Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000961.1 Hibiscus syriacus cultivar Beakdansim tig00001921_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: 72368
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:315 original size:15 final size:15
Alignment explanation
Indices: 279--314 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
269 TTTTCTGAGA
279 TATTATTATTATTATT
1 TATT-TTATTATTATT
295 TATTTTATTATTATT
1 TATTTTATTATTATT
310 T-TTTT
1 TATTTT
315 TCAGGTTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 4 0.20
15 12 0.60
16 4 0.20
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
TATTTTATTATTATT
Found at i:864 original size:29 final size:30
Alignment explanation
Indices: 822--878 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
812 GATTTCCAAA
* *
822 AAAATAGAAAAAATGAA-ACGAAAAAAGAG
1 AAAAGAGAAAAAATAAATACGAAAAAAGAG
* *
851 AAAAGAGAAGAAATAAATATGAAAAAAG
1 AAAAGAGAAAAAATAAATACGAAAAAAG
879 GAGGAAGAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 14 0.61
30 9 0.39
ACGTcount: A:0.72, C:0.02, G:0.18, T:0.09
Consensus pattern (30 bp):
AAAAGAGAAAAAATAAATACGAAAAAAGAG
Found at i:1696 original size:19 final size:18
Alignment explanation
Indices: 1672--1710 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1662 TGTTTTCTTG
*
1672 TTATTATACGCATGTATAT
1 TTATTA-ACGCATGGATAT
*
1691 TTATTAGCGCATGGATAT
1 TTATTAACGCATGGATAT
1709 TT
1 TT
1711 TGCCAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.46
Consensus pattern (18 bp):
TTATTAACGCATGGATAT
Found at i:6419 original size:2 final size:2
Alignment explanation
Indices: 6412--6444 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6402 TTTCGTAAAT
6412 TA 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 TA T
6445 TAGATTGACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16477 original size:51 final size:51
Alignment explanation
Indices: 16352--16478 Score: 184
Period size: 51 Copynumber: 2.5 Consensus size: 51
16342 GATTTGGCAC
* * * *
16352 CACGTGGAGTATAGCGCGCCCCCAGTACCGCGCTATACGCTGACTGGGTTA
1 CACGTGGGGTATAGCGCACCCCCTGTACCGCGCTATACACTGACTGGGTTA
* *
16403 CACGTGGGGTATAGTGCAACCCCTGCT-CCGCGCTATACACTGACTGGGTTA
1 CACGTGGGGTATAGCGCACCCCCTG-TACCGCGCTATACACTGACTGGGTTA
16454 CACGTGGGGTATAGCGCACCCCCTG
1 CACGTGGGGTATAGCGCACCCCCTG
16479 ATCCATTCTA
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
51 66 0.99
52 1 0.01
ACGTcount: A:0.19, C:0.31, G:0.29, T:0.20
Consensus pattern (51 bp):
CACGTGGGGTATAGCGCACCCCCTGTACCGCGCTATACACTGACTGGGTTA
Found at i:16660 original size:12 final size:12
Alignment explanation
Indices: 16640--16676 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
16630 ACCTCTCGTT
16640 CTCGCATCTCTC
1 CTCGCATCTCTC
*
16652 CTTGCATCT-T-
1 CTCGCATCTCTC
16662 CTCGCATCTCTC
1 CTCGCATCTCTC
16674 CTC
1 CTC
16677 TCTTATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
10 8 0.38
11 2 0.10
12 11 0.52
ACGTcount: A:0.08, C:0.46, G:0.08, T:0.38
Consensus pattern (12 bp):
CTCGCATCTCTC
Found at i:20122 original size:35 final size:36
Alignment explanation
Indices: 20039--20139 Score: 97
Period size: 35 Copynumber: 2.9 Consensus size: 36
20029 TTGGTATTTA
*
20039 AATACAACAAACTTACAAT-AA-GA-ATTAAATGGT
1 AATACAACAAAATTACAATAAATGATATTAAATGGT
* *
20072 ATATGATAACCAAATTACAATAAATGATATTAAATGGT
1 A-AT-ACAACAAAATTACAATAAATGATATTAAATGGT
*
20110 AATA-AACAAAATTA-ACTGAAAT-ATATTAAA
1 AATACAACAAAATTACAAT-AAATGATATTAAA
20140 AAAAAAGTCC
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
33 1 0.02
34 12 0.21
35 26 0.46
36 3 0.05
37 4 0.07
38 11 0.19
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (36 bp):
AATACAACAAAATTACAATAAATGATATTAAATGGT
Found at i:20581 original size:20 final size:20
Alignment explanation
Indices: 20552--20598 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
20542 CCCAACTCTT
*
20552 GAGAACACTCTTTTCTCAAA
1 GAGAAGACTCTTTTCTCAAA
20572 GAGAAGACTCTTTTCTCAAA
1 GAGAAGACTCTTTTCTCAAA
20592 GAGAAGA
1 GAGAAGA
20599 TTACAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (20 bp):
GAGAAGACTCTTTTCTCAAA
Found at i:21143 original size:75 final size:75
Alignment explanation
