Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004481.1 Hibiscus syriacus cultivar Beakdansim tig00009876_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: 64274
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:5051 original size:2 final size:2
Alignment explanation
Indices: 5038--5098 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
5028 CAAATGCATG
*
5038 TA TA TG 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
5080 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
5099 CATGTAACAC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5572 original size:18 final size:18
Alignment explanation
Indices: 5549--5600 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
5539 CGTAGAAATT
*
5549 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
5567 TGTCCCAAAGGACCAATA
1 TGTCCCGAAGGACCACTA
*
5585 TATCCCGAAGGACCAC
1 TGTCCCGAAGGACCAC
5601 ATAGAACAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:5621 original size:28 final size:28
Alignment explanation
Indices: 5581--5635 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
5571 CCAAAGGACC
5581 AATATATCCCGAAGGACCACATAGAACA
1 AATATATCCCGAAGGACCACATAGAACA
* *
5609 AATATGTCCCGAAGGACCACGTAGAAC
1 AATATATCCCGAAGGACCACATAGAAC
5636 CCTCGACTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.42, C:0.25, G:0.18, T:0.15
Consensus pattern (28 bp):
AATATATCCCGAAGGACCACATAGAACA
Found at i:9854 original size:18 final size:18
Alignment explanation
Indices: 9831--9882 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
9821 CGTAGAAATT
9831 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
9849 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
9867 TGCCCCGAAGGACCAC
1 TGTCCCGAAGGACCAC
9883 ATAGAACAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.27, C:0.37, G:0.23, T:0.13
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:10795 original size:11 final size:11
Alignment explanation
Indices: 10779--10815 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
10769 TGAGTGCATC
10779 GATGCATGGCT
1 GATGCATGGCT
10790 GATGCAT--C-
1 GATGCATGGCT
10798 GATGCATGGCT
1 GATGCATGGCT
10809 GATGCAT
1 GATGCAT
10816 CGATGCATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 7 0.30
9 1 0.04
10 1 0.04
11 14 0.61
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (11 bp):
GATGCATGGCT
Found at i:10797 original size:19 final size:19
Alignment explanation
Indices: 10768--10823 Score: 103
Period size: 19 Copynumber: 2.9 Consensus size: 19
10758 TCAAAATAGC
10768 CTGAGTGCATCGATGCATGG
1 CTGA-TGCATCGATGCATGG
10788 CTGATGCATCGATGCATGG
1 CTGATGCATCGATGCATGG
10807 CTGATGCATCGATGCAT
1 CTGATGCATCGATGCAT
10824 CAAATGCATT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 32 0.89
20 4 0.11
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.27
Consensus pattern (19 bp):
CTGATGCATCGATGCATGG
Found at i:10801 original size:8 final size:8
Alignment explanation
Indices: 10773--10838 Score: 51
Period size: 8 Copynumber: 7.2 Consensus size: 8
10763 ATAGCCTGAG
10773 TGCATCGA
1 TGCATCGA
10781 TGCATGGCTGA
1 TGCAT--C-GA
10792 TGCATCGA
1 TGCATCGA
10800 TGCATGGCTGA
1 TGCAT--C-GA
10811 TGCATCGA
1 TGCATCGA
*
10819 TGCATCAAA
1 TGCATC-GA
10828 TGCATTCGA
1 TGCA-TCGA
10837 TG
1 TG
10839 TTTTCATAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
8 20 0.42
9 10 0.21
10 4 0.08
11 14 0.29
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (8 bp):
TGCATCGA
Found at i:13603 original size:23 final size:22
Alignment explanation
Indices: 13572--13649 Score: 86
Period size: 21 Copynumber: 3.5 Consensus size: 22
13562 GGCCTTGTAC
13572 ATCGATGCACATTCAAGGCGTGT
1 ATCGATGCACATTCAAGG-GTGT
* * *
13595 ATCGGTGCACCTTC-ATGGTGT
1 ATCGATGCACATTCAAGGGTGT
*
13616 ATCGATGCACATTCAAAGGGATGC
1 ATCGATGCACATTC-AAGGG-TGT
13640 ATCGATGCAC
1 ATCGATGCAC
13650 TGTTAAGTGT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
21 16 0.36
22 2 0.04
23 15 0.33
24 12 0.27
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (22 bp):
ATCGATGCACATTCAAGGGTGT
Found at i:19435 original size:19 final size:17
Alignment explanation
Indices: 19411--19457 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
19401 GGACGCTTAG
*
19411 TGCATCGGTGCACTAAGAA
1 TGCATCGATGCA-TAA-AA
19430 TGCATCGATGCATAAAA
1 TGCATCGATGCATAAAA
19447 TGCATTCGATG
1 TGCA-TCGATG
19458 TTTCAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 6 0.23
18 9 0.35
19 11 0.42
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (17 bp):
TGCATCGATGCATAAAA
Found at i:19477 original size:64 final size:63
Alignment explanation
Indices: 19409--19588 Score: 204
Period size: 65 Copynumber: 2.8 Consensus size: 63
19399 TTGGACGCTT
* *
19409 AGTGCATCGGTGCACTAAG-AATGCATCGATGCATAAAATGCATTCGATGTTTCA-AAATAGC-C
1 AGTGCATCGATGCA-T-AGTAATGCATCGATGTATAAAATGCATTCGATGTTTCATAAA-A-CTC
19471 TG
62 TG
* * * *
19473 AGTGCATCGATGCATGGTTGATGCATCGATGTATCAAATGCATTCTATGTTTTCATAAAACTCTG
1 AGTGCATCGATGCATAG-TAATGCATCGATGTATAAAATGCATTCGATG-TTTCATAAAACTCTG
* *
19538 AGTGCATCGATGCATAGTATATGCATCGGTGTATGAAATGCATTCGATGTT
1 AGTGCATCGATGCATAGTA-ATGCATCGATGTATAAAATGCATTCGATGTT
19589 CAATTTATTC
Statistics
Matches: 99, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 43 0.43
65 51 0.52
66 3 0.03
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (63 bp):
AGTGCATCGATGCATAGTAATGCATCGATGTATAAAATGCATTCGATGTTTCATAAAACTCTG
Found at i:19562 original size:65 final size:65
Alignment explanation
Indices: 19429--19588 Score: 211
Period size: 65 Copynumber: 2.5 Consensus size: 65
19419 TGCACTAAGA
* *
19429 ATGCATCGATGCATAAAATGCATTCGATG-TTTCAAAATAGCCTGAGTGCATCGATGCATGGTTG
1 ATGCATCGATGTATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATGCATAGTTG
* *
