Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007852.1 Hibiscus syriacus cultivar Beakdansim tig00110212_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: 82824
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:524 original size:20 final size:20
Alignment explanation
Indices: 499--545 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
489 ATTCTTGACG
499 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
519 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
539 ATCGCAA
1 ATCGCAA
546 TGAAAATCGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.26, G:0.23, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:568 original size:19 final size:19
Alignment explanation
Indices: 544--581 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
534 TGGCTATCGC
544 AATGAAAATCGCAATGCGA
1 AATGAAAATCGCAATGCGA
*
563 AATGAAAATCGCATTGCGA
1 AATGAAAATCGCAATGCGA
582 TTTTCTCGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.18
Consensus pattern (19 bp):
AATGAAAATCGCAATGCGA
Found at i:612 original size:19 final size:16
Alignment explanation
Indices: 571--621 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 16
561 GAAATGAAAA
571 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
587 TCG--TTGCGATTTTC
1 TCGCATTGCGATTTTC
601 ATTTCGCATTGCGA-TTTC
1 ---TCGCATTGCGATTTTC
619 TCG
1 TCG
622 TTGCGATAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
14 11 0.37
15 3 0.10
16 3 0.10
17 3 0.10
18 4 0.13
19 6 0.20
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.45
Consensus pattern (16 bp):
TCGCATTGCGATTTTC
Found at i:624 original size:32 final size:32
Alignment explanation
Indices: 571--647 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 32
561 GAAATGAAAA
***
571 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGA-TTTCTCGTTGCGATAGCCATT
604 TCGCATTGCGATTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTCTCGTTGCGATAGCCATT
*
636 TCGCGTTGCGAT
1 TCGCATTGCGAT
648 AGTCTGTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 29 0.73
33 11 0.28
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (32 bp):
TCGCATTGCGATTTCTCGTTGCGATAGCCATT
Found at i:2626 original size:20 final size:19
Alignment explanation
Indices: 2591--2694 Score: 87
Period size: 19 Copynumber: 5.7 Consensus size: 19
2581 GAAACTTAAA
*
2591 ATCGCAACGTGAAATGACT
1 ATCGCAACGCGAAATGACT
*
2610 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
2630 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
2649 ATCGCAA--CGACAA--A--
1 ATCGCAACGCGA-AATGACT
*
2663 ATCGCAACGCGAAATGA-A
1 ATCGCAACGCGAAATGACT
2681 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
2695 CCAAATCGCA
Statistics
Matches: 72, Mismatches: 6, Indels: 15
0.77 0.06 0.16
Matches are distributed among these distances:
14 7 0.10
15 2 0.03
16 4 0.06
17 4 0.06
18 16 0.22
19 22 0.31
20 17 0.24
ACGTcount: A:0.41, C:0.23, G:0.22, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:2741 original size:14 final size:14
Alignment explanation
Indices: 2722--2778 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
2712 TTTCATTTCG
2722 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2736 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
2752 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
2768 CGTTGCGATTT
1 CGTTGCGATTT
2779 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.11, C:0.18, G:0.25, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2813 original size:20 final size:19
Alignment explanation
Indices: 2779--2833 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
2769 GTTGCGATTT
*
2779 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
2798 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
2818 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
2834 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:2814 original size:38 final size:32
Alignment explanation
Indices: 2705--2794 Score: 162
Period size: 32 Copynumber: 2.8 Consensus size: 32
2695 CCAAATCGCA
*
2705 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
2738 TTGCGATTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTCATTTCGCATTGCGATTTTGTCG
2770 TTGCGATTTCATTTCGCATTGCGAT
1 TTGCGATTTCATTTCGCATTGCGAT
2795 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 50 0.89
33 6 0.11
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCATTGCGATTTTGTCG
Found at i:3323 original size:18 final size:18
Alignment explanation
Indices: 3297--3341 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
3287 GTCGATCAGA
*
3297 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGAGAGG
*
3315 TGATAGCTCTGGGAGAGG
1 TGATGGCTCTGGGAGAGG
3333 TGATGGCTC
1 TGATGGCTC
3342 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:0.16, C:0.13, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGAGAGG
Found at i:4669 original size:20 final size:20
Alignment explanation
Indices: 4644--4686 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
4634 AATAGTTTCT
4644 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
4664 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
4684 GAA
1 GAA
4687 TTCGACTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.19, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:4992 original size:22 final size:22
Alignment explanation
Indices: 4965--5008 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
4955 GATGGAGATA
4965 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
4987 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
5009 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:5287 original size:21 final size:21
Alignment explanation
Indices: 5254--5354 Score: 59
Period size: 20 Copynumber: 4.9 Consensus size: 21
5244 TGCGAAAGTA
* * *
5254 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
5275 ATTATCGCATTGCGA-TAATC
1 AGTATCGCATTGCGATTTTTC
5295 AGTATCGCATTGCGA-TTTTC
1 AGTATCGCATTGCGATTTTTC
** *
5315 ACAATTCGCGTTGCGATTTACTT-
1 AGTA-TCGCATTGCGATTT--TTC
5338 A-T-TCGCATTGCGATTTT
1 AGTATCGCATTGCGATTTT
5355 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 34 0.55
21 22 0.35
22 2 0.03
23 1 0.02
24 2 0.03
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.43
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:5299 original size:41 final size:41
Alignment explanation
Indices: 5176--5313 Score: 109
Period size: 41 Copynumber: 3.4 Consensus size: 41
5166 CGCTTTGAAA
* * * * * *
5176 ATCGCATTGCGATTATGTATTATCGCGTTACGAAAGTCAGA
1 ATCGCATTGCGATTTTTTATTATCGCATTGCGAAAGTAAGT
* *** * * *
5217 ATCGCGTTGCGA-AAGTCAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTTTTTATTATCGCATTGCGAAAGTAAGT
* * *
5257 ATCTCGTTGCGATTTTTTATTATCGCATTGCGATAA-TCAGT
1 ATCGCATTGCGATTTTTTATTATCGCATTGCGA-AAGTAAGT
5298 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
5314 CACAATTCGC
Statistics
Matches: 76, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
40 31 0.41
41 43 0.57
42 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCGATTTTTTATTATCGCATTGCGAAAGTAAGT
Found at i:5302 original size:20 final size:21
Alignment explanation
Indices: 5196--5310 Score: 103
Period size: 20 Copynumber: 5.7 Consensus size: 21
5186 GATTATGTAT
*
5196 TATCGCGTTACGA-AAGTCAG
1 TATCGCGTTGCGATAAGTCAG
*
5216 AATCGCGTTGCGA-AAGTCAG
1 TATCGCGTTGCGATAAGTCAG
*
5236 TATCGCGTTGCGA-AAGTAAG
1 TATCGCGTTGCGATAAGTCAG
* *** * *
5256 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGATAAGTCAG
*
5277 TATCGCATTGCGATAA-TCAG
1 TATCGCGTTGCGATAAGTCAG
*
5297 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
5311 TTTCACAATT
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
20 64 0.82
21 14 0.18
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.32
Consensus pattern (21 bp):
TATCGCGTTGCGATAAGTCAG
Found at i:5329 original size:41 final size:41
Alignment explanation
Indices: 5299--5391 Score: 141
Period size: 41 Copynumber: 2.3 Consensus size: 41
5289 ATAATCAGTA
* *
5299 TCGCATTGCGATTTTCACAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCACAATTCGCGTTGCGATTCACGTAT
* * *
5340 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCACAATTCGCGTTGCGATTCACGTAT
5381 TCGCATTGCGA
1 TCGCATTGCGA
5392 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCACAATTCGCGTTGCGATTCACGTAT
Found at i:5343 original size:20 final size:20
Alignment explanation
Indices: 5299--5391 Score: 98
Period size: 20 Copynumber: 4.5 Consensus size: 20
5289 ATAATCAGTA
*
5299 TCGCATTGCGATTTTCAC-AAT
1 TCGCATTGCGA-TTT-ACTTAT
*
5320 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
5340 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
5361 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
5381 TCGCATTGCGA
1 TCGCATTGCGA
5392 ATTGGGAAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
19 2 0.03
