Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001079.1 Hibiscus syriacus cultivar Beakdansim tig00002138_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: 113573
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:4796 original size:12 final size:12
Alignment explanation
Indices: 4779--4804 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4769 AACGTTAATT
4779 TACTGATTGAGA
1 TACTGATTGAGA
4791 TACTGATTGAGA
1 TACTGATTGAGA
4803 TA
1 TA
4805 TAATAAAATT
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:0.08, G:0.23, T:0.35
Consensus pattern (12 bp):
TACTGATTGAGA
Found at i:5398 original size:21 final size:20
Alignment explanation
Indices: 5360--5398 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5350 AGATTATATA
*
5360 ATTGATTTTTAAATCATTTT
1 ATTGATTTTTAAAGCATTTT
5380 ATTGATTTTTAACAGCATT
1 ATTGATTTTTAA-AGCATT
5399 GCGAAGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (20 bp):
ATTGATTTTTAAAGCATTTT
Found at i:5787 original size:22 final size:22
Alignment explanation
Indices: 5745--5792 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
5735 ATGGTACATT
*
5745 TTTTCCTATATCTATGGTAT-G
1 TTTTCCTATATCTATGATATGG
* *
5766 TTTTCTTATATCCTTTGATATGG
1 TTTTCCTATAT-CTATGATATGG
5789 TTTT
1 TTTT
5793 TGTTTTCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 10 0.45
22 7 0.32
23 5 0.23
ACGTcount: A:0.17, C:0.12, G:0.12, T:0.58
Consensus pattern (22 bp):
TTTTCCTATATCTATGATATGG
Found at i:14932 original size:26 final size:26
Alignment explanation
Indices: 14896--14948 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
14886 GTATAAAACT
14896 TTAAAATTTTATATATTTTTTAATTA
1 TTAAAATTTTATATATTTTTTAATTA
14922 TTAAAATTTTATATATTTTTTAATTA
1 TTAAAATTTTATATATTTTTTAATTA
14948 T
1 T
14949 CATATGAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
TTAAAATTTTATATATTTTTTAATTA
Found at i:19519 original size:60 final size:60
Alignment explanation
Indices: 19449--19605 Score: 201
Period size: 60 Copynumber: 2.6 Consensus size: 60
19439 GTCAAATACC
* * * * *
19449 ATTTTGTAACTTTTAATAGTTAGGAGACTCAACAAAATAGTGTCTTATAGTTAGTGGATT
1 ATTTTATAACTTTTAATAGTTAGGAGACTCAACAAAATAGTATCCTATAGTTAATGGACT
* *
19509 ATTTTATAACTTTTAATAGTCA-GATGACTTAACAAAATAGTATCCTATAGTTAATGGACT
1 ATTTTATAACTTTTAATAGTTAGGA-GACTCAACAAAATAGTATCCTATAGTTAATGGACT
* *
19569 ATTTTATAATTTTTAATAGTTTAGG-GACTCAATAAAA
1 ATTTTATAACTTTTAATAG-TTAGGAGACTCAACAAAA
19606 AACACAATAT
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
59 2 0.02
60 78 0.94
61 2 0.02
62 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (60 bp):
ATTTTATAACTTTTAATAGTTAGGAGACTCAACAAAATAGTATCCTATAGTTAATGGACT
Found at i:20127 original size:2 final size:2
Alignment explanation
Indices: 20120--20144 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20110 AATTAATTGA
20120 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 A
20145 CAAACTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21589 original size:20 final size:20
Alignment explanation
Indices: 21564--21601 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
21554 TAAAGATCAC
21564 ATCTTAATTAAAACAAAATG
1 ATCTTAATTAAAACAAAATG
*
21584 ATCTTAATTAAAATAAAA
1 ATCTTAATTAAAACAAAA
21602 CGAAAGTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.32
Consensus pattern (20 bp):
ATCTTAATTAAAACAAAATG
Found at i:21875 original size:18 final size:18
Alignment explanation
Indices: 21835--21883 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
21825 GTTTATGAGG
*
21835 GAATTAGAATTTGTAAAT
1 GAATTAGAATCTGTAAAT
*
21853 AAATTAGAATCTGTGAAA-
1 GAATTAGAATCTGT-AAAT
*
21871 GAATTGGAATCTG
1 GAATTAGAATCTG
21884 AAACCTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 23 0.88
19 3 0.12
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.33
Consensus pattern (18 bp):
GAATTAGAATCTGTAAAT
Found at i:22557 original size:33 final size:33
Alignment explanation
Indices: 22520--22649 Score: 104
Period size: 32 Copynumber: 3.9 Consensus size: 33
22510 GAAACTGGAT
*
22520 TTTTTTTTTAAAAAAAATCCAACCCGATATCGA
1 TTTTTTTTTAAAAAAAATCCAACCCGATACCGA
** * * * *
22553 TTTTTTTTTAAAAACCCGACCCGACTCGA-ACCCA
1 TTTTTTTTTAAAAA--AAATCCAACCCGATACCGA
* * * *
22587 ATTTTTTTAAAAAAAAATCCGACCCGATCCCGA
1 TTTTTTTTTAAAAAAAATCCAACCCGATACCGA
*
22620 -ATTTTTTT-AAAAAAATCCAACCCGAATACC
1 TTTTTTTTTAAAAAAAATCCAACCCG-ATACC
22650 AAAATATTGA
Statistics
Matches: 74, Mismatches: 19, Indels: 9
0.73 0.19 0.09
Matches are distributed among these distances:
31 15 0.20
32 19 0.26
33 17 0.23
34 15 0.20
35 8 0.11
ACGTcount: A:0.38, C:0.25, G:0.07, T:0.31
Consensus pattern (33 bp):
TTTTTTTTTAAAAAAAATCCAACCCGATACCGA
Found at i:30722 original size:2 final size:2
Alignment explanation
Indices: 30710--30748 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
30700 AAATAATTTA
*
30710 AT AT TT 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 A
30749 GAAAATAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:33096 original size:12 final size:11
Alignment explanation
Indices: 33050--33098 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 11
33040 TTTCCTAAAA
33050 TATTTA-ATTT
1 TATTTATATTT
33060 T-TTTATATTT
1 TATTTATATTT
*
33070 TA--GATATTT
1 TATTTATATTT
33079 TATTTATATTT
1 TATTTATATTT
33090 CTATTTATA
1 -TATTTATA
33099 GTATGTTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
9 12 0.38
10 6 0.19
11 6 0.19
12 8 0.25
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (11 bp):
TATTTATATTT
Found at i:36415 original size:35 final size:33
Alignment explanation
Indices: 36365--36433 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 33
36355 GTATTTCTTT
36365 AATATAATTTCTTTATTTTATTTTATTTAATATTA
1 AATATAATTTCTTTATTTTA--TTATTTAATATTA
*
36400 AATATAATTAT-TTTATTTTATTATTTCATATTA
1 AATATAATT-TCTTTATTTTATTATTTAATATTA
36433 A
1 A
36434 CTTTAAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 13 0.41
