Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004279.1 Hibiscus syriacus cultivar Beakdansim tig00009380_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: 101568
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:675 original size:194 final size:197
Alignment explanation
Indices: 1--681 Score: 1176
Period size: 196 Copynumber: 3.5 Consensus size: 197
1 ATATGTAATTTTTCAATCTAACCGGTAC--TTATACCGGTTTTATGAGAGAATATGTCTAAAT-A
1 ATATGT-ATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAA
*
63 TGTGTCGACACTAATATAGTTTGTATCGATACTTTTTT-CCAGAATGAATGGAAACAAGGTGCAC
65 TGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAACAAGGTGCAC
127 CCAT-AAGTGTCGATCCATATATAAAAAGTGTCGATCCCCCAAAATCATCGAACCCAAAAGTATA
130 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGAT--CCCAAAATCATCGAACCCAAAAGTATA
191 ATGTA
193 ATGTA
196 ATATGTATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAA-AAT
1 ATATGTATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAAT
260 GTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCA-AATGAATGGAAACAA-GTGCACC
66 GTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAACAAGGTGCA-C
323 CCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCCAAAA--AGTA
130 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAA-CCCAAAAGTA-TA
384 ATGTA
193 ATGTA
389 ATATGTAATTTTTCAATCTAAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATA
1 ATATGT-ATTTTTCAATCT-AACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATA
454 ATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAACAAGGTGCA
64 ATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAACAAGGTGCA
519 -CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACCCAAAAGTATAA
129 CCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
582 TGTA
194 TGTA
586 ATATGT-TTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAAT
1 ATATGTATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAAT
650 GTGTCGACACTAATATAGTTTGTGTCGATACT
66 GTGTCGACACTAATATAGTTTGTGTCGATACT
682 AATTTAAATA
Statistics
Matches: 468, Mismatches: 1, Indels: 35
0.93 0.00 0.07
Matches are distributed among these distances:
192 1 0.00
193 28 0.06
194 119 0.25
195 82 0.18
196 158 0.34
197 54 0.12
198 26 0.06
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (197 bp):
ATATGTATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAAT
GTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAACAAGGTGCACC
CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TA
Found at i:2144 original size:3 final size:3
Alignment explanation
Indices: 2136--2205 Score: 59
Period size: 3 Copynumber: 23.0 Consensus size: 3
2126 TGAAGCTGAC
* * * ** * *
2136 GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT GAC GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
2184 GATT GAT GAT GAA GAT GAT GAT
1 GA-T GAT GAT GAT GAT GAT GAT
2206 CCAACAAGTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
3 48 0.94
4 3 0.06
ACGTcount: A:0.34, C:0.06, G:0.34, T:0.26
Consensus pattern (3 bp):
GAT
Found at i:2165 original size:27 final size:27
Alignment explanation
Indices: 2124--2204 Score: 108
Period size: 27 Copynumber: 3.0 Consensus size: 27
2114 GGTCGCAGAA
*
2124 GATGAAGCTGACGATGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGATGAC
*
2151 GATGAAGCTGGCGATGAAGATGATGAC
1 GATGAAGCTGACGATGAAGATGATGAC
* * *
2178 GATGATGATTGATGATGAAGATGATGA
1 GATGAAG-CTGACGATGAAGATGATGA
2205 TCCAACAAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 31 0.66
28 16 0.34
ACGTcount: A:0.35, C:0.07, G:0.35, T:0.23
Consensus pattern (27 bp):
GATGAAGCTGACGATGAAGATGATGAC
Found at i:2193 original size:19 final size:19
Alignment explanation
Indices: 2169--2205 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2159 TGGCGATGAA
*
2169 GATGATGACGATGATGATT
