Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003178.1 Hibiscus syriacus cultivar Beakdansim tig00006691_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: 95983
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6105 original size:2 final size:2
Alignment explanation
Indices: 6086--6141 Score: 91
Period size: 2 Copynumber: 29.5 Consensus size: 2
6076 TCCTCCATAG
6086 AT AT A- AT A- AT AT AT -T 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
6125 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
6142 AGAAGAGTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.06
2 48 0.94
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12633 original size:17 final size:16
Alignment explanation
Indices: 12615--12648 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
12605 ATAAATATAT
*
12615 ATATATAAT-AATCAA
1 ATATATAATAAAACAA
12630 ATATATAATAAAACAA
1 ATATATAATAAAACAA
12646 ATA
1 ATA
12649 AATAGAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (16 bp):
ATATATAATAAAACAA
Found at i:12684 original size:14 final size:14
Alignment explanation
Indices: 12611--12692 Score: 60
Period size: 14 Copynumber: 5.8 Consensus size: 14
12601 ACAAATAAAT
12611 ATATATATATAATA
1 ATATATATATAATA
*
12625 ATCAAATATATAATA
1 AT-ATATATATAATA
* * *
12640 AAACAAATA-AATA
1 ATATATATATAATA
* *
12653 GAAATAAATA-AATAA
1 -ATATATATATAAT-A
*
12668 ATATACATATAATA
1 ATATATATATAATA
12682 ATATATATATA
1 ATATATATATA
12693 TAAAGCGTAA
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
13 4 0.07
14 36 0.64
15 16 0.29
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.32
Consensus pattern (14 bp):
ATATATATATAATA
Found at i:12684 original size:18 final size:18
Alignment explanation
Indices: 12604--12690 Score: 68
Period size: 18 Copynumber: 4.6 Consensus size: 18
12594 GGAAAAAACA
12604 AATAAATATATATATATAAT
1 AATAAATATA-A-ATATAAT
* *
12624 AATCAAATATATAATAAAACA
1 AAT-AAATATA-AATATAA-T
*
12645 AATAAATAGAAATA-AAT
1 AATAAATATAAATATAAT
*
12662 AAATAAATATACATATAAT
1 -AATAAATATAAATATAAT
*
12681 AATATATATA
1 AATAAATATA
12691 TATAAAGCGT
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
18 23 0.41
19 7 0.12
20 14 0.25
21 12 0.21
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.31
Consensus pattern (18 bp):
AATAAATATAAATATAAT
Found at i:13780 original size:27 final size:27
Alignment explanation
Indices: 13721--13780 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
13711 ACATGGAACC
*
13721 AAATGAATAATAATTATATATTATAGA
1 AAATAAATAATAATTATATATTATAGA
* *
13748 ATATAAATAA-AATATATATATTATATA
1 AAATAAATAATAAT-TATATATTATAGA
13775 AAATAA
1 AAATAA
13781 TATTAATGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (27 bp):
AAATAAATAATAATTATATATTATAGA
Found at i:14649 original size:79 final size:81
Alignment explanation
Indices: 14534--14691 Score: 196
Period size: 79 Copynumber: 2.0 Consensus size: 81
14524 TTTTGTTGAT
* ** ** *
14534 ATATAGCCCTTCTTGCCTTGAGCTATGTTGTGAATGATA-TGGC-TTGAGCTGAATGGAATCGAA
1 ATATAACCCTTCTTGCCTTGAGCTATACTGCAAATGATAGTGCCTTTGAGCTGAATGGAATCGAA
*
14597 CTTGAAGGTCTTTGGC
66 CTCGAAGGTCTTTGGC
* * *
14613 ATATAACCCTT-TTAGCCTTGAGCTATACTGCAAATGATAGTGCCTTTGAGCTGAGTGTAATCTA
1 ATATAACCCTTCTT-GCCTTGAGCTATACTGCAAATGATAGTGCCTTTGAGCTGAATGGAATCGA
14677 ACTCGAAGGTCTTTG
65 ACTCGAAGGTCTTTG
14692 TTTGGCAGAT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
78 2 0.03
79 31 0.47
80 3 0.05
81 30 0.45
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (81 bp):
ATATAACCCTTCTTGCCTTGAGCTATACTGCAAATGATAGTGCCTTTGAGCTGAATGGAATCGAA
CTCGAAGGTCTTTGGC
Found at i:14774 original size:36 final size:36
Alignment explanation
Indices: 14728--15418 Score: 573
Period size: 36 Copynumber: 20.0 Consensus size: 36
14718 AGCTATGCTG
*
14728 CAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTT
1 CAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTT
* * * *
14764 CAAGAGAAACTGTCCCAAGAGAGACGAAACTTAGTTC
1 CAAGAGAAACTGTCTCAAGAGAGAC-AAAATTTGTTT
* * *
14801 CAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTT
1 CAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTT
* * *
14837 CAAG-GAAAACATAT-TC-A-A-AG----ATTTTATTT
1 CAAGAG-AAAC-TGTCTCAAGAGAGACAAAATTTGTTT
* *
14866 CAAGGGAAATTGTCTCAAGAGAGACAAAATTTGTTT
1 CAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTT
* *
14902 CAAGGGAAATTGTCTCAAGAGAGACAAAATTTGTTT
1 CAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTT
*
14938 CAAGAGAAATTGTCTCAAGAGAGACAAAATTTGTTT
1 CAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTT
* * * * * *
14974 CAAGAGAAATTGTCCCAAGAGAGATGAAACTTAGTTC
1 CAAGAGAAACTGTCTCAAGAGAGA-CAAAATTTGTTT
* * *
15011 CAAAAGAAA-TGTCTCAAGGGAGACGAAATTTGTTT
1 CAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTT
* * *
15046 CAAG-GAAAACATAT-TC-A-A-AG----ATTTTATTT
1 CAAGAG-AAAC-TGTCTCAAGAGAGACAAAATTTGTTT
*
15075 CAAGGGAAA---T-T--A-AGAGACAAAA----TTT
1 CAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTT
* * * *
15100 CAAG-GAAATTGTCTCAACAGAGACAAATTTTATTT
1 CAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTT
* *
15135 CAAGGGAAATTGTCTCAAGAGAGACAAAATTTGTTT
1 CAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTT
* *
15171 CAAGGGAAATTGTCTCAAGAGAGACAAAATTTGTTT
1 CAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTT
* *
15207 CAAGAGAAACTGTCTCAAGAGAGACCAAAACTTAGTTC
1 CAAGAGAAACTGTCTCAAGAGAGA-CAAAA-TTTGTTT
* *
15245 CAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTT
1 CAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTT
* *
15281 -AATGTA-AAACATAT-TC-A-A-AG----ATTTTGTTT
1 CAA-G-AGAAAC-TGTCTCAAGAGAGACAAAATTTGTTT
15310 CAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTT
1 CAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTT
* *
15346 CAAGTGAAACTGTCTTAAGAGAGACAAAATTTGTTT
1 CAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTT
*
15382 CAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTT
1 CAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTT
15419 TGAGTAAATT
Statistics
Matches: 541, Mismatches: 64, Indels: 99
0.77 0.09 0.14
Matches are distributed among these distances:
24 6 0.01
25 11 0.02
27 1 0.00
28 6 0.01
29 46 0.09
30 7 0.01
31 11 0.02
32 4 0.01
33 6 0.01
34 1 0.00
35 26 0.05
36 319 0.59
37 70 0.13
38 27 0.05
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (36 bp):
CAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTT
Found at i:14904 original size:21 final size:21
Alignment explanation
Indices: 14875--14980 Score: 101
Period size: 21 Copynumber: 5.6 Consensus size: 21
14865 TCAAGGGAAA
14875 TTGTCTCAAGAGAGACAAAAT
1 TTGTCTCAAGAGAGACAAAAT
*
14896 TTGTTTCAAG-G-G---AAA-
1 TTGTCTCAAGAGAGACAAAAT
14911 TTGTCTCAAGAGAGACAAAAT
1 TTGTCTCAAGAGAGACAAAAT
*
14932 TTGTTTC-A-AGAG---AAA-
1 TTGTCTCAAGAGAGACAAAAT
14947 TTGTCTCAAGAGAGACAAAAT
1 TTGTCTCAAGAGAGACAAAAT
*
14968 TTGTTTCAAGAGA
1 TTGTCTCAAGAGA
14981 AATTGTCCCA
Statistics
Matches: 68, Mismatches: 5, Indels: 24
0.70 0.05 0.25
Matches are distributed among these distances:
15 15 0.22
16 8 0.12
17 5 0.07
19 5 0.07
20 8 0.12
21 27 0.40
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (21 bp):
TTGTCTCAAGAGAGACAAAAT
Found at i:15173 original size:21 final size:21
Alignment explanation
Indices: 15144--15213 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
15134 TCAAGGGAAA
15144 TTGTCTCAAGAGAGACAAAAT
1 TTGTCTCAAGAGAGACAAAAT
*
15165 TTGTTTCAAG-G-G---AAA-
1 TTGTCTCAAGAGAGACAAAAT
15180 TTGTCTCAAGAGAGACAAAAT
1 TTGTCTCAAGAGAGACAAAAT
*
15201 TTGTTTCAAGAGA
1 TTGTCTCAAGAGA
15214 AACTGTCTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
15 9 0.22
16 4 0.10
17 1 0.03
19 1 0.03
20 4 0.10
21 21 0.52
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (21 bp):
TTGTCTCAAGAGAGACAAAAT
Found at i:15324 original size:139 final size:138
Alignment explanation
Indices: 15164--15418 Score: 404
Period size: 139 Copynumber: 1.8 Consensus size: 138
15154 AGAGACAAAA
* *
15164 TTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
*
15229 GACCAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTAATGTAAAACAT
66 GA-CAAAA-TTAGTTCCAAAAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTAATGTAAAACAT
15293 ATTCAAAGAT
129 ATTCAAAGAT
* *
15303 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGTGAAACTGTCTTAAGAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
* * * *
15368 GACAAAATTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTT
66 GACAAAATTAGTTCCAAAAGAAACTGTCTCAAGAGAGACAAAACTTTGTTT
15419 TGAGTAAATT
Statistics
Matches: 106, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
137 31 0.29
138 12 0.11
139 63 0.59
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (138 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
GACAAAATTAGTTCCAAAAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTAATGTAAAACATAT
TCAAAGAT
Found at i:15428 original size:36 final size:35
Alignment explanation
Indices: 15303--15443 Score: 135
Period size: 36 Copynumber: 3.9 Consensus size: 35
15293 ATTCAAAGAT
*
15303 TTTGTTTCAAGAG-AAACTGTCTCAAGAGAGACAAAA
1 TTTGTTT--AGAGTAAATTGTCTCAAGAGAGACAAAA
* *
15339 TTTGTTTCA-AGTGAAACTGTCTTAAGAGAGACAAAA
1 TTTGTTT-AGAGT-AAATTGTCTCAAGAGAGACAAAA
15375 TTTGTTTCAAGAG-AAATTGTCTCAAGAGAGACAAAA
1 TTTGTTT--AGAGTAAATTGTCTCAAGAGAGACAAAA
* * *
15411 CTTTGTTTTGAGTAAATTAGTTTCAAGCGAGAC
1 -TTTGTTTAGAGTAAATT-GTCTCAAGAGAGAC
15444 GCCCCATTGT
Statistics
Matches: 90, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
34 2 0.02
35 4 0.04
36 62 0.69
37 20 0.22
38 2 0.02
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (35 bp):
TTTGTTTAGAGTAAATTGTCTCAAGAGAGACAAAA
Found at i:16865 original size:83 final size:87
Alignment explanation
Indices: 16745--16971 Score: 284
Period size: 95 Copynumber: 2.6 Consensus size: 87
16735 GGCTAGCTGA
**
16745 ATCCATAAAGCTAGGGCGTTTAACCAATTG-CTCTAGAGGGACAACTCAA-TAT-GTA-AA-CAC
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCCT-TAGAGGGACAACTCAATTATAGTATAATCAC
*
16805 CATTATCAGGTTAGCTGAATCTT
65 CATTATCAGGTTAGCTGAATATT
16828 ATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGGACAACTCAAGCTTTATTGTATAGTA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGGACAACTC-A-----A-T-TATAGTA
*
16893 TAATCACCTTTATCAGGTTAGCTGAATATT
58 TAATCACCATTATCAGGTTAGCTGAATATT
* *
16923 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTTTAAAGGGACAACTCAA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGGACAACTCAA
16972 GCTTTATTGT
Statistics
Matches: 125, Mismatches: 6, Indels: 20
0.83 0.04 0.13
Matches are distributed among these distances:
83 42 0.34
84 3 0.02
89 2 0.02
92 3 0.02
93 3 0.02
94 3 0.02
95 69 0.55
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (87 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGGACAACTCAATTATAGTATAATCACC
ATTATCAGGTTAGCTGAATATT
Found at i:16970 original size:95 final size:95
Alignment explanation
Indices: 16802--16984 Score: 330
Period size: 95 Copynumber: 1.9 Consensus size: 95
16792 AATATGTAAA
* *
16802 CACCATTATCAGGTTAGCTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGG
1 CACCATTATCAGGTTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAAAGG
16867 GACAACTCAAGCTTTATTGTATAGTATAAT
66 GACAACTCAAGCTTTATTGTATAGTATAAT
* *
16897 CACCTTTATCAGGTTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCTTTAAAGG
1 CACCATTATCAGGTTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAAAGG
16962 GACAACTCAAGCTTTATTGTATA
66 GACAACTCAAGCTTTATTGTATA
16985 TACAAAATAT
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
95 84 1.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (95 bp):
CACCATTATCAGGTTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAAAGG
GACAACTCAAGCTTTATTGTATAGTATAAT
Found at i:20190 original size:24 final size:24
Alignment explanation
Indices: 20158--20207 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
20148 TCACGAAGGC
*
20158 TACTTGCTAGACATGTGCGGTGAA
1 TACTTGCTAGACATGTGCAGTGAA
20182 TACTTGCTAGACATGTGCAGTGAA
1 TACTTGCTAGACATGTGCAGTGAA
20206 TA
1 TA
20208 AATTCACATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (24 bp):
TACTTGCTAGACATGTGCAGTGAA
Found at i:21084 original size:22 final size:21
Alignment explanation
Indices: 21048--21090 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
