Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002915.1 Hibiscus syriacus cultivar Beakdansim tig00006027_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: 71936
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:9532 original size:61 final size:60
Alignment explanation
Indices: 9428--9545 Score: 155
Period size: 61 Copynumber: 1.9 Consensus size: 60
9418 ATGCAAACAA
* *
9428 TCCCTCGACTATAAGGCGTTGCTTTGTTGAATCCCTCGACTATTGAAAGTTACAAAATGG
1 TCCCTCGACTATAAGACGTTGCTTTGTTGAATCCCTCGACTATTAAAAGTTACAAAATGG
* ** * * *
9488 TCCCTCGATTATAAGACGATTTTTTTGTTGTATCCCTCGGCTATTAAAAGTTATAAAA
1 TCCCTCGACTATAAGACG-TTGCTTTGTTGAATCCCTCGACTATTAAAAGTTACAAAA
9546 CGATCACCCG
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
60 16 0.33
61 33 0.67
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (60 bp):
TCCCTCGACTATAAGACGTTGCTTTGTTGAATCCCTCGACTATTAAAAGTTACAAAATGG
Found at i:13340 original size:20 final size:20
Alignment explanation
Indices: 13289--13342 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
13279 GGTCATCCGA
*
13289 CCGAGGCCATCAGAGAGCAT
1 CCGAGGCCATCCGAGAGCAT
*
13309 CTGAGGCCATCCGAGAGCAT
1 CCGAGGCCATCCGAGAGCAT
13329 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
13343 CCGAGGCCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.33, G:0.30, T:0.11
Consensus pattern (20 bp):
CCGAGGCCATCCGAGAGCAT
Found at i:13348 original size:14 final size:14
Alignment explanation
Indices: 13329--13361 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
13319 CCGAGAGCAT
13329 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
13343 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
13357 ACGAG
1 CCGAG
13362 CTATGCGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.39, G:0.30, T:0.06
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:13356 original size:10 final size:10
Alignment explanation
Indices: 13289--13342 Score: 58
Period size: 10 Copynumber: 5.4 Consensus size: 10
13279 GGTCATCCGA
13289 CCGAGGCCAT
1 CCGAGGCCAT
*
13299 CAGAGAG-CAT
1 CCGAG-GCCAT
*
13309 CTGAGGCCAT
1 CCGAGGCCAT
13319 CCGAGAG-CAT
1 CCGAG-GCCAT
13329 CCGAGGCCAT
1 CCGAGGCCAT
13339 CCGA
1 CCGA
13343 CCGAGGCCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
9 2 0.05
10 33 0.89
11 2 0.05
ACGTcount: A:0.26, C:0.33, G:0.30, T:0.11
Consensus pattern (10 bp):
CCGAGGCCAT
Found at i:13397 original size:33 final size:33
Alignment explanation
Indices: 13360--13424 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
13350 CATCCGAACG
* *
13360 AGCTATGCGAGGGCATCCGAGGGCAA-CCGAGCT
1 AGCTATGCGAAGGAATCCGAGGG-AAGCCGAGCT
13393 AGCTATGCGAAGGAATCCGAGGGAAGCCGAGC
1 AGCTATGCGAAGGAATCCGAGGGAAGCCGAGC
13425 GAGGGTAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 2 0.07
33 27 0.93
ACGTcount: A:0.28, C:0.25, G:0.37, T:0.11
Consensus pattern (33 bp):
AGCTATGCGAAGGAATCCGAGGGAAGCCGAGCT
Found at i:13607 original size:29 final size:29
Alignment explanation
Indices: 13565--13621 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
13555 GAGCAAGGGT
13565 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
13594 AGGTCGCCCGGAGTGCATGGCGACCTAC
1 AGGTCGCCCGGAGTGCATGGCGACCTAC
13622 GGCCAACACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.19, C:0.32, G:0.35, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:13968 original size:2 final size:2
Alignment explanation
Indices: 13963--13995 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
13953 ACACACACAC
13963 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 A
13996 AGAAAAACCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14056 original size:14 final size:14
Alignment explanation
Indices: 14037--14064 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
14027 AATAGAAACT
14037 TGGTTTATTAGCCA
1 TGGTTTATTAGCCA
14051 TGGTTTATTAGCCA
1 TGGTTTATTAGCCA
14065 ATGATTAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.43
Consensus pattern (14 bp):
TGGTTTATTAGCCA
Found at i:14240 original size:9 final size:8
Alignment explanation
Indices: 14228--14340 Score: 52
Period size: 9 Copynumber: 13.2 Consensus size: 8
14218 AATATTTTAT
14228 ATATAATTA
1 ATATAA-TA
*
14237 ATATAAAA
1 ATATAATA
14245 ATATAA-A
1 ATATAATA
**
14252 ATATTTTA
1 ATATAATA
14260 TATATAATTA
1 -ATATAA-TA
*
14270 ATATAAAAA
1 ATAT-AATA
14279 ATATAA-A
1 ATATAATA
*
14286 ATATTATA
1 ATATAATA
14294 TATATAATTA
1 -ATATAA-TA
*
14304 ATATAAAAAA
1 ATAT--AATA
14314 ATATAA-A
1 ATATAATA
*
14321 ATATTATA
1 ATATAATA
14329 TATATATATA
1 -ATATA-ATA
14339 AT
1 AT
14341 TAGGACGGGG
Statistics
Matches: 81, Mismatches: 11, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
7 17 0.21
8 14 0.17
9 34 0.42
10 14 0.17
11 2 0.02
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATATAATA
Found at i:14253 original size:33 final size:34
Alignment explanation
Indices: 14216--14334 Score: 204
Period size: 34 Copynumber: 3.5 Consensus size: 34
14206 CCCGAACCTA
*
14216 AAAATATTTTATATATAATTAATAT-AAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
*
14249 AAAATATTTTATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
14283 AAAATATTATATATATAATTAATATAAAAAAATAT
1 AAAATATTATATATATAATTAATAT-AAAAAATAT