1 GATGATGAAGATGATGATT
2188 GATGATGAAGATGATGAT
1 GATGATGAAGATGATGAT
2206 CCAACAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.32, T:0.30
Consensus pattern (19 bp):
GATGATGAAGATGATGATT
Found at i:6545 original size:23 final size:23
Alignment explanation
Indices: 6514--6577 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
6504 ATAGGTAAAC
*
6514 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
6537 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
6560 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
6578 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:6584 original size:23 final size:23
Alignment explanation
Indices: 6514--6586 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
6504 ATAGGTAAAC
* **
6514 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
6537 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
6560 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
6583 ATAT
1 ATAT
6587 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:6966 original size:22 final size:23
Alignment explanation
Indices: 6933--6995 Score: 83
Period size: 22 Copynumber: 2.8 Consensus size: 23
6923 AATAGGTAAC
*
6933 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
6956 ATAT-ATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
6978 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
6996 TGGTTATATG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 19 0.54
23 16 0.46
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:7002 original size:23 final size:22
Alignment explanation
Indices: 6933--7004 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 22
6923 AATAGGTAAC
**
6933 ATATGATGTAATAGGTAGCCCTT
1 ATAT-ATGTAATAGGTAGTGCTT
*
6956 ATATATGTAATAGGTA-TCGTTT
1 ATATATGTAATAGGTAGT-GCTT
*
6978 ATATAATGTAATAGGTAGTGGTT
1 ATAT-ATGTAATAGGTAGTGCTT
7001 ATAT
1 ATAT
7005 GTAAAGTGTC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
22 18 0.43
23 23 0.55
24 1 0.02
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (22 bp):
ATATATGTAATAGGTAGTGCTT
Found at i:7198 original size:420 final size:420
Alignment explanation
Indices: 6419--7235 Score: 1470
Period size: 420 Copynumber: 1.9 Consensus size: 420
6409 TCGCAGTACA
6419 CTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAGTATCGATCCTTTTTATAAAAA
1 CTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAGTATCGATCCTTTTTATAAAAA
6484 GTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAAT
66 GTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAAT
6549 AGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAG
131 AGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAG
6614 TCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATAT
196 TCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATAT
* *
6679 TAATTTAGTAATTAAGGCGTCTAATGATTTTATTTTTTACGTTACGGTATATTATTATTAAATTA
261 TAATTTAGTAATTAAGGCGTATAATGATTTTATTTTTTACGTTACGATATATTATTATTAAATTA
6744 AAAATTCTAAATAATATTTTATAAATATAAACAATC-AATAATTTTTTTGTGCAAATGAAATTAT
326 AAAATTCTAAATAATATTTTATAAATATAAACAATCAAATAA-TTTTTTGTGCAAATGAAATTAT
6808 TAAATCAATATTGTAGGGGAAAACATGAAAC
390 TAAATCAATATTGTAGGGGAAAACATGAAAC
6839 CTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAGTATCGATCCTTTTTATAAAAA
1 CTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAGTATCGATCCTTTTTATAAAAA
6904 GTATGGACACTTTCAATATAATAGGT-AACATATGATGTAATAGGTAGCCCTTATAT-ATGTAAT
66 GTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAAT
6967 AGGTATCGTTTATATAATGTAATAGGTAGTGGTTATA-TGTAAAGTGTCTATCCTTTTTATAAAA
131 AGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT-AAA
7031 GTGTCCATACTTTTTTCACTGTGGAAAACA-TAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGA
195 --GTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGA
