Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004832.1 Hibiscus syriacus cultivar Beakdansim tig00010885_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: 94147
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:3319 original size:12 final size:11
Alignment explanation
Indices: 3285--3316 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
3275 CATTTGCTGC
3285 ATTTTTTTTTA
1 ATTTTTTTTTA
3296 ATTTTTTTTTA
1 ATTTTTTTTTA
3307 ATTTTTTTTT
1 ATTTTTTTTT
3317 TAAGTTCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
ATTTTTTTTTA
Found at i:8474 original size:61 final size:60
Alignment explanation
Indices: 8399--8512 Score: 149
Period size: 61 Copynumber: 1.9 Consensus size: 60
8389 TATTTGAATG
* * *
8399 AATTTAGAAATGAAATTAAAAGATTCAAAAAGTTTGAGGATTAATTTAAAATGAATGTCAC
1 AATTTAGAAATGAAATTAAAAGATTCAAAAA-CTTGAAGACTAATTTAAAATGAATGTCAC
** *
8460 AATTTA-AGAATGAAATTGGAAGATTCAAAAACTTGAAGACTAATTTAGAATGA
1 AATTTAGA-AATGAAATTAAAAGATTCAAAAACTTGAAGACTAATTTAAAATGA
8513 TATTCATAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
60 19 0.41
61 27 0.59
ACGTcount: A:0.49, C:0.05, G:0.16, T:0.30
Consensus pattern (60 bp):
AATTTAGAAATGAAATTAAAAGATTCAAAAACTTGAAGACTAATTTAAAATGAATGTCAC
Found at i:8785 original size:32 final size:32
Alignment explanation
Indices: 8744--8812 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
8734 AAACTAAATC
* *
8744 AATATTGAACCTAAACCGGCATTCATCCATAT
1 AATATTGAACCTAAACCAGCATTCATCAATAT
* *
8776 AATATTGAACCTAAATCAGTATTCATCAATAT
1 AATATTGAACCTAAACCAGCATTCATCAATAT
8808 AATAT
1 AATAT
8813 ATAATATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.32
Consensus pattern (32 bp):
AATATTGAACCTAAACCAGCATTCATCAATAT
Found at i:8813 original size:5 final size:5
Alignment explanation
Indices: 8811--8902 Score: 140
Period size: 5 Copynumber: 19.2 Consensus size: 5
8801 TCAATATAAT
8811 ATATA ATATA ATATA ATAT- A-ATA ATATA A-ATA ATATA ATAT- ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
8857 ATATA ATATAA ATATA ATAT- ATATA ATATA ATATA ATATA ATATA A
1 ATATA ATAT-A ATATA ATATA ATATA ATATA ATATA ATATA ATATA A
8903 CTTTACAAGT
Statistics
Matches: 81, Mismatches: 0, Indels: 12
0.87 0.00 0.13
Matches are distributed among these distances:
3 2 0.02
4 14 0.17
5 60 0.74
6 5 0.06
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:8846 original size:39 final size:37
Alignment explanation
Indices: 8803--8902 Score: 141
Period size: 39 Copynumber: 2.6 Consensus size: 37
8793 AGTATTCATC
8803 AATATAATATATAATATAATATAATATAATAATATAAAT
1 AATATAATATATAATATAATATAA-AT-ATAATATAAAT
*
8842 AATATAATATATATAATATAATATAAATATAATATATAT
1 AATAT-A-ATATATAATATAATATAAATATAATATAAAT
8881 AATAT-A-ATATAATATAATATAA
1 AATATAATATATAATATAATATAA
8903 CTTTACAAGT
Statistics
Matches: 58, Mismatches: 1, Indels: 8
0.87 0.01 0.12
Matches are distributed among these distances:
35 16 0.28
36 1 0.02
39 20 0.34
40 3 0.05
41 18 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (37 bp):
AATATAATATATAATATAATATAAATATAATATAAAT
Found at i:13022 original size:5 final size:5
Alignment explanation
Indices: 13012--13042 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
13002 CCAACAATAA
13012 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT T
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT T
13043 GACATGATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTAAT
Found at i:15118 original size:2 final size:2
Alignment explanation
Indices: 15111--15137 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
15101 TTGGGTTTTA
15111 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
15138 AATTTATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15391 original size:162 final size:161
Alignment explanation
Indices: 15115--15432 Score: 485
Period size: 162 Copynumber: 2.0 Consensus size: 161
15105 GTTTTAATAT
*
15115 ATATATATATATATATATATATAAATTTATGTTTATTTTTAAATATAAATATTTTAAATTTTATA
1 ATATATATATATATATATATATAAATTTAAGTTTATTTTTAAATATAAATATTTTAAATTTTATA
* * * * * * *
15180 AAGGTGACATATTTTATTTAACGATAGAAATTAACAACGATAACAATCCAGAAATCTAAAATAAT
66 AAGATAACATATATCATTTAACGATAAAAATTAACAACAATAACAATCCAAAAATCTAAAATAAT
*
15245 AATGTTTATAACATTA-GACACATAAATTTTA
131 AATGATTATAACATTATG-CACATAAATTTTA
*
15276 ATATATATATATATATATATATAATTTTAAGTTTATTTTTTAAATATAAATATTTTAAATTTTAT
1 ATATATATATATATATATATATAAATTTAAGTTTA-TTTTTAAATATAAATATTTTAAATTTTAT
* * *
15341 AAAGATAATATATATCATTTAACGATAAAAATTAATAACAATAGCAATCCAAAAATCTAAAATAA
65 AAAGATAACATATATCATTTAACGATAAAAATTAACAACAATAACAATCCAAAAATCTAAAATAA
*
15406 TAATGATTATAATATTATGCACATAAA
130 TAATGATTATAACATTATGCACATAAA
15433 GTATCCCAAA
Statistics
Matches: 141, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
161 33 0.23
162 107 0.76
163 1 0.01
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.40
Consensus pattern (161 bp):
ATATATATATATATATATATATAAATTTAAGTTTATTTTTAAATATAAATATTTTAAATTTTATA
AAGATAACATATATCATTTAACGATAAAAATTAACAACAATAACAATCCAAAAATCTAAAATAAT
AATGATTATAACATTATGCACATAAATTTTA
Found at i:15672 original size:20 final size:20
Alignment explanation
Indices: 15628--15925 Score: 224
Period size: 20 Copynumber: 14.6 Consensus size: 20
15618 AATGACCAAT
* *
15628 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
15647 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
15667 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
15687 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
15707 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
15727 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
15747 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
15768 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * * *
15791 AAAATCGAAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
15811 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
15831 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * * *
15854 AAAATCGAAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* *
15874 AGAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
15894 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
15914 AAAATCGCAACG
1 AAAATCGCAACG
15926 GTCAAAAGAA
Statistics
Matches: 224, Mismatches: 43, Indels: 23
0.77 0.15 0.08
Matches are distributed among these distances:
19 17 0.08
20 166 0.74
21 14 0.06
23 27 0.12
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:15852 original size:63 final size:63
Alignment explanation
Indices: 15630--15915 Score: 252
Period size: 63 Copynumber: 4.6 Consensus size: 63
15620 TGACCAATAA
* * * * * *
15630 AATCGCAACGCGATATCA-A-AATCGCAACGCGATTT---AGAAAATCGCAACGCGATTTAGAA
1 AATCGCAACGCGAT-TGAGAGAATCGCAACGCGATTTAGAAGAAAATCGAAATGCGACTGAGAG
* * * * * * * ** *
15689 AATCGCAACGCGATTTAGAAAATCGCAA--CG-TTAAAAAGAAAATCGCAACG-GTCAAAAGAA
1 AATCGCAACGCGATTGAGAGAATCGCAACGCGATTTAGAAGAAAATCGAAATGCGAC-TGAGAG
* * * *
15749 AATCGCAACGCGAGCTTCCA-AG-TTCGCAACGCGATTTAGAAGAAAATCGAAATGCGATTGATA
1 AATCGCAACGCGA--TT-GAGAGAATCGCAACGCGATTTAGAAGAAAATCGAAATGCGACTGAGA
