Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005599.1 Hibiscus syriacus cultivar Beakdansim tig00013024_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: 204908
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
File 2 of 2
Found at i:172071 original size:2 final size:2
Alignment explanation
Indices: 172059--172089 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
172049 TTTTAATTAC
*
172059 TA TA TA CA 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 T
172090 TAATTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:172127 original size:16 final size:16
Alignment explanation
Indices: 172082--172131 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
172072 ATATATATAT
* *
172082 ATATATATTAATTATTT
1 ATAT-TATTAATAATTA
*
172099 ATTTTATTTAATAATTA
1 ATATTA-TTAATAATTA
172116 ATATTATTAATAATTA
1 ATATTATTAATAATTA
172132 TTATATTCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 12 0.43
17 16 0.57
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATATTATTAATAATTA
Found at i:172145 original size:13 final size:13
Alignment explanation
Indices: 172129--172157 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
172119 TTATTAATAA
172129 TTATTATATTCAT
1 TTATTATATTCAT
172142 TTATTATATTCAT
1 TTATTATATTCAT
172155 TTA
1 TTA
172158 ATTTATACGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (13 bp):
TTATTATATTCAT
Found at i:172532 original size:2 final size:2
Alignment explanation
Indices: 172525--172552 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
172515 ACTCGAAACA
172525 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
172553 CTTCATTTGA
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:173012 original size:3 final size:3
Alignment explanation
Indices: 173004--173044 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
172994 AATGACTCTA
* *
173004 TAT TAT TAT TTT TAT TAT TTT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
173045 AGTGACATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:173284 original size:21 final size:21
Alignment explanation
Indices: 173255--173307 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
173245 ATTCTGACTA
*
173255 TCGCATTGCGATTTTTCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
173276 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
173297 TCGCAATGCGA
1 TCGCATTGCGA
173308 ATACGTAAAT
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:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:173322 original size:20 final size:20
Alignment explanation
Indices: 173297--173390 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
173287 TTTTCCTAAT
173297 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
173317 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
173337 TCACAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
173358 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
173378 TCGCAATGCGAAT
1 TCGCAATGCGAAT
173391 CTGACTATCG
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
20 45 0.73
21 17 0.27
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:173359 original size:41 final size:41
Alignment explanation
Indices: 173300--173390 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 41
173290 TCCTAATTCG
* *
173300 CAATGCGAA-TACGTAAATCGCAACGCGATTAAGTAAATCA
1 CAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAATCA
* * * *
173340 CAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAATCG
1 CAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAATCA
173381 CAATGCGAAT
1 CAATGCGAAT
173391 CTGACTATCG
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 9 0.20
41 35 0.80
ACGTcount: A:0.42, C:0.19, G:0.20, T:0.20
Consensus pattern (41 bp):
CAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAATCA
Found at i:173997 original size:19 final size:19
Alignment explanation
Indices: 173945--173998 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 19
