Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009445.1 Hibiscus syriacus cultivar Beakdansim tig00113539_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: 49403
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:6095 original size:22 final size:23
Alignment explanation
Indices: 6069--6115 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
6059 TGATCTTTAC
*
6069 ATATGATGTTTATCATGAAT-AT
1 ATATGATATTTATCATGAATGAT
6091 ATATGATATTTATCATGAATGAT
1 ATATGATATTTATCATGAATGAT
6114 AT
1 AT
6116 TTTAGGTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.45
Consensus pattern (23 bp):
ATATGATATTTATCATGAATGAT
Found at i:6263 original size:28 final size:28
Alignment explanation
Indices: 6228--6285 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
6218 TGCATATGGT
*
6228 ACTATAGTGTATAAGGACACTTAGTACA
1 ACTATAGTGTATAAGGAAACTTAGTACA
*
6256 ACTATAGTGTATAAGGAAATTTAGTACA
1 ACTATAGTGTATAAGGAAACTTAGTACA
6284 AC
1 AC
6286 ACTGTTGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (28 bp):
ACTATAGTGTATAAGGAAACTTAGTACA
Found at i:6316 original size:30 final size:30
Alignment explanation
Indices: 6282--6341 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
6272 AAATTTAGTA
* *
6282 CAACACTGTTGTGTGTAAGGACTCTCAGTG
1 CAACACTGTGGTGTGTAAGGACACTCAGTG
6312 CAACACTGTGGTGTGTAAGGACACTCAGTG
1 CAACACTGTGGTGTGTAAGGACACTCAGTG
6342 TATATGGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (30 bp):
CAACACTGTGGTGTGTAAGGACACTCAGTG
Found at i:7843 original size:22 final size:23
Alignment explanation
Indices: 7816--7867 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
7806 TATTATCAAG
*
7816 TATATAACATATTA-GTAGCGCT
1 TATATAACATAATAGGTAGCGCT
**
7838 TATATAATGTAATAGGTAGCGCT
1 TATATAACATAATAGGTAGCGCT
7861 TATATAA
1 TATATAA
7868 TAAATATGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (23 bp):
TATATAACATAATAGGTAGCGCT
Found at i:7940 original size:85 final size:84
Alignment explanation
Indices: 7795--7950 Score: 251
Period size: 85 Copynumber: 1.8 Consensus size: 84
7785 TGTTATATCA
* *
7795 TTAACCGGAAATATTATCAAGTATATAACATATTAGTAGCGCTTATATAATGTAATAGGTAGCGC
1 TTAACCGGAAATATTATCAAGTAAATAACAAATTAGTAGCGCTTATATAATGTAATAGGTAGCGC
7860 TTATATAATAAATATGCAT
66 TTATATAATAAATATGCAT
* *
7879 TTAACCGGAAATA-TATCAAGTACAATAACAAATTAGGTAGCTCTTATATAATGTAATAGGTAGT
1 TTAACCGGAAATATTATCAAGTA-AATAACAAATTA-GTAGCGCTTATATAATGTAATAGGTAGC
7943 GCTTATAT
64 GCTTATAT
7951 TGACCTTTTC
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
83 9 0.14
84 23 0.35
85 34 0.52
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (84 bp):
TTAACCGGAAATATTATCAAGTAAATAACAAATTAGTAGCGCTTATATAATGTAATAGGTAGCGC
TTATATAATAAATATGCAT
Found at i:8347 original size:186 final size:188
Alignment explanation
Indices: 8106--8545 Score: 466
Period size: 201 Copynumber: 2.3 Consensus size: 188
8096 TATTTCATTT
* *
8106 TGGA-AAAAAGTATCGACACAAACTAACAACGTGTCGATACATTAT-TTAGACCTATTCTCTCAT
1 TGGACAAAAAGTATCGACACAAATTAACAA-GTGTCGATACATTATGTT-GACCTATTCTATCAT
* * *
8169 AAAAC-CCGGTTACATTG-AAAATTACCTATTACATTATACTTAT-GGTTTTGATGTTTCCGGGA
64 AAAACTCCGGTTACATTGTAAAATTACCTAATACATTATAATTATCGGTTTCGATGTTTCCGGGA
* * *
8231 TCGATACTTTTTATAAATGTATCAACACTTTATG-GTTGCACC-C-TTTTTGGTATTCATTA
129 TCGATACTTTTAATAAATGTATCAACACTTTATGCG-TGCACCTCGTTTTT-GCATTCATCA
* * *
