Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016416.1 Corchorus olitorius cultivar O-4 contig16449, 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: 107881
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:4937 original size:184 final size:185
Alignment explanation
Indices: 4628--4997 Score: 715
Period size: 184 Copynumber: 2.0 Consensus size: 185
4618 GACAAATATC
4628 TTGGACTTCCTATCATGATTGGAAGATCTAAGAAGAGGGAGTTACTTTTTATTAAGGATCGATTA
1 TTGGACTTCCTATCATGATTGGAAGATCTAAGAAGAGGGAGTTACTTTTTATTAAGGATCGATTA
4693 ATTACTCGTGTTCGGAAATGGAATGGCAAATTCCTTTCTATTGTAGGCAAATCGATTCTCATCCG
66 ATTACTCGTGTTCGGAAATGGAATGGCAAATTCCTTTCTATTGTAGGCAAATCGATTCTCATCCG
* *
4758 ATCAATTGCCTAACCAATACCTCAA-TTCTTATCAGTGTATTCAAATTCCTTAAA
131 ATCAATTGCCCAACCAATACCTCAATTTCTTATCAATGTATTCAAATTCCTTAAA
4812 TTGGACTTCCTATCATGATTGGAAGATCTAAGAAGAGGGAGTTACTTTTTATTAAGGATCGATTA
1 TTGGACTTCCTATCATGATTGGAAGATCTAAGAAGAGGGAGTTACTTTTTATTAAGGATCGATTA
4877 ATTACTCGTGTTCGGAAATGGAATGGCAAATTCCTTTCTATTGTAGGCAAATCGATTCTCATCCG
66 ATTACTCGTGTTCGGAAATGGAATGGCAAATTCCTTTCTATTGTAGGCAAATCGATTCTCATCCG
4942 ATCAATTGCCCAACCAATACCTCAATTTCTTATCAATGTATTCAAATTCCTTAAA
131 ATCAATTGCCCAACCAATACCTCAATTTCTTATCAATGTATTCAAATTCCTTAAA
4997 T
1 T
4998 CCTTCTTGCA
Statistics
Matches: 183, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
184 154 0.84
185 29 0.16
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (185 bp):
TTGGACTTCCTATCATGATTGGAAGATCTAAGAAGAGGGAGTTACTTTTTATTAAGGATCGATTA
ATTACTCGTGTTCGGAAATGGAATGGCAAATTCCTTTCTATTGTAGGCAAATCGATTCTCATCCG
ATCAATTGCCCAACCAATACCTCAATTTCTTATCAATGTATTCAAATTCCTTAAA
Found at i:10576 original size:17 final size:16
Alignment explanation
Indices: 10536--10586 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
10526 CATGTAATCT
*
10536 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
10552 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
10569 TTAGATCACTAGTGATC
1 TT-GATCACTGGTGATC
10586 T
1 T
10587 GGGGGTGATC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:21918 original size:166 final size:166
Alignment explanation
Indices: 21644--21971 Score: 638
Period size: 166 Copynumber: 2.0 Consensus size: 166
21634 TTTGTCCAAA
21644 TATACGATATCAATGGAAGCAAGAGTAGCAAACTGTGAGAAGAAATATTAGATTCTATCATCCTA
1 TATACGATATCAATGGAAGCAAGAGTAGCAAACTGTGAGAAGAAATATTAGATTCTATCATCCTA
*
21709 AATAATTCAAACATCCTTGCGCAAATAAGAAGATCGTGACATGTAAGCAAATGGGCCAGTGAAAG
66 AATAATTCAAACATCCTTGCGCAAATAAGAAGATCATGACATGTAAGCAAATGGGCCAGTGAAAG
21774 CCTATTTCTCTCCCTCAAACATCTAAAAACAGCAAG
131 CCTATTTCTCTCCCTCAAACATCTAAAAACAGCAAG
*
21810 TATACGATATCAATGGAAGCAAGAGTAGCAAATTGTGAGAAGAAATATTAGATTCTATCATCCTA
1 TATACGATATCAATGGAAGCAAGAGTAGCAAACTGTGAGAAGAAATATTAGATTCTATCATCCTA
21875 AATAATTCAAACATCCTTGCGCAAATAAGAAGATCATGACATGTAAGCAAATGGGCCAGTGAAAG
66 AATAATTCAAACATCCTTGCGCAAATAAGAAGATCATGACATGTAAGCAAATGGGCCAGTGAAAG
21940 CCTATTTCTCTCCCTCAAACATCTAAAAACAG
131 CCTATTTCTCTCCCTCAAACATCTAAAAACAG
21972 GAGCAGAAAA
Statistics
Matches: 160, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
166 160 1.00
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (166 bp):
TATACGATATCAATGGAAGCAAGAGTAGCAAACTGTGAGAAGAAATATTAGATTCTATCATCCTA
AATAATTCAAACATCCTTGCGCAAATAAGAAGATCATGACATGTAAGCAAATGGGCCAGTGAAAG
CCTATTTCTCTCCCTCAAACATCTAAAAACAGCAAG
Found at i:23240 original size:12 final size:12
Alignment explanation
Indices: 23223--23249 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
23213 GTTGTTGAAC
23223 TGAATTAATTAG
1 TGAATTAATTAG
23235 TGAATTAATTAG
1 TGAATTAATTAG
23247 TGA
1 TGA
23250 GGTCTCGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (12 bp):
TGAATTAATTAG
Found at i:26978 original size:6 final size:6
Alignment explanation
Indices: 26967--27003 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
26957 AGTTCATATA
26967 ATGACC ATGACC ATGACC ATGACC ATGACC ATGACC A
1 ATGACC ATGACC ATGACC ATGACC ATGACC ATGACC A
