Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003320.1 Hibiscus syriacus cultivar Beakdansim tig00006992_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: 341838
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
File 2 of 2
Found at i:206107 original size:20 final size:20
Alignment explanation
Indices: 205895--206125 Score: 249
Period size: 20 Copynumber: 11.6 Consensus size: 20
205885 CGCGAACACA
*
205895 TAAATCGCAACGCGT-ATCCG
1 TAAATCGCAACG-ATAATCCG
*
205915 TAAATCGCAACG-TGTATCCG
1 TAAATCGCAACGAT-AATCCG
* *
205935 TATATCGCAACGCGT-ATCCG
1 TAAATCGCAACG-ATAATCCG
205955 TAAATCGCAATGCG-T-ATCCG
1 TAAATCGCAA--CGATAATCCG
* *
205975 TATATCGCAACGCGT-ATCCG
1 TAAATCGCAACG-ATAATCCG
205995 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGATAATCCG
* *
206015 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGATAATCCG
206035 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGATAATCCG
* *
206055 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGATAATCCG
206075 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGATAATCCG
* *
206095 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGATAATCCG
*
206115 TAAATCACAAC
1 TAAATCGCAAC
206126 ACTGAAATTT
Statistics
Matches: 186, Mismatches: 16, Indels: 18
0.85 0.07 0.08
Matches are distributed among these distances:
18 3 0.02
19 1 0.01
20 179 0.96
22 3 0.02
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (20 bp):
TAAATCGCAACGATAATCCG
Found at i:206847 original size:24 final size:24
Alignment explanation
Indices: 206808--206854 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
206798 AAATTTGGTC
206808 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
206832 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
206855 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:209386 original size:33 final size:33
Alignment explanation
Indices: 209335--209545 Score: 189
Period size: 33 Copynumber: 6.2 Consensus size: 33
209325 CGGAAATTAC
*
209335 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAAC-ATGAAAATCGCAATGCGAAATGAA
*
209368 AATCCCAACATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACATGAAAATCGCAATGC-GAAATGAA
** * *
209402 AATCGCAACGGGAGAATCGCAATGTGAAATGAA
1 AATCGCAACATGAAAATCGCAATGCGAAATGAA
* * *
209435 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCG-C
1 AATCGCAA--C---ATGAAAATCGCAATGCGA-AAT-GAA
209474 AAT-GCGAA-ATGAAAATCGCAATGCGAAATGAA
1 AATCGC-AACATGAAAATCGCAATGCGAAATGAA
* *
209506 AATCGCAACGA-GAGAATCGCAATGCGAAATTAA
1 AATCGCAAC-ATGAAAATCGCAATGCGAAATGAA
209539 AATCGCA
1 AATCGCA
209546 TTGCGATTCT
Statistics
Matches: 146, Mismatches: 18, Indels: 28
0.76 0.09 0.15
Matches are distributed among these distances:
31 1 0.01
32 9 0.06
33 82 0.56
34 29 0.20
35 1 0.01
38 15 0.10
39 8 0.05
40 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (33 bp):
AATCGCAACATGAAAATCGCAATGCGAAATGAA
Found at i:209440 original size:19 final size:19
Alignment explanation
Indices: 209416--209551 Score: 157
Period size: 19 Copynumber: 7.7 Consensus size: 19
209406 GCAACGGGAG
*
209416 AATCGCAATGTGAAATGAA
1 AATCGCAATGCGAAATGAA
209435 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
209454 AATCGCAA--CG--A-GAT
1 AATCGCAATGCGAAATGAA
209468 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
209487 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
209506 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
209520 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
209539 AATCGCATTGCGA
1 AATCGCAATGCGA
209552 TTCTCCCGTT
Statistics
Matches: 100, Mismatches: 7, Indels: 20
0.79 0.06 0.16
Matches are distributed among these distances:
14 20 0.20
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 68 0.68
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.17
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:209462 original size:52 final size:52
Alignment explanation
Indices: 209377--209551 Score: 296
Period size: 52 Copynumber: 3.3 Consensus size: 52
209367 AAATCCCAAC
* *
209377 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGGGAGAATCGCAATGTGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
209430 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
209482 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
209534 ATTAAAATCGCATTGCGA
1 ATGAAAATCGCAATGCGA
209552 TTCTCCCGTT
Statistics
Matches: 116, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
52 100 0.86
53 16 0.14
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.16
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:209600 original size:19 final size:19
Alignment explanation
Indices: 209560--209657 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
209550 GATTCTCCCG
209560 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
209580 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
209599 TTGCGA--TT-ATCTCG--
1 TTGCGATTTTCATTTCGCA
209613 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
