Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002585.1 Hibiscus syriacus cultivar Beakdansim tig00005231_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: 72206
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:2753 original size:24 final size:20
Alignment explanation
Indices: 2697--2754 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
2687 TTCCCCTTGA
2697 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
*
2717 AGTTCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
2740 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
2755 CTACCCATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.50
22 1 0.03
23 3 0.09
24 12 0.38
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:2820 original size:64 final size:63
Alignment explanation
Indices: 2742--2882 Score: 171
Period size: 64 Copynumber: 2.2 Consensus size: 63
2732 TCTTTAACAT
* *
2742 GTGCATCGATGCACTACC-CATGCATCGATACACAAATTACCTTCGATG-TT-TTCATTTTAAGG
1 GTGCATCGATGCACT-CCTCATGCATCGATACACAAATTACATTCGATGATTCTTC--TTTAAAG
*
2804 G
63 A
* * *
2805 GATGCATCGATGCACTCCTTATGCATCGATACACCAATTGCATTCGATGATTCTTCTTTAAAGA
1 G-TGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGATTCTTCTTTAAAGA
2869 GTGCATCGATGCAC
1 GTGCATCGATGCAC
2883 ATTGAATATG
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
63 16 0.24
64 47 0.69
65 2 0.03
66 3 0.04
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGATTCTTCTTTAAAGA
Found at i:15960 original size:25 final size:24
Alignment explanation
Indices: 15912--16051 Score: 158
Period size: 23 Copynumber: 5.8 Consensus size: 24
15902 TAAGATAATT
* *
15912 TTTAATGTTTTTAGGTTAGAGTGG
1 TTTAAGGTTTTTAGGTTAAAGTGG
*
15936 TTTAAGGTTTTATATGTTAAAGTGG
1 TTTAAGGTTTT-TAGGTTAAAGTGG
* * * *
15961 TTTAGGGTGTTTTAGATGAAAGGGG
1 TTTAAGGT-TTTTAGGTTAAAGTGG
*
15986 TTTAGAGTTTTTTTAGGTTAAAGTGG
1 TTTA-AG-GTTTTTAGGTTAAAGTGG
16012 TTTAAGG-TTTTAGGTTAAAGTGG
1 TTTAAGGTTTTTAGGTTAAAGTGG
16035 TTTAAGG-TTTTAGGTTA
1 TTTAAGGTTTTTAGGTTA
16052 GATTAAAATG
Statistics
Matches: 98, Mismatches: 14, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
23 33 0.34
24 10 0.10
25 33 0.34
26 21 0.21
27 1 0.01
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.46
Consensus pattern (24 bp):
TTTAAGGTTTTTAGGTTAAAGTGG
Found at i:16058 original size:51 final size:50
Alignment explanation
Indices: 15920--16046 Score: 145
Period size: 49 Copynumber: 2.6 Consensus size: 50
15910 TTTTTAATGT
* *
15920 TTTTAGGTTAGAGTGGTTTAAGGTTTTA-TATGTTAAAGTGGTTTAGGGTG
1 TTTTAGGTTAAAGTGGTTTAAGGTTTTATTA-GTTAAAGTGGTTTAGAGTG
* * * *
15970 TTTTAGATGAAAGGGGTTT-AGAGTTTTTTTAGGTTAAAGTGGTTTA-AG-G
1 TTTTAGGTTAAAGTGGTTTAAG-GTTTTATTA-GTTAAAGTGGTTTAGAGTG
16019 TTTTAGGTTAAAGTGGTTTAAGGTTTTA
1 TTTTAGGTTAAAGTGGTTTAAGGTTTTA
16047 GGTTAGATTA
Statistics
Matches: 63, Mismatches: 11, Indels: 7
0.78 0.14 0.09
Matches are distributed among these distances:
49 24 0.38
50 23 0.37
51 16 0.25
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (50 bp):
TTTTAGGTTAAAGTGGTTTAAGGTTTTATTAGTTAAAGTGGTTTAGAGTG
Found at i:16138 original size:10 final size:10
Alignment explanation
Indices: 16123--16149 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
16113 CACATACATT
16123 GAAAATATTA
1 GAAAATATTA
16133 GAAAATATTA
1 GAAAATATTA
16143 GAAAATA
1 GAAAATA
16150 CAATTACATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (10 bp):
GAAAATATTA
Found at i:16171 original size:35 final size:36
Alignment explanation
Indices: 16098--16171 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 36
16088 CTAAATGGAA
16098 AAAATTTAGAAAATACACATACATTGAAAATATTAG
1 AAAATTTAGAAAATACACATACATTGAAAATATTAG
16134 AAAATATTAGAAAATACA-ATTACA-TG-AAATATTAG
1 AAAAT-TTAGAAAATACACA-TACATTGAAAATATTAG
16169 AAA
1 AAA
16172 CAAACACATA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
35 12 0.33
36 8 0.22
37 16 0.44
ACGTcount: A:0.58, C:0.07, G:0.08, T:0.27
Consensus pattern (36 bp):
AAAATTTAGAAAATACACATACATTGAAAATATTAG
