Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001940.1 Hibiscus syriacus cultivar Beakdansim tig00003931_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: 114805
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1314 original size:2 final size:2
Alignment explanation
Indices: 1301--1347 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1291 CAGCTTAAGC
*
1301 TA TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1343 TA TA T
1 TA TA T
1348 CAATGGCTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4910 original size:64 final size:66
Alignment explanation
Indices: 4704--4913 Score: 202
Period size: 65 Copynumber: 3.2 Consensus size: 66
4694 TTTTTCAGAG
* * * **
4704 TGATGCACCGATGCACCA-ATCCATGCATCAATGCAC-CATGAATTAAATTG--AACATCGAATG
1 TGATGCATCGATGCACCATA-CCATGCACCAATGCACTCA-GGATTTTA-TGAAAACATCGAATG
4765 CATT
63 CATT
* * *
4769 TCATGCATCGATGCA-CATACCATGCACCAATGCACTGAGGATTTTATGAAAACATTGAATGCAT
1 TGATGCATCGATGCACCATACCATGCACCAATGCACTCAGGATTTTATGAAAACATCGAATGCAT
4833 T
66 T
* * * * *
4834 TGATGCATCGATGCACCA-GCCATGCATCGATGCACTCTGGCTATTT-T-AAAACATCGAATGCA
1 TGATGCATCGATGCACCATACCATGCACCAATGCACTCAGGAT-TTTATGAAAACATCGAATGCA
*
4896 CT
65 TT
4898 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
4914 TCTTAGTGCA
Statistics
Matches: 122, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
63 2 0.02
64 53 0.43
65 62 0.51
66 5 0.04
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (66 bp):
TGATGCATCGATGCACCATACCATGCACCAATGCACTCAGGATTTTATGAAAACATCGAATGCAT
T
Found at i:4913 original size:17 final size:19
Alignment explanation
Indices: 4885--4933 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
4875 TATTTTAAAA
4885 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
4903 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
4922 CACCGATGCACT
1 CATCGATGCACT
4934 GAGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:4929 original size:64 final size:63
Alignment explanation
Indices: 4754--4933 Score: 179
Period size: 65 Copynumber: 2.8 Consensus size: 63
4744 AATTAAATTG
* * *
4754 AACATCGAATGCATTTCATGCATCGATGCACATACCA-TGCACCAATGCACTGAGGATTTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCAC-T--CAGTGCACCGATGCACTCAGGATTTTATGA
4818 A
63 A
* * * *
4819 AACATTGAATGCATTTGATGCATCGATGCAC-CAGCCATGCATCGATGCACTCTGGCTATTT-T-
1 AACATCGAATGCATTTGATGCATCGATGCACTCAG---TGCACCGATGCACTCAGGAT-TTTATG
4881 AA
62 AA
*
4883 AACATCGAATGCACTTGATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTGATGCATCGATGCACTC--AGTGCACCGATGCACT
4934 GAGAGTCCAA
Statistics
Matches: 97, Mismatches: 10, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
61 2 0.02
64 44 0.45
65 46 0.47
66 3 0.03
67 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCAGTGCACCGATGCACTCAGGATTTTATGAA
Found at i:10757 original size:24 final size:23
Alignment explanation
Indices: 10730--10812 Score: 82
Period size: 23 Copynumber: 3.7 Consensus size: 23
10720 TCACTTAACA
10730 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCATCCC-TTGAAT
* *
10754 GTGCATCGATTCAT--CTTG-CT
1 GTGCATCGATGCATCCCTTGAAT
* *
10774 GATGCACCGATGCATGCCTTGAAT
1 G-TGCATCGATGCATCCCTTGAAT
*
10798 GTGCATCGATTCATC
1 GTGCATCGATGCATC
10813 TTGCTTATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
20 2 0.04
21 14 0.30
22 1 0.02
23 15 0.32
24 15 0.32
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.33
Consensus pattern (23 bp):
GTGCATCGATGCATCCCTTGAAT
Found at i:10784 original size:21 final size:20
Alignment explanation
Indices: 10753--10817 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 20
10743 TCCCTTTGAA
10753 TGTGCATCGATTCATCTTGC
1 TGTGCATCGATTCATCTTGC
* * *
10773 TGATGCACCGATGCATGCCTTGAA
1 TG-TGCATCGATTCAT--CTTG-C
10797 TGTGCATCGATTCATCTTGC
1 TGTGCATCGATTCATCTTGC
10817 T
1 T
10818 TATTTTCTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
20 3 0.09
21 15 0.43
23 15 0.43
24 2 0.06
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (20 bp):
TGTGCATCGATTCATCTTGC
Found at i:10796 original size:44 final size:45
Alignment explanation
Indices: 10731--10817 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 45
10721 CACTTAACAG
*
10731 TGCATCGATGCATCCCTTTGAATGTGCATCGATTCATCTTGCTGA
1 TGCACCGATGCATCCCTTTGAATGTGCATCGATTCATCTTGCTGA
*
10776 TGCACCGATGCATGCC-TTGAATGTGCATCGATTCATCTTGCT
1 TGCACCGATGCATCCCTTTGAATGTGCATCGATTCATCTTGCT
10818 TATTTTCTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 26 0.65
45 14 0.35
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.34
Consensus pattern (45 bp):
TGCACCGATGCATCCCTTTGAATGTGCATCGATTCATCTTGCTGA
Found at i:12365 original size:21 final size:21
Alignment explanation
Indices: 12323--12375 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
12313 ACTCCGGGAG
* * *
12323 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCTCGAGCTCCTC
*
12344 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCTCGAGCTCCTC
*
12365 CT-CCTCCTCTC
1 CTAGCTCCTCTC
12376 CGGCTCCGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.08, C:0.47, G:0.13, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCTCGAGCTCCTC
Found at i:15369 original size:13 final size:13
Alignment explanation
Indices: 15340--15373 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
15330 GGGGAGTAAT
*
15340 TTTTCAAAATTGA
1 TTTTCAAAAATGA
15353 -TTTCAAAAATGA
1 TTTTCAAAAATGA
15365 TTTTCAAAA
1 TTTTCAAAA
15374 CGAAAATCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (13 bp):
TTTTCAAAAATGA
Found at i:15521 original size:16 final size:18
Alignment explanation
Indices: 15486--15522 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
15476 TTAAGATTTT
15486 ATATTCGATTTCAAAAATA
1 ATATTCGATTTC-AAAATA
15505 ATATTCGA-TTC-AAATA
1 ATATTCGATTTCAAAATA
15521 AT
1 AT
15523 CGAATATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.39
18 3 0.17
19 8 0.44
ACGTcount: A:0.46, C:0.11, G:0.05, T:0.38
Consensus pattern (18 bp):
ATATTCGATTTCAAAATA
Found at i:20767 original size:36 final size:36
Alignment explanation
Indices: 20720--20789 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
20710 GGTGTGATTC
** *
20720 TGCTTCACTACTCTTTTGTGAAGGCTTAAGATGGTT
1 TGCTTCACTACTCTTCCGTGAAGGCATAAGATGGTT
20756 TGCTTCACTACTCTTCCGTGAAGGCATAAGATGG
1 TGCTTCACTACTCTTCCGTGAAGGCATAAGATGG
20790 CCTGGGGGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (36 bp):
TGCTTCACTACTCTTCCGTGAAGGCATAAGATGGTT
Found at i:20987 original size:42 final size:42
Alignment explanation
Indices: 20940--21029 Score: 135
Period size: 42 Copynumber: 2.1 Consensus size: 42