Indices: 21015--21222 Score: 258
Period size: 75 Copynumber: 2.8 Consensus size: 75
21005 GACCGTTGAA
* * * * *
21015 CAGGGGGGAATCGGTACCCCCT-TGGGGGGATCAGTTCCCTCCGAGCATACTGGAATTCTCGGAA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAA
**
21079 CAAAAACTGTT
66 C-AAAACCATT
* * * *
21090 TA-GGGGGAATCGGTTCCTCATATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAA
*
21154 CCAAACCATT
66 CAAAACCATT
* *
21164 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCAATCTGGAATT
1 CAGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAATT
21223 TTTGGCTTTA
Statistics
Matches: 113, Mismatches: 17, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
74 23 0.20
75 59 0.52
76 31 0.27
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.24
Consensus pattern (75 bp):
CAGGGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAA
CAAAACCATT
Found at i:21832 original size:17 final size:17
Alignment explanation
Indices: 21812--21856 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
21802 TTCATAAATT
21812 CAAAATCCAACAATCCA
1 CAAAATCCAACAATCCA
*
21829 CAAAATCAAACAATCCA
1 CAAAATCCAACAATCCA
*
21846 AAAATATCCAA
1 CAAA-ATCCAA
21857 AATGTTGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 19 0.79
18 5 0.21
ACGTcount: A:0.58, C:0.29, G:0.00, T:0.13
Consensus pattern (17 bp):
CAAAATCCAACAATCCA
Found at i:23892 original size:20 final size:20
Alignment explanation
Indices: 23863--23900 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
23853 CCCCTTCAAA
*
23863 GGGGGAATCGGTTCCCTCAG
1 GGGGGAATCGATTCCCTCAG
*
23883 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
23901 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.39, T:0.21
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAG
Found at i:29759 original size:75 final size:76
Alignment explanation
Indices: 29671--29879 Score: 264
Period size: 75 Copynumber: 2.8 Consensus size: 76
29661 GACCGTTGAA
* * *
29671 CAGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
**
29735 ACAAAAACTGTT
66 AC-AAAACCATT
* * * *
29747 TA-GGGGGAATCGGTTCCTCATAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
* *
29810 GCCAAACCATT
66 ACAAAACCATT
*
29821 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCA-ATCTGGAATT
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATA-CTGGAATT
29880 TTTGGCTTTA
Statistics
Matches: 113, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
74 7 0.06
75 74 0.65
76 32 0.28
ACGTcount: A:0.22, C:0.24, G:0.31, T:0.23
Consensus pattern (76 bp):
CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
ACAAAACCATT
Found at i:30169 original size:12 final size:12
Alignment explanation
Indices: 30152--30185 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
30142 GACTCCTCGC
30152 TGTCATCATCAT
1 TGTCATCATCAT
30164 TGTCATCATCAT
1 TGTCATCATCAT
* *
30176 CGTCACCATC
1 TGTCATCATC
30186 GTCATCGTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.32, G:0.09, T:0.35
Consensus pattern (12 bp):
TGTCATCATCAT
Found at i:30605 original size:18 final size:18
Alignment explanation
Indices: 30552--30605 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
30542 CGATGGCGCC
* * *
30552 ATCATATATGGATGCGGC
1 ATCATATATGGCTGCAGT
30570 ATCATATATGGCTGCAGT
1 ATCATATATGGCTGCAGT
30588 ATCATATATGGCTGCAGT
1 ATCATATATGGCTGCAGT
30606 GGCTGCTGGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (18 bp):
ATCATATATGGCTGCAGT
Found at i:32190 original size:111 final size:111
Alignment explanation
Indices: 32048--32380 Score: 594
Period size: 111 Copynumber: 3.0 Consensus size: 111
32038 ATTACAAAAA
* *
32048 TTAATTCTTACTCTAATAATCATTCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
32113 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
32159 TTAATTCTTAATCTAATAATAATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* * *
32224 AATTAATAGGTTAAAATGTTATCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
32270 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
32335 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
32381 ATGATTTCCA
Statistics
Matches: 210, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 210 1.00
