Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001351.1 Hibiscus syriacus cultivar Beakdansim tig00002632_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: 67803
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:499 original size:29 final size:30
Alignment explanation
Indices: 436--492 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
426 AGTGAACTGG
*
436 CGGTTCAAACCGGTTTTGCCGGTTTTCAGA
1 CGGTTCAAACCGGTTTTACCGGTTTTCAGA
**
466 CGGTTCACCCCGG-TTTACCGGTTTTCA
1 CGGTTCAAACCGGTTTTACCGGTTTTCA
493 ACCGGTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.14, C:0.28, G:0.25, T:0.33
Consensus pattern (30 bp):
CGGTTCAAACCGGTTTTACCGGTTTTCAGA
Found at i:6489 original size:59 final size:59
Alignment explanation
Indices: 6414--6526 Score: 190
Period size: 59 Copynumber: 1.9 Consensus size: 59
6404 GGTCTCCGAC
* *
6414 TATAGGGTGATACTTTGTTGAGTCTCTCGACTATTAAAAGTTACAAAATGATCATTCGT
1 TATAGGGTGATACTTTGTTGAGTCCCCCGACTATTAAAAGTTACAAAATGATCATTCGT
* *
6473 TATAGGGTGTTGCTTTGTTGAGTCCCCCGACTATTAAAAGTTACAAAATGATCA
1 TATAGGGTGATACTTTGTTGAGTCCCCCGACTATTAAAAGTTACAAAATGATCA
6527 ACCAACTATT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 50 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.35
Consensus pattern (59 bp):
TATAGGGTGATACTTTGTTGAGTCCCCCGACTATTAAAAGTTACAAAATGATCATTCGT
Found at i:7433 original size:23 final size:23
Alignment explanation
Indices: 7415--7475 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
7405 CTCGTATAAA
7415 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
7438 TGCACCGAAGTGGCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
7461 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
7476 TATAAAATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.28, C:0.26, G:0.30, T:0.16
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:7989 original size:2 final size:2
Alignment explanation
Indices: 7982--8047 Score: 116
Period size: 2 Copynumber: 33.0 Consensus size: 2
7972 ACTCATAGTC
7982 AT AT AT AT AGT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8024 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
8048 CATTTTACCT
Statistics
Matches: 62, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.02
2 60 0.97
3 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10190 original size:60 final size:60
Alignment explanation
Indices: 10060--10197 Score: 156
Period size: 60 Copynumber: 2.3 Consensus size: 60
10050 TTACACAGGT
* * *
10060 GACCATTTTGTAACTTTTAATAGTCGGGGTACTCAACAAAGCAATATCTTATAGTTGAAG
1 GACCATTTTGTAACTTTTAATAGTCGGGGTACTCAACAAAGCAATACCCTATAGTCGAAG
* * *
10120 GACCATTTTGTAACTTTTAATAGTC-GAGTGACTCAGCAAAAGC-ATCACCCTATAGTCGAGG
1 GACCATTTTGTAACTTTTAATAGTCGGGGT-ACTCAAC-AAAGCAAT-ACCCTATAGTCGAAG
*
10181 GACTATTTGTGT-ACTTT
1 GACCATTT-TGTAACTTT
10198 ACCCAATAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
59 3 0.04
60 33 0.49
61 28 0.42
62 3 0.04
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAGTCGGGGTACTCAACAAAGCAATACCCTATAGTCGAAG
Found at i:13067 original size:13 final size:13
Alignment explanation
Indices: 13049--13092 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
13039 CGCCCGATTA
13049 CCCGATTACCCGC
1 CCCGATTACCCGC
*
13062 CCCGATTATCCGC
1 CCCGATTACCCGC
*
13075 CCCGA-TACCCGA
1 CCCGATTACCCGC
13087 CCCGAT
1 CCCGAT
13093 AAATATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.18, C:0.50, G:0.16, T:0.16
Consensus pattern (13 bp):
CCCGATTACCCGC
Found at i:13120 original size:2 final size:2
Alignment explanation
Indices: 13113--13206 Score: 56
Period size: 2 Copynumber: 50.0 Consensus size: 2
13103 AATAATTATT
* *
13113 TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA -A TA AA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * * *
13152 -A TT TA AA TA -A AA AA TA TA TA TT TA TA TA TT TA -A TT TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13191 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
13207 CCTGGCCCGA
Statistics
Matches: 69, Mismatches: 17, Indels: 12
0.70 0.17 0.12
Matches are distributed among these distances:
1 6 0.09
2 63 0.91
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:13239 original size:12 final size:12
Alignment explanation
Indices: 13221--13270 Score: 91
Period size: 12 Copynumber: 4.2 Consensus size: 12
13211 GCCCGATTCT
13221 CGGCCCAATACC
1 CGGCCCAATACC
*
13233 CGACCCAATACC
1 CGGCCCAATACC
13245 CGGCCCAATACC
1 CGGCCCAATACC
13257 CGGCCCAATACC
1 CGGCCCAATACC
13269 CG
1 CG
13271 TTTAAATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.26, C:0.50, G:0.16, T:0.08
Consensus pattern (12 bp):
CGGCCCAATACC
Found at i:14102 original size:57 final size:57
Alignment explanation
Indices: 14023--14130 Score: 198
Period size: 57 Copynumber: 1.9 Consensus size: 57
14013 TCCCGAAAAT
*
14023 AAAATAAAATCTAATTTTATTTTAATTGTTTCATATAACGTTCAAAGCACTGTCCCG
1 AAAAGAAAATCTAATTTTATTTTAATTGTTTCATATAACGTTCAAAGCACTGTCCCG
*
14080 AAAAGAAAATCTAATTTTATTTTAGTTGTTTCATATAACGTTCAAAGCACT
1 AAAAGAAAATCTAATTTTATTTTAATTGTTTCATATAACGTTCAAAGCACT
14131 ACAGGAAACC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (57 bp):
AAAAGAAAATCTAATTTTATTTTAATTGTTTCATATAACGTTCAAAGCACTGTCCCG
Found at i:17988 original size:24 final size:24
Alignment explanation
Indices: 17955--18003 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
17945 AATGATCTTC
* *
17955 TGGGTATCTCCTTTTTTTTTCTTTT
1 TGGGTATCT-CTTCTGTTTTCTTTT
17980 TGGGT-TCTCTTCTGTTTTCTTTT
1 TGGGTATCTCTTCTGTTTTCTTTT
18003 T
1 T
18004 TGATGTCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 14 0.64
24 3 0.14
25 5 0.23
ACGTcount: A:0.02, C:0.16, G:0.14, T:0.67
Consensus pattern (24 bp):
