Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009119.1 Hibiscus syriacus cultivar Beakdansim tig00112608_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: 96278
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:5060 original size:15 final size:15
Alignment explanation
Indices: 5042--5072 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5032 AAATTCTAAA
5042 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
5057 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
5072 T
1 T
5073 CATCGATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:10027 original size:36 final size:38
Alignment explanation
Indices: 9969--10041 Score: 87
Period size: 37 Copynumber: 1.9 Consensus size: 38
9959 TTTAAAAACG
*
9969 TATAATATATAGTTTTTAG-AAAACAGTTATTGAAAATA
1 TATAATATATAG-ATTTAGAAAAACAGTTATTGAAAATA
* * *
10007 TATAATATATA-ATTTCGAAAAACGGTTTTTGAAAA
1 TATAATATATAGATTTAGAAAAACAGTTATTGAAAA
10042 CGTATTTTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
36 4 0.13
37 15 0.50
38 11 0.37
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.38
Consensus pattern (38 bp):
TATAATATATAGATTTAGAAAAACAGTTATTGAAAATA
Found at i:10041 original size:50 final size:50
Alignment explanation
Indices: 9979--10098 Score: 134
Period size: 50 Copynumber: 2.4 Consensus size: 50
9969 TATAATATAT
* * *
9979 AGTTTTTAGAAAACAGT-TATTGAAAATATATAATATATAATTTCGAAAAAC
1 AGTTTTT-GAAAAC-GTATATTGAAAACATAAAATATATAATTTCAAAAAAC
* * * *
10030 GGTTTTTGAAAACGTATTTTGAAAACATAAAATATATAGTTTTAAAAAAC
1 AGTTTTTGAAAACGTATATTGAAAACATAAAATATATAATTTCAAAAAAC
* *
10080 AGTTTTCGAAAATGTATAT
1 AGTTTTTGAAAACGTATAT
10099 AATATAATTT
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
49 2 0.04
50 49 0.86
51 6 0.11
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.37
Consensus pattern (50 bp):
AGTTTTTGAAAACGTATATTGAAAACATAAAATATATAATTTCAAAAAAC
Found at i:10079 original size:87 final size:87
Alignment explanation
Indices: 9945--10114 Score: 222
Period size: 87 Copynumber: 2.0 Consensus size: 87
9935 TACAGTATAA
* * *
9945 TTTTTGAAAATATTTTTAAAAACGTATAATATATAGTTTTTAGAAAACAGTTATT-GAAAATATA
1 TTTTTGAAAATATTTTTAAAAACATAAAATATATAGTTTTTAAAAAACAGTT-TTCGAAAATATA
10009 TA-ATATATAATTTCGAAAAACGG
65 TATA-ATATAATTTCGAAAAACGG
* *
10032 TTTTTGAAAACGTA-TTTTGAAAACATAAAATATATAG-TTTTAAAAAACAGTTTTCGAAAATGT
1 TTTTTGAAAA--TATTTTTAAAAACATAAAATATATAGTTTTTAAAAAACAGTTTTCGAAAATAT
*
10095 ATATAATATAATTTTGAAAA
64 ATATAATATAATTTCGAAAA
10115 CATATATATA
Statistics
Matches: 73, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
86 2 0.03
87 48 0.66
88 21 0.29
89 2 0.03
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (87 bp):
TTTTTGAAAATATTTTTAAAAACATAAAATATATAGTTTTTAAAAAACAGTTTTCGAAAATATAT
ATAATATAATTTCGAAAAACGG
Found at i:10113 original size:23 final size:25
Alignment explanation
Indices: 10082--10128 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
10072 TAAAAAACAG
**
10082 TTTTCGAAAATGTATATA-ATATAA
1 TTTTCGAAAACATATATATATATAA
10106 TTTT-GAAAACATATATATATATA
1 TTTTCGAAAACATATATATATATA
10129 TAGTTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (25 bp):
TTTTCGAAAACATATATATATATAA
Found at i:10160 original size:62 final size:60
Alignment explanation
Indices: 10045--10166 Score: 165
Period size: 62 Copynumber: 2.0 Consensus size: 60
10035 TTGAAAACGT
**
10045 ATTTTGAAAACATAAAATATATAGTTTTAAAAAACAGTTTTCGAAAATGTATATAATATA
1 ATTTTGAAAACATAAAATATATAGTTTTAAAAAACAGTTTTCGAAAACATATATAATATA
* * *
10105 ATTTTGAAAACATATATATATATATAGTTTT-TAAAACGGTTTTTGAAAACATATATAATATA
1 ATTTTGAAAACATA-A-A-ATATATAGTTTTAAAAAACAGTTTTCGAAAACATATATAATATA
10167 TATAATTTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
60 14 0.26
61 1 0.02
62 27 0.50
63 12 0.22
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.39
Consensus pattern (60 bp):
ATTTTGAAAACATAAAATATATAGTTTTAAAAAACAGTTTTCGAAAACATATATAATATA
Found at i:10213 original size:24 final size:23
Alignment explanation
Indices: 10157--10213 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
10147 TTGAAAACAT
*
10157 ATATAATATATATAATTTTTGAA
1 ATATAATTTATATAATTTTTGAA
*
10180 ATCAT-A-TTATATAGTTTTTGAAA
1 AT-ATAATTTATATAATTTTTG-AA
10203 ATATAATTTAT
1 ATATAATTTAT
