTCATCGCTCCATGT
* * *
15458 AGCCACGTGAGCCTTGTGCTTATTCTTTGATTGACCCTTTCTCTTCAATTGTGGGCAATCATATT
521 AGCCACATAAGCCTTGTGCTTATTCTTTGATTGACCCTTTCTCTTCAATTATGGGCAATCATATT
* * * *
15523 TGACATGCCCTAATTTTTTGCATTCATAGCAAATGATCGGGTCCTTTTCTTTTGGTTCATTCTTT
586 TGACATGCCCCAACTTTTTGCATTCATAGCAAATGATAGGGTCATTTTCTTTTGGTTCATTCTTT
** *
15588 AAGACTTCATTTCATTTGAATTTTCTTCCTCGGTTTGGCCTCATCATTTTTCTGAACTGTTTGAC
651 AAGACTTCATTTCATTTGAATTTTCTTCCTCGGTAAGGCCTCATCATTTTTCTGAACCGTTTGAC
*
15653 AAACAATGTCATCTCCTCGTCATCGTCATCTTCATCCGAATCACTTTCATCTTTTGTTGATTTGA
716 AAACAATGTCATCTCCTCGTCATCGTCATCTTCATCCGAATCACTCTCATCTTTTGTTGATTTGA
* * * * * * *
15718 GAGCAACTCTCACATTCTTCTTCTTCTCCATATCCTTCTTTGGCTCGCATTTTTTCTCTATGTCT
781 AAGCAACTCTCACATTCTTATTCTTCTCCATATCCTCCTTTGGCTCGCATTTTTTATCGAGGTCC
* * * *
15783 TCCTCTTCTTTAAGCATCATTTCATGTGTGAGGAGAGAGCCAATAAGCTCATCGAGAGTCAAGGA
846 ACCTCATCTTCAAGCATCATTTCATGAGTGAGGAGAGAGCCAATAAGCTCATCGAGAGTCAAGGA
15848 TTTTAAGTC
911 TTTTAAGTC
* * *
15857 CTTTAGGAACCCATATACTTTTAACGATTTTTCCATTAGAGGTTCTTCGGGGACCTATATGATTG
1 CTTTAGGAACCCATATACTTCTAACGATTTTTCCATTAGACGTTCTTCGGAGACCTATATGATTG
* *
15922 TAGTTTTTAAAACTTTTTCTAACAAAGTTGGAT-TTTGAATTTTCTCCATTTTCAAAACGTTTTG
66 TAGTTTCTAAAACTTTTTCTAACAAAGTTGG-TCTTTGAATTTTCTCCATTTTCAAAACATTTTG
* * *
15986 TTCTAACTTTATCAAAAGAAGCTTTAAGATCATCAATTTTCTTTTGATGATCATCATTGAC-CTT
130 ATCCAACTTTATCAAAAGAAGCTTTAAGATCATCAATTTCCTTTTGATGATCATCATTGACTC-T
**
16050 TAAAAGTAAATTTTACAAATCCGAATTTTTCTTTTCAAACTCTTCTAGTTTGATTTGCAAATCTT
194 TAAAAGTAAATTTTACAAATAAGAATTTTTCTTTTCAAACTCTTCTAGTTTGATTTGCAAATCTT
* * * *
16115 TGATTTTACTTTCAAAATCATTGTTCGTCTTGGATATGAGTTTATTTTCATTTTTTAATTTTGAG
259 TGATTTTACTTTCAAAATCATTGTTCGTCTTGGATATGAGATTATTTTCATTCTTCAATTTTGAA
*
16180 A-ATCATTTTTATATTTTAAAAACAATTTCTCATAATCCGAAGTCAACCCATTATATTCCTCTAA
324 ATATCATTTTTATATTTTAAAAACAATTTCTCATAATCCGAAGCCAACCCATTATATTCCTCTAA
* * * **
16244 TAACTCATCATAAGATAAATCATCTAATTCAAATGAGTTAGAGGTTACCTTAGAATCTTCCCTGA
389 TAACTCATCATAAGACAAATCATCTAAATCAAATGAGTTAGAGGTTACCTCAGAATCTTCCCCCA
* *
16309 ATGCCATCAAGAACAAGTTTGCTACTTCTTGTTCCTCTTCAT-TGAAACCTTTTTCATCGCTCCA
454 ATACCATCAAGAACAAGTTTGCTACTTCTTGTTCCTCTTCATATG-AACCTTCTTCATCGCTCCA
16373 TGTAGCCACATAAGCCTTGTGCTTATTCTTTGATTGACCCTTTCTCTTCAATTATGGGCAATCAT
518 TGTAGCCACATAAGCCTTGTGCTTATTCTTTGATTGACCCTTTCTCTTCAATTATGGGCAATCAT
**
16438 ATTTGACATGCCCCGGCTTTTTGCATTCATAGCAAATGATAGGGT-ATTTCTCTTTTGGTTCATT
583 ATTTGACATGCCCCAACTTTTTGCATTCATAGCAAATGATAGGGTCATTT-TCTTTTGGTTCATT
* * *
16502 -TTTGAGGCCTTCATTTCGTTTGAATTTTCTTCCTCGGTAAGGCCTCATCATTTTTCTGAACCGT
647 CTTT-AAGACTTCATTTCATTTGAATTTTCTTCCTCGGTAAGGCCTCATCATTTTTCTGAACCGT
* * * * *
16566 TTGGCAAACAATGTCATTTCCTCTTCATCGTCATCTTTATCTGAATCACTCTCATCTTTT-TTGG