173935 AATGAAAATC
173945 GCAACGCGTAAATGACTATT
1 GCAACGCG-AAATGACTATT
173965 GCAACGCGGAAATGACTATT
1 GCAACGC-GAAATGACTATT
173985 GCAACGCGAAATGA
1 GCAACGCGAAATGA
173999 AAATCGCAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
19 7 0.21
20 25 0.76
21 1 0.03
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.19
Consensus pattern (19 bp):
GCAACGCGAAATGACTATT
Found at i:174082 original size:33 final size:33
Alignment explanation
Indices: 174040--174161 Score: 136
Period size: 33 Copynumber: 3.5 Consensus size: 33
174030 CAAAATCGCA
* *
174040 TTGCGATTTTCATTTTGCGTTGTGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
174073 TTGCGATTTTCATTTCGTGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
174106 TTGCGATAGTCATTTCCGCGTTGCGATTTTCATTCTCTCG
1 TTGCGATTTTCATTT-CGCGTTGCG------ATTCTCTCG
174146 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
174162 AACCAAAAGA
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
33 43 0.58
34 8 0.11
39 1 0.01
40 22 0.30
ACGTcount: A:0.11, C:0.21, G:0.20, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:174138 original size:20 final size:21
Alignment explanation
Indices: 174098--174161 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 21
174088 CGTGTTGCGA
* **
174098 TTCTCTCGTTGCGATAGTCAT
1 TTCTCGCGTTGCGATTTTCAT
174119 TTC-CGCGTTGCGATTTTCA-
1 TTCTCGCGTTGCGATTTTCAT
*
174138 TTCTCTCGTTGCGATTTTCAT
1 TTCTCGCGTTGCGATTTTCAT
174159 TTC
1 TTC
174162 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 3 0.08
20 28 0.76
21 6 0.16
ACGTcount: A:0.11, C:0.25, G:0.17, T:0.47
Consensus pattern (21 bp):
TTCTCGCGTTGCGATTTTCAT
Found at i:176077 original size:94 final size:93
Alignment explanation
Indices: 175856--176131 Score: 406
Period size: 94 Copynumber: 3.0 Consensus size: 93
175846 GATTGCTTAA
* *
175856 TAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGTAT
1 TAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTAT
175917 TTGTCTTTTGTTTTGTCTTTTGGTTGAAG
66 TTGTC-TTTGTTTTGTCTTTTGGTTGAAG
175946 T--A--TATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTAT
1 TAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTAT
176007 TTGTCTTTGTTTTGTCTTTTGGTTGAAAG
66 TTGTCTTTGTTTTGTCTTTTGGTTG-AAG
* * * * * *
176036 TAAATTTGTTCGCTTGCTGCCAATTTTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAATAT
1 TAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTAT
176101 TTGTCTTTGTTTTGTCTTTTGGTTGAAG
66 TTGTCTTTGTTTTGTCTTTTGGTTGAAG
176129 TAA
1 TAA
176132 TGCAATCCAT
Statistics
Matches: 169, Mismatches: 8, Indels: 15
0.88 0.04 0.08
Matches are distributed among these distances:
86 27 0.16
88 4 0.02
89 22 0.13
90 31 0.18
92 1 0.01
93 6 0.04
94 78 0.46
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.47
Consensus pattern (93 bp):
TAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTAT
TTGTCTTTGTTTTGTCTTTTGGTTGAAG
Found at i:176266 original size:19 final size:19
Alignment explanation
Indices: 176220--176277 Score: 89
Period size: 19 Copynumber: 3.0 Consensus size: 19
176210 TCTTTTGGTT
*
176220 GAAATGAAAATCGCAATGA
1 GAAATGAAAATCGCAACGA
*
176239 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGA
176259 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
176278 CAAAATCGCA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
19 18 0.51
20 17 0.49
ACGTcount: A:0.50, C:0.16, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:176315 original size:33 final size:33
Alignment explanation
Indices: 176246--176315 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
176236 TGAGAGAATG
**
176246 AAAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACAAAAATCGCAACGAC
*
176279 AAAATCGCAACGCGAACCCAAAAATCGCAACG-C
1 AAAATCGCAACGCGAA-ACAAAAATCGCAACGAC
176312 AAAA
1 AAAA
176316 CTATAATCGC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 21 0.64
34 12 0.36
