Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007626.1 Hibiscus syriacus cultivar Beakdansim tig00023188_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: 54090
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:1628 original size:29 final size:28
Alignment explanation
Indices: 1595--1665 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 28
1585 ATTGAAAATC
*
1595 ATTATATATTATTAAAATAAAAGTATAAT
1 ATTATATATTATTAAAATAAAAGAAT-AT
* * *
1624 ATTATATATCATTAATATTAAAGAATAT
1 ATTATATATTATTAAAATAAAAGAATAT
*
1652 AATATATATTATTA
1 ATTATATATTATTA
1666 GAATTATGAG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 14 0.39
29 22 0.61
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (28 bp):
ATTATATATTATTAAAATAAAAGAATAT
Found at i:3081 original size:24 final size:24
Alignment explanation
Indices: 3054--3168 Score: 126
Period size: 24 Copynumber: 4.8 Consensus size: 24
3044 TCATATTCAT
* * *
3054 GTCAAGTTTCATATCAAAATCCAG
1 GTCAAGTATCATATCAGAATCCAA
3078 GTCAAGTATCATATCAGAATCCAA
1 GTCAAGTATCATATCAGAATCCAA
* *
3102 GTTAAGTATCAGATCAGAATCCATA
1 GTCAAGTATCATATCAGAATCCA-A
* *
3127 -TC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCATATCAGAATCCAA
*
3150 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCATATCAGAA
3169 ATCAAATCGA
Statistics
Matches: 80, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
23 2 0.03
24 75 0.94
25 3 0.04
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAA
Found at i:9538 original size:35 final size:37
Alignment explanation
Indices: 9461--9538 Score: 90
Period size: 35 Copynumber: 2.1 Consensus size: 37
9451 TTGAAAAATC
**
9461 ATTATATATTATTAAAATAAAAGTATAATATATATATC
1 ATTATATATTA-TAAAATAAAAGTATAATATATATAGA
*
9499 ATTATATATTA-AAAATATAA-TATAATAT-TATTAGA
1 ATTATATATTATAAAATAAAAGTATAATATATA-TAGA
9534 ATTAT
1 ATTAT
9539 GAGTAAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
34 2 0.06
35 15 0.42
36 8 0.22
38 11 0.31
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.44
Consensus pattern (37 bp):
ATTATATATTATAAAATAAAAGTATAATATATATAGA
Found at i:11188 original size:22 final size:22
Alignment explanation
Indices: 11163--11206 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
11153 ATAATCCTAT
11163 TATTTCAAA-ATATATTAATTTA
1 TATTT-AAATATATATTAATTTA
* *
11185 TATTTAAATATTTATTATTTTA
1 TATTTAAATATATATTAATTTA
11207 GAAATATCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TATTTAAATATATATTAATTTA
Found at i:11307 original size:29 final size:29
Alignment explanation
Indices: 11260--11322 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
11250 TCTTCGATAT
*
11260 TAAAAATAAATAATAATTAAAAAAATTTC
1 TAAAAATAAATAATAATTAAAAAAATTTA
* *
11289 TAAAAATAATATAAT-ATTAATATAATTTA
1 TAAAAATAA-ATAATAATTAAAAAAATTTA
11318 TAAAA
1 TAAAA
11323 TAGGATATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 25 0.83
30 5 0.17
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (29 bp):
TAAAAATAAATAATAATTAAAAAAATTTA
Found at i:11562 original size:22 final size:19
Alignment explanation
Indices: 11546--11589 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
11536 GAACAAAAGT
11546 AATTAAATATATAAACATATAA
1 AATTAAA-ATATAAACA-A-AA
*
11568 AATTAAAATATAAATAAAA
1 AATTAAAATATAAACAAAA
11587 AAT
1 AAT
11590 GACTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 1 0.05
21 8 0.38
22 7 0.33
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
AATTAAAATATAAACAAAA
Found at i:12898 original size:3 final size:3
Alignment explanation
Indices: 12878--12935 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
