Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003330.1 Hibiscus syriacus cultivar Beakdansim tig00007011_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: 62341
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Found at i:6559 original size:15 final size:15
Alignment explanation
Indices: 6541--6578 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
6531 AAAAAATGAA
6541 AAAATAAAAACAAAT
1 AAAATAAAAACAAAT
*
6556 AAAAT-AAAATAAAT
1 AAAATAAAAACAAAT
6570 AATAATAAA
1 AA-AATAAA
6579 TTTGTTTACC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 10 0.50
15 8 0.40
16 2 0.10
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAATAAAAACAAAT
Found at i:11229 original size:29 final size:29
Alignment explanation
Indices: 11196--11252 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
11186 TCTATTATTC
11196 TTTTACTCAACAGTGTTTAACCGTTCATA
1 TTTTACTCAACAGTGTTTAACCGTTCATA
11225 TTTTACTCAACAGTGTTTAACCGTTCAT
1 TTTTACTCAACAGTGTTTAACCGTTCAT
11253 CTAACTGACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (29 bp):
TTTTACTCAACAGTGTTTAACCGTTCATA
Found at i:11339 original size:68 final size:68
Alignment explanation
Indices: 11248--11565 Score: 423
Period size: 68 Copynumber: 4.8 Consensus size: 68
11238 TGTTTAACCG
*
11248 TTCATCTAACTGACATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
11313 CCT
66 CCT
* * * * ** * *
11316 TTTATCTAACTGGCATAAATGACACATTTCTATCAAATACACAAATAGGTCTCAAAGGCAGTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
11381 CCT
66 CCT
* * * * *
11384 TTTATCTAACTGACAT-AATGAAATCTTTCTGTCAAA--CACAGTTAGACCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
11446 CCT
66 CCT
* *
11449 TTCATCTGACTGGCATAAATGACACTTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
11514 CCT
66 CCT
* * *
11517 TCCATCTAACTGGCATAAATG-CA-CATT-TGTCAAATGCACAGTTAAGCCT
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCT
11566 ATTAATCTTT
Statistics
Matches: 216, Mismatches: 31, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
65 58 0.27
66 19 0.09
67 18 0.08
68 121 0.56
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.29
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:11557 original size:133 final size:136
Alignment explanation
Indices: 11250--11560 Score: 436
Period size: 133 Copynumber: 2.3 Consensus size: 136
11240 TTTAACCGTT
*
11250 CATCTAACTGACATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCC
1 CATCTAACTGACATAAATGACACCTTTCTGTCAAATGCACAGTTAGACCTCAAAGGCACTTAGCC
* * *
11315 TTTTATCTAACTGGCATAAATGACACATTTCTATCAAATACACAAATAGGTCTCAAAGGCAGTTA
66 TTTCATCTAACTGGCATAAATGACACATTTCTATCAAATACACAAATAGGCCTCAAAGGCACTTA
*
11380 GCCTTT
131 GCCTTC
* * *
11386 TATCTAACTGACAT-AATGAAATCTTTCTGTCAAA--CACAGTTAGACCTCAAAGGCACTTAGCC
1 CATCTAACTGACATAAATGACACCTTTCTGTCAAATGCACAGTTAGACCTCAAAGGCACTTAGCC
* * * * **
11448 TTTCATCTGACTGGCATAAATGACACTTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
66 TTTCATCTAACTGGCATAAATGACACATTTCTATCAAATACACAAATAGGCCTCAAAGGCACTTA
11513 GCCTTC
131 GCCTTC
* *
11519 CATCTAACTGGCATAAATG-CA-CATT-TGTCAAATGCACAGTTA
1 CATCTAACTGACATAAATGACACCTTTCTGTCAAATGCACAGTTA
11561 AGCCTATTAA
Statistics
Matches: 154, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
131 7 0.05
132 3 0.02
133 109 0.71
134 4 0.03
135 18 0.12
136 13 0.08