27004 ATGGGTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.35, C:0.32, G:0.16, T:0.16
Consensus pattern (6 bp):
ATGACC
Found at i:34433 original size:67 final size:64
Alignment explanation
Indices: 34307--34453 Score: 223
Period size: 59 Copynumber: 2.3 Consensus size: 64
34297 CAATCTTGGG
34307 ATGACAACTTCTGGTGTCAATAATTTCCTCAGCATGACAACTTCTGGTGTCAAGATAATAATTTG
1 ATGACAACTTCTGGTGTCAATAATTT-CT-A-CATGACAACTTCTGGTGTCAAGATAATAATTTG
34372 AT
63 AT
*
34374 ATGACAACTTCTGGTGTCAATAATTT-T-CATGACAACTTCTGGTGTCAAG---ATAATTTAAT
1 ATGACAACTTCTGGTGTCAATAATTTCTACATGACAACTTCTGGTGTCAAGATAATAATTTGAT
34433 ATGACAACTTCTGGTGTCAAT
1 ATGACAACTTCTGGTGTCAAT
34454 TAAATTTTAA
Statistics
Matches: 79, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
59 30 0.38
62 22 0.28
65 1 0.01
67 26 0.33
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Consensus pattern (64 bp):
ATGACAACTTCTGGTGTCAATAATTTCTACATGACAACTTCTGGTGTCAAGATAATAATTTGAT
Found at i:34440 original size:31 final size:30
Alignment explanation
Indices: 34340--34452 Score: 151
Period size: 31 Copynumber: 3.7 Consensus size: 30
34330 TTTCCTCAGC
34340 ATGACAACTTCTGGTGTCAAGATAATAATTTGAT
1 ATGACAACTTCTGGTGTCAAG---ATAATTT-AT
34374 ATGACAACTTCTGGTGTC-A-ATAATTT-T
1 ATGACAACTTCTGGTGTCAAGATAATTTAT
34401 CATGACAACTTCTGGTGTCAAGATAATTTAAT
1 -ATGACAACTTCTGGTGTCAAGATAATTT-AT
34433 ATGACAACTTCTGGTGTCAA
1 ATGACAACTTCTGGTGTCAA
34453 TTAAATTTTA
Statistics
Matches: 74, Mismatches: 0, Indels: 13
0.85 0.00 0.15
Matches are distributed among these distances:
27 1 0.01
28 18 0.24
29 8 0.11
30 7 0.09
31 20 0.27
32 1 0.01
33 1 0.01
34 18 0.24
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (30 bp):
ATGACAACTTCTGGTGTCAAGATAATTTAT
Found at i:34956 original size:37 final size:37
Alignment explanation
Indices: 34906--34981 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
34896 TGGAAATTAC
34906 TTAAAGGCCAAATTCAGGAATAATGTGGTGCCTCCTT
1 TTAAAGGCCAAATTCAGGAATAATGTGGTGCCTCCTT
34943 TTAAAGGCCAAATTCAGGAATAATGTGGTGCCTCCTT
1 TTAAAGGCCAAATTCAGGAATAATGTGGTGCCTCCTT
34980 TT
1 TT
34982 GGTTTTTTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (37 bp):
TTAAAGGCCAAATTCAGGAATAATGTGGTGCCTCCTT
Found at i:35511 original size:21 final size:22
Alignment explanation
Indices: 35487--35527 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
35477 TACTTAAATT
35487 TAAAAA-TCTTCTTTTATTTTA
1 TAAAAAGTCTTCTTTTATTTTA
* *
35508 TAAAAAGTTTTTTTTTATTT
1 TAAAAAGTCTTCTTTTATTT
35528 ATCATTCGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (22 bp):
TAAAAAGTCTTCTTTTATTTTA
Found at i:40041 original size:29 final size:29
Alignment explanation
Indices: 39983--40204 Score: 218
Period size: 29 Copynumber: 7.7 Consensus size: 29
39973 GGTCACTTAA
*
39983 AGGGGCATTTTGATCA-TTTTGCATGA-CC
1 AGGGGCATTTTGGTCATTTTTGCAT-ATCC
*
40011 AGGGGCATTATGGTCATTTTTGCATATCC
1 AGGGGCATTTTGGTCATTTTTGCATATCC
*
40040 AGGGGCATTTTGGTCATTTTTGCATATCA
1 AGGGGCATTTTGGTCATTTTTGCATATCC
* * ** *
40069 AAGGGCATTATGGTCATTTTCACGTATCCC
1 AGGGGCATTTTGGTCATTTTTGCATAT-CC
* ** *
40099 A-TGGCATTTTTATCATTTTTGC-TCATTC
1 AGGGGCATTTTGGTCATTTTTGCAT-ATCC
* *
40127 AGGAGCATTTTGGTCATTTTTGCACATCC
1 AGGGGCATTTTGGTCATTTTTGCATATCC
** *
40156 AATGGTATTTTGGTCATTTTTGCATATCC
1 AGGGGCATTTTGGTCATTTTTGCATATCC
* *
40185 AAGGGCATTATGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
40205 GGTTTTATTC
Statistics
Matches: 157, Mismatches: 31, Indels: 11
0.79 0.16 0.06
Matches are distributed among these distances:
28 18 0.11
29 137 0.87
30 2 0.01
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (29 bp):
AGGGGCATTTTGGTCATTTTTGCATATCC
Found at i:46463 original size:13 final size:13
Alignment explanation
Indices: 46445--46470 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46435 AAAGGGTCTT
46445 TCAACAGCAATGA
1 TCAACAGCAATGA
46458 TCAACAGCAATGA
1 TCAACAGCAATGA
46471 GTCCATGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.15, T:0.15