15812 G
63 G
* *
15813 AATCGCAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAGAAAATCGAAATGCGACTGAGAG
1 AATCGCAACGCGATTGAGAGAATCGCAACGCGATTTAGAAGAAAATCGAAATGCGACTGAGAG
15876 AATCGCAACGCGATTGAGAGAATCGCAACGCGATTTAGAA
1 AATCGCAACGCGATTGAGAGAATCGCAACGCGATTTAGAA
15916 AATCGCAACG
Statistics
Matches: 186, Mismatches: 26, Indels: 26
0.78 0.11 0.11
Matches are distributed among these distances:
57 2 0.01
58 4 0.02
59 16 0.09
60 39 0.21
61 7 0.04
62 7 0.04
63 80 0.43
64 30 0.16
65 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.18
Consensus pattern (63 bp):
AATCGCAACGCGATTGAGAGAATCGCAACGCGATTTAGAAGAAAATCGAAATGCGACTGAGAG
Found at i:16024 original size:6 final size:6
Alignment explanation
Indices: 16013--16080 Score: 129
Period size: 6 Copynumber: 11.5 Consensus size: 6
16003 GACACGTATT
16013 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
16061 ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACC
16081 CGAGACGAGA
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.08
6 57 0.92
ACGTcount: A:0.32, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:16787 original size:6 final size:6
Alignment explanation
Indices: 16771--16832 Score: 117
Period size: 6 Copynumber: 10.5 Consensus size: 6
16761 TCTCGTCTCG
16771 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
16818 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
16833 TGCGATTTTC
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.09
6 51 0.91
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:16890 original size:19 final size:20
Alignment explanation
Indices: 16850--16900 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
16840 TTCTTTTTAA
*
16850 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
16870 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
*
16889 CGTTACGATTTT
1 CGTTGCGATTTT
16901 ATTGGTCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:23949 original size:11 final size:12
Alignment explanation
Indices: 23925--23953 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
23915 TGTTACATTC
23925 AAAATATTTATA
1 AAAATATTTATA
23937 AAAATATTT-TA
1 AAAATATTTATA
23948 AAAATA
1 AAAATA
23954 AAAAATATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAAATATTTATA
Found at i:30279 original size:12 final size:12
Alignment explanation
Indices: 30262--30288 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
30252 AATATTTAGC
30262 GAGAGAGGGAGA
1 GAGAGAGGGAGA
30274 GAGAGAGGGAGA
1 GAGAGAGGGAGA
30286 GAG
1 GAG
30289 CATTTTGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (12 bp):
GAGAGAGGGAGA
Found at i:47730 original size:3 final size:3
Alignment explanation
Indices: 47724--47801 Score: 156
Period size: 3 Copynumber: 26.0 Consensus size: 3
47714 AACAACGATG
47724 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
47772 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
47802 TTTATCTTCT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:48602 original size:29 final size:29
Alignment explanation
Indices: 48560--48619 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
48550 ATTCTACAGT
48560 GATCTCGTAGGACGCCATGCAATCCAGGC
1 GATCTCGTAGGACGCCATGCAATCCAGGC
*
48589 GATCTTGTAGGACGCCATGCAATCCAGGC
1 GATCTCGTAGGACGCCATGCAATCCAGGC
48618 GA
1 GA
48620 CATACCATAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.18
Consensus pattern (29 bp):
GATCTCGTAGGACGCCATGCAATCCAGGC
Found at i:48747 original size:32 final size:32
Alignment explanation
Indices: 48704--48785 Score: 155
Period size: 32 Copynumber: 2.6 Consensus size: 32
48694 TATTATACGA
*
48704 GGAGAGATCGCCATGCAGACGAGCCAGCCAAT
1 GGAGAGGTCGCCATGCAGACGAGCCAGCCAAT
48736 GGAGAGGTCGCCATGCAGACGAGCCAGCCAAT
1 GGAGAGGTCGCCATGCAGACGAGCCAGCCAAT
48768 GGAGAGGTCGCCATGCAG
1 GGAGAGGTCGCCATGCAG
48786 TCTGGGTGAC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.28, C:0.27, G:0.35, T:0.10
Consensus pattern (32 bp):
GGAGAGGTCGCCATGCAGACGAGCCAGCCAAT
Found at i:48816 original size:29 final size:29
Alignment explanation
Indices: 48772--48863 Score: 139
Period size: 29 Copynumber: 3.2 Consensus size: 29
48762 GCCAATGGAG
* ** *
48772 AGGTCGCCATGCAGTCTGGGTGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
48801 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
*
48830 AAGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
48859 AGGTC
1 AGGTC
48864 ACCCCGGCGT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 57 1.00
ACGTcount: A:0.15, C:0.28, G:0.32, T:0.25
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:49197 original size:16 final size:18
Alignment explanation
Indices: 49176--49214 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
49166 GGAGATAAGG
*
49176 TAAATTTGTTTA-TATT-
1 TAAATTAGTTTATTATTA
49192 TAAATTAGTTTATTATTA
1 TAAATTAGTTTATTATTA
49210 TAAAT
1 TAAAT
49215 GTTAATTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 4 0.20
18 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TAAATTAGTTTATTATTA
Found at i:49382 original size:46 final size:48
Alignment explanation
Indices: 49319--49410 Score: 129
Period size: 46 Copynumber: 2.0 Consensus size: 48
49309 TTATATAGTT
49319 AAAAAATAATTAATTAGTTTGTT-TT-GTT-AATAGTT-AGTTATATAA
1 AAAAAATAATTAATTAGTTT-TTGTTAGTTAAATAGTTAAGTTATATAA
*
49364 AAAAAATTATTTAATTAGTTTTTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAA-TAATTAATTAGTTTTTGTTAGTTAAATAGTTAAGTTATAT
49411 TTGTTTGTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
45 8 0.20
46 15 0.37
47 3 0.07
48 7 0.17
49 8 0.20
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (48 bp):
AAAAAATAATTAATTAGTTTTTGTTAGTTAAATAGTTAAGTTATATAA
Found at i:55250 original size:21 final size:21
Alignment explanation
Indices: 55224--55286 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
55214 TTTTGGTGCA
*
55224 GAGGGAATCGATCCCCCCCCT
1 GAGGGAACCGATCCCCCCCCT
* **
55245 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCCCT
*
55266 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATCCCCCCC
55287 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 18 0.51
22 1 0.03
23 16 0.46
ACGTcount: A:0.21, C:0.38, G:0.25, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCCCT
Found at i:55294 original size:21 final size:21
Alignment explanation
Indices: 55268--55307 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
55258 CCCCCTTTGA
*
55268 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
55289 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
55308 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:58787 original size:33 final size:33
Alignment explanation
Indices: 58750--58827 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 33
58740 TTAGTTAGTA
58750 AGTTTATTAGTAG-TATA-TTATAATGAAAAAAAT
1 AGTTTATTAGTAGTTATAGTTAT-AT-AAAAAAAT
*
58783 AGTTTATTAGTTAGTTTTAGTTATATAAAAAAAT
1 AGTTTATTAG-TAGTTATAGTTATATAAAAAAAT
*
58817 ATTTTATTAGT
1 AGTTTATTAGT
58828 TGTTTAAGGG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