20 31 0.53
21 26 0.44
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:5364 original size:21 final size:20
Alignment explanation
Indices: 5299--5391 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
5289 ATAATCAGTA
*
5299 TCGCATTGCGATTTTCACAAT
1 TCGCATTGCGATTTAC-CAAT
* **
5320 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
*
5340 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
5361 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
5381 TCGCATTGCGA
1 TCGCATTGCGA
5392 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 28 0.48
21 30 0.52
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACCAAT
Found at i:12878 original size:17 final size:17
Alignment explanation
Indices: 12851--12889 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
12841 AATTTACAAT
12851 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
12867 TAATTATAAATAATATC
1 TAATTATAAATAATATC
12884 TAATTA
1 TAATTA
12890 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:13007 original size:9 final size:9
Alignment explanation
Indices: 12993--13027 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
12983 TATATTTAAA
12993 GGTTAATTC
1 GGTTAATTC
13002 GGTTAATTC
1 GGTTAATTC
13011 GGTTAATTC
1 GGTTAATTC
*
13020 GATTAATT
1 GGTTAATT
13028 AACCGATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.46
Consensus pattern (9 bp):
GGTTAATTC
Found at i:14904 original size:60 final size:60
Alignment explanation
Indices: 14833--14947 Score: 178
Period size: 60 Copynumber: 1.9 Consensus size: 60
14823 AAATGGTTCA
*
14833 TCGACTATAGGATACTGCTTTGTTGAGT-CTCCGACTATTAAAAAGTTACAAAATGATCCT
1 TCGACTATAGGACACTGCTTTGTTGAGTCCTCCGACTATT-AAAAGTTACAAAATGATCCT
** *
14893 TCGACTATAGGACGTTGCTTTGTTGAGTCCTTCGACTATTAAAAGTTACAAAATG
1 TCGACTATAGGACACTGCTTTGTTGAGTCCTCCGACTATTAAAAGTTACAAAATG
14948 GTCACTCAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
60 40 0.80
61 10 0.20
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (60 bp):
TCGACTATAGGACACTGCTTTGTTGAGTCCTCCGACTATTAAAAGTTACAAAATGATCCT
Found at i:14960 original size:60 final size:60
Alignment explanation
Indices: 14848--14960 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
14838 TATAGGATAC
*
14848 TGCTTTGTTGAGTCTCCGACTATTAAAAAGTTACAAAATGATCCTTCGACTATAGGACGT
1 TGCTTTGTTGAGTCTCCGACTATTAAAAAGTTACAAAATGATCCTTCAACTATAGGACGT
* *
14908 TGCTTTGTTGAGTCCTTCGACTATT-AAAAGTTACAAAATGGTCAC-TCAACTAT
1 TGCTTTGTTGAGT-CTCCGACTATTAAAAAGTTACAAAATGATC-CTTCAACTAT
14961 TCATTATGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
60 37 0.77
61 11 0.23
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35
Consensus pattern (60 bp):
TGCTTTGTTGAGTCTCCGACTATTAAAAAGTTACAAAATGATCCTTCAACTATAGGACGT
Found at i:23406 original size:40 final size:40
Alignment explanation
Indices: 23343--23419 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
23333 ACATAATGTA
** * *
23343 CATGACAATGATTTGTGTGACCTTATTAACACTGCATCTG
1 CATGACAATGATACGTATCACCTTATTAACACTGCATCTG
23383 CATGACAATGATACGTATCACCTTATTAACACTGCAT
1 CATGACAATGATACGTATCACCTTATTAACACTGCAT
23420 GTAGAACAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.32
Consensus pattern (40 bp):
CATGACAATGATACGTATCACCTTATTAACACTGCATCTG
Found at i:25705 original size:139 final size:139
Alignment explanation
Indices: 25348--25707 Score: 506
Period size: 139 Copynumber: 2.6 Consensus size: 139
25338 CTAAAATACA
* *
25348 AACGCCAATACATTGAAAATTTTGATTATTTAAAAGTTTAGAATTTGATTTTTTTATTAAGTTAA
1 AACGCCAATACATTGAAAAATTTGATTATTTAAAAGCTTAGAATTTG-TTTTTTTATTAAGTTAA
* * *
25413 AGGTAATTAAAAAAATAGCATATGTTTTAATTATTTTTAATTATTTGACAATGAATGTTGAAACC
65 AGGTGATT-ATAAAATAACATATGTTTTAATTATTTTTAATTATTTGACAATGAATGTTGAAACC
25478 ATTCTTATAAT
129 ATTCTTATAAT
*
25489 AACGCCAATACATT-AGAAAATTTGATTATTTAAAAGCTTAGAATTTATTTTTTTATTAAGTTAA
1 AACGCCAATACATTGA-AAAATTTGATTATTTAAAAGCTTAGAATTTGTTTTTTTATTAAGTTAA
** * *
25553 AAATGATTGTAAAATAACATATGTTTTAATTATTTTTAATTATTTGACAGTGAATGTTGAAACCA
65 AGGTGATTATAAAATAACATATGTTTTAATTATTTTTAATTATTTGACAATGAATGTTGAAACCA
*
25618 TTCTTGTAAT
130 TTCTTATAAT
* ** * * ** *
25628 AACGCCAATGCATTGAAAAAACTAATTATTTAAAAGCTTAAAATTTGTTTACTTATTAAATTAAA
1 AACGCCAATACATTGAAAAATTTGATTATTTAAAAGCTTAGAATTTGTTTTTTTATTAAGTTAAA
*
25693 GGTGGTTATAAAATA
66 GGTGATTATAAAATA
25708 GTATATTTAT
Statistics
Matches: 193, Mismatches: 24, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
