Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005729.1 Hibiscus syriacus cultivar Beakdansim tig00013390_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: 123944
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2153 original size:20 final size:20
Alignment explanation
Indices: 2115--2153 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2105 ATATACACAT
*
2115 TATATATTACATATTTATAA
1 TATATATTACATATGTATAA
2135 TATATATCTACAT-TGTATA
1 TATATAT-TACATATGTATA
2154 GTGTGCATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (20 bp):
TATATATTACATATGTATAA
Found at i:2181 original size:2 final size:2
Alignment explanation
Indices: 2174--2239 Score: 50
Period size: 2 Copynumber: 34.5 Consensus size: 2
2164 ATTATACTGT
* * *
2174 TA TA TA TA TA TA TA TA T- TA TA TA AA TG TT TA TA T- 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
* *
2214 GTA T- TA AA CA TA TA TA TA TA T- TA TA T
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA T
2240 GTTTTTTTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
1 4 0.08
2 45 0.88
3 2 0.04
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2195 original size:17 final size:17
Alignment explanation
Indices: 2173--2239 Score: 59
Period size: 17 Copynumber: 4.1 Consensus size: 17
2163 CATTATACTG
2173 TTATATATATATATATA
1 TTATATATATATATATA
* * *
2190 TTATATAAATGTTTATA
1 TTATATATATATATATA
* *
2207 TTATATAGTAT-TAAACA
1 TTATATA-TATATATATA
2224 -TATATATATAT-TATA
1 TTATATATATATATATA
2239 T
1 T
2240 GTTTTTTTAT
Statistics
Matches: 38, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
15 5 0.13
16 7 0.18
17 24 0.63
18 2 0.05
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (17 bp):
TTATATATATATATATA
Found at i:3416 original size:18 final size:17
Alignment explanation
Indices: 3392--3440 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
3382 ATCCAACATT
3392 TTTTCTTTTGTTTATTT-
1 TTTTCTTTTGTTT-TTTG
3409 TATTTCTTTTGTTTTTTG
1 T-TTTCTTTTGTTTTTTG
*
3427 TTTTGTTTTGTTTT
1 TTTTCTTTTGTTTT
3441 CTTTTTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 16 0.55
18 13 0.45
ACGTcount: A:0.04, C:0.04, G:0.10, T:0.82
Consensus pattern (17 bp):
TTTTCTTTTGTTTTTTG
Found at i:6886 original size:21 final size:21
Alignment explanation
Indices: 6840--6914 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
6830 TATTTAAAGA
*
6840 GTGGTCATTCGGG--ATATAT
1 GTGGTCATTCGGGACATCTAT
*
6859 ATGGTCATTCGGGACATCTAT
1 GTGGTCATTCGGGACATCTAT
6880 GTGGTCATTCGGGACATTTCTAT
1 GTGGTCATTCGGGACA--TCTAT
*
6903 GCGGTCATTCGG
1 GTGGTCATTCGG
6915 AACAAATTCA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 12 0.25
21 20 0.42
23 16 0.33
ACGTcount: A:0.19, C:0.17, G:0.29, T:0.35
Consensus pattern (21 bp):
GTGGTCATTCGGGACATCTAT
Found at i:6908 original size:23 final size:21
Alignment explanation
Indices: 6842--6914 Score: 87
Period size: 19 Copynumber: 3.5 Consensus size: 21
6832 TTTAAAGAGT
* *
6842 GGTCATTCGGGATATATAT--
1 GGTCATTCGGGACATCTATGC
*
6861 GGTCATTCGGGACATCTATGT
1 GGTCATTCGGGACATCTATGC
6882 GGTCATTCGGGACATTTCTATGC
1 GGTCATTCGGGACA--TCTATGC
6905 GGTCATTCGG
1 GGTCATTCGG
6915 AACAAATTCA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
19 17 0.36
21 14 0.30
23 16 0.34
ACGTcount: A:0.19, C:0.18, G:0.29, T:0.34
Consensus pattern (21 bp):
GGTCATTCGGGACATCTATGC
Found at i:10566 original size:20 final size:19
Alignment explanation
Indices: 10528--10566 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
10518 GTGATTTATG
*
10528 TGAATACATGTTAATGTGA
1 TGAATACATGTGAATGTGA
*
10547 TGAATCCATGTGATATGTGA
1 TGAATACATGTGA-ATGTGA
10567 ATATATATGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (19 bp):
TGAATACATGTGAATGTGA
Found at i:10711 original size:15 final size:15
Alignment explanation
Indices: 10687--10726 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
10677 ATGTTATATG
*
10687 AGCTACGTGATAAGA
1 AGCTATGTGATAAGA
10702 AGCTATGTGATAAGA
1 AGCTATGTGATAAGA
10717 AGCTATGTGA
1 AGCTATGTGA
10727 AAGTGATCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.38, C:0.10, G:0.28, T:0.25
Consensus pattern (15 bp):
AGCTATGTGATAAGA
Found at i:11892 original size:70 final size:68
Alignment explanation
Indices: 11817--11992 Score: 203
Period size: 70 Copynumber: 2.5 Consensus size: 68
11807 TACTTAAAAT
* *
11817 TTTAAAAAATATGAAAAATGAGAATATTGCAAAGTATCAATACTTATACACAAATATCGATACTT
1 TTTAAAAAATATGAAAAATGAGAA-ACTGCAAAGTATCAATA-TTATACACAAATATCAATACTT
11882 TCAAA
64 TCAAA
* * * * * * *
11887 TTTAAAAAAAATGAAAAATAAGAAAGCTGCAATGTTTCAATATTTTCCACAAATATTAATACTTT
1 TTTAAAAAATATGAAAAATGAGAAA-CTGCAAAGTATCAATATTATACACAAATATCAATACTTT
*
11952 CGAA
65 CAAA
11956 -TTAAAAAATAT-AGAAAATGAGAAGACTGCAAAGTATC
1 TTTAAAAAATATGA-AAAATGAGAA-ACTGCAAAGTATC
11993 GAACTTTTTT
Statistics
Matches: 89, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
67 1 0.01
68 29 0.33
69 24 0.27
70 35 0.39
ACGTcount: A:0.50, C:0.11, G:0.10, T:0.29
Consensus pattern (68 bp):
TTTAAAAAATATGAAAAATGAGAAACTGCAAAGTATCAATATTATACACAAATATCAATACTTTC
AAA
Found at i:12092 original size:21 final size:21
Alignment explanation
Indices: 12066--12117 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
12056 TGGTAAAATA
12066 TCGATACTTTTTCTATTATGT
1 TCGATACTTTTTCTATTATGT
12087 TCGATACTTTTTCTATTATGT
1 TCGATACTTTTTCTATTATGT
12108 TCGATACTTT
1 TCGATACTTT
12118 AACATTTGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.15, G:0.10, T:0.56
Consensus pattern (21 bp):
TCGATACTTTTTCTATTATGT
Found at i:12399 original size:105 final size:103
Alignment explanation
Indices: 12246--12674 Score: 495
Period size: 100 Copynumber: 4.2 Consensus size: 103
12236 ATATGGATAA
* *
12246 TGTAATAATAATTACAACTTAACC-GATTAAAATAAAGTAGGCGCAACATATTACGTTAAACTAG
1 TGTAA-AATATTTACAACTTAACCTGATTAAAATAAAATAGGCGCAACATATTACGTTAAACTAG
12310 CTACCAGTTTGTTTAAATGTATAATAATAATGTAATGTAAAC
65 CTACCAGTTTGTTTAAA-GTATAATAATAA--TAATGTAAAC
* * *
12352 TGTAAAATATTTACAACTTAACCTG-TTAAAATAAAATAGGTGTAACATATTACGTTAAACTAAC
1 TGTAAAATATTTACAACTTAACCTGATTAAAATAAAATAGGCGCAACATATTACGTTAAACTAGC
*
12416 TA-CATGTTTGTTTAACG-AT-ATAATAATAATGTAAAC
66 TACCA-GTTTGTTTAAAGTATAATAATAATAATGTAAAC
* * * ** * *
12452 GGTAAAATATTTACAACTTAACC-GGTTAAAATAAAAAAGATGCAACTTATTACGTTAAATTAGC
1 TGTAAAATATTTACAACTTAACCTGATTAAAATAAAATAGGCGCAACATATTACGTTAAACTAGC
