Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009371.1 Hibiscus syriacus cultivar Beakdansim tig00113242_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: 109671
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:120 original size:31 final size:32
Alignment explanation
Indices: 85--161 Score: 84
Period size: 39 Copynumber: 2.2 Consensus size: 32
75 TGTTTAGTAC
85 CTAAATTATTA-ATTTTGATCCATTTTAATAT
1 CTAAATTATTACATTTTGATCCATTTTAATAT
116 CTAAATTTTACCTATTATCATTTTGATCCATTTTAATAT
1 CTAAA---T---TATTA-CATTTTGATCCATTTTAATAT
155 CTAAATT
1 CTAAATT
162 TAAAAAAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
31 5 0.13
33 1 0.03
34 1 0.03
36 1 0.03
37 5 0.13
39 25 0.66
ACGTcount: A:0.34, C:0.13, G:0.03, T:0.51
Consensus pattern (32 bp):
CTAAATTATTACATTTTGATCCATTTTAATAT
Found at i:2152 original size:7 final size:7
Alignment explanation
Indices: 2142--2166 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2132 TTTATAGACC
2142 TTTAAAT
1 TTTAAAT
2149 TTTAAAT
1 TTTAAAT
2156 TTTAAAT
1 TTTAAAT
2163 TTTA
1 TTTA
2167 CTATATACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTTAAAT
Found at i:3546 original size:18 final size:20
Alignment explanation
Indices: 3525--3561 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
3515 TTTTCTCCTC
3525 TTCTC-CAAAGATT-TCATT
1 TTCTCGCAAAGATTCTCATT
*
3543 TTCTCGTAAAGATTCTCAT
1 TTCTCGCAAAGATTCTCAT
3562 CTTTACTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 7 0.44
20 4 0.25
ACGTcount: A:0.27, C:0.22, G:0.08, T:0.43
Consensus pattern (20 bp):
TTCTCGCAAAGATTCTCATT
Found at i:3866 original size:22 final size:22
Alignment explanation
Indices: 3841--3887 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
3831 TCGCCACCAC
3841 CGCCACTACACTTCGTTAGTTT
1 CGCCACTACACTTCGTTAGTTT
3863 CGCCACTACACTTCGTTAGTTT
1 CGCCACTACACTTCGTTAGTTT
3885 CGC
1 CGC
3888 TTTCATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.17, C:0.34, G:0.15, T:0.34
Consensus pattern (22 bp):
CGCCACTACACTTCGTTAGTTT
Found at i:4148 original size:2 final size:2
Alignment explanation
Indices: 4141--4207 Score: 74
Period size: 2 Copynumber: 36.5 Consensus size: 2
4131 CCGCCCCGAT
*
4141 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
4182 T- TA TT TA TA T- TA -A T- TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4208 TTTATATTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
1 6 0.11
2 50 0.89
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:4183 original size:7 final size:7
Alignment explanation
Indices: 4171--4222 Score: 50
Period size: 7 Copynumber: 6.9 Consensus size: 7
4161 TATATATATA
4171 TATATTT
1 TATATTT
4178 TATATTATT
1 TATA-T-TT
4187 TATATTAAT
1 TATATT--T
*
4196 TATATAT
1 TATATTT
*
4203 AATATTT
1 TATATTT
4210 TATATTT
1 TATATTT
4217 TATATT
1 TATATT
4223 AATTATATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
7 23 0.62
8 2 0.05
9 12 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (7 bp):
TATATTT
Found at i:4191 original size:30 final size:32
Alignment explanation
Indices: 4140--4240 Score: 134
Period size: 30 Copynumber: 3.1 Consensus size: 32
4130 CCCGCCCCGA
*
4140 TTATATATATATATATATATATATATATATATATATT
1 TTATAT-TATTTATAT-TA-AT-TATATATA-ATATT
4177 TTATATTATTTATATTAATTATATATAATATT
1 TTATATTATTTATATTAATTATATATAATATT
4209 TTATA-T-TTTATATTAATTATATATAATATT
1 TTATATTATTTATATTAATTATATATAATATT
4239 TT
1 TT
4241 TGGGTTCGAG
Statistics
Matches: 63, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
30 26 0.41
31 1 0.02
32 10 0.16
33 8 0.13
34 2 0.03
35 2 0.03
36 8 0.13
37 6 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (32 bp):
TTATATTATTTATATTAATTATATATAATATT
Found at i:4208 original size:16 final size:16
Alignment explanation
Indices: 4143--4238 Score: 74
Period size: 16 Copynumber: 5.8 Consensus size: 16
4133 GCCCCGATTA
4143 TATATATATATATATATAT
1 TATATATA-ATAT-TA-AT
4162 ATATATATATATATT--T
1 -TATATATA-ATATTAAT
*
4178 TATATTATTTATATTAAT
1 TATA-TA-TAATATTAAT
4196 TATATATAATATT--T
1 TATATATAATATTAAT
* *
4210 TATATTTTATATTAAT
1 TATATATAATATTAAT
4226 TATATATAATATT
1 TATATATAATATT
4239 TTTGGGTTCG
Statistics
Matches: 64, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
14 12 0.19
15 4 0.06
16 26 0.41
17 3 0.05
18 5 0.08
19 1 0.02
20 13 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATATAATATTAAT
Found at i:4214 original size:39 final size:42