Found at i:16183 original size:26 final size:25
Alignment explanation
Indices: 16135--16234 Score: 105
Period size: 26 Copynumber: 3.9 Consensus size: 25
16125 AAATATTAGA
*
16135 AAATATTAGAAAATACAATTACA-TG
1 AAATATTAGAAAAAACAA-TACATTG
16160 AAATATTAGAAACAAACACATACATTG
1 AAATATTAGAAA-AAACA-ATACATTG
* * *
16187 AAATGTTAGAAAATAAGATTACATTG
1 AAATATTAGAAAA-AACAATACATTG
16213 AAATATTAG-AAAAACACATACA
1 AAATATTAGAAAAAACA-ATACA
16235 CAAAAATAGT
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
24 3 0.05
25 19 0.30
26 24 0.38
27 17 0.27
ACGTcount: A:0.56, C:0.10, G:0.09, T:0.25
Consensus pattern (25 bp):
AAATATTAGAAAAAACAATACATTG
Found at i:16196 original size:27 final size:26
Alignment explanation
Indices: 16135--16278 Score: 109
Period size: 25 Copynumber: 5.5 Consensus size: 26
16125 AAATATTAGA
*
16135 AAATATTAGAAAATACA-ATTACA-TG
1 AAATATTAGAAAAAACACA-TACATTG
16160 AAATATTAGAAACAAACACATACATTG
1 AAATATTAGAAA-AAACACATACATTG
* * *
16187 AAATGTTAGAAAATAAGA-TTACATTG
1 AAATATTAGAAAA-AACACATACATTG
***
16213 AAATATTAG-AAAAACACATACACAA
1 AAATATTAGAAAAAACACATACATTG
* * *
16238 AAATAGTAG-AAAAGCACATACAATACTA
1 AAATATTAGAAAAAACACATAC-AT--TG
16266 AAATATTAGAAAA
1 AAATATTAGAAAA
16279 GCACAAACAT
Statistics
Matches: 95, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
24 3 0.03
25 38 0.40
26 25 0.26
27 17 0.18
28 9 0.09
29 3 0.03
ACGTcount: A:0.58, C:0.10, G:0.09, T:0.23
Consensus pattern (26 bp):
AAATATTAGAAAAAACACATACATTG
Found at i:16208 original size:52 final size:51
Alignment explanation
Indices: 16135--16234 Score: 150
Period size: 52 Copynumber: 1.9 Consensus size: 51
16125 AAATATTAGA
16135 AAATATTAGAAAATACAATTACA-TGAAATATTAGAAACAAACACATACATTG
1 AAATATTAGAAAATACAATTACATTGAAATATTAG-AA-AAACACATACATTG
*
16187 AAATGTTAGAAAATA-AGATTACATTGAAATATTAGAAAAACACATACA
1 AAATATTAGAAAATACA-ATTACATTGAAATATTAGAAAAACACATACA
16235 CAAAAATAGT
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
51 12 0.27
52 22 0.49
53 11 0.24
ACGTcount: A:0.56, C:0.10, G:0.09, T:0.25
Consensus pattern (51 bp):
AAATATTAGAAAATACAATTACATTGAAATATTAGAAAAACACATACATTG
Found at i:16241 original size:25 final size:26
Alignment explanation
Indices: 16213--16283 Score: 90
Period size: 28 Copynumber: 2.7 Consensus size: 26
16203 GATTACATTG
*
16213 AAATATTAGAAAAACACATAC-ACAA
1 AAATATTAGAAAAGCACATACAACAA
* *
16238 AAATAGTAGAAAAGCACATACAATACTA
1 AAATATTAGAAAAGCACATAC-A-ACAA
16266 AAATATTAGAAAAGCACA
1 AAATATTAGAAAAGCACA
16284 AACATAGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
25 19 0.49
28 20 0.51
ACGTcount: A:0.61, C:0.14, G:0.08, T:0.17
Consensus pattern (26 bp):
AAATATTAGAAAAGCACATACAACAA
Found at i:18228 original size:23 final size:23
Alignment explanation
Indices: 18202--18270 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
18192 GTTCTACGCA
*
18202 GTCCTTCGGGATAATTCTATGTG
1 GTCCTTCGGGAAAATTCTATGTG
* * *
18225 GTCCTTCAGGAAAATTCTACGCG
1 GTCCTTCGGGAAAATTCTATGTG
* *
18248 ATCCTTTGGGACAAA-TCTATGTG
1 GTCCTTCGGGA-AAATTCTATGTG
18271 ACACTTCGGT
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
23 33 0.92
24 3 0.08
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (23 bp):
GTCCTTCGGGAAAATTCTATGTG
Found at i:19375 original size:22 final size:22
Alignment explanation
Indices: 19330--19375 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
19320 AAGTAGAAAT
**
19330 AAATAAAATGAAAATGATTGAA
1 AAATAAAATGAAAAAAATTGAA
19352 AAATAAAATTGAAAAAAATT-AA
1 AAATAAAA-TGAAAAAAATTGAA
19374 AA
1 AA
19376 TACCTATGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.22
Consensus pattern (22 bp):
AAATAAAATGAAAAAAATTGAA
Found at i:21331 original size:8 final size:8
Alignment explanation
Indices: 21318--21351 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
21308 CAGAGATATC
21318 AGTTTGAG
1 AGTTTGAG
21326 AGTTTGAG
1 AGTTTGAG
*
21334 AATTTGAG
1 AGTTTGAG
21342 AGTTTGAG
1 AGTTTGAG
21350 AG
1 AG
21352 AGTGTAAGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.35