*
12516 TACCAGTTTGTTTAAAGGTATAACAATAATAATGTAAAC
66 TACCAGTTTGTTTAAA-GTATAATAATAATAATGTAAAC
* * * * * *
12555 -GATAAAATATTTACAACTTAA-CTGATTAAAA-AAATTATGCGCCACCTATTACATTAAACTTG
1 TG-TAAAATATTTACAACTTAACCTGATTAAAATAAAATAGGCGCAACATATTACGTTAAACTAG
*
12617 CTACCAATTTGTTTATAAG--T-ATAATAATAATGTAAAC
65 CTACCAGTTTGTTTA-AAGTATAATAATAATAATGTAAAC
**
12654 AATAAAATATTTACAACTTAA
1 TGTAAAATATTTACAACTTAA
12675 TCGTTGAAAA
Statistics
Matches: 283, Mismatches: 29, Indels: 29
0.83 0.09 0.09
Matches are distributed among these distances:
99 36 0.13
100 78 0.28
101 3 0.01
102 47 0.17
103 46 0.16
104 3 0.01
105 64 0.23
106 6 0.02
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (103 bp):
TGTAAAATATTTACAACTTAACCTGATTAAAATAAAATAGGCGCAACATATTACGTTAAACTAGC
TACCAGTTTGTTTAAAGTATAATAATAATAATGTAAAC
Found at i:12518 original size:205 final size:202
Alignment explanation
Indices: 12247--12674 Score: 549
Period size: 205 Copynumber: 2.1 Consensus size: 202
12237 TATGGATAAT
* ** *
12247 GTAATAATAATTACAACTTAACCGATTAAAATAAAGTAGGCGCAACATATTACGTTAAACTAGCT
1 GTAA-AATATTTACAACTTAACCGATTAAAATAAAAAAGACGCAACATATTACGTTAAACTAGCT
* *
12312 ACCAGTTTGTTTAAATGTATAATAATAATGTAATGTAAACTG-TAAAATATTTACAACTTAACCT
65 ACCAGTTTGTTTAAAGGTATAACAATAA--TAATGTAAAC-GATAAAATATTTACAACTTAA-CT
* * * * *
12376 G-TTAAAATAAAATAGGTGTAACATATTACGTTAAACTAACTA-CATGTTTGTTTA-ACGATATA
126 GATTAAAA-AAAATAGGCGCAACATATTACATTAAACTAACTACCA-ATTTGTTTATAAG-TATA
*
12438 ATAATAATGTAAACG
188 ATAATAATGTAAACA
* * * *
12453 GTAAAATATTTACAACTTAACCGGTTAAAATAAAAAAGATGCAACTTATTACGTTAAATTAGCTA
1 GTAAAATATTTACAACTTAACCGATTAAAATAAAAAAGACGCAACATATTACGTTAAACTAGCTA
12518 CCAGTTTGTTTAAAGGTATAACAATAATAATGTAAACGATAAAATATTTACAACTTAACTGATTA
66 CCAGTTTGTTTAAAGGTATAACAATAATAATGTAAACGATAAAATATTTACAACTTAACTGATTA
* * * * **
12583 AAAAAATTATGCGCCACCTATTACATTAAACTTGCTACCAATTTGTTTATAAGTATAATAATAAT
131 AAAAAAATAGGCGCAACATATTACATTAAACTAACTACCAATTTGTTTATAAGTATAATAATAAT
12648 GTAAACA
196 GTAAACA
*
12655 ATAAAATATTTACAACTTAA
1 GTAAAATATTTACAACTTAA
12675 TCGTTGAAAA
Statistics
Matches: 195, Mismatches: 23, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
202 74 0.38
203 39 0.20
205 78 0.40
206 4 0.02
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (202 bp):
GTAAAATATTTACAACTTAACCGATTAAAATAAAAAAGACGCAACATATTACGTTAAACTAGCTA
CCAGTTTGTTTAAAGGTATAACAATAATAATGTAAACGATAAAATATTTACAACTTAACTGATTA
AAAAAAATAGGCGCAACATATTACATTAAACTAACTACCAATTTGTTTATAAGTATAATAATAAT
GTAAACA
Found at i:12773 original size:74 final size:69
Alignment explanation
Indices: 12686--12878 Score: 224
Period size: 74 Copynumber: 2.7 Consensus size: 69
12676 CGTTGAAAAG
* ** * *
12686 ATTTTTATTAATTCGAAAGTATCGATACTTGTGGAAAAGTATCAATACTTTGCAACCTTCTTATT
1 ATTTTTTTTAATTCGAAAGTATTAATACTTGTGGAAAAGTATCGATACTTTGCAACCTTCTCATT
12751 TTCCATGT
66 TT-C---T
* * * * *
12759 TTTTTTTTTAAATTCGAAAGTCTTAATACTTGTAGAAAAATATCGATATTTTGCAACCTTCTCAT
1 ATTTTTTTT-AATTCGAAAGTATTAATACTTGTGGAAAAGTATCGATACTTTGCAACCTTCTCAT
12824 TTTCT
65 TTTCT
* * *
12829 ATTTTTTTTAATTCAAAAGTATTAATATTTGTGTAAAAGTATCGATACTT
1 ATTTTTTTTAATTCGAAAGTATTAATACTTGTGGAAAAGTATCGATACTT
12879 ATTTCCATAC
Statistics
Matches: 101, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
69 34 0.34
70 9 0.09
73 8 0.08
74 50 0.50
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (69 bp):
ATTTTTTTTAATTCGAAAGTATTAATACTTGTGGAAAAGTATCGATACTTTGCAACCTTCTCATT
TTCT
Found at i:13157 original size:202 final size:202
Alignment explanation
Indices: 12794--13327 Score: 556
Period size: 202 Copynumber: 2.6 Consensus size: 202
12784 ATACTTGTAG
* * * ** *
12794 AAAAATATCGATATTTTGCAACCTTCTCATTTTCTATTTTTTTTAATTCAAAAGTATTAATATTT
1 AAAAGTATCGATATTTTGCAGCCTTCTCATTTTCTATTTTTTTAAATTTGAAAGTATCAATATTT
* * * *
12859 GTGTAAAAGTATCGATACTTATTTCCATACATTTTATATAAAAATTTTCAATACTTTTTTATCGG
66 GTGGAAAAGTATCGATACTTA-TTCCATACATTTTATATAAAAAGTTTCGATACTCTTTTATCGG
* * * *
12924 TATCAGCTCGTTTTGTTTTATATCAGTTACC-T-TAATATAATAAC-AGTTGCTTATAAGGAAGC
130 TATCAGCTCGTTTTATTTTATATCAGTTACCTTATAAAACAATAACGA-TTACTTATAAGGAAGC
**
12986 ATGAGAAAT
194 AAAAGAAAT
** * * * *
12995 TGAAGTATCAATATTTTGCAGCCATCTCATTTTCCATTTTTTTAAAATTTGAAAGTATCGATATT
1 AAAAGTATCGATATTTTGCAGCCTTCTCATTTTCTATTTTTTT-AAATTTGAAAGTATCAATATT
* *
13060 TGTGGAAAAGTATCGATACTTATTCACATGCATTTTATATAAAAAGTTTCGGTACTCTTTTA-CT
65 TGTGGAAAAGTATCGATACTTATTC-CATACATTTTATATAAAAAGTTTCGATACTCTTTTATC-
* * * ** *
13124 GGTTTC-GCCTTGTTTTATTTTTTATTGGTTACCTTAGTAAAACAATAACGATTATTTATAAGGA
128 GGTATCAG-CTCGTTTTATTTTATATCAGTTACCTTA-TAAAACAATAACGATTACTTATAAGGA
13188 AGCAAAAGAAAT
191 AGCAAAAGAAAT
* *
13200 AAAAGTATCGATACTTTGCCGCCTTCTCATTTTTCATATATATATTATTTTTTAAATTTGAAAGT
1 AAAAGTATCGATATTTTGCAGCCTTCTCA-TTTTC-------TA-T-TTTTTTAAATTTGAAAGT
* * *
13265 ATCTATATTTGTGGAAAAGTATCGATATTTATTCGCATACATTCTATATAAAAAGTTTCGATA
56 ATCAATATTTGTGGAAAAGTATCGATACTTATTC-CATACATTTTATATAAAAAGTTTCGATA
13328 TTTTACAGGT
Statistics
Matches: 272, Mismatches: 43, Indels: 23
0.80 0.13 0.07
Matches are distributed among these distances:
201 41 0.15
202 93 0.34
203 1 0.00
205 54 0.20
206 6 0.02
213 1 0.00
214 70 0.26
215 6 0.02
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.43
Consensus pattern (202 bp):
AAAAGTATCGATATTTTGCAGCCTTCTCATTTTCTATTTTTTTAAATTTGAAAGTATCAATATTT
GTGGAAAAGTATCGATACTTATTCCATACATTTTATATAAAAAGTTTCGATACTCTTTTATCGGT
ATCAGCTCGTTTTATTTTATATCAGTTACCTTATAAAACAATAACGATTACTTATAAGGAAGCAA
AAGAAAT
Found at i:14117 original size:27 final size:27
Alignment explanation
Indices: 14087--14182 Score: 183
Period size: 27 Copynumber: 3.6 Consensus size: 27
14077 TTTAATTAAG
14087 ATTTAATTGGAATATTAGTTAAAAATT
1 ATTTAATTGGAATATTAGTTAAAAATT
14114 ATTTAATTGGAATATTAGTTAAAAATT
1 ATTTAATTGGAATATTAGTTAAAAATT
*
14141 ATTTAATTGGAATATTAGTTGAAAATT
1 ATTTAATTGGAATATTAGTTAAAAATT
14168 ATTTAATTGGAATAT
1 ATTTAATTGGAATAT
14183 GTTTATTAGA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
27 68 1.00
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (27 bp):
ATTTAATTGGAATATTAGTTAAAAATT
Found at i:14135 original size:16 final size:16
Alignment explanation
Indices: 14089--14160 Score: 56
Period size: 16 Copynumber: 5.1 Consensus size: 16
14079 TAATTAAGAT
14089 TTAATTGGAATATTAG
1 TTAATTGGAATATTAG
*
14105 TTAA----AA-ATTAT
1 TTAATTGGAATATTAG
