Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006759.1 Hibiscus syriacus cultivar Beakdansim tig00017056_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: 64324
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:5518 original size:17 final size:17
Alignment explanation
Indices: 5498--5544 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
5488 ATGATGATTT
*
5498 ATAAATAATGAAAATAA
1 ATAAATAATAAAAATAA
5515 ATAAATAATAAAAATAA
1 ATAAATAATAAAAATAA
5532 AT-AATGAATAAAA
1 ATAAAT-AATAAAA
5545 TTGATGAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 3 0.11
17 25 0.89
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.23
Consensus pattern (17 bp):
ATAAATAATAAAAATAA
Found at i:8503 original size:21 final size:22
Alignment explanation
Indices: 8479--8553 Score: 91
Period size: 23 Copynumber: 3.4 Consensus size: 22
8469 CACCGAAGTG
*
8479 CCACATA-TTTGTCCTGAAAGA
1 CCACATAGTTTGTCCTGAAGGA
*
8500 CCACATAGTTTTATCCTGAAGGA
1 CCACATAG-TTTGTCCTGAAGGA
8523 CCACATAGTTTTGTCCCT-AAGGA
1 CCACATAG-TTTGT-CCTGAAGGA
8546 CCACATAG
1 CCACATAG
8554 AACCCTCGAC
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
21 7 0.15
23 38 0.79
24 3 0.06
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (22 bp):
CCACATAGTTTGTCCTGAAGGA
Found at i:8519 original size:23 final size:23
Alignment explanation
Indices: 8490--8553 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
8480 CACATATTTG
*
8490 TCCTGAAAGACCACATAGTTTTA
1 TCCTGAAGGACCACATAGTTTTA
*
8513 TCCTGAAGGACCACATAGTTTTG
1 TCCTGAAGGACCACATAGTTTTA
8536 TCCCT-AAGGACCACATAG
1 T-CCTGAAGGACCACATAG
8554 AACCCTCGAC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 35 0.92
24 3 0.08
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (23 bp):
TCCTGAAGGACCACATAGTTTTA
Found at i:11281 original size:23 final size:22
Alignment explanation
Indices: 11248--11318 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 22
11238 TTATTATACT
*
11248 AAAATTATAATATTATATTATTA
1 AAAATTTTAATATTATATT-TTA
*
11271 AAAATTTTAATAAATATATTTTA
1 AAAATTTTAAT-ATTATATTTTA
*
11294 AATATTTTAATAGTTAATATTTTA
1 AAAATTTTAATA-TT-ATATTTTA
11318 A
1 A
11319 TTAAAATGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
22 1 0.02
23 24 0.59
24 16 0.39
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (22 bp):
AAAATTTTAATATTATATTTTA
Found at i:11372 original size:28 final size:29
Alignment explanation
Indices: 11308--11372 Score: 66
Period size: 28 Copynumber: 2.3 Consensus size: 29
11298 TTTTAATAGT
*
11308 TAATATT-TTAATTAAAATGATAATAAAT
1 TAATATTATTAATTAAAATGATAATAAAA
* *
11336 TATTA-TATTAATATGAAAT-AT-ATAAAA
1 TAATATTATTAAT-TAAAATGATAATAAAA
11363 TAATATTATT
1 TAATATTATT
11373 TCCATTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
27 10 0.33
28 15 0.50
29 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (29 bp):
TAATATTATTAATTAAAATGATAATAAAA
Found at i:14768 original size:83 final size:82
Alignment explanation
Indices: 14675--14880 Score: 225
Period size: 82 Copynumber: 2.5 Consensus size: 82
14665 AAATAAACAC
* *
14675 CGCAATAGAGTGGTAATTTAGCGGCGTTTATAGCT-CAAACGACGCAATAGAGTTGTTTATAGTG
1 CGCAATAGAGTGGTAATTTAGCGGCGTTTATA--TACAAACGACACAATAGAGTTGTTTATAGAG
* * *
14739 GCGTTTTTTCAACAAACGT
64 GCATTTGTTCAACAAACGA
* * * * *
14758 CGCAATAGAGTGGTAATTTAGCGGCGTTTTTATACAAACGCCACGATAGTGTTGTTTATAGAGTC
1 CGCAATAGAGTGGTAATTTAGCGGCGTTTATATACAAACGACACAATAGAGTTGTTTATAGAGGC
14823 ATTTGTTCAACAAACGA
66 ATTTGTTCAACAAACGA
* * * ** * *
14840 CACTATTGAGAAGTAATTTAGCGGTGTTTATCAAACAAACG
1 CGCAATAGAGTGGTAATTTAGCGGCGTTTAT-ATACAAACG
14881 TTGCAAAAGG
Statistics
Matches: 103, Mismatches: 18, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
81 1 0.01
82 63 0.61
83 39 0.38
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (82 bp):
CGCAATAGAGTGGTAATTTAGCGGCGTTTATATACAAACGACACAATAGAGTTGTTTATAGAGGC
ATTTGTTCAACAAACGA
Found at i:14795 original size:41 final size:41
Alignment explanation
Indices: 14650--14797 Score: 144
Period size: 41 Copynumber: 3.6 Consensus size: 41
14640 AAAATGATAC
* * *
14650 TTTAGCGGCATTTTTAAATAAAC-ACCGCAATAGAGTGGTAA
1 TTTAGCGGCGTTTTTATACAAACGA-CGCAATAGAGTGGTAA
* *
14691 TTTAGCGGCGTTTATAGCT-CAAACGACGCAATAGAGTTGT--
1 TTTAGCGGCGTTTTTA--TACAAACGACGCAATAGAGTGGTAA
* *
14731 TTATAGTGGCGTTTTT-TCAACAAACGTCGCAATAGAGTGGTAA