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.37
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:32723 original size:50 final size:50
Alignment explanation
Indices: 32669--32786 Score: 139
Period size: 50 Copynumber: 2.4 Consensus size: 50
32659 AGATACCCAG
* * * *
32669 GTATAGCGCAGATCAGGGGGTACGCTATACCCACGTGGCGCCAGATCATC
1 GTATAGCGCGGATCAGGGGGCACGCTATACCCACGTGGCGCCAAATCAGC
* * * *
32719 GTATATCGTGGGA-CAGGGGGCGCGCTATACCCACGTGGCGTCAAATCAGC
1 GTATAGCG-CGGATCAGGGGGCACGCTATACCCACGTGGCGCCAAATCAGC
*
32769 GTATAGCGCGGTTCAGGG
1 GTATAGCGCGGATCAGGG
32787 AGCGCGCTTT
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
49 2 0.04
50 51 0.93
51 2 0.04
ACGTcount: A:0.22, C:0.25, G:0.34, T:0.19
Consensus pattern (50 bp):
GTATAGCGCGGATCAGGGGGCACGCTATACCCACGTGGCGCCAAATCAGC
Found at i:33158 original size:18 final size:18
Alignment explanation
Indices: 33135--33181 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
33125 CGTGCTACAG
33135 GGTATGGGCACTTAGCAA
1 GGTATGGGCACTTAGCAA
33153 GGTATGGGCACTTAGCAA
1 GGTATGGGCACTTAGCAA
*
33171 GGCATGGGCAC
1 GGTATGGGCAC
33182 ACTGGGGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.26, C:0.19, G:0.36, T:0.19
Consensus pattern (18 bp):
GGTATGGGCACTTAGCAA
Found at i:38276 original size:23 final size:23
Alignment explanation
Indices: 38226--38281 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
38216 AATCGTGTTA
*
38226 AAAGACAGAGAAAAACGTGTCAT
1 AAAGGCAGAGAAAAACGTGTCAT
* *
38249 AAAGGTAGAGAAAATCGT-TCCAT
1 AAAGGCAGAGAAAAACGTGT-CAT
*
38272 TAAGGCAGAG
1 AAAGGCAGAG
38282 TTATTTGACA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.46, C:0.12, G:0.25, T:0.16
Consensus pattern (23 bp):
AAAGGCAGAGAAAAACGTGTCAT
Found at i:39108 original size:43 final size:43
Alignment explanation
Indices: 39026--39112 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
39016 GAGTGAGTGA
* **
39026 TCATCGGTGGTAATAGTGGTCGACAACGGGATTTCAGGGATAT
1 TCATCGGTGATAATAGTGGTCGACAACGACATTTCAGGGATAT
* * * *
39069 TCATTGGTGATAATGGTGGTCGACAATGACATTTTAGGGATAT
1 TCATCGGTGATAATAGTGGTCGACAACGACATTTCAGGGATAT
39112 T
1 T
39113 TTTAGAGTTC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.26, C:0.11, G:0.30, T:0.32
Consensus pattern (43 bp):
TCATCGGTGATAATAGTGGTCGACAACGACATTTCAGGGATAT
Found at i:39552 original size:18 final size:18
Alignment explanation
Indices: 39529--39593 Score: 121
Period size: 18 Copynumber: 3.6 Consensus size: 18
39519 ATGCAAAATA
*
39529 GGTACCGATACCCAAAGG
1 GGTACCAATACCCAAAGG
39547 GGTACCAATACCCAAAGG
1 GGTACCAATACCCAAAGG
39565 GGTACCAATACCCAAAGG
1 GGTACCAATACCCAAAGG
39583 GGTACCAATAC
1 GGTACCAATAC
39594 TACTTTACGT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.37, C:0.28, G:0.23, T:0.12
Consensus pattern (18 bp):
GGTACCAATACCCAAAGG
Found at i:41109 original size:19 final size:19
Alignment explanation
Indices: 41069--41107 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
41059 ATATTGAATC
41069 AAATTAAAATATATAGTTA
1 AAATTAAAATATATAGTTA
41088 AAATTAAAA-ATATA-TTA
1 AAATTAAAATATATAGTTA
41105 AAA
1 AAA
41108 AAGGGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.30
18 5 0.25
19 9 0.45
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
AAATTAAAATATATAGTTA
Found at i:41258 original size:20 final size:20
Alignment explanation
Indices: 41235--41278 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
41225 AAAAAATTTT
**
41235 AAAAAAATTTAAAAAAAATG
1 AAAAAAATGAAAAAAAAATG
41255 AAAAAAATGAAAAAAAAATG
1 AAAAAAATGAAAAAAAAATG
41275 AAAA
1 AAAA
41279 TGTAAGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.14
Consensus pattern (20 bp):
AAAAAAATGAAAAAAAAATG
Found at i:41259 original size:11 final size:11
Alignment explanation
Indices: 41235--41278 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
41225 AAAAAATTTT
**
41235 AAAAAAATTTA
1 AAAAAAATGAA
41246 AAAAAAATG--
1 AAAAAAATGAA
41255 AAAAAAATGAA
1 AAAAAAATGAA
41266 AAAAAAATGAA
1 AAAAAAATGAA
41277 AA
1 AA
41279 TGTAAGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 9 0.30
11 21 0.70
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.14
Consensus pattern (11 bp):