35 18 0.56
36 1 0.03
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (33 bp):
AATATAATTTCTTTATTTTATTATTTAATATTA
Found at i:39153 original size:15 final size:17
Alignment explanation
Indices: 39133--39165 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
39123 GAATTGAATT
39133 ATTTTTA-TC-ATTATA
1 ATTTTTATTCAATTATA
39148 ATTTTTATTCAATTATA
1 ATTTTTATTCAATTATA
39165 A
1 A
39166 CAATAAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 2 0.12
17 7 0.44
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTTTATTCAATTATA
Found at i:42898 original size:12 final size:12
Alignment explanation
Indices: 42856--42890 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
42846 CATATTGAAT
* *
42856 TTTCTTTTGAAC
1 TTTCTTTTTAAA
42868 TTTCTTTTTAAA
1 TTTCTTTTTAAA
42880 TTTCTTTTTAA
1 TTTCTTTTTAA
42891 TCTTCTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.20, C:0.11, G:0.03, T:0.66
Consensus pattern (12 bp):
TTTCTTTTTAAA
Found at i:43371 original size:186 final size:186
Alignment explanation
Indices: 43049--43421 Score: 692
Period size: 186 Copynumber: 2.0 Consensus size: 186
43039 GTGGGATCGA
43049 CTCTTACTTCTCTTTTACAACGTTAAATTTCCTTTATTATTAATTGAGAAGAATGAAATATTTTG
1 CTCTTACTTCTCTTTTACAACGTTAAATTTCCTTTATTATTAATTGAGAAGAATGAAATATTTTG
* * *
43114 ATGCGAAAAACGACGCGTGTCACTTTAGATAATGATGTCTGGCAATGAAGCCCTCAAAACTTGCG
66 ATGCAAAAAACGACGCGTGTCACTTTAGATAATGATGTCTGGCAATGAAGCCCTCAAAACTTACA
43179 ATGGGTGGTGTTGTCTGGTAGTGAAGCTCTCAAACCTTGTGAATCAGTAGATTCGG
131 ATGGGTGGTGTTGTCTGGTAGTGAAGCTCTCAAACCTTGTGAATCAGTAGATTCGG
*
43235 CTCTTACTTCTCTTTTACAACGTTAAATTTCCTTTATTATTAATTGATAAGAATGAAATATTTTG
1 CTCTTACTTCTCTTTTACAACGTTAAATTTCCTTTATTATTAATTGAGAAGAATGAAATATTTTG
43300 ATGCAAAAAACGACGCGTGTCACTTTAGATAATGATGTCTGGCAATGAAGCCCTCAAAACTTACA
66 ATGCAAAAAACGACGCGTGTCACTTTAGATAATGATGTCTGGCAATGAAGCCCTCAAAACTTACA
* *
43365 ATGGGTGGTGTTGTCTGGTAGTGAAGCTCTCAAACCTTGTGAATCCGTATATTCGG
131 ATGGGTGGTGTTGTCTGGTAGTGAAGCTCTCAAACCTTGTGAATCAGTAGATTCGG
43421 C
1 C
43422 GAAGAGAAAG
Statistics
Matches: 181, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
186 181 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (186 bp):
CTCTTACTTCTCTTTTACAACGTTAAATTTCCTTTATTATTAATTGAGAAGAATGAAATATTTTG
ATGCAAAAAACGACGCGTGTCACTTTAGATAATGATGTCTGGCAATGAAGCCCTCAAAACTTACA
ATGGGTGGTGTTGTCTGGTAGTGAAGCTCTCAAACCTTGTGAATCAGTAGATTCGG
Found at i:44186 original size:21 final size:20
Alignment explanation
Indices: 44100--44298 Score: 121
Period size: 21 Copynumber: 9.8 Consensus size: 20
44090 AAATGACCAA
**
44100 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
44119 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** * *
44139 CAGAATCGCAAATCAATTTC
1 CAAAATCGCAACGCGATTTT
44159 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
44180 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
44201 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
44221 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
* **
44242 GAAAATCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
44262 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
44283 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
44299 ACACATAAAT
Statistics
Matches: 134, Mismatches: 41, Indels: 9
0.73 0.22 0.05
Matches are distributed among these distances:
19 15 0.11
20 58 0.43
21 61 0.46
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:44248 original size:20 final size:20
Alignment explanation
Indices: 44100--44317 Score: 122
Period size: 20 Copynumber: 10.8 Consensus size: 20
44090 AAATGACCAA
44100 CAAAATCGCAACGCGAA-AT
1 CAAAATCGCAACGCGAATAT
* **
44119 AAAAATCGCAACGCG-ATCCC
1 CAAAATCGCAACGCGAAT-AT
* ** *
44139 CAGAATCGCAAATC-AATTT
1 CAAAATCGCAACGCGAATAT
* *
44158 CCAAAATCGCAACGCGATTCTT
1 -CAAAATCGCAACGCGAAT-AT
* *
44180 GAAAATCGCAATGCG-ATAGT
1 CAAAATCGCAACGCGAATA-T
* ** * *
44200 ACAAATTCGCATTGCGATTTT
1 -CAAAATCGCAACGCGAATAT
44221 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGAATAT
* ** * *
44242 GAAAATCGCATTGCGATTTT
1 CAAAATCGCAACGCGAATAT
44262 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGAATAT
* *
44283 GAAAATCGCAACGCGAACA-
1 CAAAATCGCAACGCGAATAT
44302 CATAAATCGCAACGCG
1 CA-AAATCGCAACGCG
44318 TATCCGTAAA
Statistics
Matches: 147, Mismatches: 41, Indels: 21
0.70 0.20 0.10
Matches are distributed among these distances:
18 1 0.01
19 15 0.10
20 70 0.48
21 58 0.39
22 3 0.02
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGAATAT
Found at i:44260 original size:41 final size:41
Alignment explanation
Indices: 44181--44292 Score: 174
Period size: 41 Copynumber: 2.7 Consensus size: 41
44171 GCGATTCTTG
*
44181 AAAATCGCAATGCG-ATA-GTACAAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGAATATG-A-AAA-TCGCATTGCGATTTTCC
44223 AAAATCGCAACGCGAATATGAAAATCGCATTGCGATTTTCC
1 AAAATCGCAACGCGAATATGAAAATCGCATTGCGATTTTCC
44264 AAAATCGCAACGCGAATATGAAAATCGCA
1 AAAATCGCAACGCGAATATGAAAATCGCA
44293 ACGCGAACAC
Statistics
Matches: 67, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
41 46 0.69
42 16 0.24
43 4 0.06
44 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGCGAATATGAAAATCGCATTGCGATTTTCC
Found at i:44327 original size:20 final size:20
Alignment explanation
Indices: 44265--44458 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
44255 CGATTTTCCA
* ** *
44265 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
44285 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
44305 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
44325 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
44345 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
44365 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
44385 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
44405 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
44425 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