1 TT-TAGCGGCGTTTTTAT--ACAAACGACGCAATAGAGTGGTAA
14774 TTTAGCGGCGTTTTTATACAAACG
1 TTTAGCGGCGTTTTTATACAAACG
14798 CCACGATAGT
Statistics
Matches: 87, Mismatches: 10, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
38 1 0.01
40 2 0.02
41 51 0.59
42 29 0.33
43 4 0.05
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTATACAAACGACGCAATAGAGTGGTAA
Found at i:15143 original size:41 final size:41
Alignment explanation
Indices: 15096--15173 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
15086 GTTTGTGCGA
* *
15096 AAACGCCGCAATAGCCTTGTAC-TTATCTGGCGTTTGTGATC
1 AAACGCCGCAATAGCCATGTACTTTAGC-GGCGTTTGTGATC
*
15137 AAACGCCGCAATATCCATGTACTTTAGCGGCGTTTGT
1 AAACGCCGCAATAGCCATGTACTTTAGCGGCGTTTGT
15174 AGAAAAATGC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 29 0.88
42 4 0.12
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (41 bp):
AAACGCCGCAATAGCCATGTACTTTAGCGGCGTTTGTGATC
Found at i:15279 original size:42 final size:43
Alignment explanation
Indices: 15190--15286 Score: 126
Period size: 42 Copynumber: 2.3 Consensus size: 43
15180 ATGCCGTAAT
* * *
15190 AGTTTTGTCATTTAATGGCGTTTTTTTTAATAAACACCACAGT
1 AGTTTTGTCCTTTAATGGCGTTTTTTGTAATAAACACCACAGA
*
15233 AGTTTTGTCCTTT-ATGGGCG-TTTTTGTAATAAACACCGCAGA
1 AGTTTTGTCCTTTAAT-GGCGTTTTTTGTAATAAACACCACAGA
*
15275 AGTTTGGTCCTT
1 AGTTTTGTCCTT
15287 AGAATTTTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
42 32 0.67
43 16 0.33
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (43 bp):
AGTTTTGTCCTTTAATGGCGTTTTTTGTAATAAACACCACAGA
Found at i:18396 original size:21 final size:23
Alignment explanation
Indices: 18356--18403 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
18346 TAATGATTAT
*
18356 TTTTTAATATATATATATTTAAA
1 TTTTTAATATATATACATTTAAA
*
18379 TTTTT-ATAT-TATACATTTATA
1 TTTTTAATATATATACATTTAAA
18400 TTTT
1 TTTT
18404 ATGTGTGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 14 0.61
22 4 0.17
23 5 0.22
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTTAATATATATACATTTAAA
Found at i:24158 original size:21 final size:21
Alignment explanation
Indices: 24134--24221 Score: 88
Period size: 21 Copynumber: 4.0 Consensus size: 21
24124 TGAAGCAAGG
* *
24134 GAAGCAGAGAGAGCAGTAGCA
1 GAAGCAGACAGAGCAGCAGCA
*
24155 GAAGCAGCCAGAGCAGCAGCA
1 GAAGCAGACAGAGCAGCAGCA
*
24176 GAAGCA-ACCAGAGCAGCAGCG
1 GAAGCAGA-CAGAGCAGCAGCA
*
24197 GAAGCAAAGAAAGAAGCAGCAGCA
1 GAAGC--AGACAG-AGCAGCAGCA
24221 G
1 G
24222 CACAAAGAGA
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
21 41 0.75
23 3 0.05
24 11 0.20
ACGTcount: A:0.43, C:0.22, G:0.34, T:0.01
Consensus pattern (21 bp):
GAAGCAGACAGAGCAGCAGCA
Found at i:24706 original size:85 final size:85
Alignment explanation
Indices: 24609--24773 Score: 201
Period size: 85 Copynumber: 1.9 Consensus size: 85
24599 GTTTTTAGCA
* * * *
24609 AAAACGCTGCAAAACATCAAAACCTACTACGGCATTTGTGGA-AAAAACGTCG-TAAAACATCA-
1 AAAACGCCGCAAAACAGCAAAACCTACTACGGCATTT-TAGAGAAAAACGCCGCT-AAACATCAT
*
24671 ACACCTACTGCGGCGTTTGTGGG
64 A-AACTACTGCGGCGTTTGTGGG
* * *
24694 AAAACGCCGCAAAACAGCAACACCTACTGCGGCGTTTTAGAGAAAAACGCCGCTAAACATCATAA
1 AAAACGCCGCAAAACAGCAAAACCTACTACGGCATTTTAGAGAAAAACGCCGCTAAACATCATAA
*
24759 ACTATTGCGGCGTTT
66 ACTACTGCGGCGTTT
24774 ATCTAAAAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
84 3 0.04
85 63 0.93
86 2 0.03
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.19
Consensus pattern (85 bp):
AAAACGCCGCAAAACAGCAAAACCTACTACGGCATTTTAGAGAAAAACGCCGCTAAACATCATAA
ACTACTGCGGCGTTTGTGGG
Found at i:24715 original size:42 final size:42
Alignment explanation
Indices: 24608--24857 Score: 216
Period size: 43 Copynumber: 5.8 Consensus size: 42
24598 CGTTTTTAGC
* * * *
24608 AAAAACGCTGCAAAACATCAAAACCTACTACGGCATTTGTGG
1 AAAAACGCCGCAAAACATCAACACCTACTGCGGCGTTTGTGG
* *
24650 AAAAAACGTCGTAAAACATCAACACCTACTGCGGCGTTTGTGG
1 -AAAAACGCCGCAAAACATCAACACCTACTGCGGCGTTTGTGG
* *
24693 GAAAACGCCGCAAAACAGCAACACCTACTGCGGCGTTT-TAGAG
1 AAAAACGCCGCAAAACATCAACACCTACTGCGGCGTTTGT-G-G
* * * * **
24736 AAAAACGCCGCTAAACATCATA-AACTATTGCGGCGTTTATCTAA
1 AAAAACGCCGCAAAACATCA-ACACCTACTGCGGCG-TT-TGTGG
* * * * **
24780 AAAAACGCCGCTAAATATCAACACCTATTGCGACGTTTGTCAT
1 AAAAACGCCGCAAAACATCAACACCTACTGCGGCGTTTGT-GG
* * *
24823 AAAAACGCCGCTAAATATCAACACCTATTGCGGCG
1 AAAAACGCCGCAAAACATCAACACCTACTGCGGCG
24858 CTTTTTGTTT
Statistics
