Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003351.1 Hibiscus syriacus cultivar Beakdansim tig00007056_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: 86209
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:3907 original size:21 final size:21
Alignment explanation
Indices: 3877--3951 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
3867 GATTTACATA
*
3877 TTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
** * *
3898 TTCGCGTTGCGATTTTTCCACG
1 TTCGCGTTGCGA-TAGTCGAAG
3920 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
3939 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
3952 TTATTCTAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
19 7 0.17
20 8 0.19
21 20 0.48
22 7 0.17
ACGTcount: A:0.16, C:0.21, G:0.28, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCGAAG
Found at i:3908 original size:41 final size:39
Alignment explanation
Indices: 3858--3976 Score: 130
Period size: 41 Copynumber: 2.9 Consensus size: 39
3848 ATTTCGACTA
* *
3858 TCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATTTACACATTCG--TTGCGATAGTCGAAGT
* *
3899 TCGCGTTGCGATTTTTCCACGTTCGTTGCGATAGTCGAAGT
1 TCGCGTTGCGA--TTTACACATTCGTTGCGATAGTCGAAGT
*
3940 TCGCGTTGCGATTTATTCTAAATTCGTTGCGATAGTC
1 TCGCGTTGCGATTTA--C-ACATTCGTTGCGATAGTC
3977 CAAAATCGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
39 3 0.05
41 38 0.58
42 16 0.24
43 9 0.14
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (39 bp):
TCGCGTTGCGATTTACACATTCGTTGCGATAGTCGAAGT
Found at i:4593 original size:16 final size:16
Alignment explanation
Indices: 4572--4607 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
4562 TCGTCTCGTC
4572 TCGTCTCGGGTCGTGG
1 TCGTCTCGGGTCGTGG
*
4588 TCGTCTTGGGTCGTGG
1 TCGTCTCGGGTCGTGG
4604 TCGT
1 TCGT
4608 GGTAATACGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.00, C:0.22, G:0.42, T:0.36
Consensus pattern (16 bp):
TCGTCTCGGGTCGTGG
Found at i:4749 original size:42 final size:41
Alignment explanation
Indices: 4690--4960 Score: 456
Period size: 42 Copynumber: 6.6 Consensus size: 41
4680 TACCACCAGT
* *
4690 CAACGCGAACTTGGACTATCGCAACGAATTTTGAATAAATCG
1 CAACGCGAACTTCGACTATCGCAACGAATTTGGAA-AAATCG
*
4732 CAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCA
1 CAACGCGAACTTCGACTATCGCAACGAATTTGGAA-AAATCG
4774 CAACGCGAACTTCGACTATCGCAACGAATTTGG-AAAATCG
1 CAACGCGAACTTCGACTATCGCAACGAATTTGGAAAAATCG
4814 CAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCG
1 CAACGCGAACTTCGACTATCGCAACGAATTTGGAA-AAATCG
4856 CAACGCGAACTTCGACTATCGCAACGAATTTGGAAAAATCG
1 CAACGCGAACTTCGACTATCGCAACGAATTTGGAAAAATCG
*
4897 CAACGCGAACTTCGACTATAGCAACGAATTTGG-AAAATCG
1 CAACGCGAACTTCGACTATCGCAACGAATTTGGAAAAATCG
*
4937 CAACGCGAACTTGGACTATCGCAA
1 CAACGCGAACTTCGACTATCGCAA
4961 TGCGAATATG
Statistics
Matches: 220, Mismatches: 7, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
40 67 0.30
41 40 0.18
42 113 0.51
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (41 bp):
CAACGCGAACTTCGACTATCGCAACGAATTTGGAAAAATCG
Found at i:4837 original size:82 final size:82
Alignment explanation
Indices: 4690--4960 Score: 456
Period size: 82 Copynumber: 3.3 Consensus size: 82
4680 TACCACCAGT
* *
4690 CAACGCGAACTTGGACTATCGCAACGAATTTTGAATAAATCGCAACGCGAACTTCGACTATCGCA
1 CAACGCGAACTTCGACTATCGCAACGAA-TTTGGA-AAATCGCAACGCGAACTTCGACTATCGCA
*
4755 ACGAATTTGGAATAAATCA
64 ACGAATTTGGAATAAATCG
4774 CAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAAC
1 CAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAAC
4839 GAATTTGGAATAAATCG
66 GAATTTGGAATAAATCG
*
4856 CAACGCGAACTTCGACTATCGCAACGAATTTGGAAAAATCGCAACGCGAACTTCGACTATAGCAA
1 CAACGCGAACTTCGACTATCGCAACGAATTTGG-AAAATCGCAACGCGAACTTCGACTATCGCAA
4921 CGAATTTGG-A-AAATCG
65 CGAATTTGGAATAAATCG
*
4937 CAACGCGAACTTGGACTATCGCAA