14318 AAAATATTATATATATA
1 AAAATATTATATATATA
14335 TATAATTAGG
Statistics
Matches: 83, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
33 25 0.30
34 32 0.39
35 26 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:14289 original size:25 final size:25
Alignment explanation
Indices: 14261--14318 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 25
14251 AATATTTTAT
14261 ATATAAT-TAATATAAAAAATATAAA
1 ATATAATAT-ATATAAAAAATATAAA
* **
14286 ATATTATATATATAATTAATATAAA
1 ATATAATATATATAAAAAATATAAA
14311 A-A-AATATA
1 ATATAATATA
14319 AAATATTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 5 0.18
24 1 0.04
25 21 0.75
26 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
ATATAATATATATAAAAAATATAAA
Found at i:14949 original size:19 final size:19
Alignment explanation
Indices: 14925--14961 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
14915 TCATAGGCAA
14925 AATTTTTACTACTAAAAAT
1 AATTTTTACTACTAAAAAT
14944 AATTTTTACTACTAAAAA
1 AATTTTTACTACTAAAAA
14962 ATTATCAAAC
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:0.49, C:0.11, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTTTTACTACTAAAAAT
Found at i:15694 original size:12 final size:12
Alignment explanation
Indices: 15661--15694 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
15651 ATATGTATAT
*
15661 TTTTTTTGGGGA
1 TTTTTTTGTGGA
15673 TTTCTTTTGTGGA
1 TTT-TTTTGTGGA
15686 TTTTTTTGT
1 TTTTTTTGT
15695 TTGTTTCGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.06, C:0.03, G:0.24, T:0.68
Consensus pattern (12 bp):
TTTTTTTGTGGA
Found at i:15880 original size:22 final size:24
Alignment explanation
Indices: 15856--15899 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
15846 AATAATATAA
15856 TTTT-TTTCTAACCCATATATCAT
1 TTTTCTTTCTAACCCATATATCAT
15879 TTTTCTTTCTAACCCAT-TATC
1 TTTTCTTTCTAACCCATATATC
15900 CTAATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.23, C:0.25, G:0.00, T:0.52
Consensus pattern (24 bp):
TTTTCTTTCTAACCCATATATCAT
Found at i:18087 original size:23 final size:22
Alignment explanation
Indices: 18057--18125 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 22
18047 TCGATTTTAA
18057 ATAAATAATATTTTAATCATTT
1 ATAAATAATATTTTAATCATTT
** *
18079 ATGTTATAA-ATTTATTATATC-TTA
1 AT-AAATAATA-TT-TTA-ATCATTT
18103 ATAAATAATATTTTAATCATTT
1 ATAAATAATATTTTAATCATTT
18125 A
1 A
18126 CGATATTGAT
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
21 3 0.09
22 9 0.26
23 12 0.34
24 8 0.23
25 3 0.09
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.51
Consensus pattern (22 bp):
ATAAATAATATTTTAATCATTT
Found at i:18123 original size:46 final size:46
Alignment explanation
Indices: 18056--18144 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
18046 ATCGATTTTA
* *
18056 AATAAATAATATTTTAATCATTTATGTTATAAATTTATTATATCTT
1 AATAAATAATATTTTAATCATTTACGATATAAATTTATTATATCTT
**
18102 AATAAATAATATTTTAATCATTTACGATATTGATTTATTATAT
1 AATAAATAATATTTTAATCATTTACGATATAAATTTATTATAT
18145 TTCGATCATT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (46 bp):
AATAAATAATATTTTAATCATTTACGATATAAATTTATTATATCTT
Found at i:22492 original size:14 final size:13
Alignment explanation
Indices: 22452--22492 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
22442 ATGGGCAAAT
*
22452 TTTGAAAACTATG
1 TTTGAAAACAATG
22465 TTTGAAAACAATG
1 TTTGAAAACAATG
22478 TTTGAAAATCAATG
1 TTTGAAAA-CAATG
22492 T
1 T
22493 GTAGTTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 20 0.77
14 6 0.23
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:22555 original size:14 final size:14
Alignment explanation
Indices: 22536--22564 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
22526 TTAAAATCAA
22536 AATAATTTTTTATT
1 AATAATTTTTTATT
22550 AATAATTTTTTATT
1 AATAATTTTTTATT
22564 A
1 A
22565 TTTCAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
AATAATTTTTTATT
Found at i:22980 original size:21 final size:23
Alignment explanation
Indices: 22955--23016 Score: 92
Period size: 21 Copynumber: 2.8 Consensus size: 23
22945 AACCAGAACC
22955 CATGGAGGGTATCGGTACCC-TT
1 CATGGAGGGTATCGGTACCCATT
22977 -ATGGAGGGTATCGGTACCCATT
1 CATGGAGGGTATCGGTACCCATT
* *
22999 CAAGGATGGTATCGGTAC
1 CATGGAGGGTATCGGTAC
23017 TAATGCGAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 19 0.53
22 2 0.06
23 15 0.42
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (23 bp):
CATGGAGGGTATCGGTACCCATT
Found at i:36756 original size:80 final size:80
Alignment explanation
Indices: 36618--37072 Score: 700
Period size: 80 Copynumber: 5.7 Consensus size: 80
36608 TGTAAGTCCT
* * * **
36618 TACGAACCTAAAGATATCTTGGGTA-GTCCATAAGACATATCCTTAGGTTGGTTCCCTTTGCTGT
1 TACGGACCTAAGGATATCTTGGGTAGGTCC-CAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGT
36682 GTGCATAAGGTAACCC
65 GTGCATAAGGTAACCC
36698 TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
1 TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
*
36763 TGCATAGGGTAACCC
66 TGCATAAGGTAACCC
*
36778 TACGGACCTAAGGATATATTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
1 TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
36843 TGCATAAGGTAACCC
66 TGCATAAGGTAACCC
* *
