Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005941.1 Hibiscus syriacus cultivar Beakdansim tig00013955_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: 87610
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:406 original size:14 final size:14
Alignment explanation
Indices: 371--409 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
361 TCTGTCTATA
* *
371 TGCAGAGATTTTTT
1 TGCAGGGATTTATT
385 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
400 TGCAGGGATT
1 TGCAGGGATT
410 ACTTCCCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.21, C:0.10, G:0.28, T:0.41
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:5506 original size:21 final size:21
Alignment explanation
Indices: 5482--5537 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
5472 AAACATTGAT
*
5482 TTGTTTGGATATATATGTAGA
1 TTGTTTGGATATATACGTAGA
5503 TTGTTTGGATATATACGTAGA
1 TTGTTTGGATATATACGTAGA
* *
5524 TTGTATGGACATAT
1 TTGTTTGGATATAT
5538 TTTCTGGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.29, C:0.04, G:0.23, T:0.45
Consensus pattern (21 bp):
TTGTTTGGATATATACGTAGA
Found at i:6508 original size:2 final size:2
Alignment explanation
Indices: 6501--6545 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
6491 ATTTGAAATC
6501 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
6543 AT A
1 AT A
6546 GATCTTTTCC
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:16422 original size:21 final size:20
Alignment explanation
Indices: 16381--16422 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
16371 TGGTTGTGAT
*
16381 TTTGAGGTTATGGTTATGGA
1 TTTGAGGTTATGGGTATGGA
16401 TTTGAAGGTTGATGGGTA-GGA
1 TTTG-AGGTT-ATGGGTATGGA
16422 T
1 T
16423 GAGATGCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.40
Consensus pattern (20 bp):
TTTGAGGTTATGGGTATGGA
Found at i:17116 original size:26 final size:26
Alignment explanation
Indices: 17085--17134 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
17075 TGGTTATATT
17085 AATTTTATTATTAAATTTTAAAAACC
1 AATTTTATTATTAAATTTTAAAAACC
17111 AATTTTATTATTAAATTTTAAAAA
1 AATTTTATTATTAAATTTTAAAAA
17135 ATCAGAGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (26 bp):
AATTTTATTATTAAATTTTAAAAACC
Found at i:18327 original size:29 final size:29
Alignment explanation
Indices: 18287--18353 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
18277 ACTTTTTGAC
18287 AATTA-AAGTGAAGGACAAAAG-GTTTTATA
1 AATTATAA-TGAAGGACAAAAGTG-TTTATA
** *
18316 AATTATAATGAATTACAAAATTGTTTATA
1 AATTATAATGAAGGACAAAAGTGTTTATA
18345 AATTATAAT
1 AATTATAAT
18354 AAAGTGTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 30 0.91
30 3 0.09
ACGTcount: A:0.49, C:0.03, G:0.12, T:0.36
Consensus pattern (29 bp):
AATTATAATGAAGGACAAAAGTGTTTATA
Found at i:18364 original size:29 final size:29
Alignment explanation
Indices: 18309--18375 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
18299 GGACAAAAGG
* *
18309 TTTTATAAATTATAATGAATTACAAAA-T
1 TTTTATAAATTATAATAAAGTACAAAACT
**
18337 TGTTTATAAATTATAATAAAGTGTAAAACT
1 T-TTTATAAATTATAATAAAGTACAAAACT
18367 TTTTATAAA
1 TTTTATAAA
18376 ATAAAATATC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 1 0.03
29 30 0.91
30 2 0.06
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (29 bp):
TTTTATAAATTATAATAAAGTACAAAACT
Found at i:18652 original size:22 final size:22
Alignment explanation
Indices: 18616--18697 Score: 119
Period size: 22 Copynumber: 3.7 Consensus size: 22
18606 CTACGGATGG
* *
18616 TGGAAGAAGGTTGCACGAATGC
1 TGGAAGTAGGCTGCACGAATGC
18638 TGGAAGTAGGCTGCACGAATGC
1 TGGAAGTAGGCTGCACGAATGC
*
18660 TAGAAGTAGGCTGCACGAATGC
1 TGGAAGTAGGCTGCACGAATGC
**
18682 TGGAAGCGGGCTGCAC
1 TGGAAGTAGGCTGCAC
18698 AGGTGCTGAT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.28, C:0.18, G:0.37, T:0.17
Consensus pattern (22 bp):
TGGAAGTAGGCTGCACGAATGC
Found at i:21778 original size:24 final size:24
Alignment explanation
Indices: 21746--21822 Score: 127
Period size: 24 Copynumber: 3.2 Consensus size: 24
21736 CAAAGGGCTC
*
21746 GTTCGTTCATTTACGTTCGTTTAT
1 GTTCGTTCATTTATGTTCGTTTAT
21770 GTTCGTTCATTTATGTTCGTTTAT
1 GTTCGTTCATTTATGTTCGTTTAT
* *
21794 GTTCGTTTATTTATGTTCATTTAT
1 GTTCGTTCATTTATGTTCGTTTAT
21818 GTTCG
1 GTTCG
21823 AACAGAGAGC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.13, C:0.13, G:0.17, T:0.57
Consensus pattern (24 bp):
GTTCGTTCATTTATGTTCGTTTAT
Found at i:21787 original size:10 final size:10
Alignment explanation
Indices: 21774--21821 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
21764 GTTTATGTTC
21774 GTTCATTTAT
1 GTTCATTTAT
*
21784 GTTCGTTTAT
1 GTTCATTTAT
21794 GTTCGTTTATTTAT
1 GTTC----ATTTAT
21808 GTTCATTTAT
1 GTTCATTTAT
21818 GTTC
1 GTTC
21822 GAACAGAGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
10 23 0.72
14 9 0.28
ACGTcount: A:0.15, C:0.10, G:0.15, T:0.60
Consensus pattern (10 bp):
GTTCATTTAT