209632 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
209651 TTGCGAT
1 TTGCGAT
209658 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:209654 original size:52 final size:53
Alignment explanation
Indices: 209541--209657 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
209531 GAAATTAAAA
*
209541 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTATCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
*
209594 TCGCATTGCGATTATCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTATCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
209646 TCGCATTGCGAT
1 TCGCATTGCGAT
209658 AGTCAATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTATCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:209783 original size:14 final size:14
Alignment explanation
Indices: 209764--209800 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
209754 CATCAATTAC
209764 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
209778 ACAAATCATCTTTT
1 ACAAATCAACTTTT
209792 ACAAATCAA
1 ACAAATCAA
209801 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:211800 original size:14 final size:14
Alignment explanation
Indices: 211781--211837 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
211771 GCGAAATGAA
*
211781 AATCGCAACGACAG
1 AATCGCAACGAAAG
211795 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
211812 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
211828 AATCGCAACG
1 AATCGCAACG
211838 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:211808 original size:33 final size:33
Alignment explanation
Indices: 211762--211854 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
211752 GCGAAACCAA
*
211762 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
211795 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
211828 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
211855 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:211819 original size:19 final size:19
Alignment explanation
Indices: 211725--211859 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
211715 TAGTTTACTT
* *
211725 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
211745 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
211764 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
211783 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
211797 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
211816 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
211830 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
211849 TCGCAATGCGA
1 TCGCAACGCGA
211860 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:211877 original size:19 final size:19
Alignment explanation
Indices: 211855--211983 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
211845 AAAATCGCAA
211855 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
211874 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
211888 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
211907 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
* **
211921 TGCAATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
211940 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
211959 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
211979 TGCGA
1 TGCGA
211984 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 21 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 47 0.53
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:211897 original size:33 final size:33
Alignment explanation
Indices: 211855--211946 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
211845 AAAATCGCAA
211855 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
211888 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* **
211921 TGCAATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
211947 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 53 0.96
34 2 0.04
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:212147 original size:93 final size:93
Alignment explanation
Indices: 212031--212313 Score: 550
Period size: 93 Copynumber: 3.1 Consensus size: 93
212021 ATGGATTGCA
212031 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
212095 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
212123 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
212188 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
212216 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
212281 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
212309 TTACT
1 TTACT
212314 AAGCAATCTA
Statistics
Matches: 189, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
92 4 0.02
93 185 0.98
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:214039 original size:14 final size:14
Alignment explanation
Indices: 214020--214123 Score: 100
Period size: 14 Copynumber: 6.7 Consensus size: 14
214010 TTGAAATGAA
214020 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