12868 ATTTATTTAT
* * *
12878 TAA TAA TATA TAA CAA TAA TAA TAA TAA T-A TAA TAA TAA CAA TTA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12923 -AA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA
12936 AAGTAAACTG
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 5 0.11
3 37 0.82
4 3 0.07
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:12912 original size:14 final size:14
Alignment explanation
Indices: 12878--12934 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 14
12868 ATTTATTTAT
*
12878 TAATAATATATAACAA
1 TAATAATA-ATAA-TA
12894 TAATAATAATAATA
1 TAATAATAATAATA
*
12908 TAATAATAACAAT-
1 TAATAATAATAATA
12921 TAAATAATAA-AATA
1 T-AATAATAATAATA
12935 AAAGTAAACT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
13 4 0.11
14 21 0.57
15 4 0.11
16 8 0.22
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.32
Consensus pattern (14 bp):
TAATAATAATAATA
Found at i:12926 original size:22 final size:23
Alignment explanation
Indices: 12878--12935 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
12868 ATTTATTTAT
*
12878 TAATAATAT-ATAACAATAATAA
1 TAATAATATAATAACAACAATAA
* *
12900 TAATAATATAATAATAACAATTA
1 TAATAATATAATAACAACAATAA
*
12923 -AATAATAAAATAA
1 TAATAATATAATAA
12936 AAGTAAACTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 21 0.68
23 10 0.32
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (23 bp):
TAATAATATAATAACAACAATAA
Found at i:13462 original size:224 final size:227
Alignment explanation
Indices: 13060--13621 Score: 945
Period size: 224 Copynumber: 2.5 Consensus size: 227
13050 GATGAAAATG
* *
13060 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TTTTGAAAACATCAAAAAGC
*
13125 TCCCG-AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCTAAGGCTTTGAAAAC
65 TCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCGAAGGCTTTGAAAAC
** *
13189 ATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAG
130 ATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAG
*
13254 GCTTTGAAAACATC-AAAAG-TTCCGAAGGCTT
195 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
* *
13285 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCGAAGG-CTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCT
*
13349 CCCGAAGGCTTTTTGGAAACATTATGCACTGTAGGACTTACAGATGACCCGAAGGC-TTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGA-CCGAAGGCTTTGAAAAC
13413 ATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAG
130 ATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAG
13478 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
195 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
* * *
13511 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAATAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCT
*
13576 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
13622 TGGGAAATAG
Statistics
Matches: 316, Mismatches: 16, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
223 23 0.07
224 125 0.40
225 53 0.17
226 53 0.17
227 62 0.20
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (227 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCT
CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCGAAGGCTTTGAAAACA
TCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGG
CTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
Found at i:13520 original size:76 final size:76
Alignment explanation
Indices: 13060--13621 Score: 929
Period size: 76 Copynumber: 7.5 Consensus size: 76
13050 GATGAAAATG
* * * * *
13060 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGG-CTTTGAAAACATCAAAAAGC