711 TTGACAAACAATGTCATCTCCTCGTCATCGTCATCTTCATCCGAATCACTCTCATCTTTTGTT-G
* * *
16630 ATTTGAAAGCAACTC-CA-ATGTTTTTATTCTTCTCC-T-T-CTCCTTTGGTGTCTC-TTTAATC
775 ATTTGAAAGCAACTCTCACA--TTCTTATTCTTCTCCATATCCTCCTTTGG-CTCGCATTT--T-
16689 TTATCGAGGTCCACCTCATCTTCAAGCATCATTTCATGAGTGA
834 TTATCGAGGTCCACCTCATCTTCAAGCATCATTTCATGAGTGA
16732 TGAGGGAACC
Statistics
Matches: 793, Mismatches: 70, Indels: 25
0.89 0.08 0.03
Matches are distributed among these distances:
915 11 0.01
916 5 0.01
917 14 0.02
918 468 0.59
919 294 0.37
920 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.42
Consensus pattern (919 bp):
CTTTAGGAACCCATATACTTCTAACGATTTTTCCATTAGACGTTCTTCGGAGACCTATATGATTG
TAGTTTCTAAAACTTTTTCTAACAAAGTTGGTCTTTGAATTTTCTCCATTTTCAAAACATTTTGA
TCCAACTTTATCAAAAGAAGCTTTAAGATCATCAATTTCCTTTTGATGATCATCATTGACTCTTA
AAAGTAAATTTTACAAATAAGAATTTTTCTTTTCAAACTCTTCTAGTTTGATTTGCAAATCTTTG
ATTTTACTTTCAAAATCATTGTTCGTCTTGGATATGAGATTATTTTCATTCTTCAATTTTGAAAT
ATCATTTTTATATTTTAAAAACAATTTCTCATAATCCGAAGCCAACCCATTATATTCCTCTAATA
ACTCATCATAAGACAAATCATCTAAATCAAATGAGTTAGAGGTTACCTCAGAATCTTCCCCCAAT
ACCATCAAGAACAAGTTTGCTACTTCTTGTTCCTCTTCATATGAACCTTCTTCATCGCTCCATGT
AGCCACATAAGCCTTGTGCTTATTCTTTGATTGACCCTTTCTCTTCAATTATGGGCAATCATATT
TGACATGCCCCAACTTTTTGCATTCATAGCAAATGATAGGGTCATTTTCTTTTGGTTCATTCTTT
AAGACTTCATTTCATTTGAATTTTCTTCCTCGGTAAGGCCTCATCATTTTTCTGAACCGTTTGAC
AAACAATGTCATCTCCTCGTCATCGTCATCTTCATCCGAATCACTCTCATCTTTTGTTGATTTGA
AAGCAACTCTCACATTCTTATTCTTCTCCATATCCTCCTTTGGCTCGCATTTTTTATCGAGGTCC
ACCTCATCTTCAAGCATCATTTCATGAGTGAGGAGAGAGCCAATAAGCTCATCGAGAGTCAAGGA
TTTTAAGTC
Found at i:18338 original size:20 final size:20
Alignment explanation
Indices: 18313--18358 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
18303 TTCATGGTGC
18313 ATGCATGCATCGGTGCATCG
1 ATGCATGCATCGGTGCATCG
* *
18333 ATGCATGGATTGGTGCATCG
1 ATGCATGCATCGGTGCATCG
*
18353 GTGCAT
1 ATGCAT
18359 CACTTTGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.20, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGCATGCATCGGTGCATCG
Found at i:19776 original size:97 final size:97
Alignment explanation
Indices: 19609--19791 Score: 242
Period size: 97 Copynumber: 1.9 Consensus size: 97
19599 AGATCTTAAG
* *
19609 TTTGAGTATTTGTATATGTAGAAAAACACTGCAAGAAAACTCAGCCACCAAAATCAATTGGACGA
1 TTTGAGTATTTGTATATGTAGAAAAACACTGCAAGAAAACTCAGCCACCAAAACCAATTGAACGA
*
19674 TGCGACTCAGTCCAGATTAATAAGGTCTCAAA
66 CGCGACTCAGTCCAGATTAATAAGGTCTCAAA
* * * * * * *
19706 TTTGAGTCTTTGTGTATGTAGAAAATCTA-TGCAAGAAGACTCGGTCACCAAAACCAGTTGAACG
1 TTTGAGTATTTGTATATGTAGAAAAAC-ACTGCAAGAAAACTCAGCCACCAAAACCAATTGAACG
* *
19770 GCGCGACTCAGTTCAGATTAAT
65 ACGCGACTCAGTCCAGATTAAT
19792 CAAAACAAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