214034 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
214053 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
214067 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
214086 AATCGCAACGAGAG
1 AATCGCAACGAGAG
214100 AATCGCAACGAGAG
1 AATCGCAACGAGAG
214114 AATCGCAACG
1 AATCGCAACG
214124 CGAAATGAAA
Statistics
Matches: 76, Mismatches: 4, Indels: 20
0.76 0.04 0.20
Matches are distributed among these distances:
14 44 0.58
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 20 0.26
ACGTcount: A:0.44, C:0.22, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:214052 original size:33 final size:33
Alignment explanation
Indices: 214012--214109 Score: 196
Period size: 33 Copynumber: 3.0 Consensus size: 33
214002 TCTTTTGGTT
214012 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
214045 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
214078 GAAATGAAAATCGCAACGAGAGAATCGCAACG
1 GAAATGAAAATCGCAACGAGAGAATCGCAACG
214110 AGAGAATCGC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 65 1.00
ACGTcount: A:0.46, C:0.20, G:0.24, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:214074 original size:47 final size:47
Alignment explanation
Indices: 214020--214134 Score: 135
Period size: 47 Copynumber: 2.4 Consensus size: 47
214010 TTGAAATGAA
* * *
214020 AATCGCAACGAGAGAATCGCAACGCGAAATGA-A-AATCGCAACGAGAG
1 AATCGCAACGAGA-AAT-GAAAAGCGAAACGAGAGAATCGCAACGAGAG
* * *
214067 AATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGAGAG
1 AATCGCAACGAGAAATGAAAAGCGAAACGAGAGAATCGCAACGAGAG
*
214114 AATCGCAACGCGAAATGAAAA
1 AATCGCAACGAGAAATGAAAA
214135 TCGCAATGCG
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
45 9 0.15
46 4 0.07
47 47 0.78
ACGTcount: A:0.46, C:0.21, G:0.24, T:0.09
Consensus pattern (47 bp):
AATCGCAACGAGAAATGAAAAGCGAAACGAGAGAATCGCAACGAGAG
Found at i:214176 original size:14 final size:14
Alignment explanation
Indices: 214157--214213 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
214147 TTTGGTTTCG
214157 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
214171 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
214190 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
214204 CGTTGCGATT
1 CGTTGCGATT
214214 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:214189 original size:33 final size:33
Alignment explanation
Indices: 214141--214221 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
214131 AAAATCGCAA
**
214141 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
214174 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
214207 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
214222 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:214224 original size:21 final size:21
Alignment explanation
Indices: 214198--214273 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
214188 CGCGTTGCGA
214198 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
214219 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
214239 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
214260 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
214274 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:214254 original size:41 final size:41
Alignment explanation
Indices: 214197--214274 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
214187 TCGCGTTGCG
*
214197 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
214238 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
214275 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:214395 original size:33 final size:33
Alignment explanation
Indices: 214353--214423 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
214343 AATACTAACT
*
214353 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
214386 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
214419 TGAAA
1 TGAAA
214424 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:214657 original size:22 final size:22
Alignment explanation
Indices: 214605--214659 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
214595 TGGTTGTGAG
**
214605 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
214627 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
214649 GGATTTCTTCG
1 GGATTTCTTCG
214660 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:214831 original size:20 final size:20
Alignment explanation
Indices: 214806--214939 Score: 164
Period size: 20 Copynumber: 6.7 Consensus size: 20
214796 CTTTAAATAT
214806 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
214826 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
214848 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
214867 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
214887 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
214907 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
214927 CGCGTTGCGATTT
1 CGCGTTGCGATTT
214940 TCATATTCAC
Statistics
Matches: 98, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
19 2 0.02
20 79 0.81