AAAAAAATGAA
Found at i:41278 original size:9 final size:9
Alignment explanation
Indices: 41246--41270 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
41236 AAAAAATTTA
41246 AAAAAAATG
1 AAAAAAATG
41255 AAAAAAATG
1 AAAAAAATG
41264 AAAAAAA
1 AAAAAAA
41271 AATGAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (9 bp):
AAAAAAATG
Found at i:49178 original size:21 final size:21
Alignment explanation
Indices: 49150--49207 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
49140 GAATTGACAC
*
49150 CATT-TGCATTTTCATCATTG
1 CATTATGCATTTGCATCATTG
49170 CATTATGCATTTGCATCATTG
1 CATTATGCATTTGCATCATTG
*
49191 CATTATGCAATTGCATC
1 CATTATGCATTTGCATC
49208 GTATTTTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 4 0.11
21 31 0.89
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.43
Consensus pattern (21 bp):
CATTATGCATTTGCATCATTG
Found at i:51822 original size:39 final size:38
Alignment explanation
Indices: 51750--51904 Score: 127
Period size: 38 Copynumber: 4.1 Consensus size: 38
51740 ATTTTTCTTA
* * * *
51750 AAACTTCAACTTTGTCTCCATTGA-AGTAGTTTCCCTTG
1 AAACATCAAATTTATCTCCCTTGAGA-TAGTTTCCCTTG
* *
51788 AAACATCAAATTTATCTCCCTTGGGATTGTTTTCCCTTG
1 AAACATCAAATTTATCTCCCTTGAGATAG-TTTCCCTTG
* * *
51827 AAACA-CTAGTTTGTCTCCCTTGAGATAGTTTCCCTTG
1 AAACATCAAATTTATCTCCCTTGAGATAGTTTCCCTTG
** ** * *
51864 AAACATTGAATTCT-TCTAACTCGAGATAGATTCCCTTG
1 AAACATCAAATT-TATCTCCCTTGAGATAGTTTCCCTTG
51902 AAA
1 AAA
51905 TTAAAATTTT
Statistics
Matches: 95, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
37 14 0.15
38 65 0.68
39 16 0.17
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (38 bp):
AAACATCAAATTTATCTCCCTTGAGATAGTTTCCCTTG
Found at i:52806 original size:113 final size:112
Alignment explanation
Indices: 52598--52819 Score: 295
Period size: 113 Copynumber: 2.0 Consensus size: 112
52588 AGCAATCAAG
* *
52598 GAAGAAGTTCATATAGAAGAGATTGTTCGACCTCAACATGCCCTTTATGGAAGAATAGAGGGCTT
1 GAAGAAATTCATATAGAAGAGATTGTTCGACCTCAACATGACCTTTATGGAAGAATAGAGGGCTT
* * * * *
52663 ATATAAGATAGCTCGCCTAGTCATTTCATAGAGGAAAAAATGATCTTA
66 ATATAAGAGAGCTCGCCCACTAATTCCATAGA-GAAAAAATGATCTTA
* * * *
52711 GAAGAAATTCATATAGGAGAGTTTTTTCGACGTCAACATGACCTTTATGGAAGAATAG-GGAGCT
1 GAAGAAATTCATATAGAAGAGATTGTTCGACCTCAACATGACCTTTATGGAAGAATAGAGG-GCT
*
52775 TATATAGGAGAGC-CAGCCCACTAATTCCATAGAGAAAAAATGATC
65 TATATAAGAGAGCTC-GCCCACTAATTCCATAGAGAAAAAATGATC
52820 AAGGAAGAAG
Statistics
Matches: 95, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
112 15 0.16
113 80 0.84
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (112 bp):
GAAGAAATTCATATAGAAGAGATTGTTCGACCTCAACATGACCTTTATGGAAGAATAGAGGGCTT
ATATAAGAGAGCTCGCCCACTAATTCCATAGAGAAAAAATGATCTTA
Found at i:53037 original size:3 final size:3
Alignment explanation
Indices: 53029--53150 Score: 244
Period size: 3 Copynumber: 40.7 Consensus size: 3
53019 TTACCTGACC
53029 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
53077 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
53125 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
53151 AAGTAAAGAA
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 119 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:54460 original size:2 final size:2
Alignment explanation
Indices: 54453--54488 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
54443 AATACGTAAC
54453 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54489 GCGTGAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56943 original size:2 final size:2
Alignment explanation
Indices: 56936--56974 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
56926 TTGATCAAGA
56936 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
56975 ATGAAAAGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:57892 original size:33 final size:33
Alignment explanation
Indices: 57845--57912 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
57835 GGCACTTTTT
57845 ACAGAGTTTCTTTTTACGTCAGAAGAGTTTCTA
1 ACAGAGTTTCTTTTTACGTCAGAAGAGTTTCTA
*
57878 ACAGCGTTTCTTTTTACGTCAGAAGAGTTTCTA
1 ACAGAGTTTCTTTTTACGTCAGAAGAGTTTCTA
57911 AC
1 AC
57913 GGCACATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (33 bp):