Matches: 176, Mismatches: 23, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
41 1 0.01
42 37 0.21
43 103 0.59
44 33 0.19
45 1 0.01
46 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (42 bp):
AAAAACGCCGCAAAACATCAACACCTACTGCGGCGTTTGTGG
Found at i:24827 original size:87 final size:87
Alignment explanation
Indices: 24694--24857 Score: 215
Period size: 87 Copynumber: 1.9 Consensus size: 87
24684 CGTTTGTGGG
* *
24694 AAAACGCCGCAAAACAGCAACACCTACTGCGGCGTTTTAGAGAAAAACGCCGCTAAACATCATA-
1 AAAACGCCGCAAAACAGCAACACCTACTGCGACGTTTTACAGAAAAACGCCGCTAAACATCA-AC
24758 AACTATTGCGGCGTTTATCTAAA
65 AACTATTGCGGCGTTTATCTAAA
* * * * * *
24781 AAAACGCCGCTAAATATCAACACCTATTGCGACGTTTGT-CATAAAAACGCCGCTAAATATCAAC
1 AAAACGCCGCAAAACAGCAACACCTACTGCGACGTTT-TACAGAAAAACGCCGCTAAACATCAAC
*
24845 ACCTATTGCGGCG
65 AACTATTGCGGCG
24858 CTTTTTGTTT
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
86 1 0.02
87 64 0.97
88 1 0.02
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (87 bp):
AAAACGCCGCAAAACAGCAACACCTACTGCGACGTTTTACAGAAAAACGCCGCTAAACATCAACA
ACTATTGCGGCGTTTATCTAAA
Found at i:25750 original size:33 final size:33
Alignment explanation
Indices: 25708--25811 Score: 208
Period size: 33 Copynumber: 3.2 Consensus size: 33
25698 AATGAATATC
25708 GAGATTTAATGCATTGAAATGGTGTCATTCGAA
1 GAGATTTAATGCATTGAAATGGTGTCATTCGAA
25741 GAGATTTAATGCATTGAAATGGTGTCATTCGAA
1 GAGATTTAATGCATTGAAATGGTGTCATTCGAA
25774 GAGATTTAATGCATTGAAATGGTGTCATTCGAA
1 GAGATTTAATGCATTGAAATGGTGTCATTCGAA
25807 GAGAT
1 GAGAT
25812 GAGTCAGAGA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 71 1.00
ACGTcount: A:0.34, C:0.09, G:0.25, T:0.33
Consensus pattern (33 bp):
GAGATTTAATGCATTGAAATGGTGTCATTCGAA
Found at i:26575 original size:21 final size:20
Alignment explanation
Indices: 26438--26635 Score: 86
Period size: 20 Copynumber: 9.8 Consensus size: 20
26428 AAATGACCAA
**
26438 CAAAATCGCAACGCGAAAT-
1 CAAAATCGCAACGCGATTTC
* **
26457 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTC
* **
26477 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTC
26497 CAAAATCGCAACGCGA-TTC
1 CAAAATCGCAACGCGATTTC
* * *
26516 CTGAAAATCGCAATGCGATAGTA
1 C--AAAATCGCAACGCGAT-TTC
* **
26539 CAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGA-TTTC
* *
26560 CAGAATCGCAACGCGAATAT-
1 CAAAATCGCAACGCG-ATTTC
* *
26580 GAAAATCGCAACGCGA--AC
1 CAAAATCGCAACGCGATTTC
*
26598 ACATAAATCGCAACGCGAATAT-
1 -CA-AAATCGCAACGCG-ATTTC
*
26620 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
26636 ACACATAAAT
Statistics
Matches: 133, Mismatches: 31, Indels: 30
0.69 0.16 0.15
Matches are distributed among these distances:
19 23 0.17
20 62 0.47
21 44 0.33
22 2 0.02
23 2 0.02
ACGTcount: A:0.39, C:0.26, G:0.18, T:0.17
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTC
Found at i:26664 original size:20 final size:20
Alignment explanation
Indices: 26563--26791 Score: 169
Period size: 20 Copynumber: 11.4 Consensus size: 20
26553 GATTTTCCAG
* ** *
26563 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
26583 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
* ** *
26603 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
26623 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
26643 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
26663 AACCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
26683 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
26703 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
26723 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
26743 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * * *
26763 AATTGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
26783 AATCACAAC
1 AATCGCAAC
26792 ACTGAAATTT
Statistics
Matches: 165, Mismatches: 36, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
19 3 0.02
20 159 0.96
21 3 0.02
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:26670 original size:40 final size:39
Alignment explanation
Indices: 26563--26791 Score: 206
Period size: 40 Copynumber: 5.7 Consensus size: 39
26553 GATTTTCCAG
* *
26563 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGAATCTGTAAATCGCAACGCGAAC-CATA
* *
26603 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGAATCTGTAAATCGCAACGCGAAC-CATA
* * * * * *