14116 TTAATTGGAATATTAG
1 TTAATTGGAATATTAG
*
14132 TTAA----AA-ATTAT
1 TTAATTGGAATATTAG
14143 TTAATTGGAATATTAG
1 TTAATTGGAATATTAG
14159 TT
1 TT
14161 GAAAATTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 20
0.64 0.06 0.30
Matches are distributed among these distances:
11 16 0.38
12 4 0.10
15 4 0.10
16 18 0.43
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (16 bp):
TTAATTGGAATATTAG
Found at i:17502 original size:2 final size:2
Alignment explanation
Indices: 17495--17557 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
17485 ATTCCGTGTA
17495 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17537 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
17558 CACACATATG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:26448 original size:36 final size:36
Alignment explanation
Indices: 26398--26473 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
26388 TTATAGCAAA
*
26398 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
26434 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
26470 AAAA
1 AAAA
26474 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:31451 original size:36 final size:36
Alignment explanation
Indices: 31401--31476 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
31391 TTATAGCAAA
*
31401 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
31437 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
31473 AAAA
1 AAAA
31477 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:33034 original size:84 final size:83
Alignment explanation
Indices: 32813--33040 Score: 237
Period size: 84 Copynumber: 2.7 Consensus size: 83
32803 CAAAAGCCAG
* * * * * *
32813 TATATATTGGCTATCGCGGCTTTTTTTTATATAAACGCCACTAAAGTACGTGTGTTTAGCGGTGT
1 TATATATTGGCTTTCG-GGC-TTTTTTTACATAAACGCCACTAAAGTACGCGTTTTTAGCAGAGT
*
32878 TTTCACAAAAAACGTCACTA
64 TTTCACAAAAAACGCCACTA
* * ** *
32898 TATATCTT-GTTATTGCGGTTTTTTTTTACATAAACGCCAC-ATAAGTATGCGTTTTTAGCAGAG
1 TATATATTGGCT-TT-CGGGCTTTTTTTACATAAACGCCACTA-AAGTACGCGTTTTTAGCAGAG
32961 TTTTCAC-AAAAACGCCACTA
63 TTTTCACAAAAAACGCCACTA
* * *
32981 TATATATATGGCTTTCGTGGCGTTTTTTACATAAATGCCACTAAAGTACGCGTTTGTAGC
1 TATATAT-TGGCTTTCG-GGCTTTTTTTACATAAACGCCACTAAAGTACGCGTTTTTAGC
33041 GGCTCCCAAA
Statistics
Matches: 116, Mismatches: 20, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
83 21 0.18
84 81 0.70
85 12 0.10
86 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.38
Consensus pattern (83 bp):
TATATATTGGCTTTCGGGCTTTTTTTACATAAACGCCACTAAAGTACGCGTTTTTAGCAGAGTTT
TCACAAAAAACGCCACTA
Found at i:46431 original size:26 final size:27
Alignment explanation
Indices: 46402--46453 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
46392 TTGGTTTGGT
46402 TTTAAACGG-TTCA-GTTTTTGATTCGA
1 TTTAAA-GGCTTCATGTTTTTGATTCGA
*
46428 TTTAAAGGCTTCATTTTTTTGATTCG
1 TTTAAAGGCTTCATGTTTTTGATTCG
46454 GTTCGGGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 2 0.09
26 10 0.43
27 11 0.48
ACGTcount: A:0.21, C:0.12, G:0.17, T:0.50
Consensus pattern (27 bp):
TTTAAAGGCTTCATGTTTTTGATTCGA
Found at i:46921 original size:29 final size:30
Alignment explanation
Indices: 46889--46954 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
46879 TTCATAAATT
46889 TTTAAAAATTAAGA-TATAAATTAAA-TTAA
1 TTTAAAAATTAA-ACTATAAATTAAACTTAA
* *
46918 TTTAAAACTTAAACTTTAAATTAAATCTTAA
1 TTTAAAAATTAAACTATAAATTAAA-CTTAA
46949 TTTAAA
1 TTTAAA
46955 TCTTAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 1 0.03
29 21 0.66
31 10 0.31
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.41
Consensus pattern (30 bp):
TTTAAAAATTAAACTATAAATTAAACTTAA
Found at i:46949 original size:31 final size:30
Alignment explanation
Indices: 46905--46984 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
46895 AATTAAGATA
46905 TAAATTAAA-TTAATTTAAAACTTAAACTT
1 TAAATTAAATTTAATTTAAAACTTAAACTT
* **
46934 TAAATTAAATCTTAATTTAAATCTTAATTTT
1 TAAATTAAAT-TTAATTTAAAACTTAAACTT
* *
46965 TAGATAAAATATTAATTTAA
1 TAAATTAAAT-TTAATTTAA
46985 CTCATGAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 9 0.21
31 34 0.79
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (30 bp):
TAAATTAAATTTAATTTAAAACTTAAACTT
Found at i:46961 original size:12 final size:12
Alignment explanation
Indices: 46933--46963 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
46923 AACTTAAACT
*
46933 TTAAATTAAATC
1 TTAATTTAAATC
46945 TTAATTTAAATC
1 TTAATTTAAATC
46957 TTAATTT
1 TTAATTT
46964 TTAGATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAATTTAAATC
Found at i:47996 original size:2 final size:2
Alignment explanation
Indices: 47991--48015 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47981 AAAAAAGTGT
47991 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 T
48016 TAATATTGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48290 original size:22 final size:22
Alignment explanation
Indices: 48242--48290 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
48232 TTTTAATATT
48242 TTTTAAATATAAAAAAATCTAA
1 TTTTAAATATAAAAAAATCTAA
* **
48264 ATTTAAATAATAATTAAAT-TAA
1 TTTTAAAT-ATAAAAAAATCTAA
48286 TTTTA
1 TTTTA
48291 TCTGATTAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTTAAATATAAAAAAATCTAA
Found at i:51275 original size:16 final size:18
Alignment explanation
Indices: 51239--51278 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
51229 CTCTAGCTGA
51239 TTTTTATGTCCTTGTTCT
1 TTTTTATGTCCTTGTTCT
*
51257 TTTTTATG-CTTTGTT-T
1 TTTTTATGTCCTTGTTCT
51273 TTTTTA
1 TTTTTA
51279 CATTGCAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
17 6 0.29
18 8 0.38
ACGTcount: A:0.07, C:0.10, G:0.10, T:0.72
Consensus pattern (18 bp):
TTTTTATGTCCTTGTTCT
Found at i:62907 original size:35 final size:35
Alignment explanation
Indices: 62861--62947 Score: 99
Period size: 35 Copynumber: 2.5 Consensus size: 35
62851 TAGTATTTTT
*
62861 TAAATAGTTATTATATTTTATATT-AAT-ATATTTATG
1 TAAATA-TTATT-TATTTT-TATTAAATAATATTTATA
62897 TAAATATTATTT-TTTTTATTAAAATAATATTTATA
1 TAAATATTATTTATTTTTATT-AAATAATATTTATA
*
62932 TAATTATTATTTATTT
1 TAAATATTATTTATTT
62948 AGAATTATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
32 4 0.09
33 4 0.09
34 4 0.09
35 24 0.53
36 9 0.20
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (35 bp):
TAAATATTATTTATTTTTATTAAATAATATTTATA