44446 AAATCGCAACGCG
1 AAATCGCAACGCG
44459 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:44357 original size:60 final size:60
Alignment explanation
Indices: 44265--44458 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
44255 CGATTTTCCA
* ** * *
44265 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
44325 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
44385 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
44446 AAATCGCAACGCG
1 AAATCGCAACGCG
44459 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:44875 original size:33 final size:33
Alignment explanation
Indices: 44836--44906 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
44826 TTCACTTAGA
* *
44836 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
44869 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
44902 TTTCA
1 TTTCA
44907 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:45012 original size:21 final size:20
Alignment explanation
Indices: 44986--45091 Score: 91
Period size: 21 Copynumber: 5.5 Consensus size: 20
44976 TGCAGAAGAG
44986 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
45007 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
45027 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
45048 GCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
45062 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
45081 TCGCAACGAGA
1 TCGCAACGAGA
45092 GAATCGCAAC
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 2 0.03
19 11 0.17
20 16 0.24
21 25 0.38
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.10
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:45030 original size:20 final size:21
Alignment explanation
Indices: 44984--45062 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
44974 TTTGCAGAAG
*
44984 AGTCGCAACGAGATAAATGAAA
1 AGTCGCAACGAGA-GAATGAAA
*
45006 A-TCGCAACGAGAGAATG-AC
1 AGTCGCAACGAGAGAATGAAA
*
45025 TGTCGCAACGAGAGAAATGAAA
1 AGTCGCAACGAGAG-AATGAAA
45047 AG-CGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAT
45063 CGCAACGCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.02
20 19 0.39
21 26 0.53
22 3 0.06
ACGTcount: A:0.46, C:0.16, G:0.27, T:0.11
Consensus pattern (21 bp):
AGTCGCAACGAGAGAATGAAA
Found at i:45043 original size:41 final size:38
Alignment explanation
Indices: 44979--45095 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
44969 TTCAATTTGC
* *
44979 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
45017 AGAATGACTGTCGCAACGAGAGAAATGAAAAGCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
45058 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
45091 AGAAT
1 AGAAT
45096 CGCAACGCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.10
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:45068 original size:14 final size:14
Alignment explanation
Indices: 45049--45102 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
45039 AAATGAAAAG
45049 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
*
45063 CGCAACGCGAAATGAAAAT
1 CGCAA--CG--A-GAGAAT
45082 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
45096 CGCAACG
1 CGCAACG
45103 CGAAACCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.43, C:0.24, G:0.26, T:0.07
Consensus pattern (14 bp):
CGCAACGAGAGAAT
Found at i:45078 original size:33 final size:33
Alignment explanation
Indices: 45038--45107 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
45028 CGCAACGAGA
45038 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
*
45071 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
45104 GAAA
1 GAAA
45108 CCAAAATCGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.47, C:0.20, G:0.26, T:0.07
Consensus pattern (33 bp):
GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
Found at i:45114 original size:33 final size:33
Alignment explanation
Indices: 45044--45118 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
45034 GAGAGAAATG
* **
45044 AAAAGCGCAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
45077 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
45110 AAAATCGCA
1 AAAATCGCA
45119 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.47, C:0.24, G:0.23, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:45136 original size:19 final size:19
Alignment explanation
Indices: 45114--45211 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 19
45104 GAAACCAAAA
*
45114 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
45133 TCGCGTTACGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
45149 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
45166 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
45180 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
45199 TCGCGTTGCGATT
1 TCGCGTTGCGATT
45212 CTCTCGTTGC
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 17 0.28
16 7 0.11
17 8 0.13
19 29 0.48
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:45161 original size:33 final size:33
Alignment explanation
Indices: 45119--45233 Score: 194
Period size: 33 Copynumber: 3.5 Consensus size: 33
45109 CAAAATCGCA
* *
45119 TTGCGATTTTCATTTCGCGTTACGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
45152 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
45185 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
45218 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
45234 AACCAAAAGA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:45188 original size:14 final size:14
Alignment explanation
Indices: 45169--45225 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 14
45159 TTTCATTTCG
45169 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
45183 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
45200 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
45216 CGTTGCGATT
1 CGTTGCGATT
