Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003470.1 Hibiscus syriacus cultivar Beakdansim tig00007341_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: 87039
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:2680 original size:23 final size:24
Alignment explanation
Indices: 2647--2698 Score: 97
Period size: 23 Copynumber: 2.2 Consensus size: 24
2637 AAAAATATGT
2647 CATGTCACCATTTTCGACATGTAA
1 CATGTCACCATTTTCGACATGTAA
2671 CATGT-ACCATTTTCGACATGTAA
1 CATGTCACCATTTTCGACATGTAA
2694 CATGT
1 CATGT
2699 TTTATGTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 23 0.82
24 5 0.18
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (24 bp):
CATGTCACCATTTTCGACATGTAA
Found at i:3927 original size:31 final size:31
Alignment explanation
Indices: 3889--3966 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
3879 ATATGAGGAT
** *
3889 GACTTTGACAAAGTCGTCGGCACATGAAGAC
1 GACTTTGACAAAGTCACCGGCAAATGAAGAC
* * *
3920 GATTTTGATAAAGCCACCGGCAAATGAAGAC
1 GACTTTGACAAAGTCACCGGCAAATGAAGAC
*
3951 GACTCTGACAAAGTCA
1 GACTTTGACAAAGTCA
3967 TCGACAAGTG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (31 bp):
GACTTTGACAAAGTCACCGGCAAATGAAGAC
Found at i:4498 original size:2 final size:2
Alignment explanation
Indices: 4493--4522 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4483 AAGTTCTAAG
4493 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4523 GAGAGAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5433 original size:22 final size:20
Alignment explanation
Indices: 5408--5456 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 20
5398 AAGACGGAGG
5408 AAAATATATCAAAATGTAGAGA
1 AAAATATATCAAAA-G-AGAGA
*
5430 AAAAAATATCAAAAGAGAGA
1 AAAATATATCAAAAGAGAGA
5450 AAAATAT
1 AAAATAT
5457 GCAATAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 11 0.44
21 1 0.04
22 13 0.52
ACGTcount: A:0.65, C:0.04, G:0.12, T:0.18
Consensus pattern (20 bp):
AAAATATATCAAAAGAGAGA
Found at i:5471 original size:19 final size:18
Alignment explanation
Indices: 5425--5471 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
5415 ATCAAAATGT
*
5425 AGAGAAAAAAATATCAAA
1 AGAGACAAAAATATCAAA
*
5443 AGAGAGAAAAATATGCAATA
1 AGAGACAAAAATAT-CAA-A
5463 A-AGACAAAA
1 AGAGACAAAA
5472 TTATTAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 13 0.52
19 10 0.40
20 2 0.08
ACGTcount: A:0.68, C:0.06, G:0.15, T:0.11
Consensus pattern (18 bp):
AGAGACAAAAATATCAAA
Found at i:15786 original size:2 final size:2
Alignment explanation
Indices: 15750--15776 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
15740 TCTTTTTTAA
15750 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
15777 ATTTTATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16092 original size:59 final size:59
Alignment explanation
Indices: 15998--16181 Score: 192
Period size: 59 Copynumber: 3.1 Consensus size: 59
15988 TCATATGTAA
* * * * * *
15998 CCAAACTATAACCCTCATTTTAAATTGAAT-TTTAAACTTTTGAATATTTTAATTTCATC
1 CCAAATTATGACCCTCATTCTAAATT-AGTCCTTAAACTTTTGAATATTCTAATTTCATC
* *
16057 CCAAATTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTGAACATTCTAATTTCATC
1 CCAAATTATGACCCTCATTCTAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATC
* * * * * * * *
16116 CTTAAACTATGACCCTCATTCTAAATTGGTCC-CAAGCGTTTGAATCTTCCAATTTCATC
1 C-CAAATTATGACCCTCATTCTAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATC
16175 CCAAATT
1 CCAAATT
16182 TCATCCAAAT
Statistics
Matches: 103, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
58 6 0.06
59 71 0.69
60 26 0.25
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (59 bp):
CCAAATTATGACCCTCATTCTAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATC
Found at i:16117 original size:29 final size:29
Alignment explanation
Indices: 16029--16123 Score: 79
Period size: 29 Copynumber: 3.2 Consensus size: 29
16019 AAATTGAATT
* *
16029 TTAAACTTTTGAATATTTTAATTTCATCC
1 TTAAACTTTTGAACATTCTAATTTCATCC
* * * *
16058 -CAAA-TTATGACTCTCATTCTAAATT-AGTCC
1 TTAAACTTTTGA---ACATTCTAATTTCA-TCC
16088 TTAAACTTTTGAACATTCTAATTTCATCC
1 TTAAACTTTTGAACATTCTAATTTCATCC
16117 TTAAACT
1 TTAAACT
16124 ATGACCCTCA
Statistics
Matches: 49, Mismatches: 10, Indels: 14
0.67 0.14 0.19
Matches are distributed among these distances:
27 5 0.10
28 3 0.06
29 21 0.43
30 12 0.24
31 3 0.06
32 5 0.10
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.44
Consensus pattern (29 bp):
TTAAACTTTTGAACATTCTAATTTCATCC
Found at i:17932 original size:60 final size:60
Alignment explanation
Indices: 17868--17984 Score: 216
