Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 97 of 126
Found at i:29536153 original size:24 final size:26
Alignment explanation
Indices: 29536089--29536157 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 26
29536079 CTTGTAACGG
* *
29536089 GAAAGCTTATCCGAGCTTAATAACAA
1 GAAAGCTCATACGAGCTTAATAACAA
* *
29536115 GAAA-CTCATAAGAGCTTAA-ATC-A
1 GAAAGCTCATACGAGCTTAATAACAA
*
29536138 GAAAGCTCATGCGAGCTTAA
1 GAAAGCTCATACGAGCTTAA
29536158 CGGGTAACTC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
23 5 0.14
24 15 0.42
25 12 0.33
26 4 0.11
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (26 bp):
GAAAGCTCATACGAGCTTAATAACAA
Found at i:29536373 original size:24 final size:23
Alignment explanation
Indices: 29536335--29536396 Score: 61
Period size: 24 Copynumber: 2.7 Consensus size: 23
29536325 GGAAGAACCA
*
29536335 TATATCGGAAAGCTCAAGAGAGCT
1 TATATCGGGAAGCTCAAGAGAG-T
* * *
29536359 TATATCGGGATGCTCATGTGAGT
1 TATATCGGGAAGCTCAAGAGAGT
* *
29536382 TATAGCGGGACGCTC
1 TATATCGGGAAGCTC
29536397 TTGCGAGCTA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 14 0.44
24 18 0.56
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (23 bp):
TATATCGGGAAGCTCAAGAGAGT
Found at i:29536740 original size:10 final size:11
Alignment explanation
Indices: 29536721--29536750 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
29536711 AATTTAATAA
29536721 AATTCACATTC
1 AATTCACATTC
29536732 AATTC-CATTC
1 AATTCACATTC
29536742 AATTCACAT
1 AATTCACAT
29536751 CTTAGGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.37, C:0.27, G:0.00, T:0.37
Consensus pattern (11 bp):
AATTCACATTC
Found at i:29544017 original size:9 final size:9
Alignment explanation
Indices: 29544003--29544078 Score: 59
Period size: 9 Copynumber: 8.4 Consensus size: 9
29543993 TAAACAATAT
29544003 TTTTTATAA
1 TTTTTATAA
*
29544012 TTTTTATAC
1 TTTTTATAA
29544021 TTTTTAATAA
1 TTTTT-ATAA
* *
29544031 TTTTAATAC
1 TTTTTATAA
29544040 TTTTT-T-A
1 TTTTTATAA
*
29544047 TTTTTAAATA
1 TTTTTATA-A
*
29544057 TTTTTTTGAA
1 TTTTTAT-AA
29544067 TTTTTA-AA
1 TTTTTATAA
29544075 TTTT
1 TTTT
29544079 AAAAAATTAA
Statistics
Matches: 52, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
7 5 0.10
8 7 0.13
9 20 0.38
10 19 0.37
11 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (9 bp):
TTTTTATAA
Found at i:29544024 original size:19 final size:19
Alignment explanation
Indices: 29543998--29544047 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
29543988 AAACTTAAAC
29543998 AATA-TTTTTTATAATTTT
1 AATACTTTTTTATAATTTT
* *
29544016 TATACTTTTTAATAATTTT
1 AATACTTTTTTATAATTTT
29544035 AATACTTTTTTAT
1 AATACTTTTTTAT
29544048 TTTTAAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
18 3 0.11
19 24 0.89
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (19 bp):
AATACTTTTTTATAATTTT
Found at i:29544043 original size:28 final size:26
Alignment explanation
Indices: 29543998--29544053 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 26
29543988 AAACTTAAAC
* *
29543998 AATATTTTTTATAATTTTTATACTTTTT
1 AATAATTTTAATAATTTTT-TA-TTTTT
*
29544026 AATAATTTTAATACTTTTTTATTTTT
1 AATAATTTTAATAATTTTTTATTTTT
29544052 AA
1 AA
29544054 ATATTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 7 0.28
27 2 0.08
28 16 0.64
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (26 bp):
AATAATTTTAATAATTTTTTATTTTT
Found at i:29549669 original size:2 final size:2
Alignment explanation
Indices: 29549662--29549697 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
29549652 CTGTTTCTTT
* *
29549662 TC TC TC TC CC TC TC AC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
29549698 GGGATTGGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.03, C:0.53, G:0.00, T:0.44
Consensus pattern (2 bp):
TC
Found at i:29562740 original size:16 final size:16
Alignment explanation
Indices: 29562719--29562749 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29562709 TTCAATGTGG
*
29562719 TTCTATTACTTGTTTA
1 TTCTATTACATGTTTA
29562735 TTCTATTACATGTTT
1 TTCTATTACATGTTT
29562750 GACTGATTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.13, G:0.06, T:0.61
Consensus pattern (16 bp):
TTCTATTACATGTTTA
Found at i:29563174 original size:92 final size:92
Alignment explanation
Indices: 29562843--29563154 Score: 615
Period size: 92 Copynumber: 3.4 Consensus size: 92
29562833 TTAACATGGA
29562843 GTTCATGTTTTGGTTTCTGTATTAAGTTGAAGTTTTTCTTTAAAGAAGATTGATTAGTTGGGTGA
1 GTTCATGTTTTGGTTTCTGTATTAAGTTGAAGTTTTTCTTTAAAGAAGATTGATTAGTTGGGTGA
29562908 GAGTCAAGATTTTTAATGTGTTATAAT
66 GAGTCAAGATTTTTAATGTGTTATAAT
29562935 GTTCATGTTTTGGTTTCTGTATTAAGTTGAAGTTTTTCTTTAAAGAAGATTGATTAGTTGGGTGA
1 GTTCATGTTTTGGTTTCTGTATTAAGTTGAAGTTTTTCTTTAAAGAAGATTGATTAGTTGGGTGA
29563000 GAGTCAAGATTTTTAATGTGTTATAAT
66 GAGTCAAGATTTTTAATGTGTTATAAT
29563027 GTTCATGTTTTGGTTTCTGTATTAAGTTGAAGTTTTTCTTTAAAGAAGATTGATTAGTTGGGTGA
1 GTTCATGTTTTGGTTTCTGTATTAAGTTGAAGTTTTTCTTTAAAGAAGATTGATTAGTTGGGTGA
29563092 GAGTCAAGATTTTTAATGTGTTATAAT
66 GAGTCAAGATTTTTAATGTGTTATAAT
*
29563119 GTTCATGTTTTGGTTTCTGTATTAAGTTGATGTTTT
1 GTTCATGTTTTGGTTTCTGTATTAAGTTGAAGTTTT
29563155 CCGTTTGTAT
Statistics
Matches: 219, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 219 1.00
ACGTcount: A:0.25, C:0.04, G:0.23, T:0.48
Consensus pattern (92 bp):
GTTCATGTTTTGGTTTCTGTATTAAGTTGAAGTTTTTCTTTAAAGAAGATTGATTAGTTGGGTGA
GAGTCAAGATTTTTAATGTGTTATAAT
Found at i:29565700 original size:15 final size:15
Alignment explanation
Indices: 29565670--29565703 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
29565660 TAACTCATCA
29565670 TTTAATTTTAATTTT
1 TTTAATTTTAATTTT
29565685 TTTAACTTTTAATTTT
1 TTTAA-TTTTAATTTT
29565701 TTT
1 TTT
29565704 TCAAATATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTAATTTTAATTTT
Found at i:29567556 original size:59 final size:60
Alignment explanation
Indices: 29567483--29567610 Score: 213
Period size: 60 Copynumber: 2.1 Consensus size: 60
29567473 ATCTAGTAGA
*
29567483 CAAGTTCAGGTACCAAAGTGAACG-AAAAAAAGTACAGGTACCAAAGTAGACTTAGTTGC
1 CAAGTTCAGATACCAAAGTGAACGAAAAAAAAGTACAGGTACCAAAGTAGACTTAGTTGC
* *
29567542 CAAGTTCAGATACCAAAGTGAACGAAAAAAAAGTATAGGTACCAAAGTGGACTTAGTTGC
1 CAAGTTCAGATACCAAAGTGAACGAAAAAAAAGTACAGGTACCAAAGTAGACTTAGTTGC
*
29567602 TAAGTTCAG
1 CAAGTTCAG
29567611 GGGCTAAAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
59 23 0.36
60 41 0.64
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (60 bp):
CAAGTTCAGATACCAAAGTGAACGAAAAAAAAGTACAGGTACCAAAGTAGACTTAGTTGC
Found at i:29569335 original size:95 final size:95
Alignment explanation
Indices: 29569172--29569363 Score: 323
Period size: 95 Copynumber: 2.0 Consensus size: 95
29569162 AATATAATGC
* *
29569172 TTAGACCCAACCCACACCCTACCCGGTCCATTAACATCTCATAATAATACAGTCACCGAAAGGTG
1 TTAGACCCAACCCACACCCGACCCGGTCCATCAACATCTCATAATAATACAGTCACCGAAAGGTG
*
29569237 AAATGTTGTGATAGTGCTTGGACTTTTCTT
66 AAATGTTGTGATAATGCTTGGACTTTTCTT
* *
29569267 TTAGACCCAGCCCACACCCGACCCGGTCCATCAACATCTCATAATAATACAGTCACTGATAA-GT
1 TTAGACCCAACCCACACCCGACCCGGTCCATCAACATCTCATAATAATACAGTCACCGA-AAGGT
29569331 GAAATGTTGTGATAATGCTTGGACTTTTCTT
65 GAAATGTTGTGATAATGCTTGGACTTTTCTT
29569362 TT
1 TT
29569364 TCTTTTATAG
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
95 89 0.98
96 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (95 bp):
TTAGACCCAACCCACACCCGACCCGGTCCATCAACATCTCATAATAATACAGTCACCGAAAGGTG
AAATGTTGTGATAATGCTTGGACTTTTCTT
Found at i:29595251 original size:10 final size:10
Alignment explanation
Indices: 29595238--29595271 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
29595228 GAAAAATTCT
*
29595238 TTAAAAATTG
1 TTAAAAATTA
29595248 TTAAAAATTA
1 TTAAAAATTA
*
29595258 TTAAGAATTA
1 TTAAAAATTA
29595268 TTAA
1 TTAA
29595272 TTTCTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:29595822 original size:20 final size:20
Alignment explanation
Indices: 29595783--29595826 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
29595773 CAAAACAAAA
*
29595783 TTTTAAATTTTTTTACTAAT
1 TTTTAAATTTATTTACTAAT
29595803 TTTTATAATTTATTTA-TAAT
1 TTTTA-AATTTATTTACTAAT
29595823 TTTT
1 TTTT
29595827 GCAGTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTAAATTTATTTACTAAT
Found at i:29595838 original size:20 final size:21
Alignment explanation
Indices: 29595783--29595838 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 21
29595773 CAAAACAAAA
29595783 TTTTA-AATTTTTTTACTAAT
1 TTTTACAATTTTTTTACTAAT
* *
29595803 TTTTATAATTTATTTA-TAAT
1 TTTTACAATTTTTTTACTAAT
* *
29595823 TTTTGCAGTTTTTTTA
1 TTTTACAATTTTTTTA
29595839 AAAAAATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 21 0.70
21 9 0.30
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.66
Consensus pattern (21 bp):
TTTTACAATTTTTTTACTAAT
Found at i:29595965 original size:40 final size:40
Alignment explanation
Indices: 29595894--29595969 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
29595884 AAGCGCAATT
* * *
29595894 AATATACCATGTCACTAGTCACCTTGTCATGTCATCGGTC
1 AATACACCATGTCACTAGTCAACTTGCCATGTCATCGGTC
*
29595934 AATACACCATGTCACTTGTCAACTTGCCATGTCATC
1 AATACACCATGTCACTAGTCAACTTGCCATGTCATC
29595970 AATGATGTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (40 bp):
AATACACCATGTCACTAGTCAACTTGCCATGTCATCGGTC
Found at i:29613264 original size:18 final size:18
Alignment explanation
Indices: 29613216--29613275 Score: 50
Period size: 17 Copynumber: 3.3 Consensus size: 18
29613206 GAAAAATTAT
* * *
29613216 AAAATATTTAAAACATTA
1 AAAATATTAAAAAAAATA
* *
29613234 TAAAT-TTATAAAAAATA
1 AAAATATTAAAAAAAATA
29613251 AAAATATTAAAAAAACTATA
1 AAAATATTAAAAAAA--ATA
29613271 AAAAT
1 AAAAT
29613276 TCAAGAAATA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
17 12 0.38
18 12 0.38
20 8 0.25
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAATATTAAAAAAAATA
Found at i:29615592 original size:125 final size:125
Alignment explanation
Indices: 29615370--29615740 Score: 627
Period size: 125 Copynumber: 3.0 Consensus size: 125
29615360 TTTTAGGGCT
**** *
29615370 TGGAAGAAATAATTTCGAGTTGACGTTTCTGATCAAATAGTATAAAATCGCTTCTAGCAGGATGC
1 TGGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGC
* *
29615435 TATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCA
66 TATTTGAGAAGAATTTATAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCA
*
29615495 TGGAAGAAATAATTTTTTTTTGACGTTTCTGAGAAAATAGTATAAAATCGCTTCTAGCAGGATGC
1 TGGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGC
*
29615560 TATTTGAGAAGAATTTATAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTTGGTCA
66 TATTTGAGAAGAATTTATAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCA
29615620 TGGAAGAAATAA-TTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGC
1 TGGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGC
* *
29615684 TATTTGAGAAGAATTTATGAAAATCGCGCCCTTGTGGACGCACTTTTGCTACAGTAG
66 TATTTGAGAAGAATTTAT-AAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
29615741 CATGTTTGGG
Statistics
Matches: 232, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
124 69 0.30
125 163 0.70
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (125 bp):
TGGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGC
TATTTGAGAAGAATTTATAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCA
Found at i:29618897 original size:17 final size:17
Alignment explanation
Indices: 29618830--29618897 Score: 57
Period size: 17 Copynumber: 3.8 Consensus size: 17
29618820 TATGTGAATG
*
29618830 TAAAATTATTAATT-GA
1 TAAAATTATTAATTATA
* *
29618846 TAAATTGTATTAATGATTA
1 TAAAAT-TATTAATTA-TA
*
29618865 GTAAAATTATCAAATTATA
1 -TAAAATTAT-TAATTATA
29618884 TAAAATTATTAATT
1 TAAAATTATTAATT
29618898 GTTAGTACCA
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
16 5 0.12
17 11 0.28
18 9 0.22
19 6 0.15
20 9 0.22
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (17 bp):
TAAAATTATTAATTATA
Found at i:29618920 original size:116 final size:116
Alignment explanation
Indices: 29618716--29618959 Score: 427
Period size: 116 Copynumber: 2.1 Consensus size: 116
29618706 TAAGTTTGTG
*
29618716 AAATTATTAATTGATAAATTGTATTAATGGTTAGTAAAAATTATCAAATTATATAAAATTATTAA
1 AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAAATTATCAAATTATATAAAATTATTAA
** * *
29618781 TTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAGCATTATGTGAATGTA
66 TTGTTAGTACCAGAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
29618832 AAATTATTAATTGATAAATTGTATTAATGATTAGT-AAAATTATCAAATTATATAAAATTATTAA
1 AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAAATTATCAAATTATATAAAATTATTAA
29618896 TTGTTAGTACCAGGAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
66 TTGTTAGTACCA-GAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
29618948 AAATTATTAATT
1 AAATTATTAATT
29618960 TAGTTTAGGG
Statistics
Matches: 122, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
115 41 0.34
116 81 0.66
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.39
Consensus pattern (116 bp):
AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAAATTATCAAATTATATAAAATTATTAA
TTGTTAGTACCAGAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
Found at i:29619074 original size:68 final size:67
Alignment explanation
Indices: 29618985--29619865 Score: 598
Period size: 68 Copynumber: 13.0 Consensus size: 67
29618975 AATTAAATTA
* * *
29618985 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAAGGAGTTAGGATTTTTAAGCTT
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAA-TTAAATGAGTTAGGGTTTTTAAGTTT
29619050 -AG
65 AAG
*
29619052 GGTTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTT-AATTAGGTTAGGGTTTTTAAG-
1 GG-TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAA-TTAAATGA-GTTAGGGTTTTTAAGT
29619115 TTAAGGG
63 TTAA--G
* * * *
29619122 GGTTAGGGTTTTTAAGTTT-A--GGGTTTAAGGATTTTAATTAAATTAGGTTAGGGTTTTTAAGT
1 GGTTAGGGTTTTTAA-TTTAATTAGG-TTAGGGTTTTTAATTAAATGA-GTTAGGGTTTTTAAGT
29619184 TTAAG
63 TTAAG
* * *
29619189 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAG-TT
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTAAATGA-GTTAGGGTTTTTAAGTTT
*
29619253 AATTA
65 AA--G
* *** *
29619258 GGTTAGGGTTTTTAAGTTAAGGGGGTTAGGGTTTTTAAGTTTAA-G-GTTTAGGGTTTTTAA-TT
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAA-TTAAATGAG-TTAGGGTTTTTAAGTT
*
29619320 TAATTA
64 TAA--G
* *
29619326 GGTTAGGGTTTTTAATTTAATTAGGTTAGTGGTTAGTTT--TT--A-GGGTTTA-GGATTTTAA-
1 GGTTAGGGTTTTTAATTTAATTAGGTTAG-GGTT--TTTAATTAAATGAG-TTAGGGTTTTTAAG
* *
29619384 TTAAATTA
62 TTTAA--G
* *
29619392 GGTTAGGGTTTTTAAGTTTAGA-T---TTAGGGTTTTTAATTAAATTAGGTTAGGGGTTTTAAG-
1 GGTTAGGGTTTTTAA-TTTA-ATTAGGTTAGGGTTTTTAATTAAATGA-GTTAGGGTTTTTAAGT
29619452 TTAAGGG
63 TTAA--G
* * * * * * *
29619459 GGTTAGGGTTTTTAATTAAATTAGGTTAGGATTTTTAAGTT-TAGGATTTAGAGTTTTTAA-TTA
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAA-TTAAATGAGTTAGGGTTTTTAAGTTT
*
29619522 AATTA
65 AA--G
* * *
29619527 GGTTAGGGTTTTTAA-GT--TTAGGTTTAGGGTTTTTAATTAAATTAGGTTAGTGTTTTTAAGTT
1 GGTTAGGGTTTTTAATTTAATTAGG-TTAGGGTTTTTAATTAAATGA-GTTAGGGTTTTTAAGTT
29619589 T-AG
64 TAAG
** * * * *
29619592 GGTTTAATGTTTTTAATTAAATTAGGTTAGAGTTTTTAATTTAATTAGGTTAGGGTTTTTAA-TT
1 GG-TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTAAATGA-GTTAGGGTTTTTAAGTT
*
29619656 TAATTA
64 TAA--G
* * *
29619662 GGTTAGGGTTTTTAAGTTT-A--GGGTTTAGGGTTTTTAATTAAATTAGGTTGGGGTTTTTAAGT
1 GGTTAGGGTTTTTAA-TTTAATTAGG-TTAGGGTTTTTAATTAAATGA-GTTAGGGTTTTTAAGT
29619724 TT-AG
63 TTAAG
* * *
29619728 TGTTTAGGGTTTTAAATTTAATTAGGTTAGGGTTTTTAAGTT-AATTAGGTTAGGGTTTTTAAGT
1 -GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAA-TTAAATGA-GTTAGGGTTTTTAAGT
*
29619792 TAAGAG
63 TTA-AG
* * * *
29619798 GGTCAGGGTTTTTAAGTTT-A--AGGTTTAAGG-TTTTAATTTAATTAGGTTAGGGTTTTTAA-T
1 GGTTAGGGTTTTTAA-TTTAATTAGG-TTAGGGTTTTTAATTAAATGA-GTTAGGGTTTTTAAGT
29619858 TTAAG
63 TTAAG
29619863 GGT
1 GGT
29619866 ATTAATGGTT
Statistics
Matches: 672, Mismatches: 81, Indels: 124
0.77 0.09 0.14
Matches are distributed among these distances:
61 3 0.00
63 6 0.01
64 4 0.01
65 16 0.02
66 74 0.11
67 130 0.19
68 308 0.46
69 107 0.16
70 21 0.03
71 3 0.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (67 bp):
GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTAAATGAGTTAGGGTTTTTAAGTTTA
AG
Found at i:29619117 original size:91 final size:91
Alignment explanation
Indices: 29618962--29619865 Score: 932
Period size: 91 Copynumber: 10.0 Consensus size: 91
29618952 TATTAATTTA
*
29618962 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTA
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAA-TTA
* * *
29619027 AAGGA-GTTAGGATTTTTAAGCTTAGG
65 AATGAGGTTAGGGTTTTTAAGTTTAGG
*
29619053 GTTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTT-
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAA-TTA
* *
29619117 AAGGGGGTTAGGGTTTTTAAGTTTAGG
65 AATGAGGTTAGGGTTTTTAAGTTTAGG
* * *
29619144 GTTTAAGGATTTTAATTAAATTAGGTTAGGGTTTTTAAGTT--TAAGGTTTAGGGTTTTTAATTA
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAATTAGG-TTAGGGTTTTTAATTA
* *
29619207 AATTAGGTTAGGGTTTTTAATTAAATTA-G
65 AATGAGGTTAGGGTTTTTAAGT---TTAGG
***
29619236 G-TTAGGGTTTTTAAGTT-AATTAGGTTAGGGTTTTTAAGTTAAGGGGGTTAGGGTTTTTAAGTT
1 GTTTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAA-TT
* * *
29619299 TAA-G-GTTTAGGGTTTTTAA-TTTAATTAG
64 AAATGAGGTTAGGGTTTTTAAGTTT-A--GG
* * *
29619327 G-TTAGGGTTTTTAATTTAATTAGGTTAGTGG---TT-AGTT-TTTAGGGTTTA-GGATTTTAAT
1 GTTTAGGGTTTTTAATTAAATTAGGTTAG-GGTTTTTAAGTTAATTA-GG-TTAGGGTTTTTAAT
*
29619385 TAAATTAGGTTAGGGTTTTTAAGTTTA-G
63 TAAATGAGGTTAGGGTTTTTAAGTTTAGG
* * ***
29619413 ATTTAGGGTTTTTAATTAAATTAGGTTAGGGGTTTTAAGTTAAGGGGGTTAGGGTTTTTAATTAA
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAATTAA
* *
29619478 ATTAGGTTAGGATTTTTAAGTTTAGG
66 ATGAGGTTAGGGTTTTTAAGTTTAGG
* *
29619504 ATTTAGAGTTTTTAATTAAATTAGGTTAGGGTTTTTAAG-T--TTAGGTTTAGGGTTTTTAATTA
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAATTAGG-TTAGGGTTTTTAATTA
* *
29619566 AATTAGGTTAGTGTTTTTAAGTTTAGG
65 AATGAGGTTAGGGTTTTTAAGTTTAGG
** * * *
29619593 GTTTAATGTTTTTAATTAAATTAGGTTAGAGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTA
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAATTAA
*
29619658 ATTAGGTTAGGGTTTTTAAGTTTAGG
66 ATGAGGTTAGGGTTTTTAAGTTTAGG
* * * * * *
29619684 GTTTAGGGTTTTTAATTAAATTAGGTTGGGGTTTTTAAGTTTAGT-GTTTAGGGTTTTAAATTTA
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAATTAA
*
29619748 ATTAGGTTAGGGTTTTTAAGTTAATTA-G
66 ATGAGGTTAGGGTTTTTAAG-T--TTAGG
* * * *
29619776 G-TTAGGGTTTTTAAGTTAAGA--GGGTCAGGGTTTTTAAGTT--TAAGGTTTAAGG-TTTTAAT
1 GTTTAGGGTTTTTAA-TTAA-ATTAGGTTAGGGTTTTTAAGTTAATTAGG-TTAGGGTTTTTAAT
* *
29619835 TTAATTAGGTTAGGGTTTTTAA-TTTAAGG
63 TAAATGAGGTTAGGGTTTTTAAGTTT-AGG
29619864 GT
1 GT
29619866 ATTAATGGTT
Statistics
Matches: 702, Mismatches: 68, Indels: 88
0.82 0.08 0.10
Matches are distributed among these distances:
86 5 0.01
87 33 0.05
88 20 0.03
89 106 0.15
90 150 0.21
91 345 0.49
92 30 0.04
93 13 0.02
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.48
Consensus pattern (91 bp):
GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAATTAA
ATGAGGTTAGGGTTTTTAAGTTTAGG
Found at i:29619859 original size:23 final size:23
Alignment explanation
Indices: 29618954--29619861 Score: 777
Period size: 23 Copynumber: 40.2 Consensus size: 23
29618944 AGTAAAATTA
*
29618954 TTAATTTAGTTTAGGGTTTTTAAT
1 TTAA-TTAGGTTAGGGTTTTTAAT
*
29618978 TAAATTAGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
*
29619001 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
* *
29619024 TTAA--AGGAGTTAGGATTTTTAAGC
1 TTAATTA-G-GTTAGGGTTTTTAA-T
*
29619048 TT-A--GGGTTTAGGGTTTTTAAT
1 TTAATTAGG-TTAGGGTTTTTAAT
*
29619069 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
*
29619092 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
***
29619115 TTAAGGGGGTTAGGGTTTTTAAGT
1 TTAATTAGGTTAGGGTTTTTAA-T
* * *
29619139 TT-A--GGGTTTAAGGATTTTAAT
1 TTAATTAGG-TTAGGGTTTTTAAT
*
29619160 TAAATTAGGTTAGGGTTTTTAAGT
1 TTAATTAGGTTAGGGTTTTTAA-T
29619184 TT-A--AGGTTTAGGGTTTTTAAT
1 TTAATTAGG-TTAGGGTTTTTAAT
*
29619205 TAAATTAGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
* *
29619228 TAAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
*
29619251 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
***
29619274 TTAAGGGGGTTAGGGTTTTTAAGT
1 TTAATTAGGTTAGGGTTTTTAA-T
29619298 TT-A--AGGTTTAGGGTTTTTAAT
1 TTAATTAGG-TTAGGGTTTTTAAT
29619319 TTAATTAGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
*
29619342 TTAATTAGGTTAGTGG---TTAGT
1 TTAATTAGGTTAG-GGTTTTTAAT
*
29619363 TT--TTAGGGTTTA-GGATTTTAAT
1 TTAATTA-GG-TTAGGGTTTTTAAT
*
29619385 TAAATTAGGTTAGGGTTTTTAAGT
1 TTAATTAGGTTAGGGTTTTTAA-T
29619409 TTAGA-T---TTAGGGTTTTTAAT
1 TTA-ATTAGGTTAGGGTTTTTAAT
* * *
29619429 TAAATTAGGTTAGGGGTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
