Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001814.1 Hibiscus syriacus cultivar Beakdansim tig00003673_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: 53392
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:397 original size:20 final size:20
Alignment explanation
Indices: 348--420 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
338 TTACTAAGTA
348 GTCAGTATCGATACT-ATA-G
1 GTCAGTATCGATACTCA-AGG
*
367 GTGAGTATCGATACTCAAGG
1 GTCAGTATCGATACTCAAGG
* * *
387 TTCATTATCGATACTGAAGG
1 GTCAGTATCGATACTCAAGG
407 GTCAGTATCGATAC
1 GTCAGTATCGATAC
421 CCATGGACAG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
19 15 0.33
20 30 0.67
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.30
Consensus pattern (20 bp):
GTCAGTATCGATACTCAAGG
Found at i:2660 original size:21 final size:20
Alignment explanation
Indices: 2632--2671 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
2622 ACTCGACATT
2632 ACTCAAAATTTAT-AAAGTCG
1 ACTCAAAATTT-TCAAAGTCG
2652 ACTCGAAAATTTTCAAAGTC
1 ACTC-AAAATTTTCAAAGTC
2672 AACTTTGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.30
Consensus pattern (20 bp):
ACTCAAAATTTTCAAAGTCG
Found at i:4896 original size:182 final size:181
Alignment explanation
Indices: 4246--5082 Score: 1037
Period size: 182 Copynumber: 4.6 Consensus size: 181
4236 GATACAAATA
* * * * * * * *
4246 AAAAATGTATCGATCTATAGCAATATAACATGTTAAAATATAACAAAATCGGTTTC-ATTATGAC
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGA-AATGAC
* * * * * * *
4310 AAAACCGGTAAAGTGGTACCGGATATGTTGAAAGTATCGATTAGATTGAA-ATAAGTATAAATAC
65 AAAACCGGTAAA-AGCTACCGGATATGTTGAAAGTGTCGA-TA-CTTTAATATAAGTATAGACAC
* *
4374 TTTTAGAATTTAAAAGAG--G-AGTAATAGTGTCTATAAAGTGTCGATACTTTA-
127 TTTTAGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
* *
4425 AAAAA-ATATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTAGAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACA
* * * *
4489 AAATCGGTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTATATTA-AAGTATCGACACTT
66 AAACCGGTAAA-AGCTACCGGATATGTTGAAAGTGTCGATACTT-TAATATAAGTATAGACACTT
* * *
4553 TTAGAATTTAAAAGAGAAGTAGTAATAACGCCTATAAAGTATCGATACTTTAT
129 TTAGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
* *
4606 -AAAATGTATCGATCCATAACAATATAACAGGTAAATATATGACAAAACCGATCTCGAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACA
** * * *
4670 AAACCATTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACGCTTT
66 AAACCGGTAAA-AGCTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATAGACACTTT
* * *
4735 TGGAATTTAAAAGAGAAGCATTTATAGCGCCTATAAAGTGTCGATACTTTAT
130 TAGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
* * **
4787 AAAAATGTATCGATTCATAACAATATAACATGTAAAAATATGACAAAACCAATCTCGAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACA
* * *
4852 AAACGGGTAAAATGCTACCGGATATGTTGAAAGTGCCAATACTTTAATATAAGTATAGACACTTT
66 AAACCGGTAAAA-GCTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATAGACACTTT
* * *