21 15 0.15
22 2 0.02
ACGTcount: A:0.19, C:0.18, G:0.28, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:214933 original size:40 final size:40
Alignment explanation
Indices: 214805--214939 Score: 182
Period size: 40 Copynumber: 3.4 Consensus size: 40
214795 GCTTTAAATA
*
214805 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
214846 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
214886 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
214926 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
214940 TCATATTCAC
Statistics
Matches: 80, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
40 50 0.62
41 30 0.38
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.36
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:229024 original size:14 final size:15
Alignment explanation
Indices: 228993--229031 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
228983 AAATAAAGCT
228993 TAAAGAAAACTCAAA
1 TAAAGAAAACTCAAA
*
229008 TAAAGAAAAC-GAAA
1 TAAAGAAAACTCAAA
229022 TAAAAGAAAA
1 T-AAAGAAAA
229032 AAAAGATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.72, C:0.08, G:0.10, T:0.10
Consensus pattern (15 bp):
TAAAGAAAACTCAAA
Found at i:231384 original size:14 final size:14
Alignment explanation
Indices: 231365--231397 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
231355 ATACACAGTC
231365 GATGAGCCACCAAT
1 GATGAGCCACCAAT
*
231379 GATGAGCCACCATT
1 GATGAGCCACCAAT
231393 GATGA
1 GATGA
231398 CAATATTTGA
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:0.33, C:0.24, G:0.24, T:0.18
Consensus pattern (14 bp):
GATGAGCCACCAAT
Found at i:233300 original size:13 final size:13
Alignment explanation
Indices: 233266--233305 Score: 64
Period size: 14 Copynumber: 3.1 Consensus size: 13
233256 ATTATATATG
233266 ATTTT-TAAAAAT
1 ATTTTATAAAAAT
233278 ATTTTAATAAAAAT
1 ATTTT-ATAAAAAT
233292 ATTTTATAAAAAT
1 ATTTTATAAAAAT
233305 A
1 A
233306 AAAAGTTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.19
13 9 0.35
14 12 0.46
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATTTTATAAAAAT
Found at i:234113 original size:31 final size:31
Alignment explanation
Indices: 234056--234123 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
234046 TTAACGGATG
* * *
234056 AGGGACTAAAATCGAACGGACCGATAATATT
1 AGGGACTAAAATCAAACGGAACGATAACATT
* * *
234087 AGGGACTAAAATCAAATGGAATGATAACGTT
1 AGGGACTAAAATCAAACGGAACGATAACATT
234118 AGGGAC
1 AGGGAC
234124 CATGTACCTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.43, C:0.13, G:0.25, T:0.19
Consensus pattern (31 bp):
AGGGACTAAAATCAAACGGAACGATAACATT
Found at i:236717 original size:17 final size:17
Alignment explanation
Indices: 236695--236729 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
236685 AACGGTCAAC
236695 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
236712 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
236729 G
1 G
236730 TCGGGTCGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.23, G:0.49, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:236776 original size:19 final size:19
Alignment explanation
Indices: 236754--236820 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
236744 TCGGGTCAGG
236754 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
* *
236773 TCAGACCGATCAAAACGGT
1 TCAGACCGGTCAAACCGGT
*
236792 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
236811 TCAAACCGGT
1 TCAGACCGGT
236821 TGAAAACCAA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
18 2 0.05
19 30 0.77
20 7 0.18
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.16
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:236801 original size:29 final size:29
Alignment explanation
Indices: 236766--236821 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
236756 AGACCGGTCA
*
236766 AACCGGTTCAGACCGATCAAAACGGTTCG
1 AACCGGTTCAAACCGATCAAAACGGTTCG
* * *
236795 AACCGGTTGAAACCGGTCAAACCGGTT
1 AACCGGTTCAAACCGATCAAAACGGTT
236822 GAAAACCAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.18
Consensus pattern (29 bp):
AACCGGTTCAAACCGATCAAAACGGTTCG
Found at i:236818 original size:9 final size:9
Alignment explanation
Indices: 236752--236820 Score: 57
Period size: 9 Copynumber: 7.3 Consensus size: 9
236742 GGTCGGGTCA
*
236752 GGTCAGACC
1 GGTCAAACC
236761 GGTCAAACC
1 GGTCAAACC
*
236770 GGTTCAGACC
1 GG-TCAAACC
* *
236780 GATCAAAAC
1 GGTCAAACC
*
236789 GGTTCGAACC
1 GG-TCAAACC
*
236799 GGTTGAAACC
1 GG-TCAAACC
236809 GGTCAAACC
1 GGTCAAACC
236818 GGT
1 GGT
236821 TGAAAACCAA
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
9 25 0.53
10 22 0.47
ACGTcount: A:0.29, C:0.28, G:0.28, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:236821 original size:19 final size:20
Alignment explanation
Indices: 236795--236841 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
236785 AAACGGTTCG
**
236795 AACCGGTTG-AAACCGGTCA
1 AACCGGTTGAAAACCAATCA
236814 AACCGGTTGAAAACCAATCA
1 AACCGGTTGAAAACCAATCA