Period size: 60 Copynumber: 1.9 Consensus size: 60
17858 AATAGTCGGG
17868 TGACCATTTTATAACTTTTAATAGTCGAGGGACTCAACAAAGCAACACCCTATAGTCAAA
1 TGACCATTTTATAACTTTTAATAGTCGAGGGACTCAACAAAGCAACACCCTATAGTCAAA
* *
17928 TGACCATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAGCATCACCCTATAGTC
1 TGACCATTTTATAACTTTTAATAGTCGAGGGACTCAACAAAGCAACACCCTATAGTC
17985 GAGAGATTAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (60 bp):
TGACCATTTTATAACTTTTAATAGTCGAGGGACTCAACAAAGCAACACCCTATAGTCAAA
Found at i:22652 original size:22 final size:22
Alignment explanation
Indices: 22616--22666 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
22606 TGAAGAACCT
*
22616 AATATT-TCGATTTTAACTTAA
1 AATATTATCGAATTTAACTTAA
**
22637 AATATTATCGAATTTATTTTAA
1 AATATTATCGAATTTAACTTAA
*
22659 AAAATTAT
1 AATATTAT
22667 AATCAATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (22 bp):
AATATTATCGAATTTAACTTAA
Found at i:26347 original size:60 final size:60
Alignment explanation
Indices: 26237--26350 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
26227 GTCGAATGAC
* * * * *
26237 TATTTTATAACTTTTAATAGTCGGAGAACTCAACAAAACGACGTCCTATAATAGAATAAT
1 TATTTTATAACTTTTAATAGTCGAAAAACTCAACAAAACAACATCATATAATAGAATAAT
* * * *
26297 TATTTTATAGCTTTTAATAGTCGAAAAACTCAATAAAATAATATCATATAATAG
1 TATTTTATAACTTTTAATAGTCGAAAAACTCAACAAAACAACATCATATAATAG
26351 GGAATCATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (60 bp):
TATTTTATAACTTTTAATAGTCGAAAAACTCAACAAAACAACATCATATAATAGAATAAT
Found at i:31516 original size:21 final size:20
Alignment explanation
Indices: 31492--31683 Score: 81
Period size: 21 Copynumber: 9.2 Consensus size: 20
31482 GATTCGCAAC
31492 GCGATAGTCGAAGTTCGCATT
1 GCGATAGTCGAAGTTCGC-TT
* * *
31513 GCGATTCATTCCAAATTCG-TT
1 GCGA-T-AGTCGAAGTTCGCTT
31534 GCGATAGTCGAAGTTCGCGTT
1 GCGATAGTCGAAGTTCGC-TT
* * *
31555 GCGATTCATTCCAA-ATCG-TT
1 GCGA-T-AGTCGAAGTTCGCTT
*
31575 GCGATAGTCGAAGTTCGAGTT
1 GCGATAGTCGAAGTTCG-CTT
* * * *
31596 GCAATTCATTCTAA-ATCG-TT
1 GCGA-T-AGTCGAAGTTCGCTT
*
31616 GCGATAGGCGAAGTTCGCGTT
1 GCGATAGTCGAAGTTCGC-TT
* * *
31637 GCGATTCATTCCAAATTCG-TT
1 GCGA-T-AGTCGAAGTTCGCTT
*
31658 GCGATAGGCGAAGTTCGCGTT
1 GCGATAGTCGAAGTTCGC-TT
31679 GCGAT
1 GCGAT
31684 TCATTCTAAA
Statistics
Matches: 124, Mismatches: 29, Indels: 36
0.66 0.15 0.19
Matches are distributed among these distances:
18 9 0.07
19 25 0.20
20 13 0.10
21 40 0.32
22 10 0.08
23 27 0.22
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (20 bp):
GCGATAGTCGAAGTTCGCTT
Found at i:31586 original size:41 final size:42
Alignment explanation
Indices: 31492--31708 Score: 357
Period size: 42 Copynumber: 5.2 Consensus size: 42
31482 GATTCGCAAC
*
31492 GCGATAGTCGAAGTTCGCATTGCGATTCATTCCAAATTCGTT
1 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
31534 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAA-TCGTT
1 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
* * *
31575 GCGATAGTCGAAGTTCGAGTTGCAATTCATTCTAAA-TCGTT
1 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
*
31616 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
1 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
* *
31658 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCTAAATTCGTT
1 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
31700 GCGATAGTC
1 GCGATAGTC
31709 CAAATATTGC
Statistics
Matches: 164, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
41 75 0.46
42 89 0.54
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.32
Consensus pattern (42 bp):
GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
Found at i:32493 original size:6 final size:6
Alignment explanation
Indices: 32482--32508 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
32472 TCCTGTCTCG
32482 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
32509 AATGGTAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:32667 original size:41 final size:41
Alignment explanation
Indices: 32598--32852 Score: 393
Period size: 41 Copynumber: 6.2 Consensus size: 41
32588 AATATTTGGA
* *
32598 CTATCGCAACAAATTTGTAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTCGC
* * * *
32640 ATGTCGCAACGAATTGGAATTAATCGCAATGCGAACTTCGC
1 CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGC
32681 CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGC
*
32722 CTATCGCAACGAATTGGAATTAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGC
** *
32763 CTATCGCAACGCTTTGGAATGAATCGCAACGCGAACTTCGA
1 CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGC
*
