Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006461.1 Hibiscus syriacus cultivar Beakdansim tig00015656_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: 132878
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:5224 original size:29 final size:29
Alignment explanation
Indices: 5183--5251 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
5173 AAATTATATT
* * *
5183 TTTAGTC-CTTAAACTTTTATAATTTATAC
1 TTTAGTCAC-TAAACTTTAAAAATTTACAC
*
5212 TTTAGTCACTAAAGTTTAAAAATTTACAC
1 TTTAGTCACTAAACTTTAAAAATTTACAC
*
5241 CTTAGTCACTA
1 TTTAGTCACTA
5252 GTCCAAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 33 0.97
30 1 0.03
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (29 bp):
TTTAGTCACTAAACTTTAAAAATTTACAC
Found at i:10197 original size:43 final size:44
Alignment explanation
Indices: 10105--10260 Score: 163
Period size: 43 Copynumber: 3.6 Consensus size: 44
10095 TCCTCTGTTA
* * * * * * *
10105 TGTGCAAGGTTAAGTCTTTACCGTTACCACAGGCTCATTTACTG
1 TGTGCAAGGGTAAGACCTTACAGTTTCCCCAGGCTCATTTGCTG
* *
10149 TGTGCAAGGGTAAG-CCTTACAGTTTCCCCAGGTTCCTTTGCTG
1 TGTGCAAGGGTAAGACCTTACAGTTTCCCCAGGCTCATTTGCTG
* * * *
10192 TGTGCAAGGGTAAG-CTTTATAGTTTCCCCAGGCTCTTTTGCTA
1 TGTGCAAGGGTAAGACCTTACAGTTTCCCCAGGCTCATTTGCTG
* *
10235 AGTGCAAGGGTAAGACCTTACCGTTT
1 TGTGCAAGGGTAAGACCTTACAGTTT
10261 TTGCATGTTC
Statistics
Matches: 94, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
43 73 0.78
44 21 0.22
ACGTcount: A:0.21, C:0.22, G:0.24, T:0.33
Consensus pattern (44 bp):
TGTGCAAGGGTAAGACCTTACAGTTTCCCCAGGCTCATTTGCTG
Found at i:10283 original size:87 final size:87
Alignment explanation
Indices: 10105--10292 Score: 198
Period size: 87 Copynumber: 2.1 Consensus size: 87
10095 TCCTCTGTTA
* * **
10105 TGTGCAAGGTTAAGTCTTTACCGTTACCACAGGCTCATTTACTGTGTGCAAGGGTAAGCCTTACA
1 TGTGCAAGGGTAAGTCTTTACAGTTACCACAGGCTCATTTACTAAGTGCAAGGGTAAGCCTTACA
* *
10170 GTTTCCCCAGGTTCCTTTGCTG
66 GTTTCCCCAGGTTCCTCTACTG
* * * * *
10192 TGTGCAAGGGTAAG-CTTTATAGTTTCCCCAGGCTCTTTTGCTAAGTGCAAGGGTAAGACCTTAC
1 TGTGCAAGGGTAAGTCTTTACAGTTACCACAGGCTCATTTACTAAGTGCAAGGGTAAG-CCTTAC
* *** * *
10256 CGTTTTTGCATGTTCCTCTACTT
65 AGTTTCCCCAGGTTCCTCTACTG
10279 TGTGCACAGGGTAA
1 TGTGCA-AGGGTAA
10293 ATATGTTTTA
Statistics
Matches: 82, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
86 35 0.43
87 40 0.49
88 7 0.09
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.34
Consensus pattern (87 bp):
TGTGCAAGGGTAAGTCTTTACAGTTACCACAGGCTCATTTACTAAGTGCAAGGGTAAGCCTTACA
GTTTCCCCAGGTTCCTCTACTG
Found at i:12524 original size:43 final size:43
Alignment explanation
Indices: 12435--12719 Score: 417
Period size: 43 Copynumber: 6.6 Consensus size: 43
12425 TCCTCTACTA
* * * * *
12435 TGTGCAAGGGTAAGTCCTTACCGTTACCGCAGGCTCATTTGCTG
1 TGTGCAAGGGTAAG-CCTTACAGTTTCCCCAGGTTCCTTTGCTG
*
12479 TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGTTG
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTG
*
12522 TGTGCAAGGGTAAGCCTTACAGTTTCCCGAGGTTCCTTTGCTG
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTG
* *
12565 TGTGCAAGGGTAAGCCTTACAATTTCCCTAGGTTCCTTTGCTG
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTG
12608 TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTG
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTG
* * * * *
12651 TGTGCAAGGGTAAGCTTTATAGTTTCCCCAGGATCTTTTGCTA
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTG
*
12694 TGTGCAAGGGTAAGACCTTACCGTTT
1 TGTGCAAGGGTAAG-CCTTACAGTTT
12720 TTGCATGCTC
Statistics
Matches: 220, Mismatches: 20, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
43 198 0.90
44 22 0.10
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.33
Consensus pattern (43 bp):
TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTG
Found at i:13775 original size:18 final size:18
Alignment explanation
Indices: 13748--13794 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
13738 AGTTCCAACA
* *
13748 CCATTAATATTTCTAG-T
1 CCATTGATATTTCCAGCT
13765 CCCATTGATATTTCCAGCT
1 -CCATTGATATTTCCAGCT
13784 CCATTGATATT
1 CCATTGATATT
13795 ATTAGCATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 25 0.96
19 1 0.04
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.43
Consensus pattern (18 bp):
CCATTGATATTTCCAGCT
Found at i:24340 original size:14 final size:13
Alignment explanation
Indices: 24321--24354 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
24311 CTTTCAATTC
*
24321 TTTTATTATTATTG
1 TTTTATTATT-TTA
24335 TTTTATTATTTTA
1 TTTTATTATTTTA
24348 TTTTATT
1 TTTTATT
24355 TTGTATCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (13 bp):
TTTTATTATTTTA
Found at i:25677 original size:2 final size:2
Alignment explanation
Indices: 25670--25700 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
25660 ATTTATCCTT
25670 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25701 GTTATCCCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25951 original size:13 final size:14
Alignment explanation
Indices: 25930--25974 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
25920 GGAAAAATAG
*
25930 AAGATATAAT-AAA
1 AAGAAATAATAAAA
25943 AAGAAATAATAAAA
1 AAGAAATAATAAAA
25957 AAGAAA-AGA-AAAA
1 AAGAAATA-ATAAAA
25970 AAGAA
1 AAGAA
25975 GACAAATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 19 0.66
14 10 0.34
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (14 bp):
AAGAAATAATAAAA
Found at i:25965 original size:5 final size:5
Alignment explanation
Indices: 25955--26041 Score: 51
Period size: 5 Copynumber: 17.8 Consensus size: 5
25945 GAAATAATAA
* * *
25955 AAAAG AAAAG AAAAA AAGAAG ACAAAT AAAAG AAAAG -AAAG -AAAG AAGAG
1 AAAAG AAAAG AAAAG AA-AAG A-AAAG AAAAG AAAAG AAAAG AAAAG AAAAG
* *
26005 -AGAG AAAAG AAATCA- AAAAG AAAA- AGAAG -AAAG AAAA
1 AAAAG AAAAG AAA--AG AAAAG AAAAG AAAAG AAAAG AAAA
26042 CAGAAAACAT
Statistics
Matches: 65, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
4 19 0.29
5 35 0.54
6 9 0.14
7 2 0.03
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:25970 original size:27 final size:27
Alignment explanation
Indices: 25940--26003 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
25930 AAGATATAAT
*
25940 AAAAAGAA-ATAATAAAAAAGAAAAGAA
1 AAAAAGAAGACAA-AAAAAAGAAAAGAA
*
25967 AAAAAGAAGACAAATAAAAGAAAAGAA
1 AAAAAGAAGACAAAAAAAAGAAAAGAA
*
25994 AGAAAGAAGA
1 AAAAAGAAGA
26004 GAGAGAAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 30 0.91