Found at i:63112 original size:17 final size:17
Alignment explanation
Indices: 63090--63143 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
63080 AATGTTAATA
63090 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
63107 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
63124 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
63141 TTT
1 TTT
63144 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:65606 original size:22 final size:21
Alignment explanation
Indices: 65569--65609 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
65559 ATAAATATTT
*
65569 TTAATATATTATTTATAATAA
1 TTAATATATTAGTTATAATAA
65590 TTAATATTATTAGTTATAAT
1 TTAATA-TATTAGTTATAAT
65610 TTTTTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TTAATATATTAGTTATAATAA
Found at i:66967 original size:182 final size:182
Alignment explanation
Indices: 66675--67547 Score: 1142
Period size: 183 Copynumber: 4.8 Consensus size: 182
66665 GATACAAATG
* * * * * * * *
66675 AAAAATAGATCGCTCCATAGCAATATTACAGGTACAAATATGACAAAACGGGTC-CCAAAATGAC
1 AAAAATATATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGAC
* * * *
66739 AAAACCGGTAAAACGCTACCGGATATGTGTCG--AGTGTCGATAATTTAATATAAGTATCGAAAC
66 AAAACCGG-AAAAAGTTACCGGATATAT-T-GAAAGTGTCGATAATTTAATATAAGTATCGACAC
* * *
66802 TTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAA
128 TTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTAT
* *
66857 AAAAATATATCGATCCACAACAATATAACAGGTAAAAATATGATAAAACTGGTCTCAAAAATGAC
1 AAAAATATATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGAC
* *
66922 AAAACCGGAAAAAGTTACTGGATATATTGAAAGTGTCGATAATTTAATATTAGTATCGACACTTT
66 AAAACCGGAAAAAGTTACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
66987 CTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTAT
131 CTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTAT
* * * * * * *
67039 GAAAATGTATCGATCCTTACCAATATAACAAGTAAAAATATGATAAAACATGTCTAAAAAAATGA
1 AAAAATATATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCT-CAAAAATGA
* * * *
67104 CAAAACCGAAAAAAGTTACCGGATATGTTAAAAGTGTCGATAATTTAATATAAGTATCGATACTT
65 CAAAACCGGAAAAAGTTACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTT
* * *
67169 TCTGAATTTAAAAGAGAAAAAGTTATTGCGCTTAAAAAGTGTCGACACTTTAT
130 TCTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTAT
* * * * *
67222 GAAAATGTATCGATCTATAACAATATAACAGGTAAAAATATGATAAAACAAGTCTCAAAATTGAC
1 AAAAATATATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGAC
* * * *
67287 AAAACCAGTAAAACGCTACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGAAACTT
66 AAAACC-GGAAAAAGTTACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTT
* ** * *
67352 TCTGAATTTAAAAGAGAAGAAGTTATAGCGTCTGTAAAGTGTCGATACTTTAA
130 TCTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTAT
* * * *
67405 AAAAATATATCGATCCACAATAATATAACAGGTAAAAATATGATAAAACAGGTCCCAAAATTTGA
1 AAAAATATATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAA-ATGA
* * *
67470 CAAAACCAGTAAAACA-ATACCGGATATATTGAAAGTATCGATAATTTAATATAAGTATCGACAC
65 CAAAACC-GGAAAA-AGTTACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACAC
* *
67534 TTTCTAAAATTAAA
128 TTTCTGAATTTAAA
67548 CTAAAAAGTG
Statistics
Matches: 614, Mismatches: 70, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
180 1 0.00
181 1 0.00
182 203 0.33
183 334 0.54
184 75 0.12
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (182 bp):
AAAAATATATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGAC
AAAACCGGAAAAAGTTACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
CTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTAT
Found at i:67856 original size:182 final size:181
Alignment explanation
Indices: 67549--68047 Score: 739
Period size: 182 Copynumber: 2.7 Consensus size: 181
67539 AAAATTAAAC
* *
67549 TAAAAAGTGTCGACACTTTATGAAAATGTATCAATCCATAACAATATAACAGGTAAAACTATGAT
1 TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAT
** ** *
67614 AAAATTGGTCTCAAAAATGACAAAACCGAAAAAAGTTATTGGATATATTGAAAGTGTCGATAATT
66 AAAACAGGTCT-AAAAATGACAAAACCGAAAAAAGTTACCGGATATGTTGAAAGTGTCGATAATT
*
67679 TAATATTAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCT
130 TAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCT
* * *
67731 TAAAAAGTGTCGACACTTTATTAAAATGTATCGATCCTTACCAATATAACAGGTAAAAATATGAT
1 TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAT
* *
67796 AAAACAGGTCTAAAAAATGACAAAGCC-AGAAAAAGTTACCAGATATGTTGAAAGTGTCGATAAT
66 AAAACAGGTCT-AAAAATGACAAAACCGA-AAAAAGTTACCGGATATGTTGAAAGTGTCGATAAT
*
67860 TTAATATAAGTATCGACACTTTCTTAATTTAAAAGAGAAGAAGTTATAGCGCT
129 TTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCT
* * * *
67913 TAAAAAATGTCGACACTTTATGAAAATATATCGATCCAGAACAATATAATAGGTAAAAATATGAT
1 TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAT
* * * * * *
67978 AAAACCGGTCTCAAAATGACAAAACTGGTAAATAGTTACCGGATATGTTGAAAGTGTCGATACTT
66 AAAACAGGTCTAAAAATGACAAAAC-CGAAAAAAGTTACCGGATATGTTGAAAGTGTCGATAATT
68043 TAATA
130 TAATA
68048 AGTACGCGTA
Statistics
Matches: 284, Mismatches: 30, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
181 13 0.05
182 271 0.95
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.28
Consensus pattern (181 bp):
TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAT
AAAACAGGTCTAAAAATGACAAAACCGAAAAAAGTTACCGGATATGTTGAAAGTGTCGATAATTT
AATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCT
Found at i:68458 original size:18 final size:19
Alignment explanation
Indices: 68435--68479 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
68425 TAGTTAATAT
68435 TTATAGGT-AAAAATGATA
1 TTATAGGTAAAAAATGATA
68453 TTATAGGTAAAAAATGATA
1 TTATAGGTAAAAAATGATA
*
68472 TTTTAGGT
1 TTATAGGT
68480 TGTATAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 8 0.32
19 17 0.68
ACGTcount: A:0.44, C:0.00, G:0.18, T:0.38
Consensus pattern (19 bp):
TTATAGGTAAAAAATGATA
Found at i:68608 original size:5 final size:5
Alignment explanation
Indices: 68598--68626 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
68588 TGTAAGCAGT
68598 ATTTG ATTTG ATTTG ATTTG ATTTG ATTT
1 ATTTG ATTTG ATTTG ATTTG ATTTG ATTT
68627 ACGCAAACTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.17, T:0.62
Consensus pattern (5 bp):
ATTTG
Found at i:68762 original size:18 final size:18
Alignment explanation