TGGGTATCTCTTCTGTTTTCTTTT
Found at i:19278 original size:54 final size:54
Alignment explanation
Indices: 19182--19388 Score: 222
Period size: 54 Copynumber: 3.8 Consensus size: 54
19172 TGGAAAACAT
* * * * * **
19182 GTTCACTCCCTATTCCTTCAGGGAGTAGA-AACTCGTACAATCTTTTGCCTACGG
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCG-AAAATCTTTTGCAAACGG
* *
19236 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTTGAAAATCTTCTGCAAACGG
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTTTGCAAACGG
* * *
19290 GTTCGCTCCCACTTTCTTCAGGGAGTATAGAACTCGAAAATCTTTTGAAAACGT
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTTTGCAAACGG
* * *
19344 G-TCTGCTCCCTATTCCTTCAGAGAGTAT-GAGACTCGAACAATCTT
1 GTTC-GCTCCCTCTTTCTTCAGGGAGTATAGA-ACTCGAA-AATCTT
19389 CAACAATCGT
Statistics
Matches: 131, Mismatches: 18, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
53 4 0.03
54 116 0.89
55 11 0.08
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (54 bp):
GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTTTGCAAACGG
Found at i:19409 original size:55 final size:55
Alignment explanation
Indices: 19341--19562 Score: 354
Period size: 55 Copynumber: 4.0 Consensus size: 55
19331 CTTTTGAAAA
*
19341 CGTGTCTGCTCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAAT
1 CGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAT
* * * *
19396 CGTGTCTACTCCCTATTCTTTCAGAGAGTATGAGACTCGAATAATCTTCAACAAT
1 CGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAT
* *
19451 CGTGTCTGCTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAAACTTCAACAAT
1 CGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAT
* * *
19506 CGCGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGAT
1 CGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAT
19561 CG
1 CG
19563 CTGGGAAACC
Statistics
Matches: 155, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 155 1.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (55 bp):
CGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAT
Found at i:19475 original size:110 final size:110
Alignment explanation
Indices: 19302--19562 Score: 361
Period size: 110 Copynumber: 2.4 Consensus size: 110
19292 TCGCTCCCAC
* *
19302 TTTCTTCAGGGAGTAT-AGAACTCGAA-AATCTTTTGAA-AA-CGTGTCTGCTCCCTATTCCTTC
1 TTTCTTCAGAGAGTATAAG-ACTCGAACAATC--TTCAACAATCGTGTCTGCTCCCTATTCCTTC
* * *
19363 AGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTACTCCCTA
63 AGAGAGTATAAGACTCGAACAAACTTCAACAATCGCGTCTACTCCCTA
* * *
19411 -TTCTTTCAGAGAGTATGAGACTCGAATAATCTTCAACAATCGTGTCTGCTCCCTATTCTTTCAG
1 TTTC-TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAG
*
19475 AGAGTATAAGACTCGAACAAACTTCAACAATCGCGTCTGCTCCCTA
65 AGAGTATAAGACTCGAACAAACTTCAACAATCGCGTCTACTCCCTA
*
19521 TTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCG
1 TTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCG
19563 CTGGGAAACC
Statistics
Matches: 136, Mismatches: 10, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
108 7 0.05
109 20 0.15
110 106 0.78
111 3 0.02
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (110 bp):
TTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
GAGTATAAGACTCGAACAAACTTCAACAATCGCGTCTACTCCCTA
Found at i:20573 original size:8 final size:8
Alignment explanation
Indices: 20560--20618 Score: 65
Period size: 8 Copynumber: 7.9 Consensus size: 8
20550 TCTTGAACCC
20560 TCATTTTT
1 TCATTTTT
20568 TCATTTTT
1 TCATTTTT
20576 TCA----T
1 TCATTTTT
20580 TCATTTTT
1 TCATTTTT
20588 T-ATTTTTT
1 TCA-TTTTT
*
20596 TTATTTTT
1 TCATTTTT
20604 TCATTTTT
1 TCATTTTT
20612 TCATTTT
1 TCATTTT
20619 CACTCATTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
4 4 0.09
7 1 0.02
8 38 0.86
9 1 0.02
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (8 bp):
TCATTTTT
Found at i:30599 original size:16 final size:16
Alignment explanation
Indices: 30578--30615 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
30568 AACCTTATTC
30578 ACATGATATCTACCCA
1 ACATGATATCTACCCA
30594 ACATGATATCTACCCA
1 ACATGATATCTACCCA
30610 ATCATG
1 A-CATG
30616 CTTTAGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.37, C:0.29, G:0.08, T:0.26
Consensus pattern (16 bp):
ACATGATATCTACCCA
Found at i:33502 original size:24 final size:24
Alignment explanation
Indices: 33469--33517 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
33459 AATGATCTTC
* *
33469 TGGGTGTCTCCTTTTTTTTTCTTTT
1 TGGGTGTCT-CTTCTGTTTTCTTTT
33494 TGGGT-TCTCTTCTGTTTTCTTTT
1 TGGGTGTCTCTTCTGTTTTCTTTT
33517 T
1 T
33518 TGATGTCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 14 0.64
24 3 0.14
25 5 0.23
ACGTcount: A:0.00, C:0.16, G:0.16, T:0.67
Consensus pattern (24 bp):
TGGGTGTCTCTTCTGTTTTCTTTT
Found at i:34883 original size:17 final size:16
Alignment explanation
Indices: 34858--34908 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
34848 TTTCTTTGCG
34858 TTATATTATATATTAT
1 TTATATTATATATTAT
*
34874 TTCCTATTATATA-TAT
1 TT-ATATTATATATTAT
*
34890 ATATATTATATTATTAT
1 TTATATTATA-TATTAT
34907 TT
1 TT
34909 TTTATCTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
15 7 0.25
16 8 0.29
17 13 0.46
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATATTATATATTAT
Found at i:35108 original size:2 final size:2
Alignment explanation
Indices: 35101--35152 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
35091 TACATACATT
35101 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
*
35143 TA TA TT TA TA
1 TA TA TA TA TA
35153 CTATTTATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39958 original size:16 final size:16
Alignment explanation
Indices: 39932--39965 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