97 72 0.99
98 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.26
Consensus pattern (97 bp):
TTTGAGTATTTGTATATGTAGAAAAACACTGCAAGAAAACTCAGCCACCAAAACCAATTGAACGA
CGCGACTCAGTCCAGATTAATAAGGTCTCAAA
Found at i:26666 original size:22 final size:22
Alignment explanation
Indices: 26640--26695 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
26630 ACATAATGAT
* *
26640 GTGGCTAATGGCCGCCTCCAAC
1 GTGGCCAACGGCCGCCTCCAAC
*
26662 GTGGCCAACGGCTGCCTCCAAC
1 GTGGCCAACGGCCGCCTCCAAC
26684 GTGGCCAACGGC
1 GTGGCCAACGGC
26696 TAACAACGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.18, C:0.38, G:0.30, T:0.14
Consensus pattern (22 bp):
GTGGCCAACGGCCGCCTCCAAC
Found at i:26696 original size:22 final size:22
Alignment explanation
Indices: 26653--26696 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
26643 GCTAATGGCC
26653 GCCTCCAACGTGGCCAACGGCT
1 GCCTCCAACGTGGCCAACGGCT
26675 GCCTCCAACGTGGCCAACGGCT
1 GCCTCCAACGTGGCCAACGGCT
26697 AACAACGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.41, G:0.27, T:0.14
Consensus pattern (22 bp):
GCCTCCAACGTGGCCAACGGCT
Found at i:27053 original size:14 final size:14
Alignment explanation
Indices: 27034--27062 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
27024 AATTAATCAT
27034 TCAGTATCATACAA
1 TCAGTATCATACAA
27048 TCAGTATCATACAA
1 TCAGTATCATACAA
27062 T
1 T
27063 GATCATACAA
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:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (14 bp):
TCAGTATCATACAA
Found at i:27069 original size:11 final size:13
Alignment explanation
Indices: 27036--27072 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
27026 TTAATCATTC
27036 AGTATCATACAAT
1 AGTATCATACAAT
27049 CAGTATCATACAAT
1 -AGTATCATACAAT
27063 -G-ATCATACAA
1 AGTATCATACAA
27073 GGAAAATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 9 0.39
12 1 0.04
14 13 0.57
ACGTcount: A:0.46, C:0.19, G:0.08, T:0.27
Consensus pattern (13 bp):
AGTATCATACAAT
Found at i:28117 original size:22 final size:23
Alignment explanation
Indices: 28092--28141 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
28082 TCTATAAAAA
28092 TATTTTATTAT-A-TTATATTATT
1 TATTTTATTATCATTTATATT-TT
*
28114 TA-TTTATTATCATTTTTATTTT
1 TATTTTATTATCATTTATATTTT
28136 TATTTT
1 TATTTT
28142 TTGTAAGCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 8 0.33
22 7 0.29
23 9 0.38
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (23 bp):
TATTTTATTATCATTTATATTTT
Found at i:28121 original size:16 final size:16
Alignment explanation
Indices: 28094--28138 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
28084 TATAAAAATA
28094 TTTTATTATATTAT-AT
1 TTTTATT-TATTATCAT