32804 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGA
1 CTATCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTCGC
32846 CTATCGC
1 CTATCGC
32853 GTTGCGAATC
Statistics
Matches: 195, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
41 150 0.77
42 45 0.23
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.22
Consensus pattern (41 bp):
CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGC
Found at i:32668 original size:20 final size:20
Alignment explanation
Indices: 32643--32752 Score: 75
Period size: 20 Copynumber: 5.4 Consensus size: 20
32633 ACTTCGCATG
32643 TCGCAACGAATTGGAATTAA
1 TCGCAACGAATTGGAATTAA
* **
32663 TCGCAATGCGAACTTCG-CCT-A
1 TCGCAA--CGAA-TTGGAATTAA
*
32684 TCGCAACGAATTGGAATGAA
1 TCGCAACGAATTGGAATTAA
* **
32704 TCGCAACGCGAACTTCG-CCT-A
1 TCGCAA--CGAA-TTGGAATTAA
32725 TCGCAACGAATTGGAATTAA
1 TCGCAACGAATTGGAATTAA
32745 TCGCAACG
1 TCGCAACG
32753 CGAACTTCGC
Statistics
Matches: 66, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
18 6 0.09
19 9 0.14
20 22 0.33
21 14 0.21
22 9 0.14
23 6 0.09
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAACGAATTGGAATTAA
Found at i:32772 original size:21 final size:21
Alignment explanation
Indices: 32662--32774 Score: 85
Period size: 21 Copynumber: 5.5 Consensus size: 21
32652 ATTGGAATTA
*
32662 ATCGCAATGCGAACTTCGCCT
1 ATCGCAACGCGAACTTCGCCT
* **
32683 ATCGCAA--CGAA-TTGGAAT
1 ATCGCAACGCGAACTTCGCCT
32701 GAATCGCAACGCGAACTTCGCCT
1 --ATCGCAACGCGAACTTCGCCT
* **
32724 ATCGCAA--CGAA-TTGGAATT
1 ATCGCAACGCGAACTTCG-CCT
32743 AATCGCAACGCGAACTTCGCCT
1 -ATCGCAACGCGAACTTCGCCT
32765 ATCGCAACGC
1 ATCGCAACGC
32775 TTTGGAATGA
Statistics
Matches: 70, Mismatches: 12, Indels: 20
0.69 0.12 0.20
Matches are distributed among these distances:
18 7 0.10
19 9 0.13
20 14 0.20
21 24 0.34
22 9 0.13
23 7 0.10
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGCCT
Found at i:33311 original size:13 final size:13
Alignment explanation
Indices: 33293--33321 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
33283 ACACTTTAAA
33293 ATTTTATAATTTT
1 ATTTTATAATTTT
33306 ATTTTATAATTTT
1 ATTTTATAATTTT
33319 ATT
1 ATT
33322 ATATCCTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTTATAATTTT
Found at i:34663 original size:60 final size:60
Alignment explanation
Indices: 34536--34672 Score: 154
Period size: 60 Copynumber: 2.3 Consensus size: 60
34526 ACACCTGAGT
* * * * * *
34536 GACCATTTTATAACTTTTAATGGTCAAGGGACTCAACAAAGCAACGTCCTATAGTCGATG
1 GACCATTTTGTAACTTTTAATAGTCAAGAGACTCAACAAAGCAACGTCCCATAATCGAAG
* *
34596 GATCATTTTGTAACTTTTAATAGTCAAGAGACTCAACAAAG-TA-GTACCCATTAATCGAAG
1 GACCATTTTGTAACTTTTAATAGTCAAGAGACTCAACAAAGCAACGT-CCCA-TAATCGAAG
34656 GACCATTTATGT-ACTTT
1 GACCATTT-TGTAACTTT
34673 AACCATAATT
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
58 2 0.03
59 4 0.06
60 56 0.86
61 3 0.05
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAGTCAAGAGACTCAACAAAGCAACGTCCCATAATCGAAG
Found at i:40986 original size:2 final size:2
Alignment explanation
Indices: 40979--41008 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
40969 CAGTCTATCC
40979 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
41009 GTATGCATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48998 original size:15 final size:15
Alignment explanation
Indices: 48978--49007 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
48968 TGTCACTCAC
48978 TATTATAATAATATA
1 TATTATAATAATATA
*
48993 TATTATTATAATATA
1 TATTATAATAATATA
49008 ATTTATATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTATAATAATATA
Found at i:56092 original size:20 final size:20
Alignment explanation
Indices: 56067--56260 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
56057 GATTTTCAAT
* *
56067 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
56087 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
56107 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
56127 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
56147 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
56167 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
56187 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
56207 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
56228 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
56248 AATCGCAACGCGA
1 AATCGCAACGCGA
56261 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:56112 original size:40 final size:39
Alignment explanation
Indices: 56067--56260 Score: 199
Period size: 40 Copynumber: 4.8 Consensus size: 39
56057 GATTTTCAAT
