Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009149.1 Hibiscus syriacus cultivar Beakdansim tig00112673_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: 1143513
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 1 of 6
Found at i:3805 original size:21 final size:22
Alignment explanation
Indices: 3775--3815 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3765 TTAGGATCAA
*
3775 TGGGATTAGGAATAGGATTTTG
1 TGGGATTAGGAAGAGGATTTTG
*
3797 TGGGA-TAGGAGGAGGATTT
1 TGGGATTAGGAAGAGGATTT
3816 ACAGGAGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.27, C:0.00, G:0.41, T:0.32
Consensus pattern (22 bp):
TGGGATTAGGAAGAGGATTTTG
Found at i:11398 original size:75 final size:75
Alignment explanation
Indices: 11271--11449 Score: 241
Period size: 75 Copynumber: 2.4 Consensus size: 75
11261 ACCGGTTAAC
** * * * ** * *
11271 ATAAAATAGATGCTACCTATTATGTTAAACTACCTACTGATTTATTTGAAGGTTACTAATATTGT
1 ATAAAATAGGCGCTACCTATTACGTTAAAATACATACCAATTTATTTAAAGGTTACTAATAATGT
**
11336 AAACGGTAAA
66 AAACAATAAA
*
11346 ATAAAATAGGCGCTACCTATTACGTTAAAATACATACCAATTTGTTTAAAGGTTACTAATAATGT
1 ATAAAATAGGCGCTACCTATTACGTTAAAATACATACCAATTTATTTAAAGGTTACTAATAATGT
11411 AAACAATAAA
66 AAACAATAAA
*
11421 AGAAAATAGGCGCTACCTATTACGTTAAA
1 ATAAAATAGGCGCTACCTATTACGTTAAA
11450 TAGGCACTAC
Statistics
Matches: 91, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 91 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (75 bp):
ATAAAATAGGCGCTACCTATTACGTTAAAATACATACCAATTTATTTAAAGGTTACTAATAATGT
AAACAATAAA
Found at i:11454 original size:23 final size:23
Alignment explanation
Indices: 11424--11474 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
11414 CAATAAAAGA
*
11424 AAATAGGCGCTACCTATTACGTT
1 AAATAGGCACTACCTATTACGTT
*
11447 AAATAGGCACTACTTATTACGTT
1 AAATAGGCACTACCTATTACGTT
11470 AAATA
1 AAATA
11475 AGCGTTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (23 bp):
AAATAGGCACTACCTATTACGTT
Found at i:11485 original size:23 final size:23
Alignment explanation
Indices: 11424--11495 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
11414 CAATAAAAGA
* * *
11424 AAATAGGCGCTACCTATTACGTT
1 AAATAAGCACTACTTATTACGTT
*
11447 AAATAGGCACTACTTATTACGTT
1 AAATAAGCACTACTTATTACGTT
** * *
11470 AAATAAGCGTTTCTTATTGCGTT
1 AAATAAGCACTACTTATTACGTT
11493 AAA
1 AAA
11496 CTAGCTACGG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (23 bp):
AAATAAGCACTACTTATTACGTT
Found at i:15509 original size:62 final size:62
Alignment explanation
Indices: 15412--15536 Score: 250
Period size: 62 Copynumber: 2.0 Consensus size: 62
15402 TGTTTTTTAA
15412 ACTAAGTTTCAGGTGAAGTTTAAAATTTGGTCAGTGTGCAATCTCTGATTTCATTGCATTAC
1 ACTAAGTTTCAGGTGAAGTTTAAAATTTGGTCAGTGTGCAATCTCTGATTTCATTGCATTAC
15474 ACTAAGTTTCAGGTGAAGTTTAAAATTTGGTCAGTGTGCAATCTCTGATTTCATTGCATTAC
1 ACTAAGTTTCAGGTGAAGTTTAAAATTTGGTCAGTGTGCAATCTCTGATTTCATTGCATTAC
15536 A
1 A
15537 ACAGGCTGGA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.38
Consensus pattern (62 bp):
ACTAAGTTTCAGGTGAAGTTTAAAATTTGGTCAGTGTGCAATCTCTGATTTCATTGCATTAC
Found at i:17484 original size:38 final size:37
Alignment explanation
Indices: 17423--17499 Score: 100
Period size: 38 Copynumber: 2.1 Consensus size: 37
17413 ATGATGTGAC
*
17423 ATTATCTTATGATGATATATTGATATAACTGTTAAGTT
1 ATTATCTTATGATGACATATTGATATAACTG-TAAGTT
* * * *
17461 ATTATCTTATGGTGACATGTTGATATTATTGTAAGTT
1 ATTATCTTATGATGACATATTGATATAACTGTAAGTT
17498 AT
1 AT
17500 AATGATGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
37 8 0.24
38 26 0.76
ACGTcount: A:0.31, C:0.05, G:0.16, T:0.48
Consensus pattern (37 bp):
ATTATCTTATGATGACATATTGATATAACTGTAAGTT
Found at i:22487 original size:10 final size:11
Alignment explanation
Indices: 22472--22503 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
22462 CTATTAATCC
22472 ATTATAT-TAT
1 ATTATATATAT
22482 ATTATATATAT
1 ATTATATATAT
22493 A-TATATATAT
1 ATTATATATAT
22503 A
1 A
22504 ACTAACTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 17 0.81
11 4 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
ATTATATATAT
Found at i:24070 original size:24 final size:23
Alignment explanation
Indices: 24043--24120 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 23
24033 ACCGAATTGT
24043 CACGTAGAATTTGTCCCGAAGGAC
1 CACGTAGAA-TTGTCCCGAAGGAC
* * * *
24067 CACGTAGAAATATCCCGAATGAT
1 CACGTAGAATTGTCCCGAAGGAC
* *
24090 CACATAG-ATTGTCCCAAAGGAC
1 CACGTAGAATTGTCCCGAAGGAC
*
24112 CGCGTAGAA
1 CACGTAGAA
24121 CCCTTGACTC
Statistics
Matches: 41, Mismatches: 12, Indels: 3
0.73 0.21 0.05
Matches are distributed among these distances:
22 15 0.37
23 17 0.41
24 9 0.22
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (23 bp):
CACGTAGAATTGTCCCGAAGGAC
Found at i:30981 original size:24 final size:23
Alignment explanation
Indices: 30961--31004 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
30951 GCGTAGAATT
* *
30961 TATCCCGAAGGACCACATAGAAA
1 TATCCCAAAAGACCACATAGAAA
*
30984 TATCCCAAAAGATCACATAGA
1 TATCCCAAAAGACCACATAGA
31005 TTGTCACGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.45, C:0.25, G:0.14, T:0.16
Consensus pattern (23 bp):
TATCCCAAAAGACCACATAGAAA
Found at i:37895 original size:24 final size:23
Alignment explanation
Indices: 37868--37933 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
37858 AAGGATTGCG
37868 TAGAATTTGTCCCGAAGGACCACA
1 TAGAA-TTGTCCCGAAGGACCACA
* * * * *
37892 TAGAAATATCCCAAAAGATCACA
1 TAGAATTGTCCCGAAGGACCACA
37915 TAG-ATTGTCCCGAAGGACC
1 TAGAATTGTCCCGAAGGACC
37934 GCGTAGAACC
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
22 11 0.34
23 16 0.50
24 5 0.16
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (23 bp):
TAGAATTGTCCCGAAGGACCACA
Found at i:39853 original size:61 final size:60
Alignment explanation
Indices: 39779--39916 Score: 156
Period size: 61 Copynumber: 2.3 Consensus size: 60
39769 TTTTTTGGGT
* *
39779 AAAG-TACACAAATGGTCTCCCAACTATA-TGA-TAATGCTCTGTTGAGTCCCCTTGACTATTA
1 AAAGTTACA-AAATGGTCCCCCAACTATAGGGACT--TGCTCTGTTGAGT-CCCTTGACTATTA
* * * * *
39840 AAAGTTACAAAATGATCCCCCGACTATAGGGACTTGCTTTGTTGGGTCTCTTGACTATTA
1 AAAGTTACAAAATGGTCCCCCAACTATAGGGACTTGCTCTGTTGAGTCCCTTGACTATTA
39900 AAAGTTACAAAATGGTC
1 AAAGTTACAAAATGGTC
39917 ACTCGACTAT
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
60 28 0.42
61 31 0.47
62 6 0.09
63 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (60 bp):
AAAGTTACAAAATGGTCCCCCAACTATAGGGACTTGCTCTGTTGAGTCCCTTGACTATTA
Found at i:43228 original size:58 final size:58
Alignment explanation
Indices: 43158--43292 Score: 261
Period size: 58 Copynumber: 2.3 Consensus size: 58
43148 AAGTAATTTG
43158 ACTTATAAGTCCTATTTGAGCATGTAGCTCAAATAGATTTAATGTAATATAAAACCAT
1 ACTTATAAGTCCTATTTGAGCATGTAGCTCAAATAGATTTAATGTAATATAAAACCAT
43216 ACTTATAAGTCCTATTTGAGCATGTAGCTCAAATAGATTTAATGTAATATAAAACCAT
1 ACTTATAAGTCCTATTTGAGCATGTAGCTCAAATAGATTTAATGTAATATAAAACCAT
*
43274 ACTTATAAGTCCAATTTGA
1 ACTTATAAGTCCTATTTGA
43293 AAGAAATGAA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
58 76 1.00
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (58 bp):
ACTTATAAGTCCTATTTGAGCATGTAGCTCAAATAGATTTAATGTAATATAAAACCAT
Found at i:43722 original size:16 final size:17
Alignment explanation
Indices: 43672--43723 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
43662 ATAAAAAATA
43672 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
43689 GA-TT-AAA-TTAGGAGT
1 AATTTGAAAGTTA-GAGT
43704 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
43720 AATT
1 AATT
43724 AAATTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 11 0.38
17 4 0.14
18 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:44976 original size:31 final size:30
Alignment explanation
Indices: 44928--45102 Score: 140
Period size: 30 Copynumber: 5.8 Consensus size: 30
44918 CTAAAATAAT
* *
44928 AAAACAGAAACTTAAAGGGCTAAAATAGCA
1 AAAATAGAAACTTAAAGGGCTAAAACAGCA
* * * *
44958 TAAATATAAACTTAAAAGGGATAAAACAGTA
1 AAAATAGAAACTT-AAAGGGCTAAAACAGCA
* *
44989 AAAATAGAAACTTAAAAGGATAAAACAGCAAA
1 AAAATAGAAACTTAAAGGGCTAAAACAGC--A
* * * *
45021 AAAAAAGAAACCTAAAGGACTAAAATAGC-
1 AAAATAGAAACTTAAAGGGCTAAAACAGCA
* *
45050 AAAA-A-AAACTTAAAGGGCTAAAACGGAA
1 AAAATAGAAACTTAAAGGGCTAAAACAGCA
* * * *
45078 AAAACAAAAACTTAAAAGACTAAAA
1 AAAATAGAAACTTAAAGGGCTAAAA
45103 TGGAAAAATC
Statistics
Matches: 116, Mismatches: 23, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
27 17 0.15
28 5 0.04
29 5 0.04
30 40 0.34
31 25 0.22
32 24 0.21
ACGTcount: A:0.62, C:0.11, G:0.13, T:0.14
Consensus pattern (30 bp):
AAAATAGAAACTTAAAGGGCTAAAACAGCA
Found at i:45030 original size:32 final size:32
Alignment explanation
Indices: 44965--45057 Score: 111
Period size: 32 Copynumber: 2.9 Consensus size: 32
44955 GCATAAATAT
* *
44965 AAACTTAAAAGGGATAAAACAG--TAAAAATAG
1 AAACTTAAAA-GGATAAAACAGCAAAAAAAAAG
44996 AAACTTAAAAGGATAAAACAGCAAAAAAAAAG
1 AAACTTAAAAGGATAAAACAGCAAAAAAAAAG
* *
45028 AAACCT-AAAGGACTAAAATAGCAAAAAAAA
1 AAACTTAAAAGGA-TAAAACAGCAAAAAAAA
45058 CTTAAAGGGC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
30 11 0.20
31 16 0.29
32 28 0.51
ACGTcount: A:0.66, C:0.10, G:0.13, T:0.12
Consensus pattern (32 bp):
AAACTTAAAAGGATAAAACAGCAAAAAAAAAG
Found at i:45108 original size:30 final size:30
Alignment explanation
Indices: 45053--45110 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
45043 AAATAGCAAA
* *
45053 AAAAACTTAAAGGGCTAAAACGGAAAAAAC
1 AAAAACTTAAAAGACTAAAACGGAAAAAAC
*
45083 AAAAACTTAAAAGACTAAAATGGAAAAA
1 AAAAACTTAAAAGACTAAAACGGAAAAA
45111 TCAGATAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.64, C:0.10, G:0.14, T:0.12
Consensus pattern (30 bp):
AAAAACTTAAAAGACTAAAACGGAAAAAAC
Found at i:45822 original size:10 final size:10
Alignment explanation
Indices: 45807--45848 Score: 57
Period size: 10 Copynumber: 4.0 Consensus size: 10
45797 ACCGGCGGTA
45807 GCCACGACGG
1 GCCACGACGG
*
45817 GCCACGGCGG
1 GCCACGACGG
45827 GCCACGACGG
1 GCCACGACGG
45837 AGCCCACGACGG
1 -G-CCACGACGG
45849 CTCACGGTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 18 0.64
11 1 0.04
12 9 0.32
ACGTcount: A:0.19, C:0.40, G:0.40, T:0.00
Consensus pattern (10 bp):
GCCACGACGG