39922 AGATCCAATC
39932 AAGAACAAAAAAG-AA
1 AAGAACAAAAAAGCAA
39947 AAGAAGCAAAAAAGCAA
1 AAGAA-CAAAAAAGCAA
39964 AA
1 AA
39966 AAAACAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 8 0.47
17 4 0.24
ACGTcount: A:0.76, C:0.09, G:0.15, T:0.00
Consensus pattern (16 bp):
AAGAACAAAAAAGCAA
Found at i:40000 original size:18 final size:17
Alignment explanation
Indices: 39967--40000 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
39957 AAAGCAAAAA
39967 AAACAAAGAAAAAAGAG
1 AAACAAAGAAAAAAGAG
*
39984 AAACAAGAGAAACAAGA
1 AAACAA-AGAAAAAAGA
40001 AAAAAAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.74, C:0.09, G:0.18, T:0.00
Consensus pattern (17 bp):
AAACAAAGAAAAAAGAG
Found at i:40324 original size:172 final size:174
Alignment explanation
Indices: 40054--40400 Score: 585
Period size: 172 Copynumber: 2.0 Consensus size: 174
40044 TTCCCTAAAA
*
40054 AAATGGCACATCAAGCTTCAAACTATGAGATTGATCAAGCACAATCATTCCCGAATTACTGAATC
1 AAATGGCACATCAAGCTTCAAACTATGAGATTGATCAAGCACAATCATTCCCGAATCACTGAATC
40119 ACTTCACTCGAAGATCATAGAGCATCAAGAGAGAGAAACATTTT-G-A-G-CAGGATTGAAGACA
66 ACTTCACTCGAAGATCATAGAGCATC-A-AGAGAGAAACATTTTAGTAGGACAGGATTGAAGACA
*
40180 TCATAATGAATTGATCCTTGGTTCAACACCCTGAAACACTTGTTTG
129 TCAGAATGAATTGATCCTTGGTTCAACACCCTGAAACACTTGTTTG
40226 AAATGGCACATCAAGCTTCAAACTATGAGATTGATCAAGCACAATCATTCCCGAATCACTGAATC
1 AAATGGCACATCAAGCTTCAAACTATGAGATTGATCAAGCACAATCATTCCCGAATCACTGAATC
* * * *
40291 ACTTCACTCGAAGATCATAGAGTATCAAGAGAGATACATTTTGAGTAGGACATGATTGAAGGCAT
66 ACTTCACTCGAAGATCATAGAGCATCAAGAGAGAAACATTTT-AGTAGGACAGGATTGAAGACAT
40356 CAGAATGAATTGATCCTTGGTTCAACACCCTGAAACACTTGTTTG
130 CAGAATGAATTGATCCTTGGTTCAACACCCTGAAACACTTGTTTG
40401 GGCCTATTTA
Statistics
Matches: 164, Mismatches: 6, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
170 14 0.09
171 1 0.01
172 90 0.55
173 1 0.01
174 1 0.01
175 57 0.35
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (174 bp):
AAATGGCACATCAAGCTTCAAACTATGAGATTGATCAAGCACAATCATTCCCGAATCACTGAATC
ACTTCACTCGAAGATCATAGAGCATCAAGAGAGAAACATTTTAGTAGGACAGGATTGAAGACATC
AGAATGAATTGATCCTTGGTTCAACACCCTGAAACACTTGTTTG
Found at i:40823 original size:22 final size:22
Alignment explanation
Indices: 40795--40871 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
40785 GCTACCCCAT
40795 CAAACCGTTGAGCATCAAATGA
1 CAAACCGTTGAGCATCAAATGA
40817 CAAACCGTTGAGCATCAAATGA
1 CAAACCGTTGAGCATCAAATGA
* *
40839 CAAACCTTTGAGCATCAAATGT
1 CAAACCGTTGAGCATCAAATGA
*
40861 CAAACCTTTGA
1 CAAACCGTTGA
40872 CCAAACATAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.22
Consensus pattern (22 bp):
CAAACCGTTGAGCATCAAATGA
Found at i:41836 original size:106 final size:106
Alignment explanation
Indices: 41680--43373 Score: 2400
Period size: 106 Copynumber: 16.0 Consensus size: 106
41670 ATATCGTGCC
* * * *
41680 ACTCAAGACAACACAAGTTCAACTTCACAATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
41745 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * * *
41786 ACTCCAGACAATGCAAGTTCAACTTCACAACGAAGAGACTGATGGTTGTCAATAAACAATTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* *
41851 AATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
41892 ACTCCAGACAACTCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACGACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
*
41957 AATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
41998 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTTGTTGTCAATAAACAATTTCGC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* * *
42063 AATTTCAGAGCCAATTTAAACTTCACAGCGAAGCATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
42104 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
42169 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
42210 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* *
42275 AATTTCAGAGCCAATTTTAACTTTACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
42316 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* * *
42381 AATTTCAGAGCCAATTTAAACTTCACAGCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * *
42422 ACTCAAGACAACGCAAGTTCAACTTCACAATGAAGGGACCGCTGGTTGTCAATAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* * *
42487 AATTTCATAACCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
42528 ACTCCAGATAACGCAAGTTCAACTTCACGGCGAAGGGACCGCTAGTTGTCAACAAACAACTTTTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
42593 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
42634 ACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGTTAGTTGTCAACAAACAATTTC-C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* **
42698 TAATTTCAGAGCCAATTTCAACTTTACAGTGAAGGATATTGG
66 -AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
42740 ACTCAAGATAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTC-C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
*
42804 TAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
66 -AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
42846 ACTCCAGACAACGCAAATTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
*
42911 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
42952 ACTCCAGACAACGCAAGTTCAACTTCACGAAGAAGGGACCACTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* *
43017 AATTTCAGATCCAATTTCAACTTCACAACGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
43058 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* * * *
43123 AATTTCATAGCCAATTTCAACTTCTCAGCGAAGGATCTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * *
43164 AC-CCAAGATAACACAAGCTCAACTTCACGACGAAGGGGCGGCTGATTGTCAAC-AA-AA-TT-T
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCT
** *
43224 C-A-TTCAGATTCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * * *
43264 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACGAATAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCT
** * * *
43328 CGGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
43370 ACTC
1 ACTC
43374 AGAACAATGC
Statistics
Matches: 1427, Mismatches: 150, Indels: 22
0.89 0.09 0.01
Matches are distributed among these distances:
99 1 0.00
100 75 0.05
101 4 0.00
102 3 0.00
103 4 0.00
104 3 0.00
105 4 0.00
106 1332 0.93
107 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:44194 original size:37 final size:37
Alignment explanation
Indices: 44104--44198 Score: 127
Period size: 37 Copynumber: 2.6 Consensus size: 37
44094 CCTTTTCGTC
44104 CTACTAGGATTCAAACTCCTAAAAATAGAATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGAATAGAATT
* * * *
44141 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGAATAGAATT
** *
44178 CTACTATTATTTAAACTCCTA
1 CTACTAGGATTCAAACTCCTA
44199 GTGATAGGAT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGAATAGAATT
Found at i:44681 original size:5 final size:5
Alignment explanation
Indices: 44671--44720 Score: 57
Period size: 5 Copynumber: 9.8 Consensus size: 5
44661 TTTCTTTGCG
* *
44671 TTATA TTATA TTATA TTATT TTCCTA TTATA -TATA TATATA TTATA TTAT
1 TTATA TTATA TTATA TTATA TT-ATA TTATA TTATA T-TATA TTATA TTAT
44721 TATTTTTATC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
4 4 0.11
5 26 0.68
6 8 0.21
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:44724 original size:26 final size:26
Alignment explanation
Indices: 44671--44724 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
44661 TTTCTTTGCG
* *
44671 TTATATTATATTATATTATTTTCCTA
1 TTATATTATATTATATTATATTACTA
*
44697 TTATA-TATATATATATTATATTATTA
1 TTATATTATAT-TATATTATATTACTA
44723 TT
1 TT
44725 TTTATCTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (26 bp):
TTATATTATATTATATTATATTACTA
Found at i:44761 original size:13 final size:13
Alignment explanation
Indices: 44743--44768 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44733 TGTTTACTTA
44743 TTTACTATATTTT
1 TTTACTATATTTT
44756 TTTACTATATTTT
1 TTTACTATATTTT
44769 CCTAACGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTACTATATTTT
Found at i:44937 original size:18 final size:18
Alignment explanation
Indices: 44914--44972 Score: 59
Period size: 17 Copynumber: 3.3 Consensus size: 18
44904 TTATACATAC
44914 ATTTTTATATTTTTATAT
1 ATTTTTATATTTTTATAT
44932 ATTTTT-TATTTTT-TAT
1 ATTTTTATATTTTTATAT
* * *
44948 TTTATTTATACTATTTATTT
1 ATT-TTTATA-TTTTTATAT
44968 ATTTT
1 ATTTT
44973 CATTATGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
16 5 0.15
17 10 0.30
18 8 0.24
19 6 0.18
20 4 0.12
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (18 bp):
ATTTTTATATTTTTATAT
Found at i:44955 original size:16 final size:17
Alignment explanation
Indices: 44914--44956 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 17
44904 TTATACATAC
44914 ATTTTTATATTTTTATAT
1 ATTTTT-TATTTTTATAT
44932 ATTTTTTATTTTT-TAT
1 ATTTTTTATTTTTATAT
44948 -TTTATTTAT
1 ATTT-TTTAT
44957 ACTATTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 3 0.12
16 8 0.33
17 7 0.29
18 6 0.25
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (17 bp):
ATTTTTTATTTTTATAT
Found at i:44957 original size:25 final size:25
Alignment explanation
Indices: 44914--44967 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
44904 TTATACATAC
* *
44914 ATTTTTATATTTTTATATATTTTTT
1 ATTTTTATATTTTTATATACTATTT
*
44939 ATTTTT-TATTTTATTTATACTATTT
1 ATTTTTATATTTT-TATATACTATTT
44964 ATTT
1 ATTT
44968 ATTTTCATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (25 bp):
ATTTTTATATTTTTATATACTATTT
Found at i:45706 original size:18 final size:18
Alignment explanation
Indices: 45683--45718 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
45673 TCAGTATGAC
45683 CCGTTGACATTGACCGAA
1 CCGTTGACATTGACCGAA
* *
45701 CCGTTGACTTTGGCCGAA
1 CCGTTGACATTGACCGAA
45719 AAGTCAAATT
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:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (18 bp):
CCGTTGACATTGACCGAA
Found at i:53397 original size:214 final size:214
Alignment explanation
Indices: 52704--53421 Score: 1195
Period size: 214 Copynumber: 3.3 Consensus size: 214
52694 ATTTTATGAA
* * * * *
52704 AAATATAAATTTAAGAACTAAATTGAATAAATATAAAATTACAAATTAAAATTTAAATAAATTAA
1 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
*
52769 ACAACACACATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAA
66 ACAACACACATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTTAAATTAATACAA
*
52834 AAAGTACTAAATTTTACCCATTTAAAAAGTTATGGG-TCAATTAAAAATATAAATAAGTAATAAG
131 AAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCT-AATTAAAAATATAAATAAGTAATAAG
52898 TATGAGCCAATTTCATATGC
195 TATGAGCCAATTTCATATGC
52918 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAAATTTAAATAAATTA
1 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAAT-AAAAATTTAAATAAATTA
* * *
52983 AACAGCACACATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTCTAGATTAATACA
65 AACAACACACATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTTAAATTAATAC-
*
53048 AAAAAGTACTAAATTAAACCCATTTAAAAAGTTATGGGCTAATTAAAAAATATAAATAAGTAATA
129 AAAAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCTAATT-AAAAATATAAATAAGTAATA
* * * *
53113 AGTATGAGACTATTTTAGATGC
193 AGTATGAGCCAATTTCATATGC
*
53135 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTAAAAATAAAAATTTAAATAAATTAA
1 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
* *
53200 ACAACACACATTGATGAGGGGTCAAATCGAAATAATTTTAAATTGCGAGGTTTAAATTAATACAA
