Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008156.1 Hibiscus syriacus cultivar Beakdansim tig00110722_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: 820393
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:771385 original size:20 final size:20
Alignment explanation
Indices: 771299--771392 Score: 98
Period size: 20 Copynumber: 4.7 Consensus size: 20
771289 TTTTCCTAAT
*
771299 TCGCAACGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
771319 TCGTAACGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
771339 TCGCAATGCAAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
* *
771360 TTGCAATACGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
771380 TCGCAATGCGAAT
1 TCGCAATGCGAAT
771393 CTGACTATCG
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 43 0.74
21 15 0.26
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:772115 original size:19 final size:19
Alignment explanation
Indices: 771944--772109 Score: 197
Period size: 19 Copynumber: 8.5 Consensus size: 19
771934 TTCTAAACTT
**
771944 AAAATCGCAACATGAAAATG
1 AAAATCGCAACGCG-AAATG
*
771964 AAAATCGCAACACGAAAAATG
1 AAAATCGCAACGCG--AAATG
** *
771985 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAAC--GCGAAATG
**
772006 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
772025 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
772044 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
772063 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
**
772082 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATG
772101 AAAATCGCA
1 AAAATCGCA
772110 TTGCGATTTT
Statistics
Matches: 133, Mismatches: 10, Indels: 7
0.89 0.07 0.05
Matches are distributed among these distances:
19 88 0.66
20 13 0.10
21 31 0.23
23 1 0.01
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:772192 original size:33 final size:34
Alignment explanation
Indices: 772141--772206 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
772131 GATTTTAATT
* **
772141 TCTCTTTGCGATTTTCATTT-CGCGTTGCGATTC
1 TCTCATTGCGATAGTCATTTCCGCGTTGCGATTC
772174 TCTCATTGCGATAGTCATTTCCGCGTTGCGATT
1 TCTCATTGCGATAGTCATTTCCGCGTTGCGATT
772207 TTCATTCTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 17 0.59
34 12 0.41
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (34 bp):
TCTCATTGCGATAGTCATTTCCGCGTTGCGATTC
Found at i:772211 original size:20 final size:19
Alignment explanation
Indices: 772110--772234 Score: 111
Period size: 20 Copynumber: 6.8 Consensus size: 19
772100 CAAAATCGCA
772110 TTGCGATTTTCA-TT-TCG
1 TTGCGATTTTCATTTCTCG
* *
772127 TTGCGATTTTAATTTCTCT
1 TTGCGATTTTCATTTCTCG
*
772146 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCTCG
*
772165 TTGCGA--TTC---TCTCA
1 TTGCGATTTTCATTTCTCG
** *
772179 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CTCG
772199 TTGCGATTTTCATTCTCTCG
1 TTGCGATTTTCATT-TCTCG
*
772219 TTGCGATTTTTATTTC
1 TTGCGATTTTCATTTC
772235 AACCAAAAGA
Statistics
Matches: 85, Mismatches: 14, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
14 9 0.11
16 2 0.02
17 14 0.16
18 2 0.02
19 27 0.32
20 30 0.35
21 1 0.01
ACGTcount: A:0.13, C:0.21, G:0.17, T:0.50
Consensus pattern (19 bp):
TTGCGATTTTCATTTCTCG
Found at i:774091 original size:94 final size:94
Alignment explanation
Indices: 773930--774309 Score: 656
Period size: 94 Copynumber: 4.1 Consensus size: 94
773920 TAGATTGCTT
*
773930 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
773995 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
774024 AGTAAATTTATTCGGTTACTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
774089 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * *
774118 AGTAAATTTGTTCAGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
774183 ATTTGTCTTTTTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * *
774212 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
