Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008316.1 Hibiscus syriacus cultivar Beakdansim tig00111013_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: 2380696
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 12
Found at i:639584 original size:11 final size:11
Alignment explanation
Indices: 639570--639650 Score: 64
Period size: 11 Copynumber: 7.6 Consensus size: 11
639560 TGAATCGAGT
639570 TCGAGCTTGAA
1 TCGAGCTTGAA
639581 TCGAG-TT---
1 TCGAGCTTGAA
639588 -CGAGCTTGAA
1 TCGAGCTTGAA
**
639598 TCGAGCTCAAA
1 TCGAGCTTGAA
639609 TTCGAGCTTGAA
1 -TCGAGCTTGAA
* *
639621 TCAAGCTTAAAA
1 TCGAGCTT-GAA
*
639633 TCGAGCTTTAA
1 TCGAGCTTGAA
639644 TCGAGCT
1 TCGAGCT
639651 CGAGTATCAA
Statistics
Matches: 55, Mismatches: 8, Indels: 14
0.71 0.10 0.18
Matches are distributed among these distances:
6 4 0.07
7 2 0.04
10 2 0.04
11 29 0.53
12 18 0.33
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:639612 original size:23 final size:23
Alignment explanation
Indices: 639586--639651 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
639576 TTGAATCGAG
639586 TTCGAGCTTGAATCGAGCTCAAA
1 TTCGAGCTTGAATCGAGCTCAAA
* *
639609 TTCGAGCTTGAATCAAGCTTAAA
1 TTCGAGCTTGAATCGAGCTCAAA
* *
639632 ATCGAGCTTTAATCGAGCTC
1 TTCGAGCTTGAATCGAGCTC
639652 GAGTATCAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (23 bp):
TTCGAGCTTGAATCGAGCTCAAA
Found at i:642778 original size:21 final size:21
Alignment explanation
Indices: 642752--642793 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
642742 CAAATCAAGC
642752 AAAGAGGTAAATGTGTAGATG
1 AAAGAGGTAAATGTGTAGATG
*
642773 AAAGAGGTAAATGTGTGGATG
1 AAAGAGGTAAATGTGTAGATG
642794 TTAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.36, T:0.24
Consensus pattern (21 bp):
AAAGAGGTAAATGTGTAGATG
Found at i:646838 original size:26 final size:25
Alignment explanation
Indices: 646774--646838 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 25
646764 TTTAATTCAT
*
646774 ATTAAATAATTTAATATATCGTCAC
1 ATTAAATAATTTAATATATCGTCAA
* *
646799 ATTAAATTAA-TTAATA-ATTGATTAA
1 ATTAAA-TAATTTAATATATCG-TCAA
646824 ATATAAATAATTTAA
1 AT-TAAATAATTTAA
646839 CATTCTATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
24 3 0.09
25 19 0.58
26 11 0.33
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.42
Consensus pattern (25 bp):
ATTAAATAATTTAATATATCGTCAA
Found at i:647256 original size:2 final size:2
Alignment explanation
Indices: 647249--647299 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
647239 CTCATACACG
647249 TA TA TA TA TA TA 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 TA TA TA TA TA TA
647291 TA TA TA TA T
1 TA TA TA TA T
647300 GAATATAAAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:648805 original size:57 final size:57
Alignment explanation
Indices: 648743--648871 Score: 215
Period size: 57 Copynumber: 2.3 Consensus size: 57
648733 AAAGAGAGTT
* *
648743 ATATTCTTCTTATAATTAGGTTTGAATTATCAATGATTAAAAAAATATTCTGAATAA
1 ATATTCTTCTTATAATTAGGTTCGAATTATCAATGATTAAAAAAATATTCTAAATAA
*
648800 ATATTCTTCTTATAATTAGGTTCGAGTTATCAATGATTAAAAAAATATTCTAAATAA
1 ATATTCTTCTTATAATTAGGTTCGAATTATCAATGATTAAAAAAATATTCTAAATAA
*
648857 ATATTATT-TTATAAT
1 ATATTCTTCTTATAAT
648872 CATCCTAATC
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
56 7 0.10
57 61 0.90
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (57 bp):
ATATTCTTCTTATAATTAGGTTCGAATTATCAATGATTAAAAAAATATTCTAAATAA
Found at i:649019 original size:18 final size:19
Alignment explanation
Indices: 648998--649039 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
648988 CAACTTATTG
648998 ATTAATT-ATAATAAAGT-A
1 ATTAATTAATAATAAA-TAA
649016 ATT-ATTAATAATAAATAA
1 ATTAATTAATAATAAATAA
649034 ATTAAT
1 ATTAAT
649040 ACAATTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.19
18 15 0.71
19 2 0.10
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
ATTAATTAATAATAAATAA
Found at i:649054 original size:15 final size:15
Alignment explanation
Indices: 648998--649058 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 15
648988 CAACTTATTG
648998 ATTAATTATAATA-A
1 ATTAATTATAATACA
* *
649012 AGTAATTATTAATAATA
1 ATTAATTA-TAAT-ACA
* *
649029 AATAAAT-TAATACA
1 ATTAATTATAATACA
649043 ATTAATTATAATACA
1 ATTAATTATAATACA
649058 A
1 A
649059 CGGAGAATCT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
14 14 0.38
15 16 0.43
16 1 0.03
17 6 0.16
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (15 bp):
ATTAATTATAATACA
Found at i:651758 original size:15 final size:16
Alignment explanation
Indices: 651740--651810 Score: 58
Period size: 15 Copynumber: 4.6 Consensus size: 16
651730 TAAATTTGAT
651740 TAATGTAAA-TCAAAA
1 TAATGTAAATTCAAAA
* *
651755 TAATTTAAATTTAAAA
1 TAATGTAAATTCAAAA
* *
651771 T-TTCTAAATTCAAAA
1 TAATGTAAATTCAAAA
*
651786 CTAGTGTAAA-TCAAAA
1 -TAATGTAAATTCAAAA
*
651802 TAATATAAA
1 TAATGTAAA
651811 AATTTAAAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
15 26 0.59
16 13 0.30
17 5 0.11
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.34
Consensus pattern (16 bp):
TAATGTAAATTCAAAA
Found at i:657419 original size:21 final size:21
Alignment explanation
Indices: 657395--657529 Score: 171
Period size: 21 Copynumber: 6.4 Consensus size: 21
657385 CAAAATCGCA
*
657395 TTGCGATAACACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
*
657416 TTGCGATAGCACTGTTTACCG
1 TTGCGATAGCACTGTTCACCG
* *
657437 TTGCAATAGCACTGTTCACCT
1 TTGCGATAGCACTGTTCACCG
* *
657458 TTGTGATAGTACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
*
657479 TTGCGATATCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
* * * *
657500 TTACAATAGCACTGTTCATCA
1 TTGCGATAGCACTGTTCACCG
657521 TTGCGATAG
1 TTGCGATAG
657530 TGATCAAAAT
Statistics
Matches: 95, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 95 1.00
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.33
Consensus pattern (21 bp):
TTGCGATAGCACTGTTCACCG
Found at i:657529 original size:63 final size:63
Alignment explanation
Indices: 657393--657530 Score: 204
Period size: 63 Copynumber: 2.2 Consensus size: 63
657383 TCCAAAATCG
** * *
657393 CATTGCGATAACACTGTTCACCGTTGCGATAGCACTGTTTACCGTTGCAATAGCACTGTTCAC
1 CATTGCGATAGTACTGTTCACCGTTGCGATAGCACTGTTCACCGTTACAATAGCACTGTTCAC
* * * *
657456 CTTTGTGATAGTACTGTTCACCGTTGCGATATCACTGTTCACCGTTACAATAGCACTGTTCAT
1 CATTGCGATAGTACTGTTCACCGTTGCGATAGCACTGTTCACCGTTACAATAGCACTGTTCAC
657519 CATTGCGATAGT
1 CATTGCGATAGT
657531 GATCAAAATA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (63 bp):
CATTGCGATAGTACTGTTCACCGTTGCGATAGCACTGTTCACCGTTACAATAGCACTGTTCAC
Found at i:658233 original size:21 final size:21
Alignment explanation
Indices: 658207--658248 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
658197 AATTCGCAAT
658207 GTGAACAGTGCTATCGCAACG
1 GTGAACAGTGCTATCGCAACG
*
658228 GTGAACAGTTCTATCGCAACG
1 GTGAACAGTGCTATCGCAACG
658249 CGATTTTGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (21 bp):
GTGAACAGTGCTATCGCAACG
Found at i:665200 original size:60 final size:61
Alignment explanation
Indices: 665063--665235 Score: 187
Period size: 60 Copynumber: 2.9 Consensus size: 61
665053 GTCCCTAAAT
* * * *
665063 TATGAT-CTTCATTTTAAATTGATCCCT-AAACTTTTAAATATT-CTATTTCATCCTTAAAC
1 TATGATAC-TCATTATAAATTGATCCATAAAACTTTTAAATATTCCAATTTCATCCTCAAAC
* *
665122 TATGATACTCATTATAAATT-ATTCATAAAACTTTTAAACATTCCAATTTCATCCTCAAAC
1 TATGATACTCATTATAAATTGATCCATAAAACTTTTAAATATTCCAATTTCATCCTCAAAC
* * * * *
665182 TATG-TCCATTATTCTAAATTGATCCCTAGAA-TTTTAAATATTCCAATTTCATCC
1 TATGATAC-TCATTATAAATTGATCCATAAAACTTTTAAATATTCCAATTTCATCC
665236 CCCAAATTCA
Statistics
Matches: 96, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
58 4 0.04
59 33 0.34
60 52 0.54
61 7 0.07
ACGTcount: A:0.35, C:0.20, G:0.03, T:0.42
Consensus pattern (61 bp):
TATGATACTCATTATAAATTGATCCATAAAACTTTTAAATATTCCAATTTCATCCTCAAAC
Found at i:666808 original size:23 final size:24
Alignment explanation
Indices: 666764--666815 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
666754 AAAATTATGT
*
666764 ATTTTCTTTTTAAAAATATATATA
1 ATTTTATTTTTAAAAATATATATA
* *
666788 ATTTTATTTTT-AAATTTTATATA
1 ATTTTATTTTTAAAAATATATATA
666811 ATTTT
1 ATTTT
666816 TTTAAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTTATTTTTAAAAATATATATA
Found at i:666818 original size:21 final size:23
Alignment explanation
