Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006706.1 Hibiscus syriacus cultivar Beakdansim tig00016709_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: 51675
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:578 original size:18 final size:18
Alignment explanation
Indices: 555--595 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
545 TTTAGTTCAC
*
555 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAA
573 GGAATGTAAGATTACCAA
1 GGAATGTAAGATTACCAA
591 GGAAT
1 GGAAT
596 AGGATTACTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.41, C:0.10, G:0.27, T:0.22
Consensus pattern (18 bp):
GGAATGTAAGATTACCAA
Found at i:5282 original size:21 final size:21
Alignment explanation
Indices: 5256--5297 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5246 CTTTCGCTAG
*
5256 TTGCCTATTTTTAAGAGCCAA
1 TTGCCTATTTTCAAGAGCCAA
*
5277 TTGCCTCTTTTCAAGAGCCAA
1 TTGCCTATTTTCAAGAGCCAA
5298 CTAAGAGGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (21 bp):
TTGCCTATTTTCAAGAGCCAA
Found at i:13075 original size:18 final size:15
Alignment explanation
Indices: 13052--13094 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 15
13042 GGTTAAAAAA
13052 CGGTTAAAAAATAGTGAT
1 CGGTTAAAAAATA---AT
13070 CGGTTAAACAAATAAT
1 CGGTTAAA-AAATAAT
13086 CGGTTAAAA
1 CGGTTAAAA
13095 TTTTGACCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 1 0.04
16 10 0.42
18 8 0.33
19 5 0.21
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.26
Consensus pattern (15 bp):
CGGTTAAAAAATAAT
Found at i:13169 original size:23 final size:23
Alignment explanation
Indices: 13143--13188 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
13133 ATCAAGTATA
*
13143 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
** *
13166 ATAATGTAATAGGTAGCGTTTAT
1 ATAACATAATAGGTAGCGCTTAT
13189 TTAATAAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.37
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:13199 original size:23 final size:23
Alignment explanation
Indices: 13152--13199 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
13142 AATAACATAT
**
13152 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
* *
13175 TAGGTAGCGTTTATTTAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
13198 TA
1 TA
13200 ACATTTAACC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:13224 original size:85 final size:87
Alignment explanation
Indices: 13115--13278 Score: 251
Period size: 85 Copynumber: 1.9 Consensus size: 87
13105 AATGTTATAT
* * *
13115 CATTTAACCAGAAATATCATCAAGTATAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCAGAAATATCATCAAGTACAATAACATATTAGATAACGCTTATATAATGTAATAGGT
*
13180 AGCGTTTAT-TTAATAAAATAA
66 AGCGCTTATATTAATAAAATAA
* * *
13201 CATTTAACC-GAAATATTATCAAGTACAATAACATATTAGATAACTCTTATATAATGTAATATGT
1 CATTTAACCAGAAATATCATCAAGTACAATAACATATTAGATAACGCTTATATAATGTAATAGGT
13265 AGCGCTTATATTAA
66 AGCGCTTATATTAA
13279 CCTATTTTCG
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
85 57 0.81
86 13 0.19
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.35
Consensus pattern (87 bp):
CATTTAACCAGAAATATCATCAAGTACAATAACATATTAGATAACGCTTATATAATGTAATAGGT
AGCGCTTATATTAATAAAATAA
Found at i:13698 original size:200 final size:197
Alignment explanation
Indices: 13278--14000 Score: 778
Period size: 200 Copynumber: 3.6 Consensus size: 197
13268 GCTTATATTA
** * * *
13278 ACCTATTTTCGAAGTAAACCAGTATATTTATACCGATAACATTGTAAATTTACCTATTACATTAT