774277 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
774305 AGTAA
1 AGTAA
774310 TGCAATCCAT
Statistics
Matches: 273, Mismatches: 12, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
93 26 0.10
94 247 0.90
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:774455 original size:33 final size:33
Alignment explanation
Indices: 774416--774498 Score: 130
Period size: 33 Copynumber: 2.5 Consensus size: 33
774406 ACGTAAAATG
* *
774416 AAAATCGCAACGCGAAATGAAAATCACAATGAG
1 AAAATCGCAACGCGAAATGAAAATCACAACGAC
* *
774449 AGAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAATGAAAATCACAACGAC
774482 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
774499 CCAAAAATCG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.49, C:0.22, G:0.19, T:0.10
Consensus pattern (33 bp):
AAAATCGCAACGCGAAATGAAAATCACAACGAC
Found at i:774475 original size:19 final size:19
Alignment explanation
Indices: 774360--774518 Score: 95
Period size: 19 Copynumber: 8.7 Consensus size: 19
774350 TAGTTTACTT
* *
774360 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* **
774380 TCGCAACGTGAAAAATGACTA
1 TCGCAACGCG--AAATGAAAA
**
774401 TCGCAACGTAAAATGAAAA
1 TCGCAACGCGAAATGAAAA
774420 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
* * *
774439 TCACAA--TG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
774453 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
774472 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
**
774486 TCGCAACGCGAAACCAAAAA
1 TCGCAACGCGAAA-TGAAAA
774506 TCGCAACGCGAAA
1 TCGCAACGCGAAA
774519 CCATAATCGC
Statistics
Matches: 108, Mismatches: 18, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
14 19 0.18
15 2 0.02
16 3 0.03
17 3 0.03
18 2 0.02
19 39 0.36
20 25 0.23
21 12 0.11
22 3 0.03
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:774505 original size:20 final size:20
Alignment explanation
Indices: 774482--774521 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
774472 TCGCAACGAC
774482 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAACCA
774502 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAACCA
774522 TAATCGCGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.30, G:0.15, T:0.05
Consensus pattern (20 bp):
AAAATCGCAACGCGAAACCA
Found at i:774547 original size:19 final size:19
Alignment explanation
Indices: 774525--774622 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
774515 GAAACCATAA
774525 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
774544 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
774558 TCTCGTTGTGATTTTCATT
1 TCGCGTTGCGATTTTCATT
774577 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
774591 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
774610 TTGCGTTGCGATT
1 TCGCGTTGCGATT
774623 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 9, Indels: 20
0.67 0.10 0.22
Matches are distributed among these distances:
14 18 0.30
16 6 0.10
17 6 0.10
19 30 0.50
ACGTcount: A:0.10, C:0.21, G:0.21, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:774571 original size:33 final size:33
Alignment explanation
Indices: 774528--774636 Score: 191
Period size: 33 Copynumber: 3.3 Consensus size: 33
774518 ACCATAATCG
*
774528 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
774561 CGTTGTGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
774594 CGTTGCGATTTTCATTTTGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
774627 CGTTGCGATT
1 CGTTGCGATT
774637 CATTTTGTGT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 72 1.00
ACGTcount: A:0.10, C:0.22, G:0.21, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:774599 original size:14 final size:14
Alignment explanation
Indices: 774580--774637 Score: 62
Period size: 14 Copynumber: 3.8 Consensus size: 14
774570 TTTCATTTCG
774580 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
774594 CGTTGCGATTTTCATTTT
1 CGTTGCGA--TTC--TCT
774612 GCGTTGCGATTCTCT