7095 TATTAATTTAGTAATTATAGGCGTATAATGA-TTTATTTTTTACGTTACGATATATTA-T-TTAA
258 TATTAATTTAGTAATTA-AGGCGTATAATGATTTTATTTTTTACGTTACGATATATTATTATTAA
* *
7157 ATTAAAAATTCTAAATATTATTTTATAAAATGTCAAAACAATCAAATAATTTTTTGTGCAAATGA
322 ATTAAAAATTCTAAATAATATTTTAT-AAATAT--AAACAATCAAATAATTTTTTGTGCAAATGA
7222 AATTATTAAATCAA
384 AATTATTAAATCAA
7236 ATAATTCAAA
Statistics
Matches: 385, Mismatches: 4, Indels: 16
0.95 0.01 0.04
Matches are distributed among these distances:
417 52 0.14
418 53 0.14
419 106 0.28
420 169 0.44
421 5 0.01
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40
Consensus pattern (420 bp):
CTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAGTATCGATCCTTTTTATAAAAA
GTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAAT
AGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAG
TCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATAT
TAATTTAGTAATTAAGGCGTATAATGATTTTATTTTTTACGTTACGATATATTATTATTAAATTA
AAAATTCTAAATAATATTTTATAAATATAAACAATCAAATAATTTTTTGTGCAAATGAAATTATT
AAATCAATATTGTAGGGGAAAACATGAAAC
Found at i:7929 original size:38 final size:39
Alignment explanation
Indices: 7846--7970 Score: 225
Period size: 39 Copynumber: 3.2 Consensus size: 39
7836 TCCGATGCTC
* *
7846 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
7885 ATCAAAATCCAAATCTCATATGATGCCAAGC-AAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
7923 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
7962 ATCAAAATC
1 ATCAAAATC
7971 TACAACTTGA
Statistics
Matches: 83, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
38 38 0.46
39 45 0.54
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
Found at i:8397 original size:22 final size:23
Alignment explanation
Indices: 8364--8426 Score: 83
Period size: 22 Copynumber: 2.8 Consensus size: 23
8354 AATAGGTAAC
*
8364 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
8387 ATAT-ATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
8409 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
8427 TGGTTATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 19 0.54
23 16 0.46
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:8433 original size:23 final size:22
Alignment explanation
Indices: 8364--8435 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 22
8354 AATAGGTAAC
**
8364 ATATGATGTAATAGGTAGCCCTT
1 ATAT-ATGTAATAGGTAGTGCTT
*
8387 ATATATGTAATAGGTA-TCGTTT
1 ATATATGTAATAGGTAGT-GCTT
*
8409 ATATAATGTAATAGGTAGTGGTT
1 ATAT-ATGTAATAGGTAGTGCTT
8432 ATAT
1 ATAT
8436 TTAGTAATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
22 18 0.43
23 23 0.55
24 1 0.02
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (22 bp):
ATATATGTAATAGGTAGTGCTT
Found at i:10302 original size:3 final size:3
Alignment explanation
Indices: 10294--10358 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
10284 TGAAGCTGAC
* ** *
10294 GAT GAT GAT GAT GAC GAT GAACT GGC GAT GAA GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT G-A-T GAT GAT GAT GAT GAT GAT GAT GAT
10341 GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT
10359 CCAAACAAGT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
3 49 0.94
4 1 0.02
5 2 0.04
ACGTcount: A:0.34, C:0.05, G:0.34, T:0.28
Consensus pattern (3 bp):
GAT
Found at i:14738 original size:23 final size:23
Alignment explanation
Indices: 14707--14770 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
14697 ATAGGTAAAC
*
14707 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
14730 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
14753 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
14771 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:14777 original size:23 final size:23
Alignment explanation
Indices: 14707--14779 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
14697 ATAGGTAAAC
