Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010891.1 Kokia drynarioides strain JFW-HI SEQ_125859, 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: 111560
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:28 original size:17 final size:18
Alignment explanation
Indices: 1--48 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
*
1 AAAATAAATTTAAATTTT
1 AAAACAAATTTAAATTTT
19 -AAACAAATTT-AATTTT
1 AAAACAAATTTAAATTTT
*
35 AAAATAAATTTAAA
1 AAAACAAATTTAAA
49 GAGAGTATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 6 0.23
17 18 0.69
18 2 0.08
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAACAAATTTAAATTTT
Found at i:1087 original size:49 final size:49
Alignment explanation
Indices: 799--1094 Score: 195
Period size: 49 Copynumber: 6.0 Consensus size: 49
789 ACCTAAAAAA
* * *
799 CATGAAGATTTGAAGGGAAAGGTTGAGGTCGCAACGACGAACCCAATAC
1 CATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGACGAACCTAATAC
* * * * * * * * * * *
848 CTTAGAATATGAGATGGGAAAGGTTGAGACCACAATGGCGAACCCAAAAT
1 CAT-GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGACGAACCTAATAC
* * * * * * **
898 CATGAAGGTGTGAAGGGAAAGGTTGAGGCTGAAATGGC-AAGCTCGGTAC
1 CATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGACGAACCT-AATAC
* * ** * *
947 CTTAGAAGACGTGATCGG-AAGGATTGAGGCCTCAGCGACGAATCC-AATAC
1 CAT-GAAGATGTGAAGGGAAAGG-TTGAGGCCGCAACGACGAA-CCTAATAC
* * * ** *
997 CATGAA-ATGTTATGGGAAAGGTTGAGGCCGTAACGGTGAACCTGATAC
1 CATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGACGAACCTAATAC
* *
1045 CATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGACGAACCTAGTAC
1 CATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGACGAACCTAATAC
1094 C
1 C
1095 TTTGGAACAT
Statistics
Matches: 179, Mismatches: 59, Indels: 18
0.70 0.23 0.07
Matches are distributed among these distances:
47 2 0.01
48 34 0.19
49 78 0.44
50 62 0.35
51 2 0.01
52 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.30, T:0.18
Consensus pattern (49 bp):
CATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGACGAACCTAATAC
Found at i:1186 original size:37 final size:37
Alignment explanation
Indices: 1136--1287 Score: 178
Period size: 37 Copynumber: 3.8 Consensus size: 37
1126 AAAGTGATCA
1136 TCTTCCTGATGAGATATAGAGAAGTGGATTAAATTCG
1 TCTTCCTGATGAGATATAGAGAAGTGGATTAAATTCG
* *
1173 TCTTCCTGATGAGATACAGAGAAGTGGATTGAAACAATGGGGCGGTCA
1 TCTTCCTGATGAGATATAGAGAAGTGGATT---A-AAT-------TCG
*
1221 TCTTCCTGATAAGATATAGAGAAGTGGATTAAATTCG
1 TCTTCCTGATGAGATATAGAGAAGTGGATTAAATTCG
1258 TCTTCCTGATGAGATATAGAGAAGTGGATT
1 TCTTCCTGATGAGATATAGAGAAGTGGATT
1288 GAAACAATGA
Statistics
Matches: 98, Mismatches: 6, Indels: 22
0.78 0.05 0.17
Matches are distributed among these distances:
37 60 0.61
40 1 0.01
41 3 0.03
44 3 0.03
45 1 0.01
48 30 0.31
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (37 bp):
TCTTCCTGATGAGATATAGAGAAGTGGATTAAATTCG
Found at i:1244 original size:48 final size:47
Alignment explanation
Indices: 1173--1330 Score: 192
Period size: 48 Copynumber: 3.5 Consensus size: 47
1163 ATTAAATTCG
1173 TCTTCCTGATGAGATACAGAGAAGTGGATTGAAACAATGGGGCGGTCA
1 TCTTCCTGATGAGATACAGAGAAGTGGATTGAAACAAT-GGGCGGTCA
* * *
1221 TCTTCCTGATAAGATATAGAGAAGTGGATT---A-AAT------TCG
1 TCTTCCTGATGAGATACAGAGAAGTGGATTGAAACAATGGGCGGTCA
*
1258 TCTTCCTGATGAGATATAGAGAAGTGGATTGAAACAATGAGGCGGTCA
1 TCTTCCTGATGAGATACAGAGAAGTGGATTGAAACAATG-GGCGGTCA
1306 TCTTCCTGATGAGATACAGAGAAGT
1 TCTTCCTGATGAGATACAGAGAAGT
1331 AGACAAAATC
Statistics
Matches: 93, Mismatches: 6, Indels: 22
0.77 0.05 0.18
Matches are distributed among these distances:
37 31 0.33
40 1 0.01
41 3 0.03
44 3 0.03
45 1 0.01
48 54 0.58
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (47 bp):
TCTTCCTGATGAGATACAGAGAAGTGGATTGAAACAATGGGCGGTCA
Found at i:1279 original size:85 final size:85
Alignment explanation
Indices: 1133--1330 Score: 360
Period size: 85 Copynumber: 2.3 Consensus size: 85
1123 AATAAAGTGA
1133 TCATCTTCCTGATGAGATATAGAGAAGTGGATTAAATTCGTCTTCCTGATGAGATACAGAGAAGT
1 TCATCTTCCTGATGAGATATAGAGAAGTGGATTAAATTCGTCTTCCTGATGAGATACAGAGAAGT
*
1198 GGATTGAAACAATGGGGCGG
66 GGATTGAAACAATGAGGCGG
* *
1218 TCATCTTCCTGATAAGATATAGAGAAGTGGATTAAATTCGTCTTCCTGATGAGATATAGAGAAGT
1 TCATCTTCCTGATGAGATATAGAGAAGTGGATTAAATTCGTCTTCCTGATGAGATACAGAGAAGT
1283 GGATTGAAACAATGAGGCGG
66 GGATTGAAACAATGAGGCGG
*
1303 TCATCTTCCTGATGAGATACAGAGAAGT
1 TCATCTTCCTGATGAGATATAGAGAAGT
1331 AGACAAAATC
Statistics
Matches: 108, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 108 1.00
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (85 bp):
TCATCTTCCTGATGAGATATAGAGAAGTGGATTAAATTCGTCTTCCTGATGAGATACAGAGAAGT
GGATTGAAACAATGAGGCGG
Found at i:1563 original size:207 final size:208
Alignment explanation
Indices: 1173--1668 Score: 597
Period size: 207 Copynumber: 2.4 Consensus size: 208
1163 ATTAAATTCG
* *** *
1173 TCTTCCTGATGAGATACAGAGAAGTGGATTGAAA-CAATGGGGCGGTCATCTTCCTGATAAGATA
1 TCTTCCTGATGAGATACAGAGAAGTGGGTT-AAAGCAATAAAGAGGTCATCTTCCTGATAAGATA
* * * * * *
1237 TAGAGAAGTGGATTAAATTCGTCTTCCTGATGAGATATAGAGAAGTGGATTGAAACAATGAGGCG
65 CAGAGAAGTAGACTAAATTCATCTTCCTGATGAGACATAGAGAAGTGAATTGAAACAATGAGGCG
* * *
1302 GTCATCTTCCTGATGAGATACAGAGAAGTAGACAAAATCAATGAAGCAAAGCTCAATACGAATGA
130 ATCATCTTCCTGATGAGATACAGAGAAGTAGACAAAATAAATGAAGCAAAGCTCAATACGAATAA
*
1367 GACTTCCAACCCCA
195 GACTTCAAACCCCA
* * * * *
1381 TCTTCTTGATGAGATATAGAGAAGTGGGTTAAAGCAATAAAGTGGTCATCTTCCTGATCAGTTAC
1 TCTTCCTGATGAGATACAGAGAAGTGGGTTAAAGCAATAAAGAGGTCATCTTCCTGATAAGATAC
* * * * *
1446 AGAGAAGTAGACTGAATTCATCTTTCTGATGAGGCA-AGAGAAGTGAATT-AAATTAATGAAGTC