Consensus pattern (8 bp):
AGTTTGAG
Found at i:26292 original size:109 final size:110
Alignment explanation
Indices: 26111--26719 Score: 564
Period size: 109 Copynumber: 5.6 Consensus size: 110
26101 CTACGGGTTC
* * * * ** * *
26111 GCTCCCTCTTTCTTCAGGGAGTATATA-ACTTGAA-AATCTTCTGCAAACGGGTTCTCTCCCTCT
1 GCTCCCTATTCCTTCAGAGAGTATA-AGACTCGAACAATCTTCAACAATCGGGTTCTCTCCCTAT
* *
26174 TTCTTCAGGGAGTATAGA-ACTCGAAAATCTTTTGAAAACGTGTCT
65 TTCTTCAGAGAGTATAGAGACTCGAAAATCTTTTCAAAACGTGTCT
* * *
26219 GCTCCTTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGGGTTCGT-TCCCTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGGGTTC-TCTCCCTAT
* * * *
26283 TTCTCCAGGGAGTATAGA-ACTCGAAAATCTTTTGAAAACGTGTAT
65 TTCTTCAGAGAGTATAGAGACTCGAAAATCTTTTCAAAACGTGTCT
* * *
26328 GCTCCATATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTG-TCTACTCCCTA-
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGGGTTCT-CTCCCTAT
26391 TTCTTTCAGAGAGTAT-GAGACTCGAATAATC--TTCAACAATCGTGTCT
65 TTC-TTCAGAGAGTATAGAGACTCGAA-AATCTTTTCAA-AA-CGTGTCT
* *
26438 GCTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAAACTTCAACAATCGGG-TCTACTCCCTAT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGGGTTCT-CTCCCTAT
* * * * *
26502 TTCTTCAGAGAGTATA-AGAC-CCACAATCTTCATC-AATCGCGTCT
65 TTCTTCAGAGAGTATAGAGACTCGAAAATCTT-TTCAAAACGTGTCT
* * * * *
26546 GCCCCCTATTTCTTCAGAGAGTATAAGACTC--ACAATCTTCATCAATCGTGTT-TGCCCCCTAT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGGGTTCT-CTCCCTAT
* * *
26608 TTTTTCAGAGAGTATA-AGACTCGAACAATC--TTCAACTATCGTGTAT
65 TTCTTCAGAGAGTATAGAGACTCGAA-AATCTTTTCAA--AACGTGTCT
* * * *
26654 CCCCCCTATAT-CTTCAGAGAGTATAAGAC-C-CACAATCTTCAACAAAT-GGGTTCGCTCCCTA
1 GCTCCCTAT-TCCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC-AATCGGGTTCTCTCCCTA
26715 TTTCT
64 TTTCT
26720 CTAGGGAGTA
Statistics
Matches: 428, Mismatches: 48, Indels: 50
0.81 0.09 0.10
Matches are distributed among these distances:
105 2 0.00
106 44 0.10
107 6 0.01
108 137 0.32
109 148 0.35
110 86 0.20
111 5 0.01
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.31
Consensus pattern (110 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGGGTTCTCTCCCTATT
TCTTCAGAGAGTATAGAGACTCGAAAATCTTTTCAAAACGTGTCT
Found at i:26296 original size:55 final size:55
Alignment explanation
Indices: 26103--27368 Score: 761
Period size: 51 Copynumber: 23.9 Consensus size: 55
26093 TCTTTTGCCT
* * * **
26103 ACGGGTTCGCTCCCTCTTTCTTCAGGGAGTAT-ATAACTTGAA-AATCTTCTGCAA
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGAGAACTCGAACAATCTTCAAC-A
* * *
26157 ACGGGTTCTCTCCCTCTTTCTTCAGGGAGTAT-AGAACTCGAA-AATCTTTTGAA-A
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGAGAACTCGAACAATC--TTCAACA
* * * * * *
26211 ACGTG-TCTGCTCCTTATTCCTTCAGAGAGTATGAG-ACTCGAACAATCTTCAACA
1 ACGGGTTC-GCTCCCTCTTTCTTTAGGGAGTATGAGAACTCGAACAATCTTCAACA
* ** *
26265 ATCGGGTTCGTTCCCTCTTTCTCCAGGGAGTAT-AGAACTCGAA-AATCTTTTGAA-A
1 A-CGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGAGAACTCGAACAATC--TTCAACA
* * * * * *
26320 ACGTGTAT-GCTCCATATTCCTTCAGAGAGTATGAG-ACTCGAACAATCTTCAACA
1 ACGGGT-TCGCTCCCTCTTTCTTTAGGGAGTATGAGAACTCGAACAATCTTCAACA
* * * * *
26374 ATCGTG-TCTACTCCCT-ATTCTTTCAGAGAGTATGAG-ACTCGAATAATCTTCAACA
1 A-CGGGTTC-GCTCCCTCTTTCTTT-AGGGAGTATGAGAACTCGAACAATCTTCAACA
* * * * *
26429 ATCGTG-TCTGCTCCCT-ATTCTTTCAGAGAGTATAAG-ACTCGAACAAACTTCAACA
1 A-CGGGTTC-GCTCCCTCTTTCTTT-AGGGAGTATGAGAACTCGAACAATCTTCAACA
* * * * * * *
26484 ATCGGG-TCTACTCCCTATTTCTTCAGAGAGTATAAG-AC-C-CACAATCTTCATCA
1 A-CGGGTTC-GCTCCCTCTTTCTTTAGGGAGTATGAGAACTCGAACAATCTTCAACA
* * * * * * *
26537 ATCGCG-TCTGCCCCCTATTTCTTCAGAGAGTATAAG-ACTC--ACAATCTTCATCA
1 A-CGGGTTC-GCTCCCTCTTTCTTTAGGGAGTATGAGAACTCGAACAATCTTCAACA
* * * * * *
26590 ATCGTGTTTGCCCCCTATTT-TTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACTA
1 A-CGGGTTCGCTCCCTCTTTCTTT-AGGGAGTATGAGAACTCGAACAATCTTCAAC-A
* * * * * * * * *
26646 TCGTGTATC-CCCCCTATATCTTCAGAGAGTATAAG-AC-C-CACAATCTTCAACAA