ACAGAGTTTCTTTTTACGTCAGAAGAGTTTCTA
Found at i:59934 original size:21 final size:21
Alignment explanation
Indices: 59908--59982 Score: 132
Period size: 21 Copynumber: 3.6 Consensus size: 21
59898 GCGTTGCATT
*
59908 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
59929 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
59950 TCACGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
59971 TCGCGTTGCGAT
1 TCGCGTTGCGAT
59983 TTTCCAGTTC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:59996 original size:20 final size:20
Alignment explanation
Indices: 59971--60238 Score: 123
Period size: 20 Copynumber: 13.6 Consensus size: 20
59961 TAGTTGAAAA
59971 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* *
59991 TCGCGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAGT
* * *
60013 T-GTAGTTGTGATTTTCCAAAT
1 TCG-CGTTGCGATTTTCC-AGT
* *
60034 T--CGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAGT
*
60054 T-GTCGTTGCGATTTTCCAAAT
1 TCG-CGTTGCGATTTTCC-AGT
*
60075 T--CGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
60093 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* ** **
60113 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCAGT
**
60134 T--CGTTGCGA------AAA
1 TCGCGTTGCGATTTTCCAGT
60146 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* * ** **
60166 TCGCATTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCAGT
* *
60187 TCGCGTTACGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
*
60207 TCGCATTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
60227 TCGCGTTGCGAT
1 TCGCGTTGCGAT
60239 AGTCTACAGT
Statistics
Matches: 186, Mismatches: 41, Indels: 42
0.69 0.15 0.16
Matches are distributed among these distances:
12 4 0.02
14 8 0.04
18 3 0.02
19 29 0.16
20 92 0.49
21 27 0.15
22 23 0.12
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAGT
Found at i:60020 original size:22 final size:22
Alignment explanation
Indices: 59994--60065 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 22
59984 TTCCAGTTCG
59994 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * * * **
60016 AGTTGTGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
60035 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
60057 CGTTGCGAT
1 CGTTGCGAT
60066 TTTCCAAATT
Statistics
Matches: 35, Mismatches: 12, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
19 8 0.23
20 5 0.14
21 5 0.14
22 17 0.49
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:60039 original size:41 final size:41
Alignment explanation
Indices: 59975--60084 Score: 168
Period size: 41 Copynumber: 2.7 Consensus size: 41
59965 TGAAAATCGC
*
59975 GTTGCGATTTTCC-AGTTCGCGTTGCGATAGTCTACAGTTGTA
1 GTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTTGTA
* *
60017 GTTGTGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGTC
1 GTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGTA
60058 GTTGCGATTTTCCAAATTCGTTGCGAT
1 GTTGCGATTTTCCAAATTCGTTGCGAT
60085 TTTCCATTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
41 48 0.76
42 12 0.19
43 3 0.05
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (41 bp):
GTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGTA
Found at i:60080 original size:19 final size:19
Alignment explanation
Indices: 60017--60110 Score: 82
Period size: 19 Copynumber: 4.7 Consensus size: 19
60007 TACAGTTGTA
*
60017 GTTGTGATTTTCCAAATTC
1 GTTGCGATTTTCCAAATTC
* * **
60036 GTTGCGATAGTCTACAGTTGTC
1 GTTGCGAT--TTTCCAAAT-TC
60058 GTTGCGATTTTCCAAATTC
1 GTTGCGATTTTCCAAATTC
*
60077 GTTGCGATTTTCC-ATTTCGC
1 GTTGCGATTTTCCAAATT--C
60097 GTTGCGATTTTCCA
1 GTTGCGATTTTCCA
60111 GTTCGCGTTG
Statistics
Matches: 59, Mismatches: 10, Indels: 10
0.75 0.13 0.13
Matches are distributed among these distances:
18 3 0.05
19 22 0.37
20 19 0.32
21 5 0.08
22 10 0.17
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.43
Consensus pattern (19 bp):
GTTGCGATTTTCCAAATTC
Found at i:60199 original size:41 final size:41
Alignment explanation
Indices: 60141--60218 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
60131 AAATCGTTGC
*