Found at i:21806 original size:14 final size:14
Alignment explanation
Indices: 21765--21817 Score: 60
Period size: 14 Copynumber: 4.1 Consensus size: 14
21755 TTTACGTTCG
*
21765 TTTATGTTCGTTCA
1 TTTATGTTCGTTTA
21779 TTTATGTTCG----
1 TTTATGTTCGTTTA
21789 TTTATGTTCGTTTA
1 TTTATGTTCGTTTA
*
21803 TTTATGTTCATTTA
1 TTTATGTTCGTTTA
21817 T
1 T
21818 GTTCGAACAG
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 10 0.29
14 24 0.71
ACGTcount: A:0.15, C:0.09, G:0.13, T:0.62
Consensus pattern (14 bp):
TTTATGTTCGTTTA
Found at i:22110 original size:23 final size:22
Alignment explanation
Indices: 22084--22159 Score: 84
Period size: 23 Copynumber: 3.5 Consensus size: 22
22074 GTGTTTGTGT
22084 TGTTCGTTTACTGTATTCGTTTA
1 TGTTCGTTTACTGT-TTCGTTTA
* * *
22107 TGTTCATTTATTATGTTCGTTTA
1 TGTTCGTTTACTGT-TTCGTTTA
*
22130 TGTTCGTTTAC-GTTT-GTTTG
1 TGTTCGTTTACTGTTTCGTTTA
22150 TGTTCGTTTA
1 TGTTCGTTTA
22160 TCATTTAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
20 14 0.31
21 2 0.04
22 1 0.02
23 28 0.62
ACGTcount: A:0.12, C:0.11, G:0.18, T:0.59
Consensus pattern (22 bp):
TGTTCGTTTACTGTTTCGTTTA
Found at i:22130 original size:10 final size:10
Alignment explanation
Indices: 22084--22160 Score: 64
Period size: 10 Copynumber: 7.1 Consensus size: 10
22074 GTGTTTGTGT
22084 TGTTCGTTTA
1 TGTTCGTTTA
22094 CTGTATTCGTTTA
1 -TG--TTCGTTTA
*
22107 TGTTCATTTATTA
1 TGTTC--GT-TTA
22120 TGTTCGTTTA
1 TGTTCGTTTA
22130 TGTTCGTTTA
1 TGTTCGTTTA
* * *
22140 CGTTTGTTTG
1 TGTTCGTTTA
22150 TGTTCGTTTA
1 TGTTCGTTTA
22160 T
1 T
22161 CATTTAAATG
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
10 31 0.58
11 3 0.06
12 3 0.06
13 16 0.30
ACGTcount: A:0.12, C:0.10, G:0.18, T:0.60
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:34748 original size:4 final size:4
Alignment explanation
Indices: 34739--34773 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
34729 CTGCTTTGTC
34739 CAAT CAAT CAAT CAAT CAAT CAAT CAAT CAAT CAA
1 CAAT CAAT CAAT CAAT CAAT CAAT CAAT CAAT CAA
34774 AATACAGCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (4 bp):
CAAT
Found at i:35320 original size:27 final size:25
Alignment explanation
Indices: 35273--35329 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
35263 AGAGGTGCAC
* *
35273 AAAAAATTCGAATATCTGATTTACGGA
1 AAAAAATTCGAATACCGGATTT--GGA
35300 AAAAATATTCGAA-ACCGGATTTGGA
1 AAAAA-ATTCGAATACCGGATTTGGA
35325 AAAAA
1 AAAAA
35330 CCGGTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 8 0.30
27 12 0.44
28 7 0.26
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.25
Consensus pattern (25 bp):
AAAAAATTCGAATACCGGATTTGGA
Found at i:35481 original size:21 final size:21
Alignment explanation
Indices: 35457--35504 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
35447 TTTATCCGGA
35457 AAAAAATCAGGTCTGAGATTT
1 AAAAAATCAGGTCTGAGATTT
* * * *
35478 -AAAAATCTGGTTTGGGGTTT
1 AAAAAATCAGGTCTGAGATTT
35498 AAAAAAT
1 AAAAAAT
35505 TGGATGACCG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.31
Consensus pattern (21 bp):
AAAAAATCAGGTCTGAGATTT
Found at i:35550 original size:16 final size:17
Alignment explanation
Indices: 35529--35562 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
35519 TTTTACCGGA
*
35529 TTAAAAATCGG-TTTTT
1 TTAAAAACCGGATTTTT
35545 TTAAAAACCGGATTTTT
1 TTAAAAACCGGATTTTT
35562 T
1 T
35563 CAAATCGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (17 bp):
TTAAAAACCGGATTTTT
Found at i:35697 original size:21 final size:21
Alignment explanation
Indices: 35667--35713 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
35657 TGTAAAAACT
* *
35667 GGATCGATTTATATCCGATCC
1 GGATCAATTTATATCCAATCC
* *
35688 GGATCAATTTTTATCTAATCC
1 GGATCAATTTATATCCAATCC
35709 GGATC
1 GGATC
35714 GGATTTAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (21 bp):
GGATCAATTTATATCCAATCC
Found at i:36077 original size:20 final size:21
Alignment explanation
Indices: 36052--36103 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
36042 TTTTCCCAAT
*
36052 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
36072 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
36093 TCGCAATGCGA
1 TCGCAATGCGA
36104 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:36117 original size:20 final size:20
Alignment explanation
Indices: 36092--36185 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
36082 AATTGGGAAA
36092 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
36112 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
36132 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
36153 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
36173 TTCGCAACGCGAT
1 ATCGCAATGCGAT
36186 TTACATAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.73
21 13 0.21
22 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:36738 original size:19 final size:19
Alignment explanation