236834 AACCGGTT
1 AACCGGTT
236842 TCCAGCAGCG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (20 bp):
AACCGGTTGAAAACCAATCA
Found at i:243969 original size:7 final size:7
Alignment explanation
Indices: 243957--243987 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
243947 GTCAAAGGAA
243957 GTCAACG
1 GTCAACG
243964 GTCAACG
1 GTCAACG
243971 GTCAACG
1 GTCAACG
*
243978 ATCAACG
1 GTCAACG
243985 GTC
1 GTC
243988 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:243994 original size:5 final size:5
Alignment explanation
Indices: 243984--244032 Score: 73
Period size: 5 Copynumber: 9.8 Consensus size: 5
243974 AACGATCAAC
*
243984 GGTCG GGTCG GGTCG GGTCAC GGTCG GGTC- GGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC-G GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
244033 AGACCGGTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
4 4 0.10
5 32 0.80
6 4 0.10
ACGTcount: A:0.02, C:0.22, G:0.55, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:248497 original size:18 final size:19
Alignment explanation
Indices: 248474--248518 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
248464 CTCAGTAATC
248474 TTATTCC-CTGGTAATCTT
1 TTATTCCACTGGTAATCTT
248492 TTATTCCCACTGGTAATCTT
1 TTATT-CCACTGGTAATCTT
*
248512 ATATTCC
1 TTATTCC
248519 GTGAACCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 5 0.21
19 4 0.17
20 15 0.62
ACGTcount: A:0.20, C:0.24, G:0.09, T:0.47
Consensus pattern (19 bp):
TTATTCCACTGGTAATCTT
Found at i:248506 original size:20 final size:20
Alignment explanation
Indices: 248481--248518 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
248471 ATCTTATTCC
*
248481 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTATATTCCCA
248501 CTGGTAATCTTATATTCC
1 CTGGTAATCTTATATTCC
248519 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTATATTCCCA
Found at i:251349 original size:2 final size:2
Alignment explanation
Indices: 251342--251368 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
251332 TTCTTGGTCC
251342 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 T
251369 CAGCTAGATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:253121 original size:57 final size:56
Alignment explanation
Indices: 253013--253123 Score: 132
Period size: 57 Copynumber: 2.0 Consensus size: 56
253003 AATACGTCGA
* * * * *
253013 ATCACTTACTCTGCACTCGGTTCATCATAATCATTTGTATCCAATCGCTCTCTCGT
1 ATCACTTACTCTCCACTCGGTTCATCAGAATCACTTGAATCCAATCACTCTCTCGT
* * * *
253069 ATCACTTTCTCTCCCACTTGGTTCGTCAGAATCACTTGAATCCTATCACTCTCTC
1 ATCACTTACTCT-CCACTCGGTTCATCAGAATCACTTGAATCCAATCACTCTCTC
253124 TCCGACTGAA
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
56 11 0.24
57 34 0.76
ACGTcount: A:0.21, C:0.32, G:0.10, T:0.37
Consensus pattern (56 bp):
ATCACTTACTCTCCACTCGGTTCATCAGAATCACTTGAATCCAATCACTCTCTCGT
Found at i:255944 original size:29 final size:28
Alignment explanation
Indices: 255897--256056 Score: 123
Period size: 29 Copynumber: 5.7 Consensus size: 28
255887 TAAATTCATA
255897 ATATTTTA-TTTATCTTAACTTTAAAATT
1 ATATTTTATTTTATCTTAACTTTAAAA-T
* *
255925 ATATTTTATTTTATCTTAACTTATTACAT
1 ATATTTTATTTTATCTTAACTT-TAAAAT
** * * *
255954 ATATTTTAATCGTATGTTAATTTTAATAT
1 ATATTTT-ATTTTATCTTAACTTTAAAAT
*
255983 ATATTTT-TCTTATCTTAA-TTTAAAAAT
1 ATATTTTATTTTATCTTAACTTT-AAAAT
* *
256010 ATATGTTATTTTTATCTTAAC--TACAAT
1 ATATTTTA-TTTTATCTTAACTTTAAAAT
* *
256037 ATATTATATTATTATATTAA
1 ATATTTTATT-TTATCTTAA
256057 ATTAAAAGAA
Statistics
Matches: 107, Mismatches: 17, Indels: 17
0.76 0.12 0.12
Matches are distributed among these distances:
26 5 0.05
27 37 0.35
28 9 0.08
29 42 0.39
30 14 0.13
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.56
Consensus pattern (28 bp):
ATATTTTATTTTATCTTAACTTTAAAAT
Found at i:256172 original size:23 final size:23
Alignment explanation
Indices: 256125--256185 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
256115 ATAATGAAAA
*
256125 ATTATTAAT-TTTGAAAATTAATT
1 ATTAATAATATTT-AAAATTAATT
*
256148 ATTAA-AATATTTAAAATATATTT
1 ATTAATAATATTTAAAAT-TAATT
*
256171 ATTAATAATTTTTAA
1 ATTAATAATATTTAA
256186 TAAAATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
22 8 0.25
23 16 0.50
24 8 0.25
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
ATTAATAATATTTAAAATTAATT
Found at i:256952 original size:21 final size:21
Alignment explanation
Indices: 256900--256952 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
256890 TAGAATTGTT
*
256900 AAAAATAAAAAAAATAAAGATA
1 AAAAAT-AATAAAATAAAGATA
* *
256922 TAATATAATAAAATAAAGA-A
1 AAAAATAATAAAATAAAGATA
256942 AAAAATGAATA
1 AAAAAT-AATA
256953 CCGACGATCG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 5 0.20
21 16 0.64
22 4 0.16
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (21 bp):
AAAAATAATAAAATAAAGATA
Found at i:257314 original size:27 final size:27
Alignment explanation
Indices: 257166--257516 Score: 603
Period size: 27 Copynumber: 12.8 Consensus size: 27
257156 ATTCTCCACC
