Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008342.1 Hibiscus syriacus cultivar Beakdansim tig00111069_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: 1228932
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 6
Found at i:285 original size:114 final size:116
Alignment explanation
Indices: 76--296 Score: 328
Period size: 114 Copynumber: 1.9 Consensus size: 116
66 CGCGCGGGGC
*
76 CCCCAAAAAAGGGCCCAAAAAGTATATATATATGGCGTTTTTTCCAATAAACGCCACTATAGATG
1 CCCCAAAAAAGGGCCCAAAAAGTATATATATATGGCGTTTTTTCCAATAAACACCACTATAGATG
141 GACCTATTCGACGTTTTTTTTTTTTC-AAAAACGCCACTATTATTGTGCAG
66 GACCTATTCGACGTTTTTTTTTTTTCAAAAAACGCCACTATTATTGTGCAG
* *
191 CCCCAAAAAA-TGCCCTAAAAGTATATATATAGTGGCG-TTTTTCC-AT-AACACCACTATAGAT
1 CCCCAAAAAAGGGCCCAAAAAGTATATATATA-TGGCGTTTTTTCCAATAAACACCACTATAGAT
*
252 GGACCCTATTGCGACG-TTTTTTTTTTTCAAAAAAATGCCACTATT
65 GGA-CCTATT-CGACGTTTTTTTTTTTTC-AAAAAACGCCACTATT
297 GTTGCCCTCG
Statistics
Matches: 97, Mismatches: 4, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
112 17 0.18
113 20 0.21
114 31 0.32
115 29 0.30
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.33
Consensus pattern (116 bp):
CCCCAAAAAAGGGCCCAAAAAGTATATATATATGGCGTTTTTTCCAATAAACACCACTATAGATG
GACCTATTCGACGTTTTTTTTTTTTCAAAAAACGCCACTATTATTGTGCAG
Found at i:2039 original size:20 final size:20
Alignment explanation
Indices: 2016--2055 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2006 CAAAATGTAC
*
2016 TTAAAAC-GCTAAATTAAATA
1 TTAAAACTG-TAAATAAAATA
2036 TTAAAACTGTAAATAAAATA
1 TTAAAACTGTAAATAAAATA
2056 ATAACTATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (20 bp):
TTAAAACTGTAAATAAAATA
Found at i:4825 original size:15 final size:16
Alignment explanation
Indices: 4805--4838 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
4795 CGTCTAAATA
*
4805 TATATATAT-TGTGTG
1 TATATATATGTGTATG
4820 TATATATATGTGTATG
1 TATATATATGTGTATG
4836 TAT
1 TAT
4839 TTCTAACTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (16 bp):
TATATATATGTGTATG
Found at i:6766 original size:33 final size:32
Alignment explanation
Indices: 6710--6775 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
6700 ATCGATTCAG
* *
6710 ATCAGTATTAAATTGATCCATTTTTCAGATTAA
1 ATCAATATCAAATTGATCCATTTTT-AGATTAA
* *
6743 ATCAATATCAAATTGATCGATTTTTAGCTTAA
1 ATCAATATCAAATTGATCCATTTTTAGATTAA
6775 A
1 A
6776 CCAACCTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 7 0.24
33 22 0.76
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (32 bp):
ATCAATATCAAATTGATCCATTTTTAGATTAA
Found at i:9108 original size:27 final size:28
Alignment explanation
Indices: 9077--9132 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
9067 TTTAGTTGAA
* *
9077 AGCAGGG-GAAGGAAGTTATATAAATAC
1 AGCAGGGAAAAGGAAGATATATAAATAC
9104 AGCAGGGAAAAAGGAAGATATATAAATAC
1 AGCAGGG-AAAAGGAAGATATATAAATAC
9133 CGACGTCGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 7 0.28
29 18 0.72
ACGTcount: A:0.50, C:0.07, G:0.27, T:0.16
Consensus pattern (28 bp):
AGCAGGGAAAAGGAAGATATATAAATAC
Found at i:9852 original size:5 final size:5
Alignment explanation
Indices: 9842--9867 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
9832 CATAATTCTA
9842 TTATT TTATT TTATT TTATT TTATT T
1 TTATT TTATT TTATT TTATT TTATT T
9868 CATGAGGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:30305 original size:27 final size:27
Alignment explanation
Indices: 30271--30324 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
30261 TTCTATCAAA
30271 AAACTTTATAAAATAACACCTTATAAT
1 AAACTTTATAAAATAACACCTTATAAT
* *
30298 AAACTTTATAGAATAACATCTTATAAT
1 AAACTTTATAAAATAACACCTTATAAT
30325 CGATAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.50, C:0.13, G:0.02, T:0.35
Consensus pattern (27 bp):
AAACTTTATAAAATAACACCTTATAAT
Found at i:30406 original size:27 final size:27
Alignment explanation
Indices: 30367--30418 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
30357 AAATTATATA
*
30367 TCATTCATATATTGAAAGAATAATTTG
1 TCATACATATATTGAAAGAATAATTTG
* * *
30394 TCATACATTTATTGAATGGATAATT
1 TCATACATATATTGAAAGAATAATT
30419 GATCTAAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (27 bp):
TCATACATATATTGAAAGAATAATTTG
Found at i:35548 original size:23 final size:23
Alignment explanation
Indices: 35517--35577 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
35507 TTAATGAGAT
35517 ATTT-TATGACGTTTTGGTTTTG
1 ATTTATATGACGTTTTGGTTTTG
35539 ATTTATATGACGTTTTGGTTTTG
1 ATTTATATGACGTTTTGGTTTTG
*
35562 GTTTATATGACGTTTT
1 ATTTATATGACGTTTT
35578 AATATTTGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 4 0.11
23 33 0.89
ACGTcount: A:0.16, C:0.05, G:0.21, T:0.57
Consensus pattern (23 bp):
ATTTATATGACGTTTTGGTTTTG
Found at i:44314 original size:2 final size:2
Alignment explanation
Indices: 44307--44340 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
44297 ATTTTAGTTA
* *
44307 GT GT GT GT GT GT GT GT GC GC GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
44341 ATATATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.06, G:0.50, T:0.44
Consensus pattern (2 bp):
GT
Found at i:45818 original size:24 final size:24
Alignment explanation
Indices: 45790--45845 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
45780 ATACAATAGG
45790 GAAGCGAATGAGAAAAAAATAGAT
1 GAAGCGAATGAGAAAAAAATAGAT
45814 GAAGCGAATGAGAAAAAAATAGAT
1 GAAGCGAATGAGAAAAAAATAGAT
*
45838 GAAACGAA
1 GAAGCGAA
45846 CAAGTCACAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.59, C:0.05, G:0.25, T:0.11
Consensus pattern (24 bp):
GAAGCGAATGAGAAAAAAATAGAT
Found at i:61468 original size:28 final size:28
Alignment explanation
Indices: 61428--61487 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
61418 CCGGCTTATA
61428 CGACCTTCAGCACAAAGCTGTGTTGCTC
1 CGACCTTCAGCACAAAGCTGTGTTGCTC
61456 CGACCTTCAGCACAAAGCTGTGTTGCTC
1 CGACCTTCAGCACAAAGCTGTGTTGCTC
61484 CGAC
1 CGAC
61488 TCTTATACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.23
Consensus pattern (28 bp):
CGACCTTCAGCACAAAGCTGTGTTGCTC
Found at i:64016 original size:147 final size:150
Alignment explanation
Indices: 63706--64058 Score: 469
Period size: 148 Copynumber: 2.4 Consensus size: 150
63696 ATACACAAAC
* * * *
63706 AAGATTAGGAATCCAAATTTGTTTTGTTTATTTGAAAGTTAATAAAATATAAACATAAGGGGTTC
1 AAGATTAAGAACCCAAATTTGTTTTGTTTATTTGAATGTTAAT-AAATATAAACACAAGGGGTTC
* * * * *
63771 TCTTTTTGTAGTTTGTTTGATTAGATTTTCTCGAGAAAATTAATTGAAAAGAAATACCAAGGAAA
65 TCTTCTTGTAGTTCGTTTGATCAGATTTTCTCGAGAAAATAAAATGAAAAGAAATACCAAGGAAA
*
63836 GAAACTTTATTGTTCGGAGAT
130 GAAACTTTATTGTTCAGAGAT
63857 AAGATTAAGAACCCAAATTTG-TTTGTTTATTTGAATGTTAATAAATATAAACACAA-GGGTTCT
1 AAGATTAAGAACCCAAATTTGTTTTGTTTATTTGAATGTTAATAAATATAAACACAAGGGGTTCT
* * * * * *
63920 CTTCTTGTAGTTCGTTTGGTCGGATTTTCTCGAGAAAATAAAATGAATA-TAATACCCAGTAAAG
66 CTTCTTGTAGTTCGTTTGATCAGATTTTCTCGAGAAAATAAAATGAAAAGAAATACCAAGGAAAG
*
63984 AAGCTTTATTGTTCAGAGAT
131 AAACTTTATTGTTCAGAGAT
* ** * *
64004 GAGATTAAGAACCCAAATTTGTTTTGTTTCGTTGAATATCAATAGAATATAAACA
1 AAGATTAAGAACCCAAATTTGTTTTGTTTATTTGAATGTTAATA-AATATAAACA
64059 TTGGGTTTTT
Statistics
Matches: 178, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
147 50 0.28
148 66 0.37
149 23 0.13
150 20 0.11
151 19 0.11
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (150 bp):
AAGATTAAGAACCCAAATTTGTTTTGTTTATTTGAATGTTAATAAATATAAACACAAGGGGTTCT
CTTCTTGTAGTTCGTTTGATCAGATTTTCTCGAGAAAATAAAATGAAAAGAAATACCAAGGAAAG
AAACTTTATTGTTCAGAGAT
Found at i:70965 original size:9 final size:9
Alignment explanation
Indices: 70920--70998 Score: 58
Period size: 9 Copynumber: 8.9 Consensus size: 9
70910 AATGGCTAAG
70920 AAATAAAAT
1 AAATAAAAT
*
70929 AAA-ACAAT
1 AAATAAAAT
*
70937 AAAAGAAAAT
1 -AAATAAAAT
*
70947 AAGGTAAAAT
1 AA-ATAAAAT
70957 AAATAAAAT
1 AAATAAAAT
70966 AAA-AAACA-
1 AAATAAA-AT
*
70974 AAACAAAAT
1 AAATAAAAT
70983 -AATAAAAT
1 AAATAAAAT
*
70991 ATATAAAA
1 AAATAAAA
70999 ATAACAAAAC
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
8 18 0.32
9 27 0.48
10 11 0.20
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (9 bp):
AAATAAAAT
Found at i:71008 original size:36 final size:35
Alignment explanation
Indices: 70920--71012 Score: 116
Period size: 36 Copynumber: 2.6 Consensus size: 35
70910 AATGGCTAAG
* *
70920 AAATAAAATAAAACAATAAAAGAAAATAAGGTAAAAT
1 AAATAAAATAAAA-AACAAAACAAAATAA-GTAAAAT
70957 AAATAAAATAAAAAACAAAACAAAATAA-TAAAAT
1 AAATAAAATAAAAAACAAAACAAAATAAGTAAAAT
*
70991 ATATAAAAATAACAAAACAAAA
1 AAAT-AAAATAA-AAAACAAAA
71013 TGAAGAGAAG
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
34 9 0.18
35 7 0.14
36 22 0.43
37 13 0.25
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.15
Consensus pattern (35 bp):
AAATAAAATAAAAAACAAAACAAAATAAGTAAAAT
Found at i:73744 original size:19 final size:19
Alignment explanation
Indices: 73720--73761 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
73710 AGCACCTAAA
73720 TAGGTAACATTTGTGACGT
1 TAGGTAACATTTGTGACGT
73739 TAGGTAACATTTGTGACGT
1 TAGGTAACATTTGTGACGT
73758 TAGG
1 TAGG
73762 CACCGAGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.26, C:0.10, G:0.29, T:0.36
Consensus pattern (19 bp):
TAGGTAACATTTGTGACGT
Found at i:75238 original size:19 final size:19
Alignment explanation
Indices: 75214--75253 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
75204 AAAGCAGCGG
*
75214 TAGACGTGGGTTTAGGAGT
1 TAGACGTGGGTTTAAGAGT
75233 TAGACGTGGGTTTAAGAGT
1 TAGACGTGGGTTTAAGAGT
75252 TA
1 TA
75254 AAAGGAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.25, C:0.05, G:0.38, T:0.33
Consensus pattern (19 bp):
TAGACGTGGGTTTAAGAGT
Found at i:81154 original size:2 final size:2
Alignment explanation
Indices: 81147--81178 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
81137 ATGTGTAATA
81147 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
81179 CCCCTCTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:84647 original size:39 final size:40