4917 TGGAATTTAAAAGAGAAGCAGTAATA-CTGCCTATAAAGTGCCAATACTTTAT
130 TAGAATTTAAAAGAGAAGCAGTAATAGC-GCCTATAAAGTGTCGATACTTTAT
* * * *
4969 AGAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATCGGTCTCAAAATTACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACA
* * *
5034 AAGCCGGTTAAACGCTGCCGGATATGTTGAAAGTGTCGATACTTTAATA
66 AAACCGG-TAAAAGCTACCGGATATGTTGAAAGTGTCGATACTTTAATA
5083 AGTATGCGTA
Statistics
Matches: 575, Mismatches: 70, Indels: 23
0.86 0.10 0.03
Matches are distributed among these distances:
176 2 0.00
177 30 0.05
178 82 0.14
179 7 0.01
180 36 0.06
181 158 0.27
182 256 0.45
183 4 0.01
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (181 bp):
AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACA
AAACCGGTAAAAGCTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATAGACACTTTT
AGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
Found at i:4915 original size:363 final size:356
Alignment explanation
Indices: 4247--5082 Score: 1054
Period size: 363 Copynumber: 2.3 Consensus size: 356
4237 ATACAAATAA
* * * * * *
4247 AAAATGTATCGATCTATAGCAATATAACATGTTAAAATATAACAAAATCGGTTTCATTATGACAA
1 AAAATGTATCGATCCATAACAATATAACA-GGTAAAATATGACAAAATCGGTCTCA-AATGACAA
* * * * * * *
4312 AACCGGTAAAGTGGTACCGGATATGTTGAAAGTATCGATTAGATTGAA-ATAAGTATAAATACTT
64 AACCGTTAAAGAGCTACCGGATATGTTGAAAGTGTCGA-TA-CTTTAATATAAGTATAAACACTT
* *
4376 TTAGAATTTAAAAGAGGAGTAATAGTGTCTATAAAGTGTCGATACTTTAAAAAAATATCGATCCA
127 TTAGAATTTAAAAGAGGAGTAATAGCGCCTATAAAGTGTCGATACTTTAAAAAAATATCGATCCA
**
4441 TAACAATATAACAGGTAAAAATATGACAAAACCGGTCTAGAAATGACAAAATCGGTAAAGAGCTA
192 TAACAATATAACAGGTAAAAATATGACAAAACCAATCTAGAAATGACAAAATCGGTAAAGAGCTA
* * * *
4506 CCAGATATGTTGAAAGTGTCGATACTTATATTAAAGTATCGACACTTTTAGAATTTAAAAGAGAA
257 CCAGATATGTTGAAAGTGCCAATACTTATAATAAAGTATAGACACTTTTAGAATTTAAAAGAGAA
* * *
4571 GTAGTAATAAC-GCCTATAAAGTATCGATACTTTAT
322 GCAGTAAT-ACTGCCTATAAAGTACCAATACTTTAT
* *
4606 AAAATGTATCGATCCATAACAATATAACAGGTAAATATATGACAAAACCGATCTCGAAATGACAA
1 AAAATGTATCGATCCATAACAATATAACAGGTAAA-ATATGACAAAATCGGTCTC-AAATGACAA
* * ** *
4671 AACCATTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACGCTTTT
64 AACCGTTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATAAACACTTTT
* * * *
4736 GGAATTTAAAAGAGAAGCATTTATAGCGCCTATAAAGTGTCGATACTTTATAAAAATGTATCGAT
129 AGAATTTAAAAGAG--G-AGTAATAGCGCCTATAAAGTGTCGATACTTTA-AAAAA-ATATCGAT
* * *
4801 TCATAACAATATAACATGTAAAAATATGACAAAACCAATCTCGAAATGACAAAA-CGGGTAAA-A
189 CCATAACAATATAACAGGTAAAAATATGACAAAACCAATCTAGAAATGACAAAATC-GGTAAAGA
* *
4864 TGCTACCGGATATGTTGAAAGTGCCAATACTT-TAATATAAGTATAGACACTTTTGGAATTTAAA
253 -GCTACCAGATATGTTGAAAGTGCCAATACTTATAATA-AAGTATAGACACTTTTAGAATTTAAA
*
4928 AGAGAAGCAGTAATACTGCCTATAAAGTGCCAATACTTTAT
316 AGAGAAGCAGTAATACTGCCTATAAAGTACCAATACTTTAT
*
4969 AGAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATCGGTCTCAAAATTACA
1 A-AAATGTATCGATCCATAACAATATAACAGGT-AAAATATGACAAAATCGGTCTC-AAATGACA
* * *
5034 AAGCCGGTTAAA-CGCTGCCGGATATGTTGAAAGTGTCGATACTTTAATA