* ** *
56067 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CATA
* * *
56107 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
** * * *
56147 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
* ** *
56187 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT-A
56228 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
56261 TATTTAAAGC
Statistics
Matches: 128, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.01
40 94 0.73
41 33 0.26
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (39 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACCATA
Found at i:56136 original size:60 final size:60
Alignment explanation
Indices: 56067--56260 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
56057 GATTTTCAAT
** * *
56067 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * * *** *
56127 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * **
56187 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
56248 AATCGCAACGCGA
1 AATCGCAACGCGA
56261 TATTTAAAGC
Statistics
Matches: 111, Mismatches: 22, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGAATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:56679 original size:33 final size:33
Alignment explanation
Indices: 56640--56710 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
56630 TTCACTTAGA
*
56640 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
56673 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
56706 TTTCA
1 TTTCA
56711 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:56850 original size:14 final size:14
Alignment explanation
Indices: 56831--56885 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
56821 AGAATGACTG
56831 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
56845 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
56864 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
56878 TCGCAACG
1 TCGCAACG
56886 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:56868 original size:33 final size:33
Alignment explanation
Indices: 56831--56901 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
56821 AGAATGACTG
**
56831 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
56864 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
56897 TCGCA
1 TCGCA
56902 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:56919 original size:19 final size:19
Alignment explanation
Indices: 56897--56994 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
56887 GAAACCAAAA
*
56897 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
56916 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
56930 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
56949 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
56963 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
56982 TCGCGTTGCGATT
1 TCGCGTTGCGATT
56995 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:56938 original size:14 final size:14
Alignment explanation
Indices: 56919--57008 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
56909 TTTCATTTCG
56919 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
56933 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
56952 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
56966 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
56983 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
56999 CGTTGCGATT
1 CGTTGCGATT
57009 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:56944 original size:33 final size:33
Alignment explanation
Indices: 56902--57016 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
56892 CAAAATCGCA
56902 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
56935 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
56968 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
57001 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
57017 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:58919 original size:92 final size:93
Alignment explanation
Indices: 58713--59091 Score: 735
Period size: 92 Copynumber: 4.1 Consensus size: 93
58703 TAGATTGCTT
*
58713 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
58778 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
58806 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
58870 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
58898 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
58962 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
58990 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