28110 TATTTATTTATTATCAT
1 T-TTTATTTATTATCAT
28127 TTTTATTT-TTAT
1 TTTTATTTATTAT
28139 TTTTTGTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 4 0.15
16 14 0.52
17 9 0.33
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTATTTATTATCAT
Found at i:29171 original size:20 final size:20
Alignment explanation
Indices: 29146--29255 Score: 80
Period size: 20 Copynumber: 5.3 Consensus size: 20
29136 CCCACGTGTA
*
29146 TTTATTTTTTTAAATTTTAT
1 TTTATTTTTTTATATTTTAT
*
29166 TTTATTATTTTATTATTTT-T
1 TTTATTTTTTTA-TATTTTAT
* *
29186 TCTATTTTTTCTATTTTTTA-
1 TTTATTTTTT-TATATTTTAT
* *
29206 TTTATTTTTGTTATCTATTAT
1 TTTATTTTT-TTATATTTTAT
*
29227 ATTTATTTTATTTTTATTATTAT
1 -TTTATTTT-TTTATATT-TTAT
*
29250 TATATT
1 TTTATT
29256 AATATTAATA
Statistics
Matches: 70, Mismatches: 12, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
20 40 0.57
21 8 0.11
22 17 0.24
23 5 0.07
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.75
Consensus pattern (20 bp):
TTTATTTTTTTATATTTTAT
Found at i:29234 original size:33 final size:32
Alignment explanation
Indices: 29161--29247 Score: 99
Period size: 33 Copynumber: 2.7 Consensus size: 32
29151 TTTTTTAAAT
*
29161 TTTATTTTATTATTTTATTATTTTTTCTATTTT
1 TTTATTTTATTA-TTTATTATTTTTTCTATTTA
29194 TTCTATTTT-TTATTTATT-TTTGTTATCTATTATA
1 TT-TATTTTATTATTTATTATTT-TT-TCTATT-TA
29228 TTTATTTTATT-TTTATTATT
1 TTTATTTTATTATTTATTATT
29248 ATTATATTAA
Statistics
Matches: 47, Mismatches: 1, Indels: 11
0.80 0.02 0.19
Matches are distributed among these distances:
31 3 0.06
32 8 0.17
33 23 0.49
34 13 0.28
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.76
Consensus pattern (32 bp):
TTTATTTTATTATTTATTATTTTTTCTATTTA
Found at i:29246 original size:9 final size:9
Alignment explanation
Indices: 29165--29252 Score: 60
Period size: 9 Copynumber: 9.7 Consensus size: 9
29155 TTAAATTTTA
29165 TTTTATTA-
1 TTTTATTAT
29173 TTTTATTAT
1 TTTTATTAT
29182 TTTT-TCTAT
1 TTTTAT-TAT
29191 TTTT-TCTATT
1 TTTTAT-TA-T
29201 TTTTATTTAT
1 TTTTA-TTAT
*
29211 TTTTGTTAT
1 TTTTATTAT
*
29220 CTATTA-TAT
1 -TTTTATTAT
29229 TTATT-TTAT
1 TT-TTATTAT
29238 TTTTATTAT
1 TTTTATTAT
*
29247 TATTAT
1 TTTTAT
29253 ATTAATATTA
Statistics
Matches: 66, Mismatches: 5, Indels: 17
0.75 0.06 0.19
Matches are distributed among these distances:
8 12 0.18
9 38 0.58
10 13 0.20
11 2 0.03
12 1 0.02
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.75
Consensus pattern (9 bp):
TTTTATTAT
Found at i:29378 original size:12 final size:13
Alignment explanation
Indices: 29356--29384 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
29346 TAAATCGAAT
29356 TTTTAAATTTTAA
1 TTTTAAATTTTAA
29369 TTTT-AATTTTAA
1 TTTTAAATTTTAA