1 CAACGCGAACTTCGACTATCGCAA
4961 TGCGAATATG
Statistics
Matches: 181, Mismatches: 5, Indels: 5
0.95 0.03 0.03
Matches are distributed among these distances:
81 29 0.16
82 81 0.45
83 44 0.24
84 27 0.15
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (82 bp):
CAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAAC
GAATTTGGAATAAATCG
Found at i:5000 original size:21 final size:21
Alignment explanation
Indices: 4975--5025 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
4965 AATATGTAAA
4975 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
*
4996 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
*
5017 TCGCGTTGC
1 TCGCATTGC
5026 AAATCTGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:19257 original size:17 final size:16
Alignment explanation
Indices: 19235--19268 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19225 TTCCCAAAAC
19235 TTAAAAAGAAAAAAGAA
1 TTAAAAA-AAAAAAGAA
*
19252 TTAAAAACAAAAAGAA
1 TTAAAAAAAAAAAGAA
19268 T
1 T
19269 GTTCAGTTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.74, C:0.03, G:0.09, T:0.15
Consensus pattern (16 bp):
TTAAAAAAAAAAAGAA
Found at i:23261 original size:20 final size:20
Alignment explanation
Indices: 23232--23272 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
23222 TCAAAATCAG
*
23232 CAAAATTTCATTCACAATAC
1 CAAAACTTCATTCACAATAC
23252 CAAAACTTCATTCACAATAC
1 CAAAACTTCATTCACAATAC
23272 C
1 C
23273 TCAAAGTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.27
Consensus pattern (20 bp):
CAAAACTTCATTCACAATAC
Found at i:28916 original size:10 final size:10
Alignment explanation
Indices: 28901--28925 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
28891 TTCAAAAATA
28901 AAATATTTTT
1 AAATATTTTT
28911 AAATATTTTT
1 AAATATTTTT
28921 AAATA
1 AAATA
28926 AACTTCCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
AAATATTTTT
Found at i:32770 original size:15 final size:16
Alignment explanation
Indices: 32752--32807 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 16
32742 ATCTATTCTT
32752 TTATTAATT-ATTTAA
1 TTATTAATTAATTTAA
32767 TTATTAATTAATTT-A
1 TTATTAATTAATTTAA
* *
32782 TTA--AACTAAGTTAA
1 TTATTAATTAATTTAA
*
32796 TTATAAATTAAT
1 TTATTAATTAAT
32808 ATATATTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
13 7 0.21
14 4 0.12
15 13 0.39
16 9 0.27
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (16 bp):
TTATTAATTAATTTAA
Found at i:33720 original size:18 final size:17
Alignment explanation
Indices: 33687--33730 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
33677 CTCAAAAGTA
33687 AATATTATTTTAAATAAT
1 AATATT-TTTTAAATAAT
*
33705 TATATTTTTTACAATAAT
1 AATATTTTTTA-AATAAT
33723 AATATTTT
1 AATATTTT
33731 CACCTTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
AATATTTTTTAAATAAT
Found at i:38942 original size:47 final size:46
Alignment explanation
Indices: 38873--38997 Score: 155
Period size: 47 Copynumber: 2.6 Consensus size: 46
38863 TTACTTAGAT
*
38873 GACTTCTTTTTCCCAGGTTTGGACTTTTTCATA-CAGATTCTTTCTCA
1 GACTTCTTTTTCCCGGGTTTGGACTTTTTCATATCAGATTC-TT-TCA
*
38920 GACTT-TTTTTCCACGGGTTTGGACCTTTTCATACTTGCAGATTCTTTCA
1 GACTTCTTTTTCC-CGGGTTTGGACTTTTTCATA--T-CAGATTCTTTCA
*
38969 GACTTCTTTTTCCCGGTTTTGGACTTTTT
1 GACTTCTTTTTCCCGGGTTTGGACTTTTT
38998 AGTGTTCATC
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
46 7 0.10
47 23 0.34
49 22 0.32
50 9 0.13
51 7 0.10
ACGTcount: A:0.14, C:0.22, G:0.15, T:0.48
Consensus pattern (46 bp):
GACTTCTTTTTCCCGGGTTTGGACTTTTTCATATCAGATTCTTTCA
Found at i:52096 original size:15 final size:15
Alignment explanation
Indices: 52078--52107 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
52068 AAAACCATGT
52078 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
52093 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