36858 TACGAACCTAAGGATATCTTGGGTAGGTCTCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
1 TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
*
36923 TGCATAAGATAACCC
66 TGCATAAGGTAACCC
* * *
36938 TACGGACCTAAAGATGTCTTGGGTAGG-CCCAAGGTATATCCTTAGGTTGGTTCCCTTAGCTGTG
1 TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
**
37002 TGGTTAAGGTAACCC
66 TGCATAAGGTAACCC
* * * *
37017 TACGGATCTAAGGATATCCTTGGGTAGAT-CTAAGGTATATCCTTAGGTTGGCTCCC
1 TACGGACCTAAGGATAT-CTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCC
37073 CTTTTTGCTG
Statistics
Matches: 346, Mismatches: 26, Indels: 6
0.92 0.07 0.02
Matches are distributed among these distances:
79 61 0.18
80 281 0.81
81 4 0.01
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.31
Consensus pattern (80 bp):
TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
TGCATAAGGTAACCC
Found at i:42274 original size:80 final size:80
Alignment explanation
Indices: 42141--42591 Score: 665
Period size: 80 Copynumber: 5.7 Consensus size: 80
42131 AAGTCCTTAT
* * * * * *
42141 GGACCTAAGGATATCTTGGTTA-GCCCCAAGGCATGTCTTTAAGTTGGTTCCCTTTGCTGTGTGC
1 GGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTGTGC
42205 ATAAGGTAACCCTAC
66 ATAAGGTAACCCTAC
*
42220 GGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTGTGT
1 GGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTGTGC
*
42285 ATAGGGTAACCCTAC
66 ATAAGGTAACCCTAC
42300 GGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTGTGC
1 GGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTGTGC
*
42365 ATAAGGTAACCCTAT
66 ATAAGGTAACCCTAC
* * *
42380 GTACCTAAGGATATCTTGGGTAGGTCCTAAGGTATATCCTTAAGTTGGTTCCCTTTGCTGTGTGC
1 GGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTGTGC
42445 ATAAGGTAACCCTAC
66 ATAAGGTAACCCTAC
* *
42460 GGACCTAAGGATGTCTTGGGTAGG-CCCAAGGTATATCCTTAGGTTGGTTCCCTTAGCTGTGTGC
1 GGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTGTGC
* *
42524 TTAAGGTAACCCTAT
66 ATAAGGTAACCCTAC
* * *** * *
42539 GGATCTAAGGATGTCCTCAAGTAGAT-CCAAGGTATATCCTTAGGTTGGCTCCC
1 GGACCTAAGGATAT-CTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCC
42592 CTTTTTTCTG
Statistics
Matches: 341, Mismatches: 28, Indels: 5
0.91 0.07 0.01
Matches are distributed among these distances:
79 84 0.25
80 257 0.75
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.32
Consensus pattern (80 bp):
GGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTGTGC
ATAAGGTAACCCTAC
Found at i:42571 original size:239 final size:239
Alignment explanation
Indices: 42138--42591 Score: 698
Period size: 239 Copynumber: 1.9 Consensus size: 239
42128 TGTAAGTCCT
* * *
42138 TATGGACCTAAGGATATCTTGGTTAGCCCCAAGGCATGTCTTTAAGTTGGTTCCCTTTGCTGTGT
1 TATGGACCTAAGGATATCTTGGGTAGCCCCAAGGCATATCCTTAAGTTGGTTCCCTTTGCTGTGT
42203 GCATAAGGTAACCCTACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGG
66 GCATAAGGTAACCCTACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGG
* * *** *
42268 TTCCCTTTGCTGTGTGTATAGGGTAACCCTACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGT
131 TTCCCTTAGCTGTGTGTATAAGGTAACCCTACGGACCTAAGGATATCTCAAGTAGATCCCAAGGT
*
42333 ATATCCTTAGGTTGGTTCCCTTTGCTGTGTGCATAAGGTAACCC
196 ATATCCTTAGGTTGGCTCCCTTTGCTGTGTGCATAAGGTAACCC
* * * *
42377 TATGTACCTAAGGATATCTTGGGTAGGTCCTAAGGTATATCCTTAAGTTGGTTCCCTTTGCTGTG
1 TATGGACCTAAGGATATCTTGGGTA-GCCCCAAGGCATATCCTTAAGTTGGTTCCCTTTGCTGTG
*
42442 TGCATAAGGTAACCCTACGGACCTAAGGATGTCTTGGGTAGG-CCCAAGGTATATCCTTAGGTTG
65 TGCATAAGGTAACCCTACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTG
* * *
42506 GTTCCCTTAGCTGTGTGCT-TAAGGTAACCCTATGGATCTAAGGATGTCCTCAAGTAGAT-CCAA
130 GTTCCCTTAGCTGTGTG-TATAAGGTAACCCTACGGACCTAAGGATAT-CTCAAGTAGATCCCAA
42569 GGTATATCCTTAGGTTGGCTCCC
193 GGTATATCCTTAGGTTGGCTCCC
42592 CTTTTTTCTG
Statistics
Matches: 194, Mismatches: 18, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
239 111 0.57
240 83 0.43
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.32
Consensus pattern (239 bp):
TATGGACCTAAGGATATCTTGGGTAGCCCCAAGGCATATCCTTAAGTTGGTTCCCTTTGCTGTGT
GCATAAGGTAACCCTACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGG
TTCCCTTAGCTGTGTGTATAAGGTAACCCTACGGACCTAAGGATATCTCAAGTAGATCCCAAGGT
ATATCCTTAGGTTGGCTCCCTTTGCTGTGTGCATAAGGTAACCC
Found at i:46778 original size:29 final size:29
Alignment explanation
Indices: 46736--46847 Score: 215
Period size: 29 Copynumber: 3.9 Consensus size: 29
46726 TACCGGGGGT
46736 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
46765 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
46794 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
*
46823 AGGTCGCCATGCACGCCCTGCGACC
1 AGGTCGCCATGCACGCCCGGCGACC
46848 TACCCCACGA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 82 1.00
ACGTcount: A:0.20, C:0.45, G:0.28, T:0.08
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAACC
Found at i:46876 original size:10 final size:10
Alignment explanation
Indices: 46861--46953 Score: 68
Period size: 10 Copynumber: 9.3 Consensus size: 10
46851 CCCACGACCT
46861 CCATGCACGC
1 CCATGCACGC
46871 CCATGCACGC
1 CCATGCACGC
46881 CCATGCACGC
1 CCATGCACGC
*
46891 CCA-ACGAC-C
1 CCATGC-ACGC
*
46900 TCCATGCATGC
1 -CCATGCACGC
* *