8290 TGGACCAAAAAGTATCGACACAAATTTAGCAAGTGTCGATAC-TTGATGCTGACCTATTTTATCA
1 TGGA-CAAAAAGTATCGACACAAA-TTAACAAGTGTCGATACATT-ATGTTGACCTATTCTATCA
* *
8354 TAAAACTGGTATATTTATATCGGTTACATTGTAAATTTACCTAATACATTATAATTATCGGTTTC
63 TAAAAC-----------T-CCGGTTACATTGTAAAATTACCTAATACATTATAATTATCGGTTTC
** *
8419 GATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTTTGC
116 GATGTTTCCGGGATCGATACTTTTAATAAATGTATCAACACTTTATGCGTGCACCTCGTTTTTGC
*
8484 ATTCATCC
181 ATTCATCA
* *
8492 TGGACAATAAGTATTGACACAAATTACACAAGTGTCGATACATTATGTTGACCT
1 TGGACAAAAAGTATCGACACAAATTA-ACAAGTGTCGATACATTATGTTGACCT
8546 GTTTTCTAAT
Statistics
Matches: 210, Mismatches: 21, Indels: 33
0.80 0.08 0.12
Matches are distributed among these distances:
184 4 0.02
185 2 0.01
186 48 0.23
187 6 0.03
199 11 0.05
200 26 0.12
201 93 0.44
202 15 0.07
203 5 0.02
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (188 bp):
TGGACAAAAAGTATCGACACAAATTAACAAGTGTCGATACATTATGTTGACCTATTCTATCATAA
AACTCCGGTTACATTGTAAAATTACCTAATACATTATAATTATCGGTTTCGATGTTTCCGGGATC
GATACTTTTAATAAATGTATCAACACTTTATGCGTGCACCTCGTTTTTGCATTCATCA
Found at i:8450 original size:201 final size:198
Alignment explanation
Indices: 8174--8659 Score: 599
Period size: 200 Copynumber: 2.4 Consensus size: 198
8164 CTCATAAAAC
* * **
8174 CCGGTTACATTG-AAAATTACCTATTACATTATACTTATGGTTTTGATGTTTCCGGGATCGATAC
1 CCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGTTTTGATGTTTTTGGGATCGATAC
* * *
8238 TTTTTATAAATGTATCAACACTTTATG-GTTGCACC-C-TTTTTGGTATTCATTATGGACCAAAA
66 -TTTTATAAATGTATCGACACTTTATGCG-TGCACCTCGTTTTT-GCATTCATCATGGA-CAAAA
* * *
8300 AGTATCGACACAAATTTA-GCAAGTGTCGATAC-TTGATGCTGACCTATTTTATCATAAAACTGG
127 AGTATCGACACAAA-TTACACAAGTGTCGATACATT-ATGCTGACCTATTTTATAAT-AAACCGG
8363 TATATTTATA
189 TATATTTATA
* * *
8373 TCGGTTACATTGTAAATTTACCTAATACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATA
1 CCGGTTACATTGTAAATTTACCTATTACATTATAATTAT-GGTTTTGATGTTTTTGGGATCGATA
* *
8438 CTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTTTGCATTCATCCTGGACAATAAG
65 CTTTT-ATAAATGTATCGACACTTTATGCGTGCACCTCGTTTTTGCATTCATCATGGACAAAAAG
* * * * *
8503 TATTGACACAAATTACACAAGTGTCGATACATTATGTTGACCTGTTTTCTAATTAACCGGTATAT
129 TATCGACACAAATTACACAAGTGTCGATACATTATGCTGACCTATTTTATAATAAACCGGTATAT
8568 TTATA
194 TTATA
* * *
8573 CCGGTTACATTATTAATTTACCTATTACGTTATAATTATTGGTTTTGATGTTTTTTGGG-TCGAT
1 CCGGTTACATTGTAAATTTACCTATTACATTATAATTA-TGGTTTTGATG-TTTTTGGGATCGAT
*
8637 ACTTGTATAATATGTATCGACAC
64 ACTTTTATAA-ATGTATCGACAC
8660 ATATTTAGGT
Statistics
Matches: 249, Mismatches: 27, Indels: 21
0.84 0.09 0.07
Matches are distributed among these distances:
199 15 0.06
200 109 0.44
201 105 0.42
202 15 0.06
203 5 0.02
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (198 bp):
CCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGTTTTGATGTTTTTGGGATCGATAC
TTTTATAAATGTATCGACACTTTATGCGTGCACCTCGTTTTTGCATTCATCATGGACAAAAAGTA
TCGACACAAATTACACAAGTGTCGATACATTATGCTGACCTATTTTATAATAAACCGGTATATTT
ATA
Found at i:11495 original size:195 final size:198
Alignment explanation
Indices: 11200--11611 Score: 563
Period size: 195 Copynumber: 2.1 Consensus size: 198
11190 GATGTTTTCG
* * *
11200 GTATCGACACTTTGTGCGGTCATCCTTTTTGGCATCCATTCTGAAAAAAAAAAGTATCGATACAA
1 GTATCGACACTTTATGCGTTCATCCTTTTTGGCATCCATTCTG-AAAAAAAAAGTATCGACACAA
* * *