52108 GAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:52114 original size:15 final size:15
Alignment explanation
Indices: 52081--52115 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
52071 ACCATGTTAG
* *
52081 ATAAAAAGGTAATAG
1 ATAAAAAGGTAAGAA
52096 ATAAAAAGGTAAGAA
1 ATAAAAAGGTAAGAA
52111 ATAAA
1 ATAAA
52116 TAAATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAAAGGTAAGAA
Found at i:52238 original size:28 final size:30
Alignment explanation
Indices: 52200--52273 Score: 82
Period size: 28 Copynumber: 2.5 Consensus size: 30
52190 TAAGTAAAAT
* *
52200 AAATATAAAAAATAAAGAAA-AAGAA-GAA-
1 AAATAAAAAAAATAAAGAAATAA-AACAAAC
*
52228 AAATAAAAAAAATATAGAAATAAAACAAAC
1 AAATAAAAAAAATAAAGAAATAAAACAAAC
*
52258 AAATAAAAAAAGTAAA
1 AAATAAAAAAAATAAA
52274 AATAATATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
28 20 0.53
29 4 0.11
30 14 0.37
ACGTcount: A:0.78, C:0.03, G:0.07, T:0.12
Consensus pattern (30 bp):
AAATAAAAAAAATAAAGAAATAAAACAAAC
Found at i:52249 original size:45 final size:43
Alignment explanation
Indices: 52200--52302 Score: 104
Period size: 45 Copynumber: 2.4 Consensus size: 43
52190 TAAGTAAAAT
52200 AAATATAAAAAATAAAGAAAAAGAAG-AAAAATAAAAAAAATATAG
1 AAATATAAAAAATAAAGAAAAA-AAGTAAAAAT--AAAAAATATAG
* * * * *
52245 AAATA-AAACAAACAAATAAAAAAAGTAAAAATAATATATATAT
1 AAATATAAA-AAATAAAGAAAAAAAGTAAAAATAAAAAATATAG
52288 AAA-ATAAAAAATAAA
1 AAATATAAAAAATAAA
52303 AAAGTAAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
42 7 0.14
43 14 0.29
44 6 0.12
45 22 0.45
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.17
Consensus pattern (43 bp):
AAATATAAAAAATAAAGAAAAAAAGTAAAAATAAAAAATATAG
Found at i:52252 original size:22 final size:21
Alignment explanation
Indices: 52227--52298 Score: 53
Period size: 19 Copynumber: 3.5 Consensus size: 21
52217 AAAAAGAAGA
52227 AAAATAAAAAAAATATAGAAAT
1 AAAATAAAAAAAATATA-AAAT
* *
52249 -AAA-ACAAACAA-ATAAAA-
1 AAAATAAAAAAAATATAAAAT
* * *
52266 AAAGTAAAAATAATATATATAT
1 AAAATAAAAAAAATATA-AAAT
52288 AAAATAAAAAA
1 AAAATAAAAAA
52299 TAAAAAAGTA
Statistics
Matches: 37, Mismatches: 8, Indels: 10
0.67 0.15 0.18
Matches are distributed among these distances:
18 5 0.14
19 9 0.24
20 9 0.24
21 5 0.14
22 9 0.24
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (21 bp):
AAAATAAAAAAAATATAAAAT
Found at i:52267 original size:37 final size:38
Alignment explanation
Indices: 52191--52310 Score: 115
Period size: 39 Copynumber: 3.2 Consensus size: 38
52181 ATAAAATAGT
* *
52191 AAGTAAAATAAATATA-AAA-AATAA-AGAAAAAGAAGAAA
1 AAGTAAAAAAAATATAGAAATAA-AACA-AAAAATAA-AAA
52229 AA-TAAAAAAAATATAGAAATAAAACAAACAAATAAAAA
1 AAGTAAAAAAAATATAGAAATAAAACAAA-AAATAAAAA
* * * *
52267 AAGTAAAAATAATATATATATAAAATAAAAAAT-AAAA
1 AAGTAAAAAAAATATAGAAATAAAACAAAAAATAAAAA
52304 AAGTAAA
1 AAGTAAA
52311 TATATATATA
Statistics
Matches: 71, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
37 23 0.32
38 18 0.25
39 30 0.42
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.17
Consensus pattern (38 bp):
AAGTAAAAAAAATATAGAAATAAAACAAAAAATAAAAA
Found at i:52290 original size:39 final size:37
Alignment explanation
Indices: 52226--52322 Score: 117
Period size: 39 Copynumber: 2.6 Consensus size: 37
52216 GAAAAAGAAG
* * *
52226 AAAAA-TAAAAAAAATATAGAAATAAAACAAACAAATAA
1 AAAAAGTAAAAATAATATATATATAAAACAAA-AAAT-A
*
52264 AAAAAGTAAAAATAATATATATATAAAATAAAAAATA
1 AAAAAGTAAAAATAATATATATATAAAACAAAAAATA
*
52301 AAAAAGTAAATAT-ATATATATA
1 AAAAAGTAAAAATAATATATATA
52323 AATTAATAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
36 9 0.17
37 13 0.25
38 9 0.17
39 22 0.42
ACGTcount: A:0.73, C:0.02, G:0.03, T:0.22
Consensus pattern (37 bp):
AAAAAGTAAAAATAATATATATATAAAACAAAAAATA
Found at i:52333 original size:30 final size:30
Alignment explanation