1 ACCTATTTTCTCA-TAAAACAGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTAT
* * * ** *
13343 TATTATCGGTTACGATGTTTTT-AGATCGATACAATTT-TAAATGTATCGACACTTTATGTTTGC
65 AATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGC
** * * *
13406 ACCTGGTTGGACATTCATATTTCATTTTGGAAAAAAGTATCGACACAAACTAACAACGTGTCGAT
130 ACCT-GTT-----TTGGTA-TTCATTCTGGACAAAAGTATCGACACAAATTAACAA-GTGTCGAT
13471 ACATTAT-TTAG
187 ACATTATGTT-G
* * *
13482 ACCTATTCTCTCATAAAACAAGTATATTTAAACCGGTTACATTGAAAATTTACCTATTACATTAT
1 ACCTATTTTCTCATAAAAC-AGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTAT
* * **
13547 ACTTATGGGTTTCGATGTTTCCGGGATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGC
65 AATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGC
** *
13612 ACCCT-TTTTGGTATTCATTCTGGACCAAAAGTATCGACACAAATTTATTAAGTGTCGATACTTT
130 A-CCTGTTTTGGTATTCATTCTGGA-CAAAAGTATCGACACAAA-TTAACAAGTGTCGATACATT
*
13676 ATGCTG
192 ATGTTG
* * * *
13682 ACCTATTTTATCATAAAACTGGTATATTTATATCGGTTACATTGTAAATTTACCTAATACATTAT
1 ACCTATTTTCTCATAAAAC-AGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTAT
* *
13747 AATTATCGGTTTCAATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCG-TG
65 AATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATG-GTTG
* * *
13811 CACCTCG-TTTGTGCATTCATCCTGGACAATAAGTATCGACACAAATTACACAAGTGTCAATACA
129 CACCT-GTTTTG-GTATTCATTCTGGACAA-AAGTATCGACACAAATTA-ACAAGTGTCGATACA
13875 TTATGTTG
190 TTATGTTG
* * * * * * *
13883 ACATGTTTTCTAATTAATCGGTATATTTATACCGGTTACATTGTTAATTTACCTATTACATTATA
1 ACCTATTTTCTCATAAAACAGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATA
* * *
13948 ATTATTGGTTTTGATGTTTTTTGGG-TCGATAC-TTGTATAAAATGTATCGACAC
66 ATTATCGGTTTCGATG-TTTTTGGGATCGATACTTTTTAT-AAATGTATCGACAC
14001 ATATTTAGGT
Statistics
Matches: 442, Mismatches: 62, Indels: 34
0.82 0.12 0.06
Matches are distributed among these distances:
199 17 0.04
200 238 0.54
201 72 0.16
203 5 0.01
204 67 0.15
205 14 0.03
206 26 0.06
207 3 0.01
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (197 bp):
ACCTATTTTCTCATAAAACAGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATA
ATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCA
CCTGTTTTGGTATTCATTCTGGACAAAAGTATCGACACAAATTAACAAGTGTCGATACATTATGT
TG
Found at i:16931 original size:200 final size:198
Alignment explanation
Indices: 16541--16903 Score: 514
Period size: 200 Copynumber: 1.8 Consensus size: 198
16531 TTTTTCAACA
* * * * * * *
16541 AAGTGTCGATACATGTTGTATACCTATTCTTTCATAAAATCGGTATATTTATACCGGTTACATTG
1 AAGTGTCGATACATATTATAGACCTATTCTGTCATAAAACCGGTATATGTATACCGGTTACATTA
* * *
16606 TAAATTTACCTATTATATTATAATTATGGGTTTCAATGTTTTTGGAATCGACACTTTTTGAAAAT
66 CAAAATTACCTATTACATTATAATTATGGGTTTCAATGTTTTTGGAATCGACACTTTTTGAAAAT
* * * *
16671 GTATCGACACTTTATGTGTTCACCCTTTTTGACATCCATTATGGACAAAAATTATCGACACAATA
131 GTATCAACACTTTATGCGTGCACCCTTTTGGACATCCATTATGG--AAAAATTATCGACACAATA
16736 TTAAT
194 TTAAT
*
16741 AAGTGTCGATACATATTATAGACCTATTCTGTCATAAAACCGGTATATGTATACCGGTTATATTA
1 AAGTGTCGATACATATTATAGACCTATTCTGTCATAAAACCGGTATATGTATACCGGTTACATTA
* *
16806 CAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACAC-TTTT-AATAA
66 CAAAATTACCTATTACATTATAATTATGGGTTTCAATGTTTTTGGAATCGACACTTTTTGAA-AA
16869 TTGTATCAACACTTTATGCGTGCAACCCTTTTGGA
130 -TGTATCAACACTTTATGCGTGC-ACCCTTTTGGA
16904 TCGACACTCT
Statistics
Matches: 143, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
198 2 0.01
199 6 0.04
200 125 0.87
201 10 0.07
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (198 bp):
