Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008531.1 Hibiscus syriacus cultivar Beakdansim tig00111409_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: 3817888
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 19
Found at i:3648074 original size:117 final size:117
Alignment explanation
Indices: 3647868--3648194 Score: 564
Period size: 117 Copynumber: 2.8 Consensus size: 117
3647858 AAATGTTGAG
* *
3647868 CCAAGGTTGAACAAGTTATTCTCATTATTAAATTCTTCTCCCTCGTCGGATGAGTTCTTCTCATT
1 CCAAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAGTTCTTCTCATT
* *
3647933 ATGAACTCTCCATTGTAAATGTTGATCCACCTCCTTCTGTGATGGAATCGAA
66 ATGAACTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATGGAATCGAA
* *
3647985 CCAAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTCCTTCGTCGGATGAGTTCTTCTTATT
1 CCAAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAGTTCTTCTCATT
*
3648050 ATGAACTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATGGAATTGAA
66 ATGAACTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATGGAATCGAA
* *
3648102 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTTCGGATGAGTTCTTCTCATT
1 CCAAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAGTTCTTCTCATT
*
3648167 ATGAACTCTCCACTGGAAATGTTAATCC
66 ATGAACTCTCCACTGGAAATGTTGATCC
3648195 CTCGAGCAAG
Statistics
Matches: 198, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
117 198 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (117 bp):
CCAAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAGTTCTTCTCATT
ATGAACTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATGGAATCGAA
Found at i:3652984 original size:93 final size:93
Alignment explanation
Indices: 3652825--3652999 Score: 255
Period size: 93 Copynumber: 1.9 Consensus size: 93
3652815 ACAACATCCT
* * * *
3652825 AGTGGGTCGCCCATCCTTGGATTTCCCTAGTTCAAGCATGCTTAACCACACTGTTATAAAGAGAA
1 AGTGGGTCACCCATACTTGGATTTCCCTAGTCCAAGCACGCTTAACCACACTGTTATAAAGAGAA
3652890 TGGTCA-CATTTCCTTCTAACAACTTCAC
66 TGGTCACCA-TTCCTTCTAACAACTTCAC
* * *
3652918 AGTGGGTCACCCATACTTGGATTTCCCTAGTCCAAGCACGCTTAACCACA-TAGTTCTGAAGTGA
1 AGTGGGTCACCCATACTTGGATTTCCCTAGTCCAAGCACGCTTAACCACACT-GTTATAAAGAGA
3652982 ATGGTCACCATTCCTTCT
65 ATGGTCACCATTCCTTCT
3653000 TAAAACCAAT
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
92 1 0.01
93 70 0.96
94 2 0.03
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (93 bp):
AGTGGGTCACCCATACTTGGATTTCCCTAGTCCAAGCACGCTTAACCACACTGTTATAAAGAGAA
TGGTCACCATTCCTTCTAACAACTTCAC
Found at i:3653959 original size:450 final size:452
Alignment explanation
Indices: 3652918--3654056 Score: 1779
Period size: 450 Copynumber: 2.5 Consensus size: 452
3652908 ACAACTTCAC
* *
3652918 AGTGGGTCACCCATACTTGGATTTCCCTAGTCCAAGCACGCTTAACCACATAGTTCTGAAGTGAA
1 AGTGGGTCACCCATCCTTGGATTTCCCTAGTCCAAGCACGCTTAACCACAGAGTTCTGAAGTGAA
*
3652983 TGGTCACCATTCCTTCTTAAAACCAATTGGTGATAAGTAGGTGGGTTGGTAGGCCCTTTTAACCT
66 TGGTCACCATTCCTTCTTAAAACCAATTGGTGATAAGTA----GG-T-G--GGCCATTTTAACCT
* *
3653048 CATATCTTTGTAGTAGGTGATCACTAAGTTCCCTCAAGCCAAGGTGAATTCTTATGGGGCACCCC
123 CATATCTTTGTAGTAGGTGATCACTGAGTTCCCTCAAGCCAAGGTGGATTCTTATGGGGCACCCC
* * ** * *
3653113 CCATAGTTCACCACGCTATTACAGAGCGTCGCATCTATAACGTGCTGCGGGCGGGCCAAGTGGCT
188 CCACAGTTCACCACGGTATTACAGAGCCCCGCATCTATAACGTGCTACGAGCGGGCCAAGTGGCT
* * * *
3653178 TCGCAAGACACACGTGGGCCTCGGTAGGTTGGCCAGTTACGTACCGATATCGCGCTCATACACGA
253 TCGCAAGACACACATAGGCCTCGGCAGGTTGGCCAGTTACGCACCGATATCGCGCTCATACACGA
3653243 TAGAATCCCTAAGGGTGATCACTGGGCCCCATAACCCAACAATCACCCCCTCAGCGACACCTGGG
318 TAGAATCCCTAAGGGTGATCACTGGGCCCCATAACCCAACAATCACCCCCTCAGCGACACCTGGG
* * *
3653308 GGATTCGAACCTACAACATGTTCTGATATCAATTATTAGGATCGAGTCATTCATTTCTGAAGACC
383 GAATTCAAACCTACAACATCTTCTGATATCAATTATTAGGATCGAGTCATTCATTTCTGAAGACC
3653373 TTCCT
448 TTCCT
3653378 AGTGGGTCACCCATCCTTGGATTTCCCTAGTCCAAGCACGCTTAACCACAGAGTTCTGAAGTGAA
1 AGTGGGTCACCCATCCTTGGATTTCCCTAGTCCAAGCACGCTTAACCACAGAGTTCTGAAGTGAA
** * * *
3653443 TGGTCACCATTCCTTCTTAAAACCAATTACTAATAAGTATGTGGGCCATTTTAACCTTATATCTT
66 TGGTCACCATTCCTTCTTAAAACCAATTGGTGATAAGTAGGTGGGCCATTTTAACCTCATATCTT
* *
3653508 TGTAATAGGTGATCACTGAGTTCCCTCAAGCCAAGGTGGATTCTTGTGGGGCACCCCCCACAGTT
131 TGTAGTAGGTGATCACTGAGTTCCCTCAAGCCAAGGTGGATTCTTATGGGGCACCCCCCACAGTT
*
3653573 CACCACGGTATTACAGAGCCCCACATCTATAACGTGCTACGAGCGGGCCTAAG-GGCTAT-GCAA
196 CACCACGGTATTACAGAGCCCCGCATCTATAACGTGCTACGAGCGGGCC-AAGTGGCT-TCGCAA
* *
3653636 GGCACACATAGGCCTCGGCAGGTTGGGCAGTTACGCACCGATATCGCGCTCATACACGATAGAAT
259 GACACACATAGGCCTCGGCAGGTTGGCCAGTTACGCACCGATATCGCGCTCATACACGATAGAAT
** *
3653701 CCCTAAGGGTGATCGTTGGGCCCCATAACCCAACAATCA-CCCC-CAGCGACACCTTGGGAATTC
324 CCCTAAGGGTGATCACTGGGCCCCATAACCCAACAATCACCCCCTCAGCGACACCTGGGGAATTC
*
3653764 AAACCTACAACATCTTTTGATATCAATTATTAGGATCGAGTCATTCATTTCTGAAGACCTTCCT
389 AAACCTACAACATCTTCTGATATCAATTATTAGGATCGAGTCATTCATTTCTGAAGACCTTCCT
*
3653828 AGTGGGTCACCAATCCTTGGATTTCCCTAGTCCAAGCACGCTTAACCACAGAGTTCTGAAGTGAA
1 AGTGGGTCACCCATCCTTGGATTTCCCTAGTCCAAGCACGCTTAACCACAGAGTTCTGAAGTGAA
3653893 TGGTCACCATTCCTTCTTAAAACCAATTGGTGATAAGTAGGTGGGCCATTTTAACCTCATATCTT
66 TGGTCACCATTCCTTCTTAAAACCAATTGGTGATAAGTAGGTGGGCCATTTTAACCTCATATCTT
* * * *
3653958 TGTAGTGGGTGATCACTGAGTTCCCTTAAGCCAAGGTGGATTCTTTTAGGGCA---CCCACAGTT
131 TGTAGTAGGTGATCACTGAGTTCCCTCAAGCCAAGGTGGATTCTTATGGGGCACCCCCCACAGTT
* * *
3654020 CAGCACGGCATTGCAGAGCCCCGCATCTATAACGTGC
196 CACCACGGTATTACAGAGCCCCGCATCTATAACGTGC
3654057 CTTGGCAGGT
Statistics
Matches: 630, Mismatches: 47, Indels: 17
0.91 0.07 0.02
Matches are distributed among these distances:
447 42 0.07
450 251 0.40
451 4 0.01
452 227 0.36
453 4 0.01
454 1 0.00
455 1 0.00
456 1 0.00
460 99 0.16
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (452 bp):
AGTGGGTCACCCATCCTTGGATTTCCCTAGTCCAAGCACGCTTAACCACAGAGTTCTGAAGTGAA
TGGTCACCATTCCTTCTTAAAACCAATTGGTGATAAGTAGGTGGGCCATTTTAACCTCATATCTT
TGTAGTAGGTGATCACTGAGTTCCCTCAAGCCAAGGTGGATTCTTATGGGGCACCCCCCACAGTT
CACCACGGTATTACAGAGCCCCGCATCTATAACGTGCTACGAGCGGGCCAAGTGGCTTCGCAAGA
CACACATAGGCCTCGGCAGGTTGGCCAGTTACGCACCGATATCGCGCTCATACACGATAGAATCC
CTAAGGGTGATCACTGGGCCCCATAACCCAACAATCACCCCCTCAGCGACACCTGGGGAATTCAA
ACCTACAACATCTTCTGATATCAATTATTAGGATCGAGTCATTCATTTCTGAAGACCTTCCT
Found at i:3654857 original size:15 final size:15
Alignment explanation
Indices: 3654840--3654890 Score: 84
Period size: 15 Copynumber: 3.4 Consensus size: 15
3654830 ACTACTTAAG
* *
3654840 GGTTTTTTTTGAAAG
1 GGTTTTCTTTGAAAA
3654855 GGTTTTCTTTGAAAA
1 GGTTTTCTTTGAAAA
3654870 GGTTTTCTTTGAAAA
1 GGTTTTCTTTGAAAA
3654885 GGTTTT
1 GGTTTT
3654891 GTAATGTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.22, C:0.04, G:0.24, T:0.51
Consensus pattern (15 bp):
GGTTTTCTTTGAAAA
Found at i:3658156 original size:80 final size:78
Alignment explanation
Indices: 3658017--3658164 Score: 215
Period size: 80 Copynumber: 1.9 Consensus size: 78
3658007 TAATATTTTT
* * **
3658017 GGTAAAGCGCTACCTAAAATATTACTTTTCTACCGGAAATGTTAATATTGGGTGCTACCTAAAAT
1 GGTAAAGCGCTACCTAAAACATTACTTTTCTACCAGAAATGTTAATATTGGACGCTACCTAAAAT
3658082 GTTTAACATTTCC
66 GTTTAACATTTCC
* * *
3658095 GGTAAAGCGCTACCTAAAACATTATTTTTTTCTATCAGAAATGTTAATATTGGACGTTACCTAAA
1 GGTAAAGCGCTACCTAAAACATTA--CTTTTCTACCAGAAATGTTAATATTGGACGCTACCTAAA
3658160 ATGTT
64 ATGTT
3658165 ATTTTTTCTA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
78 23 0.38
80 38 0.62
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (78 bp):
GGTAAAGCGCTACCTAAAACATTACTTTTCTACCAGAAATGTTAATATTGGACGCTACCTAAAAT
GTTTAACATTTCC
Found at i:3658234 original size:20 final size:19
Alignment explanation
Indices: 3658192--3658235 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
3658182 TTAGTTAGTG
3658192 AAAT-TAACATTTCCAGTA
1 AAATATAACATTTCCAGTA
3658210 AAATATAACATTTCCAGTA
1 AAATATAACATTTCCAGTA
3658229 AAA-ATAA
1 AAATATAA
3658236 TGTTTTAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 8 0.32
19 17 0.68
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.30
Consensus pattern (19 bp):
AAATATAACATTTCCAGTA
Found at i:3659604 original size:70 final size:70
Alignment explanation
Indices: 3659489--3659671 Score: 176
Period size: 69 Copynumber: 2.6 Consensus size: 70
3659479 ACCTCTTAAA
* * * * * * * *
3659489 ATTTTCTGATTTAATTATTTTTTAAGATATTATCAGTTTTAAAATTAAATGAAATTAAATCT-TA
1 ATTTTGTGGTTTAATTATTTTTTAGGACATGATCAATTTTAAAATT-AATAAAATTAAATCTCAA
3659553 -CCTCT
65 TCCTCT
* * *
3659558 AACTTTTTTGGTTTAATTATTTTTTAGGACATGA-CAATTTTGAAATTAATAAAATTAAGTCTCA
1 -A-TTTTGTGGTTTAATTATTTTTTAGGACATGATCAATTTTAAAATTAATAAAATTAAATCTCA
3659622 ATCCTCT
64 ATCCTCT
* * *
3659629 ATTTTGTGGTTTAATTATCTTTTAGAACATTG-TTAATTTTAAA
1 ATTTTGTGGTTTAATTATTTTTTAGGACA-TGATCAATTTTAAA
3659672 GATAAGCAAT
Statistics
Matches: 93, Mismatches: 15, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
69 38 0.41
70 24 0.26
71 31 0.33
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.49
Consensus pattern (70 bp):
ATTTTGTGGTTTAATTATTTTTTAGGACATGATCAATTTTAAAATTAATAAAATTAAATCTCAAT
CCTCT
Found at i:3660772 original size:9 final size:9
Alignment explanation
Indices: 3660758--3660782 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3660748 ATTGATAATC
3660758 ATTTAAAAT
1 ATTTAAAAT
3660767 ATTTAAAAT
1 ATTTAAAAT
3660776 ATTTAAA
1 ATTTAAA
3660783 TTAATATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
ATTTAAAAT
Found at i:3662271 original size:2 final size:2
Alignment explanation
Indices: 3662264--3662290 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3662254 ATGTACGCGC