Consensus pattern (13 bp):
TCAACAGCAATGA
Found at i:47178 original size:23 final size:23
Alignment explanation
Indices: 47129--47543 Score: 296
Period size: 23 Copynumber: 18.2 Consensus size: 23
47119 GACAAATAAG
* * *
47129 CAAAACAACAACATTTCCCAACAT
1 CAAAACAGCAACATTT-TCAACAA
* * *
47153 CAAAACAGTAACATTTTGAACAT
1 CAAAACAGCAACATTTTCAACAA
*
47176 CAAAACAGCAAAACAACATTTTCAATAGA
1 CAAAACAG-----CAACATTTTCAACA-A
* * * *
47205 AAAAACAGCAGCAATTTCAACAG
1 CAAAACAGCAACATTTTCAACAA
* *
47228 CAAAACAACAGCATTTTCAACAA
1 CAAAACAGCAACATTTTCAACAA
* *
47251 CAAAACATCAACATTTTCAACAT
1 CAAAACAGCAACATTTTCAACAA
* *
47274 CAAAACAGCAACATCTTGAACAA
1 CAAAACAGCAACATTTTCAACAA
*
47297 CAAAACAACAACATTTTCAACAGA
1 CAAAACAGCAACATTTTCAACA-A
* * * *
47321 -AAAATAGCAGCAATTTCAACAG
1 CAAAACAGCAACATTTTCAACAA
* *
47343 CAAAACATCAGCATTTTCAAC-A
1 CAAAACAGCAACATTTTCAACAA
* *
47365 CAAAATAGCAGCATTTTCAACAA
1 CAAAACAGCAACATTTTCAACAA
* *
47388 CAAAACAGTAACATTTTCAACAT
1 CAAAACAGCAACATTTTCAACAA
* *
47411 CAAAACAGCAACATCTT---GAA
1 CAAAACAGCAACATTTTCAACAA
*
47431 C---A-GGCAACATTTTCAAC-A
1 CAAAACAGCAACATTTTCAACAA
** * * * *
47449 GGAAACAGTAGCAATTTCAACAG
1 CAAAACAGCAACATTTTCAACAA
*
47472 CAAAACAGCAGCATTTTCAAC-A
1 CAAAACAGCAACATTTTCAACAA
* *
47494 CAAAATAGCAGCATTTTCAACAA
1 CAAAACAGCAACATTTTCAACAA
*
47517 C-AAACAACAACATTTTCAACAA
1 CAAAACAGCAACATTTTCAACAA
*
47539 AAAAA
1 CAAAA
47544 AAACAGAAAT
Statistics
Matches: 307, Mismatches: 65, Indels: 39
0.75 0.16 0.09
Matches are distributed among these distances:
16 9 0.03
17 1 0.00
18 1 0.00
20 2 0.01
21 1 0.00
22 68 0.22
23 181 0.59
24 26 0.08
28 11 0.04
29 7 0.02
ACGTcount: A:0.50, C:0.24, G:0.07, T:0.19
Consensus pattern (23 bp):
CAAAACAGCAACATTTTCAACAA
Found at i:47439 original size:16 final size:16
Alignment explanation
Indices: 47414--47455 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
47404 TCAACATCAA
*
47414 AACA-GCAACATCTTG
1 AACAGGCAACATCTTC
*
47429 AACAGGCAACATTTTC
1 AACAGGCAACATCTTC
*
47445 AACAGGAAACA
1 AACAGGCAACA
47456 GTAGCAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.45, C:0.24, G:0.14, T:0.17
Consensus pattern (16 bp):
AACAGGCAACATCTTC
Found at i:50154 original size:23 final size:23
Alignment explanation
Indices: 50124--50245 Score: 127
Period size: 23 Copynumber: 5.3 Consensus size: 23
50114 AAAAAACAAC
*
50124 AACAACAACATTTTGATCATCAA
1 AACAACAACATTTTGAACATCAA
50147 AACAACAACATTTTGAACATCAA
1 AACAACAACATTTTGAACATCAA
* **
50170 AACAACAACATCTTGAACAGAAA
1 AACAACAACATTTTGAACATCAA
* * * **
50193 AACAATAACATCTTCAACAGAAA
1 AACAACAACATTTTGAACATCAA
* * **
50216 AACAATAACATTTTCAACAGAAA
1 AACAACAACATTTTGAACATCAA
50239 AACAACA
1 AACAACA
50246 GCAATTTCAG
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 91 1.00
ACGTcount: A:0.55, C:0.21, G:0.05, T:0.19
Consensus pattern (23 bp):
AACAACAACATTTTGAACATCAA
Found at i:50174 original size:46 final size:46
Alignment explanation
Indices: 50124--50245 Score: 145
Period size: 46 Copynumber: 2.7 Consensus size: 46
50114 AAAAAACAAC
* ** * * **
50124 AACAACAACATTTTGATCATCAAAACAACAACATTTTGAACATCAA
1 AACAACAACATTTTGAACAGAAAAACAACAACATCTTCAACAGAAA
* *
50170 AACAACAACATCTTGAACAGAAAAACAATAACATCTTCAACAGAAA
1 AACAACAACATTTTGAACAGAAAAACAACAACATCTTCAACAGAAA
* *
50216 AACAATAACATTTTCAACAGAAAAACAACA
1 AACAACAACATTTTGAACAGAAAAACAACA
50246 GCAATTTCAG
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 63 1.00
ACGTcount: A:0.55, C:0.21, G:0.05, T:0.19
Consensus pattern (46 bp):
AACAACAACATTTTGAACAGAAAAACAACAACATCTTCAACAGAAA
Found at i:51866 original size:20 final size:19
Alignment explanation
Indices: 51841--51878 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
51831 AAAAAAATAG
51841 GTGTTGGGTATATCAGAAAC
1 GTGTTGGGTATAT-AGAAAC
51861 GTGTTGGGTATATAGAAA
1 GTGTTGGGTATATAGAAA
51879 AAATGACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.32, C:0.05, G:0.32, T:0.32
Consensus pattern (19 bp):