***
29619452 TTAAGGGGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
* *
29619475 TAAATTAGGTTAGGATTTTTAA-
1 TTAATTAGGTTAGGGTTTTTAAT
* *
29619497 GT--TTAGGATTTAGAGTTTTTAAT
1 TTAATTAGG--TTAGGGTTTTTAAT
*
29619520 TAAATTAGGTTAGGGTTTTTAA-
1 TTAATTAGGTTAGGGTTTTTAAT
*
29619542 GT--TTAGGTTTAGGGTTTTTAAT
1 TTAATTAGG-TTAGGGTTTTTAAT
* *
29619564 TAAATTAGGTTAGTGTTTTTAAGT
1 TTAATTAGGTTAGGGTTTTTAA-T
* **
29619588 TT-A--GGGTTTAATGTTTTTAAT
1 TTAATTAGG-TTAGGGTTTTTAAT
* *
29619609 TAAATTAGGTTAGAGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
29619632 TTAATTAGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
29619655 TTAATTAGGTTAGGGTTTTTAAGT
1 TTAATTAGGTTAGGGTTTTTAA-T
*
29619679 TT-A--GGGTTTAGGGTTTTTAAT
1 TTAATTAGG-TTAGGGTTTTTAAT
* *
29619700 TAAATTAGGTTGGGGTTTTTAAGT
1 TTAATTAGGTTAGGGTTTTTAA-T
* * *
29619724 TT-AGT-GTTTAGGGTTTTAAAT
1 TTAATTAGGTTAGGGTTTTTAAT
*
29619745 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
*
29619768 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
* *
29619791 TTAA-GAGGGTCAGGGTTTTTAAGT
1 TTAATTA-GGTTAGGGTTTTTAA-T
*
29619815 TT-A--AGGTTTAAGG-TTTTAAT
1 TTAATTAGG-TTAGGGTTTTTAAT
29619835 TTAATTAGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
29619858 TTAA
1 TTAA
29619862 GGGTATTAAT
Statistics
Matches: 729, Mismatches: 89, Indels: 133
0.77 0.09 0.14
Matches are distributed among these distances:
19 6 0.01
20 19 0.03
21 74 0.10
22 126 0.17
23 450 0.62
24 48 0.07
25 6 0.01
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.48
Consensus pattern (23 bp):
TTAATTAGGTTAGGGTTTTTAAT
Found at i:29619934 original size:25 final size:25
Alignment explanation
Indices: 29619904--29619951 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
29619894 TATCAAAAAT
29619904 TTTTATTTTATTACATCAAATAAAC
1 TTTTATTTTATTACATCAAATAAAC
29619929 TTTTATTTTATTACATCAAATAA
1 TTTTATTTTATTACATCAAATAA
29619952 TATCAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (25 bp):
TTTTATTTTATTACATCAAATAAAC
Found at i:29620304 original size:18 final size:18
Alignment explanation
Indices: 29620281--29620316 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29620271 CGGAAAAGGG
*
29620281 TACATACAAGGGTTAGGA
1 TACATACAAGGGCTAGGA
*
29620299 TACATATAAGGGCTAGGA
1 TACATACAAGGGCTAGGA
29620317 AACGCACCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.11, G:0.28, T:0.22
Consensus pattern (18 bp):
TACATACAAGGGCTAGGA
Found at i:29620969 original size:7 final size:7
Alignment explanation
Indices: 29620959--29620983 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29620949 TTATATACAT
29620959 AATACTA
1 AATACTA
29620966 AATACTA
1 AATACTA
29620973 AATACTA
1 AATACTA
29620980 AATA
1 AATA
29620984 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:29621191 original size:20 final size:20
Alignment explanation
Indices: 29621154--29621191 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
29621144 TTTATTTTTA
*
29621154 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
29621174 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
29621192 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:29622124 original size:12 final size:11
Alignment explanation
Indices: 29622082--29622124 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
29622072 ATTTTTATGG
*
29622082 TTTAAAAAAAA
1 TTTAAAAAATA
29622093 TTTAAAAAATA
1 TTTAAAAAATA
* *
29622104 TTTTTAAAATTA
1 -TTTAAAAAATA
29622116 TTTAAAAAA
1 TTTAAAAAA
29622125 GGGAGTTAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TTTAAAAAATA
Found at i:29622146 original size:11 final size:11
Alignment explanation
Indices: 29622130--29622171 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
29622120 AAAAAGGGAG
29622130 TTAAGAGAAAC
1 TTAAGAGAAAC
* *
29622141 TTAAGAGGAGC
1 TTAAGAGAAAC
*
29622152 TTAAGAGGAAC
1 TTAAGAGAAAC
29622163 TTAAGAGAA
1 TTAAGAGAA
29622172 TTTTTGAAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.26, T:0.19
Consensus pattern (11 bp):
TTAAGAGAAAC
Found at i:29622155 original size:22 final size:21
Alignment explanation
Indices: 29622126--29622169 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
29622116 TTTAAAAAAG
29622126 GGAGTTAAGAGAAACTTAAGA
1 GGAGTTAAGAGAAACTTAAGA
*
29622147 GGAGCTTAAGAGGAACTTAAGA
1 GGAG-TTAAGAGAAACTTAAGA
29622169 G
1 G
29622170 AATTTTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.43, C:0.07, G:0.32, T:0.18
Consensus pattern (21 bp):
GGAGTTAAGAGAAACTTAAGA
Found at i:29626715 original size:15 final size:15
Alignment explanation
Indices: 29626692--29626723 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
29626682 GATTGATTGA
29626692 GAAAAAAAATAAGAG
1 GAAAAAAAATAAGAG
*
29626707 GAAAGAAAATAAGAG
1 GAAAAAAAATAAGAG
29626722 GA
1 GA
29626724 TACCATTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.06
Consensus pattern (15 bp):
GAAAAAAAATAAGAG
Found at i:29627180 original size:20 final size:20
Alignment explanation
Indices: 29627155--29627208 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
29627145 TCTTTCTTAA
29627155 CAAAAATTAAAAATAATTTT
1 CAAAAATTAAAAATAATTTT
* *
29627175 CAAAAATTCAAAATGATTTT
1 CAAAAATTAAAAATAATTTT
*
29627195 -TAAAATTAAAAATA
1 CAAAAATTAAAAATA
29627209 TTTATAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 11 0.38
20 18 0.62
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (20 bp):
CAAAAATTAAAAATAATTTT
Found at i:29647205 original size:10 final size:10
Alignment explanation
Indices: 29647190--29647214 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
29647180 TTTTTTAATT
29647190 TAAAACTATA
1 TAAAACTATA
29647200 TAAAACTATA
1 TAAAACTATA
29647210 TAAAA
1 TAAAA
29647215 TTATTAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (10 bp):
TAAAACTATA
Found at i:29647473 original size:20 final size:20
Alignment explanation
Indices: 29647450--29647518 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
29647440 GTTAGATATT
*
29647450 TTGATAAATCTTTAAAAATA
1 TTGATAAATCTTTAGAAATA
*
29647470 TTGATAAAT-TATTAGATATA
1 TTGATAAATCT-TTAGAAATA
* * *
29647490 TTGATAAATCCTTCGAAATT
1 TTGATAAATCTTTAGAAATA
29647510 TTGATAAAT
1 TTGATAAAT
29647519 TGTTATATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 1 0.02
20 40 0.98
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (20 bp):
TTGATAAATCTTTAGAAATA
Found at i:29647494 original size:40 final size:40
Alignment explanation
Indices: 29647434--29647519 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
29647424 ATTATCTTGG
* * *
29647434 TAAATTGTTAGATATTTTGATAAATCTTTAAAAATATTGA
1 TAAATTATTAGATATATTGATAAATCCTTAAAAATATTGA
** *
29647474 TAAATTATTAGATATATTGATAAATCCTTCGAAATTTTGA
1 TAAATTATTAGATATATTGATAAATCCTTAAAAATATTGA
29647514 TAAATT
1 TAAATT
29647520 GTTATATTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (40 bp):
TAAATTATTAGATATATTGATAAATCCTTAAAAATATTGA
Found at i:29653869 original size:30 final size:29
Alignment explanation
Indices: 29653805--29653860 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
29653795 CCCAAATCGA
* *
29653805 TTAAAAATAATTTTTCTAATAAAAATTAC
1 TTAAAAATAAATTTTCTAACAAAAATTAC
29653834 TTAAAAATAAATTTTC-AACAAACAATT
1 TTAAAAATAAATTTTCTAACAAA-AATT
29653861 GATATAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.38
Consensus pattern (29 bp):
TTAAAAATAAATTTTCTAACAAAAATTAC
Found at i:29655606 original size:18 final size:19
Alignment explanation
Indices: 29655583--29655621 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
29655573 GAAACTCTAT
29655583 ATCCTTC-AGGGATTTT-AA
1 ATCCTTCTA-GGATTTTCAA
29655601 ATCCTTCTAGGATTTTCAA
1 ATCCTTCTAGGATTTTCAA
29655620 AT
1 AT
29655622 AAATTTAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (19 bp):
ATCCTTCTAGGATTTTCAA
Found at i:29663057 original size:2 final size:2
Alignment explanation
Indices: 29663050--29663092 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
29663040 TCTTATAATT
29663050 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
29663092 T
1 T
29663093 AAATATATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:29666986 original size:17 final size:18
Alignment explanation
Indices: 29666966--29667012 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
29666956 ATTTTTCGAA
29666966 AAATAA-ATTTTTTGTTC
1 AAATAATATTTTTTGTTC
*
29666983 AAATAATTTTTTTTGTTC
1 AAATAATATTTTTTGTTC
29667001 AAAT--TATTTTTT
1 AAATAATATTTTTT
29667013 TCCAGTTGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 7 0.26
17 6 0.22
18 14 0.52
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (18 bp):
AAATAATATTTTTTGTTC
Found at i:29666994 original size:18 final size:18
Alignment explanation
Indices: 29666973--29667013 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
29666963 GAAAAATAAA
29666973 TTTTTTGTTCAAATAATT
1 TTTTTTGTTCAAATAATT
*
29666991 TTTTTTGTTCAAATTATT
1 TTTTTTGTTCAAATAATT
29667009 TTTTT
1 TTTTT
29667014 CCAGTTGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTTTTGTTCAAATAATT
Found at i:29675324 original size:114 final size:114
Alignment explanation
Indices: 29675124--29675351 Score: 447
Period size: 114 Copynumber: 2.0 Consensus size: 114
29675114 TAATAGTTTT
29675124 TCTTAGGTTAAATTTCATCTACTTTATGGCATTTGAATGTTAGGGAGAGAGTCAGGGGAGAGGGA
1 TCTTAGGTTAAATTTCATCTACTTTATGGCATTTGAATGTTAGGGAGAGAGTCAGGGGAGAGGGA
29675189 GGGTCGGTAGGGGAGGAGGGGAGAGAGATAAAGGTAGGGGTAAAGGTAG
66 GGGTCGGTAGGGGAGGAGGGGAGAGAGATAAAGGTAGGGGTAAAGGTAG
*
29675238 TCTTAGGTTAAATTTCATTTACTTTATGGCATTTGAATGTTAGGGAGAGAGTCAGGGGAGAGGGA
1 TCTTAGGTTAAATTTCATCTACTTTATGGCATTTGAATGTTAGGGAGAGAGTCAGGGGAGAGGGA
29675303 GGGTCGGTAGGGGAGGAGGGGAGAGAGATAAAGGTAGGGGTAAAGGTAG
66 GGGTCGGTAGGGGAGGAGGGGAGAGAGATAAAGGTAGGGGTAAAGGTAG
29675352 AGGGAGGGAA
Statistics
Matches: 113, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
114 113 1.00
ACGTcount: A:0.29, C:0.06, G:0.41, T:0.24
Consensus pattern (114 bp):
TCTTAGGTTAAATTTCATCTACTTTATGGCATTTGAATGTTAGGGAGAGAGTCAGGGGAGAGGGA
GGGTCGGTAGGGGAGGAGGGGAGAGAGATAAAGGTAGGGGTAAAGGTAG
Found at i:29675411 original size:25 final size:23
Alignment explanation
Indices: 29675368--29675414 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
29675358 GGAATTTTTT
*
29675368 TTATTTTTTTAATATTAATATAG
1 TTATTTTTTTAATAATAATATAG
29675391 TTATTTTTAATTAATAATAATATA
1 TTATTTTT--TTAATAATAATATA
29675415 AAATTATAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
25 13 0.62
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TTATTTTTTTAATAATAATATAG