28 3 0.09
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.05
Consensus pattern (27 bp):
AAAAAGAAGACAAAAAAAAGAAAAGAA
Found at i:26003 original size:11 final size:10
Alignment explanation
Indices: 25940--26047 Score: 61
Period size: 11 Copynumber: 10.9 Consensus size: 10
25930 AAGATATAAT
*
25940 AAAAAGAAAT
1 AAAAAGAAAG
25950 AATAAA-AAAG
1 AA-AAAGAAAG
25960 -AAAAG-AA-
1 AAAAAGAAAG
25967 AAAAAG-AAG
1 AAAAAGAAAG
25976 ACAAATA-AAAG
1 A-AAA-AGAAAG
25987 -AAAAGAAAG
1 AAAAAGAAAG
*
25996 AAAGAAGAGAG
1 AAA-AAGAAAG
*
26007 AGAAAAGAAATC
1 A-AAAAGAAA-G
26019 AAAAAGAAA-
1 AAAAAGAAAG
*
26028 AAGAAGAAAG
1 AAAAAGAAAG
26038 AAAACAGAAA
1 AAAA-AGAAA
26048 ACATATCAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 27
0.70 0.05 0.24
Matches are distributed among these distances:
8 13 0.17
9 17 0.22
10 13 0.17
11 32 0.41
12 3 0.04
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:26012 original size:27 final size:27
Alignment explanation
Indices: 25955--26016 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
25945 GAAATAATAA
*
25955 AAAAGAAAAGAAAAAAAGAAGACAAAT
1 AAAAGAAAAGAAAAAAAGAAGACAAAG
* * *
25982 AAAAGAAAAGAAAGAAAGAAGAGAGAG
1 AAAAGAAAAGAAAAAAAGAAGACAAAG
26009 AAAAGAAA
1 AAAAGAAA
26017 TCAAAAAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.02
Consensus pattern (27 bp):
AAAAGAAAAGAAAAAAAGAAGACAAAG
Found at i:26034 original size:31 final size:33
Alignment explanation
Indices: 25987--26047 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 33
25977 CAAATAAAAG
*
25987 AAAAGAAAGAAAGAAGAGAGAGAAA-AGAAATCA
1 AAAAGAAAGAAAGAAGAAAGA-AAACAGAAATCA
26020 AAAAG-AA-AAAGAAGAAAGAAAACAGAAA
1 AAAAGAAAGAAAGAAGAAAGAAAACAGAAA
26048 ACATATCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 3 0.12
31 16 0.62
32 2 0.08
33 5 0.19
ACGTcount: A:0.74, C:0.03, G:0.21, T:0.02
Consensus pattern (33 bp):
AAAAGAAAGAAAGAAGAAAGAAAACAGAAATCA
Found at i:28267 original size:54 final size:55
Alignment explanation
Indices: 28021--28276 Score: 157
Period size: 55 Copynumber: 4.6 Consensus size: 55
28011 TGATTTTTTT
* * * * * * *
28021 AGAAACTAAGCCTAATTTTCA-GGGTTTCTTGGTTTTTTTTAAAATGAGTTTTATTTAA
1 AGAAGCTAAGCCTGATTTTCAGGGGTTTCTT-GATTATCTTCAAATGA--ATT-TTTAA
* * * * * *
28079 AGAAGCTATGTCC-GATTTTC-GGAAGTTTCTTGATAATTTTGAAAT-AAGTTTTCAA
1 AGAAGCTAAG-CCTGATTTTCAGG-GGTTTCTTGATTATCTTCAAATGAA-TTTTTAA
* * * *
28134 A-AGAGCTAAGCCGGATTTTCAGGGGTTTCTTGA-TATTTTCAAATGATTTTTTTA
1 AGA-AGCTAAGCCTGATTTTCAGGGGTTTCTTGATTATCTTCAAATGAATTTTTAA
* * * **
28188 GGAAAACTAAACCTGATTTTCAGGGGTTTCTTGATTA-CTTCCGATGAATTTTTAA
1 AG-AAGCTAAGCCTGATTTTCAGGGGTTTCTTGATTATCTTCAAATGAATTTTTAA
* * *
28243 AGAAGCTAAGCCTAATTTTTAGGGGCTTCTTGAT
1 AGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGAT
28277 GATAACCGTA
Statistics
Matches: 155, Mismatches: 32, Indels: 26
0.73 0.15 0.12
Matches are distributed among these distances:
54 44 0.28
55 69 0.45
56 7 0.05
57 1 0.01
58 25 0.16
59 9 0.06
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.41
Consensus pattern (55 bp):
AGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATTATCTTCAAATGAATTTTTAA
Found at i:29938 original size:91 final size:91
Alignment explanation
Indices: 29763--30039 Score: 333
Period size: 91 Copynumber: 3.0 Consensus size: 91
29753 GATAAACCAA
* * **
29763 TCAACATTTCCAGTGGAAGGGTTCATAATGAGAAGAACTCATCCAATAAGGGAGAATAAGTTCAT
1 TCAACATTTCCAGTGG-AGAGTTCATAATGAGAAAAACTCATCCAACGAGGGAGAATAAGTTCAT
*
29828 AATGAGAAA-AACTTGTTCAACCTTGGC
65 AATGA-AAAGAACTTGTTCAACCTTAGC
* * * * *
29855 AT-AACATTTCTAGTGGAGAGCTCATAATGAGAATAATTCATCCAACGAGGGAAAATAAGTTCAT
1 -TCAACATTTCCAGTGGAGAGTTCATAATGAGAAAAACTCATCCAACGAGGGAGAATAAGTTCAT
* * *
29919 ACTGAAAAGAATTTATTCAACCTTAGC
65 AATGAAAAGAACTTGTTCAACCTTAGC
* * * * *
29946 TCAACATATCCAGTGGAGAGTTTATAATGAGAAAAACTCATCCGACGAGAGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAAAACTCATCCAACGAGGGAGAATAAGTTCATA
* *
30011 ATGAGAAGAACTTGTTCAACCTCAGC
66 ATGAAAAGAACTTGTTCAACCTTAGC
30037 TCA
1 TCA
30040 TTTCCATCAC
Statistics
Matches: 155, Mismatches: 27, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
90 4 0.03
91 137 0.88
92 13 0.08
93 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (91 bp):
TCAACATTTCCAGTGGAGAGTTCATAATGAGAAAAACTCATCCAACGAGGGAGAATAAGTTCATA
ATGAAAAGAACTTGTTCAACCTTAGC
Found at i:32938 original size:25 final size:24
Alignment explanation
Indices: 32901--32948 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
32891 ATTACTATTT
*
32901 TATGTATGGTATGTACATTTTTATG
1 TATGTATGGTATGCA-ATTTTTATG
*
32926 TATGTATGTTATGCAATTTTTAT
1 TATGTATGGTATGCAATTTTTAT
32949 TTTATTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.25, C:0.04, G:0.17, T:0.54
Consensus pattern (24 bp):
TATGTATGGTATGCAATTTTTATG
Found at i:44320 original size:33 final size:34
Alignment explanation
Indices: 44283--44357 Score: 91
Period size: 33 Copynumber: 2.2 Consensus size: 34
44273 TTTGCTTGAA
* *
44283 GAAAAAAGAAGAAGAA-AAAAAATGAGTG-AAAAT
1 GAAAAAAGAA-AAAAATAAAAAATGAATGAAAAAT
*
44316 GAAAAAATAAAAAAATAAAAAATGAATGAAAAAAT
1 GAAAAAAGAAAAAAATAAAAAATGAATG-AAAAAT
44351 GAAAAAA
1 GAAAAAA
44358 TGAGGGTTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 4 0.11
33 20 0.56
35 12 0.33
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.11
Consensus pattern (34 bp):
GAAAAAAGAAAAAAATAAAAAATGAATGAAAAAT
Found at i:44351 original size:8 final size:8
Alignment explanation
Indices: 44311--44360 Score: 56
Period size: 8 Copynumber: 6.9 Consensus size: 8
44301 AAAATGAGTG
44311 AAAATGAA
1 AAAATGAA
*
44319 AAAATAAA
1 AAAATGAA
44327 AAAAT-AA
1 AAAATGAA
44334 AAAATG--
1 AAAATGAA
44340 --AATGAA
1 AAAATGAA
44346 AAAATGAA
1 AAAATGAA
44354 AAAATGA
1 AAAATGA
44361 GGGTTCAAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
4 4 0.11
7 7 0.19
8 25 0.69
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (8 bp):
AAAATGAA
Found at i:45516 original size:55 final size:55
Alignment explanation
Indices: 45365--45782 Score: 625
Period size: 55 Copynumber: 7.7 Consensus size: 55
45355 TGTTTGATGG
*
45365 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATT-TATGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGT-TGA
* *
45420 AGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
*
45473 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGACAGACGCGATTGTTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