ACGTcount: A:0.50, C:0.27, G:0.16, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGCGAAACAAAAATCGCAACGAC
Found at i:176379 original size:33 final size:33
Alignment explanation
Indices: 176340--176419 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 33
176330 CGATTTTTGG
* *
176340 TTTCGCGTTGCGATTTTGTCATTACGATTTTCA
1 TTTCGCGTTGCGATTCTCTCATTACGATTTTCA
** *
176373 TTTCGCGTTGCGATTCTCTTGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCATTACGATTTTCA
176406 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
176420 AGTCATTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCATTACGATTTTCA
Found at i:176417 original size:19 final size:19
Alignment explanation
Indices: 176364--176443 Score: 71
Period size: 19 Copynumber: 4.4 Consensus size: 19
176354 TTTGTCATTA
176364 CGATTTTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
*
176383 CGATTCTC--TT---GTTG
1 CGATTTTCATTTCGCGTTG
176397 CGATTTTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
** *
176416 CGATAGTCATTTTTCACGTTG
1 CGATTTTCA--TTTCGCGTTG
176437 CGATTTT
1 CGATTTT
176444 AAGTTCCAGA
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
14 11 0.23
16 2 0.04
17 2 0.04
19 18 0.38
21 14 0.30
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.47
Consensus pattern (19 bp):
CGATTTTCATTTCGCGTTG
Found at i:176920 original size:21 final size:21
Alignment explanation
Indices: 176896--176962 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
176886 TCATTCCTCG
176896 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
176917 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
176938 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
176959 AGAG
1 AGAG
176963 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:178333 original size:14 final size:14
Alignment explanation
Indices: 178314--178349 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
178304 ATTATTTAAT
178314 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
178328 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
178342 TGATTTGT
1 TGATTTGT
178350 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:178472 original size:19 final size:19
Alignment explanation
Indices: 178456--178502 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
178446 AAAAATGACT
*
178456 ATCACAATGCGAAATGAAA
1 ATCACAACGCGAAATGAAA
*
178475 ATCGCAACGCGAAATGAAA
1 ATCACAACGCGAAATGAAA
*
178494 ATCGCAACG
1 ATCACAACG
178503 AGGGAATCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (19 bp):
ATCACAACGCGAAATGAAA
Found at i:178531 original size:19 final size:19
Alignment explanation
Indices: 178464--178539 Score: 81
Period size: 19 Copynumber: 4.3 Consensus size: 19
178454 CTATCACAAT
*
178464 GCGAAATGAAAATCGCAAC
1 GCGAAATGAAAATCGCAAA
178483 GCGAAATGAAAATCGC-AA
1 GCGAAATGAAAATCGCAAA
**
178501 -CG--A-GGGAATCGCAAA
1 GCGAAATGAAAATCGCAAA
*
178516 GCGAAATGAAAATCGCAAC
1 GCGAAATGAAAATCGCAAA
178535 GCGAA
1 GCGAA
178540 TTTAGTTTCG
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
14 7 0.15
15 3 0.07
16 2 0.04
17 2 0.04
18 2 0.04
19 30 0.65
ACGTcount: A:0.46, C:0.20, G:0.25, T:0.09
Consensus pattern (19 bp):
GCGAAATGAAAATCGCAAA
Found at i:178570 original size:19 final size:19
Alignment explanation
Indices: 178535--178580 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
178525 AAATCGCAAC
*
178535 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
178554 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
178573 GTGATTTT
1 GCGATTTT
178581 GTCGTTGCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.13, C:0.13, G:0.26, T:0.48
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:178594 original size:33 final size:33
Alignment explanation
Indices: 178550--178709 Score: 241
Period size: 33 Copynumber: 4.8 Consensus size: 33
178540 TTTAGTTTCG
* * * *
178550 CGTTGCGATTTT-AGTTTCGCGTTGTGATTTTGT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