139 127 0.66
140 24 0.12
141 42 0.22
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (139 bp):
AACGCCAATACATTGAAAAATTTGATTATTTAAAAGCTTAGAATTTGTTTTTTTATTAAGTTAAA
GGTGATTATAAAATAACATATGTTTTAATTATTTTTAATTATTTGACAATGAATGTTGAAACCAT
TCTTATAAT
Found at i:28976 original size:24 final size:24
Alignment explanation
Indices: 28949--29003 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
28939 TTGTGCTAAG
28949 GGCTATTCTGAAGATATATAAATT
1 GGCTATTCTGAAGATATATAAATT
28973 GGCTATTCTGAAGATATATAAATT
1 GGCTATTCTGAAGATATATAAATT
*
28997 TGCTATT
1 GGCTATT
29004 ATGTTACCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (24 bp):
GGCTATTCTGAAGATATATAAATT
Found at i:30362 original size:2 final size:2
Alignment explanation
Indices: 30357--30404 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
30347 GTTATGAATA
30357 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
30399 AT AT AT
1 AT AT AT
30405 GGTTACATTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30740 original size:18 final size:18
Alignment explanation
Indices: 30706--30740 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30696 GTTCTTAAGG
*
30706 AGTGGTCATTTGAGACAT
1 AGTGGTCATTCGAGACAT
*
30724 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGAGACA
30741 AATATTCAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (18 bp):
AGTGGTCATTCGAGACAT
Found at i:40004 original size:23 final size:23
Alignment explanation
Indices: 39977--40049 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
39967 ACACTTTGCA
39977 ATATAACCACTACCTATTACATT
1 ATATAACCACTACCTATTACATT
*
40000 ATATAAACGA-TACCTATTACATT
1 ATAT-AACCACTACCTATTACATT
* * *
40023 ATATAAGCGCTACCTATTACATC
1 ATATAACCACTACCTATTACATT
40046 ATAT
1 ATAT
40050 TTTTACCTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
22 2 0.05
23 37 0.86
24 4 0.09
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.34
Consensus pattern (23 bp):
ATATAACCACTACCTATTACATT
Found at i:40526 original size:39 final size:39
Alignment explanation
Indices: 40472--40557 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
40462 CAAGTTGTAG
*
40472 ATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGA
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
* *
40511 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
40550 ATTTTGAT
1 ATTTTGAT
40558 GAGCATCGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.49
Consensus pattern (39 bp):
ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
Found at i:40839 original size:18 final size:18
Alignment explanation
Indices: 40816--40852 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
40806 CGAAATATAT
40816 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
40834 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
40852 A
1 A
40853 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:41314 original size:23 final size:23
Alignment explanation
Indices: 41288--41350 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
41278 ATATAACCAC
41288 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
41311 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
41334 TACCTATTACATCATAT
1 TACCTATTACATTATAT
41351 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:41752 original size:25 final size:25
Alignment explanation
Indices: 41695--41760 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
41685 CACTCAAAAG
*
41695 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
41720 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
41745 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
41761 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:44753 original size:183 final size:183
Alignment explanation
Indices: 44228--44720 Score: 871
Period size: 183 Copynumber: 2.7 Consensus size: 183
44218 TTAAAATTAC
*
44228 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
* *
44293 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* *
44358 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
* * *
44411 CGATACTTTTTTAAATCGTATCGACATATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
*
44476 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTACATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
44541 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
*
44594 CGACACTTTTTAACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