26643 AATCGCAACGCGTATCCGTAAACCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCTGTAAATCGCAACGCG-AACCATA
* * * ** *
26683 TATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGTA
1 AATCGCAACGCGAATCTGTAAATCGCAACGCGAA-CCATA
* ** *
26723 AATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGTA
1 AATCGCAACGCGAATCTGTAAATCGCAACGCGAA-CCATA
* * *
26763 AATTGCAACGAGAATCTGTAAATCACAAC
1 AATCGCAACGCGAATCTGTAAATCGCAAC
26792 ACTGAAATTT
Statistics
Matches: 167, Mismatches: 20, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
39 1 0.01
40 164 0.98
41 2 0.01
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.18
Consensus pattern (39 bp):
AATCGCAACGCGAATCTGTAAATCGCAACGCGAACCATA
Found at i:27523 original size:24 final size:24
Alignment explanation
Indices: 27484--27530 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
27474 AAATTTGGTC
27484 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
27508 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
27531 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:27722 original size:12 final size:12
Alignment explanation
Indices: 27705--27729 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27695 ATATAATCCT
27705 GAAGAAGAAAAA
1 GAAGAAGAAAAA
27717 GAAGAAGAAAAA
1 GAAGAAGAAAAA
27729 G
1 G
27730 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:30074 original size:20 final size:19
Alignment explanation
Indices: 30023--30212 Score: 205
Period size: 19 Copynumber: 10.7 Consensus size: 19
30013 GCAACGAGAG
30023 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
30042 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
30056 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
30076 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
30095 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
30109 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
30129 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
*
30147 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
30161 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
30181 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
30200 AATCGCATTGCGA
1 AATCGCAATGCGA
30213 TTCTCTCGTT
Statistics
Matches: 145, Mismatches: 7, Indels: 38
0.76 0.04 0.20
Matches are distributed among these distances:
13 1 0.01
14 31 0.21
15 1 0.01
16 5 0.03
17 5 0.03
18 9 0.06
19 51 0.35
20 42 0.29
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:30172 original size:52 final size:53
Alignment explanation
Indices: 30023--30206 Score: 327
Period size: 53 Copynumber: 3.5 Consensus size: 53
30013 GCAACGAGAG
* *
30023 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGGAAATGAA
30076 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
30129 AATCGCAATGCGAAATG-AAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
30181 AATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
30207 TTGCGATTCT
Statistics
Matches: 127, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
52 52 0.41
53 74 0.58
54 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
Found at i:30177 original size:86 final size:87
Alignment explanation
Indices: 29990--30188 Score: 239
Period size: 86 Copynumber: 2.3 Consensus size: 87
29980 GTATTTGACT
** * *
29990 ATCGCAACACGGAAATTACAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGA
* *
30055 AAATCGCAATGCGGAAATGAAA
66 AAATCGAAATGCGCAAATGAAA
*
30077 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGC-A-ATG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAACATG
* *
30139 CGAAAT-GAAAT-CGCAACGA-GAGA
65 -AAAATCGAAATGCGCAA--ATGAAA
30162 ATCGCAATGCGGAAATGAAAATCGCAA
1 ATCGCAATGCGGAAATGAAAATCGCAA
30189 TGCGAAATGA
Statistics
Matches: 98, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
84 4 0.04
85 20 0.20
86 53 0.54
87 21 0.21
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (87 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGA
AAATCGAAATGCGCAAATGAAA
Found at i:30315 original size:52 final size:53
Alignment explanation
Indices: 30202--30318 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
30192 GAAATGAAAA
30202 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
*
30255 TCACATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
30307 TCGCATTGCGAT
1 TCGCATTGCGAT