20930 GAAGGCTTAA
* **
20940 GATGGCCCGAAAGACTTAATCATCATGCTCGTAAGGTTTACT
1 GATGGCCCGAAAGACTTAATCATCATGCTCGAAAGACTTACT
* *
20982 GATGGCCTGAAAGACTTCATCATCATGCTCGAAAGACTTACT
1 GATGGCCCGAAAGACTTAATCATCATGCTCGAAAGACTTACT
21024 GATGGC
1 GATGGC
21030 ACTTACTGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (42 bp):
GATGGCCCGAAAGACTTAATCATCATGCTCGAAAGACTTACT
Found at i:21035 original size:13 final size:13
Alignment explanation
Indices: 21017--21041 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21007 TGCTCGAAAG
21017 ACTTACTGATGGC
1 ACTTACTGATGGC
21030 ACTTACTGATGG
1 ACTTACTGATGG
21042 GATTGCTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:24384 original size:23 final size:22
Alignment explanation
Indices: 24336--24384 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
24326 CCAGAATGTC
24336 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
24357 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
24380 AAGGA
1 AAGGA
24385 AAATTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:25171 original size:97 final size:97
Alignment explanation
Indices: 25060--25254 Score: 365
Period size: 97 Copynumber: 2.0 Consensus size: 97
25050 TCGAGGGTCT
25060 ATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACT
1 ATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACT
*
25125 TGAT-CCTTGGCATATGTATATGATTCTTAAGG
66 TGATCCCTAGG-ATATGTATATGATTCTTAAGG
25157 ATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACT
1 ATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACT
25222 TGATCCCTAGGATATGTATATGATTCTTAAGG
66 TGATCCCTAGGATATGTATATGATTCTTAAGG
25254 A
1 A
25255 ATGATATGTG
Statistics
Matches: 96, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
97 91 0.95
98 5 0.05
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (97 bp):
ATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACT
TGATCCCTAGGATATGTATATGATTCTTAAGG
Found at i:25320 original size:23 final size:23
Alignment explanation
Indices: 25277--25331 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
25267 CCTTATGGAC
*
25277 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
*
25301 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
25324 ATTATATG
1 ATTATATG
25332 AGCTGTGGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 25 0.86
24 4 0.14
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:32566 original size:16 final size:18
Alignment explanation
Indices: 32534--32573 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
32524 GGAAACAAGG
32534 TAAAATGAAACATATGAC
1 TAAAATGAAACATATGAC
32552 TAAAAT-AAA-ATATGAC
1 TAAAATGAAACATATGAC
*
32568 CAAAAT
1 TAAAAT
32574 TAAGGGAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.57
17 3 0.14
18 6 0.29
ACGTcount: A:0.60, C:0.10, G:0.07, T:0.23
Consensus pattern (18 bp):
TAAAATGAAACATATGAC
Found at i:34695 original size:34 final size:34
Alignment explanation
Indices: 34647--34713 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
34637 TTAAGACTGA
34647 TTATTTGATTGCTTGCCT-TCTCAAATGACCAGTG
1 TTATTTGATTGCTTGCCTCT-TCAAATGACCAGTG
*
34681 TTATTTG-TTGGCTTGCCTCTTCAAATGATCAGT
1 TTATTTGATT-GCTTGCCTCTTCAAATGACCAGT
34714 TTCAATAAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 2 0.07
34 27 0.90
35 1 0.03
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.43
Consensus pattern (34 bp):
TTATTTGATTGCTTGCCTCTTCAAATGACCAGTG
Found at i:37456 original size:185 final size:184
Alignment explanation
Indices: 37123--38075 Score: 947
Period size: 185 Copynumber: 5.1 Consensus size: 184
37113 TTTTTTTATT
* * * * * *
37123 AAATCGATTGCA-CCTAAAATGTTGCCAGAG-TTAAGATGAT-GGGGTTCTGAATTTCTCACGAT
1 AAATCGATTG-AGCCTAAAATGTTACCAGAGTTTAAGCTGATAGGGATTTTCAATTTCCCACGAT
*
37185 AACAAAATAAGTTAAAATAAAAGTTGTTATGAATATCTATAAGAAATCAGGTTGCACCCAAT-AA
65 AACAAAATAAGTTAAAATAAAA-ATGTTATGAATATCTATAAGAAATCAGGTTGCACCC-ATGAA
* * * * * *
37249 T-TCTATGGTCGCCAATAAAGTAGGTTGTGATATAGAATGTTAGTTTTATGTCTAATA
128 TGT-TATGGTCGCTAAGAAAGTAGGTTGTGATCTGGAATGTTAATTTTATGTTTAATA
* * * *
37306 AAATCGATTGAGCCTGAAATGTTACCAGAGTTTAAGCTAATATGGTTTTTCAATTTCCCACGATA
1 AAATCGATTGAGCCTAAAATGTTACCAGAGTTTAAGCTGATAGGGATTTTCAATTTCCCACGATA
* * * ** * *
37371 ACAAAATAAGTTAAAATCAAAACTGTTATGAATATCTATAA-AAATTAAGTTGTGCTCATTAATG
66 ACAAAATAAGTTAAAAT-AAAAATGTTATGAATATCTATAAGAAATCAGGTTGCACCCATGAATG
** * *
37435 TTATAGGTCGCTAAGAAAGTAGGTTACGATCTGAAATGTTAATTTTATGTTTGATA
130 TTAT-GGTCGCTAAGAAAGTAGGTTGTGATCTGGAATGTTAATTTTATGTTTAATA
* * * ** * ** * *
37491 AAATTGATTGTGCCTAAAATGTTAACAGAGTTTAATTTGATAGGGATTTTGAATTTCTAACAAAA
1 AAATCGATTGAGCCTAAAATGTTACCAGAGTTTAAGCTGATAGGGATTTTCAATTTCCCACGATA
* * * * * * **
37556 ATAAATTAAGTTAAATTAAAAATATTATGAATATCTAT-AGAATTCAGGTTACGTCCATGAATGT
66 ACAAAATAAGTTAAAATAAAAATGTTATGAATATCTATAAGAAATCAGGTTGCACCCATGAATGT
* * *
37620 TATGGGTTGCTAAGAAAGTAGGTTGTGATCTGGAATGTTAATTTTGTGTTTGATA
131 TAT-GGTCGCTAAGAAAGTAGGTTGTGATCTGGAATGTTAATTTTATGTTTAATA
* * * * * * *
37675 AAATCAACT-ATGCCTAAAATGTTACTAGAGTTCAAGCTGAT-GGGACTTTCAAATTTCACACAA
1 AAATCGATTGA-GCCTAAAATGTTACCAGAGTTTAAGCTGATAGGGATTTTC-AATTTCCCACGA
* * *
37738 TAACAAACTAAGTTAAAATAAAAATGTTATGAACATCTATAAGAAATCAGGTTGAACCCATGAAT
64 TAACAAAATAAGTTAAAATAAAAATGTTATGAATATCTATAAGAAATCAGGTTGCACCCATGAAT
** * * * *
37803 GTTATGTGTCATTAAGAAAGTAGGTTGTGATTTGGAATGTTAGTATTATATTTAATA
129 GTTATG-GTCGCTAAGAAAGTAGGTTGTGATCTGGAATGTTAATTTTATGTTTAATA
* * * * * *
37860 AAATCGGTTGCGCCTAAAATGTTATCAGAGTTTAAGTTGAT-GAGGCTTTTGAATTTCCCACGAT
1 AAATCGATTGAGCCTAAAATGTTACCAGAGTTTAAGCTGATAG-GGATTTTCAATTTCCCACGAT
* * *
37924 AACAAAATAAGTTAAAATAAAAAAAAATGTTATGAATATCTATAAGAAATCATGTTGCGCCCATA
65 AACAAAATAAGTTAAAAT----AAAAATGTTATGAATATCTATAAGAAATCAGGTTGCACCCATG
* * ** *
37989 AATGTTATGGGTCGCTAAAAAAGTAGGATAAGATTTGGAATGTTAATTTTATGTTTAATA
126 AATGTTAT-GGTCGCTAAGAAAGTAGGTTGTGATCTGGAATGTTAATTTTATGTTTAATA
* *
38049 AAATCGGTTGCA-CCTAAAATATTACCA
1 AAATCGATTG-AGCCTAAAATGTTACCA
38076 CAATAATAAA
Statistics
Matches: 628, Mismatches: 122, Indels: 34
0.80 0.16 0.04
Matches are distributed among these distances:
182 1 0.00
183 36 0.06
184 185 0.29
185 286 0.46
186 9 0.01
189 110 0.18
190 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (184 bp):
AAATCGATTGAGCCTAAAATGTTACCAGAGTTTAAGCTGATAGGGATTTTCAATTTCCCACGATA
ACAAAATAAGTTAAAATAAAAATGTTATGAATATCTATAAGAAATCAGGTTGCACCCATGAATGT
TATGGTCGCTAAGAAAGTAGGTTGTGATCTGGAATGTTAATTTTATGTTTAATA
Found at i:37821 original size:369 final size:368
Alignment explanation
Indices: 37123--38053 Score: 1032
Period size: 369 Copynumber: 2.5 Consensus size: 368
37113 TTTTTTTATT
* ** * * *