Indices: 68741--68779 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
68731 TTGAAATGGT
68741 AATTAGATTA-AAACTTTA
1 AATT-GATTACAAACTTTA
*
68759 AATTGATTACAAATTTTA
1 AATTGATTACAAACTTTA
68777 AAT
1 AAT
68780 GTTGACAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (18 bp):
AATTGATTACAAACTTTA
Found at i:69913 original size:198 final size:194
Alignment explanation
Indices: 69415--69944 Score: 600
Period size: 198 Copynumber: 2.7 Consensus size: 194
69405 AAGAATATGC
*
69415 GTCGATACATTTTCAAAA-AGTATCG-TCCCCAAAAACATCGAAACAAATAATTATAATGTAATA
1 GTCGATACA-TTT-AAAATTGTATCGAT-CCCAAAAACATCGAAACAAA-AATTATAATGTAATA
** * * * * * * * * * *
69478 TTTAAATTAACAATGTAACCAGTATACATATACCGATTAATTATAAAACAAGTCAACATAAAATA
62 GGTAAATTTACAATGTAACCGGTATAAATATACCGTTTTATGAGAAAATAGGTCAA-ATAAAGTA
* * * * * *
69543 TCGACACTTTTTAAGTTTGTGTTGATACTTTTTTCCAAAAGAAAGCACAAACAGGTTCACGCATA
126 TCGACACTTTGTAAGTTTGTGTCGATACTTTTGTCCAAAAGAAAGCACAAACAGGTGCAAGAATA
69608 AAGT
191 AAGT
* * * *
69612 GTCGATACATTTAAAATTGTATCGATCACAAAAACATCAAAACCGATAATTATAATGTAATAGGT
1 GTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAA-CAAAAATTATAATGTAATAGGT
* * *
69677 CAATTTACAATGTAACCGGTTTAAATTTACCAGTTTTATGAGAAAATAGGTCAGAATAAAGTATC
65 AAATTTACAATGTAACCGGTATAAATATACC-GTTTTATGAGAAAATAGGTCA-AATAAAGTATC
* * *
69742 GACACTTGTGTAA-TTTGTGTCGATACATTTTGTCCATAATGAATGC-CCAACGAGGTGCAAGAA
128 GACACTT-TGTAAGTTTGTGTCGATAC-TTTTGTCCA-AAAGAAAGCACAAAC-AGGTGCAAGAA
*
69805 TAACGT
189 TAAAGT
* *
69811 GTCGATACATTTAAAATTGTATCGATCCCAAAAGCATCGAAACAAAAATTATAATGTTATAGGTA
1 GTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACAAAAATTATAATGTAATAGGTA
* *
69876 AATTTACAATGTACCCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCTAAATAATGTATCG
66 AATTTACAATGTAACCGGTATAAATATACC-GTTTTATGAGAAAATAGGTC-AAATAAAGTATCG
69941 ACAC
129 ACAC
69945 GTAATTATCG
Statistics
Matches: 281, Mismatches: 42, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
195 4 0.01
196 64 0.23
197 55 0.20
198 98 0.35
199 60 0.21
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (194 bp):
GTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACAAAAATTATAATGTAATAGGTA
AATTTACAATGTAACCGGTATAAATATACCGTTTTATGAGAAAATAGGTCAAATAAAGTATCGAC
ACTTTGTAAGTTTGTGTCGATACTTTTGTCCAAAAGAAAGCACAAACAGGTGCAAGAATAAAGT
Found at i:70377 original size:21 final size:21
Alignment explanation
Indices: 70338--70378 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
70328 CGGTAAAAAT
* * *
70338 TACCTAAAATATTATTATTTC
1 TACCTAAAACATCAATATTTC
70359 TACCTAAAACATCAATATTT
1 TACCTAAAACATCAATATTT
70379 TTTAACATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (21 bp):
TACCTAAAACATCAATATTTC
Found at i:71051 original size:23 final size:23
Alignment explanation
Indices: 71004--71053 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
70994 AATAACATAT
**
71004 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
71027 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
71050 TAGG
1 TAGG
71054 CATTTAATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:71691 original size:197 final size:199
Alignment explanation
Indices: 71352--71723 Score: 540
Period size: 197 Copynumber: 1.9 Consensus size: 199
71342 TACAATTTTA
* * *
71352 AATGTATCGACACTTGTGTAATTTGTGTTGATACATTTTGTCCATAATGAATGCCAAACTAGGTG
1 AATGTATCGACACTTGTGTAATTTGTGTCGATACATTTTGTCCAGAATGAATGCCAAACGAGGTG
* **
71417 CACTCATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAATTGATAATTA
66 CACGCATAAAGTGTCGATACATTTA-TAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTA
*
71482 CAATGTAATAGGTAAATTTACAATG-TAGCCGGTAGAAATATACCGATTTTATGAGAAAATAGGT
130 CAATGTAATAGGTAAATTTACAATGTTA-CCGATAGAAATATACCGATTTTATGAGAAAATAGGT
71546 CTACAT
194 CTACAT
* *
71552 AATGTATCGACACGTT-T-TAAGTTTGTGTCGA-AC-TTTTTTCCAGAATGAATGCCCAACGAGG
1 AATGTATCGACAC-TTGTGTAA-TTTGTGTCGATACATTTTGTCCAGAATGAATGCCAAACGAGG
* *
71613 TGCACGCATAAAGTGTCGATACATTTA-AAATTGTATCGATCCCAAAAACATTGAAACCGATAAT
64 TGCACGCATAAAGTGTCGATACATTTATAAA-AGTATCGATCCCAAAAACATCGAAACCGATAAT
* *
71677 TATAATGTAATAGGTAAATTTACAATGTTACCGATATAAATATACCG
128 TACAATGTAATAGGTAAATTTACAATGTTACCGATAGAAATATACCG
71724 CTATAAATCT
Statistics
Matches: 155, Mismatches: 13, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
196 3 0.02
197 70 0.45
198 52 0.34
199 5 0.03
200 23 0.15
201 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.31
Consensus pattern (199 bp):
AATGTATCGACACTTGTGTAATTTGTGTCGATACATTTTGTCCAGAATGAATGCCAAACGAGGTG
CACGCATAAAGTGTCGATACATTTATAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTAC
AATGTAATAGGTAAATTTACAATGTTACCGATAGAAATATACCGATTTTATGAGAAAATAGGTCT
ACAT
Found at i:72080 original size:125 final size:125
Alignment explanation
Indices: 71904--72133 Score: 352
Period size: 125 Copynumber: 1.8 Consensus size: 125
71894 CTGGTAAAAA
* *
71904 AATAACAAAAACGGCAGCGCTTTTACCGGTTTTGTTAAGAAACCCGATAAAATGCAAAAATAATA
1 AATAACAAAAACGACAGCCCTTTTACCGGTTTTGTTAAGAAACCCGATAAAATGCAAAAATAATA
*
71969 ACAAAACCGATAGAAATAATGATGTTTTCGGTAATTTTTACCGGGTTTATTATGCACAAC
66 ACAAAACCGATAGAAATAATGATGTTTTCAGTAATTTTTACCGGGTTTATTATGCACAAC
* * * * * * *
72029 AATAACAAAACCGATAGCCCTTTTACTGGTTTTGTTAAGGAACGCGGTAAAATGCCAAAATAATA
1 AATAACAAAAACGACAGCCCTTTTACCGGTTTTGTTAAGAAACCCGATAAAATGCAAAAATAATA
* *
72094 ACAAAACCGGTAGGAATAATGATGTTTTCAGTAATTTTTA
66 ACAAAACCGATAGAAATAATGATGTTTTCAGTAATTTTTA
72134 ACAAAACCGG
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
125 93 1.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.29
Consensus pattern (125 bp):
AATAACAAAAACGACAGCCCTTTTACCGGTTTTGTTAAGAAACCCGATAAAATGCAAAAATAATA
ACAAAACCGATAGAAATAATGATGTTTTCAGTAATTTTTACCGGGTTTATTATGCACAAC
Found at i:76532 original size:35 final size:34
Alignment explanation
Indices: 76447--76533 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 34
76437 AATATAATTT
*
76447 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
*
76481 TAAATGATAA-ACAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACA-AAATTACAATAA--G-TATTAAATGG
76519 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
76534 ACCAAAATAC
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
34 6 0.13
35 22 0.49
36 2 0.04
37 4 0.09
38 11 0.24
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:76566 original size:34 final size:33
Alignment explanation