30319 AGTCATTTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:30326 original size:19 final size:19
Alignment explanation
Indices: 30221--30318 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
30211 GATTCTCTCG
30221 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
*
30241 TTGCGATTTTCATTTCACA
1 TTGCGATTTTCATTTCGCA
*
30260 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
30274 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
30293 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
30312 TTGCGAT
1 TTGCGAT
30319 AGTCATTTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 6 0.09
16 6 0.09
17 7 0.10
19 35 0.51
20 15 0.22
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:30444 original size:14 final size:14
Alignment explanation
Indices: 30425--30461 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
30415 CATCAATTAC
30425 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
30439 ACAAATCATCTTTT
1 ACAAATCAACTTTT
30453 ACAAATCAA
1 ACAAATCAA
30462 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:32407 original size:20 final size:20
Alignment explanation
Indices: 32376--32472 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
32366 TTTTGGTTGA
32376 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
32396 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
32416 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
32435 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
32450 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
32470 AAT
1 AAT
32473 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:32428 original size:21 final size:21
Alignment explanation
Indices: 32374--32438 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
32364 TCTTTTGGTT
32374 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
32395 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
32415 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
32436 GAA
1 GAA
32439 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:32442 original size:14 final size:14
Alignment explanation
Indices: 32423--32479 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
32413 GAGAAATGAA
32423 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
32437 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
32456 AATCGCAACGAGAG
1 AATCGCAACGAGAG
32470 AATCGCAACG
1 AATCGCAACG
32480 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:32455 original size:33 final size:33
Alignment explanation
Indices: 32374--32496 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
32364 TCTTTTGGTT
*
32374 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
32415 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
32448 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
32481 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
32497 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 50 0.62
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.27
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:32532 original size:14 final size:14
Alignment explanation
Indices: 32513--32569 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
32503 TTTGGTTTCG
32513 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
32527 CGTTGCAATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
32546 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
32560 CGTTGCGATT
1 CGTTGCGATT
32570 TTCATTTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:32545 original size:33 final size:33
Alignment explanation
Indices: 32508--32576 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
32498 GCGATTTTGG
32508 TTTCGCGTTGCGATTCTCTCGTTGCAATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCAATTTTCA
*
32541 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCAATTTTCA
32574 TTT
1 TTT
32577 TTCTCGTTGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.10, C:0.23, G:0.19, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCAATTTTCA
Found at i:32582 original size:21 final size:21
Alignment explanation
Indices: 32557--32630 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
32547 GTTGCGATTC
32557 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
* **
32578 TCTCGTTGCAAATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
32599 TCACGTTGCGATTTTCATTTC
1 TCTCGTTGCGATTTTCATTTT
32620 TCTCGTTGCGA