AAGTGTCGATACATATTATAGACCTATTCTGTCATAAAACCGGTATATGTATACCGGTTACATTA
CAAAATTACCTATTACATTATAATTATGGGTTTCAATGTTTTTGGAATCGACACTTTTTGAAAAT
GTATCAACACTTTATGCGTGCACCCTTTTGGACATCCATTATGGAAAAATTATCGACACAATATT
AAT
Found at i:17101 original size:251 final size:251
Alignment explanation
Indices: 16645--17136 Score: 711
Period size: 251 Copynumber: 2.0 Consensus size: 251
16635 GTTTCAATGT
* * **
16645 TTTTGGAATCGACACTTTTTGAAAATGTATCGACACTTTATGTGTTCACCCTTTTTGACATCCAT
1 TTTTGGAATCGACACTCTATGAAAATGTATCGACACTTTATAAGTTCACCCTTTTTGACATCCAT
* * * *
16710 TATGGACAAAAATTATCGACACAATATTAATAAGTGTCGATACATATTATAGACCTATTCTGTCA
66 TATGGACAAAAAGTATCGACACAATACTAATAAGTGTCGATAAATATTATAGACATATTCTGTCA
* * *
16775 TAAAACCGGTATATGTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTC
131 TAAAACCGGTATATGTATACCGGTTATATTAAAAAATTACCCATTACATTATAATTATGAGTTTC
* *
16840 GATGTTTTTGGGATCGACACTTTTAATA-ATTGTATCAACACTTTATGCGTGCAACCC
196 AATGTTTTTGGG-TCGACACTTTTAATATA-TGGATCAACACTTTATGCGTGCAACCC
* *
16897 TTTTGG-ATCGACACTCTATGAAAATGTATCGACACTTTGTAAGTTCACCCTTTTTGGCATCCAT
1 TTTTGGAATCGACACTCTATGAAAATGTATCGACACTTTATAAGTTCACCCTTTTTGACATCCAT
* * * *
16961 TCTGGACAAAAAGTATCGACACAATACTAATAAGTGTCGATAAATGTTGTAGACATATT-TTTCA
66 TATGGACAAAAAGTATCGACACAATACTAATAAGTGTCGATAAATATTATAGACATATTCTGTCA
* *
17025 TAAAACCGGTATATTTATACCGGTTATATTAAAAAATTACCCATTATATTATAATTATGAGTTTC
131 TAAAACCGGTATATGTATACCGGTTATATTAAAAAATTACCCATTACATTATAATTATGAGTTTC
** * *
17090 AATGTTTTTTGGGTCGTTACTTTTTATATATGGATCGACACTTTATG
196 AATG-TTTTTGGGTCGACACTTTTAATATATGGATCAACACTTTATG
17137 AGAAACTTTA
Statistics
Matches: 213, Mismatches: 25, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
250 94 0.44
251 113 0.53
252 6 0.03
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (251 bp):
TTTTGGAATCGACACTCTATGAAAATGTATCGACACTTTATAAGTTCACCCTTTTTGACATCCAT
TATGGACAAAAAGTATCGACACAATACTAATAAGTGTCGATAAATATTATAGACATATTCTGTCA
TAAAACCGGTATATGTATACCGGTTATATTAAAAAATTACCCATTACATTATAATTATGAGTTTC
AATGTTTTTGGGTCGACACTTTTAATATATGGATCAACACTTTATGCGTGCAACCC
Found at i:20441 original size:201 final size:201
Alignment explanation
Indices: 19907--20803 Score: 1268
Period size: 201 Copynumber: 4.6 Consensus size: 201
19897 TATTTAAATT
* *
19907 AGTATCGACACAAAATTAAAAACGTGTCGATACATGTTGTAGACCTATTATCTCATAAAACTGGT
1 AGTATCGACACAAAATTAAAAAAGTGTCGATACATATTGTAGACCTATTATCTCATAAAACTGGT
19972 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
66 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
* *
20037 GGATCAACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTATGG
131 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGG
20102 A-CAAA
196 ACCAAA
* ** * * * * * *
20107 ACTTATCGATGCAATATT-AATAAGTGTCGATACATATTATAGACCTATTCTCTCATAAAACCGA
1 A-GTATCGACACAAAATTAAAAAAGTGTCGATACATATTGTAGACCTATTATCTCATAAAACTGG
* * * *
20171 TATATGTATACCAGTTATATT-ACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTT
65 TATATTTATACCGGTTACATTGA-AAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTT
* * *
20235 TGGGATCGACACTTTTTAAAAATATATCGACACTTTATGCGTTCACCCTTTTTGGCACCCATTCT
129 TGGGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCT
20300 GGACCAAA
194 GGACCAAA
* *
20308 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTATCTCATAAAACTAGT
1 AGTATCGACACAAAATTAAAAAAGTGTCGATACATATTGTAGACCTATTATCTCATAAAACTGGT
20373 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
66 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
* * *
20438 GGATCGACATTTTTTGAAAATGTATCGACATTTTATGCGTTCACCCTTTTTGGCATCCATCCTGG