Indices: 666771--666824 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
666761 TGTATTTTCT
* *
666771 TTTTAAAAATATATATAATTTTA
1 TTTTAAAATTTTATATAATTTTA
*
666794 TTTTTAAATTTTATATAA-TTT-
1 TTTTAAAATTTTATATAATTTTA
666815 TTTTAAAATT
1 TTTTAAAATT
666825 ATTAGATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 9 0.33
22 3 0.11
23 15 0.56
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTTAAAATTTTATATAATTTTA
Found at i:674213 original size:32 final size:32
Alignment explanation
Indices: 674177--674244 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
674167 CACATGCTAT
674177 ATCATCACTTTGAATGACATGAAACATAACAC
1 ATCATCACTTTGAATGACATGAAACATAACAC
* * * * * *
674209 ATCATCATTTTTAGTGACATGACATATATCAC
1 ATCATCACTTTGAATGACATGAAACATAACAC
674241 ATCA
1 ATCA
674245 ATAATTGAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.31
Consensus pattern (32 bp):
ATCATCACTTTGAATGACATGAAACATAACAC
Found at i:694781 original size:20 final size:20
Alignment explanation
Indices: 694731--694781 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
694721 AAAAAAATTG
*
694731 AAATAATTAAATTCTCAAAT
1 AAATAATTATATTCTCAAAT
*
694751 AAA-AATATATATTTTCAAA-
1 AAATAAT-TATATTCTCAAAT
694770 AAATAATGTATA
1 AAATAAT-TATA
694782 GAAAAATTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 6 0.23
20 20 0.77
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (20 bp):
AAATAATTATATTCTCAAAT
Found at i:696075 original size:60 final size:60
Alignment explanation
Indices: 695962--696075 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
695952 ATGACTATCA
* * * *
695962 TTCTAAATTAGTTCCCAAAATTTTTAATATTTTATTTTCATCCCCAAATTATATCCTTTG
1 TTCTAAATTAGTCCCCAAAATTTTTAACATTTTAATTTCATCCCCAAACTATATCCTTTG
* *
696022 TTCTAAATT-GATCCCCAAACTTTTTCAACATTTTAATTTCAT-CCCAAGCTATAT
1 TTCTAAATTAG-TCCCCAAAATTTTT-AACATTTTAATTTCATCCCCAAACTATAT
696076 GTATATAGTA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 1 0.02
60 31 0.67
61 14 0.30
ACGTcount: A:0.31, C:0.21, G:0.04, T:0.45
Consensus pattern (60 bp):
TTCTAAATTAGTCCCCAAAATTTTTAACATTTTAATTTCATCCCCAAACTATATCCTTTG
Found at i:696448 original size:20 final size:20
Alignment explanation
Indices: 696401--696448 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
696391 TTTATTCAAC
696401 TTTTAAAA-TTATAAATTAA
1 TTTTAAAATTTATAAATTAA
696420 TTATT-AAATTTATTAAATT-A
1 TT-TTAAAATTTA-TAAATTAA
696440 TTTTAAAAT
1 TTTTAAAAT
696449 AAATATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
19 7 0.28
20 12 0.48
21 6 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTTAAAATTTATAAATTAA
Found at i:696470 original size:32 final size:32
Alignment explanation
Indices: 696408--696500 Score: 118
Period size: 32 Copynumber: 2.9 Consensus size: 32
696398 AACTTTTAAA
* * *
696408 ATTATAAATTAATTATTAAA-TTTATTAAATT
1 ATTATAAAATAAATATTAAATTTTATCAAATT
*
696439 ATTTTAAAATAAATATTAAATTTTATCAAATT
1 ATTATAAAATAAATATTAAATTTTATCAAATT
*
696471 ATTATAAAAT-TATCATTAAATTTTATCAAA
1 ATTATAAAATAAAT-ATTAAATTTTATCAAA
696501 CTTTTACATT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
31 19 0.35
32 35 0.65
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (32 bp):
ATTATAAAATAAATATTAAATTTTATCAAATT
Found at i:696480 original size:11 final size:11
Alignment explanation
Indices: 696408--696496 Score: 73
Period size: 11 Copynumber: 8.5 Consensus size: 11
696398 AACTTTTAAA
696408 ATTA-TAAATT
1 ATTATTAAATT
696418 AATTATTAAA-T
1 -ATTATTAAATT
696429 -TTATTAAATT
1 ATTATTAAATT
*
696439 ATT-TTAAAATA
1 ATTATT-AAATT
*
696450 AATATTAAATT
1 ATTATTAAATT
*
696461 -TTATCAAATT
1 ATTATTAAATT
*
696471 ATTATAAAATT
1 ATTATTAAATT
*
696482 ATCATTAAATT
1 ATTATTAAATT
696493 -TTAT
1 ATTAT
696497 CAAACTTTTA
Statistics
Matches: 63, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
9 8 0.13
10 14 0.22
11 35 0.56
12 6 0.10
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (11 bp):
ATTATTAAATT
Found at i:704326 original size:20 final size:20
Alignment explanation
Indices: 704301--704353 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
704291 CTTTACATAG
704301 TAGTATCGATACCATAGGCT
1 TAGTATCGATACCATAGGCT
704321 TAGTATCGATACCATAGGCT
1 TAGTATCGATACCATAGGCT
704341 TAGTATCGATACC
1 TAGTATCGATACC
704354 GTCAGGCCCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (20 bp):
TAGTATCGATACCATAGGCT
Found at i:704493 original size:20 final size:20
Alignment explanation
Indices: 704468--704505 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
704458 TTTTGTAGAT
704468 AAATCAT-CTACAACGGCTCC
1 AAATCATCCT-CAACGGCTCC
704488 AAATCATCCTCAACGGCT
1 AAATCATCCTCAACGGCT
704506 AGAAACGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.34, C:0.34, G:0.11, T:0.21
Consensus pattern (20 bp):
AAATCATCCTCAACGGCTCC
Found at i:706913 original size:29 final size:29
Alignment explanation
Indices: 706881--706945 Score: 130
Period size: 29 Copynumber: 2.2 Consensus size: 29
706871 TAAAAATTCA
706881 ATGACTATATTGCAAGTTTTAAATATTAG
1 ATGACTATATTGCAAGTTTTAAATATTAG
706910 ATGACTATATTGCAAGTTTTAAATATTAG
1 ATGACTATATTGCAAGTTTTAAATATTAG
706939 ATGACTA
1 ATGACTA
706946 AAATACAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (29 bp):
ATGACTATATTGCAAGTTTTAAATATTAG
Found at i:707233 original size:21 final size:20
Alignment explanation
Indices: 707205--707249 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
707195 TTAATTGATA
*
707205 AAATTAAAAATTTAATAATT
1 AAATTAAAAATTTAAGAATT
* *
707225 AAATATAAATATTTTAGAATT
1 AAAT-TAAAAATTTAAGAATT
707246 AAAT
1 AAAT
707250 GATATCATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
AAATTAAAAATTTAAGAATT
Found at i:708832 original size:19 final size:19
Alignment explanation
Indices: 708808--708844 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
708798 ATGACCAACA
708808 AAATCGCAACGCGATCTCT
1 AAATCGCAACGCGATCTCT
708827 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
708845 CATTATCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.19
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:708982 original size:20 final size:20
Alignment explanation
Indices: 708930--708982 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
708920 GATTTTAGAT
* *
708930 AATCGCAATGCAAATATGTA
1 AATCGCAATGCGAATATATA
708950 AATCGCAATGCGAATATATA
1 AATCGCAATGCGAATATATA
*
708970 AATCGCAACGCGA
1 AATCGCAATGCGA
708983 TAACACGTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (20 bp):
AATCGCAATGCGAATATATA
Found at i:708997 original size:21 final size:21
Alignment explanation
Indices: 708971--709045 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
708961 GAATATATAA
708971 ATCGCAACGCGATAACACGTG
1 ATCGCAACGCGATAACACGTG
* * *
708992 ATCGCAAAGTGAT-TCGGAC-T-
1 ATCGCAACGCGATAAC--ACGTG
*
709012 ATCGCAACGCGATAATACGTG
1 ATCGCAACGCGATAACACGTG
709033 ATCGCAACGCGAT
1 ATCGCAACGCGAT
709046 TCTGACTATC
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
19 2 0.05
20 13 0.31
21 25 0.60
22 2 0.05
ACGTcount: A:0.32, C:0.25, G:0.24, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGATAACACGTG
Found at i:709016 original size:41 final size:41
Alignment explanation
Indices: 708971--709065 Score: 145
Period size: 41 Copynumber: 2.3 Consensus size: 41
708961 GAATATATAA
*
708971 ATCGCAACGCGATAACACGTGATCGCAAAGTGATTCGGACT
1 ATCGCAACGCGATAACACGTGATCGCAAAGCGATTCGGACT
* * *
709012 ATCGCAACGCGATAATACGTGATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAACACGTGATCGCAAAGCGATTCGGACT
*
709053 ATCGCAACACGAT
1 ATCGCAACGCGAT
709066 TCTGACTAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGATAACACGTGATCGCAAAGCGATTCGGACT
Found at i:709058 original size:20 final size:20
Alignment explanation
Indices: 708992--709078 Score: 86
Period size: 20 Copynumber: 4.3 Consensus size: 20
708982 ATAACACGTG
* * *
708992 ATCGCAAAGTGATTCGGACT
1 ATCGCAACGCGATTCTGACT
**
709012 ATCGCAACGCGATAAT-ACGT
1 ATCGCAACGCGATTCTGAC-T
709032 GATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
*
709053 ATCGCAACACGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
709073 AACGCA
1 ATCGCA
709079 TCACTGAATT
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
19 2 0.04
20 36 0.65
21 15 0.27
22 2 0.04
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:709931 original size:24 final size:24
Alignment explanation
Indices: 709899--709952 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