Indices: 52258--52325 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 30
52248 TAAAACAAAC
52258 AAATAAAAAA-AGTAAAAATAATATATATATA
1 AAATAAAAAATA--AAAAATAATATATATATA
52289 AAATAAAAAATAAAAAAGTAAATATATATATA
1 AAATAAAAAATAAAAAA-T-AATATATATATA
52321 TAAAT
1 -AAAT
52326 TAATAAAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
30 5 0.15
31 11 0.33
32 13 0.39
33 4 0.12
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (30 bp):
AAATAAAAAATAAAAAATAATATATATATA
Found at i:52351 original size:34 final size:34
Alignment explanation
Indices: 52235--52333 Score: 99
Period size: 34 Copynumber: 2.7 Consensus size: 34
52225 GAAAAATAAA
* * *
52235 AAAAATATAGAAATAAAACAAACAAATAAAAAAAGT
1 AAAAATATATATATAAAATAAA-AAAT-AAAAAAGT
52271 AAAAATAATATATATATAAAATAAAAAATAAAAAAGT
1 --AAA-AATATATATATAAAATAAAAAATAAAAAAGT
* *
52308 AAATATATATATATAAATTAATAAAA
1 AAAAATATATATATAAAATAA-AAAA
52334 CTGATAATAA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
34 16 0.30
35 7 0.13
37 8 0.15
38 7 0.13
39 16 0.30
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.23
Consensus pattern (34 bp):
AAAAATATATATATAAAATAAAAAATAAAAAAGT
Found at i:52423 original size:23 final size:22
Alignment explanation
Indices: 52366--52429 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 22
52356 ATATATATCT
52366 AAAAAAATATATAC-T-AAAGTA
1 AAAAAAATAT-TACATAAAAGTA
*
52387 AAAAAGAA-AATACATAAAATGTA
1 AAAAA-AATATTACATAAAA-GTA
52410 AAAAAAATATTACATGAAAA
1 AAAAAAATATTACAT-AAAA
52430 AAAAGAAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
20 3 0.09
21 7 0.20
22 7 0.20
23 14 0.40
24 4 0.11
ACGTcount: A:0.69, C:0.05, G:0.06, T:0.20
Consensus pattern (22 bp):
AAAAAAATATTACATAAAAGTA
Found at i:52794 original size:34 final size:34
Alignment explanation
Indices: 52751--52819 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
52741 GAATCCTAGC
52751 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
* *
52785 AAAATTCTATCCTATTTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
52819 A
1 A
52820 GTAGGACGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (34 bp):
AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
Found at i:53668 original size:105 final size:105
Alignment explanation
Indices: 53368--54199 Score: 1287
Period size: 105 Copynumber: 8.0 Consensus size: 105
53358 CATTGTTCCA
* * * * ** * * *
53368 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGTTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * * *
53433 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
53474 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
53534 AGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
53574 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTTAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
53639 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
53679 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
53744 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
53784 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
53849 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
53889 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* * * *
53954 AGCGGTCCATTCGTCATGAAGTTGAACTTACGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
53994 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTAAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
54059 AGCGGTCCCTTCGTCGTGAAGTTGAATTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
54099 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * *
54164 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
54200 CCTCGAGTGC
Statistics
Matches: 674, Mismatches: 46, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
100 82 0.12
101 1 0.00
102 4 0.01
103 4 0.01
104 3 0.00
105 504 0.75