19493 ATGCATCGATGTATCAAATGCATTCTATGTTTTCATAAA-A-CTCTGAGTGCATCGATGCATAGT
1 ATGCATCGATGTATAAAATGCATTCGATGTTTTCA-AAATAGC-CTGAGTGCATCGATGCATAGT
19556 AT-
64 -TG
* *
19558 ATGCATCGGTGTATGAAATGCATTCGATGTT
1 ATGCATCGATGTATAAAATGCATTCGATGTT
19589 CAATTTATTC
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
64 27 0.32
65 54 0.64
66 4 0.05
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.33
Consensus pattern (65 bp):
ATGCATCGATGTATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATGCATAGTTG
Found at i:24746 original size:24 final size:25
Alignment explanation
Indices: 24717--24775 Score: 66
Period size: 29 Copynumber: 2.2 Consensus size: 25
24707 ATTTTATTCT
24717 TGTCTTAACTTAAAAATATATTTTA
1 TGTCTTAACTTAAAAATATATTTTA
*
24742 TTCTTACTTTAACTTAAAAATATATTTTA
1 -T-GT-C-TTAACTTAAAAATATATTTTA
24771 -GTCTT
1 TGTCTT
24776 TATATTAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
24 2 0.07
25 1 0.04
26 2 0.07
27 1 0.04
28 1 0.04
29 21 0.75
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.51
Consensus pattern (25 bp):
TGTCTTAACTTAAAAATATATTTTA
Found at i:24844 original size:121 final size:123
Alignment explanation
Indices: 24691--24918 Score: 318
Period size: 122 Copynumber: 1.9 Consensus size: 123
24681 TATTTTTATA
* * * * * * *
24691 TTAATTTATTAAATATATTTTATTCTTGTCTTAACTTA-AAAATATATTTTATTCTTACTTTAAC
1 TTAAATTATTAAATATATTCTACTCTTATCTTAAATTATAAAATATAATTAATTCTTACTTTAAC
24755 TTAAAA-ATATATTTTAGTCTTTATATTAACTTAAAAA-ATATACATTATATTCTTAAC
66 TTAAAATATATATTTTAGTC-TTATATTAACTTAAAAATATATACATTATATTCTTAAC
* *
24812 TTAAATTATTAAATATATTCTACTCTTATCTTAAATTATTAAATATAATTAATTCTTATTTTAAC
1 TTAAATTATTAAATATATTCTACTCTTATCTTAAATTATAAAATATAATTAATTCTTACTTTAAC
* * *
24877 TTAAAATATATCTTTTATTCTTATCTTAACTTAAAAATATAT
66 TTAAAATATATATTTTAGTCTTATATTAACTTAAAAATATAT
24919 TTTTATCTTA
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
121 33 0.36
122 44 0.48
123 15 0.16
ACGTcount: A:0.39, C:0.09, G:0.01, T:0.50
Consensus pattern (123 bp):
TTAAATTATTAAATATATTCTACTCTTATCTTAAATTATAAAATATAATTAATTCTTACTTTAAC
TTAAAATATATATTTTAGTCTTATATTAACTTAAAAATATATACATTATATTCTTAAC
Found at i:24923 original size:30 final size:29
Alignment explanation
Indices: 24667--24969 Score: 267
Period size: 30 Copynumber: 10.3 Consensus size: 29
24657 ATTTTTACCA
* * *
24667 TTAAAAATATATTTTATTTTTATATTAAT
1 TTAAAAATATATTTTATTCTTATCTTAAC
* *
24696 TTATTAAATATATTTTATTCTTGTCTTAAC
1 TTA-AAAATATATTTTATTCTTATCTTAAC
24726 TTAAAAATATATTTTATTCTTA-CTTTAAC
1 TTAAAAATATATTTTATTCTTATC-TTAAC
* *
24755 TTAAAAATATATTTTAGTCTTTATATTAAC
1 TTAAAAATATATTTTATTC-TTATCTTAAC
* * *
24785 TTAAAAAATATACATTATATTCTTAACTTAAA
1 TT-AAAAATAT--ATTTTATTCTTATCTTAAC
* * * *
24817 TTATTAAATATATTCTACTCTTATCTTAAA
1 TTA-AAAATATATTTTATTCTTATCTTAAC
* * * *
24847 TTATTAAATATAATTAATTCTTATTTTAAC
1 TTA-AAAATATATTTTATTCTTATCTTAAC
*
24877 TTAAAATATATCTTTTATTCTTATCTTAAC
1 TTAAAA-ATATATTTTATTCTTATCTTAAC
24907 TTAAAAATATA---T-TT-TTATCTTAAC
1 TTAAAAATATATTTTATTCTTATCTTAAC
* * * *
24931 TAAAAAATATATTATATTTTTATCTTAAA
1 TTAAAAATATATTTTATTCTTATCTTAAC
*
24960 TTTAAAATAT
1 TTAAAAATAT
24970 TATTATAATA
Statistics
Matches: 226, Mismatches: 34, Indels: 28
0.78 0.12 0.10
Matches are distributed among these distances:
24 20 0.09
25 2 0.01
26 1 0.00
27 1 0.00
28 3 0.01
29 66 0.29
30 102 0.45
31 9 0.04
32 15 0.07
33 7 0.03
ACGTcount: A:0.40, C:0.08, G:0.01, T:0.51
Consensus pattern (29 bp):
TTAAAAATATATTTTATTCTTATCTTAAC
Found at i:24940 original size:22 final size:24
Alignment explanation
Indices: 24892--24943 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
24882 ATATATCTTT
24892 TATTCTTATCTTAACTTAAAAATA
1 TATTCTTATCTTAACTTAAAAATA
* *
24916 TATTTTTATCTTAACTAAAAAATA
1 TATTCTTATCTTAACTTAAAAATA
24940 TATT
1 TATT
24944 ATATTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (24 bp):
TATTCTTATCTTAACTTAAAAATA
Found at i:24954 original size:53 final size:54
Alignment explanation
Indices: 24867--24969 Score: 136
Period size: 53 Copynumber: 1.9 Consensus size: 54
24857 TAATTAATTC
* * * * *
24867 TTATTTTAACTTAAAATATATCTTTTATTCTTATCTTAACTTAAAAATATATTT
1 TTATCTTAACTTAAAAAATATATTATATTCTTATCTTAAATTAAAAATATATTT
* *
24921 TTATCTTAAC-TAAAAAATATATTATATTTTTATCTTAAATTTAAAATAT
1 TTATCTTAACTTAAAAAATATATTATATTCTTATCTTAAATTAAAAATAT
24970 TATTATAATA
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
53 33 0.79
54 9 0.21
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (54 bp):
TTATCTTAACTTAAAAAATATATTATATTCTTATCTTAAATTAAAAATATATTT
Found at i:25025 original size:30 final size:30
Alignment explanation
Indices: 24990--25094 Score: 90
Period size: 30 Copynumber: 3.5 Consensus size: 30
24980 AAATGTAAAT
* *
24990 ATTTAAGTTAAGAATAAATTATATTTTTTA
1 ATTTAAGATAAGAATAAAGTATATTTTTTA
*
25020 ATTTAAGATAAGATTAAAGTATA-TTTTT-
1 ATTTAAGATAAGAATAAAGTATATTTTTTA
* * **
25048 ATGTTACA-AAAAGAATAAAATATATTTAATA
1 AT-TTA-AGATAAGAATAAAGTATATTTTTTA
* *
25079 AGTTAAGATAAAAATA
1 ATTTAAGATAAGAATA
25095 TATTTTTAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
28 2 0.03
29 22 0.37
30 34 0.58
31 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.09, T:0.40
Consensus pattern (30 bp):
ATTTAAGATAAGAATAAAGTATATTTTTTA
Found at i:25092 original size:25 final size:27
Alignment explanation
Indices: 25058--25129 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 27
25048 ATGTTACAAA
25058 AAGA-ATAAAATATATTTAATAA-GTT
1 AAGACATAAAATATATTTAATAATGTT
* *
25083 AAGATA-AAAATATATTT-TTAATGTT
1 AAGACATAAAATATATTTAATAATGTT
25108 AAGACATAAAAT-TGATTTAATA
1 AAGACATAAAATAT-ATTTAATA
25130 TGTGAATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
24 3 0.08
25 24 0.62
26 10 0.26
27 2 0.05
ACGTcount: A:0.53, C:0.01, G:0.08, T:0.38
Consensus pattern (27 bp):
AAGACATAAAATATATTTAATAATGTT