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (136 bp):
CATCTAACTGACATAAATGACACCTTTCTGTCAAATGCACAGTTAGACCTCAAAGGCACTTAGCC
TTTCATCTAACTGGCATAAATGACACATTTCTATCAAATACACAAATAGGCCTCAAAGGCACTTA
GCCTTC
Found at i:11867 original size:55 final size:54
Alignment explanation
Indices: 11747--11897 Score: 198
Period size: 55 Copynumber: 2.8 Consensus size: 54
11737 TTCCTATACT
* * * * * *
11747 GAAATTCATACACTTGGCATGAATTT-TTA-TTTCGCATACATAGTGCCCATAC
1 GAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATAA
11799 GAAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATATA
1 G-AAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATA-A
11855 GAAATTCATACACTTAGTATGAATTTCTTAAGTTTTTGCACAC
1 GAAATTCATACACTTAGTATGAATTTCTT-AG-TTTTGCACAC
11898 TTAGTGCCAT
Statistics
Matches: 87, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
52 1 0.01
53 23 0.26
54 3 0.03
55 47 0.54
56 3 0.03
57 10 0.11
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.36
Consensus pattern (54 bp):
GAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATAA
Found at i:14062 original size:54 final size:54
Alignment explanation
Indices: 13934--14381 Score: 429
Period size: 54 Copynumber: 8.3 Consensus size: 54
13924 TATATGTTGA
* **
13934 AATTTCTGTATTGGCACTA--TGTGCAACTTAAGAAATTCATAAT-AGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACCCAAGAAATTCATAATGAGTTTATG
* * * * **
13985 AATTTCTGTATTGGTACTGTGTGTGCAACCTAAGAAATTCATAATTTGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACCCAAGAAATTCATAATGAGTTTATG
* *
14039 AATTTCCGTATTGGCACTATGTGTGCAACCCCACAAATTCATAATGAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACCCAAGAAATTCATAATGAGTTTATG
* * *
14093 -ATTTTCGTATTGGAACTATGTGTGCAATCCCATGAAATTCATAATGAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAA-CCCAAGAAATTCATAATGAGTTTATG
* * *
14147 AATTTTCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATA
1 AATTTCCGTATTGGCACTATGTGTGCAA-CCCAAGAAATTCATAATGAGTTTATG
* * ** *
14202 AATTTCTGTATTGGCACTATGTGTGCAACCTAAGTAACTCATAAATAATGAGTTTGTG
1 AATTTCCGTATTGGCACTATGTGTGCAACCCAAG-AA---ATTCATAATGAGTTTATG
** * *** * *
14260 AATTAT-CGTATTGGCACTATGTGTATAACCTACTTAATTCACAATGAGTTTGTG
1 AATT-TCCGTATTGGCACTATGTGTGCAACCCAAGAAATTCATAATGAGTTTATG
** * * * * * * * *
14314 AATGACCGTATCGACACTATATGTGCACCCCAAGGATTTCAAAATGAGTTTGTG
1 AATTTCCGTATTGGCACTATGTGTGCAACCCAAGAAATTCATAATGAGTTTATG
*
14368 AATTTCCATATTGG
1 AATTTCCGTATTGG
14382 TACTTAGGTG
Statistics
Matches: 329, Mismatches: 57, Indels: 19
0.81 0.14 0.05
Matches are distributed among these distances:
51 17 0.05
53 48 0.15
54 143 0.43
55 78 0.24
57 1 0.00
58 41 0.12
59 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (54 bp):
AATTTCCGTATTGGCACTATGTGTGCAACCCAAGAAATTCATAATGAGTTTATG
Found at i:14364 original size:221 final size:213
Alignment explanation
Indices: 13931--14381 Score: 487
Period size: 221 Copynumber: 2.1 Consensus size: 213
13921 AGGTATATGT
* ** *
13931 TGAAATTTCTGTATTGGCACTATGTGCAACTTAAGAAATTCATAATAGTTTATGAATTTCTGTAT
1 TGAATTTTC-GTATTGGCACTATGTGCAACCCAAGAAATTCATAATAGTTTATAAATTTCTGTAT
* * * *
13996 TGGTACTGTGTGTGCAACCTAAGAAATTCATAATTTGTTTATGAATTTCCGTATTGGCACTATGT
65 TGGCACTATGTGTGCAACCTAAGAAACTCATAATTAGTTTATGAATTTCCGTATTGGCACTATGT
* * *** * * * *
14061 GTGCAACCCCACAAATTCATAATGAGTTTATGATTTTCGTATTGGAACTATGTGTGCAATCCCAT