59055 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
59083 AGTAAATTT
1 AGTAAATTT
59092 ATCCATTCAA
Statistics
Matches: 284, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 184 0.65
93 100 0.35
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:58943 original size:185 final size:185
Alignment explanation
Indices: 58713--59093 Score: 737
Period size: 185 Copynumber: 2.1 Consensus size: 185
58703 TAGATTGCTT
58713 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
58778 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
58843 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
130 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
58898 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
58963 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
66 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
59028 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
59083 AGTAAATTTAT
1 AGTAAATTTAT
59094 CCATTCAAGT
Statistics
Matches: 193, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
184 92 0.48
185 101 0.52
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (185 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:59175 original size:19 final size:19
Alignment explanation
Indices: 59135--59263 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
59125 TAGTTTACTT
* *
59135 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
59155 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
59174 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
59193 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
59207 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
59226 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
59240 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
59259 TCGCA
1 TCGCA
59264 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:59214 original size:33 final size:32
Alignment explanation
Indices: 59171--59263 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
59161 CGCGAAACCA
**
59171 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
59203 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
59236 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
59264 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:59261 original size:52 final size:52
Alignment explanation
Indices: 59135--59263 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
59125 TAGTTTACTT
**
59135 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
59187 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
59240 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
59264 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:59281 original size:19 final size:19
Alignment explanation
Indices: 59259--59393 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
59249 GAAACCAAAA
*
59259 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
59278 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
59294 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
59311 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
59327 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
59344 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
59363 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
59383 TCGTGTTGCGA
1 TCGCGTTGCGA
59394 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:59300 original size:14 final size:14
Alignment explanation
Indices: 59281--59337 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
59271 TTTCATTTCG
59281 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
59295 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
59312 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
59328 CGTTGCGATT
1 CGTTGCGATT
59338 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:59306 original size:33 final size:33
Alignment explanation
Indices: 59264--59356 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
59254 CAAAATCGCA
*
59264 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
59297 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
59330 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
59357 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:59900 original size:21 final size:20
Alignment explanation
Indices: 59846--59906 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
59836 CTCGAGAGTC
*
59846 CCCTCCCACCGTTGAAGAGG
1 CCCTCCCACCATTGAAGAGG
** *
59866 CCACTGTCATCATTGAAGAGG
1 CC-CTCCCACCATTGAAGAGG
*
59887 TCCCTCCCACCATTCAAGAG
1 -CCCTCCCACCATTGAAGAG
59907 CCCGATTCAC