Found at i:46579 original size:20 final size:20
Alignment explanation
Indices: 46554--46598 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
46544 GTTAGGGCTG
*
46554 GGTTGCTTGTTTTGGGCCTC
1 GGTTGCTTGTTTTAGGCCTC
46574 GGTTGCTTGTTTTAGGCCTC
1 GGTTGCTTGTTTTAGGCCTC
46594 GGTTG
1 GGTTG
46599 AGGGCTTGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.02, C:0.18, G:0.36, T:0.44
Consensus pattern (20 bp):
GGTTGCTTGTTTTAGGCCTC
Found at i:52270 original size:26 final size:26
Alignment explanation
Indices: 52241--52306 Score: 105
Period size: 26 Copynumber: 2.5 Consensus size: 26
52231 AAATATCCCC
*
52241 AAGCCCTAGAATGACTGAATACCTTT
1 AAGCCCTAGAATGACTGAATACCCTT
52267 AAGCCCTAGAATGACTGAATACCCTT
1 AAGCCCTAGAATGACTGAATACCCTT
* *
52293 AAGCTCTGGAATGA
1 AAGCCCTAGAATGA
52307 ATAAATCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (26 bp):
AAGCCCTAGAATGACTGAATACCCTT
Found at i:54037 original size:29 final size:32
Alignment explanation
Indices: 53998--54058 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 32
53988 TTTATTACTA
53998 GATATTGTTGAA-TTCTATTTT-TATATAAAT
1 GATATTGTTGAACTTCTATTTTATATATAAAT
* *
54028 GATATT-TTGAACTTGTATTTTATCTATAAAT
1 GATATTGTTGAACTTCTATTTTATATATAAAT
54059 TATTTTACAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 5 0.19
30 14 0.52
31 8 0.30
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.52
Consensus pattern (32 bp):
GATATTGTTGAACTTCTATTTTATATATAAAT
Found at i:55327 original size:64 final size:65
Alignment explanation
Indices: 55233--55440 Score: 230
Period size: 65 Copynumber: 3.2 Consensus size: 65
55223 TTTCAAAGTG
* **
55233 ATGCACCGATGCACCAATCTATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCATT
1 ATGCATCGATGCACCAA-CTATGCATCGATGCACTCA-GGAATATTTTGAAACATCGAATGCATT
55296 TC
64 TC
*
55298 ATGCATCGATGCA-CATACTATGCATCGATGCACTCA-GAGT-TTTATGAAAACATCGAATGCAT
1 ATGCATCGATGCACCA-ACTATGCATCGATGCACTCAGGAATATTT-TG-AAACATCGAATGCAT
*
55360 TTG
63 TTC
* * * * * *
55363 ATGCATCGATGCACCAGCCATGCATCGACGCACTCAGG-CTATTTTGAAACATCGAATACATTTT
1 ATGCATCGATGCACCAACTATGCATCGATGCACTCAGGAATATTTTGAAACATCGAATGCATTTC
55427 ATGCATCGATGCAC
1 ATGCATCGATGCAC
55441 TCTTAGTGCA
Statistics
Matches: 124, Mismatches: 11, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
62 1 0.01
63 5 0.04
64 48 0.39
65 64 0.52
66 6 0.05
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (65 bp):
ATGCATCGATGCACCAACTATGCATCGATGCACTCAGGAATATTTTGAAACATCGAATGCATTTC
Found at i:61132 original size:23 final size:21
Alignment explanation
Indices: 61080--61141 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
61070 TGCATCCCTT
*
61080 TGAATGTGCATCGATACACCA
1 TGAATGTGCATCGATGCACCA
* * *
61101 TGAAGGTGCACCGATGCACGCC
1 TGAATGTGCATCGATGCAC-CA
61123 TAGAATGTGCATCGATGCA
1 T-GAATGTGCATCGATGCA
61142 TCCGTCGGGT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 16 0.48
22 2 0.06
23 15 0.45
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (21 bp):
TGAATGTGCATCGATGCACCA
Found at i:63897 original size:46 final size:45
Alignment explanation
Indices: 63846--63952 Score: 146
Period size: 45 Copynumber: 2.4 Consensus size: 45
63836 TGCACATACT
*
63846 ATGCATTGATGCACTCAGAG-T-TTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACTCAG-GCTATTT-TG-AAACATCGAATGCATTTG
*
63892 ATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTG
*
63937 ATGAATCGATGCACTC
1 ATGCATCGATGCACTC
63953 TTAGTGCACC
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
45 33 0.59
46 20 0.36
47 3 0.05
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (45 bp):
ATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTG
Found at i:68218 original size:15 final size:15
Alignment explanation
Indices: 68181--68238 Score: 57
Period size: 15 Copynumber: 3.7 Consensus size: 15
68171 ATTCAACTTA
68181 AATTATAATAAGAGTAT
1 AATTATAATAA-A-TAT
68198 AA--ATAATAAATAT
1 AATTATAATAAATAT
*
68211 AATTATAATAAAAAAT
1 AATTATAAT-AAATAT
68227 AATTTATAATAA
1 AA-TTATAATAA
68239 TTCACTATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
13 5 0.14
14 1 0.03
15 12 0.33
16 9 0.25
17 9 0.25
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
AATTATAATAAATAT
Found at i:68235 original size:17 final size:16
Alignment explanation
Indices: 68200--68238 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
68190 AAGAGTATAA
*
68200 ATAAT-AAATATAATT
1 ATAATAAAAAATAATT
68215 ATAATAAAAAATAATTT
1 ATAATAAAAAATAA-TT
68232 ATAATAA
1 ATAATAA
68239 TTCACTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.24
16 7 0.33
17 9 0.43
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAATAAAAAATAATT
Found at i:69926 original size:44 final size:44
Alignment explanation
Indices: 69863--70301 Score: 405
Period size: 44 Copynumber: 10.3 Consensus size: 44
69853 ATTTTATGAA
*
69863 ATTG-AAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGGG
1 ATTGAAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGAG
* * *
69906 GTTGAAAAAAAATAGGGGCCTCAATTATAAAGGT-AAAAGATGGG
1 ATTGAAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAG-TGAG
** * *
69950 ATTGAAAAAAATTAGAAGCTTCAATTATAAATGTAAAAAGT-AG
1 ATTGAAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGAG
* **
69993 ATTGAAAAAAAAAATTAGGGG-CTTAATTATAAAGGTAAAAACCGAG
1 ATTG---AAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGAG
* * * *
70039 ATT-AAAAAAACTAGGGACCTCAATTATGAAGGTAGAAAGTGAG
1 ATTGAAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGAG
* *
70082 ATTGAAAAAAATTAGGGGTCTCAATTATAAAGATAAAAAGTGAG
1 ATTGAAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGAG
* ** * *
70126 ATTGAAAAAAATTAAGAACTTCAATTATAAAGGTAAAAAGTGGG
1 ATTGAAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGAG
* * * * *
70170 ATT-ACAAAAATTAGGGGTCTCATTTATAAATGTAAAAAGTGGG
1 ATTGAAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGAG
*
70213 ATTG------A--A--GG-CTCAATTATAAAGGTAAAATGTGAG
1 ATTGAAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGAG
* * * *
70246 ATT--AAAAAATTAGGGACCTTAATTATAAAAGT-AAAAGTTAG
1 ATTGAAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGAG
*
70287 ATTGAAAAATATTAG
1 ATTGAAAAAAATTAG
70302 AAAAGCCACA
Statistics
Matches: 320, Mismatches: 54, Indels: 44
0.77 0.13 0.11
Matches are distributed among these distances:
33 24 0.08
34 2 0.01
36 1 0.00
37 1 0.00
38 1 0.00
39 1 0.00
41 11 0.03
42 25 0.08
43 80 0.25
44 135 0.42
45 22 0.07
46 17 0.05
ACGTcount: A:0.48, C:0.06, G:0.21, T:0.25
Consensus pattern (44 bp):
ATTGAAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGAG
Found at i:88514 original size:16 final size:16
Alignment explanation
Indices: 88493--88528 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
88483 GTTACTGCAC
*
88493 ATAGACAAGACTTCTA
1 ATAGACAAGACCTCTA
*
88509 ATAGACAAGTCCTCTA
1 ATAGACAAGACCTCTA
88525 ATAG
1 ATAG
88529 GTCACCGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (16 bp):
ATAGACAAGACCTCTA
Found at i:96954 original size:16 final size:16
Alignment explanation
Indices: 96933--96964 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
96923 TATTTTAATC
96933 ATTAAATTTTAAACTT
1 ATTAAATTTTAAACTT
96949 ATTAAATTTTAAACTT
1 ATTAAATTTTAAACTT
96965 TTCAATTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTAAATTTTAAACTT
Found at i:101207 original size:23 final size:21
Alignment explanation
Indices: 101181--101229 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
101171 CATACCCGAA
* *
101181 ATATCATTCATGATAAATATCAT
1 ATAT-ATTCAGGAT-AACATCAT
*
101204 ATATGTTCAGGATAACATCAT
1 ATATATTCAGGATAACATCAT
101225 ATATA
1 ATATA
101230 ATGATCAGTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 11 0.50
22 7 0.32
23 4 0.18
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (21 bp):
ATATATTCAGGATAACATCAT
Found at i:109626 original size:27 final size:26
Alignment explanation
Indices: 109586--109636 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
109576 CCAGAAGACG
*
109586 CTGACTAGATCTTCTAGAAAACTGCTA
1 CTGACTAGACCTTCTAG-AAACTGCTA
*
109613 CTGACTGGACCTTCTAGAAACTGC
1 CTGACTAGACCTTCTAGAAACTGC
109637 CACGTTAGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27
Consensus pattern (26 bp):
CTGACTAGACCTTCTAGAAACTGCTA
Found at i:113128 original size:26 final size:25
Alignment explanation
Indices: 113107--113155 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
113097 CGTTAATAGG
*
113107 AAAGCATAATATTAAGCATTAATGTA
1 AAAGCAGAATATT-AGCATTAATGTA
*
113133 AAATCAGAATATTAGCATTAATG
1 AAAGCAGAATATTAGCATTAATG
113156 AAGGATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.31
Consensus pattern (25 bp):
AAAGCAGAATATTAGCATTAATGTA
Found at i:124516 original size:2 final size:2
Alignment explanation
Indices: 124501--124540 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
124491 AAGATTAATG
*
124501 TA TA TA TT TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
124541 TAATTATACA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 34 0.97
3 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:127237 original size:378 final size:374
Alignment explanation
Indices: 126463--127220 Score: 1091
Period size: 378 Copynumber: 2.0 Consensus size: 374
126453 GTTGATGCTT
*
126463 ATTAATGAT-TTTTTTAAAAAAGAAAAGAAATGGTTAGCCACCTCAGTTGTTTCGTATAACACTC
1 ATTAATGATATTTTTT--TAAA-AAAAGAAATGGTTAGCCACCTCAGTTGTTTCGTATAACACTC
* *
126527 GAATCCGTCGGGTTTGGGTTGGATTCAGATTTGGGTGTTACAACCATAAACAATACAAATATTTG
63 GAATCCGTCGGGTTTGGGTCGAATTCAGATTTGGGTGTTACAACCATAAACAATACAAATATTTG
*
126592 TAATTAAATCTAAACAAAAACTTGAACAATTCGACTCGACTCGAAATTTTTTTAAATGCAATTTA
128 TAATTAAATCTAAACAAAAACTTGAACAA-T--ACTCGACTCGAAATTTTTTTAAATACAATTTA
*
126657 AATTATAAAATAAGGCTTATCAACTCAACTGACTCGAAATTTTGACTCGACTCGACTCTATCCAA
190 AATTATAAAATAAGGCTCATCAACTCAACTGACTCGAAATTTTGACTCGACTCGACTCTA-CCAA
*
126722 TCTAATACTCACCTAGAGATAAGGCGACAATAATATTTTTTATAACTATTTAACATTGTAACTTA
254 TATAATACTCACCTAGAGATAAGGCGACAATAATATTTTTTATAACTATTTAACATTGTAACTTA
* * *
126787 TTTTTGTTTCAAATGGGTTTAATACAAATAAAAGTCTAAATTATACCCTGTTTCTC
319 TTTTTGCTTAAAATGGGTTTAATACAAATAAAAATCTAAATTATACCCTGTTTCTC
* *
126843 ATTAATGATTTTTTTTTAAAAAAAGAAATGGTTAGCCACCTCAGTTGTTTCGTATGACACTCGAA
1 ATTAATGATATTTTTTTAAAAAAAGAAATGGTTAGCCACCTCAGTTGTTTCGTATAACACTCGAA