33 11 0.28
34 20 0.50
35 5 0.12
36 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (33 bp):
AGTTTATTAGTAGTTATAGTTATATAAAAAAAT
Found at i:58905 original size:16 final size:16
Alignment explanation
Indices: 58873--58919 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
58863 TTTAAAAAGT
*
58873 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
58889 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
58905 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
58920 AAGTTTTGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:58914 original size:15 final size:14
Alignment explanation
Indices: 58894--58924 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
58884 GTTTATTAGT
58894 TTATTATATTATAAG
1 TTATTATATTA-AAG
58909 TTATTATATTAAAG
1 TTATTATATTAAAG
58923 TT
1 TT
58925 TTGTGTTGAA
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:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:59972 original size:11 final size:11
Alignment explanation
Indices: 59956--61114 Score: 207
Period size: 11 Copynumber: 96.5 Consensus size: 11
59946 CATTAAATAT
59956 TTAAATCATTA
1 TTAAATCATTA
59967 TTAAATCATTATTA
1 TTAAATC---ATTA
59981 TTAAATCATTAGTA
1 TTAAATCA-T--TA
59995 TTAAATCATTA
1 TTAAATCATTA
*
60006 CT-AA--ATTA
1 TTAAATCATTA
*
60014 TGAAATCATTAGTA
1 TTAAATCA-T--TA
60028 TTAAATCATTA
1 TTAAATCATTA
*
60039 TTATAAATAATTA
1 -T-TAAATCATTA
* * *
60052 CTAAATAATAA
1 TTAAATCATTA
* *
60063 CTAAATAATTA
1 TTAAATCATTA
60074 TTATAAAATCATTA
1 -T-T-AAATCATTA
*
60088 TTATAATAATTA
1 TTA-AATCATTA
60100 TTATCAAATCATTA
1 -T-T-AAATCATTA
*
60114 CTAAATCATCAAATCA
1 TTAAATCAT----T-A
60130 TTAAAT-A-T-
1 TTAAATCATTA
60138 TTAAATCATTA
1 TTAAATCATTA
*
60149 TCAAATCATTAGTA
1 TTAAATCA-T--TA
60163 TTAAATCATTA
1 TTAAATCATTA
* *
60174 TTATAAATAATTT
1 -T-TAAATCATTA
* *
60187 TTAAATAATAA
1 TTAAATCATTA
* *
60198 CTAAATAATTA
1 TTAAATCATTA
*
60209 TTATAAAATCATTT
1 -T-T-AAATCATTA
*
60223 TTATAATAATTA
1 TTA-AATCATTA
60235 TTATCAAATCATTA
1 -T-T-AAATCATTA
*
60249 CTAAATCATCAAATCA
1 TTAAATCAT----T-A
60265 TTAAAT-A-T-
1 TTAAATCATTA
60273 TTAAATCATTA
1 TTAAATCATTA
*
60284 TTAAATCATTT
1 TTAAATCATTA
*
60295 TTATAATGATTA
1 TTA-AATCATTA
*
60307 TTACTAAATCATTT
1 -T--TAAATCATTA
*
60321 TTATAATGATTA
1 TTA-AATCATTA
60333 TTATCAAATCATTA
1 -T-T-AAATCATTA
*
60347 CTATAATGATTATTA
1 -T-TAA--ATCATTA
*
60362 TCAAATCATTA
1 TTAAATCATTA
*
60373 CTAAATCATCAAATCA
1 TTAAATCAT----T-A
60389 TTAAAT-A-T-
1 TTAAATCATTA
60397 TTAAATCATTA
1 TTAAATCATTA
60408 TTAAATCATTA
1 TTAAATCATTA
*
60419 GTAACAAATCATTA
1 -T--TAAATCATTA
60433 TTAAATCATTAGTA
1 TTAAATCA-T--TA
*
60447 TTAAATCATCA
1 TTAAATCATTA
*
60458 CT-AA--ATTA
1 TTAAATCATTA
*
60466 TGAAATCATTAGTA
1 TTAAATCA-T--TA
60480 TTAAATCATTA
1 TTAAATCATTA
*
60491 CT-AA--ATTA
1 TTAAATCATTA
60499 TTAAATCATTAGTA
1 TTAAATCA-T--TA
60513 TTAAATCATTA
1 TTAAATCATTA
*
60524 TTATAAATAATTA
1 -T-TAAATCATTA
* * *
60537 CTAAATAATAA
1 TTAAATCATTA
* *
60548 CTAAATAATTA
1 TTAAATCATTA
60559 TTATAAAATCATTA
1 -T-T-AAATCATTA
*
60573 TTATAATGATTA
1 TTA-AATCATTA
60585 TTATCAAATCATTA
1 -T-T-AAATCATTA
*
60599 CTAAATCATCAAATCA
1 TTAAATCAT----T-A
60615 TTAAAT-A-T-
1 TTAAATCATTA
60623 TTAAATCATTA
1 TTAAATCATTA
60634 TTAAATCATTA
1 TTAAATCATTA
*
60645 GTAACAAATCATTA
1 -T--TAAATCATTA
60659 TTAAATCATTAGTA
1 TTAAATCA-T--TA
*
60673 TTAAATCATCA
1 TTAAATCATTA
*
60684 CT-AA--ATTA
1 TTAAATCATTA
*
60692 TGAAATCATTAGTA
1 TTAAATCA-T--TA
60706 TTAAATCATTA
1 TTAAATCATTA
*
60717 CT-AA--ATTA
1 TTAAATCATTA
60725 TTAAATCATTAGTA
1 TTAAATCA-T--TA
60739 TTAAATCATTA
1 TTAAATCATTA
*
60750 TTATAAATAATTA
1 -T-TAAATCATTA
* * *
60763 CTAAATAATAA
1 TTAAATCATTA
* *
60774 CTAAATAATTA
1 TTAAATCATTA
60785 TTATAAAATCATTA
1 -T-T-AAATCATTA
*
60799 TTATAATGATTA
1 TTA-AATCATTA
60811 TTATCAAATCATTA
1 -T-T-AAATCATTA
60825 TTAAATCATCAAATCA
1 TTAAATCAT----T-A
60841 TTAAAT-A-T-
1 TTAAATCATTA
60849 TTAAATCATTA
1 TTAAATCATTA
60860 TTAAATCATTA
1 TTAAATCATTA
*
60871 GTAACAAATCATTA
1 -T--TAAATCATTA
60885 TTAAATCATTAGTA
1 TTAAATCA-T--TA
*
60899 TTAAATCATCA
1 TTAAATCATTA
*
60910 CT-AA--ATTA
1 TTAAATCATTA
*
60918 TGAAATCATTAGTA
1 TTAAATCA-T--TA
60932 TTAAATCATTA
1 TTAAATCATTA
*
60943 CT-AA--ATTA
1 TTAAATCATTA
60951 TTAAATCATTAGTA
1 TTAAATCA-T--TA
60965 TTAAATCATTA
1 TTAAATCATTA
*
60976 TTATAAATAATTA
1 -T-TAAATCATTA
* * *
60989 CTAAATAATAA
1 TTAAATCATTA
* *
61000 CTAAATAATTA
1 TTAAATCATTA
61011 TTATAAAATCATTA
1 -T-T-AAATCATTA
*
61025 TTATAATGATTA
1 TTA-AATCATTA
61037 TTATCAAATCATTA
1 -T-T-AAATCATTA
* *
61051 CTAAATCATCA
1 TTAAATCATTA
*
61062 --AATCATTATTTA
1 TTAA--ATCA-TTA
61074 TTTAAATCATTA
1 -TTAAATCATTA
*
61086 TTAAATCATTT
1 TTAAATCATTA
*
61097 TTATAATGATTA
1 TTA-AATCATTA
*
61109 ATAAAT
1 TTAAAT
61115 ACATAGAAAT
Statistics
Matches: 867, Mismatches: 110, Indels: 342
0.66 0.08 0.26
Matches are distributed among these distances:
8 58 0.07
9 21 0.02
10 24 0.03
11 282 0.33
12 90 0.10
13 85 0.10
14 250 0.29
15 26 0.03
16 31 0.04
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.41
Consensus pattern (11 bp):
TTAAATCATTA
Found at i:60153 original size:46 final size:45
Alignment explanation
Indices: 60099--60293 Score: 136
Period size: 46 Copynumber: 4.3 Consensus size: 45
60089 TATAATAATT
60099 ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATC
1 ATTATCAAATCATTACTAAATCAT-AAATCATTAAATATTTAAATC
* * *
60145 ATTATCAAATCATTAGT--AT--TAAATCATT--AT-TATAAATA
1 ATTATCAAATCATTACTAAATCATAAATCATTAAATATTTAAATC
* * * * * * * * *
60183 ATTTTTAAATAATAACTAAATAAT-TATTATAAAATCATTTTTATAATAATT
1 ATTATCAAATCATTACTAAATCATAAATCATTAAAT-A---TT-T-A-AATC
60234 ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATC
1 ATTATCAAATCATTACTAAATCAT-AAATCATTAAATATTTAAATC
*
60280 ATTATTAAATCATT
1 ATTATCAAATCATT
60294 TTTATAATGA
Statistics
Matches: 110, Mismatches: 23, Indels: 32
0.67 0.14 0.19
Matches are distributed among these distances:
38 18 0.16
39 2 0.02
40 2 0.02
41 12 0.11
42 2 0.02
43 2 0.02
44 2 0.02
46 32 0.29
47 1 0.01
48 2 0.02
49 3 0.03
50 1 0.01
51 22 0.20
52 1 0.01
53 8 0.07
ACGTcount: A:0.48, C:0.10, G:0.01, T:0.42
Consensus pattern (45 bp):
ATTATCAAATCATTACTAAATCATAAATCATTAAATATTTAAATC
Found at i:60190 original size:49 final size:49
Alignment explanation
Indices: 60135--60607 Score: 178
Period size: 49 Copynumber: 9.5 Consensus size: 49
60125 AATCATTAAA
*
60135 TATTTAAATCATTA-TCAAATCATTAGTATTAAATCATTATTATAAATAAT
1 TATTTAAATCATTACT-AAATCATTAGTATAAAATCATTATTAT-AATAAT
* * * * *
60185 T-TTTAAATAATAACTAAATAATTATTATAAAATCATTTTTATAATAAT
1 TATTTAAATCATTACTAAATCATTAGTATAAAATCATTATTATAATAAT
* * * *
60233 TATTATCAAATCATTACTAAATCATCAAATCATTAAAT-A-T-TTA-AATCAT
1 TATT-T-AAATCATTACTAAATCAT-TAGT-ATAAAATCATTATTATAATAAT
** * * * *
60282 TA-TTAAATCATTTTTATAATGATTATTACT-AAATCATTTTTATAATGAT
1 TATTTAAATCATTACTA-AATCATTAGTA-TAAAATCATTATTATAATAAT
* * * * *
60331 TATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTA-AATCAT
1 TATT-T-AAATCATTACTA-AATCATTAGTATAAAATCATTATTATAATAAT