Alignment explanation
Indices: 84604--84694 Score: 139
Period size: 39 Copynumber: 2.3 Consensus size: 40
84594 ATAAACATAG
84604 CCAAATTTCATGAATGAAACCCCATTTCCATTCCCAT-TT
1 CCAAATTTCATGAATGAAACCCCATTTCCATTCCCATCTT
* *
84643 CCAAATTTCATGAATGAAACTCCATTTCCATTTCCATCTT
1 CCAAATTTCATGAATGAAACCCCATTTCCATTCCCATCTT
* *
84683 TCAATTTTCATG
1 CCAAATTTCATG
84695 TTTATCTGCT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
39 35 0.74
40 12 0.26
ACGTcount: A:0.30, C:0.27, G:0.05, T:0.37
Consensus pattern (40 bp):
CCAAATTTCATGAATGAAACCCCATTTCCATTCCCATCTT
Found at i:86084 original size:81 final size:81
Alignment explanation
Indices: 85943--86129 Score: 320
Period size: 81 Copynumber: 2.3 Consensus size: 81
85933 TTCAAAATGG
85943 TGATCTTTGTGTAATTTTGGTTCTCTCAGGAGCTAGGTTTAGTTCGTAAACCGGTCGAGGTTGAA
1 TGATCTTTGTGTAATTTTGG-T-TCTCAGGAGCTAGGTTTAGTTCGTAAACCGGTCGAGGTTGAA
*
86008 ATTTTCGGTTTGAAGGAC
64 ATTTTCGGTTCGAAGGAC
* * *
86026 TGATCTTTGTGTAATTTTGGTTCTCAGGAGCTAGGTTTAGTTCTTAAACCGGTTGAGGTTGAATT
1 TGATCTTTGTGTAATTTTGGTTCTCAGGAGCTAGGTTTAGTTCGTAAACCGGTCGAGGTTGAAAT
86091 TTTCGGTTCGAAGGAC
66 TTTCGGTTCGAAGGAC
86107 TGATCTTTGTGTAATTTTGGTTC
1 TGATCTTTGTGTAATTTTGGTTC
86130 ACATTGGTGC
Statistics
Matches: 100, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
81 79 0.79
82 1 0.01
83 20 0.20
ACGTcount: A:0.19, C:0.12, G:0.27, T:0.42
Consensus pattern (81 bp):
TGATCTTTGTGTAATTTTGGTTCTCAGGAGCTAGGTTTAGTTCGTAAACCGGTCGAGGTTGAAAT
TTTCGGTTCGAAGGAC
Found at i:86592 original size:42 final size:42
Alignment explanation
Indices: 86443--86572 Score: 206
Period size: 42 Copynumber: 3.1 Consensus size: 42
86433 AACGAATCAC
* * *
86443 CACCGATGGCTGCACGTGGTGATCAAGGACAGAAACCGGCTA
1 CACCAATGGCTGCACATGGTAATCAAGGACAGAAACCGGCTA
* *
86485 CAACAATGGCTGCACATGGTAATCAAGGACAGAAACCAGCTA
1 CACCAATGGCTGCACATGGTAATCAAGGACAGAAACCGGCTA
*
86527 CACCAATGGCTGAACATGGTAATCAAGGACAGAAACCGGCTA
1 CACCAATGGCTGCACATGGTAATCAAGGACAGAAACCGGCTA
86569 CACC
1 CACC
86573 GGTGGATGCA
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 80 1.00
ACGTcount: A:0.35, C:0.26, G:0.25, T:0.14
Consensus pattern (42 bp):
CACCAATGGCTGCACATGGTAATCAAGGACAGAAACCGGCTA
Found at i:104684 original size:30 final size:31
Alignment explanation
Indices: 104639--104707 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
104629 TAATTAATTG
104639 GATATTGA-TCTGACCCGAAATCAAAC-AATCT
1 GATATTGATTC-GACCCGAAAT-AAACTAATCT
*
104670 GAT-TTGATTCGACCCGAAATTAACTAATCT
1 GATATTGATTCGACCCGAAATAAACTAATCT
104700 GATATTGA
1 GATATTGA
104708 CCCAACCCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
29 3 0.09
30 22 0.65
31 9 0.26
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.30
Consensus pattern (31 bp):
GATATTGATTCGACCCGAAATAAACTAATCT
Found at i:114200 original size:20 final size:19
Alignment explanation
Indices: 114175--114212 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
114165 TTCCTATTGA
*
114175 AATTTTATTTCGCTCCCTAT
1 AATTTTAGTTCGC-CCCTAT
114195 AATTTTAGTTCGCCCCTA
1 AATTTTAGTTCGCCCCTA
114213 ACATAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.21, C:0.26, G:0.08, T:0.45
Consensus pattern (19 bp):
AATTTTAGTTCGCCCCTAT
Found at i:115278 original size:17 final size:18
Alignment explanation
Indices: 115253--115290 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
115243 TATATCTTTA
115253 TAATATTAAATA-TAAAT
1 TAATATTAAATAGTAAAT
* *
115270 TAATGTTAATTAGTAAAT
1 TAATATTAAATAGTAAAT
115288 TAA
1 TAA
115291 ATACAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (18 bp):
TAATATTAAATAGTAAAT
Found at i:116757 original size:39 final size:39
Alignment explanation
Indices: 116703--116778 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
116693 ATTTAGAATT
*
116703 AGATTCATAGTTTAGGGATGAAATTTGAATGTTCAAATG
1 AGATTCATAGTTTAGGGATAAAATTTGAATGTTCAAATG
116742 AGATTCATAGTTTAGGGATAAAATTTGAATGTTCAAA
1 AGATTCATAGTTTAGGGATAAAATTTGAATGTTCAAA
116779 AGTTTAAGGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (39 bp):
AGATTCATAGTTTAGGGATAAAATTTGAATGTTCAAATG
Found at i:117902 original size:60 final size:59
Alignment explanation
Indices: 117829--117950 Score: 156
Period size: 60 Copynumber: 2.1 Consensus size: 59
117819 CTCCCCCAAT
* *
117829 TATAGGTGATGCTTCATTGAGTCCCTCGACTATTAAAAGTTACAAAATGATC-CTCCGAC
1 TATAGGTGATGCTTCATTGAGTCCCTAGACTATCAAAAGTTACAAAATGATCAC-CCGAC
* ** * *
117888 TATAGAGTGTTGCTTTGTTGAGTCCCTAGACTATCAAAAGTTAGAAAATGGTCACCCGAC
1 TATAG-GTGATGCTTCATTGAGTCCCTAGACTATCAAAAGTTACAAAATGATCACCCGAC
117948 TAT
1 TAT
117951 TTATTATGTT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 5 0.09
60 48 0.89
61 1 0.02
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (59 bp):
TATAGGTGATGCTTCATTGAGTCCCTAGACTATCAAAAGTTACAAAATGATCACCCGAC
Found at i:136169 original size:4 final size:4
Alignment explanation
Indices: 136160--136185 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
136150 TTAGAACATA
136160 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
136186 TAAGTTAGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:136708 original size:24 final size:23
Alignment explanation
Indices: 136673--136726 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
136663 ATTAAATTTC
* *
136673 TTTGTTAATTACTCTTTAAGATA
1 TTTGTAAATTACACTTTAAGATA
136696 TTTGTAAATTTACACTTTAAGATA
1 TTTGTAAA-TTACACTTTAAGATA
136720 TTTGTAA
1 TTTGTAA
136727 TTATAATTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 7 0.25
24 21 0.75
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.50
Consensus pattern (23 bp):
TTTGTAAATTACACTTTAAGATA
Found at i:144936 original size:43 final size:43
Alignment explanation
Indices: 144887--144982 Score: 147
Period size: 43 Copynumber: 2.2 Consensus size: 43
144877 GCTTGATCAA
* *
144887 TGGATTTGTGTGATTATGTTTCAATGTCATTGTGGGGTTGGTT
1 TGGATTTGTGTGATTATGTTTCAATGTCACTGTGGAGTTGGTT
*
144930 TGGATTTGTGTGATTATGTTTCAATGTCACTGTGGAGTTTGTT
1 TGGATTTGTGTGATTATGTTTCAATGTCACTGTGGAGTTGGTT
*
144973 TAAGATTTGT
1 T-GGATTTGT
144983 TTGAATTTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
43 41 0.85
44 7 0.15
ACGTcount: A:0.17, C:0.05, G:0.29, T:0.49
Consensus pattern (43 bp):
TGGATTTGTGTGATTATGTTTCAATGTCACTGTGGAGTTGGTT
Found at i:149787 original size:24 final size:24
Alignment explanation
Indices: 149757--149812 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
149747 TAGAAGTTCG
149757 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
149781 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
149805 ATTGAAGC
1 ATTGAAGC
149813 GAAAGAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:150626 original size:11 final size:11
Alignment explanation
Indices: 150591--150657 Score: 52
Period size: 11 Copynumber: 6.4 Consensus size: 11
150581 ATTTTTAAAC
*
150591 ATTATAAAATGA
1 ATTATTAAAT-A
150603 A-TATTAAAT-
1 ATTATTAAATA
* *
150612 -TTATCAAATT
1 ATTATTAAATA
*
150622 ATTATAAAATA
1 ATTATTAAATA
150633 ATTATTAAAT-
1 ATTATTAAATA
*
150643 TTTATTAAATA
1 ATTATTAAATA
150654 ATTA
1 ATTA
150658 CACCATGATC
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
9 7 0.16
10 9 0.20
11 27 0.61
12 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (11 bp):
ATTATTAAATA
Found at i:150627 original size:31 final size:31
Alignment explanation
Indices: 150591--150691 Score: 100
Period size: 31 Copynumber: 3.2 Consensus size: 31
150581 ATTTTTAAAC
150591 ATTATAAAATGAATATTAAATTTATCAAATT
1 ATTATAAAATGAATATTAAATTTATCAAATT
* *
150622 ATTATAAAAT-AATTATTAAATTTTATTAAATA
1 ATTATAAAATGAA-TATTAAA-TTTATCAAATT
* **
150654 ATTACACCATG-ATCATTAAATTTATCCAAATT
1 ATTATAAAATGAAT-ATTAAATTTAT-CAAATT
150686 -TTATAA
1 ATTATAA
150692 TATTATAATA
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
30 2 0.04
31 27 0.48
32 27 0.48
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.43
Consensus pattern (31 bp):
ATTATAAAATGAATATTAAATTTATCAAATT
Found at i:150652 original size:21 final size:22
Alignment explanation
Indices: 150604--150657 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
150594 ATAAAATGAA
150604 TATTAAAT--TTATCAAATTAT
1 TATTAAATAATTATCAAATTAT
* *
150624 TATAAAATAATTATTAAATT-T
1 TATTAAATAATTATCAAATTAT
150645 TATTAAATAATTA
1 TATTAAATAATTA
150658 CACCATGATC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.24
21 13 0.45
22 9 0.31
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
TATTAAATAATTATCAAATTAT
Found at i:151107 original size:23 final size:24
Alignment explanation
Indices: 151047--151122 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
151037 CATTTAAGTG
* ** * *
151047 ATAAACGAACATAAATAAATATAT
1 ATAAATGAACATAAACGAACATAA
*
151071 ATAAATGAATATAAACGAACAT-A
1 ATAAATGAACATAAACGAACATAA
* *
151094 ATAAATTAACATAATCGAACATAA
1 ATAAATGAACATAAACGAACATAA
151118 ATAAA
1 ATAAA
151123 AATAATTTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
23 19 0.45
24 23 0.55
ACGTcount: A:0.62, C:0.09, G:0.05, T:0.24
Consensus pattern (24 bp):
ATAAATGAACATAAACGAACATAA
Found at i:155417 original size:403 final size:405
Alignment explanation
Indices: 154668--155466 Score: 1338
Period size: 403 Copynumber: 2.0 Consensus size: 405
154658 GAAATTTGTA
154668 ATTTACCTTTTTAATTTAAGTTACAAAATGGCGCGTGTGTTTGGGGAATCATGGTGTGAGAGTGT
1 ATTTACCTTTTTAATTTAAGTTACAAAATGGCGCGTGTGTTTGGGGAATCATGGTGTGAGAGTGT
154733 AAGACCAGCATTGAGCCAATCACACAGCTTTATTAGACTCAGTTGTCCAAATCCATGTGCCTTTT
66 AAGACCAGCATTGAGCCAATCACACAGCTTTATTAGACTCAGTTGTCCAAATCCATGTGCCTTTT
154798 CATGGGGAAGGTCGTCCCTCTGTTTAGGGTACCCATTGGAGCCTGTCTCCTTTTTAGCCTGTACT
131 CATGGGGAAGGTCGTCCCTCTGTTTAGGGTACCCATTGGAGCCTGTCTCCTTTTTAGCCTGTACT
* * * *
154863 AACGAGATAGGTTGTTACTCATTTGAAATTATCATTCAGTTCAGTTGTTAGAGTACAATGATCTT
196 AACCAGATAGGTTGTTACTCATTTGAAATGATCATTCAGTTCAGTTGGTAGAGTACAAGGATCTT
* * *
154928 AATTTTGAGGTCATGGGATCAAGTTCTATGGAATGTATTTTATAATTTGGAGGTCTCTTACAGAA
261 AATTTTGAGGTCATGGGATCAAATTCTATGGAAGGCATTTTATAATTTGGAGGTCTCTTACAGAA