1 ACGGGT-TCGCTCCCTCTTTCTTTAGGGAGTATGAGAACTCGAACAATCTTCAAC-A
* * *
26699 ATGGGTTCGCTCCCTATTTCTCTAGGGAGTATG-GAACTC-AGACATATTCTTC-A-A
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGAGAACTCGA-ACA-A-TCTTCAACA
* * *
26753 ACGGGTTCGCTCCCCCTTTCTCTAGGGAGTAT-AGAACTCGAACATCTCTTC-A-A
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGAGAACTCGAACA-ATCTTCAACA
* * * *
26806 ACGGGTTCGTTCCTTCCTTCTTTAAGGAGTAT-AGAACTCGAAC-ATCTTC-A-A
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGAGAACTCGAACAATCTTCAACA
* * *
26857 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTAT-AGAACTCGAAC-ATATTC-A-A
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGAGAACTCGAACAATCTTCAACA
* **
26908 ATGGGTTCGCTCCCTCTTTCTTTAGGGAGTAT-AGAACTCGAAC-ATC-TCTTC-
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGAGAACTCGAACAATCTTCAACA
*
26959 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATG-GAACTCGAAC-ATCTTCAAC-
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGAGAACTCGAACAATCTTCAACA
* * * *
27011 -TGGGTTCGCTCCTTCTTTCTTTAAGGAGTATG-GAACTCGAAC-ATCTT-TA-A
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGAGAACTCGAACAATCTTCAACA
* *
27061 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTAT-AGAACTCG--CATATCTTC-AC-
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGAGAACTCGAACA-ATCTTCAACA
* *
27112 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATG-GAACTC-AGACATCTCTTC-A-A
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGAGAACTCGA-ACA-ATCTTCAACA
* * * *
27165 ACGGGTTCGCTCCTTCTTTATTTAAGGAGTATG-GAACTCGAAC-ATCTT-TA-A
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGAGAACTCGAACAATCTTCAACA
* *
27216 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTAT-AGAACTCG--CATATCTTC-AC-
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGAGAACTCGAACA-ATCTTCAACA
* * * *
27267 ACGGGTTCGCTCCTTCCTTCTCTAGGGAGTATG-GAACTCGGAC-ATCTTC-A-A
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGAGAACTCGAACAATCTTCAACA
* * * *
27318 ACAGGTTCGCTCCCTCTTTCTCTAGGGAGTATG-GAACTCAAATAATCTTCA
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGAGAACTCGAACAATCTTCA
27369 TTTGCTTCAC
Statistics
Matches: 1030, Mismatches: 117, Indels: 131
0.81 0.09 0.10
Matches are distributed among these distances:
49 2 0.00
50 3 0.00
51 391 0.38
52 14 0.01
53 229 0.22
54 163 0.16
55 204 0.20
56 19 0.02
57 5 0.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (55 bp):
ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGAGAACTCGAACAATCTTCAACA
Found at i:26556 original size:53 final size:55
Alignment explanation
Indices: 26168--26698 Score: 511
Period size: 55 Copynumber: 9.8 Consensus size: 55
26158 CGGGTTCTCT
* * * *
26168 CCCTCTTTCTTCAGGGAGTAT-AGAACTCGAA-AATCTTTTGAA-AA-CGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATC--TTCAACAATCGTGTCTGCC
* * * * **
26222 CCTTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGGGT-TCGTT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT-GCC
* * * * * *
26277 CCCTCTTTCTCCAGGGAGTAT-AGAACTCGAA-AATCTTTTGAA-AA-CGTGTATGCT
1 CCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATC--TTCAACAATCGTGTCTGCC
* * * * *
26331 CCATATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTACT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCC
* * *
26386 CCCTA-TTCTTTCAGAGAGTATGAGACTCGAATAATCTTCAACAATCGTGTCTGCT
1 CCCTATTTC-TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCC
* * * *
26441 CCCTA-TTCTTTCAGAGAGTATAAGACTCGAACAAACTTCAACAATCGGGTCTACT
1 CCCTATTTC-TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCC
* * *
26496 CCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCC
* *
26549 CCCTATTTCTTCAGAGAGTATAAGACTC--ACAATCTTCATCAATCGTGTTTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCC
* * * *
26602 CCCTATTTTTTCAGAGAGTATAAGACTCGAACAATCTTCAACTATCGTGTATCCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCC
* *
26657 CCCTATATCTTCAGAGAGTATAAGAC-C-CACAATCTTCAACAA
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAA
26699 ATGGGTTCGC
Statistics
Matches: 410, Mismatches: 49, Indels: 37
0.83 0.10 0.07
Matches are distributed among these distances:
53 117 0.29
54 69 0.17
55 217 0.53
56 7 0.02
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (55 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCC
Found at i:26616 original size:161 final size:162
Alignment explanation
Indices: 26225--26698 Score: 514
Period size: 161 Copynumber: 2.9 Consensus size: 162
26215 GTCTGCTCCT
* * * * * *
26225 TATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGGGTTCGTTCCCTCT-TTC-TC
1 TATTCTTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATCGTG-TC-TGCCCCCTATTCTTT
* * * * * * *
26288 CAGGGAGTAT-AGAACTCGAA-AATCTTTTGAA-AA-CGTGTATGCTCCATATTCCTTCAGAGAG
63 CAGAGAGTATAAG-ACTCGAACAAAC--TTCAACAATCGGGTATACTCCCTATTTCTTCAGAGAG
* * * *
26349 TATGAGACTCGAACAATCTTCAACAATCGTGTCTACTCCC
125 TATAAGAC-C-CACAATCTTCAACAATCGCGTCTACCCCC
* * *
26389 TATTCTTTCAGAGAGTATGAGACTCGAATAATCTTCAACAATCGTGTCTGCTCCCTATTCTTTCA
1 TATTCTTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATCGTGTCTGCCCCCTATTCTTTCA
*
26454 GAGAGTATAAGACTCGAACAAACTTCAACAATCGGGTCTACTCCCTATTTCTTCAGAGAGTATAA
65 GAGAGTATAAGACTCGAACAAACTTCAACAATCGGGTATACTCCCTATTTCTTCAGAGAGTATAA
* *
26519 GACCCACAATCTTCATCAATCGCGTCTGCCCCC
130 GACCCACAATCTTCAACAATCGCGTCTACCCCC
* * *
26552 TATT-TCTTCAGAGAGTATAAGACTC-ACAATCTTCATCAATCGTGTTTGCCCCCTATTTTTTCA
1 TATTCT-TTCAGAGAGTATAAGACTCAACAATCTTCAACAATCGTGTCTGCCCCCTATTCTTTCA
* * * * * *
26615 GAGAGTATAAGACTCGAACAATCTTCAACTATCGTGTATCCCCCCTATATCTTCAGAGAGTATAA
65 GAGAGTATAAGACTCGAACAAACTTCAACAATCGGGTATACTCCCTATTTCTTCAGAGAGTATAA
26680 GACCCACAATCTTCAACAA
130 GACCCACAATCTTCAACAA
26699 ATGGGTTCGC
Statistics
Matches: 268, Mismatches: 35, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
161 109 0.41
162 6 0.02
163 55 0.21
164 63 0.24
165 35 0.13
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (162 bp):
TATTCTTTCAGAGAGTATAAGACTCAACAATCTTCAACAATCGTGTCTGCCCCCTATTCTTTCAG
AGAGTATAAGACTCGAACAAACTTCAACAATCGGGTATACTCCCTATTTCTTCAGAGAGTATAAG
ACCCACAATCTTCAACAATCGCGTCTACCCCC
Found at i:26714 original size:53 final size:56
Alignment explanation
Indices: 26107--26719 Score: 489
Period size: 55 Copynumber: 11.3 Consensus size: 56
26097 TTGCCTACGG
* * * ** * *
26107 GTTC-GCTCCCTCTTTCTTCAGGGAGTATATA-ACTTGAA-AATCTTCTGCAAACGG
1 GTTCTGCTCCCTATTTCTTCAGAGAGTATA-AGACTCGAACAATCTTCAACAATCGC
* * * *
26161 GTTCT-CTCCCTCTTTCTTCAGGGAGTAT-AGAACTCGAA-AATCTTTTGAA-AA-CGT
1 GTTCTGCTCCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATC--TTCAACAATCGC
* * * *
26215 G-TCTGCTCCTTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGG
1 GTTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGC
* * * * * *
26270 GTTC-GTTCCCTCTTTCTCCAGGGAGTAT-AGAACTCGAA-AATCTTTTGAA-AA-CGT
1 GTTCTGCTCCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATC--TTCAACAATCGC
* * * * *
26324 G-TATGCTCCATATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGT
1 GTTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGC
* * * *
26379 G-TCTACTCCCTA-TTCTTTCAGAGAGTATGAGACTCGAATAATCTTCAACAATCGT
1 GTTCTGCTCCCTATTTC-TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGC
*
26434 G-TCTGCTCCCTA-TTCTTTCAGAGAGTATAAGACTCGAACAAACTTCAACAATCG-
1 GTTCTGCTCCCTATTTC-TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGC
* * * *
26488 GGTCTACTCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGC
1 GTTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGC
* * *
26542 G-TCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC--ACAATCTTCATCAATCGT
1 GTTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGC
* * * *
26595 GTT-TGCCCCCTATTTTTTCAGAGAGTATAAGACTCGAACAATCTTCAACTATCGT
1 GTTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGC
* * * *
26650 GTATC--CCCCCTATATCTTCAGAGAGTATAAGAC-C-CACAATCTTCAACAAAT-GG
1 GT-TCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC-AATCGC
26703 GTTC-GCTCCCTATTTCT