10214 GTTATATAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
22 14 0.50
23 8 0.29
24 6 0.21
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (23 bp):
ATATAATTTATATAATTTTTGAA
Found at i:10275 original size:9 final size:8
Alignment explanation
Indices: 10248--10318 Score: 55
Period size: 7 Copynumber: 9.2 Consensus size: 8
10238 AGTATACGCT
10248 TTATATATA
1 TTAT-TATA
*
10257 TATATAATA
1 T-TATTATA
10266 TTAGTTATA
1 TTA-TTATA
10275 TTATTAT-
1 TTATTATA
*
10282 TTATTATT
1 TTATTATA
10290 TTA-TAT-
1 TTATTATA
10296 TTATTATA
1 TTATTATA
10304 TTA-TAT-
1 TTATTATA
10310 TTATT-TA
1 TTATTATA
10317 TT
1 TT
10319 TAATTTTATT
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
6 7 0.13
7 19 0.36
8 12 0.23
9 12 0.23
10 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (8 bp):
TTATTATA
Found at i:10279 original size:12 final size:11
Alignment explanation
Indices: 10259--10307 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 11
10249 TATATATATA
*
10259 TATAATATTAGT
1 TATATTATTA-T
10271 TATATTATTAT
1 TATATTATTAT
10282 T-TATTATT-T
1 TATATTATTAT
10291 TATA-T-TTAT
1 TATATTATTAT
10300 TATATTAT
1 TATATTAT
10308 ATTTATTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
8 2 0.06
9 8 0.25
10 10 0.31
11 3 0.09
12 9 0.28
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (11 bp):
TATATTATTAT
Found at i:10296 original size:29 final size:29
Alignment explanation
Indices: 10270--10328 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
10260 ATAATATTAG
10270 TTATATTATTATTTA-TTATTTTATATTTA
1 TTATATTA-TATTTATTTATTTTATATTTA
*
10299 TTATATTATATTTATTTATTTAAT-TTTA
1 TTATATTATATTTATTTATTTTATATTTA
10327 TT
1 TT
10329 TTAACAGTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (29 bp):
TTATATTATATTTATTTATTTTATATTTA
Found at i:10298 original size:14 final size:14
Alignment explanation
Indices: 10279--10328 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
10269 GTTATATTAT
10279 TATTTATTATTTTA
1 TATTTATTATTTTA
*
10293 TATTTATTATATTA
1 TATTTATTATTTTA
*
10307 TATTTATTTATTTAA
1 TATTTA-TTATTTTA
10322 T-TTTATT
1 TATTTATT
10329 TTAACAGTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 2 0.06
14 23 0.72
15 7 0.22
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TATTTATTATTTTA
Found at i:13353 original size:22 final size:22
Alignment explanation
Indices: 13297--13354 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
13287 ATATTGAAGT
*
13297 AAGTATCGGTACCATATAAGAG
1 AAGTATCGGTACTATATAAGAG
13319 AAGTATCGGTACTATATAAGAG
1 AAGTATCGGTACTATATAAGAG
13341 AAGTATCGGTACTA
1 AAGTATCGGTACTA
13355 CAAGAAGAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (22 bp):
AAGTATCGGTACTATATAAGAG
Found at i:13365 original size:20 final size:21
Alignment explanation
Indices: 13292--13362 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 21
13282 TATCGATATT
13292 GAAGTAAGTATCGGTACCATATAA
1 GAAG-AAGTATCGGTA-C-TATAA
13316 G-AGAAGTATCGGTACTATATA
1 GAAGAAGTATCGGTACTATA-A
*
13337 -AGAGAAGTATCGGTACTACAA
1 GA-AGAAGTATCGGTACTATAA
13358 GAAGA
1 GAAGA
13363 GTACTGATAC
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
20 4 0.10
21 6 0.14
22 29 0.69
23 2 0.05
24 1 0.02
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.23
Consensus pattern (21 bp):
GAAGAAGTATCGGTACTATAA
Found at i:14112 original size:23 final size:23
Alignment explanation
Indices: 14082--14172 Score: 128
Period size: 23 Copynumber: 4.0 Consensus size: 23
14072 GTCGAGGGTT
*
14082 CTATGTGGTCCTTTGGGACAAAA
1 CTATGTGGTCCTTCGGGACAAAA
* * *
14105 CTATGTGGTCTTTCAGGATAAAA
1 CTATGTGGTCCTTCGGGACAAAA
* *
14128 CTATGTGATCATTCGGGACAAAA
1 CTATGTGGTCCTTCGGGACAAAA
14151 CTATGTGGTCCTTCGGGACAAA
1 CTATGTGGTCCTTCGGGACAAA
14173 TACGTGGAAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGACAAAA
Found at i:17003 original size:24 final size:24
Alignment explanation
Indices: 16976--17048 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
16966 TCAAGAAGAC
*
16976 TCATATGCTACAAAAGCATAAGCT
1 TCATATGCTACAAAAGCACAAGCT
* * *
17000 TCATCTGTTGCAAAAGCACAAGCT
1 TCATATGCTACAAAAGCACAAGCT
* *
17024 TCAT-CGACTGCAAAAGCACAAGCT
1 TCATATG-CTACAAAAGCACAAGCT
17048 T
1 T
17049 TCGTAACTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 1 0.02