45226 TTCATTTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 18 0.47
15 1 0.03
16 5 0.13
17 5 0.13
18 1 0.03
19 8 0.21
ACGTcount: A:0.09, C:0.26, G:0.25, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:47116 original size:93 final size:93
Alignment explanation
Indices: 46926--47397 Score: 903
Period size: 93 Copynumber: 5.1 Consensus size: 93
46916 TAGATTGCTT
*
46926 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACAC--TGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
46989 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
47017 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
47082 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
47110 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
47175 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
47203 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
47268 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
47296 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
47361 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
47389 AGTAAATTT
1 AGTAAATTT
47398 ATCCATTCAA
Statistics
Matches: 374, Mismatches: 5, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
91 51 0.14
93 323 0.86
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:47481 original size:19 final size:19
Alignment explanation
Indices: 47441--47569 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
47431 TAGTTTACTT
* *
47441 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
47461 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
47480 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
47499 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
47513 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
47532 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
47546 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
47565 TCGCA
1 TCGCA
47570 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:47520 original size:33 final size:32
Alignment explanation
Indices: 47477--47569 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
47467 CGCGAAACCA
**
47477 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
47509 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
47542 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
47570 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:47567 original size:52 final size:52
Alignment explanation
Indices: 47441--47569 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
47431 TAGTTTACTT
**
47441 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
47493 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
47546 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
47570 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:47587 original size:19 final size:19
Alignment explanation
Indices: 47565--47699 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
47555 GAAACCAAAA
*
47565 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
47584 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
47600 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
47617 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
47633 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
47650 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
47669 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
47689 TCGTGTTGCGA
1 TCGCGTTGCGA
47700 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:47606 original size:14 final size:14
Alignment explanation
Indices: 47587--47643 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
47577 TTTCATTTCG
47587 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
47601 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
47618 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
47634 CGTTGCGATT
1 CGTTGCGATT
47644 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:47612 original size:33 final size:33
Alignment explanation
Indices: 47570--47662 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
47560 CAAAATCGCA
*
47570 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
47603 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
47636 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
47663 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:49660 original size:14 final size:14
Alignment explanation
Indices: 49624--49660 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
49614 GATTGTTTAA
49624 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
49638 ATGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
49652 TTGACTTGT
1 TTGATTTGT
49661 GTAATTGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.32, C:0.03, G:0.22, T:0.43
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:49789 original size:19 final size:19
Alignment explanation
Indices: 49765--49863 Score: 138
Period size: 19 Copynumber: 5.5 Consensus size: 19
49755 AAAATTGACT
49765 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
49784 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
49803 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
49817 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
49836 ATCGCAATGCGGAAATG-AA
1 ATCGCAATGC-GAAATGAAA
49855 ATCGCAATG
1 ATCGCAATG
49864 GGAGAATCGC
Statistics
Matches: 72, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 50 0.69
20 6 0.08
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:49843 original size:52 final size:52
Alignment explanation
Indices: 49765--49876 Score: 190
Period size: 52 Copynumber: 2.2 Consensus size: 52
49755 AAAATTGACT
49765 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATG-AAATCGCAACGAGAGA
* *
49817 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAATCGCAATGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAATCGCAACGAGAGA
49869 ATCGCAAT
1 ATCGCAAT