11265 ATTTAACAAGTGTCGCTACATATTATAGACCTATTCTCTCATAAAATCGGTATATTTATACCGGT
65 ATTTAACAAGTGTCGATACATATTATAGACCTATTCTCTCATAAAACCGGTATATGTATACCGGT
**
11330 TACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTT-GGATCGACACTTTT
130 TACATTACAAA-TTACCTATTACA-T-TAATTATGGGTTTCGATGTTTTTGGGATCGACAC-TTT
*
11394 TGA-AAAT
191 TAATAAAT
* * * *
11401 GTATCGACACTTT-TGCGTTCA-CC-TTTTGGCATTCATTCTG-GACAAAAATTATCGACAC-AA
1 GTATCGACACTTTATGCGTTCATCCTTTTTGGCATCCATTCTGAAAAAAAAAGTATCGACACAAA
* *
11461 TATTAAGAA-TGTCGATACATATTATAGACCTATTCTCTCATAAAACCGGTATATGTGTACCGGT
66 T-TTAACAAGTGTCGATACATATTATAGACCTATTCTCTCATAAAACCGGTATATGTATACCGGT
*
11525 TATATTACAAATTACCTATTACATTAATTATGGGTTTCGATGTTTTTGGGATCGACACTTTTAAT
130 TACATTACAAATTACCTATTACATTAATTATGGGTTTCGATGTTTTTGGGATCGACACTTTTAAT
11590 AAAT
195 AAAT
11594 GTATCGA-ACTTTATGCGT
1 GTATCGACACTTTATGCGT
11612 GCAACCCTTT
Statistics
Matches: 192, Mismatches: 15, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
192 33 0.17
193 27 0.14
194 12 0.06
195 62 0.32
196 20 0.10
198 16 0.08
199 2 0.01
200 7 0.04
201 13 0.07
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (198 bp):
GTATCGACACTTTATGCGTTCATCCTTTTTGGCATCCATTCTGAAAAAAAAAGTATCGACACAAA
TTTAACAAGTGTCGATACATATTATAGACCTATTCTCTCATAAAACCGGTATATGTATACCGGTT
ACATTACAAATTACCTATTACATTAATTATGGGTTTCGATGTTTTTGGGATCGACACTTTTAATA
AAT
Found at i:13144 original size:15 final size:15
Alignment explanation
Indices: 13102--13145 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
13092 GTTTGGATCA
*
13102 TCATCATCATCGCCG
1 TCATCATCATCGTCG
* *
13117 TCATCGTCGTCGTCG
1 TCATCATCATCGTCG
*
13132 TCATCTTCATCGTC
1 TCATCATCATCGTC
13146 ATCTTCATCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.14, C:0.36, G:0.16, T:0.34
Consensus pattern (15 bp):
TCATCATCATCGTCG
Found at i:13149 original size:12 final size:12
Alignment explanation
Indices: 13129--13159 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
13119 ATCGTCGTCG
13129 TCGTCATCTTCA
1 TCGTCATCTTCA
13141 TCGTCATCTTCA
1 TCGTCATCTTCA
*
13153 TCTTCAT
1 TCGTCAT
13160 TGACCGCTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.16, C:0.32, G:0.06, T:0.45
Consensus pattern (12 bp):
TCGTCATCTTCA
Found at i:15111 original size:199 final size:201
Alignment explanation
Indices: 14627--15165 Score: 865
Period size: 202 Copynumber: 2.7 Consensus size: 201
14617 TATTTAAATT
* * *
14627 AGTATCGACACAAAATTAAAAACGTGTCGATACATGTTGTAGACCTATTCTTTCATAAAACTGAT
1 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACTGGT
*
14692 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATAGATGCATATGTTTCTG
66 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCA-ATGTTTCTG
* *
14757 GGATCGATACTTTTTATAAAATGTATTGACACTTTATGGTTGCACTCTTTTTGGCATTCATTCTG
130 GGATCGATACTTTTTATAAAATGTATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTG
14822 AACCAAA
195 AACCAAA
* *
14829 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGA
1 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACTGGT
* *
14894 ATATTTATACCGGTTACATTGAAAATTTACCTATTATATTATACTTATGGATGC-ATGTTCCTGG
66 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCAATGTTTCTGG
*
14958 GATCGATAC-TTTTAT-AAATGTATCGACAC-TTATGGTTGCACCCTTTTTGGCATTCATTCTGG
131 GATCGATACTTTTTATAAAATGTATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGA
15020 ACCAAA
196 ACCAAA
* *