* * *
178583 CGTTGCAATTTTCATTTCGCGTTACGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
178616 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
178649 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
178682 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
178710 AGTCATTTCC
Statistics
Matches: 118, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
33 117 0.99
34 1 0.01
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:178624 original size:14 final size:14
Alignment explanation
Indices: 178602--178691 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
178592 TTTCATTTCG
*
178602 CGTTACGATTCTCT
1 CGTTGCGATTCTCT
*
178616 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
178633 CGCATTGCGATTCTCT
1 CG--TTGCGATTCTCT
*
178649 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
178666 CGCATTGCGATTCTCT
1 CG--TTGCGATTCTCT
178682 CGTTGCGATT
1 CGTTGCGATT
178692 TTCATTTCGC
Statistics
Matches: 61, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
14 21 0.34
16 14 0.23
17 14 0.23
19 12 0.20
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:178642 original size:19 final size:19
Alignment explanation
Indices: 178618--178729 Score: 100
Period size: 19 Copynumber: 6.4 Consensus size: 19
178608 GATTCTCTCG
178618 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
178637 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
178651 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
178670 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
178684 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
178703 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
178723 TTGCGAT
1 TTGCGAT
178730 AGATATTAAG
Statistics
Matches: 75, Mismatches: 7, Indels: 21
0.73 0.07 0.20
Matches are distributed among these distances:
14 12 0.16
16 14 0.19
17 14 0.19
19 25 0.33
20 10 0.13
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:178775 original size:20 final size:20
Alignment explanation
Indices: 178703--178775 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
178693 TCATTTCGCA
*
178703 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTCCGTG
**
178723 TTGCGATAG--ATATTAAGATG
1 TTGCGATAGTCAT-TTCCG-TG
178743 ATTGCGA-ACGTCATTTCCGTG
1 -TTGCGATA-GTCATTTCCGTG
178764 TTGCGATAGTCA
1 TTGCGATAGTCA
178776 AATGAATGCC
Statistics
Matches: 41, Mismatches: 5, Indels: 14
0.68 0.08 0.23
Matches are distributed among these distances:
18 2 0.05
19 3 0.07
20 21 0.51
21 10 0.24
22 3 0.07
23 2 0.05
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGTG
Found at i:181039 original size:14 final size:14
Alignment explanation
Indices: 181020--181046 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
181010 TCCCGTGGCA
181020 TTTTCTTTGGGGAC
1 TTTTCTTTGGGGAC
181034 TTTTCTTTGGGGA
1 TTTTCTTTGGGGA
181047 TTTCTTCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.11, G:0.30, T:0.52
Consensus pattern (14 bp):
TTTTCTTTGGGGAC
Found at i:181280 original size:24 final size:24
Alignment explanation
Indices: 181246--181299 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
181236 CTGAAAAATC
* *
181246 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTAACCAAG
* *
181270 ATCAAAGTCCGGGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
181294 ATCAAA
1 ATCAAA
181300 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:182188 original size:20 final size:20
Alignment explanation
Indices: 182165--182349 Score: 182
Period size: 20 Copynumber: 9.2 Consensus size: 20
182155 AGAATCTCGT
182165 TGCGATTTAC-TAAATCGCAA
1 TGCGATTTACGT-AATCGCAA
182185 TGCGA-TTACGTAAATCG-AA
1 TGCGATTTACGT-AATCGCAA
* * *
182204 GTGCGAATTAGGAAAATCGCAA
1 -TGCGATTTACG-TAATCGCAA
182226 TGCGA-TTACGTAAATCGCAA
1 TGCGATTTACGT-AATCGCAA
* *
182246 TGCGA-ATACGTAATCGCAT
1 TGCGATTTACGTAATCGCAA
* *
182265 TGCGATTTACGTAATCGTAT
1 TGCGATTTACGTAATCGCAA
*
182285 TGCGATTTACGTAATCGCAT