60141 GAAAATCGCGTTGCGATTTTCCAGTTCGCATTGCGATAGTT
1 GAAAATCGCGTTACGATTTTCCAGTTCGCATTGCGATAGTT
*
60182 GAAAATCGCGTTACGATTTTCCATTTCGCATTGCGAT
1 GAAAATCGCGTTACGATTTTCCAGTTCGCATTGCGAT
60219 TTTCCAGTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.35
Consensus pattern (41 bp):
GAAAATCGCGTTACGATTTTCCAGTTCGCATTGCGATAGTT
Found at i:60255 original size:22 final size:21
Alignment explanation
Indices: 60230--60301 Score: 67
Period size: 22 Copynumber: 3.4 Consensus size: 21
60220 TTCCAGTTCG
60230 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTT-T
* ** *
60252 CGTTGTGATTTTCTA-A-ATT
1 CGTTGCGATAGTCTACAGTTT
60271 CGTTGCGATAGTCTACAGTTAT
1 CGTTGCGATAGTCTACAGTT-T
*
60293 TGTTGCGAT
1 CGTTGCGAT
60302 TTTCCAAATT
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 13 0.34
20 2 0.05
21 2 0.05
22 21 0.55
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.42
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTTT
Found at i:60277 original size:41 final size:41
Alignment explanation
Indices: 60212--60319 Score: 137
Period size: 41 Copynumber: 2.6 Consensus size: 41
60202 CCATTTCGCA
* *
60212 TTGCGATTTTCC-AGTTCGCGTTGCGATAGTCTACAGTTGTCG
1 TTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTTATCG
* * *
60254 TTGTGATTTTCTAAATTCGTTGCGATAGTCTACAGTTATTG
1 TTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTATCG
*
60295 TTGCGATTTTCCAAATTCATTGCGA
1 TTGCGATTTTCCAAATTCGTTGCGA
60320 AAATTCGTTG
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 44 0.77
42 10 0.18
43 3 0.05
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (41 bp):
TTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTATCG
Found at i:60279 original size:61 final size:59
Alignment explanation
Indices: 59929--60241 Score: 162
Period size: 61 Copynumber: 5.3 Consensus size: 59
59919 TAATTGAAAA
* * * ** *
59929 TCGCGTTGCGATAGTTGAAAATCACGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAGT
1 TCGCATTGCGATAGTTGAAAATCGCGTTACGAT--TTTCAAAT-TCGTTGCGATTTTCCAGT
* * * * * ** * *
59991 TCGCGTTGCGATAGTCT-ACAGTTGTAGTTGTGATTTTCCAAATTCGTTGCGATAGTCTACAGT
1 TCGCATTGCGATAGT-TGAAAATCG-CGTTACGATTTT-CAAATTCGTTGCGAT--TTTCCAGT
* * ** * * * *
60054 T-GTCGTTGCGAT-TTTCCAAAT-TCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAGT
1 TCG-CATTGCGATAGTTGAAAATCGCGTTACGATTTTCAAATT--CGTTGCGATTTTCCAGT
* * *
60113 TCGCGTTGCGATAGTTGAAAAT--CGTTGCGA-----AAATCGCGTTGCGATTTTCCAGT
1 TCGCATTGCGATAGTTGAAAATCGCGTTACGATTTTCAAAT-TCGTTGCGATTTTCCAGT
* *
60166 TCGCATTGCGATAGTTGAAAATCGCGTTACGATTTTCCATTTCGCATTGCGATTTTCCAGT
1 TCGCATTGCGATAGTTGAAAATCGCGTTACGATTTTCAAATTCG--TTGCGATTTTCCAGT
*
60227 TCGCGTTGCGATAGT
1 TCGCATTGCGATAGT
60242 CTACAGTTGT
Statistics
Matches: 196, Mismatches: 34, Indels: 43
0.72 0.12 0.16
Matches are distributed among these distances:
53 38 0.19
54 2 0.01
55 7 0.04
59 30 0.15
60 19 0.10
61 50 0.26
62 26 0.13
63 24 0.12
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (59 bp):
TCGCATTGCGATAGTTGAAAATCGCGTTACGATTTTCAAATTCGTTGCGATTTTCCAGT
Found at i:60285 original size:19 final size:22
Alignment explanation
Indices: 60230--60288 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 22
60220 TTCCAGTTCG
*
60230 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGATGT
* **
60252 CGTTGTGATTTTCTA-A-AT-T
1 CGTTGCGATAGTCTACAGATGT
60271 CGTTGCGATAGTCTACAG
1 CGTTGCGATAGTCTACAG
60289 TTATTGTTGC
Statistics
Matches: 28, Mismatches: 7, Indels: 5
0.70 0.17 0.12
Matches are distributed among these distances:
19 13 0.46
20 2 0.07
21 1 0.04
22 12 0.43
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGATGT
Found at i:60437 original size:6 final size:6
Alignment explanation
Indices: 60428--60464 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
60418 CGACCACGAC
*
60428 CACGGA CACGGA CACGGA CACGGA CCCGGA CACGGA C
1 CACGGA CACGGA CACGGA CACGGA CACGGA CACGGA C
60465 CCGACCCGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.30, C:0.38, G:0.32, T:0.00
Consensus pattern (6 bp):
CACGGA
Found at i:60443 original size:18 final size:17
Alignment explanation
Indices: 60422--60461 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
60412 TTACCACGAC