* * * ** * *
154993 ATTGTTTTTAACCTAGTGTTA-GGAGCAGCCTATTATCTTGTCTTCCCTTATCCTATTACATATG
326 ACTGTTTTTAACCTAGTGTTAGGGA-CAGCATACTATCTTACCTTCCCTTACCCCATTACATATG
*
155057 GGAACAATTGACAATC
390 AGAACAATTGACAATC
*
155073 ATTTACCTTTGTTAATTTAAGTTAC-AAATGGCGCTTGTGTTTGGGGAATCATGGTGTGAGAGTG
1 ATTTACCTTT-TTAATTTAAGTTACAAAATGGCGCGTGTGTTTGGGGAATCATGGTGTGAGAGTG
155137 TAAGACCAGCATTGAGCCAATCACACAGCTTTATTAGACTCAGTTGTCCAAATCCATGTGCCTTT
65 TAAGACCAGCATTGAGCCAATCACACAGCTTTATTAGACTCAGTTGTCCAAATCCATGTGCCTTT
*
155202 TCATGGGGAAGGTCGT-CC-CTGTTTAGGGTACCCATTGGAGCCTGTCTCCTTTTTAGCCTTTAC
130 TCATGGGGAAGGTCGTCCCTCTGTTTAGGGTACCCATTGGAGCCTGTCTCCTTTTTAGCCTGTAC
*
155265 TAACCAGATAGGTTGTTACTCATTTGAAATGATCATTCAGTTCAGTTGGTAGAGTACAAGGATTT
195 TAACCAGATAGGTTGTTACTCATTTGAAATGATCATTCAGTTCAGTTGGTAGAGTACAAGGATCT
* *
155330 TAATTTTGAGGTCGTGGGATCAAA-TCTTATGGAAGGCATTTTATAATTTGGATGTCTCTTACAG
260 TAATTTTGAGGTCATGGGATCAAATTC-TATGGAAGGCATTTTATAATTTGGAGGTCTCTTACAG
* *
155394 AAACTGTTTTTAACTTAGTGTTAGGGACAGCATACTATCTTACCTTCTCTTACCCCATTACATAT
324 AAACTGTTTTTAACCTAGTGTTAGGGACAGCATACTATCTTACCTTCCCTTACCCCATTACATAT
155459 GAGAACAA
389 GAGAACAA
155467 AATACAGTCA
Statistics
Matches: 369, Mismatches: 22, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
402 2 0.01
403 219 0.59
404 5 0.01
405 129 0.35
406 14 0.04
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.36
Consensus pattern (405 bp):
ATTTACCTTTTTAATTTAAGTTACAAAATGGCGCGTGTGTTTGGGGAATCATGGTGTGAGAGTGT
AAGACCAGCATTGAGCCAATCACACAGCTTTATTAGACTCAGTTGTCCAAATCCATGTGCCTTTT
CATGGGGAAGGTCGTCCCTCTGTTTAGGGTACCCATTGGAGCCTGTCTCCTTTTTAGCCTGTACT
AACCAGATAGGTTGTTACTCATTTGAAATGATCATTCAGTTCAGTTGGTAGAGTACAAGGATCTT
AATTTTGAGGTCATGGGATCAAATTCTATGGAAGGCATTTTATAATTTGGAGGTCTCTTACAGAA
ACTGTTTTTAACCTAGTGTTAGGGACAGCATACTATCTTACCTTCCCTTACCCCATTACATATGA
GAACAATTGACAATC
Found at i:160798 original size:158 final size:158
Alignment explanation
Indices: 160510--160825 Score: 605
Period size: 158 Copynumber: 2.0 Consensus size: 158
160500 TCAATAACTT
* *
160510 GAATAACCCGCTATGAATGACCGTCTATCTGAGGTGAAATGTGGTGTTGAAATGGAGCTTAGTGC
1 GAATAACCCGCTATGAATAACCGTCTATCTGAGGTGAAATGTGGTGCTGAAATGGAGCTTAGTGC
160575 TGAAAGATTCATGTAAAGCTTCCTAAAATTGTGAAGTAAATCTGAGGTCTCTGTCCAAAATAATT
66 TGAAAGATTCATGTAAAGCTTCCTAAAATTGTGAAGTAAATCTGAGGTCTCTGTCCAAAATAATT
160640 ATGGTCGAAACTCTATGTAATCTTACTA
131 ATGGTCGAAACTCTATGTAATCTTACTA
*
160668 GAATAACCCGCTATGAATAACCGTCTATTTGAGGTGAAATGTGGTGCTGAAATGGAGCTTAGTGC
1 GAATAACCCGCTATGAATAACCGTCTATCTGAGGTGAAATGTGGTGCTGAAATGGAGCTTAGTGC
160733 TGAAAGATTCATGTAAAGCTTCCTAAAATTGTGAAGTAAATCTGAGGTCTCTGTCCAAAATAATT
66 TGAAAGATTCATGTAAAGCTTCCTAAAATTGTGAAGTAAATCTGAGGTCTCTGTCCAAAATAATT
160798 ATGGTCGAAACTCTATGTAATCTTACTA
131 ATGGTCGAAACTCTATGTAATCTTACTA
160826 TCTCATGGAT
Statistics
Matches: 155, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
158 155 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (158 bp):
GAATAACCCGCTATGAATAACCGTCTATCTGAGGTGAAATGTGGTGCTGAAATGGAGCTTAGTGC
TGAAAGATTCATGTAAAGCTTCCTAAAATTGTGAAGTAAATCTGAGGTCTCTGTCCAAAATAATT
ATGGTCGAAACTCTATGTAATCTTACTA
Found at i:168682 original size:147 final size:147
Alignment explanation
Indices: 168262--168693 Score: 392
Period size: 147 Copynumber: 2.9 Consensus size: 147
168252 TTTCTACATC
* ** ** * * * * **
168262 AACTTTATCTTCCACAAATCCAGAATTGTCCATTTCGGTAACTTCCTCCTTCAGTTCAGAAGTCG
1 AACTTTATCTGCCACAACCCCAGAATCATCCATTTCAGTAACCTCCTCCTTAAGATCAGAAGTAA
* * * * *
168327 GGTTATCTTCCTTAATTGTATTTTCAACATCTCCAAC-GTTCGACGAAATGTCAGG-CTGAACAA
66 GGTTATCTTCCTTAATTGCATTTTCAGCATCTCC-ACTGTTCGATGAAATG-CCGGACTGAACTA
*
168390 TAGTCGACTTGGCCTCAAT
129 TAGTCGACTTGGACTCAAT
* *
168409 AACTTTATCTGCCACAACCCCATAATCATCCATTTCAGTAACCTCCTCCTTAAGCTCAGAAGTAA
1 AACTTTATCTGCCACAACCCCAGAATCATCCATTTCAGTAACCTCCTCCTTAAGATCAGAAGTAA
* * * * * * *
168474 GTTTAT-TTCCCATAATTGCATTTTCTGCATC-CGCAATGTTCGATGAAATGCCAGATTGAACTG
66 GGTTATCTT-CCTTAATTGCATTTTCAGCATCTC-CACTGTTCGATGAAATGCCGGACTGAACTA
* *
168537 TTGTCGACTT-GACTACATT
129 TAGTCGACTTGGACT-CAAT
* * * * * *
168556 AACTTTGA-CTTCCACAACCCCCGAGTTATCCATTTCAGTAACCTCCTCTTTAAGATCGGATA-T
1 AACTTT-ATCTGCCACAACCCCAGAATCATCCATTTCAGTAACCTCCTCCTTAAGATCAGA-AGT
* ** *
168619 CAGGTTATCTTCCTTGGTTGCATTTTCAGCATCTTCACTGTTCGATGAAATGCCGGACTGAACTA
64 AAGGTTATCTTCCTTAATTGCATTTTCAGCATCTCCACTGTTCGATGAAATGCCGGACTGAACTA
* *
168684 CAGTAGACTT
129 TAGTCGACTT
168694 AGTCTCAAAA
Statistics
Matches: 227, Mismatches: 49, Indels: 18
0.77 0.17 0.06
Matches are distributed among these distances:
146 9 0.04
147 214 0.94
148 4 0.02
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (147 bp):
AACTTTATCTGCCACAACCCCAGAATCATCCATTTCAGTAACCTCCTCCTTAAGATCAGAAGTAA
GGTTATCTTCCTTAATTGCATTTTCAGCATCTCCACTGTTCGATGAAATGCCGGACTGAACTATA
GTCGACTTGGACTCAAT
Found at i:169619 original size:43 final size:43
Alignment explanation
Indices: 169558--169642 Score: 170
Period size: 43 Copynumber: 2.0 Consensus size: 43
169548 CTGAAATGGA
169558 GTGAATTTTACAGTGAGCTTGGAGGTCGCCATGGCATCCGGGG
1 GTGAATTTTACAGTGAGCTTGGAGGTCGCCATGGCATCCGGGG
169601 GTGAATTTTACAGTGAGCTTGGAGGTCGCCATGGCATCCGGG
1 GTGAATTTTACAGTGAGCTTGGAGGTCGCCATGGCATCCGGG
169643 CGACCTTGGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.26
Consensus pattern (43 bp):
GTGAATTTTACAGTGAGCTTGGAGGTCGCCATGGCATCCGGGG
Found at i:169660 original size:29 final size:29
Alignment explanation
Indices: 169618--169677 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
169608 TTACAGTGAG
*
169618 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGAGCGAC
169647 CTTGGAGGTCGCCATGGCATCCGAGCGAC
1 CTTGGAGGTCGCCATGGCATCCGAGCGAC
169676 CT
1 CT
169678 GTGGGCTGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.15, C:0.32, G:0.35, T:0.18
Consensus pattern (29 bp):
CTTGGAGGTCGCCATGGCATCCGAGCGAC
Found at i:170007 original size:14 final size:14
Alignment explanation
Indices: 169984--170025 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
169974 CGCTGGGCAT
*
169984 CCGAGACCATCCGA
1 CCGAGGCCATCCGA
*
169998 TCGAGGCCATCCGA
1 CCGAGGCCATCCGA
170012 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
170026 AAGCATCCGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.24, C:0.40, G:0.26, T:0.10
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:170040 original size:20 final size:20
Alignment explanation
Indices: 170012--170066 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
170002 GGCCATCCGA
170012 CCGAGGCCATCCGAAAGCAT
1 CCGAGGCCATCCGAAAGCAT
* * *
170032 CCGATGCCATCTGAGAGCAT
1 CCGAGGCCATCCGAAAGCAT
170052 CCGAGGCCATCCGAA
1 CCGAGGCCATCCGAA
170067 CGAACTATGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.35, G:0.25, T:0.13
Consensus pattern (20 bp):
CCGAGGCCATCCGAAAGCAT
Found at i:170135 original size:23 final size:23
Alignment explanation
Indices: 170053--170134 Score: 119
Period size: 23 Copynumber: 3.6 Consensus size: 23
170043 TGAGAGCATC
* *
170053 CGAGGCCATCCGAACGAACTATG
1 CGAGGGCATCCGAACGAGCTATG
*
170076 TGAGGGCATCCGAACGAGCTATG
1 CGAGGGCATCCGAACGAGCTATG
*
170099 CGAGGGCATCCGAGCGAGCTATG
1 CGAGGGCATCCGAACGAGCTATG
*
170122 CGAGGGAATCCGA
1 CGAGGGCATCCGA
170135 GGGCAACCGA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.27, C:0.26, G:0.34, T:0.13
Consensus pattern (23 bp):
CGAGGGCATCCGAACGAGCTATG
Found at i:170195 original size:29 final size:29
Alignment explanation
Indices: 170153--170209 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
170143 GAGCGAGGGT
170153 AGGTCGCCCGGAGTACATGGCAACCTACA
1 AGGTCGCCCGGAGTACATGGCAACCTACA
* *
170182 AGGTCGCCCGGAGTGCATGGCGACCTAC
1 AGGTCGCCCGGAGTACATGGCAACCTAC
170210 GTCGGATGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.23, C:0.32, G:0.32, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGTACATGGCAACCTACA
Found at i:171675 original size:16 final size:15
Alignment explanation
Indices: 171649--171678 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
171639 GGAGGAGGAG
171649 GAGGAGAAGAAGAAT
1 GAGGAGAAGAAGAAT
171664 GAGGAGGAAGAAGAA
1 GAGGA-GAAGAAGAA
171679 GAAATTGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.00, G:0.43, T:0.03
Consensus pattern (15 bp):
GAGGAGAAGAAGAAT
Found at i:171677 original size:19 final size:18
Alignment explanation
Indices: 171646--171681 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
171636 GAAGGAGGAG
171646 GAGGAGGAGAAGAAGAAT
1 GAGGAGGAGAAGAAGAAT
171664 GAGGAGGAAGAAGAAGAA
1 GAGGAGG-AGAAGAAGAA
171682 ATTGTTGCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.53, C:0.00, G:0.44, T:0.03
Consensus pattern (18 bp):
GAGGAGGAGAAGAAGAAT
Found at i:174189 original size:31 final size:34
Alignment explanation
Indices: 174125--174210 Score: 133
Period size: 31 Copynumber: 2.6 Consensus size: 34
174115 TAAAGTTAAG
174125 ATTTAATGATTATTTTATAATAATATTTCAATAA
1 ATTTAATGATTATTTTATAATAATATTTCAATAA
174159 ATTTAATGATTATTTTATAAT-A-ATTT-AATAA
1 ATTTAATGATTATTTTATAATAATATTTCAATAA
* *
174190 AATTAACGATTATTTTATAAT
1 ATTTAATGATTATTTTATAAT
174211 TATTGACAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
31 24 0.48
32 4 0.08
33 1 0.02
34 21 0.42
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.50
Consensus pattern (34 bp):
ATTTAATGATTATTTTATAATAATATTTCAATAA
Found at i:174604 original size:160 final size:157
Alignment explanation
Indices: 174358--174735 Score: 506
Period size: 160 Copynumber: 2.4 Consensus size: 157
174348 CTTAATTTCA
* * * * * * * * * *
174358 TTATTTCTTCGATTCCTCCTTCATTTTAAGTCTATATTTTT-CTAGATTTGAATCACATGTTGCT
1 TTATTTCTTCAATTCGTCATTTATTTTAAGTCCATTTTTTTACCAAATTTGAATCACATGATCCT
* * *
174422 AAACCATAGTAGAATGCATGTGTACTTTCAATTCCTCTTTTTGATAATAATTTTTTTATTTTTCA
66 AAACCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAACAA-ATTTTTATTTTTCA
174487 ATTTAGTCCTTCAATTTTTCATAATCTC
130 ATTTAGTCCTTCAATTTTTCATAATCTC
*
174515 TTTATTTCTTCAATTCGTCATTTATTTTAAGTCCATTTGTTTTACCAAATTTGAGTCACATGATC