46911 CCAGGCACGT
1 CCATGCACGC
*
46921 CCA-ACGAC-C
1 CCATGC-ACGC
*
46930 TCCATGCACGG
1 -CCATGCACGC
46941 CCATGCACGC
1 CCATGCACGC
46951 CCA
1 CCA
46954 ACGACCTCCA
Statistics
Matches: 64, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
9 3 0.05
10 58 0.91
11 3 0.05
ACGTcount: A:0.23, C:0.47, G:0.19, T:0.11
Consensus pattern (10 bp):
CCATGCACGC
Found at i:46905 original size:30 final size:30
Alignment explanation
Indices: 46871--46973 Score: 170
Period size: 30 Copynumber: 3.4 Consensus size: 30
46861 CCATGCACGC
46871 CCATGCACGCCCATGCACGCCCAACGACCT
1 CCATGCACGCCCATGCACGCCCAACGACCT
* * *
46901 CCATGCATGCCCAGGCACGTCCAACGACCT
1 CCATGCACGCCCATGCACGCCCAACGACCT
*
46931 CCATGCACGGCCATGCACGCCCAACGACCT
1 CCATGCACGCCCATGCACGCCCAACGACCT
46961 CCATGCACGCCCA
1 CCATGCACGCCCA
46974 GCTCGCCAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 65 1.00
ACGTcount: A:0.23, C:0.48, G:0.18, T:0.11
Consensus pattern (30 bp):
CCATGCACGCCCATGCACGCCCAACGACCT
Found at i:47616 original size:21 final size:21
Alignment explanation
Indices: 47591--47634 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
47581 AATTTAGTTA
47591 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
47612 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
47633 AT
1 AT
47635 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:47648 original size:28 final size:28
Alignment explanation
Indices: 47611--47671 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
47601 TAGTATAAAT
*
47611 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAATTTGTTAGTTTAAGTTATATTA
47639 TATTAATTTGTTAGTTTAAGTTATATTA
1 TATTAATTTGTTAGTTTAAGTTATATTA
*
47667 GATTA
1 TATTA
47672 TATAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (28 bp):
TATTAATTTGTTAGTTTAAGTTATATTA
Found at i:50798 original size:11 final size:10
Alignment explanation
Indices: 50782--51049 Score: 53
Period size: 10 Copynumber: 26.7 Consensus size: 10
50772 AATGATTTGA
50782 TAGTAATGATT
1 TAGTAATGA-T
50793 TAGTAATGAT
1 TAGTAATGAT
*
50803 TAGTAAT-AA
1 TAGTAATGAT
* *
50812 T-GAAATTAT
1 TAGTAATGAT
* *
50821 TATTAATTAT
1 TAGTAATGAT
*
50831 GTA-TGATTTGA-
1 -TAGT-A-ATGAT
50842 TAGTAATGATT
1 TAGTAATGA-T
50853 TAGTAATGAT
1 TAGTAATGAT
*
50863 TAGTAAT-AA
1 TAGTAATGAT
* *
50872 T-GAAATTAT
1 TAGTAATGAT
* *
50881 TATTAATTAT
1 TAGTAATGAT
*
50891 GTA-TGATTTGA-
1 -TAGT-A-ATGAT
50902 TAGTAATGATT
1 TAGTAATGA-T
50913 TAGTAATGAT
1 TAGTAATGAT
*
50923 TAGTAAT-AA
1 TAGTAATGAT
* *
50932 T-GAAATTAT
1 TAGTAATGAT
* **
50941 TATTAATTTT
1 TAGTAATGAT
* *
50951 TAATGATTTGA-
1 TAGT-A-ATGAT
50962 TAGTAATGATT
1 TAGTAATGA-T
50973 TAGTAATGAT
1 TAGTAATGAT
*
50983 TAGTAAT-AA
1 TAGTAATGAT
* *
50992 T-GAAATTAT
1 TAGTAATGAT
* *
51001 TATTAATTAT
1 TAGTAATGAT
*
51011 GTA-TGATTTGA-
1 -TAGT-A-ATGAT
51022 TAGTAATGATT
1 TAGTAATGA-T
51033 TAGTAATGAT
1 TAGTAATGAT
51043 TAGTAAT
1 TAGTAAT
51050 AATGAAATTA
Statistics
Matches: 191, Mismatches: 36, Indels: 61
0.66 0.12 0.21
Matches are distributed among these distances:
8 16 0.08
9 28 0.15
10 79 0.41
11 61 0.32
12 7 0.04
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:50800 original size:60 final size:60
Alignment explanation
Indices: 50729--51149 Score: 642
Period size: 60 Copynumber: 7.2 Consensus size: 60
50719 GTATTTATAA
*
50729 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
*
50789 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT-TTTAATGATTTGATAGTAAT
*
50849 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT-TTTAATGATTTGATAGTAAT
50909 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
*
50969 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT-TTTAATGATTTGATAGTAAT
51029 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAA-TTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
* *
51088 GA-TTAG---T-A--A-TAATAAT----TTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
51136 GA-TTAGTAATGATT
1 GATTTAGTAATGATT
51150 TGATAGTAAT
Statistics
Matches: 343, Mismatches: 7, Indels: 28
0.91 0.02 0.07
Matches are distributed among these distances:
47 10 0.03
48 25 0.07
51 8 0.02
52 2 0.01
54 1 0.00
55 1 0.00
58 6 0.02
59 21 0.06
60 265 0.77
61 4 0.01
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (60 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
Found at i:50926 original size:21 final size:20
Alignment explanation
Indices: 50902--51050 Score: 60
Period size: 21 Copynumber: 7.4 Consensus size: 20
50892 TATGATTTGA
50902 TAGTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
* * *
50923 TAGTAATA-AT-GAAATTAT
1 TAGTAATATTTAGTAATGAT
* * * *
50941 TATTAATTTTTAATGATTTGA-
1 TAGTAATATTTAGT-A-ATGAT
50962 TAGTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
* * *
50983 TAGTAATA-AT-GAAATTAT
1 TAGTAATATTTAGTAATGAT
* * *
51001 TATTAATTATGTA-TGATTTGA-
1 TAGTAA-TATTTAGT-A-ATGAT
51022 TAGTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
51043 TAGTAATA
1 TAGTAATA
51051 ATGAAATTAT
Statistics
Matches: 89, Mismatches: 25, Indels: 29
0.62 0.17 0.20
Matches are distributed among these distances:
18 23 0.26
19 5 0.06
20 11 0.12
21 40 0.45
22 10 0.11
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (20 bp):