1 CGACACTTTTTTA-AATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
*
44658 GATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
65 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
44721 ATAGCATTGC
Statistics
Matches: 294, Mismatches: 15, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
183 291 0.99
184 3 0.01
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Consensus pattern (183 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
Found at i:46227 original size:3 final size:3
Alignment explanation
Indices: 46219--46299 Score: 72
Period size: 3 Copynumber: 27.0 Consensus size: 3
46209 ACTTGTTTGG
* * * **
46219 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
46267 AGC TTC ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
46300 GTCAGCTTCA
Statistics
Matches: 59, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.23, C:0.35, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:46236 original size:12 final size:12
Alignment explanation
Indices: 46223--46311 Score: 88
Period size: 12 Copynumber: 7.4 Consensus size: 12
46213 GTTTGGATCA
* *
46223 TCATCTTCATCA
1 TCATCGTCATCT
* *
46235 TCATCATCATCA
1 TCATCGTCATCT
* *
46247 TCGTCATCATCT
1 TCATCGTCATCT
* *
46259 TCATCGCCAGCT
1 TCATCGTCATCT
*
46271 TCATCGTCATCA
1 TCATCGTCATCT
46283 TCATCGTCATCT
1 TCATCGTCATCT
*
46295 TCATCGTCAGCT
1 TCATCGTCATCT
46307 TCATC
1 TCATC
46312 TTCTGCGACC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:46242 original size:18 final size:18
Alignment explanation
Indices: 46223--46314 Score: 76
Period size: 18 Copynumber: 5.1 Consensus size: 18
46213 GTTTGGATCA
* *
46223 TCATCTTCATCATCATCA
1 TCATCATCATCATCATCT
*
46241 TCATCATCGTCATCATCT
1 TCATCATCATCATCATCT
** * * *
46259 TCATCGCCAGCTTCATCG
1 TCATCATCATCATCATCT
*
46277 TCATCATCATCGTCATCT
1 TCATCATCATCATCATCT
* * *
46295 TCATCGTCAGCTTCATCT
1 TCATCATCATCATCATCT
46313 TC
1 TC
46315 TGCGACCGCT
Statistics
Matches: 57, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.37
Consensus pattern (18 bp):
TCATCATCATCATCATCT
Found at i:46275 original size:36 final size:36
Alignment explanation
Indices: 46235--46311 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
46225 ATCTTCATCA
*
46235 TCATCATCATCATCGTCATCATCTTCATCGCCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCT
* * *
46271 TCATCGTCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCT
46307 TCATC
1 TCATC
46312 TTCTGCGACC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.21, C:0.35, G:0.09, T:0.35
Consensus pattern (36 bp):
TCATCATCATCATCATCATCATCTTCATCGCCAGCT
Found at i:46314 original size:6 final size:6
Alignment explanation
Indices: 46223--46314 Score: 67
Period size: 6 Copynumber: 15.3 Consensus size: 6
46213 GTTTGGATCA
* * * * * * * *
46223 TCATCT TCATCA TCATCA TCATCA TCGTCA TCATCT TCATCG CCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * * *
46271 TCATCG TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
46315 TGCGACCGCT
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.37
Consensus pattern (6 bp):
TCATCT
Found at i:48649 original size:397 final size:397
Alignment explanation
Indices: 47779--49341 Score: 2810
Period size: 397 Copynumber: 3.9 Consensus size: 397
47769 TTTAAATTAG
* * *
47779 TATCGACACAAACTAAAACGTGTCGACACATTATTTAGACATATTCTCTCATAAAATCGGTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAAC
47844 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
* * *
47909 GACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGACCAA
131 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACAA
* *
47974 AAATATCGACACCAACTAAA-AAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGT
196 AAATATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGT
*
48038 ATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGG
261 AAACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
48102 GATCGACAC-TTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGA
326 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGA
48165 CCAAAAA
391 CCAAAAA
*
48172 TATCGACACCAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAAC
*
48237 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTAGATGATTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
48302 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACAA
131 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACAA
* *