1 -TTATTTCTTCAATTCGTCATTTATTTTAAGTCCATTT-TTTTACCAAATTTGAATCACATGATC
174580 CTAAACCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAACAAATTTTTATTTTTC
64 CTAAACCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAACAAATTTTTATTTTTC
174645 AATTTAGTCCTTCAATTTTTCATAATCTC
129 AATTTAGTCCTTCAATTTTTCATAATCTC
* * * * * * * *
174674 TTGTTCCTTCAATTTGTAATTTAGTTTATGTCCCCTTTTTTTTACCAAATTTGAACCACATG
1 TTATTTCTTCAATTCGTCATTTATTTTAAGT--CCATTTTTTTACCAAATTTGAATCACATG
174736 CTCATATACG
Statistics
Matches: 193, Mismatches: 23, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
158 56 0.29
159 66 0.34
160 71 0.37
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.48
Consensus pattern (157 bp):
TTATTTCTTCAATTCGTCATTTATTTTAAGTCCATTTTTTTACCAAATTTGAATCACATGATCCT
AAACCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAACAAATTTTTATTTTTCAA
TTTAGTCCTTCAATTTTTCATAATCTC
Found at i:174724 original size:159 final size:160
Alignment explanation
Indices: 174403--174735 Score: 508
Period size: 159 Copynumber: 2.1 Consensus size: 160
174393 ATTTTTCTAG
* * *
174403 ATTTGAATCACATGTTGCTAAACCATAGTAGAATGCATGTGTACTTTCAATTCCTCTTTTTGATA
1 ATTTGAATCACATGATCCTAAACCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATA
* * *
174468 ATAATTTTTTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCTCTTTATTTCTTCAATTCGT
66 ACAATATTTTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCTCTTTATTCCTTCAATTCGT
* *
174533 CATTTATTTTAAGTCCATTTGTTTTACCAA
131 AATTTAGTTTAAGTCCATTTGTTTTACCAA
*
174563 ATTTGAGTCACATGATCCTAAACCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATA
1 ATTTGAATCACATGATCCTAAACCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATA
* *
174628 ACAA-ATTTTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCTC-TTGTTCCTTCAATTTGT
66 ACAATATTTTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCTCTTTATTCCTTCAATTCGT
* * *
174691 AATTTAGTTTATGTCCCCTTTTTTTTACCAA
131 AATTTAGTTTAAGT-CCATTTGTTTTACCAA
*
174722 ATTTGAACCACATG
1 ATTTGAATCACATG
174736 CTCATATACG
Statistics
Matches: 156, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
158 25 0.16
159 67 0.43
160 64 0.41
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.47
Consensus pattern (160 bp):
ATTTGAATCACATGATCCTAAACCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATA
ACAATATTTTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCTCTTTATTCCTTCAATTCGT
AATTTAGTTTAAGTCCATTTGTTTTACCAA
Found at i:174771 original size:159 final size:160
Alignment explanation
Indices: 174403--174773 Score: 419
Period size: 159 Copynumber: 2.3 Consensus size: 160
174393 ATTTTTCTAG
* * * * * * *
174403 ATTTGAATCACATGTTGC-TAAACCATAGTAGAATGCATGTGTACTTTCAATTCCTCTTTTTGAT
1 ATTTGAACCACATGAT-CATAAACCACAATAGAATACATATATACTTTCAATTCCTCTTTTTGAT
* * *
174467 AATAATTTTTTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCTCTTTATTTCTTCAATTCG
65 AACAATATTTTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCTCTTTATTCCTTCAATTCG
* *
174532 TCATTTATTTTAAGTCCATTTGTTTTACCAA
130 TAATTTAGTTTAAGTCCATTTGTTTTACCAA
** * * * * *
174563 ATTTGAGTCACATGATCCTAAACCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATA
1 ATTTGAACCACATGATCATAAACCACAATAGAATACATATATACTTTCAATTCCTCTTTTTGATA
* *
174628 ACAA-ATTTTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCTC-TTGTTCCTTCAATTTGT
66 ACAATATTTTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCTCTTTATTCCTTCAATTCGT
* * *
174691 AATTTAGTTTATGTCCCCTTTTTTTTACCAA
131 AATTTAGTTTAAGT-CCATTTGTTTTACCAA
* * * *
174722 ATTTGAACCACATGCTCATATACGACAATATG-ATACTTATATAAC-TTCAATT
1 ATTTGAACCACATGATCATAAACCACAATA-GAATACATATAT-ACTTTCAATT
174774 GTTATTTTTT
Statistics
Matches: 183, Mismatches: 24, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
158 25 0.14
159 92 0.50
160 66 0.36
ACGTcount: A:0.28, C:0.18, G:0.08, T:0.46
Consensus pattern (160 bp):
ATTTGAACCACATGATCATAAACCACAATAGAATACATATATACTTTCAATTCCTCTTTTTGATA
ACAATATTTTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCTCTTTATTCCTTCAATTCGT
AATTTAGTTTAAGTCCATTTGTTTTACCAA
Found at i:175028 original size:2 final size:2
Alignment explanation
Indices: 175021--175056 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
175011 TGAAAGAATA
175021 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
175057 TATGGTTAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:176093 original size:14 final size:15
Alignment explanation
Indices: 176072--176116 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
176062 GATTTCTTGT
176072 TTTCGATTCTACTGC
1 TTTCGATTCTACTGC
* *
176087 TTT-GATTC-GCTGT
1 TTTCGATTCTACTGC
176100 TTTCGATTCTACTGC
1 TTTCGATTCTACTGC
176115 TT
1 TT
176117 GTTACTCTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
13 6 0.25
14 10 0.42
15 8 0.33
ACGTcount: A:0.11, C:0.22, G:0.16, T:0.51
Consensus pattern (15 bp):
TTTCGATTCTACTGC
Found at i:184201 original size:26 final size:28
Alignment explanation
Indices: 184149--184203 Score: 87
Period size: 26 Copynumber: 2.0 Consensus size: 28
184139 AACGTTCACA
*
184149 GTCGAGTCCGAGTAACATAGATTTGTTT
1 GTCGAGTCCGACTAACATAGATTTGTTT
184177 GTCGAGTCCGACT-A-ATAGATTTGTTT
1 GTCGAGTCCGACTAACATAGATTTGTTT
184203 G
1 G
184204 ATTGCGTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 13 0.50
27 1 0.04
28 12 0.46
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (28 bp):
GTCGAGTCCGACTAACATAGATTTGTTT
Found at i:184402 original size:80 final size:80
Alignment explanation
Indices: 184269--184429 Score: 295
Period size: 80 Copynumber: 2.0 Consensus size: 80
184259 ATTACAATCC
*
184269 AAACTACTTTTTCAGGGTAATACACAGGAGGAGTTACCGGAATCCCTACTTGGAACATGCAGGCT
1 AAACTACTTTTTCAGGGCAATACACAGGAGGAGTTACCGGAATCCCTACTTGGAACATGCAGGCT
184334 AAACCATCTCGATCT
66 AAACCATCTCGATCT
*
184349 AAACTACTTTTTCAGGGCAATACACAGGAGGAGTTACCGGAATCCCTGCTTGGAACATGCAGGCT
1 AAACTACTTTTTCAGGGCAATACACAGGAGGAGTTACCGGAATCCCTACTTGGAACATGCAGGCT
*
184414 AAATCATCTCGATCT
66 AAACCATCTCGATCT
184429 A
1 A
184430 TCGAAGGCTC
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (80 bp):
AAACTACTTTTTCAGGGCAATACACAGGAGGAGTTACCGGAATCCCTACTTGGAACATGCAGGCT
AAACCATCTCGATCT
Found at i:187114 original size:17 final size:16
Alignment explanation
Indices: 187087--187128 Score: 75
Period size: 17 Copynumber: 2.6 Consensus size: 16
187077 AATTTACAAT
187087 TAATTTAAATAATATC
1 TAATTTAAATAATATC
187103 TAATTATAAATAATATC
1 TAATT-TAAATAATATC
187120 TAATTTAAA
1 TAATTTAAA
187129 ATTTTTTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 9 0.36
17 16 0.64
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATTTAAATAATATC
Found at i:189019 original size:41 final size:39
Alignment explanation
Indices: 188919--189023 Score: 114
Period size: 41 Copynumber: 2.8 Consensus size: 39
188909 AAACATACCT
188919 AAAA-TTTAGTTTTTG-T--ATTTTAG-A-ATCCATCGTA
1 AAAACTTTAGTTTTTGTTACATTTTAGTACAT-CATCGTA
188953 AAAACTTTAGTTTTTGTTACATTTTAGTACATCATCGTTA
1 AAAACTTTAGTTTTTGTTACATTTTAGTACATCATCG-TA
* * *
188993 AAAGCTTTATTTTTTTGTTTCATTTTAGTAC
1 AAAACTTTA-GTTTTTGTTACATTTTAGTAC
189024 CCCGTTCAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 9
0.83 0.04 0.12
Matches are distributed among these distances:
34 4 0.07
35 11 0.18
36 1 0.02
38 7 0.12
39 6 0.10
40 12 0.20
41 19 0.32
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.50
Consensus pattern (39 bp):
AAAACTTTAGTTTTTGTTACATTTTAGTACATCATCGTA
Found at i:189199 original size:7 final size:8
Alignment explanation
Indices: 189180--189206 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
189170 GATTTTGAAA
189180 AAAAAATT
1 AAAAAATT
189188 AAAAAATT
1 AAAAAATT
189196 AAAAAATT
1 AAAAAATT
189204 AAA
1 AAA
189207 TACTAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAAAATT
Found at i:194648 original size:2 final size:2
Alignment explanation
Indices: 194643--194691 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
194633 TGTTTTTTAA
194643 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
194684 AT A- AT AT A
1 AT AT AT AT A
194692 AAATATGTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:195047 original size:24 final size:23
Alignment explanation
Indices: 194996--195052 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
194986 GTGTTTATTT
*
194996 ATTTATTGTTCACAAACATGTTC
1 ATTTATTGTTCACAAACATGGTC
* **
195019 GTTTATTTGTTCATGAACATGGTC
1 ATTTA-TTGTTCACAAACATGGTC
*
195043 ATTTAGTGTT
1 ATTTATTGTT
195053 AATTTTATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
23 8 0.30
24 19 0.70
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.47
Consensus pattern (23 bp):
ATTTATTGTTCACAAACATGGTC
Found at i:196797 original size:18 final size:18
Alignment explanation
Indices: 196766--196800 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
196756 TTACCCTGCA
*
196766 ATTATATAATTTTTAATT
1 ATTATATAAATTTTAATT
*
196784 ATTATTTAAATTTTAAT
1 ATTATATAAATTTTAAT
196801 AATGAAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTATATAAATTTTAATT
Found at i:199419 original size:16 final size:16
Alignment explanation
Indices: 199398--199429 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
199388 AGTTCGTGAT
199398 TTCATTATTCATTTAA
1 TTCATTATTCATTTAA
*
199414 TTCATTCTTCATTTAA
1 TTCATTATTCATTTAA
199430 GTCTATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.16, G:0.00, T:0.56
Consensus pattern (16 bp):
TTCATTATTCATTTAA
Found at i:200945 original size:23 final size:23
Alignment explanation
Indices: 200919--200965 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
200909 ATATAAAAAA
*
200919 TTAAAAGAAATACTTTAAAAACG
1 TTAAAAGAAAGACTTTAAAAACG
200942 TTAAAAGAAAGACTTTAAAAACG
1 TTAAAAGAAAGACTTTAAAAACG
200965 T
1 T
200966 GATCTATCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.55, C:0.09, G:0.11, T:0.26
Consensus pattern (23 bp):
TTAAAAGAAAGACTTTAAAAACG
Found at i:201970 original size:39 final size:39
Alignment explanation