66 AGAGAAGTAGACTAAATTCATCTTCCTGATGAGACATAGAGAAGTGAATTGAAA-CAATG-AGGC
* * ** *
1509 -ATCATCTTCTTGATGAGATACAGAGAAGTAGACCAAATAAATGAAGTGAAGCTCAATATGAATA
129 GATCATCTTCCTGATGAGATACAGAGAAGTAGACAAAATAAATGAAGCAAAGCTCAATACGAATA
1573 AGACTTCAAACCCCA
194 AGACTTCAAACCCCA
* * ** *
1588 TCTTCCTGATAAGATACAGAGAAGTGAGTCGAAGCAATAAAGAGGTCATCTTCCTG-TGAGATAC
1 TCTTCCTGATGAGATACAGAGAAGTGGGTTAAAGCAATAAAGAGGTCATCTTCCTGATAAGATAC
* *
1652 AGAGAAGTGGATTAAAT
66 AGAGAAGTAGACTAAAT
1669 CAATGAAACA
Statistics
Matches: 244, Mismatches: 41, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
206 23 0.09
207 138 0.57
208 83 0.34
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (208 bp):
TCTTCCTGATGAGATACAGAGAAGTGGGTTAAAGCAATAAAGAGGTCATCTTCCTGATAAGATAC
AGAGAAGTAGACTAAATTCATCTTCCTGATGAGACATAGAGAAGTGAATTGAAACAATGAGGCGA
TCATCTTCCTGATGAGATACAGAGAAGTAGACAAAATAAATGAAGCAAAGCTCAATACGAATAAG
ACTTCAAACCCCA
Found at i:1683 original size:47 final size:48
Alignment explanation
Indices: 1586--1723 Score: 156
Period size: 48 Copynumber: 2.9 Consensus size: 48
1576 CTTCAAACCC
* * * *
1586 CATCTTCCTGATAAGATACAGAGAAGTGAGTCGAAGCAAT-AAAGAGGT
1 CATCTTCCTGATGAGATACAGAGAAGTGA-TCAAATCAATGAAACAGGT
*
1634 CATCTTCCTG-TGAGATACAGAGAAGTGGATTAAATCAATGAAACA-GT
1 CATCTTCCTGATGAGATACAGAGAAGT-GATCAAATCAATGAAACAGGT
* * *
1681 CATCTTCCCGATGAGATATAGAGAAGTAGACCAAATCAATGAA
1 CATCTTCCTGATGAGATACAGAGAAGT-GATCAAATCAATGAA
1724 GCGAAACTTA
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
47 33 0.43
48 44 0.57
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (48 bp):
CATCTTCCTGATGAGATACAGAGAAGTGATCAAATCAATGAAACAGGT
Found at i:1751 original size:170 final size:171
Alignment explanation
Indices: 1482--1830 Score: 443
Period size: 170 Copynumber: 2.0 Consensus size: 171
1472 TGATGAGGCA
* * **
1482 AGAGAAGTGAATTAAATTAATGAAGTCATCATCTTCTTGATGAGATACAGAGAAGTAGACCAAAT
1 AGAGAAGTGAATTAAATCAATGAAGACATCATCTTCCCGATGAGATACAGAGAAGTAGACCAAAT
* * * * * *
1547 AAATGAAGTGAAGCTCAATATGAATAAGACTTCAAACCCCATCTTCCTGATAAGATACAGAGAAG
66 AAATGAAGCGAAACTCAATACGAATAAGACTTCAAAACCCATCTTCCTGATAAGATACAAAGAAA
* * *
1612 TGAGTCGAAGCAATAAAGAGGTCATCTTCC-TGTGAGATAC
131 TGAGTCAAAGCAATAAAGAGGTCATCTTCCTTATAAGATAC
* *
1652 AGAGAAGTGGATTAAATCAATGAA-ACAGTCATCTTCCCGATGAGATATAGAGAAGTAGACCAAA
1 AGAGAAGTGAATTAAATCAATGAAGACA-TCATCTTCCCGATGAGATACAGAGAAGTAGACCAAA
* * * * *
1716 TCAATGAAGCGAAACTTAATACGAATGAA-ACTTCAAAACTCATCTTCTTGATGAGATACAAAGA
65 TAAATGAAGCGAAACTCAATACGAAT-AAGACTTCAAAACCCATCTTCCTGATAAGATACAAAGA
* * **
1780 AATGGGTTAAAGCAATAAATTGGTCATCTTCCTTATAAGATAC
129 AATGAGTCAAAGCAATAAAGAGGTCATCTTCCTTATAAGATAC
1823 AGAGAAGT
1 AGAGAAGT
1831 AGACCAAATC
Statistics
Matches: 152, Mismatches: 24, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
169 2 0.01
170 132 0.87
171 18 0.12
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (171 bp):
AGAGAAGTGAATTAAATCAATGAAGACATCATCTTCCCGATGAGATACAGAGAAGTAGACCAAAT
AAATGAAGCGAAACTCAATACGAATAAGACTTCAAAACCCATCTTCCTGATAAGATACAAAGAAA
TGAGTCAAAGCAATAAAGAGGTCATCTTCCTTATAAGATAC
Found at i:1914 original size:85 final size:83
Alignment explanation
Indices: 1766--2085 Score: 241
Period size: 85 Copynumber: 3.9 Consensus size: 83
1756 CATCTTCTTG
* * * * * * * * *
1766 ATGAGATACAAAGAAATGGGTTAAAGCAATAAATTGGTCATCTTCCTTATAAGATACAGAGAAGT
1 ATGAGATACAAAGAAGTGGATTCAATCAATGAA-CGATCATCTTCCTGATAAGATACAAAGAAGT
1831 AGACCAAATCTACCTTCCTA
65 AGACCAAATCTA-CTTCCTA
*
1851 ATGAGATACAAAGAAGTGGATTCAATCAATGAGACGATCATCTTCCTGATGAGATACAAAGAAGT
1 ATGAGATACAAAGAAGTGGATTCAATCAATGA-ACGATCATCTTCCTGATAAGATACAAAGAAGT
* *
1916 AGACCAAATC-A-AT--GA
65 AGACCAAATCTACTTCCTA
* * * * * ** * *
1931 AGCGAAGCT-CAATACAAATGAGA--C-TTC-A--AAC-CCCATCTTCCTGATGAGATACAGAGA
1 A-TG-AGATACAA-AGAAGTG-GATTCAATCAATGAACGATCATCTTCCTGATAAGATACAAAGA
*
1988 AGTAGACCAAATCTGTCTTCCTA
62 AGTAGACCAAATCT-ACTTCCTA
* * * *
2011 ATTAGATACAAAGAAGTTGATTAAATCAATGAAGCGATCATCTTCTTGATAAGATACAAAGAAGT
1 ATGAGATACAAAGAAGTGGATTCAATCAATGAA-CGATCATCTTCCTGATAAGATACAAAGAAGT
2076 AGACCAAATC
65 AGACCAAATC
2086 AATCAAGCGA
Statistics
Matches: 180, Mismatches: 36, Indels: 38
0.71 0.14 0.15
Matches are distributed among these distances:
75 36 0.20
76 2 0.01
77 3 0.02
78 8 0.04
79 4 0.02
80 8 0.04
81 6 0.03
82 9 0.05
83 4 0.02
84 2 0.01
85 97 0.54
86 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24
Consensus pattern (83 bp):
ATGAGATACAAAGAAGTGGATTCAATCAATGAACGATCATCTTCCTGATAAGATACAAAGAAGTA
GACCAAATCTACTTCCTA
Found at i:1988 original size:160 final size:160
Alignment explanation
Indices: 1804--2150 Score: 561
Period size: 160 Copynumber: 2.2 Consensus size: 160
1794 ATAAATTGGT
* *
1804 CATCTTCCTTATAAGATACAGAGAAGTAGACCAAATCTACCTTCCTAATGAGATACAAAGAAGTG
1 CATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCTACCTTCCTAATGAGATACAAAGAAGTG
* * *
1869 GATTCAATCAATG-AGACGATCATCTTCCTGATGAGATACAAAGAAGTAGACCAAATCAATGAAG
66 GATTAAATCAATGAAG-CGATCATCTTCCTGATAAGATACAAAGAAGTAGACCAAATCAATCAAG
1933 CGAAGCTCAATACAAATGAGACTTCAAACCC
130 CGAAGCTCAATACAAATGAGACTTCAAACCC
** * *
1964 CATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCTGTCTTCCTAATTAGATACAAAGAAGTT
1 CATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCTACCTTCCTAATGAGATACAAAGAAGTG
*
2029 GATTAAATCAATGAAGCGATCATCTTCTTGATAAGATACAAAGAAGTAGACCAAATCAATCAAGC
66 GATTAAATCAATGAAGCGATCATCTTCCTGATAAGATACAAAGAAGTAGACCAAATCAATCAAGC
* *
2094 GAAGCTTAATACGAATGAGACTTCAAACCC
131 GAAGCTCAATACAAATGAGACTTCAAACCC
*
2124 CATCTTTCTGATGAGATACAGAGAAGT
1 CATCTTCCTGATGAGATACAGAGAAGT
2151 GGGTCAAAGC
Statistics
Matches: 173, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