1 TCTCGTTGCGA
32631 CTCTTCTGCA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
20 5 0.12
21 32 0.76
22 5 0.12
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:32752 original size:33 final size:33
Alignment explanation
Indices: 32710--32780 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
32700 AATACTAACT
32710 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
32743 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
32776 TGAAA
1 TGAAA
32781 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:33196 original size:21 final size:20
Alignment explanation
Indices: 33160--33320 Score: 110
Period size: 20 Copynumber: 7.6 Consensus size: 20
33150 CTTTAAAAAT
33160 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
33180 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
33200 TGTCGTTGCGATTTACGGATATA
1 CG-CGTTGCGATTTACGG--ATA
33223 CGGATACGCATTGCGATTTACGGATA
1 C-G---CG--TTGCGATTTACGGATA
** *
33249 CATGTTGCGGTTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
33269 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
33289 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
33309 CGCGTTGCGATT
1 CGCGTTGCGATT
33321 CTGGAAAATC
Statistics
Matches: 112, Mismatches: 17, Indels: 24
0.73 0.11 0.16
Matches are distributed among these distances:
20 72 0.64
21 17 0.15
22 3 0.03
24 1 0.01
26 6 0.05
28 13 0.12
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:33263 original size:48 final size:49
Alignment explanation
Indices: 33172--33268 Score: 126
Period size: 48 Copynumber: 2.0 Consensus size: 49
33162 CGTTGCGATT
* * **
33172 TACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATA
1 TACGGATACGCATTGCGATTTTACGGATCATCGTTGCGATTTACGGATA
*
33221 TACGGATACGCATTGCGA-TTTACGGATACAT-GTTGCGGTTTACGGATA
1 TACGGATACGCATTGCGATTTTACGGAT-CATCGTTGCGATTTACGGATA
33269 CGCGTTGCGA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
48 24 0.57
49 18 0.43
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (49 bp):
TACGGATACGCATTGCGATTTTACGGATCATCGTTGCGATTTACGGATA
Found at i:34867 original size:37 final size:39
Alignment explanation
Indices: 34783--34871 Score: 148
Period size: 38 Copynumber: 2.4 Consensus size: 39
34773 TTCAATATGG
*
34783 AACCCGACCCGAC-CTGACCTGAATATCACACTTAAAAA
1 AACCCGACCCGACTCTGACCCGAATATCACACTTAAAAA
34821 AACCCGACCCGACTC-GACCCGAATATCACACTT-AAAA
1 AACCCGACCCGACTCTGACCCGAATATCACACTTAAAAA
34858 AACCCGACCCGACT
1 AACCCGACCCGACT
34872 GAACAAAATA
Statistics
Matches: 49, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
37 18 0.37
38 30 0.61
39 1 0.02
ACGTcount: A:0.37, C:0.38, G:0.11, T:0.13
Consensus pattern (39 bp):
AACCCGACCCGACTCTGACCCGAATATCACACTTAAAAA
Found at i:34932 original size:5 final size:5
Alignment explanation
Indices: 34922--34947 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
34912 AATTAGAAAT
34922 CCGAC CCGAC CCGAC CCGAC CCGAC C
1 CCGAC CCGAC CCGAC CCGAC CCGAC C
34948 AAAATAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.62, G:0.19, T:0.00
Consensus pattern (5 bp):
CCGAC
Found at i:34951 original size:72 final size:71
Alignment explanation
Indices: 34859--35012 Score: 245
Period size: 72 Copynumber: 2.2 Consensus size: 71
34849 CACTTAAAAA
* * *
34859 ACCCGACCCGACTGAACAAAATAAAGTTTCATCCGACCCGACCTGAATATATGAATTAGAAATCC
1 ACCCGACCCGACCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCA
*
34924 GACCCG
66 AACCCG
*
34930 ACCCGACCCGACCCGACCAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATC
1 ACCCGACCCGA-CCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATC
34995 AAACCCG
65 AAACCCG
*
35002 ACCCGATCCGA
1 ACCCGACCCGA
35013 AATAATAAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
71 11 0.14
72 65 0.86
ACGTcount: A:0.36, C:0.32, G:0.15, T:0.16
Consensus pattern (71 bp):
ACCCGACCCGACCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCA
AACCCG
Found at i:35398 original size:18 final size:18
Alignment explanation
Indices: 35375--35417 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
35365 TGATGGAATT
*
35375 CAATTCCATTAGGGATTC
1 CAATTCCATCAGGGATTC
*
35393 CAATTCTATCAGGGATTC
1 CAATTCCATCAGGGATTC
*
35411 TAATTCC
1 CAATTCC
35418 CTTGAAAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (18 bp):
CAATTCCATCAGGGATTC
Found at i:36221 original size:33 final size:33