3662264 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 A
3662291 ATAAACATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3665993 original size:21 final size:21
Alignment explanation
Indices: 3665969--3666008 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3665959 TTTATTTTAT
3665969 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
3665990 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
3666009 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:3666056 original size:33 final size:33
Alignment explanation
Indices: 3666003--3666101 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
3665993 TTTGTTTCAA
3666003 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
3666035 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
3666068 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
3666101 T
1 T
3666102 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:3666130 original size:13 final size:13
Alignment explanation
Indices: 3666087--3666141 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
3666077 TTGGAAGTAT
3666087 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
3666100 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
3666114 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
3666127 TTAAGTATTTGAA
1 TTAAGTATTTCAA
3666140 TT
1 TT
3666142 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:3666363 original size:21 final size:21
Alignment explanation
Indices: 3666337--3666393 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
3666327 TGGAGCGTGG
*
3666337 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
3666358 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
3666379 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
3666394 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:3672391 original size:19 final size:18
Alignment explanation
Indices: 3672355--3672405 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 18
3672345 ACAAATTATT
3672355 AATAATTAATTCAATTTA
1 AATAATTAATTCAATTTA
* *
3672373 AATATATTAATTTACTTTA
1 AATA-ATTAATTCAATTTA
**
3672392 TTTAATTAATTCAA
1 AATAATTAATTCAA
3672406 AGTTTTTATA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (18 bp):
AATAATTAATTCAATTTA
Found at i:3672998 original size:12 final size:14
Alignment explanation
Indices: 3672980--3673016 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
3672970 ATTTAACTAT
3672980 TTAATTTTTTTTAA
1 TTAATTTTTTTTAA
*
3672994 -T-ATTTTATTTAA
1 TTAATTTTTTTTAA
3673006 TTAATTTTTTT
1 TTAATTTTTTT
3673017 GCAGTTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 4
0.76 0.08 0.16
Matches are distributed among these distances:
12 10 0.53
13 2 0.11
14 7 0.37
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTAATTTTTTTTAA
Found at i:3673000 original size:30 final size:30
Alignment explanation
Indices: 3672935--3673006 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
3672925 TCTTTAAGGT
*
3672935 ATATTTTA-TT-ATATTTAGTATTTTGTTA
1 ATATTTTATTTAATATTTAATATTTTGTTA
* *
3672963 GTATTTTATTTAACTATTTAAT-TTTTTTTA
1 ATATTTTATTTAA-TATTTAATATTTTGTTA
3672993 ATATTTTATTTAAT
1 ATATTTTATTTAAT
3673007 TAATTTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 7 0.19
29 3 0.08
30 20 0.54
31 7 0.19
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.65
Consensus pattern (30 bp):
ATATTTTATTTAATATTTAATATTTTGTTA
Found at i:3673003 original size:17 final size:18
Alignment explanation
Indices: 3672964--3673003 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
3672954 ATTTTGTTAG
3672964 TATTTTATTTAACTATTT
1 TATTTTATTTAACTATTT
* *
3672982 AATTTTTTTTAA-TATTT
1 TATTTTATTTAACTATTT
3672999 TATTT
1 TATTT
3673004 AATTAATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (18 bp):
TATTTTATTTAACTATTT
Found at i:3678881 original size:13 final size:13
Alignment explanation
Indices: 3678863--3678888 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3678853 ATCATATATA
3678863 ATTATAAAAAAAT
1 ATTATAAAAAAAT
3678876 ATTATAAAAAAAT
1 ATTATAAAAAAAT
3678889 TACCTTATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATTATAAAAAAAT
Found at i:3681507 original size:20 final size:20
Alignment explanation
Indices: 3681479--3681528 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
3681469 CTATCGCAAA
3681479 TTCGCGTTGCAATTTTCCAT
1 TTCGCGTTGCAATTTTCCAT
* **
3681499 TTTGCGTTGTGATTTTCCAT
1 TTCGCGTTGCAATTTTCCAT
3681519 TTCGCGTTGC
1 TTCGCGTTGC
3681529 GATAGTCCAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.10, C:0.22, G:0.20, T:0.48
Consensus pattern (20 bp):
TTCGCGTTGCAATTTTCCAT
Found at i:3681537 original size:20 final size:20
Alignment explanation
Indices: 3681479--3681555 Score: 57
Period size: 20 Copynumber: 3.8 Consensus size: 20
3681469 CTATCGCAAA
* **
3681479 TTCGCGTTGCAATTTTCCAT
1 TTCGCGTTGCGATAGTCCAT
* * **
3681499 TTTGCGTTGTGATTTTCCAT
1 TTCGCGTTGCGATAGTCCAT
*
3681519 TTCGCGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCC-AT
3681540 TT-GTCGTTGCGATAGT
1 TTCG-CGTTGCGATAGT
3681556 TTCCAAATTC
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
20 32 0.68
21 15 0.32
ACGTcount: A:0.14, C:0.19, G:0.23, T:0.43
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCCAT
Found at i:3681547 original size:21 final size:19
Alignment explanation
Indices: 3681523--3681617 Score: 82
Period size: 21 Copynumber: 4.6 Consensus size: 19
3681513 TTCCATTTCG
*
3681523 CGTTGCGATAGTCCAAGTTGT
1 CGTTGCGATAGTCCAA-AT-T
3681544 CGTTGCGATAGTTTCCAAATT
1 CGTTGCGATAG--TCCAAATT
**
3681565 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTC--CAAAT-T
**
3681587 CGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCCAAATT
3681606 CGTTGCGATAGT
1 CGTTGCGATAGT
3681618 AAAAAAAAGA
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
19 13 0.22
20 3 0.05
21 26 0.43
22 13 0.22
23 5 0.08
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCCAAATT
Found at i:3681610 original size:41 final size:41
Alignment explanation
Indices: 3681523--3681617 Score: 156
Period size: 41 Copynumber: 2.3 Consensus size: 41
3681513 TTCCATTTCG
3681523 CGTTGCGATAGTCCAAGTTGTCGTTGCGATAGTTTCCAAATT
1 CGTTGCGATAGTCCAAGTTGTCGTTGCGATA-TTTCCAAATT
*
3681565 CGTTGCGATAGTCTACAGTTGTCGTTGCGAT-TTTCCAAATT
1 CGTTGCGATAGTCCA-AGTTGTCGTTGCGATATTTCCAAATT
3681606 CGTTGCGATAGT
1 CGTTGCGATAGT
3681618 AAAAAAAAGA
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
41 22 0.43
42 14 0.27
43 15 0.29
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (41 bp):
CGTTGCGATAGTCCAAGTTGTCGTTGCGATATTTCCAAATT
Found at i:3682604 original size:6 final size:6
Alignment explanation
Indices: 3682595--3682625 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
3682585 CCGTCTCGTC
3682595 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
3682626 AATACGTGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:3682771 original size:19 final size:19
Alignment explanation
Indices: 3682749--3682796 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
3682739 ACTGTAGACT
*
3682749 ATCGCAACGAATTTGGACA
1 ATCGCAACGAATTTGGAAA
3682768 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
3682787 ATCGCAACGA
1 ATCGCAACGA
3682797 CAACTTGTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.19
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:3682857 original size:21 final size:21
Alignment explanation
Indices: 3682828--3682879 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
3682818 GAAATGAAAA
3682828 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
3682849 ATCGGAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
3682870 ATCGCAACGC
1 ATCGCAACGC
3682880 AAATTTGCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:3682927 original size:19 final size:20
Alignment explanation
Indices: 3682884--3682929 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
3682874 CAACGCAAAT
*
3682884 TTGCGATATTGGAGATCACA
1 TTGCGATATTAGAGATCACA
* *
3682904 ATGCGA-ATTAGAGATCGCA
1 TTGCGATATTAGAGATCACA
3682923 TTGCGAT
1 TTGCGAT
3682930 TTTATTGGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.28
Consensus pattern (20 bp):
TTGCGATATTAGAGATCACA
Found at i:3686434 original size:124 final size:123
Alignment explanation
Indices: 3686211--3686444 Score: 274
Period size: 124 Copynumber: 1.9 Consensus size: 123
3686201 AAATATTATG
* * * *
3686211 ATTATCACCATGAAACTGCAGACAGTCAAGAAAGTAAAGAAGTGGACTTTCCTTTTGTATACCAA
1 ATTAGCACCATGAAACTGCAGACAGTCAAGAAAG-AAAGAAGTGAAATGTCCTTTTGTATACCAA
* **
3686276 AAAACTAAACTACCCTTCAAAGCTATGACAATATCAAACCATTTGGTGAAACTCTGATA
65 AAAACTAAACTACCCATCAAAGAGATGACAATATCAAACCATTTGGTGAAACTCTGATA
* * * * *
3686335 ATTAGCACCATGAAAGTGCAGATAGTCTAGAAACG-AAGAATTGAAATGTCCTTTTGTATA-CTA
1 ATTAGCACCATGAAACTGCAGACAGTCAAGAAA-GAAAGAAGTGAAATGTCCTTTTGTATACCAA
* * * *
3686398 AAAACTCAAACTACCCATCACAGAAGATGACGATATCTAGCCATTTG
65 AAAACT-AAACTACCCATCAAAG-AGATGACAATATCAAACCATTTG
3686445 ATGGGAGTTT
Statistics
Matches: 91, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
122 8 0.09
123 35 0.38
124 47 0.52
125 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.26
Consensus pattern (123 bp):
ATTAGCACCATGAAACTGCAGACAGTCAAGAAAGAAAGAAGTGAAATGTCCTTTTGTATACCAAA
AAACTAAACTACCCATCAAAGAGATGACAATATCAAACCATTTGGTGAAACTCTGATA
Found at i:3687144 original size:2 final size:2
Alignment explanation
Indices: 3687137--3687163 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3687127 TATTTTTAGG