160 171 0.99
161 2 0.01
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (160 bp):
CATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCTACCTTCCTAATGAGATACAAAGAAGTG
GATTAAATCAATGAAGCGATCATCTTCCTGATAAGATACAAAGAAGTAGACCAAATCAATCAAGC
GAAGCTCAATACAAATGAGACTTCAAACCC
Found at i:2350 original size:48 final size:48
Alignment explanation
Indices: 2298--2417 Score: 170
Period size: 48 Copynumber: 2.5 Consensus size: 48
2288 TCTTGATAAT
* *
2298 ATACAGAGAAGTGGGTCAAAGT-AATAAAGAGGTCATCTTCCTAATGAG
1 ATACAGAGAAGTAGATCAAA-TCAATAAAGAGGTCATCTTCCTAATGAG
* * *
2346 ATACAGAGAAGTAGATTAAATCAATGAAGTGGTCATCTTCCTAATGAG
1 ATACAGAGAAGTAGATCAAATCAATAAAGAGGTCATCTTCCTAATGAG
*
2394 ATACAGAGAAGTAGACCAAATCAA
1 ATACAGAGAAGTAGATCAAATCAA
2418 AGAAACGAAG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
47 1 0.02
48 63 0.98
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.23
Consensus pattern (48 bp):
ATACAGAGAAGTAGATCAAATCAATAAAGAGGTCATCTTCCTAATGAG
Found at i:2521 original size:172 final size:171
Alignment explanation
Indices: 2221--2532 Score: 437
Period size: 172 Copynumber: 1.8 Consensus size: 171
2211 CTTACTGATT
* * * ** * **
2221 AGATATAGAGAAGTAGACCAATTCAATGAAGGGGAGCTCAATGTGAGTAAAACTTCAAACCCCAT
1 AGATACAGAGAAGTAGACCAAATCAAAGAAACGAAGCTCAATGCAAGTAAAACTTCAAACCCCAT
* * * *
2286 CTTCTTGATAATATACAGAGAAGTGGGTCAAAGTAATAAAGAGGTCATCTTCCTAATGAGATACA
66 CTTCCTGATAAGATACAAAGAAATGGGTCAAAGTAATAAAGAGGTCATCTTCCTAATGAGATACA
2351 GAGAAGTAGATTAAATCAATGAAGTGGTCATCTTCCTAATG
131 GAGAAGTAGATTAAATCAATGAAGTGGTCATCTTCCTAATG
* *
2392 AGATACAGAGAAGTAGACCAAATCAAAGAAACGAAGTTCAATGCAAGTGAAACTTCAAACCCTCA
1 AGATACAGAGAAGTAGACCAAATCAAAGAAACGAAGCTCAATGCAAGTAAAACTTCAAACCC-CA
* * * *
2457 TTTTCCTGATAAGATACAAAGAAATGGGTCGAAGTAATAAA-ACGGTCATCTTTCTGATGAGATA
65 TCTTCCTGATAAGATACAAAGAAATGGGTCAAAGTAATAAAGA-GGTCATCTTCCTAATGAGATA
2521 CAGAGAAGTAGA
129 CAGAGAAGTAGA
2533 CCAAGAAATG
Statistics
Matches: 121, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
171 53 0.44
172 68 0.56
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.23
Consensus pattern (171 bp):
AGATACAGAGAAGTAGACCAAATCAAAGAAACGAAGCTCAATGCAAGTAAAACTTCAAACCCCAT
CTTCCTGATAAGATACAAAGAAATGGGTCAAAGTAATAAAGAGGTCATCTTCCTAATGAGATACA
GAGAAGTAGATTAAATCAATGAAGTGGTCATCTTCCTAATG
Found at i:4638 original size:28 final size:31
Alignment explanation
Indices: 4581--4641 Score: 92
Period size: 28 Copynumber: 2.1 Consensus size: 31
4571 AGGCCCTTAT
*
4581 TTTTTCTAAAATTATATTTTGGCCCCTAAAC
1 TTTTTCTAAAATTATATTTTGGACCCTAAAC
4612 TTTTT-TAAAATT-TATTTT-GACCCTAAAC
1 TTTTTCTAAAATTATATTTTGGACCCTAAAC
4640 TT
1 TT
4642 CTCCAAAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 11 0.38
29 6 0.21
30 7 0.24
31 5 0.17
ACGTcount: A:0.30, C:0.16, G:0.05, T:0.49
Consensus pattern (31 bp):
TTTTTCTAAAATTATATTTTGGACCCTAAAC
Found at i:4670 original size:86 final size:86
Alignment explanation
Indices: 4580--4744 Score: 199
Period size: 86 Copynumber: 1.9 Consensus size: 86
4570 AAGGCCCTTA
** * ** * * * *
4580 TTTTTT-CTAAAATTATATTTTGGCCCCTAAACTTTTTTAAAATT-TATTTTGACCCTAAACTTC
1 TTTTTTGCTAAAA-TATATTTTAACCCCCAAACTTTCCTAAAATTACATTTTAACCCCAAAATTC
* *
4643 TCCAAAAGTACATTTTGACCCC
65 TCAAAAACTACATTTTGACCCC
4665 TTTTTTGCTAAAATATATTTTAACCCCCAAACTTTCCTAAAATTACATTTTAACCCCAAAATTCT
1 TTTTTTGCTAAAATATATTTTAACCCCCAAACTTTCCTAAAATTACATTTTAACCCCAAAATTCT
*
4730 CAAAAACTTCATTTT
66 CAAAAACTACATTTT
4745 TCGACCTCGT
Statistics
Matches: 66, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
85 32 0.48
86 34 0.52
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.42
Consensus pattern (86 bp):
TTTTTTGCTAAAATATATTTTAACCCCCAAACTTTCCTAAAATTACATTTTAACCCCAAAATTCT
CAAAAACTACATTTTGACCCC
Found at i:4721 original size:29 final size:29
Alignment explanation
Indices: 4586--4724 Score: 106
Period size: 29 Copynumber: 4.8 Consensus size: 29
4576 CTTATTTTTT
* *
4586 CTAAAATTATATTTTGGCCCCTAAACTTTT
1 CTAAAATTATATTTTGACCCC-AAACTTTC
* *
4616 TTAAAATT-TATTTTGACCCTAAACTTCTC
1 CTAAAATTATATTTTGACCCCAAACTT-TC
* * *** *
4645 C-AAAAGTACATTTTGACCCC-TTTTTTG
1 CTAAAATTATATTTTGACCCCAAACTTTC
*
4672 CTAAAA-TATATTTTAACCCCCAAACTTTC
1 CTAAAATTATATTTTGA-CCCCAAACTTTC
* *
4701 CTAAAATTACATTTTAACCCCAAA
1 CTAAAATTATATTTTGACCCCAAA
4725 ATTCTCAAAA
Statistics
Matches: 84, Mismatches: 19, Indels: 13
0.72 0.16 0.11
Matches are distributed among these distances:
27 10 0.12
28 21 0.25
29 37 0.44
30 16 0.19
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (29 bp):
CTAAAATTATATTTTGACCCCAAACTTTC
Found at i:4735 original size:29 final size:30
Alignment explanation
Indices: 4681--4744 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
4671 GCTAAAATAT
* *
4681 ATTTTAACCCCCAAACTTTCCTAAAA-TTAC
1 ATTTTAACCCCCAAAATTTCCAAAAACTT-C
4711 ATTTTAA-CCCCAAAA-TTCTCAAAAACTTC
1 ATTTTAACCCCCAAAATTTC-CAAAAACTTC
4740 ATTTT
1 ATTTT
4745 TCGACCTCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 3 0.10
29 18 0.60
30 9 0.30
ACGTcount: A:0.38, C:0.27, G:0.00, T:0.36
Consensus pattern (30 bp):
ATTTTAACCCCCAAAATTTCCAAAAACTTC
Found at i:5468 original size:17 final size:18
Alignment explanation
Indices: 5436--5472 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
5426 TTTTTCTGGA
5436 TTTCGAAAACCAAATTGTT
1 TTTCGAAAACCAAATT-TT
5455 TTTC-AAAA-CAAATTTT
1 TTTCGAAAACCAAATTTT
5471 TT
1 TT
5473 GTGTTGATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.22
17 6 0.33
18 4 0.22
19 4 0.22
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (18 bp):
TTTCGAAAACCAAATTTT
Found at i:12577 original size:65 final size:65
Alignment explanation
Indices: 12498--12627 Score: 251