* * * *
126908 TCCGTCGGGTTTGGGTCGAATTCGGATTTGGGTGTTACAACCATAAATATTATAAATATTTGTAA
66 TCCGTCGGGTTTGGGTCGAATTCAGATTTGGGTGTTACAACCATAAACAATACAAATATTTGTAA
* * * * *
126973 TTAAATTTAAATAAAAATTTGAAC-A-ACTCGACTCG-ATTTTTTTTAAAATACATTTTAAATTA
131 TTAAATCTAAACAAAAACTTGAACAATACTCGACTCGAAATTTTTTT-AAATACAATTTAAATTA
* * *
127035 TAAAATAAGGCTCATCAACTCAACTGACTCGAAATTTTTTGATTCGTCTTGACTCTA-CATGATA
195 TAAAATAAGGCTCATCAACTCAACTGACTCGAAA--TTTTGACTCGACTCGACTCTACCA--ATA
*
127099 TAATACTCACCTCA-AGATAAGGCGACAATAATAATTTTTTATAACTATTTAACTTTGTAACTTA
256 TAATACTCACCT-AGAGATAAGGCGACAATAAT-ATTTTTTATAACTATTTAACATTGTAACTTA
* *
127163 TTTTTGCTTAAAATGGGTTTAATACAAA-AAAAATTTAAATTATATCTCT-TTTCTC
319 TTTTTGCTTAAAATGGGTTTAATACAAATAAAAATCTAAATTATA-CCCTGTTTCTC
127218 ATT
1 ATT
127221 TAGGTGTCGA
Statistics
Matches: 344, Mismatches: 25, Indels: 23
0.88 0.06 0.06
Matches are distributed among these distances:
372 8 0.02
373 60 0.17
375 73 0.21
376 60 0.17
377 1 0.00
378 124 0.36
379 3 0.01
380 9 0.03
381 6 0.02
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (374 bp):
ATTAATGATATTTTTTTAAAAAAAGAAATGGTTAGCCACCTCAGTTGTTTCGTATAACACTCGAA
TCCGTCGGGTTTGGGTCGAATTCAGATTTGGGTGTTACAACCATAAACAATACAAATATTTGTAA
TTAAATCTAAACAAAAACTTGAACAATACTCGACTCGAAATTTTTTTAAATACAATTTAAATTAT
AAAATAAGGCTCATCAACTCAACTGACTCGAAATTTTGACTCGACTCGACTCTACCAATATAATA
CTCACCTAGAGATAAGGCGACAATAATATTTTTTATAACTATTTAACATTGTAACTTATTTTTGC
TTAAAATGGGTTTAATACAAATAAAAATCTAAATTATACCCTGTTTCTC
Found at i:128581 original size:60 final size:60
Alignment explanation
Indices: 128461--128587 Score: 143
Period size: 60 Copynumber: 2.1 Consensus size: 60
128451 GTCGAGTGAT
* * * * ****
128461 CATTTTGTAACTTTTAATAGTTGAGGGACTCAACAAAATCACTTTCTATAGTTGGGGGAC
1 CATTTTGTAACTTTAAATAGTGGAGGGACTCAACAAAAGCAATTTCTATAGTCAAAGGAC
128521 CATTTTGTAACTTTAAATAGTCGGA-GGACTCAAC-AAAGCAATATTCTATAGTCAAAGGAC
1 CATTTTGTAACTTTAAATAGT-GGAGGGACTCAACAAAAGCAAT-TTCTATAGTCAAAGGAC
128581 C-TTTTGT
1 CATTTTGT
128588 GTACTTTATC
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
59 12 0.21
60 43 0.75
61 2 0.04
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (60 bp):
CATTTTGTAACTTTAAATAGTGGAGGGACTCAACAAAAGCAATTTCTATAGTCAAAGGAC
Found at i:132606 original size:3 final size:3
Alignment explanation
Indices: 132598--132646 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
132588 GTCAAAACCG
* * *
132598 TTA TTA TTA TTA TT- TAA CTAA CTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
132643 TTA T
1 TTA T
132647 ACATGCCAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
2 1 0.03
3 36 0.90
4 3 0.08
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:133217 original size:14 final size:13
Alignment explanation
Indices: 133199--133235 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
133189 AAGGAAAATA
133199 AAAAAATAGAAAG
1 AAAAAATAGAAAG
133212 -AAAAA-AGAAAGG
1 AAAAAATAGAAA-G
133224 AAAAAATAGAAA
1 AAAAAATAGAAA
133236 AAAGAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 5 0.24
12 6 0.29
13 5 0.24
14 5 0.24
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.05
Consensus pattern (13 bp):
AAAAAATAGAAAG
Found at i:133226 original size:12 final size:11
Alignment explanation
Indices: 133200--133245 Score: 51
Period size: 10 Copynumber: 4.3 Consensus size: 11
133190 AGGAAAATAA
133200 AAAAATAGAAAG
1 AAAAA-AGAAAG
133212 AAAAAAGAAAG
1 AAAAAAGAAAG
* *
133223 GAAAAA-ATAG
1 AAAAAAGAAAG
133233 AAAAAAG-AAG
1 AAAAAAGAAAG
133243 AAA
1 AAA
133246 CAAAACAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 13 0.45
11 11 0.38
12 5 0.17
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.04
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:133233 original size:25 final size:24
Alignment explanation
Indices: 133199--133245 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
133189 AAGGAAAATA
133199 AAAAAATAGAAAGAAAAAAGAAAGG
1 AAAAAATAGAAA-AAAAAAGAAAGG
*
133224 AAAAAATAGAAAAAAGAAGAAA
1 AAAAAATAGAAAAAAAAAGAAA
133246 CAAAACAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (24 bp):
AAAAAATAGAAAAAAAAAGAAAGG
Found at i:133244 original size:31 final size:31
Alignment explanation
Indices: 133186--133245 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
133176 GAAAAATCAG
*
133186 AGAAAGGAAAATAAAAAAATAGAAAGAAAAA
1 AGAAAGGAAAATAAAAAAAAAGAAAGAAAAA
133217 AGAAAGGAAAA-AATAGAAAAAAG-AAGAAA
1 AGAAAGGAAAATAA-A-AAAAAAGAAAGAAA
133246 CAAAACAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 2 0.08
31 18 0.69
32 6 0.23
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (31 bp):
AGAAAGGAAAATAAAAAAAAAGAAAGAAAAA
Found at i:133250 original size:21 final size:21
Alignment explanation
Indices: 133210--133259 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
133200 AAAAATAGAA
*
133210 AGAAAAAAGAAAGGAAAAAAT
1 AGAAAAAAGAAAGAAAAAAAT
*
133231 AGAAAAAAG-AAGAAACAAA-
1 AGAAAAAAGAAAGAAAAAAAT
*
133250 ACAAAAAAGA
1 AGAAAAAAGA
133260 GAGACATGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 8 0.32
20 8 0.32
21 9 0.36
ACGTcount: A:0.78, C:0.04, G:0.16, T:0.02
Consensus pattern (21 bp):
AGAAAAAAGAAAGAAAAAAAT
Found at i:134311 original size:477 final size:479
Alignment explanation
Indices: 133409--134357 Score: 1812
Period size: 477 Copynumber: 2.0 Consensus size: 479
133399 GAAGGTGGTT
133409 GGTGTTGTGTTTCTTTCAAAAGTAAAGAAAAAAGCAAAAAAAGAGAAGGGGTTAAAGAGAATGAG
1 GGTGTTGTGTTTCTTTCAAAAGTAAAGAAAAAAGCAAAAAAAGAGAAGGGGTT----A-AA-GAG
133474 AGAATGAGAGAAATGAGGGCTAGGTTTTACAAAAGCCTATAATGGGGCTTATATGGGGTCTTAAA
60 AGAATGAGAGAAATGAGGGCTAGGTTTTACAAAAGCCTATAATGGGGCTTATATGGGGTCTTAAA
133539 ACGTCGTAGTTTAGGGAAACTAGGGCATTCAGGTTTGGGCTTTAAGGGTTAATTGTTTAAGGGAG
125 ACGTCGTAGTTTAGGGAAACTAGGGCATTCAGGTTTGGGCTTTAAGGGTTAATTGTTTAAGGGAG
133604 GCTTCTTACATTAATTTGTTTCAGTTTAATCATCAATTGAGAACTTCGTTTGTTTTAATTTTGGC
190 GCTTCTTACATTAATTTGTTTCAGTTTAATCATCAATTGAGAACTTCGTTTGTTTTAATTTTGGC
133669 TTTAAGTTTCACGCGTGTTACAATTTGGTCACTTTAAGTTATTTGCTTTTGCTTATTTTAATTTC
255 TTTAAGTTTCACGCGTGTTACAATTTGGTCACTTTAAGTTATTTGCTTTTGCTTATTTTAATTTC
133734 TGGCTTGTAATTTTGAATACTTTCATTTTGGTCCCATTGACTTATTAATTGTGTTTTTGTTTCTT
320 TGGCTTGTAATTTTGAATACTTTCATTTTGGTCCCATTGACTTATTAATTGTGTTTTTGTTTCTT
133799 TTAATTTCGGGTGTGTTATTTTAAATACTTTTATTCTAGTCCCAAATATTTATGGTTTATTTTCA
385 TTAATTTCGGGTGTGTTATTTTAAATACTTTTATTCTAGTCCCAAATATTTATGGTTTATTTTCA
133864 TTTCCTAGTTTTCTTATCGGGGCGGTGTGC
450 TTTCCTAGTTTTCTTATCGGGGCGGTGTGC
133894 GGTGTTGTGTTTCTTTCAAAAGTAAAGAAAAAAGCAAAAAAAGAGAAGGGGTT-AA-AGAGAATG
1 GGTGTTGTGTTTCTTTCAAAAGTAAAGAAAAAAGCAAAAAAAGAGAAGGGGTTAAAGAGAGAATG
*
133957 AGAGAAATGAGGGCTAGGTTTTACAAAAGCTTATAATGGGGCTTATATGGGGTCTTAAAACGTCG
66 AGAGAAATGAGGGCTAGGTTTTACAAAAGCCTATAATGGGGCTTATATGGGGTCTTAAAACGTCG
*
134022 TAGTTTAGGGAAACTAGGGCATTCAGGTTTGGGCTTTGAGGGTTAATTGTTTAAGGGAGGCTTCT
131 TAGTTTAGGGAAACTAGGGCATTCAGGTTTGGGCTTTAAGGGTTAATTGTTTAAGGGAGGCTTCT
134087 TACATTAATTTGTTTCAGTTTAATCATCAATTGAGAACTTCGTTTGTTTTAATTTTGGCTTTAAG
196 TACATTAATTTGTTTCAGTTTAATCATCAATTGAGAACTTCGTTTGTTTTAATTTTGGCTTTAAG
134152 TTTCACGCGTGTTACAATTTGGTCACTTTAAGTTATTTGCTTTTGCTTATTTTAATTTCTGGCTT
261 TTTCACGCGTGTTACAATTTGGTCACTTTAAGTTATTTGCTTTTGCTTATTTTAATTTCTGGCTT
134217 GTAATTTTGAATACTTTCATTTTGGTCCCATTGACTTATTAATTGTGTTTTTGTTTCTTTTAATT
326 GTAATTTTGAATACTTTCATTTTGGTCCCATTGACTTATTAATTGTGTTTTTGTTTCTTTTAATT
134282 TCGGGTGTGTTATTTTAAATACTTTTATTCTAGTCCCAAATATTTATGGTTTATTTTCATTTCCT
391 TCGGGTGTGTTATTTTAAATACTTTTATTCTAGTCCCAAATATTTATGGTTTATTTTCATTTCCT
134347 AGTTTTCTTAT
456 AGTTTTCTTAT
134358 GTTATTTTAT
Statistics
Matches: 462, Mismatches: 2, Indels: 8
0.98 0.00 0.02
Matches are distributed among these distances:
477 407 0.88
479 2 0.00
485 53 0.11
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (479 bp):
GGTGTTGTGTTTCTTTCAAAAGTAAAGAAAAAAGCAAAAAAAGAGAAGGGGTTAAAGAGAGAATG
AGAGAAATGAGGGCTAGGTTTTACAAAAGCCTATAATGGGGCTTATATGGGGTCTTAAAACGTCG
TAGTTTAGGGAAACTAGGGCATTCAGGTTTGGGCTTTAAGGGTTAATTGTTTAAGGGAGGCTTCT
TACATTAATTTGTTTCAGTTTAATCATCAATTGAGAACTTCGTTTGTTTTAATTTTGGCTTTAAG
TTTCACGCGTGTTACAATTTGGTCACTTTAAGTTATTTGCTTTTGCTTATTTTAATTTCTGGCTT
GTAATTTTGAATACTTTCATTTTGGTCCCATTGACTTATTAATTGTGTTTTTGTTTCTTTTAATT
TCGGGTGTGTTATTTTAAATACTTTTATTCTAGTCCCAAATATTTATGGTTTATTTTCATTTCCT
AGTTTTCTTATCGGGGCGGTGTGC
Found at i:134507 original size:8 final size:8
Alignment explanation
Indices: 134466--134567 Score: 55
Period size: 8 Copynumber: 12.2 Consensus size: 8
134456 ATTTGATTTA
134466 TATACTATT
1 TATA-TATT
*
134475 TCATAAATT
1 T-ATATATT
134484 TATTATATT
1 TA-TATATT
*
134493 ATGTATATT
1 -TATATATT
134502 TATATAATT
1 TATAT-ATT
134511 T-TAGTA-T
1 TATA-TATT
* * *
134518 AACATGTT
1 TATATATT
*
134526 TATATATA
1 TATATATT
*
134534 TATATATA
1 TATATATT
*
134542 TATATATA
1 TATATATT
*
134550 TATATATA
1 TATATATT
134558 TATATATT
1 TATATATT
134566 TA
1 TA
134568 CATTTATACT
Statistics
Matches: 74, Mismatches: 12, Indels: 15
0.73 0.12 0.15
Matches are distributed among these distances:
7 2 0.03
8 47 0.64
9 21 0.28
10 4 0.05
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (8 bp):
TATATATT
Found at i:134533 original size:2 final size:2
Alignment explanation
Indices: 134526--134564 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
134516 ATAACATGTT
134526 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
134565 TTACATTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:136528 original size:20 final size:20
Alignment explanation
Indices: 136503--136545 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
136493 TCTAAAATCC
*
136503 CATTTAGGATCATATAGATG
1 CATTTAGGAGCATATAGATG
*
136523 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
136543 CAT
1 CAT
136546 GTGGTGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:143941 original size:15 final size:15
Alignment explanation
Indices: 143921--143950 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
143911 CCCATTTTGT
*
143921 TAAAAAAAGAGAAAA
1 TAAAAAAAAAGAAAA
143936 TAAAAAAAAAGAAAA
1 TAAAAAAAAAGAAAA
143951 AGAAAAAATG
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:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (15 bp):
TAAAAAAAAAGAAAA
Found at i:143951 original size:16 final size:17