37123 AAATCGATTGCACCTAAAATGTTGCCAGAG-TTAAGATGATGGGGTTCTGAATTTCTCACGATAA
1 AAATCGATTGCGCCTAAAATGTTAACAGAGTTTAAGTTGATGGGATTTTGAATTTCTCACGATAA
* * *
37187 CAAAATAAGTTAAAATAAAAGTTGTTATGAATATCTATAAGAAATCAGGTTGCACCCAATAAT-T
66 CAAAATAAGTTAAATTAAAA-ATGTTATGAATATCTATAAGAAATCAGGTTGCGCCC-ATAATGT
* * * * * * *
37251 CTAT-GGTCGCCAATAAAGTAGGTTGTGATATAGAATGTTAGTTTTATGTCTAATAAAATCGATT
129 -TATGGGTCGCTAAAAAAGTAGGTTGTGATATGGAATGTTAATTTTATGTTTAATAAAATCAACT
* * * ** * *
37315 GAGCCTGAAATGTTACCAGAGTTTAAGCTAATATGGTTTTTCAATTTCCCACGATAACAAAATAA
193 GAGCCTAAAATGTTACCAGAGTTCAAGCTAATAGGGACTTTCAATTTCACACAATAACAAAATAA
* * * ** * * *
37380 GTTAAAATCAAAACTGTTATGAATATCTATAAAAATTAAGTTGTGCTCATTAATGTTATAGGTCG
258 GTTAAAATCAAAAATGTTATGAACATCTATAAAAATCAAGTTGAACCCATGAATGTTATAGGTCA
* * *
37445 CTAAGAAAGTAGGTTACGATCTGAAATGTTAATTTTATGTTTGATA
323 CTAAGAAAGTAGGTTACGATCTGAAATGTTAATATTATATTTAATA
* * * * * *
37491 AAATTGATTGTGCCTAAAATGTTAACAGAGTTTAATTTGATAGGGATTTTGAATTTCTAACAAAA
1 AAATCGATTGCGCCTAAAATGTTAACAGAGTTTAAGTTGAT-GGGATTTTGAATTTCTCACGATA
* * * * * *
37556 ATAAATTAAGTTAAATTAAAAATATTATGAATATCTAT-AGAATTCAGGTTACGTCCATGAATGT
65 ACAAAATAAGTTAAATTAAAAATGTTATGAATATCTATAAGAAATCAGGTTGCGCCCAT-AATGT
* * * * *
37620 TATGGGTTGCTAAGAAAGTAGGTTGTGATCTGGAATGTTAATTTTGTGTTTGATAAAATCAACT-
129 TATGGGTCGCTAAAAAAGTAGGTTGTGATATGGAATGTTAATTTTATGTTTAATAAAATCAACTG
* * *
37684 ATGCCTAAAATGTTACTAGAGTTCAAGCTGAT-GGGACTTTCAAATTTCACACAATAACAAACTA
194 A-GCCTAAAATGTTACCAGAGTTCAAGCTAATAGGGACTTTC-AATTTCACACAATAACAAAATA
*
37748 AGTTAAAAT-AAAAATGTTATGAACATCTATAAGAAATCAGGTTGAACCCATGAATGTTAT-GTG
257 AGTTAAAATCAAAAATGTTATGAACATCTATAA-AAATCAAGTTGAACCCATGAATGTTATAG-G
* ** * * *
37811 TCATTAAGAAAGTAGGTTGTGATTTGGAATGTTAGTATTATATTTAATA
320 TCACTAAGAAAGTAGGTTACGATCTGAAATGTTAATATTATATTTAATA
* * * *
37860 AAATCGGTTGCGCCTAAAATGTTATCAGAGTTTAAGTTGATGAGGCTTTTGAATTTCCCACGATA
1 AAATCGATTGCGCCTAAAATGTTAACAGAGTTTAAGTTGATG-GGATTTTGAATTTCTCACGATA
* *
37925 ACAAAATAAGTTAAAATAAAAAAAAATGTTATGAATATCTATAAGAAATCATGTTGCGCCCATAA
65 ACAAAATAAGTT-AAAT---TAAAAATGTTATGAATATCTATAAGAAATCAGGTTGCGCCCAT-A
* ** *
37990 ATGTTATGGGTCGCTAAAAAAGTAGGATAAGATTTGGAATGTTAATTTTATGTTTAATAAAATC
125 ATGTTATGGGTCGCTAAAAAAGTAGGTTGTGATATGGAATGTTAATTTTATGTTTAATAAAATC
38054 GGTTGCACCT
Statistics
Matches: 461, Mismatches: 87, Indels: 24
0.81 0.15 0.04
Matches are distributed among these distances:
367 2 0.00
368 75 0.16
369 251 0.54
370 40 0.09
373 20 0.04
374 73 0.16
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (368 bp):
AAATCGATTGCGCCTAAAATGTTAACAGAGTTTAAGTTGATGGGATTTTGAATTTCTCACGATAA
CAAAATAAGTTAAATTAAAAATGTTATGAATATCTATAAGAAATCAGGTTGCGCCCATAATGTTA
TGGGTCGCTAAAAAAGTAGGTTGTGATATGGAATGTTAATTTTATGTTTAATAAAATCAACTGAG
CCTAAAATGTTACCAGAGTTCAAGCTAATAGGGACTTTCAATTTCACACAATAACAAAATAAGTT
AAAATCAAAAATGTTATGAACATCTATAAAAATCAAGTTGAACCCATGAATGTTATAGGTCACTA
AGAAAGTAGGTTACGATCTGAAATGTTAATATTATATTTAATA
Found at i:38250 original size:72 final size:72
Alignment explanation
Indices: 38168--38383 Score: 263
Period size: 72 Copynumber: 3.0 Consensus size: 72
38158 ACACGTTCAG
** * * *
38168 GTATTGAAAAAGTTGAAGATAAGATTTAAAGTTAAATATTGATACTCATGCGGTGATGATCAATA
1 GTATTGAAAAAGTTGAAGATAAGATCAAAATTTAAATATTGATACTTATGCGGTGATGATCGATA
38233 CTTTTAA
66 CTTTTAA
* * * * * *
38240 TTATTTAAAAA-ATAAAGATAAGATCAAAATTTAATATATTGATACTTAGGAGGTGATGATCGAT
1 GTATTGAAAAAGTTGAAGATAAGATCAAAATTTAA-ATATTGATACTTATGCGGTGATGATCGAT
*
38304 ATTTTTAA
65 ACTTTTAA
* * * *
38312 GTATTGAAAGAGTTGAAGATAAGATCGAAATTTAAAATATCGATACTTATGCGCTGATGATCGAT
1 GTATTGAAAAAGTTGAAGATAAGATCAAAATTT-AAATATTGATACTTATGCGGTGATGATCGAT
38377 ACTTTTA
65 ACTTTTA
38384 TATAGAAGAA
Statistics
Matches: 118, Mismatches: 23, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
71 18 0.15
72 49 0.42
73 49 0.42
74 2 0.02
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (72 bp):
GTATTGAAAAAGTTGAAGATAAGATCAAAATTTAAATATTGATACTTATGCGGTGATGATCGATA
CTTTTAA
Found at i:38357 original size:73 final size:72
Alignment explanation
Indices: 38168--38431 Score: 255
Period size: 73 Copynumber: 3.6 Consensus size: 72
38158 ACACGTTCAG
** * * *
38168 GTATTGAAAAAGTTGAAGATAAGATTTAAAGTT-AAATATTGATACTCATGCGGTGATGATCAAT
1 GTATTG-AAAAGTTGAAGATAAGATCAAAATTTAAAATATTGATACTTATGCGGTGATGATCGAT
38232 ACTTTTAA
65 ACTTTTAA
* * ** * * * *
38240 TTATTTAAAAAATAAAGATAAGATCAAAATTTAATATATTGATACTTAGGAGGTGATGATCGATA
1 GTATTGAAAAGTTGAAGATAAGATCAAAATTTAAAATATTGATACTTATGCGGTGATGATCGATA
*
38305 TTTTTAA
66 CTTTTAA
* * *
38312 GTATTGAAAGAGTTGAAGATAAGATCGAAATTTAAAATATCGATACTTATGCGCTGATGATCGAT
1 GTATTGAAA-AGTTGAAGATAAGATCAAAATTTAAAATATTGATACTTATGCGGTGATGATCGAT
38377 ACTTTT-A
65 ACTTTTAA
* * * * *
38384 -TATAGAAGAAGTTGTTGAAGATATGATCAATAGTTAAAATATAGATAC
1 GTATTGAA-AA---GTTGAAGATAAGATCAAAATTTAAAATATTGATAC
38432 ATATATTATG
Statistics
Matches: 154, Mismatches: 32, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
71 27 0.18
72 46 0.30
73 51 0.33
74 30 0.19
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.34
Consensus pattern (72 bp):
GTATTGAAAAGTTGAAGATAAGATCAAAATTTAAAATATTGATACTTATGCGGTGATGATCGATA
CTTTTAA
Found at i:38982 original size:104 final size:98
Alignment explanation
Indices: 38778--39104 Score: 337
Period size: 104 Copynumber: 3.3 Consensus size: 98
38768 CTCATAACCA
* * * *
38778 TATTTGTTATAGGTTATTATAATATAAACGGTTAACG-AATTATAACTTAAACAG--TAAAAAAA
1 TATTTGTTATAGGTTATTATAATATAAACGATTAAAGCCA-TATAACTT-AACAGATTCAAAAAA
* * * *
38840 TCACA-GTGCAACCTAATACTTTACCATAAAAACTG
64 TCA-AGGCGCAACCTATTACTTTACCATAGAAATTG
* * *
38875 TATTTGTTATATGTTATTATAATATAAACGATTAAAGCCTTATAAGTTAACCAG-TTCAAAAAAA
1 TATTTGTTATAGGTTATTATAATATAAACGATTAAAGCCATATAACTTAA-CAGATTC-------
*
38939 AAAAAAT-AAGGCGCAACCTATTACTTTACCATTGAAATTG
58 AAAAAATCAAGGCGCAACCTATTACTTTACCATAGAAATTG
* * *
38979 TATTTATTATAGGTTATTATAATATAAACGGTTAAAGCCATATAACTTAACTGATTCAAAAAATC
1 TATTTGTTATAGGTTATTATAATATAAACGATTAAAGCCATATAACTTAACAGATTCAAAAAATC
*
39044 AAGGCGCAACCTATTACGTTACCATAG-AATCATG
66 AAGGCGCAACCTATTACTTTACCATAGAAAT--TG
39078 -ATTTGTTATAGGTTATTATAATATAAA
1 TATTTGTTATAGGTTATTATAATATAAA
39105 TGGTTAAAAG
Statistics
Matches: 194, Mismatches: 21, Indels: 29
0.80 0.09 0.12
Matches are distributed among these distances:
96 2 0.01
97 54 0.28
98 52 0.27
99 2 0.01
103 3 0.02
104 74 0.38
105 7 0.04
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.34
Consensus pattern (98 bp):
TATTTGTTATAGGTTATTATAATATAAACGATTAAAGCCATATAACTTAACAGATTCAAAAAATC
AAGGCGCAACCTATTACTTTACCATAGAAATTG
Found at i:39389 original size:21 final size:20
Alignment explanation