Alignment explanation
Indices: 4139--4235 Score: 119
Period size: 39 Copynumber: 2.3 Consensus size: 42
4129 CCCCGCCCCG
4139 ATTATATATATATATATATATATATATATATATATATTTTATATTA
1 ATTATATATA-AT-TATATATATATATATAT--ATATTTTATATTA
* *
4185 TTTATAT-TAATTATATATA-ATAT-TTTATATTTTATATTA
1 ATTATATATAATTATATATATATATATATATATTTTATATTA
4224 ATTATATATAAT
1 ATTATATATAAT
4236 ATTTTTGGGT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
39 19 0.40
40 4 0.09
41 2 0.04
42 4 0.09
43 8 0.17
44 2 0.04
45 2 0.04
46 6 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (42 bp):
ATTATATATAATTATATATATATATATATATATTTTATATTA
Found at i:15644 original size:24 final size:24
Alignment explanation
Indices: 15600--15645 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
15590 TCGTCAAAGA
* *
15600 TCGAATACAAGGATCATAAACATC
1 TCGAATACAAGAATCAGAAACATC
15624 TCGAA-ACAAGAATCAAGAAACA
1 TCGAATACAAGAATC-AGAAACA
15646 AGGGGAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.52, C:0.20, G:0.13, T:0.15
Consensus pattern (24 bp):
TCGAATACAAGAATCAGAAACATC
Found at i:25615 original size:6 final size:6
Alignment explanation
Indices: 25604--25636 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
25594 TTAATGGATT
25604 AAAATA AAAATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAA
25637 GCAAAATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:25642 original size:18 final size:18
Alignment explanation
Indices: 25604--25642 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
25594 TTAATGGATT
*
25604 AAAATAAAAATAAAAATA
1 AAAATAAAAATAAAAACA
*
25622 AAAATAAAAATAAAAGCA
1 AAAATAAAAATAAAAACA
25640 AAA
1 AAA
25643 TTAAGTGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.13
Consensus pattern (18 bp):
AAAATAAAAATAAAAACA
Found at i:29275 original size:29 final size:29
Alignment explanation
Indices: 29230--29287 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
29220 GTGTTGGCCG
29230 TAGGTCGCCATGCCTTC-CGGGTGACCTAC
1 TAGGTCGCCATGCCTTCTC-GGTGACCTAC
*
29259 TAGGTCGCCATGTCTTCTCGGTGACCTAC
1 TAGGTCGCCATGCCTTCTCGGTGACCTAC
29288 AAGAGATTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 26 0.96
30 1 0.04
ACGTcount: A:0.14, C:0.33, G:0.26, T:0.28
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCTCGGTGACCTAC
Found at i:29349 original size:14 final size:14
Alignment explanation
Indices: 29330--29362 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
29320 CGCTGGGCAT
29330 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
29344 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
29358 ACGAG
1 CCGAG
29363 CTATGCGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.39, G:0.30, T:0.06
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:29460 original size:23 final size:23
Alignment explanation
Indices: 29425--29480 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
29415 CGAGGGTAGG
*
29425 TCGCCCGGATTCCCTCGCATAGC
1 TCGCTCGGATTCCCTCGCATAGC
*
29448 TCGCTCGGTTTCCCTCGCATAGC
1 TCGCTCGGATTCCCTCGCATAGC
*
29471 TCGTTCGGAT
1 TCGCTCGGAT
29481 GGCCTCGGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.11, C:0.38, G:0.23, T:0.29
Consensus pattern (23 bp):
TCGCTCGGATTCCCTCGCATAGC
Found at i:29486 original size:23 final size:23
Alignment explanation
Indices: 29425--29487 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
29415 CGAGGGTAGG
* *
29425 TCGCCCGGATTCCCTCGCATAGC
1 TCGCTCGGATGCCCTCGCATAGC
* *
29448 TCGCTCGGTTTCCCTCGCATAGC
1 TCGCTCGGATGCCCTCGCATAGC
* *
29471 TCGTTCGGATGGCCTCG
1 TCGCTCGGATGCCCTCG
29488 GTCGGATGGC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.10, C:0.38, G:0.25, T:0.27
Consensus pattern (23 bp):
TCGCTCGGATGCCCTCGCATAGC
Found at i:29492 original size:14 final size:14
Alignment explanation
Indices: 29470--29502 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
29460 CCTCGCATAG
*
29470 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
29484 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
29498 CTCGG
1 CTCGG
29503 ATGCCCAGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.30, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:54384 original size:15 final size:15
Alignment explanation
Indices: 54366--54395 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
54356 CACTCGTACA
54366 TGTCATTTAGGAACT
1 TGTCATTTAGGAACT
54381 TGTCATTTAGGAACT
1 TGTCATTTAGGAACT
54396 GTTTAGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (15 bp):
