Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001059.1 Hibiscus syriacus cultivar Beakdansim tig00002094_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: 71674
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:4821 original size:2 final size:2
Alignment explanation
Indices: 4814--4887 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
4804 GTCCATAAAC
4814 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4856 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4888 TACTTAAAAA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6070 original size:7 final size:7
Alignment explanation
Indices: 6047--6085 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
6037 TATATATATA
6047 TATTTTT
1 TATTTTT
*
6054 T-TTTTC
1 TATTTTT
6060 TATTTTT
1 TATTTTT
6067 TATTTTTT
1 TA-TTTTT
6075 TATTTTT
1 TATTTTT
6082 TATT
1 TATT
6086 GTTATTCCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 5 0.18
7 16 0.57
8 7 0.25
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.85
Consensus pattern (7 bp):
TATTTTT
Found at i:6072 original size:15 final size:15
Alignment explanation
Indices: 6049--6085 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
6039 TATATATATA
6049 TTTTT-TTTTTCTAT
1 TTTTTATTTTTCTAT
*
6063 TTTTTATTTTTTTAT
1 TTTTTATTTTTCTAT
6078 TTTTTATT
1 TTTTTATT
6086 GTTATTCCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTTATTTTTCTAT
Found at i:6248 original size:16 final size:15
Alignment explanation
Indices: 6211--6248 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
6201 TTTTATTTAT
6211 TTATTTTATTTTTCC
1 TTATTTTATTTTTCC
*
6226 TTATTTTATTTTTTC
1 TTATTTTATTTTTCC
6241 TTACTTTT
1 TTA-TTTT
6249 TGTTTTTAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (15 bp):
TTATTTTATTTTTCC
Found at i:6354 original size:4 final size:4
Alignment explanation
Indices: 6341--6376 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
6331 TATTATTATT
6341 TTTA -TTA TTTA -TT- TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
6377 TGGTTATCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 7 0.24
4 22 0.76
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:6354 original size:13 final size:13
Alignment explanation
Indices: 6329--6368 Score: 64
Period size: 14 Copynumber: 3.1 Consensus size: 13
6319 ATGTCAGCAG
6329 TTTATTA-TTATT
1 TTTATTATTTATT
6341 TTTATTATTTATT
1 TTTATTATTTATT
6354 TTTATTTATTTATT
1 TTTA-TTATTTATT
6368 T
1 T
6369 ATTTATTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 7 0.27
13 9 0.35
14 10 0.38
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTATTATTTATT
Found at i:6358 original size:22 final size:22
Alignment explanation
Indices: 6329--6376 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
6319 ATGTCAGCAG
* *
6329 TTTATTATTATTTTTATTATTTA
1 TTTATTTTTATTTAT-TTATTTA
6352 TTT-TTATTTATTTATTTATTTA
1 TTTATT-TTTATTTATTTATTTA
6374 TTT
1 TTT
6377 TGGTTATCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTATTTTTATTTATTTATTTA
Found at i:6377 original size:22 final size:23
Alignment explanation
Indices: 6335--6377 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
6325 GCAGTTTATT
*
6335 ATTATTTTTATTATTTATTTTTA
1 ATTATTTATATTATTTATTTTTA
*
6358 TTTATTTAT-TTATTTATTTT
1 ATTATTTATATTATTTATTTT
6378 GGTTATCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (23 bp):
ATTATTTATATTATTTATTTTTA
Found at i:16207 original size:2 final size:2
Alignment explanation
Indices: 16196--16227 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
16186 GTCCATACAC
16196 AT AT -T AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16228 TTTTTACTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:17316 original size:18 final size:21