130 GTACAACCCCACAAATTCACAATGAGTTTATGATGACCGTATTCGAACTATATGTGCAACCCCAA
*
14126 GAAATTCATAATGAGTTTA
195 GAAATTCAAAATGAGTTTA
*
14145 TGAATTTTCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATAAATTTCTG
1 TGAATTTTCGTATTGGCACTA--TGTGCAA-CCCAAGAAATTCATAAT-AGTTTATAAATTTCTG
* *
14210 TATTGGCACTATGTGTGCAACCTAAGTAACTCATAAATAATGAGTTTGTGAATTAT-CGTATTGG
62 TATTGGCACTATGTGTGCAACCTAAGAAACTCAT-AAT--T-AGTTTATGAATT-TCCGTATTGG
* * * *
14274 CACTATGTGTATAA-CCTACTTAATTCACAATGAGTTTGTGAATGACCGTA-TCGACACTATATG
122 CACTATGTGTACAACCCCAC-AAATTCACAATGAGTTTATG-ATGACCGTATTCGA-ACTATATG
* * *
14337 TGC-ACCCCAAGGATTTCAAAATGAGTTTG
184 TGCAACCCCAAGAAATTCAAAATGAGTTTA
* *
14366 TGAATTTCCATATTGG
1 TGAATTTTCGTATTGG
14382 TACTTAGGTG
Statistics
Matches: 195, Mismatches: 30, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
213 12 0.06
214 8 0.04
215 7 0.04
216 14 0.07
217 45 0.23
218 3 0.02
220 5 0.03
221 84 0.43
222 17 0.09
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (213 bp):
TGAATTTTCGTATTGGCACTATGTGCAACCCAAGAAATTCATAATAGTTTATAAATTTCTGTATT
GGCACTATGTGTGCAACCTAAGAAACTCATAATTAGTTTATGAATTTCCGTATTGGCACTATGTG
TACAACCCCACAAATTCACAATGAGTTTATGATGACCGTATTCGAACTATATGTGCAACCCCAAG
AAATTCAAAATGAGTTTA
Found at i:18762 original size:23 final size:24
Alignment explanation
Indices: 18712--18762 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
18702 TTATCGTGTA
*
18712 ATTTTTTCATTATTTACTTATACG
1 ATTTTGTCATTATTTACTTATACG
18736 -TTTTGTCATTATTT-CTTATTA-G
1 ATTTTGTCATTATTTACTTA-TACG
18758 ATTTT
1 ATTTT
18763 ATTTTCATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.22, C:0.10, G:0.06, T:0.63
Consensus pattern (24 bp):
ATTTTGTCATTATTTACTTATACG
Found at i:20637 original size:11 final size:12
Alignment explanation
Indices: 20606--20638 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
20596 ATTTTATCAT
20606 TGAGTTCAATTA
1 TGAGTTCAATTA
20618 TGAGTTCAATTA
1 TGAGTTCAATTA
*
20630 -GGGTTCAAT
1 TGAGTTCAAT
20639 AAATTTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.39
Consensus pattern (12 bp):
TGAGTTCAATTA
Found at i:22547 original size:14 final size:14
Alignment explanation
Indices: 22528--22556 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
22518 AATTAAACCC
22528 ATGAAATATTACAT
1 ATGAAATATTACAT
22542 ATGAAATATTACAT
1 ATGAAATATTACAT
22556 A
1 A
22557 AAAGTTTATT
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:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (14 bp):
ATGAAATATTACAT
Found at i:28751 original size:109 final size:111
Alignment explanation
Indices: 28521--28751 Score: 260
Period size: 109 Copynumber: 2.1 Consensus size: 111
28511 TAATCACTAT
* * *
28521 AGGTGACCAAAATGTAAAAAAACACTTAAATAAGAGGGACTAAACAACAAATGTTCCAATAAATA
1 AGGTGTCCAAAATGCAAAAAAACACTTAAATAAGAGGGACTAAACAACAAATATTCCAATAAATA
* *
28586 TATAACGTACATGAAAAAAGGGTAAGTAACATATTTGGTCATCGTC
66 TATAACATACATGAAAAAAGGGTAAATAACATATTTGGTCATCGTC
** * *
28632 --GTAGAT-CAAAATGCAAAAACTCGCTTAAATAAGAGGGAC-ACAA-AACAAATATTCCGATAA
1 AGGT-G-TCCAAAATGCAAAAAAACACTTAAATAAGAGGGACTA-AACAACAAATATTCCAATAA
* * * *
28692 ATATATAACATACATGATAAAGGGGTAAATAGCA-ATTTTGGTCCTCG-C
63 ATATATAACATACATGAAAAAAGGGTAAATAACATA-TTTGGTCATCGTC
28740 AGGTGTCCAAAA
1 AGGTGTCCAAAA
28752 CCAAAATGCA
Statistics
Matches: 100, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