* * * *
60382 CAAATCATTAAAT-ATT--TAAATCATTA-T-T-AAATCATTAGTAACAAATCAT
1 --TAT--TTAAATCATTACTAAATCATTAGTATAAAATCATTA-TTA-TAATAAT
* * * * *
60431 TA-TTAAATCATTAGTATTAAATCATCACTAAATTATGAAATCATTAGTATTA-AAT
1 TATTTAAATCA-T--TACTAAATCAT---T--AGTATAAAATCATTATTATAATAAT
* * *
60486 CA-TTACTAA--ATTATTAAATCATTAGTATTAAATCATTATTATAAATAAT
1 TATTTA--AATCATTACTAAATCATTAGTATAAAATCATTATTAT-AATAAT
* * * * * *
60535 TA-CTAAATAATAACTAAATAATTATTATAAAATCATTATTATAATGAT
1 TATTTAAATCATTACTAAATCATTAGTATAAAATCATTATTATAATAAT
60583 TATTATCAAATCATTACTAAATCAT
1 TATT-T-AAATCATTACTAAATCAT
60608 CAAATCATTA
Statistics
Matches: 326, Mismatches: 51, Indels: 91
0.70 0.11 0.19
Matches are distributed among these distances:
44 6 0.02
45 6 0.02
46 24 0.07
47 28 0.09
48 21 0.06
49 97 0.30
50 18 0.06
51 38 0.12
52 49 0.15
53 13 0.04
54 2 0.01
55 9 0.03
56 2 0.01
57 4 0.01
58 9 0.03
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (49 bp):
TATTTAAATCATTACTAAATCATTAGTATAAAATCATTATTATAATAAT
Found at i:60203 original size:35 final size:37
Alignment explanation
Indices: 60164--60232 Score: 106
Period size: 35 Copynumber: 1.9 Consensus size: 37
60154 TCATTAGTAT
*
60164 TAAATCATTATTAT-AAATAATTTTTA-AATAATAAC
1 TAAATAATTATTATAAAATAATTTTTATAATAATAAC
*
60199 TAAATAATTATTATAAAATCATTTTTATAATAAT
1 TAAATAATTATTATAAAATAATTTTTATAATAAT
60233 TATTATCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 13 0.43
36 11 0.37
37 6 0.20
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (37 bp):
TAAATAATTATTATAAAATAATTTTTATAATAATAAC
Found at i:60230 original size:26 final size:26
Alignment explanation
Indices: 60205--60371 Score: 145
Period size: 26 Copynumber: 6.7 Consensus size: 26
60195 TAACTAAATA
* *
60205 ATTATTATAAAATCATTTTTATAATA
1 ATTATTATCAAATCATTTTTATAATG
** *
60231 ATTATTATCAAATCATTACTA-AATC
1 ATTATTATCAAATCATTTTTATAATG
* * * *
60256 ATCA-AATCATTAA--ATATTTA-AATC
1 ATTATTATCA--AATCATTTTTATAATG
60280 ATTA-T-T-AAATCATTTTTATAATG
1 ATTATTATCAAATCATTTTTATAATG
60303 ATTATTA-CTAAATCATTTTTATAATG
1 ATTATTATC-AAATCATTTTTATAATG
**
60329 ATTATTATCAAATCATTACTATAATG
1 ATTATTATCAAATCATTTTTATAATG
60355 ATTATTATCAAATCATT
1 ATTATTATCAAATCATT
60372 ACTAAATCAT
Statistics
Matches: 116, Mismatches: 15, Indels: 20
0.77 0.10 0.13
Matches are distributed among these distances:
20 2 0.02
22 7 0.06
23 8 0.07
24 16 0.14
25 6 0.05
26 76 0.66
27 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.46
Consensus pattern (26 bp):
ATTATTATCAAATCATTTTTATAATG
Found at i:60444 original size:25 final size:25
Alignment explanation
Indices: 60399--60455 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
60389 TTAAATATTT
60399 AAATCATTATTAAATCATTAGTAAC
1 AAATCATTATTAAATCATTAGTAAC
**
60424 AAATCATTATTAAATCATTAGTATT
1 AAATCATTATTAAATCATTAGTAAC
60449 AAATCAT
1 AAATCAT
60456 CACTAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.39
Consensus pattern (25 bp):
AAATCATTATTAAATCATTAGTAAC
Found at i:60463 original size:25 final size:25
Alignment explanation
Indices: 59938--60005 Score: 73
Period size: 28 Copynumber: 2.5 Consensus size: 25
59928 TTATTATTAG
*
59938 TATTAAATCATTAAATATTTAAATCAT
1 TATTAAATCATT-AGTA-TTAAATCAT
*
59965 TATTAAATCATTATTATTAAATCATT
1 TATTAAATCATTAGTATTAAATCA-T
59991 AGTATTAAATCATTA
1 --TATTAAATCATTA
60006 CTAAATTATG
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
25 8 0.22
26 4 0.11
27 12 0.32
28 13 0.35
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.46
Consensus pattern (25 bp):
TATTAAATCATTAGTATTAAATCAT
Found at i:60472 original size:33 final size:33
Alignment explanation
Indices: 60429--60973 Score: 234
Period size: 33 Copynumber: 16.8 Consensus size: 33
60419 GTAACAAATC
60429 ATTATTAAATCATTAGTATTAAATCATCACTAA
1 ATTATTAAATCATTAGTATTAAATCATCACTAA
* *
60462 ATTATGAAATCATTAGTATTAAATCATTACTAA
1 ATTATTAAATCATTAGTATTAAATCATCACTAA
60495 ATTATTAAATCATTAGTATTAAATCAT---T--
1 ATTATTAAATCATTAGTATTAAATCATCACTAA
* * * * * *
60523 ATTA-TAAATAATTACTA-AATAATAACTAAATAA
1 ATTATTAAATCATTAGTATTA-AATCA-TCACTAA
* * *
60556 TTATTATAAAATCATTATTA-T-AATGAT---T--
1 --ATTATTAAATCATTAGTATTAAATCATCACTAA
* * *
60584 ATTATCAAATCATTACTA--AATCATCAAATCATTAA
1 ATTATTAAATCATTAGTATTAA--ATC--ATCACTAA
* *
60619 ATAT-TTAAATCA-T--TATTAAATCATTAGTAACAAA
1 AT-TATTAAATCATTAGTATTAAATC---A-TCACTAA
60653 TCATTATTAAATCATTAGTATTAAATCATCACTAA
1 --ATTATTAAATCATTAGTATTAAATCATCACTAA
* *
60688 ATTATGAAATCATTAGTATTAAATCATTACTAA
1 ATTATTAAATCATTAGTATTAAATCATCACTAA
60721 ATTATTAAATCATTAGTATTAAATCAT---T--
1 ATTATTAAATCATTAGTATTAAATCATCACTAA
* * * * * *
60749 ATTA-TAAATAATTACTA-AATAATAACTAAATAA
1 ATTATTAAATCATTAGTATTA-AATCA-TCACTAA
* * * * *
60782 TTATTATAAAATCATTATTA-TAATGATTATTATCAAA
1 --ATTATTAAATCATTAGTATTAA--ATCATCA-CTAA
* * *
60819 TCATTATTAAATCATCAAATCATTAAAT-AT--TTAAA
1 --ATTATTAAATCAT-TAGT-ATTAAATCATCACT-AA
60854 TCATTATTAAATCATTAGTA--ACAA--AT--C---
1 --ATTATTAAATCATTAGTATTA-AATCATCACTAA
60881 ATTATTAAATCATTAGTATTAAATCATCACTAA
1 ATTATTAAATCATTAGTATTAAATCATCACTAA
* *
60914 ATTATGAAATCATTAGTATTAAATCATTACTAA
1 ATTATTAAATCATTAGTATTAAATCATCACTAA
60947 ATTATTAAATCATTAGTATTAAATCAT
1 ATTATTAAATCATTAGTATTAAATCAT
60974 TATTATAAAT
Statistics
Matches: 404, Mismatches: 50, Indels: 116
0.71 0.09 0.20
Matches are distributed among these distances:
25 18 0.04
26 21 0.05
27 31 0.08
28 14 0.03
30 6 0.01
31 5 0.01
32 7 0.02
33 175 0.43
34 13 0.03
35 41 0.10
36 35 0.09
37 21 0.05
38 4 0.01
39 10 0.02
40 3 0.01
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (33 bp):
ATTATTAAATCATTAGTATTAAATCATCACTAA
Found at i:60502 original size:19 final size:19
Alignment explanation
Indices: 60445--60509 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
60435 AAATCATTAG
*
60445 TATTAAATCATCACTAAAT
1 TATTAAATCATTACTAAAT
* *
60464 TATGAAATCA-T--T--AG
1 TATTAAATCATTACTAAAT
60478 TATTAAATCATTACTAAAT
1 TATTAAATCATTACTAAAT
60497 TATTAAATCATTA
1 TATTAAATCATTA
60510 GTATTAAATC
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
14 10 0.28
15 1 0.03
16 1 0.03
17 1 0.03
19 23 0.64
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.40
Consensus pattern (19 bp):
TATTAAATCATTACTAAAT
Found at i:60561 original size:226 final size:226
Alignment explanation
Indices: 60282--61095 Score: 1493
Period size: 226 Copynumber: 3.6 Consensus size: 226
60272 TTTAAATCAT
* * * *** * *
60282 TATTAAATCATTTTTATAATGATTATTACTAAATCATTTTTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTATTATAA--ATAATTACTAAATAATAACTA-AATAATTATTATAAAATCATTA
*
60347 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAA
63 TTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAA
60412 ATCATTAGTAACAAATCATTATTAAATCATTAGTATTAAATCATCACTAAATTATGAAATCATTA
128 ATCATTAGTAACAAATCATTATTAAATCATTAGTATTAAATCATCACTAAATTATGAAATCATTA
60477 GTATTAAATCATTACTAAATTATTAAATCATTAG
193 GTATTAAATCATTACTAAATTATTAAATCATTAG
60511 TATTAAATCATTATTATAAATAATTACTAAATAATAACTAAATAATTATTATAAAATCATTATTA