TAGTAATATTTAGTAATGAT
Found at i:51089 original size:48 final size:48
Alignment explanation
Indices: 51033--51145 Score: 192
Period size: 48 Copynumber: 2.4 Consensus size: 48
51023 AGTAATGATT
51033 TAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTTAATGATTTGA
1 TAGTAATGATTAGTAATAAT-AAATTATTATTAATATTTAATGATTTGA
*
51081 TAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATAAATTATTATTAATATTTAATGATTTGA
*
51129 TATTAATGATTAGTAAT
1 TAGTAATGATTAGTAAT
51146 GATTTGATAG
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
47 13 0.21
48 49 0.79
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.47
Consensus pattern (48 bp):
TAGTAATGATTAGTAATAATAAATTATTATTAATATTTAATGATTTGA
Found at i:51097 original size:24 final size:24
Alignment explanation
Indices: 51070--51163 Score: 104
Period size: 24 Copynumber: 3.9 Consensus size: 24
51060 TTATTAATTT
51070 TAATGATTTGATAGTAATGATTAG
1 TAATGATTTGATAGTAATGATTAG
* * *
51094 TAATAATAATTTATTATTAAT-ATT--
1 TAATGAT--TTGA-TAGTAATGATTAG
*
51118 TAATGATTTGATATTAATGATTAG
1 TAATGATTTGATAGTAATGATTAG
51142 TAATGATTTGATAGTAATGATT
1 TAATGATTTGATAGTAATGATT
51164 TACGACTTGA
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
21 7 0.12
22 6 0.10
24 33 0.57
26 6 0.10
27 6 0.10
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (24 bp):
TAATGATTTGATAGTAATGATTAG
Found at i:51134 original size:14 final size:14
Alignment explanation
Indices: 51118--51164 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
51108 TATTAATATT
*
51118 TAATGATTTGATAT
1 TAATGATTTGATAG
51132 TAATGA--T--TAG
1 TAATGATTTGATAG
51142 TAATGATTTGATAG
1 TAATGATTTGATAG
51156 TAATGATTT
1 TAATGATTT
51165 ACGACTTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
10 8 0.29
12 2 0.07
14 18 0.64
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:51248 original size:7 final size:7
Alignment explanation
Indices: 51236--51269 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
51226 ATTTTTGGTT
51236 CAATGAA
1 CAATGAA
51243 CAATGAA
1 CAATGAA
51250 CAATGAA
1 CAATGAA
51257 CAATGAA
1 CAATGAA
51264 CAATGA
1 CAATGA
51270 TTTAGTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (7 bp):
CAATGAA
Found at i:51296 original size:26 final size:26
Alignment explanation
Indices: 51265--51402 Score: 96
Period size: 26 Copynumber: 5.5 Consensus size: 26
51255 AACAATGAAC
51265 AATGATTTAGTAATAATCATTATAAA
1 AATGATTTAGTAATAATCATTATAAA
*
51291 AATGA-TT--TAATAATGATT-T--A
1 AATGATTTAGTAATAATCATTATAAA
* * * * **
51311 AAT-ATTTAATGATTTGATGATT-TAGT
1 AATGATTTAGT-A-ATAATCATTATAAA
**
51337 AATGATTT-GATAATAATCATTATAGT
1 AATGATTTAG-TAATAATCATTATAAA
51363 AATGATTTAGTAATAATCATTATAAA
1 AATGATTTAGTAATAATCATTATAAA
*
51389 AATGATTTAATAAT
1 AATGATTTAGTAAT
51403 GATTTAAATA
Statistics
Matches: 90, Mismatches: 11, Indels: 22
0.73 0.09 0.18
Matches are distributed among these distances:
19 1 0.01
20 6 0.07
22 2 0.02
23 11 0.12
24 8 0.09
25 8 0.09
26 48 0.53
27 6 0.07
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (26 bp):
AATGATTTAGTAATAATCATTATAAA
Found at i:51434 original size:98 final size:98
Alignment explanation
Indices: 51265--51483 Score: 404
Period size: 98 Copynumber: 2.2 Consensus size: 98
51255 AACAATGAAC
51265 AATGATTTAGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
1 AATGATTTAGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
*
51330 ATTTAGTAATGATTTGATAATAATCATTATAGT
66 ATTTAGTAATGATTTGATAATAATCATTATAAT
51363 AATGATTTAGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
1 AATGATTTAGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
51428 ATTTAGTAATGATTTGATAATAATCATTATAAT
66 ATTTAGTAATGATTTGATAATAATCATTATAAT
*
51461 AATGATTTTA-TAATAATTATTAT
1 AATGA-TTTAGTAATAATCATTAT
51484 GTTATTATTT
Statistics
Matches: 118, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
98 114 0.97
99 4 0.03
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (98 bp):
AATGATTTAGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
ATTTAGTAATGATTTGATAATAATCATTATAAT
Found at i:51463 original size:26 final size:26
Alignment explanation
Indices: 51336--51483 Score: 121
Period size: 26 Copynumber: 5.9 Consensus size: 26
51326 GATGATTTAG
*
51336 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
51362 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
51388 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
51411 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
51434 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
* *
51460 TAATGATTTTATAATAATTATTAT
1 TAATGATTTGATAATAATCATTAT
51484 GTTATTATTT
Statistics
Matches: 95, Mismatches: 19, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
21 4 0.04
22 3 0.03
23 12 0.13
24 7 0.07
25 7 0.07
26 61 0.64
27 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Found at i:51517 original size:24 final size:24
Alignment explanation
Indices: 51445--51536 Score: 80
Period size: 24 Copynumber: 3.8 Consensus size: 24
51435 AATGATTTGA
*
51445 TAATAATCATTA-TAATAATGATT
1 TAATAATTATTACTAATAATGATT
* * * * * *
51468 TTATAATAATTATTATGTTATTATT
1 TAATAATTATTACTA-ATAATGATT
*
51493 TAGTAATTATTTA-TAATAATGATT
1 TAATAATTA-TTACTAATAATGATT