Indices: 36700--36766 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
36690 TTCGAGAATG
36700 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
36720 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
36739 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
36758 AAAATCGCA
1 AAAATCGCA
36767 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:36808 original size:20 final size:19
Alignment explanation
Indices: 36762--36927 Score: 129
Period size: 20 Copynumber: 9.1 Consensus size: 19
36752 GAAACCAAAA
*
36762 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
36781 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
36800 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
36820 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
36836 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
36853 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
36867 TCTCGTTGCGATAGTT-ATT
1 TCGCGTTGCGAT-TTTCATT
*
36886 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
36906 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
36926 TC
1 TC
36928 AACCAAAAGA
Statistics
Matches: 118, Mismatches: 14, Indels: 30
0.73 0.09 0.19
Matches are distributed among these distances:
14 20 0.17
15 1 0.01
16 1 0.01
17 5 0.04
18 1 0.01
19 42 0.36
20 47 0.40
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:36843 original size:39 final size:39
Alignment explanation
Indices: 36767--36843 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
36757 CAAAATCGCA
* **
36767 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
36806 TTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
36844 ATAGTCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:36897 original size:34 final size:33
Alignment explanation
Indices: 36815--36902 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
36805 GTTGCGATTT
* *
36815 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
36848 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
36881 TTATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
36903 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 35 0.70
34 15 0.30
ACGTcount: A:0.11, C:0.24, G:0.25, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:39008 original size:42 final size:42
Alignment explanation
Indices: 38957--39050 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
38947 CCACTCCTAT
* *
38957 CGTTGAAGAGGCCCCTATCATTCCTCG-AGA-GTCCTCTCCCAC
1 CGTTCAAGAGGCCACTATCA-TCCTCGAAGAGGTCC-CTCCCAC
* * *
38999 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCAC
*
39041 CATTCAAGAG
1 CGTTCAAGAG
39051 CCCGATTCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
41 4 0.09
42 36 0.82
43 4 0.09
ACGTcount: A:0.22, C:0.34, G:0.21, T:0.22
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCAC
Found at i:40427 original size:14 final size:14
Alignment explanation
Indices: 40408--40443 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
40398 ATTGTTTAAT
40408 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
40422 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
40436 TGATTTGT
1 TGATTTGT
40444 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:40607 original size:20 final size:19
Alignment explanation
Indices: 40550--40617 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 19
40540 AAAAAGTACT
40550 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
40569 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
40583 ATCGCAATGCGAAAATGAAA
1 ATCGCAATGCG-AAATGAAA
*
40603 ATCGCAACGCGAAAT
1 ATCGCAATGCGAAAT
40618 TAAATTCGCG
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
19 12 0.30
20 13 0.32
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:40644 original size:19 final size:19
Alignment explanation
Indices: 40622--40772 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
40612 CGAAATTAAA
40622 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
40641 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
40656 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * *
40674 TTCGCATTGC-A----AAA
1 TTCGCGTTGCGATTTTCAT
*
40688 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
40707 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
40722 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
40740 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
40759 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
40773 GGACATTAAG
Statistics
Matches: 93, Mismatches: 23, Indels: 31
0.63 0.16 0.21
Matches are distributed among these distances:
14 26 0.28
15 1 0.01
16 6 0.06
17 6 0.06
18 1 0.01
19 43 0.46
20 10 0.11
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:40668 original size:33 final size:32
Alignment explanation
Indices: 40626--40752 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
40616 ATTAAATTCG