Period size: 65 Copynumber: 2.0 Consensus size: 65
12488 CGACAAAAGA
*
12498 GTATTTGATAGAATAAGAACGACGCGTACTATCAAGTCTTCGATGAGCACATCATCAAGTTCATT
1 GTATTTGATAGAATAAGAACGACGCGCACTATCAAGTCTTCGATGAGCACATCATCAAGTTCATT
12563 GTATTTGATAGAATAAGAACGACGCGCACTATCAAGTCTTCGATGAGCACATCATCAAGTTCATT
1 GTATTTGATAGAATAAGAACGACGCGCACTATCAAGTCTTCGATGAGCACATCATCAAGTTCATT
12628 CCCTAGCATC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.28
Consensus pattern (65 bp):
GTATTTGATAGAATAAGAACGACGCGCACTATCAAGTCTTCGATGAGCACATCATCAAGTTCATT
Found at i:13313 original size:18 final size:18
Alignment explanation
Indices: 13290--13324 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13280 AGTAAATTTA
13290 ATTATTAAATTTTAAAAG
1 ATTATTAAATTTTAAAAG
* *
13308 ATTATTTATTTTTAAAA
1 ATTATTAAATTTTAAAA
13325 TTTAATAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
ATTATTAAATTTTAAAAG
Found at i:19976 original size:23 final size:22
Alignment explanation
Indices: 19940--20042 Score: 109
Period size: 23 Copynumber: 4.5 Consensus size: 22
19930 AAGTGCTGGG
19940 TAAT-AGAGGACACACAAAGTGC
1 TAATCAGAGG-CACACAAAGTGC
*
19962 TAATCAGAGCGCACACGAAGTGC
1 TAATCAGAG-GCACACAAAGTGC
*
19985 TAATCAGAGTGCACACGAAGTGC
1 TAATCAGAG-GCACACAAAGTGC
*
20008 TAATAACAGATGGCACACACAGTGC
1 TAAT--CAGA-GGCACACAAAGTGC
*
20033 TAAACAGAGG
1 TAATCAGAGG
20043 GTACGAAACG
Statistics
Matches: 71, Mismatches: 5, Indels: 10
0.83 0.06 0.12
Matches are distributed among these distances:
22 6 0.08
23 45 0.63
24 1 0.01
25 18 0.25
26 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.24, T:0.15
Consensus pattern (22 bp):
TAATCAGAGGCACACAAAGTGC
Found at i:20041 original size:48 final size:46
Alignment explanation
Indices: 19950--20041 Score: 116
Period size: 48 Copynumber: 2.0 Consensus size: 46
19940 TAATAGAGGA
*
19950 CACACAAAGTGCTAATCAGAGCGCACACGAAGTGCTAATCAGAGTG
1 CACACAAAGTGCTAATCAGAGCGCACACGAAGTGCTAAACAGAGTG
*
19996 CACACGAAGTGCTAATAACAGATG-GCACAC-ACAGTGCTAAACAGAG
1 CACACAAAGTGCTAAT--CAGA-GCGCACACGA-AGTGCTAAACAGAG
20042 GGTACGAAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
46 15 0.38
47 1 0.03
48 23 0.57
49 1 0.03
ACGTcount: A:0.39, C:0.24, G:0.23, T:0.14
Consensus pattern (46 bp):
CACACAAAGTGCTAATCAGAGCGCACACGAAGTGCTAAACAGAGTG
Found at i:20831 original size:24 final size:24
Alignment explanation
Indices: 20799--20850 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
20789 ATTTTACTCA
20799 ATCACATATTAATCCTTTCATTTT
1 ATCACATATTAATCCTTTCATTTT
20823 ATCACATATTAATCCTTTCATTTT
1 ATCACATATTAATCCTTTCATTTT
20847 ATCA
1 ATCA
20851 TTGTAAACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.48
Consensus pattern (24 bp):
ATCACATATTAATCCTTTCATTTT
Found at i:23563 original size:9 final size:8
Alignment explanation
Indices: 23548--23612 Score: 55
Period size: 9 Copynumber: 8.0 Consensus size: 8
23538 GTCAGAACAA
23548 TTTCTTCT
1 TTTCTTCT
23556 TCTTCTTCTT
1 T-TTCTTC-T
23566 TTTCTTCT
1 TTTCTTCT
23574 TTTGCTTCT
1 TTT-CTTCT
23583 TTTC--CT
1 TTTCTTCT
23589 TTGTCTTCT
1 TT-TCTTCT
*
23598 CTT-TTCT
1 TTTCTTCT
*
23605 CTTCTTCT
1 TTTCTTCT
23613 ACAACACTCT
Statistics
Matches: 49, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
6 4 0.08
7 9 0.18
8 11 0.22
9 23 0.47
10 2 0.04
ACGTcount: A:0.00, C:0.28, G:0.03, T:0.69
Consensus pattern (8 bp):
TTTCTTCT
Found at i:23570 original size:12 final size:12
Alignment explanation
Indices: 23549--23612 Score: 53
Period size: 12 Copynumber: 5.3 Consensus size: 12
23539 TCAGAACAAT
*
23549 TTCTTCTTCTTC
1 TTCTTTTTCTTC
23561 TTCTTTTTCTTC
1 TTCTTTTTCTTC
*
23573 TT-TTGCTTCTT-
1 TTCTT-TTTCTTC
*
23584 TTCCTTTGTCTTC
1 TT-CTTTTTCTTC
23597 -TCTTTTCTCTTC
1 TTCTTTT-TCTTC
23609 TTCT
1 TTCT
23613 ACAACACTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
11 8 0.20
12 28 0.68
13 5 0.12
ACGTcount: A:0.00, C:0.28, G:0.03, T:0.69
Consensus pattern (12 bp):
TTCTTTTTCTTC
Found at i:23571 original size:18 final size:18
Alignment explanation
Indices: 23548--23612 Score: 73
Period size: 18 Copynumber: 3.6 Consensus size: 18
23538 GTCAGAACAA
23548 TTTCTTCTTCTTCTTCTT
1 TTTCTTCTTCTTCTTCTT
23566 TTTCTTCTT-TTGCTTCTT
1 TTTCTTCTTCTT-CTTCTT
*
23584 TTCCTT-TGTCTTC-TCTT
1 TTTCTTCT-TCTTCTTCTT
23601 TTCTCTTCTTCT
1 TT-TCTTCTTCT
23613 ACAACACTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
17 9 0.22
18 28 0.70
19 3 0.08
ACGTcount: A:0.00, C:0.28, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTCTTCTTCTTCTTCTT
Found at i:23572 original size:15 final size:15
Alignment explanation
Indices: 23552--23612 Score: 54
Period size: 15 Copynumber: 3.9 Consensus size: 15
23542 GAACAATTTC
23552 TTCTTCTTCTTCTTT
1 TTCTTCTTCTTCTTT
23567 TTCTTCTTTTGCTTCTTT
1 TTCTTC--TT-CTTCTTT
*
23585 TCCTT-TGTCTTCTCTT
1 TTCTTCT-TCTTCT-TT
23601 TTC-TCTTCTTCT
1 TTCTTCTTCTTCT
23613 ACAACACTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
15 19 0.50
16 6 0.16
17 2 0.05
18 11 0.29
ACGTcount: A:0.00, C:0.28, G:0.03, T:0.69
Consensus pattern (15 bp):
TTCTTCTTCTTCTTT
Found at i:30592 original size:18 final size:17
Alignment explanation
Indices: 30569--30602 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
30559 TTTAAAAGAA
30569 AATCAACAAAAGATTAGT
1 AATCAACAAAAG-TTAGT
*
30587 AATCAATAAAAGTTAG
1 AATCAACAAAAGTTAG
30603 AAAAGGAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.24
Consensus pattern (17 bp):
AATCAACAAAAGTTAGT
Found at i:34497 original size:16 final size:17
Alignment explanation
Indices: 34460--34499 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
34450 AATAAATTAA
*
34460 AAATATATAAAATTATT
1 AAATATATAAAATAATT