Found at i:26897 original size:8 final size:8
Alignment explanation
Indices: 26884--26923 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
26874 GACCCGAACC
26884 GACCCGTT
1 GACCCGTT
26892 GACCC---
1 GACCCGTT
26897 GACCCGTT
1 GACCCGTT
26905 GACCCGTT
1 GACCCGTT
26913 GA-CCGTT
1 GACCCGTT
26920 GACC
1 GACC
26924 GGAGTTGACC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
5 5 0.18
7 7 0.25
8 16 0.57
ACGTcount: A:0.15, C:0.40, G:0.25, T:0.20
Consensus pattern (8 bp):
GACCCGTT
Found at i:26900 original size:13 final size:13
Alignment explanation
Indices: 26882--26910 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
26872 CCGACCCGAA
26882 CCGACCCGTTGAC
1 CCGACCCGTTGAC
26895 CCGACCCGTTGAC
1 CCGACCCGTTGAC
26908 CCG
1 CCG
26911 TTGACCGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.48, G:0.24, T:0.14
Consensus pattern (13 bp):
CCGACCCGTTGAC
Found at i:28256 original size:18 final size:18
Alignment explanation
Indices: 28230--28270 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
28220 ATTGTTCGAA
* *
28230 AAGACTGAAGTAAATGAT
1 AAGATTGAAGTAAATAAT
*
28248 AAGATTGAATTAAATAAT
1 AAGATTGAAGTAAATAAT
28266 AAGAT
1 AAGAT
28271 CGGATGGAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.02, G:0.17, T:0.27
Consensus pattern (18 bp):
AAGATTGAAGTAAATAAT
Found at i:29459 original size:23 final size:24
Alignment explanation
Indices: 29421--29488 Score: 84
Period size: 23 Copynumber: 2.9 Consensus size: 24
29411 AATTCTGTTA
* *
29421 TGATACCTGACCTGGATTATGATC
1 TGATACTTGACATGGATTATGATC
*
29445 TGATA-TTGACATGGATTCTGATC
1 TGATACTTGACATGGATTATGATC
* *
29468 TGATACTTGACTTGAATTATG
1 TGATACTTGACATGGATTATG
29489 TTTTGATTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
23 20 0.54
24 17 0.46
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TGATACTTGACATGGATTATGATC
Found at i:29472 original size:47 final size:48
Alignment explanation
Indices: 29394--29488 Score: 111
Period size: 47 Copynumber: 2.0 Consensus size: 48
29384 TAAATATTTT
* * * *
29394 ATCTGATTTTCGACTTGAATTCTGTTATGATACCTGACCTGGATTATG
1 ATCTGATATTCGACATGAATTCTGATATGATACCTGACCTGAATTATG
* * * *
29442 ATCTGATATT-GACATGGATTCTGATCTGATACTTGACTTGAATTATG
1 ATCTGATATTCGACATGAATTCTGATATGATACCTGACCTGAATTATG
29489 TTTTGATTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
47 30 0.77
48 9 0.23
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (48 bp):
ATCTGATATTCGACATGAATTCTGATATGATACCTGACCTGAATTATG
Found at i:29495 original size:24 final size:24
Alignment explanation
Indices: 29405--29488 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
29395 TCTGATTTTC
* * * *
29405 GACTTGAATTCTGTTATGATACCT
1 GACTTGAATTATGATCTGATACTT
* *
29429 GACCTGGATTATGATCTGATA-TT
1 GACTTGAATTATGATCTGATACTT
* * *
29452 GACATGGATTCTGATCTGATACTT
1 GACTTGAATTATGATCTGATACTT
29476 GACTTGAATTATG
1 GACTTGAATTATG
29489 TTTTGATTTT
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
23 20 0.42
24 28 0.58
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.39
Consensus pattern (24 bp):
GACTTGAATTATGATCTGATACTT
Found at i:31620 original size:8 final size:8
Alignment explanation
Indices: 31607--31646 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
31597 GACCCGAACC
31607 GACCCGTT
1 GACCCGTT
31615 GACCC---
1 GACCCGTT
31620 GACCCGTT
1 GACCCGTT
31628 GACCCGTT
1 GACCCGTT
31636 GA-CCGTT
1 GACCCGTT
31643 GACC
1 GACC
31647 GGAGTTGACC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
5 5 0.18
7 7 0.25
8 16 0.57
ACGTcount: A:0.15, C:0.40, G:0.25, T:0.20
Consensus pattern (8 bp):
GACCCGTT
Found at i:31623 original size:13 final size:13
Alignment explanation
Indices: 31605--31633 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
31595 CCGACCCGAA
31605 CCGACCCGTTGAC
1 CCGACCCGTTGAC
31618 CCGACCCGTTGAC
1 CCGACCCGTTGAC
31631 CCG
1 CCG
31634 TTGACCGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.48, G:0.24, T:0.14
Consensus pattern (13 bp):
CCGACCCGTTGAC
Found at i:32976 original size:18 final size:18
Alignment explanation
Indices: 32950--32990 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
32940 ATTGTTCGAA
* *
32950 AAGACTGAAGTAAATGAT
1 AAGATTGAAGTAAATAAT
*
32968 AAGATTGAATTAAATAAT
1 AAGATTGAAGTAAATAAT
32986 AAGAT
1 AAGAT
32991 CGGATGGAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.02, G:0.17, T:0.27
Consensus pattern (18 bp):
AAGATTGAAGTAAATAAT
Found at i:34178 original size:23 final size:24
Alignment explanation
Indices: 34140--34207 Score: 84
Period size: 23 Copynumber: 2.9 Consensus size: 24
34130 AATTCTGTTA
* *
34140 TGATACCTGACCTGGATTATGATC
1 TGATACTTGACATGGATTATGATC
*
34164 TGATA-TTGACATGGATTCTGATC
1 TGATACTTGACATGGATTATGATC
* *
34187 TGATACTTGACTTGAATTATG
1 TGATACTTGACATGGATTATG
34208 TTTTGATTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
23 20 0.54
24 17 0.46
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TGATACTTGACATGGATTATGATC
Found at i:34191 original size:47 final size:48
Alignment explanation
Indices: 34113--34207 Score: 111
Period size: 47 Copynumber: 2.0 Consensus size: 48
34103 TAAATATTTT
* * * *
34113 ATCTGATTTTCGACTTGAATTCTGTTATGATACCTGACCTGGATTATG
1 ATCTGATATTCGACATGAATTCTGATATGATACCTGACCTGAATTATG
* * * *
34161 ATCTGATATT-GACATGGATTCTGATCTGATACTTGACTTGAATTATG
1 ATCTGATATTCGACATGAATTCTGATATGATACCTGACCTGAATTATG
34208 TTTTGATTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
47 30 0.77
48 9 0.23
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (48 bp):
ATCTGATATTCGACATGAATTCTGATATGATACCTGACCTGAATTATG
Found at i:34214 original size:24 final size:24
Alignment explanation
Indices: 34124--34207 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
34114 TCTGATTTTC
* * * *
34124 GACTTGAATTCTGTTATGATACCT
1 GACTTGAATTATGATCTGATACTT