24 41 0.98
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.23
Consensus pattern (24 bp):
TCATATGCTACAAAAGCACAAGCT
Found at i:20470 original size:18 final size:18
Alignment explanation
Indices: 20447--20481 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20437 CTGAACTTGG
*
20447 GCACGAATGAATAAAAGC
1 GCACGAAAGAATAAAAGC
20465 GCACGAAAGAATAAAAG
1 GCACGAAAGAATAAAAG
20482 AAAAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.14, G:0.23, T:0.09
Consensus pattern (18 bp):
GCACGAAAGAATAAAAGC
Found at i:22474 original size:54 final size:54
Alignment explanation
Indices: 22409--22800 Score: 569
Period size: 54 Copynumber: 7.3 Consensus size: 54
22399 CTTTGGGGTA
* *
22409 CACACGTAGTGCCTATACGGTCGTTCATAAACTTATTATGAATTTCGTGGGTTG
1 CACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTCGTGGGTTG
* *
22463 CACACTTAGTGCCGATACAGTCGTTCATAAACATATTATGAA-TTCTGTGGGTTG
1 CACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTC-GTGGGTTG
* *
22517 CACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATAAATTCCGTGGGTTG
1 CACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTCGTGGGTTG
***
22571 CACACTTAGTGCCGATACGGAAATTCATAAA-TATATTATGAATTTCGTGGGTTG
1 CACACTTAGTGCCGATACGGTCGTTCATAAACT-TATTATGAATTTCGTGGGTTG
*
22625 CACACTTAGTTCCGATACGGTCGTTCATAAACTTATTATGAA-TTCTGTGGGTTG
1 CACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTC-GTGGGTTG
*
22679 CACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTAT-GTGGGTTG
1 CACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATT-TCGTGGGTTG
** * *
22733 CACACTTAGTGTTGATACGATCGTTTATAAACTTATTATGAA-TTCTGTGGGTTG
1 CACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTC-GTGGGTTG
22787 CACACTTAGTGCCG
1 CACACTTAGTGCCG
22801 GTAGTACACC
Statistics
Matches: 303, Mismatches: 26, Indels: 18
0.87 0.07 0.05
Matches are distributed among these distances:
52 1 0.00
53 8 0.03
54 289 0.95
55 4 0.01
56 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.35
Consensus pattern (54 bp):
CACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTCGTGGGTTG
Found at i:26197 original size:21 final size:21
Alignment explanation
Indices: 26142--26223 Score: 74
Period size: 21 Copynumber: 3.8 Consensus size: 21
26132 TATACAATTG
* *
26142 TCCCGAAGGACCACGTAGAAATA
1 TCCCAAAGGACCAC--ATAAATA
* * * * *
26165 TCCCTAATGACCATATATATT
1 TCCCAAAGGACCACATAAATA
*
26186 TCCCGAAGGACCACATAAATA
1 TCCCAAAGGACCACATAAATA
26207 TCCCAAAGGACCACATA
1 TCCCAAAGGACCACATA
26224 GAGTTGTCCC
Statistics
Matches: 47, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
21 36 0.77
23 11 0.23
ACGTcount: A:0.39, C:0.28, G:0.13, T:0.20
Consensus pattern (21 bp):
TCCCAAAGGACCACATAAATA
Found at i:26289 original size:21 final size:20
Alignment explanation
Indices: 26265--26327 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
26255 AAAGAACCAA
26265 ATATATGTCTCGAAGGACCGC
1 ATATATGT-TCGAAGGACCGC
* ***
26286 ATATATGTTCCAAAGGATTAC
1 ATATATGTT-CGAAGGACCGC
26307 ATATATGTTTCGAAGGACCGC
1 ATATATG-TTCGAAGGACCGC
26328 GTAGAACCCT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 1 0.03
21 29 0.91
22 2 0.06
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.29
Consensus pattern (20 bp):
ATATATGTTCGAAGGACCGC
Found at i:30606 original size:21 final size:21
Alignment explanation
Indices: 30580--30734 Score: 96
Period size: 21 Copynumber: 7.3 Consensus size: 21
30570 CATATAAAAT
*
30580 TGTCCCAAATGACCCCATATA
1 TGTCCCAAATGACCACATATA
* *
30601 TGTCCCGAATGACCACATAAA
1 TGTCCCAAATGACCACATATA
* * * *
30622 TATCCCGAA-GAATCACATAAAA
1 TGTCCCAAATG-ACCACAT-ATA
* *
30644 TTGTCCCTAAGGACCACATATA
1 -TGTCCCAAATGACCACATATA
* * * *
30666 TGTTCTAAAGGACCAAATATA
1 TGTCCCAAATGACCACATATA
* * * *
30687 TATACCGAAGGACCACATATA
1 TGTCCCAAATGACCACATATA
* * *
30708 TGTTCCAAAAGATCACATATA
1 TGTCCCAAATGACCACATATA
30729 TGTCCC
1 TGTCCC
30735 GAAGAACCGC
Statistics
Matches: 106, Mismatches: 24, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
20 1 0.01
21 86 0.81
22 5 0.05
23 13 0.12
24 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.24
Consensus pattern (21 bp):
TGTCCCAAATGACCACATATA
Found at i:30680 original size:65 final size:65
Alignment explanation