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.25, C:0.36, G:0.20, T:0.20
Consensus pattern (20 bp):
CCCTCCCACCATTGAAGAGG
Found at i:61314 original size:13 final size:14
Alignment explanation
Indices: 61289--61323 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
61279 ATTGTTTAAT
61289 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
61303 TGATTTGT-AAAGT
1 TGATTTGTAAAAGA
61316 TGATTTGT
1 TGATTTGT
61324 GTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:61452 original size:19 final size:19
Alignment explanation
Indices: 61430--61512 Score: 104
Period size: 19 Copynumber: 4.6 Consensus size: 19
61420 AAAAATGACT
*
61430 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
*
61449 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
61463 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
61482 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
61502 ATCGCAATGCG
1 ATCGCAATGCG
61513 TTTATAATTT
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
14 9 0.16
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 21 0.38
20 19 0.35
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:61498 original size:20 final size:20
Alignment explanation
Indices: 61462--61512 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
61452 GCAACGAGAG
61462 AATCGCAATGC-GAAATGAA
1 AATCGCAATGCGGAAATGAA
61481 AATCGCAATGCGGAAATGAA
1 AATCGCAATGCGGAAATGAA
61501 AATCGCAATGCG
1 AATCGCAATGCG
61513 TTTATAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 11 0.35
20 20 0.65
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.16
Consensus pattern (20 bp):
AATCGCAATGCGGAAATGAA
Found at i:61565 original size:19 final size:19
Alignment explanation
Indices: 61541--61814 Score: 354
Period size: 19 Copynumber: 15.4 Consensus size: 19
61531 GATTATCTCG
61541 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
61560 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
61579 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
61593 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
61612 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
61631 TTGCGATTTCCATTTCGCA
1 TTGCGATTTTCATTTCGCA
61650 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
61669 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
61688 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
61702 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
61721 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
61740 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
61754 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
61774 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
61788 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
61807 TTGCGATT
1 TTGCGATT
61815 GTATTTTCCG
Statistics
Matches: 226, Mismatches: 8, Indels: 42
0.82 0.03 0.15
Matches are distributed among these distances:
14 29 0.13
16 24 0.11
17 21 0.09
18 3 0.01
19 137 0.61
20 12 0.05
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:61581 original size:52 final size:52
Alignment explanation
Indices: 61519--61786 Score: 455
Period size: 52 Copynumber: 5.0 Consensus size: 52
61509 TGCGTTTATA
*
61519 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
61571 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
61623 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TT-C-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
61680 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
61732 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
61785 AT
1 AT
61787 GTTGGGATTT
Statistics
Matches: 207, Mismatches: 3, Indels: 11
0.94 0.01 0.05
Matches are distributed among these distances:
52 131 0.63
53 19 0.09
54 5 0.02
55 6 0.03
56 2 0.01
57 44 0.21
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:61670 original size:109 final size:105
Alignment explanation
Indices: 61519--61786 Score: 459
Period size: 109 Copynumber: 2.5 Consensus size: 105
61509 TGCGTTTATA
61519 ATTTCGCATTGCGATT-ATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
1 ATTTCGCATTGCGATTCATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
*
61583 GATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
66 GATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
61623 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 ATTTCGCATTGCGA-TT-CATCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
61688 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
62 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