* *
34148 GACCTGGATTATGATCTGATA-TT
1 GACTTGAATTATGATCTGATACTT
* * *
34171 GACATGGATTCTGATCTGATACTT
1 GACTTGAATTATGATCTGATACTT
34195 GACTTGAATTATG
1 GACTTGAATTATG
34208 TTTTGATTTT
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
23 20 0.42
24 28 0.58
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.39
Consensus pattern (24 bp):
GACTTGAATTATGATCTGATACTT
Found at i:37762 original size:15 final size:15
Alignment explanation
Indices: 37744--37773 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
37734 AAAACCATGT
37744 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
37759 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
37774 GAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:37780 original size:15 final size:15
Alignment explanation
Indices: 37747--37781 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
37737 ACCATGTTAG
* *
37747 ATAAAAAGGTAATAG
1 ATAAAAAGGTAAGAA
37762 ATAAAAAGGTAAGAA
1 ATAAAAAGGTAAGAA
37777 ATAAA
1 ATAAA
37782 TAAATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAAAGGTAAGAA
Found at i:37903 original size:13 final size:13
Alignment explanation
Indices: 37864--37919 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
37854 AGTAAGTAAT
37864 ATAAA-AAATAAA
1 ATAAAGAAATAAA
* *
37876 GAAAAAGAAAAAAA
1 -ATAAAGAAATAAA
*
37890 ATATAGAAATAAA
1 ATAAAGAAATAAA
* *
37903 ACAAATAAATAAA
1 ATAAAGAAATAAA
37916 ATAA
1 ATAA
37920 TAATAAAAAA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
13 27 0.82
14 6 0.18
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (13 bp):
ATAAAGAAATAAA
Found at i:37937 original size:29 final size:30
Alignment explanation
Indices: 37905--37975 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 30
37895 GAAATAAAAC
37905 AAATAA-ATA-AAAT-AATAATAAAAAAGTAA
1 AAATAATATAGAAATAAATAA-AAAAAA-TAA
*
37934 AAATAATATAGATATAAATAAAAAAAATAAA
1 AAATAATATAGAAATAAATAAAAAAAAT-AA
37965 AAAGTAATATA
1 AAA-TAATATA
37976 TATATATAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
29 6 0.17
30 4 0.11
31 14 0.39
32 12 0.33
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (30 bp):
AAATAATATAGAAATAAATAAAAAAAATAA
Found at i:37951 original size:49 final size:48
Alignment explanation
Indices: 37864--37973 Score: 136
Period size: 49 Copynumber: 2.3 Consensus size: 48
37854 AGTAAGTAAT
*
37864 ATAAAAAATAA-AGAAAAAGAAAAAAAATATAGAAATAAA-ACAAATAA
1 ATAAAAAATAATAGAAAAAGAAAAAAAATATAGAAATAAATA-AAAAAA
* *
37911 ATAAAATAATAATA-AAAAAGTAAAAATAATATAGATATAAATAAAAAAA
1 ATAAAA-AATAATAGAAAAAG-AAAAAAAATATAGAAATAAATAAAAAAA
37960 ATAAAAAAGTAATA
1 ATAAAAAA-TAATA
37974 TATATATATA
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
47 6 0.11
48 13 0.24
49 35 0.64
50 1 0.02
ACGTcount: A:0.75, C:0.01, G:0.05, T:0.18
Consensus pattern (48 bp):
ATAAAAAATAATAGAAAAAGAAAAAAAATATAGAAATAAATAAAAAAA
Found at i:37954 original size:32 final size:32
Alignment explanation
Indices: 37918--37981 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
37908 TAAATAAAAT
37918 AATAATAAAAAAGT-AAAAA-TAATATAGATATA
1 AATAA-AAAAAA-TAAAAAAGTAATATAGATATA
*
37950 AATAAAAAAAATAAAAAAGTAATATATATATA
1 AATAAAAAAAATAAAAAAGTAATATAGATATA
37982 TAAATTAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 1 0.03
31 11 0.38
32 17 0.59
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (32 bp):
AATAAAAAAAATAAAAAAGTAATATAGATATA
Found at i:37963 original size:9 final size:9
Alignment explanation
Indices: 37861--37967 Score: 63
Period size: 9 Copynumber: 11.0 Consensus size: 9
37851 AATAGTAAGT
*
37861 AATATAAAA
1 AATAAAAAA
37870 AATAAAGAAA
1 AATAAA-AAA
*
37880 AAGAAAAAA
1 AATAAAAAA
* *
37889 AAT-ATAGA
1 AATAAAAAA
*
37897 AATAAAACA
1 AATAAAAAA
37906 AATAAATAAAA
1 AAT-AA-AAAA
37917 TAATAATAAAA
1 -AATAA-AAAA
37928 AAGTAAAAATA
1 AA-TAAAAA-A
* *
37939 ATATAGATATA
1 A-ATA-AAAAA
37950 AATAAAAAA
1 AATAAAAAA
37959 AATAAAAAA
1 AATAAAAAA
37968 GTAATATATA
Statistics
Matches: 77, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
8 6 0.08
9 28 0.36
10 18 0.23
11 19 0.25
12 6 0.08
ACGTcount: A:0.77, C:0.01, G:0.05, T:0.18
Consensus pattern (9 bp):
AATAAAAAA
Found at i:37985 original size:30 final size:30
Alignment explanation
Indices: 37905--37985 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 30
37895 GAAATAAAAC
*
37905 AAATAA-ATAAAAT-AATAATAAAAAAGTAA
1 AAATAATATAATATAAATAA-AAAAAAGTAA
37934 AAATAATATAGATATAAATAAAAAAAA-TAAA
1 AAATAATATA-ATATAAATAAAAAAAAGT-AA
*
37965 AAAGTAATAT-ATATATATAAA
1 AAA-TAATATAATATAAATAAA
37986 TTAATAAAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
29 6 0.13
30 14 0.31
31 14 0.31
32 11 0.24
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.25
Consensus pattern (30 bp):
AAATAATATAATATAAATAAAAAAAAGTAA
Found at i:38042 original size:38 final size:38
Alignment explanation
Indices: 37905--38045 Score: 121
Period size: 38 Copynumber: 3.6 Consensus size: 38
37895 GAAATAAAAC
* *
37905 AAATAAATAAAATAATAATAAAAAAGTAA-AAATA-ATAT
1 AAATTAATAAAA-AA-AATAAAAAAGTAATATATATATAT
*
37943 AGATATAAATAAAAAAAATAAAAAAGTAATATATATATAT
1 A-A-ATTAATAAAAAAAATAAAAAAGTAATATATATATAT
*
37983 AAATTAATAAAACTGATAATAAAAAA-TAATATAT-T-TAT
1 AAATTAATAAAA---AAAATAAAAAAGTAATATATATATAT
38021 AAATATAATCTAAAAAAAATAAAAA
1 AAAT-TAA--TAAAAAAAATAAAAA
38046 TATATACTAA
Statistics
Matches: 89, Mismatches: 4, Indels: 20
0.79 0.04 0.18
Matches are distributed among these distances:
38 39 0.44
39 12 0.13
40 23 0.26
41 15 0.17
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (38 bp):
AAATTAATAAAAAAAATAAAAAAGTAATATATATATAT
Found at i:38095 original size:22 final size:21
Alignment explanation
Indices: 38041--38101 Score: 54
Period size: 23 Copynumber: 2.8 Consensus size: 21
38031 TAAAAAAAAT
38041 AAAAATATATAC-T-AAAGTAA