Indices: 76528--76611 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 33
76518 GTAATAAACA
*
76528 AAATTAACCAAAATACATTAACAA-AAAGTCCAA-C
1 AAATTAA-CAAAATAAATTAA-AATAAA-TCCAACC
76562 AAATTTAACAAAATAAATTAAAATAAATCCAACC
1 AAA-TTAACAAAATAAATTAAAATAAATCCAACC
**
76596 AAATTAATGAAATAAA
1 AAATTAACAAAATAAA
76612 GTAAGTATTA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
33 18 0.41
34 22 0.50
35 4 0.09
ACGTcount: A:0.62, C:0.14, G:0.02, T:0.21
Consensus pattern (33 bp):
AAATTAACAAAATAAATTAAAATAAATCCAACC
Found at i:76611 original size:33 final size:34
Alignment explanation
Indices: 76524--76600 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 34
76514 AATGGTAATA
* *
76524 AACAAAATTAACCAAAATACATTAACAAAAAGTCC
1 AACAAATTTAA-CAAAATAAATTAACAAAAAGTCC
76559 AACAAATTTAACAAAATAAATTAA-AATAAA-TCC
1 AACAAATTTAACAAAATAAATTAACAA-AAAGTCC
76592 AACCAAATT
1 AA-CAAATT
76601 AATGAAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
33 7 0.18
34 21 0.55
35 10 0.26
ACGTcount: A:0.61, C:0.17, G:0.01, T:0.21
Consensus pattern (34 bp):
AACAAATTTAACAAAATAAATTAACAAAAAGTCC
Found at i:78909 original size:16 final size:17
Alignment explanation
Indices: 78885--78918 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
78875 TATATCTGGA
78885 AAAAAATTAA-TTAAAT
1 AAAAAATTAATTTAAAT
*
78901 AAAATATTAATTTAAAT
1 AAAAAATTAATTTAAAT
78918 A
1 A
78919 CTTAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAAAATTAATTTAAAT
Found at i:84146 original size:20 final size:20
Alignment explanation
Indices: 84121--84169 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
84111 GATTAAATTA
*
84121 GTATCGATACTGAA-AGTAAG
1 GTATCGATAC-CAAGAGTAAG
84141 GTATCGATACCAAGAGTAAG
1 GTATCGATACCAAGAGTAAG
84161 GTATCGATA
1 GTATCGATA
84170 ATATTATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.24
Consensus pattern (20 bp):
GTATCGATACCAAGAGTAAG
Found at i:84275 original size:20 final size:20
Alignment explanation
Indices: 84250--84302 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
84240 TAGGAGAGAG
84250 GTATCGATACTATAGTTGGA
1 GTATCGATACTATAGTTGGA
* *
84270 GTATCGATACTGTAGTTGGG
1 GTATCGATACTATAGTTGGA
*
84290 GTACCGATACTAT
1 GTATCGATACTAT
84303 TAAGTCTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.34
Consensus pattern (20 bp):
GTATCGATACTATAGTTGGA
Found at i:84964 original size:2 final size:2
Alignment explanation
Indices: 84957--84986 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
84947 ACCATGACAT
84957 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
84987 TATATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:85020 original size:2 final size:2
Alignment explanation
Indices: 85013--85047 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
85003 AAATAATCAA
85013 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
85048 CAAGTCACTC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:85389 original size:21 final size:21
Alignment explanation
Indices: 85364--85435 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
85354 ACATAGAATT
*
85364 TGTCCCGAATAACCACATATA
1 TGTCCCGAATGACCACATATA
*
85385 TGTCCCGAAGGACCACATATA
1 TGTCCCGAATGACCACATATA
*
85406 TGTCCCGAATGACCACATAGA
1 TGTCCCGAATGACCACATATA
85427 TGTCCCGAA
1 TGTCCCGAA
85436 GGACTACTCC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (21 bp):
TGTCCCGAATGACCACATATA
Found at i:87463 original size:15 final size:14
Alignment explanation
Indices: 87443--87506 Score: 69
Period size: 15 Copynumber: 4.5 Consensus size: 14
87433 TATTTGACAA
87443 TGCTATGTGATAATG
1 TGCTATGTGA-AATG
87458 TGCTATGTGAAATG
1 TGCTATGTGAAATG
87472 T--TATGTGAATATG
1 TGCTATGTGAA-ATG
*
87485 TGCTAAGTGAATATG
1 TGCTATGTGAA-ATG
*
87500 TTCTATG
1 TGCTATG
87507 GAACATAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
12 8 0.19
13 4 0.09
14 5 0.12
15 26 0.60
ACGTcount: A:0.28, C:0.06, G:0.25, T:0.41
Consensus pattern (14 bp):
TGCTATGTGAAATG
Found at i:87476 original size:27 final size:27
Alignment explanation
Indices: 87441--87501 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
87431 AATATTTGAC
* *
87441 AATGCTATGTG-ATAATGTGCTATGTGA
1 AATGTTATGTGAAT-ATGTGCTAAGTGA
87468 AATGTTATGTGAATATGTGCTAAGTGA
1 AATGTTATGTGAATATGTGCTAAGTGA
87495 ATATGTT
1 A-ATGTT
87502 CTATGGAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 23 0.77
28 7 0.23
ACGTcount: A:0.31, C:0.05, G:0.25, T:0.39
Consensus pattern (27 bp):
AATGTTATGTGAATATGTGCTAAGTGA
Found at i:87765 original size:23 final size:23
Alignment explanation
Indices: 87739--87823 Score: 107
Period size: 23 Copynumber: 3.7 Consensus size: 23
87729 GGGTTCTTTA
87739 TGGTCCTTCGGGACAATCCTATG
1 TGGTCCTTCGGGACAATCCTATG
*
87762 TGGTCCTTCGAGACAATCCTATG
1 TGGTCCTTCGGGACAATCCTATG
* * * **
87785 TAGTCTTTCGGGATAAAACTATG
1 TGGTCCTTCGGGACAATCCTATG
*
87808 TGGTCATTCGGGACAA
1 TGGTCCTTCGGGACAA
87824 ATATGTGTCA
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.31
Consensus pattern (23 bp):
TGGTCCTTCGGGACAATCCTATG
Found at i:88310 original size:12 final size:12
Alignment explanation
Indices: 88293--88324 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
88283 TTTCCTCTTG
88293 TCTTCTTCTTAT
1 TCTTCTTCTTAT
*
88305 TCTTCTTCTTGT
1 TCTTCTTCTTAT
88317 TCTTCTTC
1 TCTTCTTC
88325 CCGTTAGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.03, C:0.28, G:0.03, T:0.66
Consensus pattern (12 bp):
TCTTCTTCTTAT
Found at i:94022 original size:21 final size:20
Alignment explanation
Indices: 93992--94036 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
93982 TTTAAAAGTG
93992 AAAAAATAATGAAAAATAATT
1 AAAAAATAAT-AAAAATAATT
* * *
94013 AAAAATTAATAAAATTTATT
1 AAAAAATAATAAAAATAATT
94033 AAAA
1 AAAA
94037 TAAAAAGAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (20 bp):
AAAAAATAATAAAAATAATT
Found at i:94262 original size:82 final size:81
Alignment explanation
Indices: 94157--94449 Score: 444
Period size: 82 Copynumber: 3.6 Consensus size: 81
94147 TTATTTTATT
* * *
94157 TGATATGTCAATGAAAAGT-AAATGACGTGAATAATGTAGATTCTCTGATTTTCTAAATTATTTT
1 TGATATGTCAATGAAAA-TCAAATGATGTGAATAGTGTAGATTCTCT-ATTCTCTAAATTATTTT
*
94221 ACTTTATCTGAGTTGATG
64 AGTTTATCTGAGTTGATG
* *
94239 TGATATGTCAAGGAAAATCAAATGATGTGAATAGTGTAGATTCTCTTATTCTCTAAATTATTTCA
1 TGATATGTCAATGAAAATCAAATGATGTGAATAGTGTAGATTCTC-TATTCTCTAAATTATTTTA