709889 GTATTCGAAA
709899 TTTGATCTTGGTCAATACTCAGAC
1 TTTGATCTTGGTCAATACTCAGAC
* *
709923 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACTCAGAC
709947 TTTGAT
1 TTTGAT
709953 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCAGAC
Found at i:710171 original size:14 final size:14
Alignment explanation
Indices: 710142--710178 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
710132 AGAAAAAGAA
710142 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
710157 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
710171 GAAGAAAA
1 GAAGAAAA
710179 TGCCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:712451 original size:20 final size:20
Alignment explanation
Indices: 712426--712702 Score: 219
Period size: 20 Copynumber: 14.7 Consensus size: 20
712416 CACATTCATT
712426 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
712446 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
* * *
712466 TGACTATCGTAACGTGAATT
1 TGACTATCGCAACGCGAATA
* *
712486 TGAATATCGCAACG-GGATA
1 TGACTATCGCAACGCGAATA
* * *
712505 --A-T-T-ACAATGCGAAAA
1 TGACTATCGCAACGCGAATA
**
712520 TGACTATCGCAACGCG-GGA
1 TGACTATCGCAACGCGAATA
* *
712539 T-A--ATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
*
712556 TGACTATCGCAACGCGAAAA
1 TGACTATCGCAACGCGAATA
* *
712576 TGACTATCGCAATGCGAATT
1 TGACTATCGCAACGCGAATA
* *
712596 TAACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
* *
712616 TGACTATAGCAA--CG-AGA
1 TGACTATCGCAACGCGAATA
712633 T-A--ATCGCAACGCGAA-A
1 TGACTATCGCAACGCGAATA
* *
712649 TGACTATCGCAACGCAAATT
1 TGACTATCGCAACGCGAATA
* * *
712669 TGATTATCGCAACGGGAATT
1 TGACTATCGCAACGCGAATA
712689 TGACTATCGCAACG
1 TGACTATCGCAACG
712703 AGAAAATCGC
Statistics
Matches: 205, Mismatches: 35, Indels: 34
0.75 0.13 0.12
Matches are distributed among these distances:
14 10 0.05
15 4 0.02
16 16 0.08
17 8 0.04
18 5 0.02
19 18 0.09
20 144 0.70
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (20 bp):
TGACTATCGCAACGCGAATA
Found at i:712549 original size:36 final size:36
Alignment explanation
Indices: 712490--712571 Score: 132
Period size: 36 Copynumber: 2.3 Consensus size: 36
712480 TGAATTTGAA
*
712490 TATCGCAA--CGGGATAATTACAATGCGAAAATGAC
1 TATCGCAACGCGGGATAATCACAATGCGAAAATGAC
*
712524 TATCGCAACGCGGGATAATCGCAATGCGAAAATGAC
1 TATCGCAACGCGGGATAATCACAATGCGAAAATGAC
712560 TATCGCAACGCG
1 TATCGCAACGCG
712572 AAAATGACTA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
34 8 0.18
36 36 0.82
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (36 bp):
TATCGCAACGCGGGATAATCACAATGCGAAAATGAC
Found at i:712669 original size:73 final size:73
Alignment explanation
Indices: 712561--712737 Score: 237
Period size: 73 Copynumber: 2.4 Consensus size: 73
712551 GAAAATGACT
* *
712561 ATCGCAACGCGAAAATGACTATCGCAATGCGAATTTAACTATCGCAACGCGAATTTGACTATAGC
1 ATCGCAACGCG-AAATGACTATCGCAACGCAAATTTAACTATCGCAACGCGAATTTGACTATAGC
*
712626 AACGAGATA
65 AACGAGAAA
* * * *
712635 ATCGCAACGCGAAATGACTATCGCAACGCAAATTTGATTATCGCAACGGGAATTTGACTATCGCA
1 ATCGCAACGCGAAATGACTATCGCAACGCAAATTTAACTATCGCAACGCGAATTTGACTATAGCA
712700 ACGAGAAA
66 ACGAGAAA
* * * *
712708 ATCGCAAAGTGTATTAGACTATCGCAACGC
1 ATCGCAACGCGAAAT-GACTATCGCAACGC
712738 GAATATGATG
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
73 66 0.73
74 25 0.27
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (73 bp):
ATCGCAACGCGAAATGACTATCGCAACGCAAATTTAACTATCGCAACGCGAATTTGACTATAGCA
ACGAGAAA
Found at i:712877 original size:36 final size:34
Alignment explanation
Indices: 712837--712916 Score: 114
Period size: 30 Copynumber: 2.4 Consensus size: 34
712827 TCAACTTTTA
712837 ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
1 ATCAATTAAACAA--ACAAATAAGAATTATTTACAC
712873 ATCAATT----AAACAAATAAGAATTATTTACAC
1 ATCAATTAAACAAACAAATAAGAATTATTTACAC
712903 ATCAATTAAACAAA
1 ATCAATTAAACAAA
712917 TCAACTCTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
30 28 0.70
32 2 0.05
34 3 0.08
36 7 0.17
ACGTcount: A:0.55, C:0.15, G:0.04, T:0.26
Consensus pattern (34 bp):
ATCAATTAAACAAACAAATAAGAATTATTTACAC
Found at i:712886 original size:30 final size:30
Alignment explanation
Indices: 712852--712917 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
712842 TTAAACAAGC
712852 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
712882 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
712912 ACAAAT
1 ACAAAT
712918 CAACTCTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.55, C:0.14, G:0.03, T:0.29
Consensus pattern (30 bp):
ACAAATAAGAATTATTTACACATCAATTAA
Found at i:714323 original size:21 final size:21
Alignment explanation
Indices: 714299--714401 Score: 100
Period size: 21 Copynumber: 4.9 Consensus size: 21
714289 TTGGGAAGGT
*
714299 CCTCTTCAACGATGACAGGGG
1 CCTCTTGAACGATGACAGGGG
* **
714320 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGACAGGGG
* ** *
714341 ACTCTTGAGGGATGATAGGGG
1 CCTCTTGAACGATGACAGGGG
* *
714362 CCTCTTGAACGAT-AGGAGAGG
1 CCTCTTGAACGATGA-CAGGGG
714383 CCTCTTGAACGATGACAGG
1 CCTCTTGAACGATGACAGG
714402 TGAGTCAGGC
Statistics
Matches: 63, Mismatches: 17, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
20 1 0.02
21 61 0.97
22 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.36, T:0.20
Consensus pattern (21 bp):
CCTCTTGAACGATGACAGGGG
Found at i:714355 original size:42 final size:42
Alignment explanation
Indices: 714300--714401 Score: 132
Period size: 42 Copynumber: 2.4 Consensus size: 42
714290 TGGGAAGGTC
* * * *
714300 CTCTTCAACGATGACAGGGGCCTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGATGACAGGGGCCTCTTGAACGATAGGAGAGGA
** * *
714342 CTCTTGAGGGATGATAGGGGCCTCTTGAACGATAGGAGAGGC
1 CTCTTGAACGATGACAGGGGCCTCTTGAACGATAGGAGAGGA
714384 CTCTTGAACGATGACAGG
1 CTCTTGAACGATGACAGG
714402 TGAGTCAGGC
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.24, C:0.20, G:0.36, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGATGACAGGGGCCTCTTGAACGATAGGAGAGGA
Found at i:714901 original size:20 final size:20
Alignment explanation
Indices: 714876--714919 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
714866 AATAGTTTCT
714876 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
714896 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
714916 GAAA
1 GAAA
714920 ATGATTATCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.52, C:0.23, G:0.11, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:714929 original size:20 final size:20
Alignment explanation
Indices: 714883--714933 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
714873 TCTGAAACTT
* *
714883 AAAATCGCAACACGAAACTT
1 AAAATCGCAACACGAAAATG
714903 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
**
714923 ATTATCGCAAC
1 AAAATCGCAAC
714934 GCGAGTTTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.49, C:0.24, G:0.12, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:714948 original size:20 final size:20
Alignment explanation
Indices: 714906--714974 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
714896 GAAACTTAAA
* ** *
714906 ATCGCAACACGAAAATGATT
1 ATCGCAACGCGAATTTGACT
*
714926 ATCGCAACGCGAGTTTGACT
1 ATCGCAACGCGAATTTGACT
714946 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
714966 ATCGCAACG
1 ATCGCAACG
714975 AGATAATCGC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:715049 original size:20 final size:20
Alignment explanation
Indices: 715024--715124 Score: 63
Period size: 20 Copynumber: 5.3 Consensus size: 20
715014 TAAATTCACG
715024 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
715044 TTGCGAT--T-A---TCCCG
1 TTGCGATAGTCATTTTCGCA
* *
715058 TTGCGATAGTCAAATTT-GCG
1 TTGCGATAGTC-ATTTTCGCA
** * *
715078 TTGTAATAGTCATTTCCGCT
1 TTGCGATAGTCATTTTCGCA
*
715098 TTGCGATAGTCGTTTTCGCA
1 TTGCGATAGTCATTTTCGCA
715118 TTGCGAT
1 TTGCGAT
715125 TATCCCGTTG
Statistics
Matches: 60, Mismatches: 13, Indels: 16
0.67 0.15 0.18
Matches are distributed among these distances:
14 10 0.17
16 1 0.02
17 1 0.02
18 2 0.03
19 3 0.05
20 42 0.70
21 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:715169 original size:20 final size:20
Alignment explanation
Indices: 715130--715177 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
715120 GCGATTATCC
*
715130 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAATCAAATTCG
**
715150 CGTTGCGATAATCATTTTCG
1 CGTTGCGATAATCAAATTCG
*
715170 TGTTGCGA