40626 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
40659 CGTTGCGATTTTCATTTCGCATTGCAAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGC--GATTCCT
40692 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
40725 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
40753 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:40715 original size:66 final size:66
Alignment explanation
Indices: 40619--40749 Score: 244
Period size: 66 Copynumber: 2.0 Consensus size: 66
40609 ACGCGAAATT
*
40619 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
40684 A
66 A
*
40685 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
40750 GATAGTAATT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
A
Found at i:43062 original size:12 final size:12
Alignment explanation
Indices: 43045--43069 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43035 TCTTCGGAGA
43045 CTTTTTCTTCTT
1 CTTTTTCTTCTT
43057 CTTTTTCTTCTT
1 CTTTTTCTTCTT
43069 C
1 C
43070 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:43278 original size:24 final size:24
Alignment explanation
Indices: 43244--43297 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
43234 CTGAAACATC
* *
43244 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
43268 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
43292 ATCAAA
1 ATCAAA
43298 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:44379 original size:20 final size:20
Alignment explanation
Indices: 44354--44411 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
44344 ATTCATTTGA
44354 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
44374 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
44394 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
44412 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:44454 original size:14 final size:16
Alignment explanation
Indices: 44434--44507 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
44424 TGAAAATCGC
44434 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
44449 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
44466 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
44485 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
44501 -TTGCGAT
1 ATTGCGAT
44508 AGCCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:44471 original size:19 final size:19
Alignment explanation
Indices: 44430--44497 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
44420 GAAATGAAAA
44430 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
44446 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
44463 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
44482 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
44498 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:46556 original size:20 final size:19
Alignment explanation
Indices: 46520--46605 Score: 102
Period size: 19 Copynumber: 4.5 Consensus size: 19
46510 CGAAACTTAA
*
46520 AATCGCAACGTGAAATGAC
1 AATCGCAACGCGAAATGAC
* *
46539 TATCGCAACGCGGAAATGGC
1 AATCGCAACGC-GAAATGAC
* * *
46559 TATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAC
46578 AATCGCAACGCGAAATGA-
1 AATCGCAACGCGAAATGAC
46596 AATCGCAACG
1 AATCGCAACG
46606 ACAAAATCGC
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
18 10 0.17
19 31 0.53
20 17 0.29
ACGTcount: A:0.40, C:0.22, G:0.23, T:0.15
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAC
Found at i:46564 original size:39 final size:38
Alignment explanation
Indices: 46521--46594 Score: 103
Period size: 39 Copynumber: 1.9 Consensus size: 38
46511 GAAACTTAAA
* **
46521 ATCGCAACGTGAAATGACTATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAATGAAAATCGCAACGC-GAAATGGCT
*
46560 ATCGCAATGCGAAATGAAAATCGCAACGCGAAATG
1 ATCGCAACGCGAAATGAAAATCGCAACGCGAAATG
46595 AAATCGCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 6 0.19
39 25 0.81
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (38 bp):
ATCGCAACGCGAAATGAAAATCGCAACGCGAAATGGCT
Found at i:46672 original size:14 final size:14
Alignment explanation
Indices: 46653--46710 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
46643 TTTCATTTCG
46653 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
46667 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
46683 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
46699 CGTTGCGATTTT
1 CGTTGCGATTTT
46711 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:46717 original size:33 final size:33
Alignment explanation
Indices: 46636--46726 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
46626 ACAAATCGCA
*
46636 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
46669 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
46701 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
46727 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:46762 original size:20 final size:20
Alignment explanation