Alignment explanation
Indices: 143922--143958 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
143912 CCATTTTGTT
*
143922 AAAAAAAGAGAAAATAA
1 AAAAAAAGAGAAAAGAA
143939 AAAAAAAGA-AAAAGAA
1 AAAAAAAGAGAAAAGAA
143955 AAAA
1 AAAA
143959 TGAAGCTGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (17 bp):
AAAAAAAGAGAAAAGAA
Found at i:144596 original size:20 final size:20
Alignment explanation
Indices: 144571--144613 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
144561 TCTAAAAGCC
*
144571 CATTTAGGATCATATAGATG
1 CATTTAGGAGCATATAGATG
*
144591 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
144611 CAT
1 CAT
144614 GTGGTGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:149854 original size:3 final size:3
Alignment explanation
Indices: 149848--149881 Score: 50
Period size: 3 Copynumber: 10.7 Consensus size: 3
149838 AGTAATCTTA
149848 AAT AAT AAT AAT AAT AAT AAT AACTT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA--T AAT AAT AA
149882 CGAGACGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 26 0.90
5 3 0.10
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:150221 original size:111 final size:111
Alignment explanation
Indices: 150022--150556 Score: 718
Period size: 111 Copynumber: 4.8 Consensus size: 111
150012 ATCAGTTCCG
* * * * * *
150022 CTGTCACTCAGGGAATATCAAATCTGGGGATGAGAGGGATTTGTTTCGA-TTCTTCTAAAGGGGA
1 CTGTCACTCAGGGAATATCAAATCTTGGAAT-AGAGTGATCTG-TTCCACTTCTTCT-AAGGGAA
* * * *
150086 TATCAGATTTGG-GGAAGTTGATCCATTGAATCGTGGTAGACTTATT-TC
63 TATCAGATCTGGAAG-AGTTGATCCATTGAATCGGGGTAGACTTGTTATC
* * *
150134 GTTATCACTCAGGGAAAATCAAATCTTGGAATAGAGTGATCTGTTCCACTTCTTCTAAGGGAATA
1 -CTGTCACTCAGGGAATATCAAATCTTGGAATAGAGTGATCTGTTCCACTTCTTCTAAGGGAATA
* * *
150199 TCAGATCTGGAAGAGTTGATCCATTGAATCAGGGTAGACTTGTTCTA
65 TCAGATCTGGAAGAGTTGATCCATTGAATCGGGGTAGACTTGTTATC
* *
150246 CTGTTACTCAGGGAATATCAAATCTTGGAATAGAGTGATTTGTTCCACTTCTTCTAAGGGAATAT
1 CTGTCACTCAGGGAATATCAAATCTTGGAATAGAGTGATCTGTTCCACTTCTTCTAAGGGAATAT
*
150311 CAGATCTGGAAGAGTTGATCCATTGAATCGGGGTAGACCTGTTATC
66 CAGATCTGGAAGAGTTGATCCATTGAATCGGGGTAGACTTGTTATC
* * *
150357 CTGTCACTCAGGGAATATGAAATCTTGGAATAGAGTGATCTATTCCACTTTTTCTAAGGGAATAT
1 CTGTCACTCAGGGAATATCAAATCTTGGAATAGAGTGATCTGTTCCACTTCTTCTAAGGGAATAT
* * * *
150422 TAGATATGGAAGAGTTAATCCATTGAATCGGGGTAGACTTGTT-CC
66 CAGATCTGGAAGAGTTGATCCATTGAATCGGGGTAGACTTGTTATC
* *
150467 ACTGTCACTCAGGGAATATCAAATCTTGGAATAGAGTGATCTGTTCTATTTCTTCTAAGGGAATA
1 -CTGTCACTCAGGGAATATCAAATCTTGGAATAGAGTGATCTGTTCCACTTCTTCTAAGGGAATA
* *
150532 TCAGATCTAGAAGAGTTGATTCATT
65 TCAGATCTGGAAGAGTTGATCCATT
150557 TCGCTGTCAC
Statistics
Matches: 374, Mismatches: 44, Indels: 10
0.87 0.10 0.02
Matches are distributed among these distances:
110 1 0.00
111 329 0.88
112 18 0.05
113 26 0.07
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (111 bp):
CTGTCACTCAGGGAATATCAAATCTTGGAATAGAGTGATCTGTTCCACTTCTTCTAAGGGAATAT
CAGATCTGGAAGAGTTGATCCATTGAATCGGGGTAGACTTGTTATC
Found at i:151804 original size:17 final size:17
Alignment explanation
Indices: 151781--151822 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
151771 ATCTTAAACC
151781 CTCTTTTTATTTTATTTT
1 CTCTTTTTATTTT-TTTT
*
151799 -TCTTTTTCTTTTTTTT
1 CTCTTTTTATTTTTTTT
151815 CTCTTTTT
1 CTCTTTTT
151823 TTCTTTCCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (17 bp):
CTCTTTTTATTTTTTTT
Found at i:151805 original size:12 final size:11
Alignment explanation
Indices: 151782--151847 Score: 69
Period size: 11 Copynumber: 5.6 Consensus size: 11
151772 TCTTAAACCC
*
151782 TCTTTTTATTT
1 TCTTTTTTTTT
*
151793 TATTTTTCTTTT
1 TCTTTTT-TTTT
*
151805 TCTTTTTTTTC
1 TCTTTTTTTTT
151816 TCTTTTTTTCTT
1 TCTTTTTTT-TT
151828 TCCTTTTTTCTTT
1 T-CTTTTTT-TTT
151841 TCTTTTT
1 TCTTTTT
151848 CATTTTTATA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
11 18 0.39
12 17 0.37
13 10 0.22
14 1 0.02
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (11 bp):
TCTTTTTTTTT
Found at i:151823 original size:13 final size:13
Alignment explanation
Indices: 151807--151847 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
151797 TTTCTTTTTC
151807 TTTTTTTTCTCTT
1 TTTTTTTTCTCTT
151820 TTTTTCTTTC-CTT
1 TTTTT-TTTCTCTT
151833 TTTTCTTTTCT-TT
1 TTTT-TTTTCTCTT
151846 TT
1 TT
151848 CATTTTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 20 0.80
14 5 0.20
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTTTTCTCTT
Found at i:151823 original size:25 final size:25
Alignment explanation
Indices: 151795--151847 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
151785 TTTTATTTTA
*
151795 TTTTTCTTTTTCTTTTTT-TTCTCTT
1 TTTTTC-TTTCCTTTTTTCTTCTCTT
*
151820 TTTTTCTTTCCTTTTTTCTTTTCTT
1 TTTTTCTTTCCTTTTTTCTTCTCTT
151845 TTT
1 TTT
151848 CATTTTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (25 bp):
TTTTTCTTTCCTTTTTTCTTCTCTT
Found at i:151872 original size:7 final size:6
Alignment explanation
Indices: 151790--151854 Score: 55
Period size: 6 Copynumber: 10.7 Consensus size: 6
151780 CCTCTTTTTA
* *
151790 TTTTAT TTTTCT TTTTCT TTTT-T TTCTCT TTTT-T TCTTTCCT TTTT-T
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT T-TTT-CT TTTTCT
151837 CTTTTCT TTTTCAT TTTT
1 -TTTTCT TTTTC-T TTTT
151855 ATAGTCTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
5 7 0.14
6 31 0.63
7 9 0.18
8 2 0.04
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:163525 original size:69 final size:71
Alignment explanation
Indices: 163394--163531 Score: 217
Period size: 71 Copynumber: 2.0 Consensus size: 71
163384 GAATTACCAT
* * * *
163394 ACTTTTAATATATAATATAAAGGCAAAGTAATCATGCATAAAATATATATATAAGACACCACAAC
1 ACTTTTAATATATAAAATAAAGGCAAAGAAAACATACATAAAATATATATATAAGACACCACAAC
163459 CAACAC
66 CAACAC
*
163465 ACTTTTAATATATAAAATAAAGGTAAAGAAAACATACAT-AAA-ATATATATAAGACACCACAAC
1 ACTTTTAATATATAAAATAAAGGCAAAGAAAACATACATAAAATATATATATAAGACACCACAAC
163528 CAAC
66 CAAC
163532 GTGGGTCAGT
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
69 25 0.40
70 3 0.05
71 34 0.55
ACGTcount: A:0.54, C:0.16, G:0.07, T:0.24
Consensus pattern (71 bp):
ACTTTTAATATATAAAATAAAGGCAAAGAAAACATACATAAAATATATATATAAGACACCACAAC
CAACAC
Found at i:164883 original size:3 final size:3
Alignment explanation
Indices: 164877--164911 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
164867 AGTAATCTTA
164877 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
164912 CTTAATAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:167709 original size:30 final size:30
Alignment explanation
Indices: 167653--167710 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
167643 GATTTATTTA
* *
167653 GTGACCAAATTATAAATTTGGTAAAGTTTG
1 GTGACCAAAGTATAAATTTGGAAAAGTTTG
167683 GTGACCAAAGTATAAACTTT-GAAAAGTT
1 GTGACCAAAGTATAAA-TTTGGAAAAGTT
167711 CAGGAACCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.88
31 3 0.12
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.33
Consensus pattern (30 bp):
GTGACCAAAGTATAAATTTGGAAAAGTTTG
Found at i:168926 original size:13 final size:11
Alignment explanation
Indices: 168896--168928 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
168886 TATCATTTTA
168896 AAAACACACTT
1 AAAACACACTT
168907 AAAACACACTT
1 AAAACACACTT
*
168918 GAAACACACTT
1 AAAACACACTT
168929 CTCCCCCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.52, C:0.27, G:0.03, T:0.18
Consensus pattern (11 bp):
AAAACACACTT
Found at i:171215 original size:20 final size:20
Alignment explanation
Indices: 171186--171223 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
171176 CCCCTTCAAA
*
171186 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
171206 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
171224 TGCACCAAAA
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:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:179056 original size:45 final size:45
Alignment explanation
Indices: 179007--179254 Score: 442
Period size: 45 Copynumber: 5.5 Consensus size: 45
178997 TTATTGGTTA
179007 ATAAATGGTAAGTATATTGGTAAAATAAGCTTACAAGCTTATGGG
1 ATAAATGGTAAGTATATTGGTAAAATAAGCTTACAAGCTTATGGG
179052 ATAAATGGTAAGTATATTGGTAAAATAAGCTTACAAGCTTATGGG
1 ATAAATGGTAAGTATATTGGTAAAATAAGCTTACAAGCTTATGGG
* **
179097 ATAAATGATAAGTATATTGGTAAAATAAGCTTATGAGCTTATGGG
1 ATAAATGGTAAGTATATTGGTAAAATAAGCTTACAAGCTTATGGG
*
179142 ATAAATGGTAAGTATATTGGTAAAATAAGCTAACAAGCTTATGGG
1 ATAAATGGTAAGTATATTGGTAAAATAAGCTTACAAGCTTATGGG
*
179187 ATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGG
1 ATAAATGGTAAGTATATTGGTAAAATAAGCTTACAAGCTTATGGG
*
179232 TTAAATGGTAAGTATATTGGTAA
1 ATAAATGGTAAGTATATTGGTAA
179255 GAAATTTTAT
Statistics
Matches: 193, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 193 1.00
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.32
Consensus pattern (45 bp):
ATAAATGGTAAGTATATTGGTAAAATAAGCTTACAAGCTTATGGG
Found at i:179102 original size:25 final size:25
Alignment explanation
Indices: 179029--179102 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
179019 TATATTGGTA
179029 AAATAAGCTTACAAGCTTATGGGAT
1 AAATAAGCTTACAAGCTTATGGGAT
* *
179054 AAAT--G-GT--AAG-TATATTGG-T
1 AAATAAGCTTACAAGCT-TATGGGAT
179073 AAAATAAGCTTACAAGCTTATGGGAT
1 -AAATAAGCTTACAAGCTTATGGGAT
179099 AAAT
1 AAAT
179103 GATAAGTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 18
0.62 0.07 0.31
Matches are distributed among these distances:
19 2 0.06
20 12 0.33
22 2 0.06
23 2 0.06
25 16 0.44
26 2 0.06
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.30
Consensus pattern (25 bp):
AAATAAGCTTACAAGCTTATGGGAT
Found at i:179730 original size:17 final size:17
Alignment explanation
Indices: 179708--179767 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
179698 ATAATGAATC
179708 ATAATTCATATGATATG
1 ATAATTCATATGATATG
* *
179725 ATAATTTGTTATAATGA-ATC
1 ATAA--T-TCAT-ATGATATG
179745 ATAATTCATATGATATG
1 ATAATTCATATGATATG
179762 ATAATT
1 ATAATT
179768 TTGATAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
16 4 0.12
17 15 0.44
18 1 0.03
19 1 0.03
20 9 0.26
21 4 0.12
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.43
Consensus pattern (17 bp):
ATAATTCATATGATATG
Found at i:179744 original size:37 final size:37