1 TATTAAATCATTATTATAAATAATTACTAAATAATAACTAAATAATTATTATAAAATCATTATTA
60576 TAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATC
66 TAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATC
60641 ATTAGTAACAAATCATTATTAAATCATTAGTATTAAATCATCACTAAATTATGAAATCATTAGTA
131 ATTAGTAACAAATCATTATTAAATCATTAGTATTAAATCATCACTAAATTATGAAATCATTAGTA
60706 TTAAATCATTACTAAATTATTAAATCATTAG
196 TTAAATCATTACTAAATTATTAAATCATTAG
60737 TATTAAATCATTATTATAAATAATTACTAAATAATAACTAAATAATTATTATAAAATCATTATTA
1 TATTAAATCATTATTATAAATAATTACTAAATAATAACTAAATAATTATTATAAAATCATTATTA
*
60802 TAATGATTATTATCAAATCATTATTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATC
66 TAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATC
60867 ATTAGTAACAAATCATTATTAAATCATTAGTATTAAATCATCACTAAATTATGAAATCATTAGTA
131 ATTAGTAACAAATCATTATTAAATCATTAGTATTAAATCATCACTAAATTATGAAATCATTAGTA
60932 TTAAATCATTACTAAATTATTAAATCATTAG
196 TTAAATCATTACTAAATTATTAAATCATTAG
60963 TATTAAATCATTATTATAAATAATTACTAAATAATAACTAAATAATTATTATAAAATCATTATTA
1 TATTAAATCATTATTATAAATAATTACTAAATAATAACTAAATAATTATTATAAAATCATTATTA
**
61028 TAATGATTATTATCAAATCATTACTAAATCATCAAATCATTATTTATTTAAATCATTATTAAATC
66 TAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATC
61093 ATT
131 ATT
61096 TTTATAATGA
Statistics
Matches: 572, Mismatches: 13, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
226 538 0.94
227 16 0.03
229 18 0.03
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.41
Consensus pattern (226 bp):
TATTAAATCATTATTATAAATAATTACTAAATAATAACTAAATAATTATTATAAAATCATTATTA
TAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATC
ATTAGTAACAAATCATTATTAAATCATTAGTATTAAATCATCACTAAATTATGAAATCATTAGTA
TTAAATCATTACTAAATTATTAAATCATTAG
Found at i:60586 original size:12 final size:13
Alignment explanation
Indices: 59953--61050 Score: 264
Period size: 14 Copynumber: 80.2 Consensus size: 13
59943 AATCATTAAA
59953 TATT-TAAATCAT
1 TATTATAAATCAT
59965 TA-T-TAAATCAT
1 TATTATAAATCAT
59976 TATTATTAAATCAT
1 TATTA-TAAATCAT
*
59990 TAGTATTAAATCATT
1 TATTA-TAAATCA-T
60005 ACTAAATTATGAAATCAT
1 --T--ATTAT-AAATCAT
*
60023 TAGTATTAAATCAT
1 TATTA-TAAATCAT
60037 TATTATAAAT-A-
1 TATTATAAATCAT
60048 -ATTACTAAAT-A-
1 TATTA-TAAATCAT
* *
60059 -ATAACTAAATAAT
1 TATTA-TAAATCAT
60072 TATTATAAAATCAT
1 TATTAT-AAATCAT
*
60086 TATTAT-AATAAT
1 TATTATAAATCAT
60098 TATTATCAAATCAT
1 TATTAT-AAATCAT
60112 TACTAAATCATCAAATCAT
1 TA-T---T-AT-AAATCAT
*
60131 TAAATATTTAAATCAT
1 T--AT-TATAAATCAT
*
60147 TA-T-CAAATCAT
1 TATTATAAATCAT
*
60158 TAGTATTAAATCAT
1 TATTA-TAAATCAT
*
60172 TATTATAAATAAT
1 TATTATAAATCAT
60185 T-TT-TAAAT-A-
1 TATTATAAATCAT
* *
60194 -ATAACTAAATAAT
1 TATTA-TAAATCAT
60207 TATTATAAAATCAT
1 TATTAT-AAATCAT
* *
60221 TTTTAT-AATAAT
1 TATTATAAATCAT
60233 TATTATCAAATCAT
1 TATTAT-AAATCAT
60247 TACTAAATCATCAAATCAT
1 TA-T---T-AT-AAATCAT
*
60266 TAAATATTTAAATCAT
1 T--AT-TATAAATCAT
60282 TA-T-TAAATCAT
1 TATTATAAATCAT
* *
60293 TTTTAT-AATGAT
1 TATTATAAATCAT
60305 TATTACTAAATCAT
1 TATTA-TAAATCAT
* *
60319 TTTTAT-AATGAT
1 TATTATAAATCAT
60331 TATTATCAAATCAT
1 TATTAT-AAATCAT
* *
60345 TACTAT-AATGAT
1 TATTATAAATCAT
60357 TATTATCAAATCAT
1 TATTAT-AAATCAT
60371 TACTAAATCATCAAATCAT
1 TA-T---T-AT-AAATCAT
*
60390 TAAATATTTAAATCAT
1 T--AT-TATAAATCAT
60406 TA-T-TAAATCAT
1 TATTATAAATCAT
* *
60417 TAGTAACAAATCAT
1 TA-TTATAAATCAT
60431 TA-T-TAAATCAT
1 TATTATAAATCAT
*
60442 TAGTATTAAATCAT
1 TATTA-TAAATCAT
60456 CACTAAATTATGAAATCAT
1 ---T--ATTAT-AAATCAT
*
60475 TAGTATTAAATCATT
1 TATTA-TAAATCA-T
60490 ACTAAATTATTAAATCAT
1 --T--ATTA-TAAATCAT
*
60508 TAGTATTAAATCAT
1 TATTA-TAAATCAT
60522 TATTATAAAT-A-
1 TATTATAAATCAT
60533 -ATTACTAAAT-A-
1 TATTA-TAAATCAT
* *
60544 -ATAACTAAATAAT
1 TATTA-TAAATCAT
60557 TATTATAAAATCAT
1 TATTAT-AAATCAT
*
60571 TATTAT-AATGAT
1 TATTATAAATCAT
60583 TATTATCAAATCAT
1 TATTAT-AAATCAT
60597 TACTAAATCATCAAATCAT
1 TA-T---T-AT-AAATCAT
*
60616 TAAATATTTAAATCAT
1 T--AT-TATAAATCAT
60632 TA-T-TAAATCAT
1 TATTATAAATCAT
* *
60643 TAGTAACAAATCAT
1 TA-TTATAAATCAT
60657 TA-T-TAAATCAT
1 TATTATAAATCAT
*
60668 TAGTATTAAATCAT
1 TATTA-TAAATCAT
60682 CACTAAATTATGAAATCAT
1 ---T--ATTAT-AAATCAT
*
60701 TAGTATTAAATCATT
1 TATTA-TAAATCA-T
60716 ACTAAATTATTAAATCAT
1 --T--ATTA-TAAATCAT
*
60734 TAGTATTAAATCAT
1 TATTA-TAAATCAT
60748 TATTATAAAT-A-
1 TATTATAAATCAT
60759 -ATTACTAAAT-A-
1 TATTA-TAAATCAT
* *
60770 -ATAACTAAATAAT
1 TATTA-TAAATCAT
60783 TATTATAAAATCAT
1 TATTAT-AAATCAT
*
60797 TATTAT-AATGAT
1 TATTATAAATCAT
60809 TATTATCAAATCAT
1 TATTAT-AAATCAT
60823 TA-T-TAAATCAT
1 TATTATAAATCAT
* * * * * *
60834 CA-AATCATTAAA
1 TATTATAAATCAT
60846 TATT-TAAATCAT
1 TATTATAAATCAT
60858 TA-T-TAAATCAT
1 TATTATAAATCAT
* *
60869 TAGTAACAAATCAT
1 TA-TTATAAATCAT
60883 TA-T-TAAATCAT
1 TATTATAAATCAT
*
60894 TAGTATTAAATCAT
1 TATTA-TAAATCAT
60908 CACTAAATTATGAAATCAT
1 ---T--ATTAT-AAATCAT
*
60927 TAGTATTAAATCATT
1 TATTA-TAAATCA-T
60942 ACTAAATTATTAAATCAT
1 --T--ATTA-TAAATCAT
*
60960 TAGTATTAAATCAT
1 TATTA-TAAATCAT
60974 TATTATAAAT-A-
1 TATTATAAATCAT
60985 -ATTACTAAAT-A-
1 TATTA-TAAATCAT
* *
60996 -ATAACTAAATAAT
1 TATTA-TAAATCAT
61009 TATTATAAAATCAT
1 TATTAT-AAATCAT
*
61023 TATTAT-AATGAT
1 TATTATAAATCAT
61035 TATTATCAAATCAT
1 TATTAT-AAATCAT
61049 TA
1 TA
61051 CTAAATCATC
Statistics
Matches: 854, Mismatches: 90, Indels: 282
0.70 0.07 0.23
Matches are distributed among these distances:
9 1 0.00
10 17 0.02
11 165 0.19
12 118 0.14
13 37 0.04
14 310 0.36
15 12 0.01
16 39 0.05
17 11 0.01
18 20 0.02
19 116 0.14
20 4 0.00
21 4 0.00
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.41
Consensus pattern (13 bp):
TATTATAAATCAT
Found at i:60688 original size:25 final size:25
Alignment explanation
Indices: 60495--61059 Score: 96
Period size: 25 Copynumber: 22.5 Consensus size: 25
60485 TCATTACTAA
60495 ATTATTAAATCATTAGTATTAAATC
1 ATTATTAAATCATTAGTATTAAATC
* * * *
60520 ATTATTATAA--ATAATTACTAAATA
1 ATTATTA-AATCATTAGTATTAAATC
* * * * *
60544 ATAACTAAATAATTATTATAAAATC
1 ATTATTAAATCATTAGTATTAAATC
* * *
60569 ATTATTATAATGATTATTATCAAATC
1 ATTATTA-AATCATTAGTATTAAATC
* * *
60595 ATTACTAAATCATCAAATCATTAAAT-
1 ATTATTAAATCAT-TAGT-ATTAAATC
60621 A-T-TTAAATCA-T--TATTAAATC
1 ATTATTAAATCATTAGTATTAAATC
* * * *
60641 ATTAGTAACA-AATCATTATTAAATC
1 ATTATTAA-ATCATTAGTATTAAATC
* *
60666 ATTAGTATTAAATCATCACTAAATTATGAAATC
1 A-T--TATTAAATCAT---T--AGTATTAAATC
*
60699 ATTAGTATTAAATCA-T--TACT-AA--
1 A-T--TATTAAATCATTAGTATTAAATC
60721 ATTATTAAATCATTAGTATTAAATC
1 ATTATTAAATCATTAGTATTAAATC
* * * *
60746 ATTATTATAA--ATAATTACTAAATA
1 ATTATTA-AATCATTAGTATTAAATC
* * * * *
60770 ATAACTAAATAATTATTATAAAATC
1 ATTATTAAATCATTAGTATTAAATC
* * *
60795 ATTATTATAATGATTATTATCAAATC
1 ATTATTA-AATCATTAGTATTAAATC
* *
60821 ATTATTAAATCATCAAATCATTAAAT-
1 ATTATTAAATCAT-TAGT-ATTAAATC
60847 A-T-TTAAATCA-T--TATTAAATC
1 ATTATTAAATCATTAGTATTAAATC
* * * *
60867 ATTAGTAACA-AATCATTATTAAATC
1 ATTATTAA-ATCATTAGTATTAAATC
* *
60892 ATTAGTATTAAATCATCACTAAATTATGAAATC
1 A-T--TATTAAATCAT---T--AGTATTAAATC
*