13125 TCCCG-AGGCTT
65 TCCCGAAGGCTT
13136 TTTGGAAACATCATGCACTGTAGGACTTACAGATGA-CCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
13200 CCTGAAGGCTT
66 CCCGAAGGCTT
13211 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAG-T
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
13274 TCCGAAGGCTT
66 CCCGAAGGCTT
* *
13285 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGC-TTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
13349 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
13360 TTTGGAAACATTATGCACTGTAGGACTTACAGATGACCCGAAGGC-TTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
13424 CCCAAAGGCTT
66 CCCGAAGGCTT
*
13435 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
13500 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
13511 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAATAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
13576 CCCGAAGGCTT
66 CCCGAAGGCTT
*
13587 TTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATG
13622 TGGGAAATAG
Statistics
Matches: 459, Mismatches: 22, Indels: 10
0.93 0.04 0.02
Matches are distributed among these distances:
73 11 0.02
74 81 0.18
75 178 0.39
76 189 0.41
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:13789 original size:138 final size:138
Alignment explanation
Indices: 13626--13899 Score: 428
Period size: 136 Copynumber: 2.0 Consensus size: 138
13616 CAGATGTGGG
*
13626 AAATAGTTTACTAAGTAAAAAAACTAAGGAAATTGTTTTCTTACGTTTCAACAATTTCATTTCTA
1 AAATAGTTTACTAAGTAAAAAAACTAAGGAAATCG-TTTCTTACGTTTCAACAATTTCATTT-TA
**
13691 GAAAAGATTGAATGAGAAACTATGGAAA-TCGTTTTCTC-ATTA-TTTTTCAAAATAACATGTTG
64 GAAAAGATAAAATGAGAAACTATGGAAATTC-TTTTCTCTATTATTTTTTCAAAATAACATGTTG
13753 ATTGGGTTTGT
128 ATTGGGTTTGT
*
13764 AAATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTCTTACTTTTCAACAATTTCATTTTAGA
1 AAATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTCTTACGTTTCAACAATTTCATTTTAGA
**
13829 AAAGATAAAATGAGAAACTATGGAAATTCTTTTCTCATTATTATTTTTTTGAAATAACATGTTGA
66 AAAGATAAAATGAGAAACTATGGAAATTCTTTTCTC--TATTATTTTTTCAAAATAACATGTTGA
13894 TTGGGT
129 TTGGGT
13900 AACATGACCC
Statistics
Matches: 125, Mismatches: 6, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
136 35 0.28
137 27 0.22
138 34 0.27
139 4 0.03
140 25 0.20
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.39
Consensus pattern (138 bp):
AAATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTCTTACGTTTCAACAATTTCATTTTAGA
AAAGATAAAATGAGAAACTATGGAAATTCTTTTCTCTATTATTTTTTCAAAATAACATGTTGATT
GGGTTTGT
Found at i:17220 original size:114 final size:113
Alignment explanation
Indices: 17016--17234 Score: 366
Period size: 114 Copynumber: 1.9 Consensus size: 113
17006 GATCATGCAG
* * * *
17016 TTCATCTTTCAATTCCAATGATTGGTTTTGGGGTTCCTACCGAACCAGATCAATAACTCAAAGAA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAAATCAATAACTCAAAGAA
*
17081 CACTTCCAGAAGATTCTATTCGGTCTCCTTATTTCTACTATGAGCAAA
66 CACTTCCAGAAGATACTATTCGGTCTCCTTATTTCTACTATGAGCAAA
*
17129 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAAATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAAATCA-ATAACTCAAAGA
*
17194 ACACTTCCAGAAGATACTATTGGGTCTCCTTATTTCTACTA
65 ACACTTCCAGAAGATACTATTCGGTCTCCTTATTTCTACTA
17235 CGAGACGTGG
Statistics
Matches: 98, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
113 47 0.48
114 51 0.52
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.34
Consensus pattern (113 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAAATCAATAACTCAAAGAA
CACTTCCAGAAGATACTATTCGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:21384 original size:14 final size:15
Alignment explanation
Indices: 21367--21399 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
21357 TAAAAGTATG
21367 AATGCAAA-ATGAAA
1 AATGCAAAGATGAAA
*
21381 AATGCAAAGATGCAA
1 AATGCAAAGATGAAA
21396 AATG
1 AATG
21400 AAATGCATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.58, C:0.09, G:0.18, T:0.15
Consensus pattern (15 bp):
AATGCAAAGATGAAA
Found at i:23799 original size:20 final size:21
Alignment explanation
Indices: 23749--23799 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
23739 ATAATATTAT
* *
23749 GAAAATCATAAAAAATTGAAA
1 GAAAATAATTAAAAATTGAAA
23770 GAAAATAATTAAAAATT-AAA
1 GAAAATAATTAAAAATTGAAA
23790 -AAAATGAATT
1 GAAAAT-AATT
23800 TTTAATTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 5 0.19
20 7 0.26
21 15 0.56
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.24
Consensus pattern (21 bp):
GAAAATAATTAAAAATTGAAA
Found at i:25950 original size:3 final size:3
Alignment explanation
Indices: 25930--25987 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
25920 ATTTATTTAT
* * *
25930 TAA TAA TATA TAA CAA TAA TAA TAA T-A TTA TAA TAA TAA TAA TTA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
25975 -AA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA
25988 AAGTAAACTG
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
2 5 0.11
3 38 0.83
4 3 0.07
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:25964 original size:14 final size:15
Alignment explanation
Indices: 25930--25982 Score: 65
Period size: 14 Copynumber: 3.6 Consensus size: 15
25920 ATTTATTTAT
**
25930 TAATAATATATAACAA
1 TAATAATA-ATAATTA
25946 TAATAATAAT-ATTA
1 TAATAATAATAATTA
25960 TAATAATAATAATTA
1 TAATAATAATAATTA
25975 -AATAATAA
1 TAATAATAA
25983 AATAAAAGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 20 0.59
15 6 0.18
16 8 0.24
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (15 bp):
TAATAATAATAATTA
Found at i:25964 original size:17 final size:17
Alignment explanation
Indices: 25930--25972 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
25920 ATTTATTTAT
25930 TAATAAT-ATATAACAA
1 TAATAATAATATAACAA
* *
25946 TAATAATAATATTATAA
1 TAATAATAATATAACAA
25963 TAATAATAAT
1 TAATAATAAT
25973 TAAATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 7 0.29
17 17 0.71
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
TAATAATAATATAACAA
Found at i:28330 original size:64 final size:65
Alignment explanation
Indices: 28259--28407 Score: 167
Period size: 65 Copynumber: 2.3 Consensus size: 65
28249 CTAGGGGTGC
* * *
28259 ATCGGTACACTAATTACATTCGATGTTTC-AAAGAGCCATGAGTGCATCGATGCATGG-TATGTG
1 ATCGGTACACAAAATACATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCT-TGTG
28322 A
65 A
** * * ** * *
28323 ATCGGTACACAAAATGTATTTGATGTTTCAAAATATTCAAGAGTGCATCGATGCTTGGCTTGTGC
1 ATCGGTACACAAAATACATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCTTGTGA
*
28388 ATCGGTACACAAAATGCATT
1 ATCGGTACACAAAATACATT
28408 AGATATGGGT
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
64 24 0.34
65 46 0.65
66 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (65 bp):
ATCGGTACACAAAATACATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCTTGTGA
Found at i:28769 original size:12 final size:13
Alignment explanation
Indices: 28743--28777 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
28733 TAAGATTTTC
28743 TTTGAAAATCAAT
1 TTTGAAAATCAAT
28756 TTTGAAAA-CAAT
1 TTTGAAAATCAAT
28768 TTTGCAAAAT
1 TTTG-AAAAT