Alignment explanation
Indices: 179694--179768 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
179684 CACTGTTCAC
179694 TGTTATAATGAATCATAATTCATATGATATGATAATT
1 TGTTATAATGAATCATAATTCATATGATATGATAATT
179731 TGTTATAATGAATCATAATTCATATGATATGATAATT
1 TGTTATAATGAATCATAATTCATATGATATGATAATT
179768 T
1 T
179769 TGATAATATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (37 bp):
TGTTATAATGAATCATAATTCATATGATATGATAATT
Found at i:179750 original size:20 final size:20
Alignment explanation
Indices: 179694--179750 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
179684 CACTGTTCAC
179694 TGTTATAATGAATCATAA--
1 TGTTATAATGAATCATAATT
* *
179712 T-TCAT-ATGATATGATAATT
1 TGTTATAATGA-ATCATAATT
179731 TGTTATAATGAATCATAATT
1 TGTTATAATGAATCATAATT
179751 CATATGATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
16 4 0.13
17 9 0.30
18 1 0.03
19 1 0.03
20 11 0.37
21 4 0.13
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (20 bp):
TGTTATAATGAATCATAATT
Found at i:180440 original size:50 final size:51
Alignment explanation
Indices: 180386--180511 Score: 164
Period size: 51 Copynumber: 2.5 Consensus size: 51
180376 TGTGCTGTAA
* *
180386 TTTTAATTTATGCATCTTAGTCACT-TTTATTTCTGATTTGGCCACTATTC
1 TTTTAATTTATGCATTTTAGTCACTGTTTATTTCTGATTTGGCCACTATCC
* * * *
180436 TTTTATTTTATGCATTTTAGTAACTGTTTATTTCTGATTTGGCTACTGTCC
1 TTTTAATTTATGCATTTTAGTCACTGTTTATTTCTGATTTGGCCACTATCC
* * *
180487 TTTCAATTTACGCATTTTGGTCACT
1 TTTTAATTTATGCATTTTAGTCACT
180512 ACTTTTTTTT
Statistics
Matches: 64, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
50 22 0.34
51 42 0.66
ACGTcount: A:0.19, C:0.17, G:0.12, T:0.52
Consensus pattern (51 bp):
TTTTAATTTATGCATTTTAGTCACTGTTTATTTCTGATTTGGCCACTATCC
Found at i:180539 original size:22 final size:23
Alignment explanation
Indices: 180500--180542 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
180490 CAATTTACGC
* *
180500 ATTTTGGTCACTACTTTTTTTTT
1 ATTTGGGTAACTACTTTTTTTTT
180523 ATTTGGGTAACTA-TTTTTTT
1 ATTTGGGTAACTACTTTTTTT
180543 ATTTAATTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.16, C:0.09, G:0.12, T:0.63
Consensus pattern (23 bp):
ATTTGGGTAACTACTTTTTTTTT
Found at i:184090 original size:3 final size:3
Alignment explanation
Indices: 184077--184137 Score: 108
Period size: 3 Copynumber: 21.0 Consensus size: 3
184067 TCGTCCTGTT
184077 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
184123 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
184138 CAAAATCGGG
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 4 0.07
3 52 0.93
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:184112 original size:26 final size:26
Alignment explanation
Indices: 184077--184135 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
184067 TCGTCCTGTT
*
184077 TTATTTTATTATTATTATTATTATTA
1 TTATTATATTATTATTATTATTATTA
184103 TTATTATATTATTATTATTATTATTA
1 TTATTATATTATTATTATTATTATTA
184129 TTATTAT
1 TTATTAT
184136 TACAAAATCG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (26 bp):
TTATTATATTATTATTATTATTATTA
Found at i:186392 original size:43 final size:43
Alignment explanation
Indices: 186335--186420 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
186325 CCTAATTTTT
* *
186335 ATGTTATTTGTTATGTCGTGTTTGAATTATATATGTTTTAATA
1 ATGTTATTTATTATGTCATGTTTGAATTATATATGTTTTAATA
186378 ATGTTATTTATTATGTCATGTTTGAATTATATATGTTTTAATA
1 ATGTTATTTATTATGTCATGTTTGAATTATATATGTTTTAATA
186421 TTATTATATG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.28, C:0.02, G:0.14, T:0.56
Consensus pattern (43 bp):
ATGTTATTTATTATGTCATGTTTGAATTATATATGTTTTAATA
Found at i:186415 original size:15 final size:15
Alignment explanation
Indices: 186353--186434 Score: 53
Period size: 15 Copynumber: 5.4 Consensus size: 15
186343 TGTTATGTCG
186353 TGTTTGAATTATATA
1 TGTTTGAATTATATA
* * *
186368 TGTTTTAATAATGT-
1 TGTTTGAATTATATA
* *
186382 TATTT--ATTATGTCA
1 TGTTTGAATTATAT-A
186396 TGTTTGAATTATATA
1 TGTTTGAATTATATA
*
186411 TGTTTTAATATTATTATA
1 TG-TTTGA-ATTA-TATA
186429 TGTTTG
1 TGTTTG
186435 TACTTGGAAG
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
12 6 0.12
14 8 0.16
15 14 0.27
16 10 0.20
17 7 0.14
18 6 0.12
ACGTcount: A:0.29, C:0.01, G:0.12, T:0.57
Consensus pattern (15 bp):
TGTTTGAATTATATA
Found at i:189883 original size:3 final size:3
Alignment explanation
Indices: 189875--189900 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
189865 AAGTATTAAC
189875 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
189901 CGTAATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:193256 original size:16 final size:17
Alignment explanation
Indices: 193237--193273 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
193227 AATCATTTTG
193237 GGTA-AAAGCATGCCCA
1 GGTATAAAGCATGCCCA
*
193253 GGTATAAAGCATGCCCG
1 GGTATAAAGCATGCCCA
193270 GGTA
1 GGTA
193274 GAAATGCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.32, C:0.22, G:0.30, T:0.16
Consensus pattern (17 bp):
GGTATAAAGCATGCCCA
Found at i:197611 original size:36 final size:36
Alignment explanation
Indices: 197520--197632 Score: 145
Period size: 36 Copynumber: 3.1 Consensus size: 36
197510 TTTAAAATTG
* * * *
197520 TTTCTCTCGAAACAAATGTCGTCTTGCTAGAGACAA
1 TTTCTCTTGAAACAAATTTCGTCTCGCTTGAGACAA
* * *
197556 TTTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACAA
1 TTTCTCTT-GAAACAAATTTCGTCTCGCTTGAGACAA
*
197593 TTTCTCTTGAAACAAATTTCGTCTCGCTTGAGACAG
1 TTTCTCTTGAAACAAATTTCGTCTCGCTTGAGACAA
197629 TTTC
1 TTTC
197633 CCCTGAAATG
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
36 35 0.54
37 30 0.46
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.37
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTCGTCTCGCTTGAGACAA
Found at i:197622 original size:21 final size:20
Alignment explanation
Indices: 197566--197623 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 20
197556 TTTTTCTTAA
197566 AAACAAATTTTGTCTCGCTTG
1 AAACAAA-TTTGTCTCGCTTG
*
197587 AGAC-AA-TT-TCT--CTTG
1 AAACAAATTTGTCTCGCTTG
197602 AAACAAATTTCGTCTCGCTTG
1 AAACAAATTT-GTCTCGCTTG
197623 A
1 A
197624 GACAGTTTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 12
0.67 0.05 0.28
Matches are distributed among these distances:
15 7 0.24
16 2 0.07
17 5 0.17
18 2 0.07
19 3 0.10
20 2 0.07
21 8 0.28
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (20 bp):
AAACAAATTTGTCTCGCTTG
Found at i:197866 original size:36 final size:35
Alignment explanation
Indices: 197826--197916 Score: 112
Period size: 36 Copynumber: 2.5 Consensus size: 35
197816 CTTTGAGTAT
197826 GTTTCCATTGAAACATATTTTGTCTCTCTTGAGACA
1 GTTTCC-TTGAAACATATTTTGTCTCTCTTGAGACA
* * *
197862 GTTTCCTTTGAAACATGTGTTGTCTCTCTTGAGATA
1 GTTTCC-TTGAAACATATTTTGTCTCTCTTGAGACA
*
197898 GTCTCTCTTGAAACA-ATTT
1 GTTTC-CTTGAAACATATTT
197917 ATCCCTAAAG
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
35 2 0.04
36 44 0.94
37 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (35 bp):
GTTTCCTTGAAACATATTTTGTCTCTCTTGAGACA
Found at i:197873 original size:66 final size:67
Alignment explanation
Indices: 197745--197875 Score: 219
Period size: 66 Copynumber: 2.0 Consensus size: 67
197735 CTTAAGATAT
* *
197745 AAATCTTTGAGTTTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 AAATCTTTGAGTATGTTTCCATTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
197810 CA
66 CA
* *
197812 AAATCTTTGAGTATGTTTCCATTGAAACATA-TTTTGTCTCTCTTGAGACAGTTTCCTTTGAAAC
1 AAATCTTTGAGTATGTTTCCATTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
197876 ATGTGTTGTC
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
66 32 0.53
67 28 0.47
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (67 bp):
AAATCTTTGAGTATGTTTCCATTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
CA
Found at i:197893 original size:21 final size:20
Alignment explanation
Indices: 197833--197893 Score: 51
Period size: 21 Copynumber: 3.2 Consensus size: 20
197823 TATGTTTCCA
*
197833 TTGAAACATATTTTGTCTCTC
1 TTGAAACAT-TGTTGTCTCTC
*
197854 TTGAGACA--GTT-TC-CT-
1 TTGAAACATTGTTGTCTCTC
197869 TTGAAACATGTGTTGTCTCTC
1 TTGAAACAT-TGTTGTCTCTC
197890 TTGA
1 TTGA
197894 GATAGTCTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 12
0.67 0.07 0.26
Matches are distributed among these distances:
15 7 0.23
16 2 0.06
17 2 0.06
18 5 0.16
19 2 0.06
20 2 0.06
21 11 0.35
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.44
Consensus pattern (20 bp):
TTGAAACATTGTTGTCTCTC
Found at i:198157 original size:134 final size:133
Alignment explanation
Indices: 197940--198278 Score: 441
Period size: 134 Copynumber: 2.5 Consensus size: 133
197930 GTCAGTTGTT
* * * * *
197940 CTCATCACGTAGTAATCGTGTCATCTACCGACCATATCTCCTCATCACGTAGGAGCCCCATC-AC
1 CTCATCACGTAGGAATCGTGTCATCCACCGACCAGATCTCCTCATCACGTAGGAG-CACGTCAAC
* * * * *
198004 CATTATATAACTAGCCATCCTCATCACGTAGAAACTA-TGTTCTCATCATCCCTAAAGATGGCCA
65 C-TTAGATAACCAGCCATCCTCATCACATAGAAA-TAGTGTTATCATCACCCCTAAAGATGGCCA
198068 ACCATC
128 ACCATC
* *
198074 CTCATCACGTAGGAA-CTGTGTCATCCACTGACCAGATCTCCTCATCACGTAGTAGTCACGTCAA
1 CTCATCACGTAGGAATC-GTGTCATCCACCGACCAGATCTCCTCATCACGTAGGAG-CACGTCAA
* *
198138 CCTTAGATAACCAGCCATCCTCATCGCATAGGAATAGTGTTATCATCACCCCTAAAGATGGCCAA
64 CCTTAGATAACCAGCCATCCTCATCACATAGAAATAGTGTTATCATCACCCCTAAAGATGGCCAA
198203 CCATC
129 CCATC
* * *
198208 CTCATCACGTATGAATCATGTCATCCACCGAACAGATCTCCTCATCACGTAGGAGCAGCGTCAAC
1 CTCATCACGTAGGAATCGTGTCATCCACCGACCAGATCTCCTCATCACGTAGGAGCA-CGTCAAC
*
198273 ATTAGA
65 CTTAGA
198279 GATCCAAAAT
Statistics
Matches: 179, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
133 5 0.03
134 170 0.95
135 4 0.02
ACGTcount: A:0.29, C:0.32, G:0.14, T:0.24
Consensus pattern (133 bp):
CTCATCACGTAGGAATCGTGTCATCCACCGACCAGATCTCCTCATCACGTAGGAGCACGTCAACC
TTAGATAACCAGCCATCCTCATCACATAGAAATAGTGTTATCATCACCCCTAAAGATGGCCAACC
ATC
Found at i:198616 original size:22 final size:22
Alignment explanation
Indices: 198591--198635 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
198581 ATCAACCAGC
*
198591 AGCCAACCCGAAGCCCAACTGA
1 AGCCAACCAGAAGCCCAACTGA
*
198613 AGCCAACCAGAAGCCCAATTGA
1 AGCCAACCAGAAGCCCAACTGA
198635 A
1 A