1 -CGTTGCGATTCTCT
774627 CGTTGCGATTC
1 CGTTGCGATTC
774638 ATTTTGTGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 19 0.51
15 2 0.05
16 3 0.08
17 3 0.08
18 2 0.05
19 8 0.22
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:775153 original size:42 final size:42
Alignment explanation
Indices: 775077--775165 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
775067 GACTCACCTG
* * *
775077 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * * *
775119 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
775161 TCATC
1 TCATC
775166 GTTGAAGAGA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:776687 original size:19 final size:19
Alignment explanation
Indices: 776663--776717 Score: 92
Period size: 19 Copynumber: 2.9 Consensus size: 19
776653 TTGAAGGCAA
* *
776663 AAATGAATATCGCAATGCG
1 AAATGAAAATCGCAACGCG
776682 AAATGAAAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
776701 AAATGAAAATCGCAACG
1 AAATGAAAATCGCAACG
776718 ACAAAATCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (19 bp):
AAATGAAAATCGCAACGCG
Found at i:776764 original size:19 final size:19
Alignment explanation
Indices: 776742--776859 Score: 85
Period size: 19 Copynumber: 6.7 Consensus size: 19
776732 CGAAACTAAA
776742 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
776761 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
776776 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
776794 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
776809 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
776827 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
776846 TTCTGCGTTGCGAT
1 TTC-GCGTTGCGAT
776860 AGACATTAAG
Statistics
Matches: 74, Mismatches: 14, Indels: 21
0.68 0.13 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 36 0.49
20 9 0.12
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:776788 original size:33 final size:33
Alignment explanation
Indices: 776746--776839 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
776736 ACTAAATTCG
776746 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
776779 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
776812 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
776840 AGTCATTTCT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:776858 original size:20 final size:19
Alignment explanation
Indices: 776812--776866 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
776802 GCGATTCTCT
**
776812 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
776831 CATTGCGATAGTCATTTCTG
1 CGTTGCGATAGTCATTTC-G
*
776851 CGTTGCGATAGACATT
1 CGTTGCGATAGTCATT
776867 AAGATGATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:779409 original size:24 final size:24
Alignment explanation
Indices: 779375--779428 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
779365 CTGAAAAATC
779375 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
779399 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
779423 ATCAAA
1 ATCAAA
779429 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:779442 original size:24 final size:24
Alignment explanation
Indices: 779375--779442 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
779365 CTGAAAAATC
* * *
779375 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
779399 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
779423 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
779443 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:780314 original size:20 final size:21
Alignment explanation
Indices: 780291--780417 Score: 104
Period size: 20 Copynumber: 6.3 Consensus size: 21
780281 AGAATCCCGT
780291 TGCGATTTAC-TAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
780311 TGCGA-TTACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
** **
780331 TGC-AAATACGT-AATCGCGT
1 TGCGATTTACGTAAATCGCAA
**
780350 TGCGATTTACGT-AATCGCGT