60422 CACGACCACGGACACGGA
1 CACGA-CACGGACACGGA
*
60440 CACGGACACGGACCCGGA
1 CAC-GACACGGACACGGA
60458 CACG
1 CACG
60462 GACCCGACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 17 0.85
19 2 0.10
ACGTcount: A:0.30, C:0.40, G:0.30, T:0.00
Consensus pattern (17 bp):
CACGACACGGACACGGA
Found at i:60466 original size:12 final size:12
Alignment explanation
Indices: 60425--60467 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
60415 CCACGACCAC
60425 GACCACGGACACG
1 GACC-CGGACACG
*
60438 GACACGGACACG
1 GACCCGGACACG
60450 GACCCGGACACG
1 GACCCGGACACG
60462 GACCCG
1 GACCCG
60468 ACCCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
12 25 0.89
13 3 0.11
ACGTcount: A:0.28, C:0.40, G:0.33, T:0.00
Consensus pattern (12 bp):
GACCCGGACACG
Found at i:60472 original size:5 final size:5
Alignment explanation
Indices: 60462--60488 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
60452 CCCGGACACG
60462 GACCC GACCC GACCC GACCC GACCC GA
1 GACCC GACCC GACCC GACCC GACCC GA
60489 GAAGAGACGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.56, G:0.22, T:0.00
Consensus pattern (5 bp):
GACCC
Found at i:60885 original size:39 final size:39
Alignment explanation
Indices: 60813--60891 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 39
60803 ACTATTTAAG
* * *
60813 GCTCAATCCCACATAGTATTGGGAACAAGTATTGGTAAT
1 GCTCAATCCCACATAGTATTGGAAACAACTATTGGGAAT
60852 GCTCAAATCCCACATAGTATTGGAAAC-ACTATTGGGAAT
1 GCTC-AATCCCACATAGTATTGGAAACAACTATTGGGAAT
60891 G
1 G
60892 GTATTTAAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 15 0.42
40 21 0.58
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (39 bp):
GCTCAATCCCACATAGTATTGGAAACAACTATTGGGAAT
Found at i:60993 original size:6 final size:6
Alignment explanation
Indices: 60982--61061 Score: 110
Period size: 6 Copynumber: 13.7 Consensus size: 6
60972 GTCCGTCTCA
* * * *
60982 GGTCGG GGTCGG GGTCGG GGTCGG GGTCGT GGTCG- GGTCG- GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
61028 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
61062 ATACGTGTCT
Statistics
Matches: 72, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
5 10 0.14
6 62 0.86
ACGTcount: A:0.00, C:0.17, G:0.56, T:0.26
Consensus pattern (6 bp):
GGTCGT
Found at i:61185 original size:22 final size:22
Alignment explanation
Indices: 61159--61212 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
61149 AATTTGGAAA
61159 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* *
61181 TTCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
61203 ATCGCAACGA
1 ATCGCAACGA
61213 ATTTGGAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.37, C:0.28, G:0.17, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:61289 original size:21 final size:21
Alignment explanation
Indices: 61263--61372 Score: 98
Period size: 21 Copynumber: 5.3 Consensus size: 21
61253 GAAATGGAAA
*
61263 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTGCAACT
* ** * *
61284 ATCGCAACGAGAAATGGAA-A
1 ATCGCAACGCGATTTGCAACT
*
61304 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTGCAACT
** * *
61325 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTGCAACT
*
61345 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGATTTGCAACT
61366 ATCGCAA
1 ATCGCAA
61373 TGCAAAATGC
Statistics
Matches: 65, Mismatches: 22, Indels: 4
0.71 0.24 0.04
Matches are distributed among these distances:
20 29 0.45
21 36 0.55
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATTTGCAACT
Found at i:61303 original size:82 final size:81
Alignment explanation
Indices: 61200--61381 Score: 242
Period size: 82 Copynumber: 2.2 Consensus size: 81
61190 ACAACTGTAG
** * *
61200 ACTATCGCAACGAATTTGGAAAATCGTAACGAC-ATTGT-AGACTATCGCAATACGAAATGGAAA
1 ACTATCGCAACGAAAATGGAAAATCGCAACG-CGATTGTCA-ACTATCGCAACACGAAATGGAAA
*
61263 ATCGCAACGCGATTTTCA
64 ATCGCAACGCGATTTCCA
* *
61281 ACTATCGCAACGAGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAA
1 ACTATCGCAACGA-AAATGGAAAATCGCAACGCGATTGTCAACTATCGCAACACGAAATGGAAAA
61346 TCGCAACGCGATTTCCA
65 TCGCAACGCGATTTCCA
*
61363 ACTATCGCAATGCAAAATG
1 ACTATCGCAACG-AAAATG
61382 CAATGCGAAT
Statistics