28778 TACTCCCCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:32959 original size:254 final size:250
Alignment explanation
Indices: 32478--32982 Score: 906
Period size: 253 Copynumber: 2.0 Consensus size: 250
32468 GTCAATTTAA
32478 AAACATGATCTGGAAATTTGAATCTTCAAAACCATGAGGTTGTGCCATATACACTTCTTCTTTTA
1 AAACATGATCTGGAAATTTGAATCTTCAAAACCATGAGGTTGTGCCATATACACTTCTTCTTTTA
*
32543 TAAAACCATTTAAAAATGAACTTCTAACATCCATTTTATATAATTTAAATTCATTGAAACATGCA
66 TAAAACCATTTAAAAATGAACTTCTAACATCCATTTGATATAATTTAAATTCATTGAAACATGCA
32608 AATGCTAATAAATTCTAATTGCTTCCATCCTAGCTACGGGAGCGTATGTTCATCATAGTATATGC
131 AATGCTAATAAATTCTAATTGCTTCCATCCTAGCTACGGGAGCGTATGTTCATCATAGTATATGC
32673 CCTCTTCTTGAGTATATCCTTGAGCAACAAGTCTAACCTTGTTTCTCACTATATTACC
196 CCTCTTCTTGAGTATATCCTTGAGCAACAAGTCTAA-CTTG-TTCTCACTATA-TACC
*
32731 AAACATGATCTGGAAATTTTGAATCTTCAAAACCATGAGGTTGTGCCTTATACACTTCTTC-TTT
1 AAACATGATCTGGAAA-TTTGAATCTTCAAAACCATGAGGTTGTGCCATATACACTTCTTCTTTT
*
32795 ATAAAACCATTTAAAAATGCACTTCTAACATCCATTTGATATAATTTAAATTCATTGAAACATGC
65 ATAAAACCATTTAAAAATGAACTTCTAACATCCATTTGATATAATTTAAATTCATTGAAACATGC
*
32860 AAATGCTAATAACATTCTAATTGCTTCCATCCTAGCTATGGGAGCGTATGTTTCATCATAGTATA
130 AAATGCTAATAA-ATTCTAATTGCTTCCATCCTAGCTACGGGAGCGTATG-TTCATCATAGTATA
32925 TGCCCTCTTCTTGAGTATATCCTTGAGC-ACAAGTCTAACTTGTTCTCACTATATACC
193 TGCCCTCTTCTTGAGTATATCCTTGAGCAACAAGTCTAACTTGTTCTCACTATATACC
32982 A
1 A
32983 CTTCATCAAG
Statistics
Matches: 245, Mismatches: 4, Indels: 8
0.95 0.02 0.03
Matches are distributed among these distances:
251 5 0.02
252 11 0.04
253 98 0.40
254 89 0.36
255 42 0.17
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (250 bp):
AAACATGATCTGGAAATTTGAATCTTCAAAACCATGAGGTTGTGCCATATACACTTCTTCTTTTA
TAAAACCATTTAAAAATGAACTTCTAACATCCATTTGATATAATTTAAATTCATTGAAACATGCA
AATGCTAATAAATTCTAATTGCTTCCATCCTAGCTACGGGAGCGTATGTTCATCATAGTATATGC
CCTCTTCTTGAGTATATCCTTGAGCAACAAGTCTAACTTGTTCTCACTATATACC
Found at i:33613 original size:24 final size:24
Alignment explanation
Indices: 33585--33635 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
33575 AGGGTTGTTT
33585 ATAAATATTAAATAATTTAT-AATA
1 ATAAAT-TTAAATAATTTATGAATA
**
33609 ATAAATTTATGTAATTTATGAATA
1 ATAAATTTAAATAATTTATGAATA
33633 ATA
1 ATA
33636 TTATTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
ATAAATTTAAATAATTTATGAATA
Found at i:33698 original size:28 final size:26
Alignment explanation
Indices: 33654--33719 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 26
33644 ATTGAAAATC
33654 ATTATAT-ATTATAAAATAAAAGTATAAT
1 ATTATATCATTATAAAATAAAAG---AAT
*
33682 ATTATATCATTAT-AAATTAAAGAAT
1 ATTATATCATTATAAAATAAAAGAAT
*
33707 ATAATATCATTAT
1 ATTATATCATTAT
33720 TAGAATTATG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 15 0.43
28 15 0.43
29 5 0.14
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (26 bp):
ATTATATCATTATAAAATAAAAGAAT
Found at i:34126 original size:13 final size:13
Alignment explanation
Indices: 34108--34133 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34098 TTAATTCTTG
34108 ATATATATATTAT
1 ATATATATATTAT
34121 ATATATATATTAT
1 ATATATATATTAT
34134 TATTTTATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATATATATATTAT
Found at i:35493 original size:2 final size:2
Alignment explanation
Indices: 35482--35522 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
35472 TTATAAAAGC
35482 AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35523 TTCCAAGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:36636 original size:20 final size:22
Alignment explanation
Indices: 36593--36637 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