29381 TTTT
1 TTTT
29385 CACAATTAAA
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):
TTTTAAATTTTAA
Found at i:29978 original size:20 final size:20
Alignment explanation
Indices: 29953--30022 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
29943 ATTTTCTGTT
29953 TATTTTCATTCACTTGCAAA
1 TATTTTCATTCACTTGCAAA
29973 TATTTTCA---A---GCAAA
1 TATTTTCATTCACTTGCAAA
29987 TATTTTCATTCACTTGCAAA
1 TATTTTCATTCACTTGCAAA
30007 TATTTTCATTCACTTG
1 TATTTTCATTCACTTG
30023 GTTATTTCCA
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
14 13 0.30
17 2 0.05
20 29 0.66
ACGTcount: A:0.30, C:0.19, G:0.06, T:0.46
Consensus pattern (20 bp):
TATTTTCATTCACTTGCAAA
Found at i:29987 original size:14 final size:14
Alignment explanation
Indices: 29968--29994 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29958 TCATTCACTT
29968 GCAAATATTTTCAA
1 GCAAATATTTTCAA
29982 GCAAATATTTTCA
1 GCAAATATTTTCA
29995 TTCACTTGCA
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:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (14 bp):
GCAAATATTTTCAA
Found at i:30496 original size:40 final size:40
Alignment explanation
Indices: 30450--30530 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
30440 ATCCTACGAT
30450 AACATTTATTATCTTTAATTGGATAGAAAATAAACAAAAG
1 AACATTTATTATCTTTAATTGGATAGAAAATAAACAAAAG
30490 AACATTTATTATCTTTAATTGGATAGAAAATAAACAAAAG
1 AACATTTATTATCTTTAATTGGATAGAAAATAAACAAAAG
30530 A
1 A
30531 GAAGCTGCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.32
Consensus pattern (40 bp):
AACATTTATTATCTTTAATTGGATAGAAAATAAACAAAAG
Found at i:30762 original size:27 final size:27
Alignment explanation
Indices: 30724--30787 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
30714 AAAACAAAGC
* * *
30724 AAAATAAGTTTAATATTTTTATATTTT
1 AAAATAAATTTAACATTTTTAAATTTT
*
30751 TAAATAAATTTAACATTTTTAAATTTT
1 AAAATAAATTTAACATTTTTAAATTTT
*
30778 AAAACAAATT
1 AAAATAAATT
30788 AAAATAAGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (27 bp):
AAAATAAATTTAACATTTTTAAATTTT
Found at i:31005 original size:32 final size:31
Alignment explanation
Indices: 30960--31023 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
30950 GGTTGATGGC
*
30960 TAACTTTTACACATTG-GAAAATTCATCTTTGG
1 TAACTTGTACACA-TGAG-AAATTCATCTTTGG
* *
30992 TAACTTGTGCACATGAGAATTTCATCTTTGG
1 TAACTTGTACACATGAGAAATTCATCTTTGG
31023 T
1 T
31024 CCCTAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (31 bp):
TAACTTGTACACATGAGAAATTCATCTTTGG
Found at i:33330 original size:14 final size:14
Alignment explanation
Indices: 33311--33341 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
33301 TGGCAGAGCA
33311 TATGAATCAAACAC
1 TATGAATCAAACAC
*
33325 TATGAATCGAACAC