34477 AAATAT-TAAAATAATT
1 AAATATATAAAATAATT
*
34493 TAATATA
1 AAATATA
34500 AATATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATATATAAAATAATT
Found at i:35345 original size:13 final size:12
Alignment explanation
Indices: 35327--35364 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
35317 ATATCTTCAA
35327 TTTTATTAATAAT
1 TTTTA-TAATAAT
35340 TTTTATAATAAT
1 TTTTATAATAAT
*
35352 TTTAATAA-AAT
1 TTTTATAATAAT
35363 TT
1 TT
35365 AACTTTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 5 0.21
12 14 0.58
13 5 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTTATAATAAT
Found at i:38560 original size:15 final size:15
Alignment explanation
Indices: 38540--38569 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
38530 TTTAGATGAG
38540 CACTTGTTAAAGAGT
1 CACTTGTTAAAGAGT
38555 CACTTGTTAAAGAGT
1 CACTTGTTAAAGAGT
38570 TGGTTTCATA
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:0.13, G:0.20, T:0.33
Consensus pattern (15 bp):
CACTTGTTAAAGAGT
Found at i:39058 original size:17 final size:17
Alignment explanation
Indices: 39033--39074 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
39023 GTGAAATTAG
*
39033 AACTGAATTGAGA-AAAT
1 AACTTAATTG-GATAAAT
39050 AACTTAATTGGATAAAT
1 AACTTAATTGGATAAAT
*
39067 AAATTAAT
1 AACTTAAT
39075 ATTTTGGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 2 0.09
17 20 0.91
ACGTcount: A:0.52, C:0.05, G:0.12, T:0.31
Consensus pattern (17 bp):
AACTTAATTGGATAAAT
Found at i:39718 original size:14 final size:16
Alignment explanation
Indices: 39688--39719 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
39678 TCACTCTGCT
39688 TAAAATCATTGTTTTC
1 TAAAATCATTGTTTTC
39704 TAAAAT-ATT-TTTTC
1 TAAAATCATTGTTTTC
39718 TA
1 TA
39720 TTATTTTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 3 0.19
16 6 0.38
ACGTcount: A:0.34, C:0.09, G:0.03, T:0.53
Consensus pattern (16 bp):
TAAAATCATTGTTTTC
Found at i:42934 original size:11 final size:11
Alignment explanation
Indices: 42911--42942 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
42901 TCTAAAAAGA
42911 TAAATAT-AAT
1 TAAATATAAAT
42921 TAAATATAAAT
1 TAAATATAAAT
42932 TAAATATAAAT
1 TAAATATAAAT
42943 AATATCCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.33
11 14 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TAAATATAAAT
Found at i:46017 original size:23 final size:23
Alignment explanation
Indices: 45991--46036 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
45981 CAATAAGCAT
*
45991 ATTCATGGGCAAAATCGTGGGCA
1 ATTCATGGGAAAAATCGTGGGCA
* *
46014 ATTCGTGGGAAAAATCTTGGGCA
1 ATTCATGGGAAAAATCGTGGGCA
46037 TGAAAAGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.24
Consensus pattern (23 bp):
ATTCATGGGAAAAATCGTGGGCA
Found at i:46355 original size:10 final size:10
Alignment explanation
Indices: 46325--46358 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
46315 CATATAATAA
46325 ATAAATAAAT
1 ATAAATAAAT
*
46335 AGAAA-AAAT
1 ATAAATAAAT
46344 ATAAATAAAT
1 ATAAATAAAT
46354 ATAAA
1 ATAAA
46359 AATAAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (10 bp):
ATAAATAAAT
Found at i:46365 original size:6 final size:6
Alignment explanation
Indices: 46338--46383 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
46328 AATAAATAGA
* * *
46338 AAAAAT ATAAAT AAATAT AAAAAT AAAAA- GAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
46384 ATTGGGTTGC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
5 4 0.12
6 29 0.88
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:46365 original size:23 final size:21
Alignment explanation
Indices: 46320--46384 Score: 60
Period size: 23 Copynumber: 2.9 Consensus size: 21
46310 CTGGACATAT
46320 AATAAATAAATA-AATAGAAAAA
1 AATAAATAAATATAA-A-AAAAA
46342 ATATAAATAAATATAAAAATAAA
1 A-ATAAATAAATATAAAAA-AAA
* *
46365 AAGAAAATAAAAATAAAAAA
1 AA-TAAATAAATATAAAAAA
46385 TTGGGTTGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
22 5 0.14
23 30 0.81
24 2 0.05
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.18
Consensus pattern (21 bp):
AATAAATAAATATAAAAAAAA
Found at i:56749 original size:22 final size:22
Alignment explanation
Indices: 56724--56800 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
56714 TTGATCAAGA
56724 TGGTATTCTATGCTTTCGGGGT
1 TGGTATTCTATGCTTTCGGGGT
*
56746 TGGTATTTTATGCTTTCGGGGT
1 TGGTATTCTATGCTTTCGGGGT
*
56768 TGGTATTCTATGCTTCCGGGGT
1 TGGTATTCTATGCTTTCGGGGT
* *
56790 TGATACTCTAT
1 TGGTATTCTAT
56801 TCCAAGGGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.12, C:0.14, G:0.29, T:0.45
Consensus pattern (22 bp):
TGGTATTCTATGCTTTCGGGGT
Found at i:59073 original size:20 final size:20
Alignment explanation
Indices: 59033--59072 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
59023 GACCTGTTGA
*
59033 TCATTGACCATTGACTTTTT
1 TCATTGACCATTAACTTTTT
59053 TCATTGACCATTAA-TTTTT
1 TCATTGACCATTAACTTTTT
59072 T
1 T
59073 TTTGGAAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.23, C:0.17, G:0.07, T:0.53
Consensus pattern (20 bp):
TCATTGACCATTAACTTTTT
Found at i:60572 original size:24 final size:25
Alignment explanation
Indices: 60526--60577 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
60516 GGGATTACAG
* *
60526 ATTAGAAAAACTATTATTAAATT-A
1 ATTAGAAAAAATATTACTAAATTGA
60550 ATTAGAAAAAATGATTACT-AATTGA
1 ATTAGAAAAAAT-ATTACTAAATTGA
60575 ATT
1 ATT
60578 GAATCATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.37
Consensus pattern (25 bp):
ATTAGAAAAAATATTACTAAATTGA
Found at i:63672 original size:29 final size:29
Alignment explanation
Indices: 63640--63749 Score: 82