1 CGTTGCGA
715178 CTATTCTTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAATCAAATTCG
Found at i:715176 original size:74 final size:75
Alignment explanation
Indices: 715023--715177 Score: 242
Period size: 74 Copynumber: 2.1 Consensus size: 75
715013 CTAAATTCAC
* * *
715023 GTTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAATTTGCGTTGTAATAGT
1 GTTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAATTCGCGTTGCAATAAT
715088 CATTTCCGCT
66 CATTTCCGCT
* *
715098 -TTGCGATAGTCGTTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAATTCGCGTTGCGATAAT
1 GTTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAATTCGCGTTGCAATAAT
*
715162 CATTTTCG-T
66 CATTTCCGCT
715171 GTTGCGA
1 GTTGCGA
715178 CTATTCTTCT
Statistics
Matches: 73, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
73 1 0.01
74 72 0.99
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (75 bp):
GTTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAATTCGCGTTGCAATAAT
CATTTCCGCT
Found at i:715355 original size:32 final size:31
Alignment explanation
Indices: 715296--715357 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
715286 CTACCACCGA
715296 ATGAATTTACTAAGCAATCCAAAAGACAAAT
1 ATGAATTTACTAAGCAATCCAAAAGACAAAT
*
715327 ATGAATTTACTAACTTCAA-CCAAAAGACAAA
1 ATGAATTTACTAA--GCAATCCAAAAGACAAA
715358 ACAAAGACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 13 0.46
32 12 0.43
33 3 0.11
ACGTcount: A:0.52, C:0.18, G:0.08, T:0.23
Consensus pattern (31 bp):
ATGAATTTACTAAGCAATCCAAAAGACAAAT
Found at i:717181 original size:20 final size:20
Alignment explanation
Indices: 717158--717213 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
717148 TCTGAAACTT
*
717158 AAAATCGTAACACGAAAATG
1 AAAATCGCAACACGAAAATG
717178 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
717198 ATTATCGCAACGCGAA
1 AAAATCGCAACACGAA
717214 TTTTTTCGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.50, C:0.20, G:0.16, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:717587 original size:22 final size:22
Alignment explanation
Indices: 717556--717613 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
717546 GATGGAGATA
717556 GACGGATTTCGCCGGAAATGGG
1 GACGGATTTCGCCGGAAATGGG
* * *
717578 GACGGGTTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAAATGGG
*
717600 GACGGATGTCGCCG
1 GACGGATTTCGCCG
717614 TAGAGAGTGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.17, C:0.19, G:0.45, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGGAAATGGG
Found at i:717803 original size:20 final size:20
Alignment explanation
Indices: 717778--717861 Score: 80
Period size: 20 Copynumber: 4.2 Consensus size: 20
717768 ATCGTAACGA
* *
717778 GATAGTCATAATCTCGTTGC
1 GATAGTCAGAATCGCGTTGC
717798 GATAGTCAGAATCGCGTTGC
1 GATAGTCAGAATCGCGTTGC
** *
717818 GATCACGT-ATTATCGCGTTAC
1 GAT-A-GTCAGAATCGCGTTGC
* *
717839 GATAGTCAGAATCACATTGC
1 GATAGTCAGAATCGCGTTGC
717859 GAT
1 GAT
717862 CACGTGTTAT
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
19 2 0.04
20 33 0.65
21 14 0.27
22 2 0.04
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (20 bp):
GATAGTCAGAATCGCGTTGC
Found at i:717834 original size:21 final size:21
Alignment explanation
Indices: 717808--717882 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
717798 GATAGTCAGA
717808 ATCGCGTTGCGATCACGTATT
1 ATCGCGTTGCGATCACGTATT
* **
717829 ATCGCGTTACGAT-A-GTCAGA
1 ATCGCGTTGCGATCACGT-ATT
* * *
717849 ATCACATTGCGATCACGTGTT
1 ATCGCGTTGCGATCACGTATT
717870 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
717883 TTATATATTC
Statistics
Matches: 40, Mismatches: 11, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 2 0.05
20 12 0.30
21 24 0.60
22 2 0.05
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.31
Consensus pattern (21 bp):
ATCGCGTTGCGATCACGTATT
Found at i:717859 original size:41 final size:41
Alignment explanation
Indices: 717792--717882 Score: 146
Period size: 41 Copynumber: 2.2 Consensus size: 41
717782 GTCATAATCT
* *
717792 CGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCG
1 CGTTGCGATAGTCAGAATCACATTGCGATCACGTATTATCG
* *
717833 CGTTACGATAGTCAGAATCACATTGCGATCACGTGTTATCG
1 CGTTGCGATAGTCAGAATCACATTGCGATCACGTATTATCG
717874 CGTTGCGAT
1 CGTTGCGAT
717883 TTATATATTC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (41 bp):
CGTTGCGATAGTCAGAATCACATTGCGATCACGTATTATCG
Found at i:718013 original size:19 final size:19
Alignment explanation
Indices: 717989--718025 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
717979 TGCGATAATG
* *
717989 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTACGATTTA
718008 GAGATCGCATTACGATTT
1 GAGATCGCATTACGATTT
718026 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTACGATTTA
Found at i:725862 original size:81 final size:81
Alignment explanation
Indices: 725716--725878 Score: 220
Period size: 81 Copynumber: 2.0 Consensus size: 81
725706 ACTCGAACAA
* * * * **
725716 GCGGAGGTGGAGGAGATGGTGGCAACACCACTGGAGTATTTGGTGCCAAGGATGGTGCACGTTCT
1 GCGGAGGTGGAAGAGACGGTGGCAACACCAATGGAGTACTTGGTGCCAAGGATGGAACACGTTCT
725781 TCAATA-GTGAATGGTG
66 TCAATAGGT-AATGGTG
* * **
725797 GCGGAGGTGGAAGATACGGTGGCAACACCAATGGAGTACTTGGTGCCAAGGGTGGAACATTTTCT
1 GCGGAGGTGGAAGAGACGGTGGCAACACCAATGGAGTACTTGGTGCCAAGGATGGAACACGTTCT
725862 TCAATAGGTAATGGTG
66 TCAATAGGTAATGGTG
725878 G
1 G
725879 TGAAGCTGTA
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
81 69 0.97
82 2 0.03
ACGTcount: A:0.25, C:0.15, G:0.37, T:0.23
Consensus pattern (81 bp):
GCGGAGGTGGAAGAGACGGTGGCAACACCAATGGAGTACTTGGTGCCAAGGATGGAACACGTTCT
TCAATAGGTAATGGTG
Found at i:727311 original size:2 final size:2
Alignment explanation
Indices: 727306--727350 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
727296 AGATGGGAGA
727306 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
727347 AT AT
1 AT AT
727351 TTGGACAGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:728244 original size:16 final size:16
Alignment explanation
Indices: 728218--728251 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
728208 AAAATTCCAC
728218 TTTTGTGGATATTATTT
1 TTTTGTGGATATT-TTT
728235 TTTTGT-GATATTTTT
1 TTTTGTGGATATTTTT
728250 TT
1 TT
728252 AATACACCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 6 0.35
17 6 0.35
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.71
Consensus pattern (16 bp):
TTTTGTGGATATTTTT
Found at i:728490 original size:20 final size:20
Alignment explanation
Indices: 728467--728511 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
728457 ACTTAGTTTC
* *
728467 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAAAGCGAAAGT
728487 CAAATTCGCAAAGCGAAAGT
1 CAAATTCGCAAAGCGAAAGT
728507 CAAAT
1 CAAAT
728512 GTTTTTACGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (20 bp):
CAAATTCGCAAAGCGAAAGT
Found at i:728958 original size:20 final size:19
Alignment explanation
Indices: 728929--728967 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
728919 ACCAAATTCA
*
728929 CAACGTGAAAATGAAAATCG
1 CAACGCGAAAAT-AAAATCG
*
728949 CAACGCGAAACTAAAATCG
1 CAACGCGAAAATAAAATCG
728968 TGTTACGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.13
Consensus pattern (19 bp):
CAACGCGAAAATAAAATCG
Found at i:730694 original size:21 final size:21
Alignment explanation
Indices: 730670--730717 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
730660 GTTAGGGGAA
*
730670 TTACGTCATGAGGTCGGTGCT
1 TTACGTCATGAGGTCGGTACT
730691 TTACGTCATGAGGTCGGTACT
1 TTACGTCATGAGGTCGGTACT
730712 TTACGT
1 TTACGT
730718 GAAGATAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.17, C:0.19, G:0.29, T:0.35
Consensus pattern (21 bp):
TTACGTCATGAGGTCGGTACT
Found at i:731212 original size:21 final size:21
Alignment explanation
Indices: 731123--731218 Score: 79
Period size: 21 Copynumber: 4.6 Consensus size: 21
731113 GATGCACATA
* *
731123 TCATCATTCAAGA-GCCGCTTC
1 TCATCGTTCAAGAGGCC-CCTC
*
731144 TTATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * *
731165 TCATC-ATCGAAGAAGCCTCTC
1 TCATCGTTC-AAGAGGCCCCTC
* * *
731186 CCATCGTTTAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTC
731207 TCATCGTTCAAG
1 TCATCGTTCAAG
731219 TGGTCCCGCC
Statistics
Matches: 57, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
20 2 0.04
21 51 0.89
22 4 0.07
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.27