21038 AGAAAAAAAA
*
21048 GAAAAATAAATAAATGAAAGT
1 GAAAAATAAAAAAATGAAAGT
*
21069 GAAATAATAAAAAAATGCAAGT
1 GAAA-AATAAAAAAATGAAAGT
21091 AATAGTAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.65, C:0.02, G:0.14, T:0.19
Consensus pattern (21 bp):
GAAAAATAAAAAAATGAAAGT
Found at i:21187 original size:55 final size:55
Alignment explanation
Indices: 21126--21230 Score: 167
Period size: 55 Copynumber: 1.9 Consensus size: 55
21116 ACAATGAAAA
*
21126 AAACAAATAAATAAATATATATATATATAATAATCAA-ATATAGAATAAAACAAAT
1 AAACAAATAAATAAATATATATACATATAATAAT-AATATATAGAATAAAACAAAT
* *
21181 AAACAAATAAATATATATATATACATATAATAATAATATATATAATAAAA
1 AAACAAATAAATAAATATATATACATATAATAATAATATATAGAATAAAA
21231 AATAATATAT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
54 2 0.04
55 44 0.96
ACGTcount: A:0.65, C:0.05, G:0.01, T:0.30
Consensus pattern (55 bp):
AAACAAATAAATAAATATATATACATATAATAATAATATATAGAATAAAACAAAT
Found at i:21235 original size:25 final size:25
Alignment explanation
Indices: 21139--21237 Score: 62
Period size: 25 Copynumber: 3.9 Consensus size: 25
21129 CAAATAAATA
* *
21139 AATATATATATAT-ATAATAATCA-
1 AATATATATATATAAAAATAATAAT
* * *
21162 AATATAGA-ATAAAACAAATAAACAAAT
1 AATATATATATATAA-AAAT-AA-TAAT
* *
21189 AAATATATATATATACATATAATAAT
1 -AATATATATATATAAAAATAATAAT
21215 AATATATATA-ATAAAAAATAATA
1 AATATATATATAT-AAAAATAATA
21238 TATACAAAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
22 3 0.05
23 8 0.14
24 5 0.09
25 20 0.36
26 4 0.07
27 2 0.04
28 10 0.18
29 4 0.07
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.31
Consensus pattern (25 bp):
AATATATATATATAAAAATAATAAT
Found at i:21249 original size:19 final size:19
Alignment explanation
Indices: 21183--21250 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
21173 AAACAAATAA
* *
21183 ACAAATAAATATATATATAT
1 ACAAAAAAAAATA-ATATAT
* * *
21203 ACATATAATAATAATATAT
1 ACAAAAAAAAATAATATAT
* *
21222 ATAATAAAAAATAATATAT
1 ACAAAAAAAAATAATATAT
21241 ACAAAAAAAA
1 ACAAAAAAAA
21251 TAAGTAAAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
19 28 0.74
20 10 0.26
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.29
Consensus pattern (19 bp):
ACAAAAAAAAATAATATAT
Found at i:22352 original size:27 final size:27
Alignment explanation
Indices: 22317--22376 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
22307 ACATGGAACC
* * *
22317 AAATGAATAATAATTATATATTATATA
1 AAATAAATAAAAAATATATATTATATA
*
22344 ATATAAATAAAAAATATATATTATATA
1 AAATAAATAAAAAATATATATTATATA
22371 AAATAA
1 AAATAA
22377 TATTAATGGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (27 bp):
AAATAAATAAAAAATATATATTATATA
Found at i:23150 original size:2 final size:2
Alignment explanation
Indices: 23143--23192 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
23133 GGGTTTTTGG
23143 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
23185 TA TA TA TA
1 TA TA TA TA
23193 AATAAATTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30655 original size:69 final size:68
Alignment explanation
Indices: 30611--31006 Score: 488
Period size: 69 Copynumber: 5.8 Consensus size: 68
30601 CTTATCTATT
* * *
30611 TTTGCAGACTCTGTTCCAAGCACCCCTGCTTATGCAGATAACATGTTCAAGGGGAAGAGTTCATC
1 TTTGCAGACTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTCCAA-GGGAAGAGTTCATC
30676 CTTG
65 CTTG
* *
30680 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGACAGAGTTCATC
1 TTTGCAGACTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTCCAAGGGA-AGAGTTCATC
30745 CTTG
65 CTTG
* * * *
30749 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCGGATAACATGTTCAAGGGTCAGAGTTCATC
1 TTTGCAGACTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTCCAAGGG-AAGAGTTCATC
30814 CTTG
65 CTTG
* * * * * *
30818 TTTGCAGACTCTGTTCCGAGTACTCCTGCCTATGCGGATAACATGTTCAAGGGTCAGAGTTCCTC
1 TTTGCAGACTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTCCAAGGG-AAGAGTTCATC
30883 CTTG
65 CTTG
* * * * * * **
30887 TATGCAGATTCTGTTCCAAGCACTCCTGCCTATGCGGATAATATGTTCAAGAG-TCAGTTCATCC
1 TTTGCAGACTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTCCAAGGGAAGAGTTCATCC
30951 TTG
66 TTG
* * ** * *
30954 TTTACAGATTCCATTCCAAGCACTCCTGCCTATGCGGATAACATGTTCAAGGG
1 TTTGCAGACTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTCCAAGGG
31007 GAAGGGCTCT
Statistics
Matches: 301, Mismatches: 24, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
67 58 0.19
68 4 0.01
69 239 0.79
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (68 bp):
TTTGCAGACTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTCCAAGGGAAGAGTTCATCC
TTG
Found at i:30796 original size:138 final size:137
Alignment explanation
Indices: 30611--31006 Score: 596
Period size: 138 Copynumber: 2.9 Consensus size: 137
30601 CTTATCTATT
* * * *
30611 TTTGCAGACTCTGTTCCAAGCACCCCTGCTTATGCAGATAACATGTTCAAGGGGAAGAGTTCATC
1 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCGGATAACATGTTCAAGGGG-AGAGTTCATC
*
30676 CTTGTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGACAGAGTT
65 CTTGTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCGGATAACATGTTCAAGGGACAGAGTT
30741 CATCCTTG
130 CATCCTTG
*
30749 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCGGATAACATGTTCAAGGGTCAGAGTTCATC
1 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCGGATAACATGTTCAAGGG-GAGAGTTCATC
* * * *
30814 CTTGTTTGCAGACTCTGTTCCGAGTACTCCTGCCTATGCGGATAACATGTTCAAGGGTCAGAGTT
65 CTTGTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCGGATAACATGTTCAAGGGACAGAGTT
*
30879 CCTCCTTG
130 CATCCTTG
* * * **
30887 TATGCAGATTCTGTTCCAAGCACTCCTGCCTATGCGGATAATATGTTCAA-GAGTCAGTTCATCC
1 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCGGATAACATGTTCAAGGGGAGAGTTCATCC
* **
30951 TTGTTTACAGATTCCATTCCAAGCACTCCTGCCTATGCGGATAACATGTTCAAGGG
66 TTGTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCGGATAACATGTTCAAGGG
31007 GAAGGGCTCT
Statistics
Matches: 234, Mismatches: 23, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
136 59 0.25
137 1 0.00
138 174 0.74
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (137 bp):
TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCGGATAACATGTTCAAGGGGAGAGTTCATCC
TTGTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCGGATAACATGTTCAAGGGACAGAGTTC
ATCCTTG
Found at i:30903 original size:207 final size:205
Alignment explanation
Indices: 30611--31006 Score: 630
Period size: 207 Copynumber: 1.9 Consensus size: 205
30601 CTTATCTATT
*
30611 TTTGCAGACTCTGTTCCAAGCACCCCTGCTTATGCAGATAACATGTTCAAGGGGAAGAGTTCATC
1 TTTGCAGACTCTGTTCCAAGCACCCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGTTCATC
* *
30676 CTTGTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGACAGAGTT
66 CTTGTATGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGAGAC--AGTT
* **
30741 CATCCTTGTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCGGATAACATGTTCAAGGGTCAG
129 CATCCTTGTTTACAGATTCCATTCCAAGCACTCCTGCCTATGCGGATAACATGTTCAAGGGTCAG
30806 AGTTCATCCTTG
194 AGTTCATCCTTG
* * * * ** *
30818 TTTGCAGACTCTGTTCCGAGTACTCCTGCCTATGCGGATAACATGTTCAAGGGTCAGAGTTCCTC
1 TTTGCAGACTCTGTTCCAAGCACCCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGTTCATC
* * *
30883 CTTGTATGCAGATTCTGTTCCAAGCACTCCTGCCTATGCGGATAATATGTTCAAGAGTCAGTTCA
66 CTTGTATGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGAGACAGTTCA
30948 TCCTTGTTTACAGATTCCATTCCAAGCACTCCTGCCTATGCGGATAACATGTTCAAGGG
131 TCCTTGTTTACAGATTCCATTCCAAGCACTCCTGCCTATGCGGATAACATGTTCAAGGG
31007 GAAGGGCTCT
Statistics
Matches: 173, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
205 62 0.36
207 111 0.64
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (205 bp):
TTTGCAGACTCTGTTCCAAGCACCCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGTTCATC
CTTGTATGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGAGACAGTTCA
TCCTTGTTTACAGATTCCATTCCAAGCACTCCTGCCTATGCGGATAACATGTTCAAGGGTCAGAG
TTCATCCTTG
Found at i:37230 original size:17 final size:16
Alignment explanation
Indices: 37204--37238 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
37194 TTAGGTTTTA
*
37204 AAAGGAAGAATTGAAG
1 AAAGGAAGAAGTGAAG
37220 AAAGAGAAGAAGTGAAG
1 AAAG-GAAGAAGTGAAG
37237 AA
1 AA