1 TATGAATCAAACAC
33339 TAT
1 TAT
33342 TGGAGAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.26
Consensus pattern (14 bp):
TATGAATCAAACAC
Found at i:39549 original size:40 final size:39
Alignment explanation
Indices: 39500--39588 Score: 124
Period size: 40 Copynumber: 2.3 Consensus size: 39
39490 GCAAAATTGA
* *
39500 CATCTTTGGTTGGTGACTAACTTGTACACATTGAAAAATT
1 CATCTTTGGTAGGTGACCAACTTGTACACA-TGAAAAATT
* * *
39540 CATCTTTGGTAGGTGACCAACTTGTGCACATGAGAATTT
1 CATCTTTGGTAGGTGACCAACTTGTACACATGAAAAATT
39579 CATCTTTGGT
1 CATCTTTGGT
39589 CCCTAAAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 17 0.39
40 27 0.61
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (39 bp):
CATCTTTGGTAGGTGACCAACTTGTACACATGAAAAATT
Found at i:40466 original size:31 final size:31
Alignment explanation
Indices: 40409--40473 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
40399 CAGTTATTAT
*
40409 ATTTGGTCTTTAATATTTTTATATTTAATCA
1 ATTTGGTCTTTAATATTTTTATATTTAATAA
*
40440 ATTTGGTC-TTAATTTTAATTTA-ATTTAATAA
1 ATTTGGTCTTTAATATT--TTTATATTTAATAA
40471 ATT
1 ATT
40474 AACCTTTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 7 0.23
31 19 0.63
32 4 0.13
ACGTcount: A:0.32, C:0.05, G:0.06, T:0.57
Consensus pattern (31 bp):
ATTTGGTCTTTAATATTTTTATATTTAATAA
Found at i:43993 original size:46 final size:46
Alignment explanation
Indices: 43926--44019 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
43916 AACCAAATCT
43926 CTCCATGATTTAATATGATTTATAGTCAATTGGTTATACCACTTGG
1 CTCCATGATTTAATATGATTTATAGTCAATTGGTTATACCACTTGG
43972 CTCCATGATTTAATATGATTTATAGTCAATTGGTTATACCACTTGG
1 CTCCATGATTTAATATGATTTATAGTCAATTGGTTATACCACTTGG
44018 CT
1 CT
44020 GCAGACCTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (46 bp):
CTCCATGATTTAATATGATTTATAGTCAATTGGTTATACCACTTGG
Found at i:47836 original size:16 final size:15
Alignment explanation
Indices: 47815--47854 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
47805 CTTACTCTTG
*
47815 GAGAGGAAATGAAGAA
1 GAGAGGAAA-GAAAAA
47831 GAGAGGAAAGAAAAA
1 GAGAGGAAAGAAAAA
47846 GAAGAGGAA
1 G-AGAGGAA
47855 TATATTTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.60, C:0.00, G:0.38, T:0.03
Consensus pattern (15 bp):
GAGAGGAAAGAAAAA
Found at i:52285 original size:22 final size:22
Alignment explanation
Indices: 52255--52321 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
52245 AGTTGATGGT
* * *
52255 TACATAGGTCCTTTGGGACATA
1 TACACAGGTCCTTCGGGACAAA
*
52277 TACAGAGGTCCTTCGGGACAAA
1 TACACAGGTCCTTCGGGACAAA
* *
52299 TACACAGGTCCTTCAGGAAAAA
1 TACACAGGTCCTTCGGGACAAA
52321 T
1 T
52322 TTCACATGCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (22 bp):
TACACAGGTCCTTCGGGACAAA
Done.