15026 TGTATCGACACAAAATTAAAAAAAAGTGTCAATACATGTTGTAGA-CTATTCTCTCATAAAAACT
1 AGTATCGACACAAAATT--AAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCAT-AAAACT
*
15090 GGTATATTTATACCGGTTACATTGAAAATTTACCCATTACATTATACTTATGGATGCATATGTTT
63 GGTATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCA-ATGTTT
15155 CT-GGATCGATA
127 CTGGGATCGATA
15166 AATTTTACCT
Statistics
Matches: 314, Mismatches: 18, Indels: 12
0.91 0.05 0.03
Matches are distributed among these distances:
197 53 0.17
198 25 0.08
199 90 0.29
200 27 0.09
201 7 0.02
202 112 0.36
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (201 bp):
AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACTGGT
ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCAATGTTTCTGG
GATCGATACTTTTTATAAAATGTATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGA
ACCAAA
Found at i:15448 original size:19 final size:19
Alignment explanation
Indices: 15420--15463 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
15410 TTACATTCAC
15420 ATAC-AAATTATAAATCTT
1 ATACAAAATTATAAATCTT
15438 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCTT
15457 ATA-AAAA
1 ATACAAAA
15464 AATTAACCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 8 0.32
19 17 0.68
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (19 bp):
ATACAAAATTATAAATCTT
Found at i:17293 original size:33 final size:33
Alignment explanation
Indices: 17256--17321 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
17246 CATCTTAAGA
*
17256 TCACCCCTTAACACCTCAACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
** *
17289 TCACCCCTCAACACCTTTACTTCTTTTACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
17322 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.23, C:0.44, G:0.00, T:0.33
Consensus pattern (33 bp):
TCACCCCTCAACACCTCAACTTCTTTCACCACT
Found at i:17380 original size:21 final size:21
Alignment explanation
Indices: 17355--17398 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
17345 CCCCTTATGC
17355 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
17376 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
17397 CT
1 CT
17399 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:19903 original size:182 final size:181
Alignment explanation
Indices: 19589--20062 Score: 684
Period size: 182 Copynumber: 2.6 Consensus size: 181
19579 CGTACTTATG
* *
19589 AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACC-GATTTATCATTTCGATACCGGTTT
*
19654 TATCATATTTTTACATGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACTTTAT
65 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACTTTAT
19719 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATT
130 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATT
* * *
19771 AAAGTACCGACACTTTAAATATATCCGGTAGCTCTTTACCAGATTTATCATTTCGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACC-GATTTATCATTTCGATACCGGTTT
*
19836 TGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACTTTAT
65 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACTTTAT
* * * * *
19901 AGGTGTTAAAACTGCTTCTCTTTTAAATTCACAAAGTTTCGATCCTTGTATT
130 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATT
* * **
19953 AAAGTATCGACA-TGTTCAATATATCCGGTAAG-GATTTACCGATATTGTGTTTTCG-TGACCGG
1 AAAGTATCGACACT-TTCAATATATCCGGT-AGCGCTTTACCGAT-TTATCATTTCGAT-ACCGG