51517 TAATAATTATTACTAATAAT
1 TAATAATTATTACTAATAAT
51537 TATAGAATAC
Statistics
Matches: 53, Mismatches: 12, Indels: 7
0.74 0.17 0.10
Matches are distributed among these distances:
23 13 0.25
24 23 0.43
25 14 0.26
26 3 0.06
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (24 bp):
TAATAATTATTACTAATAATGATT
Found at i:51533 original size:13 final size:12
Alignment explanation
Indices: 51444--51539 Score: 81
Period size: 11 Copynumber: 7.9 Consensus size: 12
51434 TAATGATTTG
*
51444 ATAATAATCATT
1 ATAATAATTATT
*
51456 ATAATAATGATTTT
1 ATAATAAT--TATT
51470 ATAATAATTATT
1 ATAATAATTATT
* *
51482 AT-GTTATTATT
1 ATAATAATTATT
*
51493 -TAGTAATTATTT
1 ATAATAATTA-TT
*
51505 ATAATAATGATT
1 ATAATAATTATT
51517 -TAATAATTATT
1 ATAATAATTATT
51528 ACTAATAATTAT
1 A-TAATAATTAT
51540 AGAATACTAA
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
10 1 0.01
11 23 0.34
12 17 0.25
13 17 0.25
14 10 0.15
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (12 bp):
ATAATAATTATT
Found at i:51545 original size:24 final size:24
Alignment explanation
Indices: 51496--51545 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
51486 TATTATTTAG
**
51496 TAATTATTTATAATAATGATTTAA
1 TAATTATTTATAATAATGATAGAA
*
51520 TAATTA-TTACTAATAATTATAGAA
1 TAATTATTTA-TAATAATGATAGAA
51544 TA
1 TA
51546 CTAACAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (24 bp):
TAATTATTTATAATAATGATAGAA
Found at i:51644 original size:14 final size:13
Alignment explanation
Indices: 51625--51689 Score: 50
Period size: 14 Copynumber: 5.2 Consensus size: 13
51615 TTTAAATATT
51625 TAATGATTTGATAC
1 TAATGATTT-ATAC
51639 TAATGA-TT-TAC
1 TAATGATTTATAC
*
51650 TAAT--TAT-TAC
1 TAATGATTTATAC
51660 TAATGATTTAATAC
1 TAATGATTT-ATAC
*
51674 TAATTATTTGATAC
1 TAATGATTT-ATAC
51688 TA
1 TA
51690 GTAATTATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
10 8 0.19
11 7 0.17
12 2 0.05
13 2 0.05
14 23 0.55
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
TAATGATTTATAC
Found at i:51661 original size:10 final size:11
Alignment explanation
Indices: 51636--51669 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
51626 AATGATTTGA
51636 TACTAATGATT
1 TACTAATGATT
*
51647 TACTAATTA-T
1 TACTAATGATT
51657 TACTAATGATT
1 TACTAATGATT
51668 TA
1 TA
51670 ATACTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (11 bp):
TACTAATGATT
Found at i:51679 original size:21 final size:21
Alignment explanation
Indices: 51636--51679 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
51626 AATGATTTGA
* *
51636 TACTAATGATTTACTAATTAT
1 TACTAATGATTTAATAATAAT
*
51657 TACTAATGATTTAATACTAAT
1 TACTAATGATTTAATAATAAT
51678 TA
1 TA
51680 TTTGATACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (21 bp):
TACTAATGATTTAATAATAAT
Found at i:51696 original size:17 final size:17
Alignment explanation
Indices: 51674--51706 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
51664 GATTTAATAC
51674 TAATTATTTGATACTAG
1 TAATTATTTGATACTAG
51691 TAATTATTTGATACTA
1 TAATTATTTGATACTA
51707 AACATCATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.48
Consensus pattern (17 bp):
TAATTATTTGATACTAG
Found at i:53876 original size:15 final size:14
Alignment explanation
Indices: 53853--53883 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
53843 TACAACACTA
53853 AACTTTAATATAAT
1 AACTTTAATATAAT
53867 AACTTATAATATAAT
1 AACTT-TAATATAAT
53882 AA
1 AA
53884 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:53891 original size:16 final size:16
Alignment explanation
Indices: 53858--53904 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
53848 CACTAAACTT
*
53858 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
53873 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
53889 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
53905 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:54023 original size:12 final size:12
Alignment explanation
Indices: 54007--54050 Score: 61
Period size: 12 Copynumber: 3.5 Consensus size: 12
53997 ATTATAATAT
*
54007 ACTAATAAACTT
1 ACTAATAAACTA
54019 ACTAACTAAAACTA
1 ACTAA-T-AAACTA
54033 ACTAATAAACTA
1 ACTAATAAACTA
54045 ACTAAT
1 ACTAAT
54051 TTTTATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 17 0.59
13 2 0.07
14 10 0.34
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (12 bp):
ACTAATAAACTA
Found at i:54144 original size:42 final size:43
Alignment explanation
Indices: 54095--54206 Score: 115
Period size: 42 Copynumber: 2.6 Consensus size: 43
54085 AACTATTTAA
54095 CTAACAAAAACTAATTAAATAATTTTTTT-A-TATAACTAACTAT
1 CTAACAAAAACTAATTAAATAATTTTTTTAACTAT-A-TAACTAT
* * *
54138 -TAAC-AAAACAAACTAATTAATTATTTTTAACTATATAACTAT
1 CTAACAAAAACTAATTAAATAATT-TTTTTAACTATATAACTAT
* * *
54180 CAAACATATACTAATTAAATAATTTTT
1 CTAACAAAAACTAATTAAATAATTTTT
54207 AATTTATGTA
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
41 15 0.27
42 16 0.29
43 8 0.15
44 16 0.29
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (43 bp):
CTAACAAAAACTAATTAAATAATTTTTTTAACTATATAACTAT
Found at i:54176 original size:46 final size:47
Alignment explanation
Indices: 54076--54178 Score: 124
Period size: 46 Copynumber: 2.2 Consensus size: 47