3687137 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 T
3687164 TATTTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3689135 original size:16 final size:16
Alignment explanation
Indices: 3689114--3689144 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3689104 TAATAAATAA
3689114 ACAAACATAAACGAAC
1 ACAAACATAAACGAAC
3689130 ACAAACATAAACGAA
1 ACAAACATAAACGAA
3689145 TAATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.23, G:0.06, T:0.06
Consensus pattern (16 bp):
ACAAACATAAACGAAC
Found at i:3689227 original size:10 final size:10
Alignment explanation
Indices: 3689212--3689270 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
3689202 CATTTAATAA
3689212 ATAAACGAAC
1 ATAAACGAAC
*
3689222 ATAAACAAAC
1 ATAAACGAAC
* *
3689232 AAAAAC-ATAA
1 ATAAACGA-AC
3689242 ATGAACACGAAC
1 AT-AA-ACGAAC
3689254 ATAAACGAAC
1 ATAAACGAAC
3689264 ATAAACG
1 ATAAACG
3689271 TTGGAGACCC
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
9 1 0.03
10 29 0.73
11 4 0.10
12 5 0.12
13 1 0.03
ACGTcount: A:0.63, C:0.19, G:0.08, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:3689248 original size:16 final size:16
Alignment explanation
Indices: 3689219--3689269 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
3689209 TAAATAAACG
*
3689219 AACATAAACAAACAAA
1 AACATAAACGAACAAA
* **
3689235 AACATAAATGAACACG
1 AACATAAACGAACAAA
*
3689251 AACATAAACGAACATA
1 AACATAAACGAACAAA
3689267 AAC
1 AAC
3689270 GTTGGAGACC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.65, C:0.20, G:0.06, T:0.10
Consensus pattern (16 bp):
AACATAAACGAACAAA
Found at i:3689253 original size:32 final size:30
Alignment explanation
Indices: 3689208--3689269 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 30
3689198 CGTTCATTTA
3689208 ATAAATAAACGAACATAAACAAACAAAAAC
1 ATAAATAAACGAACATAAACAAACAAAAAC
* *
3689238 ATAAATGAACACGAACATAAACGAACATAAAC
1 ATAAAT-AA-ACGAACATAAACAAACAAAAAC
3689270 GTTGGAGACC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 6 0.21
31 2 0.07
32 20 0.71
ACGTcount: A:0.65, C:0.18, G:0.06, T:0.11
Consensus pattern (30 bp):
ATAAATAAACGAACATAAACAAACAAAAAC
Found at i:3692622 original size:82 final size:82
Alignment explanation
Indices: 3692526--3692691 Score: 323
Period size: 82 Copynumber: 2.0 Consensus size: 82
3692516 CTACACATCA
*
3692526 CCAGTAAATCTCTAACTGTAGGAATAGGGTCTTACTTGTTCGGGCATTTCAGTATGCCATAGATT
1 CCAGTAAATCTCTAACTGCAGGAATAGGGTCTTACTTGTTCGGGCATTTCAGTATGCCATAGATT
3692591 CACCAAACTGCACATTT
66 CACCAAACTGCACATTT
3692608 CCAGTAAATCTCTAACTGCAGGAATAGGGTCTTACTTGTTCGGGCATTTCAGTATGCCATAGATT
1 CCAGTAAATCTCTAACTGCAGGAATAGGGTCTTACTTGTTCGGGCATTTCAGTATGCCATAGATT
3692673 CACCAAACTGCACATTT
66 CACCAAACTGCACATTT
3692690 CC
1 CC
3692692 TTTTTTCCAT
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 83 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (82 bp):
CCAGTAAATCTCTAACTGCAGGAATAGGGTCTTACTTGTTCGGGCATTTCAGTATGCCATAGATT
CACCAAACTGCACATTT
Found at i:3694197 original size:24 final size:24
Alignment explanation
Indices: 3694161--3694222 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
3694151 TATTAGGTTA
**
3694161 AACATAAATGAACGCACATAAACG
1 AACATAACCGAACGCACATAAACG
*
3694185 AACATAACCGAACGCATATAAACG
1 AACATAACCGAACGCACATAAACG
*
3694209 AACATAACGGAACG
1 AACATAACCGAACG
3694223 TTCACGAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.52, C:0.23, G:0.15, T:0.11
Consensus pattern (24 bp):
AACATAACCGAACGCACATAAACG
Found at i:3694453 original size:23 final size:23
Alignment explanation
Indices: 3694427--3694503 Score: 145
Period size: 23 Copynumber: 3.3 Consensus size: 23
3694417 TTAGTGTTAA
*
3694427 AAGTTAAACTAAATTACACTTCG
1 AAGTTACACTAAATTACACTTCG
3694450 AAGTTACACTAAATTACACTTCG
1 AAGTTACACTAAATTACACTTCG
3694473 AAGTTACACTAAATTACACTTCG
1 AAGTTACACTAAATTACACTTCG
3694496 AAGTTACA
1 AAGTTACA
3694504 TAATTATATG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (23 bp):
AAGTTACACTAAATTACACTTCG
Found at i:3694458 original size:13 final size:13
Alignment explanation
Indices: 3694440--3694503 Score: 68
Period size: 13 Copynumber: 5.4 Consensus size: 13
3694430 TTAAACTAAA
3694440 TTACACTTCGAAG
1 TTACACTTCGAAG
*
3694453 TTACAC-T--AAA
1 TTACACTTCGAAG
3694463 TTACACTTCGAAG
1 TTACACTTCGAAG
*
3694476 TTACAC-T--AAA
1 TTACACTTCGAAG
3694486 TTACACTTCGAAG
1 TTACACTTCGAAG
3694499 TTACA
1 TTACA
3694504 TAATTATATG
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
10 16 0.39
11 2 0.05
12 2 0.05
13 21 0.51
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (13 bp):
TTACACTTCGAAG
Found at i:3705207 original size:15 final size:15
Alignment explanation
Indices: 3705153--3705200 Score: 78
Period size: 15 Copynumber: 3.2 Consensus size: 15
3705143 AATTATCATT
3705153 TATTCACATAGAACA
1 TATTCACATAGAACA
* *
3705168 CATTCACATAAAACA
1 TATTCACATAGAACA
3705183 TATTCACATAGAACA
1 TATTCACATAGAACA
3705198 TAT
1 TAT
3705201 ACTCATAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.48, C:0.21, G:0.04, T:0.27
Consensus pattern (15 bp):
TATTCACATAGAACA
Found at i:3713071 original size:30 final size:29
Alignment explanation
Indices: 3713015--3713071 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
3713005 AATTTAGATA
*
3713015 GTGACCAAAATAAAAATTTTAAAAGTTTG
1 GTGACCAAAATAAAAATTTAAAAAGTTTG
* *
3713044 GTGACCAAAGTATAAACTTTAAAAAGTT
1 GTGACCAAAATA-AAAATTTAAAAAGTT
3713072 AAGGGACTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.30
Consensus pattern (29 bp):
GTGACCAAAATAAAAATTTAAAAAGTTTG
Found at i:3713561 original size:11 final size:11
Alignment explanation
Indices: 3713545--3713569 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3713535 TTTAATATTC
3713545 ATTAAAGGTAA
1 ATTAAAGGTAA
3713556 ATTAAAGGTAA
1 ATTAAAGGTAA
3713567 ATT
1 ATT
3713570 TAGCATGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (11 bp):
ATTAAAGGTAA
Found at i:3715899 original size:23 final size:23
Alignment explanation
Indices: 3715823--3715946 Score: 117
Period size: 23 Copynumber: 5.3 Consensus size: 23
3715813 TAAACTATCG
*
3715823 CGTAGAATT-TGCACCGAAGTACCA
1 CGTAGAATTGT-C-CCGAAGGACCA
* **
3715847 CGTAGAATATG-CACTGAAGTTCCA
1 CGTAGAAT-TGTC-CCGAAGGACCA
* * *
3715871 CATAGATTTGTCCCAAAGGACCA
1 CGTAGAATTGTCCCGAAGGACCA
3715894 CGTAGAATTGTCCCGAAGGACCA
1 CGTAGAATTGTCCCGAAGGACCA
* *
3715917 CGTAGAATTGTCCCGAATGACCG
1 CGTAGAATTGTCCCGAAGGACCA
3715940 CGTAGAA
1 CGTAGAA
3715947 CCCTTGACTC
Statistics
Matches: 84, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
23 57 0.68
24 26 0.31
25 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.21
Consensus pattern (23 bp):
CGTAGAATTGTCCCGAAGGACCA
Found at i:3716094 original size:15 final size:15
Alignment explanation
Indices: 3716049--3716096 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
3716039 AATTATCATT
*
3716049 TATTCACATAGAACA
1 TATTCACATAAAACA
*
3716064 CATTCACATAAAACA
1 TATTCACATAAAACA
*
3716079 TATTCACATATAACA
1 TATTCACATAAAACA
3716094 TAT
1 TAT
3716097 ACTCATAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.48, C:0.21, G:0.02, T:0.29
Consensus pattern (15 bp):
TATTCACATAAAACA
Found at i:3716103 original size:15 final size:15
Alignment explanation
Indices: 3716053--3716104 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
3716043 ATCATTTATT
* * *
3716053 CACATAGAACACATT
1 CACATAAAACATATA
*
3716068 CACATAAAACATATT
1 CACATAAAACATATA
*
3716083 CACATATAACATATA
1 CACATAAAACATATA
*
3716098 CTCATAA
1 CACATAA
3716105 TAATGAAATC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.50, C:0.23, G:0.02, T:0.25
Consensus pattern (15 bp):
CACATAAAACATATA
Found at i:3718586 original size:54 final size:54
Alignment explanation
Indices: 3718522--3718635 Score: 210
Period size: 54 Copynumber: 2.1 Consensus size: 54
3718512 AGATTTCATG
*
3718522 AATATGCATTCTTACAATTTAATCATAACATTTCAATATGCATGTATATATTTT
1 AATATGCATTCTTACAATTTAATCATAACATTTCAATATGCATGTATATATTTC
*
3718576 AATATGCATTCTTACCATTTAATCATAACATTTCAATATGCATGTATATATTTC
1 AATATGCATTCTTACAATTTAATCATAACATTTCAATATGCATGTATATATTTC
3718630 AATATG
1 AATATG
3718636 ACATATATAT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (54 bp):
AATATGCATTCTTACAATTTAATCATAACATTTCAATATGCATGTATATATTTC
Found at i:3718630 original size:20 final size:21
Alignment explanation
Indices: 3718605--3718647 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
3718595 TAATCATAAC
*
3718605 ATTTCAATATG-CATGTATAT
1 ATTTCAATATGACATATATAT
3718625 ATTTCAATATGACATATATAT
1 ATTTCAATATGACATATATAT
3718646 AT
1 AT
3718648 ACATCATGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (21 bp):
ATTTCAATATGACATATATAT
Found at i:3718854 original size:38 final size:38
Alignment explanation
Indices: 3718802--3718897 Score: 129
Period size: 38 Copynumber: 2.5 Consensus size: 38
3718792 CTCGTATAAA
* *
3718802 TGTCCCGAGGGACCTATCATCCCAAAGGATGTCATATG
1 TGTCCCGAAGGACCTATCATCCCAAAGGATGTAATATG
* * * *
3718840 TGTCCCGAAAGACCTGTCATCCCGAAGGATGTAATCTG
1 TGTCCCGAAGGACCTATCATCCCAAAGGATGTAATATG
*
3718878 TGTCCCGTAGGACCTATCAT
1 TGTCCCGAAGGACCTATCAT
3718898 ATGTCTTATA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (38 bp):
TGTCCCGAAGGACCTATCATCCCAAAGGATGTAATATG
Found at i:3719102 original size:46 final size:46
Alignment explanation
Indices: 3719046--3719158 Score: 187
Period size: 46 Copynumber: 2.5 Consensus size: 46
3719036 ATGTGTAACC
3719046 ATGT-ATTTCATATCATATCACATGTATCACGTATTACATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
*