Indices: 39303--39460 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
39293 AAATGACCAA
**
39303 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
39322 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
39342 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
39362 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
39383 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
39404 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
39424 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
39445 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
39461 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:39489 original size:20 final size:20
Alignment explanation
Indices: 39427--39640 Score: 252
Period size: 20 Copynumber: 10.7 Consensus size: 20
39417 CGATTTTCCA
* ** *
39427 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
39447 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
39467 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
39487 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
39507 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
39527 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
39547 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
39567 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
39587 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
39607 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
39628 AAATCGCAACGCG
1 AAATCGCAACGCG
39641 ATATTTAAAG
Statistics
Matches: 166, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.01
20 146 0.88
21 17 0.10
22 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:39812 original size:22 final size:22
Alignment explanation
Indices: 39787--39841 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
39777 CTATCTACGG
39787 CGAAGAAATCCGTCCCCATCTC
1 CGAAGAAATCCGTCCCCATCTC
**
39809 CGAAGATTTCCGTCCCCATCTC
1 CGAAGAAATCCGTCCCCATCTC
**
39831 CGGCGAAATCC
1 CGAAGAAATCC
39842 CTCACAACCA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.24, C:0.40, G:0.16, T:0.20
Consensus pattern (22 bp):
CGAAGAAATCCGTCCCCATCTC
Found at i:40058 original size:31 final size:33
Alignment explanation
Indices: 40023--40091 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 33
40013 TTCACTTAGA
*
40023 TTTCATTTCGCGTTACGA-T-TGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
40054 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
40087 TTTCA
1 TTTCA
40092 AGTTAGTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 16 0.48
32 1 0.03
33 16 0.48
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:40228 original size:41 final size:41
Alignment explanation
Indices: 40170--40247 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
40160 TTGCAGAAGA
*
40170 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
40211 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
40248 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:40244 original size:21 final size:21
Alignment explanation
Indices: 40171--40246 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
40161 TGCAGAAGAG
*
40171 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
***
40192 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
40212 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
40233 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
40247 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:40250 original size:14 final size:14
Alignment explanation
Indices: 40231--40287 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
40221 GAGAAATGAA
40231 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
40245 AATCGCAACGCGAAATAAA
1 AATCGCAA--CG--A-GAG
40264 AATCGCAACGAGAG
1 AATCGCAACGAGAG
40278 AATCGCAACG
1 AATCGCAACG
40288 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:40266 original size:33 final size:33
Alignment explanation
Indices: 40223--40303 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
40213 CGCAACGAGA
*
40223 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATAAAAATCGCAACGAGAGAATCGCAACGC
40256 GAAATAAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATAAAAATCGCAACGAGAGAATCGCAACGC
**
40289 GAAACCAAAATCGCA
1 GAAATAAAAATCGCA
40304 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.48, C:0.22, G:0.21, T:0.09
Consensus pattern (33 bp):
GAAATAAAAATCGCAACGAGAGAATCGCAACGC
Found at i:40321 original size:19 final size:19
Alignment explanation
Indices: 40299--40404 Score: 115
Period size: 19 Copynumber: 6.1 Consensus size: 19
40289 GAAACCAAAA
*
40299 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
40318 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
40332 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
40351 TCGCGTTGCGATTTTC---
1 TCGCGTTGCGATTTTCATT
*
40367 T--CGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
40384 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
40403 TC
1 TC
40405 AACCAAAAGA
Statistics
Matches: 72, Mismatches: 5, Indels: 20
0.74 0.05 0.21
Matches are distributed among these distances:
14 22 0.31
16 4 0.06
17 4 0.06
19 42 0.58
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:40340 original size:14 final size:14
Alignment explanation
Indices: 40321--40377 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
40311 TTTCATTTCG
40321 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
40335 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
40354 CGTTGCGATTTTCT
1 CGTTGCGATTCTCT
40368 CGTTGCGATT
1 CGTTGCGATT
40378 GTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:40397 original size:33 final size:33
Alignment explanation
Indices: 40304--40399 Score: 174
Period size: 33 Copynumber: 2.9 Consensus size: 33
40294 CAAAATCGCA
*
40304 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCTCG
40337 TTGCGATTTTCATTTCGCGTTGCGATTTTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCTCG
*
40370 TTGCGATTGTCATTTCGCGTTGCGATTTTC
1 TTGCGATTTTCATTTCGCGTTGCGATTTTC
40400 ATTTCAACCA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTCTCG
Found at i:43221 original size:12 final size:12
Alignment explanation
Indices: 43204--43228 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43194 TCTTCGGGGA
43204 CTTTTTCTTCTT
1 CTTTTTCTTCTT
43216 CTTTTTCTTCTT
1 CTTTTTCTTCTT
43228 C
1 C
43229 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:43437 original size:24 final size:24
Alignment explanation
Indices: 43403--43449 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
43393 CTGAAACATC
43403 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