36583 TTAAGATTAT
*
36593 TAAATTTTATTGAAACTTTGAA
1 TAAATTATATTGAAACTTTGAA
*
36615 TAAATTATATT-AAA-TTTTAA
1 TAAATTATATTGAAACTTTGAA
36635 TAA
1 TAA
36638 TAATAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
21 3 0.14
22 10 0.48
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (22 bp):
TAAATTATATTGAAACTTTGAA
Found at i:37295 original size:2 final size:2
Alignment explanation
Indices: 37288--37315 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
37278 TTAATTCTTG
37288 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
37316 TATTTTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39806 original size:12 final size:12
Alignment explanation
Indices: 39779--39871 Score: 55
Period size: 12 Copynumber: 7.8 Consensus size: 12
39769 ACAGAGATGT
* *
39779 CAGAAATCAAAA
1 CAGAATTCAGAA
*
39791 CAGAATTCAGAT
1 CAGAATTCAGAA
39803 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* * *
39815 CAAAATCCAGAT
1 CAGAATTCAGAA
*
39827 CAGAAATCAGAA
1 CAGAATTCAGAA
* *
39839 CAGGATTCATATA
1 CAGAATTCAGA-A
* *
39852 -AGAAATCATAA
1 CAGAATTCAGAA
39863 CAGAATTCA
1 CAGAATTCA
39872 AATCGAAAAT
Statistics
Matches: 60, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
11 3 0.05
12 54 0.90
13 3 0.05
ACGTcount: A:0.52, C:0.17, G:0.13, T:0.18
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:39806 original size:24 final size:24
Alignment explanation
Indices: 39778--39885 Score: 119
Period size: 24 Copynumber: 4.5 Consensus size: 24
39768 CACAGAGATG
*
39778 TCAGAAATCAAAACAGAATTCAGA
1 TCAGAAATCAGAACAGAATTCAGA
* * *
39802 TCAGATATCAGAACAAAATCCAGA
1 TCAGAAATCAGAACAGAATTCAGA
* *
39826 TCAGAAATCAGAACAGGATTCATA
1 TCAGAAATCAGAACAGAATTCAGA
* * *
39850 TAAGAAATCATAACAGAATTCAAA
1 TCAGAAATCAGAACAGAATTCAGA
39874 TC-GAAAATCAGA
1 TCAG-AAATCAGA
39886 TAAAACATTC
Statistics
Matches: 68, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
23 1 0.01
24 67 0.99
ACGTcount: A:0.52, C:0.17, G:0.13, T:0.19
Consensus pattern (24 bp):
TCAGAAATCAGAACAGAATTCAGA
Found at i:48755 original size:2 final size:2
Alignment explanation
Indices: 48748--48777 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
48738 AATTCCTGAC
48748 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
48778 TTTTATGAAA
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:51300 original size:20 final size:22
Alignment explanation
Indices: 51257--51301 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
51247 TTAAGATTAT
*
51257 TAAATTTTATTGAAACTTTGAA
1 TAAATTATATTGAAACTTTGAA
*
51279 TAAATTATATT-AAA-TTTTAA
1 TAAATTATATTGAAACTTTGAA
51299 TAA
1 TAA
51302 TAATAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
21 3 0.14
22 10 0.48
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (22 bp):
TAAATTATATTGAAACTTTGAA
Found at i:51529 original size:15 final size:15
Alignment explanation
Indices: 51509--51556 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
51499 AAAATAAAAG
51509 TATAATATATATAAT
1 TATAATATATATAAT
*
51524 TATAATATTACATAA-
1 TATAATA-TATATAAT
*
51539 TATAATATCATATTAT
1 TATAATAT-ATATAAT
51555 TA
1 TA
51557 GAATTATGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 1 0.04
15 18 0.67
16 8 0.30
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (15 bp):
TATAATATATATAAT
Found at i:51975 original size:2 final size:2
Alignment explanation
Indices: 51968--51999 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
51958 TTAATTCTTG
51968 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52000 TATTTTTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.