* * * *
20015 TTTTATCGACATTTTTACCTGTTATATTGATATGGATCGATACATTTT
62 TTTTATC-ATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTT
20063 AATTGGATCA
Statistics
Matches: 262, Mismatches: 25, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
181 5 0.02
182 219 0.84
183 38 0.15
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (181 bp):
AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGATTTATCATTTCGATACCGGTTTT
ATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACTTTATA
GGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATT
Found at i:24386 original size:10 final size:9
Alignment explanation
Indices: 24351--24449 Score: 90
Period size: 10 Copynumber: 10.3 Consensus size: 9
24341 GCTGCTGGAA
*
24351 ACCGGTTTA
1 ACCGGTTTG
*
24360 ACCGGTTTTCA
1 ACCGG-TTT-G
24371 ACCGGTTCTG
1 ACCGGTT-TG
24381 ACCGGTTTG
1 ACCGGTTTG
*
24390 ACCGGTTTCA
1 ACCGGTTT-G
*
24400 ACCGGTTCG
1 ACCGGTTTG
24409 AACCGGTTTG
1 -ACCGGTTTG
*
24419 ACCGGTCTG
1 ACCGGTTTG
24428 ACTCGGTTTG
1 AC-CGGTTTG
*
24438 ACCGGTCTG
1 ACCGGTTTG
24447 ACC
1 ACC
24450 CGACCCGACC
Statistics
Matches: 76, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
9 34 0.45
10 35 0.46
11 7 0.09
ACGTcount: A:0.15, C:0.28, G:0.27, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:24395 original size:19 final size:19
Alignment explanation
Indices: 24352--24449 Score: 87
Period size: 19 Copynumber: 5.1 Consensus size: 19
24342 CTGCTGGAAA
* * *
24352 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
24372 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
*
24391 CCGGTTTCAACCGGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
24411 CCGGTTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
24429 CTCGGTTTGACCGG-TCTGA
1 C-CGGTTTGACCGGTTCTGA
24448 CC
1 CC
24450 CGACCCGACC
Statistics
Matches: 68, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
18 6 0.09
19 39 0.57
20 15 0.22
21 8 0.12
ACGTcount: A:0.14, C:0.29, G:0.28, T:0.30
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:24413 original size:29 final size:30
Alignment explanation
Indices: 24350--24424 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
24340 GGCTGCTGGA
*
24350 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
24381 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
24409 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
24425 CTGACTCGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 1 0.02
29 28 0.67
30 13 0.31
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:24434 original size:29 final size:28
Alignment explanation
Indices: 24351--24449 Score: 101
Period size: 29 Copynumber: 3.4 Consensus size: 28
24341 GCTGCTGGAA
* *
24351 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TCTCAACCGGTTC-G
*
24381 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTCTCAACCGGTTCG
* *
24409 AACCGGTTTGACCGGTCT-GACTCGGTTTG
1 -ACCGGTTTGACCGGTCTCAAC-CGGTTCG
*
24438 ACCGGTCTGACC
1 ACCGGTTTGACC
24450 CGACCCGACC
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
28 14 0.23
29 35 0.56
30 13 0.21
ACGTcount: A:0.15, C:0.28, G:0.27, T:0.29
Consensus pattern (28 bp):
ACCGGTTTGACCGGTCTCAACCGGTTCG
Found at i:24456 original size:5 final size:5
Alignment explanation
Indices: 24446--24503 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