43427 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
43450 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:44160 original size:20 final size:20
Alignment explanation
Indices: 44132--44381 Score: 259
Period size: 20 Copynumber: 12.5 Consensus size: 20
44122 AAATTCCAGT
* * *
44132 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
44152 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
**
44172 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
44192 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
44212 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
44232 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
44252 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
44272 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
44292 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
44312 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
44332 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
44352 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
44372 GTTGCGATTT
1 GTTGCGATTT
44382 TAGAAAATCG
Statistics
Matches: 202, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 201 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:44433 original size:21 final size:21
Alignment explanation
Indices: 44348--44445 Score: 74
Period size: 21 Copynumber: 4.7 Consensus size: 21
44338 ATTTATGTGT
* *
44348 TCGCGTTGCGATTTTC-ATAT
1 TCGCGTTGCGATTTTCAAAAA
44368 TCGCGTTGCGATTTT-AGAAAA
1 TCGCGTTGCGATTTTCA-AAAA
** * ** **
44389 TCGCAATGCGAATTTGTACTA
1 TCGCGTTGCGATTTTCAAAAA
* *
44410 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAAAAA
44431 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
44446 GGAAACTGAT
Statistics
Matches: 60, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 15 0.25
21 45 0.75
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.38
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCAAAAA
Found at i:44441 original size:42 final size:43
Alignment explanation
Indices: 44348--44446 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
44338 ATTTATGTGT
*
44348 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTAGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTAGAAAA
** *
44389 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTTCA-AGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTT-AGAAAA
*
44431 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
44447 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 8 0.17
42 35 0.74
43 4 0.09
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTAGAAAA
Found at i:45073 original size:14 final size:14
Alignment explanation
Indices: 45054--45083 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
45044 TTTAGATTTT
*
45054 TTAAAATTACATTA
1 TTAAAAATACATTA
45068 TTAAAAATACATTA
1 TTAAAAATACATTA
45082 TT
1 TT
45084 GATGAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:47233 original size:11 final size:11
Alignment explanation
Indices: 47217--47313 Score: 90
Period size: 11 Copynumber: 8.6 Consensus size: 11
47207 TAACCCATCT
47217 TCGAGCTT-AA
1 TCGAGCTTGAA
47227 GTCGAGCTTGAA
1 -TCGAGCTTGAA
47239 TCGAGCTT-AA
1 TCGAGCTTGAA
47249 GTCGAGCTTGAA
1 -TCGAGCTTGAA
* **
47261 TCGAACTCACAA
1 TCGAGCT-TGAA
47273 TCGAGCTTGAA
1 TCGAGCTTGAA
**
47284 TCGAGCTCAAAA
1 TCGAGCT-TGAA
*
47296 TCGAGCTTCAA
1 TCGAGCTTGAA
47307 TCGAGCT
1 TCGAGCT
47314 CGAGTCTTGA
Statistics
Matches: 71, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
10 2 0.03
11 48 0.68
12 21 0.30
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:47280 original size:23 final size:22
Alignment explanation
Indices: 47217--47314 Score: 124
Period size: 23 Copynumber: 4.4 Consensus size: 22
47207 TAACCCATCT
* *
47217 TCGAGCTTAAGTCGAGCTTGAA
1 TCGAGCTCAAATCGAGCTTGAA
* *
47239 TCGAGCTTAAGTCGAGCTTGAA
1 TCGAGCTCAAATCGAGCTTGAA
*
47261 TCGAACTCACAATCGAGCTTGAA
1 TCGAGCTCA-AATCGAGCTTGAA
*
47284 TCGAGCTCAAAATCGAGCTTCAA
1 TCGAGCTC-AAATCGAGCTTGAA
47307 TCGAGCTC
1 TCGAGCTC
47315 GAGTCTTGAG
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
22 29 0.42
23 39 0.57
24 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.24
Consensus pattern (22 bp):
TCGAGCTCAAATCGAGCTTGAA
Found at i:47308 original size:34 final size:33
Alignment explanation
Indices: 47217--47313 Score: 97
Period size: 34 Copynumber: 2.9 Consensus size: 33
47207 TAACCCATCT
* * *
47217 TCGAGCTTAAGTCGAGCTTGAATCGAGCTTAAG
1 TCGAGCTAAAATCGAGCTTCAATCGAGCTTAAG
** * *
47250 TCGAGCTTGAATCGAACTCACAATCGAGCTTGAA-
1 TCGAGCTAAAATCGAGCT-TCAATCGAGCTT-AAG
47284 TCGAGCTCAAAATCGAGCTTCAATCGAGCT
1 TCGAGCT-AAAATCGAGCTTCAATCGAGCT
47314 CGAGTCTTGA
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
33 15 0.29
34 27 0.52
35 10 0.19
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (33 bp):
TCGAGCTAAAATCGAGCTTCAATCGAGCTTAAG
Found at i:47993 original size:12 final size:11
Alignment explanation
Indices: 47976--48031 Score: 51
Period size: 12 Copynumber: 4.9 Consensus size: 11
47966 TGAGGCCCTA
47976 AAAAAATTAAAT
1 AAAAAA-TAAAT
47988 AAAAAACTAAAT
1 AAAAAA-TAAAT
* *
48000 CAAATAT-AAT
1 AAAAAATAAAT
*
48010 AAAACATATAAT
1 AAAAAATA-AAT
48022 AAAAAATAAA
1 AAAAAATAAA
48032 GTGATATTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
10 8 0.22
11 3 0.08
12 25 0.69
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAAAATAAAT
Found at i:48446 original size:6 final size:6
Alignment explanation
Indices: 48421--48477 Score: 60
Period size: 6 Copynumber: 9.3 Consensus size: 6
48411 CATCCCGCAC
* * * * *
48421 TCCCCT TGCCCT TGCCCT TCCCCT TCCACT TCCACT TCCACT TCCCCT
1 TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT
48469 TCTCCCT TC
1 TC-CCCT TC
48478 TCTATTCTAC
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
6 40 0.87
7 6 0.13
ACGTcount: A:0.05, C:0.56, G:0.04, T:0.35
Consensus pattern (6 bp):
TCCCCT
Found at i:49529 original size:25 final size:25
Alignment explanation
Indices: 49495--49555 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
49485 TGGTATTTCT
49495 TAAGATACAAAAATTATTCATCCAA
1 TAAGATACAAAAATTATTCATCCAA
**
49520 TAAGATACAAATGTTATTCATCCAA
1 TAAGATACAAAAATTATTCATCCAA
*
49545 TAGGATACAAA
1 TAAGATACAAA
49556 GGTCAAAGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.28
Consensus pattern (25 bp):
TAAGATACAAAAATTATTCATCCAA
Found at i:50470 original size:15 final size:16
Alignment explanation
Indices: 50450--50482 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
50440 AAAATACAGC
50450 ATTCCC-AGTAATCTT
1 ATTCCCTAGTAATCTT
*
50465 ATTCCCTGGTAATCTT
1 ATTCCCTAGTAATCTT