Indices: 46711--46754 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
46701 TTGCGATTTT
*
46711 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
46730 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
46750 CATTT
1 CATTT
46755 TCGTGTTGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:47273 original size:18 final size:18
Alignment explanation
Indices: 47247--47291 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
47237 GTCGATCAGA
*
47247 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
47265 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
47283 TGATGGCTC
1 TGATGGCTC
47292 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:48636 original size:20 final size:20
Alignment explanation
Indices: 48611--48648 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
48601 AATAGTTTCT
48611 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
48631 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
48649 GAGAGAATCG
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:48939 original size:22 final size:22
Alignment explanation
Indices: 48912--48955 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
48902 GATGGAGATA
48912 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
48934 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
48956 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:49214 original size:21 final size:21
Alignment explanation
Indices: 49181--49281 Score: 59
Period size: 20 Copynumber: 4.9 Consensus size: 21
49171 TGCGAAAGTA
* * *
49181 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
49202 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
*
49222 AGTATCGCATTGCGATTTTCCC
1 AGTATCGCATTGCGATTTT-TC
* *
49244 AAT-TCGCGTTGCGATTTACTT-
1 AGTATCGCATTGCGATTT--TTC
49265 A-T-TCGCATTGCGATTTT
1 AGTATCGCATTGCGATTTT
49282 CCCAATTCGC
Statistics
Matches: 62, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
18 1 0.02
20 30 0.48
21 27 0.44
22 3 0.05
23 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.43
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:49229 original size:20 final size:20
Alignment explanation
Indices: 49143--49237 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
49133 GATTATATAT
* *
49143 TATCGCGTTGCGAAAGTCAA
1 TATCGCGTTGCGATAGTCAG
* *
49163 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGATAGTCAG
* ** * *
49183 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-TAGTCAG
*
49204 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
49224 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
49238 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:49256 original size:41 final size:42
Alignment explanation
Indices: 49160--49299 Score: 144
Period size: 41 Copynumber: 3.4 Consensus size: 42
49150 TTGCGAAAGT
* * * *
49160 CAATATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-T
1 CAATATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCC
* * * *
49201 TATTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCC
1 CAATATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCC
* **
49243 CAAT-TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCC
1 CAATATCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCC
49284 CAAT-TCGCGTTGCGAT
1 CAATATCGCGTTGCGAT
49300 TTACTTATTC
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 77 0.94
42 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (42 bp):
CAATATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCC
Found at i:49291 original size:21 final size:20
Alignment explanation
Indices: 49226--49318 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
49216 ATAGTCAGTA
*
49226 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
49247 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
*
49267 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
49288 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
49308 TCGCATTGCGA
1 TCGCATTGCGA
49319 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACCAAT
Found at i:49300 original size:41 final size:41
Alignment explanation
Indices: 49226--49318 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
49216 ATAGTCAGTA
49226 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
49267 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
49308 TCGCATTGCGA
1 TCGCATTGCGA
49319 ATTGGGAAAA
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:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:50975 original size:2 final size:2
Alignment explanation
Indices: 50968--51170 Score: 127
Period size: 2 Copynumber: 105.5 Consensus size: 2
50958 TGCCTATCCC
50968 TA TA TA TA TA TA TA T- TA TA GTA T- TA TA T- TA TA TA GTA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA
* *
51009 GTA TA TA GTA TA TA T- TA CA -A TA TA TA TA GTT TA T- TA TA T-
1 -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