49877 ACGATTTTAA
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
52 51 0.89
53 6 0.11
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAATCGCAACGAGAGA
Found at i:49900 original size:19 final size:19
Alignment explanation
Indices: 49878--50037 Score: 170
Period size: 19 Copynumber: 9.2 Consensus size: 19
49868 AATCGCAATA
*
49878 CGATTTTAATTTCGCATTG
1 CGATTTTCATTTCGCATTG
*
49897 CGA--TTC-TCTCG--TTG
1 CGATTTTCATTTCGCATTG
49911 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTG
49930 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTG
*
49949 CGA--TTC-TCTCG--TTG
1 CGATTTTCATTTCGCATTG
49963 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTG
49982 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTG
*
50001 CGA--TT-ATCTCG--TTG
1 CGATTTTCATTTCGCATTG
50015 CGATTTTCATTTCCGCATTG
1 CGATTTTCATTT-CGCATTG
50035 CGA
1 CGA
50038 AATGTAATGG
Statistics
Matches: 118, Mismatches: 7, Indels: 31
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.15
16 21 0.18
17 18 0.15
18 2 0.02
19 53 0.45
20 6 0.05
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
CGATTTTCATTTCGCATTG
Found at i:49915 original size:33 final size:33
Alignment explanation
Indices: 49878--50037 Score: 146
Period size: 33 Copynumber: 4.7 Consensus size: 33
49868 AATCGCAATA
*
49878 CGATTTTAATTTCGCATTGCGATTCTCTCGTTG
1 CGATTTTCATTTCGCATTGCGATTCTCTCGTTG
*
49911 CGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTG
* * * * *
49949 CGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCATTG
1 CGATT-T-TCATTTCGCA-TTGCGATTCTCTCGTTG
*
49982 CGATTTTCATTTCGCATTGCGATTATCTCGTTG
1 CGATTTTCATTTCGCATTGCGATTCTCTCGTTG
50015 CGATTTTCATTTCCGCATTGCGA
1 CGATTTTCATTT-CGCATTGCGA
50038 AATGTAATGG
Statistics
Matches: 102, Mismatches: 13, Indels: 23
0.74 0.09 0.17
Matches are distributed among these distances:
31 9 0.09
32 5 0.05
33 47 0.46
34 10 0.10
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.08
39 3 0.03
40 9 0.09
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (33 bp):
CGATTTTCATTTCGCATTGCGATTCTCTCGTTG
Found at i:49926 original size:52 final size:52
Alignment explanation
Indices: 49878--50037 Score: 293
Period size: 52 Copynumber: 3.1 Consensus size: 52
49868 AATCGCAATA
*
49878 CGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTG
49930 CGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTG
*
49982 CGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCCGCATTG
1 CGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTG
50035 CGA
1 CGA
50038 AATGTAATGG
Statistics
Matches: 105, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
52 95 0.90
53 10 0.10
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (52 bp):
CGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTG
Found at i:50120 original size:19 final size:19
Alignment explanation
Indices: 50096--50214 Score: 185
Period size: 19 Copynumber: 6.5 Consensus size: 19
50086 AAAATTGACT
50096 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
50115 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
50134 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
50153 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
50167 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
50186 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
50206 ATCGCAATG
1 ATCGCAATG
50215 GGAGAATCGC
Statistics
Matches: 92, Mismatches: 2, Indels: 11
0.88 0.02 0.10
Matches are distributed among these distances:
14 10 0.11
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 58 0.63
20 18 0.20
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:50175 original size:33 final size:36
Alignment explanation
Indices: 50096--50214 Score: 163
Period size: 33 Copynumber: 3.2 Consensus size: 36
50086 AAAATTGACT
50096 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAA
*
50134 ATCGCAATGCGAAATGAAAATCGCAA-CG-A-GAGA
1 ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
50167 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GC-G-AATGAAA
50206 ATCGCAATG
1 ATCGCAATG
50215 GGAGAATCGC
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
33 29 0.40
34 1 0.01
35 1 0.01
36 3 0.04
38 27 0.37
39 12 0.16
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (36 bp):
ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
Found at i:50244 original size:53 final size:53
Alignment explanation
Indices: 50114--50231 Score: 211
Period size: 53 Copynumber: 2.2 Consensus size: 53
50104 GCGAAATGAA
50114 AATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
* *
50166 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAATGGGAG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
50219 AATCGCAATGCGA
1 AATCGCAATGCGA
50232 TTTTCATTTC
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.44, C:0.17, G:0.25, T:0.14
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
Found at i:52563 original size:12 final size:12
Alignment explanation
Indices: 52546--52570 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52536 TCTTCGGGGA
52546 CTTTTTCTTCTT
1 CTTTTTCTTCTT
52558 CTTTTTCTTCTT
1 CTTTTTCTTCTT
52570 C
1 C
52571 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:52779 original size:24 final size:24
Alignment explanation
Indices: 52745--52791 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
52735 CTGAAACATC
52745 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
52769 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
52792 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:53501 original size:20 final size:20
Alignment explanation
Indices: 53473--53742 Score: 308
Period size: 20 Copynumber: 13.5 Consensus size: 20
53463 AAATTTCAGT
* *
53473 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
53493 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
53513 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
