Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004029.1 Hibiscus syriacus cultivar Beakdansim tig00008802_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: 61143
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4524 original size:2 final size:2
Alignment explanation
Indices: 4517--4552 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
4507 GTAAAAACTA
*
4517 AT AT AT AT CT 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
4553 GGACATACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13127 original size:20 final size:20
Alignment explanation
Indices: 13099--13136 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
13089 GATTCATTCC
*
13099 TTAACCAAAGTTCAATTATG
1 TTAAACAAAGTTCAATTATG
*
13119 TTAAACAAATTTCAATTA
1 TTAAACAAAGTTCAATTA
13137 CTTTATTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (20 bp):
TTAAACAAAGTTCAATTATG
Found at i:14897 original size:19 final size:19
Alignment explanation
Indices: 14873--14918 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
14863 AAACCCTAAA
14873 TTCCTTTTCAATCTCGAAT
1 TTCCTTTTCAATCTCGAAT
*
14892 TTCCTTTTCGATCTCGAAT
1 TTCCTTTTCAATCTCGAAT
14911 TTCCTTTT
1 TTCCTTTT
14919 TCGCTTCTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.15, C:0.26, G:0.07, T:0.52
Consensus pattern (19 bp):
TTCCTTTTCAATCTCGAAT
Found at i:15040 original size:23 final size:23
Alignment explanation
Indices: 15014--15071 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
15004 GTTGACTTGA
*
15014 ATAAGGAGTACTGAATATCTTTC
1 ATAAGGAGTACTGAATATATTTC
*
15037 ATAAGGAGTACTGAATATATTTT
1 ATAAGGAGTACTGAATATATTTC
15060 ATAAGGAGTACT
1 ATAAGGAGTACT
15072 AAAAGTTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (23 bp):
ATAAGGAGTACTGAATATATTTC
Found at i:16218 original size:23 final size:23
Alignment explanation
Indices: 16192--16249 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
16182 GTTGACTTGA
*
16192 ATAAGGAGTACTGAATATCTTTC
1 ATAAGGAGTACTGAATATATTTC
*
16215 ATAAGGAGTACTGAATATATTTT
1 ATAAGGAGTACTGAATATATTTC
16238 ATAAGGAGTACT
1 ATAAGGAGTACT
16250 AAAAGTTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (23 bp):
ATAAGGAGTACTGAATATATTTC
Found at i:18375 original size:21 final size:21
Alignment explanation
Indices: 18346--18409 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
18336 AGTCGAGGGT
18346 TTCATAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
18367 CTT-ATAGGTCCTTCGGGACATA
1 -TTCATAGGTCCTTCGGGACA-A
* *
18389 TTCACATGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
18410 ACTTCATATG
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
21 20 0.53
22 18 0.47
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (21 bp):
TTCATAGGTCCTTCGGGACAA
Found at i:19022 original size:20 final size:20
Alignment explanation
Indices: 18993--19030 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
18983 AGTTTTTATA
*
18993 CATCGGTGCATTGTAGCATG
1 CATCGATGCATTGTAGCATG
19013 CATCGATGCATTGTAGCA
1 CATCGATGCATTGTAGCA
19031 GGTTATTGTT
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:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (20 bp):
CATCGATGCATTGTAGCATG
Found at i:20623 original size:65 final size:68
Alignment explanation
Indices: 20479--20623 Score: 170
Period size: 71 Copynumber: 2.1 Consensus size: 68
20469 TTTGTGTTTG
* * * *
20479 TTTATTTTTGAAGGTGTTCATGTTTGATTCATGTTTATTTAAATTTTTAGTATCATTTTCATGTT
1 TTTATTTTTGAAGGTATTCATGTCTGATTCATGTTCATTTAAATTTTTAG-ATCA--TTCACGTT
*
20544 CGTTTA
63 CATTTA
* * *
20550 TTTATTTTTGAAGGTATTCATGTCTGGTTCGTGTTCATTTAAATTTTTA-AT-A-TCACGTTTAT
1 TTTATTTTTGAAGGTATTCATGTCTGATTCATGTTCATTTAAATTTTTAGATCATTCACGTTCAT
20612 TTA
66 TTA
20615 TTTATTTTT
1 TTTATTTTT
20624 TAAAGTGTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
65 19 0.29
68 1 0.02
69 2 0.03
71 44 0.67
ACGTcount: A:0.21, C:0.08, G:0.13, T:0.58
Consensus pattern (68 bp):
TTTATTTTTGAAGGTATTCATGTCTGATTCATGTTCATTTAAATTTTTAGATCATTCACGTTCAT
TTA
Found at i:27677 original size:20 final size:21
Alignment explanation
Indices: 27652--27744 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
27642 TTTTCCCAAT
*
27652 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
27672 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
27693 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
27713 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
27734 TCGCAATGCGA
1 TCGCAATGCGA
27745 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:27697 original size:41 final size:41
Alignment explanation
Indices: 27652--27744 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
27642 TTTTCCCAAT
27652 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