* **
14707 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
14730 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
14753 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
14776 ATAT
1 ATAT
14780 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:15165 original size:23 final size:23
Alignment explanation
Indices: 15134--15196 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
15124 ATAGGTAAAC
*
15134 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
15157 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
15180 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
15197 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:15204 original size:23 final size:23
Alignment explanation
Indices: 15134--15206 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
15124 ATAGGTAAAC
* * **
15134 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
15157 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
15180 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
15203 ATAT
1 ATAT
15207 TGTAAGTGTC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:15503 original size:24 final size:24
Alignment explanation
Indices: 15476--15522 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
15466 AAATCAATTA
*
15476 AACATTGTTGTGGGTACATTATTG
1 AACATTGTTATGGGTACATTATTG
15500 AACATTGTTATGGGTACATTATT
1 AACATTGTTATGGGTACATTATT
15523 TGGATTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.43
Consensus pattern (24 bp):
AACATTGTTATGGGTACATTATTG
Found at i:15790 original size:18 final size:18
Alignment explanation
Indices: 15769--15805 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
15759 GTAATTGGAG
15769 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
15787 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
15805 T
1 T
15806 ATATATTCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:16105 original size:39 final size:39
Alignment explanation
Indices: 16062--16187 Score: 234
Period size: 39 Copynumber: 3.2 Consensus size: 39
16052 TCCGATGCTC
* *
16062 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
16101 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
16140 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
16179 ATCAAAATC
1 ATCAAAATC
16188 TACAACTTGA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 85 1.00
ACGTcount: A:0.48, C:0.21, G:0.13, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
Found at i:16620 original size:23 final size:23
Alignment explanation
Indices: 16589--16652 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
16579 ATAGGTAAAC
*
16589 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
16612 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
16635 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
16653 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:16659 original size:23 final size:23
Alignment explanation
Indices: 16589--16661 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
16579 ATAGGTAAAC
* **
16589 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
16612 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
16635 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
16658 ATAT
1 ATAT
16662 TTAGTAATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:18024 original size:21 final size:21
Alignment explanation
Indices: 17994--18048 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
17984 ATGTTTAAAA
17994 AAATATAAAATTAAATTAAA-TC
1 AAATA-AAAATTAAA-TAAATTC
* *
18016 AAATCAAAATTCAATAAATTC
1 AAATAAAAATTAAATAAATTC
*
18037 ATATAAAAATTA
1 AAATAAAAATTA
18049 TCTTTAATCT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 4 0.15
21 19 0.70
22 4 0.15
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATAAAAATTAAATAAATTC
Found at i:25705 original size:16 final size:18
Alignment explanation
Indices: 25667--25710 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
25657 TTTATGAGAT
*
25667 AATTGAAATCTGTGAATG
1 AATTGGAATCTGTGAATG
25685 AATTGGAATCTGT-AA-G
1 AATTGGAATCTGTGAATG
25701 AATTGGAATC
1 AATTGGAATC
25711 CAATTCTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 11 0.44
17 2 0.08
18 12 0.48
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.32
Consensus pattern (18 bp):
AATTGGAATCTGTGAATG
Found at i:26328 original size:34 final size:35
Alignment explanation
Indices: 26281--26363 Score: 132
Period size: 34 Copynumber: 2.3 Consensus size: 35
26271 TTCACCCTAA
26281 ACCCGAACCCGAATATCACACTTAAAAAA-AACCCG
1 ACCCG-ACCCGAATATCACACTTAAAAAACAACCCG
*
26316 ACCCGACCCGAATATCACACTTAAAAAACCGACCCG
1 ACCCGACCCGAATATCACACTTAAAAAA-CAACCCG
26352 ACCCGACCCGAA
1 ACCCGACCCGAA
26364 ATAATAAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
34 23 0.51
35 5 0.11
36 17 0.38
ACGTcount: A:0.41, C:0.39, G:0.11, T:0.10
Consensus pattern (35 bp):
ACCCGACCCGAATATCACACTTAAAAAACAACCCG
Found at i:26622 original size:218 final size:200
Alignment explanation
Indices: 26349--26802 Score: 573
Period size: 216 Copynumber: 2.2 Consensus size: 200
26339 AAAAACCGAC
26349 CCGACCCGACCCGAAATAATAAAAAAA-A--TTTATTTAATAAAAACAGTGACTTAATCCGACCC
1 CCGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCGACCC
* *
26411 GACTCGAATTATATATATATTTTCGGTTCGGCCCGATTTTTTTCACCCTAAACCCGAACCCGACC
66 GACCCGAA-T-TATATATATTTTCGGGTCGGCCCGATTTTTTTCACCCTAAACCCGAACCCGA--
* * *
26476 CGAACCAAATATCACACTTAAAAAACCTGAGCTGACCCGAA-CAAAATAAAGTTTCATCTGA-CC
127 C---CCAAATATCACACTT----AA--T---CCGACCC-AACCAAAATAAAGTTTCACCCGACCC
26539 GACCCGAATATATGAATTAGAAA
179 GACCCGAATATATGAATTAG-AA
*
26562 TCCGACCCGACCCAAAATAATAAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCGAC
1 -CCGACCCGACCCGAAATAAT-AAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCGAC
** * *
26627 CCGACCCGAATTATATATATTTTCGGGTCGGTTCTATTTTTTTCATCCTAAACCCGAACCCGACC
64 CCGACCCGAATTATATATATTTTCGGGTCGGCCCGATTTTTTTCACCCTAAACCCGAACCCGACC
26692 CAAATATCACACTTAATCCGACCCAACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGA
129 CAAATATCACACTTAATCCGACCCAACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGA
26757 ATTAGAA
194 ATTAGAA
*
26764 ---ACCCGACCCGAAATAATAAAAAAATATTTTTATTCAATA
1 CCGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATA
26803 TATAAATAAG
Statistics
Matches: 222, Mismatches: 12, Indels: 29
0.84 0.05 0.11
Matches are distributed among these distances:
197 21 0.09
198 16 0.07
201 2 0.01
202 26 0.12
203 22 0.10
205 1 0.00
207 2 0.01
211 15 0.07
214 20 0.09
215 7 0.03
216 48 0.22
217 1 0.00
218 41 0.18
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.25
Consensus pattern (200 bp):
CCGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCGACCC
GACCCGAATTATATATATTTTCGGGTCGGCCCGATTTTTTTCACCCTAAACCCGAACCCGACCCA
AATATCACACTTAATCCGACCCAACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAAT
TAGAA
Found at i:32586 original size:21 final size:21
Alignment explanation
Indices: 32561--32603 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
32551 GGAAATGTTA
*
32561 AAAAACATTAATATTTTAGGT
1 AAAAACAATAATATTTTAGGT
* *
32582 AAAAATAATAATGTTTTAGGT
1 AAAAACAATAATATTTTAGGT
32603 A
1 A
32604 TTTTTTTACC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.02, G:0.12, T:0.37
Consensus pattern (21 bp):
AAAAACAATAATATTTTAGGT
Found at i:33935 original size:21 final size:21
Alignment explanation
Indices: 33897--33946 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
33887 GAAAAAATCG
*
33897 GATATCCGAAATTTCGGATCA
1 GATATCCGAAATTCCGGATCA
*
33918 GATATCCG-AATATCCGGATCC
1 GATATCCGAAAT-TCCGGATCA
33939 GA-ATCCGA
1 GATATCCGA