1 TGCGATTTACGTAAATCGCAA
* *
780370 TGCGATTTAGGAAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
* * *
780391 CGCGAATTT-GGGAAATCGCAA
1 TGCG-ATTTACGTAAATCGCAA
780412 TGCGAT
1 TGCGAT
780418 AGTCAGAATC
Statistics
Matches: 90, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
19 14 0.16
20 49 0.54
21 23 0.26
22 4 0.04
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (21 bp):
TGCGATTTACGTAAATCGCAA
Found at i:780404 original size:22 final size:21
Alignment explanation
Indices: 780374--780416 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
780364 TCGCGTTGCG
780374 ATTTAGGAAAATCGCAACGCGA
1 ATTTAGG-AAATCGCAACGCGA
* *
780396 ATTTGGGAAATCGCAATGCGA
1 ATTTAGGAAATCGCAACGCGA
780417 TAGTCAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (21 bp):
ATTTAGGAAATCGCAACGCGA
Found at i:787722 original size:15 final size:14
Alignment explanation
Indices: 787704--787737 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
787694 AATTGATGAG
787704 TTTTT-AAAATAAT
1 TTTTTAAAAATAAT
787717 ATTTTTAAAAATAAT
1 -TTTTTAAAAATAAT
787732 TTTTTA
1 TTTTTA
787738 GTTAAATTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTTTAAAAATAAT
Found at i:788803 original size:35 final size:37
Alignment explanation
Indices: 788732--788804 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 37
788722 ATTGGAAAAT
* *
788732 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
*
788769 ATTTATATATTTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
788804 A
1 A
788805 AATGTTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 6 0.18
36 14 0.42
37 13 0.39
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:788807 original size:37 final size:37
Alignment explanation
Indices: 788727--788807 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
788717 AACAAATTGG
* *
788727 AAAATATTTATATATTTTCTTTAAAAAATTTAAATTC
1 AAAAAATTTATATATTTTCTTTAAAAAATTAAAATTC
* *
788764 ATAAAATTTATATATTTT-TTTACAAAATTGAAAATAT-
1 AAAAAATTTATATATTTTCTTTAAAAAATT-AAAAT-TC
788801 AAAAAAT
1 AAAAAAT
788808 GTTTAATGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
36 10 0.27
37 26 0.70
38 1 0.03
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (37 bp):
AAAAAATTTATATATTTTCTTTAAAAAATTAAAATTC
Found at i:792371 original size:18 final size:17
Alignment explanation
Indices: 792344--792378 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
792334 GCACCAAGTG
792344 TGCATCGATGTATGAAA
1 TGCATCGATGTATGAAA
*
792361 TGCATTCGATGTTTGAAA
1 TGCA-TCGATGTATGAAA
792379 AATAGCCTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.34
Consensus pattern (17 bp):
TGCATCGATGTATGAAA
Found at i:792390 original size:64 final size:63
Alignment explanation
Indices: 792322--792502 Score: 209
Period size: 64 Copynumber: 2.8 Consensus size: 63
792312 TTGGAACACT
* *** *
792322 TGATGCATCGGTGCACCAAGTGTGCATCGATGTATGAAATGCATTCGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCC
** * **
792386 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCC
* * * *
792450 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTT
792503 CAATTAATTC
Statistics
Matches: 98, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
64 53 0.54
65 45 0.46
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.30
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
Found at i:792474 original size:19 final size:19
Alignment explanation
Indices: 792450--792500 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
792440 GAAAATATTC
792450 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
792469 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
792488 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
792501 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:792476 original size:65 final size:65
Alignment explanation
Indices: 792343--792502 Score: 207
Period size: 65 Copynumber: 2.5 Consensus size: 65
792333 TGCACCAAGT
* * ***