*
51048 TA T- TA TA TA TA T- TT TA GTA T- TA TA TCA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA T-A TA TA TA TA TA TA TA
* * *
51089 TA TA TA TA TT TA TT TA TT TA T- TA TA T- TA T- TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
51127 TA GTA TA TA T- TA TA T- TA TA -A TA TT TA CTA TA TA T- TA TA GTA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA
51168 TA T
1 TA T
51171 TATTAAGTAT
Statistics
Matches: 161, Mismatches: 12, Indels: 56
0.70 0.05 0.24
Matches are distributed among these distances:
1 18 0.11
2 124 0.77
3 19 0.12
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (2 bp):
TA
Found at i:51124 original size:77 final size:76
Alignment explanation
Indices: 50968--51141 Score: 221
Period size: 77 Copynumber: 2.4 Consensus size: 76
50958 TGCCTATCCC
*
50968 TATA-TATATATATATTATAGTATTATATTATATAGTATATAGTATATAGTATATATTACAATAT
1 TATATTATATATATATTATAGTATTATATCATATAGTATATAGTATATAGTATATATTACAATAT
51032 ATATAGTTTAT
66 ATATAGTTTAT
*
51043 TATATTATTATATATATTTTAGTATTATATCATATA-TATATA-TATATA-TATATATT----TA
1 TATATTA-TATATATATTATAGTATTATATCATATAGTATATAGTATATAGTATATATTACAATA
51101 T-T-TA-TTTAT
65 TATATAGTTTAT
*
51110 TATATTAT-TATATATTATAGTA-TATATTATAT
1 TATATTATATATATATTATAGTATTATATCATAT
51142 TATAATATTT
Statistics
Matches: 93, Mismatches: 4, Indels: 15
0.83 0.04 0.13
Matches are distributed among these distances:
64 9 0.10
65 13 0.14
66 1 0.01
67 12 0.13
68 2 0.02
69 1 0.01
70 3 0.03
74 8 0.09
75 10 0.11
76 8 0.09
77 26 0.28
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (76 bp):
TATATTATATATATATTATAGTATTATATCATATAGTATATAGTATATAGTATATATTACAATAT
ATATAGTTTAT
Found at i:51158 original size:77 final size:79
Alignment explanation
Indices: 50968--51174 Score: 202
Period size: 75 Copynumber: 2.6 Consensus size: 79
50958 TGCCTATCCC
* *
50968 TATATATATA-TATATTATAGTATTATATTATATAGTATATAGTATATAGTATATATTACAATAT
1 TATATATATATTATATTATAATATT-TA-TATATA-TATATAGTATATA-TATTTATTACAATAT
51032 ATATAGTTTATTATATTAT
62 ATATAG-TTATTATATTAT
* * *
51051 TATATATATTTTAGTATTAT-ATCA--TATATATATATATA-TATATATATTTATT--TATTTAT
1 TATATATATATTA-TATTATAAT-ATTTATATATATATATAGTATATATATTTATTACAATATA-
51110 TATA-TTATTATA-TAT
63 TATAGTTATTATATTAT
51125 TATAGTATATATTATATTATAATATTTACTATATAT-TATAGTATAT-TATT
1 TATA-TATATATTATATTATAATATTTA-TATATATATATAGTATATATATT
51175 AAGTATTATA
Statistics
Matches: 108, Mismatches: 6, Indels: 27
0.77 0.04 0.19
Matches are distributed among these distances:
74 14 0.13
75 18 0.17
76 14 0.13
77 16 0.15
78 7 0.06
79 6 0.06
80 6 0.06
81 6 0.06
82 2 0.02
83 9 0.08
84 3 0.03
85 7 0.06
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (79 bp):
TATATATATATTATATTATAATATTTATATATATATATAGTATATATATTTATTACAATATATAT
AGTTATTATATTAT
Found at i:51160 original size:113 final size:115
Alignment explanation
Indices: 50968--51185 Score: 281
Period size: 113 Copynumber: 1.9 Consensus size: 115
50958 TGCCTATCCC
50968 TATATATATATATATTATAGTATTATATTATATAGTATATAGTATATAGTATATATTACAATATA
1 TATATATATATATATTATAGTATTATATTATATAGTATATAGTATATAGTATATATTACAATATA
*
51033 TATAGTTTATTATATTAT--TATATATATTTTAGTATTATATCATATATATA
66 TATAGTTTATTATATTATAGTATAT-TA-TTAAGTATTATATCATATATATA
* * * *
51083 TATATATATATATATT-TATTTATT-TATTATATTATTATATA-T-TATAGTATATATTATATTA
1 TATATATATATATATTATA-GTATTATATTATA-TAGTATATAGTATATAGTATATATTACAATA
51144 TA-ATA-TTTACTATATATTATAGTATATTATTAAGTATTATAT
64 TATATAGTTTA-T-TATATTATAGTATATTATTAAGTATTATAT
51186 TTTATTTGTA
Statistics
Matches: 92, Mismatches: 5, Indels: 14
0.83 0.05 0.13
Matches are distributed among these distances:
111 4 0.04
112 4 0.04
113 39 0.42
114 12 0.13
115 33 0.36
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (115 bp):
TATATATATATATATTATAGTATTATATTATATAGTATATAGTATATAGTATATATTACAATATA
TATAGTTTATTATATTATAGTATATTATTAAGTATTATATCATATATATA
Found at i:51390 original size:34 final size:34
Alignment explanation
Indices: 51299--51443 Score: 130
Period size: 35 Copynumber: 4.1 Consensus size: 34
51289 TTGAAAACTT
* * *
51299 ATTTTTGAAAACGTATAATATATTTTTTTTAAAAAAA
1 ATTTTTGAAAACGCATAATATA--TGTTTT-AAAAAC
* * *
51336 ATAGCTTTGAAAAAGTATAATATATGTTTTAAAAAC
1 AT--TTTTGAAAACGCATAATATATGTTTTAAAAAC
*
51372 ATTTTT-AAGAACGCATAATATATAATTTTAAAAAC
1 ATTTTTGAA-AACGCATAATATAT-GTTTTAAAAAC
* *
51407 ATTTTTGAAAACGTATAATATATGCTTTTGAAAAC
1 ATTTTTGAAAACGCATAATATATG-TTTTAAAAAC
51442 AT
1 AT
51444 ATAAAATATG
Statistics
Matches: 91, Mismatches: 11, Indels: 14
0.78 0.09 0.12
Matches are distributed among these distances:
33 2 0.02
34 15 0.16
35 40 0.44
36 9 0.10
37 7 0.08
39 18 0.20
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (34 bp):
ATTTTTGAAAACGCATAATATATGTTTTAAAAAC
Found at i:51439 original size:23 final size:23
Alignment explanation
Indices: 51409--51466 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
51399 TTAAAAACAT
* *