Indices: 30573--30734 Score: 166
Period size: 65 Copynumber: 2.5 Consensus size: 65
30563 TGAGTGCCAT
* * * * * * *
30573 ATAAAATTGTCCCAAATGACCCCATATATGTCCCGAATGACCACATAAATATCCCGAAGAATCAC
1 ATAAAATTGTCCCAAAGGACCACATATATGTCCCAAAGGACCAAATAAATATACCGAAGAACCAC
* * * * *
30638 ATAAAATTGTCCCTAAGGACCACATATATGTTCTAAAGGACCAAATATATATACCGAAGGACCAC
1 ATAAAATTGTCCCAAAGGACCACATATATGTCCCAAAGGACCAAATAAATATACCGAAGAACCAC
* * * *
30703 AT-ATA-TGTTCCAAAAGATCACATATATGTCCC
1 ATAAAATTGTCCCAAAGGACCACATATATGTCCC
30735 GAAGAACCGC
Statistics
Matches: 78, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
63 21 0.27
64 2 0.03
65 55 0.71
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (65 bp):
ATAAAATTGTCCCAAAGGACCACATATATGTCCCAAAGGACCAAATAAATATACCGAAGAACCAC
Found at i:30728 original size:42 final size:42
Alignment explanation
Indices: 30652--30738 Score: 120
Period size: 42 Copynumber: 2.1 Consensus size: 42
30642 AATTGTCCCT
* *
30652 AAGGACCACATATATGTTCTAAAGGACCAAATATATATACCG
1 AAGGACCACATATATGTTCCAAAAGACCAAATATATATACCG
* * * *
30694 AAGGACCACATATATGTTCCAAAAGATCACATATATGTCCCG
1 AAGGACCACATATATGTTCCAAAAGACCAAATATATATACCG
30736 AAG
1 AAG
30739 AACCGCGTAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.23
Consensus pattern (42 bp):
AAGGACCACATATATGTTCCAAAAGACCAAATATATATACCG
Found at i:34237 original size:37 final size:37
Alignment explanation
Indices: 34171--34339 Score: 206
Period size: 37 Copynumber: 4.6 Consensus size: 37
34161 GAAAATATTT
34171 TTGAAAACATA-AA-ATATAGTTTC-AGAAAACGATTG
1 TTGAAAACATATAATATATAGTTTCGA-AAAACGATTG
*
34206 TTGAAAACGTATAATATATAGTTTCGAAAAACGATTG
1 TTGAAAACATATAATATATAGTTTCGAAAAACGATTG
* * *
34243 TTGAAAACGTATAATATATAGTTTCGAAAAACGGTTT
1 TTGAAAACATATAATATATAGTTTCGAAAAACGATTG
* * *
34280 TTGAAAACATAT-ATAATATGGTTTTG-AAAAC-ATATT
1 TTGAAAACATATAAT-ATATAGTTTCGAAAAACGAT-TG
34316 TTGAAAACATATAATATATAGTTT
1 TTGAAAACATATAATATATAGTTT
34340 TAAAAATTGG
Statistics
Matches: 120, Mismatches: 8, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
35 11 0.09
36 31 0.26
37 77 0.64
38 1 0.01
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.35
Consensus pattern (37 bp):
TTGAAAACATATAATATATAGTTTCGAAAAACGATTG
Found at i:34319 original size:13 final size:13
Alignment explanation
Indices: 34301--34327 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
34291 TATAATATGG
34301 TTTTGAAAACATA
1 TTTTGAAAACATA
34314 TTTTGAAAACATA
1 TTTTGAAAACATA
34327 T
1 T
34328 AATATATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (13 bp):
TTTTGAAAACATA
Found at i:34331 original size:73 final size:71
Alignment explanation
Indices: 34151--34397 Score: 275
Period size: 73 Copynumber: 3.4 Consensus size: 71
34141 TAATATGTAG
* * *
34151 TATAGTTTTTGAAAATATTTTTGAAAACATA-AA-ATATAGTTTCAGAAAACGATTGTTGAAAAC
1 TATAG-TTTTGAAAACATTTTTGAAAACATATAATATATAGTTTCA-AAAACGGTTTTTGAAAAC
*
34214 GTATA-ATA
64 ATATATA-A
* * *
34222 TATAGTTTCGAAAAACGATTGTTGAAAACGTATAATATATAGTTTCGAAAAACGGTTTTTGAAAA
1 TATAGTTTTG-AAAAC-ATTTTTGAAAACATATAATATATAGTTTC-AAAAACGGTTTTTGAAAA
34287 CATATATAA
63 CATATATAA
* * * *
34296 TATGGTTTTGAAAACATATTTTGAAAACATATAATATATAGTTTTAAAAATTGGTTTTCGAAAAC
1 TATAGTTTTGAAAACAT-TTTTGAAAACATATAATATATAGTTTCAAAAA-CGGTTTTTGAAAAC
*
34361 TTATATAA
64 ATATATAA
*
34369 TATAGTTTTGAAAAGATATTTTGAAAACA
1 TATAGTTTTGAAAACAT-TTTTGAAAACA
34398 CACACACACA
Statistics
Matches: 151, Mismatches: 17, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
70 4 0.03
71 9 0.06
72 20 0.13
73 77 0.51
74 39 0.26
75 2 0.01
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (71 bp):
TATAGTTTTGAAAACATTTTTGAAAACATATAATATATAGTTTCAAAAACGGTTTTTGAAAACAT
ATATAA
Found at i:34359 original size:110 final size:109
Alignment explanation
Indices: 34168--34382 Score: 260
Period size: 110 Copynumber: 2.0 Consensus size: 109
34158 TTTGAAAATA
*
34168 TTTTTGAAAACATAAAATATAGTTTCAGAAAACGATTGTTGAAAACGTATAATATATAGTTTCGA
1 TTTTTGAAAACATAAAATATAGTTTCAGAAAACGATTGTTGAAAACATATAATATATAGTTTCGA
34233 AAAACGATTGTTGAAAACGTATA-ATATATAGTTTCGAAAAACGG
66 AAAACGATTGTTGAAAACGTATATA-ATATAGTTTCGAAAAACGG
* * *
34277 TTTTTGAAAACATATATAATATGGTTT-TGAAAAC-ATATTTTGAAAACATATAATATATAGTTT
1 TTTTTGAAAACATA-A-AATATAGTTTCAGAAAACGAT-TGTTGAAAACATATAATATATAGTTT