63 AAACC-GTTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTAATA
5083 AGTATGCGTA
Statistics
Matches: 412, Mismatches: 50, Indels: 25
0.85 0.10 0.05
Matches are distributed among these distances:
357 4 0.01
358 34 0.08
359 81 0.20
360 2 0.00
361 28 0.07
362 13 0.03
363 149 0.36
364 93 0.23
365 8 0.02
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (356 bp):
AAAATGTATCGATCCATAACAATATAACAGGTAAAATATGACAAAATCGGTCTCAAATGACAAAA
CCGTTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATAAACACTTTTAG
AATTTAAAAGAGGAGTAATAGCGCCTATAAAGTGTCGATACTTTAAAAAAATATCGATCCATAAC
AATATAACAGGTAAAAATATGACAAAACCAATCTAGAAATGACAAAATCGGTAAAGAGCTACCAG
ATATGTTGAAAGTGCCAATACTTATAATAAAGTATAGACACTTTTAGAATTTAAAAGAGAAGCAG
TAATACTGCCTATAAAGTACCAATACTTTAT
Found at i:10444 original size:200 final size:198
Alignment explanation
Indices: 9918--10598 Score: 1028
Period size: 199 Copynumber: 3.4 Consensus size: 198
9908 GTAAACAAAT
9918 GTGTCGATACATTTATTAAA-AGTATCGATCCCAAAAACATCGAAACCGATAATTATAATATAAT
1 GTGTCGATACATTTA--AAATAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATATAAT
* * *
9982 AGGTAAATTTACAATGTAACCAGTAGAAATATACCGGTTTTATGAGAAAATATGTCTACATAATG
64 AGGTAAATTTACAATGTAACCGGTAGAAATATATCGGTTTTATGAGAAAATAGGTCTACATAATG
* * * *
10047 TATCGATACTTTATAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGACAAACTAGGTGCACG
129 TATCAACACTTTTTAAATTTGTGTCGATACTTTTTTTCCAGAATGAATGAC-AACTAGGTGCACG
10112 CATAAA
193 CATAAA
* *
10118 GTGTCAATACATTTAAAATTA-TATCGATCCCAAAAACATCGAAACCGATAATTACAATATAATA
1 GTGTCGATACATTTAAAA-TAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATATAATA
* * * *
10182 GGTAAATTTAAAATGTAACCGGTAGAAATATATCGATTTTATGAGAGAATAGGTCAACATAATGT
65 GGTAAATTTACAATGTAACCGGTAGAAATATATCGGTTTTATGAGAAAATAGGTCTACATAATGT
10247 ATCAACACTTTTTAAATTTGTGTCGATACTTTTTTTCCAGAATGAATGACATACTAGGTGCACGC
130 ATCAACACTTTTTAAATTTGTGTCGATACTTTTTTTCCAGAATGAATGACA-ACTAGGTGCACGC
10312 ATAAA
194 ATAAA
* *
10317 GTGTCGATACATTTATTAAA-AGTATCGATCCCAAAAATATCGAAACCGATAATTATAATGTAAT
1 GTGTCGATACATTTA--AAATAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATATAAT
* * *
10381 AGGTAAATTTACAATGTAATCGGTATAAATATATTGGTTTTATGAGAAAATAGGTCTACATAATG
64 AGGTAAATTTACAATGTAACCGGTAGAAATATATCGGTTTTATGAGAAAATAGGTCTACATAATG
* *
10446 TATCAACACTTTTTAAATTTGTGTCGATA-TTTTTTGTCCAGAATGAATGCCCAACGAGGTGCAC
129 TATCAACACTTTTTAAATTTGTGTCGATACTTTTTT-TCCAGAATGAATG-ACAACTAGGTGCAC
10510 GCATAAA
192 GCATAAA
* * *
10517 GTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAT
1 GTGTCGATACATTTAAAATAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATATAATAG
* *
10582 GTAACTTTGCAATGTAA
66 GTAAATTTACAATGTAA
10599 TTGTTTATGT
Statistics
Matches: 441, Mismatches: 31, Indels: 19
0.90 0.06 0.04
Matches are distributed among these distances:
198 7 0.02
199 243 0.55
200 186 0.42
201 5 0.01
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (198 bp):
GTGTCGATACATTTAAAATAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATATAATAG
GTAAATTTACAATGTAACCGGTAGAAATATATCGGTTTTATGAGAAAATAGGTCTACATAATGTA
TCAACACTTTTTAAATTTGTGTCGATACTTTTTTTCCAGAATGAATGACAACTAGGTGCACGCAT
AAA
Found at i:10759 original size:23 final size:23
Alignment explanation
Indices: 10733--10783 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
10723 TCAATAATTA
**
10733 ACCTATTTTATTATATAAGC-GCT
1 ACCTATTACATTATATAAGCAG-T
10756 ACCTATTACATTATATAAGCAGT
1 ACCTATTACATTATATAAGCAGT
10779 ACCTA
1 ACCTA
10784 ATATGTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCAGT
Found at i:10862 original size:16 final size:17
Alignment explanation
Indices: 10843--10878 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
10833 CGATCTAAAT
*
10843 TTTAACCGATTAC-TTA
1 TTTAACCAATTACGTTA
10859 TTTAACCAATTACGTTA
1 TTTAACCAATTACGTTA
10876 TTT
1 TTT
10879 TTTAAACGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.47
Consensus pattern (17 bp):
TTTAACCAATTACGTTA
Found at i:14045 original size:23 final size:24
Alignment explanation
Indices: 14008--14064 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
13998 CCGGTTTTTT
*
14008 AAAAAATCGATTTTTAATCCGGTA
1 AAAAAACCGATTTTTAATCCGGTA
14032 AAAAAACCGATTTTTAATCCGGTA
1 AAAAAACCGATTTTTAATCCGGTA
14056 AAAAAACCG
1 AAAAAACCG
14065 GTCGTCCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.26
Consensus pattern (24 bp):
AAAAAACCGATTTTTAATCCGGTA
Found at i:16790 original size:27 final size:27
Alignment explanation
Indices: 16749--16800 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
16739 GTGCGTCTTT
* *
16749 TTTTTAAATTTAATAATATTTTTATGC
1 TTTTTAAATTTAATAAAAATTTTATGC
16776 TTTTT-AATTTCAATAAAAATTTTAT
1 TTTTTAAATTT-AATAAAAATTTTAT
16801 AAATATCAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (27 bp):
TTTTTAAATTTAATAAAAATTTTATGC
Found at i:26724 original size:2 final size:2
Alignment explanation
Indices: 26717--26753 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
26707 TGTTTACCAA
26717 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
26754 CAATAAAGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27848 original size:4 final size:4
Alignment explanation
Indices: 27841--27905 Score: 130
Period size: 4 Copynumber: 16.2 Consensus size: 4
27831 CAAACACACG
27841 CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA
1 CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA
27889 CGCA CGCA CGCA CGCA C
1 CGCA CGCA CGCA CGCA C
27906 ACACACACAC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 61 1.00
ACGTcount: A:0.25, C:0.51, G:0.25, T:0.00
Consensus pattern (4 bp):
CGCA
Found at i:27910 original size:2 final size:2
Alignment explanation
Indices: 27903--27934 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
27893 CGCACGCACG
27903 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
27935 TACATACATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:28468 original size:36 final size:36
Alignment explanation
Indices: 28439--28542 Score: 102
Period size: 36 Copynumber: 2.9 Consensus size: 36