TGTCATTTAGGAACT
Found at i:54739 original size:2 final size:2
Alignment explanation
Indices: 54732--54774 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
54722 ACATACATAC
54732 AT AT AT 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 AT AT AT
54774 A
1 A
54775 ATGCTTTCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:58666 original size:12 final size:12
Alignment explanation
Indices: 58649--58674 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
58639 TGAATATGAA
58649 AATTTAAATACT
1 AATTTAAATACT
58661 AATTTAAATACT
1 AATTTAAATACT
58673 AA
1 AA
58675 ACACGTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (12 bp):
AATTTAAATACT
Found at i:61058 original size:2 final size:2
Alignment explanation
Indices: 61051--61077 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
61041 AATGCAATGA
61051 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 A
61078 CAAGACAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:63690 original size:22 final size:20
Alignment explanation
Indices: 63631--63681 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
63621 AAACTGAACA
* *
63631 ATTAAAAAGTTACTCTAATTG
1 ATTAAAAA-TAACTATAATTG
63652 ATTAAAAATAACTATAATTG
1 ATTAAAAATAACTATAATTG
*
63672 ATTATAAATA
1 ATTAAAAATA
63682 TCTTTATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (20 bp):
ATTAAAAATAACTATAATTG
Found at i:70902 original size:63 final size:63
Alignment explanation
Indices: 70798--70919 Score: 145
Period size: 63 Copynumber: 1.9 Consensus size: 63
70788 ATATCGTGGT
* * * * **
70798 CATGTAATAATGATATCGGACGACGCCGCTACTGCTATATAACAAGTGCCATTGCGGTAGCGC
1 CATGCAATAACGATATCGGACGACACCACTACCACTATATAACAAGTGCCATTGCGGTAGCGC
* * * **
70861 CATGCAATAACGATATCGGACGACACCACTACCATTTTATAACGAGTGTTATTGCGGTA
1 CATGCAATAACGATATCGGACGACACCACTACCACTATATAACAAGTGCCATTGCGGTA
70920 AAGAACCATT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
63 48 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.25
Consensus pattern (63 bp):
CATGCAATAACGATATCGGACGACACCACTACCACTATATAACAAGTGCCATTGCGGTAGCGC
Found at i:72862 original size:212 final size:212
Alignment explanation
Indices: 72536--72938 Score: 585
Period size: 212 Copynumber: 1.9 Consensus size: 212
72526 TGTAATTGTT
* *
72536 TAGGCTGGTTCGTTTTCCGGTTTGATGAATTCAATTTGCATACACATAATCTTAATCCAGGCATT
1 TAGGCTGGTTCATTTTCCGGTTCGATGAATTCAATTTGCATACACATAATCTT-ATCCAGGCATT
* * * *
72601 GCTTGTATGCCTTGTAAGAATGAAATTAGGCAAATGCAGGCCCTTGAACCATAGTGATAAGCTTA
65 GCTTGTATGCCTTGTAAGAATGAAATTAGGAAAATGCAGGCCATTGAACCATAATGATAAGCTCA
** *
72666 TGTAAC-TCTAGCATTGGTTTTGATTTTAATCTAGATTAAGATTGTAACAATCATGTCGGTTCTA
130 TGTAACTTC-AGCATTGGTTTCAATCTTAATCTAGATTAAGATTGTAACAATCATGTCGGTTCTA
72730 TGCGTTGATTTTCTGTGTG
194 TGCGTTGATTTTCTGTGTG
* * * *
72749 TAGGTTGGTTCATTTTTCGGTTCGATGAATTCGATTTGCATACACATATTTCTT-TCCAGGCATT
1 TAGGCTGGTTCATTTTCCGGTTCGATGAATTCAATTTGCATACACATA-ATCTTATCCAGGCATT
* * * * * *
72813 GCTTGTATGCCTTGTATGCATGAAGTTGGGAAAATGTAGGCCATTGAACCATAATGCTAAGCTCA
65 GCTTGTATGCCTTGTAAGAATGAAATTAGGAAAATGCAGGCCATTGAACCATAATGATAAGCTCA
*
72878 TGTAACTTCAGCATTGGTTTCAATCTTAATCTAGATTAAGATTGTAACAATCGTGTCGGTT
130 TGTAACTTCAGCATTGGTTTCAATCTTAATCTAGATTAAGATTGTAACAATCATGTCGGTT
72939 AAGCGCTGAT
Statistics
Matches: 168, Mismatches: 20, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
212 119 0.71
213 45 0.27
214 4 0.02
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (212 bp):
TAGGCTGGTTCATTTTCCGGTTCGATGAATTCAATTTGCATACACATAATCTTATCCAGGCATTG
CTTGTATGCCTTGTAAGAATGAAATTAGGAAAATGCAGGCCATTGAACCATAATGATAAGCTCAT
GTAACTTCAGCATTGGTTTCAATCTTAATCTAGATTAAGATTGTAACAATCATGTCGGTTCTATG
CGTTGATTTTCTGTGTG
Found at i:79966 original size:228 final size:227
Alignment explanation
Indices: 79528--80012 Score: 873
Period size: 229 Copynumber: 2.1 Consensus size: 227
79518 GTAAATTATC
* * *
79528 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
*
79593 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
79658 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
*
79723 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAAC-TTAAAAAAAGTATA
*
79756 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
79821 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
*
79886 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATG-AACACTATTAAAAAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