60925 ATTAGTATTAAATCA-T--TACT-AA--
1 A-T--TATTAAATCATTAGTATTAAATC
60947 ATTATTAAATCATTAGTATTAAATC
1 ATTATTAAATCATTAGTATTAAATC
* * * *
60972 ATTATTATAA--ATAATTACTAAATA
1 ATTATTA-AATCATTAGTATTAAATC
* * * * *
60996 ATAACTAAATAATTATTATAAAATC
1 ATTATTAAATCATTAGTATTAAATC
* * *
61021 ATTATTATAATGATTATTATCAAATC
1 ATTATTA-AATCATTAGTATTAAATC
*
61047 ATTACTAAATCAT
1 ATTATTAAATCAT
61060 CAAATCATTA
Statistics
Matches: 404, Mismatches: 76, Indels: 120
0.67 0.13 0.20
Matches are distributed among these distances:
19 34 0.08
20 6 0.01
21 4 0.01
22 16 0.04
23 12 0.03
24 64 0.16
25 107 0.26
26 81 0.20
27 14 0.03
28 14 0.03
29 2 0.00
33 50 0.12
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.40
Consensus pattern (25 bp):
ATTATTAAATCATTAGTATTAAATC
Found at i:60728 original size:19 final size:19
Alignment explanation
Indices: 60671--60735 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
60661 AAATCATTAG
*
60671 TATTAAATCATCACTAAAT
1 TATTAAATCATTACTAAAT
* *
60690 TATGAAATCA-T--T--AG
1 TATTAAATCATTACTAAAT
60704 TATTAAATCATTACTAAAT
1 TATTAAATCATTACTAAAT
60723 TATTAAATCATTA
1 TATTAAATCATTA
60736 GTATTAAATC
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
14 10 0.28
15 1 0.03
16 1 0.03
17 1 0.03
19 23 0.64
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.40
Consensus pattern (19 bp):
TATTAAATCATTACTAAAT
Found at i:60798 original size:49 final size:46
Alignment explanation
Indices: 60688--60804 Score: 135
Period size: 49 Copynumber: 2.5 Consensus size: 46
60678 TCATCACTAA
* * * * *
60688 ATTATGAAATCATTAGTATTAAATCATTACTAAATTATTAAATCATT
1 ATTATAAAATCATTATTA-TAAATAATTACTAAATTACTAAATAATT
* *
60735 AGTATTAAATCATTATTATAAATAATTACTAAATAATAACTAAATAATT
1 ATTATAAAATCATTATTATAAATAATTACTAAAT--T-ACTAAATAATT
60784 ATTATAAAATCATTATTATAA
1 ATTATAAAATCATTATTATAA
60805 TGATTATTAT
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 15 0.25
47 15 0.25
48 1 0.02
49 28 0.47
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.41
Consensus pattern (46 bp):
ATTATAAAATCATTATTATAAATAATTACTAAATTACTAAATAATT
Found at i:60837 original size:19 final size:19
Alignment explanation
Indices: 60813--60868 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
60803 AATGATTATT
60813 ATCAAATCATTATTAAATC
1 ATCAAATCATTATTAAATC
60832 ATCAAATC---ATTAAAT-
1 ATCAAATCATTATTAAATC
*
60847 ATTTAAATCATTATTAAATC
1 A-TCAAATCATTATTAAATC
60867 AT
1 AT
60869 TAGTAACAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
15 1 0.03
16 13 0.42
19 16 0.52
20 1 0.03
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (19 bp):
ATCAAATCATTATTAAATC
Found at i:60954 original size:19 final size:19
Alignment explanation
Indices: 60897--60961 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
60887 AAATCATTAG
*
60897 TATTAAATCATCACTAAAT
1 TATTAAATCATTACTAAAT
* *
60916 TATGAAATCA-T--T--AG
1 TATTAAATCATTACTAAAT
60930 TATTAAATCATTACTAAAT
1 TATTAAATCATTACTAAAT
60949 TATTAAATCATTA
1 TATTAAATCATTA
60962 GTATTAAATC
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
14 10 0.28
15 1 0.03
16 1 0.03
17 1 0.03
19 23 0.64
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.40
Consensus pattern (19 bp):
TATTAAATCATTACTAAAT
Found at i:61024 original size:49 final size:46
Alignment explanation
Indices: 60914--61030 Score: 135
Period size: 49 Copynumber: 2.5 Consensus size: 46
60904 TCATCACTAA
* * * * *
60914 ATTATGAAATCATTAGTATTAAATCATTACTAAATTATTAAATCATT
1 ATTATAAAATCATTATTA-TAAATAATTACTAAATTACTAAATAATT
* *
60961 AGTATTAAATCATTATTATAAATAATTACTAAATAATAACTAAATAATT
1 ATTATAAAATCATTATTATAAATAATTACTAAAT--T-ACTAAATAATT
61010 ATTATAAAATCATTATTATAA
1 ATTATAAAATCATTATTATAA
61031 TGATTATTAT
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 15 0.25
47 15 0.25
48 1 0.02
49 28 0.47
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.41
Consensus pattern (46 bp):
ATTATAAAATCATTATTATAAATAATTACTAAATTACTAAATAATT
Found at i:64219 original size:28 final size:28
Alignment explanation
Indices: 64167--64220 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
64157 ATAATCTAAT
**
64167 ATATAACTTAAACTAACAATTTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
64195 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
64221 ATTTATACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:64227 original size:28 final size:28
Alignment explanation
Indices: 64163--64227 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
64153 TTATATAATC
**
64163 TAATATATAACTTAAACTAACAATTTAA
1 TAATATATAACTTAAACTAACAAACTAA
64191 T-ATAATATAACTTAAACTAACAAACTAA
1 TAAT-ATATAACTTAAACTAACAAACTAA
*
64219 TAATTTATA
1 TAATATATA
64228 CTAACAAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 2 0.06
28 28 0.88
29 2 0.06
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (28 bp):
TAATATATAACTTAAACTAACAAACTAA
Found at i:64230 original size:21 final size:21
Alignment explanation
Indices: 64197--64245 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
64187 TTAATATAAT
64197 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
64218 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
64239 ATTAACT
1 A-TAACT
64246 AAATTTCTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:64913 original size:10 final size:10
Alignment explanation
Indices: 64898--64943 Score: 56
Period size: 10 Copynumber: 4.3 Consensus size: 10
64888 TGGAGGTCGT
*
64898 TGGGCGTGCC
1 TGGGCGTGCA
64908 TGGGCGTGCA
1 TGGGCGTGCA
64918 TGGAGGTCGTGCA
1 T-G-GG-CGTGCA
64931 TGGGCGTGCA
1 TGGGCGTGCA
64941 TGG
1 TGG
64944 AGGTCGTTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
10 19 0.59
11 3 0.09
12 3 0.09
13 7 0.22
ACGTcount: A:0.09, C:0.20, G:0.50, T:0.22
Consensus pattern (10 bp):
TGGGCGTGCA
Found at i:64913 original size:30 final size:30
Alignment explanation
Indices: 64877--64959 Score: 108
Period size: 30 Copynumber: 3.0 Consensus size: 30
64867 CTTTGGCGAG
64877 CTGGGCGTGCATGGAGGTCGTTGGGCGTGC
1 CTGGGCGTGCATGGAGGTCGTTGGGCGTGC
64907 CTGGGCGTGCATGGA-G--G-T---CGTGC
1 CTGGGCGTGCATGGAGGTCGTTGGGCGTGC
*
64930 ATGGGCGTGCATGGAGGTCGTTGGGCGTGC
1 CTGGGCGTGCATGGAGGTCGTTGGGCGTGC
64960 ATGGCGACCT
Statistics
Matches: 45, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
23 19 0.42
24 1 0.02
26 2 0.04
27 2 0.04
29 1 0.02
30 20 0.44
ACGTcount: A:0.08, C:0.19, G:0.49, T:0.23
Consensus pattern (30 bp):
CTGGGCGTGCATGGAGGTCGTTGGGCGTGC
Found at i:64930 original size:13 final size:13
Alignment explanation
Indices: 64912--64950 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
64902 CGTGCCTGGG
64912 CGTGCATGGAGGT
1 CGTGCATGGAGGT
64925 CGTGCAT-G-GG-
1 CGTGCATGGAGGT
64935 CGTGCATGGAGGT
1 CGTGCATGGAGGT
64948 CGT
1 CGT
64951 TGGGCGTGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
10 7 0.30
11 3 0.13
12 3 0.13
13 10 0.43
ACGTcount: A:0.13, C:0.18, G:0.46, T:0.23
Consensus pattern (13 bp):
CGTGCATGGAGGT
Found at i:64934 original size:23 final size:22
Alignment explanation