54066 CAACAAACAA
*
54076 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTT
1 ATATAAC-TAACTATTTAACTAACAAAAACTAATTAAATAATTTTTCT
*
54124 ATATAACTAACTA-TTAAC-AA-AACAAACTAATT-AATTATTTTTAACT
1 ATATAACTAACTATTTAACTAACAA-AAACTAATTAAATAATTTTT--CT
54170 ATATAACTA
1 ATATAACTA
54179 TCAAACATAT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
44 11 0.22
45 11 0.22
46 15 0.30
47 6 0.12
48 7 0.14
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.39
Consensus pattern (47 bp):
ATATAACTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTCT
Found at i:54234 original size:41 final size:39
Alignment explanation
Indices: 54147--54234 Score: 88
Period size: 41 Copynumber: 2.2 Consensus size: 39
54137 TTAACAAAAC
*
54147 AAACTAATTAATTATTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
54187 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATT-AATAATTTTTAA-CTATATA-ACTATAAACAT
54228 AAACTAA
1 AAACTAA
54235 CAATCATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
40 8 0.21
41 21 0.54
42 5 0.13
43 5 0.13
ACGTcount: A:0.47, C:0.10, G:0.01, T:0.42
Consensus pattern (39 bp):
AAACTAATTAATAATTTTTAACTATATAACTATAAACAT
Found at i:54299 original size:16 final size:18
Alignment explanation
Indices: 54270--54308 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
54260 ACTAATTAAC
*
54270 ATTTATAATAATAAACTA
1 ATTTATAATAATAAACAA
54288 ATTTA-AAT-ATAAACAA
1 ATTTATAATAATAAACAA
54304 ATTTA
1 ATTTA
54309 CCTTATCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTATAATAATAAACAA
Found at i:54597 original size:49 final size:49
Alignment explanation
Indices: 54520--54626 Score: 175
Period size: 49 Copynumber: 2.2 Consensus size: 49
54510 TAGGATCACA
*
54520 TGGCATGC-TGTAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCT
1 TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTAT-T
54569 TGGCATGCATGCAGGCATGCAGC-GGGAGCAGGAGCACGTGAAGTTATT
1 TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATT
54617 TGGC-TGCATG
1 TGGCATGCATG
54627 TGCATGCATG
Statistics
Matches: 56, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
47 6 0.11
48 5 0.09
49 32 0.57
50 13 0.23
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.21
Consensus pattern (49 bp):
TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATT
Found at i:54694 original size:29 final size:29
Alignment explanation
Indices: 54661--54755 Score: 163
Period size: 29 Copynumber: 3.3 Consensus size: 29
54651 TGGACGCCGG
54661 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
54690 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
** *
54719 GGCGACCTACAAGGTCGCCCAGACTGCAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
54748 GGCGACCT
1 GGCGACCT
54756 CTCTATTGGC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.23, C:0.33, G:0.31, T:0.14
Consensus pattern (29 bp):
GGCGACCTACAAGGTCGCCGGGACTACAT
Found at i:54784 original size:32 final size:32
Alignment explanation
Indices: 54742--54813 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
54732 GTCGCCCAGA
*
54742 CTGCATGGCGACCTCTCTATTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
* *
54774 TTGCATGGCGACCTCTCCGTTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
54806 CTGCATGG
1 CTGCATGG
54814 TGAGTATATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.08, C:0.31, G:0.31, T:0.31
Consensus pattern (32 bp):
CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
Found at i:56347 original size:17 final size:16
Alignment explanation
Indices: 56310--56350 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
56300 TGGAATTATT
56310 ATAATATTTTAAATAA
1 ATAATATTTTAAATAA
* *
56326 TTAATTTTTTATAATAA
1 ATAATATTTTA-AATAA
56343 ATAATATT
1 ATAATATT
56351 AATTATTATA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATAATATTTTAAATAA
Found at i:56365 original size:22 final size:22
Alignment explanation
Indices: 56318--56370 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
56308 TTATAATATT
*
56318 TTAAAT-AATTAATTTTTTATA
1 TTAAATAAATTAATTTATTATA
*
56339 ATAAATAATATTAA-TTATTATA
1 TTAAATAA-ATTAATTTATTATA
56361 TTAAATAAAT
1 TTAAATAAAT
56371 ATCATAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 7 0.26
22 15 0.56
23 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTAAATAAATTAATTTATTATA
Found at i:59719 original size:138 final size:138
Alignment explanation
Indices: 59370--59989 Score: 1066
Period size: 138 Copynumber: 4.5 Consensus size: 138
59360 TGGGGGGCAT
* * *
59370 CTTCCATTATTTTGTCATATAATATGTTATCATTGCCCTATTATGTCACTCTTGTCCCCCGGGGA
1 CTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGGGA
* * *
59435 ACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTGAAAACACGTT-CCGG
66 ACTATTCATGTCAGTACCTATTATTTCTGAAGGGACTTGGCAAAGTGGTGAAAGCGCGTTCCCGG
59499 GGG-GCGC
131 GGGCGCGC
*
59506 CTTCCATTATTTTGTTAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGGGA
1 CTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGGGA
*
59571 ACTATTCATGTCAGTACCTATTATTTCTGAAGGGACTTGGCAAAGTGGTGAAAGTGCGTTCCCGG
66 ACTATTCATGTCAGTACCTATTATTTCTGAAGGGACTTGGCAAAGTGGTGAAAGCGCGTTCCCGG
59636 GGGCGCGC
131 GGGCGCGC