66 ACAACACACATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTTAAATTAATACAA
53265 AAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCTAATTAAAAATATAAATAAGTAATAAGT
131 AAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCTAATTAAAAATATAAATAAGTAATAAGT
*
53330 ATGGGCCAATTTCATATGC
196 ATGAGCCAATTTCATATGC
* **
53349 AAATATAATTTTAAGGACTAAATTGAACAAATACGAAATTACAAATAAAGTTTTAAATAAATTAA
1 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
53414 ACAACACA
66 ACAACACA
53422 AAGGGATCAA
Statistics
Matches: 469, Mismatches: 31, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
214 148 0.32
215 120 0.26
216 117 0.25
217 84 0.18
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (214 bp):
AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
ACAACACACATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTTAAATTAATACAA
AAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCTAATTAAAAATATAAATAAGTAATAAGT
ATGAGCCAATTTCATATGC
Found at i:53531 original size:2 final size:2
Alignment explanation
Indices: 53520--53776 Score: 106
Period size: 2 Copynumber: 125.0 Consensus size: 2
53510 TTGAAACAAC
*
53520 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
53560 CTA TA TA GTT TA TA TT TA TA T- TA T- TA TA TA CTA TA TA TA AA
1 -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* *
53601 CTA TA TA T- TA TA TA TA T- TA -A TCA TA AA CTA TA TA TA CA -A
1 -TA TA TA TA TA TA TA TA TA TA TA T-A TA TA -TA TA TA TA TA TA
* * * *
53640 TG TA TA AA CTA TA -A TA CTA TA TA GTT TA CA TA TGA -A CTA TA TA
1 TA TA TA TA -TA TA TA TA -TA TA TA -TA TA TA TA T-A TA -TA TA TA
* * * * *
53683 AA CTA TT TA TA TA GTA TA TA CTA CA TA TA TA -A TC TA TA GTT TA
1 TA -TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA
* *
53726 TA TT TA TA TA CTA TA TA T- TA TA TA TA TA AA CTA TA TA TA CTA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA
53768 TA TA GTA TA
1 TA TA -TA TA
53777 ATTTACATAT
Statistics
Matches: 191, Mismatches: 33, Indels: 62
0.67 0.12 0.22
Matches are distributed among these distances:
1 12 0.06
2 152 0.80
3 27 0.14
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:53574 original size:41 final size:39
Alignment explanation
Indices: 53517--53636 Score: 129
Period size: 41 Copynumber: 3.0 Consensus size: 39
53507 AAATTGAAAC
53517 AACTATA-ATATATATATATATATATATATATA-TATAATATA
1 AACTATATAT-TATATATATAT-TAT-TATATACTAT-ATATA
*
53558 AACTATATAGTTTATATTTATATTATTATATACTATATATA
1 AACTATATA--TTATATATATATTATTATATACTATATATA
* * *
53599 AACTATATATTATATATAT-TAATCATAAACTATATATA
1 AACTATATATTATATATATATTATTATATACTATATATA
53637 CAATGTATAA
Statistics
Matches: 70, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
38 16 0.23
39 9 0.13
41 27 0.39
42 7 0.10
43 10 0.14
44 1 0.01
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.46
Consensus pattern (39 bp):
AACTATATATTATATATATATTATTATATACTATATATA
Found at i:53588 original size:39 final size:43
Alignment explanation
Indices: 53517--53771 Score: 158
Period size: 40 Copynumber: 6.0 Consensus size: 43
53507 AAATTGAAAC
53517 AACTATA-A-TATATATATATATATATATATATA-TATAATATA
1 AACTATATATTATATATATATATATATATATATACTAT-ATATA
*
53558 AACTATATAGTT-TATATTTATAT-TAT-TATATACTATATATA
1 AACTATATA-TTATATATATATATATATATATATACTATATATA
* * *
53599 AACTATATATTATATATATTAATCATAAACTATATATACAATGTATA
1 AACTATATATTATATATA-T-AT-ATATA-TATATATACTATATATA
* * * * *
53646 AACTATAATACTATATAGTTTACATATGAACTATATAAACTATTTATA
1 AACTAT-ATATTATATA-TATATATAT--A-TATATATACTATATATA
* * * * * *
53694 TAGTATATACTACATATATA-ATCTATAGT-T-TA-TATTTATA
1 AACTATATATTATATATATATATATATA-TATATACTATATATA
* *
53734 TACTATATATTATATATATA-A-A-CTATATATACTATATA
1 AACTATATATTATATATATATATATATATATATACTATATA
53772 GTATAATTTA
Statistics
Matches: 171, Mismatches: 24, Indels: 39
0.73 0.10 0.17
Matches are distributed among these distances:
37 1 0.01
38 3 0.02
39 2 0.01
40 33 0.19
41 33 0.19
42 11 0.06
43 14 0.08
44 3 0.02
45 4 0.02
46 7 0.04
47 29 0.17
48 30 0.18
49 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.44
Consensus pattern (43 bp):
AACTATATATTATATATATATATATATATATATACTATATATA
Found at i:53596 original size:9 final size:9
Alignment explanation
Indices: 53518--53771 Score: 92
Period size: 9 Copynumber: 27.9 Consensus size: 9
53508 AATTGAAACA
53518 ACTATA-AT
1 ACTATATAT
53526 A-TATATAT
1 ACTATATAT
53534 A-TATATAT
1 ACTATATAT
53542 A-TATATAT
1 ACTATATAT
*
53550 A-TAATATAA
1 ACT-ATATAT
53559 ACTATATAGTTT
1 ACTATATA---T
*
53571 A-TATTTAT
1 ACTATATAT
*
53579 ATTATTATAT
1 ACTA-TATAT
53589 ACTATATAT
1 ACTATATAT
53598 AAACTATATAT
1 --ACTATATAT
53609 --TATATAT
1 ACTATATAT
* *
53616 ATTAATCATAA
1 ACT-AT-ATAT
53627 ACTATATAT
1 ACTATATAT
* *
53636 ACAATGTATAA
1 AC--TATATAT
53647 ACTATA-AT
1 ACTATATAT
53655 ACTATATAGTTT
1 ACTATATA---T
53667 AC-ATATGA-
1 ACTATAT-AT
*
53675 ACTATATAA
1 ACTATATAT
*
53684 ACTATTTAT
1 ACTATATAT
53693 A-TAGTATAT
1 ACTA-TATAT
*
53702 ACTACATAT
1 ACTATATAT
*
53711 A-TA-ATCT
1 ACTATATAT
*
53718 A-TAGTTTAT
1 ACTA-TATAT
*
53727 A-TTTATAT
1 ACTATATAT
53735 ACTATATATT
1 ACTATATA-T
53745 A-TATATAT
1 ACTATATAT
53753 AAACTATATAT
1 --ACTATATAT
53764 ACTATATA
1 ACTATATA
53772 GTATAATTTA
Statistics
Matches: 192, Mismatches: 22, Indels: 63
0.69 0.08 0.23
Matches are distributed among these distances:
7 17 0.09
8 43 0.22
9 73 0.38
10 17 0.09
11 37 0.19
12 5 0.03
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.44
Consensus pattern (9 bp):
ACTATATAT
Found at i:53617 original size:43 final size:42
Alignment explanation
Indices: 53517--53672 Score: 128
Period size: 41 Copynumber: 3.6 Consensus size: 42
53507 AAATTGAAAC
53517 AACTATAATATATATATA--TATATATATATATATATAATATA