106 76 0.11
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:55016 original size:65 final size:67
Alignment explanation
Indices: 54843--54998 Score: 199
Period size: 68 Copynumber: 2.3 Consensus size: 67
54833 AGATATCTGT
* * * * ** *
54843 TGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGAGT
54908 TTG
65 TTG
* *
54911 TGTTTCAAGAGTAACTGTCTCAAAGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAG-GTT
1 TGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
54975 T-
66 TG
*
54976 TGTTTCAAGGGAAACTGTCTCAA
1 TGTTTCAAGAGAAACTGTCTCAA
54999 GATAGACGAA
Statistics
Matches: 77, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
65 21 0.27
66 3 0.04
67 22 0.29
68 31 0.40
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.32
Consensus pattern (67 bp):
TGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
TG
Found at i:55026 original size:36 final size:35
Alignment explanation
Indices: 54975--55254 Score: 261
Period size: 36 Copynumber: 8.0 Consensus size: 35
54965 TTCAAAGGTT
* *
54975 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
55011 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
55046 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
55084 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
* *
55113 TTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
55148 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
55185 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
55220 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
55255 CTCTTCTAGT
Statistics
Matches: 201, Mismatches: 27, Indels: 32
0.77 0.10 0.12
Matches are distributed among these distances:
28 2 0.01
29 16 0.08
30 1 0.00
31 1 0.00
32 2 0.01
33 1 0.00
34 1 0.00
35 10 0.05
36 132 0.66
37 33 0.16
38 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:55085 original size:138 final size:137
Alignment explanation
Indices: 54923--55236 Score: 414
Period size: 138 Copynumber: 2.3 Consensus size: 137
54913 TTTCAAGAGT
* * * * *
54923 AACTGTCTCAAAGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGGTTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
* *
54988 AACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGT
66 AACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGT
55052 TCCAAAAGA
129 TCCAAAAGA
** * * * * *
55061 AACTGTCTCAAGGGAGACGGAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTTAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
* * * * *
55126 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTT
66 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
*
55191 CAAGAGA
131 CAAAAGA
*
55198 AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
55237 TGTCTCAAGA
Statistics
Matches: 150, Mismatches: 25, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
137 49 0.33
138 101 0.67
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (137 bp):
AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
CAAAAGA
Found at i:55192 original size:101 final size:103
Alignment explanation
Indices: 55011--55199 Score: 283
Period size: 102 Copynumber: 1.9 Consensus size: 103
55001 TAGACGAAAA
*
55011 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
*
55076 GACGGAATTTGTTTCAA-AGAAAACATATTCAAATATT
66 GACGAAATTTGTTTCAAGAGAAAACATATTCAAATATT
* * * * ** *
55113 TTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAATTTA-TTTCAAGGGAAACTGTCTCAAGATA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
55177 GACGAAATTTGTTTCAAGAGAAA
66 GACGAAATTTGTTTCAAGAGAAA
55200 CTGTCTCAAG
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 36 0.47
102 41 0.53
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (103 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
GACGAAATTTGTTTCAAGAGAAAACATATTCAAATATT