1 AAAAATAT-TACATAAAAGTAA
* *
38061 AAAAGAAAATACATAAAATGTAA
1 AAAA-ATATTACATAAAA-GTAA
38084 AAAAATATTACATGAAAA
1 AAAAATATTACAT-AAAA
38102 AAAGAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
20 7 0.22
21 3 0.09
22 10 0.31
23 12 0.38
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (21 bp):
AAAAATATTACATAAAAGTAA
Found at i:38475 original size:34 final size:34
Alignment explanation
Indices: 38421--38489 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
38411 GAATCCTAGC
38421 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
* * *
38455 AAAATTTTATCCTATTTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
38489 A
1 A
38490 GTAGGACAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (34 bp):
AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
Found at i:39250 original size:106 final size:104
Alignment explanation
Indices: 38951--39844 Score: 861
Period size: 105 Copynumber: 8.5 Consensus size: 104
38941 AATATTGTTC
* * * * *
38951 CGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAAT-TGAAAATGTTTGTTGACA
** * * * *
39016 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
64 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * *
39057 CGAGTCTAATATCCTTCGCTGTGAAGATGAAATTGACTCTG-AA-CG-AAAT-CTTGTTGACAAT
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAAAATGTTTGTTGACAAC
39118 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
39157 CGAGTCCAATATCCTTCACTGCGAAGTTGAAATTGGCTCTGAAATTTGAAAAATGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA-TTG-AAAATGTTTGTTGACA
39222 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
64 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * ** * *
39263 CGAGTGGCACGATATCCTCCG-TCGTGGAGTT-AAAATCGCGGATGAAACTGAAAAGTTGTTCGT
1 CGAGT--C-CAATATCCTTCGCT-GTGAAGTTGAAATTGGC-TCTGAAATTGAAAA--TGTTTGT
*
39326 TGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
59 TGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * *
39372 CGGGTAGCACGATATCC-TCTGTCATG-G-AGTTGAAATCGGCTCTGGAATTGGGAAATTGTTTG
1 CGAGT--C-CAATATCCTTC-G-C-TGTGAAGTTGAAATTGGCTCTGAAATT--GAAAATGTTTG
*
39434 TTGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
58 TTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * **
39481 CGAGTCCAATATCCTTCGCTGTGAAGTTGAGATTGGCTCCGAAA-T-----TGCTTGTCGACAGT
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAAAATGTTTGTTGACAAC
* * * *
39540 CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
66 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * *
39579 TGGGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGAAACTAGGAAAT-TATTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA-TTGAAAATGT-TTGTTGACA
39643 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
64 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* ** * *
39684 GGAGTCCAATATCCTTCATTATGAAGTTGAAATTGGCTCTGAAATTGAGAA-GTTGTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAAAATG-T-TTGTTGACA
** * * * * *
39748 GGCAGCGGTCCCTTCGTCGTGAAGTTTAATTTGCGTTGTCT
64 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
39789 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-GTTTG
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAAAATGTTTG
39845 GCTTCGAGCT
Statistics
Matches: 659, Mismatches: 96, Indels: 69
0.80 0.12 0.08
Matches are distributed among these distances:
98 84 0.13
100 81 0.12
101 5 0.01
102 1 0.00
103 4 0.01
104 8 0.01
105 183 0.28
106 113 0.17
107 7 0.01
108 11 0.02
109 150 0.23
110 6 0.01
111 5 0.01
112 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (104 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAAAATGTTTGTTGACAAC
CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:39484 original size:218 final size:206
Alignment explanation
Indices: 38951--39835 Score: 748
Period size: 206 Copynumber: 4.2 Consensus size: 206
38941 AATATTGTTC
* * * * *
38951 CGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCACTGCGAAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACA
** * * * *
39016 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCTAATATCCTTCGCTGTGA
66 ACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTCCGCTGTGA
* * ** *
39081 AGATGAAATTGACTCTGAACGAAATCTTGTTGACAATCAGCCGTCCCTTCGTTGTGAAGTTGAAC
131 AGATAAAATCGACGATGAACGAAATCTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAAC
39146 TTGTGTTGTCT
196 TTGTGTTGTCT
* * * *
39157 CGAGTCCAATATCCTTCACTGCGAAGTTGAAATTGGCTCTGAAATTTGAAAAATGTTTGTTGACA
1 CGAGTCCAATATCCTTCACTGCGAAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACA
*
39222 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGC-ACGATATCCTCCG-T
66 ACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGT--CTA--ATATCCTCCGCT
* * * *
39285 CGTGGAGTTAAAATCG-CGGATGAAACTGAAAAGTTGTTCGTTGACAACCAGTCGTCCCTTCGTT
127 -GTGAAGATAAAATCGAC-GATG-AAC-G-AAA--TCTT-GTTGACAACCAGCCGTCCCTTCGTT
39349 GTGAAGTTGAACTTGTGTTGTCT
184 GTGAAGTTGAACTTGTGTTGTCT
* * *
39372 CGGGTAGCACGATATCCTCTGTCA-TG-G-AGTTGAAATCGGCTCTGGAATTGGGAAATTGTTTG
1 CGAGT--C-CAATAT-C-CT-TCACTGCGAAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTG
* *
39434 TTGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCG
60 TTGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTCCG
* * * * * * * ** * *
39499 CTGTGAAGTTGAGATTG--GCT--CCGAAATTGCTTGTCGACAGTCAGCCGCCCCTTCGCTGTGA
125 CTGTGAAGATAAAATCGACGATGAACGAAA-T-CTTGTTGACAACCAGCCGTCCCTTCGTTGTGA
* *
39560 AGTTGAGCTTGTGCTGTCT
188 AGTTGAACTTGTGTTGTCT
* * * * * * * * * *
39579 TGGGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGAAACTAGGAAATT-ATTGTTGACA
1 CGAGTCCAATATCCTTCACTGCGAAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACA
* * * * ** *
39643 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCATTATGA
66 ACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTCCGCTGTGA
* * * * ** * * ** * *
39708 AGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGCAGCGGTCCCTTCGTCGTGAAGT
131 AGATAAAATCGACGATG-AA-CGA-AA--TCTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGT
* * *
39773 TTAATTTGCGTTGTCT
191 TGAACTTGTGTTGTCT
* ** * *
39789 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTG
1 CGAGTCCAATATCCTTCACTGCGAAGTTGAAATTGGCTCTGGAATTG
39836 AGAAGTTTGG
Statistics
Matches: 560, Mismatches: 87, Indels: 60
0.79 0.12 0.08
Matches are distributed among these distances:
201 2 0.00
202 4 0.01
203 81 0.14
204 29 0.05
205 3 0.01
206 96 0.17
207 47 0.08
208 8 0.01
209 25 0.04
210 85 0.15
211 3 0.01
212 3 0.01
213 2 0.00
214 3 0.01
215 70 0.12
216 2 0.00
217 2 0.00
218 86 0.15
219 2 0.00
220 4 0.01
221 3 0.01
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (206 bp):
CGAGTCCAATATCCTTCACTGCGAAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTCCGCTGTGA
AGATAAAATCGACGATGAACGAAATCTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAAC
TTGTGTTGTCT
Found at i:40340 original size:36 final size:36
Alignment explanation
Indices: 40300--40369 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
40290 AAGATATTTG
** * *
40300 TTGTTTCAAGGGAAACGGTCTTAAGGGAGATAAATT
1 TTGTTTCAAGAAAAACGGTCTCAAGAGAGATAAATT
* *
40336 TTGTTTTAAGAAAAACTGTCTCAAGAGAGATAAA
1 TTGTTTCAAGAAAAACGGTCTCAAGAGAGATAAA
40370 ACTTAGTTCC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.30
Consensus pattern (36 bp):
TTGTTTCAAGAAAAACGGTCTCAAGAGAGATAAATT
Found at i:40526 original size:103 final size:103
Alignment explanation
Indices: 40343--40570 Score: 248
Period size: 103 Copynumber: 2.2 Consensus size: 103
40333 ATTTTGTTTT
* * * *
40343 AAGA-AAAACTGTCTCAAGAGAGATAAAACTTAGTTCCAAAAGAAATTGTCTCACGGGGAGATGA
1 AAGAGAAAACTGTCTCAAGAGAGATAAAACTTAGTTCCAAAAGAAACTGTCTCACAGAGAGACGA
40407 AATTAGTTCCAAGGAAACATATTCAAAGATGATGCTTC
66 AATTAGTTCCAAGGAAACATATTCAAAGATGATGCTTC
* * * * *
40445 AAGAGAAAACTGTCTCAAGGGAGATAAAATTTTGTTTCAAGAGAAACTGTCTCA-AGAGAGACGA
1 AAGAGAAAACTGTCTCAAGAGAGATAAAACTTAGTTCCAAAAGAAACTGTCTCACAGAGAGACGA
* ** * * * * *
40509 AATTCA-TTTCAAGGGAAATGTTTTCAATGTTTATGTTTC
66 AATT-AGTTCCAA-GGAAACATATTCAAAGATGATGCTTC
*
40548 AAGAG-AAACTATCTCAAGAGAGA
1 AAGAGAAAACTGTCTCAAGAGAGA
40571 CGAAATTCAT
Statistics
Matches: 104, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
102 36 0.35
103 68 0.65
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (103 bp):
AAGAGAAAACTGTCTCAAGAGAGATAAAACTTAGTTCCAAAAGAAACTGTCTCACAGAGAGACGA
AATTAGTTCCAAGGAAACATATTCAAAGATGATGCTTC
Found at i:40581 original size:65 final size:65
Alignment explanation
Indices: 40473--40642 Score: 297
Period size: 65 Copynumber: 2.6 Consensus size: 65
40463 GGGAGATAAA
40473 ATTT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAAT
1 ATTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAAT
* *
40537 GTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAAT
1 ATTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAAT
* *
40602 ATTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 ATTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATT
40643 TTGTTTCGAG
Statistics
Matches: 99, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
64 3 0.03
65 96 0.97
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (65 bp):
ATTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAAT
Found at i:40643 original size:167 final size:169
Alignment explanation
Indices: 40442--40759 Score: 523
Period size: 167 Copynumber: 1.9 Consensus size: 169
40432 AAGATGATGC
* *
40442 TTCAAGAGAAAACTGTCTCAAGGGAGATAAAATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC
1 TTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
* *
40507 GAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
66 AAAATTAATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
*
40572 GAAA-TTCATTTCAAGGGAAATGTTTTCAATATTTATGT
131 AAAATTTCATTTCAAGGGAAATGTTTTCAATATTTATGT
* *
40610 TTCAAGAG-AAACTGTCTCAAGGGAGACAAAATTTTGTTTCGAGGGAAACTATCTCAAGAGAGAC
1 TTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
* *
40674 AAAATTAATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAC
66 AAAATTAATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
**
40739 AAAATTTTGTTTCAAGGGAAA
131 AAAATTTCATTTCAAGGGAAA
40760 CTATCTCAAG
Statistics
Matches: 138, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
167 116 0.84
168 22 0.16
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (169 bp):
TTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
AAAATTAATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
AAAATTTCATTTCAAGGGAAATGTTTTCAATATTTATGT
Found at i:40648 original size:102 final size:102
Alignment explanation
Indices: 40542--41274 Score: 1323
Period size: 102 Copynumber: 7.2 Consensus size: 102
40532 TCAATGTTTA
* * *
40542 TGTTTCAAGAGAAACTATCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATATTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
40607 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* *
40644 TGTTTCGAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
40709 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
40746 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
40811 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
40848 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
40913 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
40950 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
41015 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
41052 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
41117 TGTTTCAAGAGAAACTGTCTCAATGGAGACAGAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* *