1 AACTAT-ATATATATATATTTATATATATATATATATAATATA
53558 AACTATATAGT-T-TATATTTATAT-TAT-TATATACTATATATA
1 AACTATATA-TATATATATTTATATATATATATATA-TA-ATATA
* * *
53599 AACTATATATTATATATATTAATCATAAACTATATATACAATGTATA
1 AACTATATA-TATATATATTTAT-ATATA-TATATATATAA--TATA
*
53646 AACTATA-ATACTATATAGTTTACATAT
1 AACTATATATA-TATATA-TTTATATAT
53673 GAACTATATA
Statistics
Matches: 93, Mismatches: 7, Indels: 25
0.74 0.06 0.20
Matches are distributed among these distances:
39 10 0.11
40 9 0.10
41 27 0.29
42 1 0.01
43 8 0.09
44 2 0.02
45 4 0.04
46 12 0.13
47 20 0.22
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.44
Consensus pattern (42 bp):
AACTATATATATATATATTTATATATATATATATATAATATA
Found at i:53825 original size:18 final size:18
Alignment explanation
Indices: 53804--53841 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
53794 ATATAAAAAC
53804 TATATAAACTATAGTTTA
1 TATATAAACTATAGTTTA
53822 TATATAAACTATAGTTTA
1 TATATAAACTATAGTTTA
53840 TA
1 TA
53842 GTTGATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (18 bp):
TATATAAACTATAGTTTA
Found at i:53841 original size:47 final size:47
Alignment explanation
Indices: 53708--53841 Score: 123
Period size: 47 Copynumber: 2.8 Consensus size: 47
53698 ATATACTACA
* *
53708 TATATAATCTATAGTTTATATTTATATACTATA-TATTATATATATAAAC
1 TATATAAACTATAGTTTATA--TATATACTATAGT-TTATATATAAAAAC
* * * *
53757 TATATATACTATA-TAGTATA-ATTTAC-ATATGAATTATATATAAAAAC
1 TATATAAACTATAGT-TTATATATATACTATA-G-TTTATATATAAAAAC
*
53804 TATATAAACTATAGTTTATATATAAACTATAGTTTATA
1 TATATAAACTATAGTTTATATATATACTATAGTTTATA
53842 GTTGATATTT
Statistics
Matches: 67, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
45 3 0.04
46 5 0.07
47 34 0.51
48 7 0.10
49 18 0.27
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.45
Consensus pattern (47 bp):
TATATAAACTATAGTTTATATATATACTATAGTTTATATATAAAAAC
Found at i:53894 original size:18 final size:18
Alignment explanation
Indices: 53873--53912 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
53863 ATATAAATTA
*
53873 TATAGTTGATATATGAAC
1 TATAGTTGACATATGAAC
*
53891 TATAGTTTACATATGAAC
1 TATAGTTGACATATGAAC
53909 TATA
1 TATA
53913 TGTAAAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (18 bp):
TATAGTTGACATATGAAC
Found at i:53935 original size:60 final size:59
Alignment explanation
Indices: 53773--53936 Score: 174
Period size: 60 Copynumber: 2.8 Consensus size: 59
53763 TACTATATAG
* * *
53773 TATAATTTACATATGAATTATATATAAAAACTATATAAAC--TATAGTTTATATATAAAC
1 TATAGTTTACATATGAA-TATATGTAAAAACTATATAAACTATATAGTTGATATATAAAC
* * * * *
53831 TATAGTTTATAGT-TGATATTTATGTATAAACTATATAAATTATATAGTTGATATATGAAC
1 TATAGTTTACA-TATGA-ATATATGTAAAAACTATATAAACTATATAGTTGATATATAAAC
*
53891 TATAGTTTACATATGAACTATATGTAAAAA-TCATATCAACTATATA
1 TATAGTTTACATATGAA-TATATGTAAAAACT-ATATAAACTATATA
53937 CTATAGTTGA
Statistics
Matches: 86, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
58 30 0.35
59 5 0.06
60 51 0.59
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (59 bp):
TATAGTTTACATATGAATATATGTAAAAACTATATAAACTATATAGTTGATATATAAAC
Found at i:53984 original size:15 final size:15
Alignment explanation
Indices: 53938--53997 Score: 65
Period size: 15 Copynumber: 4.3 Consensus size: 15
53928 AACTATATAC
* *
53938 TATAGTTGATATTTA
1 TATAGTTTATACTTA
*
53953 TATA--TTATA-TAA
1 TATAGTTTATACTTA
53965 TATAGTTTATACTTA
1 TATAGTTTATACTTA
53980 TATAGTTTATAC-TA
1 TATAGTTTATACTTA
53994 TATA
1 TATA
53998 AATTCAAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
12 6 0.15
13 4 0.10
14 11 0.28
15 18 0.46
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.52
Consensus pattern (15 bp):
TATAGTTTATACTTA
Found at i:53990 original size:27 final size:27
Alignment explanation
Indices: 53931--53995 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
53921 TCATATCAAC
*
53931 TATATACTATAGTTGATATTTATATAT
1 TATATACTATAGTTGATACTTATATAT
* *
53958 TATATAATATAGTTTATACTTATATAGT
1 TATATACTATAGTTGATACTTATATA-T
53986 T-TATACTATA
1 TATATACTATA
53996 TAAATTCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 31 0.94
28 2 0.06
ACGTcount: A:0.38, C:0.05, G:0.06, T:0.51
Consensus pattern (27 bp):
TATATACTATAGTTGATACTTATATAT
Found at i:54085 original size:18 final size:16
Alignment explanation
Indices: 54062--54351 Score: 63
Period size: 18 Copynumber: 17.4 Consensus size: 16
54052 ATAAACGATT
54062 TATATAGTATATACTAC
1 TATATAGTATATA-TAC
54079 ATATATAGTTTATATATAC
1 -TATATAG--TATATATAC
*
54098 TATATAGTTTACATATGAAC
1 TATATAG--TATATAT--AC
*
54118 TATATA-TA-A-AAAC
1 TATATAGTATATATAC
*
54131 TATATA-TATA-A-AG
1 TATATAGTATATATAC
* *
54144 TATATGGTATATACAAAC
1 TATATAGTATAT--ATAC
*
54162 TATATA-T-TATATAG
1 TATATAGTATATATAC
54176 T-TATTAGTATATATAAAC
1 TATA-TAGTATATAT--AC
*
54194 TATATAATATATATATAC
1 TATAT-A-GTATATATAC
* *
54212 TATATATTATATAGTTC
1 TATATAGTATATA-TAC
54229 -AT-TAGTATATATAAAC
1 TATATAGTATATAT--AC
* * *
54245 TATACATTATATAGTTC
1 TATATAGTATATA-TAC
54262 -AT-TAGTATATATAAAC
1 TATATAGTATATAT--AC
* * *
54278 TATACATTATATATAG
1 TATATAGTATATATAC
54294 T-TCATTAGTATATATAAAC
1 TAT-A-TAGTATATAT--AC
* *
54313 TATATATTATATAGTTC
1 TATATAGTATATA-TAC
54330 -AT-TAGTATATATGAC
1 TATATAGTATATAT-AC
54345 ATATATA
1 -TATATA
54352 TTAATTTATT
Statistics
Matches: 204, Mismatches: 30, Indels: 76
0.66 0.10 0.25
Matches are distributed among these distances:
13 18 0.09
14 14 0.07
15 27 0.13
16 26 0.13
17 23 0.11
18 63 0.31
19 11 0.05
20 22 0.11
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (16 bp):
TATATAGTATATATAC
Found at i:54113 original size:20 final size:18
Alignment explanation
Indices: 54069--54123 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 18