3719091 ATGTCATTTCATATCATATCACATGTATCACGTATTGCATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
*
3719137 ATATCATTTCATAT-A-ATCACAT
1 ATGTCATTTCATATCATATCACAT
3719159 AGCTTATCTC
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
44 7 0.11
45 5 0.08
46 53 0.82
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.42
Consensus pattern (46 bp):
ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
Found at i:3719593 original size:34 final size:36
Alignment explanation
Indices: 3719547--3719616 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
3719537 TTCATTTAGG
3719547 GGGGAATAGATA-CCCCCA-GGGGGAATCTGTTCCC
1 GGGGAATAGATACCCCCCAGGGGGGAATCTGTTCCC
*
3719581 GGGGAATCGATACCCCCCAGGGGGGAATCTGTTCCC
1 GGGGAATAGATACCCCCCAGGGGGGAATCTGTTCCC
3719617 CCTGTACATA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
34 11 0.33
35 6 0.18
36 16 0.48
ACGTcount: A:0.21, C:0.29, G:0.33, T:0.17
Consensus pattern (36 bp):
GGGGAATAGATACCCCCCAGGGGGGAATCTGTTCCC
Found at i:3722475 original size:2 final size:2
Alignment explanation
Indices: 3722468--3722494 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3722458 TGCCTTAATC
3722468 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 A
3722495 GGATCCACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3723050 original size:2 final size:2
Alignment explanation
Indices: 3723043--3723067 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3723033 ATCAAATTAT
3723043 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
3723068 TCCAATGATA
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:3724757 original size:34 final size:34
Alignment explanation
Indices: 3724718--3724794 Score: 154
Period size: 34 Copynumber: 2.3 Consensus size: 34
3724708 AGATTTCATG
3724718 AATATGCATTCTTACCATTTAATCATAACATTTC
1 AATATGCATTCTTACCATTTAATCATAACATTTC
3724752 AATATGCATTCTTACCATTTAATCATAACATTTC
1 AATATGCATTCTTACCATTTAATCATAACATTTC
3724786 AATATGCAT
1 AATATGCAT
3724795 GTATATATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.36, C:0.19, G:0.04, T:0.40
Consensus pattern (34 bp):
AATATGCATTCTTACCATTTAATCATAACATTTC
Found at i:3724806 original size:20 final size:21
Alignment explanation
Indices: 3724781--3724823 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
3724771 TAATCATAAC
*
3724781 ATTTCAATATG-CATGTATAT
1 ATTTCAATATGACATATATAT
3724801 ATTTCAATATGACATATATAT
1 ATTTCAATATGACATATATAT
3724822 AT
1 AT
3724824 ACATCATGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (21 bp):
ATTTCAATATGACATATATAT
Found at i:3725029 original size:38 final size:38
Alignment explanation
Indices: 3724978--3725074 Score: 131
Period size: 38 Copynumber: 2.6 Consensus size: 38
3724968 CTCGTATAAA
* * * *
3724978 TGTCCCGAGGGACCTATCATCCCGAAGGATGTCATATG
1 TGTCCCGAAGGACCTATCATACCGAAGGATATAATATG
* *
3725016 TGTCCCGAAGGACCTGTCATACCGAAGGATATAATCTG
1 TGTCCCGAAGGACCTATCATACCGAAGGATATAATATG
*
3725054 TGTCCCGTAGGACCTATCATA
1 TGTCCCGAAGGACCTATCATA
3725075 TGTCTTATAG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.25
Consensus pattern (38 bp):
TGTCCCGAAGGACCTATCATACCGAAGGATATAATATG
Found at i:3725278 original size:46 final size:46
Alignment explanation
Indices: 3725222--3725334 Score: 187
Period size: 46 Copynumber: 2.5 Consensus size: 46
3725212 AAGTGTAACC
3725222 ATGT-ATTTCATATCATATCACATGTATCACGTATTACATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
*
3725267 ATGTCATTTCATATCATATCACATGTATCACGTATTGCATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
*
3725313 ATATCATTTCATAT-A-ATCACAT
1 ATGTCATTTCATATCATATCACAT
3725335 AGCTTATCTC
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
44 7 0.11
45 5 0.08
46 53 0.82
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.42
Consensus pattern (46 bp):
ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
Found at i:3731560 original size:17 final size:17
Alignment explanation
Indices: 3731535--3731591 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 17
3731525 ACTGTTGAAA
* *
3731535 CACTTAGTGCATCGGTG
1 CACTAAGTGCATCGATG
3731552 CACTAAGTGTGCATCGATG
1 CACTAA--GTGCATCGATG
3731571 CACTAAGTGTGCATCGATG
1 CACTAA--GTGCATCGATG
3731590 CA
1 CA
3731592 TAAAATGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.14
19 31 0.86
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (17 bp):
CACTAAGTGCATCGATG
Found at i:3731565 original size:19 final size:19
Alignment explanation
Indices: 3731541--3731591 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
3731531 GAAACACTTA
*
3731541 GTGCATCGGTGCACTAAGT
1 GTGCATCGATGCACTAAGT
3731560 GTGCATCGATGCACTAAGT
1 GTGCATCGATGCACTAAGT
3731579 GTGCATCGATGCA
1 GTGCATCGATGCA
3731592 TAAAATGCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (19 bp):
GTGCATCGATGCACTAAGT
Found at i:3731721 original size:20 final size:20
Alignment explanation
Indices: 3731685--3731722 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3731675 CAATTTATTC
*
3731685 ATTGGTGCATTGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
3731705 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
3731723 CCCTTTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.13, G:0.34, T:0.34
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:3734327 original size:27 final size:25
Alignment explanation
Indices: 3734262--3734311 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 25
3734252 GGTAAACATA
3734262 TATATATACATATACAAAAAAAATCG
1 TATA-ATACATATACAAAAAAAATCG
*
3734288 TATAAAACATATACAAAATAAAAT
1 TATAATACATATACAAAA-AAAAT
3734312 ACTGGTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.62, C:0.10, G:0.02, T:0.26
Consensus pattern (25 bp):
TATAATACATATACAAAAAAAATCG
Found at i:3741726 original size:20 final size:20
Alignment explanation
Indices: 3741701--3741740 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3741691 GAAAAAAGAT
3741701 TTATGATTTTCTTATGTTAA
1 TTATGATTTTCTTATGTTAA
3741721 TTATGATTTTCTTATGTTAA
1 TTATGATTTTCTTATGTTAA
3741741 AAACCCTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.05, G:0.10, T:0.60
Consensus pattern (20 bp):
TTATGATTTTCTTATGTTAA
Found at i:3742006 original size:14 final size:14
Alignment explanation
Indices: 3741987--3742016 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3741977 TGTGTAATAT
*
3741987 ATATATGTTTGCTG
1 ATATATGTTTACTG
3742001 ATATATGTTTACTG
1 ATATATGTTTACTG
3742015 AT
1 AT
3742017 TGCAGAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.50
Consensus pattern (14 bp):
ATATATGTTTACTG
Found at i:3742147 original size:15 final size:15
Alignment explanation
Indices: 3742086--3742148 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
3742076 ATAATATATG
3742086 TGATAATATGTTTA-
1 TGATAATATGTTTAC
* *
3742100 AGAATGATATGTTTAC
1 TG-ATAATATGTTTAC
3742116 TGAT--TATGTGTT-C
1 TGATAATATGT-TTAC
*
3742129 TGATAATATGTTTAT
1 TGATAATATGTTTAC
3742144 TGATA
1 TGATA
3742149 GAATTATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
13 10 0.26
14 5 0.13
15 23 0.59
16 1 0.03
ACGTcount: A:0.32, C:0.03, G:0.17, T:0.48
Consensus pattern (15 bp):
TGATAATATGTTTAC
Found at i:3742191 original size:18 final size:18
Alignment explanation
Indices: 3742170--3742227 Score: 59
Period size: 17 Copynumber: 3.3 Consensus size: 18
3742160 TTATTAATGT
3742170 TATGTTTTTTATAGAATA
1 TATGTTTTTTATAGAATA
* *
3742188 TATG-TTCTGATAGAAT-
1 TATGTTTTTTATAGAATA
*
3742204 TAT-TTGTTTTATAAAATA
1 TATGTT-TTTTATAGAATA
3742222 TATGTT
1 TATGTT
3742228 CTGATATGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
16 4 0.13
17 18 0.58
18 7 0.23
19 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (18 bp):
TATGTTTTTTATAGAATA
Found at i:3742202 original size:17 final size:17
Alignment explanation
Indices: 3742180--3742233 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
3742170 TATGTTTTTT
3742180 ATAGAATATATGTTCTG
1 ATAGAATATATGTTCTG
* *
3742197 ATAGAATTATTTGTT-TT
1 ATAGAA-TATATGTTCTG
*
3742214 ATAAAATATATGTTCTG
1 ATAGAATATATGTTCTG
3742231 ATA
1 ATA
3742234 TGTTTATTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
16 7 0.23
17 16 0.53
18 7 0.23
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (17 bp):
ATAGAATATATGTTCTG
Found at i:3742311 original size:18 final size:18
Alignment explanation
Indices: 3742267--3742312 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
3742257 TATTAATAGA
3742267 ATATATGTTGTGATAGAAT
1 ATATATGTT-TGATAGAAT
*
3742286 -TATTTGTTTGCAT-GAAT
1 ATATATGTTTG-ATAGAAT
3742303 ATATATGTTT
1 ATATATGTTT
3742313 TGTATGAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.50
Consensus pattern (18 bp):
ATATATGTTTGATAGAAT
Found at i:3743955 original size:20 final size:20
Alignment explanation
Indices: 3743930--3743967 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3743920 GACATGTTAA
3743930 AGAATGCATCGATACACTGT
1 AGAATGCATCGATACACTGT
* *
3743950 AGAATGTATCGATGCACT
1 AGAATGCATCGATACACT
3743968 TCAAGGGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATACACTGT
Found at i:3744796 original size:32 final size:32
Alignment explanation
Indices: 3744755--3744846 Score: 98
Period size: 32 Copynumber: 2.9 Consensus size: 32
3744745 AGTCGAGGGT
3744755 TTACCTATGTTCTAAGGAACATATGGACAAAA
1 TTACCTATGTTCTAAGGAACATATGGACAAAA
*** * **
3744787 TTACCTATG-TCTTTCGAGACATATGGATAGTA
1 TTACCTATGTTCTAAGGA-ACATATGGACAAAA
*
3744819 -TAACTATGTTCTAAGGAACATATGGACA
1 TTACCTATGTTCTAAGGAACATATGGACA
3744847 GTTTACCTAG
Statistics
Matches: 47, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