*
45528 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
*
45583 AGATT-TCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGA
1 AGATTGT-TCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
* *
45638 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
* * * *
45693 AGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
* * *
45746 AGATTGTCCGAGT-TCTATACTCTCTAAAGAAAGAGGG
1 AGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGG
45783 AGCGAACCCG
Statistics
Matches: 335, Mismatches: 20, Indels: 16
0.90 0.05 0.04
Matches are distributed among these distances:
53 94 0.28
54 6 0.02
55 235 0.70
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.28
Consensus pattern (55 bp):
AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
Found at i:47909 original size:25 final size:24
Alignment explanation
Indices: 47872--47919 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
47862 ATTACTATTT
*
47872 TATGTATGGTATGTACATTTTTATG
1 TATGTATGGTATGCA-ATTTTTATG
*
47897 TATGTATGTTATGCAATTTTTAT
1 TATGTATGGTATGCAATTTTTAT
47920 TTTATTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.25, C:0.04, G:0.17, T:0.54
Consensus pattern (24 bp):
TATGTATGGTATGCAATTTTTATG
Found at i:53298 original size:27 final size:26
Alignment explanation
Indices: 53254--53306 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
53244 TTCCAGAAGG
53254 TGCTGACTAGATCCTCTAGAAAACTAC
1 TGCTGACTAGATCCTCTAG-AAACTAC
*
53281 TGCTGACTGGA-CCTTCTAGAAACTAC
1 TGCTGACTAGATCC-TCTAGAAACTAC
53307 CACGTCGGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (26 bp):
TGCTGACTAGATCCTCTAGAAACTAC
Found at i:55083 original size:16 final size:17
Alignment explanation
Indices: 55062--55094 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
55052 AAATTTTGTC
55062 ATATTTA-ATAATTTAT
1 ATATTTACATAATTTAT
55078 ATATTTACTATAATTTA
1 ATATTTAC-ATAATTTA
55095 AAAAACATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATTTACATAATTTAT
Found at i:56255 original size:12 final size:12
Alignment explanation
Indices: 56238--56277 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
56228 ACAATAATTA
56238 AAATATATACAT
1 AAATATATACAT
*
56250 AAATATACACAT
1 AAATATATACAT
*
56262 ACATATATTACAT
1 AAATATA-TACAT
56275 AAA
1 AAA
56278 AATGTAAGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
12 17 0.74
13 6 0.26
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATATATACAT
Found at i:56891 original size:13 final size:13
Alignment explanation
Indices: 56870--56929 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
56860 ATTTTGTTAG
56870 TATTTTATTTAAT
1 TATTTTATTTAAT
* *
56883 TATTGTA-TTATT
1 TATTTTATTTAAT
56895 TAATTTT-TTT-AT
1 T-ATTTTATTTAAT
56907 TATTTTATTTAAT
1 TATTTTATTTAAT
56920 TATTTTATTT
1 TATTTTATTT
56930 TTTACAGTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 5 0.13
12 10 0.26
13 24 0.62
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.72
Consensus pattern (13 bp):
TATTTTATTTAAT
Found at i:56895 original size:21 final size:20
Alignment explanation
Indices: 56870--56933 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
56860 ATTTTGTTAG
56870 TATTTTATTTAATTATTGTAT
1 TATTTTATTTAATTATT-TAT
*
56891 TA-TTTAATT--TT-TTTAT
1 TATTTTATTTAATTATTTAT
56907 TATTTTATTTAATTATTTTAT
1 TATTTTATTTAATTA-TTTAT
56928 T-TTTTA
1 TATTTTA
56934 CAGTTATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
16 5 0.14
17 8 0.22
18 2 0.06
19 2 0.06
20 11 0.31
21 8 0.22
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.72
Consensus pattern (20 bp):
TATTTTATTTAATTATTTAT
Found at i:56911 original size:37 final size:37
Alignment explanation
Indices: 56860--56933 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
56850 AATTAATCAT
56860 ATTTTGTTAGTATTTTATTTAATTATTGTATTATTTA
1 ATTTTGTTAGTATTTTATTTAATTATTGTATTATTTA
* * * *
56897 ATTTTTTTATTATTTTATTTAATTATTTTATTTTTTA
1 ATTTTGTTAGTATTTTATTTAATTATTGTATTATTTA
56934 CAGTTATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (37 bp):
ATTTTGTTAGTATTTTATTTAATTATTGTATTATTTA
Found at i:56916 original size:16 final size:16
Alignment explanation
Indices: 56874--56916 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
56864 TGTTAGTATT
* *
56874 TTATTTAATTATTGTA
1 TTATTTAATTTTTTTA
56890 TTATTTAATTTTTTTA
1 TTATTTAATTTTTTTA
*
56906 TTATTTTATTT
1 TTATTTAATTT
56917 AATTATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
TTATTTAATTTTTTTA
Found at i:57196 original size:8 final size:8
Alignment explanation
Indices: 57179--57226 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 8
57169 TTTATAACTG
*
57179 TAAAAAAA
1 TAAAATAA
57187 TAAAATAA
1 TAAAATAA
*
57195 TAAAAAAA
1 TAAAATAA
*
57203 TTAAATAA
1 TAAAATAA
*
57211 TACAATAA
1 TAAAATAA
*
57219 TTAAATAA
1 TAAAATAA
57227 AATACTAACA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (8 bp):
TAAAATAA
Found at i:57200 original size:16 final size:16
Alignment explanation
Indices: 57179--57226 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
57169 TTTATAACTG
*
57179 TAAAAAAATAAAATAA
1 TAAAAAAATTAAATAA
57195 TAAAAAAATTAAATAA
1 TAAAAAAATTAAATAA
* *
57211 TACAATAATTAAATAA
1 TAAAAAAATTAAATAA
57227 AATACTAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (16 bp):
TAAAAAAATTAAATAA
Found at i:61007 original size:18 final size:18
Alignment explanation
Indices: 60984--61026 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
60974 TTTATTTTTA
60984 ATATTGTGAGGGTAAACT
1 ATATTGTGAGGGTAAACT
61002 ATATTGTGAGGGTAAACT
1 ATATTGTGAGGGTAAACT
*
61020 ACATTGT
1 ATATTGT
61027 TCACCACTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.35
Consensus pattern (18 bp):
ATATTGTGAGGGTAAACT
Found at i:63108 original size:12 final size:12
Alignment explanation
Indices: 63091--63129 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
63081 ACAATAATTA
63091 AAATATATACAT
1 AAATATATACAT
*
63103 AAATATACACAT
1 AAATATATACAT
* *
63115 ACATATATACTT
1 AAATATATACAT
63127 AAA
1 AAA
63130 AATGTAAGTC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (12 bp):
AAATATATACAT
Found at i:65514 original size:32 final size:31
Alignment explanation
Indices: 65463--65544 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 31
65453 CAAATATAGG
**
65463 TGTTTTGTTTCAAGGGAAACAGA-TGCAAAGA
1 TGTTTTGTTTCAAAAGAAACAGACT-CAAAGA
*
65494 TAGTTTTGTTTCAAAAGAAACATACTCAAAGA
1 T-GTTTTGTTTCAAAAGAAACAGACTCAAAGA