108 3 0.03
109 63 0.63
110 34 0.34
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.23
Consensus pattern (111 bp):
AGGTGTCCAAAATGCAAAAAAACACTTAAATAAGAGGGACTAAACAACAAATATTCCAATAAATA
TATAACATACATGAAAAAAGGGTAAATAACATATTTGGTCATCGTC
Found at i:29180 original size:2 final size:2
Alignment explanation
Indices: 29175--29234 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
29165 TTTTTTTTAA
29175 AT 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 AT
29217 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
29235 TTCAAAATTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29704 original size:3 final size:3
Alignment explanation
Indices: 29691--29804 Score: 165
Period size: 3 Copynumber: 37.3 Consensus size: 3
29681 AATGGGGTTG
* *
29691 TAA TAAA TAA TAA TATT TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
29738 TAG TAA TAG TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
29786 TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA T
29805 TGGAAAATGG
Statistics
Matches: 99, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
3 95 0.96
4 4 0.04
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:30929 original size:41 final size:42
Alignment explanation
Indices: 30879--30991 Score: 115
Period size: 42 Copynumber: 2.7 Consensus size: 42
30869 ATCTTGCCCG
** *
30879 AAGGTCTTATAGATGGTCCGAAGGACTTA-TTATCTTGCTCAA
1 AAGG-CTTATAGATGGTCCGAAGGACTTAGGCATCATGCTCAA
* * *
30921 AAGGCTTATAGATGATCTGAAGGATTTAGGCATCATGCTCAA
1 AAGGCTTATAGATGGTCCGAAGGACTTAGGCATCATGCTCAA
*
30963 AAGACTTACT-GATGG-CTCGAAGGACTTAG
1 AAGGCTTA-TAGATGGTC-CGAAGGACTTAG
30992 TAAGCAAGAA
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
41 22 0.38
42 35 0.60
43 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (42 bp):
AAGGCTTATAGATGGTCCGAAGGACTTAGGCATCATGCTCAA
Found at i:31184 original size:239 final size:238
Alignment explanation
Indices: 30655--31229 Score: 857
Period size: 239 Copynumber: 2.4 Consensus size: 238
30645 AAACATCCTA
* *
30655 CCCGAAGGACTTACCATCTTGCTCAAAAGGCTTATAGATGACCCGAAGGATTTAGGCATCATTCT
1 CCCGAAGGACTTATCATCTTGCTCAAAAGGCTTATAGATGACCCGAAGGATTTAGGCATCATGCT
* * *
30720 CGAAAGACTTACTAATGGCCCGAAGGACTTAGAAGTAAGAAACTTTGGAAATCTTTTTCTTACTT
66 CGAAAGACTTACTGATGG-CCGAAGGACTTAGAAGCAAGAAACTTTGGAAATCGTTTTCTTAC-T
* *
30785 TTTCAAAAAAAATCAATTTTCAGAAAAGATTTAAATGAGAAACTTTGGAAATCTCTTTCTCATTT
129 TTTCAAAAAAAATCAATTTTAAGAAAAGATTTAAATGAGAAACTTTGGAAATCGCTTTCTCATTT
30850 TTGAGAATCATATGAAAACATCTTGCCCGAAGGTCTTATAGATGG
194 TTGAGAATCATATGAAAACATCTTGCCCGAAGGTCTTATAGATGG
* * * *
30895 TCCGAAGGACTTATTATCTTGCTCAAAAGGCTTATAGATGATCTGAAGGATTTAGGCATCATGCT
1 CCCGAAGGACTTATCATCTTGCTCAAAAGGCTTATAGATGACCCGAAGGATTTAGGCATCATGCT
*
30960 CAAAAGACTTACTGATGGCTCGAAGGACTTAGTAAGCAAGAAACTTTGGAAATCGTTTTCTTAC-
66 CGAAAGACTTACTGATGGC-CGAAGGACTTAG-AAGCAAGAAACTTTGGAAATCGTTTTCTTACT
* *
31024 TTT-AAAAAAAATCAATTTTAAGAAAATATTTAAATGAGAAAGTTTGGAAATCGCTTTCTCATTC
129 TTTCAAAAAAAATCAATTTTAAGAAAAGATTTAAATGAGAAACTTTGGAAATCGCTTTCTCATT-
* ** * *
31088 TTTGAGAATCATGTGAAAACATCTTGTTCGATGGTCTTATGGATGG
193 TTTGAGAATCATATGAAAACATCTTGCCCGAAGGTCTTATAGATGG
* * * * *
31134 CCCGAATGACTTATCATCTTGGTTAAAAGACTTATAGATGACCCGAAGGATTTAAGCATCATGCT
1 CCCGAAGGACTTATCATCTTGCTCAAAAGGCTTATAGATGACCCGAAGGATTTAGGCATCATGCT
*