50481 AT
1 AT
50483 ATTCCCACTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.42
Consensus pattern (16 bp):
ATTCCCTAGTAATCTT
Found at i:50506 original size:20 final size:20
Alignment explanation
Indices: 50470--50507 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
50460 ATCTTATTCC
* *
50470 CTGGTAATCTTATATTCCCA
1 CTGGTAATCATACATTCCCA
50490 CTGGTAATCATACATTCC
1 CTGGTAATCATACATTCC
50508 GTGAACCAAA
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:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATCATACATTCCCA
Found at i:53212 original size:23 final size:23
Alignment explanation
Indices: 53161--53206 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
53151 ATAAATGACA
53161 AACACATAATGTTTTTGTTCTTT
1 AACACATAATGTTTTTGTTCTTT
53184 AACACATAATGTTTTTGTTCTTT
1 AACACATAATGTTTTTGTTCTTT
53207 GGCACAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.52
Consensus pattern (23 bp):
AACACATAATGTTTTTGTTCTTT
Found at i:56028 original size:22 final size:22
Alignment explanation
Indices: 55980--56030 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
55970 AAAGTGCCTC
*
55980 AGCACTGATACAAAATTGCATT
1 AGCACTGATACAAAATTCCATT
*
56002 TGCACTGATACAAAAGTTCCA-T
1 AGCACTGATACAAAA-TTCCATT
56024 AGCACTG
1 AGCACTG
56031 GAAAAGAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (22 bp):
AGCACTGATACAAAATTCCATT
Found at i:56533 original size:21 final size:21
Alignment explanation
Indices: 56507--56580 Score: 139
Period size: 21 Copynumber: 3.5 Consensus size: 21
56497 TGAGACCCAT
56507 AGTATCGATACCCCTTGAAGG
1 AGTATCGATACCCCTTGAAGG
56528 AGTATCGATACCCCTTGAAGG
1 AGTATCGATACCCCTTGAAGG
56549 AGTATCGATACCCCTTGAAGG
1 AGTATCGATACCCCTTGAAGG
*
56570 AGTATCAATAC
1 AGTATCGATAC
56581 TTCCTTCATT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (21 bp):
AGTATCGATACCCCTTGAAGG
Found at i:57283 original size:23 final size:23
Alignment explanation
Indices: 57257--57336 Score: 124
Period size: 23 Copynumber: 3.4 Consensus size: 23
57247 GAAGCTCACA
57257 AGAGGAAAAATATGAAGAATAGG
1 AGAGGAAAAATATGAAGAATAGG
*
57280 AGAGGGAAAATATGAAGAATAGG
1 AGAGGAAAAATATGAAGAATAGG
**
57303 AGAGGGCAAATATGAAGAATAGG
1 AGAGGAAAAATATGAAGAATAGG
57326 AGAGGGAAAAA
1 AGA-GGAAAAA
57337 AAGATAAATG
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
23 47 0.90
24 5 0.10
ACGTcount: A:0.54, C:0.01, G:0.34, T:0.11
Consensus pattern (23 bp):
AGAGGAAAAATATGAAGAATAGG
Found at i:58358 original size:21 final size:21
Alignment explanation
Indices: 58334--58381 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
58324 CCAAAGGACA
*
58334 ATCCATCG-AGGAAAAAGATCG
1 ATCCATCGAAAGAAAAA-ATCG
*
58355 ATCCCTCGAAAGAAAAAATCG
1 ATCCATCGAAAGAAAAAATCG
58376 ATCCAT
1 ATCCAT
58382 TTGTTGTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.44, C:0.23, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCCATCGAAAGAAAAAATCG
Found at i:75820 original size:42 final size:42
Alignment explanation
Indices: 75773--75855 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
75763 TAAGCAATTT
* *
75773 AAGTCCTTAGTGTAATCAGTAAGTCTTTCGAGCATGATGATG
1 AAGTCCTTAGGGCAATCAGTAAGTCTTTCGAGCATGATGATG
* * * *
75815 AAGTCCTTCGGGCCATCAGTAAGTCTTTTGAGTATGATGAT
1 AAGTCCTTAGGGCAATCAGTAAGTCTTTCGAGCATGATGAT
75856 TAAATCATTC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.34
Consensus pattern (42 bp):
AAGTCCTTAGGGCAATCAGTAAGTCTTTCGAGCATGATGATG
Found at i:75867 original size:42 final size:42
Alignment explanation
Indices: 75787--75868 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
75777 CCTTAGTGTA
* *
75787 ATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCC
1 ATCAGTAAGTCTTTCGAGCATGATGATGAAATCATTCGGGCC
* * *
75829 ATCAGTAAGTCTTTTGAGTATGATGATTAAATCATTCGGG
1 ATCAGTAAGTCTTTCGAGCATGATGATGAAATCATTCGGG
75869 TAATTTGTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (42 bp):
ATCAGTAAGTCTTTCGAGCATGATGATGAAATCATTCGGGCC
Found at i:76261 original size:13 final size:13
Alignment explanation
Indices: 76243--76267 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
76233 TGAAGAAAAC
76243 CCATCAGTAAGTG
1 CCATCAGTAAGTG
76256 CCATCAGTAAGT
1 CCATCAGTAAGT
76268 CTTTCGAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:77005 original size:53 final size:53
Alignment explanation
Indices: 76721--76980 Score: 421
Period size: 53 Copynumber: 4.9 Consensus size: 53
76711 AGAATCACAC
*
76721 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
* * *
76774 CAGAAGATTGTTCGAGTTCTACTCCATGAAGCAAGAGGGAGAGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
* *
76827 TAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAAAGGGAGCGAACCCGTAAG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
* * * *
76880 CAGAAGATTGTTTGAGTTCTACTCCTTGAAGCAAGAGGGAGTGAACCCGTAAA
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
*
76933 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAATAGGGAGCGAACCC
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCC
76981 ATTTTTAAAA
Statistics
Matches: 190, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 190 1.00
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.21
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
Found at i:83709 original size:20 final size:20
Alignment explanation
Indices: 83684--83722 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
83674 AAAATTCGAT
* *
83684 AGTATCGATATTTATGTAAA
1 AGTATCAATATTTAAGTAAA
83704 AGTATCAATATTTAAGTAA
1 AGTATCAATATTTAAGTAA
83723 TAGTTATAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.05, G:0.13, T:0.38
Consensus pattern (20 bp):
AGTATCAATATTTAAGTAAA
Found at i:83883 original size:102 final size:102
Alignment explanation
Indices: 83749--84247 Score: 624
Period size: 102 Copynumber: 5.0 Consensus size: 102
83739 TATTACATAT
* * *
83749 AAACCGGATTTGTTATAGGTTATTATAATATAAACGATTAAAGCCTTATAACTTAACCAGTTTAA
1 AAACTGGATTTGTTATAGGTTATTATAATATAAACGATTAAAGTCTTATAACTTAACCAGTTCAA
*
83814 AAATAAAATCAAGGCACAACTTATTACGTTACCA-TCG
66 AAATAAAATCAAGGCGCAACTTATTACGTTACCACT-G
*
83851 AAACTGGATTTGTTATAGGTTATTATAATATAAACGATTAAAGTCTTATAACTTAACTAGTTCAA
1 AAACTGGATTTGTTATAGGTTATTATAATATAAACGATTAAAGTCTTATAACTTAACCAGTTCAA
* * * *
83916 AAATAAAATCAAGGTGCAACCTATTACATTATCACTG
66 AAATAAAATCAAGGCGCAACTTATTACGTTACCACTG
*** * * *
83953 AAACCATATTTGTCATAGGTTATTATAATATAAACAATTAAAGTCTTATAACTTAACCAATTCAA
1 AAACTGGATTTGTTATAGGTTATTATAATATAAACGATTAAAGTCTTATAACTTAACCAGTTCAA
* *
84018 AAATAAAATAAAGGCGCAACCTATTACGTTACCA-TCG
66 AAATAAAATCAAGGCGCAACTTATTACGTTACCACT-G
* * * * *
84055 AAACTGTATTTGTCATAGG----T-TAATATAAACGGTTAAAGCCTTATAACTTAATC-GATTCA