1 GTTCTGCTCCCTATTTCT
26720 CTAGGGAGTA
Statistics
Matches: 475, Mismatches: 53, Indels: 63
0.80 0.09 0.11
Matches are distributed among these distances:
52 3 0.01
53 131 0.28
54 114 0.24
55 215 0.45
56 12 0.03
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.31
Consensus pattern (56 bp):
GTTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGC
Found at i:26872 original size:51 final size:51
Alignment explanation
Indices: 26696--27356 Score: 799
Period size: 51 Copynumber: 12.8 Consensus size: 51
26686 CAATCTTCAA
* * * * *
26696 CAAATGGGTTCGCTCCCTATTTCTCTAGGGAGTATGGAACTCAGACATATTCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAGGGAGTATGGAACTC-GA-ACA-TCTT
** * *
26750 CAAACGGGTTCGCTCCCCCTTTCTCTAGGGAGTATAGAACTCGAACATCTCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAGGGAGTATGGAACTCGAACA--TCTT
* * * *
26803 CAAACGGGTTCGTTCCTTCCTTCTTTAAGGAGTATAGAACTCGAACATCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAGGGAGTATGGAACTCGAACATCTT
* * *
26854 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATATT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAGGGAGTATGGAACTCGAACATCTT
* * *
26905 CAAATGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAGGGAGTATGGAACTCGAACA--TCTT
* *
26958 C--ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAGGGAGTATGGAACTCGAACATCTT
*
27007 C-AACTGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAACATCTT
1 CAAAC-GGGTTCGCTCCTTCTTTCTTTAGGGAGTATGGAACTCGAACATCTT
* * * * *
27058 TAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGCATATCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAGGGAGTATGGAACTCGAACATCTT
* * *
27109 CACACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC-AGACATCTCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAGGGAGTATGGAACTCGA-ACA--TCTT
* *
27162 CAAACGGGTTCGCTCCTTCTTTATTTAAGGAGTATGGAACTCGAACATCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAGGGAGTATGGAACTCGAACATCTT
* * * * *
27213 TAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGCATATCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAGGGAGTATGGAACTCGAACATCTT
* * * *
27264 CACACGGGTTCGCTCCTTCCTTCTCTAGGGAGTATGGAACTCGGACATCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAGGGAGTATGGAACTCGAACATCTT
* * *
27315 CAAACAGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC
1 CAAACGGGTTCGCTCCTTCTTTCTTTAGGGAGTATGGAACTC
27357 AAATAATCTT
Statistics
Matches: 538, Mismatches: 59, Indels: 23
0.87 0.10 0.04
Matches are distributed among these distances:
49 5 0.01
50 2 0.00
51 392 0.73
52 5 0.01
53 95 0.18
54 39 0.07
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.33
Consensus pattern (51 bp):
CAAACGGGTTCGCTCCTTCTTTCTTTAGGGAGTATGGAACTCGAACATCTT
Found at i:27796 original size:36 final size:36
Alignment explanation
Indices: 27738--27927 Score: 238
Period size: 36 Copynumber: 5.2 Consensus size: 36
27728 ACTCTTCTGA
* * **
27738 GAAGGCTTAAAATGGATATGCTTCACTACTT-TTTGGT
1 GAAGGCTTAAGATGG-TTTGCTTCACTA-TTCTCCGGT
* * *
27775 GAAGACTTAAGATGGTTTGCTTCACTACTCTCTGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* *
27811 GAAGACTTATGATGGTTTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* * *
27847 GAAGGCTTCAGATTGATTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
*
27883 GAAGGCTTCAGATGGTTTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
27919 GAAGGCTTA
1 GAAGGCTTA
27928 GGATTGACTT
Statistics
Matches: 136, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
35 1 0.01
36 122 0.90
37 13 0.10
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (36 bp):
GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
Found at i:30096 original size:16 final size:16
Alignment explanation
Indices: 30078--30107 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30068 TTCATTCTTT
30078 TTTTC-ATTTTTCTCA
1 TTTTCAATTTTTCTCA
30093 TTTTCAATTTTTCTC
1 TTTTCAATTTTTCTC
30108 TTTCTTTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.20, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTCAATTTTTCTCA
Found at i:32792 original size:20 final size:21
Alignment explanation
Indices: 32767--32821 Score: 85
Period size: 20 Copynumber: 2.7 Consensus size: 21
32757 CATGCGATGT
32767 GGTCTTCTCGTCTTTACG-AA
1 GGTCTTCTCGTCTTTACGAAA
* *
32787 GGTCTTCTCGTCGTTATGAAA
1 GGTCTTCTCGTCTTTACGAAA
32808 GGTCTTCTCGTCTT
1 GGTCTTCTCGTCTT
32822 GATGAATAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.13, C:0.24, G:0.22, T:0.42
Consensus pattern (21 bp):
GGTCTTCTCGTCTTTACGAAA
Found at i:32811 original size:21 final size:21
Alignment explanation
Indices: 32767--32882 Score: 114
Period size: 21 Copynumber: 5.6 Consensus size: 21
32757 CATGCGATGT
* *
32767 GGTCTTCTCGTCTTTACG-AA
1 GGTCTTCTCGTCTTGATGAAA
32787 GGTCTTCTCGTCGTT-ATGAAA
1 GGTCTTCTCGTC-TTGATGAAA
32808 GGTCTTCTCGTCTTGATGAATA
1 GGTCTTCTCGTCTTGATGAA-A
*
32830 -GTATTCTCGTCTTGATG-AA
1 GGTCTTCTCGTCTTGATGAAA
* * *
32849 TGACATTCTCGTCTTGATGAAT
1 GGTC-TTCTCGTCTTGATGAAA
*
32871 GCTCTTCTCGTC
1 GGTCTTCTCGTC
32883 CTTGGTACGA
Statistics
Matches: 81, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.01
20 18 0.22
21 59 0.73
22 3 0.04
ACGTcount: A:0.17, C:0.22, G:0.21, T:0.41
Consensus pattern (21 bp):
GGTCTTCTCGTCTTGATGAAA
Found at i:38277 original size:2 final size:2
Alignment explanation
Indices: 38272--38437 Score: 332
Period size: 2 Copynumber: 83.0 Consensus size: 2
38262 GTGTGATATA
38272 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
38314 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
38356 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
38398 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
38438 CTTACATAAG
Statistics
Matches: 164, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 164 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:39477 original size:21 final size:21
Alignment explanation
Indices: 39451--39490 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
39441 TACGAAAGTT
39451 ACTGTAGCAGTGAATCGATGC
1 ACTGTAGCAGTGAATCGATGC
*
39472 ACTGTAGCAGTGCATCGAT
1 ACTGTAGCAGTGAATCGAT
39491 ACACAATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (21 bp):
ACTGTAGCAGTGAATCGATGC
Found at i:40080 original size:33 final size:34
Alignment explanation
Indices: 40009--40106 Score: 148
Period size: 34 Copynumber: 3.0 Consensus size: 34
39999 TATAAGAATA
*
40009 TGTTTGTGGTCCTAACTTTCAAAACTTCTCATTG
1 TGTTTGTGGTCCTAACTTTCAAAACTTCTCATTC
40043 TGTTTGTGGTCCTAACTTTCAAAA-TTCTCATTC
1 TGTTTGTGGTCCTAACTTTCAAAACTTCTCATTC
* *
40076 TGTTTGTGGTCC-CAC-TTCAAAACTTTTCATT
1 TGTTTGTGGTCCTAACTTTCAAAACTTCTCATT
40107 AAGTTTCTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
31 7 0.12
32 9 0.15
33 20 0.33
34 24 0.40
ACGTcount: A:0.20, C:0.21, G:0.13, T:0.45
Consensus pattern (34 bp):
TGTTTGTGGTCCTAACTTTCAAAACTTCTCATTC
Found at i:40820 original size:6 final size:6
Alignment explanation
Indices: 40811--40865 Score: 76
Period size: 6 Copynumber: 9.2 Consensus size: 6
40801 AATGTAAATA
* *
40811 TGAATT TGAATT TGTAA-T TGAAGT TGAATT TGAATT TGAATT TGCATT
1 TGAATT TGAATT TG-AATT TGAATT TGAATT TGAATT TGAATT TGAATT
40859 TGAATT T
1 TGAATT T
40866 TATTTTCTAG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
5 2 0.05
6 40 0.91
7 2 0.05
ACGTcount: A:0.31, C:0.02, G:0.18, T:0.49
Consensus pattern (6 bp):
TGAATT
Found at i:41749 original size:13 final size:13
Alignment explanation
Indices: 41731--41768 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
41721 AAACAAATAT
*
41731 TAAAAATATTACA
1 TAAAAATATTAAA
41744 TAAAAATATTAAA
1 TAAAAATATTAAA
*
41757 TACAAATATTAA
1 TAAAAATATTAA
41769 TGTTCCAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAAAATATTAAA
Found at i:42432 original size:117 final size:117
Alignment explanation
Indices: 42221--42456 Score: 400
Period size: 117 Copynumber: 2.0 Consensus size: 117
42211 TCTGAACTAT
* * *
42221 TAGGTTGGGCATGTACCCATGCAGCGGTGGCATTTGAACTGGTGTGCTGGGCATGTACACCTGTG