*
65526 T-TTTGTTTTTCAAAAGAAA
1 TGTTT-TGTTTCAAAAGAAA
65545 TTGTCTCAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
30 3 0.07
31 14 0.32
32 26 0.59
33 1 0.02
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (31 bp):
TGTTTTGTTTCAAAAGAAACAGACTCAAAGA
Found at i:65757 original size:32 final size:32
Alignment explanation
Indices: 65721--65788 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 32
65711 GATCGTTCAT
65721 TGTTAAATCCCCAAAGATG-CCTCAACATTCGA
1 TGTTAAATCCCCAAAGATGCCCT-AACATTCGA
*
65753 TGTTAAATCTCCAAAGATGCCCTAACATTCGA
1 TGTTAAATCCCCAAAGATGCCCTAACATTCGA
65785 TGTT
1 TGTT
65789 TCTTGCTTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 31 0.91
33 3 0.09
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.29
Consensus pattern (32 bp):
TGTTAAATCCCCAAAGATGCCCTAACATTCGA
Found at i:68799 original size:32 final size:32
Alignment explanation
Indices: 68763--68824 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
68753 ATTAAAAATG
68763 ACACAAACAAAAGAAAAGAAA-TAAGTTAGTGT
1 ACACAAACAAAAGAAAAGAAATTAA-TTAGTGT
*
68795 ACACAAACAAAAGAAAATAAATTAATTAGT
1 ACACAAACAAAAGAAAAGAAATTAATTAGT
68825 ACATGTAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 25 0.89
33 3 0.11
ACGTcount: A:0.61, C:0.10, G:0.11, T:0.18
Consensus pattern (32 bp):
ACACAAACAAAAGAAAAGAAATTAATTAGTGT
Found at i:71665 original size:3 final size:3
Alignment explanation
Indices: 71646--71683 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
71636 ATGTATAATG
*
71646 TAA TAT TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA T
71684 TTTTTGTAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:72998 original size:9 final size:9
Alignment explanation
Indices: 72975--73028 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
72965 TTTCAAATTT
72975 TAAAAAATCA
1 TAAAAAAT-A
*
72985 GAAAAAATA
1 TAAAAAATA
72994 TAAAAAATA
1 TAAAAAATA
*
73003 TACAAAATA
1 TAAAAAATA
73012 -AAAAAATTA
1 TAAAAAA-TA
*
73021 CAAAAAAT
1 TAAAAAAT
73029 TAGTATGATT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
8 5 0.13
9 20 0.53
10 13 0.34
ACGTcount: A:0.74, C:0.06, G:0.02, T:0.19
Consensus pattern (9 bp):
TAAAAAATA
Found at i:73014 original size:16 final size:16
Alignment explanation
Indices: 72988--73025 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 16
72978 AAAATCAGAA
72988 AAAATATAAAAAATATAC
1 AAAATA-AAAAAAT-TAC
73006 AAAATAAAAAAATTAC
1 AAAATAAAAAAATTAC
73022 AAAA
1 AAAA
73026 AATTAGTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.35
17 7 0.35
18 6 0.30
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAATAAAAAAATTAC
Found at i:74925 original size:5 final size:5
Alignment explanation
Indices: 74909--74939 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
74899 CATTCAATGG
74909 TTAAT ATTAAT TTAAT TTAAT TTAAT TTAAT
1 TTAAT -TTAAT TTAAT TTAAT TTAAT TTAAT
74940 CATAGTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TTAAT
Found at i:82591 original size:3 final size:3
Alignment explanation
Indices: 82583--82628 Score: 65
Period size: 3 Copynumber: 14.7 Consensus size: 3
82573 AGTATTTTTA
*
82583 AAT AAT AAT AAT AAT AAT ACT AAT AAT AAT AAT AACTT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA--T AAT AAT AA
82629 CGAGTTGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 36 0.92
5 3 0.08
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:82867 original size:41 final size:41
Alignment explanation
Indices: 82813--82909 Score: 158
Period size: 41 Copynumber: 2.4 Consensus size: 41
82803 GATCCATTCT
**
82813 GCTGTCACTCAGGGAAGATTGAATCATTGCAGACTTGTTCC
1 GCTGTCACTCAGGGAAGATTGAATCAGGGCAGACTTGTTCC
82854 GCTGTCACTCAGGGAAGATTGAATCAGGGCAGACTTGTTCC
1 GCTGTCACTCAGGGAAGATTGAATCAGGGCAGACTTGTTCC
* *
82895 GTTGTCACTAAGGGA
1 GCTGTCACTCAGGGA
82910 CTATCAAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (41 bp):
GCTGTCACTCAGGGAAGATTGAATCAGGGCAGACTTGTTCC
Found at i:86723 original size:17 final size:18
Alignment explanation
Indices: 86701--86746 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
86691 ATTAATGAAT
**
86701 AAAATGCAATGCGAAAA-
1 AAAATGCAATGAAAAAAG
86718 AAAATGCAATGAAAAAAG
1 AAAATGCAATGAAAAAAG
86736 AAAATGCAATG
1 AAAATGCAATG
86747 TGGATGCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.61, C:0.09, G:0.17, T:0.13
Consensus pattern (18 bp):
AAAATGCAATGAAAAAAG
Found at i:91005 original size:3 final size:3
Alignment explanation
Indices: 90997--91134 Score: 192
Period size: 3 Copynumber: 46.7 Consensus size: 3
90987 GTGGGTTGTA
90997 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
** * * **
91044 AAT AAT AAT AAT AAT AAT AAT AA- AAT GTT AGT ATT TTT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
91089 AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
91135 AATGTTAGTA
Statistics
Matches: 123, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
2 6 0.05
3 116 0.94
4 1 0.01
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:91124 original size:68 final size:68
Alignment explanation
Indices: 91015--91167 Score: 290
Period size: 68 Copynumber: 2.2 Consensus size: 68
91005 TAATAATAAT
91015 AATAATAATAATAATAATAATAATATAATAATAATAATAATAATAATAATAAAATGTTAGTATTT
1 AATAATAATAATAATAATAATAATATAATAATAATAATAATAATAATAATAAAATGTTAGTATTT
91080 TTA
66 TTA
91083 AATAATAATAATAATAATAATAATA-ATATAATAATAATAATAATAATAATAAAATGTTAGTATT
1 AATAATAATAATAATAATAATAATATA-ATAATAATAATAATAATAATAATAAAATGTTAGTATT
91147 TTTA
65 TTTA
91151 AATAATAATAATAATAA
1 AATAATAATAATAATAA
91168 CTTAATAAGA
Statistics
Matches: 84, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
67 1 0.01
68 83 0.99
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (68 bp):
AATAATAATAATAATAATAATAATATAATAATAATAATAATAATAATAATAAAATGTTAGTATTT
TTA
Found at i:93444 original size:15 final size:14
Alignment explanation
Indices: 93424--93456 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
93414 AAAAATACAT
93424 ATATATATATATAAA
1 ATATATATAT-TAAA
93439 ATATATATATTAAA
1 ATATATATATTAAA
93453 ATAT
1 ATAT
93457 TAAATTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATATATATTAAA
Found at i:93456 original size:21 final size:22
Alignment explanation
Indices: 93405--93461 Score: 53
Period size: 23 Copynumber: 2.5 Consensus size: 22
93395 TGACCCCCTG
*
93405 AAAATATTAAAAAATACATATAT
1 AAAATA-TAAAATATACATATAT
* *
93428 ATATATATAAAATATATATAT-T