257166 TACGTATATCCATGTATATTTACTTTTT
1 TACGTATATCCATGTATATTTA-TTTTT
257194 TACGTATATCCATGTATATTTATTTCTT
1 TACGTATATCCATGTATATTTATTT-TT
*
257222 TACATATATCCATGTATATTTATTTTTT
1 TACGTATATCCATGTATATTTA-TTTTT
257250 TACGTATATCCATGTATATTTATTTCTT
1 TACGTATATCCATGTATATTTATTT-TT
257278 TACGTATATCCATGTATATTTATTTTT
1 TACGTATATCCATGTATATTTATTTTT
*
257305 TACTTATATCCATGTATATTTATTTTT
1 TACGTATATCCATGTATATTTATTTTT
257332 TACGTATATCCATGTATATTTATTTTT
1 TACGTATATCCATGTATATTTATTTTT
257359 TACGTATATCCATGTATATTTATTTTTT
1 TACGTATATCCATGTATATTTA-TTTTT
* *
257387 TAGGTATATTCATGTATATTTATTTTTT
1 TACGTATATCCATGTATATTTA-TTTTT
257415 TACGTATATCCATGTATATTTATTTTT
1 TACGTATATCCATGTATATTTATTTTT
257442 TACGTATATCCATGTATATTTATTTTT
1 TACGTATATCCATGTATATTTATTTTT
257469 TACGTATATCCATGTATATTTATTTTT
1 TACGTATATCCATGTATATTTATTTTT
*
257496 TACGTATATTCATGTATATTT
1 TACGTATATCCATGTATATTT
257517 TTTACAATTT
Statistics
Matches: 310, Mismatches: 9, Indels: 9
0.95 0.03 0.03
Matches are distributed among these distances:
27 161 0.52
28 146 0.47
29 3 0.01
ACGTcount: A:0.26, C:0.11, G:0.07, T:0.56
Consensus pattern (27 bp):
TACGTATATCCATGTATATTTATTTTT
Found at i:257381 original size:137 final size:137
Alignment explanation
Indices: 257166--257516 Score: 630
Period size: 137 Copynumber: 2.5 Consensus size: 137
257156 ATTCTCCACC
*
257166 TACGTATATCCATGTATATTTACTTTTTTACGTATATCCATGTATATTTATTTCTTTACATATAT
1 TACGTATATCCATGTATATTTA-TTTTTTACGTATATCCATGTATATTTATTT-TTTACGTATAT
257231 CCATGTATATTTATTTTTTTACGTATATCCATGTATATTTATTTCTTTACGTATATCCATGTATA
64 CCATGTATATTTATTTTTTTACGTATATCCATGTATATTTATTTCTTTACGTATATCCATGTATA
257296 TTTATTTTT
129 TTTATTTTT
*
257305 TACTTATATCCATGTATATTTATTTTTTACGTATATCCATGTATATTTATTTTTTACGTATATCC
1 TACGTATATCCATGTATATTTATTTTTTACGTATATCCATGTATATTTATTTTTTACGTATATCC
* * *
257370 ATGTATATTTATTTTTTTAGGTATATTCATGTATATTTATTTTTTTACGTATATCCATGTATATT
66 ATGTATATTTATTTTTTTACGTATATCCATGTATATTTATTTCTTTACGTATATCCATGTATATT
257435 TATTTTT
131 TATTTTT
*
257442 TACGTATATCCATGTATATTTATTTTTTACGTATATCCATGTATATTTATTTTTTACGTATATTC
1 TACGTATATCCATGTATATTTATTTTTTACGTATATCCATGTATATTTATTTTTTACGTATATCC
257507 ATGTATATTT
66 ATGTATATTT
257517 TTTACAATTT
Statistics
Matches: 205, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
137 154 0.75
138 30 0.15
139 21 0.10
ACGTcount: A:0.26, C:0.11, G:0.07, T:0.56
Consensus pattern (137 bp):
TACGTATATCCATGTATATTTATTTTTTACGTATATCCATGTATATTTATTTTTTACGTATATCC
ATGTATATTTATTTTTTTACGTATATCCATGTATATTTATTTCTTTACGTATATCCATGTATATT
TATTTTT
Found at i:258744 original size:23 final size:23
Alignment explanation
Indices: 258718--258797 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 23
258708 GTGTGGTTTA
* *
258718 TGTTCATTTATGTTTGTTTGTTT
1 TGTTCATTTATGTTCGTTTGTTG
* **
258741 TGTTCATTTACGTTCGTTAATTG
1 TGTTCATTTATGTTCGTTTGTTG
* *
258764 TGTTCGTTTATGTTCGTTTCTTG
1 TGTTCATTTATGTTCGTTTGTTG
*
258787 TGTTCGTTTAT
1 TGTTCATTTAT
258798 ATTTGTTCGC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.61
Consensus pattern (23 bp):
TGTTCATTTATGTTCGTTTGTTG
Found at i:275209 original size:213 final size:211
Alignment explanation
Indices: 274835--275424 Score: 781
Period size: 213 Copynumber: 2.8 Consensus size: 211
274825 CAAGTTATCT
* * *
274835 GGAAGGTAAACAAGGTTTTCACAGTTGTTCAATCTCAAATCAGTAAGACCAATGAGATTCTCCAT
1 GGAAGGCAAACAAGGTTTTCACAGTTGTTCAATCT-AAATCAGAAAGACCAGTGAGATTCTCCAT
* * * * *
274900 CGAGGACGGTAATTTCTTCAATGCCGTTCCGCTTAAATCAAGAGTTATCAACCTCTCCATAGTGT
65 TGAAGATGGTAATTTCTTCAATGCTGTTCC-CTTAAATCAAGAGTTATCAACCTCTCCATGGTGT
* *
274965 CCAAGATTTCTGGGAAAATCTCCAATCTTGAGCAGCCTCCAAGAAAGAAATCCTCAAGAGATTTC
129 CCAAGATTTCTGGGAAAATCTCCAATCTTGAGCAGCCCCCAAGAAAGAAACCCTCAAGAGATTTC
*
275030 AATTTATAGAA-GCTGTGA
194 AATTTATA-AAGGCTGTCA
* *
275048 GGAAGGCAAACAAGGTTTTCACAGTTGTTCATTCTAAAATGCTG-AAGACCAGTGAGATTCTCCA
1 GGAAGGCAAACAAGGTTTTCACAGTTGTTCAATCT-AAAT-CAGAAAGACCAGTGAGATTCTCCA
* *
275112 TTGATGATGGTAATTTCTTCAATGCTGTTCCACTTAAATCAAGAGTTATCAAACTCTCCATGGTG
64 TTGAAGATGGTAATTTCTTCAATGCTGTTCC-CTTAAATCAAGAGTTATCAACCTCTCCATGGTG
* ** * ** *
275177 TCCAAGATTTCTGGGAAATTCTCCAATCTTGAGCAGCCCCCAAGATGGAGACCCTGGAGTGATTT
128 TCCAAGATTTCTGGGAAAATCTCCAATCTTGAGCAGCCCCCAAGAAAGAAACCCTCAAGAGATTT
*
275242 CAATTTATAAAGGCTGTCC
193 CAATTTATAAAGGCTGTCA
* * *
275261 GGAAGGCAAACAAGGTTTTCACAGTTGTTCAAGCTCAATTCAGAAAGACC-GATAAGATTCTCCA
1 GGAAGGCAAACAAGGTTTTCACAGTTGTTCAATCT-AAATCAGAAAGACCAG-TGAGATTCTCCA
* * ** *
275325 TTGAAGATGGTAATTCCTTCAAAGCTGTTTCCCTTAAATCAAGAACTCTCAACCTCTCCATGGTG
64 TTGAAGATGGTAATTTCTTCAATGCTG-TTCCCTTAAATCAAGAGTTATCAACCTCTCCATGGTG
* *
275390 TCTAAGATTTCTGGGAAAGTCTCCAATCTTGAGCA
128 TCCAAGATTTCTGGGAAAATCTCCAATCTTGAGCA
275425 ACACGCTAGA
Statistics
Matches: 334, Mismatches: 38, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
212 5 0.01
213 323 0.97
214 6 0.02
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (211 bp):
GGAAGGCAAACAAGGTTTTCACAGTTGTTCAATCTAAATCAGAAAGACCAGTGAGATTCTCCATT