53533 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
53553 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
53573 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
53593 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
*
53613 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
53633 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
53653 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
53673 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCTC
* *
53693 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
* ** *
53713 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCTC
53733 GTTGCGATTT
1 GTTGCGATTT
53743 TGGAAAATCG
Statistics
Matches: 216, Mismatches: 32, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
20 215 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:53759 original size:21 final size:21
Alignment explanation
Indices: 53729--53811 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
53719 ATTTTCATAT
*
53729 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
53750 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
53771 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
53792 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
53812 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:53802 original size:42 final size:43
Alignment explanation
Indices: 53709--53807 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
53699 ATTTATGTGT
* *
53709 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
53750 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
53792 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
53808 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:55729 original size:16 final size:17
Alignment explanation
Indices: 55691--55722 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
55681 TTTTGAAAAT
55691 AAAGTAAAAGCTAAGGG
1 AAAGTAAAAGCTAAGGG
55708 AAAGTAAAAG-TAAGG
1 AAAGTAAAAGCTAAGG
55723 TTAAGTAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.56, C:0.03, G:0.28, T:0.12
Consensus pattern (17 bp):
AAAGTAAAAGCTAAGGG
Found at i:61044 original size:15 final size:16
Alignment explanation
Indices: 61024--61057 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
61014 ATTATTATAT
*
61024 TTTTATTATA-TTTCA
1 TTTTATCATATTTTCA
61039 TTTTATCATATTTTCA
1 TTTTATCATATTTTCA
61055 TTT
1 TTT
61058 ATACAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTATCATATTTTCA
Found at i:62010 original size:29 final size:29
Alignment explanation
Indices: 61962--62046 Score: 77
Period size: 29 Copynumber: 2.9 Consensus size: 29
61952 ATAAAAACAT
* *
61962 AAAAGATAGAATAAGAAAAA-ATAATATAA-
1 AAAAGAAAGAAAAAGAAAAAGA-AA-ATAAC
*
61991 TAAAGAAAAGAAAAAGAAAAAGAAAATAAC
1 AAAAG-AAAGAAAAAGAAAAAGAAAATAAC
*
62021 AAAAGAAAGTAAAAGAAATAA-AAAAT
1 AAAAGAAAGAAAAAGAAA-AAGAAAAT
62047 TAGAAAAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
29 25 0.53
30 21 0.45
31 1 0.02
ACGTcount: A:0.75, C:0.01, G:0.12, T:0.12
Consensus pattern (29 bp):
AAAAGAAAGAAAAAGAAAAAGAAAATAAC
Found at i:62034 original size:23 final size:21
Alignment explanation
Indices: 62003--62045 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
61993 AAGAAAAGAA
62003 AAAGAAAAAGAAAATAACAAAAG
1 AAAGAAAAAG-AAATAA-AAAAG
*
62026 AAAGTAAAAGAAATAAAAAA
1 AAAGAAAAAGAAATAAAAAA
62046 TTAGAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 6 0.32
23 9 0.47
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (21 bp):
AAAGAAAAAGAAATAAAAAAG
Found at i:63047 original size:2 final size:2
Alignment explanation
Indices: 63040--63083 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
63030 TTGTATTTTA
63040 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
63082 AT
1 AT
63084 GTTAATATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:63745 original size:2 final size:2
Alignment explanation
Indices: 63738--63763 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
63728 CGACTATGCC
63738 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
63764 GGGTGGATCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72045 original size:16 final size:17
Alignment explanation
Indices: 72024--72059 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
72014 CATAAATATT
*
72024 ATTAATAAAATAAA-TA
1 ATTAATAAAAAAAATTA
72040 ATTAATAAAAAAAATTA
1 ATTAATAAAAAAAATTA
72057 ATT
1 ATT
72060 TTCAGAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATTAATAAAAAAAATTA
Found at i:76604 original size:17 final size:17
Alignment explanation
Indices: 76582--76614 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
76572 ATTAATTTAT
*
76582 AAAAATAAAATTAATAA
1 AAAAATAAAATAAATAA
76599 AAAAATAAAATAAATA
1 AAAAATAAAATAAATA
76615 TTTTTAAAAA
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:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAATAAAATAAATAA
Found at i:76623 original size:21 final size:21
Alignment explanation
Indices: 76599--76650 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
76589 AAATTAATAA
76599 AAAAATAAAATAAATATTTTT
1 AAAAATAAAATAAATATTTTT
76620 AAAAATAAAATAAATATTTTT
1 AAAAATAAAATAAATATTTTT
76641 AAAAATAAAA
1 AAAAATAAAA
76651 AATATGGACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAAATAAAATAAATATTTTT
Found at i:76651 original size:22 final size:22
Alignment explanation
Indices: 76580--76651 Score: 94
Period size: 21 Copynumber: 3.3 Consensus size: 22
76570 TTATTAATTT
**
76580 ATAAAAATAAA-ATTAATAAAA
1 ATAAAAATAAATATTTTTAAAA
*
76601 AAATAAAATAAATATTTTTAAAA
1 ATA-AAAATAAATATTTTTAAAA
76624 AT-AAAATAAATATTTTTAAAA
1 ATAAAAATAAATATTTTTAAAA
76645 ATAAAAA
1 ATAAAAA
76652 ATATGGACAA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
21 23 0.52
22 12 0.27
23 9 0.20
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
ATAAAAATAAATATTTTTAAAA