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:732667 original size:14 final size:14
Alignment explanation
Indices: 732648--732687 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
732638 TTTTGATTAA
732648 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
** *
732662 TTGATTTGTTTAAT
1 TTGATTTGTAAAAG
732676 TTGATTTGTAAA
1 TTGATTTGTAAA
732688 TAAGAATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:732864 original size:20 final size:20
Alignment explanation
Indices: 732839--732881 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
732829 GATTTTTGAT
*
732839 TTGCGAAATTGACTTTCGCG
1 TTGCGAAATTAACTTTCGCG
*
732859 TTGCGAATTTAACTTTCGCG
1 TTGCGAAATTAACTTTCGCG
732879 TTG
1 TTG
732882 ATCGCAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.40
Consensus pattern (20 bp):
TTGCGAAATTAACTTTCGCG
Found at i:733111 original size:39 final size:39
Alignment explanation
Indices: 733057--733143 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
733047 TCAAGTTGTA
733057 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
* *
733096 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
733135 GATTTTGAT
1 GATTTTGAT
733144 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:733476 original size:18 final size:18
Alignment explanation
Indices: 733453--733489 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
733443 CGGAATTTAT
733453 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
733471 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
733489 A
1 A
733490 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:733506 original size:24 final size:25
Alignment explanation
Indices: 733451--733508 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
733441 GCCGGAATTT
733451 ATATTGAAATTCAAACTCAAATTGAA
1 ATATT-AAATTCAAACTCAAATTGAA
* *
733477 AT-TTAAATTCAAACTCCAATT-AC
1 ATATTAAATTCAAACTCAAATTGAA
733500 ATATTAAAT
1 ATATTAAAT
733509 GAATTTGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 3 0.10
24 22 0.76
25 2 0.07
26 2 0.07
ACGTcount: A:0.48, C:0.14, G:0.03, T:0.34
Consensus pattern (25 bp):
ATATTAAATTCAAACTCAAATTGAA
Found at i:733911 original size:25 final size:25
Alignment explanation
Indices: 733877--733928 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
733867 TTATTTTTCC
*
733877 AAATAATGTACCCATAACAATGTTT
1 AAATAATGTACCCACAACAATGTTT
733902 AAATAATGTACCCACAACAATGTTT
1 AAATAATGTACCCACAACAATGTTT
733927 AA
1 AA
733929 TTGATTTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.29
Consensus pattern (25 bp):
AAATAATGTACCCACAACAATGTTT
Found at i:734079 original size:20 final size:20
Alignment explanation
Indices: 734025--734082 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 20
734015 TCGGTTTGCG
734025 ATTTCGCGTTGCGAATTTGA
1 ATTTCGCGTTGCGAATTTGA
* *
734045 AATTC-AGTTGCGAATTTGA
1 ATTTCGCGTTGCGAATTTGA
* *
734064 CTTTCGCGTTGTGAATTTG
1 ATTTCGCGTTGCGAATTTG
734083 GAAAATCGCA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.41
Consensus pattern (20 bp):
ATTTCGCGTTGCGAATTTGA
Found at i:739354 original size:29 final size:31
Alignment explanation
Indices: 739321--739379 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
739311 AAATAGAATA
*
739321 TAAATAAAAT-A-ACAATACAAGGGCTTATC
1 TAAATAAAATGATAAAATACAAGGGCTTATC
*
739350 TAAATAAAATGATAAAATTCAAGGGCTTAT
1 TAAATAAAATGATAAAATACAAGGGCTTAT
739380 TTAGTATATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 10 0.38
30 1 0.04
31 15 0.58
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.27
Consensus pattern (31 bp):
TAAATAAAATGATAAAATACAAGGGCTTATC
Found at i:744381 original size:20 final size:20
Alignment explanation
Indices: 744337--744580 Score: 112
Period size: 20 Copynumber: 11.8 Consensus size: 20
744327 AATGACCAAT
* *
744337 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
744356 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
744376 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
* **
744396 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
744417 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
744440 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
744460 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
744480 ATAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* * * **
744500 AGAGTCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
744521 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
744544 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* *
744564 AGAATCGCAATGCGATT
1 AAAATCGCAACGCGATT
744581 GAGAGAGTCT
Statistics
Matches: 168, Mismatches: 48, Indels: 17
0.72 0.21 0.07
Matches are distributed among these distances:
19 17 0.10
20 97 0.58
21 26 0.15
23 28 0.17
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:744486 original size:104 final size:104
Alignment explanation
Indices: 744337--744580 Score: 348
Period size: 104 Copynumber: 2.4 Consensus size: 104
744327 AATGACCAAT
* * * **
744337 AAAATCGCAACGCGA-T-ATCAAAATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAGAAAA
1 AAAATCGCAATGCGATTGAT-AGAATCGCAATGCGATTTAGAAAATCGCAACGCGAAAAAGAAAA
744400 TCGCAACGCGAGCTTCCAAGTTCGCAACGCGATTTAGAAG
65 TCGCAACGCGAGCTTCCAAGTTCGCAACGCGATTTAGAAG
* * * *** * *
744440 AAAATCGCAATGCGATTGATAGAATCGCAATGCGATTTATATAATCGCAATGCGATTGAGAGAGT
1 AAAATCGCAATGCGATTGATAGAATCGCAATGCGATTTAGAAAATCGCAACGCGAAAAAGAAAAT
744505 CGCAACGCGAGCTTCCAAGTTCGCAACGCGATTTAGAAG
66 CGCAACGCGAGCTTCCAAGTTCGCAACGCGATTTAGAAG
744544 AAAATCGCAATGCGATTGATAGAATCGCAATGCGATT
1 AAAATCGCAATGCGATTGATAGAATCGCAATGCGATT
744581 GAGAGAGTCT
Statistics
Matches: 126, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
103 14 0.11
104 110 0.87
105 2 0.02
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.21
Consensus pattern (104 bp):
AAAATCGCAATGCGATTGATAGAATCGCAATGCGATTTAGAAAATCGCAACGCGAAAAAGAAAAT
CGCAACGCGAGCTTCCAAGTTCGCAACGCGATTTAGAAG
Found at i:744581 original size:20 final size:20
Alignment explanation
Indices: 744442--744655 Score: 133
Period size: 20 Copynumber: 10.8 Consensus size: 20
744432 TTTAGAAGAA
744442 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
* *
744462 AATCGCAATGCGATTTATAT
1 AATCGCAATGCGATTGATAG
*
744482 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGATAG
* * *
744502 AGTCGCAACGCGAGCTTCCA-AG
1 AATCGCAATGCGA--TT-GATAG
* *
744524 -TTCGCAACGCGATTTAGA-AG
1 AATCGCAATGCGA-TT-GATAG
744544 AAAATCGCAATGCGATTGATAG
1 --AATCGCAATGCGATTGATAG
*
744566 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGATAG
* ** *
744586 AGT--C--TTAGA-AGA-A-
1 AATCGCAATGCGATTGATAG
* *
744599 AATCGCAATGCGATTTATAT
1 AATCGCAATGCGATTGATAG
*
744619 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGATAG
* *
744639 AGTCGCAACGCGATTGA
1 AATCGCAATGCGATTGA
744656 CGTTGAAAAT
Statistics
Matches: 151, Mismatches: 29, Indels: 28
0.73 0.14 0.13
Matches are distributed among these distances:
13 2 0.01
14 1 0.01
15 3 0.02
16 3 0.02
17 3 0.02
18 2 0.01
19 1 0.01
20 104 0.69
21 13 0.09
22 8 0.05
23 11 0.07
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (20 bp):
AATCGCAATGCGATTGATAG
Found at i:744623 original size:53 final size:53
Alignment explanation
Indices: 744537--744642 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
744527 GCAACGCGAT
744537 TTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAGAGTC
1 TTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAGAGTC
* *
744590 TTAGAAGAAAATCGCAATGCGATTTATATAATCGCAATGCGATTGAGAGAGTC
1 TTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAGAGTC
744643 GCAACGCGAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.25
Consensus pattern (53 bp):
TTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAGAGTC
Found at i:745575 original size:20 final size:20
Alignment explanation
Indices: 745550--745638 Score: 101
Period size: 20 Copynumber: 4.5 Consensus size: 20
745540 ATCTTTTTAA
*
745550 CGTTGCGATTCTCTTAATCG
1 CGTTGCGATTCTCTAAATCG
* * *
745570 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTCTCTAAATCG
*
745590 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTCTCTAAATCG
*
745610 CGTTGCGATT-T-TGATATCG
1 CGTTGCGATTCTCT-AAATCG
745629 CGTTGCGATT
1 CGTTGCGATT
745639 TTATTGGTCA
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
18 1 0.02
19 16 0.27
20 43 0.72
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTCTCTAAATCG
Found at i:745639 original size:39 final size:40