54059 ATTTATATAG
54069 TATATACTACATATATAGTT
1 TATATA-TAC-TATATAGTT
54089 TATATATACTATATAGTT
1 TATATATACTATATAGTT
*
54107 TACATATGAACTATATA
1 TATATAT--ACTATATA
54124 TAAAAACTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 15 0.47
19 3 0.09
20 14 0.44
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (18 bp):
TATATATACTATATAGTT
Found at i:54167 original size:13 final size:13
Alignment explanation
Indices: 54115--54148 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
54105 TTTACATATG
54115 AACTATATATAAA
1 AACTATATATAAA
*
54128 AACTATATATATA
1 AACTATATATAAA
*
54141 AAGTATAT
1 AACTATAT
54149 GGTATATACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (13 bp):
AACTATATATAAA
Found at i:54198 original size:50 final size:51
Alignment explanation
Indices: 54133--54341 Score: 182
Period size: 50 Copynumber: 4.1 Consensus size: 51
54123 ATAAAAACTA
* **
54133 TATATATAAAGTATATGGTATATACAAACTATATATTATATAGTT-ATTAG
1 TATATATAAACTATATAATATATACAAACTATATATTATATAGTTCATTAG
* *
54183 TATATATAAACTATATAATATATATATACTATATATTATATAGTTCATTAG
1 TATATATAAACTATATAATATATACAAACTATATATTATATAGTTCATTAG
* * * * * *
54234 TATATATAAACTATACATTATATAGTTCATTAGTATATA-TAAACTA-TACATTA-
1 TATATATAAACTAT--ATAATATA-TACA-AACTATATATTATA-TAGTTCATTAG
* * *
54287 TATATAGT--TC-AT-TAGTATATATAAACTATATATTATATAGTTCATTAG
1 TATATA-TAAACTATATAATATATACAAACTATATATTATATAGTTCATTAG
54335 TATATAT
1 TATATAT
54342 GACATATATA
Statistics
Matches: 129, Mismatches: 20, Indels: 23
0.75 0.12 0.13
Matches are distributed among these distances:
46 9 0.07
47 12 0.09
48 11 0.09
50 40 0.31
51 21 0.16
52 1 0.01
53 13 0.10
54 12 0.09
55 10 0.08
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (51 bp):
TATATATAAACTATATAATATATACAAACTATATATTATATAGTTCATTAG
Found at i:54241 original size:2 final size:2
Alignment explanation
Indices: 54062--54224 Score: 50
Period size: 2 Copynumber: 77.0 Consensus size: 2
54052 ATAAACGATT
* * *
54062 TA TA TA GTA TA TA CTA CA TA TA TA GTT TA TA TA TA CTA TA TA GTT
1 TA TA TA -TA TA TA -TA TA TA TA TA -TA TA TA TA TA -TA TA TA -TA
* * * * *
54107 TA CA TA TGA -A CTA TA TA TA AA AA CTA TA TA TA TA AA GTA TA TGG
1 TA TA TA T-A TA -TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA T-A
* *
54151 TA TA TA CA AA CTA TA TA T- TA TA TA GT- TA T- TA GTA TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA
*
54191 AA CTA TA TA -A TA TA TA TA TA CTA TA TA T- TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
54225 GTTCATTAGT
Statistics
Matches: 121, Mismatches: 19, Indels: 42
0.66 0.10 0.23
Matches are distributed among these distances:
1 6 0.05
2 95 0.79
3 20 0.17
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (2 bp):
TA
Found at i:54272 original size:68 final size:68
Alignment explanation
Indices: 54201--54341 Score: 241
Period size: 68 Copynumber: 2.1 Consensus size: 68
54191 AACTATATAA
* *
54201 TATATATATACTATATA-T-TATATAGTTCATTAGTATATATAAACTATACATTATATAGTTCAT
1 TATATATAAACTATACATTATATATAGTTCATTAGTATATATAAACTATACATTATATAGTTCAT
54264 TAG
66 TAG
*
54267 TATATATAAACTATACATTATATATAGTTCATTAGTATATATAAACTATATATTATATAGTTCAT
1 TATATATAAACTATACATTATATATAGTTCATTAGTATATATAAACTATACATTATATAGTTCAT
54332 TAG
66 TAG
54335 TATATAT
1 TATATAT
54342 GACATATATA
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
66 15 0.21
67 1 0.01
68 54 0.77
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (68 bp):
TATATATAAACTATACATTATATATAGTTCATTAGTATATATAAACTATACATTATATAGTTCAT
TAG
Found at i:54352 original size:35 final size:33
Alignment explanation
Indices: 54201--54354 Score: 238
Period size: 33 Copynumber: 4.6 Consensus size: 33
54191 AACTATATAA
*
54201 TATATATATACTATATATTATATAGTTCATTAG
1 TATATATAAACTATATATTATATAGTTCATTAG
*
54234 TATATATAAACTATACATTATATAGTTCATTAG
1 TATATATAAACTATATATTATATAGTTCATTAG
*
54267 TATATATAAACTATACATTATATATAGTTCATTAG
1 TATATATAAACTATATA-T-TATATAGTTCATTAG
54302 TATATATAAACTATATATTATATAGTTCATTAG
1 TATATATAAACTATATATTATATAGTTCATTAG
*
54335 TATATAT-GACATATATATTA
1 TATATATAAAC-TATATATTA
54355 ATTTATTAAT
Statistics
Matches: 114, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.02
33 79 0.69
34 2 0.02
35 31 0.27
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (33 bp):
TATATATAAACTATATATTATATAGTTCATTAG
Found at i:54485 original size:61 final size:61
Alignment explanation
Indices: 54411--54552 Score: 216
Period size: 61 Copynumber: 2.3 Consensus size: 61
54401 TATAAGGATC
54411 AAATTGAACAAATTTGAAATATGAAGCTTAAATTAATAAATTGTA-AT-ATTAAATTTGAACT
1 AAATTGAACAAATTTGAAATATGAAGCTTAAATTAATAAA-T-TACATCATTAAATTTGAACT
* * *
54472 AAATTGAAGAAATTTGAAATATGAAGCTTACATTAATATATTACATCATTAAATTTGAACT
1 AAATTGAACAAATTTGAAATATGAAGCTTAAATTAATAAATTACATCATTAAATTTGAACT
*
54533 AAATTGAACAAATTTAAAAT
1 AAATTGAACAAATTTGAAAT
54553 TAGGAGACAA
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
59 2 0.03
60 3 0.04
61 69 0.93
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.35
Consensus pattern (61 bp):
AAATTGAACAAATTTGAAATATGAAGCTTAAATTAATAAATTACATCATTAAATTTGAACT
Found at i:54618 original size:13 final size:13
Alignment explanation
Indices: 54600--54624 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54590 ACACGCGGGT
54600 CAAAACCCAAACC
1 CAAAACCCAAACC
54613 CAAAACCCAAAC
1 CAAAACCCAAAC
54625 AAACCCGTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.44, G:0.00, T:0.00
Consensus pattern (13 bp):
CAAAACCCAAACC
Found at i:55175 original size:12 final size:12
Alignment explanation
Indices: 55155--55230 Score: 64
Period size: 12 Copynumber: 6.3 Consensus size: 12
55145 TCTTAACCAT
*
55155 AACCCAAACTTG
1 AACCCAAACCTG