33947 TTTTTTTAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (21 bp):
GATATCCGAAATTCCGGATCA
Found at i:38581 original size:23 final size:27
Alignment explanation
Indices: 38533--38604 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 27
38523 TACTTTAGTT
* *
38533 TAATAAAAAAATTATATGAATAAATA-AA
1 TAATAAAATAATT-TA-AAATAAATATAA
38561 -AAT-AAA-AATTTAAAATAAATATAA
1 TAATAAAATAATTTAAAATAAATATAA
38585 TTAATAAAATAATTTAAAAT
1 -TAATAAAATAATTTAAAAT
38605 TTTAAAAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
23 8 0.21
24 4 0.11
25 4 0.11
26 6 0.16
27 6 0.16
28 10 0.26
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (27 bp):
TAATAAAATAATTTAAAATAAATATAA
Found at i:55685 original size:21 final size:21
Alignment explanation
Indices: 55659--55700 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
55649 GTTTTATTTA
55659 TGATCACCGCCCATCTATATC
1 TGATCACCGCCCATCTATATC
*
55680 TGATCACCTCCCATCTATATC
1 TGATCACCGCCCATCTATATC
55701 CATACTCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.38, G:0.07, T:0.31
Consensus pattern (21 bp):
TGATCACCGCCCATCTATATC
Found at i:58765 original size:30 final size:30
Alignment explanation
Indices: 58729--58794 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
58719 AGTGAACCGG
*
58729 CGGTTCAAACCGATT-TTTCCGGTTTTCAGC
1 CGGTTCAAACCGATTCTAT-CGGTTTTCAGC
** *
58759 CGGTTCACCCCGGTTCTATCGGTTTTCAGC
1 CGGTTCAAACCGATTCTATCGGTTTTCAGC
58789 CGGTTC
1 CGGTTC
58795 TACCGGTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 29 0.94
31 2 0.06
ACGTcount: A:0.12, C:0.30, G:0.23, T:0.35
Consensus pattern (30 bp):
CGGTTCAAACCGATTCTATCGGTTTTCAGC
Found at i:78309 original size:24 final size:24
Alignment explanation
Indices: 78282--78353 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
78272 AAACGGAGAT
*
78282 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
78306 ATCAGATATCATAACAGAA-TCAAT
1 ATCAGAAATCAAAACAGAATTC-AG
*
78330 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
78354 GTAATGTATC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
23 2 0.05
24 35 0.90
25 2 0.05
ACGTcount: A:0.51, C:0.17, G:0.11, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:78386 original size:48 final size:48
Alignment explanation
Indices: 78280--78373 Score: 127
Period size: 48 Copynumber: 2.0 Consensus size: 48
78270 GTAAACGGAG
* * *
78280 ATATCAGAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCA
1 ATATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAACAGAATCA
* *
78328 ATATCAGAAATCAGAACAGAATTCAGGTAATG-TATCAGAACAGAAT
1 ATATCAGAAATCAAAACAGAATTCAGATAA-GATATCAGAACAGAAT
78374 TCAAGTCGGA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 39 0.98
49 1 0.03
ACGTcount: A:0.50, C:0.15, G:0.13, T:0.22
Consensus pattern (48 bp):
ATATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAACAGAATCA
Found at i:87453 original size:188 final size:183
Alignment explanation
Indices: 87120--87756 Score: 586
Period size: 188 Copynumber: 3.4 Consensus size: 183
87110 ATTGGAGGGC
* * * *
87120 AAAGGGAAGTTTTTGAGTGTTGATGATTAAGTAGAAGACCC-TTCGTCTCCACTATTGCAAATGG
1 AAAGGGAAGTTATTGAGTGTTGATGATTAAATAGAAGACCCTTTTGTCTCCACTCTTGCAAATGG
* * * * * * * * **
87184 AGAGGCCCATATGCATGCATATGTATG---TATGTC-T--AAAAGTAT-ACATG-TA-TGCATGC
66 AGAGGTCCATATGCATGCATGTATATGTACTATGACATGCATAGGTATGTC-TGAAATTATATGC
* * *
87240 ATGCTTGCTCCTCAATATGGGTCTT-G-ACTCTAAAGCATATGTACATGAACAT
130 ATGCATGCTCCTCAATATGGGTCTTAGAACTCTTAAGCATATATACATGAACAT
* * * * *
87292 AAATGGAAGTTCTTGAGTGCTGATAATTAAATAGAAGACCCTTTTGTCTCCACTGTTGCAAATGG
1 AAAGGGAAGTTATTGAGTGTTGATGATTAAATAGAAGACCCTTTTGTCTCCACTCTTGCAAATGG
* * * *
87357 AGAGGTCCATATTCATGTCATAGTATATGCA-TATGTATGCATGTATCATGTATGTCTGAAATTA
66 AGAGGTCCATATGCATG-CAT-GTATATGTACTATG-A--CATGCAT-AGGTATGTCTGAAATTA
* * *
87421 TAAATGCATGCATGCTTCTCAACATGGGTCTTGAGATAAACCACTCTTAAGCATATATACATGCA