Alignment explanation
Indices: 36184--36291 Score: 119
Period size: 33 Copynumber: 3.3 Consensus size: 33
36174 GGGTCTTCCT
* *
36184 TTCGCCGCTGAAATCGGCCAGAAAATCGATTTC
1 TTCGCCGCCGAAACCGGCCAGAAAATCGATTTC
*
36217 TTCGCCGCCGAAACCGGCCAGACAATCGATTTC
1 TTCGCCGCCGAAACCGGCCAGAAAATCGATTTC
** * * *
36250 TTCTACGCC-AAAGCAGCCCACAAAATCGATTTC
1 TTCGCCGCCGAAA-CCGGCCAGAAAATCGATTTC
*
36283 TTCGTCGCC
1 TTCGCCGCC
36292 TTCGTCATCG
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
32 3 0.05
33 60 0.95
ACGTcount: A:0.26, C:0.33, G:0.19, T:0.22
Consensus pattern (33 bp):
TTCGCCGCCGAAACCGGCCAGAAAATCGATTTC
Found at i:36896 original size:32 final size:32
Alignment explanation
Indices: 36855--36917 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
36845 TCCTCGACAG
36855 TTTCCCCTCATTCAGATCCACGAGTGCAATAT
1 TTTCCCCTCATTCAGATCCACGAGTGCAATAT
36887 TTTCCCCTCATTCAGATCCACGAGTGCAATA
1 TTTCCCCTCATTCAGATCCACGAGTGCAATA
36918 ATGATTTGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.25, C:0.32, G:0.13, T:0.30
Consensus pattern (32 bp):
TTTCCCCTCATTCAGATCCACGAGTGCAATAT
Found at i:42759 original size:14 final size:14
Alignment explanation
Indices: 42740--42767 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42730 GCGGGTGCGT
42740 GTTGATTACCTTTA
1 GTTGATTACCTTTA
42754 GTTGATTACCTTTA
1 GTTGATTACCTTTA
42768 ATTGCGTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.50
Consensus pattern (14 bp):
GTTGATTACCTTTA
Found at i:43665 original size:2 final size:2
Alignment explanation
Indices: 43658--43716 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
43648 TTCAAGATAC
43658 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43700 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
43717 TATGTTTGAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:43777 original size:14 final size:14
Alignment explanation
Indices: 43758--43788 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
43748 TCATCTAAAT
43758 CATCAAACATTCAA
1 CATCAAACATTCAA
*
43772 CATCAAGCATTCAA
1 CATCAAACATTCAA
43786 CAT
1 CAT
43789 TTAATTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.29, G:0.03, T:0.23
Consensus pattern (14 bp):
CATCAAACATTCAA
Found at i:46786 original size:17 final size:18
Alignment explanation
Indices: 46759--46796 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
46749 TTTACCTCTC
46759 TAAACTAAAAAATTATAA
1 TAAACTAAAAAATTATAA
46777 TAAA-TAAAAAATTATAA
1 TAAACTAAAAAATTATAA
46794 TAA
1 TAA
46797 TTTTTTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAACTAAAAAATTATAA
Found at i:51779 original size:29 final size:29
Alignment explanation
Indices: 51734--51791 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
51724 GTGTTGGCCG
*
51734 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
* *
51763 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
51792 AAGAGATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.14, C:0.36, G:0.28, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:51914 original size:14 final size:14
Alignment explanation
Indices: 51836--51875 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
51826 CTGGGCATCT
* *
51836 GAGGCTATCCGATC
1 GAGGCCATCCGACC
51850 GAGGCCATCCGACC
1 GAGGCCATCCGACC
51864 GAGGCCATCCGA
1 GAGGCCATCCGA
51876 GAGCATCCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.23, C:0.35, G:0.30, T:0.12
Consensus pattern (14 bp):
GAGGCCATCCGACC
Found at i:51949 original size:33 final size:33
Alignment explanation
Indices: 51906--51980 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
51896 CCGAGGCCAT
* * * *
51906 CCGAACGAGCTATGTGAGGGCATCCTAGGGCAA-
1 CCGAGCGAGCTATGCGAGGGAATCCGAGGG-AAG
51939 CCGAGCGAGCTATGCGAGGGAATCCGAGGGAAG
1 CCGAGCGAGCTATGCGAGGGAATCCGAGGGAAG
51972 CCGAGCGAG
1 CCGAGCGAG
51981 GGTAGGTCGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
32 2 0.05
33 35 0.95
ACGTcount: A:0.27, C:0.24, G:0.39, T:0.11
Consensus pattern (33 bp):
CCGAGCGAGCTATGCGAGGGAATCCGAGGGAAG
Found at i:52017 original size:29 final size:29
Alignment explanation
Indices: 51984--52097 Score: 219
Period size: 29 Copynumber: 3.9 Consensus size: 29
51974 GAGCGAGGGT
*
51984 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
52013 AGGTCGCCCGGAGGGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
52042 AGGTCGCCCGGAGGGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
52071 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
52098 TGTGTTGGGC
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 84 1.00
ACGTcount: A:0.20, C:0.31, G:0.38, T:0.11
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:57611 original size:68 final size:68
Alignment explanation
Indices: 57502--57632 Score: 244
Period size: 68 Copynumber: 1.9 Consensus size: 68
57492 TTTCTTTCCC
*
57502 AGAGCCAATCTTCAAGCACTCTAATCTTAGTTAGCTTGAGCCAAGGTAAGATTATGAATCACCAT
1 AGAGCCAATCTTCAAGCACTCTAATCTTAGTTAGCTTGAGCCAAGATAAGATTATGAATCACCAT
57567 TCA
66 TCA
*
57570 AGAGCCAATCTTTAAGCACTCTAATCTTAGTTAGCTTGAGCCAAGATAAGATTATGAATCACC
1 AGAGCCAATCTTCAAGCACTCTAATCTTAGTTAGCTTGAGCCAAGATAAGATTATGAATCACC
57633 CTTCTTCAAG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.28
Consensus pattern (68 bp):
AGAGCCAATCTTCAAGCACTCTAATCTTAGTTAGCTTGAGCCAAGATAAGATTATGAATCACCAT
TCA
Found at i:58745 original size:35 final size:36
Alignment explanation
Indices: 58655--58818 Score: 110
Period size: 39 Copynumber: 4.4 Consensus size: 36
58645 GTTTTTTTAA
*
58655 AAAAACGTTTTGAAAACTTATATACAATATATAAGTTTT
1 AAAAACATTTTGAAAA-TTATATACAATATAT-A-TTTT
58694 AAAAACATTTTGAAAATTATATA-ACATATAT-TTTT
1 AAAAACATTTTGAAAATTATATACA-ATATATATTTT
* * *
58729 GAAATCATTTTG-AAA--ATAT--AATGTATAGTTTAAAT
1 AAAAACATTTTGAAAATTATATACAATATATA-TTT---T
* *
58764 AAAAACATTTTTGAAAATTTTATATAATATATAGTTTTT
1 AAAAACA-TTTTGAAAATTATATACAATATATA--TTTT
58803 AAAAA-ATTTTGGAAAA
1 AAAAACATTTT-GAAAA
58819 CTCATAATAT
Statistics
Matches: 102, Mismatches: 9, Indels: 29
0.73 0.06 0.21
Matches are distributed among these distances:
30 5 0.05
31 1 0.01
32 7 0.07
34 3 0.03
35 20 0.20
36 5 0.05
37 8 0.08
38 19 0.19
39 24 0.24
41 7 0.07
42 3 0.03
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (36 bp):
AAAAACATTTTGAAAATTATATACAATATATATTTT
Found at i:58834 original size:73 final size:68
Alignment explanation
Indices: 58688--58856 Score: 163
Period size: 73 Copynumber: 2.4 Consensus size: 68
58678 ACAATATATA
**
58688 AGTTT-TAAAAACA-TTTTGAAAATTATATAACATATATTTTTGAAATCATTTTGAAAATATAAT
1 AGTTTATAAAAACATTTTTGAAAATTATATAACATATATTTTTGAAAAAATTTTGAAAATATAA-
58751 GTAT
65 GTAT
*
58755 AGTTTAAATAAAAACATTTTTGAAAATTTTATATAATATATAGTTTTT-AAAAAATTTTGGAAAA
1 AGTTT--ATAAAAACATTTTTGAAAA--TTATATAACATATA-TTTTTGAAAAAATTTT-GAAAA
58819 CTCATAA-TAT
60 -T-ATAAGTAT
*
58829 --TTT-TAAAAATCATTTTTGAAAACTATAT
1 AGTTTATAAAAA-CATTTTTGAAAATTATAT
58857 GGTATATAGT
Statistics
Matches: 87, Mismatches: 4, Indels: 21
0.78 0.04 0.19
Matches are distributed among these distances:
67 5 0.06
68 5 0.06
69 6 0.07
70 20 0.23
71 9 0.10
72 3 0.03
73 21 0.24
74 13 0.15
75 1 0.01
76 4 0.05
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.43
Consensus pattern (68 bp):
AGTTTATAAAAACATTTTTGAAAATTATATAACATATATTTTTGAAAAAATTTTGAAAATATAAG
TAT
Found at i:58980 original size:18 final size:18
Alignment explanation
Indices: 58959--58997 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
58949 ATTATTTCCT
*
58959 TTCATTTTA-TTCACTTTA
1 TTCATTTAATTTCA-TTTA
58977 TTCATTTAATTTCATTTA
1 TTCATTTAATTTCATTTA
58995 TTC
1 TTC
58998 TGTTTATGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (18 bp):
TTCATTTAATTTCATTTA
Found at i:61577 original size:3 final size:3
Alignment explanation
Indices: 61571--61627 Score: 79
Period size: 3 Copynumber: 20.7 Consensus size: 3
61561 TTTTCAACAA
61571 AAT AAT AAT AAT AAT -AT AAT -AT AAT AA- AAT AAT -AT AAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
61614 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
61628 CTGCTAGTGA
Statistics
Matches: 49, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
2 10 0.20
3 39 0.80
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:61591 original size:8 final size:8
Alignment explanation
Indices: 61571--61627 Score: 69
Period size: 8 Copynumber: 6.6 Consensus size: 8
61561 TTTTCAACAA
61571 AATAATAAT
1 AATAAT-AT
61580 AATAATAT
1 AATAATAT
*
61588 AATATAATAA
1 -A-ATAATAT
61598 AATAATAT
1 AATAATAT
61606 AATAATAT
1 AATAATAT
61614 AATAATAAT
1 AATAAT-AT
61623 AATAA
1 AATAA
61628 CTGCTAGTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
8 22 0.51
9 15 0.35
10 6 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AATAATAT
Done.