1 TAGGCTGGGCATGTACCCATGCAGCGATGGCATTTGAACTGGTGTGCTAGGCATGTACACCTGTG
*
42286 GGCTCATAATCAGTGGAGATGATAGATGTTGTGATGGTTCCGGTGGTGCTAC
66 GGCTCATAATCAGTGGAGATGATAGATGTTGTGATGGTTCCAGTGGTGCTAC
* * *
42338 TAGGCTGGGCATGTACCCCTGCGGCGATGGCATTTGAACTGGTGTGCTAGGCATGTACACTTGTG
1 TAGGCTGGGCATGTACCCATGCAGCGATGGCATTTGAACTGGTGTGCTAGGCATGTACACCTGTG
*
42403 GGCTCATAATCAGTGGAGATGATGGATGTTGTGATGGTTCCAGTGGTGCTAC
66 GGCTCATAATCAGTGGAGATGATAGATGTTGTGATGGTTCCAGTGGTGCTAC
42455 TA
1 TA
42457 ATGCTGAACC
Statistics
Matches: 111, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
117 111 1.00
ACGTcount: A:0.19, C:0.17, G:0.34, T:0.29
Consensus pattern (117 bp):
TAGGCTGGGCATGTACCCATGCAGCGATGGCATTTGAACTGGTGTGCTAGGCATGTACACCTGTG
GGCTCATAATCAGTGGAGATGATAGATGTTGTGATGGTTCCAGTGGTGCTAC
Found at i:43965 original size:17 final size:17
Alignment explanation
Indices: 43943--43975 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
43933 ATAATTTTTT
*
43943 TATTATATTTTATTAAA
1 TATTATATTATATTAAA
43960 TATTATATTATATTAA
1 TATTATATTATATTAA
43976 CGATAGGCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTATATTATATTAAA
Found at i:44719 original size:21 final size:21
Alignment explanation
Indices: 44694--44737 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
44684 TTGTTATCCC
44694 TCTAAAGATGATTTTCAGAGA
1 TCTAAAGATGATTTTCAGAGA
* *
44715 TCTAAATATTATTTTCAGAGA
1 TCTAAAGATGATTTTCAGAGA
44736 TC
1 TC
44738 ATCTAATCCC
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:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (21 bp):
TCTAAAGATGATTTTCAGAGA
Found at i:46769 original size:2 final size:2
Alignment explanation
Indices: 46762--46837 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
46752 GATGTGTAAG
46762 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46804 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46838 TTAGTCATCT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50728 original size:18 final size:18
Alignment explanation
Indices: 50705--50747 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
50695 GGCCTTTCCT
50705 GACTTCTTGAAGTTGGTA
1 GACTTCTTGAAGTTGGTA
50723 GACTTCTTGAAGTTGGTA
1 GACTTCTTGAAGTTGGTA
*
50741 GCCTTCT
1 GACTTCT
50748 GAGGTTTCGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.19, C:0.16, G:0.26, T:0.40
Consensus pattern (18 bp):
GACTTCTTGAAGTTGGTA
Found at i:64944 original size:24 final size:24
Alignment explanation
Indices: 64915--64960 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
64905 ATTGAGAAAA
*
64915 GAGTTAGGGATTTTGAATTTACAG
1 GAGTTAGGGATTTTGAAATTACAG
64939 GAGTTAGGGATTTTGAAATTAC
1 GAGTTAGGGATTTTGAAATTAC
64961 CGGATGCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.04, G:0.28, T:0.37
Consensus pattern (24 bp):
GAGTTAGGGATTTTGAAATTACAG
Found at i:65033 original size:18 final size:18
Alignment explanation
Indices: 65007--65042 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
64997 AGATGATAAT
* *
65007 TGGGTTGAATGAGTCAAC
1 TGGGCTGAAGGAGTCAAC
65025 TGGGCTGAAGGAGTCAAC
1 TGGGCTGAAGGAGTCAAC
65043 AGATAAGGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.36, T:0.22
Consensus pattern (18 bp):
TGGGCTGAAGGAGTCAAC
Found at i:70079 original size:24 final size:24
Alignment explanation
Indices: 70051--70096 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
70041 ATTGAGAAAA
*
70051 GAGTTA-AGGATTTTGAATTTACAG
1 GAGTTAGA-GATTTTGAAATTACAG
70075 GAGTTAGAGATTTTGAAATTAC
1 GAGTTAGAGATTTTGAAATTAC
70097 CAAATGCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (24 bp):
GAGTTAGAGATTTTGAAATTACAG
Found at i:70163 original size:18 final size:18
Alignment explanation
Indices: 70140--70178 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
70130 AGGAGATGAT
* *
70140 AACTGGGCTGAATGAGTC
1 AACTGGACTGAAGGAGTC
70158 AACTGGACTGAAGGAGTC
1 AACTGGACTGAAGGAGTC
70176 AAC
1 AAC
70179 AGATAAAGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.18, G:0.31, T:0.18
Consensus pattern (18 bp):
AACTGGACTGAAGGAGTC
Done.