Alignment explanation
Indices: 17295--17333 Score: 57
Period size: 18 Copynumber: 2.0 Consensus size: 21
17285 CTTATTTTTA
17295 TTTATT-TAA-ATAT-TATAT
1 TTTATTATAATATATATATAT
17313 TTTATTATAATATATATATAT
1 TTTATTATAATATATATATAT
17334 ATTCTTTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 3 0.17
20 4 0.22
21 5 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTATTATAATATATATATAT
Found at i:17348 original size:61 final size:61
Alignment explanation
Indices: 17282--17415 Score: 141
Period size: 61 Copynumber: 2.2 Consensus size: 61
17272 AATTTCTTTT
* *
17282 TTTCTTATTTTTATTT-ATTTAAATATTAT-ATTTTA-TTATAATATATATATATATTCTTTCC
1 TTTCTTATTTTTATTTAATTTAAATA-TATCATTTTACAT-TAATATATATATATATT-TTTAC
* ** * *
17343 TTTCTTA-CTTTATTTAATTTATTTATATCATTTTACATTAATATTTATATATATTTTTAG
1 TTTCTTATTTTTATTTAATTTAAATATATCATTTTACATTAATATATATATATATTTTTAC
17403 TTTCTTACTTTTT
1 TTTCTTA-TTTTT
17416 TCTTTTGTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
60 20 0.33
61 36 0.60
62 4 0.07
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.63
Consensus pattern (61 bp):
TTTCTTATTTTTATTTAATTTAAATATATCATTTTACATTAATATATATATATATTTTTAC
Found at i:18221 original size:22 final size:22
Alignment explanation
Indices: 18180--18246 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
18170 CTCGTATAAA
18180 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
18203 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
* *
18225 TGCACCGTAGTGTCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
18247 GATGTCCATA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
22 30 0.71
23 12 0.29
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.21
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:19960 original size:21 final size:21
Alignment explanation
Indices: 19936--19980 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
19926 TCTTGTTCGT
* *
19936 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
19957 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
19978 TTG
1 TTG
19981 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:23157 original size:22 final size:22
Alignment explanation
Indices: 23116--23182 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
23106 CTCGTATAAA
23116 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
23139 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
23161 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
23183 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:24896 original size:21 final size:21
Alignment explanation
Indices: 24872--24916 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
24862 TCTTGTTCGT
24872 TTGAAGGGGTATCAG-TTCCCC
1 TTGAAGGGGTA-CAGATTCCCC
* *
24893 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACAGATTCCCC
24914 TTG
1 TTG
24917 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACAGATTCCCC
Found at i:25729 original size:24 final size:25
Alignment explanation
Indices: 25702--25753 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
25692 ATTTGTTTGG
25702 TTTCCGGATTTTATTTATTTTA-TT
1 TTTCCGGATTTTATTTATTTTACTT
** *
25726 TTTCCTTATTTTATTTTTTTTACTT
1 TTTCCGGATTTTATTTATTTTACTT
25751 TTT
1 TTT
25754 GTTTTTAGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.13, C:0.10, G:0.04, T:0.73
Consensus pattern (25 bp):
TTTCCGGATTTTATTTATTTTACTT
Found at i:25752 original size:15 final size:14
Alignment explanation
Indices: 25709--25752 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
25699 TGGTTTCCGG
*
25709 ATTTTATTTATTTT
1 ATTTTTTTTATTTT
*
25723 ATTTTTCCTTATTTT
1 ATTTTT-TTTATTTT
25738 ATTTTTTTTACTTTT
1 ATTTTTTTTA-TTTT
25753 TGTTTTTAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (14 bp):