28429 TTGAGATCGC
*
28439 TTTCTC-AAAAACAACTTTTGTCTCGCTTGAGATAA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGATAA
* * * * *
28474 TTTTTCTAAAAACAAATTTTGTCTTGCTGGAAACAA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGATAA
** * * *
28510 TTTCTCCCAAAACAAATTTCGACTTGCTTGAGA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGA
28543 CATTTTTCTC
Statistics
Matches: 55, Mismatches: 13, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
35 5 0.09
36 50 0.91
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (36 bp):
TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGATAA
Found at i:28763 original size:28 final size:28
Alignment explanation
Indices: 28732--28793 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
28722 TCTTGAGACA
* *
28732 GTTTCTCTTGAAACAAGTCTTTGAGTTT
1 GTTTCTCTTCAAACAAATCTTTGAGTTT
* *
28760 GTTTCTTTTCAAACAAATTTTTGAGTTT
1 GTTTCTCTTCAAACAAATCTTTGAGTTT
28788 GTTTCT
1 GTTTCT
28794 ACTAACAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.21, C:0.13, G:0.15, T:0.52
Consensus pattern (28 bp):
GTTTCTCTTCAAACAAATCTTTGAGTTT
Found at i:29014 original size:63 final size:64
Alignment explanation
Indices: 28897--29017 Score: 165
Period size: 64 Copynumber: 1.9 Consensus size: 64
28887 CTATAAGAAC
** *
28897 AAAAATCTTTGAGTCTGTTTCTCTGAAAACAATTTTTTTGTCACTTGAGACAATTTCTGTGGAA
1 AAAAATCTTTGAGTCTGTTTCTCTGAAAACAATAATTTTGTCACTCGAGACAATTTCTGTGGAA
* * *
28961 AAAAATCTTTGAGTTTGTTTCTTTTG-AAACAA-AATTTTGTCTCTCGAGACAATTTCT
1 AAAAATCTTTGAGTCTGTTTC-TCTGAAAACAATAATTTTGTCACTCGAGACAATTTCT
29018 TTTGAAAATG
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
63 21 0.42
64 26 0.52
65 3 0.06
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (64 bp):
AAAAATCTTTGAGTCTGTTTCTCTGAAAACAATAATTTTGTCACTCGAGACAATTTCTGTGGAA
Found at i:29115 original size:67 final size:63
Alignment explanation
Indices: 28897--29115 Score: 174
Period size: 67 Copynumber: 3.3 Consensus size: 63
28887 CTATAAGAAC
** ** * * *
28897 AAAAATCTTTGAGTCTGTTTCTCTGAAAACAATTTTTTTGTCACTTGAGACAATTTCTGTGG-AA
1 AAAAATCTTTGAGTCTGTTTCT-TTTAAACAAAATTTGTCTC-CTTGAGACAATTTCTTTGGAAA
* * *
28961 AAAAATCTTTGAGTTTGTTTCTTTTGAAACAAAATTTTGTCT-CTCGAGACAATTTCTTTTGAAA
1 AAAAATCTTTGAGTCTGTTTCTTTT-AAACAAAA-TTTGTCTCCTTGAGACAATTTCTTTGGAAA
*** * *
29025 ATGCCTATCTTTGAGATC-ATTTCTATTTAAACAAAATTTGTCTCCCTTGAGGCAATTTCTTTGG
1 A--AAAATCTTTGAG-TCTGTTTCT-TTTAAACAAAATTTGTCT-CCTTGAGACAATTTCTTTGG
29089 AAA
61 AAA
*
29092 CATAAAATCATTGAGTCTGTTTCT
1 -A-AAAATCTTTGAGTCTGTTTCT
29116 CTTGAAATAA
Statistics
Matches: 120, Mismatches: 24, Indels: 19
0.74 0.15 0.12
Matches are distributed among these distances:
63 17 0.14
64 30 0.25
65 12 0.10
66 24 0.20
67 36 0.30
68 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.42
Consensus pattern (63 bp):
AAAAATCTTTGAGTCTGTTTCTTTTAAACAAAATTTGTCTCCTTGAGACAATTTCTTTGGAAA
Found at i:29139 original size:32 final size:31
Alignment explanation
Indices: 29102--29216 Score: 108