GTGTTGGGTATATAGAAAC
Found at i:51916 original size:7 final size:7
Alignment explanation
Indices: 51899--51930 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
51889 ATTTAATTAA
51899 TTGGG-T
1 TTGGGCT
51905 TTGGGCT
1 TTGGGCT
51912 TTGGGCT
1 TTGGGCT
51919 TTGGGCT
1 TTGGGCT
51926 TTGGG
1 TTGGG
51931 TTGGGTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.20
7 20 0.80
ACGTcount: A:0.00, C:0.09, G:0.47, T:0.44
Consensus pattern (7 bp):
TTGGGCT
Found at i:51923 original size:14 final size:13
Alignment explanation
Indices: 51899--51945 Score: 60
Period size: 14 Copynumber: 3.5 Consensus size: 13
51889 ATTTAATTAA
51899 TTGGGTTTGGGCT
1 TTGGGTTTGGGCT
51912 TTGGGCTTTGGGCT
1 TTGGG-TTTGGGCT
*
51926 TTGGG-TTGGGTAT
1 TTGGGTTTGGG-CT
51939 TTGGGTT
1 TTGGGTT
51946 GGGTATATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 5 0.17
13 11 0.37
14 14 0.47
ACGTcount: A:0.02, C:0.06, G:0.45, T:0.47
Consensus pattern (13 bp):
TTGGGTTTGGGCT
Found at i:51943 original size:13 final size:13
Alignment explanation
Indices: 51925--51951 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
51915 GGCTTTGGGC
51925 TTTGGGTTGGGTA
1 TTTGGGTTGGGTA
51938 TTTGGGTTGGGTA
1 TTTGGGTTGGGTA
51951 T
1 T
51952 ATCATAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.00, G:0.44, T:0.48
Consensus pattern (13 bp):
TTTGGGTTGGGTA
Found at i:53456 original size:28 final size:28
Alignment explanation
Indices: 53400--53459 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
53390 ACCTTATAAT
* * *
53400 AAATTGAATAACCTGATAAGACGCCAAA
1 AAATTGAATAACCTGATAAAAAGCAAAA
*
53428 AAATTGAATAACCTGATAATAAAGAAAAA
1 AAATTGAATAACCTGATAA-AAAGCAAAA
53457 AAA
1 AAA
53460 GATAGTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.18
Consensus pattern (28 bp):
AAATTGAATAACCTGATAAAAAGCAAAA
Found at i:60118 original size:30 final size:30
Alignment explanation
Indices: 60082--60182 Score: 148
Period size: 30 Copynumber: 3.4 Consensus size: 30
60072 AAATTCTGAG
* *
60082 GATGATTTTGACTCGGATGTGGATCCCGAA
1 GATGATTTTGACCCGGATGAGGATCCCGAA
* *
60112 GATGATTTTGGCCCAGATGAGGATCCCGAA
1 GATGATTTTGACCCGGATGAGGATCCCGAA
60142 GATGATTTTGACCCGGATGAGGATCCCGAA
1 GATGATTTTGACCCGGATGAGGATCCCGAA
* *
60172 GAAGAGTTTGA
1 GATGATTTTGA
60183 GGAGTCAGCC
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.26
Consensus pattern (30 bp):
GATGATTTTGACCCGGATGAGGATCCCGAA
Found at i:63801 original size:39 final size:41
Alignment explanation
Indices: 63757--63852 Score: 118
Period size: 35 Copynumber: 2.5 Consensus size: 41
63747 TGCTTTTGAT
63757 GGGAACTTTCCCACTTTGAAAATTG-AAACCAAAA-CTGAC
1 GGGAACTTTCCCACTTTGAAAATTGAAAACCAAAACCTGAC
*
63796 GGGAACTTT-CC-C--TG--AATTGAAAACTAAAACCTGAC
1 GGGAACTTTCCCACTTTGAAAATTGAAAACCAAAACCTGAC
*
63831 GGGAACTTTCCCAATTTGAAAA
1 GGGAACTTTCCCACTTTGAAAA
63853 AGAGCTAGAT
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
33 5 0.11
34 8 0.17
35 16 0.34
36 2 0.04
37 1 0.02
38 2 0.04
39 11 0.23
41 2 0.04
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.24
Consensus pattern (41 bp):
GGGAACTTTCCCACTTTGAAAATTGAAAACCAAAACCTGAC
Found at i:63888 original size:52 final size:52
Alignment explanation
Indices: 63831--64213 Score: 610
Period size: 52 Copynumber: 7.4 Consensus size: 52
63821 AAAACCTGAC
*
63831 GGGAACTTTCCCAATTTGAAAAAGAGCTAGATTGAATACTTTTAAAACTGGT
1 GGGAACTTTCCCAATTTGAAAAAGAGCTAGATTGAATACTTTGAAAACTGGT
63883 GGGAACTTTCCCAATTTGAAAAAGAGCTAGATTGAATACTTTGAAAACTGGT
1 GGGAACTTTCCCAATTTGAAAAAGAGCTAGATTGAATACTTTGAAAACTGGT
63935 GGGAACTTTCCCAATTT-AAAAA-AGCTAGATTGAATACTTTGAAAACTGGT
1 GGGAACTTTCCCAATTTGAAAAAGAGCTAGATTGAATACTTTGAAAACTGGT
*
63985 GGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTGAAAACTGGT
1 GGGAACTTTCCCAATTTGAAAAAGAGCTAGATTGAATACTTTGAAAACTGGT
* * *
64037 GGGAACTTTCTCAATTTAAAAAAAAGCTAGATTGAATACTTTGAAAACTGGT
1 GGGAACTTTCCCAATTTGAAAAAGAGCTAGATTGAATACTTTGAAAACTGGT
* * *