Matches: 89, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
81 14 0.16
82 73 0.82
83 2 0.02
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (81 bp):
ACTATCGCAACGAAAATGGAAAATCGCAACGCGATTGTCAACTATCGCAACACGAAATGGAAAAT
CGCAACGCGATTTCCA
Found at i:61309 original size:20 final size:20
Alignment explanation
Indices: 61252--61356 Score: 93
Period size: 20 Copynumber: 5.2 Consensus size: 20
61242 TATCGCAATA
61252 CGAAATGGAAAATCGCAACG
1 CGAAATGGAAAATCGCAACG
** ** *
61272 CGATTTTCAACTATCGCAACG
1 CGAAATGGAA-AATCGCAACG
*
61293 AGAAATGGAAAATCGCAACG
1 CGAAATGGAAAATCGCAACG
** ** *
61313 CGATTTTCAACTATCGCAACG
1 CGAAATGGAA-AATCGCAACG
61334 CGAAATGGAAAATCGCAACG
1 CGAAATGGAAAATCGCAACG
61354 CGA
1 CGA
61357 TTTCCAACTA
Statistics
Matches: 61, Mismatches: 22, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (20 bp):
CGAAATGGAAAATCGCAACG
Found at i:61381 original size:41 final size:41
Alignment explanation
Indices: 61200--61381 Score: 219
Period size: 41 Copynumber: 4.5 Consensus size: 41
61190 ACAACTGTAG
** * *
61200 ACTATCGCAACG-AATTTGGAAAATCGTAACGAC-ATTGT-A
1 ACTATCGCAACGCAAAATGGAAAATCGCAACG-CGATTTTCA
** *
61239 GACTATCGCAATACGAAATGGAAAATCGCAACGCGATTTTCA
1 -ACTATCGCAACGCAAAATGGAAAATCGCAACGCGATTTTCA
61281 ACTATCGCAACG-AGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCA-AAATGGAAAATCGCAACGCGATTTTCA
* *
61322 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTCCA
1 ACTATCGCAACGCAAAATGGAAAATCGCAACGCGATTTTCA
*
61363 ACTATCGCAATGCAAAATG
1 ACTATCGCAACGCAAAATG
61382 CAATGCGAAT
Statistics
Matches: 123, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
40 11 0.09
41 111 0.90
42 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (41 bp):
ACTATCGCAACGCAAAATGGAAAATCGCAACGCGATTTTCA
Found at i:62412 original size:17 final size:17
Alignment explanation
Indices: 62361--62432 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
62351 AATTAAGAGT
* *
62361 TAGTCTAATAAATGAAC
1 TAGTTTAATTAATGAAC
* * *
62378 TAGTTTGATGAATAAAC
1 TAGTTTAATTAATGAAC
62395 TAGTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
*
62412 TCACTTT-ATTCAATGAAC
1 T-AGTTTAATT-AATGAAC
62430 TAG
1 TAG
62433 ATGCATGAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
17 32 0.73
18 12 0.27
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.36
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:62922 original size:15 final size:16
Alignment explanation
Indices: 62877--62921 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
62867 CCGAAAAAAA
*
62877 TCAGATATCTGAAAA-T
1 TCAGATATC-CAAAATT
62893 TCAGATATCCAAAATT
1 TCAGATATCCAAAATT
*
62909 TCATATATCCAAA
1 TCAGATATCCAAA
62922 TATCTGGATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 4 0.15
16 22 0.85
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (16 bp):
TCAGATATCCAAAATT
Found at i:64165 original size:75 final size:75
Alignment explanation
Indices: 64071--64262 Score: 264
Period size: 72 Copynumber: 2.6 Consensus size: 75
64061 TCTTATGGAT
* * *
64071 TTTATTGTTCTAGAGTTAATATTATGGTTTGAATCTTGAGATTTGATATTTTAATATTGTGGTTT
1 TTTATTGTTCTAGACTTAATATTGTGGTTTGAATCTTGAGATTTGATATTTTAATATTGTGGGTT
* *
64136 CTTTATAGAC
66 CTTTATAAAA
*
64146 TTTATTGTTATAGACTTAATATTGTGGTTTG-A--TTGAGATTTGATATTTTAATATTGTGGGTT
1 TTTATTGTTCTAGACTTAATATTGTGGTTTGAATCTTGAGATTTGATATTTTAATATTGTGGGTT
*
64208 GTTTATAAAA
66 CTTTATAAAA
* * * *
64218 TTTATTGTTCTAAATTTAATATTGTGATTTGAGTCTTGAGATTTG
1 TTTATTGTTCTAGACTTAATATTGTGGTTTGAATCTTGAGATTTG
64263 TTTATGGTTT
Statistics
Matches: 102, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
72 63 0.62
74 1 0.01
75 38 0.37
ACGTcount: A:0.26, C:0.04, G:0.18, T:0.52
Consensus pattern (75 bp):
TTTATTGTTCTAGACTTAATATTGTGGTTTGAATCTTGAGATTTGATATTTTAATATTGTGGGTT
CTTTATAAAA
Found at i:68220 original size:16 final size:15
Alignment explanation
Indices: 68199--68241 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
68189 TCTTAAGGTA
*
68199 AAAAAATAAAAATTT
1 AAAAAATAAAAAATT
*
68214 CAAAAAACAAAAAATT
1 -AAAAAATAAAAAATT
*
68230 AAAAATTAAAAA
1 AAAAAATAAAAA
68242 CGATCAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAAAATAAAAAATT
Done.