* * * * *
34340 -TAAAAATTGGTT-TTCGAAAACTTATATAATATAGTTTTGAAAA
63 CGAAAAA-CGATTGTT-GAAAACGTATATAATATAGTTTCGAAAA
34383 GATATTTTGA
Statistics
Matches: 91, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
109 23 0.25
110 58 0.64
111 10 0.11
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.37
Consensus pattern (109 bp):
TTTTTGAAAACATAAAATATAGTTTCAGAAAACGATTGTTGAAAACATATAATATATAGTTTCGA
AAAACGATTGTTGAAAACGTATATAATATAGTTTCGAAAAACGG
Found at i:34372 original size:37 final size:35
Alignment explanation
Indices: 34282--34397 Score: 96
Period size: 36 Copynumber: 3.2 Consensus size: 35
34272 AACGGTTTTT
* *
34282 GAAAACATAT-ATAATATGGTTTTGAAAACAT-ATTTT
1 GAAAACATATAAT-ATATAGTTTT-AAAA-ATGGTTTT
34318 GAAAACATATAATATATAGTTTTAAAAATTGGTTTT
1 GAAAACATATAATATATAGTTTTAAAAA-TGGTTTT
* *
34354 CGAAAACTTAT-ATAATATAGTTTTGAAAAGAT-ATTTT
1 -GAAAACATATAAT-ATATAGTTTT-AAAA-ATGGTTTT
34391 GAAAACA
1 GAAAACA
34398 CACACACACA
Statistics
Matches: 68, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
34 1 0.01
35 5 0.07
36 31 0.46
37 25 0.37
38 5 0.07
39 1 0.01
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (35 bp):
GAAAACATATAATATATAGTTTTAAAAATGGTTTT
Found at i:34450 original size:22 final size:23
Alignment explanation
Indices: 34425--34479 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
34415 ATATATATAT
34425 ATATATATATATA-TGTGTGAAA
1 ATATATATATATAGTGTGTGAAA
* *
34447 ATATAT-TATATAGTTTTTGAAA
1 ATATATATATATAGTGTGTGAAA
34469 ATATA-ATATAT
1 ATATATATATAT
34480 GTTATATAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 6 0.21
22 23 0.79
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (23 bp):
ATATATATATATAGTGTGTGAAA
Found at i:34458 original size:2 final size:2
Alignment explanation
Indices: 34409--34438 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
34399 ACACACACAC
34409 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
34439 GTGTGAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34510 original size:31 final size:29
Alignment explanation
Indices: 34447--34512 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
34437 ATGTGTGAAA
* *
34447 ATATATTATATAGTTTTTGAAAATATAAT
1 ATATGTTATATAGTTTTTAAAAATATAAT
*
34476 ATATGTTATATAGTTTTTAAATAAATATAGT
1 ATATGTTATATAGTTTTT-AA-AAATATAAT
34507 ATATGT
1 ATATGT
34513 ATTATATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 17 0.53
30 1 0.03
31 14 0.44
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (29 bp):
ATATGTTATATAGTTTTTAAAAATATAAT
Found at i:34542 original size:15 final size:15
Alignment explanation
Indices: 34514--34594 Score: 64
Period size: 16 Copynumber: 5.3 Consensus size: 15
34504 AGTATATGTA
34514 TTATATTATATATTAT
1 TTATATTAT-TATTAT
34530 TTATATTATTATT-T
1 TTATATTATTATTAT
34544 ATTAT-TT-TTA-TAT
1 -TTATATTATTATTAT
34557 TTAT-TATATTATATCAT
1 TTATAT-TATTAT-T-AT
34574 ATTATATTATTATTTAT
1 -TTATATTATTA-TTAT
34591 TTAT
1 TTAT
34595 TTAATTTCAT
Statistics
Matches: 55, Mismatches: 0, Indels: 20
0.73 0.00 0.27
Matches are distributed among these distances:
12 6 0.11
13 5 0.09
14 6 0.11
15 8 0.15
16 14 0.25
17 4 0.07
18 10 0.18
19 2 0.04
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATATTATTATTAT
Found at i:34562 original size:46 final size:46
Alignment explanation
Indices: 34506--34596 Score: 141
Period size: 46 Copynumber: 2.0 Consensus size: 46
34496 ATAAATATAG
34506 TATATGTATTATATTATAT-ATTATTTATATTATTATTTA-TTATTTT
1 TATATGTATTATATTATATCA-TA-TTATATTATTATTTATTTATTTT
*
34552 TATATTTATTATATTATATCATATTATATTATTATTTATTTATTT
1 TATATGTATTATATTATATCATATTATATTATTATTTATTTATTT
34597 AATTTCATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
45 15 0.36
46 26 0.62
47 1 0.02
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (46 bp):
TATATGTATTATATTATATCATATTATATTATTATTTATTTATTTT
Found at i:34577 original size:30 final size:29
Alignment explanation
Indices: 34512--34595 Score: 91
Period size: 30 Copynumber: 2.8 Consensus size: 29
34502 ATAGTATATG
*
34512 TATTATATTATATATTATTTATATTATTATT
1 TATTATATTATAT-TTA-TTATATTATTATA
*
34543 TATTATTTTTATATTTATTATATTA-TATCA
1 TATTA-TATTATATTTATTATATTATTAT-A
34573 TATTATATTATTATTTATT-TATT
1 TATTATATTA-TATTTATTATATT