27693 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
27734 TCGCAATGCGA
1 TCGCAATGCGA
27745 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:27757 original size:41 final size:41
Alignment explanation
Indices: 27671--27805 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
27661 GAATAAGTAA
* *
27671 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
27712 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
27753 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
27794 TTCGCAACGCGA
1 ATCGCAACGCGA
27806 TTTACATAGC
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:27779 original size:21 final size:20
Alignment explanation
Indices: 27730--27780 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
27720 GCGAATTGGG
* *
27730 AAAATCGCAATGCGATACTG
1 AAAATCGCAATGCGATAATA
**
27750 ACTATCGCAATGCGATAATAA
1 AAAATCGCAATGCGATAAT-A
27771 AAAATCGCAA
1 AAAATCGCAA
27781 CGAGATACTT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.20
Consensus pattern (20 bp):
AAAATCGCAATGCGATAATA
Found at i:28371 original size:19 final size:19
Alignment explanation
Indices: 28326--28373 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
28316 TTCGAGAATG
*
28326 AAAATCGCAACGCGGAAAT
1 AAAATCGCAACGCGGAAAC
*
28345 AACTATCGCAACGC-GAAACC
1 AA-AATCGCAACGCGGAAA-C
28365 AAAATCGCA
1 AAAATCGCA
28374 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.46, C:0.27, G:0.17, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGGAAAC
Found at i:28391 original size:19 final size:19
Alignment explanation
Indices: 28369--28553 Score: 156
Period size: 19 Copynumber: 10.1 Consensus size: 19
28359 GAAACCAAAA
*
28369 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
28388 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
28407 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
28426 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
* *
28446 TCGTGTTGCGATTGTC--T
1 TCGCGTTGCGATTTTCATT
* **
28463 T---GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
28479 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
28493 TCTCATTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
28512 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
28532 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
28552 TC
1 TC
28554 AACCAAAAGA
Statistics
Matches: 135, Mismatches: 18, Indels: 26
0.75 0.10 0.15
Matches are distributed among these distances:
14 19 0.14
16 4 0.03
17 4 0.03
19 60 0.44
20 47 0.35
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:28446 original size:39 final size:38
Alignment explanation
Indices: 28369--28553 Score: 156
Period size: 33 Copynumber: 5.1 Consensus size: 38
28359 GAAACCAAAA
*
28369 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
28407 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * * **
28446 TCGTGTTGCGATTGTC--TT---GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* * **
28479 TCGCGTTGCGA--TTC---TCTCATTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
28512 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
28552 TC
1 TC
28554 AACCAAAAGA
Statistics
Matches: 120, Mismatches: 16, Indels: 21
0.76 0.10 0.13
Matches are distributed among these distances:
30 1 0.01
31 2 0.02
33 36 0.30
34 10 0.08
36 2 0.02
37 2 0.02
38 21 0.17
39 29 0.24
40 17 0.14
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:28530 original size:20 final size:20
Alignment explanation
Indices: 28507--28553 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
28497 ATTGCGATAG
28507 TCATTTCCGCGTTGCGATTC
1 TCATTTCCGCGTTGCGATTC
* *
28527 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCGATTC
28547 TCATTTC
1 TCATTTC
28554 AACCAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATTC
Found at i:30629 original size:21 final size:21
Alignment explanation
Indices: 30605--30671 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
30595 TCATTCCTTG
30605 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
30626 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
30647 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
30668 AGAG
1 AGAG
30672 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:32049 original size:14 final size:14
Alignment explanation
Indices: 32030--32065 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
32020 ATTGTTTAAT
32030 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
32044 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
32058 TGATTTGT
1 TGATTTGT
32066 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:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:32246 original size:19 final size:19
Alignment explanation
Indices: 32224--32392 Score: 152