Found at i:55387 original size:35 final size:35
Alignment explanation
Indices: 55273--55391 Score: 100
Period size: 36 Copynumber: 3.3 Consensus size: 35
55263 GTGAAAACGG
*
55273 TCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAA
1 TCTCAAGTGAGACAAATC-TGTTTTAAGAAAAACAA
* * * * * *
55309 TCAT-GAGTGAAATAAATCT-TCTTTCGAGTAAAACAG
1 TC-TCAAGTGAGACAAATCTGT-TTT-AAGAAAAACAA
*
55345 TCCCAAGTGAGACAAAGTCTGTTTTAAG-AAAACAA
1 TCTCAAGTGAGACAAA-TCTGTTTTAAGAAAAACAA
55380 TCTCAAGTGAGA
1 TCTCAAGTGAGA
55392 TAATCATCTG
Statistics
Matches: 63, Mismatches: 14, Indels: 13
0.70 0.16 0.14
Matches are distributed among these distances:
34 1 0.02
35 21 0.33
36 33 0.52
37 7 0.11
38 1 0.02
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (35 bp):
TCTCAAGTGAGACAAATCTGTTTTAAGAAAAACAA
Found at i:55761 original size:18 final size:18
Alignment explanation
Indices: 55734--55769 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
55724 TGTTGAATCC
* *
55734 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
55752 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
55770 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:56209 original size:22 final size:22
Alignment explanation
Indices: 56183--56231 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
56173 TTGTGTTTGG
* *
56183 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
56205 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
56227 TCAAA
1 TCAAA
56232 AGATTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:56238 original size:22 final size:22
Alignment explanation
Indices: 56195--56238 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
56185 AAAGGTTTGG
* * *
56195 CATTTGATGCTCAAAGGTTTGA
1 CATTGGATGCTCAAAAGATTGA
56217 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGCTCAAAAGATTGA
56239 TGGGGTAGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGCTCAAAAGATTGA
Found at i:56886 original size:20 final size:20
Alignment explanation
Indices: 56859--56916 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
56849 CTTTTTGTCC
56859 CTTT-TTTTTTATTTTTGTT
1 CTTTCTTTTTTATTTTTGTT
* *
56878 CTTTCTTTTTTGTTCTTGTT
1 CTTTCTTTTTTATTTTTGTT
* *
56898 TTTTCCTTTTTTCTTTTTG
1 CTTT-CTTTTTTATTTTTG
56917 CCCTTTTGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 4 0.12
20 16 0.50
21 12 0.38
ACGTcount: A:0.02, C:0.12, G:0.07, T:0.79
Consensus pattern (20 bp):
CTTTCTTTTTTATTTTTGTT
Found at i:58057 original size:8 final size:8
Alignment explanation
Indices: 58041--58079 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
58031 AATGTAGATG
58041 AAAATGCA
1 AAAATGCA
*
58049 AAAAGGCA
1 AAAATGCA
58057 AAAATGC-
1 AAAATGCA
58064 AAAATGCA
1 AAAATGCA
*
58072 AGAATGCA
1 AAAATGCA
58080 TGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:58067 original size:15 final size:15
Alignment explanation
Indices: 58041--58079 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
58031 AATGTAGATG
58041 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
58057 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
58072 AGAATGCA
1 AAAATGCA
58080 TGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:60515 original size:15 final size:15
Alignment explanation
Indices: 60497--60526 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
60487 AAAACCATGT
60497 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
60512 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
60527 GAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:60533 original size:15 final size:15
Alignment explanation
Indices: 60500--60534 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
60490 ACCATGTTAG
* *
60500 ATAAAAAGGTAATAG
1 ATAAAAAGGTAAGAA
60515 ATAAAAAGGTAAGAA
1 ATAAAAAGGTAAGAA
60530 ATAAA
1 ATAAA
60535 TAAATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAAAGGTAAGAA
Found at i:60586 original size:20 final size:21
Alignment explanation
Indices: 60545--60586 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
60535 TAAATTAATT
*
60545 AAATTAAAATAAAGAGAAAAG
1 AAATTAAAATAAAAAGAAAAG
*
60566 AAATT-AAATAAAAAGATAAG
1 AAATTAAAATAAAAAGAAAAG
60586 A
1 A
60587 TAAAGAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (21 bp):
AAATTAAAATAAAAAGAAAAG
Found at i:60685 original size:28 final size:28
Alignment explanation
Indices: 60624--60687 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
60614 TAAAATAAAT
*
60624 ATAAAAAATAAAGAAAAAGAAGAAAAAG
1 ATAAAAAATAAAGAAAAAGAACAAAAAG
* *
60652 AAAAAAAATATAGAAATAA-AACAAATAA-
1 ATAAAAAATAAAGAAA-AAGAACAAA-AAG
60680 ATAAAAAA
1 ATAAAAAA
60688 AGTAAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.80, C:0.02, G:0.08, T:0.11
Consensus pattern (28 bp):
ATAAAAAATAAAGAAAAAGAACAAAAAG
Found at i:60695 original size:9 final size:8
Alignment explanation
Indices: 60614--60732 Score: 51
Period size: 9 Copynumber: 13.5 Consensus size: 8
60604 AAATAGTAAG
60614 TAAAATAAA
1 TAAAA-AAA
60623 TATAAAAAA
1 TA-AAAAAA
60632 TAAAGAAAAA
1 T-AA-AAAAA
*
60642 GAAGAAAAA
1 TAA-AAAAA
*
60651 GAAAAAAAA
1 -TAAAAAAA
* *
60660 TATAGAAA
1 TAAAAAAA
60668 TAAAACAAA
1 TAAAA-AAA
60677 TAAATAAAA
1 TAAA-AAAA
*
60686 AAAGTAAAAA
1 TAA--AAAAA
* *
60696 T-AATATA
1 TAAAAAAA
*
60703 TATATAAAA
1 TA-AAAAAA
60712 TAAAAAAA
1 TAAAAAAA
60720 TAAAAAAA
1 TAAAAAAA
60728 GTAAA
1 -TAAA
60733 TATATATATA
Statistics
Matches: 84, Mismatches: 15, Indels: 22
0.69 0.12 0.18
Matches are distributed among these distances:
7 4 0.05
8 21 0.25
9 42 0.50
10 16 0.19
11 1 0.01
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.17
Consensus pattern (8 bp):
TAAAAAAA
Found at i:60710 original size:30 final size:29
Alignment explanation
Indices: 60676--60756 Score: 81
Period size: 31 Copynumber: 2.7 Consensus size: 29
60666 AATAAAACAA
* * *
60676 ATAAATAAAAAAAGTAAAAATAATATATAT
1 ATAAATAAAAAAA-TAAAAAAAGTAAATAT
60706 ATAAAATAAAAAAATAAAAAAAGTAAATAT
1 ATA-AATAAAAAAATAAAAAAAGTAAATAT
**
60736 ATATATATAAATTAATAAAAA
1 ATA-A-ATAAAAAAATAAAAA
60757 TGATATTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
30 20 0.47
31 23 0.53
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (29 bp):
ATAAATAAAAAAATAAAAAAAGTAAATAT
Found at i:60710 original size:39 final size:39
Alignment explanation
Indices: 60637--60744 Score: 130
Period size: 39 Copynumber: 2.8 Consensus size: 39
60627 AAAAATAAAG
* * * *
60637 AAAAAGAAGAAAAAG-AAAAAAAATATAGAAATAAAACAA
1 AAAAATAA-AAAAAGTAAAAATAATATATATATAAAACAA
* *
60676 ATAAATAAAAAAAGTAAAAATAATATATATATAAAATAA
1 AAAAATAAAAAAAGTAAAAATAATATATATATAAAACAA
*
60715 AAAAATAAAAAAAGTAAATAT-ATATATATA
1 AAAAATAAAAAAAGTAAAAATAATATATATA
60745 AATTAATAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
38 15 0.25
39 45 0.75
ACGTcount: A:0.74, C:0.01, G:0.06, T:0.19
Consensus pattern (39 bp):
AAAAATAAAAAAAGTAAAAATAATATATATATAAAACAA
Found at i:60753 original size:39 final size:40
Alignment explanation
Indices: 60678--60805 Score: 133
Period size: 39 Copynumber: 3.2 Consensus size: 40
60668 TAAAACAAAT
*
60678 AAATAAAAAAAGTAAAAATAATATATATATAA--AATAAAA
1 AAATAAAAAAAGTAAATAT-ATATATATATAATTAATAAAA
60717 AAATAAAAAAAGTAAATATATATATATA-AATTAATAAAA
1 AAATAAAAAAAGTAAATATATATATATATAATTAATAAAA
* * *
60756 ATGATATTAAAAA-TAATATATTTATATATATAATCT-A-AAAA
1 A-AATA-AAAAAAGTAA-ATATATATATATATAAT-TAATAAAA
60797 AAATAAAAA
1 AAATAAAAA
60806 TATATACTAA
Statistics
Matches: 76, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
37 2 0.03
38 9 0.12
39 29 0.38
40 9 0.12
41 22 0.29
42 4 0.05
43 1 0.01
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (40 bp):
AAATAAAAAAAGTAAATATATATATATATAATTAATAAAA