Indices: 64902--64963 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 22
64892 GGTCGTTGGG
64902 CGTGCCTGGGCGTGCATGGAGGT
1 CGTG-CTGGGCGTGCATGGAGGT
64925 CGTGCATGGGCGTGCATGGAGGT
1 CGTGC-TGGGCGTGCATGGAGGT
64948 CGT--TGGGCGTGCATGG
1 CGTGCTGGGCGTGCATGG
64964 CGACCTACCA
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
20 13 0.34
22 1 0.03
23 24 0.63
ACGTcount: A:0.10, C:0.19, G:0.48, T:0.23
Consensus pattern (22 bp):
CGTGCTGGGCGTGCATGGAGGT
Found at i:64977 original size:29 final size:29
Alignment explanation
Indices: 64952--65059 Score: 216
Period size: 29 Copynumber: 3.7 Consensus size: 29
64942 GGAGGTCGTT
64952 GGGCGTGCATGGCGACCTACCAGGTCGCC
1 GGGCGTGCATGGCGACCTACCAGGTCGCC
64981 GGGCGTGCATGGCGACCTACCAGGTCGCC
1 GGGCGTGCATGGCGACCTACCAGGTCGCC
65010 GGGCGTGCATGGCGACCTACCAGGTCGCC
1 GGGCGTGCATGGCGACCTACCAGGTCGCC
65039 GGGCGTGCATGGCGACCTACC
1 GGGCGTGCATGGCGACCTACC
65060 CCCGGGACTG
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 79 1.00
ACGTcount: A:0.14, C:0.34, G:0.38, T:0.14
Consensus pattern (29 bp):
GGGCGTGCATGGCGACCTACCAGGTCGCC
Found at i:65817 original size:2 final size:2
Alignment explanation
Indices: 65812--65838 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
65802 ATATATACAC
65812 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
65839 TGTTGAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:73190 original size:349 final size:349
Alignment explanation
Indices: 72546--73811 Score: 1691
Period size: 349 Copynumber: 3.6 Consensus size: 349
72536 TGACCTATTA
** * **
72546 GTGTTGCAGTGAGGAGATGGTTTTGAGATGTGTTGATAA-AACAAATGGACCATGACGGTTAGAG
1 GTGTTGCAACGAGGAGATGGTTTTGAGATGTGTTGATAAGAA-AAATGGATCACAACGGTTAGAG
* * *
72610 GCAGTTCATCCCTTTTTAATTTGGGTGGAGAGTCGTAAGTAATTGACAAGTGTCAAGGTTCTTTG
65 GCAGTTCATCCCTTTTTAATTTGGGTGGAGAGTCGTAAGTCATTGACAAGTGTCAAGATTCTCTG
* * * *
72675 TCTTTATGAAGATATAGAAAACAATTGAATAGGGAGGAAAAATGAAGAGTTTGATCCCTTCTCTC
130 TCTTCATGAAGAGATAGAAAAGAATTGAATATGGAGGAAAAATGAAGAGTTTGATCCCTTCTCTC
* * * * *
72740 GGTCTTAATCGAGAGAATTTATTAGTATTGGTGTCGACGT-TAAGTTTATTATCGTTTCTCGTAG
195 GGTCTTAATCGAGAGACTTTATTAGTACTGGTGTCGAC-TATAAGTTTATTATCATTACTTGTAG
* * * *
72804 GTTGATATTCTTAGTAGATACGATCAACTATCAATAGATTTAACCAATGCTTGAAAGAACCTAGA
259 GTTGATAGTCTTAGTAGATATGATCAACTAACAATAGATTTAACCAATGCTTGAAAGAACCTTGA
* * *
72869 GAAAACTGTCATGCGGGATGGATTGT
324 GAAAACCGTCATGCGCGATGGATCGT
** *
72895 GTGTTGCAGTGAAGAGATGGTTTTGAGATGTGTTGATAAGAAAAATGGATCACAACGGTTAGAGG
1 GTGTTGCAACGAGGAGATGGTTTTGAGATGTGTTGATAAGAAAAATGGATCACAACGGTTAGAGG
* *** ** *
72960 TAGTTCATTTATTTTTAATTTGAATGGAGAGTCGTAAATCATTGACAAGTGTCAAGATTCTCTGT
66 CAGTTCATCCCTTTTTAATTTGGGTGGAGAGTCGTAAGTCATTGACAAGTGTCAAGATTCTCTGT
* * *
73025 CTTCATGAAGAGATA-AAAGAGAATTGAATATGGA-TAAAGAATGAAGAGTATGATCCATTCTCT
131 CTTCATGAAGAGATAGAAA-AGAATTGAATATGGAGGAAA-AATGAAGAGTTTGATCCCTTCTCT
* * * *
73088 TGGTTTTAATCGAGAGACTTTATTAGTACTGGTGTCAACTATAATTTTATTATCATTACTTGTAG
194 CGGTCTTAATCGAGAGACTTTATTAGTACTGGTGTCGACTATAAGTTTATTATCATTACTTGTAG
* * * *
73153 ATTGATAGTCTTAGTAGATATGATAAACTAACAATAGATTTAACCAGTGCTTGAATGAACCTTGA
259 GTTGATAGTCTTAGTAGATATGATCAACTAACAATAGATTTAACCAATGCTTGAAAGAACCTTGA
*
73218 GAAAACCGTAATGCGCGATGGATCGT
324 GAAAACCGTCATGCGCGATGGATCGT
* * * **
73244 GTGCTGCAACGAGGAGATGGTTTTGAGATGTGTTGATAAGATAAATGGATCACGACGGTTAGAAA
1 GTGTTGCAACGAGGAGATGGTTTTGAGATGTGTTGATAAGAAAAATGGATCACAACGGTTAGAGG
* *
73309 CAATTCATCCCTTTTTAATTTGGGTGGAGAGTGGTAAGTCATTGACAAGTGTCAAGATTCTCTGT
66 CAGTTCATCCCTTTTTAATTTGGGTGGAGAGTCGTAAGTCATTGACAAGTGTCAAGATTCTCTGT
** * * *
73374 CTTCATGAAGAGATAGAAAAGGGTTGAATAAGTAGGAAAAATGAAGAGTTTGATCCGTTCTCTCG
131 CTTCATGAAGAGATAGAAAAGAATTGAATATGGAGGAAAAATGAAGAGTTTGATCCCTTCTCTCG
* *
73439 GTCTTAATCTAGAGACTTTATTAGTACTTGTGTCGACTATAAGTTTATTATCATTA-TTCGTAGG
196 GTCTTAATCGAGAGACTTTATTAGTACTGGTGTCGACTATAAGTTTATTATCATTACTT-GTAGG
* * * * * *
73503 TTGATAGTCTTAGTAGATATGATCAATTGATAATAGATTTAACCAACGCTTGAAAGAACATTGGG
260 TTGATAGTCTTAGTAGATATGATCAACTAACAATAGATTTAACCAATGCTTGAAAGAACCTTGAG
* **
73568 AATACCGTCATATGCGATGGATCGT
325 AAAACCGTCATGCGCGATGGATCGT
* *
73593 GTGTTGCAACGAGGAGATGGTTTTGAGATATGTTGATAAGACAAATGGATCACAACGGTTAGAGG
1 GTGTTGCAACGAGGAGATGGTTTTGAGATGTGTTGATAAGAAAAATGGATCACAACGGTTAGAGG
* * * *
73658 CAGTTCATCCCTTTTTAATTTGGGTGGAGAGTTGTAAGTCATAGACAAGTGCCAAGATTCTCTAT
66 CAGTTCATCCCTTTTTAATTTGGGTGGAGAGTCGTAAGTCATTGACAAGTGTCAAGATTCTCTGT
** * * *
73723 CTTCATGAAGAGATAGAAAATG-ACCGAATATGGAGTAAAAATGAAGAGTTTTAACCCTTCTCTC
131 CTTCATGAAGAGATAGAAAA-GAATTGAATATGGAGGAAAAATGAAGAGTTTGATCCCTTCTCTC
* *
73787 GATCTTAATCGAGACAC-TTATTAGT
195 GGTCTTAATCGAGAGACTTTATTAGT
73812 GAGATGTGTT
Statistics
Matches: 800, Mismatches: 109, Indels: 17
0.86 0.12 0.02
Matches are distributed among these distances:
348 17 0.02
349 774 0.97
350 9 0.01
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (349 bp):
GTGTTGCAACGAGGAGATGGTTTTGAGATGTGTTGATAAGAAAAATGGATCACAACGGTTAGAGG
CAGTTCATCCCTTTTTAATTTGGGTGGAGAGTCGTAAGTCATTGACAAGTGTCAAGATTCTCTGT
CTTCATGAAGAGATAGAAAAGAATTGAATATGGAGGAAAAATGAAGAGTTTGATCCCTTCTCTCG
GTCTTAATCGAGAGACTTTATTAGTACTGGTGTCGACTATAAGTTTATTATCATTACTTGTAGGT
TGATAGTCTTAGTAGATATGATCAACTAACAATAGATTTAACCAATGCTTGAAAGAACCTTGAGA
AAACCGTCATGCGCGATGGATCGT
Found at i:73963 original size:195 final size:196
Alignment explanation
Indices: 73616--74007 Score: 561
Period size: 195 Copynumber: 2.0 Consensus size: 196
73606 GAGATGGTTT
* *
73616 TGAGATATGTTGATAAGACAAATGGATCACAACGGTTAGAGGCAGTTCATCCCTTTTTAATTTGG
1 TGAGATATGTTGATAAGACAAACGGATCACAACGGTTAGAGGCAATTCATCCCTTTTTAATTTGG
* *
73681 GTGGAGAGTTGTAAGTCATAGACAAGTGCCAAGATTCTCTATCTTCATGAAGAGATAGAAAATGA
66 GTGGAGAGTCGTAAGTCATAGACAAGTGCCAAGATTCTCTATCTTCATGAAGAGATAGAAAAGGA
* * * * *
73746 CCGAATATGGAGTAAAAATGAAGAGTTTTAACCCTTCTCTCGATCTTAATCGAGACAC-TTATTA
131 CCGAATATGAAGGAAAAATGAAGAGTTTGAACCATTATCTCGATCTTAATCGAGACACTTTATTA
73810 G
196 G
* * * * *
73811 TGAGATGTGTTGATAAGACAAACGGATTACGATGGTTAGAGTCAATTCATCCCTTTTTAATTTGG
1 TGAGATATGTTGATAAGACAAACGGATCACAACGGTTAGAGGCAATTCATCCCTTTTTAATTTGG
* * * *
73876 GTGGAGAGTCGTAAGTCATTGACAAGTGTCAAGATTCTCTGTCTTCATGAAGAGATAGACAAGGA
66 GTGGAGAGTCGTAAGTCATAGACAAGTGCCAAGATTCTCTATCTTCATGAAGAGATAGAAAAGGA
** * * * *
73941 TTGAATATGAAGGAAGAATGAAGAGTTTGATCCATTATCTCGATTTTAATCGAGAGACTTTATTA
131 CCGAATATGAAGGAAAAATGAAGAGTTTGAACCATTATCTCGATCTTAATCGAGACACTTTATTA
74006 G
196 G
74007 T
1 T
74008 ACTGGTGACG
Statistics
Matches: 172, Mismatches: 24, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
195 164 0.95
196 8 0.05
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (196 bp):
TGAGATATGTTGATAAGACAAACGGATCACAACGGTTAGAGGCAATTCATCCCTTTTTAATTTGG
GTGGAGAGTCGTAAGTCATAGACAAGTGCCAAGATTCTCTATCTTCATGAAGAGATAGAAAAGGA
CCGAATATGAAGGAAAAATGAAGAGTTTGAACCATTATCTCGATCTTAATCGAGACACTTTATTA
G
Found at i:81801 original size:45 final size:45
Alignment explanation
Indices: 81752--81865 Score: 183
Period size: 45 Copynumber: 2.5 Consensus size: 45
81742 ATTCGATCAG
* * * * *
81752 ATTTATTTGTATATATTTTTTGTTCGAGTTATGATCTTTTGTCAA