Period size: 19 Copynumber: 9.7 Consensus size: 19
32214 CGAAATTAAA
*
32224 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
32243 TTCGTATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
32262 TTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
32281 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
32297 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
32314 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
32328 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
32347 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
32363 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
32380 TTCGCAATGCGAT
1 TTCGCATTGCGAT
32393 AGTAATTTCC
Statistics
Matches: 119, Mismatches: 16, Indels: 30
0.72 0.10 0.18
Matches are distributed among these distances:
14 23 0.19
16 13 0.11
17 13 0.11
19 70 0.59
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:32310 original size:33 final size:33
Alignment explanation
Indices: 32228--32392 Score: 206
Period size: 33 Copynumber: 4.8 Consensus size: 33
32218 ATTAAATTCG
* *
32228 CGTTGCGATTTTCATTTCGTATTGCGATTTTCATTT
1 CGTTGCGATTTTCATTTCGCATTGCGA--TTC-TCT
*
32264 CGCATTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CG--TTGCGATTTTCATTTCGCATTGCGATTCTCT
* **
32299 CGTTGCGATTTTCATTTCGCATTGCGAAAT-TAG
1 CGTTGCGATTTTCATTTCGCATTGCG-ATTCTCT
32332 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
32365 CGTTGCGATTTTCATTTCGCAATGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
32393 AGTAATTTCC
Statistics
Matches: 114, Mismatches: 11, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
32 2 0.02
33 78 0.68
34 2 0.02
35 3 0.03
36 5 0.04
38 24 0.21
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:32359 original size:66 final size:66
Alignment explanation
Indices: 32268--32391 Score: 230
Period size: 66 Copynumber: 1.9 Consensus size: 66
32258 TCATTTCGCA
*
32268 TTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAAATTAGC
1 TTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCAATGCGAAATTAGC
32333 G
66 G
*
32334 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCAATGCGA
1 TTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCAATGCGA
32392 TAGTAATTTC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.42
Consensus pattern (66 bp):
TTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCAATGCGAAATTAGC
G
Found at i:34710 original size:12 final size:12
Alignment explanation
Indices: 34693--34717 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34683 TCTTCGGGGA
34693 CTTTTTCTTCTT
1 CTTTTTCTTCTT
34705 CTTTTTCTTCTT
1 CTTTTTCTTCTT
34717 C
1 C
34718 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:37688 original size:19 final size:18
Alignment explanation
Indices: 37662--37767 Score: 103
Period size: 19 Copynumber: 5.9 Consensus size: 18
37652 ACGAAACTTA
37662 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
*
37680 ACTATCGCAACGCGGAAATGG
1 A-AATCGCAACGC-GAAAT-G
** *
37701 CTATCGCAATGCGAAATG
1 AAATCGCAACGCGAAATG
*
37719 AAAATCGCAA--CGACA--
1 -AAATCGCAACGCGAAATG
37734 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
37752 AAATCGCAACGCGAAA
1 AAATCGCAACGCGAAA
37768 CACAAATCGC
Statistics
Matches: 73, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 4 0.05
18 18 0.25
19 22 0.30
20 15 0.21
21 1 0.01
ACGTcount: A:0.42, C:0.24, G:0.22, T:0.12
Consensus pattern (18 bp):
AAATCGCAACGCGAAATG
Found at i:37688 original size:39 final size:37
Alignment explanation
Indices: 37645--37778 Score: 102
Period size: 39 Copynumber: 3.6 Consensus size: 37
37635 TAGTTTACTT
*
37645 TCGCAACACGAAACTTAAAATCGCAACGCGAAATGACTA
1 TCGCAACACGAAAC-TAAAATCGCAACGCGAAATGA-AA
* *** *
37684 TCGCAACGCGGAAA-TGGCTATCGCAATGCGAAATGAAAA
1 TCGCAACAC-GAAACT-AAAATCGCAACGCGAAATG-AAA
37723 TCGC-A-ACG--AC-AAAATCGCAACGCGAAATGAAA
1 TCGCAACACGAAACTAAAATCGCAACGCGAAATGAAA
*
37755 TCGCAACGCGAAAC-ACAAATCGCA
1 TCGCAACACGAAACTA-AAATCGCA
37779 TTGCGATTTT
Statistics
Matches: 74, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
32 7 0.09
33 16 0.22
34 3 0.04
36 4 0.05
37 9 0.12
38 2 0.03
39 28 0.38
40 5 0.07
ACGTcount: A:0.43, C:0.25, G:0.19, T:0.13
Consensus pattern (37 bp):
TCGCAACACGAAACTAAAATCGCAACGCGAAATGAAA
Found at i:37776 original size:19 final size:18
Alignment explanation
Indices: 37734--37778 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
37724 CGCAACGACA
**
37734 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAAAC
37752 AAATCGCAACGCGAAACAC
1 AAATCGCAACGCGAAA-AC
37771 AAATCGCA
1 AAATCGCA
37779 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.09
Consensus pattern (18 bp):
AAATCGCAACGCGAAAAC
Found at i:37796 original size:19 final size:19
Alignment explanation