Found at i:29692664 original size:16 final size:17
Alignment explanation
Indices: 29692643--29692677 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
29692633 AATTGAAATT
*
29692643 AATTAATTAA-TTTCTC
1 AATTAAATAATTTTCTC
29692659 AATTAAATAATTTTCTC
1 AATTAAATAATTTTCTC
29692676 AA
1 AA
29692678 CCTGATTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTAAATAATTTTCTC
Found at i:29695617 original size:49 final size:49
Alignment explanation
Indices: 29695560--29695659 Score: 173
Period size: 49 Copynumber: 2.0 Consensus size: 49
29695550 TCCTTTACAT
* *
29695560 CACCAAGCCCAAATCCTAGTAAACCCAACTAGCCTGAAGTTTTAAGACC
1 CACCAAGCCCAAATCCTAGTAAACCCAACTAACCTAAAGTTTTAAGACC
*
29695609 CACCAAGCCCAAATCCTAGTAAACCCAACTAACCTAAAGTTTTAATACC
1 CACCAAGCCCAAATCCTAGTAAACCCAACTAACCTAAAGTTTTAAGACC
29695658 CA
1 CA
29695660 GCCCAAGCAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.39, C:0.33, G:0.09, T:0.19
Consensus pattern (49 bp):
CACCAAGCCCAAATCCTAGTAAACCCAACTAACCTAAAGTTTTAAGACC
Found at i:29695634 original size:25 final size:25
Alignment explanation
Indices: 29695560--29695635 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 25
29695550 TCCTTTACAT
29695560 CACCAAGCCCAAATCCTAGTAAACC
1 CACCAAGCCCAAATCCTAGTAAACC
* * * * *
29695585 CAACTAGCCTGAAGT--T-TTAAGACC
1 CACCAAGCC-CAAATCCTAGTAA-ACC
29695609 CACCAAGCCCAAATCCTAGTAAACC
1 CACCAAGCCCAAATCCTAGTAAACC
29695634 CA
1 CA
29695636 ACTAACCTAA
Statistics
Matches: 36, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
23 6 0.17
24 11 0.31
25 13 0.36
26 6 0.17
ACGTcount: A:0.38, C:0.36, G:0.11, T:0.16
Consensus pattern (25 bp):
CACCAAGCCCAAATCCTAGTAAACC
Found at i:29700742 original size:11 final size:11
Alignment explanation
Indices: 29700726--29700757 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
29700716 TGGCGAACTT
*
29700726 TGTCAAATTAC
1 TGTCAAATTAA
29700737 TGTCAAATTAA
1 TGTCAAATTAA
29700748 TGTCAAATTA
1 TGTCAAATTA
29700758 TTGTGATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (11 bp):
TGTCAAATTAA
Found at i:29703629 original size:43 final size:43
Alignment explanation
Indices: 29703561--29703664 Score: 131
Period size: 43 Copynumber: 2.4 Consensus size: 43
29703551 AGATCGTACA
* * *
29703561 ATGCCTAC-GTCCCAGACGAGGTCTTACATGT-AATCAAATATCG
1 ATGCC-ACTGTCCCAGACAAGATCTTACACGTAAATCAAATA-CG
*
29703604 ATGCCACTGTCCCAGACAAGATCTTACACGTAAATCATATACG
1 ATGCCACTGTCCCAGACAAGATCTTACACGTAAATCAAATACG
*
29703647 ATGCCAATGTCCCAGACA
1 ATGCCACTGTCCCAGACA
29703665 TGGTCTTTCT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
42 2 0.04
43 44 0.81
44 8 0.15
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACAAGATCTTACACGTAAATCAAATACG
Found at i:29704881 original size:16 final size:17
Alignment explanation
Indices: 29704860--29704891 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
29704850 TGTTCATACT
29704860 AAAAAGAAAA-GAAAAC
1 AAAAAGAAAAGGAAAAC
29704876 AAAAAGAAAAGGAAAA
1 AAAAAGAAAAGGAAAA
29704892 GTCTTACCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAGGAAAAC
Found at i:29705685 original size:3 final size:3
Alignment explanation
Indices: 29705635--29705713 Score: 59
Period size: 3 Copynumber: 25.7 Consensus size: 3
29705625 TAATGTGTGC
* * * * * *
29705635 TAT TATT TAT TAC TAT TAT ATAT TAT TCT TAA CAC TAT TAT AAT TAT
1 TAT TA-T TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
29705682 TAT TAT TAG CAT TAT TAT TAT TAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
29705714 AATACCTTTT
Statistics
Matches: 57, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
3 51 0.89
4 6 0.11
ACGTcount: A:0.37, C:0.06, G:0.01, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:29705697 original size:24 final size:23
Alignment explanation
Indices: 29705646--29705714 Score: 77
Period size: 24 Copynumber: 3.0 Consensus size: 23
29705636 ATTATTTATT
*
29705646 ACTATTATA-TATTATTCTTAAC
1 ACTATTATATTATTATTATTAAC
*
29705668 ACTATTATAATTATTATTATTAGC
1 ACTATTAT-ATTATTATTATTAAC
* *
29705692 ATTATTATTATTAATATTATTAA
1 ACTATTA-TATTATTATTATTAA
29705715 ATACCTTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
22 8 0.21
23 1 0.03
24 29 0.74
25 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.52
Consensus pattern (23 bp):
ACTATTATATTATTATTATTAAC
Found at i:29710593 original size:6 final size:6
Alignment explanation
Indices: 29710564--29710616 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
29710554 AATCAAAGTC
* * * *
29710564 AAAATG AAAATG AAAAAG AGAAAAG AAAAATG AAAAGG AAAAAG AAAAGG
1 AAAAAG AAAAAG AAAAAG A-AAAAG AAAAA-G AAAAAG AAAAAG AAAAAG
29710614 AAA
1 AAA
29710617 GGCCAAGGCG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
6 30 0.73
7 11 0.27
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.06
Consensus pattern (6 bp):
AAAAAG
Found at i:29710598 original size:26 final size:25
Alignment explanation
Indices: 29710564--29710616 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 25
29710554 AATCAAAGTC
*
29710564 AAAATGAAAATGAAAAAGAGAAAAGA
1 AAAATGAAAAGGAAAAAGA-AAAAGA
*
29710590 AAAATGAAAAGGAAAAAGAAAAGGA
1 AAAATGAAAAGGAAAAAGAAAAAGA
29710615 AA
1 AA
29710617 GGCCAAGGCG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.06
Consensus pattern (25 bp):
AAAATGAAAAGGAAAAAGAAAAAGA
Found at i:29710599 original size:19 final size:20
Alignment explanation
Indices: 29710570--29710611 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
29710560 AGTCAAAATG
29710570 AAAATGAAAAA-GAGAAAAGA
1 AAAATGAAAAAGGA-AAAAGA
29710590 AAAATG-AAAAGGAAAAAGA
1 AAAATGAAAAAGGAAAAAGA
29710609 AAA
1 AAA
29710612 GGAAAGGCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (20 bp):
AAAATGAAAAAGGAAAAAGA
Found at i:29710613 original size:12 final size:12
Alignment explanation
Indices: 29710564--29710616 Score: 61
Period size: 13 Copynumber: 4.2 Consensus size: 12
29710554 AATCAAAGTC
* *
29710564 AAAATGAAAATG
1 AAAAAGAAAAGG
*
29710576 AAAAAGAGAAAAG
1 AAAAAGA-AAAGG
29710589 AAAAATGAAAAGG
1 AAAAA-GAAAAGG
29710602 AAAAAGAAAAGG
1 AAAAAGAAAAGG
29710614 AAA
1 AAA
29710617 GGCCAAGGCG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
12 16 0.44
13 18 0.50
14 2 0.06
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.06
Consensus pattern (12 bp):
AAAAAGAAAAGG
Found at i:29711001 original size:21 final size:22
Alignment explanation
Indices: 29710961--29711005 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
29710951 GGATTTCAAG
*
29710961 AACAAAAAAGAAAGAGATGAAA
1 AACAAAAAAGAAAGAAATGAAA
*
29710983 AACAAAAATGAAA-AAATGAAA
1 AACAAAAAAGAAAGAAATGAAA
29711004 AA
1 AA
29711006 TGAAAGAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.07
Consensus pattern (22 bp):
AACAAAAAAGAAAGAAATGAAA
Found at i:29712376 original size:24 final size:24
Alignment explanation
Indices: 29712344--29712392 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
29712334 AACAGCGAAG
29712344 CAGATCGAAAACAAAACCTTGCCT
1 CAGATCGAAAACAAAACCTTGCCT
*
29712368 CAGATCGAAAACAAAGCCTTGCCT
1 CAGATCGAAAACAAAACCTTGCCT
29712392 C
1 C
29712393 CATCGGTTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.39, C:0.31, G:0.14, T:0.16
Consensus pattern (24 bp):
CAGATCGAAAACAAAACCTTGCCT
Found at i:29712454 original size:111 final size:111
Alignment explanation
Indices: 29712260--29712479 Score: 395
Period size: 111 Copynumber: 2.0 Consensus size: 111
29712250 ATCAGTGAAT
* *
29712260 ATCGAAAACAAAGCCTTGCCTCCATCGATTGCAGTGGAGCTGGTTAAAGATAGCAGATATTGCCT
1 ATCGAAAACAAAGCCTTGCCTCCATCGATTGCAGTGGAGCTGGTTAAAGATAACAGATATTGCAT
29712325 TCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAACCTTGCCTCAG
66 TCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAACCTTGCCTCAG
* *
29712371 ATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGATCTTGCAT
1 ATCGAAAACAAAGCCTTGCCTCCATCGATTGCAGTGGAGCTGGTTAAAGATAACAGATATTGCAT
*
29712436 TCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTC
66 TCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAACCTTGCCTC
29712480 CATCGATTGC
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 104 1.00
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.22
Consensus pattern (111 bp):
ATCGAAAACAAAGCCTTGCCTCCATCGATTGCAGTGGAGCTGGTTAAAGATAACAGATATTGCAT
TCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAACCTTGCCTCAG
Found at i:29712516 original size:87 final size:87
Alignment explanation
Indices: 29712368--29713134 Score: 1146
Period size: 87 Copynumber: 8.8 Consensus size: 87
29712358 AACCTTGCCT
29712368 CAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGATCTTG
1 CAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGATCTTG
*
29712433 CATTCCTGCGTTAACAGCGAAG
66 CCTTCCTGCGTTAACAGCGAAG
* * *
29712455 CAGATCGAAAACAAAGCCTTGCCTCCATCGATTGCAGTGGAGCTGATTAAAGATAATAGATCTTG
1 CAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGATCTTG
29712520 CC-TCCTGCGTTAACAGCGAAG
66 CCTTCCTGCGTTAACAGCGAAG
* * * * *
29712541 CATACCGAAAACAAAGCCTTGCCTCCATCGATTACAGTGGAGCTGGTTAAAGATAGCAGATCTTG
1 CAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGATCTTG
*
29712606 CCTTCTTGCGTTAACAGCGAAG
66 CCTTCCTGCGTTAACAGCGAAG
* * * ** * *
29712628 CAAACCGAAAACAAAGCTTTGCCTCCATCAATTGCAGTGGAGCTGGTTAAATATAGCAGATCTTG
1 CAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGATCTTG
* *
29712693 CCTTACTGCGTTAACAACGAAG
66 CCTTCCTGCGTTAACAGCGAAG
* * *
29712715 CAGATCGAAAATAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTG
1 CAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGATCTTG
*
29712780 CCTTCCTGCGTTAACAGCGAAA
66 CCTTCCTGCGTTAACAGCGAAG
*
29712802 CAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGGTCTTG
1 CAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGATCTTG
* *
29712867 CCTTTCTGTGTTAACAGCGAAG
66 CCTTCCTGCGTTAACAGCGAAG
* * *
29712889 CAGA-CTGAAAACAAAGCCTTGCCTCCATCGGTTACAGTAGAGCTGGTTAAAGATAACAGGTCTT
1 CAGATC-GAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGATCTT
* *
29712953 GCCTTTCTGTGTTAACAGCGAAG
65 GCCTTCCTGCGTTAACAGCGAAG
* * *
29712976 CAGA-CTGAAAACAAAGCCTTGCCTCCATCGGTTACAGTAGAGCTGGTTAAAGATAACAGGTCTT
1 CAGATC-GAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGATCTT
* *
29713040 GCCTTTCTGTGTTAACAGCGAAG
65 GCCTTCCTGCGTTAACAGCGAAG
*
29713063 CAGA-CTGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTT
1 CAGATC-GAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGATCTT
29713127 GCCTTCCT