64089 GGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTGCAAACTTGAT
1 GGGAACTTTCCCAATTTGAAAAAGAGCTAGATTGAATACTTTGAAAAC-TGGT
* * * *
64142 GGGAACTTTCCCAATTTTAAAAA-AGCTTAAATTGAATACTTTGAAAATTGAT
1 GGGAACTTTCCCAATTTGAAAAAGAGC-TAGATTGAATACTTTGAAAACTGGT
*
64194 GGGAACTTTCTCAATTTGAA
1 GGGAACTTTCCCAATTTGAA
64214 GACTTTAAAA
Statistics
Matches: 310, Mismatches: 17, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
50 45 0.15
51 10 0.03
52 211 0.68
53 44 0.14
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (52 bp):
GGGAACTTTCCCAATTTGAAAAAGAGCTAGATTGAATACTTTGAAAACTGGT
Found at i:64020 original size:154 final size:157
Alignment explanation
Indices: 63821--64213 Score: 632
Period size: 154 Copynumber: 2.5 Consensus size: 157
63811 ATTGAAAACT
* * * *
63821 AAAACCTGACGGGAACTTTCCCAATTTGAAAAAGAGCTAGATTGAATACTTTTAAAACTGGTGGG
1 AAAACTTGATGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTGAAAACTGGTGGG
* *
63886 AACTTTCCCAATTTGAAAAAGAGCTAGATTGAATACTTTGAAAACTGGTGGGAACTTTCCCAATT
66 AACTTTCTCAATTTGAAAAAAAGCTAGATTGAATACTTTGAAAACTGGTGGGAACTTTCCCAATT
*
63951 T-AAAAA-AGCTAGATTGAATACTTTG
131 TGAAAAAGAGCTAAATTGAATACTTTG
*
63976 AAAAC-TGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTGAAAACTGGTGGG
1 AAAACTTGATGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTGAAAACTGGTGGG
*
64040 AACTTTCTCAATTTAAAAAAAAGCTAGATTGAATACTTTGAAAACTGGTGGGAACTTTCCCAATT
66 AACTTTCTCAATTTGAAAAAAAGCTAGATTGAATACTTTGAAAACTGGTGGGAACTTTCCCAATT
64105 TGAAAAAGAGCTAAATTGAATACTTTG
131 TGAAAAAGAGCTAAATTGAATACTTTG
* * * *
64132 CAAACTTGATGGGAACTTTCCCAATTTTAAAAA-AGCTTAAATTGAATACTTTGAAAATTGATGG
1 AAAACTTGATGGGAACTTTCCCAATTTGAAAAAGAGC-TAAATTGAATACTTTGAAAACTGGTGG
64196 GAACTTTCTCAATTTGAA
65 GAACTTTCTCAATTTGAA
64214 GACTTTAAAA
Statistics
Matches: 220, Mismatches: 14, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
154 118 0.54
155 10 0.05
156 25 0.11
157 67 0.30
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (157 bp):
AAAACTTGATGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTGAAAACTGGTGGG
AACTTTCTCAATTTGAAAAAAAGCTAGATTGAATACTTTGAAAACTGGTGGGAACTTTCCCAATT
TGAAAAAGAGCTAAATTGAATACTTTG
Found at i:64235 original size:37 final size:37
Alignment explanation
Indices: 64173--64289 Score: 166
Period size: 37 Copynumber: 3.2 Consensus size: 37
64163 AAAGCTTAAA
*
64173 TTGAATACTTTGAAAA-TTGATGGGAACTTTCTCAAT
1 TTGAAAACTTTGAAAACTTGATGGGAACTTTCTCAAT
* *
64209 TTGAAGACTTTAAAAACTTGATGGGAACTTT-TCCAAT
1 TTGAAAACTTTGAAAACTTGATGGGAACTTTCT-CAAT
* *
64246 TTGAAAACTATGAAGACTTGATGGGAACTTTCTCAAT
1 TTGAAAACTTTGAAAACTTGATGGGAACTTTCTCAAT
64283 TTGAAAA
1 TTGAAAA
64290 ACTAAGTTGA
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
36 15 0.21
37 56 0.78
38 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (37 bp):
TTGAAAACTTTGAAAACTTGATGGGAACTTTCTCAAT
Found at i:64986 original size:26 final size:26
Alignment explanation
Indices: 64968--65028 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
64958 TAATAAGTAG
64968 AAGCCCAAAGCCTAGATAATAAATCA
1 AAGCCCAAAGCCTAGATAATAAATCA
64994 AAGCCCAAAGCCTAGATAATAAATCA
1 AAGCCCAAAGCCTAGATAATAAATCA
65020 AAGCCCAAA
1 AAGCCCAAA
65029 AAATTATACC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.51, C:0.25, G:0.11, T:0.13
Consensus pattern (26 bp):
AAGCCCAAAGCCTAGATAATAAATCA
Found at i:65754 original size:1 final size:1
Alignment explanation
Indices: 65750--65778 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
65740 AAGGGTAAGG
65750 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
65779 ACTTCGGTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:75475 original size:55 final size:55
Alignment explanation
Indices: 75410--75520 Score: 195
Period size: 55 Copynumber: 2.0 Consensus size: 55
75400 AACGAAGATG
75410 AAGATGATCACCAACACGCAAGATAATCAATGCATAAAAGAGGCAAATCATATAT
1 AAGATGATCACCAACACGCAAGATAATCAATGCATAAAAGAGGCAAATCATATAT
* * *
75465 AAGATGATCACCAACATGCAAGATAATCAATGCGTAAAAGAGGCAAATCCTATAT