1 TGCGATTTACGTAATCGCAA
* *
182305 TGCGATTTACGTATTCGCAT
1 TGCGATTTACGTAATCGCAA
* *
182325 TGCGATTTACGTATTCGCAT
1 TGCGATTTACGTAATCGCAA
182345 TGCGA
1 TGCGA
182350 ATTAGAAAAA
Statistics
Matches: 148, Mismatches: 10, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
19 18 0.12
20 114 0.77
21 14 0.09
22 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (20 bp):
TGCGATTTACGTAATCGCAA
Found at i:182220 original size:21 final size:21
Alignment explanation
Indices: 182176--182391 Score: 119
Period size: 20 Copynumber: 10.7 Consensus size: 21
182166 GCGATTTACT
*
182176 AAATCGCAATGCG-ATTACGT
1 AAATCGCAATGCGAATTACGA
*
182196 AAATCG-AAGTGCGAATTAGGA
1 AAATCGCAA-TGCGAATTACGA
*
182217 AAATCGCAATGCG-ATTACGT
1 AAATCGCAATGCGAATTACGA
182237 AAATCGCAATGCGAA-TACG-
1 AAATCGCAATGCGAATTACGA
* * *
182256 TAATCGCATTGCGATTTACG-
1 AAATCGCAATGCGAATTACGA
* * * *
182276 TAATCGTATTGCGATTTACG-
1 AAATCGCAATGCGAATTACGA
* * *
182296 TAATCGCATTGCGATTTACG-
1 AAATCGCAATGCGAATTACGA
* * * *
182316 TATTCGCATTGCGATTTACG-
1 AAATCGCAATGCGAATTACGA
* * *
182336 TATTCGCATTGCGAATTA-GAA
1 AAATCGCAATGCGAATTACG-A
* * ** *
182357 AAATCGTAACGCGAATTTGGG
1 AAATCGCAATGCGAATTACGA
182378 AAATCGCAATGCGA
1 AAATCGCAATGCGA
182392 TAGTCAGAAT
Statistics
Matches: 168, Mismatches: 20, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
19 15 0.09
20 110 0.65
21 40 0.24
22 3 0.02
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (21 bp):
AAATCGCAATGCGAATTACGA
Found at i:182227 original size:41 final size:40
Alignment explanation
Indices: 182165--182392 Score: 162
Period size: 40 Copynumber: 5.7 Consensus size: 40
182155 AGAATCTCGT
* *
182165 TGCGATTTACTAAATCGCAATGCGA-TTACGTAAATCGAA
1 TGCGAATTACGAAATCGCAATGCGATTTACGTAAATCGAA
*
182204 GTGCGAATTAGGAAAATCGCAATGCGA-TTACGTAAATCGCAA
1 -TGCGAATTACG-AAATCGCAATGCGATTTACGTAAATCG-AA
* * *
182246 TGCGAA-TACGTAATCGCATTGCGATTTACGT-AATCGTAT
1 TGCGAATTACGAAATCGCAATGCGATTTACGTAAATCG-AA
* * * * *
182285 TGCGATTTACGTAATCGCATTGCGATTTACGT-ATTCGCAT
1 TGCGAATTACGAAATCGCAATGCGATTTACGTAAATCG-AA
* * * * * *
182325 TGCGATTTACGTATTCGCATTGCGAATTA-GAAAAATCGTAA
1 TGCGAATTACGAAATCGCAATGCGATTTACG-TAAATCG-AA
* **
182366 CGCGAATTTGGGAAATCGCAATGCGAT
1 TGCGAA-TTACGAAATCGCAATGCGAT
182393 AGTCAGAATC
Statistics
Matches: 156, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
39 24 0.15
40 75 0.48
41 41 0.26
42 16 0.10
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (40 bp):
TGCGAATTACGAAATCGCAATGCGATTTACGTAAATCGAA
Found at i:182316 original size:60 final size:60
Alignment explanation
Indices: 182164--182349 Score: 225
Period size: 60 Copynumber: 3.1 Consensus size: 60
182154 CAGAATCTCG
* * * * *
182164 TTGCGATTTAC-TAAATCGCAATGCGATTACGTAAATCGAAGTGCGAATTAGGAAAATCGCA
1 TTGCGATTTACGTAAATCGCAATGCGATTACGT-AATCGCATTGCGATTTACG-TAATCGCA
* * *
182225 ATGCGA-TTACGTAAATCGCAATGCGAATACGTAATCGCATTGCGATTTACGTAATCGTA
1 TTGCGATTTACGTAAATCGCAATGCGATTACGTAATCGCATTGCGATTTACGTAATCGCA
* * *
182284 TTGCGATTTACGT-AATCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTAAATCGCAATGCGA-TTACGTAATCGCATTGCGATTTACGTAATCGCA
182344 TTGCGA
1 TTGCGA
182350 ATTAGAAAAA
Statistics
Matches: 108, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
59 23 0.21
60 60 0.56
61 25 0.23
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (60 bp):
TTGCGATTTACGTAAATCGCAATGCGATTACGTAATCGCATTGCGATTTACGTAATCGCA
Found at i:185805 original size:16 final size:16
Alignment explanation
Indices: 185784--185818 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
185774 ATGCAAACAT
185784 GAAATGTCTACTGGTA
1 GAAATGTCTACTGGTA
185800 GAAATGTCTACTGGTA
1 GAAATGTCTACTGGTA
185816 GAA
1 GAA
185819 TAGGTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (16 bp):
GAAATGTCTACTGGTA
Found at i:195333 original size:15 final size:15
Alignment explanation
Indices: 195313--195346 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