Found at i:60770 original size:36 final size:34
Alignment explanation
Indices: 60674--60811 Score: 100
Period size: 37 Copynumber: 3.8 Consensus size: 34
60664 GAAATAAAAC
*
60674 AAATAAATAAAA-AAAGTAAAAATAATATATATATA
1 AAATAAA-AAAATAAAATAAAAAT-ATATATATATA
*
60709 AAATAAAAAAATAAAAAAAGTAAATATATATATATA
1 AAATAAAAAAATAAAATAA--AAATATATATATATA
* * * *
60745 AATTAATAAAAATGATATTAAAAATAATATATTTATA
1 AAATAA-AAAAAT-AAAATAAAAAT-ATATATATATA
* *
60782 TATATAATCTAAAA-AAAATAAAAATATATA
1 -AAATAA--AAAAATAAAATAAAAATATATA
60812 CTAAAGTAAA
Statistics
Matches: 82, Mismatches: 13, Indels: 15
0.75 0.12 0.14
Matches are distributed among these distances:
34 4 0.05
35 12 0.15
36 25 0.30
37 29 0.35
38 8 0.10
39 4 0.05
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (34 bp):
AAATAAAAAAATAAAATAAAAATATATATATATA
Found at i:60856 original size:23 final size:22
Alignment explanation
Indices: 60801--60862 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
60791 TAAAAAAAAT
60801 AAAAATATATAC-T-AAAGTAAA
1 AAAAATAT-TACATAAAAGTAAA
*
60822 AAAGAA-AATACATAAAATGTAAA
1 AAA-AATATTACATAAAA-GTAAA
60845 AAAAATATTACATGAAAA
1 AAAAATATTACAT-AAAA
60863 AAAAAGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
20 3 0.09
21 5 0.15
22 7 0.21
23 14 0.42
24 4 0.12
ACGTcount: A:0.68, C:0.05, G:0.06, T:0.21
Consensus pattern (22 bp):
AAAAATATTACATAAAAGTAAA
Found at i:61232 original size:34 final size:34
Alignment explanation
Indices: 61189--61257 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
61179 GAATCCTAGC
61189 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
*
61223 AAAATTCTATCATATTTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
61257 A
1 A
61258 GTAGGACGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (34 bp):
AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
Found at i:71164 original size:17 final size:16
Alignment explanation
Indices: 71142--71177 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
71132 TCCACTCTCC
71142 TCATTTATCTTCTCATT
1 TCATTTATCTT-TCATT
*
71159 TCATTTTTCTTTCATT
1 TCATTTATCTTTCATT
71175 TCA
1 TCA
71178 ACCAAAGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.17, C:0.22, G:0.00, T:0.61
Consensus pattern (16 bp):
TCATTTATCTTTCATT
Found at i:76251 original size:24 final size:25
Alignment explanation
Indices: 76224--76283 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 25
76214 TAATAAAAAA
76224 ATTAACTTAATAAATAT-TTTT-TGT
1 ATTAACTTAATAAATATGTTTTAT-T
*
76248 ATTAGA-TTACTAAATATGTTTTATT
1 ATTA-ACTTAATAAATATGTTTTATT
76273 ATTAACTTAAT
1 ATTAACTTAAT
76284 TCAAAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
24 15 0.50
25 14 0.47
26 1 0.03
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (25 bp):
ATTAACTTAATAAATATGTTTTATT
Found at i:76448 original size:27 final size:27
Alignment explanation
Indices: 76418--76479 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
76408 CATAACATAT
76418 ATTTTTAAATAAAAATAAAAATAAAAC
1 ATTTTTAAATAAAAATAAAAATAAAAC
* * * *
76445 ATTTTTAAATTAAATTAATAATAAAAT
1 ATTTTTAAATAAAAATAAAAATAAAAC
*
76472 ATATTTAA
1 ATTTTTAA
76480 TAAGTTAGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (27 bp):
ATTTTTAAATAAAAATAAAAATAAAAC
Found at i:83517 original size:53 final size:53
Alignment explanation
Indices: 83459--83564 Score: 158
Period size: 53 Copynumber: 2.0 Consensus size: 53
83449 TGTACTCGGT
* * *
83459 TCATTTATATACACAAATAAATTTGTTTGAAAGTTCGTTTATTAACTCGTTTA
1 TCATTTATATACACAAATAAACTTGTTTAAAAATTCGTTTATTAACTCGTTTA
* * *
83512 TCATTTATGTACACGAATAAACTTGTTTAAAAATTCGTTTATTGACTCGTTTA
1 TCATTTATATACACAAATAAACTTGTTTAAAAATTCGTTTATTAACTCGTTTA
83565 CTCAGTTCTC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.44
Consensus pattern (53 bp):
TCATTTATATACACAAATAAACTTGTTTAAAAATTCGTTTATTAACTCGTTTA
Done.