1 AAGATGATCACCAACACGCAAGATAATCAATGCATAAAAGAGGCAAATCATATAT
75520 A
1 A
75521 TTCTAATTAA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.19
Consensus pattern (55 bp):
AAGATGATCACCAACACGCAAGATAATCAATGCATAAAAGAGGCAAATCATATAT
Found at i:75973 original size:2 final size:2
Alignment explanation
Indices: 75966--75993 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
75956 AGGAAAACTT
75966 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
75994 GTAAGTAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:77172 original size:12 final size:12
Alignment explanation
Indices: 77155--77180 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
77145 TTAATTAATA
77155 ATTGTAATTAAC
1 ATTGTAATTAAC
77167 ATTGTAATTAAC
1 ATTGTAATTAAC
77179 AT
1 AT
77181 ATTTAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (12 bp):
ATTGTAATTAAC
Found at i:82627 original size:41 final size:41
Alignment explanation
Indices: 82570--82653 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
82560 GCCCATGAGC
82570 AAGTCTAATCATAAGTATGTGTAGACACCAAAATTTGGGCT
1 AAGTCTAATCATAAGTATGTGTAGACACCAAAATTTGGGCT
82611 AAGTCTAATCATAAGTATGTGTAGACACCAAAATTTGGGCT
1 AAGTCTAATCATAAGTATGTGTAGACACCAAAATTTGGGCT
82652 AA
1 AA
82654 TTAATTTTGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (41 bp):
AAGTCTAATCATAAGTATGTGTAGACACCAAAATTTGGGCT
Found at i:86610 original size:17 final size:16
Alignment explanation
Indices: 86564--86612 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
86554 CTATGGAGAT
*
86564 CATGGAGAGGATG-AG
1 CATGGAGAGCATGAAG
*
86579 CATGGAGTGCAATGAAG
1 CATGGAGAGC-ATGAAG
86596 CATGGAGAAGCATGAAG
1 CATGGAG-AGCATGAAG
86613 ATCAAGGAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 8 0.29
16 3 0.11
17 15 0.54
18 2 0.07
ACGTcount: A:0.37, C:0.10, G:0.39, T:0.14
Consensus pattern (16 bp):
CATGGAGAGCATGAAG
Found at i:89750 original size:535 final size:531
Alignment explanation
Indices: 88545--89615 Score: 1560
Period size: 535 Copynumber: 2.0 Consensus size: 531
88535 CAATCCTTAT
* ** * * *
88545 ATATCCCTCTCATTAGTTATTAGTGAATTGACATAAAGACAGCATCAA-GCAACAAATTCAGGTC
1 ATATCCCTCTCATAAAATATTAGTCAATTGACATAAAGACAGCA-GAAGGCAACAAAGTC--GTC
* * *
88609 ACAGCAGCAATATTCCATAAAGATTTACCAGGCACTTATTAACCAATCAACACGACAAGAATTAA
63 ACAGCAGCAATATT-C-TAAAGATTTACCAGACACTTATTAACCAATCAATACGACAAGACTTAA
88674 ACAGAACTTACTGAAAACTGAGACATAATGTAAATTAGAGCTAGCTCAACTTAATGAGGCAATAA
126 ACAGAACTTACTGAAAACTGAGACATAATGTAAATTAGAGCTAGCTCAACTTAATGAGGCAATAA
*
88739 GAGTTGTAAGAATTAGTGAAACTACATGATTATAAACCGAAGCAATAAGTAAGATAGAATGAAGT
191 GAGTTGTAAGAATGAGTGAAACTACATGATTATAAACCGAAGCAATAAGTAAGATAGAATGAAGT
*
88804 GAATATACCTCAGATTTCTTCAGAATGCCATTTGGATCACATGTTACAATCCAACCAAGACGCCA
256 GAATATACCCCAGATTTCTTCAGAATGCCATTTGGATCACATGTTACAATCCAACCAAGACGCCA
88869 ACCGGGAACAATCCATTTCTTTGATATAGTTACCAGTGTAAGAACAGGCACAACAGATGCAAACT
321 ACCGGGAACAATCCATTTCTTTGATATAGTTACCAGTGTAAGAACAGGCACAACAGATGCAAACT
*
88934 TGCCCATGGGTATAAATGGATTGCTCCCAAAAGTTAGATAGCCATAAACCTCATCAACAATGACA
386 TGCCCATGGGTATAAATGGATTGCTCCCAAAAGTTAGATAGCCATAAACCTCATCAACAATAACA
* * * * * * * * **** * *
88999 TATTCCAAGCTTTTGTATTAAAGTTAAGTTTATCAATCAAAGAGAGTTTCTTTTGAAAATTTAGC
451 TATTCCAAGCTTTTGCATTAAAGTCAACTTGAACAACCAAACAGAGATAAAATTGAAAATCTAGA
* * * * *
89064 TTCATTTATACCTTAT
516 TACATATAGACATTAA
* ** * * * *
89080 ATATCCCTCTCATTAGTTATTAGTGAATTGACATAAAGACAGCAGCATGCAACAAATTCAGGTCA
1 ATATCCCTCTCATAAAATATTAGTCAATTGACATAAAGACAGCAGAAGGCAACAAAGTC--GTCA
*
89145 CAGCAGCAATATTCCATAAAGATTTACCAGGCACTTATTAACCAATCAATACGACAAGACTTAAA
64 CAGCAGCAATATT-C-TAAAGATTTACCAGACACTTATTAACCAATCAATACGACAAGACTTAAA
89210 CAGAACTTACTGAAAACTGAGACATAATGTAAATTAGAGCTAGCTCAACTTAATGAGGCAATAAG
127 CAGAACTTACTGAAAACTGAGACATAATGTAAATTAGAGCTAGCTCAACTTAATGAGGCAATAAG
89275 AGTTGTAAGAATGAGTGAAACTACATGATTATAAACCGAAGCAATAAGTAAGATAGAATGAAGTG
192 AGTTGTAAGAATGAGTGAAACTACATGATTATAAACCGAAGCAATAAGTAAGATAGAATGAAGTG