51409 TTTTGAAAACGTATAATATATGC
1 TTTTGAAAACATATAAAATATGC
*
51432 TTTTGAAAACATATAAAATATGG
1 TTTTGAAAACATATAAAATATGC
*
51455 TTTTAAAAACAT
1 TTTTGAAAACAT
51467 TTTTGAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (23 bp):
TTTTGAAAACATATAAAATATGC
Found at i:51524 original size:38 final size:38
Alignment explanation
Indices: 51432--51514 Score: 118
Period size: 38 Copynumber: 2.2 Consensus size: 38
51422 TAATATATGC
*
51432 TTTTG-AAAACATATA-A-AATATGGTTTTAAAAACAT
1 TTTTGAAAAACATATATATAATATAGTTTTAAAAACAT
*
51467 TTTTGAAAAACATATATATAATATAGTTTTGAAAACATT
1 TTTTGAAAAACATATATATAATATAGTTTTAAAAACA-T
51506 TTTTGAAAA
1 TTTTGAAAA
51515 TGTATATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
35 5 0.12
36 10 0.24
37 1 0.02
38 16 0.38
39 10 0.24
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (38 bp):
TTTTGAAAAACATATATATAATATAGTTTTAAAAACAT
Found at i:51623 original size:2 final size:2
Alignment explanation
Indices: 51618--51645 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
51608 TTTCCTTTTA
51618 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
51646 TAAGCTTATT
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:51683 original size:23 final size:21
Alignment explanation
Indices: 51651--51701 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 21
51641 TATATTAAGC
*
51651 TTATTATTATTTTATATATTATA
1 TTATTTTTATTTT-TAT-TTATA
*
51674 TTATTTTTATTTTTATTTTTA
1 TTATTTTTATTTTTATTTATA
51695 TT-TTTTT
1 TTATTTTT
51702 GGGATCAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 5 0.19
21 6 0.23
22 3 0.12
23 12 0.46
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (21 bp):
TTATTTTTATTTTTATTTATA
Found at i:51689 original size:17 final size:19
Alignment explanation
Indices: 51651--51699 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
51641 TATATTAAGC
51651 TTATTATTA-TTTTATATA
1 TTATTATTATTTTTATATA
*
51669 TTA-TATTATTTTTAT-TT
1 TTATTATTATTTTTATATA
*
51686 TTATTTTTATTTTT
1 TTATTATTATTTTT
51700 TTGGGATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (19 bp):
TTATTATTATTTTTATATA
Found at i:51697 original size:6 final size:6
Alignment explanation
Indices: 51674--51699 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
51664 ATATATTATA
51674 TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TT
51700 TTGGGATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:53856 original size:13 final size:13
Alignment explanation
Indices: 53834--53863 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
53824 AGAGCAAAAA
*
53834 AAAATCAAAAATC
1 AAAATAAAAAATC
53847 AAAATAAAAAATC
1 AAAATAAAAAATC
53860 AAAA
1 AAAA
53864 GCTTAAAGCT
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:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (13 bp):
AAAATAAAAAATC
Found at i:63149 original size:32 final size:32
Alignment explanation
Indices: 63103--63168 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
63093 AAGTCAAGAC
* *
63103 GCCAAGTCAGAAATGGGAGGCACGAATTCGGT
1 GCCAAGTCAAAAATGGGAGGCACAAATTCGGT
63135 GCCAAGTCAAAAATGGGAGGCACAAATTCGGT
1 GCCAAGTCAAAAATGGGAGGCACAAATTCGGT
63167 GC
1 GC
63169 AATTAATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.33, C:0.20, G:0.32, T:0.15
Consensus pattern (32 bp):
GCCAAGTCAAAAATGGGAGGCACAAATTCGGT
Found at i:68664 original size:29 final size:29
Alignment explanation
Indices: 68630--68688 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
68620 CCTAAATTAA
68630 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
*
68659 TTTGATTTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
68688 T
1 T
68689 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.51
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:69471 original size:17 final size:17
Alignment explanation
Indices: 69449--69487 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
69439 TATTGTGAAA
69449 CAGGCTTTTAAAAAGGC
1 CAGGCTTTTAAAAAGGC
*
69466 CAGGCTTTTAAACAGGC
1 CAGGCTTTTAAAAAGGC
69483 CAGGC
1 CAGGC
69488 CGAGCCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.21
Consensus pattern (17 bp):
CAGGCTTTTAAAAAGGC
Found at i:69832 original size:40 final size:40
Alignment explanation
Indices: 69757--69834 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
69747 TCATTTATTT
** *
69757 ATTAAATGAACGAACATGAACAAGATTTTGCGTTCGTTTA
1 ATTAAATGAACGAACATGAACAAGAGCTAGCGTTCGTTTA
*
69797 ATTAAATGAACGAACATGAACAAAGGGCTAG-GTTCGTT
1 ATTAAATGAACGAACATGAAC-AAGAGCTAGCGTTCGTT
69835 CATTTACGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 28 0.85
41 5 0.15
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (40 bp):
ATTAAATGAACGAACATGAACAAGAGCTAGCGTTCGTTTA
Found at i:69876 original size:10 final size:10
Alignment explanation
Indices: 69861--69903 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
69851 CGTTTGATTA
69861 TATGTTCGTT
1 TATGTTCGTT
69871 TATGTTCGTTCAT
1 TATGTTCG-T--T