34596 TAATTTCATT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
29 11 0.23
30 21 0.45
31 8 0.17
32 7 0.15
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (29 bp):
TATTATATTATATTTATTATATTATTATA
Found at i:35759 original size:29 final size:29
Alignment explanation
Indices: 35700--35759 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
35690 TTTCAATAAA
* *
35700 TTCAATTTGATCCTTTATTTTTAATTATT
1 TTCAATTTGATCCTTTAATTTAAATTATT
35729 TTCAATTTGATCCTTATAATTTAAATT-TT
1 TTCAATTTGATCCTT-TAATTTAAATTATT
35758 TT
1 TT
35760 GTTTATTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.27, C:0.10, G:0.03, T:0.60
Consensus pattern (29 bp):
TTCAATTTGATCCTTTAATTTAAATTATT
Found at i:35801 original size:18 final size:17
Alignment explanation
Indices: 35769--35816 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
35759 TGTTTATTTC
35769 TTTTATTT-ATTTAAAT
1 TTTTATTTAATTTAAAT
35785 TTTTATTTAATTTTAAAT
1 TTTTATTTAA-TTTAAAT
*
35803 TTTTATTTACTTTA
1 TTTTATTTAATTTA
35817 TTCTAACCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 8 0.28
17 5 0.17
18 16 0.55
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTATTTAATTTAAAT
Found at i:41732 original size:65 final size:64
Alignment explanation
Indices: 41612--41735 Score: 153
Period size: 65 Copynumber: 1.9 Consensus size: 64
41602 TACTGATTAG
* * * *
41612 TATGTTAATATTATTTTTATAAATATTTGTAGTTGTATTTTACCTTTTCTGGATTTATTGTTTTT
1 TATGTTAATATTATTTTTATAAATATTTGTAATTGTATATAACATTTTC-GGATTTATTGTTTTT
*
41677 TATGTTAATATTATTTTTAT-AATATTTTTATATTGTATAATAACATTTTAC-GATTTATT
1 TATGTTAATATTATTTTTATAAATATTTGTA-ATTGTAT-ATAACATTTT-CGGATTTATT
41736 ATCATAGTGT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
64 9 0.18
65 34 0.67
66 7 0.14
67 1 0.02
ACGTcount: A:0.28, C:0.04, G:0.08, T:0.60
Consensus pattern (64 bp):
TATGTTAATATTATTTTTATAAATATTTGTAATTGTATATAACATTTTCGGATTTATTGTTTTT
Found at i:42181 original size:5 final size:5
Alignment explanation
Indices: 42166--42301 Score: 173
Period size: 5 Copynumber: 27.2 Consensus size: 5
42156 ATCTCAAATC
* * * * * * *
42166 GCTAT GATAT GTTAT GTTAT GTTAT GCTAT GATAT GCTAC GCTAT GTTAT
1 GCTAT GCTAT GCTAT GCTAT GCTAT GCTAT GCTAT GCTAT GCTAT GCTAT
*
42216 GCTAT GCTAT GCTAT GATAT GCTAT GCTAT GCTAT GCTAT GCTAT GCTAT
1 GCTAT GCTAT GCTAT GCTAT GCTAT GCTAT GCTAT GCTAT GCTAT GCTAT
* * *
42266 GTTAT GATAT GCTAT GTTAT GCTAT GCTAT GCTAT G
1 GCTAT GCTAT GCTAT GCTAT GCTAT GCTAT GCTAT G
42302 TTATATTATA
Statistics
Matches: 115, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 115 1.00
ACGTcount: A:0.23, C:0.13, G:0.21, T:0.43
Consensus pattern (5 bp):
GCTAT
Found at i:44636 original size:37 final size:37
Alignment explanation
Indices: 44586--44660 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
44576 TAATTTTTGC
44586 ACTTTAGTTACGGTTTTGATTCTTGAGGTACTAAGAA
1 ACTTTAGTTACGGTTTTGATTCTTGAGGTACTAAGAA
44623 ACTTTAGTTACGGTTTTGATTCTTGAGGTACTAAGAA
1 ACTTTAGTTACGGTTTTGATTCTTGAGGTACTAAGAA
44660 A
1 A
44661 GCTTAAGGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (37 bp):
ACTTTAGTTACGGTTTTGATTCTTGAGGTACTAAGAA
Found at i:45235 original size:22 final size:21
Alignment explanation
Indices: 45205--45245 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
45195 CGGTACCGGG
45205 ATAGGGTATCAGTACCCTAGC
1 ATAGGGTATCAGTACCCTAGC
*
45226 ATAGAGGTATCGGTACCCTA
1 ATAG-GGTATCAGTACCCTA
45246 AGGGTAGTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.24
Consensus pattern (21 bp):
ATAGGGTATCAGTACCCTAGC
Found at i:46790 original size:18 final size:18
Alignment explanation
Indices: 46767--46818 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
46757 TATGTGATAT
46767 GTGGTCCTTC-GGAACATA
1 GTGGTCCTTCAGG-ACATA
*
46785 GTGGTCCTTCAGGGCATA
1 GTGGTCCTTCAGGACATA
46803 GTGGTCCTTCAGGACA
1 GTGGTCCTTCAGGACA
46819 AATTTTACGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 29 0.94
19 2 0.06
ACGTcount: A:0.19, C:0.23, G:0.31, T:0.27
Consensus pattern (18 bp):
GTGGTCCTTCAGGACATA
Found at i:56999 original size:24 final size:24
Alignment explanation
Indices: 56970--57047 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
56960 TAGTACTGAT
56970 ACAAAAATGTAACATATGCATTAA
1 ACAAAAATGTAACATATGCATTAA