*
89340 CATATACCCCAGATTTCTTCAGAATGCCATTTGGATCACATGTTACAATCCAACCAAGACGCCAA
257 AATATACCCCAGATTTCTTCAGAATGCCATTTGGATCACATGTTACAATCCAACCAAGACGCCAA
89405 CCGGGAACAATCCATTTCTTTGATATAGTTACCAGTGTAAGAACAGGCACAACAGATGCAAACTT
322 CCGGGAACAATCCATTTCTTTGATATAGTTACCAGTGTAAGAACAGGCACAACAGATGCAAACTT
89470 GCCCATGGGTATAAATGGATTGCTCCCAAAAGTTAGATAGCCATAAACCTCATCAACAATAACAT
387 GCCCATGGGTATAAATGGATTGCTCCCAAAAGTTAGATAGCCATAAACCTCATCAACAATAACAT
** *
89535 ATTCCAAGCTTTCTTGCAGTTTCAG-CAACCTTGGAACCACCAAACA-A-ATAAAATT-AAAGAC
452 ATTCCAAGC-TT-TTGCA-TTAAAGTCAA-CTT-GAACAACCAAACAGAGATAAAATTGAAA-A-
*
89596 TCTA-ATACATATAGATATTA
510 TCTAGATACATATAGACATTA
89616 GCAATTCCAG
Statistics
Matches: 498, Mismatches: 30, Indels: 14
0.92 0.06 0.03
Matches are distributed among these distances:
534 1 0.00
535 454 0.91
536 5 0.01
537 20 0.04
538 10 0.02
539 8 0.02
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.26
Consensus pattern (531 bp):
ATATCCCTCTCATAAAATATTAGTCAATTGACATAAAGACAGCAGAAGGCAACAAAGTCGTCACA
GCAGCAATATTCTAAAGATTTACCAGACACTTATTAACCAATCAATACGACAAGACTTAAACAGA
ACTTACTGAAAACTGAGACATAATGTAAATTAGAGCTAGCTCAACTTAATGAGGCAATAAGAGTT
GTAAGAATGAGTGAAACTACATGATTATAAACCGAAGCAATAAGTAAGATAGAATGAAGTGAATA
TACCCCAGATTTCTTCAGAATGCCATTTGGATCACATGTTACAATCCAACCAAGACGCCAACCGG
GAACAATCCATTTCTTTGATATAGTTACCAGTGTAAGAACAGGCACAACAGATGCAAACTTGCCC
ATGGGTATAAATGGATTGCTCCCAAAAGTTAGATAGCCATAAACCTCATCAACAATAACATATTC
CAAGCTTTTGCATTAAAGTCAACTTGAACAACCAAACAGAGATAAAATTGAAAATCTAGATACAT
ATAGACATTAA
Found at i:91541 original size:29 final size:29
Alignment explanation
Indices: 91504--91577 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
91494 AATTATTAGT
91504 TTGAAATTTAATTAGTTAATTATTCTTAA
1 TTGAAATTTAATTAGTTAATTATTCTTAA
*
91533 TTGAAATTTAATTAAAATTAATTATTCTTAA
1 TTGAAATTTAATT--AGTTAATTATTCTTAA
91564 TT--AATTT-ATTAGTT
1 TTGAAATTTAATTAGTT
91578 TGACTTAGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 3 0.07
28 3 0.07
29 18 0.44
31 17 0.41
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (29 bp):
TTGAAATTTAATTAGTTAATTATTCTTAA
Found at i:91554 original size:31 final size:29
Alignment explanation
Indices: 91488--91565 Score: 97
Period size: 31 Copynumber: 2.7 Consensus size: 29
91478 TTAATTATTC
**
91488 TTAATTAATTATTAGT--TTGAAATTTAA
1 TTAATTAATTATTCTTAATTGAAATTTAA
*
91515 TTAGTTAATTATTCTTAATTGAAATTTAA
1 TTAATTAATTATTCTTAATTGAAATTTAA
91544 TTAAAATTAATTATTCTTAATT
1 TT--AATTAATTATTCTTAATT
91566 AATTTATTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 13 0.30
29 13 0.30
31 17 0.40
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (29 bp):
TTAATTAATTATTCTTAATTGAAATTTAA
Found at i:93657 original size:18 final size:19
Alignment explanation
Indices: 93614--93658 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
93604 AAATAAATCA
93614 TTTCTTTGACTTATTATAT
1 TTTCTTTGACTTATTATAT
* * *
93633 TTCCTTT-ACTTATTTTGT
1 TTTCTTTGACTTATTATAT
93651 TTTCTTTG
1 TTTCTTTG
93659 TTTCTTTGTA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.13, C:0.13, G:0.07, T:0.67
Consensus pattern (19 bp):
TTTCTTTGACTTATTATAT
Found at i:104209 original size:40 final size:40
Alignment explanation
Indices: 104154--104479 Score: 503
Period size: 40 Copynumber: 8.2 Consensus size: 40
104144 GATCAGTCTT
* *
104154 GTGTTGTCTAAATACCCAGTTTGCCCTTCCCCATCGGAAG
1 GTGTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAG
*
104194 GTGTTGTTTAAATACCCAGTTTGCCCTTCCCCATCGGAAG
1 GTGTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAG
*
104234 GTGTTGTTTAAATACCCAATTTGCCCTTCCCCACCGGAAG
1 GTGTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAG
104274 GTGTTGTTTAAATACCCA-TTTGCCCTTCCCCACCGGAAG
1 GTGTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAG
104313 GTGTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAG
1 GTGTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAG
104353 GTGTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAG
1 GTGTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAG
* * * *
104393 GTGTTGTTTAAATA-CCAGTTTGCCTTTCCCTACTGGAAA
1 GTGTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAG
* * ** * * *
104432 GTGTTGTCTAAATTCTTAGTTTGCCCTTCCTCATCGGGAG
1 GTGTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAG
104472 GTGTTGTT
1 GTGTTGTT
104480 CCTATTCCTT
Statistics
Matches: 265, Mismatches: 19, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
39 72 0.27
40 193 0.73
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (40 bp):
GTGTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAG
Found at i:104311 original size:119 final size:120
Alignment explanation
Indices: 104154--104479 Score: 512
Period size: 119 Copynumber: 2.7 Consensus size: 120
104144 GATCAGTCTT
* *
104154 GTGTTGTCTAAATACCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAATACCCAGTTTGCC
1 GTGTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCCAGTTTGCC
104219 CTTCCCCATCGGAAGGTGTTGTTTAAATACCCAATTTGCCCTTCCCCACCGGAAG
66 CTTCCCCATCGGAAGGTGTTGTTTAAATACCCAATTTGCCCTTCCCCACCGGAAG
104274 GTGTTGTTTAAATACCCA-TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCCAGTTTGCC
1 GTGTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCCAGTTTGCC
* *
104338 CTTCCCCACCGGAAGGTGTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAG
66 CTTCCCCATCGGAAGGTGTTGTTTAAATACCCAATTTGCCCTTCCCCACCGGAAG
* * * * * * **
104393 GTGTTGTTTAAATA-CCAGTTTGCCTTTCCCTACTGGAAAGTGTTGTCTAAATTCTTAGTTTGCC
1 GTGTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCCAGTTTGCC
* *
104457 CTTCCTCATCGGGAGGTGTTGTT
66 CTTCCCCATCGGAAGGTGTTGTT
104480 CCTATTCCTT
Statistics
Matches: 190, Mismatches: 15, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
118 3 0.02
119 170 0.89
120 17 0.09
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (120 bp):
GTGTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCCAGTTTGCC
CTTCCCCATCGGAAGGTGTTGTTTAAATACCCAATTTGCCCTTCCCCACCGGAAG
Found at i:104336 original size:79 final size:80
Alignment explanation
Indices: 104154--104479 Score: 503
Period size: 79 Copynumber: 4.1 Consensus size: 80
104144 GATCAGTCTT
* *
104154 GTGTTGTCTAAATACCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAATACCCAGTTTGCC
1 GTGTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCCAGTTTGCC
*
104219 CTTCCCCATCGGAAG
66 CTTCCCCACCGGAAG
*
104234 GTGTTGTTTAAATACCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCCA-TTTGCC
1 GTGTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCCAGTTTGCC
104298 CTTCCCCACCGGAAG
66 CTTCCCCACCGGAAG
104313 GTGTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCCAGTTTGCC
1 GTGTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCCAGTTTGCC
104378 CTTCCCCACCGGAAG
66 CTTCCCCACCGGAAG
* * * * * * **
104393 GTGTTGTTTAAATA-CCAGTTTGCCTTTCCCTACTGGAAAGTGTTGTCTAAATTCTTAGTTTGCC
1 GTGTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCCAGTTTGCC
* * *
104457 CTTCCTCATCGGGAG
66 CTTCCCCACCGGAAG
104472 GTGTTGTT
1 GTGTTGTT
104480 CCTATTCCTT
Statistics
Matches: 229, Mismatches: 16, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
79 139 0.61
80 90 0.39
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (80 bp):
GTGTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCCAGTTTGCC
CTTCCCCACCGGAAG
Found at i:107854 original size:30 final size:27
Alignment explanation
Indices: 107769--107851 Score: 121
Period size: 30 Copynumber: 3.0 Consensus size: 27
107759 ATTAATTTAG
107769 ACTTATTATTATTATAATAATTATTAA
1 ACTTATTATTATTATAATAATTATTAA
*
107796 ACTTATTATTAGTGGTATTATAATTATTAA
1 ACTTATTATTA-T--TATAATAATTATTAA
*
107826 ACTTATTATTATAATAATAATTATTA
1 ACTTATTATTATTATAATAATTATTA
107852 TTAGTGGTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
27 23 0.46
28 1 0.02
29 1 0.02
30 25 0.50
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (27 bp):
ACTTATTATTATTATAATAATTATTAA
Done.