31 22 0.47
32 25 0.53
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (32 bp):
TTACCTATGTTCTAAGGAACATATGGACAAAA
Found at i:3744861 original size:31 final size:31
Alignment explanation
Indices: 3744753--3744880 Score: 114
Period size: 31 Copynumber: 4.1 Consensus size: 31
3744743 AGAGTCGAGG
3744753 GTTTACCTATGTTCTAAGGAACATATGGACAA
1 GTTTACCTATGTTCTAAGGAACATATGGAC-A
** *** *
3744785 AATTACCTATG-TCTTTCGAGACATATGGATA
1 GTTTACCTATGTTCTAAGGA-ACATATGGACA
* *
3744816 GTATAACTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTAAGGAACATATGGACA
* ** * *
3744847 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTAAGGAACATATGGACA
3744878 GTT
1 GTT
3744881 GCCGAGGTTC
Statistics
Matches: 73, Mismatches: 21, Indels: 5
0.74 0.21 0.05
Matches are distributed among these distances:
31 50 0.68
32 23 0.32
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.33
Consensus pattern (31 bp):
GTTTACCTATGTTCTAAGGAACATATGGACA
Found at i:3744900 original size:30 final size:31
Alignment explanation
Indices: 3744839--3744905 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
3744829 CTAAGGAACA
* *
3744839 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAGTTTACCGAGGTTCTTCAGGACC
* * *
3744870 TATGGACAG-TTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTTACCGAGGTTCTTCAGGACC
3744900 TATGGA
1 TATGGA
3744906 TAGGTCCTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 22 0.71
31 9 0.29
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (31 bp):
TATGGACAGTTTACCGAGGTTCTTCAGGACC
Found at i:3745818 original size:54 final size:54
Alignment explanation
Indices: 3745735--3746185 Score: 548
Period size: 54 Copynumber: 8.4 Consensus size: 54
3745725 TTCGTTAGGG
* * * * * *
3745735 TGCACACGTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCCGTAGGA
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCTGTGGGT
* * * * * *
3745789 TACACATTTAGTGTTGATATGGTTGTTCATAAACACATTATGAATT-TCGTGGGT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCT-GTGGGT
* *
3745843 TGCACACTTAGTGTCGATACGATCATTCATAAACATATTATGAATTCTGTGGGT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCTGTGGGT
* * * * * *
3745897 TGCACACTTGGTGTCGATACGGTCATTCATAAATATGTTATGAATTTTGTGGTT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCTGTGGGT
* * *
3745951 TGCACACTTAGTGCCGATACGGTCGTTCATAAACATGTTATGAATTATGTGGGT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCTGTGGGT
** * *
3746005 TGCACACTTAGTACCGATACGGTGGTTCATAAACATATTATGAATTTTGTGGGT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCTGTGGGT
** *
3746059 TGCACACTTAGTGTCGATATAGTCGTTCATAAACATATTATGAATTCCGTGGGT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCTGTGGGT
* * *
3746113 TGCACACTTAGTGCCGATA-GGATCATTCATAAACATATTATGAATT-TCGTGGTT
1 TGCACACTTAGTGTCGATACGG-TCGTTCATAAACATATTATGAATTCT-GTGGGT
*
3746167 TGCACACTTAATGTCGATA
1 TGCACACTTAGTGTCGATA
3746186 GTACACATAG
Statistics
Matches: 343, Mismatches: 50, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
53 1 0.00
54 341 0.99
55 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (54 bp):
TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCTGTGGGT
Found at i:3748215 original size:45 final size:45
Alignment explanation
Indices: 3748160--3748259 Score: 137
Period size: 45 Copynumber: 2.2 Consensus size: 45
3748150 CTAAACATAA
* *
3748160 TGAACCTGAAATTGATGAACCAGAACCAGTTGAGCCATAAATCAG
1 TGAACCTGAAATTAATGAACCAGAACCAGCTGAGCCATAAATCAG
* * * * *
3748205 TGAACTTGAAATTAATGAACTAGAATCAGCTGAGCCATAAATTAA
1 TGAACCTGAAATTAATGAACCAGAACCAGCTGAGCCATAAATCAG
3748250 TGAACCTGAA
1 TGAACCTGAA
3748260 CCAGCTGAGC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (45 bp):
TGAACCTGAAATTAATGAACCAGAACCAGCTGAGCCATAAATCAG
Found at i:3748285 original size:30 final size:31
Alignment explanation
Indices: 3748212--3748285 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 31
3748202 CAGTGAACTT
*
3748212 GAAATTAATGAA-CTAGAATCAGCTGAGCCA
1 GAAATTAATGAACCTAGAACCAGCTGAGCCA
* *
3748242 TAAATTAATGAACCT-GAACCAGCTGAGCTA
1 GAAATTAATGAACCTAGAACCAGCTGAGCCA
3748272 GAAATTAATGAACC
1 GAAATTAATGAACC
3748286 CGAAATTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 37 0.95
31 2 0.05
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.22
Consensus pattern (31 bp):
GAAATTAATGAACCTAGAACCAGCTGAGCCA
Found at i:3748291 original size:75 final size:75
Alignment explanation
Indices: 3748167--3748330 Score: 195
Period size: 75 Copynumber: 2.2 Consensus size: 75
3748157 TAATGAACCT
* * * * ** *
3748167 GAAATTGATGAACCAGAACCAGTTGAGCCATAAATCAGTGAACTTGAAATTAATGAA-CTAGAAT
1 GAAATTAATGAACCAGAACCAGCTGAGCCAGAAATCAATGAACCCGAAATTAATGAATC-AGAAC
3748231 CAGCTGAGCCA
65 CAGCTGAGCCA
* * * *
3748242 TAAATTAATGAACCTGAACCAGCTGAGCTAGAAATTAATGAACCCGAAATTAATGAATCAGAACC
1 GAAATTAATGAACCAGAACCAGCTGAGCCAGAAATCAATGAACCCGAAATTAATGAATCAGAACC
*
3748307 AGCTGATCCA
66 AGCTGAGCCA
*
3748317 GAAATTAATTAACC
1 GAAATTAATGAACC
3748331 CAAAGTTAAT
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
75 73 0.99
76 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.22
Consensus pattern (75 bp):
GAAATTAATGAACCAGAACCAGCTGAGCCAGAAATCAATGAACCCGAAATTAATGAATCAGAACC
AGCTGAGCCA
Found at i:3748292 original size:45 final size:44
Alignment explanation
Indices: 3748243--3748358 Score: 151
Period size: 45 Copynumber: 2.6 Consensus size: 44
3748233 GCTGAGCCAT
* *
3748243 AAATTAATGAACCTGAACCAGCTGAGCTAGAAATTAATGAACCC
1 AAATTAATGAACCAGAACCAGCTGAGCCAGAAATTAATGAACCC
* * *
3748287 GAAATTAATGAATCAGAACCAGCTGATCCAGAAATTAATTAACCC
1 -AAATTAATGAACCAGAACCAGCTGAGCCAGAAATTAATGAACCC
* *
3748332 AAAGTTAATGAACCGGAACCTGCTGAG
1 AAA-TTAATGAACCAGAACCAGCTGAG
3748359 GTGAGGATAT
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 3 0.05
45 58 0.95
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.21
Consensus pattern (44 bp):
AAATTAATGAACCAGAACCAGCTGAGCCAGAAATTAATGAACCC
Found at i:3750250 original size:26 final size:26
Alignment explanation
Indices: 3750212--3750274 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
3750202 AACTTGCTAA
*
3750212 TACATATTATTCATGCATAGTGTTAT
1 TACATATTGTTCATGCATAGTGTTAT
* *
3750238 TACATATTGTTCATTCATATTGTTAT
1 TACATATTGTTCATGCATAGTGTTAT
* *
3750264 TGCATAGTGTT
1 TACATATTGTT
3750275 ATTACATATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.27, C:0.11, G:0.13, T:0.49
Consensus pattern (26 bp):
TACATATTGTTCATGCATAGTGTTAT
Found at i:3750282 original size:26 final size:26
Alignment explanation
Indices: 3750227--3750385 Score: 173
Period size: 26 Copynumber: 6.0 Consensus size: 26
3750217 ATTATTCATG
* *
3750227 CATAGTGTTATTACATATTGTTCATT-
1 CATATTGTTATTGCATATTGTT-ATTA
*
3750253 CATATTGTTATTGCATAGTGTTATTA
1 CATATTGTTATTGCATATTGTTATTA
3750279 CATATTGTTCA-TGCATATTGTTATTA
1 CATATTGTT-ATTGCATATTGTTATTA
3750305 CATATTGTTCA-TGCATATTGTTATTA
1 CATATTGTT-ATTGCATATTGTTATTA
* *
3750331 CATATTGGAATACTTGAAT-TTGTTATTA
1 CATATT-G-TTA-TTGCATATTGTTATTA
3750359 CATAACTTGTTATTGCATATTGTTATT
1 CAT-A-TTGTTATTGCATATTGTTATT
3750386 GTGTTAATGC
Statistics
Matches: 116, Mismatches: 8, Indels: 16
0.83 0.06 0.11
Matches are distributed among these distances:
25 3 0.03
26 74 0.64
27 8 0.07
28 23 0.20
29 6 0.05
30 2 0.02
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.50
Consensus pattern (26 bp):
CATATTGTTATTGCATATTGTTATTA
Found at i:3750386 original size:13 final size:13
Alignment explanation
Indices: 3750225--3750386 Score: 143
Period size: 13 Copynumber: 12.2 Consensus size: 13
3750215 ATATTATTCA
*
3750225 TGCATAGTGTTAT
1 TGCATATTGTTAT
*
3750238 TACATATTGTTCAT
1 TGCATATTGTT-AT
3750252 T-CATATTGTTAT
1 TGCATATTGTTAT
*
3750264 TGCATAGTGTTAT
1 TGCATATTGTTAT
*
3750277 TACATATTGTTCA-
1 TGCATATTGTT-AT
3750290 TGCATATTGTTAT
1 TGCATATTGTTAT
*
3750303 TACATATTGTTCA-
1 TGCATATTGTT-AT
3750316 TGCATATTGTTAT
1 TGCATATTGTTAT
* *
3750329 TACATATTGGAATACT
1 TGCATATT-G-TTA-T
*
3750345 TGAAT-TTGTTAT
1 TGCATATTGTTAT
*
3750357 TACATAACTTGTTAT
1 TGCAT-A-TTGTTAT
3750372 TGCATATTGTTAT
1 TGCATATTGTTAT
3750385 TG
1 TG
3750387 TGTTAATGCT
Statistics
Matches: 121, Mismatches: 16, Indels: 24
0.75 0.10 0.15
Matches are distributed among these distances:
12 9 0.07
13 85 0.70
14 8 0.07
15 15 0.12
16 4 0.03
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49
Consensus pattern (13 bp):
TGCATATTGTTAT
Found at i:3751135 original size:16 final size:16
Alignment explanation
Indices: 3751095--3751128 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3751085 TTATTGCATT
*
3751095 TTTTAGATTTAATTTG
1 TTTTAGATTAAATTTG
3751111 TTTTAGATTAAATTTG
1 TTTTAGATTAAATTTG
3751127 TT
1 TT
3751129 ATTGATTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.62
Consensus pattern (16 bp):
TTTTAGATTAAATTTG
Found at i:3755701 original size:105 final size:105
Alignment explanation
Indices: 3755532--3755758 Score: 271
Period size: 105 Copynumber: 2.2 Consensus size: 105
3755522 CTGACAGAGT
* * ** * ** * * *
3755532 TACCTTGAATCAAGGGTACTATGGGACTGGACATTTATCTAATTGTATGGACTCTTGAAGCTTGG
1 TACCTTGACTCAAGGGTACAATGGGACTGGACATCCATATAACAGTATAGACCCTTAAAGCTTGG
*
3755597 TTTGTTATTGGAGCTTCCT-AACGATTCTGACTAG-CATAAC
66 TTTGTTATTGGAGCTT-CTAAACGATTCTGA-TAGACACAAC
*
3755637 TACCTTGACTCAAGGGTACAATGGGACTGGGCATCCATATAACAGTATAGACCCTTAAAGCTTGG
1 TACCTTGACTCAAGGGTACAATGGGACTGGACATCCATATAACAGTATAGACCCTTAAAGCTTGG
* * *
3755702 TTTGTTGTTGGAGCTTCTAAACGATTTTGATTGACACAAC
66 TTTGTTATTGGAGCTTCTAAACGATTCTGATAGACACAAC