GAAGATGGTAATTTCTTCAATGCTGTTCCCTTAAATCAAGAGTTATCAACCTCTCCATGGTGTCC
AAGATTTCTGGGAAAATCTCCAATCTTGAGCAGCCCCCAAGAAAGAAACCCTCAAGAGATTTCAA
TTTATAAAGGCTGTCA
Found at i:278389 original size:2 final size:2
Alignment explanation
Indices: 278382--278409 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
278372 GGTGACTGCG
278382 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
278410 TTGATTGTCC
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:279837 original size:20 final size:17
Alignment explanation
Indices: 279793--279840 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 17
279783 GTTCTGATAA
279793 TTTTAAAAATTTTATTT
1 TTTTAAAAATTTTATTT
*
279810 TTTAAAAAATTATTATATT
1 TTTTAAAAATT-TTAT-TT
279829 TATTTAAAAATT
1 T-TTTAAAAATT
279841 CTAATTTCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 10 0.38
18 4 0.15
19 3 0.12
20 9 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTAAAAATTTTATTT
Found at i:280817 original size:21 final size:21
Alignment explanation
Indices: 280776--280818 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
280766 GGTTTTGTTA
* * *
280776 TTTTTTTATCGGTTTTGTTAT
1 TTTTTTTATCAGCTTTATTAT
280797 TTTTTTTATCAGCTTTATTAT
1 TTTTTTTATCAGCTTTATTAT
280818 T
1 T
280819 ATTGGACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.07, G:0.09, T:0.70
Consensus pattern (21 bp):
TTTTTTTATCAGCTTTATTAT
Found at i:281400 original size:19 final size:20
Alignment explanation
Indices: 281376--281437 Score: 74
Period size: 19 Copynumber: 3.1 Consensus size: 20
281366 TTACGTAAAT
281376 TATTATAATATTAAAATT-A
1 TATTATAATATTAAAATTAA
*
281395 TATTATAATGTTAAAATTAA
1 TATTATAATATTAAAATTAA
* *
281415 TATTA-AATAATATAATATAA
1 TATTATAATATTAAAAT-TAA
281435 TAT
1 TAT
281438 AGTTTTCGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 25 0.68
20 12 0.32
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
TATTATAATATTAAAATTAA
Found at i:281566 original size:42 final size:42
Alignment explanation
Indices: 281519--281600 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
281509 ATTACATTAG
* **
281519 AAAATCAATTACAACTACTAAACATTGAAAAATATTTTTCAT
1 AAAATCAAATACAACTACTAAACACCGAAAAATATTTTTCAT
** *
281561 AAAATCAAATACAGTTATTAAACACCGAAAAATATTTTTC
1 AAAATCAAATACAACTACTAAACACCGAAAAATATTTTTC
281601 GAAAAAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.50, C:0.15, G:0.04, T:0.32
Consensus pattern (42 bp):
AAAATCAAATACAACTACTAAACACCGAAAAATATTTTTCAT
Found at i:281882 original size:13 final size:13
Alignment explanation
Indices: 281864--281893 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
281854 GAGACCAACT
281864 TCCGTGGAAGACC
1 TCCGTGGAAGACC
*
281877 TCCGTGGGAGACC
1 TCCGTGGAAGACC
281890 TCCG
1 TCCG
281894 ACAATTATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.33, G:0.33, T:0.17
Consensus pattern (13 bp):
TCCGTGGAAGACC
Found at i:303841 original size:31 final size:31
Alignment explanation
Indices: 303803--303865 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
303793 AGTTGGAACT
303803 CTTCCAATGACTGGCCCCCACAACGGTCGAG
1 CTTCCAATGACTGGCCCCCACAACGGTCGAG
*
303834 CTTCCAATGACTGGCTCCCACAACGGTCGAG
1 CTTCCAATGACTGGCCCCCACAACGGTCGAG
303865 C
1 C
303866 ATTATGCTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.22, C:0.38, G:0.22, T:0.17
Consensus pattern (31 bp):
CTTCCAATGACTGGCCCCCACAACGGTCGAG
Found at i:303973 original size:20 final size:20
Alignment explanation
Indices: 303900--303972 Score: 121
Period size: 20 Copynumber: 3.6 Consensus size: 20
303890 TTGGTTCACG
*
303900 GAATATAAGATTACATGTGA
1 GAATGTAAGATTACATGTGA
303920 GAATGTAAGATTACATGTGA
1 GAATGTAAGATTACATGTGA
303940 GAATGTAAGATTATC-TGTGA
1 GAATGTAAGATTA-CATGTGA
303960 GAATGTAAGATTA
1 GAATGTAAGATTA
303973 TTAGGAATAT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 50 0.98
21 1 0.02
ACGTcount: A:0.41, C:0.04, G:0.23, T:0.32
Consensus pattern (20 bp):
GAATGTAAGATTACATGTGA
Found at i:309939 original size:31 final size:33
Alignment explanation
Indices: 309901--309962 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 33
309891 AAATTACATG
*
309901 TTTAGTACTTAAA-TT-ATTAGTTTTGATTTAT
1 TTTAGTACCTAAACTTAATTAGTTTTGATTTAT
* *
309932 TTTAGTACCTAAACTTAATTATTTTTTATTT
1 TTTAGTACCTAAACTTAATTAGTTTTGATTT
309963 TTCATTCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 12 0.46
32 2 0.08
33 12 0.46
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.58
Consensus pattern (33 bp):
TTTAGTACCTAAACTTAATTAGTTTTGATTTAT
Found at i:319994 original size:29 final size:29
Alignment explanation
Indices: 319949--320006 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
319939 GTGTTAGCCG
* *
319949 TAGGTTGTCATGCCTTTCGGGCGACCTAC
1 TAGGTCGTCATGCCTTTCGGGCGAACTAC
* *
319978 TAGGTCGTCATGTCTTTCTGGCGAACTAC
1 TAGGTCGTCATGCCTTTCGGGCGAACTAC
320007 AAGAGATTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.33
Consensus pattern (29 bp):
TAGGTCGTCATGCCTTTCGGGCGAACTAC
Found at i:320070 original size:14 final size:14