131 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGG
20503 ACCAAA
196 ACCAAA
*
20509 AGTATCGACACAAAATTAAAAAAGTGTCGATACATATTGTAGACCTATTCTCTCATAAAA-TCGG
1 AGTATCGACACAAAATTAAAAAAGTGTCGATACATATTGTAGACCTATTATCTCATAAAACT-GG
* * * *
20573 TATATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTTGATGTTTCT
65 TATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTT
* *
20638 GGGATCGACAC--TTT----ATG---CG------T-T-C--AC-CCTTTT-TGGCATCCATTCTG
130 GGGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTG
20682 GACCAAA
195 GACCAAA
* *
20689 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACTGGT
1 AGTATCGACACAAAATTAAAAAAGTGTCGATACATATTGTAGACCTATTATCTCATAAAACTGGT
* *
20754 ATATTTATACCGGTTACATTGAAAATTTACCTATTATATTATACTTATGG
66 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGG
20804 ATGCATATGT
Statistics
Matches: 633, Mismatches: 57, Indels: 34
0.87 0.08 0.05
Matches are distributed among these distances:
180 128 0.20
181 6 0.01
182 1 0.00
184 1 0.00
185 1 0.00
186 1 0.00
192 2 0.00
195 3 0.00
199 4 0.01
200 174 0.27
201 311 0.49
202 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (201 bp):
AGTATCGACACAAAATTAAAAAAGTGTCGATACATATTGTAGACCTATTATCTCATAAAACTGGT
ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGG
ACCAAA
Found at i:20763 original size:180 final size:180
Alignment explanation
Indices: 20461--20825 Score: 608
Period size: 180 Copynumber: 2.0 Consensus size: 180
20451 TTGAAAATGT
*
20461 ATCGACATTTTATGCGTTCACCCTTTTTGGCATCCATCCTGGACCAAAAGTATCGACACAAAATT
1 ATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATCCTGGACCAAAAGTATCGACACAAAATT
*
20526 AAAAAAGTGTCGATACATATTGTAGACCTATTCTCTCATAAAATCGGTATATTTATACTGGTTAC
66 AAAAAAGTGTCGATACATATTGTAGACCTATTCTCTCATAAAATCGGTATATTTATACCGGTTAC
* * **
20591 ATTGTAAATTTACCTATTACATTATAATTATGGGT-TTTGATGTTTCTGGG
131 ATTGAAAATTTACCTATTACATTATAATTATGGATGCAT-ATGTTTCTGGG
*
20641 ATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGGACCAAAAGTATCGACACAAAATT
1 ATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATCCTGGACCAAAAGTATCGACACAAAATT
*
20706 AAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAA-CTGGTATATTTATACCGGTTA
66 AAAAAAGTGTCGATACATATTGTAGACCTATTCTCTCATAAAATC-GGTATATTTATACCGGTTA
* *
20770 CATTGAAAATTTACCTATTATATTATACTTATGGATGCATATGTTTCTGGG
130 CATTGAAAATTTACCTATTACATTATAATTATGGATGCATATGTTTCTGGG
20821 ATCGA
1 ATCGA
20826 TAAATTTTAC
Statistics
Matches: 173, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
179 1 0.01
180 171 0.99
181 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (180 bp):
ATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATCCTGGACCAAAAGTATCGACACAAAATT
AAAAAAGTGTCGATACATATTGTAGACCTATTCTCTCATAAAATCGGTATATTTATACCGGTTAC
ATTGAAAATTTACCTATTACATTATAATTATGGATGCATATGTTTCTGGG
Found at i:21705 original size:4 final size:4
Alignment explanation
Indices: 21696--21720 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
21686 AATGTCCTTT
21696 CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA C
21721 CAATCTCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:22949 original size:33 final size:33
Alignment explanation
Indices: 22912--22980 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
22902 CATCTTAAGA
*
22912 TCACCCCTTAACACCTCAACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
* *
22945 TCACCCCTCAACACCTCTACTTCTTTCATCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
22978 TCA
1 TCA