* * ** * *
56994 ACAAAATTG-ATCGATAACCATCAT
1 ACAAAAATGTAAC-ATATGCATTAA
*
57018 ACGAAAATGTAA-ATTATGCATTAA
1 ACAAAAATGTAACA-TATGCATTAA
57042 ACAAAA
1 ACAAAA
57048 TCGTTCAATA
Statistics
Matches: 37, Mismatches: 14, Indels: 6
0.65 0.25 0.11
Matches are distributed among these distances:
23 3 0.08
24 33 0.89
25 1 0.03
ACGTcount: A:0.53, C:0.14, G:0.09, T:0.24
Consensus pattern (24 bp):
ACAAAAATGTAACATATGCATTAA
Found at i:58270 original size:54 final size:54
Alignment explanation
Indices: 58072--58268 Score: 304
Period size: 55 Copynumber: 3.6 Consensus size: 54
58062 ATTGTTTGAG
* * *
58072 TGTGTATCAGTACACTGAGGAGTGTATCAATACACTCCAAACATCGAATGCAATT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACACT-CAAACATCGAATGTAATT
* *
58127 TGTGTATCGGTACACTGAGAAGTGTATCGATACACTCAAAACATCGAATGTCATT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACACTC-AAACATCGAATGTAATT
*
58182 TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAACATCGAATGTAATT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACACTCAAACATCGAATGTAATT
* *
58236 TATGTATCGGTACACTAAGGAGTGTATCGATAC
1 TGTGTATCGGTACACTGAGGAGTGTATCGATAC
58269 CCCCCAGTTA
Statistics
Matches: 131, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
54 48 0.37
55 83 0.63
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (54 bp):
TGTGTATCGGTACACTGAGGAGTGTATCGATACACTCAAACATCGAATGTAATT
Found at i:64849 original size:20 final size:20
Alignment explanation
Indices: 64824--64878 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
64814 TTGTATGAGT
*
64824 GTGTATCGGTACACTGATAA
1 GTGTATCGGTACACTGAGAA
*
64844 GTGTATCGGTACACTGAGGA
1 GTGTATCGGTACACTGAGAA
64864 GTGTATCGGTACACT
1 GTGTATCGGTACACT
64879 CCAAATATCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.29
Consensus pattern (20 bp):
GTGTATCGGTACACTGAGAA
Found at i:64905 original size:55 final size:55
Alignment explanation
Indices: 64844--65036 Score: 268
Period size: 55 Copynumber: 3.6 Consensus size: 55
64834 ACACTGATAA
* *
64844 GTGTATCGGTACACTGAGGAGTGTATCGGTACACTCCAAATATCGAATGAAATTT
1 GTGTATCGGTACACTGAGGAGTGTATCGATACACTCCAAACATCGAATGAAATTT
* * * **
64899 GTGTATCGGCACACTGAGGAGTGTATTGATACACTCAAAACATCGAATGTCATTT
1 GTGTATCGGTACACTGAGGAGTGTATCGATACACTCCAAACATCGAATGAAATTT
* * *
64954 GTGTATCGGTACACTGAGGAGTGTATCGATAC-CTTCAAACATTGAATGCAATTT
1 GTGTATCGGTACACTGAGGAGTGTATCGATACACTCCAAACATCGAATGAAATTT
65008 GTGTATCGGTACACT---GAGTGTATCGATAC
1 GTGTATCGGTACACTGAGGAGTGTATCGATAC
65037 CCCTAGTTAT
Statistics
Matches: 124, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
51 14 0.11
54 32 0.26
55 78 0.63
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (55 bp):
GTGTATCGGTACACTGAGGAGTGTATCGATACACTCCAAACATCGAATGAAATTT
Found at i:65426 original size:21 final size:21
Alignment explanation
Indices: 65384--65433 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
65374 GTGTTAGGAA
* * *
65384 AATATGAGCTTTGAACAGGTG
1 AATATGAACTTCGAACAAGTG
*
65405 AATATGAACTTCGAATAAGTG
1 AATATGAACTTCGAACAAGTG
*
65426 AATGTGAA
1 AATATGAA
65434 TATACTCTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (21 bp):
AATATGAACTTCGAACAAGTG
Found at i:65666 original size:21 final size:22
Alignment explanation
Indices: 65584--65667 Score: 70
Period size: 23 Copynumber: 3.9 Consensus size: 22
65574 TCTTCCGGGA
**
65584 CAAA-TATGTGGCACTTCGGTG
1 CAAACTATGTGGCACTTCGAAG
*
65605 -AAACCTTATGTGGCACTTCGATG
1 CAAA-C-TATGTGGCACTTCGAAG
65628 CAAACTATGTGGTC-CTTC-AAG
1 CAAACTATGTGG-CACTTCGAAG
65649 -ACAACTATGTGGCACTTCG
1 CA-AACTATGTGGCACTTCG
65668 GTATAAATTA
Statistics
Matches: 53, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
20 5 0.09
21 16 0.30
22 11 0.21
23 18 0.34
24 3 0.06
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (22 bp):
CAAACTATGTGGCACTTCGAAG
Found at i:67128 original size:23 final size:23
Alignment explanation
Indices: 67044--67127 Score: 96
Period size: 23 Copynumber: 3.7 Consensus size: 23
67034 CACCACAGCT
*
67044 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * * *
67067 CGTAGAATTGTATCGAAGTGTCG
1 CGTAGAATTGCACCGAAGTGCCA
* *
67090 CGTAGAATTACACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
67113 TGTAGAATTGCACCG
1 CGTAGAATTGCACCG
67128 TGGTGCCATA