792343 GTGCATCGATGTATGAAATGCATTCGATG-TTTGAAAAATAGCCTGATGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
* **
792407 GTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGA-TGCATCGATGCATGGAG
792471 A
65 A
* *
792472 GTGCATCGGTGCATGGAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
792503 CAATTAATTC
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 36 0.43
65 47 0.57
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
Found at i:792542 original size:65 final size:64
Alignment explanation
Indices: 792344--792551 Score: 187
Period size: 65 Copynumber: 3.2 Consensus size: 64
792334 GCACCAAGTG
* * * * * *
792344 TGCATCGATGTATGAAATGCATTCGATGTTTGAAAA-ATAGCCTGATGCATCGATGCATGGCTTG
1 TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAATAT-TCATGATGCATCGATGCATGAC-TG
792408 -
64 A
* * *
792408 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGA--
1 TGCATCGGTGCATGAAATGCATTCGATG-TTTCAAAATATTCATGA-TGCATCGATGCAT-GACT
792470 GA
63 GA
* *
792472 GTGCATCGGTGCATGGAATGCATTCGATG-TTC-AATTAATTCATTGATGCATCGATGCATGTAC
1 -TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAAT-ATTCA-TGATGCATCGATGCATG-AC
792535 TGA
62 TGA
792538 TGCATCGGTGCATG
1 TGCATCGGTGCATG
792552 CCTTTGAATA
Statistics
Matches: 122, Mismatches: 10, Indels: 23
0.79 0.06 0.15
Matches are distributed among these distances:
62 3 0.02
63 9 0.07
64 42 0.34
65 63 0.52
66 5 0.04
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.31
Consensus pattern (64 bp):
TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAATATTCATGATGCATCGATGCATGACTGA
Found at i:792919 original size:25 final size:25
Alignment explanation
Indices: 792891--792942 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
792881 CTTACTCCCC
792891 CTTACTATAACACATCTTAAATTTT
1 CTTACTATAACACATCTTAAATTTT
*
792916 CTTACTATATCACATCTTAAATTTT
1 CTTACTATAACACATCTTAAATTTT
792941 CT
1 CT
792943 CCCCCTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.46
Consensus pattern (25 bp):
CTTACTATAACACATCTTAAATTTT
Found at i:800933 original size:64 final size:63
Alignment explanation
Indices: 800863--801043 Score: 200
Period size: 64 Copynumber: 2.8 Consensus size: 63
800853 CGTTGGAACT
* ***
800863 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCC
** * * **
800927 TGATGCATCGATGCATGGCTTGTGAATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCC
* * * * *
800991 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCAATGTT
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTT
801044 CAATTAATTC
Statistics
Matches: 96, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
64 53 0.55
65 43 0.45
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
Found at i:801015 original size:19 final size:19
Alignment explanation
Indices: 800991--801029 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
800981 GAAAATATTC
800991 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
801010 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
801029 A
1 A
801030 ATGCATTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.38, T:0.21
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:801026 original size:65 final size:65
Alignment explanation
Indices: 800884--801043 Score: 198
Period size: 65 Copynumber: 2.5 Consensus size: 65
800874 TGCACCAAGT
* ***
800884 GTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGATGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
* * **
800948 GTGAATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGA-TGCATCGATGCATGGAG
801012 A
65 A
* * *
801013 GTGCATCGGTGCATGGAATGCATTCAATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
801044 CAATTAATTC
Statistics
Matches: 81, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
64 36 0.44
65 45 0.56
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
Found at i:801283 original size:20 final size:21
Alignment explanation