Period size: 29 Copynumber: 3.9 Consensus size: 29
63630 AGGCTTATTC
* *
63640 ATAATAGATTCATCCACAAAGGCTCACAT
1 ATAATAAATTCAGCCACAAAGGCTCACAT
* * * * *
63669 ATAACAAAATCAACCCCAAAGGCT--CTT
1 ATAATAAATTCAGCCACAAAGGCTCACAT
* * *
63696 TTAACAAAATT-AGCCAAAAAGGCTCACAT
1 ATAA-TAAATTCAGCCACAAAGGCTCACAT
* *
63725 ATAATAGATTCAGCCGCAAAGGCTC
1 ATAATAAATTCAGCCACAAAGGCTC
63750 TTTTTCGATA
Statistics
Matches: 59, Mismatches: 18, Indels: 8
0.69 0.21 0.09
Matches are distributed among these distances:
27 15 0.25
28 8 0.14
29 36 0.61
ACGTcount: A:0.43, C:0.25, G:0.12, T:0.21
Consensus pattern (29 bp):
ATAATAAATTCAGCCACAAAGGCTCACAT
Found at i:67839 original size:27 final size:27
Alignment explanation
Indices: 67802--67857 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
67792 TCAAATCTTG
*
67802 TAATATCATCA-TATACATGTCATTCAA
1 TAATATAATCATTATACAT-TCATTCAA
*
67829 TAATATAATCATTTTACATTCATTCAA
1 TAATATAATCATTATACATTCATTCAA
67856 TA
1 TA
67858 CATTGCATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.41, C:0.16, G:0.02, T:0.41
Consensus pattern (27 bp):
TAATATAATCATTATACATTCATTCAA
Found at i:71753 original size:15 final size:15
Alignment explanation
Indices: 71735--71782 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
71725 AAACAACACA
*
71735 CATATAATCAATTCG
1 CATATAATCAGTTCG
* *
71750 CATACAA-CAGTTCA
1 CATATAATCAGTTCG
71764 CATATAATCAGTTCG
1 CATATAATCAGTTCG
71779 CATA
1 CATA
71783 CAATAGTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.40, C:0.23, G:0.08, T:0.29
Consensus pattern (15 bp):
CATATAATCAGTTCG
Found at i:71765 original size:29 final size:29
Alignment explanation
Indices: 71733--71796 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
71723 ACAAACAACA
71733 CACATATAATCAATTCGCATACAACAGTT
1 CACATATAATCAATTCGCATACAACAGTT
* *
71762 CACATATAATCAGTTCGCATACAATAGTT
1 CACATATAATCAATTCGCATACAACAGTT
*
71791 AACATA
1 CACATA
71797 CAATAAGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (29 bp):
CACATATAATCAATTCGCATACAACAGTT
Found at i:71796 original size:14 final size:14
Alignment explanation
Indices: 71750--71801 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
71740 AATCAATTCG
*
71750 CATACAACAGTTCA
1 CATACAATAGTTCA
* *
71764 CATATAATCAGTTCG
1 CATACAAT-AGTTCA
*
71779 CATACAATAGTTAA
1 CATACAATAGTTCA
71793 CATACAATA
1 CATACAATA
71802 AGTTTAAGCT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
14 19 0.61
15 12 0.39
ACGTcount: A:0.44, C:0.21, G:0.08, T:0.27
Consensus pattern (14 bp):
CATACAATAGTTCA
Found at i:71805 original size:29 final size:29
Alignment explanation
Indices: 71746--71805 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
71736 ATATAATCAA
* * *
71746 TTCGCATACAACAGTTCACATATAATCAG
1 TTCGCATACAACAGTTAACATACAATAAG
*
71775 TTCGCATACAATAGTTAACATACAATAAG
1 TTCGCATACAACAGTTAACATACAATAAG
71804 TT
1 TT
71806 TAAGCTTGCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (29 bp):
TTCGCATACAACAGTTAACATACAATAAG
Found at i:77319 original size:43 final size:43
Alignment explanation
Indices: 77258--77398 Score: 221
Period size: 43 Copynumber: 3.3 Consensus size: 43
77248 TCACTTGGCG
77258 TAAATGGAAGACTCATGTCTTGGGATGAGCATGAGATTATGTA
1 TAAATGGAAGACTCATGTCTTGGGATGAGCATGAGATTATGTA
77301 TAAATGGAAGACTCATGTCTTGGGATGAGCATGAGATTATGTA
1 TAAATGGAAGACTCATGTCTTGGGATGAGCATGAGATTATGTA
* * * * * *
77344 TAAATGAAAGACTCGTGACTCGGAATGAGCATGAGATTATGTT
1 TAAATGGAAGACTCATGTCTTGGGATGAGCATGAGATTATGTA
77387 TAAA-GGAAGACT
1 TAAATGGAAGACT
77399 TATGACTCTG
Statistics
Matches: 91, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
42 7 0.08
43 84 0.92
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.28
Consensus pattern (43 bp):
TAAATGGAAGACTCATGTCTTGGGATGAGCATGAGATTATGTA
Found at i:82873 original size:2 final size:2
Alignment explanation
Indices: 82866--82900 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
82856 CTCATGCTTT
82866 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
82901 TAAATTATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:84605 original size:17 final size:18
Alignment explanation
Indices: 84567--84608 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
84557 ATCTTGTCAT
84567 TTTTATATTTTTCTTAAA
1 TTTTATATTTTTCTTAAA
84585 -TTTAT-TTTTT-TATAAA
1 TTTTATATTTTTCT-TAAA
84601 TTTTATAT
1 TTTTATAT
84609 AAAAGTATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
15 1 0.05
16 9 0.43
17 10 0.48
18 1 0.05
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTATATTTTTCTTAAA
Found at i:84724 original size:5 final size:5
Alignment explanation
Indices: 84714--84781 Score: 50
Period size: 5 Copynumber: 13.4 Consensus size: 5
84704 AAATGTTTTT
* * * * *
84714 TTAAA TTAAA TTACATA TTAAC TTAGAG CTAAA TT-CA TTAAA TT-AT
1 TTAAA TTAAA TTA-A-A TTAAA TTA-AA TTAAA TTAAA TTAAA TTAAA
84760 TTAAA TTAAA TTAAA TTAAA TT
1 TTAAA TTAAA TTAAA TTAAA TT
84782 TAAAAAAATT
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
4 6 0.12
5 34 0.69
6 5 0.10
7 4 0.08
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (5 bp):
TTAAA
Found at i:85660 original size:28 final size:28
Alignment explanation
Indices: 85629--85693 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
85619 TTAATCTCAC
*
85629 ATTAATTAGAGAATACTCTTAATTCCAT
1 ATTAACTAGAGAATACTCTTAATTCCAT
*
85657 ATTAACTAGAGAATACTCTTAATTCCAC
1 ATTAACTAGAGAATACTCTTAATTCCAT
*
85685 ATTGACTAG
1 ATTAACTAG
85694 CTCATTTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.35
Consensus pattern (28 bp):
ATTAACTAGAGAATACTCTTAATTCCAT
Found at i:86056 original size:23 final size:24
Alignment explanation