79950 GAAACATAAATTACATAACTTAAAAAAAGTATA
195 GAAACATAAATTACATAACTTAAAAAAAGTATA
79983 TATCATTTTTATAAAAGTGTCCATACTTAT
1 TATCATTTTTATAAAAGTGTCCATACTTAT
80013 AAAAGTAGGT
Statistics
Matches: 248, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
227 43 0.17
228 73 0.29
229 132 0.53
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTAAAAAAAGTATA
Found at i:80313 original size:20 final size:19
Alignment explanation
Indices: 80290--80336 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
80280 CGATATACCA
80290 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
80310 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
80330 GGTAAAA
1 GGTAAAA
80337 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:80376 original size:181 final size:182
Alignment explanation
Indices: 80079--80550 Score: 682
Period size: 181 Copynumber: 2.6 Consensus size: 182
80069 GATCCAAATT
* * * *
80079 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGA-CAAACCGGTATA-GAAATGAT
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTA-ACAAAATGAT
* * * * *
80142 AAAACCGGTCAAGCGCA-ACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACT
65 AAAACCGGTAAAACG-ATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACT
* * *
80206 TCGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
129 TCGTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
*
80260 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
* *
80325 AAACCGGTAAAACGTTACCGGATATATTAAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
** *
80389 GTGAATTTAAAAGAGAAGCAGTTATAGCGCCTATAATGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
* * *
80441 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
* * *
80506 AAACCAGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTT
80551 CGTAAGTACG
Statistics
Matches: 262, Mismatches: 26, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
181 207 0.79
182 55 0.21
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
Found at i:80494 original size:20 final size:19
Alignment explanation
Indices: 80471--80517 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
80461 CGATATAACA
80471 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
80491 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
*
80511 AGTAAAA
1 GGTAAAA
80518 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.11, G:0.15, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:82759 original size:21 final size:21
Alignment explanation
Indices: 82732--82784 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
82722 AAGACAATCA
*
82732 AGAGTCGAAGAGAAACTCGAT
1 AGAGTCGAAGAGAAACTCGAG
* *
82753 CGAGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
82774 AGAGTCGAAGA
1 AGAGTCGAAGA
82785 TACACTTGAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.40, C:0.15, G:0.32, T:0.13
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:84684 original size:18 final size:19
Alignment explanation
Indices: 84640--84687 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
84630 AATGTAGGGT
84640 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
84659 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
84678 T-ATTTTGTAT
1 TAATTTTGTAT
84688 GTGAATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:85269 original size:198 final size:199
Alignment explanation
Indices: 84801--85747 Score: 1434
Period size: 199 Copynumber: 4.9 Consensus size: 199
84791 CAATATGGCC
* * *
84801 AACAGGGTGCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCAATCCCAAAAACATCGAAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
* * *
84864 CCAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAAGTCTACTGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
* *
84928 GAATATGTCTAAATAATGTGTAGACACTAATATAGTTTGTGTCGATATTTTTTTTCCATAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
84993 TGGAA
195 TGGAA
* *
84998 AACTGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAATGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
85063 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
85128 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
85193 GGAA
196 GGAA
85197 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
* ** *
85261 CAAAAGTATAATATAATATGTAATTTTTCAATCTAATTGGTACAATTATACCGGTTTTATGAGAT
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
* *