1 AAACTGGATTTGTTATAGGTTATTATAATATAAACGATTAAAGTCTTATAACTTAACCAG-TTCA
84114 AAAATAAAATCAAGGCGCAA-TCTATTAC-TTACCACTG
65 AAAATAAAATCAAGGCGCAACT-TATTACGTTACCACTG
* * * *
84151 AAATTGGATTTGTTATAGATTATTATAATATAAACGGTTAAAGTCTTATAACTTAACCAGTTAAA
1 AAACTGGATTTGTTATAGGTTATTATAATATAAACGATTAAAGTCTTATAACTTAACCAGTTCAA
* *
84216 AAATAAAATCAATGCACAACCTT-TTACGTTAC
66 AAATAAAATCAAGGCGCAA-CTTATTACGTTAC
84248 TATCCCGACC
Statistics
Matches: 345, Mismatches: 38, Indels: 28
0.84 0.09 0.07
Matches are distributed among these distances:
96 22 0.06
97 59 0.17
98 1 0.00
100 1 0.00
101 57 0.17
102 203 0.59
103 2 0.01
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (102 bp):
AAACTGGATTTGTTATAGGTTATTATAATATAAACGATTAAAGTCTTATAACTTAACCAGTTCAA
AAATAAAATCAAGGCGCAACTTATTACGTTACCACTG
Found at i:85124 original size:15 final size:14
Alignment explanation
Indices: 85098--85129 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
85088 TAATAAAATA
85098 ATTTATTTAATATT
1 ATTTATTTAATATT
85112 ATTTATGTTAATATT
1 ATTTAT-TTAATATT
85127 ATT
1 ATT
85130 GCACGAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (14 bp):
ATTTATTTAATATT
Found at i:85453 original size:25 final size:23
Alignment explanation
Indices: 85425--85481 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 23
85415 ATTATTAGTT
*
85425 ATATTAATAATTTATTAGAATAAAA
1 ATATTAATAA--TATTAAAATAAAA
*
85450 ATATTATTATAATATTAAAATTAAA
1 ATATTA--ATAATATTAAAATAAAA
85475 ATATTAA
1 ATATTAA
85482 ATTATATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
23 1 0.04
25 23 0.82
27 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
ATATTAATAATATTAAAATAAAA
Found at i:85473 original size:42 final size:42
Alignment explanation
Indices: 85385--85473 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
85375 AATAAATATG
* * * *
85385 ATTAATTATTTATTATAATAAAAATATTATATTATTAGTTAT
1 ATTAATAATTTATTAGAATAAAAATATTATATTAATAGTTAA
85427 ATTAATAATTTATTAGAATAAAAATATTAT-TATAATA-TTAAA
1 ATTAATAATTTATTAGAATAAAAATATTATAT-TAATAGTT-AA
85469 ATTAA
1 ATTAA
85474 AATATTAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
41 3 0.07
42 38 0.93
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (42 bp):
ATTAATAATTTATTAGAATAAAAATATTATATTAATAGTTAA
Found at i:85519 original size:22 final size:21
Alignment explanation
Indices: 85479--85567 Score: 80
Period size: 22 Copynumber: 4.1 Consensus size: 21
85469 ATTAAAATAT
85479 TAAATTATATTTTGGAAATTATTAA
1 TAAA-TATATTTT--AAA-TATTAA
85504 TAAATATATTTTAAATATT--
1 TAAATATATTTTAAATATTAA
85523 T-AATA-A-TTTAATATTATTAA
1 TAAATATATTTTAA-A-TATTAA
85543 TAAATATATTTTAAATATTTAA
1 TAAATATATTTTAAATA-TTAA
85565 TAA
1 TAA
85568 TGTAATAATA
Statistics
Matches: 56, Mismatches: 0, Indels: 19
0.75 0.00 0.25
Matches are distributed among these distances:
16 5 0.09
17 2 0.04
18 8 0.14
19 1 0.02
20 1 0.02
21 10 0.18
22 12 0.21
23 5 0.09
24 8 0.14
25 4 0.07
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
TAAATATATTTTAAATATTAA
Found at i:85545 original size:39 final size:39
Alignment explanation
Indices: 85496--85580 Score: 152
Period size: 39 Copynumber: 2.2 Consensus size: 39
85486 TATTTTGGAA
*
85496 ATTATTAATAAATATATTTTAAATATTTAATAATTTAAT
1 ATTATTAATAAATATATTTTAAATATTTAATAATGTAAT
85535 ATTATTAATAAATATATTTTAAATATTTAATAATGTAAT
1 ATTATTAATAAATATATTTTAAATATTTAATAATGTAAT
*
85574 AATATTA
1 ATTATTA
85581 TTTTATGAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (39 bp):
ATTATTAATAAATATATTTTAAATATTTAATAATGTAAT
Found at i:89549 original size:210 final size:210
Alignment explanation
Indices: 89187--89608 Score: 835
Period size: 210 Copynumber: 2.0 Consensus size: 210
89177 TGCTTCAAAT
89187 GAACTCTTGAGCTTTTGCTTCATTATCACAAATATGCATGTCTTATGCATATGTTTCCATATGTC
1 GAACTCTTGAGCTTTTGCTTCATTATCACAAATATGCATGTCTTATGCATATGTTTCCATATGTC
89252 AATAGTGTGTGATTTAGAATTTGAGATAGTCAACTTCCTTTGAGGATTATTTTATATTTAAGAAA
66 AATAGTGTGTGATTTAGAATTTGAGATAGTCAACTTCCTTTGAGGATTATTTTATATTTAAGAAA
89317 TATGACTACTGTAGTAAATCAATATTTCTTCTAGAAGATGATTAATCAAGCTTCTTGAAAGTGTG
131 TATGACTACTGTAGTAAATCAATATTTCTTCTAGAAGATGATTAATCAAGCTTCTTGAAAGTGTG
89382 GCCCTTAGGCCATAA
196 GCCCTTAGGCCATAA
*
89397 GAACTCTTGATCTTTTGCTTCATTATCACAAATATGCATGTCTTATGCATATGTTTCCATATGTC
1 GAACTCTTGAGCTTTTGCTTCATTATCACAAATATGCATGTCTTATGCATATGTTTCCATATGTC
89462 AATAGTGTGTGATTTAGAATTTGAGATAGTCAACTTCCTTTGAGGATTATTTTATATTTAAGAAA
66 AATAGTGTGTGATTTAGAATTTGAGATAGTCAACTTCCTTTGAGGATTATTTTATATTTAAGAAA
89527 TATGACTACTGTAGTAAATCAATATTTCTTCTAGAAGATGATTAATCAAGCTTCTTGAAAGTGTG
131 TATGACTACTGTAGTAAATCAATATTTCTTCTAGAAGATGATTAATCAAGCTTCTTGAAAGTGTG
89592 GCCCTTAGGCCATAA
196 GCCCTTAGGCCATAA
89607 GA
1 GA
89609 GGGTCATGCT
Statistics
Matches: 211, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
210 211 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.39
Consensus pattern (210 bp):
GAACTCTTGAGCTTTTGCTTCATTATCACAAATATGCATGTCTTATGCATATGTTTCCATATGTC
AATAGTGTGTGATTTAGAATTTGAGATAGTCAACTTCCTTTGAGGATTATTTTATATTTAAGAAA
TATGACTACTGTAGTAAATCAATATTTCTTCTAGAAGATGATTAATCAAGCTTCTTGAAAGTGTG
GCCCTTAGGCCATAA
Found at i:93023 original size:20 final size:20
Alignment explanation
Indices: 93000--93062 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 20
92990 ATCTAAATTC
93000 TAAACAGATTACCTAACAAT
1 TAAACAGATTACCTAACAAT
* **
93020 TAAACATATTATAGATAAACAAT
1 TAAACAGA-T-TACCT-AACAAT
93043 TAAACAGATTACCTTAACAA
1 TAAACAGATTACC-TAACAA
93063 AATAACAAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
20 7 0.21
21 8 0.24
22 5 0.15
23 13 0.39
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (20 bp):
TAAACAGATTACCTAACAAT
Found at i:93218 original size:24 final size:27
Alignment explanation
Indices: 93157--93210 Score: 81
Period size: 29 Copynumber: 1.9 Consensus size: 27
93147 CCAATATATA
*
93157 AACAATTAAACAAATTACATTGAAGAT
1 AACAATTAAACAAATTACAGTGAAGAT
93184 GAAGCAATTAAACAAATTACAGTGAAG
1 -AA-CAATTAAACAAATTACAGTGAAG
93211 TAAATTAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.54, C:0.11, G:0.13, T:0.22
Consensus pattern (27 bp):
AACAATTAAACAAATTACAGTGAAGAT
Found at i:101802 original size:23 final size:23
Alignment explanation
Indices: 101757--101805 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
101747 TGACTAAAAT
* *
101757 AAAATAACATAAAAGCAACATGC
1 AAAATAAAATAAAAGCAAAATGC
101780 AAAATTAAAATAAAA-CAAAATGC
1 AAAA-TAAAATAAAAGCAAAATGC
101803 AAA
1 AAA
101806 TGTGACTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.67, C:0.12, G:0.06, T:0.14
Consensus pattern (23 bp):
AAAATAAAATAAAAGCAAAATGC
Found at i:102065 original size:27 final size:27