198636 ACCCATCAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.36, G:0.18, T:0.07
Consensus pattern (22 bp):
AGCCAACCAGAAGCCCAACTGA
Found at i:200708 original size:17 final size:18
Alignment explanation
Indices: 200679--200712 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
200669 TAACGCATAC
200679 CAATTTTTGTCTTAAAAA
1 CAATTTTTGTCTTAAAAA
200697 CAATTTTT-TCTTAAAA
1 CAATTTTTGTCTTAAAA
200713 TTGTTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (18 bp):
CAATTTTTGTCTTAAAAA
Found at i:200846 original size:25 final size:24
Alignment explanation
Indices: 200805--200896 Score: 107
Period size: 25 Copynumber: 3.8 Consensus size: 24
200795 ATTCAAAATC
*
200805 ATAATT-TTTTTTCAAAATAA-AGT
1 ATAATTATTTTTTTAAAATAATA-T
200828 CATAATTATTTTTTTAAAATAATAT
1 -ATAATTATTTTTTTAAAATAATAT
*
200853 TTAATTATTTTTTTTAAAATAATAT
1 ATAATTA-TTTTTTTAAAATAATAT
*
200878 TTAATTATTTTTTCTAAAA
1 ATAATTATTTTTT-TAAAA
200897 AAATGGTTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
24 18 0.29
25 43 0.69
26 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (24 bp):
ATAATTATTTTTTTAAAATAATAT
Found at i:206822 original size:2 final size:2
Alignment explanation
Indices: 206817--206842 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
206807 ATACGTCTAC
206817 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
206843 GCATAAGCTA
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:206973 original size:18 final size:19
Alignment explanation
Indices: 206936--206984 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
206926 GTCATAATAC
206936 CCATATATACAATATAGCAT
1 CCATATATA-AATATAGCAT
*
206956 CCATATATAATTAT-GCAT
1 CCATATATAAATATAGCAT
* *
206974 ACGTATATAAA
1 CCATATATAAA
206985 AATATTTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 12 0.48
19 4 0.16
20 9 0.36
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.33
Consensus pattern (19 bp):
CCATATATAAATATAGCAT
Found at i:207637 original size:131 final size:133
Alignment explanation
Indices: 207467--207707 Score: 369
Period size: 131 Copynumber: 1.8 Consensus size: 133
207457 GAGTCTGAAT
* * * *
207467 CATAATAATGTGGATCATACCCAGGATATGGTCACCACAAGGTCGAATCGAATAATAGAAACAAT
1 CATAATAATGTGGATCATACCCAGAATATGGTCACCACAACGTCAAATCGAATAATAGAAACAAC
*
207532 AAATAAATAAAT-A-AACAATGGTTAGAGTGCAATAAAATAAAAGTCAGTAGTTAGCAGAGTCCA
66 AAATAAATAAATAATAACAATGGTTAAAGTGCAATAAAATAAAAGTCAGTAGTTAGCAGAGTCCA
207595 AAC
131 AAC
* * * * *
207598 CATAGTAATGTGGATCATACCCCGAATCTGGTCAGCACAACGTCAAATCGAATATTAGAAACAAC
1 CATAATAATGTGGATCATACCCAGAATATGGTCACCACAACGTCAAATCGAATAATAGAAACAAC
207663 AAATAAATAAATAAATAACAATGGTTAAAGTGCAATAAAATAAAA
66 AAATAAATAAAT-AATAACAATGGTTAAAGTGCAATAAAATAAAA
207708 CTTAGTGGTT
Statistics
Matches: 97, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
131 68 0.70
133 1 0.01
134 28 0.29
ACGTcount: A:0.48, C:0.15, G:0.16, T:0.22
Consensus pattern (133 bp):
CATAATAATGTGGATCATACCCAGAATATGGTCACCACAACGTCAAATCGAATAATAGAAACAAC
AAATAAATAAATAATAACAATGGTTAAAGTGCAATAAAATAAAAGTCAGTAGTTAGCAGAGTCCA
AAC
Found at i:208833 original size:139 final size:139
Alignment explanation
Indices: 208627--209183 Score: 658
Period size: 139 Copynumber: 4.0 Consensus size: 139
208617 ATCTGGAGAC
* * * * * *
208627 AATTTGGTGACAACATGATTCCTACGTGATGAGGAAGTCTAATTGCCTAAGGATGACGCTGCTCC
1 AATTTGGAGACAACACGATTCCTACGTGATGAGGAAGTCTGATTGTCTTAGGATGACACTGCTCC
* * * * *
208692 TACACGTTGAGGAGATCTGGTCAGTGGATGACATTGTTCCTACATGATGAGGACATCTAGCCAAC
66 TACGCGTTGAGGAGATCTGGTCAGTGGACGACATTATTCCTACGTGATGAGGACGTCTAGCCAAC
208757 TTTAGGGAT
131 TTTAGGGAT
* * * * * * *
208766 AACTTAGAGACAACACGATTCCTATGTGATGAGGAATTCTGATTATCTTAGTATGACACTACTCC
1 AATTTGGAGACAACACGATTCCTACGTGATGAGGAAGTCTGATTGTCTTAGGATGACACTGCTCC
* * * * **
208831 TACGTGTTGAGGAGACCTGGT-ATGTGGACGACATTGTTCCTATGTGATGAGGACGTCTAGCCGT
66 TACGCGTTGAGGAGATCTGGTCA-GTGGACGACATTATTCCTACGTGATGAGGACGTCTAGCCAA
208895 CTTTAGGGAT
130 CTTTAGGGAT
* * * *
208905 GATTTGGAGACAACATGGTTCCTACGTGATGAGGAAGTCTGATTGTCTGAGGATGACGA-TGCTC
1 AATTTGGAGACAACACGATTCCTACGTGATGAGGAAGTCTGATTGTCTTAGGATGAC-ACTGCTC
* *
208969 CTACGCGTTAAGGAGATCTGGTCTA-TGGAAGACATTATTCCTACGTGATGAGGACGTCTAG-CA
65 CTACGCGTTGAGGAGATCTGGTC-AGTGGACGACATTATTCCTACGTGATGAGGACGTCTAGCCA
*
209032 ATCATTAGGGAT
129 A-CTTTAGGGAT
* * * *
209044 AATTTGGAGACAACACGGTTGCTACGTGATAAGGAAGTCTGATTGT-TTGAGGATGATGACT-CT
1 AATTTGGAGACAACACGATTCCTACGTGATGAGGAAGTCTGATTGTCTT-AGGATGA-CACTGCT
* * * *
209107 CCTACGCGTTGAGGAGATCTGTTCGGTGGACGTCATTATTCCTACGTGATGAGGACGTCTAGCCG
64 CCTACGCGTTGAGGAGATCTGGTCAGTGGACGACATTATTCCTACGTGATGAGGACGTCTAGCCA
*
209172 TCTTTAGGGAT
129 ACTTTAGGGAT
209183 A
1 A
209184 TTTTTTTTTC
Statistics
Matches: 352, Mismatches: 56, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
138 3 0.01
139 345 0.98
140 3 0.01
141 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (139 bp):
AATTTGGAGACAACACGATTCCTACGTGATGAGGAAGTCTGATTGTCTTAGGATGACACTGCTCC
TACGCGTTGAGGAGATCTGGTCAGTGGACGACATTATTCCTACGTGATGAGGACGTCTAGCCAAC
TTTAGGGAT
Found at i:209138 original size:278 final size:277
Alignment explanation
Indices: 208628--209186 Score: 766
Period size: 278 Copynumber: 2.0 Consensus size: 277
208618 TCTGGAGACA
* *
208628 ATTTGGTGACAACATGATTCCTACGTGATGAGGAAGTCTAATTGCCTAAGGATGACGCTGCTCCT
1 ATTTGGAGACAACATGATTCCTACGTGATGAGGAAGTCTAATTGCCTAAGGATGACGATGCTCCT
* * * *
208693 ACACGTTGAGGAGATCTGGTCAGTGGATGACATTGTTCCTACATGATGAGGACATCTAGCCAACT
66 ACACGTTAAGGAGATCTGGTCAGTGGAAGACATTATTCCTACATGATGAGGACATCTAGCCAACA
* * * *
208758 TTAGGGATAACTTAGAGACAACACGATTCCTATGTGATGAGGAATTCTGATTATCTTAGTATGAC
131 TTAGGGATAACTTAGAGACAACACGATTCCTACGTGATAAGGAAGTCTGATTATCTTAGGATGAC
* * * *
208823 ACTACTCCTACGTGTTGAGGAGACCTGGTATGTGGACGACATTGTTCCTATGTGATGAGGACGTC
196 ACTACTCCTACGCGTTGAGGAGACCTGGTAGGTGGACGACATTATTCCTACGTGATGAGGACGTC
208888 TAGCCGTCTTTAGGGAT
261 TAGCCGTCTTTAGGGAT
* * * *
208905 GATTTGGAGACAACATGGTTCCTACGTGATGAGGAAGTCTGATTGTCTGAGGATGACGATGCTCC
1 -ATTTGGAGACAACATGATTCCTACGTGATGAGGAAGTCTAATTGCCTAAGGATGACGATGCTCC
* * *
208970 TACGCGTTAAGGAGATCTGGTCTA-TGGAAGACATTATTCCTACGTGATGAGGACGTCTAG-CAA
65 TACACGTTAAGGAGATCTGGTC-AGTGGAAGACATTATTCCTACATGATGAGGACATCTAGCCAA
* * * * *
209033 TCATTAGGGATAATTTGGAGACAACACGGTTGCTACGTGATAAGGAAGTCTGATTGT-TTGAGGA
129 -CATTAGGGATAACTTAGAGACAACACGATTCCTACGTGATAAGGAAGTCTGATTATCTT-AGGA
* * * * *
209097 TGATGACT-CTCCTACGCGTTGAGGAGATCTGTTCGGTGGACGTCATTATTCCTACGTGATGAGG
192 TGA-CACTACTCCTACGCGTTGAGGAGACCTGGTAGGTGGACGACATTATTCCTACGTGATGAGG
209161 ACGTCTAGCCGTCTTTAGGGAT
256 ACGTCTAGCCGTCTTTAGGGAT
209183 ATTT
1 ATTT
209187 TTTTTTCAAG
Statistics
Matches: 246, Mismatches: 31, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
277 9 0.04
278 233 0.95
279 4 0.02
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (277 bp):
ATTTGGAGACAACATGATTCCTACGTGATGAGGAAGTCTAATTGCCTAAGGATGACGATGCTCCT
ACACGTTAAGGAGATCTGGTCAGTGGAAGACATTATTCCTACATGATGAGGACATCTAGCCAACA
TTAGGGATAACTTAGAGACAACACGATTCCTACGTGATAAGGAAGTCTGATTATCTTAGGATGAC
ACTACTCCTACGCGTTGAGGAGACCTGGTAGGTGGACGACATTATTCCTACGTGATGAGGACGTC
TAGCCGTCTTTAGGGAT
Found at i:209304 original size:37 final size:37
Alignment explanation
Indices: 209254--209374 Score: 162
Period size: 33 Copynumber: 3.4 Consensus size: 37
209244 CAATTGTTTA
*
209254 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTT
*
209291 TGTTTCAAGAGAAACTG--T--AGCGAGACGAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTT
* *
209324 TGTTTCGAGAGAAATTGTCTCAAGCGAGACAAAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTT
*
209360 TGTTTCAAGGGAAAC
1 TGTTTCAAGAGAAAC
209375 AATCTCAATT
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
33 28 0.39
35 2 0.03
36 14 0.19
37 28 0.39
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTT
Found at i:209381 original size:36 final size:36
Alignment explanation
Indices: 209190--209478 Score: 173
Period size: 37 Copynumber: 8.4 Consensus size: 36
209180 GATATTTTTT
209190 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
* ** ** *
209226 TTTCAAGGGAAACAATCTC-A-ATTG-----TTTATG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT-TG
209256 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTG
* *
209293 TTTCAAGAGAAACTG--T--AGCGAGACGAAACTTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATTTG
* * *
209326 TTTCGAGAGAAATTGTCTCAAGCGAGACAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
* ** ** *
209362 TTTCAAGGGAAACAATCTC-A-ATTG-----TTTATG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT-TG
* * * *
209392 TTTCAAAAGAAATTATCTCAAGAGAGATAAAACTTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTG
* * *
209429 TTTTAAGAGAAACTGTCTCAAGCGAGACGAAACTTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATTTG
*
209466 TTTCGAGAGAAAC
1 TTTCAAGAGAAAC
209479 AACCTCAACG
Statistics
Matches: 187, Mismatches: 42, Indels: 47
0.68 0.15 0.17
Matches are distributed among these distances:
29 4 0.02
30 35 0.19
31 2 0.01
32 4 0.02
33 24 0.13
34 6 0.03
35 4 0.02
36 37 0.20
37 64 0.34
38 7 0.04
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (36 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
Found at i:209411 original size:66 final size:67
Alignment explanation
Indices: 209190--209441 Score: 287
Period size: 66 Copynumber: 3.7 Consensus size: 67
209180 GATATTTTTT
*
209190 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACAATCTCAATTGTTTA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAATTGTTTA
209254 TG
66 TG
** ** *
209256 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTAGCGAGA-CGAA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACAATCTC-A-ATTG--
*
209320 ACTT-TG
62 -TTTATG
* * * *
209326 TTTCGAGAGAAATTGTCTCAAGCGAGACAAAA-TTTGTTTCAAGGGAAACAATCTCAATTGTTTA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAATTGTTTA
209390 TG
66 TG
* * * * *
209392 TTTCAAAAGAAATTATCTCAAGAGAGATAAAACTTTGTTTTAAGAGAAAC
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAAC
209442 TGTCTCAAGC
Statistics
Matches: 153, Mismatches: 24, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
65 2 0.01
66 61 0.40
67 34 0.22
68 4 0.03
69 19 0.12
70 31 0.20
71 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (67 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAATTGTTTA
TG
Found at i:209439 original size:136 final size:138
Alignment explanation
Indices: 209190--209478 Score: 474
Period size: 136 Copynumber: 2.1 Consensus size: 138
209180 GATATTTTTT
*
209190 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAATTGTTTAT
1 TTTCGAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAATTGTTTAT
* *
209255 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTG-T-AGCGAGACG
66 GTTTCAAAAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGCTAAGCGAGACG
209318 AAACTTTG
131 AAACTTTG
* *
209326 TTTCGAGAGAAATTGTCTCAAGCGAGACAAAATTTGTTTCAAGGGAAACAATCTCAATTGTTTAT
1 TTTCGAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAATTGTTTAT
* * *
209391 GTTTCAAAAGAAATTATCTCAAGAGAGATAAAACTTTGTTTTAAGAGAAACTGTCTCAAGCGAGA
66 GTTTCAAAAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTG-CT-AAGCGAGA
209456 CGAAACTTTG
129 CGAAACTTTG
209466 TTTCGAGAGAAAC
1 TTTCGAGAGAAAC
209479 AACCTCAACG
Statistics
Matches: 140, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
136 110 0.79
138 1 0.01
140 29 0.21
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (138 bp):
TTTCGAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAATTGTTTAT
GTTTCAAAAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGCTAAGCGAGACG
AAACTTTG
Found at i:209535 original size:104 final size:101
Alignment explanation
Indices: 209425--209681 Score: 282
Period size: 104 Copynumber: 2.5 Consensus size: 101
209415 GAGATAAAAC
* * *
209425 TTTGTTTTAAGAGAAACTGTCTCAAGCGAGACGAAACTTTGTTTCGAGAGAAACAACCTCAACGG
1 TTTGTTTTAAGAGAAACTGTCTCAAGCGAGACGAAA-TTTGTTTTGAGAAAAACAACCTCAAAGG
209490 TTTATCAACTTTGTTACAAGTGAAACAATTTCAGAATT
65 -TTATCAACTTTGTTACAAGTGAAACAATTTCAGAATT
* * * * * * *
209528 TTGTGTTTTGAGGGAAAATTGTCTCAAACGAAACGAAATTTGTTTTTAAGAAAAACAATCTCAAA
1 TT-TGTTTTAAGAG-AAACTGTCTCAAGCGAGACGAAATTTG-TTTTGAGAAAAACAACCTCAAA
* * * *
209593 TGTTATCAATTTTGTTTCAAGTGAAACAATTTTAGAATT
63 GGTTATCAACTTTGTTACAAGTGAAACAATTTCAGAATT
* * * *
209632 TTTGTTTCGAAGAAAAACTGTCTAAAGTGAGAC-AAATTTTGTTTTGAGAA
1 TTTGTTT-TAAGAGAAACTGTCTCAAGCGAGACGAAA-TTTGTTTTGAGAA
209682 CAAATCTCAA
Statistics
Matches: 125, Mismatches: 24, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
102 11 0.09
103 25 0.20
104 51 0.41
105 38 0.30
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (101 bp):
TTTGTTTTAAGAGAAACTGTCTCAAGCGAGACGAAATTTGTTTTGAGAAAAACAACCTCAAAGGT
TATCAACTTTGTTACAAGTGAAACAATTTCAGAATT
Found at i:209718 original size:100 final size:99
Alignment explanation
Indices: 209510--209834 Score: 304
Period size: 100 Copynumber: 3.2 Consensus size: 99
209500 TTGTTACAAG
* * * * * * *
209510 TGAAACAATTTCAGAATTTTGTGTTTTGAGGGAAAATTGTCTCAAACGAAACGAAATTTGTTTTT
1 TGAAACAATTTCA-AAATTTGT-TTTT-AAGAAAAACTGTCTCAAACGAGACAAAATTTATTTTT
* ** *
209575 AAGAAAAACAATCTCAAATGTTATCAATTTTGTTTCA-A
63 AAG--AAACAATCTCAAGTGAGATAAATTTTGTTTCAGA
* * *
209613 GTGAAACAATTTTAGAATTT-TTGTTTCGAAGAAAAACTGTCT-AAAGTGAGAC-AAATTT-TGT
1 -TGAAACAATTTCAAAATTTGTT-TTT--AAGAAAAACTGTCTCAAA-CGAGACAAAATTTAT-T
*
209674 TTTGAG-AACAAATCTCAAGTGAGATAAATTTTGTTTCAGA
60 TTTAAGAAAC-AATCTCAAGTGAGATAAATTTTGTTTCAGA
* *
209714 TGAAACAACTTCAAAATTTGTTTTTAAGAAAAATTGTCTCAAACGAGACAAAATTTATTTTTAAG
1 TGAAACAATTTCAAAATTTGTTTTTAAGAAAAACTGTCTCAAACGAGACAAAATTTATTTTTAAG
*
209779 AAATCAATCTCAAGTGAGATCAATTTTGTTTCAAGA
66 AAA-CAATCTCAAGTGAGATAAATTTTGTTTC-AGA
*
209815 -AAAACAATTTCAAAATTTGT
1 TGAAACAATTTCAAAATTTGT
209835 GGAAATCTGT
Statistics
Matches: 186, Mismatches: 22, Indels: 30
0.78 0.09 0.13
Matches are distributed among these distances:
98 18 0.10
99 18 0.10
100 90 0.48
101 9 0.05
102 19 0.10
103 20 0.11
104 12 0.06
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (99 bp):
TGAAACAATTTCAAAATTTGTTTTTAAGAAAAACTGTCTCAAACGAGACAAAATTTATTTTTAAG
AAACAATCTCAAGTGAGATAAATTTTGTTTCAGA
Found at i:211782 original size:22 final size:22
Alignment explanation
Indices: 211741--211784 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
211731 TTATTTTCAA
*
211741 AATTTTGAAAAATATCAAAAAT
1 AATTTTGAAAAATATAAAAAAT
*
211763 AATTTTGAAAAATGAAAAAAAA
1 AATTTTGAAAAAT-ATAAAAAA
211785 AAATATTGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (22 bp):
AATTTTGAAAAATATAAAAAAT
Found at i:213104 original size:66 final size:66
Alignment explanation
Indices: 212947--213298 Score: 474
Period size: 66 Copynumber: 5.3 Consensus size: 66
212937 GAATACCATG
* * * *
212947 AGTGGCACCTTTTATGTCGATAATGCACCGTTATGCATTAAACAAAATTGATCGATAATTTT-AT
1 AGTGGCACCTTTTATGCCGATAATGCACTGTTATGCATTAATCAAAATCGATCGATAATTTTCAT
213011 T
66 T
* * *
213012 AGTGGCACCTTTTATGTCGATAATGCACTGTTACGCATTAATCAAAATCGATTGATAATTTTCAT
1 AGTGGCACCTTTTATGCCGATAATGCACTGTTATGCATTAATCAAAATCGATCGATAATTTTCAT
213077 T
66 T
* * *
213078 AGTGGCGCCTTTTATGCCGATAATGCACCGTTATGCATTAATCAAAATCGATTGATAATTTTCAT
1 AGTGGCACCTTTTATGCCGATAATGCACTGTTATGCATTAATCAAAATCGATCGATAATTTTCAT
213143 T
66 T
* * *
213144 AGTGGCACATTTTATGTCGATAATGCA-TCGTTATGCATTAATCAAAGTCGATCGATAATTTTCA
1 AGTGGCACCTTTTATGCCGATAATGCACT-GTTATGCATTAATCAAAATCGATCGATAATTTTCA
213208 TT
65 TT
* * * * *
213210 AGTGGAACTTTTTTATGCCAATAATGCACTGATATGCATTAATCAAAATCGATCAATAATTTTCA
1 AGTGGCAC-CTTTTATGCCGATAATGCACTGTTATGCATTAATCAAAATCGATCGATAATTTTCA
213275 TT
65 TT
* * * *
213277 AATGGCTCCGTTTATACCGATA
1 AGTGGCACCTTTTATGCCGATA
213299 TGTACCTATG
Statistics
Matches: 254, Mismatches: 29, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
65 57 0.22
66 141 0.56
67 55 0.22
68 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37
Consensus pattern (66 bp):
AGTGGCACCTTTTATGCCGATAATGCACTGTTATGCATTAATCAAAATCGATCGATAATTTTCAT
T
Found at i:215145 original size:17 final size:17
Alignment explanation
Indices: 215123--215187 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 17
215113 GTGCTTATTG
215123 TCTTCTTTTTCTCTTTT
1 TCTTCTTTTTCTCTTTT
*
215140 TCTTCTTTCTTGTCTTTGT
1 TCTTCTTT-TTCTCTTT-T
* *
215159 TCTT-TTCTT-TGTTTT
1 TCTTCTTTTTCTCTTTT
215174 T-TTC-TTTTCTCTTT
1 TCTTCTTTTTCTCTTT
215188 GCTTTTTAGT
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
14 5 0.13
15 6 0.15
16 4 0.10
17 10 0.26
18 9 0.23
19 5 0.13
ACGTcount: A:0.00, C:0.20, G:0.05, T:0.75
Consensus pattern (17 bp):
TCTTCTTTTTCTCTTTT
Found at i:215176 original size:12 final size:12
Alignment explanation
Indices: 215137--215180 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
215127 CTTTTTCTCT
215137 TTTTCTTCT-TTC
1 TTTTCTT-TGTTC
*
215149 TTGTCTTTGTTC
1 TTTTCTTTGTTC
*
215161 TTTTCTTTGTTT
1 TTTTCTTTGTTC
215173 TTTTCTTT
1 TTTTCTTT
215181 TCTCTTTGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 1 0.04
12 27 0.96
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (12 bp):
TTTTCTTTGTTC
Found at i:215186 original size:24 final size:23
Alignment explanation
Indices: 215129--215194 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 23
215119 ATTGTCTTCT
215129 TTTTCTCTTTTTCTTCTTTCTTGTC
1 TTTTCTC-TTTTCTT-TTTCTTGTC
* *
215154 TTTGT-TCTTTTCTTTGTTTTTTTC
1 TTT-TCTCTTTTCTTT-TTCTTGTC
*
215178 TTTTCTCTTTGCTTTTT
1 TTTTCTCTTTTCTTTTT
215195 AGTTTTTGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
23 4 0.11
24 25 0.71
25 5 0.14
26 1 0.03
ACGTcount: A:0.00, C:0.18, G:0.06, T:0.76
Consensus pattern (23 bp):
TTTTCTCTTTTCTTTTTCTTGTC
Found at i:215208 original size:8 final size:8
Alignment explanation
Indices: 215185--215231 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 8
215175 TTCTTTTCTC
215185 TTTGCTTT
1 TTTGCTTT
*
215193 TTAG--TT
1 TTTGCTTT
215199 TTTGCTTT
1 TTTGCTTT
*
215207 TTTTC-TT
1 TTTGCTTT
215214 TTTGCTTT
1 TTTGCTTT
215222 TTTGCTTT
1 TTTGCTTT
215230 TT
1 TT
215232 GCTATTTTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
6 5 0.16
7 6 0.19
8 21 0.66
ACGTcount: A:0.02, C:0.11, G:0.11, T:0.77
Consensus pattern (8 bp):
TTTGCTTT
Found at i:215215 original size:15 final size:15
Alignment explanation
Indices: 215178--215251 Score: 78
Period size: 15 Copynumber: 5.0 Consensus size: 15
215168 TGTTTTTTTC
*
215178 TTTTCTCTTTGC-TT
1 TTTTCTTTTTGCTTT
**
215192 TTTAGTTTTTGCTTT
1 TTTTCTTTTTGCTTT
215207 TTTTCTTTTTGCTTT
1 TTTTCTTTTTGCTTT
* *
215222 TTTGCTTTTTGCTAT
1 TTTTCTTTTTGCTTT
* *
215237 TTTCCTCTTTGCTTT
1 TTTTCTTTTTGCTTT
215252 GATTTAATGT
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
14 9 0.18
15 40 0.82
ACGTcount: A:0.03, C:0.16, G:0.09, T:0.72
Consensus pattern (15 bp):
TTTTCTTTTTGCTTT
Found at i:215231 original size:30 final size:29
Alignment explanation
Indices: 215178--215251 Score: 103
Period size: 30 Copynumber: 2.5 Consensus size: 29
215168 TGTTTTTTTC
*
215178 TTTTCTCTTTGCTTTTTAGTTTTTGCTTT
1 TTTTCTCTTTGCTTTTTAGTTTTTGCTAT
* *
215207 TTTTCTTTTTGCTTTTTTGCTTTTTGCTAT
1 TTTTCTCTTTGCTTTTTAG-TTTTTGCTAT
*
215237 TTTCCTCTTTGCTTT
1 TTTTCTCTTTGCTTT
215252 GATTTAATGT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 17 0.44
30 22 0.56
ACGTcount: A:0.03, C:0.16, G:0.09, T:0.72
Consensus pattern (29 bp):
TTTTCTCTTTGCTTTTTAGTTTTTGCTAT
Found at i:215239 original size:8 final size:7
Alignment explanation
Indices: 215185--215251 Score: 64
Period size: 7 Copynumber: 9.1 Consensus size: 7
215175 TTCTTTTCTC
215185 TTTGCTT
1 TTTGCTT
215192 TTTAG-TT
1 TTT-GCTT
215199 TTTGCTTT
1 TTTGC-TT
*
215207 TTTTCTT
1 TTTGCTT
215214 TTTGCTTT
1 TTTGC-TT
215222 TTTGCTT
1 TTTGCTT
215229 TTTGCTAT
1 TTTGCT-T
* *
215237 TTTCCTC
1 TTTGCTT
215244 TTTGCTT
1 TTTGCTT
215251 T
1 T
215252 GATTTAATGT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
6 1 0.02
7 28 0.57
8 20 0.41
ACGTcount: A:0.03, C:0.15, G:0.10, T:0.72
Consensus pattern (7 bp):
TTTGCTT
Found at i:219634 original size:42 final size:41
Alignment explanation
Indices: 219571--219721 Score: 151
Period size: 41 Copynumber: 3.5 Consensus size: 41
219561 ATAGGTCAAA
219571 AAACGCCGCAAAAGGTCGATATCTATAGCGGCG-TTTTGGAAC
1 AAACGCCGCAAAAGGTCGATATCTAT--CGGCGTTTTTGGAAC
* * *
219613 AAACGTCGTAAAAGGTTGATATCTATCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCGATATCTATCGGCGTTTTTGGAAC
* * * * *
219654 AAACGCTGCAAACGGTCGAGATCTATCGCGGCATTTTTTGGTTAC
1 AAACGCCGCAAAAGGTCGATATCTAT--CGGC-GTTTTTGG-AAC
*
219699 AAACGCCGCAAAATGTCAGATAT