*
3755742 TACC-CGACTCAAGGGTA
1 TACCTTGACTCAAGGGTA
3755759 TATTGAGGTC
Statistics
Matches: 104, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
104 16 0.15
105 88 0.85
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (105 bp):
TACCTTGACTCAAGGGTACAATGGGACTGGACATCCATATAACAGTATAGACCCTTAAAGCTTGG
TTTGTTATTGGAGCTTCTAAACGATTCTGATAGACACAAC
Found at i:3758508 original size:24 final size:24
Alignment explanation
Indices: 3758481--3758526 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
3758471 TAAACACTCA
3758481 CATGAACCTTAGTTTTTCCTCTCG
1 CATGAACCTTAGTTTTTCCTCTCG
*
3758505 CATGAACTTTAGTTTTTCCTCT
1 CATGAACCTTAGTTTTTCCTCT
3758527 TGCAGTTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.17, C:0.26, G:0.11, T:0.46
Consensus pattern (24 bp):
CATGAACCTTAGTTTTTCCTCTCG
Found at i:3760502 original size:22 final size:22
Alignment explanation
Indices: 3760468--3760515 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
3760458 TTTCGTTTAT
* *
3760468 AAAACATTTAATTCACTTTAAAA
1 AAAACATTAAATTAAC-TTAAAA
*
3760491 AAAACA-TAAATTAACTTAAAT
1 AAAACATTAAATTAACTTAAAA
3760512 AAAA
1 AAAA
3760516 TAACAAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 9 0.41
22 7 0.32
23 6 0.27
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAACATTAAATTAACTTAAAA
Found at i:3760782 original size:2 final size:2
Alignment explanation
Indices: 3760775--3760800 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3760765 AATGAAATCA
3760775 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
3760801 CATTATTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3760983 original size:52 final size:53
Alignment explanation
Indices: 3760916--3761032 Score: 155
Period size: 52 Copynumber: 2.2 Consensus size: 53
3760906 TCCCATATTT
*
3760916 TGCACACATAATGCCGAAAATGTTATTCATCCACAT-GACGAATTCCGTGAAA
1 TGCACACATAATGCCGAAAAGGTTATTCATCCACATAGACGAATTCCGTGAAA
* * * * *
3760968 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCTGTGAAA
1 TGCACACATAATGCCGAAAAGGTTATTCATCCACATA-GACGAATTCCGTGAAA
*
3761022 TGCACATATAA
1 TGCACACATAA
3761033 CAGCCTCAAC
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
52 32 0.59
54 22 0.41
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.26
Consensus pattern (53 bp):
TGCACACATAATGCCGAAAAGGTTATTCATCCACATAGACGAATTCCGTGAAA
Found at i:3761866 original size:66 final size:64
Alignment explanation
Indices: 3761794--3761917 Score: 169
Period size: 66 Copynumber: 1.9 Consensus size: 64
3761784 ATTGTTCAAG
* * *
3761794 GTGTATCGATGCACATGAAGTGTATCGATGCACTCC-TTTAAAATAAAAAAACATCGAATGCCAT
1 GTGTATCGATGCACAAGAAGTGCATCGATGCAC-CCGCTTAAAAT--AAAAACATCGAATGCCAT
3761858 CA
63 CA
* *
3761860 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCGCTTAAAATACAAACATCGAATG
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCGCTTAAAATAAAAACATCGAATG
3761918 GGATTTATGT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
64 13 0.25
65 2 0.04
66 37 0.71
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (64 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCACCCGCTTAAAATAAAAACATCGAATGCCATCA
Found at i:3769406 original size:18 final size:18
Alignment explanation
Indices: 3769383--3769443 Score: 104
Period size: 18 Copynumber: 3.4 Consensus size: 18
3769373 AGGGATTATC
* *
3769383 AGTGGTCTTTCGGGACAT
1 AGTGGTCCTTCAGGACAT
3769401 AGTGGTCCTTCAGGACAT
1 AGTGGTCCTTCAGGACAT
3769419 AGTGGTCCTTCAGGACAT
1 AGTGGTCCTTCAGGACAT
3769437 AGTGGTC
1 AGTGGTC
3769444 ATTCGGGATA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTCAGGACAT
Found at i:3770058 original size:54 final size:54
Alignment explanation
Indices: 3769980--3770425 Score: 649
Period size: 54 Copynumber: 8.3 Consensus size: 54
3769970 GGGTGTTACA
* * * *
3769980 GCACACTTAATTCCGAAATGGTTATTCATCCACATAAGATGAATTCCGTGAAAT
1 GCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAAT
* * ** *
3770034 GCACTCTTAGTGTCGAAACGGTTATTCATCTGCATATGATGAATTCCGTGAAAT
1 GCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAAT
* * *
3770088 ACACACTTAGTGCCGAAACGATTATTCATCCACATATGATGAATTCCGTGAAAT
1 GCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAAT
* *
3770142 GCACACTTAGTGCCAAAACAGTTATTCATCCACATAGGATGAATTCCGTGAAAT
1 GCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAAT
* * * *
3770196 GCACAATTAGTGCCTAAACGATTATTCATCCACATAGGATGAATTCCATGAAAT
1 GCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAAT
* * *
3770250 GCACACTTAGTGTCGAAACGGTTATTCATCCACATAGGATGAATTTCGTGAATT
1 GCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAAT
* * * *
3770304 GCACACTTAGTGCCAAAACGCTTATACATTCACATAGGATGAATTCCGTGAAAT
1 GCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAAT
* *
3770358 GCACACTTAGTGTCGAAATGGTTATTCATCCACATAGGATGAATTCCGTGAAAT
1 GCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAAT
3770412 GCACACTTAGTGCC
1 GCACACTTAGTGCC
3770426 TATTTGGTAA
Statistics
Matches: 347, Mismatches: 45, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 347 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (54 bp):
GCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAAT
Found at i:3770906 original size:19 final size:19
Alignment explanation
Indices: 3770841--3770914 Score: 71
Period size: 19 Copynumber: 3.7 Consensus size: 19
3770831 CGATGTTACC
3770841 TGGTATCGATACCTTAACT-A
1 TGGTATCGATACCTT--CTCA
*
3770861 TGGTATCGATA-CTAGCATACTA
1 TGGTATCGATACCT-TC-T-C-A
3770883 TGGTATCGATACCTTCTCA
1 TGGTATCGATACCTTCTCA
3770902 TGGTATCGATACC
1 TGGTATCGATACC
3770915 ATTTTTGCAT
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
18 1 0.02
19 17 0.37
20 12 0.26
21 1 0.02
22 13 0.28
23 2 0.04
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (19 bp):
TGGTATCGATACCTTCTCA
Found at i:3770963 original size:20 final size:20
Alignment explanation
Indices: 3770938--3770987 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
3770928 GTTTCAAAAT
3770938 GGTATCGATACCTT-CCCTTC
1 GGTATCGATA-CTTCCCCTTC
*
3770958 GGTATCGATACTTCCCCTTT
1 GGTATCGATACTTCCCCTTC
*
3770978 GGTATTGATA
1 GGTATCGATA
3770988 TTGATTGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 3 0.11
20 24 0.89
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.38
Consensus pattern (20 bp):
GGTATCGATACTTCCCCTTC
Found at i:3777268 original size:54 final size:54
Alignment explanation
Indices: 3777158--3777602 Score: 561
Period size: 54 Copynumber: 8.3 Consensus size: 54
3777148 TTTTGTATTT
* * * * *
3777158 TGCACACATAGTGCCAAAACGATTATTCAT--TCATAGGATAAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * *
3777210 TGCACACTTAGTGCTGAAACGGTTATTCATCCATATAGGATAAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * *
3777264 TGCACACTTAGTACCGAAACGGTTATTCATCCACATATGATGAATTCCATGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * * * * *
3777318 TGCACATTTAGTGCTGAAACGATTATCCATCCACATAGGATGAATTACATAAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
** * * * *
3777372 TGCGTACTAAGTGCCGAAACGGTTATTCATTCACATGGGATGAAATCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
** * * *
3777426 TGCACACTTAGTGCCGAAACGGTTATTTTTCCACATATGATGAATTTCTTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
**
3777480 TGCACACTTAGTGTTGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * *
3777534 TGCACACTTAGTGTCGAAATGGTTATTTATCCACATAGGATGAATTTCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
3777588 TGCACACTTAGTGCC
1 TGCACACTTAGTGCC
3777603 TAATTGGTAA
Statistics
Matches: 335, Mismatches: 56, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
52 26 0.08
54 309 0.92
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Consensus pattern (54 bp):
TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
Found at i:3777949 original size:20 final size:21
Alignment explanation
Indices: 3777921--3777979 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 21
3777911 ATTTATGGCT
*
3777921 CCATAGTATCGATACCCT-TA
1 CCATGGTATCGATACCCTATA
* *
3777941 CCATGGTATTGATACTACTATA
1 CCATGGTATCGATAC-CCTATA
* *
3777963 CTATGGTACCGATACCC
1 CCATGGTATCGATACCC
3777980 CCTTCCGGTA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 13 0.43
21 3 0.10
22 14 0.47
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.31
Consensus pattern (21 bp):
CCATGGTATCGATACCCTATA
Found at i:3778141 original size:20 final size:19
Alignment explanation
Indices: 3778116--3778185 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 19
3778106 GTTTCAAAAT
*
3778116 GGTATCGATACCTTCCCTTC
1 GGTATCGATA-CTCCCCTTC
*
3778136 GGTATCGATACTCCCCATTT
1 GGTATCGATACTCCCC-TTC
*
3778156 GGTATCAATACTCCCCCTTC
1 GGTATCGATACT-CCCCTTC
3778176 GGTATCGATA
1 GGTATCGATA
3778186 TTGATTGAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
19 5 0.12
20 34 0.79
21 4 0.09
ACGTcount: A:0.20, C:0.31, G:0.16, T:0.33
Consensus pattern (19 bp):
GGTATCGATACTCCCCTTC
Found at i:3780136 original size:43 final size:43
Alignment explanation
Indices: 3780053--3780138 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 43
3780043 TCGATTTTAC
* * **
3780053 AGTAATATCACCAATAAATCAAACCATGTTTTGGAGAAAGTAT
1 AGTAATATCACCAACAAATCAAACCATGTATTAAAGAAAGTAT
* * * *
3780096 AGTAATATCACTAACAGATCAAACCTTGTATTAAATAAAGTAT
1 AGTAATATCACCAACAAATCAAACCATGTATTAAAGAAAGTAT
3780139 CTTTTATGAG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (43 bp):
AGTAATATCACCAACAAATCAAACCATGTATTAAAGAAAGTAT
Found at i:3780951 original size:21 final size:21
Alignment explanation
Indices: 3780925--3780967 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