1 A-AAATATAAAATATACATATAT
*
93450 AAAATATTAAAT
1 AAAATATAAAAT
93462 TTAACCCCCT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
21 9 0.32
22 2 0.07
23 13 0.46
24 4 0.14
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAATATAAAATATACATATAT
Found at i:95265 original size:43 final size:42
Alignment explanation
Indices: 95186--95279 Score: 125
Period size: 43 Copynumber: 2.2 Consensus size: 42
95176 TGATAAGGTT
* *
95186 TAGGGTTTAGAGTTTAGAGTTTATGTGATATGATTTAAGATC
1 TAGGGTTTAGAGTTTAGAGTTTATATGACATGATTTAAGATC
* * * *
95228 TAGGGTTTAGTGTTTAGGGGTTTATATGACATGATTTAAGGTT
1 TAGGGTTTAGAGTTTA-GAGTTTATATGACATGATTTAAGATC
95271 TAGGGTTTA
1 TAGGGTTTA
95280 TATGGTAGGA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
42 15 0.33
43 30 0.67
ACGTcount: A:0.26, C:0.02, G:0.29, T:0.44
Consensus pattern (42 bp):
TAGGGTTTAGAGTTTAGAGTTTATATGACATGATTTAAGATC
Found at i:95291 original size:28 final size:28
Alignment explanation
Indices: 95239--95307 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
95229 AGGGTTTAGT
*
95239 GTTTAGGGGTTTATATGACATGATTTAAG
1 GTTTA-GGGTTTATATGACAGGATTTAAG
**
95268 GTTTAGGGTTTATATGGTAGGATTTAAG
1 GTTTAGGGTTTATATGACAGGATTTAAG
*
95296 ATTTAGGGTTTA
1 GTTTAGGGTTTA
95308 CATATTAGAG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 31 0.86
29 5 0.14
ACGTcount: A:0.26, C:0.01, G:0.29, T:0.43
Consensus pattern (28 bp):
GTTTAGGGTTTATATGACAGGATTTAAG
Found at i:97549 original size:23 final size:23
Alignment explanation
Indices: 97519--97581 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
97509 TTTGGCTAAC
* *
97519 AATTGAGCTTGAGTTGAGTTTAA
1 AATTGAGCTTGAATTGAGCTTAA
97542 AATTGAGCTTGAATTGAGCTTAA
1 AATTGAGCTTGAATTGAGCTTAA
* * *
97565 AATCGAGTTTCAATTGA
1 AATTGAGCTTGAATTGA
97582 ATTCAAGTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (23 bp):
AATTGAGCTTGAATTGAGCTTAA
Found at i:97558 original size:11 final size:11
Alignment explanation
Indices: 97519--97562 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
97509 TTTGGCTAAC
97519 AATTGAGCTTG
1 AATTGAGCTTG
* * *
97530 AGTTGAGTTTAA
1 AATTGAGCTT-G
97542 AATTGAGCTTG
1 AATTGAGCTTG
97553 AATTGAGCTT
1 AATTGAGCTT
97563 AAAATCGAGT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
11 18 0.69
12 8 0.31
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.39
Consensus pattern (11 bp):
AATTGAGCTTG
Found at i:98415 original size:235 final size:235
Alignment explanation
Indices: 97999--98441 Score: 559
Period size: 235 Copynumber: 1.9 Consensus size: 235
97989 TTTGGGGGGG
* *
97999 GGGGGCCATTTAATTTTTTTTAGCAAACCAAGAATATTAATAACGCCTATCATGTTTTTCTTGAG
1 GGGGGCCATTTAATTTTTTTGAGCAAACCAAAAATATTAATAACGCCTATCATGTTTTTCTTGAG
* * * * *
98064 AAAATAGATAATTAGAGGAATAGATTTGATATGGATATGTACTCGAGTTAAATTTTATCTTGTTT
66 AAAATAGATAATTAGAGGAATAGATTTGATATGGACATGCACTCAAGTCAAATTTTATCTCGTTT
* * * * * ** *
98129 ATTAATTGGATATTCCTATATTGATTTACGTATTTTGGGATCAGTAAACGAAATACTAACATTTT
131 ATTAACTAGATATTCCTACATTAACTTACGTAGATCGGGATCAGTAAACGAAATACTAACATTTT
98194 CAACATCAACAACAATGGCAGAACTAAACACTATTTTCTA
196 CAACATCAACAACAATGGCAGAACTAAACACTATTTTCTA
* * *
98234 GGGGG-CATTTAAATTTTTTTGAGCAAACCAAAAATATTAATAATGTCTATCATGTTTTTCTTGC
1 GGGGGCCATTT-AATTTTTTTGAGCAAACCAAAAATATTAATAACGCCTATCATGTTTTTCTTGA
* * * *
98298 GAAAATAGATAATTAGAGGAATATATTTGTTATGGGCATGCACTCAAGTCAAATTTTATGTCG-T
65 GAAAATAGATAATTAGAGGAATAGATTTGATATGGACATGCACTCAAGTCAAATTTTATCTCGTT
* * ** * * **
98362 TATTAACTAGATATTCTTACATTAACTTACTTAAGATCGCGTTTTA-TAAACGAAATATTAATGT
130 TATTAACTAGATATTCCTACATTAACTTACGT-AGATCG-GGATCAGTAAACGAAATACTAACAT
*
98426 TTTCAACCTCAACAAC
193 TTTCAACATCAACAAC
98442 TATAGACATA
Statistics
Matches: 174, Mismatches: 31, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
234 31 0.18
235 140 0.80
236 3 0.02
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.37
Consensus pattern (235 bp):
GGGGGCCATTTAATTTTTTTGAGCAAACCAAAAATATTAATAACGCCTATCATGTTTTTCTTGAG
AAAATAGATAATTAGAGGAATAGATTTGATATGGACATGCACTCAAGTCAAATTTTATCTCGTTT
ATTAACTAGATATTCCTACATTAACTTACGTAGATCGGGATCAGTAAACGAAATACTAACATTTT
CAACATCAACAACAATGGCAGAACTAAACACTATTTTCTA
Found at i:98994 original size:2 final size:2
Alignment explanation
Indices: 98983--99023 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
98973 TAATATTTTA
*
98983 AT AT AT -T AT AT AT AT AT AT AT AT AT GT 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
99024 TTATTTTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:99578 original size:3 final size:3
Alignment explanation
Indices: 99564--99611 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
99554 TTAAAATGAT
* *
99564 TAA TAA -AA TAA TAA TAA TAA TAG TAG TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
99610 TA
1 TA
99612 TTTTTGGTAG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 4 0.10
3 37 0.90
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:99997 original size:40 final size:42
Alignment explanation
Indices: 99901--100137 Score: 202
Period size: 40 Copynumber: 5.5 Consensus size: 42
99891 AAGGGTGATA
* *
99901 ACACGGTTCCTACGCGATGAGGAAGG-CTGGTTATCTAGGGG-TG
1 ACACGGTTCCTACGTGATGAGG-AGGTCTGG-T-TCTGGGGGATG
*
99944 ACACGGCTCCTACGTGATGAGGAGGTCTGG-TC-GGGGGATG
1 ACACGGTTCCTACGTGATGAGGAGGTCTGGTTCTGGGGGATG
* ** *
99984 ACACGGTTCCTACGTGATGAGGATGG-CAGGTCATCTTTAGGAATGATT
1 ACACGGTTCCTACGTGATGAGGA-GGTCTGGT--TC--T-GG-GGGATG
* *
100032 ACACGGTTCCTATGTGATGAGGACGTCTGGTTATCTGGGGG-TG
1 ACACGGTTCCTACGTGATGAGGAGGTCTGG-T-TCTGGGGGATG
* *
100075 ACACGGCTCCTACGTGATGAGGAGGTCT-GATC-GGGGGATG
1 ACACGGTTCCTACGTGATGAGGAGGTCTGGTTCTGGGGGATG
*
100115 ACACGGTTCCTACGCGATGAGGA
1 ACACGGTTCCTACGTGATGAGGA
100138 CGGCATGCCA
Statistics
Matches: 160, Mismatches: 20, Indels: 31
0.76 0.09 0.15
Matches are distributed among these distances:
39 9 0.06
40 54 0.34
41 2 0.01
42 4 0.03
43 52 0.32
44 1 0.01
45 2 0.01
46 1 0.01
47 3 0.02
48 31 0.19
49 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.36, T:0.24
Consensus pattern (42 bp):
ACACGGTTCCTACGTGATGAGGAGGTCTGGTTCTGGGGGATG
Found at i:100086 original size:131 final size:132
Alignment explanation
Indices: 99800--100155 Score: 464
Period size: 131 Copynumber: 2.7 Consensus size: 132
99790 GGTTTGGTCG
* * * * * * * * *
99800 TCTAAGGGTGACACGACTCCTACGTGATAAGGAGATCTGGTCGGTGAATGATACGGCTCATACGT
1 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCCTACGT
* **