37239 GAAGGCGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.60, C:0.00, G:0.31, T:0.09
Consensus pattern (16 bp):
AAAGGAAGAAGTGAAG
Found at i:53666 original size:21 final size:21
Alignment explanation
Indices: 53642--53755 Score: 228
Period size: 21 Copynumber: 5.4 Consensus size: 21
53632 GGATTTCAAA
53642 CCGATCCGGATCGGTTTTTAT
1 CCGATCCGGATCGGTTTTTAT
53663 CCGATCCGGATCGGTTTTTAT
1 CCGATCCGGATCGGTTTTTAT
53684 CCGATCCGGATCGGTTTTTAT
1 CCGATCCGGATCGGTTTTTAT
53705 CCGATCCGGATCGGTTTTTAT
1 CCGATCCGGATCGGTTTTTAT
53726 CCGATCCGGATCGGTTTTTAT
1 CCGATCCGGATCGGTTTTTAT
53747 CCGATCCGG
1 CCGATCCGG
53756 TTTTTTCTCA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 93 1.00
ACGTcount: A:0.14, C:0.25, G:0.25, T:0.36
Consensus pattern (21 bp):
CCGATCCGGATCGGTTTTTAT
Found at i:53868 original size:15 final size:15
Alignment explanation
Indices: 53850--53905 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
53840 TAACCGGTTT
53850 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
53865 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
53882 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
53897 CGATTTTAA
1 CGGTTTTAA
53906 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:53878 original size:17 final size:17
Alignment explanation
Indices: 53853--53903 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
53843 CCGGTTTCGG
53853 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
53870 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
53885 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
53902 TT
1 TT
53904 AATATTCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:54374 original size:33 final size:33
Alignment explanation
Indices: 54327--54425 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
54317 AACTCAACAT
* * *
54327 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
54360 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
54393 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
54425 A
1 A
54426 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:56791 original size:15 final size:14
Alignment explanation
Indices: 56759--56799 Score: 66
Period size: 13 Copynumber: 2.9 Consensus size: 14
56749 TCCCGGATAA
56759 AAACCGGTTTTTTT
1 AAACCGGTTTTTTT
56773 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
56786 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
56800 ATCCGGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.52
15 12 0.48
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.49
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:57737 original size:24 final size:25
Alignment explanation
Indices: 57691--57738 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
57681 GTTTCAAATT
57691 TTTTCGGTTATCAATTTTTAGATCAA
1 TTTTCGGTTAT-AATTTTTAGATCAA
*
57717 TTTTCGGTTAT-TTTTTTAGATC
1 TTTTCGGTTATAATTTTTAGATC
57739 GGATTAGATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.48
26 11 0.52
ACGTcount: A:0.21, C:0.10, G:0.12, T:0.56
Consensus pattern (25 bp):
TTTTCGGTTATAATTTTTAGATCAA
Found at i:58580 original size:16 final size:16
Alignment explanation
Indices: 58561--58601 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
58551 CAAATCAAGT
58561 CAAACTCAACAATACC
1 CAAACTCAACAATACC
* *
58577 CAAACCCAACAATACT
1 CAAACTCAACAATACC
58593 CAAACTCAA
1 CAAACTCAA
58602 ATCGACTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.51, C:0.37, G:0.00, T:0.12
Consensus pattern (16 bp):
CAAACTCAACAATACC
Found at i:62288 original size:21 final size:21
Alignment explanation
Indices: 62250--62289 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
62240 CCAATGTACC
*
62250 ACATATATGTTCCAAAGGATT
1 ACATATATGATCCAAAGGATT
62271 ACATATAT-ATCCAGAAGGA
1 ACATATATGATCCA-AAGGA
62290 CCACGTAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (21 bp):
ACATATATGATCCAAAGGATT
Found at i:66625 original size:15 final size:15
Alignment explanation
Indices: 66598--66644 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
66588 ACTTGGTCAC
66598 TTTCGGTGCAAATGG
1 TTTCGGTGCAAATGG
* * *
66613 TTTTGGTGGAAATTGC
1 TTTCGGTGCAAA-TGG