65 GCCTTCCT
29713135 AAGCACTAGC
Statistics
Matches: 634, Mismatches: 44, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
86 81 0.13
87 553 0.87
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (87 bp):
CAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGATCTTG
CCTTCCTGCGTTAACAGCGAAG
Found at i:29713472 original size:44 final size:44
Alignment explanation
Indices: 29713380--29713474 Score: 102
Period size: 44 Copynumber: 2.2 Consensus size: 44
29713370 TCGCATCAGG
* ** *
29713380 TCTTATCTCTCTGAAGTTGCAGCGGAGCAGACTGAGAAAACAAG
1 TCTTATCCCTCTGAAGTCACAGCGGAGCAGACTGAGAAAACAAA
* * * *
29713424 TCTTATCCCTCTGAAGTCACAGTGGGGCAGATTGA-AGAAGCAAA
1 TCTTATCCCTCTGAAGTCACAGCGGAGCAGACTGAGA-AAACAAA
29713468 TCTTATC
1 TCTTATC
29713475 TCCTTGAGGT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
43 1 0.02
44 41 0.98
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (44 bp):
TCTTATCCCTCTGAAGTCACAGCGGAGCAGACTGAGAAAACAAA
Found at i:29714446 original size:16 final size:17
Alignment explanation
Indices: 29714425--29714457 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
29714415 TTGTTCATAC
29714425 TAAAAAGAAAA-GAAAA
1 TAAAAAGAAAAGGAAAA
29714441 TAAAAAGAAAAGGAAAA
1 TAAAAAGAAAAGGAAAA
29714458 GCCTTACCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (17 bp):
TAAAAAGAAAAGGAAAA
Found at i:29715188 original size:3 final size:3
Alignment explanation
Indices: 29715176--29715241 Score: 51
Period size: 3 Copynumber: 21.7 Consensus size: 3
29715166 TAATGTGTGC
* * * * * * *
29715176 TAT TATT TAT TAT TAT TAT TAA CAC TAT TAT AAT CAT TAT TAG CAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
29715222 TAT TAT TAT TAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
29715242 AATACCTTTT
Statistics
Matches: 48, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:29735730 original size:6 final size:6
Alignment explanation
Indices: 29735719--29735747 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
29735709 ATGTTTGGAC
29735719 GAAAAG GAAAAG GAAAAG GAAAAG GAAAA
1 GAAAAG GAAAAG GAAAAG GAAAAG GAAAA
29735748 TACAAGGGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (6 bp):
GAAAAG
Found at i:29737058 original size:11 final size:11
Alignment explanation
Indices: 29737031--29737074 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
29737021 TTTGATCACT
*
29737031 TAATTATTTAA
1 TAATTATTAAA
29737042 -AATTATTAAA
1 TAATTATTAAA
29737052 TAATTATTAAA
1 TAATTATTAAA
* *
29737063 TTATTAATAAA
1 TAATTATTAAA
29737074 T
1 T
29737075 TTTCATTTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.31
11 20 0.69
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TAATTATTAAA
Found at i:29738160 original size:99 final size:99
Alignment explanation
Indices: 29737989--29738182 Score: 291
Period size: 99 Copynumber: 2.0 Consensus size: 99
29737979 TTGTTGGCAG
* ** * *
29737989 AGGCCAATATTAACTTTGATAAACCATAAATAACATTTATTTTTAAAAAGTAAGTGTTATCTCCA
1 AGGCCAATAGTAACTTTGATAAACCATAAATAACATTTATTTAAAAAAAGTAAGGGTTACCTCCA
29738054 TTAAAATTTTGCCTTATTTGAGTATTTTTATATT
66 TTAAAATTTTGCCTTATTTGAGTATTTTTATATT
* * * *
29738088 AGGCCAATAGTAACTTTGGTAAACCATATATAACATTTATTTAAAAAAAAGTAAGGGTTCCCT-T
1 AGGCCAATAGTAACTTTGATAAACCATAAATAACATTTATTT-AAAAAAAGTAAGGGTTACCTCC
29738152 ATTAAAATTTTGCCTTATTTGAGTATTTTTA
65 ATTAAAATTTTGCCTTATTTGAGTATTTTTA
29738183 ATAGTTGAAT
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
99 70 0.82
100 15 0.18
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (99 bp):
AGGCCAATAGTAACTTTGATAAACCATAAATAACATTTATTTAAAAAAAGTAAGGGTTACCTCCA
TTAAAATTTTGCCTTATTTGAGTATTTTTATATT
Found at i:29739402 original size:11 final size:11
Alignment explanation
Indices: 29739361--29739402 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
29739351 CCTTCAAAAA
29739361 TTCTCTTAAGT
1 TTCTCTTAAGT
*
29739372 TACTCTTAAGT
1 TTCTCTTAAGT
*
29739383 TCCTCTTAAGT
1 TTCTCTTAAGT
*
29739394 TTCTTTTAA
1 TTCTCTTAA
29739403 CTCCTTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.21, C:0.19, G:0.07, T:0.52
Consensus pattern (11 bp):
TTCTCTTAAGT
Found at i:29739584 original size:15 final size:15
Alignment explanation
Indices: 29739564--29739617 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
29739554 TTTTTAAATA
*
29739564 TTATTTAAGAATTTT
1 TTATTTATGAATTTT
*
29739579 TTATTTATGCATTTT
1 TTATTTATGAATTTT
*
29739594 TAGATATTTATTAATTTT
1 T---TATTTATGAATTTT
29739612 TTATTT
1 TTATTT
29739618 GTTATAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
15 19 0.59
18 13 0.41
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.65
Consensus pattern (15 bp):
TTATTTATGAATTTT
Found at i:29741722 original size:25 final size:25
Alignment explanation
Indices: 29741694--29741741 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
29741684 TATTTTGATA
29741694 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
29741719 TTATTTGATGTAATAAAATAGAA
1 TTATTTGATGTAATAAAATAGAA
29741742 ATTTTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.40
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:29741927 original size:28 final size:23
Alignment explanation
Indices: 29741784--29742243 Score: 439
Period size: 23 Copynumber: 20.2 Consensus size: 23
29741774 ATTAATACCC
29741784 TTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
* *
29741807 TTTAATTAAAAACCTTAAACCCT-A
1 TTAAATTAAAAACCCT-AA-CCTAA
* ***
29741831 --AACTTAAAAACCCTAACCCCC
1 TTAAATTAAAAACCCTAACCTAA
*
29741852 TTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
*
29741875 TTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
29741898 TTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
29741921 TTAAATTAAAAACCCTAAACCCTAA
1 TTAAATTAAAAACCCT-AA-CCTAA
* **
29741946 --ACA-TAAAAACCCTAACCCCA
1 TTAAATTAAAAACCCTAACCTAA
*
29741966 TTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
* **
29741989 TTAACTTAAAAGTCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
*
29742012 TTAAATTAAAAACCTTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
*
29742035 TTTAATTAAAAACCCTAAACCCT-A
1 TTAAATTAAAAACCCT-AA-CCTAA
*
29742059 --AACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
* *
29742080 TTTAATTAAAAACCTTAAACCCT-A
1 TTAAATTAAAAACCCT-AA-CCTAA
* **
29742104 --AACTTAAAAACCCTAA-CTCCC
1 TTAAATTAAAAACCCTAACCT-AA
* *
29742125 TTAACTTAAAAACTCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
29742148 TTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
*
29742171 TTTAATTAAAAACCCTAAACCCT-A
1 TTAAATTAAAAACCCT-AA-CCTAA
*
29742195 --AACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
* *
29742216 TTTAATTAAAAACCCTAAACTAAA
1 TTAAATTAAAAACCCTAACCT-AA
29742240 TTAA
1 TTAA
29742244 TAATTTTACT
Statistics
Matches: 362, Mismatches: 47, Indels: 55
0.78 0.10 0.12
Matches are distributed among these distances:
19 2 0.01
20 11 0.03
21 12 0.03
22 57 0.16
23 242 0.67
24 21 0.06
25 17 0.05
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (23 bp):
TTAAATTAAAAACCCTAACCTAA
Found at i:29741975 original size:114 final size:115
Alignment explanation
Indices: 29741784--29742243 Score: 584
Period size: 114 Copynumber: 4.0 Consensus size: 115
29741774 ATTAATACCC
* * *
29741784 TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCTTAAACCCTAAACTTAAAAACCCTAACC
1 TTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAACCCTAAACATAAAAACCCTAACC
*
29741849 CCCTTAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCTAACCT-AA
66 CCATTAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCTAACCTAAA
29741898 TTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAACCCTAAACATAAAAACCCTAACC
1 TTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAACCCTAAACATAAAAACCCTAACC
**
29741963 CCATTAACTTAAAAACCCTAACCTAATTAACTTAAAAGTCCTAACCT-AA
66 CCATTAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCTAACCTAAA
* * *
29742012 TTAAATTAAAAACCTTAACCTAATTTAATTAAAAACCCTAAACCCTAAACTTAAAAACCCTAACC
1 TTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAACCCTAAACATAAAAACCCTAACC
** * ***
29742077 TAATTTAA-TTAAAAACCTTAAACCCT-A--AACTTAAAAACCCTAA-CTCCC
66 CCA-TTAACTTAAAAACCCT-AA-CCTAATTAACTTAAAAACCCTAACCTAAA
* *
29742125 TTAACTTAAAAACTCTAACCTAATTAAATTAAAAACCCT-AA-CCTAATTTA-ATTAAAAACCCT
1 TTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAACCCTAA---ACA-TAAAAACCCT
* * *
29742187 AAACCC-TAAACTTAAAAACCCTAACCTAATTTAA-TTAAAAACCCTAAACTAAA
62 AACCCCATTAACTTAAAAACCCTAACCTAA-TTAACTTAAAAACCCTAACCTAAA
29742240 TTAA
1 TTAA
29742244 TAATTTTACT
Statistics
Matches: 303, Mismatches: 29, Indels: 27
0.84 0.08 0.08
Matches are distributed among these distances:
111 8 0.03
112 10 0.03
113 59 0.19
114 208 0.69
115 15 0.05
116 3 0.01
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (115 bp):
TTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAACCCTAAACATAAAAACCCTAACC
CCATTAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCTAACCTAAA
Found at i:29742087 original size:68 final size:67
Alignment explanation
Indices: 29741780--29742244 Score: 472
Period size: 68 Copynumber: 6.8 Consensus size: 67
29741770 AACCATTAAT
* *
29741780 ACCCTTAAA-TTAAAAACCCTAACCTAATTTAATTAAAAACCTTAAACCCTAA--ACTTAAAAAC
1 ACCC-TAAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCT-AA-CCTAATTAATTAAAAAC
29741842 CCTAA
63 CCTAA
* *
29741847 CCCCCTTAACTTAAAAACCCTAACCTAA-TTAACTTAAAAACCCTAACCTAATTAAATTAAAAAC
1 -ACCCTAAACTTAAAAACCCTAACCTAATTTAA-TTAAAAACCCTAACCTAATT-AATTAAAAAC
29741911 CCT-A
63 CCTAA
* **
29741915 A-CCTAATTAAATTAAAAACCCTAAACCCTAA---ACA-TAAAAACCCTAACCCCATTAACTTAA
1 ACCCT-A--AACTTAAAAACCCT-AA-CCTAATTTA-ATTAAAAACCCTAACCTAATTAA-TTAA
29741975 AAACCCT-A
59 AAACCCTAA
** * *
29741983 A-CCTAATTAACTTAAAAGTCCTAACCTAATTAAATTAAAAACCTTAACCTAATTTAATTAAAAA
1 ACCCT-A--AACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAA-TTAATTAAAAA
29742047 CCCTAA
62 CCCTAA
* *
29742053 ACCCTAAACTTAAAAACCCTAACCTAATTTAATTAAAAACCTTAAACCCTAA--ACTTAAAAACC
1 ACCCTAAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCT-AA-CCTAATTAATTAAAAACC
29742116 CTAA
64 CTAA
* * * *
29742120 CTCCCTTAACTTAAAAACTCTAACCTAATTAAATTAAAAACCCTAACCTAATTTAATTAAAAACC
1 -ACCCTAAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAA-TTAATTAAAAACC
29742185 CTAA
64 CTAA
*
29742189 ACCCTAAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACTAAATTAAT
1 ACCCTAAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCT-AATTAAT
29742245 AATTTTACTT