Indices: 201910--201986 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 39
201900 TTTTAGAATC
201910 CATCGTAAAAACTTTAGTTTTTGTTACATTTTAGTACAT
1 CATCGTAAAAACTTTAGTTTTTGTTACATTTTAGTACAT
* * *
201949 CATCGTTAAAAGCTTTATTTTTTGTTTCATTTTAGTAC
1 CATCG-TAAAAACTTTAGTTTTTGTTACATTTTAGTAC
201987 CCGTTCAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 5 0.15
40 29 0.85
ACGTcount: A:0.27, C:0.13, G:0.10, T:0.49
Consensus pattern (39 bp):
CATCGTAAAAACTTTAGTTTTTGTTACATTTTAGTACAT
Found at i:202703 original size:17 final size:17
Alignment explanation
Indices: 202676--202714 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
202666 AATTTACAAT
202676 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
202692 TAATTATAAATAATATC
1 TAATTATAAATAATATC
202709 TAATTA
1 TAATTA
202715 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:210494 original size:216 final size:215
Alignment explanation
Indices: 209740--210594 Score: 1446
Period size: 215 Copynumber: 4.0 Consensus size: 215
209730 AGTATCACAA
* * * * *
209740 TTTAACATCTAAAAAGGACAGAATGATTGATTTACGGGCTGACTATAGGAAATCATTAGATCTCA
1 TTTAACATCTAAAAAAGACAGAATGATCGATTTACAGACTGACTATCGGAAATCATTAGATCTCA
*
209805 ACAAAATCT-ATTAACAAATCCACTTCATAAAATATTAATCACTTATTCATACTAAAAGCAAATA
66 ACAAAATCTCA-TAACAAATCCACCTCATAAAATATTAATCACTTATTCATACTAAAAGCAAATA
*
209869 TCATATAAATCAGGAAGTCAATACAACGATCTTAAAGAAAAGGCAAACCATTCTAGAAAATAATT
130 TCATATAAATCAGGAAGTCAATACAACGATCTTAAAGAAAAGGCAAACAATTCTAGAAAATAATT
209934 AAATAGATCTCAACAAAACAG
195 AAATAGATCTCAACAAAACAG
* * *
209955 TTTAACATGTAAAAAAGACAGAATGATCGATATACAGACTGGCTAT-GAGAAATCATTAGATCTC
1 TTTAACATCTAAAAAAGACAGAATGATCGATTTACAGACTGACTATCG-GAAATCATTAGATCTC
*
210019 AACAAAATCTCATAACAAATCCACCTCATAAAATATTAATCACTTATTCATACTAAAAGCAAATT
65 AACAAAATCTCATAACAAATCCACCTCATAAAATATTAATCACTTATTCATACTAAAAGCAAATA
* *
210084 TCATATAAATCAGGAAGTCAATACATCGATCTTAAAGAAAAGGCAAACCATTCTAGAAAATAATT
130 TCATATAAATCAGGAAGTCAATACAACGATCTTAAAGAAAAGGCAAACAATTCTAGAAAATAATT
210149 AAATAGATCTCAACAAAACAG
195 AAATAGATCTCAACAAAACAG
* *
210170 TTTAACATCTAAAAAAGACAGAATGATCGATTTACAGACTGGCTATCAGAAATCATTAGATCTCA
1 TTTAACATCTAAAAAAGACAGAATGATCGATTTACAGACTGACTATCGGAAATCATTAGATCTCA
*
210235 ACAAAATCTCATAACAAATCCACCTCATAAAATATTAATCACTTATTCATACTAAAAGCAAATTT
66 ACAAAATCTCATAACAAATCCACCTCATAAAATATTAATCACTTATTCATACTAAAAGCAAATAT
210300 CATATAAATCAGGAAGTCAATACAACGATCTTAAAGAAAAGGCAAAACAATTCTAGAAAATAATT
131 CATATAAATCAGGAAGTCAATACAACGATCTTAAAGAAAAGGC-AAACAATTCTAGAAAATAATT
210365 AAATAGATCTCAACAAAACA-
195 AAATAGATCTCAACAAAACAG
* * *
210385 TAATAACATCTAAAAAAGACCGAATGATCGATTTACAGATTGACTATCGGAAATCATTAGATCTC
1 T-TTAACATCTAAAAAAGACAGAATGATCGATTTACAGACTGACTATCGGAAATCATTAGATCTC
* *
210450 AACAAAATCTCATAACAAATCCACTTCGTAAAATATTAATCACTTATTCATACTAAAAGCAAATA
65 AACAAAATCTCATAACAAATCCACCTCATAAAATATTAATCACTTATTCATACTAAAAGCAAATA
210515 TCATATAAATCAGGAAGTCAATACAACGATCTTAAAGAAAAGGCAAAACAATTCTAGAAAATAAT
130 TCATATAAATCAGGAAGTCAATACAACGATCTTAAAGAAAAGGC-AAACAATTCTAGAAAATAAT
210580 TAAATAGATCCTCAA
194 TAAATAGAT-CTCAA
210595 TTACTACAAT
Statistics
Matches: 611, Mismatches: 23, Indels: 10
0.95 0.04 0.02
Matches are distributed among these distances:
214 1 0.00
215 370 0.61
216 235 0.38
217 5 0.01
ACGTcount: A:0.48, C:0.17, G:0.10, T:0.25
Consensus pattern (215 bp):
TTTAACATCTAAAAAAGACAGAATGATCGATTTACAGACTGACTATCGGAAATCATTAGATCTCA
ACAAAATCTCATAACAAATCCACCTCATAAAATATTAATCACTTATTCATACTAAAAGCAAATAT
CATATAAATCAGGAAGTCAATACAACGATCTTAAAGAAAAGGCAAACAATTCTAGAAAATAATTA
AATAGATCTCAACAAAACAG
Found at i:210547 original size:431 final size:432
Alignment explanation
Indices: 209740--210594 Score: 1452
Period size: 431 Copynumber: 2.0 Consensus size: 432
209730 AGTATCACAA
* * * *
209740 TTTAACATCTAAAAAGGACAGAATGATTGATTTACGGGCTGACTATAGGAAATCATTAGATCTCA
1 TTTAACATCTAAAAAAGACAGAATGATCGATTTACAGACTGACTATAGGAAATCATTAGATCTCA
*
209805 ACAAAATCTATTAACAAATCCACTTCATAAAATATTAATCACTTATTCATACTAAAAGCAAATAT
66 ACAAAATCTATTAACAAATCCACCTCATAAAATATTAATCACTTATTCATACTAAAAGCAAATAT
*
209870 CATATAAATCAGGAAGTCAATACAACGATCTTAAAGAAAAGGCAAACCATTCTAGAAAATAATTA
131 CATATAAATCAGGAAGTCAATACAACGATCTTAAAGAAAAGGCAAACAATTCTAGAAAATAATTA
* * *
209935 AATAGATCTCAACAAAACAGTTTAACATGTAAAAAAGACAGAATGATCGATATACAGACTGGCTA
196 AATAGATCTCAACAAAACAGTATAACATCTAAAAAAGACAGAATGATCGATATACAGACTGACTA
210000 TGAGAAATCATTAGATCTCAACAAAATCTCATAACAAATCCACCTCATAAAATATTAATCACTTA
261 TGAGAAATCATTAGATCTCAACAAAATCTCATAACAAATCCACCTCATAAAATATTAATCACTTA
* *
210065 TTCATACTAAAAGCAAATTTCATATAAATCAGGAAGTCAATACATCGATCTTAAAGAAAAGGC-A
326 TTCATACTAAAAGCAAATATCATATAAATCAGGAAGTCAATACAACGATCTTAAAGAAAAGGCAA
*
210129 AACCATTCTAGAAAATAATTAAATAGAT-CTCAACAAAACAG
391 AACAATTCTAGAAAATAATTAAATAGATCCTCAACAAAACAG
*
210170 TTTAACATCTAAAAAAGACAGAATGATCGATTTACAGACTGGCTATCA-GAAATCATTAGATCTC
1 TTTAACATCTAAAAAAGACAGAATGATCGATTTACAGACTGACTAT-AGGAAATCATTAGATCTC
210234 AACAAAATCTCA-TAACAAATCCACCTCATAAAATATTAATCACTTATTCATACTAAAAGCAAAT
65 AACAAAATCT-ATTAACAAATCCACCTCATAAAATATTAATCACTTATTCATACTAAAAGCAAAT
*
210298 TTCATATAAATCAGGAAGTCAATACAACGATCTTAAAGAAAAGGCAAAACAATTCTAGAAAATAA
129 ATCATATAAATCAGGAAGTCAATACAACGATCTTAAAGAAAAGGC-AAACAATTCTAGAAAATAA
* * *
210363 TTAAATAGATCTCAACAAAACA-TAATAACATCTAAAAAAGACCGAATGATCGATTTACAGATTG
193 TTAAATAGATCTCAACAAAACAGT-ATAACATCTAAAAAAGACAGAATGATCGATATACAGACTG
* *
210427 ACTATCG-GAAATCATTAGATCTCAACAAAATCTCATAACAAATCCACTTCGTAAAATATTAATC
257 ACTAT-GAGAAATCATTAGATCTCAACAAAATCTCATAACAAATCCACCTCATAAAATATTAATC
210491 ACTTATTCATACTAAAAGCAAATATCATATAAATCAGGAAGTCAATACAACGATCTTAAAGAAAA
321 ACTTATTCATACTAAAAGCAAATATCATATAAATCAGGAAGTCAATACAACGATCTTAAAGAAAA
210556 GGCAAAACAATTCTAGAAAATAATTAAATAGATCCTCAA
386 GGCAAAACAATTCTAGAAAATAATTAAATAGATCCTCAA
210595 TTACTACAAT
Statistics
Matches: 399, Mismatches: 19, Indels: 11
0.93 0.04 0.03
Matches are distributed among these distances:
430 163 0.41
431 202 0.51
432 29 0.07
433 5 0.01
ACGTcount: A:0.48, C:0.17, G:0.10, T:0.25
Consensus pattern (432 bp):
TTTAACATCTAAAAAAGACAGAATGATCGATTTACAGACTGACTATAGGAAATCATTAGATCTCA
ACAAAATCTATTAACAAATCCACCTCATAAAATATTAATCACTTATTCATACTAAAAGCAAATAT
CATATAAATCAGGAAGTCAATACAACGATCTTAAAGAAAAGGCAAACAATTCTAGAAAATAATTA
AATAGATCTCAACAAAACAGTATAACATCTAAAAAAGACAGAATGATCGATATACAGACTGACTA
TGAGAAATCATTAGATCTCAACAAAATCTCATAACAAATCCACCTCATAAAATATTAATCACTTA
TTCATACTAAAAGCAAATATCATATAAATCAGGAAGTCAATACAACGATCTTAAAGAAAAGGCAA
AACAATTCTAGAAAATAATTAAATAGATCCTCAACAAAACAG
Found at i:214117 original size:112 final size:113
Alignment explanation
Indices: 213921--214126 Score: 371
Period size: 112 Copynumber: 1.8 Consensus size: 113
213911 CGCGCAGGGC
*
213921 CCCCAAAAAAGGGCCCAAAAAAGTATATATATAGTGGCGTTTTTCCAATAAACGCCACTATAGAT
1 CCCCAAAAAAGGGCCCAAAAAAGTATATATATAGTGGCGTTTTTCCAATAAACACCACTATAGAT
213986 GGACCTATTGCGACG-TTTTTTCAAAAAACGCCACTATTATTGTGCAG
66 GGACCTATTGCGACGTTTTTTTCAAAAAACGCCACTATTATTGTGCAG
*
214033 CCCCAAAAAA-TGCCCTAAAAAAGTATATATATAGTGGCGTTTTTCCAATAAACACCACTATAGA
1 CCCCAAAAAAGGGCCC-AAAAAAGTATATATATAGTGGCGTTTTTCCAATAAACACCACTATAGA
214097 TGGACCTATTGCGACGTTTTTTTCAAAAAA
65 TGGACCTATTGCGACGTTTTTTTCAAAAAA
214127 AATGCCACTA
Statistics
Matches: 90, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
111 4 0.04
112 73 0.81
113 13 0.14
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (113 bp):
CCCCAAAAAAGGGCCCAAAAAAGTATATATATAGTGGCGTTTTTCCAATAAACACCACTATAGAT
GGACCTATTGCGACGTTTTTTTCAAAAAACGCCACTATTATTGTGCAG
Found at i:215914 original size:20 final size:20
Alignment explanation
Indices: 215891--215930 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
215881 AAAAATGTAC
*
215891 TTAAAAC-GCTAAATTAAATA
1 TTAAAACTG-TAAATAAAATA
215911 TTAAAACTGTAAATAAAATA
1 TTAAAACTGTAAATAAAATA
215931 ATAACTATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (20 bp):
TTAAAACTGTAAATAAAATA
Found at i:218728 original size:15 final size:16
Alignment explanation
Indices: 218708--218741 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
218698 CGTCTAAATA
*
218708 TATATATAT-TGTGTG
1 TATATATATGTGTATG
218723 TATATATATGTGTATG
1 TATATATATGTGTATG
218739 TAT
1 TAT
218742 TTCTAACTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (16 bp):
TATATATATGTGTATG
Found at i:220664 original size:33 final size:32
Alignment explanation
Indices: 220608--220673 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
220598 ATCGATTCAG
* *
220608 ATCAGTATTAAATTGATCCATTTTTCAGATTAA
1 ATCAATATCAAATTGATCCATTTTT-AGATTAA
* *
220641 ATCAATATCAAATTGATCGATTTTTAGCTTAA
1 ATCAATATCAAATTGATCCATTTTTAGATTAA
220673 A
1 A
220674 CCAACCTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 7 0.24
33 22 0.76
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (32 bp):
ATCAATATCAAATTGATCCATTTTTAGATTAA
Found at i:223012 original size:27 final size:28
Alignment explanation
Indices: 222981--223036 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
222971 TTTAGTTGAA
* *
222981 AGCAGGG-GAAGGAAGTTATATAAATAC
1 AGCAGGGAAAAGGAAGATATATAAATAC
223008 AGCAGGGAAAAAGGAAGATATATAAATAC
1 AGCAGGG-AAAAGGAAGATATATAAATAC
223037 CGACGTCGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 7 0.28
29 18 0.72
ACGTcount: A:0.50, C:0.07, G:0.27, T:0.16
Consensus pattern (28 bp):
AGCAGGGAAAAGGAAGATATATAAATAC
Found at i:223757 original size:5 final size:5
Alignment explanation
Indices: 223747--223772 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
223737 CATAATTCTA
223747 TTATT TTATT TTATT TTATT TTATT T
1 TTATT TTATT TTATT TTATT TTATT T
223773 CATGAGGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:226461 original size:2 final size:2
Alignment explanation
Indices: 226454--226479 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
226444 TAATAGTCTC
226454 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
226480 TTTTCAAGTA
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:242226 original size:27 final size:27
Alignment explanation