66629 TTTCGGTGCAAATGG
1 TTTCGGTGCAAATGG
66644 T
1 T
66645 CCAATTTAAC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.19, C:0.11, G:0.32, T:0.38
Consensus pattern (15 bp):
TTTCGGTGCAAATGG
Found at i:66641 original size:16 final size:16
Alignment explanation
Indices: 66597--66641 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
66587 AACTTGGTCA
66597 CTTTCGGTGCAAA-TG
1 CTTTCGGTGCAAATTG
* * *
66612 GTTTTGGTGGAAATTG
1 CTTTCGGTGCAAATTG
66628 CTTTCGGTGCAAAT
1 CTTTCGGTGCAAAT
66642 GGTCCAATTT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.20, C:0.13, G:0.29, T:0.38
Consensus pattern (16 bp):
CTTTCGGTGCAAATTG
Found at i:66929 original size:22 final size:21
Alignment explanation
Indices: 66888--66931 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
66878 ACTTTCGGTG
**
66888 TTTTATTTTTTTTTTGACAAT
1 TTTTATTTTTTTTTCAACAAT
66909 TTTTATTCTTTTTTTCAACAAT
1 TTTTATT-TTTTTTTCAACAAT
66931 T
1 T
66932 GCTGTCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTTATTTTTTTTTCAACAAT
Found at i:73107 original size:23 final size:23
Alignment explanation
Indices: 73047--73108 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
73037 AAACTTTAGG
73047 TGGTTG-AAAGTTGACAACAATAA
1 TGGTTGAAAAG-TGACAACAATAA
* * * *
73070 TGGTTCATAATTGACACCAATAA
1 TGGTTGAAAAGTGACAACAATAA
73093 TGGTTGAAAAGTGACA
1 TGGTTGAAAAGTGACA
73109 TGGGAAAATT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
23 29 0.94
24 2 0.06
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.27
Consensus pattern (23 bp):
TGGTTGAAAAGTGACAACAATAA
Found at i:73291 original size:26 final size:26
Alignment explanation
Indices: 73262--73325 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 26
73252 AAATTTTCTT
*
73262 GAGAATTGTTTTCTCCTTTTTATTAAGA
1 GAGAATTG--TTCTCCTTTTTATCAAGA
*
73290 GAGAATTGTTCTCTTTTTTATCAAGA
1 GAGAATTGTTCTCCTTTTTATCAAGA
73316 GAGAATTGTT
1 GAGAATTGTT
73326 ATTGTTTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 26 0.76
28 8 0.24
ACGTcount: A:0.27, C:0.09, G:0.17, T:0.47
Consensus pattern (26 bp):
GAGAATTGTTCTCCTTTTTATCAAGA
Found at i:74417 original size:23 final size:23
Alignment explanation
Indices: 74391--74445 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
74381 AAACTTTAGG
74391 TGGTTGAAAGTTGGCAACAATAA
1 TGGTTGAAAGTTGGCAACAATAA
* * *
74414 TGGTTCATAGTTGGCACCAATAA
1 TGGTTGAAAGTTGGCAACAATAA
74437 TGGTTGAAA
1 TGGTTGAAA
74446 AGTGACATGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (23 bp):
TGGTTGAAAGTTGGCAACAATAA
Found at i:76197 original size:23 final size:22
Alignment explanation
Indices: 76171--76225 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 22
76161 AAACTTTAGG
76171 TGGTTGAAAGTTGGCAACAATAA
1 TGGTTGAAA-TTGGCAACAATAA
* *
76194 TGGTTCATAATTGGCACCAATAA
1 TGGTTGA-AATTGGCAACAATAA
76217 TGGTTGAAA
1 TGGTTGAAA
76226 AGTGACATGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.07
23 24 0.86
24 2 0.07
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (22 bp):
TGGTTGAAATTGGCAACAATAA
Found at i:77827 original size:68 final size:68
Alignment explanation
Indices: 77636--77916 Score: 278
Period size: 68 Copynumber: 4.1 Consensus size: 68
77626 TTAATTTTCT
* * *
77636 ATTAATGGTTAAAGAAAAAATTCGGTTAATTCGATTCGGTTAATAATTTTCAAATAAATTTTGGT
1 ATTAATGGTTAAAGAAAAAAATCGGTTAATTTGATTCGGTTAATAATTTTCAAATAAATTTCGGT
77701 TCG
66 TCG
* ** * * * *
77704 ATTAATGGTT-AAGGAAAAAAT-AATTTATTTTATTCGGTTAATAATTTTAAAATAAATTTCGAT
1 ATTAATGGTTAAAGAAAAAAATCGGTTAATTTGATTCGGTTAATAATTTTCAAATAAATTTCGGT
77767 TCG
66 TCG
* * * *
77770 ATTAATGGTTAAAGAAAAAAATCGGTTGATTTGGTTTGGTTAATAATTTTCAAATAAAGTTCGGT
1 ATTAATGGTTAAAGAAAAAAATCGGTTAATTTGATTCGGTTAATAATTTTCAAATAAATTTCGGT
*
77835 TTG
66 TCG
** *** * *
77838 ATTAACAGTTAAAGAAAAATAATTTATTTTATGTGATTAATTCGGTTAATAATTTTCAAATAAAT
1 ATTAATGGTTAAAGAAAAA-AA--TCGGTTA-AT--TTGATTCGGTTAATAATTTTCAAATAAAT
* *
77903 TTGGGATCG
60 TTCGGTTCG
77912 ATTAA
1 ATTAA
77917 CAGTCAAATA
Statistics
Matches: 170, Mismatches: 35, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
66 47 0.28
67 19 0.11
68 62 0.36
69 2 0.01