ATTTTTTTTATTTT
Found at i:27926 original size:28 final size:28
Alignment explanation
Indices: 27894--27952 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
27884 ACATATTTAA
27894 AAGT-AATCAATAAAACAAATATAGTAGC
1 AAGTAAAT-AATAAAACAAATATAGTAGC
* *
27922 AAGTAAATAATAAAACAGATATATTAGC
1 AAGTAAATAATAAAACAAATATAGTAGC
27950 AAG
1 AAG
27953 GAAAGATACA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 25 0.89
29 3 0.11
ACGTcount: A:0.58, C:0.08, G:0.12, T:0.22
Consensus pattern (28 bp):
AAGTAAATAATAAAACAAATATAGTAGC
Found at i:30690 original size:31 final size:31
Alignment explanation
Indices: 30643--30701 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
30633 GCTAAATAGT
* *
30643 AAATACATAAATTTAAAGGACCAAAAAAAAC
1 AAATACAGAAACTTAAAGGACCAAAAAAAAC
30674 AAATACAGAAACTTAAAGGACCAAAAAA
1 AAATACAGAAACTTAAAGGACCAAAAAA
30702 CAAAAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.64, C:0.14, G:0.08, T:0.14
Consensus pattern (31 bp):
AAATACAGAAACTTAAAGGACCAAAAAAAAC
Found at i:30718 original size:29 final size:29
Alignment explanation
Indices: 30651--30728 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 29
30641 GTAAATACAT
*
30651 AAATTTAAAGGACCAAAAAAAACAAATACAG
1 AAATTTAAAGGACC--AAAAAACAAAAACAG
*
30682 AAACTTAAAGGACCAAAAAACAAAAACA-
1 AAATTTAAAGGACCAAAAAACAAAAACAG
30710 AACATTTAAA-GATCCAAAA
1 AA-ATTTAAAGGA-CCAAAA
30729 TAGTAAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 4 0.10
29 25 0.60
31 13 0.31
ACGTcount: A:0.64, C:0.15, G:0.08, T:0.13
Consensus pattern (29 bp):
AAATTTAAAGGACCAAAAAACAAAAACAG
Found at i:30759 original size:30 final size:29
Alignment explanation
Indices: 30725--30828 Score: 97
Period size: 29 Copynumber: 3.6 Consensus size: 29
30715 TTAAAGATCC
30725 AAAATAGTAAAAATAGACATTTAAGGGATT
1 AAAATAGTAAAAATAGA-ATTTAAGGGATT
* * * *
30755 AAAATAGAAAAAAATA-TATATAAAGGATT
1 AAAATAG-TAAAAATAGAATTTAAGGGATT
* *
30784 AAAATAGTAAAAACATAATCTTAAAGGG-TT
1 AAAATAGTAAAAATAGAAT-TT-AAGGGATT
30814 -AAATAGTAAAAATAG
1 AAAATAGTAAAAATAG
30829 CAACTAAAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
28 6 0.10
29 32 0.54
30 10 0.17
31 11 0.19
ACGTcount: A:0.59, C:0.03, G:0.13, T:0.25
Consensus pattern (29 bp):
AAAATAGTAAAAATAGAATTTAAGGGATT
Found at i:32796 original size:131 final size:130
Alignment explanation
Indices: 32627--32865 Score: 325
Period size: 131 Copynumber: 1.8 Consensus size: 130
32617 TTTCCTACAC
* * ***
32627 GATGAGGACGGCTGGTTATCTAGGGGTGACATGGCTCCTACATGATGAGGAGGTATGATCGGGAG
1 GATGAGGACGGCTGGTTATCTAGAGATGACACAACTCCTACATGATGAGGAGGTATGATCGGG-G
* * *
32692 ATGACACGGTTCCTACGTGATGAGGATGGTAGACCATATTTAGGGATGATAACACAGTTCCTATG
65 ATGACACAGTTCCTACATGATGAGGACGGTAGACCATATTTAGGGATGATAACACAGTTCCTATG
32757 T
130 T
* * * * *
32758 GATGAGGACGGCTGGTTATCTAGATATGACACAACTCCTACATGATGAGGATGTCTGGTCGGGGT
1 GATGAGGACGGCTGGTTATCTAGAGATGACACAACTCCTACATGATGAGGAGGTATGATCGGGGA
* * *
32823 TGACGCAGTTCCTACATGATGAGGACGGTAGGCCATCTTTAGG
66 TGACACAGTTCCTACATGATGAGGACGGTAGACCATATTTAGG
32866 TATTTGTTTC
Statistics
Matches: 92, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
130 38 0.41
131 54 0.59
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.26
Consensus pattern (130 bp):
GATGAGGACGGCTGGTTATCTAGAGATGACACAACTCCTACATGATGAGGAGGTATGATCGGGGA
TGACACAGTTCCTACATGATGAGGACGGTAGACCATATTTAGGGATGATAACACAGTTCCTATGT
Found at i:33525 original size:104 final size:104
Alignment explanation
Indices: 33333--33530 Score: 276
Period size: 104 Copynumber: 1.9 Consensus size: 104
33323 CGGTTTTGAA
* * * *
33333 AATCTCAAGTGAGATTAATTTTATTTCAAGTAAAACAACTTTGAAATTTGTATTATGAGGGAAAA
1 AATCTCAAGTGAGATTAATTTTATTTCAAGTAAAACAAATTCGAAATTTGTATTATAAGGAAAAA