48367 AAATATCGAGACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTTATAAAACCGGT
196 AAATATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGT
*
48432 AAACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATATTGG
261 AAACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
48497 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGA
326 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGA
48562 CCAAAAA
391 CCAAAAA
*
48569 TATCGACACCAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAAC
*
48634 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTAGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
48699 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACAA
131 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACAA
* *
48764 AAATATCGACACAAACTAAATTAGTGTTGACACATTATTTAGACATATTCTCTGATAAAACCGGT
196 AAATATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGT
48829 AAACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
261 AAACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
* *
48894 GATCGACACTTTTTATATATGGATCGACACTTTGTGGTTGCACCCTGTTTTCCATTCATTCTGGA
326 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGA
*
48959 ACAAAAA
391 CCAAAAA
*
48966 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
1 TATCGACACAAACTAAA-AAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
*
49031 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
65 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
49096 CGACACTTTTTATATATGGATCAACACTTTATGGTTGCACCCTGTTTTCCATTCATTATGGAACA
130 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
49161 AAAATATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
195 AAAATATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
* *
49226 TAAACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTT
260 TAAACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTT
* * *
49291 GGGATTGACACTTTTTATATATGGATCGACACTTTATGGTTACACCCTGTT
324 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
49342 GGCCATATTG
Statistics
Matches: 1128, Mismatches: 36, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
393 205 0.18
394 100 0.09
395 13 0.01
396 4 0.00
397 461 0.41
398 286 0.25
399 59 0.05
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36
Consensus pattern (397 bp):
TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAAC
TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACAA
AAATATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGT
AAACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGA
CCAAAAA
Found at i:48683 original size:198 final size:199
Alignment explanation
Indices: 47779--49341 Score: 2771
Period size: 199 Copynumber: 7.9 Consensus size: 199
47769 TTTAAATTAG
* * *
47779 TATCGACACAAACTAAA-ACGTGTCGACACATTATTTAGACATATTCTCTCATAAAATCGGTATA
1 TATCGACACAAACTAAATAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
47843 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * *
47908 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGACCA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
47973 AAAA
196 AAAA
* *
47977 TATCGACACCAACTAAA-AAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAATAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
48041 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
48105 CGACAC-TTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGACCA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
48168 AAAA
196 AAAA
*
48172 TATCGACACCAACTAAA-AAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
1 TATCGACACAAACTAAATAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
*
48236 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTAGATGATTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
48301 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
48366 AAAA
196 AAAA
* * *
48370 TATCGAGACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTTATAAAACCGGTAAA
1 TATCGACACAAACTAAATAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
*
48435 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATATTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
48500 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGACCA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
48565 AAAA
196 AAAA
*
48569 TATCGACACCAACTAAA-AAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
1 TATCGACACAAACTAAATAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
*
48633 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTAGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
48698 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
48763 AAAA
196 AAAA
* * *
48767 TATCGACACAAACTAAATTAGTGTTGACACATTATTTAGACATATTCTCTGATAAAACCGGTAAA
1 TATCGACACAAACTAAATAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
48832 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
48897 CGACACTTTTTATATATGGATCGACACTTTGTGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
48962 AAAA
196 AAAA
*
48966 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
1 TATCGACACAAACTAAATAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
*
49031 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
49096 CGACACTTTTTATATATGGATCAACACTTTATGGTTGCACCCTGTTTTCCATTCATTATGGAACA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
49161 AAAA
196 AAAA
*
49165 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
1 TATCGACACAAACTAAATAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
* *
49230 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
* *
49295 TTGACACTTTTTATATATGGATCGACACTTTATGGTTACACCCTGTT
130 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
49342 GGCCATATTG
Statistics
Matches: 1319, Mismatches: 40, Indels: 10
0.96 0.03 0.01
Matches are distributed among these distances:
195 174 0.13
196 18 0.01
197 18 0.01
198 378 0.29
199 671 0.51
200 60 0.05
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36
Consensus pattern (199 bp):
TATCGACACAAACTAAATAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
AAAA
Found at i:49497 original size:19 final size:19
Alignment explanation
Indices: 49451--49499 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
49441 TTATATTCAC
*
49451 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
49470 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
49489 ATACAAAATTA
1 ATACAAAATTA
49500 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:51327 original size:33 final size:33
Alignment explanation
Indices: 51290--51355 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
51280 CATCTTAATA
*
51290 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
51323 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
51356 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:51414 original size:21 final size:21
Alignment explanation
Indices: 51389--51432 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
51379 CCCCTTATGC
51389 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
51410 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
51431 CT
1 CT
51433 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:53853 original size:20 final size:20
Alignment explanation
Indices: 53826--53872 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
53816 TCCGGTAACG
53826 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
53845 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
53866 TTTTACC
1 TTTTACC
53873 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:54401 original size:228 final size:228
Alignment explanation
Indices: 53921--54864 Score: 1772
Period size: 228 Copynumber: 4.2 Consensus size: 228
53911 ACTTTTATAC
*
53921 GTATGAACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
1 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
53986 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC-AAAAAT
66 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAAT
54050 TATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAG
131 TATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAG
54115 ATAATAATAAATATGTTTTCCACAGTGAAATAA
196 ATAATAATAAATATGTTTTCCACAGTGAAATAA
*
54148 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATCTTTCAATTT
1 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
54213 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAAA
66 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC-AAAAAA
54278 TTA-TTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
130 TTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
54342 GATAATAATAAATATGTTTTCCACAGTGAAATAA
195 GATAATAATAAATATGTTTTCCACAGTGAAATAA
54376 GTATGGACACTTTTATAAAAATGATATATA-TATTTTTTAAAGTTATGTAATTTATGTTTCAATT
1 GTATGGACACTTTTATAAAAATGATATATACT-TTTTTTAAAGTTATGTAATTTATGTTTCAATT