24436 TGACCGGTCT
* *
24446 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
24495 GACCC GACC
1 GACCC GACC
24504 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:24472 original size:22 final size:22
Alignment explanation
Indices: 24446--24510 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
24436 TGACCGGTCT
24446 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
24468 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
24490 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
24511 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:24512 original size:7 final size:7
Alignment explanation
Indices: 24500--24537 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
24490 GACCCGACCC
24500 GACCGTT
1 GACCGTT
24507 GACCGTT
1 GACCGTT
24514 GACCGTT
1 GACCGTT
24521 GACCGTT
1 GACCGTT
24528 GACCGTT
1 GACCGTT
24535 GAC
1 GAC
24538 TTTCTTTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:31710 original size:20 final size:20
Alignment explanation
Indices: 31685--31760 Score: 77
Period size: 20 Copynumber: 3.8 Consensus size: 20
31675 GGCTGCTGGA
31685 AACCGGTTTAACCGGTTTTC
1 AACCGGTTTAACCGGTTTTC
*
31705 AACCGGTTCTGACCGGTTTT-
1 AACCGGTT-TAACCGGTTTTC
*
31725 GACCGGTTTCAACCGG--TTC
1 AACCGGTTT-AACCGGTTTTC
*
31744 GAACCGGTTTGACCGGT
1 -AACCGGTTTAACCGGT
31761 CTGACTCGGT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
18 2 0.04
19 6 0.13
20 28 0.61
21 10 0.22
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.30
Consensus pattern (20 bp):
AACCGGTTTAACCGGTTTTC
Found at i:31721 original size:10 final size:10
Alignment explanation
Indices: 31706--31785 Score: 73
Period size: 10 Copynumber: 8.3 Consensus size: 10
31696 CCGGTTTTCA
31706 ACCGGTTCTG
1 ACCGGTTCTG
*
31716 ACCGGTTTTG
1 ACCGGTTCTG
*
31726 ACCGGTT-TCA
1 ACCGGTTCT-G
31736 ACCGGTTC-G
1 ACCGGTTCTG
31745 AACCGGTT-TG
1 -ACCGGTTCTG
31755 ACCGG-TCTG
1 ACCGGTTCTG
31764 ACTCGGTT-TG
1 AC-CGGTTCTG
31774 ACCGG-TCTG
1 ACCGGTTCTG
31783 ACC
1 ACC
31786 CGACCCGACC
Statistics
Matches: 59, Mismatches: 3, Indels: 17
0.75 0.04 0.22
Matches are distributed among these distances:
8 2 0.03
9 18 0.31
10 38 0.64
11 1 0.02
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.29
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:31722 original size:30 final size:30
Alignment explanation
Indices: 31685--31760 Score: 111
Period size: 30 Copynumber: 2.5 Consensus size: 30
31675 GGCTGCTGGA
*
31685 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGGTTTTCAACCGGTTC-G
31716 -ACCGGTTTTGACCGG-TTTCAACCGGTTCG
1 AACCGG-TTTGACCGGTTTTCAACCGGTTCG
31745 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
31761 CTGACTCGGT
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
29 10 0.24
30 23 0.56
31 8 0.20
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.30
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTTCAACCGGTTCG
Found at i:31780 original size:19 final size:19
Alignment explanation
Indices: 31748--31784 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
31738 CGGTTCGAAC
31748 CGGTTTGACCGGTCTGACT
1 CGGTTTGACCGGTCTGACT
31767 CGGTTTGACCGGTCTGAC
1 CGGTTTGACCGGTCTGAC
31785 CCGACCCGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.11, C:0.27, G:0.32, T:0.30
Consensus pattern (19 bp):
CGGTTTGACCGGTCTGACT