*
55167 AACCTAAACCTG
1 AACCCAAACCTG
*
55179 AAACCAAACCCT-
1 AACCCAAA-CCTG
* *
55191 AACTCAAACCTA
1 AACCCAAACCTG
* *
55203 AACCCAGACCCG
1 AACCCAAACCTG
*
55215 AACCCAGACCTG
1 AACCCAAACCTG
55227 AACC
1 AACC
55231 TGAATCTGAA
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
11 3 0.06
12 45 0.88
13 3 0.06
ACGTcount: A:0.42, C:0.39, G:0.08, T:0.11
Consensus pattern (12 bp):
AACCCAAACCTG
Found at i:55189 original size:30 final size:31
Alignment explanation
Indices: 55149--55206 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
55139 TCATCTTCTT
**
55149 AACCATAACCCAAACTTGAACCTAAACCTGA
1 AACCATAACCCAAACTCAAACCTAAACCTGA
*
55180 AACCA-AACCCTAACTCAAACCTAAACC
1 AACCATAACCCAAACTCAAACCTAAACC
55207 CAGACCCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.47, C:0.36, G:0.03, T:0.14
Consensus pattern (31 bp):
AACCATAACCCAAACTCAAACCTAAACCTGA
Found at i:55256 original size:30 final size:30
Alignment explanation
Indices: 55213--55283 Score: 70
Period size: 30 Copynumber: 2.4 Consensus size: 30
55203 AACCCAGACC
* * * ** *
55213 CGAACCCAGACCTGAACCTGAATCTGAATT
1 CGAATCCAAACCTGAACCCGAATCCAAAAT
**
55243 CGAATCCAAACCTGTTCCCGAATCCAAAAT
1 CGAATCCAAACCTGAACCCGAATCCAAAAT
55273 CGAATCCAAAC
1 CGAATCCAAAC
55284 TATTCGAAAC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.37, C:0.32, G:0.13, T:0.18
Consensus pattern (30 bp):
CGAATCCAAACCTGAACCCGAATCCAAAAT
Found at i:57896 original size:20 final size:20
Alignment explanation
Indices: 57871--57911 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
57861 AAATACTTGG
57871 TGCTTGTTTCTGTTTGATAT
1 TGCTTGTTTCTGTTTGATAT
57891 TGCTTGTTTCTGTTTGATAT
1 TGCTTGTTTCTGTTTGATAT
57911 T
1 T
57912 TGTAAGGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.10, C:0.10, G:0.20, T:0.61
Consensus pattern (20 bp):
TGCTTGTTTCTGTTTGATAT
Found at i:58029 original size:15 final size:15
Alignment explanation
Indices: 58011--58055 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
58001 TAGGATGCTT
58011 GCTGAATTGATGCAA
1 GCTGAATTGATGCAA
**
58026 GCTGAATTGATGCTT
1 GCTGAATTGATGCAA
58041 GCTGAATTGATGCAA
1 GCTGAATTGATGCAA
58056 TGATGCTTGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (15 bp):
GCTGAATTGATGCAA
Found at i:58084 original size:23 final size:23
Alignment explanation
Indices: 58035--58087 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
58025 AGCTGAATTG
* *
58035 ATGCTTGCTGAATTGATGCAATG
1 ATGCTTGCTGAATTGATACAATA
* *
58058 ATGCTTGCTGAATTGGTACATTA
1 ATGCTTGCTGAATTGATACAATA
58081 ATGCTTG
1 ATGCTTG
58088 TCAGTTGTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.38
Consensus pattern (23 bp):
ATGCTTGCTGAATTGATACAATA
Found at i:58703 original size:18 final size:18
Alignment explanation
Indices: 58682--58767 Score: 70
Period size: 18 Copynumber: 4.9 Consensus size: 18
58672 AAATTTATAT
* *
58682 TATAAGAATTATAATTAA
1 TATAAAAATTAGAATTAA
58700 TATAAAAATTAGAATTAA
1 TATAAAAATTAGAATTAA
* *
58718 TAT-AAAACTA-AATTTAG
1 TATAAAAATTAGAA-TTAA
** *
58735 TATTCAAATTATAATTAA
1 TATAAAAATTAGAATTAA
*
58753 TCTAAAAATTA-AATT
1 TATAAAAATTAGAATT
58768 TCAAAAAGTA
Statistics
Matches: 55, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
16 2 0.04
17 16 0.29
18 35 0.64
19 2 0.04
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
TATAAAAATTAGAATTAA
Found at i:66658 original size:19 final size:20
Alignment explanation
Indices: 66608--66660 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
66598 ATCAGGTAAA
* *
66608 AATATGACTAAACCGGGTTC
1 AATATGACAAAACCCGGTTC
*
66628 AATATAACAAAACCCGGTTC
1 AATATGACAAAACCCGGTTC
66648 AA-ATGACAAAACC
1 AATATGACAAAACC
66661 GGTAAAGCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 10 0.34
20 19 0.66
ACGTcount: A:0.45, C:0.23, G:0.13, T:0.19
Consensus pattern (20 bp):
AATATGACAAAACCCGGTTC
Found at i:67152 original size:169 final size:168
Alignment explanation
Indices: 66867--67187 Score: 483
Period size: 169 Copynumber: 1.9 Consensus size: 168
66857 TATCTACTAG
*
66867 ATATGTTGAAGGTATCGATCTTTAATAAGTATATGATAATAATATCGATACTTTAGGAATTTAAA
1 ATATGTTGAAGGTATCGATCTTTAATAAGTATATGATAATAATATCAATACTTTAGGAATTTAAA
* * *
66932 ATAATTGCAATATGCGCCATAAAGTATCGATACTTTATAAACATGTATCGATACATAACAATATA
66 AGAATTACAATATGCGCCATAAAGTATCGATACTTTATAAACATATATCGATACATAACAATATA
66997 -AGAGGT-AAAAATATGACAAAACTTAAAGTGCTACCGA
131 GA-AGGTAAAAAATATGACAAAACTTAAAGTGCTACCGA
*
67034 ATATGTTGAAGGTATCGATACTTTAATAAGTATATGCA-AGATATTATCAATACTTTAGGAATTT
1 ATATGTTGAAGGTATCGAT-CTTTAATAAGTATATG-ATA-ATAATATCAATACTTTAGGAATTT
*
67098 AAAAGAATTACAATAATGACGCCTATAAAGTA-CGATACTTTAT-AA-ATATATCGATATATAAC
63 AAAAGAATTACAAT-ATG-CGCC-ATAAAGTATCGATACTTTATAAACATATATCGATACATAAC
67160 AATATAGAAGGTAAAAAATATGACAAAA
125 AATATAGAAGGTAAAAAATATGACAAAA
67188 TTAGTTTCAG
Statistics
Matches: 140, Mismatches: 6, Indels: 13
0.88 0.04 0.08
Matches are distributed among these distances:
167 19 0.14
168 17 0.12
169 60 0.43
170 21 0.15
171 15 0.11
172 8 0.06
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (168 bp):
ATATGTTGAAGGTATCGATCTTTAATAAGTATATGATAATAATATCAATACTTTAGGAATTTAAA
AGAATTACAATATGCGCCATAAAGTATCGATACTTTATAAACATATATCGATACATAACAATATA
GAAGGTAAAAAATATGACAAAACTTAAAGTGCTACCGA
Found at i:67337 original size:29 final size:29
Alignment explanation
Indices: 67303--67359 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
67293 AAGAAAACGT
67303 ATCGAAAATATCGACACCTGACACAAAAA
1 ATCGAAAATATCGACACCTGACACAAAAA
*
67332 ATCGAAAGTATCGACACCTGACACAAAA
1 ATCGAAAATATCGACACCTGACACAAAA
67360 GTATCGAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.49, C:0.25, G:0.12, T:0.14
Consensus pattern (29 bp):
ATCGAAAATATCGACACCTGACACAAAAA
Done.