54440 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
65 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
54505 TTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
130 TTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
54570 GATAATAATAAATATGTTTTCCACAGTGAAATAA
195 GATAATAATAAATATGTTTTCCACAGTGAAATAA
54604 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
1 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
*
54669 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACACAAAAT
66 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAAT
54734 TATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAG
131 TATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAG
*
54799 ATAATAATAAATATATTTT-CACAGTGAAATAA
196 ATAATAATAAATATGTTTTCCACAGTGAAATAA
* * *
54831 GTATGAACACTTTTATAAAAAGGATAGATA-TTTT
1 GTATGGACACTTTTATAAAAATGATATATACTTTT
54865 ACAATATAAC
Statistics
Matches: 704, Mismatches: 8, Indels: 11
0.97 0.01 0.02
Matches are distributed among these distances:
226 4 0.01
227 171 0.24
228 520 0.74
229 9 0.01
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.44
Consensus pattern (228 bp):
GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAAT
TATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAG
ATAATAATAAATATGTTTTCCACAGTGAAATAA
Found at i:61243 original size:23 final size:23
Alignment explanation
Indices: 61195--61243 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
61185 TCACCTCTTG
* * * *
61195 AAATTTTAGAAGTTTGTCCCTTA
1 AAATTTTAAAAGTTCGTCACTCA
61218 AAATTTTAAAAGTTCGTCACTCA
1 AAATTTTAAAAGTTCGTCACTCA
61241 AAA
1 AAA
61244 ATTAAAATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (23 bp):
AAATTTTAAAAGTTCGTCACTCA
Found at i:64489 original size:18 final size:18
Alignment explanation
Indices: 64466--64500 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
64456 TTCCATCCGG
*
64466 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
64484 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
64501 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:69647 original size:18 final size:18
Alignment explanation
Indices: 69624--69658 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
69614 TTCCATCCGG
*
69624 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
69642 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
69659 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:70953 original size:7 final size:7
Alignment explanation
Indices: 70933--70965 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
70923 GTGGTTAACG
70933 ACGGTCA
1 ACGGTCA
70940 ACGGGTCA
1 AC-GGTCA
70948 ACGGTCA
1 ACGGTCA
70955 ACGGTCA
1 ACGGTCA
70962 ACGG
1 ACGG
70966 GTCGAGTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.27, C:0.27, G:0.33, T:0.12
Consensus pattern (7 bp):
ACGGTCA
Found at i:71004 original size:13 final size:13
Alignment explanation
Indices: 70957--70986 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
70947 AACGGTCAAC
70957 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
70970 AGTCAACGGGTCG
1 GGTCAACGGGTCG
70983 GGTC
1 GGTC
70987 GGGTCAACGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:71006 original size:18 final size:18
Alignment explanation
Indices: 70963--71009 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
70953 CAACGGTCAA
*
70963 CGGGTCGAGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
70981 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
70999 CGGGTCGGGTC
1 CGGGTCGGGTC
71010 GGGTTGTGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.11, C:0.23, G:0.49, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:77277 original size:3 final size:3
Alignment explanation
Indices: 77265--77301 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
77255 CATTTTTGAA
77265 AAT AAT -AT AAT AAT AAT -AT AAT AAT AAAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AA
77302 GCAATAGCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.13
3 24 0.77
4 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:77281 original size:11 final size:11
Alignment explanation
Indices: 77265--77301 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
77255 CATTTTTGAA
77265 AATAATATAAT
1 AATAATATAAT
77276 AATAATATAAT
1 AATAATATAAT
77287 AATAA-ATAAT
1 AATAATATAAT
77297 AATAA
1 AATAA
77302 GCAATAGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AATAATATAAT
Done.