125 T--ATGCATGCATGCTCCTCAATATGGGTCTT-AG----A--ACTCTTAAGCATATATACATGAA
87486 CAT
181 CAT
* * *
87489 AAAGGGAAGTTATTGAGTGTTGATGATTAAATAGAAGGCCCTTATT-TCTCCAGTCTTGCAAATA
1 AAAGGGAAGTTATTGAGTGTTGATGATTAAATAGAAGACCCTT-TTGTCTCCACTCTTGCAAATG
*
87553 GAGAGGTCCATATGCATGCATGTATATGTACTATGACATGCATAGGTATGTCTGTAATTATA--C
65 GAGAGGTCCATATGCATGCATGTATATGTACTATGACATGCATAGGTATGTCTGAAATTATATGC
* * * *
87616 ATGCATGCTCCCCAATATGGGTCTTGAGATAAACCACTCTTGAGCATATATTCATGTACAT
130 ATGCATGCTCCTCAATATGGGTCTT-AG----A--ACTCTTAAGCATATATACATGAACAT
* * *
87677 GAAGGGAAGTTATAGAGTTTTGATGATTAAATAGAAGACCCTTTTGTCTCCACTCTTGCAAATGG
1 AAAGGGAAGTTATTGAGTGTTGATGATTAAATAGAAGACCCTTTTGTCTCCACTCTTGCAAATGG
87742 AGAGGTCCATATGCA
66 AGAGGTCCATATGCA
87757 CTATGGCAAG
Statistics
Matches: 387, Mismatches: 49, Indels: 42
0.81 0.10 0.09
Matches are distributed among these distances:
172 36 0.09
173 36 0.09
174 3 0.01
175 5 0.01
177 4 0.01
180 1 0.00
181 1 0.00
183 1 0.00
184 7 0.02
185 2 0.01
186 1 0.00
187 2 0.01
188 153 0.40
190 2 0.01
192 16 0.04
193 6 0.02
195 9 0.02
196 7 0.02
197 93 0.24
198 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Consensus pattern (183 bp):
AAAGGGAAGTTATTGAGTGTTGATGATTAAATAGAAGACCCTTTTGTCTCCACTCTTGCAAATGG
AGAGGTCCATATGCATGCATGTATATGTACTATGACATGCATAGGTATGTCTGAAATTATATGCA
TGCATGCTCCTCAATATGGGTCTTAGAACTCTTAAGCATATATACATGAACAT
Found at i:87550 original size:197 final size:188
Alignment explanation
Indices: 87266--87756 Score: 644
Period size: 188 Copynumber: 2.6 Consensus size: 188
87256 ATGGGTCTTG
* * * * * *
87266 ACTCTAAAGCATATGTACATGAACATAAATGGAAGTTCTTGAGTGCTGATAATTAAATAGAAGAC
1 ACTCTTAAGCATATATACATGAACATAAAGGGAAGTTATTGAGTGTTGATGATTAAATAGAAGAC
* * *
87331 CCTTTTGTCTCCACTGTTGCAAATGGAGAGGTCCATATTCATGTCATAGTATATGCA-TATGTAT
66 CCTTTTGTCTCCACTCTTGCAAATGGAGAGGTCCATATGCATG-CAT-GTATATGTACTATG-A-
* * * *
87395 GCATGTATCATGTATGTCTGAAATTATAAATGCATGCATGCTTCTCAACATGGGTCTTGAGATAA
127 -CATGCAT-AGGTATGTCTGAAATTAT--A--CATGCATGCTCCCCAACATGGGTCTTGAGATAA
87460 ACC
186 ACC
* *
87463 ACTCTTAAGCATATATACATGCACATAAAGGGAAGTTATTGAGTGTTGATGATTAAATAGAAGGC
1 ACTCTTAAGCATATATACATGAACATAAAGGGAAGTTATTGAGTGTTGATGATTAAATAGAAGAC
* *
87528 CCTTATT-TCTCCAGTCTTGCAAATAGAGAGGTCCATATGCATGCATGTATATGTACTATGACAT
66 CCTT-TTGTCTCCACTCTTGCAAATGGAGAGGTCCATATGCATGCATGTATATGTACTATGACAT
* *
87592 GCATAGGTATGTCTGTAATTATACATGCATGCTCCCCAATATGGGTCTTGAGATAAACC
130 GCATAGGTATGTCTGAAATTATACATGCATGCTCCCCAACATGGGTCTTGAGATAAACC
* * * * * *
87651 ACTCTTGAGCATATATTCATGTACATGAAGGGAAGTTATAGAGTTTTGATGATTAAATAGAAGAC
1 ACTCTTAAGCATATATACATGAACATAAAGGGAAGTTATTGAGTGTTGATGATTAAATAGAAGAC
87716 CCTTTTGTCTCCACTCTTGCAAATGGAGAGGTCCATATGCA
66 CCTTTTGTCTCCACTCTTGCAAATGGAGAGGTCCATATGCA
87757 CTATGGCAAG
Statistics
Matches: 263, Mismatches: 28, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
187 2 0.01
188 127 0.48
190 1 0.00
192 16 0.06
193 6 0.02
195 9 0.03
196 7 0.03
197 93 0.35
198 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (188 bp):
ACTCTTAAGCATATATACATGAACATAAAGGGAAGTTATTGAGTGTTGATGATTAAATAGAAGAC
CCTTTTGTCTCCACTCTTGCAAATGGAGAGGTCCATATGCATGCATGTATATGTACTATGACATG
CATAGGTATGTCTGAAATTATACATGCATGCTCCCCAACATGGGTCTTGAGATAAACC
Found at i:89573 original size:2 final size:2
Alignment explanation
Indices: 89562--89599 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
89552 TTGATGAATT
89562 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
89600 CCAAGTTAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:90408 original size:3 final size:3
Alignment explanation
Indices: 90400--90432 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
90390 AACCTATTAT
90400 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
90433 TCAATTGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Done.