Alignment explanation
Indices: 102035--102087 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
102025 AACATTAACT
*
102035 AAAATTCATAAATTAAA-AATACAACAC
1 AAAATTCATAAA-TAAATAATAAAACAC
*
102062 AAAATTCATGAATAAATAATAAAACA
1 AAAATTCATAAATAAATAATAAAACA
102088 GAATACATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.64, C:0.11, G:0.02, T:0.23
Consensus pattern (27 bp):
AAAATTCATAAATAAATAATAAAACAC
Found at i:103654 original size:15 final size:14
Alignment explanation
Indices: 103629--103658 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
103619 TGCCACAGAA
103629 ATAAAATAAATAAT
1 ATAAAATAAATAAT
103643 ATAAATATAAATAAT
1 ATAAA-ATAAATAAT
103658 A
1 A
103659 ATGATAGTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAAAATAAATAAT
Found at i:103690 original size:3 final size:3
Alignment explanation
Indices: 103684--103723 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
103674 GTAGTAGTAG
103684 TAA TAA TAA TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
103724 CGGTCTCCGA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:104317 original size:45 final size:45
Alignment explanation
Indices: 104260--104406 Score: 267
Period size: 45 Copynumber: 3.3 Consensus size: 45
104250 GTTCCGCTTC
* *
104260 TTCTTTAGGGAAACTTAGATCTAAAAACATTGATTCATTCCACTT
1 TTCTTTAAGGAAACTTAGATCTAAAAACATTGATTCATTCCACTG
*
104305 TTCTTTAAGGAAACTTAGATATAAAAACATTGATTCATTCCACTG
1 TTCTTTAAGGAAACTTAGATCTAAAAACATTGATTCATTCCACTG
104350 TTCTTTAAGGAAACTTAGATCTAAAAACATTGATTCATTCCACTG
1 TTCTTTAAGGAAACTTAGATCTAAAAACATTGATTCATTCCACTG
104395 TTCTTTAAGGAA
1 TTCTTTAAGGAA
104407 GATCAAATCA
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 98 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (45 bp):
TTCTTTAAGGAAACTTAGATCTAAAAACATTGATTCATTCCACTG
Found at i:105441 original size:42 final size:41
Alignment explanation
Indices: 105347--105446 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 41
105337 GGTCTTATGG
* * * * *
105347 ATGGCCCAAAGGACTTATCATCTTGCTTGAAAGACTTACGG
1 ATGGCCCGAAGGACTTAGCATCATGCTCGAAAGACTTACGA
* * * *
105388 ATGACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACTA
1 ATGGCCCGAAGGACTT-AGCATCATGCTCGAAAGACTTACGA
105430 ATGGCCCGAAGGACTTA
1 ATGGCCCGAAGGACTTA
105447 CTAAGTAAGA
Statistics
Matches: 46, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
41 13 0.28
42 33 0.72
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (41 bp):
ATGGCCCGAAGGACTTAGCATCATGCTCGAAAGACTTACGA
Found at i:105666 original size:245 final size:240
Alignment explanation
Indices: 104964--105704 Score: 1058
Period size: 241 Copynumber: 3.1 Consensus size: 240
104954 TGGAAATAGT
* ** *** *
104964 TTACTAGGTAAGAAACTTTGGAAACCGTTTTCTTACTTTTCAAAA-ATTTCAATTTTCATAAAA-
1 TTACTAAGTAAGAAACTTTGGAAATTGTTTTCTTACTTTTCAAAAGAAACCAATTTTCAGAAAAG
* * * *
105027 GATTAAATGAGAAAATTTGGAAATCGTTTTCTTATTTTTCAAAAAACATGTGAAAACAT-CTTGC
66 GTTTAAATGAGAAACTTTGGAAATTGTTTTCTTATTTTTTAAAAAACATGTGAAAACATCCTT-C
* *
105091 CCGAAGGTCTTATGGATGACCCGAATGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGA
130 CCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGA-CCGA
* *
105156 AGGATTTAAGCATCATGCTCAAAAGATTTACTGATGGCCCGAAGGAC
194 AGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGAC
* * *
105203 TTACTAAGCAATAAACTTTGAAAATTGTTTTCTTACTTTTCAAAAGAAACCAAATTTT-AGAAAA
1 TTACTAAGTAAGAAACTTTGGAAATTGTTTTCTTACTTTTCAAAAGAAACC-AATTTTCAGAAAA
* * * * *
105267 GTTTTAAATGAGAAACTTTGGAAATTGTTTTCTCATTTTTTGAAAAACAAGTGAAAACATCCTAC
65 GGTTTAAATGAGAAACTTTGGAAATTGTTTTCTTATTTTTTAAAAAACATGTGAAAACATCCTTC
* * *
105332 CCGAAGGTCTTATGGATGGCCCAAAGGACTTATCATCTTGCTTGAAAGACTTACGGATGACCTGA
130 CCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACC-GA
*
105397 AGGATTTAAGCATCATGCTCGAAAGACTTACTAATGGCCCGAAGGAC
194 AGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGAC
* *
105444 TTACTAAGTAAGAAACTTTGGAAATTGTTTTCTTACATTTCAAAAGAAACCAATTTTCCGAAAAG
1 TTACTAAGTAAGAAACTTTGGAAATTGTTTTCTTACTTTTCAAAAGAAACCAATTTTCAGAAAAG
* **
105509 GTTTAAATAAGAAACTTTGGAAATTACTTTCTTATTTTTTAAAAAAAAATCATGTGAAAACATCC
66 GTTTAAATGAGAAACTTTGGAAATTGTTTTCTTATTTTTT---AAAAAA-CATGTGAAAACATCC
*
105574 TTCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTTACAGATGACT
127 TTCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGAC-
* *
105639 CGAAGGATTTAAGCATAATGCTCGAAAGACTTACTGTTGGCCCGAAGGAC
191 CGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGAC
105689 TTACTAAGTAAGAAAC
1 TTACTAAGTAAGAAAC
105705 CCGTGAAAAT
Statistics
Matches: 444, Mismatches: 47, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
239 39 0.09
240 15 0.03
241 247 0.56
242 2 0.00
244 5 0.01
245 135 0.30
246 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (240 bp):
TTACTAAGTAAGAAACTTTGGAAATTGTTTTCTTACTTTTCAAAAGAAACCAATTTTCAGAAAAG
GTTTAAATGAGAAACTTTGGAAATTGTTTTCTTATTTTTTAAAAAACATGTGAAAACATCCTTCC
CGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCGAAG
GATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGAC
Found at i:105685 original size:42 final size:41
Alignment explanation
Indices: 105591--105691 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 41
105581 AGGTCTTATG
* **
105591 GATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTTACA
1 GATGGCCCGAAGGACTTAGCATAATGCTCAAAAGACTTACA
* * * * *
105632 GATGACTCGAAGGATTTAAGCATAATGCTCGAAAGACTTACT
1 GATGGCCCGAAGGACTT-AGCATAATGCTCAAAAGACTTACA
*
105674 GTTGGCCCGAAGGACTTA
1 GATGGCCCGAAGGACTTA
105692 CTAAGTAAGA
Statistics
Matches: 47, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
41 15 0.32
42 32 0.68
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.25
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTAGCATAATGCTCAAAAGACTTACA
Found at i:109655 original size:15 final size:15
Alignment explanation
Indices: 109635--109664 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
109625 TGTTTCTTTT
109635 TCATTATCTAAGCCA
1 TCATTATCTAAGCCA
109650 TCATTATCTAAGCCA
1 TCATTATCTAAGCCA
109665 AATGCTTTAG
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:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (15 bp):
TCATTATCTAAGCCA
Found at i:110392 original size:23 final size:23
Alignment explanation
Indices: 110362--110416 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
110352 CTCTCAGGGG
*
110362 GGGTATCGGTACCCATTCAAAGA
1 GGGTATCGATACCCATTCAAAGA
*
110385 GGGTATCGATACCCATTCAAAGG
1 GGGTATCGATACCCATTCAAAGA
110408 GGGTATCGA
1 GGGTATCGA
110417 ACCTACCGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (23 bp):
GGGTATCGATACCCATTCAAAGA
Done.