Indices: 86014--86059 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
86004 TCACGAACAA
*
86014 GCTCGTTTAAAAGCTTGTTTATTG
1 GCTCGTTTAAAAGCTCGTTTATTG
*
86038 GCTCGTTT-ATAGCTCGTTTATT
1 GCTCGTTTAAAAGCTCGTTTATT
86060 TATTAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.17, C:0.15, G:0.20, T:0.48
Consensus pattern (24 bp):
GCTCGTTTAAAAGCTCGTTTATTG
Found at i:86641 original size:16 final size:16
Alignment explanation
Indices: 86610--86639 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
86600 AAAATATTTA
86610 AATTTACTTATTAAAT
1 AATTTACTTATTAAAT
86626 AATTTA-TTATTAAA
1 AATTTACTTATTAAA
86640 ATTAAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTTACTTATTAAAT
Found at i:86920 original size:24 final size:24
Alignment explanation
Indices: 86875--86920 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
86865 TTCACTTCCC
*
86875 AGTTAATTATAATTAAATTAAATA
1 AGTTAATTATAATTAAAGTAAATA
* *
86899 AGTTAATTTTAATTGAAGTAAA
1 AGTTAATTATAATTAAAGTAAA
86921 ATATAATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (24 bp):
AGTTAATTATAATTAAAGTAAATA
Found at i:88162 original size:127 final size:127
Alignment explanation
Indices: 88017--88270 Score: 472
Period size: 127 Copynumber: 2.0 Consensus size: 127
88007 TATAAACAAC
* *
88017 AAATAAAATCATAAACTCAGAAAAGAAATGAAACCAAAATCTTTGCTAAAAAAATATCCAAATTT
1 AAATAAAATCATAAACTCAGAAAAGAAATGAAACCAAAATCTTTACTAAAAAAATACCCAAATTT
* *
88082 ATACAAAGATAATGGAGGAAAACTCTCTTTTAAATTCTTCTTCAGGCATCTCCATTTTTTCT
66 ATACAAAGATAATGGAGGAAAACGCTCTTTCAAATTCTTCTTCAGGCATCTCCATTTTTTCT
88144 AAATAAAATCATAAACTCAGAAAAGAAATGAAACCAAAATCTTTACTAAAAAAATACCCAAATTT
1 AAATAAAATCATAAACTCAGAAAAGAAATGAAACCAAAATCTTTACTAAAAAAATACCCAAATTT
88209 ATACAAAGATAATGGAGGAAAACGCTCTTTCAAATTCTTCTTCAGGCATCTCCATTTTTTCT
66 ATACAAAGATAATGGAGGAAAACGCTCTTTCAAATTCTTCTTCAGGCATCTCCATTTTTTCT
88271 CTTCTTCTTA
Statistics
Matches: 123, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
127 123 1.00
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.30
Consensus pattern (127 bp):
AAATAAAATCATAAACTCAGAAAAGAAATGAAACCAAAATCTTTACTAAAAAAATACCCAAATTT
ATACAAAGATAATGGAGGAAAACGCTCTTTCAAATTCTTCTTCAGGCATCTCCATTTTTTCT
Found at i:88286 original size:17 final size:16
Alignment explanation
Indices: 88263--88308 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
88253 GGCATCTCCA
88263 TTTTTTCTCTTCTTCT
1 TTTTTTCTCTTCTTCT
*
88279 TATTTT-TCTTCTTTCT
1 TTTTTTCTCTTC-TTCT
88295 TTTTTTCTCTTCTT
1 TTTTTTCTCTTCTT
88309 AAACCTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 5 0.19
16 16 0.62
17 5 0.19
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTTCTCTTCTTCT
Found at i:95274 original size:18 final size:19
Alignment explanation
Indices: 95253--95297 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
95243 TAAATTTTAT
95253 TAAATTTTAATAAAAA-TA
1 TAAATTTTAATAAAAATTA
*
95271 TAAATTTTATTAAAAATTA
1 TAAATTTTAATAAAAATTA
*
95290 GAAATTTT
1 TAAATTTT
95298 TTTAATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
TAAATTTTAATAAAAATTA
Found at i:95294 original size:19 final size:18
Alignment explanation
Indices: 95254--95302 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
95244 AAATTTTATT
* *
95254 AAATTTTAATAAAAATAT
1 AAATTTTATTAAAAATAG
95272 AAATTTTATTAAAAATTAG
1 AAATTTTATTAAAAA-TAG
*
95291 AAATTTTTTTAA
1 AAATTTTATTAA
95303 TAAAAACAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 14 0.52
19 13 0.48
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
AAATTTTATTAAAAATAG
Found at i:95369 original size:31 final size:32
Alignment explanation
Indices: 95314--95390 Score: 129
Period size: 31 Copynumber: 2.4 Consensus size: 32
95304 AAAAACAGTA
*
95314 AAAAATTATAAAATAATTTTGTAAACTTTTAT
1 AAAAATTATAAAATAAATTTGTAAACTTTTAT
*
95346 AAAAATTATAAAA-AAATTTGTAAATTTTTAT
1 AAAAATTATAAAATAAATTTGTAAACTTTTAT
95377 AAAAATTATAAAAT
1 AAAAATTATAAAAT
95391 GCATTAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
31 29 0.69
32 13 0.31
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (32 bp):
AAAAATTATAAAATAAATTTGTAAACTTTTAT
Found at i:95654 original size:8 final size:8
Alignment explanation
Indices: 95641--95722 Score: 55
Period size: 8 Copynumber: 9.8 Consensus size: 8
95631 GATTTTATAA
95641 AATTTTAT
1 AATTTTAT
95649 AATTTT-T
1 AATTTTAT
*
95656 --TTCTAT
1 AATTTTAT
95662 -ATTTCTAT
1 AATTT-TAT
95670 ATATTTTAT
1 A-ATTTTAT
95679 AATTTTAT
1 AATTTTAT
95687 AGAATTTTTAT
1 --AA-TTTTAT
95698 AATTTTAT
1 AATTTTAT
95706 AGAATTTTTAT
1 --AA-TTTTAT
95717 AATTTT
1 AATTTT
95723 TTCTAATTTT
Statistics
Matches: 61, Mismatches: 2, Indels: 22
0.72 0.02 0.26
Matches are distributed among these distances:
5 3 0.05
6 1 0.02
7 3 0.05
8 26 0.43
9 8 0.13
10 8 0.13
11 12 0.20
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (8 bp):
AATTTTAT
Found at i:95655 original size:19 final size:19
Alignment explanation
Indices: 95633--95756 Score: 60
Period size: 19 Copynumber: 6.4 Consensus size: 19
95623 TTTCTTACGA
95633 TTTTATAAAATTTTATAAT
1 TTTTATAAAATTTTATAAT
* * *
95652 TTTTTTCTATATTTCTAT-AT
1 TTTTAT-AAAATTT-TATAAT
95672 ATTTTAT--AATTTTATAGAAT
1 -TTTTATAAAATTTTAT--AAT
95692 TTTTAT--AATTTTATAGAAT
1 TTTTATAAAATTTTAT--AAT
** *
95711 TTTTATAATTTTTTCTAAT
1 TTTTATAAAATTTTATAAT
* * *
95730 TTTAATAAAATTTAAATATT
1 TTTTATAAAATTT-TATAAT
95750 TTTTATA
1 TTTTATA
95757 GTTTTTTATT
Statistics
Matches: 81, Mismatches: 15, Indels: 17
0.72 0.13 0.15
Matches are distributed among these distances:
17 3 0.04
18 4 0.05
19 43 0.53
20 18 0.22
21 13 0.16
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTATAAAATTTTATAAT
Found at i:95697 original size:11 final size:11
Alignment explanation
Indices: 95681--95717 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
95671 TATTTTATAA
95681 TTTTATAGAAT
1 TTTTATAGAAT
95692 TTTTAT--AA-
1 TTTTATAGAAT
95700 TTTTATAGAAT
1 TTTTATAGAAT
95711 TTTTATA
1 TTTTATA
95718 ATTTTTTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 6 0.26
9 2 0.09
10 2 0.09
11 13 0.57
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (11 bp):
TTTTATAGAAT
Found at i:95723 original size:29 final size:30
Alignment explanation
Indices: 95681--95761 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 30
95671 TATTTTATAA
* *
95681 TTTTATAGAATTTTTATAATTTT-ATAGAAT
1 TTTTATA-ATTTTTTATAATTTTAATAAAAT
*
95711 TTTTATAATTTTTTCTAATTTTAATAAAAT
1 TTTTATAATTTTTTATAATTTTAATAAAAT
** *
95741 TTAAAT-ATTTTTTATAGTTTT
1 TTTTATAATTTTTTATAATTTT
95762 TTATTAACAT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 26 0.60
30 17 0.40
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60
Consensus pattern (30 bp):
TTTTATAATTTTTTATAATTTTAATAAAAT
Found at i:95778 original size:30 final size:31
Alignment explanation
Indices: 95729--95786 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
95719 TTTTTTCTAA
95729 TTTTAATAAAATTTAAATATTTTTTATAGTT
1 TTTTAATAAAATTTAAATATTTTTTATAGTT
* *
95760 TTTTATTAACATTT-AATATTTTTTATA
1 TTTTAATAAAATTTAAATATTTTTTATA
95787 AATTTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 13 0.52
31 12 0.48
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (31 bp):
TTTTAATAAAATTTAAATATTTTTTATAGTT
Found at i:95793 original size:30 final size:31
Alignment explanation
Indices: 95729--95793 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
95719 TTTTTTCTAA
**
95729 TTTTAATAAAATTTAAATATTTTTTATAGTT
1 TTTTAATAAAATTTAAATATTTTTTATAAAT
* *
95760 TTTTATTAACATTT-AATATTTTTTATAAAT
1 TTTTAATAAAATTTAAATATTTTTTATAAAT
95790 TTTT
1 TTTT
95794 TTATTTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 18 0.60
31 12 0.40
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (31 bp):
TTTTAATAAAATTTAAATATTTTTTATAAAT
Found at i:95793 original size:31 final size:31
Alignment explanation
Indices: 95729--95794 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
95719 TTTTTTCTAA
*
95729 TTTTAATAAAATTTAAATATTTTTTATAGTT
1 TTTTAATAAAATTTAAATATTTTTTATAATT
* *
95760 TTTTATTAACATTT-AATATTTTTTATAAATT
1 TTTTAATAAAATTTAAATATTTTTTAT-AATT
95791 TTTT
1 TTTT
95795 TATTTTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 12 0.39
31 19 0.61
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (31 bp):
TTTTAATAAAATTTAAATATTTTTTATAATT
Found at i:99494 original size:42 final size:42
Alignment explanation
Indices: 99387--99494 Score: 96
Period size: 42 Copynumber: 2.5 Consensus size: 42
99377 GTTAGGCGCA
* *
99387 CTTTCTACTAACATGTTAGGGAAAACTCGTCCAACTGGGCAAC
1 CTTTCTACTAACAT-TCAGGGAAAACTCGTCCAAATGGGCAAC
** * * *
99430 CTTTCTAC-ATA-ATTGGCA-GGAAATTTTGTCCAAATTGGCAAG
1 CTTTCTACTA-ACATT--CAGGGAAAACTCGTCCAAATGGGCAAC
99472 CTTTCTACTAACATTCAGGGAAA
1 CTTTCTACTAACATTCAGGGAAA
99495 GTGCACCCAG
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
41 3 0.06
42 35 0.67
43 14 0.27
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (42 bp):
CTTTCTACTAACATTCAGGGAAAACTCGTCCAAATGGGCAAC
Found at i:104017 original size:23 final size:23
Alignment explanation
Indices: 103973--104022 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
103963 TTCGTGAATA
*** *
103973 TAAACGAACATGTTTGTAAACGT
1 TAAACGAACATGTTCACAAACGC
*
103996 TAAACGAACATGTTCACGAACGC
1 TAAACGAACATGTTCACAAACGC
104019 TAAA
1 TAAA
104023 TGAATCGAGC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (23 bp):
TAAACGAACATGTTCACAAACGC
Found at i:107081 original size:19 final size:19
Alignment explanation
Indices: 107046--107107 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
107036 AAGAAAAAAT
* *
107046 AAAATAA-TTTTAGAATTG
1 AAAATAATTTTTAAAATTC
107064 AAAATAATTTTTAAAATTC
1 AAAATAATTTTTAAAATTC
*
107083 AAAAT-ATTTATAAAAATTC
1 AAAATAATTT-TTAAAATTC
107102 TAAAAT
1 -AAAAT
107108 TTTTATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 11 0.29
19 22 0.58
20 5 0.13
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (19 bp):
AAAATAATTTTTAAAATTC
Found at i:107112 original size:20 final size:19
Alignment explanation
Indices: 107076--107113 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
107066 AATAATTTTT
107076 AAAATTCAAAATATTTATA
1 AAAATTCAAAATATTTATA
*
107095 AAAATTCTAAAATTTTTAT
1 AAAATTC-AAAATATTTAT
107114 TTTTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATTCAAAATATTTATA
Found at i:107350 original size:23 final size:23
Alignment explanation
Indices: 107307--107351 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
107297 GAAACAAGAT
**
107307 TTTAATTTAACATTATTAATTTG
1 TTTAATTTAACATTAACAATTTG
107330 TTTAATTTAAC-TTGAACAATTT
1 TTTAATTTAACATT-AACAATTT
107352 CACTTAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.53
Consensus pattern (23 bp):
TTTAATTTAACATTAACAATTTG
Found at i:109183 original size:33 final size:34
Alignment explanation
Indices: 109107--109183 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 34
109097 CCTATTTACT
* * * **
109107 TAAAATAAATAATTTTAGTCAAAATGAAATTAGA
1 TAAAATAAACAAATTTAATCAAAACAAAATTAGA
109141 -AAAAT-AACAAATTTAATCAAAACAAAATTA-A
1 TAAAATAAACAAATTTAATCAAAACAAAATTAGA
109172 TAAAATAAACAA
1 TAAAATAAACAA
109184 CTTTGACTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
31 1 0.03
32 25 0.69
33 10 0.28
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (34 bp):
TAAAATAAACAAATTTAATCAAAACAAAATTAGA
Done.