Indices: 242192--242245 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
242182 TTCTATCAAA
242192 AAACTTTATAAAATAACACCTTATAAT
1 AAACTTTATAAAATAACACCTTATAAT
* *
242219 AAACTTTATAGAATAACATCTTATAAT
1 AAACTTTATAAAATAACACCTTATAAT
242246 CGATAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.50, C:0.13, G:0.02, T:0.35
Consensus pattern (27 bp):
AAACTTTATAAAATAACACCTTATAAT
Found at i:247219 original size:41 final size:41
Alignment explanation
Indices: 247172--247253 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
247162 ATATTTTAAC
247172 CAAACATTTCAATTTTTATCAAAATAACTTTTATTTAATAA
1 CAAACATTTCAATTTTTATCAAAATAACTTTTATTTAATAA
*
247213 CAAACATTTCAATTTTTATCAAAATAACTTTTATTTGATAA
1 CAAACATTTCAATTTTTATCAAAATAACTTTTATTTAATAA
247254 AAAATATTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.43, C:0.12, G:0.01, T:0.44
Consensus pattern (41 bp):
CAAACATTTCAATTTTTATCAAAATAACTTTTATTTAATAA
Found at i:247563 original size:23 final size:23
Alignment explanation
Indices: 247496--247552 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
247486 TGAGATATTT
247496 TATGACGTTTTGGTTTTGGTTTA
1 TATGACGTTTTGGTTTTGGTTTA
247519 TATGACGTTTTGGTTTTGGTTTA
1 TATGACGTTTTGGTTTTGGTTTA
247542 TATGACGTTTT
1 TATGACGTTTT
247553 AATATTTGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.14, C:0.05, G:0.25, T:0.56
Consensus pattern (23 bp):
TATGACGTTTTGGTTTTGGTTTA
Found at i:258010 original size:27 final size:27
Alignment explanation
Indices: 257930--258021 Score: 114
Period size: 27 Copynumber: 3.3 Consensus size: 27
257920 AACCCCCACA
257930 CCCATCATTCCCTTCACCGGTGCTCT-
1 CCCATCATTCCCTTCACCGGTGCTCTC
** *
257956 CCCATTCCGCCTCTCATTCACCGGTGCTCTC
1 CCCA-T-C-ATTC-CCTTCACCGGTGCTCTC
257987 CCCATCATTCCCTTCACCGGTGCTCTC
1 CCCATCATTCCCTTCACCGGTGCTCTC
258014 CCCATCAT
1 CCCATCAT
258022 CCCCATGCTT
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
26 4 0.07
27 25 0.45
28 3 0.05
29 3 0.05
30 16 0.29
31 4 0.07
ACGTcount: A:0.12, C:0.48, G:0.11, T:0.29
Consensus pattern (27 bp):
CCCATCATTCCCTTCACCGGTGCTCTC
Found at i:267677 original size:3 final size:3
Alignment explanation
Indices: 267669--267730 Score: 52
Period size: 3 Copynumber: 20.3 Consensus size: 3
267659 ATGTTATTTA
* * * * * *
267669 TAT TAT TAT TAT TAT AAT TAT AAT TAT AAT AAT AAT AAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
267717 TAA TAT ATAT TAT T
1 TAT TAT -TAT TAT T
267731 TAATATTACA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
3 47 0.94
4 3 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:269161 original size:13 final size:12
Alignment explanation
Indices: 269124--269160 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
269114 ATATATAATA
269124 AATATTTATTTT
1 AATATTTATTTT
*
269136 AATAAATTATTTT
1 AAT-ATTTATTTT
269149 AATATTTATTTT
1 AATATTTATTTT
269161 TCATATGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
AATATTTATTTT
Found at i:280543 original size:13 final size:14
Alignment explanation
Indices: 280525--280582 Score: 70
Period size: 13 Copynumber: 4.4 Consensus size: 14
280515 TAAAAAAAAG
*
280525 AGAAAAG-AAGCAA
1 AGAAAAGAAAGAAA
280538 AGAAAAGAAAGAAA
1 AGAAAAGAAAGAAA
*
280552 A-AAAAGAAAAAAA
1 AGAAAAGAAAGAAA
280565 AGAAAAG-AA-AAA
1 AGAAAAGAAAGAAA
280577 AGAAAA
1 AGAAAA
280583 AGAGGGGTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
12 9 0.22
13 21 0.51
14 11 0.27
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (14 bp):
AGAAAAGAAAGAAA
Found at i:280548 original size:9 final size:9
Alignment explanation
Indices: 280536--280585 Score: 66
Period size: 9 Copynumber: 5.6 Consensus size: 9
280526 GAAAAGAAGC
*
280536 AAAGAAAAG
1 AAAGAAAAA
280545 AAAGAAAAA
1 AAAGAAAAA
280554 AAAGAAAAA
1 AAAGAAAAA
280563 AAAGAAAAGA
1 AAAGAAAA-A
*
280573 AAA-AAGAA
1 AAAGAAAAA
280581 AAAGA
1 AAAGA
280586 GGGGTCAAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
8 4 0.11
9 29 0.78
10 4 0.11
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:280582 original size:5 final size:5
Alignment explanation
Indices: 280536--280575 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
280526 GAAAAGAAGC
280536 AAAGA AAAG- AAAGA AAA-A AAAGA AAA-A AAAGA AAAGA AAA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAA
280576 AAGAAAAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 12 0.38
5 20 0.62
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:280583 original size:13 final size:13
Alignment explanation
Indices: 280518--280585 Score: 68
Period size: 13 Copynumber: 5.1 Consensus size: 13
280508 ATAATAATAA
280518 AAAAAAGAGAAAAG
1 AAAAAAGA-AAAAG
*
280532 AAGCAAAG-AAAAG
1 AA-AAAAGAAAAAG
280545 AAAGAAA-AAAAAG
1 AAA-AAAGAAAAAG
*
280558 AAAAAAAAGAAAAG
1 AAAAAAGA-AAAAG
280572 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
280585 A
1 A
280586 GGGGTCAAGG
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
12 3 0.07
13 25 0.54
14 14 0.30
15 4 0.09
ACGTcount: A:0.81, C:0.01, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:281870 original size:83 final size:83
Alignment explanation
Indices: 281731--282778 Score: 1809
Period size: 83 Copynumber: 12.6 Consensus size: 83
281721 AACAAATGCC
* * * *
281731 ATGTGCCCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATC
281796 ATTGAATTTGGAAGAAT-A
66 ATTGAATTTGGAAG-ATGA
* * *
281814 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATC
281879 ATTGAATTTGGAAGAAT-A
66 ATTGAATTTGGAAG-ATGA
281897 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATC
281962 ATTGAATTTGGAAGAAT-A
66 ATTGAATTTGGAAG-ATGA
* *
281980 ATGTGCTCATAGCATCTTCTAGAAGTGTTTTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATC
282045 ATTGAATTTGGAAGATGA
66 ATTGAATTTGGAAGATGA
* * * * *
282063 ATATGCTCATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATC
282128 ATTGAATTTGGAAGATGA
66 ATTGAATTTGGAAGATGA
282146 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATC
282211 ATTGAATTTGGAAGATGA
66 ATTGAATTTGGAAGATGA
* *
282229 ATGTGCTCATAGCATCTTCTGGAAGTGGTCTTTGATTTATCTGATCTGGTTTGGCAGAACCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATC
282294 ATTGAATTTGGAAGATGA
66 ATTGAATTTGGAAGATGA
* * * *
282312 ATGTGCTCATAGCATCTTCTGGAAGTGGTCTTTGAGTTATCTGATCTGGTTTGGAAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATC
282377 ATTGAATTTGGAAGAAT-A
66 ATTGAATTTGGAAG-ATGA
282395 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATC
282460 ATTGAATTTGGAAGATGA
66 ATTGAATTTGGAAGATGA
*
282478 ATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATC
282543 ATTGAATTTGGAAGATGA
66 ATTGAATTTGGAAGATGA
*
282561 ATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATC
282626 ATTGAATTTGGAAGATGA
66 ATTGAATTTGGAAGATGA
282644 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATC
282709 ATTGAATTTGGAAGA-GTA
66 ATTGAATTTGGAAGATG-A
*
282727 ATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
282779 AGTAGGAACC
Statistics
Matches: 930, Mismatches: 31, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
82 5 0.01
83 923 0.99
84 2 0.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (83 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATC
ATTGAATTTGGAAGATGA
Found at i:283704 original size:113 final size:113
Alignment explanation
Indices: 283506--284178 Score: 1088
Period size: 113 Copynumber: 6.0 Consensus size: 113
283496 TAGCAAAGAT
*
283506 TCAAATCCATCACTTGATGGATTAGATTTTCCAAATCGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATTAGCTTTTCCAAATCGAGTTCATAATGAGAAGAACTCATCTGA
*
283571 AGAATGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
283619 TCAAATCCATCACTTGATGGATTAGCTTTTCCAAATCGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATTAGCTTTTCCAAATCGAGTTCATAATGAGAAGAACTCATCTGA
283684 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
283732 TCAAATCCATCACTTGATGGATTAGCTTTTCCAAATCGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATTAGCTTTTCCAAATCGAGTTCATAATGAGAAGAACTCATCTGA
* * *
283797 AGAAGAAAGAAGAAGTTCACAATGAGAAGAATTTGTTCAACCGTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* **
283845 TCAAATCCATAACTTGATGGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATTAGCTTTTCCAAATCGAGTTCATAATGAGAAGAACTCATCTGA
*
283910 AGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * **
283958 TCAAATCCATAACTTGATGGATTAGATTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATTAGCTTTTCCAAATCGAGTTCATAATGAGAAGAACTCATCTGA
*
284023 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
284071 TCAAATCCATCACTTGATGGATCAACTTTTCTAGAA--GAAGTTCATAATGAGAAGAACTCATC-
1 TCAAATCCATCACTTGATGGATTAGCTTTTCCA-AATCG-AGTTCATAATGAGAAGAACTCATCT
* * ** *
284133 --AGGA-GAAGAAGAAGTTCATAATAAGAAGAGCTTATTCAACCTTTTG
64 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
284179 AATGACTCTA
Statistics
Matches: 530, Mismatches: 28, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
109 37 0.07
110 3 0.01
112 1 0.00
113 489 0.92
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATTAGCTTTTCCAAATCGAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:284125 original size:17 final size:17
Alignment explanation
Indices: 284103--284161 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
284093 CAACTTTTCT
284103 AGAAGAAGTTCATAATG
1 AGAAGAAGTTCATAATG
*
284120 AGAAGAA-CTCATCAGGA-G
1 AGAAGAAGTTCAT-A--ATG
*
284138 AAGAAGAAGTTCATAATA
1 -AGAAGAAGTTCATAATG
284156 AGAAGA
1 AGAAGA
284162 GCTTATTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
16 4 0.12
17 15 0.45
18 1 0.03
19 9 0.27
20 4 0.12
ACGTcount: A:0.51, C:0.08, G:0.24, T:0.17
Consensus pattern (17 bp):
AGAAGAAGTTCATAATG
Found at i:284416 original size:3 final size:3
Alignment explanation
Indices: 284408--284484 Score: 82
Period size: 3 Copynumber: 25.3 Consensus size: 3
284398 ATGTTATTTA
* * * * *
284408 TAT TAT TAT TAT TAT TAT AAT AAT TAT TAT TAT AAT TAT AAT TAT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