41154 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTCATTTAAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
41219 TGTTTCAAGAGAAACTGTCTCAAGGGAGAC-AAA---
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
41252 -GTTTCAAGGGAAACTGTCTCAAG
1 TGTTTCAAGGGAAACTATCTCAAG
41275 GGAAACTGTC
Statistics
Matches: 613, Mismatches: 18, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
97 22 0.04
101 2 0.00
102 589 0.96
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (102 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:41241 original size:15 final size:15
Alignment explanation
Indices: 41223--41292 Score: 70
Period size: 15 Copynumber: 4.5 Consensus size: 15
41213 TGTTTATGTT
41223 TCAAGAGAAACTGTC
1 TCAAGAGAAACTGTC
* *
41238 TCAAGGGAGACAA-AGTT
1 TCAA--GAGA-AACTGTC
*
41255 TCAAGGGAAACTGTC
1 TCAAGAGAAACTGTC
*
41270 TCAAGGGAAACTGTC
1 TCAAGAGAAACTGTC
41285 TCAAGAGA
1 TCAAGAGA
41293 GACAATAGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
14 2 0.04
15 31 0.69
17 10 0.22
18 2 0.04
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.19
Consensus pattern (15 bp):
TCAAGAGAAACTGTC
Found at i:42192 original size:22 final size:22
Alignment explanation
Indices: 42167--42217 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
42157 TTGTGTTTGG
42167 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
42189 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
42211 TCAAAGG
1 TCAAAGG
42218 ATTGATGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:45865 original size:14 final size:15
Alignment explanation
Indices: 45840--45868 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
45830 AAAACCATGT
45840 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
45855 TAGAT-AAAAGGTAA
1 TAGATAAAAAGGTAA
45869 GAAATAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:45920 original size:31 final size:29
Alignment explanation
Indices: 45883--45944 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 29
45873 TAAATTAATT
45883 AATTAAATTAAA-ATAAAATAAAGAGAAAACA
1 AATTAAA-TAAAGATAAAAT-AA-AGAAAACA
*
45914 AATTAAATAAAGATAAGATAAAGAAAACA
1 AATTAAATAAAGATAAAATAAAGAAAACA
45943 AA
1 AA
45945 GATAAAATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 10 0.34
30 6 0.21
31 13 0.45
ACGTcount: A:0.71, C:0.03, G:0.08, T:0.18
Consensus pattern (29 bp):
AATTAAATAAAGATAAAATAAAGAAAACA
Found at i:46052 original size:38 final size:39
Alignment explanation
Indices: 46010--46142 Score: 127
Period size: 38 Copynumber: 3.5 Consensus size: 39
46000 TAAAACAAAT
46010 AAATAAAATAATAATAAAAAGTAAAAATA-ATATATATA
1 AAATAAAATAATAATAAAAAGTAAAAATATATATATATA
*
46048 AAATAAAA-AA-AATAAAAAAGTAAATATATATATATATA
1 AAATAAAATAATAAT-AAAAAGTAAAAATATATATATATA
* * *
46086 ATTAATAAAACTGATAATAAAAA-T-AATATATTTATATATA
1 A--AATAAAA-TAATAATAAAAAGTAAAAATATATATATATA
**
46126 ATCTAAAA-AA-AATAAAA
1 AAATAAAATAATAATAAAA
46143 TATATACTAA
Statistics
Matches: 82, Mismatches: 6, Indels: 17
0.78 0.06 0.16
Matches are distributed among these distances:
35 7 0.09
36 4 0.05
37 15 0.18
38 23 0.28
40 23 0.28
41 1 0.01
42 6 0.07
43 3 0.04
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (39 bp):
AAATAAAATAATAATAAAAAGTAAAAATATATATATATA
Found at i:46052 original size:42 final size:40
Alignment explanation
Indices: 46006--46126 Score: 117
Period size: 42 Copynumber: 3.0 Consensus size: 40
45996 GAAATAAAAC
46006 AAATAAATAAAATAATAATAAAAAGTAAAAATAATATATATA
1 AAAT-AATAAAATAATAATAAAAAGTAAAAAT-ATATATATA
*
46048 AAATAA-AAAA-AAT-A-AAAAAGTAAATATATATATATA
1 AAATAATAAAATAATAATAAAAAGTAAAAATATATATATA
* * * *
46084 TAATTAATAAAACTGATAATAAAAA-TAATATATTTATATATA
1 -AAATAATAAAA-TAATAATAAAAAGTAA-AAATATATATATA
46126 A
1 A
46127 TCTAAAAAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
36 9 0.13
37 17 0.25
38 5 0.07
39 3 0.04
40 6 0.09
41 7 0.10
42 21 0.31
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (40 bp):
AAATAATAAAATAATAATAAAAAGTAAAAATATATATATA
Found at i:46079 original size:36 final size:37
Alignment explanation
Indices: 46010--46142 Score: 119
Period size: 37 Copynumber: 3.5 Consensus size: 37
46000 TAAAACAAAT
*
46010 AAATAAAATAATAAT-AAAAAGTAAAAATAATATATATA
1 AAATAAAA-AATAATAAAAAAGTAAATAT-ATATATATA
46048 AAATAAAAAA-AATAAAAAAGTAAATATATATATATA
1 AAATAAAAAATAATAAAAAAGTAAATATATATATATA
* * * *
46084 TAATTAATAAAACTGATAATAAAAATAATATATTTATATATA
1 -AAATAA-AAAA-TAATAA-AAAAGTAA-ATATATATATATA
**
46126 ATCTAAAAAA-AATAAAA
1 AAATAAAAAATAATAAAA
46143 TATATACTAA
Statistics
Matches: 80, Mismatches: 8, Indels: 15
0.78 0.08 0.15
Matches are distributed among these distances:
36 12 0.15
37 21 0.26
38 16 0.20
40 8 0.10
41 11 0.14
42 12 0.15
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (37 bp):
AAATAAAAAATAATAAAAAAGTAAATATATATATATA
Found at i:46554 original size:32 final size:34
Alignment explanation
Indices: 46513--46579 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
46503 GAATCCTAGC
46513 AAAATTCTAT-C-ATCTTTAGGAGTTTGAATCCT
1 AAAATTCTATCCTATCTTTAGGAGTTTGAATCCT
*
46545 AAAATTCTATCCTATTTTTAGGAGTTTGAATCCT
1 AAAATTCTATCCTATCTTTAGGAGTTTGAATCCT
46579 A
1 A
46580 GTAGGACGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 10 0.31
33 1 0.03
34 21 0.66
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (34 bp):
AAAATTCTATCCTATCTTTAGGAGTTTGAATCCT
Found at i:47805 original size:23 final size:22
Alignment explanation
Indices: 47772--47820 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
47762 AAGGAAAAAT
*
47772 AAAATAAAATAAAAAAAAAGAAC
1 AAAATAAAAT-AAAAAAAAGAAA
*
47795 AAAATAGAATAAAAAAAAGAAA
1 AAAATAAAATAAAAAAAAGAAA
47817 AAAA
1 AAAA
47821 AAGGAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.84, C:0.02, G:0.06, T:0.08
Consensus pattern (22 bp):
AAAATAAAATAAAAAAAAGAAA