61732 ATTTCGCATTGCGATTC-TCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCAT
1 ATTTCGCATTGCGATTCATCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCAT
61787 GTTGGGATTT
Statistics
Matches: 155, Mismatches: 3, Indels: 11
0.92 0.02 0.07
Matches are distributed among these distances:
104 29 0.19
105 19 0.12
106 4 0.03
107 6 0.04
108 2 0.01
109 95 0.61
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (105 bp):
ATTTCGCATTGCGATTCATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
GATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:64114 original size:12 final size:12
Alignment explanation
Indices: 64097--64121 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
64087 TCTTCGGGGA
64097 CTTTTTCTTCTT
1 CTTTTTCTTCTT
64109 CTTTTTCTTCTT
1 CTTTTTCTTCTT
64121 C
1 C
64122 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:64330 original size:24 final size:24
Alignment explanation
Indices: 64296--64342 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
64286 CTGAAACATC
64296 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
64320 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
64343 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:65046 original size:20 final size:20
Alignment explanation
Indices: 65018--65407 Score: 457
Period size: 20 Copynumber: 19.4 Consensus size: 20
65008 AAATTTCAGT
* * * *
65018 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
65038 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
65058 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
65078 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
65098 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
65118 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
65138 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
65158 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
65178 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
65198 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
65218 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * *
65238 GTTGCGATTTTATGTATTA-TC
1 GTTGCGA-TTTACGGA-TACGC
65259 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
65279 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
65299 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
65319 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
65339 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
65359 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
65379 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
65399 GTTGCGATT
1 GTTGCGATT
65408 ATTGAAAATC
Statistics
Matches: 323, Mismatches: 36, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
19 7 0.02
20 295 0.91
21 19 0.06
22 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:67617 original size:23 final size:23
Alignment explanation
Indices: 67573--67617 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
67563 ATTATTATAT
*
67573 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
67596 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
67618 AGCTGTGATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:72165 original size:16 final size:15
Alignment explanation
Indices: 72144--72186 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
72134 TGTTATCATC
*
72144 TCAAATTCCTAAATTT
1 TCAAATTCCTAAA-CT
*
72160 TCAAATTCTTAAACT
1 TCAAATTCCTAAACT
72175 T-AAATTCCTAAA
1 TCAAATTCCTAAA
72187 ATATCAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 10 0.42
15 2 0.08
16 12 0.50
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.40
Consensus pattern (15 bp):
TCAAATTCCTAAACT
Found at i:77434 original size:103 final size:103
Alignment explanation
Indices: 77313--77509 Score: 376
Period size: 103 Copynumber: 1.9 Consensus size: 103
77303 AAAAGATGAA
*
77313 ATGGATGAAAATAAAAATGTCTTGAACCAAGAAGAAGCAGGAGCTTCCGCAAGGCTTTACTGCTG
1 ATGGATGAAAACAAAAATGTCTTGAACCAAGAAGAAGCAGGAGCTTCCGCAAGGCTTTACTGCTG
77378 TGAAAGTTCGCACCTTCGTCGGAGAAAAATATGAAATG
66 TGAAAGTTCGCACCTTCGTCGGAGAAAAATATGAAATG
*
77416 ATGGATGAAAACAAAAATGTCTTGAACCAAGAAGAAGCGGGAGCTTCCGCAAGGCTTTACTGCTG
1 ATGGATGAAAACAAAAATGTCTTGAACCAAGAAGAAGCAGGAGCTTCCGCAAGGCTTTACTGCTG
77481 TGAAAGTTCGCACCTTCGTCGGAGAAAAA
66 TGAAAGTTCGCACCTTCGTCGGAGAAAAA
77510 GATGCGTCGC
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 92 1.00
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (103 bp):
ATGGATGAAAACAAAAATGTCTTGAACCAAGAAGAAGCAGGAGCTTCCGCAAGGCTTTACTGCTG
TGAAAGTTCGCACCTTCGTCGGAGAAAAATATGAAATG
Done.