*
69884 TATGTTCATT
1 TATGTTCGTT
69894 TATGTTCGTT
1 TATGTTCGTT
69904 CATTTATGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
10 18 0.64
11 1 0.04
12 1 0.04
13 8 0.29
ACGTcount: A:0.14, C:0.12, G:0.16, T:0.58
Consensus pattern (10 bp):
TATGTTCGTT
Found at i:69895 original size:23 final size:24
Alignment explanation
Indices: 69861--69914 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 24
69851 CGTTTGATTA
*
69861 TATGTTCGTTTATGTTCGTTCA-T
1 TATGTTCATTTATGTTCGTTCATT
69884 TATGTTCATTTATGTTCGTTCATT
1 TATGTTCATTTATGTTCGTTCATT
69908 TATGTTC
1 TATGTTC
69915 GAACAGAGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 21 0.72
24 8 0.28
ACGTcount: A:0.15, C:0.13, G:0.15, T:0.57
Consensus pattern (24 bp):
TATGTTCATTTATGTTCGTTCATT
Found at i:69906 original size:14 final size:14
Alignment explanation
Indices: 69864--69915 Score: 60
Period size: 14 Copynumber: 4.1 Consensus size: 14
69854 TTGATTATAT
*
69864 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
69878 GTTCA-TTA---T-
1 GTTCATTTATGTTC
69887 GTTCATTTATGTTC
1 GTTCATTTATGTTC
69901 GTTCATTTATGTTC
1 GTTCATTTATGTTC
69915 G
1 G
69916 AACAGAGGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
9 5 0.16
10 4 0.12
13 4 0.12
14 19 0.59
ACGTcount: A:0.13, C:0.13, G:0.17, T:0.56
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:70133 original size:129 final size:129
Alignment explanation
Indices: 69999--70258 Score: 493
Period size: 129 Copynumber: 2.0 Consensus size: 129
69989 CAAATTAACT
*
69999 TTAAGATTTTATTATGTTCATATAGTTTATTTATGATTTATGTATGTTTTTGTCGTATTCGAACA
1 TTAAGATTTTATTATGTTCATATAGCTTATTTATGATTTATGTATGTTTTTGTCGTATTCGAACA
*
70064 AATTAACTCTAAAGTTGCAGGTTATATTAATGAATTGTTATTCTTGTTGTTTACTTTTTTTCCA
66 AATTAACTCTAAAGTTGCAGGTTATATTAATGAATTGTTATTCTTGTTGTTTACTTTTTTTACA
70128 TTAAGATTTTATTATGTTCATATAGCTTATTTATGATTTATGTATGTTTTTGTCGTATTCGAACA
1 TTAAGATTTTATTATGTTCATATAGCTTATTTATGATTTATGTATGTTTTTGTCGTATTCGAACA
*
70193 AATTAGCTCTAAAGTTGCAGGTTATATTAATGAATTGTTATTCTTGTTGTTTACTTTTTTTACA
66 AATTAACTCTAAAGTTGCAGGTTATATTAATGAATTGTTATTCTTGTTGTTTACTTTTTTTACA
70257 TT
1 TT
70259 CGTTTGTTGT
Statistics
Matches: 128, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 128 1.00
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.52
Consensus pattern (129 bp):
TTAAGATTTTATTATGTTCATATAGCTTATTTATGATTTATGTATGTTTTTGTCGTATTCGAACA
AATTAACTCTAAAGTTGCAGGTTATATTAATGAATTGTTATTCTTGTTGTTTACTTTTTTTACA
Found at i:70407 original size:16 final size:16
Alignment explanation
Indices: 70386--70418 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
70376 ACAAAAAAAT
70386 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTTG
70402 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTTG
70418 T
1 T
70419 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.06, G:0.24, T:0.64
Consensus pattern (16 bp):
TGTTCGTTTATGTTTG
Found at i:74466 original size:29 final size:29
Alignment explanation
Indices: 74432--74490 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
74422 CCTAAATTAA
74432 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
74461 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
74490 T
1 T
74491 AGGTGAAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:76488 original size:19 final size:19
Alignment explanation
Indices: 76450--76492 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
76440 TTTTAAAAGG
* *
76450 AAAAAAATTAAATTTATTT
1 AAAAAAATCAAAGTTATTT
76469 ATAAAAAATCAAAGTT-TTT
1 A-AAAAAATCAAAGTTATTT
76488 AAAAA
1 AAAAA
76493 TTATAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 4 0.19
19 5 0.24
20 12 0.57
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
AAAAAAATCAAAGTTATTT
Found at i:78137 original size:2 final size:2
Alignment explanation
Indices: 78130--78162 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
78120 TATTTATAAA
78130 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
78163 TTTCTTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:83991 original size:16 final size:16
Alignment explanation
Indices: 83968--84000 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
83958 TATTATACTT
83968 GAAAAAAAGGGAAAAAA
1 GAAAAAAA-GGAAAAAA
83985 GAAAAAAAGGAAAAAA
1 GAAAAAAAGGAAAAAA
84001 TTGAACCAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
GAAAAAAAGGAAAAAA
Found at i:84486 original size:33 final size:33
Alignment explanation
Indices: 84449--84512 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
84439 GTCTGGAAAC
* *
84449 AGAAGTA-CCTCTACGATATGAACATAAACAACG
1 AGAAGTATCC-CTACAAAATGAACATAAACAACG
*
84482 AGAAGTATCCCTACAAAATGAGCATAAACAA
1 AGAAGTATCCCTACAAAATGAACATAAACAA
84513 TCATTTCTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 25 0.93
34 2 0.07
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.17
Consensus pattern (33 bp):
AGAAGTATCCCTACAAAATGAACATAAACAACG
Done.