Alignment explanation
Indices: 320051--320105 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 14
320041 CTGGGCATCT
320051 GAGGCCATCCGACC
1 GAGGCCATCCGACC
320065 GAGGCCAT----CC
1 GAGGCCATCCGACC
*
320075 GAGGTCATCCGACC
1 GAGGCCATCCGACC
* *
320089 GAGGTCATCCGAAC
1 GAGGCCATCCGACC
320103 GAG
1 GAG
320106 CTATGCGAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
10 9 0.26
14 26 0.74
ACGTcount: A:0.24, C:0.35, G:0.31, T:0.11
Consensus pattern (14 bp):
GAGGCCATCCGACC
Found at i:320078 original size:24 final size:24
Alignment explanation
Indices: 320046--320100 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
320036 ATATGCTGGG
*
320046 CATCTGAGGCCATCCGACCGAGGC
1 CATCCGAGGCCATCCGACCGAGGC
* *
320070 CATCCGAGGTCATCCGACCGAGGT
1 CATCCGAGGCCATCCGACCGAGGC
320094 CATCCGA
1 CATCCGA
320101 ACGAGCTATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.22, C:0.36, G:0.27, T:0.15
Consensus pattern (24 bp):
CATCCGAGGCCATCCGACCGAGGC
Found at i:320170 original size:33 final size:33
Alignment explanation
Indices: 320087--320155 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
320077 GGTCATCCGA
* * * *
320087 CCGAGGTCATCCGAACGAGCTATGCGAGGGCAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
320120 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
320153 CCG
1 CCG
320156 TTGGAAGCCG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.25, C:0.28, G:0.36, T:0.12
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
Found at i:320935 original size:3 final size:3
Alignment explanation
Indices: 320929--320958 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
320919 TAGATGTTAC
320929 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
320959 TTTAAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:321788 original size:11 final size:11
Alignment explanation
Indices: 321726--321795 Score: 56
Period size: 11 Copynumber: 6.4 Consensus size: 11
321716 TGATACAATA
*
321726 TAAAATGAATT
1 TAAAATAAATT
*
321737 AAAACATAACATT
1 TAAA-ATAA-ATT
321750 TAAAA-AAA-T
1 TAAAATAAATT
321759 TAAAA-AAATT
1 TAAAATAAATT
**
321769 TAATTTAAATT
1 TAAAATAAATT
321780 TAAAATAAATT
1 TAAAATAAATT
321791 ATAAA
1 -TAAA
321796 TTATAAATTA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
9 9 0.19
10 5 0.11
11 19 0.40
12 8 0.17
13 6 0.13
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (11 bp):
TAAAATAAATT
Found at i:321998 original size:34 final size:32
Alignment explanation
Indices: 321943--322005 Score: 74
Period size: 34 Copynumber: 1.9 Consensus size: 32
321933 CCATAATTCA
*
321943 AAAATATTTTTTAAAAATATTATTAAATTATTTT
1 AAAATATTTGTTAAAAATATTA--AAATTATTTT
*
321977 AAAATAATTTGTT-AAACTATTAAAATTAT
1 AAAAT-ATTTGTTAAAAATATTAAAATTAT
322006 AAAATGAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
32 7 0.27
34 13 0.50
35 6 0.23
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (32 bp):
AAAATATTTGTTAAAAATATTAAAATTATTTT
Found at i:329137 original size:2 final size:2
Alignment explanation
Indices: 329130--329174 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
329120 AGTTTTAAGG
329130 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
329172 AT A
1 AT A
329175 AAGTTTATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:329797 original size:86 final size:87
Alignment explanation
Indices: 329619--329816 Score: 294
Period size: 86 Copynumber: 2.3 Consensus size: 87
329609 GTAAATTTAA
* * *
329619 AATAA-TTTCTTAACCATAATTTTATCCACAGATCAATTATAAATTTAATAACATAAAAATAATT
1 AATAATTTTCTTATCCATAATCTTATCCAAAGATCAATTATAAATTTAATAACATAAAAATAATT
* *
329683 AATAAAAATATTTGTTATCAAT
66 AATAAAAAAATTTGTTATCAAG
* * *
329705 AATAATTTTCTTATCCATAATCTTATCCAAAGATCAATTATAAATTTAAT-ATAT-AATATATTT
1 AATAATTTTCTTATCCATAATCTTATCCAAAGATCAATTATAAATTTAATAACATAAAAATAATT
329768 AATAAAAAAAATTTGTTATCAAG
66 AAT-AAAAAAATTTGTTATCAAG
329791 AATAATTTTCTTATCCATAATCTTAT
1 AATAATTTTCTTATCCATAATCTTAT
329817 GCTTATTTCA
Statistics
Matches: 102, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
85 10 0.10
86 51 0.50
87 41 0.40
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.41
Consensus pattern (87 bp):
AATAATTTTCTTATCCATAATCTTATCCAAAGATCAATTATAAATTTAATAACATAAAAATAATT
AATAAAAAAATTTGTTATCAAG
Found at i:340447 original size:55 final size:56
Alignment explanation
Indices: 340382--340506 Score: 148
Period size: 57 Copynumber: 2.2 Consensus size: 56
340372 TATTTTTTAG
* * * *
340382 ATATATTCGATTCT-GAGCCCTTATTTTTATGCTTCTTAATAGA-AACAACTGATAA
1 ATATATTCGATTCTAGACCCCCTATTTGTATGCTTATTAAT-GACAACAACTGATAA
*
340437 ATATATTCGATT-TAAAGACCCCCTATTTGTATGCTTATTAATGACAACAACTGATAG
1 ATATATTCGATTCT--AGACCCCCTATTTGTATGCTTATTAATGACAACAACTGATAA
*
340494 AGATATTCGATTC
1 ATATATTCGATTC
340507 GGGCTCCTAT
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
54 1 0.02
55 12 0.20
56 2 0.03
57 44 0.75
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.38
Consensus pattern (56 bp):
ATATATTCGATTCTAGACCCCCTATTTGTATGCTTATTAATGACAACAACTGATAA
Done.