Statistics
Matches: 341, Mismatches: 30, Indels: 52
0.81 0.07 0.12
Matches are distributed among these distances:
66 18 0.05
67 29 0.09
68 201 0.59
69 70 0.21
70 15 0.04
71 8 0.02
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (67 bp):
ACCCTAAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTAATTAAAAACCCT
AA
Found at i:29742225 original size:91 final size:91
Alignment explanation
Indices: 29741784--29742243 Score: 507
Period size: 91 Copynumber: 5.0 Consensus size: 91
29741774 ATTAATACCC
* *
29741784 TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCTTAAACCCTAAACTTAAAAACCCTAACC
1 TTAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAAACTTAAAAACCCTAACC
**
29741849 -CCCTTAACTTAAAAACCCTAACCTAA
66 TAACTTAA-TTAAAAACCCTAACCTAA
* *
29741875 TTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCT-AA-CCTAATTAAATTAAAAACCCTA
1 TTAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCT-A--AACTTAAAAACCCT-
**
29741938 AACCCTAA---ACA-TAAAAACCCTAACCCCA
62 AA-CCTAACTTA-ATTAAAAACCCTAACCTAA
** * *
29741966 TTAACTTAAAAACCCTAACCTAA-TTAACTTAAAAGTCCT-AA-CCTAATTAAATTAAAAACCTT
1 TTAACTTAAAAACCCTAACCTAATTTAA-TTAAAAACCCTAAACCCT-A--AACTTAAAAACCCT
*
29742028 AACCTAATTTAATTAAAAACCCTAAACCCT-A
62 AACCTAACTTAATTAAAAACCCT-AA-CCTAA
*
29742059 --AACTTAAAAACCCTAACCTAATTTAATTAAAAACCTTAAACCCTAAACTTAAAAACCCTAA-C
1 TTAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAAACTTAAAAACCCTAACC
** *
29742121 TCCCTTAACTTAAAAACTCTAACCTAA
66 TAACTTAA-TTAAAAACCCTAACCTAA
*
29742148 TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAAACTTAAAAACCCTAACC
1 TTAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAAACTTAAAAACCCTAACC
* *
29742213 TAATTTAATTAAAAACCCTAAACTAAA
66 TAACTTAATTAAAAACCCTAACCT-AA
29742240 TTAA
1 TTAA
29742244 TAATTTTACT
Statistics
Matches: 317, Mismatches: 29, Indels: 45
0.81 0.07 0.12
Matches are distributed among these distances:
88 3 0.01
89 17 0.05
90 32 0.10
91 208 0.66
92 44 0.14
93 9 0.03
94 4 0.01
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (91 bp):
TTAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAAACTTAAAAACCCTAACC
TAACTTAATTAAAAACCCTAACCTAA
Found at i:29742444 original size:115 final size:115
Alignment explanation
Indices: 29742238--29742597 Score: 603
Period size: 116 Copynumber: 3.1 Consensus size: 115
29742228 CCCTAAACTA
* **
29742238 AATTAATAATTTTACTTTCACATAATGTTAGATTTGGAAAAATGTTTTTTCCTGGTACTAACAAT
1 AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATG-TTTTGACTGGTACTAACAAT
*
29742303 TAATAATTTTATATAATTTGATAATTTTACTAATCATTAATACAATTTATC
65 TAATAATTTTATATAATTTGATAATTTTACTAACCATTAATACAATTTATC
* * *
29742354 ATTTAATAATTTTACATTCACATAATGTTAGATTTGAAAAAATGTTTTGACTAGTACTAACAATT
1 AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATT
*
29742419 AATAATTTTATATAATTTGATAATTTTTAGTAACCATTAATACAATTTATC
66 AATAATTTTATATAATTTGATAA-TTTTACTAACCATTAATACAATTTATC
*
29742470 AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATATTTTGACTGGTACTAACAATT
1 AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATT
*
29742535 AATAATTTTATATAATTTGATAGTTTTTACTAACCATTAATACAATTTATC
66 AATAATTTTATATAATTTGATA-ATTTTACTAACCATTAATACAATTTATC
29742586 AATTAATAATTT
1 AATTAATAATTT
29742598 CACAAACTTA
Statistics
Matches: 228, Mismatches: 14, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
115 41 0.18
116 187 0.82
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (115 bp):
AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATT
AATAATTTTATATAATTTGATAATTTTACTAACCATTAATACAATTTATC
Found at i:29742480 original size:55 final size:54
Alignment explanation
Indices: 29742414--29742597 Score: 145
Period size: 55 Copynumber: 3.2 Consensus size: 54
29742404 CTAGTACTAA
29742414 CAATTAATAATTTTATATAATTTGATAATTTTTAGTAACCATTAATACAATTTAT
1 CAATTAATAATTTTATATAATTTGATAATTTTTA-TAACCATTAATACAATTTAT
* * * ** * ** * ** * *
29742469 CAATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATATT-TTGACTGGTACTAA
1 CAATTAATAATTTTATA-T-A-AT-TTGATA-ATTTTTATAACCATTAAT-AC-AAT-TTAT
*
29742530 CAATTAATAATTTTATATAATTTGATAGTTTTTACTAACCATTAATACAATTTAT
1 CAATTAATAATTTTATATAATTTGATAATTTTTA-TAACCATTAATACAATTTAT
29742585 CAATTAATAATTT
1 CAATTAATAATTT
29742598 CACAAACTTA
Statistics
Matches: 92, Mismatches: 27, Indels: 20
0.66 0.19 0.14
Matches are distributed among these distances:
55 31 0.34
56 6 0.07
57 12 0.13
58 6 0.07
59 12 0.13
60 7 0.08
61 18 0.20
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.45
Consensus pattern (54 bp):
CAATTAATAATTTTATATAATTTGATAATTTTTATAACCATTAATACAATTTAT
Found at i:29742544 original size:61 final size:61
Alignment explanation
Indices: 29742356--29742544 Score: 169
Period size: 61 Copynumber: 3.2 Consensus size: 61
29742346 AATTTATCAT
*
29742356 TTAATAATTTTACATTCACATAATGTTAGATTTGAAAAAATGTTTTGACTAGTACTAACAA
1 TTAATAATTTTACATTCACATAATGTTAGATTTGAAAAAATATTTTGACTAGTACTAACAA
* * * * ** ** * * * *
29742417 TTAATAATTTTATA-T-A-AT-TTGATA-ATTTTTAGTAACCATTAAT-AC-AAT-TTATCAA
1 TTAATAATTTTACATTCACATAATGTTAGA-TTTGAAAAAATATT-TTGACTAGTACTAACAA
* *
29742472 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATATTTTGACTGGTACTAACAA
1 TTAATAATTTTACATTCACATAATGTTAGATTTGAAAAAATATTTTGACTAGTACTAACAA
29742533 TTAATAATTTTA
1 TTAATAATTTTA
29742545 TATAATTTGA
Statistics
Matches: 91, Mismatches: 27, Indels: 20
0.66 0.20 0.14
Matches are distributed among these distances:
55 18 0.20
56 4 0.04
57 15 0.16
58 6 0.07
59 15 0.16
60 3 0.03
61 30 0.33
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (61 bp):
TTAATAATTTTACATTCACATAATGTTAGATTTGAAAAAATATTTTGACTAGTACTAACAA
Found at i:29744941 original size:124 final size:124
Alignment explanation
Indices: 29744783--29745130 Score: 572
Period size: 124 Copynumber: 2.8 Consensus size: 124
29744773 CAAACATGCT
*
29744783 ACTGTAGCAAAAGCGCGTCCACGAGGGCGTGATTTTACAAATTCTTCTCAAATAGCATTC-TGCT
1 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCA-TCATGCT
*
29744847 AGAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAAAATATTTCTTCCATGGCCG
65 AGAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAAAATATTTCTTCCATGACCG
*
29744907 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCTTGCTA
1 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCATGCTA
* * * **
29744972 GAATCAATTTTATACTATTTGCTCAGAAACATCAAAAAAAATTATTTCTTCCATGACTT
66 GAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAAAATATTTCTTCCATGACCG
* *
29745031 ACTGTAGTAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCATGCTA
1 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCATGCTA
* *
29745096 GAAGCGATTTTATACTATTTGATCAGAAACGTCAA
66 GAAGCGATTTTATACTATTTGCTCAGAAACATCAA
29745131 CTCGAAATTA
Statistics
Matches: 209, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
123 2 0.01
124 207 0.99
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.29
Consensus pattern (124 bp):
ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCATGCTA
GAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAAAATATTTCTTCCATGACCG
Found at i:29747655 original size:6 final size:6
Alignment explanation
Indices: 29747644--29747670 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
29747634 TGTAATGCAA
29747644 AAATGC AAATGC AAATGC AAATGC AAA
1 AAATGC AAATGC AAATGC AAATGC AAA
29747671 GTAGCCAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (6 bp):
AAATGC
Found at i:29752043 original size:13 final size:13
Alignment explanation
Indices: 29752010--29752045 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
29752000 ATATATATTT
29752010 AAAAATT-ATATA
1 AAAAATTAATATA
29752022 AAAAA-TAATATA
1 AAAAATTAATATA
29752034 AAAAATTAATAT
1 AAAAATTAATAT
29752046 GGGTGGATCG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.05
12 15 0.68
13 6 0.27
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAAATTAATATA
Found at i:29760890 original size:6 final size:6
Alignment explanation
Indices: 29760879--29760906 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
29760869 CTCTTTTCTT
29760879 CTCTAC CTCTAC CTCTAC CTCTAC CTCT
1 CTCTAC CTCTAC CTCTAC CTCTAC CTCT
29760907 TACACTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.50, G:0.00, T:0.36
Consensus pattern (6 bp):
CTCTAC
Found at i:29765537 original size:22 final size:22
Alignment explanation
Indices: 29765503--29765545 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
29765493 AACAATAATA
29765503 ATAATAATAAAAT-AGTAGCAAT
1 ATAATAATAAAATGA-TAGCAAT
* *
29765525 ATAATAGTGAAATGATAGCAA
1 ATAATAATAAAATGATAGCAA
29765546 AACAATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.56, C:0.05, G:0.14, T:0.26
Consensus pattern (22 bp):
ATAATAATAAAATGATAGCAAT
Found at i:29768497 original size:3 final size:3
Alignment explanation
Indices: 29768489--29768521 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
29768479 TTTCATCACC
29768489 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29768522 AATAAGAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:29775786 original size:22 final size:22
Alignment explanation
Indices: 29775761--29775804 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
29775751 TTTTCCCCCC
29775761 TAATTATATATT-TTAATTATTT
1 TAATTAT-TATTATTAATTATTT
*
29775783 TAATTATTTTTATTAATTATTT
1 TAATTATTATTATTAATTATTT
29775805 GATTAGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TAATTATTATTATTAATTATTT
Found at i:29778369 original size:6 final size:6
Alignment explanation
Indices: 29778358--29778382 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
29778348 TTGTATTACA
29778358 TTTATT TTTATT TTTATT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT T
29778383 CAAGTTCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:29786400 original size:4 final size:4
Alignment explanation
Indices: 29786391--29786427 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
29786381 ACGTATGTTG
*
29786391 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA AGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
29786428 AGCTTATACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (4 bp):
TGTA
Found at i:29789388 original size:51 final size:51
Alignment explanation
Indices: 29789268--29789445 Score: 155
Period size: 51 Copynumber: 3.5 Consensus size: 51
29789258 TGGTCACGTA
* * * * * *
29789268 TGTAGTACTATGTGGAGGCTACTACGTGTACCGGAATGAT-A-GGTCGCATG
1 TGTAGTACTATGTGCAGGCTACTATGCGTACAGG-ATGATAATGATCACATG
* * * ** *