31199 CGAAAGACTTATTGATGGCCTGAAGGACTTA
66 CGAAAGACTTACTGATGGCC-GAAGGACTTA
31230 CTCATCAAGA
Statistics
Matches: 301, Mismatches: 30, Indels: 9
0.89 0.09 0.03
Matches are distributed among these distances:
238 57 0.19
239 128 0.43
240 87 0.29
241 29 0.10
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (238 bp):
CCCGAAGGACTTATCATCTTGCTCAAAAGGCTTATAGATGACCCGAAGGATTTAGGCATCATGCT
CGAAAGACTTACTGATGGCCGAAGGACTTAGAAGCAAGAAACTTTGGAAATCGTTTTCTTACTTT
TCAAAAAAAATCAATTTTAAGAAAAGATTTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTT
GAGAATCATATGAAAACATCTTGCCCGAAGGTCTTATAGATGG
Found at i:31236 original size:42 final size:41
Alignment explanation
Indices: 31123--31236 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 41
31113 GTTCGATGGT
* * * * *
31123 CTTATGGATGGCCCGAATGACTTATCATCTTGGTTAAAAGA
1 CTTATAGATGGCCCGAAGGACTTATCATCATGCTCAAAAGA
* * * *
31164 CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTT-ATCATCATGCTCAAAAGA
* *
31206 CTTATTGATGGCCTGAAGGACTTACTCATCA
1 CTTATAGATGGCCCGAAGGACTTA-TCATCA
31237 AGAAACCCTT
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
41 20 0.35
42 37 0.65
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTATCATCATGCTCAAAAGA
Found at i:31367 original size:57 final size:57
Alignment explanation
Indices: 31231--31369 Score: 158
Period size: 58 Copynumber: 2.4 Consensus size: 57
31221 AAGGACTTAC
* * **
31231 TCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAAAAACCTTCATTTATAGTTA
1 TCATCAAGAAACCCTTGAAAATCAAGCTTAGCTTCTTAAAAA-CTTCATTGATAGCAA
* * *
31289 TCATCAAGAAA-CCTCTAAAAATTAGGCTTAGCTTCTTTAAAAA-TTCATTGGA-AGCAA
1 TCATCAAGAAACCCT-TGAAAATCAAGCTTAGCTTC-TTAAAAACTTCATT-GATAGCAA
31346 TCATCAAGAAACCCTTGAAAATCA
1 TCATCAAGAAACCCTTGAAAATCA
31370 GGGTAGCTCA
Statistics
Matches: 68, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
57 30 0.44
58 31 0.46
59 7 0.10
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.30
Consensus pattern (57 bp):
TCATCAAGAAACCCTTGAAAATCAAGCTTAGCTTCTTAAAAACTTCATTGATAGCAA
Found at i:31478 original size:55 final size:55
Alignment explanation
Indices: 31397--31815 Score: 452
Period size: 55 Copynumber: 7.6 Consensus size: 55
31387 GTTCATCATG
* *
31397 TCAAGAAACCTT-TGAAAATTAGACTTAGTTTCTTTGAAAACTCATTTAAAACTCA
1 TCAAGAAA-CTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATCA
* * * *
31452 TCAAGAAACTTCTAAAAATTAGACTTAGTTTCTTTGTAAACTCATTTAAAAATTA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATCA
31507 TCAAGAAACTTCTGAAAATCAGACTTTAGTTTCTTTGAAAACTCATTTAAAAATCA
1 TCAAGAAACTTCTGAAAATCAGAC-TTAGTTTCTTTGAAAACTCATTTAAAAATCA
* * ** *
31563 TCAAGAAACTTTTGAAAATCAGACTTATTTTCTTTGAAAGGTAATTTAAAAATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATCA
* * * * **
31618 TCAAGAAACTTCTTAAAACCAGATTTAGTTTATTTGAAAGGTCATTTAAAAAATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTT-AAAAATCA
* * ** *
31674 TCAAGAAACTTCTAAAAATCAGAC--ACTTTCTTTGAAAGGTCATTTAAGAATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATCA
** * * * * * *
31727 TCAAGAAACTTCCAAAAATCAAACTTAGCTTTTTTTCG-AAACTTATTTGAAAGTTA
1 TCAAGAAACTTCTGAAAATCAGACTTAG-TTTCTTT-GAAAACTCATTTAAAAATCA
* * *
31783 TCAAGAAAC-CCTTGAAAATTAGGCTTAGTTTCT
1 TCAAGAAACTTC-TGAAAATCAGACTTAGTTTCT
31816 ATAAATTCTT
Statistics
Matches: 312, Mismatches: 44, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