Found at i:31792 original size:5 final size:5
Alignment explanation
Indices: 31782--31839 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
31772 TGACCGGTCT
* *
31782 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
31831 GACCC GACC
1 GACCC GACC
31840 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:31808 original size:22 final size:22
Alignment explanation
Indices: 31782--31846 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
31772 TGACCGGTCT
31782 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
31804 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
31826 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
31847 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:31848 original size:7 final size:7
Alignment explanation
Indices: 31836--31873 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
31826 GACCCGACCC
31836 GACCGTT
1 GACCGTT
31843 GACCGTT
1 GACCGTT
31850 GACCGTT
1 GACCGTT
31857 GACCGTT
1 GACCGTT
31864 GACCGTT
1 GACCGTT
31871 GAC
1 GAC
31874 TTTCTTTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:35916 original size:39 final size:39
Alignment explanation
Indices: 35860--35949 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 39
35850 CGTTTTTTTT
*
35860 AATCGTATATTAAGACTGTCGCAGGTGATCATTTCCGGA
1 AATCGTATATTAAGACTGTCGCAGGTGATCATTTCCAGA
* *
35899 AGTCGTATATTAAGACTGTCGCAGGTGATCATTTTCAGA
1 AATCGTATATTAAGACTGTCGCAGGTGATCATTTCCAGA
35938 AATCGTATATTA
1 AATCGTATATTA
35950 CAAGATGCAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (39 bp):
AATCGTATATTAAGACTGTCGCAGGTGATCATTTCCAGA
Found at i:41530 original size:31 final size:32
Alignment explanation
Indices: 41490--41551 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
41480 GATTTCGAAA
* *
41490 AATATAAGATGTGATCACTTTCGTTTTTATTT
1 AATATAAGATATGATCACTTTCATTTTTATTT
* *
41522 AATA-AAGATATGGTCACTTTTATTTTTATT
1 AATATAAGATATGATCACTTTCATTTTTATT
41552 AATTAATATG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.31, C:0.08, G:0.11, T:0.50
Consensus pattern (32 bp):
AATATAAGATATGATCACTTTCATTTTTATTT
Found at i:41724 original size:29 final size:27
Alignment explanation
Indices: 41691--41764 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 27
41681 TAAATATTAC
41691 TATAAAATATATTTTTAAATTAAGTTAA
1 TATAAAATATA-TTTTAAATTAAGTTAA
41719 TA-ATAAATATA-TTT-AA-TAAGTTAA
1 TATA-AAATATATTTTAAATTAAGTTAA
*
41743 TATAAAA-ATACTTTTAAGTTAA
1 TATAAAATATA-TTTTAAATTAA
41765 TATATATAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 13
0.74 0.02 0.25
Matches are distributed among these distances:
23 3 0.08
24 13 0.33
25 6 0.15
26 4 0.10
27 4 0.10
28 9 0.23
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (27 bp):
TATAAAATATATTTTAAATTAAGTTAA
Found at i:41763 original size:22 final size:21
Alignment explanation
Indices: 41710--41778 Score: 75
Period size: 24 Copynumber: 3.0 Consensus size: 21
41700 TATTTTTAAA
*
41710 TTAAGTTAATAATAAATATATT
1 TTAAGTTAAT-ATAAAAATATT
41732 TAATAAGTTAATATAAAAATACTT
1 T--TAAGTTAATATAAAAATA-TT
41756 TTAAGTTAATATATATAAATATT
1 TTAAGTTAATATA-A-AAATATT
41779 ATGAATTTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
22 13 0.32
23 11 0.27
24 17 0.41
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (21 bp):
TTAAGTTAATATAAAAATATT
Found at i:42496 original size:24 final size:23