85326 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGCCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
85391 GGAA
196 GGAA
* *
85395 AACAGGGTGCGTGCACCCATAAAGTGTCGATCC------CAAAA---TC-AT--C--GA--A-C-
1 AACA--G-G-GTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
*
85442 --CCAAAA-GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
62 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
*
85504 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAG-TTGTGTCGATA-TTTTTTCCCAGAAT
127 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAAT
85567 GAATGG-A
192 GAATGGAA
85574 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
85638 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAT
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
85703 AATATGTCTAAATAATGTGTCGACACGT--TATAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACAC-TAATATAGTTTGTGTCGATA
85748 CTAATTTAAA
Statistics
Matches: 689, Mismatches: 31, Indels: 62
0.88 0.04 0.08
Matches are distributed among these distances:
175 23 0.03
176 1 0.00
177 1 0.00
179 5 0.01
180 23 0.03
181 10 0.01
182 89 0.13
183 7 0.01
184 2 0.00
186 2 0.00
187 1 0.00
188 1 0.00
189 1 0.00
190 2 0.00
191 1 0.00
192 2 0.00
193 2 0.00
194 10 0.01
195 96 0.14
196 5 0.01
197 28 0.04
198 171 0.25
199 181 0.26
200 1 0.00
201 1 0.00
202 23 0.03
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (199 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
GGAA
Found at i:85540 original size:182 final size:176
Alignment explanation
Indices: 85234--85747 Score: 685
Period size: 195 Copynumber: 2.8 Consensus size: 176
85224 CCATATATAA
* *
85234 AAAGTGTCGATCCC-AAATCATCGAACCCAAAAGTATAATATAATATGTAATTTTTCAATCTAAT
1 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
* *
85298 TGGTACAATTATACCGGTTTTATGAGATAATATGTATAAATAATGTGTCGACACTAATATAGTTT
66 CGGTACAATTATACCGGTTTTATGAGATAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
* *
85363 GTGCCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCGTGCACCCAT
131 GTGTCGATA-TTTTTTCCCAGAATGAATGG-AAACA--G-G-GTGCACCCAT
85415 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
1 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
*
85480 CGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAG-TT
66 CGGTACAATTATACCGGTTTTATGAGATAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
85544 GTGTCGATATTTTTTCCCAGAATGAATGGAAACAGGGTGCACCCAT
131 GTGTCGATATTTTTTCCCAGAATGAATGGAAACAGGGTGCACCCAT
*
85590 AAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAAT
1 AAAGTGTCGATCC--------------C-A---AA--ATCATCGAACCCAAAAGTATAATGTAAT
85655 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTCTAAATAATG
46 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTCTAAATAATG
85720 TGTCGACACGT--TATAGTTTGTGTCGATA
111 TGTCGACAC-TAATATAGTTTGTGTCGATA
85748 CTAATTTAAA
Statistics
Matches: 301, Mismatches: 9, Indels: 32
0.88 0.03 0.09
Matches are distributed among these distances:
175 23 0.08
176 1 0.00
177 1 0.00
179 5 0.02
180 19 0.06
181 24 0.08
182 107 0.36
189 1 0.00
190 1 0.00
193 1 0.00
194 5 0.02
195 112 0.37
196 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.32
Consensus pattern (176 bp):
AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
CGGTACAATTATACCGGTTTTATGAGATAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
GTGTCGATATTTTTTCCCAGAATGAATGGAAACAGGGTGCACCCAT
Found at i:87218 original size:18 final size:18
Alignment explanation
Indices: 87197--87258 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
87187 AGCCGTCGCA
87197 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* * *
87215 GAAGATGACGATGATGAT
1 GAAGATGAAGCTGACGAT
* *
87233 GACGATGAAGCTGGCGAT
1 GAAGATGAAGCTGACGAT
87251 GAAGATGA
1 GAAGATGA
87259 TGACGATGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.37, C:0.10, G:0.35, T:0.18
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:87221 original size:6 final size:6
Alignment explanation
Indices: 87197--87288 Score: 67
Period size: 6 Copynumber: 15.3 Consensus size: 6
87187 AGCCGTCGCA
* * * * * *
87197 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
** * * * * *
87245 GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
87289 TGATCCAAAC
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:87232 original size:3 final size:3
Alignment explanation
Indices: 87212--87292 Score: 72