71 3 0.02
72 1 0.01
74 36 0.21
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.41
Consensus pattern (68 bp):
ATTAATGGTTAAAGAAAAAAATCGGTTAATTTGATTCGGTTAATAATTTTCAAATAAATTTCGGT
TCG
Found at i:77969 original size:26 final size:25
Alignment explanation
Indices: 77895--77975 Score: 90
Period size: 26 Copynumber: 3.1 Consensus size: 25
77885 AATAATTTTC
* * * *
77895 AAATAAATTTGGGATCGATTAACAGTC
1 AAAT-AATTTCGGTTCGATTAA-TGTT
*
77922 AAATAATTTTGGTTCGATTAATGGTT
1 AAATAATTTCGGTTCGATTAAT-GTT
77948 AAATAATTTCGGTTCGATTAATGTT
1 AAATAATTTCGGTTCGATTAATGTT
77973 AAA
1 AAA
77976 GAAAAAAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
25 6 0.12
26 38 0.79
27 4 0.08
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.38
Consensus pattern (25 bp):
AAATAATTTCGGTTCGATTAATGTT
Found at i:78024 original size:94 final size:93
Alignment explanation
Indices: 77920--78137 Score: 350
Period size: 94 Copynumber: 2.3 Consensus size: 93
77910 CGATTAACAG
* *
77920 TCAAAT-AATTTTGGTTCGATTAATGGTTAAATAATTTCGGTTCGATTAATGTTAAAGAAAAAAA
1 TCAAATAAATTTTGGTTCGATTAACGGTTAAATAATTTCAGTTCGATTAATGTTAAAGAAAAAAA
*
77984 TTCGGTTAATTTGGTTCGGTTAATAAATTT
66 -TCGGTTAATTTGGTTCGATTAAT-AATTT
*
78014 T-AAATAAATTTTGGTTCGATTAACGGTCAAATAATTTCAGTTCGATTAATGTTAAAGAAAAAAA
1 TCAAATAAATTTTGGTTCGATTAACGGTTAAATAATTTCAGTTCGATTAATGTTAAAGAAAAAAA
*
78078 TCGGTTGATTTGGTTCGATTAATAATTT
66 TCGGTTAATTTGGTTCGATTAATAATTT
*
78106 TCAAATAAATTTCGGTTCGATTAACGGTTAAA
1 TCAAATAAATTTTGGTTCGATTAACGGTTAAA
78138 GAAAAATTAA
Statistics
Matches: 115, Mismatches: 7, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
92 6 0.05
93 53 0.46
94 56 0.49
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (93 bp):
TCAAATAAATTTTGGTTCGATTAACGGTTAAATAATTTCAGTTCGATTAATGTTAAAGAAAAAAA
TCGGTTAATTTGGTTCGATTAATAATTT
Found at i:78902 original size:33 final size:33
Alignment explanation
Indices: 78860--78930 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
78850 TACAAGAAGA
* *
78860 AAATCGGCGCAAGAGCAAGAAAGACATGCCAAT
1 AAATCGGCGCAAGACCAAGAAAGACATGCAAAT
78893 AAATCGGCGCAAGACCAAGAAAGACATGCAAAT
1 AAATCGGCGCAAGACCAAGAAAGACATGCAAAT
78926 AAATC
1 AAATC
78931 TGCAACAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.21, G:0.21, T:0.10
Consensus pattern (33 bp):
AAATCGGCGCAAGACCAAGAAAGACATGCAAAT
Found at i:82530 original size:34 final size:34
Alignment explanation
Indices: 82471--82537 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
82461 TTCTTGAGAG
*
82471 TTGTTTTCTCCTTTTTATCAAGAGAGAA-TTGTTA
1 TTGTTTTCTCCTTTTGATC-AGAGAGAAGTTGTTA
82505 TTGTTTTCTCCTTGTTAGATC-GAGAGAAGTTGT
1 TTGTTTTCTCCTT-TT-GATCAGAGAGAAGTTGT
82538 AATTCCTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 20 0.69
35 6 0.21
36 3 0.10
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (34 bp):
TTGTTTTCTCCTTTTGATCAGAGAGAAGTTGTTA
Found at i:83997 original size:23 final size:22
Alignment explanation
Indices: 83955--83998 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
83945 TGAAATAATA
*
83955 TATTTATTAAAAATGTTATTTT
1 TATTTATTAAAAATGATATTTT
83977 TATTTAATTAAAATAT-ATATTT
1 TATTT-ATTAAAA-ATGATATTT
83999 AATTGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
23 12 0.63
24 2 0.11
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TATTTATTAAAAATGATATTTT
Found at i:84572 original size:24 final size:24
Alignment explanation
Indices: 84527--84572 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
84517 TAAATAATAA
* * *
84527 ATTAAGATTATATTTTTGTTAAAT
1 ATTAAGATCATATTTCTATTAAAT
*
84551 ATTAAGATCGTATTTCTATTAA
1 ATTAAGATCATATTTCTATTAA
84573 TGCTTTAATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (24 bp):
ATTAAGATCATATTTCTATTAAAT
Found at i:87500 original size:18 final size:18
Alignment explanation
Indices: 87477--87514 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
87467 GATTAAAATA
87477 TATCAAT-TAGTATATATG
1 TATCAATGTAGTAT-TATG
*
87495 TATCAATGTATTATTATG
1 TATCAATGTAGTATTATG
87513 TA
1 TA
87515 GATTTAGAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47
Consensus pattern (18 bp):
TATCAATGTAGTATTATG
Done.