33398 TGTCTCAAGTGAGACGAAATTTGTTTTAAAATAAACAAC
66 TGTCTCAAGTGAGACGAAATTTGTTTTAAAATAAACAAC
* *
33437 AATCTCAAGTGAGATTAATTTT-TTTCAAGTTAAGCAAATTCGAAATTTGTATCTCA-AAGGAAA
1 AATCTCAAGTGAGATTAATTTTATTTCAAGTAAAACAAATTCGAAATTTGTAT-T-ATAAGGAAA
* *
33500 AATGTCTCAAGCT-AGATGAAGTTTGTTTTAA
64 AATGTCTCAAG-TGAGACGAAATTTGTTTTAA
33531 GAGAAATTGT
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
103 26 0.31
104 55 0.66
105 2 0.02
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (104 bp):
AATCTCAAGTGAGATTAATTTTATTTCAAGTAAAACAAATTCGAAATTTGTATTATAAGGAAAAA
TGTCTCAAGTGAGACGAAATTTGTTTTAAAATAAACAAC
Found at i:33561 original size:36 final size:36
Alignment explanation
Indices: 33521--33608 Score: 106
Period size: 36 Copynumber: 2.4 Consensus size: 36
33511 CTAGATGAAG
* *
33521 TTTGTTTTAAGAGAAATTGTCTTAAGTGAGACAAAA-
1 TTTGTTTTAAGA-AAACTGTCTCAAGTGAGACAAAAT
* *
33557 TTTGTTTTTTATAAAACTGTCTCAAGTGAGACAAAAT
1 TTTG-TTTTAAGAAAACTGTCTCAAGTGAGACAAAAT
*
33594 TTTGTTTCAAGAAAA
1 TTTGTTTTAAGAAAA
33609 ACACCCTCAA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
36 33 0.77
37 10 0.23
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.39
Consensus pattern (36 bp):
TTTGTTTTAAGAAAACTGTCTCAAGTGAGACAAAAT
Found at i:33610 original size:37 final size:36
Alignment explanation
Indices: 33496--33610 Score: 101
Period size: 36 Copynumber: 3.2 Consensus size: 36
33486 TATCTCAAAG
** *
33496 GAAAAA-TGTCTCAAGCT-AGATGAAGTTTGTTTTAA
1 GAAAAACTGTCTCAAG-TGAGACAAAATTTGTTTTAA
* * * *
33531 GAGAAATTGTCTTAAGTGAGACAAAATTTGTTTTTTA
1 GAAAAACTGTCTCAAGTGAGACAAAATTTG-TTTTAA
* *
33568 -TAAAACTGTCTCAAGTGAGACAAAATTTTGTTTCAA
1 GAAAAACTGTCTCAAGTGAGACAAAA-TTTGTTTTAA
33604 GAAAAAC
1 GAAAAAC
33611 ACCCTCAAAG
Statistics
Matches: 62, Mismatches: 13, Indels: 8
0.75 0.16 0.10
Matches are distributed among these distances:
35 6 0.10
36 42 0.68
37 14 0.23
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (36 bp):
GAAAAACTGTCTCAAGTGAGACAAAATTTGTTTTAA
Found at i:33847 original size:16 final size:16
Alignment explanation
Indices: 33826--33869 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
33816 CGCATGTAAC
*
33826 ATGTATGTATGTGTTG
1 ATGTATGTATGTATTG
33842 ATGTATGTATGTATTG
1 ATGTATGTATGTATTG
33858 ATGTATGTATGT
1 ATGTATGTATGT
33870 TGATCTGTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (16 bp):
ATGTATGTATGTATTG
Found at i:39592 original size:30 final size:29
Alignment explanation
Indices: 39533--39589 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
39523 TCTAAACAGT
* *
39533 AAATACATAAAGTTAAAGAACCAAAAAAC
1 AAATACAAAAACTTAAAGAACCAAAAAAC
*
39562 AAATACAAAAACTTAAAGGACCAAAAAA
1 AAATACAAAAACTTAAAGAACCAAAAAA
39590 ACATTTAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (29 bp):
AAATACAAAAACTTAAAGAACCAAAAAAC
Found at i:39654 original size:29 final size:29
Alignment explanation
Indices: 39604--39706 Score: 104
Period size: 29 Copynumber: 3.5 Consensus size: 29
39594 TTAAAGATCC
*
39604 AAAATAGTAAAAACAGACATTTAAGGGATT
1 AAAATAGTAAAAATAGA-ATTTAAGGGATT
* * *
39634 AAAATAG-AAAAATACATATTTAAAGGACT
1 AAAATAGTAAAAATAGA-ATTTAAGGGATT
*
39663 AAAACAGTAAAAATAGAATCTTGAAGGG-TT
1 AAAATAGTAAAAATAGAAT-TT-AAGGGATT
39693 -AAATAGTAAAAATA
1 AAAATAGTAAAAATA
39707 ACAACTAAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
29 38 0.63
30 18 0.30
31 4 0.07
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.23
Consensus pattern (29 bp):
AAAATAGTAAAAATAGAATTTAAGGGATT
Found at i:39672 original size:59 final size:59
Alignment explanation
Indices: 39604--39727 Score: 148
Period size: 59 Copynumber: 2.1 Consensus size: 59
39594 TTAAAGATCC
* * *
39604 AAAATAGTAAAAACAGACAT-TT-AAGGGATTAAAATAG-AAAAAT-ACATATTTAAAGGACT