94304 GTTTATCTGAGTTGATG
65 GTTTATCTGAGTTGATG
* *
94321 TGATATGTCAATGAAAAACAAATGATGTAAATAGTGTAGATTCTCATATTCTCTAAATTATTTTA
1 TGATATGTCAATGAAAATCAAATGATGTGAATAGTGTAGATTCTC-TATTCTCTAAATTATTTTA
94386 GTTTATCTGAGTTGATG
65 GTTTATCTGAGTTGATG
* * *
94403 TAATATGTCAATGAAAATTAAAGGATGTGAATAGTGTAGATTCTCTA
1 TGATATGTCAATGAAAATCAAATGATGTGAATAGTGTAGATTCTCTA
94450 AATTTGATAT
Statistics
Matches: 193, Mismatches: 16, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
81 3 0.02
82 189 0.98
83 1 0.01
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (81 bp):
TGATATGTCAATGAAAATCAAATGATGTGAATAGTGTAGATTCTCTATTCTCTAAATTATTTTAG
TTTATCTGAGTTGATG
Found at i:99875 original size:33 final size:33
Alignment explanation
Indices: 99833--99899 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
99823 CCTAGTACAG
99833 ATGGTGGACACGACCTTATGTGTCATACGGATT
1 ATGGTGGACACGACCTTATGTGTCATACGGATT
99866 ATGGTGGACACGACCTTATGTGTCATACGGATT
1 ATGGTGGACACGACCTTATGTGTCATACGGATT
99899 A
1 A
99900 GCACTACGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (33 bp):
ATGGTGGACACGACCTTATGTGTCATACGGATT
Found at i:99997 original size:20 final size:20
Alignment explanation
Indices: 99959--100001 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
99949 TATATTGGGC
* **
99959 TATTGTCTATTGTTTATGGT
1 TATTGTCTATGGTAAATGGT
99979 TATTGTCTATGGTAAATGGT
1 TATTGTCTATGGTAAATGGT
99999 TAT
1 TAT
100002 GGAATAATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.05, G:0.21, T:0.53
Consensus pattern (20 bp):
TATTGTCTATGGTAAATGGT
Found at i:100061 original size:44 final size:46
Alignment explanation
Indices: 100013--100104 Score: 161
Period size: 44 Copynumber: 2.0 Consensus size: 46
100003 GAATAATTGC
100013 AAGTGTATTGGTAAAATAAGCTTACGAGCTTATGG-A-TAAATGGT
1 AAGTGTATTGGTAAAATAAGCTTACGAGCTTATGGTATTAAATGGT
*
100057 AAGTGTATTGGTAAAATAATCTTACGAGCTTATGGTATTAAATGGT
1 AAGTGTATTGGTAAAATAAGCTTACGAGCTTATGGTATTAAATGGT
100103 AA
1 AA
100105 AATATTGCAC
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 34 0.76
45 1 0.02
46 10 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.34
Consensus pattern (46 bp):
AAGTGTATTGGTAAAATAAGCTTACGAGCTTATGGTATTAAATGGT
Found at i:102694 original size:37 final size:37
Alignment explanation
Indices: 102641--102737 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 37
102631 CCTTTTCGTC
102641 CTACTAGGATTCAAACTCCTAAAAATAAGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAAGATAGAATT
* * * *
102678 TTGCTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAAGATAGAATT
* *
102715 CTACTATGATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
102738 GATAGGATCC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAAGATAGAATT
Found at i:103298 original size:19 final size:19
Alignment explanation
Indices: 103270--103307 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
103260 ATTCATTTGA
*
103270 TTATTTTTTA-ATACTATAT
1 TTATTATTTATATA-TATAT
103289 TTATTATTTATATATATAT
1 TTATTATTTATATATATAT
103308 ATATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
TTATTATTTATATATATAT
Found at i:103616 original size:4 final size:4
Alignment explanation
Indices: 103609--103636 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
103599 TTAATATCTC
103609 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
103637 TTCCTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:103656 original size:12 final size:13
Alignment explanation
Indices: 103609--103696 Score: 60
Period size: 12 Copynumber: 7.0 Consensus size: 13
103599 TTAATATCTC
103609 ATTTATTTA-TTT
1 ATTTATTTATTTT
103621 ATTTATTTA-TTT
1 ATTTATTTATTTT
**
103633 ATTT-TTCCTTTT
1 ATTTATTTATTTT
103645 ATTTTATTT-TTTT
1 A-TTTATTTATTTT
*
103658 ACTTATTT-TTATT
1 ATTTATTTATT-TT
* * *
103671 CTTCATTTTTTTT
1 ATTTATTTATTTT
*
103684 ATTTATTCATTTT
1 ATTTATTTATTTT
103697 TTCCCTCTAA
Statistics
Matches: 60, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
11 2 0.03
12 28 0.47
13 26 0.43
14 4 0.07
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (13 bp):
ATTTATTTATTTT
Found at i:103684 original size:16 final size:17
Alignment explanation
Indices: 103614--103698 Score: 68
Period size: 17 Copynumber: 5.1 Consensus size: 17
103604 ATCTCATTTA
* *
103614 TTTATTTATTTA-TTTA
1 TTTATTTATTCATTTTT
*
103630 TTTATTT-TTCCTTTTAT
1 TTTATTTATTCATTTT-T
* * *
103647 TTTATTTTTTTACTTATT
1 TTTATTTATTCA-TTTTT
*
103665 TTTA-TTCTTCATTTTT
1 TTTATTTATTCATTTTT
103681 TTTATTTATTCATTTTT
1 TTTATTTATTCATTTTT
103698 T
1 T
103699 CCCTCTAACA
Statistics
Matches: 54, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
15 2 0.04
16 18 0.33
17 24 0.44
18 7 0.13
19 3 0.06
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTTATTCATTTTT
Found at i:108151 original size:11 final size:11
Alignment explanation
Indices: 108137--108170 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
108127 AACAAAAAGG
108137 GCAAAAAAAAA
1 GCAAAAAAAAA
108148 GCAAAAAAAAA
1 GCAAAAAAAAA
*
108159 ACAAAAGAAAAA
1 GCAAAA-AAAAA
108171 AGAAAGACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.82, C:0.09, G:0.09, T:0.00
Consensus pattern (11 bp):
GCAAAAAAAAA
Found at i:108154 original size:12 final size:12
Alignment explanation
Indices: 108139--108197 Score: 59
Period size: 12 Copynumber: 4.8 Consensus size: 12
108129 CAAAAAGGGC
108139 AAAAAAAAAGCA
1 AAAAAAAAAGCA
108151 AAAAAAAAA-CA
1 AAAAAAAAAGCA
108162 AAAGAAAAAAG-A
1 AAA-AAAAAAGCA
* *
108174 AAGACAAAAATCA
1 AA-AAAAAAAGCA
108187 AAAAGAAAAAG
1 AAAA-AAAAAG
108198 GGACAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
11 5 0.13
12 24 0.63
13 9 0.24
ACGTcount: A:0.81, C:0.07, G:0.10, T:0.02
Consensus pattern (12 bp):
AAAAAAAAAGCA
Found at i:108876 original size:22 final size:22
Alignment explanation
Indices: 108804--108880 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
108794 GCTACCCCAT
*
108804 CAAACCGTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
**
108826 CAAACCCATGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
108848 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
108870 CAAACCTTTGA
1 CAAACCTTTGA
108881 CCAAACATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.38, C:0.29, G:0.14, T:0.19
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:109871 original size:106 final size:106