59644 CTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGGGA
1 CTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGGGA
*
59709 ACTATTCATGTCAGTACCTATTATTTCTGAAGGGACTTGGCAAAGTGGTGAAAGTGCGTTCCCGG
66 ACTATTCATGTCAGTACCTATTATTTCTGAAGGGACTTGGCAAAGTGGTGAAAGCGCGTTCCCGG
59774 GGGCGCGC
131 GGGCGCGC
*
59782 CTTCCATTATTTTGTCAGAGAATATGTTATCATGGCCCTATTATGTCACTCATGTCCCCCGGGGA
1 CTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGGGA
*
59847 ACTATTCATGTCAGTACCTATTATTTCT-AAGGGGACTTGGCAAAGTGGTGAAAGCGCATTCCCG
66 ACTATTCATGTCAGTACCTATTATTTCTGAA-GGGACTTGGCAAAGTGGTGAAAGCGCGTTCCCG
*
59911 GGGGCGTGC
130 GGGGCGCGC
* * * *
59920 CTTACATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACTCATGTCCACCGAGGA
1 CTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGGGA
59985 ACTAT
66 ACTAT
59990 AGATGGATGG
Statistics
Matches: 463, Mismatches: 18, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
136 117 0.25
137 9 0.02
138 337 0.73
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (138 bp):
CTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGGGA
ACTATTCATGTCAGTACCTATTATTTCTGAAGGGACTTGGCAAAGTGGTGAAAGCGCGTTCCCGG
GGGCGCGC
Found at i:60148 original size:23 final size:23
Alignment explanation
Indices: 60122--60224 Score: 78
Period size: 23 Copynumber: 4.7 Consensus size: 23
60112 ATGTGAAGTT
60122 TGAATAAATTGGATAAAATGTTA
1 TGAATAAATTGGATAAAATGTTA
* *
60145 TGAATAAATTGAAT-AAATGTAAA
1 TGAATAAATTGGATAAAATGT-TA
*
60168 GTG-ATCAATTGG-T----TGTT-
1 -TGAATAAATTGGATAAAATGTTA
*
60185 TGAATATATTGGATAAAATGTTA
1 TGAATAAATTGGATAAAATGTTA
* *
60208 TGGATAAATTGAATAAA
1 TGAATAAATTGGATAAA
60225 TGTGAAGTGA
Statistics
Matches: 61, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
16 2 0.03
17 7 0.11
18 1 0.02
19 3 0.05
22 11 0.18
23 35 0.57
24 2 0.03
ACGTcount: A:0.45, C:0.01, G:0.18, T:0.36
Consensus pattern (23 bp):
TGAATAAATTGGATAAAATGTTA
Found at i:60187 original size:63 final size:63
Alignment explanation
Indices: 60119--60243 Score: 207
Period size: 63 Copynumber: 2.0 Consensus size: 63
60109 GTTATGTGAA
60119 GTTTGAATAAATTGGATAAAATGTTATGAATAAATTGAATAAATGTAAAGTGATCAA-TTGGTT
1 GTTTGAATAAATTGGATAAAATGTTATGAATAAATTGAATAAATGTAAAGTGAT-AAGTTGGTT
* * *
60182 GTTTGAATATATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGT
1 GTTTGAATAAATTGGATAAAATGTTATGAATAAATTGAATAAATGTAAAGTGATAAGTTGGT
60244 CGTGACATTG
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 2 0.03
63 56 0.97
ACGTcount: A:0.41, C:0.01, G:0.22, T:0.37
Consensus pattern (63 bp):
GTTTGAATAAATTGGATAAAATGTTATGAATAAATTGAATAAATGTAAAGTGATAAGTTGGTT
Found at i:67989 original size:16 final size:16
Alignment explanation
Indices: 67919--67989 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 16
67909 CTAAACTAAG
*
67919 AATT-ATTTAAAATTT
1 AATTAATTTAATATTT
*
67934 GATTCACATTT-ATATTT
1 AATT-A-ATTTAATATTT
* *
67951 AATTAATTAAATATAT
1 AATTAATTTAATATTT
*
67967 AAATAATTTAATATTT
1 AATTAATTTAATATTT
*
67983 AGTTAAT
1 AATTAAT
67990 AATTATATAA
Statistics
Matches: 42, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
15 6 0.14
16 24 0.57
17 8 0.19
18 4 0.10
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (16 bp):
AATTAATTTAATATTT
Found at i:67997 original size:31 final size:31
Alignment explanation
Indices: 67941--68001 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
67931 TTTGATTCAC
67941 ATTTATATTTAATTAATTAAATATATAAATA
1 ATTTATATTTAATTAATTAAATATATAAATA
* *
67972 ATTTAATATTTAGTTAA-TAATTATATAAAT
1 ATTT-ATATTTAATTAATTAAATATATAAAT
68002 TAAATAATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 16 0.59
32 11 0.41
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (31 bp):
ATTTATATTTAATTAATTAAATATATAAATA
Found at i:68070 original size:72 final size:72
Alignment explanation
Indices: 67985--68119 Score: 182
Period size: 72 Copynumber: 1.9 Consensus size: 72
67975 TAATATTTAG
* * * * *
67985 TTAATAATTATATAAATTAAATAATGATATTGATGAAATAT-AATCTAAAATATTTTTTTCAAAT
1 TTAACAATTATATAAAGTAAATAATGATATCGATGAAATATAAAT-TAAAAAACTTTTTTCAAAT
68049 AATTTTTT
65 AATTTTTT
* * *
68057 TTAACAATTATATAAAGTAAATATTGATGTCGGTGAAATATAAATTAAAAAACTTTTTTCAAA
1 TTAACAATTATATAAAGTAAATAATGATATCGATGAAATATAAATTAAAAAACTTTTTTCAAA
68120 CTCTTTATAT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
72 51 0.94
73 3 0.06
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (72 bp):
TTAACAATTATATAAAGTAAATAATGATATCGATGAAATATAAATTAAAAAACTTTTTTCAAATA
ATTTTTT
Found at i:68867 original size:12 final size:10
Alignment explanation
Indices: 68839--68865 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
68829 ATCACACCAA
68839 TTCTCTCAAT
1 TTCTCTCAAT
68849 TTCTCTCAAT
1 TTCTCTCAAT
68859 TTCTCTC
1 TTCTCTC
68866 TCGGTTTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.15, C:0.33, G:0.00, T:0.52
Consensus pattern (10 bp):
TTCTCTCAAT
Found at i:68937 original size:17 final size:18
Alignment explanation
Indices: 68905--68938 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
68895 TAATATTATG
*
68905 TATTTAATTTTTTTACTT
1 TATTTAATTATTTTACTT
68923 TATTTAA-TATTTTACT
1 TATTTAATTATTTTACT
68939 AATATAATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (18 bp):
TATTTAATTATTTTACTT
Done.