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:67133 original size:23 final size:23
Alignment explanation
Indices: 67091--67136 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
67081 GAAGTGTCGC
67091 GTAGAATTACACCGTAGTGCCAT
1 GTAGAATTACACCGTAGTGCCAT
* *
67114 GTAGAATTGCACCGTGGTGCCAT
1 GTAGAATTACACCGTAGTGCCAT
67137 ATAATAATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (23 bp):
GTAGAATTACACCGTAGTGCCAT
Found at i:68815 original size:22 final size:20
Alignment explanation
Indices: 68762--68816 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
68752 TTCAGACTAA
68762 ATAGTATTGATACTCATCCT
1 ATAGTATTGATACTCATCCT
* * * *
68782 ACAGTATCGATACTTCCTTTCT
1 ATAGTATTGATAC-T-CATCCT
68804 ATAGTATTGATAC
1 ATAGTATTGATAC
68817 ATACTTCGGT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 11 0.41
21 1 0.04
22 15 0.56
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (20 bp):
ATAGTATTGATACTCATCCT
Found at i:69165 original size:20 final size:21
Alignment explanation
Indices: 69122--69165 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
69112 AAACTAACTT
** *
69122 ACATCCATAAATCTCCTTATA
1 ACATCCATAAATCTCCAAAGA
69143 ACATCCA-AAATCTCCAAAGA
1 ACATCCATAAATCTCCAAAGA
69163 ACA
1 ACA
69166 CTCAAAACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.45, C:0.30, G:0.02, T:0.23
Consensus pattern (21 bp):
ACATCCATAAATCTCCAAAGA
Found at i:71314 original size:6 final size:6
Alignment explanation
Indices: 71303--71336 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
71293 TGGAAGAGTA
71303 GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAG
1 GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAG
71337 ACGGAGGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.68, T:0.15
Consensus pattern (6 bp):
GGAGGT
Found at i:71342 original size:18 final size:18
Alignment explanation
Indices: 71303--71343 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
71293 TGGAAGAGTA
**
71303 GGAGGTGGAGGTGGAGGT
1 GGAGGTGGAGGTGGAGAC
71321 GGAGGTGGAGGTGGAGAC
1 GGAGGTGGAGGTGGAGAC
71339 GGAGG
1 GGAGG
71344 AAGGGGAGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.02, G:0.66, T:0.12
Consensus pattern (18 bp):
GGAGGTGGAGGTGGAGAC
Found at i:73843 original size:13 final size:13
Alignment explanation
Indices: 73834--73858 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
73824 ATCTATGAAG
73834 CGCATTTATGACA
1 CGCATTTATGACA
73847 CGCATTTATGAC
1 CGCATTTATGAC
73859 TCATATTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (13 bp):
CGCATTTATGACA
Found at i:81538 original size:19 final size:19
Alignment explanation
Indices: 81516--81568 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
81506 TTTCTATCAC
81516 ATTTTTCTTTTAAATTAAT
1 ATTTTTCTTTTAAATTAAT
* * *
81535 ATTTTTAGTTTT-ATTTTAT
1 ATTTTT-CTTTTAAATTAAT
*
81554 ATTTTTCTTTCAAAT
1 ATTTTTCTTTTAAAT
81569 AATTTAAGAT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
18 3 0.12
19 19 0.73
20 4 0.15
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTTTCTTTTAAATTAAT
Found at i:81843 original size:19 final size:20
Alignment explanation
Indices: 81816--81860 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
81806 AAATTAAATT
81816 ATTAA-TAAAAAATATAAAA
1 ATTAATTAAAAAATATAAAA
**
81835 A-TAATTAAACTATATAAAA
1 ATTAATTAAAAAATATAAAA
81854 ATTAATT
1 ATTAATT
81861 TTTTTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 3 0.14
19 14 0.64
20 5 0.23
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
ATTAATTAAAAAATATAAAA
Found at i:83481 original size:21 final size:21
Alignment explanation
Indices: 83455--83497 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
83445 AATCCTTATC
83455 AGTTTAAATTCAAGTAAAATT
1 AGTTTAAATTCAAGTAAAATT
83476 AGTTTAAATTCAAGTAAAATT
1 AGTTTAAATTCAAGTAAAATT
83497 A
1 A
83498 AACTTTTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (21 bp):
AGTTTAAATTCAAGTAAAATT
Found at i:87998 original size:4 final size:4
Alignment explanation
Indices: 87989--88017 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
87979 TCTAATTATA
87989 TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG T
88018 GGACATGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Done.