Period size: 3 Copynumber: 27.0 Consensus size: 3
87202 TGAAGCTGAC
* * * * * ** *
87212 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
87260 GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
87293 CCAAACAAGT
Statistics
Matches: 59, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.36, C:0.06, G:0.35, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:87251 original size:36 final size:36
Alignment explanation
Indices: 87200--87276 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
87190 CGTCGCAGAA
*
87200 GATGAAGCTGACGATGAAGATGACGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
* * *
87236 GATGAAGCTGGCGATGAAGATGATGACGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
87272 GATGA
1 GATGA
87277 TGATGAAGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.35, C:0.09, G:0.35, T:0.21
Consensus pattern (36 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGAC
Found at i:87292 original size:12 final size:12
Alignment explanation
Indices: 87200--87288 Score: 88
Period size: 12 Copynumber: 7.4 Consensus size: 12
87190 CGTCGCAGAA
*
87200 GATGAAGCTGAC
1 GATGAAGATGAC
87212 GATGAAGATGAC
1 GATGAAGATGAC
*
87224 GATGATGATGAC
1 GATGAAGATGAC
* *
87236 GATGAAGCTGGC
1 GATGAAGATGAC
*
87248 GATGAAGATGAT
1 GATGAAGATGAC
* * *
87260 GACGATGATGAT
1 GATGAAGATGAC
* *
87272 GATGATGATGAA
1 GATGAAGATGAC
87284 GATGA
1 GATGA
87289 TGATCCAAAC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.21
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:87292 original size:18 final size:18
Alignment explanation
Indices: 87197--87288 Score: 76
Period size: 18 Copynumber: 5.1 Consensus size: 18
87187 AGCCGTCGCA
*
87197 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGACGAT
* *
87215 GAAGATGACGATGATGAT
1 GAAGATGAAGATGACGAT
* * *
87233 GACGATGAAGCTGGCGAT
1 GAAGATGAAGATGACGAT
* * *
87251 GAAGATGATGACGATGAT
1 GAAGATGAAGATGACGAT
* * *
87269 GATGATGATGATGAAGAT
1 GAAGATGAAGATGACGAT
87287 GA
1 GA
87289 TGATCCAAAC
Statistics
Matches: 57, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.21
Consensus pattern (18 bp):
GAAGATGAAGATGACGAT
Found at i:89061 original size:184 final size:182
Alignment explanation
Indices: 88785--89278 Score: 853
Period size: 184 Copynumber: 2.7 Consensus size: 182
88775 GCAATGCTAT
*
88785 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATCTT
1 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
*
88850 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTGTTAAAAAGTGTCGACA
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATT-TAAAAAAGTGTCGACA
*
88915 TTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAAC
130 TTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
88968 CGGTATAAATATACCGGTTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATAT
1 CGGTATAAATATACCGG-TTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATAT
* *
89033 TGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTATCGAC
65 TGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATAC-ATTTAAAAAAGTGTCGAC
*
89098 ATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAAC
129 ATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
* * * * *
89152 CGGTATAAATATACCGATTTTATGAGCGAATAGGTCTACAACCTATATCAACACTTTATAATAGT
1 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
89217 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCG
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA-CATTTAAAAAAGTGTCG
89279 GTAATTTTAA
Statistics
Matches: 295, Mismatches: 13, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
183 119 0.40
184 173 0.59
185 3 0.01
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Consensus pattern (182 bp):
CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTTAAAAAAGTGTCGACAT
TTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
Found at i:91767 original size:25 final size:25
Alignment explanation
Indices: 91739--91803 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
91729 TTATTATTAA
91739 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
91764 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
91789 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
91804 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:92194 original size:22 final size:23
Alignment explanation
Indices: 92138--92200 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
92128 AATATGTAAA
*