29789318 TATTGTATTATGTGCAGGCTACTATGCGTACAGGAT-AGTTTTGATCACGTG
1 TGTAGTACTATGTGCAGGCTACTATGCGTACAGGATGA-TAATGATCACATG
* * * ** *
29789369 TGTAGTACTATGTGAAGGCTACTACGTGTATTGGATGATAATGGTCACATG
1 TGTAGTACTATGTGCAGGCTACTATGCGTACAGGATGATAATGATCACATG
29789420 TGTAGTACTATGTGCAGGCTACTATG
1 TGTAGTACTATGTGCAGGCTACTATG
29789446 TGAACCGAAC
Statistics
Matches: 99, Mismatches: 25, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
48 1 0.01
49 3 0.03
50 27 0.27
51 67 0.68
52 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (51 bp):
TGTAGTACTATGTGCAGGCTACTATGCGTACAGGATGATAATGATCACATG
Found at i:29789388 original size:101 final size:102
Alignment explanation
Indices: 29789261--29789445 Score: 275
Period size: 101 Copynumber: 1.8 Consensus size: 102
29789251 AAAGTGATGG
* * *
29789261 TCACGTATGTAGTACTATGTGGAGGCTACTACGTGTACCGGAATGAT-A-GGTCGCATGTATTGT
1 TCACGTATGTAGTACTATGTGAAGGCTACTACGTGTACCGG-ATGATAATGGTCACATGTATAGT
*
29789324 ATTATGTGCAGGCTACTATGCGTACAGGATAGTTTTGA
65 ACTATGTGCAGGCTACTATGCGTACAGGATAGTTTTGA
* ** *
29789362 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATTGGATGATAATGGTCACATGTGTAGTA
1 TCACGTATGTAGTACTATGTGAAGGCTACTACGTGTACCGGATGATAATGGTCACATGTATAGTA
29789427 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
29789446 TGAACCGAAC
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
100 5 0.07
101 38 0.51
102 31 0.42
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (102 bp):
TCACGTATGTAGTACTATGTGAAGGCTACTACGTGTACCGGATGATAATGGTCACATGTATAGTA
CTATGTGCAGGCTACTATGCGTACAGGATAGTTTTGA
Found at i:29789517 original size:45 final size:45
Alignment explanation
Indices: 29789449--29789543 Score: 165
Period size: 45 Copynumber: 2.1 Consensus size: 45
29789439 TACTATGTGA
*
29789449 ACCGAACATCATTGATAAGTAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTGATAAGTAAGGTGGTTGCTATGTGCTGAATCC
29789494 ACCGAACATCATTGATTAA-TAAGGTGGTTGCTATGTGCTGAATCC
1 ACCGAACATCATTGA-TAAGTAAGGTGGTTGCTATGTGCTGAATCC
29789539 ACCGA
1 ACCGA
29789544 GTATCTGTTA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 45 0.94
46 3 0.06
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.29
Consensus pattern (45 bp):
ACCGAACATCATTGATAAGTAAGGTGGTTGCTATGTGCTGAATCC
Found at i:29792661 original size:3 final size:3
Alignment explanation
Indices: 29792653--29792683 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
29792643 TAAAAGGGGT
29792653 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
29792684 GAGATCTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:29793765 original size:20 final size:20
Alignment explanation
Indices: 29793740--29793778 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29793730 TTAAATTTAA
*
29793740 TTTAATATCAACATAATAAC
1 TTTAATATCAAAATAATAAC
*
29793760 TTTAATATTAAAATAATAA
1 TTTAATATCAAAATAATAA
29793779 AATACTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTAATATCAAAATAATAAC
Found at i:29798330 original size:22 final size:23
Alignment explanation
Indices: 29798269--29798320 Score: 88
Period size: 22 Copynumber: 2.3 Consensus size: 23
29798259 AGTAAAAAAA
*
29798269 TTAAGAAAGAATTTGAGATA-TT
1 TTAAGAGAGAATTTGAGATATTT
29798291 TTAAGAGAGAATTTGAGATATTT
1 TTAAGAGAGAATTTGAGATATTT
29798314 TTAAGAG
1 TTAAGAG
29798321 TTGATTGAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (23 bp):
TTAAGAGAGAATTTGAGATATTT
Found at i:29798991 original size:27 final size:27
Alignment explanation
Indices: 29798946--29799017 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 27
29798936 GGGATTTTAT
*
29798946 ATATGTTATTATTAATTAGTTTCAAACTA
1 ATATGTT-TTATTATTTAGTTTCAAAC-A
*
29798975 A-ATGTTTTATTATTTAGTTTCACACA
1 ATATGTTTTATTATTTAGTTTCAAACA
*
29799001 ATATATTTTATTATTTA
1 ATATGTTTTATTATTTA
29799018 TTTATTATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
26 2 0.05
27 31 0.79
28 5 0.13
29 1 0.03
ACGTcount: A:0.35, C:0.07, G:0.06, T:0.53
Consensus pattern (27 bp):
ATATGTTTTATTATTTAGTTTCAAACA
Found at i:29800177 original size:21 final size:21
Alignment explanation
Indices: 29800151--29800203 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
29800141 TTTTTGATGA
29800151 AGGTATCGATACCTTAGGCCT
1 AGGTATCGATACCTTAGGCCT
* *
29800172 AGGTATTGATACC-TAGGCTT
1 AGGTATCGATACCTTAGGCCT
29800192 A--TATCGATACCT
1 AGGTATCGATACCT
29800204 ACCTCAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 9 0.32
20 7 0.25
21 12 0.43
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (21 bp):
AGGTATCGATACCTTAGGCCT
Found at i:29800202 original size:18 final size:19
Alignment explanation
Indices: 29800153--29800204 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
29800143 TTTGATGAAG
29800153 GTATCGATACCTTAGGCCTA
1 GTATCGATACC-TAGGCCTA
* *
29800173 GGTATTGATACCTAGGCTTA
1 -GTATCGATACCTAGGCCTA
29800193 -TATCGATACCTA
1 GTATCGATACCTA
29800205 CCTCAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 11 0.39
20 7 0.25
21 10 0.36
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (19 bp):
GTATCGATACCTAGGCCTA
Found at i:29800738 original size:24 final size:25
Alignment explanation
Indices: 29800702--29800748 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
29800692 TAAAATTTAC
29800702 TATTAATAGTATA-AAATAAAATAA
1 TATTAATAGTATAGAAATAAAATAA
** *
29800726 TATTAATTTTATAGACATAAAAT
1 TATTAATAGTATAGAAATAAAAT
29800749 TTACATCACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.38
Consensus pattern (25 bp):
TATTAATAGTATAGAAATAAAATAA
Found at i:29804573 original size:21 final size:21
Alignment explanation
Indices: 29804547--29804597 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
29804537 AAAATTACTA
*
29804547 TTTTTTTTACTGTTTTCTTGT
1 TTTTTTTTACTATTTTCTTGT
* *
29804568 TTTTTTTAATTATTTTCTTGT
1 TTTTTTTTACTATTTTCTTGT
29804589 TGTTTTTTT
1 T-TTTTTTT
29804598 TTCACTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.08, C:0.06, G:0.08, T:0.78
Consensus pattern (21 bp):
TTTTTTTTACTATTTTCTTGT
Found at i:29805244 original size:120 final size:120
Alignment explanation
Indices: 29805021--29805250 Score: 307
Period size: 120 Copynumber: 1.9 Consensus size: 120
29805011 CTCTAGTCCC
* * *
29805021 AAGTATCCTCAATACATCAATTGATCGTCCAAGCTGAAATTATATACATGTCAGGTTACCCGTCC
1 AAGTATCCTCAATACATCAATTGATCGTCCAAGCTGAAAATATATACAAGTCAGGTTACCCATCC
* *
29805086 GGACTAAACCTTTAAATTAACATCAAGTTGCTCATCTGAGCTAAAGTTGTATCCT
66 GGACTAAACCTTTAAACTAACATCAAGTTACTCATCTGAGCTAAAGTTGTATCCT
* * * * * *
29805141 AAGTATTCTCAATTCATCAATTGCTCGTCCAAGTTGAAAATATATAGAAGTCAGGTTACCCATCT
1 AAGTATCCTCAATACATCAATTGATCGTCCAAGCTGAAAATATATACAAGTCAGGTTACCCATCC
* * * * * *
29805206 GGGCTAAACTTTTGAACTAACATTAGGTTACTCGTCTGAGCTAAA
66 GGACTAAACCTTTAAACTAACATCAAGTTACTCATCTGAGCTAAA
29805251 CCTGTGTCAC
Statistics
Matches: 93, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
120 93 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (120 bp):
AAGTATCCTCAATACATCAATTGATCGTCCAAGCTGAAAATATATACAAGTCAGGTTACCCATCC
GGACTAAACCTTTAAACTAACATCAAGTTACTCATCTGAGCTAAAGTTGTATCCT
Found at i:29815455 original size:50 final size:50
Alignment explanation
Indices: 29815331--29815435 Score: 192
Period size: 50 Copynumber: 2.1 Consensus size: 50
29815321 TATAAAAAAT
*
29815331 TAATAATGTTAACAACATAATAATTAACTATTTAAAATTAAATAATTTAA
1 TAATAATGTTAACAACATAATAATTAACTAATTAAAATTAAATAATTTAA
*
29815381 TAATAATGTTAACAACATAATAATTAACTAATTAAAATTTAATAATTTAA
1 TAATAATGTTAACAACATAATAATTAACTAATTAAAATTAAATAATTTAA
29815431 TAATA
1 TAATA
29815436 TTTTCCTACC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (50 bp):
TAATAATGTTAACAACATAATAATTAACTAATTAAAATTAAATAATTTAA
Found at i:29815723 original size:18 final size:18
Alignment explanation
Indices: 29815702--29815736 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
29815692 TATAGTTGTA
29815702 GGAATTATGACCGTTGGG
1 GGAATTATGACCGTTGGG
29815720 GGAATTATGACCGTTGG
1 GGAATTATGACCGTTGG
29815737 CTAGAAAGCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.11, G:0.37, T:0.29
Consensus pattern (18 bp):
GGAATTATGACCGTTGGG
Found at i:29816018 original size:14 final size:14
Alignment explanation
Indices: 29815999--29816025 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29815989 ATTTTTATTA
29815999 TTTTTATAGTTTAG
1 TTTTTATAGTTTAG
29816013 TTTTTATAGTTTA
1 TTTTTATAGTTTA
29816026 ATTAACCATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (14 bp):
TTTTTATAGTTTAG
Found at i:29820146 original size:31 final size:34
Alignment explanation
Indices: 29820071--29820146 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 34
29820061 CTTAAAAAAT
*
29820071 ATTTTTTAATTCTTTTATTTTTTTTTACATTATTTC
1 ATTTTTT--TTCTTTTATTTTTTTTTACATTATTCC
*
29820107 --TTTCTTTCTTTT-TTTTTTTTT-CATT-TTCC
1 ATTTTTTTTCTTTTATTTTTTTTTACATTATTCC
29820136 ATTTTTTTTCT
1 ATTTTTTTTCT
29820147 AACGTATGGC
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
29 3 0.09
30 4 0.11
31 17 0.49
32 7 0.20
34 4 0.11
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (34 bp):
ATTTTTTTTCTTTTATTTTTTTTTACATTATTCC
Found at i:29830374 original size:30 final size:31
Alignment explanation
Indices: 29830340--29830407 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 31
29830330 AGTTTGCATA
* *
29830340 TATGAATTCGCTATGATCATGAAG-TTCTTT
1 TATGAATTCGCTATGATCATAAAGTTTCTTC
* *
29830370 TATGAATTTGCTATGTTCATAAAGTTTCTTC
1 TATGAATTCGCTATGATCATAAAGTTTCTTC
29830401 TATGAAT
1 TATGAAT
29830408 CCGTCTGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 21 0.64
31 12 0.36
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.46
Consensus pattern (31 bp):
TATGAATTCGCTATGATCATAAAGTTTCTTC
Found at i:29830482 original size:45 final size:45
Alignment explanation
Indices: 29830428--29830536 Score: 139
Period size: 45 Copynumber: 2.4 Consensus size: 45
29830418 GAATCTGTTT
* * * *
29830428 TATCCATGAAGT-TTCTTCTATGAATTTTCATGTATGAGTTTGCCA
1 TATCCATGAA-TCTTCTTCTATAAATCTGCATGTATGAGTCTGCCA
* * *
29830473 TATCTATGAATCATCTTCAATAAATCTGCATGTATGAGTCTGCCA
1 TATCCATGAATCTTCTTCTATAAATCTGCATGTATGAGTCTGCCA
29830518 TATCCATGAATCTTCTTCT
1 TATCCATGAATCTTCTTCT
29830537 TTTGCATGTA
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
44 1 0.02
45 52 0.98
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (45 bp):
TATCCATGAATCTTCTTCTATAAATCTGCATGTATGAGTCTGCCA
Found at i:29845335 original size:19 final size:20
Alignment explanation
Indices: 29845302--29845339 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