Period size: 31 Copynumber: 3.7 Consensus size: 31
29092 CATAAAATCA
*
29102 TTGAGTCTGTTTCTCTTGAAATAAAACCATCT
1 TTGAGTCTGTTTCTCTTGAAA-AAAATCATCT
* * ** *
29134 TTGAGT-AGTTTCTTTTGAAACACCATTATCT
1 TTGAGTCTGTTTCTCTTGAAA-AAAATCATCT
* *
29165 TTGAGTCTGTTTCTTTTGAAAAAAATCACCT
1 TTGAGTCTGTTTCTCTTGAAAAAAATCATCT
*
29196 TTGAGTC-GATTTCCCTTGAAA
1 TTGAGTCTG-TTTCTCTTGAAA
29217 CCTTTATACT
Statistics
Matches: 67, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
30 1 0.01
31 47 0.70
32 19 0.28
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (31 bp):
TTGAGTCTGTTTCTCTTGAAAAAAATCATCT
Found at i:29154 original size:62 final size:62
Alignment explanation
Indices: 29080--29201 Score: 156
Period size: 62 Copynumber: 2.0 Consensus size: 62
29070 CTTGAGGCAA
* *
29080 TTTCTTTGGAAACA-TAAAATCATTGAGTCTGTTTCTCTTGAAATAAAACCATCTTTGAGTAG
1 TTTCTTTGGAAACACCAAAATCATTGAGTCTGTTTCTCTTGAAA-AAAACCACCTTTGAGTAG
* ** * * *
29142 TTTCTTTTGAAACACCATTATCTTTGAGTCTGTTTCTTTTGAAAAAAATCACCTTTGAGT
1 TTTCTTTGGAAACACCAAAATCATTGAGTCTGTTTCTCTTGAAAAAAACCACCTTTGAGT
29202 CGATTTCCCT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
62 27 0.53
63 24 0.47
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.42
Consensus pattern (62 bp):
TTTCTTTGGAAACACCAAAATCATTGAGTCTGTTTCTCTTGAAAAAAACCACCTTTGAGTAG
Found at i:29198 original size:31 final size:32
Alignment explanation
Indices: 29080--29202 Score: 119
Period size: 31 Copynumber: 3.9 Consensus size: 32
29070 CTTGAGGCAA
* *
29080 TTTCTTTGGAAACATAAA--ATCATTGAGTCTG
1 TTTCTTTTGAAACA-AAATCATCTTTGAGTCTG
* * * *
29111 TTTCTCTTGAAATAAAACCATCTTTGAGT-AG
1 TTTCTTTTGAAACAAAATCATCTTTGAGTCTG
** *
29142 TTTCTTTTGAAACACCATTATCTTTGAGTCTG
1 TTTCTTTTGAAACAAAATCATCTTTGAGTCTG
*
29174 TTTCTTTTGAAA-AAAATCACCTTTGAGTC
1 TTTCTTTTGAAACAAAATCATCTTTGAGTC
29203 GATTTCCCTT
Statistics
Matches: 73, Mismatches: 16, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
30 3 0.04
31 48 0.66
32 22 0.30
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.41
Consensus pattern (32 bp):
TTTCTTTTGAAACAAAATCATCTTTGAGTCTG
Found at i:29685 original size:135 final size:132
Alignment explanation
Indices: 29227--29739 Score: 437
Period size: 135 Copynumber: 3.9 Consensus size: 132
29217 CCTTTATACT
* * * *
29227 TAAAGATGGCCAAGAACTCTTCATCACGTATGAG-CAGTGTCATCCCCCGACCAGATTTCCCCAG
1 TAAAGATGACCAAGAACTCTTCATCACGTATGAGCCA-TGTCAT-CCCCGACTAGATCTCCCCAT
* * * **
29291 CAGAGT-GGAATCGTGTCAACCTCAGATAACCAG--TCGTCCCCA-GTAGAGTGGAACCGTGTTA
64 CA-TGTAGGAATCGTGTCAACCTTAGATAACCAGACTCTTCATCACGT--A-T-GAACCGTGTTA
*
29352 TCACCCTTCC
124 TCA-CATTCC
* *
29362 TAAAGATGACCAA-AACTCTTTATCACGTATGAGCCATGTCATCACCAGACCT-GATCTCCCCAT
1 TAAAGATGACCAAGAACTCTTCATCACGTATGAGCCATGTCATC-CCCGA-CTAGATCTCCCCAT
* * * * * * * * *
29425 CACGTAGGAGTTGTTTCAA-CTTAGATAATCAGCCGTCCTCATCACGTAGGAACCGTTTTATCAC
64 CATGTAGGAATCGTGTCAACCTTAGATAACCAGAC-TCTTCATCACGTATGAACCGTGTTATCAC
29489 ATT--
128 ATTCC
* * * * *
29492 T--AGATGGCC-AGAACTCTTCATCACGTATGAGCCATGTCATCACCCGACTAAATTTCCTCATT