Found at i:85556 original size:18 final size:18
Alignment explanation
Indices: 85533--85570 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
85523 GTTTTAATCT
85533 ACCCGACCCGACCCGAGA
1 ACCCGACCCGACCCGAGA
85551 ACCCGACCCGACCCGAGA
1 ACCCGACCCGACCCGAGA
85569 AC
1 AC
85571 AAGGAATCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.50, G:0.21, T:0.00
Consensus pattern (18 bp):
ACCCGACCCGACCCGAGA
Found at i:87009 original size:18 final size:18
Alignment explanation
Indices: 86986--87022 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
86976 TAATAATAAC
86986 TTTA-TTATCAAACTTTAT
1 TTTATTTAT-AAACTTTAT
87004 TTTATTTATAAACTTTAT
1 TTTATTTATAAACTTTAT
87022 T
1 T
87023 ATCACATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTATTTATAAACTTTAT
Found at i:95318 original size:2 final size:2
Alignment explanation
Indices: 95311--95345 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
95301 CCCAGGTATG
95311 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 T
95346 TCAAATCTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:103374 original size:71 final size:71
Alignment explanation
Indices: 103272--103413 Score: 194
Period size: 71 Copynumber: 2.0 Consensus size: 71
103262 GTCAAAGGGG
* * * *
103272 GGCATCATTTCTCCCCCAATGGGCCCCAAATATGATAATCAATGTGCATAGAACGTTACAATAAG
1 GGCATCATTTCTCCCCCAATGGACCCCAAATAAGATAATCAATGTGCATAGAACATAACAATAAG
103337 TCAAGC
66 TCAAGC
* * * * * *
103343 GGCATTATTTCTTCCCCAATTGATCCCAAATAAGATAATCAATGTGCATAGCACATAACAATATG
1 GGCATCATTTCTCCCCCAATGGACCCCAAATAAGATAATCAATGTGCATAGAACATAACAATAAG
103408 TCAAGC
66 TCAAGC
103414 AACATTATAG
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (71 bp):
GGCATCATTTCTCCCCCAATGGACCCCAAATAAGATAATCAATGTGCATAGAACATAACAATAAG
TCAAGC
Found at i:104594 original size:34 final size:34
Alignment explanation
Indices: 104547--104623 Score: 129
Period size: 34 Copynumber: 2.3 Consensus size: 34
104537 TATAATCTGA
104547 TCCTCCATATTGATTTAAATTCAAATACAC-CAAT
1 TCCTCCATATTGATTTAAATTCAAATACACTC-AT
*
104581 TCCTCCATGTTGATTTAAATTCAAATACACTCAT
1 TCCTCCATATTGATTTAAATTCAAATACACTCAT
104615 TCCTCCATA
1 TCCTCCATA
104624 CACATTACAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
34 39 0.98
35 1 0.03
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (34 bp):
TCCTCCATATTGATTTAAATTCAAATACACTCAT
Found at i:105303 original size:160 final size:156
Alignment explanation
Indices: 105017--105322 Score: 470
Period size: 160 Copynumber: 1.9 Consensus size: 156
105007 GAGAGAAACT
*
105017 AATTTCCTATTGTAGACAAGAAAATTCCAAAACAATTTTTGGCATTATTATAAGCATATCAATAC
1 AATTTCCTATTGTAAACAAGAAAATTCCAAAACAATTTTTGGCATTATTATAAGCATATCAATAC
* * * *
105082 AGAAAATGAGCTGGCCATCAATATAGACTAGCCATCCAACCGATTATAGAAAATTATTCAACCAA
66 AGAAAATGAGCTGACCACCAATACAGACTAGCCATCCAACCGATTATAGAAAATAATTCAACCAA
105147 CATGCCCCAA-TACACAGTTACCAACC
131 CATG-CCCAAGTACACAGTTACCAACC
* * *
105173 AATTTCCTATTGTAAATAAGAAAATTCCCAAAGAATTTTTGGCATTATTATAAGCATTCAAGTCA
1 AATTTCCTATTGTAAACAAGAAAATTCCAAAACAATTTTTGGCATTATTATAAGCA-T--A-TCA
* *
105238 ATGCAGAAAATGAGCTGACCACCAGTACAGACTAGCCATCCAACCGATTATAGAAAATAATTCAA
62 ATACAGAAAATGAGCTGACCACCAATACAGACTAGCCATCCAACCGATTATAGAAAATAATTCAA
105303 CCAACATGCCCAAGTACACA
127 CCAACATGCCCAAGTACACA
105323 CGGTCAGCAA
Statistics
Matches: 135, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
156 52 0.39
157 1 0.01
159 6 0.04
160 76 0.56
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.25
Consensus pattern (156 bp):
AATTTCCTATTGTAAACAAGAAAATTCCAAAACAATTTTTGGCATTATTATAAGCATATCAATAC
AGAAAATGAGCTGACCACCAATACAGACTAGCCATCCAACCGATTATAGAAAATAATTCAACCAA
CATGCCCAAGTACACAGTTACCAACC
Found at i:107696 original size:107 final size:107
Alignment explanation
Indices: 107570--107849 Score: 391
Period size: 107 Copynumber: 2.6 Consensus size: 107
107560 CGTCTATTTA
* *
107570 AAGTTGATGGGACCTTAGAAATTTGACGATAACAAAATAGGTTAATTATTTAATTTGTTATTAAT
1 AAGTTGATGGG-CCTTAGAAATTCGACGATAACAAAATAGGTTAATTATTTATTTTGTTATTAAT
*
107635 ATTATCAATATATTAGGTAGAGCATAAAATATTATCAAAGATT
65 ATTATCAATATATTAGGTAGAGCATAAAATATTACCAAAGATT
* * * *
107678 AAGTTGATGGGTCTTAGAAATCCGACGATAACAAAATAGATTAATTACTTATTTTGTTATTAATA
1 AAGTTGATGGGCCTTAGAAATTCGACGATAACAAAATAGGTTAATTATTTATTTTGTTATTAATA
* * * *
107743 TTATCAATATATTAGGTAGCGCCTAAAATGTTACCAAAGTTT
66 TTATCAATATATTAGGTAGAGCATAAAATATTACCAAAGATT
* * * * *
107785 AAGCTGATGGACCTTCGAAATTCGACGACAACAAAATAGGTTAATT-TCTTATTTTGTTATAAAT
1 AAGTTGATGGGCCTTAGAAATTCGACGATAACAAAATAGGTTAATTAT-TTATTTTGTTATTAAT
107849 A
65 A
107850 AATATTAACA
Statistics
Matches: 151, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
107 140 0.93
108 11 0.07
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (107 bp):
AAGTTGATGGGCCTTAGAAATTCGACGATAACAAAATAGGTTAATTATTTATTTTGTTATTAATA
TTATCAATATATTAGGTAGAGCATAAAATATTACCAAAGATT
Found at i:108486 original size:23 final size:23
Alignment explanation
Indices: 108460--108517 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
108450 CGGTAGCTAG
* *
108460 TTTAATGTAATAGGTACCGCTTA
1 TTTAACGTAATAGGTACAGCTTA
*
108483 TTTAACGTAATAGGTAGAGCTTA
1 TTTAACGTAATAGGTACAGCTTA
*
108506 TTTAACATAATA
1 TTTAACGTAATA
108518 AGTAGCGTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (23 bp):
TTTAACGTAATAGGTACAGCTTA
Found at i:108531 original size:23 final size:23
Alignment explanation
Indices: 108478--108522 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
108468 AATAGGTACC
* *
108478 GCTTATTTAACGTAATAGGTAGA
1 GCTTATTTAACATAATAAGTAGA
108501 GCTTATTTAACATAATAAGTAG
1 GCTTATTTAACATAATAAGTAG
108523 CGTCTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.36
Consensus pattern (23 bp):
GCTTATTTAACATAATAAGTAGA
Found at i:108604 original size:23 final size:23
Alignment explanation
Indices: 108578--108627 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
108568 TGGTAACTAG
*
108578 TTTAACGTAATAGATAACGCTTA