1 AAACGCCGCAAAAGGTC-GATAT
219722 ATAGCGGCAT
Statistics
Matches: 88, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
40 5 0.06
41 29 0.33
42 23 0.26
43 4 0.05
44 7 0.08
45 16 0.18
46 4 0.05
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (41 bp):
AAACGCCGCAAAAGGTCGATATCTATCGGCGTTTTTGGAAC
Found at i:219729 original size:44 final size:44
Alignment explanation
Indices: 219571--219734 Score: 142
Period size: 44 Copynumber: 3.8 Consensus size: 44
219561 ATAGGTCAAA
* * *
219571 AAACGCCGCAAAAGGTCGATATCTATAGCGGC--GTTTTGGAAC
1 AAACGCCGCAAAAGGTCGAGATATATAGCGGCATTTTTTGGAAC
* * * * * *
219613 AAACGTCGTAAAAGGT--TGATATCTATCGGC-GTTTTTGGAAC
1 AAACGCCGCAAAAGGTCGAGATATATAGCGGCATTTTTTGGAAC
* * * * *
219654 AAACGCTGCAAACGGTCGAGATCTATCGCGGCATTTTTTGGTTAC
1 AAACGCCGCAAAAGGTCGAGATATATAGCGGCATTTTTTGG-AAC
*
219699 AAACGCCGCAAAATGTC-AGATATATAGCGGCATTTT
1 AAACGCCGCAAAAGGTCGAGATATATAGCGGCATTTT
219735 CGAATAAACG
Statistics
Matches: 93, Mismatches: 24, Indels: 8
0.74 0.19 0.06
Matches are distributed among these distances:
40 9 0.10
41 21 0.23
42 14 0.15
43 9 0.10
44 24 0.26
45 16 0.17
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.27
Consensus pattern (44 bp):
AAACGCCGCAAAAGGTCGAGATATATAGCGGCATTTTTTGGAAC
Found at i:226136 original size:16 final size:16
Alignment explanation
Indices: 226111--226153 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
226101 GTGTTAATAA
*
226111 TTAGCGGTTAGGAAGG
1 TTAGCGGTTAGGAAAG
*
226127 TTAGCAGTTAGGAAAG
1 TTAGCGGTTAGGAAAG
226143 TTAGCGGTTAG
1 TTAGCGGTTAG
226154 CAGAGTCTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.28, C:0.07, G:0.37, T:0.28
Consensus pattern (16 bp):
TTAGCGGTTAGGAAAG
Found at i:226329 original size:108 final size:109
Alignment explanation
Indices: 226139--226351 Score: 268
Period size: 108 Copynumber: 2.0 Consensus size: 109
226129 AGCAGTTAGG
* * * **
226139 AAAGTTAGCGGTTAGCAGAGTCTGAACCGTAATAATGTGGATCATACCCTGGATATAGTCACCAC
1 AAAGTTAGCGGTTAGCAGAGTCCGAACCATAATAATGTAGATCATACCCCAGATATAGTCACCAC
** *
226204 AAGGTCAAATCTTATAATTCAAAC-A-AAATAAAATAAATATAAA
66 AAGGTCAAATCGAATAATACAAACAATAAAT-AAATAAATATAAA
* * * * *
226247 AAAGTTAGTGGTTAGCAGAGTCCGAACCATAATAATGTAGATCATTCCCCAGATCTGGTTACCAC
1 AAAGTTAGCGGTTAGCAGAGTCCGAACCATAATAATGTAGATCATACCCCAGATATAGTCACCAC
* *
226312 AAGGTCGAATCGAATAATAGAAACAATAAATAAATAAATA
66 AAGGTCAAATCGAATAATACAAACAATAAATAAATAAATA
226352 AATAAATAAA
Statistics
Matches: 88, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
108 74 0.84
109 10 0.11
110 4 0.05
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.24
Consensus pattern (109 bp):
AAAGTTAGCGGTTAGCAGAGTCCGAACCATAATAATGTAGATCATACCCCAGATATAGTCACCAC
AAGGTCAAATCGAATAATACAAACAATAAATAAATAAATATAAA
Found at i:226345 original size:4 final size:4
Alignment explanation
Indices: 226336--226364 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
226326 TAATAGAAAC
226336 AATA AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA AATA A
226365 TGGTTAGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:226527 original size:29 final size:29
Alignment explanation
Indices: 226495--226570 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
226485 TAAATAACAA
**
226495 TGGTTAA-AGTGAAATAAAATAAAATTTAG
1 TGGTTAATA-TGAAATAAAATAAAAGCTAG
*
226524 TGGTTAATATGTAATAAAATAAAAGCTAG
1 TGGTTAATATGAAATAAAATAAAAGCTAG
*
226553 TGGTTAATATGCAATAAA
1 TGGTTAATATGAAATAAA
226571 TAATATTGTC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 41 0.98
30 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.17, T:0.32
Consensus pattern (29 bp):
TGGTTAATATGAAATAAAATAAAAGCTAG
Found at i:235948 original size:14 final size:14
Alignment explanation
Indices: 235929--235979 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
235919 AGTCAACGGG
235929 TTGACTCGGACGAA
1 TTGACTCGGACGAA
* *
235943 TTGACTCAGATCGAG
1 TTGACTCGGA-CGAA
*
235958 TTGACTCGAAC-AA
1 TTGACTCGGACGAA
235971 TTTGACTCG
1 -TTGACTCG
235980 ATGACTAGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
13 1 0.03
14 18 0.60
15 11 0.37
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (14 bp):
TTGACTCGGACGAA
Found at i:238533 original size:15 final size:15
Alignment explanation
Indices: 238510--238543 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
238500 CAATCTCAAA
*
238510 TTCGATAATTTTAAG
1 TTCGATAATTTTAAC
*
238525 TTCGGTAATTTTAAC
1 TTCGATAATTTTAAC
238540 TTCG
1 TTCG
238544 TGAGTTTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.47
Consensus pattern (15 bp):
TTCGATAATTTTAAC
Found at i:248608 original size:30 final size:30
Alignment explanation
Indices: 248572--248628 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
248562 CTATCAAATG
248572 AGCCAGGATTAAAAGTTCCTTCCTCTAATT
1 AGCCAGGATTAAAAGTTCCTTCCTCTAATT
248602 AGCCAGGATTAAAAGTTCCTTCCTCTA
1 AGCCAGGATTAAAAGTTCCTTCCTCTA
248629 TGGAAATTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.32
Consensus pattern (30 bp):
AGCCAGGATTAAAAGTTCCTTCCTCTAATT
Found at i:249416 original size:14 final size:14
Alignment explanation
Indices: 249397--249427 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
249387 CAAGTATCGT
249397 AGAAATTCATTTAC
1 AGAAATTCATTTAC
249411 AGAAATTCATTTAC
1 AGAAATTCATTTAC
249425 AGA
1 AGA
249428 GGCATTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32
Consensus pattern (14 bp):
AGAAATTCATTTAC
Found at i:251078 original size:17 final size:17
Alignment explanation
Indices: 251056--251088 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
251046 TAAAATTATA
*
251056 ATTCGATTTTGATTTTG
1 ATTCGATTTCGATTTTG
251073 ATTCGATTTCGATTTT
1 ATTCGATTTCGATTTT
251089 AATATTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.09, G:0.15, T:0.58
Consensus pattern (17 bp):
ATTCGATTTCGATTTTG
Found at i:251968 original size:2 final size:2
Alignment explanation
Indices: 251961--251995 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
251951 ATACTTTATT
251961 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
251996 TTTACTTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:262871 original size:16 final size:17
Alignment explanation
Indices: 262836--262873 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
262826 GAAAAAATTG
*
262836 AAAAAGAGAACAAAAGA
1 AAAAAGAGAACAAAACA
*
262853 AAAAAGAGAA-AGAACA
1 AAAAAGAGAACAAAACA
262869 AAAAA
1 AAAAA
262874 TAAGGTGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAGAGAACAAAACA
Found at i:263497 original size:14 final size:14
Alignment explanation
Indices: 263478--263504 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
263468 GATCAGAACT
263478 TCAAGATTCCAGAG
1 TCAAGATTCCAGAG
263492 TCAAGATTCCAGA
1 TCAAGATTCCAGA
263505 CATGCAATCG
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:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (14 bp):
TCAAGATTCCAGAG
Found at i:264179 original size:106 final size:106
Alignment explanation
Indices: 263989--264185 Score: 243
Period size: 106 Copynumber: 1.9 Consensus size: 106
263979 CATGCTCAAC
* *** *
263989 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAACTTCCC
1 ACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTAACTGTCAACAAACAACTTCCC
* *
264054 AATTTACGAGTCAATTTCAACTTCACAGCGAAGGATATTAG
66 AATTCACGAGCCAATTTCAACTTCACAGCGAAGGATATTAG
* * * * * *
264095 ACTCGAGACATCACAAGCTCAACTTCACAGCGAAGGGGCGGCTAACTGTCAACAAACAATTTCCT
1 ACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTAACTGTCAACAAACAACTTCCC
**
264160 GGTTC-CAGAGCCAATTTCAACTTCAC
66 AATTCAC-GAGCCAATTTCAACTTCAC
264186 GACGGAGAAT
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
105 1 0.01
106 74 0.99
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (106 bp):
ACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTAACTGTCAACAAACAACTTCCC
AATTCACGAGCCAATTTCAACTTCACAGCGAAGGATATTAG
Found at i:265325 original size:20 final size:20
Alignment explanation
Indices: 265303--265390 Score: 65
Period size: 20 Copynumber: 4.3 Consensus size: 20
265293 ATTATTATTA
265303 TTTATTTCATTTATACTTTAT
1 TTTATTT-ATTTATACTTTAT
*
265324 TTTATTTATTTATA-TATA-
1 TTTATTTATTTATACTTTAT
* *
265342 TGTATTT-TTTTTACTTTGAT
1 TTTATTTATTTATACTTT-AT
* * *
265362 TTTCATATTCTTTATAATTTCT
1 TTT-AT-TTATTTATACTTTAT
265384 TTTATTT
1 TTTATTT
265391 CTGTTTTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 13
0.72 0.11 0.18
Matches are distributed among these distances:
17 5 0.09
18 8 0.15
19 4 0.08
20 11 0.21
21 11 0.21
22 6 0.11
23 8 0.15
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.68
Consensus pattern (20 bp):
TTTATTTATTTATACTTTAT
Found at i:265424 original size:19 final size:19
Alignment explanation
Indices: 265383--265429 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
265373 TTATAATTTC
* *
265383 TTTTATTTCTGTTTTTTTA
1 TTTTATTACTATTTTTTTA
265402 -TTTATTACTATTTTTTTA
1 TTTTATTACTATTTTTTTA
*
265420 TTTTAATACT
1 TTTTATTACT
265430 TATTATTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.72
Consensus pattern (19 bp):
TTTTATTACTATTTTTTTA
Found at i:265605 original size:5 final size:5
Alignment explanation
Indices: 265591--265659 Score: 63
Period size: 5 Copynumber: 14.0 Consensus size: 5
265581 TTTAACTTAC
* *
265591 ATTTT TTTTT ATTTT -TTTT ATTTT -CTTT ATTTT A-TTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
* *
265638 TTTTCT ATTTT CTTTGT ATTTT
1 ATTT-T ATTTT ATTT-T ATTTT
265660 TCCTCATTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
4 11 0.22
5 32 0.63
6 8 0.16
ACGTcount: A:0.13, C:0.04, G:0.01, T:0.81
Consensus pattern (5 bp):
ATTTT
Found at i:265607 original size:9 final size:9
Alignment explanation
Indices: 265593--265660 Score: 68
Period size: 9 Copynumber: 7.6 Consensus size: 9
265583 TAACTTACAT
265593 TTTTTTTTA
1 TTTTTTTTA
265602 TTTTTTTTA
1 TTTTTTTTA
*
265611 TTTTCTTTA
1 TTTTTTTTA
*
265620 TTTTATTTA
1 TTTTTTTTA
*
265629 -TTTTATT-
1 TTTTTTTTA
*
265636 TTTTTTCTA
1 TTTTTTTTA
265645 TTTTCTTTGTA
1 TTTT-TTT-TA
265656 TTTTT
1 TTTTT
265661 CCTCATTATT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
8 10 0.21
9 29 0.60
10 3 0.06
11 6 0.12
ACGTcount: A:0.12, C:0.04, G:0.01, T:0.82
Consensus pattern (9 bp):
TTTTTTTTA
Done.