1 TAAAGATGACCAAGAACTCTTCATCACGTATGAGCCATGTCATC-CCCGACTAGATCTCCCCATC
* *
29554 ATGTAGGAATCGTGTCAATCCTT-GATAACCAGAACTCTTCATCACGTATGAGCCGAGTTATCAC
65 ATGTAGGAATCGTGTCAA-CCTTAGATAACCAG-ACTCTTCATCACGTATGAACCGTGTTATCAC
29618 TATTCC
128 -ATTCC
*
29624 TAAAGATGACCAAGAACTCTTCATCACGTATGAG-CAGTGTCATCCCCTGACTAGATCTCCTCAT
1 TAAAGATGACCAAGAACTCTTCATCACGTATGAGCCA-TGTCATCCCC-GACTAGATCTCCCCAT
* * * * *
29688 TATGTAGGAGTCTTGTC-ACCTTTAGACAACCCGAACTCTTCATCACGTATGA
64 CATGTAGGAATCGTGTCAACC-TTAGATAACCAG-ACTCTTCATCACGTATGA
29740 GCAGTGTCGT
Statistics
Matches: 312, Mismatches: 43, Indels: 46
0.78 0.11 0.11
Matches are distributed among these distances:
127 3 0.01
128 63 0.20
129 32 0.10
130 8 0.03
132 4 0.01
133 29 0.09
134 65 0.21
135 100 0.32
136 6 0.02
137 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (132 bp):
TAAAGATGACCAAGAACTCTTCATCACGTATGAGCCATGTCATCCCCGACTAGATCTCCCCATCA
TGTAGGAATCGTGTCAACCTTAGATAACCAGACTCTTCATCACGTATGAACCGTGTTATCACATT
CC
Found at i:29909 original size:3 final size:3
Alignment explanation
Indices: 29901--29964 Score: 56
Period size: 3 Copynumber: 20.7 Consensus size: 3
29891 CCGGGTCGAA
* * * * *
29901 TAT TAT TAT TAT TAT TAT TAT TAT TAC TAC TAC AAC TAT TAT TAT TAAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
*
29950 TAAT TAT TTT TAT TA
1 T-AT TAT TAT TAT TA
29965 CATTTTACAG
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
3 47 0.87
4 7 0.13
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:33028 original size:14 final size:14
Alignment explanation
Indices: 33009--33040 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
32999 TGGCTAGTTG
33009 GCAACTACTTGTAA
1 GCAACTACTTGTAA
*
33023 GCAACTAGTTGTAA
1 GCAACTACTTGTAA
33037 GCAA
1 GCAA
33041 TTTAGAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (14 bp):
GCAACTACTTGTAA
Found at i:40275 original size:2 final size:2
Alignment explanation
Indices: 40268--40298 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
40258 GATCCTGCCC
40268 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40299 AAGTTTGGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52162 original size:20 final size:21
Alignment explanation
Indices: 52131--52178 Score: 89
Period size: 20 Copynumber: 2.3 Consensus size: 21
52121 TGTGTGTACC
52131 GTACACTCTCAAGGTGTATCG
1 GTACACTCTCAAGGTGTATCG
52152 GTACACT-TCAAGGTGTATCG
1 GTACACTCTCAAGGTGTATCG
52172 GTACACT
1 GTACACT
52179 GTGTGTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 20 0.74
21 7 0.26
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (21 bp):
GTACACTCTCAAGGTGTATCG
Found at i:52366 original size:17 final size:18
Alignment explanation
Indices: 52333--52367 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
52323 CTTTTTAATT
52333 GTTTCAAAAATATTTTAA
1 GTTTCAAAAATATTTTAA
*
52351 GTTTCAAACA-ATTTTAA
1 GTTTCAAAAATATTTTAA
52368 ACTTAAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.43
Consensus pattern (18 bp):
GTTTCAAAAATATTTTAA
Done.