1 AAAACAGTAAAAACAGA-ATCTTGAAGGG-TT-AAATAGTAAAAATAACA-ACTAAAAGGACT
*
39663 AAAACAGTAAAAATAGAATCTTGAAGGGTTAAATAGTAAAAATAACAACTAAAAGGACT
1 AAAACAGTAAAAACAGAATCTTGAAGGGTTAAATAGTAAAAATAACAACTAAAAGGACT
39722 AAAACA
1 AAAACA
39728 ACAAACACAT
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
58 8 0.14
59 41 0.72
60 8 0.14
ACGTcount: A:0.57, C:0.08, G:0.14, T:0.21
Consensus pattern (59 bp):
AAAACAGTAAAAACAGAATCTTGAAGGGTTAAATAGTAAAAATAACAACTAAAAGGACT
Found at i:39778 original size:60 final size:59
Alignment explanation
Indices: 39694--39806 Score: 136
Period size: 60 Copynumber: 1.9 Consensus size: 59
39684 TGAAGGGTTA
*
39694 AATAGTAAAAATAACAACTAAAAGGACTAAAACAACAAACACATAAACTTAAAGAACTAC
1 AATAGTAAAAACAACAACTAAAAGGACT-AAACAACAAACACATAAACTTAAAGAACTAC
** * * ** **
39754 AATAGTAAAAACATGAACTTAAAGGGCTAAACAGTAATTACATAAACTTAAAG
1 AATAGTAAAAACAACAACTAAAAGGACTAAACAACAAACACATAAACTTAAAG
39807 GGCTAAACAG
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
59 21 0.48
60 23 0.52
ACGTcount: A:0.58, C:0.14, G:0.10, T:0.19
Consensus pattern (59 bp):
AATAGTAAAAACAACAACTAAAAGGACTAAACAACAAACACATAAACTTAAAGAACTAC
Found at i:39796 original size:29 final size:29
Alignment explanation
Indices: 39764--39822 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
39754 AATAGTAAAA
* *
39764 ACATGAACTTAAAGGGCTAAACAGTAATT
1 ACATAAACTTAAAGGGCTAAACAGAAATT
39793 ACATAAACTTAAAGGGCTAAACAGAAATT
1 ACATAAACTTAAAGGGCTAAACAGAAATT
39822 A
1 A
39823 AACTAACTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.49, C:0.14, G:0.15, T:0.22
Consensus pattern (29 bp):
ACATAAACTTAAAGGGCTAAACAGAAATT
Found at i:42740 original size:3 final size:3
Alignment explanation
Indices: 42734--42781 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
42724 AATAATAATA
*
42734 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
42781 A
1 A
42782 ACATATAGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:44681 original size:19 final size:19
Alignment explanation
Indices: 44659--44697 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
44649 AAATTCAGAG
*
44659 TAAATTAATTAAATTTTAA
1 TAAATTAATCAAATTTTAA
*
44678 TAAATTAATCATATTTTAA
1 TAAATTAATCAAATTTTAA
44697 T
1 T
44698 TTTATATTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAATTAATCAAATTTTAA
Found at i:47189 original size:20 final size:20
Alignment explanation
Indices: 47166--47203 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
47156 CTAAGTTTAA
47166 TAATTTAATTGA-CAAAATTT
1 TAATTTAA-TGATCAAAATTT
47186 TAATTTAATGATCAAAAT
1 TAATTTAATGATCAAAAT
47204 GGAACAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (20 bp):
TAATTTAATGATCAAAATTT
Found at i:49552 original size:24 final size:24
Alignment explanation
Indices: 49498--49544 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
49488 TTTCTATCAA
* * *
49498 AGTCAACGATCAACAGTCAACGGC
1 AGTCAACGGTCAAAAGTCAACAGC
49522 AGTCAACGGTCAAAAGTCAACAG
1 AGTCAACGGTCAAAAGTCAACAG
49545 TGGTCAACAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.40, C:0.26, G:0.21, T:0.13
Consensus pattern (24 bp):
AGTCAACGGTCAAAAGTCAACAGC
Found at i:50998 original size:28 final size:28
Alignment explanation
Indices: 50944--51000 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
50934 TGACTTTTTT
* *
50944 ATATTATATTGTCGAGTTAATGCTTGAA
1 ATATTATATTATCGAGCTAATGCTTGAA
* *
50972 ATATTATATTATCGAGCTAGTGTTTGAA
1 ATATTATATTATCGAGCTAATGCTTGAA
51000 A
1 A
51001 ATAGAGATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (28 bp):
ATATTATATTATCGAGCTAATGCTTGAA
Found at i:51069 original size:21 final size:22
Alignment explanation
Indices: 51045--51104 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
51035 AAGTTTATCT