Alignment explanation
Indices: 745550--745640 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 40
745540 ATCTTTTTAA
* * *
745550 CGTTGCGATTCTCTTAATCGCATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCGCATTGCGATTCTCTCAATCG
* *
745590 CGTTGCGATTTTCTAAATCGCGTTGCGATT-T-TGATATCG
1 CGTTGCGATTTTCTAAATCGCATTGCGATTCTCTCA-ATCG
745629 CGTTGCGATTTT
1 CGTTGCGATTTT
745641 ATTGGTCATT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
38 2 0.04
39 16 0.36
40 27 0.60
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.41
Consensus pattern (40 bp):
CGTTGCGATTTTCTAAATCGCATTGCGATTCTCTCAATCG
Found at i:747010 original size:6 final size:6
Alignment explanation
Indices: 746999--747030 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
746989 CGACGTCGTT
746999 CGGCGA CGGCGA CGGCGA CGGCGA CGGCGA CG
1 CGGCGA CGGCGA CGGCGA CGGCGA CGGCGA CG
747031 ATCAAGGCGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.34, G:0.50, T:0.00
Consensus pattern (6 bp):
CGGCGA
Found at i:750070 original size:23 final size:23
Alignment explanation
Indices: 750016--750071 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
750006 CTAATAAAGG
*
750016 ATTGAATT-AAAATTTTATTTTA
1 ATTGAATTGAAAATGTTATTTTA
* * *
750038 ATAGATTTGAAAATGTTATTTTT
1 ATTGAATTGAAAATGTTATTTTA
750061 ATTGAATTGAA
1 ATTGAATTGAA
750072 TTAAAAAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (23 bp):
ATTGAATTGAAAATGTTATTTTA
Found at i:756839 original size:17 final size:17
Alignment explanation
Indices: 756817--756853 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
756807 TTCTATAATA
756817 TATATATATATACGATG
1 TATATATATATACGATG
756834 TATATATATATACGATG
1 TATATATATATACGATG
756851 TAT
1 TAT
756854 CACTCAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (17 bp):
TATATATATATACGATG
Found at i:761279 original size:12 final size:12
Alignment explanation
Indices: 761262--761318 Score: 53
Period size: 12 Copynumber: 4.4 Consensus size: 12
761252 ATGTAATAAA
761262 TATTTATAATAT
1 TATTTATAATAT
*
761274 TATTTAATAAATTAAA
1 TATTT-AT-AA-T-AT
761290 TATTATATAATA-
1 TATT-TATAATAT
761302 TATTTATAATAT
1 TATTTATAATAT
761314 TATTT
1 TATTT
761319 CTTTAAAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
11 7 0.18
12 14 0.37
13 3 0.08
14 3 0.08
15 3 0.08
16 7 0.18
17 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TATTTATAATAT
Found at i:761290 original size:28 final size:28
Alignment explanation
Indices: 761258--761315 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
761248 TTTTATGTAA
761258 TAAATATT-TATAATATTATTTAATAA-AT
1 TAAATATTATATAATA-TATTT-ATAATAT
761286 TAAATATTATATAATATATTTATAATAT
1 TAAATATTATATAATATATTTATAATAT
761314 TA
1 TA
761316 TTTCTTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 4 0.14
28 17 0.61
29 7 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
TAAATATTATATAATATATTTATAATAT
Found at i:761291 original size:19 final size:21
Alignment explanation
Indices: 761265--761318 Score: 76
Period size: 19 Copynumber: 2.7 Consensus size: 21
761255 TAATAAATAT
761265 TTATAATATTATTTAATA-AA
1 TTATAATATTATTTAATATAA
* *
761285 TTA-AATATTATATAATATAT
1 TTATAATATTATTTAATATAA
761305 TTATAATATTATTT
1 TTATAATATTATTT
761319 CTTTAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 13 0.45
20 7 0.24
21 9 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTATAATATTATTTAATATAA
Found at i:761812 original size:22 final size:22
Alignment explanation
Indices: 761786--761832 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
761776 TTAGATCATC
761786 AATAAAAAATATAAAAATATAA
1 AATAAAAAATATAAAAATATAA
** * *
761808 AATAAACTATATGAGAATATAA
1 AATAAAAAATATAAAAATATAA
761830 AAT
1 AAT
761833 TTCCAAAGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (22 bp):
AATAAAAAATATAAAAATATAA
Found at i:763204 original size:10 final size:10
Alignment explanation
Indices: 763189--763238 Score: 73
Period size: 10 Copynumber: 4.9 Consensus size: 10
763179 ATTTTTTAAT
763189 GATTAAATTA
1 GATTAAATTA
*
763199 GATTAAAGTA
1 GATTAAATTA
763209 GATTAAATTA
1 GATTAAATTA
*
763219 GATTAAAGATA
1 GATTAAA-TTA
763230 GATTAAATT
1 GATTAAATT
763239 GTAACATAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
10 26 0.74
11 9 0.26
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (10 bp):
GATTAAATTA
Found at i:763214 original size:20 final size:21
Alignment explanation
Indices: 763189--763238 Score: 93
Period size: 20 Copynumber: 2.4 Consensus size: 21
763179 ATTTTTTAAT
763189 GATTAAATTAGATTAAAG-TA
1 GATTAAATTAGATTAAAGATA
763209 GATTAAATTAGATTAAAGATA
1 GATTAAATTAGATTAAAGATA
763230 GATTAAATT
1 GATTAAATT
763239 GTAACATAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (21 bp):
GATTAAATTAGATTAAAGATA
Found at i:764069 original size:4 final size:4
Alignment explanation
Indices: 764060--764095 Score: 63
Period size: 4 Copynumber: 8.8 Consensus size: 4
764050 GAAAATGATA
764060 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAGAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA-AG AAA
764096 TCATCGACCT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 27 0.87
5 4 0.13
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:765588 original size:13 final size:13
Alignment explanation
Indices: 765570--765596 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
765560 GAGGGCAATT
765570 AAAATTAATTTTA
1 AAAATTAATTTTA
765583 AAAATTAATTTTA
1 AAAATTAATTTTA
765596 A
1 A
765597 TTTTTATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAAATTAATTTTA
Found at i:770407 original size:43 final size:43
Alignment explanation
Indices: 770339--770438 Score: 137
Period size: 43 Copynumber: 2.3 Consensus size: 43
770329 ACTTATGTAA
* *
770339 GTCTAATTATGGATTCAGTCCCTACTTTCTACAGTTTTAATTT
1 GTCTAATTATGGATTCAGTCCCTACTTTCTACAGTTTCAATTG
* * * *
770382 GTCTAATTATGGGTTTAGTCGCTACTTTCTACAGTTTCAGTTG
1 GTCTAATTATGGATTCAGTCCCTACTTTCTACAGTTTCAATTG
*
770425 GTCTAATTCTGGAT
1 GTCTAATTATGGAT
770439 CTAGCCCCTC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.45
Consensus pattern (43 bp):
GTCTAATTATGGATTCAGTCCCTACTTTCTACAGTTTCAATTG
Found at i:772169 original size:30 final size:30
Alignment explanation
Indices: 772133--772192 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
772123 GTGTCTGTTA
*
772133 CTAAACTTCTCAGAAATATTAACAAGAATT
1 CTAAACTTCTCAGAAATATGAACAAGAATT
* * *
772163 CTAAACTTTTCAGGAATATGAACAATAATT
1 CTAAACTTCTCAGAAATATGAACAAGAATT
772193 AAGCATTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (30 bp):
CTAAACTTCTCAGAAATATGAACAAGAATT
Found at i:776717 original size:15 final size:15
Alignment explanation
Indices: 776669--776729 Score: 67
Period size: 15 Copynumber: 4.3 Consensus size: 15
776659 GTTTTCCATG
776669 TTTTACTAT-ATTTAA
1 TTTTA-TATGATTTAA
776684 TTTTA-A-GATTTAA
1 TTTTATATGATTTAA
*
776697 -TTTATATGTTTTAA
1 TTTTATATGATTTAA
*
776711 TTTTATATAATTTAA
1 TTTTATATGATTTAA
776726 TTTT
1 TTTT
776730 TTGATTATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
12 4 0.10
13 8 0.21
14 6 0.15
15 21 0.54
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (15 bp):
TTTTATATGATTTAA
Found at i:784181 original size:2 final size:2
Alignment explanation
Indices: 784174--784223 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
784164 TGACTACCGT
784174 TA TA TA TA TA TA 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 TA TA TA TA TA TA
784216 TA TA TA TA
1 TA TA TA TA
784224 ATAAAAATAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:784973 original size:12 final size:12
Alignment explanation
Indices: 784956--784981 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
784946 TTTTGTTTAA
784956 ATCATAGATTCT
1 ATCATAGATTCT
784968 ATCATAGATTCT
1 ATCATAGATTCT
784980 AT
1 AT
784982 AATCTATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (12 bp):
ATCATAGATTCT
Found at i:785690 original size:2 final size:2
Alignment explanation
Indices: 785683--785714 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
785673 GCAATACTTA
785683 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
785715 TGTTGCCTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:806359 original size:2 final size:2
Alignment explanation
Indices: 806352--806394 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
806342 ATTGGTTTAA
* * *
806352 AT AT AT AT AT TT CT CT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