22981 TCTATTTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.23, C:0.45, G:0.00, T:0.32
Consensus pattern (33 bp):
TCACCCCTCAACACCTCAACTTCTTTCACCACT
Found at i:23036 original size:21 final size:21
Alignment explanation
Indices: 23011--23052 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
23001 CACCTTATGC
23011 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
23032 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
23053 TTTGATTGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.31, G:0.12, T:0.40
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:23157 original size:15 final size:15
Alignment explanation
Indices: 23137--23199 Score: 117
Period size: 15 Copynumber: 4.2 Consensus size: 15
23127 ACTCTGTTTT
*
23137 CCCTCACCGTCATCC
1 CCCTCATCGTCATCC
23152 CCCTCATCGTCATCC
1 CCCTCATCGTCATCC
23167 CCCTCATCGTCATCC
1 CCCTCATCGTCATCC
23182 CCCTCATCGTCATCC
1 CCCTCATCGTCATCC
23197 CCC
1 CCC
23200 AATACAACCA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.13, C:0.57, G:0.06, T:0.24
Consensus pattern (15 bp):
CCCTCATCGTCATCC
Found at i:25397 original size:20 final size:19
Alignment explanation
Indices: 25343--25388 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
25333 CTGGTAGCGC
*
25343 TTTACCGGTTTTATCATTT
1 TTTACCAGTTTTATCATTT
*
25362 TGATACCAGTTTTATCATATT
1 T-TTACCAGTTTTATCAT-TT
25383 TTTACC
1 TTTACC
25389 TGTTATATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 18 0.82
21 3 0.14
ACGTcount: A:0.22, C:0.17, G:0.09, T:0.52
Consensus pattern (19 bp):
TTTACCAGTTTTATCATTT
Found at i:25555 original size:20 final size:20
Alignment explanation
Indices: 25527--25581 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
25517 GGTAGTTCTT
*
25527 TACCAGTTTTATCATTTCGA
1 TACCGGTTTTATCATTTCGA
25547 TACCGGTTTTATCATTTCGA
1 TACCGGTTTTATCATTTCGA
*
25567 TACCGGTTTTGTCAT
1 TACCGGTTTTATCAT
25582 ATTTTTACCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (20 bp):
TACCGGTTTTATCATTTCGA
Found at i:25691 original size:202 final size:202
Alignment explanation
Indices: 25345--25722 Score: 648
Period size: 202 Copynumber: 1.9 Consensus size: 202
25335 GGTAGCGCTT
*
25345 TACCGGTTTTATCATTTTGATACCAGTTTTATCATATTTTTACCTGTTATATCGTTGTGGAACGA
1 TACCGGTTTTATCATTTCGATACCAGTTTTATCATATTTTTACCTGTTATATCGTTGTGGAACGA
*
25410 TACATTTTTATAAAGTATCGACACTTTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAG
66 TACATTTTTATAAAGTATCGACACTTTATAGGCGCTAAAAATGCTTCTCTTTTAAATTCACAAAG
** *
25475 TGTCGATACTTATATTAATGTACCGACACTTTAAATATATCCGGTAGTTCTTTACCAGTTTTATC
131 TGTCGATACTTATATTAAAATACCGACACGTTAAATATATCCGGTAGTTCTTTACCAGTTTTATC
25540 ATTTCGA
196 ATTTCGA
* * *
25547 TACCGGTTTTATCATTTCGATACCGGTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGA
1 TACCGGTTTTATCATTTCGATACCAGTTTTATCATATTTTTACCTGTTATATCGTTGTGGAACGA
*
25612 TACATTTTTATAAAGTATCGACACTTTATAGGCGTTAAAAATGCTTCTCTTTTAAATTCACAAAG
66 TACATTTTTATAAAGTATCGACACTTTATAGGCGCTAAAAATGCTTCTCTTTTAAATTCACAAAG
* * *
25677 TGTCGATCCTTATATTAAAATATCGACACGTTCAATATATCCGGTA
131 TGTCGATACTTATATTAAAATACCGACACGTTAAATATATCCGGTA
25723 AGGATTTACA
Statistics
Matches: 164, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
202 164 1.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.41
Consensus pattern (202 bp):
TACCGGTTTTATCATTTCGATACCAGTTTTATCATATTTTTACCTGTTATATCGTTGTGGAACGA
TACATTTTTATAAAGTATCGACACTTTATAGGCGCTAAAAATGCTTCTCTTTTAAATTCACAAAG
TGTCGATACTTATATTAAAATACCGACACGTTAAATATATCCGGTAGTTCTTTACCAGTTTTATC
ATTTCGA
Found at i:28402 original size:18 final size:18