1 TTTAACGTAATAGATAACGCCTA
*
108601 TTTAACGTAATAGATATCGCCTA
1 TTTAACGTAATAGATAACGCCTA
108624 TTTA
1 TTTA
108628 TCATAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (23 bp):
TTTAACGTAATAGATAACGCCTA
Found at i:108626 original size:118 final size:117
Alignment explanation
Indices: 108411--108706 Score: 405
Period size: 118 Copynumber: 2.5 Consensus size: 117
108401 TTAAGTTGTA
* * * *
108411 TATTTTACCGTTTACATTATTATTAACCTTTAAACAAACCGGTAGCTAGTTTAATGTAATAGGTA
1 TATTTTACCGTTTAC--TATTATTAACATTTAAACAAACTGGTAGCTAGTTTAACGTAATAGATA
* * * *
108476 CCGCTTATTTAACGTAATAGGTAGAGCTTATTTAACATAATAAGTAGCGTCTATTT
64 ACGCTTATTTAACGTAATAGATAGAGCCTATTTAACATAAT-A-TAGCATCTATTT
* * * *
108532 TATTTTATCGTTTAC-ATTATTAACTTTTAAACAATCTGGTAACTAGTTTAACGTAATAGATAAC
1 TATTTTACCGTTTACTATTATTAACATTTAAACAAACTGGTAGCTAGTTTAACGTAATAGATAAC
** *
108596 GCTTATTTAACGTAATAGATATCGCCTATTTATCATAATATAGCATCTATTT
66 GCTTATTTAACGTAATAGATAGAGCCTATTTAACATAATATAGCATCTATTT
108648 TATTTTACCGTTTACATATTATTAACATTTAAACAAACTGGTAGCTAGTTTAACGTAAT
1 TATTTTACCGTTTAC-TATTATTAACATTTAAACAAACTGGTAGCTAGTTTAACGTAAT
108707 TGGTAGCACC
Statistics
Matches: 155, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
116 25 0.16
117 1 0.01
118 115 0.74
121 14 0.09
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (117 bp):
TATTTTACCGTTTACTATTATTAACATTTAAACAAACTGGTAGCTAGTTTAACGTAATAGATAAC
GCTTATTTAACGTAATAGATAGAGCCTATTTAACATAATATAGCATCTATTT
Found at i:108634 original size:23 final size:23
Alignment explanation
Indices: 108578--108635 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
108568 TGGTAACTAG
* *
108578 TTTAACGTAATAGATAACGCTTA
1 TTTAACATAATAGATAACGCCTA
* *
108601 TTTAACGTAATAGATATCGCCTA
1 TTTAACATAATAGATAACGCCTA
*
108624 TTTATCATAATA
1 TTTAACATAATA
108636 TAGCATCTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (23 bp):
TTTAACATAATAGATAACGCCTA
Found at i:108774 original size:75 final size:75
Alignment explanation
Indices: 108636--108952 Score: 327
Period size: 75 Copynumber: 4.3 Consensus size: 75
108626 TATCATAATA
* * * *
108636 TAGCATCTATTTTATTTTACCGTTTACA-TATTATTAACATTTAAACAAACTGGTA-GCTAGTTT
1 TAGCACCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAACCGGTATG-TAGTTT
*
108699 AACGTAATTGG
65 AACGTAATAGG
* *
108710 TAGCACCTAATTTATTTTATCGTTTACATTATTAGTAACCTTTAAACAAACCGGTATGTAGTTTA
1 TAGCACCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAACCGGTATGTAGTTTA
** *
108775 ATATAATAAG
66 ACGTAATAGG
*** * * *** *
108785 TAATGCCTATTTTATTTTACCGTTTACATTATTAGAAACTTTTAAACAAACATATAGGTA-TTTC
1 TAGCACCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAACCGGTATGTAGTTT-
108849 AACGTAATAGG
65 AACGTAATAGG
** * * * * *
108860 TAGCGTCTATTTTATTTTA-CGGTTACATTATTAGTAACCTTAAAAAAAATCAGTATGTAGTTTA
1 TAGCACCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAACCGGTATGTAGTTTA
108924 ACGTAATAGG
66 ACGTAATAGG
** *
108934 TAGCGTCTGTTTTATTTTA
1 TAGCACCTATTTTATTTTA
108953 ACCGGTTAAG
Statistics
Matches: 201, Mismatches: 38, Indels: 8
0.81 0.15 0.03
Matches are distributed among these distances:
74 87 0.43
75 113 0.56
76 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (75 bp):
TAGCACCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAACCGGTATGTAGTTTA
ACGTAATAGG
Found at i:108892 original size:149 final size:149
Alignment explanation
Indices: 108642--108924 Score: 392
Period size: 149 Copynumber: 1.9 Consensus size: 149
108632 AATATAGCAT
** *
108642 CTATTTTATTTTACCGTTTACATATTATTAACATTTAAACAAACTGGTAGCTAGTTTAACGTAAT
1 CTATTTTATTTTACCGTTTACATATTAGAAACATTTAAACAAACTGATAGCTAGTTTAACGTAAT
* * * * *
108707 TGGTAGCACCTAATTTATTTTATCGTTTACATTATTAGTAACCTTTAAACAAACCGGTATGTAGT
66 AGGTAGCACCTAATTTATTTTATCGGTTACATTATTAGTAACCTTAAAAAAAACCAGTATGTAGT
108772 TTAATATAATAAGTAATGC
131 TTAATATAATAAGTAATGC
* *
108791 CTATTTTATTTTACCGTTTACATTATTAGAAACTTTTAAACAAACAT-ATAGGTA-TTTCAACGT
1 CTATTTTATTTTACCGTTTACA-TATTAGAAACATTTAAACAAAC-TGATAGCTAGTTT-AACGT
** * *
108854 AATAGGTAGCGTCTATTTTATTTTA-CGGTTACATTATTAGTAACCTTAAAAAAAATCAGTATGT
63 AATAGGTAGCACCTAATTTATTTTATCGGTTACATTATTAGTAACCTTAAAAAAAACCAGTATGT
108918 AGTTTAA
128 AGTTTAA
108925 CGTAATAGGT
Statistics
Matches: 117, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
149 66 0.56
150 50 0.43
151 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (149 bp):
CTATTTTATTTTACCGTTTACATATTAGAAACATTTAAACAAACTGATAGCTAGTTTAACGTAAT
AGGTAGCACCTAATTTATTTTATCGGTTACATTATTAGTAACCTTAAAAAAAACCAGTATGTAGT
TTAATATAATAAGTAATGC
Found at i:108947 original size:149 final size:149
Alignment explanation
Indices: 108624--108952 Score: 389
Period size: 149 Copynumber: 2.2 Consensus size: 149
108614 ATATCGCCTA
* * **
108624 TTTATCATAAT-A-TAGCATCTATTTTATTTTACCGTTTACATATTATTAACATTTAAACAAACT
1 TTTAACATAATAAGTAGCGTCTATTTTATTTTACCGTTTACATATTAGAAACATTTAAACAAACT
* * *
108687 GGTAGCTAGTTTAACGTAATTGGTAGCACCTAATTTATTTTATCGTTTACATTATTAGTAACCTT
66 GATAGCTAGTTTAACGTAATAGGTAGCACCTAATTTATTTTATCGGTTACATTATTAGTAACCTT
* * *
108752 TAAACAAACCGGTATGTAG
131 AAAAAAAACCAGTATGTAG
* ** * *
108771 TTTAATATAATAAGTAATGCCTATTTTATTTTACCGTTTACATTATTAGAAACTTTTAAACAAAC
1 TTTAACATAATAAGTAGCGTCTATTTTATTTTACCGTTTACA-TATTAGAAACATTTAAACAAAC
* ** *
108836 AT-ATAGGTA-TTTCAACGTAATAGGTAGCGTCTATTTTATTTTA-CGGTTACATTATTAGTAAC
65 -TGATAGCTAGTTT-AACGTAATAGGTAGCACCTAATTTATTTTATCGGTTACATTATTAGTAAC
*
108898 CTTAAAAAAAATCAGTATGTAG
128 CTTAAAAAAAACCAGTATGTAG
* * *
108920 TTTAACGTAATAGGTAGCGTCTGTTTTATTTTA
1 TTTAACATAATAAGTAGCGTCTATTTTATTTTA
108953 ACCGGTTAAG
Statistics
Matches: 150, Mismatches: 27, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
147 9 0.06
148 1 0.01
149 89 0.59
150 50 0.33
151 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (149 bp):
TTTAACATAATAAGTAGCGTCTATTTTATTTTACCGTTTACATATTAGAAACATTTAAACAAACT
GATAGCTAGTTTAACGTAATAGGTAGCACCTAATTTATTTTATCGGTTACATTATTAGTAACCTT
AAAAAAAACCAGTATGTAG
Done.