53 29 0.09
54 22 0.07
55 142 0.46
56 118 0.38
57 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.35
Consensus pattern (55 bp):
TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATCA
Found at i:31553 original size:111 final size:110
Alignment explanation
Indices: 31397--31791 Score: 476
Period size: 111 Copynumber: 3.6 Consensus size: 110
31387 GTTCATCATG
* *
31397 TCAAGAAACCTT-TGAAAATTAGACTTAGTTTCTTTGAAAACTCATTTAAAACTCATCAAGAAAC
1 TCAAGAAA-CTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATCATCAAGAAAC
* * *
31461 TTCTAAAAATTAGACTTAGTTTCTTTGTAAA-CTCATTTAAAAATTA
65 TTCTAAAAATCAGACTTAGTTTCTTTG-AAAGGTCATTTAAAAATCA
31507 TCAAGAAACTTCTGAAAATCAGACTTTAGTTTCTTTGAAAACTCATTTAAAAATCATCAAGAAAC
1 TCAAGAAACTTCTGAAAATCAGAC-TTAGTTTCTTTGAAAACTCATTTAAAAATCATCAAGAAAC
* * * *
31572 TTTTGAAAATCAGACTTATTTTCTTTGAAAGGTAATTTAAAAATCA
65 TTCTAAAAATCAGACTTAGTTTCTTTGAAAGGTCATTTAAAAATCA
* * * * **
31618 TCAAGAAACTTCTTAAAACCAGATTTAGTTTATTTGAAAGGTCATTTAAAAAATCATCAAGAAAC
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTT-AAAAATCATCAAGAAAC
* *
31683 TTCTAAAAATCAGAC--ACTTTCTTTGAAAGGTCATTTAAGAATCA
65 TTCTAAAAATCAGACTTAGTTTCTTTGAAAGGTCATTTAAAAATCA
** * * * * * *
31727 TCAAGAAACTTCCAAAAATCAAACTTAGCTTTTTTTCG-AAACTTATTTGAAAGTTATCAAGAAA
1 TCAAGAAACTTCTGAAAATCAGACTTAG-TTTCTTT-GAAAACTCATTTAAAAATCATCAAGAAA
31791 C
64 C
31792 CCTTGAAAAT
Statistics
Matches: 247, Mismatches: 32, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
109 66 0.27
110 55 0.22
111 126 0.51
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.34
Consensus pattern (110 bp):
TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATCATCAAGAAACT
TCTAAAAATCAGACTTAGTTTCTTTGAAAGGTCATTTAAAAATCA
Found at i:31859 original size:52 final size:54
Alignment explanation
Indices: 31772--31872 Score: 138
Period size: 52 Copynumber: 1.9 Consensus size: 54
31762 TCGAAACTTA
* *
31772 TTTGAAAGTTATCAAGAAACCCTTGAAAATTAGGCTTAGTTTC-TATAAATTCT
1 TTTGAAAGTCATCAAGAAACCCTTGAAAATCAGGCTTAGTTTCTTATAAATTCT
31825 TTTGAAAG-CATCAAGAATACCC-T-AACAATCAGGCTTAGTTTCTTATAA
1 TTTGAAAGTCATCAAGAA-ACCCTTGAA-AATCAGGCTTAGTTTCTTATAA
31873 GAAATGTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
51 2 0.05
52 24 0.56
53 17 0.40
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (54 bp):
TTTGAAAGTCATCAAGAAACCCTTGAAAATCAGGCTTAGTTTCTTATAAATTCT
Found at i:35910 original size:45 final size:45
Alignment explanation
Indices: 35859--36093 Score: 343
Period size: 45 Copynumber: 5.3 Consensus size: 45
35849 GAATACCATG
** * *
35859 AGTGGCACCTTTTATGTTGATGATGCACCGTTATGCATTTTCTTT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
*
35904 AGTGGCACCTTTTATGCTGATAATGCACCGTTATGCATTTTCATT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
*
35949 AGTGG----TTTTATGCCGATAATGCACCTTTATGCATTTTCATT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
* * *
35990 AGTGGCACCTTTTATACCGATAATGCACCGCTATGAATTTTCATT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
* *
36035 AGTGGCACATTTTATGCCGATAATGCATCGTTATGCATTTTCATT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
36080 AGTGGCACCTTTTA
1 AGTGGCACCTTTTA
36094 GGCCTTCATT
Statistics
Matches: 171, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
41 39 0.23
45 132 0.77
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (45 bp):
AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
Found at i:36013 original size:86 final size:87
Alignment explanation
Indices: 35881--36093 Score: 329
Period size: 86 Copynumber: 2.4 Consensus size: 87
35871 TATGTTGATG
* * * * *
35881 ATGCACCGTTATGCATTTTCTTTAGTGGCACCTTTTATGCTGATAATGCACCGTTATGCATTTTC
1 ATGCACCGTTATGCATTTTCATTAGTGGCACCTTTTATACCGATAATGCACCGCTATGAATTTTC
35946 ATTAGTGG-TTTTATGCCGATA
66 ATTAGTGGATTTTATGCCGATA
*
35967 ATGCACCTTTATGCATTTTCATTAGTGGCACCTTTTATACCGATAATGCACCGCTATGAATTTTC
1 ATGCACCGTTATGCATTTTCATTAGTGGCACCTTTTATACCGATAATGCACCGCTATGAATTTTC
36032 ATTAGTGGCACATTTTATGCCGATA
66 ATTAGTGG---ATTTTATGCCGATA
*
36057 ATGCATCGTTATGCATTTTCATTAGTGGCACCTTTTA
1 ATGCACCGTTATGCATTTTCATTAGTGGCACCTTTTA
36094 GGCCTTCATT
Statistics
Matches: 115, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
86 67 0.58
90 48 0.42
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (87 bp):
ATGCACCGTTATGCATTTTCATTAGTGGCACCTTTTATACCGATAATGCACCGCTATGAATTTTC
ATTAGTGGATTTTATGCCGATA
Found at i:38364 original size:25 final size:24
Alignment explanation
Indices: 38323--38370 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
38313 TTGAAAGTTT
38323 ATGTCCTTTATCATTCCAAAAATC
1 ATGTCCTTTATCATTCCAAAAATC
* * *
38347 ATGTCCCTTTTTCCTTCCATAAAT
1 ATGT-CCTTTATCATTCCAAAAAT
38371 GTATGTGTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.27, C:0.27, G:0.04, T:0.42
Consensus pattern (24 bp):
ATGTCCTTTATCATTCCAAAAATC
Found at i:40866 original size:16 final size:17
Alignment explanation
Indices: 40847--40879 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40837 TTTCTAATTT
*
40847 TTTTC-TTCTTTTTGTA
1 TTTTCTTTCCTTTTGTA
40863 TTTTCTTTCCTTTTGTA
1 TTTTCTTTCCTTTTGTA
40880 CTCAAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.06, C:0.15, G:0.06, T:0.73
Consensus pattern (17 bp):
TTTTCTTTCCTTTTGTA
Found at i:40876 original size:27 final size:26
Alignment explanation
Indices: 40801--40876 Score: 68
Period size: 27 Copynumber: 3.0 Consensus size: 26
40791 TGGCTTTGCT
* *
40801 TTCTTTTTG-AATTTC-TTCTTTTTT
1 TTCTTTTTGTATTTTCTTTCTTTTTC
* *
40825 TTCTTTTTTTCTTTTCTAATT-TTTTTC
1 TTCTTTTTGTATTTTCT--TTCTTTTTC
*
40852 TTCTTTTTGTATTTTCTTTCCTTTT
1 TTCTTTTTGTATTTTCTTTCTTTTT
40877 GTACTCAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
24 8 0.20
25 6 0.15
26 4 0.10
27 20 0.50
28 2 0.05
ACGTcount: A:0.07, C:0.14, G:0.03, T:0.76
Consensus pattern (26 bp):
TTCTTTTTGTATTTTCTTTCTTTTTC
Found at i:46344 original size:22 final size:23
Alignment explanation
Indices: 46301--46344 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
46291 AATTGCTTCT
* *
46301 TGTGAAAATCAACCCATTCATGA
1 TGTGAAAATCAACCAATCCATGA
*
46324 TGTGAAGA-CAACCAATCCATG
1 TGTGAAAATCAACCAATCCATG
46345 CCCAAAATGA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.23
Consensus pattern (23 bp):
TGTGAAAATCAACCAATCCATGA
Found at i:48652 original size:45 final size:45
Alignment explanation
Indices: 48591--48828 Score: 255
Period size: 45 Copynumber: 5.2 Consensus size: 45
48581 ATGGGTGGCT
* * *
48591 CCTTTTATGCCTATAATGCACTATTATGCCTTTTC-TTAAGTGACA
1 CCTTTTATGCCGATAATGCACTGTTATGCATTTTCATT-AGTGACA
* * * *
48636 CATTTTATACCGATAATGTACCGTTATGCATTTTCATTAGTGACA
1 CCTTTTATGCCGATAATGCACTGTTATGCATTTTCATTAGTGACA
* * *