Found at i:47821 original size:23 final size:22
Alignment explanation
Indices: 47766--47821 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
47756 AAAATCAAGG
*
47766 AAAAATAAAATAAAATAAAAAA
1 AAAAAAAAAATAAAATAAAAAA
* *
47788 AAAGAACAAAATAGAATAAAAAA
1 AAA-AAAAAAATAAAATAAAAAA
47811 AAGAAAAAAAA
1 AA-AAAAAAAA
47822 AGGAAAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.10
23 25 0.86
24 1 0.03
ACGTcount: A:0.84, C:0.02, G:0.05, T:0.09
Consensus pattern (22 bp):
AAAAAAAAAATAAAATAAAAAA
Found at i:47822 original size:10 final size:10
Alignment explanation
Indices: 47766--47828 Score: 54
Period size: 10 Copynumber: 6.0 Consensus size: 10
47756 AAAATCAAGG
*
47766 AAAAATAAAA
1 AAAAAGAAAA
* *
47776 TAAAATAAAA
1 AAAAAGAAAA
*
47786 AAAAAGAACA
1 AAAAAGAAAA
*
47796 AAATAGAATAAA
1 AAAAAG-A-AAA
47808 AAAAAGAAAA
1 AAAAAGAAAA
47818 AAAAAGGAAAA
1 AAAAA-GAAAA
47829 TTGGGTTGCC
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
10 29 0.67
11 7 0.16
12 7 0.16
ACGTcount: A:0.83, C:0.02, G:0.08, T:0.08
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:52726 original size:20 final size:20
Alignment explanation
Indices: 52671--52726 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
52661 GATACTGACC
**
52671 CTTTA-GTATCGATACATAA
1 CTTTAGGTATCGATACCCAA
* *
52690 CCTTGGGTATCGATACCCAA
1 CTTTAGGTATCGATACCCAA
52710 CTTTAGGTATCGATACC
1 CTTTAGGTATCGATACC
52727 GACTTACTGA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 3 0.10
20 27 0.90
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (20 bp):
CTTTAGGTATCGATACCCAA
Found at i:57275 original size:29 final size:29
Alignment explanation
Indices: 57232--57349 Score: 143
Period size: 29 Copynumber: 4.1 Consensus size: 29
57222 CCTTGAGTTC
*
57232 TCAGTAATGTTCATGGGCTTAT-AAAGATA
1 TCAGTAATGTACAT-GGCTTATAAAAGATA
* *
57261 TCAGTACTGTACATGTC-TAT-AAAGATA
1 TCAGTAATGTACATGGCTTATAAAAGATA
57288 TCAGTAATGTACATGGCTTATAAAAGATA
1 TCAGTAATGTACATGGCTTATAAAAGATA
** *
57317 TCAGTACCGTACATGGGCCTATAAAAGATA
1 TCAGTAATGTACAT-GGCTTATAAAAGATA
57347 TCA
1 TCA
57350 AAATACATGG
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
27 25 0.32
28 5 0.06
29 31 0.40
30 17 0.22
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (29 bp):
TCAGTAATGTACATGGCTTATAAAAGATA
Found at i:57287 original size:27 final size:28
Alignment explanation
Indices: 57254--57349 Score: 122
Period size: 27 Copynumber: 3.4 Consensus size: 28
57244 ATGGGCTTAT
*
57254 AAAGATATCAGTACTGTACATGTCTAT-
1 AAAGATATCAGTACTGTACATGCCTATA
* *
57281 AAAGATATCAGTAATGTACATGGCTTATA
1 AAAGATATCAGTACTGTACAT-GCCTATA
*
57310 AAAGATATCAGTACCGTACATGGGCCTATA
1 AAAGATATCAGTACTGTACAT--GCCTATA
57340 AAAGATATCA
1 AAAGATATCA
57350 AAATACATGG
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
27 20 0.33
28 4 0.07
29 19 0.32
30 17 0.28
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.28
Consensus pattern (28 bp):
AAAGATATCAGTACTGTACATGCCTATA
Found at i:57303 original size:56 final size:58
Alignment explanation
Indices: 57232--57349 Score: 170
Period size: 56 Copynumber: 2.1 Consensus size: 58
57222 CCTTGAGTTC
* * *
57232 TCAGTAATGTTCATGGGCTTAT-AAAGATATCAGTACTGTACAT-GTCTAT-AAAGATA
1 TCAGTAATGTACAT-GGCTTATAAAAGATATCAGTACCGTACATGGCCTATAAAAGATA
57288 TCAGTAATGTACATGGCTTATAAAAGATATCAGTACCGTACATGGGCCTATAAAAGATA
1 TCAGTAATGTACATGGCTTATAAAAGATATCAGTACCGTACAT-GGCCTATAAAAGATA
57347 TCA
1 TCA
57350 AAATACATGG
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
55 7 0.13
56 33 0.60
58 5 0.09
59 10 0.18
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (58 bp):
TCAGTAATGTACATGGCTTATAAAAGATATCAGTACCGTACATGGCCTATAAAAGATA
Found at i:58425 original size:18 final size:18
Alignment explanation
Indices: 58402--58446 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
58392 TTTTTTGCAT
58402 TTCCTTAGTTTCAAAATC
1 TTCCTTAGTTTCAAAATC
58420 TTCCTTAGTTTCAAAATC
1 TTCCTTAGTTTCAAAATC
58438 TTCCTTAGT
1 TTCCTTAGT
58447 GTGTTGATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.24, C:0.22, G:0.07, T:0.47
Consensus pattern (18 bp):
TTCCTTAGTTTCAAAATC
Found at i:60637 original size:15 final size:16
Alignment explanation
Indices: 60614--60649 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
60604 AAAATTATAT
*
60614 ATATGGTTTTTAAAA-
1 ATATAGTTTTTAAAAC
60629 ATATAGTTTTTAAAAC
1 ATATAGTTTTTAAAAC
60645 ATATA
1 ATATA
60650 ATATATAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (16 bp):
ATATAGTTTTTAAAAC
Found at i:60728 original size:20 final size:20
Alignment explanation
Indices: 60694--60793 Score: 86
Period size: 20 Copynumber: 5.3 Consensus size: 20
60684 AAACATATAT
*
60694 AATATA-TATAATTTTTGAA
1 AATATATTATAGTTTTTGAA
60713 AATATATTATAGTTTTTGAA
1 AATATATTATAGTTTTTGAA
* * *
60733 AACATATTACAGTGTTTG--
1 AATATATTATAGTTTTTGAA
* *
60751 -ATA-A-CATAATTTTTGAA
1 AATATATTATAGTTTTTGAA
* *
60768 AATATATTAGAGTTTTTGGA
1 AATATATTATAGTTTTTGAA
60788 AATATA
1 AATATA
60794 ATGTATGTTA
Statistics
Matches: 62, Mismatches: 13, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
15 7 0.11
16 1 0.02
17 2 0.03
18 3 0.05
19 7 0.11
20 42 0.68
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (20 bp):
AATATATTATAGTTTTTGAA
Found at i:60795 original size:35 final size:35
Alignment explanation
Indices: 60720--60795 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 35
60710 GAAAATATAT
*
60720 TATAGTTTTTGAAAACATATTACAGTGTTTGATAA
1 TATAATTTTTGAAAACATATTACAGTGTTTGATAA
* * * *
60755 CATAATTTTTGAAAATATATTAGAGTTTTTGGA-AA
1 TATAATTTTTGAAAACATATTACAGTGTTT-GATAA
60790 TATAAT
1 TATAAT
60796 GTATGTTATA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
35 32 0.94
36 2 0.06
ACGTcount: A:0.39, C:0.04, G:0.13, T:0.43
Consensus pattern (35 bp):
TATAATTTTTGAAAACATATTACAGTGTTTGATAA
Done.