99865 GATGAAG-TGTTATGGCCATCTTTAGGAAGGGTGATAACACGGTTCCTACGCGATGAGGAAGGCT
66 GATGAGGATGGCA-GGCCATCTTTAGGAA--GTGATAACACGGTTCCTACGCGATGAGGAAGGCT
99929 GGTTA
128 GGTTA
99934 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCCTACGT
1 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCCTACGT
* * * * * *
99999 GATGAGGATGGCAGGTCATCTTTAGGAA-TGATTACACGGTTCCTATGTGATGAGGACGTCTGGT
66 GATGAGGATGGCAGGCCATCTTTAGGAAGTGATAACACGGTTCCTACGCGATGAGGAAGGCTGGT
100063 TA
131 TA
* * *
100065 TCTGGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGATCGGGGGATGACACGGTTCCTACGC
1 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCCTACGT
* *
100130 GATGAGGACGGCATGCCATCTTTAGG
66 GATGAGGATGGCAGGCCATCTTTAGG
100156 GATAATGTAT
Statistics
Matches: 197, Mismatches: 24, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
131 118 0.60
134 76 0.39
135 3 0.02
ACGTcount: A:0.22, C:0.19, G:0.34, T:0.25
Consensus pattern (132 bp):
TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCCTACGT
GATGAGGATGGCAGGCCATCTTTAGGAAGTGATAACACGGTTCCTACGCGATGAGGAAGGCTGGT
TA
Found at i:100318 original size:66 final size:64
Alignment explanation
Indices: 100257--100404 Score: 197
Period size: 66 Copynumber: 2.3 Consensus size: 64
100247 GTGTTTCAGG
* * * *
100257 ACAAACATACTCAAAGATTTTCCTTCAAAAGATATTGTCTCAAGAGAGATAAAATTTTGTTTCTA
1 ACAAACATACTCAAAGATTTTCCTTCAAAAGAAACTGTCTC-A-AGACACAAAATTTTGTTTCTA
100322 A
64 A
* * *
100323 AGAAACATACTCAAAGATTTTTCTTCAAAAGAAACTGTCTCAAGACACAAAATTTTGTTTCCAA
1 ACAAACATACTCAAAGATTTTCCTTCAAAAGAAACTGTCTCAAGACACAAAATTTTGTTTCTAA
* *
100387 ATAAACAGACTCAAAGAT
1 ACAAACATACTCAAAGAT
100405 GGGTTATGTC
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
64 35 0.48
65 1 0.01
66 37 0.51
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (64 bp):
ACAAACATACTCAAAGATTTTCCTTCAAAAGAAACTGTCTCAAGACACAAAATTTTGTTTCTAA
Found at i:100612 original size:32 final size:32
Alignment explanation
Indices: 100564--100627 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
100554 TTCACATCAG
* *
100564 GATGTTGACTCCCCAAATACGCCCCAACATTC
1 GATGTTGAATCCCCAAAGACGCCCCAACATTC
* * *
100596 GATGTTGAATCTCCAAAGATGCCCCATCATTC
1 GATGTTGAATCCCCAAAGACGCCCCAACATTC
100628 ATTATTTCTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.28, C:0.33, G:0.14, T:0.25
Consensus pattern (32 bp):
GATGTTGAATCCCCAAAGACGCCCCAACATTC
Found at i:101707 original size:25 final size:25
Alignment explanation
Indices: 101673--101728 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
101663 GTGCTTCTTG
*
101673 TCTTCTTTTTTTCTTCATTTG-T-TTT
1 TCTTTTTTTTTTC-TC-TTTGATATTT
101698 TCTTTTTTTTTTCTCTTTGATATTT
1 TCTTTTTTTTTTCTCTTTGATATTT
101723 TCTTTT
1 TCTTTT
101729 CATTTATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 4 0.14
24 3 0.11
25 21 0.75
ACGTcount: A:0.05, C:0.14, G:0.04, T:0.77
Consensus pattern (25 bp):
TCTTTTTTTTTTCTCTTTGATATTT
Found at i:109827 original size:21 final size:21
Alignment explanation
Indices: 109801--109840 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
109791 CCCCCTTTGA
*
109801 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
109822 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
109841 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:112303 original size:61 final size:61
Alignment explanation
Indices: 112233--112426 Score: 197
Period size: 61 Copynumber: 3.2 Consensus size: 61
112223 ATTTTAATAT
112233 TTCGATATAACAAATTAAGTTAAATGGATTTTAAGATTTTCCAAATGATTTTCTAAGTATA
1 TTCGATATAACAAATTAAGTTAAATGGATTTTAAGATTTTCCAAATGATTTTCTAAGTATA
* ** * * **
112294 TTCGATATAAC-TATTCGAA-TATCAAA-ACATTACTCCAA-ATATTTCAAAAACA-TTT-TAA-
1 TTCGATATAACAAATT--AAGT-T-AAATGGATT--T-TAAGAT-TTTCCAAATGATTTTCTAAG
112352 TAT-
58 TATA
112355 TTCGATATAACAAATTAAGTTAAATGGATTTTAAGATTTTCCAAATGATTTTCTAAGTATA
1 TTCGATATAACAAATTAAGTTAAATGGATTTTAAGATTTTCCAAATGATTTTCTAAGTATA
112416 TTCGATATAAC
1 TTCGATATAAC
112427 TATTCGAATA
Statistics
Matches: 103, Mismatches: 14, Indels: 32
0.69 0.09 0.21
Matches are distributed among these distances:
57 10 0.10
58 6 0.06
59 6 0.06
60 12 0.12
61 35 0.34
62 12 0.12
63 6 0.06
64 6 0.06
65 10 0.10
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (61 bp):
TTCGATATAACAAATTAAGTTAAATGGATTTTAAGATTTTCCAAATGATTTTCTAAGTATA
Found at i:112436 original size:122 final size:122
Alignment explanation
Indices: 112219--112472 Score: 499
Period size: 122 Copynumber: 2.1 Consensus size: 122
112209 GAGATTGTTG
112219 AAACATTTTAATATTTCGATATAACAAATTAAGTTAAATGGATTTTAAGATTTTCCAAATGATTT
1 AAACATTTTAATATTTCGATATAACAAATTAAGTTAAATGGATTTTAAGATTTTCCAAATGATTT
112284 TCTAAGTATATTCGATATAACTATTCGAATATCAAAACATTACTCCAAATATTTCAA
66 TCTAAGTATATTCGATATAACTATTCGAATATCAAAACATTACTCCAAATATTTCAA
112341 AAACATTTTAATATTTCGATATAACAAATTAAGTTAAATGGATTTTAAGATTTTCCAAATGATTT
1 AAACATTTTAATATTTCGATATAACAAATTAAGTTAAATGGATTTTAAGATTTTCCAAATGATTT
112406 TCTAAGTATATTCGATATAACTATTCGAATATCAAAACATTACTCCAAATATTTCAA
66 TCTAAGTATATTCGATATAACTATTCGAATATCAAAACATTACTCCAAATATTTCAA
112463 AAATCATTTT
1 AAA-CATTTT
112473 TGATCCTTAC
Statistics
Matches: 131, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
122 125 0.95
123 6 0.05
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (122 bp):
AAACATTTTAATATTTCGATATAACAAATTAAGTTAAATGGATTTTAAGATTTTCCAAATGATTT
TCTAAGTATATTCGATATAACTATTCGAATATCAAAACATTACTCCAAATATTTCAA
Found at i:115459 original size:29 final size:30
Alignment explanation
Indices: 115331--115584 Score: 146
Period size: 30 Copynumber: 8.6 Consensus size: 30
115321 CAGTAAATAA
* *
115331 AGAAACTTAAAGGACTAAAATAACTAAAAT
1 AGAAACTTAAAGGACTAAAATAGCTAAAAC
* * * * *
115361 AAAAAGTTAAAGGACCAAAATAGCAAAAAT
1 AGAAACTTAAAGGACTAAAATAGCTAAAAC
* *
115391 AAAAACTTAAAGGACTAAAATAGCTAAAAT
1 AGAAACTTAAAGGACTAAAATAGCTAAAAC
* * *
115421 AGAAAGTTAAAGGACTAAAGT-GGTAAAAC
1 AGAAACTTAAAGGACTAAAATAGCTAAAAC
* ** *
115450 ATAAACTTAAAGGGTTAAAATA---ATAAC
1 AGAAACTTAAAGGACTAAAATAGCTAAAAC
** * *
115477 CTAAACTTAAGGGTCT-AAATAGC-AAATAC
1 AGAAACTTAAAGGACTAAAATAGCTAAA-AC
* * * * *
115506 A-AACATTTAAAGAACTAAAATAACAAAAAT
1 AGAA-ACTTAAAGGACTAAAATAGCTAAAAC
* * * *
115536 AAAAACTTAAGGGACTAAAAT-GGTATTAAC
1 AGAAACTTAAAGGACTAAAATAGCTA-AAAC
* *
115566 AGAAACTAAAAGGGCTAAA
1 AGAAACTTAAAGGACTAAA
115585 CATTAATTAC
Statistics
Matches: 172, Mismatches: 43, Indels: 18
0.74 0.18 0.08
Matches are distributed among these distances:
26 5 0.03
27 16 0.09
28 4 0.02
29 33 0.19