806394 A
1 A
806395 ATTAAAGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:807094 original size:21 final size:20
Alignment explanation
Indices: 807069--807119 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
807059 TATTATTTAA
807069 AAATAATTTTAGAA-TAATATT
1 AAATAATTTTA-AATTAA-ATT
807090 AAAT-ATTTTAAATTTAAATT
1 AAATAATTTTAAA-TTAAATT
807110 AAATAATTTT
1 AAATAATTTT
807120 GAAACAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 2 0.07
20 13 0.48
21 12 0.44
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
AAATAATTTTAAATTAAATT
Found at i:831274 original size:20 final size:20
Alignment explanation
Indices: 831251--831417 Score: 271
Period size: 20 Copynumber: 8.3 Consensus size: 20
831241 GAATACGTAA
* *
831251 ATCGCAACGCAAATCTGACT
1 ATCGCAACGCGATTCTGACT
*
831271 ATCGTAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
831291 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
831311 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
831331 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
831351 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
831371 ATCGCAACGCGATTTTGACT
1 ATCGCAACGCGATTCTGACT
* *
831391 ATCGTAATGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
831411 ATCGCAA
1 ATCGCAA
831418 TACTGAATTT
Statistics
Matches: 136, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 136 1.00
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:832310 original size:24 final size:24
Alignment explanation
Indices: 832259--832312 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
832249 GTATTCGAAA
*
832259 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
832283 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
832307 TTTGAT
1 TTTGAT
832313 GATTTTTCAG
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:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:834751 original size:20 final size:19
Alignment explanation
Indices: 834726--834797 Score: 108
Period size: 20 Copynumber: 3.6 Consensus size: 19
834716 GACATTCATT
834726 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAA-A
*
834746 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGC-GAAA
834766 TGACTATCGCAACGCGAAAA
1 TGACTATCGCAACGCG-AAA
834786 TGACTATCGCAA
1 TGACTATCGCAA
834798 TGAGAGAATC
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
19 1 0.02
20 44 0.92
21 3 0.06
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (19 bp):
TGACTATCGCAACGCGAAA
Found at i:834828 original size:33 final size:34
Alignment explanation
Indices: 834771--834866 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 34
834761 GGAAATGACT
* ** *
834771 ATCGCAACGCGAAAATGACTATCGCAATGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
834805 ATCGCAATGCG-AAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
834838 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCGAAAATGAAAATCGCAACG
834867 CGAATTTAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 30 0.53
34 27 0.47
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.14
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
Found at i:834862 original size:20 final size:19
Alignment explanation
Indices: 834804--834870 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
834794 GCAATGAGAG
834804 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
834823 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
834837 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
834857 AATCGCAACGCGAA
1 AATCGCAATGCGAA
834871 TTTAGTTTCG
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
19 11 0.28
20 13 0.33
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:834922 original size:14 final size:14
Alignment explanation
Indices: 834903--834970 Score: 73
Period size: 14 Copynumber: 4.5 Consensus size: 14
834893 CATTTTCGCA
834903 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
834917 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
834931 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
834948 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
834964 TTACGAT
1 TTGCGAT
834971 AGTCATTTCC
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
14 26 0.57
16 7 0.15
17 7 0.15
19 6 0.13
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:834959 original size:33 final size:33
Alignment explanation
Indices: 834917--834979 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
834907 GATTCTCTCG
* **
834917 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTCTCTCGTTACGATAGTCATTTCGCA
834950 TTGCGATTCTCTCGTTACGATAGTCATTTC
1 TTGCGATTCTCTCGTTACGATAGTCATTTC
834980 CGCGTTGTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.44
Consensus pattern (33 bp):
TTGCGATTCTCTCGTTACGATAGTCATTTCGCA
Found at i:836566 original size:42 final size:42
Alignment explanation
Indices: 836468--836570 Score: 109
Period size: 42 Copynumber: 2.5 Consensus size: 42
836458 TTGGGATGGA
* * * *
836468 CCTCTTCAACGATGACAGTGGCCTCTTAAACGGTGGGAGGGG
1 CCTCTTGAACGATGACAGGGGCCTCTTAAACGATGGGAGAGG
* ** * *
836510 ACTCTTGAGGGATGATAGGGGCCTCTTGAACGATAGGG-GAGG
1 CCTCTTGAACGATGACAGGGGCCTCTTAAACGAT-GGGAGAGG
836552 CCTCTTGAACGATGACAGG
1 CCTCTTGAACGATGACAGG
836571 TGAGTCGGGC
Statistics
Matches: 47, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
42 44 0.94
43 3 0.06
ACGTcount: A:0.23, C:0.20, G:0.35, T:0.21
Consensus pattern (42 bp):
CCTCTTGAACGATGACAGGGGCCTCTTAAACGATGGGAGAGG
Found at i:837079 original size:20 final size:20
Alignment explanation
Indices: 837054--837158 Score: 129
Period size: 20 Copynumber: 5.2 Consensus size: 20
837044 CTTAAAATCA
*
837054 CAACGCAAAAATGACTATCG
1 CAACGCGAAAATGACTATCG
837074 CAACGCGAAAATGACTATCG
1 CAACGCGAAAATGACTATCG
*
837094 CAATGCGAAAATGACTATCG
1 CAACGCGAAAATGACTATCG
* **
837114 CAATGCGAATTTGACTATCG
1 CAACGCGAAAATGACTATCG
* * **
837134 TAATGCGAATTTGACTATCG
1 CAACGCGAAAATGACTATCG
837154 CAACG
1 CAACG
837159 AGAGAATCGC
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 78 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (20 bp):
CAACGCGAAAATGACTATCG
Found at i:837116 original size:40 final size:40
Alignment explanation
Indices: 837061--837158 Score: 142
Period size: 40 Copynumber: 2.5 Consensus size: 40
837051 TCACAACGCA
837061 AAAATGACTATCGCAACGCGAAAATGACTATCGCAATGCG
1 AAAATGACTATCGCAACGCGAAAATGACTATCGCAATGCG
* ** *
837101 AAAATGACTATCGCAATGCGAATTTGACTATCGTAATGCG
1 AAAATGACTATCGCAACGCGAAAATGACTATCGCAATGCG
**
837141 AATTTGACTATCGCAACG
1 AAAATGACTATCGCAACG
837159 AGAGAATCGC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.23
Consensus pattern (40 bp):
AAAATGACTATCGCAACGCGAAAATGACTATCGCAATGCG
Found at i:837228 original size:20 final size:20
Alignment explanation
Indices: 837203--837359 Score: 108
Period size: 20 Copynumber: 8.5 Consensus size: 20
837193 GATACTTTCG
**
837203 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
837223 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
* *
837243 TTGTGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
837263 TTGCGAT--T--TTGTT-G--
1 TTGCGATAGTCATT-TTCGCA
* **
837277 TTACGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
837296 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
837310 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
*
837330 TTGCTATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
837350 TTGCGATAGT
1 TTGCGATAGT
837360 AAACTATTCT
Statistics
Matches: 109, Mismatches: 14, Indels: 28
0.72 0.09 0.19
Matches are distributed among these distances:
14 13 0.12
16 12 0.11
17 6 0.06
18 5 0.05
19 6 0.06
20 67 0.61
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.43
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:839265 original size:20 final size:20
Alignment explanation
Indices: 839242--839350 Score: 114
Period size: 20 Copynumber: 5.5 Consensus size: 20
839232 TCTGAAACTT
839242 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
839262 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * *
839282 ACTATCGCAACGCG-AAATA
1 AAAATCGCAACACGAAAATG
*
839301 AAAATCACAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
839321 ACTATCACAATGCG-AAATG
1 AAAATCGCAACACGAAAATG
839340 AAAATCGCAAC
1 AAAATCGCAAC
839351 GACAGAATCG
Statistics
Matches: 71, Mismatches: 17, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