Alignment explanation
Indices: 109681--111373 Score: 2535
Period size: 106 Copynumber: 16.0 Consensus size: 106
109671 ATATCGTGCC
* * * * * *
109681 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACCGTTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
109746 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
109787 ACTCCAGACAACACAAGTTCAACTTCACGAAGAAGGGACCGTTGGTTGTCAATAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
109852 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
109893 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACGACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
109958 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
109999 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
110064 AATTTCAGAGCTAATTTCAACTTCACAGCGAAGGATTTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
** *
110105 ACTTAAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
110170 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
110211 ACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* * *
110276 AATTTCAGAACCAATTTCAACTTTACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
110317 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCATTAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
110382 AATTTCAGAGCCAATTTCAACTTCACAGCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
110423 ACTCAAGATAACG-AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
**
110487 AATTTCAGAGCCAATTTCAACTTCACTTCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
110528 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTATCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
110593 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
110634 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGAACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
110699 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
110740 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAATAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
110805 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
110846 ACTCCATACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
110911 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
110952 AGTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
111017 AATTTTAGAGCCAATTTCAACTTCACAGCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
111058 ACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTAAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
111123 AATTTCAGAGCCAATTTCAACTTCTCAGCGAAGGATCTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
111164 AC-CCAAGACAACACAAGCTCAACTTCACGACGAAGAGG-CGGCTGATTGTCAA-CAA-AA-TT-
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACGAAG-GGACCGCTGGTTGTCAATAAACAACTTC
* *
111223 TC-A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
64 CCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
111264 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTTTCAACAAACAATTTCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAATAAACAACTTCC
** * * *
111328 CGGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGA
65 CAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
111370 ACTC
1 ACTC
111374 AGAACAATGC
Statistics
Matches: 1447, Mismatches: 127, Indels: 26
0.90 0.08 0.02
Matches are distributed among these distances:
99 3 0.00
100 74 0.05
101 4 0.00
102 3 0.00
103 4 0.00
104 4 0.00
105 101 0.07
106 1252 0.87
107 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:112448 original size:19 final size:19
Alignment explanation
Indices: 112412--112450 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
112402 TATATAGTCC
*
112412 TTTTATTTATTGTATATAT
1 TTTTATTTATTATATATAT
*
112431 TTTTATTTATTATTTATAT
1 TTTTATTTATTATATATAT
112450 T
1 T
112451 ATTGTCATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (19 bp):
TTTTATTTATTATATATAT
Found at i:112650 original size:2 final size:2
Alignment explanation
Indices: 112643--112723 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
112633 GTATTATTAC
112643 TA TA TA TA 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
112685 TA TA 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 TA TA T
112724 GTAATTATCT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:112852 original size:29 final size:29
Alignment explanation
Indices: 112819--112877 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
112809 ATATGTATAC
112819 TTTTATATTTGG-TTTATATATTTATTTAT
1 TTTTATATTTGGTTTTAT-TATTTATTTAT
* *
112848 TTTTATGTTTGGTTTTATTATTTGTTTAT
1 TTTTATATTTGGTTTTATTATTTATTTAT
112877 T
1 T
112878 ACTATCATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.19, C:0.00, G:0.10, T:0.71
Consensus pattern (29 bp):
TTTTATATTTGGTTTTATTATTTATTTAT
Found at i:112985 original size:29 final size:29
Alignment explanation
Indices: 112947--113029 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 29
112937 TATTTTTTAA
* *
112947 TATTTCATTTATTTATTTATTTTTCCTT-T
1 TATTTTATTTATTTATTTATTTTT-ATTCT
* *
112976 TATTTTATTTTTTTACTTATTTTTATTCT
1 TATTTTATTTATTTATTTATTTTTATTCT
*
113005 TCATTTT-TTTCATTTATTCATTTTT
1 T-ATTTTATTT-ATTTATTTATTTTT
113030 TTCCTCTAAC
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
28 2 0.05
29 26 0.59
30 16 0.36
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.73
Consensus pattern (29 bp):
TATTTTATTTATTTATTTATTTTTATTCT
Found at i:116623 original size:19 final size:19
Alignment explanation
Indices: 116577--116623 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
116567 GCATTAATGA
116577 AGAAGCAAAAACATAAAAG
1 AGAAGCAAAAACATAAAAG
* * *
116596 AAAAACAAAAAC-TAGAAG
1 AGAAGCAAAAACATAAAAG
116614 CAGAAGCAAA
1 -AGAAGCAAA
116624 TCGTTGCCGG
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.68, C:0.13, G:0.15, T:0.04
Consensus pattern (19 bp):
AGAAGCAAAAACATAAAAG
Found at i:123524 original size:14 final size:14
Alignment explanation
Indices: 123505--123535 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
123495 GCCTAAATGG
123505 AGCCCAAATTATAA
1 AGCCCAAATTATAA
123519 AGCCCAAATTATAA
1 AGCCCAAATTATAA
123533 AGC
1 AGC
123536 TTGGATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.23, G:0.10, T:0.19
Consensus pattern (14 bp):
AGCCCAAATTATAA
Done.