48681 CCTTTTATGTCGATAATGGATTGTTATGCATTTTCATTAGTGACA
1 CCTTTTATGCCGATAATGCACTGTTATGCATTTTCATTAGTGACA
* * **
48726 CCTTTTTTATGTCAATAATGCA-TCGTTATGCATTTTCATTAGTGGTA
1 CC--TTTTATGCCGATAATGCACT-GTTATGCATTTTCATTAGTGACA
* * * * *
48773 CTTTTTATGCCAATAATGCACCGTTATGCATTTTTATTAGTGGCA
1 CCTTTTATGCCGATAATGCACTGTTATGCATTTTCATTAGTGACA
48818 CCTTTTATGCC
1 CCTTTTATGCC
48829 TTCATTTTAG
Statistics
Matches: 165, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
45 124 0.75
46 3 0.02
47 38 0.23
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.43
Consensus pattern (45 bp):
CCTTTTATGCCGATAATGCACTGTTATGCATTTTCATTAGTGACA
Found at i:48779 original size:92 final size:92
Alignment explanation
Indices: 48591--48823 Score: 256
Period size: 92 Copynumber: 2.6 Consensus size: 92
48581 ATGGGTGGCT
* ** * * ** *
48591 CCTTTTATGCCTATAATGCACTATTATGCCTTTTC-TTAAGTGACA-C-ATTTTATACCGATAAT
1 CCTTTTATGCCAATAATGCACCGTTATGCATTTTCATT-AGTGACACCTTTTTTATGTCAATAAT
*
48653 GTACCGTTATGCATTTTCATTAGTGACA
65 GCACCGTTATGCATTTTCATTAGTGACA
* * * **
48681 CCTTTTATGTCGATAATGGATTGTTATGCATTTTCATTAGTGACACCTTTTTTATGTCAATAATG
1 CCTTTTATGCCAATAATGCACCGTTATGCATTTTCATTAGTGACACCTTTTTTATGTCAATAATG
* **
48746 CATCGTTATGCATTTTCATTAGTGGTA
66 CACCGTTATGCATTTTCATTAGTGACA
* * *
48773 CTTTTTATGCCAATAATGCACCGTTATGCATTTTTATTAGTGGCACCTTTT
1 CCTTTTATGCCAATAATGCACCGTTATGCATTTTCATTAGTGACACCTTTT
48824 ATGCCTTCAT
Statistics
Matches: 118, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
90 36 0.31
91 3 0.03
92 79 0.67
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.44
Consensus pattern (92 bp):
CCTTTTATGCCAATAATGCACCGTTATGCATTTTCATTAGTGACACCTTTTTTATGTCAATAATG
CACCGTTATGCATTTTCATTAGTGACA
Found at i:53066 original size:29 final size:28
Alignment explanation
Indices: 53016--53077 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
53006 ACAAAGCACA
*
53016 AGAAAAAACAAAAGGAAATCAAGTTAGT
1 AGAAAAAACAAAAAGAAATCAAGTTAGT
53044 AGAAACAATACAAAAAG-AATCAAGTTAGT
1 AGAAA-AA-ACAAAAAGAAATCAAGTTAGT
*
53073 TGAAA
1 AGAAA
53078 TGATTATTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 5 0.17
29 18 0.60
30 7 0.23
ACGTcount: A:0.60, C:0.08, G:0.16, T:0.16
Consensus pattern (28 bp):
AGAAAAAACAAAAAGAAATCAAGTTAGT
Found at i:55518 original size:110 final size:110
Alignment explanation
Indices: 55306--55545 Score: 324
Period size: 110 Copynumber: 2.2 Consensus size: 110
55296 CAATCACTAC
* *
55306 ATGTTACCAAAATGCAAAAACACACTTAAATATAAGGGACTAAACAACAAATATTCCAATAAATA
1 ATGTTACCAAAATGCAAAAACACACTTAAATATAAGGAACAAAACAACAAATATTCCAATAAATA
* * * *
55371 TATAACGTACATGAGCAAGGGGTAAATAATAGATTTGGTCCTTGCA
66 TATAACATACATGAACAAGGGGTAAATAATAGATTTGGTACTCG-A
* * *
55417 A-GTTAACAAAATGCAAAAACACACTTAAATA-AGAGGAACAAAACAATAAATATTCCAATAAGT
1 ATGTTACCAAAATGCAAAAACACACTTAAATATA-AGGAACAAAACAACAAATATTCCAATAAAT
* *
55480 ATATAGCATACATGAACAAGGGGTAAATAGTA-ATTTTGGTACTCGA
65 ATATAACATACATGAACAAGGGGTAAATAATAGA-TTTGGTACTCGA
*
55526 ATGTGACCAAAATGCAAAAA
1 ATGTTACCAAAATGCAAAAA
55546 TGCATTTATA
Statistics
Matches: 113, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
109 4 0.04
110 108 0.96
111 1 0.01
ACGTcount: A:0.48, C:0.14, G:0.15, T:0.23
Consensus pattern (110 bp):
ATGTTACCAAAATGCAAAAACACACTTAAATATAAGGAACAAAACAACAAATATTCCAATAAATA
TATAACATACATGAACAAGGGGTAAATAATAGATTTGGTACTCGA
Done.