Alignment explanation
Indices: 28379--28426 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
28369 CCAAAACTTC
28379 AACTCCATCTTCAACCGT
1 AACTCCATCTTCAACCGT
28397 AACTCCATCTTCAACCGT
1 AACTCCATCTTCAACCGT
28415 AACTCCATCTTC
1 AACTCCATCTTC
28427 CTTTTCCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.27, C:0.40, G:0.04, T:0.29
Consensus pattern (18 bp):
AACTCCATCTTCAACCGT
Found at i:28994 original size:24 final size:23
Alignment explanation
Indices: 28957--29005 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
28947 ATTTTTTATA
*
28957 TATTATAATATTATATATTTAAT
1 TATTATAATATTATATATTAAAT
*
28980 TATTAATAATTTTATATATTAAAT
1 TATT-ATAATATTATATATTAAAT
29004 TA
1 TA
29006 AACTAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTATAATATTATATATTAAAT
Found at i:28999 original size:16 final size:17
Alignment explanation
Indices: 28953--29001 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 17
28943 AATTATTTTT
*
28953 TATATATTATAATATT-A
1 TATATTTTAT-ATATTAA
*
28970 TATATTTAAT-TATTAA
1 TATATTTTATATATTAA
28986 TA-ATTTTATATATTAA
1 TATATTTTATATATTAA
29002 ATTAAACTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 10 0.37
16 9 0.33
17 8 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATATTTTATATATTAA
Found at i:29424 original size:7 final size:7
Alignment explanation
Indices: 29414--29438 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29404 AATAAAATTT
29414 AAAATAG
1 AAAATAG
29421 AAAATAG
1 AAAATAG
29428 AAAATAG
1 AAAATAG
29435 AAAA
1 AAAA
29439 GAAAAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAATAG
Found at i:30443 original size:5 final size:5
Alignment explanation
Indices: 30435--30498 Score: 74
Period size: 5 Copynumber: 12.0 Consensus size: 5
30425 TCTGACCAGA
* *
30435 CCGAC CCGAC CCGAC CCGAC CGTTGAC CCGAC CCGAC CCGAC CCGAC CGTTGAC
1 CCGAC CCGAC CCGAC CCGAC C--CGAC CCGAC CCGAC CCGAC CCGAC C--CGAC
30489 CCGAC CCGAC
1 CCGAC CCGAC
30499 TGTTGTCCGT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
5 43 0.84
7 8 0.16
ACGTcount: A:0.19, C:0.53, G:0.22, T:0.06
Consensus pattern (5 bp):
CCGAC
Found at i:30464 original size:17 final size:17
Alignment explanation
Indices: 30442--30503 Score: 66
Period size: 17 Copynumber: 4.1 Consensus size: 17
30432 AGACCGACCC
30442 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
30459 GACCCGA--C--CC---
1 GACCCGACCCGACCGTT
30469 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
*
30486 GACCCGACCCGACTGTT
1 GACCCGACCCGACCGTT
30503 G
1 G
30504 TCCGTTGACC
Statistics
Matches: 37, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
10 7 0.19
12 1 0.03
13 2 0.05
14 2 0.05
15 1 0.03
17 24 0.65
ACGTcount: A:0.18, C:0.47, G:0.24, T:0.11
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:30465 original size:27 final size:27
Alignment explanation
Indices: 30435--30498 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
30425 TCTGACCAGA
30435 CCGACCCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCCGACCGTTGAC
30462 CCGACCCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCCGACCGTTGAC
30489 CCGACCCGAC
1 CCGACCCGAC
30499 TGTTGTCCGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.19, C:0.53, G:0.22, T:0.06
Consensus pattern (27 bp):
CCGACCCGACCCGACCCGACCGTTGAC
Found at i:32728 original size:13 final size:13
Alignment explanation
Indices: 32710--32739 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
32700 CAGGGTGCTG
32710 TGGCGATGTTAGA
1 TGGCGATGTTAGA