51045 AAAATTCAATTTTATAAA-AAA
1 AAAATTCAATTTTATAAATAAA
* * * *
51066 AAAATTTAAATATATAAATAAT
1 AAAATTCAATTTTATAAATAAA
51088 AAAA-TCATATTTTATAA
1 AAAATTCA-ATTTTATAA
51105 CTTTTTTATA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAATTCAATTTTATAAATAAA
Found at i:53515 original size:23 final size:21
Alignment explanation
Indices: 53488--53542 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 21
53478 TAGTCTACTA
53488 ATATTATAAAAATTCCTTAAAAT
1 ATATTATAAAAATT--TTAAAAT
*
53511 ATATTTATTAATAATTTTAAAAT
1 ATA-TTA-TAAAAATTTTAAAAT
*
53534 ATAATATAA
1 ATATTATAA
53543 TATTTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 3 0.11
22 2 0.07
23 13 0.46
24 3 0.11
25 7 0.25
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (21 bp):
ATATTATAAAAATTTTAAAAT
Found at i:53543 original size:21 final size:23
Alignment explanation
Indices: 53504--53550 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
53494 TAAAAATTCC
*
53504 TTAAAATATATTTATTAATAATT
1 TTAAAATATATATATTAATAATT
*
53527 TTAAAATATA-ATA-TAATATTT
1 TTAAAATATATATATTAATAATT
53548 TTA
1 TTA
53551 TTTTTATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.45
22 2 0.09
23 10 0.45
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTAAAATATATATATTAATAATT
Found at i:56044 original size:3 final size:3
Alignment explanation
Indices: 56036--56161 Score: 132
Period size: 3 Copynumber: 40.0 Consensus size: 3
56026 CGAGTCTTTT
56036 TTA TTA TTA TTTA TTTA TTA TTA TTA TT- TTAA TTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
* *
56083 TTA TGTA TTA CATA TT- TTGC TTA TTTA TTA TTA TTA TTA TTA TT- TTAA
1 TTA T-TA TTA -TTA TTA TT-A TTA -TTA TTA TTA TTA TTA TTA TTA TT-A
56131 TTA TTA TTA TTA TTA TTA TTA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
56162 CATATTTTGC
Statistics
Matches: 109, Mismatches: 3, Indels: 22
0.81 0.02 0.16
Matches are distributed among these distances:
2 6 0.06
3 79 0.72
4 24 0.22
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:57656 original size:30 final size:30
Alignment explanation
Indices: 57617--57750 Score: 121
Period size: 30 Copynumber: 4.5 Consensus size: 30
57607 TGCTAATATC
*
57617 ATTTGAGTCCCTTAATTTTCTATTTTTACT
1 ATTTTAGTCCCTTAATTTTCTATTTTTACT
* * * *** *
57647 ATTTTAGTCCTTTAAATGTCTGCATTTATT
1 ATTTTAGTCCCTTAATTTTCTATTTTTACT
* *
57677 A-TTTAGCCCCTTAAGTTTCTATTTTTACT
1 ATTTTAGTCCCTTAATTTTCTATTTTTACT
*
57706 ATTTTAG-CCCTTTAAGTTTT-TATTTTTGCT
1 ATTTTAGTCCC-TTAA-TTTTCTATTTTTACT
*
57736 ATTTTAGTCCTTTAA
1 ATTTTAGTCCCTTAA
57751 ATTCTTGTTT
Statistics
Matches: 81, Mismatches: 19, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
29 24 0.30
30 52 0.64
31 5 0.06
ACGTcount: A:0.21, C:0.16, G:0.08, T:0.55
Consensus pattern (30 bp):
ATTTTAGTCCCTTAATTTTCTATTTTTACT
Found at i:57768 original size:30 final size:29
Alignment explanation
Indices: 57640--57778 Score: 95
Period size: 30 Copynumber: 4.7 Consensus size: 29
57630 AATTTTCTAT
57640 TTTTACTATTTTAGTCCTTTAAATGTC-TG
1 TTTTACTATTTTAGTCCTTTAAAT-TCTTG
* * * * *
57669 CATTTATTA-TTTAGCCCCTTAAGTTTCTAT-
1 -TTTTACTATTTTAGTCCTTTAA-ATTCT-TG
* * * *
57699 TTTTACTATTTTAGCCCTTTAAGTTTTTAT
1 TTTTACTATTTTAGTCCTTTAAATTCTT-G
*
57729 TTTTGCTATTTTAGTCCTTTAAATTCTTG
1 TTTTACTATTTTAGTCCTTTAAATTCTTG
**
57758 TTTGTACTATTTCGGTCCTTT
1 TTT-TACTATTTTAGTCCTTT
57779 GAGTGTATGT
Statistics
Matches: 84, Mismatches: 18, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
28 1 0.01
29 25 0.30
30 57 0.68
31 1 0.01
ACGTcount: A:0.19, C:0.16, G:0.09, T:0.56
Consensus pattern (29 bp):
TTTTACTATTTTAGTCCTTTAAATTCTTG
Found at i:58595 original size:17 final size:18
Alignment explanation
Indices: 58560--58597 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