19 26 0.37
20 45 0.63
ACGTcount: A:0.51, C:0.22, G:0.14, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:839314 original size:39 final size:39
Alignment explanation
Indices: 839245--839350 Score: 158
Period size: 39 Copynumber: 2.7 Consensus size: 39
839235 GAAACTTAAA
*
839245 ATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACT
1 ATCGCAACGCG-AAATGAAAATCGCAACACGAAAATGACT
* *
839285 ATCGCAACGCGAAATAAAAATCACAACACGAAAATGACT
1 ATCGCAACGCGAAATGAAAATCGCAACACGAAAATGACT
* *
839324 ATCACAATGCGAAATGAAAATCGCAAC
1 ATCGCAACGCGAAATGAAAATCGCAAC
839351 GACAGAATCG
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
39 49 0.83
40 10 0.17
ACGTcount: A:0.50, C:0.23, G:0.14, T:0.13
Consensus pattern (39 bp):
ATCGCAACGCGAAATGAAAATCGCAACACGAAAATGACT
Found at i:839749 original size:22 final size:22
Alignment explanation
Indices: 839687--839752 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
839677 TGACCATGAA
* *
839687 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
839709 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
839731 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
839753 GGATGTCGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:839960 original size:20 final size:20
Alignment explanation
Indices: 839937--840002 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
839927 GTAAATCGCA
839937 TTGCGATAGTCAAAATCGTG
1 TTGCGATAGTCAAAATCGTG
* *
839957 TTGCGA-A-TCTGGAAACTGGT-
1 TTGCGATAGTC---AAAATCGTG
*
839977 TTGCGATAGTCAAAATCGCG
1 TTGCGATAGTCAAAATCGTG
839997 TTGCGA
1 TTGCGA
840003 ATCTGGAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 12
0.67 0.10 0.23
Matches are distributed among these distances:
18 2 0.06
19 6 0.17
20 18 0.51
21 7 0.20
22 2 0.06
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (20 bp):
TTGCGATAGTCAAAATCGTG
Found at i:839992 original size:40 final size:40
Alignment explanation
Indices: 839937--840044 Score: 162
Period size: 40 Copynumber: 2.7 Consensus size: 40
839927 GTAAATCGCA
*
839937 TTGCGATAGTCAAAATCGTGTTGCGAATCTGGAAACTGGT
1 TTGCGATAGTCAAAATCGTGTTGCGAATCTGGAAACTGAT
*
839977 TTGCGATAGTCAAAATCGCGTTGCGAATCTGGAAACTGAT
1 TTGCGATAGTCAAAATCGTGTTGCGAATCTGGAAACTGAT
* ** *
840017 TTGCGATACTGGAGATCGTGTTGCGAAT
1 TTGCGATAGTCAAAATCGTGTTGCGAAT
840045 TATCGATCGC
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.30
Consensus pattern (40 bp):
TTGCGATAGTCAAAATCGTGTTGCGAATCTGGAAACTGAT
Found at i:851458 original size:28 final size:28
Alignment explanation
Indices: 851427--851485 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
851417 TTAATCCTTT
*
851427 ATTAAATTTTAATTTTAATAAAAACATA
1 ATTAAATTATAATTTTAATAAAAACATA
* * * *
851455 ATTATATTATGATTTTTATTAAAACATA
1 ATTAAATTATAATTTTAATAAAAACATA
851483 ATT
1 ATT
851486 TATTTATTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (28 bp):
ATTAAATTATAATTTTAATAAAAACATA
Found at i:858942 original size:18 final size:18
Alignment explanation
Indices: 858899--858961 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
858889 CAAAAAGCAT
*
858899 AAATTTAAAAATTTATAA
1 AAATTTAAAAATATATAA
*
858917 TCAA--TAAAAATAT-TAA
1 -AAATTTAAAAATATATAA
*
858933 AAATATTAAAATTATATAA
1 AAAT-TTAAAAATATATAA
858952 AAATTTAAAA
1 AAATTTAAAA
858962 TTTACCCCGT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
15 2 0.06
16 3 0.08
17 8 0.22
18 14 0.39
19 9 0.25
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATTTAAAAATATATAA
Found at i:858954 original size:11 final size:9
Alignment explanation
Indices: 858921--858961 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
858911 TTATAATCAA
858921 TAAAAATAT
1 TAAAAATAT
858930 TAAAAATAT
1 TAAAAATAT
*
858939 TAAAATTAT
1 TAAAAATAT
858948 ATAAAAAT-T
1 -TAAAAATAT
858957 TAAAA
1 TAAAA
858962 TTTACCCCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 5 0.17
9 18 0.62
10 6 0.21
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
TAAAAATAT
Found at i:866326 original size:2 final size:2
Alignment explanation
Indices: 866319--866349 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
866309 ATACATACAC
866319 AT AT 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 AT AT A
866350 AGAGTTCTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:866652 original size:17 final size:17
Alignment explanation
Indices: 866630--866662 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
866620 TTTGACATAG
866630 TGCTTGTGAGTTTTTCA
1 TGCTTGTGAGTTTTTCA
*
866647 TGCTTGTGATTTTTTC
1 TGCTTGTGAGTTTTTC
866663 GAAAGTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.58
Consensus pattern (17 bp):
TGCTTGTGAGTTTTTCA
Found at i:871771 original size:30 final size:30
Alignment explanation
Indices: 871715--871808 Score: 154
Period size: 30 Copynumber: 3.1 Consensus size: 30
871705 GAAGGACCTA
* *
871715 TCCAGAGGTCACAAAGA-CCCCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
871744 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
871774 TCCAGAGGTCATAAAGATCCTCGGTAAACTG
1 TCCAGAGGTCATAAAGATCCTCGGT-AACTG
871805 TCCA
1 TCCA
871809 TATGTCTCGA
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
29 16 0.26
30 36 0.59
31 9 0.15
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:872560 original size:22 final size:22
Alignment explanation
Indices: 872516--872557 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
872506 TAAATCAATT
*
872516 TCATATAACTCCTATAATCTTC
1 TCATATAACTCCTATAACCTTC
*
872538 TCATATAACTTC-ATAACCTT
1 TCATATAACTCCTATAACCTT
872558 TCTTATGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.40
Consensus pattern (22 bp):
TCATATAACTCCTATAACCTTC
Found at i:873034 original size:21 final size:21
Alignment explanation
Indices: 873004--873048 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
872994 ATTCTGTCGT
* *
873004 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
873025 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
873046 TTG
1 TTG
873049 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:877453 original size:2 final size:2
Alignment explanation
Indices: 877446--877486 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
877436 GTATGAAGGA
877446 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
877487 TACATATTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:877899 original size:2 final size:2
Alignment explanation
Indices: 877894--877932 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
877884 ATATATCCGT
877894 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
877933 GCTAATGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:878427 original size:61 final size:61
Alignment explanation
Indices: 878343--878553 Score: 237
Period size: 61 Copynumber: 3.5 Consensus size: 61
878333 AAATAAGTAT
* * ** * * *
878343 CTAATTAAAATAAGCTAGGCTTATTAGGCTCAATTATTGATTAATTTAATTAAATAAGGAC
1 CTAATTGAAAGAAGCTAAACTTATTAGGCTCAATTATTAATTAATTTAACTAATTAAGGAC
* *
878404 CTAATTGAAAGATA-CTAAACTTATTAGGCTTC-ATTATTAATCAATTTAACTAATTAAGGAT
1 CTAATTGAAAGA-AGCTAAACTTATTAGGC-TCAATTATTAATTAATTTAACTAATTAAGGAC
* * *** * * *
878465 CTAATTGCAAGAAGCCAAACTTATTACATTTAATTATTAATTAATTTAACTACTTATGGAC
1 CTAATTGAAAGAAGCTAAACTTATTAGGCTCAATTATTAATTAATTTAACTAATTAAGGAC
878526 CTAATTGAAAGAAGCTAAACTTATTAGG
1 CTAATTGAAAGAAGCTAAACTTATTAGG
878554 TTAAAAAATT
Statistics
Matches: 123, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
60 2 0.02
61 118 0.96
62 3 0.02
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (61 bp):
CTAATTGAAAGAAGCTAAACTTATTAGGCTCAATTATTAATTAATTTAACTAATTAAGGAC
Found at i:884442 original size:81 final size:81
Alignment explanation
Indices: 884302--884459 Score: 262
Period size: 81 Copynumber: 2.0 Consensus size: 81
884292 GTCTCTTGCA
* * *
884302 CAACTGGCTCGGTAGCTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTG
1 CAACCGGCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTG
884367 CGAACCATTCTTGGTG
66 CGAACCATTCTTGGTG
* * *
884383 CAACCGGCTCAGTAACTTCCTTCTCTACACCTCTGTGAGAGCTTGTTGCTCCGCCATTTCGTGTG
1 CAACCGGCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTG
884448 CGAACCATTCTT
66 CGAACCATTCTT
884460 TGTAACTCGC
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 71 1.00
ACGTcount: A:0.16, C:0.31, G:0.22, T:0.32
Consensus pattern (81 bp):
CAACCGGCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTG
CGAACCATTCTTGGTG
Done.