1 ATTTATTCGTATTTATCTTTTGTTCGAGTTATGACCCTTTGTCAA
81797 ATTTATTCGTATTTATCTTTTGTTCGAGTTATGACCCTTTGTCAA
1 ATTTATTCGTATTTATCTTTTGTTCGAGTTATGACCCTTTGTCAA
81842 ATTTATTCGTATTTATCTTTTGTT
1 ATTTATTCGTATTTATCTTTTGTT
81866 TAATTATAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 64 1.00
ACGTcount: A:0.20, C:0.11, G:0.12, T:0.57
Consensus pattern (45 bp):
ATTTATTCGTATTTATCTTTTGTTCGAGTTATGACCCTTTGTCAA
Found at i:82906 original size:31 final size:31
Alignment explanation
Indices: 82871--82954 Score: 75
Period size: 35 Copynumber: 2.6 Consensus size: 31
82861 AACCTTTTTT
82871 ATATTTTTAATTTTGTAAA-AAAATTATATAA
1 ATATTTTTAATTTTGTAAAGAAAA-TATATAA
82902 ATATTATGAATTTAATTTT-TAAAGAAAATATATAA
1 ATA-T-T---TTTAATTTTGTAAAGAAAATATATAA
*
82937 AT-TTTTTACAATTTGTAA
1 ATATTTTTA-ATTTTGTAA
82955 TATTATACAA
Statistics
Matches: 44, Mismatches: 1, Indels: 16
0.72 0.02 0.26
Matches are distributed among these distances:
29 4 0.09
30 4 0.09
31 6 0.14
32 2 0.05
33 2 0.05
35 13 0.30
36 13 0.30
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (31 bp):
ATATTTTTAATTTTGTAAAGAAAATATATAA
Found at i:85944 original size:21 final size:21
Alignment explanation
Indices: 85919--85959 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
85909 TTGTGAACAG
*
85919 TGCTACAGTACATCGATGCAT
1 TGCTACAGTACACCGATGCAT
*
85940 TGCTACAGTGCACCGATGCA
1 TGCTACAGTACACCGATGCA
85960 CTAAAATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (21 bp):
TGCTACAGTACACCGATGCAT
Found at i:88163 original size:20 final size:20
Alignment explanation
Indices: 88134--88226 Score: 114
Period size: 20 Copynumber: 4.6 Consensus size: 20
88124 TTTCCCAATT
*
88134 CGCAATGCGAATAAGTAAAA
1 CGCAACGCGAATAAGTAAAA
** *
88154 CGCAACGCGAATTGGGAAAA
1 CGCAACGCGAATAAGTAAAA
*
88174 TCGCAACGCGAATAAGTAAAT
1 -CGCAACGCGAATAAGTAAAA
*
88195 CGCAACGCGAATAAGTAAAT
1 CGCAACGCGAATAAGTAAAA
*
88215 CACAACGCGAAT
1 CGCAACGCGAAT
88227 TGGGAAAATC
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 47 0.75
21 16 0.25
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.14
Consensus pattern (20 bp):
CGCAACGCGAATAAGTAAAA
Found at i:88259 original size:20 final size:19
Alignment explanation
Indices: 88234--88348 Score: 68
Period size: 20 Copynumber: 5.7 Consensus size: 19
88224 AATTGGGAAA
* *
88234 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATAAT-ACT
* *
88254 ATCGCAATGCGATAATACAAA
1 ATCGCAACGCGATAATAC--T
* *
88275 ATCGCAACGAGATATTTACT
1 ATCGCAACGCGATA-ATACT
* **
88295 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAAT-ACT
*
88315 TTCGCAACGCGATAATACAT
1 ATCGCAACGCGATAATAC-T
*
88335 AATCGCAATGCGAT
1 -ATCGCAACGCGAT
88349 TTTCAAAGCG
Statistics
Matches: 75, Mismatches: 14, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
19 5 0.07
20 44 0.59
21 23 0.31
22 3 0.04
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.25
Consensus pattern (19 bp):
ATCGCAACGCGATAATACT
Found at i:88540 original size:21 final size:21
Alignment explanation
Indices: 88514--88556 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
88504 CACTCTCTCA
88514 CCCATCTCCGACGAAATCCGT
1 CCCATCTCCGACGAAATCCGT
*
88535 CCCATCTCCGGCGAAATCCGT
1 CCCATCTCCGACGAAATCCGT
88556 C
1 C
88557 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.44, G:0.16, T:0.19
Consensus pattern (21 bp):
CCCATCTCCGACGAAATCCGT
Found at i:88858 original size:20 final size:20
Alignment explanation
Indices: 88819--88877 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
88809 GCGATTCTCT
**
88819 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
88839 CGTTGTGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
88859 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
88878 AGAAACTATT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:90216 original size:18 final size:18
Alignment explanation
Indices: 90195--90239 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
90185 TCCACTTCGG
*
90195 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
90213 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
90231 GAGCCATCA
1 GAGCCATCA
90240 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:90729 original size:20 final size:20
Alignment explanation
Indices: 90704--90749 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
90694 GAGTTTACTT
90704 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
90724 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
90744 TCGCAA
1 TCGCAA
90750 TGCGAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:90758 original size:19 final size:19
Alignment explanation
Indices: 90715--90773 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
90705 CGCAACACGA
*
90715 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAATGC-G
*
90735 AAATGGCTATCGCAATGCG
1 AAATGACTATCGCAATGCG
**
90754 AAATGAAAATCGCAATGCG
1 AAATGACTATCGCAATGCG
90773 A
1 A
90774 TTTTGTCGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (19 bp):
AAATGACTATCGCAATGCG
Found at i:90826 original size:20 final size:19
Alignment explanation
Indices: 90792--90847 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
90782 TTGCGATTTT
*
90792 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
90811 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
90831 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
90848 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:92706 original size:14 final size:14
Alignment explanation
Indices: 92687--92722 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
92677 GATGTTTAAT
92687 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
92701 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
92715 TGATTTGT
1 TGATTTGT
92723 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:92861 original size:19 final size:19
Alignment explanation
Indices: 92839--92887 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
92829 ATCGCAACGA
92839 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
92858 GAAAATTGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
92877 GAAAATCGCAA
1 GAAAATCGCAA
92888 CGAGGAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.49, C:0.14, G:0.20, T:0.16
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:92949 original size:20 final size:20
Alignment explanation
Indices: 92924--92961 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
92914 TTGCATTGCG
* *
92924 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCAATAGCC
92944 ATTTTCGCGTTGCAATAG
1 ATTTTCGCGTTGCAATAG
92962 TCAAATGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCAATAGCC
Found at i:94048 original size:23 final size:23
Alignment explanation
Indices: 93997--94049 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
93987 AGTATTCGAA
* * *
93997 ATTTGATCTTGGTCAATACCCGG
1 ATTTGATATTGGTCAATACACAG
*
94020 ACTTGATATTGGTCAATACACAG
1 ATTTGATATTGGTCAATACACAG
94043 ATTTGAT
1 ATTTGAT
94050 GATGTTTCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (23 bp):
ATTTGATATTGGTCAATACACAG
Done.