30 109 0.63
31 5 0.03
ACGTcount: A:0.57, C:0.10, G:0.13, T:0.20
Consensus pattern (30 bp):
AGAAACTTAAAGGACTAAAATAGCTAAAAC
Found at i:115553 original size:30 final size:30
Alignment explanation
Indices: 115333--115556 Score: 174
Period size: 30 Copynumber: 7.6 Consensus size: 30
115323 GTAAATAAAG
* *
115333 AAACTTAAAGGACTAAAATAACTAAAATAA
1 AAACTTAAAGGACTAAAATAGCAAAAATAA
* *
115363 AAAGTTAAAGGACCAAAATAGCAAAAATAA
1 AAACTTAAAGGACTAAAATAGCAAAAATAA
* *
115393 AAACTTAAAGGACTAAAATAGCTAAAATAG
1 AAACTTAAAGGACTAAAATAGCAAAAATAA
* * * *
115423 AAAGTTAAAGGACTAAAGTGGTAAAACAT--
1 AAACTTAAAGGACTAAAATAGCAAAA-ATAA
** **
115452 AAACTTAAAGGGTTAAAATA--ATAACCT--
1 AAACTTAAAGGACTAAAATAGCA-AAAATAA
* * * *
115479 AAACTTAAGGGTCT-AAATAGCAAATACAA
1 AAACTTAAAGGACTAAAATAGCAAAAATAA
* * * *
115508 ACATTTAAAGAACTAAAATAACAAAAATAA
1 AAACTTAAAGGACTAAAATAGCAAAAATAA
*
115538 AAACTTAAGGGACTAAAAT
1 AAACTTAAAGGACTAAAAT
115557 GGTATTAACA
Statistics
Matches: 149, Mismatches: 38, Indels: 14
0.74 0.19 0.07
Matches are distributed among these distances:
26 5 0.03
27 15 0.10
28 3 0.02
29 24 0.16
30 100 0.67
31 2 0.01
ACGTcount: A:0.58, C:0.10, G:0.12, T:0.20
Consensus pattern (30 bp):
AAACTTAAAGGACTAAAATAGCAAAAATAA
Found at i:118863 original size:282 final size:282
Alignment explanation
Indices: 118349--118908 Score: 883
Period size: 282 Copynumber: 2.0 Consensus size: 282
118339 GTATTTATGT
**
118349 AGATGACATAGTTCTTGCAGGAAAGAACTTGGAGCTATTAAATGAGATTCAGACTTTTCTTCAGC
1 AGATGACATAGTTCTTGCAGGAAAGAACTTGGAGCTATTAAAAAAGATTCAGACTTTTCTTCAGC
* *
118414 AACATTTTAAACTAAAAATCCCAGATCCTTTGAAATATTTTCTTGGTTTTGAGATTGCTCGAAAT
66 AACATTTTAAACTAAAAATCCCAGATCCTTTGAAATATTTTCTTGGTTTTGAGACTGCTCAAAAT
* *
118479 GCTACTGGGATCTCTTTGTCCAAAGACATCATACATTACAACTTTCGGAAGACACCGATACTCTT
131 GCTACTGGGATCACTTTGTCCAAAGACATCATACATTACAACTTTCGGAAGACACCGATACTCAT
* *
118544 GGTAAGAAACCTGTTCATCTATCAATTTTTCCCTCTCATAAATTGAGTTTTCATGAAGGTGAGTT
196 GGTAAGAAACCTGCTCATCTATCAATTTTTCCCTCTCATAAATTGAGTATTCATGAAGGTGAGTT
* *
118609 ATTGTTTGATCCTTAACTGTGG
261 ATTGTCTGATCCTCAACTGTGG
*
118631 AGATGACATAGTTCTTGCAGGAAAGAACTTGGAGCTATTAAAAAAGGTTCAGACTTTTCTTCAGC
1 AGATGACATAGTTCTTGCAGGAAAGAACTTGGAGCTATTAAAAAAGATTCAGACTTTTCTTCAGC
* * *
118696 AACA-TTTAAGCTAAAAATCCTAGGTCCTTTGAAATATTTTCTTGGTTTTGAGACTGCTCAAAAT
66 AACATTTTAAACTAAAAATCCCAGATCCTTTGAAATATTTTCTTGGTTTTGAGACTGCTCAAAAT
* * * * **
118760 TCTACTGGGATCACTTTGTCACAAAGACATTATGCATTATAACTTTTC-GAAGACATTGATACTC
131 GCTACTGGGATCACTTTGTC-CAAAGACATCATACATTACAAC-TTTCGGAAGACACCGATACTC
*
118824 ATGGTAAGAAACCTGCTGATCTATCAATTGTTT-CCTCTCATAAATTGAGTATTCATGAAGGTGA
194 ATGGTAAGAAACCTGCTCATCTATCAATT-TTTCCCTCTCATAAATTGAGTATTCATGAAGGTGA
118888 GTTATTGTCTGATCCTCAACT
258 GTTATTGTCTGATCCTCAACT
118909 ATATTGAAGG
Statistics
Matches: 254, Mismatches: 21, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
281 73 0.29
282 174 0.69
283 7 0.03
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Consensus pattern (282 bp):
AGATGACATAGTTCTTGCAGGAAAGAACTTGGAGCTATTAAAAAAGATTCAGACTTTTCTTCAGC
AACATTTTAAACTAAAAATCCCAGATCCTTTGAAATATTTTCTTGGTTTTGAGACTGCTCAAAAT
GCTACTGGGATCACTTTGTCCAAAGACATCATACATTACAACTTTCGGAAGACACCGATACTCAT
GGTAAGAAACCTGCTCATCTATCAATTTTTCCCTCTCATAAATTGAGTATTCATGAAGGTGAGTT
ATTGTCTGATCCTCAACTGTGG
Found at i:121242 original size:29 final size:29
Alignment explanation
Indices: 121208--121266 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
121198 CTTAAATTAA
121208 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
121237 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
121266 T
1 T
121267 AGGTGAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:125086 original size:21 final size:20
Alignment explanation
Indices: 125060--125201 Score: 162
Period size: 21 Copynumber: 6.8 Consensus size: 20
125050 AGGGTGTCAA
*
125060 AGTGCATTCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
125081 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA-CCCTGC
125102 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA-CCCTGC
125123 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCCATGCACCCTG--C
* *
125144 TAGTGCATCGATGCACCATGC
1 -AGTGCATCCATGCACCCTGC
125165 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCCATGCACCCTG--C
125186 TAGTGCATCCATGCAC
1 -AGTGCATCCATGCAC
125202 TCAAACACCG
Statistics
Matches: 107, Mismatches: 6, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.07
20 13 0.12
21 57 0.53
22 27 0.25
23 3 0.03
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.23
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:125094 original size:13 final size:13
Alignment explanation
Indices: 125091--125178 Score: 55
Period size: 13 Copynumber: 6.9 Consensus size: 13
125081 AGTGCATCCA
*
125091 TGCATCCCTGCAG
1 TGCATCCATGCAG
125104 TGCATCCATGCA-
1 TGCATCCATGCAG
125116 T-C--CC-TGCAG
1 TGCATCCATGCAG
*
125125 TGCATCCATGCACC
1 TGCATCCATGCA-G
*
125139 TGCA-CTAGTGCATCG
1 TGCATCCA-TGCA--G
125154 ATGCA-CCATGCAG
1 -TGCATCCATGCAG
125167 TGCATCCATGCA
1 TGCATCCATGCA
125179 CCTGCACTAG
Statistics
Matches: 60, Mismatches: 5, Indels: 20
0.71 0.06 0.24
Matches are distributed among these distances:
8 4 0.07
9 3 0.05
10 1 0.02
11 1 0.02
12 7 0.12
13 25 0.42
14 8 0.13
15 5 0.08
16 6 0.10
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.23
Consensus pattern (13 bp):
TGCATCCATGCAG
Found at i:125121 original size:42 final size:41
Alignment explanation
Indices: 125060--125201 Score: 189
Period size: 42 Copynumber: 3.4 Consensus size: 41
125050 AGGGTGTCAA
*
125060 AGTGCATTCATGCACCCCTGCAGTGCATCCATGCATCCCTG-C-
1 AGTGCATCCATGCA-CCCTGCAGTGCATCCATGCA--CCTGACT
125102 AGTGCATCCATGCATCCCTGCAGTGCATCCATGCACCTGCACT
1 AGTGCATCCATGCA-CCCTGCAGTGCATCCATGCACCTG-ACT
* *
125145 AGTGCATCGATGCACCATGCAGTGCATCCATGCACCTGCACT
1 AGTGCATCCATGCACCCTGCAGTGCATCCATGCACCTG-ACT
125187 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
125202 TCAAACACCG
Statistics
Matches: 92, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
40 4 0.04
42 75 0.82
43 13 0.14
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.23
Consensus pattern (41 bp):
AGTGCATCCATGCACCCTGCAGTGCATCCATGCACCTGACT
Found at i:125247 original size:20 final size:20
Alignment explanation
Indices: 125222--125316 Score: 136
Period size: 20 Copynumber: 4.7 Consensus size: 20
125212 AATGCAATTA
*
125222 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTGCT
**
125242 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-CTGCT
125263 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
*
125283 GTGCATCCATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
*
125303 GTGCATCCATGCAT
1 GTGCATCGATGCAT
125317 GAAGGCTGCA
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 51 0.75
21 17 0.25
ACGTcount: A:0.18, C:0.29, G:0.23, T:0.29
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:125269 original size:41 final size:40
Alignment explanation
Indices: 125222--125316 Score: 136
Period size: 41 Copynumber: 2.4 Consensus size: 40
125212 AATGCAATTA
* *
125222 GTGCATCGATGCATCCTTCTGTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCCTGCTGTGCATCCATGCATC-AGGCT
**
125263 GTGCATCGATGCATCCTGCTGTGCATCCATGCATCCTGCT
1 GTGCATCGATGCATCCTGCTGTGCATCCATGCATCAGGCT
*
125303 GTGCATCCATGCAT
1 GTGCATCGATGCAT
125317 GAAGGCTGCA
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 16 0.33
41 33 0.67
ACGTcount: A:0.18, C:0.29, G:0.23, T:0.29
Consensus pattern (40 bp):
GTGCATCGATGCATCCTGCTGTGCATCCATGCATCAGGCT
Found at i:125325 original size:24 final size:20
Alignment explanation
Indices: 125061--125316 Score: 149
Period size: 21 Copynumber: 12.7 Consensus size: 20
125051 GGGTGTCAAA
* * *
125061 GTGCATTCATGCACCCCTGCA
1 GTGCATCCATGCA-TCCTGCT
*
125082 GTGCATCCATGCATCCCTGCA
1 GTGCATCCATGCAT-CCTGCT
*
125103 GTGCATCCATGCATCCCTGCA
1 GTGCATCCATGCAT-CCTGCT
125124 GTGCATCCATGCA-CCTGCACT
1 GTGCATCCATGCATCCTG--CT
* *
125145 AGTGCATCGATGCA-CCATGCA
1 -GTGCATCCATGCATCC-TGCT
125166 GTGCATCCATGCA-CCTGCACT
1 GTGCATCCATGCATCCTG--CT
125187 AGTGCATCCATGCA--CT-C-
1 -GTGCATCCATGCATCCTGCT
*** *
125204 AAACA-CCGAATGCAAT--T--A
1 GTGCATCC--ATGC-ATCCTGCT
* *
125222 GTGCATCGATGCATCCTTCT
1 GTGCATCCATGCATCCTGCT
* **
125242 GTGCATCGATGCATCAAGGCT
1 GTGCATCCATGCATC-CTGCT
*
125263 GTGCATCGATGCATCCTGCT
1 GTGCATCCATGCATCCTGCT
125283 GTGCATCCATGCATCCTGCT
1 GTGCATCCATGCATCCTGCT
125303 GTGCATCCATGCAT
1 GTGCATCCATGCAT
125317 GAAGGCTGCA
Statistics
Matches: 195, Mismatches: 21, Indels: 39
0.76 0.08 0.15
Matches are distributed among these distances:
15 2 0.01
16 4 0.02
17 8 0.04
18 6 0.03
19 7 0.04
20 65 0.33
21 74 0.38
22 27 0.14
23 2 0.01
ACGTcount: A:0.22, C:0.33, G:0.20, T:0.25
Consensus pattern (20 bp):
GTGCATCCATGCATCCTGCT
Found at i:125457 original size:21 final size:21
Alignment explanation
Indices: 125428--125467 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
125418 TTTTAGTAGA
125428 AAAATCATCTCCAAACGGCTCC
1 AAAATCATC-CCAAACGGCTCC
*
125450 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCAAACGGCT
125468 ATATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 4 0.24
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCAAACGGCTCC
Found at i:126633 original size:19 final size:20
Alignment explanation
Indices: 126609--126656 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
126599 AACGATTTTC
*
126609 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
126628 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
126648 TTTTGAAAA
1 TTTTGAAAA
126657 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:127914 original size:28 final size:28
Alignment explanation
Indices: 127883--127943 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 28
127873 TTGATATAAC
* *
127883 AATTTAA-GGCAAAATGTTTTTGGACTT
1 AATTTAATGACAAAATATTTTTGGACTT
*
127910 GAATTTAATTTACAAAATATTTTTGGACTT
1 -AATTTAA-TGACAAAATATTTTTGGACTT
127940 AATT
1 AATT
127944 GAATTTATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.25
29 4 0.14
30 17 0.61
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (28 bp):
AATTTAATGACAAAATATTTTTGGACTT
Found at i:127961 original size:29 final size:30
Alignment explanation
Indices: 127892--127950 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
127882 CAATTTAAGG
*
127892 CAAAATGTTTTTGGACTTGAATTTAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
*
127922 CAAAATATTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
127951 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.46
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:128136 original size:21 final size:21
Alignment explanation
Indices: 128092--128195 Score: 122
Period size: 21 Copynumber: 5.0 Consensus size: 21
128082 AATGCAATTA
***
128092 GTGCATCGATGCATC-CTTCT
1 GTGCATCGATGCATCAAGGCT
128112 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCAAGGCT
128133 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCAAGGCT
**
128154 GTGCATCGATGCATC-CTGCT
1 GTGCATCGATGCATCAAGGCT
* * *
128174 GTTCATCCATGCATGAAGGCT
1 GTGCATCGATGCATCAAGGCT
128195 G
1 G
128196 CAACGGCTAG
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
20 30 0.42
21 42 0.58
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GTGCATCGATGCATCAAGGCT
Found at i:128175 original size:41 final size:42
Alignment explanation
Indices: 128092--128195 Score: 122
Period size: 41 Copynumber: 2.5 Consensus size: 42
128082 AATGCAATTA
***
128092 GTGCATCGATGCATC-CTTCTGTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCAAGGCTGTGCATCGATGCATCAAGGCT
**
128133 GTGCATCGATGCATCAAGGCTGTGCATCGATGCATC-CTGCT
1 GTGCATCGATGCATCAAGGCTGTGCATCGATGCATCAAGGCT
* * *
128174 GTTCATCCATGCATGAAGGCTG
1 GTGCATCGATGCATCAAGGCTG
128196 CAACGGCTAG
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
41 37 0.69
42 17 0.31
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (42 bp):
GTGCATCGATGCATCAAGGCTGTGCATCGATGCATCAAGGCT
Found at i:129888 original size:29 final size:28
Alignment explanation
Indices: 129854--129911 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 28
129844 ACCTAATTAA
129854 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAA-TTAGT
129883 TTTGATGTCATTGCTTACATCAATTAGT
1 TTTGATGTCATTGCTTACATCAATTAGT
129911 T
1 T
129912 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.48
Consensus pattern (28 bp):
TTTGATGTCATTGCTTACATCAATTAGT
Found at i:132447 original size:25 final size:25
Alignment explanation
Indices: 132399--132448 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
132389 TTATTTTCTT
*
132399 TTTCTATAAAATTCTTTAAGTTTAA
1 TTTCTATAAAATTCTTTAAATTTAA
*
132424 TTTCTCTAAAATT-TTATAAATTTAA
1 TTTCTATAAAATTCTT-TAAATTTAA
132449 ATTAAGCGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (25 bp):
TTTCTATAAAATTCTTTAAATTTAA
Done.