92138 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
92161 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
92184 ATAT-ATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
92201 TGGTATATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 12 0.33
23 24 0.67
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:96119 original size:27 final size:27
Alignment explanation
Indices: 96081--96143 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
96071 TCGCGAACCG
96081 GAGTCGAATCTCTCAGCAGAGGGATAT
1 GAGTCGAATCTCTCAGCAGAGGGATAT
*
96108 GAGTCGAATCTCTCAGGAGAGGGATAT
1 GAGTCGAATCTCTCAGCAGAGGGATAT
*
96135 GAGCCGAAT
1 GAGTCGAAT
96144 GATCAACTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.30, C:0.17, G:0.32, T:0.21
Consensus pattern (27 bp):
GAGTCGAATCTCTCAGCAGAGGGATAT
Found at i:99685 original size:113 final size:114
Alignment explanation
Indices: 99061--99755 Score: 1017
Period size: 113 Copynumber: 6.0 Consensus size: 114
99051 AGCTGTGGGA
99061 ACCATGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
1 ACCATGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
* *
99126 ATAGGAAAACCATAATCAAGCTTCATT-TTTTCAAATAAAACAATTTTG
66 ATAGGAAAACCATAACCAAGCTTCATTCTTTTCATATAAAACAATTTTG
*
99174 ACCATGCTATTCAGAGGCAAGAATGACTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
1 ACCATGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
* *
99239 ATAGGATTATAGGAAACCATAACCGAGCTTCATTCTTTTCATATCAAACAATTTTG
66 ATAGG-----A--AAACCATAACCAAGCTTCATTCTTTTCATATAAAACAATTTTG
*
99295 ACCACGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
1 ACCATGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
99360 ATAGGAAAACCATAACCAAGCTTCATTCTTTTCATAT--AA-AATTTTG
66 ATAGGAAAACCATAACCAAGCTTCATTCTTTTCATATAAAACAATTTTG
*
99406 ACCATGCTA-TCAGAGGCAAGAATGACTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
1 ACCATGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
* *
99470 ATAGGATTATAGGAAAACCATAACCGAGCTTCATTCTTTTCATATCAAACAATTTTGACCACG
66 --------ATAGGAAAACCATAACCAAGCTTCATTCTTTTCATATAAAACAATTTT------G
99533 ACCATGCTA-TCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
1 ACCATGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
99597 ATAGGAAAACCATAACCAAGCTTCATTC-TTTCATATAAAACAATTTTG
66 ATAGGAAAACCATAACCAAGCTTCATTCTTTTCATATAAAACAATTTTG
*
99645 ACCATGCTATTCAGAGGCAAGAATGATTGCAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
1 ACCATGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
* * * *
99710 ATAAGAAAACAATAATCAAGCTTCATTTTTTTTCATATAAAACAAT
66 ATAGGAAAACCATAACCAAGCTTCA-TTCTTTTCATATAAAACAAT
99756 CTCTCGAACA
Statistics
Matches: 535, Mismatches: 19, Indels: 54
0.88 0.03 0.09
Matches are distributed among these distances:
110 54 0.10
111 15 0.03
112 12 0.02
113 145 0.27
114 32 0.06
115 16 0.03
116 1 0.00
118 55 0.10
119 27 0.05
120 21 0.04
121 93 0.17
127 64 0.12
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (114 bp):
ACCATGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
ATAGGAAAACCATAACCAAGCTTCATTCTTTTCATATAAAACAATTTTG
Found at i:99706 original size:350 final size:341
Alignment explanation
Indices: 99061--99751 Score: 1034
Period size: 350 Copynumber: 2.0 Consensus size: 341
99051 AGCTGTGGGA
*
99061 ACCATGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
1 ACCATGCTATTCAGAGGCAAGAATGACTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
*
99126 ATAGGAAAACCATAATCAAGCTTCATTTTTTCAAATAAAACAATTTTGACCATGCTATTCAGAGG
66 ATAGGAAAACCATAACCAAGCTTCATTTTTTCAAATAAAACAATTTTGACCATGCTATTCAGAGG
99191 CAAGAATGACTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAACATAGGATTATAGGAAAC
131 CAAGAATGACTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAACATAGG----TA-GAAAC
* *
99256 CATAACCGAGCTTCATTCTTTTCATATCAAACAATTTTGACCACGCTATTCAGAGGCAAGAATGA
191 CATAACCAAGCTTCATTCTTTTCATATAAAACAATTTTGACCACGCTATTCAGAGGCAAGAATGA
* * *
99321 TTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAACATAGGAAAACCATAACCAAGCTTCA-
256 TTGCAAACATCCCAATTCTCCTAAATTTCTGAAACAAACATAAGAAAACAATAACCAAGCTTCAT
99385 TTCTTTTCATATAAAATTTTG
321 TTCTTTTCATATAAAATTTTG
99406 ACCATGCTA-TCAGAGGCAAGAATGACTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
1 ACCATGCTATTCAGAGGCAAGAATGACTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
* * *
99470 ATAGGATTATAGGAAAACCATAACCGAGCTTCATTCTTTTCATATCAAACAATTTTGACCACGAC
66 --------ATAGGAAAACCATAACCAAGCTTCATT-TTTTCAAATAAAACAATTTT------GAC