29845292 TTGTTAAAAG
*
29845302 TAAAAATCATTAAAATTATT
1 TAAAAATCATAAAAATTATT
29845322 TAAAAAT-ATAAAAATTAT
1 TAAAAATCATAAAAATTAT
29845340 AAAATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAAAATCATAAAAATTATT
Found at i:29850736 original size:21 final size:21
Alignment explanation
Indices: 29850702--29850752 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
29850692 ATTAATCTCT
* *
29850702 TCCAATAAAAATTACAAAATAA
1 TCCAA-AATAATTACAAAAAAA
*
29850724 TCCAAAATAATTATAAAAAAA
1 TCCAAAATAATTACAAAAAAA
*
29850745 TTCAAAAT
1 TCCAAAAT
29850753 TTATATTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.25
Consensus pattern (21 bp):
TCCAAAATAATTACAAAAAAA
Found at i:29854061 original size:25 final size:25
Alignment explanation
Indices: 29854007--29854061 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
29853997 AAAAACTAAC
**
29854007 AAAAA-TTAAAATAAATATTTTCCA
1 AAAAATTTAAAATAAATATTTTAAA
* *
29854031 ACAAATTTAAAATAAATTTTTTAAA
1 AAAAATTTAAAATAAATATTTTAAA
29854056 AAAAAT
1 AAAAAT
29854062 CTTTATACTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 4 0.16
25 21 0.84
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (25 bp):
AAAAATTTAAAATAAATATTTTAAA
Found at i:29854185 original size:22 final size:22
Alignment explanation
Indices: 29854160--29854202 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
29854150 GAAATGTTAG
*
29854160 CAAAACAGTGGGAAAACAACAA
1 CAAAACAGTGGAAAAACAACAA
*
29854182 CAAAATAGTGGAAAAACAACA
1 CAAAACAGTGGAAAAACAACA
29854203 GTTTTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.60, C:0.16, G:0.16, T:0.07
Consensus pattern (22 bp):
CAAAACAGTGGAAAAACAACAA
Found at i:29860124 original size:5 final size:5
Alignment explanation
Indices: 29860108--29860146 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
29860098 GCCTAAGATG
* *
29860108 TGAAT TGGAT TGAAT TGAAT ATGAAT TGTAT TGAAT TGA
1 TGAAT TGAAT TGAAT TGAAT -TGAAT TGAAT TGAAT TGA
29860147 GCTAAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.36, C:0.00, G:0.23, T:0.41
Consensus pattern (5 bp):
TGAAT
Found at i:29868360 original size:31 final size:32
Alignment explanation
Indices: 29868304--29868364 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
29868294 TATAAAATGA
*
29868304 TCACACAACTATTTGACTTTTTTCTTTTTTGG
1 TCACACAACTATTTGACATTTTTCTTTTTTGG
*
29868336 TCACCCAACTATTTGA-ATTTTTCTTTTTT
1 TCACACAACTATTTGACATTTTTCTTTTTT
29868365 AGTTATCAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 12 0.44
32 15 0.56
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.54
Consensus pattern (32 bp):
TCACACAACTATTTGACATTTTTCTTTTTTGG
Found at i:29881139 original size:60 final size:60
Alignment explanation
Indices: 29881037--29881168 Score: 183
Period size: 60 Copynumber: 2.2 Consensus size: 60
29881027 TACACTAGTA
* ** *
29881037 GTCAGCCAACTATTAATAAATTTATCTTTTGGTCATTTAACTATGAAAAGTTATAAAATG
1 GTCACCCAACTATTAATAAATTTATCTTTTGGTCATCAAACTATGAAAAGTTACAAAATG
* * * * *
29881097 GTTATCCAACTATTAGTAAATTTCTTTTTTGGTCATCAAACTATGAAAAGTTACAAAATG
1 GTCACCCAACTATTAATAAATTTATCTTTTGGTCATCAAACTATGAAAAGTTACAAAATG
29881157 GTCACCCAACTA
1 GTCACCCAACTA
29881169 CTCAATTTTG
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.36
Consensus pattern (60 bp):
GTCACCCAACTATTAATAAATTTATCTTTTGGTCATCAAACTATGAAAAGTTACAAAATG
Found at i:29881183 original size:60 final size:59
Alignment explanation
Indices: 29881054--29881191 Score: 152
Period size: 60 Copynumber: 2.3 Consensus size: 59
29881044 AACTATTAAT
* * ** * * * *
29881054 AAATTTATCTTTTGGTCATTTAACTATGAAAAGTTATAAAATGGTTATCCAACTATTAG
1 AAATTTCTTTTTTGGTCATCAAACTATGAAAAGTTACAAAATGGTCACCCAACTATCAG
29881113 TAAATTTCTTTTTTGGTCATCAAACTATGAAAAGTTACAAAATGGTCACCCAACTACTCA-
1 -AAATTTCTTTTTTGGTCATCAAACTATGAAAAGTTACAAAATGGTCACCCAACTA-TCAG
**
29881173 ATTTTGTCTTTTTTGGTCA
1 AAATT-TCTTTTTTGGTCA
29881192 CTAACTGGCT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
59 3 0.05
60 61 0.92
61 2 0.03
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (59 bp):
AAATTTCTTTTTTGGTCATCAAACTATGAAAAGTTACAAAATGGTCACCCAACTATCAG
Found at i:29882768 original size:28 final size:29
Alignment explanation
Indices: 29882731--29882790 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
29882721 TAATAGTGTT
29882731 TAAATTTATTATTATAATTTAAATTGTAA
1 TAAATTTATTATTATAATTTAAATTGTAA
* * *
29882760 TAAA-TTATTATTTTCATTTATATTGTAA
1 TAAATTTATTATTATAATTTAAATTGTAA
29882788 TAA
1 TAA
29882791 CAGATTTTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (29 bp):
TAAATTTATTATTATAATTTAAATTGTAA
Found at i:29883875 original size:81 final size:80
Alignment explanation
Indices: 29883738--29883889 Score: 295
Period size: 81 Copynumber: 1.9 Consensus size: 80
29883728 GCCTTTAAAT
29883738 ATCTTTATAATTAGGTTTTATTATTTTTTTAATTTTCCCCTTTAATTTATTTTAATTTCAATTTA
1 ATCTTTATAATTAGGTTTTATTATTTTTTTAATTTTCCCCTTTAATTTATTTTAATTTCAATTTA
29883803 ACCCTTTATGTGAAA
66 ACCCTTTATGTGAAA
29883818 ATNCTTTATAATTAGGTTTTATTATTTTTTTAATTTTCCCCTTTAATTTATTTTAATTTCAATTT
1 AT-CTTTATAATTAGGTTTTATTATTTTTTTAATTTTCCCCTTTAATTTATTTTAATTTCAATTT
29883883 AACCCTT
65 AACCCTT
29883890 CTTGAACGAC
Statistics
Matches: 71, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
80 2 0.03
81 69 0.97
ACGTcount: A:0.26, C:0.12, G:0.04, T:0.57
Consensus pattern (80 bp):
ATCTTTATAATTAGGTTTTATTATTTTTTTAATTTTCCCCTTTAATTTATTTTAATTTCAATTTA
ACCCTTTATGTGAAA
Found at i:29884605 original size:25 final size:25
Alignment explanation
Indices: 29884557--29884605 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
29884547 ATTACCTTTT
* *
29884557 TTATTTTTTTATTCATTTACTTATA
1 TTATTTTTTGATGCATTTACTTATA
29884582 TTATTTTTATGATGCATTTA-TTAT
1 TTATTTTT-TGATGCATTTACTTAT
29884606 TGTTATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.24, C:0.06, G:0.04, T:0.65
Consensus pattern (25 bp):
TTATTTTTTGATGCATTTACTTATA
Found at i:29887151 original size:31 final size:31
Alignment explanation
Indices: 29887108--29887172 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
29887098 AGCCAGCTGG
*
29887108 TGACAAAAAAAGATAA-A-ATTGAATAGTTGGA
1 TGACAAAAAAAGA-AATATACT-AATAGTTGGA
*
29887139 TGACCAAAAAAGAAATATACTAATAGTTGGA
1 TGACAAAAAAAGAAATATACTAATAGTTGGA
29887170 TGA
1 TGA
29887173 TAACTAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 2 0.07
31 26 0.87
32 2 0.07
ACGTcount: A:0.52, C:0.06, G:0.18, T:0.23
Consensus pattern (31 bp):
TGACAAAAAAAGAAATATACTAATAGTTGGA
Found at i:29890133 original size:12 final size:12
Alignment explanation
Indices: 29890086--29890144 Score: 52
Period size: 12 Copynumber: 4.9 Consensus size: 12
29890076 ACTTAATTAC
29890086 TTTAATATTAAA
1 TTTAATATTAAA
*
29890098 TTAAAT-TTAAAA
1 TTTAATATT-AAA
*
29890110 TTT-ATCTATAAA
1 TTTAATAT-TAAA
29890122 TATTAA-ATTAAA
1 T-TTAATATTAAA
29890134 TTTAATATTAA
1 TTTAATATTAA
29890145 GATAATCACT
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
11 8 0.21
12 25 0.66
13 4 0.11
14 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (12 bp):
TTTAATATTAAA
Found at i:29890483 original size:19 final size:19
Alignment explanation
Indices: 29890456--29890495 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
29890446 TTAGACCATC
*
29890456 AGTCTGATTTCACATAACA
1 AGTCCGATTTCACATAACA
*
29890475 AGTCCGATTTCACATAGCA
1 AGTCCGATTTCACATAACA
29890494 AG
1 AG
29890496 CCTGGTTCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.28
Consensus pattern (19 bp):
AGTCCGATTTCACATAACA
Found at i:29895368 original size:42 final size:42
Alignment explanation
Indices: 29895309--29895395 Score: 129
Period size: 42 Copynumber: 2.1 Consensus size: 42
29895299 TGTGGATGGT
* * *
29895309 TTTGTTTCCCATTTGGGATTTTTTGGGTATCTCAAGATTGCC
1 TTTGTTTCCCATTTGGGATATTTTGAGTATCCCAAGATTGCC
* *
29895351 TTTGTTTCCCGTTTGGGATATTTTGAGTATCCCAGGATTGCC
1 TTTGTTTCCCATTTGGGATATTTTGAGTATCCCAAGATTGCC
29895393 TTT
1 TTT
29895396 CTTGCTTGAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.14, C:0.17, G:0.22, T:0.47
Consensus pattern (42 bp):
TTTGTTTCCCATTTGGGATATTTTGAGTATCCCAAGATTGCC
Found at i:29897310 original size:40 final size:40
Alignment explanation
Indices: 29897235--29897377 Score: 141
Period size: 40 Copynumber: 3.6 Consensus size: 40
29897225 AGCACACCAG
* * *
29897235 TTTGGCACCCAGTGTCTCATCAGA-TAATTCTAAGTAATAA
1 TTTGACACCCAGTGTCTCATC-GACTAATCCAAAGTAATAA
* * *
29897275 TTTGACACCTAGTGTCTCATCGACTAAACCGAAGT-A-AA
1 TTTGACACCCAGTGTCTCATCGACTAATCCAAAGTAATAA
* * * *
29897313 -TTGGCACCCAGTGCCTCATCGAATTAATCCAAAGTAGTAA
1 TTTGACACCCAGTGTCTCATCG-ACTAATCCAAAGTAATAA
*
29897353 ATTGACACCCAGTGTCTCATCGACT
1 TTTGACACCCAGTGTCTCATCGACT
29897378 CGAAGTCGAA
Statistics
Matches: 83, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
37 18 0.22
38 12 0.14
39 3 0.04
40 31 0.37
41 19 0.23
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.28
Consensus pattern (40 bp):
TTTGACACCCAGTGTCTCATCGACTAATCCAAAGTAATAA
Found at i:29904115 original size:13 final size:13
Alignment explanation
Indices: 29904097--29904123 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29904087 TTTCGGTTTA
29904097 ATTTAAACAATAT
1 ATTTAAACAATAT
29904110 ATTTAAACAATAT
1 ATTTAAACAATAT
29904123 A
1 A
29904124 GTTGTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (13 bp):
ATTTAAACAATAT
Found at i:29905682 original size:23 final size:23
Alignment explanation
Indices: 29905647--29905691 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
29905637 CCTTATTTAA
**
29905647 TTCAAATTGATTAT-AATATTATC
1 TTCAAATAAATTATCAA-ATTATC
29905670 TTCAAATAAATTATCAAATTAT
1 TTCAAATAAATTATCAAATTAT
29905692 AAAATGACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (23 bp):
TTCAAATAAATTATCAAATTATC
Found at i:29908878 original size:29 final size:28
Alignment explanation
Indices: 29908845--29908931 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
29908835 TCATAAGAAC
29908845 ATTTTATGAAATTATATTTAATAATAATT
1 ATTTTAT-AAATTATATTTAATAATAATT
* * *
29908874 A-TTT-TAAATTGTATTAAATCAT-A-T
1 ATTTTATAAATTATATTTAATAATAATT
* *
29908898 ATTTTAATTAAAATATATTTAATATTAATT
1 ATTTT-A-TAAATTATATTTAATAATAATT
29908928 ATTT
1 ATTT
29908932 CAAATTTTCA
Statistics
Matches: 44, Mismatches: 8, Indels: 11
0.70 0.13 0.17
Matches are distributed among these distances:
24 2 0.05
25 4 0.09
26 14 0.32
27 1 0.02
28 16 0.36
29 2 0.05
30 5 0.11
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (28 bp):
ATTTTATAAATTATATTTAATAATAATT
Done.