58550 GCAGACCAAA
58560 TTTTGTCTTATAAAATGT
1 TTTTGTCTTATAAAATGT
* *
58578 TTTTTTCTTA-AAATTGT
1 TTTTGTCTTATAAAATGT
58595 TTT
1 TTT
58598 AAAAGACGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.63
Consensus pattern (18 bp):
TTTTGTCTTATAAAATGT
Found at i:63993 original size:36 final size:36
Alignment explanation
Indices: 63950--64184 Score: 350
Period size: 36 Copynumber: 6.6 Consensus size: 36
63940 TCTTAAAATG
*
63950 AATTTTGTCTCGCTTGAGACAGTTTTCTTAAAAACA
1 AATTGTGTCTCGCTTGAGACAGTTTTCTTAAAAACA
* * *
63986 AATTTTGTCTCACTTGATACAGTTTTCTTAAAAACA
1 AATTGTGTCTCGCTTGAGACAGTTTTCTTAAAAACA
* *
64022 AATTGTGTCTCGCTTGAGACAATTTTCTTAAAAACC
1 AATTGTGTCTCGCTTGAGACAGTTTTCTTAAAAACA
*
64058 AATTGTGTCTCGCTTGAGACAGTTTTCTTAGAAACA
1 AATTGTGTCTCGCTTGAGACAGTTTTCTTAAAAACA
*
64094 AATTGTGTCTCGCTTGAGATAGTTTTCTTAAAAACA
1 AATTGTGTCTCGCTTGAGACAGTTTTCTTAAAAACA
*
64130 AATTGTGTATCGCTTGAGACAGTTTTCTTAAAAACGA
1 AATTGTGTCTCGCTTGAGACAGTTTTCTTAAAAAC-A
*
64167 ACTT-TGTCT--CTTGAGACA
1 AATTGTGTCTCGCTTGAGACA
64185 ATTTCTAATT
Statistics
Matches: 182, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
34 9 0.05
36 169 0.93
37 4 0.02
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (36 bp):
AATTGTGTCTCGCTTGAGACAGTTTTCTTAAAAACA
Found at i:64469 original size:63 final size:63
Alignment explanation
Indices: 64304--64499 Score: 196
Period size: 66 Copynumber: 3.0 Consensus size: 63
64294 TCTTTAAGAC
* * * * * *
64304 CGTTTCCCTTGAAATGAATTTTGTCTCATTTGAGGCAGTTTCCCATGAAGCACCGATCTTTGAGA
1 CGTTTCCCTTGAAACGAATTTTGTCTCATTTGAGACAGTTT-CCTTTAAACATC-ATCTTTGAG-
*
64369 A
63 T
* * * **
64370 CGTTTCCCTTAAAAACAAAATTTGTCTCGCTTGAGACAGTTTCCTTTAAACATCATCTTTGAGT
1 CGTTTCCCTT-GAAACGAATTTTGTCTCATTTGAGACAGTTTCCTTTAAACATCATCTTTGAGT
*
64434 CGTTTCCCTTGAAACGAATTTTGTCTC-TTTCGAGACAGTTTCTTTTGAAACACATCATCTTTGA
1 CGTTTCCCTTGAAACGAATTTTGTCTCATTT-GAGACAGTTTCCTTT--AA-ACATCATCTTTGA
64498 GT
62 GT
64500 TTGTTTTTTC
Statistics
Matches: 108, Mismatches: 17, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
62 2 0.02
63 28 0.26
64 10 0.09
65 11 0.10
66 33 0.31
67 24 0.22
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (63 bp):
CGTTTCCCTTGAAACGAATTTTGTCTCATTTGAGACAGTTTCCTTTAAACATCATCTTTGAGT
Found at i:64550 original size:28 final size:28
Alignment explanation
Indices: 64471--64572 Score: 116
Period size: 28 Copynumber: 3.5 Consensus size: 28
64461 TTTCGAGACA
*
64471 GTTTCTTTTGAAACACATCATCTTTGAGTTT
1 GTTTCTTTTGAAACA-A--ATCTTTGAGTCT
*
64502 GTTTTTTCTTGAAACAAATCTTTGAGTCT
1 GTTTCTT-TTGAAACAAATCTTTGAGTCT
*
64531 GTTTCTTTTGAAACAAATCTTTCAGTC-
1 GTTTCTTTTGAAACAAATCTTTGAGTCT
*
64558 GATTTCTCTTGAAAC
1 G-TTTCTTTTGAAAC
64573 CATAATCCCT
Statistics
Matches: 64, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
27 1 0.02
28 31 0.48
29 17 0.27
31 7 0.11
32 8 0.12
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.46
Consensus pattern (28 bp):
GTTTCTTTTGAAACAAATCTTTGAGTCT
Found at i:64846 original size:133 final size:129
Alignment explanation
Indices: 64596--64834 Score: 309
Period size: 133 Copynumber: 1.8 Consensus size: 129
64586 GATGGCCAGC
* * * * * *
64596 CGTCCTCATCACGTAGGAACCGTGTTATCATTTCTAAAGATGGCCAAAACTCTTCATCACGTATG
1 CGTCCACATCACGTAGGAACCGAGCTATCATTCCTAAAGATGACCAAAAATCTTCATCACGTATG
*
64661 ATCCGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGATCCGTGTCACCCATATAACCTGT
66 ATCAGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGATCCGTGTCACCCATATAACCTGT
* *
64725 CGTCCACATCGCGTAGGAACCGAGCTATCACCCTTCCTAAAGATGACTAAGAAATCTTCATCACG
1 CGTCCACATCACGTAGGAACCGAGCTATCA---TTCCTAAAGATGACCAA-AAATCTTCATCACG
* * * *
64790 TATGAGT-AGTGTCATCCCCCGACCATATCTCCTCATCATGTAGGA
62 TATGA-TCAGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGA
64835 GTTGTGTCAC
Statistics
Matches: 92, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
129 26 0.28
132 14 0.15
133 51 0.55
134 1 0.01
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.26
Consensus pattern (129 bp):
CGTCCACATCACGTAGGAACCGAGCTATCATTCCTAAAGATGACCAAAAATCTTCATCACGTATG
ATCAGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGATCCGTGTCACCCATATAACCTGT
Found at i:65051 original size:11 final size:11
Alignment explanation
Indices: 65036--65077 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
65026 TGGATATTTT
65036 TTATTAT-TTA
1 TTATTATATTA
65046 TTTATT-TATTA
1 -TTATTATATTA
65057 TTATTATATTA
1 TTATTATATTA
65068 TTATTA-ATTA
1 TTATTATATTA
65078 ATATATTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 10 0.34
11 19 0.66
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTATTATATTA
Found at i:65057 original size:18 final size:19
Alignment explanation
Indices: 65030--65084 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 19
65020 TTTGTCTGGA
*
65030 TATTTTTTATTATT-TATT
1 TATTTATTATTATTATATT
65048 TATTTATTATTATTATA-T
1 TATTTATTATTATTATATT
*
65066 TA-TTATTAATTAATATATT
1 TATTTATT-ATTATTATATT
65085 ACATATTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 5 0.16
18 24 0.75
19 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTTATTATTATTATATT
Found at i:69496 original size:49 final size:48
Alignment explanation
Indices: 69439--69548 Score: 125
Period size: 49 Copynumber: 2.2 Consensus size: 48
69429 AAATTTTAAC
* *
69439 ATAAAATATATTT-TTAAATGAA-ATAAAATATTTTTAAATTAAGTTTAT
1 ATAAAATATATTTAATAAATGAATATAAAAT-TTTTTAAATTAA-TATAT
* * *
69487 AATAAAATATATTTAATAAGTTAATATAAAATTTTTTAAGTTAATATAT
1 -ATAAAATATATTTAATAAATGAATATAAAATTTTTTAAATTAATATAT
69536 ATAAAATTATATT
1 ATAAAA-TATATT
69549 ATATAATCAG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
48 6 0.11
49 23 0.43
50 17 0.32
51 7 0.13
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (48 bp):
ATAAAATATATTTAATAAATGAATATAAAATTTTTTAAATTAATATAT
Found at i:69891 original size:38 final size:39
Alignment explanation
Indices: 69780--69896 Score: 127
Period size: 38 Copynumber: 3.1 Consensus size: 39
69770 TTTTAAAAAC
69780 AATTTAGAATGTTA-ATGTGAAATAA-TTAAGAAATTAAG
1 AATTTAGAATGTTAGA-GTGAAATAATTTAAGAAATTAAG
** *
69818 AATTTAGAATGTTATG-GTGTCA-AATTTAAGAAATTAGG
1 AATTTAGAATGTTA-GAGTGAAATAATTTAAGAAATTAAG
* * *
69856 ATTTTAGAATGTTAGAGTGAAATAATTTGAG-AATTATG
1 AATTTAGAATGTTAGAGTGAAATAATTTAAGAAATTAAG
69894 AAT
1 AAT
69897 AAAAATTTAA
Statistics
Matches: 65, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
37 3 0.05
38 55 0.85
39 7 0.11
ACGTcount: A:0.44, C:0.01, G:0.19, T:0.37
Consensus pattern (39 bp):
AATTTAGAATGTTAGAGTGAAATAATTTAAGAAATTAAG
Found at i:71405 original size:100 final size:95
Alignment explanation
Indices: 71239--71418 Score: 220
Period size: 99 Copynumber: 1.8 Consensus size: 95
71229 ATAAGTTGTA
* * * *
71239 TTTGAGTAGTTTGGTAAGTTTAGTTTAAATATTTTTATTTTTATTGGATATATAAATTATTGGAC
1 TTTGAGTAGTTTGGTAAATTTAGTTTAAATATTTTTATTTTTATTGGAAATAGAAATTATTAGAC
*
71304 TATTTATTTTGTTTTACAGATTAAATCGTAT
66 TATTT-TTTTGATTTACAGATTAAATCGTAT
* *
71335 TTTGAGTGGTTTGGTAAATTTA-TTTAAATTTTAATGTTTTATTTTTA-TGTAAATAGAAATTAA
1 TTTGAGTAGTTTGGTAAATTTAGTTTAAA---T-AT-TTTTATTTTTATTGGAAATAGAAATT-A
71398 TTAGACTATTTTTTTGATTTA
60 TTAGACTATTTTTTTGATTTA
71419 ACATATTTTT
Statistics
Matches: 71, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
95 6 0.08
96 20 0.28
98 1 0.01
99 22 0.31
100 22 0.31
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.54
Consensus pattern (95 bp):
TTTGAGTAGTTTGGTAAATTTAGTTTAAATATTTTTATTTTTATTGGAAATAGAAATTATTAGAC
TATTTTTTTGATTTACAGATTAAATCGTAT
Done.