Indices: 801260--801299 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
801250 GAATCGAATA
801260 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
801280 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
801300 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:802341 original size:20 final size:20
Alignment explanation
Indices: 802316--802371 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
802306 AAAACCCGAA
*
802316 GGGGGTATCGGTACCCTTAT
1 GGGGGTATCGGTACCCTCAT
802336 GGGGGTATCGGTACCCTCAT
1 GGGGGTATCGGTACCCTCAT
*
802356 GGGGGTATAGGTACCC
1 GGGGGTATCGGTACCC
802372 ATTCAAAGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.16, C:0.21, G:0.38, T:0.25
Consensus pattern (20 bp):
GGGGGTATCGGTACCCTCAT
Found at i:802393 original size:23 final size:23
Alignment explanation
Indices: 802358--802402 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
802348 ACCCTCATGG
*
802358 GGGTATAGGTACCCATTCAAAGA
1 GGGTATAGATACCCATTCAAAGA
*
802381 GGGTATCGATACCCATTCAAAG
1 GGGTATAGATACCCATTCAAAG
802403 GGGGCATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.22
Consensus pattern (23 bp):
GGGTATAGATACCCATTCAAAGA
Found at i:802415 original size:23 final size:23
Alignment explanation
Indices: 802367--802416 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
802357 GGGGTATAGG
* *
802367 TACCCATTCAAAGAGGGTATCGA
1 TACCCATTCAAAGAGGGCATCAA
* *
802390 TACCCATTCAAAGGGGGCATTAA
1 TACCCATTCAAAGAGGGCATCAA
802413 TACC
1 TACC
802417 TAACGTACAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (23 bp):
TACCCATTCAAAGAGGGCATCAA
Found at i:806071 original size:20 final size:21
Alignment explanation
Indices: 806033--806071 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
806023 ACGCTTTAAA
* *
806033 ATCATCAATTTTCTTTTGATG
1 ATCATCAATTTACTCTTGATG
806054 ATCATC-ATTTACTCTTGA
1 ATCATCAATTTACTCTTGA
806072 AAGTAAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.49
Consensus pattern (21 bp):
ATCATCAATTTACTCTTGATG
Found at i:808603 original size:29 final size:30
Alignment explanation
Indices: 808568--808634 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
808558 AAGTCAATGT
* * *
808568 AACCACCGAATTATTT-TTTGTTTCAATCA
1 AACCACCGAACTATTTAATTGATTCAATCA
* *
808597 GACCACCAAACTATTTAATTGATTCAATCA
1 AACCACCGAACTATTTAATTGATTCAATCA
808627 AACCACCG
1 AACCACCG
808635 GCCATTAATT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
29 13 0.43
30 17 0.57
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.31
Consensus pattern (30 bp):
AACCACCGAACTATTTAATTGATTCAATCA
Found at i:809152 original size:68 final size:68
Alignment explanation
Indices: 809073--809311 Score: 276
Period size: 68 Copynumber: 3.6 Consensus size: 68
809063 TAAATAAATT
** *** *
809073 ATTTTTTCTTTAACCATTAATTAAATTTAAATTTATTTGAAAATTATTAACCGAACCGAATTAAT
1 ATTTTTTCTTTAACCATTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAAT
809138 CAA
66 CAA
* ** *
809141 ATTTTTTCTTTAACCATTAATCGAACCGAAATTTATTTGGAAATTATTAACCGAATAAAATAAAT
1 ATTTTTTCTTTAACCATTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAAT
*
809206 --T
66 CAA
* * *
809207 A-TTTTTCTTTAACCGTTAATCGAACCGAAATGTATTT-AAAATTATTAACCGAACCAAATTAAC
1 ATTTTTTCTTTAACCATTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAAT
*
809270 CGA
66 CAA
809273 ATTTGTTTCTTTAA-CATTAATCGAACC-AAGA-TTATTTGA
1 ATTT-TTTCTTTAACCATTAATCGAACCGAA-ATTTATTTGA
809312 CCGTTAATCG
Statistics
Matches: 144, Mismatches: 21, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
64 21 0.15
65 34 0.24
66 9 0.06
67 16 0.11
68 64 0.44
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (68 bp):
ATTTTTTCTTTAACCATTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAAT
CAA
Found at i:809362 original size:94 final size:94
Alignment explanation
Indices: 809214--809447 Score: 373
Period size: 94 Copynumber: 2.5 Consensus size: 94
809204 ATTATTTTTC
* *
809214 TTTAACCGTTAATCGAACCGAAATGTATTT-AAAATTATTAACCGAACCAAATTAACCGAATTTG
1 TTTAACCGTTAATCGAATCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGAATTTG
809278 TTTCTTTAACATTAATCGAACC-AAGATTA
66 TTTCTTTAACATTAATCGAACCGAA-ATTA
* * *
809307 TTTGACCGTTAATCGAATCGAAATTTATTTGAAAATTATTAACTGAACCAAATTAACCGAATTTT
1 TTTAACCGTTAATCGAATCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGAATTTG
*
809372 TTTCTTTAACGTTAATCGAACCGAAATTA
66 TTTCTTTAACATTAATCGAACCGAAATTA
* *
809401 TTTAACTGTTAATCGAATCGAAATTTATTTGAATATTATTAACCGAA
1 TTTAACCGTTAATCGAATCGAAATTTATTTGAAAATTATTAACCGAA
809448 TTTTTTTCTT
Statistics
Matches: 129, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
93 27 0.21
94 100 0.78
95 2 0.02
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (94 bp):
TTTAACCGTTAATCGAATCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGAATTTG
TTTCTTTAACATTAATCGAACCGAAATTA
Found at i:809414 original size:26 final size:26
Alignment explanation
Indices: 809376--809430 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
809366 AATTTTTTTC
809376 TTTAACGTTAATCGAACCGAAA-TTA
1 TTTAACGTTAATCGAACCGAAATTTA
*
809401 TTTAACTGTTAATCGAATCGAAATTTA
1 TTTAAC-GTTAATCGAACCGAAATTTA
809428 TTT
1 TTT
809431 GAATATTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 6 0.22
26 15 0.56
27 6 0.22
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (26 bp):
TTTAACGTTAATCGAACCGAAATTTA
Found at i:809493 original size:81 final size:80
Alignment explanation
Indices: 809358--809530 Score: 258
Period size: 81 Copynumber: 2.1 Consensus size: 80
809348 ACTGAACCAA
* * * *
809358 ATTAACCGAATTTTTTTCTTTAACGTTAATCGAACCGAAATTATTTAACTGTTAATCGAATCGAA
1 ATTAACCGAATTTTTTTCTTTAACATTAATCGAACCGAAATTATTTAACCGTTAATCGAACCCAA
809423 ATTTATTTGAATA-TT
66 ATTTATTTGAA-AGTT
* * *
809438 ATTAACCGAATTTTTTTCTTTAACCATTAATCGAATCGGAATTATTTGACCGTTAATCGAACCCA
1 ATTAACCGAATTTTTTTCTTTAA-CATTAATCGAACCGAAATTATTTAACCGTTAATCGAACCCA
809503 AATTTATTTGAAAGTT
65 AATTTATTTGAAAGTT
809519 ATTAACCGAATT
1 ATTAACCGAATT
809531 AACTTAATAA
Statistics
Matches: 84, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
80 24 0.29
81 60 0.71
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.40
Consensus pattern (80 bp):
ATTAACCGAATTTTTTTCTTTAACATTAATCGAACCGAAATTATTTAACCGTTAATCGAACCCAA
ATTTATTTGAAAGTT
Found at i:809806 original size:27 final size:27
Alignment explanation
Indices: 809776--809915 Score: 119
Period size: 26 Copynumber: 5.3 Consensus size: 27
809766 ATTCAGTTAA
* *
809776 TAATTTTCAAATAAATTTGGGTTCGAT
1 TAATGTTCAAATAAATTTCGGTTCGAT
* * *
809803 TAATGGTCAAAT-AATTTCGATTCAAT
1 TAATGTTCAAATAAATTTCGGTTCGAT
* *
809829 TAATGGTT-AAAGAAAATTTTCGGTT--AA
1 TAAT-GTTCAAA-TAAA-TTTCGGTTCGAT
* *
809856 TAATTTTCAAATAAATTTTGGTTCGAT
1 TAATGTTCAAATAAATTTCGGTTCGAT
* *
809883 TAATGGTCAAAT-AATTTTGGTTCGAT
1 TAATGTTCAAATAAATTTCGGTTCGAT
809909 TAATGTT
1 TAATGTT
809916 AAAGAAAAGA
Statistics
Matches: 90, Mismatches: 16, Indels: 15
0.74 0.13 0.12
Matches are distributed among these distances:
25 7 0.08
26 43 0.48
27 31 0.34
28 2 0.02
29 7 0.08
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (27 bp):
TAATGTTCAAATAAATTTCGGTTCGAT
Found at i:809935 original size:80 final size:80
Alignment explanation
Indices: 809766--809936 Score: 263
Period size: 80 Copynumber: 2.1 Consensus size: 80
809756 AATTTATTTT
809766 ATTCAGTTAATAATTTTCAAATAAATTTGGGTTCGATTAATGGTCAAATAATTTCGATTCAATTA
1 ATTCAGTTAATAATTTTCAAATAAATTTGGGTTCGATTAATGGTCAAATAATTTCGATTCAATTA
*
809831 ATGGTTAAAGAAAAT
66 ATGGTTAAAGAAAAA
* * * * * *
809846 TTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAATGGTCAAATAATTTTGGTTCGATTA
1 ATTCAGTTAATAATTTTCAAATAAATTTGGGTTCGATTAATGGTCAAATAATTTCGATTCAATTA
809911 AT-GTTAAAGAAAAGA
66 ATGGTTAAAGAAAA-A
809926 ATTCAGTTAAT
1 ATTCAGTTAAT
809937 TTGGTTTGGT
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
79 11 0.14
80 70 0.86
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (80 bp):