Indices: 37774--37855 Score: 95
Period size: 18 Copynumber: 4.6 Consensus size: 19
37764 GAAACACAAA
37774 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
37793 TCGCGTTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
* *
37811 TCGCTTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
37827 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
37844 TCGCATTGCGAT
1 TCGCATTGCGAT
37856 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
14 6 0.11
15 3 0.06
16 4 0.07
17 4 0.07
18 20 0.37
19 17 0.31
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:37874 original size:20 final size:19
Alignment explanation
Indices: 37840--37894 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
37830 TTGCGATTTT
*
37840 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
37859 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
37879 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
37895 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:38397 original size:18 final size:18
Alignment explanation
Indices: 38376--38411 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
38366 ATGATGGCTA
*
38376 TGGGTGAGGTGATAGCTC
1 TGGGCGAGGTGATAGCTC
*
38394 TGGGCGAGGTGATGGCTC
1 TGGGCGAGGTGATAGCTC
38412 CCGAAGTGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.14, G:0.47, T:0.25
Consensus pattern (18 bp):
TGGGCGAGGTGATAGCTC
Found at i:39754 original size:20 final size:20
Alignment explanation
Indices: 39729--39766 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
39719 AATAGTTTCT
39729 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
39749 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
39767 GAGAGAATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:39815 original size:19 final size:19
Alignment explanation
Indices: 39793--39843 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
39783 GAAACTAAAA
39793 TCGCGTTGCGATTTGCATT
1 TCGCGTTGCGATTTGCATT
39812 TCGCGTTGCGATTTGCATT
1 TCGCGTTGCGATTTGCATT
*
39831 TCGCGTTCCGATT
1 TCGCGTTGCGATT
39844 CTTGGTTGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.10, C:0.24, G:0.25, T:0.41
Consensus pattern (19 bp):
TCGCGTTGCGATTTGCATT
Found at i:40305 original size:20 final size:20
Alignment explanation
Indices: 40280--40373 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
40270 GATTATGTAT
40280 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
40300 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
40320 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
40341 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
40361 TATCGCATTGCGA
1 TATCGCGTTGCGA
40374 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:40345 original size:41 final size:41
Alignment explanation
Indices: 40300--40377 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
40290 CGAAAGTCAG
* * *
40300 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
40341 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
40378 CCCAATTCGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:40374 original size:20 final size:20
Alignment explanation
Indices: 40260--40374 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
40250 CGCTTTGAAA
*
40260 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
40281 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
40301 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
40321 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
40342 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
40362 ATCGCATTGCGAT
1 ATCGCATTGCGAT
40375 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:40392 original size:21 final size:21
Alignment explanation
Indices: 40363--40496 Score: 130
Period size: 20 Copynumber: 6.5 Consensus size: 21
40353 ATAGTCAGTA
40363 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
40384 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
40404 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
40425 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
*
40445 TCGCATTGTGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
40466 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
40486 TCGCATTGCGA
1 TCGCATTGCGA
40497 ATTGGAAAAA
Statistics
Matches: 88, Mismatches: 23, Indels: 5
0.76 0.20 0.04
Matches are distributed among these distances:
20 47 0.53
21 41 0.47
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:40393 original size:41 final size:41
Alignment explanation
Indices: 40363--40496 Score: 232
Period size: 41 Copynumber: 3.3 Consensus size: 41
40353 ATAGTCAGTA
*
40363 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACGTAT
*
40404 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACGTAT
* *
40445 TCGCATTGTGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACGTAT
40486 TCGCATTGCGA
1 TCGCATTGCGA
40497 ATTGGAAAAA
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 91 1.00
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACGTAT
Found at i:40413 original size:82 final size:82
Alignment explanation
Indices: 40343--40496 Score: 240
Period size: 82 Copynumber: 1.9 Consensus size: 82
40333 TTTTTTATTA
40343 TCGCATTGCGATAGTCA-GTA-TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTC
1 TCGCATTGCGAT--TCACGTATTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTC
40406 GCATTGCGATTTTCCCAAT
64 GCATTGCGATTTTCCCAAT
* * * *
40425 TCGCGTTGCGATTTACTTATTCGCATTGTGATTTTCCCAATTCGCGTTGCGATTTACTTATTCGC
1 TCGCATTGCGATTCACGTATTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCGC
40490 ATTGCGA
66 ATTGCGA
40497 ATTGGAAAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
80 2 0.03
81 2 0.03
82 62 0.94
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.40
Consensus pattern (82 bp):
TCGCATTGCGATTCACGTATTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCGC
ATTGCGATTTTCCCAAT
Found at i:41526 original size:21 final size:21
Alignment explanation
Indices: 41487--41527 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
41477 TTGCTGCCAT
* *
41487 GGTATCGATACCATGCTACAG
1 GGTACCGATACCATACTACAG
*
41508 GGTACCGATACCCTACTACA
1 GGTACCGATACCATACTACA
41528 ATACTGCTAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (21 bp):
GGTACCGATACCATACTACAG
Found at i:42120 original size:18 final size:18
Alignment explanation
Indices: 42097--42131 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
42087 ACTGAATATT
42097 TGTCCC-AAAGGACCACTA
1 TGTCCCGAAA-GACCACTA
42115 TGTCCCGAAAGACCACT
1 TGTCCCGAAAGACCACT
42132 GATAATCCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.31, C:0.34, G:0.17, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAAGACCACTA
Found at i:45796 original size:13 final size:13
Alignment explanation
Indices: 45771--45804 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
45761 TCATAACGTC
*
45771 ATAATTCAAACTT
1 ATAATTTAAACTT
*
45784 ATGATTTAAACTT
1 ATAATTTAAACTT
45797 ATAATTTA
1 ATAATTTA
45805 CTTGAAAGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (13 bp):
ATAATTTAAACTT
Found at i:49784 original size:32 final size:32
Alignment explanation
Indices: 49748--49814 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
49738 AAGTTCCATT
49748 AATGGATATCAAACCAGGTTAAATTAAATTAA
1 AATGGATATCAAACCAGGTTAAATTAAATTAA
49780 AATGGATATCAAACCAGGTTAAATTAAATTAA
1 AATGGATATCAAACCAGGTTAAATTAAATTAA
49812 AAT
1 AAT
49815 AAATTTAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.28
Consensus pattern (32 bp):
AATGGATATCAAACCAGGTTAAATTAAATTAA
Found at i:50720 original size:21 final size:21
Alignment explanation
Indices: 50683--50737 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
50673 ATTCGTAATG
*
50683 CGAAAATC-AATTTCGCAACA
1 CGAAAATCGAAATTCGCAACA
*
50703 CGAAAATCGAAATTCGCAACG
1 CGAAAATCGAAATTCGCAACA
*
50724 CGAAAGTCGAAATT
1 CGAAAATCGAAATT
50738 TGACACGTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 8 0.26
21 23 0.74
ACGTcount: A:0.44, C:0.22, G:0.16, T:0.18
Consensus pattern (21 bp):
CGAAAATCGAAATTCGCAACA
Found at i:50911 original size:19 final size:19
Alignment explanation
Indices: 50880--50930 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
50870 TGGAACCTAT
50880 GTTGCGAAATTTGA-ATTCGC
1 GTTGCG-AATTTGAGA-TCGC
*
50900 GTTGTGAATTTGAGATCGC
1 GTTGCGAATTTGAGATCGC
50919 GTTGCGAATTTG
1 GTTGCGAATTTG
50931 TTGGTCATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 22 0.79
20 6 0.21
ACGTcount: A:0.22, C:0.12, G:0.29, T:0.37
Consensus pattern (19 bp):
GTTGCGAATTTGAGATCGC
Found at i:52344 original size:39 final size:40
Alignment explanation
Indices: 52300--52378 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
52290 GGTTTCTTTG
* * *
52300 TTTATGATG-TCAACCCTCCCTTCTGTTTATCGATTTTTT
1 TTTATGATGACCAACCCTCCCTCCTATTTATCGATTTTTT
* *
52339 TTTATGATGACCAACCCTCTCTCCTATTTATCTATTTTTT
1 TTTATGATGACCAACCCTCCCTCCTATTTATCGATTTTTT
52379 AAAATTTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
39 9 0.26
40 25 0.74
ACGTcount: A:0.18, C:0.24, G:0.08, T:0.51
Consensus pattern (40 bp):
TTTATGATGACCAACCCTCCCTCCTATTTATCGATTTTTT
Found at i:54399 original size:15 final size:15
Alignment explanation
Indices: 54362--54399 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
54352 TTATTATAAA
54362 TTATAAATATTTTTT
1 TTATAAATATTTTTT
*
54377 TT-TTAATATTTTTT
1 TTATAAATATTTTTT
*
54391 TTATCAATA
1 TTATAAATA
54400 ATACATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATAAATATTTTTT
Done.