284456 TAT AAT TAT TAT TAT TAA TAT ATAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT T
284485 TAATATTACA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
3 58 0.95
4 3 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:284423 original size:12 final size:12
Alignment explanation
Indices: 284408--284484 Score: 91
Period size: 12 Copynumber: 6.3 Consensus size: 12
284398 ATGTTATTTA
*
284408 TATTATTATTAT
1 TATTATTATAAT
*
284420 TATTATAATAAT
1 TATTATTATAAT
284432 TATTATTATAAT
1 TATTATTATAAT
*
284444 TATAATTATAAT
1 TATTATTATAAT
* *
284456 TATAATTATTAT
1 TATTATTATAAT
*
284468 TATTAATATATAT
1 TATTATTATA-AT
284481 TATT
1 TATT
284485 TAATATTACA
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
12 50 0.89
13 6 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TATTATTATAAT
Found at i:285617 original size:24 final size:23
Alignment explanation
Indices: 285571--285618 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
285561 TAATAAATAA
**
285571 TATTTTAATCAATATTTTTAATT
1 TATTTTAATCAATATTTCAAATT
*
285594 TATTTTAATCTGATATTTCAAATT
1 TATTTTAATC-AATATTTCAAATT
285618 T
1 T
285619 TAGATAAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.58
Consensus pattern (23 bp):
TATTTTAATCAATATTTCAAATT
Found at i:285882 original size:13 final size:13
Alignment explanation
Indices: 285866--285905 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
285856 ATATAATAAA
285866 TAAATATTTATTT
1 TAAATATTTATTT
*
285879 TAAATAAATTATTT
1 TAAAT-ATTTATTT
285893 T-AATATTTATTT
1 TAAATATTTATTT
285905 T
1 T
285906 TCAATATTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:300863 original size:20 final size:21
Alignment explanation
Indices: 300840--300890 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
300830 TTTGAGTTAA
*
300840 TTAAAATATGTTT-AAAGTGT
1 TTAAAATATGTTTAAAACTGT
* *
300860 TTAAAATGTGTTTAAAACTTT
1 TTAAAATATGTTTAAAACTGT
300881 TTAAAATATG
1 TTAAAATATG
300891 AAAAATACTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (21 bp):
TTAAAATATGTTTAAAACTGT
Found at i:300870 original size:11 final size:11
Alignment explanation
Indices: 300840--300876 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
300830 TTTGAGTTAA
*
300840 TTAAAATATGT
1 TTAAAATGTGT
300851 TT-AAA-GTGT
1 TTAAAATGTGT
300860 TTAAAATGTGT
1 TTAAAATGTGT
300871 TTAAAA
1 TTAAAA
300877 CTTTTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
9 5 0.22
10 6 0.26
11 12 0.52
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (11 bp):
TTAAAATGTGT
Found at i:300931 original size:12 final size:12
Alignment explanation
Indices: 300914--300942 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
300904 AGTCACTATT
300914 TGACATTGTTCA
1 TGACATTGTTCA
300926 TGACATTGTTCA
1 TGACATTGTTCA
300938 T-ACAT
1 TGACAT
300943 GGGTAATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (12 bp):
TGACATTGTTCA
Found at i:302891 original size:30 final size:31
Alignment explanation
Indices: 302834--302911 Score: 117
Period size: 30 Copynumber: 2.5 Consensus size: 31
302824 TTTTAAGAGT
302834 ACTCATAATAACAAATATTGAAAAAAATTAG
1 ACTCATAATAACAAATATTGAAAAAAATTAG
302865 ACAT-ATAATAA-AAAGTATTG-AAAAAATTAG
1 AC-TCATAATAACAAA-TATTGAAAAAAATTAG
302895 ACTCATAATAACAAATA
1 ACTCATAATAACAAATA
302912 AATATTAGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
29 1 0.02
30 24 0.56
31 17 0.40
32 1 0.02
ACGTcount: A:0.59, C:0.09, G:0.06, T:0.26
Consensus pattern (31 bp):
ACTCATAATAACAAATATTGAAAAAAATTAG
Found at i:302988 original size:30 final size:30
Alignment explanation
Indices: 302952--303010 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
302942 TATGCCCCTA
302952 ATAATAAATATTGA-AAAAATTGGATCCTTG
1 ATAATAAATATTGATAAAAATTGGA-CCTTG
*
302982 ATAATAAGTATTGATAAAAATTGGACCTT
1 ATAATAAATATTGATAAAAATTGGACCTT
303011 TTATTGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.46, C:0.07, G:0.14, T:0.34
Consensus pattern (30 bp):
ATAATAAATATTGATAAAAATTGGACCTTG
Found at i:303022 original size:22 final size:22
Alignment explanation
Indices: 302990--303054 Score: 103
Period size: 22 Copynumber: 2.9 Consensus size: 22
302980 TGATAATAAG
*
302990 TATTGATAAAAATTGGACCTTT
1 TATTGAAAAAAATTGGACCTTT
*
303012 TATTGAAAAAAATTGGACATTT
1 TATTGAAAAAAATTGGACCTTT
303034 TATTGAAAAAAAATTGGACCT
1 TATTG-AAAAAAATTGGACCT
303055 ATAATGATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 25 0.64
23 14 0.36
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (22 bp):
TATTGAAAAAAATTGGACCTTT
Found at i:303877 original size:56 final size:56
Alignment explanation
Indices: 303816--304006 Score: 231
Period size: 56 Copynumber: 3.4 Consensus size: 56
303806 TTTTATTTTT
* * * *
303816 TAGATATATTTAATTTCGGGGCCTCTATTTTTATATTTCTTAATGGCAACAACTGA
1 TAGATATACTCAATTTCGGGGCCCCTATTTTTATACTTCTTAATGGCAACAACTGA
* * * ** *
303872 TAGATATACTCGATTTTGGAGCCCCTATTTTTATACTTCTTAATGAAAATAACTGA
1 TAGATATACTCAATTTCGGGGCCCCTATTTTTATACTTCTTAATGGCAACAACTGA
* * *
303928 TAGATATACTCAATTTC-GGCCCCCTATTTTTATGCTTATTAATGGCAACAACTGA
1 TAGATATACTCAATTTCGGGGCCCCTATTTTTATACTTCTTAATGGCAACAACTGA
* * *
303983 TATATATACTCGATTTCGAGGCCC
1 TAGATATACTCAATTTCGGGGCCC
304007 TTTCGAGACC
Statistics
Matches: 111, Mismatches: 23, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
55 46 0.41
56 65 0.59
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (56 bp):
TAGATATACTCAATTTCGGGGCCCCTATTTTTATACTTCTTAATGGCAACAACTGA
Found at i:304497 original size:59 final size:59
Alignment explanation
Indices: 304367--304497 Score: 156
Period size: 59 Copynumber: 2.2 Consensus size: 59
304357 TGGGGTGACC
* * * * * *
304367 ATTTTGTAACTTTTAATAGTCGATGAACTTAACAAAGTAACATTCTATAGTCGGTGATT
1 ATTTTGTAACTTTTAATAATCGAGGAACTTAAAAAAGTAACATCCTATAGTCGGGGAAT
* * **
304426 ATTTTATAACTTTTAATAATCGAGGGACTTAAAAAAGTAGTATCCTATAGTCGGGGAAT
1 ATTTTGTAACTTTTAATAATCGAGGAACTTAAAAAAGTAACATCCTATAGTCGGGGAAT
304485 ATTTGTGT-ACTTT
1 ATTT-TGTAACTTT
304498 ACCCTATATT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 58 0.97
60 2 0.03
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.39
Consensus pattern (59 bp):
ATTTTGTAACTTTTAATAATCGAGGAACTTAAAAAAGTAACATCCTATAGTCGGGGAAT
Found at i:309814 original size:24 final size:23
Alignment explanation
Indices: 309761--309815 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
309751 ATCAAAAATA
*
309761 AATAAATGGAATTCAACTTAATTT
1 AATAAATAGAATTCAAC-TAATTT
309785 AA-AAATAGAAGTTCAA-TAATTT
1 AATAAATAGAA-TTCAACTAATTT
309807 ACATAAATA
1 A-ATAAATA
309816 TAAGAGTGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 7 0.26
23 8 0.30
24 12 0.44
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (23 bp):
AATAAATAGAATTCAACTAATTT
Found at i:310314 original size:23 final size:23
Alignment explanation
Indices: 310288--310378 Score: 92
Period size: 23 Copynumber: 4.0 Consensus size: 23
310278 CACATAAAAA
* * * *
310288 TGTCCAGAAGGACCACATTGTAT
1 TGTCCCGAAGGACCACGTAGAAT
* * * *
310311 TGTCCCGAAAGACAACGTGGAAA
1 TGTCCCGAAGGACCACGTAGAAT
310334 TGTCCCGAAGGACCACGTAGAAT
1 TGTCCCGAAGGACCACGTAGAAT
**
310357 TGTCCCGAAGGACTGCGTAGAA
1 TGTCCCGAAGGACCACGTAGAA
310379 CCCTCAACTC
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (23 bp):
TGTCCCGAAGGACCACGTAGAAT
Found at i:310488 original size:16 final size:14
Alignment explanation
Indices: 310454--310492 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
310444 TTTACACATT
*
310454 TCACATAGCTTATA
1 TCACATAGCATATA
310468 TCACATAGACATATAA
1 TCACATAG-CATAT-A
310484 TCACATAGC
1 TCACATAGC
310493 TCATTGTCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 8 0.36
15 5 0.23
16 9 0.41
ACGTcount: A:0.41, C:0.23, G:0.08, T:0.28
Consensus pattern (14 bp):
TCACATAGCATATA
Found at i:310504 original size:15 final size:14
Alignment explanation
Indices: 310450--310518 Score: 59
Period size: 15 Copynumber: 4.7 Consensus size: 14
310440 ACCATTTACA
310450 CATTTCACATAGCT
1 CATTTCACATAGCT
* *
310464 TATATCACATAGACAT
1 CATTTCACATAG-C-T
*
310480 -ATAATCACATAGCT
1 CAT-TTCACATAGCT
310494 CATTGTCACATAGCT
1 CATT-TCACATAGCT
*
310509 TATTTCACAT
1 CATTTCACAT
310519 TTTCATATCA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
14 17 0.37
15 19 0.41
16 10 0.22
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.35
Consensus pattern (14 bp):
CATTTCACATAGCT
Found at i:310546 original size:42 final size:45
Alignment explanation
Indices: 310455--310585 Score: 135
Period size: 42 Copynumber: 3.0 Consensus size: 45
310445 TTACACATTT
*** * * * *
310455 CACATAGCTTATATCA-CATAGACATATAATCACATAGCTCATTGT
1 CACATAGCTTATATCACCATTTTCA-GTAATCACATAGGTCAATGC
*
310500 CACATAGCTTATTTCA-CATTTTCA-T-ATCACATAGGTCAATGC
1 CACATAGCTTATATCACCATTTTCAGTAATCACATAGGTCAATGC
*
310542 CACATAGCTTATATCACCTTTTTCATGTAATCACATAGGTCAAT
1 CACATAGCTTATATCACCATTTTCA-GTAATCACATAGGTCAAT
310586 ATCATATAGC
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
42 29 0.40
43 8 0.11
45 21 0.29
46 15 0.21
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (45 bp):
CACATAGCTTATATCACCATTTTCAGTAATCACATAGGTCAATGC
Found at i:311175 original size:2 final size:2
Alignment explanation
Indices: 311168--311257 Score: 180
Period size: 2 Copynumber: 45.0 Consensus size: 2
311158 AACATGTTCC
311168 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
311210 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
311252 AT AT AT
1 AT AT AT
311258 TACTTACAAT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 88 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:312018 original size:11 final size:11
Alignment explanation
Indices: 312002--312035 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
311992 TTTCGTATCT
312002 ACCACCTACCC
1 ACCACCTACCC
312013 ACCACCTACCC
1 ACCACCTACCC
312024 ACCACCTACCC
1 ACCACCTACCC
312035 A
1 A
312036 TCCTTATACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.29, C:0.62, G:0.00, T:0.09
Consensus pattern (11 bp):
ACCACCTACCC