ATTCAGTTAATAATTTTCAAATAAATTTGGGTTCGATTAATGGTCAAATAATTTCGATTCAATTA
ATGGTTAAAGAAAAA
Found at i:810053 original size:39 final size:37
Alignment explanation
Indices: 809942--810128 Score: 105
Period size: 39 Copynumber: 5.2 Consensus size: 37
809932 TTAATTTGGT
*
809942 TTGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAA
1 TTGGTTAATAA-TTTCAAATAAATTTTGGTTCGATTAA
* * * ** *
809980 -TGGTTAGAGAA---AAAATAATTTTTTATTCGGTTAA
1 TTGGTTA-ATAATTTCAAATAAATTTTGGTTCGATTAA
810014 TTAGGTTAATAATTTCCAAATAAATTTTGGTTCGATTAA
1 TT-GGTTAATAATTT-CAAATAAATTTTGGTTCGATTAA
* **
810053 -TGGTTAA-AGA----AAA-AAA-TTTGGTT-AATTCGG
1 TTGGTTAATA-ATTTCAAATAAATTTTGGTTCGATT-AA
*
810083 TTCGGTTAATAATTTTTAAATAAATTTTGGTTCGATTAA
1 TT-GGTTAATAA-TTTCAAATAAATTTTGGTTCGATTAA
810122 -TGGTTAA
1 TTGGTTAA
810129 ATAAAAAACA
Statistics
Matches: 110, Mismatches: 19, Indels: 41
0.65 0.11 0.24
Matches are distributed among these distances:
29 3 0.03
30 7 0.06
31 4 0.04
32 10 0.09
33 1 0.01
34 17 0.15
35 4 0.04
36 6 0.05
37 22 0.20
38 8 0.07
39 25 0.23
40 3 0.03
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.43
Consensus pattern (37 bp):
TTGGTTAATAATTTCAAATAAATTTTGGTTCGATTAA
Found at i:810091 original size:142 final size:141
Alignment explanation
Indices: 809890--810147 Score: 401
Period size: 142 Copynumber: 1.8 Consensus size: 141
809880 GATTAATGGT
* * *
809890 CAAATAATTTTGGTTCGATTAATGTTAAAGAAAAGAATTCAGTTAATTTGGTTTGGTTAATAATT
1 CAAATAATTTTGGTTCGATTAATGTTAAAGAAAAAAATTCAGTTAATTCGGTTCGGTTAATAATT
* *
809955 TTCAAATAAATTTCGGTTCGATTAATGGTTAGAGAAAAAATAATTT-TTTATTCGGTTAATTAGG
66 TTCAAATAAATTTCGGTTCGATTAATGGTTAAAGAAAAAACAATTTATTTATTCGGTTAATTAGG
810019 TTAATAATTTC
131 TTAATAATTTC
**
810030 CAAATAAATTTTGGTTCGATTAATGGTTAAAGAAAAAAATTTGGTTAATTCGGTTCGGTTAATAA
1 CAAAT-AATTTTGGTTCGATTAAT-GTTAAAGAAAAAAATTCAGTTAATTCGGTTCGGTTAATAA
* * *
810095 TTTTTAAATAAATTTTGGTTCGATTAATGGTTAAATAAAAAACAATTTATTTA
64 TTTTCAAATAAATTTCGGTTCGATTAATGGTTAAAGAAAAAACAATTTATTTA
810148 AACAAATAGT
Statistics
Matches: 105, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
140 5 0.05
141 18 0.17
142 78 0.74
143 4 0.04
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.41
Consensus pattern (141 bp):
CAAATAATTTTGGTTCGATTAATGTTAAAGAAAAAAATTCAGTTAATTCGGTTCGGTTAATAATT
TTCAAATAAATTTCGGTTCGATTAATGGTTAAAGAAAAAACAATTTATTTATTCGGTTAATTAGG
TTAATAATTTC
Found at i:810120 original size:69 final size:68
Alignment explanation
Indices: 809889--810136 Score: 304
Period size: 69 Copynumber: 3.6 Consensus size: 68
809879 CGATTAATGG
* * * *
809889 TCAAAT-AATTTTGGTTCGATTAAT-GTTAAAGAAAAGAATTCAGTTAATTTGGTTTGGTTAATA
1 TCAAATAAATTTTGGTTCGATTAATGGTTAAAGAAAAAAATT-TGTTAATTCGGTTAGGTTAATA
809952 ATTT
65 ATTT
* * *
809956 TCAAATAAATTTCGGTTCGATTAATGGTTAGAGAAAAAATAATTT-TTTATTCGGTTAATTAGGT
1 TCAAATAAATTTTGGTTCGATTAATGGTTAAAG-AAAAA-AATTTGTTAATTCGG----TTAGGT
810020 TAATAATTT
60 TAATAATTT
* *
810029 CCAAATAAATTTTGGTTCGATTAATGGTTAAAGAAAAAAATTTGGTTAATTCGGTTCGGTTAATA
1 TCAAATAAATTTTGGTTCGATTAATGGTTAAAGAAAAAAATTT-GTTAATTCGGTTAGGTTAATA
810094 ATTT
65 ATTT
* *
810098 TTAAATAAATTTTGGTTCGATTAATGGTTAAATAAAAAA
1 TCAAATAAATTTTGGTTCGATTAATGGTTAAAGAAAAAA
810137 CAATTTATTT
Statistics
Matches: 156, Mismatches: 15, Indels: 18
0.83 0.08 0.10
Matches are distributed among these distances:
67 6 0.04
68 17 0.11
69 63 0.40
70 4 0.03
71 9 0.06
72 5 0.03
73 52 0.33
ACGTcount: A:0.38, C:0.05, G:0.16, T:0.41
Consensus pattern (68 bp):
TCAAATAAATTTTGGTTCGATTAATGGTTAAAGAAAAAAATTTGTTAATTCGGTTAGGTTAATAA
TTT
Found at i:814868 original size:14 final size:14
Alignment explanation
Indices: 814849--814881 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
814839 TGGGGAGTAA
*
814849 TCCCTGTAAATAAT
1 TCCCTGCAAATAAT
814863 TCCCTGCAAATAAT
1 TCCCTGCAAATAAT
814877 TCCCT
1 TCCCT
814882 ACATAGAAAT
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:0.30, C:0.30, G:0.06, T:0.33
Consensus pattern (14 bp):
TCCCTGCAAATAAT
Done.