Alignment explanation
Indices: 42466--42568 Score: 75
Period size: 24 Copynumber: 4.3 Consensus size: 23
42456 TTTTATCTTT
42466 GTATTTTAGTTTAAATAGGTTTTA
1 GTATTTTA-TTTAAATAGGTTTTA
* *
42490 GTATTTTAATTAAATTTAGGATATTA
1 GTATTTTATTTAAA--TAGG-TTTTA
* **
42516 -T-TTTTATTTGAACTTTGTTTTA
1 GTATTTTATTT-AAATAGGTTTTA
*
42538 GGTATTTTAGTTTAAGTAGGTTTTA
1 -GTATTTTA-TTTAAATAGGTTTTA
42563 GTATTT
1 GTATTT
42569 AATTAGGATT
Statistics
Matches: 61, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
22 4 0.07
23 7 0.11
24 22 0.36
25 21 0.34
26 7 0.11
ACGTcount: A:0.27, C:0.01, G:0.16, T:0.56
Consensus pattern (23 bp):
GTATTTTATTTAAATAGGTTTTA
Found at i:42558 original size:73 final size:70
Alignment explanation
Indices: 42466--42650 Score: 225
Period size: 73 Copynumber: 2.6 Consensus size: 70
42456 TTTTATCTTT
* **
42466 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTA-AATTTAGGATATTATTTTTAT-TTGAAC
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGAATTTAGAATATTATTTAAATATT--A-
42529 TTTGTTTTAG
63 -TT-TTTTAG
* *
42539 GTATTTTAGTTTAAGTAGGTTTTAGTA-TTTAATTAGGATTTAGAATATTATTTAAATATTATTT
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGAATTTAGAATATTATTTAAATATTATTT
42603 TTTAG
66 TTTAG
* *
42608 GTATTTTATTTTAAATA-GTTTTAAGTATTTTAATTAGGATTTA
1 GTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAGAATTTA
42651 AGATGTTTTA
Statistics
Matches: 101, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
68 5 0.05
69 25 0.25
70 17 0.17
72 9 0.09
73 43 0.43
74 2 0.02
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.55
Consensus pattern (70 bp):
GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGAATTTAGAATATTATTTAAATATTATTT
TTTAG
Found at i:43333 original size:7 final size:7
Alignment explanation
Indices: 43323--43378 Score: 55
Period size: 7 Copynumber: 8.1 Consensus size: 7
43313 TCTTTACTAA
43323 TATTATT
1 TATTATT
43330 TATTATT
1 TATTATT
43337 TATTATT
1 TATTATT
**
43344 T-TCCCTT
1 TAT-TATT
43351 T-TTATT
1 TATTATT
43357 TATTA-T
1 TATTATT
43363 TATTATTT
1 TATTA-TT
43371 TATTATT
1 TATTATT
43378 T
1 T
43379 TTTCTTTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
6 10 0.24
7 25 0.61
8 6 0.15
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.71
Consensus pattern (7 bp):
TATTATT
Found at i:43422 original size:35 final size:35
Alignment explanation
Indices: 43356--43422 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
43346 CCCTTTTTAT
* * * *
43356 TTATTATTATTATTTTATTATTTTTTCTTTTTAAA
1 TTATAATTATTATTTTATTATATTATATTTTTAAA
43391 TTATAATTATTTATTTTATT-TATTATATTTTT
1 TTATAATTA-TTATTTTATTATATTATATTTTT
43423 CAACTTCATC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 17 0.63
36 10 0.37
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.72
Consensus pattern (35 bp):
TTATAATTATTATTTTATTATATTATATTTTTAAA
Found at i:48780 original size:5 final size:5
Alignment explanation
Indices: 48770--48827 Score: 57
Period size: 5 Copynumber: 11.8 Consensus size: 5
48760 TCGTTCTATT
* * * *
48770 TTTTA TTTTA TTTCA TTTTA TTTTCG TTTTA -TTTC GTTTA -TTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA
48819 TTTTA TTTT
1 TTTTA TTTT
48828 TTTAGAACTT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
4 7 0.16
5 33 0.75
6 4 0.09
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (5 bp):
TTTTA
Done.