3780915 TGGAAAAAAT
*
3780925 ATATTTATAAT-ATTTTTATAA
1 ATATTTAGAATAATTTTT-TAA
3780946 ATATTTAGAATAATTTTTTAA
1 ATATTTAGAATAATTTTTTAA
3780967 A
1 A
3780968 ACTTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
ATATTTAGAATAATTTTTTAA
Found at i:3781778 original size:54 final size:55
Alignment explanation
Indices: 3781577--3781976 Score: 517
Period size: 55 Copynumber: 7.3 Consensus size: 55
3781567 TTATGTGTAC
* *
3781577 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATAAGTTGATGAATAACTG
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
* **
3781632 TACAGACACTATGTGTGCAAATCCACATAATTCATCATGAGTTGATGAATAACCG
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
* **
3781687 TACAGGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAGTCG
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
* * * *
3781742 TACA-TCACTATGTGTTCAAATCCATGGAATTGATCATGAGTTGATGAATAACCG
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
* * *
3781796 TACAGGCACTATGTGTGC-AACCCACAGG-ATTCACCATTAGTTGATGAATAACCG
1 TACAGGCACTATGTGTGCAAATCCAC-GGAATTCATCATGAGTTGATGAATAACCG
* * *
3781850 TACATGCAGTATGTGTGCAAACCCAC-GAGATTCATCATGAGTTGATGAATAACCG
1 TACAGGCACTATGTGTGCAAATCCACGGA-ATTCATCATGAGTTGATGAATAACCG
* * * *
3781905 TACAGGCATTATGTGTGC-AACCCACGGAATTCATTATGAGTTGATGAAT-TCCG
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
*
3781958 TATAGGCACTACT-TGTGCA
1 TACAGGCACTA-TGTGTGCA
3781977 TTATAATAAA
Statistics
Matches: 303, Mismatches: 34, Indels: 17
0.86 0.10 0.05
Matches are distributed among these distances:
53 18 0.06
54 119 0.39
55 166 0.55
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (55 bp):
TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
Found at i:3781809 original size:109 final size:106
Alignment explanation
Indices: 3781577--3781953 Score: 477
Period size: 109 Copynumber: 3.5 Consensus size: 106
3781567 TTATGTGTAC
* * * *
3781577 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATAAGTTGATGAATAACTGTACAGACACT
1 TACAGGCACTATGTGTGC-AACCCACGAAATTCATCATGAGTTGATGAATAAC-GTACA-TCACT
*
3781642 ATGTGTGCAAATCCACATAATTCATCATGAGTTGATGAATAACCG
63 ATGTGTGCAAATCCA-AGAATTCATCATGAGTTGATGAATAACCG
* *
3781687 TACAGGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAGTCGTACATCACTA
1 TACAGGCACTATGTGTGC-AACCCACGAAATTCATCATGAGTTGATGAATA-ACGTACATCACTA
* * *
3781752 TGTGTTCAAATCCATGGAATTGATCATGAGTTGATGAATAACCG
64 TGTGTGCAAATCCA-AGAATTCATCATGAGTTGATGAATAACCG
* * * *
3781796 TACAGGCACTATGTGTGCAACCCAC-AGGATTCACCATTAGTTGATGAATAACCGTACATGCAGT
1 TACAGGCACTATGTGTGCAACCCACGA-AATTCATCATGAGTTGATGAATAA-CGTACAT-CACT
* *
3781860 ATGTGTGCAAACCCACGAGATTCATCATGAGTTGATGAATAACCG
63 ATGTGTGCAAATCCAAGA-ATTCATCATGAGTTGATGAATAACCG
* * *
3781905 TACAGGCATTATGTGTGCAACCCACGGAATTCATTATGAGTTGATGAAT
1 TACAGGCACTATGTGTGCAACCCACGAAATTCATCATGAGTTGATGAAT
3781954 TCCGTATAGG
Statistics
Matches: 236, Mismatches: 25, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
107 1 0.00
108 35 0.15
109 145 0.61
110 54 0.23
111 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (106 bp):
TACAGGCACTATGTGTGCAACCCACGAAATTCATCATGAGTTGATGAATAACGTACATCACTATG
TGTGCAAATCCAAGAATTCATCATGAGTTGATGAATAACCG
Found at i:3782842 original size:20 final size:19
Alignment explanation
Indices: 3782813--3782850 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
3782803 GGAGAAAAAA
3782813 GAAAGAAGAAGAAAGATAG
1 GAAAGAAGAAGAAAGATAG
3782832 GAAAGGAAGAAGAAAGATA
1 GAAA-GAAGAAGAAAGATA
3782851 TAAAAGGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.63, C:0.00, G:0.32, T:0.05
Consensus pattern (19 bp):
GAAAGAAGAAGAAAGATAG
Found at i:3782856 original size:20 final size:20
Alignment explanation
Indices: 3782817--3782857 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3782807 AAAAAAGAAA
*
3782817 GAAGAAGAAAGATAGGAAAG
1 GAAGAAGAAAGATAGAAAAG
*
3782837 GAAGAAGAAAGATATAAAAG
1 GAAGAAGAAAGATAGAAAAG
3782857 G
1 G
3782858 CAATTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.32, T:0.07
Consensus pattern (20 bp):
GAAGAAGAAAGATAGAAAAG
Found at i:3782929 original size:14 final size:13
Alignment explanation
Indices: 3782905--3782935 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
3782895 AATTAATTTA
3782905 TATTATATTAAAT
1 TATTATATTAAAT
3782918 TATTATTATTAAAT
1 TATTA-TATTAAAT
3782932 TATT
1 TATT
3782936 GTTGTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TATTATATTAAAT
Found at i:3783142 original size:145 final size:128
Alignment explanation
Indices: 3782919--3783272 Score: 381
Period size: 145 Copynumber: 2.6 Consensus size: 128
3782909 ATATTAAATT
* * *
3782919 ATTATTATTAAATTATTGTTGTTTAAAAAATTAAATTTTTACATATTTATTTGAAGAAATAAAGT
1 ATTA-TATTAAATTATTGTTGTTTAAAAAATTAAATTTTTACAGATTCATTTGAAGAAAGAAAG-
*
3782984 AAATGAAGAAGAAAGAAATATGAAAGTATTTTTAAATTTTCTGTAGTTGTGTAAATTAGTTAGTT
64 AAATGAAGAAGAAAGAAATACG-AAG-----TT--ATTTTCTGTAGTTGTGT-AA--A-TTAGTT
*
3783049 AGTTAGTTAGTTTAG
117 AG-T--TTAGTTTAA
* *
3783064 ATTATATTAAATTATAGTTGTTTAAAAAATTAAATTGTTTAGAGATTCATTTGAAGAAAGAAATG
1 ATTATATTAAATTATTGTTGTTTAAAAAATTAAATT-TTTACAGATTCATTTGAAGAAAGAAA-G
* * *
3783129 AAAGGAAGAAGAAAGAAATACGAAGTTATTTTTTGTTGTTGTGTAAATTAGTTAGTTTAGTTTAA
64 AAATGAAGAAGAAAGAAATACGAAGTTATTTTCTGTAGTTGTGTAAATTAGTTAGTTTAGTTTAA
* **
3783194 ATTATATTAAATTATTTTTGTTT---AAATTATTTTTTTACAGATTCATTTGAAGAAAGAAAGGA
1 ATTATATTAAATTATTGTTGTTTAAAAAATTAAATTTTTACAGATTCATTTGAAGAAAGAAA-GA
*
3783256 AATGAAGAAAAAAGAAA
65 AATGAAGAAGAAAGAAA
3783273 ATAAAGGAAA
Statistics
Matches: 189, Mismatches: 18, Indels: 23
0.82 0.08 0.10
Matches are distributed among these distances:
126 42 0.22
127 8 0.04
130 29 0.15
132 1 0.01
133 8 0.04
134 1 0.01
136 2 0.01
137 15 0.08
139 2 0.01
144 34 0.18
145 46 0.24
146 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.15, T:0.41
Consensus pattern (128 bp):
ATTATATTAAATTATTGTTGTTTAAAAAATTAAATTTTTACAGATTCATTTGAAGAAAGAAAGAA
ATGAAGAAGAAAGAAATACGAAGTTATTTTCTGTAGTTGTGTAAATTAGTTAGTTTAGTTTAA
Found at i:3783263 original size:17 final size:16
Alignment explanation
Indices: 3783241--3783274 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3783231 CAGATTCATT
*
3783241 TGAAGAAAGAAAGGAAA
1 TGAAGAAA-AAAGAAAA
3783258 TGAAGAAAAAAGAAAA
1 TGAAGAAAAAAGAAAA
3783274 T
1 T
3783275 AAAGGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.09
Consensus pattern (16 bp):
TGAAGAAAAAAGAAAA
Found at i:3783296 original size:20 final size:20
Alignment explanation
Indices: 3783242--3783297 Score: 58
Period size: 25 Copynumber: 2.5 Consensus size: 20
3783232 AGATTCATTT
*
3783242 GAAGAAAGAAAGGAAATGAA
1 GAAGAAATAAAGGAAATGAA
3783262 GAAAAAAGAAAATAAAGGAAATGAA
1 G----AAG-AAATAAAGGAAATGAA
3783287 GAAGAAATAAA
1 GAAGAAATAAA
3783298 TACGAAGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
20 8 0.27
21 3 0.10
24 3 0.10
25 16 0.53
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (20 bp):
GAAGAAATAAAGGAAATGAA
Found at i:3783561 original size:20 final size:20
Alignment explanation
Indices: 3783536--3783576 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3783526 TCATTTCATT
3783536 TAAAGGTCTTAACCTTTCAA
1 TAAAGGTCTTAACCTTTCAA
3783556 TAAAGGTCTTAACCTTTCAA
1 TAAAGGTCTTAACCTTTCAA
3783576 T
1 T
3783577 CCTCTCCCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.37
Consensus pattern (20 bp):
TAAAGGTCTTAACCTTTCAA
Found at i:3788578 original size:52 final size:52
Alignment explanation
Indices: 3788519--3789124 Score: 1059
Period size: 52 Copynumber: 11.7 Consensus size: 52
3788509 TTCGCTCTCT
* * *
3788519 TTTTCTTCAGGGAGTAGAACTCGAACGATAATCTTCCTACGAGACTGCCCAA
1 TTTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGTCTGCCCAA
* *
3788571 TTTTCTTCAGGGACTAGAACTCAAACAATAATCTTCCTACGAGACTGCCCAA
1 TTTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGTCTGCCCAA
* *
3788623 TTTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGTCCAA
1 TTTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGTCTGCCCAA
3788675 TTTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGTCTGCCCAA
1 TTTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGTCTGCCCAA
* *
3788727 TTTTCTTCAAGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAA
1 TTTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGTCTGCCCAA
3788779 TTTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGTCTGCCCAA
1 TTTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGTCTGCCCAA
** *
3788831 TTTTCTTCAAAGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAA
1 TTTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGTCTGCCCAA
*
3788883 TTTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAA
1 TTTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGTCTGCCCAA
* *
3788935 TTTTCTTCAGGGACTAGAACTTGAACAATAATCTTCCTACGGGTCTGCCCAA
1 TTTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGTCTGCCCAA
*
3788987 TTTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAA
1 TTTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGTCTGCCCAA
*
3789039 TTTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAA
1 TTTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGTCTGCCCAA
3789091 TTTTCTTCAGGGACTAGAACTCGAACAATAATCT
1 TTTTCTTCAGGGACTAGAACTCGAACAATAATCT
3789125 CCAACGATCG
Statistics
Matches: 532, Mismatches: 22, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 532 1.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (52 bp):
TTTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGTCTGCCCAA
Found at i:3789179 original size:55 final size:55
Alignment explanation
Indices: 3789120--3789399 Score: 456
Period size: 55 Copynumber: 5.1 Consensus size: 55
3789110 CTCGAACAAT
*
3789120 AATCTCCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* *
3789175 AATCTTCAACAATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
*
3789230 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGA-TC-CAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * *
3789283 AATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAT
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * *
3789338 AATCTTCAACGATCGCGTCTGCCCCCAATTTATTCATAGAGTATAAGACTCGAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
3789393 AATCTTC
1 AATCTTC
3789400 TTTTGCTTCA
Statistics
Matches: 207, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
53 48 0.23
54 4 0.02
55 155 0.75
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (55 bp):
AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
Found at i:3789329 original size:108 final size:110
Alignment explanation
Indices: 3789120--3789399 Score: 474
Period size: 108 Copynumber: 2.6 Consensus size: 110
3789110 CTCGAACAAT
*
3789120 AATCTCCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
3789185 AATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
66 AATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
* *
3789230 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGA-TC-CACAATCTTCATC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
* *
3789293 AATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAT
66 AATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
* * *
3789338 AATCTTCAACGATCGCGTCTGCCCCCAATTTATTCATAGAGTATAAGACTCGAACAATCTTC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTC
3789400 TTTTGCTTCA
Statistics
Matches: 159, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
108 99 0.62
109 4 0.03
110 56 0.35
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (110 bp):
AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
AATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
Found at i:3790564 original size:7 final size:7
Alignment explanation
Indices: 3790552--3790635 Score: 66
Period size: 7 Copynumber: 11.7 Consensus size: 7
3790542 TGAACCCCCC
3790552 TTTTATT
1 TTTTATT
3790559 TTTTATTT
1 TTTTA-TT
*
3790567 TTTTTTT
1 TTTTATT
*
3790574 CTTCTTCTT
1 -TT-TTATT
3790583 TTTTATT
1 TTTTATT
3790590 TTTT-TT
1 TTTTATT
*
3790596 ATTT-TT
1 TTTTATT
*
3790602 TTTCATTT
1 TTTTA-TT
3790610 TTTTCATT
1 TTTT-ATT
3790618 TTTTA-T
1 TTTTATT
3790624 TTTTATT
1 TTTTATT
3790631 TTTTA
1 TTTTA
3790636 AGCAAAACCC
Statistics
Matches: 63, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
6 15 0.24
7 22 0.35
8 21 0.33
9 5 0.08
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTATT
Found at i:3790571 original size:9 final size:9
Alignment explanation
Indices: 3790552--3790635 Score: 69
Period size: 10 Copynumber: 8.6 Consensus size: 9
3790542 TGAACCCCCC
3790552 TTTTATTTTT
1 TTTTA-TTTT
*
3790562 TATTTTTTTT
1 T-TTTATTTT
*
3790572 TTCTTCTTCTT
1 TT-TTATT-TT
3790583 TTTTATTTT
1 TTTTATTTT
3790592 TTTTATTTT
1 TTTTATTTT
3790601 TTTTCATTTT
1 TTTT-ATTTT
*
3790611 TTTCATTTT
1 TTTTATTTT
*
3790620 TTATTTTTATT
1 TT-TTATT-TT
3790631 TTTTA
1 TTTTA
3790636 AGCAAAACCC
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
9 23 0.38
10 27 0.44
11 11 0.18
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTATTTT
Found at i:3791763 original size:3 final size:3
Alignment explanation
Indices: 3791749--3791783 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
3791739 GTACCAAGGC
3791749 CTT CTAT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CT-T CTT CTT CTT CTT CTT CTT CTT CTT CTT C
3791784 AATGGGTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:3802084 original size:20 final size:20
Alignment explanation
Indices: 3802059--3802099 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3802049 TCATTTCATT
3802059 TAAAGGTCTTAACCTTTCAA
1 TAAAGGTCTTAACCTTTCAA
3802079 TAAAGGTCTTAACCTTTCAA
1 TAAAGGTCTTAACCTTTCAA
3802099 T
1 T
3802100 CCTCTCCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.37
Consensus pattern (20 bp):
TAAAGGTCTTAACCTTTCAA
Found at i:3804978 original size:22 final size:22
Alignment explanation
Indices: 3804948--3804994 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 22
3804938 GTTGCCCAGA
*
3804948 ATAGAGGAAATCGGTACCCCTTC
1 ATAGAGG-AATCGATACCCCTTC
3804971 ATAG-GGAATCGATACCCCTTC
1 ATAGAGGAATCGATACCCCTTC
3804992 ATA
1 ATA
3804995 ATATTCAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.74
22 2 0.09
23 4 0.17
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (22 bp):
ATAGAGGAATCGATACCCCTTC
Found at i:3805068 original size:20 final size:21
Alignment explanation
Indices: 3805029--3805070 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3805019 GCTGTTGAAC
3805029 AGGGGGGAATCGGTACCCCCT
1 AGGGGGGAATCGGTACCCCCT
3805050 AGGGGGGAATCGGTACCCCCT
1 AGGGGGGAATCGGTACCCCCT
3805071 GGACATTCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.29, G:0.38, T:0.14
Consensus pattern (21 bp):
AGGGGGGAATCGGTACCCCCT
Found at i:3805131 original size:20 final size:20
Alignment explanation
Indices: 3805106--3805168 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
3805096 AAAACCTGCA
3805106 GGGGGGTATCTGTACCCCCT
1 GGGGGGTATCTGTACCCCCT
3805126 GGGGGGTATCTGTACCCCCT
1 GGGGGGTATCTGTACCCCCT
* *
3805146 GGGGGGAATCTATACCCCCT
1 GGGGGGTATCTGTACCCCCT
3805166 GGG
1 GGG
3805169 CAATCTTGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.13, C:0.29, G:0.37, T:0.22
Consensus pattern (20 bp):
GGGGGGTATCTGTACCCCCT
Found at i:3805290 original size:29 final size:31
Alignment explanation
Indices: 3805258--3805317 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
3805248 AAACTTTGAA
3805258 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
3805287 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
3805318 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:3805502 original size:22 final size:22
Alignment explanation
Indices: 3805477--3805522 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
3805467 AAGCTCCCCC
3805477 TTTTCATTAAGAAATTGAATTT
1 TTTTCATTAAGAAATTGAATTT
*
3805499 TTTTTATTAAGAAATTGAATTT
1 TTTTCATTAAGAAATTGAATTT
3805521 TT
1 TT
3805523 CAAACTAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.54
Consensus pattern (22 bp):
TTTTCATTAAGAAATTGAATTT
Found at i:3807542 original size:34 final size:32
Alignment explanation
Indices: 3807488--3807557 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
3807478 ACCTTACAAC
* *
3807488 TCCCTAGTTTTTCCGGGCTAAACTATAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
3807520 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
3807554 TCCC
1 TCCC
3807558 CTTTATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.21, C:0.31, G:0.14, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:3807796 original size:20 final size:22
Alignment explanation
Indices: 3807771--3807810 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3807761 AGTCGTATAT
3807771 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
3807791 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
3807811 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:3807862 original size:21 final size:21
Alignment explanation
Indices: 3807838--3807880 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3807828 CCCAGAATAG
*
3807838 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
*
3807859 AGGGAATCGATACCCTTTCAT
1 AGGGAATCGATACCCCTTCAT
3807880 A
1 A
3807881 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:3807953 original size:19 final size:20
Alignment explanation
Indices: 3807916--3807957 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
3807906 CTGTTGAACA
3807916 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
3807936 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
3807956 GG
1 GG
3807958 ACATTCTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.29, G:0.43, T:0.14
Consensus pattern (20 bp):
GGGGGGAATCGGTACCCCCT
Found at i:3808012 original size:15 final size:15
Alignment explanation
Indices: 3807992--3808021 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3807982 AAACCTGCAG
*
3807992 GGGGTATCTGTACCC
1 GGGGTAACTGTACCC
3808007 GGGGTAACTGTACCC
1 GGGGTAACTGTACCC
3808022 CCTGGGGGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.27, G:0.33, T:0.23
Consensus pattern (15 bp):
GGGGTAACTGTACCC
Found at i:3808205 original size:34 final size:29
Alignment explanation
Indices: 3808137--3808196 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
3808127 AAACTTTGAA
*
3808137 TAAATTCAATTAAGTCCAAAAATATTTTG
1 TAAATTCAATTAAGTCCAAAAACATTTTG
3808166 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
3808197 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATTTTG
Found at i:3810705 original size:28 final size:28
Alignment explanation
Indices: 3810686--3810756 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
3810676 AAGCGTTGAC
*
3810686 TCGACGACATAATGTTTTAAGTAATACT
1 TCGACGACATAATGTTTTAAGCAATACT
* *
3810714 TTGACGACATAATGTTTTAAGCAGTACT
1 TCGACGACATAATGTTTTAAGCAATACT
* *
3810742 TTGATGACATAATGT
1 TCGACGACATAATGT
3810757 CAATGGAGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.37
Consensus pattern (28 bp):
TCGACGACATAATGTTTTAAGCAATACT
Done.