*
99535 CATGCTA-TCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAACAT
116 CATGCTATTCAGAGGCAAGAATGACTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAACAT
*
99599 AGG-A-AAACCATAACCAAGCTTCATTC-TTTCATATAAAACAATTTTGACCATGCTATTCAGAG
181 AGGTAGAAACCATAACCAAGCTTCATTCTTTTCATATAAAACAATTTTGACCACGCTATTCAGAG
*
99661 GCAAGAATGATTGCAAACATCCCAATTCTCCTAAATTTCTGAAACAAACATAAGAAAACAATAAT
246 GCAAGAATGATTGCAAACATCCCAATTCTCCTAAATTTCTGAAACAAACATAAGAAAACAATAAC
*
99726 CAAGCTTCATTTTTTTTCATATAAAA
311 CAAGCTTCATTTCTTTTCATATAAAA
99752 CAATCTCTCG
Statistics
Matches: 316, Mismatches: 14, Indels: 26
0.89 0.04 0.07
Matches are distributed among these distances:
344 54 0.17
345 9 0.03
350 104 0.33
351 36 0.11
352 25 0.08
353 19 0.06
358 59 0.19
359 10 0.03
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (341 bp):
ACCATGCTATTCAGAGGCAAGAATGACTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAAC
ATAGGAAAACCATAACCAAGCTTCATTTTTTCAAATAAAACAATTTTGACCATGCTATTCAGAGG
CAAGAATGACTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAACATAGGTAGAAACCATAA
CCAAGCTTCATTCTTTTCATATAAAACAATTTTGACCACGCTATTCAGAGGCAAGAATGATTGCA
AACATCCCAATTCTCCTAAATTTCTGAAACAAACATAAGAAAACAATAACCAAGCTTCATTTCTT
TTCATATAAAATTTTG
Found at i:100488 original size:12 final size:12
Alignment explanation
Indices: 100473--100497 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
100463 ACGGAGCTAC
100473 TTAAGGAGTGGG
1 TTAAGGAGTGGG
100485 TTAAGGAGTGGG
1 TTAAGGAGTGGG
100497 T
1 T
100498 GGGGTTCTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.48, T:0.28
Consensus pattern (12 bp):
TTAAGGAGTGGG
Found at i:100898 original size:54 final size:52
Alignment explanation
Indices: 100835--100942 Score: 144
Period size: 52 Copynumber: 2.0 Consensus size: 52
100825 CACTCAGCCA
* ***
100835 TACACACAATCTTGTTTACATATTTGTGGGAGATTATTGACTAATCCCATTAAT
1 TACACACAATCTCGTTTAC--ATTTGCCAGAGATTATTGACTAATCCCATTAAT
* *
100889 TACACACAATCTCGTTTACATTTGCCATAGATTATTGACTAATCTCATTAAT
1 TACACACAATCTCGTTTACATTTGCCAGAGATTATTGACTAATCCCATTAAT
100941 TA
1 TA
100943 ATTTGCAGAG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
52 30 0.62
54 18 0.38
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (52 bp):
TACACACAATCTCGTTTACATTTGCCAGAGATTATTGACTAATCCCATTAAT
Found at i:103778 original size:21 final size:22
Alignment explanation
Indices: 103740--103782 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
103730 AATGTCAGAG
*
103740 GGGAACCGATTCCCCTGCTACA
1 GGGAACCGATTACCCTGCTACA
103762 GGGAACCGA-TACCCTGCTACA
1 GGGAACCGATTACCCTGCTACA
103783 TTACTGCTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.26, C:0.35, G:0.23, T:0.16
Consensus pattern (22 bp):
GGGAACCGATTACCCTGCTACA
Found at i:104549 original size:28 final size:28
Alignment explanation
Indices: 104515--104572 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
104505 GGTAATCAAT
*
104515 CCATATGTCCCGAAGAACATAGGTAAAC
1 CCATATGTCCCGAAAAACATAGGTAAAC
104543 CCATATGTCCCGAAAAACATAGGTAAAC
1 CCATATGTCCCGAAAAACATAGGTAAAC
104571 CC
1 CC
104573 TCGACCCTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.28, G:0.16, T:0.17
Consensus pattern (28 bp):
CCATATGTCCCGAAAAACATAGGTAAAC
Found at i:107792 original size:33 final size:34
Alignment explanation
Indices: 107754--107832 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
107744 CTTTAAACCT
*
107754 TAAACCCTAAA-TCTTAAAACCT-AAAATAGATCC
1 TAAACCCTAAACTC-TAAAACATGAAAATAGATCC
* * *
107787 TAAACCCTAGACTCTAAGACATGAAAATATATCC
1 TAAACCCTAAACTCTAAAACATGAAAATAGATCC
107821 TAAACCCTAAAC
1 TAAACCCTAAAC
107833 CTCGAATATC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
33 16 0.41
34 23 0.59
ACGTcount: A:0.47, C:0.25, G:0.05, T:0.23
Consensus pattern (34 bp):
TAAACCCTAAACTCTAAAACATGAAAATAGATCC
Found at i:108715 original size:23 final size:23
Alignment explanation
Indices: 108671--108742 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 23
108661 AAGAGATCAA
* *
108671 ATTTTCATAAAATAATATAAATT
1 ATTTTCATAAAATAAAAAAAATT
108694 ATTTTCATAAAATAAAAAAAA-T
1 ATTTTCATAAAATAAAAAAAATT
* *
108716 AGTTTTTAGAAAATATAAATAAAATT
1 A-TTTTCATAAAATA-AAA-AAAATT
108742 A
1 A
108743 AAGTTTAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
22 2 0.05
23 30 0.73
24 3 0.07
25 4 0.10
26 2 0.05
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (23 bp):
ATTTTCATAAAATAAAAAAAATT
Done.