195303 GGAATGAACG
* *
195313 TTTTAGGGATTTCAA
1 TTTTAGGAATTCCAA
195328 TTTTAGGAATTCCAA
1 TTTTAGGAATTCCAA
195343 TTTT
1 TTTT
195347 GAGAACACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.50
Consensus pattern (15 bp):
TTTTAGGAATTCCAA
Found at i:195890 original size:6 final size:6
Alignment explanation
Indices: 195879--195909 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
195869 GACACGTATT
195879 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
195910 GACGACGGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:196432 original size:6 final size:6
Alignment explanation
Indices: 196416--196447 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
196406 TCTCCTCTCG
196416 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
196448 AATACGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:196560 original size:16 final size:17
Alignment explanation
Indices: 196539--196575 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
196529 ATCGCAACGA
196539 CAACTGTAGACTA-TCG
1 CAACTGTAGACTATTCG
196555 CAACTGTAGACTATTCG
1 CAACTGTAGACTATTCG
196572 CAAC
1 CAAC
196576 GCGAACTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (17 bp):
CAACTGTAGACTATTCG
Found at i:196594 original size:20 final size:20
Alignment explanation
Indices: 196569--196681 Score: 64
Period size: 20 Copynumber: 5.5 Consensus size: 20
196559 TGTAGACTAT
*
196569 TCGCAACGCGAACTGAAAAA
1 TCGCAACGCGAAATGAAAAA
* ** * **
196589 TCGCAACACGATTTTCAACTA
1 TCGCAACGCGA-AATGAAAAA
* *
196610 TCGCAACGCGAAATGGAAAT
1 TCGCAACGCGAAATGAAAAA
** * **
196630 TCGCAACGCGATTTTCAACTA
1 TCGCAACGCGA-AATGAAAAA
*
196651 TCGCAACGCGAAATGTAAAA
1 TCGCAACGCGAAATGAAAAA
*
196671 TCGTAACGCGA
1 TCGCAACGCGA
196682 TTTTCAACTA
Statistics
Matches: 63, Mismatches: 28, Indels: 4
0.66 0.29 0.04
Matches are distributed among these distances:
20 36 0.57
21 27 0.43
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAAATGAAAAA
Found at i:196614 original size:21 final size:21
Alignment explanation
Indices: 196588--196721 Score: 148
Period size: 21 Copynumber: 6.5 Consensus size: 21
196578 GAACTGAAAA
*
196588 ATCGCAACACGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
196609 ATCGCAACGCGAAATGGAAAT
1 ATCGCAACGCGATTTTCAACT
196630 -TCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* * *
196650 ATCGCAACGCGAAATGT-AA-A
1 ATCGCAACGCG-ATTTTCAACT
*
196670 ATCGTAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
196691 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
196712 ATCGCAACGC
1 ATCGCAACGC
196722 AAAATACAAC
Statistics
Matches: 90, Mismatches: 19, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
19 3 0.03
20 27 0.30
21 57 0.63
22 3 0.03
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:196617 original size:41 final size:41
Alignment explanation
Indices: 196564--196702 Score: 215
Period size: 41 Copynumber: 3.4 Consensus size: 41
196554 GCAACTGTAG
* *
196564 ACTATTCGCAACGCGAACTGAAAAATCGCAACACGATTTTCA
1 ACTA-TCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
* *
196606 ACTATCGCAACGCGAAATGGAAATTCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
* *
196647 ACTATCGCAACGCGAAATGTAAAATCGTAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
196688 ACTATCGCAACGCGA
1 ACTATCGCAACGCGA
196703 TTTTCAACTA
Statistics
Matches: 90, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
41 86 0.96
42 4 0.04
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
Found at i:196731 original size:21 final size:21
Alignment explanation
Indices: 196686--196731 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
196676 ACGCGATTTT
* ** *
196686 CAACTATCGCAACGCGATTTT
1 CAACTATCGCAACGCAAAATA
196707 CAACTATCGCAACGCAAAATA
1 CAACTATCGCAACGCAAAATA
196728 CAAC
1 CAAC
196732 GCGAATTTGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.30, G:0.11, T:0.20
Consensus pattern (21 bp):
CAACTATCGCAACGCAAAATA
Done.