32723 TGGCGATGTTAGA
1 TGGCGATGTTAGA
32736 TGGC
1 TGGC
32740 AATGCCTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.20, C:0.10, G:0.40, T:0.30
Consensus pattern (13 bp):
TGGCGATGTTAGA
Found at i:33122 original size:18 final size:18
Alignment explanation
Indices: 33096--33157 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
33086 TATTGAAAAC
*
33096 CCGATAAACCGAACCGAA
1 CCGAAAAACCGAACCGAA
33114 CCGAAAAACCCGAACCGTTAA
1 CCGAAAAA-CCGAACCG--AA
*
33135 ---AAAAACTGAACCGAA
1 CCGAAAAACCGAACCGAA
33150 CCGAAAAA
1 CCGAAAAA
33158 ATCAGTGTCG
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
15 2 0.06
17 7 0.19
18 17 0.47
19 8 0.22
21 2 0.06
ACGTcount: A:0.50, C:0.29, G:0.15, T:0.06
Consensus pattern (18 bp):
CCGAAAAACCGAACCGAA
Found at i:38194 original size:19 final size:19
Alignment explanation
Indices: 38166--38208 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
38156 GCAGCTGGAA
*
38166 AACCGGTTTGACCGGTCTG
1 AACCGATTTGACCGGTCTG
*
38185 AACCGATTTGATCGGTCTG
1 AACCGATTTGACCGGTCTG
38204 AACCG
1 AACCG
38209 GTCTGACCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.21, C:0.26, G:0.28, T:0.26
Consensus pattern (19 bp):
AACCGATTTGACCGGTCTG
Found at i:44168 original size:24 final size:24
Alignment explanation
Indices: 44136--44182 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
44126 TCTATTCCAT
44136 GGACTTGACAATTTTAACATGTCC
1 GGACTTGACAATTTTAACATGTCC
44160 GGACTTGACAATTTTAACATGTC
1 GGACTTGACAATTTTAACATGTC
44183 AATATCGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (24 bp):
GGACTTGACAATTTTAACATGTCC
Found at i:47011 original size:22 final size:21
Alignment explanation
Indices: 46986--47042 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
46976 TAATATGAAC
46986 ATAATATAATTAAAATTTAAT-T
1 ATAATATAATTAAAA--TAATGT
*
47008 ATAATATAAATAAAATAATGT
1 ATAATATAATTAAAATAATGT
*
47029 ATATTATAATTAAA
1 ATAATATAATTAAA
47043 TCTTTATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.13
21 13 0.42
22 14 0.45
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
ATAATATAATTAAAATAATGT
Found at i:48238 original size:20 final size:20
Alignment explanation
Indices: 48213--48256 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
48203 GAACTTCCTG
* *
48213 GAACTGGTTCGAGTTAACTC
1 GAACTGGTTCGAGTCAACCC
*
48233 GAACTGGTTTGAGTCAACCC
1 GAACTGGTTCGAGTCAACCC
48253 GAAC
1 GAAC
48257 CGACCTGAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (20 bp):
GAACTGGTTCGAGTCAACCC
Found at i:48265 original size:20 final size:20
Alignment explanation
Indices: 48242--48284 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
48232 CGAACTGGTT
*
48242 TGAGTCAACCCGAACCGACC
1 TGAGTCAACCCAAACCGACC
* *
48262 TGAGTCAACTCAAACCGATC
1 TGAGTCAACCCAAACCGACC
48282 TGA
1 TGA
48285 CATGTTGACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.33, G:0.19, T:0.16
Consensus pattern (20 bp):
TGAGTCAACCCAAACCGACC
Found at i:50292 original size:32 final size:33
Alignment explanation
Indices: 50215--50293 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
50205 CCTCGATATG
* * *
50215 TTCCCTTGGGTAGGCTCTCAGGCCCCAAGGTGC
1 TTCCCTTGGGTAGGCTATAAGGCCCCAAGGTGA
*
50248 TACCCTTGGGTAGGCTATAAGGCCCCAAGGT-A
1 TTCCCTTGGGTAGGCTATAAGGCCCCAAGGTGA
*
50280 TTCCCTTAGGTAGG
1 TTCCCTTGGGTAGG
50294 GTCGCACTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 12 0.30
33 28 0.70
ACGTcount: A:0.18, C:0.28, G:0.29, T:0.25
Consensus pattern (33 bp):
TTCCCTTGGGTAGGCTATAAGGCCCCAAGGTGA
Done.