Found at i:314251 original size:14 final size:13
Alignment explanation
Indices: 314227--314261 Score: 61
Period size: 14 Copynumber: 2.6 Consensus size: 13
314217 TTTGCATTCC
314227 ACAATTTTTATAA
1 ACAATTTTTATAA
314240 ACAATTTGTTATAA
1 ACAATTT-TTATAA
314254 ACAATTTT
1 ACAATTTT
314262 AAAATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.46
Consensus pattern (13 bp):
ACAATTTTTATAA
Found at i:317197 original size:26 final size:30
Alignment explanation
Indices: 317144--317199 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 30
317134 CTTTATCATC
317144 ACTTAAAATAATATTATTTAAAATATTTTA
1 ACTTAAAATAATATTATTTAAAATATTTTA
317174 ACTT-AAA-AATA-TATTT-AAATATTTTA
1 ACTTAAAATAATATTATTTAAAATATTTTA
317200 TTATTAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 10 0.38
27 5 0.19
28 4 0.15
29 3 0.12
30 4 0.15
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (30 bp):
ACTTAAAATAATATTATTTAAAATATTTTA
Found at i:317254 original size:96 final size:98
Alignment explanation
Indices: 317089--317284 Score: 235
Period size: 96 Copynumber: 2.0 Consensus size: 98
317079 TTTTAGCTTA
* *
317089 TTAAATATATATTATTTTATTTTAATGTAAAAATATATATTTTATCTTTATCATCACTTAAAATA
1 TTAAATATATATTATTTTAATTTAATATAAAAATATATATTTTATCTTTATCATCACTTAAAATA
*
317154 ATATTAT-TTAAAATATTTTAACTTAAAAATATAT
66 ATATTATATT--AATATTTTAAATTAAAAATATAT
*
317188 TTAAATAT-T-TTATTATTAATTTAATAT-AAAA-ATATATTTTAT-TCTTATCTTCACTTAAAA
1 TTAAATATATATTATT-TTAATTTAATATAAAAATATATATTTTATCT-TTATCATCACTTAAAA
* **
317248 -ATATATTCTATTCTTATTTTAAATTAAAAATATAT
64 TA-ATATTATATTAATATTTTAAATTAAAAATATAT
317283 TT
1 TT
317285 TATTCTTATC
Statistics
Matches: 86, Mismatches: 7, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
95 24 0.28
96 32 0.37
97 11 0.13
98 11 0.13
99 8 0.09
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.51
Consensus pattern (98 bp):
TTAAATATATATTATTTTAATTTAATATAAAAATATATATTTTATCTTTATCATCACTTAAAATA
ATATTATATTAATATTTTAAATTAAAAATATAT
Found at i:317269 original size:58 final size:57
Alignment explanation
Indices: 317192--317306 Score: 169
Period size: 58 Copynumber: 2.0 Consensus size: 57
317182 ATATATTTAA
*
317192 ATATTTTATTATTAATTT-AATATAAAAATATATTTTATTCTTATCTTCACTTAAAAAT
1 ATATTCTATTATTAATTTAAAT-TAAAAATATATTTTATTCTTATCTT-ACTTAAAAAT
* * *
317250 ATATTCTATTCTTATTTTAAATTAAAAATATATTTTATTCTTATCTTATTTAAAAAT
1 ATATTCTATTATTAATTTAAATTAAAAATATATTTTATTCTTATCTTACTTAAAAAT
317307 CTTAACTTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
57 9 0.17
58 40 0.77
59 3 0.06
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (57 bp):
ATATTCTATTATTAATTTAAATTAAAAATATATTTTATTCTTATCTTACTTAAAAAT
Found at i:317293 original size:29 final size:28
Alignment explanation
Indices: 317192--317306 Score: 142
Period size: 29 Copynumber: 4.0 Consensus size: 28
317182 ATATATTTAA
*
317192 ATATTTTATTATTAAT-TTAATATAAAAAT
1 ATATTTTATTCTT-ATCTTAAT-TAAAAAT
*
317221 ATATTTTATTCTTATCTTCACTTAAAAAT
1 ATATTTTATTCTTATCTT-AATTAAAAAT
* *
317250 ATATTCTATTCTTATTTTAAATTAAAAAT
1 ATATTTTATTCTTATCTT-AATTAAAAAT
*
317279 ATATTTTATTCTTATCTTATTTAAAAAT
1 ATATTTTATTCTTATCTTAATTAAAAAT
317307 CTTAACTTAA
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
28 11 0.15
29 62 0.83
30 2 0.03
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (28 bp):
ATATTTTATTCTTATCTTAATTAAAAAT
Found at i:320871 original size:56 final size:55
Alignment explanation
Indices: 320802--320942 Score: 219
Period size: 56 Copynumber: 2.5 Consensus size: 55
320792 TATTTTCTAA
*
320802 ATATACTCAATTTCGAAGCCCCTATTTTTATGCTTCTTAATGGCAACAACTGATAG
1 ATATACTCAATTTCG-GGCCCCTATTTTTATGCTTCTTAATGGCAACAACTGATAG
*
320858 ATATACTCGATTTCGGGCCCCCTATTTTTATGCTTCTTAATGGCAACAACTGATAG
1 ATATACTCAATTTCGGG-CCCCTATTTTTATGCTTCTTAATGGCAACAACTGATAG
* *
320914 ATATACTCTATTTTGGGGCCCCTATTTTT
1 ATATACTC-AATTTCGGGCCCCTATTTTT
320943 TGGGGCCCTA
Statistics
Matches: 78, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
55 1 0.01
56 71 0.91
57 6 0.08
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (55 bp):
ATATACTCAATTTCGGGCCCCTATTTTTATGCTTCTTAATGGCAACAACTGATAG
Found at i:322418 original size:125 final size:125
Alignment explanation
Indices: 322255--322506 Score: 335
Period size: 125 Copynumber: 2.0 Consensus size: 125
322245 TTTGGACAAG
* * * * *
322255 GTATTGAACATGTATTCGATACTCATACAAAGGGTATATCCTTATATCTGACACACACAGAGAAT
1 GTATCGAACACGTATTCGATACTCACACAAAGAGTATATCCTTATATCGGACACACACAGAGAAT
* *
322320 AATGTAGACATTTGGAA-TTTCGAAACTTCCCTTGAGATTAGGGATTCATCAGCAATATTT
66 AATCTAGACATTTGGAACTTT-GAAACTTCCCTTGAGATGAGGGATTCATCAGCAATATTT
* * * * **
322380 GTATCGAACACGTATTTGATACTCACACATAGAGTATATTCTTATATCGGACACTCACATCGAAT
1 GTATCGAACACGTATTCGATACTCACACAAAGAGTATATCCTTATATCGGACACACACAGAGAAT
* * * *
322445 ATTCTAGACATTTGGAACTTTGGAACTTCCTTTGAGATGAGGGATTCATCGGCAATATTT
66 AATCTAGACATTTGGAACTTTGAAACTTCCCTTGAGATGAGGGATTCATCAGCAATATTT
322505 GT
1 GT
322507 GATTTGGCTA
Statistics
Matches: 109, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
125 106 0.97
126 3 0.03
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (125 bp):
GTATCGAACACGTATTCGATACTCACACAAAGAGTATATCCTTATATCGGACACACACAGAGAAT
AATCTAGACATTTGGAACTTTGAAACTTCCCTTGAGATGAGGGATTCATCAGCAATATTT
Found at i:323484 original size:2 final size:2
Alignment explanation
Indices: 323477--323503 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
323467 AATATGAGGA
323477 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
323504 GTTAGAGAAT
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:328669 original size:18 final size:18
Alignment explanation
Indices: 328646--328698 Score: 106
Period size: 18 Copynumber: 2.9 Consensus size: 18
328636 ACCGGTCAAC
328646 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
328664 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
328682 GGTCAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
328699 AACGGGTCGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.49, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:328673 original size:13 final size:13
Alignment explanation
Indices: 328657--328707 Score: 57
Period size: 13 Copynumber: 3.5 Consensus size: 13
328647 GTCAACGGGT
328657 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
328670 CGGGTCGGGTCGGGTCAA
1 CGGGT-----CGGGTCAA
328688 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
328701 CGGGTCG
1 CGGGTCG
328708 TGACCGGTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
13 20 0.61
18 13 0.39
ACGTcount: A:0.12, C:0.24, G:0.49, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:328717 original size:31 final size:31
Alignment explanation
Indices: 328657--328718 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
328647 GTCAACGGGT
* *
328657 CGGGTCGGGTCAACGGGTCGGGTCGGGTCAA
1 CGGGTCGGGTCAACGGGTCGGGACCGGTCAA
*
328688 CGGGTCGGGTCAACGGGTCGTGACCGGTCAA
1 CGGGTCGGGTCAACGGGTCGGGACCGGTCAA
328719 ACCGGTCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.15, C:0.24, G:0.45, T:0.16
Consensus pattern (31 bp):
CGGGTCGGGTCAACGGGTCGGGACCGGTCAA
Found at i:328730 original size:10 final size:10
Alignment explanation
Indices: 328710--328764 Score: 78
Period size: 10 Copynumber: 5.6 Consensus size: 10
328700 ACGGGTCGTG
328710 ACCGGTC-AA
1 ACCGGTCAAA
328719 ACCGGTCAAA
1 ACCGGTCAAA
328729 ACCGGTTCAAA
1 ACCGG-TCAAA
*
328740 ACCGGT-TAA
1 ACCGGTCAAA
328749 ACCGGTCAAA
1 ACCGGTCAAA
328759 ACCGGT
1 ACCGGT
328765 TTCCAGCGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
9 15 0.37
10 16 0.39
11 10 0.24
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:328765 original size:19 final size:19
Alignment explanation
Indices: 328710--328765 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
328700 ACGGGTCGTG
*
328710 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGT-TAA
328729 ACCGGTTCAAAACCGGTTAA
1 ACCGG-TCAAAACCGGTTAA
328749 ACCGGTCAAAACCGGTT
1 ACCGGTCAAAACCGGTT
328766 TCCAGCGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 17 0.50
20 9 0.26
21 8 0.24
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAAACCGGTTAA
Found at i:330225 original size:30 final size:31
Alignment explanation
Indices: 330186--330252 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 31
330176 GAATGACCTA
* * * *
330186 TCCAAAGGTCATAAAGAACCTCGG-CAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
* *
330216 TCCATAGGTCCCGAAGAACCTAGGTAAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
330247 TCCATA
1 TCCATA
330253 TGTTCCTTAG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
30 19 0.63
31 11 0.37
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.19
Consensus pattern (31 bp):
TCCATAGGTCACAAAGAACCTAGGTAAACTG
Found at i:330265 original size:31 final size:32
Alignment explanation
Indices: 330211--330287 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 32
330201 GAACCTCGGC
* * *
330211 AACTGTCCATAGGTCCCGAAGAACCTAGGTA-
1 AACTGTCCATATGTCCCGAAGAACATAGATAT
* **
330242 AACTGTCCATATGTTCCTTAGAACATAGATAT
1 AACTGTCCATATGTCCCGAAGAACATAGATAT
330274 AA-TGTCCATATGTC
1 AACTGTCCATATGTC
330288 TCAAAAGACA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 36 0.95
32 2 0.05
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (32 bp):
AACTGTCCATATGTCCCGAAGAACATAGATAT
Found at i:330327 original size:32 final size:32
Alignment explanation
Indices: 330276--330382 Score: 196
Period size: 32 Copynumber: 3.3 Consensus size: 32
330266 ATAGATATAA
*
330276 TGTCCATATGTCTCAAAAGACATAGGTAATTC
1 TGTCCATATGTCTCGAAAGACATAGGTAATTC
*
330308 TGTCCATATATCTCGAAAGACATAGGTAATTC
1 TGTCCATATGTCTCGAAAGACATAGGTAATTC
330340 TGTCCATATGTCTCGAAAGACATAGGTAATTC
1 TGTCCATATGTCTCGAAAGACATAGGTAATTC
330372 TGTCCATATGT
1 TGTCCATATGT
330383 TCTGTAGAAC
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 72 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Consensus pattern (32 bp):
TGTCCATATGTCTCGAAAGACATAGGTAATTC
Done.